Multiple sequence alignment - TraesCS1A01G300000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G300000 chr1A 100.000 4170 0 0 1 4170 494798446 494802615 0.000000e+00 7701.0
1 TraesCS1A01G300000 chr1A 95.349 43 2 0 194 236 443024679 443024721 7.480000e-08 69.4
2 TraesCS1A01G300000 chr1D 91.283 3304 156 56 941 4170 397284911 397288156 0.000000e+00 4385.0
3 TraesCS1A01G300000 chr1D 89.759 166 13 3 234 399 397283482 397283643 4.220000e-50 209.0
4 TraesCS1A01G300000 chr1D 95.614 114 4 1 39 152 397283330 397283442 9.210000e-42 182.0
5 TraesCS1A01G300000 chr1D 97.500 40 1 0 4131 4170 397379167 397379206 7.480000e-08 69.4
6 TraesCS1A01G300000 chr1B 89.478 3317 190 64 941 4170 532693134 532696378 0.000000e+00 4045.0
7 TraesCS1A01G300000 chr1B 90.863 197 8 3 1 197 532690116 532690302 5.350000e-64 255.0
8 TraesCS1A01G300000 chr1B 89.305 187 17 2 475 661 532662405 532662588 9.020000e-57 231.0
9 TraesCS1A01G300000 chr1B 85.849 212 9 6 1 197 532661787 532661992 5.460000e-49 206.0
10 TraesCS1A01G300000 chr1B 90.541 148 14 0 514 661 532692600 532692747 3.290000e-46 196.0
11 TraesCS1A01G300000 chr2D 95.537 1210 50 2 1199 2408 432871710 432870505 0.000000e+00 1932.0
12 TraesCS1A01G300000 chr2D 93.333 90 4 1 2471 2558 432870494 432870405 9.410000e-27 132.0
13 TraesCS1A01G300000 chr3D 82.341 1914 312 22 1165 3065 452619466 452617566 0.000000e+00 1639.0
14 TraesCS1A01G300000 chr3A 82.288 1914 311 24 1165 3064 595061499 595059600 0.000000e+00 1631.0
15 TraesCS1A01G300000 chr3A 97.619 42 1 0 195 236 727377513 727377472 5.780000e-09 73.1
16 TraesCS1A01G300000 chr3A 95.349 43 2 0 194 236 163626988 163627030 7.480000e-08 69.4
17 TraesCS1A01G300000 chr3B 95.652 46 2 0 192 237 694171832 694171787 1.610000e-09 75.0
18 TraesCS1A01G300000 chr6D 97.619 42 1 0 195 236 47270733 47270692 5.780000e-09 73.1
19 TraesCS1A01G300000 chr6D 97.619 42 1 0 195 236 426281999 426282040 5.780000e-09 73.1
20 TraesCS1A01G300000 chr5A 97.619 42 1 0 195 236 623013102 623013061 5.780000e-09 73.1
21 TraesCS1A01G300000 chrUn 95.349 43 2 0 194 236 318992593 318992635 7.480000e-08 69.4
22 TraesCS1A01G300000 chr7D 93.478 46 3 0 191 236 151024029 151024074 7.480000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G300000 chr1A 494798446 494802615 4169 False 7701.000000 7701 100.000000 1 4170 1 chr1A.!!$F2 4169
1 TraesCS1A01G300000 chr1D 397283330 397288156 4826 False 1592.000000 4385 92.218667 39 4170 3 chr1D.!!$F2 4131
2 TraesCS1A01G300000 chr1B 532690116 532696378 6262 False 1498.666667 4045 90.294000 1 4170 3 chr1B.!!$F2 4169
3 TraesCS1A01G300000 chr1B 532661787 532662588 801 False 218.500000 231 87.577000 1 661 2 chr1B.!!$F1 660
4 TraesCS1A01G300000 chr2D 432870405 432871710 1305 True 1032.000000 1932 94.435000 1199 2558 2 chr2D.!!$R1 1359
5 TraesCS1A01G300000 chr3D 452617566 452619466 1900 True 1639.000000 1639 82.341000 1165 3065 1 chr3D.!!$R1 1900
6 TraesCS1A01G300000 chr3A 595059600 595061499 1899 True 1631.000000 1631 82.288000 1165 3064 1 chr3A.!!$R1 1899

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
151 167 0.109086 CTCTGACGTGAATGTCGCCT 60.109 55.0 0.0 0.0 41.87 5.52 F
1002 3618 0.179097 GCCCTCCACTTCGTCTCATC 60.179 60.0 0.0 0.0 0.00 2.92 F
1318 3955 0.880278 TGTTTGACGACCTGCTGCTC 60.880 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 3722 0.957395 ATTGCGGCAACCAGACTCAG 60.957 55.000 18.94 0.0 0.00 3.35 R
1978 4621 1.443872 GTCGTACGTCTGGCCACTG 60.444 63.158 16.05 0.0 0.00 3.66 R
3228 5898 0.373716 GGCTAAAGAATCGCACCACG 59.626 55.000 0.00 0.0 45.62 4.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 1.201343 GAGGCGAGCGACTGTTAATC 58.799 55.000 1.53 0.00 30.74 1.75
147 163 4.041049 CAGCTATCTCTGACGTGAATGTC 58.959 47.826 0.00 0.00 39.37 3.06
151 167 0.109086 CTCTGACGTGAATGTCGCCT 60.109 55.000 0.00 0.00 41.87 5.52
152 168 0.317160 TCTGACGTGAATGTCGCCTT 59.683 50.000 0.00 0.00 41.87 4.35
155 171 0.865769 GACGTGAATGTCGCCTTTGT 59.134 50.000 0.00 0.00 0.00 2.83
187 203 2.715532 TTCGTTGCTCTCGGCTTGCT 62.716 55.000 0.00 0.00 42.39 3.91
197 213 3.090037 TCTCGGCTTGCTACTTTCTACT 58.910 45.455 0.00 0.00 0.00 2.57
198 214 3.128938 TCTCGGCTTGCTACTTTCTACTC 59.871 47.826 0.00 0.00 0.00 2.59
199 215 2.165845 TCGGCTTGCTACTTTCTACTCC 59.834 50.000 0.00 0.00 0.00 3.85
200 216 2.738964 CGGCTTGCTACTTTCTACTCCC 60.739 54.545 0.00 0.00 0.00 4.30
201 217 2.502130 GGCTTGCTACTTTCTACTCCCT 59.498 50.000 0.00 0.00 0.00 4.20
202 218 3.431068 GGCTTGCTACTTTCTACTCCCTC 60.431 52.174 0.00 0.00 0.00 4.30
203 219 3.431068 GCTTGCTACTTTCTACTCCCTCC 60.431 52.174 0.00 0.00 0.00 4.30
