Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 23 of 25
Found at i:3357866 original size:31 final size:31
Alignment explanation
Indices: 3357806--3357888 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
3357796 GACCAAACTT
* * *
3357806 AAAATGACCTGAAACCAAAATGACTCAAACCC
1 AAAATGACCT-AACCCAAAATAACCCAAACCC
3357838 AAAATGACCTAACCCAAAATAACCCAAACCC
1 AAAATGACCTAACCCAAAATAACCCAAACCC
* *
3357869 AAAATAACTCTAACACAAAA
1 AAAATGAC-CTAACCCAAAA
3357889 ATGACTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
31 25 0.56
32 20 0.44
ACGTcount: A:0.54, C:0.29, G:0.05, T:0.12
Consensus pattern (31 bp):
AAAATGACCTAACCCAAAATAACCCAAACCC
Found at i:3358239 original size:20 final size:19
Alignment explanation
Indices: 3358196--3358241 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
3358186 AATATTTACT
3358196 ATATTT-AATATTTGTTTA
1 ATATTTAAATATTTGTTTA
*
3358214 ACATTTAAATTATTT-TTTAA
1 ATATTTAAA-TATTTGTTT-A
3358234 ATATTTAA
1 ATATTTAA
3358242 TTTTTTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATTTAAATATTTGTTTA
Found at i:3358243 original size:19 final size:20
Alignment explanation
Indices: 3358196--3358248 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
3358186 AATATTTACT
3358196 ATATTTAA-TATTTGTTTAAC
1 ATATTTAATTATTT-TTTAAC
*
3358216 AT-TTAAATTATTTTTTAA-
1 ATATTTAATTATTTTTTAAC
3358234 ATATTTAATT-TTTTT
1 ATATTTAATTATTTTT
3358249 AAGTGAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 7 0.24
19 15 0.52
20 7 0.24
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
ATATTTAATTATTTTTTAAC
Found at i:3359146 original size:51 final size:52
Alignment explanation
Indices: 3359065--3359192 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
3359055 GAAAATGTAT
* * * *
3359065 CAATATGTTTTTCATTGTATCGATACATTCTGGG-TTTTGACCCAAATATAA
1 CAATATATTCTTCAATGTATCGATAAATTCTGGGTTTTTGACCCAAATATAA
3359116 CAATATATTCTTCAATGTATCGATAAATTCTGGGTTTTTGACCCAAATATAA
1 CAATATATTCTTCAATGTATCGATAAATTCTGGGTTTTTGACCCAAATATAA
* * *
3359168 CGATACATTCTTCAATATATCGATA
1 CAATATATTCTTCAATGTATCGATA
3359193 CATACAGGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 30 0.43
52 39 0.57
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (52 bp):
CAATATATTCTTCAATGTATCGATAAATTCTGGGTTTTTGACCCAAATATAA
Found at i:3360835 original size:22 final size:21
Alignment explanation
Indices: 3360812--3360851 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3360802 AATCATTTTA
3360812 AAATATTA-AATCATTTTTCAT
1 AAATATTATAAT-ATTTTTCAT
*
3360833 AAATTTTATAATATTTTTC
1 AAATATTATAATATTTTTC
3360852 CTTGAAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATATTATAATATTTTTCAT
Found at i:3364135 original size:11 final size:12
Alignment explanation
Indices: 3364109--3364133 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3364099 TTATAAATAA
3364109 TTATTTTATTTT
1 TTATTTTATTTT
3364121 TTATTTTATTTT
1 TTATTTTATTTT
3364133 T
1 T
3364134 ATAAATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:3364947 original size:23 final size:23
Alignment explanation
Indices: 3364899--3364947 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3364889 TTGTTTTATT
* *
3364899 TATTTTAAAAATATTTAATTGTA
1 TATTTTAAAAATATTAAATTGAA
*
3364922 TATTTTATAAATAATTAAATT-AA
1 TATTTTAAAAAT-ATTAAATTGAA
3364945 TAT
1 TAT
3364948 ATATTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTTTAAAAATATTAAATTGAA
Found at i:3365299 original size:17 final size:16
Alignment explanation
Indices: 3365279--3365314 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3365269 ATACTTTTAT
3365279 ATATATTATAAATAATA
1 ATATATTATAAAT-ATA
*
3365296 ATATATTCTAAATATA
1 ATATATTATAAATATA
3365312 ATA
1 ATA
3365315 GTCAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATTATAAATATA
Found at i:3365614 original size:30 final size:31
Alignment explanation
Indices: 3365580--3365659 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
3365570 TTAGAATATA
3365580 ATTTTAATTTAG-GAAAAAATATATTTACAT
1 ATTTTAATTTAGAGAAAAAATATATTTACAT
* *
3365610 ATTTTCAAATTT-GATAAAAAATATATTTATAT
1 ATTTT--AATTTAGAGAAAAAATATATTTACAT
*
3365642 TTTTTAATTTA-A-AAAAAA
1 ATTTTAATTTAGAGAAAAAA
3365660 CTATTTAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
29 6 0.14
30 11 0.26
31 1 0.02
32 25 0.58
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (31 bp):
ATTTTAATTTAGAGAAAAAATATATTTACAT
Found at i:3366322 original size:22 final size:21
Alignment explanation
Indices: 3366297--3366338 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3366287 AAAAAATTTA
* *
3366297 ATATATTTATTTTAAAGATAAT
1 ATATATTGAATTT-AAGATAAT
3366319 ATATATTGAATTTAAGATAA
1 ATATATTGAATTTAAGATAA
3366339 ACATAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATATTGAATTTAAGATAAT
Found at i:3366397 original size:16 final size:17
Alignment explanation
Indices: 3366361--3366398 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3366351 TAATATGCAC
*
3366361 TTTAATTAAAATTTAAG
1 TTTAATTAAAAGTTAAG
3366378 -TTAATTAAAAGTT-AG
1 TTTAATTAAAAGTTAAG
3366393 TTTAAT
1 TTTAAT
3366399 AGTAATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
TTTAATTAAAAGTTAAG
Found at i:3367158 original size:29 final size:29
Alignment explanation
Indices: 3367125--3367225 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 29
3367115 GAAAAAAATA
3367125 TTAAA-AAATTCTTAAATTTTATTTTTTAT
1 TTAAATAAATT-TTAAATTTTATTTTTTAT
* * *
3367154 TTAAATAAAATTTTATATTTT-TATTATAT
1 TTAAAT-AAATTTTAAATTTTATTTTTTAT
* *
3367183 TTAAATAAATTTTTATTATTTATTTTTTAT
1 TTAAATAAATTTTAAAT-TTTATTTTTTAT
3367213 TTAAATAAATTTT
1 TTAAATAAATTTT
3367226 TATTTCAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.13
29 20 0.33
30 27 0.45
31 5 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TTAAATAAATTTTAAATTTTATTTTTTAT
Found at i:3367203 original size:30 final size:30
Alignment explanation
Indices: 3367142--3367229 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
3367132 ATTCTTAAAT
* *
3367142 TTTATTTTTTATTTAAATAAAATTTTA-TA
1 TTTATTTTATATTTAAATAAATTTTTATTA
3367171 TTT-TTATTATATTTAAATAAATTTTTATTA
1 TTTATT-TTATATTTAAATAAATTTTTATTA
*
3367201 TTTATTTTTTATTTAAATAAATTTTTATT
1 TTTATTTTATATTTAAATAAATTTTTATT
3367230 TCAAAAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 2 0.04
29 22 0.42
30 27 0.51
31 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTATTTTATATTTAAATAAATTTTTATTA
Found at i:3368215 original size:14 final size:14
Alignment explanation
Indices: 3368198--3368244 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
3368188 TTAAAATTTA
3368198 AATAAAAATATAAT
1 AATAAAAATATAAT
*
3368212 AATAAAAGTATAAT
1 AATAAAAATATAAT
* *
3368226 -ATAAAAATAAAAA
1 AATAAAAATATAAT
3368239 AATAAA
1 AATAAA
3368245 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (14 bp):
AATAAAAATATAAT
Found at i:3368243 original size:19 final size:19
Alignment explanation
Indices: 3368204--3368253 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
3368194 TTTAAATAAA
* **
3368204 AATATAATAATAAAAGTAT
1 AATATAAAAATAAAAAAAT
3368223 AATATAAAAATAAAAAAAT
1 AATATAAAAATAAAAAAAT
*
3368242 AA-ATTAAAATAA
1 AATATAAAAATAA
3368254 TATAATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATATAAAAATAAAAAAAT
Found at i:3368265 original size:18 final size:18
Alignment explanation
Indices: 3368229--3368296 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
3368219 GTATAATATA
* **
3368229 AAAATAAAAAAATAAATT
1 AAAATAATAAAATTTATT
*
3368247 AAAATAATATAATTTATT
1 AAAATAATAAAATTTATT
* *
3368265 AATATATTAAAATTTA-T
1 AAAATAATAAAATTTATT
3368282 ATAAATATATAAAAT
1 A-AAATA-ATAAAAT
3368297 ATAATATAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 2 0.05
18 31 0.79
19 6 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATAATAAAATTTATT
Found at i:3368302 original size:14 final size:14
