Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007703.1 Hibiscus syriacus cultivar Beakdansim tig00109916_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1017536
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:2667 original size:182 final size:184
Alignment explanation
Indices: 2061--2729 Score: 1188
Period size: 184 Copynumber: 3.7 Consensus size: 184
2051 TTTTAAATGG
*
2061 TATGGACATAAAGTACCGACAC-ATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
2125 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
2190 GATGTGTAAAATTTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
2244 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCCGCGC
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATT-CGCTC
*
2309 AT-AGACCGGTATATTTATACCGGTTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
65 ATAAAACCGGTATATTTATACCGG-TTATATTACAAAATTATCTATTACATTATAATTATGGGTT
*
2373 CCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCC-A
129 CCGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
2428 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
2493 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTAT-ATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
2557 GATGTGT-AAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2610 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCG-TGC
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT-C
* **
2674 ATAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
65 ATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
2730 ATGTTGAAAG
Statistics
Matches: 466, Mismatches: 13, Indels: 14
0.95 0.03 0.03
Matches are distributed among these distances:
181 44 0.09
182 131 0.28
183 58 0.12
184 135 0.29
185 98 0.21
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:4191 original size:3 final size:3
Alignment explanation
Indices: 4183--4266 Score: 78
Period size: 3 Copynumber: 28.0 Consensus size: 3
4173 ACTTTTTTGG
* * * ** *
4183 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
4231 TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
4267 GTCAGCTTCA
Statistics
Matches: 62, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:4200 original size:12 final size:12
Alignment explanation
Indices: 4183--4281 Score: 72
Period size: 12 Copynumber: 8.0 Consensus size: 12
4173 ACTTTTTTGG
4183 ATCATCATCTTC
1 ATCATCATCTTC
4195 ATCATCATCATCATC
1 ATCATCATC-T--TC
*
4210 GTCATCATCTTC
1 ATCATCATCTTC
** *
4222 ATCGCCAGCTTC
1 ATCATCATCTTC
* *
4234 ATCGTCATCATC
1 ATCATCATCTTC
*
4246 ATCATCATCGTC
1 ATCATCATCTTC
* *
4258 ATCTTCATCGTC
1 ATCATCATCTTC
* *
4270 AGCTTCATCTTC
1 ATCATCATCTTC
4282 TGCGACCGAT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
12 59 0.83
13 1 0.01
14 1 0.01
15 10 0.14
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.36
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:4260 original size:42 final size:42
Alignment explanation
Indices: 4196--4278 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
4186 ATCATCTTCA
*
4196 TCATCATCATCATCGTCATCATCTTCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
* *
4238 TCATCATCATCATCATCGTCATCTTCATCGTCAGCTTCATC
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATC
4279 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
Found at i:4277 original size:18 final size:18
Alignment explanation
Indices: 4214--4281 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
4204 ATCATCGTCA
*
4214 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* *
4232 TCATCGTCATCATCATCATCAT
1 TCATC-T--TCATCGTCAGC-T
4254 CGTCATCTTCATCGTCAGCT
1 --TCATCTTCATCGTCAGCT
4274 TCATCTTC
1 TCATCTTC
4282 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:4281 original size:6 final size:6
Alignment explanation
Indices: 4187--4281 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
4177 TTTTGGATCA
* * * * * *
4187 TCATCT TCATCA TCATCA TCATCGT CATCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATC-T --TCATCT TCATCT TCATCT TCATCT
* * * * *
4238 TCATCA TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
4282 TGCGACCGAT
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
6 64 0.91
8 1 0.01
9 5 0.07
ACGTcount: A:0.21, C:0.35, G:0.07, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:6448 original size:196 final size:198
Alignment explanation
Indices: 5725--7117 Score: 2408
Period size: 196 Copynumber: 7.1 Consensus size: 198
5715 ATTAAATTAG
5725 TATCGACACAAA-TAT-TTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5788 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5853 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTA-TGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
5918 AAAA
195 AAAA
*
5922 TATCGA-ACAAACTATATTAGTGTCG--ACATTATTTAGACATATTCTCTCAT-AAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5983 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
6047 CGACACGTTTTATATATGGATTGACACTTTA-GGTGCACCTTGTTTTTAATTCATTCTGGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
6110 AAA
196 AAA
6113 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
6176 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
6241 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCTTG-TTTTAATTCATTCTGGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
6305 AAA
196 AAA
6308 TATCGACACAAACTATATTA-TGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
6372 ATTGTACCGTTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
6437 CGACACTTTTTATATATGGATCGACACTTTATTGTGCACCTTGTTTTTAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
6502 AAA
196 AAA
*
6505 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTA-TCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
6569 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGAGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
6634 CGACACTTTTT-TATATGGATCGACACTTTATGAGTGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATG-GTGCACCTTGTTTTTAATTCATTCTGGGAAA
6697 AAAA
195 AAAA
*
6701 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
6765 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTTGGGTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTTGGGTTCGATGATTTTGGGA
* *
6830 TCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTA-TGGTGCACCTTGTTTTTAATTCATTCTGGGAA
6895 AAAAA
194 AAAAA
*
6900 TATCG-CACAAACTATATTAGTGTCGACACATTA-TTAGACTTA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
6961 ATTGTACC-GTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
7024 CGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTG-TTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTA-TGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
7085 AAAA
195 AAAA
*
7089 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
7118 TGACCCTTAA
Statistics
Matches: 1153, Mismatches: 23, Indels: 47
0.94 0.02 0.04
Matches are distributed among these distances:
189 13 0.01
190 36 0.03
191 44 0.04
192 52 0.05
193 52 0.05
194 251 0.22
195 84 0.07
196 283 0.25
197 221 0.19
198 102 0.09
199 15 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
AAA
Found at i:9054 original size:33 final size:33
Alignment explanation
Indices: 9017--9082 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
9007 CATCTTAATA
*
9017 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
9050 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
9083 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:11212 original size:24 final size:24
Alignment explanation
Indices: 11175--11227 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
11165 CCGTTCTATC
11175 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
11199 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
11223 TATTT
1 TATTT
11228 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:11417 original size:20 final size:19
Alignment explanation
Indices: 11371--11417 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
11361 TCCGGTATCA
*
11371 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
11390 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
11411 TTTTACC
1 TTTTACC
11418 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:11565 original size:20 final size:20
Alignment explanation
Indices: 11539--11584 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
11529 CACTTTTAAA
11539 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
11558 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
11579 TTTACC
1 TTTACC
11585 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:12012 original size:223 final size:222
Alignment explanation
Indices: 11648--12089 Score: 748
Period size: 223 Copynumber: 2.0 Consensus size: 222
11638 TTAAAACTGC
11648 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
11713 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATATT
66 TTAATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATATATT
* *
11778 TAGCATTTAAATTTAACAATATTAACCAAATATAATAAT-ATATGTTTTCAACAGTGAAATAAGT
131 TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAATATATTTTC-ACAGTGAAATAAGT
*
11842 ATGGACACTTTTATAAAAATGATATACT
195 ATGGACACTTTTATAAAAAGGATATACT
11870 TTTTGAAAGTTATGTAATTTATGTTTCAAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAA
1 TTTT-AAAGTTATGTAATTTATGTTTC-AATTTATTTAATAGTGTTTCATGTTTTCCACCTACAA
*
11934 TATTAATTTAATAATTTCATTTACACAAAA-ATTATTTGATTGTTTTGATATTTTATAAAATATT
64 TATTAATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATA-T
*
11998 ATTTAG-ATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAAT
128 ATTTAGCA-TTTAAATTTAACAATATTAACCAAAGATAATAAT-AATATATTTTCACAGTGAAAT
12062 AAGTATGGACACTTTTATAAAAAGGATA
191 AAGTATGGACACTTTTATAAAAAGGATA
12090 GATAATTTAC
Statistics
Matches: 208, Mismatches: 6, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
222 36 0.17
223 121 0.58
224 42 0.20
225 9 0.04
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (222 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATATATT
TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAATATATTTTCACAGTGAAATAAGTA
TGGACACTTTTATAAAAAGGATATACT
Found at i:12406 original size:2 final size:2
Alignment explanation
Indices: 12399--12443 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
12389 CTAATGGTTA
12399 AT AT AT AT AT -T 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
12440 AT AT
1 AT AT
12444 TTTGAAGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12699 original size:12 final size:12
Alignment explanation
Indices: 12682--12708 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12672 TTTATGATCA
12682 AAATATTATTTT
1 AAATATTATTTT
12694 AAATATTATTTT
1 AAATATTATTTT
12706 AAA
1 AAA
12709 AAATAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATATTATTTT
Found at i:23172 original size:21 final size:20
Alignment explanation
Indices: 23148--23199 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
23138 TAAATATAAA
*
23148 GGTTTAGAGATCAGGGTTTAG
1 GGTTTAGAG-TCAGGGGTTAG
* *
23169 GGTTTATGTGTTAGGGGTTAG
1 GGTTTA-GAGTCAGGGGTTAG
23190 GGTTTAGAGT
1 GGTTTAGAGT
23200 TTAAAGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 21 0.81
22 2 0.08
ACGTcount: A:0.19, C:0.02, G:0.40, T:0.38
Consensus pattern (20 bp):
GGTTTAGAGTCAGGGGTTAG
Found at i:23209 original size:42 final size:42
Alignment explanation
Indices: 23163--23287 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 42
23153 AGAGATCAGG
* * *
23163 GTTTAGGGTTTATGTGTTAGGGGTTAGGGTTTAGAGTTTAAA
1 GTTTAAGGTTTATGTGTTAGGGTTTAAGGTTTAGAGTTTAAA
* * * * **
23205 GTTTAAGGTTTATGTGATATGATTTAAGGTTTATAGTTTAGG
1 GTTTAAGGTTTATGTGTTAGGGTTTAAGGTTTAGAGTTTAAA
** * *
23247 GTTTAAGGTTTATGAATTAGAGTTTATGGTTTAGAGTTTAA
1 GTTTAAGGTTTATGTGTTAGGGTTTAAGGTTTAGAGTTTAA
23288 GTTATACACA
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.46
Consensus pattern (42 bp):
GTTTAAGGTTTATGTGTTAGGGTTTAAGGTTTAGAGTTTAAA
Found at i:23214 original size:21 final size:21
Alignment explanation
Indices: 23190--23287 Score: 67
Period size: 21 Copynumber: 4.7 Consensus size: 21
23180 TAGGGGTTAG
23190 GGTTTAGAGTTTAAAGTTTAA
1 GGTTTAGAGTTTAAAGTTTAA
* * *
23211 GGTTTA-TG-TGATATGATTTAA
1 GGTTTAGAGTTTA-AAG-TTTAA
* **
23232 GGTTTATAGTTTAGGGTTTAA
1 GGTTTAGAGTTTAAAGTTTAA
* * *
23253 GGTTTATGA-ATTAGAGTTTAT
1 GGTTTA-GAGTTTAAAGTTTAA
23274 GGTTTAGAGTTTAA
1 GGTTTAGAGTTTAA
23288 GTTATACACA
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.03
20 5 0.09
21 46 0.79
22 3 0.05
23 2 0.03
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
GGTTTAGAGTTTAAAGTTTAA
Found at i:23244 original size:14 final size:14
Alignment explanation
Indices: 23227--23288 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
23217 TGTGATATGA
*
23227 TTTAAGGTTTATAG
1 TTTAAGGTTTAGAG
*
23241 TTTAGGGTTTA-AGG
1 TTTAAGGTTTAGA-G
* **
23255 TTTATGAATTAGAG
1 TTTAAGGTTTAGAG
*
23269 TTTATGGTTTAGAG
1 TTTAAGGTTTAGAG
23283 TTTAAG
1 TTTAAG
23289 TTATACACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 1 0.03
14 37 0.95
15 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (14 bp):
TTTAAGGTTTAGAG
Found at i:25707 original size:12 final size:12
Alignment explanation
Indices: 25687--25717 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25677 CGAGTTTGAG
25687 TCGAGCTCAAAA
1 TCGAGCTCAAAA
*
25699 TCTAGCTCAAAA
1 TCGAGCTCAAAA
25711 TCGAGCT
1 TCGAGCT
25718 TCAATCGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (12 bp):
TCGAGCTCAAAA
Found at i:25778 original size:16 final size:16
Alignment explanation
Indices: 25754--25785 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25744 ACTCTTGAAT
*
25754 TTTTTGAGTTTGAGTC
1 TTTTCGAGTTTGAGTC
25770 TTTTCGAGTTTGAGTC
1 TTTTCGAGTTTGAGTC
25786 AAGTTTCAAT
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:0.12, C:0.09, G:0.25, T:0.53
Consensus pattern (16 bp):
TTTTCGAGTTTGAGTC
Found at i:27133 original size:13 final size:13
Alignment explanation
Indices: 27114--27157 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
27104 TTTTCTTTAA
27114 TTATTTAATTATT
1 TTATTTAATTATT
27127 ATT-TTT-ATTATT
1 -TTATTTAATTATT
27139 TTATTTAATTATT
1 TTATTTAATTATT
*
27152 TAATTT
1 TTATTT
27158 TTTTGCAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 2 0.07
12 9 0.33
13 14 0.52
14 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTAATTATT
Found at i:27423 original size:8 final size:8
Alignment explanation
Indices: 27410--27462 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
27400 TTATAACTAC
27410 AAAATAAT
1 AAAATAAT
27418 AAAATAAT
1 AAAATAAT
27426 AAAAT--T
1 AAAATAAT
27432 -AAATAAT
1 AAAATAAT
*
27439 TAAATAAT
1 AAAATAAT
*
27447 TAAATAAT
1 AAAATAAT
27455 AAAATAAT
1 AAAATAAT
27463 TAATACAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
7 1 0.02
8 35 0.85
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAATAAT
Found at i:27435 original size:21 final size:21
Alignment explanation
Indices: 27411--27451 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27401 TATAACTACA
27411 AAATAATAAAATAATAAAATT
1 AAATAATAAAATAATAAAATT
* *
27432 AAATAATTAAATAATTAAAT
1 AAATAATAAAATAATAAAAT
27452 AATAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAATAAAATAATAAAATT
Found at i:29125 original size:72 final size:72
Alignment explanation
Indices: 28994--29166 Score: 211
Period size: 72 Copynumber: 2.4 Consensus size: 72
28984 ATGATAATGA
* * * * * * *
28994 TGGTGATCATGATGATGGGCAAAATCATGGAGGTCATGATTATGACCGTGAGCAAGTTTATGTCC
1 TGGTGATCATGATGGTGGGCACAATCATGGAGGTCAAGACTATGAACATGAGCAAGTTTACGTCC
29059 ACGGTCG
66 ACGGTCG
* ** * *
29066 TGGTGATCATGATGGTGGACACAATCATGGTTGTCAAGACTATGAACATGATCATGTTTACGTCC
1 TGGTGATCATGATGGTGGGCACAATCATGGAGGTCAAGACTATGAACATGAGCAAGTTTACGTCC
* *
29131 ATGGTCT
66 ACGGTCG
*
29138 TGGGGATCATGATGGTGGGCACAATCATG
1 TGGTGATCATGATGGTGGGCACAATCATG
29167 TGGAGCTTGA
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 85 1.00
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (72 bp):
TGGTGATCATGATGGTGGGCACAATCATGGAGGTCAAGACTATGAACATGAGCAAGTTTACGTCC
ACGGTCG
Found at i:51307 original size:128 final size:128
Alignment explanation
Indices: 51075--51335 Score: 425
Period size: 128 Copynumber: 2.0 Consensus size: 128
51065 ATTTCGTTCA
* *
51075 ATTCCAAGAGTCTTGTTTCTCTAGCAAGCTGAGCATCCATGTTTAACTTTTTGATGGCCCAGTAG
1 ATTCCAAGAGTCTTCTTTCTCCAGCAAGCTGAGCATCCATGTTTAACTTTTTGATGGCCCAGTAG
* * * * * *
51140 GCTCTATGTTCTAATTCTACAGGTTAATTACATTCTTTTCCATAGACCAGTTTGAACGGTGAC
66 GCTCTATGTTCTAATTCAACAGGTAAATGACATTATTTTCCATAGAACAGTTTAAACGGTGAC
*
51203 ATTCCAAGAGTCTTCTTTCTCCAGCAAGCTGAGGATCCATGTTTAACTTTTTGATGGCCCAGTAG
1 ATTCCAAGAGTCTTCTTTCTCCAGCAAGCTGAGCATCCATGTTTAACTTTTTGATGGCCCAGTAG
51268 GCTCTATGTTCTAATTCAACAGG-AAGATGACATTATTTTCCATAGAACAGTTTAAACGGTGAC
66 GCTCTATGTTCTAATTCAACAGGTAA-ATGACATTATTTTCCATAGAACAGTTTAAACGGTGAC
51331 ATTCC
1 ATTCC
51336 CAACGGTGTC
Statistics
Matches: 123, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
127 1 0.01
128 122 0.99
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (128 bp):
ATTCCAAGAGTCTTCTTTCTCCAGCAAGCTGAGCATCCATGTTTAACTTTTTGATGGCCCAGTAG
GCTCTATGTTCTAATTCAACAGGTAAATGACATTATTTTCCATAGAACAGTTTAAACGGTGAC
Found at i:60850 original size:44 final size:44
Alignment explanation
Indices: 60802--60901 Score: 173
Period size: 44 Copynumber: 2.2 Consensus size: 44
60792 ATTTTCTTGC
60802 TTTAATAAAATTATTAAATATATATTTTTAAAGTGATCATACCA
1 TTTAATAAAATTATTAAATATATATTTTTAAAGTGATCATACCA
*
60846 TTTAATAAAATTATTAATTATATATTTTTAAAGTGATCATACCA
1 TTTAATAAAATTATTAAATATATATTTTTAAAGTGATCATACCA
*
60890 TTTGGATAAAAT
1 TTT-AATAAAAT
60902 CGATTGAACC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
44 46 0.87
45 7 0.13
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (44 bp):
TTTAATAAAATTATTAAATATATATTTTTAAAGTGATCATACCA
Found at i:61137 original size:10 final size:10
Alignment explanation
