Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 42
Found at i:3604 original size:21 final size:21
Alignment explanation
Indices: 3580--3631 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
3570 GGAGTGGTCA
*
3580 TTCGGTACATCTATGTGGTTC
1 TTCGGGACATCTATGTGGTTC
3601 TTCGGGACATCTATGTGGTTC
1 TTCGGGACATCTATGTGGTTC
*
3622 TTCAGGACAT
1 TTCGGGACAT
3632 TTCTACGCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
TTCGGGACATCTATGTGGTTC
Found at i:5094 original size:27 final size:27
Alignment explanation
Indices: 5041--5096 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
5031 TAAGATTGTG
* * **
5041 AAGTGCTTCATCATTGTGGCATTGCTT
1 AAGTACTTCATCATTCTGGCACCGCTT
*
5068 AAGTACTTCATCATTCTGTCACCGCTT
1 AAGTACTTCATCATTCTGGCACCGCTT
5095 AA
1 AA
5097 TCTTTTTCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (27 bp):
AAGTACTTCATCATTCTGGCACCGCTT
Found at i:11907 original size:22 final size:22
Alignment explanation
Indices: 11879--11921 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11869 GGCTTCAAGC
*
11879 TTGTTTTGTATTTGGGCCCTAG
1 TTGTTTTGAATTTGGGCCCTAG
11901 TTGTTTTGAATTTGGGCCCTA
1 TTGTTTTGAATTTGGGCCCTA
11922 TTTTGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (22 bp):
TTGTTTTGAATTTGGGCCCTAG
Found at i:11967 original size:3 final size:3
Alignment explanation
Indices: 11961--11986 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11951 ATTTATTATT
11961 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
11987 TAAATGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12219 original size:14 final size:15
Alignment explanation
Indices: 12200--12229 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12190 ACTTATTTTG
12200 ACAAAAAGA-ATATT
1 ACAAAAAGATATATT
12214 ACAAAAAGATATATT
1 ACAAAAAGATATATT
12229 A
1 A
12230 TTGCTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (15 bp):
ACAAAAAGATATATT
Found at i:12914 original size:12 final size:12
Alignment explanation
Indices: 12899--12971 Score: 78
Period size: 12 Copynumber: 5.8 Consensus size: 12
12889 ATAATTATAA
12899 TTTTATTTTTAT
1 TTTTATTTTTAT
12911 TTTTATTTTTAT
1 TTTTATTTTTAT
*
12923 TTTTATTTATTTT
1 TTTTATTT-TTAT
12936 TATTTATTTATT-T
1 T-TTTATTT-TTAT
12949 TTTTATTTATTTAT
1 TTTTA-TT-TTTAT
12963 TTTT-TTTTT
1 TTTTATTTTT
12972 GTTTAAACTG
Statistics
Matches: 55, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
11 3 0.05
12 26 0.47
13 10 0.18
14 16 0.29
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:12933 original size:4 final size:4
Alignment explanation
Indices: 12924--12964 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
12914 TATTTTTATT
*
12924 TTTA TTTA -TT- TTTA TTTA TTTA TTTT TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
12965 TTTTTTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 4 0.12
4 29 0.88
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTA
Found at i:12933 original size:16 final size:16
Alignment explanation
Indices: 12899--12976 Score: 92
Period size: 16 Copynumber: 4.9 Consensus size: 16
12889 ATAATTATAA
12899 TTTTATTTTTATTTTTAT
1 TTTTATTTTTA--TTTAT
12917 TTTTATTTTTATTTAT
1 TTTTATTTTTATTTAT
12933 TTTTA--TTTATTTAT
1 TTTTATTTTTATTTAT
12947 TTTT-TTATTTATTTAT
1 TTTTATT-TTTATTTAT
*
12963 TTTT-TTTTTGTTTA
1 TTTTATTTTTATTTA
12977 AACTGATAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
14 13 0.23
15 7 0.12
16 25 0.45
18 11 0.20
ACGTcount: A:0.17, C:0.00, G:0.01, T:0.82
Consensus pattern (16 bp):
TTTTATTTTTATTTAT
Found at i:13400 original size:13 final size:13
Alignment explanation
Indices: 13382--13446 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
13372 CAGATGAATC
13382 AAAAATTTAAATA
1 AAAAATTTAAATA
**
13395 AAAAATAAAAATA
1 AAAAATTTAAATA
* *
13408 AATAA-TTAATCTTA
1 AAAAATTTAA--ATA
*
13422 TAAAATTTAAATA
1 AAAAATTTAAATA
*
13435 TAAAATTTAAAT
1 AAAAATTTAAAT
13447 TTTATGTGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
12 2 0.05
13 29 0.73
14 5 0.12
15 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAATTTAAATA
Found at i:21819 original size:16 final size:16
Alignment explanation
Indices: 21800--21831 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21790 ACTTTTGAGT
21800 AATATTTAAAAGTATA
1 AATATTTAAAAGTATA
*
21816 AATATTTGAAAGTATA
1 AATATTTAAAAGTATA
21832 CTAACATTTT
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:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
AATATTTAAAAGTATA
Found at i:23181 original size:177 final size:177
Alignment explanation
Indices: 22943--23276 Score: 403
Period size: 178 Copynumber: 1.9 Consensus size: 177
22933 AATTTGTCAC
* * *
22943 AAACGTGAATATCATTATTTTTGTGACAATGTTTTTTGTAATAATTAGTAAAACTTATAGTTACA
1 AAACGTGAATATCACTATTTTTGTGACAA-GTTTTTTGTAACAATAAGTAAAACTTATAGTTAC-
*
23008 AAATT-TGTCACTATATGAATTT-TTTGGCGTA-AAACAATATT-GAGGA-AATC-TTTGTGACA
64 AAATTATGTCACTACAT-AATTTCTTT-GCGTACAAA-AA-ATTGGA-GATAATCATTTGTGACA
*
23067 ATATATTTTGTCACTATAATTAAAACATATAACGACAAACATTATTTTTACTAA
124 ATACATTTTGTCACTATAATTAAAACATATAACGACAAACATTATTTTTACTAA
* * * * *
23121 AAACTTGAATCTCACTATTTGTTGTGACAA-TTTTTTGTAACAATAATTATAGCTTATAGTTACA
1 AAACGTGAATATCACTATTT-TTGTGACAAGTTTTTTGTAACAATAAGTAAAACTTATAGTTACA
* ** *
23185 AATTATGTCACTACATTATTTCGTTTTTGTACAAAAAATTGGAGATAATCATTTGTGACTATACA
65 AATTATGTCACTACATAATTTC-TTTGCGTACAAAAAATTGGAGATAATCATTTGTGACAATACA
*
23250 TTTTGTCACTATAATTAAAATATATAA
129 TTTTGTCACTATAATTAAAACATATAA
23277 TTACAAAAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
176 14 0.11
177 49 0.37
178 61 0.46
179 9 0.07
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (177 bp):
AAACGTGAATATCACTATTTTTGTGACAAGTTTTTTGTAACAATAAGTAAAACTTATAGTTACAA
ATTATGTCACTACATAATTTCTTTGCGTACAAAAAATTGGAGATAATCATTTGTGACAATACATT
TTGTCACTATAATTAAAACATATAACGACAAACATTATTTTTACTAA
Found at i:26198 original size:19 final size:20
Alignment explanation
Indices: 26174--26216 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
26164 AGCATTTATC
*
26174 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
26193 TTCATTAAAAATCATGTTTT
1 TTCATTAAAAATCATGTATT
26213 TTCA
1 TTCA
26217 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:26608 original size:35 final size:35
Alignment explanation
Indices: 26560--26635 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
26550 TACTTTCTAT
* *
26560 ACCATCTTTCATCTCCATATCACGCCTATATCATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
* *
26595 ACCATCTTCCATCTGCATTTCACGCCTATATAATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
26630 ACCATC
1 ACCATC
26636 CCATTATCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.26, C:0.37, G:0.04, T:0.33
Consensus pattern (35 bp):
ACCATCTTCCATCTCCATATCACGCCTATATAATC
Found at i:26846 original size:15 final size:15
Alignment explanation
Indices: 26826--26866 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
26816 CTAATTTCAT
26826 ATTTCCATTTCAATC
1 ATTTCCATTTCAATC
26841 ATTTCCATTTCAATC
1 ATTTCCATTTCAATC
26856 ATTTCCATTTC
1 ATTTCCATTTC
26867 TATTTCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTCCATTTCAATC
Found at i:33969 original size:105 final size:105
Alignment explanation
Indices: 33779--33989 Score: 253
Period size: 105 Copynumber: 2.0 Consensus size: 105
33769 CTTCTAATTT
** * * *
33779 TTCTAGTGAGACGGGTCAGGCTATTGTGAATGCAAGTGTTACTCCTCTGGGAGTAACAGTTCAGT
1 TTCTAGTGAGACGAATCAGGCTATTGTGAATGCAAGTGTTACTCCTCTAGAAGTAACAGTTCAGA
* * *
33844 AAGAGGTAGCTGATGTAACCTCAGATAGTACAGCTGAGGA
66 AAAAGGTAGCTGATGCAACCTCAGATAGTACAACTGAGGA
* * * * * *
33884 TTCTGGTGAGACGAATCAGGCTACTT-TGGATGTAGGTGTTACTCCTCTAGAAGTAGCAGTTTAG
1 TTCTAGTGAGACGAATCAGGCTA-TTGTGAATGCAAGTGTTACTCCTCTAGAAGTAACAGTTCAG
* * *
33948 AAAAAGGTAGTTGGTGCAACCTCAGATAGTAGAACTGAGGA
65 AAAAAGGTAGCTGATGCAACCTCAGATAGTACAACTGAGGA
33989 T
1 T
33990 AATGTGTTGG
Statistics
Matches: 88, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
105 86 0.98
106 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (105 bp):
TTCTAGTGAGACGAATCAGGCTATTGTGAATGCAAGTGTTACTCCTCTAGAAGTAACAGTTCAGA
AAAAGGTAGCTGATGCAACCTCAGATAGTACAACTGAGGA
Found at i:40666 original size:24 final size:24
Alignment explanation
Indices: 40639--40688 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
40629 GTTCACATGA
40639 TTGTTTTATCTGATGTGCAATGTG
1 TTGTTTTATCTGATGTGCAATGTG
*
40663 TTGTTTTATCTGATTTGCAATGTG
1 TTGTTTTATCTGATGTGCAATGTG
40687 TT
1 TT
40689 TATATGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.22, T:0.54
Consensus pattern (24 bp):
TTGTTTTATCTGATGTGCAATGTG
Found at i:45671 original size:21 final size:21
Alignment explanation
Indices: 45647--45698 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
45637 GGAGTGGTCA
*
45647 TTCGGTACATCTATGTGGTTC
1 TTCGGGACATCTATGTGGTTC
45668 TTCGGGACATCTATGTGGTTC
1 TTCGGGACATCTATGTGGTTC
*
45689 TTCAGGACAT
1 TTCGGGACAT
45699 TTCTACGCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
TTCGGGACATCTATGTGGTTC
Found at i:46640 original size:38 final size:38
Alignment explanation
Indices: 46598--46681 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
46588 TTCAAAACAC
*
46598 CCCAACATGATACATGCTAATATGAGCCTTCAAAATGT
1 CCCAACATGATACATGCTAATATGAACCTTCAAAATGT
* ** ** * *
46636 CCCAACGTTCTTTATGCTGATGTGAACCTTCAAAATGT
1 CCCAACATGATACATGCTAATATGAACCTTCAAAATGT
46674 CCCAACAT
1 CCCAACAT
46682 TCCAAGTTGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (38 bp):
CCCAACATGATACATGCTAATATGAACCTTCAAAATGT
Found at i:47177 original size:27 final size:27
Alignment explanation
Indices: 47124--47179 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
