Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009036.1 Hibiscus syriacus cultivar Beakdansim tig00112443_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: 1934717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:150540 original size:13 final size:13
Alignment explanation
Indices: 150522--150547 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150512 ACAGACGCGC
150522 ATATGAAGACTGT
1 ATATGAAGACTGT
150535 ATATGAAGACTGT
1 ATATGAAGACTGT
150548 TTAACTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
ATATGAAGACTGT
Found at i:151873 original size:44 final size:44
Alignment explanation
Indices: 151818--151909 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
151808 AAATATTTAT
*
151818 TAAATGTAACGATCAGAGTTTTTTAATTTTATTATTTATTTCAG
1 TAAATGTAACGATCAAAGTTTTTTAATTTTATTATTTATTTCAG
151862 TAAATGTAACGATCAAAGTTTTTTAATTTTATTATTTATTTCAG
1 TAAATGTAACGATCAAAGTTTTTTAATTTTATTATTTATTTCAG
151906 TAAA
1 TAAA
151910 ATTAAATGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.49
Consensus pattern (44 bp):
TAAATGTAACGATCAAAGTTTTTTAATTTTATTATTTATTTCAG
Found at i:163967 original size:37 final size:37
Alignment explanation
Indices: 163917--163990 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
163907 AACAAGTTTA
*
163917 TATGAAAACCTAATTGGTTGATCAATGATCATACCAG
1 TATGAAAACCTAATTGGTTAATCAATGATCATACCAG
163954 TATGAAAACCTAATTGGTTAATCAATGATCATACCAG
1 TATGAAAACCTAATTGGTTAATCAATGATCATACCAG
163991 GGAATTGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (37 bp):
TATGAAAACCTAATTGGTTAATCAATGATCATACCAG
Found at i:180251 original size:55 final size:54
Alignment explanation
Indices: 180192--180836 Score: 335
Period size: 55 Copynumber: 12.1 Consensus size: 54
180182 GGGATAAGTG
* * * *
180192 AGACTTGAAAAATCTTCAAATGACGAGTCTGTTCCCTATTCCTTCAG-GAAGTATA
1 AGACTTGAACAATCTTCAAA-AACGAGTCTGCTCCCTATTCATTCAGAG-AGTATA
* * * *
180247 AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGTATA
1 AGACTTGAACAATCTTCA-AAAACGAGTCTGCTCCCTATTCATTCAGAGAGTATA
* * * *
180302 AGAC-TGAACAATCTTCAATAAAAC-AGGTCCGCTCTCTACTCCTTCAGAGAGTAT-
1 AGACTTGAACAATCTTC-A-AAAACGA-GTCTGCTCCCTATTCATTCAGAGAGTATA
* * * * *
180356 AGAACTCGGAA-AATCTTCAATAAAC-AGGCCCGCTCTCTATTCTTTCAGAGAGTATA
1 AG-ACT-TGAACAATCTTCAA-AAACGA-GTCTGCTCCCTATTCATTCAGAGAGTATA
* * * *
180412 GGAC-T---CAATCTTTAACAAACGTGT-TCGCTCCCTATTCCTTCAGAGAGTAT-
1 AGACTTGAACAATCTTCAA-AAACGAGTCT-GCTCCCTATTCATTCAGAGAGTATA
* * * * * *
180462 AGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-
1 AG-ACTTGAACAATCTTCA-AAAACGAGTCTGCTCCCTATTCATTCAGAGAGTATA
* * * * *
180517 AGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATTCATTCAGAGAGTAT-
1 AG-ACTTGAACAATCTTCA-AAAACGAGTCTGCTCCCTATTCATTCAGAGAGTATA
* ** *
180572 AGAACTCGAACAATCTTCAACAAACTTGT-TCGCTCCCTATTCCTTCAGAGAGTATA
1 AG-ACTTGAACAATCTTCAA-AAACGAGTCT-GCTCCCTATTCATTCAGAGAGTATA
* * ** *
180628 GGAC-T---CAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATA
1 AGACTTGAACAATCTTCAA-AAACGAGTCTGCTCCCTATTCATTCAGAGAGTATA
* * ** * *
180679 GGAC-T---CAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTTGAACAATCTTCAA-AAACGAGTCTGCTCCCTATTCATTCAGAGAGTATA
* * ** * *
180730 GGAC-T---CAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTTGAACAATCTTCAA-AAACGAGTCTGCTCCCTATTCATTCAGAGAGTATA
* ** * *
180781 GGAC-T---CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTTGAACAATCTTCAA-AAACGAGTCTGCTCCCTATTCATTCAGAGAGTATA
*
180832 GGACT
1 AGACT
180837 CAATCTTCAA
Statistics
Matches: 519, Mismatches: 47, Indels: 51
0.84 0.08 0.08
Matches are distributed among these distances:
50 1 0.00
51 234 0.45
54 15 0.03
55 253 0.49
56 13 0.03
57 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (54 bp):
AGACTTGAACAATCTTCAAAAACGAGTCTGCTCCCTATTCATTCAGAGAGTATA
Found at i:180447 original size:51 final size:51
Alignment explanation
Indices: 180224--180851 Score: 645
Period size: 51 Copynumber: 11.8 Consensus size: 51
180214 ACGAGTCTGT
* *
180224 TCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAA-TGTGTCTGC
1 TCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACAAACT-TGTCCGC
* * * * **
180279 TCTCTATTCATTCAGAGAGTATAAGACTGAACAATCTTCAATAAAACAGGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT---CAATCTTCAA-CAAACTTGTCCGC
* * * * ** *
180334 TCTCTACTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACAGGCCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAACTTGTCCGC
* * * * *
180389 TCTCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAACGTGTTCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* **
180440 TCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATA-AAACGGGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACAAACTTGTCCGC
* * **
180495 TCTCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATA-AAACGGGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACAAACTTGTCCGC
* * * *
180550 TCTCTATTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACTTGTTCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACTTGTCCGC
*
180605 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* *
180656 TCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
*
180707 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
180758 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
180809 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
180852 GAATTTGCTT
Statistics
Matches: 519, Mismatches: 40, Indels: 32
0.88 0.07 0.05
Matches are distributed among these distances:
51 255 0.49
52 1 0.00
53 1 0.00
54 13 0.03
55 238 0.46
56 11 0.02
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (51 bp):
TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
Found at i:180621 original size:216 final size:213
Alignment explanation
Indices: 180224--180852 Score: 784
Period size: 216 Copynumber: 3.0 Consensus size: 213
180214 ACGAGTCTGT
* *
180224 TCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTATT
1 TCCCTATTCCTTCAGAG-AGTATAGA-ACTCG-ACAATCTTCATAAAACGTGTCCGCTCTCTATT
* *
180287 CATTCAGAGAGTATA-AGACTGAACAATCTTCAATAAAACAGGTCCGCTCTCTACTCCTTCAGAG
63 CCTTCAGAGAGTATAGA-ACTG-ACAATCTTC-ATAAAACAGGTCCGCTCTCTATTCCTTCAGAG
* ** * * *
180351 AGTATAGAACTCGGAA-AATCTTCAATAAACAGGCCCGCTCTCTATTCTTTCAGAGAGTATAGGA
125 AGTATAGAACTC-GAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGA
* *
180415 CTCAATCTTTAACAAACGTGTTCGC
189 CTCAATCTTCAACAAACGTGTCCGC
*
180440 TCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATTCC
1 TCCCTATTCCTTCAGAGAGTATAGAACTCGA-CAATCTTCATAAAACGTGTCCGCTCTCTATTCC
* *
180505 TTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATTCATTCAGAGAGT
65 TTCAGAGAGTATAGAACT-GA-CAATCTTCATAAAACAGGTCCGCTCTCTATTCCTTCAGAGAGT
*
180570 ATAGAACTCGAACAATCTTCAACAAACTTGTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTCA
128 ATAGAACTCGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCA
* *
180635 ATCTTCAACGAACTTGTCCGC
193 ATCTTCAACAAACGTGTCCGC
* * * * *
180656 TCCCTATTCATTCAGAGAGTATAGGACT---CAATCTTCA-ACGAACTTGTCCGCTCCCTATTCC
1 TCCCTATTCCTTCAGAGAGTATAGAACTCGACAATCTTCATA-AAACGTGTCCGCTCTCTATTCC
* * ** *
180717 TTCAGAGAGTATAGGACT--CAATCTTCA-ACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTA
65 TTCAGAGAGTATAGAACTGACAATCTTCATA-AAACAGGTCCGCTCTCTATTCCTTCAGAGAGTA
*
180779 TAGGACT----CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAA
129 TAGAACTCGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAA
180840 TCTTCAACAAACG
194 TCTTCAACAAACG
180853 AATTTGCTTC
Statistics
Matches: 370, Mismatches: 34, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
204 64 0.17
207 1 0.00
208 43 0.12
211 1 0.00
212 44 0.12
215 4 0.01
216 201 0.54
217 12 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (213 bp):
TCCCTATTCCTTCAGAGAGTATAGAACTCGACAATCTTCATAAAACGTGTCCGCTCTCTATTCCT
TCAGAGAGTATAGAACTGACAATCTTCATAAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATA
GAACTCGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATC
TTCAACAAACGTGTCCGC
Found at i:182195 original size:8 final size:8
Alignment explanation
Indices: 182168--182275 Score: 50
Period size: 9 Copynumber: 13.4 Consensus size: 8
182158 CCTCCTTTTA
182168 TTTCTCTTT
1 TTTCTC-TT
*
182177 TTTTTCATT
1 TTTCTC-TT
182186 TTTCTCTT
1 TTTCTCTT
*
182194 TTTAT-TT
1 TTTCTCTT
*
182201 TTCTTTCTT
1 TT-TCTCTT
*
182210 TTTTTCATT
1 TTTCTC-TT
*
182219 TTTAT-TT
1 TTTCTCTT
182226 TTTCTCATT
1 TTTCTC-TT
182235 TTT-TC-T
1 TTTCTCTT
182241 TTTCT-TCT
1 TTTCTCT-T
182249 TTTCT-TCT
1 TTTCTCT-T
182257 TTT-TCTT
1 TTTCTCTT
182264 TTTCTCATT
1 TTTCTC-TT
182273 TTT
1 TTT
182276 ATTTTTATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
6 4 0.05
7 16 0.20
8 29 0.36
9 32 0.40
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTCTCTT
Found at i:182195 original size:14 final size:14
Alignment explanation
Indices: 182178--182293 Score: 51
Period size: 14 Copynumber: 7.8 Consensus size: 14
182168 TTTCTCTTTT
182178 TTTTCATTTTTCTC
1 TTTTCATTTTTCTC
*
182192 TTTTTATTTTTCTTTC
1 TTTTCATTTTTC--TC
* *
182208 TTTTTTTCATTTTTATTT
1 ---TTTTCATTTTT-CTC
182226 TTTCTCATTTTT-TC
1 TTT-TCATTTTTCTC
*
182240 TTTTCTTCTTTTCTTC
1 TTTTCAT-TTTTC-TC
182256 TTTTTC-TTTTTCTC
1 -TTTTCATTTTTCTC
* *
182270 ATTTTTATTTTTAT-
1 -TTTTCATTTTTCTC
182284 TTTT-ATTTTT
1 TTTTCATTTTT
182294 TCATTTTTCG
Statistics
Matches: 81, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
12 6 0.07
13 7 0.09
14 25 0.31
15 14 0.17
16 13 0.16
17 5 0.06
18 1 0.01
19 10 0.12
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCATTTTTCTC
Found at i:182195 original size:16 final size:16
Alignment explanation
Indices: 182163--182281 Score: 78
Period size: 15 Copynumber: 7.7 Consensus size: 16
182153 TGAACCCTCC
* *
182163 TTTT-ATTTCTCTTTT
1 TTTTCATTTTTCTCTT
182178 TTTTCATTTTTCTC-T
1 TTTTCATTTTTCTCTT
182193 TTTT-ATTTTTCTTTCTTT
1 TTTTCATTTTTC--TC-TT
*
182211 TTTTCATTTTTAT-TT
1 TTTTCATTTTTCTCTT
182226 TTTCTCATTTTT-TCTT
1 TTT-TCATTTTTCTCTT
182242 TTCTTC--TTTTCT-TCT
1 TT-TTCATTTTTCTCT-T
*
182257 TTTTC-TTTTTCTCAT
1 TTTTCATTTTTCTCTT
182272 TTTT-ATTTTT
1 TTTTCATTTTT
182282 ATTTTTATTT
Statistics
Matches: 86, Mismatches: 4, Indels: 28
0.73 0.03 0.24
Matches are distributed among these distances:
14 15 0.17
15 35 0.41
16 23 0.27
17 2 0.02
18 5 0.06
19 6 0.07
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCATTTTTCTCTT
Found at i:182243 original size:6 final size:6
Alignment explanation
Indices: 182185--182317 Score: 56
Period size: 6 Copynumber: 20.7 Consensus size: 6
182175 TTTTTTTCAT
* * *
182185 TTTTCTC TTTTTA TTTTTC TTTCTT- TTTTTC ATTTTTAT TTTTTC TCATTTTT
1 TTTT-TC TTTTTC TTTTTC TTT-TTC TTTTTC -TTTTT-C TTTTTC T--TTTTC
* * * * *
182238 TCTTTTC TTCTT- TTCTTC TTTTTC TTTTTCTC ATTTTTA TTTTTA TTTTTAT
1 T-TTTTC TTTTTC TTTTTC TTTTTC -TTTT-TC -TTTTTC TTTTTC TTTTT-C
*
182290 TTTTTC ATTTTTC GTTTT- TTTTTC TTTT
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTT
182318 ATTTCTTCTT
Statistics
Matches: 99, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
5 11 0.11
6 40 0.40
7 37 0.37
8 11 0.11
ACGTcount: A:0.07, C:0.14, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:182317 original size:8 final size:8
Alignment explanation
Indices: 182175--182324 Score: 80
Period size: 8 Copynumber: 18.2 Consensus size: 8
