Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 20 of 27
Found at i:2961083 original size:20 final size:20
Alignment explanation
Indices: 2961042--2961080 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2961032 CATTATTCTA
2961042 AATTTTTTATAATTATATTT
1 AATTTTTTATAATTATATTT
2961062 AATTTTTTAT-ATTATATTT
1 AATTTTTTATAATTATATTT
2961081 TAAATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTTTATAATTATATTT
Found at i:2962163 original size:66 final size:66
Alignment explanation
Indices: 2962092--2962294 Score: 370
Period size: 66 Copynumber: 3.1 Consensus size: 66
2962082 TGTTCAATGC
* *
2962092 TTTATTATTAAATATATATTTTAATATAACAAATATTTCAGTTCAGTAAGATAATATTTTCAATT
1 TTTATTATTACATATATATTTCAATATAACAAATATTTCAGTTCAGTAAGATAATATTTTCAATT
2962157 T
66 T
2962158 TTTATTATTACATATATATTTCAATATAACAAATATTTCAGTTCAGTAAGATAATATTTTCAATT
1 TTTATTATTACATATATATTTCAATATAACAAATATTTCAGTTCAGTAAGATAATATTTTCAATT
2962223 T
66 T
* *
2962224 TTTATTATTACATATATATTTCAATATAACAAATATTCCAGTTCAGTAAGATAATATTTTTAATT
1 TTTATTATTACATATATATTTCAATATAACAAATATTTCAGTTCAGTAAGATAATATTTTCAATT
2962289 T
66 T
2962290 TTTAT
1 TTTAT
2962295 AATAAATTTT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 133 1.00
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.48
Consensus pattern (66 bp):
TTTATTATTACATATATATTTCAATATAACAAATATTTCAGTTCAGTAAGATAATATTTTCAATT
T
Found at i:2963130 original size:22 final size:22
Alignment explanation
Indices: 2963102--2963144 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2963092 AATAGGTTAG
2963102 ATAAACGCTTAAAGTTGCTTTA
1 ATAAACGCTTAAAGTTGCTTTA
* *
2963124 ATAAACGTTTAAGGTTGCTTT
1 ATAAACGCTTAAAGTTGCTTT
2963145 GATGAACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
ATAAACGCTTAAAGTTGCTTTA
Found at i:2963195 original size:16 final size:16
Alignment explanation
Indices: 2963168--2963204 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2963158 TTATTAATTA
2963168 TAATTAAGTTTATATT
1 TAATTAAGTTTATATT
2963184 GTAATT-AGTTTATATT
1 -TAATTAAGTTTATATT
2963200 TAATT
1 TAATT
2963205 TGCATTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 10 0.50
17 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (16 bp):
TAATTAAGTTTATATT
Found at i:2963882 original size:43 final size:43
Alignment explanation
Indices: 2963833--2963915 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
2963823 CAATATTATG
*
2963833 ATAATTTATACTATGATGAACTGATATGTTAAATATTAAGAAA
1 ATAATTTATACTATGATGAACTGATAGGTTAAATATTAAGAAA
* *
2963876 ATAATTTATACTATGTTGAGCTGATAGGTTAAATATTAAG
1 ATAATTTATACTATGATGAACTGATAGGTTAAATATTAAG
2963916 TACTGAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (43 bp):
ATAATTTATACTATGATGAACTGATAGGTTAAATATTAAGAAA
Found at i:2964981 original size:18 final size:19
Alignment explanation
Indices: 2964958--2964996 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2964948 ATATAAATGT
2964958 ATAAAAGT-AAAAAAAAAA
1 ATAAAAGTGAAAAAAAAAA
* *
2964976 ATAAAATTGATAAAAAAAA
1 ATAAAAGTGAAAAAAAAAA
2964995 AT
1 AT
2964997 TAGATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (19 bp):
ATAAAAGTGAAAAAAAAAA
Found at i:2966645 original size:20 final size:20
Alignment explanation
Indices: 2966622--2966668 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2966612 TTTTAATATT
2966622 TATTT-ATAGTTAAAATTATA
1 TATTTAATA-TTAAAATTATA
*
2966642 TATTTAATATTTAAATTAT-
1 TATTTAATATTAAAATTATA
2966661 T-TTTAATA
1 TATTTAATA
2966669 CTATCTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 1 0.04
20 14 0.56
21 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTTAATATTAAAATTATA
Found at i:2967497 original size:6 final size:6
Alignment explanation
Indices: 2967486--2967518 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2967476 TATAATCTAC
2967486 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
2967519 AATTACACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTAT
Found at i:2968401 original size:15 final size:16
Alignment explanation
Indices: 2968383--2968412 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2968373 ATTTTATGAA
2968383 AAAGAAAAAG-GAAAG
1 AAAGAAAAAGAGAAAG
2968398 AAAGAAAAAGAGAAA
1 AAAGAAAAAGAGAAA
2968413 AAATTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAGAAAG
Found at i:2968961 original size:16 final size:16
Alignment explanation
Indices: 2968934--2968974 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2968924 ATTTTTAAAT
2968934 AAATTTTA-TTAATTA
1 AAATTTTATTTAATTA
*
2968949 TAATTTTATTTAATTA
1 AAATTTTATTTAATTA
2968965 AAATATTTAT
1 AAAT-TTTAT
2968975 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 10 0.45
17 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTTTATTTAATTA
Found at i:2969139 original size:15 final size:14
Alignment explanation
Indices: 2969115--2969149 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2969105 CTTGGGTGAA
*
2969115 AAAGAAAGAAGAAAG
1 AAAGAGAGAAG-AAG
2969130 AAAGAGAGAAGAAG
1 AAAGAGAGAAGAAG
2969144 AAAGAG
1 AAAGAG
2969150 TGAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AAAGAGAGAAGAAG
Found at i:2969216 original size:10 final size:10
Alignment explanation
Indices: 2969201--2969259 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
2969191 TTTAAAATAT
2969201 TATATTTTTA
1 TATATTTTTA
2969211 TATATTTTT-
1 TATATTTTTA
* *
2969220 TATATATTAA
1 TATATTTTTA
*
2969230 TA-ATTTATTT
1 TATATTT-TTA
*
2969240 TA-ATTTATA
1 TATATTTTTA
2969249 TATATTTTTA
1 TATATTTTTA
2969259 T
1 T
2969260 GTATAATTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
9 13 0.34
10 25 0.66
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TATATTTTTA
Found at i:2969239 original size:32 final size:31
Alignment explanation
Indices: 2969169--2969240 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
2969159 TATATATATG
* *
2969169 TTTATATTTATAATTTTTTGTATTTAAAATA
1 TTTATTTTTATAATTTTTTATATTTAAAATA
*
2969200 TTATATTTTTATATATTTTTTATATATTAATA-A
1 TT-TATTTTTATA-ATTTTTTATAT-TTAAAATA
2969233 TTTATTTT
1 TTTATTTT
2969241 AATTTATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 2 0.06
32 15 0.43
33 13 0.37
34 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (31 bp):
TTTATTTTTATAATTTTTTATATTTAAAATA
Found at i:2969273 original size:16 final size:16
Alignment explanation
Indices: 2969229--2969275 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2969219 TTATATATTA
*
2969229 ATAATTTATTTTAATTT
1 ATAATTTATTTT-ATGT
*
2969246 AT-ATATATTTTTATGT
1 ATAATTTA-TTTTATGT
2969262 ATAATTTATTTTAT
1 ATAATTTATTTTAT
2969276 ATATGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
ATAATTTATTTTATGT
Found at i:2969319 original size:13 final size:13
Alignment explanation
Indices: 2969301--2969325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2969291 TTTAAGTGTT
2969301 TATATTTTTTATG
1 TATATTTTTTATG
2969314 TATATTTTTTAT
1 TATATTTTTTAT
2969326 TATTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TATATTTTTTATG
Found at i:2969361 original size:19 final size:19
Alignment explanation
Indices: 2969333--2969397 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
2969323 TATTATTGAA
2969333 AATA-TTATAAATTTATGT
1 AATATTTATAAATTTATGT
*
2969351 AATATTTATAAATATT-TTT
1 AATATTTATAAAT-TTATGT
* * *
2969370 TATATTTGTATATTTATGT
1 AATATTTATAAATTTATGT
*
2969389 CATATTTAT
1 AATATTTAT
2969398 TTTTTTGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 6 0.16
19 29 0.78
20 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
AATATTTATAAATTTATGT
Found at i:2969976 original size:31 final size:32
Alignment explanation
Indices: 2969940--2970001 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
2969930 AATAAAATAA
* *
2969940 ATTTATATAAATTTTTACATGTTAAT-TATTT
1 ATTTATATAAATTTTGACATATTAATGTATTT
* *
2969971 ATTTATTTATATTTTGACATATTAATGTATT
1 ATTTATATAAATTTTGACATATTAATGTATT
2970002 CGTACCGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (32 bp):