Alignment explanation
Indices: 3368189--3368304 Score: 53
Period size: 14 Copynumber: 8.0 Consensus size: 14
3368179 ATCAAAATTT
*
3368189 TAAAATTTAA-ATA
1 TAAAATATAATATA
3368202 -AAAATATAATA-A
1 TAAAATATAATATA
3368214 TAAAAGTATAATATA
1 TAAAA-TATAATATA
* *
3368229 -AAAATA-AAAAAA
1 TAAAATATAATATA
* *
3368241 TAAATTAAAATAATA
1 TAAAATATAAT-ATA
**
3368256 TAATTTATTAATATA
1 TAAAATA-TAATATA
3368271 TTAAAATTTATATAAATATA
1 -T-AAA---ATAT-AATATA
3368291 TAAAATATAATATA
1 TAAAATATAATATA
3368305 ATTTAAAAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
12 13 0.16
13 12 0.15
14 19 0.24
15 16 0.20
16 4 0.05
17 2 0.03
18 3 0.04
19 2 0.03
20 8 0.10
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (14 bp):
TAAAATATAATATA
Found at i:3368994 original size:2 final size:2
Alignment explanation
Indices: 3368987--3369016 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3368977 CCTATCCTTC
3368987 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3369017 ATCCAAAAGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3373807 original size:30 final size:30
Alignment explanation
Indices: 3373773--3373832 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3373763 TGTAAGTTAA
* *
3373773 AAATTTTTAGTT-TTATTTAATTATATTATT
1 AAATTTTTA-TTATTAATAAATTATATTATT
3373803 AAATTTTTATTATTAATAAATTATATTATT
1 AAATTTTTATTATTAATAAATTATATTATT
3373833 TAAGTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
AAATTTTTATTATTAATAAATTATATTATT
Found at i:3373848 original size:13 final size:13
Alignment explanation
Indices: 3373832--3373857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3373822 ATTATATTAT
3373832 TTAAGTAATTTTA
1 TTAAGTAATTTTA
3373845 TTAAGTAATTTTA
1 TTAAGTAATTTTA
3373858 ATAAAAAAGT
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:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TTAAGTAATTTTA
Found at i:3374008 original size:14 final size:13
Alignment explanation
Indices: 3373989--3374067 Score: 53
Period size: 12 Copynumber: 6.4 Consensus size: 13
3373979 AATTAATTTA
3373989 TTAATAATAAAAAT
1 TTAATAAT-AAAAT
*
3374003 TTAATAATATAA-
1 TTAATAATAAAAT
3374015 TT--TAATAAAAT
1 TTAATAATAAAAT
* *
3374026 TAAATAATTATAAT
1 TTAATAA-TAAAAT
*
3374040 TT-AT-ATAAAAA
1 TTAATAATAAAAT
*
3374051 TTAAT-ATTAAAT
1 TTAATAATAAAAT
3374063 TTAAT
1 TTAAT
3374068 GATTCGAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
10 7 0.14
11 7 0.14
12 15 0.29
13 8 0.16
14 14 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAATAATAAAAT
Found at i:3374026 original size:10 final size:11
Alignment explanation
Indices: 3373993--3374067 Score: 55
Period size: 11 Copynumber: 6.4 Consensus size: 11
3373983 AATTTATTAA
3373993 TAATAAAAATT
1 TAATAAAAATT
3374004 TAATAATATAATT
1 TAATAA-A-AATT
3374017 TAAT-AAAATT
1 TAATAAAAATT
*
3374027 AAATAATTATAATT
1 TAATAA--A-AATT
3374041 TATATAAAAA-T
1 TA-ATAAAAATT
*
3374052 TAATATTAAATT
1 TAATA-AAAATT
3374064 TAAT
1 TAAT
3374068 GATTCGAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
10 10 0.19
11 14 0.27
12 9 0.17
13 10 0.19
14 5 0.10
15 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATAAAAATT
Found at i:3374031 original size:23 final size:23
Alignment explanation
Indices: 3373993--3374067 Score: 91
Period size: 23 Copynumber: 3.2 Consensus size: 23
3373983 AATTTATTAA
3373993 TAATAAAAATTTAATAATATAATT
1 TAATAAAAA-TTAATAATATAATT
3374017 TAAT-AAAATTAAATAATTATAATT
1 TAATAAAAATT-AATAA-TATAATT
*
3374041 TATATAAAAATTAATATTA-AATT
1 TA-ATAAAAATTAATAATATAATT
3374064 TAAT
1 TAAT
3374068 GATTCGAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
22 4 0.09
23 15 0.33
24 15 0.33
25 6 0.13
26 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAAAAATTAATAATATAATT
Found at i:3374037 original size:24 final size:24
Alignment explanation
Indices: 3373993--3374067 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
3373983 AATTTATTAA
3373993 TAATAAAAATTTAATAA-TATAATT
1 TAATAAAAA-TTAATAATTATAATT
3374017 TAAT-AAAATTAAATAATTATAATT
1 TAATAAAAATT-AATAATTATAATT
3374041 TATATAAAAATTAAT-ATTA-AATT
1 TA-ATAAAAATTAATAATTATAATT
3374064 TAAT
1 TAAT
3374068 GATTCGAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.09
23 15 0.32
24 17 0.36
25 5 0.11
26 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAAAAATTAATAATTATAATT
Found at i:3375435 original size:3 final size:3
Alignment explanation
Indices: 3375421--3375468 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
3375411 TTGTTGGAAA
* * *
3375421 AAT AAG AAT AAT AAT AAT AAT AAT AAT AACT -AT TAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
3375466 AAT
1 AAT
3375469 TATTATTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:3375470 original size:15 final size:15
Alignment explanation
Indices: 3375428--3375474 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
3375418 AAAAATAAGA
* *
3375428 ATAATAATAATAATA
1 ATAATAATAATTATT
3375443 ATAATAACT-ATTATT
1 ATAATAA-TAATTATT
3375458 ATAATAATAATTATT
1 ATAATAATAATTATT
3375473 AT
1 AT
3375475 TAATTTGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAATAATTATT
Found at i:3375472 original size:18 final size:18
Alignment explanation
Indices: 3375440--3375476 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3375430 AATAATAATA
3375440 ATAATAATAACTATTATT
1 ATAATAATAACTATTATT
*
3375458 ATAATAATAATTATTATT
1 ATAATAATAACTATTATT
3375476 A
1 A
3375477 ATTTGGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAATAATAACTATTATT
Found at i:3375817 original size:16 final size:16
Alignment explanation
Indices: 3375798--3375846 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3375788 AAATATTATA
3375798 TATTTTATATAAATTT
1 TATTTTATATAAATTT
* *
3375814 TATTATAT-TAATAATT
1 TATTTTATATAA-ATTT
*
3375830 TATATTATATAAATTT
1 TATTTTATATAAATTT
3375846 T
1 T
3375847 GATATATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTATATAAATTT
Found at i:3375835 original size:18 final size:18
Alignment explanation
Indices: 3375772--3375839 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
3375762 TTATTGTTAG
3375772 TTTATAATTATATTTAA-AA
1 TTTAT-ATTATA-TTAATAA
*
3375791 TATTATA-TATTTTATATAAA
1 T-TTATATTATATTA-AT-AA
3375811 TTT-TATTATATTAATAA
1 TTTATATTATATTAATAA
3375828 TTTATATTATAT
1 TTTATATTATAT
3375840 AAATTTTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
17 8 0.20
18 16 0.39
19 10 0.24
20 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATATTATATTAATAA
Found at i:3375843 original size:32 final size:33
Alignment explanation
Indices: 3375802--3375872 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
3375792 ATTATATATT
3375802 TTATATAAATTTT-ATTATATTAATA-ATTTATA
1 TTATATAAATTTTGA-TATATTAATATATTTATA
* *
3375834 TTATATAAATTTTGATATATTTATATATTTTTA
1 TTATATAAATTTTGATATATTAATATATTTATA
3375867 TTATAT
1 TTATAT
3375873 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TTATATAAATTTTGATATATTAATATATTTATA
Found at i:3375882 original size:18 final size:19
Alignment explanation
Indices: 3375796--3375893 Score: 84
Period size: 18 Copynumber: 5.4 Consensus size: 19
3375786 TAAAATATTA
*
3375796 TATATTTTATATAAATTTTAT
1 TATA-TTTATAT-ATTTTTAT
* *
3375817 TATATTAATA-ATTTATAT
1 TATATTTATATATTTTTAT
*
3375835 TATA--TA-A-ATTTTGA-
1 TATATTTATATATTTTTAT
3375849 TATATTTATATATTTTTAT
1 TATATTTATATATTTTTAT
*
3375868 TATATTTTTAT-TTTTTAT
1 TATATTTATATATTTTTAT
3375886 TATATTTA
1 TATATTTA
3375894 AAATTATATT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 4 0.06
15 6 0.10
16 3 0.05
17 1 0.02
18 30 0.48
19 10 0.16
20 5 0.08
21 4 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (19 bp):
TATATTTATATATTTTTAT
Found at i:3375992 original size:27 final size:24
Alignment explanation
Indices: 3375952--3376028 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 24
