Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 15 of 253
Found at i:4317018 original size:30 final size:30
Alignment explanation
Indices: 4316982--4317096 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
4316972 ACTTTTCTCA
*
4316982 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
4317012 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
4317042 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
4317072 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
4317097 CTTGTACCTA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.25, C:0.50, G:0.03, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:4317665 original size:13 final size:12
Alignment explanation
Indices: 4317647--4317696 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
4317637 GTATATTATA
4317647 TATTATACTATTT
1 TATTATA-TATTT
4317660 TATTATATATCTT
1 TATTATATAT-TT
*
4317673 TAATATTATATTT
1 TATTA-TATATTT
4317686 TA-TATAT-TTT
1 TATTATATATTT
4317696 T
1 T
4317697 TTTTTCTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 4 0.12
11 3 0.09
12 5 0.15
13 17 0.50
14 5 0.15
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTATATATTT
Found at i:4317742 original size:22 final size:24
Alignment explanation
Indices: 4317714--4317771 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
4317704 ACATGTTATC
4317714 TATGTATATATCTT-A-ACTATAT
1 TATGTATATATCTTAACACTATAT
* *
4317736 TATGTATGTATTTTTAACACTATAT
1 TATGTATATA-TCTTAACACTATAT
*
4317761 TATGTACATAT
1 TATGTATATAT
4317772 TTTTAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 9 0.31
23 3 0.10
24 2 0.07
25 15 0.52
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (24 bp):
TATGTATATATCTTAACACTATAT
Found at i:4317763 original size:25 final size:24
Alignment explanation
Indices: 4317729--4317797 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
4317719 ATATATCTTA
4317729 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTAT-TATTTTTAAC
* *
4317754 ACTATATTATGTACATATTTTTAAT
1 ACTATATTATGTA-TTATTTTTAAC
*
4317779 A-T-TATCATGTATTATTTTT
1 ACTATATTATGTATTATTTTT
4317798 TATATATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 7 0.18
23 8 0.21
24 1 0.03
25 23 0.59
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.55
Consensus pattern (24 bp):
ACTATATTATGTATTATTTTTAAC
Found at i:4325477 original size:18 final size:19
Alignment explanation
Indices: 4325456--4325583 Score: 56
Period size: 18 Copynumber: 6.9 Consensus size: 19
4325446 TTAGTTATAA
4325456 TAAAAATAAAAATAATA-C
1 TAAAAATAAAAATAATAGC
*
4325474 T--AAAT-ATAATAATAG-
1 TAAAAATAAAAATAATAGC
* * *
4325489 TGATATTCAAAAAATAATAGC
1 TAAAAAT-AAA-AATAATAGC
* *
4325510 TATAAA-AAAAATAATAACC
1 TAAAAATAAAAATAAT-AGC
*
4325529 ATAACAATAAAGAATAATAGC
1 -TAAAAATAAA-AATAATAGC
* *
4325550 -AAAAATAATAATAATA-A
1 TAAAAATAAAAATAATAGC
* *
4325567 TAATAATAATAATAATA
1 TAAAAATAAAAATAATA
4325584 ATAATGAAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
15 9 0.11
16 4 0.05
17 2 0.02
18 29 0.35
19 13 0.16
20 12 0.15
21 7 0.09
22 6 0.07
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (19 bp):
TAAAAATAAAAATAATAGC
Found at i:4325765 original size:3 final size:3
Alignment explanation
Indices: 4325553--4325745 Score: 119
Period size: 3 Copynumber: 63.3 Consensus size: 3
4325543 TAATAGCAAA
* *
4325553 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAA- AAC AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * * * * *
4325598 AAT ATT AAGT TAC AAT AGT AA- AAT AAT AAT AGT GAT AAT AAT AGT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
4325643 -AT ATT AGAT AAC AAT ACT AA- GAT AAT AAGT AAT AAT AAT AGAGT -AT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT A-A-T AAT
* * *
4325689 AAAT AAT AGT TAT GAA- AAT AAT AAC AAGT AAT AAT AAT AAT AAT AAT
1 -AAT AAT AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
4325736 AAT AAT AAT A
1 AAT AAT AAT A
4325746 GTGACGATAG
Statistics
Matches: 145, Mismatches: 30, Indels: 30
0.71 0.15 0.15
Matches are distributed among these distances:
2 9 0.06
3 120 0.83
4 15 0.10
5 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4325939 original size:23 final size:23
Alignment explanation
Indices: 4325888--4325933 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
4325878 GTTAATAACA
4325888 ATAATAATAATATGTAAAAATAG
1 ATAATAATAATATGTAAAAATAG
*
4325911 AAAATAATAATATGGTAAAAATA
1 ATAATAATAATAT-GTAAAAATA
4325934 TTAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (23 bp):
ATAATAATAATATGTAAAAATAG
Found at i:4326806 original size:17 final size:18
Alignment explanation
Indices: 4326776--4326809 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4326766 ATAGGTTCTA
*
4326776 AAAAAATAATAAAATAAC
1 AAAAAATAAGAAAATAAC
4326794 AAAAAA-AAGAAAATAA
1 AAAAAATAAGAAAATAA
4326810 TAAACCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAAAATAAGAAAATAAC
Found at i:4327695 original size:44 final size:43
Alignment explanation
Indices: 4327624--4327992 Score: 192
Period size: 43 Copynumber: 8.5 Consensus size: 43
4327614 AATTTTCAGC
* *
4327624 CTGTTACCCTACTGCTTAGAGGGTTAAGGCCCATCGCCTTCGAT
1 CTGTTTCCCTACTGCTTAG-GGGTTAAGGCCCATCACCTTCGAT
* *
4327668 CTGTTTCCCGACTGCTTAGGGGTTTAAGGCCCATCACCTTTGAT
1 CTGTTTCCCTACTGCTTAGGGG-TTAAGGCCCATCACCTTCGAT
* ** * ** *
4327712 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTAT-AAATTC-AGC
1 CTGTTTCCCTACTGCTTAGGG-GTTAAGGCCCATCACCTTCGA-T
* ***** ** * *
4327755 CTGTTACCCTACTGCTTAGGGGGTTAAGATTTGT-AAATTCAAC
1 CTGTTTCCCTACTGCTTA-GGGGTTAAGGCCCATCACCTTCGAT
* ** ** ** *
4327798 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTC-AGC
1 CTGTTTCCCTACTGCTTA-GGGGTTAAGGCCCATCACCTTCGA-T
* * *
4327841 CTGTTACCCTACTGCCTAGGGGTTTAAGGCCCACCACCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGG-TTAAGGCCCATCACCTTCGAT
** * ** ** * ** * *
4327885 CTGTTTCTTTACTGCTTAGGGTGATAAGATCTGTAAATTTAG-C
1 CTGTTTCCCTACTGCTTAGGG-GTTAAGGCCCATCACCTTCGAT
* *
4327928 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCACCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGG-TTAAGGCCCATCACCTTCGAT
4327972 CTGTTTCCCTACTGCTTAGGG
1 CTGTTTCCCTACTGCTTAGGG
4327993 AATTAAGATC
Statistics
Matches: 255, Mismatches: 58, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
42 7 0.03
43 129 0.51
44 116 0.45
45 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (43 bp):
CTGTTTCCCTACTGCTTAGGGGTTAAGGCCCATCACCTTCGAT
Found at i:4327929 original size:87 final size:87
Alignment explanation
Indices: 4327668--4328045 Score: 517
Period size: 87 Copynumber: 4.4 Consensus size: 87
4327658 CGCCTTCGAT
* * *
4327668 CTGTTTCCCGACTGCTTAGGGGTTTAAGGCCCATCACCTTTGATCTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGG
*
4327733 TGATAAGATCTATAAATTCAGC
66 TGATAAGATCTGTAAATTCAGC
* ***** ** * * *
4327755 CTGTTACCCTACTGCTTAGGGGGTTAAGATTTGT-AAATTCAACCTGTTACCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGG
* *
4327819 GGTTAAGATCTGTAAATTCAGC
66 TGATAAGATCTGTAAATTCAGC
* * **
4327841 CTGTTACCCTACTGCCTAGGGGTTTAAGGCCCACCACCTTCGATCTGTTTCTTTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGG
*
4327906 TGATAAGATCTGTAAATTTAGC
66 TGATAAGATCTGTAAATTCAGC
*
4327928 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGG
*
4327993 -AATTAAGATCTGTAAATTCAGC
66 TGA-TAAGATCTGTAAATTCAGC
4328015 CTGTTACCCTACTGCTTAGGGGTTTAAGGCC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCC
4328046 TGTGGATTTA
Statistics
Matches: 246, Mismatches: 43, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
86 70 0.28
87 176 0.72
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (87 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGG
TGATAAGATCTGTAAATTCAGC
Found at i:4328042 original size:43 final size:43
Alignment explanation
Indices: 4327712--4328042 Score: 292
Period size: 43 Copynumber: 7.7 Consensus size: 43
4327702 CACCTTTGAT
* * *
4327712 CTGTTTCCCTACTGCTTA-GGGTGATAAGATCTATAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGT-TTAAGATCTGTAAATTCAGC
* * *
4327755 CTGTTACCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAAC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGATCTGTAAATTCAGC
*
4327798 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGATCTGTAAATTCAGC
* ** *** ** *
4327841 CTGTTACCCTACTGCCTAGGGGTTTAAGGCCCACCACCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGTTTAA-GATCTGTAAATTCAG-C
* ** * *
4327885 CTGTTTCTTTACTGCTTA-GGGTGATAAGATCTGTAAATTTAGC
1 CTGTTACCCTACTGCTTAGGGGT-TTAAGATCTGTAAATTCAGC
* ** ** ** *
4327928 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCACCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGATCTGT-AAATTCAG-C
* **
4327972 CTGTTTCCCTACTGCTTAGGGAATTAAGATCTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGATCTGTAAATTCAGC
4328015 CTGTTACCCTACTGCTTAGGGGTTTAAG
1 CTGTTACCCTACTGCTTAGGGGTTTAAG
4328043 GCCTGTGGAT
Statistics
Matches: 220, Mismatches: 59, Indels: 18
0.74 0.20 0.06
Matches are distributed among these distances:
43 159 0.72
44 61 0.28
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGATCTGTAAATTCAGC
Found at i:4329893 original size:30 final size:30
Alignment explanation
Indices: 4329857--4330031 Score: 296
Period size: 30 Copynumber: 5.8 Consensus size: 30
4329847 ACTTTTCTCA
*
4329857 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
4329887 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
4329917 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
4329947 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
4329977 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
4330007 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
4330032 CTTGTACCTA
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 135 1.00
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:4329922 original size:60 final size:60
Alignment explanation