ATTTATATAAATTTTGACATATTAATGTATTT
Found at i:2971889 original size:16 final size:16
Alignment explanation
Indices: 2971870--2971954 Score: 80
Period size: 16 Copynumber: 5.2 Consensus size: 16
2971860 TTTGATATAG
2971870 TTTAGATTTGAATTTA
1 TTTAGATTTGAATTTA
* *
2971886 TTTAAATTTGAGTTTA
1 TTTAGATTTGAATTTA
*
2971902 TTTAGATTTAAATTTA
1 TTTAGATTTGAATTTA
* * *
2971918 TTTGGATTTAGATTTTGG
1 TTTAGATTT-GAATTT-A
* *
2971936 TTTGGATTTAAATTTA
1 TTTAGATTTGAATTTA
2971952 TTT
1 TTT
2971955 TATATTATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
16 38 0.69
17 8 0.15
18 9 0.16
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (16 bp):
TTTAGATTTGAATTTA
Found at i:2971896 original size:32 final size:32
Alignment explanation
Indices: 2971860--2971920 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2971850 TAGATTGTAG
*
2971860 TTTGA-TATAGTTTAGATTTGAATTTATTTAAA
1 TTTGAGTATA-TTTAGATTTAAATTTATTTAAA
*
2971892 TTTGAGTTTATTTAGATTTAAATTTATTT
1 TTTGAGTATATTTAGATTTAAATTTATTT
2971921 GGATTTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (32 bp):
TTTGAGTATATTTAGATTTAAATTTATTTAAA
Found at i:2971911 original size:22 final size:21
Alignment explanation
Indices: 2971885--2971932 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2971875 ATTTGAATTT
2971885 ATTTAAATTTGAGTTT-ATTTAG
1 ATTTAAATTT-A-TTTGATTTAG
2971907 ATTTAAATTTATTTGGATTTAG
1 ATTTAAATTTATTT-GATTTAG
2971929 ATTT
1 ATTT
2971933 TGGTTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.12
21 1 0.04
22 20 0.83
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
ATTTAAATTTATTTGATTTAG
Found at i:2971983 original size:24 final size:24
Alignment explanation
Indices: 2971956--2972015 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
2971946 AATTTATTTT
*
2971956 ATATTATTTTTTATTTTAT-ATTAA
1 ATATTATTTTTT-TTATATAATTAA
* * *
2971980 ATATAATTATTTTTATATAATTTA
1 ATATTATTTTTTTTATATAATTAA
2972004 ATATTTATTTTT
1 ATA-TTATTTTT
2972016 AAAAAGTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 5 0.18
24 17 0.61
25 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
ATATTATTTTTTTTATATAATTAA
Found at i:2972053 original size:27 final size:29
Alignment explanation
Indices: 2972019--2972086 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
2972009 TATTTTTAAA
2972019 AAGTAAA-TTATTAAATTATTA-ATTTTT
1 AAGTAAATTTATTAAATTATTATATTTTT
*
2972046 AAGTAAATTTTTATTATATTATTATATTTTT
1 AAGTAAA--TTTATTAAATTATTATATTTTT
*
2972077 AA-TATATTTA
1 AAGTAAATTTA
2972087 ATTATTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 7 0.20
28 4 0.11
30 16 0.46
31 8 0.23
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
AAGTAAATTTATTAAATTATTATATTTTT
Found at i:2972092 original size:19 final size:19
Alignment explanation
Indices: 2972052--2972093 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2972042 TTTTAAGTAA
* *
2972052 ATTTTTATTATATTATTAT
1 ATTTTTAATATATTAATAT
2972071 ATTTTTAATATATTTAAT-T
1 ATTTTTAATATA-TTAATAT
2972090 ATTT
1 ATTT
2972094 ATTTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTAATATATTAATAT
Found at i:2972138 original size:16 final size:16
Alignment explanation
Indices: 2972117--2972159 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
2972107 TATATTTATA
2972117 TATATAATTAATTTGT
1 TATATAATTAATTTGT
*
2972133 TATATAAAATTAATTTTT
1 TATAT--AATTAATTTGT
*
2972151 TAAATAATT
1 TATATAATT
2972160 TATTATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TATATAATTAATTTGT
Found at i:2972157 original size:18 final size:18
Alignment explanation
Indices: 2972122--2972157 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2972112 TTATATATAT
*
2972122 AATTAATTTGTTATATAA
1 AATTAATTTGTTAAATAA
*
2972140 AATTAATTTTTTAAATAA
1 AATTAATTTGTTAAATAA
2972158 TTTATTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTAATTTGTTAAATAA
Found at i:2973363 original size:16 final size:16
Alignment explanation
Indices: 2973319--2973374 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
2973309 AAATTCGGGT
2973319 TCGGGTTTGGG-TCAATC
1 TCGGGTTTGGGTTC--TC
* *
2973336 TTGGGTTCGGGTTCTC
1 TCGGGTTTGGGTTCTC
*
2973352 TCGGGTTTGGGTTCTT
1 TCGGGTTTGGGTTCTC
2973368 TCGGGTT
1 TCGGGTT
2973375 CGGGCTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 22 0.67
17 9 0.27
18 2 0.06
ACGTcount: A:0.04, C:0.16, G:0.38, T:0.43
Consensus pattern (16 bp):
TCGGGTTTGGGTTCTC
Found at i:2973391 original size:16 final size:16
Alignment explanation
Indices: 2973372--2973426 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
2973362 GTTCTTTCGG
*
2973372 GTTCGGGCTTTTTTGA
1 GTTCGGGCTTTCTTGA
*
2973388 GTTCGGGCTTTCTTGG
1 GTTCGGGCTTTCTTGA
* * *
2973404 GTTCGGGCTATCTCGG
1 GTTCGGGCTTTCTTGA
2973420 GTTCGGG
1 GTTCGGG
2973427 TAATTTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.04, C:0.18, G:0.38, T:0.40
Consensus pattern (16 bp):
GTTCGGGCTTTCTTGA
Found at i:2973424 original size:32 final size:30
Alignment explanation
Indices: 2973334--2973427 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 30
2973324 TTTGGGTCAA
* * *
2973334 TCTTGGGTTCGGGTTCTCTCGGGTTTGGGT
1 TCTTGGGTTCGGGCTATCTCGGGTTCGGGT
* * * *
2973364 TCTTTCGGGTTCGGGCTTTTTTGAGTTCGGGCTT
1 TC-TT-GGGTTCGGGCTATCTCGGGTTCGGG--T
2973398 TCTTGGGTTCGGGCTATCTCGGGTTCGGGT
1 TCTTGGGTTCGGGCTATCTCGGGTTCGGGT
2973428 AATTTTGGAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
30 3 0.06
31 2 0.04
32 40 0.80
33 2 0.04
34 3 0.06
ACGTcount: A:0.02, C:0.18, G:0.37, T:0.43
Consensus pattern (30 bp):
TCTTGGGTTCGGGCTATCTCGGGTTCGGGT
Found at i:2973434 original size:48 final size:48
Alignment explanation
Indices: 2973319--2973434 Score: 110
Period size: 48 Copynumber: 2.4 Consensus size: 48
2973309 AAATTCGGGT
* * * * * * *
2973319 TCGGGTTTGGGTCAATCTTGGGTTCGGGTTCTCTCGGGTTTGGGTTCTT
1 TCGGGTTCGGGT-AATTTTGAGTTCGGGTTCTCTCGGGTTCGGGCTATC
* *
2973368 TCGGGTTCGGGCT-TTTTTGAGTTCGGGCTT-TCTTGGGTTCGGGCTATC
1 TCGGGTTCGGG-TAATTTTGAGTTCGGG-TTCTCTCGGGTTCGGGCTATC
2973416 TCGGGTTCGGGTAATTTTG
1 TCGGGTTCGGGTAATTTTG
2973435 GATTCGCTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
47 1 0.02
48 40 0.74
49 12 0.22
50 1 0.02
ACGTcount: A:0.05, C:0.16, G:0.36, T:0.42
Consensus pattern (48 bp):
TCGGGTTCGGGTAATTTTGAGTTCGGGTTCTCTCGGGTTCGGGCTATC
Found at i:2975411 original size:2 final size:2
Alignment explanation
Indices: 2975404--2975440 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2975394 AAAGCTCTTT
2975404 TA 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 TA T
2975441 TTGTTAGTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2976624 original size:16 final size:18
Alignment explanation
Indices: 2976592--2976628 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
2976582 TATTTTATAT
2976592 TTTAATAATATTGATAAA
1 TTTAATAATATTGATAAA
2976610 TTTAA-AATA-TGATAAA
1 TTTAATAATATTGATAAA
2976626 TTT
1 TTT
2976629 TATATCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 4 0.21
18 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
TTTAATAATATTGATAAA
Found at i:2976630 original size:17 final size:19
Alignment explanation
Indices: 2976590--2976630 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
2976580 TATATTTTAT
2976590 ATTTTAATAATATTGATAA
1 ATTTTAATAATATTGATAA
2976609 A-TTTAA-AATA-TGATAA
1 ATTTTAATAATATTGATAA
2976625 ATTTTA
1 ATTTTA
2976631 TATCATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 5 0.24
19 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTTTAATAATATTGATAA
Found at i:2978598 original size:33 final size:33
Alignment explanation
Indices: 2978556--2978622 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2978546 TACTAGAATC
* *
2978556 AGCATATCTGCGTTCTCCCTTTCCAGCTTGGTT
1 AGCATATCTGCATTCTCCCTTACCAGCTTGGTT
2978589 AGCATATCTGCATTCTCCCTTACCAGCTTGGTT
1 AGCATATCTGCATTCTCCCTTACCAGCTTGGTT
2978622 A
1 A
2978623 TTTATCCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.37
Consensus pattern (33 bp):
