Multiple sequence alignment - TraesCS5A01G156800

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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 TraesCS5A01G156800 chr5A 100.000 5230 0 0 1 5230 335681510 335676281 0.000000e+00 9659.0
1 TraesCS5A01G156800 chr5A 85.294 68 9 1 13 80 475718742 475718676 9.400000e-08 69.4
2 TraesCS5A01G156800 chr5D 92.567 5274 265 46 2 5230 253187101 253181910 0.000000e+00 7450.0
3 TraesCS5A01G156800 chr5B 93.741 4170 141 32 1114 5230 285507174 285503072 0.000000e+00 6144.0
4 TraesCS5A01G156800 chr5B 82.671 277 47 1 1 277 285562722 285562447 1.450000e-60 244.0
5 TraesCS5A01G156800 chr5B 88.024 167 13 2 846 1012 285507810 285507651 1.920000e-44 191.0
6 TraesCS5A01G156800 chrUn 85.393 178 24 2 5049 5224 224666734 224666911 3.220000e-42 183.0
7 TraesCS5A01G156800 chrUn 79.574 235 22 6 4937 5171 67091990 67091782 1.520000e-30 145.0
8 TraesCS5A01G156800 chr3D 75.258 194 40 7 108 296 603729126 603729316 9.330000e-13 86.1


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 TraesCS5A01G156800 chr5A 335676281 335681510 5229 True 9659.0 9659 100.0000 1 5230 1 chr5A.!!$R1 5229
1 TraesCS5A01G156800 chr5D 253181910 253187101 5191 True 7450.0 7450 92.5670 2 5230 1 chr5D.!!$R1 5228
2 TraesCS5A01G156800 chr5B 285503072 285507810 4738 True 3167.5 6144 90.8825 846 5230 2 chr5B.!!$R2 4384

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
240 241 0.036952 CTTCCCGCACATCACTGACT 60.037 55.000 0.00 0.00 0.00 3.41 F
241 242 0.037326 TTCCCGCACATCACTGACTC 60.037 55.000 0.00 0.00 0.00 3.36 F
452 453 0.102300 AGGCAAAGGCGTTTGTGTTC 59.898 50.000 27.25 16.65 44.37 3.18 F
497 498 0.179029 ACCCACAACTTCACTTCCCG 60.179 55.000 0.00 0.00 0.00 5.14 F
605 607 0.179235 CCGGTCGCATTTGTGTAACG 60.179 55.000 0.00 0.00 42.39 3.18 F
679 681 0.312416 TTTGCATGAAAACCGTCCGG 59.688 50.000 3.76 3.76 42.03 5.14 F
968 974 1.113788 CGGGGGTCGTCTGGTAAATA 58.886 55.000 0.00 0.00 0.00 1.40 F
1450 1833 1.137479 CGCCCCGTTCCTGTTAGATTA 59.863 52.381 0.00 0.00 0.00 1.75 F
3047 3462 0.972883 TGGGCCTGTGTTAATTTGGC 59.027 50.000 4.53 0.00 42.56 4.52 F
3588 4003 0.751643 CCCTTCCCTGTAAATGCGGG 60.752 60.000 0.00 0.00 39.41 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 2162 0.320374 TAACTGAACCAGACGCCCAG 59.680 55.000 0.45 0.00 35.18 4.45 R
1888 2274 5.652452 AGGAAGCAATGGGTGTAGATTTTAC 59.348 40.000 0.00 0.00 0.00 2.01 R
2274 2661 7.826252 ACATCTGGAATATATATTCACCAGCAC 59.174 37.037 28.37 14.75 42.92 4.40 R
2493 2882 4.404715 AGCATGGCAGCTAAAGATTCATTT 59.595 37.500 9.26 0.00 44.50 2.32 R
2499 2888 2.950309 CAGAAGCATGGCAGCTAAAGAT 59.050 45.455 11.01 0.00 45.89 2.40 R
2879 3294 7.781324 ATCCTTTAGCTCATTCTTCCAAAAA 57.219 32.000 0.00 0.00 0.00 1.94 R
3046 3461 2.634982 TCAAGAAATGTGCCATTCGC 57.365 45.000 1.57 0.00 38.31 4.70 R
3480 3895 1.486997 ATAGGAGGCATGCCAGCGAT 61.487 55.000 37.18 21.59 38.92 4.58 R
4102 4517 0.515127 ACAACACACACACACACACG 59.485 50.000 0.00 0.00 0.00 4.49 R
4884 5324 0.966875 AAGCATCGCAAATGGCCTGA 60.967 50.000 3.32 0.00 40.31 3.86 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
24 25 4.719369 GCCGACTTGCCGACGAGT 62.719 66.667 0.00 0.00 43.65 4.18
26 27 2.087009 CCGACTTGCCGACGAGTTC 61.087 63.158 0.00 0.00 40.85 3.01
39 40 1.446966 GAGTTCGCTGGAGGTGAGC 60.447 63.158 0.00 0.00 35.73 4.26
44 45 3.749064 GCTGGAGGTGAGCGACGA 61.749 66.667 0.00 0.00 0.00 4.20
45 46 3.069980 GCTGGAGGTGAGCGACGAT 62.070 63.158 0.00 0.00 0.00 3.73
53 54 2.278013 GAGCGACGATGACCCGAC 60.278 66.667 0.00 0.00 0.00 4.79
68 69 0.039074 CCGACGATGTAGGAGGCATC 60.039 60.000 0.00 0.00 39.32 3.91
88 89 1.451927 GATGACGAGCCAATGCCCA 60.452 57.895 0.00 0.00 38.69 5.36
90 91 3.499737 GACGAGCCAATGCCCACG 61.500 66.667 0.00 0.00 38.69 4.94
102 103 1.078426 GCCCACGCCTGTCTATGTT 60.078 57.895 0.00 0.00 0.00 2.71
135 136 2.646719 CAGGCGCATGTGCACTTT 59.353 55.556 30.73 11.67 42.21 2.66
139 140 0.240945 GGCGCATGTGCACTTTAACT 59.759 50.000 30.73 0.00 42.21 2.24
143 144 1.729149 GCATGTGCACTTTAACTCCGC 60.729 52.381 19.41 5.84 41.59 5.54
144 145 1.135689 CATGTGCACTTTAACTCCGCC 60.136 52.381 19.41 0.00 0.00 6.13
159 160 2.751436 GCCATGGCGAAGGAGCAA 60.751 61.111 23.48 0.00 39.27 3.91
