Multiple sequence alignment - TraesCS2B01G094100

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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 TraesCS2B01G094100 chr2B 100.000 6411 0 0 1 6411 54527836 54534246 0.000000e+00 11839
1 TraesCS2B01G094100 chr2B 85.849 318 36 6 1 313 117996515 117996828 4.790000e-86 329
2 TraesCS2B01G094100 chr2B 83.333 240 38 2 2379 2617 43959103 43959341 3.010000e-53 220
3 TraesCS2B01G094100 chr2B 80.723 166 26 6 2343 2507 320514458 320514298 2.430000e-24 124
4 TraesCS2B01G094100 chr2D 91.245 5597 287 76 1 5511 32787851 32793330 0.000000e+00 7433
5 TraesCS2B01G094100 chr2D 89.534 879 40 22 5555 6408 32793330 32794181 0.000000e+00 1066
6 TraesCS2B01G094100 chr2D 84.252 381 45 10 1 374 398470424 398470796 2.200000e-94 357
7 TraesCS2B01G094100 chr2D 84.298 363 47 7 1 357 76756239 76756597 4.760000e-91 346
8 TraesCS2B01G094100 chr2D 84.362 243 36 2 2379 2620 5131802 5131561 2.990000e-58 237
9 TraesCS2B01G094100 chr2A 90.569 2937 197 41 2325 5217 36038791 36041691 0.000000e+00 3816
10 TraesCS2B01G094100 chr2A 87.357 1400 88 40 977 2329 36037401 36038758 0.000000e+00 1522
11 TraesCS2B01G094100 chr2A 88.588 885 42 19 5555 6411 36042018 36042871 0.000000e+00 1020
12 TraesCS2B01G094100 chr2A 87.421 318 31 6 1 313 77242774 77243087 2.200000e-94 357
13 TraesCS2B01G094100 chr2A 84.211 342 24 11 470 802 36036512 36036832 8.080000e-79 305
14 TraesCS2B01G094100 chr2A 83.929 224 34 2 2398 2620 559846650 559846428 5.040000e-51 213
15 TraesCS2B01G094100 chr7B 86.624 314 35 6 1 312 238643826 238644134 2.210000e-89 340
16 TraesCS2B01G094100 chr7B 85.000 220 31 2 2398 2616 459351600 459351382 8.370000e-54 222
17 TraesCS2B01G094100 chr5B 80.211 475 76 15 1 465 614046155 614045689 2.210000e-89 340
18 TraesCS2B01G094100 chr1B 86.349 315 33 7 2 311 673629182 673628873 1.030000e-87 335
19 TraesCS2B01G094100 chr1B 85.849 318 36 5 1 313 575920765 575920452 4.790000e-86 329
20 TraesCS2B01G094100 chr3A 82.624 282 42 7 2336 2616 411838054 411837779 6.420000e-60 243
21 TraesCS2B01G094100 chr3A 84.064 251 30 6 1749 1998 411838646 411838405 3.860000e-57 233
22 TraesCS2B01G094100 chr4A 84.689 209 29 3 2398 2605 707655801 707656007 8.430000e-49 206


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 TraesCS2B01G094100 chr2B 54527836 54534246 6410 False 11839.00 11839 100.00000 1 6411 1 chr2B.!!$F2 6410
1 TraesCS2B01G094100 chr2D 32787851 32794181 6330 False 4249.50 7433 90.38950 1 6408 2 chr2D.!!$F3 6407
2 TraesCS2B01G094100 chr2A 36036512 36042871 6359 False 1665.75 3816 87.68125 470 6411 4 chr2A.!!$F2 5941
3 TraesCS2B01G094100 chr3A 411837779 411838646 867 True 238.00 243 83.34400 1749 2616 2 chr3A.!!$R1 867

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
983 1406 0.036577 ATCAGCCGCATATGCTCTCC 60.037 55.000 24.56 10.25 36.81 3.71 F
1195 1636 0.243636 GGCTTCGATTGGTTGGTTGG 59.756 55.000 0.00 0.00 0.00 3.77 F
2142 2661 0.255890 TATTCTGCCAACCTGCCTCC 59.744 55.000 0.00 0.00 0.00 4.30 F
2452 3029 0.609131 CCGGTGGTCTCCTTTTGCAT 60.609 55.000 0.00 0.00 0.00 3.96 F
2694 3271 1.135402 GGTTCAGCCCAAATAGCAACG 60.135 52.381 0.00 0.00 0.00 4.10 F
4494 5117 1.227823 CGAACTCAACAGTGCCCCA 60.228 57.895 0.00 0.00 31.06 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2427 0.184451 CCCCATGATCCCTGACCAAG 59.816 60.000 0.0 0.0 0.00 3.61 R
2206 2725 0.515127 TAGGCGTGTGTTGATTTGCG 59.485 50.000 0.0 0.0 0.00 4.85 R
3327 3907 2.543578 CTGCTTTCTTGCGGCTACA 58.456 52.632 0.0 0.0 35.36 2.74 R
3334 3914 3.128938 AGATCTTCATGCTGCTTTCTTGC 59.871 43.478 0.0 0.0 0.00 4.01 R
4575 5198 0.323725 GGCCACCATGAACCATCACT 60.324 55.000 0.0 0.0 38.69 3.41 R
6242 6952 0.179086 GGCAGGCAGAGAGAAGTAGC 60.179 60.000 0.0 0.0 0.00 3.58 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
66 67 1.946650 GTAGGCTCAGCATCGACGC 60.947 63.158 0.00 0.00 0.00 5.19
67 68 3.138930 TAGGCTCAGCATCGACGCC 62.139 63.158 0.00 0.00 40.99 5.68
71 72 1.522355 CTCAGCATCGACGCCCAAT 60.522 57.895 0.00 0.00 0.00 3.16
115 116 0.250338 GCGGACAACTTCACTTCCCT 60.250 55.000 0.00 0.00 0.00 4.20
116 117 1.512926 CGGACAACTTCACTTCCCTG 58.487 55.000 0.00 0.00 0.00 4.45
118 119 1.545651 GGACAACTTCACTTCCCTGGG 60.546 57.143 6.33 6.33 0.00 4.45
156 157 1.238439 CGGAAGCAGAGCTGGAAAAA 58.762 50.000 0.00 0.00 39.62 1.94
159 160 0.964700 AAGCAGAGCTGGAAAAAGCC 59.035 50.000 0.00 0.00 44.68 4.35
229 230 2.946762 GCGATCATTTAGCCCGCC 59.053 61.111 0.00 0.00 39.97 6.13
264 265 9.787532 CTTTCATGTATTTGTAATGAAATCCGT 57.212 29.630 9.70 0.00 44.79 4.69
266 267 8.499403 TCATGTATTTGTAATGAAATCCGTCA 57.501 30.769 0.00 0.00 0.00 4.35
305 306 5.842327 CCGTCGTGTTTATATAAAATTCGGC 59.158 40.000 9.48 13.49 0.00 5.54
333 334 2.288213 TGCACGAGTTCTGTCCAGTTAG 60.288 50.000 0.00 0.00 0.00 2.34
343 344 8.974060 AGTTCTGTCCAGTTAGTTTGAATTAA 57.026 30.769 0.00 0.00 0.00 1.40
377 378 5.847111 ATACGGCTAGTGTTGAATGACTA 57.153 39.130 0.00 0.00 0.00 2.59
396 397 1.739338 ATCTCTCGCATCCGTGTCCC 61.739 60.000 0.00 0.00 35.54 4.46
