Multiple sequence alignment - TraesCS4A01G050700

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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 TraesCS4A01G050700 chr4A 100.000 3262 0 0 1 3262 41914819 41918080 0.000000e+00 6024.0
1 TraesCS4A01G050700 chr4A 100.000 543 0 0 3718 4260 41918536 41919078 0.000000e+00 1003.0
2 TraesCS4A01G050700 chr4A 87.741 881 76 13 104 979 41852246 41853099 0.000000e+00 1000.0
3 TraesCS4A01G050700 chr4D 93.048 2618 119 29 683 3262 422552904 422550312 0.000000e+00 3768.0
4 TraesCS4A01G050700 chr4D 93.554 543 34 1 3718 4260 422550249 422549708 0.000000e+00 808.0
5 TraesCS4A01G050700 chr4D 84.696 477 52 11 108 574 422554256 422553791 1.400000e-124 457.0
6 TraesCS4A01G050700 chr4D 74.542 601 109 28 1823 2409 421925654 421925084 5.540000e-54 222.0
7 TraesCS4A01G050700 chr4B 91.148 2474 118 45 806 3243 519408189 519405781 0.000000e+00 3262.0
8 TraesCS4A01G050700 chr4B 81.946 709 71 16 104 801 519411310 519410648 8.050000e-152 547.0
9 TraesCS4A01G050700 chr4B 92.241 348 24 3 3782 4128 519405676 519405331 1.380000e-134 490.0
10 TraesCS4A01G050700 chr4B 90.226 133 13 0 4128 4260 519405209 519405077 1.570000e-39 174.0
11 TraesCS4A01G050700 chr4B 95.098 102 4 1 1 102 426691784 426691884 4.410000e-35 159.0
12 TraesCS4A01G050700 chr7B 95.960 99 4 0 4 102 143206846 143206748 1.230000e-35 161.0
13 TraesCS4A01G050700 chr1B 95.098 102 5 0 1 102 335780545 335780444 1.230000e-35 161.0
14 TraesCS4A01G050700 chr1B 95.050 101 5 0 1 101 330362905 330363005 4.410000e-35 159.0
15 TraesCS4A01G050700 chr5D 95.050 101 5 0 1 101 246277792 246277892 4.410000e-35 159.0
16 TraesCS4A01G050700 chr5D 97.368 38 1 0 2468 2505 68233041 68233078 9.890000e-07 65.8
17 TraesCS4A01G050700 chr5D 91.111 45 4 0 2469 2513 68091509 68091465 1.280000e-05 62.1
18 TraesCS4A01G050700 chr2D 95.050 101 5 0 1 101 447738714 447738614 4.410000e-35 159.0
19 TraesCS4A01G050700 chr2B 95.050 101 5 0 1 101 39547342 39547442 4.410000e-35 159.0
20 TraesCS4A01G050700 chr2B 91.964 112 7 2 1 112 383579723 383579832 5.700000e-34 156.0
21 TraesCS4A01G050700 chr7D 93.396 106 7 0 1 106 206067646 206067541 1.590000e-34 158.0
22 TraesCS4A01G050700 chr6D 93.023 43 2 1 2470 2512 65506057 65506098 1.280000e-05 62.1
23 TraesCS4A01G050700 chr6B 94.872 39 2 0 2469 2507 686365194 686365232 1.280000e-05 62.1
24 TraesCS4A01G050700 chr6A 97.222 36 1 0 2470 2505 83250790 83250755 1.280000e-05 62.1
25 TraesCS4A01G050700 chr1D 97.059 34 0 1 2466 2498 452260416 452260449 5.950000e-04 56.5


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 TraesCS4A01G050700 chr4A 41914819 41919078 4259 False 3513.500000 6024 100.000000 1 4260 2 chr4A.!!$F2 4259
1 TraesCS4A01G050700 chr4A 41852246 41853099 853 False 1000.000000 1000 87.741000 104 979 1 chr4A.!!$F1 875
2 TraesCS4A01G050700 chr4D 422549708 422554256 4548 True 1677.666667 3768 90.432667 108 4260 3 chr4D.!!$R2 4152
3 TraesCS4A01G050700 chr4D 421925084 421925654 570 True 222.000000 222 74.542000 1823 2409 1 chr4D.!!$R1 586
4 TraesCS4A01G050700 chr4B 519405077 519411310 6233 True 1118.250000 3262 88.890250 104 4260 4 chr4B.!!$R1 4156

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
36 37 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96 F
1546 4861 0.103572 TCGGGGCGTTATCTTGTAGC 59.896 55.000 0.00 0.00 0.00 3.58 F
1766 5083 0.938713 CGGTGCTACCACGACAAAAA 59.061 50.000 0.00 0.00 43.00 1.94 F
1767 5084 1.533731 CGGTGCTACCACGACAAAAAT 59.466 47.619 0.00 0.00 43.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 5063 0.104487 TTTTGTCGTGGTAGCACCGA 59.896 50.000 18.90 15.63 42.58 4.69 R
2956 6298 1.144969 CCGTTTTCTCTTGCAGCGTA 58.855 50.000 0.00 0.00 0.00 4.42 R
3063 6405 1.751351 TGCGCTCACTATACTTGCTCT 59.249 47.619 9.73 0.00 0.00 4.09 R
3728 7070 4.085733 TGCCTTAGCCTGCAAAAGAATAA 58.914 39.130 5.99 0.00 38.69 1.40 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
20 21 1.254954 ACGTAGACACACTCTTCCCC 58.745 55.000 0.00 0.00 0.00 4.81
21 22 1.203025 ACGTAGACACACTCTTCCCCT 60.203 52.381 0.00 0.00 0.00 4.79
22 23 1.473278 CGTAGACACACTCTTCCCCTC 59.527 57.143 0.00 0.00 0.00 4.30
