Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 21 of 31
Found at i:10128795 original size:18 final size:18
Alignment explanation
Indices: 10128737--10128795 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
10128727 TTTAATTTTA
*
10128737 ATTTT-TTTTTAT-TTTC
1 ATTTTCTTTTTTTCTTTC
10128753 ATTTTTCCTTTTTTTC--TC
1 A-TTTT-CTTTTTTTCTTTC
*
10128771 ATATTCTTTTTTTCTTTC
1 ATTTTCTTTTTTTCTTTC
10128789 ATTTTCT
1 ATTTTCT
10128796 CATATTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 10 0.29
17 7 0.21
18 11 0.32
19 6 0.18
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTCTTTTTTTCTTTC
Found at i:10130501 original size:47 final size:47
Alignment explanation
Indices: 10130396--10130530 Score: 139
Period size: 47 Copynumber: 2.9 Consensus size: 47
10130386 TATGAAAGGA
* * *
10130396 TTATTAAAATATAGTCAAGGATAGTTTTAAT-TTTTGGTATAAATATG
1 TTATTAAATTATAGTCAAGGGTA-ATTTAATCTTTTGGTATAAATATG
* * *
10130443 TGATTAAATTATAGTCAAGGGTAATTTAATCTTTTGTTATAAATATT
1 TTATTAAATTATAGTCAAGGGTAATTTAATCTTTTGGTATAAATATG
* * * * * *
10130490 TTATTATATTATAATTAAGGG-CATTTTATCTTTTGGCATAA
1 TTATTAAATTATAGTCAAGGGTAATTTAATCTTTTGGTATAA
10130531 GTATTTTCGT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
46 22 0.30
47 51 0.70
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (47 bp):
TTATTAAATTATAGTCAAGGGTAATTTAATCTTTTGGTATAAATATG
Found at i:10153462 original size:16 final size:15
Alignment explanation
Indices: 10153441--10153471 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
10153431 CATCCAATGT
10153441 GAAAATTAATTGTTTC
1 GAAAATTAATT-TTTC
10153457 GAAAATTAATTTTTC
1 GAAAATTAATTTTTC
10153472 CTCTATAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (15 bp):
GAAAATTAATTTTTC
Found at i:10155816 original size:2 final size:2
Alignment explanation
Indices: 10155809--10155849 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
10155799 CCACTTTTCC
* *
10155809 AT AT AT AT AA AT AT AT AA 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 AT AT A
10155850 GAGCACCTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:10164872 original size:13 final size:13
Alignment explanation
Indices: 10164856--10164897 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
10164846 AGCATAAAAG
10164856 TAAACATATGAAA
1 TAAACATATGAAA
*
10164869 TAAA-ATA-GCATA
1 TAAACATATG-AAA
10164881 TAAACATATGAAA
1 TAAACATATGAAA
10164894 TAAA
1 TAAA
10164898 ATAGCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 13 0.54
14 1 0.04
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (13 bp):
TAAACATATGAAA
Found at i:10164914 original size:25 final size:25
Alignment explanation
Indices: 10164856--10164907 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
10164846 AGCATAAAAG
10164856 TAAACATATGAAATAAAATAGCATA
1 TAAACATATGAAATAAAATAGCATA
10164881 TAAACATATGAAATAAAATAGCATA
1 TAAACATATGAAATAAAATAGCATA
10164906 TA
1 TA
10164908 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (25 bp):
TAAACATATGAAATAAAATAGCATA
Found at i:10166442 original size:21 final size:20
Alignment explanation
Indices: 10166413--10166454 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
10166403 TACATTTTGT
10166413 TTCAAATGTATAGATACATA
1 TTCAAATGTATAGATACATA
* *
10166433 TTCATAATGTATTGATATATA
1 TTCA-AATGTATAGATACATA
10166454 T
1 T
10166455 GATCACGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (20 bp):
TTCAAATGTATAGATACATA
Found at i:10166935 original size:17 final size:18
Alignment explanation
Indices: 10166913--10166951 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
10166903 GAGTATGAGT
10166913 TTTAGCTAAAA-AAATAG
1 TTTAGCTAAAAGAAATAG
10166930 TTTAGCTAAAAGTAAATAG
1 TTTAGCTAAAAG-AAATAG
10166949 TTT
1 TTT
10166952 CAAAAGTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
19 9 0.45
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (18 bp):
TTTAGCTAAAAGAAATAG
Found at i:10169080 original size:35 final size:36
Alignment explanation
Indices: 10169024--10169107 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
10169014 GAGAATAATG
* *
10169024 AGAATAACTAAAA-CAAGTGAAGTACAACTTCATGT
1 AGAACAACTAAAATCAAGTGAAGTACAACTTCATGC
* ** *
10169059 AGAACAACTAAAATTAA-TGAAGTATTATTTCATGC
1 AGAACAACTAAAATCAAGTGAAGTACAACTTCATGC
10169094 AGAACAACTAAAAT
1 AGAACAACTAAAAT
10169108 AAATAGAGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 40 0.95
36 2 0.05
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (36 bp):
AGAACAACTAAAATCAAGTGAAGTACAACTTCATGC
Found at i:10170507 original size:22 final size:22
Alignment explanation
Indices: 10170482--10170550 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 22
10170472 AATATCATTG
* *
10170482 ATAACTAAATTATTAATTTTAT
1 ATAATTAAATTATTAATTTTAA
*
10170504 ATAATTAAATATATAAAATTATTAA
1 ATAATTAAAT-TAT-TAATT-TTAA
10170529 ATTAATTAAAATTATTAATTTT
1 A-TAATT-AAATTATTAATTTT
10170551 TTTCTAACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 9 0.24
23 3 0.08
24 6 0.16
25 8 0.21
26 8 0.21
27 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATTAAATTATTAATTTTAA
Found at i:10170530 original size:8 final size:8
Alignment explanation
Indices: 10170487--10170546 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
10170477 CATTGATAAC
10170487 TAAATTAT
1 TAAATTAT
10170495 T-AATT-T
1 TAAATTAT
* *
10170501 TATATAAT
1 TAAATTAT
10170509 TAAATATAT
1 TAAAT-TAT
*
10170518 AAAATTAT
1 TAAATTAT
10170526 TAAATTAAT
1 TAAATT-AT
10170535 TAAAATTAT
1 T-AAATTAT
10170544 TAA
1 TAA
10170547 TTTTTTTCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
6 2 0.05
7 6 0.15
8 16 0.39
9 12 0.29
10 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAAATTAT
Found at i:10171684 original size:6 final size:6
Alignment explanation
Indices: 10171657--10171705 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
10171647 ATATTAAAAA
* * *
10171657 AATTTT AATTAT ATTTAA AATTAT AATTAT AATTAT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
10171705 A
1 A
10171706 TCTTGAATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTAT
Found at i:10173357 original size:2 final size:2
Alignment explanation
Indices: 10173350--10173375 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10173340 GCATACAAAA
10173350 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
10173376 TGCTTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10176599 original size:37 final size:34
Alignment explanation
Indices: 10176556--10176630 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 34
10176546 CTGGTCCGGC
10176556 GCCGGGG-GGGTCGGGGGCGCGCCCGGGCGCGCCCGCG
1 GCCGGGGCGGG-C-GGGGC-CGCCC-GGCGCGCCCGCG
* *
10176593 GCCGGGGCGGGCGGGGCCGCGCGGCGCGGCCGCG
1 GCCGGGGCGGGCGGGGCCGCCCGGCGCGCCCGCG
10176627 GCCG
1 GCCG
10176631 CGCAAGCCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 15 0.43
35 4 0.11
36 5 0.14
37 8 0.23
38 3 0.09
ACGTcount: A:0.00, C:0.39, G:0.60, T:0.01
Consensus pattern (34 bp):
GCCGGGGCGGGCGGGGCCGCCCGGCGCGCCCGCG
Found at i:10176618 original size:13 final size:13
Alignment explanation
Indices: 10176602--10176659 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
10176592 GGCCGGGGCG
*
10176602 GGCGGGGCCGCGC
1 GGCGCGGCCGCGC
10176615 GGCGCGGCCGCGGC
1 GGCGCGGCCGC-GC
* *
10176629 CGCGCAAGCCGCG-