Indices: 4329857--4330031 Score: 332
Period size: 60 Copynumber: 2.9 Consensus size: 60
4329847 ACTTTTCTCA
*
4329857 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
4329917 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
*
4329977 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCA
4330032 CTTGTACCTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 113 1.00
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (60 bp):
ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:4330612 original size:25 final size:25
Alignment explanation
Indices: 4330536--4330733 Score: 102
Period size: 25 Copynumber: 7.8 Consensus size: 25
4330526 ATATTTCTTA
* * *
4330536 ATATTATATTATATATATTCTTTTAAT
1 ATATTAT-GTATATATATT-TTATACT
* ** *
4330563 ATATTAGGTATAT-T-TTAAATTCT
1 ATATTATGTATATATATTTTATACT
*
4330586 ATATTACGTATATATATTTTATACT
1 ATATTATGTATATATATTTTATACT
* * * * *
4330611 ATTTTATTTATATATCTTTAATATT
1 ATATTATGTATATATATTTTATACT
* *
4330636 ATATTATTATATATATATTTTTCTAC-
1 ATATTA-TGTATATATA-TTTTATACT
* * *
4330662 ATGTTATCTTATGTATATATCTTA-ACT
1 ATATTAT-GTA--TATATATTTTATACT
*
4330689 ATATTATGTATATAT-TTTTAACACT
1 ATATTATGTATATATATTTT-ATACT
*
4330714 ATATTATGTACATAT-TTTTA
1 ATATTATGTATATATATTTTA
4330734 ATATTATCAC
Statistics
Matches: 130, Mismatches: 31, Indels: 23
0.71 0.17 0.12
Matches are distributed among these distances:
23 17 0.13
24 10 0.08
25 53 0.41
26 24 0.18
27 20 0.15
28 6 0.05
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.56
Consensus pattern (25 bp):
ATATTATGTATATATATTTTATACT
Found at i:4330652 original size:14 final size:13
Alignment explanation
Indices: 4330594--4330656 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 13
4330584 CTATATTACG
4330594 TATATATA-TTT-
1 TATATATATTTTA
*
4330605 TATA-CTATTTTA
1 TATATATATTTTA
*
4330617 TTTATATATCTTTA
1 TATATATAT-TTTA
4330631 -ATATTATATTATTA
1 TATA-TATATT-TTA
4330645 TATATATATTTT
1 TATATATATTTT
4330657 TCTACATGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 2 0.05
11 7 0.17
12 3 0.07
13 8 0.20
14 18 0.44
15 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATATATTTTA
Found at i:4330873 original size:16 final size:16
Alignment explanation
Indices: 4330854--4330934 Score: 69
Period size: 16 Copynumber: 4.8 Consensus size: 16
4330844 ATTTCTATTT
4330854 TATTTT-TTATTTTCAA
1 TATTTTATTATTTT-AA
4330870 TATTAATTATTATTATTCTAA
1 TATT--TTATTA-T-TT-TAA
4330891 TATTTTGA-TATTTTAA
1 TATTTT-ATTATTTTAA
4330907 TATTTTA-TATTTTATA
1 TATTTTATTATTTTA-A
4330923 TATTTTATTATT
1 TATTTTATTATT
4330935 CACATCATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
15 8 0.14
16 21 0.38
17 6 0.11
18 3 0.05
19 7 0.12
20 2 0.04
21 8 0.14
22 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (16 bp):
TATTTTATTATTTTAA
Found at i:4330918 original size:7 final size:8
Alignment explanation
Indices: 4330883--4330934 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
4330873 TAATTATTAT
*
4330883 TATTCTAA
1 TATTTTAA
*
4330891 TATTTTGA
1 TATTTTAA
4330899 TATTTTAA
1 TATTTTAA
4330907 TATTTT-A
1 TATTTTAA
4330914 TATTTTATA
1 TATTTTA-A
*
4330923 TATTTTAT
1 TATTTTAA
4330931 TATT
1 TATT
4330935 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:4337118 original size:26 final size:26
Alignment explanation
Indices: 4337082--4337134 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
4337072 CACATCTGTA
4337082 CGAACATCTACGGGAGCAACTCCTTT
1 CGAACATCTACGGGAGCAACTCCTTT
4337108 CGAACATCTACGGGAGCAACTCCTTT
1 CGAACATCTACGGGAGCAACTCCTTT
4337134 C
1 C
4337135 TCTCTGGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (26 bp):
CGAACATCTACGGGAGCAACTCCTTT
Found at i:4338554 original size:71 final size:69
Alignment explanation
Indices: 4338432--4338605 Score: 208
Period size: 71 Copynumber: 2.5 Consensus size: 69
4338422 CTTTCCAAGG
** *
4338432 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
*
4338497 TTTTT
65 GTTTT
** * *
4338502 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAG-AGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
4338567 TGTTTT
64 TGTTTT
** *
4338573 -AAATTGACTCATATTGCGAGAG-GAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGTGAGTTGAGCCT
4338606 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
67 10 0.11
68 2 0.02
69 18 0.20
71 59 0.65
72 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTATG
TTTT
Found at i:4338724 original size:71 final size:70
Alignment explanation
Indices: 4338609--4338827 Score: 248
Period size: 71 Copynumber: 3.1 Consensus size: 70
4338599 TAAGCCTTTT
* * *
4338609 AATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCA-AGACGCTGAGG
1 AATTTTTGTTTATCAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTCAGACACGCTGAGG
4338672 TAATTTC
65 T-ATTTC
*
4338679 AATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTTTGTTTATCAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTCA-GACACGCTGAG
* *
4338744 GTGTTTT
64 GTATTTC
* * **
4338751 AA-TTTTGTTCATCAAAAAT-TACTCATATTGCAGAGGTGAGTTGAGCCTTGGCTCACACGCTGA
1 AATTTTTGTTTATCAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCC-T--CAGACACGCTGA
4338814 GGTATTTTC
63 GGTA-TTTC
4338823 AATTT
1 AATTT
4338828 CTGGTTTTCA
Statistics
Matches: 128, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
69 16 0.12
70 25 0.20
71 63 0.49
72 11 0.09
73 13 0.10
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (70 bp):
AATTTTTGTTTATCAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCAGACACGCTGAGGT
ATTTC
Found at i:4338837 original size:14 final size:14
Alignment explanation
Indices: 4338818--4338852 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
4338808 CGCTGAGGTA
4338818 TTTTCAATTTCTGG
1 TTTTCAATTTCTGG
*
4338832 TTTTCAATTTCTGT
1 TTTTCAATTTCTGG
4338846 TTTTCAA
1 TTTTCAA
4338853 AAATCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGG
Found at i:4338900 original size:87 final size:84
Alignment explanation
Indices: 4338745--4339088 Score: 313
Period size: 89 Copynumber: 4.1 Consensus size: 84
4338735 CACGCTGAGG
* *
4338745 TGTTTT-AATTTTGTTCATCAAAAATTACTCATATTGCAGAGGTGAGTTGAGCCTTGGCTCACAC
1 TGTTTTCAATTTTGTTCATCAAAAATGACTCATATTGCAGAGGTGAGTTGAGCCTCGGC-CACAC
*
4338809 GCTGAGGTATTTTCAATTTC
65 GCTGAGGTAATTTCAATTTC
** *
4338829 TGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GA
1 T-GTTTTCAATTT-TGTTCATCAAAAAT-GACTCATATTGC-AGAGGTGAGTTGAGCCTCGGCCA
4338893 CACGCTGAGGTAATTTCAATTTC
62 CACGCTGAGGTAATTTCAATTTC
* *
4338916 TG--------TTTG-TCA--AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACA
1 TGTTTTCAATTTTGTTCATCAAAAATGACTCATATTGC-AGAGGTGAGTTGAGCCTCGGC-CACA
* * ** *
4338970 TGCTGAAGTCTTTTCAATTTT
64 CGCTGAGGTAATTTCAATTTC
** *
4338991 TGTTCTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TGTT-TTCAATTT-TGTTC--ATCAAAAAT-GACTCATATTGC-AGAGGTGAGTTGAGCCTC-GG
4339056 --ACACGCTGAGGTAATTTCAATTTC
59 CCACACGCTGAGGTAATTTCAATTTC
4339080 TGTTTTCAA
1 TGTTTTCAA
4339089 AATTCAACTT
Statistics
Matches: 214, Mismatches: 22, Indels: 44
0.76 0.08 0.16
Matches are distributed among these distances:
73 32 0.15
74 5 0.02
75 21 0.10
76 1 0.00
77 2 0.01
78 2 0.01
84 3 0.01
85 7 0.03
86 8 0.04
87 36 0.17
88 17 0.08
89 42 0.20
90 5 0.02
91 31 0.14
92 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (84 bp):
TGTTTTCAATTTTGTTCATCAAAAATGACTCATATTGCAGAGGTGAGTTGAGCCTCGGCCACACG
CTGAGGTAATTTCAATTTC
Found at i:4339064 original size:164 final size:161
Alignment explanation
Indices: 4338675--4339277 Score: 663
Period size: 164 Copynumber: 3.8 Consensus size: 161
4338665 GCTGAGGTAA
* ***
4338675 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTCTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* * * *
4338740 TGAGGT-GTTTTAATTT-TGTTCATCAAAAATT-ACTCATATTGC-AGAGGTGAGTTGAGCCTTG
66 TGAGGTAATTTCAATTTCTGTT-TTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
*
4338801 GCTCACACGCTGAGGTATTTTCAATTTCTGGT
130 GCTCACACGCTGAAGTATTTTCAATTTCTGGT
*** * *
4338833 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
1 TTTCAATTTCTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
4338898 TGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
66 TGAGGTAATTTCAATTTCTGTTT-TCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* * *
4338963 GCTCACATGCTGAAGTCTTTTCAATTT-TTGT
130 GCTCACACGCTGAAGTATTTTCAATTTCTGGT
4338994 TCTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 T-TTCAATTTCTGTT--TAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* **
4339059 CGCTGAGGTAATTTCAATTTCTGTTTTC-AAAATTCAACTTATATTGCGAGAAATGAGTTGAGCC
63 CGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATT-AACTCATATTGCGAGAGGTGAGTTGAGCC
* * *
4339123 TCAAG---ACACGTTGAGGTATTTTCAATTTCT-GT
127 TC-GGCTCACACGCTGAAGTATTTTCAATTTCTGGT
*
4339155 TTTC-A---------AAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACA
1 TTTCAATTTCTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
* * * *
4339209 TGCTGAGGTATTTTCAATTTCTGTTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
63 CGCTGAGGTAATTTCAATTTCTG---TTTT---CAAAAATTAACTCATATTGCGAGAGGTGAGTT
4339274 GAGC
122 GAGC
4339278 TTCAGATTAC
Statistics
Matches: 391, Mismatches: 33, Indels: 44
0.84 0.07 0.09
Matches are distributed among these distances:
147 2 0.01
148 40 0.10
150 24 0.06
153 4 0.01
156 25 0.06
157 5 0.01
158 67 0.17
159 9 0.02
160 16 0.04
161 37 0.09
162 62 0.16
163 30 0.08
164 70 0.18
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (161 bp):
TTTCAATTTCTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAATTTCTGTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
CTCACACGCTGAAGTATTTTCAATTTCTGGT
Found at i:4339299 original size:80 final size:78
Alignment explanation
Indices: 4338996--4339302 Score: 341
Period size: 72 Copynumber: 4.0 Consensus size: 78
4338986 ATTTTTGTTC
* * *
4338996 TTCAATTTCTG--TTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GA