23 24 2.810164 GTAGACACACTCTTCCCCTCT 58.190 52.381 0.00 0.00 0.00 3.69
24 25 1.931635 AGACACACTCTTCCCCTCTC 58.068 55.000 0.00 0.00 0.00 3.20
25 26 0.528470 GACACACTCTTCCCCTCTCG 59.472 60.000 0.00 0.00 0.00 4.04
26 27 0.178958 ACACACTCTTCCCCTCTCGT 60.179 55.000 0.00 0.00 0.00 4.18
27 28 0.969894 CACACTCTTCCCCTCTCGTT 59.030 55.000 0.00 0.00 0.00 3.85
28 29 0.969894 ACACTCTTCCCCTCTCGTTG 59.030 55.000 0.00 0.00 0.00 4.10
29 30 0.390472 CACTCTTCCCCTCTCGTTGC 60.390 60.000 0.00 0.00 0.00 4.17
30 31 0.543174 ACTCTTCCCCTCTCGTTGCT 60.543 55.000 0.00 0.00 0.00 3.91
31 32 1.272536 ACTCTTCCCCTCTCGTTGCTA 60.273 52.381 0.00 0.00 0.00 3.49
32 33 2.035632 CTCTTCCCCTCTCGTTGCTAT 58.964 52.381 0.00 0.00 0.00 2.97
33 34 1.757118 TCTTCCCCTCTCGTTGCTATG 59.243 52.381 0.00 0.00 0.00 2.23
34 35 0.178068 TTCCCCTCTCGTTGCTATGC 59.822 55.000 0.00 0.00 0.00 3.14
35 36 0.975556 TCCCCTCTCGTTGCTATGCA 60.976 55.000 0.00 0.00 36.47 3.96
36 37 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
37 38 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
38 39 1.069823 CCCTCTCGTTGCTATGCATCT 59.930 52.381 0.19 0.00 38.76 2.90
39 40 2.402305 CCTCTCGTTGCTATGCATCTC 58.598 52.381 0.19 0.00 38.76 2.75
40 41 2.402305 CTCTCGTTGCTATGCATCTCC 58.598 52.381 0.19 0.00 38.76 3.71
41 42 2.034878 TCTCGTTGCTATGCATCTCCT 58.965 47.619 0.19 0.00 38.76 3.69
42 43 3.222603 TCTCGTTGCTATGCATCTCCTA 58.777 45.455 0.19 0.00 38.76 2.94
43 44 3.636764 TCTCGTTGCTATGCATCTCCTAA 59.363 43.478 0.19 0.00 38.76 2.69
44 45 4.099419 TCTCGTTGCTATGCATCTCCTAAA 59.901 41.667 0.19 0.00 38.76 1.85
45 46 4.960938 TCGTTGCTATGCATCTCCTAAAT 58.039 39.130 0.19 0.00 38.76 1.40
46 47 6.015434 TCTCGTTGCTATGCATCTCCTAAATA 60.015 38.462 0.19 0.00 38.76 1.40
47 48 6.159293 TCGTTGCTATGCATCTCCTAAATAG 58.841 40.000 0.19 0.00 38.76 1.73
48 49 6.015434 TCGTTGCTATGCATCTCCTAAATAGA 60.015 38.462 0.19 0.00 38.76 1.98
49 50 6.815641 CGTTGCTATGCATCTCCTAAATAGAT 59.184 38.462 0.19 0.00 38.76 1.98
50 51 7.009999 CGTTGCTATGCATCTCCTAAATAGATC 59.990 40.741 0.19 0.00 38.76 2.75
51 52 7.730672 TGCTATGCATCTCCTAAATAGATCT 57.269 36.000 0.19 0.00 31.71 2.75
52 53 8.143673 TGCTATGCATCTCCTAAATAGATCTT 57.856 34.615 0.19 0.00 31.71 2.40
53 54 8.039538 TGCTATGCATCTCCTAAATAGATCTTG 58.960 37.037 0.19 0.00 31.71 3.02
54 55 7.011295 GCTATGCATCTCCTAAATAGATCTTGC 59.989 40.741 0.19 0.69 31.22 4.01
55 56 5.233225 TGCATCTCCTAAATAGATCTTGCG 58.767 41.667 0.00 0.00 31.22 4.85
56 57 5.221521 TGCATCTCCTAAATAGATCTTGCGT 60.222 40.000 0.00 0.00 31.22 5.24
57 58 5.119898 GCATCTCCTAAATAGATCTTGCGTG 59.880 44.000 0.00 0.00 31.22 5.34
58 59 6.450545 CATCTCCTAAATAGATCTTGCGTGA 58.549 40.000 0.00 0.00 31.22 4.35
59 60 6.078202 TCTCCTAAATAGATCTTGCGTGAG 57.922 41.667 0.00 1.23 0.00 3.51
60 61 8.731337 CATCTCCTAAATAGATCTTGCGTGAGC 61.731 44.444 0.00 0.00 44.14 4.26
71 72 4.617875 CGTGAGCGGAGGGATTTT 57.382 55.556 0.00 0.00 0.00 1.82
72 73 2.854522 CGTGAGCGGAGGGATTTTT 58.145 52.632 0.00 0.00 0.00 1.94
93 94 6.595772 TTTTTGAAATTGCATGCTACGTTT 57.404 29.167 20.33 13.51 0.00 3.60
94 95 6.595772 TTTTGAAATTGCATGCTACGTTTT 57.404 29.167 20.33 9.00 0.00 2.43
95 96 5.820926 TTGAAATTGCATGCTACGTTTTC 57.179 34.783 20.33 17.25 0.00 2.29
96 97 4.233789 TGAAATTGCATGCTACGTTTTCC 58.766 39.130 20.33 4.72 0.00 3.13
97 98 3.932545 AATTGCATGCTACGTTTTCCA 57.067 38.095 20.33 0.00 0.00 3.53
98 99 3.932545 ATTGCATGCTACGTTTTCCAA 57.067 38.095 20.33 0.30 0.00 3.53
99 100 2.697431 TGCATGCTACGTTTTCCAAC 57.303 45.000 20.33 0.00 0.00 3.77
100 101 1.950216 TGCATGCTACGTTTTCCAACA 59.050 42.857 20.33 0.00 32.54 3.33
101 102 2.556189 TGCATGCTACGTTTTCCAACAT 59.444 40.909 20.33 0.00 32.54 2.71
102 103 3.005261 TGCATGCTACGTTTTCCAACATT 59.995 39.130 20.33 0.00 32.54 2.71
174 176 3.380471 ACACCAATAGCCAGCCAATAA 57.620 42.857 0.00 0.00 0.00 1.40
197 199 7.736447 AACTCTCCTTGAAAGATACACAAAG 57.264 36.000 0.00 0.00 0.00 2.77
200 202 5.997746 TCTCCTTGAAAGATACACAAAGTGG 59.002 40.000 1.93 0.00 37.94 4.00
204 206 6.403866 TTGAAAGATACACAAAGTGGCAAT 57.596 33.333 1.93 0.00 37.94 3.56
205 207 5.771469 TGAAAGATACACAAAGTGGCAATG 58.229 37.500 1.93 0.00 37.94 2.82
246 249 5.924475 ATTTAAGGACACAAACTCTCACG 57.076 39.130 0.00 0.00 0.00 4.35
