Multiple sequence alignment - TraesCS4D01G218800

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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 TraesCS4D01G218800 chr4D 100.000 9620 0 0 1 9620 374120096 374110477 0.000000e+00 17765.0
1 TraesCS4D01G218800 chr4D 97.778 45 0 1 3586 3629 281196158 281196202 1.040000e-09 76.8
2 TraesCS4D01G218800 chr4A 94.764 5309 189 34 3970 9230 90318795 90324062 0.000000e+00 8181.0
3 TraesCS4D01G218800 chr4A 94.809 3333 88 29 680 3968 90315461 90318752 0.000000e+00 5118.0
4 TraesCS4D01G218800 chr4A 86.244 647 74 4 1 632 90314668 90315314 0.000000e+00 688.0
5 TraesCS4D01G218800 chr4A 90.258 349 19 4 9273 9618 90324062 90324398 8.870000e-120 442.0
6 TraesCS4D01G218800 chr4A 88.288 333 31 8 5518 5849 277904944 277905269 9.060000e-105 392.0
7 TraesCS4D01G218800 chr4A 88.060 335 34 6 5520 5852 626723072 626722742 9.060000e-105 392.0
8 TraesCS4D01G218800 chr4A 85.448 268 29 9 6084 6345 277905508 277905771 4.430000e-68 270.0
9 TraesCS4D01G218800 chr4A 89.286 168 16 2 6154 6319 314686736 314686903 9.790000e-50 209.0
10 TraesCS4D01G218800 chr4A 91.216 148 8 5 3820 3965 200094843 200094987 7.620000e-46 196.0
11 TraesCS4D01G218800 chr4A 92.199 141 7 4 3828 3965 626312747 626312886 7.620000e-46 196.0
12 TraesCS4D01G218800 chr4A 86.188 181 22 3 6166 6344 626722456 626722277 9.860000e-45 193.0
13 TraesCS4D01G218800 chr4A 92.647 68 4 1 9393 9460 90324093 90324159 7.950000e-16 97.1
14 TraesCS4D01G218800 chr4A 97.826 46 1 0 3584 3629 360655661 360655706 8.010000e-11 80.5
15 TraesCS4D01G218800 chr4A 93.333 45 2 1 3586 3629 236156486 236156530 2.240000e-06 65.8
16 TraesCS4D01G218800 chr4B 95.011 5091 162 36 3968 9026 460336345 460331315 0.000000e+00 7910.0
17 TraesCS4D01G218800 chr4B 94.560 1636 52 18 746 2372 460339608 460338001 0.000000e+00 2494.0
18 TraesCS4D01G218800 chr4B 93.407 1623 37 19 2373 3968 460337958 460336379 0.000000e+00 2340.0
19 TraesCS4D01G218800 chr4B 81.011 653 95 14 45 681 460345419 460344780 8.680000e-135 492.0
20 TraesCS4D01G218800 chr4B 86.926 283 26 10 5579 5859 295687635 295687362 3.370000e-79 307.0
21 TraesCS4D01G218800 chr4B 91.195 159 12 1 9026 9182 460330690 460330532 2.100000e-51 215.0
22 TraesCS4D01G218800 chr4B 85.294 204 29 1 6098 6300 295687115 295686912 9.790000e-50 209.0
23 TraesCS4D01G218800 chr4B 82.143 252 16 7 9393 9616 460329972 460329722 1.280000e-43 189.0
24 TraesCS4D01G218800 chr4B 95.455 66 3 0 9276 9341 460330380 460330315 1.320000e-18 106.0
25 TraesCS4D01G218800 chr7B 91.637 837 44 15 5516 6346 693911422 693912238 0.000000e+00 1134.0
26 TraesCS4D01G218800 chr7B 95.652 46 2 0 3584 3629 366050618 366050663 3.730000e-09 75.0
27 TraesCS4D01G218800 chr5D 87.834 337 35 6 5518 5852 542428666 542428998 3.260000e-104 390.0
28 TraesCS4D01G218800 chr1B 87.768 327 35 5 5517 5841 636820148 636819825 2.540000e-100 377.0
29 TraesCS4D01G218800 chr1B 82.335 334 42 8 6020 6346 636819650 636819327 3.420000e-69 274.0
30 TraesCS4D01G218800 chr5B 87.164 335 34 8 5519 5849 484885974 484885645 1.180000e-98 372.0
31 TraesCS4D01G218800 chr5B 80.370 433 59 13 5935 6343 484885574 484885144 1.210000e-78 305.0
32 TraesCS4D01G218800 chrUn 93.007 143 7 3 3828 3968 398232359 398232500 1.270000e-48 206.0
33 TraesCS4D01G218800 chrUn 92.361 144 7 4 3828 3968 231459831 231459689 1.640000e-47 202.0
34 TraesCS4D01G218800 chrUn 92.361 144 7 4 3828 3968 275537077 275536935 1.640000e-47 202.0
35 TraesCS4D01G218800 chr7A 92.361 144 7 4 3828 3968 19561541 19561683 1.640000e-47 202.0
36 TraesCS4D01G218800 chr7A 91.667 144 8 4 3828 3968 726414025 726413883 7.620000e-46 196.0
37 TraesCS4D01G218800 chr7D 90.728 151 11 3 3820 3968 168778062 168777913 2.120000e-46 198.0
38 TraesCS4D01G218800 chr7D 95.745 47 1 1 3584 3629 90603322 90603276 3.730000e-09 75.0
39 TraesCS4D01G218800 chr7D 93.617 47 2 1 3584 3629 316584223 316584177 1.730000e-07 69.4
40 TraesCS4D01G218800 chr6B 91.667 144 8 4 3828 3968 151878991 151878849 7.620000e-46 196.0
41 TraesCS4D01G218800 chr6D 93.750 48 2 1 3584 3630 240796719 240796672 4.820000e-08 71.3


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 TraesCS4D01G218800 chr4D 374110477 374120096 9619 True 17765.00 17765 100.000000 1 9620 1 chr4D.!!$R1 9619
1 TraesCS4D01G218800 chr4A 90314668 90324398 9730 False 2905.22 8181 91.744400 1 9618 5 chr4A.!!$F6 9617
2 TraesCS4D01G218800 chr4A 277904944 277905771 827 False 331.00 392 86.868000 5518 6345 2 chr4A.!!$F7 827
3 TraesCS4D01G218800 chr4A 626722277 626723072 795 True 292.50 392 87.124000 5520 6344 2 chr4A.!!$R1 824
4 TraesCS4D01G218800 chr4B 460329722 460339608 9886 True 2209.00 7910 91.961833 746 9616 6 chr4B.!!$R3 8870
5 TraesCS4D01G218800 chr4B 460344780 460345419 639 True 492.00 492 81.011000 45 681 1 chr4B.!!$R1 636
6 TraesCS4D01G218800 chr4B 295686912 295687635 723 True 258.00 307 86.110000 5579 6300 2 chr4B.!!$R2 721
7 TraesCS4D01G218800 chr7B 693911422 693912238 816 False 1134.00 1134 91.637000 5516 6346 1 chr7B.!!$F2 830
