Multiple sequence alignment - TraesCS1B01G096700

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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 TraesCS1B01G096700 chr1B 100.000 7670 0 0 1 7670 100655578 100647909 0.000000e+00 14164.0
1 TraesCS1B01G096700 chr1B 87.795 508 48 4 5459 5952 661570268 661569761 3.990000e-162 582.0
2 TraesCS1B01G096700 chr1B 87.071 495 49 8 5471 5952 30662717 30662225 5.230000e-151 545.0
3 TraesCS1B01G096700 chr1B 86.667 495 51 8 5471 5952 30650951 30650459 1.130000e-147 534.0
4 TraesCS1B01G096700 chr1B 96.241 133 3 2 2338 2469 100653110 100653241 4.660000e-52 217.0
5 TraesCS1B01G096700 chr1D 93.856 3288 129 33 3778 7014 63023857 63020592 0.000000e+00 4885.0
6 TraesCS1B01G096700 chr1D 93.072 2064 94 23 1799 3839 63025894 63023857 0.000000e+00 2974.0
7 TraesCS1B01G096700 chr1D 97.318 895 21 2 909 1802 63028528 63027636 0.000000e+00 1517.0
8 TraesCS1B01G096700 chr1D 94.947 752 31 4 1 745 125835778 125835027 0.000000e+00 1171.0
9 TraesCS1B01G096700 chr1D 84.792 480 33 13 7009 7463 63020566 63020102 5.460000e-121 446.0
10 TraesCS1B01G096700 chr1D 86.452 310 14 8 7162 7466 62940990 62940704 1.610000e-81 315.0
11 TraesCS1B01G096700 chr1D 91.787 207 12 3 7465 7670 62940755 62940553 4.530000e-72 283.0
12 TraesCS1B01G096700 chr1D 93.529 170 8 3 748 915 63032254 63032086 4.600000e-62 250.0
13 TraesCS1B01G096700 chr1D 93.902 164 4 3 7009 7171 62941390 62941232 7.690000e-60 243.0
14 TraesCS1B01G096700 chr1D 94.958 119 5 1 5216 5333 62941541 62941423 1.310000e-42 185.0
15 TraesCS1B01G096700 chr1D 84.270 89 9 5 4986 5071 474927900 474927986 1.770000e-11 82.4
16 TraesCS1B01G096700 chr1D 92.157 51 4 0 7465 7515 63020152 63020102 1.070000e-08 73.1
17 TraesCS1B01G096700 chr1D 81.319 91 15 2 4979 5069 353551556 353551644 1.070000e-08 73.1
18 TraesCS1B01G096700 chr1D 94.872 39 2 0 5177 5215 62941608 62941570 2.310000e-05 62.1
19 TraesCS1B01G096700 chr1A 93.192 2776 126 27 2464 5215 61390477 61387741 0.000000e+00 4021.0
20 TraesCS1B01G096700 chr1A 92.092 1568 69 22 796 2343 61392004 61390472 0.000000e+00 2158.0
21 TraesCS1B01G096700 chr1A 89.658 1141 68 14 5272 6377 61386820 61385695 0.000000e+00 1408.0
22 TraesCS1B01G096700 chr1A 91.566 747 58 3 1 745 282598271 282597528 0.000000e+00 1026.0
23 TraesCS1B01G096700 chr1A 87.279 621 49 18 6416 7014 61385517 61384905 0.000000e+00 682.0
24 TraesCS1B01G096700 chr1A 86.765 476 24 13 7009 7466 61384879 61384425 1.920000e-135 494.0
25 TraesCS1B01G096700 chr1A 89.855 207 13 4 7465 7670 61384477 61384278 7.640000e-65 259.0
26 TraesCS1B01G096700 chr1A 91.781 73 5 1 5216 5288 61387712 61387641 4.900000e-17 100.0
27 TraesCS1B01G096700 chr7A 87.921 505 47 7 5462 5952 119788649 119788145 3.990000e-162 582.0
28 TraesCS1B01G096700 chr7A 87.500 504 49 7 5463 5952 194170051 194169548 3.110000e-158 569.0
29 TraesCS1B01G096700 chrUn 87.500 512 50 7 5455 5952 1081402 1080891 5.160000e-161 579.0
30 TraesCS1B01G096700 chrUn 87.500 512 50 7 5455 5952 403580805 403581316 5.160000e-161 579.0
31 TraesCS1B01G096700 chrUn 93.077 130 8 1 2338 2467 50320436 50320564 1.020000e-43 189.0
32 TraesCS1B01G096700 chr5A 87.698 504 48 7 5463 5952 670274192 670273689 6.680000e-160 575.0
33 TraesCS1B01G096700 chr5B 87.500 504 49 7 5463 5952 184296022 184295519 3.110000e-158 569.0
34 TraesCS1B01G096700 chr5B 87.449 494 48 8 5471 5951 405525581 405525089 2.420000e-154 556.0
35 TraesCS1B01G096700 chr5B 90.476 42 4 0 5028 5069 478522779 478522820 1.000000e-03 56.5
36 TraesCS1B01G096700 chr6B 87.255 510 46 6 5460 5952 601870405 601870912 1.440000e-156 564.0
37 TraesCS1B01G096700 chr6B 92.481 133 9 1 2336 2468 209249731 209249862 1.020000e-43 189.0
38 TraesCS1B01G096700 chr5D 87.129 505 51 8 5462 5952 319916039 319915535 1.870000e-155 560.0
39 TraesCS1B01G096700 chr5D 86.310 504 55 8 5463 5952 288444505 288444002 3.150000e-148 536.0
40 TraesCS1B01G096700 chr2D 86.310 504 52 9 5463 5952 362162057 362162557 4.070000e-147 532.0
41 TraesCS1B01G096700 chr2D 93.077 130 8 1 2338 2467 240320096 240320224 1.020000e-43 189.0
42 TraesCS1B01G096700 chr2D 100.000 28 0 0 5042 5069 492055678 492055651 1.400000e-02 52.8
43 TraesCS1B01G096700 chr3B 85.545 505 57 10 5461 5951 436516574 436516072 1.480000e-141 514.0
44 TraesCS1B01G096700 chr4D 93.077 130 8 1 2338 2467 465674322 465674450 1.020000e-43 189.0
45 TraesCS1B01G096700 chr6D 91.367 139 9 3 2338 2475 126108390 126108254 3.650000e-43 187.0
46 TraesCS1B01G096700 chr3D 92.424 132 9 1 2336 2467 573868970 573869100 3.650000e-43 187.0