47114 TAAGATTGTG
* * **
47124 AAGTGCTTCATCATTGTGGCATTGCTT
1 AAGTACTTCATCATTCTGGCACCGCTT
*
47151 AAGTACTTCATCATTCTGTCACCGCTT
1 AAGTACTTCATCATTCTGGCACCGCTT
47178 AA
1 AA
47180 TCTTTTTCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (27 bp):
AAGTACTTCATCATTCTGGCACCGCTT
Found at i:54058 original size:3 final size:3
Alignment explanation
Indices: 54052--54089 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
54042 TATTATTTAT
54052 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54090 TAAATGCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:54321 original size:14 final size:15
Alignment explanation
Indices: 54302--54331 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54292 ACTTATTTTG
54302 ACAAAAAGA-ATATT
1 ACAAAAAGATATATT
54316 ACAAAAAGATATATT
1 ACAAAAAGATATATT
54331 A
1 A
54332 TTGCTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (15 bp):
ACAAAAAGATATATT
Found at i:54994 original size:11 final size:11
Alignment explanation
Indices: 54980--55042 Score: 67
Period size: 11 Copynumber: 5.5 Consensus size: 11
54970 TATAATTATA
54980 ATTTTATTTTT
1 ATTTTATTTTT
54991 ATTTTATTTTT
1 ATTTTATTTTT
55002 -TTTTATTTTTT
1 ATTTTA-TTTTT
55013 ATTTTTATTATTT
1 A-TTTTATT-TTT
55026 ATTTATTATTTTT
1 A-TT-TTATTTTT
55039 -TTTT
1 ATTTT
55043 TGTTTAAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.15
11 18 0.38
12 2 0.04
13 15 0.32
14 5 0.11
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:55010 original size:7 final size:7
Alignment explanation
Indices: 54981--55043 Score: 69
Period size: 7 Copynumber: 9.3 Consensus size: 7
54971 ATAATTATAA
54981 TTTTA-T
1 TTTTATT
54987 TTTTATT
1 TTTTATT
*
54994 TTATTTTT
1 TT-TTATT
55002 TTTTATT
1 TTTTATT
55009 TTTTA-T
1 TTTTATT
55015 TTTTATT
1 TTTTATT
*
55022 ATTTATT
1 TTTTATT
*
55029 TATTATT
1 TTTTATT
55036 TTTT-TT
1 TTTTATT
55042 TT
1 TT
55044 GTTTAAACTG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 15 0.31
7 27 0.56
8 6 0.12
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:55031 original size:34 final size:35
Alignment explanation
Indices: 54981--55048 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
54971 ATAATTATAA
54981 TTTTATTTTTATTTTATT-TTTTTTTATTT-TTTAT
1 TTTTATTTTTATTTTATTATTTTTTT-TTTGTTTAT
55015 TTTTATTATTTA-TTTATTATTTTTTTTTTGTTTA
1 TTTTATT-TTTATTTTATTATTTTTTTTTTGTTTA
55049 AACTGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 16 0.52
35 15 0.48
ACGTcount: A:0.16, C:0.00, G:0.01, T:0.82
Consensus pattern (35 bp):
TTTTATTTTTATTTTATTATTTTTTTTTTGTTTAT
Found at i:55290 original size:20 final size:20
Alignment explanation
Indices: 55239--55292 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
55229 TTCGATCCCT
* *
55239 TATATTTATAATATTTTTCAA
1 TATATTTTTAAT-TTTTTAAA
*
55260 TATGA-TCTTAATTTTTTAAA
1 TAT-ATTTTTAATTTTTTAAA
55280 TATATTTTTAATT
1 TATATTTTTAATT
55293 GAATACTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 8 0.30
22 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (20 bp):
TATATTTTTAATTTTTTAAA
Found at i:55468 original size:13 final size:13
Alignment explanation
Indices: 55450--55514 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
55440 CAGATGAATC
55450 AAAAATTTAAATA
1 AAAAATTTAAATA
**
55463 AAAAATAAAAATA
1 AAAAATTTAAATA
* *
55476 AATAA-TTAATCTTA
1 AAAAATTTAA--ATA
*
55490 TAAAATTTAAATA
1 AAAAATTTAAATA
*
55503 TAAAATTTAAAT
1 AAAAATTTAAAT
55515 TTTATGTGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
12 2 0.05
13 29 0.73
14 5 0.12
15 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAATTTAAATA
Found at i:63837 original size:16 final size:16
Alignment explanation
Indices: 63818--63849 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
63808 ACTTTTGAGT
63818 AATATTTAAAAGTATA
1 AATATTTAAAAGTATA
*
63834 AATATTTGAAAGTATA
1 AATATTTAAAAGTATA
63850 CTAACATTTT
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:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
AATATTTAAAAGTATA
Found at i:65194 original size:180 final size:180
Alignment explanation
Indices: 64953--65289 Score: 409
Period size: 181 Copynumber: 1.9 Consensus size: 180
64943 AATTTGTCAC
* * *
64953 AAACGTGAATATCATTATTTTTGTGACAATGTTTTTTGTAATAATTAGTAAAACTTATAGTTACA
1 AAACGTGAATATCACTATTTTTGTGACAA-GTTTTTTGTAACAATAAGTAAAACTTATAGTTAC-
*
65018 AAATT-TGTCACTATATGAATTT-TTTGGCGTA-AAACAATATT-GAGGA-AATC-TTTGTGACA
64 AAATTATGTCACTACAT-AATTTCTTT-GCGTACAAA-AA-ATTGGA-GATAATCATTTGTGACA
*
65077 ATATATTTTGTCACTATAATTAAAACATATAACGACAAACATTATTATTTTTACTAA
124 ATACATTTTGTCACTATAATTAAAACATATAACGACAAACATTATTATTTTTACTAA
* * * * *
65134 AAACTTGAATCTCACTATTTGTTGTGACAA-TTTTTTGTAACAATAATTATAGCTTATAGTTACA
1 AAACGTGAATATCACTATTT-TTGTGACAAGTTTTTTGTAACAATAAGTAAAACTTATAGTTACA
* ** *
65198 AATTATGTCACTACATTATTTCGTTTTTGTACAAAAAATTGGAGATAATCATTTGTGACTATACA
65 AATTATGTCACTACATAATTTC-TTTGCGTACAAAAAATTGGAGATAATCATTTGTGACAATACA
*
65263 TTTTGTCACTATAATTAAAATATATAA
129 TTTTGTCACTATAATTAAAACATATAA
65290 TTACAAAAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
179 14 0.11
180 49 0.37
181 61 0.46
182 9 0.07
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (180 bp):
AAACGTGAATATCACTATTTTTGTGACAAGTTTTTTGTAACAATAAGTAAAACTTATAGTTACAA
ATTATGTCACTACATAATTTCTTTGCGTACAAAAAATTGGAGATAATCATTTGTGACAATACATT
TTGTCACTATAATTAAAACATATAACGACAAACATTATTATTTTTACTAA
Found at i:68207 original size:19 final size:20
Alignment explanation
Indices: 68183--68225 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
68173 AGCATTTATC
*
68183 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
68202 TTCATTAAAAATCATGTTTT
1 TTCATTAAAAATCATGTATT
68222 TTCA
1 TTCA
68226 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:68617 original size:35 final size:35
Alignment explanation
Indices: 68569--68644 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
68559 TACTTTCTAT
* *
68569 ACCATCTTTCATCTCCATATCACGCCTATATCATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
*
68604 ACCATCTTCCATCTCCATTTCACGCCTATATAATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
68639 ACCATC
1 ACCATC
68645 CCATTATCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.26, C:0.38, G:0.03, T:0.33
Consensus pattern (35 bp):
ACCATCTTCCATCTCCATATCACGCCTATATAATC
Found at i:68855 original size:15 final size:15
Alignment explanation
Indices: 68835--68875 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
68825 CTAATTTCAT
68835 ATTTCCATTTCAATC
1 ATTTCCATTTCAATC
68850 ATTTCCATTTCAATC
1 ATTTCCATTTCAATC
68865 ATTTCCATTTC
1 ATTTCCATTTC
68876 TATTTCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTCCATTTCAATC
Found at i:75975 original size:105 final size:105
Alignment explanation
Indices: 75785--75995 Score: 253
Period size: 105 Copynumber: 2.0 Consensus size: 105
75775 CTTCTAATTT
** * * *
75785 TTCTAGTGAGACGGGTCAGGCTATTGTGAATGCAAGTGTTACTCCTCTGGGAGTAACAGTTCAGT
1 TTCTAGTGAGACGAATCAGGCTATTGTGAATGCAAGTGTTACTCCTCTAGAAGTAACAGTTCAGA
* * *
75850 AAGAGGTAGCTGATGTAACCTCAGATAGTACAGCTGAGGA
66 AAAAGGTAGCTGATGCAACCTCAGATAGTACAACTGAGGA
* * * * * *
75890 TTCTGGTGAGACGAATCAGGCTACTT-TGGATGTAGGTGTTACTCCTCTAGAAGTAGCAGTTTAG
1 TTCTAGTGAGACGAATCAGGCTA-TTGTGAATGCAAGTGTTACTCCTCTAGAAGTAACAGTTCAG
* * *
75954 AAAAAGGTAGTTGGTGCAACCTCAGATAGTAGAACTGAGGA
65 AAAAAGGTAGCTGATGCAACCTCAGATAGTACAACTGAGGA
75995 T
1 T
75996 AATGTGTTGG
Statistics
Matches: 88, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
105 86 0.98
106 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (105 bp):
TTCTAGTGAGACGAATCAGGCTATTGTGAATGCAAGTGTTACTCCTCTAGAAGTAACAGTTCAGA
AAAAGGTAGCTGATGCAACCTCAGATAGTACAACTGAGGA
Found at i:82648 original size:24 final size:24
Alignment explanation
Indices: 82621--82670 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
82611 GTTCACATGA
82621 TTGTTTTATCTGATGTGCAATGTG
1 TTGTTTTATCTGATGTGCAATGTG
*
82645 TTGTTTTATCTGATTTGCAATGTG
1 TTGTTTTATCTGATGTGCAATGTG
82669 TT
1 TT
82671 TATATGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.22, T:0.54
Consensus pattern (24 bp):
TTGTTTTATCTGATGTGCAATGTG
Found at i:89681 original size:44 final size:43
Alignment explanation
Indices: 89608--89781 Score: 242
Period size: 44 Copynumber: 4.0 Consensus size: 43
89598 ACCATGAGTG
* **
89608 GAACCTGTCTGCCAATAATGCATAGTTATGCATTTTCATTTAT
1 GAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
*
89651 GACACCTTTCTGCCAATAATGCACCTTTATGCATTTTCATTTAT
1 GA-ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
* * * *
89695 GGTACCTTACTGCCAATAATGCACCATTATGCATTTTTATTTAT
1 -GAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
89739 GGAACCTTTCTGCCAATAATGCACCGTT-TGCATTTTCATTTAT
1 -GAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
89782 TTTAGAGCAG
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
43 16 0.14
44 100 0.85
45 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (43 bp):
GAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
Found at i:100510 original size:40 final size:40
Alignment explanation
Indices: 100429--100589 Score: 261
Period size: 40 Copynumber: 4.0 Consensus size: 40
100419 TGCAGGTTTA
*
100429 TAATACACTTCAGTGTATATGGT-GACACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
**
100468 TAATACACTTCGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
*
100508 TAATACACTTCGGTGTATATGGTGGACACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
* *
100548 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
100588 TA
1 TA
100590 GCACTACGGT
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 22 0.20
40 90 0.80