204 220 2.376109 TGCTACTTTCTACTCCCTCCG 58.624 52.381 0.00 0.00 0.00 4.63
205 221 2.291411 TGCTACTTTCTACTCCCTCCGT 60.291 50.000 0.00 0.00 0.00 4.69
206 222 2.759535 GCTACTTTCTACTCCCTCCGTT 59.240 50.000 0.00 0.00 0.00 4.44
207 223 3.195182 GCTACTTTCTACTCCCTCCGTTT 59.805 47.826 0.00 0.00 0.00 3.60
208 224 4.322574 GCTACTTTCTACTCCCTCCGTTTT 60.323 45.833 0.00 0.00 0.00 2.43
209 225 5.105595 GCTACTTTCTACTCCCTCCGTTTTA 60.106 44.000 0.00 0.00 0.00 1.52
210 226 5.813513 ACTTTCTACTCCCTCCGTTTTAA 57.186 39.130 0.00 0.00 0.00 1.52
211 227 6.178607 ACTTTCTACTCCCTCCGTTTTAAA 57.821 37.500 0.00 0.00 0.00 1.52
212 228 6.776744 ACTTTCTACTCCCTCCGTTTTAAAT 58.223 36.000 0.00 0.00 0.00 1.40
213 229 7.229308 ACTTTCTACTCCCTCCGTTTTAAATT 58.771 34.615 0.00 0.00 0.00 1.82
214 230 8.377799 ACTTTCTACTCCCTCCGTTTTAAATTA 58.622 33.333 0.00 0.00 0.00 1.40
215 231 8.552083 TTTCTACTCCCTCCGTTTTAAATTAC 57.448 34.615 0.00 0.00 0.00 1.89
216 232 7.486407 TCTACTCCCTCCGTTTTAAATTACT 57.514 36.000 0.00 0.00 0.00 2.24
217 233 7.550712 TCTACTCCCTCCGTTTTAAATTACTC 58.449 38.462 0.00 0.00 0.00 2.59
218 234 5.173664 ACTCCCTCCGTTTTAAATTACTCG 58.826 41.667 0.00 0.00 0.00 4.18
219 235 5.151297 TCCCTCCGTTTTAAATTACTCGT 57.849 39.130 0.00 0.00 0.00 4.18
220 236 5.170748 TCCCTCCGTTTTAAATTACTCGTC 58.829 41.667 0.00 0.00 0.00 4.20
221 237 4.032104 CCCTCCGTTTTAAATTACTCGTCG 59.968 45.833 0.00 0.00 0.00 5.12
222 238 4.491441 CCTCCGTTTTAAATTACTCGTCGC 60.491 45.833 0.00 0.00 0.00 5.19
223 239 3.986572 TCCGTTTTAAATTACTCGTCGCA 59.013 39.130 0.00 0.00 0.00 5.10
224 240 4.090354 TCCGTTTTAAATTACTCGTCGCAG 59.910 41.667 0.00 0.00 0.00 5.18
225 241 4.090354 CCGTTTTAAATTACTCGTCGCAGA 59.910 41.667 0.00 0.00 0.00 4.26
226 242 5.388682 CCGTTTTAAATTACTCGTCGCAGAA 60.389 40.000 0.00 0.00 39.69 3.02
227 243 6.066410 CGTTTTAAATTACTCGTCGCAGAAA 58.934 36.000 0.00 0.00 39.69 2.52
228 244 6.735063 CGTTTTAAATTACTCGTCGCAGAAAT 59.265 34.615 0.00 0.00 39.69 2.17
229 245 7.267600 CGTTTTAAATTACTCGTCGCAGAAATT 59.732 33.333 0.00 0.00 39.69 1.82
230 246 8.355806 GTTTTAAATTACTCGTCGCAGAAATTG 58.644 33.333 0.00 0.00 39.69 2.32
231 247 5.856126 AAATTACTCGTCGCAGAAATTGA 57.144 34.783 0.00 0.00 39.69 2.57
232 248 6.422776 AAATTACTCGTCGCAGAAATTGAT 57.577 33.333 0.00 0.00 39.69 2.57
253 269 0.676466 TACAACGGCTGCCAATCTGG 60.676 55.000 20.29 3.29 41.55 3.86
257 273 1.377725 CGGCTGCCAATCTGGTTCT 60.378 57.895 20.29 0.00 40.46 3.01
263 279 3.565902 GCTGCCAATCTGGTTCTAATACC 59.434 47.826 0.00 0.00 40.46 2.73
268 284 5.690097 GCCAATCTGGTTCTAATACCATCCA 60.690 44.000 0.00 0.00 46.63 3.41
269 285 5.765182 CCAATCTGGTTCTAATACCATCCAC 59.235 44.000 0.00 0.00 46.63 4.02
285 305 1.173043 CCACTTTGGTGTGTGTGTGT 58.827 50.000 0.00 0.00 41.53 3.72
315 335 2.237143 TCACACCATTTTTGTTGGCCAA 59.763 40.909 16.05 16.05 37.81 4.52
380 401 2.970324 GCGTGGGCGTGAACTTCA 60.970 61.111 0.00 0.00 40.81 3.02
395 416 6.145534 CGTGAACTTCATGAGCAAACTAACTA 59.854 38.462 5.16 0.00 35.46 2.24
400 421 3.935203 TCATGAGCAAACTAACTAGCTGC 59.065 43.478 0.00 0.00 37.48 5.25
401 422 3.685139 TGAGCAAACTAACTAGCTGCT 57.315 42.857 7.57 7.57 44.00 4.24
403 424 2.933260 GAGCAAACTAACTAGCTGCTCC 59.067 50.000 20.64 10.15 46.40 4.70
404 425 2.010497 GCAAACTAACTAGCTGCTCCC 58.990 52.381 4.91 0.00 34.44 4.30
405 426 2.355209 GCAAACTAACTAGCTGCTCCCT 60.355 50.000 4.91 0.00 34.44 4.20
406 427 3.870299 GCAAACTAACTAGCTGCTCCCTT 60.870 47.826 4.91 0.00 34.44 3.95
407 428 3.897141 AACTAACTAGCTGCTCCCTTC 57.103 47.619 4.91 0.00 0.00 3.46
409 430 1.751924 CTAACTAGCTGCTCCCTTCGT 59.248 52.381 4.91 0.00 0.00 3.85
410 431 0.977395 AACTAGCTGCTCCCTTCGTT 59.023 50.000 4.91 0.00 0.00 3.85
411 432 0.533032 ACTAGCTGCTCCCTTCGTTC 59.467 55.000 4.91 0.00 0.00 3.95
412 433 0.532573 CTAGCTGCTCCCTTCGTTCA 59.467 55.000 4.91 0.00 0.00 3.18
414 435 1.188219 AGCTGCTCCCTTCGTTCAGA 61.188 55.000 0.00 0.00 0.00 3.27
416 437 1.433534 CTGCTCCCTTCGTTCAGAAC 58.566 55.000 2.85 2.85 34.66 3.01
417 438 1.001406 CTGCTCCCTTCGTTCAGAACT 59.999 52.381 11.60 0.00 34.66 3.01
419 440 2.832129 TGCTCCCTTCGTTCAGAACTAT 59.168 45.455 11.60 0.00 34.66 2.12
421 442 4.254492 GCTCCCTTCGTTCAGAACTATTT 58.746 43.478 11.60 0.00 34.66 1.40
422 443 4.093556 GCTCCCTTCGTTCAGAACTATTTG 59.906 45.833 11.60 0.00 34.66 2.32
423 444 5.223449 TCCCTTCGTTCAGAACTATTTGT 57.777 39.130 11.60 0.00 34.66 2.83
424 445 5.235516 TCCCTTCGTTCAGAACTATTTGTC 58.764 41.667 11.60 0.00 34.66 3.18
425 446 4.091509 CCCTTCGTTCAGAACTATTTGTCG 59.908 45.833 11.60 0.00 34.66 4.35
426 447 4.434330 CCTTCGTTCAGAACTATTTGTCGC 60.434 45.833 11.60 0.00 34.66 5.19