47 TraesCS1B01G096700 chr2B 92.366 131 9 1 2337 2467 526754063 526754192 1.310000e-42 185.0
48 TraesCS1B01G096700 chr2B 91.241 137 10 2 2336 2472 677806375 677806509 1.310000e-42 185.0
49 TraesCS1B01G096700 chr7B 80.645 124 16 7 6386 6505 531433379 531433498 1.060000e-13 89.8
50 TraesCS1B01G096700 chr7B 82.558 86 10 4 6422 6505 531155104 531155022 3.840000e-08 71.3
51 TraesCS1B01G096700 chr7B 92.308 39 3 0 5029 5067 450642272 450642310 1.000000e-03 56.5
52 TraesCS1B01G096700 chr7B 90.244 41 2 2 225 264 639229662 639229701 1.400000e-02 52.8
53 TraesCS1B01G096700 chr7D 79.675 123 18 6 6386 6505 501829141 501829259 1.770000e-11 82.4
54 TraesCS1B01G096700 chr7D 81.053 95 8 10 4980 5069 51998854 51998765 4.970000e-07 67.6
55 TraesCS1B01G096700 chr4A 91.111 45 4 0 5022 5066 734342145 734342189 2.310000e-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 TraesCS1B01G096700 chr1B 100647909 100655578 7669 True 14164.000000 14164 100.000000 1 7670 1 chr1B.!!$R3 7669
1 TraesCS1B01G096700 chr1B 661569761 661570268 507 True 582.000000 582 87.795000 5459 5952 1 chr1B.!!$R4 493
2 TraesCS1B01G096700 chr1D 63020102 63032254 12152 True 1690.850000 4885 92.454000 748 7515 6 chr1D.!!$R3 6767
3 TraesCS1B01G096700 chr1D 125835027 125835778 751 True 1171.000000 1171 94.947000 1 745 1 chr1D.!!$R1 744
4 TraesCS1B01G096700 chr1D 62940553 62941608 1055 True 217.620000 315 92.394200 5177 7670 5 chr1D.!!$R2 2493
5 TraesCS1B01G096700 chr1A 61384278 61392004 7726 True 1303.142857 4021 90.088857 796 7670 7 chr1A.!!$R2 6874
6 TraesCS1B01G096700 chr1A 282597528 282598271 743 True 1026.000000 1026 91.566000 1 745 1 chr1A.!!$R1 744
7 TraesCS1B01G096700 chr7A 119788145 119788649 504 True 582.000000 582 87.921000 5462 5952 1 chr7A.!!$R1 490
8 TraesCS1B01G096700 chr7A 194169548 194170051 503 True 569.000000 569 87.500000 5463 5952 1 chr7A.!!$R2 489
9 TraesCS1B01G096700 chrUn 1080891 1081402 511 True 579.000000 579 87.500000 5455 5952 1 chrUn.!!$R1 497
10 TraesCS1B01G096700 chrUn 403580805 403581316 511 False 579.000000 579 87.500000 5455 5952 1 chrUn.!!$F2 497
11 TraesCS1B01G096700 chr5A 670273689 670274192 503 True 575.000000 575 87.698000 5463 5952 1 chr5A.!!$R1 489
12 TraesCS1B01G096700 chr5B 184295519 184296022 503 True 569.000000 569 87.500000 5463 5952 1 chr5B.!!$R1 489
13 TraesCS1B01G096700 chr6B 601870405 601870912 507 False 564.000000 564 87.255000 5460 5952 1 chr6B.!!$F2 492
14 TraesCS1B01G096700 chr5D 319915535 319916039 504 True 560.000000 560 87.129000 5462 5952 1 chr5D.!!$R2 490
15 TraesCS1B01G096700 chr5D 288444002 288444505 503 True 536.000000 536 86.310000 5463 5952 1 chr5D.!!$R1 489
16 TraesCS1B01G096700 chr2D 362162057 362162557 500 False 532.000000 532 86.310000 5463 5952 1 chr2D.!!$F2 489
17 TraesCS1B01G096700 chr3B 436516072 436516574 502 True 514.000000 514 85.545000 5461 5951 1 chr3B.!!$R1 490

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
805 813 0.991146 TAGTCAATCCAGGCCTTGCA 59.009 50.000 0.00 0.0 0.00 4.08 F
1522 5104 0.666274 CGCAGCTGTGGTAACGAAGA 60.666 55.000 19.78 0.0 42.51 2.87 F
3200 8550 0.035881 GAGCTGCAGCCTGGCATATA 59.964 55.000 34.39 3.1 43.97 0.86 F
3389 8741 0.257039 AGCCTGCTTCCTTGTATGGG 59.743 55.000 0.00 0.0 0.00 4.00 F
4392 9811 1.238439 GCAAGTGCATACGGCCATAT 58.762 50.000 2.24 0.0 43.89 1.78 F
5556 11881 1.536418 CCAGGAGGAGGGACACACA 60.536 63.158 0.00 0.0 36.89 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 5201 0.193574 TCCCTGTGGTTCCTTCCTCT 59.806 55.0 0.00 0.00 0.00 3.69 R
3371 8723 0.034089 ACCCATACAAGGAAGCAGGC 60.034 55.0 0.00 0.00 0.00 4.85 R
4136 9555 0.745845 GAGCCTGCGGACAATGACAT 60.746 55.0 0.00 0.00 0.00 3.06 R
5212 10639 0.546122 AACTGGGTTCTGTGCTCACA 59.454 50.0 2.48 2.48 39.32 3.58 R
5569 11894 0.249868 CTGCTCGTTTGGTGAGGACA 60.250 55.0 0.00 0.00 33.99 4.02 R
7262 14080 0.036388 CTACATGACCACTTGCGGGT 60.036 55.0 0.00 0.00 42.61 5.28 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
47 48 3.964031 ACTGGGTTGAAACATTGCCTTAA 59.036 39.130 0.00 0.00 0.00 1.85
135 136 6.039493 TGTGTCCTCTCGGTCTAATAATTCTC 59.961 42.308 0.00 0.00 0.00 2.87
348 354 1.065551 GCACATAGCGAATTTGGGACC 59.934 52.381 0.00 0.00 0.00 4.46
364 370 3.118408 TGGGACCGTGATTAATCTCCAAG 60.118 47.826 18.29 8.66 0.00 3.61
395 401 1.019673 AGCATAGCATGGTTGAAGCG 58.980 50.000 1.12 0.00 37.84 4.68
451 457 4.517453 TCTTGGGATAACAAAGTTTCCACG 59.483 41.667 10.82 0.00 0.00 4.94
452 458 3.150767 TGGGATAACAAAGTTTCCACGG 58.849 45.455 10.82 0.00 0.00 4.94