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
Found at i:100780 original size:45 final size:45
Alignment explanation
Indices: 100689--100913 Score: 330
Period size: 45 Copynumber: 5.0 Consensus size: 45
100679 GTAAGCATGC
*
100689 AAATAAGCTTAAGAGCTTATGG--TATAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTA-AATGGTAAGTATATTGGTA
* * *
100733 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGCATGTTGATA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
* *
100778 AAATAAGCTTACGAGCTTATGGATTAAATGGTCAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
100823 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
* * *
100868 AAATAAGTTTACGAGCTTATGCGA-TAAATGATATGTATATTGGTA
1 AAATAAGCTTACGAGCTTATG-GATTAAATGGTAAGTATATTGGTA
100913 A
1 A
100914 GAAAGTTGTA
Statistics
Matches: 166, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
44 21 0.13
45 141 0.85
46 4 0.02
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
Found at i:103817 original size:46 final size:46
Alignment explanation
Indices: 103716--103931 Score: 253
Period size: 46 Copynumber: 4.7 Consensus size: 46
103706 CACCCCTATG
*
103716 CATTTCATTTATGGCATCCTTTCATG--CCTTTTATACGA-TATTATG
1 CATTTCATTTATGGCATCCTTTCATGCCCCTTTT-TAC-ACTATTATA
* * * *
103761 CATTTCATTTATAGCATCCTATCATGCCCCTTTTTACATTATTATT
1 CATTTCATTTATGGCATCCTTTCATGCCCCTTTTTACACTATTATA
* * *
103807 TATTTCATTTATGGCATCCTTTCATTCCCC-TTTTACACTGTTATA
1 CATTTCATTTATGGCATCCTTTCATGCCCCTTTTTACACTATTATA
* * ** *
103852 CATTTTATTTTATGGCATTCTTTCATGCATCTTCTTACACTATTATA
1 CATTTCA-TTTATGGCATCCTTTCATGCCCCTTTTTACACTATTATA
103899 CATTTCATTTATGGCATCCTTTCATG-CCCTTTT
1 CATTTCATTTATGGCATCCTTTCATGCCCCTTTT
103932 AAACGAGCAT
Statistics
Matches: 143, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
45 46 0.32
46 72 0.50
47 25 0.17
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (46 bp):
CATTTCATTTATGGCATCCTTTCATGCCCCTTTTTACACTATTATA
Found at i:104075 original size:68 final size:68
Alignment explanation
Indices: 103963--104705 Score: 954
Period size: 68 Copynumber: 11.0 Consensus size: 68
103953 TAGTCTTTTA
* * * *
103963 CTCAAAGGCACTTAGACTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAATTGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
*
104028 AGC
66 GGC
* * * * ** * *
104031 CTCAAAGGCACTTATCTTTTCATTTAATTGGCATAATTTCCACCTTTTTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104096 GGC
66 GGC
* * * * * *
104099 CTCAAAGGCACTTAGCTTTTCATCTAATTGGCCTAATTCACACATTTATGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104164 GGC
66 GGC
* * * *
104167 CTCAAAGGCACTTAGCCTTTCATCTAACTGGGATAATTGACACATTTCTATCAACTGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104232 GGC
66 GGC
* *
104235 CTCAAAGGCACTTAGCCTTTCATCTAACTGGC--AATTGACACCCTT-TGTAAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104297 GGC
66 GGC
* * * * * *
104300 CT-AAAGACAATTAGCCTTTCATCTAAATGGCATAATTGACACCTTTTTTTCAAATGCACGGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104364 GGC
66 GGC
* * * * **
104367 CTCAAAGACACTTAGCCTTTCATCTAACTGGCATAATTGACAACTTTCTGTCAAATGTATAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104432 GGC
66 GGC
* * * *
104435 CTCAAAGGTACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCGCAATTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
*
104500 AGC
66 GGC
* * * * *
104503 CTCAAAGGCTCTTAACCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATACACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104568 GGC
66 GGC
* * *
104571 CTCAAAGGCACTTATCCTTTCATCTAACTAGCTTAATTGACACCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104636 GGC
66 GGC
* * * * * *
104639 CTCAACGGCACTTAGCCTTTCATTTAATTTGCATAATTGACACCTTTTTGTCAAATACACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
104704 GG
66 GG
104706 TTATTAATCT
Statistics
Matches: 587, Mismatches: 84, Indels: 8
0.86 0.12 0.01
Matches are distributed among these distances:
64 26 0.04
65 19 0.03
66 23 0.04
67 19 0.03
68 500 0.85
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
GGC
Found at i:104963 original size:55 final size:55
Alignment explanation
Indices: 104904--105083 Score: 245
Period size: 55 Copynumber: 3.2 Consensus size: 55
104894 CTGATAATTG
* * * * *
104904 CACATATATTTCCCATACGAAAATTCATACACTTAGTATGGATTTATTAAGTTTA
1 CACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
*
104959 CACATATAGTGCCCATAC-AGAAATTCATCCTCTTAGTATGAATTTCTTAAGTTTA
1 CACATATAGTGCCCATACGA-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
* *
105014 CACATATAGTGCCCATACGGAAATTCATCCACTTAGTATGAATTTCTCAAGTTTTTA
1 CACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG--TTTA
*
105071 CACATTTAGTGCC
1 CACATATAGTGCC
105084 ATTTGGTAAT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
54 1 0.01
55 94 0.85
57 16 0.14
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (55 bp):
CACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
Found at i:107743 original size:46 final size:45
Alignment explanation
Indices: 107649--107887 Score: 183
Period size: 46 Copynumber: 5.3 Consensus size: 45
107639 TTCATTGAGA
* ** * * *
107649 GCATCCATTCATACTTATAATACACCA-TATGCATCTCAATTATC
1 GCATCCTTTCATACCCATAATACACCATTATGCATTTCATTTATG
* * * *
107693 GCATCCTTTCGTACCGATAATGCACCCCTTATGCATTTCATTTATG
1 GCATCCTTTCATACCCATAATACA-CCATTATGCATTTCATTTATG
* ** * *
107739 GCATCCTTTCATACCCTTTTTACACTATTATACATTTCATTTATG
1 GCATCCTTTCATACCCATAATACACCATTATGCATTTCATTTATG
* * ** * * *
107784 GCATCCTTTCATGCCCCTTTTTTCACTATTATACATTTCATTTATG
1 GCATCCTTTCAT-ACCCATAATACACCATTATGCATTTCATTTATG
* * * ** * *
107830 GCATCCTTCCATGCCCCTTTTTACACTATTATACATTTCATTTATG
1 GCATCCTTTCAT-ACCCATAATACACCATTATGCATTTCATTTATG
107876 GCATCCTTTCAT
1 GCATCCTTTCAT
107888 GCCCTTTTAT
Statistics
Matches: 169, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
44 19 0.11
45 32 0.19
46 118 0.70
ACGTcount: A:0.24, C:0.27, G:0.07, T:0.42
Consensus pattern (45 bp):
GCATCCTTTCATACCCATAATACACCATTATGCATTTCATTTATG
Found at i:107907 original size:46 final size:46
Alignment explanation
Indices: 107721--107895 Score: 300
Period size: 46 Copynumber: 3.8 Consensus size: 46
107711 AATGCACCCC
* *
107721 TTATGCATTTCATTTATGGCATCCTTTCAT-ACCCTTTTTACACTA
1 TTATACATTTCATTTATGGCATCCTTTCATGCCCCTTTTTACACTA
*
107766 TTATACATTTCATTTATGGCATCCTTTCATGCCCCTTTTTTCACTA
1 TTATACATTTCATTTATGGCATCCTTTCATGCCCCTTTTTACACTA
*
107812 TTATACATTTCATTTATGGCATCCTTCCATGCCCCTTTTTACACTA
1 TTATACATTTCATTTATGGCATCCTTTCATGCCCCTTTTTACACTA
107858 TTATACATTTCATTTATGGCATCCTTTCATG-CCCTTTT
1 TTATACATTTCATTTATGGCATCCTTTCATGCCCCTTTT
107896 ATATGACATT
Statistics
Matches: 123, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
45 36 0.29
46 87 0.71
ACGTcount: A:0.21, C:0.26, G:0.07, T:0.47
Consensus pattern (46 bp):
TTATACATTTCATTTATGGCATCCTTTCATGCCCCTTTTTACACTA
Found at i:108012 original size:68 final size:68
Alignment explanation
Indices: 107935--108395 Score: 651
Period size: 68 Copynumber: 6.8 Consensus size: 68
107925 GTTTTTACTT
* * * **
107935 AAAGGCACTTAGCCTTTCATCTAACTGACATGATTGACACCTTTTTGTCAAATGCACAACTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
108000 CTC
66 CTC
* * * **
108003 AAAGGCACTTAGCCTTTCATCAAACTGACATAATTGACACCTTTTTGTCAAATGCACAACTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
108068 CTC
66 CTC
* *
108071 AAAGGTACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGTTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
108136 CTC
66 CTC
*
108139 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAAGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
108204 CTC
66 CTC
* * *
108207 AAAGGCACTTAGCCTTTCATCTAACGGGTATAATTGACACCTTTCTGTCAAATGCACAGTTAGTC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
108272 CTC
66 CTC
* * * * * *
108275 AAAGGAACTTAGGCTTTCATCTAACTGGCATAATTAAAACCATTATGTCAAATGCACAGTTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
108340 CTC
66 CTC
* * * * *
108343 AAATGCACTTAGCATTTCATAT-A--GGCATAATTGGCACCTTTCTTTCAAA-GCAC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
108396 TTAGCCTTTC
Statistics
Matches: 357, Mismatches: 36, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
64 4 0.01
65 20 0.06
67 1 0.00
68 332 0.93
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (68 bp):
AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
CTC
Found at i:108430 original size:48 final size:46
Alignment explanation
Indices: 108341--108444 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 46
108331 CAGTTAGGCC
**
108341 TCAAATGCACTTAGCATTTCATATAGGCATAATTGGCACCTTTCTT-
1 TCAAATGCACTTAGCATTTCATATAGGCATAATTGAAACCTTT-TTG
* *
108387 TCAAA-GCACTTAGCCTTTCATCTAATTGGCATAATTGAAACCTTTTTG
1 TCAAATGCACTTAGCATTTCA--T-ATAGGCATAATTGAAACCTTTTTG
108435 TCAAATGCAC
1 TCAAATGCAC
108445 AATTAGGCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
45 14 0.29
46 5 0.10
47 3 0.06
48 23 0.47
49 4 0.08
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (46 bp):
TCAAATGCACTTAGCATTTCATATAGGCATAATTGAAACCTTTTTG
Found at i:108724 original size:55 final size:55
Alignment explanation
Indices: 108654--108872 Score: 339
Period size: 55 Copynumber: 4.0 Consensus size: 55
108644 CTGATAATTG
* * * * *
108654 CACATATATTTCCCATATAGAAATTCAGCCACTTAGTATGGATTTCTTAAGTTTA
1 CACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
108709 CACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
1 CACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
* * * *
108764 CACATATAGTGCCCATACATAAATTCATACACTTAGTATAAATTTATTAAGTTTA