161 162 1.377725 CCATGGCGAAGGAGCAACT 60.378 57.895 0.00 0.00 39.27 3.16
163 164 1.293924 CATGGCGAAGGAGCAACTAG 58.706 55.000 0.00 0.00 39.27 2.57
164 165 0.462759 ATGGCGAAGGAGCAACTAGC 60.463 55.000 0.00 0.00 46.19 3.42
176 177 2.686558 CAACTAGCGTTGCATGTGTT 57.313 45.000 0.00 0.00 43.47 3.32
177 178 2.998772 CAACTAGCGTTGCATGTGTTT 58.001 42.857 0.00 0.00 43.47 2.83
178 179 2.686558 ACTAGCGTTGCATGTGTTTG 57.313 45.000 0.00 0.00 0.00 2.93
179 180 1.266718 ACTAGCGTTGCATGTGTTTGG 59.733 47.619 0.00 0.00 0.00 3.28
180 181 0.039617 TAGCGTTGCATGTGTTTGGC 60.040 50.000 0.00 0.00 0.00 4.52
181 182 1.591059 GCGTTGCATGTGTTTGGCA 60.591 52.632 0.00 0.00 35.41 4.92
183 184 1.500108 CGTTGCATGTGTTTGGCATT 58.500 45.000 0.00 0.00 37.39 3.56
185 186 1.799994 GTTGCATGTGTTTGGCATTCC 59.200 47.619 0.00 0.00 37.39 3.01
187 188 0.737019 GCATGTGTTTGGCATTCCGG 60.737 55.000 0.00 0.00 34.14 5.14
188 189 0.737019 CATGTGTTTGGCATTCCGGC 60.737 55.000 0.00 0.00 41.67 6.13
189 190 2.126502 GTGTTTGGCATTCCGGCG 60.127 61.111 0.00 0.00 45.16 6.46
190 191 3.369400 TGTTTGGCATTCCGGCGG 61.369 61.111 22.51 22.51 45.16 6.13
205 206 3.905678 CGGGCGTAGGAGGAGCAG 61.906 72.222 0.00 0.00 0.00 4.24
215 216 1.216710 GAGGAGCAGCGCTACAACT 59.783 57.895 10.99 6.71 42.99 3.16
218 219 1.687494 GGAGCAGCGCTACAACTTCG 61.687 60.000 10.99 0.00 39.71 3.79
228 229 2.791501 TACAACTTCGCCCTTCCCGC 62.792 60.000 0.00 0.00 0.00 6.13
229 230 3.948719 AACTTCGCCCTTCCCGCA 61.949 61.111 0.00 0.00 0.00 5.69
230 231 4.699522 ACTTCGCCCTTCCCGCAC 62.700 66.667 0.00 0.00 0.00 5.34
231 232 4.697756 CTTCGCCCTTCCCGCACA 62.698 66.667 0.00 0.00 0.00 4.57
232 233 3.976701 CTTCGCCCTTCCCGCACAT 62.977 63.158 0.00 0.00 0.00 3.21
233 234 3.969250 TTCGCCCTTCCCGCACATC 62.969 63.158 0.00 0.00 0.00 3.06
234 235 4.776322 CGCCCTTCCCGCACATCA 62.776 66.667 0.00 0.00 0.00 3.07
235 236 3.134127 GCCCTTCCCGCACATCAC 61.134 66.667 0.00 0.00 0.00 3.06
236 237 2.671070 CCCTTCCCGCACATCACT 59.329 61.111 0.00 0.00 0.00 3.41
237 238 1.746615 CCCTTCCCGCACATCACTG 60.747 63.158 0.00 0.00 0.00 3.66
238 239 1.296392 CCTTCCCGCACATCACTGA 59.704 57.895 0.00 0.00 0.00 3.41
239 240 1.021390 CCTTCCCGCACATCACTGAC 61.021 60.000 0.00 0.00 0.00 3.51
240 241 0.036952 CTTCCCGCACATCACTGACT 60.037 55.000 0.00 0.00 0.00 3.41
241 242 0.037326 TTCCCGCACATCACTGACTC 60.037 55.000 0.00 0.00 0.00 3.36
242 243 1.184970 TCCCGCACATCACTGACTCA 61.185 55.000 0.00 0.00 0.00 3.41
256 257 0.744771 GACTCACGGAGGGCCAAATC 60.745 60.000 6.18 0.00 33.35 2.17
261 262 1.262640 ACGGAGGGCCAAATCTACGT 61.263 55.000 10.84 10.84 44.68 3.57
263 264 0.831307 GGAGGGCCAAATCTACGTCT 59.169 55.000 6.18 0.00 0.00 4.18
269 270 3.132467 GGGCCAAATCTACGTCTAGTTCT 59.868 47.826 4.39 0.00 0.00 3.01
281 282 2.098443 GTCTAGTTCTTGAGCGAGGAGG 59.902 54.545 0.00 0.00 0.00 4.30
283 284 1.448717 GTTCTTGAGCGAGGAGGCC 60.449 63.158 0.00 0.00 0.00 5.19
284 285 1.913262 TTCTTGAGCGAGGAGGCCA 60.913 57.895 5.01 0.00 0.00 5.36
286 287 0.397114 TCTTGAGCGAGGAGGCCATA 60.397 55.000 5.01 0.00 0.00 2.74
308 309 1.944676 GCTATGGACGAGAACGCCG 60.945 63.158 0.00 0.00 43.96 6.46
310 311 3.420214 TATGGACGAGAACGCCGGC 62.420 63.158 19.07 19.07 43.96 6.13
313 314 3.774702 GACGAGAACGCCGGCAAC 61.775 66.667 28.98 16.56 43.96 4.17
314 315 4.295119 ACGAGAACGCCGGCAACT 62.295 61.111 28.98 21.21 43.96 3.16
315 316 3.777925 CGAGAACGCCGGCAACTG 61.778 66.667 28.98 12.87 0.00 3.16
316 317 4.090057 GAGAACGCCGGCAACTGC 62.090 66.667 28.98 10.48 44.31 4.40
344 345 4.690719 CGGGCCGCTACAACCACA 62.691 66.667 15.42 0.00 0.00 4.17
368 369 2.180204 GGCCCATTCACGTCCATCG 61.180 63.158 0.00 0.00 46.00 3.84
369 370 2.823829 GCCCATTCACGTCCATCGC 61.824 63.158 0.00 0.00 44.19 4.58
389 390 2.203640 ACCTCACCTCCGCTGACA 60.204 61.111 0.00 0.00 0.00 3.58
391 392 1.194781 ACCTCACCTCCGCTGACAAT 61.195 55.000 0.00 0.00 0.00 2.71
395 396 1.079819 ACCTCCGCTGACAATGTCG 60.080 57.895 9.00 5.02 34.95 4.35
424 425 1.254284 ACTCAGGCGAGGAAGAGTGG 61.254 60.000 10.29 0.00 44.17 4.00
432 433 0.543749 GAGGAAGAGTGGGACATGGG 59.456 60.000 0.00 0.00 44.52 4.00
435 436 0.543749 GAAGAGTGGGACATGGGAGG 59.456 60.000 0.00 0.00 44.52 4.30
