Multiple sequence alignment - TraesCS6A01G150700

Loading Multiple Alignment...

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 TraesCS6A01G150700 chr6A 100.000 3464 0 0 1 3464 134681028 134684491 0.000000e+00 6397.0
1 TraesCS6A01G150700 chr6A 98.698 845 11 0 2620 3464 268834741 268835585 0.000000e+00 1500.0
2 TraesCS6A01G150700 chr6A 84.130 1172 122 30 957 2086 91976535 91977684 0.000000e+00 1075.0
3 TraesCS6A01G150700 chr6A 99.244 397 3 0 2620 3016 268839583 268839979 0.000000e+00 717.0
4 TraesCS6A01G150700 chr6A 98.741 397 5 0 2620 3016 134688493 134688889 0.000000e+00 706.0
5 TraesCS6A01G150700 chr6A 92.308 182 14 0 2152 2333 91977823 91978004 3.430000e-65 259.0
6 TraesCS6A01G150700 chr6B 93.115 1525 76 14 604 2113 198948350 198949860 0.000000e+00 2207.0
7 TraesCS6A01G150700 chr6B 85.977 1141 117 24 962 2079 149730338 149731458 0.000000e+00 1181.0
8 TraesCS6A01G150700 chr6B 95.161 248 11 1 2117 2364 198950024 198950270 1.170000e-104 390.0
9 TraesCS6A01G150700 chr6B 91.758 182 15 0 2152 2333 149731568 149731749 1.600000e-63 254.0
10 TraesCS6A01G150700 chr6D 91.597 1083 51 11 577 1645 110165453 110166509 0.000000e+00 1459.0
11 TraesCS6A01G150700 chr6D 85.125 1163 120 32 958 2086 76010901 76012044 0.000000e+00 1140.0
12 TraesCS6A01G150700 chr6D 85.292 1149 118 26 961 2079 76050472 76051599 0.000000e+00 1138.0
13 TraesCS6A01G150700 chr6D 86.809 796 91 10 2672 3461 297407875 297408662 0.000000e+00 876.0
14 TraesCS6A01G150700 chr6D 90.406 542 52 0 36 577 97240306 97240847 0.000000e+00 713.0
15 TraesCS6A01G150700 chr6D 85.060 502 70 4 2117 2614 110213521 110214021 1.110000e-139 507.0
16 TraesCS6A01G150700 chr6D 85.987 471 38 15 1655 2118 110213031 110213480 2.420000e-131 479.0
17 TraesCS6A01G150700 chr6D 88.940 217 20 3 2117 2333 76051671 76051883 7.370000e-67 265.0
18 TraesCS6A01G150700 chr6D 100.000 35 0 0 1 35 424744155 424744121 8.020000e-07 65.8
19 TraesCS6A01G150700 chrUn 85.565 1150 118 33 961 2086 78169958 78168833 0.000000e+00 1160.0
20 TraesCS6A01G150700 chrUn 87.692 195 23 1 2139 2333 78168718 78168525 3.480000e-55 226.0
21 TraesCS6A01G150700 chr2B 87.827 879 67 35 2612 3464 367703760 367702896 0.000000e+00 994.0
22 TraesCS6A01G150700 chr2B 94.092 457 27 0 3006 3462 166754561 166754105 0.000000e+00 695.0
23 TraesCS6A01G150700 chr2B 77.881 859 135 42 2620 3462 788429903 788430722 1.870000e-132 483.0
24 TraesCS6A01G150700 chr2B 77.532 859 138 41 2620 3462 788405550 788406369 1.880000e-127 466.0
25 TraesCS6A01G150700 chr2B 100.000 35 0 0 1 35 370497195 370497229 8.020000e-07 65.8
26 TraesCS6A01G150700 chr2B 94.286 35 2 0 1 35 638975332 638975298 2.000000e-03 54.7
27 TraesCS6A01G150700 chr2A 87.900 876 65 35 2617 3464 729546924 729547786 0.000000e+00 992.0