1 CACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
* *
108819 CACATATAGTGCCCATACAAAAATTCATCCACTTAGTAAGAATTTCTTAAGTTT
1 CACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
108873 TTGCGCACTT
Statistics
Matches: 150, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 150 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (55 bp):
CACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
Found at i:109253 original size:22 final size:19
Alignment explanation
Indices: 109221--109273 Score: 52
Period size: 22 Copynumber: 2.6 Consensus size: 19
109211 ATCGATACCC
*
109221 CTACCATGGTATCAATACT
1 CTACTATGGTATCAATACT
* *
109240 ACTATACTATGGTACCGATACT
1 -C--TACTATGGTATCAATACT
109262 CTACTATGGTAT
1 CTACTATGGTAT
109274 TGATGCCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 10 0.37
20 1 0.04
21 1 0.04
22 15 0.56
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (19 bp):
CTACTATGGTATCAATACT
Found at i:110466 original size:70 final size:70
Alignment explanation
Indices: 110377--110516 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 70
110367 AGAGCAAGTC
* *
110377 TTGCTCCATGATACATACATCACAAGGCTCATATCAAAAGAAAATGGACTAACATTTAAATTGTT
1 TTGCTCCATGATACATACATCACAAGACTCATACCAAAAGAAAATGGACTAACATTTAAATTGTT
110442 TCACA
66 TCACA
*
110447 TTGCTCCATGATACATACATCACAAGACTCATACCAAAAGAAGATGGACTAACATTTAAATTGTT
1 TTGCTCCATGATACATACATCACAAGACTCATACCAAAAGAAAATGGACTAACATTTAAATTGTT
110512 TCACA
66 TCACA
110517 CCACAAAGCC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (70 bp):
TTGCTCCATGATACATACATCACAAGACTCATACCAAAAGAAAATGGACTAACATTTAAATTGTT
TCACA
Found at i:111112 original size:54 final size:54
Alignment explanation
Indices: 111027--111248 Score: 195
Period size: 54 Copynumber: 4.1 Consensus size: 54
111017 TTCATTGAGA
* * * *
111027 TGCACA-TGTAGTGCCTATACGGTTCTCCATCAACGTATGATGAA-TTCTGTGGGT
1 TGCACACT-TAGTGCCTATACCGTTGTTCATCAACATATGATGAATTTC-GTGGGT
* *
111081 TGCACACTTAGTGGCTATACCGTTGTTCATC-A-ATATGATGAATTTCGCGGGT
1 TGCACACTTAGTGCCTATACCGTTGTTCATCAACATATGATGAATTTCGTGGGT
* * * * * * * *
111133 TGCACACTTAGTGCATATA-CGATGGTTTAGCAAAACATGGTGAATTTGGTGGGT
1 TGCACACTTAGTGCCTATACCG-TTGTTCATCAACATATGATGAATTTCGTGGGT
* * * * *
111187 TGTACACTTGGTGCCTATACGGTTGTTCATCAACATTTGATGAATTAT-GTGGTT
1 TGCACACTTAGTGCCTATACCGTTGTTCATCAACATATGATGAATT-TCGTGGGT
111241 TGCACACT
1 TGCACACT
111249 CACTTAATGC
Statistics
Matches: 133, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
51 2 0.02
52 37 0.28
53 5 0.04
54 86 0.65
55 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACCGTTGTTCATCAACATATGATGAATTTCGTGGGT
Found at i:111140 original size:52 final size:53
Alignment explanation
Indices: 111027--111152 Score: 150
Period size: 52 Copynumber: 2.4 Consensus size: 53
111017 TTCATTGAGA
* *
111027 TGCACA-TGTAGTGCCTATACGGTTCTCCATCAACGTATGATGAATTCTGTGGGT
1 TGCACACT-TAGTGCCTATACCGTTCTCCATCAAC-TATGATGAATTCTGCGGGT
* * *
111081 TGCACACTTAGTGGCTATACCGTTGTTCATCAA-TATGATGAATT-TCGCGGGT
1 TGCACACTTAGTGCCTATACCGTTCTCCATCAACTATGATGAATTCT-GCGGGT
*
111133 TGCACACTTAGTGCATATAC
1 TGCACACTTAGTGCCTATAC
111153 GATGGTTTAG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
51 1 0.02
52 34 0.54
54 27 0.43
55 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (53 bp):
TGCACACTTAGTGCCTATACCGTTCTCCATCAACTATGATGAATTCTGCGGGT
Found at i:111639 original size:22 final size:22
Alignment explanation
Indices: 111612--111668 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
111602 TACCCCTACC
*
111612 ATGGTATTGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
111634 ATGGTATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
*
111656 ATGGTATCAATAC
1 ATGGTATCGATAC
111669 CCCCTTTCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (22 bp):
ATGGTATCGATACTTCTATACT
Found at i:117837 original size:215 final size:216
Alignment explanation
Indices: 117404--117896 Score: 568
Period size: 215 Copynumber: 2.3 Consensus size: 216
117394 TTTATTGAGA
* *** * * *
117404 TGCACACGTAGTGCCTATACGGCCATTCAT-AAACATATTATGAATT-CATTGGTTCGCACA-TA
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAAA-ATATGATGAATTCCGTGGGTT-GCACACT-
* * * *
117466 TAGTGCCTATACGATTGTTCATCAACATATGATGAATTTCGTGGGTTTCACACTTAGTGCCTATA
63 TAGTGCCTATACGATTGTTCATCAACATAAGATGAATTTCGCGGGTTGCACACTTAGTGCATATA
* * * * * * *
117531 CGGTTGTTCATCAACATATGATGAATTCCATGTGTTGCACAGTTTGTGCCTATACGGTTCTCCAT
128 CGATGGTTCATCAAAACATGATGAATTCCATGGGTTGCACAGTTAGTGCCTATACGATTCTCCAT
* * *
117596 CAACATATGATGAATTCTGTGGGT
193 AAACACATGAAGAATTCTGTGGGT
** **
117620 TGCACACTTAGTGGTTATACGGTTGTTCATCAAAATATGATG-ATTTTGTGGGTTGCACACTTAG
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAAAATATGATGAATTCCGTGGGTTGCACACTTAG
* *
117684 TGCCTATACGGTTGTTCATCAACATAAGATGAATTTTGCGGGTTGCACACTTAGTGCATATACGA
66 TGCCTATACGATTGTTCATCAACATAAGATGAATTTCGCGGGTTGCACACTTAGTGCATATACGA
* * ** * *
117749 TGGTTCAGT-AAAACATGATGAATTTCGTGGGTTGCAC-GCTTAGTTTCTATACGATTGTTCATA
131 TGGTTCA-TCAAAACATGATGAATTCCATGGGTTGCACAG-TTAGTGCCTATACGATTCTCCATA
117812 AACACATGAAGAATT-TCGTGGGT
194 AACACATGAAGAATTCT-GTGGGT
* *
117835 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCGTGGTTTGCACACT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAAAATATGATGAATTCCGTGGGTTGCACACT
117897 CACTTAGTGC
Statistics
Matches: 232, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
214 2 0.01
215 173 0.75
216 54 0.23
217 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (216 bp):
TGCACACTTAGTGCCTATACGGTTGTTCATCAAAATATGATGAATTCCGTGGGTTGCACACTTAG
TGCCTATACGATTGTTCATCAACATAAGATGAATTTCGCGGGTTGCACACTTAGTGCATATACGA
TGGTTCATCAAAACATGATGAATTCCATGGGTTGCACAGTTAGTGCCTATACGATTCTCCATAAA
CACATGAAGAATTCTGTGGGT
Found at i:117896 original size:54 final size:54
Alignment explanation
Indices: 117404--117896 Score: 573
Period size: 54 Copynumber: 9.1 Consensus size: 54
117394 TTTATTGAGA
* *** * * * *
117404 TGCACACGTAGTGCCTATACGGCCATTCATAAACATATTATGAA-TTCATTGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
*
117457 TCGCACA-TATAGTGCCTATACGATTGTTCATCAACATATGATGAATTTCGTGGGT
1 T-GCACACT-TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
* * * *
117512 TTCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCATGTGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
* * * *
117566 TGCACAGTTTGTGCCTATACGGTTCTCCATCAACATATGATGAA-TTCTGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTC-GTGGGT
** * *
117620 TGCACACTTAGTGGTTATACGGTTGTTCATCAAAATATGATG-ATTTTGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
* * *
117673 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATAAGATGAATTTTGCGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
* * * * *
117727 TGCACACTTAGTGCATATACGATGGTTCAGT-AAAACATGATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCA-TCAACATATGATGAATTTCGTGGGT
* ** * * * *
117781 TGCACGCTTAGTTTCTATACGATTGTTCATAAACACATGAAGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
* *
117835 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCGTGGTT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
117889 TGCACACT
1 TGCACACT
117897 CACTTAGTGC
Statistics
Matches: 372, Mismatches: 59, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
53 49 0.13
54 313 0.84
55 10 0.03
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
Found at i:119642 original size:12 final size:11
Alignment explanation
Indices: 119620--119661 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
119610 TGGATTATGA
119620 TATTATTTTAT
1 TATTATTTTAT
119631 TATTAGTTTTAT
1 TATTA-TTTTAT
*
119643 TTTTATTTTAGT
1 TATTATTTTA-T
119655 TATTATT
1 TATTATT
119662 CATTGTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:119644 original size:17 final size:17
Alignment explanation
Indices: 119620--119661 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
119610 TGGATTATGA
119620 TATTATTTTATTATTAGT
1 TATTATTTTATT-TTAGT
119638 T-TTATTTTTATTTTAGT
1 TATTA-TTTTATTTTAGT
119655 TATTATT
1 TATTATT
119662 CATTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (17 bp):
TATTATTTTATTTTAGT
Found at i:119648 original size:18 final size:18
Alignment explanation
Indices: 119620--119661 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
119610 TGGATTATGA
119620 TATTA-TTTTATTATTAGT
1 TATTATTTTTATT-TTAGT
119638 T-TTATTTTTATTTTAGT
1 TATTATTTTTATTTTAGT
119655 TATTATT
1 TATTATT
119662 CATTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (18 bp):
TATTATTTTTATTTTAGT
Found at i:121771 original size:19 final size:20
Alignment explanation
Indices: 121747--121791 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
121737 CTATGAATGA
*
121747 ATAAAATTTAATG-CAAAAG
1 ATAAAATTCAATGTCAAAAG
*
121766 ATAAAATTCAATGTGAAAAG
1 ATAAAATTCAATGTCAAAAG
121786 -TAAAAT
1 ATAAAAT
121792 GCAAATGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (20 bp):
ATAAAATTCAATGTCAAAAG
Found at i:121803 original size:19 final size:19
Alignment explanation
Indices: 121756--121803 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
121746 AATAAAATTT
*
121756 AATGCAAAAGATAAAATTC
1 AATGCAAAAGATAAAATGC
*
121775 AATGTGAAAAG-TAAAATGC
1 AATG-CAAAAGATAAAATGC
121794 AAATGCAAAA
1 -AATGCAAAA
121804 TGCAAAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (19 bp):
AATGCAAAAGATAAAATGC
Found at i:124772 original size:27 final size:29
Alignment explanation
Indices: 124734--124793 Score: 90
Period size: 27 Copynumber: 2.1 Consensus size: 29
124724 ATTGGTATTA
124734 TAAAATTGCCCCTGAAA-TGTAAAATGA-C
1 TAAAATTGCCCCT-AAAGTGTAAAATGACC
124762 TAAAA-TGCCCCTAAAGTGTAAAATGACC