474 480 4.687483 GGTGAAAACCAATGCATCTTTCTG 59.313 41.667 17.36 6.68 0.00 3.02
477 483 6.258507 GTGAAAACCAATGCATCTTTCTGTTT 59.741 34.615 17.36 11.05 0.00 2.83
517 523 6.095300 CCACCAGAACTGTGCAATAATATCAA 59.905 38.462 0.00 0.00 0.00 2.57
572 578 5.474578 AAGACTGACATAGCAAAGACAGA 57.525 39.130 0.00 0.00 33.02 3.41
613 619 9.750125 CTGCTTTTAACAGAATTTCTTTACCTT 57.250 29.630 0.00 0.00 37.32 3.50
667 673 9.118300 CAATTAGCCTCTGTTTAATTCTCTCAT 57.882 33.333 0.00 0.00 0.00 2.90
669 675 9.995003 ATTAGCCTCTGTTTAATTCTCTCATAG 57.005 33.333 0.00 0.00 0.00 2.23
731 737 2.761208 CAGGGAGTCCGAGATACTTGTT 59.239 50.000 2.26 0.00 38.33 2.83
745 753 6.810911 AGATACTTGTTATAGTGCCTCAGTG 58.189 40.000 0.00 0.00 0.00 3.66
746 754 3.600388 ACTTGTTATAGTGCCTCAGTGC 58.400 45.455 0.00 0.00 0.00 4.40
805 813 0.991146 TAGTCAATCCAGGCCTTGCA 59.009 50.000 0.00 0.00 0.00 4.08
821 829 1.971167 GCAATGTTGAGCCGACCCA 60.971 57.895 0.00 0.00 0.00 4.51
842 850 2.110011 ACAGGGTCAGGTTTGCCTAAAT 59.890 45.455 0.00 0.00 44.97 1.40
844 852 3.056607 CAGGGTCAGGTTTGCCTAAATTG 60.057 47.826 0.00 0.00 44.97 2.32
845 853 2.897326 GGGTCAGGTTTGCCTAAATTGT 59.103 45.455 0.00 0.00 44.97 2.71
846 854 3.056821 GGGTCAGGTTTGCCTAAATTGTC 60.057 47.826 0.00 0.00 44.97 3.18
853 863 1.022451 TGCCTAAATTGTCCGGTCGC 61.022 55.000 0.00 0.00 0.00 5.19
879 890 2.552315 TCCGAACATTTGAGGTTTGAGC 59.448 45.455 0.00 0.00 32.46 4.26
1522 5104 0.666274 CGCAGCTGTGGTAACGAAGA 60.666 55.000 19.78 0.00 42.51 2.87
1669 5251 2.102252 GAGTGGTGGCCTGAGATAGAAG 59.898 54.545 3.32 0.00 0.00 2.85
1689 5271 1.966451 CGAGTTGGTGGAACTGGGC 60.966 63.158 0.00 0.00 45.48 5.36
1756 5338 6.038985 CGAGGTGAATGCCTGTATATATCTG 58.961 44.000 0.00 0.00 39.34 2.90
1792 5382 9.554395 TGTTCTGTTTCTAGTTCAAACATATGA 57.446 29.630 10.38 1.91 41.69 2.15
1812 7138 8.573885 CATATGAAGTCAATAGGAATGTTGCAT 58.426 33.333 0.00 0.00 0.00 3.96
1893 7220 9.232473 ACTTTCTAGGTTCATTTATTCTTGTCC 57.768 33.333 0.00 0.00 0.00 4.02
1911 7238 6.657966 TCTTGTCCGAACTCAGAAATAGTAGA 59.342 38.462 0.00 0.00 0.00 2.59
1918 7245 8.407064 CCGAACTCAGAAATAGTAGAAGTGTAT 58.593 37.037 0.00 0.00 0.00 2.29
1939 7266 8.190122 GTGTATTATCATTTTGAATGCCTGACA 58.810 33.333 0.00 0.00 0.00 3.58
2034 7362 9.403583 ACCAACTTTTGTTTTTGAGTCTAGATA 57.596 29.630 0.00 0.00 41.35 1.98
2044 7372 8.977505 GTTTTTGAGTCTAGATAGATGCAGATC 58.022 37.037 0.00 0.00 34.39 2.75
2078 7406 2.555325 CACTGCCATGTGTGAGATTTGT 59.445 45.455 5.20 0.00 36.38 2.83
2189 7521 3.646162 TGGCCTCAGTCTTAGTTTCTTGA 59.354 43.478 3.32 0.00 0.00 3.02
2351 7683 0.606604 TGCAAAGTACTCCCTCCGTC 59.393 55.000 0.00 0.00 0.00 4.79
2355 7687 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
2359 7691 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2361 7693 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2364 7696 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2366 7698 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2368 7700 3.568007 TCCGTCCCAAAATTCTTGTCTTG 59.432 43.478 0.00 0.00 0.00 3.02
2369 7701 3.568007 CCGTCCCAAAATTCTTGTCTTGA 59.432 43.478 0.00 0.00 0.00 3.02
2373 7705 6.363357 CGTCCCAAAATTCTTGTCTTGAATTC 59.637 38.462 0.00 0.00 41.54 2.17
2377 7709 7.141363 CCAAAATTCTTGTCTTGAATTCGTCT 58.859 34.615 0.04 0.00 41.54 4.18
2379 7711 9.107367 CAAAATTCTTGTCTTGAATTCGTCTAC 57.893 33.333 0.04 0.00 41.54 2.59
2383 7715 8.462143 TTCTTGTCTTGAATTCGTCTACATAC 57.538 34.615 0.04 0.00 0.00 2.39
2384 7716 6.745907 TCTTGTCTTGAATTCGTCTACATACG 59.254 38.462 0.04 0.00 44.19 3.06
2395 7727 8.734218 ATTCGTCTACATACGGATGTATCTAT 57.266 34.615 20.64 7.80 45.42 1.98
2396 7728 8.557592 TTCGTCTACATACGGATGTATCTATT 57.442 34.615 20.64 0.00 45.42 1.73
2399 7731 7.903946 CGTCTACATACGGATGTATCTATTCAC 59.096 40.741 20.64 8.14 45.42 3.18
2400 7732 8.948145 GTCTACATACGGATGTATCTATTCACT 58.052 37.037 20.64 0.00 45.42 3.41
2408 7740 9.261180 ACGGATGTATCTATTCACTAAAATGTG 57.739 33.333 0.00 0.00 39.15 3.21
2409 7741 9.476202 CGGATGTATCTATTCACTAAAATGTGA 57.524 33.333 0.00 0.00 44.17 3.58
2422 7754 9.476202 TCACTAAAATGTGAATAGATACATCCG 57.524 33.333 0.00 0.00 43.08 4.18
2441 7773 5.823209 TCCGTATGTAGACGAATTCAAGA 57.177 39.130 6.22 0.00 45.82 3.02
2446 7778 6.745907 CGTATGTAGACGAATTCAAGACAAGA 59.254 38.462 6.22 0.00 45.82 3.02
2454 7786 6.215845 ACGAATTCAAGACAAGAATTTTGGG 58.784 36.000 6.22 0.00 43.60 4.12
2616 7948 2.552599 TCGTTGACAATAGGGTTGCA 57.447 45.000 0.00 0.00 0.00 4.08
2659 7991 6.128445 CGATGATGCAGTTCAAGTTAGTCTTT 60.128 38.462 0.00 0.00 33.63 2.52
2724 8069 6.210185 CACCTCCTTTCCTTGAATTTGAGAAT 59.790 38.462 0.00 0.00 0.00 2.40