427 448 3.644823 TCGTTCAGAACTATTTGTCGCA 58.355 40.909 11.60 0.00 0.00 5.10
457 677 0.683504 ACGTACGAGCCCTCTGGAAT 60.684 55.000 24.41 0.00 0.00 3.01
481 705 5.723672 TCCTACCAGTAGAACTTGAACAG 57.276 43.478 6.39 0.00 35.21 3.16
484 708 5.010719 CCTACCAGTAGAACTTGAACAGACA 59.989 44.000 6.39 0.00 35.21 3.41
490 714 4.558538 AGAACTTGAACAGACAATGTGC 57.441 40.909 0.00 0.00 43.00 4.57
541 2795 6.759272 TGGTAGTAATAGTGCAATCATCTCC 58.241 40.000 0.00 0.00 0.00 3.71
547 2801 1.065926 AGTGCAATCATCTCCGCTTCA 60.066 47.619 0.00 0.00 0.00 3.02
552 2806 3.609807 GCAATCATCTCCGCTTCAAAAAC 59.390 43.478 0.00 0.00 0.00 2.43
579 2837 5.235305 AGTTGATATGGTCGTGCATTTTC 57.765 39.130 0.00 0.00 0.00 2.29
588 2846 2.670414 GTCGTGCATTTTCTGAGGAGAG 59.330 50.000 0.00 0.00 0.00 3.20
600 2859 8.608844 TTTTCTGAGGAGAGAAAAGTTGATAC 57.391 34.615 0.00 0.00 43.72 2.24
610 2869 4.680110 AGAAAAGTTGATACAGTCGTGACG 59.320 41.667 0.00 0.00 36.20 4.35
628 2887 2.673368 GACGCCGATGAAATGAAAGAGT 59.327 45.455 0.00 0.00 0.00 3.24
661 3148 2.807906 CGTGTCACTGTGCAACGCA 61.808 57.895 17.65 4.23 42.39 5.24
663 3150 2.051882 GTCACTGTGCAACGCAGC 60.052 61.111 8.01 0.00 44.75 5.25
665 3152 3.585020 CACTGTGCAACGCAGCCA 61.585 61.111 8.01 0.00 44.75 4.75
666 3153 3.585990 ACTGTGCAACGCAGCCAC 61.586 61.111 8.01 0.00 44.75 5.01
667 3154 3.585020 CTGTGCAACGCAGCCACA 61.585 61.111 0.00 2.68 42.39 4.17
668 3155 2.906388 TGTGCAACGCAGCCACAT 60.906 55.556 0.00 0.00 42.39 3.21
669 3156 2.429571 GTGCAACGCAGCCACATG 60.430 61.111 0.00 0.00 40.08 3.21
670 3157 4.345962 TGCAACGCAGCCACATGC 62.346 61.111 0.00 0.00 42.95 4.06
673 3160 2.039974 CAACGCAGCCACATGCCTA 61.040 57.895 0.00 0.00 43.49 3.93
678 3182 1.709147 GCAGCCACATGCCTAAGACG 61.709 60.000 0.00 0.00 42.71 4.18
689 3193 2.039216 TGCCTAAGACGATTTCCAACCA 59.961 45.455 0.00 0.00 0.00 3.67
690 3194 3.279434 GCCTAAGACGATTTCCAACCAT 58.721 45.455 0.00 0.00 0.00 3.55
691 3195 4.080807 TGCCTAAGACGATTTCCAACCATA 60.081 41.667 0.00 0.00 0.00 2.74
718 3234 0.454600 CCTGCACATTGATCAGGCAC 59.545 55.000 13.17 0.00 40.63 5.01
720 3236 0.606130 TGCACATTGATCAGGCACGT 60.606 50.000 8.70 0.00 0.00 4.49
723 3239 1.395954 CACATTGATCAGGCACGTGAG 59.604 52.381 22.23 8.30 0.00 3.51
724 3240 1.012086 CATTGATCAGGCACGTGAGG 58.988 55.000 22.23 7.50 0.00 3.86
725 3241 0.904649 ATTGATCAGGCACGTGAGGA 59.095 50.000 22.23 13.13 0.00 3.71
726 3242 0.247460 TTGATCAGGCACGTGAGGAG 59.753 55.000 22.23 5.53 0.00 3.69
727 3243 1.142748 GATCAGGCACGTGAGGAGG 59.857 63.158 22.23 3.18 0.00 4.30
728 3244 1.608717 GATCAGGCACGTGAGGAGGT 61.609 60.000 22.23 0.88 0.00 3.85
772 3316 2.750237 GCCGGGTCACCAATCCAC 60.750 66.667 2.18 0.00 36.13 4.02
775 3319 2.359011 GGGTCACCAATCCACCCC 59.641 66.667 0.00 0.00 43.79 4.95
776 3320 2.543797 GGGTCACCAATCCACCCCA 61.544 63.158 0.00 0.00 43.79 4.96
830 3374 2.242572 CGATCCAGCGCTCCACATG 61.243 63.158 7.13 0.00 0.00 3.21
836 3380 2.125147 GCGCTCCACATGCCACTA 60.125 61.111 0.00 0.00 0.00 2.74
837 3381 1.745115 GCGCTCCACATGCCACTAA 60.745 57.895 0.00 0.00 0.00 2.24
838 3382 1.982073 GCGCTCCACATGCCACTAAC 61.982 60.000 0.00 0.00 0.00 2.34
839 3383 0.391661 CGCTCCACATGCCACTAACT 60.392 55.000 0.00 0.00 0.00 2.24
864 3408 7.230747 TGACATCTTCCTTCCTTCAAACAATA 58.769 34.615 0.00 0.00 0.00 1.90
870 3414 1.083489 TCCTTCAAACAATAGCGCCG 58.917 50.000 2.29 0.00 0.00 6.46
881 3425 5.030874 ACAATAGCGCCGATAAAATAAGC 57.969 39.130 2.29 0.00 0.00 3.09
930 3474 7.603963 AAAAACAATAAACAAAACGGCTTCT 57.396 28.000 0.00 0.00 0.00 2.85
931 3475 7.603963 AAAACAATAAACAAAACGGCTTCTT 57.396 28.000 0.00 0.00 0.00 2.52
932 3476 6.822073 AACAATAAACAAAACGGCTTCTTC 57.178 33.333 0.00 0.00 0.00 2.87
933 3477 6.144078 ACAATAAACAAAACGGCTTCTTCT 57.856 33.333 0.00 0.00 0.00 2.85
934 3478 6.206498 ACAATAAACAAAACGGCTTCTTCTC 58.794 36.000 0.00 0.00 0.00 2.87
935 3479 3.710326 AAACAAAACGGCTTCTTCTCC 57.290 42.857 0.00 0.00 0.00 3.71
939 3483 1.752833 AACGGCTTCTTCTCCGGTT 59.247 52.632 0.00 0.00 44.41 4.44
976 3592 2.598439 CGTCGCGCTCGTATATATACCC 60.598 54.545 15.70 5.37 36.96 3.69
977 3593 1.594397 TCGCGCTCGTATATATACCCG 59.406 52.381 15.70 15.53 36.96 5.28
984 3600 0.595825 GTATATATACCCGCGCCCGC 60.596 60.000 11.27 1.98 37.85 6.13
985 3601 1.737355 TATATATACCCGCGCCCGCC 61.737 60.000 0.00 0.00 37.98 6.13
1001 3617 1.901085 GCCCTCCACTTCGTCTCAT 59.099 57.895 0.00 0.00 0.00 2.90
1002 3618 0.179097 GCCCTCCACTTCGTCTCATC 60.179 60.000 0.00 0.00 0.00 2.92
1003 3619 1.479709 CCCTCCACTTCGTCTCATCT 58.520 55.000 0.00 0.00 0.00 2.90
1004 3620 1.407258 CCCTCCACTTCGTCTCATCTC 59.593 57.143 0.00 0.00 0.00 2.75