1 GGCGC-GGCCGCGC
10176642 GGCGCGG-CGCGC
1 GGCGCGGCCGCGC
10176654 GG-GCGG
1 GGCGCGG
10176660 GGCTGGGGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
11 8 0.22
12 3 0.08
13 14 0.38
14 7 0.19
15 5 0.14
ACGTcount: A:0.03, C:0.40, G:0.57, T:0.00
Consensus pattern (13 bp):
GGCGCGGCCGCGC
Found at i:10177048 original size:26 final size:26
Alignment explanation
Indices: 10177019--10177082 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 26
10177009 CCGCCCGGAG
10177019 CGGGCCGCGGGGC-GCGGCCGGCGCGC
1 CGGGCCGCGGGGCGGCGGCC-GCGCGC
*
10177045 CGGGCGCTGCGGGGCGGCGGGCGCGCGC
1 CGGGC-C-GCGGGGCGGCGGCCGCGCGC
*
10177073 CGGTCCGCGG
1 CGGGCCGCGG
10177083 CCAGGCCGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 9 0.27
27 2 0.06
28 17 0.52
29 5 0.15
ACGTcount: A:0.00, C:0.39, G:0.58, T:0.03
Consensus pattern (26 bp):
CGGGCCGCGGGGCGGCGGCCGCGCGC
Found at i:10180984 original size:14 final size:14
Alignment explanation
Indices: 10180944--10180975 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
10180934 GAGTTTGGAG
*
10180944 AGAGAGAGAGAGAC
1 AGAGACAGAGAGAC
10180958 AGAGACAGAGAGAC
1 AGAGACAGAGAGAC
10180972 AGAG
1 AGAG
10180976 GGAGTGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAGACAGAGAGAC
Found at i:10183068 original size:17 final size:18
Alignment explanation
Indices: 10183033--10183069 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
10183023 CAAGTAAATT
10183033 TTAAGTAGTGTTAATTAA
1 TTAAGTAGTGTTAATTAA
10183051 TTAAGTA-T-TTACATTAA
1 TTAAGTAGTGTTA-ATTAA
10183068 TT
1 TT
10183070 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 8 0.44
18 7 0.39
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAAGTAGTGTTAATTAA
Found at i:10183081 original size:15 final size:17
Alignment explanation
Indices: 10183032--10183085 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
10183022 TCAAGTAAAT
10183032 TTTAAGTAGTGTTAATTAA
1 TTTAAGTA-T-TTAATTAA
10183051 -TTAAGTATTTACATTAA
1 TTTAAGTATTTA-ATTAA
10183068 TTTAA-T-TTTAATTAA
1 TTTAAGTATTTAATTAA
10183083 TTT
1 TTT
10183086 TTTCAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.24
16 7 0.21
17 7 0.21
18 11 0.33
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (17 bp):
TTTAAGTATTTAATTAA
Found at i:10187371 original size:15 final size:15
Alignment explanation
Indices: 10187340--10187388 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
10187330 CATTTGGTGT
*
10187340 ATTGTTAGAAATGTG
1 ATTGTTAGAAATATG
*
10187355 ATTGTTAGATATATG
1 ATTGTTAGAAATATG
** *
10187370 ATTACTAGAAATACG
1 ATTGTTAGAAATATG
10187385 ATTG
1 ATTG
10187389 CTGGGAATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (15 bp):
ATTGTTAGAAATATG
Found at i:10188170 original size:38 final size:38
Alignment explanation
Indices: 10188121--10188202 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
10188111 ACTTTCATTT
* * *
10188121 TTCTCTCCTTCCTTGTTGCTCTATGGTGATGGATTGTTC
1 TTCT-TCCTTCCTCGTTGCTATATGGTGATGGACTGTTC
* *
10188160 TTCTTCCTTCCTCGTTGCTATTTGTTGATGGACTGTTC
1 TTCTTCCTTCCTCGTTGCTATATGGTGATGGACTGTTC
10188198 TTCTT
1 TTCTT
10188203 TTCTTTGCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
38 34 0.89
39 4 0.11
ACGTcount: A:0.07, C:0.23, G:0.18, T:0.51
Consensus pattern (38 bp):
TTCTTCCTTCCTCGTTGCTATATGGTGATGGACTGTTC
Found at i:10198836 original size:2 final size:2
Alignment explanation
Indices: 10198829--10198855 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10198819 AAAGGATATA
10198829 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
10198856 TACATTACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10204418 original size:2 final size:2
Alignment explanation
Indices: 10204411--10204442 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10204401 AGGAAATGGA
10204411 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
10204443 CATGCATCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:10206366 original size:15 final size:14
Alignment explanation
Indices: 10206345--10206379 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
10206335 GTATTGTCCA
10206345 TTCTTTTTC-TTTT
1 TTCTTTTTCTTTTT
10206358 TTCTCTTTTCTTTTT
1 TTCT-TTTTCTTTTT
10206373 TTCTTTT
1 TTCTTTT
10206380 CACCCCAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 8 0.40
15 8 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:10206371 original size:13 final size:14
Alignment explanation
Indices: 10206345--10206380 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
10206335 GTATTGTCCA
10206345 TTCT-TTTTCTTTT
1 TTCTCTTTTCTTTT
10206358 TTCTCTTTTCTTTT
1 TTCTCTTTTCTTTT
10206372 TT-TCTTTTC
1 TTCTCTTTTC
10206381 ACCCCAGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTCTTTTCTTTT
Found at i:10210850 original size:6 final size:6
Alignment explanation
Indices: 10210839--10210871 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10210829 GCAAAGAGCT
10210839 TTTTTG TTTTTG TTTTTG TTTTT- TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
10210872 CACTTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (6 bp):
TTTTTG
Found at i:10211036 original size:4 final size:4
Alignment explanation
Indices: 10211027--10211053 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10211017 CCAATGAAGA
10211027 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
10211054 TTTTTTAGGT
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:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:10216944 original size:2 final size:2
Alignment explanation
Indices: 10216937--10216965 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10216927 TACACATACA
10216937 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 A
10216966 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10218988 original size:42 final size:42
Alignment explanation
Indices: 10218929--10219011 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
10218919 ACTCACCCTG
10218929 AAAGATCAGGCACGATTACGAACCAATGCAGGAATCATTGCA
1 AAAGATCAGGCACGATTACGAACCAATGCAGGAATCATTGCA
*
10218971 AAAGATCAGGCACGATTATGAACCAATGCAGGAATCATTGC
1 AAAGATCAGGCACGATTACGAACCAATGCAGGAATCATTGC
10219012 TCCAGACTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (42 bp):
AAAGATCAGGCACGATTACGAACCAATGCAGGAATCATTGCA
Found at i:10232054 original size:2 final size:2
Alignment explanation
Indices: 10232049--10232074 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10232039 GAGAGACCAC
10232049 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10232075 GACAACAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10232302 original size:2 final size:2
Alignment explanation
Indices: 10232295--10232327 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10232285 GTTGACATAA
10232295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10232328 AATCTATCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10237065 original size:33 final size:33
Alignment explanation
Indices: 10236992--10237058 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
10236982 TGGCCTAATA
*
10236992 TGAAGGATA-CTTCAATAACCAGTTATCAAGGT
1 TGAAGAATACCTTCAATAACCAGTTATCAAGGT
10237024 TGAAGAATACCTTC-ATAACCAGTTATCAAGGT
1 TGAAGAATACCTTCAATAACCAGTTATCAAGGT
10237056 TGA
1 TGA