8 TraesCS4D01G218800 chr1B 636819327 636820148 821 True 325.50 377 85.051500 5517 6346 2 chr1B.!!$R1 829
9 TraesCS4D01G218800 chr5B 484885144 484885974 830 True 338.50 372 83.767000 5519 6343 2 chr5B.!!$R1 824

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
684 783 0.110238 CAACAATCGGACGTGCCAAG 60.110 55.0 0.00 0.00 35.94 3.61 F
689 806 0.250124 ATCGGACGTGCCAAGTTTCA 60.250 50.0 0.00 0.00 35.94 2.69 F
1456 1578 1.045350 CCTCTCCGGAGCTGGAATGA 61.045 60.0 28.46 10.76 37.64 2.57 F
2669 2863 0.039618 ATTTGGACCGGCTGGAACAT 59.960 50.0 21.41 0.00 38.20 2.71 F
3502 3717 1.059098 TCACCAGTGATCCTGTTGCT 58.941 50.0 0.00 0.00 39.74 3.91 F
4857 5151 0.106708 ACTGTGTGTTGTGCCTCGAT 59.893 50.0 0.00 0.00 0.00 3.59 F
5759 6071 0.460284 ATTTGGCTGTACCTCGAGCG 60.460 55.0 6.99 2.92 40.22 5.03 F
6800 7323 0.389391 ATCTTGGGTATGAGGTCGCG 59.611 55.0 0.00 0.00 0.00 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1972 3.005684 TGCTGCAACATTGGAGGTAAAAG 59.994 43.478 14.07 0.00 45.44 2.27 R
2406 2596 4.717233 AAGCAATGACATAAATCGGCAA 57.283 36.364 0.00 0.00 0.00 4.52 R
3307 3501 1.080995 GCAAGTCTAGCAGCGGACAG 61.081 60.000 18.98 13.44 35.18 3.51 R
3875 4095 1.216178 CCCCCTCAAATGCAAAGCG 59.784 57.895 0.00 0.00 0.00 4.68 R
5363 5657 1.207089 TGCTCTTACAAGCTACGGCAT 59.793 47.619 0.00 0.00 42.94 4.40 R
5948 6272 1.169661 CGTGTAAGTGGCTGCCCAAA 61.170 55.000 17.53 0.00 44.33 3.28 R
7714 8239 1.849039 AGATCAAGGGGAAGTCCATGG 59.151 52.381 4.97 4.97 37.91 3.66 R
8642 9195 0.379669 CCTCAACCAATCGCATCTGC 59.620 55.000 0.00 0.00 37.78 4.26 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
140 141 6.140377 TGAAAAATCTTTTGGGAGGTAACCT 58.860 36.000 0.00 0.00 36.03 3.50
155 156 4.842380 AGGTAACCTTCCTAGCACAAGTAA 59.158 41.667 0.00 0.00 33.04 2.24
156 157 5.308759 AGGTAACCTTCCTAGCACAAGTAAA 59.691 40.000 0.00 0.00 33.04 2.01
157 158 5.999600 GGTAACCTTCCTAGCACAAGTAAAA 59.000 40.000 0.00 0.00 0.00 1.52
166 167 8.685838 TCCTAGCACAAGTAAAAAGTAACAAT 57.314 30.769 0.00 0.00 0.00 2.71
168 169 8.349983 CCTAGCACAAGTAAAAAGTAACAATGT 58.650 33.333 0.00 0.00 0.00 2.71
169 170 7.985634 AGCACAAGTAAAAAGTAACAATGTG 57.014 32.000 0.00 0.00 38.07 3.21
188 190 1.070105 GTGCGGTCACAACCCACTA 59.930 57.895 8.20 0.00 43.21 2.74
346 348 1.377987 ATGGCGGTTTATGGCGTGT 60.378 52.632 0.00 0.00 34.03 4.49
403 405 4.395854 TGTGCGATGCTCTAAATGAATGTT 59.604 37.500 0.00 0.00 0.00 2.71
418 420 4.196193 TGAATGTTTTGAGTCAACGAGGT 58.804 39.130 4.68 0.00 0.00 3.85
420 422 5.995282 TGAATGTTTTGAGTCAACGAGGTAT 59.005 36.000 4.68 0.00 0.00 2.73
437 439 2.290641 GGTATGACAAACGATGATGGCC 59.709 50.000 0.00 0.00 0.00 5.36
499 515 2.355310 CCTATTCGTGGGGTGCTAAACA 60.355 50.000 0.00 0.00 0.00 2.83
518 534 2.555325 ACATGTCTGGTGCTGAATGTTG 59.445 45.455 0.00 0.00 0.00 3.33
540 556 8.181573 TGTTGATTTTATTGATTAGCGGTCTTC 58.818 33.333 0.00 0.00 0.00 2.87
559 575 1.518056 CGCTTTGGTGGCATGAGTGT 61.518 55.000 0.00 0.00 0.00 3.55
574 590 2.076863 GAGTGTTGCTAGCAAATCCGT 58.923 47.619 30.83 14.25 37.70 4.69
576 592 3.262420 AGTGTTGCTAGCAAATCCGTAG 58.738 45.455 30.83 0.00 37.70 3.51
577 593 2.006888 TGTTGCTAGCAAATCCGTAGC 58.993 47.619 30.83 16.32 39.76 3.58
603 620 2.223479 GGCACTGTCGTTGTTGATTTGT 60.223 45.455 0.00 0.00 0.00 2.83
623 640 4.469657 TGTTTGGTTGCATTCTAGGTCTT 58.530 39.130 0.00 0.00 0.00 3.01
624 641 5.626142 TGTTTGGTTGCATTCTAGGTCTTA 58.374 37.500 0.00 0.00 0.00 2.10
640 739 9.947433 TCTAGGTCTTATTTTTCGGTTATCAAA 57.053 29.630 0.00 0.00 0.00 2.69
654 753 6.040729 TCGGTTATCAAAGATGTTATACGGGA 59.959 38.462 0.00 0.00 0.00 5.14
660 759 5.424252 TCAAAGATGTTATACGGGAGTCCTT 59.576 40.000 9.58 0.00 45.66 3.36
681 780 0.802494 AATCAACAATCGGACGTGCC 59.198 50.000 0.00 0.00 0.00 5.01
682 781 0.321210 ATCAACAATCGGACGTGCCA 60.321 50.000 0.00 0.00 35.94 4.92
683 782 0.533085 TCAACAATCGGACGTGCCAA 60.533 50.000 0.00 0.00 35.94 4.52
684 783 0.110238 CAACAATCGGACGTGCCAAG 60.110 55.000 0.00 0.00 35.94 3.61
689 806 0.250124 ATCGGACGTGCCAAGTTTCA 60.250 50.000 0.00 0.00 35.94 2.69
733 850 7.446319 TCACTCTGATTTATGAAATGGCATAGG 59.554 37.037 0.00 0.00 32.75 2.57
734 851 7.230108 CACTCTGATTTATGAAATGGCATAGGT 59.770 37.037 0.00 0.00 32.75 3.08
758 875 5.303165 TCGCTCTCTCACGAGGTTTATATA 58.697 41.667 0.00 0.00 37.86 0.86
879 999 1.660575 CGATATCCACGTCACCGCC 60.661 63.158 0.00 0.00 37.70 6.13
931 1052 1.074090 TTGACCCCCACCTGTCAGA 60.074 57.895 0.00 0.00 42.05 3.27
1399 1521 3.456365 AGATCGACGCTGCAGCCT 61.456 61.111 32.07 21.68 37.91 4.58
1456 1578 1.045350 CCTCTCCGGAGCTGGAATGA 61.045 60.000 28.46 10.76 37.64 2.57
1645 1767 2.230130 TCTGCGATTGGGGGATTTTT 57.770 45.000 0.00 0.00 0.00 1.94
1766 1888 8.483307 TCAGTGTTTTAGAACGTTTTTAGTCT 57.517 30.769 0.46 0.00 38.65 3.24
1774 1896 6.203808 AGAACGTTTTTAGTCTTTGGCTTT 57.796 33.333 0.46 0.00 0.00 3.51
2210 2333 4.376514 GGTTTGTTTTGTTGTTGGTGTTCG 60.377 41.667 0.00 0.00 0.00 3.95
2265 2388 6.944234 ATGTTCCTACTATAAAAAGCTGCC 57.056 37.500 0.00 0.00 0.00 4.85
2321 2468 4.481463 GGATATCAACCGTTGTGTTTTGG 58.519 43.478 11.01 0.00 0.00 3.28
