Multiple sequence alignment - TraesCS4A01G053900

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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 TraesCS4A01G053900 chr4A 100.000 4971 0 0 1 4971 45345690 45350660 0.000000e+00 9180.0
1 TraesCS4A01G053900 chr4D 93.304 3898 179 22 853 4686 419303716 419299837 0.000000e+00 5677.0
2 TraesCS4A01G053900 chr4D 94.019 418 25 0 4402 4819 419258020 419257603 7.020000e-178 634.0
3 TraesCS4A01G053900 chr4B 93.711 1924 85 14 1000 2913 517216197 517214300 0.000000e+00 2850.0
4 TraesCS4A01G053900 chr4B 89.015 1056 52 16 3397 4413 517213610 517212580 0.000000e+00 1249.0
5 TraesCS4A01G053900 chr4B 94.617 483 23 3 2915 3395 517214252 517213771 0.000000e+00 745.0
6 TraesCS4A01G053900 chr4B 93.514 185 11 1 4641 4824 517212049 517211865 1.760000e-69 274.0
7 TraesCS4A01G053900 chr4B 93.085 188 12 1 4419 4606 517212232 517212046 1.760000e-69 274.0
8 TraesCS4A01G053900 chr4B 94.375 160 7 2 4812 4971 657859936 657859779 1.380000e-60 244.0
9 TraesCS4A01G053900 chr6A 86.439 848 68 18 1 827 387149131 387148310 0.000000e+00 885.0
10 TraesCS4A01G053900 chr6A 92.500 160 11 1 4812 4971 425899695 425899853 1.390000e-55 228.0
11 TraesCS4A01G053900 chr3A 91.788 548 40 3 1 545 686792959 686793504 0.000000e+00 758.0
12 TraesCS4A01G053900 chr3A 84.324 185 19 3 650 824 686793845 686794029 6.620000e-39 172.0
13 TraesCS4A01G053900 chr6B 81.076 576 56 19 315 850 119906590 119906028 1.290000e-110 411.0
14 TraesCS4A01G053900 chr2A 94.479 163 8 1 4809 4971 719682481 719682642 2.970000e-62 250.0
15 TraesCS4A01G053900 chr2A 94.702 151 8 0 4821 4971 563223077 563222927 8.320000e-58 235.0
16 TraesCS4A01G053900 chr2A 78.000 200 23 15 4565 4748 553061945 553061751 6.810000e-19 106.0
17 TraesCS4A01G053900 chr1D 95.484 155 6 1 4817 4971 10600976 10600823 3.840000e-61 246.0
18 TraesCS4A01G053900 chr6D 95.364 151 7 0 4821 4971 153202254 153202404 1.790000e-59 241.0
19 TraesCS4A01G053900 chr6D 94.194 155 9 0 4817 4971 48674764 48674918 2.310000e-58 237.0
20 TraesCS4A01G053900 chr5D 95.302 149 7 0 4820 4968 93068556 93068704 2.310000e-58 237.0
21 TraesCS4A01G053900 chr5D 77.387 199 24 15 4566 4748 194790007 194789814 1.140000e-16 99.0
22 TraesCS4A01G053900 chr7D 93.631 157 8 2 4815 4971 156361632 156361786 2.990000e-57 233.0
23 TraesCS4A01G053900 chr3B 76.000 200 25 15 4566 4748 698968965 698969158 1.150000e-11 82.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G053900 chr4A 45345690 45350660 4970 False 9180.0 9180 100.0000 1 4971 1 chr4A.!!$F1 4970
1 TraesCS4A01G053900 chr4D 419299837 419303716 3879 True 5677.0 5677 93.3040 853 4686 1 chr4D.!!$R2 3833
2 TraesCS4A01G053900 chr4B 517211865 517216197 4332 True 1078.4 2850 92.7884 1000 4824 5 chr4B.!!$R2 3824
3 TraesCS4A01G053900 chr6A 387148310 387149131 821 True 885.0 885 86.4390 1 827 1 chr6A.!!$R1 826
4 TraesCS4A01G053900 chr3A 686792959 686794029 1070 False 465.0 758 88.0560 1 824 2 chr3A.!!$F1 823
5 TraesCS4A01G053900 chr6B 119906028 119906590 562 True 411.0 411 81.0760 315 850 1 chr6B.!!$R1 535

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
526 538 0.179073 GATGCATGTGCCGGAGTAGT 60.179 55.0 5.05 0.00 41.18 2.73 F
1264 1560 0.247460 TGCTCGACTCTGGTGATTGG 59.753 55.0 0.00 0.00 0.00 3.16 F
1522 1818 0.321564 CTGATGTCACCGGCAAGGAA 60.322 55.0 0.00 0.00 45.00 3.36 F
1763 2059 0.957888 GGAACTGCTGTCCAGAAGGC 60.958 60.0 7.21 0.00 44.64 4.35 F
2785 3081 0.385751 ACCGGCGTATGACTCATGAG 59.614 55.0 21.37 21.37 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2035 0.034059 CTGGACAGCAGTTCCTCGTT 59.966 55.000 0.00 0.0 0.00 3.85 R
2256 2552 0.039618 TTCACTTGGATCAAGCCCCC 59.960 55.000 7.48 0.0 44.43 5.40 R
2764 3060 1.335810 TCATGAGTCATACGCCGGTAC 59.664 52.381 5.03 0.0 0.00 3.34 R
3755 4270 1.445066 CTCTGCTGACGCGATGTGT 60.445 57.895 15.93 0.0 39.65 3.72 R
4451 5334 0.110486 TGGGCCAAACAAGTCTCCTC 59.890 55.000 2.13 0.0 0.00 3.71 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
200 202 8.757877 CAAAAAGGAGTGGGGAAATATGATAAA 58.242 33.333 0.00 0.00 0.00 1.40
226 228 3.003378 GGGTGCTGACAAACTACTTGAAC 59.997 47.826 0.00 0.00 38.50 3.18
229 231 4.332819 GTGCTGACAAACTACTTGAACTGT 59.667 41.667 0.00 0.00 38.50 3.55
239 241 4.654262 ACTACTTGAACTGTCTGGGAAAGA 59.346 41.667 0.00 0.00 0.00 2.52
246 248 2.373502 ACTGTCTGGGAAAGAAAGAGGG 59.626 50.000 0.00 0.00 42.31 4.30
301 306 2.272146 GAAGGGATCTGGCGGCAA 59.728 61.111 14.48 4.62 0.00 4.52
355 361 3.160748 GGCTGAGGAGGAGAGGGC 61.161 72.222 0.00 0.00 0.00 5.19
420 432 2.415608 CGGCGGCAGAAGACTAGGA 61.416 63.158 10.53 0.00 0.00 2.94
425 437 2.920524 CGGCAGAAGACTAGGACTAGA 58.079 52.381 13.00 0.00 36.97 2.43
468 480 1.758514 GGCGACAGAGGAGATGGGA 60.759 63.158 0.00 0.00 0.00 4.37
484 496 2.302587 GGGACAACCAAAGGGATGAA 57.697 50.000 0.00 0.00 39.20 2.57
502 514 2.715532 AAGAGAACGAGCTGCGGCAA 62.716 55.000 21.93 0.00 46.49 4.52
526 538 0.179073 GATGCATGTGCCGGAGTAGT 60.179 55.000 5.05 0.00 41.18 2.73
527 539 1.068588 GATGCATGTGCCGGAGTAGTA 59.931 52.381 5.05 0.00 41.18 1.82
528 540 0.459899 TGCATGTGCCGGAGTAGTAG 59.540 55.000 5.05 0.00 41.18 2.57
529 541 0.460311 GCATGTGCCGGAGTAGTAGT 59.540 55.000 5.05 0.00 34.31 2.73
530 542 1.679680 GCATGTGCCGGAGTAGTAGTA 59.320 52.381 5.05 0.00 34.31 1.82
531 543 2.287668 GCATGTGCCGGAGTAGTAGTAG 60.288 54.545 5.05 0.00 34.31 2.57