1 TTCAATTTCTGTTTTC-AAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGATTA
* *
4339057 CACGCTGAGGTAAT
65 CACACTGAGGTATT
* ** *
4339071 TTCAATTTCTGTTTTC----AAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCA-A-GAC
1 TTCAATTTCTGTTTTCAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGATTAC
**
4339130 ACGTTGAGGTATT
66 ACACTGAGGTATT
*
4339143 TTCAATTTCTGTTTTCAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTT-C
1 TTCAATTTCTGTTTTCAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGATTAC
4339206 ACATGCTGAGGTATT
66 ACA--CTGAGGTATT
* * *
4339221 TTCAATTTCTGTTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATT
1 TTCAATTTCTG--TTTTCAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGATT
*
4339286 ACACACTGTGGTATT
64 ACACACTGAGGTATT
4339301 TT
1 TT
4339303 TTTCAATTCA
Statistics
Matches: 199, Mismatches: 18, Indels: 25
0.82 0.07 0.10
Matches are distributed among these distances:
72 65 0.33
75 11 0.06
76 38 0.19
77 3 0.02
78 20 0.10
80 55 0.28
81 3 0.02
82 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (78 bp):
TTCAATTTCTGTTTTCAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGATTAC
ACACTGAGGTATT
Found at i:4339515 original size:71 final size:73
Alignment explanation
Indices: 4339435--4339575 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 73
4339425 TCAAAATCAG
* *
4339435 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTT-G-TGTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
4339498 AATTTCAA
66 AATTTCAA
* *
4339506 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTTTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
4339571 AATTT
66 AATTT
4339576 ATGTTTCAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 53 0.83
72 1 0.02
73 10 0.16
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (73 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
AATTTCAA
Found at i:4339603 original size:160 final size:160
Alignment explanation
Indices: 4339427--4339729 Score: 459
Period size: 160 Copynumber: 1.9 Consensus size: 160
4339417 CTACTTTTTC
* * ** *
4339427 AAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTG
1 AAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTC-AAG-ACGCTGAGGTAATTTCAATTTT-
**
4339492 TGTTT-T-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTT
63 TGTTTGTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTT
*
4339555 CAATTTTC-GTTTTTTTAATTTATGTTTCAAAA
128 CAAATTTCTGTTTTTTTAATTTATGTTTCAAAA
*
4339587 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACGCTGAGGTAATTTCAATTTTTGT
1 AAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCAAGACGCTGAGGTAATTTCAATTTTTGT
*
4339652 TTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTA
66 TTGT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
4339717 AATTTCTGTTTTT
130 AATTTCTGTTTTT
4339730 CAAAAATCAA
Statistics
Matches: 129, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
157 5 0.04
158 22 0.17
159 1 0.01
160 95 0.74
161 6 0.05
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (160 bp):
AAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCAAGACGCTGAGGTAATTTCAATTTTTGT
TTGTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
ATTTCTGTTTTTTTAATTTATGTTTCAAAA
Found at i:4339688 original size:71 final size:73
Alignment explanation
Indices: 4339586--4339767 Score: 278
Period size: 74 Copynumber: 2.5 Consensus size: 73
4339576 ATGTTTCAAA
* * *
4339586 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCA-AGACGCTGAGGTA-ATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGACACGCTGAGGTATATTTAAATTTC
4339649 TGTTTGTC
66 TGTTTGTC
* *
4339657 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCA-GACACGCTGAGGTATATTTAAATTT
*
4339722 CTGTTTTTC
65 CTGTTTGTC
*
4339731 AAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
4339768 TGGGTTCACA
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
71 38 0.38
73 12 0.12
74 51 0.50
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGACACGCTGAGGTATATTTAAATTTC
TGTTTGTC
Found at i:4340515 original size:30 final size:30
Alignment explanation
Indices: 4340479--4340653 Score: 296
Period size: 30 Copynumber: 5.8 Consensus size: 30
4340469 ACTTTTCTCA
*
4340479 ACTAGCCACTCCTTTTCCACCAGCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
*
4340509 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
*
4340539 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
4340569 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
*
4340599 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
* *
4340629 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCCTTTTCCACCACCA
4340654 CTTGTACCTA
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 136 1.00
ACGTcount: A:0.25, C:0.49, G:0.04, T:0.23
Consensus pattern (30 bp):
ACTAGCCACTCCTTTTCCACCACCAACTCC
Found at i:4341178 original size:23 final size:23
Alignment explanation
Indices: 4341141--4341270 Score: 74
Period size: 23 Copynumber: 5.5 Consensus size: 23
4341131 CCTTTTTTGT
4341141 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
4341164 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
**
4341186 TATTAGGTATATT-TTAA-ATTCTA
1 TATTATATATATTCTTAATA-T-TA
* *
4341209 TATTACGTATATATATTTTATACTATTT
1 TATTA--TATATAT-TCTTA-A-TATTA
4341237 TATT-TATATA-TCTTTAATATTA
1 TATTATATATATTC-TTAATATTA
*
4341259 TATTATTTATAT
1 TATTATATATAT
4341271 ATATATTTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
21 3 0.04
22 23 0.28
23 25 0.31
24 7 0.09
25 11 0.14
26 1 0.01
27 3 0.04
28 6 0.07
29 1 0.01
30 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:4341234 original size:25 final size:25
Alignment explanation
Indices: 4341158--4341356 Score: 95
Period size: 25 Copynumber: 7.8 Consensus size: 25
4341148 ATATTTCTTA
* * *
4341158 ATATTATATTATATATATTCTTTTAAT
1 ATATTAT-GTATATATATT-TTATACT
* ** *
4341185 ATATTAGGTATAT-T-TTAAATTCT
1 ATATTATGTATATATATTTTATACT
*
4341208 ATATTACGTATATATATTTTATACT
1 ATATTATGTATATATATTTTATACT
* * * * *
4341233 ATTTTATTTATATATCTTTAATATT
1 ATATTATGTATATATATTTTATACT
* *
4341258 ATATTATTTATATATATATTT-TTCT
1 ATATTATGTATATATAT-TTTATACT
* * *
4341283 ACATGTTATCTTATGTATATATCTTA-ACT
1 --ATATTAT-GTA--TATATATTTTATACT
*
4341312 ATATTATGTATATAT-TTTTAACACT
1 ATATTATGTATATATATTTT-ATACT
*
4341337 ATATTATGTACATAT-TTTTA
1 ATATTATGTATATATATTTTA
4341357 ATATTATCAC
Statistics
Matches: 132, Mismatches: 29, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
23 17 0.13
24 10 0.08
25 64 0.48
26 9 0.07
27 18 0.14
28 3 0.02
29 4 0.03
30 7 0.05
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.56
Consensus pattern (25 bp):
ATATTATGTATATATATTTTATACT
Found at i:4341496 original size:16 final size:16
Alignment explanation
Indices: 4341477--4341557 Score: 69
Period size: 16 Copynumber: 4.8 Consensus size: 16
4341467 ATTTCTATTT
4341477 TATTTT-TTATTTTCAA
1 TATTTTATTATTTT-AA
4341493 TATTAATTATTATTATTCTAA
1 TATT--TTATTA-T-TT-TAA
4341514 TATTTTGA-TATTTTAA
1 TATTTT-ATTATTTTAA
4341530 TATTTTA-TATTTTATA
1 TATTTTATTATTTTA-A
4341546 TATTTTATTATT
1 TATTTTATTATT
4341558 CACATCATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
15 8 0.14
16 21 0.38
17 6 0.11
18 3 0.05
19 7 0.12
20 2 0.04
21 8 0.14
22 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (16 bp):
TATTTTATTATTTTAA
Found at i:4341541 original size:7 final size:8
Alignment explanation
Indices: 4341506--4341557 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
4341496 TAATTATTAT
*
4341506 TATTCTAA
1 TATTTTAA
*
4341514 TATTTTGA
1 TATTTTAA
4341522 TATTTTAA
1 TATTTTAA
4341530 TATTTT-A
1 TATTTTAA
4341537 TATTTTATA
1 TATTTTA-A
*
4341546 TATTTTAT
1 TATTTTAA
4341554 TATT
1 TATT
4341558 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:4348004 original size:23 final size:23
Alignment explanation
Indices: 4347974--4348019 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4347964 CTTTTCTGTT
4347974 TCTGTTACTTCATCGAGATTGAG
1 TCTGTTACTTCATCGAGATTGAG
4347997 TCTGTTACTTCATCGAGATTGAG
1 TCTGTTACTTCATCGAGATTGAG
4348020 GACCACAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (23 bp):
TCTGTTACTTCATCGAGATTGAG
Found at i:4348533 original size:9 final size:9
Alignment explanation
Indices: 4348515--4348546 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4348505 TACAATGCTG
4348515 ATGC-ATGA
1 ATGCAATGA
4348523 ATGCAATGA
1 ATGCAATGA
4348532 ATGCAATGA
1 ATGCAATGA
4348541 ATGCAA
1 ATGCAA
4348547 AAAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (9 bp):
ATGCAATGA
Found at i:4352082 original size:24 final size:24
Alignment explanation
Indices: 4352055--4352174 Score: 62
Period size: 26 Copynumber: 4.8 Consensus size: 24
4352045 TAATAGCAAT
4352055 AATAATAATAATAATAATGAAAAA
1 AATAATAATAATAATAATGAAAAA
* * * * *
4352079 AATATTAAGTTACAATAGTAAAATAA
1 AATAATAA-TAATAATAATGAAA-AA
* * * *
4352105 TAATAGTAATAATAATAGTGATAAT
1 -AATAATAATAATAATAATGAAAAA
* * *
4352130 AATAGTATATTAGATAACAAT-AATAA
1 AATA--ATAATA-ATAATAATGAAAAA
4352156 AATAATAAGTAATAATAAT
1 AATAATAA-TAATAATAAT
4352175 AGAGTATAAA
Statistics
Matches: 69, Mismatches: 20, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
24 21 0.30
25 13 0.19
26 22 0.32
27 13 0.19
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (24 bp):
AATAATAATAATAATAATGAAAAA
Found at i:4352246 original size:3 final size:3
Alignment explanation
Indices: 4352052--4352226 Score: 101
Period size: 3 Copynumber: 57.3 Consensus size: 3
4352042 GAATAATAGC
* * * * *
4352052 AAT AAT AAT AAT AAT AAT AAT GAA- AAA AAT ATT AAGT TAC AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AAT
* * * * *
4352098 AA- AAT AAT AAT AGT AAT AAT AAT AGT GAT AAT AAT AGT -AT ATT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
4352145 AAC AAT AAT AA- AAT AAT AAGT AAT AAT AAT AGAGT -AT AAAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT A-A-T AAT -AAT AAT AAT
