Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
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: 2064896
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 13
Found at i:137441 original size:16 final size:16
Alignment explanation
Indices: 137420--137462 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
137410 TAATTTTTTT
*
137420 ATTTAAATTTAAATAA
1 ATTTAAAATTAAATAA
*
137436 ATTTAAAATTAAATTA
1 ATTTAAAATTAAATAA
137452 ATTTAATAATT
1 ATTTAA-AATT
137463 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTAAAATTAAATAA
Found at i:137916 original size:13 final size:12
Alignment explanation
Indices: 137841--137922 Score: 52
Period size: 13 Copynumber: 7.2 Consensus size: 12
137831 TTTAATTCGT
137841 AATTA-AATTT-
1 AATTATAATTTA
*
137851 ATTTATAATTTA
1 AATTATAATTTA
137863 AATTATAATTTA
1 AATTATAATTTA
137875 AA--A-AA-TTA
1 AATTATAATTTA
*
137883 AAAT-TAATTTA
1 AATTATAATTTA
**
137894 TTTTAATAATTTA
1 AATT-ATAATTTA
*
137907 AATTATTAATTAA
1 AATTA-TAATTTA
137920 AAT
1 AAT
137923 AAAATATTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 5 0.09
9 2 0.04
10 7 0.13
11 9 0.16
12 14 0.25
13 18 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTATAATTTA
Found at i:138580 original size:23 final size:23
Alignment explanation
Indices: 138554--138598 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
138544 TTTTAAATAA
138554 TAAAATAAAATATTAAAT-TAAAT
1 TAAAATAAAATA-TAAATGTAAAT
* *
138577 TAAATTTAAATATAAATGTAAA
1 TAAAATAAAATATAAATGTAAA
138599 AAATTTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAAATAAAATATAAATGTAAAT
Found at i:138592 original size:12 final size:12
Alignment explanation
Indices: 138530--138598 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
138520 ATTATTTATG
*
138530 AAATTTAAAAAT
1 AAATTTAAATAT
**
138542 ATTTTTAAATAAT
1 AAATTTAAAT-AT
* *
138555 AAAATAAAATATT
1 AAATTTAAATA-T
138568 AAA-TTAAAT-T
1 AAATTTAAATAT
138578 AAATTTAAATAT
1 AAATTTAAATAT
*
138590 AAATGTAAA
1 AAATTTAAA
138599 AAATTTCTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
10 4 0.09
11 6 0.14
12 22 0.50
13 12 0.27
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
AAATTTAAATAT
Found at i:141165 original size:16 final size:15
Alignment explanation
Indices: 141123--141154 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
141113 TTTTATTTAA
*
141123 ATTAAATATAAAAAT
1 ATTAATTATAAAAAT
141138 ATTAATTATAAAAAT
1 ATTAATTATAAAAAT
141153 AT
1 AT
141155 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAATTATAAAAAT
Found at i:141859 original size:34 final size:34
Alignment explanation
Indices: 141780--141859 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
141770 AAATCAATAT
*
141780 ATATTTTTAAACAAACTTAAATAAATAATTAAAA
1 ATATTTTTAAATAAACTTAAATAAATAATTAAAA
141814 ATATTTTTAAATAAACTTAAATAAATAATTAAAA
1 ATATTTTTAAATAAACTTAAATAAATAATTAAAA
141848 ATATTTTTAAAT
1 ATATTTTTAAAT
141860 CGTAATTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (34 bp):
ATATTTTTAAATAAACTTAAATAAATAATTAAAA
Found at i:142342 original size:17 final size:17
Alignment explanation
Indices: 142309--142342 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
142299 AGTTAAGTTC
* *
142309 AATTCTTTTTAATTTTA
1 AATTCTTTTAAAATTTA
142326 AATTCTTTTAAAATTTA
1 AATTCTTTTAAAATTTA
142343 TCACATAATA
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:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTCTTTTAAAATTTA
Found at i:143013 original size:12 final size:12
Alignment explanation
Indices: 142960--143024 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
142950 ATAAAAATAA
142960 AATTTAAGTATTT
1 AATTTAAGTA-TT
142973 AATTATAAGT-TT
1 AATT-TAAGTATT
142985 --TTTAAGTATT
1 AATTTAAGTATT
*
142995 AAATTAA-TATAT
1 AATTTAAGTAT-T
*
143007 AATTTAAGTACT
1 AATTTAAGTATT
143019 AATTTA
1 AATTTA
143025 TATATTTACC
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
9 5 0.12
10 4 0.09
11 3 0.07
12 20 0.47
13 6 0.14
14 5 0.12
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (12 bp):
AATTTAAGTATT
Found at i:143022 original size:23 final size:24
Alignment explanation
Indices: 142985--143029 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
142975 TTATAAGTTT
*
142985 TTTAAGTATTAAATTAATATATAA
1 TTTAAGTACTAAATTAATATATAA
*
143009 TTTAAGTACT-AATTTATATAT
1 TTTAAGTACTAAATTAATATAT
143030 TTACCCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
TTTAAGTACTAAATTAATATATAA
Found at i:143275 original size:11 final size:11
Alignment explanation
Indices: 143247--143285 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
143237 AGTTAAATTT
143247 AAATTTGATTC
1 AAATTTGATTC
143258 AAAATTTGATTC
1 -AAATTTGATTC
*
143270 AAATTTAATT-
1 AAATTTGATTC
143280 AAATTT
1 AAATTT
143286 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 6 0.23
11 9 0.35
12 11 0.42
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (11 bp):
AAATTTGATTC
Found at i:145839 original size:19 final size:19
Alignment explanation
Indices: 145815--145852 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
145805 AATATGATAA
145815 TCTGGATCCAAATAAATTG
1 TCTGGATCCAAATAAATTG
145834 TCTGGATCCAAATAAATTG
1 TCTGGATCCAAATAAATTG
145853 CAATCTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
TCTGGATCCAAATAAATTG
Found at i:147121 original size:18 final size:18
Alignment explanation
Indices: 147098--147140 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
147088 AATATAATAT
* *
147098 AAAAATTAATTTTTTAAA
1 AAAAATTAAATTTATAAA
147116 AAAAATTAAATTTATAAA
1 AAAAATTAAATTTATAAA
147134 AAAAATT
1 AAAAATT
147141 TATAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATTAAATTTATAAA
Found at i:147141 original size:13 final size:13
Alignment explanation
Indices: 147123--147148 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
147113 AAAAAAAATT
147123 AAATTTATAAAAA
1 AAATTTATAAAAA
147136 AAATTTATAAAAA
1 AAATTTATAAAAA
147149 TAAAAATATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTTATAAAAA
Found at i:147169 original size:19 final size:19
Alignment explanation
Indices: 147147--147186 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
147137 AATTTATAAA
*
147147 AATAAAAATATTTATATTT
1 AATAAAAATATTTAAATTT
**
147166 AATATTAATATTTAAATTT
1 AATAAAAATATTTAAATTT
147185 AA
1 AA
147187 ATAATATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAAAAATATTTAAATTT
Found at i:147171 original size:13 final size:13
Alignment explanation
Indices: 147153--147185 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
147143 TAAAAATAAA
147153 AATATTTATATTT
1 AATATTTATATTT
*
147166 AATATTAATATTT
1 AATATTTATATTT
147179 AA-ATTTA
1 AATATTTA
147186 AATAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:147240 original size:28 final size:28
Alignment explanation
Indices: 147187--147240 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
147177 TTAAATTTAA
***
147187 ATAATATAAAAATATTTTAAATATAATT
1 ATAATATAAAAATAAAATAAATATAATT
147215 ATAATATAAAAATAAAAATAAA-ATAA
1 ATAATATAAAAAT-AAAATAAATATAA
147241 AACTCGCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 17 0.77
29 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATAAAAATAAAATAAATATAATT
Found at i:148159 original size:24 final size:27
Alignment explanation
Indices: 148106--148163 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
148096 TTATGACGAG
*
148106 AAAT-TTATTATAATTTAGTATATAAT
1 AAATATTATTATAATTTAATATATAAT
148132 AAATATTATTATAA-TTAAT-TATAA-
1 AAATATTATTATAATTTAATATATAAT
148156 AAATATTA
1 AAATATTA
148164 ATGAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 8 0.27