10237059 TTGAATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (33 bp):
TGAAGAATACCTTCAATAACCAGTTATCAAGGT
Found at i:10265067 original size:7 final size:8
Alignment explanation
Indices: 10265051--10265076 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
10265041 GATTCCCGGC
10265051 AAAAGAAA
1 AAAAGAAA
10265059 AAAAGAAA
1 AAAAGAAA
10265067 AAAAGAAA
1 AAAAGAAA
10265075 AA
1 AA
10265077 GGAAAACCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:10265640 original size:2 final size:2
Alignment explanation
Indices: 10265633--10265657 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10265623 TTGTAGAAGA
10265633 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
10265658 AAAGATTTAA
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:10267996 original size:17 final size:19
Alignment explanation
Indices: 10267974--10268058 Score: 59
Period size: 21 Copynumber: 4.4 Consensus size: 19
10267964 AGCATCGTAC
10267974 AATTTA-AAATT-TAAATA
1 AATTTATAAATTATAAATA
10267991 AATTTATAAATTATAAATTTA
1 AATTTATAAATTATAAA--TA
* * * *
10268012 TATTTTTAATTTTAAAAATA
1 AATTTATAA-ATTATAAATA
* *
10268032 TAATTAATAAATAATAAA-A
1 -AATTTATAAATTATAAATA
10268051 AATTTATA
1 AATTTATA
10268059 TTTATATATC
Statistics
Matches: 51, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
17 6 0.12
18 12 0.24
19 5 0.10
20 7 0.14
21 15 0.29
22 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTATAAATTATAAATA
Found at i:10269579 original size:29 final size:27
Alignment explanation
Indices: 10269543--10269602 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
10269533 AATGTTTATG
*
10269543 TATAAATTAAATATATATATAATGTATT
1 TATAAATTAAATATATATATAATAT-TT
* *
10269571 TATACAATTATATATATTTATAATATTT
1 TATA-AATTAAATATATATATAATATTT
10269599 TATA
1 TATA
10269603 TTATAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
TATAAATTAAATATATATATAATATTT
Found at i:10269836 original size:16 final size:16
Alignment explanation
Indices: 10269817--10269850 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10269807 CTATTATATT
*
10269817 TTAAGTATATTATTAA
1 TTAAGTATATTATCAA
*
10269833 TTAAGTTTATTATCAA
1 TTAAGTATATTATCAA
10269849 TT
1 TT
10269851 TTTTTGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAGTATATTATCAA
Found at i:10277717 original size:4 final size:4
Alignment explanation
Indices: 10277708--10277738 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
10277698 AAAGAGAATC
10277708 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
10277739 TTCTATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:10281045 original size:18 final size:17
Alignment explanation
Indices: 10281021--10281060 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
10281011 TTCTTTTTCT
*
10281021 TTTTTTTTTAATTATATCA
1 TTTTTTATT-ATTATA-CA
10281040 TTTTTTATTATTATACA
1 TTTTTTATTATTATACA
10281057 TTTT
1 TTTT
10281061 AATGCGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 6 0.30
19 8 0.40
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTATTATTATACA
Found at i:10281049 original size:15 final size:18
Alignment explanation
Indices: 10281024--10281060 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
10281014 TTTTTCTTTT
10281024 TTTTTTAATTA-TAT-CA
1 TTTTTTAATTATTATACA
10281040 TTTTTT-ATTATTATACA
1 TTTTTTAATTATTATACA
10281057 TTTT
1 TTTT
10281061 AATGCGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 9 0.47
17 6 0.32
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTAATTATTATACA
Found at i:10283090 original size:21 final size:20
Alignment explanation
Indices: 10283039--10283091 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
10283029 TTGAGTGGTG
10283039 TTATAATT--AAAATAATAA
1 TTATAATTAAAAAATAATAA
*
10283057 TTATAATTAAAAAATTAATAT
1 TTATAATTAAAAAA-TAATAA
10283078 TTA-AATTATAAAAA
1 TTATAATTA-AAAAA
10283092 AATTTATCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.27
20 9 0.30
21 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTATAATTAAAAAATAATAA
Found at i:10284849 original size:25 final size:25
Alignment explanation
Indices: 10284820--10284868 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
10284810 AATTAATACT
*
10284820 ATTAATCTTCATGCAATAAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
* *
10284845 ATTAATCTTTATATAATAAATAAA
1 ATTAATCTTCATACAATAAATAAA
10284869 TATTTGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (25 bp):
ATTAATCTTCATACAATAAATAAAC
Found at i:10285038 original size:16 final size:16
Alignment explanation
Indices: 10285017--10285049 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10285007 CAAGGCTCCA
10285017 ACTTCAATTTTTAACG
1 ACTTCAATTTTTAACG
10285033 ACTTCAATTTTTAACG
1 ACTTCAATTTTTAACG
10285049 A
1 A
10285050 TTTTGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ACTTCAATTTTTAACG
Found at i:10285307 original size:12 final size:12
Alignment explanation
Indices: 10285290--10285328 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10285280 AACAAATCTA
10285290 ATAAATTAAATT
1 ATAAATTAAATT
* *
10285302 ATAAATAAAACT
1 ATAAATTAAATT
*
10285314 ATAAAATAAATT
1 ATAAATTAAATT
10285326 ATA
1 ATA
10285329 TAGTTACCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAATTAAATT
Found at i:10287692 original size:41 final size:41
Alignment explanation
Indices: 10287647--10287767 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 41
10287637 AAATGTCACT
10287647 TATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAA
1 TATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAA
* * * * **
10287688 TATCA-AATGATTTATCA----TTAAT-TAAAATGT--CACT
1 TATCATTA-CATTTATCAGGTGTTAATATAAAAAGTAAAAAA
10287722 TATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAA
1 TATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAA
10287763 TATCA
1 TATCA
10287768 AATGATTATG
Statistics
Matches: 59, Mismatches: 12, Indels: 18
0.66 0.13 0.20
Matches are distributed among these distances:
34 14 0.24
35 1 0.02
36 7 0.12
37 5 0.08
38 5 0.08
39 7 0.12
40 1 0.02
41 19 0.32
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.36
Consensus pattern (41 bp):
TATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAA
Found at i:10287709 original size:74 final size:75
Alignment explanation
Indices: 10287625--10287774 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
10287615 AGTTAATTAA
10287625 TTATCATTAATT-AAATGTCACTTATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAAT
1 TTATCATTAATTAAAATGTCACTTATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAAT
10287689 ATCAAATGAT
66 ATCAAATGAT
10287699 TTATCATTAATTAAAATGTCACTTATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAAT
1 TTATCATTAATTAAAATGTCACTTATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAAT
10287764 ATCAAATGAT
66 ATCAAATGAT
10287774 T
1 T
10287775 ATGTCATCAT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 12 0.16
75 63 0.84
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (75 bp):
TTATCATTAATTAAAATGTCACTTATCATTACATTTATCAGGTGTTAATATAAAAAGTAAAAAAT
ATCAAATGAT
Found at i:10289836 original size:7 final size:7
Alignment explanation
Indices: 10289819--10289857 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
10289809 TAGTATAACT
10289819 GTATA-A
1 GTATATA
10289825 GTATATA