397 398 3.432051 CTCTCGCATCCGTGTCCCC 62.432 68.421 0.00 0.00 35.54 4.81
429 430 1.903183 TGTTCATGACCGGATGTGGTA 59.097 47.619 9.46 0.00 44.01 3.25
430 431 2.503765 TGTTCATGACCGGATGTGGTAT 59.496 45.455 9.46 0.00 44.01 2.73
465 466 0.247736 GCGATCGGAGATGGCCTTAT 59.752 55.000 18.30 0.00 45.12 1.73
467 468 2.341257 CGATCGGAGATGGCCTTATTG 58.659 52.381 7.38 0.00 45.12 1.90
511 512 2.700722 CCCAGAGGTAGAAAGAAGGC 57.299 55.000 0.00 0.00 0.00 4.35
512 513 2.192263 CCCAGAGGTAGAAAGAAGGCT 58.808 52.381 0.00 0.00 0.00 4.58
513 514 2.573915 CCCAGAGGTAGAAAGAAGGCTT 59.426 50.000 0.00 0.00 35.37 4.35
514 515 3.369997 CCCAGAGGTAGAAAGAAGGCTTC 60.370 52.174 19.53 19.53 31.82 3.86
515 516 3.369997 CCAGAGGTAGAAAGAAGGCTTCC 60.370 52.174 23.09 8.66 31.82 3.46
516 517 3.517500 CAGAGGTAGAAAGAAGGCTTCCT 59.482 47.826 23.09 15.36 31.82 3.36
517 518 3.517500 AGAGGTAGAAAGAAGGCTTCCTG 59.482 47.826 23.09 0.00 32.13 3.86
518 519 2.573915 AGGTAGAAAGAAGGCTTCCTGG 59.426 50.000 23.09 0.00 32.13 4.45
519 520 2.356227 GGTAGAAAGAAGGCTTCCTGGG 60.356 54.545 23.09 0.00 32.13 4.45
520 521 0.038890 AGAAAGAAGGCTTCCTGGGC 59.961 55.000 23.09 8.99 32.13 5.36
521 522 0.251341 GAAAGAAGGCTTCCTGGGCA 60.251 55.000 23.09 0.00 32.13 5.36
522 523 0.188342 AAAGAAGGCTTCCTGGGCAA 59.812 50.000 23.09 0.00 32.13 4.52
523 524 0.540597 AAGAAGGCTTCCTGGGCAAC 60.541 55.000 23.09 0.00 32.13 4.17
556 570 1.168714 GGCAACTTCCAGGTAGCAAG 58.831 55.000 0.00 0.00 0.00 4.01
605 619 0.674534 ACTCGTCCACCACTCAACTC 59.325 55.000 0.00 0.00 0.00 3.01
606 620 0.673985 CTCGTCCACCACTCAACTCA 59.326 55.000 0.00 0.00 0.00 3.41
607 621 1.068588 CTCGTCCACCACTCAACTCAA 59.931 52.381 0.00 0.00 0.00 3.02
608 622 1.202486 TCGTCCACCACTCAACTCAAC 60.202 52.381 0.00 0.00 0.00 3.18
609 623 1.594331 GTCCACCACTCAACTCAACC 58.406 55.000 0.00 0.00 0.00 3.77
621 635 0.755327 ACTCAACCCAACCCAGCAAC 60.755 55.000 0.00 0.00 0.00 4.17
662 680 4.825085 TGGAATAACAAGACAACCCAAGAC 59.175 41.667 0.00 0.00 0.00 3.01
697 715 5.245977 AGCAATAAAACAAGTAGCCAACCAT 59.754 36.000 0.00 0.00 0.00 3.55
716 737 7.177921 CCAACCATGGCATAGATTTAGAATCAT 59.822 37.037 13.04 0.00 40.58 2.45
717 738 9.234827 CAACCATGGCATAGATTTAGAATCATA 57.765 33.333 13.04 0.00 0.00 2.15
718 739 8.798859 ACCATGGCATAGATTTAGAATCATAC 57.201 34.615 13.04 0.00 0.00 2.39
719 740 8.609483 ACCATGGCATAGATTTAGAATCATACT 58.391 33.333 13.04 0.00 0.00 2.12
720 741 8.890718 CCATGGCATAGATTTAGAATCATACTG 58.109 37.037 0.00 0.00 0.00 2.74
740 761 1.912110 GTAGATCACGTTCGCACACTC 59.088 52.381 0.00 0.00 0.00 3.51
762 783 2.537560 CGCAACGGCATGGAGATCC 61.538 63.158 0.00 0.00 41.24 3.36
808 837 2.079925 GGATATGCTCCGCTTCAATCC 58.920 52.381 0.00 0.00 33.29 3.01
809 838 2.550855 GGATATGCTCCGCTTCAATCCA 60.551 50.000 0.00 0.00 33.29 3.41
810 839 2.708216 TATGCTCCGCTTCAATCCAA 57.292 45.000 0.00 0.00 0.00 3.53
811 840 1.386533 ATGCTCCGCTTCAATCCAAG 58.613 50.000 0.00 0.00 0.00 3.61
812 841 1.308069 TGCTCCGCTTCAATCCAAGC 61.308 55.000 0.00 0.00 44.67 4.01
819 856 1.542492 CTTCAATCCAAGCAGCCAGT 58.458 50.000 0.00 0.00 0.00 4.00
845 882 2.110967 CAGATGCTCAACCCGCTGG 61.111 63.158 0.00 0.00 37.80 4.85
846 883 3.512516 GATGCTCAACCCGCTGGC 61.513 66.667 0.00 0.00 33.59 4.85
850 887 2.589540 CTCAACCCGCTGGCCATA 59.410 61.111 5.51 0.00 33.59 2.74
851 888 1.149174 CTCAACCCGCTGGCCATAT 59.851 57.895 5.51 0.00 33.59 1.78
852 889 0.396435 CTCAACCCGCTGGCCATATA 59.604 55.000 5.51 0.00 33.59 0.86
858 895 2.017049 CCCGCTGGCCATATAATTAGC 58.983 52.381 5.51 1.80 0.00 3.09
861 898 3.127548 CCGCTGGCCATATAATTAGCAAG 59.872 47.826 5.51 0.00 0.00 4.01
863 900 3.760684 GCTGGCCATATAATTAGCAAGCT 59.239 43.478 5.51 0.00 46.64 3.74
880 917 0.462759 GCTCCCATCACTGTACCAGC 60.463 60.000 0.00 0.00 34.37 4.85
883 920 1.596934 CCATCACTGTACCAGCGGT 59.403 57.895 5.58 5.58 40.16 5.68
886 923 0.460311 ATCACTGTACCAGCGGTAGC 59.540 55.000 7.56 4.74 39.02 3.58
899 936 0.597637 CGGTAGCGTCCCACATCATC 60.598 60.000 6.07 0.00 0.00 2.92
925 962 5.277538 GCCACTTCTTTAGCGGATTGATTAG 60.278 44.000 0.00 0.00 0.00 1.73
927 964 4.816925 ACTTCTTTAGCGGATTGATTAGCC 59.183 41.667 0.00 0.00 0.00 3.93
940 977 3.631250 TGATTAGCCATTTTCTGGGGTC 58.369 45.455 0.00 0.00 46.06 4.46
953 990 2.266055 GGGTCAGAGGCGGAAGTG 59.734 66.667 0.00 0.00 0.00 3.16
982 1405 2.662006 TATCAGCCGCATATGCTCTC 57.338 50.000 24.56 13.19 36.81 3.20
983 1406 0.036577 ATCAGCCGCATATGCTCTCC 60.037 55.000 24.56 10.25 36.81 3.71
1057 1489 3.297134 TTTCTATTGCCCCATCCTCAC 57.703 47.619 0.00 0.00 0.00 3.51
1105 1538 2.586792 CCACTAGGTGCTCAGCCC 59.413 66.667 0.00 0.00 31.34 5.19
1116 1549 2.164422 GTGCTCAGCCCATTTTCTTACC 59.836 50.000 0.00 0.00 0.00 2.85
1118 1551 2.424956 GCTCAGCCCATTTTCTTACCAG 59.575 50.000 0.00 0.00 0.00 4.00
1193 1634 1.202879 TCAGGCTTCGATTGGTTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
1194 1635 1.068333 CAGGCTTCGATTGGTTGGTTG 60.068 52.381 0.00 0.00 0.00 3.77
1195 1636 0.243636 GGCTTCGATTGGTTGGTTGG 59.756 55.000 0.00 0.00 0.00 3.77
1196 1637 0.958822 GCTTCGATTGGTTGGTTGGT 59.041 50.000 0.00 0.00 0.00 3.67