437 438 2.204136 AGTGGGACATGGGAGGCA 60.204 61.111 0.00 0.00 44.52 4.75
445 446 1.978617 CATGGGAGGCAAAGGCGTT 60.979 57.895 0.00 0.00 42.47 4.84
452 453 0.102300 AGGCAAAGGCGTTTGTGTTC 59.898 50.000 27.25 16.65 44.37 3.18
460 461 1.069227 GGCGTTTGTGTTCCATGTCTC 60.069 52.381 0.00 0.00 0.00 3.36
471 472 3.175438 TCCATGTCTCACTCTTCCTCA 57.825 47.619 0.00 0.00 0.00 3.86
472 473 3.717576 TCCATGTCTCACTCTTCCTCAT 58.282 45.455 0.00 0.00 0.00 2.90
475 476 3.073274 TGTCTCACTCTTCCTCATCGA 57.927 47.619 0.00 0.00 0.00 3.59
476 477 2.750166 TGTCTCACTCTTCCTCATCGAC 59.250 50.000 0.00 0.00 0.00 4.20
497 498 0.179029 ACCCACAACTTCACTTCCCG 60.179 55.000 0.00 0.00 0.00 5.14
505 506 0.539051 CTTCACTTCCCGGAGCTCAT 59.461 55.000 17.19 0.00 0.00 2.90
508 509 1.306141 ACTTCCCGGAGCTCATGGA 60.306 57.895 22.17 19.61 0.00 3.41
509 510 1.333636 ACTTCCCGGAGCTCATGGAG 61.334 60.000 22.17 15.55 0.00 3.86
523 524 1.748329 ATGGAGCGGCGAAGATGCTA 61.748 55.000 12.98 0.00 39.51 3.49
534 536 3.797039 CGAAGATGCTAGACATGGGAAA 58.203 45.455 0.00 0.00 39.84 3.13
551 553 2.035961 GGAAAAACAAGGACTTGGAGGC 59.964 50.000 15.72 2.34 44.45 4.70
557 559 4.452733 GGACTTGGAGGCCCGACG 62.453 72.222 0.00 0.00 37.46 5.12
560 562 4.394712 CTTGGAGGCCCGACGCTT 62.395 66.667 0.00 0.00 37.74 4.68
562 564 2.311688 CTTGGAGGCCCGACGCTTAT 62.312 60.000 0.00 0.00 37.74 1.73
563 565 1.044231 TTGGAGGCCCGACGCTTATA 61.044 55.000 0.00 0.00 37.74 0.98
565 567 0.320697 GGAGGCCCGACGCTTATAAT 59.679 55.000 0.00 0.00 37.74 1.28
571 573 3.998341 GGCCCGACGCTTATAATGATTTA 59.002 43.478 0.00 0.00 37.74 1.40
573 575 4.092968 GCCCGACGCTTATAATGATTTAGG 59.907 45.833 0.00 0.00 0.00 2.69
574 576 4.092968 CCCGACGCTTATAATGATTTAGGC 59.907 45.833 0.00 0.00 0.00 3.93
578 580 6.253727 CGACGCTTATAATGATTTAGGCTAGG 59.746 42.308 0.00 0.00 0.00 3.02
588 590 5.667466 TGATTTAGGCTAGGTTAACTTCCG 58.333 41.667 5.42 0.00 0.00 4.30
589 591 4.476628 TTTAGGCTAGGTTAACTTCCGG 57.523 45.455 5.42 0.00 0.00 5.14
590 592 1.948391 AGGCTAGGTTAACTTCCGGT 58.052 50.000 0.00 0.00 0.00 5.28
591 593 1.829849 AGGCTAGGTTAACTTCCGGTC 59.170 52.381 0.00 0.00 0.00 4.79
600 602 0.591170 AACTTCCGGTCGCATTTGTG 59.409 50.000 0.00 0.00 0.00 3.33
604 606 1.149987 TCCGGTCGCATTTGTGTAAC 58.850 50.000 0.00 0.00 37.35 2.50
605 607 0.179235 CCGGTCGCATTTGTGTAACG 60.179 55.000 0.00 0.00 42.39 3.18
606 608 0.785378 CGGTCGCATTTGTGTAACGA 59.215 50.000 0.00 0.00 42.39 3.85
615 617 6.739100 TCGCATTTGTGTAACGAAAATATGTC 59.261 34.615 0.00 0.00 44.81 3.06
623 625 8.496751 TGTGTAACGAAAATATGTCGAAAATGA 58.503 29.630 14.21 0.00 42.39 2.57
638 640 4.558470 CGAAAATGAAATGAATGTGGTCCG 59.442 41.667 0.00 0.00 0.00 4.79
641 643 5.505173 AATGAAATGAATGTGGTCCGATC 57.495 39.130 0.00 0.00 0.00 3.69
651 653 6.828273 TGAATGTGGTCCGATCTAAATGAAAT 59.172 34.615 0.00 0.00 0.00 2.17
672 674 6.790285 AATTCATCCAGTTTGCATGAAAAC 57.210 33.333 20.07 20.07 39.40 2.43
674 676 2.791383 TCCAGTTTGCATGAAAACCG 57.209 45.000 23.25 14.68 40.26 4.44
679 681 0.312416 TTTGCATGAAAACCGTCCGG 59.688 50.000 3.76 3.76 42.03 5.14
707 711 7.518731 TTAAATTCCGCTTGAAAATGTATGC 57.481 32.000 0.00 0.00 36.33 3.14
734 738 5.920193 ATTTGAGGTACATGGTTGAATGG 57.080 39.130 0.00 0.00 31.46 3.16
735 739 4.380843 TTGAGGTACATGGTTGAATGGT 57.619 40.909 0.00 0.00 31.46 3.55
743 747 1.749258 GGTTGAATGGTCGGCTCCC 60.749 63.158 0.00 0.00 0.00 4.30
753 757 2.279517 CGGCTCCCGTATCACTGC 60.280 66.667 0.00 0.00 42.73 4.40
754 758 2.786495 CGGCTCCCGTATCACTGCT 61.786 63.158 0.00 0.00 42.73 4.24
757 761 1.360551 CTCCCGTATCACTGCTCGG 59.639 63.158 0.00 0.00 42.22 4.63
762 766 1.138883 GTATCACTGCTCGGACGCA 59.861 57.895 2.91 2.91 38.40 5.24
768 772 3.647649 CTGCTCGGACGCATCCACA 62.648 63.158 0.00 0.00 46.67 4.17
784 788 2.571202 TCCACAGATGTATGGCTTGTCA 59.429 45.455 0.00 0.00 35.81 3.58
792 796 7.148018 ACAGATGTATGGCTTGTCAATTTTAGG 60.148 37.037 0.00 0.00 0.00 2.69
804 808 4.726304 TTTAGGGGCCCGCGTTGG 62.726 66.667 18.95 0.00 37.55 3.77
828 833 2.232208 GTGCCTTGAAGGGGATTGAAAG 59.768 50.000 13.99 0.00 35.37 2.62
841 846 2.609921 GAAAGGGGTCGAGGGGGT 60.610 66.667 0.00 0.00 0.00 4.95
842 847 2.121644 AAAGGGGTCGAGGGGGTT 60.122 61.111 0.00 0.00 0.00 4.11
