Multiple sequence alignment - TraesCS6D01G201900

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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 TraesCS6D01G201900 chr6D 100.000 5535 0 0 1 5535 284403308 284397774 0.000000e+00 10222.0
1 TraesCS6D01G201900 chr6A 91.631 4959 182 81 279 5102 404701167 404696307 0.000000e+00 6643.0
2 TraesCS6D01G201900 chr6A 92.419 277 14 4 5246 5518 404696305 404696032 6.720000e-104 388.0
3 TraesCS6D01G201900 chr6A 82.394 284 26 15 2 277 404701482 404701215 5.580000e-55 226.0
4 TraesCS6D01G201900 chr6B 93.051 3727 116 47 279 3921 445012734 445009067 0.000000e+00 5315.0
5 TraesCS6D01G201900 chr6B 91.851 1129 43 17 3991 5102 445008675 445007579 0.000000e+00 1530.0
6 TraesCS6D01G201900 chr6B 84.000 275 24 11 5244 5518 445007581 445007327 4.280000e-61 246.0
7 TraesCS6D01G201900 chr1D 95.522 134 6 0 5113 5246 458883641 458883508 1.210000e-51 215.0
8 TraesCS6D01G201900 chr5D 93.662 142 7 2 5113 5254 498927138 498927277 1.560000e-50 211.0
9 TraesCS6D01G201900 chr5D 92.958 142 8 2 5113 5254 501708673 501708812 7.270000e-49 206.0
10 TraesCS6D01G201900 chr5D 92.029 138 10 1 5113 5250 478161218 478161354 5.660000e-45 193.0
11 TraesCS6D01G201900 chr5B 93.662 142 7 2 5113 5254 625449931 625450070 1.560000e-50 211.0
12 TraesCS6D01G201900 chr5B 93.662 142 7 2 5113 5254 629078053 629078192 1.560000e-50 211.0
13 TraesCS6D01G201900 chr5B 93.662 142 7 2 5113 5254 632808243 632808104 1.560000e-50 211.0
14 TraesCS6D01G201900 chr2D 94.737 133 7 0 5113 5245 519335095 519335227 2.020000e-49 207.0
15 TraesCS6D01G201900 chrUn 89.655 145 12 3 5122 5266 31210865 31210724 1.220000e-41 182.0
16 TraesCS6D01G201900 chr1B 80.165 121 20 3 2894 3012 608995038 608994920 2.750000e-13 87.9


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 TraesCS6D01G201900 chr6D 284397774 284403308 5534 True 10222.000000 10222 100.000000 1 5535 1 chr6D.!!$R1 5534
1 TraesCS6D01G201900 chr6A 404696032 404701482 5450 True 2419.000000 6643 88.814667 2 5518 3 chr6A.!!$R1 5516
2 TraesCS6D01G201900 chr6B 445007327 445012734 5407 True 2363.666667 5315 89.634000 279 5518 3 chr6B.!!$R1 5239

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
704 802 0.030638 GCGTCCATGAGAGAGAGAGC 59.969 60.000 0.0 0.0 0.00 4.09 F
915 1021 1.279749 AAATCCGTTCCCCTCTCCCC 61.280 60.000 0.0 0.0 0.00 4.81 F
1841 1967 2.102553 GAGCTCACCTACGTCGCC 59.897 66.667 9.4 0.0 0.00 5.54 F
3618 3822 0.249322 CGAAATATCGGACCAGGCGT 60.249 55.000 0.0 0.0 45.32 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2402 0.108615 CAGAACGTACCCAGAGCAGG 60.109 60.0 0.00 0.0 0.0 4.85 R
2687 2849 1.234615 AAGGAAACGACGGCATGTGG 61.235 55.0 0.00 0.0 0.0 4.17 R
3835 4047 0.251121 TTTGCCATCCCGACACACAT 60.251 50.0 0.00 0.0 0.0 3.21 R
5186 5767 0.177836 CACCATGGACTGCATACGGA 59.822 55.0 21.47 0.0 0.0 4.69 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
32 33 4.399303 GTGACTAAAGCAATGTGGGCTAAT 59.601 41.667 0.00 0.00 41.66 1.73
72 73 4.467795 TCTGAAATGGAAGAAGACGAGGAT 59.532 41.667 0.00 0.00 0.00 3.24
101 121 4.728772 TGATGAACTTTCCCACATTGAGT 58.271 39.130 0.00 0.00 0.00 3.41
102 122 4.761739 TGATGAACTTTCCCACATTGAGTC 59.238 41.667 0.00 0.00 0.00 3.36
109 129 5.882557 ACTTTCCCACATTGAGTCATATGAC 59.117 40.000 25.47 25.47 45.08 3.06
150 170 7.093552 TGCCATTGCCATTTGTTAGTAGTTAAT 60.094 33.333 0.00 0.00 36.33 1.40
151 171 8.410141 GCCATTGCCATTTGTTAGTAGTTAATA 58.590 33.333 0.00 0.00 0.00 0.98
176 196 8.588290 ATTAATGGCCATTTGTTAGTAGTTCA 57.412 30.769 34.85 10.40 32.50 3.18
181 201 4.092968 GCCATTTGTTAGTAGTTCAGACGG 59.907 45.833 0.00 0.00 0.00 4.79
269 289 9.314133 TCTATGTAATATGGTAAGATCACTGCT 57.686 33.333 0.00 0.00 0.00 4.24
272 292 5.537300 AATATGGTAAGATCACTGCTCGT 57.463 39.130 0.00 0.00 0.00 4.18
287 353 1.543614 CTCGTGAGACTGCATCTTCG 58.456 55.000 0.00 3.15 38.00 3.79
317 383 1.242076 GCTCAGTGCTGTCAACCAAT 58.758 50.000 0.00 0.00 38.95 3.16
319 385 1.808945 CTCAGTGCTGTCAACCAATCC 59.191 52.381 0.00 0.00 0.00 3.01
321 387 0.478072 AGTGCTGTCAACCAATCCCA 59.522 50.000 0.00 0.00 0.00 4.37
322 388 1.133513 AGTGCTGTCAACCAATCCCAA 60.134 47.619 0.00 0.00 0.00 4.12
323 389 1.270550 GTGCTGTCAACCAATCCCAAG 59.729 52.381 0.00 0.00 0.00 3.61
324 390 0.244721 GCTGTCAACCAATCCCAAGC 59.755 55.000 0.00 0.00 0.00 4.01
