Multiple sequence alignment - TraesCS2B01G421500

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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 TraesCS2B01G421500 chr2B 100.000 6280 0 0 1 6280 606611139 606617418 0.000000e+00 11598.0
1 TraesCS2B01G421500 chr2B 84.680 359 35 8 1 339 488640772 488640414 2.170000e-89 340.0
2 TraesCS2B01G421500 chr2B 82.031 128 23 0 2393 2520 780015944 780015817 6.660000e-20 110.0
3 TraesCS2B01G421500 chr2B 74.375 160 38 1 2279 2438 655598242 655598398 1.460000e-06 65.8
4 TraesCS2B01G421500 chr2D 93.674 3462 126 24 1 3400 514944513 514947943 0.000000e+00 5094.0
5 TraesCS2B01G421500 chr2D 94.558 2389 99 17 3427 5792 514947942 514950322 0.000000e+00 3663.0
6 TraesCS2B01G421500 chr2D 94.562 331 16 1 5796 6126 514950420 514950748 1.560000e-140 510.0
7 TraesCS2B01G421500 chr2D 75.613 693 154 13 4595 5278 19643999 19643313 4.690000e-86 329.0
8 TraesCS2B01G421500 chr2D 92.357 157 7 5 6124 6277 514950788 514950942 1.060000e-52 219.0
9 TraesCS2B01G421500 chr2D 84.466 206 28 4 5572 5773 606702501 606702296 3.840000e-47 200.0
10 TraesCS2B01G421500 chr2D 82.031 128 23 0 2393 2520 651070908 651070781 6.660000e-20 110.0
11 TraesCS2B01G421500 chr2D 85.106 94 12 2 3344 3435 612817253 612817346 1.860000e-15 95.3
12 TraesCS2B01G421500 chr2D 94.595 37 2 0 5522 5558 588738611 588738647 2.450000e-04 58.4
13 TraesCS2B01G421500 chr2A 92.150 2586 164 22 2964 5525 658908111 658910681 0.000000e+00 3615.0
14 TraesCS2B01G421500 chr2A 93.826 2057 75 14 910 2960 658906052 658908062 0.000000e+00 3048.0
15 TraesCS2B01G421500 chr2A 92.169 332 23 3 5796 6126 658911072 658911401 3.430000e-127 466.0
16 TraesCS2B01G421500 chr2A 93.286 283 14 5 5509 5789 658910693 658910972 4.530000e-111 412.0
17 TraesCS2B01G421500 chr2A 76.197 689 151 11 4595 5275 20561283 20561966 1.000000e-92 351.0
18 TraesCS2B01G421500 chr2A 91.558 154 8 5 6127 6277 658911444 658911595 2.290000e-49 207.0
19 TraesCS2B01G421500 chr2A 74.675 154 36 2 2280 2433 759149528 759149678 1.460000e-06 65.8
20 TraesCS2B01G421500 chr1D 86.150 361 29 8 1 340 370203109 370203469 2.770000e-98 370.0
21 TraesCS2B01G421500 chr1D 87.440 207 21 4 446 648 370204073 370204278 3.790000e-57 233.0
22 TraesCS2B01G421500 chr1D 86.111 216 23 6 5584 5793 213703158 213702944 6.330000e-55 226.0
23 TraesCS2B01G421500 chr1D 85.926 135 16 3 6148 6280 249227484 249227351 2.360000e-29 141.0
24 TraesCS2B01G421500 chr1D 86.000 100 10 4 3338 3435 250421651 250421748 3.100000e-18 104.0
25 TraesCS2B01G421500 chr5D 86.072 359 30 7 1 339 243287123 243287481 9.950000e-98 368.0
26 TraesCS2B01G421500 chr1B 85.960 349 36 9 2 339 445589395 445589741 1.660000e-95 361.0
27 TraesCS2B01G421500 chr1B 82.913 357 39 7 1 336 564001354 564001709 1.020000e-77 302.0
28 TraesCS2B01G421500 chr1B 84.579 214 26 6 5586 5793 306893325 306893537 8.250000e-49 206.0
29 TraesCS2B01G421500 chr1B 83.645 214 28 6 5586 5793 306710055 306710267 1.790000e-45 195.0
30 TraesCS2B01G421500 chr7D 85.278 360 31 10 1 339 192688519 192688877 1.000000e-92 351.0
31 TraesCS2B01G421500 chr7D 84.848 132 14 6 6134 6262 388029931 388030059 1.840000e-25 128.0
32 TraesCS2B01G421500 chr6D 85.352 355 35 7 1 339 464820903 464821256 1.000000e-92 351.0
33 TraesCS2B01G421500 chrUn 85.278 360 30 8 1 339 48284549 48284906 3.600000e-92 350.0
34 TraesCS2B01G421500 chrUn 74.855 688 162 10 4595 5275 272323786 272324469 1.020000e-77 302.0
35 TraesCS2B01G421500 chrUn 74.746 689 161 12 4595 5275 16721838 16722521 4.760000e-76 296.0