248 251 1.120530 AGGACACAAACTCTCACGGT 58.879 50.000 0.00 0.00 0.00 4.83
256 260 0.241481 AACTCTCACGGTCTCTTCGC 59.759 55.000 0.00 0.00 0.00 4.70
265 269 3.053896 TCTCTTCGCCAGCGTCGA 61.054 61.111 12.32 8.61 40.74 4.20
317 321 2.156098 GACCTTATTCCAACACGCCAA 58.844 47.619 0.00 0.00 0.00 4.52
319 323 1.883275 CCTTATTCCAACACGCCAACA 59.117 47.619 0.00 0.00 0.00 3.33
320 324 2.491693 CCTTATTCCAACACGCCAACAT 59.508 45.455 0.00 0.00 0.00 2.71
390 394 0.826672 AAACGAGACAGACGGGTCCT 60.827 55.000 0.00 0.00 38.59 3.85
395 399 2.600769 ACAGACGGGTCCTCGCTT 60.601 61.111 0.00 0.00 0.00 4.68
407 411 3.939837 CTCGCTTCTCTTGCCGCCA 62.940 63.158 0.00 0.00 0.00 5.69
436 440 3.357166 CTCGAACGAGGAATAAGAGGG 57.643 52.381 15.22 0.00 38.51 4.30
466 470 4.752879 GCGGCGTGTAGGGAAGCA 62.753 66.667 9.37 0.00 0.00 3.91
513 518 2.305927 TGGGAGAAGGAGGAATGTGTTC 59.694 50.000 0.00 0.00 0.00 3.18
575 589 3.991773 TCGGAAGACCAAAACGTTGATAG 59.008 43.478 0.00 0.00 33.56 2.08
612 627 2.096614 CCATACAAACACACCGTTCGTC 60.097 50.000 0.00 0.00 36.59 4.20
677 699 2.821366 CAGCGCACCACCCATCTC 60.821 66.667 11.47 0.00 0.00 2.75
804 4096 1.905449 CAGGCGGTAACTCGTAAGTC 58.095 55.000 0.00 0.00 33.48 3.01
823 4115 3.766691 TAACGCCTCCCTCGTGCC 61.767 66.667 0.00 0.00 40.36 5.01
841 4134 0.255318 CCAGGCAAAGGCATCTCTCT 59.745 55.000 0.00 0.00 43.71 3.10
842 4135 1.666054 CAGGCAAAGGCATCTCTCTC 58.334 55.000 0.00 0.00 43.71 3.20
843 4136 0.545646 AGGCAAAGGCATCTCTCTCC 59.454 55.000 0.00 0.00 43.71 3.71
845 4138 1.474855 GGCAAAGGCATCTCTCTCCTC 60.475 57.143 0.00 0.00 43.71 3.71
846 4139 1.209019 GCAAAGGCATCTCTCTCCTCA 59.791 52.381 0.00 0.00 40.72 3.86
847 4140 2.158784 GCAAAGGCATCTCTCTCCTCAT 60.159 50.000 0.00 0.00 40.72 2.90
848 4141 3.684981 GCAAAGGCATCTCTCTCCTCATT 60.685 47.826 0.00 0.00 40.72 2.57
849 4142 4.128643 CAAAGGCATCTCTCTCCTCATTC 58.871 47.826 0.00 0.00 0.00 2.67
903 4196 4.503314 CCGGACCGCGTACCCTTC 62.503 72.222 8.86 0.00 0.00 3.46
904 4197 3.446570 CGGACCGCGTACCCTTCT 61.447 66.667 4.92 0.00 0.00 2.85
1063 4377 1.671742 GAGAAGGAGAACACCGCCA 59.328 57.895 0.00 0.00 37.17 5.69
1066 4380 3.883744 AAGGAGAACACCGCCAGCG 62.884 63.158 4.75 4.75 37.17 5.18
1409 4723 2.202222 GTCTGACAATGCGTGCGC 60.202 61.111 9.85 9.85 42.35 6.09
1438 4752 2.504175 AGTCATTTTAGAGGGCGGCTTA 59.496 45.455 9.56 0.00 0.00 3.09
1487 4802 1.002624 TGGGATTCGGTCCTGTTGC 60.003 57.895 7.54 0.00 46.91 4.17
1508 4823 4.580167 TGCTATGTCAAGGTGATAAATGGC 59.420 41.667 0.00 0.00 0.00 4.40
1528 4843 4.996122 TGGCATCACACATTTTGGAATTTC 59.004 37.500 0.00 0.00 0.00 2.17
1546 4861 0.103572 TCGGGGCGTTATCTTGTAGC 59.896 55.000 0.00 0.00 0.00 3.58
1581 4896 2.439135 GGAATTTGGGGGATTGGATTGG 59.561 50.000 0.00 0.00 0.00 3.16
1746 5063 7.444629 ACGATGAATGCAATGAAATATAGCT 57.555 32.000 0.00 0.00 0.00 3.32
1761 5078 2.506438 GCTCGGTGCTACCACGAC 60.506 66.667 0.00 0.00 43.00 4.34
1766 5083 0.938713 CGGTGCTACCACGACAAAAA 59.061 50.000 0.00 0.00 43.00 1.94
1767 5084 1.533731 CGGTGCTACCACGACAAAAAT 59.466 47.619 0.00 0.00 43.00 1.82
1768 5085 2.664424 CGGTGCTACCACGACAAAAATG 60.664 50.000 0.00 0.00 43.00 2.32
1885 5202 2.365635 AGCGCCACTATGAGGGGT 60.366 61.111 2.29 0.00 42.17 4.95
1971 5288 4.023193 CCTTGCGGTTTCATATATTGACCC 60.023 45.833 4.24 0.00 32.84 4.46
1979 5296 5.483685 TTCATATATTGACCCCTTCCTCG 57.516 43.478 0.00 0.00 32.84 4.63
2004 5321 1.895131 GAGTGTAGTTACCCGGGACAA 59.105 52.381 32.02 18.17 0.00 3.18
2066 5383 4.625564 CGTATGGGCCTAAACTTTCCTCTT 60.626 45.833 4.53 0.00 0.00 2.85
2076 5393 7.281324 GCCTAAACTTTCCTCTTATCTCCTTTC 59.719 40.741 0.00 0.00 0.00 2.62
2130 5447 3.427098 GCCAACTTACAACGGCCTAAATC 60.427 47.826 0.00 0.00 38.67 2.17
2239 5564 2.355010 AACCTTCTGCTGAACTTGCT 57.645 45.000 1.33 0.00 0.00 3.91
2440 5769 7.658179 ATTTGCACATACCTATCAACTATCG 57.342 36.000 0.00 0.00 0.00 2.92
2443 5772 5.535030 TGCACATACCTATCAACTATCGTCT 59.465 40.000 0.00 0.00 0.00 4.18
2460 5789 5.100344 TCGTCTCTATGTCAAGTACTCCT 57.900 43.478 0.00 0.00 0.00 3.69
2463 5792 5.354513 CGTCTCTATGTCAAGTACTCCTTCA 59.645 44.000 0.00 0.00 0.00 3.02
2464 5793 6.038825 CGTCTCTATGTCAAGTACTCCTTCAT 59.961 42.308 0.00 2.30 0.00 2.57