AGCATATCTGCATTCTCCCTTACCAGCTTGGTT
Found at i:2978637 original size:23 final size:23
Alignment explanation
Indices: 2978604--2978650 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2978594 ATCTGCATTC
*
2978604 TCCCTTACCAGCTTGGTTATTTA
1 TCCCTTACCAGCTTGGATATTTA
* *
2978627 TCCCTTTCCAGTTTGGATATTTA
1 TCCCTTACCAGCTTGGATATTTA
2978650 T
1 T
2978651 TGAATCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (23 bp):
TCCCTTACCAGCTTGGATATTTA
Found at i:2987248 original size:42 final size:42
Alignment explanation
Indices: 2987187--2987318 Score: 167
Period size: 42 Copynumber: 3.1 Consensus size: 42
2987177 TAGCCCTCAA
* *
2987187 AGAGAAAGAAGAGAAAGGAGGGATGATAGGAGGAGAGACAAG
1 AGAGATAGTAGAGAAAGGAGGGATGATAGGAGGAGAGACAAG
* *
2987229 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACATG
1 AGAGATAGTAGAGAAAGGAGGGATGATAGGAGGAGAGACAAG
* * * * *
2987271 AGAGATAATAGAGAGAGGAAGGATGACAGGAGGACGAGAGAAG
1 AGAGATAGTAGAGAAAGGAGGGATGATAGGAGGA-GAGACAAG
2987314 A-AGAT
1 AGAGAT
2987319 GGAAGAGTGA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 72 0.91
43 7 0.09
ACGTcount: A:0.46, C:0.03, G:0.42, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAAAGGAGGGATGATAGGAGGAGAGACAAG
Found at i:2992228 original size:28 final size:28
Alignment explanation
Indices: 2992188--2992259 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
2992178 GGAATAAAGC
**
2992188 CGGGGTTGGAGTATCCCCTCGGA-AGTAA
1 CGGGGTTGGAGTATCCCCGAGGAGA-TAA
*
2992216 CGGGGTTGGAGTATCCCCGATGAGATAA
1 CGGGGTTGGAGTATCCCCGAGGAGATAA
*
2992244 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2992260 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAGATAA
Found at i:2992409 original size:51 final size:53
Alignment explanation
Indices: 2992281--2992417 Score: 172
Period size: 53 Copynumber: 2.6 Consensus size: 53
2992271 AAATTGGTAT
* * ** *
2992281 TTTTGGAAATAAAATCGAAGTTGGAGTATCCCCAATTAAAGGAAAAATTGGTG
1 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCAATTAAAGGAAAAATTAGTG
**
2992334 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCAATT-GTGGAAAAATTAGTG
1 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCAATTAAAGGAAAAATTAGTG
*
2992386 -TTT-ACTAATAAAACCGGGGTTGGAGTATCCCC
1 TTTTGA-AAATAAAACCGGGGTTGGAGTATCCCC
2992418 TCAAAAATAA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
50 1 0.01
51 29 0.39
52 12 0.16
53 33 0.44
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (53 bp):
TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCAATTAAAGGAAAAATTAGTG
Found at i:2992463 original size:27 final size:27
Alignment explanation
Indices: 2992400--2992475 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
2992390 CTAATAAAAC
* *
2992400 CGGGGTTGGAGTATCCCCTCAAAAATAA
1 CGGGGTTGGAGTATCCCC-GATAAATAA
* *
2992428 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATAAATAA
2992455 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2992476 TGTGAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 26 0.59
28 18 0.41
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:2994833 original size:20 final size:20
Alignment explanation
Indices: 2994806--2994860 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2994796 TAAAATTTCC
*
2994806 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
2994826 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
2994846 AAATGTATCGATACA
1 AAATGTATCGATACA
2994861 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:2994904 original size:19 final size:18
Alignment explanation
Indices: 2994880--2994951 Score: 84
Period size: 19 Copynumber: 4.2 Consensus size: 18
2994870 CAGTAGCTAA
2994880 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2994899 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2994914 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2994931 TTATGTATCGATACAAA-
1 TTATGTATCGATACAAAC
2994948 TTAT
1 TTAT
2994952 TGAATTTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.23
14 1 0.02
16 2 0.04
17 4 0.09
18 4 0.09
19 25 0.53
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2994920 original size:13 final size:13
Alignment explanation
Indices: 2994902--2994926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2994892 ACAATACTTA
2994902 TGTATCGATACAT
1 TGTATCGATACAT
2994915 TGTATCGATACA
1 TGTATCGATACA
2994927 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2994924 original size:32 final size:32
Alignment explanation
Indices: 2994883--2994945 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2994873 TAGCTAATTA
*
2994883 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2994915 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2994946 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2995728 original size:55 final size:55
Alignment explanation
Indices: 2995633--2996530 Score: 1334
Period size: 55 Copynumber: 16.3 Consensus size: 55
2995623 ATAAACTGTA
* * * * * *
2995633 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2995688 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
2995743 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2995798 TCCTGCTCTTTGAGGACTGGGAAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT--GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* **
2995853 TCCTGTTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2995908 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2995963 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2996018 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2996073 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2996128 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
2996183 TCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * * *
2996238 TCCTGCTTTTTGAGGACTGGAAGGCGCCACCAATTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2996293 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2996348 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2996403 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2996458 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2996513 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
2996531 AAAAAGCGGA
Statistics
Matches: 776, Mismatches: 48, Indels: 38
0.90 0.06 0.04
Matches are distributed among these distances:
53 4 0.01
54 21 0.03
55 727 0.94
56 20 0.03
57 4 0.01
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:2995797 original size:29 final size:28
Alignment explanation
Indices: 2995707--2996512 Score: 119
Period size: 28 Copynumber: 29.2 Consensus size: 28
2995697 TTGAGGACTG
2995707 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * ** *
2995735 GAAAGGTGTCCTGC-TCTT-TG-GGGAATG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
2995762 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
2995790 AAGAGGTGTCCTGC-TCTT-TGAGGACTGGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCT-TT
2995819 AAA--TGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
**** * * *
2995845 GAAAGGTGTCC-TGTTCTT-TGAGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
**
2995872 AAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
2995900 AAGAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
2995927 GAAGGCGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
2995955 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
2995982 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
2996010 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
2996038 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
2996065 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
2996092 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
2996120 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
2996148 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
* * * **
2996175 GAAAGGTGTCCTA-C-TCTT-TGAGGACTGG
1 -AAAGGTG-CC-ACCAACTTGTGTGGGCTTT
*
