Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold77
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: 1374688
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.34
Warning! 47366 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:136114 original size:14 final size:14
Alignment explanation
Indices: 136095--136122 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
136085 ATTTTTTATT
136095 TTAAATATATTTTA
1 TTAAATATATTTTA
136109 TTAAATATATTTTA
1 TTAAATATATTTTA
136123 AATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:136225 original size:5 final size:5
Alignment explanation
Indices: 136215--136258 Score: 67
Period size: 5 Copynumber: 9.4 Consensus size: 5
136205 CAATTAAAAT
136215 TTAAA TTAAA TT-AA TTAAA -T-AA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
136259 TTTAATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 28 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:136243 original size:22 final size:22
Alignment explanation
Indices: 136206--136274 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
136196 ACTCTATATC
136206 AATTAAA-ATTTAAATTAAATT
1 AATTAAATATTTAAATTAAATT
*
136227 AATTAAATAATTAAATTAAATT
1 AATTAAATATTTAAATTAAATT
* *
136249 AAATTAAAT-TTTTAATTAAATC
1 -AATTAAATATTTAAATTAAATT
136271 AATT
1 AATT
136275 TCAACATACT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.26
22 23 0.55
23 8 0.19
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTAAATATTTAAATTAAATT
Found at i:137062 original size:50 final size:50
Alignment explanation
Indices: 136987--137102 Score: 196
Period size: 50 Copynumber: 2.3 Consensus size: 50
136977 ATTATTTTTT
* *
136987 ATCAACCTTTGATAATCGAGAGAGGTGATCGTAATTGTTGACTATTCTTC
1 ATCAACCTTTGACAATCGAGAGAGGTGATCGTAATTGTTAACTATTCTTC
* *
137037 ATCAACCTTTGGCAATCGAGAGAGGTGATTGTAATTGTTAACTATTCTTC
1 ATCAACCTTTGACAATCGAGAGAGGTGATCGTAATTGTTAACTATTCTTC
137087 ATCAACCTTTGACAAT
1 ATCAACCTTTGACAAT
137103 AGAAAAATGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (50 bp):
ATCAACCTTTGACAATCGAGAGAGGTGATCGTAATTGTTAACTATTCTTC
Found at i:137122 original size:50 final size:50
Alignment explanation
Indices: 136987--137129 Score: 153
Period size: 50 Copynumber: 2.9 Consensus size: 50
136977 ATTATTTTTT
* * * * * *
136987 ATCAACCTTTGATAATCGAGAGAGGTGA-TCGTAATTGTTGACTATTCTTC
1 ATCAACCTTTGACAATAGAAAAAGGTGACT-ATAATTGTTAACTATTCTTC
* * * * * *
137037 ATCAACCTTTGGCAATCGAGAGAGGTGATTGTAATTGTTAACTATTCTTC
1 ATCAACCTTTGACAATAGAAAAAGGTGACTATAATTGTTAACTATTCTTC
*
137087 ATCAACCTTTGACAATAGAAAAATGTGACTATAATTGTTAACT
1 ATCAACCTTTGACAATAGAAAAAGGTGACTATAATTGTTAACT
137130 CTAAGCATTT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 81 0.99
51 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (50 bp):
ATCAACCTTTGACAATAGAAAAAGGTGACTATAATTGTTAACTATTCTTC
Found at i:141265 original size:17 final size:17
Alignment explanation
Indices: 141243--141326 Score: 56
Period size: 17 Copynumber: 5.1 Consensus size: 17
141233 TTCGTATATA
141243 ATTATATATTTTATTAT
1 ATTATATATTTTATTAT
*
141260 ATTATA-ATTATATT-T
1 ATTATATATTTTATTAT
141275 A-TA-ATATTTTA-TAT
1 ATTATATATTTTATTAT
*
141289 -TTATATAAATTTTAATAT
1 ATTATAT--ATTTTATTAT
*
141307 GTTA-ATAATTTATATTAT
1 ATTATAT-ATTT-TATTAT
141325 AT
1 AT
141327 AAATTTTGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
13 2 0.04
14 10 0.19
15 4 0.07
16 7 0.13
17 17 0.31
18 11 0.20
19 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
ATTATATATTTTATTAT
Found at i:141292 original size:22 final size:21
Alignment explanation
Indices: 141247--141294 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
141237 TATATAATTA
*
141247 TATATTTTATTATATTATAAT
1 TATATTTTAATATATTATAAT
* *
141268 TATATTTATAATATTTTATATT
1 TATATTT-TAATATATTATAAT
141290 TATAT
1 TATAT
141295 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTTTAATATATTATAAT
Found at i:141293 original size:45 final size:47
Alignment explanation
Indices: 141239--141346 Score: 116
Period size: 49 Copynumber: 2.3 Consensus size: 47
141229 ATAATTCGTA
* *
141239 TATAATTATATATTTTATTATATT-ATAA-TTATATT-TATAATATTT
1 TATATTTATATATTTTAATATATTAATAATTTATATTATATAA-ATTT
*
141284 TATATTTATATAAATTTTAATATGTTAATAATTTATATTATATAAATTT
1 TATATTTATAT--ATTTTAATATATTAATAATTTATATTATATAAATTT
* *
141333 T-GATTCATATATTT
1 TATATTTATATATTT
141347 CTATCATGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
45 10 0.19
46 4 0.08
47 11 0.21
48 11 0.21
49 12 0.23
50 5 0.09
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (47 bp):
TATATTTATATATTTTAATATATTAATAATTTATATTATATAAATTT
Found at i:141306 original size:18 final size:17
Alignment explanation
Indices: 141267--141333 Score: 72
Period size: 16 Copynumber: 4.1 Consensus size: 17
141257 TATATTATAA
*
141267 TTATATTTATA-ATATT
1 TTATATTTATATAAATT
141283 TTATATTTATATAAATT
1 TTATATTTATATAAATT
141300 TTAATATGTTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
141316 TTATA-TTATATAAATT
1 TTATATTTATATAAATT
141332 TT
1 TT
141334 GATTCATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 5 0.11
16 17 0.39
17 8 0.18
18 6 0.14
19 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:141343 original size:48 final size:47
Alignment explanation
Indices: 141245--141343 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 47
141235 CGTATATAAT
* * * *
141245 TATATATTTTATTATATTATAATTATATTTATAATATTTTATATTTA
1 TATAAATTTTAATATATTATAATTATATTTATAATATTTTAGATTCA
*
141292 TATAAATTTTAATATGTTAATAATTTATATTATATAA-ATTTT-GATTCA
1 TATAAATTTTAATATATT-ATAA-TTATATT-TATAATATTTTAGATTCA
141340 TATA
1 TATA
141344 TTTCTATCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
47 15 0.34
48 12 0.27
49 12 0.27
50 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (47 bp):
TATAAATTTTAATATATTATAATTATATTTATAATATTTTAGATTCA
Found at i:145653 original size:44 final size:43
Alignment explanation
Indices: 145569--145658 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 43
145559 TCTAATTATT
*
145569 TTTTAAATTTAAATTAAAAATTATAATAGTTTAATTATTTAAA
1 TTTTAAATTTAAATTAAAAATTATAATAGTATAATTATTTAAA
* * *
145612 TTTTAAATTTTAAATTAAGAATTGTAATAGTAT-CTTAATTTAAA
1 TTTTAAA-TTTAAATTAAAAATTATAATAGTATAATT-ATTTAAA
145656 TTT
1 TTT
145659 AAAAAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 9 0.22
44 32 0.78
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (43 bp):
TTTTAAATTTAAATTAAAAATTATAATAGTATAATTATTTAAA
Found at i:145851 original size:19 final size:19
Alignment explanation
Indices: 145824--145865 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
145814 ATTATATCTA
*
145824 TAATAATATTA-TCTTTTAT
1 TAATAATATAACT-TTTTAT
*
145843 TAATGATATAACTTTTTAT
1 TAATAATATAACTTTTTAT
145862 TAAT
1 TAAT
145866 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (19 bp):
TAATAATATAACTTTTTAT
Found at i:145852 original size:27 final size:27
Alignment explanation
Indices: 145795--145853 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
145785 AATACTTTTT
*
145795 TATAATAATAAAATCTATTATTATATC
1 TATAATAATAAAATCTATTATTATATA
** *
145822 TATAATAATATTATCTTTTATTA-ATGA
1 TATAATAATAAAATCTATTATTATAT-A
145849 TATAA
1 TATAA
145854 CTTTTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (27 bp):
TATAATAATAAAATCTATTATTATATA
Found at i:146150 original size:28 final size:29
Alignment explanation
Indices: 146090--146154 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
146080 TTTTCGTTAA
* * *
146090 TTAAAATAGTAATATTTTGATAATTTATT
1 TTAAAATAATAATATTTTAAAAATTTATT
*
146119 TTAAATTAATAATATTTTAAAAATTTATT
1 TTAAAATAATAATATTTTAAAAATTTATT
*
146148 TAAAAAT
1 TTAAAAT
146155 CAACAGTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTAAAATAATAATATTTTAAAAATTTATT
Found at i:147433 original size:27 final size:27
Alignment explanation
Indices: 147403--147466 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