2468 5797 6.897966 TCTATGTCAAGTACTCCTTCATTCCT 59.102 38.462 0.00 0.00 0.00 3.36
2469 5798 5.825593 TGTCAAGTACTCCTTCATTCCTT 57.174 39.130 0.00 0.00 0.00 3.36
2470 5799 5.551233 TGTCAAGTACTCCTTCATTCCTTG 58.449 41.667 0.00 0.00 0.00 3.61
2472 5801 6.183361 TGTCAAGTACTCCTTCATTCCTTGAA 60.183 38.462 0.00 0.00 42.09 2.69
2473 5802 6.147985 GTCAAGTACTCCTTCATTCCTTGAAC 59.852 42.308 0.00 0.00 39.44 3.18
2474 5803 6.043243 TCAAGTACTCCTTCATTCCTTGAACT 59.957 38.462 0.00 0.00 39.44 3.01
2475 5804 7.234782 TCAAGTACTCCTTCATTCCTTGAACTA 59.765 37.037 0.00 0.00 39.44 2.24
2476 5805 7.554959 AGTACTCCTTCATTCCTTGAACTAA 57.445 36.000 0.00 0.00 39.44 2.24
2477 5806 7.974504 AGTACTCCTTCATTCCTTGAACTAAA 58.025 34.615 0.00 0.00 39.44 1.85
2478 5807 8.437575 AGTACTCCTTCATTCCTTGAACTAAAA 58.562 33.333 0.00 0.00 39.44 1.52
2481 5810 6.369629 TCCTTCATTCCTTGAACTAAAACCA 58.630 36.000 0.00 0.00 39.44 3.67
2483 5812 5.682943 TCATTCCTTGAACTAAAACCACG 57.317 39.130 0.00 0.00 0.00 4.94
2484 5813 5.369833 TCATTCCTTGAACTAAAACCACGA 58.630 37.500 0.00 0.00 0.00 4.35
2485 5814 5.237779 TCATTCCTTGAACTAAAACCACGAC 59.762 40.000 0.00 0.00 0.00 4.34
2488 5817 5.127491 TCCTTGAACTAAAACCACGACAAT 58.873 37.500 0.00 0.00 0.00 2.71
2489 5818 6.289834 TCCTTGAACTAAAACCACGACAATA 58.710 36.000 0.00 0.00 0.00 1.90
2490 5819 6.766944 TCCTTGAACTAAAACCACGACAATAA 59.233 34.615 0.00 0.00 0.00 1.40
2491 5820 7.446013 TCCTTGAACTAAAACCACGACAATAAT 59.554 33.333 0.00 0.00 0.00 1.28
2493 5822 9.458374 CTTGAACTAAAACCACGACAATAATTT 57.542 29.630 0.00 0.00 0.00 1.82
2495 5824 9.239002 TGAACTAAAACCACGACAATAATTTTG 57.761 29.630 0.00 0.00 0.00 2.44
2496 5825 8.582433 AACTAAAACCACGACAATAATTTTGG 57.418 30.769 0.00 0.00 0.00 3.28
2497 5826 7.942990 ACTAAAACCACGACAATAATTTTGGA 58.057 30.769 0.00 0.00 0.00 3.53
2498 5827 7.863877 ACTAAAACCACGACAATAATTTTGGAC 59.136 33.333 0.00 0.00 0.00 4.02
2586 5926 7.450014 TGGACAAAGAATTTCATAAGCCTAACA 59.550 33.333 0.00 0.00 35.03 2.41
2587 5927 8.303876 GGACAAAGAATTTCATAAGCCTAACAA 58.696 33.333 0.00 0.00 35.03 2.83
2606 5948 8.077991 CCTAACAATTGATACATGTATTGCAGG 58.922 37.037 19.19 18.12 32.58 4.85
2607 5949 5.835257 ACAATTGATACATGTATTGCAGGC 58.165 37.500 19.19 6.44 32.58 4.85
2613 5955 2.923121 ACATGTATTGCAGGCGATTCT 58.077 42.857 0.00 0.00 30.99 2.40
2625 5967 5.822519 TGCAGGCGATTCTTAATATCTTGTT 59.177 36.000 0.00 0.00 0.00 2.83
2657 5999 2.298729 TGTAAGCACATTTTTGGAGCCC 59.701 45.455 0.00 0.00 0.00 5.19
2679 6021 4.036498 CCTCAGCATTTGCCTCTCTTAATG 59.964 45.833 0.00 0.00 43.38 1.90
2683 6025 6.830324 TCAGCATTTGCCTCTCTTAATGTTAT 59.170 34.615 0.00 0.00 43.38 1.89
2860 6202 4.262592 GGTTCACAATCAGCCCAAAGATTT 60.263 41.667 0.00 0.00 32.43 2.17
2904 6246 8.063200 TCAAATCTTGCTGAATCATTGAATCT 57.937 30.769 3.52 0.00 0.00 2.40
2907 6249 6.594284 TCTTGCTGAATCATTGAATCTACG 57.406 37.500 3.52 0.00 0.00 3.51
2916 6258 8.337532 TGAATCATTGAATCTACGTTATGCTTG 58.662 33.333 0.00 0.00 0.00 4.01
2956 6298 6.220930 TGACATTTACGTCTGCTAGAACTTT 58.779 36.000 0.00 0.00 36.82 2.66
3063 6405 6.095860 CAGTATTCAAATCTGAAGGCCATCAA 59.904 38.462 12.50 3.89 44.68 2.57
3187 6529 1.141881 GTGTCGATGATGGCCTCGT 59.858 57.895 11.41 4.53 36.33 4.18
3246 6588 1.985473 AGTGAAAGGCTGACAATGCA 58.015 45.000 0.00 0.00 0.00 3.96
3247 6589 2.309613 AGTGAAAGGCTGACAATGCAA 58.690 42.857 0.00 0.00 0.00 4.08
3802 7144 5.539979 TGATCTAGCAAGAATCTCTCATGC 58.460 41.667 0.00 0.00 46.85 4.06
3805 7147 0.942962 GCAAGAATCTCTCATGCCCG 59.057 55.000 0.00 0.00 41.87 6.13
3824 7166 1.268437 CGCCTGTAGGTAGTTAGTCGC 60.268 57.143 0.00 0.00 37.57 5.19
3874 7217 5.108517 GCTATCTAGCTGCATCTGTAATCC 58.891 45.833 1.02 0.00 45.62 3.01
3911 7254 5.998981 TGACCGGAATGTTTTTGTACATAGT 59.001 36.000 9.46 0.00 37.76 2.12
3953 7296 4.201910 CGTGGTCAATGATAAAATTCCGCT 60.202 41.667 0.00 0.00 0.00 5.52
3989 7332 4.455190 GGCCATGTTTTTGTTGCATACATT 59.545 37.500 0.00 0.00 36.44 2.71
4035 7378 6.037940 TGAAGTGATCAGCATATTCTCAAAGC 59.962 38.462 0.00 0.00 33.04 3.51
4159 7624 7.807977 ATCATCCATAAAGTGCTTAAACGAT 57.192 32.000 0.00 0.00 0.00 3.73
4160 7625 8.902540 ATCATCCATAAAGTGCTTAAACGATA 57.097 30.769 0.00 0.00 0.00 2.92
4186 7651 4.992381 AACTGACAGCGATTTGAGTAAC 57.008 40.909 1.25 0.00 0.00 2.50