2996203 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
* ** * *
2996230 AAGAGGTG--TCCTGCTT-TTTGAGGAC-TG
1 AA-AGGTGCCACCAACTTGTGTG-GG-CTTT
* * *
2996257 GAAGGCGCCACCAATTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
2996285 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
2996312 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
2996340 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
2996367 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
2996395 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
2996423 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
2996450 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
2996477 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
2996505 AAGAGGTG
1 AA-AGGTG
2996513 TCCTGCTCTT
Statistics
Matches: 511, Mismatches: 180, Indels: 172
0.59 0.21 0.20
Matches are distributed among these distances:
24 1 0.00
25 38 0.07
26 101 0.20
27 109 0.21
28 122 0.24
29 101 0.20
30 38 0.07
31 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:2997566 original size:11 final size:11
Alignment explanation
Indices: 2997528--2997566 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2997518 CTTTGTTTTG
2997528 TTTTTTTG-TT
1 TTTTTTTGCTT
**
2997538 TTTTTTCCCTT
1 TTTTTTTGCTT
2997549 TTTTTTTGCTT
1 TTTTTTTGCTT
2997560 TTTTTTT
1 TTTTTTT
2997567 TGAAGAGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:3002765 original size:17 final size:17
Alignment explanation
Indices: 3002743--3002776 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3002733 ACATCGATTC
*
3002743 TTGACTGTGGCTTCCTT
1 TTGACTGTGCCTTCCTT
*
3002760 TTGACTTTGCCTTCCTT
1 TTGACTGTGCCTTCCTT
3002777 CTTACCTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGACTGTGCCTTCCTT
Found at i:3009583 original size:79 final size:78
Alignment explanation
Indices: 3009472--3009678 Score: 227
Period size: 79 Copynumber: 2.6 Consensus size: 78
3009462 GAGATAATAA
* * * * * * *
3009472 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
3009537 -TTAGAAAAAACAAT
65 TTTAGAAAAAA-AAC
* *
3009551 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * * *
3009616 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* * *
3009630 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGAAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
3009679 GAGATAACGA
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 1 0.01
79 99 0.93
80 7 0.07
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:3009841 original size:52 final size:51
Alignment explanation
Indices: 3009689--3009860 Score: 193
Period size: 52 Copynumber: 3.3 Consensus size: 51
3009679 GAGATAACGA
** * * *
3009689 GGTTGGAGTATCATCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGA
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGT-GTTTT-AAAATAAAATCGG
* ** *
3009741 AGTTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAAATTGGTGTTTT-AAAATAAAATCGG
* *
3009794 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTACCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTA-AAATAAAATCGG
3009846 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
3009861 TCGGAAATAA
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
51 1 0.01
52 57 0.56
53 33 0.32
54 11 0.11
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTAAAATAAAATCGG
Found at i:3009906 original size:27 final size:28
Alignment explanation
Indices: 3009843--3009918 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
3009833 CCAATAAAAT
***
3009843 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
3009871 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
3009898 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
3009919 TGTGAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:3012289 original size:13 final size:13
Alignment explanation
Indices: 3012271--3012296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3012261 ACAAAGATCC
3012271 ATGTATCGATACA
1 ATGTATCGATACA
3012284 ATGTATCGATACA
1 ATGTATCGATACA
3012297 TTTCCTTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3012340 original size:19 final size:18
Alignment explanation
Indices: 3012316--3012383 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3012306 CAGTAGCTAA
3012316 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3012335 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3012350 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3012367 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3012384 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3012356 original size:13 final size:13
Alignment explanation
Indices: 3012338--3012362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3012328 ACAATACTTA
3012338 TGTATCGATACAT
1 TGTATCGATACAT
3012351 TGTATCGATACA
1 TGTATCGATACA
3012363 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3012360 original size:32 final size:32
Alignment explanation
Indices: 3012319--3012381 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3012309 TAGCTAATTA
*
3012319 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3012351 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3012382 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3014484 original size:16 final size:16
Alignment explanation
Indices: 3014438--3014536 Score: 76
Period size: 16 Copynumber: 6.1 Consensus size: 16
3014428 AAATTTTCGA
3014438 GTCATTTTCGAGTTCAG
1 GTCA-TTTCGAGTTCAG
* *
3014455 GTAATTT-TAGGTTCAG
1 GTCATTTCGA-GTTCAG
*
3014471 GTCATTTCAAGTTC-G
1 GTCATTTCGAGTTCAG
* *
3014486 AATTATTTCGAGTTCAG
1 -GTCATTTCGAGTTCAG
**
3014503 GTTGTTTCGAGTTCAG
1 GTCATTTCGAGTTCAG
* *
3014519 GTCATTTTGAATTCAG
1 GTCATTTCGAGTTCAG
3014535 GT
1 GT
3014537 TAATCGAGTT
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
15 2 0.03
16 58 0.89
17 5 0.08
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.42
Consensus pattern (16 bp):
GTCATTTCGAGTTCAG
Found at i:3015461 original size:16 final size:16
Alignment explanation
Indices: 3015427--3015479 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
3015417 GTTCAATTCA
* *
3015427 TTTTAGGTTTAAGTTAT
1 TTTTA-GTTTGAGTCAT
3015444 TTTTAGTTTGAGTCAT
1 TTTTAGTTTGAGTCAT
*
3015460 TTCGTA-TTTGAGTCAT
1 TT-TTAGTTTGAGTCAT
3015476 TTTT
1 TTTT
3015480 GGGTTCAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 23 0.74
17 7 0.23
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (16 bp):
TTTTAGTTTGAGTCAT
Found at i:3015989 original size:22 final size:24
Alignment explanation
Indices: 3015951--3015995 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
3015941 ATCATATTAC
3015951 TTCATTTTTTTTAAAATCTATGCT
1 TTCATTTTTTTTAAAATCTATGCT
3015975 TTCA-TTTTTTT-AAATCTATGC
1 TTCATTTTTTTTAAAATCTATGC
3015996 ATGACAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.48
23 7 0.33
24 4 0.19
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.58
Consensus pattern (24 bp):
TTCATTTTTTTTAAAATCTATGCT
Found at i:3016859 original size:17 final size:17
Alignment explanation
Indices: 3016839--3016873 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3016829 GTTTTCTAGC
3016839 CTTTTTAATTTTAAAGT
1 CTTTTTAATTTTAAAGT
3016856 CTTTTTAATTTTAAAGT
1 CTTTTTAATTTTAAAGT
3016873 C
1 C
3016874 AACTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (17 bp):
CTTTTTAATTTTAAAGT
Found at i:3021115 original size:12 final size:12
Alignment explanation
Indices: 3021094--3021126 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3021084 TCGTATTTGT
3021094 TTTTAT-TTTTA
1 TTTTATATTTTA
3021105 TTTTATATTTTA
1 TTTTATATTTTA
*
3021117 TTTTTTATTT
1 TTTTATATTT
3021127 AGTGTATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATATTTTA
Found at i:3021850 original size:17 final size:17
Alignment explanation
Indices: 3021828--3021860 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3021818 CAAAAAATAA
3021828 AATTAAA-GATATATTAT
1 AATTAAATGATA-ATTAT