532 544 2.795231 TGTGCCGGAGTAGTAGTAGT 57.205 50.000 5.05 0.00 0.00 2.73
571 583 1.677966 CGACGAGGAGAGGTCCCAA 60.678 63.158 0.00 0.00 45.26 4.12
575 587 1.613630 GAGGAGAGGTCCCAAGGCA 60.614 63.158 0.00 0.00 45.26 4.75
579 591 3.637273 GAGGTCCCAAGGCACCGT 61.637 66.667 0.00 0.00 37.79 4.83
615 632 0.693049 GCCTCCTCTTTTCCAGGTCA 59.307 55.000 0.00 0.00 32.20 4.02
626 661 4.379243 CAGGTCAAGCGGCGGAGT 62.379 66.667 9.78 0.00 0.00 3.85
663 917 0.869730 GAAGCGTTACCTTTTGCGGA 59.130 50.000 0.00 0.00 0.00 5.54
675 929 2.302587 TTTGCGGAAGGGGAGATTTT 57.697 45.000 0.00 0.00 0.00 1.82
686 940 3.099141 GGGGAGATTTTCAGCCAAATCA 58.901 45.455 13.35 0.00 43.14 2.57
687 941 3.515104 GGGGAGATTTTCAGCCAAATCAA 59.485 43.478 13.35 0.00 43.14 2.57
755 1019 5.751509 CCTGTATTTATGTGATTTCCGACGA 59.248 40.000 0.00 0.00 0.00 4.20
776 1040 1.213537 GTTTCAGTGCGCATGCCAT 59.786 52.632 15.91 0.00 41.78 4.40
777 1041 1.074319 GTTTCAGTGCGCATGCCATG 61.074 55.000 15.91 8.27 41.78 3.66
824 1088 3.758554 ACCAAATCCAATTCAGAACCTCG 59.241 43.478 0.00 0.00 0.00 4.63
827 1091 5.278957 CCAAATCCAATTCAGAACCTCGTTT 60.279 40.000 0.00 0.00 0.00 3.60
828 1092 5.376854 AATCCAATTCAGAACCTCGTTTG 57.623 39.130 0.00 0.00 0.00 2.93
830 1094 4.456535 TCCAATTCAGAACCTCGTTTGAA 58.543 39.130 0.00 0.00 32.22 2.69
832 1096 5.534654 TCCAATTCAGAACCTCGTTTGAAAT 59.465 36.000 0.00 0.00 31.83 2.17
833 1097 5.630680 CCAATTCAGAACCTCGTTTGAAATG 59.369 40.000 0.00 0.00 31.83 2.32
834 1098 4.829064 TTCAGAACCTCGTTTGAAATGG 57.171 40.909 0.00 0.00 0.00 3.16
835 1099 4.079980 TCAGAACCTCGTTTGAAATGGA 57.920 40.909 0.00 0.00 0.00 3.41
836 1100 4.456535 TCAGAACCTCGTTTGAAATGGAA 58.543 39.130 0.00 0.00 0.00 3.53
850 1114 1.398692 ATGGAACCAAACGCAGTGTT 58.601 45.000 0.00 0.00 45.00 3.32
851 1115 2.039818 TGGAACCAAACGCAGTGTTA 57.960 45.000 0.00 0.00 45.00 2.41
852 1116 1.944024 TGGAACCAAACGCAGTGTTAG 59.056 47.619 0.00 0.00 45.00 2.34
853 1117 2.215196 GGAACCAAACGCAGTGTTAGA 58.785 47.619 0.00 0.00 45.00 2.10
854 1118 2.223377 GGAACCAAACGCAGTGTTAGAG 59.777 50.000 0.00 0.00 45.00 2.43
855 1119 2.902705 ACCAAACGCAGTGTTAGAGA 57.097 45.000 0.00 0.00 45.00 3.10
856 1120 3.188159 ACCAAACGCAGTGTTAGAGAA 57.812 42.857 0.00 0.00 45.00 2.87
862 1126 4.054780 ACGCAGTGTTAGAGAACTTCAA 57.945 40.909 0.00 0.00 42.51 2.69
867 1131 6.073548 CGCAGTGTTAGAGAACTTCAAATTCT 60.074 38.462 0.00 0.00 39.15 2.40
901 1165 7.281999 TGTTTGAAATGGAATCAAAAGAAACCC 59.718 33.333 3.51 0.00 45.43 4.11
910 1174 6.239092 GGAATCAAAAGAAACCCGAGGTAAAA 60.239 38.462 0.00 0.00 33.12 1.52
919 1183 5.970501 AACCCGAGGTAAAAGGAAGATAT 57.029 39.130 0.00 0.00 33.12 1.63
928 1192 7.450903 AGGTAAAAGGAAGATATATGTTCGGG 58.549 38.462 14.51 0.00 31.43 5.14
945 1209 2.362503 GGGGGCCCACTGTAAAGC 60.363 66.667 26.86 1.47 35.81 3.51
965 1229 4.425520 AGCGAGATAGAGAAACGGAAAAG 58.574 43.478 0.00 0.00 0.00 2.27
978 1242 1.340600 CGGAAAAGGGGATAAGGCACA 60.341 52.381 0.00 0.00 0.00 4.57
995 1259 4.012721 ACTCCCCCTTCTCCGCCT 62.013 66.667 0.00 0.00 0.00 5.52
1081 1355 3.801997 CCCTCCATTCCCGCAGCT 61.802 66.667 0.00 0.00 0.00 4.24
1118 1392 3.672397 CAGCTACGCGCATCGACG 61.672 66.667 5.73 0.00 42.61 5.12
1264 1560 0.247460 TGCTCGACTCTGGTGATTGG 59.753 55.000 0.00 0.00 0.00 3.16
1267 1563 2.886081 CTCGACTCTGGTGATTGGAAG 58.114 52.381 0.00 0.00 0.00 3.46
1522 1818 0.321564 CTGATGTCACCGGCAAGGAA 60.322 55.000 0.00 0.00 45.00 3.36
1729 2025 1.210478 GGATCAAGGCTGCACTTCCTA 59.790 52.381 0.50 0.00 31.24 2.94
1739 2035 3.360867 CTGCACTTCCTAGAAGAGAGGA 58.639 50.000 11.17 0.00 41.52 3.71
1748 2044 3.379057 CCTAGAAGAGAGGAACGAGGAAC 59.621 52.174 0.00 0.00 35.99 3.62
1763 2059 0.957888 GGAACTGCTGTCCAGAAGGC 60.958 60.000 7.21 0.00 44.64 4.35
1825 2121 6.405508 CCATAGAGCTGTTTGATTCAATGCTT 60.406 38.462 17.20 12.13 30.05 3.91
1831 2127 3.243334 TGTTTGATTCAATGCTTGCGTCA 60.243 39.130 0.00 0.00 0.00 4.35
1939 2235 2.041620 TGAGTTCATGAAGGGGAAAGGG 59.958 50.000 8.80 0.00 0.00 3.95
2146 2442 2.185310 AACTGTGGGGAAGGCTAGCG 62.185 60.000 9.00 0.00 0.00 4.26
2158 2454 1.205893 AGGCTAGCGGAGAACTCTTTG 59.794 52.381 9.00 0.00 0.00 2.77
2179 2475 4.894784 TGAGTGGAACCTTGATGACTTAC 58.105 43.478 0.00 0.00 37.80 2.34
2183 2479 4.567159 GTGGAACCTTGATGACTTACGATC 59.433 45.833 0.00 0.00 0.00 3.69
2469 2765 6.878317 TGTACCATCTTCTAACATCTTCAGG 58.122 40.000 0.00 0.00 0.00 3.86
2573 2869 7.235399 AGCTTTTCCAAGGAATTAAATCCAAGA 59.765 33.333 12.15 2.69 42.27 3.02
2578 2874 6.321181 TCCAAGGAATTAAATCCAAGAATCCG 59.679 38.462 12.15 0.00 42.27 4.18
2638 2934 4.191544 TGTCTTGTGAAAGACTTGGTCAG 58.808 43.478 16.99 0.00 47.00 3.51
2764 3060 2.603173 GCCAAAAGTCGCTCTGAAAGTG 60.603 50.000 0.00 0.00 36.80 3.16
2785 3081 0.385751 ACCGGCGTATGACTCATGAG 59.614 55.000 21.37 21.37 0.00 2.90
2809 3105 1.626654 GCTCACCGGACACATTCACG 61.627 60.000 9.46 0.00 0.00 4.35
2937 3279 8.534496 AGCTAGCTGGTAATGATTTTGAATTTT 58.466 29.630 18.57 0.00 0.00 1.82
3208 3551 4.666512 TCTTGCCTAGGCTTTGATTTTCT 58.333 39.130 33.07 0.00 42.51 2.52
3216 3559 7.414651 GCCTAGGCTTTGATTTTCTTAGTCTTC 60.415 40.741 27.17 0.00 38.26 2.87
3217 3560 7.607991 CCTAGGCTTTGATTTTCTTAGTCTTCA 59.392 37.037 0.00 0.00 0.00 3.02
3294 3638 4.099266 TCTGAATTTGTTGTTCCAAGTGGG 59.901 41.667 0.00 0.00 35.41 4.61
3328 3672 4.297510 TGCACAAATGAAATTCACTTCGG 58.702 39.130 0.00 0.00 33.67 4.30