* *
4352192 TAT GAA- AAT AAT AAC AAGT AAT AAT AAT AAT AAT A
1 AAT -AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT A
4352227 GTGACGATAG
Statistics
Matches: 130, Mismatches: 27, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
2 10 0.08
3 104 0.80
4 15 0.12
5 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4352420 original size:23 final size:23
Alignment explanation
Indices: 4352369--4352414 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
4352359 GTTAATAACA
4352369 ATAATAATAATATGTAAAAATAG
1 ATAATAATAATATGTAAAAATAG
*
4352392 AAAATAATAATATGGTAAAAATA
1 ATAATAATAATAT-GTAAAAATA
4352415 TTAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (23 bp):
ATAATAATAATATGTAAAAATAG
Found at i:4353233 original size:5 final size:5
Alignment explanation
Indices: 4353223--4353248 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4353213 AATAGGTTCT
4353223 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
4353249 CAAAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:4353262 original size:17 final size:18
Alignment explanation
Indices: 4353232--4353265 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4353222 TAAATAAAAT
*
4353232 AAAATAAAATAAAATAAC
1 AAAATAAAAGAAAATAAC
4353250 AAAA-AAAAGAAAATAA
1 AAAATAAAAGAAAATAA
4353266 TAAACCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAATAAAAGAAAATAAC
Found at i:4355001 original size:23 final size:23
Alignment explanation
Indices: 4354975--4355018 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4354965 AGCTTAGGGT
*
4354975 TTCGAAACCAATAAAATTGTGGC
1 TTCGAAACCAATAAAACTGTGGC
*
4354998 TTCGAAACTAATAAAACTGTG
1 TTCGAAACCAATAAAACTGTG
4355019 TTGAGTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (23 bp):
TTCGAAACCAATAAAACTGTGGC
Found at i:4358280 original size:31 final size:31
Alignment explanation
Indices: 4358243--4358308 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
4358233 AGTTAAAGAT
4358243 TTAAGATATAATATCATTAGCT-AGTTAAGTC
1 TTAAGATATAATATCATTAGCTGA-TTAAGTC
*
4358274 TTAAGATATAATATCATTAGCTGATTAAGTT
1 TTAAGATATAATATCATTAGCTGATTAAGTC
4358305 TTAA
1 TTAA
4358309 CTCAATTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (31 bp):
TTAAGATATAATATCATTAGCTGATTAAGTC
Found at i:4362691 original size:23 final size:22
Alignment explanation
Indices: 4362661--4362704 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
4362651 CGTTTAACTA
4362661 ATACTTAATACCTTTTGTATAT
1 ATACTTAATACCTTTTGTATAT
4362683 ATACATTAATACCTTTTGTATA
1 ATAC-TTAATACCTTTTGTATA
4362705 ATGTTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.48
Consensus pattern (22 bp):
ATACTTAATACCTTTTGTATAT
Found at i:4368185 original size:21 final size:22
Alignment explanation
Indices: 4368141--4368188 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
4368131 TTAGTTTTAA
* *
4368141 TTATTTTAATTTAAAATGTATT
1 TTATATTAATTTAAAATCTATT
*
4368163 TTATATTAATTT-AATTCTATT
1 TTATATTAATTTAAAATCTATT
4368184 TTATA
1 TTATA
4368189 ATTATTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATATTAATTTAAAATCTATT
Found at i:4370668 original size:19 final size:18
Alignment explanation
Indices: 4370626--4370681 Score: 78
Period size: 17 Copynumber: 3.1 Consensus size: 18
4370616 ACAAAATAAT
*
4370626 AATTTTTTAAAACACGAA
1 AATTTTTTGAAACACGAA
*
4370644 GA-TTTTTGAAACACGAA
1 AATTTTTTGAAACACGAA
4370661 AATTTTTTGAAAACACGAA
1 AATTTTTTG-AAACACGAA
4370680 AA
1 AA
4370682 CACAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.45
18 7 0.21
19 11 0.33
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (18 bp):
AATTTTTTGAAACACGAA
Found at i:4370762 original size:20 final size:19
Alignment explanation
Indices: 4370626--4370903 Score: 101
Period size: 19 Copynumber: 15.1 Consensus size: 19
4370616 ACAAAATAAT
4370626 AATTTTTT-AAAACACGAA
1 AATTTTTTGAAAACACGAA
*
4370644 GA-TTTTTG-AAACACGAA
1 AATTTTTTGAAAACACGAA
4370661 AATTTTTTGAAAACACGAAAACACAA
1 AATTTTTTGAAAACACG-------AA
**
4370687 AATATTTTT---AACACGGG
1 AAT-TTTTTGAAAACACGAA
4370704 AA-TTTTTGAAAACACGACA
1 AATTTTTTGAAAACACGA-A
** **
4370723 GTTTTTTTTTAAACACGAA
1 AATTTTTTGAAAACACGAA
4370742 AATTTTTTGAAAACAC-AGA
1 AATTTTTTGAAAACACGA-A
* *
4370761 AATTTTTTGAAAACAAGGA
1 AATTTTTTGAAAACACGAA
* * * *
4370780 AA-TTTTAG-ATACATGAG
1 AATTTTTTGAAAACACGAA
*
4370797 AATTCTTTG---ACACGAA
1 AATTTTTTGAAAACACGAA
* * *
4370813 AA-ATTTTGAAAACATGAG
1 AATTTTTTGAAAACACGAA
** *
4370831 AA--TTCCGAAAACATG--
1 AATTTTTTGAAAACACGAA
* *
4370846 AATTTTTT-AAAACATG-T
1 AATTTTTTGAAAACACGAA
* *
4370863 AATTTTTTAAAAAACACGAG
1 AATTTTTT-GAAAACACGAA
4370883 AATTTTTTGAAAACACGAA
1 AATTTTTTGAAAACACGAA
4370902 AA
1 AA
4370904 CATGAAAATT
Statistics
Matches: 195, Mismatches: 37, Indels: 55
0.68 0.13 0.19
Matches are distributed among these distances:
15 11 0.06
16 15 0.08
17 45 0.23
18 30 0.15
19 57 0.29
20 21 0.11
24 6 0.03
26 5 0.03
27 5 0.03
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (19 bp):
AATTTTTTGAAAACACGAA
Found at i:4370834 original size:17 final size:16
Alignment explanation
Indices: 4370813--4370868 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
4370803 TTGACACGAA
4370813 AAATTTTGAAAACATG
1 AAATTTTGAAAACATG
**
4370829 AGAATTCCGAAAACATG
1 A-AATTTTGAAAACATG
* *
4370846 AATTTTTTAAAACATG
1 AAATTTTGAAAACATG
*
4370862 TAATTTT
1 AAATTTT
4370869 TTAAAAAACA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (16 bp):
AAATTTTGAAAACATG
Found at i:4370859 original size:16 final size:17
Alignment explanation
Indices: 4370838--4370874 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
4370828 GAGAATTCCG
4370838 AAAACATG-AATTTTTT
1 AAAACATGTAATTTTTT
4370854 AAAACATGTAATTTTTT
1 AAAACATGTAATTTTTT
4370871 AAAA
1 AAAA
4370875 AACACGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
AAAACATGTAATTTTTT
Found at i:4370913 original size:27 final size:25
Alignment explanation
Indices: 4370873--4370923 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4370863 AATTTTTTAA
*
4370873 AAAACACGAGAATTTTTTGAAAACACG
1 AAAACACGA-AA-ATTTTGAAAACACG
*
4370900 AAAACATGAAAATTTTGAAAACAC
1 AAAACACGAAAATTTTGAAAACAC
4370924 AGGCAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 2 0.09
27 8 0.36
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (25 bp):
AAAACACGAAAATTTTGAAAACACG
Found at i:4371034 original size:24 final size:23
Alignment explanation
Indices: 4370981--4371072 Score: 104
Period size: 24 Copynumber: 4.2 Consensus size: 23
4370971 TTGTTTTTTG
*
4370981 TTTT-ATTTTAAAACACGAAAAT
1 TTTTCATTTTAAAACGCGAAAAT
*
4371003 TTTTCATTTGAAAACGCGAAAATT
1 TTTTCATTTTAAAACGCGAAAA-T
4371027 TTTTCATTTTAAAACGCG--AAT
1 TTTTCATTTTAAAACGCGAAAAT
* *
4371048 TTTT--TTTTAAAACACGAAAAC
1 TTTTCATTTTAAAACGCGAAAAT
4371069 TTTT
1 TTTT
4371073 GAAAACGCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
19 11 0.18
21 11 0.18
22 6 0.10
23 15 0.25
24 18 0.30
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (23 bp):
TTTTCATTTTAAAACGCGAAAAT
Found at i:4371072 original size:19 final size:18
Alignment explanation
Indices: 4371051--4371085 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4371041 CGCGAATTTT
*
4371051 TTTTTAAAACACGAAAAC
1 TTTTGAAAACACGAAAAC
*
4371069 TTTTGAAAACGCGAAAA
1 TTTTGAAAACACGAAAA
4371086 GTCGAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (18 bp):
TTTTGAAAACACGAAAAC
Found at i:4371714 original size:14 final size:14
Alignment explanation
Indices: 4371695--4371725 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4371685 GAGCTGCACG
4371695 GGTGGGCCACTGCT
1 GGTGGGCCACTGCT
*
4371709 GGTGGGCTACTGCT
1 GGTGGGCCACTGCT
4371723 GGT
1 GGT
4371726 CCACCAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.23, G:0.45, T:0.26
Consensus pattern (14 bp):
GGTGGGCCACTGCT
Found at i:4371785 original size:7 final size:7
Alignment explanation
Indices: 4371746--4371776 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4371736 TAGCCTGCTG
4371746 TTTTTTA
1 TTTTTTA
4371753 TTTTTTA
1 TTTTTTA
4371760 TTTTTTA
1 TTTTTTA
4371767 TTTTTTA
1 TTTTTTA
4371774 TTT
1 TTT
4371777 CTTTTTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:4371792 original size:21 final size:21
Alignment explanation
Indices: 4371768--4371812 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
4371758 TATTTTTTAT
4371768 TTTTTATT-TCTTTTTTCTCTC
1 TTTTTATTCTCTTTTTTCT-TC
*
4371789 TTTTTCTTCCTCTTTTTTCTTC
1 TTTTTATT-CTCTTTTTTCTTC
4371811 TT
1 TT
4371813 CTCTTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 4 0.19
23 10 0.48
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTATTCTCTTTTTTCTTC
Found at i:4371817 original size:21 final size:23
Alignment explanation
Indices: 4371776--4371823 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
4371766 ATTTTTTATT
*
4371776 TCTTTTTTCTCTCTTTTTCTTCC
1 TCTTTTTTCTCTCTTTCTCTTCC
*
4371799 TCTTTTTTCT-TC-TTCTCTTCT
1 TCTTTTTTCTCTCTTTCTCTTCC
4371820 TCTT
1 TCTT
4371824 GTCTCAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 2 0.09
23 10 0.43
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (23 bp):
TCTTTTTTCTCTCTTTCTCTTCC
Found at i:4372368 original size:29 final size:29
Alignment explanation
Indices: 4372335--4372421 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
4372325 TGTAATTTTT
*
4372335 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
4372364 TGAAATTTTAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAGGGT-TAAAATGAAATTTAA
* *
4372393 AGAAAGTTTAAGGGTCAAAATGAAATTTA
1 AGAAAATTT-AGGGTTAAAATGAAATTTA
4372422 GGAAAAGTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
29 30 0.64
30 17 0.36
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.32
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:4372417 original size:30 final size:30
Alignment explanation
Indices: 4372350--4372450 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