1 GTATATA
10289832 GTATATA
1 GTATATA
10289839 GTATATA
1 GTATATA
10289846 GTATATA
1 GTATATA
10289853 GTATA
1 GTATA
10289858 CATGCATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (7 bp):
GTATATA
Found at i:10293127 original size:3 final size:3
Alignment explanation
Indices: 10293114--10293146 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
10293104 AAGCCACAAA
10293114 AAT AA- AAT AAT AAT AAT AAT AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10293147 GGTTATAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:10293140 original size:14 final size:14
Alignment explanation
Indices: 10293114--10293146 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10293104 AAGCCACAAA
10293114 AATAAAATAATAAT
1 AATAAAATAATAAT
10293128 AATAATAAT-ATAAT
1 AATAA-AATAATAAT
10293142 AATAA
1 AATAA
10293147 GGTTATAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAAATAATAAT
Found at i:10293140 original size:17 final size:17
Alignment explanation
Indices: 10293114--10293146 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10293104 AAGCCACAAA
10293114 AATAAAATAATAATAAT
1 AATAAAATAATAATAAT
*
10293131 AATAATATAATAATAA
1 AATAAAATAATAATAA
10293147 GGTTATAGGA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAAATAATAATAAT
Found at i:10293633 original size:13 final size:13
Alignment explanation
Indices: 10293615--10293650 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
10293605 CCTTTTGCTA
10293615 GCATTTGCATCCT
1 GCATTTGCATCCT
10293628 GCATTTGCATCCT
1 GCATTTGCATCCT
*
10293641 GCATCTGCAT
1 GCATTTGCAT
10293651 ATCTGACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.36
Consensus pattern (13 bp):
GCATTTGCATCCT
Found at i:10301253 original size:19 final size:19
Alignment explanation
Indices: 10301229--10301274 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
10301219 GCAATTGCAA
10301229 GTTGGTTAACAGATAACTG
1 GTTGGTTAACAGATAACTG
10301248 GTTGGTTAACAGATAACTG
1 GTTGGTTAACAGATAACTG
10301267 GTTGGTTA
1 GTTGGTTA
10301275 TTGGATGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (19 bp):
GTTGGTTAACAGATAACTG
Found at i:10313044 original size:2 final size:2
Alignment explanation
Indices: 10313037--10313065 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10313027 ATTCTCCTCT
10313037 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10313066 CATACTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10314198 original size:2 final size:2
Alignment explanation
Indices: 10314186--10314232 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
10314176 TGACTTTTGT
* * * *
10314186 GA GA GA TA GA GA GA GA GA GA CA GA GA GA GA GA GA GG GA GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10314228 GA GA G
1 GA GA G
10314233 GGAGGGACAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.45, C:0.02, G:0.51, T:0.02
Consensus pattern (2 bp):
GA
Found at i:10314226 original size:16 final size:16
Alignment explanation
Indices: 10314193--10314254 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
10314183 TGTGAGAGAT
**
10314193 AGAGAGAGAGAGACAG
1 AGAGAGAGAGAGGGAG
10314209 AGAGAGAGAGAGGGAG
1 AGAGAGAGAGAGGGAG
* * *
10314225 AGGGAGAGGGAGGGAC
1 AGAGAGAGAGAGGGAG
* *
10314241 AGAAAAAGAGAGGG
1 AGAGAGAGAGAGGG
10314255 TGTTTGCATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.45, C:0.03, G:0.52, T:0.00
Consensus pattern (16 bp):
AGAGAGAGAGAGGGAG
Found at i:10314633 original size:15 final size:16
Alignment explanation
Indices: 10314615--10314652 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
10314605 GTTTTCGAGT
10314615 TTGTTGTT-ATTGTTG
1 TTGTTGTTCATTGTTG
*
10314630 TTGTT-TTCATTTTTG
1 TTGTTGTTCATTGTTG
10314645 TTGTTGTT
1 TTGTTGTT
10314653 TGCGTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.80
16 2 0.10
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.71
Consensus pattern (16 bp):
TTGTTGTTCATTGTTG
Found at i:10314633 original size:27 final size:24
Alignment explanation
Indices: 10314603--10314652 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
10314593 TTTTTGTATA
10314603 TTGTTTTCGAGTTTGTTGTTATTGTTG
1 TTGTTTTC-A-TTT-TTGTTATTGTTG
*
10314630 TTGTTTTCATTTTTGTTGTTGTT
1 TTGTTTTCATTTTTGTTATTGTT
10314653 TGCGTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 3 0.14
26 1 0.05
27 8 0.36
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (24 bp):
TTGTTTTCATTTTTGTTATTGTTG
Found at i:10315352 original size:2 final size:2
Alignment explanation
Indices: 10315345--10315380 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10315335 TGTGATGCAC
*
10315345 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10315381 GAAGTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:10319586 original size:23 final size:23
Alignment explanation
Indices: 10319548--10319612 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
10319538 AAACGTTATT
10319548 AATATTAATATGTTTAAAATATTAA
1 AATATTAATA--TTTAAAATATTAA
* **
10319573 AATATTAGTATTTAATTTATTAA
1 AATATTAATATTTAAAATATTAA
*
10319596 ATTATTAATATATTAAA
1 AATATTAATAT-TTAAA
10319613 TTTTTAACGA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 20 0.61
24 4 0.12
25 9 0.27
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
AATATTAATATTTAAAATATTAA
Found at i:10319609 original size:16 final size:16
Alignment explanation
Indices: 10319584--10319619 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10319574 ATATTAGTAT
*
10319584 TTAATTTATTAAATTA
1 TTAATATATTAAATTA
*
10319600 TTAATATATTAAATTT
1 TTAATATATTAAATTA
10319616 TTAA
1 TTAA
10319620 CGAGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATATATTAAATTA
Found at i:10319665 original size:23 final size:24
Alignment explanation
Indices: 10319625--10319675 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
10319615 TTTAACGAGT
*
10319625 ATAAATAAAAAATAAAAAATGTA-A
1 ATAAAGAAAAAATAAAAAAT-TATA
10319649 ATAAAGAAAAAAT-AAAAATTATA
1 ATAAAGAAAAAATAAAAAATTATA
10319672 ATAA
1 ATAA
10319676 TATTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 2 0.08
23 11 0.44
24 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (24 bp):
ATAAAGAAAAAATAAAAAATTATA
Found at i:10319707 original size:15 final size:16
Alignment explanation
Indices: 10319687--10319720 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10319677 ATTTTAATAA
10319687 TAAATTATT-AAATTT
1 TAAATTATTAAAATTT
*
10319702 TAAATTTTTAAAATTT
1 TAAATTATTAAAATTT
10319718 TAA
1 TAA
10319721 TGAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTATTAAAATTT
Found at i:10321180 original size:18 final size:18
Alignment explanation
Indices: 10321157--10321193 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
10321147 GCGAGAACAC
10321157 TACACTATAACTTTTTAA
1 TACACTATAACTTTTTAA
10321175 TACACTATAACTTTTTAA
1 TACACTATAACTTTTTAA
10321193 T
1 T
10321194 GCATTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (18 bp):
TACACTATAACTTTTTAA
Found at i:10321453 original size:17 final size:18
Alignment explanation
Indices: 10321431--10321465 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10321421 GTCAAGATTG
10321431 ATCAAAAATATT-ATTTA
1 ATCAAAAATATTAATTTA
*
10321448 ATCAAAATTATTAATTTA
1 ATCAAAAATATTAATTTA
10321466 TCCAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
