Multiple sequence alignment - TraesCS7A01G272000

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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 TraesCS7A01G272000 chr7A 100.000 4665 0 0 1 4665 285429191 285433855 0.000000e+00 8615.0
1 TraesCS7A01G272000 chr7A 100.000 1395 0 0 5028 6422 285434218 285435612 0.000000e+00 2577.0
2 TraesCS7A01G272000 chr7A 85.171 263 26 10 5948 6200 547357240 547357499 2.300000e-64 257.0
3 TraesCS7A01G272000 chr7A 77.240 413 57 24 6012 6409 206012574 206012964 2.350000e-49 207.0
4 TraesCS7A01G272000 chr7A 87.931 58 5 1 2836 2893 439003330 439003275 4.160000e-07 67.6
5 TraesCS7A01G272000 chr7D 92.324 1915 71 18 306 2209 262360883 262362732 0.000000e+00 2652.0
6 TraesCS7A01G272000 chr7D 89.693 1174 82 15 2214 3375 262362778 262363924 0.000000e+00 1461.0
7 TraesCS7A01G272000 chr7D 89.099 688 50 13 3657 4337 262364203 262364872 0.000000e+00 832.0
8 TraesCS7A01G272000 chr7D 94.798 519 20 3 5028 5541 262365665 262366181 0.000000e+00 802.0
9 TraesCS7A01G272000 chr7D 88.728 346 20 8 4325 4664 262365305 262365637 7.750000e-109 405.0
10 TraesCS7A01G272000 chr7D 91.089 202 14 3 1 201 262360685 262360883 2.950000e-68 270.0
11 TraesCS7A01G272000 chr7D 92.500 40 3 0 4151 4190 496722331 496722292 2.500000e-04 58.4
12 TraesCS7A01G272000 chr7D 100.000 28 0 0 2142 2169 262362753 262362780 1.200000e-02 52.8
13 TraesCS7A01G272000 chr7B 96.554 1422 34 10 938 2353 241563849 241562437 0.000000e+00 2340.0
14 TraesCS7A01G272000 chr7B 92.786 1303 62 15 3384 4665 241561314 241560023 0.000000e+00 1857.0
15 TraesCS7A01G272000 chr7B 93.152 1066 62 2 2319 3384 241562401 241561347 0.000000e+00 1554.0
16 TraesCS7A01G272000 chr7B 88.128 935 71 13 1 933 241570589 241569693 0.000000e+00 1075.0
17 TraesCS7A01G272000 chr7B 95.354 495 21 2 5028 5522 241559996 241559504 0.000000e+00 785.0
18 TraesCS7A01G272000 chr7B 95.276 127 5 1 5630 5756 241559330 241559205 3.930000e-47 200.0
19 TraesCS7A01G272000 chr7B 79.605 304 42 11 6038 6332 403410031 403410323 3.930000e-47 200.0
20 TraesCS7A01G272000 chr7B 86.842 152 9 8 5500 5650 241559492 241559351 6.660000e-35 159.0
21 TraesCS7A01G272000 chr7B 100.000 35 0 0 2319 2353 241562436 241562402 1.490000e-06 65.8
22 TraesCS7A01G272000 chr7B 87.719 57 4 3 2629 2684 7200974 7201028 5.380000e-06 63.9
23 TraesCS7A01G272000 chr5D 91.294 425 36 1 1277 1700 424318760 424319184 4.320000e-161 579.0
24 TraesCS7A01G272000 chr5D 96.629 178 6 0 999 1176 424318504 424318681 4.870000e-76 296.0
25 TraesCS7A01G272000 chr5A 90.118 425 41 1 1277 1700 538311871 538312295 9.410000e-153 551.0
26 TraesCS7A01G272000 chr5A 83.922 510 49 16 5877 6374 14850615 14851103 2.110000e-124 457.0
27 TraesCS7A01G272000 chr5A 80.917 545 61 23 5877 6409 532474810 532475323 2.170000e-104 390.0
28 TraesCS7A01G272000 chr5A 80.212 566 66 24 5874 6419 538811755 538811216 3.630000e-102 383.0
29 TraesCS7A01G272000 chr5A 80.787 432 48 17 5968 6388 14851103 14851510 8.090000e-79 305.0
30 TraesCS7A01G272000 chr5A 96.629 178 6 0 999 1176 538311626 538311803 4.870000e-76 296.0
31 TraesCS7A01G272000 chr5B 89.882 425 42 1 1277 1700 513590239 513590663 4.380000e-151 545.0
32 TraesCS7A01G272000 chr5B 96.067 178 7 0 999 1176 513589530 513589707 2.270000e-74 291.0
33 TraesCS7A01G272000 chr3D 82.847 548 61 27 5880 6409 519618101 519617569 1.630000e-125 460.0
34 TraesCS7A01G272000 chr3B 78.328 646 95 29 5787 6411 634771160 634771781 6.080000e-100 375.0
35 TraesCS7A01G272000 chr3B 89.796 49 5 0 3159 3207 586455834 586455882 5.380000e-06 63.9
36 TraesCS7A01G272000 chr3B 90.196 51 2 3 2629 2678 774457994 774458042 5.380000e-06 63.9
37 TraesCS7A01G272000 chr1B 76.736 576 77 34 5886 6409 553006416 553006986 1.060000e-67 268.0
38 TraesCS7A01G272000 chr1B 81.522 92 14 3 2825 2915 332082064 332082153 8.930000e-09 73.1
39 TraesCS7A01G272000 chr1B 91.667 48 1 3 2630 2677 266106879 266106835 5.380000e-06 63.9
40 TraesCS7A01G272000 chr2A 79.898 393 41 28 5886 6247 109603983 109604368 2.970000e-63 254.0
41 TraesCS7A01G272000 chr2A 79.878 164 28 5 3813 3974 138867260 138867420 1.460000e-21 115.0
42 TraesCS7A01G272000 chr1D 82.237 304 42 10 6114 6409 76089172 76089471 1.070000e-62 252.0