36 TraesCS2B01G421500 chr7B 76.555 627 134 10 4591 5213 126175361 126174744 1.300000e-86 331.0
37 TraesCS2B01G421500 chr7B 86.395 147 17 3 5584 5728 184480669 184480524 2.340000e-34 158.0
38 TraesCS2B01G421500 chr4D 84.358 358 35 8 1 337 270612889 270612532 1.300000e-86 331.0
39 TraesCS2B01G421500 chr4D 88.060 67 5 3 3895 3960 460779169 460779105 6.750000e-10 76.8
40 TraesCS2B01G421500 chr4D 88.462 52 4 2 5515 5566 509275119 509275168 1.890000e-05 62.1
41 TraesCS2B01G421500 chr5A 83.520 358 40 9 1 339 51540241 51540598 3.650000e-82 316.0
42 TraesCS2B01G421500 chr5A 85.235 149 16 6 6135 6280 494555727 494555582 1.410000e-31 148.0
43 TraesCS2B01G421500 chr5A 97.059 34 1 0 5525 5558 474876853 474876886 2.450000e-04 58.4
44 TraesCS2B01G421500 chr3B 81.944 360 44 4 1 339 728313750 728313391 1.030000e-72 285.0
45 TraesCS2B01G421500 chr3B 80.112 357 36 12 2 337 508487717 508487375 3.790000e-57 233.0
46 TraesCS2B01G421500 chr3B 75.100 249 48 3 2702 2937 12841626 12841379 3.100000e-18 104.0
47 TraesCS2B01G421500 chr3B 84.536 97 11 4 3342 3435 123056332 123056237 6.700000e-15 93.5
48 TraesCS2B01G421500 chr3B 85.057 87 13 0 2851 2937 13247723 13247809 8.670000e-14 89.8
49 TraesCS2B01G421500 chr3B 73.222 239 61 1 2280 2518 13413888 13414123 4.030000e-12 84.2
50 TraesCS2B01G421500 chr3A 82.173 359 34 10 1 339 445876361 445876709 1.330000e-71 281.0
51 TraesCS2B01G421500 chr3A 80.657 274 31 7 86 339 695741035 695740764 6.420000e-45 193.0
52 TraesCS2B01G421500 chr3A 79.452 146 29 1 2377 2522 16233526 16233382 1.110000e-17 102.0
53 TraesCS2B01G421500 chr3A 79.452 146 29 1 2377 2522 17332556 17332700 1.110000e-17 102.0
54 TraesCS2B01G421500 chr3A 85.714 84 12 0 2854 2937 17378257 17378174 8.670000e-14 89.8
55 TraesCS2B01G421500 chr4B 89.498 219 21 2 4 220 242752160 242751942 6.200000e-70 276.0
56 TraesCS2B01G421500 chr4B 88.356 146 14 3 6134 6277 178379314 178379458 8.370000e-39 172.0
57 TraesCS2B01G421500 chr4B 86.525 141 12 7 6134 6272 135745463 135745328 1.410000e-31 148.0
58 TraesCS2B01G421500 chr4B 89.091 55 2 4 5507 5559 636798568 636798620 1.460000e-06 65.8
59 TraesCS2B01G421500 chr6A 83.854 192 26 4 5604 5792 420845027 420845216 1.800000e-40 178.0
60 TraesCS2B01G421500 chr6A 80.749 187 29 3 448 633 517658333 517658153 8.490000e-29 139.0
61 TraesCS2B01G421500 chr6A 89.583 96 10 0 446 541 29650367 29650272 8.550000e-24 122.0
62 TraesCS2B01G421500 chr6A 79.570 186 21 8 372 541 29683579 29683395 3.980000e-22 117.0
63 TraesCS2B01G421500 chr6A 86.364 88 12 0 3351 3438 93285788 93285701 5.180000e-16 97.1
64 TraesCS2B01G421500 chr6A 97.059 34 1 0 5523 5556 201091703 201091670 2.450000e-04 58.4
65 TraesCS2B01G421500 chr7A 81.921 177 22 5 5602 5772 589038975 589039147 2.360000e-29 141.0
66 TraesCS2B01G421500 chr7A 84.733 131 16 4 6134 6262 438210944 438211072 1.840000e-25 128.0
67 TraesCS2B01G421500 chr3D 81.633 147 19 8 6135 6277 147457266 147457408 1.430000e-21 115.0
68 TraesCS2B01G421500 chr3D 72.989 348 72 12 2607 2937 5330011 5330353 1.110000e-17 102.0
69 TraesCS2B01G421500 chr3D 79.054 148 31 0 2377 2524 5375431 5375284 1.110000e-17 102.0
70 TraesCS2B01G421500 chr3D 74.704 253 50 3 2698 2937 41595278 41595027 4.010000e-17 100.0
71 TraesCS2B01G421500 chr3D 85.870 92 13 0 3344 3435 302930478 302930387 1.440000e-16 99.0
72 TraesCS2B01G421500 chr3D 87.209 86 11 0 3350 3435 409967707 409967792 1.440000e-16 99.0