Indices: 61122--61279 Score: 155
Period size: 8 Copynumber: 18.1 Consensus size: 10
61112 GCCTTTATGC
61122 TATATATATA
1 TATATATATA
61132 TATATATATA
1 TATATATATA
61142 TATATATATA
1 TATATATATA
61152 TATATATA-A
1 TATATATATA
61161 TATA-ATATA
1 TATATATATA
61170 -ATATA-ATA
1 TATATATATA
61178 TA-ATATA-A
1 TATATATATA
61186 TATA-ATATA
1 TATATATATA
61195 -ATATA-ATA
1 TATATATATA
61203 TA-ATATA-A
1 TATATATATA
61211 TATA-ATATA
1 TATATATATA
61220 -ATATA-ATA
1 TATATATATA
61228 TA-ATATA-A
1 TATATATATA
61236 TATA-ATATA
1 TATATATATA
61245 -ATATA-ATA
1 TATATATATA
61253 TATATATA-A
1 TATATATATA
61262 TATA-ATATA
1 TATATATATA
61271 -ATATA-ATA
1 TATATATATA
61279 T
1 T
61280 TTAGAAGATC
Statistics
Matches: 126, Mismatches: 0, Indels: 45
0.74 0.00 0.26
Matches are distributed among these distances:
8 63 0.50
9 34 0.27
10 29 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATATATA
Found at i:61147 original size:20 final size:20
Alignment explanation
Indices: 61122--61279 Score: 155
Period size: 17 Copynumber: 9.1 Consensus size: 20
61112 GCCTTTATGC
61122 TATATATATATATATATATA
1 TATATATATATATATATATA
61142 TATATATATATATATATA-A
1 TATATATATATATATATATA
61161 TATA-ATATA-ATATA-ATA
1 TATATATATATATATATATA
61178 TA-ATATA-ATATA-ATATA
1 TATATATATATATATATATA
61195 -ATATA-ATATA-ATATA-A
1 TATATATATATATATATATA
61211 TATA-ATATA-ATATA-ATA
1 TATATATATATATATATATA
61228 TA-ATATA-ATATA-ATATA
1 TATATATATATATATATATA
61245 -ATATA-ATATATATATA-A
1 TATATATATATATATATATA
61262 TATA-ATATA-ATATA-ATA
1 TATATATATATATATATATA
61279 T
1 T
61280 TTAGAAGATC
Statistics
Matches: 118, Mismatches: 0, Indels: 43
0.73 0.00 0.27
Matches are distributed among these distances:
16 17 0.14
17 64 0.54
18 14 0.12
19 5 0.04
20 18 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATATATATATATATATA
Found at i:61165 original size:5 final size:5
Alignment explanation
Indices: 61125--61279 Score: 256
Period size: 5 Copynumber: 29.8 Consensus size: 5
61115 TTTATGCTAT
61125 ATATA TATATA TATATA TATATA TATATA TATATA ATATA ATATA ATATA
1 ATATA -ATATA -ATATA -ATATA -ATATA -ATATA ATATA ATATA ATATA
61175 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
61225 ATATA ATATA ATATA ATATA ATATA ATATA TATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATATA ATATA
61276 ATAT
1 ATAT
61280 TTAGAAGATC
Statistics
Matches: 148, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
5 114 0.77
6 34 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:62539 original size:10 final size:10
Alignment explanation
Indices: 62526--62555 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
62516 ACTTTCACTC
62526 TTTTTCTTTA
1 TTTTTCTTTA
62536 TTTTTCTTTA
1 TTTTTCTTTA
62546 TTTTTCTTTA
1 TTTTTCTTTA
62556 AAGTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTA
Found at i:64167 original size:204 final size:204
Alignment explanation
Indices: 63812--64191 Score: 616
Period size: 204 Copynumber: 1.9 Consensus size: 204
63802 GGGAGGATCA
* * * *
63812 ACTTATTGAAAGCACATTCAACTTCATGGGAACAAACTTAGCAATATTGTTCGCTAAGAGGAAAC
1 ACTTATTGAAAGAACATTCAACTTCATAGGAACAAACTTAACAAAATTGTTCGCTAAGAGGAAAC
* *
63877 TGAGATCGAAATCAATTATTATTGAAACAACATAATCAGAGTCGGTCTTTTACTAACATAAACGT
66 TGAGATCGAAATCAATTATTATTGAAACAACATAATCAGAGTCGATCTTTTACGAACATAAACGT
*
63942 TTTTTGATCTACAACATAGTTGTTTATTAGGTCAATTTTCGAAAATCGATATCAAATGTTGCACT
131 TTTTTGATCTACAACATAGTTGTTTATTAGGTCAATTTTCCAAAATCGATATCAAATGTTGCACT
64007 TGGGAATAC
196 TGGGAATAC
* * * *
64016 ACTTATTGAAAGAACATTCGACTTCCTAGGAATACACTTAACAAAATTGTTCGCTAAGAGGAAAC
1 ACTTATTGAAAGAACATTCAACTTCATAGGAACAAACTTAACAAAATTGTTCGCTAAGAGGAAAC
** * *
64081 TGAGATCGTCATCAATTATTATTGAAACAACATAATCAGAGTTGATCTTTTACGAACTTAAACGT
66 TGAGATCGAAATCAATTATTATTGAAACAACATAATCAGAGTCGATCTTTTACGAACATAAACGT
*
64146 TTTTTGATCTACAATATAGTTGTTTATTAGGTCAATTTTCCAAAAT
131 TTTTTGATCTACAACATAGTTGTTTATTAGGTCAATTTTCCAAAAT
64192 TGGTATAAAA
Statistics
Matches: 160, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
204 160 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (204 bp):
ACTTATTGAAAGAACATTCAACTTCATAGGAACAAACTTAACAAAATTGTTCGCTAAGAGGAAAC
TGAGATCGAAATCAATTATTATTGAAACAACATAATCAGAGTCGATCTTTTACGAACATAAACGT
TTTTTGATCTACAACATAGTTGTTTATTAGGTCAATTTTCCAAAATCGATATCAAATGTTGCACT
TGGGAATAC
Found at i:67782 original size:54 final size:54
Alignment explanation
Indices: 67719--67827 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
67709 GAGTAGACGA
67719 TATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTAT
1 TATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTAT
67773 TATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTAT
1 TATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTAT
67827 T
1 T
67828 TGGTTCTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.52
Consensus pattern (54 bp):
TATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTAT
Found at i:75732 original size:35 final size:35
Alignment explanation
Indices: 75693--75823 Score: 172
Period size: 35 Copynumber: 3.7 Consensus size: 35
75683 TGGTTTGGGT
* *
75693 TGTGTTCTTCCGCAGTTCATTATGTTAGTTTTCTA
1 TGTGTTCTTCAGCAGTTCAGTATGTTAGTTTTCTA
* * * *
75728 TGTGTTGTTCCGCAGTTCATTATGTTAGTTTTCTG
1 TGTGTTCTTCAGCAGTTCAGTATGTTAGTTTTCTA
* *
75763 TTTTTTCTTCAGCAGTTCAGTATGTTAGTTTTCTA
1 TGTGTTCTTCAGCAGTTCAGTATGTTAGTTTTCTA
* *
75798 TTTGTTCTTCAGCGGTTCAGTATGTT
1 TGTGTTCTTCAGCAGTTCAGTATGTT
75824 CTGTAAGAGA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 86 1.00
ACGTcount: A:0.14, C:0.15, G:0.19, T:0.52
Consensus pattern (35 bp):
TGTGTTCTTCAGCAGTTCAGTATGTTAGTTTTCTA
Found at i:78363 original size:18 final size:17
Alignment explanation
Indices: 78323--78356 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
78313 TATATTTTTC
78323 TTCATA-TTTTTTCATA
1 TTCATATTTTTTTCATA
78339 TTCATATTTTTTTCATA
1 TTCATATTTTTTTCATA
78356 T
1 T
78357 GTGATATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCATATTTTTTTCATA
Found at i:90890 original size:10 final size:10
Alignment explanation
Indices: 90875--90955 Score: 55
Period size: 10 Copynumber: 8.1 Consensus size: 10
90865 GTGTTTGTGT
90875 TGTTCGTTTA
1 TGTTCGTTTA
90885 TGTTCGTTTA
1 TGTTCGTTTA
90895 T-TGT-GTTTA
1 TGT-TCGTTTA
*
90904 T-TT--ATTA
1 TGTTCGTTTA
*
90911 TGTTCGTTCGTTTG
1 TGTTC----GTTTA
90925 TGTTCGTTTA
1 TGTTCGTTTA
*
90935 CGTTCGTTTA
1 TGTTCGTTTA
90945 TGTTCGTTTA
1 TGTTCGTTTA
90955 T
1 T
90956 CATTTAATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
7 4 0.07
8 3 0.05
9 8 0.14
10 35 0.61
14 7 0.12
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.60
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:90940 original size:20 final size:20
Alignment explanation
Indices: 90915--90954 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
90905 TTATTATGTT
*
90915 CGTTCGTTTGTGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
90935 CGTTCGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
90955 TCATTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.15, G:0.23, T:0.55
Consensus pattern (20 bp):
CGTTCGTTTATGTTCGTTTA
Found at i:91041 original size:16 final size:16
Alignment explanation
Indices: 91020--91052 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
91010 AAAAAAAATT
91020 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
91036 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
91052 T
1 T
91053 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:94535 original size:6 final size:6
Alignment explanation
Indices: 94526--94557 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
94516 GTAGGAATTG
94526 GAATCT GAATCT GAATCT GAATCT GAAATCT G
1 GAATCT GAATCT GAATCT GAATCT G-AATCT G
94558 TTTGGTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (6 bp):
GAATCT
Found at i:96044 original size:32 final size:31
Alignment explanation
Indices: 95998--96059 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
95988 ATATCGGGTT
*
95998 GGGTCAGGTTAATATTGGATCAATTAGATTTC
1 GGGTCAGGTCAATATTGGATCAATT-GATTTC
* *
96030 GGGTCGGGTCAATATTGGATCAGTTGATTT
1 GGGTCAGGTCAATATTGGATCAATTGATTT
96060 TTTGTTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37
Consensus pattern (31 bp):
GGGTCAGGTCAATATTGGATCAATTGATTTC
Found at i:96675 original size:18 final size:19
Alignment explanation
Indices: 96638--96675 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
96628 TCTTAAATTT
* *
96638 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
96657 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
96675 T
1 T
96676 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:97438 original size:14 final size:14
Alignment explanation
Indices: 97419--97448 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
97409 TTTAGATTTT
*
97419 TTAAAATTACATTA
1 TTAAAAATACATTA
97433 TTAAAAATACATTA
1 TTAAAAATACATTA
97447 TT
1 TT
97449 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:97616 original size:14 final size:14
Alignment explanation