2333 2480 5.233050 CGTTGTGTTTTGGTTGCATGAAATA 59.767 36.000 0.00 0.00 0.00 1.40
2360 2507 6.849151 AGGAAAAGGGTATAGTGTTTTCTGT 58.151 36.000 10.78 1.34 38.43 3.41
2496 2686 7.092716 ACTTTATTGAAACACATGAATGCCTC 58.907 34.615 0.00 0.00 0.00 4.70
2500 2690 3.253921 TGAAACACATGAATGCCTCACTG 59.746 43.478 0.00 0.00 36.69 3.66
2503 2693 2.224597 ACACATGAATGCCTCACTGTCA 60.225 45.455 0.00 0.00 36.69 3.58
2543 2733 5.012561 AGTCTAGTCTGAAATCTGGTGCTTT 59.987 40.000 0.00 0.00 0.00 3.51
2669 2863 0.039618 ATTTGGACCGGCTGGAACAT 59.960 50.000 21.41 0.00 38.20 2.71
2684 2878 3.068024 TGGAACATGTTTGAGTTTGGCTC 59.932 43.478 13.36 0.00 44.36 4.70
2685 2879 3.319122 GGAACATGTTTGAGTTTGGCTCT 59.681 43.478 13.36 0.00 44.41 4.09
3307 3501 1.166531 AAGCTTGTTGCCGTGGACTC 61.167 55.000 0.00 0.00 44.23 3.36
3386 3581 5.581126 TTGCTGCTATCTTTGTTATTGGG 57.419 39.130 0.00 0.00 0.00 4.12
3448 3643 9.988350 CTGTTTTGGTAAATTATACTGCTACAG 57.012 33.333 0.00 0.00 37.52 2.74
3502 3717 1.059098 TCACCAGTGATCCTGTTGCT 58.941 50.000 0.00 0.00 39.74 3.91
3508 3723 1.421268 AGTGATCCTGTTGCTGTGGAA 59.579 47.619 0.00 0.00 33.20 3.53
3645 3862 1.273759 TGTCCTGATCTGCTTCAGCT 58.726 50.000 0.00 0.00 41.50 4.24
3736 3954 3.711086 TGAAGCTAGATTCTCGTGATGC 58.289 45.455 20.62 0.00 0.00 3.91
3814 4032 3.743521 TGACTCTTGATGGTGTTCCTTG 58.256 45.455 0.00 0.00 34.23 3.61
3822 4040 3.444742 TGATGGTGTTCCTTGCATTGATC 59.555 43.478 0.00 0.00 34.23 2.92
3826 4044 3.444742 GGTGTTCCTTGCATTGATCATCA 59.555 43.478 0.00 0.00 0.00 3.07
3827 4045 4.098960 GGTGTTCCTTGCATTGATCATCAT 59.901 41.667 0.00 0.00 0.00 2.45
3828 4046 5.300034 GGTGTTCCTTGCATTGATCATCATA 59.700 40.000 0.00 0.00 0.00 2.15
3829 4047 6.015688 GGTGTTCCTTGCATTGATCATCATAT 60.016 38.462 0.00 0.00 0.00 1.78
3882 4102 2.473530 TGCTATTGCATACGCTTTGC 57.526 45.000 0.00 0.00 45.31 3.68
3889 4109 2.866198 TGCATACGCTTTGCATTTGAG 58.134 42.857 3.66 0.00 44.73 3.02
3890 4110 2.187707 GCATACGCTTTGCATTTGAGG 58.812 47.619 0.00 0.00 39.90 3.86
4012 4276 9.856162 GTAACCATTAAAACAATCCCTATCCTA 57.144 33.333 0.00 0.00 0.00 2.94
4033 4297 7.041721 TCCTAGTATTGCTGATGTGTTAACAG 58.958 38.462 8.98 0.00 40.39 3.16
4087 4351 8.612619 GTTAGGACAATGGTTTAGTATCACATG 58.387 37.037 0.00 0.00 0.00 3.21
4259 4523 1.873591 GACAATGTTCCGCAGTTCTGT 59.126 47.619 1.78 0.00 0.00 3.41
4615 4893 5.036737 CCAAAAGCTATTTATCAAGTGGCG 58.963 41.667 0.00 0.00 0.00 5.69
4806 5089 1.593196 TGAGCCATGCGTAATTAGGC 58.407 50.000 20.54 20.54 45.54 3.93
4807 5090 0.875059 GAGCCATGCGTAATTAGGCC 59.125 55.000 23.42 10.80 46.35 5.19
4808 5091 0.182537 AGCCATGCGTAATTAGGCCA 59.817 50.000 23.42 13.88 46.35 5.36
4809 5092 0.310854 GCCATGCGTAATTAGGCCAC 59.689 55.000 23.42 9.51 39.42 5.01
4810 5093 0.951558 CCATGCGTAATTAGGCCACC 59.048 55.000 23.42 1.47 36.33 4.61
4811 5094 1.674359 CATGCGTAATTAGGCCACCA 58.326 50.000 23.42 8.65 36.33 4.17
4812 5095 2.229792 CATGCGTAATTAGGCCACCAT 58.770 47.619 23.42 10.38 36.33 3.55
4813 5096 3.407698 CATGCGTAATTAGGCCACCATA 58.592 45.455 23.42 7.68 36.33 2.74
4814 5097 3.120321 TGCGTAATTAGGCCACCATAG 57.880 47.619 23.42 0.00 36.33 2.23
4815 5098 1.804748 GCGTAATTAGGCCACCATAGC 59.195 52.381 17.40 0.00 0.00 2.97
4816 5099 2.808933 GCGTAATTAGGCCACCATAGCA 60.809 50.000 17.40 0.00 0.00 3.49
4857 5151 0.106708 ACTGTGTGTTGTGCCTCGAT 59.893 50.000 0.00 0.00 0.00 3.59
5089 5383 5.521010 TGTACTGAGTAACCAAGTGTTTTCG 59.479 40.000 0.00 0.00 38.42 3.46
5254 5548 7.180322 TGATGCCAAAACATATAAACCACAT 57.820 32.000 0.00 0.00 0.00 3.21
5363 5657 5.771666 AGCAAAGAATCTGATTTGGAACTCA 59.228 36.000 4.11 0.00 36.99 3.41
5367 5661 4.643784 AGAATCTGATTTGGAACTCATGCC 59.356 41.667 4.11 0.00 0.00 4.40
5384 5678 1.001520 TGCCGTAGCTTGTAAGAGCAA 59.998 47.619 0.00 0.00 45.12 3.91
5538 5837 0.534873 GGTGTGTTTGGTTTGTGCCT 59.465 50.000 0.00 0.00 0.00 4.75
5642 5941 5.736951 AGCCAATGTACTTGCCAAAATTA 57.263 34.783 0.00 0.00 33.20 1.40
5690 5993 3.479370 GCCACTAGCTGAGTTGCG 58.521 61.111 0.00 0.00 37.11 4.85
5759 6071 0.460284 ATTTGGCTGTACCTCGAGCG 60.460 55.000 6.99 2.92 40.22 5.03
5959 6283 3.399440 CAAAACTATTTTGGGCAGCCA 57.601 42.857 15.19 0.00 44.75 4.75
6061 6405 5.412594 CACATAGCTACCCATGCGATTAATT 59.587 40.000 0.00 0.00 35.28 1.40
6130 6482 2.595124 AAACCAAAAACGGAGCAAGG 57.405 45.000 0.00 0.00 0.00 3.61
6144 6497 1.635487 AGCAAGGCCCACATAAAGAGA 59.365 47.619 0.00 0.00 0.00 3.10
6386 6909 7.692460 TGTCATCTTTATGTCTGCTTGAATT 57.308 32.000 0.00 0.00 34.50 2.17
6420 6943 8.613482 GTCTATTAATTAAAGAAGTGGCCTGTC 58.387 37.037 3.32 0.00 0.00 3.51
6513 7036 9.699703 GTTGTTTCTGTAGAGAAAGATAGAAGT 57.300 33.333 14.89 0.00 46.63 3.01
6599 7122 8.657074 TCTGTTATGATACAAATAGGGAAACG 57.343 34.615 0.00 0.00 0.00 3.60
6797 7320 2.224402 GGCAGATCTTGGGTATGAGGTC 60.224 54.545 0.00 0.00 0.00 3.85
6800 7323 0.389391 ATCTTGGGTATGAGGTCGCG 59.611 55.000 0.00 0.00 0.00 5.87
6996 7519 1.408266 GCCGGGTATGTGAAATGGTCT 60.408 52.381 2.18 0.00 0.00 3.85
7083 7606 8.462016 CAGGCTTCTGCTAAAATTACTTAACAT 58.538 33.333 0.00 0.00 39.59 2.71
7108 7631 3.129113 TCACATCAAGCACCATATGTTGC 59.871 43.478 16.81 16.81 30.32 4.17