1005 3621 1.407258 CCTCCACTTCGTCTCATCTCC 59.593 57.143 0.00 0.00 0.00 3.71
1006 3622 2.095461 CTCCACTTCGTCTCATCTCCA 58.905 52.381 0.00 0.00 0.00 3.86
1007 3623 2.692557 CTCCACTTCGTCTCATCTCCAT 59.307 50.000 0.00 0.00 0.00 3.41
1013 3629 1.950216 TCGTCTCATCTCCATTCTCCG 59.050 52.381 0.00 0.00 0.00 4.63
1046 3662 2.592861 GCACTCCATCGGCATCCC 60.593 66.667 0.00 0.00 0.00 3.85
1059 3675 2.624364 CGGCATCCCATTCATTCATTCA 59.376 45.455 0.00 0.00 0.00 2.57
1060 3676 3.257375 CGGCATCCCATTCATTCATTCAT 59.743 43.478 0.00 0.00 0.00 2.57
1061 3677 4.262292 CGGCATCCCATTCATTCATTCATT 60.262 41.667 0.00 0.00 0.00 2.57
1071 3687 3.373748 TCATTCATTCATTCAACCCGACG 59.626 43.478 0.00 0.00 0.00 5.12
1091 3707 1.508088 CATCCAAAGCCTTCACGCC 59.492 57.895 0.00 0.00 0.00 5.68
1303 3940 2.049433 CTCCTCGTCGCCGTGTTT 60.049 61.111 0.00 0.00 35.01 2.83
1318 3955 0.880278 TGTTTGACGACCTGCTGCTC 60.880 55.000 0.00 0.00 0.00 4.26
1319 3956 1.664649 TTTGACGACCTGCTGCTCG 60.665 57.895 8.04 8.04 35.96 5.03
1320 3957 4.724602 TGACGACCTGCTGCTCGC 62.725 66.667 9.33 4.16 39.77 5.03
1570 4210 4.838486 GACCTCCTCACGCTCGCG 62.838 72.222 10.06 10.06 46.03 5.87
1676 4316 2.833582 GGGAGATCGTGCCGGAGA 60.834 66.667 5.05 0.25 0.00 3.71
1723 4363 2.750237 GTGGCCATCAACGACCCC 60.750 66.667 9.72 0.00 0.00 4.95
1888 4528 2.584391 GGACTCCAAGGTGGACGCT 61.584 63.158 0.00 0.00 42.67 5.07
1976 4619 4.309950 GCGACCCCGTTGTGTCCT 62.310 66.667 0.00 0.00 38.24 3.85
1978 4621 2.346365 GACCCCGTTGTGTCCTCC 59.654 66.667 0.00 0.00 0.00 4.30
2266 4909 3.003763 GCCTCGTTCTCCCCTGGT 61.004 66.667 0.00 0.00 0.00 4.00
2465 5108 0.169451 CAAGAAGCGCATCATGCACA 59.831 50.000 15.84 0.00 45.36 4.57
2560 5203 4.008933 ACCGTGCTCAGCCTGTCC 62.009 66.667 0.00 0.00 0.00 4.02
2662 5305 3.151906 AGCACCAAGAAGGACGCT 58.848 55.556 0.00 0.00 42.30 5.07
2665 5308 1.016653 GCACCAAGAAGGACGCTCTC 61.017 60.000 0.00 0.00 41.22 3.20
2704 5347 2.971452 GCGGAGAGGGAGAACGTT 59.029 61.111 0.00 0.00 0.00 3.99
2961 5604 3.200593 GCAGGTGCTGGCGATCAG 61.201 66.667 0.00 0.00 46.03 2.90
3147 5816 4.626172 GTCGTGAACTCATTCTTAGGAACC 59.374 45.833 0.00 0.00 35.69 3.62
3158 5827 3.811083 TCTTAGGAACCGCTGAAAAACA 58.189 40.909 0.00 0.00 0.00 2.83
3250 5920 0.393808 GGTGCGATTCTTTAGCCCCA 60.394 55.000 0.00 0.00 0.00 4.96
3285 5956 8.131100 ACACAAACACAGAGTAATTGAATCAAG 58.869 33.333 1.10 0.00 0.00 3.02
3292 5963 6.432162 ACAGAGTAATTGAATCAAGTGTGCAT 59.568 34.615 6.17 0.00 0.00 3.96
3293 5964 7.607607 ACAGAGTAATTGAATCAAGTGTGCATA 59.392 33.333 6.17 0.00 0.00 3.14
3294 5965 7.907045 CAGAGTAATTGAATCAAGTGTGCATAC 59.093 37.037 5.29 5.29 0.00 2.39
3317 5988 4.474226 ACAGAACATTCGTTGCTTCTTC 57.526 40.909 0.00 0.00 34.75 2.87
3331 6005 2.096860 GCTTCTTCCGTTCTTCGTTGTC 60.097 50.000 0.00 0.00 37.94 3.18
3333 6007 0.161024 CTTCCGTTCTTCGTTGTCGC 59.839 55.000 0.00 0.00 37.94 5.19
3349 6023 3.575630 TGTCGCTGTGAGATCTTGTAAC 58.424 45.455 0.00 0.00 0.00 2.50
3364 6042 8.956426 AGATCTTGTAACACAAAGTGAAAGAAA 58.044 29.630 3.88 0.00 37.69 2.52
3365 6043 9.567848 GATCTTGTAACACAAAGTGAAAGAAAA 57.432 29.630 3.88 0.00 37.69 2.29
3399 6077 3.405823 ACAAATTGTGCCCATTCTTGG 57.594 42.857 0.00 0.00 43.23 3.61
3446 6127 5.914898 AATTTTGTACTAGTTGATGGGCC 57.085 39.130 0.00 0.00 0.00 5.80
3448 6129 4.374689 TTTGTACTAGTTGATGGGCCAA 57.625 40.909 11.89 0.00 0.00 4.52
3450 6131 3.681593 TGTACTAGTTGATGGGCCAAAC 58.318 45.455 11.89 12.12 0.00 2.93
3451 6132 3.329520 TGTACTAGTTGATGGGCCAAACT 59.670 43.478 23.23 23.23 0.00 2.66
3454 6135 2.514458 AGTTGATGGGCCAAACTAGG 57.486 50.000 19.55 0.00 0.00 3.02
3456 6137 1.818674 GTTGATGGGCCAAACTAGGTG 59.181 52.381 11.89 0.00 0.00 4.00
3495 6181 2.390599 CCCGTGATGAGTGGTTGCG 61.391 63.158 0.00 0.00 0.00 4.85
3496 6182 2.390599 CCGTGATGAGTGGTTGCGG 61.391 63.158 0.00 0.00 0.00 5.69
3497 6183 2.870372 GTGATGAGTGGTTGCGGC 59.130 61.111 0.00 0.00 0.00 6.53
3528 6221 2.766660 AGGCCAGCCTTTCTTCCC 59.233 61.111 5.04 0.00 45.70 3.97
3529 6222 1.854507 AGGCCAGCCTTTCTTCCCT 60.855 57.895 5.04 0.00 45.70 4.20
3530 6223 1.379176 GGCCAGCCTTTCTTCCCTC 60.379 63.158 0.00 0.00 0.00 4.30
3531 6224 1.379176 GCCAGCCTTTCTTCCCTCC 60.379 63.158 0.00 0.00 0.00 4.30
3532 6225 1.304617 CCAGCCTTTCTTCCCTCCC 59.695 63.158 0.00 0.00 0.00 4.30
3533 6226 1.500783 CCAGCCTTTCTTCCCTCCCA 61.501 60.000 0.00 0.00 0.00 4.37
3534 6227 0.034670 CAGCCTTTCTTCCCTCCCAG 60.035 60.000 0.00 0.00 0.00 4.45
3535 6228 1.379176 GCCTTTCTTCCCTCCCAGC 60.379 63.158 0.00 0.00 0.00 4.85
3536 6229 1.304617 CCTTTCTTCCCTCCCAGCC 59.695 63.158 0.00 0.00 0.00 4.85
3537 6230 1.078143 CTTTCTTCCCTCCCAGCCG 60.078 63.158 0.00 0.00 0.00 5.52