4217 7682 3.065925 GCAATAGGACTTCAGAATGGTGC 59.934 47.826 0.00 0.00 36.16 5.01
4218 7683 4.264253 CAATAGGACTTCAGAATGGTGCA 58.736 43.478 0.00 0.00 36.16 4.57
4232 7697 3.467374 TGGTGCAGCGATCATTACATA 57.533 42.857 11.91 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.040813 AGGGGAAGAGTGTGTCTACGTA 59.959 50.000 0.00 0.00 32.65 3.57
1 2 1.203025 AGGGGAAGAGTGTGTCTACGT 60.203 52.381 0.00 0.00 32.65 3.57
2 3 1.473278 GAGGGGAAGAGTGTGTCTACG 59.527 57.143 0.00 0.00 32.65 3.51
3 4 2.756207 GAGAGGGGAAGAGTGTGTCTAC 59.244 54.545 0.00 0.00 32.65 2.59
4 5 2.618302 CGAGAGGGGAAGAGTGTGTCTA 60.618 54.545 0.00 0.00 32.65 2.59
5 6 1.888826 CGAGAGGGGAAGAGTGTGTCT 60.889 57.143 0.00 0.00 36.94 3.41
6 7 0.528470 CGAGAGGGGAAGAGTGTGTC 59.472 60.000 0.00 0.00 0.00 3.67
7 8 0.178958 ACGAGAGGGGAAGAGTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
8 9 0.969894 AACGAGAGGGGAAGAGTGTG 59.030 55.000 0.00 0.00 0.00 3.82
9 10 0.969894 CAACGAGAGGGGAAGAGTGT 59.030 55.000 0.00 0.00 0.00 3.55
10 11 0.390472 GCAACGAGAGGGGAAGAGTG 60.390 60.000 0.00 0.00 0.00 3.51
11 12 0.543174 AGCAACGAGAGGGGAAGAGT 60.543 55.000 0.00 0.00 0.00 3.24
12 13 1.475403 TAGCAACGAGAGGGGAAGAG 58.525 55.000 0.00 0.00 0.00 2.85
13 14 1.757118 CATAGCAACGAGAGGGGAAGA 59.243 52.381 0.00 0.00 0.00 2.87
14 15 1.808133 GCATAGCAACGAGAGGGGAAG 60.808 57.143 0.00 0.00 0.00 3.46
15 16 0.178068 GCATAGCAACGAGAGGGGAA 59.822 55.000 0.00 0.00 0.00 3.97
16 17 0.975556 TGCATAGCAACGAGAGGGGA 60.976 55.000 0.00 0.00 34.76 4.81
17 18 0.107456 ATGCATAGCAACGAGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
18 19 1.069823 AGATGCATAGCAACGAGAGGG 59.930 52.381 0.00 0.00 43.62 4.30
19 20 2.402305 GAGATGCATAGCAACGAGAGG 58.598 52.381 0.00 0.00 43.62 3.69
20 21 2.035704 AGGAGATGCATAGCAACGAGAG 59.964 50.000 0.00 0.00 43.62 3.20
21 22 2.034878 AGGAGATGCATAGCAACGAGA 58.965 47.619 0.00 0.00 43.62 4.04
22 23 2.522836 AGGAGATGCATAGCAACGAG 57.477 50.000 0.00 0.00 43.62 4.18
23 24 4.400529 TTTAGGAGATGCATAGCAACGA 57.599 40.909 0.00 0.00 43.62 3.85
24 25 6.159293 TCTATTTAGGAGATGCATAGCAACG 58.841 40.000 0.00 0.00 43.62 4.10
25 26 8.040132 AGATCTATTTAGGAGATGCATAGCAAC 58.960 37.037 0.00 0.00 43.62 4.17
26 27 8.143673 AGATCTATTTAGGAGATGCATAGCAA 57.856 34.615 0.00 0.00 43.62 3.91
27 28 7.730672 AGATCTATTTAGGAGATGCATAGCA 57.269 36.000 0.00 0.00 44.86 3.49
28 29 7.011295 GCAAGATCTATTTAGGAGATGCATAGC 59.989 40.741 0.00 0.00 33.71 2.97
29 30 7.222417 CGCAAGATCTATTTAGGAGATGCATAG 59.778 40.741 0.00 0.00 43.02 2.23
30 31 7.038048 CGCAAGATCTATTTAGGAGATGCATA 58.962 38.462 0.00 0.00 43.02 3.14
31 32 5.873712 CGCAAGATCTATTTAGGAGATGCAT 59.126 40.000 0.00 0.00 43.02 3.96
32 33 5.221521 ACGCAAGATCTATTTAGGAGATGCA 60.222 40.000 0.00 0.00 43.62 3.96
33 34 5.119898 CACGCAAGATCTATTTAGGAGATGC 59.880 44.000 0.00 0.00 43.62 3.91
34 35 6.450545 TCACGCAAGATCTATTTAGGAGATG 58.549 40.000 0.00 0.00 43.62 2.90
35 36 6.656632 TCACGCAAGATCTATTTAGGAGAT 57.343 37.500 0.00 0.00 43.62 2.75
36 37 5.508153 GCTCACGCAAGATCTATTTAGGAGA 60.508 44.000 0.00 0.00 43.62 3.71
37 38 4.683781 GCTCACGCAAGATCTATTTAGGAG 59.316 45.833 0.00 0.94 43.62 3.69
38 39 4.621991 GCTCACGCAAGATCTATTTAGGA 58.378 43.478 0.00 0.00 43.62 2.94
39 40 3.426859 CGCTCACGCAAGATCTATTTAGG 59.573 47.826 0.00 0.00 43.62 2.69
40 41 3.426859 CCGCTCACGCAAGATCTATTTAG 59.573 47.826 0.00 0.00 43.62 1.85
41 42 3.067601 TCCGCTCACGCAAGATCTATTTA 59.932 43.478 0.00 0.00 43.62 1.40
42 43 2.159099 TCCGCTCACGCAAGATCTATTT 60.159 45.455 0.00 0.00 43.62 1.40
43 44 1.409064 TCCGCTCACGCAAGATCTATT 59.591 47.619 0.00 0.00 43.62 1.73
44 45 1.000827 CTCCGCTCACGCAAGATCTAT 60.001 52.381 0.00 0.00 43.62 1.98
45 46 0.382158 CTCCGCTCACGCAAGATCTA 59.618 55.000 0.00 0.00 43.62 1.98
46 47 1.140589 CTCCGCTCACGCAAGATCT 59.859 57.895 0.00 0.00 43.62 2.75
47 48 1.880340 CCTCCGCTCACGCAAGATC 60.880 63.158 0.00 0.00 43.62 2.75
48 49 2.185350 CCTCCGCTCACGCAAGAT 59.815 61.111 0.00 0.00 43.62 2.40
49 50 4.069232 CCCTCCGCTCACGCAAGA 62.069 66.667 0.00 0.00 43.62 3.02
51 52 2.463589 AAATCCCTCCGCTCACGCAA 62.464 55.000 0.00 0.00 38.22 4.85
52 53 2.463589 AAAATCCCTCCGCTCACGCA 62.464 55.000 0.00 0.00 38.22 5.24
