Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 20
Found at i:2863445 original size:36 final size:36
Alignment explanation
Indices: 2863379--2864037 Score: 896
Period size: 36 Copynumber: 18.4 Consensus size: 36
2863369 TTTGAGATTA
2863379 TTTCCCTTGAAACAAA-TTT-TCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2863413 TTTCTCTCGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * ** *
2863449 TTTCCCTTAAAACAAGTTTCCTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2863485 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * * *
2863521 TTTCCCTCT-AAACATATTTGGTCTCCCTTGAGATAA
1 TTTCCCT-TGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
2863557 TTTCCCTTAAAATAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2863593 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAA
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2863629 TTTCCCTTTAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2863665 TTTCCCTTTAAACAAA-TTT-TCTCTCTTAAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
2863699 TTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2863735 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAA
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
2863771 TTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
2863807 TTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2863843 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAA
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
2863879 TTTCCCTTGAAACAAATTTTGTCTCTCTTGATACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2863915 TTTCCCTTGAAACACATTTTGTCTCTCTTGAGACAT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
2863951 TTTCCCATGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2863987 TTTCCTTTAAAACAAATTTTTGTCTCTTTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
*
2864024 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2864038 CCACTCTTTG
Statistics
Matches: 552, Mismatches: 66, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
34 41 0.07
35 9 0.02
36 471 0.85
37 31 0.06
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2863621 original size:21 final size:21
Alignment explanation
Indices: 2863595--2863659 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
2863585 TGAGACAGTT
2863595 TCCCTTGAAACAAATTTCGTC
1 TCCCTTGAAACAAATTTCGTC
*
2863616 TCCCTTGAGAC-AA--T--T-
1 TCCCTTGAAACAAATTTCGTC
*
2863631 TCCCTTTAAACAAATTTCGTC
1 TCCCTTGAAACAAATTTCGTC
2863652 TCCCTTGA
1 TCCCTTGA
2863660 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 9 0.26
16 3 0.09
18 2 0.06
20 3 0.09
21 17 0.50
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.35
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTCGTC
Found at i:2863871 original size:21 final size:20
Alignment explanation
Indices: 2863845--2863909 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
2863835 TGAGACAGTT
2863845 TCCCTTGAAACAAATTTCGTC
1 TCCCTTGAAACAAATTT-GTC
*
2863866 TCCCTTGAGAC-AA--T-T-
1 TCCCTTGAAACAAATTTGTC
2863881 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAA-TTTGTC
*
2863902 TCTCTTGA
1 TCCCTTGA
2863910 TACAGTTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
15 10 0.29
16 3 0.09
18 1 0.03
19 1 0.03
20 3 0.09
21 17 0.49
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (20 bp):
TCCCTTGAAACAAATTTGTC
Found at i:2864576 original size:5 final size:5
Alignment explanation
Indices: 2864568--2864593 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2864558 ATTAATACTA
2864568 TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
2864594 TTGTTTACAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:2865688 original size:32 final size:32
Alignment explanation
Indices: 2865652--2865739 Score: 78
Period size: 32 Copynumber: 2.8 Consensus size: 32
2865642 TTCTTCACGG
2865652 TTTTTATTTAATTCTTCTATTTTATTTTATTA
1 TTTTTATTTAATTCTTCTATTTTATTTTATTA
** * *
2865684 TTTTT-TTTAAAACTAACT-TATTATTATTATTA
1 TTTTTATTTAATTCT-TCTATTTTATT-TTATTA
*
2865716 -TTTTATTTATTTC-T-TATTTTATTT
1 TTTTTATTTAATTCTTCTATTTTATTT
2865740 ATGTATCTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 11
0.68 0.14 0.17
Matches are distributed among these distances:
29 2 0.05
30 6 0.14
31 17 0.40
32 18 0.42
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (32 bp):
TTTTTATTTAATTCTTCTATTTTATTTTATTA
Found at i:2865861 original size:15 final size:14
Alignment explanation
Indices: 2865841--2865892 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2865831 ATATTTTTAG
2865841 TTTTTTATTTTATT
1 TTTTTTATTTTATT
* * *
2865855 CTTTTTTACTATATA
1 -TTTTTTATTTTATT
2865870 TTTTTTA-TTTATT
1 TTTTTTATTTTATT
2865883 TATTTTTATT
1 T-TTTTTATT
2865893 AAATACTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 5 0.17
14 13 0.43
15 12 0.40
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTATTTTATT
Found at i:2866254 original size:42 final size:42
Alignment explanation
Indices: 2866177--2866266 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 42
2866167 TTAATTTTCC
*
2866177 CCCTTTTGATCTATTTTTATTTTTACTTATTTTTTTCTTTTT
1 CCCTTTTGATCTATTTTTATTTTTACTTATTTTTTTATTTTT
2866219 CCCTTTTGAT-TGA-TTTTATTATTTA-TTATTTTTTTTATTTTT
1 CCCTTTTGATCT-ATTTTTATT-TTTACTTA-TTTTTTTATTTTT
*
2866261 TCCTTT
1 CCCTTT
2866267 GCCCTTTGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
41 11 0.26
42 32 0.74
ACGTcount: A:0.13, C:0.12, G:0.03, T:0.71
Consensus pattern (42 bp):
CCCTTTTGATCTATTTTTATTTTTACTTATTTTTTTATTTTT
Found at i:2866257 original size:50 final size:50
Alignment explanation
Indices: 2866188--2866299 Score: 131
Period size: 50 Copynumber: 2.2 Consensus size: 50
2866178 CCTTTTGATC
* *
2866188 TATTT-TTATTTTTACTTATTTTTTTCTTTTTCCCTTTTGATTGATTT-TAT
1 TATTTATTATTTTTACTTA-TTTTTTCCTTTGCCC-TTTGATTGATTTATAT
* *
2866238 TATTTATTATTTTT-TTTATTTTTTCCTTTGCCCTTTGATTTATTTAATAT
1 TATTTATTATTTTTACTTATTTTTTCCTTTGCCCTTTGATTGATTT-ATAT
*
2866288 TTTTTATTATTT
1 TATTTATTATTT
2866300 GTTATCTAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
48 11 0.20
49 13 0.24
50 22 0.41
51 8 0.15
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (50 bp):
TATTTATTATTTTTACTTATTTTTTCCTTTGCCCTTTGATTGATTTATAT
Found at i:2871291 original size:40 final size:40
Alignment explanation
Indices: 2871236--2871316 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2871226 AGTGCACCAG
2871236 AGATAATCCTCATAATCCCATCTTTTGCCCTCACTTCTAA
1 AGATAATCCTCATAATCCCATCTTTTGCCCTCACTTCTAA
*
2871276 AGATAATCCTCATAATCCCATCTTTTTCCCTCACTTCTAA
1 AGATAATCCTCATAATCCCATCTTTTGCCCTCACTTCTAA
2871316 A
1 A
2871317 CCTTTTGACT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.32, G:0.04, T:0.36
Consensus pattern (40 bp):
AGATAATCCTCATAATCCCATCTTTTGCCCTCACTTCTAA
Found at i:2877748 original size:25 final size:25
Alignment explanation
Indices: 2877718--2877768 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2877708 ACTTTCAGTT
2877718 AATTTCATTTGAGCATCACCAATTA
1 AATTTCATTTGAGCATCACCAATTA
2877743 AATTTCATTTGAGCATCACCAATTA
1 AATTTCATTTGAGCATCACCAATTA
2877768 A
1 A
2877769 TTAAACAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (25 bp):
AATTTCATTTGAGCATCACCAATTA
Found at i:2877822 original size:25 final size:25
Alignment explanation
Indices: 2877794--2877859 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
2877784 ATACAACAAA
2877794 AAAAATTTAAAAAACACTAAATAAT
1 AAAAATTTAAAAAACACTAAATAAT
* * * *
2877819 AAAAATATTCAAACA-ATTAAGTAAT
1 AAAAAT-TTAAAAAACACTAAATAAT
* *
2877844 AAAAAATTAACAAACA
1 AAAAATTTAAAAAACA
2877860 AAATAAATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
24 5 0.16
25 20 0.65
26 6 0.19
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.23
Consensus pattern (25 bp):
AAAAATTTAAAAAACACTAAATAAT
Found at i:2877857 original size:26 final size:26
Alignment explanation
Indices: 2877793--2877860 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
2877783 GATACAACAA
*
2877793 AAAAAATTTAAAAAAC-ACTAAATAAT
1 AAAAAA-TTAACAAACAACTAAATAAT
* *
2877819 AAAAATATT--CAAACAATTAAGTAAT
1 AAAAA-ATTAACAAACAACTAAATAAT
2877844 AAAAAATTAACAAACAA
1 AAAAAATTAACAAACAA
2877861 AATAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.20
25 13 0.37
26 14 0.40
27 1 0.03
ACGTcount: A:0.68, C:0.09, G:0.01, T:0.22
Consensus pattern (26 bp):
AAAAAATTAACAAACAACTAAATAAT
Found at i:2877879 original size:17 final size:16
Alignment explanation
Indices: 2877833--2877880 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
2877823 ATATTCAAAC
2877833 AATTAAGTAAT-AAAA
1 AATTAAGTAATAAAAA
** *
2877848 AATTAACAAACAAAATA
1 AATTAAGTAATAAAA-A
2877865 AATTAAGTAATAAAAA
1 AATTAAGTAATAAAAA
2877881 GTAAATAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
15 8 0.32
16 4 0.16
17 13 0.52
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (16 bp):
AATTAAGTAATAAAAA
Found at i:2878027 original size:12 final size:12
Alignment explanation