182165 TTATTTCTCT
182175 TTTTTTTC
1 TTTTTTTC
*
182183 ATTTTTCTC
1 -TTTTTTTC
182192 TTTTTATT-
1 TTTTT-TTC
*
182200 TTTCTTTC
1 TTTTTTTC
182208 TTTTTTTC
1 TTTTTTTC
*
182216 ATTTTTAT-
1 -TTTTTTTC
*
182224 TTTTTCTC
1 TTTTTTTC
*
182232 ATTTTTTC
1 TTTTTTTC
*
182240 TTTTCTTC
1 TTTTTTTC
*
182248 TTTTCTTC
1 TTTTTTTC
182256 --TTTTTC
1 TTTTTTTC
*
182262 TTTTTCTC
1 TTTTTTTC
182270 ATTTTTATT-
1 -TTTTT-TTC
182279 TTTATTTT-
1 TTT-TTTTC
182287 TATTTTTTC
1 T-TTTTTTC
182296 ATTTTTCGTT-
1 -TTTTT--TTC
182306 TTTTTTTC
1 TTTTTTTC
182314 TTTTATTTC
1 TTTT-TTTC
182323 TT
1 TT
182325 CTTCAAGCGA
Statistics
Matches: 112, Mismatches: 13, Indels: 32
0.71 0.08 0.20
Matches are distributed among these distances:
6 5 0.04
7 10 0.09
8 55 0.49
9 38 0.34
10 2 0.02
11 2 0.02
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:182326 original size:12 final size:11
Alignment explanation
Indices: 182193--182327 Score: 50
Period size: 11 Copynumber: 12.2 Consensus size: 11
182183 ATTTTTCTCT
182193 TTTTATTTTTC
1 TTTTATTTTTC
*
182204 TTTCTTTTTTTC
1 TTT-TATTTTTC
182216 ATTTTTATTTTT-
1 --TTTTATTTTTC
* *
182228 TCTCATTTTTTC
1 TTTTA-TTTTTC
*
182240 TTTTCTTCTTT-
1 TTTTATT-TTTC
* *
182251 TCTTCTTTTTC
1 TTTTATTTTTC
**
182262 TTTT-TCTCAT-
1 TTTTAT-TTTTC
*
182272 TTTTATTTTTA
1 TTTTATTTTTC
*
182283 TTTT-TATTT-
1 TTTTATTTTTC
*
182292 TTTCATTTTTC
1 TTTTATTTTTC
182303 GTTTT-TTTTTC
1 -TTTTATTTTTC
182314 TTTTATTTCTTC
1 TTTTATTT-TTC
182326 TT
1 TT
182328 CAAGCGAAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 29
0.67 0.12 0.21
Matches are distributed among these distances:
9 3 0.03
10 25 0.27
11 35 0.38
12 20 0.22
13 6 0.07
14 3 0.03
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:198450 original size:15 final size:15
Alignment explanation
Indices: 198430--198462 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
198420 ACATTACTCA
198430 CCCCGCATCCGCCCG
1 CCCCGCATCCGCCCG
198445 CCCCGCATCCGCCCG
1 CCCCGCATCCGCCCG
198460 CCC
1 CCC
198463 AGCTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.70, G:0.18, T:0.06
Consensus pattern (15 bp):
CCCCGCATCCGCCCG
Found at i:200191 original size:16 final size:16
Alignment explanation
Indices: 200170--200201 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
200160 AGGTCACCGT
200170 GACGCAATATTAACGC
1 GACGCAATATTAACGC
200186 GACGCAATATTAACGC
1 GACGCAATATTAACGC
200202 AACGTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (16 bp):
GACGCAATATTAACGC
Found at i:200210 original size:16 final size:16
Alignment explanation
Indices: 200171--200210 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
200161 GGTCACCGTG
*
200171 ACGCAATATTAACGCG
1 ACGCAATATTAACGCA
200187 ACGCAATATTAACGCA
1 ACGCAATATTAACGCA
*
200203 ACGTAATA
1 ACGCAATA
200211 AAATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (16 bp):
ACGCAATATTAACGCA
Found at i:202540 original size:24 final size:24
Alignment explanation
Indices: 202455--202564 Score: 116
Period size: 24 Copynumber: 4.6 Consensus size: 24
202445 TCATGTTCGT
* *
202455 GAACGTATTCGTTTATATGTTCAC
1 GAACGTGTTCATTTATATGTTCAC
*
202479 GAATGTGTTCA-TTAGTATGTTCAC
1 GAACGTGTTCATTTA-TATGTTCAC
*
202503 GAATGTGTTCATTTATATGTTCAC
1 GAACGTGTTCATTTATATGTTCAC
* * *
202527 AAACGTGTTCATTTAGA-GTTCAT
1 GAACGTGTTCATTTATATGTTCAC
* *
202550 GAACATGTTCGTTTA
1 GAACGTGTTCATTTA
202565 GCGTTTGTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
23 20 0.27
24 51 0.69
25 3 0.04
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (24 bp):
GAACGTGTTCATTTATATGTTCAC
Found at i:203079 original size:17 final size:18
Alignment explanation
Indices: 203040--203086 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
203030 TGTTTATGAG
203040 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
203058 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
203075 GGAATTGGAATC
1 GGAATTGGAATC
203087 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:203861 original size:200 final size:200
Alignment explanation
Indices: 203485--203861 Score: 557
Period size: 200 Copynumber: 1.9 Consensus size: 200
203475 ATAAAGTTTC
* * *
203485 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAAGAGTGACTTAATTGGAAAAAA
1 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAA
203550 TATATAGAGAGAGGGGTATTATTGTAATTATTCCTAAATATAAGGTAAAATTATATATTTTTTGG
66 TATATAGAGAGAGGGGTATTATTGTAATTATTCCTAAATATAAGGTAAAATTATATATTTTTT-G
* *
203615 GTCGGGTCGGGTATTTTTCACACTAAACCCGACCCGACCCGACCCGAATATATGAATTAGAAATC
130 G-CGGGTCGAGTATTTTCCACACTAAACCCGACCCGACCCGACCCGAATATATGAATTAGAAATC
203680 CGACCCG
194 CGACCCG
*
203687 ACCCGACCTGAAATAAT-AAAAAA-TATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAA
1 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAA
* *
203750 -ATTATAGATAGAGGGGTATTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATATTT
66 TA-TATAGAGAGAGGGGTATTATTGTAATTATTCCT-AA-ATATAAGGTAAAATTATATAT-TTT
* * *
203814 TT-G-GGGTCGAGTATTTTCCACCCTAAACCCGAACTCGACCTGACCCGA
127 TTGGCGGGTCGAGTATTTTCCACACTAAACCCG-ACCCGACCCGACCCGA
203862 CCTGAATATC
Statistics
Matches: 159, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
199 26 0.16
200 82 0.52
201 9 0.06
202 37 0.23
203 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (200 bp):
ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAA
TATATAGAGAGAGGGGTATTATTGTAATTATTCCTAAATATAAGGTAAAATTATATATTTTTTGG
CGGGTCGAGTATTTTCCACACTAAACCCGACCCGACCCGACCCGAATATATGAATTAGAAATCCG
ACCCG
Found at i:213349 original size:40 final size:38
Alignment explanation
Indices: 213287--213363 Score: 100
Period size: 40 Copynumber: 2.0 Consensus size: 38
213277 AAGTTCATTT
* * **
213287 ATTTTAGTTTATTTATCAAATGAACGAGCATGAACAAG
1 ATTTTAGTTCATTTAACAAATGAACGAAAATGAACAAG
213325 ATTTTATGTTCATTTAACTAAATGAACGAAAATGAACAA
1 ATTTTA-GTTCATTTAAC-AAATGAACGAAAATGAACAA
213364 AAGGCTCGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 6 0.18
39 9 0.27
40 18 0.55
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (38 bp):
ATTTTAGTTCATTTAACAAATGAACGAAAATGAACAAG
Found at i:213427 original size:14 final size:14
Alignment explanation
Indices: 213408--213476 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
213398 TGATAATTTT
213408 TTCATTTATGTTCG
1 TTCATTTATGTTCG
* *
213422 TTCATTTGTGTTGG
1 TTCATTTATGTTCG
* * *
213436 TTCGTGTATGTTCA
1 TTCATTTATGTTCG
**
213450 TTTTTTTATGTTCG
1 TTCATTTATGTTCG
*
213464 TTCGTTTATGTTC
1 TTCATTTATGTTC
213477 TCCATATTTG
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (14 bp):
TTCATTTATGTTCG
Found at i:213690 original size:14 final size:14
Alignment explanation
Indices: 213654--213693 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
213644 CCCAATTAAT
*
213654 TTTATGTTCGTTCA
1 TTTATGTTTGTTCA
213668 TTTATGTTTGTTCA
1 TTTATGTTTGTTCA
*
213682 TTTGTGTTTGTT
1 TTTATGTTTGTT
213694 TATGGTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.65
Consensus pattern (14 bp):
TTTATGTTTGTTCA
Found at i:213706 original size:24 final size:24
Alignment explanation
Indices: 213668--213720 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
213658 TGTTCGTTCA
* * *
213668 TTTATGTTTGTTCATTTGTGTTTG
1 TTTATGGTTGATCATTTGTGCTTG
213692 TTTATGGTTGATCATTTGTGCTTG
1 TTTATGGTTGATCATTTGTGCTTG
213716 TTTAT
1 TTTAT
213721 CATTTAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.11, C:0.06, G:0.21, T:0.62
Consensus pattern (24 bp):
TTTATGGTTGATCATTTGTGCTTG
Found at i:218350 original size:18 final size:19
Alignment explanation
Indices: 218329--218373 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
218319 GTCTCGTACA
*
218329 ACCACTA-TGTCCCGAATG
1 ACCACTATTGTCCCGAAGG
218347 ACCACTGTATTGTCCCGAAGG
1 ACCAC--TATTGTCCCGAAGG
218368 ACCACT
1 ACCACT
218374 GTAACCCTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 5 0.22
19 1 0.04
20 2 0.09
21 15 0.65
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (19 bp):
ACCACTATTGTCCCGAAGG
Found at i:218362 original size:21 final size:21
Alignment explanation
Indices: 218336--218376 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
218326 ACAACCACTA
*
218336 TGTCCCGAATGACCACTGTAT
1 TGTCCCGAAGGACCACTGTAT
218357 TGTCCCGAAGGACCACTGTA
1 TGTCCCGAAGGACCACTGTA
218377 ACCCTCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGTAT
Found at i:221145 original size:2 final size:2
Alignment explanation
Indices: 221138--221182 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
221128 GCTGTAACTT
221138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
221180 TA T
1 TA T
221183 TATTTGTCGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:221952 original size:17 final size:17
Alignment explanation
Indices: 221939--221971 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
221929 CGAATGCATT
221939 CCATGCATCGATGCACA
1 CCATGCATCGATGCACA
*
221956 CCATGCACCGATGCAC
1 CCATGCATCGATGCAC
221972 TGAGGATTTT
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:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCATCGATGCACA
Found at i:222014 original size:46 final size:45
Alignment explanation
Indices: 221958--222064 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
221948 GATGCACACC
* * *
221958 ATGCACCGATGCACT-GAGGAT-TTTATAAGAACATCGAATGCATTTG
1 ATGCATCGATGCACTCG-GGATATTT-TAA-AACATCAAATGCACTTG
*
222004 ATGCATCGATGCACTCGGGCTATTTTAAAACATCAAATGCACTTG
1 ATGCATCGATGCACTCGGGATATTTTAAAACATCAAATGCACTTG
222049 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
222065 TTAGTGCACC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 31 0.56
46 20 0.36
47 4 0.07
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (45 bp):
ATGCATCGATGCACTCGGGATATTTTAAAACATCAAATGCACTTG
Found at i:232336 original size:21 final size:21
Alignment explanation
Indices: 232283--232339 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
232273 CCACTATGTT
*
232283 CGAAGGACCACTGTATTGTCC
1 CGAAGGACCATTGTATTGTCC
*
232304 CGAATGACCATTGTATTGTCC
1 CGAAGGACCATTGTATTGTCC
*
232325 CGAAGGATCATTGTA
1 CGAAGGACCATTGTA
232340 ACCCTCGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
CGAAGGACCATTGTATTGTCC
Found at i:233225 original size:20 final size:22
Alignment explanation
Indices: 233190--233271 Score: 78
Period size: 24 Copynumber: 3.6 Consensus size: 22
233180 TTCCCCTTGA
* *
233190 AGTGCATCGGTACATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
233210 AGTGCATCGATGCATTCCTTAAC
1 AGTGCATCGATGCATT-CTTAAC
233233 ATGTGCATCGATGCATTCCTTAAC
1 A-GTGCATCGATGCATT-CTTAAC
* *
233257 ATGTACATCAATGCA
1 A-GTGCATCGATGCA
233272 CTATCCATGC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
20 14 0.26
21 1 0.02
22 1 0.02
23 3 0.06
24 35 0.65
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:233243 original size:24 final size:24
Alignment explanation
Indices: 233211--233271 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
233201 ACATTCTACA
233211 GTGCATCGATGCATTCCTTAACAT
1 GTGCATCGATGCATTCCTTAACAT
233235 GTGCATCGATGCATTCCTTAACAT
1 GTGCATCGATGCATTCCTTAACAT
* *
233259 GTACATCAATGCA
1 GTGCATCGATGCA
233272 CTATCCATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATTCCTTAACAT
Found at i:235328 original size:17 final size:17
Alignment explanation
Indices: 235293--235327 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