4372340 ATTTAGGATT
* *
4372350 AAAATGAAATTTAATGAAA-TTTTAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
4372379 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* **
4372409 AAAATGAAATTT-AGGAAAAGTTTGGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
4372439 AAAATGCAATTT
1 AAAATGAAATTT
4372451 TTATTTTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.30
30 42 0.70
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.31
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:4372906 original size:54 final size:55
Alignment explanation
Indices: 4372722--4372940 Score: 308
Period size: 54 Copynumber: 4.1 Consensus size: 55
4372712 CACGTGAGCC
* *
4372722 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
4372777 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAA
* * *
4372829 AAGGCTCAACTTACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
4372883 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
4372938 AAG
1 AAG
4372941 TAGAAATTGA
Statistics
Matches: 148, Mismatches: 8, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
50 14 0.09
52 34 0.23
54 51 0.34
55 37 0.25
57 6 0.04
58 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:4372918 original size:106 final size:104
Alignment explanation
Indices: 4372722--4372932 Score: 325
Period size: 107 Copynumber: 2.0 Consensus size: 104
4372712 CACGTGAGCC
* *
4372722 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT-CAAAAGGCTCAAC
*
4372787 TCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAA
65 TCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAA
* * *
4372829 AAGGCTCAACTTACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTCAAAAGGCTCAAC
4372893 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
65 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
4372933 TTGAAAAGTA
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
104 16 0.16
106 35 0.36
107 36 0.37
108 10 0.10
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (104 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTCAAAAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
Found at i:4372938 original size:14 final size:14
Alignment explanation
Indices: 4372919--4372953 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4372909 GAGTTGATTT
4372919 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
4372933 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
4372947 TTGAAAA
1 TTGAAAA
4372954 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:4373203 original size:86 final size:89
Alignment explanation
Indices: 4373044--4373297 Score: 324
Period size: 91 Copynumber: 2.9 Consensus size: 89
4373034 AATAGAAATT
* * *
4373044 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
4373109 TTGA--TTTGAAAAGTAGA-ATT-A
65 TTGATTTTTGAAAAGTAGAGATTAA
** * * *
4373130 GTAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
*
4373193 TTGATTTTTGAAAAGTATAGATTGAA
65 TTGATTTTTGAAAAGTAGAGATT-AA
*
4373219 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
4373283 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
4373298 ACAAAAATTA
Statistics
Matches: 143, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
83 3 0.02
84 33 0.23
86 34 0.24
87 3 0.02
89 24 0.17
91 43 0.30
93 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (89 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAGATTAA
Found at i:4373697 original size:122 final size:120
Alignment explanation
Indices: 4373571--4373795 Score: 274
Period size: 122 Copynumber: 1.9 Consensus size: 120
4373561 GCGTGCCCCG
* * * * **
4373571 AGGCTCAACTCACTTCTCGCAATATAAGTTGATTTTTTAAA-A-AATTTAAAAATACCGCAACGT
1 AGGCTCAACTCACCTCTCGCAATATAAG-TCA-ATTTAAAACATAAACTAAAAATACCGCAACGT
** *
4373634 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
64 G-CCCGAGGCTCAACTCACTTCTCGCAATATGA-TTGATTTTGAAAAACAAAAATTAAA
* * * **
4373693 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATAAGTCAATTTAAAACATAAACTAAAAATACCGCAACGTGC
4373758 CCGAGGCTCAACTCACTTCTCGCAATATGATTGATTTT
66 CCGAGGCTCAACTCACTTCTCGCAATATGATTGATTTT
4373796 TTTAAAAAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
120 14 0.16
121 31 0.36
122 42 0.48
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (120 bp):
AGGCTCAACTCACCTCTCGCAATATAAGTCAATTTAAAACATAAACTAAAAATACCGCAACGTGC
CCGAGGCTCAACTCACTTCTCGCAATATGATTGATTTTGAAAAACAAAAATTAAA
Found at i:4374202 original size:193 final size:192
Alignment explanation
Indices: 4373255--4374250 Score: 1820
Period size: 192 Copynumber: 5.2 Consensus size: 192
4373245 CATGTGAGCC
** *
4373255 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
*
4373320 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACATCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
* * ***
4373385 AACTCATTTCTTGCAATATGAGTTGATTTTTTTTTTAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
4373448 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
* *
4373513 ACCTCTCGCAATATTAGTCAATTTAAAACATAAACTAAAAGTACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
* *
4373578 ACTCACTTCTCGCAATATAAGTTGA-TTTTTTAAAAAATTTAAAAATACCGCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
4373639 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
4373704 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTG-CCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
4373768 ACTCACTTCTCGCAATATGA-TTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
4373829 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAAC-AAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
4373893 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
4373958 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTT
4374021 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
4374086 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGGCGTGCCCCGAGGCTC
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTC-GGCGTGCCCCGAGGCTC
4374151 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
4374214 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
4374251 CCTTGGAAAG
Statistics
Matches: 780, Mismatches: 17, Indels: 12
0.96 0.02 0.01
Matches are distributed among these distances:
189 77 0.10
190 140 0.18
191 159 0.20
192 190 0.24
193 164 0.21
194 50 0.06
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (192 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:4385587 original size:44 final size:43
Alignment explanation
Indices: 4385510--4385599 Score: 153
Period size: 44 Copynumber: 2.1 Consensus size: 43
4385500 TGTTTAATTC
*
4385510 TAGACACGACTCTCAAAAGGCTTCCCAGCGGAGTCGCCAGCTG
1 TAGACACGACTCTCAAAAAGCTTCCCAGCGGAGTCGCCAGCTG
*
4385553 TAGACACGACTCTCAAAAAGCTTTCCCAGCGGAGTCGCTAGCTG
1 TAGACACGACTCTCAAAAAGC-TTCCCAGCGGAGTCGCCAGCTG
4385597 TAG
1 TAG
4385600 CGACCTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 20 0.45
44 24 0.55
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (43 bp):
TAGACACGACTCTCAAAAAGCTTCCCAGCGGAGTCGCCAGCTG
Found at i:4386013 original size:16 final size:16
Alignment explanation
Indices: 4385959--4386064 Score: 56
Period size: 16 Copynumber: 6.2 Consensus size: 16
4385949 GAAACAACTT
*
4385959 TTTTTCGAAACACGAAA
1 TTTTTAGAAACACG-AA
* *
4385976 TATTTTAAAATACAAGAA
1 T-TTTTAGAA-ACACGAA
4385994 -TTTTAGAAACACGAA
1 TTTTTAGAAACACGAA
*
4386009 TTTTTTAAAAAAACACGAAA
1 -TTTTT--AGAAACACG-AA
*
4386029 ATTTT-GAAACACGAGAA
1 TTTTTAGAAACAC--GAA
4386046 TTTTT-GAAAACACGAA
1 TTTTTAG-AAACACGAA
4386062 TTT
1 TTT
4386065 ATTTTAAAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
15 6 0.09
16 19 0.27
17 12 0.17
18 15 0.21
19 16 0.23
20 2 0.03
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.31
Consensus pattern (16 bp):
TTTTTAGAAACACGAA
Found at i:4386024 original size:53 final size:54
Alignment explanation
Indices: 4385966--4386073 Score: 148
Period size: 53 Copynumber: 2.0 Consensus size: 54
4385956 CTTTTTTTCG
*
4385966 AAACACGAAATATTTTAAAATACAAGAATTTTAG-AAACACGAATTT-TTTAAAA
1 AAACACGAAA-ATTTTAAAACACAAGAATTTTAGAAAACACGAATTTATTTAAAA
* * * *
4386019 AAACACGAAAATTTTGAAACACGAGAATTTTTGAAAACACGAATTTATTTTAAA
1 AAACACGAAAATTTTAAAACACAAGAATTTTAGAAAACACGAATTTATTTAAAA
4386073 A
1 A
4386074 CACATTTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 19 0.40
53 22 0.46
54 7 0.15
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.30
Consensus pattern (54 bp):
AAACACGAAAATTTTAAAACACAAGAATTTTAGAAAACACGAATTTATTTAAAA
Found at i:4386084 original size:17 final size:17
Alignment explanation
Indices: 4386047--4386095 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
4386037 ACACGAGAAT
4386047 TTTTGAAAACACGAATTTA
1 TTTT-AAAACAC-AATTTA
*
4386066 TTTTAAAACACATTTTA
1 TTTTAAAACACAATTTA
*
4386083 TTTGAAAACACAA
1 TTTTAAAACACAA
4386096 AAATTTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 16 0.59
18 7 0.26
19 4 0.15
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (17 bp):
TTTTAAAACACAATTTA
Found at i:4386145 original size:18 final size:18
Alignment explanation
Indices: 4386112--4386209 Score: 60
Period size: 18 Copynumber: 5.5 Consensus size: 18
4386102 TGATAAATTA
**
4386112 TGAAACACGAGGATTTTT
1 TGAAACACGAAAATTTTT
*
4386130 TGAAACACGAAAA-TTTA
1 TGAAACACGAAAATTTTT
* **
4386147 TGAAACAATGTCAATTTTT
1 TGAAAC-ACGAAAATTTTT
4386166 TGAAAACACG-AAA--TTT
1 TG-AAACACGAAAATTTTT
** *
4386182 TGAAAGTCGAGAATTTTT
1 TGAAACACGAAAATTTTT
4386200 TGAAAACACG
1 TG-AAACACG
4386210 GATTATTTAA
Statistics
Matches: 59, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
15 5 0.08
16 7 0.12
17 9 0.15
18 22 0.37
19 12 0.20
20 4 0.07
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (18 bp):
TGAAACACGAAAATTTTT
Found at i:4386151 original size:35 final size:35
Alignment explanation
Indices: 4386109--4386209 Score: 116