1 TAAAATTGCCCCTAAAGTGTAAAATGACC
124790 TAAA
1 TAAA
124794 TTATCTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 3 0.10
27 17 0.57
28 10 0.33
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (29 bp):
TAAAATTGCCCCTAAAGTGTAAAATGACC
Found at i:128718 original size:21 final size:20
Alignment explanation
Indices: 128676--128725 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
128666 ATTCCTCTTG
128676 GTATCGATACCTCCACATCA
1 GTATCGATACCTCCACATCA
*
128696 GTATCGATACTACTTCA-ATCA
1 GTATCGATAC--CTCCACATCA
128717 GTATCGATA
1 GTATCGATA
128726 TTATTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (20 bp):
GTATCGATACCTCCACATCA
Found at i:139928 original size:53 final size:51
Alignment explanation
Indices: 139865--139967 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
139855 TAAGGAAACT
*
139865 AAATGCTAATTTACAAACTCATTATGAGTACCATGAATGCACACATAGTGCCA
1 AAATGCTAA-TT-CAAACTCATTATGAATACCATGAATGCACACATAGTGCCA
* *
139918 AAATGGTAATTCACACTCATTATGAATACCATGAATGCACACATAGTGCC
1 AAATGCTAATTCAAACTCATTATGAATACCATGAATGCACACATAGTGCC
139968 GAAAGTACAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 37 0.79
52 2 0.04
53 8 0.17
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (51 bp):
AAATGCTAATTCAAACTCATTATGAATACCATGAATGCACACATAGTGCCA
Found at i:148063 original size:18 final size:17
Alignment explanation
Indices: 148035--148082 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 17
148025 CTTCGGATTC
148035 AAGTTAGTTTCTAAATT
1 AAGTTAGTTTCTAAATT
148052 AAGTTCAGTTTCTAAATT
1 AAGTT-AGTTTCTAAATT
148070 AAGTTTAGTTTCT
1 AAG-TTAGTTTCT
148083 GACGTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.17
18 22 0.76
19 2 0.07
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (17 bp):
AAGTTAGTTTCTAAATT
Found at i:149634 original size:12 final size:13
Alignment explanation
Indices: 149615--149651 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
149605 ATGGATGTTT
149615 TCTTTGATTTCTG
1 TCTTTGATTTCTG
*
149628 T-TTTGATCTCT-
1 TCTTTGATTTCTG
149639 TCTTTGATTTCTG
1 TCTTTGATTTCTG
149652 ATATCTCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.08, C:0.16, G:0.14, T:0.62
Consensus pattern (13 bp):
TCTTTGATTTCTG
Found at i:151646 original size:2 final size:2
Alignment explanation
Indices: 151639--151664 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
151629 TCATACACCC
151639 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
151665 GACCACAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:155891 original size:12 final size:12
Alignment explanation
Indices: 155874--155901 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
155864 AACAATGTTG
155874 AGAATCCAAGAA
1 AGAATCCAAGAA
155886 AGAATCCAAGAA
1 AGAATCCAAGAA
155898 AGAA
1 AGAA
155902 CCCACATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.14, G:0.18, T:0.07
Consensus pattern (12 bp):
AGAATCCAAGAA
Found at i:166040 original size:54 final size:54
Alignment explanation
Indices: 165939--166145 Score: 234
Period size: 54 Copynumber: 3.8 Consensus size: 54
165929 CTACTTATTC
* * * * *
165939 TATGAATTTCTTATGTTTTCACATATAGTTCCCATACGAAAATTCACACACTTAG
1 TATGAATTTCTTA-GTTTGCACACATAGTGCCCATACGGAAAGTCACACACTTAG
* *
165994 TATGAATTTATTAGTTTGCACACATAATGCCCATACGGAAAGTCACACACTTAG
1 TATGAATTTCTTAGTTTGCACACATAGTGCCCATACGGAAAGTCACACACTTAG
* * * * *
166048 TATGAATTTCTTAGTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAT
1 TATGAATTTCTTAGTTTGCACACATAGTGCCCATACGGAAAGTCACACACTTAG
* * * *
166102 TATGAATTTCATAACTTTTTGCACACAAAGTGCCCATACAGAAA
1 TATGAATTTC-TTA--GTTTGCACACATAGTGCCCATACGGAAA
166146 TTCATAAACT
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
54 92 0.70
55 14 0.11
57 25 0.19
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (54 bp):
TATGAATTTCTTAGTTTGCACACATAGTGCCCATACGGAAAGTCACACACTTAG
Found at i:166090 original size:108 final size:111
Alignment explanation
Indices: 165939--166145 Score: 269
Period size: 108 Copynumber: 1.9 Consensus size: 111
165929 CTACTTATTC
* * * * *
165939 TATGAATTTCTTATGTTTTCACATATAGTTCCCATACGAAAATTCACACACTTAGTATGAATTT-
1 TATGAATTTCTTATGTTTGCACACATAGTGCCCATACGAAAATTCACAAACTAAGTATGAATTTC
* *
166003 ATTA-GTTTGCACACATAA-TGCCCATACGGAAAGTCACACACTTAG
66 ATAACGTTTGCACACA-AAGTGCCCATACAGAAAGTCACACACTTAG
* * *
166048 TATGAATTTCTTA-GTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTC
1 TATGAATTTCTTATGTTTGCACACATAGTGCCCATACGAAAATTCACAAACTAAGTATGAATTTC
*
166112 ATAACTTTTTGCACACAAAGTGCCCATACAGAAA
66 ATAAC-GTTTGCACACAAAGTGCCCATACAGAAA
166146 TTCATAAACT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
108 42 0.51
109 16 0.19
110 2 0.02
111 23 0.28
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (111 bp):
TATGAATTTCTTATGTTTGCACACATAGTGCCCATACGAAAATTCACAAACTAAGTATGAATTTC
ATAACGTTTGCACACAAAGTGCCCATACAGAAAGTCACACACTTAG
Found at i:166146 original size:57 final size:56
Alignment explanation
Indices: 166008--166233 Score: 229
Period size: 57 Copynumber: 4.2 Consensus size: 56
165998 AATTTATTAG
* * * * * * * *
166008 TTTGCACACATAA-TGCCCATACGGAAAGTCACACACTTAGTATGAATTTCTTA--G
1 TTTGCACACA-AAGTGCCCATACAGAAATTCATAAACTAATTATGAATTTCTAACTT
* *
166062 TTTGCACACATAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCATAACTT
1 TTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATGAATTTC-TAACTT
166119 TTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATG-------AACTT
1 TTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATGAATTTCTAACTT
* ** *
166168 TTTGCTCACAAAGTGCCCATATTGAAATTCATAAACTAATTATTAATTTCTTAACTT
1 TTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATGAATTTC-TAACTT
166225 TTTGCACAC
1 TTTGCACAC
166234 TCAGTGCCAT
Statistics
Matches: 145, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
49 45 0.31
53 1 0.01
54 42 0.29
55 2 0.01
57 55 0.38
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (56 bp):
TTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATGAATTTCTAACTT
Found at i:166186 original size:49 final size:49
Alignment explanation
Indices: 166114--166210 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
166104 TGAATTTCAT
166114 AACTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATG
1 AACTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATG
* **
166163 AACTTTTTGCTCACAAAGTGCCCATATTGAAATTCATAAACTAATTAT
1 AACTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTAT
166211 TAATTTCTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (49 bp):
AACTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATG
Found at i:168717 original size:15 final size:15
Alignment explanation
Indices: 168697--168728 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
168687 TAACGACTCT
168697 TCAAGTCTTGATACA
1 TCAAGTCTTGATACA
*
168712 TCAAGTCTTGATGCA
1 TCAAGTCTTGATACA
168727 TC
1 TC
168729 TTATTCCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (15 bp):
TCAAGTCTTGATACA
Found at i:171841 original size:14 final size:14
Alignment explanation
Indices: 171822--171858 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
171812 ATTTATTTAC
171822 TATATTCAT-TTTTT
1 TATATT-ATATTTTT
171836 TATATTATATTTTT
1 TATATTATATTTTT
171850 TATA-TATAT
1 TATATTATAT
171859 CTTATATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TATATTATATTTTT
Found at i:171886 original size:14 final size:14
Alignment explanation
Indices: 171850--171893 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
171840 TTATATTTTT
*
171850 TATATATATCT-TA
1 TATATATATGTATA
171863 TATCAT-TATGTATA
1 TAT-ATATATGTATA
171877 TATATATATGTATA
1 TATATATATGTATA
171891 TAT
1 TAT
171894 GTATTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (14 bp):
TATATATATGTATA
Found at i:171947 original size:43 final size:43
Alignment explanation
Indices: 171900--171997 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
171890 ATATGTATTA
171900 ATTTTTCTATTTACTATTTATATATATATATTCTTA-ATATTCT
1 ATTTTTCTATTTACTATTTATATAT-TATATTCTTACATATTCT
* * * * * *
171943 ATTTTTGTTTTTATTATTTATATATTATATTTTTACTTTATTTT
1 ATTTTTCTATTTACTATTTATATATTATATTCTTAC-ATATTCT
171987 ATTTTTCTATT
1 ATTTTTCTATT
171998 ATTTTTTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
42 9 0.20
43 22 0.49
44 14 0.31
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (43 bp):
ATTTTTCTATTTACTATTTATATATTATATTCTTACATATTCT
Found at i:172000 original size:43 final size:43
Alignment explanation
Indices: 171900--172067 Score: 116
Period size: 43 Copynumber: 3.9 Consensus size: 43
171890 ATATGTATTA
* * * * *
171900 ATTTTTCTATTTACTATTTATATATATATATTCTTA-ATATTCT
1 ATTTTTCTACTTATTATTTATATAT-TATATTTTTATTTATTTT
* **
171943 ATTTTTGTTTTTATTATTTATATATTATATTTTTACTTTATTTT
1 ATTTTTCTACTTATTATTTATATATTATATTTTTA-TTTATTTT
* *
171987 ATTTTTCTA-TTATT-TTTTTAATATCATATATCTTTA--T-TTTT
1 ATTTTTCTACTTATTATTTAT-ATAT--TATATTTTTATTTATTTT
* *
172028 ATTTTTTTACTTAGTA-TTATATATTTATTATTTTTATTTA
1 ATTTTTCTACTTATTATTTATATA-TTA-TATTTTTATTTA
172068 GTAAATACTA
Statistics
Matches: 99, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
40 2 0.02
41 22 0.22
42 22 0.22
43 32 0.32
44 12 0.12
45 9 0.09
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.67
Consensus pattern (43 bp):
ATTTTTCTACTTATTATTTATATATTATATTTTTATTTATTTT
Found at i:172138 original size:17 final size:18
Alignment explanation
Indices: 172107--172140 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
172097 TTTTTATTCA
172107 TTTTTAATTTCTTTTACC
1 TTTTTAATTTCTTTTACC
*
172125 TTTTTTATTT-TTTTAC
1 TTTTTAATTTCTTTTAC
172141 TCCATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTAATTTCTTTTACC
Found at i:174626 original size:18 final size:17
Alignment explanation
Indices: 174575--174639 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
174565 CAAAACATTA
*
174575 AATGAGCTAGTTTAATT
1 AATGAACTAGTTTAATT
*
174592 AATGAACCAGTTTAATT
1 AATGAACTAGTTTAATT
* *
174609 GAATTAACTAGATTAATT
1 -AATGAACTAGTTTAATT
*
174627 ATTGAACTAGTTT
1 AATGAACTAGTTT
174640 TTTTAATAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 25 0.64
18 14 0.36
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (17 bp):
AATGAACTAGTTTAATT
Found at i:183749 original size:23 final size:21
Alignment explanation
Indices: 183697--183758 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
183687 TTTTGGTGCA
*
183697 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
183717 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
183738 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
183759 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:183779 original size:20 final size:21
Alignment explanation
Indices: 183740--183779 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
183730 CCCCCTTTGA
*
183740 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
183761 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
183780 TGGGGCTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:185924 original size:19 final size:19
Alignment explanation
Indices: 185900--185939 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
185890 GTGTTTTAAG
185900 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
185919 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
185938 TG
1 TG
185940 GGAGAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
TGTGTTTTAAAATGATAAA
Found at i:195274 original size:49 final size:49
Alignment explanation
Indices: 195221--195358 Score: 204
Period size: 49 Copynumber: 2.8 Consensus size: 49
195211 GGTGCTAAAA
* *
195221 TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGT
** ** *
195270 TAAATGCATAACATTGCATTTCTCCATAAAATGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGT
*
195319 TAAATGCATAACGGTGCATTTCGACATAAATGGTGCCACT
1 TAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
195359 CATTGTATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 77 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (49 bp):
TAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGT
Found at i:200001 original size:22 final size:21
Alignment explanation
Indices: 199959--199998 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
199949 GAGTTTATTT
*
199959 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
199980 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
199999 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:202029 original size:45 final size:45
Alignment explanation
Indices: 201979--202073 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
201969 CGATGTTTTG
* *
201979 AAAATGC-CTGAGTGCATCAATGCATGGTCTTGTGCATCGATGCAT
1 AAAATGCACTGAGTGCATCAATGCATGGT-ATGTGCATCAATGCAT
* *
202024 CAAATGCACTGAGTGCATCGATGCATGGTATGTGCATCAATGCAT
1 AAAATGCACTGAGTGCATCAATGCATGGTATGTGCATCAATGCAT
202069 AAAAT
1 AAAAT
202074 ACATTCGATG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 24 0.55
46 20 0.45
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
AAAATGCACTGAGTGCATCAATGCATGGTATGTGCATCAATGCAT
Found at i:210999 original size:31 final size:32
Alignment explanation
Indices: 210964--211039 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
210954 GAATGACCTG
210964 AACCCGAATTGAA-CCGAA-AATATGATACCCA
1 AACCCGAATTGAATCCGAATAATATGA-ACCCA
* *
210995 AACCCGAATTGAATCTGAATGATATGAACCCA
1 AACCCGAATTGAATCCGAATAATATGAACCCA
*
211027 AACCTGAGATTGA
1 AACCCGA-ATTGA
211040 CCTAGTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 13 0.33
32 15 0.38
33 11 0.28
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (32 bp):
AACCCGAATTGAATCCGAATAATATGAACCCA
Found at i:214483 original size:12 final size:12
Alignment explanation
Indices: 214468--214493 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
214458 TTCAAATATT
214468 AAAATAAAAATG
1 AAAATAAAAATG
214480 AAAATAAAAATG
1 AAAATAAAAATG
214492 AA
1 AA
214494 TGAAAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:214698 original size:53 final size:50
Alignment explanation
Indices: 214590--214738 Score: 129
Period size: 53 Copynumber: 2.9 Consensus size: 50
214580 GGGTTTAGGG
* * * * * * *
214590 TTAGAGAATGAACAGAGACAAAAGATGAAGAGGCTTGATTTGAGTTTGGGG
1 TTAGAGAATGAACAGAGAC-AAAGATGAAAAGGCTAGGTTAGGGTATGGGA
214641 TTAGAGAATATGAACAGAGACAGAAGATGAAAAGGCTAGGTTAGGGTATGGGA
1 TTAGAG-A-ATGAACAGAGACA-AAGATGAAAAGGCTAGGTTAGGGTATGGGA
* * * * *
214694 TTAGAGGGGATGAACTGAGATAAAG-TGAATAGGCTCGGTTAGGGT
1 TTAGA--GAATGAACAGAGACAAAGATGAAAAGGCTAGGTTAGGGT
214739 TTAGGTTTAG
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
51 24 0.30
52 5 0.06
53 51 0.63
55 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.35, T:0.22
Consensus pattern (50 bp):
TTAGAGAATGAACAGAGACAAAGATGAAAAGGCTAGGTTAGGGTATGGGA
Found at i:214749 original size:51 final size:53
Alignment explanation
Indices: 214650--214749 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 53
214640 GTTAGAGAAT
*
214650 ATGAACAGAGACAGAAGATGAAAAGGCTAGGTTAGGGTATGGGATTAGAGGGG
1 ATGAACAGAGACAGAAGATGAAAAGGCTAGGTTAGGGTATAGGATTAGAGGGG
* * * * * *
214703 ATGAACTGAGATA-AAG-TGAATAGGCTCGGTTAGGGTTTAGGTTTAGA
1 ATGAACAGAGACAGAAGATGAAAAGGCTAGGTTAGGGTATAGGATTAGA
214750 TTTGGGTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 26 0.65
52 3 0.08
53 11 0.28
ACGTcount: A:0.35, C:0.06, G:0.36, T:0.23
Consensus pattern (53 bp):
ATGAACAGAGACAGAAGATGAAAAGGCTAGGTTAGGGTATAGGATTAGAGGGG
Found at i:214781 original size:6 final size:6
Alignment explanation
Indices: 214772--214882 Score: 98
Period size: 6 Copynumber: 18.5 Consensus size: 6
214762 TCCAGTTCTA
* * * *
214772 GTTTGG GTTTGG GTTTGG GATCGG GTTTGG GATCGG GTTTGG GTTT-G
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * * *
214819 GTTTCGG GTCTGG GTTCGA GTTTGG GTTTGG GTTTAG GTTCGG TTTTGG
1 GTTT-GG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* *
214868 GTTTAG GTTAGG GTT
1 GTTTGG GTTTGG GTT
214883 AGTGTTATAG
Statistics
Matches: 80, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
5 5 0.06
6 71 0.89
7 4 0.05
ACGTcount: A:0.05, C:0.05, G:0.45, T:0.44
Consensus pattern (6 bp):
GTTTGG
Found at i:215582 original size:61 final size:61
Alignment explanation
Indices: 215507--215640 Score: 214
Period size: 61 Copynumber: 2.2 Consensus size: 61
215497 TAGTTGTAAG
*
215507 TTTGTTCAATTTAGTACAAATTTAATGATACAATGTATTAATTTAATCTTCATATTTAAAA
1 TTTGTTCAATTTAGTACAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
* * * * *
215568 TTTGTTCAATTTAGTATAAATTTAATGTTGCAATTTATTAGTTTAAACTTCATATTTAAAA
1 TTTGTTCAATTTAGTACAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
215629 TTTGTTCAATTT
1 TTTGTTCAATTT
215641 GATCCTTATA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.49
Consensus pattern (61 bp):
TTTGTTCAATTTAGTACAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
Found at i:215756 original size:11 final size:10
Alignment explanation
Indices: 215726--215895 Score: 56
Period size: 11 Copynumber: 16.8 Consensus size: 10
215716 ACTAATGAAC
215726 TATATA-ATA
1 TATATATATA
*
215735 TATAGTCTATA
1 TATA-TATATA
215746 TATACTATATA
1 TATA-TATATA
*
215757 GTTTATATATA
1 -TATATATATA
*
215768 CTA-ATAAACTA
1 -TATATATA-TA
215779 TATA-ATATA
1 TATATATATA
* *
215788 TAGTTTATAAA
1 TA-TATATATA
215799 TAT-TAT-TA
1 TATATATATA
215807 TA-ATATATA
1 TATATATATA
215816 TATATATAGT-
1 TATATATA-TA
* *
215826 TCATATGTAAA
1 T-ATATATATA
*
215837 CTATACAT-TA
1 -TATATATATA
*
215847 TATATAAACTA
1 TATATATA-TA
*
215858 TATATGTAGTA
1 TATATATA-TA
215869 TATA-AGTAT-
1 TATATA-TATA
215878 TCATATATATA
1 T-ATATATATA
215889 -ATATATA
1 TATATATA
215896 CTTTGAATTT
Statistics
Matches: 119, Mismatches: 22, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
8 6 0.05
9 28 0.24
10 25 0.21
11 56 0.47
12 4 0.03
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (10 bp):
TATATATATA
Found at i:215763 original size:51 final size:51
Alignment explanation
Indices: 215691--215819 Score: 168
Period size: 51 Copynumber: 2.5 Consensus size: 51
215681 GTTTATATTA
* * *
215691 ATAAATTAATATATAGGTTATATATACTAATGAACTATATAATATATAGTCT
1 ATAAA-TACTATATAGTTTATATATACTAATAAACTATATAATATATAGTCT
* *
215743 ATATATACTATATAGTTTATATATACTAATAAACTATATAATATATAGTTT
1 ATAAATACTATATAGTTTATATATACTAATAAACTATATAATATATAGTCT
* * *
215794 ATAAATATTATTATAATATATATATA
1 ATAAATACTA-TATAGTTTATATATA
215820 TATAGTTCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
51 50 0.75
52 17 0.25
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (51 bp):
ATAAATACTATATAGTTTATATATACTAATAAACTATATAATATATAGTCT
Found at i:215781 original size:33 final size:33
Alignment explanation
Indices: 215742--215831 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 33
215732 ATATATAGTC
215742 TATATATACTATATAGTTTATATATACTA-ATAA
1 TATATATA-TATATAGTTTATATATACTATATAA
* *
215775 -ACTATATAATATATAGTTTATAAATATTATTATAA
1 TA-TATAT-ATATATAGTTTATATATACTA-TATAA
*
215810 TATATATATATATAGTTCATAT
1 TATATATATATATAGTTTATAT
215832 GTAAACTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
32 1 0.02
33 23 0.48
34 14 0.29
35 9 0.19
36 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (33 bp):
TATATATATATATAGTTTATATATACTATATAA
Found at i:215910 original size:2 final size:2
Alignment explanation
Indices: 215726--215895 Score: 56