25 5 0.17
26 8 0.27
27 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
AAATATTATTATAATTTAATATATAAT
Found at i:148196 original size:14 final size:15
Alignment explanation
Indices: 148142--148199 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
148132 AAATATTATT
*
148142 ATAATTAATTATAAA
1 ATAATTAATCATAAA
*
148157 A-ATATTAATGA-AAA
1 ATA-ATTAATCATAAA
148171 ATAATTAAATCATAAA
1 ATAATT-AATCATAAA
148187 ATAATT-ATCATAA
1 ATAATTAATCATAA
148200 TGCCGTATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 15 0.41
15 13 0.35
16 9 0.24
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (15 bp):
ATAATTAATCATAAA
Found at i:148336 original size:20 final size:21
Alignment explanation
Indices: 148292--148344 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
148282 TTAATTTTTT
* * *
148292 AAATTTAAACTAAACATAAAT
1 AAATTTAAATTTAACATAAAA
148313 AAATTTAAATTTAA-ATAAAA
1 AAATTTAAATTTAACATAAAA
*
148333 AAATTAAAATTT
1 AAATTTAAATTT
148345 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTTAAATTTAACATAAAA
Found at i:149565 original size:11 final size:11
Alignment explanation
Indices: 149549--149590 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
149539 CTAATCAATT
*
149549 TAAATATTAAA
1 TAAATAATAAA
149560 TAAATAATAAA
1 TAAATAATAAA
149571 T--ATAATAAA
1 TAAATAATAAA
*
149580 TAATTAATAAA
1 TAAATAATAAA
149591 AATACTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:149579 original size:16 final size:16
Alignment explanation
Indices: 149558--149588 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
149548 TTAAATATTA
149558 AATAAATAATAAATAT
1 AATAAATAATAAATAT
*
149574 AATAAATAATTAATA
1 AATAAATAATAAATA
149589 AAAATACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAATAATAAATAT
Found at i:150208 original size:19 final size:19
Alignment explanation
Indices: 150177--150271 Score: 54
Period size: 19 Copynumber: 4.9 Consensus size: 19
150167 CTTAGACTTG
150177 AAAATCAAT-TTTATTATTT
1 AAAAT-AATATTTATTATTT
**
150196 AAAATAATATTTAAAAATTT
1 AAAATAATATTT-ATTATTT
*
150216 AAAA-AA-ATTTTTTATATT
1 AAAATAATATTTATTAT-TT
* * *
150234 AAAATTTATAATTA-AATTT
1 AAAA-TAATATTTATTATTT
*
150253 AAATAAAATATTTATTATT
1 AAA-ATAATATTTATTATT
150272 ATTTATCAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 15
0.66 0.16 0.18
Matches are distributed among these distances:
17 2 0.04
18 13 0.24
19 21 0.38
20 16 0.29
21 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATAATATTTATTATTT
Found at i:150226 original size:38 final size:38
Alignment explanation
Indices: 150183--150271 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 38
150173 CTTGAAAATC
*
150183 AATTTTATTATTTAAAA-TAATATTTAAAAATTTAAA-AA
1 AATTTTATTATTTAAAATTAATAATT--AAATTTAAATAA
*
150221 AATTTT-TTATATTAAAATTTATAATTAAATTTAAATAA
1 AATTTTATTAT-TTAAAATTAATAATTAAATTTAAATAA
150259 AATATTTATTATT
1 AAT-TTTATTATT
150272 ATTTATCAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
37 13 0.30
38 17 0.39
39 10 0.23
40 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
AATTTTATTATTTAAAATTAATAATTAAATTTAAATAA
Found at i:151505 original size:14 final size:15
Alignment explanation
Indices: 151486--151523 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
151476 TGAGTTTAAA
151486 TTTAATTTTT-ATTT
1 TTTAATTTTTAATTT
151500 TTTAATTTTTAATTT
1 TTTAATTTTTAATTT
151515 TTTATATTT
1 TTTA-ATTT
151524 AAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.45
15 8 0.36
16 4 0.18
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTAATTTTTAATTT
Found at i:151524 original size:21 final size:21
Alignment explanation
Indices: 151486--151525 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
151476 TGAGTTTAAA
*
151486 TTTAATTTTTATTTTTTAATT
1 TTTAATTTTTATTATTTAATT
151507 TTTAATTTTT-TATATTTAA
1 TTTAATTTTTAT-TATTTAA
151526 AAAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTAATTTTTATTATTTAATT
Found at i:155420 original size:2 final size:2
Alignment explanation
Indices: 155408--155444 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
155398 GAGCCAAACA
155408 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155445 CTCCGTTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:155581 original size:27 final size:26
Alignment explanation
Indices: 155534--155600 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 26
155524 ATAAATTTTG
* *
155534 ATATATTTATTTATTCGTATTTTATT
1 ATATATTTATTTATTCATATTATATT
*
155560 CATATATTT-TTTTTATCATATTATATT
1 -ATATATTTATTTAT-TCATATTATATT
*
155587 ATAT-TTTAATTATT
1 ATATATTTATTTATT
155601 TTTATATGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
25 4 0.12
26 11 0.33
27 18 0.55
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (26 bp):
ATATATTTATTTATTCATATTATATT
Found at i:155770 original size:11 final size:10
Alignment explanation
Indices: 155728--155812 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 10
155718 GTAATCTATG
*
155728 TATATTATCA
1 TATATTATAA
155738 TAT-TTATAA
1 TATATTATAA
*
155747 -AT-TT-TTA
1 TATATTATAA
155754 TATATTATAA
1 TATATTATAA
155764 CTATATT-TAA
1 -TATATTATAA
*
155774 AATATTAT-A
1 TATATTATAA
155783 TAT-TTAT-A
1 TATATTATAA
* *
155791 TAAATTTTAA
1 TATATTATAA
155801 TATATTAATAA
1 TATATT-ATAA
155812 T
1 T
155813 TTATATTAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
7 2 0.03
8 13 0.22
9 18 0.31
10 15 0.26
11 10 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (10 bp):
TATATTATAA
Found at i:155797 original size:47 final size:48
Alignment explanation
Indices: 155729--155828 Score: 134
Period size: 47 Copynumber: 2.1 Consensus size: 48
155719 TAATCTATGT
* *
155729 ATATTATCATATTTATAAATTTTTATATATT-ATAA-CTATATTTAAA
1 ATATTATCATATTTATAAATTTTAATATATTAATAATCTATATTAAAA
*
155775 ATATTAT-ATATTTATATAAATTTTAATATATTAATAATTTATATTAAAA
1 ATATTATCATA-TT-TATAAATTTTAATATATTAATAATCTATATTAAAA
155824 ATATT
1 ATATT
155829 TTTTTGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
45 3 0.06
46 9 0.19
47 17 0.36
48 4 0.09
49 14 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (48 bp):
ATATTATCATATTTATAAATTTTAATATATTAATAATCTATATTAAAA
Found at i:156296 original size:42 final size:40
Alignment explanation
Indices: 156249--156352 Score: 104
Period size: 41 Copynumber: 2.5 Consensus size: 40
156239 TATGTGTAAC
*
156249 ATATA-TTATATAA-ATTTTAATATGTATATATATTTATATTAT
1 ATATATTTA-ATAATATTTT-ATATGTAT-TATAATTAT-TTAT
* *
156291 ATATATTTAATAATATTTTATATTTATTATAATTATTTTT
1 ATATATTTAATAATATTTTATATGTATTATAATTATTTAT
* *
156331 ATATAATGTAATTATATTTTAT
1 ATAT-ATTTAATAATATTTTAT
156353 TTAAAATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
40 7 0.13
41 23 0.43
42 16 0.30
43 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (40 bp):
ATATATTTAATAATATTTTATATGTATTATAATTATTTAT
Found at i:156311 original size:21 final size:21
Alignment explanation
Indices: 156287--156352 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
156277 TATATTTATA
*
156287 TTATATATATTTAATAATATT
1 TTATATATATTTAATTATATT
*
156308 TTATATTTATTATAATTAT-TT
1 TTATATATATT-TAATTATATT
*
156329 TTATATA-ATGTAATTATATT
1 TTATATATATTTAATTATATT
156349 TTAT
1 TTAT
156353 TTAAAATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 7 0.18
20 8 0.21
21 18 0.46
22 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATATATATTTAATTATATT
Found at i:156322 original size:19 final size:19
Alignment explanation
Indices: 156292--156364 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 19
156282 TTATATTATA
156292 TATATTTAATAA-TA-TTT
