Multiple sequence alignment - TraesCS5A01G208200

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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 TraesCS5A01G208200 chr5A 100.000 5241 0 0 1 5241 421822441 421827681 0.000000e+00 9679.0
1 TraesCS5A01G208200 chr5A 97.162 881 24 1 1932 2811 602838315 602839195 0.000000e+00 1487.0
2 TraesCS5A01G208200 chr5A 96.939 882 26 1 1932 2812 483275702 483276583 0.000000e+00 1478.0
3 TraesCS5A01G208200 chr5A 87.821 312 36 2 4054 4364 421834243 421834553 1.070000e-96 364.0
4 TraesCS5A01G208200 chr5A 90.710 183 11 4 4579 4756 290391868 290391687 6.780000e-59 239.0
5 TraesCS5A01G208200 chr5D 92.316 1809 94 25 2810 4587 323908209 323910003 0.000000e+00 2529.0
6 TraesCS5A01G208200 chr5D 91.284 1044 46 10 900 1925 323907204 323908220 0.000000e+00 1382.0
7 TraesCS5A01G208200 chr5D 96.172 209 7 1 5034 5241 323910578 323910786 1.810000e-89 340.0
8 TraesCS5A01G208200 chr5D 85.535 318 45 1 4054 4371 323917031 323917347 1.090000e-86 331.0
9 TraesCS5A01G208200 chr5D 89.394 264 17 6 1 257 323906347 323906606 6.550000e-84 322.0
10 TraesCS5A01G208200 chr5D 93.966 116 4 3 4746 4860 323910001 323910114 6.980000e-39 172.0
11 TraesCS5A01G208200 chr5D 98.276 58 1 0 4858 4915 323910146 323910203 9.290000e-18 102.0
12 TraesCS5A01G208200 chr5B 92.276 1476 67 17 3140 4587 375617333 375618789 0.000000e+00 2050.0
13 TraesCS5A01G208200 chr5B 94.227 1074 47 5 866 1929 375615909 375616977 0.000000e+00 1626.0
14 TraesCS5A01G208200 chr5B 93.878 392 16 4 4858 5241 375619781 375620172 7.560000e-163 584.0
15 TraesCS5A01G208200 chr5B 91.317 334 20 2 2810 3141 375616962 375617288 1.040000e-121 448.0
16 TraesCS5A01G208200 chr5B 87.662 308 33 3 4061 4364 375644366 375644672 2.320000e-93 353.0
17 TraesCS5A01G208200 chr5B 87.730 163 14 5 7 163 375615120 375615282 8.960000e-43 185.0
18 TraesCS5A01G208200 chr3D 97.508 883 16 4 1932 2812 329443460 329442582 0.000000e+00 1504.0
19 TraesCS5A01G208200 chr1D 97.052 882 25 1 1932 2812 223523693 223524574 0.000000e+00 1483.0
20 TraesCS5A01G208200 chr1D 91.111 180 12 2 4578 4754 238940209 238940387 1.890000e-59 241.0
21 TraesCS5A01G208200 chr2A 96.939 882 26 1 1932 2812 624463112 624462231 0.000000e+00 1478.0
22 TraesCS5A01G208200 chr2A 79.449 1489 201 57 2811 4251 737235647 737237078 0.000000e+00 957.0
23 TraesCS5A01G208200 chr2A 85.366 615 81 6 950 1562 737234708 737235315 3.440000e-176 628.0
24 TraesCS5A01G208200 chr2A 85.965 57 6 2 561 617 740871727 740871673 5.670000e-05 60.2
25 TraesCS5A01G208200 chr7D 97.039 878 25 1 1932 2808 465339685 465340562 0.000000e+00 1476.0
26 TraesCS5A01G208200 chr7D 92.571 175 9 2 4578 4749 39001278 39001451 1.130000e-61 248.0
27 TraesCS5A01G208200 chr7A 96.932 880 26 1 1932 2810 664228870 664227991 0.000000e+00 1474.0
28 TraesCS5A01G208200 chr7A 92.486 173 9 2 4584 4753 115807688 115807517 1.460000e-60 244.0
29 TraesCS5A01G208200 chr4D 96.829 883 26 2 1932 2812 242938085 242938967 0.000000e+00 1474.0
30 TraesCS5A01G208200 chr2B 96.825 882 27 1 1932 2812 214596226 214595345 0.000000e+00 1472.0
31 TraesCS5A01G208200 chr2B 79.150 1458 190 58 2811 4220 736726538 736727929 0.000000e+00 904.0
32 TraesCS5A01G208200 chr2B 85.342 614 82 5 950 1562 736725609 736726215 3.440000e-176 628.0
33 TraesCS5A01G208200 chr2D 79.555 1482 201 54 2811 4245 605829211 605830637 0.000000e+00 965.0
34 TraesCS5A01G208200 chr2D 82.899 614 76 11 950 1562 605828294 605828879 4.650000e-145 525.0
35 TraesCS5A01G208200 chr2D 93.976 166 6 2 4585 4747 647970257 647970093 1.130000e-61 248.0
36 TraesCS5A01G208200 chr4B 93.491 169 6 4 4585 4750 667612094 667612260 4.050000e-61 246.0
37 TraesCS5A01G208200 chr3B 92.941 170 8 2 4581 4747 655849589 655849421 1.460000e-60 244.0
38 TraesCS5A01G208200 chr6A 91.111 180 10 4 4582 4756 24072063 24071885 6.780000e-59 239.0
39 TraesCS5A01G208200 chr3A 87.500 208 14 10 4582 4783 70479042 70479243 4.080000e-56 230.0
40 TraesCS5A01G208200 chr6D 100.000 28 0 0 563 590 461449164 461449191 9.000000e-03 52.8


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 TraesCS5A01G208200 chr5A 421822441 421827681 5240 False 9679.000000 9679 100.0000 1 5241 1 chr5A.!!$F1 5240
1 TraesCS5A01G208200 chr5A 602838315 602839195 880 False 1487.000000 1487 97.1620 1932 2811 1 chr5A.!!$F4 879
2 TraesCS5A01G208200 chr5A 483275702 483276583 881 False 1478.000000 1478 96.9390 1932 2812 1 chr5A.!!$F3 880