3538 6231 1.842381 CTTTCTTCCCTCCCAGCCGT 61.842 60.000 0.00 0.00 0.00 5.68
3596 6297 4.891727 ATAAGTCGCGCGGCTGGG 62.892 66.667 39.67 4.08 0.00 4.45
3606 6307 4.473520 CGGCTGGGAACGCTCCAT 62.474 66.667 7.26 0.00 44.51 3.41
3609 6310 1.153086 GCTGGGAACGCTCCATGAT 60.153 57.895 7.26 0.00 44.51 2.45
3610 6311 0.749454 GCTGGGAACGCTCCATGATT 60.749 55.000 7.26 0.00 44.51 2.57
3611 6312 1.303309 CTGGGAACGCTCCATGATTC 58.697 55.000 7.26 0.00 44.51 2.52
3612 6313 0.461870 TGGGAACGCTCCATGATTCG 60.462 55.000 7.26 0.00 44.51 3.34
3708 6409 3.576356 GGTGCGCATCCATCCACG 61.576 66.667 15.91 0.00 0.00 4.94
3712 6413 4.681421 CGCATCCATCCACGCTAT 57.319 55.556 0.00 0.00 0.00 2.97
3713 6414 2.156542 CGCATCCATCCACGCTATG 58.843 57.895 0.00 0.00 0.00 2.23
3714 6415 1.871772 GCATCCATCCACGCTATGC 59.128 57.895 0.00 0.00 36.51 3.14
3715 6416 0.604780 GCATCCATCCACGCTATGCT 60.605 55.000 0.00 0.00 39.80 3.79
3716 6417 1.338105 GCATCCATCCACGCTATGCTA 60.338 52.381 0.00 0.00 39.80 3.49
3717 6418 2.679059 GCATCCATCCACGCTATGCTAT 60.679 50.000 0.00 0.00 39.80 2.97
3718 6419 2.749280 TCCATCCACGCTATGCTATG 57.251 50.000 0.00 0.00 0.00 2.23
3719 6420 1.970640 TCCATCCACGCTATGCTATGT 59.029 47.619 0.00 0.00 0.00 2.29
3757 6458 7.231722 CACTACTCCACTGCTAATCTAACCTAT 59.768 40.741 0.00 0.00 0.00 2.57
3758 6459 8.446394 ACTACTCCACTGCTAATCTAACCTATA 58.554 37.037 0.00 0.00 0.00 1.31
3804 6505 1.071699 TGGTTCCTTTCTTGTCCCTCG 59.928 52.381 0.00 0.00 0.00 4.63
3829 6530 1.078143 GATGCACTCCAGGGTGTCC 60.078 63.158 0.00 0.00 39.21 4.02
3830 6531 2.543067 GATGCACTCCAGGGTGTCCC 62.543 65.000 0.00 0.00 45.90 4.46
3852 6553 0.449388 CGCTTCACATGGGCTCTTTC 59.551 55.000 0.00 0.00 0.00 2.62
3854 6555 1.615384 GCTTCACATGGGCTCTTTCCT 60.615 52.381 0.00 0.00 0.00 3.36
3872 6573 5.920193 TTCCTGAATTTGACCATTGATCC 57.080 39.130 0.00 0.00 0.00 3.36
3886 6587 1.729284 TGATCCGCCGTTCCTTTAAC 58.271 50.000 0.00 0.00 34.52 2.01
3892 6593 0.242825 GCCGTTCCTTTAACCCAAGC 59.757 55.000 0.00 0.00 34.33 4.01
3905 6606 1.599047 CCAAGCACTCCTGGTCGAT 59.401 57.895 0.00 0.00 0.00 3.59
3936 6637 1.266175 CTTGGTGCTTCAGTGCTTCTG 59.734 52.381 3.68 3.68 44.85 3.02
3970 6689 3.265479 CCTATCATCTTTCCATCTCCCCC 59.735 52.174 0.00 0.00 0.00 5.40
4008 6727 2.669391 CGTTGCTTCTTCTCAAATGGCC 60.669 50.000 0.00 0.00 0.00 5.36
4015 6734 1.203994 CTTCTCAAATGGCCAAGGCAG 59.796 52.381 10.96 3.91 42.43 4.85
4078 6798 2.804828 CTTCTTCCGTGGCCAGGACC 62.805 65.000 26.78 3.72 37.53 4.46
4085 6805 3.319198 TGGCCAGGACCGGTTCTC 61.319 66.667 14.22 2.03 0.00 2.87
4089 6809 4.052229 CAGGACCGGTTCTCGCGT 62.052 66.667 14.22 0.00 37.59 6.01
4090 6810 4.052229 AGGACCGGTTCTCGCGTG 62.052 66.667 10.55 3.13 37.59 5.34
4091 6811 4.047059 GGACCGGTTCTCGCGTGA 62.047 66.667 9.42 6.33 37.59 4.35
4092 6812 2.049802 GACCGGTTCTCGCGTGAA 60.050 61.111 18.79 18.79 37.59 3.18
4093 6813 1.662446 GACCGGTTCTCGCGTGAAA 60.662 57.895 23.54 5.87 37.59 2.69
4094 6814 1.883725 GACCGGTTCTCGCGTGAAAC 61.884 60.000 24.92 24.92 37.59 2.78
4115 6842 7.437862 TGAAACTGAAATTAAAATGTGCCTGAC 59.562 33.333 0.00 0.00 0.00 3.51
4118 6845 6.265196 ACTGAAATTAAAATGTGCCTGACAGA 59.735 34.615 3.32 0.00 38.23 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 1.834378 TCAGAGATAGCTGGCCGGG 60.834 63.158 15.02 1.86 36.55 5.73
151 167 1.223187 GAAAGAAGGCGACGGACAAA 58.777 50.000 0.00 0.00 0.00 2.83
152 168 0.942410 CGAAAGAAGGCGACGGACAA 60.942 55.000 0.00 0.00 0.00 3.18
155 171 0.942410 CAACGAAAGAAGGCGACGGA 60.942 55.000 0.00 0.00 0.00 4.69
187 203 6.916360 TTAAAACGGAGGGAGTAGAAAGTA 57.084 37.500 0.00 0.00 0.00 2.24
197 213 5.151297 ACGAGTAATTTAAAACGGAGGGA 57.849 39.130 0.00 0.00 0.00 4.20
198 214 4.032104 CGACGAGTAATTTAAAACGGAGGG 59.968 45.833 0.00 0.00 0.00 4.30
199 215 4.491441 GCGACGAGTAATTTAAAACGGAGG 60.491 45.833 0.00 0.00 0.00 4.30
200 216 4.090354 TGCGACGAGTAATTTAAAACGGAG 59.910 41.667 0.00 0.00 0.00 4.63
201 217 3.986572 TGCGACGAGTAATTTAAAACGGA 59.013 39.130 0.00 0.00 0.00 4.69
202 218 4.090354 TCTGCGACGAGTAATTTAAAACGG 59.910 41.667 0.00 0.00 0.00 4.44
203 219 5.181235 TCTGCGACGAGTAATTTAAAACG 57.819 39.130 0.00 0.00 0.00 3.60
204 220 8.355806 CAATTTCTGCGACGAGTAATTTAAAAC 58.644 33.333 0.00 0.00 0.00 2.43
205 221 8.283992 TCAATTTCTGCGACGAGTAATTTAAAA 58.716 29.630 0.00 0.00 0.00 1.52
206 222 7.798801 TCAATTTCTGCGACGAGTAATTTAAA 58.201 30.769 0.00 0.00 0.00 1.52
207 223 7.354025 TCAATTTCTGCGACGAGTAATTTAA 57.646 32.000 0.00 0.00 0.00 1.52
208 224 6.954616 TCAATTTCTGCGACGAGTAATTTA 57.045 33.333 0.00 0.00 0.00 1.40
209 225 5.856126 TCAATTTCTGCGACGAGTAATTT 57.144 34.783 0.00 0.00 0.00 1.82