2746 8091 0.733729 CTGGCATGCTCTTCTTGCTC 59.266 55.000 18.92 0.00 43.21 4.26
2748 8093 0.733729 GGCATGCTCTTCTTGCTCTG 59.266 55.000 18.92 0.00 43.21 3.35
2814 8160 5.995282 AGTAGGTCGACATTCAGAGAGATAG 59.005 44.000 18.91 0.00 0.00 2.08
2816 8162 3.550561 GTCGACATTCAGAGAGATAGCG 58.449 50.000 11.55 0.00 0.00 4.26
2850 8196 3.381590 TCTGATAGAACGACATGGTCCTG 59.618 47.826 0.00 0.00 0.00 3.86
2968 8315 1.004560 CTCTGTTTGGCCGAGCTCA 60.005 57.895 15.40 1.85 0.00 4.26
3068 8415 1.228367 CTGGCCAGAGGTTGCTTGT 60.228 57.895 29.88 0.00 0.00 3.16
3071 8418 0.538287 GGCCAGAGGTTGCTTGTTCT 60.538 55.000 0.00 0.00 0.00 3.01
3082 8429 8.049721 AGAGGTTGCTTGTTCTAGCTTATAAAT 58.950 33.333 0.00 0.00 41.76 1.40
3199 8549 1.228184 GAGCTGCAGCCTGGCATAT 60.228 57.895 34.39 14.14 43.97 1.78
3200 8550 0.035881 GAGCTGCAGCCTGGCATATA 59.964 55.000 34.39 3.10 43.97 0.86
3213 8563 5.707298 GCCTGGCATATAGTCACATAATTGT 59.293 40.000 15.17 0.00 36.15 2.71
3302 8654 7.910441 ATGTAATTTTGATTTTGAAGCCAGG 57.090 32.000 0.00 0.00 0.00 4.45
3307 8659 6.363167 TTTTGATTTTGAAGCCAGGATCAT 57.637 33.333 0.00 0.00 30.73 2.45
3357 8709 7.891183 ATGCGACTGGAGTAATATTGATTAC 57.109 36.000 0.00 0.48 45.37 1.89
3389 8741 0.257039 AGCCTGCTTCCTTGTATGGG 59.743 55.000 0.00 0.00 0.00 4.00
3427 8779 1.403679 CGTGTGTTGGTCACCACATTT 59.596 47.619 0.00 0.00 45.61 2.32
3579 8931 3.950397 TCGGAGCACCAGAAATATTGTT 58.050 40.909 0.00 0.00 35.59 2.83
4073 9489 2.512692 TCTTGCAATGCTGGGTATGT 57.487 45.000 6.82 0.00 0.00 2.29
4076 9492 5.303259 TCTTGCAATGCTGGGTATGTATA 57.697 39.130 6.82 0.00 0.00 1.47
4077 9493 5.063204 TCTTGCAATGCTGGGTATGTATAC 58.937 41.667 6.82 0.00 0.00 1.47
4119 9538 9.750882 CTTGTTTATGATCTTGCATATGTATCG 57.249 33.333 4.29 0.00 31.34 2.92
4229 9648 5.607477 TGTAGAATTCATCGTGTATTCCCC 58.393 41.667 8.44 5.85 35.56 4.81
4355 9774 4.058721 GTTGCAAACTTGTGATTCCCTT 57.941 40.909 0.00 0.00 45.32 3.95
4357 9776 3.030291 TGCAAACTTGTGATTCCCTTGT 58.970 40.909 0.00 0.00 0.00 3.16
4392 9811 1.238439 GCAAGTGCATACGGCCATAT 58.762 50.000 2.24 0.00 43.89 1.78
4499 9921 4.647564 TTTGAGCTGAGGGAAGAAAGAT 57.352 40.909 0.00 0.00 0.00 2.40
5018 10445 6.596497 CCACAATATAGGACGGTTTTACAAGT 59.404 38.462 0.00 0.00 0.00 3.16
5024 10451 5.996669 AGGACGGTTTTACAAGTTAACAG 57.003 39.130 8.61 2.39 0.00 3.16
5036 10463 5.343249 ACAAGTTAACAGAGCTTGCAAAAG 58.657 37.500 8.61 0.00 42.20 2.27
5106 10533 2.620779 TGTTGTGTTGTTGTTCGTGG 57.379 45.000 0.00 0.00 0.00 4.94
5124 10551 3.919804 CGTGGAAATTGCACACCTAAATG 59.080 43.478 17.34 0.00 38.73 2.32
5132 10559 3.000041 TGCACACCTAAATGCTAAGTCG 59.000 45.455 0.00 0.00 42.55 4.18
5212 10639 8.827832 TCCAATGAAAATGACATCCTAGAAAT 57.172 30.769 0.00 0.00 0.00 2.17
5461 11753 5.507482 GGAAGCACTTAACCTTTTCCACTTC 60.507 44.000 0.00 0.00 35.35 3.01
5556 11881 1.536418 CCAGGAGGAGGGACACACA 60.536 63.158 0.00 0.00 36.89 3.72
5569 11894 2.484770 GGACACACACATACACACCACT 60.485 50.000 0.00 0.00 0.00 4.00
5647 11975 2.134630 CTTGCCTTGTCCAGCCTCCT 62.135 60.000 0.00 0.00 0.00 3.69
5649 11977 0.621571 TGCCTTGTCCAGCCTCCTAT 60.622 55.000 0.00 0.00 0.00 2.57
5674 12002 2.074729 ATGCCGAGGTAGCTAGACTT 57.925 50.000 3.38 0.00 0.00 3.01
5686 12014 2.023888 AGCTAGACTTAGGGCCTCAAGA 60.024 50.000 10.74 0.00 0.00 3.02
5736 12064 3.697045 CCGAAGAAGACCACATCTCTAGT 59.303 47.826 0.00 0.00 36.27 2.57
5758 12086 3.697747 TCCGGGCCAACGTACCTG 61.698 66.667 4.39 0.00 0.00 4.00
5765 12093 2.740826 CAACGTACCTGCCACCCG 60.741 66.667 0.00 0.00 0.00 5.28
5767 12095 3.524648 AACGTACCTGCCACCCGTG 62.525 63.158 0.00 0.00 0.00 4.94
5780 12108 2.125512 CCGTGTGTGCCTAGGAGC 60.126 66.667 14.75 4.35 0.00 4.70
5877 12205 4.899239 CCGGACGCCCATGCTCTC 62.899 72.222 0.00 0.00 34.43 3.20
5879 12207 2.490148 CGGACGCCCATGCTCTCTA 61.490 63.158 0.00 0.00 34.43 2.43
5880 12208 1.810606 CGGACGCCCATGCTCTCTAT 61.811 60.000 0.00 0.00 34.43 1.98
5881 12209 0.320247 GGACGCCCATGCTCTCTATG 60.320 60.000 0.00 0.00 34.43 2.23
5884 12212 0.949588 CGCCCATGCTCTCTATGCTG 60.950 60.000 0.00 0.00 34.43 4.41
6063 12401 4.760047 CCGCCACCCAAGGTCTCG 62.760 72.222 0.00 0.00 31.02 4.04
6065 12403 2.047179 GCCACCCAAGGTCTCGTC 60.047 66.667 0.00 0.00 31.02 4.20
6073 12411 0.179134 CAAGGTCTCGTCGGTCATCC 60.179 60.000 0.00 0.00 0.00 3.51
6074 12412 0.323542 AAGGTCTCGTCGGTCATCCT 60.324 55.000 0.00 0.00 0.00 3.24
6075 12413 0.748729 AGGTCTCGTCGGTCATCCTC 60.749 60.000 0.00 0.00 0.00 3.71
6076 12414 0.748729 GGTCTCGTCGGTCATCCTCT 60.749 60.000 0.00 0.00 0.00 3.69
6099 12437 3.338126 CTCGTACGGCAGCCTCGTT 62.338 63.158 16.52 0.00 41.38 3.85