53 54 1.305930 AAAAATCCCTCCGCTCACGC 61.306 55.000 0.00 0.00 38.22 5.34
54 55 2.854522 AAAAATCCCTCCGCTCACG 58.145 52.632 0.00 0.00 39.67 4.35
70 71 6.595772 AAACGTAGCATGCAATTTCAAAAA 57.404 29.167 21.98 0.00 0.00 1.94
71 72 6.292596 GGAAAACGTAGCATGCAATTTCAAAA 60.293 34.615 21.98 0.00 30.40 2.44
72 73 5.176590 GGAAAACGTAGCATGCAATTTCAAA 59.823 36.000 21.98 0.00 30.40 2.69
73 74 4.683781 GGAAAACGTAGCATGCAATTTCAA 59.316 37.500 21.98 0.00 30.40 2.69
74 75 4.233789 GGAAAACGTAGCATGCAATTTCA 58.766 39.130 21.98 0.00 30.40 2.69
75 76 4.233789 TGGAAAACGTAGCATGCAATTTC 58.766 39.130 21.98 19.23 0.00 2.17
76 77 4.250116 TGGAAAACGTAGCATGCAATTT 57.750 36.364 21.98 12.49 0.00 1.82
77 78 3.932545 TGGAAAACGTAGCATGCAATT 57.067 38.095 21.98 5.18 0.00 2.32
78 79 3.005261 TGTTGGAAAACGTAGCATGCAAT 59.995 39.130 21.98 1.90 0.00 3.56
79 80 2.359214 TGTTGGAAAACGTAGCATGCAA 59.641 40.909 21.98 0.00 0.00 4.08
80 81 1.950216 TGTTGGAAAACGTAGCATGCA 59.050 42.857 21.98 2.77 0.00 3.96
81 82 2.697431 TGTTGGAAAACGTAGCATGC 57.303 45.000 10.51 10.51 0.00 4.06
82 83 4.793071 TCAATGTTGGAAAACGTAGCATG 58.207 39.130 0.00 0.00 0.00 4.06
83 84 4.759693 TCTCAATGTTGGAAAACGTAGCAT 59.240 37.500 0.00 0.00 0.00 3.79
84 85 4.130857 TCTCAATGTTGGAAAACGTAGCA 58.869 39.130 0.00 0.00 0.00 3.49
85 86 4.742438 TCTCAATGTTGGAAAACGTAGC 57.258 40.909 0.00 0.00 0.00 3.58
86 87 5.912955 GGTTTCTCAATGTTGGAAAACGTAG 59.087 40.000 0.00 0.00 35.62 3.51
87 88 5.504337 CGGTTTCTCAATGTTGGAAAACGTA 60.504 40.000 23.55 2.54 44.24 3.57
88 89 4.678622 GGTTTCTCAATGTTGGAAAACGT 58.321 39.130 12.97 0.00 35.62 3.99
89 90 3.728718 CGGTTTCTCAATGTTGGAAAACG 59.271 43.478 21.13 21.13 44.07 3.60
90 91 4.048504 CCGGTTTCTCAATGTTGGAAAAC 58.951 43.478 0.00 11.45 34.55 2.43
91 92 3.068873 CCCGGTTTCTCAATGTTGGAAAA 59.931 43.478 0.00 2.12 32.88 2.29
92 93 2.625790 CCCGGTTTCTCAATGTTGGAAA 59.374 45.455 0.00 5.74 0.00 3.13
93 94 2.235016 CCCGGTTTCTCAATGTTGGAA 58.765 47.619 0.00 0.00 0.00 3.53
94 95 1.144093 ACCCGGTTTCTCAATGTTGGA 59.856 47.619 0.00 0.00 0.00 3.53
95 96 1.539827 GACCCGGTTTCTCAATGTTGG 59.460 52.381 0.00 0.00 0.00 3.77
96 97 2.226330 TGACCCGGTTTCTCAATGTTG 58.774 47.619 0.00 0.00 0.00 3.33
97 98 2.649531 TGACCCGGTTTCTCAATGTT 57.350 45.000 0.00 0.00 0.00 2.71
98 99 2.504367 CTTGACCCGGTTTCTCAATGT 58.496 47.619 0.00 0.00 0.00 2.71
99 100 1.200020 GCTTGACCCGGTTTCTCAATG 59.800 52.381 0.00 0.00 0.00 2.82
100 101 1.534729 GCTTGACCCGGTTTCTCAAT 58.465 50.000 0.00 0.00 0.00 2.57
101 102 0.536460 GGCTTGACCCGGTTTCTCAA 60.536 55.000 0.00 0.83 0.00 3.02
102 103 1.072505 GGCTTGACCCGGTTTCTCA 59.927 57.895 0.00 0.00 0.00 3.27
174 176 6.708054 CACTTTGTGTATCTTTCAAGGAGAGT 59.292 38.462 0.00 0.00 0.00 3.24
197 199 3.070302 TGGTTCCCTTTAAACATTGCCAC 59.930 43.478 0.00 0.00 0.00 5.01
200 202 4.698575 TGTTGGTTCCCTTTAAACATTGC 58.301 39.130 0.00 0.00 0.00 3.56
205 207 9.647797 CCTTAAATATGTTGGTTCCCTTTAAAC 57.352 33.333 0.00 0.00 0.00 2.01
226 229 3.133362 ACCGTGAGAGTTTGTGTCCTTAA 59.867 43.478 0.00 0.00 0.00 1.85
228 231 1.485066 ACCGTGAGAGTTTGTGTCCTT 59.515 47.619 0.00 0.00 0.00 3.36
246 249 2.507324 GACGCTGGCGAAGAGACC 60.507 66.667 21.77 0.00 42.83 3.85
248 251 2.622962 TTCGACGCTGGCGAAGAGA 61.623 57.895 21.77 11.14 42.17 3.10
265 269 1.025812 CCTAGCCTCGACGTCTGATT 58.974 55.000 14.70 4.69 0.00 2.57
317 321 1.221840 GATGAGGTGGTGGCGATGT 59.778 57.895 0.00 0.00 0.00 3.06
319 323 0.548031 ATTGATGAGGTGGTGGCGAT 59.452 50.000 0.00 0.00 0.00 4.58
320 324 0.392863 CATTGATGAGGTGGTGGCGA 60.393 55.000 0.00 0.00 0.00 5.54
390 394 4.002506 TGGCGGCAAGAGAAGCGA 62.003 61.111 10.22 0.00 0.00 4.93
395 399 4.069232 CTCGGTGGCGGCAAGAGA 62.069 66.667 29.60 20.70 0.00 3.10
489 493 0.914644 CATTCCTCCTTCTCCCAGCA 59.085 55.000 0.00 0.00 0.00 4.41
513 518 4.758251 TGGTCCTGGCGCATGTCG 62.758 66.667 10.83 5.35 42.12 4.35
612 627 2.657237 GTGGAGGGGACGTGACAG 59.343 66.667 0.00 0.00 0.00 3.51
677 699 0.949105 CGAACCGTTGGAGTTGGGAG 60.949 60.000 0.00 0.00 0.00 4.30
804 4096 2.202570 CACGAGGGAGGCGTTACG 60.203 66.667 0.00 0.00 40.44 3.18
823 4115 1.666054 GAGAGAGATGCCTTTGCCTG 58.334 55.000 0.00 0.00 36.33 4.85
900 4193 4.002316 CCTTGGCTTTGAGAGAAGAGAAG 58.998 47.826 0.00 0.00 0.00 2.85