3 TraesCS5A01G208200 chr5D 323906347 323910786 4439 False 807.833333 2529 93.5680 1 5241 6 chr5D.!!$F2 5240
4 TraesCS5A01G208200 chr5B 375615120 375620172 5052 False 978.600000 2050 91.8856 7 5241 5 chr5B.!!$F2 5234
5 TraesCS5A01G208200 chr3D 329442582 329443460 878 True 1504.000000 1504 97.5080 1932 2812 1 chr3D.!!$R1 880
6 TraesCS5A01G208200 chr1D 223523693 223524574 881 False 1483.000000 1483 97.0520 1932 2812 1 chr1D.!!$F1 880
7 TraesCS5A01G208200 chr2A 624462231 624463112 881 True 1478.000000 1478 96.9390 1932 2812 1 chr2A.!!$R1 880
8 TraesCS5A01G208200 chr2A 737234708 737237078 2370 False 792.500000 957 82.4075 950 4251 2 chr2A.!!$F1 3301
9 TraesCS5A01G208200 chr7D 465339685 465340562 877 False 1476.000000 1476 97.0390 1932 2808 1 chr7D.!!$F2 876
10 TraesCS5A01G208200 chr7A 664227991 664228870 879 True 1474.000000 1474 96.9320 1932 2810 1 chr7A.!!$R2 878
11 TraesCS5A01G208200 chr4D 242938085 242938967 882 False 1474.000000 1474 96.8290 1932 2812 1 chr4D.!!$F1 880
12 TraesCS5A01G208200 chr2B 214595345 214596226 881 True 1472.000000 1472 96.8250 1932 2812 1 chr2B.!!$R1 880
13 TraesCS5A01G208200 chr2B 736725609 736727929 2320 False 766.000000 904 82.2460 950 4220 2 chr2B.!!$F1 3270
14 TraesCS5A01G208200 chr2D 605828294 605830637 2343 False 745.000000 965 81.2270 950 4245 2 chr2D.!!$F1 3295

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
827 1007 0.535780 AAAACCGGTCGGAACCTTCC 60.536 55.0 16.9 0.0 44.04 3.46 F
829 1009 0.542702 AACCGGTCGGAACCTTCCTA 60.543 55.0 16.9 0.0 45.33 2.94 F
850 1030 0.675522 AACCTCACGTTATTGGGCCG 60.676 55.0 0.0 0.0 30.96 6.13 F
2607 2878 1.617947 ATGTCAAGAGAGGTCGGGGC 61.618 60.0 0.0 0.0 0.00 5.80 F
3058 3342 1.917872 TTTGGTCATACCCTGTTGGC 58.082 50.0 0.0 0.0 37.50 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 2229 0.452987 CACCACATCATCCGCAAAGG 59.547 55.000 0.00 0.00 42.97 3.11 R
2544 2815 0.543277 TATGCACTGGAGCTTCTGGG 59.457 55.000 3.68 0.00 34.99 4.45 R
2704 2975 0.761187 GGCTCTGGCACATGGATAGA 59.239 55.000 0.00 0.00 38.20 1.98 R
4111 4512 1.141657 ACATGGATGAATCGACCAGGG 59.858 52.381 12.75 6.73 39.36 4.45 R
4860 5262 1.066430 GGGGTCGTCTTATTCTGTGCA 60.066 52.381 0.00 0.00 0.00 4.57 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
30 32 7.921786 TTTGTCAATACCTATGAGACCAAAG 57.078 36.000 0.00 0.00 0.00 2.77
44 46 6.454795 TGAGACCAAAGTGGAATTATTTTGC 58.545 36.000 0.18 0.00 40.96 3.68
125 133 5.496556 CACATCACATCCAAGTTTACCCTA 58.503 41.667 0.00 0.00 0.00 3.53
131 139 7.867921 TCACATCCAAGTTTACCCTATTACAT 58.132 34.615 0.00 0.00 0.00 2.29
133 141 7.013274 CACATCCAAGTTTACCCTATTACATGG 59.987 40.741 0.00 0.00 32.25 3.66
158 166 3.684305 GGATGCCACAAAATGTAAAAGCC 59.316 43.478 0.00 0.00 0.00 4.35
175 183 7.773224 TGTAAAAGCCATGCTATGTATAGTTGT 59.227 33.333 1.28 0.00 38.25 3.32
177 185 5.551305 AGCCATGCTATGTATAGTTGTGA 57.449 39.130 1.28 0.00 36.99 3.58
210 218 4.201647 GCATGAAGCCAATTTTGATCAACG 60.202 41.667 7.89 0.00 37.23 4.10
221 229 8.233868 CCAATTTTGATCAACGATGTTGTAGTA 58.766 33.333 7.89 0.00 0.00 1.82
222 230 9.605955 CAATTTTGATCAACGATGTTGTAGTAA 57.394 29.630 7.89 0.00 0.00 2.24
253 261 8.928733 ACAAATGATGATGTAAATCAACTTTGC 58.071 29.630 18.70 2.37 37.58 3.68
255 263 9.491675 AAATGATGATGTAAATCAACTTTGCAA 57.508 25.926 0.00 0.00 41.80 4.08
256 264 9.661563 AATGATGATGTAAATCAACTTTGCAAT 57.338 25.926 0.00 0.00 41.80 3.56
276 364 6.309436 GCAATTGCAAGAGAAATAAAAAGGC 58.691 36.000 25.36 0.00 41.59 4.35
277 365 6.073112 GCAATTGCAAGAGAAATAAAAAGGCA 60.073 34.615 25.36 0.00 41.59 4.75
278 366 7.520292 GCAATTGCAAGAGAAATAAAAAGGCAA 60.520 33.333 25.36 0.00 42.10 4.52
280 368 7.424227 TTGCAAGAGAAATAAAAAGGCAATG 57.576 32.000 0.00 0.00 34.23 2.82
281 369 5.409214 TGCAAGAGAAATAAAAAGGCAATGC 59.591 36.000 0.00 0.00 0.00 3.56
290 378 8.675705 AAATAAAAAGGCAATGCAGTTAAGTT 57.324 26.923 7.79 0.00 0.00 2.66
299 387 5.064579 GCAATGCAGTTAAGTTGTTTGGTTT 59.935 36.000 0.00 0.00 0.00 3.27
320 408 6.144402 GGTTTCATTGCATAGTTGTTCACAAG 59.856 38.462 0.00 0.00 36.39 3.16
350 508 2.255252 GCGGCGTGCATGAAAACT 59.745 55.556 10.93 0.00 45.45 2.66
409 567 9.538508 TCATATGATTAGATAATGATTCGGCTG 57.461 33.333 0.00 0.00 0.00 4.85
410 568 9.538508 CATATGATTAGATAATGATTCGGCTGA 57.461 33.333 0.00 0.00 0.00 4.26
525 689 9.658475 TGTGTTCACGTAATTCTAGAAAAATTG 57.342 29.630 9.71 3.98 0.00 2.32
596 760 7.540400 TCATAACACTTAAAAATGTTCGCATGG 59.460 33.333 0.00 0.00 39.67 3.66