6168 12506 3.810623 AGTAGGTCCATGTTCCCCTTAA 58.189 45.455 0.00 0.00 0.00 1.85
6265 12603 0.035881 ACCAGTCTACCTCGACGACA 59.964 55.000 0.00 0.00 38.90 4.35
6304 12642 2.344093 AAGGTCTGTGAGGGTATGGT 57.656 50.000 0.00 0.00 0.00 3.55
6339 12693 6.995686 TCTTACTGCTGGTTCAGTGAAAAATA 59.004 34.615 7.25 0.00 45.95 1.40
6366 12720 0.602638 CAGCTGGCGGTGTAAAGTCA 60.603 55.000 5.57 0.00 34.04 3.41
6447 12944 8.925161 TTTGTCTTCTTGTTTTTCCATTGTAG 57.075 30.769 0.00 0.00 0.00 2.74
6450 12947 8.617809 TGTCTTCTTGTTTTTCCATTGTAGTAC 58.382 33.333 0.00 0.00 0.00 2.73
6451 12948 8.837389 GTCTTCTTGTTTTTCCATTGTAGTACT 58.163 33.333 0.00 0.00 0.00 2.73
6463 12960 9.701098 TTCCATTGTAGTACTAAGTACTGTTTG 57.299 33.333 3.61 0.00 46.99 2.93
6506 13003 2.378547 AGATGCCCTTTGGGTGTCTTAA 59.621 45.455 4.42 0.00 46.51 1.85
6509 13006 2.712087 TGCCCTTTGGGTGTCTTAACTA 59.288 45.455 4.42 0.00 46.51 2.24
6641 13141 8.583810 TCGGTTTTCTAATGGTATTATCTTCG 57.416 34.615 0.00 0.00 0.00 3.79
6659 13159 1.302351 GTGCCTTGCAGAGCTCACT 60.302 57.895 17.77 0.00 40.08 3.41
6695 13195 1.471676 CGTGCAGTAGAAGGGTCCATC 60.472 57.143 0.00 0.00 0.00 3.51
6718 13218 2.356665 TTTGTAGTTCCAGCTTGGCA 57.643 45.000 0.00 0.00 37.47 4.92
6757 13274 4.769688 ACGGCTGAGATATTCACAATTGA 58.230 39.130 13.59 0.00 0.00 2.57
6832 13349 5.695851 ATTCGAGGAATTAACATGATGCC 57.304 39.130 0.00 0.00 0.00 4.40
6889 13406 4.237724 GTCTAAAGCATTCCAAACAAGGC 58.762 43.478 0.00 0.00 33.15 4.35
6899 13417 1.404035 CCAAACAAGGCGGTATAAGGC 59.596 52.381 0.00 0.00 0.00 4.35
6900 13418 2.088423 CAAACAAGGCGGTATAAGGCA 58.912 47.619 5.94 0.00 36.55 4.75
6917 13435 3.873910 AGGCACAGTACATATGAACACC 58.126 45.455 10.38 1.60 0.00 4.16
6918 13436 2.607635 GGCACAGTACATATGAACACCG 59.392 50.000 10.38 0.00 0.00 4.94
6952 13470 1.861542 TTCGGCCAACGCATCCAAAG 61.862 55.000 2.24 0.00 43.86 2.77
6976 13494 6.070538 AGCAGGTTCTCTTGTAAGACATACAT 60.071 38.462 0.00 0.00 43.84 2.29
7072 13636 2.035632 TGCATGGTCCGAAAAACCTTT 58.964 42.857 0.00 0.00 37.69 3.11
7100 13664 3.819368 TCATTTGTGTCTGAAGGCTTGA 58.181 40.909 3.46 0.00 0.00 3.02
7138 13702 3.849911 TCTACTCGTTGCATTTCTGAGG 58.150 45.455 0.00 0.00 0.00 3.86
7236 14054 3.839293 ACTAGTGAAACGATGTGAGAGC 58.161 45.455 0.00 0.00 45.86 4.09
7240 14058 2.802816 GTGAAACGATGTGAGAGCTGTT 59.197 45.455 0.00 0.00 0.00 3.16
7277 14095 2.268076 GCAACCCGCAAGTGGTCAT 61.268 57.895 0.00 0.00 39.53 3.06
7349 14169 6.207417 TGATTGAAGTGGAAGGACAAAATCTC 59.793 38.462 0.00 0.00 0.00 2.75
7393 14214 5.059833 GCAAGGGATAAGGATACAGAACAG 58.940 45.833 0.00 0.00 41.41 3.16
7440 14261 6.042777 TCTTATCAATAGTCAAAGGCACTCG 58.957 40.000 0.00 0.00 38.49 4.18
7488 14312 9.717942 ATATCTTATCAATAGTCAAAGGCACTC 57.282 33.333 0.00 0.00 38.49 3.51
7489 14313 7.187824 TCTTATCAATAGTCAAAGGCACTCT 57.812 36.000 0.00 0.00 38.49 3.24
7490 14314 7.268586 TCTTATCAATAGTCAAAGGCACTCTC 58.731 38.462 0.00 0.00 38.49 3.20
7491 14315 4.890158 TCAATAGTCAAAGGCACTCTCA 57.110 40.909 0.00 0.00 38.49 3.27
7492 14316 5.227569 TCAATAGTCAAAGGCACTCTCAA 57.772 39.130 0.00 0.00 38.49 3.02
7493 14317 5.620206 TCAATAGTCAAAGGCACTCTCAAA 58.380 37.500 0.00 0.00 38.49 2.69
7494 14318 6.061441 TCAATAGTCAAAGGCACTCTCAAAA 58.939 36.000 0.00 0.00 38.49 2.44
7495 14319 6.545666 TCAATAGTCAAAGGCACTCTCAAAAA 59.454 34.615 0.00 0.00 38.49 1.94
7528 14352 5.847111 TCCTACATATGTATATGGACGGC 57.153 43.478 15.81 0.00 43.38 5.68
7531 14355 3.093814 ACATATGTATATGGACGGCGGA 58.906 45.455 13.24 0.00 43.38 5.54
7545 14373 2.925563 ACGGCGGAAGTAAAGTAAATCG 59.074 45.455 13.24 0.00 0.00 3.34
7548 14376 3.373130 GGCGGAAGTAAAGTAAATCGCTT 59.627 43.478 0.00 0.00 41.36 4.68
7549 14377 4.567959 GGCGGAAGTAAAGTAAATCGCTTA 59.432 41.667 0.00 0.00 41.36 3.09
7550 14378 5.235831 GGCGGAAGTAAAGTAAATCGCTTAT 59.764 40.000 0.00 0.00 41.36 1.73
7551 14379 6.238293 GGCGGAAGTAAAGTAAATCGCTTATT 60.238 38.462 0.00 0.00 41.36 1.40
7556 14384 9.486857 GAAGTAAAGTAAATCGCTTATTTGTCC 57.513 33.333 4.62 0.00 38.29 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.481313 CAGTGGATGTTCACAGGATATTACAG 59.519 42.308 0.00 0.00 39.93 2.74
47 48 0.820871 GATGTGGGACGAAGAGCTCT 59.179 55.000 11.45 11.45 0.00 4.09
220 221 3.806949 AATGAAAGGGCTTGAGGTGTA 57.193 42.857 0.00 0.00 0.00 2.90
313 314 0.387929 TGTGCGAGAGTTCCGAAAGT 59.612 50.000 0.00 0.00 0.00 2.66
339 345 4.080015 TGGAGATTAATCACGGTCCCAAAT 60.080 41.667 17.56 0.00 0.00 2.32
348 354 7.852945 GCTAAACAATCTTGGAGATTAATCACG 59.147 37.037 17.56 0.00 42.67 4.35
395 401 5.367060 GGTATGGGATTCAGGGATCTATACC 59.633 48.000 13.66 13.66 38.06 2.73