3357 3701 8.299570 CACATGGCTTTATTTTCTACTTGACTT 58.700 33.333 0.00 0.00 0.00 3.01
3364 3708 9.528018 CTTTATTTTCTACTTGACTTTTTGGCA 57.472 29.630 0.00 0.00 0.00 4.92
3395 3898 7.849804 TTTGCTAGCCTAAAAGAACTGATAG 57.150 36.000 13.29 0.00 0.00 2.08
3412 3915 4.058124 TGATAGATTGCATGGTCGTAAGC 58.942 43.478 0.00 0.00 37.18 3.09
3465 3968 2.677836 GACTCGACATTTTGGCTATGCA 59.322 45.455 0.00 0.00 0.00 3.96
3527 4030 9.132521 CATTTAAGCTAACTGTTTGAGATTTGG 57.867 33.333 6.17 0.00 0.00 3.28
3529 4032 3.189287 AGCTAACTGTTTGAGATTTGGCG 59.811 43.478 6.17 0.00 0.00 5.69
3534 4037 2.161855 TGTTTGAGATTTGGCGCTCAT 58.838 42.857 7.64 0.00 40.51 2.90
3546 4049 3.726607 TGGCGCTCATGTTTTTGATTTT 58.273 36.364 7.64 0.00 0.00 1.82
3591 4106 7.959658 ATCACCATTCATTTCCATACTGAAA 57.040 32.000 0.00 0.00 38.51 2.69
3592 4107 7.395190 TCACCATTCATTTCCATACTGAAAG 57.605 36.000 0.00 0.00 37.63 2.62
3755 4270 0.592637 CAAGGTCGTTCATGCTGCAA 59.407 50.000 6.36 0.00 0.00 4.08
3828 4343 1.980844 GAACGTGCAATGCAATCACAG 59.019 47.619 10.44 0.05 41.47 3.66
3899 4437 3.888323 TGTTTGAGTAAAGAATGCTGGCA 59.112 39.130 0.00 0.00 0.00 4.92
3921 4459 7.090173 GGCACATTTTATGTTCACTGTAATGT 58.910 34.615 0.00 0.00 42.70 2.71
3925 4463 8.296713 ACATTTTATGTTCACTGTAATGTGACC 58.703 33.333 0.00 0.00 45.32 4.02
3968 4506 6.073058 GCGAGGAATATGCTGTTTGATATCAA 60.073 38.462 14.23 14.23 0.00 2.57
3976 4514 5.002464 GCTGTTTGATATCAACAGCCAAT 57.998 39.130 34.24 0.00 44.92 3.16
3977 4515 4.802039 GCTGTTTGATATCAACAGCCAATG 59.198 41.667 34.24 19.30 44.92 2.82
3985 4523 0.322098 CAACAGCCAATGGGTCGGTA 60.322 55.000 0.00 0.00 36.17 4.02
4061 4601 1.202758 ACGAAGCAGTGAACCCAATGA 60.203 47.619 0.00 0.00 40.52 2.57
4092 4632 3.660865 AGTCGGAAAATGTACTGTCCAC 58.339 45.455 0.00 0.00 0.00 4.02
4093 4633 2.740447 GTCGGAAAATGTACTGTCCACC 59.260 50.000 0.00 0.00 0.00 4.61
4094 4634 2.635915 TCGGAAAATGTACTGTCCACCT 59.364 45.455 0.00 0.00 0.00 4.00
4095 4635 3.833650 TCGGAAAATGTACTGTCCACCTA 59.166 43.478 0.00 0.00 0.00 3.08
4096 4636 4.283978 TCGGAAAATGTACTGTCCACCTAA 59.716 41.667 0.00 0.00 0.00 2.69
4098 4638 5.557866 GGAAAATGTACTGTCCACCTAACT 58.442 41.667 0.00 0.00 0.00 2.24
4099 4639 5.411669 GGAAAATGTACTGTCCACCTAACTG 59.588 44.000 0.00 0.00 0.00 3.16
4100 4640 4.553330 AATGTACTGTCCACCTAACTGG 57.447 45.455 0.00 0.00 42.93 4.00
4134 4674 5.059833 TGAACAAAAAGTGGTTGCTTTTGT 58.940 33.333 6.37 6.37 44.88 2.83
4159 4699 6.848451 TCGCTTTCATATTTTGGGAAACTAC 58.152 36.000 0.00 0.00 0.00 2.73
4287 4828 2.180946 TGTGCCACTATCCATCTCCT 57.819 50.000 0.00 0.00 0.00 3.69
4305 4846 7.720957 CCATCTCCTGTTCAAATTATGGATGTA 59.279 37.037 0.00 0.00 35.68 2.29
4319 4860 1.065418 GGATGTACCACCAACTCCAGG 60.065 57.143 0.00 0.00 38.79 4.45
4341 4882 3.447586 GGAAGAAATTGGACTAAAGCCCC 59.552 47.826 0.00 0.00 0.00 5.80
4344 4885 1.852633 AATTGGACTAAAGCCCCTGC 58.147 50.000 0.00 0.00 37.95 4.85
4362 4903 0.236711 GCGCGACGATAGCCTAAGTA 59.763 55.000 12.10 0.00 42.67 2.24
4397 4938 1.811266 CTCGTTGTCGCCTCCCATG 60.811 63.158 0.00 0.00 36.96 3.66
4398 4939 2.819595 CGTTGTCGCCTCCCATGG 60.820 66.667 4.14 4.14 0.00 3.66
4417 5300 4.970662 TGGCTCATTTCTTTCTATGTGC 57.029 40.909 0.00 0.00 39.36 4.57
4422 5305 4.832248 TCATTTCTTTCTATGTGCGACCT 58.168 39.130 0.00 0.00 0.00 3.85
4441 5324 2.163010 CCTGTCACTTTGCCACATCATC 59.837 50.000 0.00 0.00 0.00 2.92
4444 5327 3.004629 TGTCACTTTGCCACATCATCAAC 59.995 43.478 0.00 0.00 0.00 3.18
4460 5343 2.348472 TCAACAATGGGGAGGAGACTT 58.652 47.619 0.00 0.00 44.43 3.01
4524 5407 4.398044 GGTGGTTGAAAGAAAACTCACTCA 59.602 41.667 0.00 0.00 33.21 3.41
4538 5421 1.899142 TCACTCACGTCCATTCCATCA 59.101 47.619 0.00 0.00 0.00 3.07
4607 5490 4.279420 GGGGATTAGGATGCACTTTCAATC 59.721 45.833 0.00 0.00 0.00 2.67
4771 5654 9.846248 GCATGATCATTTGGGTATATTAGAAAC 57.154 33.333 5.16 0.00 0.00 2.78
4804 5687 1.315257 GCAAATCCGGTGGAGTGCAT 61.315 55.000 15.61 0.00 42.60 3.96
4816 5699 5.584649 CGGTGGAGTGCATAGAGAATAAAAA 59.415 40.000 0.00 0.00 0.00 1.94
4841 5724 9.525826 AAAAATGGGTTTTTATCATTTATGCCA 57.474 25.926 0.00 0.00 43.70 4.92
4842 5725 8.504812 AAATGGGTTTTTATCATTTATGCCAC 57.495 30.769 0.00 0.00 38.74 5.01
4843 5726 6.865834 TGGGTTTTTATCATTTATGCCACT 57.134 33.333 0.00 0.00 0.00 4.00
4844 5727 7.962995 TGGGTTTTTATCATTTATGCCACTA 57.037 32.000 0.00 0.00 0.00 2.74
4845 5728 8.006298 TGGGTTTTTATCATTTATGCCACTAG 57.994 34.615 0.00 0.00 0.00 2.57
4846 5729 7.617723 TGGGTTTTTATCATTTATGCCACTAGT 59.382 33.333 0.00 0.00 0.00 2.57
4847 5730 8.474831 GGGTTTTTATCATTTATGCCACTAGTT 58.525 33.333 0.00 0.00 0.00 2.24
4848 5731 9.301153 GGTTTTTATCATTTATGCCACTAGTTG 57.699 33.333 0.00 0.00 0.00 3.16
4849 5732 9.855021 GTTTTTATCATTTATGCCACTAGTTGT 57.145 29.630 0.00 0.00 0.00 3.32
4850 5733 9.853555 TTTTTATCATTTATGCCACTAGTTGTG 57.146 29.630 0.00 0.00 45.80 3.33
4851 5734 8.574251 TTTATCATTTATGCCACTAGTTGTGT 57.426 30.769 4.03 0.00 44.81 3.72
4852 5735 6.683974 ATCATTTATGCCACTAGTTGTGTC 57.316 37.500 4.03 0.00 44.81 3.67
4853 5736 5.804639 TCATTTATGCCACTAGTTGTGTCT 58.195 37.500 4.03 0.00 44.81 3.41
4854 5737 5.874810 TCATTTATGCCACTAGTTGTGTCTC 59.125 40.000 4.03 0.00 44.81 3.36
4855 5738 4.882842 TTATGCCACTAGTTGTGTCTCA 57.117 40.909 4.03 0.08 44.81 3.27
4856 5739 2.526304 TGCCACTAGTTGTGTCTCAC 57.474 50.000 4.03 0.00 44.81 3.51
4857 5740 2.039418 TGCCACTAGTTGTGTCTCACT 58.961 47.619 4.03 0.00 44.81 3.41
