Multiple sequence alignment - TraesCS6A01G351300

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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 TraesCS6A01G351300 chr6A 100.000 4591 0 0 949 5539 583272768 583268178 0.000000e+00 8479.0
1 TraesCS6A01G351300 chr6A 100.000 660 0 0 1 660 583273716 583273057 0.000000e+00 1219.0
2 TraesCS6A01G351300 chr6B 90.766 4202 229 69 991 5108 659236784 659232658 0.000000e+00 5463.0
3 TraesCS6A01G351300 chr6B 82.051 312 42 8 5150 5457 659230770 659230469 2.560000e-63 254.0
4 TraesCS6A01G351300 chr6B 91.176 68 6 0 593 660 659236999 659236932 5.910000e-15 93.5
5 TraesCS6A01G351300 chr6D 92.647 3713 161 57 949 4599 436225639 436221977 0.000000e+00 5241.0
6 TraesCS6A01G351300 chr6D 85.586 1006 69 30 4549 5539 436221987 436221043 0.000000e+00 985.0
7 TraesCS6A01G351300 chr6D 82.902 696 57 36 8 660 436226804 436226128 2.240000e-158 569.0
8 TraesCS6A01G351300 chrUn 84.539 304 29 14 203 495 270353991 270354287 9.080000e-73 285.0
9 TraesCS6A01G351300 chr7D 84.539 304 29 14 203 495 631658219 631657923 9.080000e-73 285.0
10 TraesCS6A01G351300 chr4B 79.000 200 37 4 4269 4467 497554178 497554373 1.250000e-26 132.0
11 TraesCS6A01G351300 chr4A 78.713 202 34 8 4269 4467 59484247 59484442 5.830000e-25 126.0


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 TraesCS6A01G351300 chr6A 583268178 583273716 5538 True 4849.000000 8479 100.000000 1 5539 2 chr6A.!!$R1 5538
1 TraesCS6A01G351300 chr6B 659230469 659236999 6530 True 1936.833333 5463 87.997667 593 5457 3 chr6B.!!$R1 4864
2 TraesCS6A01G351300 chr6D 436221043 436226804 5761 True 2265.000000 5241 87.045000 8 5539 3 chr6D.!!$R1 5531

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
498 532 0.035458 GATCTGGATAAGCCCCGTGG 59.965 60.0 0.0 0.0 34.97 4.94 F
532 566 0.250513 CCCTCCTTCTTCCACCTTCG 59.749 60.0 0.0 0.0 0.00 3.79 F
533 567 0.391793 CCTCCTTCTTCCACCTTCGC 60.392 60.0 0.0 0.0 0.00 4.70 F
534 568 0.610687 CTCCTTCTTCCACCTTCGCT 59.389 55.0 0.0 0.0 0.00 4.93 F
2712 2967 0.249699 ACATTGTGCCGTCGTTCAGA 60.250 50.0 0.0 0.0 0.00 3.27 F
2805 3060 0.102120 CGAGCAGTGAGGTCATCTCC 59.898 60.0 0.0 0.0 44.97 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 2619 1.226575 CACGATGACGCTCCGCTTA 60.227 57.895 0.00 0.00 43.96 3.09 R
2613 2868 2.839162 CCAATCCCCCAATGCCGG 60.839 66.667 0.00 0.00 0.00 6.13 R
2661 2916 2.181525 CGCCTGAAATTTGGGCCG 59.818 61.111 19.78 13.64 42.58 6.13 R
2805 3060 0.363512 CGCACAGACGATTCAAGACG 59.636 55.000 0.00 0.00 34.06 4.18 R
3960 4264 0.098728 GCCGATCCAACAAATCCGTG 59.901 55.000 0.00 0.00 0.00 4.94 R
4713 5080 0.670854 GCGCGAGAGGAAGAGGTTTT 60.671 55.000 12.10 0.00 0.00 2.43 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
93 94 2.999739 TTTGGACACCCGCTCGGTTC 63.000 60.000 7.59 1.02 45.36 3.62
102 103 2.693762 CGCTCGGTTCGGTAGACCA 61.694 63.158 0.00 0.00 35.14 4.02
105 106 1.606224 GCTCGGTTCGGTAGACCAAAA 60.606 52.381 0.00 0.00 35.14 2.44
115 116 2.546789 GGTAGACCAAAACACGGTTCAG 59.453 50.000 0.00 0.00 36.69 3.02
124 125 1.398692 ACACGGTTCAGCCACAAAAT 58.601 45.000 0.00 0.00 36.97 1.82
147 148 2.560542 TGGCACGGAAAGCACATTTTAT 59.439 40.909 0.00 0.00 0.00 1.40
150 151 4.102649 GCACGGAAAGCACATTTTATACC 58.897 43.478 0.00 0.00 0.00 2.73
151 152 4.668289 CACGGAAAGCACATTTTATACCC 58.332 43.478 0.00 0.00 0.00 3.69
152 153 3.697542 ACGGAAAGCACATTTTATACCCC 59.302 43.478 0.00 0.00 0.00 4.95
153 154 3.067601 CGGAAAGCACATTTTATACCCCC 59.932 47.826 0.00 0.00 0.00 5.40
154 155 3.067601 GGAAAGCACATTTTATACCCCCG 59.932 47.826 0.00 0.00 0.00 5.73
177 178 3.955101 TTTTCCCGGTGCGCGTTG 61.955 61.111 8.43 0.00 0.00 4.10
183 184 4.368808 CGGTGCGCGTTGTCCTTG 62.369 66.667 8.43 0.00 0.00 3.61
184 185 3.276846 GGTGCGCGTTGTCCTTGT 61.277 61.111 8.43 0.00 0.00 3.16
187 188 1.063327 TGCGCGTTGTCCTTGTTTG 59.937 52.632 8.43 0.00 0.00 2.93
188 189 2.292916 GCGCGTTGTCCTTGTTTGC 61.293 57.895 8.43 0.00 0.00 3.68
189 190 2.003443 CGCGTTGTCCTTGTTTGCG 61.003 57.895 0.00 0.00 38.04 4.85
190 191 1.657181 GCGTTGTCCTTGTTTGCGG 60.657 57.895 0.00 0.00 0.00 5.69
191 192 1.725066 CGTTGTCCTTGTTTGCGGT 59.275 52.632 0.00 0.00 0.00 5.68
192 193 0.591236 CGTTGTCCTTGTTTGCGGTG 60.591 55.000 0.00 0.00 0.00 4.94
193 194 0.869880 GTTGTCCTTGTTTGCGGTGC 60.870 55.000 0.00 0.00 0.00 5.01
194 195 2.051345 GTCCTTGTTTGCGGTGCG 60.051 61.111 0.00 0.00 0.00 5.34
195 196 2.515057 TCCTTGTTTGCGGTGCGT 60.515 55.556 0.00 0.00 0.00 5.24
196 197 2.353376 CCTTGTTTGCGGTGCGTG 60.353 61.111 0.00 0.00 0.00 5.34