28 TraesCS6A01G150700 chr2A 93.846 130 4 2 2620 2745 729551797 729551926 3.530000e-45 193.0
29 TraesCS6A01G150700 chr4B 87.830 871 67 34 2620 3464 25485227 25486084 0.000000e+00 985.0
30 TraesCS6A01G150700 chr4B 84.810 869 91 34 2620 3464 6567844 6568695 0.000000e+00 835.0
31 TraesCS6A01G150700 chr4B 82.576 660 83 24 2810 3461 668009803 668010438 1.400000e-153 553.0
32 TraesCS6A01G150700 chr7B 87.227 869 76 30 2620 3464 682252264 682253121 0.000000e+00 957.0
33 TraesCS6A01G150700 chr4A 86.521 868 81 30 2619 3464 718613102 718612249 0.000000e+00 922.0
34 TraesCS6A01G150700 chr4A 95.252 337 12 4 2691 3026 718796794 718796461 6.580000e-147 531.0
35 TraesCS6A01G150700 chr5D 86.614 762 84 14 2704 3461 434912222 434912969 0.000000e+00 826.0
36 TraesCS6A01G150700 chr5D 90.775 542 50 0 36 577 246019113 246019654 0.000000e+00 725.0
37 TraesCS6A01G150700 chr5D 90.239 543 50 2 36 577 525606283 525606823 0.000000e+00 706.0
38 TraesCS6A01G150700 chr5A 85.229 765 89 16 2705 3461 52496439 52497187 0.000000e+00 765.0
39 TraesCS6A01G150700 chr5A 86.765 204 22 3 1883 2084 391754666 391754466 4.500000e-54 222.0
40 TraesCS6A01G150700 chr1B 83.081 857 107 21 940 1764 3881770 3882620 0.000000e+00 745.0
41 TraesCS6A01G150700 chr1B 89.493 552 58 0 36 587 659526493 659525942 0.000000e+00 699.0
42 TraesCS6A01G150700 chr1B 81.149 801 96 32 988 1764 3907258 3908027 2.980000e-165 592.0
43 TraesCS6A01G150700 chr1B 81.854 507 67 13 1282 1764 4044337 4044842 1.500000e-108 403.0
44 TraesCS6A01G150700 chr1B 85.075 268 33 3 1821 2086 3908139 3908401 2.050000e-67 267.0
45 TraesCS6A01G150700 chr1B 85.130 269 30 5 1821 2086 4044955 4045216 2.050000e-67 267.0
46 TraesCS6A01G150700 chr2D 91.160 543 48 0 36 578 552731959 552731417 0.000000e+00 737.0
47 TraesCS6A01G150700 chr2D 90.590 542 51 0 36 577 593406697 593406156 0.000000e+00 719.0
48 TraesCS6A01G150700 chr3D 91.144 542 48 0 36 577 15261064 15260523 0.000000e+00 736.0
49 TraesCS6A01G150700 chr3D 90.642 545 49 2 36 580 104820861 104821403 0.000000e+00 723.0
50 TraesCS6A01G150700 chr7D 90.590 542 51 0 36 577 423695151 423694610 0.000000e+00 719.0
51 TraesCS6A01G150700 chr7D 78.462 780 138 24 2691 3461 173199906 173199148 1.870000e-132 483.0
52 TraesCS6A01G150700 chr3B 99.000 400 3 1 2619 3017 770301663 770302062 0.000000e+00 715.0
53 TraesCS6A01G150700 chr3B 82.675 658 90 18 2810 3464 54164320 54163684 2.330000e-156 562.0
54 TraesCS6A01G150700 chr3B 82.549 659 90 18 2810 3464 54088097 54087460 1.090000e-154 556.0
55 TraesCS6A01G150700 chr4D 86.480 392 46 6 1001 1390 439820577 439820191 1.150000e-114 424.0
56 TraesCS6A01G150700 chr4D 88.571 245 28 0 1514 1758 439819914 439819670 7.270000e-77 298.0
57 TraesCS6A01G150700 chr3A 85.176 425 50 8 1001 1423 9066642 9066229 1.150000e-114 424.0