147393 TAGCCATCAA
*
147403 TTTTAATAAATAAAAAGGAACCACCAT
1 TTTTAACAAATAAAAAGGAACCACCAT
* * * *
147430 TTTTGACAAATATAAAGGAATCGCCAT
1 TTTTAACAAATAAAAAGGAACCACCAT
*
147457 TTTTGACAAA
1 TTTTAACAAA
147467 CACAAATGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (27 bp):
TTTTAACAAATAAAAAGGAACCACCAT
Found at i:151981 original size:27 final size:27
Alignment explanation
Indices: 151949--152022 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
151939 ACAAGCCATC
*
151949 ATTTTTTACAAACAAAAAAGAACCACT
1 ATTTTTCACAAACAAAAAAGAACCACT
* * *
151976 ATTTTTGACAAACATAAAAA-AATCATT
1 ATTTTTCACAAACA-AAAAAGAACCACT
*
152003 ATTTTTCACAAACACAAAAG
1 ATTTTTCACAAACAAAAAAG
152023 GTAACTTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.10
27 31 0.77
28 5 0.12
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.28
Consensus pattern (27 bp):
ATTTTTCACAAACAAAAAAGAACCACT
Found at i:153916 original size:22 final size:22
Alignment explanation
Indices: 153859--153918 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
153849 TTAAATAGGC
153859 CAATAACAT-AATAT-A-AGAA
1 CAATAACATAAATATGATAGAA
* * *
153878 AAATAA-GTGAAACATGATAGAA
1 CAATAACAT-AAATATGATAGAA
153900 CAATAACATAAATATGATA
1 CAATAACATAAATATGATA
153919 TGAATATACG
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 5 0.17
20 4 0.13
21 1 0.03
22 18 0.60
23 1 0.03
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.22
Consensus pattern (22 bp):
CAATAACATAAATATGATAGAA
Found at i:154065 original size:12 final size:12
Alignment explanation
Indices: 154050--154114 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
154040 TTTAACTCAT
*
154050 TTTTCTTTTTTC
1 TTTTCTTCTTTC
154062 TTTT-TTCTTTC
1 TTTTCTTCTTTC
154073 TCTTTC-TCTTTC
1 T-TTTCTTCTTTC
*
154085 TTTTACTCCTTTC
1 TTTT-CTTCTTTC
154098 TTTTTCTTCCTTTC
1 -TTTTCTT-CTTTC
154112 TTT
1 TTT
154115 AAAAAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
11 10 0.23
12 15 0.34
13 10 0.23
14 9 0.20
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:154928 original size:2 final size:2
Alignment explanation
Indices: 154921--154949 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
154911 TCGTTGGTGT
154921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
154950 GATAATATGC
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:155602 original size:15 final size:15
Alignment explanation
Indices: 155582--155622 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
155572 AAATTTAAAA
155582 ATTAAATATATTTAT
1 ATTAAATATATTTAT
155597 ATTAAATAAATATTTAT
1 ATTAAAT--ATATTTAT
*
155614 ATTCAATAT
1 ATTAAATAT
155623 TTATATCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAAATATATTTAT
Found at i:155609 original size:17 final size:17
Alignment explanation
Indices: 155589--155621 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
155579 AAAATTAAAT
155589 ATATTTATATTAAATAA
1 ATATTTATATTAAATAA
*
155606 ATATTTATATTCAATA
1 ATATTTATATTAAATA
155622 TTTATATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTTATATTAAATAA
Found at i:160244 original size:28 final size:28
Alignment explanation
Indices: 160184--160244 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
160174 TATATATTTC
*
160184 TAATATATATTAAAATTAAAAATATATA
1 TAATATATATTAAAATTAAAAATAAATA
* *
160212 AAATATATGTTAAATATTAAAAA-AAATA
1 TAATATATATTAAA-ATTAAAAATAAATA
160240 TAATA
1 TAATA
160245 GTAATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
TAATATATATTAAAATTAAAAATAAATA
Found at i:160909 original size:21 final size:21
Alignment explanation
Indices: 160885--160926 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
160875 TCATTCTTAG
160885 ATTTGAATAACATAAGATTGT
1 ATTTGAATAACATAAGATTGT
*
160906 ATTTGAATAACATAGGATTGT
1 ATTTGAATAACATAAGATTGT
160927 GATGTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (21 bp):
ATTTGAATAACATAAGATTGT
Found at i:161697 original size:18 final size:19
Alignment explanation
Indices: 161670--161707 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
161660 ATCACAATTT
161670 AAAATATATTATAATATTA
1 AAAATATATTATAATATTA
* *
161689 AAAAT-TATTTTTATATTA
1 AAAATATATTATAATATTA
161707 A
1 A
161708 TATTTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATATTATAATATTA
Found at i:166525 original size:21 final size:20
Alignment explanation
Indices: 166482--166526 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
166472 TTTTACTCAG
*
166482 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTGTTA
*
166502 ATGTATCGATGCATTTAGTTA
1 ATGTATCGATACATTT-GTTA
166523 ATGT
1 ATGT
166527 TGAGCATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (20 bp):
ATGTATCGATACATTTGTTA
Found at i:170541 original size:2 final size:2
Alignment explanation
Indices: 170534--170558 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
170524 TCCGATATCG
170534 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
170559 GATGAATCCA
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:171971 original size:15 final size:15
Alignment explanation
Indices: 171951--171980 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
171941 CAATCTTGAA
171951 TATATTTTATTTTAT
1 TATATTTTATTTTAT
171966 TATATTTTATTTTAT
1 TATATTTTATTTTAT
171981 GATGATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATATTTTATTTTAT
Found at i:172132 original size:19 final size:17
Alignment explanation
Indices: 172099--172137 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
172089 ATACAAAAAA
172099 ATAATTAAAATATAAAT
1 ATAATTAAAATATAAAT
172116 ATAATATAAATATATAAAT
1 ATAAT-TAAA-ATATAAAT
172135 ATA
1 ATA
172138 TCAATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 4 0.20
19 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATTAAAATATAAAT
Found at i:173450 original size:2 final size:2
Alignment explanation
Indices: 173445--173481 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
173435 TCTCTCCTTT
173445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
173482 CAAAAGTTTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:174178 original size:19 final size:19
Alignment explanation
Indices: 174150--174195 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
174140 ATTATTTATA
**
174150 TTTA-TAATAATATTTTCT
1 TTTATTAATAATATAATCT
174168 TTTATTAATAATATAATCT
1 TTTATTAATAATATAATCT
174187 TTTATTAAT
1 TTTATTAAT
174196 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATTAATAATATAATCT
Found at i:174220 original size:3 final size:3
Alignment explanation
Indices: 174212--174258 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
174202 AAATACCTAC
* *
174212 ATA ATA ATA ACT- TTA ATA AT- ATT ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
174256 ATA
1 ATA
174259 GTAGGCGAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
2 3 0.08
3 34 0.89
4 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:174251 original size:23 final size:23
Alignment explanation
Indices: 174212--174255 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
174202 AAATACCTAC
*
174212 ATAATAATAACTTTAATAATATT
1 ATAATAATAACTATAATAATATT
174235 ATAATAATAA-TAATAATAATA
1 ATAATAATAACT-ATAATAATA
174256 ATAGTAGGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAATAATAACTATAATAATATT
Found at i:175585 original size:15 final size:14
Alignment explanation
Indices: 175562--175601 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
175552 CATAGACAAC
175562 ATATAAATCTATAAA
1 ATAT-AATCTATAAA
*
175577 ATATCAATCTATTAA
1 ATAT-AATCTATAAA
175592 ATATAATCTA
1 ATATAATCTA
175602 AGATTGACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAATCTATAAA
Found at i:186888 original size:22 final size:21
Alignment explanation
Indices: 186863--186906 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
186853 TTAAAAAATT
* *
186863 AAATGAATATAATTTTTATTTA