210 226 5.351465 ACATCAATTTCTGCGACGAGTAATT 59.649 36.000 0.00 2.98 0.00 1.40
211 227 4.870426 ACATCAATTTCTGCGACGAGTAAT 59.130 37.500 0.00 0.00 0.00 1.89
212 228 4.242475 ACATCAATTTCTGCGACGAGTAA 58.758 39.130 0.00 0.00 0.00 2.24
213 229 3.845178 ACATCAATTTCTGCGACGAGTA 58.155 40.909 0.00 0.00 0.00 2.59
214 230 2.688507 ACATCAATTTCTGCGACGAGT 58.311 42.857 0.00 0.00 0.00 4.18
215 231 3.612423 TGTACATCAATTTCTGCGACGAG 59.388 43.478 0.00 0.00 0.00 4.18
216 232 3.580731 TGTACATCAATTTCTGCGACGA 58.419 40.909 0.00 0.00 0.00 4.20
217 233 3.989705 TGTACATCAATTTCTGCGACG 57.010 42.857 0.00 0.00 0.00 5.12
218 234 4.081761 CGTTGTACATCAATTTCTGCGAC 58.918 43.478 0.00 0.00 38.38 5.19
219 235 3.124466 CCGTTGTACATCAATTTCTGCGA 59.876 43.478 0.00 0.00 38.38 5.10
220 236 3.416277 CCGTTGTACATCAATTTCTGCG 58.584 45.455 0.00 0.00 38.38 5.18
221 237 3.119849 AGCCGTTGTACATCAATTTCTGC 60.120 43.478 0.00 0.00 38.38 4.26
222 238 4.406069 CAGCCGTTGTACATCAATTTCTG 58.594 43.478 0.00 0.00 38.38 3.02
223 239 3.119849 GCAGCCGTTGTACATCAATTTCT 60.120 43.478 0.00 0.00 38.38 2.52
224 240 3.171277 GCAGCCGTTGTACATCAATTTC 58.829 45.455 0.00 0.00 38.38 2.17
225 241 2.094752 GGCAGCCGTTGTACATCAATTT 60.095 45.455 0.00 0.00 38.38 1.82
226 242 1.472480 GGCAGCCGTTGTACATCAATT 59.528 47.619 0.00 0.00 38.38 2.32
227 243 1.094785 GGCAGCCGTTGTACATCAAT 58.905 50.000 0.00 0.00 38.38 2.57
228 244 0.250510 TGGCAGCCGTTGTACATCAA 60.251 50.000 7.03 0.00 0.00 2.57
229 245 0.250510 TTGGCAGCCGTTGTACATCA 60.251 50.000 7.03 0.00 0.00 3.07
230 246 1.064060 GATTGGCAGCCGTTGTACATC 59.936 52.381 7.03 0.00 0.00 3.06
231 247 1.094785 GATTGGCAGCCGTTGTACAT 58.905 50.000 7.03 0.00 0.00 2.29
232 248 0.036164 AGATTGGCAGCCGTTGTACA 59.964 50.000 7.03 0.00 0.00 2.90
268 284 1.539388 CACACACACACACACCAAAGT 59.461 47.619 0.00 0.00 0.00 2.66
269 285 1.539388 ACACACACACACACACCAAAG 59.461 47.619 0.00 0.00 0.00 2.77
315 335 1.114722 CACACAAGGCATGGTTGGGT 61.115 55.000 0.00 0.00 42.41 4.51
321 341 3.751246 CCGGCACACAAGGCATGG 61.751 66.667 0.00 0.00 0.00 3.66
365 386 0.798776 CTCATGAAGTTCACGCCCAC 59.201 55.000 7.96 0.00 0.00 4.61
368 389 0.874390 TTGCTCATGAAGTTCACGCC 59.126 50.000 7.96 0.00 0.00 5.68
369 390 2.031682 AGTTTGCTCATGAAGTTCACGC 60.032 45.455 7.96 11.60 0.00 5.34
380 401 4.213564 AGCAGCTAGTTAGTTTGCTCAT 57.786 40.909 0.00 0.00 40.05 2.90
395 416 1.188219 TCTGAACGAAGGGAGCAGCT 61.188 55.000 0.00 0.00 0.00 4.24
400 421 5.238583 ACAAATAGTTCTGAACGAAGGGAG 58.761 41.667 14.35 6.04 36.23 4.30
401 422 5.223449 ACAAATAGTTCTGAACGAAGGGA 57.777 39.130 14.35 0.00 36.23 4.20
402 423 4.091509 CGACAAATAGTTCTGAACGAAGGG 59.908 45.833 14.35 8.51 36.23 3.95
403 424 4.434330 GCGACAAATAGTTCTGAACGAAGG 60.434 45.833 14.35 7.57 36.23 3.46
404 425 4.149922 TGCGACAAATAGTTCTGAACGAAG 59.850 41.667 14.35 7.11 36.23 3.79
405 426 4.052608 TGCGACAAATAGTTCTGAACGAA 58.947 39.130 14.35 7.83 36.23 3.85
406 427 3.644823 TGCGACAAATAGTTCTGAACGA 58.355 40.909 14.35 10.20 36.23 3.85
407 428 3.673338 TCTGCGACAAATAGTTCTGAACG 59.327 43.478 14.35 3.21 36.23 3.95
409 430 6.612247 TTTTCTGCGACAAATAGTTCTGAA 57.388 33.333 0.00 0.00 0.00 3.02
410 431 6.602179 CATTTTCTGCGACAAATAGTTCTGA 58.398 36.000 0.00 0.00 0.00 3.27
411 432 5.284660 GCATTTTCTGCGACAAATAGTTCTG 59.715 40.000 0.00 0.00 41.97 3.02
412 433 5.393962 GCATTTTCTGCGACAAATAGTTCT 58.606 37.500 0.00 0.00 41.97 3.01
426 447 2.721797 GCTCGTACGTGTGCATTTTCTG 60.722 50.000 16.05 0.00 0.00 3.02
427 448 1.459592 GCTCGTACGTGTGCATTTTCT 59.540 47.619 16.05 0.00 0.00 2.52
438 658 0.683504 ATTCCAGAGGGCTCGTACGT 60.684 55.000 16.05 0.00 34.09 3.57
439 659 1.315690 TATTCCAGAGGGCTCGTACG 58.684 55.000 9.53 9.53 34.09 3.67
440 660 2.231721 GGATATTCCAGAGGGCTCGTAC 59.768 54.545 0.00 0.00 36.28 3.67
441 661 2.110188 AGGATATTCCAGAGGGCTCGTA 59.890 50.000 0.00 0.00 39.61 3.43
457 677 7.122353 GTCTGTTCAAGTTCTACTGGTAGGATA 59.878 40.741 7.76 0.00 34.06 2.59
468 688 5.368145 AGCACATTGTCTGTTCAAGTTCTA 58.632 37.500 0.00 0.00 35.29 2.10
481 705 2.766313 TGACACTGGTAGCACATTGTC 58.234 47.619 15.11 15.11 45.67 3.18
484 708 4.943705 CCTAAATGACACTGGTAGCACATT 59.056 41.667 3.41 3.41 0.00 2.71
490 714 7.348080 TCATACTCCTAAATGACACTGGTAG 57.652 40.000 0.00 0.00 0.00 3.18
541 2795 3.516615 TCAACTTTGGGTTTTTGAAGCG 58.483 40.909 0.00 0.00 35.74 4.68
547 2801 5.303333 ACGACCATATCAACTTTGGGTTTTT 59.697 36.000 0.00 0.00 35.74 1.94
552 2806 2.097466 GCACGACCATATCAACTTTGGG 59.903 50.000 0.00 0.00 34.72 4.12
579 2837 6.696411 ACTGTATCAACTTTTCTCTCCTCAG 58.304 40.000 0.00 0.00 0.00 3.35
588 2846 4.663389 GCGTCACGACTGTATCAACTTTTC 60.663 45.833 0.00 0.00 0.00 2.29