73 TraesCS2B01G421500 chr3D 73.783 267 61 6 2257 2522 5329646 5329904 5.180000e-16 97.1
74 TraesCS2B01G421500 chr3D 74.330 261 44 12 2694 2937 5375092 5374838 8.670000e-14 89.8
75 TraesCS2B01G421500 chr3D 73.810 252 54 5 2698 2937 41425560 41425309 8.670000e-14 89.8
76 TraesCS2B01G421500 chr3D 92.857 42 0 2 4183 4221 199243759 199243800 2.450000e-04 58.4
77 TraesCS2B01G421500 chr1A 86.000 100 10 4 3338 3435 320485576 320485673 3.100000e-18 104.0
78 TraesCS2B01G421500 chr5B 93.478 46 2 1 5525 5570 696590273 696590229 4.060000e-07 67.6
79 TraesCS2B01G421500 chr6B 89.796 49 4 1 5522 5570 11959847 11959800 1.890000e-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 TraesCS2B01G421500 chr2B 606611139 606617418 6279 False 11598.0 11598 100.00000 1 6280 1 chr2B.!!$F1 6279
1 TraesCS2B01G421500 chr2D 514944513 514950942 6429 False 2371.5 5094 93.78775 1 6277 4 chr2D.!!$F3 6276
2 TraesCS2B01G421500 chr2D 19643313 19643999 686 True 329.0 329 75.61300 4595 5278 1 chr2D.!!$R1 683
3 TraesCS2B01G421500 chr2A 658906052 658911595 5543 False 1549.6 3615 92.59780 910 6277 5 chr2A.!!$F3 5367
4 TraesCS2B01G421500 chr2A 20561283 20561966 683 False 351.0 351 76.19700 4595 5275 1 chr2A.!!$F1 680
5 TraesCS2B01G421500 chr1D 370203109 370204278 1169 False 301.5 370 86.79500 1 648 2 chr1D.!!$F2 647
6 TraesCS2B01G421500 chrUn 272323786 272324469 683 False 302.0 302 74.85500 4595 5275 1 chrUn.!!$F3 680
7 TraesCS2B01G421500 chrUn 16721838 16722521 683 False 296.0 296 74.74600 4595 5275 1 chrUn.!!$F1 680
8 TraesCS2B01G421500 chr7B 126174744 126175361 617 True 331.0 331 76.55500 4591 5213 1 chr7B.!!$R1 622

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
430 1014 0.170116 TAAAGCAAATTCGCCAGCCG 59.830 50.000 0.0 0.0 38.61 5.52 F
1153 1783 0.108585 ACGTGTTGCCTTGACCATCT 59.891 50.000 0.0 0.0 0.00 2.90 F
1183 1818 0.875040 TTTGCGCGAACCGTCTACAA 60.875 50.000 12.1 0.0 39.71 2.41 F
2195 2830 1.266550 CGCATGTTCAGACGACGAATG 60.267 52.381 0.0 0.0 0.00 2.67 F
3097 3800 0.463474 ACTACGACGACCTAGAGGCC 60.463 60.000 0.0 0.0 39.32 5.19 F
3219 3922 0.818040 GCAAACAACAGGACCTCGGT 60.818 55.000 0.0 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1900 0.038455 ACTCACGAGGTCTAGCAGGT 59.962 55.000 0.00 0.0 0.00 4.00 R
2709 3351 0.040692 TACGCGCTGACGGTATCATC 60.041 55.000 5.73 0.0 40.57 2.92 R
3088 3791 1.227973 GCCCATTTCGGCCTCTAGG 60.228 63.158 0.00 0.0 43.66 3.02 R
3925 4634 0.390603 CCGCGGTGTCAAGGTAATGA 60.391 55.000 19.50 0.0 0.00 2.57 R
4791 5523 1.072159 GGCTGAGGCACACTGTTCT 59.928 57.895 0.00 0.0 40.87 3.01 R
5351 6086 1.993370 CTAGTTTGGTAGCACACGAGC 59.007 52.381 8.13 0.0 0.00 5.03 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
52 53 6.406370 TGTCATAATTGTACTCCAAGTCCAG 58.594 40.000 0.00 0.00 36.25 3.86
111 112 6.707440 TTACACAACCAGTCATGATGTTTT 57.293 33.333 0.00 0.00 0.00 2.43
202 205 7.393234 CCAAATGCCCTATTAATATCCTTTCGA 59.607 37.037 0.00 0.00 0.00 3.71
206 209 7.284074 TGCCCTATTAATATCCTTTCGACAAA 58.716 34.615 0.00 0.00 0.00 2.83
207 210 7.776030 TGCCCTATTAATATCCTTTCGACAAAA 59.224 33.333 0.00 0.00 0.00 2.44
355 939 1.742268 GAGCAAATCTGACAGCCCTTC 59.258 52.381 0.00 0.00 0.00 3.46
360 944 1.661463 ATCTGACAGCCCTTCCTTCA 58.339 50.000 0.00 0.00 0.00 3.02
388 972 1.873165 GCCGAAGCAAATCCGACAA 59.127 52.632 0.00 0.00 39.53 3.18
404 988 2.224548 CGACAACCCTTTCTTCTTCCCT 60.225 50.000 0.00 0.00 0.00 4.20
424 1008 3.408150 CTGTCGACTAAAGCAAATTCGC 58.592 45.455 17.92 0.00 0.00 4.70
430 1014 0.170116 TAAAGCAAATTCGCCAGCCG 59.830 50.000 0.00 0.00 38.61 5.52