325 391 1.619654 CTGTCAACCAATCCCAAGCA 58.380 50.000 0.00 0.00 0.00 3.91
326 392 1.270550 CTGTCAACCAATCCCAAGCAC 59.729 52.381 0.00 0.00 0.00 4.40
369 435 1.270274 TGCTGTGCAGTTAGCCAAATG 59.730 47.619 13.20 0.00 44.83 2.32
370 436 1.270550 GCTGTGCAGTTAGCCAAATGT 59.729 47.619 6.32 0.00 44.83 2.71
422 488 0.965866 AGTCGGGCTCAATCAGACGA 60.966 55.000 0.00 0.00 36.97 4.20
535 601 6.564125 GCGAATATCTACCAAAGTCGAAATGG 60.564 42.308 10.04 10.04 40.16 3.16
542 608 4.062991 ACCAAAGTCGAAATGGTCAGTAC 58.937 43.478 11.18 0.00 43.90 2.73
543 609 3.122948 CCAAAGTCGAAATGGTCAGTACG 59.877 47.826 4.62 0.00 0.00 3.67
544 610 3.655276 AAGTCGAAATGGTCAGTACGT 57.345 42.857 0.00 0.00 0.00 3.57
545 611 4.771590 AAGTCGAAATGGTCAGTACGTA 57.228 40.909 0.00 0.00 0.00 3.57
567 635 1.478105 GAGCAACCCACCATTTCATCC 59.522 52.381 0.00 0.00 0.00 3.51
704 802 0.030638 GCGTCCATGAGAGAGAGAGC 59.969 60.000 0.00 0.00 0.00 4.09
730 828 2.681390 CGGATAGAGATAGAGACGGGGG 60.681 59.091 0.00 0.00 0.00 5.40
882 980 4.767892 CCTGCCCCCTTCCCCTCT 62.768 72.222 0.00 0.00 0.00 3.69
915 1021 1.279749 AAATCCGTTCCCCTCTCCCC 61.280 60.000 0.00 0.00 0.00 4.81
916 1022 3.715848 ATCCGTTCCCCTCTCCCCC 62.716 68.421 0.00 0.00 0.00 5.40
1088 1198 2.125512 CCCGCCTCTGTACTGCAC 60.126 66.667 0.00 0.00 0.00 4.57
1151 1261 4.424566 CCACACGGGTCGTACGGG 62.425 72.222 16.52 1.68 38.32 5.28
1593 1715 6.160664 TGTATTCCGTTTTCTGATCGAAAC 57.839 37.500 10.79 9.54 41.13 2.78
1733 1859 4.129737 TACCTGGCGACGCTGCTC 62.130 66.667 20.77 3.07 34.52 4.26
1841 1967 2.102553 GAGCTCACCTACGTCGCC 59.897 66.667 9.40 0.00 0.00 5.54
2111 2243 5.106515 GGAGTGAGATTTGGTGCTAGTTTTC 60.107 44.000 0.00 0.00 0.00 2.29
2125 2257 9.860898 GGTGCTAGTTTTCTATTGATTGATTTT 57.139 29.630 0.00 0.00 0.00 1.82
2191 2335 6.634436 CGAGGAAATGATTAATTAACTGCTGC 59.366 38.462 0.00 0.00 0.00 5.25
2237 2381 9.220767 GGAAAAGAACGCTGGATTAATCTATAT 57.779 33.333 14.95 0.00 0.00 0.86
2283 2434 2.180159 CTGGGTACGTTCTGGGTGGG 62.180 65.000 0.00 0.00 0.00 4.61
2521 2674 6.127647 ACTCATGTTCTTTTGCTGTCAGAAAA 60.128 34.615 3.32 2.32 0.00 2.29
2523 2676 4.997565 TGTTCTTTTGCTGTCAGAAAAGG 58.002 39.130 23.06 17.72 38.94 3.11
2624 2778 8.873215 TTCGTTAAAATTGTTCATGGCTTTTA 57.127 26.923 0.00 0.00 0.00 1.52
2625 2779 8.514136 TCGTTAAAATTGTTCATGGCTTTTAG 57.486 30.769 0.00 0.00 0.00 1.85
2642 2796 7.067008 TGGCTTTTAGCTCTTATATGAAACACC 59.933 37.037 0.00 0.00 41.99 4.16
2687 2849 6.720012 AACAAAACAAAAGTTGTGTCATCC 57.280 33.333 0.00 0.00 44.59 3.51
2712 2874 1.632948 GCCGTCGTTTCCTTGGTAGC 61.633 60.000 0.00 0.00 0.00 3.58
2714 2876 1.068474 CGTCGTTTCCTTGGTAGCTG 58.932 55.000 0.00 0.00 0.00 4.24
2718 2881 2.629137 TCGTTTCCTTGGTAGCTGTGTA 59.371 45.455 0.00 0.00 0.00 2.90
2749 2912 4.603131 TCTGGTTAATACGTGTAGAGGGT 58.397 43.478 0.00 0.00 0.00 4.34
2798 2961 3.321396 TCTTTGGATGAATTGTGCAGCAA 59.679 39.130 0.00 4.56 41.89 3.91
2867 3039 8.920509 TGTTCATCATCATCATGTTGATTTTC 57.079 30.769 15.20 3.67 38.16 2.29
2870 3042 8.747538 TCATCATCATCATGTTGATTTTCTCT 57.252 30.769 15.20 0.00 35.33 3.10
2880 3052 3.469008 TGATTTTCTCTGTGTCCGTGT 57.531 42.857 0.00 0.00 0.00 4.49
2932 3104 0.912486 GGAGTACATGCCCCTGTTCT 59.088 55.000 0.00 0.00 30.48 3.01
3383 3578 1.804326 CCCGCGGACAGAAGTAACG 60.804 63.158 30.73 0.00 0.00 3.18
3404 3599 1.544825 GGGCCCTTTCTTTGCTTCCC 61.545 60.000 17.04 0.00 0.00 3.97
3405 3600 0.542938 GGCCCTTTCTTTGCTTCCCT 60.543 55.000 0.00 0.00 0.00 4.20
3406 3601 0.605083 GCCCTTTCTTTGCTTCCCTG 59.395 55.000 0.00 0.00 0.00 4.45
3539 3742 6.421485 AGAGTCGTTATTAGTAGGACCAAGA 58.579 40.000 0.00 0.00 0.00 3.02
3618 3822 0.249322 CGAAATATCGGACCAGGCGT 60.249 55.000 0.00 0.00 45.32 5.68
3835 4047 5.483811 TGAATAATTACTGTTGGCGTCAGA 58.516 37.500 14.02 0.00 36.81 3.27
3865 4077 3.186205 CGGGATGGCAAAAACATGTTTTC 59.814 43.478 31.10 21.22 41.45 2.29
3987 4202 1.070758 CCTGTGAGGTGTAGCTTGTGT 59.929 52.381 0.00 0.00 0.00 3.72
4011 4548 0.824109 TGTATGGCACGAGAGGAAGG 59.176 55.000 0.00 0.00 0.00 3.46
4021 4558 4.821589 GAGGAAGGCGGCGAGGTG 62.822 72.222 12.98 0.00 0.00 4.00
4132 4671 3.264897 CCGCTGATGCACGGTAGC 61.265 66.667 5.36 4.57 44.46 3.58
4156 4695 0.181824 GGTACACCACAACACAGGGT 59.818 55.000 0.00 0.00 35.64 4.34
4157 4696 1.417145 GGTACACCACAACACAGGGTA 59.583 52.381 0.00 0.00 35.64 3.69