1 TATATTTAATAATTATTTT
156309 TATATTTATTATAATTATTTT
1 TATATTTA--ATAATTATTTT
*
156330 TATA--TAATGTAATTATATT
1 TATATTTAA--TAATTATTTT
156349 T-TATTTAA-AATTATTT
1 TATATTTAATAATTATTT
156365 AATTTAATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
17 16 0.35
18 2 0.04
19 16 0.35
20 5 0.11
21 7 0.15
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
TATATTTAATAATTATTTT
Found at i:156536 original size:14 final size:15
Alignment explanation
Indices: 156505--156554 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 15
156495 AAATTTTAAA
156505 ATATTA-AT-AATTT
1 ATATTATATAAATTT
156518 ATATTATATAAATTT
1 ATATTATATAAATTT
**
156533 -TATTATATTTATTT
1 ATATTATATAAATTT
156547 AT-TTATAT
1 ATATTATAT
156555 TTATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 6 0.19
14 20 0.62
15 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTATATAAATTT
Found at i:156574 original size:22 final size:22
Alignment explanation
Indices: 156531--156607 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
156521 TTATATAAAT
156531 TTTATTATATTTATT-TATTTATA
1 TTTATT-TATTTATTATA-TTATA
*
156554 TTTATTTTTTTATTATATTATA
1 TTTATTTATTTATTATATTATA
*
156576 TTTTAATTATTT-TTATATTATA
1 -TTTATTTATTTATTATATTATA
156598 -TTATTATATT
1 TTTATT-TATT
156608 AATAGGTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
20 4 0.09
21 4 0.09
22 22 0.47
23 17 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATTTATTTATTATATTATA
Found at i:156584 original size:11 final size:12
Alignment explanation
Indices: 156505--156608 Score: 67
Period size: 13 Copynumber: 8.5 Consensus size: 12
156495 AAATTTTAAA
*
156505 ATATTAATAATTT
1 ATATT-ATATTTT
156518 ATATTATATAAATTT
1 ATATTATAT---TTT
156533 -TATTATATTTAT
1 ATATTATATTT-T
*
156545 TTATT-TATATTT
1 ATATTATAT-TTT
*
156557 AT-TT-TTTTATT
1 ATATTATATT-TT
156568 ATATTATATTTT
1 ATATTATATTTT
156580 A-ATTAT-TTTT
1 ATATTATATTTT
156590 ATATTATATTATT
1 ATATTATATT-TT
156603 ATATTA
1 ATATTA
156609 ATAGGTTAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 24
0.73 0.04 0.23
Matches are distributed among these distances:
10 6 0.08
11 20 0.27
12 16 0.21
13 22 0.29
14 8 0.11
15 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:156585 original size:27 final size:28
Alignment explanation
Indices: 156530--156610 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 28
156520 ATTATATAAA
*
156530 TTTTATTATATTTATTTATTTATATTTATTT
1 TTTTATTATA-TTA-TTATTT-TAATTATTT
156561 TTTTATTATATTA-TATTTTAATTATTT
1 TTTTATTATATTATTATTTTAATTATTT
* *
156588 TTATATTATATTATTATATTAAT
1 TTTTATTATATTATTATTTTAAT
156611 AGGTTAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 20 0.43
28 13 0.28
30 3 0.07
31 10 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTATTATATTATTATTTTAATTATTT
Found at i:156608 original size:5 final size:5
Alignment explanation
Indices: 156516--156601 Score: 58
Period size: 5 Copynumber: 17.8 Consensus size: 5
156506 TATTAATAAT
* *
156516 TTATA TTATA -TAAA TTTTA TTATA TT-TA TT-TA TTTATA TT-TA TT-T-
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA
* * *
156561 TTTTA TTATA TTATA TTTTAA TTATTT TTATA TTATA TTAT
1 TTATA TTATA TTATA TTAT-A TTA-TA TTATA TTATA TTAT
156602 TATATTAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
3 2 0.03
4 15 0.23
5 39 0.60
6 8 0.12
7 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
TTATA
Found at i:156645 original size:18 final size:18
Alignment explanation
Indices: 156624--156678 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
156614 TTAAAATTTA
156624 TATAAAATATTAAATTAT
1 TATAAAATATTAAATTAT
*
156642 TATAAATATATAAAAATT-T
1 TATAAA-ATAT-TAAATTAT
*
156661 T-TAAAAT-TTAAAATAT
1 TATAAAATATTAAATTAT
156677 TA
1 TA
156679 ATATATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
15 4 0.13
16 3 0.10
17 2 0.07
18 10 0.33
19 6 0.20
20 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAATATTAAATTAT
Found at i:156698 original size:14 final size:16
Alignment explanation
Indices: 156646--156712 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
156636 AATTATTATA
* *
156646 AATATATAAAAATTTTT
1 AATATATTAAAA-TATT
*
156663 AAAAT-TTAAAATATT
1 AATATATTAAAATATT
156678 AATATATTAAAAT-TT
1 AATATATTAAAATATT
*
156693 -ATATA-T-AAATATA
1 AATATATTAAAATATT
156706 AATATAT
1 AATATAT
156713 ATTGATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
12 4 0.10
13 2 0.05
14 10 0.24
15 9 0.22
16 12 0.29
17 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATTAAAATATT
Found at i:156713 original size:14 final size:14
Alignment explanation
Indices: 156671--156713 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
156661 TTAAAATTTA
156671 AAATATTAATATATT
1 AAATATTAATATA-T
*
156686 AAA-ATTTATATAT
1 AAATATTAATATAT
*
156699 AAATATAAATATAT
1 AAATATTAATATAT
156713 A
1 A
156714 TTGATAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.17
14 17 0.71
15 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATTAATATAT
Found at i:161998 original size:2 final size:2
Alignment explanation
Indices: 161991--162015 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
161981 CTATTTGTTC
161991 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 A
162016 AACTCCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:166058 original size:24 final size:24
Alignment explanation
Indices: 166031--166078 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
166021 GCCAGAATTA
166031 GATCTTGATTGTTGAAACCAATAT
1 GATCTTGATTGTTGAAACCAATAT
166055 GATCTTGATTGTTGAAACCAATAT
1 GATCTTGATTGTTGAAACCAATAT
166079 TTGAAGACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (24 bp):
GATCTTGATTGTTGAAACCAATAT
Found at i:166224 original size:8 final size:8
Alignment explanation
Indices: 166213--166359 Score: 76
Period size: 8 Copynumber: 18.0 Consensus size: 8
166203 AATTATAATA
166213 ATTTATAT
1 ATTTATAT
166221 ATTTATATCAT
1 A-TT-TAT-AT
166232 ATTTATAT
1 ATTTATAT
166240 ATTT-TATT
1 ATTTATA-T
166248 ATGTTATA-
1 AT-TTATAT
166256 A-TTATAT
1 ATTTATAT
166263 -TTTATAT
1 ATTTATAT
166270 ATTT-TAT
1 ATTTATAT
166277 ATTTATAT
1 ATTTATAT
166285 AAATTTTAATAT
1 --A-TTT-ATAT
*
166297 ATTAATA-
1 ATTTATAT
166304 ATTTAT-T
1 ATTTATAT
*
166311 -TTATATAA
1 ATT-TATAT
166319 ATTTTATAT
1 A-TTTATAT
* *
166328 ATATCTAT
1 ATTTATAT
*
166336 ATATATAT
1 ATTTATAT
*
166344 ATATATAT
1 ATTTATAT
*
166352 ATGTATAT
1 ATTTATAT
166360 TTTCATACTA
Statistics
Matches: 112, Mismatches: 8, Indels: 38
0.71 0.05 0.24
Matches are distributed among these distances:
6 7 0.06
7 23 0.21
8 47 0.42
9 14 0.12
10 11 0.10
11 6 0.05
12 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (8 bp):
ATTTATAT
Found at i:166269 original size:49 final size:48
Alignment explanation
Indices: 166214--166339 Score: 141
Period size: 47 Copynumber: 2.6 Consensus size: 48
166204 ATTATAATAA
* *
166214 TTTATATATTTATATCATATTTATATATTTTATTATGTT-ATAATTATAT
1 TTTATATATTTATAT-ATATTTATATATTTTAATATATTAATAATT-TAT
*
166263 TTTATATATTT-TATAT-TTATATAAATTTTAATATATTAATAATTTAT
1 TTTATATATTTATATATATT-TATATATTTTAATATATTAATAATTTAT
*
166310 TTTATATAAATTTTATATATATCTATATAT
1 TTTATAT--A-TTTATATATATTTATATAT
166340 ATATATATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
46 2 0.03
47 27 0.42
48 9 0.14
49 12 0.18
50 3 0.05
51 11 0.17
52 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (48 bp):
TTTATATATTTATATATATTTATATATTTTAATATATTAATAATTTAT
Found at i:166328 original size:2 final size:2
Alignment explanation
Indices: 166323--166359 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
166313 ATATAAATTT