Indices: 2878009--2878068 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
2877999 ACTCCTCACT
2878009 CTCATCATCATC
1 CTCATCATCATC
*
2878021 TTCATCATCATC
1 CTCATCATCATC
* *
2878033 CTCATCCTCCTC
1 CTCATCATCATC
* * *
2878045 CTCCTCCTCCTC
1 CTCATCATCATC
2878057 CTCATCATCATC
1 CTCATCATCATC
2878069 AGGAGCATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (12 bp):
CTCATCATCATC
Found at i:2878039 original size:6 final size:6
Alignment explanation
Indices: 2878009--2878068 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
2877999 ACTCCTCACT
* * * * * *
2878009 CTCATC ATCATC TTCATC ATCATC CTCATC CTCCTC CTCCTC CTCCTC
1 CTCATC CTCATC CTCATC CTCATC CTCATC CTCATC CTCATC CTCATC
*
2878057 CTCATC ATCATC
1 CTCATC CTCATC
2878069 AGGAGCATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (6 bp):
CTCATC
Found at i:2888701 original size:19 final size:19
Alignment explanation
Indices: 2888677--2888717 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2888667 CAATCTTTTC
*
2888677 TAAAGAGGATTTGTGGATT
1 TAAAGAGGATTTGTGGAGT
* *
2888696 TAAAGATGATTTTTGGAGT
1 TAAAGAGGATTTGTGGAGT
2888715 TAA
1 TAA
2888718 TTAAAGAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (19 bp):
TAAAGAGGATTTGTGGAGT
Found at i:2890334 original size:64 final size:63
Alignment explanation
Indices: 2890266--2890443 Score: 191
Period size: 64 Copynumber: 2.8 Consensus size: 63
2890256 TGAAACACTT
* * * * *
2890266 AGTGCATCGGTGCACCAAGTGTGCATCGATGCGTAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAAGCC-A
* * *
2890330 AGTGCATCGGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTTGATGTTTTAATAAAAGCCA
1 AGTGCATCGGTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAAGCCA
* * *
2890394 AGTGCAT-GATGCATAGAGAGTGCATCGATGCATGGAATGCATTCGATGTT
1 AGTGCATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
2890444 CAATTTATTC
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 35 0.36
64 53 0.55
65 7 0.07
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (63 bp):
AGTGCATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAAGCCA
Found at i:2892928 original size:44 final size:43
Alignment explanation
Indices: 2892873--2893092 Score: 273
Period size: 44 Copynumber: 5.0 Consensus size: 43
2892863 TGTTACCGAA
* * *
2892873 ATAAGTGAAAATGTATAACGATGCATTATTGGCAGAAAGATGTC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAG-TGCC
* *
2892917 ATAAATGAAAATGCATAAC-AGTGCAATATTGGTAGAAATGTGCC
1 ATAAATGAAAATGCATAACGA-TGCATTATTGGCAGAAA-GTGCC
* *
2892961 ATAAATGAAAATACATAACGATGTATTATTGGCAGAAAGATGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAG-TGCC
* *
2893005 ATAAATGAAAATGCATAACGGT-CATTATTGGTAGAAATGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAA-GTGCC
* *
2893048 ATAAATGAAAATGCATAACGATGTATTATTGACAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAA-GTGCC
2893092 A
1 A
2893093 CTCATAAAAG
Statistics
Matches: 152, Mismatches: 18, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
43 40 0.26
44 110 0.72
45 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (43 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGTGCC
Found at i:2893071 original size:87 final size:88
Alignment explanation
Indices: 2892873--2893092 Score: 352
Period size: 87 Copynumber: 2.5 Consensus size: 88
2892863 TGTTACCGAA
* * * *
2892873 ATAAGTGAAAATGTATAACGATGCATTATTGGCAGAAAGATGTCATAAATGAAAATGCATAACAG
1 ATAAATGAAAATGCATAACGATGTATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACAG
2892938 TGCAATATTGGTAGAAATGTGCC
66 TGCAATATTGGTAGAAATGTGCC
* *
2892961 ATAAATGAAAATACATAACGATGTATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACGG
1 ATAAATGAAAATGCATAACGATGTATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACAG
*
2893026 T-CATTATTGGTAGAAATGTGCC
66 TGCAATATTGGTAGAAATGTGCC
* *
2893048 ATAAATGAAAATGCATAACGATGTATTATTGACAGAAAGGTGCCA
1 ATAAATGAAAATGCATAACGATGTATTATTGGCAGAAAGATGCCA
2893093 CTCATAAAAG
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
87 62 0.51
88 60 0.49
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (88 bp):
ATAAATGAAAATGCATAACGATGTATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACAG
TGCAATATTGGTAGAAATGTGCC
Found at i:2893996 original size:26 final size:30
Alignment explanation
Indices: 2893953--2894029 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
2893943 TGTTGCTTGA
*
2893953 CTCGACTCATTGCTCGTTAAAA-T-TT-TT-
1 CTCGACTC-GTGCTCGTTAAAAGTATTGTTG
2893980 CTCGACTCGTGCTCGTTAAAAGTACTTGTTG
1 CTCGACTCGTGCTCGTTAAAAGTA-TTGTTG
*
2894011 CTCGACTCGTGCTTGTTAA
1 CTCGACTCGTGCTCGTTAA
2894030 CTTTGTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 12 0.28
27 9 0.21
29 2 0.05
30 2 0.05
31 18 0.42
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (30 bp):
CTCGACTCGTGCTCGTTAAAAGTATTGTTG
Found at i:2895874 original size:23 final size:23
Alignment explanation
Indices: 2895844--2895949 Score: 137
Period size: 23 Copynumber: 4.7 Consensus size: 23
2895834 AGTCGAGGTT
*
2895844 CTATGTGGTTCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
*
2895867 CTATGTGGTCCTTCGGGATAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* * *
2895890 CTATGTGGTTCTTTGGGAAAAAC
1 CTATGTGGTCCTTCGGGACAAAC
2895913 CTATGTGGTCCTTCGGGACAAA-
1 CTATGTGGTCCTTCGGGACAAAC
2895935 -TATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
2895950 TGCAAATTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
20 1 0.01
21 13 0.18
23 60 0.81
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:2897040 original size:21 final size:20
Alignment explanation
Indices: 2896998--2897053 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
2896988 TATTTTTCTT
*
2896998 AGAATCGATCCCCTCTAAAA
1 AGAATCGATCCCTTCTAAAA
* *
2897018 AGGATCGATCCCTTTTAAAAA
1 AGAATCGATCCCTTCT-AAAA
2897039 AGAATCGATCCCTTC
1 AGAATCGATCCCTTC
2897054 ATTGTGTAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (20 bp):
AGAATCGATCCCTTCTAAAA
Found at i:2899676 original size:20 final size:20
Alignment explanation
Indices: 2899609--2899678 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
2899599 ATATCTAGAG
*
2899609 TTAATTAAATATATATTTTAA
1 TTAATTAAATATA-AATTTAA
* *
2899630 -TAATCCCAAATATTTAATTTCAA
1 TTAAT--TAAATA-TAAATTT-AA
2899653 TTAATTAAATATAAATTTAA
1 TTAATTAAATATAAATTTAA
2899673 TTAATT
1 TTAATT
2899679 TGAAATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 12 0.31
21 6 0.15
22 14 0.36
23 3 0.08
24 4 0.10
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTAAATATAAATTTAA
Found at i:2899686 original size:20 final size:21
Alignment explanation
Indices: 2899609--2899678 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
2899599 ATATCTAGAG
* *
2899609 TTAATTAAATATATATTTTAA
1 TTAATTAAATATAAATTTCAA
* *
2899630 -TAATCCCAAATATTTAATTTCAA
1 TTAAT--TAAATA-TAAATTTCAA
2899653 TTAATTAAATATAAATTT-AA
1 TTAATTAAATATAAATTTCAA
2899673 TTAATT
1 TTAATT
2899679 TGAAATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 12 0.31
21 6 0.15
22 10 0.26
23 7 0.18
24 4 0.10
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTAAATATAAATTTCAA
Found at i:2903792 original size:43 final size:42
Alignment explanation
Indices: 2903739--2903876 Score: 162
Period size: 43 Copynumber: 3.4 Consensus size: 42
2903729 TGATTTTTAA
2903739 TTGCAACCTAATTTATTGTATAGAAACCTAATTTCTTTTTAGG
1 TTGCAACCTAATTTATTGTATAGAAACCT-ATTTCTTTTTAGG
*** *
2903782 TTGCAACCTAATTTATCAAATAGAAA-C-A--T-GTTTTA-G
1 TTGCAACCTAATTTATTGTATAGAAACCTATTTCTTTTTAGG
*
2903818 TTGCAACCTAATTTATTGTATAGAAACCTGATTCCTTTTTAGG
1 TTGCAACCTAATTTATTGTATAGAAACCT-ATTTCTTTTTAGG
*
2903861 TTGCAACCTGATTTAT
1 TTGCAACCTAATTTAT
2903877 CAAATTGAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
36 24 0.31
37 6 0.08
38 1 0.01
39 1 0.01
40 1 0.01
42 6 0.08
43 39 0.50
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (42 bp):
TTGCAACCTAATTTATTGTATAGAAACCTATTTCTTTTTAGG
Found at i:2903823 original size:36 final size:37
Alignment explanation
Indices: 2903775--2903913 Score: 129
Period size: 36 Copynumber: 3.6 Consensus size: 37
2903765 CCTAATTTCT
2903775 TTTTAGGTTGCAACCTAATTTATCAAATAGAAACATG
1 TTTTAGGTTGCAACCTAATTTATCAAATAGAAACATG
*** *
2903812 TTTTA-GTTGCAACCTAATTTATTGTATAGAAACCTGATTCCT
1 TTTTAGGTTGCAACCTAATTTATCAAATAGAAA-C--A-T--G
* *
2903854 TTTTAGGTTGCAACCTGATTTATCAAATTGAAACATG
1 TTTTAGGTTGCAACCTAATTTATCAAATAGAAACATG
* *
2903891 TTTTTA-GTTGTAACCTAGTTTAT
1 -TTTTAGGTTGCAACCTAATTTAT
2903914 TGTATTGAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
36 24 0.30
37 20 0.25
38 5 0.06
39 2 0.02
40 2 0.02
42 6 0.07
43 22 0.27
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTTAGGTTGCAACCTAATTTATCAAATAGAAACATG
Found at i:2903921 original size:37 final size:37
Alignment explanation
Indices: 2903723--2903924 Score: 111
Period size: 43 Copynumber: 5.1 Consensus size: 37
2903713 AAGTCTCGTG
* * * *
2903723 GAAACCTGATTTTTAATTGCAACCTAATTTATTGTATA
1 GAAACATG-TTTTTAGTTGCAACCTAGTTTATTGTATT
* * *** *