235283 AAAGTTATGA
235293 TTAGGGATTTGAGAGTT
1 TTAGGGATTTGAGAGTT
*
235310 TTAGGTATTTGAG-GTT
1 TTAGGGATTTGAGAGTT
235326 TT
1 TT
235328 TTGTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (17 bp):
TTAGGGATTTGAGAGTT
Found at i:235767 original size:13 final size:14
Alignment explanation
Indices: 235749--235781 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
235739 TGTCACGTTC
235749 AAAATA-TTTTTTA
1 AAAATATTTTTTTA
235762 AAAATATTTTTTTA
1 AAAATATTTTTTTA
235776 AAAATA
1 AAAATA
235782 AAAAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTTTTTTA
Found at i:243549 original size:20 final size:20
Alignment explanation
Indices: 243524--243569 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
243514 ATAAGTCGAG
243524 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
243544 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
243564 AGATGT
1 AGATGT
243570 TTATAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.22
Consensus pattern (20 bp):
AGATGTAGGGAAATAGAAAT
Found at i:244543 original size:23 final size:23
Alignment explanation
Indices: 244510--244577 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
244500 ATTATTATAT
244510 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
244533 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
244556 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
244578 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:250134 original size:18 final size:19
Alignment explanation
Indices: 250099--250135 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
250089 CACGGAATGT
250099 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
250119 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
250136 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:259207 original size:33 final size:32
Alignment explanation
Indices: 259162--259229 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
259152 GATATTAATA
259162 AATAAAAATAAATATTAAAATTTTAATAAT-TTT
1 AATAAAAAT-AA-ATTAAAATTTTAATAATGTTT
* * *
259195 AATAAAACTAAATTATAATTTTTATAATGTTT
1 AATAAAAATAAATTAAAATTTTAATAATGTTT
259227 AAT
1 AAT
259230 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 15 0.48
32 8 0.26
33 8 0.26
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (32 bp):
AATAAAAATAAATTAAAATTTTAATAATGTTT
Found at i:259445 original size:37 final size:37
Alignment explanation
Indices: 259369--259445 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
259359 ATAATGATTT
* * * *
259369 AAATATATAGAATTAAAATATAAATAAACAATGAGTA
1 AAATAAATAAAATTAAAATATAAATAAAAAATGAATA
259406 AAATAAATAAAATTAAAAT-TAAATATAAAAA-GTAATA
1 AAATAAATAAAATTAAAATATAAATA-AAAAATG-AATA
259443 AAA
1 AAA
259446 CTTATAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
36 7 0.21
37 27 0.79
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (37 bp):
AAATAAATAAAATTAAAATATAAATAAAAAATGAATA
Found at i:261276 original size:113 final size:113
Alignment explanation
Indices: 260930--261940 Score: 1451
Period size: 113 Copynumber: 8.9 Consensus size: 113
260920 AGAGGGCAAT
260930 GTTGAACAAATTCTTCTCATTATGAAC-TCTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
1 GTTGAACAAATTCTTCTCATTATGAACTTC-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
* * * * *
260994 AACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCGAAAA
65 AACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCGAAAA
* *
261043 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
**** * * * * * * **
261107 ACTCGCCCTGGCAATGTTGATCTATCGAATGATGAATTCAAGCGAAAA
66 ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCGAAAA
* *
261155 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATTAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
261220 ACTTTTTCTGGAAAAGCTAATCCATCAAATGATGGATTTGAGC-AAAA
66 ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCGAAAA
* *
261267 GGTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
1 -GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
261332 AACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTCGAGCGAAAA
65 AACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTT-GAGCGAAAA
* *
261382 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*** * * * * * **
261447 AC-TCGCCTTGGCAATGCTGATCTATCGAATGATGAATTCAAGCGAAAA
66 ACTTTTTC-TGGAAAAGCTGATCCATCAAATGATGGATTTGAGCGAAAA
* * *
261495 GTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATTAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
261560 ACTTATTCTGGAAAAGCTAATCCATCAAATGATGGATTTGAGC-AAAA
66 ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCGAAAA
* *
261607 GGTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
1 -GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
261672 AACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC-AAAA
65 AACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCGAAAA
* *
261720 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATG
1 -GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
261785 AACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC-AAAA
65 AACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCGAAAA
* * * *
261833 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAAATGAGTTCTTATCATTATG
1 -GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
*
261898 AACTTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
65 AAC-TTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
261941 ATCTTTGCTA
Statistics
Matches: 819, Mismatches: 70, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
112 112 0.14
113 569 0.69
114 134 0.16
115 4 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCGAAAA
Found at i:261528 original size:20 final size:20
Alignment explanation
Indices: 261505--261568 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
261495 GTTGAACAAG
261505 TTCTTCTCATTATGAACTTA
1 TTCTTCTCATTATGAACTTA
261525 TTCTTCCTTC-TTCA-G-A-TTA
1 TTCTT-C-TCATT-ATGAACTTA
261544 GTTCTTCTCATTATGAACTTA
1 -TTCTTCTCATTATGAACTTA
261565 TTCT
1 TTCT
261569 GGAAAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
18 3 0.08
19 7 0.19
20 16 0.44
21 7 0.19
22 3 0.08
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.52
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTTA
Found at i:261548 original size:340 final size:340
Alignment explanation
Indices: 260930--261940 Score: 1656
Period size: 340 Copynumber: 3.0 Consensus size: 340
260920 AGAGGGCAAT
* *
260930 GTTGAACAAATTCTTCTCATTATGAACTCTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * *
260995 ACTTTCTCTGGAAAAGTTGATCCATCGAATGAT-GAATTCGAGCGAAAAGTTGAACAAGTTCTTC
66 ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTCGAGCGAAAAGTTGAACAAGTTCTTC
*
261059 TTATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGCCCTGGCAATG
131 TTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGCCTTGGCAATG
*
261123 TTGATCTATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
196 CTGATCTATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
261188 TTCCTTCTTCAGATTAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTAATCCATCAAATGAT
261 TTCCTTCTTCAGATTAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTAATCCATCAAATGAT
261253 GGATTTGAGCAAAAG
326 GGATTTGAGCAAAAG
261268 GTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
261333 ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTCGAGCGAAAAGTTGAACAAGTTCTTC
66 ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTCGAGCGAAAAGTTGAACAAGTTCTTC
261398 TTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGCCTTGGCAATG
131 TTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGCCTTGGCAATG
*
261463 CTGATCTATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTC
196 CTGATCTATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
*
261528 TTCCTTCTTCAGATTAGTTCTTCTCATTATGAACTTATTCTGGAAAAGCTAATCCATCAAATGAT
261 TTCCTTCTTCAGATTAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTAATCCATCAAATGAT
261593 GGATTTGAGCAAAAG
326 GGATTTGAGCAAAAG
261608 GTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
261673 ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTT-GAGC-AAAAGGTTGAACAAATTCTT
66 ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTCGAGCGAAAA-GTTGAACAAGTTCTT
* * * *** *
261736 CTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT-TTTTCTGGAAA
130 CTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGCCT-TGGCAA
* * * * ** * *
261800 AGCTGATCCATCAAATGATGGATTTGAGC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
194 TGCTGATCTATCGAATGATGAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTC
* * * * * *
261864 TTCTTCATTCTTCAAATGAGTTCTTATCATTATGAACTTTTTTCTGGAAAAGCTGATCCATCAAG
258 TTCTTCCTTCTTCAGATTAGTTCTTCTCATTATGAAC-TTTTTCTGGAAAAGCTAATCCATCAAA
261929 TGATGGATTTGA
322 TGATGGATTTGA
261941 ATCTTTGCTA
Statistics
Matches: 633, Mismatches: 34, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
338 102 0.16
339 205 0.32
340 326 0.52
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (340 bp):
GTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTCGAGCGAAAAGTTGAACAAGTTCTTC
TTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGCCTTGGCAATG
CTGATCTATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
TTCCTTCTTCAGATTAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTAATCCATCAAATGAT
GGATTTGAGCAAAAG
Found at i:262396 original size:22 final size:22
Alignment explanation
Indices: 262340--262396 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
262330 AATAAAGCTT
* * *
262340 TCATTTTTGAAAAGAGAATCTG
1 TCATCTTTGAAGAGAGAATCTA
*
262362 TCATCTTTAAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
262384 TCATCTTTGAAGA
1 TCATCTTTGAAGA
262397 ATGTAGATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:262832 original size:54 final size:54
Alignment explanation
Indices: 262750--262917 Score: 266
Period size: 54 Copynumber: 3.1 Consensus size: 54
262740 TCAGAATAGC
* * *
262750 ATGTTCGTAAAACATTTGAC-GGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAAG-ACATTCATCCTTTCCTGTGGTTTCTGCTCAG
*
262804 ATGTTCGTAAAACATTTGACAAGACATTCATCCTTTCCTGTAGTTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAAGACATTCATCCTTTCCTGTGGTTTCTGCTCAG
* *
262858 ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTTAG
1 ATGTTCGTAAAACATTTGACAAGACATTCATCCTTTCCTGTGGTTTCTGCTCAG
262912 ATGTTC
1 ATGTTC
262918 TCAATCATTG
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 105 0.99
55 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (54 bp):
ATGTTCGTAAAACATTTGACAAGACATTCATCCTTTCCTGTGGTTTCTGCTCAG
Found at i:265187 original size:115 final size:114
Alignment explanation
Indices: 264982--265198 Score: 353
Period size: 115 Copynumber: 1.9 Consensus size: 114
264972 ATGCAGTTCA
* * * *
264982 TCTTTCAATTCCAATGATTAGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTTAAAGAACAC
1 TCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
* *
265047 TTCCAGAAGGTGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCG
66 TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCG
* *
265096 TCTTTCAAATCCAATGATTGGTTTTGGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
1 TCTTTCAAATCCAATGATTAGTTCT-GGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