ATCAAAAATATTAATTTA
Found at i:10332767 original size:26 final size:27
Alignment explanation
Indices: 10332686--10332767 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 27
10332676 TAATTCTAAA
* * *
10332686 GATAATTTTGCCACAAG-AAGTGGATG
1 GATAATTTTACTACCAGAAAGTGGATG
* * *
10332712 GATAATTTTGCTACCAGAAA-TAGATA
1 GATAATTTTACTACCAGAAAGTGGATG
*
10332738 GATAATTTTATTACCA-AAAGTGGATG
1 GATAATTTTACTACCAGAAAGTGGATG
10332764 GATA
1 GATA
10332768 CCTTAATCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
25 3 0.07
26 41 0.89
27 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (27 bp):
GATAATTTTACTACCAGAAAGTGGATG
Found at i:10339922 original size:3 final size:3
Alignment explanation
Indices: 10339914--10340030 Score: 189
Period size: 3 Copynumber: 39.0 Consensus size: 3
10339904 GTAGAAGCAA
*
10339914 AAG AAG AAG AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
10339962 AAG AAG AAA AAG AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
10340010 AAG AAG AAG AAA AAG CAG AAG
1 AAG AAG AAG AAG AAG AAG AAG
10340031 GAAAAAAAAT
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10355507 original size:28 final size:28
Alignment explanation
Indices: 10355470--10355536 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
10355460 TTTCCAAATG
*
10355470 TCCAAAGTATAAACCATTTCATGGCAAAA
1 TCCAAAGTATAAACCACTTCATGG-AAAA
**
10355499 -CCAAAGTATAAGTCACTTCATGGAAAA
1 TCCAAAGTATAAACCACTTCATGGAAAA
10355526 TCCAAAGTATA
1 TCCAAAGTATA
10355537 GCATTTGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 4 0.12
28 30 0.88
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (28 bp):
TCCAAAGTATAAACCACTTCATGGAAAA
Found at i:10358469 original size:19 final size:19
Alignment explanation
Indices: 10358445--10358482 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
10358435 TTTCAAAAAA
10358445 ATAAATGAAGTCAAGCTAG
1 ATAAATGAAGTCAAGCTAG
10358464 ATAAATGAAGTCAAGCTAG
1 ATAAATGAAGTCAAGCTAG
10358483 TTGGCTACAG
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:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (19 bp):
ATAAATGAAGTCAAGCTAG
Found at i:10358663 original size:45 final size:45
Alignment explanation
Indices: 10358599--10358694 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
10358589 GAAAATAAGA
10358599 TGTTGCTGCTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
1 TGTTGCTGCTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
10358644 TGTTGCTGCTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
1 TGTTGCTGCTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
10358689 TGTTGC
1 TGTTGC
10358695 CTACTAATCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (45 bp):
TGTTGCTGCTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
Found at i:10358703 original size:45 final size:45
Alignment explanation
Indices: 10358599--10358705 Score: 180
Period size: 45 Copynumber: 2.4 Consensus size: 45
10358589 GAAAATAAGA
*
10358599 TGTTGCTGCTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
1 TGTTGCTACTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
*
10358644 TGTTGCTGCTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
1 TGTTGCTACTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
10358689 TGTTGCCTAC-TAATCAA
1 TGTTG-CTACTTAATCAA
10358706 GTAATATGGT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
45 57 0.95
46 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (45 bp):
TGTTGCTACTTAATCAACAGTTGAAGCAGAATACATTGCTACTAC
Found at i:10360661 original size:39 final size:38
Alignment explanation
Indices: 10360594--10360749 Score: 152
Period size: 39 Copynumber: 4.0 Consensus size: 38
10360584 GATTTCATTT
* * * *
10360594 CATTCATAAATTGATATCCATCATATGAATAAACCAAGA
1 CATTCATAAAGTAATCTTCATCATATGAATAAACCAA-A
* * * *
10360633 CATTCATAGAGTAATGTTTATCACATGAATAAACCAAA
1 CATTCATAAAGTAATCTTCATCATATGAATAAACCAAA
* *
10360671 TCATTCATAAATTAATCTTCGTCATATGAATAAACCAAAA
1 -CATTCATAAAGTAATCTTCATCATATGAATAAACC-AAA
* *
10360711 CATTCATAAA-TCATTCTTTCATCATATGAATAAATCAAA
1 CATTCATAAAGT-AATC-TTCATCATATGAATAAACCAAA
10360750 ATAGAAAATA
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 75 0.77
40 20 0.21
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (38 bp):
CATTCATAAAGTAATCTTCATCATATGAATAAACCAAA
Found at i:10370215 original size:6 final size:6
Alignment explanation
Indices: 10370206--10370231 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10370196 TTCTTCTTCC
10370206 ATTAAA ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA AT
10370232 ATTTTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:10370617 original size:24 final size:24
Alignment explanation
Indices: 10370575--10370620 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
10370565 TCATTTTTTT
* **
10370575 CTCTCTCTTAGGGTTTCAACAACA
1 CTCTCTCTTAAGGACTCAACAACA
10370599 CTCTCTCTTAAGGACTCAACAA
1 CTCTCTCTTAAGGACTCAACAA
10370621 AATTTTAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (24 bp):
CTCTCTCTTAAGGACTCAACAACA
Found at i:10381792 original size:2 final size:2
Alignment explanation
Indices: 10381785--10381828 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
10381775 ACCAAAATTC
* *
10381785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
10381827 AT
1 AT
10381829 CCTATCCTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10401165 original size:2 final size:2
Alignment explanation
Indices: 10401120--10401146 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10401110 TTCACAATAC
10401120 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
10401147 TTTTAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10401698 original size:3 final size:3
Alignment explanation
Indices: 10401623--10401684 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
10401613 CCAAATATAC
10401623 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10401671 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
10401685 CCCTACCTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:10401749 original size:2 final size:2
Alignment explanation
Indices: 10401742--10401770 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10401732 TACCTACATC
10401742 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10401771 ACCAAATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10401849 original size:2 final size:2
Alignment explanation
Indices: 10401842--10401868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10401832 ATATCTTTCC
10401842 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
10401869 TCTACCTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10402770 original size:23 final size:25
Alignment explanation
Indices: 10402725--10402795 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 25
10402715 ATGTTATGTT
10402725 AAAAAAATTATTAAATATCATATTG
1 AAAAAAATTATTAAATATCATATTG
*
10402750 AAAAAATATTATTAATTATATGTCATATTAA
1 AAAAAA-ATTATTAA--ATA--TCATATT-G
10402781 AAAAAAATTATTAAA
1 AAAAAAATTATTAAA
10402796 CGTCATGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 6 0.15
26 8 0.21
28 4 0.10
30 15 0.38
31 6 0.15
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (25 bp):
AAAAAAATTATTAAATATCATATTG
Found at i:10402800 original size:26 final size:26