504 1088 1.536284 CGACTAATTCCGAGGCTCACC 60.536 57.143 15.95 0.00 0.00 4.02
505 1089 1.480954 GACTAATTCCGAGGCTCACCA 59.519 52.381 15.95 0.00 39.06 4.17
606 1193 0.531532 CCCGCAAACACAAATTGGCA 60.532 50.000 0.00 0.00 0.00 4.92
636 1224 5.009631 CACTCAAACTTGGTGGAATGGATA 58.990 41.667 4.20 0.00 0.00 2.59
645 1259 3.041940 GAATGGATACGGCGCGGG 61.042 66.667 19.75 7.77 42.51 6.13
789 1404 7.233632 CCATAGATATGAAGAAAATGGACCCA 58.766 38.462 1.32 0.00 35.48 4.51
796 1411 6.078456 TGAAGAAAATGGACCCACATATCT 57.922 37.500 0.00 0.00 32.03 1.98
798 1413 7.638444 TGAAGAAAATGGACCCACATATCTAA 58.362 34.615 0.00 0.00 31.11 2.10
801 1416 7.283329 AGAAAATGGACCCACATATCTAAGAC 58.717 38.462 0.00 0.00 30.16 3.01
834 1449 2.223805 GGATGGTCAAATTTGCGGGATC 60.224 50.000 13.54 10.85 0.00 3.36
867 1482 1.420532 AAAACAGCCTCCACCCCGTA 61.421 55.000 0.00 0.00 0.00 4.02
875 1490 1.818959 CTCCACCCCGTAAACCGACA 61.819 60.000 0.00 0.00 39.56 4.35
877 1492 2.030958 CACCCCGTAAACCGACAGC 61.031 63.158 0.00 0.00 39.56 4.40
902 1517 0.605319 TGTCGGATGTCCTGGTTTGC 60.605 55.000 0.00 0.00 0.00 3.68
955 1584 1.007479 ACCCGGGTCCTTGTGTATAGA 59.993 52.381 24.16 0.00 0.00 1.98
1088 1717 4.443881 CCTGGTTATAACTTCCTTACCCGG 60.444 50.000 15.05 0.00 0.00 5.73
1101 1731 1.624336 TACCCGGTATAAGCAGCGAT 58.376 50.000 0.00 0.00 41.79 4.58
1153 1783 0.108585 ACGTGTTGCCTTGACCATCT 59.891 50.000 0.00 0.00 0.00 2.90
1183 1818 0.875040 TTTGCGCGAACCGTCTACAA 60.875 50.000 12.10 0.00 39.71 2.41
1205 1840 3.760684 ACGGATCTAGTCGGTAACTTTGT 59.239 43.478 0.00 0.00 38.47 2.83
1263 1898 3.131400 GGCAGAACCTTCGAAGATCTACT 59.869 47.826 26.61 13.94 35.04 2.57
1264 1899 4.382147 GGCAGAACCTTCGAAGATCTACTT 60.382 45.833 26.61 7.21 37.17 2.24
1265 1900 5.163540 GGCAGAACCTTCGAAGATCTACTTA 60.164 44.000 26.61 0.00 35.53 2.24
1266 1901 5.744819 GCAGAACCTTCGAAGATCTACTTAC 59.255 44.000 26.61 11.91 39.13 2.34
1309 1944 2.224113 GGATATGAAAGCGACGGGGTTA 60.224 50.000 0.00 0.00 34.69 2.85
1614 2249 3.115892 CTGCGGCGCGTTAAAGGA 61.116 61.111 28.09 5.67 0.00 3.36
1692 2327 2.987149 GTCCACTGATGTCTACGTGTTG 59.013 50.000 0.00 0.00 0.00 3.33
1713 2348 2.819595 GACGATGGCGCCATGTGT 60.820 61.111 44.96 38.01 42.48 3.72
1968 2603 2.594592 GGCACCGACCAACAGCTT 60.595 61.111 0.00 0.00 0.00 3.74
1979 2614 2.945668 ACCAACAGCTTGTTCAAGAGTC 59.054 45.455 15.52 0.00 38.77 3.36
2023 2658 2.490903 CCTGGCAATCTGACCTTCTTTG 59.509 50.000 0.00 0.00 0.00 2.77
2036 2671 3.793144 CTTTGGCTCCGCGTCTGC 61.793 66.667 4.92 5.99 37.91 4.26
2195 2830 1.266550 CGCATGTTCAGACGACGAATG 60.267 52.381 0.00 0.00 0.00 2.67
2253 2888 2.805671 CGAATCACCAAGCACAACTACA 59.194 45.455 0.00 0.00 0.00 2.74
2331 2967 1.612146 TTCGATGGGCACAGGAGGA 60.612 57.895 0.00 0.00 0.00 3.71
2387 3023 2.749044 CAGCTGCCCATGAGCGTT 60.749 61.111 0.00 0.00 41.61 4.84
2401 3037 3.490759 CGTTGCTAGCACCCGCAG 61.491 66.667 19.17 1.40 42.27 5.18
2504 3140 1.377856 GCAAGAGTTCCTCCCAGGC 60.378 63.158 0.00 0.00 34.61 4.85
2591 3227 4.796231 GACGATGACGGCGCAGGT 62.796 66.667 13.26 7.89 44.46 4.00
2595 3231 4.704833 ATGACGGCGCAGGTGCTT 62.705 61.111 13.26 0.00 39.32 3.91
2623 3265 3.712881 GCGTGTGGGCTTCGTGAC 61.713 66.667 0.00 0.00 0.00 3.67
2678 3320 3.342627 TGGTTCAAAGCGGCGTCG 61.343 61.111 4.29 4.29 39.81 5.12
2752 3394 1.909302 CCTAGAAAGGGAGCCTGAACA 59.091 52.381 0.00 0.00 39.48 3.18
3034 3737 6.507958 TCACAGTTCTTTTGACATGAAACA 57.492 33.333 0.00 0.00 0.00 2.83
3063 3766 2.512515 GCCCCACGAGATCTGTGC 60.513 66.667 15.68 5.52 36.01 4.57