1 AAATCAATATAA-TTATATTTA
*
186885 AAATCAATTTAATTATATTTA
1 AAATCAATATAATTATATTTA
186906 A
1 A
186907 TATATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATCAATATAATTATATTTA
Found at i:187123 original size:13 final size:13
Alignment explanation
Indices: 187103--187127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187093 AATTTAAGTA
187103 TATATATTAAAAG
1 TATATATTAAAAG
187116 TATATATTAAAA
1 TATATATTAAAA
187128 TATTAGAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TATATATTAAAAG
Found at i:187532 original size:19 final size:20
Alignment explanation
Indices: 187510--187550 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
187500 ATTTAATTTG
187510 AAATAATA-ATTTTAAATTA
1 AAATAATATATTTTAAATTA
*
187529 AAATAATATATTTTTAATTA
1 AAATAATATATTTTAAATTA
187549 AA
1 AA
187551 TTTAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATAATATATTTTAAATTA
Found at i:191330 original size:30 final size:29
Alignment explanation
Indices: 191291--191347 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
191281 AGCAAGGAGG
*
191291 ATAACTTGACTGTGAGATTGATTATTAAA
1 ATAACTTGACTGTGAGATTAATTATTAAA
*
191320 ATAACATTGACTGTGATATTAATTATTA
1 ATAAC-TTGACTGTGAGATTAATTATTA
191348 TAGTGGTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (29 bp):
ATAACTTGACTGTGAGATTAATTATTAAA
Found at i:192075 original size:3 final size:3
Alignment explanation
Indices: 192062--192102 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
192052 ATCTCTTAGC
192062 ATT AGTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
192103 GATGTATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:192887 original size:2 final size:2
Alignment explanation
Indices: 192882--192927 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
192872 ATCTCTCCTC
192882 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
192924 AT AT
1 AT AT
192928 TACACAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194530 original size:27 final size:27
Alignment explanation
Indices: 194499--194565 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
194489 AAAATATTAT
*
194499 TTTTTTAATTTACATTTAATATTTAAA-A
1 TTTTTTAATTTA-A-TAAATATTTAAACA
*
194527 TTTTTTATATTGAATAAATATTTAAACA
1 TTTTTTA-ATTTAATAAATATTTAAACA
*
194555 -GTTTTAATTTA
1 TTTTTTAATTTA
194566 TTTAAGGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 4 0.12
27 16 0.48
28 9 0.27
29 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (27 bp):
TTTTTTAATTTAATAAATATTTAAACA
Found at i:195426 original size:2 final size:2
Alignment explanation
Indices: 195419--195448 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
195409 TAGATTCCTC
195419 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
195449 TACGAATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196892 original size:16 final size:16
Alignment explanation
Indices: 196853--196884 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
196843 ATTTAGAGAG
196853 GAAAAAAACAAAAATA
1 GAAAAAAACAAAAATA
*
196869 GAAAAAAACCAAAATA
1 GAAAAAAACAAAAATA
196885 AAACAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.09, G:0.06, T:0.06
Consensus pattern (16 bp):
GAAAAAAACAAAAATA
Found at i:197055 original size:47 final size:47
Alignment explanation
Indices: 197001--197095 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
196991 CGTGTACTCC
*
197001 AAGTTTGATTGACCTCCACAAATGCTATTGGTGACTTGACTTAGATA
1 AAGTTTGATTCACCTCCACAAATGCTATTGGTGACTTGACTTAGATA
*
197048 AAGTTTGATTCATCTCCACAAATGCTATTGGTGACTTGACTTAGATA
1 AAGTTTGATTCACCTCCACAAATGCTATTGGTGACTTGACTTAGATA
197095 A
1 A
197096 TGGATAATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (47 bp):
AAGTTTGATTCACCTCCACAAATGCTATTGGTGACTTGACTTAGATA
Found at i:197940 original size:44 final size:44
Alignment explanation
Indices: 197877--197965 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
197867 CAATCTTTAC
197877 AATTCATCCCATATTTTCTTCCATTCACACTTCCATCATTTTCA
1 AATTCATCCCATATTTTCTTCCATTCACACTTCCATCATTTTCA
* *
197921 AATTCCTCCCATATTTTCTTCCATTCACATTTCCATCATTTTCA
1 AATTCATCCCATATTTTCTTCCATTCACACTTCCATCATTTTCA
197965 A
1 A
197966 GGAAATTGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (44 bp):
AATTCATCCCATATTTTCTTCCATTCACACTTCCATCATTTTCA
Found at i:200308 original size:19 final size:19
Alignment explanation
Indices: 200280--200321 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
200270 GATAATTTTT
200280 TAAA-ATAATAAAAAAACA
1 TAAATATAATAAAAAAACA
* *
200298 TAAATATAATATAAATACA
1 TAAATATAATAAAAAAACA
200317 TAAAT
1 TAAAT
200322 TTGATTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAATATAATAAAAAAACA
Found at i:206555 original size:27 final size:27
Alignment explanation
Indices: 206525--206605 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
206515 TTATAATTAT
206525 TTTTAAAATATTATATATTTATATAAA
1 TTTTAAAATATTATATATTTATATAAA
* *
206552 TTTTAAAAAATTA-ATAATTTAAGTTTAAA
1 TTTTAAAATATTATAT-ATTT-A-TATAAA
* * *
206581 TTTTGACATATTCATATTTTTATAT
1 TTTTAAAATATT-ATATATTTATAT
206606 TTTATTATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
26 2 0.05
27 16 0.38
28 3 0.07
29 15 0.36
30 4 0.10
31 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTTAAAATATTATATATTTATATAAA
Found at i:206621 original size:21 final size:22
Alignment explanation
Indices: 206595--206648 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
206585 GACATATTCA
*
206595 TATTTTTATATTTTATTAT-AT
1 TATTTTTATATTATATTATAAT
*
206616 TATTTTTATATTATATTTTAAT
1 TATTTTTATATTATATTATAAT
206638 TATTTTTATAT
1 TATTTTTATAT
206649 ATCGTATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTTATATTATATTATAAT
Found at i:208048 original size:2 final size:2
Alignment explanation
Indices: 208041--208072 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
208031 TTTCCTTTTG
208041 TC TC TC TC ATC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC T
208073 TCTGATAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:208274 original size:16 final size:16
Alignment explanation
Indices: 208250--208281 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
208240 GAATTGGTTT
208250 TATAAAAGTTTAATAA
1 TATAAAAGTTTAATAA
*
208266 TATATAAGTTTAATAA
1 TATAAAAGTTTAATAA
208282 ATGAGTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
TATAAAAGTTTAATAA
Found at i:208673 original size:20 final size:18
Alignment explanation
Indices: 208636--208674 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
208626 GTTCAAGCTC
*
208636 AATAAAAGAAAAGATACA
1 AATAAAAAAAAAGATACA
208654 AATAAAAAAAGAAGAGTACA
1 AATAAAAAAA-AAGA-TACA
208674 A
1 A
208675 TGTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.72, C:0.05, G:0.13, T:0.10
Consensus pattern (18 bp):
AATAAAAAAAAAGATACA
Found at i:211398 original size:20 final size:20
Alignment explanation
Indices: 211370--211412 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
211360 TATGATTAAC
211370 ACATAACTTAGATACTATTT
1 ACATAACTTAGATACTATTT
*
211390 ACATGACTTAGATACTATTT
1 ACATAACTTAGATACTATTT
211410 ACA
1 ACA
211413 AGTTCAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (20 bp):
ACATAACTTAGATACTATTT
Found at i:214186 original size:20 final size:20
Alignment explanation
Indices: 214161--214217 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
214151 ATTTCATATT
*
214161 TTTTTCTTTTTTTCTTTTTC
1 TTTTTCTTTATTTCTTTTTC
* *
214181 TTTTTCTTTCTTTCTTCTTC
1 TTTTTCTTTATTTCTTTTTC
* *
214201 ATCTTCTTTATTTCTTT
1 TTTTTCTTTATTTCTTT
214218 CTTACCTAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTCTTTATTTCTTTTTC
Found at i:214939 original size:27 final size:25
Alignment explanation
Indices: 214886--214939 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
214876 CTTATTTTCC
*
214886 TTCCTTTTTTTTTTTTGCTTTTTGT
1 TTCCTTTTTTTTTTTTGCTTTTAGT
214911 TTCCTTTTTGATTTTTTTG-TTGTTAGT