Indices: 97599--97625 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
97589 AACCCTAAGG
97599 CCTAAATCCTAAAC
1 CCTAAATCCTAAAC
97613 CCTAAATCCTAAA
1 CCTAAATCCTAAA
97626 TCTAATTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTAAATCCTAAAC
Found at i:97903 original size:15 final size:15
Alignment explanation
Indices: 97883--97914 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
97873 CATAATGTAA
97883 ACGGAGATTTGATGT
1 ACGGAGATTTGATGT
97898 ACGGAGATTTGATGT
1 ACGGAGATTTGATGT
97913 AC
1 AC
97915 AAATACAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.31
Consensus pattern (15 bp):
ACGGAGATTTGATGT
Found at i:102943 original size:39 final size:39
Alignment explanation
Indices: 102879--102970 Score: 139
Period size: 39 Copynumber: 2.3 Consensus size: 39
102869 TAATACAAAA
*
102879 TCGCAACGCGATACTGACTTTCGCAACGCGATACTGACTT
1 TCGCAACGCGAT-TTGACTTTCGCAACGCGATACTGACTT
* *
102919 TCGCAACGCGATTTGACTTTCGCAACTCGATTCTGACTT
1 TCGCAACGCGATTTGACTTTCGCAACGCGATACTGACTT
*
102958 TCGCAACGAGATT
1 TCGCAACGCGATT
102971 CTGAAAATCG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 36 0.75
40 12 0.25
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (39 bp):
TCGCAACGCGATTTGACTTTCGCAACGCGATACTGACTT
Found at i:102970 original size:20 final size:20
Alignment explanation
Indices: 102879--102974 Score: 149
Period size: 20 Copynumber: 4.8 Consensus size: 20
102869 TAATACAAAA
*
102879 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
102899 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
102919 TCGCAACGCGATT-TGACTT
1 TCGCAACGCGATTCTGACTT
*
102938 TCGCAACTCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
102958 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
102975 AAATCGCAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 18 0.25
20 53 0.75
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:103222 original size:20 final size:20
Alignment explanation
Indices: 103197--103272 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 20
103187 TAACGGGGAA
*
103197 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
103217 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
103237 ATCGCAACGCGAAAAT-AGCT
1 ATCGCAACGCGAAAATGA-CT
*
103257 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
103273 CGCAATGCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:103315 original size:33 final size:33
Alignment explanation
Indices: 103278--103348 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
103268 AAAATCGCAA
*
103278 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
103311 TGCGATTTTTATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
103344 TGCGA
1 TGCGA
103349 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:104967 original size:41 final size:42
Alignment explanation
Indices: 104922--105013 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
104912 CCTCTTCAAC
* **
104922 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGAAGGGGACTCTTGAGG
* *
104963 GATGATAGGGGCCTCTTGAACGATTGAAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGAAGGGGACTCTTGAGG
105005 GATGACAGG
1 GATGACAGG
105014 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGAAGGGGACTCTTGAGG
Found at i:104978 original size:21 final size:20
Alignment explanation
Indices: 104949--105009 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
104939 GAACGGTGGG
104949 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGA-A
* **
104970 GGGGCCTCTTGAACGATTGAA
1 GGGGACTCTTGAGGGA-TGAA
104991 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
105010 CAGGTGAGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.23
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGAA
Found at i:105375 original size:20 final size:20
Alignment explanation
Indices: 105350--105402 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
105340 GAATAATAGT
*
105350 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
105370 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
105390 TGACTATCGCAAC
1 TTACTTTCGCAAC
105403 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:105430 original size:20 final size:20
Alignment explanation
Indices: 105356--105423 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
105346 TAGTTTACTT
* * * *
105356 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
105376 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
105396 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
105416 TCGCAACG
1 TCGCAACG
105424 AAAAAATAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:105509 original size:19 final size:19
Alignment explanation
Indices: 105487--105548 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
105477 ACAAATGGCA
105487 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
105506 TTGCGA-TTT--TTT--CG
1 TTGCGATTTTCATTTCGCG
*
105520 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
105539 TTGCGATTTT
1 TTGCGATTTT
105549 GTCGTTGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 8 0.22
15 3 0.08
16 3 0.08
17 3 0.08
18 3 0.08
19 17 0.46
ACGTcount: A:0.11, C:0.18, G:0.19, T:0.52
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:105523 original size:14 final size:14
Alignment explanation
Indices: 105504--105562 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
105494 TTTCATTTCG
105504 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
105518 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
*
105535 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
105551 CGTTGCGATTTT
1 CGTTGCGATTTT
105563 CATTTCACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 18 0.46
15 3 0.08
16 4 0.10
17 5 0.13
18 3 0.08
19 6 0.15
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:105529 original size:33 final size:33
Alignment explanation
Indices: 105487--105578 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
105477 ACAAATGGCA
* *
105487 TTGCGATTTTCATTTCGCGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
105520 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
105553 TTGCGATTTTCATTTCACATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
105579 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:105577 original size:19 final size:18
Alignment explanation
Indices: 105485--105578 Score: 69
Period size: 19 Copynumber: 5.5 Consensus size: 18
105475 ACACAAATGG
105485 CATTGCGATTTTCATTTC
1 CATTGCGATTTTCATTTC
*
105503 GCGTTGCGA-TTT--TTT-
1 -CATTGCGATTTTCATTTC
*
105518 CGTTGCGATTTTCATTTC
1 CATTGCGATTTTCATTTC
*
105536 GCATTGCGA-TTT--TGT-
1 -CATTGCGATTTTCATTTC
*
105551 CGTTGCGATTTTCATTTC
1 CATTGCGATTTTCATTTC
105569 ACATTGCGAT
1 -CATTGCGAT
105579 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 15 0.25
15 6 0.10
16 5 0.08
17 5 0.08
18 6 0.10
19 22 0.37
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (18 bp):
CATTGCGATTTTCATTTC
Found at i:105585 original size:19 final size:20
Alignment explanation
Indices: 105563--105606 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
105553 TTGCGATTTT
105563 CATTT-CACATTGCGATAGC
1 CATTTCCACATTGCGATAGC
* *
105582 CATTTCCGCATTGCGATAGT
1 CATTTCCACATTGCGATAGC
105602 CATTT
1 CATTT
105607 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (20 bp):
CATTTCCACATTGCGATAGC
Found at i:106094 original size:18 final size:18
Alignment explanation
Indices: 106071--106118 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
106061 CGGGTCGATC
106071 AGGTGATGGCTCTGGGTA
1 AGGTGATGGCTCTGGGTA
* *
106089 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTA
106107 AGGTGATGGCTC
1 AGGTGATGGCTC
106119 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTA
Found at i:106988 original size:20 final size:20
Alignment explanation
Indices: 106963--107005 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
106953 AATAGTTTCT
106963 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
* *
106983 GAAAATGACAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
107003 GAA
1 GAA
107006 TTTAACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:107533 original size:20 final size:20
Alignment explanation
Indices: 107505--107597 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
107495 GATTATGTAT
*
107505 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
107525 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
107545 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
107565 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
107585 TATCGCGTTGCGA
1 TATCGCGTTGCGA
107598 TTTTGTATTA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:107611 original size:21 final size:21
Alignment explanation
Indices: 107585--107643 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
107575 CGAAAGTCAG
107585 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
107606 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
*
107627 TATCGCGTTGTGATTTT