598 762 5.596845 ACACTTAAAAATGTTCGCATGGTT 58.403 33.333 0.00 0.00 37.97 3.67
650 823 7.504924 AAATTCGTCCTGTATTCAGAAAACA 57.495 32.000 0.12 0.00 43.76 2.83
651 824 7.687941 AATTCGTCCTGTATTCAGAAAACAT 57.312 32.000 0.12 0.00 43.76 2.71
679 852 5.793675 TGTGCATTTGAAAAATGTTCAACG 58.206 33.333 12.82 0.00 38.05 4.10
686 859 9.566624 CATTTGAAAAATGTTCAACGTGTATTC 57.433 29.630 0.00 0.00 38.05 1.75
690 867 7.696872 TGAAAAATGTTCAACGTGTATTCGAAA 59.303 29.630 0.00 0.00 34.70 3.46
693 870 8.568732 AAATGTTCAACGTGTATTCGAAAAAT 57.431 26.923 0.00 0.00 34.70 1.82
697 874 9.108449 TGTTCAACGTGTATTCGAAAAATATTG 57.892 29.630 0.00 3.68 34.70 1.90
827 1007 0.535780 AAAACCGGTCGGAACCTTCC 60.536 55.000 16.90 0.00 44.04 3.46
829 1009 0.542702 AACCGGTCGGAACCTTCCTA 60.543 55.000 16.90 0.00 45.33 2.94
835 1015 2.039480 GGTCGGAACCTTCCTAAAACCT 59.961 50.000 2.60 0.00 45.33 3.50
850 1030 0.675522 AACCTCACGTTATTGGGCCG 60.676 55.000 0.00 0.00 30.96 6.13
894 1114 3.941483 ACGAGTGAGATTTAGCATTTGGG 59.059 43.478 0.00 0.00 0.00 4.12
903 1123 4.864704 TTTAGCATTTGGGGTTCAAGAC 57.135 40.909 0.00 0.00 36.62 3.01
928 1168 3.762247 CACATTGCCAAGCCCGGG 61.762 66.667 19.09 19.09 0.00 5.73
929 1169 3.978193 ACATTGCCAAGCCCGGGA 61.978 61.111 29.31 0.00 0.00 5.14
945 1185 4.767255 GAGCCCGCACCCTGTCAG 62.767 72.222 0.00 0.00 0.00 3.51
958 1205 1.688735 CCTGTCAGGACTCAAGACACA 59.311 52.381 14.26 0.00 37.67 3.72
1023 1271 3.697747 CCCGCCAAGTGGTACCGA 61.698 66.667 7.57 0.00 37.57 4.69
1570 1825 5.095490 GCGATTAAATTGTTGAACCTCAGG 58.905 41.667 0.00 0.00 0.00 3.86
1585 1840 4.593956 ACCTCAGGCTAATTCTTTCAAGG 58.406 43.478 0.00 0.00 0.00 3.61
1586 1841 4.289672 ACCTCAGGCTAATTCTTTCAAGGA 59.710 41.667 0.00 0.00 0.00 3.36
1737 2003 6.382859 TGACAAAATAGACCATCTACCAGCTA 59.617 38.462 0.00 0.00 30.79 3.32
1794 2064 4.611310 TTCAGTTAGTAGTGATCGACGG 57.389 45.455 0.00 0.00 33.82 4.79
1806 2076 4.034048 AGTGATCGACGGAAATTTGCATAC 59.966 41.667 10.49 0.00 0.00 2.39
1902 2172 6.848562 AACCCCTCATTTTGTCCTAGATAT 57.151 37.500 0.00 0.00 0.00 1.63
1959 2229 3.370953 GGAGATATCCCATGGTGTATGCC 60.371 52.174 11.73 8.26 35.37 4.40
2026 2296 8.931568 GGGGTAAATAGGAAGTTAGAGTTATGA 58.068 37.037 0.00 0.00 0.00 2.15
2082 2353 8.616076 GCTTAGTAGAACTAAACCGAGTACATA 58.384 37.037 0.00 0.00 39.89 2.29
2380 2651 5.296813 GACTAAAAGGCGACATGTTCAAT 57.703 39.130 0.00 0.00 0.00 2.57
2397 2668 4.901197 TCAATAGTTAGGTGTGGCAGAA 57.099 40.909 0.00 0.00 0.00 3.02
2544 2815 2.912624 GCATATTCAGCGCAGGCCC 61.913 63.158 11.47 0.00 41.24 5.80
2571 2842 2.004808 CTCCAGTGCATAGCGGACGA 62.005 60.000 0.00 0.00 41.69 4.20
2607 2878 1.617947 ATGTCAAGAGAGGTCGGGGC 61.618 60.000 0.00 0.00 0.00 5.80
2704 2975 2.597510 GGGGTGCGTGGAAGCTTT 60.598 61.111 0.00 0.00 38.13 3.51
2812 3084 5.136711 GCTTTGTTGTTGTTGTTGTTGTTC 58.863 37.500 0.00 0.00 0.00 3.18
2813 3085 5.659048 TTTGTTGTTGTTGTTGTTGTTCC 57.341 34.783 0.00 0.00 0.00 3.62
2814 3086 4.322080 TGTTGTTGTTGTTGTTGTTCCA 57.678 36.364 0.00 0.00 0.00 3.53
2815 3087 4.887748 TGTTGTTGTTGTTGTTGTTCCAT 58.112 34.783 0.00 0.00 0.00 3.41
2816 3088 4.926238 TGTTGTTGTTGTTGTTGTTCCATC 59.074 37.500 0.00 0.00 0.00 3.51
2817 3089 5.167845 GTTGTTGTTGTTGTTGTTCCATCT 58.832 37.500 0.00 0.00 0.00 2.90
2818 3090 5.398603 TGTTGTTGTTGTTGTTCCATCTT 57.601 34.783 0.00 0.00 0.00 2.40
2819 3091 5.406649 TGTTGTTGTTGTTGTTCCATCTTC 58.593 37.500 0.00 0.00 0.00 2.87
2820 3092 5.184864 TGTTGTTGTTGTTGTTCCATCTTCT 59.815 36.000 0.00 0.00 0.00 2.85
2821 3093 6.375736 TGTTGTTGTTGTTGTTCCATCTTCTA 59.624 34.615 0.00 0.00 0.00 2.10
2864 3138 9.117145 CTTATTATTACAGTGTGTTTGTTGCAG 57.883 33.333 5.88 0.00 0.00 4.41
2987 3261 6.870971 TGTGTTCCTAACAATACTGAAACC 57.129 37.500 0.00 0.00 44.16 3.27
2990 3264 7.163441 GTGTTCCTAACAATACTGAAACCCTA 58.837 38.462 0.00 0.00 44.16 3.53
3012 3286 5.559148 AAGAGGAATCATGATGGAGGTAC 57.441 43.478 9.46 0.00 0.00 3.34
3035 3317 8.951243 GTACTGCTATCATTTTCTTCCTTTTCT 58.049 33.333 0.00 0.00 0.00 2.52
3058 3342 1.917872 TTTGGTCATACCCTGTTGGC 58.082 50.000 0.00 0.00 37.50 4.52
3065 3349 4.278310 GTCATACCCTGTTGGCCTTAATT 58.722 43.478 3.32 0.00 37.83 1.40
3126 3418 7.071069 AGATGAGACTCATACCAAATGCATA 57.929 36.000 17.96 0.00 37.20 3.14
3239 3577 5.015710 TGATGTCTAGATCTATACAGGGCCT 59.984 44.000 21.33 0.00 0.00 5.19
3272 3620 7.540474 TGGGATGTCCTCTATTGATAAGTAC 57.460 40.000 0.00 0.00 36.20 2.73
3274 3622 7.734865 TGGGATGTCCTCTATTGATAAGTACAT 59.265 37.037 0.00 0.00 36.20 2.29
3275 3623 8.598041 GGGATGTCCTCTATTGATAAGTACATT 58.402 37.037 0.00 0.00 35.95 2.71