3088 3791 2.306799 ACGAACAGAACTACGACGAC 57.693 50.000 0.00 0.00 0.00 4.34
3097 3800 0.463474 ACTACGACGACCTAGAGGCC 60.463 60.000 0.00 0.00 39.32 5.19
3175 3878 5.776519 CCGACTACACGGTATCTATCTAC 57.223 47.826 0.00 0.00 46.70 2.59
3176 3879 5.233225 CCGACTACACGGTATCTATCTACA 58.767 45.833 0.00 0.00 46.70 2.74
3219 3922 0.818040 GCAAACAACAGGACCTCGGT 60.818 55.000 0.00 0.00 0.00 4.69
3232 3935 1.033574 CCTCGGTCGGCTCTATTCTT 58.966 55.000 0.00 0.00 0.00 2.52
3236 3939 2.099263 TCGGTCGGCTCTATTCTTTCAG 59.901 50.000 0.00 0.00 0.00 3.02
3307 4015 2.484889 ACTCCTTGCTCTCGTTTTCAC 58.515 47.619 0.00 0.00 0.00 3.18
3320 4029 6.731164 TCTCGTTTTCACTTAATTGAAACCC 58.269 36.000 17.66 11.66 43.57 4.11
3321 4030 6.319152 TCTCGTTTTCACTTAATTGAAACCCA 59.681 34.615 17.66 4.31 43.57 4.51
3328 4037 6.915349 TCACTTAATTGAAACCCAATAACGG 58.085 36.000 0.00 0.00 44.28 4.44
3445 4154 3.509184 ACCGAGGGAGTAGTTAACTGAAC 59.491 47.826 18.56 9.30 39.07 3.18
3447 4156 4.483311 CGAGGGAGTAGTTAACTGAACAC 58.517 47.826 18.56 8.19 40.86 3.32
3498 4207 8.500753 TTCCATTTTCTACTTGTACGCATTAT 57.499 30.769 0.00 0.00 0.00 1.28
3505 4214 6.811954 TCTACTTGTACGCATTATGGATTCA 58.188 36.000 0.00 0.00 0.00 2.57
3523 4232 9.659135 ATGGATTCAATTAATAAAGTGATGGGA 57.341 29.630 0.00 0.00 39.27 4.37
3621 4330 1.743623 CCGCGATAACAACAGGCCA 60.744 57.895 8.23 0.00 0.00 5.36
3706 4415 1.480954 TGTCTAGCGGATTGGTCTTCC 59.519 52.381 0.00 0.00 0.00 3.46
3757 4466 1.220206 CGCAGAGAATGTGGGAGCT 59.780 57.895 0.00 0.00 45.53 4.09
3820 4529 2.126031 GCAAGGGAGGTCGTCGAC 60.126 66.667 17.16 17.16 0.00 4.20
3822 4531 3.060615 AAGGGAGGTCGTCGACGG 61.061 66.667 35.05 18.25 40.29 4.79
3823 4532 3.557903 AAGGGAGGTCGTCGACGGA 62.558 63.158 35.05 20.20 40.29 4.69
3878 4587 3.460648 GCTAACGGCAATGAGGAGT 57.539 52.632 0.00 0.00 41.35 3.85
3905 4614 5.698832 TCCATTTTCTGCATTTTGACGTAG 58.301 37.500 0.00 0.00 0.00 3.51
3925 4634 1.621072 GGAGATAGCCCTCCGGATCAT 60.621 57.143 3.57 0.00 42.80 2.45
4008 4717 6.649557 TGATATGCAGACAATTAGCTCTGATG 59.350 38.462 9.94 0.00 36.75 3.07
4034 4743 5.105106 TCACAAATCCGGTTCTTCTATAGCA 60.105 40.000 0.00 0.00 0.00 3.49
4052 4761 3.829948 AGCAAAACTGCATCTGATTTCG 58.170 40.909 0.00 0.00 37.25 3.46
4069 4778 5.242838 TGATTTCGTTGGCAAAAGAACCTAT 59.757 36.000 15.92 9.39 34.17 2.57
4118 4827 3.006537 ACGTGTCATAAGTGGTAGCAACT 59.993 43.478 0.00 0.00 0.00 3.16
4221 4935 8.258007 TCACTATATTTGTTTACAGAGGGAGTG 58.742 37.037 0.00 0.00 0.00 3.51
4223 4937 4.724279 ATTTGTTTACAGAGGGAGTGGT 57.276 40.909 0.00 0.00 0.00 4.16
4339 5064 6.697641 TCCTATGGTATACCTCCAAATTCC 57.302 41.667 22.41 0.00 38.52 3.01
4421 5146 3.191791 GTCCAACTAACGCTCTTCTCTCT 59.808 47.826 0.00 0.00 0.00 3.10
4542 5274 6.015519 AGCTACTTTTTATGGTTTCACATGCA 60.016 34.615 0.00 0.00 32.39 3.96
4580 5312 5.183140 CCCTATGAACCGAATTGACTTTGTT 59.817 40.000 0.00 0.00 0.00 2.83
4581 5313 6.086222 CCTATGAACCGAATTGACTTTGTTG 58.914 40.000 0.00 0.00 0.00 3.33
4582 5314 4.974368 TGAACCGAATTGACTTTGTTGT 57.026 36.364 0.00 0.00 0.00 3.32
4723 5455 3.391382 GCTGCCACCGTCCTACCT 61.391 66.667 0.00 0.00 0.00 3.08
4764 5496 1.025812 CTATCACTCGTTCGGGCTCT 58.974 55.000 0.00 0.00 0.00 4.09
4791 5523 9.415008 GTCTCAATCCTAATCTATATGCCTCTA 57.585 37.037 0.00 0.00 0.00 2.43
4959 5691 2.425592 CTCTGGTCGGCACACCAA 59.574 61.111 7.37 0.00 46.19 3.67
5251 5986 3.788766 GCTCGTTGCGGCATTCGT 61.789 61.111 20.89 0.00 41.72 3.85
5399 6134 6.928348 TTAGTTCAGATCAAACCAGTAGGA 57.072 37.500 7.22 0.00 38.69 2.94
5448 6183 2.353208 GCCCGACCAACATGCATTTTTA 60.353 45.455 0.00 0.00 0.00 1.52