1 TATCGCGTTGCGATTTT
107644 CCAAATTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.49
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTGTAT
Found at i:107722 original size:21 final size:22
Alignment explanation
Indices: 107670--107722 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
107660 ATTTACTTAT
*
107670 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGAGAAAA
* **
107691 TCGAAACGCGAAATT-AGAAAA
1 TCGCATTGCGAAATTGAGAAAA
107712 TCGCATTGCGA
1 TCGCATTGCGA
107723 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGAGAAAA
Found at i:107973 original size:37 final size:37
Alignment explanation
Indices: 107932--108030 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
107922 TATTAATATA
*
107932 ATATTAATATATAAATATTAAGTATAAGTATATAATT
1 ATATTAATATATAAATATTAAGTATAAATATATAATT
* *
107969 ATATTAATATATAAATATTAAGGATAAATGTATAATT
1 ATATTAATATATAAATATTAAGTATAAATATATAATT
*
108006 ATATTAATA-A-AAATATATAATTATA
1 ATATTAATATATAAATAT-TAAGTATA
108031 TTGATTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
35 6 0.11
36 7 0.12
37 43 0.77
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (37 bp):
ATATTAATATATAAATATTAAGTATAAATATATAATT
Found at i:108090 original size:18 final size:18
Alignment explanation
Indices: 108053--108118 Score: 78
Period size: 18 Copynumber: 3.5 Consensus size: 18
108043 ACATCATTTA
108053 AATAATTAAATAATAATAAT
1 AATAATT-AA-AATAATAAT
*
108073 AATAATTAAAATATTAAT
1 AATAATTAAAATAATAAT
* *
108091 AATAATTAAAGTAAAAAT
1 AATAATTAAAATAATAAT
108109 AAATAATTAA
1 -AATAATTAA
108119 GTAGAGTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
18 23 0.56
19 11 0.27
20 7 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAATTAAAATAATAAT
Found at i:108120 original size:18 final size:18
Alignment explanation
Indices: 108051--108121 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 18
108041 CAACATCATT
* *
108051 TAAATAATTAAATAATAA
1 TAAATAATTAAGTAAAAA
*
108069 T-AATAA-TAATTAAAATA
1 TAAATAATTAAGTAAAA-A
108086 TTAATAATAATTAAAGTAAAAA
1 -T-A-AATAATT-AAGTAAAAA
108108 TAAATAATTAAGTA
1 TAAATAATTAAGTA
108122 GAGTATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
16 7 0.16
17 6 0.14
18 7 0.16
19 7 0.16
20 1 0.02
21 6 0.14
22 2 0.05
23 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TAAATAATTAAGTAAAAA
Found at i:108923 original size:48 final size:48
Alignment explanation
Indices: 108855--109184 Score: 321
Period size: 48 Copynumber: 7.1 Consensus size: 48
108845 GTGCTGGTGC
* * * *
108855 TGGTGCAGGAGTCGGAGGCTTATATGGTATG-GTAGGAGG-CTTGACTGG
1 TGGTGCAGGAGACGGTGGCTTATATGGT-GGAGTTGG-GGCCTTGACTGG
*
108903 TGGTGCAGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTTGACTGG
1 TGGTGCAGGAGACGGTGGCTTATATGGTGGAGTTGGGGCCTTGACTGG
*
108951 TGGTGCAGGATACGGTGG------T--T----TTGGGGCCTTGACTGG
1 TGGTGCAGGAGACGGTGGCTTATATGGTGGAGTTGGGGCCTTGACTGG
* *
108987 TGGTGCAGGAGACGGTGGCTTATACGGTGGTGTTGGGGCCTTGACTGG
1 TGGTGCAGGAGACGGTGGCTTATATGGTGGAGTTGGGGCCTTGACTGG
* * **
109035 TGGTGCTGGAGACGGGGGCTTATATGGTGGAGTTGGGGCCTTGGTTGG
1 TGGTGCAGGAGACGGTGGCTTATATGGTGGAGTTGGGGCCTTGACTGG
* * * * * * *
109083 -GTGTACTGGAGATGGTGGCTTATATGGTGGTGTAGGGGGCTTGACTGC
1 TG-GTGCAGGAGACGGTGGCTTATATGGTGGAGTTGGGGCCTTGACTGG
* * * *
109131 TGGTACTGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTTGCCTGG
1 TGGTGCAGGAGACGGTGGCTTATATGGTGGAGTTGGGGCCTTGACTGG
109179 TGGTGC
1 TGGTGC
109185 TGGGGTTGGA
Statistics
Matches: 234, Mismatches: 32, Indels: 32
0.79 0.11 0.11
Matches are distributed among these distances:
36 33 0.14
40 1 0.00
44 1 0.00
47 4 0.02
48 194 0.83
49 1 0.00
ACGTcount: A:0.13, C:0.13, G:0.45, T:0.28
Consensus pattern (48 bp):
TGGTGCAGGAGACGGTGGCTTATATGGTGGAGTTGGGGCCTTGACTGG
Found at i:108964 original size:36 final size:36
Alignment explanation
Indices: 108924--109004 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
108914 ACGGTGGCTT
108924 ATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAGG
1 ATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAGG
**
108960 ATACGGTGGTTTTGGGGCCTTGACTGGTGGTGCAGG
1 ATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAGG
*
108996 AGACGGTGG
1 ATACGGTGG
109005 CTTATACGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.14, C:0.14, G:0.47, T:0.26
Consensus pattern (36 bp):
ATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAGG
Found at i:109035 original size:84 final size:84
Alignment explanation
Indices: 108894--109049 Score: 285
Period size: 84 Copynumber: 1.9 Consensus size: 84
108884 TGGTAGGAGG
108894 CTTGACTGGTGGTGCAGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAG
1 CTTGACTGGTGGTGCAGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAG
*
108959 GATACGGTGGTTTTGGGGC
66 GAGACGGTGGTTTTGGGGC
* *
108978 CTTGACTGGTGGTGCAGGAGACGGTGGCTTATACGGTGGTGTTGGGGCCTTGACTGGTGGTGCTG
1 CTTGACTGGTGGTGCAGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAG
109043 GAGACGG
66 GAGACGG
109050 GGGCTTATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.13, C:0.15, G:0.46, T:0.27
Consensus pattern (84 bp):
CTTGACTGGTGGTGCAGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAG
GAGACGGTGGTTTTGGGGC
Found at i:109100 original size:132 final size:137
Alignment explanation
Indices: 108852--109187 Score: 346
Period size: 132 Copynumber: 2.4 Consensus size: 137
108842 GGGGTGCTGG
* * * * * *
108852 TGCTGGTGCAGGAGTCGGAGGCTTATATGGT-ATGGTAGGAGG-CTTGACTGGTGGTGCAGGAGA
1 TGCTGGTGCAGGAGACGGTGGCTTATACGGTGGT-GTTGG-GGCCTTGACTGGTGGTGCTGGAGA
* * *
108915 CGGTGGCTTATACGGTGGAGTTGGGGCCTTGACTGGTGGTGCAGGATACGGTGG-T-T-T-T-GG
64 CGGGGGCTTATACGGTGGAGTTGGGGCCTTGACTGGTGGTACAGGAGACGGTGGTTGTGTGTAGG
108975 GGCCTTGAC
129 GGCCTTGAC
*
108984 TGGTGGTGCAGGAGACGGTGGCTTATACGGTGGTGTTGGGGCCTTGACTGGTGGTGCTGGAGACG
1 TGCTGGTGCAGGAGACGGTGGCTTATACGGTGGTGTTGGGGCCTTGACTGGTGGTGCTGGAGACG
* ** * *
109049 GGGGCTTATATGGTGGAGTTGGGGCCTTGGTTGG-GTGTACTGGAGATGGTGGCTTATATGGTGG
66 GGGGCTTATACGGTGGAGTTGGGGCCTTGACTGGTG-GTACAGGAGACGGTGG----T-T-GT-G
*
109113 TGTAGGGGGCTTGAC
123 TGTAGGGGCCTTGAC
* * * *
109128 TGCTGGTACTGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTTGCCTGGTGGTGCTGG
1 TGCTGGTGCAGGAGACGGTGGCTTATACGGTGGTGTTGGGGCCTTGACTGGTGGTGCTGG
109188 GGTTGGAAGT
Statistics
Matches: 168, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
131 3 0.02
132 95 0.57
133 1 0.01
138 1 0.01
140 1 0.01
142 1 0.01
143 1 0.01
144 65 0.39
ACGTcount: A:0.13, C:0.13, G:0.46, T:0.28
Consensus pattern (137 bp):
TGCTGGTGCAGGAGACGGTGGCTTATACGGTGGTGTTGGGGCCTTGACTGGTGGTGCTGGAGACG
GGGGCTTATACGGTGGAGTTGGGGCCTTGACTGGTGGTACAGGAGACGGTGGTTGTGTGTAGGGG
CCTTGAC
Found at i:109202 original size:144 final size:144
Alignment explanation
Indices: 108964--109226 Score: 355
Period size: 144 Copynumber: 1.8 Consensus size: 144
108954 TGCAGGATAC
* * * * *
108964 GGTGGTTTTGGGGCCTTGACTGGTGGTGCAGGAGACGGTGGCTTATACGGTGGTGTTGGGGCCTT
1 GGTGGTGTAGGGGCCTTGACTGCTGGTACAGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTT
** * * * *
109029 GACTGGTGGTGCTGGAGACGGGGGCTTATATGGTGGAGTTGGGGCCTTGGTTGGGTGTACTGGAG
66 GACTGGTGGTGCTGGAGACGGAAGCTTATACGGGGGAGTAGGGGACTTGGTTGGGTGTACTGGAG
109094 ATGGTGGCTTATAT
131 ATGGTGGCTTATAT
* *
109108 GGTGGTGTAGGGGGCTTGACTGCTGGTACTGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTT
1 GGTGGTGTAGGGGCCTTGACTGCTGGTACAGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTT
* * ** * *
109173 GCCTGGTGGTGCTGGGGTTGGAAGTTTATACGGGGGAGTAGGGGACTTTGTTGG
66 GACTGGTGGTGCTGGAGACGGAAGCTTATACGGGGGAGTAGGGGACTTGGTTGG
109227 TGGTGCTACA
Statistics
Matches: 100, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
144 100 1.00
ACGTcount: A:0.12, C:0.12, G:0.46, T:0.30
Consensus pattern (144 bp):
GGTGGTGTAGGGGCCTTGACTGCTGGTACAGGAGACGGTGGCTTATACGGTGGAGTTGGGGCCTT
GACTGGTGGTGCTGGAGACGGAAGCTTATACGGGGGAGTAGGGGACTTGGTTGGGTGTACTGGAG
ATGGTGGCTTATAT
Found at i:111921 original size:17 final size:17
Alignment explanation
Indices: 111901--111938 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
111891 GAAAGTCAAC
*
111901 GGTCAACGGTTGGATCG
1 GGTCAACGGTCGGATCG
*
111918 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGATCG
111935 GGTC
1 GGTC
111939 GGGTCAACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.45, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGATCG
Found at i:111943 original size:22 final size:22
Alignment explanation
Indices: 111915--111960 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
111905 AACGGTTGGA
111915 TCGGGTCAACGGTCGGGTCGGG
1 TCGGGTCAACGGTCGGGTCGGG
111937 TCGGGTCAACGGTCGGGTCGGG
1 TCGGGTCAACGGTCGGGTCGGG
111959 TC
1 TC
111961 AGACCGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.09, C:0.24, G:0.48, T:0.20
Consensus pattern (22 bp):
TCGGGTCAACGGTCGGGTCGGG
Found at i:112004 original size:19 final size:19
Alignment explanation
Indices: 111963--112056 Score: 61
Period size: 19 Copynumber: 4.8 Consensus size: 19
111953 GTCGGGTCAG