7112 7635 2.093890 CAAGCACCATATGTTGCAGGA 58.906 47.619 24.88 0.00 0.00 3.86
7113 7636 2.492881 CAAGCACCATATGTTGCAGGAA 59.507 45.455 24.88 0.00 0.00 3.36
7114 7637 3.022557 AGCACCATATGTTGCAGGAAT 57.977 42.857 24.88 3.22 0.00 3.01
7115 7638 3.368248 AGCACCATATGTTGCAGGAATT 58.632 40.909 24.88 2.51 0.00 2.17
7247 7772 8.382875 GGTTTGTGTTCTGAATTTTGAAAAGAG 58.617 33.333 0.00 0.00 0.00 2.85
7295 7820 2.168936 AGCCATATGTTTGCACCCAATG 59.831 45.455 1.24 0.00 0.00 2.82
7396 7921 6.833933 AGACAACTTCTCCAAAACCACTATTT 59.166 34.615 0.00 0.00 0.00 1.40
7397 7922 7.342026 AGACAACTTCTCCAAAACCACTATTTT 59.658 33.333 0.00 0.00 31.87 1.82
7516 8041 7.721402 TGGTTTCTGCTTCTAAATTTGCTTTA 58.279 30.769 0.00 0.00 0.00 1.85
7545 8070 0.412244 AGGTACTAGGGGACTGTGCA 59.588 55.000 0.77 0.00 43.88 4.57
7553 8078 1.214062 GGGACTGTGCACTCTCTCG 59.786 63.158 19.41 2.17 0.00 4.04
7554 8079 1.244697 GGGACTGTGCACTCTCTCGA 61.245 60.000 19.41 0.00 0.00 4.04
7633 8158 0.539901 TAGGGAGGGACTATGAGCGC 60.540 60.000 0.00 0.00 41.55 5.92
7889 8414 4.965814 TCTCTTTGTATCATCCATGGCTC 58.034 43.478 6.96 0.00 0.00 4.70
7914 8439 7.119699 TCAGTTGCATACAAGAAATAGGAAGTG 59.880 37.037 0.00 0.00 36.16 3.16
7929 8454 5.662674 AGGAAGTGTCTGTATAGTTCACC 57.337 43.478 11.36 0.00 33.73 4.02
7976 8501 6.245408 TCCTTGTATGGTAATTTCTGTTGCT 58.755 36.000 0.00 0.00 0.00 3.91
7977 8502 6.150976 TCCTTGTATGGTAATTTCTGTTGCTG 59.849 38.462 0.00 0.00 0.00 4.41
7978 8503 5.309323 TGTATGGTAATTTCTGTTGCTGC 57.691 39.130 0.00 0.00 0.00 5.25
8026 8552 3.611025 TGTTTTCCTGGTCCATTTCCT 57.389 42.857 0.00 0.00 0.00 3.36
8027 8553 3.230134 TGTTTTCCTGGTCCATTTCCTG 58.770 45.455 0.00 0.00 0.00 3.86
8053 8579 2.163815 CTCCCTGCTGCTCATCTTTTTG 59.836 50.000 0.00 0.00 0.00 2.44
8055 8581 1.891150 CCTGCTGCTCATCTTTTTGGT 59.109 47.619 0.00 0.00 0.00 3.67
8084 8613 2.945668 GTTCCCACTGGTTGCTCATATC 59.054 50.000 0.00 0.00 0.00 1.63
8207 8738 8.691661 TCTAAGCTTTTGATTTCTTTACCACT 57.308 30.769 3.20 0.00 0.00 4.00
8218 8749 8.095169 TGATTTCTTTACCACTTCTAGTTCTCC 58.905 37.037 0.00 0.00 0.00 3.71
8268 8799 5.744171 AGATTGACACTACATATGCCAACA 58.256 37.500 1.58 0.00 0.00 3.33
8326 8857 4.700213 TCTGCCTTTTGTTCTTACTATGCC 59.300 41.667 0.00 0.00 0.00 4.40
8327 8858 3.438781 TGCCTTTTGTTCTTACTATGCCG 59.561 43.478 0.00 0.00 0.00 5.69
8328 8859 3.730963 GCCTTTTGTTCTTACTATGCCGC 60.731 47.826 0.00 0.00 0.00 6.53
8330 8861 1.647346 TTGTTCTTACTATGCCGCCG 58.353 50.000 0.00 0.00 0.00 6.46
8331 8862 0.533491 TGTTCTTACTATGCCGCCGT 59.467 50.000 0.00 0.00 0.00 5.68
8332 8863 1.750206 TGTTCTTACTATGCCGCCGTA 59.250 47.619 0.00 0.00 0.00 4.02
8333 8864 2.363038 TGTTCTTACTATGCCGCCGTAT 59.637 45.455 0.00 0.00 0.00 3.06
8334 8865 3.181473 TGTTCTTACTATGCCGCCGTATT 60.181 43.478 0.00 0.00 0.00 1.89
8335 8866 3.738830 TCTTACTATGCCGCCGTATTT 57.261 42.857 0.00 0.00 0.00 1.40
8336 8867 3.386486 TCTTACTATGCCGCCGTATTTG 58.614 45.455 0.00 0.00 0.00 2.32
8337 8868 2.894763 TACTATGCCGCCGTATTTGT 57.105 45.000 0.00 0.00 0.00 2.83
8338 8869 2.894763 ACTATGCCGCCGTATTTGTA 57.105 45.000 0.00 0.00 0.00 2.41
8339 8870 3.396260 ACTATGCCGCCGTATTTGTAT 57.604 42.857 0.00 0.00 0.00 2.29
8340 8871 3.323243 ACTATGCCGCCGTATTTGTATC 58.677 45.455 0.00 0.00 0.00 2.24
8341 8872 2.248280 ATGCCGCCGTATTTGTATCA 57.752 45.000 0.00 0.00 0.00 2.15
8342 8873 2.248280 TGCCGCCGTATTTGTATCAT 57.752 45.000 0.00 0.00 0.00 2.45
8343 8874 2.139917 TGCCGCCGTATTTGTATCATC 58.860 47.619 0.00 0.00 0.00 2.92
8344 8875 2.139917 GCCGCCGTATTTGTATCATCA 58.860 47.619 0.00 0.00 0.00 3.07
8345 8876 2.742053 GCCGCCGTATTTGTATCATCAT 59.258 45.455 0.00 0.00 0.00 2.45
8346 8877 3.181520 GCCGCCGTATTTGTATCATCATC 60.182 47.826 0.00 0.00 0.00 2.92
8347 8878 3.993736 CCGCCGTATTTGTATCATCATCA 59.006 43.478 0.00 0.00 0.00 3.07
8348 8879 4.631377 CCGCCGTATTTGTATCATCATCAT 59.369 41.667 0.00 0.00 0.00 2.45
8349 8880 5.446340 CCGCCGTATTTGTATCATCATCATG 60.446 44.000 0.00 0.00 0.00 3.07
8350 8881 5.446340 CGCCGTATTTGTATCATCATCATGG 60.446 44.000 0.00 0.00 0.00 3.66
8351 8882 5.412594 GCCGTATTTGTATCATCATCATGGT 59.587 40.000 0.00 0.00 0.00 3.55
8352 8883 6.402550 GCCGTATTTGTATCATCATCATGGTC 60.403 42.308 0.00 0.00 0.00 4.02
8353 8884 6.650390 CCGTATTTGTATCATCATCATGGTCA 59.350 38.462 0.00 0.00 0.00 4.02
8354 8885 7.148523 CCGTATTTGTATCATCATCATGGTCAG 60.149 40.741 0.00 0.00 0.00 3.51
8369 8922 5.355071 TCATGGTCAGATTGAGTATTGCAAC 59.645 40.000 0.00 0.00 0.00 4.17
8410 8963 5.045869 ACTCCTTGCAGTTGGTAGCTAAATA 60.046 40.000 0.00 0.00 0.00 1.40
8487 9040 2.649312 TGAGGAATGGGTGGAAGATGTT 59.351 45.455 0.00 0.00 0.00 2.71
8638 9191 4.529731 GCCAAGATGAGGGGCCCC 62.530 72.222 35.90 35.90 41.90 5.80
8648 9201 2.158810 AGGGGCCCCTATGCAGATG 61.159 63.158 43.85 0.00 46.14 2.90
8649 9202 2.282745 GGGCCCCTATGCAGATGC 60.283 66.667 12.23 0.00 42.50 3.91
8942 9500 4.013728 TGTGCCTGTAAAAGTGTTGAAGT 58.986 39.130 0.00 0.00 0.00 3.01
8996 9554 2.613977 GCTAGTTCTGATGGTGTGTGCT 60.614 50.000 0.00 0.00 0.00 4.40
9028 9586 3.620488 TGTCTGCCTCCATATTTTGTCC 58.380 45.455 0.00 0.00 0.00 4.02