197 198 3.024043 CTTGTTTGCGGTGCGTGC 61.024 61.111 0.00 0.00 0.00 5.34
302 303 2.871022 CGGATAGACGGATAGGGATACG 59.129 54.545 0.00 0.00 45.63 3.06
329 330 2.426261 GGCCGTTTCGTTTGACGC 60.426 61.111 0.00 0.00 42.21 5.19
334 335 2.895865 TTTCGTTTGACGCCCGCA 60.896 55.556 0.00 0.00 42.21 5.69
335 336 3.170810 TTTCGTTTGACGCCCGCAC 62.171 57.895 0.00 0.00 42.21 5.34
372 373 1.660355 GCGCTCGTCTATCCATCCA 59.340 57.895 0.00 0.00 0.00 3.41
380 396 5.680922 GCTCGTCTATCCATCCATCCAATAG 60.681 48.000 0.00 0.00 0.00 1.73
455 471 2.438434 GGGGCAGGACCGTCATTG 60.438 66.667 0.00 0.00 40.62 2.82
498 532 0.035458 GATCTGGATAAGCCCCGTGG 59.965 60.000 0.00 0.00 34.97 4.94
522 556 1.778383 TTGGTTGCCCCCTCCTTCT 60.778 57.895 0.00 0.00 0.00 2.85
523 557 1.368268 TTGGTTGCCCCCTCCTTCTT 61.368 55.000 0.00 0.00 0.00 2.52
526 560 1.465188 TTGCCCCCTCCTTCTTCCA 60.465 57.895 0.00 0.00 0.00 3.53
527 561 1.789576 TTGCCCCCTCCTTCTTCCAC 61.790 60.000 0.00 0.00 0.00 4.02
529 563 1.229984 CCCCCTCCTTCTTCCACCT 60.230 63.158 0.00 0.00 0.00 4.00
531 565 0.621082 CCCCTCCTTCTTCCACCTTC 59.379 60.000 0.00 0.00 0.00 3.46
532 566 0.250513 CCCTCCTTCTTCCACCTTCG 59.749 60.000 0.00 0.00 0.00 3.79
533 567 0.391793 CCTCCTTCTTCCACCTTCGC 60.392 60.000 0.00 0.00 0.00 4.70
534 568 0.610687 CTCCTTCTTCCACCTTCGCT 59.389 55.000 0.00 0.00 0.00 4.93
558 599 2.119495 GATCCTGGTCCAAGCTAGGAA 58.881 52.381 4.78 0.00 42.20 3.36
559 600 1.276622 TCCTGGTCCAAGCTAGGAAC 58.723 55.000 0.00 0.00 45.91 3.62
562 603 1.221021 GGTCCAAGCTAGGAACGGG 59.779 63.158 0.00 0.00 39.92 5.28
565 606 0.976073 TCCAAGCTAGGAACGGGAGG 60.976 60.000 0.00 0.00 33.93 4.30
566 607 0.976073 CCAAGCTAGGAACGGGAGGA 60.976 60.000 0.00 0.00 0.00 3.71
567 608 1.123928 CAAGCTAGGAACGGGAGGAT 58.876 55.000 0.00 0.00 0.00 3.24
634 680 6.888632 GTCTCGTTTATATATACCTCCTCCCA 59.111 42.308 0.00 0.00 0.00 4.37
638 684 2.226962 TATATACCTCCTCCCACGCC 57.773 55.000 0.00 0.00 0.00 5.68
1665 1920 1.137282 GTCGGATTCTTCCTCCACTCC 59.863 57.143 0.00 0.00 40.17 3.85
1695 1950 1.388065 CCTCCGAGATCTTCCGCACT 61.388 60.000 0.00 0.00 0.00 4.40
1830 2085 2.869503 ATTACCAGTCCAAGCGCGGG 62.870 60.000 8.83 14.15 0.00 6.13
2049 2304 2.509916 CTGGGGATGGAGCAGCTC 59.490 66.667 14.69 14.69 0.00 4.09
2406 2661 0.803768 CTGAGTTCGTGGGATGCTCG 60.804 60.000 0.00 0.00 31.28 5.03
2457 2712 2.711922 ATGGAGCGTGGAGTCCGTC 61.712 63.158 4.30 0.00 35.37 4.79
2613 2868 1.425428 CAAGGACCATTTCTCGCGC 59.575 57.895 0.00 0.00 0.00 6.86
2661 2916 2.281484 TTCAAGGTGGTGGCGCTC 60.281 61.111 7.64 0.23 0.00 5.03
2712 2967 0.249699 ACATTGTGCCGTCGTTCAGA 60.250 50.000 0.00 0.00 0.00 3.27
2805 3060 0.102120 CGAGCAGTGAGGTCATCTCC 59.898 60.000 0.00 0.00 44.97 3.71
3008 3264 0.169009 GTGTTGCTTTGCTCCGGATC 59.831 55.000 3.57 0.00 0.00 3.36
3029 3285 2.607771 CCTTGTTGACCGCTTTTGATGG 60.608 50.000 0.00 0.00 0.00 3.51
3076 3336 4.078363 TGCGAATTAAGCAAAGTAGCAC 57.922 40.909 5.70 0.00 38.57 4.40
3077 3337 3.500299 TGCGAATTAAGCAAAGTAGCACA 59.500 39.130 5.70 0.00 38.57 4.57
3078 3338 4.023622 TGCGAATTAAGCAAAGTAGCACAA 60.024 37.500 5.70 0.00 38.57 3.33
3079 3339 4.320953 GCGAATTAAGCAAAGTAGCACAAC 59.679 41.667 0.00 0.00 34.46 3.32
3080 3340 5.448438 CGAATTAAGCAAAGTAGCACAACA 58.552 37.500 0.00 0.00 36.85 3.33
3083 3343 7.463469 AATTAAGCAAAGTAGCACAACAAAC 57.537 32.000 0.00 0.00 36.85 2.93
3084 3344 4.448537 AAGCAAAGTAGCACAACAAACA 57.551 36.364 0.00 0.00 36.85 2.83
3085 3345 4.032703 AGCAAAGTAGCACAACAAACAG 57.967 40.909 0.00 0.00 36.85 3.16
3086 3346 3.443681 AGCAAAGTAGCACAACAAACAGT 59.556 39.130 0.00 0.00 36.85 3.55
3087 3347 3.547468 GCAAAGTAGCACAACAAACAGTG 59.453 43.478 0.00 0.00 38.74 3.66
3088 3348 4.732784 CAAAGTAGCACAACAAACAGTGT 58.267 39.130 0.00 0.00 44.64 3.55
3106 3366 6.877236 ACAGTGTCATCCAAGAAAACATTTT 58.123 32.000 0.00 0.00 0.00 1.82
3107 3367 6.980397 ACAGTGTCATCCAAGAAAACATTTTC 59.020 34.615 8.73 8.73 45.22 2.29
3109 3369 7.492020 CAGTGTCATCCAAGAAAACATTTTCAA 59.508 33.333 17.12 2.98 46.81 2.69
3110 3370 7.707893 AGTGTCATCCAAGAAAACATTTTCAAG 59.292 33.333 17.12 9.76 46.81 3.02
3111 3371 7.706179 GTGTCATCCAAGAAAACATTTTCAAGA 59.294 33.333 17.12 11.26 46.81 3.02
3112 3372 8.423349 TGTCATCCAAGAAAACATTTTCAAGAT 58.577 29.630 17.12 12.64 46.81 2.40
3113 3373 8.706035 GTCATCCAAGAAAACATTTTCAAGATG 58.294 33.333 22.43 22.43 46.81 2.90
3114 3374 7.385752 TCATCCAAGAAAACATTTTCAAGATGC 59.614 33.333 22.99 2.39 46.81 3.91
3115 3375 6.580788 TCCAAGAAAACATTTTCAAGATGCA 58.419 32.000 17.12 0.00 46.81 3.96
3116 3376 7.218614 TCCAAGAAAACATTTTCAAGATGCAT 58.781 30.769 17.12 0.00 46.81 3.96