1 TTCCTTTTT--TTTTTTTGCTT-TTAGT
214938 TT
1 TT
214940 ATGATTAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 9 0.36
26 2 0.08
27 14 0.56
ACGTcount: A:0.04, C:0.09, G:0.11, T:0.76
Consensus pattern (25 bp):
TTCCTTTTTTTTTTTTGCTTTTAGT
Found at i:215496 original size:32 final size:32
Alignment explanation
Indices: 215451--215956 Score: 468
Period size: 32 Copynumber: 16.6 Consensus size: 32
215441 AAAATGGTGA
* *
215451 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* ** *
215483 TTTTAAAAGGGTTGCCACCGA-AAGTGTGGAC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * *
215514 TTTTGAAAA-GGTTCCCATCAACTTGTGTGGGC
1 -TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
*
215546 TTTGAAAAGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * *
215578 TTTGAAATGAGTTACCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* *
215610 TTTGAAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
*
215642 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
*
215674 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* *
215706 TTTGAAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * * *
215738 TTTGAAATGGTTTACCACCGACTTGTGTAGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * *
215770 TTTG-AAATGG-TGCTACTGAC-T-TGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* *
215798 TTTG-AAA-GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* *
215826 TTTG-AAA-GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * * *
215854 TTTG-AAA-GGATGCCACCAACTTGTATGGAC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * *
215884 TTTGGAAA--GATGCCACTGAC-T-TGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* **
215912 TTTGAAAA--GATGCCACTAAC-T-TGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
215940 TTTGAAAAGGG-TGCCAC
1 TTTGAAAAGGGTTGCCAC
215957 AAAGTTGTGA
Statistics
Matches: 419, Mismatches: 46, Indels: 21
0.86 0.09 0.04
Matches are distributed among these distances:
27 2 0.00
28 115 0.27
29 9 0.02
30 27 0.06
31 29 0.07
32 237 0.57
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (32 bp):
TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
Found at i:215984 original size:27 final size:27
Alignment explanation
Indices: 215944--216824 Score: 1055
Period size: 27 Copynumber: 32.2 Consensus size: 27
215934 GTGGGCTTTG
** *
215944 AAAAGGGTGCCACAAAGTTGTGAACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
215971 AAAAGGGTGTCACAGAGTTATGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
215999 AAAAGAGTGCCACGGAGTTATGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
216027 AAAAGGGTGCCACAGAGTTGTGGAATT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
216054 AAAAGAGATGCTACGGAGTTATGGACTT
1 AAAAG-GGTGCCACGGAGTTGTGGACTT
216082 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
216109 AAAAGGGTACCACAGAGTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
216136 AAAAGGGATGCCACAGAGTTGTGGACTTT
1 AAAAGGG-TGCCACGGAGTTGTGGAC-TT
216165 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** * *
216192 AAAAGGGTGCCGTGGAGTCGTGAACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
216219 AAAAGGGATGCCACGGAGTTGTAGACTT
1 AAAAGGG-TGCCACGGAGTTGTGGACTT
* *
216247 AAAAGGGTGCCACGAAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
216274 AAAAGGGTGTCACGGAGTTGTGAACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
216302 AAAAGGGTGCCATGGAGTTGTGGACCT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
216329 AAAAAGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
216356 AAAAGGGGGCTACAGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
216383 AAAAGGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
216410 AAAAGGGTGCCACGGACTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
216437 AAAAGGGTGCCATGGACTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
216465 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* **
216492 TAAAGGGTGCCATAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
216520 AAAAGGGTGCCACGAAATTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
216547 AAAAGGATGCCACAGAGTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
216574 AAAAGGGTGCCACAGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
216601 AAAAGGGTGCTACGGAG-TGATAGACTT
1 AAAAGGGTGCCACGGAGTTG-TGGACTT
216628 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
216655 AAAAGGGTACCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
216683 AAAAGGCTGTCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
**
216711 AAAA-GGTGCCACAAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** * *
216737 AAAAGAATGCCATGGAGTTGTGGATTTT
1 AAAAGGGTGCCACGGAGTTGTGGA-CTT
*
216765 AAAAGGATGCCACGGAGTTGTGGACTCT
1 AAAAGGGTGCCACGGAGTTGTGGACT-T
*
216793 AAAAGGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
216820 TAAAG
1 AAAAG
216825 AGGTCACAGT
Statistics
Matches: 735, Mismatches: 105, Indels: 28
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.01
27 441 0.60
28 278 0.38
29 9 0.01
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.24
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:216009 original size:55 final size:54
Alignment explanation
Indices: 215944--216824 Score: 1055
Period size: 55 Copynumber: 16.1 Consensus size: 54
215934 GTGGGCTTTG
** * * * *
215944 AAAAGGGTGCCACAAAGTTGTGAACTTAAAAGGGTGTCACAGAGTTATGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TT
* * * *
215999 AAAAGAGTGCCACGGAGTTATGGACTTTAAAAGGGTGCCACAGAGTTGTGGAATT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT
* * *
216054 AAAAGAGATGCTACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
216109 AAAAGGGTACCACAGAGTTGTAGACTTAAAAGGGATGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGAC-TT
** * *
216165 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCGTGGAGTCGTGAACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* * *
216219 AAAAGGGATGCCACGGAGTTGTAGACTTAAAAGGGTGCCACGAAGTTATGGACTT
1 AAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
216274 AAAAGGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGCCATGGAGTTGTGGACCT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT
* * * * * *
216329 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGGGCTACAGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* * *
216383 AAAAGGGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGACTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* *
216437 AAAAGGGTGCCATGGACTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT
* ** * *
216492 TAAAGGGTGCCATAGAGTTGTGGACTTTAAAAGGGTGCCACGAAATTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT
* * * * *
216547 AAAAGGATGCCACAGAGTTGTAGACTTAAAAGGGTGCCACAGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* *
216601 AAAAGGGTGCTACGGAG-TGATAGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTG-TGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* * *
216655 AAAAGGGTACCACGGAGTTGTGGACTTTAAAAGGCTGTCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TT
** ** * *
216711 AAAA-GGTGCCACAAAGTTGTGGACTTAAAAGAATGCCATGGAGTTGTGGATTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA-CTT
* *
216765 AAAAGGATGCCACGGAGTTGTGGACTCTAAAAGGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACT-TAAAAGGGTGCCACGGAGTTGTGGACTT
*
216820 TAAAG
1 AAAAG
216825 AGGTCACAGT
Statistics
Matches: 706, Mismatches: 106, Indels: 28
0.84 0.13 0.03
Matches are distributed among these distances:
53 2 0.00
54 255 0.36
55 348 0.49
56 101 0.14
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.24
Consensus pattern (54 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:216146 original size:82 final size:81
Alignment explanation
Indices: 215944--216824 Score: 1055
Period size: 82 Copynumber: 10.7 Consensus size: 81
215934 GTGGGCTTTG