43 TraesCS7A01G272000 chr1D 95.349 43 1 1 2637 2678 196818373 196818415 4.160000e-07 67.6
44 TraesCS7A01G272000 chr1A 84.783 92 11 3 2825 2915 307039927 307039838 8.870000e-14 89.8
45 TraesCS7A01G272000 chr1A 91.837 49 3 1 2643 2691 129728252 129728205 4.160000e-07 67.6
46 TraesCS7A01G272000 chr1A 91.837 49 1 3 2630 2678 238670293 238670248 1.490000e-06 65.8
47 TraesCS7A01G272000 chr6B 89.041 73 3 5 3778 3849 25821432 25821500 1.150000e-12 86.1
48 TraesCS7A01G272000 chr2B 88.679 53 6 0 2643 2695 645479733 645479681 1.490000e-06 65.8
49 TraesCS7A01G272000 chr4A 81.818 77 11 2 6263 6336 201172025 201171949 1.930000e-05 62.1


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 TraesCS7A01G272000 chr7A 285429191 285435612 6421 False 5596.000000 8615 100.000000 1 6422 2 chr7A.!!$F3 6421
1 TraesCS7A01G272000 chr7D 262360685 262366181 5496 False 924.971429 2652 92.247286 1 5541 7 chr7D.!!$F1 5540
2 TraesCS7A01G272000 chr7B 241569693 241570589 896 True 1075.000000 1075 88.128000 1 933 1 chr7B.!!$R1 932
3 TraesCS7A01G272000 chr7B 241559205 241563849 4644 True 994.400000 2340 94.280571 938 5756 7 chr7B.!!$R2 4818
4 TraesCS7A01G272000 chr5D 424318504 424319184 680 False 437.500000 579 93.961500 999 1700 2 chr5D.!!$F1 701
5 TraesCS7A01G272000 chr5A 538311626 538312295 669 False 423.500000 551 93.373500 999 1700 2 chr5A.!!$F3 701
6 TraesCS7A01G272000 chr5A 532474810 532475323 513 False 390.000000 390 80.917000 5877 6409 1 chr5A.!!$F1 532
7 TraesCS7A01G272000 chr5A 538811216 538811755 539 True 383.000000 383 80.212000 5874 6419 1 chr5A.!!$R1 545
8 TraesCS7A01G272000 chr5A 14850615 14851510 895 False 381.000000 457 82.354500 5877 6388 2 chr5A.!!$F2 511
9 TraesCS7A01G272000 chr5B 513589530 513590663 1133 False 418.000000 545 92.974500 999 1700 2 chr5B.!!$F1 701
10 TraesCS7A01G272000 chr3D 519617569 519618101 532 True 460.000000 460 82.847000 5880 6409 1 chr3D.!!$R1 529
11 TraesCS7A01G272000 chr3B 634771160 634771781 621 False 375.000000 375 78.328000 5787 6411 1 chr3B.!!$F2 624
12 TraesCS7A01G272000 chr1B 553006416 553006986 570 False 268.000000 268 76.736000 5886 6409 1 chr1B.!!$F2 523

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
279 280 0.179018 ATAGAAGATGCGGGTTGCCC 60.179 55.0 0.00 0.0 45.60 5.36 F
367 368 0.240945 CGCGCCTTCAGGTTGATTTT 59.759 50.0 0.00 0.0 37.57 1.82 F
1192 1196 0.247460 GTAGGCGACCTAAAACCCGT 59.753 55.0 7.11 0.0 37.91 5.28 F
3044 3655 0.764369 ACCACTCTTCTCCACTGCCA 60.764 55.0 0.00 0.0 0.00 4.92 F
3715 4368 0.107606 TCTTCTCCTCGTCCTCCTCG 60.108 60.0 0.00 0.0 0.00 4.63 F
4266 4939 0.185901 TTCTTGGCTGGCAGAGGTTT 59.814 50.0 20.86 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1264 1745 0.618981 ACCTGGGAAATTCGAGGGAC 59.381 55.000 12.53 0.00 37.02 4.46 R
2317 2848 1.749634 GGCTGAGCAAAGAGAATGCAT 59.250 47.619 6.82 0.00 46.22 3.96 R
3142 3753 0.753479 GAGCTCGAGGAGTCCATGGA 60.753 60.000 11.44 11.44 31.39 3.41 R
4364 5484 1.379044 AAAATGCCAGCTCTCCGGG 60.379 57.895 0.00 0.00 0.00 5.73 R
5394 6527 0.539669 CTTTCGGGCCACCCTTCTTT 60.540 55.000 4.39 0.00 42.67 2.52 R
5827 7032 0.238553 CGATGCGAGCTCGATTCCTA 59.761 55.000 38.74 16.65 43.02 2.94 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
51 52 3.226347 GTTGTGTAGCATCAAAACTCGC 58.774 45.455 6.86 0.00 34.00 5.03
80 81 1.296715 GTCCGCCCAACTCAGACAT 59.703 57.895 0.00 0.00 0.00 3.06
157 158 5.125417 GGGCTTCATTCTTGTATAGTTTGCA 59.875 40.000 0.00 0.00 0.00 4.08
160 161 6.963805 GCTTCATTCTTGTATAGTTTGCAGAC 59.036 38.462 0.00 0.00 0.00 3.51
177 178 3.437049 GCAGACCTTGTGTGTCCTTATTC 59.563 47.826 0.00 0.00 33.09 1.75
195 196 9.405587 TCCTTATTCTTTTTATTTTTGTCGCAG 57.594 29.630 0.00 0.00 0.00 5.18
204 205 1.878953 TTTTGTCGCAGTTCCTCTCC 58.121 50.000 0.00 0.00 0.00 3.71
216 217 2.066393 CCTCTCCCGGAGATTGCCA 61.066 63.158 17.80 0.00 44.45 4.92
219 220 0.690744 TCTCCCGGAGATTGCCATGA 60.691 55.000 13.54 0.00 33.35 3.07
224 225 1.408683 CCGGAGATTGCCATGAAGGAA 60.409 52.381 0.00 0.00 41.22 3.36
226 227 2.681976 CGGAGATTGCCATGAAGGAAGT 60.682 50.000 0.00 0.00 41.22 3.01
228 229 3.129988 GGAGATTGCCATGAAGGAAGTTG 59.870 47.826 0.00 0.00 41.22 3.16