2903761 GAAACCTAATTTCTTTTTAGGTTGCAACCTAATTTATCAAATA
1 GAAA-C--A--TGTTTTTA-GTTGCAACCTAGTTTATTGTATT
* *
2903804 GAAACATG-TTTTAGTTGCAACCTAATTTATTGTATA
1 GAAACATGTTTTTAGTTGCAACCTAGTTTATTGTATT
* ***
2903840 GAAACCTGATTCCTTTTTAGGTTGCAACCT-GATTTATCAAATT
1 GAAA-C--A-T-GTTTTTA-GTTGCAACCTAG-TTTATTGTATT
*
2903883 GAAACATGTTTTTAGTTGTAACCTAGTTTATTGTATT
1 GAAACATGTTTTTAGTTGCAACCTAGTTTATTGTATT
2903920 GAAAC
1 GAAAC
2903925 TTGATTCATT
Statistics
Matches: 128, Mismatches: 21, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
36 24 0.19
37 28 0.22
38 12 0.09
39 3 0.02
40 3 0.02
42 13 0.10
43 45 0.35
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (37 bp):
GAAACATGTTTTTAGTTGCAACCTAGTTTATTGTATT
Found at i:2903949 original size:79 final size:79
Alignment explanation
Indices: 2903723--2903949 Score: 314
Period size: 79 Copynumber: 2.8 Consensus size: 79
2903713 AAGTCTCGTG
* * *
2903723 GAAACCTGATTTTTAATTGCAACCTAATTTATTGTATAGAAACCTAATTTCTTTTTAGGTTGCAA
1 GAAACATG-TTTTTAGTTGCAACCTAATTTATTGTATAGAAACCTGA-TTCTTTTTAGGTTGCAA
*
2903788 CCTAATTTATCAAATA
64 CCTGATTTATCAAATA
2903804 GAAACATG-TTTTAGTTGCAACCTAATTTATTGTATAGAAACCTGATTCCTTTTTAGGTTGCAAC
1 GAAACATGTTTTTAGTTGCAACCTAATTTATTGTATAGAAACCTGATT-CTTTTTAGGTTGCAAC
*
2903868 CTGATTTATCAAATT
65 CTGATTTATCAAATA
* * * * *
2903883 GAAACATGTTTTTAGTTGTAACCTAGTTTATTGTATTGAAACTTGATTCATTTTTA-ATTGCAAC
1 GAAACATGTTTTTAGTTGCAACCTAATTTATTGTATAGAAACCTGATTC-TTTTTAGGTTGCAAC
2903947 CTG
65 CTG
2903950 GTTTTGCTTA
Statistics
Matches: 133, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
78 2 0.02
79 83 0.62
80 41 0.31
81 7 0.05
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (79 bp):
GAAACATGTTTTTAGTTGCAACCTAATTTATTGTATAGAAACCTGATTCTTTTTAGGTTGCAACC
TGATTTATCAAATA
Found at i:2911140 original size:43 final size:42
Alignment explanation
Indices: 2911074--2911297 Score: 207
Period size: 42 Copynumber: 5.5 Consensus size: 42
2911064 TAGAAACCTG
2911074 ATTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTC
1 ATTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTC
** ***
2911116 ATTTTTAGGTTGCAACCTGGTTTATCAAATAG-AA-AT-A--C
1 ATTTTTA-GTTGCAACCTAATTTATTGTATAGAAACATGATTC
* * *
2911154 GTTTTTAGTTGCAACCTAATTGATTGTATAGAAACTTGATTC
1 ATTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTC
* * * ***
2911196 CTTTATAGGTTGCAACCTGATTTATCAAATAG-AA-AT-A--C
1 ATTTTTA-GTTGCAACCTAATTTATTGTATAGAAACATGATTC
* *
2911234 GTTTTTAGTTGCAACCTAATTTATTGTATAGAAACCTGATTC
1 ATTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTC
*
2911276 CTTTTTAGTTGCAACCTAATTT
1 ATTTTTAGTTGCAACCTAATTT
2911298 TGCTTATAGA
Statistics
Matches: 141, Mismatches: 29, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
37 38 0.27
38 17 0.12
39 2 0.01
40 4 0.03
41 3 0.02
42 39 0.28
43 38 0.27
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (42 bp):
ATTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTC
Found at i:2911168 original size:37 final size:38
Alignment explanation
Indices: 2911117--2911257 Score: 142
Period size: 37 Copynumber: 3.6 Consensus size: 38
2911107 ACATGATTCA
*
2911117 TTTTTAGGTTGCAACCTGGTTTATCAAATAGAAATACG
1 TTTTTAGGTTGCAACCTGATTTATCAAATAGAAATACG
* * *** *
2911155 TTTTTA-GTTGCAACCTAATTGATTGTATAGAAACTTGATTCC
1 TTTTTAGGTTGCAACCTGATTTATCAAATAGAAA--T-A--CG
*
2911197 TTTATAGGTTGCAACCTGATTTATCAAATAGAAATACG
1 TTTTTAGGTTGCAACCTGATTTATCAAATAGAAATACG
*
2911235 TTTTTA-GTTGCAACCTAATTTAT
1 TTTTTAGGTTGCAACCTGATTTAT
2911258 TGTATAGAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 13
0.74 0.15 0.12
Matches are distributed among these distances:
37 37 0.46
38 12 0.15
39 1 0.01
40 2 0.02
41 1 0.01
42 6 0.07
43 22 0.27
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (38 bp):
TTTTTAGGTTGCAACCTGATTTATCAAATAGAAATACG
Found at i:2911208 original size:80 final size:80
Alignment explanation
Indices: 2911075--2911297 Score: 376
Period size: 80 Copynumber: 2.8 Consensus size: 80
2911065 AGAAACCTGA
* *
2911075 TTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTCATTTTTAGGTTGCAACCTGGTTTA
1 TTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTCCTTTTTAGGTTGCAACCTGATTTA
2911140 TCAAATAGAAATACG
66 TCAAATAGAAATACG
* * *
2911155 TTTTTAGTTGCAACCTAATTGATTGTATAGAAACTTGATTCCTTTATAGGTTGCAACCTGATTTA
1 TTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTCCTTTTTAGGTTGCAACCTGATTTA
2911220 TCAAATAGAAATACG
66 TCAAATAGAAATACG
* *
2911235 TTTTTAGTTGCAACCTAATTTATTGTATAGAAACCTGATTCCTTTTTA-GTTGCAACCTAATTT
1 TTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTCCTTTTTAGGTTGCAACCTGATTT
2911298 TGCTTATAGA
Statistics
Matches: 134, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 14 0.10
80 120 0.90
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (80 bp):
TTTTTAGTTGCAACCTAATTTATTGTATAGAAACATGATTCCTTTTTAGGTTGCAACCTGATTTA
TCAAATAGAAATACG
Found at i:2911637 original size:130 final size:130
Alignment explanation
Indices: 2911399--2911639 Score: 358
Period size: 130 Copynumber: 1.9 Consensus size: 130
2911389 TGCTGGGTTT
* * * *
2911399 TTTACACTTAAATCCTTAAATTTATAAAAGTTTCAATGTGGTCTCATATAATTTTCTTCTATTTG
1 TTTACACTTAAATCCTTAAATTTATAAAAGTGTCAATGTGGTCCCATAAAATTATCTTCTATTTG
**
2911464 TAGTTTGGTCCTTTGATTGTGAAATAATTATTGTTTAGTCCTTAATATTTGTTATTTTATAGTTA
66 TAGTTTGGTCCTTTGATTGTGAAATAATTATAATTTAGTCCTTAATATTTGTTATTTTATAGTTA
* * * *
2911529 TTTATACTTAGATCCTTAAATTTATAAAAGTGTCAATGTGGTCCCATAAAATTATCTTTTATTTT
1 TTTACACTTAAATCCTTAAATTTATAAAAGTGTCAATGTGGTCCCATAAAATTATCTTCTATTTG
* *
2911594 TAGTTTGGT-CTCTTGATTGTTAAGTAATTATAATTTAGTCCTTAAT
66 TAGTTTGGTCCT-TTGATTGTGAAATAATTATAATTTAGTCCTTAAT
2911640 GTTATAAAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
129 2 0.02
130 96 0.98
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (130 bp):
TTTACACTTAAATCCTTAAATTTATAAAAGTGTCAATGTGGTCCCATAAAATTATCTTCTATTTG
TAGTTTGGTCCTTTGATTGTGAAATAATTATAATTTAGTCCTTAATATTTGTTATTTTATAGTTA
Found at i:2913041 original size:20 final size:20
Alignment explanation
Indices: 2913016--2913065 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2913006 AATAAGTCAG
2913016 TAGTACCGATACCCAAAGGT
1 TAGTACCGATACCCAAAGGT
* * *
2913036 TAGTA-CGATACTCAGATGT
1 TAGTACCGATACCCAAAGGT
*
2913055 CAGTACCGATA
1 TAGTACCGATA
2913066 TTGAGGGGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
TAGTACCGATACCCAAAGGT
Found at i:2921012 original size:160 final size:158
Alignment explanation
Indices: 2920781--2921096 Score: 614
Period size: 160 Copynumber: 2.0 Consensus size: 158
2920771 ATGTCAAATC
2920781 AATATTGAGTCATTAATGCCATATCTTTCCCCCTCTCGTTTTGACGAATTCCCCGAAGAAACTAC
1 AATATTGAGTCATTAATGCCATATCTTTCCCCCTCTCGTTTTGACGAATTCCCCGAAGAAACTAC
2920846 CCATTAACTTTCCAGAAAAACCAACTTACATTCAATCTTCCTCATCGTGCACACCATCTTTTCTC
66 CCATTAACTTTCCAGAAAAACCAACTTACATTCAATCTTCCTCATCGTGCACACCATCTTTTCTC
2920911 CCTCAAAAATTTTTCCCATCAAAATTCA
131 CCTCAAAAATTTTTCCCATCAAAATTCA
2920939 AATATTGAGTCATTAATGCCATATCTTTTCCCCCTCTCGTTTTGACCGAATTCCCCGAAGAAACT
1 AATATTGAGTCATTAATGCCATATC-TTTCCCCCTCTCGTTTTGA-CGAATTCCCCGAAGAAACT
2921004 ACCCATTAACTTTCCAGAAAAACCAACTTACATTCAATCTTCCTCATCGTGCACACCATCTTTTC
64 ACCCATTAACTTTCCAGAAAAACCAACTTACATTCAATCTTCCTCATCGTGCACACCATCTTTTC
2921069 TCCCTCAAAAATTTTTCCCATCAAAATT
129 TCCCTCAAAAATTTTTCCCATCAAAATT
2921097 TCCCCCATTG
Statistics
Matches: 156, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
158 25 0.16
159 19 0.12
160 112 0.72
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (158 bp):
AATATTGAGTCATTAATGCCATATCTTTCCCCCTCTCGTTTTGACGAATTCCCCGAAGAAACTAC
CCATTAACTTTCCAGAAAAACCAACTTACATTCAATCTTCCTCATCGTGCACACCATCTTTTCTC
CCTCAAAAATTTTTCCCATCAAAATTCA
Found at i:2926178 original size:21 final size:18
Alignment explanation
Indices: 2926144--2926191 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
2926134 GGATGAACAC
2926144 TATCGATACCGATGTAATTGG
1 TATCGATACCGATG---TTGG
**
2926165 TATCGATATTGATGTTGG
1 TATCGATACCGATGTTGG
2926183 TATCGATAC
1 TATCGATAC
2926192 TACGAGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 12 0.50
21 12 0.50
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (18 bp):
TATCGATACCGATGTTGG
Found at i:2933962 original size:42 final size:43
Alignment explanation
Indices: 2933903--2933984 Score: 157
Period size: 42 Copynumber: 1.9 Consensus size: 43
2933893 AACTAAAGGT
2933903 GCAATCATGGTATTCATAATGTGTTT-TGAATCACCATTTCGA
1 GCAATCATGGTATTCATAATGTGTTTGTGAATCACCATTTCGA
2933945 GCAATCATGGTATTCATAATGTGTTTGTGAATCACCATTT
1 GCAATCATGGTATTCATAATGTGTTTGTGAATCACCATTT
2933985 TGATATACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
42 26 0.67
43 13 0.33
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (43 bp):
GCAATCATGGTATTCATAATGTGTTTGTGAATCACCATTTCGA
Found at i:2936958 original size:15 final size:15
Alignment explanation
Indices: 2936938--2936969 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2936928 TTGAAAAACA
2936938 TTTTCAACTCCTAAC
1 TTTTCAACTCCTAAC