843 848 1.777127 AAAGGGGTCGAGGGGGTTT 60.777 57.895 0.00 0.00 0.00 3.27
844 849 2.076597 AAAGGGGTCGAGGGGGTTTG 62.077 60.000 0.00 0.00 0.00 2.93
845 850 2.931649 GGGGTCGAGGGGGTTTGA 60.932 66.667 0.00 0.00 0.00 2.69
847 852 1.689412 GGGTCGAGGGGGTTTGAAT 59.311 57.895 0.00 0.00 0.00 2.57
849 854 1.282738 GGGTCGAGGGGGTTTGAATAA 59.717 52.381 0.00 0.00 0.00 1.40
851 856 3.014623 GGTCGAGGGGGTTTGAATAAAG 58.985 50.000 0.00 0.00 0.00 1.85
853 858 4.323715 GGTCGAGGGGGTTTGAATAAAGTA 60.324 45.833 0.00 0.00 0.00 2.24
854 859 5.247862 GTCGAGGGGGTTTGAATAAAGTAA 58.752 41.667 0.00 0.00 0.00 2.24
876 882 3.602205 AAATCCCTATTGAGCCCTTCC 57.398 47.619 0.00 0.00 0.00 3.46
887 893 1.561542 GAGCCCTTCCAATCCTCTTGA 59.438 52.381 0.00 0.00 0.00 3.02
899 905 3.672295 CTCTTGAGAGGGGCCGCAC 62.672 68.421 23.39 16.40 38.48 5.34
908 914 4.662961 GGGCCGCACTGCAAAACC 62.663 66.667 0.00 0.00 0.00 3.27
915 921 1.724582 GCACTGCAAAACCTCCGTGT 61.725 55.000 0.00 0.00 0.00 4.49
967 973 1.902556 CGGGGGTCGTCTGGTAAAT 59.097 57.895 0.00 0.00 0.00 1.40
968 974 1.113788 CGGGGGTCGTCTGGTAAATA 58.886 55.000 0.00 0.00 0.00 1.40
969 975 1.202452 CGGGGGTCGTCTGGTAAATAC 60.202 57.143 0.00 0.00 0.00 1.89
970 976 1.139654 GGGGGTCGTCTGGTAAATACC 59.860 57.143 2.53 2.53 46.62 2.73
971 977 1.139654 GGGGTCGTCTGGTAAATACCC 59.860 57.143 7.14 0.00 45.87 3.69
972 978 1.139654 GGGTCGTCTGGTAAATACCCC 59.860 57.143 7.14 0.26 45.87 4.95
1274 1656 2.731801 TAGGGGCTAGGGCGGATCTG 62.732 65.000 0.00 0.00 39.81 2.90
1294 1676 2.881266 CTCTCCTCTCTCTCGCGCG 61.881 68.421 26.76 26.76 0.00 6.86
1329 1711 1.959226 ACATTTCGTGCTTCCGCGT 60.959 52.632 4.92 0.00 44.80 6.01
1330 1712 1.225745 CATTTCGTGCTTCCGCGTC 60.226 57.895 4.92 0.00 44.80 5.19
1373 1756 2.951229 TCTTGTCTCTTTTCCCCCAC 57.049 50.000 0.00 0.00 0.00 4.61
1450 1833 1.137479 CGCCCCGTTCCTGTTAGATTA 59.863 52.381 0.00 0.00 0.00 1.75
1451 1834 2.802057 CGCCCCGTTCCTGTTAGATTAG 60.802 54.545 0.00 0.00 0.00 1.73
1493 1879 9.952030 TCTACATGTAACCATTTGATAGTTTGA 57.048 29.630 7.06 0.00 0.00 2.69
1578 1964 3.914312 ACAGCAATATAGCTCGCGTAAT 58.086 40.909 5.77 0.00 44.54 1.89
1579 1965 3.675225 ACAGCAATATAGCTCGCGTAATG 59.325 43.478 5.77 0.00 44.54 1.90
1716 2102 4.662145 CATTAAGCATCAACGGTTTCTCC 58.338 43.478 0.00 0.00 0.00 3.71
1757 2143 5.948992 ACAGTGCTCCTTTTGTTATTCTC 57.051 39.130 0.00 0.00 0.00 2.87
1760 2146 7.398024 ACAGTGCTCCTTTTGTTATTCTCTAT 58.602 34.615 0.00 0.00 0.00 1.98
1761 2147 7.335422 ACAGTGCTCCTTTTGTTATTCTCTATG 59.665 37.037 0.00 0.00 0.00 2.23
1888 2274 4.755123 CCATTAAACCTAGGCTATGTTCGG 59.245 45.833 14.34 5.54 0.00 4.30
2274 2661 4.124851 ACGCTCTAGGATTTTGTACTGG 57.875 45.455 0.00 0.00 0.00 4.00
2376 2765 7.996098 TTGGCAGATTTTAGCTTAGTAACTT 57.004 32.000 0.00 0.00 0.00 2.66
2493 2882 3.901222 TCCTCTGTTATGACCAACTGACA 59.099 43.478 0.00 0.00 34.11 3.58
2499 2888 6.770303 TCTGTTATGACCAACTGACAAATGAA 59.230 34.615 0.00 0.00 33.17 2.57
2549 2938 7.939782 TGATGTTAACTGAAAGAAGCATTTGA 58.060 30.769 7.22 0.00 37.43 2.69
2640 3052 5.418840 AGGTCTTCAATATTCGGCAAAATGT 59.581 36.000 0.00 0.00 0.00 2.71
2984 3399 9.912634 CTTCTAGATGTTCTTGAAGGATATCTC 57.087 37.037 15.00 0.00 45.81 2.75
3046 3461 3.979101 AATGGGCCTGTGTTAATTTGG 57.021 42.857 4.53 0.00 0.00 3.28
3047 3462 0.972883 TGGGCCTGTGTTAATTTGGC 59.027 50.000 4.53 0.00 42.56 4.52
3189 3604 9.013229 TGTAAACAAGTCTTATGATGCTCAATT 57.987 29.630 0.00 0.00 0.00 2.32
3332 3747 8.815912 AGTCAATAAAAACCTTTATCTGCCATT 58.184 29.630 0.00 0.00 36.84 3.16
3333 3748 9.435688 GTCAATAAAAACCTTTATCTGCCATTT 57.564 29.630 0.00 0.00 36.84 2.32
3358 3773 8.572828 TGTGCATACTTGTTTACTTGAAATTG 57.427 30.769 0.00 0.00 0.00 2.32
3446 3861 4.275810 AGCCAACATTGAATACTGAGCAT 58.724 39.130 0.00 0.00 0.00 3.79
3480 3895 2.309755 AGGCCACCATCTTCATCTTCAA 59.690 45.455 5.01 0.00 0.00 2.69
3508 3923 1.496429 CATGCCTCCTATGGGAAGGTT 59.504 52.381 12.85 2.25 41.69 3.50
3520 3935 2.311542 TGGGAAGGTTGGCATCACTTAT 59.688 45.455 0.00 0.00 0.00 1.73
3521 3936 3.525609 TGGGAAGGTTGGCATCACTTATA 59.474 43.478 0.00 0.00 0.00 0.98
3527 3942 5.930135 AGGTTGGCATCACTTATAACCTAG 58.070 41.667 0.00 0.00 44.29 3.02