1241 1682 1.991339 GCCAGTATAAAGGGCGGGGT 61.991 60.000 0.00 0.00 38.04 4.95
1243 1684 0.834612 CAGTATAAAGGGCGGGGTCA 59.165 55.000 0.00 0.00 0.00 4.02
1254 1695 4.393778 GGGGTCACCGGAGAGGGA 62.394 72.222 9.46 0.00 46.96 4.20
1561 2013 1.709082 CCCCCAATCCCAATCCCAA 59.291 57.895 0.00 0.00 0.00 4.12
1572 2031 1.203300 CCAATCCCAACCCTTTCCCTT 60.203 52.381 0.00 0.00 0.00 3.95
1575 2034 0.485543 TCCCAACCCTTTCCCTTTCC 59.514 55.000 0.00 0.00 0.00 3.13
1660 2137 4.803426 GCGACGGAGGAGCTGGTG 62.803 72.222 0.00 0.00 0.00 4.17
1755 2232 1.134068 GCAGGTACCTCTCCATTTCCC 60.134 57.143 12.84 0.00 0.00 3.97
1765 2242 3.496331 TCTCCATTTCCCTGTCAAAACC 58.504 45.455 0.00 0.00 0.00 3.27
1782 2259 4.455070 AAACCTGCTCTTCCCTTTTACT 57.545 40.909 0.00 0.00 0.00 2.24
1783 2260 5.578157 AAACCTGCTCTTCCCTTTTACTA 57.422 39.130 0.00 0.00 0.00 1.82
1784 2261 4.554960 ACCTGCTCTTCCCTTTTACTAC 57.445 45.455 0.00 0.00 0.00 2.73
2051 2555 1.929836 GATCTTCTTGCCTGTGCTACG 59.070 52.381 0.00 0.00 38.71 3.51
2052 2556 0.966179 TCTTCTTGCCTGTGCTACGA 59.034 50.000 0.00 0.00 38.71 3.43
2062 2566 2.159517 CCTGTGCTACGAAAGGAATTGC 60.160 50.000 0.00 0.00 30.92 3.56
2070 2574 3.135994 ACGAAAGGAATTGCGTACTGTT 58.864 40.909 0.00 0.00 34.93 3.16
2142 2661 0.255890 TATTCTGCCAACCTGCCTCC 59.744 55.000 0.00 0.00 0.00 4.30
2143 2662 2.505364 ATTCTGCCAACCTGCCTCCC 62.505 60.000 0.00 0.00 0.00 4.30
2159 2678 1.984570 CCCTGCCTCGGAGTCTTGA 60.985 63.158 4.02 0.00 0.00 3.02
2183 2702 6.748132 ACCATGTTCAGTTAACCATGAAAAG 58.252 36.000 18.56 9.55 37.19 2.27
2188 2707 3.572255 TCAGTTAACCATGAAAAGGCACC 59.428 43.478 0.88 0.00 0.00 5.01
2205 2724 5.855045 AGGCACCGATAAAACTAGAATAGG 58.145 41.667 0.00 0.00 44.97 2.57
2206 2725 4.451435 GGCACCGATAAAACTAGAATAGGC 59.549 45.833 0.00 0.00 44.97 3.93
2207 2726 4.150098 GCACCGATAAAACTAGAATAGGCG 59.850 45.833 0.00 0.00 44.97 5.52
2208 2727 4.150098 CACCGATAAAACTAGAATAGGCGC 59.850 45.833 0.00 0.00 44.97 6.53
2211 2730 5.235616 CCGATAAAACTAGAATAGGCGCAAA 59.764 40.000 10.83 0.00 44.97 3.68
2212 2731 6.073222 CCGATAAAACTAGAATAGGCGCAAAT 60.073 38.462 10.83 0.00 44.97 2.32
2213 2732 7.010023 CGATAAAACTAGAATAGGCGCAAATC 58.990 38.462 10.83 1.16 44.97 2.17
2215 2734 6.509418 AAAACTAGAATAGGCGCAAATCAA 57.491 33.333 10.83 0.00 44.97 2.57
2216 2735 5.485662 AACTAGAATAGGCGCAAATCAAC 57.514 39.130 10.83 0.00 44.97 3.18
2217 2736 4.513442 ACTAGAATAGGCGCAAATCAACA 58.487 39.130 10.83 0.00 44.97 3.33
2218 2737 3.764885 AGAATAGGCGCAAATCAACAC 57.235 42.857 10.83 0.00 0.00 3.32
2219 2738 3.081061 AGAATAGGCGCAAATCAACACA 58.919 40.909 10.83 0.00 0.00 3.72
2222 2759 2.364311 GGCGCAAATCAACACACGC 61.364 57.895 10.83 0.00 45.19 5.34
2239 2776 2.753452 CACGCCTAGTTAAGTCCTCTCA 59.247 50.000 0.00 0.00 0.00 3.27
2240 2777 3.381908 CACGCCTAGTTAAGTCCTCTCAT 59.618 47.826 0.00 0.00 0.00 2.90
2241 2778 4.579340 CACGCCTAGTTAAGTCCTCTCATA 59.421 45.833 0.00 0.00 0.00 2.15
2242 2779 5.241949 CACGCCTAGTTAAGTCCTCTCATAT 59.758 44.000 0.00 0.00 0.00 1.78
2243 2780 6.430308 CACGCCTAGTTAAGTCCTCTCATATA 59.570 42.308 0.00 0.00 0.00 0.86
2244 2781 6.430616 ACGCCTAGTTAAGTCCTCTCATATAC 59.569 42.308 0.00 0.00 0.00 1.47
2245 2782 6.655848 CGCCTAGTTAAGTCCTCTCATATACT 59.344 42.308 0.00 0.00 0.00 2.12
2286 2823 4.637483 ACACATCAAACACAAGTTCCTG 57.363 40.909 0.00 0.00 36.84 3.86
2289 2826 3.632145 ACATCAAACACAAGTTCCTGGTC 59.368 43.478 0.00 0.00 36.84 4.02
2376 2950 4.141367 TGTTGTCTTGGGGTGTTCTTCATA 60.141 41.667 0.00 0.00 0.00 2.15
2452 3029 0.609131 CCGGTGGTCTCCTTTTGCAT 60.609 55.000 0.00 0.00 0.00 3.96
2481 3058 6.649973 CCTAACTTCAATGCTCTCTATCCATG 59.350 42.308 0.00 0.00 0.00 3.66
2486 3063 6.183810 TCAATGCTCTCTATCCATGAATGT 57.816 37.500 0.00 0.00 0.00 2.71
2540 3117 9.435688 AACAAGGAATATTTTATGGCAAAGAAC 57.564 29.630 0.00 0.00 0.00 3.01
2642 3219 4.910195 ACAGCATCTCAATCTACAACCAA 58.090 39.130 0.00 0.00 0.00 3.67
2650 3227 8.986847 CATCTCAATCTACAACCAAGATGATAC 58.013 37.037 3.92 0.00 40.52 2.24
2694 3271 1.135402 GGTTCAGCCCAAATAGCAACG 60.135 52.381 0.00 0.00 0.00 4.10
2748 3325 4.386867 TCAGATAATGGTCGAGTGAACC 57.613 45.455 0.00 0.00 0.00 3.62
2776 3353 3.082165 CTCTTGGAGCTGATGCCAG 57.918 57.895 0.00 0.00 43.22 4.85
3029 3607 1.661463 TGGTTGAAGCTGAGGGATCT 58.339 50.000 0.00 0.00 0.00 2.75
3129 3707 3.511146 CAGCCACCTATTGTCACCATTTT 59.489 43.478 0.00 0.00 0.00 1.82
3138 3716 7.068226 ACCTATTGTCACCATTTTACATAAGCC 59.932 37.037 0.00 0.00 0.00 4.35
3198 3776 4.837860 TGCAACTCCTAACATCCCATTTTT 59.162 37.500 0.00 0.00 0.00 1.94
3327 3907 5.965486 AGGGAGGAACTTGAAGGTTTATTT 58.035 37.500 0.00 0.00 41.55 1.40
3334 3914 5.622770 ACTTGAAGGTTTATTTGTAGCCG 57.377 39.130 0.00 0.00 0.00 5.52
3336 3916 3.413327 TGAAGGTTTATTTGTAGCCGCA 58.587 40.909 0.00 0.00 0.00 5.69
3381 3961 6.320164 TGGCAAGAAGTAAAGAAAAAGCTACA 59.680 34.615 0.00 0.00 0.00 2.74
3517 4097 9.075678 CCATAAATATTCTCAAGCAGGAAAGAT 57.924 33.333 0.00 0.00 0.00 2.40
3850 4434 7.519008 GCTTCTTACGCTGTTATATTTGATGCT 60.519 37.037 0.00 0.00 0.00 3.79