3118 3378 8.991026 CCAAGAAAACATTTTCAAGATGCATAA 58.009 29.630 17.12 0.00 46.81 1.90
3126 3386 9.715121 ACATTTTCAAGATGCATAAAAATGAGT 57.285 25.926 30.91 19.35 44.34 3.41
3129 3389 8.915871 TTTCAAGATGCATAAAAATGAGTAGC 57.084 30.769 0.00 0.00 0.00 3.58
3137 3397 5.576774 GCATAAAAATGAGTAGCAACCAACC 59.423 40.000 0.00 0.00 0.00 3.77
3176 3441 0.466124 AGCATAGCTCCTCCGAAACC 59.534 55.000 0.00 0.00 30.62 3.27
3182 3447 1.219393 CTCCTCCGAAACCAGCCTC 59.781 63.158 0.00 0.00 0.00 4.70
3186 3451 1.005394 TCCGAAACCAGCCTCGAAC 60.005 57.895 0.00 0.00 37.23 3.95
3206 3471 0.366871 CGTCGACATTCTTGCTTCCG 59.633 55.000 17.16 0.00 0.00 4.30
3213 3478 2.293399 ACATTCTTGCTTCCGGAACAAC 59.707 45.455 14.35 6.48 0.00 3.32
3214 3479 1.314730 TTCTTGCTTCCGGAACAACC 58.685 50.000 14.35 2.63 0.00 3.77
3217 3482 1.001378 CTTGCTTCCGGAACAACCTTG 60.001 52.381 14.35 2.53 36.31 3.61
3231 3496 3.545724 CCTTGGGAGGTTACGGTTC 57.454 57.895 0.00 0.00 38.32 3.62
3241 3506 0.971386 GTTACGGTTCTGGAGGGTGA 59.029 55.000 0.00 0.00 0.00 4.02
3258 3523 3.181506 GGGTGAGAAGTGATTGATTTCGC 60.182 47.826 0.00 0.00 0.00 4.70
3278 3544 3.142174 GCCCATGAACCTAAGCATAGAC 58.858 50.000 0.00 0.00 0.00 2.59
3296 3562 4.715527 AGACGGTTACTGTTCCAGTATC 57.284 45.455 0.00 4.79 44.85 2.24
3298 3564 2.498885 ACGGTTACTGTTCCAGTATCCC 59.501 50.000 18.87 14.01 46.17 3.85
3299 3565 2.764572 CGGTTACTGTTCCAGTATCCCT 59.235 50.000 18.87 0.00 46.17 4.20
3300 3566 3.197116 CGGTTACTGTTCCAGTATCCCTT 59.803 47.826 18.87 0.00 46.17 3.95
3301 3567 4.323257 CGGTTACTGTTCCAGTATCCCTTT 60.323 45.833 18.87 0.00 46.17 3.11
3302 3568 5.105228 CGGTTACTGTTCCAGTATCCCTTTA 60.105 44.000 18.87 0.00 46.17 1.85
3303 3569 6.346896 GGTTACTGTTCCAGTATCCCTTTAG 58.653 44.000 15.85 0.00 44.85 1.85
3304 3570 6.346896 GTTACTGTTCCAGTATCCCTTTAGG 58.653 44.000 5.03 0.00 44.85 2.69
3311 3577 5.286221 TCCAGTATCCCTTTAGGCTTTAGT 58.714 41.667 0.00 0.00 34.51 2.24
3335 3601 9.294614 AGTTAGAAGAGAGCATTCAAATCTTTT 57.705 29.630 0.00 0.00 30.62 2.27
3348 3614 5.240891 TCAAATCTTTTGTTTGTGGTTGCA 58.759 33.333 0.39 0.00 37.70 4.08
3349 3615 5.350914 TCAAATCTTTTGTTTGTGGTTGCAG 59.649 36.000 0.39 0.00 37.70 4.41
3351 3617 4.527509 TCTTTTGTTTGTGGTTGCAGAA 57.472 36.364 0.00 0.00 0.00 3.02
3353 3619 6.214191 TCTTTTGTTTGTGGTTGCAGAATA 57.786 33.333 0.00 0.00 0.00 1.75
3355 3621 5.590530 TTTGTTTGTGGTTGCAGAATAGT 57.409 34.783 0.00 0.00 0.00 2.12
3356 3622 4.566545 TGTTTGTGGTTGCAGAATAGTG 57.433 40.909 0.00 0.00 0.00 2.74
3361 3627 2.412089 GTGGTTGCAGAATAGTGACGTC 59.588 50.000 9.11 9.11 0.00 4.34
3363 3629 2.611971 GGTTGCAGAATAGTGACGTCCA 60.612 50.000 14.12 0.00 0.00 4.02
3364 3630 3.262420 GTTGCAGAATAGTGACGTCCAT 58.738 45.455 14.12 3.81 0.00 3.41
3365 3631 3.610040 TGCAGAATAGTGACGTCCATT 57.390 42.857 14.12 9.79 0.00 3.16
3367 3633 3.056179 TGCAGAATAGTGACGTCCATTGA 60.056 43.478 14.12 0.00 0.00 2.57
3368 3634 4.122776 GCAGAATAGTGACGTCCATTGAT 58.877 43.478 14.12 0.00 0.00 2.57
3369 3635 5.163457 TGCAGAATAGTGACGTCCATTGATA 60.163 40.000 14.12 0.00 0.00 2.15
3370 3636 5.928839 GCAGAATAGTGACGTCCATTGATAT 59.071 40.000 14.12 0.00 0.00 1.63
3374 3640 8.088981 AGAATAGTGACGTCCATTGATATAACC 58.911 37.037 14.12 0.00 0.00 2.85
3486 3752 1.467543 CCGGTGATGAGACTGTACACG 60.468 57.143 0.00 0.00 33.08 4.49
3558 3824 4.907034 CACGACGAGGCCGATCCG 62.907 72.222 0.00 2.82 40.77 4.18
3930 4231 1.153509 GCCACATGCTTGATTGCCC 60.154 57.895 6.60 0.00 36.87 5.36
3950 4254 3.629142 CCCCCGGAACAATCTATATCC 57.371 52.381 0.73 0.00 0.00 2.59
3960 4264 5.968528 ACAATCTATATCCTCTCCACGAC 57.031 43.478 0.00 0.00 0.00 4.34
3963 4267 3.400255 TCTATATCCTCTCCACGACACG 58.600 50.000 0.00 0.00 0.00 4.49
3973 4277 0.237235 CCACGACACGGATTTGTTGG 59.763 55.000 0.00 0.00 35.44 3.77
3980 4284 1.351707 CGGATTTGTTGGATCGGCG 59.648 57.895 0.00 0.00 0.00 6.46
4101 4413 9.862371 TGGCGCTATTTGATTTTATTTTAGAAA 57.138 25.926 7.64 0.00 0.00 2.52
4117 4429 3.692257 AGAAAGTAGCAGCATCTGTGT 57.308 42.857 0.00 0.00 33.43 3.72
4118 4430 4.808414 AGAAAGTAGCAGCATCTGTGTA 57.192 40.909 0.00 0.00 33.43 2.90
4128 4440 1.328680 GCATCTGTGTATCACTTGCCG 59.671 52.381 1.72 0.00 35.11 5.69
4144 4456 2.747460 CGGCACCACCACCATCTG 60.747 66.667 0.00 0.00 39.03 2.90
4160 4489 4.245660 CCATCTGTGTATCGTTGTCTTGT 58.754 43.478 0.00 0.00 0.00 3.16
4170 4499 4.285807 TCGTTGTCTTGTTTTGACATGG 57.714 40.909 0.00 0.00 42.95 3.66
4184 4513 8.896744 TGTTTTGACATGGATGAAATATCTCTC 58.103 33.333 0.00 0.00 0.00 3.20
4193 4522 5.105917 GGATGAAATATCTCTCCTCTCCGTC 60.106 48.000 0.00 0.00 0.00 4.79