* *
166323 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
166360 TTTCATACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:166346 original size:49 final size:48
Alignment explanation
Indices: 166214--166347 Score: 130
Period size: 49 Copynumber: 2.7 Consensus size: 48
166204 ATTATAATAA
* * *
166214 TTTATATA-TTTATATCATATTTATATATTTTATTATGTTATAATTATAT
1 TTTATATATTTTATAT-ATATATATATATTATA-TATGTAATAATTATAT
* * *
166263 TTTATATATTTTATATTTATATAAATTTTAATATAT-TAATAATT-TAT
1 TTTATATATTTTATATATATATATATATT-ATATATGTAATAATTATAT
*
166310 TTTATATAAATTTTATATATATCTATATATATATATAT
1 TTTATAT--ATTTTATATATATATATATAT-TATATAT
166348 ATATATGTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
47 10 0.14
48 7 0.10
49 43 0.61
50 10 0.14
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (48 bp):
TTTATATATTTTATATATATATATATATTATATATGTAATAATTATAT
Found at i:168569 original size:33 final size:33
Alignment explanation
Indices: 168527--168590 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
168517 ACTTAAATTC
*
168527 GAATATGTGTCGAGCATGAGTAGGTCAAGAACA
1 GAATATGTGTCGAGCATGAGTAGATCAAGAACA
168560 GAATATGTGTCGAGCATGAGTAGATCAAGAA
1 GAATATGTGTCGAGCATGAGTAGATCAAGAA
168591 AAATGAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.30, T:0.22
Consensus pattern (33 bp):
GAATATGTGTCGAGCATGAGTAGATCAAGAACA
Found at i:170301 original size:29 final size:27
Alignment explanation
Indices: 170255--170312 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
170245 TTAATTATTA
170255 AAAAATAAATTATTTATATTATT-ATAT
1 AAAAATAAATTATTTATA-TATTAATAT
*
170282 AAAAATAATTATATATTATATATTAATAT
1 AAAAATAAAT-TAT-TTATATATTAATAT
170311 AA
1 AA
170313 TATGTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 9 0.33
28 7 0.26
29 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAAATAAATTATTTATATATTAATAT
Found at i:170320 original size:24 final size:24
Alignment explanation
Indices: 170255--170313 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
170245 TTAATTATTA
170255 AAAAATAAATTATTTATATTATTATAT
1 AAAAAT-AATTA--TATATTATTATAT
170282 AAAAATAATTATATATTA-TATAT
1 AAAAATAATTATATATTATTATAT
* *
170305 TAATATAAT
1 AAAAATAAT
170314 ATGTATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 12 0.40
24 7 0.23
26 5 0.17
27 6 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAAATAATTATATATTATTATAT
Found at i:172187 original size:28 final size:28
Alignment explanation
Indices: 172121--172183 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 28
172111 AAATTAAAAT
172121 ATTTATTTAAAAACAATAAAAATATAAA
1 ATTTATTTAAAAACAATAAAAATATAAA
* * *
172149 ATTTATTTAAAAATAA-AATAATATTAA
1 ATTTATTTAAAAACAATAAAAATATAAA
172176 ATTTATTT
1 ATTTATTT
172184 TAAATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
ATTTATTTAAAAACAATAAAAATATAAA
Found at i:174732 original size:18 final size:17
Alignment explanation
Indices: 174704--174740 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
174694 AATTTTATTT
174704 TAAATTTAATAAAAAAA
1 TAAATTTAATAAAAAAA
*
174721 TAAATATTAATATAAAAA
1 TAAAT-TTAATAAAAAAA
174739 TA
1 TA
174741 TTAAATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATTTAATAAAAAAA
Found at i:175094 original size:29 final size:28
Alignment explanation
Indices: 175037--175099 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 28
175027 TTGGATTTTG
*
175037 TTCTTTCAAAATAATAAAAAAAAAAGCT
1 TTCTTTCAAAATAAAAAAAAAAAAAGCT
175065 TTCTTTCAAAATTAAAAAAAAAAAAAGCT
1 TTCTTTCAAAA-TAAAAAAAAAAAAAGCT
175094 TTCTTT
1 TTCTTT
175100 TGAAATAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.33
Consensus pattern (28 bp):
TTCTTTCAAAATAAAAAAAAAAAAAGCT
Found at i:176297 original size:5 final size:5
Alignment explanation
Indices: 176287--176315 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
176277 TAAATTATAA
176287 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
176316 AAATATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:177583 original size:35 final size:35
Alignment explanation
Indices: 177534--177635 Score: 95
Period size: 35 Copynumber: 2.9 Consensus size: 35
177524 ATTCAGATTG
177534 ATTT-AATTTAAATTATTATTTTAATAATAAAAAAT
1 ATTTAAATTT-AATTATTATTTTAATAATAAAAAAT
* *
177569 ATTTAAATTTAATTATAAATATTAAT-ATAAAAAAT
1 ATTTAAATTTAATTAT-TATTTTAATAATAAAAAAT
* ** *
177604 A-ATATTTTTAATT-TTATTATGAATAATAAAAA
1 ATTTAAATTTAATTATTATT-TTAATAATAAAAA
177636 TAGACTTTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
32 2 0.04
33 5 0.09
34 16 0.29
35 20 0.36
36 12 0.22
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (35 bp):
ATTTAAATTTAATTATTATTTTAATAATAAAAAAT
Found at i:180627 original size:18 final size:18
Alignment explanation
Indices: 180599--180633 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
180589 AAAAACACAA
180599 CCATACTTTAAGCAAAATC
1 CCATACTTTAAG-AAAATC
180618 CCAT-CTTTAAGAAAAT
1 CCATACTTTAAGAAAAT
180634 GAGAATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (18 bp):
CCATACTTTAAGAAAATC
Found at i:183906 original size:6 final size:6
Alignment explanation
Indices: 183889--183965 Score: 91
Period size: 6 Copynumber: 12.7 Consensus size: 6
183879 AGTGGGAAGA
* * *
183889 ATATTAT ATATTT ATATTT ATATAT GTATGT ATATTT ATATTT ATATTT
1 ATATT-T ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
* * *
183938 ATATAT GTATGT ATATTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATAT
183966 ATGTATGTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
6 55 0.92
7 5 0.08
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (6 bp):
ATATTT
Found at i:183922 original size:24 final size:24
Alignment explanation
Indices: 183895--183975 Score: 108
Period size: 24 Copynumber: 3.1 Consensus size: 24
183885 AAGAATATTA
183895 TATATTTATATTTATATATGTATG
1 TATATTTATATTTATATATGTATG
183919 TATATTTATATTTATATTTATATATGTATG
1 ------TATATTTATATTTATATATGTATG
183949 TATATTTATATTTATATATGTATG
1 TATATTTATATTTATATATGTATG
183973 TAT
1 TAT
183976 GTAAGATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
24 27 0.53
30 24 0.47
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (24 bp):
TATATTTATATTTATATATGTATG
Found at i:183929 original size:30 final size:30
Alignment explanation
Indices: 183889--183978 Score: 148
Period size: 30 Copynumber: 3.0 Consensus size: 30
183879 AGTGGGAAGA
183889 ATATTATATATTTATATTTATATATGTATGT
1 ATATT-TATATTTATATTTATATATGTATGT
183920 ATATTTATATTTATATTTATATATGTATGT
1 ATATTTATATTTATATTTATATATGTATGT
*
183950 ATATTTATATTTATA--TATGTATGTATGT
1 ATATTTATATTTATATTTATATATGTATGT
183978 A
1 A
183979 AGATTGACAA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
28 13 0.22
30 40 0.69
31 5 0.09
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (30 bp):
ATATTTATATTTATATTTATATATGTATGT
Found at i:183976 original size:8 final size:8
Alignment explanation
Indices: 183889--183978 Score: 55
Period size: 8 Copynumber: 11.9 Consensus size: 8
183879 AGTGGGAAGA
183889 ATAT-TAT
1 ATATGTAT
183896 ATAT-T-T
1 ATATGTAT
*
183902 ATATTTAT
1 ATATGTAT
183910 ATATGTAT
1 ATATGTAT
* * *
183918 GTATATTT
1 ATATGTAT
183926 ATAT-T-T
1 ATATGTAT
*
183932 ATATTTAT
1 ATATGTAT
183940 ATATGTAT
1 ATATGTAT
* * *
183948 GTATATTT
1 ATATGTAT
*
183956 ATATTTAT
1 ATATGTAT
183964 ATATGTAT
1 ATATGTAT
*
183972 GTATGTA
1 ATATGTA
183979 AGATTGACAA
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
6 10 0.15
7 8 0.12
8 47 0.72
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (8 bp):
ATATGTAT
Found at i:184609 original size:23 final size:22
Alignment explanation