4858 5741 3.227614 TGCCACTAGTTGTGTCTCACTA 58.772 45.455 4.03 0.00 44.81 2.74
4859 5742 3.005472 TGCCACTAGTTGTGTCTCACTAC 59.995 47.826 4.03 6.41 44.81 2.73
4861 5744 4.616373 GCCACTAGTTGTGTCTCACTACTC 60.616 50.000 16.88 3.44 44.27 2.59
4862 5745 4.519350 CCACTAGTTGTGTCTCACTACTCA 59.481 45.833 16.88 6.78 44.27 3.41
4863 5746 5.335269 CCACTAGTTGTGTCTCACTACTCAG 60.335 48.000 16.88 14.63 44.27 3.35
4864 5747 5.239744 CACTAGTTGTGTCTCACTACTCAGT 59.760 44.000 16.88 15.07 44.27 3.41
4865 5748 5.828859 ACTAGTTGTGTCTCACTACTCAGTT 59.171 40.000 16.88 1.09 44.27 3.16
4866 5749 5.599999 AGTTGTGTCTCACTACTCAGTTT 57.400 39.130 10.15 0.00 44.27 2.66
4867 5750 5.978814 AGTTGTGTCTCACTACTCAGTTTT 58.021 37.500 10.15 0.00 44.27 2.43
4868 5751 5.812642 AGTTGTGTCTCACTACTCAGTTTTG 59.187 40.000 10.15 0.00 44.27 2.44
4869 5752 4.119862 TGTGTCTCACTACTCAGTTTTGC 58.880 43.478 1.72 0.00 35.11 3.68
4870 5753 3.495001 GTGTCTCACTACTCAGTTTTGCC 59.505 47.826 0.00 0.00 30.46 4.52
4871 5754 3.133901 TGTCTCACTACTCAGTTTTGCCA 59.866 43.478 0.00 0.00 30.46 4.92
4872 5755 4.202357 TGTCTCACTACTCAGTTTTGCCAT 60.202 41.667 0.00 0.00 30.46 4.40
4873 5756 4.757149 GTCTCACTACTCAGTTTTGCCATT 59.243 41.667 0.00 0.00 30.46 3.16
4874 5757 5.932303 GTCTCACTACTCAGTTTTGCCATTA 59.068 40.000 0.00 0.00 30.46 1.90
4875 5758 6.091441 GTCTCACTACTCAGTTTTGCCATTAG 59.909 42.308 0.00 0.00 30.46 1.73
4876 5759 6.014584 TCTCACTACTCAGTTTTGCCATTAGA 60.015 38.462 0.00 0.00 30.46 2.10
4877 5760 6.530120 TCACTACTCAGTTTTGCCATTAGAA 58.470 36.000 0.00 0.00 30.46 2.10
4878 5761 6.995686 TCACTACTCAGTTTTGCCATTAGAAA 59.004 34.615 0.00 0.00 30.46 2.52
4879 5762 7.665559 TCACTACTCAGTTTTGCCATTAGAAAT 59.334 33.333 0.00 0.00 30.46 2.17
4880 5763 8.299570 CACTACTCAGTTTTGCCATTAGAAATT 58.700 33.333 0.00 0.00 30.46 1.82
4881 5764 9.515226 ACTACTCAGTTTTGCCATTAGAAATTA 57.485 29.630 0.00 0.00 0.00 1.40
4882 5765 9.774742 CTACTCAGTTTTGCCATTAGAAATTAC 57.225 33.333 0.00 0.00 0.00 1.89
4883 5766 8.177119 ACTCAGTTTTGCCATTAGAAATTACA 57.823 30.769 0.00 0.00 0.00 2.41
4884 5767 8.637986 ACTCAGTTTTGCCATTAGAAATTACAA 58.362 29.630 0.00 0.00 0.00 2.41
4885 5768 8.810652 TCAGTTTTGCCATTAGAAATTACAAC 57.189 30.769 0.00 0.00 0.00 3.32
4886 5769 8.637986 TCAGTTTTGCCATTAGAAATTACAACT 58.362 29.630 0.00 0.00 0.00 3.16
4887 5770 8.702438 CAGTTTTGCCATTAGAAATTACAACTG 58.298 33.333 0.00 0.00 0.00 3.16
4888 5771 7.384932 AGTTTTGCCATTAGAAATTACAACTGC 59.615 33.333 0.00 0.00 0.00 4.40
4889 5772 6.588719 TTGCCATTAGAAATTACAACTGCT 57.411 33.333 0.00 0.00 0.00 4.24
4890 5773 6.194796 TGCCATTAGAAATTACAACTGCTC 57.805 37.500 0.00 0.00 0.00 4.26
4891 5774 5.709631 TGCCATTAGAAATTACAACTGCTCA 59.290 36.000 0.00 0.00 0.00 4.26
4892 5775 6.208402 TGCCATTAGAAATTACAACTGCTCAA 59.792 34.615 0.00 0.00 0.00 3.02
4893 5776 7.090173 GCCATTAGAAATTACAACTGCTCAAA 58.910 34.615 0.00 0.00 0.00 2.69
4894 5777 7.598493 GCCATTAGAAATTACAACTGCTCAAAA 59.402 33.333 0.00 0.00 0.00 2.44
4895 5778 9.474920 CCATTAGAAATTACAACTGCTCAAAAA 57.525 29.630 0.00 0.00 0.00 1.94
4898 5781 7.412137 AGAAATTACAACTGCTCAAAAATGC 57.588 32.000 0.00 0.00 0.00 3.56
4899 5782 6.424812 AGAAATTACAACTGCTCAAAAATGCC 59.575 34.615 0.00 0.00 0.00 4.40
4900 5783 4.662468 TTACAACTGCTCAAAAATGCCA 57.338 36.364 0.00 0.00 0.00 4.92
4901 5784 3.756933 ACAACTGCTCAAAAATGCCAT 57.243 38.095 0.00 0.00 0.00 4.40
4902 5785 3.656559 ACAACTGCTCAAAAATGCCATC 58.343 40.909 0.00 0.00 0.00 3.51
4903 5786 2.642139 ACTGCTCAAAAATGCCATCG 57.358 45.000 0.00 0.00 0.00 3.84
4904 5787 1.888512 ACTGCTCAAAAATGCCATCGT 59.111 42.857 0.00 0.00 0.00 3.73
4905 5788 2.297033 ACTGCTCAAAAATGCCATCGTT 59.703 40.909 0.00 0.00 0.00 3.85
4906 5789 2.919229 CTGCTCAAAAATGCCATCGTTC 59.081 45.455 0.00 0.00 0.00 3.95
4907 5790 2.262211 GCTCAAAAATGCCATCGTTCC 58.738 47.619 0.00 0.00 0.00 3.62
4908 5791 2.352617 GCTCAAAAATGCCATCGTTCCA 60.353 45.455 0.00 0.00 0.00 3.53
4909 5792 3.676873 GCTCAAAAATGCCATCGTTCCAT 60.677 43.478 0.00 0.00 0.00 3.41
4910 5793 3.847542 TCAAAAATGCCATCGTTCCATG 58.152 40.909 0.00 0.00 0.00 3.66
4911 5794 3.509184 TCAAAAATGCCATCGTTCCATGA 59.491 39.130 0.00 0.00 0.00 3.07
4912 5795 3.788333 AAAATGCCATCGTTCCATGAG 57.212 42.857 0.00 0.00 0.00 2.90
4913 5796 2.715749 AATGCCATCGTTCCATGAGA 57.284 45.000 0.00 0.00 0.00 3.27
4914 5797 2.945080 ATGCCATCGTTCCATGAGAT 57.055 45.000 0.00 0.00 0.00 2.75
4915 5798 1.957668 TGCCATCGTTCCATGAGATG 58.042 50.000 0.00 4.04 40.86 2.90
4916 5799 1.210234 TGCCATCGTTCCATGAGATGT 59.790 47.619 14.58 0.00 39.89 3.06
4917 5800 2.292267 GCCATCGTTCCATGAGATGTT 58.708 47.619 14.58 0.00 39.89 2.71
4918 5801 2.684881 GCCATCGTTCCATGAGATGTTT 59.315 45.455 14.58 0.00 39.89 2.83
4919 5802 3.129287 GCCATCGTTCCATGAGATGTTTT 59.871 43.478 14.58 0.00 39.89 2.43
4920 5803 4.731773 GCCATCGTTCCATGAGATGTTTTC 60.732 45.833 14.58 3.64 39.89 2.29
4921 5804 4.637534 CCATCGTTCCATGAGATGTTTTCT 59.362 41.667 14.58 0.00 39.89 2.52
4936 5819 8.767478 AGATGTTTTCTCAAAAATGCCATTAG 57.233 30.769 0.00 0.00 36.77 1.73
4937 5820 8.587608 AGATGTTTTCTCAAAAATGCCATTAGA 58.412 29.630 0.00 0.00 36.77 2.10
4938 5821 9.374838 GATGTTTTCTCAAAAATGCCATTAGAT 57.625 29.630 0.00 0.00 36.77 1.98
4944 5827 9.631257 TTCTCAAAAATGCCATTAGATATCTCA 57.369 29.630 8.95 0.00 0.00 3.27
4945 5828 9.631257 TCTCAAAAATGCCATTAGATATCTCAA 57.369 29.630 8.95 3.03 0.00 3.02