5690 6457 9.840427 ACTTAATTGCATGTGTAGAAACATAAC 57.160 29.630 0.00 0.00 38.75 1.89
5739 6508 7.489757 CCTTTAAGACTAGCTCAGTATTGACAC 59.510 40.741 11.19 0.00 39.06 3.67
5768 6537 9.635520 ATCTTGTTTTCTTGATCATGAACATTC 57.364 29.630 20.34 12.55 0.00 2.67
5772 6541 9.897744 TGTTTTCTTGATCATGAACATTCTTAC 57.102 29.630 20.34 11.60 0.00 2.34
5775 6544 8.722480 TTCTTGATCATGAACATTCTTACGAT 57.278 30.769 17.55 0.00 0.00 3.73
5792 6561 9.631452 TTCTTACGATGCTATCAATAATGAGAG 57.369 33.333 0.00 0.00 45.63 3.20
5829 6692 7.255486 CCTTAGACCATGAGAATATCGTACACA 60.255 40.741 0.00 0.00 0.00 3.72
5835 6698 5.425577 TGAGAATATCGTACACAGAGCTC 57.574 43.478 5.27 5.27 0.00 4.09
5847 6710 0.829333 CAGAGCTCTGTGCCATAGGT 59.171 55.000 31.71 0.00 44.23 3.08
5855 6718 1.536766 CTGTGCCATAGGTTGTGTGTG 59.463 52.381 0.00 0.00 0.00 3.82
5858 6721 1.133637 TGCCATAGGTTGTGTGTGGTT 60.134 47.619 0.00 0.00 32.56 3.67
5987 6851 3.398406 GGTCCCGAAAAACATGCATTTT 58.602 40.909 0.00 8.98 33.13 1.82
5988 6852 3.812609 GGTCCCGAAAAACATGCATTTTT 59.187 39.130 9.88 9.88 42.94 1.94
6118 6983 9.685828 TGCAACTTTACTACAAATTAATTGACC 57.314 29.630 0.39 0.00 41.85 4.02
6132 7039 8.477419 AATTAATTGACCCAACTTTGAGAGAA 57.523 30.769 0.00 0.00 0.00 2.87
6216 7125 8.888579 TCGAATATGAGATTAGGAGAAAAACC 57.111 34.615 0.00 0.00 0.00 3.27
6266 7175 4.019051 CCAATATGATCCCTAGTCATGCCA 60.019 45.833 4.92 0.00 36.96 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.801483 TCATCGAGGATGAGAGGGATC 58.199 52.381 0.00 0.00 43.11 3.36
206 209 9.249053 ACCCCAAAATTAAGAAACACAAAAATT 57.751 25.926 0.00 0.00 0.00 1.82
207 210 8.815565 ACCCCAAAATTAAGAAACACAAAAAT 57.184 26.923 0.00 0.00 0.00 1.82
355 939 4.883354 GGCAGGCGGGGATGAAGG 62.883 72.222 0.00 0.00 0.00 3.46
388 972 1.348036 CGACAGGGAAGAAGAAAGGGT 59.652 52.381 0.00 0.00 0.00 4.34
404 988 2.158841 GGCGAATTTGCTTTAGTCGACA 59.841 45.455 19.50 0.48 39.54 4.35
424 1008 0.960861 GGGGAAGAAGAAACGGCTGG 60.961 60.000 0.00 0.00 0.00 4.85
430 1014 2.038837 CCGGCGGGGAAGAAGAAAC 61.039 63.158 20.56 0.00 38.47 2.78
504 1088 2.637025 CGGTTGGTTCCAGCGTTG 59.363 61.111 0.00 0.00 0.00 4.10
505 1089 2.406002 ATCCGGTTGGTTCCAGCGTT 62.406 55.000 0.00 0.00 36.30 4.84
606 1193 1.528309 CAAGTTTGAGTGCGGGGGT 60.528 57.895 0.00 0.00 0.00 4.95
685 1299 3.382832 CGTTCCCGCCTCCACTCT 61.383 66.667 0.00 0.00 0.00 3.24
703 1317 2.663063 CGAACTTCTTTCCGCTTGCTTC 60.663 50.000 0.00 0.00 0.00 3.86
708 1322 0.586802 GCACGAACTTCTTTCCGCTT 59.413 50.000 0.00 0.00 0.00 4.68
778 1393 6.969043 TGTCTTAGATATGTGGGTCCATTTT 58.031 36.000 0.00 0.00 0.00 1.82
809 1424 2.428171 CCGCAAATTTGACCATCCTGAT 59.572 45.455 22.31 0.00 0.00 2.90
813 1428 1.181786 TCCCGCAAATTTGACCATCC 58.818 50.000 22.31 1.90 0.00 3.51
815 1430 2.738743 AGATCCCGCAAATTTGACCAT 58.261 42.857 22.31 7.15 0.00 3.55
817 1432 4.554723 CGAATAGATCCCGCAAATTTGACC 60.555 45.833 22.31 4.10 0.00 4.02
819 1434 3.563808 CCGAATAGATCCCGCAAATTTGA 59.436 43.478 22.31 0.76 0.00 2.69
820 1435 3.304659 CCCGAATAGATCCCGCAAATTTG 60.305 47.826 14.03 14.03 0.00 2.32
821 1436 2.884639 CCCGAATAGATCCCGCAAATTT 59.115 45.455 0.00 0.00 0.00 1.82
834 1449 1.309499 TGTTTTGCCGGCCCGAATAG 61.309 55.000 26.77 0.00 0.00 1.73
875 1490 3.535561 CAGGACATCCGACAAAATAGCT 58.464 45.455 0.00 0.00 42.08 3.32
877 1492 3.873910 ACCAGGACATCCGACAAAATAG 58.126 45.455 0.00 0.00 42.08 1.73
902 1517 1.154225 GTTGGCGCCACAAATCTCG 60.154 57.895 32.95 0.00 31.17 4.04
924 1553 0.976590 GACCCGGGTAAGGAGAGCTT 60.977 60.000 30.38 0.00 0.00 3.74