3278 3626 9.698309 ATGTCCTCTATTGATAAGTACATTTCG 57.302 33.333 0.00 0.00 0.00 3.46
3341 3707 3.882288 TGTTGTGCTTGATGAACTTAGCA 59.118 39.130 0.00 0.00 41.01 3.49
3342 3708 4.023792 TGTTGTGCTTGATGAACTTAGCAG 60.024 41.667 0.00 0.00 43.61 4.24
3416 3790 5.350640 CCTTCCGAGCTTTAAATTCGTAAGT 59.649 40.000 17.87 0.00 31.12 2.24
3417 3791 6.128363 CCTTCCGAGCTTTAAATTCGTAAGTT 60.128 38.462 17.87 0.00 31.12 2.66
3418 3792 7.063780 CCTTCCGAGCTTTAAATTCGTAAGTTA 59.936 37.037 17.87 0.00 31.12 2.24
3466 3847 5.440610 AGGGTCATCTCATTATTTGGACAC 58.559 41.667 0.00 0.00 0.00 3.67
3549 3935 7.290110 AGTTCAAATAAACTGAAAGAAGGGG 57.710 36.000 0.00 0.00 38.06 4.79
3550 3936 6.267699 AGTTCAAATAAACTGAAAGAAGGGGG 59.732 38.462 0.00 0.00 38.06 5.40
3604 3995 3.244582 TGGACCTGCCTGTAACTCTTTA 58.755 45.455 0.00 0.00 37.63 1.85
3609 4000 5.246307 ACCTGCCTGTAACTCTTTATGAAC 58.754 41.667 0.00 0.00 0.00 3.18
3619 4010 3.935203 ACTCTTTATGAACCATCAGTGCG 59.065 43.478 0.00 0.00 39.39 5.34
3628 4019 4.142271 TGAACCATCAGTGCGTTTCTTTTT 60.142 37.500 0.00 0.00 0.00 1.94
3682 4073 9.030301 CAAATCTCGTTAACAAAATTTTCTGGT 57.970 29.630 6.39 0.00 0.00 4.00
3725 4116 9.791838 GTTAACAAGAAATTTCAAAAATAGCGG 57.208 29.630 19.99 0.38 0.00 5.52
3762 4155 9.685276 TGAATCTAATATGTTGACCAGTGAAAT 57.315 29.630 0.00 0.00 0.00 2.17
3792 4185 6.435292 TCTGCCTTCTTAGGACTTAAAGTT 57.565 37.500 0.00 0.00 45.05 2.66
3830 4223 5.076873 CAAAACTTCCCACCAAAGGAGATA 58.923 41.667 0.00 0.00 34.08 1.98
3844 4245 6.350445 CCAAAGGAGATAAACATTTCTGTGGG 60.350 42.308 0.00 0.00 35.22 4.61
3894 4295 6.915843 ACTACAGTTGCGGTTTTATTTTCAAG 59.084 34.615 0.00 0.00 0.00 3.02
3896 4297 6.512297 ACAGTTGCGGTTTTATTTTCAAGAT 58.488 32.000 0.00 0.00 0.00 2.40
3897 4298 7.653647 ACAGTTGCGGTTTTATTTTCAAGATA 58.346 30.769 0.00 0.00 0.00 1.98
3971 4372 6.152661 GTGGTTTATGTCCAAGATCATTTCCA 59.847 38.462 0.00 0.00 36.68 3.53
4111 4512 0.436531 CACTCGCAAAGAAGTCGCTC 59.563 55.000 0.00 0.00 0.00 5.03
4204 4605 0.170561 CGGCAGTTCAGTACGCTACT 59.829 55.000 0.00 0.00 40.28 2.57
4245 4646 0.833287 GCTGTGAGGGCTTAGATCCA 59.167 55.000 0.00 0.00 0.00 3.41
4354 4755 7.640616 TGTGCTGAAATGTAATCAATTTGTG 57.359 32.000 0.00 0.00 0.00 3.33
4545 4946 4.707030 TTGAACATGAACATCTGATGCC 57.293 40.909 17.24 10.09 0.00 4.40
4564 4965 2.029290 GCCGTCGTAACTATCATGGGAT 60.029 50.000 0.00 0.00 37.55 3.85
4593 4994 6.435292 TCTTGGCTATATTTTACTCCCTCC 57.565 41.667 0.00 0.00 0.00 4.30
4594 4995 4.884668 TGGCTATATTTTACTCCCTCCG 57.115 45.455 0.00 0.00 0.00 4.63
4595 4996 4.228824 TGGCTATATTTTACTCCCTCCGT 58.771 43.478 0.00 0.00 0.00 4.69
4596 4997 4.657039 TGGCTATATTTTACTCCCTCCGTT 59.343 41.667 0.00 0.00 0.00 4.44
4597 4998 5.131475 TGGCTATATTTTACTCCCTCCGTTT 59.869 40.000 0.00 0.00 0.00 3.60
4598 4999 5.699915 GGCTATATTTTACTCCCTCCGTTTC 59.300 44.000 0.00 0.00 0.00 2.78
4599 5000 6.464039 GGCTATATTTTACTCCCTCCGTTTCT 60.464 42.308 0.00 0.00 0.00 2.52
4600 5001 7.256083 GGCTATATTTTACTCCCTCCGTTTCTA 60.256 40.741 0.00 0.00 0.00 2.10
4601 5002 8.146412 GCTATATTTTACTCCCTCCGTTTCTAA 58.854 37.037 0.00 0.00 0.00 2.10
4606 5007 9.916360 ATTTTACTCCCTCCGTTTCTAAATATT 57.084 29.630 0.00 0.00 0.00 1.28
4607 5008 9.743581 TTTTACTCCCTCCGTTTCTAAATATTT 57.256 29.630 5.89 5.89 0.00 1.40
4611 5012 8.935741 ACTCCCTCCGTTTCTAAATATTTATCT 58.064 33.333 8.34 0.00 0.00 1.98
4612 5013 9.780186 CTCCCTCCGTTTCTAAATATTTATCTT 57.220 33.333 8.34 0.00 0.00 2.40
4690 5091 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4691 5092 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4692 5093 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4693 5094 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4694 5095 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4695 5096 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4696 5097 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4697 5098 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4698 5099 3.932710 TCACTCATTTTGCTCCGTATGTC 59.067 43.478 0.00 0.00 0.00 3.06
4699 5100 3.684305 CACTCATTTTGCTCCGTATGTCA 59.316 43.478 0.00 0.00 0.00 3.58
4700 5101 3.684788 ACTCATTTTGCTCCGTATGTCAC 59.315 43.478 0.00 0.00 0.00 3.67
4701 5102 3.935203 CTCATTTTGCTCCGTATGTCACT 59.065 43.478 0.00 0.00 0.00 3.41
4702 5103 4.323417 TCATTTTGCTCCGTATGTCACTT 58.677 39.130 0.00 0.00 0.00 3.16
4703 5104 4.154015 TCATTTTGCTCCGTATGTCACTTG 59.846 41.667 0.00 0.00 0.00 3.16