3375942 TTATCGAATT
3375952 TTAATTTAATTAAATTATATTTAATATA
1 TTAATTT--TTAAATTATATTT-ATA-A
3375980 TTAATATTTTAAATCATAATATTTATAA
1 TTAAT-TTTTAAAT--T-ATATTTATAA
*
3376008 TTTATTTTTAAATTATGATTT
1 TTAATTTTTAAATTAT-ATTT
3376029 TTTAATATGA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
24 2 0.05
25 5 0.12
27 14 0.33
28 10 0.23
29 6 0.14
30 6 0.14
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (24 bp):
TTAATTTTTAAATTATATTTATAA
Found at i:3376548 original size:29 final size:26
Alignment explanation
Indices: 3376484--3376549 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 26
3376474 TTATTATATG
*
3376484 ATATAAATATAATATAAAAATAATTA
1 ATATATATATAATATAAAAATAATTA
*
3376510 AAATATTATATAATATGAAAAAATAATTTA
1 ATATA-TATATAATAT--AAAAATAA-TTA
3376540 ATATATATAT
1 ATATATATAT
3376550 CAAAATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 4 0.12
27 9 0.27
29 13 0.39
30 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
ATATATATATAATATAAAAATAATTA
Found at i:3379395 original size:22 final size:22
Alignment explanation
Indices: 3379342--3379412 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
3379332 AAAATCATTA
* **
3379342 ATATTTTAAAAATTTTATAAAT
1 ATATATTAAAAATAATATAAAT
* *
3379364 ATATAATAAAAATAATATGAAT
1 ATATATTAAAAATAATATAAAT
*
3379386 ATATCTTAAATACACTAA-ATAAAT
1 ATATATTAAA-A-A-TAATATAAAT
3379410 ATA
1 ATA
3379413 AAAAACACAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 25 0.66
23 1 0.03
24 9 0.24
25 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (22 bp):
ATATATTAAAAATAATATAAAT
Found at i:3382436 original size:15 final size:15
Alignment explanation
Indices: 3382416--3382445 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3382406 TAATTATATA
3382416 TTTAAAGATATAAAT
1 TTTAAAGATATAAAT
*
3382431 TTTAAATATATAAAT
1 TTTAAAGATATAAAT
3382446 ATCTATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TTTAAAGATATAAAT
Found at i:3382840 original size:20 final size:20
Alignment explanation
Indices: 3382815--3382954 Score: 58
Period size: 20 Copynumber: 7.5 Consensus size: 20
3382805 TTCATGATTT
3382815 TTTTATATTATATTTATATA
1 TTTTATATTATATTTATATA
* *
3382835 TTTTAT-TATATAATAAT-TA
1 TTTTATAT-TATATTTATATA
* * *
3382854 TATTTAAAATA-ATTATATAAA
1 T-TTTATATTATATT-TATATA
3382875 TTTTA-A-TATA-TTA-ATA
1 TTTTATATTATATTTATATA
* *
3382891 ATTAATATTATA--TA-A-A
1 TTTTATATTATATTTATATA
*
3382907 TTTTA-A-AATATTTATATA
1 TTTTATATTATATTTATATA
*
3382925 TTTTATATTATTATTT-TACA
1 TTTTATATTA-TATTTATATA
3382945 TTTTA-ATTAT
1 TTTTATATTAT
3382955 TTTTTTAAAC
Statistics
Matches: 90, Mismatches: 15, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
14 3 0.03
15 1 0.01
16 11 0.12
17 7 0.08
18 14 0.16
19 13 0.14
20 34 0.38
21 7 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATATTATATTTATATA
Found at i:3382843 original size:23 final size:23
Alignment explanation
Indices: 3382811--3382856 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3382801 ATAATTCATG
* * *
3382811 ATTTTTTTATATTATATTTATAT
1 ATTTTATTATATAATAATTATAT
3382834 ATTTTATTATATAATAATTATAT
1 ATTTTATTATATAATAATTATAT
3382857 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTATTATATAATAATTATAT
Found at i:3382882 original size:18 final size:18
Alignment explanation
Indices: 3382861--3382912 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 18
3382851 TTATATTTAA
3382861 AATAATTATATAAATTTT
1 AATAATTATATAAATTTT
3382879 AATATATTA-AT-AA--TT
1 AATA-ATTATATAAATTTT
3382894 AAT-ATTATATAAATTTT
1 AATAATTATATAAATTTT
3382911 AA
1 AA
3382913 AATATTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
13 4 0.14
14 2 0.07
15 7 0.24
17 6 0.21
18 6 0.21
19 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATAATTATATAAATTTT
Found at i:3382922 original size:18 final size:19
Alignment explanation
Indices: 3382856--3382929 Score: 72
Period size: 18 Copynumber: 4.2 Consensus size: 19
3382846 AATAATTATA
3382856 TTTAAAATAATTATATAAAT
1 TTTAAAAT-ATTATATAAAT
*
3382876 TTTAATATATTA-AT-AA-
1 TTTAAAATATTATATAAAT
3382892 -TT--AATATTATATAAAT
1 TTTAAAATATTATATAAAT
*
3382908 TTTAAAATATT-TATATAT
1 TTTAAAATATTATATAAAT
3382926 TTTA
1 TTTA
3382930 TATTATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
13 6 0.13
14 2 0.04
15 4 0.09
17 4 0.09
18 12 0.27
19 10 0.22
20 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAAAATATTATATAAAT
Found at i:3382955 original size:19 final size:20
Alignment explanation
Indices: 3382924--3382961 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3382914 ATATTTATAT
3382924 ATTTTATATTATTATTTTAC
1 ATTTTATATTATTATTTTAC
*
3382944 ATTTTA-ATTATTTTTTTA
1 ATTTTATATTATTATTTTA
3382962 AACCATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTATATTATTATTTTAC
Found at i:3383673 original size:28 final size:27
Alignment explanation
Indices: 3383642--3383723 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 27
3383632 ATTGTTGTTC
3383642 ATATTAATTTTACATCATATTTAAAATA
1 ATATTAATTTTA-ATCATATTTAAAATA
* * * *
3383670 ATATAAATTTTAAT-ATATATATATATTT
1 ATATTAATTTTAATCATAT-T-TAAAATA
* *
3383698 ATATTATTTTTTATCATATTTAAAAT
1 ATATTAATTTTAATCATATTTAAAAT
3383724 TATCGAATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
26 4 0.10
27 7 0.17
28 27 0.64
29 4 0.10
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
ATATTAATTTTAATCATATTTAAAATA
Found at i:3385192 original size:3 final size:3
Alignment explanation
Indices: 3385186--3385210 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3385176 AAGAAGAAGA
3385186 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
3385211 TATCTCAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:3386413 original size:16 final size:16
Alignment explanation
Indices: 3386389--3386432 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3386379 TAAAAAAATG
3386389 AAATGTTAAAAAAACAA
1 AAAT-TTAAAAAAACAA
* * *
3386406 AGATTTAAAATAATAA
1 AAATTTAAAAAAACAA
3386422 AAATTTAAAAA
1 AAATTTAAAAA
3386433 TATGAAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (16 bp):
AAATTTAAAAAAACAA
Found at i:3387001 original size:2 final size:2
Alignment explanation
Indices: 3386994--3387024 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3386984 CATTACCATA
*
3386994 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3387025 GGGCTTCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3388218 original size:17 final size:17
Alignment explanation
Indices: 3388196--3388229 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3388186 TGGTATTATT
*
3388196 TTCTTTTGTTCTTTTTC
1 TTCTTTTGTTCATTTTC
*
3388213 TTCTTTTTTTCATTTTC
1 TTCTTTTGTTCATTTTC
3388230 ATATTTCTTT
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:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (17 bp):
TTCTTTTGTTCATTTTC
Found at i:3388664 original size:3 final size:3
Alignment explanation
Indices: 3388656--3388701 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3388646 TATCCTCTCC
3388656 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3388702 GGTCCTTCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3388906 original size:21 final size:22
Alignment explanation
Indices: 3388880--3388933 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
3388870 CGATTCATAG
*
3388880 TTAATTTTTAAATATATA-AAT
1 TTAATTTTTAAATATAAATAAT
*
3388901 TTAATTTATT-TATATAAATAAT
1 TTAATTT-TTAAATATAAATAAT
3388923 TTAATTTTTAA
1 TTAATTTTTAA
3388934 TTTGTAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTTTTAAATATAAATAAT
Found at i:3388921 original size:23 final size:22
Alignment explanation
Indices: 3388886--3388929 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3388876 ATAGTTAATT
*
3388886 TTTAAATATATAAATTTAATTTA
1 TTTAAATAAAT-AATTTAATTTA
*
3388909 TTTATATAAATAATTTAATTT
1 TTTAAATAAATAATTTAATTT