4463 4792 2.044252 AAGATGCTGCAGGGGCTG 60.044 61.111 17.12 0.00 41.91 4.85
4540 4869 2.850568 AGGAAGGAAACGGGGTATGAAT 59.149 45.455 0.00 0.00 0.00 2.57
4543 4872 4.820173 GGAAGGAAACGGGGTATGAATAAG 59.180 45.833 0.00 0.00 0.00 1.73
4547 4914 0.250166 ACGGGGTATGAATAAGCCGC 60.250 55.000 0.00 0.00 35.27 6.53
4568 4935 2.800544 CCGACGATGATGTCAATAACCC 59.199 50.000 0.00 0.00 38.84 4.11
4569 4936 2.471370 CGACGATGATGTCAATAACCCG 59.529 50.000 0.00 0.00 38.84 5.28
4576 4943 6.582677 ATGATGTCAATAACCCGTGAAAAA 57.417 33.333 0.00 0.00 0.00 1.94
4612 4979 3.916776 ACGACGATGATGATGATGATTCG 59.083 43.478 0.00 0.00 0.00 3.34
4614 4981 4.240888 GACGATGATGATGATGATTCGGT 58.759 43.478 0.00 0.00 0.00 4.69
4615 4982 4.240888 ACGATGATGATGATGATTCGGTC 58.759 43.478 0.00 0.00 0.00 4.79
4617 4984 4.687483 CGATGATGATGATGATTCGGTCAA 59.313 41.667 0.00 0.00 40.97 3.18
4652 5019 5.880332 TGGTTTTAGGATTAGCTGCAGTTAG 59.120 40.000 16.64 0.00 0.00 2.34
4685 5052 7.990917 ACAGGTTTCTTTCTTCTTTCTTCTTC 58.009 34.615 0.00 0.00 0.00 2.87
4686 5053 7.831690 ACAGGTTTCTTTCTTCTTTCTTCTTCT 59.168 33.333 0.00 0.00 0.00 2.85
4687 5054 8.681806 CAGGTTTCTTTCTTCTTTCTTCTTCTT 58.318 33.333 0.00 0.00 0.00 2.52
4688 5055 8.898761 AGGTTTCTTTCTTCTTTCTTCTTCTTC 58.101 33.333 0.00 0.00 0.00 2.87
4689 5056 8.898761 GGTTTCTTTCTTCTTTCTTCTTCTTCT 58.101 33.333 0.00 0.00 0.00 2.85
4713 5080 9.985730 TCTTATTCTTCTTCTGGTTTACGTTTA 57.014 29.630 0.00 0.00 0.00 2.01
4737 5104 4.785512 CTTCCTCTCGCGCACGCT 62.786 66.667 13.70 0.00 39.84 5.07
4799 5171 0.584876 GTTTGTTCCTTCCGGTCACG 59.415 55.000 0.00 0.00 40.55 4.35
4836 5208 4.507756 TGACGATGACGATGAAATCAATCC 59.492 41.667 0.00 0.00 45.97 3.01
4866 5241 2.925966 AATGATTCTTTCAGCCCCCA 57.074 45.000 0.00 0.00 37.89 4.96
4867 5242 3.409804 AATGATTCTTTCAGCCCCCAT 57.590 42.857 0.00 0.00 37.89 4.00
4868 5243 2.148446 TGATTCTTTCAGCCCCCATG 57.852 50.000 0.00 0.00 0.00 3.66
4905 5281 5.895928 AGTATATCGTTGATCCATCCATCG 58.104 41.667 0.00 0.00 0.00 3.84
4959 5339 5.691896 CATATATGGATGGATGCAGTGGAT 58.308 41.667 4.68 0.00 0.00 3.41
4995 5375 1.215014 GCACGCTTTTCACCTTTGCC 61.215 55.000 0.00 0.00 0.00 4.52
5076 5470 0.177604 CAGATCAGACCAGGTGCTCC 59.822 60.000 0.00 0.00 0.00 4.70
5084 5478 1.414550 GACCAGGTGCTCCTTATCTCC 59.585 57.143 4.10 0.00 43.07 3.71
5107 5501 4.598894 CCGCCAGCATCCTCGGAG 62.599 72.222 0.00 0.00 44.23 4.63
5108 5502 3.842923 CGCCAGCATCCTCGGAGT 61.843 66.667 4.02 0.00 0.00 3.85
5109 5503 2.490148 CGCCAGCATCCTCGGAGTA 61.490 63.158 4.02 0.00 0.00 2.59
5110 5504 1.365633 GCCAGCATCCTCGGAGTAG 59.634 63.158 4.02 0.00 0.00 2.57
5111 5505 1.109920 GCCAGCATCCTCGGAGTAGA 61.110 60.000 4.02 0.00 0.00 2.59
5112 5506 1.626686 CCAGCATCCTCGGAGTAGAT 58.373 55.000 4.02 0.00 0.00 1.98
5113 5507 1.967066 CCAGCATCCTCGGAGTAGATT 59.033 52.381 4.02 0.00 0.00 2.40
5114 5508 2.366916 CCAGCATCCTCGGAGTAGATTT 59.633 50.000 4.02 0.00 0.00 2.17
5116 5510 4.054671 CAGCATCCTCGGAGTAGATTTTC 58.945 47.826 4.02 0.00 0.00 2.29
5118 5512 4.407296 AGCATCCTCGGAGTAGATTTTCTT 59.593 41.667 4.02 0.00 0.00 2.52
5121 5515 3.705072 TCCTCGGAGTAGATTTTCTTCCC 59.295 47.826 4.02 0.00 0.00 3.97
5122 5516 3.491104 CCTCGGAGTAGATTTTCTTCCCG 60.491 52.174 4.02 0.00 32.92 5.14
5132 5526 3.412237 TTTTCTTCCCGTTCCTGGTAG 57.588 47.619 0.00 0.00 0.00 3.18
5158 7399 2.233186 AGCAACGGGAGACTAACCTAAC 59.767 50.000 0.00 0.00 0.00 2.34
5163 7404 2.830293 GGGAGACTAACCTAACCCACT 58.170 52.381 0.00 0.00 37.50 4.00
5166 7407 1.907255 AGACTAACCTAACCCACTGCC 59.093 52.381 0.00 0.00 0.00 4.85
5175 7416 4.232061 CCCACTGCCAACCCCCAA 62.232 66.667 0.00 0.00 0.00 4.12
5185 7426 1.382522 CAACCCCCAACTGATCATCG 58.617 55.000 0.00 0.00 0.00 3.84
5189 7430 1.889105 CCCAACTGATCATCGCCCG 60.889 63.158 0.00 0.00 0.00 6.13
5216 7457 3.883489 TCACACAGGGATATCTCTGTACG 59.117 47.826 32.78 25.86 41.71 3.67
5217 7458 3.004839 CACACAGGGATATCTCTGTACGG 59.995 52.174 32.78 23.95 41.71 4.02
5285 7527 2.142357 GAGCCAAACTTCAACGGCCC 62.142 60.000 0.00 0.00 46.08 5.80
5301 7543 1.140852 GGCCCAAGCAAGTTTTCCTTT 59.859 47.619 0.00 0.00 42.56 3.11
5310 7552 3.681417 GCAAGTTTTCCTTTGCCATGATC 59.319 43.478 0.00 0.00 0.00 2.92
5344 7586 0.676184 TTCGTTGTCAGAGAGCAGCT 59.324 50.000 0.00 0.00 0.00 4.24
5345 7587 0.038801 TCGTTGTCAGAGAGCAGCTG 60.039 55.000 10.11 10.11 34.71 4.24
5383 7626 4.748679 AGTGCGTACGACGGTCGC 62.749 66.667 28.67 24.16 45.12 5.19
5432 7675 1.075525 CCGGAGAGGGACATGGGTA 60.076 63.158 0.00 0.00 35.97 3.69
5436 7679 1.974236 GGAGAGGGACATGGGTAGATG 59.026 57.143 0.00 0.00 0.00 2.90
5470 7713 2.480610 CGGTGGAATGGAATGCCCG 61.481 63.158 0.00 0.00 43.77 6.13