2936953 TTTTCAACTCCTAAC
1 TTTTCAACTCCTAAC
2936968 TT
1 TT
2936970 GGATAGTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTTCAACTCCTAAC
Found at i:2939803 original size:25 final size:25
Alignment explanation
Indices: 2939775--2939843 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
2939765 CAAGAAAAGT
*
2939775 AATCAAAATATAATTTAAGACAATC
1 AATCAAAATATAATTTAAAACAATC
* *
2939800 AATC-ATATCATAATTTAAAATAATC
1 AATCAAAAT-ATAATTTAAAACAATC
* * *
2939825 AATTACAACATAATTTAAA
1 AATCAAAATATAATTTAAA
2939844 TTATTTATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
24 3 0.09
25 31 0.89
26 1 0.03
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (25 bp):
AATCAAAATATAATTTAAAACAATC
Found at i:2941040 original size:24 final size:24
Alignment explanation
Indices: 2941006--2941068 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
2940996 CAGTCGTAAC
*
2941006 TGCCGCATAGAATTTGCACCAAAG
1 TGCCACATAGAATTTGCACCAAAG
* * * *
2941030 TGCCACGTAGAATATGCATCGAAG
1 TGCCACATAGAATTTGCACCAAAG
2941054 TGCCACATAG-ATTTG
1 TGCCACATAGAATTTG
2941069 TCCCTAAGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
TGCCACATAGAATTTGCACCAAAG
Found at i:2941111 original size:24 final size:24
Alignment explanation
Indices: 2941056--2941128 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
2941046 CATCGAAGTG
* *
2941056 CCACATAG-ATTTGTCCCTAAGGA
1 CCACATAGAAGTTGTCCCGAAGGA
* * *
2941079 CCGCGTAGAAGTTGTCCCGAGGGA
1 CCACATAGAAGTTGTCCCGAAGGA
* *
2941103 CCACATAGAA-TTATCTCGAAGGA
1 CCACATAGAAGTTGTCCCGAAGGA
2941126 CCA
1 CCA
2941129 TGTAGAATTT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (24 bp):
CCACATAGAAGTTGTCCCGAAGGA
Found at i:2941338 original size:15 final size:16
Alignment explanation
Indices: 2941289--2941339 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
2941279 TACTCATAGT
2941289 TCATATTCACATAGAA
1 TCATATTCACATAGAA
*
2941305 T-ATCTTCACATAGAA
1 TCATATTCACATAGAA
*
2941320 -CATATTCATATA-AA
1 TCATATTCACATAGAA
2941334 TCATAT
1 TCATAT
2941340 ACTTTTAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.07
15 27 0.90
16 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (16 bp):
TCATATTCACATAGAA
Found at i:2941995 original size:27 final size:28
Alignment explanation
Indices: 2941934--2941999 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
2941924 CCCGAACCCG
*
2941934 ACCCGACCCGAATTTCACAATTAAAAAA
1 ACCCGACCCGAATATCACAATTAAAAAA
* *
2941962 ACCCGACCCGTATATCACACTT-AAAAA
1 ACCCGACCCGAATATCACAATTAAAAAA
2941989 ACCCGACCCGA
1 ACCCGACCCGA
2942000 CCCGAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.41, C:0.35, G:0.09, T:0.15
Consensus pattern (28 bp):
ACCCGACCCGAATATCACAATTAAAAAA
Found at i:2942296 original size:36 final size:37
Alignment explanation
Indices: 2942207--2942298 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
2942197 TTTTCACCCT
* *
2942207 AAACCCGAACTCGACCCGACCCGAATATCACACTTAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACAATTAAA
* * *
2942245 AAAACCGACCCGACCCGACCCGAATAT-ATGAATT-AG
1 AAACCCGACCCGACCCGACCCGAATATCA-CAATTAAA
2942281 AAACCCGACCCGACCCGA
1 AAACCCGACCCGACCCGA
2942299 AATAATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 19 0.40
37 22 0.47
38 6 0.13
ACGTcount: A:0.38, C:0.37, G:0.14, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACAATTAAA
Found at i:2947405 original size:23 final size:23
Alignment explanation
Indices: 2947379--2947476 Score: 81
Period size: 23 Copynumber: 4.2 Consensus size: 23
2947369 AAGTGCCACA
* *
2947379 TAGATTTGTCCCGAAGGACCGTG
1 TAGAATTGTCCCGAAGGACCGCG
* * *
2947402 TAGAATTCGTCCCGAATGA-TGACA
1 TAGAATT-GTCCCGAAGGACCG-CG
* *
2947426 TAGAATTATCCCGAAGGACCACG
1 TAGAATTGTCCCGAAGGACCGCG
* * *
2947449 TATAATTGTCTCGAAGGACCGTG
1 TAGAATTGTCCCGAAGGACCGCG
2947472 TAGAA
1 TAGAA
2947477 CCCTCGACTC
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
23 39 0.70
24 17 0.30
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCGCG
Found at i:2948947 original size:45 final size:45
Alignment explanation
Indices: 2948828--2949132 Score: 481
Period size: 45 Copynumber: 6.8 Consensus size: 45
2948818 ATATAAATCT
2948828 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAAT-CCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
2948873 ATTACCATTT-ATCCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
2948917 CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTACCAATAAA
1 CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
2948962 CTTACAATTTAATCCATAAGCTCATAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
2949007 CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTACTAATATA
1 CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTACCAATATA
**
2949052 CTTATAATTTAATCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
2949097 CTTGCCA-TTATTCCATAAGCTCATAAGCTTATTTTA
1 CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTA
2949133 ATGATTATCA
Statistics
Matches: 241, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
44 67 0.28
45 174 0.72
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (45 bp):
CTTACCATTTAATCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:2952245 original size:23 final size:23
Alignment explanation
Indices: 2952210--2952254 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2952200 TTTATATTAA
2952210 AAATTTAAAGGTGTAAAATTATT
1 AAATTTAAAGGTGTAAAATTATT
* * *
2952233 AAATTTTAGGGTGTGAAATTAT
1 AAATTTAAAGGTGTAAAATTAT
2952255 ATTATCGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (23 bp):
AAATTTAAAGGTGTAAAATTATT
Found at i:2954899 original size:2 final size:2
Alignment explanation
Indices: 2954892--2954941 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2954882 TTTTCTCTTC
2954892 AT AT AT AT AT AT AT AT 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 AT AT AT
2954934 AT AT AT AT
1 AT AT AT AT
2954942 TTACCTTCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2958476 original size:23 final size:22
Alignment explanation
Indices: 2958440--2958490 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
2958430 AGATAATTTA
*
2958440 AAATAACATTATTTCAAATAAAT
1 AAATAACATGATTTCAAA-AAAT
* **
2958463 AAATAATATGATTTTGAAAAAT
1 AAATAACATGATTTCAAAAAAT
2958485 AAATAA
1 AAATAA
2958491 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATAACATGATTTCAAAAAAT
Found at i:2958501 original size:19 final size:22
Alignment explanation
Indices: 2958459--2958501 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2958449 TATTTCAAAT
2958459 AAATAAATAATATGATTTTGAA
1 AAATAAATAATATGATTTTGAA
2958481 AAATAAATAA-AT-ATTTT-AA
1 AAATAAATAATATGATTTTGAA
2958500 AA
1 AA
2958502 TATTTACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 2 0.10
22 10 0.48
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
AAATAAATAATATGATTTTGAA
Found at i:2959680 original size:2 final size:2
Alignment explanation
Indices: 2959632--2959666 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2959622 TTATTGATTT
2959632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2959667 CAAATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2960456 original size:28 final size:28
Alignment explanation
Indices: 2960415--2960468 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
2960405 TATCCCCTCA
*
2960415 TTTTATGATCAATTATACTTTACCTTAT
1 TTTTATGATCAATTATAATTTACCTTAT
* *
2960443 TTTTATGATTAATTATAATTTGCCTT
1 TTTTATGATCAATTATAATTTACCTT
2960469 TTAAATTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (28 bp):
TTTTATGATCAATTATAATTTACCTTAT
Found at i:2962542 original size:42 final size:43
Alignment explanation
Indices: 2962481--2962640 Score: 220
Period size: 42 Copynumber: 3.8 Consensus size: 43
2962471 AAATAGGTCA
*
2962481 AGATCTATCGCGGCGTTTTTGGA-ACAAACGCCGCAAAATGTC
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATGTC
* * *
2962523 AGATCTATAGCGGCATTTTTGGATACAAACGTCGCAAAAAG-C
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATGTC
*
2962565 TAGATCTATAGCGGCGTTTTAGGA-ACAAACGCCGCAAAATGTC
1 -AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATGTC
* *
2962608 ATATCTATAGCGGCGTTTTT-TATACAAACGCCG
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCCG
2962641 TGAATTAAAA
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 65 0.63
43 37 0.36
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATGTC
Found at i:2962627 original size:85 final size:84
Alignment explanation
Indices: 2962481--2962637 Score: 260
Period size: 85 Copynumber: 1.9 Consensus size: 84
2962471 AAATAGGTCA
* *
2962481 AGATCTATCGCGGCGTTTTTGGAACAAACGCCGCAAAATGTCAGATCTATAGCGGCATTTTTGGA
1 AGATCTATAGCGGCGTTTTAGGAACAAACGCCGCAAAATGTCAGATCTATAGCGGCATTTTT-GA
2962546 TACAAACGTCGCAAAAAGCT
65 TACAAACGTCGCAAAAAGCT
* * *
2962566 AGATCTATAGCGGCGTTTTAGGAACAAACGCCGCAAAATGTCATATCTATAGCGGCGTTTTTTAT
1 AGATCTATAGCGGCGTTTTAGGAACAAACGCCGCAAAATGTCAGATCTATAGCGGCATTTTTGAT
2962631 ACAAACG