4177 4716 5.405571 GGGTATTACGTCATGTGCTATTCTG 59.594 44.000 0.00 0.00 0.00 3.02
4264 4819 5.337491 GGCCAACACATTTCTTGGATTATGT 60.337 40.000 0.00 0.00 39.58 2.29
4288 4843 8.766151 TGTTTTGTTTTTCTGGTTACAAACTTC 58.234 29.630 0.00 0.00 39.43 3.01
4300 4855 5.499047 GTTACAAACTTCTGTTCTCCGTTG 58.501 41.667 0.00 0.00 34.96 4.10
4303 4858 2.156343 ACTTCTGTTCTCCGTTGCTC 57.844 50.000 0.00 0.00 0.00 4.26
4398 4953 0.034059 GGGCAGATCATCCTGTACGG 59.966 60.000 0.00 0.00 36.57 4.02
4438 4993 2.765807 CAGATCCTGGAGGCCCGT 60.766 66.667 0.00 0.00 34.29 5.28
4547 5102 4.141914 GCCACTACTAGAAGCAATACCACT 60.142 45.833 0.00 0.00 0.00 4.00
4548 5103 5.068723 GCCACTACTAGAAGCAATACCACTA 59.931 44.000 0.00 0.00 0.00 2.74
4549 5104 6.505272 CCACTACTAGAAGCAATACCACTAC 58.495 44.000 0.00 0.00 0.00 2.73
4622 5182 2.190161 TGAATCATGTACGTACGCTGC 58.810 47.619 20.18 7.06 0.00 5.25
4688 5254 4.353383 ACTACCCTTGAAAGACCTGTTC 57.647 45.455 0.00 0.00 0.00 3.18
4714 5280 4.755266 TCTTGTCTCCTTTATGCCTACC 57.245 45.455 0.00 0.00 0.00 3.18
4761 5328 4.832608 GGCTAACCGCGACCCTGG 62.833 72.222 8.23 0.00 40.44 4.45
4762 5329 4.078516 GCTAACCGCGACCCTGGT 62.079 66.667 8.23 0.00 41.20 4.00
4765 5332 4.636435 AACCGCGACCCTGGTTGG 62.636 66.667 8.23 4.05 46.41 3.77
4770 5337 2.046314 CGACCCTGGTTGGCGAAT 60.046 61.111 0.00 0.00 0.00 3.34
4771 5338 2.106683 CGACCCTGGTTGGCGAATC 61.107 63.158 0.00 0.00 0.00 2.52
4772 5339 1.749258 GACCCTGGTTGGCGAATCC 60.749 63.158 0.00 0.00 0.00 3.01
4773 5340 2.824041 CCCTGGTTGGCGAATCCG 60.824 66.667 0.00 0.00 37.80 4.18
4959 5534 6.867816 GCAGTTGTCTATCTCTATCAATCTGG 59.132 42.308 0.00 0.00 0.00 3.86
5053 5630 5.520649 GTCGACCTAGGATTGACTTTTGATC 59.479 44.000 17.98 0.00 0.00 2.92
5102 5683 3.195661 CGCCTGGATCCTTAGTTTGTAC 58.804 50.000 14.23 0.00 0.00 2.90
5103 5684 3.118738 CGCCTGGATCCTTAGTTTGTACT 60.119 47.826 14.23 0.00 38.44 2.73
5104 5685 4.443621 GCCTGGATCCTTAGTTTGTACTC 58.556 47.826 14.23 0.00 35.78 2.59
5105 5686 4.683671 GCCTGGATCCTTAGTTTGTACTCC 60.684 50.000 14.23 0.00 35.78 3.85
5106 5687 4.141688 CCTGGATCCTTAGTTTGTACTCCC 60.142 50.000 14.23 0.00 35.78 4.30
5107 5688 4.695606 TGGATCCTTAGTTTGTACTCCCT 58.304 43.478 14.23 0.00 35.78 4.20
5108 5689 4.715297 TGGATCCTTAGTTTGTACTCCCTC 59.285 45.833 14.23 0.00 35.78 4.30
5109 5690 4.101274 GGATCCTTAGTTTGTACTCCCTCC 59.899 50.000 3.84 0.00 35.78 4.30
5110 5691 3.094572 TCCTTAGTTTGTACTCCCTCCG 58.905 50.000 0.00 0.00 35.78 4.63
5111 5692 2.830321 CCTTAGTTTGTACTCCCTCCGT 59.170 50.000 0.00 0.00 35.78 4.69
5112 5693 3.260128 CCTTAGTTTGTACTCCCTCCGTT 59.740 47.826 0.00 0.00 35.78 4.44
5113 5694 4.262765 CCTTAGTTTGTACTCCCTCCGTTT 60.263 45.833 0.00 0.00 35.78 3.60
5114 5695 3.851458 AGTTTGTACTCCCTCCGTTTT 57.149 42.857 0.00 0.00 0.00 2.43
5115 5696 3.473625 AGTTTGTACTCCCTCCGTTTTG 58.526 45.455 0.00 0.00 0.00 2.44
5116 5697 3.135167 AGTTTGTACTCCCTCCGTTTTGA 59.865 43.478 0.00 0.00 0.00 2.69
5117 5698 2.825861 TGTACTCCCTCCGTTTTGAC 57.174 50.000 0.00 0.00 0.00 3.18
5118 5699 1.000060 TGTACTCCCTCCGTTTTGACG 60.000 52.381 0.00 0.00 0.00 4.35
5119 5700 1.270550 GTACTCCCTCCGTTTTGACGA 59.729 52.381 0.00 0.00 34.64 4.20
5120 5701 0.317479 ACTCCCTCCGTTTTGACGAG 59.683 55.000 0.00 0.00 34.64 4.18
5121 5702 0.601558 CTCCCTCCGTTTTGACGAGA 59.398 55.000 0.00 0.00 34.64 4.04
5122 5703 1.204941 CTCCCTCCGTTTTGACGAGAT 59.795 52.381 0.00 0.00 34.64 2.75
5123 5704 1.621814 TCCCTCCGTTTTGACGAGATT 59.378 47.619 0.00 0.00 34.64 2.40
5124 5705 2.000447 CCCTCCGTTTTGACGAGATTC 59.000 52.381 0.00 0.00 34.64 2.52
5125 5706 2.000447 CCTCCGTTTTGACGAGATTCC 59.000 52.381 0.00 0.00 34.64 3.01
5126 5707 2.611971 CCTCCGTTTTGACGAGATTCCA 60.612 50.000 0.00 0.00 34.64 3.53
5127 5708 2.409975 TCCGTTTTGACGAGATTCCAC 58.590 47.619 0.00 0.00 34.64 4.02
5128 5709 2.036733 TCCGTTTTGACGAGATTCCACT 59.963 45.455 0.00 0.00 34.64 4.00
5129 5710 3.256383 TCCGTTTTGACGAGATTCCACTA 59.744 43.478 0.00 0.00 34.64 2.74
5130 5711 4.081862 TCCGTTTTGACGAGATTCCACTAT 60.082 41.667 0.00 0.00 34.64 2.12
5131 5712 4.032900 CCGTTTTGACGAGATTCCACTATG 59.967 45.833 0.00 0.00 34.64 2.23
5132 5713 4.032900 CGTTTTGACGAGATTCCACTATGG 59.967 45.833 0.00 0.00 35.27 2.74
5133 5714 5.175859 GTTTTGACGAGATTCCACTATGGA 58.824 41.667 0.00 0.00 46.61 3.41
5134 5715 8.082850 CGTTTTGACGAGATTCCACTATGGAC 62.083 46.154 0.00 0.00 40.04 4.02