9058 10241 1.131315 GATGCAGCCTCGGAACTTTTC 59.869 52.381 0.00 0.00 0.00 2.29
9061 10244 0.875059 CAGCCTCGGAACTTTTCACC 59.125 55.000 0.00 0.00 0.00 4.02
9093 10276 0.250467 GAGCTGCTGTCCAGAAACCA 60.250 55.000 7.01 0.00 44.64 3.67
9104 10287 1.745087 CCAGAAACCATTAGCATGCGT 59.255 47.619 13.01 0.00 0.00 5.24
9183 10369 4.757149 ACAGCGGCCAATCTCTTTAATATC 59.243 41.667 2.24 0.00 0.00 1.63
9203 10490 4.840401 TCGCGATATTTCAAACTGACAG 57.160 40.909 3.71 0.00 0.00 3.51
9217 10504 5.511386 AACTGACAGAATCTGGAAGGATT 57.489 39.130 15.38 0.77 38.47 3.01
9231 10518 4.722361 GAAGGATTCCGTGAAGTACTCT 57.278 45.455 0.00 0.00 39.83 3.24
9232 10519 5.831702 GAAGGATTCCGTGAAGTACTCTA 57.168 43.478 0.00 0.00 39.83 2.43
9233 10520 5.579564 AAGGATTCCGTGAAGTACTCTAC 57.420 43.478 0.00 0.00 0.00 2.59
9234 10521 4.597004 AGGATTCCGTGAAGTACTCTACA 58.403 43.478 0.00 0.00 0.00 2.74
9235 10522 4.398673 AGGATTCCGTGAAGTACTCTACAC 59.601 45.833 13.96 13.96 0.00 2.90
9236 10523 4.398673 GGATTCCGTGAAGTACTCTACACT 59.601 45.833 18.57 6.62 0.00 3.55
9237 10524 5.448904 GGATTCCGTGAAGTACTCTACACTC 60.449 48.000 18.57 12.32 0.00 3.51
9238 10525 4.011966 TCCGTGAAGTACTCTACACTCA 57.988 45.455 18.57 7.23 0.00 3.41
9239 10526 3.750130 TCCGTGAAGTACTCTACACTCAC 59.250 47.826 18.57 15.41 38.95 3.51
9240 10527 3.501062 CCGTGAAGTACTCTACACTCACA 59.499 47.826 18.46 0.00 40.72 3.58
9241 10528 4.023450 CCGTGAAGTACTCTACACTCACAA 60.023 45.833 18.46 0.00 40.72 3.33
9242 10529 4.910456 CGTGAAGTACTCTACACTCACAAC 59.090 45.833 18.46 0.00 40.72 3.32
9243 10530 5.277876 CGTGAAGTACTCTACACTCACAACT 60.278 44.000 18.46 0.00 40.72 3.16
9244 10531 5.915758 GTGAAGTACTCTACACTCACAACTG 59.084 44.000 15.17 0.00 40.55 3.16
9245 10532 5.826208 TGAAGTACTCTACACTCACAACTGA 59.174 40.000 0.00 0.00 0.00 3.41
9246 10533 6.320418 TGAAGTACTCTACACTCACAACTGAA 59.680 38.462 0.00 0.00 0.00 3.02
9247 10534 6.074544 AGTACTCTACACTCACAACTGAAC 57.925 41.667 0.00 0.00 0.00 3.18
9248 10535 3.966154 ACTCTACACTCACAACTGAACG 58.034 45.455 0.00 0.00 0.00 3.95
9249 10536 3.630769 ACTCTACACTCACAACTGAACGA 59.369 43.478 0.00 0.00 0.00 3.85
9250 10537 4.278669 ACTCTACACTCACAACTGAACGAT 59.721 41.667 0.00 0.00 0.00 3.73
9251 10538 5.472478 ACTCTACACTCACAACTGAACGATA 59.528 40.000 0.00 0.00 0.00 2.92
9252 10539 6.151312 ACTCTACACTCACAACTGAACGATAT 59.849 38.462 0.00 0.00 0.00 1.63
9253 10540 6.322491 TCTACACTCACAACTGAACGATATG 58.678 40.000 0.00 0.00 0.00 1.78
9254 10541 3.679980 ACACTCACAACTGAACGATATGC 59.320 43.478 0.00 0.00 0.00 3.14
9255 10542 3.679502 CACTCACAACTGAACGATATGCA 59.320 43.478 0.00 0.00 0.00 3.96
9256 10543 3.928992 ACTCACAACTGAACGATATGCAG 59.071 43.478 0.00 0.00 35.81 4.41
9257 10544 4.176271 CTCACAACTGAACGATATGCAGA 58.824 43.478 0.00 0.00 33.94 4.26
9258 10545 4.758688 TCACAACTGAACGATATGCAGAT 58.241 39.130 0.00 0.00 33.94 2.90
9259 10546 5.178061 TCACAACTGAACGATATGCAGATT 58.822 37.500 0.00 0.00 33.94 2.40
9260 10547 5.643348 TCACAACTGAACGATATGCAGATTT 59.357 36.000 0.00 0.00 33.94 2.17
9261 10548 5.735892 CACAACTGAACGATATGCAGATTTG 59.264 40.000 0.00 0.00 33.94 2.32
9262 10549 5.643348 ACAACTGAACGATATGCAGATTTGA 59.357 36.000 6.65 0.00 33.94 2.69
9263 10550 6.317140 ACAACTGAACGATATGCAGATTTGAT 59.683 34.615 6.65 0.00 33.94 2.57
9264 10551 7.495606 ACAACTGAACGATATGCAGATTTGATA 59.504 33.333 6.65 0.00 33.94 2.15
9265 10552 7.649370 ACTGAACGATATGCAGATTTGATAG 57.351 36.000 0.00 0.00 33.94 2.08
9266 10553 6.146837 ACTGAACGATATGCAGATTTGATAGC 59.853 38.462 0.00 0.00 33.94 2.97
9267 10554 5.990996 TGAACGATATGCAGATTTGATAGCA 59.009 36.000 0.00 0.00 41.73 3.49
9313 10600 0.677731 TGCCAAGAAATCCTCGCCTG 60.678 55.000 0.00 0.00 0.00 4.85
9341 10628 7.990314 TGATGAACTCAACGGGATATTGATTAA 59.010 33.333 0.00 0.00 35.57 1.40
9355 10672 3.144657 TGATTAAGGCATCCGCATCAT 57.855 42.857 0.00 0.00 41.24 2.45
9456 11037 2.729378 GCATCAGGCGCAAAGAAAC 58.271 52.632 10.83 0.00 0.00 2.78
9493 11074 9.625747 AATATCAGTTTTCCAACCATTGTTTTT 57.374 25.926 0.00 0.00 32.70 1.94
9520 11126 7.296856 TGGGGTGTAATCATCAATAATGTCAT 58.703 34.615 0.00 0.00 36.68 3.06
9564 11171 1.751563 CAACCGGCCCATTGGTTTT 59.248 52.632 9.83 0.00 46.04 2.43
9604 11211 6.043822 TGGAATCCATCTATCCGTCCAAATTA 59.956 38.462 0.00 0.00 35.96 1.40
9618 11225 3.621268 TCCAAATTAAGATGTTCGAGCCG 59.379 43.478 0.00 0.00 0.00 5.52
9619 11226 3.374058 CCAAATTAAGATGTTCGAGCCGT 59.626 43.478 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.566760 TTGAGATATGGCAACGTGAAATTAT 57.433 32.000 0.00 0.00 42.51 1.28
6 7 6.267817 CAATTGAGATATGGCAACGTGAAAT 58.732 36.000 0.00 0.00 42.51 2.17
11 12 3.016031 TGCAATTGAGATATGGCAACGT 58.984 40.909 10.34 0.00 42.51 3.99
12 13 3.313249 TCTGCAATTGAGATATGGCAACG 59.687 43.478 10.34 0.00 42.51 4.10
38 39 3.491766 TGGAATTCTCCCACCTCTAGT 57.508 47.619 5.23 0.00 41.64 2.57
79 80 4.643334 TGGCTTGATCATCCAGAGATTTTG 59.357 41.667 11.84 0.00 0.00 2.44
80 81 4.643784 GTGGCTTGATCATCCAGAGATTTT 59.356 41.667 15.22 0.00 0.00 1.82
85 86 1.211212 TGGTGGCTTGATCATCCAGAG 59.789 52.381 15.22 2.62 0.00 3.35