451 457 4.687483 CAGAAAGATGCATTGGTTTTCACC 59.313 41.667 19.71 0.00 44.56 4.02
452 458 5.291971 ACAGAAAGATGCATTGGTTTTCAC 58.708 37.500 19.71 0.61 31.83 3.18
474 480 3.696548 GGTGGGGAGATGATGAAGAAAAC 59.303 47.826 0.00 0.00 0.00 2.43
477 483 2.507058 CTGGTGGGGAGATGATGAAGAA 59.493 50.000 0.00 0.00 0.00 2.52
517 523 8.377799 ACCAAAAGGAATTTGCAAAGAGATTAT 58.622 29.630 18.19 0.00 45.79 1.28
613 619 5.241506 GGATGGAGAAACAATTGTCAACAGA 59.758 40.000 12.39 0.00 30.64 3.41
731 737 4.665833 ATAAACGCACTGAGGCACTATA 57.334 40.909 0.00 0.00 41.55 1.31
792 800 0.899720 CAACATTGCAAGGCCTGGAT 59.100 50.000 12.85 0.00 0.00 3.41
805 813 0.606401 CTGTGGGTCGGCTCAACATT 60.606 55.000 0.00 0.00 0.00 2.71
842 850 3.998672 GACCAGGCGACCGGACAA 61.999 66.667 9.46 0.00 0.00 3.18
853 863 1.271379 ACCTCAAATGTTCGGACCAGG 60.271 52.381 0.00 0.00 0.00 4.45
879 890 5.568677 TCAAAACGCGAATCATCAAATTGAG 59.431 36.000 15.93 0.00 0.00 3.02
1299 4881 4.208686 CGGAGGTCGCTGTAGGCC 62.209 72.222 0.00 0.00 37.74 5.19
1505 5087 1.673033 CCCTCTTCGTTACCACAGCTG 60.673 57.143 13.48 13.48 0.00 4.24
1515 5097 2.647158 GCTCCGGTCCCTCTTCGTT 61.647 63.158 0.00 0.00 0.00 3.85
1522 5104 4.741239 ACCCATGCTCCGGTCCCT 62.741 66.667 0.00 0.00 0.00 4.20
1619 5201 0.193574 TCCCTGTGGTTCCTTCCTCT 59.806 55.000 0.00 0.00 0.00 3.69
1669 5251 1.966451 CCAGTTCCACCAACTCGGC 60.966 63.158 0.00 0.00 44.14 5.54
1689 5271 0.674895 CCCACTTCTCCGCTTCTTGG 60.675 60.000 0.00 0.00 0.00 3.61
1792 5382 7.701539 TTACATGCAACATTCCTATTGACTT 57.298 32.000 0.00 0.00 0.00 3.01
1796 5386 7.933396 TCTGATTACATGCAACATTCCTATTG 58.067 34.615 0.00 0.00 0.00 1.90
1893 7220 9.790389 AATACACTTCTACTATTTCTGAGTTCG 57.210 33.333 0.00 0.00 0.00 3.95
1911 7238 8.970020 TCAGGCATTCAAAATGATAATACACTT 58.030 29.630 3.91 0.00 0.00 3.16
1918 7245 7.440198 TGTTTGTCAGGCATTCAAAATGATAA 58.560 30.769 3.91 0.00 33.80 1.75
1939 7266 9.021807 TCTACTAGCACAGTTCTACTATTGTTT 57.978 33.333 0.00 0.00 38.80 2.83
2034 7362 8.703743 AGTGATAGTAGAAAAAGATCTGCATCT 58.296 33.333 0.00 2.84 41.59 2.90
2044 7372 6.372659 ACACATGGCAGTGATAGTAGAAAAAG 59.627 38.462 19.31 0.00 42.05 2.27
2078 7406 4.285863 ACTGGGTCAAACCAAAATTCAGA 58.714 39.130 0.00 0.00 41.02 3.27
2214 7546 4.908601 TGGACTACCACAATGAAGACAT 57.091 40.909 0.00 0.00 41.77 3.06
2351 7683 6.215845 ACGAATTCAAGACAAGAATTTTGGG 58.784 36.000 6.22 0.00 43.60 4.12
2355 7687 8.378172 TGTAGACGAATTCAAGACAAGAATTT 57.622 30.769 6.22 0.00 43.60 1.82
2359 7691 6.745907 CGTATGTAGACGAATTCAAGACAAGA 59.254 38.462 6.22 0.00 45.82 3.02
2361 7693 5.803461 CCGTATGTAGACGAATTCAAGACAA 59.197 40.000 6.22 0.00 45.82 3.18
2364 7696 5.823209 TCCGTATGTAGACGAATTCAAGA 57.177 39.130 6.22 0.00 45.82 3.02
2366 7698 5.898174 ACATCCGTATGTAGACGAATTCAA 58.102 37.500 6.22 0.00 44.66 2.69
2383 7715 9.476202 TCACATTTTAGTGAATAGATACATCCG 57.524 33.333 0.00 0.00 44.92 4.18
2396 7728 9.476202 CGGATGTATCTATTCACATTTTAGTGA 57.524 33.333 0.00 0.00 46.12 3.41
2401 7733 9.778741 ACATACGGATGTATCTATTCACATTTT 57.221 29.630 12.79 0.00 44.77 1.82
2404 7736 9.462606 TCTACATACGGATGTATCTATTCACAT 57.537 33.333 20.64 0.00 45.42 3.21
2405 7737 8.727910 GTCTACATACGGATGTATCTATTCACA 58.272 37.037 20.64 0.00 45.42 3.58
2408 7740 8.194433 TCGTCTACATACGGATGTATCTATTC 57.806 38.462 20.64 7.26 45.42 1.75
2409 7741 8.557592 TTCGTCTACATACGGATGTATCTATT 57.442 34.615 20.64 0.00 45.42 1.73
2414 7746 7.210718 TGAATTCGTCTACATACGGATGTAT 57.789 36.000 20.64 4.21 45.42 2.29
2422 7754 8.462143 TTCTTGTCTTGAATTCGTCTACATAC 57.538 34.615 0.04 0.00 0.00 2.39
2424 7756 8.553459 AATTCTTGTCTTGAATTCGTCTACAT 57.447 30.769 0.04 0.00 39.15 2.29
2426 7758 9.107367 CAAAATTCTTGTCTTGAATTCGTCTAC 57.893 33.333 0.04 0.00 41.54 2.59
2428 7760 7.141363 CCAAAATTCTTGTCTTGAATTCGTCT 58.859 34.615 0.04 0.00 41.54 4.18
2429 7761 6.363357 CCCAAAATTCTTGTCTTGAATTCGTC 59.637 38.462 0.04 0.00 41.54 4.20
2432 7764 6.363357 CGTCCCAAAATTCTTGTCTTGAATTC 59.637 38.462 0.00 0.00 41.54 2.17
2436 7768 3.568007 CCGTCCCAAAATTCTTGTCTTGA 59.432 43.478 0.00 0.00 0.00 3.02
2437 7769 3.568007 TCCGTCCCAAAATTCTTGTCTTG 59.432 43.478 0.00 0.00 0.00 3.02
2441 7773 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2446 7778 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2454 7786 4.971939 AGTTATCTAGTACTCCCTCCGTC 58.028 47.826 0.00 0.00 0.00 4.79
2488 7820 3.070302 TGCCAATGAAAAAGGGTAACACC 59.930 43.478 0.00 0.00 37.60 4.16
2590 7922 3.270027 CCCTATTGTCAACGATTGCTGA 58.730 45.455 0.00 0.00 0.00 4.26
2616 7948 3.897657 TCGTATCTGTAATCCCTCCCT 57.102 47.619 0.00 0.00 0.00 4.20