Alignment explanation
Indices: 10402725--10402838 Score: 84
Period size: 26 Copynumber: 4.2 Consensus size: 26
10402715 ATGTTATGTT
*
10402725 AAAAAAATTATTAAATATCATATTGAA
1 AAAAAAATTATTAAATGTCATATT-AA
* *
10402752 AAAATATTATTAATTATATGTCATATTAA
1 AAAA-A-AATT-ATTAAATGTCATATTAA
* * *
10402781 AAAAAAATTATTAAACGTCATGTTTA
1 AAAAAAATTATTAAATGTCATATTAA
*** * * *
10402807 AAAATTGTTATTACATGTAATATTTA
1 AAAAAAATTATTAAATGTCATATTAA
10402833 AAAAAA
1 AAAAAA
10402839 TATATATGTT
Statistics
Matches: 67, Mismatches: 17, Indels: 7
0.74 0.19 0.08
Matches are distributed among these distances:
26 36 0.54
27 7 0.10
28 2 0.03
29 9 0.13
30 13 0.19
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (26 bp):
AAAAAAATTATTAAATGTCATATTAA
Found at i:10402882 original size:26 final size:26
Alignment explanation
Indices: 10402780--10402903 Score: 78
Period size: 24 Copynumber: 4.9 Consensus size: 26
10402770 TGTCATATTA
* * *
10402780 AAAAAAAATTATTAAACGTCATGTTT
1 AAAAAATATTATTACACGTAATGTTT
* * * *
10402806 AAAAATTGTTATTACATGTAATATTT
1 AAAAAATATTATTACACGTAATGTTT
* * * *
10402832 AAAAAA-A-TA-TATATGTTATTTTTT
1 AAAAAATATTATTACACG-TAATGTTT
*
10402856 AAAAAATATTATTACACGTTATGTTT
1 AAAAAATATTATTACACGTAATGTTT
* *
10402882 --ACAATATTATCACACGTAATGT
1 AAAAAATATTATTACACGTAATGT
10402904 ATGGAAAAAT
Statistics
Matches: 74, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
23 5 0.07
24 33 0.45
25 1 0.01
26 31 0.42
27 4 0.05
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (26 bp):
AAAAAATATTATTACACGTAATGTTT
Found at i:10405856 original size:27 final size:26
Alignment explanation
Indices: 10405824--10405910 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 26
10405814 TTATAAAATG
*
10405824 TTATTATTACACATTATGTTAAAAAAA
1 TTATTATTA-ACGTTATGTTAAAAAAA
*
10405851 TTATTA-T-ATGTTAT-TTAAAAAATA
1 TTATTATTAACGTTATGTTAAAAAA-A
*
10405875 TTATTGTTATACGTTATGTTTAAAAAAA
1 TTATTATTA-ACGTTATG-TTAAAAAAA
10405903 GTTATTAT
1 -TTATTAT
10405911 ACATCATGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
23 8 0.17
24 11 0.23
25 1 0.02
26 1 0.02
27 12 0.25
28 1 0.02
29 14 0.29
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (26 bp):
TTATTATTAACGTTATGTTAAAAAAA
Found at i:10405870 original size:21 final size:20
Alignment explanation
Indices: 10405845--10405884 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
10405835 CATTATGTTA
10405845 AAAAAATTATTATATGTTATTT
1 AAAAAA-TATTAT-TGTTATTT
10405867 AAAAAATATTATTGTTAT
1 AAAAAATATTATTGTTAT
10405885 ACGTTATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 6 0.33
22 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAAAATATTATTGTTATTT
Found at i:10405873 original size:51 final size:53
Alignment explanation
Indices: 10405813--10405911 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 53
10405803 AAAACACATG
* *
10405813 TTTATAAAATGTTATTATTACACATTATG-TTAAAAAAA-TTATTATATGTTA
1 TTTAAAAAATATTATTATTACACATTATGTTTAAAAAAAGTTATTATATGTTA
* * *
10405864 TTTAAAAAATATTATTGTTATACGTTATGTTTAAAAAAAGTTATTATA
1 TTTAAAAAATATTATTATTACACATTATGTTTAAAAAAAGTTATTATA
10405912 CATCATGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 24 0.59
52 9 0.22
53 8 0.20
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (53 bp):
TTTAAAAAATATTATTATTACACATTATGTTTAAAAAAAGTTATTATATGTTA
Found at i:10405907 original size:29 final size:27
Alignment explanation
Indices: 10405810--10405908 Score: 73
Period size: 29 Copynumber: 3.7 Consensus size: 27
10405800 ATAAAAACAC
** * *
10405810 ATGTTTATAAAATGTTATTATTACACATT
1 ATGTTTA-AAAAAATTATT-TTATACGTT
*
10405839 ATG-TTAAAAAAATTA--TTATATGTT
1 ATGTTTAAAAAAATTATTTTATACGTT
10405863 A--TTTAAAAAATATTATTGTTATACGTT
1 ATGTTTAAAAAA-ATTATT-TTATACGTT
10405890 ATGTTTAAAAAAAGTTATT
1 ATGTTTAAAAAAA-TTATT
10405909 ATACATCATG
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
23 8 0.14
24 11 0.20
27 16 0.29
28 4 0.07
29 17 0.30
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (27 bp):
ATGTTTAAAAAAATTATTTTATACGTT
Found at i:10406136 original size:24 final size:24
Alignment explanation
Indices: 10406104--10406161 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
10406094 TCATGTTTAC
*
10406104 AATATTGTTGCATG-CTATGTATAGA
1 AATA-TGTTGCACGTCT-TGTATAGA
*
10406129 AATATGTTACACGTCTTGTATAGA
1 AATATGTTGCACGTCTTGTATAGA
*
10406153 ATTATGTTG
1 AATATGTTG
10406162 TTACACATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (24 bp):
AATATGTTGCACGTCTTGTATAGA
Found at i:10411035 original size:2 final size:2
Alignment explanation
Indices: 10411028--10411059 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10411018 TAGGAAGCAC
*
10411028 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10411060 TAGGTCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10419580 original size:16 final size:17
Alignment explanation
Indices: 10419556--10419590 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
10419546 ATAAACTTCA
*
10419556 TTTACATTTTTTATTAT
1 TTTACATTTTTTATAAT
10419573 TTTA-ATTTTTTATAAT
1 TTTACATTTTTTATAAT
10419589 TT
1 TT
10419591 CTTTTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTACATTTTTTATAAT
Found at i:10421074 original size:13 final size:13
Alignment explanation
Indices: 10421055--10421096 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
10421045 TTAAACATTA
10421055 AGAATT-ATGTTT
1 AGAATTAATGTTT
*
10421067 GGGAATTAATGTTT
1 -AGAATTAATGTTT
10421081 AGAATTAATGTTT
1 AGAATTAATGTTT
10421094 AGA
1 AGA
10421097 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (13 bp):
AGAATTAATGTTT
Found at i:10421238 original size:85 final size:85
Alignment explanation
Indices: 10420913--10421223 Score: 425
Period size: 85 Copynumber: 3.7 Consensus size: 85
10420903 ACTTTAATAA
* * *
10420913 TTAGAATTATTGTTTGAATAATTAATTAAAATGATT--T--GATGCTAGAATTAAACATTAAGAA
1 TTAGAATTATTATTTGAATATTTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTAAGAA
10420974 TTATGTTTGGGAATTAATGT
66 TTATGTTTGGGAATTAATGT
** * *
10420994 TTAGAATTATTATTTGGGTATTTAATTAAAATAATTGGTAATATGTTAGAATTAAACATTAAGAA
1 TTAGAATTATTATTTGAATATTTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTAAGAA
10421059 TTATGTTTGGGAATTAATGT
66 TTATGTTTGGGAATTAATGT
* * * * * * * *
10421079 TTAGAATTAATGTTT-AGATTTTTAAATAAAATGATTAGTAATATGGTAGAATTAAATATTAAAA
1 TTAGAATTATTATTTGA-ATATTTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTAAGA
*
10421143 ATTATGTTTGGGAACTAATGT
65 ATTATGTTTGGGAATTAATGT
*
10421164 TTAGAATTATTATTTGAATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAACATT
1 TTAGAATTATTATTTGAATATTTAATTAAAATGATTGGTAATATGCTAGAATTAAACATT
10421224 GGAATTTATA
Statistics
Matches: 199, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
81 31 0.16
83 1 0.01
85 166 0.83
86 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.43
Consensus pattern (85 bp):
TTAGAATTATTATTTGAATATTTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTAAGAA
TTATGTTTGGGAATTAATGT
Found at i:10423644 original size:24 final size:25
Alignment explanation
Indices: 10423617--10423671 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
10423607 AACTTTTGAA
10423617 ATTAATGTTTATATATT-AATAAAG
1 ATTAATGTTTATATATTGAATAAAG
* *
10423641 ATTAATGTTTATTTATTGCATAAAG