140 141 8.508883 TTGTTACTTTTTACTTGTGCTAGGAA 57.491 30.769 0.00 0.00 0.00 3.36
155 156 2.691011 ACCGCACCACATTGTTACTTTT 59.309 40.909 0.00 0.00 0.00 2.27
156 157 2.292292 GACCGCACCACATTGTTACTTT 59.708 45.455 0.00 0.00 0.00 2.66
157 158 1.877443 GACCGCACCACATTGTTACTT 59.123 47.619 0.00 0.00 0.00 2.24
166 167 2.515057 GGTTGTGACCGCACCACA 60.515 61.111 0.00 0.00 44.51 4.17
188 190 4.960469 TCGTGTCCTTTCTTCTATACCCAT 59.040 41.667 0.00 0.00 0.00 4.00
195 197 5.524971 TGTCTTTCGTGTCCTTTCTTCTA 57.475 39.130 0.00 0.00 0.00 2.10
236 238 5.720371 TGTTATAACTTGCAAACATGCCT 57.280 34.783 16.33 0.00 0.00 4.75
298 300 6.946340 TCTTAGATCCAAGCAACTATGTGAA 58.054 36.000 0.00 0.00 0.00 3.18
403 405 4.594123 TGTCATACCTCGTTGACTCAAA 57.406 40.909 4.86 0.00 42.17 2.69
418 420 2.571212 GGGCCATCATCGTTTGTCATA 58.429 47.619 4.39 0.00 0.00 2.15
420 422 0.679640 GGGGCCATCATCGTTTGTCA 60.680 55.000 4.39 0.00 0.00 3.58
448 450 0.687354 AGCTCGTAGCAATATGGGGG 59.313 55.000 9.09 0.00 45.56 5.40
449 451 3.238108 CTAGCTCGTAGCAATATGGGG 57.762 52.381 9.09 0.00 45.56 4.96
499 515 3.144657 TCAACATTCAGCACCAGACAT 57.855 42.857 0.00 0.00 0.00 3.06
540 556 1.210931 CACTCATGCCACCAAAGCG 59.789 57.895 0.00 0.00 0.00 4.68
559 575 1.286501 CGCTACGGATTTGCTAGCAA 58.713 50.000 26.06 26.06 33.78 3.91
574 590 4.111016 CGACAGTGCCCGACGCTA 62.111 66.667 0.00 0.00 36.85 4.26
577 593 3.403057 CAACGACAGTGCCCGACG 61.403 66.667 11.75 3.29 0.00 5.12
584 600 4.265085 CCAAACAAATCAACAACGACAGTG 59.735 41.667 0.00 0.00 0.00 3.66
586 602 4.420168 ACCAAACAAATCAACAACGACAG 58.580 39.130 0.00 0.00 0.00 3.51
587 603 4.442375 ACCAAACAAATCAACAACGACA 57.558 36.364 0.00 0.00 0.00 4.35
603 620 7.775053 AAATAAGACCTAGAATGCAACCAAA 57.225 32.000 0.00 0.00 0.00 3.28
640 739 7.289317 TGATTAAAGGACTCCCGTATAACATCT 59.711 37.037 0.00 0.00 37.58 2.90
648 747 5.486735 TTGTTGATTAAAGGACTCCCGTA 57.513 39.130 0.00 0.00 37.58 4.02
654 753 4.630069 CGTCCGATTGTTGATTAAAGGACT 59.370 41.667 9.23 0.00 43.26 3.85
660 759 2.417239 GGCACGTCCGATTGTTGATTAA 59.583 45.455 0.00 0.00 0.00 1.40
681 780 9.840427 AAGTGGTTCGATTTATAATGAAACTTG 57.160 29.630 10.28 0.00 0.00 3.16
683 782 9.226606 TGAAGTGGTTCGATTTATAATGAAACT 57.773 29.630 10.28 4.40 35.17 2.66
684 783 9.274065 GTGAAGTGGTTCGATTTATAATGAAAC 57.726 33.333 0.00 4.54 35.17 2.78
689 806 8.258007 TCAGAGTGAAGTGGTTCGATTTATAAT 58.742 33.333 0.00 0.00 35.17 1.28
879 999 4.287967 ACGGCGCGTCACGTTTTG 62.288 61.111 12.89 0.00 46.11 2.44
951 1073 5.215160 GTGCTACAGTGAGTTTGGAATTTG 58.785 41.667 0.00 0.00 0.00 2.32
1605 1727 8.576442 CGCAGAATCCCCATTAAAATTAGTTAT 58.424 33.333 0.00 0.00 0.00 1.89
1615 1737 3.221771 CCAATCGCAGAATCCCCATTAA 58.778 45.455 0.00 0.00 43.58 1.40
1849 1972 3.005684 TGCTGCAACATTGGAGGTAAAAG 59.994 43.478 14.07 0.00 45.44 2.27
2057 2180 7.860872 ACTTTCGGAGCATTTTAAAAACTACAG 59.139 33.333 4.44 3.50 0.00 2.74
2210 2333 7.961827 CGATATATACCTCTAACCGACAAACTC 59.038 40.741 0.00 0.00 0.00 3.01
2321 2468 6.710295 ACCCTTTTCCTTTTATTTCATGCAAC 59.290 34.615 0.00 0.00 0.00 4.17
2333 2480 8.638873 CAGAAAACACTATACCCTTTTCCTTTT 58.361 33.333 0.00 0.00 34.49 2.27
2406 2596 4.717233 AAGCAATGACATAAATCGGCAA 57.283 36.364 0.00 0.00 0.00 4.52
2496 2686 8.539770 ACTATAGAACTGAAACAATGACAGTG 57.460 34.615 6.78 0.41 42.81 3.66
2543 2733 6.665248 CCACATCATACCTAGACCAGATATCA 59.335 42.308 5.32 0.00 0.00 2.15
3307 3501 1.080995 GCAAGTCTAGCAGCGGACAG 61.081 60.000 18.98 13.44 35.18 3.51
3386 3581 1.270041 GCTGGCAGGCAGTATCTCTAC 60.270 57.143 24.09 2.21 0.00 2.59
3448 3643 6.654161 TCCAGACTACTGTAAAGTCAGACTAC 59.346 42.308 2.64 0.00 44.77 2.73
3449 3644 6.776744 TCCAGACTACTGTAAAGTCAGACTA 58.223 40.000 2.64 0.00 44.77 2.59
3502 3717 2.548057 GTGATCGCTTTGTTCTTCCACA 59.452 45.455 0.00 0.00 0.00 4.17
3508 3723 5.633830 ATCAAATGTGATCGCTTTGTTCT 57.366 34.783 20.59 10.98 40.69 3.01
3645 3862 2.591429 CCACAACACAGCTGCGGA 60.591 61.111 15.27 0.00 0.00 5.54
3874 4094 1.535204 CCCCCTCAAATGCAAAGCGT 61.535 55.000 0.00 0.00 0.00 5.07
3875 4095 1.216178 CCCCCTCAAATGCAAAGCG 59.784 57.895 0.00 0.00 0.00 4.68
3890 4110 7.384524 AATACTAATACTCCTTAACACCCCC 57.615 40.000 0.00 0.00 0.00 5.40
4012 4276 5.352569 GCTCTGTTAACACATCAGCAATACT 59.647 40.000 3.59 0.00 38.10 2.12
4033 4297 2.998316 AGATGCTCCTTGTTAGGCTC 57.002 50.000 0.00 0.00 41.69 4.70
4087 4351 6.372103 TCCATCCATTTGAAAAATTGATGTGC 59.628 34.615 18.16 0.00 0.00 4.57
4337 4601 7.224557 AGTGAAATGTCCAATTTTGTAACTTGC 59.775 33.333 0.00 0.00 0.00 4.01
4409 4687 8.654215 GGTAAGTAAAAGAATGTAAGTTCCTCG 58.346 37.037 0.00 0.00 0.00 4.63
4528 4806 4.080863 GTCATCACATCCCTCTTTACACCT 60.081 45.833 0.00 0.00 0.00 4.00
4806 5089 2.498167 GCATCTTAGGTGCTATGGTGG 58.502 52.381 10.61 0.00 39.45 4.61
4807 5090 2.498167 GGCATCTTAGGTGCTATGGTG 58.502 52.381 17.49 0.00 42.16 4.17
4808 5091 1.421646 GGGCATCTTAGGTGCTATGGT 59.578 52.381 17.49 0.00 42.16 3.55
4809 5092 1.421268 TGGGCATCTTAGGTGCTATGG 59.579 52.381 17.49 0.00 42.16 2.74
4810 5093 2.936919 TGGGCATCTTAGGTGCTATG 57.063 50.000 17.49 0.00 42.16 2.23