5473 7716 3.226537 GGAATGGAATGCCCGGGC 61.227 66.667 39.40 39.40 35.17 6.13
5474 7717 3.595758 GAATGGAATGCCCGGGCG 61.596 66.667 39.00 7.25 45.51 6.13
5475 7718 4.122149 AATGGAATGCCCGGGCGA 62.122 61.111 39.00 28.05 45.51 5.54
5476 7719 3.435525 AATGGAATGCCCGGGCGAT 62.436 57.895 39.00 30.34 45.51 4.58
5477 7720 3.850098 ATGGAATGCCCGGGCGATC 62.850 63.158 39.00 34.99 45.51 3.69
5479 7722 4.602259 GAATGCCCGGGCGATCGA 62.602 66.667 39.00 23.27 45.51 3.59
5492 7735 1.391485 GCGATCGATCCATCATTTCGG 59.609 52.381 21.57 2.78 33.82 4.30
5493 7736 1.995484 CGATCGATCCATCATTTCGGG 59.005 52.381 19.51 0.00 33.82 5.14
5499 7742 2.869101 TCCATCATTTCGGGTCACAA 57.131 45.000 0.00 0.00 0.00 3.33
5502 7745 1.811965 CATCATTTCGGGTCACAAGCA 59.188 47.619 0.00 0.00 0.00 3.91
5503 7746 1.234821 TCATTTCGGGTCACAAGCAC 58.765 50.000 0.00 0.00 0.00 4.40
5504 7747 0.110238 CATTTCGGGTCACAAGCACG 60.110 55.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.263185 CGTGCTTATCTTTTATTTGACGGG 58.737 41.667 0.00 0.00 0.00 5.28
1 2 5.263185 CCGTGCTTATCTTTTATTTGACGG 58.737 41.667 0.00 0.00 36.97 4.79
2 3 4.728608 GCCGTGCTTATCTTTTATTTGACG 59.271 41.667 0.00 0.00 0.00 4.35
3 4 4.728608 CGCCGTGCTTATCTTTTATTTGAC 59.271 41.667 0.00 0.00 0.00 3.18
4 5 4.393680 ACGCCGTGCTTATCTTTTATTTGA 59.606 37.500 0.00 0.00 0.00 2.69
5 6 4.658071 ACGCCGTGCTTATCTTTTATTTG 58.342 39.130 0.00 0.00 0.00 2.32
6 7 4.634443 AGACGCCGTGCTTATCTTTTATTT 59.366 37.500 0.00 0.00 0.00 1.40
36 37 7.703058 ATAAACTGTTTGAAGGGAATACAGG 57.297 36.000 15.69 0.00 40.29 4.00
65 66 1.834188 GGGTGTCCAAAATGTCGGAT 58.166 50.000 0.00 0.00 32.83 4.18
93 94 1.528161 GAACCGTGTTTTGGTCTACCG 59.472 52.381 0.00 0.00 39.29 4.02
102 103 1.178276 TTGTGGCTGAACCGTGTTTT 58.822 45.000 0.00 0.00 43.94 2.43
105 106 1.066908 CATTTTGTGGCTGAACCGTGT 59.933 47.619 0.00 0.00 43.94 4.49
124 125 1.106351 AATGTGCTTTCCGTGCCACA 61.106 50.000 0.00 0.00 0.00 4.17
177 178 2.051345 CGCACCGCAAACAAGGAC 60.051 61.111 0.00 0.00 0.00 3.85
302 303 4.699522 AAACGGCCGCTGGGTCTC 62.700 66.667 28.58 0.00 35.04 3.36
309 310 2.589442 TCAAACGAAACGGCCGCT 60.589 55.556 28.58 11.40 0.00 5.52
353 354 1.080434 GGATGGATAGACGAGCGCC 60.080 63.158 2.29 0.00 0.00 6.53
404 420 1.526686 GACGGTTCGGGTTGGGTTT 60.527 57.895 0.00 0.00 0.00 3.27
405 421 2.111669 GACGGTTCGGGTTGGGTT 59.888 61.111 0.00 0.00 0.00 4.11
406 422 3.944945 GGACGGTTCGGGTTGGGT 61.945 66.667 0.00 0.00 0.00 4.51
407 423 4.710167 GGGACGGTTCGGGTTGGG 62.710 72.222 0.00 0.00 0.00 4.12
408 424 3.943691 TGGGACGGTTCGGGTTGG 61.944 66.667 0.00 0.00 0.00 3.77
410 426 4.303993 CGTGGGACGGTTCGGGTT 62.304 66.667 0.00 0.00 38.08 4.11
517 551 0.391793 GGAGCGAAGGTGGAAGAAGG 60.392 60.000 0.00 0.00 39.88 3.46
522 556 0.537188 GATCAGGAGCGAAGGTGGAA 59.463 55.000 0.00 0.00 39.88 3.53
523 557 1.330655 GGATCAGGAGCGAAGGTGGA 61.331 60.000 0.00 0.00 39.88 4.02
526 560 1.333636 CCAGGATCAGGAGCGAAGGT 61.334 60.000 0.00 0.00 46.54 3.50
527 561 1.333636 ACCAGGATCAGGAGCGAAGG 61.334 60.000 10.14 0.00 0.00 3.46
529 563 1.330655 GGACCAGGATCAGGAGCGAA 61.331 60.000 10.14 0.00 0.00 4.70
531 565 1.617018 TTGGACCAGGATCAGGAGCG 61.617 60.000 10.14 0.00 0.00 5.03
532 566 0.179936 CTTGGACCAGGATCAGGAGC 59.820 60.000 10.14 2.46 0.00 4.70
533 567 0.179936 GCTTGGACCAGGATCAGGAG 59.820 60.000 7.99 0.00 0.00 3.69
534 568 0.252881 AGCTTGGACCAGGATCAGGA 60.253 55.000 7.99 0.00 0.00 3.86
558 599 0.178958 CCACCTAGCTATCCTCCCGT 60.179 60.000 0.00 0.00 0.00 5.28
559 600 0.900647 CCCACCTAGCTATCCTCCCG 60.901 65.000 0.00 0.00 0.00 5.14
560 601 1.195442 GCCCACCTAGCTATCCTCCC 61.195 65.000 0.00 0.00 0.00 4.30
562 603 1.536943 CGGCCCACCTAGCTATCCTC 61.537 65.000 0.00 0.00 0.00 3.71
565 606 2.584391 CCCGGCCCACCTAGCTATC 61.584 68.421 0.00 0.00 0.00 2.08
566 607 2.402557 ATCCCGGCCCACCTAGCTAT 62.403 60.000 0.00 0.00 0.00 2.97
567 608 3.096089 ATCCCGGCCCACCTAGCTA 62.096 63.158 0.00 0.00 0.00 3.32
604 650 7.765360 AGGAGGTATATATAAACGAGACGAGAG 59.235 40.741 0.00 0.00 0.00 3.20
970 1216 1.607628 CCGGTCCTTCTATCGATTCGT 59.392 52.381 1.71 0.00 0.00 3.85
973 1219 1.962100 GGTCCGGTCCTTCTATCGATT 59.038 52.381 10.82 0.00 0.00 3.34
975 1221 0.816825 CGGTCCGGTCCTTCTATCGA 60.817 60.000 15.98 0.00 0.00 3.59
978 1224 4.272245 CCGGTCCGGTCCTTCTAT 57.728 61.111 23.02 0.00 42.73 1.98
998 1253 3.071206 AGGAGAGCGACGGCATGT 61.071 61.111 0.00 0.00 43.41 3.21
999 1254 2.584418 CAGGAGAGCGACGGCATG 60.584 66.667 0.00 0.00 43.41 4.06
1143 1398 3.458163 TGGGAGACGATGACCCGC 61.458 66.667 0.00 0.00 45.91 6.13