4704 5105 2.831685 TTGCTCCGTATGTCACTTGT 57.168 45.000 0.00 0.00 0.00 3.16
4705 5106 2.831685 TGCTCCGTATGTCACTTGTT 57.168 45.000 0.00 0.00 0.00 2.83
4706 5107 2.412870 TGCTCCGTATGTCACTTGTTG 58.587 47.619 0.00 0.00 0.00 3.33
4707 5108 2.036604 TGCTCCGTATGTCACTTGTTGA 59.963 45.455 0.00 0.00 0.00 3.18
4708 5109 3.064207 GCTCCGTATGTCACTTGTTGAA 58.936 45.455 0.00 0.00 35.39 2.69
4709 5110 3.496884 GCTCCGTATGTCACTTGTTGAAA 59.503 43.478 0.00 0.00 35.39 2.69
4710 5111 4.154195 GCTCCGTATGTCACTTGTTGAAAT 59.846 41.667 0.00 0.00 36.08 2.17
4711 5112 5.671329 GCTCCGTATGTCACTTGTTGAAATC 60.671 44.000 0.00 0.00 33.75 2.17
4712 5113 5.547465 TCCGTATGTCACTTGTTGAAATCT 58.453 37.500 0.00 0.00 33.75 2.40
4713 5114 5.637810 TCCGTATGTCACTTGTTGAAATCTC 59.362 40.000 0.00 0.00 33.75 2.75
4714 5115 5.639506 CCGTATGTCACTTGTTGAAATCTCT 59.360 40.000 0.00 0.00 33.75 3.10
4715 5116 6.401474 CCGTATGTCACTTGTTGAAATCTCTG 60.401 42.308 0.00 0.00 33.75 3.35
4716 5117 5.954296 ATGTCACTTGTTGAAATCTCTGG 57.046 39.130 0.00 0.00 35.39 3.86
4717 5118 5.034852 TGTCACTTGTTGAAATCTCTGGA 57.965 39.130 0.00 0.00 35.39 3.86
4718 5119 5.436175 TGTCACTTGTTGAAATCTCTGGAA 58.564 37.500 0.00 0.00 35.39 3.53
4719 5120 5.885352 TGTCACTTGTTGAAATCTCTGGAAA 59.115 36.000 0.00 0.00 35.39 3.13
4720 5121 6.038603 TGTCACTTGTTGAAATCTCTGGAAAG 59.961 38.462 0.00 0.00 35.39 2.62
4721 5122 6.260936 GTCACTTGTTGAAATCTCTGGAAAGA 59.739 38.462 0.00 0.00 35.39 2.52
4722 5123 6.260936 TCACTTGTTGAAATCTCTGGAAAGAC 59.739 38.462 0.00 0.00 0.00 3.01
4723 5124 6.038603 CACTTGTTGAAATCTCTGGAAAGACA 59.961 38.462 0.00 0.00 0.00 3.41
4724 5125 6.603201 ACTTGTTGAAATCTCTGGAAAGACAA 59.397 34.615 0.00 0.00 0.00 3.18
4725 5126 7.122650 ACTTGTTGAAATCTCTGGAAAGACAAA 59.877 33.333 0.00 0.00 0.00 2.83
4726 5127 7.587037 TGTTGAAATCTCTGGAAAGACAAAT 57.413 32.000 0.00 0.00 0.00 2.32
4727 5128 8.690203 TGTTGAAATCTCTGGAAAGACAAATA 57.310 30.769 0.00 0.00 0.00 1.40
4728 5129 9.300681 TGTTGAAATCTCTGGAAAGACAAATAT 57.699 29.630 0.00 0.00 0.00 1.28
4745 5146 9.823647 AGACAAATATTTATGAATCGAGTGAGT 57.176 29.630 0.00 0.00 0.00 3.41
4845 5247 8.548877 ACTATATTTTACATGTGGGTGAGAACT 58.451 33.333 9.11 0.00 0.00 3.01
4936 6223 3.117663 TCATATTGGGTTGAAGTAGGCCC 60.118 47.826 0.00 0.00 41.42 5.80
4989 6276 3.771160 CAGGGTTAGGCGCTCGGT 61.771 66.667 7.64 0.00 38.41 4.69
5091 6642 1.379977 ACGGAGAGATGGCGGAAGA 60.380 57.895 0.00 0.00 0.00 2.87
5107 6658 3.200593 GACGCTAGCTCCGGTCGA 61.201 66.667 13.93 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.506168 TTTGGTCTCATAGGTATTGACAAATC 57.494 34.615 0.00 0.00 0.00 2.17
30 32 4.638865 ACTAGTCCCGCAAAATAATTCCAC 59.361 41.667 0.00 0.00 0.00 4.02
82 84 2.823747 TGGTTAGAGTACAGTCGTGCAT 59.176 45.455 0.00 0.00 0.00 3.96
83 85 2.030540 GTGGTTAGAGTACAGTCGTGCA 60.031 50.000 0.00 0.00 0.00 4.57
84 86 2.030540 TGTGGTTAGAGTACAGTCGTGC 60.031 50.000 0.00 0.00 0.00 5.34
87 89 4.082949 TGTGATGTGGTTAGAGTACAGTCG 60.083 45.833 0.00 0.00 0.00 4.18
88 90 5.386958 TGTGATGTGGTTAGAGTACAGTC 57.613 43.478 0.00 0.00 0.00 3.51
89 91 5.105310 GGATGTGATGTGGTTAGAGTACAGT 60.105 44.000 0.00 0.00 0.00 3.55
90 92 5.105351 TGGATGTGATGTGGTTAGAGTACAG 60.105 44.000 0.00 0.00 0.00 2.74
125 133 3.668141 TGTGGCATCCTTCCATGTAAT 57.332 42.857 0.00 0.00 35.81 1.89
131 139 2.607499 ACATTTTGTGGCATCCTTCCA 58.393 42.857 0.00 0.00 0.00 3.53
133 141 5.120674 GCTTTTACATTTTGTGGCATCCTTC 59.879 40.000 0.00 0.00 0.00 3.46
158 166 7.326454 AGCCTATCACAACTATACATAGCATG 58.674 38.462 0.00 0.00 33.68 4.06
175 183 1.349026 GCTTCATGCCCTAGCCTATCA 59.651 52.381 0.00 0.00 38.69 2.15
252 260 6.073112 TGCCTTTTTATTTCTCTTGCAATTGC 60.073 34.615 23.69 23.69 42.50 3.56
253 261 7.424227 TGCCTTTTTATTTCTCTTGCAATTG 57.576 32.000 0.00 0.00 0.00 2.32
255 263 7.361457 GCATTGCCTTTTTATTTCTCTTGCAAT 60.361 33.333 0.00 0.00 44.92 3.56
256 264 6.073112 GCATTGCCTTTTTATTTCTCTTGCAA 60.073 34.615 0.00 0.00 40.06 4.08
264 352 8.310406 ACTTAACTGCATTGCCTTTTTATTTC 57.690 30.769 6.12 0.00 0.00 2.17
269 357 5.427378 ACAACTTAACTGCATTGCCTTTTT 58.573 33.333 6.12 0.00 0.00 1.94
273 361 4.370917 CAAACAACTTAACTGCATTGCCT 58.629 39.130 6.12 0.00 0.00 4.75
275 363 4.119136 ACCAAACAACTTAACTGCATTGC 58.881 39.130 0.46 0.46 0.00 3.56
276 364 6.312426 TGAAACCAAACAACTTAACTGCATTG 59.688 34.615 0.00 0.00 0.00 2.82
277 365 6.402222 TGAAACCAAACAACTTAACTGCATT 58.598 32.000 0.00 0.00 0.00 3.56
278 366 5.971763 TGAAACCAAACAACTTAACTGCAT 58.028 33.333 0.00 0.00 0.00 3.96