4811 5094 3.395607 TCATTGGGCATCTTAGGTGCTAT 59.604 43.478 17.49 6.01 42.16 2.97
4812 5095 2.777114 TCATTGGGCATCTTAGGTGCTA 59.223 45.455 17.49 4.22 42.16 3.49
4813 5096 1.565759 TCATTGGGCATCTTAGGTGCT 59.434 47.619 17.49 0.00 42.16 4.40
4814 5097 1.952296 CTCATTGGGCATCTTAGGTGC 59.048 52.381 9.28 9.28 41.78 5.01
4815 5098 3.287867 ACTCATTGGGCATCTTAGGTG 57.712 47.619 0.00 0.00 0.00 4.00
4816 5099 4.101741 GTCTACTCATTGGGCATCTTAGGT 59.898 45.833 0.00 0.00 0.00 3.08
4857 5151 8.079809 CGGGTTTCTAAGAAAATAAGAAAAGCA 58.920 33.333 0.00 0.00 40.03 3.91
5069 5363 6.780706 ATACGAAAACACTTGGTTACTCAG 57.219 37.500 0.00 0.00 39.29 3.35
5233 5527 6.015095 TGTCATGTGGTTTATATGTTTTGGCA 60.015 34.615 0.00 0.00 0.00 4.92
5291 5585 7.656412 ACAAGTTATGTTTGTCATTACATGCA 58.344 30.769 10.01 0.00 40.06 3.96
5363 5657 1.207089 TGCTCTTACAAGCTACGGCAT 59.793 47.619 0.00 0.00 42.94 4.40
5367 5661 4.928661 ACAATTGCTCTTACAAGCTACG 57.071 40.909 5.05 0.00 42.94 3.51
5384 5678 6.742109 GCATTCAGCAATACTTCCATACAAT 58.258 36.000 0.00 0.00 44.79 2.71
5642 5941 7.472334 AATGAAGTCTCAGCAATTTTACCAT 57.528 32.000 0.00 0.00 34.23 3.55
5690 5993 4.333926 CCAGCTACTCCTACAAAGCATTTC 59.666 45.833 0.00 0.00 35.03 2.17
5861 6175 7.262772 CACTACTAATTATCTTGGTTCGGTCA 58.737 38.462 0.00 0.00 0.00 4.02
5948 6272 1.169661 CGTGTAAGTGGCTGCCCAAA 61.170 55.000 17.53 0.00 44.33 3.28
5959 6283 3.181454 GGATGGATCAATCCCGTGTAAGT 60.181 47.826 17.51 0.00 46.59 2.24
6061 6405 2.736144 AAAAGACATCAGTACGGCGA 57.264 45.000 16.62 0.00 0.00 5.54
6193 6705 2.745884 CCAATTCGTGGGCGCAGA 60.746 61.111 10.83 0.95 44.64 4.26
6640 7163 3.761218 TGTTGCCTGAAACAAGAAAGACA 59.239 39.130 0.00 0.00 37.12 3.41
6800 7323 2.812178 CAGGCGGCATTGCTTTGC 60.812 61.111 13.08 10.13 42.01 3.68
6996 7519 8.885494 AACGTGTTATACCAACTAACAGTAAA 57.115 30.769 0.00 0.00 39.17 2.01
7083 7606 7.030075 CAACATATGGTGCTTGATGTGAATA 57.970 36.000 8.04 0.00 32.92 1.75
7247 7772 3.616219 TGGTGCCACATAAACTCCATAC 58.384 45.455 0.00 0.00 0.00 2.39
7295 7820 6.155475 ACTTCATAGAGACAGATGGCTTAC 57.845 41.667 0.00 0.00 30.09 2.34
7397 7922 9.914834 AGCCATACATTTTACTTAGTTATCCAA 57.085 29.630 0.00 0.00 0.00 3.53
7456 7981 4.179579 GCAGGCGCATCCCGTTTC 62.180 66.667 10.83 0.00 39.71 2.78
7516 8041 3.041946 CCCCTAGTACCTCTGAAATGCT 58.958 50.000 0.00 0.00 0.00 3.79
7553 8078 8.654230 TCAGCAATGATACTATGAAAAGTCTC 57.346 34.615 0.00 0.00 0.00 3.36
7554 8079 9.453572 TTTCAGCAATGATACTATGAAAAGTCT 57.546 29.630 0.00 0.00 34.66 3.24
7714 8239 1.849039 AGATCAAGGGGAAGTCCATGG 59.151 52.381 4.97 4.97 37.91 3.66
7889 8414 7.094634 ACACTTCCTATTTCTTGTATGCAACTG 60.095 37.037 0.00 0.00 0.00 3.16
7929 8454 7.172703 AGGAAACGAACTTGAAAATACCTACAG 59.827 37.037 0.00 0.00 0.00 2.74
7976 8501 5.449862 CCAAATAATAGCTGCTTAAACGGCA 60.450 40.000 7.79 0.17 44.76 5.69
7977 8502 4.976116 CCAAATAATAGCTGCTTAAACGGC 59.024 41.667 7.79 1.20 42.55 5.68
7978 8503 4.976116 GCCAAATAATAGCTGCTTAAACGG 59.024 41.667 7.79 1.73 0.00 4.44
8026 8552 2.284478 AGCAGCAGGGAGAGAGCA 60.284 61.111 0.00 0.00 0.00 4.26
8027 8553 1.688269 ATGAGCAGCAGGGAGAGAGC 61.688 60.000 0.00 0.00 0.00 4.09
8084 8613 2.614057 GGAAGATGCTACGGTTCATTGG 59.386 50.000 0.00 0.00 0.00 3.16
8268 8799 2.171448 GTGGCTAGGGATGAACAGACAT 59.829 50.000 0.00 0.00 0.00 3.06
8326 8857 5.446340 CCATGATGATGATACAAATACGGCG 60.446 44.000 4.80 4.80 0.00 6.46
8327 8858 5.412594 ACCATGATGATGATACAAATACGGC 59.587 40.000 0.00 0.00 0.00 5.68
8328 8859 6.650390 TGACCATGATGATGATACAAATACGG 59.350 38.462 0.00 0.00 0.00 4.02
8330 8861 8.837788 TCTGACCATGATGATGATACAAATAC 57.162 34.615 0.00 0.00 0.00 1.89
8332 8863 8.793592 CAATCTGACCATGATGATGATACAAAT 58.206 33.333 0.00 0.00 0.00 2.32
8333 8864 7.994334 TCAATCTGACCATGATGATGATACAAA 59.006 33.333 0.00 0.00 0.00 2.83
8334 8865 7.511268 TCAATCTGACCATGATGATGATACAA 58.489 34.615 0.00 0.00 0.00 2.41
8335 8866 7.069877 TCAATCTGACCATGATGATGATACA 57.930 36.000 0.00 0.00 0.00 2.29
8336 8867 7.160049 ACTCAATCTGACCATGATGATGATAC 58.840 38.462 0.00 0.00 0.00 2.24
8337 8868 7.312415 ACTCAATCTGACCATGATGATGATA 57.688 36.000 0.00 0.00 0.00 2.15
8338 8869 6.189036 ACTCAATCTGACCATGATGATGAT 57.811 37.500 0.00 0.00 0.00 2.45
8339 8870 5.625568 ACTCAATCTGACCATGATGATGA 57.374 39.130 0.00 0.00 0.00 2.92
8340 8871 7.573283 GCAATACTCAATCTGACCATGATGATG 60.573 40.741 0.00 0.00 0.00 3.07
8341 8872 6.430308 GCAATACTCAATCTGACCATGATGAT 59.570 38.462 0.00 0.00 0.00 2.45
8342 8873 5.761726 GCAATACTCAATCTGACCATGATGA 59.238 40.000 0.00 0.00 0.00 2.92
8343 8874 5.529800 TGCAATACTCAATCTGACCATGATG 59.470 40.000 0.00 0.00 0.00 3.07
8344 8875 5.687780 TGCAATACTCAATCTGACCATGAT 58.312 37.500 0.00 0.00 0.00 2.45
8345 8876 5.101648 TGCAATACTCAATCTGACCATGA 57.898 39.130 0.00 0.00 0.00 3.07
8346 8877 5.449588 GGTTGCAATACTCAATCTGACCATG 60.450 44.000 0.59 0.00 0.00 3.66
8347 8878 4.641989 GGTTGCAATACTCAATCTGACCAT 59.358 41.667 0.59 0.00 0.00 3.55
8348 8879 4.009675 GGTTGCAATACTCAATCTGACCA 58.990 43.478 0.59 0.00 0.00 4.02
8349 8880 4.009675 TGGTTGCAATACTCAATCTGACC 58.990 43.478 0.59 0.00 0.00 4.02