1194 1449 2.243160 ATTTAAACCCGAACGGCGCG 62.243 55.000 6.90 0.00 39.11 6.86
1665 1920 4.089757 TCGGAGGAGGGGAAGGGG 62.090 72.222 0.00 0.00 0.00 4.79
1809 2064 1.429148 CGCGCTTGGACTGGTAATCC 61.429 60.000 5.56 0.00 36.70 3.01
1812 2067 2.047655 CCGCGCTTGGACTGGTAA 60.048 61.111 5.56 0.00 0.00 2.85
1830 2085 3.663754 CGTAGTACTCGATGCCGATGTAC 60.664 52.174 0.00 13.97 44.62 2.90
2364 2619 1.226575 CACGATGACGCTCCGCTTA 60.227 57.895 0.00 0.00 43.96 3.09
2613 2868 2.839162 CCAATCCCCCAATGCCGG 60.839 66.667 0.00 0.00 0.00 6.13
2661 2916 2.181525 CGCCTGAAATTTGGGCCG 59.818 61.111 19.78 13.64 42.58 6.13
2805 3060 0.363512 CGCACAGACGATTCAAGACG 59.636 55.000 0.00 0.00 34.06 4.18
2925 3180 2.366533 TCTCACCTAGTGAAGTAGCCG 58.633 52.381 0.00 0.00 42.26 5.52
2971 3227 2.229784 ACACCGTACCAACTAGCAGTAC 59.770 50.000 7.25 7.25 34.37 2.73
3008 3264 2.607771 CCATCAAAAGCGGTCAACAAGG 60.608 50.000 0.00 0.00 0.00 3.61
3044 3300 4.201910 TGCTTAATTCGCATGCTTTCCTAC 60.202 41.667 17.13 0.00 31.40 3.18
3048 3304 4.622740 ACTTTGCTTAATTCGCATGCTTTC 59.377 37.500 17.13 0.00 37.22 2.62
3071 3331 3.563808 GGATGACACTGTTTGTTGTGCTA 59.436 43.478 0.00 0.00 39.17 3.49
3072 3332 2.358898 GGATGACACTGTTTGTTGTGCT 59.641 45.455 0.00 0.00 39.17 4.40
3073 3333 2.098934 TGGATGACACTGTTTGTTGTGC 59.901 45.455 0.00 0.00 39.17 4.57
3075 3335 4.269183 TCTTGGATGACACTGTTTGTTGT 58.731 39.130 0.00 0.00 39.17 3.32
3076 3336 4.898829 TCTTGGATGACACTGTTTGTTG 57.101 40.909 0.00 0.00 39.17 3.33
3077 3337 5.913137 TTTCTTGGATGACACTGTTTGTT 57.087 34.783 0.00 0.00 39.17 2.83
3078 3338 5.184864 TGTTTTCTTGGATGACACTGTTTGT 59.815 36.000 0.00 0.00 43.10 2.83
3079 3339 5.649557 TGTTTTCTTGGATGACACTGTTTG 58.350 37.500 0.00 0.00 0.00 2.93
3080 3340 5.913137 TGTTTTCTTGGATGACACTGTTT 57.087 34.783 0.00 0.00 0.00 2.83
3083 3343 6.979817 TGAAAATGTTTTCTTGGATGACACTG 59.020 34.615 16.53 0.00 45.14 3.66
3084 3344 7.111247 TGAAAATGTTTTCTTGGATGACACT 57.889 32.000 16.53 0.00 45.14 3.55
3085 3345 7.706179 TCTTGAAAATGTTTTCTTGGATGACAC 59.294 33.333 16.53 0.00 45.14 3.67
3086 3346 7.780064 TCTTGAAAATGTTTTCTTGGATGACA 58.220 30.769 16.53 0.00 45.14 3.58
3087 3347 8.706035 CATCTTGAAAATGTTTTCTTGGATGAC 58.294 33.333 23.74 3.59 45.14 3.06
3088 3348 7.385752 GCATCTTGAAAATGTTTTCTTGGATGA 59.614 33.333 27.33 15.59 45.14 2.92
3106 3366 7.628769 TGCTACTCATTTTTATGCATCTTGA 57.371 32.000 0.19 0.00 0.00 3.02
3107 3367 7.221452 GGTTGCTACTCATTTTTATGCATCTTG 59.779 37.037 0.19 0.00 0.00 3.02
3109 3369 6.377996 TGGTTGCTACTCATTTTTATGCATCT 59.622 34.615 0.19 0.00 0.00 2.90
3110 3370 6.563422 TGGTTGCTACTCATTTTTATGCATC 58.437 36.000 0.19 0.00 0.00 3.91
3111 3371 6.528537 TGGTTGCTACTCATTTTTATGCAT 57.471 33.333 3.79 3.79 0.00 3.96
3112 3372 5.973899 TGGTTGCTACTCATTTTTATGCA 57.026 34.783 0.00 0.00 0.00 3.96
3113 3373 5.576774 GGTTGGTTGCTACTCATTTTTATGC 59.423 40.000 0.00 0.00 0.00 3.14
3114 3374 5.799936 CGGTTGGTTGCTACTCATTTTTATG 59.200 40.000 0.00 0.00 0.00 1.90
3115 3375 5.105917 CCGGTTGGTTGCTACTCATTTTTAT 60.106 40.000 0.00 0.00 0.00 1.40
3116 3376 4.216687 CCGGTTGGTTGCTACTCATTTTTA 59.783 41.667 0.00 0.00 0.00 1.52
3118 3378 2.556622 CCGGTTGGTTGCTACTCATTTT 59.443 45.455 0.00 0.00 0.00 1.82
3119 3379 2.159382 CCGGTTGGTTGCTACTCATTT 58.841 47.619 0.00 0.00 0.00 2.32
3120 3380 1.821216 CCGGTTGGTTGCTACTCATT 58.179 50.000 0.00 0.00 0.00 2.57
3121 3381 3.551259 CCGGTTGGTTGCTACTCAT 57.449 52.632 0.00 0.00 0.00 2.90
3137 3397 3.304391 GCTCTAGCTGTGAATCTAGACCG 60.304 52.174 0.00 0.00 37.10 4.79
3170 3435 2.380410 CGGTTCGAGGCTGGTTTCG 61.380 63.158 0.00 0.00 38.13 3.46
3186 3451 0.721718 GGAAGCAAGAATGTCGACGG 59.278 55.000 11.62 0.00 0.00 4.79
3196 3461 0.472471 AGGTTGTTCCGGAAGCAAGA 59.528 50.000 19.50 2.28 41.99 3.02
3214 3479 1.338769 CCAGAACCGTAACCTCCCAAG 60.339 57.143 0.00 0.00 0.00 3.61
3217 3482 0.535797 CTCCAGAACCGTAACCTCCC 59.464 60.000 0.00 0.00 0.00 4.30
3226 3491 0.247736 CTTCTCACCCTCCAGAACCG 59.752 60.000 0.00 0.00 0.00 4.44
3231 3496 2.568956 TCAATCACTTCTCACCCTCCAG 59.431 50.000 0.00 0.00 0.00 3.86
3241 3506 3.071874 TGGGCGAAATCAATCACTTCT 57.928 42.857 0.00 0.00 0.00 2.85
3258 3523 3.393800 CGTCTATGCTTAGGTTCATGGG 58.606 50.000 6.78 0.00 0.00 4.00
3296 3562 7.184067 TCTCTTCTAACTAAAGCCTAAAGGG 57.816 40.000 0.00 0.00 35.18 3.95
3298 3564 7.324178 TGCTCTCTTCTAACTAAAGCCTAAAG 58.676 38.462 0.00 0.00 0.00 1.85
3299 3565 7.241042 TGCTCTCTTCTAACTAAAGCCTAAA 57.759 36.000 0.00 0.00 0.00 1.85
3300 3566 6.852420 TGCTCTCTTCTAACTAAAGCCTAA 57.148 37.500 0.00 0.00 0.00 2.69