3851 4435 7.177498 TCTTACGCTGTTATATTTGATGCTG 57.823 36.000 0.00 0.00 0.00 4.41
3852 4436 6.761242 TCTTACGCTGTTATATTTGATGCTGT 59.239 34.615 0.00 0.00 0.00 4.40
3853 4437 5.160699 ACGCTGTTATATTTGATGCTGTG 57.839 39.130 0.00 0.00 0.00 3.66
3854 4438 3.970610 CGCTGTTATATTTGATGCTGTGC 59.029 43.478 0.00 0.00 0.00 4.57
4013 4608 5.172460 TGTAGTTTTAGGTTGCGTTTTCC 57.828 39.130 0.00 0.00 0.00 3.13
4050 4646 6.128172 CCAGATTTTGTAGTTCCATGTCTGTC 60.128 42.308 0.00 0.00 31.17 3.51
4069 4665 5.863935 TCTGTCGTCATATGAACTGAAACAG 59.136 40.000 7.07 13.48 38.63 3.16
4141 4737 2.440539 AGCTTGAAGTACTGTGGACG 57.559 50.000 0.00 0.00 0.00 4.79
4190 4786 4.201861 GCTTGAGCCATTTACTTAGTCTGC 60.202 45.833 0.00 0.00 34.31 4.26
4231 4842 7.307632 GCTTGTGAGTTGTGATGGCTAATATAG 60.308 40.741 0.00 0.00 0.00 1.31
4473 5096 3.371380 GGAGCCTTCATGACCATCTCTTT 60.371 47.826 0.00 0.00 0.00 2.52
4494 5117 1.227823 CGAACTCAACAGTGCCCCA 60.228 57.895 0.00 0.00 31.06 4.96
4522 5145 2.202298 GGAAAATCCGTGCACGCG 60.202 61.111 33.17 24.75 38.18 6.01
4545 5168 2.026879 GCGGAGATCTCGAGTGCC 59.973 66.667 16.46 8.69 0.00 5.01
4575 5198 4.148079 TCCTGCATTCATGTAAACCACAA 58.852 39.130 0.00 0.00 41.55 3.33
4576 5199 4.218200 TCCTGCATTCATGTAAACCACAAG 59.782 41.667 0.00 0.00 41.55 3.16
4689 5312 0.387202 ACTCGAAGGATCATCCAGCG 59.613 55.000 6.42 9.14 39.61 5.18
4713 5336 2.158842 GGATTCTAGACTGCTGGCACAT 60.159 50.000 0.00 0.00 38.20 3.21
4734 5357 7.497249 GCACATAAGTCTGATATCAACTCCTTT 59.503 37.037 16.06 7.56 0.00 3.11
4747 5370 4.283978 TCAACTCCTTTGGTACCGTGATAA 59.716 41.667 7.57 0.00 35.69 1.75
4847 5470 2.430694 TGTCGTCGATCTTGGATCCAAT 59.569 45.455 27.20 14.08 35.20 3.16
4907 5530 1.098050 GAATTTGGGCTCGAGTGCAT 58.902 50.000 15.13 0.00 34.04 3.96
4908 5531 1.474077 GAATTTGGGCTCGAGTGCATT 59.526 47.619 15.13 5.81 34.04 3.56
4914 5537 0.179062 GGCTCGAGTGCATTGGAGAT 60.179 55.000 22.50 0.00 34.04 2.75
5064 5687 3.455469 GGGGTGACGTACGAGGGG 61.455 72.222 24.41 0.00 0.00 4.79
5073 5696 3.221389 TACGAGGGGCGCGCTATT 61.221 61.111 32.29 16.28 46.04 1.73
5076 5699 4.587189 GAGGGGCGCGCTATTCGT 62.587 66.667 32.29 18.42 41.07 3.85
5129 5752 0.037882 CTGAAGCTGAAGCACCTCGA 60.038 55.000 4.90 0.00 45.16 4.04
5231 5890 2.026542 TGATGATTCTCCAGCTGCTGTT 60.027 45.455 26.41 7.35 0.00 3.16
5269 5928 6.147437 AGCTAGTAGATATGTAGAGCCCTT 57.853 41.667 0.00 0.00 0.00 3.95
5292 5951 4.081476 TCTGTGTACATACATGCTTCTGCT 60.081 41.667 0.00 0.00 38.63 4.24
5311 5970 3.824443 TGCTACTTCTGTACAGCAGTGTA 59.176 43.478 30.68 19.48 45.23 2.90
5330 5989 5.821995 AGTGTACTACTAGCTTAGTGTAGGC 59.178 44.000 8.13 6.91 39.81 3.93
5364 6023 9.617975 GTGAATGGAATTTTTGTTTTTGTTCAA 57.382 25.926 0.00 0.00 36.07 2.69
5416 6077 6.817765 TTCTCTGTTCATTGGTGGTATTTC 57.182 37.500 0.00 0.00 0.00 2.17
5429 6090 3.673809 GTGGTATTTCTGTGTCGTCTGAC 59.326 47.826 0.00 0.00 45.71 3.51
5499 6174 3.318275 TCAGGATATCGAGGTTTCTTCCG 59.682 47.826 0.00 0.00 0.00 4.30
5511 6186 3.004944 GGTTTCTTCCGTTAAACATGGCA 59.995 43.478 0.00 0.00 37.33 4.92
5512 6187 4.321675 GGTTTCTTCCGTTAAACATGGCAT 60.322 41.667 0.00 0.00 37.33 4.40
5513 6188 4.433186 TTCTTCCGTTAAACATGGCATG 57.567 40.909 25.31 25.31 0.00 4.06
5514 6189 2.752354 TCTTCCGTTAAACATGGCATGG 59.248 45.455 29.49 11.59 33.60 3.66
5515 6190 0.814457 TCCGTTAAACATGGCATGGC 59.186 50.000 29.49 13.29 33.60 4.40
5532 6207 4.994756 CCAGCCCCCGCCTTTGTT 62.995 66.667 0.00 0.00 34.57 2.83
5533 6208 2.917227 CAGCCCCCGCCTTTGTTT 60.917 61.111 0.00 0.00 34.57 2.83
5534 6209 2.123033 AGCCCCCGCCTTTGTTTT 60.123 55.556 0.00 0.00 34.57 2.43
5535 6210 1.764454 AGCCCCCGCCTTTGTTTTT 60.764 52.632 0.00 0.00 34.57 1.94
5564 6239 3.161450 GCCAGCCCCCGTCTGATA 61.161 66.667 0.00 0.00 33.54 2.15
5566 6241 2.063979 CCAGCCCCCGTCTGATACA 61.064 63.158 0.00 0.00 33.54 2.29
5627 6302 4.006319 GGCTGCTTAGGCTGAATATAAGG 58.994 47.826 7.94 0.00 39.31 2.69
5637 6312 4.010349 GCTGAATATAAGGTACATGGGCC 58.990 47.826 0.00 0.00 0.00 5.80
5641 6316 0.763035 ATAAGGTACATGGGCCCGTC 59.237 55.000 15.72 2.43 0.00 4.79
5646 6321 2.063979 TACATGGGCCCGTCCTCTG 61.064 63.158 15.72 4.91 34.39 3.35
5686 6371 4.115199 CCCAGCTAGCCACCCACC 62.115 72.222 12.13 0.00 0.00 4.61
5687 6372 4.115199 CCAGCTAGCCACCCACCC 62.115 72.222 12.13 0.00 0.00 4.61
5688 6373 3.329889 CAGCTAGCCACCCACCCA 61.330 66.667 12.13 0.00 0.00 4.51
5689 6374 3.330720 AGCTAGCCACCCACCCAC 61.331 66.667 12.13 0.00 0.00 4.61
5690 6375 4.426313 GCTAGCCACCCACCCACC 62.426 72.222 2.29 0.00 0.00 4.61
5691 6376 3.728373 CTAGCCACCCACCCACCC 61.728 72.222 0.00 0.00 0.00 4.61
5698 6383 4.671590 CCCACCCACCCGTTTCCC 62.672 72.222 0.00 0.00 0.00 3.97
5701 6386 1.901464 CACCCACCCGTTTCCCTTG 60.901 63.158 0.00 0.00 0.00 3.61
6024 6734 2.365105 TTCTCCCCCGCCCTACAG 60.365 66.667 0.00 0.00 0.00 2.74
6026 6736 4.475444 CTCCCCCGCCCTACAGGA 62.475 72.222 0.00 0.00 38.24 3.86
6240 6950 3.668821 TCTCACATCCCATTCCATACCT 58.331 45.455 0.00 0.00 0.00 3.08
6241 6951 4.826616 TCTCACATCCCATTCCATACCTA 58.173 43.478 0.00 0.00 0.00 3.08