3388930 TTAATTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAATAAATAATTTAATTTA
Found at i:3390396 original size:47 final size:47
Alignment explanation
Indices: 3390317--3390433 Score: 130
Period size: 47 Copynumber: 2.5 Consensus size: 47
3390307 GAAATTAATG
* * *
3390317 AAATTAATATATTATTTATATTAAATTCAATAAATGA-GAATGAGATA
1 AAATTAATATATTATTTAAATTAAATTCAATAAA-AATGAATGAAATA
* * *
3390364 AAATTAATATATCATGTTAAATTTAA-TGAATAAAAATGAATGAAATA
1 AAATTAATATATTAT-TTAAATTAAATTCAATAAAAATGAATGAAATA
*
3390411 AAATTAATAAATTATATTAAATT
1 AAATTAATATATTAT-TTAAATT
3390434 CAATATATCT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 50 0.85
48 8 0.14
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (47 bp):
AAATTAATATATTATTTAAATTAAATTCAATAAAAATGAATGAAATA
Found at i:3390415 original size:231 final size:225
Alignment explanation
Indices: 3389948--3390433 Score: 522
Period size: 231 Copynumber: 2.1 Consensus size: 225
3389938 AATTATAAAT
*
3389948 ATGATAAAATTAA-TAATGTATTAAATTTAATGAAAGAGAAAATATTAATTGATAATAACTTTTA
1 ATGATAAAATTAATTATTGTATTAAATTTAATGAAAGAGAAAATATTAATTGATAATAACTTTTA
*
3390012 TATTATATTTTTAATAATTTAACCATTGAAATTCAATTAAAAAGAGCTAAAATGAAATTCAAAAA
66 TATTATATTTTTAATAATTTAACCATTGAAAATCAATTAAAAAGAGCTAAAA-GAAATTCAAAAA
*
3390077 GTAAAGAATAAAATTTATATATTATATTAAATTTATAGAATAAGAATGAGATAAAATTAATATAT
130 GTAAAGAATAAAATTTATATATTATATTAAATTAATAGAATAAGAATGAGATAAAATTAATATAT
* * **
3390142 TATATTAAACACAATGAAAGAGATAAAATTTT
195 CATATT-AACACAATGAAAGAGATAAAAATGA
* * *
3390174 TTGGTAAAATTAATTTATTGTATTAAATTTAAATTAATGATGAGAAAATATTAATTGATAATAA-
1 ATGATAAAATTAA-TTATTGTATTAAATTT-AATGAA--A-GAGAAAATATTAATTGATAATAAC
** * * * **
3390238 TTTTATATTATATTTTTTGTAATTTAACCATTTAAAATCTATTAAAAATATTTAAACA-AAATTC
61 TTTTATATTATATTTTTAATAATTTAACCATTGAAAATCAATTAAAAAGAGCTAAA-AGAAATTC
* * *
3390302 AAAAAG-AAATTAATGAAATTAATATATTATTTATATTAAATTCAATA-AATGAGAATGAGATAA
125 AAAAAGTAAA-GAATAAAATT--TATA-TA-TTATATTAAATT-AATAGAATAAGAATGAGATAA
* * * *
3390365 AATTAATATATCATGTT-A-A-ATTTAATGA-ATAAAAATGA
184 AATTAATATATCATATTAACACAATGAAAGAGATAAAAATGA
* *
3390403 ATGAAATAAAATTAATAAATTATATTAAATT
1 ATG--ATAAAATTAAT-TATTGTATTAAATT
3390434 CAATATATCT
Statistics
Matches: 216, Mismatches: 28, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
226 11 0.05
228 14 0.06
229 17 0.08
230 27 0.12
231 71 0.33
232 29 0.13
233 2 0.01
234 42 0.19
235 3 0.01
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (225 bp):
ATGATAAAATTAATTATTGTATTAAATTTAATGAAAGAGAAAATATTAATTGATAATAACTTTTA
TATTATATTTTTAATAATTTAACCATTGAAAATCAATTAAAAAGAGCTAAAAGAAATTCAAAAAG
TAAAGAATAAAATTTATATATTATATTAAATTAATAGAATAAGAATGAGATAAAATTAATATATC
ATATTAACACAATGAAAGAGATAAAAATGA
Found at i:3391026 original size:15 final size:16
Alignment explanation
Indices: 3390988--3391029 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3390978 ATTTTATCTA
*
3390988 AAAAATGAAAAAAACTT
1 AAAAAT-AAAAAAACAT
*
3391005 AATAATAAAAAAA-AT
1 AAAAATAAAAAAACAT
3391020 AAAAATAAAA
1 AAAAATAAAA
3391030 CATTCTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 10 0.45
16 7 0.32
17 5 0.23
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAATAAAAAAACAT
Found at i:3391344 original size:21 final size:21
Alignment explanation
Indices: 3391296--3391369 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
3391286 GATTTCGATT
* *
3391296 AAATTAAAAATTATAATGACGATG
1 AAATTAAATATTATAAT-A--ATA
* *
3391320 AAATTTATTATTATAATAATA
1 AAATTAAATATTATAATAATA
3391341 AAATTAAATATTATAATAATA
1 AAATTAAATATTATAATAATA
3391362 AAATTAAA
1 AAATTAAA
3391370 AGTAATAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 29 0.66
23 1 0.02
24 14 0.32
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (21 bp):
AAATTAAATATTATAATAATA
Found at i:3391581 original size:20 final size:20
Alignment explanation
Indices: 3391556--3391615 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
3391546 CATATTTTAA
3391556 ATTAAAAATAAATAATAATT
1 ATTAAAAATAAATAATAATT
*
3391576 ATTAAATAATCACAT-A-AATT
1 ATTAAA-AAT-AAATAATAATT
3391596 ATT-AAAA-AAATAATAATT
1 ATTAAAAATAAATAATAATT
3391614 AT
1 AT
3391616 ATGAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 8 0.24
19 2 0.06
20 13 0.38
21 4 0.12
22 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTAAAAATAAATAATAATT
Found at i:3391584 original size:18 final size:17
Alignment explanation
Indices: 3391561--3391634 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 17
3391551 TTTAAATTAA
3391561 AAATAAATAATAATTATT
1 AAAT-AATAATAATTATT
3391579 AAATAATCACATAAATTATT
1 AAATAAT-A-AT-AATTATT
*
3391599 AAAAAAATAATAATTATAT
1 -AAATAATAATAATTAT-T
* *
3391618 GAATAATTATAATTATT
1 AAATAATAATAATTATT
3391635 TAAAAGCTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
17 4 0.09
18 24 0.51
19 5 0.11
20 8 0.17
21 6 0.13
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
AAATAATAATAATTATT
Found at i:3393097 original size:25 final size:25
Alignment explanation
Indices: 3393037--3393097 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
3393027 ATAATATTTA
*
3393037 TTAATTATTTAATATAAGTATAACTT
1 TTAA-TATTTAATATAAATATAACTT
* *
3393063 TTAGTTTTTAATATAAATATAAC-T
1 TTAATATTTAATATAAATATAACTT
3393087 TTAATAATTTA
1 TTAAT-ATTTA
3393098 TTTTTTAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 5 0.17
25 21 0.72
26 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (25 bp):
TTAATATTTAATATAAATATAACTT
Found at i:3393125 original size:34 final size:32
Alignment explanation
Indices: 3393062--3393127 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
3393052 AAGTATAACT
*
3393062 TTTAGTTTTTAATATAAATATAACTTTAATAA
1 TTTAGTTTTTAATATAAACATAACTTTAATAA
* * *
3393094 TTTATTTTTTAATATATACATAA-TTTATTAA
1 TTTAGTTTTTAATATAAACATAACTTTAATAA
3393125 TTT
1 TTT
3393128 TTAATTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (32 bp):
TTTAGTTTTTAATATAAACATAACTTTAATAA
Found at i:3393798 original size:21 final size:20
Alignment explanation
Indices: 3393774--3393815 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3393764 TACTAATAGT
3393774 TATATAAATTTTTAAAAAAGA
1 TATAT-AATTTTTAAAAAAGA
* *
3393795 TATATCATTTTTAAGAAAGA
1 TATATAATTTTTAAAAAAGA
3393815 T
1 T
3393816 TATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (20 bp):
TATATAATTTTTAAAAAAGA
Found at i:3393806 original size:20 final size:20
Alignment explanation
Indices: 3393781--3393825 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
3393771 AGTTATATAA
3393781 ATTTTTAAAAAAGA-TATATC
1 ATTTTTAAAAAAGATTAT-TC
*
3393801 ATTTTTAAGAAAGATTATTC
1 ATTTTTAAAAAAGATTATTC
3393821 ATTTT
1 ATTTT
3393826 ATATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTTTTAAAAAAGATTATTC
Found at i:3394226 original size:18 final size:16
Alignment explanation
Indices: 3394169--3394261 Score: 75
Period size: 17 Copynumber: 5.6 Consensus size: 16
3394159 CTTGATTTTT
3394169 AATTTATATCTAAATAAA
1 AATTTAT-T-TAAATAAA
* *
3394187 ATATTAATTTAAATCAA
1 A-ATTTATTTAAATAAA
*
3394204 TATTTCATTTCAAATAAA
1 AATTT-ATTT-AAATAAA
*
3394222 AATTTATTTAAATATA
1 AATTTATTTAAATAAA
3394238 AATTTA---AAGATAAA
1 AATTTATTTAA-ATAAA
3394252 AATTTATTTA
1 AATTTATTTA
3394262 GATATAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
13 2 0.03
14 10 0.17
16 15 0.25
17 16 0.27
18 12 0.20
19 5 0.08
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (16 bp):
AATTTATTTAAATAAA
Found at i:3394733 original size:16 final size:15
Alignment explanation
Indices: 3394686--3394734 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
3394676 TATTAATGTT
3394686 ATTAAA-AT-TTATA
1 ATTAAATATATTATA
*
3394699 A-TAAATATATGATA
1 ATTAAATATATTATA
3394713 TATTAAATATAATTATA
1 -ATTAAATAT-ATTATA
3394730 ATTAA
1 ATTAA
3394735 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 4 0.14
13 3 0.10