58 TraesCS6A01G150700 chr7A 74.598 870 154 55 2619 3462 607608919 607609747 1.550000e-83 320.0
59 TraesCS6A01G150700 chr7A 100.000 33 0 0 1 33 215323597 215323629 1.040000e-05 62.1
60 TraesCS6A01G150700 chr1D 100.000 33 0 0 3 35 359676609 359676577 1.040000e-05 62.1
61 TraesCS6A01G150700 chr5B 100.000 31 0 0 3 33 133344347 133344317 1.340000e-04 58.4


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 TraesCS6A01G150700 chr6A 134681028 134684491 3463 False 6397.0 6397 100.0000 1 3464 1 chr6A.!!$F1 3463
1 TraesCS6A01G150700 chr6A 268834741 268839979 5238 False 1108.5 1500 98.9710 2620 3464 2 chr6A.!!$F4 844
2 TraesCS6A01G150700 chr6A 91976535 91978004 1469 False 667.0 1075 88.2190 957 2333 2 chr6A.!!$F3 1376
3 TraesCS6A01G150700 chr6B 198948350 198950270 1920 False 1298.5 2207 94.1380 604 2364 2 chr6B.!!$F2 1760
4 TraesCS6A01G150700 chr6B 149730338 149731749 1411 False 717.5 1181 88.8675 962 2333 2 chr6B.!!$F1 1371
5 TraesCS6A01G150700 chr6D 110165453 110166509 1056 False 1459.0 1459 91.5970 577 1645 1 chr6D.!!$F3 1068
6 TraesCS6A01G150700 chr6D 76010901 76012044 1143 False 1140.0 1140 85.1250 958 2086 1 chr6D.!!$F1 1128
7 TraesCS6A01G150700 chr6D 297407875 297408662 787 False 876.0 876 86.8090 2672 3461 1 chr6D.!!$F4 789
8 TraesCS6A01G150700 chr6D 97240306 97240847 541 False 713.0 713 90.4060 36 577 1 chr6D.!!$F2 541
9 TraesCS6A01G150700 chr6D 76050472 76051883 1411 False 701.5 1138 87.1160 961 2333 2 chr6D.!!$F5 1372
10 TraesCS6A01G150700 chr6D 110213031 110214021 990 False 493.0 507 85.5235 1655 2614 2 chr6D.!!$F6 959
11 TraesCS6A01G150700 chrUn 78168525 78169958 1433 True 693.0 1160 86.6285 961 2333 2 chrUn.!!$R1 1372
12 TraesCS6A01G150700 chr2B 367702896 367703760 864 True 994.0 994 87.8270 2612 3464 1 chr2B.!!$R2 852
13 TraesCS6A01G150700 chr2B 788429903 788430722 819 False 483.0 483 77.8810 2620 3462 1 chr2B.!!$F3 842
14 TraesCS6A01G150700 chr2B 788405550 788406369 819 False 466.0 466 77.5320 2620 3462 1 chr2B.!!$F2 842
15 TraesCS6A01G150700 chr2A 729546924 729547786 862 False 992.0 992 87.9000 2617 3464 1 chr2A.!!$F1 847
16 TraesCS6A01G150700 chr4B 25485227 25486084 857 False 985.0 985 87.8300 2620 3464 1 chr4B.!!$F2 844
17 TraesCS6A01G150700 chr4B 6567844 6568695 851 False 835.0 835 84.8100 2620 3464 1 chr4B.!!$F1 844
18 TraesCS6A01G150700 chr4B 668009803 668010438 635 False 553.0 553 82.5760 2810 3461 1 chr4B.!!$F3 651
19 TraesCS6A01G150700 chr7B 682252264 682253121 857 False 957.0 957 87.2270 2620 3464 1 chr7B.!!$F1 844
20 TraesCS6A01G150700 chr4A 718612249 718613102 853 True 922.0 922 86.5210 2619 3464 1 chr4A.!!$R1 845
21 TraesCS6A01G150700 chr5D 434912222 434912969 747 False 826.0 826 86.6140 2704 3461 1 chr5D.!!$F2 757