233 234 2.087646 GCCATGAAGGAAGTTGAGGAC 58.912 52.381 0.00 0.00 41.22 3.85
240 241 1.777272 AGGAAGTTGAGGACCTGCTTT 59.223 47.619 0.00 0.00 0.00 3.51
241 242 1.882623 GGAAGTTGAGGACCTGCTTTG 59.117 52.381 0.00 0.00 0.00 2.77
244 245 1.228552 TTGAGGACCTGCTTTGGGC 60.229 57.895 0.00 0.00 42.22 5.36
276 277 0.947244 GGCATAGAAGATGCGGGTTG 59.053 55.000 3.61 0.00 45.41 3.77
279 280 0.179018 ATAGAAGATGCGGGTTGCCC 60.179 55.000 0.00 0.00 45.60 5.36
355 356 2.048127 GGAGTTCTCACGCGCCTT 60.048 61.111 5.73 0.00 0.00 4.35
367 368 0.240945 CGCGCCTTCAGGTTGATTTT 59.759 50.000 0.00 0.00 37.57 1.82
377 378 5.815233 TCAGGTTGATTTTAATTTGGGCA 57.185 34.783 0.00 0.00 0.00 5.36
403 405 5.834204 ACTAGTAGTTTCAGGTGAGAAGTGT 59.166 40.000 0.00 0.00 0.00 3.55
423 425 0.336737 AGTCTTCATCCTCGGGGACT 59.663 55.000 5.91 0.00 45.43 3.85
424 426 1.196012 GTCTTCATCCTCGGGGACTT 58.804 55.000 5.91 0.00 45.43 3.01
425 427 1.134670 GTCTTCATCCTCGGGGACTTG 60.135 57.143 5.91 1.08 45.43 3.16
426 428 1.195115 CTTCATCCTCGGGGACTTGA 58.805 55.000 5.91 4.38 45.43 3.02
427 429 1.555075 CTTCATCCTCGGGGACTTGAA 59.445 52.381 17.44 17.44 45.43 2.69
428 430 1.651737 TCATCCTCGGGGACTTGAAA 58.348 50.000 5.91 0.00 45.43 2.69
429 431 1.555075 TCATCCTCGGGGACTTGAAAG 59.445 52.381 5.91 0.00 45.43 2.62
449 451 8.154649 TGAAAGTTGAAACTGAATTAGAGTCC 57.845 34.615 0.00 0.00 39.66 3.85
450 452 6.787085 AAGTTGAAACTGAATTAGAGTCCG 57.213 37.500 0.00 0.00 39.66 4.79
454 456 4.527038 TGAAACTGAATTAGAGTCCGGACT 59.473 41.667 36.89 36.89 45.84 3.85
472 474 3.130516 GGACTGGATCATACGAGTTCACA 59.869 47.826 0.00 0.00 0.00 3.58
488 490 4.067896 GTTCACATGCTCGGAATCCATAT 58.932 43.478 0.00 0.00 0.00 1.78
494 496 5.877012 ACATGCTCGGAATCCATATTGTATC 59.123 40.000 0.00 0.00 0.00 2.24
495 497 4.832248 TGCTCGGAATCCATATTGTATCC 58.168 43.478 0.00 0.00 0.00 2.59
496 498 4.192317 GCTCGGAATCCATATTGTATCCC 58.808 47.826 0.00 0.00 0.00 3.85
497 499 4.080863 GCTCGGAATCCATATTGTATCCCT 60.081 45.833 0.00 0.00 0.00 4.20
530 532 6.998968 ACCTCTTTGATTCACATGATTCTC 57.001 37.500 0.00 0.00 0.00 2.87
604 607 5.893255 TCCTAGATGATTTGGGATTGTTTGG 59.107 40.000 0.00 0.00 0.00 3.28
616 619 5.896106 TGGGATTGTTTGGTTGCATCATATA 59.104 36.000 0.00 0.00 0.00 0.86
699 702 9.429109 AGGAAGTGGTTAAGGAAAATCTTAAAA 57.571 29.630 0.00 0.00 39.86 1.52
839 843 1.387119 AAGGAGCCCTTGGAGGAATT 58.613 50.000 5.76 0.00 42.96 2.17
933 937 2.288458 CCGGACTGCGAAAGTAAACAAA 59.712 45.455 0.00 0.00 40.07 2.83
934 938 3.285745 CGGACTGCGAAAGTAAACAAAC 58.714 45.455 0.00 0.00 40.07 2.93
935 939 3.242478 CGGACTGCGAAAGTAAACAAACA 60.242 43.478 0.00 0.00 40.07 2.83
936 940 4.553938 CGGACTGCGAAAGTAAACAAACAT 60.554 41.667 0.00 0.00 40.07 2.71
941 945 8.319143 ACTGCGAAAGTAAACAAACATATACT 57.681 30.769 0.00 0.00 37.36 2.12
952 956 5.416947 ACAAACATATACTCACCGGAACTC 58.583 41.667 9.46 0.00 0.00 3.01
1192 1196 0.247460 GTAGGCGACCTAAAACCCGT 59.753 55.000 7.11 0.00 37.91 5.28
1531 2012 1.125633 TTGGCTTCGACCCCTATACC 58.874 55.000 2.56 0.00 0.00 2.73
1624 2105 1.741401 CTCCAACTCCATGCGCGAA 60.741 57.895 12.10 0.00 0.00 4.70
1859 2345 1.141254 AGATGCTCCAAGAGATGCCAG 59.859 52.381 0.00 0.00 0.00 4.85
2043 2532 2.416547 CTCAAGGTGTTAGTGGAATGCG 59.583 50.000 0.00 0.00 0.00 4.73
2212 2743 6.568869 AGTAACTGCTCATGTGAAGATAGAC 58.431 40.000 9.80 2.34 0.00 2.59
2222 2753 7.027760 TCATGTGAAGATAGACGTTCTAACAC 58.972 38.462 13.93 13.93 31.96 3.32
2245 2776 3.868062 TGACAAATGGGGGAGGATTTTT 58.132 40.909 0.00 0.00 0.00 1.94
2286 2817 7.502120 AGTGATTATATGCCAATTGACTGAC 57.498 36.000 7.12 0.00 0.00 3.51
2291 2822 7.801716 TTATATGCCAATTGACTGACCTAAC 57.198 36.000 7.12 0.00 0.00 2.34
2297 2828 5.070001 CCAATTGACTGACCTAACTGGAAA 58.930 41.667 7.12 0.00 39.71 3.13
2317 2848 8.306313 TGGAAAGCTCATGTCTAGAGTTTATA 57.694 34.615 0.00 0.00 35.84 0.98
2414 3015 8.200792 AGTACAAAGCTAGATCAAGTTCCTATG 58.799 37.037 0.00 0.00 0.00 2.23
2441 3042 8.081633 TCTGTTTTTATCGACTGCATTCAAATT 58.918 29.630 4.82 0.00 0.00 1.82
2479 3080 7.429374 AATTGAGTGAGATAGGAGTGATTCA 57.571 36.000 0.00 0.00 0.00 2.57
2483 3084 7.062957 TGAGTGAGATAGGAGTGATTCATGTA 58.937 38.462 0.00 0.00 0.00 2.29
2501 3102 4.014569 TGTATGTGCTTGCCACTTTAGA 57.985 40.909 0.00 0.00 44.92 2.10