279 367 5.392767 TGAAACCAAACAACTTAACTGCA 57.607 34.783 0.00 0.00 0.00 4.41
280 368 6.704819 CAATGAAACCAAACAACTTAACTGC 58.295 36.000 0.00 0.00 0.00 4.40
281 369 6.312426 TGCAATGAAACCAAACAACTTAACTG 59.688 34.615 0.00 0.00 0.00 3.16
290 378 5.911752 ACAACTATGCAATGAAACCAAACA 58.088 33.333 0.00 0.00 0.00 2.83
299 387 6.389830 AACTTGTGAACAACTATGCAATGA 57.610 33.333 0.00 0.00 0.00 2.57
320 408 2.173964 CACGCCGCAAAAATAGCTAAC 58.826 47.619 0.00 0.00 0.00 2.34
384 542 9.538508 TCAGCCGAATCATTATCTAATCATATG 57.461 33.333 0.00 0.00 0.00 1.78
494 658 9.658475 TTTCTAGAATTACGTGAACACATTTTG 57.342 29.630 5.89 0.00 0.00 2.44
500 664 9.659830 ACAATTTTTCTAGAATTACGTGAACAC 57.340 29.630 5.89 0.00 0.00 3.32
524 688 9.535878 GACCAATATTTTTGAAAGGTACAAACA 57.464 29.630 0.00 0.00 37.05 2.83
525 689 9.535878 TGACCAATATTTTTGAAAGGTACAAAC 57.464 29.630 0.00 0.00 37.05 2.93
625 798 8.610248 TGTTTTCTGAATACAGGACGAATTTA 57.390 30.769 9.20 0.00 43.60 1.40
629 802 6.708502 TGAATGTTTTCTGAATACAGGACGAA 59.291 34.615 16.61 0.78 43.60 3.85
632 805 8.299570 ACATTGAATGTTTTCTGAATACAGGAC 58.700 33.333 16.61 11.43 41.63 3.85
634 807 7.062605 GCACATTGAATGTTTTCTGAATACAGG 59.937 37.037 8.30 6.81 42.70 4.00
635 808 7.595875 TGCACATTGAATGTTTTCTGAATACAG 59.404 33.333 8.30 6.87 42.70 2.74
649 822 8.789881 AACATTTTTCAAATGCACATTGAATG 57.210 26.923 22.89 20.36 0.00 2.67
650 823 8.622157 TGAACATTTTTCAAATGCACATTGAAT 58.378 25.926 22.89 11.92 0.00 2.57
651 824 7.982224 TGAACATTTTTCAAATGCACATTGAA 58.018 26.923 20.02 20.02 0.00 2.69
795 975 5.412286 CCGACCGGTTTTTCCTTTTTCTATA 59.588 40.000 9.42 0.00 0.00 1.31
804 984 0.535780 GGTTCCGACCGGTTTTTCCT 60.536 55.000 9.42 0.00 35.91 3.36
827 1007 3.128068 GGCCCAATAACGTGAGGTTTTAG 59.872 47.826 0.00 0.00 40.09 1.85
829 1009 1.890489 GGCCCAATAACGTGAGGTTTT 59.110 47.619 0.00 0.00 40.09 2.43
835 1015 2.437002 GCCGGCCCAATAACGTGA 60.437 61.111 18.11 0.00 0.00 4.35
861 1041 4.838486 CACTCGTCTCCGGCGCTC 62.838 72.222 7.64 0.00 33.95 5.03
863 1043 4.838486 CTCACTCGTCTCCGGCGC 62.838 72.222 0.00 0.00 33.95 6.53
864 1044 1.994507 AATCTCACTCGTCTCCGGCG 61.995 60.000 0.00 0.00 33.95 6.46
874 1094 4.273318 ACCCCAAATGCTAAATCTCACTC 58.727 43.478 0.00 0.00 0.00 3.51
894 1114 5.618640 GCAATGTGAGATTCTGTCTTGAACC 60.619 44.000 0.00 0.00 37.29 3.62
903 1123 2.159282 GGCTTGGCAATGTGAGATTCTG 60.159 50.000 0.00 0.00 0.00 3.02
928 1168 4.767255 CTGACAGGGTGCGGGCTC 62.767 72.222 0.00 0.00 0.00 4.70
945 1185 0.667792 GACGGCTGTGTCTTGAGTCC 60.668 60.000 0.80 0.00 35.95 3.85
1382 1636 1.153289 CATGACCTGGGAGAAGGCG 60.153 63.158 0.00 0.00 41.46 5.52
1530 1785 3.907894 TCGCCACTGGTTCAATTAAAC 57.092 42.857 0.00 0.00 0.00 2.01
1570 1825 7.597386 AGTGTGAATTCCTTGAAAGAATTAGC 58.403 34.615 2.27 0.33 42.53 3.09
1586 1841 8.520351 GCCTTTTGTAATTAGGTAGTGTGAATT 58.480 33.333 0.00 0.00 0.00 2.17
1689 1954 3.951306 TGTTGTTCGCTTGAAAGATGTG 58.049 40.909 0.00 0.00 32.31 3.21
1737 2003 5.011738 TCCTGAAATTAGAAGTCGAACTGGT 59.988 40.000 0.00 0.00 0.00 4.00
1794 2064 8.243426 TGATCAGGTAAGTTGTATGCAAATTTC 58.757 33.333 14.21 9.33 39.49 2.17
1806 2076 6.312426 GTGAGACTCAATGATCAGGTAAGTTG 59.688 42.308 6.76 0.00 0.00 3.16
1871 2141 5.061721 ACAAAATGAGGGGTTAACAGAGT 57.938 39.130 8.10 0.00 0.00 3.24
1925 2195 7.892241 CCATGGGATATCTCCTTGTATTTGAAT 59.108 37.037 2.85 0.00 41.74 2.57
1926 2196 7.147141 ACCATGGGATATCTCCTTGTATTTGAA 60.147 37.037 18.09 0.00 41.74 2.69
1927 2197 6.332635 ACCATGGGATATCTCCTTGTATTTGA 59.667 38.462 18.09 0.00 41.74 2.69
1928 2198 6.432162 CACCATGGGATATCTCCTTGTATTTG 59.568 42.308 18.09 0.00 41.74 2.32
1929 2199 6.103205 ACACCATGGGATATCTCCTTGTATTT 59.897 38.462 18.09 0.00 41.74 1.40
1930 2200 5.612688 ACACCATGGGATATCTCCTTGTATT 59.387 40.000 18.09 0.00 41.74 1.89
1959 2229 0.452987 CACCACATCATCCGCAAAGG 59.547 55.000 0.00 0.00 42.97 3.11
2026 2296 4.278419 CCTTTCGATTCCAAGGTTTGTCTT 59.722 41.667 5.58 0.00 35.67 3.01
2082 2353 4.267349 AGTAGTACTGAAACCGCACATT 57.733 40.909 5.39 0.00 0.00 2.71
2380 2651 3.343617 GCATTTCTGCCACACCTAACTA 58.656 45.455 0.00 0.00 42.88 2.24
2397 2668 4.274214 CACATCCATCTCAACATACGCATT 59.726 41.667 0.00 0.00 0.00 3.56
2453 2724 5.711036 ACCCCAACTCTATCTCGTATATCAC 59.289 44.000 0.00 0.00 0.00 3.06
2544 2815 0.543277 TATGCACTGGAGCTTCTGGG 59.457 55.000 3.68 0.00 34.99 4.45
2571 2842 1.337823 ACATTCTCCGCACGCTTTAGT 60.338 47.619 0.00 0.00 0.00 2.24
2607 2878 2.679837 CTCCCATGTCAAATTCGGTCTG 59.320 50.000 0.00 0.00 0.00 3.51