3021845 AATTAAATGATAATTA
1 AATTAAATGATAATTA
3021861 ATTATAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
AATTAAATGATAATTAT
Found at i:3021907 original size:42 final size:42
Alignment explanation
Indices: 3021854--3021940 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
3021844 TAATTAAATG
3021854 ATAATTAATTATAATACA-AAGACAAAATTTTTTAAATTCATT
1 ATAATTAATTATAATACACAAG-CAAAATTTTTTAAATTCATT
* *
3021896 ATAATTAATTATAATACACATGCACAATTTTTTAAATTCATT
1 ATAATTAATTATAATACACAAGCAAAATTTTTTAAATTCATT
3021938 ATA
1 ATA
3021941 CTTTTAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.41
Consensus pattern (42 bp):
ATAATTAATTATAATACACAAGCAAAATTTTTTAAATTCATT
Found at i:3022893 original size:27 final size:26
Alignment explanation
Indices: 3022847--3022953 Score: 92
Period size: 27 Copynumber: 4.0 Consensus size: 26
3022837 TATATAATTT
3022847 TTAAATTT-ATATTAATATAAAAAAAA
1 TTAAATTTAATATTAA-ATAAAAAAAA
* * *
3022873 TTAAATTTAATATCACAATAAAATGATA
1 TTAAATTTAATATTA-AATAAAA-AAAA
* *
3022901 TT-ACTTTAATTATTAAATAAAAATAA
1 TTAAATTTAA-TATTAAATAAAAAAAA
*
3022927 TTAAATTTATAATATTAAATAATAAAA
1 TTAAA-TT-TAATATTAAATAAAAAAA
3022954 TAAAAATATA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
26 11 0.17
27 25 0.40
28 24 0.38
29 3 0.05
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (26 bp):
TTAAATTTAATATTAAATAAAAAAAA
Found at i:3022942 original size:28 final size:28
Alignment explanation
Indices: 3022855--3022948 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
3022845 TTTTAAATTT
*
3022855 ATATTAATATAAAAAAAATTAAA-TT-TA
1 ATATTAA-ATAAAAATAATTAAATTTATA
* *
3022882 ATATCACAAT-AAAATGATATT-ACTTTA-A
1 ATATTA-AATAAAAAT-A-ATTAAATTTATA
*
3022910 TTATTAAATAAAAATAATTAAATTTATA
1 ATATTAAATAAAAATAATTAAATTTATA
3022938 ATATTAAATAA
1 ATATTAAATAA
3022949 TAAAATAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
26 7 0.13
27 18 0.35
28 27 0.52
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (28 bp):
ATATTAAATAAAAATAATTAAATTTATA
Found at i:3023022 original size:22 final size:23
Alignment explanation
Indices: 3022979--3023025 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3022969 AATTTAATTT
* **
3022979 TTTAATTATAATTTTTTTAAAAA
1 TTTAATAATAATTTTTAAAAAAA
3023002 TTTAATAAT-ATTTTTAAAAAAA
1 TTTAATAATAATTTTTAAAAAAA
3023024 TT
1 TT
3023026 ATTCACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAATAATAATTTTTAAAAAAA
Found at i:3025712 original size:20 final size:20
Alignment explanation
Indices: 3025661--3025723 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
3025651 ATATATATTA
3025661 TAATTAAATTTAAATAATAAATT
1 TAATTAAA-TTAAAT-A-AAATT
*
3025684 TTATT--ATTAAATAAAATT
1 TAATTAAATTAAATAAAATT
* *
3025702 TAATTAAATTAATTTAAATT
1 TAATTAAATTAAATAAAATT
3025722 TA
1 TA
3025724 TAAAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 9 0.26
19 1 0.03
20 19 0.56
21 1 0.03
23 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATTAAATTAAATAAAATT
Found at i:3028322 original size:23 final size:23
Alignment explanation
Indices: 3028296--3028343 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3028286 TTTTTCTTGC
3028296 TTTA-TTAACATTTTAGAATAGTT
1 TTTAGTTAA-ATTTTAGAATAGTT
*
3028319 TTTAGTTAAATTTTAGAATTGTT
1 TTTAGTTAAATTTTAGAATAGTT
3028342 TT
1 TT
3028344 ACCTAGTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (23 bp):
TTTAGTTAAATTTTAGAATAGTT
Found at i:3028377 original size:197 final size:197
Alignment explanation
Indices: 3028117--3028507 Score: 545
Period size: 197 Copynumber: 2.0 Consensus size: 197
3028107 AGCTTTTTCG
* *
3028117 TAGTTTTTAGTTAAATTTTAAAATTGTTTTACCTAGTGACATGTATCAGTTAGTTTCTGTAAATT
1 TAGTTTTTAGTTAAATTTTAAAATTGTTTTACCTAGTGACATGTACCAGTTAGTTTCTGTAAATA
* * * * *
3028182 TAT-TTTTTTATTTGCTTTTTGTTAGCATTTTATCATCCACGTTATGTTAAAATTAAGAAATTTT
66 TATATTTTTTATTTGCATTTTGTTAACA-TTCATCATCCACATTATGTTAAAATTAAGAAATTGT
* **
3028246 TTTATCCACAGCAAGATATTAGTTGGTTTTCTAAGTTCCTTTTTTC-TTGCTTTATTAACATTTT
130 TTTATCCACAGAAAG-TATTAACTGGTTTTCTAAGTTCCTTTTTTCTTTGCTTTATTAACATTTT
3028310 AGAA
194 AGAA
* * *
3028314 TAGTTTTTAGTTAAATTTTAGAATTGTTTTACCTAGTGACATGTACCCGTT-GATTTTTGTAAAT
1 TAGTTTTTAGTTAAATTTTAAAATTGTTTTACCTAGTGACATGTACCAGTTAG-TTTCTGTAAAT
* * **
3028378 ATATATTTTTTATTTGCATTTTGTTAACATTCATCATCCACATTATGTTAAATTTTAGTTATTGT
65 ATATATTTTTTATTTGCATTTTGTTAACATTCATCATCCACATTATGTTAAAATTAAGAAATTGT
** **
3028443 TTTATCTGCAGAAAGTATTAACTGGTTTTCTAAGTTTGTTTTTTCTTTGCTTTATTAACATTTTA
130 TTTATCCACAGAAAGTATTAACTGGTTTTCTAAGTTCCTTTTTTCTTTGCTTTATTAACATTTTA
3028508 TCATGCACGT
Statistics
Matches: 170, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
196 27 0.16
197 121 0.71
198 22 0.13
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.51
Consensus pattern (197 bp):
TAGTTTTTAGTTAAATTTTAAAATTGTTTTACCTAGTGACATGTACCAGTTAGTTTCTGTAAATA
TATATTTTTTATTTGCATTTTGTTAACATTCATCATCCACATTATGTTAAAATTAAGAAATTGTT
TTATCCACAGAAAGTATTAACTGGTTTTCTAAGTTCCTTTTTTCTTTGCTTTATTAACATTTTAG
AA
Found at i:3031657 original size:18 final size:18
Alignment explanation
Indices: 3031636--3031673 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3031626 GTACTTTTAA
3031636 AAATCAATATCAAGTTCC
1 AAATCAATATCAAGTTCC
*
3031654 AAATTAATATCAAGTTCC
1 AAATCAATATCAAGTTCC
3031672 AA
1 AA
3031674 GTTCCAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (18 bp):
AAATCAATATCAAGTTCC
Found at i:3037224 original size:23 final size:23
Alignment explanation
Indices: 3037196--3037240 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3037186 CATTTAAATA
* *
3037196 AAATAAATTTGTACGTAAATATT
1 AAATAAATATGTACATAAATATT
*
3037219 AAATAAATATGTTCATAAATAT
1 AAATAAATATGTACATAAATAT
3037241 ATAATCGAAC
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:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATAAATATGTACATAAATATT
Found at i:3043483 original size:51 final size:51
Alignment explanation
Indices: 3043382--3043530 Score: 208
Period size: 51 Copynumber: 2.9 Consensus size: 51
3043372 CGAAATATGA
* *
3043382 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATATATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTT-ATAGTGTATCGATACATCTGGGC
* * *
3043434 AAATATGCCTTCATGTATCAATACATTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTTATAGTGTATCGATACATCTGGGC
***
3043485 AAATTTGCCTACATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTACATGTATCGATACATTTAT-AGTGTATCGATACAT
3043531 TTGAGTAATG
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 46 0.53
52 40 0.47
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTACATGTATCGATACATTTATAGTGTATCGATACATCTGGGC
Found at i:3043596 original size:19 final size:19
Alignment explanation
Indices: 3043572--3043656 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
3043562 TAGCTTATAT
3043572 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
3043591 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
3043610 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
3043623 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAC-TTA
3043643 TGTATCGATACAAA
1 TGTATCGATACAAA
3043657 TCGTTGAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.19
14 1 0.02
16 2 0.04
19 30 0.53
20 13 0.23
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:3043628 original size:13 final size:13
Alignment explanation
Indices: 3043610--3043634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3043600 ACAACACTTA
3043610 TGTATCGATACAT
1 TGTATCGATACAT
3043623 TGTATCGATACA
1 TGTATCGATACA
3043635 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3043632 original size:32 final size:33
Alignment explanation
Indices: 3043591--3043654 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
3043581 ACAAAACTTA
3043591 TGTATCGATACAACAC-TTATGTATCGATACAT
1 TGTATCGATACAACACTTTATGTATCGATACAT
3043623 TGTATCGATACAACACTTTATGTATCGATACA
1 TGTATCGATACAACACTTTATGTATCGATACA