3301 3567 7.124298 TGAATGCTCTCTTCTAACTAAAGCCTA 59.876 37.037 0.00 0.00 0.00 3.93
3302 3568 5.948742 ATGCTCTCTTCTAACTAAAGCCT 57.051 39.130 0.00 0.00 0.00 4.58
3303 3569 6.109359 TGAATGCTCTCTTCTAACTAAAGCC 58.891 40.000 0.00 0.00 0.00 4.35
3304 3570 7.602517 TTGAATGCTCTCTTCTAACTAAAGC 57.397 36.000 0.00 0.00 0.00 3.51
3311 3577 9.071276 ACAAAAGATTTGAATGCTCTCTTCTAA 57.929 29.630 9.62 0.00 0.00 2.10
3335 3601 4.036262 GTCACTATTCTGCAACCACAAACA 59.964 41.667 0.00 0.00 0.00 2.83
3348 3614 8.088981 GGTTATATCAATGGACGTCACTATTCT 58.911 37.037 18.91 6.98 0.00 2.40
3349 3615 7.331193 GGGTTATATCAATGGACGTCACTATTC 59.669 40.741 18.91 0.00 0.00 1.75
3351 3617 6.497259 AGGGTTATATCAATGGACGTCACTAT 59.503 38.462 18.91 5.64 0.00 2.12
3353 3619 4.654262 AGGGTTATATCAATGGACGTCACT 59.346 41.667 18.91 0.00 0.00 3.41
3355 3621 4.202315 CCAGGGTTATATCAATGGACGTCA 60.202 45.833 18.91 3.91 0.00 4.35
3356 3622 4.315803 CCAGGGTTATATCAATGGACGTC 58.684 47.826 7.13 7.13 0.00 4.34
3361 3627 3.524095 TGGCCAGGGTTATATCAATGG 57.476 47.619 0.00 0.00 0.00 3.16
3363 3629 5.969086 AGAATTGGCCAGGGTTATATCAAT 58.031 37.500 5.11 0.00 0.00 2.57
3364 3630 5.402054 AGAATTGGCCAGGGTTATATCAA 57.598 39.130 5.11 0.00 0.00 2.57
3365 3631 5.103728 TGAAGAATTGGCCAGGGTTATATCA 60.104 40.000 5.11 2.01 0.00 2.15
3367 3633 5.402054 TGAAGAATTGGCCAGGGTTATAT 57.598 39.130 5.11 0.00 0.00 0.86
3368 3634 4.871871 TGAAGAATTGGCCAGGGTTATA 57.128 40.909 5.11 0.00 0.00 0.98
3369 3635 3.756082 TGAAGAATTGGCCAGGGTTAT 57.244 42.857 5.11 0.00 0.00 1.89
3370 3636 3.756082 ATGAAGAATTGGCCAGGGTTA 57.244 42.857 5.11 0.00 0.00 2.85
3374 3640 1.551430 TGCAATGAAGAATTGGCCAGG 59.449 47.619 5.11 0.00 45.05 4.45
3438 3704 2.352912 GGTCTTCTTCCAGTCGAAGTCC 60.353 54.545 0.00 0.00 46.97 3.85
3447 3713 1.153745 CTCGGCGGTCTTCTTCCAG 60.154 63.158 7.21 0.00 0.00 3.86
3486 3752 4.222847 GATCCGTCGGTGGCCTCC 62.223 72.222 14.20 14.20 0.00 4.30
3558 3824 2.027625 CTGGCACGAACCGAAGTCC 61.028 63.158 0.00 0.00 0.00 3.85
3570 3836 4.400961 AGCTCCTTCGCCTGGCAC 62.401 66.667 20.29 0.00 0.00 5.01
3630 3896 3.650950 TGCTGGCCCCTCTTCACC 61.651 66.667 0.00 0.00 0.00 4.02
3717 4010 0.737219 GACTAGCAGCAGCCCAATTG 59.263 55.000 0.00 0.00 43.56 2.32
3760 4061 2.183555 GCCAAGTCTACGACCCCG 59.816 66.667 0.00 0.00 42.50 5.73
3776 4077 6.442952 TGTTCAACATGTTTTATAGTGGTGC 58.557 36.000 8.77 0.00 0.00 5.01
3777 4078 7.918033 TGTTGTTCAACATGTTTTATAGTGGTG 59.082 33.333 8.77 0.00 0.00 4.17
3778 4079 8.001881 TGTTGTTCAACATGTTTTATAGTGGT 57.998 30.769 8.77 0.00 0.00 4.16
3779 4080 7.114811 GCTGTTGTTCAACATGTTTTATAGTGG 59.885 37.037 16.89 0.00 31.47 4.00
3780 4081 7.862372 AGCTGTTGTTCAACATGTTTTATAGTG 59.138 33.333 16.89 0.00 31.47 2.74
3861 4162 4.001652 CGGATTGGATTGGATCAGATCTG 58.998 47.826 17.07 17.07 0.00 2.90
3862 4163 3.906218 TCGGATTGGATTGGATCAGATCT 59.094 43.478 10.36 0.00 0.00 2.75
3863 4164 4.277515 TCGGATTGGATTGGATCAGATC 57.722 45.455 1.18 1.18 0.00 2.75
3864 4165 4.324099 GGATCGGATTGGATTGGATCAGAT 60.324 45.833 0.00 0.00 39.04 2.90
3865 4166 3.008375 GGATCGGATTGGATTGGATCAGA 59.992 47.826 0.00 0.00 36.18 3.27
3930 4231 3.182152 AGGATATAGATTGTTCCGGGGG 58.818 50.000 0.00 0.00 33.35 5.40
3950 4254 1.336887 ACAAATCCGTGTCGTGGAGAG 60.337 52.381 0.00 0.00 39.30 3.20
3960 4264 0.098728 GCCGATCCAACAAATCCGTG 59.901 55.000 0.00 0.00 0.00 4.94
3963 4267 1.724582 CCCGCCGATCCAACAAATCC 61.725 60.000 0.00 0.00 0.00 3.01
4047 4356 2.795329 TGCTCTCCTCCAAATCCAAAC 58.205 47.619 0.00 0.00 0.00 2.93
4048 4357 3.157087 GTTGCTCTCCTCCAAATCCAAA 58.843 45.455 0.00 0.00 0.00 3.28
4049 4358 2.376518 AGTTGCTCTCCTCCAAATCCAA 59.623 45.455 0.00 0.00 0.00 3.53
4101 4413 3.703556 AGTGATACACAGATGCTGCTACT 59.296 43.478 0.00 0.00 36.74 2.57
4103 4415 4.436332 CAAGTGATACACAGATGCTGCTA 58.564 43.478 0.00 0.00 36.74 3.49
4117 4429 1.376683 GTGGTGCCGGCAAGTGATA 60.377 57.895 34.66 11.12 0.00 2.15
4118 4430 2.672996 GTGGTGCCGGCAAGTGAT 60.673 61.111 34.66 0.00 0.00 3.06
4128 4440 1.973281 CACAGATGGTGGTGGTGCC 60.973 63.158 0.00 0.00 44.04 5.01
4138 4450 4.245660 ACAAGACAACGATACACAGATGG 58.754 43.478 0.00 0.00 0.00 3.51
4141 4453 5.813157 TCAAAACAAGACAACGATACACAGA 59.187 36.000 0.00 0.00 0.00 3.41
4144 4456 5.802064 TGTCAAAACAAGACAACGATACAC 58.198 37.500 0.00 0.00 42.57 2.90
4160 4489 8.277197 AGGAGAGATATTTCATCCATGTCAAAA 58.723 33.333 11.64 0.00 34.18 2.44
4170 4499 5.391523 CGACGGAGAGGAGAGATATTTCATC 60.392 48.000 0.00 0.00 0.00 2.92
4184 4513 3.054503 ACGACCACGACGGAGAGG 61.055 66.667 0.00 0.00 42.66 3.69
4268 4597 2.125912 CAGAGCACGAAGTCGGGG 60.126 66.667 4.94 0.00 41.61 5.73