14 4 0.14
15 1 0.03
16 12 0.41
17 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTAAATATATTATA
Found at i:3394990 original size:13 final size:14
Alignment explanation
Indices: 3394972--3395004 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3394962 ATTAATTATC
3394972 ATATTATTA-AAAA
1 ATATTATTATAAAA
3394985 ATATTATTATAAAA
1 ATATTATTATAAAA
*
3394999 AAATTA
1 ATATTA
3395005 ACATCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTATTATAAAA
Found at i:3395263 original size:59 final size:59
Alignment explanation
Indices: 3395189--3395312 Score: 173
Period size: 59 Copynumber: 2.1 Consensus size: 59
3395179 TCTTTAAATT
* *
3395189 TTAA-AACGCATTAATTTAGTTTTTGATCTTACGTTCT-TAATCAAT-AAGATCTTTTTCG
1 TTAATAACGCATTAATTAAATTTTTGATCTTACGTTCTGT-ATCAATCAA-ATCTTTTTCG
* *
3395247 TTAATAACGTATTAATTAAATTTTTGATCTTACGTTCTGTATCAATCAAATTTTTTTCG
1 TTAATAACGCATTAATTAAATTTTTGATCTTACGTTCTGTATCAATCAAATCTTTTTCG
3395306 TTAATAA
1 TTAATAA
3395313 AACTATTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
58 4 0.07
59 52 0.88
60 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (59 bp):
TTAATAACGCATTAATTAAATTTTTGATCTTACGTTCTGTATCAATCAAATCTTTTTCG
Found at i:3396380 original size:33 final size:32
Alignment explanation
Indices: 3396327--3396397 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
3396317 TGATATATAT
* * *
3396327 ATATCAAATTTTATATAATATAAATTA-TTAA
1 ATATAAAAATTTATATAATATAAAATATTTAA
3396358 CATATAAAAATTTATATAAATATAAAATATTTAA
1 -ATATAAAAATTTATAT-AATATAAAATATTTAA
3396392 ATATAA
1 ATATAA
3396398 TTATATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 14 0.41
33 16 0.47
34 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAAAAATTTATATAATATAAAATATTTAA
Found at i:3396394 original size:15 final size:15
Alignment explanation
Indices: 3396273--3396445 Score: 81
Period size: 15 Copynumber: 11.0 Consensus size: 15
3396263 AATAATTAAA
3396273 ATAT-AATATAAAAT
1 ATATAAATATAAAAT
*
3396287 ATGATAAGACATAAAAT
1 AT-ATAA-ATATAAAAT
3396304 A-ATAACATA-AACATGAT
1 ATATAA-ATATAA-A--AT
* *
3396321 ATATATATATCAAATT
1 ATATAAATAT-AAAAT
* *
3396337 TTATATAATATAAATT
1 ATATA-AATATAAAAT
3396353 AT-TAACATATAAAAATTT
1 ATATAA-ATAT-AAAA--T
3396371 ATATAAATATAAAAT
1 ATATAAATATAAAAT
* *
3396386 ATTTAAATAT-AATT
1 ATATAAATATAAAAT
*
3396400 ATATAAAAATAAAAT
1 ATATAAATATAAAAT
*
3396415 AAAATAAA-AT-AAAT
1 -ATATAAATATAAAAT
3396429 AATATAAATATATAAAT
1 -ATATAAATATA-AAAT
3396446 TACCATATAA
Statistics
Matches: 123, Mismatches: 16, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
14 27 0.22
15 32 0.26
16 21 0.17
17 27 0.22
18 11 0.09
19 5 0.04
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (15 bp):
ATATAAATATAAAAT
Found at i:3396443 original size:8 final size:8
Alignment explanation
Indices: 3396370--3396445 Score: 58
Period size: 8 Copynumber: 10.1 Consensus size: 8
3396360 TATAAAAATT
3396370 TATATAAA
1 TATATAAA
3396378 TATA-AAA
1 TATATAAA
*
3396385 TAT-TTAA
1 TATATAAA
*
3396392 -ATATAAT
1 TATATAAA
3396399 TATATAAA
1 TATATAAA
3396407 -A-ATAAA
1 TATATAAA
3396413 -ATA-AAA
1 TATATAAA
*
3396419 TAAAATAAA
1 T-ATATAAA
3396428 TAATATAAA
1 T-ATATAAA
3396437 TATATAAA
1 TATATAAA
3396445 T
1 T
3396446 TACCATATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
6 11 0.20
7 12 0.22
8 20 0.36
9 12 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TATATAAA
Found at i:3399043 original size:126 final size:126
Alignment explanation
Indices: 3398818--3399070 Score: 470
Period size: 126 Copynumber: 2.0 Consensus size: 126
3398808 AGTTTCAGGT
* * * *
3398818 GTTGCAATAGATGAGGGTCTGGTTGCTGTACCACAGCATCTGAATATAAGTGAAGGTGGGGAGAA
1 GTTGCAATAGATGAGGATCTGGTTGCTGCACCACAGCATATGAATATAAATGAAGGTGGGGAGAA
3398883 AGCTGAAGAAATAAAAGTGGAGGGTTATGGAAATGTTTTTGATAAAGCTGTCACTACTGAA
66 AGCTGAAGAAATAAAAGTGGAGGGTTATGGAAATGTTTTTGATAAAGCTGTCACTACTGAA
3398944 GTTGCAATAGATGAGGATCTGGTTGCTGCACCACAGCATATGAATATAAATGAAGGTGGGGAGAA
1 GTTGCAATAGATGAGGATCTGGTTGCTGCACCACAGCATATGAATATAAATGAAGGTGGGGAGAA
3399009 AGCTGAAGAAATAAAAGTGGAGGGTTATGGAAATGTTTTTGATAAAGCTGTCACTACTGAA
66 AGCTGAAGAAATAAAAGTGGAGGGTTATGGAAATGTTTTTGATAAAGCTGTCACTACTGAA
3399070 G
1 G
3399071 CTCCTCATGA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (126 bp):
GTTGCAATAGATGAGGATCTGGTTGCTGCACCACAGCATATGAATATAAATGAAGGTGGGGAGAA
AGCTGAAGAAATAAAAGTGGAGGGTTATGGAAATGTTTTTGATAAAGCTGTCACTACTGAA
Found at i:3402518 original size:2 final size:2
Alignment explanation
Indices: 3402513--3402538 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3402503 TATATATATA
3402513 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
3402539 ATAATCAGGA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3404754 original size:10 final size:10
Alignment explanation
Indices: 3404741--3404774 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
3404731 TAGGATGCAA
3404741 TATAAAATTT
1 TATAAAATTT
*
3404751 TATAAATTTT
1 TATAAAATTT
3404761 TATAAAATTT
1 TATAAAATTT
3404771 TATA
1 TATA
3404775 CATGCTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TATAAAATTT
Found at i:3407023 original size:2 final size:2
Alignment explanation
Indices: 3407016--3407041 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3407006 CTTTTGTTGT
3407016 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3407042 AGGGCAGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3408595 original size:21 final size:20
Alignment explanation
Indices: 3408560--3408608 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3408550 CACTTTGGTG
3408560 TTTTGTTTTTATGATAATAATA
1 TTTT-TTTTTATGAT-ATAATA
* * *
3408582 TTTTTTTTTCTGATGTCATA
1 TTTTTTTTTATGATATAATA
3408602 TTTTTTT
1 TTTTTTT
3408609 ATCATGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.46
21 9 0.38
22 4 0.17
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTTTTTTATGATATAATA
Found at i:3410293 original size:19 final size:20
Alignment explanation
Indices: 3410266--3410304 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3410256 AAATAATAAA
3410266 CGAAATTAA-ATTTATAATT
1 CGAAATTAATATTTATAATT
* *
3410285 CGAATTTAATTTTTATAATT
1 CGAAATTAATATTTATAATT
3410305 AAAAGTTATC
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:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
CGAAATTAATATTTATAATT
Found at i:3410729 original size:6 final size:6
Alignment explanation
Indices: 3410718--3410784 Score: 54
Period size: 6 Copynumber: 11.5 Consensus size: 6
3410708 TACATTAATT
*
3410718 ATATAA ATATAA ATA-AA ATATAA ATTATTAA ATAT-- ATA-AA ATTTTAA
1 ATATAA ATATAA ATATAA ATATAA A-TA-TAA ATATAA ATATAA A-TATAA
*
3410765 ATATAA ATATAC AT-TAA ATA
1 ATATAA ATATAA ATATAA ATA
3410785 AATTTTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
4 3 0.06
5 10 0.20
6 25 0.51
7 7 0.14
8 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAA
Found at i:3410752 original size:14 final size:14
Alignment explanation
Indices: 3410714--3410772 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 14
3410704 ATATTACATT
3410714 AATTATATAAATATA
1 AATTAT-TAAATATA
3410729 AA-TA--AAATATA
1 AATTATTAAATATA
3410740 AATTATTAAATATATAA
1 AATTATT-AA-ATAT-A
3410757 AATT-TTAAATATA
1 AATTATTAAATATA
3410770 AAT
1 AAT
3410773 ATACATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
11 9 0.24
12 2 0.05
13 4 0.11
14 6 0.16
15 6 0.16
16 6 0.16
17 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTATTAAATATA
Found at i:3410756 original size:16 final size:16
Alignment explanation
Indices: 3410711--3410769 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
3410701 TTAATATTAC
*
3410711 ATTAATTATATAAATAT
1 ATTAAATATATAAAT-T
*
3410728 AAATAAA-ATATAAATT
1 -ATTAAATATATAAATT
3410744 ATTAAATATATAAAATT
1 ATTAAATATAT-AAATT
3410761 -TTAAATATA
1 ATTAAATATA