6242 6952 4.840680 TCTCACATCCCATTCCATACCTAG 59.159 45.833 0.00 0.00 0.00 3.02
6245 6955 4.532126 CACATCCCATTCCATACCTAGCTA 59.468 45.833 0.00 0.00 0.00 3.32
6246 6956 4.532521 ACATCCCATTCCATACCTAGCTAC 59.467 45.833 0.00 0.00 0.00 3.58
6247 6957 4.487282 TCCCATTCCATACCTAGCTACT 57.513 45.455 0.00 0.00 0.00 2.57
6248 6958 4.827789 TCCCATTCCATACCTAGCTACTT 58.172 43.478 0.00 0.00 0.00 2.24
6249 6959 4.838986 TCCCATTCCATACCTAGCTACTTC 59.161 45.833 0.00 0.00 0.00 3.01
6250 6960 4.841246 CCCATTCCATACCTAGCTACTTCT 59.159 45.833 0.00 0.00 0.00 2.85
6253 6963 6.071616 CCATTCCATACCTAGCTACTTCTCTC 60.072 46.154 0.00 0.00 0.00 3.20
6254 6964 5.915744 TCCATACCTAGCTACTTCTCTCT 57.084 43.478 0.00 0.00 0.00 3.10
6255 6965 5.626142 TCCATACCTAGCTACTTCTCTCTG 58.374 45.833 0.00 0.00 0.00 3.35
6256 6966 4.217550 CCATACCTAGCTACTTCTCTCTGC 59.782 50.000 0.00 0.00 0.00 4.26
6257 6967 2.661718 ACCTAGCTACTTCTCTCTGCC 58.338 52.381 0.00 0.00 0.00 4.85
6258 6968 2.243736 ACCTAGCTACTTCTCTCTGCCT 59.756 50.000 0.00 0.00 0.00 4.75
6259 6969 2.622942 CCTAGCTACTTCTCTCTGCCTG 59.377 54.545 0.00 0.00 0.00 4.85
6260 6970 0.823460 AGCTACTTCTCTCTGCCTGC 59.177 55.000 0.00 0.00 0.00 4.85
6261 6971 0.179086 GCTACTTCTCTCTGCCTGCC 60.179 60.000 0.00 0.00 0.00 4.85
6262 6972 1.484038 CTACTTCTCTCTGCCTGCCT 58.516 55.000 0.00 0.00 0.00 4.75
6263 6973 1.136695 CTACTTCTCTCTGCCTGCCTG 59.863 57.143 0.00 0.00 0.00 4.85
6264 6974 1.449956 CTTCTCTCTGCCTGCCTGC 60.450 63.158 0.00 0.00 0.00 4.85
6343 7053 1.588861 GCGATGGTTCTTCTCGTTAGC 59.411 52.381 0.00 0.00 34.96 3.09
6372 7082 1.359848 TTCGCCGAGAAAGCTTGATC 58.640 50.000 0.00 0.00 35.61 2.92
6374 7084 0.802222 CGCCGAGAAAGCTTGATCGA 60.802 55.000 26.51 0.00 37.35 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 1.512926 CAGGGAAGTGAAGTTGTCCG 58.487 55.000 0.00 0.00 0.00 4.79
229 230 4.876107 ACAAATACATGAAAGCGGTCCTAG 59.124 41.667 0.00 0.00 0.00 3.02
266 267 4.693566 ACACGACGGATTTCATGTAAACAT 59.306 37.500 0.00 0.00 36.96 2.71
284 285 5.523188 ACGGCCGAATTTTATATAAACACGA 59.477 36.000 35.90 5.15 0.00 4.35
323 324 8.684386 TCACATTAATTCAAACTAACTGGACA 57.316 30.769 0.00 0.00 0.00 4.02
343 344 8.988934 CAACACTAGCCGTATATATTTTCACAT 58.011 33.333 0.00 0.00 0.00 3.21
357 358 4.402793 AGATAGTCATTCAACACTAGCCGT 59.597 41.667 0.00 0.00 32.87 5.68
365 366 4.718940 TGCGAGAGATAGTCATTCAACA 57.281 40.909 0.00 0.00 0.00 3.33
377 378 1.736586 GGACACGGATGCGAGAGAT 59.263 57.895 15.49 0.00 0.00 2.75
404 405 0.108329 ATCCGGTCATGAACACGGAC 60.108 55.000 28.74 4.98 46.47 4.79
408 409 1.086696 CCACATCCGGTCATGAACAC 58.913 55.000 12.13 0.00 0.00 3.32
442 443 1.521457 GCCATCTCCGATCGCAACA 60.521 57.895 10.32 0.00 0.00 3.33
465 466 5.163395 GGGTAAAAATTGGGTTGTCTGTCAA 60.163 40.000 0.00 0.00 0.00 3.18
467 468 4.262292 GGGGTAAAAATTGGGTTGTCTGTC 60.262 45.833 0.00 0.00 0.00 3.51
511 512 1.531365 TGCTTGGTTGCCCAGGAAG 60.531 57.895 0.00 0.00 43.15 3.46
512 513 1.832167 GTGCTTGGTTGCCCAGGAA 60.832 57.895 0.00 0.00 43.15 3.36
513 514 2.203480 GTGCTTGGTTGCCCAGGA 60.203 61.111 0.00 0.00 43.15 3.86
514 515 3.673484 CGTGCTTGGTTGCCCAGG 61.673 66.667 0.00 0.00 43.15 4.45
515 516 4.347453 GCGTGCTTGGTTGCCCAG 62.347 66.667 0.00 0.00 43.15 4.45
516 517 4.892965 AGCGTGCTTGGTTGCCCA 62.893 61.111 0.00 0.00 39.65 5.36
517 518 4.347453 CAGCGTGCTTGGTTGCCC 62.347 66.667 0.00 0.00 0.00 5.36
518 519 4.347453 CCAGCGTGCTTGGTTGCC 62.347 66.667 0.00 0.00 0.00 4.52
519 520 3.259425 CTCCAGCGTGCTTGGTTGC 62.259 63.158 0.00 0.00 0.00 4.17
520 521 2.620112 CCTCCAGCGTGCTTGGTTG 61.620 63.158 0.00 0.00 0.00 3.77
521 522 2.281761 CCTCCAGCGTGCTTGGTT 60.282 61.111 0.00 0.00 0.00 3.67
534 548 0.393132 GCTACCTGGAAGTTGCCTCC 60.393 60.000 0.00 0.00 33.17 4.30
556 570 0.375803 ACCGATTTGTTTATCCGCGC 59.624 50.000 0.00 0.00 0.00 6.86
605 619 1.333636 TTGGTTGCTGGGTTGGGTTG 61.334 55.000 0.00 0.00 0.00 3.77
606 620 0.618968 TTTGGTTGCTGGGTTGGGTT 60.619 50.000 0.00 0.00 0.00 4.11
607 621 1.002274 TTTGGTTGCTGGGTTGGGT 59.998 52.632 0.00 0.00 0.00 4.51
608 622 1.333636 TGTTTGGTTGCTGGGTTGGG 61.334 55.000 0.00 0.00 0.00 4.12
609 623 0.539051 TTGTTTGGTTGCTGGGTTGG 59.461 50.000 0.00 0.00 0.00 3.77
621 635 3.164268 TCCAGGGTGATCAATTGTTTGG 58.836 45.455 5.13 1.90 33.44 3.28
716 737 2.485038 TGTGCGAACGTGATCTACAGTA 59.515 45.455 0.00 0.00 0.00 2.74
717 738 1.268625 TGTGCGAACGTGATCTACAGT 59.731 47.619 0.00 0.00 0.00 3.55
718 739 1.649171 GTGTGCGAACGTGATCTACAG 59.351 52.381 0.00 0.00 0.00 2.74
719 740 1.268625 AGTGTGCGAACGTGATCTACA 59.731 47.619 0.00 0.00 0.00 2.74
720 741 1.912110 GAGTGTGCGAACGTGATCTAC 59.088 52.381 0.00 0.00 0.00 2.59
731 752 2.202810 TTGCGTGTGAGTGTGCGA 60.203 55.556 0.00 0.00 0.00 5.10
762 783 2.478709 GGATTCCCGAGATCGATCGATG 60.479 54.545 33.86 19.46 45.56 3.84
802 831 1.679944 GCTACTGGCTGCTTGGATTGA 60.680 52.381 0.00 0.00 38.06 2.57
805 834 1.225704 GGCTACTGGCTGCTTGGAT 59.774 57.895 0.00 0.00 41.46 3.41
806 835 2.189191 CTGGCTACTGGCTGCTTGGA 62.189 60.000 0.00 0.00 41.46 3.53
807 836 1.748122 CTGGCTACTGGCTGCTTGG 60.748 63.158 0.00 0.00 41.46 3.61