5142 5723 0.606096 TCCACTATGGACCACACACG 59.394 55.000 0.00 0.00 42.67 4.49
5143 5724 0.606096 CCACTATGGACCACACACGA 59.394 55.000 0.00 0.00 40.96 4.35
5144 5725 1.001520 CCACTATGGACCACACACGAA 59.998 52.381 0.00 0.00 40.96 3.85
5145 5726 2.549134 CCACTATGGACCACACACGAAA 60.549 50.000 0.00 0.00 40.96 3.46
5146 5727 2.478894 CACTATGGACCACACACGAAAC 59.521 50.000 0.00 0.00 0.00 2.78
5147 5728 2.103432 ACTATGGACCACACACGAAACA 59.897 45.455 0.00 0.00 0.00 2.83
5148 5729 2.045561 ATGGACCACACACGAAACAA 57.954 45.000 0.00 0.00 0.00 2.83
5149 5730 1.822506 TGGACCACACACGAAACAAA 58.177 45.000 0.00 0.00 0.00 2.83
5150 5731 2.160205 TGGACCACACACGAAACAAAA 58.840 42.857 0.00 0.00 0.00 2.44
5151 5732 2.755655 TGGACCACACACGAAACAAAAT 59.244 40.909 0.00 0.00 0.00 1.82
5152 5733 3.112580 GGACCACACACGAAACAAAATG 58.887 45.455 0.00 0.00 0.00 2.32
5153 5734 3.112580 GACCACACACGAAACAAAATGG 58.887 45.455 0.00 0.00 0.00 3.16
5154 5735 2.755655 ACCACACACGAAACAAAATGGA 59.244 40.909 0.00 0.00 0.00 3.41
5155 5736 3.383185 ACCACACACGAAACAAAATGGAT 59.617 39.130 0.00 0.00 0.00 3.41
5156 5737 3.735240 CCACACACGAAACAAAATGGATG 59.265 43.478 0.00 0.00 0.00 3.51
5157 5738 4.498850 CCACACACGAAACAAAATGGATGA 60.499 41.667 0.00 0.00 0.00 2.92
5158 5739 5.039984 CACACACGAAACAAAATGGATGAA 58.960 37.500 0.00 0.00 0.00 2.57
5159 5740 5.691305 CACACACGAAACAAAATGGATGAAT 59.309 36.000 0.00 0.00 0.00 2.57
5160 5741 5.920273 ACACACGAAACAAAATGGATGAATC 59.080 36.000 0.00 0.00 0.00 2.52
5161 5742 6.151691 CACACGAAACAAAATGGATGAATCT 58.848 36.000 0.00 0.00 0.00 2.40
5162 5743 7.040755 ACACACGAAACAAAATGGATGAATCTA 60.041 33.333 0.00 0.00 0.00 1.98
5163 5744 7.271223 CACACGAAACAAAATGGATGAATCTAC 59.729 37.037 0.00 0.00 0.00 2.59
5164 5745 7.040755 ACACGAAACAAAATGGATGAATCTACA 60.041 33.333 0.00 0.00 0.00 2.74
5165 5746 7.271223 CACGAAACAAAATGGATGAATCTACAC 59.729 37.037 0.00 0.00 0.00 2.90
5166 5747 7.174946 ACGAAACAAAATGGATGAATCTACACT 59.825 33.333 0.00 0.00 0.00 3.55
5167 5748 8.023128 CGAAACAAAATGGATGAATCTACACTT 58.977 33.333 0.00 0.00 0.00 3.16
5174 5755 9.807649 AAATGGATGAATCTACACTTAAAATGC 57.192 29.630 0.00 0.00 0.00 3.56
5175 5756 7.936496 TGGATGAATCTACACTTAAAATGCA 57.064 32.000 0.00 0.00 0.00 3.96
5176 5757 8.523915 TGGATGAATCTACACTTAAAATGCAT 57.476 30.769 0.00 0.00 0.00 3.96
5177 5758 8.623903 TGGATGAATCTACACTTAAAATGCATC 58.376 33.333 0.00 0.00 0.00 3.91
5178 5759 8.844244 GGATGAATCTACACTTAAAATGCATCT 58.156 33.333 0.00 0.00 0.00 2.90
5190 5771 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
5194 5775 7.953158 AATGCATCTATATACATCCGTATGC 57.047 36.000 0.00 0.00 38.79 3.14
5195 5776 6.463995 TGCATCTATATACATCCGTATGCA 57.536 37.500 0.00 0.00 38.79 3.96
5196 5777 6.507023 TGCATCTATATACATCCGTATGCAG 58.493 40.000 0.00 0.00 38.79 4.41
5197 5778 6.096846 TGCATCTATATACATCCGTATGCAGT 59.903 38.462 0.00 0.00 38.79 4.40
5198 5779 6.638873 GCATCTATATACATCCGTATGCAGTC 59.361 42.308 0.00 0.00 38.79 3.51
5199 5780 6.694877 TCTATATACATCCGTATGCAGTCC 57.305 41.667 0.00 0.00 38.79 3.85
5200 5781 6.184789 TCTATATACATCCGTATGCAGTCCA 58.815 40.000 0.00 0.00 38.79 4.02
5201 5782 5.939764 ATATACATCCGTATGCAGTCCAT 57.060 39.130 0.00 0.00 38.79 3.41
5202 5783 2.245159 ACATCCGTATGCAGTCCATG 57.755 50.000 0.00 0.00 36.50 3.66
5203 5784 1.202687 ACATCCGTATGCAGTCCATGG 60.203 52.381 4.97 4.97 36.50 3.66
5204 5785 1.131638 ATCCGTATGCAGTCCATGGT 58.868 50.000 12.58 0.00 35.34 3.55
5205 5786 0.177836 TCCGTATGCAGTCCATGGTG 59.822 55.000 12.58 4.64 35.34 4.17
5206 5787 0.815213 CCGTATGCAGTCCATGGTGG 60.815 60.000 12.58 3.64 39.43 4.61
5207 5788 0.177836 CGTATGCAGTCCATGGTGGA 59.822 55.000 12.58 5.20 45.98 4.02
5219 5800 5.102953 TCCATGGTGGAATCTCTACAAAG 57.897 43.478 12.58 0.00 45.00 2.77
5220 5801 4.782691 TCCATGGTGGAATCTCTACAAAGA 59.217 41.667 12.58 0.00 45.00 2.52
5221 5802 4.878397 CCATGGTGGAATCTCTACAAAGAC 59.122 45.833 2.57 0.00 40.96 3.01
5222 5803 5.338708 CCATGGTGGAATCTCTACAAAGACT 60.339 44.000 2.57 0.00 40.96 3.24
5223 5804 5.825593 TGGTGGAATCTCTACAAAGACTT 57.174 39.130 0.00 0.00 28.51 3.01
5224 5805 6.928348 TGGTGGAATCTCTACAAAGACTTA 57.072 37.500 0.00 0.00 28.51 2.24
5225 5806 7.496346 TGGTGGAATCTCTACAAAGACTTAT 57.504 36.000 0.00 0.00 28.51 1.73
5226 5807 8.603898 TGGTGGAATCTCTACAAAGACTTATA 57.396 34.615 0.00 0.00 28.51 0.98