3410770 AATATACATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 5 0.14
16 14 0.39
17 13 0.36
18 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAATATATAAATT
Found at i:3411390 original size:24 final size:24
Alignment explanation
Indices: 3411338--3411390 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3411328 TTCCACTTGA
*
3411338 ATTATTTTTAATTATAATTTATCT
1 ATTATTTTTAATTAAAATTTATCT
*
3411362 A-TATTTTTTATTCAAAATTTAT-T
1 ATTATTTTTAATT-AAAATTTATCT
3411385 ATTATT
1 ATTATT
3411391 GTCAACTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATTTTTAATTAAAATTTATCT
Found at i:3411653 original size:29 final size:28
Alignment explanation
Indices: 3411617--3411716 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 28
3411607 GATGTAGAGC
3411617 ATAA-ATATAATATAAAAAAATAATTAAA
1 ATAAGATATAATATAAAAAAAT-ATTAAA
* *
3411645 ATAAGATATGATATAAAAAAATATATAAT
1 ATAAGATATAATATAAAAAAATAT-TAAA
** *
3411674 ATAAGATA-AATATGTAAATATATTAAA
1 ATAAGATATAATATAAAAAAATATTAAA
**
3411701 AT-TTATATAATATAAA
1 ATAAGATATAATATAAA
3411717 TTATGAATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
26 3 0.05
27 11 0.19
28 17 0.29
29 27 0.47
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (28 bp):
ATAAGATATAATATAAAAAAATATTAAA
Found at i:3411661 original size:17 final size:16
Alignment explanation
Indices: 3411617--3411687 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 16
3411607 GATGTAGAGC
*
3411617 ATAAATATAATATAAA
1 ATAAATATGATATAAA
3411633 A-AAATA--AT-TAAA
1 ATAAATATGATATAAA
3411645 ATAAGATATGATATAAA
1 ATAA-ATATGATATAAA
* * *
3411662 AAAATATATAATATAAG
1 ATAA-ATATGATATAAA
3411679 ATAAATATG
1 ATAAATATG
3411688 TAAATATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 5 0.11
13 4 0.09
14 3 0.07
15 5 0.11
16 7 0.16
17 20 0.45
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
ATAAATATGATATAAA
Found at i:3411741 original size:15 final size:15
Alignment explanation
Indices: 3411691--3411741 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 15
3411681 AAATATGTAA
3411691 ATATAT-TAAAATTT
1 ATATATATAAAATTT
3411705 ATATA-ATATAAA-TT
1 ATATATATA-AAATTT
3411719 ATGA-ATATAAAATTT
1 AT-ATATATAAAATTT
3411734 ATATATAT
1 ATATATAT
3411742 TTTACAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 16 0.52
15 15 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
ATATATATAAAATTT
Found at i:3412296 original size:44 final size:44
Alignment explanation
Indices: 3412243--3412328 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
3412233 TCTTTCCTTC
* * * *
3412243 CTTTCTTTTTTTTATCAGAACTAAAAAATAATTAAATATGGCTT
1 CTTTATTTTTTTCATCAAAACTAAAAAATAAATAAATATGGCTT
* * *
3412287 CTTTATTTTTTTCATTAAAATTAAAATATAAATAAATATGGC
1 CTTTATTTTTTTCATCAAAACTAAAAAATAAATAAATATGGC
3412329 AAACCATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (44 bp):
CTTTATTTTTTTCATCAAAACTAAAAAATAAATAAATATGGCTT
Found at i:3413238 original size:16 final size:16
Alignment explanation
Indices: 3413197--3413244 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3413187 ATTAAAATAT
3413197 TAATTATATTTTA-TA
1 TAATTATATTTTATTA
*
3413212 TATATTCTATTTTATTA
1 TA-ATTATATTTTATTA
*
3413229 TAATAATA-TTTATTA
1 TAATTATATTTTATTA
3413244 T
1 T
3413245 TAAATTGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 10 0.36
16 14 0.50
17 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTATATTTTATTA
Found at i:3413585 original size:6 final size:6
Alignment explanation
Indices: 3413543--3413581 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
3413533 TGCTCCCTGG
* *
3413543 CATTGC CATTGC CATTGC CATTAC CATTGC CATGGC CAT
1 CATTGC CATTGC CATTGC CATTGC CATTGC CATTGC CAT
3413582 GGCCCCCCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (6 bp):
CATTGC
Found at i:3413741 original size:2 final size:2
Alignment explanation
Indices: 3413734--3413762 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3413724 AAATGAATAT
3413734 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3413763 GGACTTGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3414807 original size:2 final size:2
Alignment explanation
Indices: 3414800--3414827 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3414790 ACTAAAAACT
3414800 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
3414828 AGTCATGGGG
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):
TA
Found at i:3416442 original size:2 final size:2
Alignment explanation
Indices: 3416435--3416462 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3416425 TAACACCTTT
3416435 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
3416463 GCAAGTTTAA
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):
TA
Found at i:3416655 original size:2 final size:2
Alignment explanation
Indices: 3416648--3416676 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3416638 GTCACCTAAC
3416648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3416677 GTTTTATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3417175 original size:3 final size:3
Alignment explanation
Indices: 3417167--3417231 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
3417157 GTTAAAAGAC
3417167 ATA ATA ATA 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 ATA ATA ATA
3417214 ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
3417232 TTATTATTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3418309 original size:24 final size:25
Alignment explanation
Indices: 3418260--3418310 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
3418250 TAATATATAT
*
3418260 TTTTTAAATTTATATTATTATAAAA
1 TTTTTAAATTTAAATTATTATAAAA
*
3418285 TTTTT-AATTTGAAATTA-TATTAAA
1 TTTTTAAATTT-AAATTATTATAAAA
3418309 TT
1 TT
3418311 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTTAAATTTAAATTATTATAAAA
Found at i:3418320 original size:21 final size:21
Alignment explanation
Indices: 3418263--3418345 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
3418253 TATATATTTT
* *
3418263 TTAAATTTATATTATTATAAAA
1 TTAAATTTAAATTA-TATTAAA
*
3418285 TTTTTAATTTGAAATTATATTAAA
1 --TTAAATTT-AAATTATATTAAA
* *
3418309 TTAAATTTAAATAATAAT-AA
1 TTAAATTTAAATTATATTAAA
*
3418329 TAATAATTTAAATTATA
1 TTA-AATTTAAATTATA
3418346 GGTATTTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 4 0.08
21 20 0.41
22 7 0.14
24 13 0.27
25 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
TTAAATTTAAATTATATTAAA
Found at i:3418581 original size:17 final size:18
Alignment explanation
Indices: 3418556--3418611 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
3418546 AAATAATACT
3418556 TATTATTTAATATTAATA
1 TATTATTTAATATTAATA
*
3418574 TATT-TTTAATATATAATT
1 TATTATTTAATAT-TAATA
*
3418592 TATTATTTAATATAAATA
1 TATTATTTAATATTAATA
3418610 TA
1 TA
3418612 ATTTTAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.24
18 17 0.52
19 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTTAATATTAATA
Found at i:3418600 original size:19 final size:19
Alignment explanation
Indices: 3418555--3418605 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 19
3418545 TAAATAATAC
3418555 TTATTATTTAATAT-TAAT
1 TTATTATTTAATATATAAT
*
3418573 ATATT-TTTAATATATAAT
1 TTATTATTTAATATATAAT
3418591 TTATTATTTAATATA
1 TTATTATTTAATATA
3418606 AATATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 12 0.41
19 9 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATTTAATATATAAT
Found at i:3418617 original size:17 final size:17
Alignment explanation
Indices: 3418556--3418618 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
3418546 AAATAATACT
*
3418556 TATTATTTAATATTAATA
1 TATT-TTTAATATAAATA
*
3418574 TATTTTTAATATATAATT
1 TATTTTTAATATA-AATA
3418592 TATTATTTAATATAAATA
1 TATT-TTTAATATAAATA
*
3418610 TAATTTTAA
1 TATTTTTAA
3418619 CAATTCTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
17 13 0.33