4948 5831 9.806203 CAAAAATGCCATTAGATATCTCAAACA 57.194 29.630 8.95 3.34 0.00 2.83
4950 5833 9.976511 AAAATGCCATTAGATATCTCAAACATG 57.023 29.630 8.95 5.36 0.00 3.21
4951 5834 8.701908 AATGCCATTAGATATCTCAAACATGT 57.298 30.769 8.95 0.00 0.00 3.21
4952 5835 7.734924 TGCCATTAGATATCTCAAACATGTC 57.265 36.000 8.95 0.00 0.00 3.06
4953 5836 7.281841 TGCCATTAGATATCTCAAACATGTCA 58.718 34.615 8.95 0.00 0.00 3.58
4954 5837 7.940688 TGCCATTAGATATCTCAAACATGTCAT 59.059 33.333 8.95 0.00 0.00 3.06
4955 5838 8.449397 GCCATTAGATATCTCAAACATGTCATC 58.551 37.037 8.95 0.00 0.00 2.92
4956 5839 8.654215 CCATTAGATATCTCAAACATGTCATCG 58.346 37.037 8.95 0.00 0.00 3.84
4957 5840 9.201127 CATTAGATATCTCAAACATGTCATCGT 57.799 33.333 8.95 0.00 0.00 3.73
4958 5841 9.770097 ATTAGATATCTCAAACATGTCATCGTT 57.230 29.630 8.95 0.00 0.00 3.85
4959 5842 7.706281 AGATATCTCAAACATGTCATCGTTC 57.294 36.000 0.00 0.00 0.00 3.95
4960 5843 6.703607 AGATATCTCAAACATGTCATCGTTCC 59.296 38.462 0.00 0.00 0.00 3.62
4961 5844 4.001618 TCTCAAACATGTCATCGTTCCA 57.998 40.909 0.00 0.00 0.00 3.53
4962 5845 4.578871 TCTCAAACATGTCATCGTTCCAT 58.421 39.130 0.00 0.00 0.00 3.41
4963 5846 5.003160 TCTCAAACATGTCATCGTTCCATT 58.997 37.500 0.00 0.00 0.00 3.16
4964 5847 6.169800 TCTCAAACATGTCATCGTTCCATTA 58.830 36.000 0.00 0.00 0.00 1.90
4965 5848 6.313658 TCTCAAACATGTCATCGTTCCATTAG 59.686 38.462 0.00 0.00 0.00 1.73
4966 5849 6.169800 TCAAACATGTCATCGTTCCATTAGA 58.830 36.000 0.00 0.00 0.00 2.10
4967 5850 6.823182 TCAAACATGTCATCGTTCCATTAGAT 59.177 34.615 0.00 0.00 0.00 1.98
4968 5851 6.609237 AACATGTCATCGTTCCATTAGATG 57.391 37.500 0.00 0.00 42.11 2.90
4969 5852 5.674525 ACATGTCATCGTTCCATTAGATGT 58.325 37.500 0.00 0.00 41.63 3.06
4970 5853 6.115446 ACATGTCATCGTTCCATTAGATGTT 58.885 36.000 0.00 0.00 41.63 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.719709 CTCGCGTACAGATGGACGA 59.280 57.895 21.29 0.27 41.60 4.20
11 12 1.939785 GCTCGCGTACAGATGGACG 60.940 63.158 13.23 13.23 41.97 4.79
17 18 2.787129 CGATAAAATGCTCGCGTACAGA 59.213 45.455 5.77 0.00 0.00 3.41
200 202 1.045407 TAGTTTGTCAGCACCCGAGT 58.955 50.000 0.00 0.00 0.00 4.18
226 228 2.639839 TCCCTCTTTCTTTCCCAGACAG 59.360 50.000 0.00 0.00 31.27 3.51
229 231 3.275848 TCTCCCTCTTTCTTTCCCAGA 57.724 47.619 0.00 0.00 0.00 3.86
239 241 1.981495 CCACTCCACTTCTCCCTCTTT 59.019 52.381 0.00 0.00 0.00 2.52
246 248 0.615850 CCCCTTCCACTCCACTTCTC 59.384 60.000 0.00 0.00 0.00 2.87
301 306 0.254178 ATGCTCGTTGCCATCTCCTT 59.746 50.000 1.30 0.00 42.00 3.36
320 325 2.119495 GCCTTCAGTTCCCATCTCCTA 58.881 52.381 0.00 0.00 0.00 2.94
355 361 4.133373 CCCTCCCATGCCACCAGG 62.133 72.222 0.00 0.00 38.23 4.45
409 421 4.710324 CCACGATCTAGTCCTAGTCTTCT 58.290 47.826 0.00 0.00 34.84 2.85
420 432 0.385751 CATGGACGCCACGATCTAGT 59.614 55.000 0.50 0.00 35.80 2.57
425 437 2.501128 CTCCATGGACGCCACGAT 59.499 61.111 11.44 0.00 35.80 3.73
446 458 1.760086 ATCTCCTCTGTCGCCCCAG 60.760 63.158 0.00 0.00 0.00 4.45
468 480 4.145052 GTTCTCTTCATCCCTTTGGTTGT 58.855 43.478 0.00 0.00 33.73 3.32
470 482 3.072476 TCGTTCTCTTCATCCCTTTGGTT 59.928 43.478 0.00 0.00 0.00 3.67
471 483 2.637872 TCGTTCTCTTCATCCCTTTGGT 59.362 45.455 0.00 0.00 0.00 3.67
474 486 2.569404 AGCTCGTTCTCTTCATCCCTTT 59.431 45.455 0.00 0.00 0.00 3.11
484 496 3.226429 TTGCCGCAGCTCGTTCTCT 62.226 57.895 0.00 0.00 40.80 3.10
526 538 5.405279 CTCCTCCTCCTCCTACTACTACTA 58.595 50.000 0.00 0.00 0.00 1.82
527 539 4.237018 CTCCTCCTCCTCCTACTACTACT 58.763 52.174 0.00 0.00 0.00 2.57
528 540 3.328637 CCTCCTCCTCCTCCTACTACTAC 59.671 56.522 0.00 0.00 0.00 2.73
529 541 3.600433 CCTCCTCCTCCTCCTACTACTA 58.400 54.545 0.00 0.00 0.00 1.82
530 542 2.424793 CCTCCTCCTCCTCCTACTACT 58.575 57.143 0.00 0.00 0.00 2.57
531 543 1.426215 CCCTCCTCCTCCTCCTACTAC 59.574 61.905 0.00 0.00 0.00 2.73
532 544 1.835895 CCCTCCTCCTCCTCCTACTA 58.164 60.000 0.00 0.00 0.00 1.82
626 661 1.131303 TCGCTCCTTCTTTTCCCCCA 61.131 55.000 0.00 0.00 0.00 4.96
663 917 2.999185 TTGGCTGAAAATCTCCCCTT 57.001 45.000 0.00 0.00 0.00 3.95
675 929 1.541147 CTTCGGCTTTGATTTGGCTGA 59.459 47.619 0.00 0.00 39.25 4.26
742 1006 2.798283 TGAAACAGTCGTCGGAAATCAC 59.202 45.455 0.00 0.00 0.00 3.06
755 1019 1.283793 GCATGCGCACTGAAACAGT 59.716 52.632 14.90 0.00 46.51 3.55
776 1040 3.194542 CCCTAAATTCCAATTCGGTTGCA 59.805 43.478 0.00 0.00 36.46 4.08
777 1041 3.430236 CCCCTAAATTCCAATTCGGTTGC 60.430 47.826 0.00 0.00 36.46 4.17
780 1044 4.536295 ATCCCCTAAATTCCAATTCGGT 57.464 40.909 0.00 0.00 35.57 4.69
824 1088 3.190874 TGCGTTTGGTTCCATTTCAAAC 58.809 40.909 0.00 0.00 43.75 2.93
827 1091 2.028130 ACTGCGTTTGGTTCCATTTCA 58.972 42.857 0.00 0.00 0.00 2.69
828 1092 2.223711 ACACTGCGTTTGGTTCCATTTC 60.224 45.455 0.00 0.00 0.00 2.17
830 1094 1.398692 ACACTGCGTTTGGTTCCATT 58.601 45.000 0.00 0.00 0.00 3.16
832 1096 1.944024 CTAACACTGCGTTTGGTTCCA 59.056 47.619 0.00 0.00 39.14 3.53
833 1097 2.215196 TCTAACACTGCGTTTGGTTCC 58.785 47.619 0.00 0.00 39.14 3.62
834 1098 3.128349 TCTCTAACACTGCGTTTGGTTC 58.872 45.455 0.00 0.00 39.14 3.62
835 1099 3.188159 TCTCTAACACTGCGTTTGGTT 57.812 42.857 0.00 0.00 39.14 3.67
836 1100 2.870411 GTTCTCTAACACTGCGTTTGGT 59.130 45.455 0.00 0.00 39.14 3.67
847 1111 8.871125 AGGAGTAGAATTTGAAGTTCTCTAACA 58.129 33.333 6.20 0.00 38.12 2.41
851 1115 9.041354 ACATAGGAGTAGAATTTGAAGTTCTCT 57.959 33.333 6.20 4.56 37.18 3.10
852 1116 9.660180 AACATAGGAGTAGAATTTGAAGTTCTC 57.340 33.333 6.20 0.10 37.18 2.87