** * * * * *
215944 AAAAGGGTGCCACAAAGTTGTGAACTTAAAAGGGTGTCACAGAGTTATGGACTTTAAAAGAGTGC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
*
216009 CACGGAGTTATGGACTTT
65 CACGGAGTTGTGGAC-TT
* * * * *
216027 AAAAGGGTGCCACAGAGTTGTGGAATTAAAAGAGATGCTACGGAGTTATGGACTTAAAAGGGTGC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
216092 CACGGAGTTGTGGACTT
65 CACGGAGTTGTGGACTT
* * * *
216109 AAAAGGGTACCACAGAGTTGTAGACTTAAAAGGGATGCCACAGAGTTGTGGACTTTAAAAGGGTG
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGAC-TTAAAAGGGTG
216174 CCACGGAGTTGTGGACTT
64 CCACGGAGTTGTGGACTT
** * * *
216192 AAAAGGGTGCCGTGGAGTCGTGAACTTAAAAGGGATGCCACGGAGTTGTAGACTTAAAAGGGTGC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGC
* *
216257 CACGAAGTTATGGACTT
65 CACGGAGTTGTGGACTT
* * * * *
216274 AAAAGGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGCCATGGAGTTGTGGACCTAAAAAGGTGC
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
*
216339 CACAGAGTTGTGGACTT
65 CACGGAGTTGTGGACTT
* * * * *
216356 AAAAGGGGGCTACAGAGTTATGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGGGTGCC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* *
216421 ACGGACTTGTAGACTT
66 ACGGAGTTGTGGACTT
* * *
216437 AAAAGGGTGCCATGGACTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGC
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
**
216502 CATAGAGTTGTGGACTTT
65 CACGGAGTTGTGGAC-TT
* * * * *
216520 AAAAGGGTGCCACGAAATTGTGGACTTAAAAGGATGCCACAGAGTTGTAGACTTAAAAGGGTGCC
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* *
216585 ACAGAGTTATGGACTT
66 ACGGAGTTGTGGACTT
* * *
216601 AAAAGGGTGCTACGGAG-TGATAGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTAC
1 AAAAGGGTGCCACGGAGTTG-TGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
216665 CACGGAGTTGTGGACTTT
65 CACGGAGTTGTGGAC-TT
* * ** **
216683 AAAAGGCTGTCACGGAGTTGTGGACTTTAAAA-GGTGCCACAAAGTTGTGGACTTAAAAGAATGC
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
* *
216747 CATGGAGTTGTGGATTTT
65 CACGGAGTTGTGGA-CTT
* * *
216765 AAAAGGATGCCACGGAGTTGTGGACTCTAAAAGGGTGCCACGGAGTTATGGACTTTAAAG
1 AAAAGGGTGCCACGGAGTTGTGGACT-TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
216825 AGGTCACAGT
Statistics
Matches: 686, Mismatches: 99, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
80 2 0.00
81 138 0.20
82 339 0.49
83 191 0.28
84 16 0.02
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.24
Consensus pattern (81 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
ACGGAGTTGTGGACTT
Found at i:218174 original size:15 final size:16
Alignment explanation
Indices: 218136--218177 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
218126 CCCTTTTTTA
218136 TTTTGCTTTTGCAATT
1 TTTTGCTTTTGCAATT
218152 TTTT-CTTTT-C-ATT
1 TTTTGCTTTTGCAATT
218165 TTTTGGCTTTTGC
1 TTTT-GCTTTTGC
218178 TTTTGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.30
14 1 0.04
15 10 0.43
16 5 0.22
ACGTcount: A:0.07, C:0.14, G:0.12, T:0.67
Consensus pattern (16 bp):
TTTTGCTTTTGCAATT
Found at i:224620 original size:9 final size:9
Alignment explanation
Indices: 224606--224635 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
224596 CCATTTCATA
224606 TTTTTTTCT
1 TTTTTTTCT
224615 TTTTTTTCT
1 TTTTTTTCT
224624 TTTTCTTTCT
1 TTTT-TTTCT
224634 TT
1 TT
224636 CTTCTTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.65
10 7 0.35
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:224628 original size:15 final size:17
Alignment explanation
Indices: 224608--224663 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 17
224598 ATTTCATATT
224608 TTTTTCTTT-TTT-TTC
1 TTTTTCTTTCTTTCTTC
224623 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
224640 TTCATCTTCTTTCTTTCTTTC
1 TT--T-TTCTTTCTTTC-TTC
224661 TTT
1 TTT
224664 CCTAACTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.26
16 3 0.09
17 5 0.14
19 2 0.06
20 11 0.31
21 5 0.14
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:227844 original size:22 final size:23
Alignment explanation
Indices: 227800--227844 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
227790 TATGATCTCT
* *
227800 TTTATAAAATAAAATATTTTTAA
1 TTTATAAAATAAAATAATCTTAA
*
227823 TTTA-AAAATTAAATAATCTTAA
1 TTTATAAAATAAAATAATCTTAA
227845 CCATTGCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTATAAAATAAAATAATCTTAA
Found at i:234986 original size:1 final size:1
Alignment explanation
Indices: 234982--235006 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
234972 TTTTTTTTTT
234982 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
235007 CACATGGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:240677 original size:19 final size:19
Alignment explanation
Indices: 240639--240677 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
240629 TGAACGTAAT
* * *
240639 TTTAATATATATATATATA
1 TTTAATATACACATACATA
240658 TTTAATATACACATACATA
1 TTTAATATACACATACATA
240677 T
1 T
240678 AAGTGTATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTAATATACACATACATA
Found at i:242869 original size:13 final size:13
Alignment explanation
Indices: 242837--242881 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
242827 GTATTTTGAT
242837 TATTTATATTTTAAAA
1 TATTTATA-TTT--AA
242853 TATTTATATTTAA
1 TATTTATATTTAA
*
242866 TATTTATTTTTAA
1 TATTTATATTTAA
242879 TAT
1 TAT
242882 ATATTCAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 17 0.61
15 3 0.11
16 8 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:243339 original size:23 final size:23
Alignment explanation
Indices: 243313--243356 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
243303 TACTTATATT
243313 TATATATAAATAT-TAAATATAAA
1 TATATAT-AATATGTAAATATAAA
*
243336 TATATATTATATGTAAATATA
1 TATATATAATATGTAAATATA
243357 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TATATATAATATGTAAATATAAA
Found at i:243342 original size:17 final size:17
Alignment explanation
Indices: 243322--243361 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
243312 TTATATATAA
243322 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
* *
243339 ATATTATATGTAAATAT
1 ATATTAAATATAAATAT
243356 AT-TTAA
1 ATATTAA
243362 TTTTATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:244546 original size:18 final size:19
Alignment explanation
Indices: 244523--244558 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
244513 AAATTTTTTA
244523 CGAATATA-ATTATTTGTT
1 CGAATATATATTATTTGTT
*
244541 CGAATATATCTTATTTGT
1 CGAATATATATTATTTGT
244559 ATAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (19 bp):
CGAATATATATTATTTGTT
Found at i:250194 original size:52 final size:52
Alignment explanation
Indices: 250046--250174 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
250036 CGAAATATGA
*
250046 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
250098 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
250150 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
250175 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:250201 original size:13 final size:13
Alignment explanation
Indices: 250183--250241 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
250173 CAAAGATCAG
250183 TGTATCGATACAA
1 TGTATCGATACAA
250196 TGTATCGATAC-A
1 TGTATCGATACAA
*
250208 T-T-T-GA-ATAA
1 TGTATCGATACAA
250217 TGTATCGATACAA
1 TGTATCGATACAA
250230 TGTATCGATACA
1 TGTATCGATACA
250242 TTTGAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 1 0.03
9 4 0.10
10 2 0.05
11 2 0.05
12 4 0.10
13 26 0.67
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:250226 original size:34 final size:34
Alignment explanation
Indices: 250183--250262 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
250173 CAAAGATCAG
250183 TGTATCGATACAATGTATCGATACATTTGAATAA
1 TGTATCGATACAATGTATCGATACATTTGAATAA
250217 TGTATCGATACAATGTATCGATACATTTGAATAA