2704 2975 0.761187 GGCTCTGGCACATGGATAGA 59.239 55.000 0.00 0.00 38.20 1.98
2812 3084 9.599322 GCACAATATAAAACGAATAGAAGATGG 57.401 33.333 0.00 0.00 0.00 3.51
2939 3213 5.818136 TTCCTATCCTCAAGCAAAAATCG 57.182 39.130 0.00 0.00 0.00 3.34
2987 3261 4.596643 ACCTCCATCATGATTCCTCTTAGG 59.403 45.833 5.16 7.62 36.46 2.69
2990 3264 5.071519 CAGTACCTCCATCATGATTCCTCTT 59.928 44.000 5.16 0.00 0.00 2.85
3035 3317 4.464597 GCCAACAGGGTATGACCAAAAATA 59.535 41.667 0.00 0.00 41.02 1.40
3058 3342 8.906867 ACAATCAATGAGTCCATACAATTAAGG 58.093 33.333 0.00 0.00 31.59 2.69
3065 3349 6.475504 AGTCAACAATCAATGAGTCCATACA 58.524 36.000 0.00 0.00 31.59 2.29
3239 3577 2.180086 AGAGGACATCCCATACTAGCCA 59.820 50.000 0.00 0.00 37.41 4.75
3324 3690 4.582869 ACATCTGCTAAGTTCATCAAGCA 58.417 39.130 0.00 0.00 42.41 3.91
3341 3707 4.582240 TGCGACAGATCATCTTCTACATCT 59.418 41.667 0.00 0.00 0.00 2.90
3342 3708 4.679197 GTGCGACAGATCATCTTCTACATC 59.321 45.833 0.00 0.00 0.00 3.06
3389 3762 3.727970 CGAATTTAAAGCTCGGAAGGTGC 60.728 47.826 12.44 0.00 32.35 5.01
3418 3792 9.995003 CTCTGAACTATTGCTAGAAAGGATATT 57.005 33.333 0.00 0.00 0.00 1.28
3492 3873 8.878211 ACAGATAAAGGTGTAGATCATGATCAT 58.122 33.333 31.99 20.79 40.22 2.45
3493 3874 8.146412 CACAGATAAAGGTGTAGATCATGATCA 58.854 37.037 31.99 18.05 40.22 2.92
3494 3875 8.147058 ACACAGATAAAGGTGTAGATCATGATC 58.853 37.037 25.42 25.42 45.77 2.92
3534 3917 4.265856 AGTTTCCCCCTTCTTTCAGTTT 57.734 40.909 0.00 0.00 0.00 2.66
3604 3995 2.783135 AGAAACGCACTGATGGTTCAT 58.217 42.857 3.26 0.00 0.00 2.57
3609 4000 3.308530 GGAAAAAGAAACGCACTGATGG 58.691 45.455 0.00 0.00 0.00 3.51
3619 4010 5.798910 TCGAGTAACAACGGAAAAAGAAAC 58.201 37.500 0.00 0.00 0.00 2.78
3628 4019 2.553602 TGCTAACTCGAGTAACAACGGA 59.446 45.455 20.39 2.34 0.00 4.69
3682 4073 8.607713 TCTTGTTAACAGAAATATTGGTAGGGA 58.392 33.333 8.56 0.00 0.00 4.20
3700 4091 9.535878 ACCGCTATTTTTGAAATTTCTTGTTAA 57.464 25.926 18.64 2.03 0.00 2.01
3767 4160 7.021998 ACTTTAAGTCCTAAGAAGGCAGATT 57.978 36.000 0.00 0.00 43.31 2.40
3768 4161 6.628644 ACTTTAAGTCCTAAGAAGGCAGAT 57.371 37.500 0.00 0.00 43.31 2.90
3770 4163 6.314152 GCTAACTTTAAGTCCTAAGAAGGCAG 59.686 42.308 0.00 0.00 43.31 4.85
3783 4176 5.451381 GCAGGTTTTGGTGCTAACTTTAAGT 60.451 40.000 0.00 0.00 36.71 2.24
3787 4180 2.763448 TGCAGGTTTTGGTGCTAACTTT 59.237 40.909 0.00 0.00 40.54 2.66
3792 4185 2.763448 AGTTTTGCAGGTTTTGGTGCTA 59.237 40.909 0.00 0.00 40.54 3.49
3830 4223 7.506938 CCTATTATCCATCCCACAGAAATGTTT 59.493 37.037 0.00 0.00 0.00 2.83
3971 4372 1.859427 CGTGTCAGCCTTGCAAGCAT 61.859 55.000 21.43 8.37 0.00 3.79
4111 4512 1.141657 ACATGGATGAATCGACCAGGG 59.858 52.381 12.75 6.73 39.36 4.45
4204 4605 1.538634 GCCATGAGTTGTTGCAAGCAA 60.539 47.619 0.00 2.89 0.00 3.91
4245 4646 8.270030 TCATGATATTCTGAAACTTCCATCTGT 58.730 33.333 0.00 0.00 0.00 3.41
4284 4685 4.860802 TGATGTTACCATGATCTTGGGT 57.139 40.909 26.54 17.46 41.35 4.51
4297 4698 3.308866 GTCCTGGCATACGTTGATGTTAC 59.691 47.826 0.00 0.00 0.00 2.50
4545 4946 4.238761 ACATCCCATGATAGTTACGACG 57.761 45.455 0.00 0.00 0.00 5.12
4611 5012 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
4612 5013 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
4613 5014 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
4614 5015 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
4615 5016 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
4616 5017 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
4617 5018 8.562892 CATATGTGGTAGTCCATTTGAAATCTC 58.437 37.037 0.00 0.00 46.20 2.75
4618 5019 7.503566 CCATATGTGGTAGTCCATTTGAAATCT 59.496 37.037 0.00 0.00 46.20 2.40
4619 5020 7.502226 TCCATATGTGGTAGTCCATTTGAAATC 59.498 37.037 8.51 0.00 46.20 2.17
4620 5021 7.353525 TCCATATGTGGTAGTCCATTTGAAAT 58.646 34.615 8.51 0.00 46.20 2.17
4621 5022 6.726379 TCCATATGTGGTAGTCCATTTGAAA 58.274 36.000 8.51 0.00 46.20 2.69
4622 5023 6.320434 TCCATATGTGGTAGTCCATTTGAA 57.680 37.500 8.51 0.00 46.20 2.69
4623 5024 5.966853 TCCATATGTGGTAGTCCATTTGA 57.033 39.130 8.51 0.00 46.20 2.69
4624 5025 6.064060 ACATCCATATGTGGTAGTCCATTTG 58.936 40.000 8.51 0.00 44.79 2.32
4625 5026 6.266131 ACATCCATATGTGGTAGTCCATTT 57.734 37.500 8.51 0.00 44.79 2.32
4626 5027 5.912149 ACATCCATATGTGGTAGTCCATT 57.088 39.130 8.51 0.00 44.79 3.16
4627 5028 8.860517 ATATACATCCATATGTGGTAGTCCAT 57.139 34.615 8.51 3.29 45.99 3.41
4628 5029 9.421399 CTATATACATCCATATGTGGTAGTCCA 57.579 37.037 8.51 1.36 45.99 4.02