2610 3216 6.641474 TCATTTGCAATGCCAATTTCATCTA 58.359 32.000 1.53 0.00 0.00 1.98
2678 3289 8.557592 ACGTCTTATAAAAGTTTAAAGAGGGG 57.442 34.615 20.45 11.75 34.54 4.79
2715 3326 7.987268 AATTTTCTTTCAAAAGTCGGTTCTC 57.013 32.000 2.63 0.00 37.31 2.87
2735 3346 8.470805 GGTTCTCTCATGTCAATAGTCTAAGAA 58.529 37.037 0.00 0.00 0.00 2.52
2762 3373 3.238497 CCGGACGCCCCATATCCA 61.238 66.667 0.00 0.00 32.35 3.41
2997 3608 3.674050 ATACCCCAGCCGGACGACT 62.674 63.158 5.05 0.00 0.00 4.18
3032 3643 2.158385 ACCTCACTCTCTTGACCACTCT 60.158 50.000 0.00 0.00 0.00 3.24
3044 3655 0.764369 ACCACTCTTCTCCACTGCCA 60.764 55.000 0.00 0.00 0.00 4.92
3070 3681 2.069430 CCCTTCCTCTCTCTGCCCC 61.069 68.421 0.00 0.00 0.00 5.80
3080 3691 3.710631 TCTGCCCCATCCCCTCCT 61.711 66.667 0.00 0.00 0.00 3.69
3094 3705 4.804420 TCCTCTCCGCCATGGCCT 62.804 66.667 30.79 0.00 37.80 5.19
3165 3776 1.450669 GGACTCCTCGAGCTCGTCT 60.451 63.158 33.33 13.71 40.80 4.18
3251 3862 1.122019 AGCTCCTCCTCGTTGGTGTT 61.122 55.000 0.00 0.00 37.07 3.32
3332 3943 4.501285 GCCTTCCCCGGTTAGGCC 62.501 72.222 21.86 0.00 46.94 5.19
3381 3992 3.710722 CAGCTGCTCCTTCCGGGT 61.711 66.667 0.00 0.00 36.25 5.28
3406 4050 1.779025 GAGGGTCGCGCGTATCACTA 61.779 60.000 30.98 5.11 0.00 2.74
3441 4085 1.153289 CCACTTCCATCCGCTCTGG 60.153 63.158 0.00 0.00 40.09 3.86
3584 4228 2.499289 TGCAAAAATGTGGTGGTGTTCT 59.501 40.909 0.00 0.00 0.00 3.01
3625 4269 1.548269 GAGAGGTTGGTGAGTCAGAGG 59.452 57.143 0.00 0.00 0.00 3.69
3627 4271 0.472734 AGGTTGGTGAGTCAGAGGCT 60.473 55.000 0.00 0.00 0.00 4.58
3706 4359 2.123342 GCGTTGATCATCTTCTCCTCG 58.877 52.381 0.00 0.00 0.00 4.63
3709 4362 3.712187 GTTGATCATCTTCTCCTCGTCC 58.288 50.000 0.00 0.00 0.00 4.79
3710 4363 3.304911 TGATCATCTTCTCCTCGTCCT 57.695 47.619 0.00 0.00 0.00 3.85
3711 4364 3.218453 TGATCATCTTCTCCTCGTCCTC 58.782 50.000 0.00 0.00 0.00 3.71
3712 4365 2.060050 TCATCTTCTCCTCGTCCTCC 57.940 55.000 0.00 0.00 0.00 4.30
3713 4366 1.566703 TCATCTTCTCCTCGTCCTCCT 59.433 52.381 0.00 0.00 0.00 3.69
3714 4367 1.953686 CATCTTCTCCTCGTCCTCCTC 59.046 57.143 0.00 0.00 0.00 3.71
3715 4368 0.107606 TCTTCTCCTCGTCCTCCTCG 60.108 60.000 0.00 0.00 0.00 4.63
3716 4369 1.077644 TTCTCCTCGTCCTCCTCGG 60.078 63.158 0.00 0.00 0.00 4.63
3738 4391 2.178521 GGCACGACTGACGACGAT 59.821 61.111 0.00 0.00 45.77 3.73
3745 4398 0.798771 GACTGACGACGATGCTCCAC 60.799 60.000 0.00 0.00 0.00 4.02
3779 4432 1.458827 CTACGCCTATCTACGTCGGAC 59.541 57.143 0.00 0.00 42.46 4.79
3890 4546 2.586293 GGGCAAATGTGGGCTGCTT 61.586 57.895 0.00 0.00 36.32 3.91
3955 4611 4.783903 CCGCAAATTAGGCAACCG 57.216 55.556 3.32 0.00 37.17 4.44
3959 4615 1.516169 CAAATTAGGCAACCGCGGC 60.516 57.895 28.58 11.81 39.92 6.53
3961 4617 1.654023 AAATTAGGCAACCGCGGCTC 61.654 55.000 28.58 14.50 42.62 4.70
3987 4652 7.563888 AGATGCTCTAATACTTGTGTACGTA 57.436 36.000 0.00 0.00 0.00 3.57
4120 4785 3.416156 TGCACATTGTGTAACTGGCATA 58.584 40.909 17.64 0.00 38.04 3.14
4149 4814 6.017109 TGTGACTCATTTAGTGAAAGAAAGCC 60.017 38.462 0.00 0.00 39.07 4.35
4174 4847 7.343316 CCACTCCCTCTGTCCTATAATATAAGG 59.657 44.444 0.00 0.00 0.00 2.69
4266 4939 0.185901 TTCTTGGCTGGCAGAGGTTT 59.814 50.000 20.86 0.00 0.00 3.27
4364 5484 7.255381 GCATATCTGCCATCCCAAATATATGTC 60.255 40.741 0.00 0.00 42.88 3.06
4446 5566 2.332514 CTGTTGCTGTGTTGCCCG 59.667 61.111 0.00 0.00 0.00 6.13
4505 5626 4.096984 GGGAAGGCAAACATTACATGAGAG 59.903 45.833 0.00 0.00 0.00 3.20
4625 5749 4.021981 TGCATATCCTCTTGTATCGTCAGG 60.022 45.833 0.00 0.00 0.00 3.86
5062 6190 5.279206 CGAGAGTGGCATATCCTCTTGTATT 60.279 44.000 6.79 0.00 38.71 1.89
5223 6356 7.757526 TGGTTTGTCTTCCATTTATATTGTCG 58.242 34.615 0.00 0.00 0.00 4.35
5224 6357 7.608376 TGGTTTGTCTTCCATTTATATTGTCGA 59.392 33.333 0.00 0.00 0.00 4.20
5446 6579 6.627243 TGTACTAATGATTTAGCACAGTCGT 58.373 36.000 0.00 0.00 36.98 4.34
5490 6623 6.521162 TCTGTTTATGTTCACAGCTTGTCTA 58.479 36.000 0.00 0.00 40.33 2.59
5495 6628 5.633830 ATGTTCACAGCTTGTCTATTTGG 57.366 39.130 0.00 0.00 0.00 3.28
5542 6709 3.764218 TGGCCGAGGGTTGTTTATTTTA 58.236 40.909 0.00 0.00 0.00 1.52
5594 6761 2.178876 ATCCCCGTCATGTTGTGCGA 62.179 55.000 0.00 0.00 31.82 5.10
5596 6763 1.206578 CCCGTCATGTTGTGCGAAC 59.793 57.895 0.00 0.00 31.82 3.95