1 TGTATCGATACAATGTATCGATACATTTGAATAA
250251 TGTATCGATACA
1 TGTATCGATACA
250263 TTTTTTGGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATTTGAATAA
Found at i:250308 original size:19 final size:19
Alignment explanation
Indices: 250284--250382 Score: 87
Period size: 13 Copynumber: 5.7 Consensus size: 19
250274 TAGCTTAAAT
250284 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
250303 TGTATCGATAC---A-TTA
1 TGTATCGATACAAAACTTA
*
250318 --TATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
250335 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
250348 TGTATCGATACAAACACTTTA
1 TGTATCGATACAAA-AC-TTA
250369 TGTATCGATACAAA
1 TGTATCGATACAAA
250383 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 20 0.30
14 1 0.02
15 3 0.05
16 3 0.05
17 4 0.06
19 20 0.30
20 1 0.02
21 14 0.21
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:250327 original size:32 final size:32
Alignment explanation
Indices: 250286--250380 Score: 154
Period size: 32 Copynumber: 2.9 Consensus size: 32
250276 GCTTAAATTG
250286 TATCGATACAAAACTTATGTATCGATACATTA
1 TATCGATACAAAACTTATGTATCGATACATTA
* *
250318 TATCGATACAACACTTATGTATCGATACATTG
1 TATCGATACAAAACTTATGTATCGATACATTA
250350 TATCGATACAAACACTTTATGTATCGATACA
1 TATCGATACAAA-AC-TTATGTATCGATACA
250381 AATCGTTGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 41 0.71
33 2 0.03
34 15 0.26
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTA
Found at i:253180 original size:17 final size:17
Alignment explanation
Indices: 253158--253192 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
253148 GATAAGTTCT
*
253158 ATTATAAGATTGTCTTG
1 ATTATAAGATTATCTTG
253175 ATTATAAGATTATCTTG
1 ATTATAAGATTATCTTG
253192 A
1 A
253193 ATATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (17 bp):
ATTATAAGATTATCTTG
Found at i:254944 original size:20 final size:20
Alignment explanation
Indices: 254921--254997 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
254911 AAGTACCCAG
*
254921 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
254941 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
254961 ATATATTGACACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
254981 ATGTATCGATATATTTT
1 ATGTATCGATACATTTT
254998 ATCTTTTTAC
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:258967 original size:78 final size:78
Alignment explanation
Indices: 258879--259038 Score: 257
Period size: 78 Copynumber: 2.1 Consensus size: 78
258869 CTTATTTGTT
* * *
258879 CAAGCTCAATTCATTTATACCTTACATTTGAACAAAGTTCATTTGATTTAAATAAACCGGGCTTG
1 CAAGCCCAATTCATTTATACCTTACATTTGAACAAAATTCATTTGATTTAAATAAACCGAGCTTG
258944 AACCAAGCTCAAA
66 AACCAAGCTCAAA
* * **
258957 CAAGCCCAATTCATTTATACCTTATATTTGAGCAAAATTCATTTGATTTAAATAAATTGAGCTTG
1 CAAGCCCAATTCATTTATACCTTACATTTGAACAAAATTCATTTGATTTAAATAAACCGAGCTTG
259022 AACCAAGCTCAAA
66 AACCAAGCTCAAA
259035 CAAG
1 CAAG
259039 TATATGAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.31
Consensus pattern (78 bp):
CAAGCCCAATTCATTTATACCTTACATTTGAACAAAATTCATTTGATTTAAATAAACCGAGCTTG
AACCAAGCTCAAA
Found at i:259430 original size:21 final size:21
Alignment explanation
Indices: 259406--259489 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
259396 TATCAGTTTA
*
259406 TTTATATAATCATTTTTAAAT
1 TTTATATAATAATTTTTAAAT
* * **
259427 TTTATAAAATGAGATTTAAAT
1 TTTATATAATAATTTTTAAAT
*
259448 TTTAATATTTATAATTTTTTAAATT
1 TTT-ATA-TAATAA-TTTTTAAA-T
*
259473 TTTATATTATAATTTTT
1 TTTATATAATAATTTTT
259490 TTTGTATTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
21 20 0.40
22 8 0.16
23 9 0.18
24 9 0.18
25 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTATATAATAATTTTTAAAT
Found at i:259491 original size:24 final size:24
Alignment explanation
Indices: 259441--259490 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
259431 TAAAATGAGA
259441 TTTAAATTTTAATATTTATAATTT
1 TTTAAATTTTAATATTTATAATTT
*
259465 TTTAAATTTTTATA-TTATAATTT
1 TTTAAATTTTAATATTTATAATTT
259488 TTT
1 TTT
259491 TTGTATTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTAAATTTTAATATTTATAATTT
Found at i:259551 original size:19 final size:20
Alignment explanation
Indices: 259517--259556 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
259507 AACTTTACGA
*
259517 ATAAAATAATAAAATATTAC
1 ATAAAATAATAAAATAATAC
*
259537 ATAATATAA-AAAATAATAC
1 ATAAAATAATAAAATAATAC
259556 A
1 A
259557 AAGATGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAATAATAAAATAATAC
Found at i:259679 original size:43 final size:47
Alignment explanation
Indices: 259595--259680 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 47
259585 AATTTTATCT
* *
259595 AATATAAATTATTACTATATCAAAATTTATACAAATATAATATTTTA
1 AATATAAATTATTAATATATCAAAATATATACAAATATAATATTTTA
*
259642 AATAT-AATTA-TAATATAT-AAAA-ATATATAAATATAATAT
1 AATATAAATTATTAATATATCAAAATATATACAAATATAATAT
259681 AAATTACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 15 0.42
44 4 0.11
45 7 0.19
46 5 0.14
47 5 0.14
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (47 bp):
AATATAAATTATTAATATATCAAAATATATACAAATATAATATTTTA
Found at i:261503 original size:17 final size:17
Alignment explanation
Indices: 261475--261519 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
261465 ATAATATGAA
261475 TTATTAACATATTA-AAT
1 TTATTAA-ATATTATAAT
261492 TTATATAAATA-TATAAT
1 TTAT-TAAATATTATAAT
261509 TTATTAAATAT
1 TTATTAAATAT
261520 AATTATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
17 14 0.56
18 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATTAAATATTATAAT
Found at i:261535 original size:16 final size:15
Alignment explanation
Indices: 261489--261537 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 15
261479 TAACATATTA
261489 AATTTATATAAATATAT
1 AATTTA-AT-AATATAT
*
261506 AATTTATTAA-ATAT
1 AATTTAATAATATAT
261520 AATTATAATAATATAT
1 AATT-TAATAATATAT
261536 AA
1 AA
261538 ACATAAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 7 0.25
17 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTAATAATATAT
Found at i:261538 original size:22 final size:22
Alignment explanation
Indices: 261494--261543 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
261484 TATTAAATTT
*
261494 ATATAAATATATAATTTATTAA
1 ATATAAATATATAATATATTAA
*
261516 ATATAATTATAATAATATA-TAA
1 ATATAAATAT-ATAATATATTAA
*
261538 ACATAA
1 ATATAA
261544 GGAGAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAAATATATAATATATTAA
Found at i:261937 original size:13 final size:14
Alignment explanation
Indices: 261919--261950 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
261909 ATTTGGTAAG
261919 AAAATT-AAAAAAT
1 AAAATTAAAAAAAT
261932 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
261946 AAAAT
1 AAAAT
261951 CTTGGCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAAAAAAAT
Found at i:263793 original size:15 final size:14
Alignment explanation
Indices: 263773--263830 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 14
263763 AACATACTAA
263773 TCTTTCTATTTCTTC
1 TCTTTCT-TTTCTTC
263788 TCTTTCTTTTTCCTCTC
1 TCTTTC-TTTT-CT-TC
*
263805 TCATTCTTTTCTTC
1 TCTTTCTTTTCTTC
*
263819 TTCTTTTTTTTC
1 -TCTTTCTTTTC
263831 ACTATAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.06
15 20 0.56
16 7 0.19
17 7 0.19
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (14 bp):
TCTTTCTTTTCTTC
Found at i:267514 original size:16 final size:16
Alignment explanation
Indices: 267452--267514 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
267442 TAAATCTAAT
267452 TAACTCAAAATCAAAA
1 TAACTCAAAATCAAAA
* * *
267468 TGACTCGAAATCGAAA
1 TAACTCAAAATCAAAA
* * **
267484 TAATTTAAACCCAAAA
1 TAACTCAAAATCAAAA
*
267500 TAACTTAAAATCAAA
1 TAACTCAAAATCAAA
267515 GTGATTCAAA
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.56, C:0.17, G:0.05, T:0.22
Consensus pattern (16 bp):