600 2859 1.006825 TTTCATCGGCGTCACGACTG 61.007 55.000 0.00 0.00 46.64 3.51
610 2869 5.220681 GGTTCTACTCTTTCATTTCATCGGC 60.221 44.000 0.00 0.00 0.00 5.54
628 2887 2.985282 ACGGTCCGTGCGGTTCTA 60.985 61.111 18.08 0.00 39.18 2.10
663 3150 2.614057 GGAAATCGTCTTAGGCATGTGG 59.386 50.000 0.00 0.00 0.00 4.17
665 3152 3.627395 TGGAAATCGTCTTAGGCATGT 57.373 42.857 0.00 0.00 0.00 3.21
666 3153 3.065371 GGTTGGAAATCGTCTTAGGCATG 59.935 47.826 0.00 0.00 0.00 4.06
667 3154 3.279434 GGTTGGAAATCGTCTTAGGCAT 58.721 45.455 0.00 0.00 0.00 4.40
668 3155 2.039216 TGGTTGGAAATCGTCTTAGGCA 59.961 45.455 0.00 0.00 0.00 4.75
669 3156 2.706890 TGGTTGGAAATCGTCTTAGGC 58.293 47.619 0.00 0.00 0.00 3.93
670 3157 6.183360 GGTTTATGGTTGGAAATCGTCTTAGG 60.183 42.308 0.00 0.00 0.00 2.69
673 3160 4.461431 GGGTTTATGGTTGGAAATCGTCTT 59.539 41.667 0.00 0.00 0.00 3.01
678 3182 2.159156 GCCGGGTTTATGGTTGGAAATC 60.159 50.000 2.18 0.00 0.00 2.17
689 3193 0.324275 AATGTGCAGGCCGGGTTTAT 60.324 50.000 2.18 0.00 0.00 1.40
690 3194 1.075836 AATGTGCAGGCCGGGTTTA 59.924 52.632 2.18 0.00 0.00 2.01
691 3195 2.203625 AATGTGCAGGCCGGGTTT 60.204 55.556 2.18 0.00 0.00 3.27
718 3234 4.135153 CGGCCTGACCTCCTCACG 62.135 72.222 0.00 0.00 35.61 4.35
720 3236 4.704103 AGCGGCCTGACCTCCTCA 62.704 66.667 0.00 0.00 35.61 3.86
723 3239 3.254024 TTGAAGCGGCCTGACCTCC 62.254 63.158 0.00 0.00 35.61 4.30
724 3240 2.035442 GTTGAAGCGGCCTGACCTC 61.035 63.158 0.00 0.00 35.61 3.85
725 3241 2.032681 GTTGAAGCGGCCTGACCT 59.967 61.111 0.00 0.00 35.61 3.85
726 3242 2.032681 AGTTGAAGCGGCCTGACC 59.967 61.111 0.00 0.00 0.00 4.02
727 3243 2.970974 GCAGTTGAAGCGGCCTGAC 61.971 63.158 0.00 0.00 0.00 3.51
728 3244 2.669569 GCAGTTGAAGCGGCCTGA 60.670 61.111 0.00 0.00 0.00 3.86
772 3316 2.523168 GGTTGTTGGGGTGTGGGG 60.523 66.667 0.00 0.00 0.00 4.96
775 3319 1.184970 GGATGGGTTGTTGGGGTGTG 61.185 60.000 0.00 0.00 0.00 3.82
776 3320 1.155155 GGATGGGTTGTTGGGGTGT 59.845 57.895 0.00 0.00 0.00 4.16
830 3374 3.618690 AGGAAGATGTCAGTTAGTGGC 57.381 47.619 0.00 0.00 0.00 5.01
836 3380 4.982241 TGAAGGAAGGAAGATGTCAGTT 57.018 40.909 0.00 0.00 0.00 3.16
837 3381 4.982241 TTGAAGGAAGGAAGATGTCAGT 57.018 40.909 0.00 0.00 0.00 3.41
838 3382 5.065914 TGTTTGAAGGAAGGAAGATGTCAG 58.934 41.667 0.00 0.00 0.00 3.51
839 3383 5.047566 TGTTTGAAGGAAGGAAGATGTCA 57.952 39.130 0.00 0.00 0.00 3.58
864 3408 1.860676 TCGCTTATTTTATCGGCGCT 58.139 45.000 7.64 0.00 44.51 5.92
870 3414 7.761220 GCGGTGTTATTTTCGCTTATTTTATC 58.239 34.615 0.00 0.00 44.10 1.75
881 3425 2.417239 TGCCTTAGCGGTGTTATTTTCG 59.583 45.455 0.00 0.00 44.31 3.46
922 3466 1.186267 AGAACCGGAGAAGAAGCCGT 61.186 55.000 9.46 0.00 45.85 5.68
928 3472 1.874345 GCGTGGAGAACCGGAGAAGA 61.874 60.000 9.46 0.00 39.42 2.87
929 3473 1.446272 GCGTGGAGAACCGGAGAAG 60.446 63.158 9.46 0.00 39.42 2.85
930 3474 2.654877 GCGTGGAGAACCGGAGAA 59.345 61.111 9.46 0.00 39.42 2.87
931 3475 3.744719 CGCGTGGAGAACCGGAGA 61.745 66.667 9.46 0.00 39.42 3.71
936 3480 3.723348 GTTGGCGCGTGGAGAACC 61.723 66.667 8.43 0.00 0.00 3.62
937 3481 2.970324 TGTTGGCGCGTGGAGAAC 60.970 61.111 8.43 4.53 0.00 3.01
938 3482 2.970324 GTGTTGGCGCGTGGAGAA 60.970 61.111 8.43 0.00 0.00 2.87
1001 3617 2.695666 GGATGAGAACGGAGAATGGAGA 59.304 50.000 0.00 0.00 0.00 3.71
1002 3618 2.432146 TGGATGAGAACGGAGAATGGAG 59.568 50.000 0.00 0.00 0.00 3.86
1003 3619 2.466846 TGGATGAGAACGGAGAATGGA 58.533 47.619 0.00 0.00 0.00 3.41
1004 3620 2.988010 TGGATGAGAACGGAGAATGG 57.012 50.000 0.00 0.00 0.00 3.16
1005 3621 3.055591 CGATGGATGAGAACGGAGAATG 58.944 50.000 0.00 0.00 0.00 2.67
1006 3622 2.546795 GCGATGGATGAGAACGGAGAAT 60.547 50.000 0.00 0.00 0.00 2.40
1007 3623 1.202417 GCGATGGATGAGAACGGAGAA 60.202 52.381 0.00 0.00 0.00 2.87
1013 3629 1.521457 TGCGGCGATGGATGAGAAC 60.521 57.895 12.98 0.00 0.00 3.01
1046 3662 5.745294 GTCGGGTTGAATGAATGAATGAATG 59.255 40.000 0.00 0.00 0.00 2.67
1059 3675 1.451387 GGATGGCGTCGGGTTGAAT 60.451 57.895 0.00 0.00 0.00 2.57
1060 3676 2.046700 GGATGGCGTCGGGTTGAA 60.047 61.111 0.00 0.00 0.00 2.69
1061 3677 2.398840 TTTGGATGGCGTCGGGTTGA 62.399 55.000 0.00 0.00 0.00 3.18
1071 3687 1.508088 CGTGAAGGCTTTGGATGGC 59.492 57.895 0.00 0.00 0.00 4.40
1105 3721 2.038814 TTGCGGCAACCAGACTCAGA 62.039 55.000 12.11 0.00 0.00 3.27
1106 3722 0.957395 ATTGCGGCAACCAGACTCAG 60.957 55.000 18.94 0.00 0.00 3.35
1107 3723 1.073025 ATTGCGGCAACCAGACTCA 59.927 52.632 18.94 0.00 0.00 3.41
1108 3724 1.503542 CATTGCGGCAACCAGACTC 59.496 57.895 18.94 0.00 0.00 3.36
1109 3725 1.973281 CCATTGCGGCAACCAGACT 60.973 57.895 18.94 0.00 0.00 3.24