8350 8881 5.575957 CATGGTTGCAATACTCAATCTGAC 58.424 41.667 0.59 0.00 0.00 3.51
8351 8882 5.823209 CATGGTTGCAATACTCAATCTGA 57.177 39.130 0.59 0.00 0.00 3.27
8369 8922 5.028549 AGGAGTACAACAATCTAGCATGG 57.971 43.478 0.00 0.00 0.00 3.66
8487 9040 1.134401 GCGTTCCCTTCATCCATCAGA 60.134 52.381 0.00 0.00 0.00 3.27
8635 9188 1.162698 CAATCGCATCTGCATAGGGG 58.837 55.000 2.72 0.00 42.21 4.79
8638 9191 2.874086 TCAACCAATCGCATCTGCATAG 59.126 45.455 2.72 0.00 42.21 2.23
8639 9192 2.874086 CTCAACCAATCGCATCTGCATA 59.126 45.455 2.72 0.00 42.21 3.14
8640 9193 1.674441 CTCAACCAATCGCATCTGCAT 59.326 47.619 2.72 0.00 42.21 3.96
8641 9194 1.089112 CTCAACCAATCGCATCTGCA 58.911 50.000 2.72 0.00 42.21 4.41
8642 9195 0.379669 CCTCAACCAATCGCATCTGC 59.620 55.000 0.00 0.00 37.78 4.26
8643 9196 1.742761 ACCTCAACCAATCGCATCTG 58.257 50.000 0.00 0.00 0.00 2.90
8645 9198 2.627945 TGTACCTCAACCAATCGCATC 58.372 47.619 0.00 0.00 0.00 3.91
8646 9199 2.779755 TGTACCTCAACCAATCGCAT 57.220 45.000 0.00 0.00 0.00 4.73
8648 9201 3.498397 CCATATGTACCTCAACCAATCGC 59.502 47.826 1.24 0.00 0.00 4.58
8649 9202 3.498397 GCCATATGTACCTCAACCAATCG 59.502 47.826 1.24 0.00 0.00 3.34
8942 9500 4.364415 AACACAAGCGCTCTTAAAAACA 57.636 36.364 12.06 0.00 0.00 2.83
9028 9586 2.313172 GGCTGCATCCAGATACGCG 61.313 63.158 3.53 3.53 41.77 6.01
9058 10241 1.300465 CTCATGATCGGCTCCGGTG 60.300 63.158 8.59 0.00 40.25 4.94
9061 10244 1.664017 CAGCTCATGATCGGCTCCG 60.664 63.158 5.03 1.14 41.35 4.63
9104 10287 2.612604 GATGCATGTTGCTTCATTGCA 58.387 42.857 2.46 14.71 45.31 4.08
9183 10369 4.840401 TCTGTCAGTTTGAAATATCGCG 57.160 40.909 0.00 0.00 0.00 5.87
9217 10504 3.750130 GTGAGTGTAGAGTACTTCACGGA 59.250 47.826 15.70 8.04 44.96 4.69
9230 10517 5.004821 GCATATCGTTCAGTTGTGAGTGTAG 59.995 44.000 0.00 0.00 32.98 2.74
9231 10518 4.862574 GCATATCGTTCAGTTGTGAGTGTA 59.137 41.667 0.00 0.00 32.98 2.90
9232 10519 3.679980 GCATATCGTTCAGTTGTGAGTGT 59.320 43.478 0.00 0.00 32.98 3.55
9233 10520 3.679502 TGCATATCGTTCAGTTGTGAGTG 59.320 43.478 0.00 0.00 32.98 3.51
9234 10521 3.925379 TGCATATCGTTCAGTTGTGAGT 58.075 40.909 0.00 0.00 32.98 3.41
9235 10522 4.176271 TCTGCATATCGTTCAGTTGTGAG 58.824 43.478 0.00 0.00 32.98 3.51
9236 10523 4.186856 TCTGCATATCGTTCAGTTGTGA 57.813 40.909 0.00 0.00 0.00 3.58
9237 10524 5.475273 AATCTGCATATCGTTCAGTTGTG 57.525 39.130 0.00 0.00 0.00 3.33
9238 10525 5.643348 TCAAATCTGCATATCGTTCAGTTGT 59.357 36.000 0.00 0.00 0.00 3.32
9239 10526 6.110543 TCAAATCTGCATATCGTTCAGTTG 57.889 37.500 0.00 0.00 0.00 3.16
9240 10527 6.932356 ATCAAATCTGCATATCGTTCAGTT 57.068 33.333 0.00 0.00 0.00 3.16
9241 10528 6.146837 GCTATCAAATCTGCATATCGTTCAGT 59.853 38.462 0.00 0.00 0.00 3.41
9242 10529 6.146673 TGCTATCAAATCTGCATATCGTTCAG 59.853 38.462 0.00 0.00 0.00 3.02
9243 10530 5.990996 TGCTATCAAATCTGCATATCGTTCA 59.009 36.000 0.00 0.00 0.00 3.18
9244 10531 6.471976 TGCTATCAAATCTGCATATCGTTC 57.528 37.500 0.00 0.00 0.00 3.95
9245 10532 8.037166 TCTATGCTATCAAATCTGCATATCGTT 58.963 33.333 6.92 0.00 44.16 3.85
9246 10533 7.550712 TCTATGCTATCAAATCTGCATATCGT 58.449 34.615 6.92 0.00 44.16 3.73
9247 10534 7.998753 TCTATGCTATCAAATCTGCATATCG 57.001 36.000 6.92 0.00 44.16 2.92
9251 10538 9.692749 CAAAAATCTATGCTATCAAATCTGCAT 57.307 29.630 0.00 0.00 46.22 3.96
9252 10539 8.905850 TCAAAAATCTATGCTATCAAATCTGCA 58.094 29.630 0.00 0.00 39.83 4.41
9253 10540 9.909644 ATCAAAAATCTATGCTATCAAATCTGC 57.090 29.630 0.00 0.00 0.00 4.26
9260 10547 9.524106 CAGCAAAATCAAAAATCTATGCTATCA 57.476 29.630 0.00 0.00 40.62 2.15
9261 10548 9.525409 ACAGCAAAATCAAAAATCTATGCTATC 57.475 29.630 0.00 0.00 40.62 2.08
9262 10549 9.525409 GACAGCAAAATCAAAAATCTATGCTAT 57.475 29.630 0.00 0.00 40.62 2.97
9263 10550 7.697710 CGACAGCAAAATCAAAAATCTATGCTA 59.302 33.333 0.00 0.00 40.62 3.49
9264 10551 6.529125 CGACAGCAAAATCAAAAATCTATGCT 59.471 34.615 0.00 0.00 43.13 3.79
9265 10552 6.689547 CGACAGCAAAATCAAAAATCTATGC 58.310 36.000 0.00 0.00 0.00 3.14
9266 10553 6.689547 GCGACAGCAAAATCAAAAATCTATG 58.310 36.000 0.00 0.00 44.35 2.23
9267 10554 6.875926 GCGACAGCAAAATCAAAAATCTAT 57.124 33.333 0.00 0.00 44.35 1.98
9283 10570 3.818787 CTTGGCATGGGCGACAGC 61.819 66.667 0.00 0.00 42.47 4.40
9313 10600 2.029838 ATCCCGTTGAGTTCATCAGC 57.970 50.000 0.00 0.00 39.68 4.26
9355 10672 5.793026 AAAAACAGAAATTTCTTTGCGCA 57.207 30.435 18.16 5.66 34.74 6.09
9428 11006 2.916052 GCCTGATGCGGATGCCATG 61.916 63.158 0.00 0.00 41.78 3.66
9456 11037 7.479980 TGGAAAACTGATATTATTCGCCAAAG 58.520 34.615 0.00 0.00 0.00 2.77
9491 11072 8.820831 ACATTATTGATGATTACACCCCAAAAA 58.179 29.630 0.00 0.00 39.15 1.94
9493 11074 7.617329 TGACATTATTGATGATTACACCCCAAA 59.383 33.333 0.00 0.00 39.15 3.28
9494 11075 7.122048 TGACATTATTGATGATTACACCCCAA 58.878 34.615 0.00 0.00 39.15 4.12
9496 11077 7.765695 ATGACATTATTGATGATTACACCCC 57.234 36.000 0.00 0.00 39.15 4.95
9497 11078 9.725019 TCTATGACATTATTGATGATTACACCC 57.275 33.333 0.00 0.00 39.15 4.61
9564 11171 4.072131 GGATTCCAAACACTGCAACTCTA 58.928 43.478 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.