808 837 3.900855 CTGGCTACTGGCTGCTTG 58.099 61.111 0.00 0.00 41.46 4.01
812 841 1.980784 ATCTGGCTGGCTACTGGCTG 61.981 60.000 2.00 0.00 40.94 4.85
813 842 1.692042 ATCTGGCTGGCTACTGGCT 60.692 57.895 2.00 0.00 40.94 4.75
815 844 1.525535 GCATCTGGCTGGCTACTGG 60.526 63.158 2.00 0.00 40.25 4.00
816 845 4.137879 GCATCTGGCTGGCTACTG 57.862 61.111 2.00 0.00 40.25 2.74
838 875 2.017049 GCTAATTATATGGCCAGCGGG 58.983 52.381 13.05 0.00 37.18 6.13
845 882 4.335416 TGGGAGCTTGCTAATTATATGGC 58.665 43.478 0.00 0.00 0.00 4.40
846 883 6.094603 GTGATGGGAGCTTGCTAATTATATGG 59.905 42.308 0.00 0.00 0.00 2.74
847 884 6.883217 AGTGATGGGAGCTTGCTAATTATATG 59.117 38.462 0.00 0.00 0.00 1.78
848 885 6.883217 CAGTGATGGGAGCTTGCTAATTATAT 59.117 38.462 0.00 0.00 0.00 0.86
849 886 6.183361 ACAGTGATGGGAGCTTGCTAATTATA 60.183 38.462 0.00 0.00 0.00 0.98
850 887 5.068636 CAGTGATGGGAGCTTGCTAATTAT 58.931 41.667 0.00 0.00 0.00 1.28
851 888 4.080356 ACAGTGATGGGAGCTTGCTAATTA 60.080 41.667 0.00 0.00 0.00 1.40
852 889 3.285484 CAGTGATGGGAGCTTGCTAATT 58.715 45.455 0.00 0.00 0.00 1.40
858 895 1.278985 TGGTACAGTGATGGGAGCTTG 59.721 52.381 0.00 0.00 0.00 4.01
880 917 0.597637 GATGATGTGGGACGCTACCG 60.598 60.000 0.00 0.00 40.97 4.02
883 920 0.104855 GCTGATGATGTGGGACGCTA 59.895 55.000 0.00 0.00 40.97 4.26
886 923 1.091771 GTGGCTGATGATGTGGGACG 61.092 60.000 0.00 0.00 0.00 4.79
889 926 1.064906 AGAAGTGGCTGATGATGTGGG 60.065 52.381 0.00 0.00 0.00 4.61
940 977 2.507992 CGCTCACTTCCGCCTCTG 60.508 66.667 0.00 0.00 0.00 3.35
946 983 0.966920 ATATACCCCGCTCACTTCCG 59.033 55.000 0.00 0.00 0.00 4.30
953 990 1.215647 CGGCTGATATACCCCGCTC 59.784 63.158 0.00 0.00 33.77 5.03
1057 1489 5.107375 CGATGAGGCAAAGAAACCATTTTTG 60.107 40.000 0.00 0.00 35.47 2.44
1105 1538 3.124636 CGGACGGAACTGGTAAGAAAATG 59.875 47.826 0.00 0.00 0.00 2.32
1116 1549 2.664436 GGCGAAACGGACGGAACTG 61.664 63.158 0.00 0.00 0.00 3.16
1118 1551 3.770424 CGGCGAAACGGACGGAAC 61.770 66.667 0.00 0.00 0.00 3.62
1174 1615 1.068333 CAACCAACCAATCGAAGCCTG 60.068 52.381 0.00 0.00 0.00 4.85
1193 1634 1.596934 GGTCAAGCCGAGATCACCA 59.403 57.895 0.00 0.00 0.00 4.17
1194 1635 4.522971 GGTCAAGCCGAGATCACC 57.477 61.111 0.00 0.00 0.00 4.02
1220 1661 0.535102 CCCGCCCTTTATACTGGCTG 60.535 60.000 0.00 0.00 43.12 4.85
1221 1662 1.705997 CCCCGCCCTTTATACTGGCT 61.706 60.000 0.00 0.00 43.12 4.75
1222 1663 1.228154 CCCCGCCCTTTATACTGGC 60.228 63.158 0.00 0.00 41.85 4.85
1223 1664 0.108019 GACCCCGCCCTTTATACTGG 59.892 60.000 0.00 0.00 0.00 4.00
1224 1665 0.834612 TGACCCCGCCCTTTATACTG 59.165 55.000 0.00 0.00 0.00 2.74
1225 1666 0.835276 GTGACCCCGCCCTTTATACT 59.165 55.000 0.00 0.00 0.00 2.12
1226 1667 0.179037 GGTGACCCCGCCCTTTATAC 60.179 60.000 0.00 0.00 36.97 1.47
1228 1669 3.004090 GGTGACCCCGCCCTTTAT 58.996 61.111 0.00 0.00 36.97 1.40
1241 1682 0.033991 CTCTCTTCCCTCTCCGGTGA 60.034 60.000 6.00 6.00 0.00 4.02
1243 1684 1.308326 CCTCTCTTCCCTCTCCGGT 59.692 63.158 0.00 0.00 0.00 5.28
1254 1695 1.076339 CGCCTCCTCTCCCTCTCTT 60.076 63.158 0.00 0.00 0.00 2.85
1296 1742 1.370437 CGGGCTCAGGATCTCCATG 59.630 63.158 0.00 0.00 38.89 3.66
1335 1781 1.135460 CCGTAGACGAACTGGTTCCTC 60.135 57.143 3.07 6.22 43.02 3.71
1546 1998 0.339510 AGGGTTGGGATTGGGATTGG 59.660 55.000 0.00 0.00 0.00 3.16
1547 1999 2.252535 AAGGGTTGGGATTGGGATTG 57.747 50.000 0.00 0.00 0.00 2.67
1548 2000 2.561984 GGAAAGGGTTGGGATTGGGATT 60.562 50.000 0.00 0.00 0.00 3.01
1549 2001 1.008327 GGAAAGGGTTGGGATTGGGAT 59.992 52.381 0.00 0.00 0.00 3.85
1550 2002 0.411848 GGAAAGGGTTGGGATTGGGA 59.588 55.000 0.00 0.00 0.00 4.37
1553 2005 2.325661 AAGGGAAAGGGTTGGGATTG 57.674 50.000 0.00 0.00 0.00 2.67
1554 2006 2.494627 GGAAAGGGAAAGGGTTGGGATT 60.495 50.000 0.00 0.00 0.00 3.01
1555 2007 1.078823 GGAAAGGGAAAGGGTTGGGAT 59.921 52.381 0.00 0.00 0.00 3.85
1556 2008 0.485543 GGAAAGGGAAAGGGTTGGGA 59.514 55.000 0.00 0.00 0.00 4.37
1561 2013 3.576861 CAAGAAAGGAAAGGGAAAGGGT 58.423 45.455 0.00 0.00 0.00 4.34
1572 2031 3.738982 TCTCATTCGTGCAAGAAAGGAA 58.261 40.909 18.90 4.29 33.43 3.36
1575 2034 4.033817 GGAGATCTCATTCGTGCAAGAAAG 59.966 45.833 23.85 14.63 33.43 2.62
1624 2101 1.884926 CTGAGCCGCCGGAATCTTC 60.885 63.158 7.68 0.00 0.00 2.87
1755 2232 1.882623 GGGAAGAGCAGGTTTTGACAG 59.117 52.381 0.00 0.00 0.00 3.51
1765 2242 5.407407 TCTGTAGTAAAAGGGAAGAGCAG 57.593 43.478 0.00 0.00 0.00 4.24
1826 2303 7.418337 TTGGTCAGCTAATTGATCTGTACTA 57.582 36.000 0.00 0.00 0.00 1.82
1856 2334 2.493278 CACCTGTGGCCAAAGGAAATAG 59.507 50.000 43.31 23.92 37.01 1.73
1931 2427 0.184451 CCCCATGATCCCTGACCAAG 59.816 60.000 0.00 0.00 0.00 3.61
2021 2517 2.744202 GGCAAGAAGATCATGTCGTGTT 59.256 45.455 0.00 0.00 0.00 3.32
2051 2555 4.742438 TCAACAGTACGCAATTCCTTTC 57.258 40.909 0.00 0.00 0.00 2.62
2052 2556 5.163602 TGTTTCAACAGTACGCAATTCCTTT 60.164 36.000 0.00 0.00 34.30 3.11
2062 2566 7.117241 AGTGATAACATGTTTCAACAGTACG 57.883 36.000 17.78 0.00 43.04 3.67
2070 2574 6.539173 ACCCACTTAGTGATAACATGTTTCA 58.461 36.000 17.78 16.14 35.23 2.69