Indices: 184560--184605 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
184550 AAATATTTTT
184560 TATTTAAATTTAATTATAAAAA
1 TATTTAAATTTAATTATAAAAA
184582 TATTTAAATATTAA-TATAAAAA
1 TATTTAAAT-TTAATTATAAAAA
184604 TA
1 TA
184606 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTTAAATTTAATTATAAAAA
Found at i:188957 original size:2 final size:2
Alignment explanation
Indices: 188950--188975 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
188940 ATTTACAAAC
188950 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
188976 TGTGCGTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:189423 original size:2 final size:2
Alignment explanation
Indices: 189416--189443 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
189406 TGGCGTGCAT
189416 GA 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 GA
189444 AACTTACATC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:190642 original size:2 final size:2
Alignment explanation
Indices: 190635--190685 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
190625 TCACATACTT
190635 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
190677 AG AG AG AG A
1 AG AG AG AG A
190686 TGAAAGAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:190728 original size:26 final size:26
Alignment explanation
Indices: 190699--190779 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
190689 AAGAGAAAAA
190699 AAATCCAAGATGCAGAAAAGCTGAAC
1 AAATCCAAGATGCAGAAAAGCTGAAC
* ** * *
190725 AAATTAACCAA-A---AGTATTGCTTAAA
1 AAA-T--CCAAGATGCAGAAAAGCTGAAC
190750 AAATCCAAGATGCAGAAAAGCTGAAC
1 AAATCCAAGATGCAGAAAAGCTGAAC
190776 AAAT
1 AAAT
190780 TGACCAAAAC
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
22 4 0.11
23 1 0.03
24 1 0.03
25 11 0.29
26 15 0.39
27 1 0.03
28 1 0.03
29 4 0.11
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.17
Consensus pattern (26 bp):
AAATCCAAGATGCAGAAAAGCTGAAC
Found at i:190772 original size:51 final size:51
Alignment explanation
Indices: 190696--190806 Score: 195
Period size: 51 Copynumber: 2.2 Consensus size: 51
190686 TGAAAGAGAA
*
190696 AAAAAATCCAAGATGCAGAAAAGCTGAACAAATTAACCAAAAGTATTGCTT
1 AAAAAATCCAAGATGCAGAAAAGCTGAACAAATTAACCAAAACTATTGCTT
*
190747 AAAAAATCCAAGATGCAGAAAAGCTGAACAAATTGACCAAAACTATTGCTT
1 AAAAAATCCAAGATGCAGAAAAGCTGAACAAATTAACCAAAACTATTGCTT
190798 AAAATAATC
1 AAAA-AATC
190807 AACAACTGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (51 bp):
AAAAAATCCAAGATGCAGAAAAGCTGAACAAATTAACCAAAACTATTGCTT
Found at i:199160 original size:33 final size:34
Alignment explanation
Indices: 199122--199201 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
199112 ATTAATATGA
* *
199122 ATATAATATGAATATATAAATGTGT-TAAAATTT
1 ATATAATATGAATATATAAATGTATAAAAAATTT
* *
199155 ATATAATATAAAT-TATTAATGTATAAAAAATTT
1 ATATAATATGAATATATAAATGTATAAAAAATTT
*
199188 ATATAA-ATGTATAT
1 ATATAATATGAATAT
199202 GTTATTTATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 13 0.33
33 26 0.67
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.42
Consensus pattern (34 bp):
ATATAATATGAATATATAAATGTATAAAAAATTT
Found at i:200843 original size:22 final size:22
Alignment explanation
Indices: 200797--200845 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
200787 ATTAAAATTT
* *
200797 TTTTTAGATTCAAAATTTATGA
1 TTTTTAAATTCAAAATTTATAA
200819 TTTTTAAATTCATAAATTTA-AA
1 TTTTTAAATTCA-AAATTTATAA
200841 TTTTT
1 TTTTT
200846 TTATTTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTTTAAATTCAAAATTTATAA
Found at i:201434 original size:32 final size:32
Alignment explanation
Indices: 201397--201461 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
201387 TTTTAAGTAG
201397 TAAAGAAATTGTGTTAATAGGTTAAGTCGAGT
1 TAAAGAAATTGTGTTAATAGGTTAAGTCGAGT
201429 TAAAGAAATTGTGTTAATAGGTTAAGTCGAGT
1 TAAAGAAATTGTGTTAATAGGTTAAGTCGAGT
201461 T
1 T
201462 GGGTTTAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (32 bp):
TAAAGAAATTGTGTTAATAGGTTAAGTCGAGT
Found at i:202973 original size:24 final size:26
Alignment explanation
Indices: 202946--202993 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
202936 TTGTACTTAA
202946 ATTTATTTAA-AAA-ATAATTTATTT
1 ATTTATTTAATAAATATAATTTATTT
*
202970 ATTTATTTAATAAATTTAATTTAT
1 ATTTATTTAATAAATATAATTTAT
202994 ATTGAATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 3 0.14
26 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTATTTAATAAATATAATTTATTT
Found at i:203649 original size:20 final size:19
Alignment explanation
Indices: 203619--203753 Score: 85
Period size: 18 Copynumber: 7.2 Consensus size: 19
203609 TCAGTAATAC
203619 ATATATTTATATTATATTT
1 ATATATTTATATTATATTT
203638 ATATATTT-TA-TATA-TT
1 ATATATTTATATTATATTT
*
203654 ATA-A-TTATATTTAAAATATT
1 ATATATTTATA-TT-ATAT-TT
*
203674 ATATATTTATA-TAAATTT
1 ATATATTTATATTATATTT
203692 -TAATATATTATAATT-TATATT
1 AT-ATAT-TTAT-ATTATAT-TT
*
203713 ATATCAATTT-TAATATATTT
1 ATAT--ATTTATATTATATTT
203733 ATATA-TTATATTATA-TT
1 ATATATTTATATTATATTT
203750 ATAT
1 ATAT
203754 TTAATCATTA
Statistics
Matches: 94, Mismatches: 4, Indels: 38
0.69 0.03 0.28
Matches are distributed among these distances:
14 2 0.02
15 3 0.03
16 5 0.05
17 14 0.15
18 17 0.18
19 16 0.17
20 17 0.18
21 10 0.11
22 8 0.09
23 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATTTATATTATATTT
Found at i:203735 original size:32 final size:31
Alignment explanation
Indices: 203675--203748 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 31
203665 TAAAATATTA
203675 TATATTTATATAAATTTTAATATATTATA-ATT
1 TATA-TTATATAAATTTTAATATATTATATA-T
*
203707 TATATTATATCAATTTTAATATATTTATATAT
1 TATATTATATAAATTTTAATATA-TTATATAT
203739 TATATTATAT
1 TATATTATAT
203749 TATATTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
31 18 0.46
32 20 0.51
33 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
TATATTATATAAATTTTAATATATTATATAT
Found at i:203880 original size:2 final size:2
Alignment explanation
Indices: 203873--203904 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
203863 TGGTGTACCA
203873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
203905 TATTGAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:204971 original size:36 final size:36
Alignment explanation
Indices: 204888--204972 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 36
204878 AAAGATTATG
*
204888 TTATTAATTTAATTTAATTTAAATTAAATTTAAAAA
1 TTATTTATTTAATTTAATTTAAATTAAATTTAAAAA
** * ** *
204924 CAATTTTTTTAATTTAA-TTAAATTTGATTTAAATTA
1 TTATTTATTTAATTTAATTTAAATTAAATTTAAA-AA
204960 TTATTTATTTAAT
1 TTATTTATTTAAT
204973 AAAAATTATT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
35 14 0.37
36 24 0.63
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (36 bp):
TTATTTATTTAATTTAATTTAAATTAAATTTAAAAA
Found at i:205575 original size:24 final size:24
Alignment explanation
Indices: 205555--205602 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
205545 ATGATTTTAT
205555 AATTTAAAATTAATTTTATTTAAA
1 AATTTAAAATTAATTTTATTTAAA
* *
205579 AATTTATAATT-ATTTT-TTAAAA
1 AATTTAAAATTAATTTTATTTAAA
205601 AA
1 AA
205603 AATACATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTTAAAATTAATTTTATTTAAA
Found at i:206423 original size:23 final size:23
Alignment explanation
Indices: 206344--206438 Score: 74
Period size: 23 Copynumber: 4.1 Consensus size: 23
206334 GCATTTCAAA
*
206344 TAAAATATTATAATATATT-TTT
1 TAAAATATTATAATATATTATAT
*
206366 TATAAATATTATTATA-ATTAATAT
1 TA-AAATATTATAATATATT-ATAT
* *
206390 TGAATAGATATGATAATATATTATGT
1 T-AA-A-ATATTATAATATATTATAT
206416 TAAAATATTAT-ATAT-TT-TAT