1110 3726 2.568090 CCATTGCGGCAACCAGAC 59.432 61.111 18.94 0.00 0.00 3.51
1156 3793 4.253257 GGCGCCGACGAGGAGTAG 62.253 72.222 12.58 0.00 45.00 2.57
1976 4619 2.632544 CGTACGTCTGGCCACTGGA 61.633 63.158 0.00 0.00 0.00 3.86
1978 4621 1.443872 GTCGTACGTCTGGCCACTG 60.444 63.158 16.05 0.00 0.00 3.66
2515 5158 3.399181 TTCTCCTTCGCCCGCCAT 61.399 61.111 0.00 0.00 0.00 4.40
2641 5284 1.671742 GTCCTTCTTGGTGCTCGGA 59.328 57.895 0.00 0.00 37.07 4.55
3147 5816 4.653806 TTTTTGGTTGTGTTTTTCAGCG 57.346 36.364 0.00 0.00 0.00 5.18
3228 5898 0.373716 GGCTAAAGAATCGCACCACG 59.626 55.000 0.00 0.00 45.62 4.94
3250 5920 1.204467 CTGTGTTTGTGTTTGCCCACT 59.796 47.619 0.00 0.00 36.30 4.00
3256 5926 8.633075 ATTCAATTACTCTGTGTTTGTGTTTG 57.367 30.769 0.00 0.00 0.00 2.93
3285 5956 4.625742 ACGAATGTTCTGTAGTATGCACAC 59.374 41.667 0.00 0.00 0.00 3.82
3292 5963 5.779922 AGAAGCAACGAATGTTCTGTAGTA 58.220 37.500 0.00 0.00 35.72 1.82
3293 5964 4.632153 AGAAGCAACGAATGTTCTGTAGT 58.368 39.130 0.00 0.00 35.72 2.73
3294 5965 5.389935 GGAAGAAGCAACGAATGTTCTGTAG 60.390 44.000 0.00 0.00 35.72 2.74
3331 6005 3.317150 TGTGTTACAAGATCTCACAGCG 58.683 45.455 9.48 0.00 34.74 5.18
3333 6007 6.479990 TCACTTTGTGTTACAAGATCTCACAG 59.520 38.462 12.39 6.71 39.53 3.66
3365 6043 8.899771 GGGCACAATTTGTACAACTAGTATTAT 58.100 33.333 8.07 0.00 34.67 1.28
3366 6044 7.883833 TGGGCACAATTTGTACAACTAGTATTA 59.116 33.333 8.07 0.00 34.67 0.98
3371 6049 5.643379 ATGGGCACAATTTGTACAACTAG 57.357 39.130 8.07 3.38 0.00 2.57
3399 6077 2.098770 GCAATCTGCCAAGATGAGGAAC 59.901 50.000 0.00 0.00 42.60 3.62
3433 6114 3.054361 ACCTAGTTTGGCCCATCAACTAG 60.054 47.826 21.17 21.17 33.43 2.57
3434 6115 2.916934 ACCTAGTTTGGCCCATCAACTA 59.083 45.455 0.00 7.60 0.00 2.24
3435 6116 1.710809 ACCTAGTTTGGCCCATCAACT 59.289 47.619 0.00 6.11 0.00 3.16
3446 6127 1.342082 CGCGACGACCACCTAGTTTG 61.342 60.000 0.00 0.00 0.00 2.93
3448 6129 2.564975 CGCGACGACCACCTAGTT 59.435 61.111 0.00 0.00 0.00 2.24
3450 6131 2.478890 ATCCGCGACGACCACCTAG 61.479 63.158 8.23 0.00 0.00 3.02
3451 6132 2.438975 ATCCGCGACGACCACCTA 60.439 61.111 8.23 0.00 0.00 3.08
3555 6256 2.577593 GGGTACCGTGCACTCCTC 59.422 66.667 16.19 2.99 40.86 3.71
3596 6297 1.089481 TGCCGAATCATGGAGCGTTC 61.089 55.000 0.00 0.00 0.00 3.95
3602 6303 1.820906 GCTGCTGCCGAATCATGGA 60.821 57.895 3.85 0.00 0.00 3.41
3606 6307 1.878070 CTTTGCTGCTGCCGAATCA 59.122 52.632 13.47 0.00 38.71 2.57
3609 6310 3.673484 GGCTTTGCTGCTGCCGAA 61.673 61.111 13.47 7.16 37.11 4.30
3627 6328 1.301322 GAAGGCTAGCTGGATCGGC 60.301 63.158 15.72 1.67 35.73 5.54
3708 6409 5.715429 CTAGCATAGCAACATAGCATAGC 57.285 43.478 0.00 0.00 36.85 2.97
3733 6434 7.768807 ATAGGTTAGATTAGCAGTGGAGTAG 57.231 40.000 0.00 0.00 0.00 2.57
3757 6458 4.275689 GGATTGTCAATGCCGAATCATGTA 59.724 41.667 1.88 0.00 0.00 2.29
3758 6459 3.067180 GGATTGTCAATGCCGAATCATGT 59.933 43.478 1.88 0.00 0.00 3.21
3804 6505 0.809241 CCTGGAGTGCATCTCGCTTC 60.809 60.000 9.29 0.00 43.60 3.86
3829 6530 3.818787 GCCCATGTGAAGCGCAGG 61.819 66.667 11.47 0.00 0.00 4.85
3830 6531 2.749044 AGCCCATGTGAAGCGCAG 60.749 61.111 11.47 0.00 0.00 5.18
3852 6553 3.489738 GCGGATCAATGGTCAAATTCAGG 60.490 47.826 0.00 0.00 0.00 3.86
3854 6555 2.426738 GGCGGATCAATGGTCAAATTCA 59.573 45.455 0.00 0.00 0.00 2.57
3872 6573 0.519961 CTTGGGTTAAAGGAACGGCG 59.480 55.000 4.80 4.80 39.12 6.46
3886 6587 1.903877 ATCGACCAGGAGTGCTTGGG 61.904 60.000 0.00 0.00 45.06 4.12
3892 6593 2.205074 GCATGTTATCGACCAGGAGTG 58.795 52.381 0.00 0.00 0.00 3.51
3944 6645 4.041444 GGAGATGGAAAGATGATAGGCACT 59.959 45.833 0.00 0.00 46.37 4.40
3970 6689 0.456221 ACGTGAGGCTGATTAGGACG 59.544 55.000 0.00 0.00 0.00 4.79
4026 6746 0.605589 AAAGACAACGCCTACCTGCC 60.606 55.000 0.00 0.00 0.00 4.85
4078 6798 0.937699 TCAGTTTCACGCGAGAACCG 60.938 55.000 18.63 9.96 42.21 4.44
4085 6805 6.281056 CACATTTTAATTTCAGTTTCACGCG 58.719 36.000 3.53 3.53 0.00 6.01
4089 6809 7.437862 GTCAGGCACATTTTAATTTCAGTTTCA 59.562 33.333 0.00 0.00 0.00 2.69
4090 6810 7.437862 TGTCAGGCACATTTTAATTTCAGTTTC 59.562 33.333 0.00 0.00 0.00 2.78
4091 6811 7.271511 TGTCAGGCACATTTTAATTTCAGTTT 58.728 30.769 0.00 0.00 0.00 2.66
4092 6812 6.815089 TGTCAGGCACATTTTAATTTCAGTT 58.185 32.000 0.00 0.00 0.00 3.16
4093 6813 6.265196 TCTGTCAGGCACATTTTAATTTCAGT 59.735 34.615 0.00 0.00 33.23 3.41
4094 6814 6.680810 TCTGTCAGGCACATTTTAATTTCAG 58.319 36.000 0.00 0.00 33.23 3.02
4115 6842 8.498054 TTGACTTTTCAGGAGCTATAATTCTG 57.502 34.615 0.00 0.00 31.71 3.02
4118 6845 6.319911 GCCTTGACTTTTCAGGAGCTATAATT 59.680 38.462 0.00 0.00 30.19 1.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.