265161 CTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
65 CTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
265199 CGAGAACGTG
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 22 0.23
115 72 0.77
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (114 bp):
TCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCG
Found at i:267496 original size:13 final size:13
Alignment explanation
Indices: 267478--267516 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
267468 TCAATTTTCC
267478 TTTTTCTTCTTTT
1 TTTTTCTTCTTTT
267491 TTTTTCTT-TTTT
1 TTTTTCTTCTTTT
267503 TTTCTTCTTTCTTT
1 TTT-TTC-TTCTTT
267517 GCTGGATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.30
13 11 0.48
14 2 0.09
15 3 0.13
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTCTTCTTTT
Found at i:267497 original size:10 final size:10
Alignment explanation
Indices: 267472--267508 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
267462 CTTGATTCAA
*
267472 TTTTCCTTTT
1 TTTTCTTTTT
*
267482 TCTTCTTTTT
1 TTTTCTTTTT
267492 TTTTCTTTTT
1 TTTTCTTTTT
267502 TTTTCTT
1 TTTTCTT
267509 CTTTCTTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:273221 original size:33 final size:32
Alignment explanation
Indices: 273176--273243 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
273166 GATATTAATA
273176 AATAAAAATAAATATTAAAATTTTAATAAT-TTT
1 AATAAAAAT-AA-ATTAAAATTTTAATAATGTTT
* * *
273209 AATAAAACTAAATTATAATTTTTATAATGTTT
1 AATAAAAATAAATTAAAATTTTAATAATGTTT
273241 AAT
1 AAT
273244 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 15 0.48
32 8 0.26
33 8 0.26
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (32 bp):
AATAAAAATAAATTAAAATTTTAATAATGTTT
Found at i:273459 original size:37 final size:37
Alignment explanation
Indices: 273383--273459 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
273373 ATAATGATTT
* * * *
273383 AAATATATAGAATTAAAATATAAATAAACAATGAGTA
1 AAATAAATAAAATTAAAATATAAATAAAAAATGAATA
273420 AAATAAATAAAATTAAAAT-TAAATATAAAAA-GTAATA
1 AAATAAATAAAATTAAAATATAAATA-AAAAATG-AATA
273457 AAA
1 AAA
273460 CTTATAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
36 7 0.21
37 27 0.79
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (37 bp):
AAATAAATAAAATTAAAATATAAATAAAAAATGAATA
Found at i:283372 original size:4 final size:4
Alignment explanation
Indices: 283363--283493 Score: 262
Period size: 4 Copynumber: 32.8 Consensus size: 4
283353 TGAAAAAACA
283363 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
283411 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
283459 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
283494 TATACCATTG
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 127 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:292605 original size:39 final size:35
Alignment explanation
Indices: 292561--292662 Score: 96
Period size: 39 Copynumber: 2.7 Consensus size: 35
292551 GAAAAATACG
292561 TATATAATATATAATTTTTTAAAAACATTTTAGAACATA
1 TATATAATATATAATTTTTT-AAAACATTTTA-AA-A-A
* * **
292600 TATATAATATATATAATTGTTAAAATGTTTTAAAAA
1 TATATAATATATA-ATTTTTTAAAACATTTTAAAAA
* *
292636 TATATGATATATAGTTTTTTGAAAACA
1 TATATAATATATAATTTTTT-AAAACA
292663 CATATAATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
35 4 0.08
36 17 0.33
37 1 0.02
38 2 0.04
39 22 0.43
40 5 0.10
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (35 bp):
TATATAATATATAATTTTTTAAAACATTTTAAAAA
Found at i:292763 original size:39 final size:40
Alignment explanation
Indices: 292708--292826 Score: 188
Period size: 39 Copynumber: 3.0 Consensus size: 40
292698 ATATAATATA
292708 TAGAAAACGTTTTTGAAAACTTATATATATTATATAGTTT
1 TAGAAAACGTTTTTGAAAACTTATATATATTATATAGTTT
*
292748 T-GAAAACGTTTTTGAAAACATT-TACATATTATATAGTTT
1 TAGAAAACGTTTTTGAAAAC-TTATATATATTATATAGTTT
* *
292787 TAAAAAACGTTTTTGAAAACTTATATATAATATATAGTTT
1 TAGAAAACGTTTTTGAAAACTTATATATATTATATAGTTT
292827 AAAAATCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
39 37 0.51
40 35 0.49
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (40 bp):
TAGAAAACGTTTTTGAAAACTTATATATATTATATAGTTT
Found at i:292839 original size:39 final size:39
Alignment explanation
Indices: 292669--292831 Score: 175
Period size: 39 Copynumber: 4.4 Consensus size: 39
292659 AACACATATA
* **
292669 ATATAGTTTTGAAAATATTTTT-AAAA--TATATATAAT
1 ATATAGTTTTAAAAACGTTTTTGAAAACTTATATATAAT
*
292705 ATATAG-----AAAACGTTTTTGAAAACTTATATATATT
1 ATATAGTTTTAAAAACGTTTTTGAAAACTTATATATAAT
* * *
292739 ATATAGTTTTGAAAACGTTTTTGAAAACATT-TACATATT
1 ATATAGTTTTAAAAACGTTTTTGAAAAC-TTATATATAAT
292778 ATATAGTTTTAAAAAACGTTTTTGAAAACTTATATATAAT
1 ATATAGTTTT-AAAAACGTTTTTGAAAACTTATATATAAT
292818 ATATAG-TTTAAAAA
1 ATATAGTTTTAAAAA
292832 TCATTTTTAA
Statistics
Matches: 109, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
31 9 0.08
32 4 0.04
34 15 0.14
36 6 0.06
38 5 0.05
39 39 0.36
40 31 0.28
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (39 bp):
ATATAGTTTTAAAAACGTTTTTGAAAACTTATATATAAT
Found at i:293373 original size:18 final size:18
Alignment explanation
Indices: 293350--293385 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
293340 CGGAACCATT
293350 GTAAACCGGACATCAACA
1 GTAAACCGGACATCAACA
* *
293368 GTAAACTGGGCATCAACA
1 GTAAACCGGACATCAACA
293386 ATACACAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (18 bp):
GTAAACCGGACATCAACA
Found at i:294173 original size:19 final size:19
Alignment explanation
Indices: 294149--294187 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
294139 TAGTTCTTGG
*
294149 TTATTTCATTTTATTTTTT
1 TTATTTCATATTATTTTTT
*
294168 TTATTTTATATTATTTTTT
1 TTATTTCATATTATTTTTT
294187 T
1 T
294188 CCATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (19 bp):
TTATTTCATATTATTTTTT
Found at i:296882 original size:22 final size:23
Alignment explanation
Indices: 296841--296883 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
296831 CAACCTTAAT
296841 TCCTAATAAAATAATAAATCTGA
1 TCCTAATAAAATAATAAATCTGA
* *
296864 TCCTAA-AAGATAATTAATCT
1 TCCTAATAAAATAATAAATCT
296884 TCCTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (23 bp):
TCCTAATAAAATAATAAATCTGA
Found at i:296887 original size:20 final size:21
Alignment explanation
Indices: 296840--296888 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
296830 CCAACCTTAA
296840 TTCCTAATAAAATAATAAATC
1 TTCCTAATAAAATAATAAATC
* *
296861 TGATCCTAA-AAGATAATTAATC
1 T--TCCTAATAAAATAATAAATC
296883 TTCCTA
1 TTCCTA
296889 TATTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 5 0.21
21 1 0.04
22 12 0.50
23 6 0.25
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (21 bp):
TTCCTAATAAAATAATAAATC
Found at i:304061 original size:84 final size:83
Alignment explanation
Indices: 303943--304721 Score: 720
Period size: 84 Copynumber: 9.4 Consensus size: 83
303933 GCTAAAGACA
* * *
303943 AGAAGGGCTATTTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
304008 TGCAGCATAACTTAACTCA
65 TGCAGCATAACTTAAGTCT
* * * * *
304027 AGAAAGGTTATCTGCCAACCAAAGACATTCGAGTTAGACTATGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
304092 TACAGCATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCT
* ** * * * * *
304111 AAAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATT
1 AGAAGGGCTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
* * * *
304173 TACATCATAACTCAAGGCT
65 TGCAGCATAACTTAAGTCT
* * * *
304192 AGACGGGTTATCTTTCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGCTATC-TGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
304256 TGCAGCACAACTTAAGTCT
65 TGCAGCATAACTTAAGTCT
* * * * * *
304275 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGATCGACTACGCTCAGCT-CAACGACACATCAT
1 AGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* *
304339 TTGCAGCATAGCTTAAGTCG
64 TTGCAGCATAACTTAAGTCT
* * * * ** *
304359 AGAAAGGCTATCTG---CGAAAGATCTTCGAGTTCGACTACGCTCAACTCTGAGGCATATCATTT
1 AGAAGGGCTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
304421 ACAGCATAACTCAAGGCT
66 GCAGCATAACTTAAGTCT
* *
304439 AGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
304503 TGCAGCATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCT
* * ** * * *
304522 AGAAGGGCTATCTG---CCAAAGACCCTCGAGTTC-AGTTACATTTAGCTTCGAGGACACATCAT
1 AGAAGGGCTATCTGCAACCAAAGACCTTCGAGTTCGA-CTACGCTCAGCTCCAAGG-CACATCAT
* * *
304583 TTACAGCATAACTCAAGGCT
64 TTGCAGCATAACTTAAGTCT
* ** *
304603 AGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGGTCAGCTCCAAGGCACATCATTT
1 AGAAGGGCTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * *
304668 GCAGTATAGCCTAAGTCG
66 GCAGCATAACTTAAGTCT
* * *
304686 AGAAGGGCTATCTGCCAATCGAAGACCTCCGAGTTC
1 AGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTC
304722 AATTACATTC
Statistics
Matches: 554, Mismatches: 122, Indels: 38
0.78 0.17 0.05
Matches are distributed among these distances:
79 1 0.00
80 114 0.21
81 73 0.13
82 2 0.00
83 145 0.26
84 218 0.39
85 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (83 bp):
AGAAGGGCTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCT
Found at i:304387 original size:164 final size:161
Alignment explanation
Indices: 303963--304785 Score: 772
Period size: 164 Copynumber: 5.0 Consensus size: 161
303953 TTTGCCAACT
* * *
303963 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAACTCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * * * *
304028 GAAAGGTTATCTGCCAACCAAAGACATTCGAGTTAGACTATGCTCAGCTCCAAGGCACATCATTT
65 GAAGGGCTATCTG----CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * * *
304093 ACAGCATAGCTTAAGTCGAAAAGGGCTATCTG--CC
126 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGCACC
** * * * * * * * * * *
304127 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACATCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TC-AAGGCACATCATTTGCAGCATAGCTTAAGTCG
* * * *
304192 AGACGGGTTATCTTTCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTT
64 AGAAGGGCTATC-TGC--CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * * *
304257 GCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACA
126 ACAGCATAACTCAAGGCTAGAAGGGTTATCTG-C-ACC
* * *
304295 AAAGACCTTTGAGATCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGA
* * * * ** *
304360 GAAAGGCTATCTGCGAAAGATCTTCGAGTTCGACTACGCTCAACTCTGAGGCATATCATTTACAG
65 GAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAG
304425 CATAACTCAAGGCTAGAAGGGTTATCTGTCACC
130 CATAACTCAAGGCTAGAAGGGTTATCTG-CACC
*
304458 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * ** * * *
304523 GAAGGGCTATCTGCCAAAGACCCTCGAGTTC-AGTTACATTTAGCTTCGAGGACACATCATTTAC
65 GAAGGGCTATCTGCCAAAGACCTTCGAGTTCGA-CTACGCTCAGCTCCAAGG-CACATCATTTAC
*
304587 AGCATAACTCAAGGCTAGAAGGGTTATCTGTTACC
128 AGCATAACTCAAGGCTAGAAGGGTTATCTG-CACC
* * *
304622 AAAGACCTTCGAGTTCGACTACGGTCAGCTCCAAGGCACATCATTTGCAGTATAGCCTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * * ** * *
304687 GAAGGGCTATCTGCCAATCGAAGACCTCCGAGTTCAATTACATTCAGCT-CAGAGGCAAACCAAA
65 GAAGGGCTATCTGCC-A---AAGACCTTCGAGTTCGACTACGCTCAGCTCCA-AGGCACATC--A
* * *
304751 TTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTG
123 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
304786 TCAATAAAAT
Statistics
Matches: 552, Mismatches: 87, Indels: 35