2142 2661 1.216710 GTCAAGACTCCGAGGCAGG 59.783 63.158 3.49 0.00 0.00 4.85
2143 2662 1.216710 GGTCAAGACTCCGAGGCAG 59.783 63.158 3.49 0.00 0.00 4.85
2146 2665 0.898320 ACATGGTCAAGACTCCGAGG 59.102 55.000 0.00 0.00 0.00 4.63
2150 2669 3.409026 ACTGAACATGGTCAAGACTCC 57.591 47.619 15.67 0.00 0.00 3.85
2159 2678 6.239289 CCTTTTCATGGTTAACTGAACATGGT 60.239 38.462 17.25 0.00 40.09 3.55
2183 2702 4.451435 GCCTATTCTAGTTTTATCGGTGCC 59.549 45.833 0.00 0.00 0.00 5.01
2188 2707 5.900339 TTGCGCCTATTCTAGTTTTATCG 57.100 39.130 4.18 0.00 0.00 2.92
2205 2724 2.364311 GGCGTGTGTTGATTTGCGC 61.364 57.895 0.00 0.00 43.46 6.09
2206 2725 0.515127 TAGGCGTGTGTTGATTTGCG 59.485 50.000 0.00 0.00 0.00 4.85
2207 2726 1.535462 ACTAGGCGTGTGTTGATTTGC 59.465 47.619 0.00 0.00 0.00 3.68
2208 2727 3.896648 AACTAGGCGTGTGTTGATTTG 57.103 42.857 0.00 0.00 0.00 2.32
2211 2730 4.243270 GACTTAACTAGGCGTGTGTTGAT 58.757 43.478 9.01 0.00 0.00 2.57
2212 2731 3.553508 GGACTTAACTAGGCGTGTGTTGA 60.554 47.826 9.01 2.19 29.87 3.18
2213 2732 2.735134 GGACTTAACTAGGCGTGTGTTG 59.265 50.000 9.01 0.00 29.87 3.33
2215 2734 2.230750 GAGGACTTAACTAGGCGTGTGT 59.769 50.000 0.00 0.00 29.87 3.72
2216 2735 2.492484 AGAGGACTTAACTAGGCGTGTG 59.508 50.000 0.00 0.00 29.87 3.82
2217 2736 2.754002 GAGAGGACTTAACTAGGCGTGT 59.246 50.000 0.00 0.00 29.87 4.49
2218 2737 2.753452 TGAGAGGACTTAACTAGGCGTG 59.247 50.000 0.00 0.00 29.87 5.34
2219 2738 3.083122 TGAGAGGACTTAACTAGGCGT 57.917 47.619 0.00 0.00 29.87 5.68
2241 2778 9.938280 TGTTTGCAAAACAGAGTAGTATAGTAT 57.062 29.630 14.67 0.00 0.00 2.12
2242 2779 9.199982 GTGTTTGCAAAACAGAGTAGTATAGTA 57.800 33.333 14.67 0.00 0.00 1.82
2243 2780 7.713507 TGTGTTTGCAAAACAGAGTAGTATAGT 59.286 33.333 14.67 0.00 0.00 2.12
2244 2781 8.083462 TGTGTTTGCAAAACAGAGTAGTATAG 57.917 34.615 14.67 0.00 0.00 1.31
2245 2782 8.615878 ATGTGTTTGCAAAACAGAGTAGTATA 57.384 30.769 14.67 0.00 0.00 1.47
2286 2823 5.587844 ACAATGAAGCATCTTACATCTGACC 59.412 40.000 0.00 0.00 0.00 4.02
2289 2826 6.965500 GTGAACAATGAAGCATCTTACATCTG 59.035 38.462 0.00 0.00 0.00 2.90
2381 2955 3.206150 GGATAATGGTCGCTGTTCACAT 58.794 45.455 0.00 0.00 0.00 3.21
2382 2956 2.027653 TGGATAATGGTCGCTGTTCACA 60.028 45.455 0.00 0.00 0.00 3.58
2384 2958 2.236146 ACTGGATAATGGTCGCTGTTCA 59.764 45.455 0.00 0.00 0.00 3.18
2391 2965 2.868583 CTCAGCAACTGGATAATGGTCG 59.131 50.000 0.00 0.00 31.51 4.79
2452 3029 7.770897 GGATAGAGAGCATTGAAGTTAGGAAAA 59.229 37.037 0.00 0.00 0.00 2.29
2481 3058 6.582672 GCCTTTAACTTGAAGCAACTACATTC 59.417 38.462 0.00 0.00 0.00 2.67
2486 3063 4.518970 CCTGCCTTTAACTTGAAGCAACTA 59.481 41.667 0.00 0.00 0.00 2.24
2540 3117 2.420628 TTTCACAAAATGCTGGAGCG 57.579 45.000 0.00 0.00 45.83 5.03
2642 3219 8.718158 TCTTTCTGGTCATCATAGTATCATCT 57.282 34.615 0.00 0.00 0.00 2.90
2650 3227 5.867903 AGTCCTCTTTCTGGTCATCATAG 57.132 43.478 0.00 0.00 0.00 2.23
2694 3271 2.665185 AAGCACGGGTTCAGCGTC 60.665 61.111 0.00 0.00 0.00 5.19
2725 3302 5.104941 TGGTTCACTCGACCATTATCTGATT 60.105 40.000 0.00 0.00 42.06 2.57
2776 3353 8.534333 TGATATTCTCATATTGTAGAAACGGC 57.466 34.615 0.00 0.00 35.47 5.68
3029 3607 4.327680 GCTCAAGAAAAGCTTCCTTCCTA 58.672 43.478 0.00 0.00 36.80 2.94
3058 3636 4.419522 TTTGACTCTATTTCTTTGCGCC 57.580 40.909 4.18 0.00 0.00 6.53
3161 3739 4.520492 AGGAGTTGCACAGTAAAAGGAATG 59.480 41.667 0.00 0.00 0.00 2.67
3198 3776 6.472016 TGCATAGTTTCCTTCACAGTATTCA 58.528 36.000 0.00 0.00 0.00 2.57
3327 3907 2.543578 CTGCTTTCTTGCGGCTACA 58.456 52.632 0.00 0.00 35.36 2.74
3334 3914 3.128938 AGATCTTCATGCTGCTTTCTTGC 59.871 43.478 0.00 0.00 0.00 4.01
3336 3916 3.695060 CCAGATCTTCATGCTGCTTTCTT 59.305 43.478 0.00 0.00 0.00 2.52
3381 3961 3.834813 TCATAGAAGAGTCCAACACAGCT 59.165 43.478 0.00 0.00 0.00 4.24
3517 4097 8.762645 TCTATCTTCTTTCTTATGAGCCTTTGA 58.237 33.333 0.00 0.00 0.00 2.69
3635 4215 7.065085 GCACATCTAACAGTGTCAATTGTCTAT 59.935 37.037 5.13 0.00 38.02 1.98
3737 4317 6.892485 TGAATCATCACACTCCTGTTCATAT 58.108 36.000 0.00 0.00 0.00 1.78
3858 4442 9.754382 GCCATGTTCAATAATTGATTAATCACT 57.246 29.630 17.76 10.03 39.84 3.41
4050 4646 4.929211 TGGTCTGTTTCAGTTCATATGACG 59.071 41.667 4.48 0.00 32.61 4.35
4098 4694 7.336931 GCTTGATTATGTTCCAAGGAGAAAGTA 59.663 37.037 0.00 0.00 38.11 2.24
4141 4737 4.868734 AGTAGACCAAACGTATTGCTTAGC 59.131 41.667 0.00 0.00 0.00 3.09
4190 4786 8.546244 CAACTCACAAGCAGAACATATATACAG 58.454 37.037 0.00 0.00 0.00 2.74
4271 4883 8.110860 ACCTTGTTTATACAACCATTGAAGAG 57.889 34.615 0.00 0.00 39.29 2.85
4292 4905 9.734984 AATAATAGTTAGTGCTACACAAACCTT 57.265 29.630 0.00 0.00 36.74 3.50
4473 5096 1.891919 GGCACTGTTGAGTTCGCCA 60.892 57.895 0.00 0.00 39.86 5.69
4494 5117 0.894835 GGATTTTCCATGGCAACGGT 59.105 50.000 6.96 0.00 36.28 4.83
4522 5145 0.526524 CTCGAGATCTCCGCCACAAC 60.527 60.000 17.13 0.00 0.00 3.32
4575 5198 0.323725 GGCCACCATGAACCATCACT 60.324 55.000 0.00 0.00 38.69 3.41
4576 5199 0.323725 AGGCCACCATGAACCATCAC 60.324 55.000 5.01 0.00 38.69 3.06
4689 5312 2.284190 GCCAGCAGTCTAGAATCCAAC 58.716 52.381 0.00 0.00 0.00 3.77