111963 ACCGGTCAAACC-AGTTC-A
1 ACCGGTCAAACCGA-TTCGA
111981 GACCGGTCAAACCGATTCGA
1 -ACCGGTCAAACCGATTCGA
* * *
112001 ACCGGTTGAAACCG-GTCAA
1 ACCGG-TCAAACCGATTCGA
*
112020 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGATTCG--A
*
112041 ACCGGTTAAACCGATT
1 ACCGGTCAAACCGATT
112057 TCCAGCAGCC
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
18 2 0.03
19 33 0.55
20 17 0.28
21 8 0.13
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGATTCGA
Found at i:112013 original size:10 final size:10
Alignment explanation
Indices: 111963--112053 Score: 75
Period size: 9 Copynumber: 9.4 Consensus size: 10
111953 GTCGGGTCAG
111963 ACCGG-TCAA
1 ACCGGTTCAA
* *
111972 ACCAGTTCAG
1 ACCGGTTCAA
111982 ACCGG-TCAA
1 ACCGGTTCAA
* *
111991 ACCGATTCGA
1 ACCGGTTCAA
*
112001 ACCGGTTGAA
1 ACCGGTTCAA
112011 ACCGG-TCAA
1 ACCGGTTCAA
112020 ACCGG-TCAGA
1 ACCGGTTCA-A
*
112030 ACCGGTTGAAA
1 ACCGGTT-CAA
112041 ACCGGTT-AA
1 ACCGGTTCAA
112050 ACCG
1 ACCG
112054 ATTTCCAGCA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
9 28 0.42
10 28 0.42
11 9 0.14
12 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:112015 original size:29 final size:31
Alignment explanation
Indices: 111982--112056 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
111972 ACCAGTTCAG
111982 ACCGGTCAAACCGATTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGATTCAGAACCGGTTGAAA
*
112011 ACCGGTCAAACCG-GTCAGAACCGGTTGAAA
1 ACCGGTCAAACCGATTCAGAACCGGTTGAAA
*
112041 ACCGGTTAAACCGATT
1 ACCGGTCAAACCGATT
112057 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
30 14 0.35
31 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGATTCAGAACCGGTTGAAA
Found at i:119248 original size:17 final size:17
Alignment explanation
Indices: 119228--119264 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
119218 AAGTCAACGA
119228 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
*
119245 TCAACGGTCTGGTCGGG
1 TCAACGGTCGGGTCGGG
119262 TCA
1 TCA
119265 GACCGGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.41, T:0.22
Consensus pattern (17 bp):
TCAACGGTCGGGTCGGG
Found at i:119278 original size:9 final size:9
Alignment explanation
Indices: 119260--119358 Score: 56
Period size: 9 Copynumber: 10.3 Consensus size: 9
119250 GGTCTGGTCG
*
119260 GGTCAGACC
1 GGTCAAACC
119269 GGTCAAACC
1 GGTCAAACC
*
119278 GGTTCAGACC
1 GG-TCAAACC
119288 GGTCAAACC
1 GGTCAAACC
**
119297 AATTCGAAA-C
1 -GGTC-AAACC
*
119307 GGTTGAAACC
1 GG-TCAAACC
119317 GGTCAAACC
1 GGTCAAACC
119326 GGTCAGAACC
1 GGTCA-AACC
* *
119336 AGTTGAAAACC
1 -GGT-CAAACC
*
119347 GGTTAAACC
1 GGTCAAACC
119356 GGT
1 GGT
119359 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
9 38 0.55
10 21 0.30
11 9 0.13
12 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:119316 original size:39 final size:40
Alignment explanation
Indices: 119266--119359 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 40
119256 GTCGGGTCAG
* *
119266 ACCGGTCAAACCGGTTCAGACCGGTCA-AACCAATTCG-AA
1 ACCGGTTAAACCGGTTCAAACCGGTCAGAACCAATT-GAAA
*
119305 A-CGGTTGAAACCGG-TCAAACCGGTCAGAACCAGTTGAAA
1 ACCGGTT-AAACCGGTTCAAACCGGTCAGAACCAATTGAAA
119344 ACCGGTTAAACCGGTT
1 ACCGGTTAAACCGGTT
119360 TCCAGCAGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
38 16 0.34
39 25 0.53
40 6 0.13
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (40 bp):
ACCGGTTAAACCGGTTCAAACCGGTCAGAACCAATTGAAA
Found at i:119335 original size:19 final size:19
Alignment explanation
Indices: 119260--119358 Score: 53
Period size: 19 Copynumber: 5.2 Consensus size: 19
119250 GGTCTGGTCG
119260 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
119278 GGTTCAG-ACCGGTCAAACC
1 GG-TCAGAACCGGTCAAACC
** * *
119297 AATTC-GAAACGGTTGAAACC
1 -GGTCAGAACCGG-TCAAACC
119317 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * * *
119336 AGTTGAAAACCGGTTAAACC
1 -GGTCAGAACCGGTCAAACC
119356 GGT
1 GGT
119359 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
18 5 0.08
19 35 0.57
20 13 0.21
21 8 0.13
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:125270 original size:6 final size:6
Alignment explanation
Indices: 125259--125303 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
125249 CCTCAAACAC
125259 TCACCT TCACCT TCACCT TCACCT TCACCT TCACCT TCACCT TCA
1 TCACCT TCACCT TCACCT TCACCT TCACCT TCACCT TCACCT TCA
125304 TTCCTATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.18, C:0.49, G:0.00, T:0.33
Consensus pattern (6 bp):
TCACCT
Found at i:125692 original size:12 final size:12
Alignment explanation
Indices: 125675--125723 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
125665 TTCAAAAAAG
125675 TTTTATATTTAA
1 TTTTATATTTAA
*
125687 TTTTATATTAAA
1 TTTTATATTTAA
*
125699 TTTGAT-TTTAA
1 TTTTATATTTAA
125710 TTTTA-ATATTAA
1 TTTTATAT-TTAA
125722 TT
1 TT
125724 GTTTAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:125795 original size:66 final size:68
Alignment explanation
Indices: 125682--125845 Score: 236
Period size: 66 Copynumber: 2.5 Consensus size: 68
125672 AAGTTTTATA
* * *
125682 TTTAATTTTATATTAAATT-T-GATTTTAATTTTAATATTAATTGTTTAAATAAATTAAATATTA
1 TTTAATATTATATTATATTATAGATATTAATTTTAATATTAATTGTTTAAATAAATTAAATATTA
125745 ATT
66 ATT
125748 TTTAATATTATATTATATTATAGATATTAATTTTAATATTAA-T-TTTAAATAAATTAAATATTA
1 TTTAATATTATATTATATTATAGATATTAATTTTAATATTAATTGTTTAAATAAATTAAATATTA
125811 ATT
66 ATT
125814 TTT--TA--ATATTATATTATAGATATTTAATTTTA
1 TTTAATATTATATTATATTATAGATA-TTAATTTTA
125846 TATCATATTA
Statistics
Matches: 92, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
62 17 0.18
63 9 0.10
64 2 0.02
66 43 0.47
67 2 0.02
68 19 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (68 bp):
TTTAATATTATATTATATTATAGATATTAATTTTAATATTAATTGTTTAAATAAATTAAATATTA
ATT
Found at i:125809 original size:22 final size:22
Alignment explanation
Indices: 125714--125815 Score: 86
Period size: 22 Copynumber: 4.5 Consensus size: 22
125704 TTTTAATTTT
125714 AATATTAATTGTTTAAATAAATTA
1 AATATTAA-T-TTTAAATAAATTA
*
125738 AATATTAATTTTTAAT--ATT-
1 AATATTAATTTTAAATAAATTA
* * *
125757 -ATATTATATTATAGATATTAATTTT
1 AATATTA-ATTTTA-A-A-TAAATTA
125782 AATATTAATTTTAAATAAATTA
1 AATATTAATTTTAAATAAATTA
125804 AATATTAATTTT
1 AATATTAATTTT
125816 TTAATATTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
18 6 0.10
19 4 0.06
20 4 0.06
21 1 0.02
22 24 0.38
23 2 0.03
24 11 0.17
25 5 0.08
26 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATATTAATTTTAAATAAATTA
Found at i:125856 original size:16 final size:16
Alignment explanation
Indices: 125805--125871 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
125795 AATAAATTAA
*
125805 ATATTAATT-TTTTA-
1 ATATTAATTATTATAT
*
125819 ATATT-A-TATTATAG
1 ATATTAATTATTATAT
125833 ATATTTAATT-TTATAT
1 ATA-TTAATTATTATAT
*
125849 CATATTAATTATTTTAT
1 -ATATTAATTATTATAT
125866 ATATTA
1 ATATTA
125872 TTAAAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 1 0.02
13 5 0.12
14 8 0.19
15 2 0.05
16 18 0.42
17 9 0.21
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
ATATTAATTATTATAT
Found at i:125864 original size:19 final size:18
Alignment explanation
Indices: 125840--125901 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
125830 TAGATATTTA
125840 ATTTTATATCATATTAATT
1 ATTTTATAT-ATATTAATT
*
125859 ATTTTATATATTATTAA-A
1 ATTTTATATA-TATTAATT
*
125877 ATTTTATATTTATTTTAATT
1 ATTTTATA--TATATTAATT
125897 ATTTT
1 ATTTT
125902 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 9 0.25
19 20 0.56
20 7 0.19
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTATATATATTAATT
Found at i:125906 original size:19 final size:19
Alignment explanation
Indices: 125851--125907 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
125841 TTTTATATCA
*
125851 TATTAATTATTTTATATAT
1 TATTAATTATTTTATTTAT
*
125870 TATTAAAATT-TTATATTTAT
1 TATT--AATTATTTTATTTAT
125890 T-TTAATTATTTTGATTTA
1 TATTAATTATTTT-ATTTA
125908 AGTTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 4 0.13
18 3 0.10
19 11 0.35
20 9 0.29
21 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTAATTATTTTATTTAT
Found at i:126425 original size:31 final size:31
Alignment explanation
Indices: 126367--126426 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
126357 TAGTTGTATG
* **
126367 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTACAAAACTAA
126398 AATTATTTAAATCTCAGTATTACAAAACT
1 AATTATTTAAATCTCAGTATTACAAAACT
126427 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTACAAAACTAA
Found at i:129005 original size:43 final size:42
Alignment explanation
Indices: 128955--129113 Score: 146
Period size: 42 Copynumber: 3.8 Consensus size: 42
128945 AAATAAAAAG
*
128955 CACCGCAATAGGTTCAAACATTTAGTGGCATTTTTTTAACAAA
1 CACCGCAATAAGTTCAAACATTTAGTGGCATTTTTTT-ACAAA
* * *
128998 CACCGCAATAAATTCAAACATTTAGTGGC-TTTTTCTTATAAG
1 CACCGCAATAAGTTCAAACATTTAGTGGCATTTTT-TTACAAA
* * * * *
129040 CGCCGCAATAATTTCAGACATTTAGCGACA-TTTTTTACAAA