0.82 0.13 0.05
Matches are distributed among these distances:
162 2 0.00
163 99 0.18
164 287 0.52
165 37 0.07
166 4 0.01
167 38 0.07
168 51 0.09
169 34 0.06
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (161 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGC
ATAACTCAAGGCTAGAAGGGTTATCTGCACC
Found at i:304692 original size:247 final size:244
Alignment explanation
Indices: 303943--304721 Score: 816
Period size: 247 Copynumber: 3.1 Consensus size: 244
303933 GCTAAAGACA
* * * *
303943 AGAAGGGCTATTTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
304008 TGCAGCATAACTTAACTCAAGAAAGGTTATCTGCCAACCAAAGACATTCGAGTT-AG-ACTATGC
65 TGCAGCATAACTTAAGTCAAGAAGGGTTATCTG-C--CCAAAGACCTTCGAGTTCAGTAC-AT--
* * *
304071 TCAGCTCCAAGG-CACATCATTTACAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCC
124 TCAGCTTCAAGGACACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCT
* * * * *
304135 CCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACA-TCATAACTCAAGGCT
189 TCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTACAGT-ATAACTCAAGGCT
* * *
304192 AGACGGGTTATCTTTCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTT
1 AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * * * **
304257 GCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGATCGACTACGCTCA
66 GCAGCATAACTTAAGTCAAGAAGGGTTATCTGCC--C-AAAGACCTTCGAGTTC-AGTACATTCA
* * * * *
304322 GC-TCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTGCGAAAGATCTTCG
127 GCTTCAAGGACACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCG
* ** *
304386 AGTTCGACTACGCTCAACTCTGAGGCATATCATTTACAGCATAACTCAAGGCT
192 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGTATAACTCAAGGCT
* *
304439 AGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * *
304504 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCTCGAGTTCAGTTACATTTAGCT
66 GCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCCAAAGACCTTCGAGTTCAG-TACATTCAGCT
* * * * * *
304568 TCGAGGACACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCG
130 TCAAGGACACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCTTCG
* * * * * *
304633 AGTTCGACTACGGTCAGCTCCAAGGCACATCATTTGCAGTATAGC-CTAAGTCG
192 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGTATAACTC-AAGGCT
* * * *
304686 AGAAGGGCTATCTGCCAATCGAAGACCTCCGAGTTC
1 AGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTC
304722 AATTACATTC
Statistics
Matches: 437, Mismatches: 78, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
242 1 0.00
243 20 0.05
244 41 0.09
245 1 0.00
246 2 0.00
247 190 0.43
248 165 0.38
249 14 0.03
250 1 0.00
251 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (244 bp):
AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCCAAAGACCTTCGAGTTCAGTACATTCAGCTT
CAAGGACACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTT
CGACTACGCTCAGCTCCAAGGCATATCATTTACAGTATAACTCAAGGCT
Found at i:305397 original size:11 final size:11
Alignment explanation
Indices: 305331--305397 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 11
305321 ATATTTTATT
305331 TTAT-TATATA
1 TTATCTATATA
*
305341 -TATATATATA
1 TTATCTATATA
*
305351 -TATATATATA
1 TTATCTATATA
*
305361 -TATATATATA
1 TTATCTATATA
*
305371 TATATATATATA
1 T-TATCTATATA
*
305383 TTATCTATATG
1 TTATCTATATA
305394 TTAT
1 TTAT
305398 ATAGTTTGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
9 3 0.06
10 26 0.50
11 12 0.23
12 11 0.21
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (11 bp):
TTATCTATATA
Found at i:305400 original size:2 final size:2
Alignment explanation
Indices: 305335--305392 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
305325 TTTATTTTAT
305335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
305377 TA TA TA T- TA TC TA TA T
1 TA TA TA TA TA TA TA TA T
305393 GTTATATAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:305628 original size:37 final size:36
Alignment explanation
Indices: 305519--305698 Score: 131
Period size: 39 Copynumber: 5.0 Consensus size: 36
305509 TGATATATAG
* * * * *
305519 GTTTTTGAAAAC-ATATACTATATAGTTCTGAAAAT
1 GTTTTTGAAAACTTTATATTATATAGTTTTAAAAAC
* * * *
305554 ATTTTT-AAAA-TATATATAATATA--TATAAAAA-
1 GTTTTTGAAAACTTTATATTATATAGTTTTAAAAAC
*
305585 GTTTTTTGAAAACTTGTATATTATATAGTTTTGAAAAC
1 G-TTTTTGAAAACTT-TATATTATATAGTTTTAAAAAC
*
305623 GTTTTTGAAAAAATTTACATATTATATAGTTTTAAAAAC
1 GTTTTTG-AAAACTTT--ATATTATATAGTTTTAAAAAC
*
305662 GTTTTTTAAAACTTATATATAATATATAG-TTTAAAAA
1 GTTTTTGAAAACTT-TATAT--TATATAGTTTTAAAAA
305699 TCATTTTGAA
Statistics
Matches: 117, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
32 11 0.09
33 4 0.03
34 15 0.13
35 15 0.13
37 17 0.15
38 21 0.18
39 34 0.29
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
GTTTTTGAAAACTTTATATTATATAGTTTTAAAAAC
Found at i:305688 original size:39 final size:38
Alignment explanation
Indices: 305555--305698 Score: 135
Period size: 39 Copynumber: 3.9 Consensus size: 38
305545 TCTGAAAATA
305555 TTTTTAAAA--TATATATAATATATA---TAAAAA-GT
1 TTTTTAAAACTTATATATAATATATAGTTTAAAAACGT
* *
305587 TTTTTGAAAACTTGTATAT--TATATAGTTTTGAAAACGT
1 TTTTT-AAAACTTATATATAATATATAG-TTTAAAAACGT
* * * *
305625 TTTTGAAAAAATT-TACATATTATATAGTTTTAAAAACGT
1 TTTT-TAAAACTTATATATAATATATAG-TTTAAAAACGT
305664 TTTTTAAAACTTATATATAATATATAGTTTAAAAA
1 TTTTTAAAACTTATATATAATATATAGTTTAAAAA
305699 TCATTTTGAA
Statistics
Matches: 90, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
32 5 0.06
33 10 0.11
35 6 0.07
37 9 0.10
38 26 0.29
39 34 0.38
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (38 bp):
TTTTTAAAACTTATATATAATATATAGTTTAAAAACGT
Found at i:306974 original size:18 final size:18
Alignment explanation
Indices: 306951--306987 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
306941 TAGTTCTTGG
*
306951 TTATTTCATTTTATTTTT
1 TTATTTCATATTATTTTT
*
306969 TTATTTTATATTATTTTT
1 TTATTTCATATTATTTTT
306987 T
1 T
306988 CCATTTTTTG
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:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATTTCATATTATTTTT
Found at i:310845 original size:45 final size:44
Alignment explanation
Indices: 310789--310897 Score: 121
Period size: 46 Copynumber: 2.4 Consensus size: 44
310779 TGCACCAATC
310789 CATGCATCGATGCACCATGAAATAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACCA-GAAATAAA-TGAAACATCGAATGCATTT
*** **
310834 CATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCAC-CAGAAATAAATG-AAACATCGAATGCATTT
*
310880 GATGCATCGATGCACCAG
1 CATGCATCGATGCACCAG
310898 CAATGCATCG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
44 2 0.04
45 21 0.38
46 32 0.58
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (44 bp):
CATGCATCGATGCACCAGAAATAAATGAAACATCGAATGCATTT
Found at i:310941 original size:64 final size:65
Alignment explanation
Indices: 310835--310958 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
310825 AATGCATTTC
**
310835 ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGCA
1 ATGCATCGATGCACTCAGACTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGCA
* *
310900 ATGCATCGATGCACTCAGACTATTT-TG-AAACATCGAATGCATTTTATGCATCGGTGCAC
1 ATGCATCGATGCACTCAGACT-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCAC
310959 TAGTGCACCG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
64 30 0.56
65 21 0.39
66 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (65 bp):
ATGCATCGATGCACTCAGACTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGCA
Found at i:311434 original size:30 final size:30
Alignment explanation
Indices: 311400--311538 Score: 91
Period size: 30 Copynumber: 4.8 Consensus size: 30
311390 TTCATCAAAA
*
311400 TATTAATTATTAAAATATTTAA-AATATATT
1 TATTAA-TATTAAAATATATAATAATATATT
*
311430 TATTAATATTTAAAATAATATAATATTATATT
1 TATTAATA-TTAAAAT-ATATAATAATATATT
* *
311462 T-TTAATATTATAATA-A-AATAATAAATT
1 TATTAATATTAAAATATATAATAATATATT
* *
311489 ATATT-ATA--ATAATATA-AGATATTATATT
1 -TATTAATATTAAAATATATA-ATAATATATT
*
311517 T-TT-ATTTTAAAAATATATAATA
1 TATTAATATT-AAAATATATAATA
311539 TTTTTTATAT
Statistics
Matches: 89, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
26 10 0.11
27 12 0.13
28 13 0.15
29 15 0.17
30 20 0.22
31 11 0.12
32 8 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
TATTAATATTAAAATATATAATAATATATT
Found at i:311460 original size:22 final size:23
Alignment explanation
Indices: 311413--311476 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
311403 TAATTATTAA
*
311413 AATATTTAAAAT-ATAT-TTATT
1 AATATTTAAAATAATATAATATT
311434 AATATTTAAAATAATATAATATT
1 AATATTTAAAATAATATAATATT
** *
311457 -ATATTTTTAATATTATAATA
1 AATATTTAAAATAATATAATA
311477 AAATAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 12 0.32
22 21 0.57
23 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTTAAAATAATATAATATT
Found at i:311470 original size:31 final size:30
Alignment explanation
Indices: 311424--311570 Score: 95
Period size: 30 Copynumber: 5.1 Consensus size: 30
311414 ATATTTAAAA
311424 TATATTTATTAATATTTAAAATAATATAATAT
1 TATATTT-TT-ATATTTAAAATAATATAATAT
* *
311456 TATATTTTTA-ATATTATAATAAAATAATA-
1 TATATTTTTATAT-TTAAAATAATATAATAT
*
311485 -A-A---TTATA-TTATAATAATATAAGATAT
1 TATATTTTTATATTTAAAATAATAT-A-ATAT
311511 TATATTTTTAT-TTTAAAA-ATATATAATAT
1 TATATTTTTATATTTAAAATA-ATATAATAT
* *
311540 T-T-TTTATATATTTAATAATGA-ATAATAT
1 TATATTTTTATATTTAA-AATAATATAATAT
311568 TAT
1 TAT
311571 TAATATAATA
Statistics
Matches: 93, Mismatches: 6, Indels: 35
0.69 0.04 0.26
Matches are distributed among these distances:
23 11 0.12
24 4 0.04
25 4 0.04
27 8 0.09
28 16 0.17
29 11 0.12
30 17 0.18
31 15 0.16
32 7 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
TATATTTTTATATTTAAAATAATATAATAT
Found at i:311491 original size:18 final size:18
Alignment explanation
Indices: 311468--311502 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
311458 TATTTTTAAT
311468 ATTATAATAAAATAATAA
1 ATTATAATAAAATAATAA
* *
311486 ATTATATTATAATAATA
1 ATTATAATAAAATAATA
311503 TAAGATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATAAAATAATAA
Found at i:311495 original size:23 final size:23
Alignment explanation
Indices: 311466--311516 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
311456 TATATTTTTA
*
311466 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAAGAAATT
* *
311489 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAAGAAATT
311512 ATATT
1 ATATT
311517 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAAGAAATT
Found at i:312003 original size:14 final size:15
Alignment explanation
Indices: 311982--312068 Score: 79
Period size: 15 Copynumber: 5.9 Consensus size: 15
311972 TTCCAAAAAT
*
311982 GTAATTCATTTTCTA
1 GTAATTCATTTTCCA
**
311997 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
312011 GTAATTCATTTTGCA
1 GTAATTCATTTTCCA
*
312026 GTAATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
** *
312041 GTAATTCAAATTACA
1 GTAATTCATTTTCCA
312056 GTAATTCATTTTC
1 GTAATTCATTTTC
312069 TAGAAAACCA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
14 15 0.26
15 39 0.67
16 4 0.07
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:312015 original size:29 final size:30
Alignment explanation
Indices: 311982--312063 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