901 4194 3.244700 CCCTTGGCTTTGAGAGAAGAGAA 60.245 47.826 0.00 0.00 0.00 2.87
902 4195 2.304180 CCCTTGGCTTTGAGAGAAGAGA 59.696 50.000 0.00 0.00 0.00 3.10
903 4196 2.709213 CCCTTGGCTTTGAGAGAAGAG 58.291 52.381 0.00 0.00 0.00 2.85
904 4197 1.271597 GCCCTTGGCTTTGAGAGAAGA 60.272 52.381 0.00 0.00 46.69 2.87
980 4294 2.851104 CGTTGGGCGTCGAGTTTC 59.149 61.111 0.00 0.00 35.54 2.78
1047 4361 2.035442 GCTGGCGGTGTTCTCCTTC 61.035 63.158 0.00 0.00 0.00 3.46
1240 4554 3.773154 GGAGCCCTCCCTCCTCCT 61.773 72.222 2.81 0.00 46.39 3.69
1409 4723 4.035675 GCCCTCTAAAATGACTCGGATTTG 59.964 45.833 0.00 0.00 0.00 2.32
1438 4752 1.002773 ACGAACTTCGCACCCCTAAAT 59.997 47.619 11.15 0.00 45.12 1.40
1487 4802 6.487668 TGATGCCATTTATCACCTTGACATAG 59.512 38.462 0.00 0.00 30.03 2.23
1508 4823 4.626604 CCCGAAATTCCAAAATGTGTGATG 59.373 41.667 0.00 0.00 0.00 3.07
1528 4843 0.179094 TGCTACAAGATAACGCCCCG 60.179 55.000 0.00 0.00 0.00 5.73
1546 4861 3.495193 CAAATTCCAGAATGCACGACTG 58.505 45.455 8.91 8.91 31.97 3.51
1581 4896 2.230130 TGATTGATTCACCCCCAACC 57.770 50.000 0.00 0.00 0.00 3.77
1677 4994 9.653287 CAATAAGGATGACATGTACGGTATAAT 57.347 33.333 0.00 0.00 0.00 1.28
1680 4997 7.015292 AGACAATAAGGATGACATGTACGGTAT 59.985 37.037 0.00 0.00 0.00 2.73
1684 5001 6.273071 TCAGACAATAAGGATGACATGTACG 58.727 40.000 0.00 0.00 0.00 3.67
1746 5063 0.104487 TTTTGTCGTGGTAGCACCGA 59.896 50.000 18.90 15.63 42.58 4.69
1753 5070 2.158652 TGTCCCCATTTTTGTCGTGGTA 60.159 45.455 0.00 0.00 0.00 3.25
1754 5071 1.324383 GTCCCCATTTTTGTCGTGGT 58.676 50.000 0.00 0.00 0.00 4.16
1756 5073 3.658757 AATGTCCCCATTTTTGTCGTG 57.341 42.857 0.00 0.00 38.10 4.35
1757 5074 5.993748 AATAATGTCCCCATTTTTGTCGT 57.006 34.783 0.00 0.00 41.50 4.34
1758 5075 6.090628 CACAAATAATGTCCCCATTTTTGTCG 59.909 38.462 16.58 12.28 42.39 4.35
1760 5077 7.072263 TCACAAATAATGTCCCCATTTTTGT 57.928 32.000 15.15 15.15 43.42 2.83
1761 5078 8.564509 AATCACAAATAATGTCCCCATTTTTG 57.435 30.769 14.40 14.40 41.46 2.44
1766 5083 7.256494 ACAAAATCACAAATAATGTCCCCAT 57.744 32.000 0.00 0.00 41.46 4.00
1767 5084 6.678568 ACAAAATCACAAATAATGTCCCCA 57.321 33.333 0.00 0.00 41.46 4.96
1768 5085 6.128309 GCAACAAAATCACAAATAATGTCCCC 60.128 38.462 0.00 0.00 41.46 4.81
1885 5202 5.784023 TCCACCAACCAATCTACTAGGATA 58.216 41.667 0.00 0.00 0.00 2.59
1979 5296 1.517913 GGGTAACTACACTCGCCGC 60.518 63.158 0.00 0.00 0.00 6.53
1990 5307 1.677552 CAGCTTGTCCCGGGTAACT 59.322 57.895 22.86 13.32 0.00 2.24
1991 5308 2.038837 GCAGCTTGTCCCGGGTAAC 61.039 63.158 22.86 13.46 0.00 2.50
2004 5321 0.316204 GACACCAAGCAATTGCAGCT 59.684 50.000 30.89 13.05 45.97 4.24
2066 5383 4.780021 ACAAAGAGAGGCAGAAAGGAGATA 59.220 41.667 0.00 0.00 0.00 1.98
2076 5393 3.891422 AGAGATGACAAAGAGAGGCAG 57.109 47.619 0.00 0.00 0.00 4.85
2130 5447 6.038382 TCTCTTCGTACTTCCTACAGCATTAG 59.962 42.308 0.00 0.00 0.00 1.73
2231 5556 9.489084 AGGAAATTTACCAAAAATAGCAAGTTC 57.511 29.630 0.00 0.00 0.00 3.01
2239 5564 9.303116 TCAGTGCTAGGAAATTTACCAAAAATA 57.697 29.630 0.00 0.00 0.00 1.40
2440 5769 6.761099 TGAAGGAGTACTTGACATAGAGAC 57.239 41.667 0.00 0.00 40.21 3.36
2443 5772 6.897966 AGGAATGAAGGAGTACTTGACATAGA 59.102 38.462 0.00 0.00 40.21 1.98
2460 5789 5.823570 TCGTGGTTTTAGTTCAAGGAATGAA 59.176 36.000 0.00 0.00 45.71 2.57
2463 5792 5.127491 TGTCGTGGTTTTAGTTCAAGGAAT 58.873 37.500 0.00 0.00 0.00 3.01
2464 5793 4.515361 TGTCGTGGTTTTAGTTCAAGGAA 58.485 39.130 0.00 0.00 0.00 3.36
2468 5797 9.804758 AAAATTATTGTCGTGGTTTTAGTTCAA 57.195 25.926 0.00 0.00 0.00 2.69
2469 5798 9.239002 CAAAATTATTGTCGTGGTTTTAGTTCA 57.761 29.630 0.00 0.00 0.00 3.18
2470 5799 8.696175 CCAAAATTATTGTCGTGGTTTTAGTTC 58.304 33.333 0.00 0.00 0.00 3.01
2472 5801 7.863877 GTCCAAAATTATTGTCGTGGTTTTAGT 59.136 33.333 0.00 0.00 0.00 2.24
2473 5802 7.327518 GGTCCAAAATTATTGTCGTGGTTTTAG 59.672 37.037 0.00 0.00 0.00 1.85
2474 5803 7.146648 GGTCCAAAATTATTGTCGTGGTTTTA 58.853 34.615 0.00 0.00 0.00 1.52
2475 5804 5.986741 GGTCCAAAATTATTGTCGTGGTTTT 59.013 36.000 0.00 0.00 0.00 2.43
2476 5805 5.534407 GGTCCAAAATTATTGTCGTGGTTT 58.466 37.500 0.00 0.00 0.00 3.27
2477 5806 4.320641 CGGTCCAAAATTATTGTCGTGGTT 60.321 41.667 0.00 0.00 0.00 3.67