1 TAAAATATTATAATATATTATAT
206436 TAA
1 TAA
206439 TATTTTGATA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
20 5 0.08
21 2 0.03
22 9 0.15
23 18 0.31
24 5 0.08
25 4 0.07
26 13 0.22
27 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TAAAATATTATAATATATTATAT
Found at i:206438 original size:20 final size:21
Alignment explanation
Indices: 206405--206453 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
206395 AGATATGATA
*
206405 ATATATTATGTTAAAATATT-
1 ATATATTATATTAAAATATTG
* * *
206425 ATATATTTTATTAATATTTTG
1 ATATATTATATTAAAATATTG
206446 ATATATTA
1 ATATATTA
206454 AAATTTATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
ATATATTATATTAAAATATTG
Found at i:206775 original size:15 final size:16
Alignment explanation
Indices: 206748--206802 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
206738 TGTATCTATA
206748 TTATATTTA-TATATT
1 TTATATTTATTATATT
*
206763 TTAT-TTTATTATA-A
1 TTATATTTATTATATT
**
206777 TTATATTTAAAATATT
1 TTATATTTATTATATT
206793 TTATATTTAT
1 TTATATTTAT
206803 ATTTTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 8 0.25
15 15 0.47
16 9 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATTTATTATATT
Found at i:206800 original size:37 final size:35
Alignment explanation
Indices: 206750--206835 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 35
206740 TATCTATATT
206750 ATATTTATATATTT-TATTTTATTATAATTATATTTAA-A
1 ATATTT-TATATTTATATTTT-TT-TAA-TATA-TTAATA
206788 ATATTTTATATTTATATTTTTTTAATATATTAATA
1 ATATTTTATATTTATATTTTTTTAATATATTAATA
206823 ATTCATTTTATAT
1 A-T-ATTTTATAT
206836 AAATTTTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
34 4 0.09
35 6 0.14
36 4 0.09
37 18 0.41
38 12 0.27
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (35 bp):
ATATTTTATATTTATATTTTTTTAATATATTAATA
Found at i:207625 original size:21 final size:23
Alignment explanation
Indices: 207599--207641 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
207589 AATTATATTT
207599 AAAATAT-TTTAT-ATTTATATA
1 AAAATATATTTATAATTTATATA
207620 AAAATATATTTATAATTTATAT
1 AAAATATATTTATAATTTATAT
207642 TATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAATATATTTATAATTTATATA
Found at i:207652 original size:16 final size:16
Alignment explanation
Indices: 207606--207653 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
207596 TTTAAAATAT
207606 TTTATATTTATATAAAA
1 TTTATA-TTATATAAAA
*
207623 -ATATATT-TAT--AA
1 TTTATATTATATAAAA
207635 TTTATATTATATAAAA
1 TTTATATTATATAAAA
207651 TTT
1 TTT
207654 TAAATACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
12 2 0.08
13 6 0.24
14 6 0.24
15 2 0.08
16 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTATATTATATAAAA
Found at i:208332 original size:16 final size:17
Alignment explanation
Indices: 208302--208335 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
208292 TAAATTAAAA
208302 AAATTATATATTTTATT
1 AAATTATATATTTTATT
208319 AAATTATA-ATTTTATT
1 AAATTATATATTTTATT
208335 A
1 A
208336 TTTGAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTATATATTTTATT
Found at i:209905 original size:19 final size:19
Alignment explanation
Indices: 209881--209940 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
209871 TATTTTATAT
*
209881 TTTTTAAAATATAAATTAA
1 TTTTTATAATATAAATTAA
*
209900 TTTTTATTAATA-AAATTTA
1 TTTTTA-TAATATAAATTAA
* *
209919 TTTTTATTATTTAAATTAA
1 TTTTTATAATATAAATTAA
209938 TTT
1 TTT
209941 ATACATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.09
19 27 0.79
20 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTATAATATAAATTAA
Found at i:209959 original size:19 final size:18
Alignment explanation
Indices: 209929--209978 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 18
209919 TTTTTATTAT
209929 TTAAATTAATTT-ATACATA
1 TTAAATT-ATTTAATA-ATA
209948 TTATAATTATTTAATAATA
1 TTA-AATTATTTAATAATA
209967 TTAAATATATTT
1 TTAAAT-TATTT
209979 TATCAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.11
19 18 0.64
20 7 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAATTATTTAATAATA
Found at i:211080 original size:2 final size:2
Alignment explanation
Indices: 211075--211116 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
211065 TTTTCTTTGA
211075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
211117 TCAAGTGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:211759 original size:17 final size:18
Alignment explanation
Indices: 211727--211764 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
211717 TCCATTATAA
*
211727 TTTGATTTTAT-CAAAAT
1 TTTGATTTTATAAAAAAT
*
211744 TTTGATTTTTTAAAAAAT
1 TTTGATTTTATAAAAAAT
211762 TTT
1 TTT
211765 TACTAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTGATTTTATAAAAAAT
Found at i:212504 original size:3 final size:3
Alignment explanation
Indices: 212496--212530 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
212486 TTTTTATGCC
212496 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
212531 GTTCACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:213680 original size:29 final size:29
Alignment explanation
Indices: 213653--213718 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 29
213643 AAATTTATAT
*
213653 TAATATAAATATTTTAAATATAATTATAATA
1 TAATA-AAATA-TATAAATATAATTATAATA
213684 TAATAAAATATATAAATATAA-TATAA-A
1 TAATAAAATATATAAATATAATTATAATA
213711 TACATAAA
1 TA-ATAAA
213719 TTATTAACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 3 0.09
28 10 0.30
29 10 0.30
30 5 0.15
31 5 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
TAATAAAATATATAAATATAATTATAATA
Found at i:213687 original size:5 final size:5
Alignment explanation
Indices: 213669--213709 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
213659 AAATATTTTA
*
213669 AATAT AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AA
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AA
213710 ATACATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 6 0.19
5 20 0.65
6 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:213717 original size:13 final size:11
Alignment explanation
Indices: 213653--213712 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
213643 AAATTTATAT
213653 TAATATAAATA
1 TAATATAAATA
*
213664 T--TTTAAATA
1 TAATATAAATA
213673 TAAT-TATAATA
1 TAATATA-AATA
213684 T-A-ATAAA-A
1 TAATATAAATA
213692 T-ATATAAATA
1 TAATATAAATA
213702 TAATATAAATA
1 TAATATAAATA
213713 CATAAATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
8 3 0.07
9 15 0.37
10 7 0.17
11 16 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATATAAATA
Found at i:214225 original size:17 final size:16
Alignment explanation
Indices: 214200--214233 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
214190 ATTTTCATAT
*
214200 TAAATTTATATTTATA
1 TAAATTTATAATTATA
214216 TAAATATTATAATTATA
1 TAAAT-TTATAATTATA
214233 T
1 T
214234 TTAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTTATAATTATA
Found at i:214251 original size:29 final size:28
Alignment explanation
Indices: 214219--214311 Score: 102
Period size: 27 Copynumber: 3.3 Consensus size: 28
214209 ATTTATATAA
214219 ATATTATAATTATATTTAAAATATTATTT
1 ATATTAT-ATTATATTTAAAATATTATTT
* *
214248 ATATTATATAAATTTTTAAAATA--ATTAT
1 ATATTATAT-TATATTTAAAATATTATT-T
*
214276 ATATTATATTATATTTAAATTATT-TTT
1 ATATTATATTATATTTAAAATATTATTT
*
214303 ATATAATAT
1 ATATTATAT
214312 CAAATTTTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
27 22 0.41
28 14 0.26
29 18 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATTATATTATATTTAAAATATTATTT
Found at i:214284 original size:28 final size:27
Alignment explanation
Indices: 214247--214370 Score: 101
Period size: 28 Copynumber: 4.4 Consensus size: 27
214237 AAATATTATT
*
214247 TATATTATATAAATTTTTAAAATAATTA
1 TATATTATATAAA-TTTTAAATTAATTA
* * *
214275 TATATTATAT-TATATTTAAATTATTTT
1 TATATTATATAAAT-TTTAAATTAATTA
* * *
214302 TATATAATATCAAATTTTATATTATATTT
1 TATATTATAT-AAATTTTAAATTA-ATTA
214331 TA-ATTATATCAAATTTTAAATTATATT-
1 TATATTATAT-AAATTTTAAATTA-ATTA
214358 TATATTCATATAA
1 TATATT-ATATAA
214371 CTATATAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
26 1 0.01
27 22 0.28
28 46 0.57
29 11 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TATATTATATAAATTTTAAATTAATTA
Found at i:214339 original size:16 final size:17
Alignment explanation
Indices: 214278--214400 Score: 61
Period size: 17 Copynumber: 6.8 Consensus size: 17
214268 ATAATTATAT
214278 ATTATATTATA-TTTAA
1 ATTATATTATATTTTAA
* *
214294 ATTATTTTTATATAATATCAA
1 ATTA-TATTATAT--T-TTAA
214315 ATTTTATATTATATTTT-A
1 A--TTATATTATATTTTAA
* *
214333 ATTATATCAAATTTTAA
1 ATTATATTATATTTTAA
*
214350 ATTATATTTATATTCATATA
1 ATTATA-TTATATT-TTA-A
* * * *
214370 ACTATATAAAATTTAAA
1 ATTATATTATATTTTAA
*
214387 ATTATATTAAATTT
1 ATTATATTATATTT
214401 ATTTTCAACC
Statistics
Matches: 80, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
16 16 0.20
17 26 0.32
18 8 0.10
19 8 0.10
20 8 0.10
21 4 0.05
22 7 0.09
23 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATATTATATTTTAA
Found at i:214349 original size:56 final size:55
Alignment explanation
Indices: 214232--214362 Score: 140
Period size: 56 Copynumber: 2.3 Consensus size: 55
214222 TTATAATTAT
* * * *
214232 ATTTAAAATATTATTTATATTATATAAATTTTTAAAATAATTATATATTATATTAT
1 ATTTAAATTATT-TTTATATAATATAAATTTTTAAAATAATTATATATTATATCAA
* * *
214288 ATTTAAATTATTTTTATATAATATCAAA-TTTTATATTATATTTTA-ATTATATCAA
1 ATTTAAATTATTTTTATATAATAT-AAATTTTTAAAATA-ATTATATATTATATCAA
*
214343 ATTTTAAATTATATTTATAT
1 A-TTTAAATTATTTTTATAT
214363 TCATATAACT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
55 28 0.44
56 36 0.56
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (55 bp):
ATTTAAATTATTTTTATATAATATAAATTTTTAAAATAATTATATATTATATCAA
Found at i:214398 original size:17 final size:17
Alignment explanation
Indices: 214318--214401 Score: 62
Period size: 17 Copynumber: 4.8 Consensus size: 17
214308 ATATCAAATT
* *
214318 TTATATTATATTT-TAA
1 TTATATTAAATTTAAAA
* *
214334 TTATATCAAATTTTAAA
1 TTATATTAAATTTAAAA
* *
214351 TTATATTTATATTCATATAA
1 TTATA-TTAAATT--TAAAA
* *
214371 CTATATAAAATTTAAAA
1 TTATATTAAATTTAAAA
214388 TTATATTAAATTTA
1 TTATATTAAATTTA
214402 TTTTCAACCC
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
16 11 0.22
17 23 0.45
18 5 0.10
19 5 0.10
20 7 0.14
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATATTAAATTTAAAA
Found at i:214830 original size:2 final size:2
Alignment explanation
Indices: 214825--214854 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
214815 GATATATAGT
214825 GA GA 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 GA GA
214855 TGGTGGGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:215055 original size:2 final size:2
Alignment explanation
Indices: 215048--215072 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
215038 TTTTCTTTCT
215048 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
215073 ATATAAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:224495 original size:16 final size:19
Alignment explanation
Indices: 224454--224495 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
224444 TTTAATATTT
*
224454 TAAATATAATTATAATATA
1 TAAAAATAATTATAATATA
224473 TAAAAATAA-TATAA-ATA
1 TAAAAATAATTATAATATA
224490 -AAAAAT
1 TAAAAAT
224496 TTTCAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 5 0.23
19 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATAATTATAATATA
Found at i:224743 original size:18 final size:18
Alignment explanation
Indices: 224722--224758 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
224712 ATTATATTAC
224722 TTTAAAATATTTATATTT
1 TTTAAAATATTTATATTT
**
224740 TTTATTATATTTATATTT
1 TTTAAAATATTTATATTT
224758 T
1 T
224759 AATTATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTAAAATATTTATATTT
Found at i:224787 original size:34 final size:34
Alignment explanation
Indices: 224744--224854 Score: 109
Period size: 34 Copynumber: 3.2 Consensus size: 34
224734 ATATTTTTTA
*
224744 TTATATTTATATTTTAATTATATTATATTTTAAT
1 TTATTTTTATATTTTAATTATATTATATTTTAAT
* **
224778 TTATTTTTATCA-TATAATTATATCGTATTTTAAT
1 TTATTTTTAT-ATTTTAATTATATTATATTTTAAT
* *
224812 ATATTTAATATATTTT-ATCATATAATTATATTTTAAT
1 TTATTT-TTATATTTTAAT--TAT-ATTATATTTTAAT
224849 TTATTT
1 TTATTT
224855 AATATATCAT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
34 36 0.59
35 6 0.10
36 3 0.05
37 16 0.26
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (34 bp):
TTATTTTTATATTTTAATTATATTATATTTTAAT
Found at i:224795 original size:18 final size:20
Alignment explanation
Indices: 224774--224842 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
224764 TATTATATTT
224774 TAATT-TAT-TTTTATCATA
1 TAATTATATATTTTATCATA
224792 TAATTATATCGTATTTTA--ATA
1 TAATTATA---TATTTTATCATA
*
224813 TATTTAATATATTTTATCATA
1 TAATT-ATATATTTTATCATA
224834 TAATTATAT
1 TAATTATAT
224843 TTTAATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
20 4 0.10
21 14 0.34
22 4 0.10
23 5 0.12
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (20 bp):
TAATTATATATTTTATCATA
Found at i:224820 original size:9 final size:9
Alignment explanation
Indices: 224806--224861 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
224796 TATATCGTAT
224806 TTTAATATA
1 TTTAATATA
224815 TTTAATATA
1 TTTAATATA
224824 TTT--TATCA
1 TTTAATAT-A
*
224832 TATAATTATA
1 TTTAA-TATA
*
224842 TTTTAATTTA
1 -TTTAATATA
224852 TTTAATATA
1 TTTAATATA
224861 T
1 T
224862 CATAAGAGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 21 0.55
10 4 0.11
11 7 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAATATA
Found at i:224827 original size:19 final size:19
Alignment explanation
Indices: 224803--224861 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
224793 AATTATATCG
224803 TATTTTAATATATTTAATA
1 TATTTTAATATATTTAATA
224822 TATTTT-ATCATA--TAATTA
1 TATTTTAAT-ATATTTAA-TA
*
224840 TATTTTAATTTATTTAATA
1 TATTTTAATATATTTAATA
224859 TAT
1 TAT
224862 CATAAGAGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 3 0.09
18 12 0.35
19 16 0.47
20 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTAATATATTTAATA
Found at i:225718 original size:2 final size:2
Alignment explanation
Indices: 225711--225740 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
225701 AAATTCAATG
225711 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
225741 GTAGCCACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:226103 original size:33 final size:32
Alignment explanation
Indices: 226065--226144 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
226055 ATAATAAAAC
*
226065 ATAATATTAATATATGAATATATCAAATTTTAT
1 ATAATATTAATATAT-AATATATCAAAATTTAT
* * * *
226098 GTAATATAAATTTATAATATATTAAAATTTAT
1 ATAATATTAATATATAATATATCAAAATTTAT
226130 ATAAATATATAATAT
1 AT-AATAT-TAATAT
226145 TTTAAATATG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
32 16 0.43
33 17 0.46
34 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (32 bp):
ATAATATTAATATATAATATATCAAAATTTAT
Found at i:226611 original size:18 final size:18
Alignment explanation