TAACTCAAAATCAAAA
Found at i:268771 original size:27 final size:24
Alignment explanation
Indices: 268727--268785 Score: 57
Period size: 27 Copynumber: 2.4 Consensus size: 24
268717 AAATATATAT
268727 TATAAATATTAAAATTTAAATTTTAAA
1 TATAAATATTAAAATTT--A-TTTAAA
***
268754 TATAAATATTATTTTTTATTTAAA
1 TATAAATATTAAAATTTATTTAAA
268778 -ATAAATAT
1 TATAAATAT
268786 ATGAACTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 8 0.28
24 6 0.21
25 1 0.03
27 14 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATAAATATTAAAATTTATTTAAA
Found at i:269378 original size:4 final size:4
Alignment explanation
Indices: 269369--269403 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
269359 ATAATTTTTA
*
269369 TATT TATT TATT TACT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
269404 AATATGGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:270500 original size:15 final size:16
Alignment explanation
Indices: 270480--270513 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
270470 GCATGATAAT
270480 AAATTATTTAA-TTAA
1 AAATTATTTAATTTAA
270495 AAATTATTTAATTTAA
1 AAATTATTTAATTTAA
270511 AAA
1 AAA
270514 AAATCACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTATTTAATTTAA
Found at i:275918 original size:21 final size:22
Alignment explanation
Indices: 275892--275937 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
275882 AAAATATGAT
275892 ATTTAATAAATTTAG-ATTTAA
1 ATTTAATAAATTTAGTATTTAA
*
275913 ATTTAATAAATTTAGTGTTTAA
1 ATTTAATAAATTTAGTATTTAA
275935 ATT
1 ATT
275938 CAGCATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTTAATAAATTTAGTATTTAA
Found at i:275921 original size:85 final size:85
Alignment explanation
Indices: 275832--275990 Score: 194
Period size: 85 Copynumber: 1.9 Consensus size: 85
275822 GATAATATAA
* * * * * *
275832 AATAAATTTAAAGTTTGAATT-TGACATATATAATTTTTTATTTTAATAATAAAATATGATATTT
1 AATAAATTTAAAGTTTAAATTCAG-CATATATAATCTCTTATTTTAATAATAAAAGATGATATAT
*
275896 AATAAATTTAGATTTAAATTT
65 AACAAATTTAGATTTAAATTT
** * * *
275917 AATAAATTTAGTGTTTAAATTCAGCATTTATAATCTCTTATTTTATTAATAAGAGATGATATATA
1 AATAAATTTAAAGTTTAAATTCAGCATATATAATCTCTTATTTTAATAATAAAAGATGATATATA
275982 ACAAATTTA
66 ACAAATTTA
275991 ATATTCAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
85 60 0.98
86 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (85 bp):
AATAAATTTAAAGTTTAAATTCAGCATATATAATCTCTTATTTTAATAATAAAAGATGATATATA
ACAAATTTAGATTTAAATTT
Found at i:277026 original size:18 final size:20
Alignment explanation
Indices: 276991--277032 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
276981 TTTTTGCTTA
276991 AAATCTTTTAAATATTAAAT
1 AAATCTTTTAAATATTAAAT
277011 AAAT-TTTTAAAT-TTAAAT
1 AAATCTTTTAAATATTAAAT
277029 AAAT
1 AAAT
277033 AACTTGACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.45
19 8 0.36
20 4 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATCTTTTAAATATTAAAT
Found at i:278123 original size:15 final size:16
Alignment explanation
Indices: 278103--278140 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
278093 TATATGCAAA
278103 TATAAATA-TTAAAAT
1 TATAAATAGTTAAAAT
*
278118 TATAAATAGTTAATAT
1 TATAAATAGTTAAAAT
*
278134 CATAAAT
1 TATAAAT
278141 TTTTAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TATAAATAGTTAAAAT
Found at i:281907 original size:23 final size:23
Alignment explanation
Indices: 281852--281899 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
281842 GAAAGATTCG
*
281852 AATTTTAAATATAATTAATGCTA
1 AATTTTAAATATAATTAATGATA
281875 AATTTTAAATATAATT-AT-ATA
1 AATTTTAAATATAATTAATGATA
281896 AATT
1 AATT
281900 AATTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 6 0.25
22 2 0.08
23 16 0.67
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTTAAATATAATTAATGATA
Found at i:281909 original size:30 final size:30
Alignment explanation
Indices: 281860--281924 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
281850 CGAATTTTAA
281860 ATATAATTAATGCTAAATTTTAAATATAATT
1 ATATAATTAAT-CTAAATTTTAAATATAATT
* *
281891 ATATAAATTAAT-TAAATTTTAAATTTTATT
1 ATAT-AATTAATCTAAATTTTAAATATAATT
281921 ATAT
1 ATAT
281925 TTAATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 20 0.65
31 4 0.13
32 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
ATATAATTAATCTAAATTTTAAATATAATT
Found at i:281971 original size:17 final size:17
Alignment explanation
Indices: 281951--281997 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
281941 TTTTAAATAT
* *
281951 TTAAATTTTTAATTAAA
1 TTAAATATTCAATTAAA
281968 TTAAACTATTCAATTAAA
1 TTAAA-TATTCAATTAAA
281986 -TAAATATATCAA
1 TTAAATAT-TCAA
281998 AAATCTGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 3 0.12
17 13 0.50
18 10 0.38
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATATTCAATTAAA
Found at i:282500 original size:1 final size:1
Alignment explanation
Indices: 282494--282519 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
282484 TGAGAAAAGG
282494 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
282520 CCCATCACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:283665 original size:2 final size:2
Alignment explanation
Indices: 283655--283690 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
283645 TTTAAAATAC
*
283655 AT AT TT 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
283691 GACATTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:284985 original size:25 final size:26
Alignment explanation
Indices: 284957--285009 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
284947 TATCTTAAAC
*
284957 ATGATAAATATATA-AAAAATAACAT
1 ATGATAAATAAATACAAAAATAACAT
*
284982 ATGATAAATAAATACATAAATAACAT
1 ATGATAAATAAATACAAAAATAACAT
285008 AT
1 AT
285010 AAATACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (26 bp):
ATGATAAATAAATACAAAAATAACAT
Found at i:286239 original size:18 final size:17
Alignment explanation
Indices: 286192--286258 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
286182 CGTATTATAA
286192 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
286208 TTATATTTATATAAATT
1 TTATATTTATATAAATT
286225 TTGATATGTTA-AT-AATT
1 TT-ATAT-TTATATAAATT
*
286242 AT-TA-TTATATAAATT
1 TTATATTTATATAAATT
286257 TT
1 TT
286259 GAAAAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 7 0.16
16 9 0.21
17 11 0.26
18 8 0.19
19 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:288294 original size:2 final size:2
Alignment explanation
Indices: 288287--288329 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
288277 TACATTCAAC
*
288287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
288329 T
1 T
288330 GAAAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:288815 original size:13 final size:12
Alignment explanation
Indices: 288778--288824 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 12
288768 CTTATCTCAA
*
288778 ATTTTATATTAA
1 ATTTTATATTAT
*
288790 ATTTTA-AATAT
1 ATTTTATATTAT
288801 -TTTTATATTAT
1 ATTTTATATTAT
288812 A-TTTATATTAT
1 ATTTTATATTAT
288823 AT
1 AT
288825 AATCAAATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 5 0.17
11 18 0.62
12 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTATATTAT
Found at i:293754 original size:16 final size:15
Alignment explanation
Indices: 293733--293772 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
293723 CCAACATATC
293733 TTTCTTCTTTTTCTTT
1 TTTCTT-TTTTTCTTT
*
293749 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTCTTT
293764 TTTCATTTT
1 TTTC-TTTT
293773 GCCATAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTTTTTCTTT
Found at i:293764 original size:13 final size:13
Alignment explanation
Indices: 293731--293763 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
293721 AACCAACATA
*
293731 TCTTTCTTCTTTT
1 TCTTTTTTCTTTT
293744 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