5597 6764 1.227999 CCCGTCATGTTGTGCGAACT 61.228 55.000 0.00 0.00 31.82 3.01
5598 6765 0.110688 CCGTCATGTTGTGCGAACTG 60.111 55.000 0.00 0.00 31.82 3.16
5599 6766 0.581529 CGTCATGTTGTGCGAACTGT 59.418 50.000 0.00 0.00 31.82 3.55
5600 6767 1.790043 CGTCATGTTGTGCGAACTGTA 59.210 47.619 0.00 0.00 31.82 2.74
5601 6768 2.411748 CGTCATGTTGTGCGAACTGTAT 59.588 45.455 0.00 0.00 31.82 2.29
5613 6780 5.747197 GTGCGAACTGTATAAGCTTAGCTAA 59.253 40.000 7.32 5.94 38.25 3.09
5618 6785 6.115448 ACTGTATAAGCTTAGCTAATGGGG 57.885 41.667 7.32 0.01 38.25 4.96
5619 6786 5.013183 ACTGTATAAGCTTAGCTAATGGGGG 59.987 44.000 7.32 0.00 38.25 5.40
5621 6788 2.736670 AAGCTTAGCTAATGGGGGTG 57.263 50.000 7.32 0.00 38.25 4.61
5622 6789 1.596496 AGCTTAGCTAATGGGGGTGT 58.404 50.000 4.30 0.00 36.99 4.16
5623 6790 1.923148 AGCTTAGCTAATGGGGGTGTT 59.077 47.619 4.30 0.00 36.99 3.32
5624 6791 3.120108 AGCTTAGCTAATGGGGGTGTTA 58.880 45.455 4.30 0.00 36.99 2.41
5625 6792 3.118000 AGCTTAGCTAATGGGGGTGTTAC 60.118 47.826 4.30 0.00 36.99 2.50
5626 6793 3.816994 CTTAGCTAATGGGGGTGTTACC 58.183 50.000 6.64 0.00 37.60 2.85
5628 6795 0.464916 GCTAATGGGGGTGTTACCGG 60.465 60.000 0.00 0.00 39.83 5.28
5646 6851 1.230324 GGAAGCTTAGCTAATGGGCG 58.770 55.000 7.32 0.00 38.25 6.13
5665 6870 2.067605 TTACCGGGCCGTGGATGAT 61.068 57.895 26.32 3.43 0.00 2.45
5684 6889 4.298626 TGATAAGTGGGCTGAGATAACCT 58.701 43.478 0.00 0.00 0.00 3.50
5756 6961 1.377725 ACATTGGAGCCTTGGAGCG 60.378 57.895 0.00 0.00 38.01 5.03
5757 6962 2.117156 CATTGGAGCCTTGGAGCGG 61.117 63.158 0.00 0.00 38.01 5.52
5758 6963 3.350031 ATTGGAGCCTTGGAGCGGG 62.350 63.158 0.00 0.00 38.01 6.13
5760 6965 4.168291 GGAGCCTTGGAGCGGGAG 62.168 72.222 0.00 0.00 38.01 4.30
5837 7042 2.478831 GGAGCTGCTTTAGGAATCGAG 58.521 52.381 2.53 0.00 0.00 4.04
5844 7049 2.748605 CTTTAGGAATCGAGCTCGCAT 58.251 47.619 30.97 21.14 39.60 4.73
5863 7069 2.476499 GCGCGAAGTCAAGCCTTC 59.524 61.111 12.10 0.00 37.96 3.46
5864 7070 2.029844 GCGCGAAGTCAAGCCTTCT 61.030 57.895 12.10 0.00 38.95 2.85
5867 7073 1.512926 GCGAAGTCAAGCCTTCTTCA 58.487 50.000 6.68 0.00 38.95 3.02
5868 7074 2.079925 GCGAAGTCAAGCCTTCTTCAT 58.920 47.619 6.68 0.00 38.95 2.57
5869 7075 2.159599 GCGAAGTCAAGCCTTCTTCATG 60.160 50.000 6.68 0.00 38.95 3.07
5870 7076 2.159599 CGAAGTCAAGCCTTCTTCATGC 60.160 50.000 6.68 0.00 38.95 4.06
5871 7077 2.875094 AGTCAAGCCTTCTTCATGCT 57.125 45.000 0.00 0.00 36.79 3.79
5872 7078 3.151912 AGTCAAGCCTTCTTCATGCTT 57.848 42.857 0.00 0.00 45.69 3.91
5878 7084 2.238144 AGCCTTCTTCATGCTTAGCTGA 59.762 45.455 5.60 4.08 29.17 4.26
5884 7090 3.753272 TCTTCATGCTTAGCTGAACAACC 59.247 43.478 5.60 0.00 0.00 3.77
5906 7112 5.352016 ACCGTGATTTTAATAGCGCTAACAA 59.648 36.000 22.98 15.07 0.00 2.83
5909 7115 8.227791 CCGTGATTTTAATAGCGCTAACAATAT 58.772 33.333 22.98 16.92 0.00 1.28
5910 7117 9.040543 CGTGATTTTAATAGCGCTAACAATATG 57.959 33.333 22.98 5.33 0.00 1.78
6131 7363 6.693315 TCATTGTTTTCGGAAAAGAGTTCT 57.307 33.333 15.75 0.00 0.00 3.01
6141 7373 5.526111 TCGGAAAAGAGTTCTTCATTTTCGT 59.474 36.000 5.74 0.00 42.91 3.85
6373 8061 7.912056 TGGATTTGAACAAAAACATCAAACA 57.088 28.000 4.12 0.00 43.50 2.83
6383 8071 7.610865 ACAAAAACATCAAACAAGGAAGAAGA 58.389 30.769 0.00 0.00 0.00 2.87
6388 8076 8.479313 AACATCAAACAAGGAAGAAGAAAAAC 57.521 30.769 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.127895 CGTCCTCCTCAGACTTCTTGTAG 59.872 52.174 0.00 0.00 31.83 2.74
10 11 1.889829 CGTCCTCCTCAGACTTCTTGT 59.110 52.381 0.00 0.00 31.83 3.16
51 52 3.103911 GGCGGACGTGTCGAACAG 61.104 66.667 11.42 0.00 0.00 3.16
135 136 6.963805 GTCTGCAAACTATACAAGAATGAAGC 59.036 38.462 0.00 0.00 0.00 3.86
157 158 5.568620 AAGAATAAGGACACACAAGGTCT 57.431 39.130 0.00 0.00 35.61 3.85
160 161 9.981114 AAATAAAAAGAATAAGGACACACAAGG 57.019 29.630 0.00 0.00 0.00 3.61
177 178 6.918022 AGAGGAACTGCGACAAAAATAAAAAG 59.082 34.615 0.00 0.00 41.55 2.27
195 196 0.179070 GCAATCTCCGGGAGAGGAAC 60.179 60.000 29.03 15.92 42.26 3.62
204 205 0.181114 TCCTTCATGGCAATCTCCGG 59.819 55.000 0.00 0.00 35.26 5.14
216 217 2.290577 GCAGGTCCTCAACTTCCTTCAT 60.291 50.000 0.00 0.00 0.00 2.57
219 220 1.439543 AGCAGGTCCTCAACTTCCTT 58.560 50.000 0.00 0.00 0.00 3.36
224 225 0.111253 CCCAAAGCAGGTCCTCAACT 59.889 55.000 0.00 0.00 0.00 3.16