855 1119 9.793259 TCAAACATAGGAGTAGAATTTGAAGTT 57.207 29.630 0.00 0.00 33.06 2.66
856 1120 9.793259 TTCAAACATAGGAGTAGAATTTGAAGT 57.207 29.630 5.40 0.00 38.79 3.01
862 1126 9.753674 TTCCATTTCAAACATAGGAGTAGAATT 57.246 29.630 0.00 0.00 0.00 2.17
867 1131 9.527157 TTTGATTCCATTTCAAACATAGGAGTA 57.473 29.630 0.00 0.00 37.97 2.59
876 1140 7.518211 CGGGTTTCTTTTGATTCCATTTCAAAC 60.518 37.037 0.00 0.00 41.45 2.93
901 1165 7.328737 CCGAACATATATCTTCCTTTTACCTCG 59.671 40.741 0.00 0.00 0.00 4.63
928 1192 2.362503 GCTTTACAGTGGGCCCCC 60.363 66.667 22.27 8.15 0.00 5.40
945 1209 4.113354 CCCTTTTCCGTTTCTCTATCTCG 58.887 47.826 0.00 0.00 0.00 4.04
965 1229 1.532238 GGGAGTGTGCCTTATCCCC 59.468 63.158 0.00 0.00 44.89 4.81
978 1242 3.986116 GAGGCGGAGAAGGGGGAGT 62.986 68.421 0.00 0.00 0.00 3.85
1081 1355 0.918983 GGGTGATGGGTGGAGATGAA 59.081 55.000 0.00 0.00 0.00 2.57
1118 1392 2.155279 GGGCTCAGAGAAAAGGTTGAC 58.845 52.381 0.00 0.00 0.00 3.18
1147 1441 3.272334 GCCGCGCCGAGAATGAAT 61.272 61.111 0.00 0.00 0.00 2.57
1228 1522 1.669115 CAGTGGACGGAGCACCTTG 60.669 63.158 0.00 0.00 0.00 3.61
1264 1560 1.683385 GCAAATGGGATACAGGGCTTC 59.317 52.381 0.00 0.00 39.74 3.86
1267 1563 1.708341 ATGCAAATGGGATACAGGGC 58.292 50.000 0.00 0.00 39.74 5.19
1331 1627 2.032528 CTGGCTGAAGGAACCGCA 59.967 61.111 0.00 0.00 0.00 5.69
1729 2025 2.823154 CAGTTCCTCGTTCCTCTCTTCT 59.177 50.000 0.00 0.00 0.00 2.85
1739 2035 0.034059 CTGGACAGCAGTTCCTCGTT 59.966 55.000 0.00 0.00 0.00 3.85
1748 2044 0.252479 ATCAGCCTTCTGGACAGCAG 59.748 55.000 0.00 0.00 40.69 4.24
1763 2059 1.948145 GGATTGGCTCAGCTTCATCAG 59.052 52.381 0.00 0.00 0.00 2.90
1847 2143 3.488090 GGAGTTACAGGCGTGCGC 61.488 66.667 6.26 8.17 41.06 6.09
1984 2280 2.096248 GAGATATAGCCCTCGGTCCTG 58.904 57.143 0.00 0.00 0.00 3.86
2146 2442 3.071747 AGGTTCCACTCAAAGAGTTCTCC 59.928 47.826 0.00 0.00 41.37 3.71
2158 2454 3.927142 CGTAAGTCATCAAGGTTCCACTC 59.073 47.826 0.00 0.00 0.00 3.51
2179 2475 4.083324 ACAAATGTGCTAACCAACAGATCG 60.083 41.667 0.00 0.00 0.00 3.69
2256 2552 0.039618 TTCACTTGGATCAAGCCCCC 59.960 55.000 7.48 0.00 44.43 5.40
2257 2553 1.004745 TCTTCACTTGGATCAAGCCCC 59.995 52.381 7.48 0.00 44.43 5.80
2469 2765 6.370994 CCATGTATATTGATCAGGCTCAAGTC 59.629 42.308 0.00 0.00 38.47 3.01
2512 2808 2.623889 GCATCGACCAGACCTATACAGT 59.376 50.000 0.00 0.00 0.00 3.55
2513 2809 2.887783 AGCATCGACCAGACCTATACAG 59.112 50.000 0.00 0.00 0.00 2.74
2752 3048 1.352156 GCCGGTACACTTTCAGAGCG 61.352 60.000 1.90 0.00 0.00 5.03
2764 3060 1.335810 TCATGAGTCATACGCCGGTAC 59.664 52.381 5.03 0.00 0.00 3.34
2797 3093 4.094887 ACAGATAAATGCGTGAATGTGTCC 59.905 41.667 0.00 0.00 0.00 4.02
2809 3105 7.642669 TGCAAGCTCTTATAACAGATAAATGC 58.357 34.615 0.00 0.00 0.00 3.56
3208 3551 7.768582 TCCTTTCATATTGCGAATGAAGACTAA 59.231 33.333 7.84 0.00 42.58 2.24
3216 3559 5.297776 AGGACTTCCTTTCATATTGCGAATG 59.702 40.000 0.00 0.00 46.09 2.67
3217 3560 5.440610 AGGACTTCCTTTCATATTGCGAAT 58.559 37.500 0.00 0.00 46.09 3.34
3247 3590 9.102757 AGAAATATAAGCACTCACACAGTTATG 57.897 33.333 0.00 0.00 30.26 1.90
3294 3638 4.362279 TCATTTGTGCAAAGAACAGAAGC 58.638 39.130 3.70 0.00 33.32 3.86
3328 3672 5.954335 AGTAGAAAATAAAGCCATGTGTGC 58.046 37.500 0.00 0.00 0.00 4.57
3357 3701 3.995705 GCTAGCAAATGTGAATGCCAAAA 59.004 39.130 10.63 0.00 43.57 2.44
3364 3708 7.177392 AGTTCTTTTAGGCTAGCAAATGTGAAT 59.823 33.333 18.24 2.91 0.00 2.57
3395 3898 3.194861 TGTAGCTTACGACCATGCAATC 58.805 45.455 0.00 0.00 0.00 2.67
3443 3946 2.939103 GCATAGCCAAAATGTCGAGTCT 59.061 45.455 0.00 0.00 0.00 3.24
3448 3951 4.530388 CAGTATGCATAGCCAAAATGTCG 58.470 43.478 6.67 0.00 0.00 4.35
3514 4017 1.603456 TGAGCGCCAAATCTCAAACA 58.397 45.000 2.29 0.00 36.50 2.83
3518 4021 1.825090 AACATGAGCGCCAAATCTCA 58.175 45.000 2.29 0.00 42.72 3.27
3527 4030 4.208873 TGACAAAATCAAAAACATGAGCGC 59.791 37.500 0.00 0.00 33.02 5.92
3546 4049 7.201785 GGTGATTCTAAAGAACCAAGTTTGACA 60.202 37.037 0.00 0.00 36.80 3.58
3591 4106 3.152341 CCTCCTGCAATGTTCAGAAACT 58.848 45.455 0.00 0.00 36.30 2.66
3592 4107 2.887152 ACCTCCTGCAATGTTCAGAAAC 59.113 45.455 0.00 0.00 33.54 2.78
3593 4108 3.149196 GACCTCCTGCAATGTTCAGAAA 58.851 45.455 0.00 0.00 33.54 2.52
3755 4270 1.445066 CTCTGCTGACGCGATGTGT 60.445 57.895 15.93 0.00 39.65 3.72
3803 4318 3.688673 TGATTGCATTGCACGTTCAGATA 59.311 39.130 11.66 0.00 38.71 1.98
3828 4343 6.600822 TGTAGTGACAGTAGGTAGGTTACATC 59.399 42.308 0.00 0.00 0.00 3.06
3875 4390 4.261572 GCCAGCATTCTTTACTCAAACACA 60.262 41.667 0.00 0.00 0.00 3.72
3876 4391 4.229876 GCCAGCATTCTTTACTCAAACAC 58.770 43.478 0.00 0.00 0.00 3.32
3925 4463 4.799949 CCTCGCATTTGTTTGACCATATTG 59.200 41.667 0.00 0.00 0.00 1.90
3942 4480 2.984562 TCAAACAGCATATTCCTCGCA 58.015 42.857 0.00 0.00 0.00 5.10
3968 4506 0.907704 TCTACCGACCCATTGGCTGT 60.908 55.000 0.00 0.00 31.43 4.40
3972 4510 3.206150 CAGAATTCTACCGACCCATTGG 58.794 50.000 7.86 0.00 35.11 3.16
3974 4512 4.569719 AACAGAATTCTACCGACCCATT 57.430 40.909 7.86 0.00 0.00 3.16
3976 4514 5.895534 ACTATAACAGAATTCTACCGACCCA 59.104 40.000 7.86 0.00 0.00 4.51
3977 4515 6.214399 CACTATAACAGAATTCTACCGACCC 58.786 44.000 7.86 0.00 0.00 4.46
4061 4601 3.006967 ACATTTTCCGACTACAGAGCACT 59.993 43.478 0.00 0.00 0.00 4.40
4107 4647 6.625873 AAGCAACCACTTTTTGTTCAAAAA 57.374 29.167 18.23 18.23 33.80 1.94