Period size: 34 Copynumber: 2.9 Consensus size: 35
4386099 TTTTGATAAA
*
4386109 TTATGAAACACGAGGATTTTTTG-AAACACGAAAAT
1 TTATGAAACACGAGAATTTTTTGAAAACACG-AAAT
* **
4386144 TTATGAAACAATGTCAATTTTTTGAAAACACGAAAT
1 TTATGAAAC-ACGAGAATTTTTTGAAAACACGAAAT
**
4386180 TT-TGAAAGTCGAGAATTTTTTGAAAACACG
1 TTATGAAACACGAGAATTTTTTGAAAACACG
4386210 GATTATTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
34 18 0.33
35 14 0.25
36 16 0.29
37 7 0.13
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (35 bp):
TTATGAAACACGAGAATTTTTTGAAAACACGAAAT
Found at i:4386350 original size:16 final size:17
Alignment explanation
Indices: 4386262--4386367 Score: 64
Period size: 16 Copynumber: 6.5 Consensus size: 17
4386252 TTTGAAATAC
* *
4386262 GAGATTTTTGAAAAGA-
1 GAGAATTTTGAAAACAT
* *
4386278 GGGAAATTTGAAAACAT
1 GAGAATTTTGAAAACAT
*
4386295 GAAAATTTTG-AAACACT
1 GAGAATTTTGAAAACA-T
*
4386312 -AG-A-TTTGAAAACAC
1 GAGAATTTTGAAAACAT
4386326 GA-AGATTTTG-AAACAT
1 GAGA-ATTTTGAAAACAT
* *
4386342 GAGAATTTTTAAAACAC
1 GAGAATTTTGAAAACAT
*
4386359 GAGGATTTT
1 GAGAATTTT
4386368 TTGAAATACG
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
14 4 0.06
15 7 0.10
16 31 0.46
17 26 0.38
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (17 bp):
GAGAATTTTGAAAACAT
Found at i:4386366 original size:17 final size:17
Alignment explanation
Indices: 4386319--4386368 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
4386309 ACTAGATTTG
*
4386319 AAAACACGAAGA-TTTT
1 AAAACACGAGGATTTTT
* * *
4386335 GAAACATGAGAATTTTT
1 AAAACACGAGGATTTTT
4386352 AAAACACGAGGATTTTT
1 AAAACACGAGGATTTTT
4386369 TGAAATACGA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (17 bp):
AAAACACGAGGATTTTT
Found at i:4386475 original size:16 final size:17
Alignment explanation
Indices: 4386454--4386485 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4386444 AATTTTAAAT
4386454 ACGAGAATTG-TGAAAC
1 ACGAGAATTGTTGAAAC
4386470 ACGAGAATTGTTGAAA
1 ACGAGAATTGTTGAAA
4386486 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22
Consensus pattern (17 bp):
ACGAGAATTGTTGAAAC
Found at i:4386523 original size:53 final size:50
Alignment explanation
Indices: 4386391--4386531 Score: 140
Period size: 52 Copynumber: 2.7 Consensus size: 50
4386381 ATTAAACATG
* * ** *
4386391 AAAATTTTTAAAAAC-AATTTTTGAAACACGAGAATTTATTTTAAAACATA
1 AAAAATTTTAAATACGAATTTTTGAAACACGAGAA-TTATTGAAAAAAATA
* * *
4386441 AAAAATTTTAAATACGAGAATTGTGAAACACGAGAATTGTTGAAAAAAATAA
1 AAAAATTTTAAATACGA-ATTTTTGAAACACGAGAATTATTGAAAAAAAT-A
* *
4386493 AAAAATTTTGAAATACGAATTTTTTTAAACACGAAAATT
1 AAAAATTTT-AAATACGAA-TTTTTGAAACACGAGAATT
4386532 TTAGAAATAT
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
50 13 0.18
51 11 0.15
52 27 0.36
53 23 0.31
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (50 bp):
AAAAATTTTAAATACGAATTTTTGAAACACGAGAATTATTGAAAAAAATA
Found at i:4386599 original size:34 final size:34
Alignment explanation
Indices: 4386493--4386611 Score: 116
Period size: 34 Copynumber: 3.4 Consensus size: 34
4386483 AAAAAAATAA
* * **
4386493 AAAAATTTTGAAATA-CGAATTTTTTTAAACACG
1 AAAAATTTTGAAAAATGGAATTTTTAAAAACACG
*
4386526 -AAAATTTTAGAAATATGGAAATTTTTTAAAAAAACACG
1 AAAAATTTT-GAAAAATGG-AA-TTTTT--AAAAACACG
*
4386564 AAAAATTTTGAAAAATGGAATTTTTGAAAACACG
1 AAAAATTTTGAAAAATGGAATTTTTAAAAACACG
*
4386598 AAAATTTTTGAAAA
1 AAAAATTTTGAAAA
4386612 CACGAAAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
32 8 0.11
33 6 0.08
34 22 0.30
35 2 0.03
36 10 0.14
37 2 0.03
38 15 0.21
39 8 0.11
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (34 bp):
AAAAATTTTGAAAAATGGAATTTTTAAAAACACG
Found at i:4386605 original size:18 final size:18
Alignment explanation
Indices: 4386556--4386624 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
4386546 ATTTTTTAAA
*
4386556 AAAACACGAAAAATTTTG
1 AAAACACGAAAATTTTTG
* *
4386574 AAAA-ATG-GAATTTTTG
1 AAAACACGAAAATTTTTG
4386590 AAAACACGAAAATTTTTG
1 AAAACACGAAAATTTTTG
4386608 AAAACACGAAAATTTTT
1 AAAACACGAAAATTTTT
4386625 CTGATTTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
16 11 0.25
17 4 0.09
18 29 0.66
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.29
Consensus pattern (18 bp):
AAAACACGAAAATTTTTG
Found at i:4386624 original size:72 final size:70
Alignment explanation
Indices: 4386466--4386624 Score: 167
Period size: 72 Copynumber: 2.2 Consensus size: 70
4386456 GAGAATTGTG
* * * * **
4386466 AAACACGAGAATTGTTGAAAAAAATAAAAAAATTTTGAAATACGAATTTTTTTAAACACGAAAAT
1 AAACACGAAAATT-TTTAAAAAAACAAAAAAATTTTGAAAAACGAATTTTTGAAAACACGAAAAT
4386531 TTTAGA
65 TTTAGA
** * * *
4386537 AATA-TGGAAATTTTTTAAAAAAACACGAAAAATTTTGAAAAATGGAATTTTTGAAAACACGAAA
1 AA-ACACGAAAATTTTTAAAAAAACA-AAAAAATTTTGAAAAA-CGAATTTTTGAAAACACGAAA
*
4386601 ATTTTTGA
63 ATTTTAGA
4386609 AAACACGAAAATTTTT
1 AAACACGAAAATTTTT
4386625 CTGATTTTCA
Statistics
Matches: 69, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
70 10 0.14
71 22 0.32
72 37 0.54
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (70 bp):
AAACACGAAAATTTTTAAAAAAACAAAAAAATTTTGAAAAACGAATTTTTGAAAACACGAAAATT
TTAGA
Found at i:4386752 original size:20 final size:19
Alignment explanation
Indices: 4386727--4386767 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
4386717 TCTTACCTTA
4386727 TTTTTGAAAACACGAGAAAT
1 TTTTTGAAAACACGA-AAAT
*
4386747 TTTTTGAAGACACGAAAAT
1 TTTTTGAAAACACGAAAAT
4386766 TT
1 TT
4386768 CGAAACGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (19 bp):
TTTTTGAAAACACGAAAAT
Found at i:4387293 original size:23 final size:23
Alignment explanation
Indices: 4387262--4387322 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
4387252 CCGCATTTGG
4387262 GCTGCTTCTTTCTTCTTCTTTTT
1 GCTGCTTCTTTCTTCTTCTTTTT
*
4387285 TCTGCTTCTTTCTTCTTCTTTTT
1 GCTGCTTCTTTCTTCTTCTTTTT
4387308 GCTGCTT-TTT-TTCTT
1 GCTGCTTCTTTCTTCTT
4387323 TGTTTTTTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.14
22 3 0.08
23 28 0.78
ACGTcount: A:0.00, C:0.25, G:0.08, T:0.67
Consensus pattern (23 bp):
GCTGCTTCTTTCTTCTTCTTTTT
Found at i:4387331 original size:23 final size:23
Alignment explanation
Indices: 4387262--4387329 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
4387252 CCGCATTTGG
4387262 GCTGCTTCTTTCTTCTTCTTTTTT
1 GCTGCTTCTTTCTTCTT-TTTTTT
*
4387286 -CTGCTTCTTTCTTCTTCTTTTT
1 GCTGCTTCTTTCTTCTTTTTTTT
4387308 GCTGCTT-TTT-TTCTTTGTTTTT
1 GCTGCTTCTTTCTTCTTT-TTTTT
4387330 TGGCTGGCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.12
22 13 0.32
23 22 0.55
ACGTcount: A:0.00, C:0.22, G:0.09, T:0.69
Consensus pattern (23 bp):
GCTGCTTCTTTCTTCTTTTTTTT
Found at i:4387446 original size:21 final size:20
Alignment explanation
Indices: 4387407--4387447 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4387397 ATTATTTTTA
*
4387407 TTTTTTCTTTCCCTTTTCTT
1 TTTTTTCTTTCCCTCTTCTT
*
4387427 TTTTTTCTTTCTTCTCTTCTT
1 TTTTTTCTTTC-CCTCTTCTT
4387448 CTTCCTTCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTCTTTCCCTCTTCTT
Found at i:4387824 original size:29 final size:29
Alignment explanation
Indices: 4387791--4387901 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 29
4387781 TGTAATTTTT
*
4387791 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
4387820 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
4387850 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* *
4387879 GGAAAAGTTTAGGGGTCAAAATG
1 AGAAAA-TTTA-GGGTTAAAATG
4387902 CAACTTTTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
29 14 0.21
30 51 0.76
31 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.29
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:4387846 original size:30 final size:30
Alignment explanation
Indices: 4387806--4387901 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
4387796 ATTTAGGATT
*
4387806 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
4387836 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
4387866 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
4387896 AAAATG
1 AAAATG
4387902 CAACTTTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.04
30 55 0.96
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.28
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:4390565 original size:19 final size:18
Alignment explanation
Indices: 4390541--4390587 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
4390531 TGTTCTTATT
*
4390541 TATTTATGTTTATAATTAA
1 TATTTAT-TTTATAAATAA
*
4390560 TATTTATTTTTTAAATAA
1 TATTTATTTTATAAATAA
4390578 T-TTTATTTTA
1 TATTTATTTTA
4390588 AATCTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.32
18 10 0.40
19 7 0.28
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTTATTTTATAAATAA
Found at i:4394147 original size:31 final size:31
Alignment explanation
Indices: 4394106--4394164 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
4394096 AACAGTCTAG
4394106 TGACTAAAATAAAAACTTTTGAATAATTCGT
1 TGACTAAAATAAAAACTTTTGAATAATTCGT
* **
4394137 TGACTTAAATAAAATTTTTTGAATAATT
1 TGACTAAAATAAAAACTTTTGAATAATT
4394165 ATGAATTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (31 bp):
TGACTAAAATAAAAACTTTTGAATAATTCGT
Found at i:4395170 original size:28 final size:29
Alignment explanation
Indices: 4395110--4395184 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
4395100 ACAAAAAAAT
* *
4395110 TTATAAAGAATAATT-AAAATTATAAATTA
1 TTATAAA-ATTAATTAAAAATCATAAATTA
4395139 TTAT-AAATTAATTAAAAATCATAAAATT-
1 TTATAAAATTAATTAAAAATCAT-AAATTA
*
4395167 TTATAAAATAAATTAAAA
1 TTATAAAATTAATTAAAA
4395185 CAAAGCTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.15
28 13 0.32
29 21 0.52
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (29 bp):
TTATAAAATTAATTAAAAATCATAAATTA
Found at i:4395421 original size:18 final size:18
Alignment explanation
Indices: 4395410--4395445 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4395400 ATTTTATACG
4395410 TTTTAATAATTTCTAAAA