66 ACAAACG
2962638 CCGTGAATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 9 0.13
85 58 0.87
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (84 bp):
AGATCTATAGCGGCGTTTTAGGAACAAACGCCGCAAAATGTCAGATCTATAGCGGCATTTTTGAT
ACAAACGTCGCAAAAAGCT
Found at i:2962760 original size:21 final size:21
Alignment explanation
Indices: 2962724--2962799 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
2962714 ATTATTCAAT
* * **
2962724 AAACTTGACATCCATAACATC
1 AAACTTGAAATTCATAACAAA
*
2962745 AAACTTGAAATTCATATCAAAA
1 AAACTTGAAATTCATAAC-AAA
*
2962767 AAACTTGAAATTCATAACAAG
1 AAACTTGAAATTCATAACAAA
2962788 AAACTTGAAATT
1 AAACTTGAAATT
2962800 TATATTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 29 0.62
22 18 0.38
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (21 bp):
AAACTTGAAATTCATAACAAA
Found at i:2964470 original size:16 final size:15
Alignment explanation
Indices: 2964427--2964462 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
2964417 GACTGAAGAG
*
2964427 AACCAACTATAGAAA
1 AACCAACTACAGAAA
2964442 AACCAACTACAGAAA
1 AACCAACTACAGAAA
2964457 AACCAA
1 AACCAA
2964463 TAGACAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.25, G:0.06, T:0.08
Consensus pattern (15 bp):
AACCAACTACAGAAA
Found at i:2977283 original size:14 final size:14
Alignment explanation
Indices: 2977253--2977293 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2977243 TTCACTCATC
*
2977253 GAGTCAACTCGGTCT
1 GAGTCAAC-CCGTCT
2977268 GAGTCAACCCGTCT
1 GAGTCAACCCGTCT
2977282 GAGTCAACCCGT
1 GAGTCAACCCGT
2977294 TGACTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (14 bp):
GAGTCAACCCGTCT
Found at i:2983250 original size:19 final size:19
Alignment explanation
Indices: 2983226--2983263 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2983216 GGGTATGATG
2983226 GGTATTTTGAGTGCAAAAT
1 GGTATTTTGAGTGCAAAAT
2983245 GGTATTTTGAGTGCAAAAT
1 GGTATTTTGAGTGCAAAAT
2983264 CCCAAGAATA
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:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (19 bp):
GGTATTTTGAGTGCAAAAT
Found at i:2984618 original size:20 final size:18
Alignment explanation
Indices: 2984595--2984636 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 18
2984585 TTTTTTCTTA
2984595 TTTATTTTTATATAGTTTAC
1 TTTATTTTTATAT--TTTAC
2984615 TTTA--TTTATATTTTAC
1 TTTATTTTTATATTTTAC
2984631 TTTATT
1 TTTATT
2984637 CTTTTTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
16 9 0.45
18 7 0.35
20 4 0.20
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTATTTTTATATTTTAC
Found at i:2984629 original size:16 final size:16
Alignment explanation
Indices: 2984605--2984636 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2984595 TTTATTTTTA
2984605 TATAGTTTACTTTATT
1 TATAGTTTACTTTATT
*
2984621 TATATTTTACTTTATT
1 TATAGTTTACTTTATT
2984637 CTTTTTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (16 bp):
TATAGTTTACTTTATT
Found at i:2990292 original size:18 final size:18
Alignment explanation
Indices: 2990271--2990312 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
2990261 TTATTTTTTC
2990271 TTTTATCTTTA-TCTTTAT
1 TTTTATCTTTATTC-TTAT
2990289 TTTTATCTTTATTCTTAT
1 TTTTATCTTTATTCTTAT
2990307 TTTTAT
1 TTTTAT
2990313 TATTCGTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATCTTTATTCTTAT
Found at i:2990301 original size:12 final size:12
Alignment explanation
Indices: 2990260--2990313 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
2990250 AAATAACAAA
2990260 TTTATTTTT-TC
1 TTTATTTTTATC
*
2990271 TTTTATCTTTATC
1 -TTTATTTTTATC
2990284 TTTATTTTTATC
1 TTTATTTTTATC
* *
2990296 TTTATTCTTATT
1 TTTATTTTTATC
2990308 TTTATT
1 TTTATT
2990314 ATTCGTGGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
12 35 0.95
13 2 0.05
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTTATC
Found at i:2994946 original size:30 final size:32
Alignment explanation
Indices: 2994873--2994959 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
2994863 TCTCGAAAAT
* *
2994873 AGTCATTGACCATTGACCGTTGATCGTTGGCC
1 AGTCATTGACCATTGACAGTTGATCGTTGACC
2994905 AGTCATTGACCATTGACAGTTGATCG-T-ACC
1 AGTCATTGACCATTGACAGTTGATCGTTGACC
* * *
2994935 ATTCGTTGACCATTGACTGTTGATC
1 AGTCATTGACCATTGACAGTTGATC
2994960 ATCGTTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 24 0.48
31 1 0.02
32 25 0.50
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (32 bp):
AGTCATTGACCATTGACAGTTGATCGTTGACC
Found at i:2998160 original size:20 final size:20
Alignment explanation
Indices: 2998135--2998173 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2998125 TTAAAGAACA
*
2998135 AGTATCGATACTAACCCTAT
1 AGTATCAATACTAACCCTAT
*
2998155 AGTATCAATACTCACCCTA
1 AGTATCAATACTAACCCTA
2998174 CATGATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (20 bp):
AGTATCAATACTAACCCTAT
Found at i:3003063 original size:29 final size:29
Alignment explanation
Indices: 3003029--3003087 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3003019 CCTAAATTAA
* *
3003029 TTTGATGTAATTGCTTACATTAATTTAGT
1 TTTGATGTAATTGCTTAAATCAATTTAGT
*
3003058 TTTGATGTCATTGCTTAAATCAATTTAGT
1 TTTGATGTAATTGCTTAAATCAATTTAGT
3003087 T
1 T
3003088 AGGTGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTAATTGCTTAAATCAATTTAGT
Found at i:3007596 original size:3 final size:3
Alignment explanation
Indices: 3007588--3007642 Score: 83
Period size: 3 Copynumber: 17.7 Consensus size: 3
3007578 CCAGAGACCG
*
3007588 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
3007634 TTTA TTA TT
1 -TTA TTA TT
3007643 TATATTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3007662 original size:7 final size:7
Alignment explanation
Indices: 3007588--3007661 Score: 81
Period size: 6 Copynumber: 11.3 Consensus size: 7
3007578 CCAGAGACCG
3007588 TTATTA-
1 TTATTAT
3007594 TTATTA-
1 TTATTAT
3007600 TTATTA-
1 TTATTAT
3007606 TTATTA-
1 TTATTAT
3007612 TTATTAT
1 TTATTAT
3007619 CATTATTAT
1 --TTATTAT
3007628 TTATTAT
1 TTATTAT
3007635 TTATTAT
1 TTATTAT
3007642 TTA-TAT
1 TTATTAT
3007648 TTATT-T
1 TTATTAT
3007654 TT-TTAT
1 TTATTAT
3007660 TT
1 TT
3007662 TATTTCTGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.03
6 36 0.57
7 18 0.29
9 7 0.11
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTAT
Found at i:3010961 original size:13 final size:13
Alignment explanation
Indices: 3010943--3010969 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3010933 ATGTGTGACA
3010943 TGATTTGTATGAG
1 TGATTTGTATGAG
3010956 TGATTTGTATGAG
1 TGATTTGTATGAG
3010969 T
1 T
3010970 ATATGCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (13 bp):
TGATTTGTATGAG
Found at i:3011577 original size:31 final size:31
Alignment explanation
Indices: 3011542--3011609 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
3011532 GTCGAGGGTT
*
3011542 TACCTGTGTTCTATA-AAACATATGGACAATA
1 TACCTATGTTCTA-AGAAACATATGGACAATA
* *
3011573 TACCTATGTTCTAAGGAACATATGGACAATT
1 TACCTATGTTCTAAGAAACATATGGACAATA
3011604 TACCTA
1 TACCTA
3011610 GATTCTTCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAAGAAACATATGGACAATA
Found at i:3014795 original size:13 final size:13
Alignment explanation
Indices: 3014777--3014814 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3014767 AAATAACATC
3014777 TTTTGCATTTGCA
1 TTTTGCATTTGCA
*
3014790 TTTTGCATATGCA
1 TTTTGCATTTGCA
3014803 TTTT-CATTTGCA
1 TTTTGCATTTGCA
3014815 ATGTGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTTGCATTTGCA
Found at i:3015613 original size:18 final size:18
Alignment explanation
Indices: 3015582--3015627 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3015572 CTAATGAGAT
3015582 ATTTAAAT-AATAAAAATG
1 ATTTAAATAAAT-AAAATG
*
3015600 A-TTAAATAAATAAAGTG
1 ATTTAAATAAATAAAATG
3015617 ATTTAAATAAA
1 ATTTAAATAAA
3015628 AATAAGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
ATTTAAATAAATAAAATG
Found at i:3016246 original size:24 final size:24
Alignment explanation
Indices: 3016214--3016259 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3016204 ATTTTTGAAA
3016214 AAAAAAACTTGAAAAATAAAAATT
1 AAAAAAACTTGAAAAATAAAAATT
* *
3016238 AAAAGAACTTGAAAAGTAAAAA
1 AAAAAAACTTGAAAAATAAAAA
3016260 GAGAAAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (24 bp):
AAAAAAACTTGAAAAATAAAAATT
Found at i:3017324 original size:22 final size:24
Alignment explanation
Indices: 3017299--3017351 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
3017289 TTTTCATGTC
3017299 TTTTTTCAACATTT-TTTCTT-CT
1 TTTTTTCAACATTTGTTTCTTCCT
* * *
3017321 TTTTTTGAACTTTTGTTTTTTCCT
1 TTTTTTCAACATTTGTTTCTTCCT
3017345 TTTTTTC
1 TTTTTTC
3017352 GATGGAGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 12 0.48
23 5 0.20
24 8 0.32
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTTTCAACATTTGTTTCTTCCT
Found at i:3021114 original size:17 final size:17
Alignment explanation
Indices: 3021090--3021138 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 17