1 CACCGCAATAAGTTCAAACATTTAGTGGCATTTTTTTACAAA
* * *
129081 CGCCGCAA-AAGGTT-ACGACATTTAGTAGCATTT
1 CACCGCAATAA-GTTCA-AACATTTAGTGGCATTT
129114 AGAATAAAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
40 3 0.03
41 26 0.27
42 38 0.40
43 29 0.30
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (42 bp):
CACCGCAATAAGTTCAAACATTTAGTGGCATTTTTTTACAAA
Found at i:129047 original size:42 final size:43
Alignment explanation
Indices: 128952--129075 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
128942 TGTAAATAAA
**
128952 AAGCACCGCAATAGGTTCAAACATTTAGTGGCATTTTTTTAAC
1 AAGCACCGCAATAAATTCAAACATTTAGTGGCATTTTTTTAAC
* *
128995 AAACACCGCAATAAATTCAAACATTTAGTGGC-TTTTTCTT-AT
1 AAGCACCGCAATAAATTCAAACATTTAGTGGCATTTTT-TTAAC
* * * * *
129037 AAGCGCCGCAATAATTTCAGACATTTAGCGACATTTTTT
1 AAGCACCGCAATAAATTCAAACATTTAGTGGCATTTTTT
129076 ACAAACGCCG
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 33 0.48
43 36 0.52
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (43 bp):
AAGCACCGCAATAAATTCAAACATTTAGTGGCATTTTTTTAAC
Found at i:129338 original size:25 final size:24
Alignment explanation
Indices: 129295--129343 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
129285 CAAGCACACA
*
129295 GTTCAACATTAAGTGAAATGTAAT
1 GTTCAACATTAAGTAAAATGTAAT
*
129319 GTTCAATATTCAAGTAAAATGTAAT
1 GTTCAACATT-AAGTAAAATGTAAT
129344 AACAACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (24 bp):
GTTCAACATTAAGTAAAATGTAAT
Found at i:131423 original size:19 final size:20
Alignment explanation
Indices: 131391--131428 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
131381 GTGTTGTAAC
*
131391 ACACAAATCTATGCAAGTAT
1 ACACAAATCGATGCAAGTAT
131411 ACAC-AATCGATGCAAGTA
1 ACACAAATCGATGCAAGTA
131429 ATATAGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (20 bp):
ACACAAATCGATGCAAGTAT
Found at i:133467 original size:16 final size:14
Alignment explanation
Indices: 133443--133477 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
133433 ACACTTAAAC
133443 TTTTTAATTTTTCAA
1 TTTTTAATTTTTC-A
133458 TTTTTCAATTTTTCA
1 TTTTT-AATTTTTCA
133473 TTTTT
1 TTTTT
133478 TAGCACTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTAATTTTTCA
Found at i:133478 original size:8 final size:8
Alignment explanation
Indices: 133443--133477 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
133433 ACACTTAAAC
133443 TTTTT-AA
1 TTTTTCAA
133450 TTTTTCAA
1 TTTTTCAA
133458 TTTTTCAA
1 TTTTTCAA
133466 TTTTTC-A
1 TTTTTCAA
133473 TTTTT
1 TTTTT
133478 TAGCACTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 11 0.41
8 16 0.59
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTCAA
Found at i:135472 original size:17 final size:17
Alignment explanation
Indices: 135452--135500 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
135442 CAACAGGTTT
*
135452 CAGATTCCAATTCCTGA
1 CAGATTCCAATTCCTCA
* *
135469 CAGATTCTAATTCATTCA
1 CAGATTCCAATTC-CTCA
*
135487 CAGTTTCCAATTCC
1 CAGATTCCAATTCC
135501 CTCAGAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (17 bp):
CAGATTCCAATTCCTCA
Found at i:144029 original size:32 final size:32
Alignment explanation
Indices: 143988--144059 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
143978 GTGATTTTAG
*
143988 GGAGAGAAGTAAGAGAGGCCTGGAGATAATAA
1 GGAGAGAAGTAAGAGAGGCATGGAGATAATAA
*
144020 GGAGAGAAGTAAGAGAGTCATGGAGATAATAA
1 GGAGAGAAGTAAGAGAGGCATGGAGATAATAA
144052 -GAGAGAAG
1 GGAGAGAAG
144060 AGAAAAAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 8 0.21
32 30 0.79
ACGTcount: A:0.46, C:0.04, G:0.38, T:0.12
Consensus pattern (32 bp):
GGAGAGAAGTAAGAGAGGCATGGAGATAATAA
Found at i:144927 original size:34 final size:31
Alignment explanation
Indices: 144873--144948 Score: 80
Period size: 34 Copynumber: 2.4 Consensus size: 31
144863 TTTTTAGTAA
* * *
144873 TTTTATATTTAATGTATTAAATATCTTAATAAT
1 TTTTATATTTTATATATTAAAT-T-TCAATAAT
*
144906 TGTTTATATTTTATATTTTAAATTTCAATAAT
1 T-TTTATATTTTATATATTAAATTTCAATAAT
*
144938 TTTTTTATTTT
1 TTTTATATTTT
144949 TCAAAAAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 9 0.24
32 8 0.22
33 2 0.05
34 18 0.49
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (31 bp):
TTTTATATTTTATATATTAAATTTCAATAAT
Found at i:156184 original size:30 final size:29
Alignment explanation
Indices: 156150--156215 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
156140 TTTGTTTTTT
**
156150 TAAAAATA-AAAATATTTTAAATTTTAAATA
1 TAAAAATATAAAATA--TTAAAAATTAAATA
156180 T-AAAATATAAAATATTAAAAATTAAATA
1 TAAAAATATAAAATATTAAAAATTAAATA
156208 TAAAAATA
1 TAAAAATA
156216 CAATTAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 13 0.41
29 12 0.38
30 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
TAAAAATATAAAATATTAAAAATTAAATA
Found at i:156185 original size:7 final size:7
Alignment explanation
Indices: 156175--156212 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
156165 TTTAAATTTT
156175 AAATATA
1 AAATATA
156182 AAATATA
1 AAATATA
156189 AAATATTA
1 AAATA-TA
*
156197 AAA-ATT
1 AAATATA
156203 AAATATA
1 AAATATA
156210 AAA
1 AAA
156213 ATACAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.15
7 18 0.67
8 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATATA
Found at i:156197 original size:21 final size:21
Alignment explanation
Indices: 156149--156212 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
156139 ATTTGTTTTT
* *
156149 TTAAAAATAAAAATATTTTAAATT
1 TTAAAAAT-AAAATA--TAAAATA
*
156173 TTAAATATAAAATATAAAATA
1 TTAAAAATAAAATATAAAATA
*
156194 TTAAAAATTAAATATAAAA
1 TTAAAAATAAAATATAAAA
156213 ATACAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 22 0.63
23 6 0.17
24 7 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAAAATAAAATATAAAATA
Found at i:157104 original size:28 final size:27
Alignment explanation
Indices: 157056--157131 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
157046 AATCTTTTTA
* *
157056 TTTAAAAAATCAAATAAGCCCTTAAAC
1 TTTAAAAAATCAATTTAGCCCTTAAAC
* *
157083 TTTTAAAAAATCAATTTGGCCCTTGAAC
1 -TTTAAAAAATCAATTTAGCCCTTAAAC
*
157111 TTGAAAAGAATCAATTTAGCC
1 TTTAAAA-AATCAATTTAGCC
157132 TATTTGCCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 6 0.15
28 35 0.85
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (27 bp):
TTTAAAAAATCAATTTAGCCCTTAAAC
Found at i:157525 original size:31 final size:31
Alignment explanation
Indices: 157483--157555 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
157473 TAAAATAAAC
157483 TTTGGTCACTTATGTTATTGTTTCATTAAGT
1 TTTGGTCACTTATGTTATTGTTTCATTAAGT
* *
157514 TTTTGTCACTTATGTTATTGTTTTATTAAGT
1 TTTGGTCACTTATGTTATTGTTTCATTAAGT
157545 TTTGGTCACTT
1 TTTGGTCACTT
157556 GGACGTTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.58
Consensus pattern (31 bp):
TTTGGTCACTTATGTTATTGTTTCATTAAGT
Found at i:162952 original size:21 final size:21
Alignment explanation
Indices: 162926--162965 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
162916 ATTTTACACT
162926 GAGTGTACCGATACACCTAGA
1 GAGTGTACCGATACACCTAGA
*
162947 GAGTGTGCCGATACACCTA
1 GAGTGTACCGATACACCTA
162966 CTCTCCTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (21 bp):
GAGTGTACCGATACACCTAGA
Found at i:168677 original size:21 final size:21
Alignment explanation
Indices: 168653--168708 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
168643 ATCCTCGCTA
168653 TGTATCGATACACTATGAATG
1 TGTATCGATACACTATGAATG
168674 TGTATCGATACACTATGAATG
1 TGTATCGATACACTATGAATG
168695 TGTATCGATACACT
1 TGTATCGATACACT
168709 CAAGAGTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (21 bp):
TGTATCGATACACTATGAATG
Found at i:169229 original size:13 final size:13
Alignment explanation
Indices: 169211--169248 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
169201 ATAATATGAT
169211 TTTTCAAATATTG
1 TTTTCAAATATTG
*
169224 TTTTC-AATATAG
1 TTTTCAAATATTG
*
169236 TTTTCAAAAATTG
1 TTTTCAAATATTG
169249 CCTATTAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (13 bp):
TTTTCAAATATTG
Found at i:169836 original size:15 final size:15
Alignment explanation
Indices: 169816--169844 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
169806 TAACATCTTT
169816 GGTTTAGATAACGAG
1 GGTTTAGATAACGAG
169831 GGTTTAGATAACGA
1 GGTTTAGATAACGA
169845 AAAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.31, T:0.28
Consensus pattern (15 bp):
GGTTTAGATAACGAG
Found at i:170664 original size:2 final size:2
Alignment explanation
Indices: 170657--170681 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
170647 CTTGGATGTT
170657 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 T
170682 GGTTATTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:171506 original size:21 final size:21
Alignment explanation
Indices: 171480--171519 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
171470 ATTTTACACT
171480 GAGTGTACCGATACACCTAGA
1 GAGTGTACCGATACACCTAGA
171501 GAGTGTACCGATACACCTA
1 GAGTGTACCGATACACCTA