4108 4648 6.625873 AAAGCAACCACTTTTTGTTCAAAA 57.374 29.167 6.61 6.61 36.47 2.44
4109 4649 6.038714 ACAAAAGCAACCACTTTTTGTTCAAA 59.961 30.769 8.32 0.00 45.29 2.69
4110 4650 5.529060 ACAAAAGCAACCACTTTTTGTTCAA 59.471 32.000 8.32 0.00 45.29 2.69
4111 4651 5.059833 ACAAAAGCAACCACTTTTTGTTCA 58.940 33.333 8.32 0.00 45.29 3.18
4112 4652 5.605564 ACAAAAGCAACCACTTTTTGTTC 57.394 34.783 8.32 0.00 45.29 3.18
4113 4653 5.333721 CGAACAAAAGCAACCACTTTTTGTT 60.334 36.000 20.61 20.61 45.29 2.83
4114 4654 4.151512 CGAACAAAAGCAACCACTTTTTGT 59.848 37.500 8.32 8.32 45.29 2.83
4115 4655 4.636975 CGAACAAAAGCAACCACTTTTTG 58.363 39.130 7.22 7.22 45.29 2.44
4116 4656 3.124466 GCGAACAAAAGCAACCACTTTTT 59.876 39.130 0.00 0.00 45.29 1.94
4118 4658 2.094234 AGCGAACAAAAGCAACCACTTT 60.094 40.909 0.00 0.00 41.60 2.66
4121 4661 1.921243 AAGCGAACAAAAGCAACCAC 58.079 45.000 0.00 0.00 35.48 4.16
4134 4674 6.339587 AGTTTCCCAAAATATGAAAGCGAA 57.660 33.333 0.00 0.00 0.00 4.70
4159 4699 7.425309 CACCGATGTACATGTAAAAGAAATTCG 59.575 37.037 14.43 7.27 0.00 3.34
4256 4796 6.268847 TGGATAGTGGCACAAACCTAATTTTT 59.731 34.615 21.41 0.00 44.16 1.94
4305 4846 0.401395 TCTTCCCTGGAGTTGGTGGT 60.401 55.000 0.00 0.00 0.00 4.16
4316 4857 4.158579 GGCTTTAGTCCAATTTCTTCCCTG 59.841 45.833 0.00 0.00 0.00 4.45
4319 4860 3.447586 GGGGCTTTAGTCCAATTTCTTCC 59.552 47.826 2.37 0.00 42.93 3.46
4341 4882 0.999228 CTTAGGCTATCGTCGCGCAG 60.999 60.000 8.75 0.00 0.00 5.18
4344 4885 2.896243 ATACTTAGGCTATCGTCGCG 57.104 50.000 0.00 0.00 0.00 5.87
4362 4903 4.073293 ACGAGGTGAAGACTTGACAAAT 57.927 40.909 7.12 0.00 0.00 2.32
4397 4938 3.623060 TCGCACATAGAAAGAAATGAGCC 59.377 43.478 0.00 0.00 36.66 4.70
4398 4939 4.494855 GGTCGCACATAGAAAGAAATGAGC 60.495 45.833 0.00 0.00 36.65 4.26
4417 5300 0.813610 TGTGGCAAAGTGACAGGTCG 60.814 55.000 0.00 0.00 35.04 4.79
4422 5305 2.861274 TGATGATGTGGCAAAGTGACA 58.139 42.857 0.00 0.00 29.15 3.58
4441 5324 2.224867 ACAAGTCTCCTCCCCATTGTTG 60.225 50.000 0.00 0.00 0.00 3.33
4444 5327 2.821969 CAAACAAGTCTCCTCCCCATTG 59.178 50.000 0.00 0.00 0.00 2.82
4451 5334 0.110486 TGGGCCAAACAAGTCTCCTC 59.890 55.000 2.13 0.00 0.00 3.71
4460 5343 3.464720 TGGATAGAATTGGGCCAAACA 57.535 42.857 24.97 8.94 0.00 2.83
4524 5407 1.628340 TGGACTTGATGGAATGGACGT 59.372 47.619 0.00 0.00 0.00 4.34
4538 5421 1.033746 CCATGCGCCTCAATGGACTT 61.034 55.000 17.29 0.00 38.35 3.01
4580 5463 3.637821 AGTGCATCCTAATCCCCTAGA 57.362 47.619 0.00 0.00 0.00 2.43
4607 5490 8.208718 TGTAATCGATTACCAAAATGAGGAAG 57.791 34.615 34.19 0.00 41.41 3.46
4647 5530 7.087409 AGATCATGATTACATTTTGTGCGAA 57.913 32.000 10.14 0.00 34.15 4.70
4682 5565 3.828875 AAGGGAGCTCTTGTATAGCAC 57.171 47.619 14.64 0.00 42.62 4.40
4689 5572 5.509670 GCACAAATTTAAAGGGAGCTCTTGT 60.510 40.000 14.64 9.82 0.00 3.16
4691 5574 4.588528 TGCACAAATTTAAAGGGAGCTCTT 59.411 37.500 14.64 2.56 0.00 2.85
4729 5612 9.923143 AATGATCATGCATTTACATTCCATAAG 57.077 29.630 9.46 0.00 35.01 1.73
4732 5615 7.659799 CCAAATGATCATGCATTTACATTCCAT 59.340 33.333 9.46 5.15 44.30 3.41
4771 5654 4.747108 CCGGATTTGCACACTATAGAAGAG 59.253 45.833 6.78 0.00 0.00 2.85
4781 5664 0.889186 ACTCCACCGGATTTGCACAC 60.889 55.000 9.46 0.00 0.00 3.82
4816 5699 8.955388 GTGGCATAAATGATAAAAACCCATTTT 58.045 29.630 0.00 0.00 43.52 1.82
4820 5703 6.865834 AGTGGCATAAATGATAAAAACCCA 57.134 33.333 0.00 0.00 0.00 4.51
4821 5704 8.007405 ACTAGTGGCATAAATGATAAAAACCC 57.993 34.615 0.00 0.00 0.00 4.11
4824 5707 9.853555 CACAACTAGTGGCATAAATGATAAAAA 57.146 29.630 0.00 0.00 44.69 1.94
4839 5722 7.685614 ACTGAGTAGTGAGACACAACTAGTGG 61.686 46.154 0.00 0.00 43.53 4.00
4840 5723 5.239744 ACTGAGTAGTGAGACACAACTAGTG 59.760 44.000 0.00 0.00 44.24 2.74
4841 5724 5.378332 ACTGAGTAGTGAGACACAACTAGT 58.622 41.667 4.75 0.00 36.74 2.57
4842 5725 5.950758 ACTGAGTAGTGAGACACAACTAG 57.049 43.478 4.75 0.00 36.74 2.57
4843 5726 6.710597 AAACTGAGTAGTGAGACACAACTA 57.289 37.500 4.75 0.00 37.19 2.24
4844 5727 5.599999 AAACTGAGTAGTGAGACACAACT 57.400 39.130 4.75 0.00 37.19 3.16
4845 5728 5.502544 GCAAAACTGAGTAGTGAGACACAAC 60.503 44.000 4.75 0.00 37.19 3.32
4846 5729 4.570772 GCAAAACTGAGTAGTGAGACACAA 59.429 41.667 4.75 0.00 37.19 3.33
4847 5730 4.119862 GCAAAACTGAGTAGTGAGACACA 58.880 43.478 4.75 0.00 37.19 3.72
4848 5731 3.495001 GGCAAAACTGAGTAGTGAGACAC 59.505 47.826 0.09 0.00 37.19 3.67
4849 5732 3.133901 TGGCAAAACTGAGTAGTGAGACA 59.866 43.478 0.09 0.00 37.19 3.41
4850 5733 3.728845 TGGCAAAACTGAGTAGTGAGAC 58.271 45.455 0.09 0.00 37.19 3.36
4851 5734 4.623932 ATGGCAAAACTGAGTAGTGAGA 57.376 40.909 0.00 0.00 37.19 3.27
4852 5735 6.166279 TCTAATGGCAAAACTGAGTAGTGAG 58.834 40.000 0.00 0.00 37.19 3.51
4853 5736 6.109156 TCTAATGGCAAAACTGAGTAGTGA 57.891 37.500 0.00 0.00 37.19 3.41
4854 5737 6.801539 TTCTAATGGCAAAACTGAGTAGTG 57.198 37.500 0.00 0.00 37.19 2.74
4855 5738 8.409358 AATTTCTAATGGCAAAACTGAGTAGT 57.591 30.769 0.00 0.00 39.32 2.73
4856 5739 9.774742 GTAATTTCTAATGGCAAAACTGAGTAG 57.225 33.333 0.00 0.00 0.00 2.57
4857 5740 9.290988 TGTAATTTCTAATGGCAAAACTGAGTA 57.709 29.630 0.00 0.00 0.00 2.59
4858 5741 8.177119 TGTAATTTCTAATGGCAAAACTGAGT 57.823 30.769 0.00 0.00 0.00 3.41
4859 5742 8.915654 GTTGTAATTTCTAATGGCAAAACTGAG 58.084 33.333 0.00 0.00 0.00 3.35
4860 5743 8.637986 AGTTGTAATTTCTAATGGCAAAACTGA 58.362 29.630 0.00 0.00 0.00 3.41
4861 5744 8.702438 CAGTTGTAATTTCTAATGGCAAAACTG 58.298 33.333 0.00 0.00 35.28 3.16