3021080 ATAATGAGAT
3021090 ATTTAAATAATAAAAGTG
1 ATTTAAATAA-AAAAGTG
3021108 A-TTAAATAAATAAAGTG
1 ATTTAAATAAA-AAAGTG
3021125 ATTTAAATAAAAAA
1 ATTTAAATAAAAAA
3021139 AAAGAATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.03
17 18 0.62
18 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (17 bp):
ATTTAAATAAAAAAGTG
Found at i:3021121 original size:18 final size:19
Alignment explanation
Indices: 3021090--3021139 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
3021080 ATAATGAGAT
3021090 ATTTAAAT-AATAAAAGTG
1 ATTTAAATAAATAAAAGTG
3021108 A-TTAAATAAAT-AAAGTG
1 ATTTAAATAAATAAAAGTG
3021125 ATTTAAATAAA-AAAA
1 ATTTAAATAAATAAAA
3021140 AAGAATAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (19 bp):
ATTTAAATAAATAAAAGTG
Found at i:3026250 original size:15 final size:16
Alignment explanation
Indices: 3026230--3026261 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3026220 TGAATTTGCG
3026230 TCATTTCAT-CATACA
1 TCATTTCATACATACA
3026245 TCATTTCATACATACA
1 TCATTTCATACATACA
3026261 T
1 T
3026262 ATATAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.41
Consensus pattern (16 bp):
TCATTTCATACATACA
Found at i:3026643 original size:42 final size:42
Alignment explanation
Indices: 3026546--3026644 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
3026536 TATTTAATAG
* * *
3026546 GTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAA
1 GTCATTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGCATAA
* * * *
3026588 ATCATTCGAGTCATCTGTAAGTCTTTTGAGCAAGATG-ATAA
1 GTCATTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGCATAA
3026629 GTCATTCGGGGTCATC
1 GTCATTC-GGGTCATC
3026645 CATAAGACCT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 9 0.19
42 38 0.81
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (42 bp):
GTCATTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGCATAA
Found at i:3027272 original size:134 final size:135
Alignment explanation
Indices: 3026981--3027320 Score: 477
Period size: 134 Copynumber: 2.5 Consensus size: 135
3026971 CAAATCGAAT
** * *
3026981 TTGATTCAATCTTATCTGATGAACAGTGGAATGAATCAACGTTTCCATATATGATTTTCCCTGAA
1 TTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCATATCTGATTTTCCCTGAA
* * *
3027046 GAAGCAGTGTAACAGATCCATATTTTTTCCAGATTTGATATTTCCTGAGGAATAGTGGAACAAGT
66 GAAGCAGAGTAACAGAGCCATATTTTTTCCAGATTTGATATTTCCTGAGGAACAGTGGAACAAGT
3027111 CTGCC
131 CTGCC
* * * *
3027116 TCGATTCAATCTTCCCTAAAGAACAGTAGAATGAATCAACGTTTTCATATCTGATTTTCCCTGAA
1 TTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCATATCTGATTTTCCCTGAA
* * * *
3027181 GAAGCAGCAG-AACA-AGCCCTCTTTTTTCCAGATTTGATCTTTCTTGAGGAACAGTGGAACAAG
66 GAAGCAG-AGTAACAGAGCCATATTTTTTCCAGATTTGATATTTCCTGAGGAACAGTGGAACAAG
* *
3027244 TTTTCC
130 TCTGCC
* *
3027250 TTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTACCCTGAA
1 TTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCATATCTGATTTTCCCTGAA
*
3027315 AAAGCA
66 GAAGCA
3027321 ATGGAGCAGA
Statistics
Matches: 180, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
134 111 0.62
135 68 0.38
136 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (135 bp):
TTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCATATCTGATTTTCCCTGAA
GAAGCAGAGTAACAGAGCCATATTTTTTCCAGATTTGATATTTCCTGAGGAACAGTGGAACAAGT
CTGCC
Found at i:3030262 original size:31 final size:32
Alignment explanation
Indices: 3030219--3030285 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
3030209 CAATTATATC
*
3030219 TTTT-TAATGGCTAAGA-TATAACCACTCTAGT
1 TTTTCTAATGGCTAA-ACTAGAACCACTCTAGT
*
3030250 TTTTCTAA-GGCTAAACTAGAACCACTCTTGT
1 TTTTCTAATGGCTAAACTAGAACCACTCTAGT
3030281 TTTTC
1 TTTTC
3030286 GAGGTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 1 0.03
31 28 0.88
32 3 0.09
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (32 bp):
TTTTCTAATGGCTAAACTAGAACCACTCTAGT
Found at i:3036866 original size:31 final size:31
Alignment explanation
Indices: 3036803--3036864 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
3036793 ATTCAGATTC
*
3036803 TAACACAATCAATAAAGTCTTTTACAAATTT
1 TAACACAATCAATAAAGTCTTGTACAAATTT
* * *
3036834 TAACACACT-AATAAATTCTTGTACAAGTTT
1 TAACACAATCAATAAAGTCTTGTACAAATTT
3036864 T
1 T
3036865 TATCTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (31 bp):
TAACACAATCAATAAAGTCTTGTACAAATTT
Found at i:3041300 original size:35 final size:34
Alignment explanation
Indices: 3041215--3041301 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
3041205 AAAATAATTT
*
3041215 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
3041249 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
3041287 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
3041302 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:3043597 original size:17 final size:18
Alignment explanation
Indices: 3043577--3043615 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3043567 ATTATATAAG
3043577 TAAAATA-TTAAATAAAT
1 TAAAATATTTAAATAAAT
3043594 TAAAATATTTAAATAAAT
1 TAAAATATTTAAATAAAT
3043612 TAAA
1 TAAA
3043616 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATATTTAAATAAAT
Found at i:3050595 original size:33 final size:33
Alignment explanation
Indices: 3050528--3050595 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
3050518 TCAACTCCTG
* * *
3050528 ACTTAAACCCTAAGTTATAAACTCCTAACTTAA
1 ACTTAAACCCTAAATCATAAACTCCTAACCTAA
3050561 ACTTAAACCCTAAATCATAAA-TCCTAACCCTAA
1 ACTTAAACCCTAAATCATAAACTCCTAA-CCTAA
3050594 AC
1 AC
3050596 CCTACCTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.26
Consensus pattern (33 bp):
ACTTAAACCCTAAATCATAAACTCCTAACCTAA
Found at i:3052377 original size:16 final size:16
Alignment explanation
Indices: 3052356--3052389 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3052346 TTGGTCGAAT
3052356 TCGTTGCTCCTTAAGC
1 TCGTTGCTCCTTAAGC
**
3052372 TCGTTGCTTGTTAAGC
1 TCGTTGCTCCTTAAGC
3052388 TC
1 TC
3052390 ACCAAAATTT
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:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (16 bp):
TCGTTGCTCCTTAAGC
Found at i:3061813 original size:43 final size:43
Alignment explanation
Indices: 3061759--3062001 Score: 258
Period size: 42 Copynumber: 5.7 Consensus size: 43
3061749 TTTTGGCCAT
* * *
3061759 AAACGCCGCTAATTCTTTTATCTTTAGTGGCATTTTTTCCCAC
1 AAACGCCGCTAATTCTATTGTCTTTAGTGGCATTTTTTACCAC
** * *
3061802 AAACGTTGCTAATTCTCTTGTCTTTAGTGGCA-TTTTTACCAT
1 AAACGCCGCTAATTCTATTGTCTTTAGTGGCATTTTTTACCAC
* * *
3061844 AAACGCCGCTAATGCTATTGTTTTTAGTGGC-TTTTTTCCCAC
1 AAACGCCGCTAATTCTATTGTCTTTAGTGGCATTTTTTACCAC
* * *
3061886 AAACACCGCTAATTCTCTTGTCTTTAGTGGC-GTTTTTACCAC
1 AAACGCCGCTAATTCTATTGTCTTTAGTGGCATTTTTTACCAC
*** * ** * *
3061928 AAAAATCGCTTATGATATTGTTTTTAGTGGCATTTTTTGCCAC
1 AAACGCCGCTAATTCTATTGTCTTTAGTGGCATTTTTTACCAC
* *
3061971 AAACGCCGCTAATGCTATTGTTTTTAGTGGC
1 AAACGCCGCTAATTCTATTGTCTTTAGTGGC
3062002 GTTTGTAATA
Statistics
Matches: 165, Mismatches: 33, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
42 102 0.62
43 63 0.38
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (43 bp):
AAACGCCGCTAATTCTATTGTCTTTAGTGGCATTTTTTACCAC
Found at i:3061908 original size:84 final size:85
Alignment explanation
Indices: 3061755--3062001 Score: 325
Period size: 84 Copynumber: 2.9 Consensus size: 85
3061745 GTGTTTTTGG
* * * * **
3061755 CCATAAACGCCGCTAATTCTTTTATCTTTAGTGGCATTTTTTCCCACAAACGTTGCTAATTCTCT
1 CCATAAACGCCGCTAATGCTATTGTTTTTAGTGGCATTTTTTCCCACAAACGCCGCTAATTCTCT
3061820 TGTCTTTAGTGGCATTTTTA
66 TGTCTTTAGTGGCATTTTTA
*
3061840 CCATAAACGCCGCTAATGCTATTGTTTTTAGTGGC-TTTTTTCCCACAAACACCGCTAATTCTCT
1 CCATAAACGCCGCTAATGCTATTGTTTTTAGTGGCATTTTTTCCCACAAACGCCGCTAATTCTCT
*
3061904 TGTCTTTAGTGGCGTTTTTA
66 TGTCTTTAGTGGCATTTTTA
* *** * * * * *
3061924 CCACAAAAATCGCTTATGATATTGTTTTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGCTAT
1 CCATAAACGCCGCTAATGCTATTGTTTTTAGTGGCATTTTTTCCCACAAACGCCGCTAATTCTCT
*
3061989 TGTTTTTAGTGGC
66 TGTCTTTAGTGGC
3062002 GTTTGTAATA
Statistics
Matches: 142, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
84 74 0.52
85 68 0.48
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (85 bp):
CCATAAACGCCGCTAATGCTATTGTTTTTAGTGGCATTTTTTCCCACAAACGCCGCTAATTCTCT
TGTCTTTAGTGGCATTTTTA
Found at i:3062504 original size:28 final size:28
Alignment explanation
Indices: 3062459--3062514 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3062449 TTGTCATCCG
*
3062459 AGGCTGAATATTGGTGCAACCCTACATA
1 AGGCTGAATATTGATGCAACCCTACATA
* *
3062487 AGGCTGAGTGTTGATGCAACCCTACATA
1 AGGCTGAATATTGATGCAACCCTACATA
3062515 CAAAGTTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (28 bp):
AGGCTGAATATTGATGCAACCCTACATA
Found at i:3064777 original size:81 final size:83
Alignment explanation
Indices: 3064600--3064798 Score: 224
Period size: 81 Copynumber: 2.4 Consensus size: 83
3064590 TATTTTAATC
* * ** *
3064600 ATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTACTTTATTGTGAAATTTGTTGAAAAAATG