4699 5322 1.905215 AGACTTATGTGCCAGCAGTCT 59.095 47.619 5.84 5.84 0.00 3.24
4713 5336 7.496346 ACCAAAGGAGTTGATATCAGACTTA 57.504 36.000 16.56 0.00 39.87 2.24
4734 5357 1.484653 AGCTGCATTATCACGGTACCA 59.515 47.619 13.54 0.00 0.00 3.25
4747 5370 5.160607 TGTTTACCAGTTAGTAGCTGCAT 57.839 39.130 8.42 2.06 32.93 3.96
4884 5507 2.437716 TCGAGCCCAAATTCCGCC 60.438 61.111 0.00 0.00 0.00 6.13
4890 5513 0.813184 CAATGCACTCGAGCCCAAAT 59.187 50.000 13.61 0.89 0.00 2.32
4907 5530 1.063942 TCAGCTCCGGTCTATCTCCAA 60.064 52.381 0.00 0.00 0.00 3.53
4908 5531 0.551396 TCAGCTCCGGTCTATCTCCA 59.449 55.000 0.00 0.00 0.00 3.86
4979 5602 2.299297 CACAGGAAGAAGGACGGTACTT 59.701 50.000 5.02 5.02 0.00 2.24
5064 5687 2.615618 CACTCACGAATAGCGCGC 59.384 61.111 26.66 26.66 46.04 6.86
5070 5693 2.927028 TCCTCGATCCACTCACGAATA 58.073 47.619 0.00 0.00 35.70 1.75
5073 5696 1.025041 CATCCTCGATCCACTCACGA 58.975 55.000 0.00 0.00 34.90 4.35
5076 5699 1.402896 GGCCATCCTCGATCCACTCA 61.403 60.000 0.00 0.00 0.00 3.41
5129 5752 3.566210 CGTGGTTGGGGGTGAGGT 61.566 66.667 0.00 0.00 0.00 3.85
5187 5810 7.175104 TCATCATCATCATCATCATTCACCAT 58.825 34.615 0.00 0.00 0.00 3.55
5269 5928 4.081476 AGCAGAAGCATGTATGTACACAGA 60.081 41.667 0.00 0.00 45.49 3.41
5311 5970 4.208746 CTGGCCTACACTAAGCTAGTAGT 58.791 47.826 3.32 4.13 37.23 2.73
5314 5973 3.103080 ACTGGCCTACACTAAGCTAGT 57.897 47.619 3.32 0.00 42.65 2.57
5317 5976 0.250513 GCACTGGCCTACACTAAGCT 59.749 55.000 3.32 0.00 0.00 3.74
5330 5989 3.947910 AAATTCCATTCACTGCACTGG 57.052 42.857 0.00 0.00 0.00 4.00
5374 6035 9.214957 ACAGAGAAAAATAATGATTCGTACACA 57.785 29.630 0.00 0.00 0.00 3.72
5416 6077 7.582435 ACAAAATAATAGTCAGACGACACAG 57.418 36.000 0.00 0.00 45.23 3.66
5487 6162 4.615223 GCCATGTTTAACGGAAGAAACCTC 60.615 45.833 0.00 0.00 35.17 3.85
5515 6190 4.994756 AACAAAGGCGGGGGCTGG 62.995 66.667 0.00 0.00 38.81 4.85
5516 6191 2.038814 AAAAACAAAGGCGGGGGCTG 62.039 55.000 0.00 0.00 38.81 4.85
5517 6192 1.764454 AAAAACAAAGGCGGGGGCT 60.764 52.632 0.00 0.00 41.24 5.19
5518 6193 2.825982 AAAAACAAAGGCGGGGGC 59.174 55.556 0.00 0.00 0.00 5.80
5547 6222 3.161450 TATCAGACGGGGGCTGGC 61.161 66.667 0.00 0.00 34.20 4.85
5548 6223 2.032860 CTGTATCAGACGGGGGCTGG 62.033 65.000 0.00 0.00 32.44 4.85
5549 6224 1.443407 CTGTATCAGACGGGGGCTG 59.557 63.158 0.00 0.00 32.44 4.85
5550 6225 3.956377 CTGTATCAGACGGGGGCT 58.044 61.111 0.00 0.00 32.44 5.19
5555 6230 1.409427 GTTCTCCCCTGTATCAGACGG 59.591 57.143 0.00 0.00 32.44 4.79
5556 6231 1.409427 GGTTCTCCCCTGTATCAGACG 59.591 57.143 0.00 0.00 32.44 4.18
5586 6261 4.339247 CAGCCCAATACAATACCCAGAAAG 59.661 45.833 0.00 0.00 0.00 2.62
5588 6263 3.897239 CAGCCCAATACAATACCCAGAA 58.103 45.455 0.00 0.00 0.00 3.02
5589 6264 2.422803 GCAGCCCAATACAATACCCAGA 60.423 50.000 0.00 0.00 0.00 3.86
5590 6265 1.956477 GCAGCCCAATACAATACCCAG 59.044 52.381 0.00 0.00 0.00 4.45
5591 6266 1.568597 AGCAGCCCAATACAATACCCA 59.431 47.619 0.00 0.00 0.00 4.51
5592 6267 2.364972 AGCAGCCCAATACAATACCC 57.635 50.000 0.00 0.00 0.00 3.69
5596 6271 2.091665 AGCCTAAGCAGCCCAATACAAT 60.092 45.455 0.00 0.00 43.56 2.71
5627 6302 2.064581 AGAGGACGGGCCCATGTAC 61.065 63.158 24.92 13.83 37.37 2.90
5637 6312 2.740055 GTGCAGCACAGAGGACGG 60.740 66.667 21.22 0.00 34.08 4.79
5652 6327 1.971695 GGCTTTTGTCCTCCCGGTG 60.972 63.158 0.00 0.00 0.00 4.94
5684 6369 2.347691 GACAAGGGAAACGGGTGGGT 62.348 60.000 0.00 0.00 0.00 4.51
5686 6371 1.964373 CGACAAGGGAAACGGGTGG 60.964 63.158 0.00 0.00 0.00 4.61
5687 6372 0.533308 TTCGACAAGGGAAACGGGTG 60.533 55.000 0.00 0.00 0.00 4.61
5688 6373 0.399075 ATTCGACAAGGGAAACGGGT 59.601 50.000 0.00 0.00 0.00 5.28
5689 6374 1.530323 AATTCGACAAGGGAAACGGG 58.470 50.000 0.00 0.00 0.00 5.28
5690 6375 2.412325 CGAAATTCGACAAGGGAAACGG 60.412 50.000 10.18 0.00 43.74 4.44
5691 6376 2.477375 TCGAAATTCGACAAGGGAAACG 59.523 45.455 14.59 0.00 44.82 3.60
5733 6418 1.586564 GGATTGCCGTCTCGTCTCG 60.587 63.158 0.00 0.00 0.00 4.04
6007 6717 2.365105 CTGTAGGGCGGGGGAGAA 60.365 66.667 0.00 0.00 0.00 2.87
6202 6912 3.729716 GTGAGAAATGATAGCGTACCGAC 59.270 47.826 0.00 0.00 0.00 4.79
6223 6933 3.602608 AGCTAGGTATGGAATGGGATGT 58.397 45.455 0.00 0.00 0.00 3.06
6240 6950 2.028130 GCAGGCAGAGAGAAGTAGCTA 58.972 52.381 0.00 0.00 0.00 3.32
6241 6951 0.823460 GCAGGCAGAGAGAAGTAGCT 59.177 55.000 0.00 0.00 0.00 3.32
6242 6952 0.179086 GGCAGGCAGAGAGAAGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
6245 6955 1.981636 CAGGCAGGCAGAGAGAAGT 59.018 57.895 0.00 0.00 0.00 3.01
6246 6956 1.449956 GCAGGCAGGCAGAGAGAAG 60.450 63.158 0.00 0.00 0.00 2.85
6247 6957 2.667418 GCAGGCAGGCAGAGAGAA 59.333 61.111 0.00 0.00 0.00 2.87
6248 6958 3.397439 GGCAGGCAGGCAGAGAGA 61.397 66.667 0.00 0.00 43.51 3.10
6273 6983 0.250684 TGTTCCGATGAAGCAGGCAA 60.251 50.000 0.00 0.00 0.00 4.52
6343 7053 1.750351 TCTCGGCGAATTTACGATCG 58.250 50.000 14.88 14.88 41.81 3.69
6372 7082 1.399714 TATGCCTGGGTAGTGACTCG 58.600 55.000 0.00 0.00 0.00 4.18
6374 7084 3.780294 TCAAATATGCCTGGGTAGTGACT 59.220 43.478 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.