3585 4000 3.017442 GTCTTCCCTTCCCTGTAAATGC 58.983 50.000 0.00 0.00 0.00 3.56
3588 4003 0.751643 CCCTTCCCTGTAAATGCGGG 60.752 60.000 0.00 0.00 39.41 6.13
3646 4061 1.557099 TCGCAGACATCAGGTACCTT 58.443 50.000 13.15 0.00 0.00 3.50
3686 4101 2.435422 TGTCACATACCCATGCTGTTG 58.565 47.619 0.00 0.00 35.39 3.33
3874 4289 1.574702 GGAAAGCCCGAAACCTGACG 61.575 60.000 0.00 0.00 0.00 4.35
3894 4309 2.479730 CGACATCTTGGAGGTTAGGACG 60.480 54.545 0.00 0.00 0.00 4.79
3926 4341 4.116961 GTTGTTTGCTTTTGTACCTTCCC 58.883 43.478 0.00 0.00 0.00 3.97
4097 4512 1.128513 TTGATATTAGACTGCGCGCG 58.871 50.000 28.44 28.44 0.00 6.86
4098 4513 1.275471 TGATATTAGACTGCGCGCGC 61.275 55.000 45.02 45.02 42.35 6.86
4099 4514 2.254671 GATATTAGACTGCGCGCGCG 62.255 60.000 45.73 45.73 45.51 6.86
4242 4657 5.499139 TGATTCAACGAGCTTCTTTTGTT 57.501 34.783 0.00 0.00 0.00 2.83
4243 4658 5.273170 TGATTCAACGAGCTTCTTTTGTTG 58.727 37.500 0.00 0.00 40.85 3.33
4251 4666 5.458779 ACGAGCTTCTTTTGTTGCAAATTAC 59.541 36.000 0.00 0.00 0.00 1.89
4264 4679 8.909708 TGTTGCAAATTACATCTAATACTTGC 57.090 30.769 0.00 4.19 36.97 4.01
4349 4786 5.796350 AGCGCTATTGTATTCTTTTTCGT 57.204 34.783 8.99 0.00 0.00 3.85
4415 4852 8.433421 TTGTACTTTCTTCTTTCGTCTTCATT 57.567 30.769 0.00 0.00 0.00 2.57
4564 5001 5.204833 CAACCACATGTAAACAAGTCTTCG 58.795 41.667 0.00 0.00 0.00 3.79
4695 5132 9.945633 AACTGGTATGTACCCCAAAAATTATAT 57.054 29.630 6.74 0.00 45.87 0.86
4702 5139 8.196378 TGTACCCCAAAAATTATATTATGCCC 57.804 34.615 0.00 0.00 0.00 5.36
4839 5276 3.391665 CTGCATCCCCAGACGACCC 62.392 68.421 0.00 0.00 34.77 4.46
4867 5304 0.329261 TTGGAGACTGGAATGCAGGG 59.671 55.000 6.73 0.00 0.00 4.45
4884 5324 2.753029 GGCAGCCTCACCAGAAGT 59.247 61.111 3.29 0.00 0.00 3.01
4919 5359 4.670347 GATGCTTGATTGCTTCTCCTTTC 58.330 43.478 0.00 0.00 35.22 2.62
4929 5369 2.350868 GCTTCTCCTTTCGGCTGAAAAC 60.351 50.000 20.77 2.55 43.21 2.43
4931 5371 0.517316 CTCCTTTCGGCTGAAAACGG 59.483 55.000 20.77 18.51 43.21 4.44
5043 5485 8.547967 TTGACTAGACATACTCATTTCCAAAC 57.452 34.615 0.00 0.00 0.00 2.93
5073 5515 7.771183 ACAAAAATCAAGAAAGCAACTAGTCA 58.229 30.769 0.00 0.00 0.00 3.41
5160 5602 4.901868 TGTTTTCCTGACCATACTGTACC 58.098 43.478 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.049433 AACTCGTCGGCAAGTCGG 60.049 61.111 0.00 0.00 32.44 4.79
9 10 2.426183 CGAACTCGTCGGCAAGTCG 61.426 63.158 0.00 0.00 46.45 4.18
39 40 1.654440 CATCGTCGGGTCATCGTCG 60.654 63.158 0.00 0.00 41.41 5.12
44 45 1.319541 CTCCTACATCGTCGGGTCAT 58.680 55.000 0.00 0.00 0.00 3.06
45 46 0.750546 CCTCCTACATCGTCGGGTCA 60.751 60.000 0.00 0.00 0.00 4.02
53 54 0.891373 ATCGGATGCCTCCTACATCG 59.109 55.000 6.46 0.00 43.98 3.84
68 69 2.537560 GGCATTGGCTCGTCATCGG 61.538 63.158 2.42 0.00 40.87 4.18
88 89 4.617875 GCCAACATAGACAGGCGT 57.382 55.556 0.00 0.00 37.41 5.68
90 91 5.999941 TGGTGAAGCCAACATAGACAGGC 63.000 52.174 0.00 0.00 45.94 4.85
143 144 0.107703 TAGTTGCTCCTTCGCCATGG 60.108 55.000 7.63 7.63 0.00 3.66
144 145 1.293924 CTAGTTGCTCCTTCGCCATG 58.706 55.000 0.00 0.00 0.00 3.66
159 160 1.266718 CCAAACACATGCAACGCTAGT 59.733 47.619 0.00 0.00 0.00 2.57
161 162 0.039617 GCCAAACACATGCAACGCTA 60.040 50.000 0.00 0.00 0.00 4.26
163 164 0.945265 ATGCCAAACACATGCAACGC 60.945 50.000 0.00 0.00 38.69 4.84
164 165 1.456544 GAATGCCAAACACATGCAACG 59.543 47.619 0.00 0.00 38.69 4.10
165 166 1.799994 GGAATGCCAAACACATGCAAC 59.200 47.619 0.00 0.00 38.69 4.17
170 171 1.591183 GCCGGAATGCCAAACACAT 59.409 52.632 5.05 0.00 0.00 3.21
171 172 2.913765 CGCCGGAATGCCAAACACA 61.914 57.895 5.05 0.00 0.00 3.72
172 173 2.126502 CGCCGGAATGCCAAACAC 60.127 61.111 5.05 0.00 0.00 3.32
188 189 3.905678 CTGCTCCTCCTACGCCCG 61.906 72.222 0.00 0.00 0.00 6.13
189 190 4.228567 GCTGCTCCTCCTACGCCC 62.229 72.222 0.00 0.00 0.00 6.13
190 191 4.577246 CGCTGCTCCTCCTACGCC 62.577 72.222 0.00 0.00 0.00 5.68
200 201 1.704582 CGAAGTTGTAGCGCTGCTC 59.295 57.895 25.90 17.93 40.44 4.26
215 216 3.969250 GATGTGCGGGAAGGGCGAA 62.969 63.158 0.00 0.00 0.00 4.70
218 219 3.134127 GTGATGTGCGGGAAGGGC 61.134 66.667 0.00 0.00 0.00 5.19
228 229 1.403382 CCTCCGTGAGTCAGTGATGTG 60.403 57.143 0.00 0.00 0.00 3.21
229 230 0.891373 CCTCCGTGAGTCAGTGATGT 59.109 55.000 0.00 0.00 0.00 3.06