4540 4869 1.299850 CATCATCGTCGGCGGCTTA 60.300 57.895 10.62 0.00 38.89 3.09
4543 4872 3.330853 GACATCATCGTCGGCGGC 61.331 66.667 10.62 3.25 38.89 6.53
4547 4914 2.800544 GGGTTATTGACATCATCGTCGG 59.199 50.000 0.00 0.00 38.84 4.79
4576 4943 3.868757 TCGTCGTCATCATCCTTCTTT 57.131 42.857 0.00 0.00 0.00 2.52
4577 4944 3.381590 TCATCGTCGTCATCATCCTTCTT 59.618 43.478 0.00 0.00 0.00 2.52
4578 4945 2.952310 TCATCGTCGTCATCATCCTTCT 59.048 45.455 0.00 0.00 0.00 2.85
4579 4946 3.355626 TCATCGTCGTCATCATCCTTC 57.644 47.619 0.00 0.00 0.00 3.46
4585 4952 3.988379 TCATCATCATCGTCGTCATCA 57.012 42.857 0.00 0.00 0.00 3.07
4588 4955 3.988379 TCATCATCATCATCGTCGTCA 57.012 42.857 0.00 0.00 0.00 4.35
4612 4979 1.981256 ACCACACCAACTGATTGACC 58.019 50.000 0.00 0.00 38.15 4.02
4614 4981 4.582656 CCTAAAACCACACCAACTGATTGA 59.417 41.667 0.00 0.00 38.15 2.57
4615 4982 4.582656 TCCTAAAACCACACCAACTGATTG 59.417 41.667 0.00 0.00 35.40 2.67
4617 4984 4.447138 TCCTAAAACCACACCAACTGAT 57.553 40.909 0.00 0.00 0.00 2.90
4652 5019 7.987750 AGAAGAAAGAAACCTGTTTATCCTC 57.012 36.000 0.00 0.00 32.11 3.71
4685 5052 8.535690 ACGTAAACCAGAAGAAGAATAAGAAG 57.464 34.615 0.00 0.00 0.00 2.85
4686 5053 8.897872 AACGTAAACCAGAAGAAGAATAAGAA 57.102 30.769 0.00 0.00 0.00 2.52
4687 5054 8.897872 AAACGTAAACCAGAAGAAGAATAAGA 57.102 30.769 0.00 0.00 0.00 2.10
4691 5058 9.726232 GTTTTAAACGTAAACCAGAAGAAGAAT 57.274 29.630 1.70 0.00 31.00 2.40
4713 5080 0.670854 GCGCGAGAGGAAGAGGTTTT 60.671 55.000 12.10 0.00 0.00 2.43
4714 5081 1.079750 GCGCGAGAGGAAGAGGTTT 60.080 57.895 12.10 0.00 0.00 3.27
4737 5104 1.363246 TGGGGCGGGCATATGTATAA 58.637 50.000 4.29 0.00 0.00 0.98
4799 5171 6.908820 TCGTCATCGTCAACTACATATACAAC 59.091 38.462 0.00 0.00 38.33 3.32
4836 5208 6.183359 GCTGAAAGAATCATTTTTCTTGCTCG 60.183 38.462 6.50 0.66 43.42 5.03
4890 5266 2.616510 GGGGATCGATGGATGGATCAAC 60.617 54.545 0.54 5.81 41.87 3.18
4905 5281 2.736670 AGGTTGCAATAGTGGGGATC 57.263 50.000 0.59 0.00 0.00 3.36
4976 5356 1.215014 GGCAAAGGTGAAAAGCGTGC 61.215 55.000 0.00 0.00 0.00 5.34
4995 5375 2.469826 TCTGGTCGTAATAATGCAGCG 58.530 47.619 0.00 0.00 0.00 5.18
5034 5414 2.203252 CGGTGGGCATCCATCCAG 60.203 66.667 0.00 0.00 46.09 3.86
5076 5470 1.301009 GGCGGCGGAAGGAGATAAG 60.301 63.158 9.78 0.00 0.00 1.73
5101 5495 3.130693 ACGGGAAGAAAATCTACTCCGAG 59.869 47.826 16.94 0.00 37.11 4.63
5105 5499 4.870991 CAGGAACGGGAAGAAAATCTACTC 59.129 45.833 0.00 0.00 0.00 2.59
5106 5500 4.833390 CAGGAACGGGAAGAAAATCTACT 58.167 43.478 0.00 0.00 0.00 2.57
5121 5515 4.859629 GTTGCTTTATCTACCAGGAACG 57.140 45.455 0.00 0.00 30.50 3.95
5122 5516 3.621715 CCGTTGCTTTATCTACCAGGAAC 59.378 47.826 0.00 0.00 35.98 3.62
5132 5526 3.869832 GGTTAGTCTCCCGTTGCTTTATC 59.130 47.826 0.00 0.00 0.00 1.75
5158 7399 4.232061 TTGGGGGTTGGCAGTGGG 62.232 66.667 0.00 0.00 0.00 4.61
5163 7404 1.076549 GATCAGTTGGGGGTTGGCA 59.923 57.895 0.00 0.00 0.00 4.92
5166 7407 1.382522 CGATGATCAGTTGGGGGTTG 58.617 55.000 0.09 0.00 0.00 3.77
5175 7416 0.464373 AAATGCGGGCGATGATCAGT 60.464 50.000 0.09 0.00 0.00 3.41
5185 7426 2.568090 CCTGTGTGAAATGCGGGC 59.432 61.111 0.00 0.00 0.00 6.13
5189 7430 4.514441 CAGAGATATCCCTGTGTGAAATGC 59.486 45.833 6.09 0.00 0.00 3.56
5244 7486 1.091771 AGGAAATGTCGCATGCCTCG 61.092 55.000 13.15 0.00 0.00 4.63
5253 7495 2.678336 GTTTGGCTCCTAGGAAATGTCG 59.322 50.000 13.77 0.61 0.00 4.35
5285 7527 2.903798 TGGCAAAGGAAAACTTGCTTG 58.096 42.857 6.73 0.00 40.66 4.01
5301 7543 4.317359 CCAACCGTGATCATGGCA 57.683 55.556 30.24 0.00 41.20 4.92
5310 7552 0.591170 ACGAAGATTTGCCAACCGTG 59.409 50.000 0.00 0.00 0.00 4.94
5344 7586 2.046411 CAGCACGGCCATGTACCA 60.046 61.111 2.24 0.00 0.00 3.25
5345 7587 2.046314 ACAGCACGGCCATGTACC 60.046 61.111 2.24 0.00 0.00 3.34
5411 7654 4.899239 CATGTCCCTCTCCGGCGC 62.899 72.222 0.00 0.00 0.00 6.53
5415 7658 0.106167 TCTACCCATGTCCCTCTCCG 60.106 60.000 0.00 0.00 0.00 4.63
5470 7713 1.734465 GAAATGATGGATCGATCGCCC 59.266 52.381 18.81 14.33 0.00 6.13
5473 7716 1.995484 CCCGAAATGATGGATCGATCG 59.005 52.381 18.81 9.36 38.82 3.69
5474 7717 2.996621 GACCCGAAATGATGGATCGATC 59.003 50.000 17.36 17.36 38.82 3.69
5475 7718 2.368548 TGACCCGAAATGATGGATCGAT 59.631 45.455 0.00 0.00 38.82 3.59
5476 7719 1.760029 TGACCCGAAATGATGGATCGA 59.240 47.619 0.00 0.00 38.82 3.59
5477 7720 1.867233 GTGACCCGAAATGATGGATCG 59.133 52.381 0.00 0.00 36.39 3.69
5478 7721 2.917933 TGTGACCCGAAATGATGGATC 58.082 47.619 0.00 0.00 0.00 3.36
5479 7722 3.282021 CTTGTGACCCGAAATGATGGAT 58.718 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.