293757 T-TTTTTT
1 TCTTTTTT
293764 TTTCATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:297556 original size:35 final size:35
Alignment explanation
Indices: 297506--297581 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
297496 TATTTTTATT
* *
297506 ATTTTTTAAACATAAATTAAATTGAATAAATTTTAA
1 ATTTTTTAAACATAAATCAAATTAAAT-AATTTTAA
*
297542 ATTTTTT-AATATAAATCAAATTAAATAATTTTAA
1 ATTTTTTAAACATAAATCAAATTAAATAATTTTAA
*
297576 AATTTT
1 ATTTTT
297582 GATTTAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 13 0.36
35 16 0.44
36 7 0.19
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (35 bp):
ATTTTTTAAACATAAATCAAATTAAATAATTTTAA
Found at i:297969 original size:22 final size:22
Alignment explanation
Indices: 297955--297996 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
297945 AAATATTTAT
297955 TTTAAATTAATTAAATTAAATA
1 TTTAAATTAATTAAATTAAATA
*
297977 TTTAAATTAATTTAATTAAA
1 TTTAAATTAATTAAATTAAA
297997 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATTAATTAAATTAAATA
Found at i:297973 original size:27 final size:27
Alignment explanation
Indices: 297917--297996 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 27
297907 AATTTTTTAA
*
297917 AAAT-TTTAAATTTAATT-ATTATAATTTT
1 AAATATTTAAATTAAATTAATTA-AA--TT
**
297945 AAATATTTATTTTAAATTAATTAAATT
1 AAATATTTAAATTAAATTAATTAAATT
*
297972 AAATATTTAAATTAATTTAATTAAA
1 AAATATTTAAATTAAATTAATTAAA
297997 ATTATTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 24 0.55
28 4 0.09
29 12 0.27
30 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATATTTAAATTAAATTAATTAAATT
Found at i:297983 original size:13 final size:13
Alignment explanation
Indices: 297943--297986 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
297933 TATTATAATT
**
297943 TTAAATATTTATT
1 TTAAATATTTAAA
*
297956 TTAAATTAATTAAA
1 TTAAA-TATTTAAA
297970 TTAAATATTTAAA
1 TTAAATATTTAAA
297983 TTAA
1 TTAA
297987 TTTAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAATATTTAAA
Found at i:298214 original size:14 final size:14
Alignment explanation
Indices: 298178--298215 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
298168 GATTTGTCAC
298178 ATATATTTTTTTTAA
1 ATATA-TTTTTTTAA
298193 AT-TAATTTTTTTAA
1 ATAT-ATTTTTTTAA
298207 ATATATTTT
1 ATATATTTT
298216 AAGATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATATTTTTTTAA
Found at i:299339 original size:24 final size:25
Alignment explanation
Indices: 299316--299417 Score: 97
Period size: 24 Copynumber: 4.2 Consensus size: 25
299306 TAAAAAATAT
*
299316 AATAAATTATT-TTTATAATAATATT
1 AATAAATTATTATTTATAATAAT-TA
* * *
299341 TATATATTTTTA-TTATTAA-AATTA
1 AATAAATTATTATTTA-TAATAATTA
*
299365 AATAAATTATTATTTA-ATTAATTA
1 AATAAATTATTATTTATAATAATTA
*
299389 AATAAATTATTATTTA-ATTAATTA
1 AATAAATTATTATTTATAATAATTA
299413 AATAA
1 AATAA
299418 TAATCAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
23 1 0.02
24 44 0.68
25 17 0.26
26 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AATAAATTATTATTTATAATAATTA
Found at i:299427 original size:24 final size:24
Alignment explanation
Indices: 299360--299427 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
299350 TTATTATTAA
* *
299360 AATTAAATAAATTATTATTTAATT
1 AATTAAATAAATAATAATTTAATT
* *
299384 AATTAAATAAATTATTATTTAATT
1 AATTAAATAAATAATAATTTAATT
299408 AATTAAAT-AATAATCAATTT
1 AATTAAATAAATAAT-AATTT
299428 TCTTCCCTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.12
24 36 0.88
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTAAATAAATAATAATTTAATT
Found at i:300404 original size:3 final size:3
Alignment explanation
Indices: 300396--300426 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
300386 TGATAGCAAA
300396 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
300427 ATTTTGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:301561 original size:90 final size:91
Alignment explanation
Indices: 301448--301622 Score: 257
Period size: 90 Copynumber: 1.9 Consensus size: 91
301438 ATTTTGAGAC
*
301448 ATTACTTAATTAATTAAAATATTTTTATTTTA-TTTTATTTTTAAAATATATTTAAAATATTAAT
1 ATTACTTAATTAATTAAAATATTTTTA-TTTAGTTTTACTTTTAAAATATATTTAAAATATTAAT
*
301512 ATATTAATA-TAAAATAATTTGATGTT
65 ATATTAATAGAAAAATAATTTGATGTT
* * * *
301538 ATTATTTAATTAA-TACAAGTATTTTTATTTAGTTTTACTTTTAAAATATCTTTTAAATATTAAT
1 ATTACTTAATTAATTA-AAATATTTTTATTTAGTTTTACTTTTAAAATATATTTAAAATATTAAT
301602 ATATTAATAGAAAAATAATTT
65 ATATTAATAGAAAAATAATTT
301623 TTAAATAGTG
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
89 6 0.08
90 60 0.79
91 10 0.13
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (91 bp):
ATTACTTAATTAATTAAAATATTTTTATTTAGTTTTACTTTTAAAATATATTTAAAATATTAATA
TATTAATAGAAAAATAATTTGATGTT
Found at i:308060 original size:21 final size:20
Alignment explanation
Indices: 308028--308068 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
308018 TTATTTAAAT
* *
308028 TTAATTATAAAATATTTTTA
1 TTAATAATAAAATAATTTTA
308048 TTAATAATAAAAATAATTTTA
1 TTAATAAT-AAAATAATTTTA
308069 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATAATAAAATAATTTTA
Found at i:312668 original size:16 final size:16
Alignment explanation
Indices: 312619--312676 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
312609 TTTTGATTAT
*
312619 TTTAAATTATTTTAAA
1 TTTAAATTTTTTTAAA
* * *
312635 TTTGAATCATTTCT-AA
1 TTTAAAT-TTTTTTAAA
312651 TTTAAATTTTTTTAAA
1 TTTAAATTTTTTTAAA
*
312667 TTCAAATTTT
1 TTTAAATTTT
312677 AAATTTTTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 4 0.12
16 25 0.78
17 3 0.09
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTAAATTTTTTTAAA
Found at i:316125 original size:3 final size:3
Alignment explanation
Indices: 316117--316161 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
316107 TATCCTAGAT
316117 ATA ATA ATA ATA ATA 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
316162 GTAGTAATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:317466 original size:18 final size:18
Alignment explanation
Indices: 317431--317464 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
317421 ACGTGTGTAT
*
317431 TTTTTAATTATTATTTTA
1 TTTTTAAATATTATTTTA
317449 TTTTTAAATA-TATTTT
1 TTTTTAAATATTATTTT
317465 TAAGATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTAAATATTATTTTA
Found at i:318399 original size:15 final size:15
Alignment explanation
Indices: 318377--318428 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
318367 TATAATCATG
318377 TATA-AAATAATTTT
1 TATATAAATAATTTT
318391 TATATAAATAAATTTT
1 TATATAAAT-AATTTT
*
318407 AATATATTAATAATTTAT
1 --TATATAAATAATTT-T
318425 TATA
1 TATA
318429 ACTTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 4 0.12
15 4 0.12
16 10 0.31
17 5 0.16
18 9 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATAAATAATTTT
Found at i:319113 original size:2 final size:2
Alignment explanation
Indices: 319101--319134 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
319091 TATCTAACAC
*
319101 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
319135 ATAAACACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:319631 original size:29 final size:28
Alignment explanation
Indices: 319581--319641 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
319571 AAATTGGTAA
319581 TTTTTTAAAATAAAAAAGTTAGAAATTAT
1 TTTTTTAAAATAAAAAAGTTAGAAA-TAT
* * *
319610 TTTTTTCAAAT-AAGAAGATTAGTAATAT
1 TTTTTTAAAATAAAAAAG-TTAGAAATAT
319638 TTTT
1 TTTT
319642 AAATAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (28 bp):
TTTTTTAAAATAAAAAAGTTAGAAATAT
Found at i:320611 original size:2 final size:2
Alignment explanation
Indices: 320604--320639 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
320594 TTAAGTACTT
320604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
320640 AAAGATAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.