1 ATTGTGGCGTTTGTATAAAAACACCGCTAAAGTACTACTCTATTACGAAATTTGTTGAAAAAATA
* * *
3064665 CAATTATAGATGAATCCT
66 CAACTATAGATAAACCCT
* * * * **
3064683 ATTATGGCATTTGTATAAAAGCACCGCTAAAGTATTA-TACTATTACGGTA-TTGTTG-AAAAAT
1 ATTGTGGCGTTTGTATAAAAACACCGCTAAAGTACTACT-CTATTACGAAATTTGTTGAAAAAAT
*
3064745 ACCACTATAGATAAACCCT
65 ACAACTATAGATAAACCCT
*
3064764 ATTGTGGCGTTTGTATAAAAACGCCGCTAAAGTAC
1 ATTGTGGCGTTTGTATAAAAACACCGCTAAAGTAC
3064799 CACTATGTAG
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
81 50 0.53
82 7 0.07
83 38 0.40
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (83 bp):
ATTGTGGCGTTTGTATAAAAACACCGCTAAAGTACTACTCTATTACGAAATTTGTTGAAAAAATA
CAACTATAGATAAACCCT
Found at i:3064862 original size:40 final size:41
Alignment explanation
Indices: 3064765--3064894 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 41
3064755 ATAAACCCTA
* * *
3064765 TTGTGGCGTTTGTATAAAAACGCCGCTAAAGTACCACT-ATG
1 TTGTGGCATTTATAAAAAAACGCCGCTAAAGTACCACTCA-G
* * * * *
3064806 TAGCGGCGTTTGT-AAAAAATGCCGCTAAAGTACCACTCAG
1 TTGTGGCATTTATAAAAAAACGCCGCTAAAGTACCACTCAG
* * *
3064846 TTGTGGTATTTATAAAAAAAACGTCGCTAAAGTACCACTCTG
1 TTGTGGCATTTAT-AAAAAAACGCCGCTAAAGTACCACTCAG
3064888 TTGTGGC
1 TTGTGGC
3064895 GTTTTTTTGA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
40 31 0.42
41 12 0.16
42 30 0.41
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
TTGTGGCATTTATAAAAAAACGCCGCTAAAGTACCACTCAG
Found at i:3064908 original size:42 final size:42
Alignment explanation
Indices: 3064765--3064900 Score: 143
Period size: 42 Copynumber: 3.3 Consensus size: 42
3064755 ATAAACCCTA
* *
3064765 TTGTGGCGTTTGTAT-AAAAACGCCGCTAAAGTACCACTATG
1 TTGTGGCGTTTTTATAAAAAACGCCGCTAAAGTACCACTCTG
* * * * *
3064806 TAGCGGCG--TTTGTAAAAAATGCCGCTAAAGTACCACTCAG
1 TTGTGGCGTTTTTATAAAAAACGCCGCTAAAGTACCACTCTG
** * * *
3064846 TTGTGGTATTTATAAAAAAAACGTCGCTAAAGTACCACTCTG
1 TTGTGGCGTTTTTATAAAAAACGCCGCTAAAGTACCACTCTG
3064888 TTGTGGCGTTTTT
1 TTGTGGCGTTTTT
3064901 TTGAAAAATG
Statistics
Matches: 72, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
39 3 0.04
40 27 0.38
41 6 0.08
42 36 0.50
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (42 bp):
TTGTGGCGTTTTTATAAAAAACGCCGCTAAAGTACCACTCTG
Found at i:3071390 original size:22 final size:22
Alignment explanation
Indices: 3071364--3071409 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3071354 GATAAACACC
3071364 ATCAACATTAACATAAAAATAT
1 ATCAACATTAACATAAAAATAT
3071386 ATCAACATTAACATAAAAATAT
1 ATCAACATTAACATAAAAATAT
3071408 AT
1 AT
3071410 ATAATAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (22 bp):
ATCAACATTAACATAAAAATAT
Found at i:3072703 original size:17 final size:16
Alignment explanation
Indices: 3072662--3072703 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
3072652 AAATACATTT
3072662 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
3072678 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
3072695 TAAAA-AATT
1 TAAAATAATT
3072704 GATCTGCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:3074718 original size:2 final size:2
Alignment explanation
Indices: 3074711--3074772 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3074701 CTGTCTACAG
3074711 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3074753 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3074773 GTAGATGTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3077188 original size:15 final size:16
Alignment explanation
Indices: 3077158--3077190 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3077148 ATATAAAATT
3077158 TAAAACTAATATTTTA
1 TAAAACTAATATTTTA
*
3077174 TAAAATTAA-ATTTTA
1 TAAAACTAATATTTTA
3077189 TA
1 TA
3077191 TTTGGAATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAACTAATATTTTA
Found at i:3077875 original size:17 final size:17
Alignment explanation
Indices: 3077855--3077919 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
3077845 TAAATATTTT
3077855 TTTTAAATAAATTTCTC
1 TTTTAAATAAATTTCTC
* * *
3077872 TTTTACATAAGAAATATTTTT
1 TTTT--A-AATAAAT-TTCTC
3077893 TTTTAAATAAATTTCTC
1 TTTTAAATAAATTTCTC
*
3077910 TTTTACATAA
1 TTTTAAATAA
3077920 GATATCATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 16 0.43
18 6 0.16
19 2 0.05
20 6 0.16
21 7 0.19
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTTAAATAAATTTCTC
Found at i:3077901 original size:38 final size:37
Alignment explanation
Indices: 3077846--3077921 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 37
3077836 ATTCCCTTTT
3077846 AAATATTTTTTTTAAATAAATTTCTCTTTTACATAAG
1 AAATATTTTTTTTAAATAAATTTCTCTTTTACATAAG
3077883 AAATATTTTTTTTTAAATAAATTTCTCTTTTACATAAG
1 AAATA-TTTTTTTTAAATAAATTTCTCTTTTACATAAG
3077921 A
1 A
3077922 TATCATTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 5 0.13
38 33 0.87
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (37 bp):
AAATATTTTTTTTAAATAAATTTCTCTTTTACATAAG
Found at i:3077913 original size:21 final size:21
Alignment explanation
Indices: 3077851--3077913 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
3077841 CTTTTAAATA
3077851 TTTTTTTTAAATAAATTTCTC
1 TTTTTTTTAAATAAATTTCTC
*** * *
3077872 TTTTACAT-AAGAAA--TAT-
1 TTTTTTTTAAATAAATTTCTC
3077889 TTTTTTTTAAATAAATTTCTC
1 TTTTTTTTAAATAAATTTCTC
3077910 TTTT
1 TTTT
3077914 ACATAAGATA
Statistics
Matches: 28, Mismatches: 10, Indels: 8
0.61 0.22 0.17
Matches are distributed among these distances:
17 5 0.18
18 7 0.25
20 7 0.25
21 9 0.32
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTTTTTAAATAAATTTCTC
Found at i:3079147 original size:3 final size:3
Alignment explanation
Indices: 3079139--3079206 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
3079129 GAATTGAAAC
3079139 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
3079187 AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AG
3079207 TCAAACGTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:3082563 original size:20 final size:21
Alignment explanation
Indices: 3082527--3082565 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3082517 TTTAGTTCGA
3082527 TTAATGTATACTAATTTTAAT
1 TTAATGTATACTAATTTTAAT
3082548 TTAAT-TATA-TATATTTTA
1 TTAATGTATACTA-ATTTTA
3082566 TGAACAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 10 0.59
21 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
TTAATGTATACTAATTTTAAT
Found at i:3083019 original size:16 final size:16
Alignment explanation
Indices: 3082998--3083037 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
3082988 TTAATTTAAT
3082998 TTATAAAGCTTTAAAA
1 TTATAAAGCTTTAAAA
3083014 TTATAAAGCTTTAAAA
1 TTATAAAGCTTTAAAA
3083030 TTATAAAG
1 TTATAAAG
3083038 TATTCAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (16 bp):
TTATAAAGCTTTAAAA
Found at i:3084114 original size:22 final size:22
Alignment explanation
Indices: 3084067--3084114 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3084057 TGGTAAATTC
** *
3084067 AAAAAATTAAAAGGTCAGTTTG
1 AAAAAATTAAAAGACCAATTTG
*
3084089 -AAAAATTAAATGACCAATTTG
1 AAAAAATTAAAAGACCAATTTG
3084110 AAAAA
1 AAAAA
3084115 TCAATGAGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (22 bp):
AAAAAATTAAAAGACCAATTTG
Found at i:3085042 original size:38 final size:38
Alignment explanation
Indices: 3084983--3085065 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
3084973 GCTTATCAAA
*
3084983 ATATCCAAAATCCATAAATATTAAGCAAATAATCCAAC
1 ATATCCAAAATACATAAATATTAAGCAAATAATCCAAC
*
3085021 ATATCCAAAATAC-TAGCATATTAAGCAAATAATCCAAC
1 ATATCCAAAATACATA-AATATTAAGCAAATAATCCAAC
3085059 ATATCCA
1 ATATCCA
3085066 TATATGATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 2 0.05
38 40 0.95
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.24
Consensus pattern (38 bp):
ATATCCAAAATACATAAATATTAAGCAAATAATCCAAC
Found at i:3086402 original size:29 final size:28
Alignment explanation
Indices: 3086357--3086411 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
3086347 TTCGAATAAA
3086357 TTCAACTAGATGAAAAAACCTAAAAACG
1 TTCAACTAGATGAAAAAACCTAAAAACG
* *
3086385 TTCAATCTAGATGCAAAAATCTAAAAA
1 TTCAA-CTAGATGAAAAAACCTAAAAA
3086412 GAAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (28 bp):
TTCAACTAGATGAAAAAACCTAAAAACG
Found at i:3086738 original size:3 final size:3
Alignment explanation
Indices: 3086730--3086789 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
3086720 ATTGATTTAT
* * *
3086730 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3086778 TTA TTA TTA TTA
1 TTA TTA TTA TTA
3086790 AATATATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3086797 original size:12 final size:11
Alignment explanation
Indices: 3086735--3086801 Score: 61
Period size: 12 Copynumber: 6.2 Consensus size: 11
3086725 TTTATTTATT
*
3086735 ATTATTATTATT
1 ATTATTATTA-A
3086747 ATTATTATTATA
1 ATTATTATTA-A
3086759 ATTATTA-TAA
1 ATTATTATTAA
*
3086769 A-TATTATTATT
1 ATTATTATTA-A
3086780 ATTATTATTAA