1 ATTAATGTTTATATATTGAATAAAG
*
10423666 AATAAT
1 ATTAAT
10423672 ATTATTAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (25 bp):
ATTAATGTTTATATATTGAATAAAG
Found at i:10426112 original size:174 final size:175
Alignment explanation
Indices: 10425855--10426201 Score: 459
Period size: 174 Copynumber: 2.0 Consensus size: 175
10425845 TTGATTCGTG
** *
10425855 GTTGTTTATATTTTAGGAATAATGTGTTGATTCATGCTAAGATTGATTGATTGCTGGTATTTGGT
1 GTTGTTTATATTTTAGGAATAATGCATTAATTCATGCTAAGATTGATTGATTGCTGGTATTTGGT
* * *
10425920 ATTAATTTTAGTTGTATA-TGTTATTCGTTGTTAGC-GATA-TTTAATTGGAAATAATGTATT-G
66 ATTAATTCTAGTTGTATATTG-GATTCATTGTTA-CTGATATTTTAATTGGAAATAATGTATTAG
* * *
10425981 ATTGATAGATGCTGTTATTTTGGCTATTGAATATGTTGATTCATGGTT
129 -TTCATAGATACTGGTATTTTGGCTATTGAATATGTTGATTCATGGTT
* * ** **
10426029 GTTGTTTATATTTTGGGAATAATGCATTAATTCATGGTTGGATTGATTGATTGCTGGTATTTTTT
1 GTTGTTTATATTTTAGGAATAATGCATTAATTCATGCTAAGATTGATTGATTGCTGGTATTTGGT
* * *
10426094 ATTAATTCTAGTTGTATATTGGATTCATTGTTACTGGTATTTTAATTGGGAATAATGTGTTAGTT
66 ATTAATTCTAGTTGTATATTGGATTCATTGTTACTGATATTTTAATTGGAAATAATGTATTAGTT
* *
10426159 CATGGATACTGGTATTTTGGCTTTTGAATATGTTGATTCATGG
131 CATAGATACTGGTATTTTGGCTATTGAATATGTTGATTCATGG
10426202 GCATAAGTGA
Statistics
Matches: 149, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
173 1 0.01
174 86 0.58
175 61 0.41
176 1 0.01
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.48
Consensus pattern (175 bp):
GTTGTTTATATTTTAGGAATAATGCATTAATTCATGCTAAGATTGATTGATTGCTGGTATTTGGT
ATTAATTCTAGTTGTATATTGGATTCATTGTTACTGATATTTTAATTGGAAATAATGTATTAGTT
CATAGATACTGGTATTTTGGCTATTGAATATGTTGATTCATGGTT
Found at i:10431710 original size:12 final size:12
Alignment explanation
Indices: 10431693--10431730 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
10431683 AGTTCGGCTT
*
10431693 AAAATTTTGTCA
1 AAAATTATGTCA
10431705 AAAATTATGTCA
1 AAAATTATGTCA
*
10431717 AAAATCATGTCA
1 AAAATTATGTCA
10431729 AA
1 AA
10431731 TTTGAAGCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (12 bp):
AAAATTATGTCA
Found at i:10449654 original size:19 final size:19
Alignment explanation
Indices: 10449622--10449659 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10449612 CGATTGATAA
* *
10449622 GTTACTAATGAAATATTTT
1 GTTACCAATAAAATATTTT
10449641 GTTACCAATAAAATATTTT
1 GTTACCAATAAAATATTTT
10449660 ATTAGCAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (19 bp):
GTTACCAATAAAATATTTT
Found at i:10449668 original size:19 final size:19
Alignment explanation
Indices: 10449632--10449668 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10449622 GTTACTAATG
*
10449632 AAATATTTTGTTACCAATA
1 AAATATTTTATTACCAATA
*
10449651 AAATATTTTATTAGCAAT
1 AAATATTTTATTACCAAT
10449669 GAGTTTGCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (19 bp):
AAATATTTTATTACCAATA
Found at i:10462991 original size:27 final size:23
Alignment explanation
Indices: 10462938--10462996 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 23
10462928 TATTTTGTTG
10462938 TTCAATTTAGTTCTTAAATTTTA
1 TTCAATTTAGTTCTTAAATTTTA
10462961 TTCAATTTAGTGTACTTTAAATTTTTA
1 TTCAATTTAGT-T-C-TTAAA-TTTTA
10462988 TTCAATTTA
1 TTCAATTTA
10462997 ATTCCTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.34
24 1 0.03
25 1 0.03
26 5 0.16
27 14 0.44
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (23 bp):
TTCAATTTAGTTCTTAAATTTTA
Found at i:10474996 original size:2 final size:2
Alignment explanation
Indices: 10474989--10475013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10474979 TTAATGCTGG
10474989 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
10475014 GAAAAGCTGC
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:10478380 original size:30 final size:30
Alignment explanation
Indices: 10478316--10478380 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
10478306 AATTATTAGT
*
10478316 TATAAGAGTTTATTTAACTTAAAATAAAAA
1 TATAAGAGTTTATTTAACTCAAAATAAAAA
* * *
10478346 TATAAGAGTTTATTTAACTCAGAATAGAAG
1 TATAAGAGTTTATTTAACTCAAAATAAAAA
10478376 TATAA
1 TATAA
10478381 TGATTCGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (30 bp):
TATAAGAGTTTATTTAACTCAAAATAAAAA
Found at i:10493011 original size:176 final size:176
Alignment explanation
Indices: 10492815--10493166 Score: 514
Period size: 176 Copynumber: 2.0 Consensus size: 176
10492805 TTATCTAGAA
*
10492815 AAACAAACATAAATGGGGAAAAAGAAAAAATAATTAAGTTTTCTTTGTAGACAAAAGAAA-ATTA
1 AAACAAACATAAATGGGGAAAAAGAAAAAAGAATTAAGTTTTCTTTGTAGA-AAAA-AAATATTA
* *
10492879 AAAAAAA-AAAGAAATGTCAACTAAG-AGGCTTTTATTTTTAATTTTTTTGACACAATGCCTG-A
64 AAAAAAAGAAACAAAGGTCAACT-AGTAGGCTTTTATTTTTAATTTTTTTGACACAATGCCTGAA
* * *
10492941 AGAACCCTTGAACTATTTTAAAAAATTTAAATAAATTTTTATTTTTATAT
128 AAAACCCTTGAACTACTTTAAAAAATTCAAATAAATTTTTA-TTTTATAT
*
10492991 AAACAAACATAAATGGGGAAAAAGAAAAAAGAATTAAGTTTTCTTTGTAGAAAAAAAATTTTAAA
1 AAACAAACATAAATGGGGAAAAAGAAAAAAGAATTAAGTTTTCTTTGTAGAAAAAAAATATTAAA
* * * * * *
10493056 AAAAAGGAACAAAGGTTAAGTAGTAGGGTTTTATTTTTAATTTTTTTGACATAATGCTTGAAAAA
66 AAAAAGAAACAAAGGTCAACTAGTAGGCTTTTATTTTTAATTTTTTTGACACAATGCCTGAAAAA
*
10493121 ACCCTTGAACTACTTTAAAAAATTCAAATAAGTTTTTATTTTATAT
131 ACCCTTGAACTACTTTAAAAAATTCAAATAAATTTTTATTTTATAT
10493167 TGTGTTCAAG
Statistics
Matches: 158, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
174 3 0.02
175 16 0.10
176 101 0.64
177 38 0.24
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.34
Consensus pattern (176 bp):
AAACAAACATAAATGGGGAAAAAGAAAAAAGAATTAAGTTTTCTTTGTAGAAAAAAAATATTAAA
AAAAAGAAACAAAGGTCAACTAGTAGGCTTTTATTTTTAATTTTTTTGACACAATGCCTGAAAAA
ACCCTTGAACTACTTTAAAAAATTCAAATAAATTTTTATTTTATAT
Found at i:10494302 original size:16 final size:16
Alignment explanation
Indices: 10494281--10494317 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
10494271 TGTGTTAATG
10494281 TTATAAAAATTA-TAA
1 TTATAAAAATTATTAA
10494296 CTTAT-AAAATTATTAA
1 -TTATAAAAATTATTAA
10494312 TTATAA
1 TTATAA
10494318 TTTATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TTATAAAAATTATTAA
Found at i:10494612 original size:16 final size:16
Alignment explanation
Indices: 10494592--10494629 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
10494582 TGGCATTAAC
10494592 ATTATAAAAATTA-TA
1 ATTATAAAAATTATTA
10494607 ATT-TATAAAATTATTA
1 ATTATA-AAAATTATTA
10494623 ATTATAA
1 ATTATAA
10494630 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.10
15 10 0.50
16 6 0.30
17 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATAAAAATTATTA
Found at i:10501579 original size:15 final size:15
Alignment explanation
Indices: 10501559--10501589 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10501549 AAGTTTTATT
*
10501559 AAGTTAGCAGATACC
1 AAGTTAGCAAATACC
10501574 AAGTTAGCAAATACC
1 AAGTTAGCAAATACC
10501589 A
1 A
10501590 GTTGAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (15 bp):
AAGTTAGCAAATACC
Found at i:10502829 original size:2 final size:2
Alignment explanation
Indices: 10502822--10502850 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10502812 GCATTTCAAA
10502822 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 A
10502851 AAAACTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10503131 original size:2 final size:2
Alignment explanation