226 227 1.228552 GCCCAAAGCAGGTCCTCAA 60.229 57.895 0.00 0.00 42.97 3.02
228 229 2.747855 CGCCCAAAGCAGGTCCTC 60.748 66.667 0.00 0.00 44.04 3.71
233 234 4.362476 GCCAACGCCCAAAGCAGG 62.362 66.667 0.00 0.00 44.04 4.85
244 245 2.109538 CTATGCCAGCATCGCCAACG 62.110 60.000 8.71 0.00 37.82 4.10
291 292 4.524053 GTCCTTATACCAAAGGTTCCCAG 58.476 47.826 2.76 0.00 45.37 4.45
298 299 3.275999 CGTTGGGTCCTTATACCAAAGG 58.724 50.000 0.00 0.00 45.04 3.11
308 309 0.602905 CGAAGAAGCGTTGGGTCCTT 60.603 55.000 0.00 0.00 0.00 3.36
313 314 2.033194 GTCCCGAAGAAGCGTTGGG 61.033 63.158 0.00 0.00 41.43 4.12
352 353 5.643348 GCCCAAATTAAAATCAACCTGAAGG 59.357 40.000 0.00 0.00 42.17 3.46
355 356 5.541868 TCTGCCCAAATTAAAATCAACCTGA 59.458 36.000 0.00 0.00 0.00 3.86
367 368 7.011499 TGAAACTACTAGTCTGCCCAAATTA 57.989 36.000 0.00 0.00 0.00 1.40
377 378 6.207810 CACTTCTCACCTGAAACTACTAGTCT 59.792 42.308 0.00 0.00 0.00 3.24
403 405 1.569548 AGTCCCCGAGGATGAAGACTA 59.430 52.381 0.00 0.00 46.41 2.59
423 425 8.621286 GGACTCTAATTCAGTTTCAACTTTCAA 58.379 33.333 0.00 0.00 37.08 2.69
424 426 7.042051 CGGACTCTAATTCAGTTTCAACTTTCA 60.042 37.037 0.00 0.00 37.08 2.69
425 427 7.291567 CGGACTCTAATTCAGTTTCAACTTTC 58.708 38.462 0.00 0.00 37.08 2.62
426 428 6.204882 CCGGACTCTAATTCAGTTTCAACTTT 59.795 38.462 0.00 0.00 37.08 2.66
427 429 5.701290 CCGGACTCTAATTCAGTTTCAACTT 59.299 40.000 0.00 0.00 37.08 2.66
428 430 5.011738 TCCGGACTCTAATTCAGTTTCAACT 59.988 40.000 0.00 0.00 40.60 3.16
429 431 5.120363 GTCCGGACTCTAATTCAGTTTCAAC 59.880 44.000 27.64 0.00 0.00 3.18
449 451 2.357952 TGAACTCGTATGATCCAGTCCG 59.642 50.000 0.00 0.00 0.00 4.79
450 452 3.130516 TGTGAACTCGTATGATCCAGTCC 59.869 47.826 0.00 0.00 0.00 3.85
454 456 3.132824 AGCATGTGAACTCGTATGATCCA 59.867 43.478 0.00 0.00 0.00 3.41
472 474 5.431765 GGATACAATATGGATTCCGAGCAT 58.568 41.667 0.00 0.00 0.00 3.79
488 490 7.569599 AGAGGTTCTAAAAGAAGGGATACAA 57.430 36.000 0.00 0.00 34.42 2.41
494 496 7.448469 TGAATCAAAGAGGTTCTAAAAGAAGGG 59.552 37.037 0.00 0.00 34.42 3.95
495 497 8.293157 GTGAATCAAAGAGGTTCTAAAAGAAGG 58.707 37.037 0.00 0.00 34.42 3.46
496 498 8.840321 TGTGAATCAAAGAGGTTCTAAAAGAAG 58.160 33.333 0.00 0.00 34.42 2.85
497 499 8.746052 TGTGAATCAAAGAGGTTCTAAAAGAA 57.254 30.769 0.00 0.00 0.00 2.52
507 509 6.479006 TGAGAATCATGTGAATCAAAGAGGT 58.521 36.000 1.35 0.00 42.56 3.85
560 563 6.158023 AGGATTGAGATGAAAATGGCATTC 57.842 37.500 14.04 3.32 0.00 2.67
644 647 5.241728 GGTTTCTAGCATCCACTCAAAACTT 59.758 40.000 0.00 0.00 30.63 2.66
839 843 7.618512 AGAAGGTAAACTACATAGGCAAGACTA 59.381 37.037 0.00 0.00 0.00 2.59
933 937 2.963782 GGGAGTTCCGGTGAGTATATGT 59.036 50.000 0.00 0.00 36.71 2.29
934 938 2.299297 GGGGAGTTCCGGTGAGTATATG 59.701 54.545 0.00 0.00 36.71 1.78
935 939 2.090943 TGGGGAGTTCCGGTGAGTATAT 60.091 50.000 0.00 0.00 36.71 0.86
936 940 1.288633 TGGGGAGTTCCGGTGAGTATA 59.711 52.381 0.00 0.00 36.71 1.47
941 945 1.758592 CTTTGGGGAGTTCCGGTGA 59.241 57.895 0.00 0.00 36.71 4.02
952 956 1.303643 AGAGGCTTTCGCTTTGGGG 60.304 57.895 0.00 0.00 36.09 4.96
1186 1190 4.968311 AGGGGGAACGGACGGGTT 62.968 66.667 0.00 0.00 0.00 4.11
1212 1681 4.338539 GTCGATCCGGCGGCGTAT 62.339 66.667 30.09 20.99 0.00 3.06
1264 1745 0.618981 ACCTGGGAAATTCGAGGGAC 59.381 55.000 12.53 0.00 37.02 4.46
1911 2397 6.443849 TGTCCTTCTCATATGGTTAGGTTCTT 59.556 38.462 2.13 0.00 0.00 2.52
1912 2398 5.964477 TGTCCTTCTCATATGGTTAGGTTCT 59.036 40.000 2.13 0.00 0.00 3.01
1913 2399 6.049790 GTGTCCTTCTCATATGGTTAGGTTC 58.950 44.000 2.13 6.09 0.00 3.62
2032 2521 2.693074 TCTAGACATGCGCATTCCACTA 59.307 45.455 22.81 18.43 0.00 2.74
2043 2532 4.310769 ACACACAGAAACTCTAGACATGC 58.689 43.478 0.00 0.00 0.00 4.06
2187 2677 7.467403 CGTCTATCTTCACATGAGCAGTTACTA 60.467 40.741 0.00 0.00 0.00 1.82
2212 2743 4.379394 CCCCATTTGTCATGTGTTAGAACG 60.379 45.833 0.00 0.00 0.00 3.95
2222 2753 2.761786 ATCCTCCCCCATTTGTCATG 57.238 50.000 0.00 0.00 0.00 3.07
2250 2781 9.625747 TGGCATATAATCACTTGTAAGAATTGA 57.374 29.630 0.00 0.00 0.00 2.57
2259 2790 7.557358 TCAGTCAATTGGCATATAATCACTTGT 59.443 33.333 13.47 0.00 0.00 3.16
2286 2817 4.213564 AGACATGAGCTTTCCAGTTAGG 57.786 45.455 0.00 0.00 39.47 2.69