18 17 0.44
19 9 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTTAATATAAATA
Found at i:3418706 original size:25 final size:25
Alignment explanation
Indices: 3418677--3418734 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3418667 TTTTATTTAT
*
3418677 ATTTTATTATTTAATATAAATATAA
1 ATTTTAATATTTAATATAAATATAA
* * **
3418702 ATTTTAATATTTATTATATATATTC
1 ATTTTAATATTTAATATAAATATAA
3418727 ATTTTAAT
1 ATTTTAAT
3418735 CTAATATCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTAATATTTAATATAAATATAA
Found at i:3419957 original size:35 final size:34
Alignment explanation
Indices: 3419918--3419988 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 34
3419908 AGTATATGTG
3419918 TATATATATAATAAAGAATTAAAAAT-AATTAAAAT
1 TATATATATAATAAAGAA-TAAAAATGAA-TAAAAT
* * * *
3419953 TATATTTATATTAAATAATAAATATGAATAAAAT
1 TATATATATAATAAAGAATAAAAATGAATAAAAT
3419987 TA
1 TA
3419989 AATTTATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 14 0.45
35 17 0.55
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (34 bp):
TATATATATAATAAAGAATAAAAATGAATAAAAT
Found at i:3420055 original size:16 final size:15
Alignment explanation
Indices: 3420026--3420059 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3420016 TGAAAATGAT
3420026 ATTTATTAAATAATA
1 ATTTATTAAATAATA
*
3420041 ATTTAATTAATTAATA
1 ATTT-ATTAAATAATA
3420057 ATT
1 ATT
3420060 AAAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATTAAATAATA
Found at i:3420538 original size:19 final size:20
Alignment explanation
Indices: 3420488--3420538 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3420478 TTTTGGTGAA
* * *
3420488 ATAAAAATTTTATTAAATTG
1 ATAAAAATTTAATCAAATGG
3420508 ATAAAAATTTAATCAAATGG
1 ATAAAAATTTAATCAAATGG
3420528 AT-AAAATTTAA
1 ATAAAAATTTAA
3420539 AAAAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (20 bp):
ATAAAAATTTAATCAAATGG
Found at i:3420585 original size:22 final size:23
Alignment explanation
Indices: 3420551--3420595 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3420541 AAATTATTTT
3420551 TTTAAAAAATTAAATA-ATTAAA
1 TTTAAAAAATTAAATATATTAAA
** *
3420573 TTTAAAATTTTAATTATATTAAA
1 TTTAAAAAATTAAATATATTAAA
3420596 AAGTTATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTAAAAAATTAAATATATTAAA
Found at i:3420667 original size:22 final size:22
Alignment explanation
Indices: 3420641--3420682 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3420631 AAATTTTTAT
*
3420641 ATTAAATTAAATAATTTAATCA
1 ATTAAATTAAATAAATTAATCA
* *
3420663 ATTAATTTAATTAAATTAAT
1 ATTAAATTAAATAAATTAAT
3420683 AACCGCAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAAATTAAATAAATTAATCA
Found at i:3420789 original size:16 final size:16
Alignment explanation
Indices: 3420768--3420818 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3420758 TTATATTCAA
3420768 TAATTATATTAAATTT
1 TAATTATATTAAATTT
* *
3420784 TAATTATTTTAAAATT
1 TAATTATATTAAATTT
*
3420800 AAATT-TAATTAAATTT
1 TAATTAT-ATTAAATTT
3420816 TAA
1 TAA
3420819 ATAATAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTATATTAAATTT
Found at i:3420820 original size:22 final size:22
Alignment explanation
Indices: 3420775--3420819 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
3420765 CAATAATTAT
3420775 ATTAAATTTTAATTATTTTAAA
1 ATTAAATTTTAATTATTTTAAA
3420797 ATTAAA-TTTAATTAAATTTTAAA
1 ATTAAATTTTAATT--ATTTTAAA
3420820 TAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
23 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTAAATTTTAATTATTTTAAA
Found at i:3421250 original size:39 final size:39
Alignment explanation
Indices: 3421156--3421257 Score: 141
Period size: 39 Copynumber: 2.6 Consensus size: 39
3421146 CTTCAAAACC
* * *
3421156 AAATTGTACGGTCCAGATCATTCAATCGGGACAGACTGT
1 AAATTGTACGGTCCAGATCATTTAATCGAGACAGACAGT
*
3421195 AAATTGTACCGTCCAGATCATTTAATCGAGACAGACAGT
1 AAATTGTACGGTCCAGATCATTTAATCGAGACAGACAGT
* *
3421234 AAATTGTAAGGACCAGATCGATTT
1 AAATTGTACGGTCCAGATC-ATTT
3421258 CTCAGTACCC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 51 0.93
40 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (39 bp):
AAATTGTACGGTCCAGATCATTTAATCGAGACAGACAGT
Found at i:3421437 original size:16 final size:16
Alignment explanation
Indices: 3421418--3421528 Score: 75
Period size: 16 Copynumber: 6.9 Consensus size: 16
3421408 TAACAAAAAT
3421418 TAAATATAATATAATA
1 TAAATATAATATAATA
*
3421434 TAAATATAATATTATTTAA
1 TAAATATAATA-TA-AT-A
* *
3421453 TAAATATATTA-AATT
1 TAAATATAATATAATA
* *
3421468 TATATATAA-ATTATA
1 TAAATATAATATAATA
* *
3421483 AAATATATAATATATTA
1 TAA-ATATAATATAATA
* *
3421500 AAAATA-AATTTAATA
1 TAAATATAATATAATA
*
3421515 TAAAAATAATATAA
1 TAAATATAATATAA
3421529 ATATTATTTA
Statistics
Matches: 71, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
14 1 0.01
15 21 0.30
16 27 0.38
17 10 0.14
18 1 0.01
19 11 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATATAATATAATA
Found at i:3421441 original size:11 final size:11
Alignment explanation
Indices: 3421420--3421532 Score: 66
Period size: 11 Copynumber: 11.0 Consensus size: 11
3421410 ACAAAAATTA
3421420 AATAT-AATAT
1 AATATAAATAT
3421430 AATATAAATAT
1 AATATAAATAT
*
3421441 AATAT-TAT-T
1 AATATAAATAT
*
3421450 TA-ATAAATAT
1 AATATAAATAT
*
3421460 -AT-TAAATTT
1 AATATAAATAT
3421469 ATATATAAATTAT
1 A-ATATAAA-TAT
*
3421482 AA-A-ATATAT
1 AATATAAATAT
*
3421491 AATAT-ATTA-
1 AATATAAATAT
* *
3421500 AAAATAAATTT
1 AATATAAATAT
*
3421511 AATATAAAAAT
1 AATATAAATAT
3421522 AATATAAATAT
1 AATATAAATAT
3421533 TATTTATATA
Statistics
Matches: 76, Mismatches: 15, Indels: 23
0.67 0.13 0.20
Matches are distributed among these distances:
8 2 0.03
9 20 0.26
10 15 0.20
11 31 0.41
12 5 0.07
13 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATAAATAT
Found at i:3421499 original size:19 final size:19
Alignment explanation
Indices: 3421426--3421505 Score: 63
Period size: 20 Copynumber: 4.1 Consensus size: 19
3421416 ATTAAATATA
* *
3421426 ATATAATATAAATATAATATT
1 ATATAATA-AATTATAA-AAT
* *
3421447 ATTTAATAAATATATTAAAT
1 ATATAATAAAT-TATAAAAT
*
3421467 TTATATATAAATTATAAAAT
1 ATATA-ATAAATTATAAAAT
*
3421487 ATATAATATATTA-AAAAT
1 ATATAATAAATTATAAAAT
3421505 A
1 A
3421506 AATTTAATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
18 6 0.12
19 7 0.15
20 18 0.38
21 17 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAATAAATTATAAAAT
Found at i:3421780 original size:20 final size:20
Alignment explanation
Indices: 3421757--3421813 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 20
3421747 TGTATTATTT
3421757 TTATTAAATTTAAATAAAAA
1 TTATTAAATTTAAATAAAAA
*
3421777 TTA-TACA-TTAAATATAAAA
1 TTATTAAATTTAAATA-AAAA
* *
3421796 -TATTTAGTTTAAA-AAAAA
1 TTATTAAATTTAAATAAAAA
3421814 GCACAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
18 13 0.43
19 9 0.30
20 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TTATTAAATTTAAATAAAAA
Found at i:3422732 original size:11 final size:11
Alignment explanation
Indices: 3422716--3422751 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3422706 ATAATTAAAT
3422716 TTTAAATTATA
1 TTTAAATTATA
3422727 TTTAAATTATA
1 TTTAAATTATA
*
3422738 TTT-TATTATA
1 TTTAAATTATA
3422748 TTTA
1 TTTA
3422752 TTATATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAAATTATA
Found at i:3422747 original size:21 final size:21
Alignment explanation
Indices: 3422721--3422784 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
3422711 TAAATTTTAA
3422721 ATTATATTTAAATTATATTTT
1 ATTATATTTAAATTATATTTT
3422742 ATTATATTTATTATATTAT-TTTT
1 ATTATATTTA--A-ATTATATTTT
3422765 ATGTATA-TTAAA-TATATTTT
1 AT-TATATTTAAATTATATTTT
3422785 TCATGTCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.08
20 5 0.13
21 11 0.29
23 10 0.26
24 9 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTATATTTAAATTATATTTT
Found at i:3422771 original size:24 final size:24
Alignment explanation
Indices: 3422732--3422782 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3422722 TTATATTTAA
* *
3422732 ATTATATTTTATTATATTTATTAT
1 ATTATATTTTATTATATTAAATAT
3422756 ATTAT-TTTTATGTATATTAAATAT
1 ATTATATTTTAT-TATATTAAATAT
3422780 ATT
1 ATT
3422783 TTTCATGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTATATTTTATTATATTAAATAT
Found at i:3423706 original size:12 final size:13
Alignment explanation
Indices: 3423666--3423708 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
3423656 AAATATTTAG
3423666 ATATTAATATATA
1 ATATTAATATATA
* *
3423679 TTATTATATATTTA
1 ATATTA-ATATATA
3423693 ATATTAA-ATATA
1 ATATTAATATATA
3423705 ATAT
1 ATAT
3423709 AGATAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 8 0.32
13 6 0.24
14 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTAATATATA
Found at i:3424020 original size:21 final size:21
Alignment explanation
Indices: 3423996--3424035 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3423986 TGCATAAATG
3423996 TTTTAT-TTAGTATAATTTATA
1 TTTTATATTAGTA-AATTTATA
*
3424017 TTTTATATTATTAAATTTA
1 TTTTATATTAGTAAATTTA
3424036 ATATCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTATATTAGTAAATTTATA
Found at i:3424722 original size:13 final size:13
Alignment explanation
Indices: 3424699--3424732 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3424689 TGTTATTATT
3424699 TATAA-AAAAATA
1 TATAATAAAAATA
3424711 TATAATAAAAATA
1 TATAATAAAAATA
*
3424724 TAAAATAAA
1 TATAATAAA
3424733 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TATAATAAAAATA
Found at i:3425071 original size:18 final size:17
Alignment explanation
Indices: 3425050--3425092 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3425040 GTTAAAAAAA
3425050 TTATAATTTATATTATAT
1 TTATAATTT-TATTATAT
3425068 TTATATATTTTATTATAT
1 TTATA-ATTTTATTATAT
3425086 TT-TAATT
1 TTATAATT
3425093 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.12
17 2 0.08
18 15 0.62
19 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATTTTATTATAT
Found at i:3425079 original size:20 final size:20
Alignment explanation
Indices: 3425051--3425212 Score: 69
Period size: 20 Copynumber: 8.2 Consensus size: 20
3425041 TTAAAAAAAT
*
3425051 TATAATTTATATTATATTTA
1 TATATTTTATATTATATTTA
3425071 TATA-TTT-TATTATATTT-
1 TATATTTTATATTATATTTA
*
3425088 TAATTATTTTTAAATTAT-TTT-
1 T-A-TA-TTTTATATTATATTTA
*
3425109 TAT-TTTTATA-AAT-TTTAA
1 TATATTTTATATTATATTT-A
*
3425127 TACATTATTA-ATT-TATATTA
1 TATATT-TTATATTATAT-TTA
** *
3425147 TATATGTTT-TAAGATATGTA
1 TATAT-TTTATATTATATTTA
* *
3425167 TTTATTTTGTATCATATATTTA
1 TATATTTTATAT--TATATTTA
3425189 -ATATTTTATATGTATATTTA
1 TATATTTTATAT-TATATTTA
3425209 TATA
1 TATA
3425213 ATTATATTTA
Statistics
Matches: 107, Mismatches: 16, Indels: 37
0.67 0.10 0.23
Matches are distributed among these distances:
16 5 0.05
17 7 0.07
18 13 0.12
19 13 0.12
20 33 0.31
21 25 0.23
22 11 0.10
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.60
Consensus pattern (20 bp):
TATATTTTATATTATATTTA
Found at i:3425086 original size:10 final size:10
Alignment explanation
Indices: 3425049--3425112 Score: 55
Period size: 11 Copynumber: 6.3 Consensus size: 10
3425039 TGTTAAAAAA
3425049 ATTATAATTTAT
1 ATTAT-ATTT-T
3425061 ATTATA-TTT
1 ATTATATTTT
3425070 A-TATATTTT
1 ATTATATTTT
3425079 ATTATATTTT
1 ATTATATTTT
3425089 AATTAT-TTTT
1 -ATTATATTTT
3425099 AAATTAT-TTTT
1 --ATTATATTTT
3425110 ATT
1 ATT
3425113 TTTATAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.08
9 9 0.19
10 14 0.29
11 16 0.33
12 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTATATTTT
Found at i:3425198 original size:14 final size:14
Alignment explanation
Indices: 3425180--3425222 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3425170 ATTTTGTATC
3425180 ATATATTTAATATTT
1 ATATATTT-ATATTT
*
3425195 -TATATGTATATTT
1 ATATATTTATATTT
*
3425208 ATATAATTATATTT
1 ATATATTTATATTT
3425222 A
1 A
3425223 AAAATTAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
ATATATTTATATTT
Found at i:3425217 original size:20 final size:20
Alignment explanation
Indices: 3425181--3425219 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3425171 TTTTGTATCA
*
3425181 TATATTTAATATTTTATATG
1 TATATTTAATATATTATATG
3425201 TATATTT-ATATAATTATAT
1 TATATTTAATAT-ATTATAT
3425220 TTAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATATTTAATATATTATATG
Found at i:3426919 original size:8 final size:8
Alignment explanation
Indices: 3426861--3426978 Score: 52
Period size: 9 Copynumber: 14.4 Consensus size: 8
3426851 AAATAATAAT
3426861 TAAA-ATA
1 TAAATATA
3426868 T-AATAT-
1 TAAATATA
3426874 TAAATATGA
1 TAAATAT-A
3426883 TAAA-ATA
1 TAAATATA
*
3426890 TAAAAAATA
1 T-AAATATA
3426899 TAAATATTA
1 TAAATA-TA
3426908 TATAAGTATA
1 TA-AA-TATA
3426918 TAAATATAA
1 TAAATAT-A
3426927 TAAA-AT-
1 TAAATATA
**
3426933 TATTTAATA
1 TAAAT-ATA
*
3426942 TAAGT-TA
1 TAAATATA
*
3426949 TTAATATA
1 TAAATATA
3426957 TCAAAATAATA
1 T--AAAT-ATA
3426968 TAAATATA
1 TAAATATA
3426976 TAA
1 TAA
3426979 TGTAAATACA
Statistics
Matches: 86, Mismatches: 8, Indels: 33
0.68 0.06 0.26
Matches are distributed among these distances:
6 5 0.06
7 15 0.17
8 25 0.29
9 26 0.30
10 9 0.10
11 6 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (8 bp):
TAAATATA
Found at i:3426975 original size:19 final size:18
Alignment explanation
Indices: 3426867--3426978 Score: 77
Period size: 19 Copynumber: 5.9 Consensus size: 18
3426857 TAATTAAAAT
3426867 ATAATATTAAATATGATAAA
1 ATAATA-TAAATAT-ATAAA
*
3426887 AT-ATA-AAAAATATAAA
1 ATAATATAAATATATAAA
* *
3426903 TATTATATAAGTATATAAA
1 -ATAATATAAATATATAAA
* *
3426922 TATAATA-AAATTATTTAAT
1 -ATAATATAAA-TATATAAA
*
3426941 ATAAGTTATTAATATATCAAA
1 ATAA--TATAAATATAT-AAA
3426962 ATAATATAAATATATAA
1 ATAATATAAATATATAA
3426979 TGTAAATACA
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
16 5 0.07
17 7 0.10
18 11 0.15
19 34 0.47
20 8 0.11
21 8 0.11
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAATATAAATATATAAA
Found at i:3426978 original size:13 final size:13
Alignment explanation
Indices: 3426846--3426986 Score: 59
Period size: 13 Copynumber: 10.8 Consensus size: 13
3426836 ATATACACAA
*
3426846 AATAAAAATA-AT
1 AATATAAATATAT
3426858 AAT-TAAA-ATAT
1 AATATAAATATAT
3426869 AATATTAAATATGAT
1 AATA-TAAATAT-AT
*
3426884 AAAATATAAAAAATAT
1 --AATAT-AAATATAT
*
3426900 AA-AT-ATTATAT
1 AATATAAATATAT
3426911 AAGTATATAA-ATAT
1 AA-TATA-AATATAT
*
3426925 AATA-AAATTATTT
1 AATATAAA-TATAT
*
3426938 AATATAAGT-TATT
1 AATATAAATATA-T
3426951 AATATATCAA-A-AT
1 AATATA--AATATAT
3426964 AATATAAATATAT
1 AATATAAATATAT
*
3426977 AATGTAAATA
1 AATATAAATA
3426987 CAAAAATTAC
Statistics
Matches: 98, Mismatches: 10, Indels: 41
0.66 0.07 0.28
Matches are distributed among these distances:
10 1 0.01
11 19 0.19
12 6 0.06
13 43 0.44
14 13 0.13
15 4 0.04
16 3 0.03
17 9 0.09
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:3427259 original size:26 final size:26
Alignment explanation
Indices: 3427225--3427283 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
3427215 AATAAGTTAT
3427225 AAATAAATTAAAATAATAATAAAAATA
1 AAAT-AATTAAAATAATAATAAAAATA
** *
3427252 AAATAATTATTATAATAATAAAATTA
1 AAATAATTAAAATAATAATAAAAATA
3427278 AAATAA
1 AAATAA
3427284 ATTATGAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAATTAAAATAATAATAAAAATA
Found at i:3433535 original size:2 final size:2
Alignment explanation
Indices: 3433528--3433565 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3433518 CATGACTTTT
* *
3433528 TA TA TA TA TA TA TA TA TG TT 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
3433566 AAAGAAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Done.