3043655 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAACACTTTATGTATCGATACAT
Found at i:3048575 original size:2 final size:2
Alignment explanation
Indices: 3048568--3048600 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3048558 TATTGAATAC
*
3048568 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3048601 AATTCAAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3053770 original size:14 final size:13
Alignment explanation
Indices: 3053725--3053827 Score: 53
Period size: 13 Copynumber: 7.5 Consensus size: 13
3053715 ATAATACTCT
*
3053725 TTGGCACACGTAC
1 TTGGCACAGGTAC
* *
3053738 CTCGCACAGGTAC
1 TTGGCACAGGTAC
*
3053751 TTGGCACAGGTGC
1 TTGGCACAGGTAC
*
3053764 TTTGGCACATGTATC
1 -TTGGCACAGGTA-C
* * *
3053779 TTTGGTATAAGTATC
1 -TTGGCACAGGTA-C
*
3053794 TTTGGTACAGGTAC
1 -TTGGCACAGGTAC
* *
3053808 TTTGACACAGGTAT
1 -TTGGCACAGGTAC
3053822 TTGGCA
1 TTGGCA
3053828 TAAGCACTTT
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
13 25 0.35
14 22 0.31
15 24 0.34
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (13 bp):
TTGGCACAGGTAC
Found at i:3053783 original size:15 final size:15
Alignment explanation
Indices: 3053741--3053872 Score: 73
Period size: 14 Copynumber: 9.3 Consensus size: 15
3053731 CACGTACCTC
3053741 GCACAGGTA-C-TTG
1 GCACAGGTATCTTTG
*
3053754 GCACAGGT-GCTTTG
1 GCACAGGTATCTTTG
*
3053768 GCACATGTATCTTTG
1 GCACAGGTATCTTTG
* * *
3053783 GTATAAGTATCTTTG
1 GCACAGGTATCTTTG
*
3053798 GTACAGGTA-CTTTG
1 GCACAGGTATCTTTG
*
3053812 ACACAGGTA--TTTG
1 GCACAGGTATCTTTG
* * *
3053825 GCATAAGCA-CTTTG
1 GCACAGGTATCTTTG
* * *
3053839 ACACAGATACCTTTG
1 GCACAGGTATCTTTG
*
3053854 GCACGGGTA-CTTTG
1 GCACAGGTATCTTTG
*
3053868 ACACA
1 GCACA
3053873 AGTACCTGGC
Statistics
Matches: 91, Mismatches: 23, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
13 18 0.20
14 38 0.42
15 35 0.38
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (15 bp):
GCACAGGTATCTTTG
Found at i:3053821 original size:29 final size:28
Alignment explanation
Indices: 3053741--3053877 Score: 107
Period size: 29 Copynumber: 4.9 Consensus size: 28
3053731 CACGTACCTC
* *
3053741 GCACAGGTAC-TTGGCACAGGTGCTTTG
1 GCACAGGTACTTTGACACAGGTACTTTG
* ** * *
3053768 GCACATGTATCTTTGGTATAAGTATCTTTG
1 GCACAGGTA-CTTTGACACAGGTA-CTTTG
*
3053798 GTACAGGTACTTTGACACAGGTA-TTTG
1 GCACAGGTACTTTGACACAGGTACTTTG
* * * *
3053825 GCATAAGCACTTTGACACAGATACCTTTG
1 GCACAGGTACTTTGACACAGGTA-CTTTG
* *
3053854 GCACGGGTACTTTGACACAAGTAC
1 GCACAGGTACTTTGACACAGGTAC
3053878 CTGGCATAGT
Statistics
Matches: 83, Mismatches: 22, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
27 30 0.36
28 2 0.02
29 39 0.47
30 12 0.14
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (28 bp):
GCACAGGTACTTTGACACAGGTACTTTG
Found at i:3061361 original size:117 final size:117
Alignment explanation
Indices: 3061155--3061619 Score: 583
Period size: 117 Copynumber: 4.0 Consensus size: 117
3061145 TGATTGTACA
* * *
3061155 GGCCGTAGCTATAATCACTCATATATTGGCCTAAGTCATTTATTCGAAAAATATTGAATAATCTA
1 GGCCGCAGCTATAATCACTCATATATTGGCCTAAGTCATTTATTCGAAAAAGATTGAATAATCTG
* * *
3061220 TTTCATTTAAGGTTGAGATACAATCTCCCTACTGAAGTAGATAGTTCCTTTT
66 CTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATAGTTCCTTTT
* * *
3061272 GGCCGCAGCTATGATCGCTCATATATTGACCTAAGTCATTTATTCGAAAAAGATTGAATAATCTG
1 GGCCGCAGCTATAATCACTCATATATTGGCCTAAGTCATTTATTCGAAAAAGATTGAATAATCTG
* * *
3061337 CTTCATTTAAGGTTGAGCTACAATCTCCCTAATGAAATGGATAGTTCCCTTT
66 CTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATAGTTCCTTTT
* * * * *
3061389 GGCCGCAGCTATGATTACTCATATATT-GCCTAAGTCATTTATTCAAAAAAGGTTGAATAATTTG
1 GGCCGCAGCTATAATCACTCATATATTGGCCTAAGTCATTTATTCGAAAAAGATTGAATAATCTG
*
3061453 CTTCATTTAAGGTTGAGATAGAATCTCCCTAATGAAGTGGATAGTT-CTCTTT
66 CTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATAGTTCCT-TTT
* ** * ** * *
3061505 GGCCGCAGCTATAATCGCTCATACGTTGGCCTAAGTCACTTATTTTAAAAAGGGTTGAATAATTT
1 GGCCGCAGCTATAATCACTCATATATTGGCCTAAGTCATTTATTCGAAAAA-GATTGAATAATCT
* ** * * * * *
3061570 ACTTTGTTTTAGGTTGAGATTCGATCTCCCTAATCAAAGTGGATGGTTCC
65 GCTTCATTTAAGGTTGAGATACAATCTCCCTAAT-GAAGTGGATAGTTCC
3061620 CCTTTGACCA
Statistics
Matches: 304, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
115 1 0.00
116 101 0.33
117 150 0.49
118 40 0.13
119 11 0.04
120 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (117 bp):
GGCCGCAGCTATAATCACTCATATATTGGCCTAAGTCATTTATTCGAAAAAGATTGAATAATCTG
CTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATAGTTCCTTTT
Found at i:3062513 original size:31 final size:32
Alignment explanation
Indices: 3062455--3062515 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
3062445 AGAACCTATG
* *
3062455 TTATATTAAGTTATTAACTCTTGGATAATACA
1 TTATATTAAGTTATTAACTCATAGATAATACA
* *
3062487 TTATATTGAG-TATTATCTCATAGATAATA
1 TTATATTAAGTTATTAACTCATAGATAATA
3062516 TGAATAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (32 bp):
TTATATTAAGTTATTAACTCATAGATAATACA
Found at i:3062978 original size:15 final size:15
Alignment explanation
Indices: 3062948--3062976 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3062938 AATTAATTAC
3062948 ATTTCTTTATTTTTT
1 ATTTCTTTATTTTTT
3062963 ATTT-TTTATTTTTT
1 ATTTCTTTATTTTTT
3062977 TAATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
ATTTCTTTATTTTTT
Found at i:3063243 original size:27 final size:27
Alignment explanation
Indices: 3063195--3063249 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3063185 TTTTTGGCAC
* * *
3063195 AGGTACTTAGCATATATGCTTTAACAT
1 AGGTACTTAACACATATACTTTAACAT
* *
3063222 AGGTACTTAACACATGTACTTTGACAT
1 AGGTACTTAACACATATACTTTAACAT
3063249 A
1 A
3063250 AGAATCTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (27 bp):
AGGTACTTAACACATATACTTTAACAT
Found at i:3063323 original size:14 final size:15
Alignment explanation
Indices: 3063293--3063334 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
3063283 ACTTGGCATA
3063293 GGCACAAGTACCTTT
1 GGCACAAGTACCTTT
*
3063308 GGCACATGTA-CTTT
1 GGCACAAGTACCTTT
*
3063322 GGCATAAGTACCT
1 GGCACAAGTACCT
3063335 GGCATAGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (15 bp):
GGCACAAGTACCTTT
Found at i:3065674 original size:5 final size:5
Alignment explanation
Indices: 3065635--3065672 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
3065625 AAAGTTAAAG
*
3065635 TTTTC TTTTC CTTTC TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
3065673 TTCAATTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:3067241 original size:2 final size:2
Alignment explanation
Indices: 3067234--3067282 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3067224 GCTTGCTAAG
3067234 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
3067276 TA TA TA T
1 TA TA TA T
3067283 TTTGTAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3067779 original size:25 final size:24
Alignment explanation
Indices: 3067745--3067791 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
3067735 TGTTTAGTTT
3067745 TCGATTTTAATT-GATATGAGATAA
1 TCGATTTTAATTGGAT-TGAGATAA
3067769 TCGATATTTAATTGGATTGAGAT
1 TCGAT-TTTAATTGGATTGAGAT
3067792 TGATTTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 13 0.62
26 3 0.14
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (24 bp):
TCGATTTTAATTGGATTGAGATAA
Found at i:3075659 original size:29 final size:29
Alignment explanation
Indices: 3075609--3075682 Score: 69
Period size: 30 Copynumber: 2.5 Consensus size: 29
3075599 TTTTATTTAG
* * *
3075609 ATAATTTTTTATGTTTTTATTT-TACGTAT
1 ATAAATTTTTAT-TTTTAATTTATACGTAA
**
3075638 ATAAATTTTTATTTTTGAATTTATATTTAA
1 ATAAATTTTTATTTTT-AATTTATACGTAA
*
3075668 ATAAAATTTTATTTT
1 ATAAATTTTTATTTT
3075683 AAGTAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.11
29 15 0.41
30 18 0.49
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (29 bp):
ATAAATTTTTATTTTTAATTTATACGTAA
Found at i:3075691 original size:18 final size:18
Alignment explanation