2291 2822 4.734398 ACTCTAGACATGAGCTTTCCAG 57.266 45.455 0.00 0.00 35.12 3.86
2297 2828 7.295322 TGCATATAAACTCTAGACATGAGCT 57.705 36.000 0.00 0.00 35.12 4.09
2317 2848 1.749634 GGCTGAGCAAAGAGAATGCAT 59.250 47.619 6.82 0.00 46.22 3.96
2379 2980 8.123639 TGATCTAGCTTTGTACTAAAGTGAGT 57.876 34.615 14.90 0.00 0.00 3.41
2414 3015 5.927030 TGAATGCAGTCGATAAAAACAGAC 58.073 37.500 9.92 0.00 0.00 3.51
2441 3042 7.939782 TCTCACTCAATTTTAGTTTCATTGCA 58.060 30.769 0.00 0.00 0.00 4.08
2479 3080 4.588899 TCTAAAGTGGCAAGCACATACAT 58.411 39.130 0.00 0.00 0.00 2.29
2483 3084 3.146104 ACTCTAAAGTGGCAAGCACAT 57.854 42.857 0.00 0.00 33.32 3.21
2501 3102 7.968956 CGTTAGTACAGATGAACAAGTATCACT 59.031 37.037 0.00 0.00 0.00 3.41
2538 3144 3.610040 ACAACAGATGACGCCTATGAA 57.390 42.857 0.00 0.00 0.00 2.57
2735 3346 1.217244 GGCGTCCGGTTGTAGATGT 59.783 57.895 0.00 0.00 0.00 3.06
2791 3402 2.289694 GCTTCTTTCTGTCCAGGCAGTA 60.290 50.000 9.83 0.00 37.70 2.74
2939 3550 3.006133 TGCGTGGGCCATAGTGGA 61.006 61.111 10.70 0.00 40.96 4.02
2997 3608 3.314693 AGTGAGGTTTGACTAGGGTTCA 58.685 45.455 0.00 0.00 0.00 3.18
3032 3643 1.198713 GAGGAGATGGCAGTGGAGAA 58.801 55.000 0.00 0.00 0.00 2.87
3044 3655 1.503347 GAGAGAGGAAGGGGAGGAGAT 59.497 57.143 0.00 0.00 0.00 2.75
3070 3681 3.237741 GGCGGAGAGGAGGGGATG 61.238 72.222 0.00 0.00 0.00 3.51
3094 3705 4.467084 GCTGCCGGATCCGTTCCA 62.467 66.667 31.22 22.46 45.78 3.53
3142 3753 0.753479 GAGCTCGAGGAGTCCATGGA 60.753 60.000 11.44 11.44 31.39 3.41
3145 3756 1.077357 ACGAGCTCGAGGAGTCCAT 60.077 57.895 40.58 13.79 43.02 3.41
3479 4123 3.857854 GTCGTCGTCGCTAGCGGA 61.858 66.667 34.76 22.90 40.25 5.54
3484 4128 2.447887 GGTCTCGTCGTCGTCGCTA 61.448 63.158 7.01 0.00 38.33 4.26
3521 4165 2.089887 TTTGCCGAGGTGTACGAGCA 62.090 55.000 0.00 0.00 36.09 4.26
3562 4206 3.055530 AGAACACCACCACATTTTTGCAA 60.056 39.130 0.00 0.00 0.00 4.08
3584 4228 2.244117 GACTCCTTGAGCCCGATGCA 62.244 60.000 0.00 0.00 44.83 3.96
3619 4263 3.196207 AAAAGCCGCCAGCCTCTGA 62.196 57.895 0.00 0.00 45.47 3.27
3643 4287 4.147449 TCCCTCACGAGCCATGCG 62.147 66.667 0.00 0.00 0.00 4.73
3699 4343 2.590645 CCGAGGAGGACGAGGAGA 59.409 66.667 0.00 0.00 45.00 3.71
3706 4359 4.459089 GCCACTGCCGAGGAGGAC 62.459 72.222 0.00 0.00 45.00 3.85
3712 4365 4.363990 AGTCGTGCCACTGCCGAG 62.364 66.667 0.00 0.00 39.62 4.63
3713 4366 4.662961 CAGTCGTGCCACTGCCGA 62.663 66.667 0.00 0.00 37.58 5.54
3714 4367 4.662961 TCAGTCGTGCCACTGCCG 62.663 66.667 0.00 0.00 43.18 5.69
3715 4368 3.044305 GTCAGTCGTGCCACTGCC 61.044 66.667 0.00 0.00 43.18 4.85
3716 4369 3.406361 CGTCAGTCGTGCCACTGC 61.406 66.667 0.00 0.00 43.18 4.40
3762 4415 0.235144 CAGTCCGACGTAGATAGGCG 59.765 60.000 0.00 0.00 0.00 5.52
3890 4546 2.994995 ATCCGCGGACAGTGACCA 60.995 61.111 33.75 4.52 0.00 4.02
3987 4652 5.415389 AGCACAGCCAAGTTTTCAAAATTTT 59.585 32.000 0.00 0.00 0.00 1.82
4060 4725 4.732285 AAGCAACAATACAGAGTCAACG 57.268 40.909 0.00 0.00 0.00 4.10
4120 4785 8.506168 TTCTTTCACTAAATGAGTCACAAAGT 57.494 30.769 0.00 0.00 38.99 2.66
4149 4814 7.896496 ACCTTATATTATAGGACAGAGGGAGTG 59.104 40.741 0.00 0.00 35.45 3.51
4226 4899 5.892686 AGAAGTAATACTCCCTCAGTACCAC 59.107 44.000 0.00 0.00 40.60 4.16
4304 4977 6.655003 CCAAAGATACTACAAAGACCACACAT 59.345 38.462 0.00 0.00 0.00 3.21
4364 5484 1.379044 AAAATGCCAGCTCTCCGGG 60.379 57.895 0.00 0.00 0.00 5.73
4446 5566 3.486383 TGGATTTTTGGTCACAGGTCTC 58.514 45.455 0.00 0.00 0.00 3.36
4505 5626 5.353400 GGCTAATCCAGGTTAAACACTGTAC 59.647 44.000 0.00 0.00 32.90 2.90
4591 5715 8.523915 ACAAGAGGATATGCATTTAAACATGA 57.476 30.769 3.54 0.00 0.00 3.07
4625 5749 9.346725 CAATAGAAGACAAACCAAAGATTTAGC 57.653 33.333 0.00 0.00 0.00 3.09
5062 6190 6.594788 ATTCAAGGCAGATTTAAGCTGAAA 57.405 33.333 14.78 0.00 35.39 2.69
5153 6281 7.557358 ACAAGAGGATATGCATTTCAACATACA 59.443 33.333 17.37 0.00 31.87 2.29
5154 6282 7.934457 ACAAGAGGATATGCATTTCAACATAC 58.066 34.615 17.37 0.00 31.87 2.39
5223 6356 5.067023 GGGGAGATCAAATCAGTGTCATTTC 59.933 44.000 0.00 0.00 0.00 2.17
5224 6357 4.952335 GGGGAGATCAAATCAGTGTCATTT 59.048 41.667 0.00 0.00 0.00 2.32
5394 6527 0.539669 CTTTCGGGCCACCCTTCTTT 60.540 55.000 4.39 0.00 42.67 2.52
5446 6579 1.976132 GCTAGAGGAGCCATGTGCCA 61.976 60.000 0.00 0.00 46.41 4.92