5227 5808 9.213777 TGGTGGAATCTCTACAAAGACTTATAT 57.786 33.333 0.00 0.00 28.51 0.86
5239 5820 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
5240 5821 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
5241 5822 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
5242 5823 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
5266 5847 9.326413 GGAGTAATAACAGTGTGCTAAATGTAT 57.674 33.333 0.00 0.00 0.00 2.29
5282 5863 0.402121 GTATCCAATCTGAGGGGCCC 59.598 60.000 17.12 17.12 0.00 5.80
5311 5892 8.875803 GTGCATGATTTCACAATTTATGTTCAT 58.124 29.630 0.00 0.00 41.46 2.57
5403 5987 3.127548 CCAGATTTGATTGTGGAGGAACG 59.872 47.826 0.00 0.00 31.04 3.95
5422 6006 0.880278 GCTGAGCTTCCACACAACGA 60.880 55.000 0.00 0.00 0.00 3.85
5423 6007 1.581934 CTGAGCTTCCACACAACGAA 58.418 50.000 0.00 0.00 0.00 3.85
5427 6011 4.130857 TGAGCTTCCACACAACGAATTAA 58.869 39.130 0.00 0.00 0.00 1.40
5445 6029 0.687354 AAGGCATCTCCAACGTGACT 59.313 50.000 0.00 0.00 37.29 3.41
5448 6032 0.037326 GCATCTCCAACGTGACTCCA 60.037 55.000 0.00 0.00 0.00 3.86
5518 6102 4.037208 GGACACGGGATTCTATACTTCGAA 59.963 45.833 0.00 0.00 0.00 3.71
5519 6103 5.450965 GGACACGGGATTCTATACTTCGAAA 60.451 44.000 0.00 0.00 0.00 3.46
5520 6104 5.346522 ACACGGGATTCTATACTTCGAAAC 58.653 41.667 0.00 0.00 0.00 2.78
5521 6105 5.126707 ACACGGGATTCTATACTTCGAAACT 59.873 40.000 0.00 0.00 0.00 2.66
5522 6106 6.040878 CACGGGATTCTATACTTCGAAACTT 58.959 40.000 0.00 0.00 0.00 2.66
5523 6107 6.198591 CACGGGATTCTATACTTCGAAACTTC 59.801 42.308 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.425606 CACATTGCTTTAGTCACTTTAACCTT 58.574 34.615 0.00 0.00 0.00 3.50
72 73 5.323581 TGTGGGAAAGTTCATCAATCATCA 58.676 37.500 0.00 0.00 0.00 3.07
101 121 7.282224 GGCAGTACCAAATTAACAGTCATATGA 59.718 37.037 0.00 0.00 38.86 2.15
102 122 7.417612 GGCAGTACCAAATTAACAGTCATATG 58.582 38.462 0.00 0.00 38.86 1.78
150 170 9.688091 TGAACTACTAACAAATGGCCATTAATA 57.312 29.630 30.84 20.75 0.00 0.98
151 171 8.588290 TGAACTACTAACAAATGGCCATTAAT 57.412 30.769 30.84 20.74 0.00 1.40
152 172 7.885922 TCTGAACTACTAACAAATGGCCATTAA 59.114 33.333 30.84 15.44 0.00 1.40
153 173 7.335924 GTCTGAACTACTAACAAATGGCCATTA 59.664 37.037 30.84 14.63 0.00 1.90
154 174 6.151144 GTCTGAACTACTAACAAATGGCCATT 59.849 38.462 25.73 25.73 0.00 3.16
155 175 5.648092 GTCTGAACTACTAACAAATGGCCAT 59.352 40.000 14.09 14.09 0.00 4.40
156 176 5.001232 GTCTGAACTACTAACAAATGGCCA 58.999 41.667 8.56 8.56 0.00 5.36
157 177 4.092968 CGTCTGAACTACTAACAAATGGCC 59.907 45.833 0.00 0.00 0.00 5.36
158 178 4.092968 CCGTCTGAACTACTAACAAATGGC 59.907 45.833 0.00 0.00 0.00 4.40
159 179 5.347907 GTCCGTCTGAACTACTAACAAATGG 59.652 44.000 0.00 0.00 0.00 3.16
160 180 6.089551 CAGTCCGTCTGAACTACTAACAAATG 59.910 42.308 0.00 0.00 46.27 2.32
161 181 6.157211 CAGTCCGTCTGAACTACTAACAAAT 58.843 40.000 0.00 0.00 46.27 2.32
162 182 5.526115 CAGTCCGTCTGAACTACTAACAAA 58.474 41.667 0.00 0.00 46.27 2.83
163 183 5.117355 CAGTCCGTCTGAACTACTAACAA 57.883 43.478 0.00 0.00 46.27 2.83
164 184 4.761235 CAGTCCGTCTGAACTACTAACA 57.239 45.455 0.00 0.00 46.27 2.41
175 195 2.029918 TGACAGTTCATCAGTCCGTCTG 60.030 50.000 0.00 0.00 44.85 3.51
176 196 2.239400 TGACAGTTCATCAGTCCGTCT 58.761 47.619 0.00 0.00 32.64 4.18
181 201 7.426929 ACTAACAAATGACAGTTCATCAGTC 57.573 36.000 0.00 0.00 42.00 3.51
192 212 7.847096 TCAATCCTAGCTACTAACAAATGACA 58.153 34.615 0.00 0.00 0.00 3.58
269 289 0.456824 GCGAAGATGCAGTCTCACGA 60.457 55.000 18.95 0.00 38.22 4.35
287 353 2.199291 GCACTGAGCATTATGGTTGC 57.801 50.000 0.00 1.04 44.79 4.17
317 383 1.773856 TTCGTCCATGGTGCTTGGGA 61.774 55.000 12.58 0.00 34.85 4.37
319 385 0.240945 GTTTCGTCCATGGTGCTTGG 59.759 55.000 12.58 0.00 35.45 3.61
321 387 1.686355 TTGTTTCGTCCATGGTGCTT 58.314 45.000 12.58 0.00 0.00 3.91
322 388 1.812571 GATTGTTTCGTCCATGGTGCT 59.187 47.619 12.58 0.00 0.00 4.40
323 389 1.812571 AGATTGTTTCGTCCATGGTGC 59.187 47.619 12.58 5.32 0.00 5.01
324 390 2.094258 CGAGATTGTTTCGTCCATGGTG 59.906 50.000 12.58 6.00 33.57 4.17
325 391 2.346803 CGAGATTGTTTCGTCCATGGT 58.653 47.619 12.58 0.00 33.57 3.55
422 488 4.703897 GGCTTCCTTTTGCCTTTACTTTT 58.296 39.130 0.00 0.00 45.26 2.27
535 601 2.094390 TGGGTTGCTCATACGTACTGAC 60.094 50.000 0.00 0.37 0.00 3.51
542 608 1.750193 AATGGTGGGTTGCTCATACG 58.250 50.000 0.00 0.00 0.00 3.06