Indices: 226590--226649 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
226580 TTTAAAATTT
226590 ATATAATATAAATTATAA
1 ATATAATATAAATTATAA
* *
226608 ATAT-ATCATTATTTATAA
1 ATATAAT-ATAAATTATAA
* *
226626 ATATAA-A-ATATTTTAA
1 ATATAATATAAATTATAA
226642 ATATAATA
1 ATATAATA
226650 ATAACACAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 11 0.33
17 4 0.12
18 17 0.52
19 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATATAAATTATAA
Found at i:226642 original size:16 final size:18
Alignment explanation
Indices: 226602--226652 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
226592 ATAATATAAA
*
226602 TTATAAATAT-ATCATTAT
1 TTATAAATATAAT-AATAT
226620 TTATAAATATAA-AATAT
1 TTATAAATATAATAATAT
226637 TT-TAAATATAATAATA
1 TTATAAATATAATAATA
226653 ACACAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.30
17 10 0.33
18 10 0.33
19 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATAAATATAATAATAT
Found at i:226966 original size:28 final size:27
Alignment explanation
Indices: 226915--226967 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
226905 TTAATACATT
*
226915 ATTTTTAATAAATTTAATTATAAATCA
1 ATTTTTAATAAATTTAAATATAAATCA
226942 ATTTTTATATAATATTTAAAT-TAAAT
1 ATTTTTA-ATAA-ATTTAAATATAAAT
226968 AAACTTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 9 0.39
29 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTTTAATAAATTTAAATATAAATCA
Found at i:227341 original size:16 final size:16
Alignment explanation
Indices: 227288--227343 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
227278 AAAAATATAT
227288 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
* * *
227304 CTATAT-TAATAATTT-
1 ATTTATATAA-ATTTTA
227319 ATATTATATAAATTTTA
1 AT-TTATATAAATTTTA
227336 ATTTATAT
1 ATTTATAT
227344 TAATATAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 4 0.13
16 21 0.70
17 5 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:227358 original size:22 final size:21
Alignment explanation
Indices: 227313--227359 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
227303 ACTATATTAA
**
227313 TAATTTATATTATATAAATTT
1 TAATTTATATTATATAAAAAT
227334 TAATTTATATTAATATAAAAAT
1 TAATTTATATT-ATATAAAAAT
227356 TAAT
1 TAAT
227360 ATAAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTATATTATATAAAAAT
Found at i:227624 original size:27 final size:27
Alignment explanation
Indices: 227577--227678 Score: 75
Period size: 27 Copynumber: 3.7 Consensus size: 27
227567 ATTAATTTAT
*
227577 ATATT-TATA-TTATAATTATATTTAAA
1 ATATTATATATTTAT-ATAATATTTAAA
*
227603 ATATTATATATTTATATAATATTTAAT
1 ATATTATATATTTATATAATATTTAAA
* * *
227630 ATGTTAATATATTT-TTTTATATTTATAAAA
1 ATATT-ATATATTTATATAATA-TT-T-AAA
*
227660 AAATTATATTATTTATATA
1 ATATTATA-TATTTATATA
227679 TTATATTATA
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
26 5 0.09
27 23 0.40
28 14 0.24
29 4 0.07
30 10 0.17
31 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
ATATTATATATTTATATAATATTTAAA
Found at i:228798 original size:15 final size:15
Alignment explanation
Indices: 228778--228809 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
228768 TTAAATTATT
228778 ATATAAAAAAATAAA
1 ATATAAAAAAATAAA
*
228793 ATATAAAAAATTAAA
1 ATATAAAAAAATAAA
228808 AT
1 AT
228810 TTAATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
ATATAAAAAAATAAA
Found at i:228846 original size:33 final size:29
Alignment explanation
Indices: 228802--228867 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
228792 AATATAAAAA
228802 ATTAAAATTTAATTAATAATTATATTATTTTAT
1 ATTAAAATTTAA-TAA-AA-T-TATTATTTTAT
*
228835 ATTAAATTTTAATAAAATTATTATTTTAT
1 ATTAAAATTTAATAAAATTATTATTTTAT
228864 -TTAA
1 ATTAA
228868 TAAATAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.12
29 11 0.34
30 1 0.03
31 2 0.06
32 3 0.09
33 11 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTAAAATTTAATAAAATTATTATTTTAT
Found at i:228880 original size:20 final size:21
Alignment explanation
Indices: 228842--228880 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
228832 TATATTAAAT
* *
228842 TTTAATAAAATTATTATTTTA
1 TTTAATAAAATAATAATTTTA
228863 TTTAAT-AAATAATAATTT
1 TTTAATAAAATAATAATTT
228881 AAATTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAATAAAATAATAATTTTA
Found at i:230181 original size:28 final size:29
Alignment explanation
Indices: 230134--230216 Score: 102
Period size: 28 Copynumber: 2.9 Consensus size: 29
230124 ATGTATGTAT
230134 TATATTTATATTATAAATTTTGATATATTAA
1 TATATTTATATTAT--ATTTTGATATATTAA
*
230165 TA-ATTTATATTATATTTTGATATATTTA
1 TATATTTATATTATATTTTGATATATTAA
*
230193 TATATTCATA-TATA-TTT-ATATATT
1 TATATTTATATTATATTTTGATATATT
230217 TTTTAAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
26 7 0.14
27 3 0.06
28 20 0.41
29 6 0.12
30 11 0.22
31 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (29 bp):
TATATTTATATTATATTTTGATATATTAA
Found at i:230190 original size:10 final size:9
Alignment explanation
Indices: 230144--230240 Score: 60
Period size: 9 Copynumber: 10.8 Consensus size: 9
230134 TATATTTATA
*
230144 TTATAAATT
1 TTATATATT
230153 TTGATATA-T
1 TT-ATATATT
*
230162 TAATA-ATT
1 TTATATATT
230170 TATATTATATT
1 T-TA-TATATT
230181 TTGATATA-T
1 TT-ATATATT
230190 TTATATA-T
1 TTATATATT
*
230198 TCATATATAT
1 TTATATAT-T
230208 TTATATATT
1 TTATATATT
* *
230217 TTTTAAATT
1 TTATATATT
*
230226 TTATTTATT
1 TTATATATT
230235 TT-TATA
1 TTATATA
230241 GTAATTCTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
7 1 0.01
8 20 0.29
9 24 0.35
10 19 0.28
11 5 0.07
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (9 bp):
TTATATATT
Found at i:230195 original size:8 final size:8
Alignment explanation
Indices: 230120--230217 Score: 57
Period size: 8 Copynumber: 12.5 Consensus size: 8
230110 AATTTTAAAA
*
230120 ATTTATGT
1 ATTTATAT
*
230128 ATGTATTAT
1 ATTTA-TAT
230137 ATTTATAT
1 ATTTATAT
* *
230145 -TATAAAT
1 ATTTATAT
230152 -TTTGATAT
1 ATTT-ATAT
230160 A-TTA-AT
1 ATTTATAT
*
230166 AATT-TAT
1 ATTTATAT
230173 A-TTATAT
1 ATTTATAT
230180 -TTTGATAT
1 ATTT-ATAT
230188 ATTTATAT
1 ATTTATAT
230196 ATTCATATAT
1 ATT--TATAT
230206 ATTTATAT
1 ATTTATAT
230214 ATTT
1 ATTT
230218 TTTAAATTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
6 5 0.07
7 18 0.25
8 32 0.44
9 9 0.12
10 8 0.11
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (8 bp):
ATTTATAT
Found at i:230454 original size:11 final size:11
Alignment explanation
Indices: 230440--230478 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
230430 ATTTAAATTT
*
230440 AATTTTTATCA
1 AATTTTTATAA
*
230451 AATTTTAATAA
1 AATTTTTATAA
*
230462 AATTTTTAAAA
1 AATTTTTATAA
230473 AATTTT
1 AATTTT
230479 AAATTATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTTTATAA
Found at i:231203 original size:2 final size:2
Alignment explanation
Indices: 231196--231226 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
231186 AAGATTATCC
*
231196 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
231227 CCTGAGAGTC
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:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:234986 original size:18 final size:18
Alignment explanation
Indices: 234965--235015 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
234955 ATATAATATG
234965 TTATATAAATATAAATTA
1 TTATATAAATATAAATTA
* **
234983 TTATATGAATATATTTTA
1 TTATATAAATATAAATTA
235001 TTA-A-AAATA-AAATTA
1 TTATATAAATATAAATTA
235016 AATGAGTCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 1 0.04
18 18 0.67
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TTATATAAATATAAATTA
Done.