5490 6623 5.595133 TCCTTCGGAAACAGTTAAACCAAAT 59.405 36.000 0.00 0.00 0.00 2.32
5495 6628 5.065602 ACAAGTCCTTCGGAAACAGTTAAAC 59.934 40.000 0.00 0.00 31.38 2.01
5513 6680 0.822121 AACCCTCGGCCAAACAAGTC 60.822 55.000 2.24 0.00 0.00 3.01
5542 6709 2.511452 AAGCACCTCCGTCAGCAGT 61.511 57.895 0.00 0.00 0.00 4.40
5583 6750 4.093408 AGCTTATACAGTTCGCACAACATG 59.907 41.667 0.00 0.00 0.00 3.21
5594 6761 6.465894 CCCCCATTAGCTAAGCTTATACAGTT 60.466 42.308 12.54 0.00 40.44 3.16
5596 6763 5.013183 ACCCCCATTAGCTAAGCTTATACAG 59.987 44.000 12.54 0.00 40.44 2.74
5597 6764 4.911522 ACCCCCATTAGCTAAGCTTATACA 59.088 41.667 12.54 0.00 40.44 2.29
5598 6765 5.221864 ACACCCCCATTAGCTAAGCTTATAC 60.222 44.000 12.54 2.56 40.44 1.47
5599 6766 4.911522 ACACCCCCATTAGCTAAGCTTATA 59.088 41.667 12.54 0.00 40.44 0.98
5600 6767 3.722101 ACACCCCCATTAGCTAAGCTTAT 59.278 43.478 12.54 0.00 40.44 1.73
5601 6768 3.120108 ACACCCCCATTAGCTAAGCTTA 58.880 45.455 12.54 5.94 40.44 3.09
5613 6780 1.996086 CTTCCGGTAACACCCCCAT 59.004 57.895 0.00 0.00 33.75 4.00
5618 6785 1.066358 AGCTAAGCTTCCGGTAACACC 60.066 52.381 0.00 0.00 33.89 4.16
5619 6786 2.381725 AGCTAAGCTTCCGGTAACAC 57.618 50.000 0.00 0.00 33.89 3.32
5621 6788 3.808174 CCATTAGCTAAGCTTCCGGTAAC 59.192 47.826 12.54 0.00 40.44 2.50
5622 6789 3.181458 CCCATTAGCTAAGCTTCCGGTAA 60.181 47.826 12.54 17.31 40.44 2.85
5623 6790 2.367567 CCCATTAGCTAAGCTTCCGGTA 59.632 50.000 12.54 2.66 40.44 4.02
5624 6791 1.141053 CCCATTAGCTAAGCTTCCGGT 59.859 52.381 12.54 3.75 40.44 5.28
5625 6792 1.884235 CCCATTAGCTAAGCTTCCGG 58.116 55.000 12.54 0.00 40.44 5.14
5626 6793 1.230324 GCCCATTAGCTAAGCTTCCG 58.770 55.000 12.54 0.00 40.44 4.30
5628 6795 1.954927 ACGCCCATTAGCTAAGCTTC 58.045 50.000 12.54 1.01 40.44 3.86
5646 6851 2.319890 ATCATCCACGGCCCGGTAAC 62.320 60.000 8.57 0.00 0.00 2.50
5659 6864 5.241662 GTTATCTCAGCCCACTTATCATCC 58.758 45.833 0.00 0.00 0.00 3.51
5665 6870 4.616553 TGTAGGTTATCTCAGCCCACTTA 58.383 43.478 0.00 0.00 0.00 2.24
5684 6889 8.796475 CCTGGTACTACTACTACAAAAGTTGTA 58.204 37.037 1.22 1.22 41.54 2.41
5724 6929 4.491676 CTCCAATGTGCAATTCTTCTTGG 58.508 43.478 0.00 0.00 34.37 3.61
5725 6930 3.924686 GCTCCAATGTGCAATTCTTCTTG 59.075 43.478 0.00 0.00 0.00 3.02
5767 6972 3.273084 TTTGTTCGCTGCGCCGAA 61.273 55.556 18.65 15.93 44.09 4.30
5768 6973 4.007940 GTTTGTTCGCTGCGCCGA 62.008 61.111 18.65 4.42 35.09 5.54
5769 6974 3.798639 TTGTTTGTTCGCTGCGCCG 62.799 57.895 18.65 1.29 0.00 6.46
5770 6975 1.142778 TTTTGTTTGTTCGCTGCGCC 61.143 50.000 18.65 10.80 0.00 6.53
5771 6976 0.642800 TTTTTGTTTGTTCGCTGCGC 59.357 45.000 18.65 0.00 0.00 6.09
5813 7018 1.072266 TTCCTAAAGCAGCTCCCCAA 58.928 50.000 0.00 0.00 0.00 4.12
5814 7019 1.212935 GATTCCTAAAGCAGCTCCCCA 59.787 52.381 0.00 0.00 0.00 4.96
5815 7020 1.811941 CGATTCCTAAAGCAGCTCCCC 60.812 57.143 0.00 0.00 0.00 4.81
5816 7021 1.139058 TCGATTCCTAAAGCAGCTCCC 59.861 52.381 0.00 0.00 0.00 4.30
5817 7022 2.478831 CTCGATTCCTAAAGCAGCTCC 58.521 52.381 0.00 0.00 0.00 4.70
5827 7032 0.238553 CGATGCGAGCTCGATTCCTA 59.761 55.000 38.74 16.65 43.02 2.94
5844 7049 3.858868 AAGGCTTGACTTCGCGCGA 62.859 57.895 31.40 31.40 0.00 5.87
5850 7055 3.080319 AGCATGAAGAAGGCTTGACTTC 58.920 45.455 17.37 17.37 45.59 3.01
5863 7069 3.425359 CGGTTGTTCAGCTAAGCATGAAG 60.425 47.826 0.00 0.00 0.00 3.02
5864 7070 2.483877 CGGTTGTTCAGCTAAGCATGAA 59.516 45.455 0.00 0.00 0.00 2.57
5867 7073 1.806542 CACGGTTGTTCAGCTAAGCAT 59.193 47.619 0.00 0.00 0.00 3.79
5868 7074 1.202592 TCACGGTTGTTCAGCTAAGCA 60.203 47.619 0.00 0.00 0.00 3.91
5869 7075 1.508632 TCACGGTTGTTCAGCTAAGC 58.491 50.000 0.00 0.00 0.00 3.09
5870 7076 4.749245 AAATCACGGTTGTTCAGCTAAG 57.251 40.909 0.00 0.00 0.00 2.18
5871 7077 6.621316 TTAAAATCACGGTTGTTCAGCTAA 57.379 33.333 0.00 0.00 0.00 3.09
5872 7078 6.811253 ATTAAAATCACGGTTGTTCAGCTA 57.189 33.333 0.00 0.00 0.00 3.32
5878 7084 4.155280 AGCGCTATTAAAATCACGGTTGTT 59.845 37.500 8.99 0.00 0.00 2.83
5884 7090 9.040543 CATATTGTTAGCGCTATTAAAATCACG 57.959 33.333 19.60 0.30 0.00 4.35
5906 7112 4.873746 AGCACGGCTATAGTTCACATAT 57.126 40.909 0.84 0.00 36.99 1.78
6373 8061 9.554395 TTTCTGTTTTTGTTTTTCTTCTTCCTT 57.446 25.926 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.