543 609 3.088532 TGAAATGGTGGGTTGCTCATAC 58.911 45.455 0.00 0.00 0.00 2.39
544 610 3.448093 TGAAATGGTGGGTTGCTCATA 57.552 42.857 0.00 0.00 0.00 2.15
545 611 2.307496 TGAAATGGTGGGTTGCTCAT 57.693 45.000 0.00 0.00 0.00 2.90
587 661 1.477377 GGGTGGGTTGGTCGTACTTTT 60.477 52.381 0.00 0.00 0.00 2.27
704 802 2.933906 GTCTCTATCTCTATCCGGCTCG 59.066 54.545 0.00 0.00 0.00 5.03
882 980 1.555075 CGGATTTCTGGACTTGGAGGA 59.445 52.381 0.00 0.00 0.00 3.71
915 1021 2.123640 GACGAGAGGGAGGGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
916 1022 1.454847 CAGACGAGAGGGAGGGAGG 60.455 68.421 0.00 0.00 0.00 4.30
917 1023 2.124693 GCAGACGAGAGGGAGGGAG 61.125 68.421 0.00 0.00 0.00 4.30
918 1024 2.043852 GCAGACGAGAGGGAGGGA 60.044 66.667 0.00 0.00 0.00 4.20
919 1025 2.363018 TGCAGACGAGAGGGAGGG 60.363 66.667 0.00 0.00 0.00 4.30
920 1026 2.716017 GGTGCAGACGAGAGGGAGG 61.716 68.421 0.00 0.00 0.00 4.30
921 1027 2.716017 GGGTGCAGACGAGAGGGAG 61.716 68.421 0.00 0.00 0.00 4.30
922 1028 2.680352 GGGTGCAGACGAGAGGGA 60.680 66.667 0.00 0.00 0.00 4.20
923 1029 4.135153 CGGGTGCAGACGAGAGGG 62.135 72.222 4.04 0.00 0.00 4.30
1259 1371 4.222847 CGGGCCGCTCTAGGGAAC 62.223 72.222 15.42 0.00 0.00 3.62
1396 1508 0.761802 GGGGATAGGAAGAGCACCAG 59.238 60.000 0.00 0.00 0.00 4.00
1733 1859 0.108992 GCACCCACATCATGCAGTTG 60.109 55.000 0.00 0.00 39.23 3.16
1841 1967 0.820871 CGGAGAAGGTGAGGAAGAGG 59.179 60.000 0.00 0.00 0.00 3.69
2111 2243 9.838339 ACCTACTGGACTAAAATCAATCAATAG 57.162 33.333 0.00 0.00 37.04 1.73
2125 2257 2.165167 CGACAACCACCTACTGGACTA 58.835 52.381 0.00 0.00 43.95 2.59
2130 2262 0.391597 ACACCGACAACCACCTACTG 59.608 55.000 0.00 0.00 0.00 2.74
2139 2283 1.732732 CGATCTCCTGACACCGACAAC 60.733 57.143 0.00 0.00 0.00 3.32
2191 2335 8.662781 TTTTCCTATGGTTATTCTCATTCGAG 57.337 34.615 0.00 0.00 40.98 4.04
2237 2381 5.123186 CAGGCGTTGGTCAATCAAATTAGTA 59.877 40.000 0.00 0.00 0.00 1.82
2238 2382 4.079253 AGGCGTTGGTCAATCAAATTAGT 58.921 39.130 0.00 0.00 0.00 2.24
2258 2402 0.108615 CAGAACGTACCCAGAGCAGG 60.109 60.000 0.00 0.00 0.00 4.85
2283 2434 3.904824 CGTGTACTCGCGTATTCTATTCC 59.095 47.826 5.77 0.00 41.80 3.01
2521 2674 8.093927 TGAACAAAAAGAACATGAGTTTTTCCT 58.906 29.630 0.00 0.00 38.30 3.36
2523 2676 9.906111 GATGAACAAAAAGAACATGAGTTTTTC 57.094 29.630 0.00 0.00 38.30 2.29
2654 2816 3.567478 TTTGTTTTGTTTGGGATGGGG 57.433 42.857 0.00 0.00 0.00 4.96
2687 2849 1.234615 AAGGAAACGACGGCATGTGG 61.235 55.000 0.00 0.00 0.00 4.17
2714 2876 9.525409 ACGTATTAACCAGATTATGAAGTACAC 57.475 33.333 0.00 0.00 0.00 2.90
2718 2881 9.745880 CTACACGTATTAACCAGATTATGAAGT 57.254 33.333 0.00 0.00 0.00 3.01
2749 2912 4.273969 CAGGCAGTAAAACGGAAACAACTA 59.726 41.667 0.00 0.00 0.00 2.24
2798 2961 9.442047 TCCATTTTACAGACAATTGTTTGTTTT 57.558 25.926 32.09 15.55 46.01 2.43
2867 3039 2.821546 TCTGAAAACACGGACACAGAG 58.178 47.619 0.00 0.00 32.04 3.35
2870 3042 4.439426 CCATTTTCTGAAAACACGGACACA 60.439 41.667 17.06 0.00 32.37 3.72
2880 3052 5.243730 GGTCTGGATCACCATTTTCTGAAAA 59.756 40.000 17.04 17.04 45.87 2.29
2932 3104 4.373116 GAGCGAGGCCACGGACAA 62.373 66.667 24.15 0.00 0.00 3.18
3383 3578 1.536418 AAGCAAAGAAAGGGCCCCC 60.536 57.895 21.43 8.44 0.00 5.40
3539 3742 0.695462 TGCTAGATGGGCCATGGAGT 60.695 55.000 26.77 8.12 0.00 3.85
3804 4016 6.725246 CCAACAGTAATTATTCATTCGGACC 58.275 40.000 0.00 0.00 0.00 4.46
3835 4047 0.251121 TTTGCCATCCCGACACACAT 60.251 50.000 0.00 0.00 0.00 3.21
3865 4077 7.985634 TTTTTCTCTTGGAATTTCAACGAAG 57.014 32.000 0.00 0.00 33.53 3.79
4067 4604 1.167851 CACACGCATTGATTGGGAGT 58.832 50.000 0.00 0.00 41.57 3.85
4088 4626 1.002087 GCGGACGGATAGATCCCAAAT 59.998 52.381 2.89 0.00 44.24 2.32
4153 4692 5.405571 CAGAATAGCACATGACGTAATACCC 59.594 44.000 0.00 0.00 0.00 3.69
4156 4695 6.156748 ACCAGAATAGCACATGACGTAATA 57.843 37.500 0.00 0.00 0.00 0.98
4157 4696 5.023533 ACCAGAATAGCACATGACGTAAT 57.976 39.130 0.00 0.00 0.00 1.89
4243 4792 9.044150 ACAAAACATAATCCAAGAAATGTGTTG 57.956 29.630 16.85 16.85 46.21 3.33
4264 4819 8.983724 CAGAAGTTTGTAACCAGAAAAACAAAA 58.016 29.630 1.44 0.00 41.85 2.44
4288 4843 0.734253 CGGAGAGCAACGGAGAACAG 60.734 60.000 0.00 0.00 0.00 3.16
4303 4858 1.472480 CCAATTTAACCCACAGCGGAG 59.528 52.381 0.00 0.00 36.56 4.63
4438 4993 3.950794 CTGGTCGGCCTTGCGCTTA 62.951 63.158 7.97 0.00 37.74 3.09