4629 5030 9.642343 TCTATATACATCCATATGTGGTAGTCC 57.358 37.037 8.51 0.00 45.99 3.85
4631 5032 9.990868 TGTCTATATACATCCATATGTGGTAGT 57.009 33.333 8.51 10.44 45.99 2.73
4668 5069 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4669 5070 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4670 5071 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4671 5072 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4672 5073 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4673 5074 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4674 5075 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4675 5076 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4676 5077 3.932710 GACATACGGAGCAAAATGAGTGA 59.067 43.478 0.00 0.00 0.00 3.41
4677 5078 3.684305 TGACATACGGAGCAAAATGAGTG 59.316 43.478 0.00 0.00 0.00 3.51
4678 5079 3.684788 GTGACATACGGAGCAAAATGAGT 59.315 43.478 0.00 0.00 0.00 3.41
4679 5080 3.935203 AGTGACATACGGAGCAAAATGAG 59.065 43.478 0.00 0.00 0.00 2.90
4680 5081 3.937814 AGTGACATACGGAGCAAAATGA 58.062 40.909 0.00 0.00 0.00 2.57
4681 5082 4.083324 ACAAGTGACATACGGAGCAAAATG 60.083 41.667 0.00 0.00 0.00 2.32
4682 5083 4.072131 ACAAGTGACATACGGAGCAAAAT 58.928 39.130 0.00 0.00 0.00 1.82
4683 5084 3.472652 ACAAGTGACATACGGAGCAAAA 58.527 40.909 0.00 0.00 0.00 2.44
4684 5085 3.120321 ACAAGTGACATACGGAGCAAA 57.880 42.857 0.00 0.00 0.00 3.68
4685 5086 2.805671 CAACAAGTGACATACGGAGCAA 59.194 45.455 0.00 0.00 0.00 3.91
4686 5087 2.036604 TCAACAAGTGACATACGGAGCA 59.963 45.455 0.00 0.00 0.00 4.26
4687 5088 2.683968 TCAACAAGTGACATACGGAGC 58.316 47.619 0.00 0.00 0.00 4.70
4688 5089 5.639506 AGATTTCAACAAGTGACATACGGAG 59.360 40.000 0.00 0.00 35.39 4.63
4689 5090 5.547465 AGATTTCAACAAGTGACATACGGA 58.453 37.500 0.00 0.00 35.39 4.69
4690 5091 5.639506 AGAGATTTCAACAAGTGACATACGG 59.360 40.000 0.00 0.00 35.39 4.02
4691 5092 6.401474 CCAGAGATTTCAACAAGTGACATACG 60.401 42.308 0.00 0.00 35.39 3.06
4692 5093 6.650807 TCCAGAGATTTCAACAAGTGACATAC 59.349 38.462 0.00 0.00 35.39 2.39
4693 5094 6.768483 TCCAGAGATTTCAACAAGTGACATA 58.232 36.000 0.00 0.00 35.39 2.29
4694 5095 5.624159 TCCAGAGATTTCAACAAGTGACAT 58.376 37.500 0.00 0.00 35.39 3.06
4695 5096 5.034852 TCCAGAGATTTCAACAAGTGACA 57.965 39.130 0.00 0.00 35.39 3.58
4696 5097 6.260936 TCTTTCCAGAGATTTCAACAAGTGAC 59.739 38.462 0.00 0.00 35.39 3.67
4697 5098 6.260936 GTCTTTCCAGAGATTTCAACAAGTGA 59.739 38.462 0.00 0.00 0.00 3.41
4698 5099 6.038603 TGTCTTTCCAGAGATTTCAACAAGTG 59.961 38.462 0.00 0.00 0.00 3.16
4699 5100 6.122277 TGTCTTTCCAGAGATTTCAACAAGT 58.878 36.000 0.00 0.00 0.00 3.16
4700 5101 6.624352 TGTCTTTCCAGAGATTTCAACAAG 57.376 37.500 0.00 0.00 0.00 3.16
4701 5102 7.403312 TTTGTCTTTCCAGAGATTTCAACAA 57.597 32.000 0.00 0.00 0.00 2.83
4702 5103 7.587037 ATTTGTCTTTCCAGAGATTTCAACA 57.413 32.000 0.00 0.00 0.00 3.33
4719 5120 9.823647 ACTCACTCGATTCATAAATATTTGTCT 57.176 29.630 11.05 0.00 0.00 3.41
4732 5133 9.350357 GTAAATAAGTTGTACTCACTCGATTCA 57.650 33.333 0.00 0.00 0.00 2.57
4733 5134 8.521860 CGTAAATAAGTTGTACTCACTCGATTC 58.478 37.037 0.00 0.00 0.00 2.52
4734 5135 7.487189 CCGTAAATAAGTTGTACTCACTCGATT 59.513 37.037 0.00 0.00 0.00 3.34
4735 5136 6.971184 CCGTAAATAAGTTGTACTCACTCGAT 59.029 38.462 0.00 0.00 0.00 3.59
4736 5137 6.149308 TCCGTAAATAAGTTGTACTCACTCGA 59.851 38.462 0.00 0.00 0.00 4.04
4737 5138 6.317088 TCCGTAAATAAGTTGTACTCACTCG 58.683 40.000 0.00 0.00 0.00 4.18
4738 5139 7.484324 GTCTCCGTAAATAAGTTGTACTCACTC 59.516 40.741 0.00 0.00 0.00 3.51
4739 5140 7.176340 AGTCTCCGTAAATAAGTTGTACTCACT 59.824 37.037 0.00 0.00 0.00 3.41
4740 5141 7.311408 AGTCTCCGTAAATAAGTTGTACTCAC 58.689 38.462 0.00 0.00 0.00 3.51
4741 5142 7.458409 AGTCTCCGTAAATAAGTTGTACTCA 57.542 36.000 0.00 0.00 0.00 3.41
4810 5212 8.215050 CCACATGTAAAATATAGTCACCCCTAA 58.785 37.037 0.00 0.00 0.00 2.69
4852 5254 3.503748 GTCTTATTCTGTGCAGTTTGCCT 59.496 43.478 0.00 0.00 44.23 4.75
4860 5262 1.066430 GGGGTCGTCTTATTCTGTGCA 60.066 52.381 0.00 0.00 0.00 4.57
4861 5263 1.653151 GGGGTCGTCTTATTCTGTGC 58.347 55.000 0.00 0.00 0.00 4.57
4862 5264 1.922570 CGGGGTCGTCTTATTCTGTG 58.077 55.000 0.00 0.00 0.00 3.66
4989 6276 1.672030 TCGCGTAAGACCCGAGTGA 60.672 57.895 5.77 0.00 43.02 3.41
5091 6642 3.507009 GTCGACCGGAGCTAGCGT 61.507 66.667 9.46 0.06 0.00 5.07
5107 6658 4.021925 GGAGTTGCAGGAGCCCGT 62.022 66.667 0.00 0.00 41.13 5.28


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

AutoCloner maintained by Alex Coulton.