230 231 0.174389 CCCTCCGTGAGTCAGTGATG 59.826 60.000 0.00 0.00 0.00 3.07
231 232 1.608717 GCCCTCCGTGAGTCAGTGAT 61.609 60.000 0.00 0.00 0.00 3.06
232 233 2.276116 GCCCTCCGTGAGTCAGTGA 61.276 63.158 0.00 0.00 0.00 3.41
233 234 2.262915 GCCCTCCGTGAGTCAGTG 59.737 66.667 0.00 0.00 0.00 3.66
234 235 2.997897 GGCCCTCCGTGAGTCAGT 60.998 66.667 0.00 0.00 0.00 3.41
235 236 2.111999 TTTGGCCCTCCGTGAGTCAG 62.112 60.000 0.00 0.00 34.14 3.51
236 237 1.488705 ATTTGGCCCTCCGTGAGTCA 61.489 55.000 0.00 0.00 34.14 3.41
237 238 0.744771 GATTTGGCCCTCCGTGAGTC 60.745 60.000 0.00 0.00 34.14 3.36
238 239 1.201429 AGATTTGGCCCTCCGTGAGT 61.201 55.000 0.00 0.00 34.14 3.41
239 240 0.830648 TAGATTTGGCCCTCCGTGAG 59.169 55.000 0.00 0.00 34.14 3.51
240 241 0.539986 GTAGATTTGGCCCTCCGTGA 59.460 55.000 0.00 0.00 34.14 4.35
241 242 0.810031 CGTAGATTTGGCCCTCCGTG 60.810 60.000 0.00 0.00 34.14 4.94
242 243 1.262640 ACGTAGATTTGGCCCTCCGT 61.263 55.000 0.00 0.00 34.14 4.69
256 257 3.242478 CCTCGCTCAAGAACTAGACGTAG 60.242 52.174 0.00 0.00 0.00 3.51
261 262 2.370349 CCTCCTCGCTCAAGAACTAGA 58.630 52.381 0.00 0.00 0.00 2.43
263 264 0.818296 GCCTCCTCGCTCAAGAACTA 59.182 55.000 0.00 0.00 0.00 2.24
269 270 0.687757 ACTATGGCCTCCTCGCTCAA 60.688 55.000 3.32 0.00 0.00 3.02
283 284 3.643763 GTTCTCGTCCATAGCCACTATG 58.356 50.000 7.49 7.49 42.28 2.23
284 285 2.293677 CGTTCTCGTCCATAGCCACTAT 59.706 50.000 0.00 0.00 0.00 2.12
286 287 0.456221 CGTTCTCGTCCATAGCCACT 59.544 55.000 0.00 0.00 0.00 4.00
299 300 4.090057 GCAGTTGCCGGCGTTCTC 62.090 66.667 23.90 9.88 34.31 2.87
341 342 1.303236 TGAATGGGCCGACCTTGTG 60.303 57.895 0.00 0.00 41.11 3.33
344 345 2.046314 CGTGAATGGGCCGACCTT 60.046 61.111 0.00 0.00 41.11 3.50
349 350 2.124736 ATGGACGTGAATGGGCCG 60.125 61.111 0.00 0.00 0.00 6.13
383 384 0.745845 ATGGCCTCGACATTGTCAGC 60.746 55.000 16.61 14.38 32.09 4.26
385 386 0.392863 CCATGGCCTCGACATTGTCA 60.393 55.000 16.61 3.66 32.09 3.58
389 390 0.179000 GAGTCCATGGCCTCGACATT 59.821 55.000 7.11 1.00 0.00 2.71
391 392 1.607801 CTGAGTCCATGGCCTCGACA 61.608 60.000 17.57 0.45 0.00 4.35
395 396 2.191641 GCCTGAGTCCATGGCCTC 59.808 66.667 16.05 16.05 40.71 4.70
409 410 1.985116 GTCCCACTCTTCCTCGCCT 60.985 63.158 0.00 0.00 0.00 5.52
411 412 0.460987 CATGTCCCACTCTTCCTCGC 60.461 60.000 0.00 0.00 0.00 5.03
424 425 2.054453 GCCTTTGCCTCCCATGTCC 61.054 63.158 0.00 0.00 0.00 4.02
432 433 0.102300 AACACAAACGCCTTTGCCTC 59.898 50.000 7.93 0.00 40.57 4.70
435 436 0.179124 TGGAACACAAACGCCTTTGC 60.179 50.000 7.93 0.00 40.57 3.68
452 453 3.490590 CGATGAGGAAGAGTGAGACATGG 60.491 52.174 0.00 0.00 0.00 3.66
460 461 1.202200 GGTCGTCGATGAGGAAGAGTG 60.202 57.143 7.79 0.00 0.00 3.51
471 472 0.677288 TGAAGTTGTGGGTCGTCGAT 59.323 50.000 0.00 0.00 0.00 3.59
472 473 0.249155 GTGAAGTTGTGGGTCGTCGA 60.249 55.000 0.00 0.00 0.00 4.20
475 476 1.474498 GGAAGTGAAGTTGTGGGTCGT 60.474 52.381 0.00 0.00 0.00 4.34
476 477 1.226746 GGAAGTGAAGTTGTGGGTCG 58.773 55.000 0.00 0.00 0.00 4.79
505 506 2.355445 CTAGCATCTTCGCCGCTCCA 62.355 60.000 0.00 0.00 37.20 3.86
508 509 1.066587 GTCTAGCATCTTCGCCGCT 59.933 57.895 0.00 0.00 39.80 5.52
509 510 0.598680 ATGTCTAGCATCTTCGCCGC 60.599 55.000 0.00 0.00 30.67 6.53
510 511 1.135046 CATGTCTAGCATCTTCGCCG 58.865 55.000 0.00 0.00 35.19 6.46
514 515 5.415701 TGTTTTTCCCATGTCTAGCATCTTC 59.584 40.000 0.00 0.00 35.19 2.87
523 524 4.184649 AGTCCTTGTTTTTCCCATGTCT 57.815 40.909 0.00 0.00 0.00 3.41
534 536 0.178961 GGGCCTCCAAGTCCTTGTTT 60.179 55.000 0.84 0.00 38.85 2.83
551 553 4.092968 GCCTAAATCATTATAAGCGTCGGG 59.907 45.833 0.00 0.00 0.00 5.14
553 555 6.253727 CCTAGCCTAAATCATTATAAGCGTCG 59.746 42.308 0.00 0.00 0.00 5.12
554 556 7.097834 ACCTAGCCTAAATCATTATAAGCGTC 58.902 38.462 0.00 0.00 0.00 5.19
562 564 7.929785 CGGAAGTTAACCTAGCCTAAATCATTA 59.070 37.037 0.88 0.00 0.00 1.90
563 565 6.766467 CGGAAGTTAACCTAGCCTAAATCATT 59.234 38.462 0.88 0.00 0.00 2.57
565 567 5.395990 CCGGAAGTTAACCTAGCCTAAATCA 60.396 44.000 0.00 0.00 0.00 2.57
571 573 1.829849 GACCGGAAGTTAACCTAGCCT 59.170 52.381 9.46 0.00 0.00 4.58
573 575 1.918595 CGACCGGAAGTTAACCTAGC 58.081 55.000 9.46 0.00 0.00 3.42