Indices: 3075657--3075690 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3075647 TATTTTTGAA
3075657 TTTATATTTAAATAAAAT
1 TTTATATTTAAATAAAAT
*
3075675 TTTAT-TTTAAGTAAAA
1 TTTATATTTAAATAAAA
3075691 AATTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTATATTTAAATAAAAT
Found at i:3075873 original size:31 final size:30
Alignment explanation
Indices: 3075820--3075879 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
3075810 TAAAAATTAT
**
3075820 ATTAATATAAAATAATTTTTTAAATTTTTC
1 ATTAATATAAAATAATAATTTAAATTTTTC
* *
3075850 ATTAATTTATAAATAATAATTTAAGTTTTT
1 ATTAATATA-AAATAATAATTTAAATTTTT
3075880 ATACTAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTAATATAAAATAATAATTTAAATTTTTC
Found at i:3075997 original size:30 final size:28
Alignment explanation
Indices: 3075975--3076047 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
3075965 ATTTAAATTA
3075975 AAATTAAAAATTTTAAAAAAATTATAATAT
1 AAATT-AAAA-TTTAAAAAAATTATAATAT
*
3076005 AAATTAAAATTT-AAAAATTTATTTAATAT
1 AAATTAAAATTTAAAAAAATTA--TAATAT
*
3076034 AAATTAAAAATTAA
1 AAATTAAAATTTAA
3076048 TAATCTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 8 0.21
28 3 0.08
29 21 0.55
30 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATTAAAATTTAAAAAAATTATAATAT
Found at i:3076031 original size:29 final size:29
Alignment explanation
Indices: 3075999--3076063 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
3075989 AAAAAAATTA
* *
3075999 TAATATAAATTAAAATTTAAAAATTTATT
1 TAATATAAATTAAAAATTAAAAATCTATT
*
3076028 TAATATAAATTAAAAATTAATAATCTATT
1 TAATATAAATTAAAAATTAAAAATCTATT
3076057 TCAATAT
1 T-AATAT
3076064 CATAAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
TAATATAAATTAAAAATTAAAAATCTATT
Found at i:3076555 original size:37 final size:37
Alignment explanation
Indices: 3076509--3076609 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 37
3076499 AAAAAAGAAA
* *
3076509 AAAAAATTATATATTTATATTTATATTTTTTATAT-TT
1 AAAATATTATATATTT-TATTTATATTTTTTACATATT
*
3076546 AAAATATTATAT-TTTTA--TAAATTTTTTACATATT
1 AAAATATTATATATTTTATTTATATTTTTTACATATT
*
3076580 AATAAT-TTATTTTATTTTATTTATATTTTT
1 AA-AATATTA-TATATTTTATTTATATTTTT
3076610 ATGTAAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
33 12 0.23
34 7 0.13
35 7 0.13
36 8 0.15
37 11 0.21
38 8 0.15
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (37 bp):
AAAATATTATATATTTTATTTATATTTTTTACATATT
Found at i:3077149 original size:22 final size:23
Alignment explanation
Indices: 3077114--3077183 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 23
3077104 TCGTATTATT
3077114 TTTTATTTAAAATATTATATTTTTA
1 TTTTATTT--AATATTATATTTTTA
*
3077139 TTTT-TTTAATATTA-ATAATTTA
1 TTTTATTTAATATTATAT-TTTTA
* *
3077161 TTTTATTTCAT-GTATATTTTTA
1 TTTTATTTAATATTATATTTTTA
3077183 T
1 T
3077184 ATGTACATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
21 2 0.05
22 22 0.58
23 7 0.18
24 3 0.08
25 4 0.11
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (23 bp):
TTTTATTTAATATTATATTTTTA
Found at i:3077485 original size:20 final size:20
Alignment explanation
Indices: 3077454--3077528 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
3077444 TTTTATCCAG
*
3077454 ATGTATCGATACATTTTTCA
1 ATGTATCAATACATTTTTCA
* * * *
3077474 ATATATCAATACATGTATGA
1 ATGTATCAATACATTTTTCA
* * *
3077494 ATGTATCGATATATTCTTCA
1 ATGTATCAATACATTTTTCA
3077514 ATGTATCAATACATT
1 ATGTATCAATACATT
3077529 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (20 bp):
ATGTATCAATACATTTTTCA
Found at i:3077514 original size:40 final size:39
Alignment explanation
Indices: 3077454--3077531 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
3077444 TTTTATCCAG
*
3077454 ATGTATCGATACATTTTTCAATATATCAATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCAATACAT-TATGA
* *
3077494 ATGTATCGATATATTCTTCAATGTATCAATACATTATG
1 ATGTATCGATACATTCTTCAATATATCAATACATTATG
3077532 TCTTTTTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCAATACATTATGA
Found at i:3081182 original size:16 final size:15
Alignment explanation
Indices: 3081155--3081196 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
3081145 ATTTTTAAAT
3081155 AAATTTTATTAATTA
1 AAATTTTATTAATTA
*
3081170 TAATTTTATTTAATTA
1 AAATTTTA-TTAATTA
3081186 AAATTTT-TTAA
1 AAATTTTATTAA
3081197 ATATTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATTTTATTAATTA
Found at i:3081287 original size:25 final size:25
Alignment explanation
Indices: 3081259--3081322 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
3081249 GAACTACAAG
3081259 CATGCCTATGGTGATGACACATGTT
1 CATGCCTATGGTGATGACACATGTT
*
3081284 CATGCCTATGGTGATGACACGTGTT
1 CATGCCTATGGTGATGACACATGTT
*
3081309 CATGCCTATAGTGA
1 CATGCCTATGGTGA
3081323 CGAGAGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (25 bp):
CATGCCTATGGTGATGACACATGTT
Found at i:3081503 original size:14 final size:15
Alignment explanation
Indices: 3081484--3081515 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3081474 GAGAAAAAAA
3081484 TTTAAGGGTTTA-AT
1 TTTAAGGGTTTATAT
3081498 TTTAAGGGTTTATAT
1 TTTAAGGGTTTATAT
3081513 TTT
1 TTT
3081516 TATTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (15 bp):
TTTAAGGGTTTATAT
Found at i:3081636 original size:32 final size:33
Alignment explanation
Indices: 3081552--3081636 Score: 84
Period size: 37 Copynumber: 2.5 Consensus size: 33
3081542 TTATAAATTT
*
3081552 ATGTAATATTTATAAATATTTTTATATTTGTATATTC
1 ATGTAATATTTAT---T-TTTTTATATTTGTATATTA
*
3081589 ATGTAATATTTATTTTTTTATA-TTGTATTTTA
1 ATGTAATATTTATTTTTTTATATTTGTATATTA
* *
3081621 AT-TAATTTTTAATTTT
1 ATGTAATATTTATTTTT
3081637 GTATTCATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 12 0.27
32 10 0.23
33 8 0.18
34 1 0.02
37 13 0.30
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (33 bp):
ATGTAATATTTATTTTTTTATATTTGTATATTA
Found at i:3082106 original size:11 final size:10
Alignment explanation
Indices: 3082084--3082117 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3082074 GGCTGAGAAG
3082084 AAAAAGAAAA
1 AAAAAGAAAA
* *
3082094 AAGAGGAAAA
1 AAAAAGAAAA
3082104 AAAAAGAAAA
1 AAAAAGAAAA
3082114 AAAA
1 AAAA
3082118 TTTATATCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:3082190 original size:19 final size:20
Alignment explanation
Indices: 3082152--3082190 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3082142 TTTTTTATAT
* *
3082152 AAAATTTTATATTGTTATAA
1 AAAATTTTATATAGTAATAA
3082172 AAAATTTTA-ATAGTAATAA
1 AAAATTTTATATAGTAATAA
3082191 TTATTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATTTTATATAGTAATAA
Found at i:3082528 original size:15 final size:16
Alignment explanation
Indices: 3082492--3082531 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3082482 TTTAATATTT
*
3082492 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
3082509 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
3082524 ATAAAATT
1 ATAAAATT
3082532 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:3082534 original size:16 final size:17
Alignment explanation
Indices: 3082492--3082534 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3082482 TTTAATATTT
*
3082492 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
3082509 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
3082524 ATAAAATTTAT
1 ATAAAATTTAT
3082535 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:3083553 original size:26 final size:28
Alignment explanation
Indices: 3083523--3083577 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
3083513 ATAACATAAA
*
3083523 AATAATTTAATTT-TTATTAAA-AATAT
1 AATAAATTAATTTATTATTAAATAATAT
* *
3083549 AATAAATTATTTTATTTTTAAATAATAT
1 AATAAATTAATTTATTATTAAATAATAT
3083577 A
1 A
3083578 TTTAAGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.46
27 7 0.29
28 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATAAATTAATTTATTATTAAATAATAT
Found at i:3083724 original size:18 final size:21
Alignment explanation