22 TraesCS6A01G150700 chr5D 246019113 246019654 541 False 725.0 725 90.7750 36 577 1 chr5D.!!$F1 541
23 TraesCS6A01G150700 chr5D 525606283 525606823 540 False 706.0 706 90.2390 36 577 1 chr5D.!!$F3 541
24 TraesCS6A01G150700 chr5A 52496439 52497187 748 False 765.0 765 85.2290 2705 3461 1 chr5A.!!$F1 756
25 TraesCS6A01G150700 chr1B 3881770 3882620 850 False 745.0 745 83.0810 940 1764 1 chr1B.!!$F1 824
26 TraesCS6A01G150700 chr1B 659525942 659526493 551 True 699.0 699 89.4930 36 587 1 chr1B.!!$R1 551
27 TraesCS6A01G150700 chr1B 3907258 3908401 1143 False 429.5 592 83.1120 988 2086 2 chr1B.!!$F2 1098
28 TraesCS6A01G150700 chr1B 4044337 4045216 879 False 335.0 403 83.4920 1282 2086 2 chr1B.!!$F3 804
29 TraesCS6A01G150700 chr2D 552731417 552731959 542 True 737.0 737 91.1600 36 578 1 chr2D.!!$R1 542
30 TraesCS6A01G150700 chr2D 593406156 593406697 541 True 719.0 719 90.5900 36 577 1 chr2D.!!$R2 541
31 TraesCS6A01G150700 chr3D 15260523 15261064 541 True 736.0 736 91.1440 36 577 1 chr3D.!!$R1 541
32 TraesCS6A01G150700 chr3D 104820861 104821403 542 False 723.0 723 90.6420 36 580 1 chr3D.!!$F1 544
33 TraesCS6A01G150700 chr7D 423694610 423695151 541 True 719.0 719 90.5900 36 577 1 chr7D.!!$R2 541
34 TraesCS6A01G150700 chr7D 173199148 173199906 758 True 483.0 483 78.4620 2691 3461 1 chr7D.!!$R1 770
35 TraesCS6A01G150700 chr3B 54163684 54164320 636 True 562.0 562 82.6750 2810 3464 1 chr3B.!!$R2 654
36 TraesCS6A01G150700 chr3B 54087460 54088097 637 True 556.0 556 82.5490 2810 3464 1 chr3B.!!$R1 654
37 TraesCS6A01G150700 chr4D 439819670 439820577 907 True 361.0 424 87.5255 1001 1758 2 chr4D.!!$R1 757
38 TraesCS6A01G150700 chr7A 607608919 607609747 828 False 320.0 320 74.5980 2619 3462 1 chr7A.!!$F2 843

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
907 942 0.109132 CCAATGCAACGGAAGAAGGC 60.109 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2590 3112 0.105401 GGGGAGAGGTAGAGGGAAGG 60.105 65.0 0.0 0.0 0.0 3.46 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
17 18 4.619227 ACGTTGGACCGTGGGCTG 62.619 66.667 0.00 0.00 40.08 4.85
18 19 4.619227 CGTTGGACCGTGGGCTGT 62.619 66.667 0.00 0.00 0.00 4.40
19 20 2.203294 GTTGGACCGTGGGCTGTT 60.203 61.111 0.00 0.00 0.00 3.16
20 21 2.112297 TTGGACCGTGGGCTGTTC 59.888 61.111 0.00 0.00 0.00 3.18
21 22 3.818121 TTGGACCGTGGGCTGTTCG 62.818 63.158 0.00 0.00 0.00 3.95
22 23 4.309950 GGACCGTGGGCTGTTCGT 62.310 66.667 0.00 0.00 0.00 3.85
23 24 3.041940 GACCGTGGGCTGTTCGTG 61.042 66.667 0.00 0.00 0.00 4.35
24 25 4.619227 ACCGTGGGCTGTTCGTGG 62.619 66.667 0.00 0.00 0.00 4.94
25 26 4.308458 CCGTGGGCTGTTCGTGGA 62.308 66.667 0.00 0.00 0.00 4.02
26 27 3.041940 CGTGGGCTGTTCGTGGAC 61.042 66.667 0.00 0.00 0.00 4.02
27 28 2.426023 GTGGGCTGTTCGTGGACT 59.574 61.111 0.00 0.00 0.00 3.85
28 29 1.668151 GTGGGCTGTTCGTGGACTC 60.668 63.158 0.00 0.00 0.00 3.36