4547 5102 5.526115 CGCTTCAATCGGGAGTTAATAGTA 58.474 41.667 0.00 0.00 0.00 1.82
4548 5103 4.369182 CGCTTCAATCGGGAGTTAATAGT 58.631 43.478 0.00 0.00 0.00 2.12
4549 5104 3.184581 GCGCTTCAATCGGGAGTTAATAG 59.815 47.826 0.00 0.00 0.00 1.73
4688 5254 5.435291 AGGCATAAAGGAGACAAGATGAAG 58.565 41.667 0.00 0.00 0.00 3.02
4756 5323 2.824041 CGGATTCGCCAACCAGGG 60.824 66.667 0.00 0.00 38.09 4.45
4766 5333 3.659089 AACCAGGGTCGCGGATTCG 62.659 63.158 6.13 0.00 39.81 3.34
4767 5334 2.106683 CAACCAGGGTCGCGGATTC 61.107 63.158 6.13 0.00 0.00 2.52
4768 5335 2.046314 CAACCAGGGTCGCGGATT 60.046 61.111 6.13 0.00 0.00 3.01
4769 5336 4.096003 CCAACCAGGGTCGCGGAT 62.096 66.667 6.13 0.00 0.00 4.18
4774 5341 4.096003 ATCCGCCAACCAGGGTCG 62.096 66.667 0.00 0.00 38.09 4.79
4775 5342 2.124695 GATCCGCCAACCAGGGTC 60.125 66.667 0.00 0.00 38.09 4.46
4776 5343 2.933287 TGATCCGCCAACCAGGGT 60.933 61.111 0.00 0.00 38.09 4.34
4886 5453 4.332819 CCGGCCAAAACAAATACAAACAAA 59.667 37.500 2.24 0.00 0.00 2.83
4889 5456 2.803386 CCCGGCCAAAACAAATACAAAC 59.197 45.455 2.24 0.00 0.00 2.93
4890 5457 2.698797 TCCCGGCCAAAACAAATACAAA 59.301 40.909 2.24 0.00 0.00 2.83
4891 5458 2.317040 TCCCGGCCAAAACAAATACAA 58.683 42.857 2.24 0.00 0.00 2.41
4895 5462 3.169908 AGTATTCCCGGCCAAAACAAAT 58.830 40.909 2.24 0.00 0.00 2.32
4959 5534 1.201414 CGGTTGCACCCCTGATTAAAC 59.799 52.381 0.00 0.00 33.75 2.01
5107 5688 8.994207 CCATAGTGGAATCTCGTCAAAACGGA 62.994 46.154 0.00 0.00 44.27 4.69
5108 5689 6.918800 CCATAGTGGAATCTCGTCAAAACGG 61.919 48.000 0.00 0.00 44.27 4.44
5109 5690 4.032900 CCATAGTGGAATCTCGTCAAAACG 59.967 45.833 0.00 0.00 45.01 3.60
5110 5691 5.175859 TCCATAGTGGAATCTCGTCAAAAC 58.824 41.667 0.00 0.00 45.00 2.43
5111 5692 5.414789 TCCATAGTGGAATCTCGTCAAAA 57.585 39.130 0.00 0.00 45.00 2.44
5123 5704 0.606096 CGTGTGTGGTCCATAGTGGA 59.394 55.000 0.00 0.00 45.98 4.02
5124 5705 0.606096 TCGTGTGTGGTCCATAGTGG 59.394 55.000 0.00 0.00 39.43 4.00
5125 5706 2.448926 TTCGTGTGTGGTCCATAGTG 57.551 50.000 0.00 0.00 0.00 2.74
5126 5707 2.103432 TGTTTCGTGTGTGGTCCATAGT 59.897 45.455 0.00 0.00 0.00 2.12
5127 5708 2.761559 TGTTTCGTGTGTGGTCCATAG 58.238 47.619 0.00 0.00 0.00 2.23
5128 5709 2.912690 TGTTTCGTGTGTGGTCCATA 57.087 45.000 0.00 0.00 0.00 2.74
5129 5710 2.045561 TTGTTTCGTGTGTGGTCCAT 57.954 45.000 0.00 0.00 0.00 3.41
5130 5711 1.822506 TTTGTTTCGTGTGTGGTCCA 58.177 45.000 0.00 0.00 0.00 4.02
5131 5712 2.923605 TTTTGTTTCGTGTGTGGTCC 57.076 45.000 0.00 0.00 0.00 4.46
5132 5713 3.112580 CCATTTTGTTTCGTGTGTGGTC 58.887 45.455 0.00 0.00 0.00 4.02
5133 5714 2.755655 TCCATTTTGTTTCGTGTGTGGT 59.244 40.909 0.00 0.00 0.00 4.16
5134 5715 3.428746 TCCATTTTGTTTCGTGTGTGG 57.571 42.857 0.00 0.00 0.00 4.17
5135 5716 4.605968 TCATCCATTTTGTTTCGTGTGTG 58.394 39.130 0.00 0.00 0.00 3.82
5136 5717 4.909696 TCATCCATTTTGTTTCGTGTGT 57.090 36.364 0.00 0.00 0.00 3.72
5137 5718 6.151691 AGATTCATCCATTTTGTTTCGTGTG 58.848 36.000 0.00 0.00 0.00 3.82
5138 5719 6.331369 AGATTCATCCATTTTGTTTCGTGT 57.669 33.333 0.00 0.00 0.00 4.49
5139 5720 7.271223 GTGTAGATTCATCCATTTTGTTTCGTG 59.729 37.037 0.00 0.00 0.00 4.35
5140 5721 7.174946 AGTGTAGATTCATCCATTTTGTTTCGT 59.825 33.333 0.00 0.00 0.00 3.85
5141 5722 7.530010 AGTGTAGATTCATCCATTTTGTTTCG 58.470 34.615 0.00 0.00 0.00 3.46
5148 5729 9.807649 GCATTTTAAGTGTAGATTCATCCATTT 57.192 29.630 0.00 0.00 0.00 2.32
5149 5730 8.970020 TGCATTTTAAGTGTAGATTCATCCATT 58.030 29.630 0.00 0.00 0.00 3.16
5150 5731 8.523915 TGCATTTTAAGTGTAGATTCATCCAT 57.476 30.769 0.00 0.00 0.00 3.41
5151 5732 7.936496 TGCATTTTAAGTGTAGATTCATCCA 57.064 32.000 0.00 0.00 0.00 3.41
5152 5733 8.844244 AGATGCATTTTAAGTGTAGATTCATCC 58.156 33.333 0.00 0.00 0.00 3.51
5164 5745 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
5168 5749 8.830580 GCATACGGATGTATATAGATGCATTTT 58.169 33.333 9.90 0.00 38.38 1.82
5169 5750 7.986889 TGCATACGGATGTATATAGATGCATTT 59.013 33.333 9.90 0.00 38.38 2.32
5170 5751 7.500141 TGCATACGGATGTATATAGATGCATT 58.500 34.615 9.90 1.23 38.38 3.56
5171 5752 7.054491 TGCATACGGATGTATATAGATGCAT 57.946 36.000 9.90 0.00 40.68 3.96
5172 5753 6.096846 ACTGCATACGGATGTATATAGATGCA 59.903 38.462 9.90 7.54 39.28 3.96
5173 5754 6.507900 ACTGCATACGGATGTATATAGATGC 58.492 40.000 9.90 0.00 39.28 3.91
5174 5755 7.142021 GGACTGCATACGGATGTATATAGATG 58.858 42.308 9.90 0.00 39.28 2.90