171520 CGCTCCTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.20
Consensus pattern (21 bp):
GAGTGTACCGATACACCTAGA
Found at i:174363 original size:23 final size:22
Alignment explanation
Indices: 174329--174371 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
174319 ACATAAATTT
174329 AAATG-AAAAAAATAGATAACTA
1 AAATGAAAAAAAAT-GATAACTA
*
174351 AAATGGAACAAAAATGATAAC
1 AAAT-GAAAAAAAATGATAAC
174372 GAGAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.65, C:0.07, G:0.12, T:0.16
Consensus pattern (22 bp):
AAATGAAAAAAAATGATAACTA
Found at i:175423 original size:18 final size:18
Alignment explanation
Indices: 175397--175431 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
175387 ATTACATATT
*
175397 TTAACTTAAATTTACATA
1 TTAAATTAAATTTACATA
175415 TTAAATTAAATTTACAT
1 TTAAATTAAATTTACAT
175432 CTTCACTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAATTAAATTTACATA
Found at i:175517 original size:59 final size:57
Alignment explanation
Indices: 175445--175700 Score: 181
Period size: 59 Copynumber: 4.2 Consensus size: 57
175435 CACTTTCAAC
* *
175445 AAATAAATTTTATTTTTATC-CTAACTTAAAAATATATTTTATTTTCATCTTTAACTTAA
1 AAATATATTTTATTTTTATCTC-AATTTAAAAATATATTTTATTTT-ATC-TTAACTTAA
* ** * *
175504 AAATATATATTATTCATATTTCAATTTAAATGATATATTTTATTATTATCTTAACTTTTAA
1 AAATATATTTTATTTTTATCTCAATTTAAA-AATATATTTTATT-TTATCTTAAC--TTAA
* * * * * * *
175565 AACTATTTTTTATCTTAATGGGACTCAATTTTAAAAATTATATTTTATTTTTATTTTAATTTTA
1 AAATATATTTTATTTTTAT----CTCAA-TTTAAAAA-TATATTTTA-TTTTATCTTAACTTAA
* * * * *
175629 AAATATATTTTATTTTTATTTTAATTTAAAATTTTATTTTAGTCTTATCTTAACTTAA
1 AAATATATTTTATTTTTATCTCAATTTAAAAATATATTTTA-TTTTATCTTAACTTAA
* *
175687 AAATGTATGTTATT
1 AAATATATTTTATT
175701 CTTAATTTAA
Statistics
Matches: 151, Mismatches: 34, Indels: 25
0.72 0.16 0.12
Matches are distributed among these distances:
58 32 0.21
59 34 0.23
60 19 0.13
61 18 0.12
64 18 0.12
65 5 0.03
66 23 0.15
67 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (57 bp):
AAATATATTTTATTTTTATCTCAATTTAAAAATATATTTTATTTTATCTTAACTTAA
Found at i:175703 original size:29 final size:29
Alignment explanation
Indices: 175445--175713 Score: 173
Period size: 29 Copynumber: 8.9 Consensus size: 29
175435 CACTTTCAAC
* * ** *
175445 AAATAAATTTTATTTTTATCCTAACTTAA
1 AAATATATTTTATTCTTATTTTAATTTAA
*
175474 AAATATATTTTATT-TTCATCTTTAACTTAA
1 AAATATATTTTATTCTT-AT-TTTAATTTAA
* * *
175504 AAATATATATTATTCATATTTCAATTTAA
1 AAATATATTTTATTCTTATTTTAATTTAA
* * *
175533 ATGATATATTTTATTATTATCTTAACTTTTAA
1 A-AATATATTTTATTCTTATTTTAA--TTTAA
* * * *
175565 AACTATTTTTTA-TCTTAATGGGACTCAATTTTAA
1 AAATATATTTTATTCTT-AT----TTTAA-TTTAA
* *
175599 AAATTATATTTTATTTTTATTTTAATTTTA
1 AAA-TATATTTTATTCTTATTTTAATTTAA
*
175629 AAATATATTTTATTTTTATTTTAATTTAA
1 AAATATATTTTATTCTTATTTTAATTTAA
* * * * *
175658 AATTTTATTTTAGTCTTATCTTAACTTAA
1 AAATATATTTTATTCTTATTTTAATTTAA
* * *
175687 AAATGTATGTTATTCTTAATTTAATTT
1 AAATATATTTTATTCTTATTTTAATTT
175714 TTTAGAAAAA
Statistics
Matches: 189, Mismatches: 38, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
28 2 0.01
29 92 0.49
30 50 0.26
31 14 0.07
32 6 0.03
34 8 0.04
35 14 0.07
36 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.55
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAATTTAA
Found at i:176045 original size:44 final size:44
Alignment explanation
Indices: 175995--176082 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
175985 CCAGAATGGT
175995 AGAGAATAAATTATTAAATTTAATCAAAACTAAATAAATTTGGC
1 AGAGAATAAATTATTAAATTTAATCAAAACTAAATAAATTTGGC
*
176039 AGAGAATAAATTATTAAATTTAATCAAAATTAAATAAATTTGGC
1 AGAGAATAAATTATTAAATTTAATCAAAACTAAATAAATTTGGC
176083 CCTCGTACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (44 bp):
AGAGAATAAATTATTAAATTTAATCAAAACTAAATAAATTTGGC
Found at i:178252 original size:21 final size:22
Alignment explanation
Indices: 178218--178259 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
178208 TTGTCATAAT
178218 TTTATTATAAATTTAAAAAATC
1 TTTATTATAAATTTAAAAAATC
*
178240 TTTATTA-AAATTTTAAAAAT
1 TTTATTATAAATTTAAAAAAT
178260 GTGAAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTATTATAAATTTAAAAAATC
Found at i:178342 original size:28 final size:25
Alignment explanation
Indices: 178280--178400 Score: 82
Period size: 28 Copynumber: 4.5 Consensus size: 25
178270 TATAAAAACC
* *
178280 TTTTATTAATTA-AAATTAGGACAAT
1 TTTTATAAATTACAAA-AAGGACAAT
*
178305 TTTTATAAATTAAGAAAAAGGACAATT
1 TTTTATAAATT-ACAAAAAGGACAA-T
* *
178332 TGTTTCTAAATTACAAAAAGGATAAAGT
1 T-TTTATAAATTACAAAAAGGA-CAA-T
* *
178360 TGTTTATAAATAACAATAAAGGGCAAAAT
1 T-TTTATAAATTACAA-AAA-GG-ACAAT
178389 TTTTATAAATTA
1 TTTTATAAATTA
178401 TAACGATTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
25 10 0.13
26 8 0.10
27 14 0.18
28 36 0.46
29 5 0.06
30 5 0.06
31 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (25 bp):
TTTTATAAATTACAAAAAGGACAAT
Found at i:180324 original size:18 final size:18
Alignment explanation
Indices: 180301--180337 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
180291 AACCATAAAA
* *
180301 AAATTTCCAAATTAATCT
1 AAATTTCAAAACTAATCT
180319 AAATTTCAAAACTAATCT
1 AAATTTCAAAACTAATCT
180337 A
1 A
180338 TTAAAAATCA
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:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTTCAAAACTAATCT
Found at i:186152 original size:18 final size:17
Alignment explanation
Indices: 186104--186156 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 17
186094 TTGGACTCCT
* *
186104 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
186122 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
186140 AGTGCATTCGATGCATG
1 AGTGCA-TCGATGCATG
186157 GCTTGTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 13 0.42
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:186218 original size:64 final size:65
Alignment explanation
Indices: 186135--186305 Score: 193
Period size: 64 Copynumber: 2.6 Consensus size: 65
186125 TGCATCGATG
* * * *
186135 CATGAAGTGCATTCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTTGATGTTTTAATTAA
1 CATG-AGTGCA-TCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTAA
186200 AT
64 AT
* ** * * *
186202 CA-GAGTGCATCGATGCATGAAGAGTGCATCGGTGCATGAAATGCATTCGATGTTTCAATTTATT
1 CATGAGTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTAAAT
186266 CATTGA-TGCATCGATGCATGGTATTGATGCATCGGTGCAT
1 CA-TGAGTGCATCGATGCATGG-ATTG-TGCATCGGTGCAT
186306 TCCTTTGAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
64 47 0.54
65 20 0.23
66 5 0.06
67 15 0.17
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (65 bp):
CATGAGTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTAAAT
Found at i:186227 original size:19 final size:19
Alignment explanation
Indices: 186203--186253 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
186193 TAATTAAATC
186203 AGAGTGCATCGATGCATGA
1 AGAGTGCATCGATGCATGA
*
186222 AGAGTGCATCGGTGCATGA
1 AGAGTGCATCGATGCATGA
186241 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
186254 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Found at i:188874 original size:24 final size:23
Alignment explanation
Indices: 188803--188882 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
188793 AATGGTCTTG
*
188803 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
188826 TGCATCG--GTACA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
188847 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
*
188871 TGCATTGATGCA
1 TGCATCGATGCA
188883 TTGTTAAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.24
24 16 0.35
25 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:194746 original size:64 final size:63
Alignment explanation
Indices: 194677--194856 Score: 183
Period size: 64 Copynumber: 2.8 Consensus size: 63
194667 TTGGACTCCT
* *
194677 AGTGCATCGGTGCACTATGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCACTATGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCAG
* * *
194738 CCTGGTGCATCGATGCATGGCT-T--GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAA
1 ---AGTGCATCGATGCA---CTATGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-TAA
194800 ATCAG
59 ATCAG
* *
194805 AGTGCATCGATGCA-TGAAGAGTGCATCGGTGCATGAAATGCATTCGATGTTT
1 AGTGCATCGATGCACT-ATGAGTGCATCGATGCATGAAATGCATTCGATGTTT
194857 CAATTTATTC
Statistics
Matches: 97, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
60 1 0.01
64 87 0.90
66 5 0.05
67 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCACTATGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCAG
Found at i:194827 original size:19 final size:19
Alignment explanation
Indices: 194803--194853 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
194793 TAATTAAATC
194803 AGAGTGCATCGATGCATGA
1 AGAGTGCATCGATGCATGA
*
194822 AGAGTGCATCGGTGCATGA
1 AGAGTGCATCGATGCATGA
194841 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
194854 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Done.