Indices: 10503124--10503148 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10503114 GGAAGACAAA
10503124 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
10503149 AACAAAGAGA
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:10512770 original size:23 final size:24
Alignment explanation
Indices: 10512735--10512779 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
10512725 GTTGACTAAT
*
10512735 TTTTTAATACA-TTTTTATTTTCA
1 TTTTAAATACATTTTTTATTTTCA
*
10512758 TTTTAAATTCATTTTTTATTTT
1 TTTTAAATACATTTTTTATTTT
10512780 AAACTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTAAATACATTTTTTATTTTCA
Found at i:10512793 original size:18 final size:17
Alignment explanation
Indices: 10512748--10512794 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
10512738 TTAATACATT
*
10512748 TTTATTTTCATTTTAAA
1 TTTATTTTTATTTTAAA
*
10512765 TTCATTTTTTATTTTAAA
1 TTTA-TTTTTATTTTAAA
10512783 CTTTATTTTTAT
1 -TTTATTTTTAT
10512795 CGTAAAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTTTATTTTAAA
Found at i:10515887 original size:1 final size:1
Alignment explanation
Indices: 10515881--10515924 Score: 79
Period size: 1 Copynumber: 44.0 Consensus size: 1
10515871 ACCCAAACCA
*
10515881 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
10515925 ATCCCGGCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.98, G:0.02, T:0.00
Consensus pattern (1 bp):
C
Found at i:10520158 original size:3 final size:3
Alignment explanation
Indices: 10520150--10520197 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
10520140 TTGTCCTCTG
* *
10520150 TCT TCT TCT TCT CCT TCT CCT TCT TCTT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT
10520196 TC
1 TC
10520198 AACCCATGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:10521345 original size:17 final size:18
Alignment explanation
Indices: 10521309--10521353 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
10521299 TATAATTAAC
10521309 TCTTAATATGATAGAAATT
1 TCTTAATATGATA-AAATT
*
10521328 TCTTAATATGCT-AAATT
1 TCTTAATATGATAAAATT
*
10521345 TTTTAATAT
1 TCTTAATAT
10521354 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
19 11 0.46
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (18 bp):
TCTTAATATGATAAAATT
Found at i:10524174 original size:22 final size:24
Alignment explanation
Indices: 10524134--10524184 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
10524124 TGCAATGGAA
* *
10524134 AAATTCATTAAATTTATCAACAT-
1 AAATTCATCAAATTCATCAACATC
10524157 AAATTCA-CAAATTCATCAACATC
1 AAATTCATCAAATTCATCAACATC
10524180 AAATT
1 AAATT
10524185 TCATAAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATTCATCAAATTCATCAACATC
Found at i:10524196 original size:24 final size:22
Alignment explanation
Indices: 10524149--10524196 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
10524139 CATTAAATTT
*
10524149 ATCAACATAAATTCACAAATTC
1 ATCAACATAAATTCACAAACTC
*
10524171 ATCAACATCAAATTTCATAAACTC
1 ATCAACAT-AAA-TTCACAAACTC
10524195 AT
1 AT
10524197 AATAATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 3 0.14
24 11 0.50
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (22 bp):
ATCAACATAAATTCACAAACTC
Found at i:10525498 original size:15 final size:17
Alignment explanation
Indices: 10525478--10525512 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10525468 ACAATTCTAG
10525478 TTAAT-AAATT-TTTTA
1 TTAATAAAATTATTTTA
10525493 TTAATAAAATTATTTTA
1 TTAATAAAATTATTTTA
10525510 TTA
1 TTA
10525513 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 5 0.28
17 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAATAAAATTATTTTA
Found at i:10525750 original size:14 final size:15
Alignment explanation
Indices: 10525731--10525768 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
10525721 CAAAATCTGA
*
10525731 ATTATTATTA-ATTT
1 ATTATTATAATATTT
10525745 ATTATT-TAATATTT
1 ATTATTATAATATTT
10525759 ATTATTATAA
1 ATTATTATAA
10525769 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 16 0.76
15 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATTATAATATTT
Found at i:10525811 original size:18 final size:17
Alignment explanation
Indices: 10525779--10525813 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10525769 AAAATAAAAA
10525779 TAAAATTTAAATTTAAT
1 TAAAATTTAAATTTAAT
*
10525796 TAAAATTATTAATTTAAT
1 TAAAATT-TAAATTTAAT
10525814 AAGTAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATTTAAATTTAAT
Found at i:10528244 original size:19 final size:20
Alignment explanation
Indices: 10528207--10528244 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
10528197 TAGTTACTTA
*
10528207 TTTATATATTATGCCTTTTT
1 TTTATATATTAAGCCTTTTT
10528227 TTTA-ATATTAAG-CTTTTT
1 TTTATATATTAAGCCTTTTT
10528245 GGAAAGGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTATATATTAAGCCTTTTT
Found at i:10534743 original size:30 final size:30
Alignment explanation
Indices: 10534709--10534767 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
10534699 TTATAAAAAC
* *
10534709 TTATTTGACTCAAAATAAAATTTCAAAAGT
1 TTATTTGACTCAAAATAAAAATACAAAAGT
* *
10534739 TTATTTGATTTAAAATAAAAATACAAAAG
1 TTATTTGACTCAAAATAAAAATACAAAAG
10534768 GCTTAATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (30 bp):
TTATTTGACTCAAAATAAAAATACAAAAGT
Found at i:10535192 original size:31 final size:30
Alignment explanation
Indices: 10535144--10535219 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
10535134 TCAATGAAAT
* * * *
10535144 TTAAATAAATCTTTAT-TTTTT-TATTGCA
1 TTAAATAAGTTTTTATATTTTTATTTTGAA
*
10535172 TTCAATAAGGTTTTTATATTTTTATTTTGAA
1 TTAAATAA-GTTTTTATATTTTTATTTTGAA
10535203 TTAAATAAGTTTTTATA
1 TTAAATAAGTTTTTATA
10535220 ATTAATGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.18
29 6 0.15
30 14 0.36
31 12 0.31
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (30 bp):
TTAAATAAGTTTTTATATTTTTATTTTGAA
Found at i:10535193 original size:29 final size:29
Alignment explanation
Indices: 10535144--10535219 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
10535134 TCAATGAAAT
* * * *
10535144 TTAAATAAATCTTTATTTTTTTA-TTGCA
1 TTAAATAAGTTTTTATATTTTTATTTGAA
*
10535172 TTCAATAAGGTTTTTATATTTTTATTTTGAA
1 TTAAATAA-GTTTTTATATTTTTA-TTTGAA
10535203 TTAAATAAGTTTTTATA
1 TTAAATAAGTTTTTATA
10535220 ATTAATGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.18
29 12 0.31
30 9 0.23
31 11 0.28
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (29 bp):
TTAAATAAGTTTTTATATTTTTATTTGAA
Found at i:10535424 original size:30 final size:30
Alignment explanation
Indices: 10535390--10535458 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
10535380 GTTATTAGGG
* *
10535390 TTTATTTGATTCAAAATAAAATTACAAGAA
1 TTTATTTGATTCAAAATAAAAATACAAAAA
*
10535420 TTTATTTGATTCAAAATAAAAATATAAAAA
1 TTTATTTGATTCAAAATAAAAATACAAAAA
*
10535450 TTTAATTGA
1 TTTATTTGA
10535459 ATGCAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (30 bp):
TTTATTTGATTCAAAATAAAAATACAAAAA
Found at i:10536153 original size:2 final size:2
Alignment explanation
Indices: 10536141--10536171 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10536131 AAGTTGGTTG
*
10536141 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10536172 TATGTAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.