1 TTTTAATAATTTCTAAAA
*
4395428 TTTTAATAATTTATAAAA
1 TTTTAATAATTTCTAAAA
4395446 AAAACTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAATAATTTCTAAAA
Found at i:4395502 original size:30 final size:30
Alignment explanation
Indices: 4395466--4395541 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 30
4395456 AAAAAATCAT
*
4395466 TTTAATTATTTTATAATATTTTTTATAAAA
1 TTTAATTATTTTATAATATATTTTATAAAA
* * **
4395496 TTTAATTATTTGA-ATTATATTTTATAATT
1 TTTAATTATTTTATAATATATTTTATAAAA
* *
4395525 TTTTATTTTTTTATAAT
1 TTTAATTATTTTATAAT
4395542 TTCGAAATGA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (30 bp):
TTTAATTATTTTATAATATATTTTATAAAA
Found at i:4396183 original size:17 final size:16
Alignment explanation
Indices: 4396161--4396210 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
4396151 GCCACACCAA
*
4396161 AAAAAATTTAAAATTAT
1 AAAAAATTTAAAA-AAT
*
4396178 AAAAAATTCAAAAAAT
1 AAAAAATTTAAAAAAT
*
4396194 AAAAAGTTTATAAAAAT
1 AAAAAATTTA-AAAAAT
4396211 TCAAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAAAATTTAAAAAAT
Found at i:4396339 original size:51 final size:51
Alignment explanation
Indices: 4396263--4396366 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
4396253 AGCTACCATG
*
4396263 TTTAAAATTTTAATGATTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
1 TTTAAAAATTTAATGATTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
*
4396314 TTTAAAAATTTAATGGTTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
1 TTTAAAAATTTAATGATTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
4396365 TT
1 TT
4396367 GAAAGGTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (51 bp):
TTTAAAAATTTAATGATTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
Found at i:4397389 original size:18 final size:18
Alignment explanation
Indices: 4397350--4397397 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
4397340 ATTGTAATTA
4397350 TTTTATAATTTGAATGATT
1 TTTTATAATTT-AATGATT
4397369 TTTTATAATTTATTATG-TT
1 TTTTATAATTTA--ATGATT
4397388 TTTT-TAATTT
1 TTTTATAATTT
4397398 CGAAATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.26
19 17 0.63
20 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
TTTTATAATTTAATGATT
Found at i:4399176 original size:15 final size:15
Alignment explanation
Indices: 4399156--4399184 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4399146 CACTAGTTTT
4399156 GGCAAAGGGAGGATA
1 GGCAAAGGGAGGATA
4399171 GGCAAAGGGAGGAT
1 GGCAAAGGGAGGAT
4399185 CTCAAGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.48, T:0.07
Consensus pattern (15 bp):
GGCAAAGGGAGGATA
Found at i:4400065 original size:20 final size:21
Alignment explanation
Indices: 4400022--4400067 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
4400012 ACTATTTTGT
4400022 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
4400042 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
4400061 TATGGGC
1 TATGGGC
4400068 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:4409218 original size:12 final size:11
Alignment explanation
Indices: 4409201--4409252 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 11
4409191 CAAGTAATTT
4409201 AAAAATTATAAA
1 AAAAATTA-AAA
4409213 AAAAATTAAAA
1 AAAAATTAAAA
4409224 ATTAAGAATTAAAA
1 A--AA-AATTAAAA
*
4409238 TAAAAAATAAAA
1 -AAAAATTAAAA
4409250 AAA
1 AAA
4409253 GTATGAAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 7 0.20
12 15 0.43
13 4 0.11
14 8 0.23
15 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (11 bp):
AAAAATTAAAA
Found at i:4409233 original size:26 final size:27
Alignment explanation
Indices: 4409199--4409251 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4409189 AACAAGTAAT
* *
4409199 TTAAAAATTATAA-AAAAAATTAAAAA
1 TTAAAAATTAAAATAAAAAATAAAAAA
*
4409225 TTAAGAATTAAAATAAAAAATAAAAAA
1 TTAAAAATTAAAATAAAAAATAAAAAA
4409252 AGTATGAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (27 bp):
TTAAAAATTAAAATAAAAAATAAAAAA
Found at i:4412578 original size:23 final size:24
Alignment explanation
Indices: 4412550--4412594 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
4412540 TAATAATTTT
4412550 ATAAATATTAATCA-TTTATAAAA
1 ATAAATATTAATCAGTTTATAAAA
* *
4412573 ATAAATTTTAATTAGTTTATAA
1 ATAAATATTAATCAGTTTATAA
4412595 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAAATATTAATCAGTTTATAAAA
Found at i:4412643 original size:21 final size:20
Alignment explanation
Indices: 4412592--4412655 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
4412582 AATTAGTTTA
* *
4412592 TAATAATTTTTTATAAAATT
1 TAATAATTTTTTTTATAATT
*
4412612 TAATAAATTTTTTTATAATT
1 TAATAATTTTTTTTATAATT
*
4412632 TGAATGATTTTTTTATTATAATT
1 T-AAT-AATTTTTT-TTATAATT
4412655 T
1 T
4412656 TTTATTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 18 0.50
21 3 0.08
22 6 0.17
23 9 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TAATAATTTTTTTTATAATT
Found at i:4417527 original size:14 final size:14
Alignment explanation
Indices: 4417508--4417536 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4417498 ATAACAATGG
4417508 TTTTTATCATGATT
1 TTTTTATCATGATT
4417522 TTTTTATCATGATT
1 TTTTTATCATGATT
4417536 T
1 T
4417537 GAAACAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTTATCATGATT
Found at i:4421526 original size:45 final size:45
Alignment explanation
Indices: 4421453--4421540 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
4421443 GCATGATACT
4421453 ATTAAATTAGTGATTTTGCTTGTAGCCTTATACTCTTGGCCTACA
1 ATTAAATTAGTGATTTTGCTTGTAGCCTTATACTCTTGGCCTACA
* * *
4421498 ATTAGATTGGTGATTTTTCTTGTAGCCTTATACTCTTGGCCTA
1 ATTAAATTAGTGATTTTGCTTGTAGCCTTATACTCTTGGCCTA
4421541 TCTTCCAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (45 bp):
ATTAAATTAGTGATTTTGCTTGTAGCCTTATACTCTTGGCCTACA
Found at i:4425955 original size:42 final size:38
Alignment explanation
Indices: 4425909--4425996 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 38
4425899 TAATTAAAAT
4425909 TTTTAAAATTTAAA-AAGTTTAACAAAATATATAAAAAATATA
1 TTTTAAAATTTAAATAA-TTT-A-AAAA-AT-TAAAAAATATA
*
4425951 TTTTAAAATTTAAATTTATTTAAAAAATTAAAAAATATA
1 TTTTAAAATTTAAA-TAATTTAAAAAATTAAAAAATATA
4425990 TTTTAAA
1 TTTTAAA
4425997 TTTTTTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
39 18 0.42
40 2 0.05
41 4 0.09
42 15 0.35
43 3 0.07
44 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (38 bp):
TTTTAAAATTTAAATAATTTAAAAAATTAAAAAATATA
Found at i:4425970 original size:18 final size:18
Alignment explanation
Indices: 4425944--4425982 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4425934 AATATATAAA
* *
4425944 AAATATATTTTAAAATTT
1 AAATATATTTAAAAAATT
*
4425962 AAATTTATTTAAAAAATT
1 AAATATATTTAAAAAATT
4425980 AAA
1 AAA
4425983 AAATATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATATTTAAAAAATT
Found at i:4429201 original size:16 final size:16
Alignment explanation
Indices: 4429180--4429219 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4429170 CTTTAATCCT
*
4429180 TTTATTTACTT-ATTTA
1 TTTATTCACTTGA-TTA
4429196 TTTATTCACTTGATTA
1 TTTATTCACTTGATTA
4429212 TTTATTCA
1 TTTATTCA
4429220 TTATTCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTATTCACTTGATTA
Found at i:4429288 original size:27 final size:27
Alignment explanation
Indices: 4429189--4429281 Score: 72
Period size: 27 Copynumber: 3.6 Consensus size: 27
4429179 TTTTATTTAC
*
4429189 TTATTTATTTATTCAC-T-TGATT-AT
1 TTATTTATTTATTCACATATCATTCAT
* *
4429213 TTATTCA-TTATTCTTTACAT-TTATTCAT
1 TTATTTATTTATTC---ACATATCATTCAT
* *
4429241 TTATTTGTTTATTCACATATCATTCCT
1 TTATTTATTTATTCACATATCATTCAT
4429268 TTATTTATTT-TTCA
1 TTATTTATTTATTCA
4429282 TCTTATCCCG
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
23 6 0.11
24 6 0.11
26 10 0.18
27 20 0.36
28 7 0.13
29 6 0.11
ACGTcount: A:0.24, C:0.13, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATTTATTTATTCACATATCATTCAT
Found at i:4429367 original size:3 final size:3
Alignment explanation
Indices: 4429359--4429413 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
4429349 GTTTGTGCCT
4429359 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4429407 TTA TTA T
1 TTA TTA T
4429414 CATCATCTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4434570 original size:48 final size:48
Alignment explanation
Indices: 4434498--4434593 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
4434488 TCTCTAAAGG
*
4434498 TTGAATAAGACGGGGATAACGAATAAAGTAGAATTAACCCTAAATCTT
1 TTGAATAAGACGGGGACAACGAATAAAGTAGAATTAACCCTAAATCTT
*
4434546 TTGAATAAGACGAGGG-CAATGAATAAAGTAGAATTAACCCTAAATCTT
1 TTGAATAAGACG-GGGACAACGAATAAAGTAGAATTAACCCTAAATCTT
4434594 CTTTGTCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 42 0.93
49 3 0.07
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (48 bp):
TTGAATAAGACGGGGACAACGAATAAAGTAGAATTAACCCTAAATCTT
Found at i:4436561 original size:130 final size:125
Alignment explanation
Indices: 4436269--4436562 Score: 279
Period size: 130 Copynumber: 2.3 Consensus size: 125
4436259 AAAAGAGTCC
* ** * * *
4436269 CAAAAATCTTAAAACACAAAAAAAATATAAAATCTTAATCTATTTCAAATTCACTTAAAATTTAA
1 CAAAAATCTTAAAACTC-TGAAAATTATAAAATATTAATCTATTTAAAATTCACTTAAAATTTAA
**** *
4436334 AAAAATATAAAAAAACTAAAAAATCATTAAAATTCCCAAAAAAATATTTTTTTTAAATCCA
65 AAAAATATAAAAAAACTAAAAAATCATTAAAATTCCCAAAAAAATATTTTAAAAAAACCCA
* * *
4436395 GAAAAATCTTAAAACTCTGAAATTTTTTTAAAAAAATATTAATCTATTTAAAATTCACTTAAAAA
1 CAAAAATCTTAAAACTCTGAAA----ATT-ATAAAATATTAATCTATTTAAAATTCACTT-AAAA
* *
4436460 TTT-TAAAAATATAAAAAAATTAAAAAATCATTAAAATT-CCAAAAAAATATATATTGAAAAAAA
60 TTTAAAAAAATATAAAAAAACTAAAAAATCATTAAAATTCCCAAAAAAATAT-T-TT--AAAAAA
*
4436523 CACCCC
121 -ACCCA
*
4436529 CAAAAGATCTTATAACT-TAGAAAATTATAAAATA
1 CAAAA-ATCTTAAAACTCT-GAAAATTATAAAATA
4436563 AACTTTTAAA
Statistics
Matches: 134, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
125 3 0.02
126 15 0.11
129 13 0.10
130 68 0.51