574 576 1.203052 TGCGACCGGAAGTTAACCTAG 59.797 52.381 9.46 0.00 0.00 3.02
578 580 2.224784 ACAAATGCGACCGGAAGTTAAC 59.775 45.455 9.46 0.00 0.00 2.01
588 590 2.953640 TTCGTTACACAAATGCGACC 57.046 45.000 0.00 0.00 0.00 4.79
589 591 6.521821 ACATATTTTCGTTACACAAATGCGAC 59.478 34.615 0.00 0.00 0.00 5.19
590 592 6.604012 ACATATTTTCGTTACACAAATGCGA 58.396 32.000 0.00 0.00 0.00 5.10
591 593 6.289821 CGACATATTTTCGTTACACAAATGCG 60.290 38.462 0.57 0.00 0.00 4.73
615 617 4.558470 CGGACCACATTCATTTCATTTTCG 59.442 41.667 0.00 0.00 0.00 3.46
623 625 6.828273 TCATTTAGATCGGACCACATTCATTT 59.172 34.615 0.00 0.00 0.00 2.32
633 635 6.486657 TGGATGAATTTCATTTAGATCGGACC 59.513 38.462 12.96 6.45 37.20 4.46
638 640 9.028185 GCAAACTGGATGAATTTCATTTAGATC 57.972 33.333 21.09 8.22 37.20 2.75
641 643 8.712285 ATGCAAACTGGATGAATTTCATTTAG 57.288 30.769 12.96 14.91 37.20 1.85
672 674 2.853963 CGGAATTTAAAAACCGGACGG 58.146 47.619 21.00 9.56 41.41 4.79
674 676 3.564235 AGCGGAATTTAAAAACCGGAC 57.436 42.857 26.06 16.26 44.61 4.79
683 685 6.252441 CGCATACATTTTCAAGCGGAATTTAA 59.748 34.615 0.00 0.00 41.30 1.52
707 711 5.364778 TCAACCATGTACCTCAAATATCCG 58.635 41.667 0.00 0.00 0.00 4.18
743 747 1.939785 GCGTCCGAGCAGTGATACG 60.940 63.158 0.00 0.00 37.05 3.06
762 766 3.200605 TGACAAGCCATACATCTGTGGAT 59.799 43.478 0.00 0.00 37.72 3.41
768 772 6.322201 CCCTAAAATTGACAAGCCATACATCT 59.678 38.462 0.00 0.00 0.00 2.90
776 780 1.207089 GGCCCCTAAAATTGACAAGCC 59.793 52.381 0.00 0.00 0.00 4.35
777 781 1.207089 GGGCCCCTAAAATTGACAAGC 59.793 52.381 12.23 0.00 0.00 4.01
779 783 1.551452 CGGGCCCCTAAAATTGACAA 58.449 50.000 18.66 0.00 0.00 3.18
784 788 1.304630 AACGCGGGCCCCTAAAATT 60.305 52.632 18.66 0.00 0.00 1.82
804 808 0.332972 AATCCCCTTCAAGGCACCTC 59.667 55.000 0.00 0.00 32.73 3.85
807 811 1.923356 TTCAATCCCCTTCAAGGCAC 58.077 50.000 0.00 0.00 32.73 5.01
811 815 2.225369 ACCCCTTTCAATCCCCTTCAAG 60.225 50.000 0.00 0.00 0.00 3.02
812 816 1.792651 ACCCCTTTCAATCCCCTTCAA 59.207 47.619 0.00 0.00 0.00 2.69
828 833 1.859841 ATTCAAACCCCCTCGACCCC 61.860 60.000 0.00 0.00 0.00 4.95
854 859 4.264804 TGGAAGGGCTCAATAGGGATTTTT 60.265 41.667 0.00 0.00 0.00 1.94
899 905 2.673368 GAGATACACGGAGGTTTTGCAG 59.327 50.000 0.00 0.00 0.00 4.41
902 908 3.179830 CTCGAGATACACGGAGGTTTTG 58.820 50.000 6.58 0.00 0.00 2.44
908 914 0.945813 GGTCCTCGAGATACACGGAG 59.054 60.000 15.71 0.00 0.00 4.63
915 921 0.395311 ACAAGCGGGTCCTCGAGATA 60.395 55.000 15.71 0.00 0.00 1.98
967 973 3.372025 GGGTTCTCGTCTAAGTAGGGGTA 60.372 52.174 0.00 0.00 0.00 3.69
968 974 2.622714 GGGTTCTCGTCTAAGTAGGGGT 60.623 54.545 0.00 0.00 0.00 4.95
969 975 2.030371 GGGTTCTCGTCTAAGTAGGGG 58.970 57.143 0.00 0.00 0.00 4.79
970 976 2.030371 GGGGTTCTCGTCTAAGTAGGG 58.970 57.143 0.00 0.00 0.00 3.53
971 977 2.950975 GAGGGGTTCTCGTCTAAGTAGG 59.049 54.545 0.00 0.00 32.18 3.18
972 978 2.950975 GGAGGGGTTCTCGTCTAAGTAG 59.049 54.545 0.00 0.00 43.34 2.57
1078 1085 1.341913 GGCCTCCCTCCCTTCTCTTC 61.342 65.000 0.00 0.00 0.00 2.87
1110 1117 0.523546 CGTCCATGTCGTCTCTTCCG 60.524 60.000 0.00 0.00 0.00 4.30
1274 1656 2.542907 CGCGAGAGAGAGGAGAGGC 61.543 68.421 0.00 0.00 0.00 4.70
1294 1676 0.970937 TGTGGAGATCCTGGACGGAC 60.971 60.000 0.00 0.00 46.80 4.79
1348 1730 4.518249 GGGGAAAAGAGACAAGATGTAGG 58.482 47.826 0.00 0.00 0.00 3.18
1373 1756 1.512734 GCGCGCATTTCAGTTCCAG 60.513 57.895 29.10 0.00 0.00 3.86
1493 1879 1.302832 CGCAAAAGCTGGACCCTCT 60.303 57.895 0.00 0.00 0.00 3.69
1578 1964 7.394016 TGTAATTGAAACTGGAGAAGCTATCA 58.606 34.615 0.00 0.00 0.00 2.15
1579 1965 7.849804 TGTAATTGAAACTGGAGAAGCTATC 57.150 36.000 0.00 0.00 0.00 2.08
1760 2146 1.833630 CCCAGCTGTTCTATGTCCTCA 59.166 52.381 13.81 0.00 0.00 3.86
1761 2147 1.474143 GCCCAGCTGTTCTATGTCCTC 60.474 57.143 13.81 0.00 0.00 3.71
1776 2162 0.320374 TAACTGAACCAGACGCCCAG 59.680 55.000 0.45 0.00 35.18 4.45
1888 2274 5.652452 AGGAAGCAATGGGTGTAGATTTTAC 59.348 40.000 0.00 0.00 0.00 2.01
2274 2661 7.826252 ACATCTGGAATATATATTCACCAGCAC 59.174 37.037 28.37 14.75 42.92 4.40
2493 2882 4.404715 AGCATGGCAGCTAAAGATTCATTT 59.595 37.500 9.26 0.00 44.50 2.32
2499 2888 2.950309 CAGAAGCATGGCAGCTAAAGAT 59.050 45.455 11.01 0.00 45.89 2.40