2478 5807 3.189702 CGGTCCAAAATTATTGTCGTGGT 59.810 43.478 0.00 0.00 0.00 4.16
2481 5810 3.677190 TCCGGTCCAAAATTATTGTCGT 58.323 40.909 0.00 0.00 0.00 4.34
2483 5812 3.380320 CCCTCCGGTCCAAAATTATTGTC 59.620 47.826 0.00 0.00 0.00 3.18
2484 5813 3.010808 TCCCTCCGGTCCAAAATTATTGT 59.989 43.478 0.00 0.00 0.00 2.71
2485 5814 3.626930 TCCCTCCGGTCCAAAATTATTG 58.373 45.455 0.00 0.00 0.00 1.90
2488 5817 4.475747 ACTATTCCCTCCGGTCCAAAATTA 59.524 41.667 0.00 0.00 0.00 1.40
2489 5818 2.919772 ATTCCCTCCGGTCCAAAATT 57.080 45.000 0.00 0.00 0.00 1.82
2490 5819 2.850568 ACTATTCCCTCCGGTCCAAAAT 59.149 45.455 0.00 0.00 0.00 1.82
2491 5820 2.271777 ACTATTCCCTCCGGTCCAAAA 58.728 47.619 0.00 0.00 0.00 2.44
2493 5822 1.961133 AACTATTCCCTCCGGTCCAA 58.039 50.000 0.00 0.00 0.00 3.53
2495 5824 1.690893 GGTAACTATTCCCTCCGGTCC 59.309 57.143 0.00 0.00 0.00 4.46
2496 5825 2.391678 TGGTAACTATTCCCTCCGGTC 58.608 52.381 0.00 0.00 37.61 4.79
2497 5826 2.555732 TGGTAACTATTCCCTCCGGT 57.444 50.000 0.00 0.00 37.61 5.28
2498 5827 2.704065 ACATGGTAACTATTCCCTCCGG 59.296 50.000 0.00 0.00 37.61 5.14
2586 5926 4.821260 TCGCCTGCAATACATGTATCAATT 59.179 37.500 18.52 2.23 0.00 2.32
2587 5927 4.388485 TCGCCTGCAATACATGTATCAAT 58.612 39.130 18.52 0.66 0.00 2.57
2606 5948 7.246674 TCCACAACAAGATATTAAGAATCGC 57.753 36.000 0.00 0.00 0.00 4.58
2607 5949 7.519008 GCCTCCACAACAAGATATTAAGAATCG 60.519 40.741 0.00 0.00 0.00 3.34
2613 5955 6.663093 ACATTGCCTCCACAACAAGATATTAA 59.337 34.615 0.00 0.00 31.03 1.40
2625 5967 1.202867 TGTGCTTACATTGCCTCCACA 60.203 47.619 0.00 0.00 0.00 4.17
2651 5993 2.421399 GGCAAATGCTGAGGGCTCC 61.421 63.158 5.25 0.00 42.39 4.70
2652 5994 1.379576 AGGCAAATGCTGAGGGCTC 60.380 57.895 5.25 0.00 42.39 4.70
2657 5999 4.639310 ACATTAAGAGAGGCAAATGCTGAG 59.361 41.667 5.25 0.00 41.70 3.35
2683 6025 7.857404 TGAAGGGGGAAACATGTTATAAAAA 57.143 32.000 12.39 0.00 0.00 1.94
2688 6030 5.402630 AGTTTGAAGGGGGAAACATGTTAT 58.597 37.500 12.39 2.16 35.00 1.89
2860 6202 8.519799 GATTTGATTAATCTTACCCAAGGACA 57.480 34.615 16.24 0.00 39.67 4.02
2898 6240 4.137116 AGCCAAGCATAACGTAGATTCA 57.863 40.909 0.00 0.00 0.00 2.57
2904 6246 3.142951 ACACAAAGCCAAGCATAACGTA 58.857 40.909 0.00 0.00 0.00 3.57
2907 6249 4.119136 ACAAACACAAAGCCAAGCATAAC 58.881 39.130 0.00 0.00 0.00 1.89
2916 6258 3.502191 TGTCAGAACAAACACAAAGCC 57.498 42.857 0.00 0.00 30.70 4.35
2956 6298 1.144969 CCGTTTTCTCTTGCAGCGTA 58.855 50.000 0.00 0.00 0.00 4.42
3063 6405 1.751351 TGCGCTCACTATACTTGCTCT 59.249 47.619 9.73 0.00 0.00 4.09
3728 7070 4.085733 TGCCTTAGCCTGCAAAAGAATAA 58.914 39.130 5.99 0.00 38.69 1.40
3752 7094 9.367160 ACCCCTAATCCACTAATAATGAATTTG 57.633 33.333 0.00 0.00 0.00 2.32
3802 7144 1.680207 GACTAACTACCTACAGGCGGG 59.320 57.143 0.00 0.00 39.32 6.13
3805 7147 1.268437 CGCGACTAACTACCTACAGGC 60.268 57.143 0.00 0.00 39.32 4.85
3824 7166 1.917303 GTAAATGCAACCGAAATGGCG 59.083 47.619 0.00 0.00 43.94 5.69
3853 7196 4.158579 CCGGATTACAGATGCAGCTAGATA 59.841 45.833 3.06 0.00 0.00 1.98
3874 7217 1.074319 CCGGTCACACGTTGATACCG 61.074 60.000 17.23 17.23 43.45 4.02
3911 7254 0.965439 GGCACCACCAACATGCTAAA 59.035 50.000 0.00 0.00 39.38 1.85
3953 7296 2.318908 ACATGGCCTGAAAGCTTTCAA 58.681 42.857 34.71 23.92 45.61 2.69
3969 7312 5.846994 GCACAATGTATGCAACAAAAACATG 59.153 36.000 0.00 0.00 42.70 3.21
4035 7378 0.906775 ATTTGCTGGCCCCATTTCAG 59.093 50.000 0.00 0.00 0.00 3.02
4076 7419 1.292061 TACTGTTGTGCACACGTTCC 58.708 50.000 21.56 5.89 0.00 3.62
4077 7420 3.095738 GTTTACTGTTGTGCACACGTTC 58.904 45.455 21.56 10.96 0.00 3.95
4155 7620 4.895224 TCGCTGTCAGTTATCTTATCGT 57.105 40.909 0.93 0.00 0.00 3.73
4159 7624 6.631016 ACTCAAATCGCTGTCAGTTATCTTA 58.369 36.000 0.93 0.00 0.00 2.10
4160 7625 5.482908 ACTCAAATCGCTGTCAGTTATCTT 58.517 37.500 0.93 0.00 0.00 2.40
4186 7651 4.744570 TGAAGTCCTATTGCTACTGAACG 58.255 43.478 0.00 0.00 0.00 3.95
4217 7682 5.784177 AGGTTACCTATGTAATGATCGCTG 58.216 41.667 0.15 0.00 39.08 5.18
4218 7683 6.350277 GCTAGGTTACCTATGTAATGATCGCT 60.350 42.308 11.97 0.00 39.08 4.93
4232 7697 2.017113 GCCGCAATTGCTAGGTTACCT 61.017 52.381 26.86 9.57 39.32 3.08


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

AutoCloner maintained by Alex Coulton.