1 ATTATTATTAA
3086791 A-TA-TATTAA
1 ATTATTATTAA
3086800 AT
1 AT
3086802 ATATATATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
9 12 0.25
10 6 0.12
11 4 0.08
12 26 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTATTATTAA
Found at i:3089414 original size:9 final size:9
Alignment explanation
Indices: 3089400--3089424 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3089390 TTACATGTAA
3089400 ATTTAAATT
1 ATTTAAATT
3089409 ATTTAAATT
1 ATTTAAATT
3089418 ATTTAAA
1 ATTTAAA
3089425 AGCATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTAAATT
Found at i:3099549 original size:9 final size:9
Alignment explanation
Indices: 3099535--3099569 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
3099525 TATTATGCTT
3099535 GAAAAAAAA
1 GAAAAAAAA
3099544 GAAAAAAAAAA
1 G--AAAAAAAA
3099555 GAAAAAAAA
1 GAAAAAAAA
3099564 GAAAAA
1 GAAAAA
3099570 GGAGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.62
11 9 0.38
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:3099552 original size:11 final size:11
Alignment explanation
Indices: 3099536--3099563 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3099526 ATTATGCTTG
3099536 AAAAAAAAGAA
1 AAAAAAAAGAA
3099547 AAAAAAAAGAA
1 AAAAAAAAGAA
3099558 AAAAAA
1 AAAAAA
3099564 GAAAAAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:3103452 original size:17 final size:16
Alignment explanation
Indices: 3103430--3103463 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3103420 TAAAAACAGT
3103430 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3103447 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3103463 A
1 A
3103464 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3105586 original size:15 final size:15
Alignment explanation
Indices: 3105566--3105596 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3105556 AGGGTTCTTT
3105566 CATAACATTATTTAA
1 CATAACATTATTTAA
3105581 CATAACATTATTTAA
1 CATAACATTATTTAA
3105596 C
1 C
3105597 CATATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (15 bp):
CATAACATTATTTAA
Found at i:3106442 original size:31 final size:31
Alignment explanation
Indices: 3106407--3106477 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
3106397 AAGCACACAC
*
3106407 GTTAAGTAATTACTTAGTGAGTTATAATATT
1 GTTAAGTAATTACTTAGTGAGTCATAATATT
3106438 GTTAAGTAATTACTTAGTGAGTCATAATATT
1 GTTAAGTAATTACTTAGTGAGTCATAATATT
*
3106469 GTAAAGTAA
1 GTTAAGTAA
3106478 CCTTTATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (31 bp):
GTTAAGTAATTACTTAGTGAGTCATAATATT
Found at i:3106735 original size:45 final size:45
Alignment explanation
Indices: 3106684--3106937 Score: 330
Period size: 45 Copynumber: 5.6 Consensus size: 45
3106674 ATTTTATGTT
* * * *
3106684 GATAATGCACCCATATGCATT-TCAACTATGGCACCCTTTCATACC
1 GATAATGCACCCATATGCATTAT-AATTTTGGCATCCTTTCATGCC
* *
3106729 TATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCC
1 GATAATGCACCCATATGCATTATAATTTTGGCATCCTTTCATGCC
* * *
3106774 GATAATGCACCTATATGCATTATTATTTTGGCATCCTTTCATGCT
1 GATAATGCACCCATATGCATTATAATTTTGGCATCCTTTCATGCC
* * **
3106819 GATAATGCACCCATATGTATTATTAGCTTGGCATCCTTTCATGCC
1 GATAATGCACCCATATGCATTATAATTTTGGCATCCTTTCATGCC
* * *
3106864 GATAATACACCCATATGCAATATTATTTTGGCATCCTTTCATGCC
1 GATAATGCACCCATATGCATTATAATTTTGGCATCCTTTCATGCC
* *
3106909 GATAATGCATCCATATGCATTATCATTTT
1 GATAATGCACCCATATGCATTATAATTTT
3106938 TTTTCATTCA
Statistics
Matches: 185, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 184 0.99
46 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (45 bp):
GATAATGCACCCATATGCATTATAATTTTGGCATCCTTTCATGCC
Found at i:3106857 original size:135 final size:135
Alignment explanation
Indices: 3106683--3106937 Score: 397
Period size: 135 Copynumber: 1.9 Consensus size: 135
3106673 AATTTTATGT
* *
3106683 TGATAATGCACCCATATGCATTTCAACTATGGCACCCTTTCATACCTATAATGCACCCATATGCA
1 TGATAATGCACCCATATGCATTTCAACTATGGCACCCTTTCATACCGATAATACACCCATATGCA
* *
3106748 TTATTATTTTGGCATCCTTTCATGCCGATAATGCA-CCTATATGCATTATTATTTTGGCATCCTT
66 ATATTATTTTGGCATCCTTTCATGCCGATAATGCATCC-ATATGCATTATCATTTTGGCATCCTT
3106812 TCATGC
130 TCATGC
* * * * *
3106818 TGATAATGCACCCATATGTATTATTAGCT-TGGCATCCTTTCATGCCGATAATACACCCATATGC
1 TGATAATGCACCCATATGCATT-TCAACTATGGCACCCTTTCATACCGATAATACACCCATATGC
3106882 AATATTATTTTGGCATCCTTTCATGCCGATAATGCATCCATATGCATTATCATTTT
65 AATATTATTTTGGCATCCTTTCATGCCGATAATGCATCCATATGCATTATCATTTT
3106938 TTTTCATTCA
Statistics
Matches: 109, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
135 103 0.94
136 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (135 bp):
TGATAATGCACCCATATGCATTTCAACTATGGCACCCTTTCATACCGATAATACACCCATATGCA
ATATTATTTTGGCATCCTTTCATGCCGATAATGCATCCATATGCATTATCATTTTGGCATCCTTT
CATGC
Found at i:3110627 original size:34 final size:33
Alignment explanation
Indices: 3110588--3110658 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
3110578 TTTTGTAAAG
* *
3110588 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCATG-AAAAACTA
* *
3110622 GGGAAAGGTTCTAGTTTATCCCATGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCATGAAAAACTA
3110655 GGGA
1 GGGA
3110659 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCATGAAAAACTA
Found at i:3113324 original size:21 final size:19
Alignment explanation
Indices: 3113282--3113342 Score: 88
Period size: 21 Copynumber: 3.1 Consensus size: 19
3113272 TATATTTTCC
3113282 AACAATTGATATC-TTTTT
1 AACAATTGATATCTTTTTT
3113300 AACAATTGATATCCTTTTGTT
1 AACAATTGATAT-CTTTT-TT
3113321 AACAATTGATATCTTTTATT
1 AACAATTGATATCTTTT-TT
3113341 AA
1 AA
3113343 ATATTTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 12 0.31
19 1 0.03
20 12 0.31
21 14 0.36
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (19 bp):
AACAATTGATATCTTTTTT
Found at i:3114039 original size:34 final size:33
Alignment explanation
Indices: 3114000--3114070 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
3113990 TTTTGTAAAG
* * *
3114000 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCATG-AAAAACTA
* *
3114034 GGGAAAGGTTATAGTTTATCCCATGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCATGAAAAACTA
3114067 GGGA
1 GGGA
3114071 GTTGTAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTATAGCTTAGCCCATGAAAAACTA
Found at i:3114753 original size:120 final size:120
Alignment explanation
Indices: 3114540--3114777 Score: 440
Period size: 120 Copynumber: 2.0 Consensus size: 120
3114530 CGAAGTGTTG
* * *
3114540 ATAATTGAAAATAAATATTTATGGAATCGAATAAGCATTTTTTAGAAGTTTGAAATGTGGATGGA
1 ATAATGGAAAATAAATATTTATAGAATCGAATAAGCATTTTTCAGAAGTTTGAAATGTGGATGGA
3114605 AAACATGATTTAGTTTTATATCGATTTAAGTATCGATTTTATTTCTATCAAACCT
66 AAACATGATTTAGTTTTATATCGATTTAAGTATCGATTTTATTTCTATCAAACCT
3114660 ATAATGGAAAATAAATATTTATAGAATCGAATAAGCATTTTTCAGAAGTTTGAAATGTGGATGGA
1 ATAATGGAAAATAAATATTTATAGAATCGAATAAGCATTTTTCAGAAGTTTGAAATGTGGATGGA
*
3114725 AAATATGATTTAGTTTTATATCGATTTAAGTATCGATTTTATTTCTATCAAAC
66 AAACATGATTTAGTTTTATATCGATTTAAGTATCGATTTTATTTCTATCAAAC
3114778 TTTATATTTA
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 114 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.39
Consensus pattern (120 bp):
ATAATGGAAAATAAATATTTATAGAATCGAATAAGCATTTTTCAGAAGTTTGAAATGTGGATGGA
AAACATGATTTAGTTTTATATCGATTTAAGTATCGATTTTATTTCTATCAAACCT
Found at i:3122193 original size:2 final size:2
Alignment explanation
Indices: 3122186--3122230 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3122176 TCAATCTACA
3122186 AT AT AT AT AT AT AT AT 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 AT AT AT
3122228 AT A
1 AT A
3122231 ATTTACGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3122379 original size:13 final size:13
Alignment explanation
Indices: 3122358--3122422 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
3122348 AATGACGCTC
* *
3122358 AATGCGCGTTATA
1 AATGTGCGTCATA
3122371 AATGTGCGTCATA
1 AATGTGCGTCATA
*
3122384 AATGTGAGTCATA
1 AATGTGCGTCATA
* *
3122397 AATGCGTGTCATA
1 AATGTGCGTCATA
*
3122410 AATGCGCGTCATA
1 AATGTGCGTCATA
3122423 GATTTATGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:3122387 original size:26 final size:26
Alignment explanation
Indices: 3122358--3122422 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
3122348 AATGACGCTC
* *
3122358 AATGCGCGTTATAAATGTGCGTCATA
1 AATGCGCGTCATAAATGCGCGTCATA
* * *
3122384 AATGTGAGTCATAAATGCGTGTCATA
1 AATGCGCGTCATAAATGCGCGTCATA
3122410 AATGCGCGTCATA
1 AATGCGCGTCATA
3122423 GATTTATGAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (26 bp):
AATGCGCGTCATAAATGCGCGTCATA
Found at i:3127342 original size:16 final size:17
Alignment explanation
Indices: 3127323--3127355 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3127313 TATGATGATA
3127323 GATTTTAA-ATGTTTAT
1 GATTTTAAGATGTTTAT
3127339 GATTTTAAGATGTTTAT
1 GATTTTAAGATGTTTAT
3127356 AAATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (17 bp):
GATTTTAAGATGTTTAT
Done.