4862 5745 7.384932 GCAGTTGTAATTTCTAATGGCAAAACT 59.615 33.333 0.00 0.00 0.00 2.66
4863 5746 7.384932 AGCAGTTGTAATTTCTAATGGCAAAAC 59.615 33.333 0.00 0.00 0.00 2.43
4864 5747 7.441017 AGCAGTTGTAATTTCTAATGGCAAAA 58.559 30.769 0.00 0.00 0.00 2.44
4865 5748 6.991938 AGCAGTTGTAATTTCTAATGGCAAA 58.008 32.000 0.00 0.00 0.00 3.68
4866 5749 6.208402 TGAGCAGTTGTAATTTCTAATGGCAA 59.792 34.615 0.00 0.00 0.00 4.52
4867 5750 5.709631 TGAGCAGTTGTAATTTCTAATGGCA 59.290 36.000 0.00 0.00 0.00 4.92
4868 5751 6.194796 TGAGCAGTTGTAATTTCTAATGGC 57.805 37.500 0.00 0.00 0.00 4.40
4869 5752 9.474920 TTTTTGAGCAGTTGTAATTTCTAATGG 57.525 29.630 0.00 0.00 0.00 3.16
4872 5755 8.977505 GCATTTTTGAGCAGTTGTAATTTCTAA 58.022 29.630 0.00 0.00 0.00 2.10
4873 5756 7.598493 GGCATTTTTGAGCAGTTGTAATTTCTA 59.402 33.333 0.00 0.00 0.00 2.10
4874 5757 6.424812 GGCATTTTTGAGCAGTTGTAATTTCT 59.575 34.615 0.00 0.00 0.00 2.52
4875 5758 6.202570 TGGCATTTTTGAGCAGTTGTAATTTC 59.797 34.615 0.00 0.00 0.00 2.17
4876 5759 6.054295 TGGCATTTTTGAGCAGTTGTAATTT 58.946 32.000 0.00 0.00 0.00 1.82
4877 5760 5.609423 TGGCATTTTTGAGCAGTTGTAATT 58.391 33.333 0.00 0.00 0.00 1.40
4878 5761 5.212532 TGGCATTTTTGAGCAGTTGTAAT 57.787 34.783 0.00 0.00 0.00 1.89
4879 5762 4.662468 TGGCATTTTTGAGCAGTTGTAA 57.338 36.364 0.00 0.00 0.00 2.41
4880 5763 4.615682 CGATGGCATTTTTGAGCAGTTGTA 60.616 41.667 0.00 0.00 0.00 2.41
4881 5764 3.656559 GATGGCATTTTTGAGCAGTTGT 58.343 40.909 0.00 0.00 0.00 3.32
4882 5765 2.664568 CGATGGCATTTTTGAGCAGTTG 59.335 45.455 0.00 0.00 0.00 3.16
4883 5766 2.297033 ACGATGGCATTTTTGAGCAGTT 59.703 40.909 0.00 0.00 0.00 3.16
4884 5767 1.888512 ACGATGGCATTTTTGAGCAGT 59.111 42.857 0.00 0.00 0.00 4.40
4885 5768 2.642139 ACGATGGCATTTTTGAGCAG 57.358 45.000 0.00 0.00 0.00 4.24
4886 5769 2.352617 GGAACGATGGCATTTTTGAGCA 60.353 45.455 0.00 0.00 0.00 4.26
4887 5770 2.262211 GGAACGATGGCATTTTTGAGC 58.738 47.619 0.00 0.00 0.00 4.26
4888 5771 3.574284 TGGAACGATGGCATTTTTGAG 57.426 42.857 0.00 0.00 0.00 3.02
4889 5772 3.509184 TCATGGAACGATGGCATTTTTGA 59.491 39.130 0.00 0.00 0.00 2.69
4890 5773 3.847542 TCATGGAACGATGGCATTTTTG 58.152 40.909 0.00 0.00 0.00 2.44
4891 5774 3.763360 TCTCATGGAACGATGGCATTTTT 59.237 39.130 0.00 0.00 0.00 1.94
4892 5775 3.355378 TCTCATGGAACGATGGCATTTT 58.645 40.909 0.00 0.00 0.00 1.82
4893 5776 3.003394 TCTCATGGAACGATGGCATTT 57.997 42.857 0.00 0.00 0.00 2.32
4894 5777 2.715749 TCTCATGGAACGATGGCATT 57.284 45.000 0.00 0.00 0.00 3.56
4895 5778 2.158711 ACATCTCATGGAACGATGGCAT 60.159 45.455 0.00 0.00 39.00 4.40
4896 5779 1.210234 ACATCTCATGGAACGATGGCA 59.790 47.619 14.88 0.00 39.00 4.92
4897 5780 1.959042 ACATCTCATGGAACGATGGC 58.041 50.000 14.88 0.00 39.00 4.40
4898 5781 4.637534 AGAAAACATCTCATGGAACGATGG 59.362 41.667 14.88 0.00 39.00 3.51
4899 5782 5.808042 AGAAAACATCTCATGGAACGATG 57.192 39.130 11.18 11.18 40.18 3.84
4911 5794 8.587608 TCTAATGGCATTTTTGAGAAAACATCT 58.412 29.630 19.21 0.00 42.61 2.90
4912 5795 8.761575 TCTAATGGCATTTTTGAGAAAACATC 57.238 30.769 19.21 0.00 37.56 3.06
4918 5801 9.631257 TGAGATATCTAATGGCATTTTTGAGAA 57.369 29.630 19.21 6.56 0.00 2.87
4919 5802 9.631257 TTGAGATATCTAATGGCATTTTTGAGA 57.369 29.630 19.21 14.84 0.00 3.27
4922 5805 9.806203 TGTTTGAGATATCTAATGGCATTTTTG 57.194 29.630 19.21 9.33 0.00 2.44
4924 5807 9.976511 CATGTTTGAGATATCTAATGGCATTTT 57.023 29.630 19.21 6.64 0.00 1.82
4925 5808 9.139734 ACATGTTTGAGATATCTAATGGCATTT 57.860 29.630 19.21 2.85 0.00 2.32
4926 5809 8.701908 ACATGTTTGAGATATCTAATGGCATT 57.298 30.769 18.01 18.01 0.00 3.56
4927 5810 7.940688 TGACATGTTTGAGATATCTAATGGCAT 59.059 33.333 4.89 0.00 27.09 4.40
4928 5811 7.281841 TGACATGTTTGAGATATCTAATGGCA 58.718 34.615 4.89 10.08 29.55 4.92
4929 5812 7.734924 TGACATGTTTGAGATATCTAATGGC 57.265 36.000 4.89 7.76 0.00 4.40
4930 5813 8.654215 CGATGACATGTTTGAGATATCTAATGG 58.346 37.037 4.89 0.00 0.00 3.16
4931 5814 9.201127 ACGATGACATGTTTGAGATATCTAATG 57.799 33.333 4.89 7.56 0.00 1.90
4932 5815 9.770097 AACGATGACATGTTTGAGATATCTAAT 57.230 29.630 4.89 0.00 0.00 1.73
4933 5816 9.249457 GAACGATGACATGTTTGAGATATCTAA 57.751 33.333 4.89 0.00 0.00 2.10
4934 5817 7.867909 GGAACGATGACATGTTTGAGATATCTA 59.132 37.037 4.89 0.00 0.00 1.98
4935 5818 6.703607 GGAACGATGACATGTTTGAGATATCT 59.296 38.462 4.47 4.47 0.00 1.98
4936 5819 6.479990 TGGAACGATGACATGTTTGAGATATC 59.520 38.462 0.00 0.00 0.00 1.63
4937 5820 6.348498 TGGAACGATGACATGTTTGAGATAT 58.652 36.000 0.00 0.00 0.00 1.63
4938 5821 5.729510 TGGAACGATGACATGTTTGAGATA 58.270 37.500 0.00 0.00 0.00 1.98
4939 5822 4.578871 TGGAACGATGACATGTTTGAGAT 58.421 39.130 0.00 0.00 0.00 2.75
4940 5823 4.001618 TGGAACGATGACATGTTTGAGA 57.998 40.909 0.00 0.00 0.00 3.27
4941 5824 4.952262 ATGGAACGATGACATGTTTGAG 57.048 40.909 0.00 0.00 0.00 3.02
4942 5825 6.169800 TCTAATGGAACGATGACATGTTTGA 58.830 36.000 0.00 0.00 0.00 2.69
4943 5826 6.421377 TCTAATGGAACGATGACATGTTTG 57.579 37.500 0.00 0.00 0.00 2.93
4944 5827 6.599244 ACATCTAATGGAACGATGACATGTTT 59.401 34.615 0.00 0.00 38.27 2.83
4945 5828 6.115446 ACATCTAATGGAACGATGACATGTT 58.885 36.000 0.00 0.00 38.27 2.71
4946 5829 5.674525 ACATCTAATGGAACGATGACATGT 58.325 37.500 0.00 0.00 38.27 3.21
4947 5830 6.609237 AACATCTAATGGAACGATGACATG 57.391 37.500 5.59 0.00 38.27 3.21


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

AutoCloner maintained by Alex Coulton.