Indices: 3083683--3083725 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3083673 AATTTATTTT
*
3083683 ATAATTAAATTTTTATTAATA
1 ATAATTAAATATTTATTAATA
3083704 ATAATTAAA-ATTTA-TAA-A
1 ATAATTAAATATTTATTAATA
3083722 ATAA
1 ATAA
3083726 AAATAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 4 0.19
21 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTAAATATTTATTAATA
Found at i:3083724 original size:21 final size:22
Alignment explanation
Indices: 3083683--3083734 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
3083673 AATTTATTTT
* *
3083683 ATAATT-AAATTTTTATTAATA
1 ATAATTAAAATTTATATAAATA
3083704 ATAATTAAAATTTATA-AAATA
1 ATAATTAAAATTTATATAAATA
* *
3083725 AAAATAAAAA
1 ATAATTAAAA
3083735 GTCTCAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATTAAAATTTATATAAATA
Found at i:3084911 original size:2 final size:2
Alignment explanation
Indices: 3084906--3084946 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3084896 TTAGGTGCTT
3084906 TA TA TA 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 TA TA TA T
3084947 GGACAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3085764 original size:28 final size:28
Alignment explanation
Indices: 3085728--3085783 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3085718 CCCTTAATGG
* * *
3085728 GTGTCTGTGATATTTGTTTGGCCCAAAA
1 GTGTCTGTGATATATATATGGCCCAAAA
*
3085756 GTGTGTGTGATATATATATGGCCCAAAA
1 GTGTCTGTGATATATATATGGCCCAAAA
3085784 ATATGCGTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (28 bp):
GTGTCTGTGATATATATATGGCCCAAAA
Found at i:3086493 original size:26 final size:25
Alignment explanation
Indices: 3086462--3086520 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
3086452 TCTGAAGTGG
3086462 GTGTGTGACA-TATTTGGTCCTAAAAT
1 GTGTGTGACATTATTTGGT-CT-AAAT
*
3086488 GTGTGTGATATTTATTTGGTCTAAAT
1 GTGTGTGACA-TTATTTGGTCTAAAT
*
3086514 GGGTGTG
1 GTGTGTG
3086521 TGATAATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 19 0.66
27 2 0.07
28 8 0.28
ACGTcount: A:0.22, C:0.07, G:0.29, T:0.42
Consensus pattern (25 bp):
GTGTGTGACATTATTTGGTCTAAAT
Found at i:3086524 original size:28 final size:28
Alignment explanation
Indices: 3086459--3086525 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
3086449 GGTTCTGAAG
*
3086459 TGGGTGTGTGACATATTTGGTCCTAAAA
1 TGGGTGTGTGATATATTTGGTCCTAAAA
3086487 T--GTGTGTGATATTTATTTGGT-CT-AAA
1 TGGGTGTGTGATA--TATTTGGTCCTAAAA
3086513 TGGGTGTGTGATA
1 TGGGTGTGTGATA
3086526 ATAGTTTAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 13 0.38
27 2 0.06
28 19 0.56
ACGTcount: A:0.22, C:0.06, G:0.30, T:0.42
Consensus pattern (28 bp):
TGGGTGTGTGATATATTTGGTCCTAAAA
Found at i:3086651 original size:81 final size:79
Alignment explanation
Indices: 3086494--3086652 Score: 176
Period size: 81 Copynumber: 2.0 Consensus size: 79
3086484 AAATGTGTGT
* * * * * * *
3086494 GATATTTATTTGGTCTAAATGGGTGTGTGATAATAGTTTAGCCCTAAAGTGGGTATTTAATATTT
1 GATATTTATTTGGCCCAAACGGGAGTGTGATAATAATTTAGCCCTAAAGTCGGTATTTAATATCT
3086559 TATTCGGCCTAAATAG
66 TA-T-GGCCTAAATAG
* * *
3086575 GATATTTATTTGGCCCAAACGGGAGTGTGATAATAATTTGGCCTTAAAGTCGGTGTTTGACATAT
1 GATATTTATTTGGCCCAAACGGGAGTGTGATAATAATTTAGCCCTAAAGTCGGTATTT-A-ATAT
3086640 CTTA-GGCCCTAAA
64 CTTATGG-CCTAAA
3086653 ATTGGAGCGT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
80 2 0.03
81 55 0.85
82 1 0.02
83 7 0.11
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (79 bp):
GATATTTATTTGGCCCAAACGGGAGTGTGATAATAATTTAGCCCTAAAGTCGGTATTTAATATCT
TATGGCCTAAATAG
Found at i:3086841 original size:27 final size:28
Alignment explanation
Indices: 3086818--3086871 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
3086808 AAATTGGCGC
* *
3086818 TAAATGGGTGTG-ATATTTATTTGGCCA
1 TAAATGAGTGTGAATACTTATTTGGCCA
3086845 TAAATGAGTGTGAATACTTATTTGGCC
1 TAAATGAGTGTGAATACTTATTTGGCC
3086872 CAAAAGGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (28 bp):
TAAATGAGTGTGAATACTTATTTGGCCA
Found at i:3097595 original size:24 final size:23
Alignment explanation
Indices: 3097560--3097604 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
3097550 ATTTCTAAAT
3097560 TTTTTGTGAAATCTCTCTTTATTA
1 TTTTTGTGAAATCTC-CTTTATTA
*
3097584 TTTTTG-GAAAATTTCCTTTAT
1 TTTTTGTG-AAATCTCCTTTAT
3097605 ATTAATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTTTGTGAAATCTCCTTTATTA
Found at i:3097922 original size:16 final size:16
Alignment explanation
Indices: 3097903--3097936 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3097893 TTAGTTCTTT
*
3097903 TTTAATTTAATAATAA
1 TTTAATTTAACAATAA
3097919 TTTAATTTAACAATAA
1 TTTAATTTAACAATAA
3097935 TT
1 TT
3097937 AAAGATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAATTTAACAATAA
Found at i:3098813 original size:18 final size:18
Alignment explanation
Indices: 3098789--3098837 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
3098779 TTATTTTCAT
3098789 TATTTATTAAA-TTAAAA
1 TATTTATTAAATTTAAAA
3098806 TGATTTATTTAATATTTAAAA
1 T-ATTTA-TTAA-ATTTAAAA
*
3098827 TATTTTTTAAA
1 TATTTATTAAA
3098838 ATATATCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 1 0.04
18 6 0.22
19 8 0.30
20 5 0.19
21 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TATTTATTAAATTTAAAA
Found at i:3099448 original size:18 final size:17
Alignment explanation
Indices: 3099418--3099451 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3099408 CTTAATTTGA
*
3099418 ATTTATTTTGGTTTTTC
1 ATTTATTTCGGTTTTTC
3099435 ATTTGATTTCGGTTTTT
1 ATTT-ATTTCGGTTTTT
3099452 GTTTTTTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.68
Consensus pattern (17 bp):
ATTTATTTCGGTTTTTC
Found at i:3100456 original size:16 final size:16
Alignment explanation
Indices: 3100437--3100473 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
3100427 ATTCAAACTA
*
3100437 TTTTGGATCTAAATTAT
1 TTTTGG-TCTAAATTAC
3100454 TTTTGGTCTAAATTAC
1 TTTTGGTCTAAATTAC
3100470 TTTT
1 TTTT
3100474 TGTCCAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTTGGTCTAAATTAC
Found at i:3100459 original size:17 final size:17
Alignment explanation
Indices: 3100437--3100475 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
3100427 ATTCAAACTA
3100437 TTTTGGATCTAAATTA-T
1 TTTTGG-TCTAAATTACT
3100454 TTTTGGTCTAAATTACT
1 TTTTGGTCTAAATTACT
3100471 TTTTG
1 TTTTG
3100476 TCCAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.56
Consensus pattern (17 bp):
TTTTGGTCTAAATTACT
Found at i:3101124 original size:2 final size:2
Alignment explanation
Indices: 3101117--3101144 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3101107 GTCATAACTC
3101117 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
3101145 CCTTTTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3101291 original size:2 final size:2
Alignment explanation
Indices: 3101284--3101311 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3101274 TGTTGATGAA
3101284 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
3101312 GATTAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3109059 original size:19 final size:19
Alignment explanation
Indices: 3109035--3109072 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3109025 ACATAATATT
3109035 AATTTTTAAATAAATCATA
1 AATTTTTAAATAAATCATA
* *
3109054 AATTTTTAATTATATCATA
1 AATTTTTAAATAAATCATA
3109073 TTTACATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTTTAAATAAATCATA
Found at i:3109191 original size:22 final size:22
Alignment explanation
Indices: 3109166--3109225 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 22
3109156 AAAATTTGAT
3109166 TATTTAATTTAATAAAAATAAA
1 TATTTAATTTAATAAAAATAAA
* *
3109188 TATTTATAACTTAAATAAAAATTAA
1 TA-TT-TAA-TTTAATAAAAATAAA
3109213 T-TTTAAATTTAAT
1 TATTT-AATTTAAT
3109226 GACTCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 8 0.26
23 6 0.19
24 3 0.10
25 14 0.45
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTTAATTTAATAAAAATAAA
Done.