2724 8069 0.885879 CAAGAAGAGCATGCCAGCAA 59.114 50.000 15.66 0.00 36.85 3.91
2746 8091 2.593346 CCTGCTACAGAAGGCTACAG 57.407 55.000 0.00 0.00 33.21 2.74
2783 8128 3.767131 TGAATGTCGACCTACTTCCATGA 59.233 43.478 14.12 0.00 0.00 3.07
2816 8162 4.667948 CGTTCTATCAGATTGCGAATTTGC 59.332 41.667 10.99 10.99 0.00 3.68
2968 8315 4.147321 TCAGAGCTCAAATTTTGAAGCCT 58.853 39.130 17.77 13.96 39.58 4.58
3082 8429 5.185635 AGCCAGAAAAGCTTAATGTGCATTA 59.814 36.000 0.00 0.90 37.24 1.90
3276 8628 8.231837 CCTGGCTTCAAAATCAAAATTACATTG 58.768 33.333 0.00 0.00 0.00 2.82
3278 8630 7.678837 TCCTGGCTTCAAAATCAAAATTACAT 58.321 30.769 0.00 0.00 0.00 2.29
3302 8654 9.846248 ATTGCTTTTAGTTCACAGTTAATGATC 57.154 29.630 0.00 0.00 0.00 2.92
3307 8659 8.220755 ACAGATTGCTTTTAGTTCACAGTTAA 57.779 30.769 0.00 0.00 0.00 2.01
3357 8709 3.587797 AGCAGGCTTGTGATGAATTTG 57.412 42.857 0.00 0.00 0.00 2.32
3371 8723 0.034089 ACCCATACAAGGAAGCAGGC 60.034 55.000 0.00 0.00 0.00 4.85
3389 8741 0.788391 CGTGCCGTCAAGTCCTAAAC 59.212 55.000 0.00 0.00 0.00 2.01
3579 8931 9.689976 CATGTTTGACAAACTGTAAATATTCCA 57.310 29.630 26.80 6.97 41.90 3.53
4053 9469 2.806434 ACATACCCAGCATTGCAAGAA 58.194 42.857 11.91 0.00 0.00 2.52
4136 9555 0.745845 GAGCCTGCGGACAATGACAT 60.746 55.000 0.00 0.00 0.00 3.06
4499 9921 2.969821 AACCATAGCAACCCAACTCA 57.030 45.000 0.00 0.00 0.00 3.41
5036 10463 4.876107 CCTCCGTCCCACAATATAATATGC 59.124 45.833 0.00 0.00 0.00 3.14
5040 10467 3.583086 CTCCCTCCGTCCCACAATATAAT 59.417 47.826 0.00 0.00 0.00 1.28
5106 10533 6.389906 ACTTAGCATTTAGGTGTGCAATTTC 58.610 36.000 0.00 0.00 43.63 2.17
5124 10551 6.562518 ACAGACTAAGATAAACCGACTTAGC 58.437 40.000 0.00 0.00 43.64 3.09
5212 10639 0.546122 AACTGGGTTCTGTGCTCACA 59.454 50.000 2.48 2.48 39.32 3.58
5482 11777 5.019907 TCAATGCAATGAAACGCAAAATG 57.980 34.783 0.85 0.00 42.37 2.32
5498 11793 4.036734 TGTTGTTCTCTTCCTGTTCAATGC 59.963 41.667 0.00 0.00 0.00 3.56
5556 11881 2.037251 GTGAGGACAGTGGTGTGTATGT 59.963 50.000 0.00 0.00 36.88 2.29
5569 11894 0.249868 CTGCTCGTTTGGTGAGGACA 60.250 55.000 0.00 0.00 33.99 4.02
5647 11975 2.899900 AGCTACCTCGGCATTCATGATA 59.100 45.455 0.00 0.00 0.00 2.15
5649 11977 1.123077 AGCTACCTCGGCATTCATGA 58.877 50.000 0.00 0.00 0.00 3.07
5674 12002 3.458163 CGCGGTCTTGAGGCCCTA 61.458 66.667 0.00 0.00 0.00 3.53
5686 12014 3.049674 CAATGGCTGTGACGCGGT 61.050 61.111 12.47 0.00 0.00 5.68
5765 12093 2.125512 CGGCTCCTAGGCACACAC 60.126 66.667 2.96 0.00 41.44 3.82
5884 12212 2.278596 CTGGCAATGCGATGCTGC 60.279 61.111 12.54 0.00 45.68 5.25
5921 12259 3.493303 GAGATGGTGGCCTCCCCC 61.493 72.222 21.06 12.25 0.00 5.40
6015 12353 7.652105 GGTTTGGAAGAAAATGTAAGTCCTTTC 59.348 37.037 0.00 0.00 0.00 2.62
6063 12401 2.218603 GAGAGAGAGAGGATGACCGAC 58.781 57.143 0.00 0.00 41.83 4.79
6065 12403 1.225855 CGAGAGAGAGAGGATGACCG 58.774 60.000 0.00 0.00 41.83 4.79
6073 12411 0.934496 CTGCCGTACGAGAGAGAGAG 59.066 60.000 18.76 0.00 0.00 3.20
6074 12412 1.090625 GCTGCCGTACGAGAGAGAGA 61.091 60.000 18.76 0.00 0.00 3.10
6075 12413 1.353804 GCTGCCGTACGAGAGAGAG 59.646 63.158 18.76 0.00 0.00 3.20
6076 12414 2.113433 GGCTGCCGTACGAGAGAGA 61.113 63.158 18.76 0.00 0.00 3.10
6099 12437 2.759973 CCACTCCTCTGGCCGCTA 60.760 66.667 0.00 0.00 0.00 4.26
6304 12642 0.685097 AGCAGTAAGAAACGCCCTCA 59.315 50.000 0.00 0.00 0.00 3.86
6366 12720 6.163135 CCATATAGGTCGTCTTCTTCCTTT 57.837 41.667 0.00 0.00 0.00 3.11
6413 12769 6.773976 AAACAAGAAGACAAAATGACCAGA 57.226 33.333 0.00 0.00 0.00 3.86
6447 12944 8.033626 AGTATCAAGGCAAACAGTACTTAGTAC 58.966 37.037 14.13 14.13 39.10 2.73
6450 12947 7.907214 AAGTATCAAGGCAAACAGTACTTAG 57.093 36.000 0.00 0.00 31.34 2.18
6451 12948 9.595823 GATAAGTATCAAGGCAAACAGTACTTA 57.404 33.333 0.00 0.00 37.48 2.24
6452 12949 8.100791 TGATAAGTATCAAGGCAAACAGTACTT 58.899 33.333 0.00 0.00 39.58 2.24
6453 12950 7.620880 TGATAAGTATCAAGGCAAACAGTACT 58.379 34.615 0.00 0.00 39.58 2.73
6454 12951 7.764443 TCTGATAAGTATCAAGGCAAACAGTAC 59.236 37.037 2.79 0.00 41.72 2.73
6635 13135 1.023513 GCTCTGCAAGGCACGAAGAT 61.024 55.000 5.79 0.00 33.79 2.40
6641 13141 1.302351 AGTGAGCTCTGCAAGGCAC 60.302 57.895 16.19 2.34 33.79 5.01
6659 13159 2.076100 GCACGTGTTCTCATTGATCCA 58.924 47.619 18.38 0.00 0.00 3.41
6695 13195 3.989817 GCCAAGCTGGAACTACAAAAATG 59.010 43.478 6.40 0.00 40.96 2.32
6718 13218 2.632377 CCGTTACTGAGGCATGACAAT 58.368 47.619 0.00 0.00 0.00 2.71
6743 13260 6.036408 GCCAAAGGCTTTCAATTGTGAATATC 59.964 38.462 10.08 0.00 46.69 1.63
6829 13346 9.268268 CTAGGAAAATTTATGACGTATTAGGCA 57.732 33.333 0.00 0.00 0.00 4.75