975 1604 1.352622 TTGAGGTTGTGTCCAGGGCT 61.353 55.000 0.00 0.00 0.00 5.19
1183 1818 3.760684 ACAAAGTTACCGACTAGATCCGT 59.239 43.478 0.00 0.00 37.72 4.69
1185 1820 6.096001 TCCTTACAAAGTTACCGACTAGATCC 59.904 42.308 0.00 0.00 37.72 3.36
1205 1840 6.156256 TCTCTTTTGGATCGAATTCCTCCTTA 59.844 38.462 17.99 7.65 36.68 2.69
1263 1898 2.290768 ACTCACGAGGTCTAGCAGGTAA 60.291 50.000 0.00 0.00 0.00 2.85
1264 1899 1.281287 ACTCACGAGGTCTAGCAGGTA 59.719 52.381 0.00 0.00 0.00 3.08
1265 1900 0.038455 ACTCACGAGGTCTAGCAGGT 59.962 55.000 0.00 0.00 0.00 4.00
1266 1901 1.178276 AACTCACGAGGTCTAGCAGG 58.822 55.000 0.00 0.00 0.00 4.85
1614 2249 1.381872 ATAGTCGCCCAGGCTGAGT 60.382 57.895 17.94 10.81 39.32 3.41
1692 2327 2.890474 ATGGCGCCATCGTCGAAC 60.890 61.111 36.10 0.26 44.55 3.95
1919 2554 2.808315 CGATCCAGTGGACGAGGG 59.192 66.667 15.86 0.00 32.98 4.30
1968 2603 0.687354 GGGGAGCAGACTCTTGAACA 59.313 55.000 0.00 0.00 42.98 3.18
1979 2614 3.631046 GATAGGCCGGGGGAGCAG 61.631 72.222 2.18 0.00 0.00 4.24
2036 2671 4.473520 CTACGCCCCAGGTGCAGG 62.474 72.222 0.00 0.00 36.54 4.85
2105 2740 1.299850 GCACCCTTGTTGGTTTCGC 60.300 57.895 0.00 0.00 36.12 4.70
2195 2830 3.235195 GTCGTGTCACTGTCATACTCAC 58.765 50.000 0.65 0.00 0.00 3.51
2253 2888 1.900498 GCTGCTGCTTTGTGGGACT 60.900 57.895 8.53 0.00 36.03 3.85
2401 3037 2.958016 ACAACACGTCGACGGTGC 60.958 61.111 37.89 0.79 44.95 5.01
2450 3086 2.783288 GGGGACGAGGGATGTCGAC 61.783 68.421 9.11 9.11 42.85 4.20
2590 3226 3.482783 GCCTCGTCGCAGAAGCAC 61.483 66.667 0.00 0.00 39.69 4.40
2593 3229 3.175240 CACGCCTCGTCGCAGAAG 61.175 66.667 0.00 0.00 38.32 2.85
2594 3230 3.973516 ACACGCCTCGTCGCAGAA 61.974 61.111 0.00 0.00 38.32 3.02
2595 3231 4.700365 CACACGCCTCGTCGCAGA 62.700 66.667 0.00 0.00 38.32 4.26
2621 3263 0.529378 CCTTGCAATCCAGGCTTGTC 59.471 55.000 0.00 0.00 0.00 3.18
2623 3265 0.529378 GTCCTTGCAATCCAGGCTTG 59.471 55.000 0.00 0.00 0.00 4.01
2709 3351 0.040692 TACGCGCTGACGGTATCATC 60.041 55.000 5.73 0.00 40.57 2.92
2752 3394 5.770663 ACGACATCTCCATAGTAAGCATAGT 59.229 40.000 0.00 0.00 0.00 2.12
3034 3737 1.607467 GTGGGGCAGCACCTGAAAT 60.607 57.895 16.83 0.00 39.10 2.17
3063 3766 3.364023 GTCGTAGTTCTGTTCGTTGATGG 59.636 47.826 0.00 0.00 0.00 3.51
3088 3791 1.227973 GCCCATTTCGGCCTCTAGG 60.228 63.158 0.00 0.00 43.66 3.02
3097 3800 1.433064 CACCCAATCGCCCATTTCG 59.567 57.895 0.00 0.00 0.00 3.46
3171 3874 6.591448 CAGTGAACAGATTAATGCTGTGTAGA 59.409 38.462 16.33 4.28 45.27 2.59
3173 3876 6.230472 ACAGTGAACAGATTAATGCTGTGTA 58.770 36.000 16.33 9.25 45.27 2.90
3174 3877 5.065914 ACAGTGAACAGATTAATGCTGTGT 58.934 37.500 16.33 9.84 45.27 3.72
3175 3878 5.618056 ACAGTGAACAGATTAATGCTGTG 57.382 39.130 16.33 9.41 45.27 3.66
3219 3922 2.604046 GGCTGAAAGAATAGAGCCGA 57.396 50.000 0.00 0.00 41.61 5.54
3232 3935 4.478206 TGAAAAATGTTTGGTGGCTGAA 57.522 36.364 0.00 0.00 0.00 3.02
3236 3939 7.614124 ATTGATATGAAAAATGTTTGGTGGC 57.386 32.000 0.00 0.00 0.00 5.01
3307 4015 6.915349 TCACCGTTATTGGGTTTCAATTAAG 58.085 36.000 0.00 0.00 43.04 1.85
3320 4029 5.551760 AATTGAGAAGCTCACCGTTATTG 57.448 39.130 0.00 0.00 40.46 1.90
3321 4030 7.681939 TTAAATTGAGAAGCTCACCGTTATT 57.318 32.000 0.00 0.00 40.46 1.40
3407 4116 9.085645 ACTCCCTCGGTAAAGAAAAATAAAATT 57.914 29.630 0.00 0.00 0.00 1.82
3415 4124 5.813513 AACTACTCCCTCGGTAAAGAAAA 57.186 39.130 0.00 0.00 0.00 2.29
3472 4181 6.811253 ATGCGTACAAGTAGAAAATGGAAA 57.189 33.333 0.00 0.00 0.00 3.13
3498 4207 8.912988 GTCCCATCACTTTATTAATTGAATCCA 58.087 33.333 0.00 0.00 0.00 3.41