5175 5756 6.833933 TGGACTGCATACGGATGTATATAGAT 59.166 38.462 9.90 0.00 39.28 1.98
5176 5757 6.184789 TGGACTGCATACGGATGTATATAGA 58.815 40.000 9.90 0.00 39.28 1.98
5177 5758 6.451064 TGGACTGCATACGGATGTATATAG 57.549 41.667 9.90 3.34 39.28 1.31
5178 5759 6.183360 CCATGGACTGCATACGGATGTATATA 60.183 42.308 5.56 0.00 39.28 0.86
5179 5760 5.395657 CCATGGACTGCATACGGATGTATAT 60.396 44.000 5.56 0.00 39.28 0.86
5180 5761 4.081697 CCATGGACTGCATACGGATGTATA 60.082 45.833 5.56 0.00 39.28 1.47
5181 5762 3.306989 CCATGGACTGCATACGGATGTAT 60.307 47.826 5.56 0.00 42.03 2.29
5182 5763 2.037121 CCATGGACTGCATACGGATGTA 59.963 50.000 5.56 3.37 35.30 2.29
5183 5764 1.202687 CCATGGACTGCATACGGATGT 60.203 52.381 5.56 0.00 35.30 3.06
5184 5765 1.202687 ACCATGGACTGCATACGGATG 60.203 52.381 21.47 2.22 36.02 3.51
5185 5766 1.131638 ACCATGGACTGCATACGGAT 58.868 50.000 21.47 0.00 0.00 4.18
5186 5767 0.177836 CACCATGGACTGCATACGGA 59.822 55.000 21.47 0.00 0.00 4.69
5187 5768 0.815213 CCACCATGGACTGCATACGG 60.815 60.000 21.47 0.38 40.96 4.02
5188 5769 0.177836 TCCACCATGGACTGCATACG 59.822 55.000 21.47 0.00 42.67 3.06
5197 5778 4.782691 TCTTTGTAGAGATTCCACCATGGA 59.217 41.667 21.47 0.00 46.61 3.41
5198 5779 4.878397 GTCTTTGTAGAGATTCCACCATGG 59.122 45.833 11.19 11.19 39.43 3.66
5199 5780 5.738909 AGTCTTTGTAGAGATTCCACCATG 58.261 41.667 0.00 0.00 0.00 3.66
5200 5781 6.380079 AAGTCTTTGTAGAGATTCCACCAT 57.620 37.500 0.00 0.00 0.00 3.55
5201 5782 5.825593 AAGTCTTTGTAGAGATTCCACCA 57.174 39.130 0.00 0.00 0.00 4.17
5214 5795 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
5215 5796 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
5216 5797 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
5217 5798 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
5218 5799 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
5219 5800 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
5220 5801 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
5221 5802 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
5222 5803 8.731591 ATTACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
5223 5804 9.827198 TTATTACTCCCTCCGTTCCTAAATATA 57.173 33.333 0.00 0.00 0.00 0.86
5224 5805 8.591940 GTTATTACTCCCTCCGTTCCTAAATAT 58.408 37.037 0.00 0.00 0.00 1.28
5225 5806 7.564660 TGTTATTACTCCCTCCGTTCCTAAATA 59.435 37.037 0.00 0.00 0.00 1.40
5226 5807 6.384886 TGTTATTACTCCCTCCGTTCCTAAAT 59.615 38.462 0.00 0.00 0.00 1.40
5227 5808 5.721000 TGTTATTACTCCCTCCGTTCCTAAA 59.279 40.000 0.00 0.00 0.00 1.85
5228 5809 5.271598 TGTTATTACTCCCTCCGTTCCTAA 58.728 41.667 0.00 0.00 0.00 2.69
5229 5810 4.870636 TGTTATTACTCCCTCCGTTCCTA 58.129 43.478 0.00 0.00 0.00 2.94
5230 5811 3.705072 CTGTTATTACTCCCTCCGTTCCT 59.295 47.826 0.00 0.00 0.00 3.36
5231 5812 3.450096 ACTGTTATTACTCCCTCCGTTCC 59.550 47.826 0.00 0.00 0.00 3.62
5232 5813 4.081807 ACACTGTTATTACTCCCTCCGTTC 60.082 45.833 0.00 0.00 0.00 3.95
5233 5814 3.836562 ACACTGTTATTACTCCCTCCGTT 59.163 43.478 0.00 0.00 0.00 4.44
5234 5815 3.194968 CACACTGTTATTACTCCCTCCGT 59.805 47.826 0.00 0.00 0.00 4.69
5235 5816 3.782046 CACACTGTTATTACTCCCTCCG 58.218 50.000 0.00 0.00 0.00 4.63
5236 5817 3.197983 AGCACACTGTTATTACTCCCTCC 59.802 47.826 0.00 0.00 0.00 4.30
5237 5818 4.473477 AGCACACTGTTATTACTCCCTC 57.527 45.455 0.00 0.00 0.00 4.30
5238 5819 6.368779 TTTAGCACACTGTTATTACTCCCT 57.631 37.500 0.00 0.00 0.00 4.20
5239 5820 6.598064 ACATTTAGCACACTGTTATTACTCCC 59.402 38.462 0.00 0.00 0.00 4.30
5240 5821 7.611213 ACATTTAGCACACTGTTATTACTCC 57.389 36.000 0.00 0.00 0.00 3.85
5242 5823 9.326413 GGATACATTTAGCACACTGTTATTACT 57.674 33.333 0.00 0.00 0.00 2.24
5266 5847 2.127065 TGGGCCCCTCAGATTGGA 59.873 61.111 22.27 0.00 0.00 3.53
5282 5863 6.308524 ACATAAATTGTGAAATCATGCACGTG 59.691 34.615 12.28 12.28 37.11 4.49
5403 5987 0.880278 TCGTTGTGTGGAAGCTCAGC 60.880 55.000 0.00 0.00 0.00 4.26
5422 6006 3.689649 GTCACGTTGGAGATGCCTTAATT 59.310 43.478 0.00 0.00 37.63 1.40
5423 6007 3.055094 AGTCACGTTGGAGATGCCTTAAT 60.055 43.478 0.00 0.00 37.63 1.40
5427 6011 0.247736 GAGTCACGTTGGAGATGCCT 59.752 55.000 0.00 0.00 37.63 4.75
5445 6029 4.585162 ACAAATATGGTGTCCGTTTTTGGA 59.415 37.500 19.67 0.00 41.97 3.53


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

AutoCloner maintained by Alex Coulton.