6889 13406 6.020971 TCATATGTACTGTGCCTTATACCG 57.979 41.667 1.90 0.00 0.00 4.02
6899 13417 4.802039 GGTACGGTGTTCATATGTACTGTG 59.198 45.833 21.34 11.63 36.52 3.66
6900 13418 4.708421 AGGTACGGTGTTCATATGTACTGT 59.292 41.667 18.66 18.66 36.52 3.55
6917 13435 1.924524 CCGAACTATGCACAAGGTACG 59.075 52.381 0.00 0.00 0.00 3.67
6918 13436 1.664151 GCCGAACTATGCACAAGGTAC 59.336 52.381 0.00 0.00 0.00 3.34
6952 13470 5.479306 TGTATGTCTTACAAGAGAACCTGC 58.521 41.667 0.00 0.00 37.87 4.85
6976 13494 1.134340 ACCGACACCAGCAAAACTGTA 60.134 47.619 0.00 0.00 45.68 2.74
6995 13513 0.670162 ACACTGCTGCCATTGTTCAC 59.330 50.000 0.00 0.00 31.63 3.18
7072 13636 4.262121 CCTTCAGACACAAATGATGGCAAA 60.262 41.667 0.00 0.00 34.95 3.68
7100 13664 4.020543 AGTAGAAGAGAAGCGGTGATCTT 58.979 43.478 12.77 12.77 34.78 2.40
7138 13702 1.480954 TCCAAACCATAGCCGACTCTC 59.519 52.381 0.00 0.00 0.00 3.20
7236 14054 2.086869 CATTGCCTACCTCCACAACAG 58.913 52.381 0.00 0.00 0.00 3.16
7240 14058 1.302949 GGCATTGCCTACCTCCACA 59.697 57.895 20.66 0.00 46.69 4.17
7260 14078 1.172180 ACATGACCACTTGCGGGTTG 61.172 55.000 0.00 0.00 39.19 3.77
7261 14079 0.398696 TACATGACCACTTGCGGGTT 59.601 50.000 0.00 0.00 39.19 4.11
7262 14080 0.036388 CTACATGACCACTTGCGGGT 60.036 55.000 0.00 0.00 42.61 5.28
7263 14081 0.036388 ACTACATGACCACTTGCGGG 60.036 55.000 0.00 0.00 0.00 6.13
7264 14082 1.464608 CAACTACATGACCACTTGCGG 59.535 52.381 0.00 0.00 0.00 5.69
7265 14083 2.096268 CACAACTACATGACCACTTGCG 60.096 50.000 0.00 0.00 0.00 4.85
7266 14084 2.350772 GCACAACTACATGACCACTTGC 60.351 50.000 0.00 0.00 0.00 4.01
7349 14169 3.242543 GCAATCACGAGAACCTAGCAATG 60.243 47.826 0.00 0.00 0.00 2.82
7393 14214 8.860780 AGATTGGAAGAAAGGATATATGCTTC 57.139 34.615 18.53 12.34 37.48 3.86
7466 14290 7.044181 TGAGAGTGCCTTTGACTATTGATAAG 58.956 38.462 0.00 0.00 0.00 1.73
7467 14291 6.946340 TGAGAGTGCCTTTGACTATTGATAA 58.054 36.000 0.00 0.00 0.00 1.75
7468 14292 6.544928 TGAGAGTGCCTTTGACTATTGATA 57.455 37.500 0.00 0.00 0.00 2.15
7469 14293 5.426689 TGAGAGTGCCTTTGACTATTGAT 57.573 39.130 0.00 0.00 0.00 2.57
7470 14294 4.890158 TGAGAGTGCCTTTGACTATTGA 57.110 40.909 0.00 0.00 0.00 2.57
7471 14295 5.947228 TTTGAGAGTGCCTTTGACTATTG 57.053 39.130 0.00 0.00 0.00 1.90
7472 14296 6.959639 TTTTTGAGAGTGCCTTTGACTATT 57.040 33.333 0.00 0.00 0.00 1.73
7502 14326 8.418662 GCCGTCCATATACATATGTAGGATTTA 58.581 37.037 19.80 8.36 38.73 1.40
7503 14327 7.272978 GCCGTCCATATACATATGTAGGATTT 58.727 38.462 19.80 6.46 38.73 2.17
7504 14328 6.461092 CGCCGTCCATATACATATGTAGGATT 60.461 42.308 19.80 6.80 38.73 3.01
7505 14329 5.009710 CGCCGTCCATATACATATGTAGGAT 59.990 44.000 19.80 12.94 38.73 3.24
7506 14330 4.337274 CGCCGTCCATATACATATGTAGGA 59.663 45.833 19.80 17.24 38.73 2.94
7507 14331 4.499188 CCGCCGTCCATATACATATGTAGG 60.499 50.000 19.80 15.43 38.73 3.18
7508 14332 4.337274 TCCGCCGTCCATATACATATGTAG 59.663 45.833 19.80 7.48 38.73 2.74
7509 14333 4.271661 TCCGCCGTCCATATACATATGTA 58.728 43.478 17.65 17.65 38.73 2.29
7510 14334 3.093814 TCCGCCGTCCATATACATATGT 58.906 45.455 13.93 13.93 38.73 2.29
7511 14335 3.793797 TCCGCCGTCCATATACATATG 57.206 47.619 0.00 0.00 39.80 1.78
7512 14336 3.767673 ACTTCCGCCGTCCATATACATAT 59.232 43.478 0.00 0.00 0.00 1.78
7513 14337 3.159472 ACTTCCGCCGTCCATATACATA 58.841 45.455 0.00 0.00 0.00 2.29
7514 14338 1.968493 ACTTCCGCCGTCCATATACAT 59.032 47.619 0.00 0.00 0.00 2.29
7515 14339 1.405872 ACTTCCGCCGTCCATATACA 58.594 50.000 0.00 0.00 0.00 2.29
7516 14340 3.648339 TTACTTCCGCCGTCCATATAC 57.352 47.619 0.00 0.00 0.00 1.47
7517 14341 3.638160 ACTTTACTTCCGCCGTCCATATA 59.362 43.478 0.00 0.00 0.00 0.86
7518 14342 2.433239 ACTTTACTTCCGCCGTCCATAT 59.567 45.455 0.00 0.00 0.00 1.78
7519 14343 1.826720 ACTTTACTTCCGCCGTCCATA 59.173 47.619 0.00 0.00 0.00 2.74
7528 14352 8.173130 ACAAATAAGCGATTTACTTTACTTCCG 58.827 33.333 0.00 0.00 35.45 4.30
7531 14355 9.005777 TGGACAAATAAGCGATTTACTTTACTT 57.994 29.630 0.00 0.00 35.45 2.24
7545 14373 8.986477 ATTTGTTAGTTCATGGACAAATAAGC 57.014 30.769 6.96 0.00 45.62 3.09
7548 14376 7.148154 CCGGATTTGTTAGTTCATGGACAAATA 60.148 37.037 6.96 0.00 46.71 1.40
7550 14378 5.048364 CCGGATTTGTTAGTTCATGGACAAA 60.048 40.000 6.96 10.00 43.56 2.83
7551 14379 4.457603 CCGGATTTGTTAGTTCATGGACAA 59.542 41.667 6.96 1.69 0.00 3.18
7556 14384 4.006989 TCCACCGGATTTGTTAGTTCATG 58.993 43.478 9.46 0.00 0.00 3.07
7633 14462 2.419198 CTCAAGGAGGCCGATCCG 59.581 66.667 5.42 0.00 44.65 4.18


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

AutoCloner maintained by Alex Coulton.