2879 3294 7.781324 ATCCTTTAGCTCATTCTTCCAAAAA 57.219 32.000 0.00 0.00 0.00 1.94
2998 3413 7.879677 TGATGAACTTCTGAATAAGCAAGAGAA 59.120 33.333 0.00 0.00 0.00 2.87
3010 3425 4.021192 GGCCCATTTTGATGAACTTCTGAA 60.021 41.667 0.00 0.00 0.00 3.02
3046 3461 2.634982 TCAAGAAATGTGCCATTCGC 57.365 45.000 1.57 0.00 38.31 4.70
3047 3462 6.324819 ACTAAATCAAGAAATGTGCCATTCG 58.675 36.000 1.57 0.00 0.00 3.34
3129 3544 4.829492 GCCCTTACCAAGCATCATAATTCT 59.171 41.667 0.00 0.00 0.00 2.40
3130 3545 4.584325 TGCCCTTACCAAGCATCATAATTC 59.416 41.667 0.00 0.00 0.00 2.17
3131 3546 4.545678 TGCCCTTACCAAGCATCATAATT 58.454 39.130 0.00 0.00 0.00 1.40
3132 3547 4.183223 TGCCCTTACCAAGCATCATAAT 57.817 40.909 0.00 0.00 0.00 1.28
3139 3554 3.730215 TTAGAATGCCCTTACCAAGCA 57.270 42.857 0.00 0.00 41.50 3.91
3189 3604 9.725206 ACTTCCTTAAACAGTTAGGATATCCTA 57.275 33.333 25.03 25.03 46.48 2.94
3332 3747 9.029243 CAATTTCAAGTAAACAAGTATGCACAA 57.971 29.630 0.00 0.00 0.00 3.33
3333 3748 8.194104 ACAATTTCAAGTAAACAAGTATGCACA 58.806 29.630 0.00 0.00 0.00 4.57
3358 3773 5.235616 TGAGACAAATTCTACACAACGGAAC 59.764 40.000 0.00 0.00 33.22 3.62
3446 3861 1.612146 TGGCCTCCTCATGTTCCGA 60.612 57.895 3.32 0.00 0.00 4.55
3480 3895 1.486997 ATAGGAGGCATGCCAGCGAT 61.487 55.000 37.18 21.59 38.92 4.58
3508 3923 5.366482 TTGCTAGGTTATAAGTGATGCCA 57.634 39.130 0.00 0.00 0.00 4.92
3520 3935 4.650972 AAGGTGGAACATTGCTAGGTTA 57.349 40.909 0.00 0.00 40.56 2.85
3521 3936 3.525800 AAGGTGGAACATTGCTAGGTT 57.474 42.857 0.00 0.00 40.56 3.50
3527 3942 8.546597 ACAAAATTATAAAGGTGGAACATTGC 57.453 30.769 0.00 0.00 41.66 3.56
3585 4000 6.143278 GCAAATTAAAAGTCAAGTGTTACCCG 59.857 38.462 0.00 0.00 0.00 5.28
3588 4003 7.169140 CCTGGCAAATTAAAAGTCAAGTGTTAC 59.831 37.037 0.00 0.00 0.00 2.50
3626 4041 1.557099 AGGTACCTGATGTCTGCGAA 58.443 50.000 15.42 0.00 0.00 4.70
3748 4163 5.569355 TCATCTTTCCTTGTATTGGAAGCA 58.431 37.500 0.00 0.00 43.48 3.91
3874 4289 2.159085 CCGTCCTAACCTCCAAGATGTC 60.159 54.545 0.00 0.00 0.00 3.06
3894 4309 6.273071 ACAAAAGCAAACAACTCTGATAACC 58.727 36.000 0.00 0.00 0.00 2.85
3926 4341 5.355071 AGGCAAAGGCAAAGAAAAGAAAAAG 59.645 36.000 0.00 0.00 43.71 2.27
3989 4404 2.674796 AAGATTCTACTCGGCACCAC 57.325 50.000 0.00 0.00 0.00 4.16
4002 4417 4.447290 GGAGCTCTTCCACCTTAAGATTC 58.553 47.826 14.64 0.00 46.01 2.52
4098 4513 4.918060 CACACACACACACGCGCG 62.918 66.667 30.96 30.96 0.00 6.86
4099 4514 3.860125 ACACACACACACACGCGC 61.860 61.111 5.73 0.00 0.00 6.86
4100 4515 2.021243 CACACACACACACACGCG 59.979 61.111 3.53 3.53 0.00 6.01
4101 4516 0.792729 CAACACACACACACACACGC 60.793 55.000 0.00 0.00 0.00 5.34
4102 4517 0.515127 ACAACACACACACACACACG 59.485 50.000 0.00 0.00 0.00 4.49
4103 4518 3.815337 TTACAACACACACACACACAC 57.185 42.857 0.00 0.00 0.00 3.82
4242 4657 6.605194 TGGGCAAGTATTAGATGTAATTTGCA 59.395 34.615 23.07 9.53 40.81 4.08
4243 4658 6.918022 GTGGGCAAGTATTAGATGTAATTTGC 59.082 38.462 17.52 17.52 39.54 3.68
4264 4679 1.971505 TATCCTTGAGCAGCCGTGGG 61.972 60.000 0.00 0.00 0.00 4.61
4377 4814 7.708752 AGAAGAAAGTACAATGCTCTATAGTGC 59.291 37.037 17.86 17.86 35.32 4.40
4564 5001 4.262249 GCTACATCATCAACTCCTCTACCC 60.262 50.000 0.00 0.00 0.00 3.69
4695 5132 4.920640 TGTGTTTTTCTTTCGGGCATAA 57.079 36.364 0.00 0.00 0.00 1.90
4702 5139 2.159170 TGCCCCTTGTGTTTTTCTTTCG 60.159 45.455 0.00 0.00 0.00 3.46
4839 5276 1.081892 CCAGTCTCCAACAGAATGCG 58.918 55.000 0.00 0.00 44.50 4.73
4867 5304 1.376553 GACTTCTGGTGAGGCTGCC 60.377 63.158 11.65 11.65 0.00 4.85
4884 5324 0.966875 AAGCATCGCAAATGGCCTGA 60.967 50.000 3.32 0.00 40.31 3.86
4919 5359 2.697431 TGAAATTCCGTTTTCAGCCG 57.303 45.000 2.41 0.00 39.91 5.52
4929 5369 5.880054 ACCTACATCTGTTTGAAATTCCG 57.120 39.130 0.00 0.00 0.00 4.30
4931 5371 9.612620 CAAGTTACCTACATCTGTTTGAAATTC 57.387 33.333 0.00 0.00 0.00 2.17
5043 5485 7.529158 AGTTGCTTTCTTGATTTTTGTTTTGG 58.471 30.769 0.00 0.00 0.00 3.28
5073 5515 6.716628 TGCAAAAATAAGAGGAATGTCTGTCT 59.283 34.615 0.00 0.00 0.00 3.41
5088 5530 3.120627 GCCGCAGCTGCAAAAATAA 57.879 47.368 36.03 0.00 42.21 1.40


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

AutoCloner maintained by Alex Coulton.