3621 4330 2.526873 AGACGGCAGAACCCAGGT 60.527 61.111 0.00 0.00 33.26 4.00
3706 4415 1.070445 GGAGCCTGATGATGACGGG 59.930 63.158 0.00 0.00 36.91 5.28
3815 4524 0.862283 GCAGAATCGTCTCCGTCGAC 60.862 60.000 5.18 5.18 40.07 4.20
3820 4529 0.803768 CACTGGCAGAATCGTCTCCG 60.804 60.000 23.66 0.00 28.78 4.63
3822 4531 1.470632 CCTCACTGGCAGAATCGTCTC 60.471 57.143 23.66 0.00 28.78 3.36
3823 4532 0.534412 CCTCACTGGCAGAATCGTCT 59.466 55.000 23.66 0.00 32.85 4.18
3878 4587 5.634439 CGTCAAAATGCAGAAAATGGAATGA 59.366 36.000 0.00 0.00 30.55 2.57
3885 4594 5.705441 TCTCCTACGTCAAAATGCAGAAAAT 59.295 36.000 0.00 0.00 0.00 1.82
3925 4634 0.390603 CCGCGGTGTCAAGGTAATGA 60.391 55.000 19.50 0.00 0.00 2.57
4008 4717 6.238130 GCTATAGAAGAACCGGATTTGTGAAC 60.238 42.308 9.46 0.00 0.00 3.18
4034 4743 4.549458 CCAACGAAATCAGATGCAGTTTT 58.451 39.130 0.00 0.00 0.00 2.43
4052 4761 4.082408 GTGGGTATAGGTTCTTTTGCCAAC 60.082 45.833 0.00 0.00 0.00 3.77
4069 4778 2.093500 TCTCGACGTAGCTAAGTGGGTA 60.093 50.000 17.36 5.20 0.00 3.69
4118 4827 8.177119 AGCTATTTGTTCATAAACAGGTTTGA 57.823 30.769 7.63 0.00 45.72 2.69
4165 4874 8.969267 CGCTCTTATATTTCTTTACGAATGAGT 58.031 33.333 0.00 0.00 0.00 3.41
4166 4875 8.969267 ACGCTCTTATATTTCTTTACGAATGAG 58.031 33.333 0.00 0.00 0.00 2.90
4169 4878 8.867112 TCACGCTCTTATATTTCTTTACGAAT 57.133 30.769 0.00 0.00 0.00 3.34
4171 4880 8.132995 TGATCACGCTCTTATATTTCTTTACGA 58.867 33.333 0.00 0.00 0.00 3.43
4329 5054 9.408648 ACTTGTGGTTATTATAGGAATTTGGAG 57.591 33.333 0.00 0.00 0.00 3.86
4421 5146 1.811965 CCCTGCGTTTCATGAATCACA 59.188 47.619 9.40 7.93 0.00 3.58
4444 5169 2.113139 CCCACTTTCCACGGCAGT 59.887 61.111 0.00 0.00 0.00 4.40
4542 5274 2.368548 TCATAGGGCATGCTCGTTACAT 59.631 45.455 18.92 0.00 34.35 2.29
4580 5312 7.508687 AGATGGTATCTGCATAATTACACACA 58.491 34.615 0.00 0.00 38.44 3.72
4581 5313 7.969536 AGATGGTATCTGCATAATTACACAC 57.030 36.000 0.00 0.00 38.44 3.82
4582 5314 7.812669 CGTAGATGGTATCTGCATAATTACACA 59.187 37.037 7.50 0.00 41.39 3.72
4764 5496 7.898100 AGAGGCATATAGATTAGGATTGAGACA 59.102 37.037 0.00 0.00 0.00 3.41
4791 5523 1.072159 GGCTGAGGCACACTGTTCT 59.928 57.895 0.00 0.00 40.87 3.01
5351 6086 1.993370 CTAGTTTGGTAGCACACGAGC 59.007 52.381 8.13 0.00 0.00 5.03
5399 6134 1.064906 CATCCTTGCCACCATGTCTCT 60.065 52.381 0.00 0.00 0.00 3.10
5690 6457 5.048504 GGCATGACAACATATCTATTGGTGG 60.049 44.000 0.00 0.00 36.07 4.61
5739 6508 8.294577 TGTTCATGATCAAGAAAACAAGATCAG 58.705 33.333 14.54 3.41 46.84 2.90
5768 6537 7.893824 GCTCTCATTATTGATAGCATCGTAAG 58.106 38.462 16.00 0.00 46.17 2.34
5792 6561 5.918608 TCATGGTCTAAGGAAGAACTATGC 58.081 41.667 0.00 0.00 42.96 3.14
5847 6710 8.553459 AAAACAAATATCAAAACCACACACAA 57.447 26.923 0.00 0.00 0.00 3.33
5900 6764 7.120726 GGACATAGTAGCAAAAACACAATACCT 59.879 37.037 0.00 0.00 0.00 3.08
6092 6957 9.685828 GGTCAATTAATTTGTAGTAAAGTTGCA 57.314 29.630 0.00 0.00 36.65 4.08
6172 7079 6.493449 TTCGAGAATCAATGCAATAACACA 57.507 33.333 0.00 0.00 33.17 3.72
6173 7080 9.110617 CATATTCGAGAATCAATGCAATAACAC 57.889 33.333 1.11 0.00 33.17 3.32
6174 7081 9.054922 TCATATTCGAGAATCAATGCAATAACA 57.945 29.630 1.11 0.00 33.17 2.41
6175 7082 9.539139 CTCATATTCGAGAATCAATGCAATAAC 57.461 33.333 1.11 0.00 34.79 1.89
6177 7084 9.662947 ATCTCATATTCGAGAATCAATGCAATA 57.337 29.630 1.11 0.00 44.92 1.90
6216 7125 7.598118 TGTTTATGTTTCTACACATGCAATTGG 59.402 33.333 7.72 0.00 37.93 3.16


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

AutoCloner maintained by Alex Coulton.