Period size: 2 Copynumber: 84.0 Consensus size: 2
215716 ACTAATGAAC
* *
215726 TA TA TA -A TA TA TA GTC TA TA TA TA CTA TA TA GTT 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
* * *
215768 CTA -A TA AA CTA TA TA -A TA TA TA GTT TA TA AA TA T- TA T- TA
1 -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
215807 TA -A TA TA TA TA TA TA TA GT- TCA TA TG TA AA CTA TA CA T- TA
1 TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA -TA TA TA TA TA
* *
215847 TA TA TA AA CTA TA TA TG TA GTA TA TA -A GTA T- TCA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA TA -TA TA T-A TA TA TA TA
215889 -A TA TA TA
1 TA TA TA TA
215896 CTTTGAATTT
Statistics
Matches: 124, Mismatches: 20, Indels: 48
0.65 0.10 0.25
Matches are distributed among these distances:
1 11 0.09
2 97 0.78
3 16 0.13
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:215937 original size:27 final size:27
Alignment explanation
Indices: 215907--216011 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
215897 TTTGAATTTA
* * * ** *
215907 TATAGTATAAATTATATAAGTAAAAAT
1 TATAGTATATAGTATATAAATATCAAC
215934 TATA-TATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
215960 TATAGTATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
215987 TATAGTATATAGTATATAAATATCA
1 TATAGTATATAGTATATAAATATCA
216012 TTACAGTTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
26 20 0.28
27 51 0.72
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATCAAC
Found at i:216189 original size:31 final size:32
Alignment explanation
Indices: 216151--216281 Score: 117
Period size: 31 Copynumber: 4.1 Consensus size: 32
216141 ATAAATAGTT
* *
216151 TATATAGTTCATACGTAAACTATATA-TTTTA
1 TATATAGTTCATATGTAAACTATATACTTATA
*
216182 TATATAGTTCATATGTAAACTACTAAACTATATA
1 TATATAGTTCATATGTAAACTA-TATACT-TATA
* * * *
216216 TATTATAGTTTACTA-GT-TATTATATAGTTTATA
1 TA-TATAGTTCA-TATGTAAACTATATA-CTTATA
*
216249 CATATAGTTCATATGTAAACTATATA-TTATA
1 TATATAGTTCATATGTAAACTATATACTTATA
216280 TA
1 TA
216282 GTTTACATAT
Statistics
Matches: 79, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
31 29 0.37
32 13 0.16
33 16 0.20
34 9 0.11
35 10 0.13
36 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (32 bp):
TATATAGTTCATATGTAAACTATATACTTATA
Found at i:216390 original size:2 final size:2
Alignment explanation
Indices: 216378--216786 Score: 106
Period size: 2 Copynumber: 208.5 Consensus size: 2
216368 AACCCTAACC
* *
216378 AT AT A- AT AT AT AT AT AT -T AT AA ACT AT AT AT -T TT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
216417 A- AT AA AGT AT AT A- AT TT AT AC AT AGT AT AT AT -T ACT -T AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT
* * *
216456 A- AT AT AC AT AT AT A- AT AT A- ACT -T GT AT AGT TT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT
* * * *
216495 AT -T CAT AT AG AT AT AT AA ACT AT AT AGT AT AT GGT AT AT AT AG
1 AT AT -AT AT AT AT AT AT AT A-T AT AT A-T AT AT -AT AT AT AT AT
* * *
216538 AT -T AT AC AT A- AT AT AT AT AT AGT -T TT AT AT A- AC AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
216576 AT A- AT AT A- AT AT AA ACT AT AGT TT TT AT -T AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * *
216616 AT AT AA AGT AT AT AGT TT AT A- AT A- AT AT AGT TT AT AC AT AC
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * *
216657 AT AT AT AT AT AT A- AT AT AA AT AT AA ACT AT AA AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
* * *
216700 AGT AT AT A- AT AT AT AT ACT TT AT AT AT AC ACT AT AT A- AT TT
1 A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* *
216741 AT AT -T A- AT AA ACT AT AT AGT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
216783 -T AT A
1 AT AT A
216787 ATGTTTCAAA
Statistics
Matches: 295, Mismatches: 58, Indels: 108
0.64 0.13 0.23
Matches are distributed among these distances:
1 31 0.11
2 240 0.81
3 24 0.08
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:216398 original size:11 final size:11
Alignment explanation
Indices: 216378--216786 Score: 92
Period size: 11 Copynumber: 36.9 Consensus size: 11
216368 AACCCTAACC
216378 ATATAATATAT
1 ATATAATATAT
* *
216389 ATATATTATAA
1 ATATAATATAT
*
216400 ACTAT-ATATTTT
1 A-TATAATA-TAT
*
216412 ATATTAATAAAGT
1 ATA-TAATATA-T
*
216425 ATATAATTTAT
1 ATATAATATAT
* *
216436 ACATAGTATAT
1 ATATAATATAT
*
216447 AT-TACT-TAT
1 ATATAATATAT
*
216456 A-AT-ATACAT
1 ATATAATATAT
216465 ATATAATATAACTT
1 ATATAATAT-A--T
* * *
216479 GTATAGTTTAT
1 ATATAATATAT
216490 ATATAAT-TCAT
1 ATATAATAT-AT
*
216501 ATA-GATATAT
1 ATATAATATAT
*
216511 A-A-ACTATAT
1 ATATAATATAT
*
216520 AGTAT-ATGGTAT
1 A-TATAAT-ATAT
216532 ATATAGAT-TAT
1 ATATA-ATATAT
*
216543 ACATAATATAT
1 ATATAATATAT
* *
216554 ATATAGT-TTT
1 ATATAATATAT
*
216564 ATATAACATAT
1 ATATAATATAT
216575 A-ATAATATA-
1 ATATAATATAT
216584 ATATAA-ACTAT
1 ATATAATA-TAT
*
216595 AGT-T--TTTAT
1 A-TATAATATAT
216604 -TATAATATAT
1 ATATAATATAT
*
216614 ATAT-ATAAAGT
1 ATATAATATA-T
* *
216625 ATATAGTTTAT
1 ATATAATATAT
216636 A-ATAATATAGT
1 ATATAATATA-T
* *
216647 TTATACATACAT
1 ATATA-ATATAT
216659 ATAT-ATATAT
1 ATATAATATAT
*
216669 AATATAAATATAA
1 -ATAT-AATATAT
*
216682 ACTATAAAGTTTAT
1 A-TAT-AA-TATAT
*
216696 ATATAGTATAT
1 ATATAATATAT
216707 A-ATATATATACT
1 ATATA-ATATA-T
* *
216719 TTATATATACACT
1 ATATA-ATATA-T
*
216732 ATATAATTTAT
1 ATATAATATAT
*
216743 AT-TAATAAACT
1 ATATAATATA-T
* *
216754 ATATAGTTTAT
1 ATATAATATAT
216765 ATATATATATAT
1 ATATA-ATATAT
*
216777 ATATATTATA
1 ATATAATATA
216787 ATGTTTCAAA
Statistics
Matches: 285, Mismatches: 66, Indels: 94
0.64 0.15 0.21
Matches are distributed among these distances:
7 1 0.00
8 2 0.01
9 20 0.07
10 60 0.21
11 104 0.36
12 45 0.16
13 42 0.15
14 11 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (11 bp):
ATATAATATAT
Found at i:216643 original size:15 final size:15
Alignment explanation
Indices: 216625--216674 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
216615 TATATAAAGT
216625 ATATAGTTTATAATA
1 ATATAGTTTATAATA
216640 ATATAGTTTATACATA
1 ATATAGTTTATA-ATA
*
216656 CATATA-TATAT-ATA
1 -ATATAGTTTATAATA
216670 ATATA
1 ATATA
216675 AATATAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 3 0.09
15 12 0.38
16 7 0.22
17 5 0.16
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (15 bp):
ATATAGTTTATAATA
Found at i:216705 original size:9 final size:8
Alignment explanation
Indices: 216693--216786 Score: 63
Period size: 9 Copynumber: 11.8 Consensus size: 8
216683 CTATAAAGTT
216693 TATATATA
1 TATATATA
216701 GTATATA-A
1 -TATATATA
216709 TATATATA
1 TATATATA
*
216717 CTTTATATA
1 -TATATATA
*
216726 TACACTATA
1 TATA-TATA
*
216735 TA-ATTTA
1 TATATATA
216742 TAT-TA-A
1 TATATATA
*
216748 TAAACTATA
1 TATA-TATA
*
216757 TAGTTTATA
1 TA-TATATA
216766 TATATATA
1 TATATATA
216774 TATATATA
1 TATATATA
216782 T-TATA
1 TATATA
216787 ATGTTTCAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
6 3 0.04
7 16 0.24
8 21 0.31
9 28 0.41
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (8 bp):
TATATATA
Found at i:216706 original size:27 final size:27
Alignment explanation
Indices: 216676--216727 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
216666 TATAATATAA
*
216676 ATATAA-ACTATAAAGTTTATATATAGT
1 ATATAATA-TATAAACTTTATATATAGT
*
216703 ATATAATATATATACTTTATATATA
1 ATATAATATATAAACTTTATATATA
216728 CACTATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
ATATAATATATAAACTTTATATATAGT
Found at i:216712 original size:47 final size:45
Alignment explanation
Indices: 216563--216744 Score: 55
Period size: 47 Copynumber: 4.0 Consensus size: 45
216553 TATATAGTTT
*
216563 TATATA-ACATATA-ATAATAT-AATATAAACTAT--AGTTT-T-
1 TATATATATATATATATAATATAAATATAAACTATAAAGTTTATA
* * * *
216601 TAT-TATA-ATATATAT-ATATAAAGTATATAGTTTATAA-TAATATA
1 TATATATATATATATATAATATAAA-TATAAACTATA-AAGT-TTATA
* * *
216645 GTTTATACATACATATATATATATAATATAAATATAAACTATAAAGTTTATA
1 -TATATATATATATATATA-ATATAA-AT--ATA-AA-CTATAAAGTTTATA
* * * *
216697 TATAGTATATAATATATATACTTTATATATACACTATATAA-TTTATA
1 TATA-TATAT-ATATATATAATATAAATATAAACTATA-AAGTTTATA
216744 T
1 T
216745 TAATAAACTA
Statistics
Matches: 102, Mismatches: 18, Indels: 39
0.64 0.11 0.25
Matches are distributed among these distances:
37 11 0.11
38 8 0.08
39 7 0.07
41 1 0.01
42 2 0.02
43 1 0.01
45 2 0.02
46 3 0.03
47 19 0.19
48 3 0.03
49 10 0.10
50 1 0.01
51 8 0.08
52 14 0.14
53 12 0.12
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (45 bp):
TATATATATATATATATAATATAAATATAAACTATAAAGTTTATA
Found at i:216770 original size:71 final size:72
Alignment explanation
Indices: 216624--216782 Score: 206
Period size: 69 Copynumber: 2.3 Consensus size: 72
216614 ATATATAAAG
* *
216624 TATATAGTTTATAATA-ATATAGTTTATACATACATATATATATATAATATAAATATAAACTATA
1 TATATAGTATATAATATATATACTTTATACATACATATATATATATAATATAAATATAAACTATA
216688 AAGTTTA
66 AAGTTTA
* * *
216695 TATATAGTATATAATATATATACTTTATATATACACTATATA-AT-TTATAT-TA-ATAAACTAT
1 TATATAGTATATAATATATATACTTTATACATACA-TATATATATATAATATAAATATAAACTAT
*
216756 ATAGTTTA
65 AAAGTTTA
216764 TATATA-TATAT-ATATATAT
1 TATATAGTATATAATATATAT
216783 TATAATGTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
67 8 0.10
68 5 0.06
69 22 0.28
70 1 0.01
71 20 0.25
72 18 0.22
73 6 0.08
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (72 bp):
TATATAGTATATAATATATATACTTTATACATACATATATATATATAATATAAATATAAACTATA
AAGTTTA
Found at i:221498 original size:10 final size:9
Alignment explanation
Indices: 221474--221529 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