311972 TTCCAAAAAT
311982 GTAATTCATTTT-CTAG-AATTCAAATTCCA
1 GTAATTCATTTTGC-AGTAATTCAAATTCCA
*
312011 GTAATTCATTTTGCAGTAATTCAAATTTCA
1 GTAATTCATTTTGCAGTAATTCAAATTCCA
** *
312041 GTAATTCAAATTACAGTAATTCA
1 GTAATTCATTTTGCAGTAATTCA
312064 TTTTCTAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
29 14 0.30
30 33 0.70
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (30 bp):
GTAATTCATTTTGCAGTAATTCAAATTCCA
Found at i:312018 original size:15 final size:15
Alignment explanation
Indices: 311998--312063 Score: 87
Period size: 15 Copynumber: 4.4 Consensus size: 15
311988 CATTTTCTAG
*
311998 AATTCAAATTCCAGT
1 AATTCAAATTACAGT
** *
312013 AATTCATTTTGCAGT
1 AATTCAAATTACAGT
*
312028 AATTCAAATTTCAGT
1 AATTCAAATTACAGT
312043 AATTCAAATTACAGT
1 AATTCAAATTACAGT
312058 AATTCA
1 AATTCA
312064 TTTTCTAGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (15 bp):
AATTCAAATTACAGT
Found at i:312050 original size:45 final size:44
Alignment explanation
Indices: 311982--312067 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 44
311972 TTCCAAAAAT
* *
311982 GTAATTCATTTTCTAGAATTCAAATTCCAGTAATTCATTTTGCA
1 GTAATTCAATTTCTAGAATTCAAATTACAGTAATTCATTTTGCA
312026 GTAATTCAAATTTC-AGTAATTCAAATTACAGTAATTCATTTT
1 GTAATTC-AATTTCTAG-AATTCAAATTACAGTAATTCATTTT
312068 CTAGAAAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 9 0.24
45 29 0.76
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (44 bp):
GTAATTCAATTTCTAGAATTCAAATTACAGTAATTCATTTTGCA
Found at i:314279 original size:57 final size:56
Alignment explanation
Indices: 314191--314304 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 56
314181 TACCTGAAAA
*
314191 ACTTGATACATTTGATGGTCTTGACATACAACTTAACTACGATAGATTGTTTATACC
1 ACTTGATACATTTGATAGTCTTGACATACAAC-TAACTACGATAGATTGTTTATACC
314248 ACTTGATACATTTGATAGTCTTGACATACAACTAACTACGATAGATTGTTTATACC
1 ACTTGATACATTTGATAGTCTTGACATACAACTAACTACGATAGATTGTTTATACC
314304 A
1 A
314305 ATAACACTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 25 0.45
57 31 0.55
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (56 bp):
ACTTGATACATTTGATAGTCTTGACATACAACTAACTACGATAGATTGTTTATACC
Found at i:314302 original size:26 final size:27
Alignment explanation
Indices: 314216--314302 Score: 72
Period size: 30 Copynumber: 3.1 Consensus size: 27
314206 TGGTCTTGAC
314216 ATACAACTTAACTACGATAGATTGTTT
1 ATACAACTTAACTACGATAGATTGTTT
* * * *
314243 ATACCACTTGA-TAC-ATTTGATAGTCTT
1 ATACAACTTAACTACGA-TAGATTGT-TT
314270 GACATACAAC-TAACTACGATAGATTGTTT
1 ---ATACAACTTAACTACGATAGATTGTTT
314299 ATAC
1 ATAC
314303 CAATAACACT
Statistics
Matches: 45, Mismatches: 8, Indels: 15
0.66 0.12 0.22
Matches are distributed among these distances:
25 1 0.02
26 13 0.29
27 11 0.24
29 4 0.09
30 15 0.33
31 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (27 bp):
ATACAACTTAACTACGATAGATTGTTT
Found at i:314890 original size:13 final size:13
Alignment explanation
Indices: 314856--314880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
314846 TTTGAGATAT
314856 TATATTTTTCTAA
1 TATATTTTTCTAA
314869 TATATTTTTCTA
1 TATATTTTTCTA
314881 TTGATTTTTT
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:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTTTTCTAA
Found at i:319756 original size:8 final size:8
Alignment explanation
Indices: 319745--319797 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
319735 AAATTTTGGC
319745 TTTTTTGT
1 TTTTTTGT
319753 TTTTTT-T
1 TTTTTTGT
*
319760 TGTTTTGT
1 TTTTTTGT
*
319768 CTTTTTGTCT
1 -TTTTT-TGT
319778 TTTTTTGT
1 TTTTTTGT
319786 TTTTTT-T
1 TTTTTTGT
319793 TTTTT
1 TTTTT
319798 GAAAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
7 12 0.32
8 15 0.39
9 9 0.24
10 2 0.05
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (8 bp):
TTTTTTGT
Found at i:319765 original size:24 final size:23
Alignment explanation
Indices: 319738--319788 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
319728 TTTTTTGAAA
*
319738 TTTTGGCTTTTTTGTTTTTTTTTG
1 TTTTGGC-TTTTTGTCTTTTTTTG
*
319762 TTTTGTCTTTTTGTCTTTTTTTG
1 TTTTGGCTTTTTGTCTTTTTTTG
319785 TTTT
1 TTTT
319789 TTTTTTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (23 bp):
TTTTGGCTTTTTGTCTTTTTTTG
Found at i:319774 original size:32 final size:32
Alignment explanation
Indices: 319738--319798 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
319728 TTTTTTGAAA
319738 TTTTGGC-TTTTTTGTTTTTTTTTGTTTTGTCT
1 TTTTGGCTTTTTTTGTTTTTTTTT-TTTTGTCT
*
319770 TTTTGTCTTTTTTTGTTTTTTTTTTTTTG
1 TTTTGGCTTTTTTTGTTTTTTTTTTTTTG
319799 AAAAAAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (32 bp):
TTTTGGCTTTTTTTGTTTTTTTTTTTTTGTCT
Found at i:319795 original size:23 final size:23
Alignment explanation
Indices: 319745--319796 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
319735 AAATTTTGGC
*
319745 TTTTTTGTTTTTTTTTGTTTTGT
1 TTTTTTGTCTTTTTTTGTTTTGT
* *
319768 CTTTTTGTCTTTTTTTGTTTTTT
1 TTTTTTGTCTTTTTTTGTTTTGT
319791 TTTTTT
1 TTTTTT
319797 TGAAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.87
Consensus pattern (23 bp):
TTTTTTGTCTTTTTTTGTTTTGT
Found at i:334842 original size:17 final size:17
Alignment explanation
Indices: 334810--334841 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
334800 CCACGTGTTA
334810 AAAAATGAATGAAAAAT
1 AAAAATGAATGAAAAAT
334827 AAAAATG-ATGAAAAA
1 AAAAATGAATGAAAAA
334842 AATTGTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (17 bp):
AAAAATGAATGAAAAAT
Found at i:341626 original size:23 final size:23
Alignment explanation
Indices: 341591--341634 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
341581 CTCAATTTAT
* *
341591 TTTTGCCAAGACATTTCCATTCA
1 TTTTACCAAGACATCTCCATTCA
*
341614 TTTTACCACGACATCTCCATT
1 TTTTACCAAGACATCTCCATT
341635 TGCTTCCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.30, G:0.07, T:0.39
Consensus pattern (23 bp):
TTTTACCAAGACATCTCCATTCA
Found at i:343506 original size:22 final size:22
Alignment explanation
Indices: 343478--343522 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
343468 TCCTTTCATC
343478 TAGAATGTTATGCGAAGACTTA
1 TAGAATGTTATGCGAAGACTTA
343500 TAGAATGTTATGCGAAGACTTA
1 TAGAATGTTATGCGAAGACTTA
343522 T
1 T
343523 TTATTAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (22 bp):
TAGAATGTTATGCGAAGACTTA
Found at i:344930 original size:81 final size:81
Alignment explanation
Indices: 344810--346088 Score: 1896
Period size: 81 Copynumber: 15.8 Consensus size: 81
344800 GGCATATAGT
** * * *
344810 CTTTCATCTAACTTACATGATTGAAACATTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
344875 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
344891 CTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
344956 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
344972 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCCATGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
* * *
345037 CTCAAAGGCATATAGC
66 CTCAAAGGTATTTAAC
* * * *
345053 CTTTCATCTAACTTGCATGATTGACACCTTTCTG-CAAATGCACAGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
*
345117 CTCAAAGATATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
345133 CTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCATAACTAGGTTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
345198 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* *
345214 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCTATTACTCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
*
345279 CTCAATGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
345295 ATTTCATCTAGCTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCTATTACTCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
* *
345360 CTCATATGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
345376 ATTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
345441 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * * *
345457 CTTTCATCTAACTGACACAATTGACACATTTCTATCAAATACACAGCTAGGTTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
345522 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
345538 CTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCTATTAATATTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
* *
345603 TTCAAATGTATTTAAC
66 CTCAAAGGTATTTAAC
* *
345619 ATTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
345684 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
*
345700 ATTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
*
345765 CTAAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
345781 CTTTCATCTAACTGGCATAATTGAGACATTTATGTCAAATGCACAGCTAAG-TCATTAATATTTT
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCT-ATTAATCTTTT
* *
345845 AGTTAAAGGTATTTAAC
65 ACTCAAAGGTATTTAAC
* * * * * *
345862 ATTTCATCTAACTGACATAATTGGCACCTTTCTGTCAAATGCACAGGTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
*
345927 CTCAAAGATATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
345943 CTTTCATCTAACTGGAATAATCGACACCTTTCTGTTAAATGCACAGCTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
*
346008 CTCAATGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
346024 CTTTCATATAAATAGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
346089 TTTTGGAATA
Statistics
Matches: 1081, Mismatches: 114, Indels: 6
0.90 0.09 0.00
Matches are distributed among these distances:
80 70 0.06
81 1011 0.94
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (81 bp):
CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTA
CTCAAAGGTATTTAAC
Found at i:354960 original size:20 final size:21
Alignment explanation
Indices: 354935--354995 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
354925 TTTTGGTGCA
*
354935 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
354955 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
354976 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
354996 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.23
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:355003 original size:20 final size:20
Alignment explanation
Indices: 354978--355015 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
354968 CCCCCTTTGA
*
354978 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
354998 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
355016 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:368301 original size:2 final size:2
Alignment explanation
Indices: 368294--368340 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
368284 TTTATCCTAA
368294 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
368336 AT AT A
1 AT AT A
368341 ATGAAACCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:369721 original size:31 final size:31
Alignment explanation
Indices: 369653--369721 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
369643 TTAGATAAAC
* *
369653 TAATA-TTTATTCATTTAATTATTTTTGTAA
1 TAATATTTTAATCATTTAATTATTTTTATAA
** * *
369683 TTTTATTTTAATCGTTTAATTTTTTTTATAA
1 TAATATTTTAATCATTTAATTATTTTTATAA
369714 TAATATTT
1 TAATATTT
369722 AAAATTATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (31 bp):
TAATATTTTAATCATTTAATTATTTTTATAA
Found at i:371807 original size:20 final size:20
Alignment explanation
Indices: 371774--371812 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