131 11 0.08
133 2 0.01
134 8 0.06
135 14 0.10
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (125 bp):
CAAAAATCTTAAAACTCTGAAAATTATAAAATATTAATCTATTTAAAATTCACTTAAAATTTAAA
AAAATATAAAAAAACTAAAAAATCATTAAAATTCCCAAAAAAATATTTTAAAAAAACCCA
Found at i:4443171 original size:18 final size:18
Alignment explanation
Indices: 4443150--4443190 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4443140 CCCCATGTTA
4443150 TGCGAAC-CCCTTTGCAGG
1 TGCGAACGCCC-TTGCAGG
*
4443168 TGCGAACGCCCTTGCATG
1 TGCGAACGCCCTTGCAGG
4443186 TGCGA
1 TGCGA
4443191 GCCCTGTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.22
Consensus pattern (18 bp):
TGCGAACGCCCTTGCAGG
Found at i:4443425 original size:36 final size:36
Alignment explanation
Indices: 4443380--4443515 Score: 105
Period size: 36 Copynumber: 3.8 Consensus size: 36
4443370 TTTATATAAA
*
4443380 ATGCAAACCCTAGGTAATATGTGAACCGAGTATATC
1 ATGCAAACCCTAGGTAATATGTGAACCCAGTATATC
* * ** * * *
4443416 ATGCGAACCCTAGGTACTATACG-AGCTATATATATC
1 ATGCAAACCCTAGGTAATATGTGAACCCA-GTATATC
** * * *
4443452 ATGTGAACCTTAGGTAATATG-CAACGCCTGTATATC
1 ATGCAAACCCTAGGTAATATGTGAAC-CCAGTATATC
* *
4443488 ATGCAAATCCTAGGTACTATGTGAACCC
1 ATGCAAACCCTAGGTAATATGTGAACCC
4443516 CATTGTGTTA
Statistics
Matches: 74, Mismatches: 22, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
35 3 0.04
36 67 0.91
37 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (36 bp):
ATGCAAACCCTAGGTAATATGTGAACCCAGTATATC
Found at i:4446259 original size:26 final size:26
Alignment explanation
Indices: 4446229--4446336 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
4446219 TGAAATGCCC
4446229 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
4446255 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
4446281 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
4446307 ATCATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAACCCATT
4446333 ATCA
1 ATCA
4446337 ATTTGTACTA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:4446645 original size:28 final size:29
Alignment explanation
Indices: 4446602--4446673 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
4446592 GTTACAATAT
4446602 GTGTG-ACCCTACATGTACGAAC-CCTAG
1 GTGTGAACCCTACATGTACGAACTCCTAG
* *
4446629 GTGTGAACCCTATATGTGCGAACTCCTAG
1 GTGTGAACCCTACATGTACGAACTCCTAG
**
4446658 GTGCAAACCCTACATG
1 GTGTGAACCCTACATG
4446674 CGTGAACCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 5 0.13
28 15 0.39
29 18 0.47
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (29 bp):
GTGTGAACCCTACATGTACGAACTCCTAG
Found at i:4446680 original size:29 final size:28
Alignment explanation
Indices: 4446607--4446726 Score: 89
Period size: 29 Copynumber: 4.2 Consensus size: 28
4446597 AATATGTGTG
** **
4446607 ACCCTACATGTACGAACCCTAGGTGTGA
1 ACCCTACATGCGCGAACCCTAGGTGCAA
* *
4446635 ACCCTATATGTGCGAACTCCTAGGTGCAA
1 ACCCTACATGCGCGAAC-CCTAGGTGCAA
* *
4446664 ACCCTACATGCGTGAACCCATATGTGCAA
1 ACCCTACATGCGCGAACCC-TAGGTGCAA
* * * *
4446693 A-CATATATGTGCGAACCCTGTATGTGCAA
1 ACCCTACATGCGCGAACCC--TAGGTGCAA
4446722 ACCCT
1 ACCCT
4446727 GCTTATGTAT
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
28 30 0.41
29 42 0.57
30 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (28 bp):
ACCCTACATGCGCGAACCCTAGGTGCAA
Found at i:4446718 original size:15 final size:15
Alignment explanation
Indices: 4446684--4446727 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
4446674 CGTGAACCCA
* *
4446684 TATGTGCAAA-CATA
1 TATGTGCAAACCCTG
*
4446698 TATGTGCGAACCCTG
1 TATGTGCAAACCCTG
4446713 TATGTGCAAACCCTG
1 TATGTGCAAACCCTG
4446728 CTTATGTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (15 bp):
TATGTGCAAACCCTG
Found at i:4450347 original size:132 final size:131
Alignment explanation
Indices: 4450168--4450460 Score: 322
Period size: 132 Copynumber: 2.2 Consensus size: 131
4450158 AACGGGAGAT
* * * ** ** * *
4450168 TGCAACCCAGCATGATAGGGCACTACTCCCCAAATTTCCAAACATCGAGTATTTCCTTTATTTTA
1 TGCAACCCAGCACGATAGGGCACGA-TTCCCAAATCACCAAACATCGAACATTTCCTTCATTTCA
* ** * *
4450233 AAGAGTTTCTAGAAA-ACGTGAGTGAGGTTCCGAAGGAATC-TTCGATTGTTTTGAACAAATGAA
65 AAGAGTTTCTAGAAACA-ATGAGTGAAATTCCAAAGGAA-CGTTCGATTATTTTGAACAAAT-AA
4450296 AAAAGC
127 AAAA-C
*
4450302 -GCAACCCAGCACGATAGGGCACGATTCTCAAATCACCAAACATCGAACATTTCCTTCATTTCAA
1 TGCAACCCAGCACGATAGGGCACGATTCCCAAATCACCAAACATCGAACATTTCCTTCATTTCAA
* * * * *
4450366 AGAGTTTTTAGAAACAATGAGTGAAATTCTAAAGGGACGTTCGATTATTTTGAGCAAATAAGAAA
66 AGAGTTTCTAGAAACAATGAGTGAAATTCCAAAGGAACGTTCGATTATTTTGAACAAATAAAAAA
4450431 C
131 C
* *
4450432 TGCAACCCAACACGTTAGGGCACGATTCC
1 TGCAACCCAGCACGATAGGGCACGATTCC
4450461 ACGAATTGTC
Statistics
Matches: 133, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
130 1 0.01
131 31 0.23
132 78 0.59
133 23 0.17
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (131 bp):
TGCAACCCAGCACGATAGGGCACGATTCCCAAATCACCAAACATCGAACATTTCCTTCATTTCAA
AGAGTTTCTAGAAACAATGAGTGAAATTCCAAAGGAACGTTCGATTATTTTGAACAAATAAAAAA
C
Found at i:4464666 original size:26 final size:26
Alignment explanation
Indices: 4464637--4464718 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
4464627 TGGTACAAAT
*
4464637 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
4464663 TGATAATGGATTAGGTAAATGCTCTA
1 TGATAATGGATTAGGTAAATGTTCCA
*
4464689 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
4464715 TGAT
1 TGAT
4464719 GGGCATTTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:4473911 original size:18 final size:18
Alignment explanation
Indices: 4473888--4473924 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4473878 CGACTAAAAG
4473888 GAGGGGAATTATGGTTTT
1 GAGGGGAATTATGGTTTT
4473906 GAGGGGAATTATGGTTTT
1 GAGGGGAATTATGGTTTT
4473924 G
1 G
4473925 TTTCAATGGT
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:0.22, C:0.00, G:0.41, T:0.38
Consensus pattern (18 bp):
GAGGGGAATTATGGTTTT
Found at i:4474339 original size:23 final size:24
Alignment explanation
Indices: 4474310--4474369 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
4474300 GTCCACTTGG
4474310 TTTTATTTTTATTTCAATTGA-GT
1 TTTTATTTTTATTTCAATTGATGT
* *
4474333 TTTTATTATTATTTCAATTTATGT
1 TTTTATTTTTATTTCAATTGATGT
4474357 TTTTATTCTTTAT
1 TTTTATT-TTTAT
4474370 GATTCTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 19 0.59
24 9 0.28
25 4 0.12
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (24 bp):
TTTTATTTTTATTTCAATTGATGT
Found at i:4482343 original size:22 final size:21
Alignment explanation
Indices: 4482325--4482366 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
4482315 AAATTTATGT
4482325 TTTTATTCATTTTTATTTAAGA
1 TTTTATT-ATTTTTATTTAAGA
*
4482347 TTTTATTATTTATTTTTTAA
1 TTTTATTATTT-TTATTTAA
4482367 AATTATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTATTATTTTTATTTAAGA
Found at i:4482503 original size:31 final size:29
Alignment explanation
Indices: 4482464--4482558 Score: 118
Period size: 31 Copynumber: 3.1 Consensus size: 29
4482454 AAAATTTCTA
4482464 TTTTAAAATTTTCATTATACATGTATTTTT
1 TTTTAAAATTTTCATTATACAT-TATTTTT
*
4482494 TTTTCAAAATTTATACATTATACATTATATATTA
1 TTTT-AAAATTT-T-CATTATACATTAT-T-TTT
*
4482528 TTTTAAAATTTTTATTATACATTATTTTT
1 TTTTAAAATTTTCATTATACATTATTTTT
4482557 TT
1 TT
4482559 ATATATTGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
29 4 0.07
30 5 0.09
31 19 0.33
32 5 0.09
33 18 0.32
34 6 0.11
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (29 bp):
TTTTAAAATTTTCATTATACATTATTTTT
Found at i:4482680 original size:3 final size:3
Alignment explanation
Indices: 4482668--4482699 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4482658 TTAAAACGCC
4482668 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4482700 ATATATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:4490242 original size:98 final size:98
Alignment explanation
Indices: 4490068--4490248 Score: 256
Period size: 98 Copynumber: 1.8 Consensus size: 98
4490058 AAGCCATAAG
* * *
4490068 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTAAAGATAACGAATCTTATCTCCCTGAAGTTGT
4490133 AGTGGAACAGATTGAAGCTATAAATAAAACAGA
66 AGTGGAACAGATTGAAGCTATAAATAAAACAGA
* * * * * *
4490166 TCTTATCTCTCTTAAGTTGTAGTAGAGCAGAGTGAAGATAAC-AGGTCTTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTAAAGATAACGA-ATCTTATCTCCCTGAAGTTG
*
4490230 TAGTGGAGCAGATTGAAGC
65 TAGTGGAACAGATTGAAGC
4490249 CACCATCCTT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 1 0.01
98 71 0.99
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (98 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTAAAGATAACGAATCTTATCTCCCTGAAGTTGT
AGTGGAACAGATTGAAGCTATAAATAAAACAGA
Found at i:4490283 original size:44 final size:44
Alignment explanation
Indices: 4490160--4490284 Score: 135
Period size: 45 Copynumber: 2.8 Consensus size: 44
4490150 CTATAAATAA
* *
4490160 AACAGATCTTATCTCTCTTAAGTTGTAGTAGAGCAGAGTGAAGAT
1 AACAG-TCTTATCTCTCTGAAGTTGTAGTAGAGCAGAGTGAAGAC
* * * *
4490205 AACAGGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCC
1 AACA-GTCTTATCTCTCTGAAGTTGTAGTAGAGCAGAGTGAAGAC
* * *
4490250 ACCA-TCCTTATCTCTCTGAAGTTGCAATAGAGCAG
1 AACAGT-CTTATCTCTCTGAAGTTGTAGTAGAGCAG
4490285 GATAAAAATA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.01
44 25 0.37
45 40 0.60
46 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
AACAGTCTTATCTCTCTGAAGTTGTAGTAGAGCAGAGTGAAGAC
Found at i:4493272 original size:21 final size:22
Alignment explanation
Indices: 4493246--4493293 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
4493236 TGTCCACTTG
4493246 GTTTTTTTTTATTTCAATTGA-
1 GTTTTTTTTTATTTCAATTGAT
*
4493267 G-TTTTTTTTATTTCAATTTAT
1 GTTTTTTTTTATTTCAATTGAT
4493288 GTTTTT
1 GTTTTT
4493294 ATTCTTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 18 0.75
21 2 0.08
22 4 0.17
ACGTcount: A:0.17, C:0.04, G:0.08, T:0.71
Consensus pattern (22 bp):
GTTTTTTTTTATTTCAATTGAT
Done.