221464 GGCTGCTAGA
*
221474 AACCGGTTA
1 AACCGGTTT
221483 AACCGGTTT
1 AACCGGTTT
221492 CAACCGGTTAT
1 -AACCGGTT-T
*
221503 GACCGGTTT
1 AACCGGTTT
*
221512 GACCGGTTT
1 AACCGGTTT
221521 CAACCGGTT
1 -AACCGGTT
221530 CGAATCGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 18 0.44
10 22 0.54
11 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:221498 original size:19 final size:18
Alignment explanation
Indices: 221474--221529 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
221464 GGCTGCTAGA
221474 AACCGGTTAAACCGGTTT
1 AACCGGTTAAACCGGTTT
*
221492 CAACCGGTTATGACCGGTTT
1 -AACCGGTTA-AACCGGTTT
* *
221512 GACCGGTTTCAACCGGTT
1 AACCGG-TTAAACCGGTT
221530 CGAATCGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (18 bp):
AACCGGTTAAACCGGTTT
Found at i:221577 original size:17 final size:17
Alignment explanation
Indices: 221575--221609 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
221565 CCCGACCCGA
221575 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
*
221592 CCGACCCGACTGTTGAC
1 CCGACCCGACCGTTGAC
221609 C
1 C
221610 GTTGACCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:228703 original size:9 final size:10
Alignment explanation
Indices: 228689--228736 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
228679 GGCTGCGAGA
228689 AACCGGTTT-
1 AACCGGTTTC
228698 AACCGGTTTTC
1 AACCGG-TTTC
228709 AACCGGTTAT-
1 AACCGGTT-TC
*
228719 GACCGGTTTC
1 AACCGGTTTC
228729 AACCGGTT
1 AACCGGTT
228737 CGAATCGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.21
10 19 0.58
11 7 0.21
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:228714 original size:20 final size:20
Alignment explanation
Indices: 228689--228736 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
228679 GGCTGCGAGA
228689 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTATAACCGG-TTTC
*
228709 AACCGGTTATGACCGGTTTC
1 AACCGGTTATAACCGGTTTC
228729 AACCGGTT
1 AACCGGTT
228737 CGAATCGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (20 bp):
AACCGGTTATAACCGGTTTC
Found at i:228746 original size:30 final size:28
Alignment explanation
Indices: 228690--228754 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
228680 GCTGCGAGAA
228690 ACCGGTTTAACCGGTTTTCAACCGGTTATG
1 ACCGGTTTAACCGG-TTTCAACCGGTT-TG
*
228720 ACCGGTTTCAACCGG-TTCGAATCGGTTTG
1 ACCGGTTT-AACCGGTTTC-AACCGGTTTG
228749 ACCGGT
1 ACCGGT
228755 CTGACCCGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 11 0.34
30 15 0.47
31 6 0.19
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (28 bp):
ACCGGTTTAACCGGTTTCAACCGGTTTG
Found at i:228777 original size:16 final size:16
Alignment explanation
Indices: 228756--228809 Score: 99
Period size: 16 Copynumber: 3.3 Consensus size: 16
228746 TTGACCGGTC
228756 TGACCCGACCCGACGT
1 TGACCCGACCCGACGT
228772 TGACCCGACCCGACGT
1 TGACCCGACCCGACGT
228788 TGACCCGACCCGACCGT
1 TGACCCGACCCGA-CGT
228805 TGACC
1 TGACC
228810 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 29 0.78
17 8 0.22
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.13
Consensus pattern (16 bp):
TGACCCGACCCGACGT
Found at i:230895 original size:16 final size:16
Alignment explanation
Indices: 230874--230940 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
230864 TTTATGCTCG
230874 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
230890 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
230906 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
230922 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
230936 TTTAT
1 TTTAT
230941 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:230912 original size:32 final size:32
Alignment explanation
Indices: 230871--230932 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
230861 ACGTTTATGC
230871 TCGTTTATGTTCGTGTTCATTTATGTTCGTGT
1 TCGTTTATGTTCGTGTTCATTTATGTTCGTGT
*
230903 TCGTTTATGTTCGTGTTCGTTTATGTTCGT
1 TCGTTTATGTTCGTGTTCATTTATGTTCGT
230933 TTATTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
TCGTTTATGTTCGTGTTCATTTATGTTCGTGT
Found at i:231853 original size:20 final size:21
Alignment explanation
Indices: 231805--231864 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
231795 AACTCAGTTT
*
231805 TCAA-ATTCGCAACGCGAATA
1 TCAAGATTCGCAACGCGATTA
* *
231825 TCCAGATTCGCAACGCGATTG
1 TCAAGATTCGCAACGCGATTA
231846 T-AAGATTCGCAACGCGATT
1 TCAAGATTCGCAACGCGATT
231865 TTGAAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGATTCGCAACGCGATTA
Found at i:231918 original size:22 final size:22
Alignment explanation
Indices: 231864--231920 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
231854 GCAACGCGAT
*
231864 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
231886 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
231905 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
231921 TTGCGATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 16 0.53
20 2 0.07
21 2 0.07
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:231935 original size:22 final size:19
Alignment explanation
Indices: 231869--231935 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
231859 GCGATTTTGA
*
231869 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
231888 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
231909 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
231932 AAAA
1 AAAA
231936 ATCCAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 16 0.41
21 1 0.03
22 8 0.21
23 2 0.05
24 2 0.05
25 10 0.26
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:232309 original size:19 final size:20
Alignment explanation
Indices: 232276--232331 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
232266 TTGCGATTTT
**
232276 GAACTTGGACTATCGCAA-C
1 GAACTTGGAAAATCGCAACC
*
232295 GAATTTGGAAAATCGCAACGC
1 GAACTTGGAAAATCGCAAC-C
232316 GAACTTGGAAAATCGC
1 GAACTTGGAAAATCGC
232332 GTTGCGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (20 bp):
GAACTTGGAAAATCGCAACC
Found at i:232338 original size:21 final size:21
Alignment explanation
Indices: 232287--232347 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
232277 AACTTGGACT
232287 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAATTTGGAAA
*
232306 ATCGCAACGCGAACTTGGAAA
1 ATCGCAACGCGAATTTGGAAA
***
232327 ATCGCGTTGCGAATTTGGAAA
1 ATCGCAACGCGAATTTGGAAA
232348 CTGAGTTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 7 0.20
21 28 0.80
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAATTTGGAAA
Found at i:238075 original size:20 final size:21
Alignment explanation
Indices: 238039--238080 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
238029 TTTTAGTCGC
*
238039 TCAATTTTAATA-TTTTTAAT
1 TCAATTTTAATACTTTTGAAT
238059 TCAATTGTTAA-ACTTTTGAAT
1 TCAATT-TTAATACTTTTGAAT
238080 T
1 T
238081 ATTCATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCAATTTTAATACTTTTGAAT
Found at i:240223 original size:16 final size:17
Alignment explanation
Indices: 240202--240233 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
240192 CCATCTATGC
240202 TCTTCA-TTTTAACTTA
1 TCTTCATTTTTAACTTA
240218 TCTTCATTTTTAACTT
1 TCTTCATTTTTAACTT
240234 CTATTAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (17 bp):
TCTTCATTTTTAACTTA
Found at i:240980 original size:40 final size:40
Alignment explanation
Indices: 240891--241004 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
240881 GTTCGGTTCG
** * * * *
240891 TTTATGTTCATGAACAAGCTTTTTTATC-AACTC-GTACA
1 TTTATGTTCATGAACAAGCTCGTTTACCTGATTCTTTACA
*
240929 TTTATGTTCATGAACAAGCTCGTTTACCTGGTTCTTTACA
1 TTTATGTTCATGAACAAGCTCGTTTACCTGATTCTTTACA
240969 TTTATGTTCATGAACAAGCTCGTTTACCTGATTCTT
1 TTTATGTTCATGAACAAGCTCGTTTACCTGATTCTT
241005 CTTTTTCTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
38 25 0.38
39 2 0.03
40 39 0.59
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (40 bp):
TTTATGTTCATGAACAAGCTCGTTTACCTGATTCTTTACA
Found at i:243862 original size:3 final size:3
Alignment explanation
Indices: 243850--243878 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
243840 ATGGGAATTG
243850 TGT T-T TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
243879 ATAGGTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TGT
Found at i:246365 original size:21 final size:21
Alignment explanation
Indices: 246341--246409 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
246331 AAATAAAGGC
246341 TAAATTATAGAAAACGTGTCA
1 TAAATTATAGAAAACGTGTCA
** *
246362 TAAAACAGAGAAAATCGTGTCA
1 TAAATTATAGAAAA-CGTGTCA
* *
246384 TGAAATT-TATTAAAACGTGACA
1 T-AAATTATA-GAAAACGTGTCA
246406 TAAA
1 TAAA
246410 GACAACATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
21 14 0.38
22 16 0.43
23 7 0.19
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.26
Consensus pattern (21 bp):
TAAATTATAGAAAACGTGTCA
Found at i:246464 original size:29 final size:26
Alignment explanation
Indices: 246408--246458 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
246398 ACGTGACATA
246408 AAGACAACATTATTAAACAATAAAAT
1 AAGACAACATTATTAAACAATAAAAT
246434 AAGACAACATTATTAAACAATAAAA
1 AAGACAACATTATTAAACAATAAAA
246459 AAATAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.63, C:0.12, G:0.04, T:0.22
Consensus pattern (26 bp):
AAGACAACATTATTAAACAATAAAAT
Found at i:247751 original size:2 final size:2
Alignment explanation
Indices: 247744--247773 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
247734 GTAAAATAAG
247744 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
247774 CATTGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.