371764 TTCGTGTTTG
* *
371774 GCCGCCGATGAACGACGGCC
1 GCCGCAGATCAACGACGGCC
*
371794 GCCGCAGATCAACGGCGGC
1 GCCGCAGATCAACGACGGC
371813 GGCAAGGCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.38, G:0.36, T:0.05
Consensus pattern (20 bp):
GCCGCAGATCAACGACGGCC
Found at i:372332 original size:22 final size:24
Alignment explanation
Indices: 372289--372347 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
372279 CATCATATCA
*
372289 TTTTCATTTTATTTACTATA-T-T
1 TTTTTATTTTATTTACTATATTCT
*
372311 TTTTTATTTTATTTTC-ATTATTCCT
1 TTTTTATTTTATTTACTA-TATT-CT
372336 TTTTTATTTTAT
1 TTTTTATTTTAT
372348 ATGTACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 16 0.52
23 1 0.03
25 13 0.42
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTATTTTATTTACTATATTCT
Found at i:372462 original size:26 final size:26
Alignment explanation
Indices: 372396--372471 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 26
372386 TTTAGTTTTT
*
372396 TTTAT-TTATTACTATTATATATATC
1 TTTATATTATTACCATTATATATATC
* * * * *
372421 TTTTTATTTTTCCCATTGTTTATATC
1 TTTATATTATTACCATTATATATATC
*
372447 TTTATATTATTACCATCATATATAT
1 TTTATATTATTACCATTATATATAT
372472 TATTTTTATA
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
25 4 0.11
26 34 0.89
ACGTcount: A:0.28, C:0.12, G:0.01, T:0.59
Consensus pattern (26 bp):
TTTATATTATTACCATTATATATATC
Found at i:383961 original size:105 final size:105
Alignment explanation
Indices: 383779--384684 Score: 1483
Period size: 105 Copynumber: 8.6 Consensus size: 105
383769 CAAGTTCAAT
*
383779 GGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGAT
1 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
383844 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
66 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
383884 GGACCGTTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
1 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
383949 ATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
66 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
383989 GGACCGCTGGTTGTCAACAAACA--TCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGAT
1 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
384052 ATTGGACTACAGACAACGCAAGTTCAACTTCACGACGAAG
66 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
384092 GGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAATTTCACAATGAAGGAT
1 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
384157 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
66 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
384197 GGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATGTCAACTTCACAACGAAGGAT
1 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
384262 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAG
66 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* **
384302 GGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCTGCTTCACAACGAAGGAT
1 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
384367 ATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAG
66 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
384407 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTTAACTTCACAACGAAGGAT
1 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
384472 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
66 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
384512 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTTAGAGCCAATTTTAACTTCACAACGAAGGAT
1 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
384577 GTTGGACTCCAGACAACGCAAGTTCAAACTTCATGACGAAG
66 ATTGGACTCCAGACAACGCAAGTTC-AACTTCACGACGAAG
* * * ** * *
384618 GGACCGCTGGTTGTCAATAAACAACTTCTCAATTTTAGAGCTCGTTTTCAACTTCACGACGAGGG
1 GGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGC-CAATTTCAACTTCACAACGAAGG
384683 AT
64 AT
384685 TTCGTGCTCG
Statistics
Matches: 752, Mismatches: 44, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
103 97 0.13
105 583 0.78
106 35 0.05
107 17 0.02
108 20 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (105 bp):
GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
Found at i:385656 original size:20 final size:20
Alignment explanation
Indices: 385623--385661 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
385613 TTCGTGTTTG
*
385623 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
* *
385643 GCCGCGGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
385662 GGCAAGGCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.38, G:0.38, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:386264 original size:17 final size:17
Alignment explanation
Indices: 386220--386271 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
386210 TATATGTACA
*
386220 TATTTGATTATAGTTATT
1 TATTT-ATTTTAGTTATT
386238 TATTTATTTTAGTT-TT
1 TATTTATTTTAGTTATT
* *
386254 TAGTTTTTTTTATTTATT
1 TA-TTTATTTTAGTTATT
386272 ACTATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 4 0.14
17 18 0.62
18 7 0.24
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (17 bp):
TATTTATTTTAGTTATT
Found at i:386348 original size:27 final size:27
Alignment explanation
Indices: 386259--386348 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
386249 GTTTTTAGTT
*
386259 TTTTTTATTTATTACTATTATATATATC
1 TTTTTTA-TTATTACCATTATATATATC
* * * *
386287 TTTTTTATTTTTCCCATTGTTTATATC
1 TTTTTTATTATTACCATTATATATATC
* *
386314 TTTATTATTATTACCATCATATATAT-
1 TTTTTTATTATTACCATTATATATATC
386340 TATTTTTAT
1 T-TTTTTAT
386349 ATTCTATATT
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
26 1 0.02
27 41 0.84
28 7 0.14
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (27 bp):
TTTTTTATTATTACCATTATATATATC
Found at i:387027 original size:21 final size:21
Alignment explanation
Indices: 386965--387027 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
386955 ATTACTGTGG
* **
386965 ACTGTCACATCAATATTGTGG
1 ACTGTCACATCAACATTGTAA
** * *
386986 ACTGTCATGTCAGCATCGTAA
1 ACTGTCACATCAACATTGTAA
387007 ACTGTCACATCAACATTGTAA
1 ACTGTCACATCAACATTGTAA
387028 TGGTTAACAT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (21 bp):
ACTGTCACATCAACATTGTAA
Found at i:390348 original size:25 final size:25
Alignment explanation
Indices: 390320--390374 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
390310 TTAATATTTT
* *
390320 TATTTAATCATATT-AAAAATATGAA
1 TATTT-ATCACATTAAAAAATATAAA
*
390345 TATTTTTCACATTAAAAAATATAAA
1 TATTTATCACATTAAAAAATATAAA
390370 TATTT
1 TATTT
390375 TTCATTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TATTTATCACATTAAAAAATATAAA
Found at i:390349 original size:31 final size:33
Alignment explanation
Indices: 390291--390351 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
390281 ATATTATTAA
* *
390291 TAATTATATATAAAACATATTAATATTTTTATT
1 TAATCATATATAAAACATATGAATATTTTTATT
390324 TAATCATAT-TAAAA-ATATGAATATTTTT
1 TAATCATATATAAAACATATGAATATTTTT
390352 CACATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 13 0.50
32 5 0.19
33 8 0.31
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (33 bp):
TAATCATATATAAAACATATGAATATTTTTATT
Found at i:390388 original size:25 final size:24
Alignment explanation
Indices: 390334--390387 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
390324 TAATCATATT
*
390334 AAAAATATGAATATTTTTCACATTA
1 AAAAATATAAATATTTTT-ACATTA
390359 AAAAATATAAATATTTTT-CATTA
1 AAAAATATAAATATTTTTACATTA
390382 ACAAAA
1 A-AAAA
390388 AGTATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 4 0.15
25 17 0.63
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (24 bp):
AAAAATATAAATATTTTTACATTA
Found at i:390901 original size:18 final size:19
Alignment explanation
Indices: 390875--390916 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
390865 TTTAATAAAA
* *
390875 ATAAAAAATATTTA-AATT
1 ATAATAAATATTTACAATC
*
390893 ATAATAAATGTTTACAATC
1 ATAATAAATATTTACAATC
390912 ATAAT
1 ATAAT
390917 TTATTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAATAAATATTTACAATC
Found at i:391659 original size:31 final size:31
Alignment explanation
Indices: 391583--391660 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
391573 CTTTTAAAAC
*
391583 TTGCAATATAATCCCTCAAAATTTAGTCCGT
1 TTGCAATATAGTCCCTCAAAATTTAGTCCGT
* *
391614 TTGCAATATTGTCCCTCAACATTTAGTCCGT
1 TTGCAATATAGTCCCTCAAAATTTAGTCCGT
*
391645 TTGCAATATGGTCCCT
1 TTGCAATATAGTCCCT
391661 GACGTAACTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (31 bp):
TTGCAATATAGTCCCTCAAAATTTAGTCCGT
Found at i:392937 original size:31 final size:31
Alignment explanation
Indices: 392899--392964 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
392889 AGTTACGTCG
392899 GGGACCATATTGCAAACCG-ACTAAATGTTGA
1 GGGACCATATTGCAAA-CGAACTAAATGTTGA
* *
392930 GGGACCATGTTGCAAACGAACTAAATGTTGG
1 GGGACCATATTGCAAACGAACTAAATGTTGA
392961 GGGA
1 GGGA
392965 TTATATTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (31 bp):
GGGACCATATTGCAAACGAACTAAATGTTGA
Found at i:393417 original size:58 final size:57
Alignment explanation
Indices: 393329--393497 Score: 162
Period size: 58 Copynumber: 2.9 Consensus size: 57
393319 ATATGACCCT
* * *
393329 CATTTTAAATTAATCCTTAAACTTTAAACATTTCAATTTCATCTCTAAATTATGA-CTAA
1 CATTCTAAATTAGTCCTCAAACTTT-AACATTTCAATTTCATC-CTAAATTATGATCT-A
* * * * *
393388 CATTCT-AATTAGTCCTCAAACTTCTAACATTCCATTTTCATCCCCAAACTATGATCTT
1 CATTCTAAATTAGTCCTCAAACTT-TAACATTTCAATTTCAT-CCTAAATTATGATCTA
* * * *
393446 CATTTTAAATTAGGCCTCAAACTTTTTACATTTCAATTTGATCCTAAATTAT
1 CATTCTAAATTAGTCCTCAAAC-TTTAACATTTCAATTTCATCCTAAATTAT
393498 ACGTATATAC
Statistics
Matches: 89, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
58 51 0.57
59 36 0.40
60 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (57 bp):
CATTCTAAATTAGTCCTCAAACTTTAACATTTCAATTTCATCCTAAATTATGATCTA
Found at i:393477 original size:59 final size:57
Alignment explanation
Indices: 393310--393489 Score: 164
Period size: 59 Copynumber: 3.1 Consensus size: 57
393300 TGCATCATAT
* * * * *
393310 ATCCCCAATATATGACCCTCATTTTAAATTAATCCTTAAACTTTAAACATTTCAATTTC
1 ATCCCCAA-ATATGA-CTTCATTTTAAATTAGTCCTCAAACTTTTAACATTCCAATTTC
* * * * * *
393369 ATCTCTAAATTATGACTAACATTCT-AATTAGTCCTCAAACTTCTAACATTCCATTTTC
1 ATCCCCAAA-TATGACT-TCATTTTAAATTAGTCCTCAAACTTTTAACATTCCAATTTC
* * * *
393427 ATCCCCAAACTATGATCTTCATTTTAAATTAGGCCTCAAACTTTTTACATTTCAATTTG
1 ATCCCCAAA-TATGA-CTTCATTTTAAATTAGTCCTCAAACTTTTAACATTCCAATTTC
393486 ATCC
1 ATCC
393490 TAAATTATAC
Statistics
Matches: 95, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
58 46 0.48
59 49 0.52
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (57 bp):
ATCCCCAAATATGACTTCATTTTAAATTAGTCCTCAAACTTTTAACATTCCAATTTC
Found at i:393705 original size:60 final size:60
Alignment explanation
Indices: 393619--393782 Score: 188
Period size: 60 Copynumber: 2.8 Consensus size: 60
393609 TTTGGATGAA
* * * * * ***
393619 TTTGGGGAT-AAATTGGAA-GATGCAAAAGTTTAGGGACCAATTTTGAATGATATTGATAG
1 TTTGGGGATGAAATTGGAATG-TTCAAAAGTTTAAGGACTAATTTAGAATGAGAGCCATAG
*
393678 TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGATTAATTTAGAATGAGAGCCATAG
1 TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGCCATAG
** * *
393738 TTTTAGGATGAAATTAGAATGTTTAAAAGTTTAAGGACTAATTTA
1 TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTA
393783 TATTAAGGGT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 9 0.10
60 79 0.89
61 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (60 bp):
TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGCCATAG
Found at i:393715 original size:29 final size:29
Alignment explanation
Indices: 393683--393774 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
393673 GATAGTTTGG
*
393683 GGATGAAATTGGAATGTTCAAAAGTTTAA
1 GGATGAAATTAGAATGTTCAAAAGTTTAA
* * ** * * *
393712 GGATTAATTTAGAATGAGAGCCATAGTTTTA
1 GGATGAAATTAGAAT--GTTCAAAAGTTTAA
*
393743 GGATGAAATTAGAATGTTTAAAAGTTTAA
1 GGATGAAATTAGAATGTTCAAAAGTTTAA
393772 GGA
1 GGA
393775 CTAATTTATA
Statistics
Matches: 45, Mismatches: 16, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
29 23 0.51
31 22 0.49
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (29 bp):
GGATGAAATTAGAATGTTCAAAAGTTTAA
Found at i:393797 original size:60 final size:60
Alignment explanation
Indices: 393674--393803 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 60
393664 AATGATATTG
* * * *
393674 ATAGTTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGATTAATTTAGAATGAGAGCC
1 ATAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATAAGAGCC
* * * * * *
393734 ATAGTTTTAGGATGAAATTAGAATGTTTAAAAGTTTAAGGACTAATTTATATTAAGGGTC
1 ATAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATAAGAGCC
393794 ATAGTTTGAG
1 ATAGTTTGAG
393804 AACATGTGTG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (60 bp):
ATAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATAAGAGCC
Found at i:398040 original size:2 final size:2
Alignment explanation
Indices: 398033--398059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
398023 TATATTAAAT
398033 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 T
398060 GGGAAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:398894 original size:3 final size:3
Alignment explanation
Indices: 398881--398929 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
398871 TAGTTTGAAA
398881 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
398928 AA
1 AA
398930 CAGATTCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:399881 original size:139 final size:134
Alignment explanation
Indices: 399574--399928 Score: 410
Period size: 139 Copynumber: 2.6 Consensus size: 134
399564 ACAAGAGGTT
* * *
399574 GAACAAGTTCTTCTTATTATGAACTTCTT-TTTCTTCTTCAGGTGAGTTCTTCTCATTATGAA-T
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATGAGTTCTTCTCATTATGAACT
* * * * * *
399637 TCCTTCTGGAAATGATGATCCTCAAAAGAGGTGTTGATTCAACTTCATATGTGATGAATTAAGGC
65 T-CATCTGGAAATGTTGATCCTCAAAAGAGGTGTTCATTCAACTCCATAGGTGATGAATCAAGGC
* *
399702 AAGGTT
129 AAAGTC
* * * *
399708 GAATAAGTTATTATCATTATGAACTTCTTCTTCCTTTTCAGACGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAACTT
* * ** *
399773 CGTCTGAAAATGTTGATCCTCAAGTGAGGTTCTTCTTTCATTCAACTCCATAGGTGATGAATCAA
66 CATCTGGAAATGTTGATCCTCAAAAGAGG----T-GTTCATTCAACTCCATAGGTGATGAATCAA
399838 -GCTAAAGTC
126 GGC-AAAGTC
* *
399847 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAACTT
*
399912 TATCTGGAAATGTTGAT
66 CATCTGGAAATGTTGAT
399929 GCTGATCTAT
Statistics
Matches: 185, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
134 73 0.39
135 7 0.04
138 3 0.02
139 102 0.55
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (134 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAACTT
CATCTGGAAATGTTGATCCTCAAAAGAGGTGTTCATTCAACTCCATAGGTGATGAATCAAGGCAA
AGTC
Found at i:400167 original size:113 final size:113
Alignment explanation
Indices: 399959--400394 Score: 626
Period size: 113 Copynumber: 3.9 Consensus size: 113
399949 GATAGAGTTA
* * * *
399959 AGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTT-TTTCTTCTTCAGATAAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
400023 CATTATGAACTTTA-TCTGGAAAAGTTAATCCATCGAGTGATGAATTTG
66 CATTATGAAC-TTACTCTGGAAAAGTTGATCCATCAAGTGATGAATTTG
* *
400071 AGCAAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * **
400136 CATTATGAACTCTAC-CTGGCAATGCTGATCCATCAAATGATGAATTCA
66 CATTATGAACT-TACTCTGGAAAAGTTGATCCATCAAGTGATGAATTTG
* *
400184 AACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTGTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
400249 TATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTG
66 CATTATGAACTTACTCTGGAAAAGTTGATCCATCAAGTGATGAATTTG
**
400297 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
400362 CATTATGAACTTTCTCTGGAAATGTTGATCCAT
66 CATTATGAACTTACTCTGGAAAAGTTGATCCAT
400395 TGTGATGGAT
Statistics
Matches: 287, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
112 39 0.14
113 248 0.86
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTTACTCTGGAAAAGTTGATCCATCAAGTGATGAATTTG
Found at i:400269 original size:226 final size:225
Alignment explanation
Indices: 399961--400394 Score: 699
Period size: 226 Copynumber: 1.9 Consensus size: 225
399951 TAGAGTTAAG
* * *
399961 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCTTCTTCAGATAAGTTCTTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATAAGTTCTTCTCAT
* *
400026 TATGAACTTTATCTGGAAAAGTTAATCCATCGAGTGATGAATTTGAGCAAAAGGTTAAACAAATT
66 TATGAACTTTATCTGGAAAAGTTAATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAACT
*
400091 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGG
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGG
*
400155 CAATGCTGATCCATCAAATGATGAATTCAAA
195 AAATGCTGATCCATCAAATGATGAATTCAAA
* *
400186 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTGTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATAAGTTCTTCTCA
* * * * *
400251 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
65 TTATGAACTTTATCTGGAAAAGTTAATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAC
*
400316 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGG
*
400381 AAATGTTGATCCAT
195 AAATGCTGATCCAT
400395 TGTGATGGAT
Statistics
Matches: 191, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
225 38 0.20
226 153 0.80
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (225 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTATCTGGAAAAGTTAATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAACT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGA
AATGCTGATCCATCAAATGATGAATTCAAA
Found at i:403683 original size:114 final size:114
Alignment explanation
Indices: 403492--403718 Score: 409
Period size: 114 Copynumber: 2.0 Consensus size: 114
403482 GACTATCATC
* * *
403492 AAATTCATCTTTTAAATCCAATGATTGGTTATAGGGTTCATACCGAACCAGATCATATAACTCAA
1 AAATTCATCTTTCAAATCCAATGATTGGTTATAGGGTTCATACCAAACCAGATCAGATAACTCAA
403557 AGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGT
66 AGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGT
* *
403606 AAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
1 AAATTCATCTTTCAAATCCAATGATTGGTTATAGGGTTCATACCAAACCAGATCAGATAACTCAA
403671 AGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 AGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
403719 AACGTGGAAC
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (114 bp):
AAATTCATCTTTCAAATCCAATGATTGGTTATAGGGTTCATACCAAACCAGATCAGATAACTCAA
AGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGT
Found at i:405388 original size:32 final size:32
Alignment explanation
Indices: 405347--405409 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
405337 TGAAGAAATG
* *
405347 ATTGTTATGCTCATCTTGTAGAGATACTTCTC
1 ATTGTTATGCTCATATCGTAGAGATACTTCTC
405379 ATTGTTATGCTCATATCGTAGAGATACTTCT
1 ATTGTTATGCTCATATCGTAGAGATACTTCT
405410 TGTGTCTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (32 bp):
ATTGTTATGCTCATATCGTAGAGATACTTCTC
Found at i:405911 original size:9 final size:8
Alignment explanation
Indices: 405894--405956 Score: 83
Period size: 8 Copynumber: 7.8 Consensus size: 8
405884 CTTGGTTCAA
405894 TTTTTCTT
1 TTTTTCTT
*
405902 TTTTTCCT
1 TTTTTCTT
405910 TTTTTC-T
1 TTTTTCTT
405917 TTTTTCTT
1 TTTTTCTT
405925 CTTTTTCTT
1 -TTTTTCTT
*
405934 TTTTTCCT
1 TTTTTCTT
405942 TTTTTCTAT
1 TTTTTCT-T
405951 TTTTTC
1 TTTTTC
405957 AAGCATAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
7 7 0.14
8 27 0.55
9 15 0.31
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:405915 original size:16 final size:16
Alignment explanation
Indices: 405894--405956 Score: 92
Period size: 16 Copynumber: 3.9 Consensus size: 16
405884 CTTGGTTCAA
405894 TTTTTCTTTTTTTCCT
1 TTTTTCTTTTTTTCCT
*
405910 TTTTTC-TTTTTTCTT
1 TTTTTCTTTTTTTCCT
405925 CTTTTTCTTTTTTTCCT
1 -TTTTTCTTTTTTTCCT
405942 TTTTTCTATTTTTTC
1 TTTTTCT-TTTTTTC
405957 AAGCATAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
15 8 0.19
16 19 0.45
17 15 0.36
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTTTCCT
Found at i:406409 original size:165 final size:165
Alignment explanation
Indices: 406147--406608 Score: 728
Period size: 165 Copynumber: 2.8 Consensus size: 165
406137 TAGATCGCTC
* * ** * * *
406147 TCTTGGAACTCTCTCAGATGTACTTTCTTGTTGTGATCTTTCATCATCCACTTCTGATACATCTA
1 TCTTGGAACTCTCTTAGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
* * **
406212 CCCATGGCAAATAACTTTCAAT-ACATTCTCATCAATAAACCTTAATTGATCAAATCAAGCTTGG
66 CCCATGGCAAATAGCTTTCAATCTCA-TCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGG
*
406276 ATCTATTCAATCTCCTTTTTTAGCACTAGATCAACA
130 ATCTATCCAATCTCCTTTTTTAGCACTAGATCAACA
* *
406312 TCTTGGAACTCTCTTGGATGTACTTTCTTGTTATGATATTTCATCATCCGTTTTTGATATATCTG
1 TCTTGGAACTCTCTTAGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
*
406377 CCTATGGCAAATAGCTTTCAATCTCATCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGGA
66 CCCATGGCAAATAGCTTTCAATCTCATCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGGA
*
406442 TCTATCCAGTCTCCTTTTTTAGCACTAGATCAACA
131 TCTATCCAATCTCCTTTTTTAGCACTAGATCAACA
406477 TCTTGGAACTCTCTTAGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
1 TCTTGGAACTCTCTTAGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
* * * *
406542 CCCATGGCAAATAGCTTTCAATCTCATCTTATCAATAAGGTTTAATTGATCAAATCGAGTTTGGA
66 CCCATGGCAAATAGCTTTCAATCTCATCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGGA
406607 TC
131 TC
406609 CCTTCAGCCT
Statistics
Matches: 273, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
165 271 0.99
166 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (165 bp):
TCTTGGAACTCTCTTAGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
CCCATGGCAAATAGCTTTCAATCTCATCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGGA
TCTATCCAATCTCCTTTTTTAGCACTAGATCAACA
Found at i:412988 original size:3 final size:3
Alignment explanation
Indices: 412980--413032 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
412970 TAGTTTGAAA
412980 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
413028 AAT AA
1 AAT AA
413033 CAGATTCAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:414213 original size:7 final size:7
Alignment explanation
Indices: 414201--414237 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
414191 TGGGGTCGGC
414201 AGAAGCG
1 AGAAGCG
414208 AGAAGCG
1 AGAAGCG
414215 AGAAGCG
1 AGAAGCG
414222 AGAAGCG
1 AGAAGCG
414229 AGAAGCG
1 AGAAGCG
414236 AG
1 AG
414238 GCAGCTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.43, T:0.00
Consensus pattern (7 bp):
AGAAGCG
Done.