29 30 2.432628 GGGCTGTTCGTGGACTCG 60.433 66.667 0.00 0.00 0.00 4.18
30 31 2.432628 GGCTGTTCGTGGACTCGG 60.433 66.667 0.00 0.00 0.00 4.63
31 32 2.338984 GCTGTTCGTGGACTCGGT 59.661 61.111 0.00 0.00 0.00 4.69
32 33 1.733399 GCTGTTCGTGGACTCGGTC 60.733 63.158 0.00 0.00 0.00 4.79
33 34 1.442184 CTGTTCGTGGACTCGGTCG 60.442 63.158 0.00 0.00 32.65 4.79
34 35 2.126417 CTGTTCGTGGACTCGGTCGT 62.126 60.000 0.00 0.00 32.65 4.34
86 88 1.068741 CAACCCTAGCCGTCATCTACC 59.931 57.143 0.00 0.00 0.00 3.18
101 105 4.163649 TCATCTACCGTTCCTCTCTCTGTA 59.836 45.833 0.00 0.00 0.00 2.74
154 158 1.366366 CACGGTTTGTCGGGAGAGT 59.634 57.895 0.00 0.00 41.26 3.24
214 218 5.144359 CGGAAGAACGACAATAAGGTTTTG 58.856 41.667 0.00 0.00 35.47 2.44
220 224 3.158676 CGACAATAAGGTTTTGGGGGAA 58.841 45.455 0.00 0.00 0.00 3.97
255 259 4.764771 TCCCGATCCGTCCCCGTT 62.765 66.667 0.00 0.00 0.00 4.44
283 287 1.276421 GCCTCTGCTTCCACTACTTCA 59.724 52.381 0.00 0.00 33.53 3.02
286 290 1.272490 TCTGCTTCCACTACTTCACCG 59.728 52.381 0.00 0.00 0.00 4.94
318 322 4.606071 GCTGATGACGAAGCCACT 57.394 55.556 0.00 0.00 33.12 4.00
337 341 3.008485 CACTAAGAAGAAGGCCTCAACCT 59.992 47.826 5.23 0.00 43.91 3.50
439 443 5.930837 TCATGTGATGGCCGTATATATGA 57.069 39.130 13.72 13.72 0.00 2.15
445 449 5.232202 GTGATGGCCGTATATATGATGTTCG 59.768 44.000 0.00 0.00 0.00 3.95
474 478 3.680642 TCGGTTCTATGTACTGTACGC 57.319 47.619 12.87 0.18 0.00 4.42
475 479 3.273434 TCGGTTCTATGTACTGTACGCT 58.727 45.455 12.87 5.90 0.00 5.07
501 505 5.303333 TCACATGCTTAGGTATCGGTATGAA 59.697 40.000 0.00 0.00 0.00 2.57
546 550 9.632638 ATGCTTACTGTTTATTCATGGATTAGT 57.367 29.630 0.00 0.00 0.00 2.24
562 566 7.519032 TGGATTAGTTTAGTGGAAAAAGTGG 57.481 36.000 0.00 0.00 0.00 4.00
600 604 1.274596 GTCCAATAGGTACGTGCACG 58.725 55.000 35.99 35.99 39.88 5.34
601 605 0.173935 TCCAATAGGTACGTGCACGG 59.826 55.000 39.21 23.04 38.93 4.94
616 621 0.595588 CACGGTGCAATTTGGCTACA 59.404 50.000 0.00 0.00 34.04 2.74
617 622 0.596082 ACGGTGCAATTTGGCTACAC 59.404 50.000 0.00 0.00 34.04 2.90
618 623 0.595588 CGGTGCAATTTGGCTACACA 59.404 50.000 0.00 0.00 32.89 3.72
717 722 5.614013 GCACTTTGGATTGTACTGTAACGAC 60.614 44.000 0.00 0.00 0.00 4.34
732 737 2.257371 GACGAGCACAGTACGCCA 59.743 61.111 0.00 0.00 0.00 5.69
739 744 0.882927 GCACAGTACGCCACCTTTCA 60.883 55.000 0.00 0.00 0.00 2.69
755 760 3.370846 CCTTTCATGGTCTGCTGGTGATA 60.371 47.826 0.00 0.00 0.00 2.15
756 761 2.988010 TCATGGTCTGCTGGTGATAC 57.012 50.000 0.00 0.00 0.00 2.24
757 762 2.187100 TCATGGTCTGCTGGTGATACA 58.813 47.619 0.00 0.00 0.00 2.29
758 763 2.093500 TCATGGTCTGCTGGTGATACAC 60.093 50.000 0.00 0.00 0.00 2.90
759 764 1.644509 TGGTCTGCTGGTGATACACT 58.355 50.000 0.00 0.00 34.40 3.55
760 765 2.815158 TGGTCTGCTGGTGATACACTA 58.185 47.619 0.00 0.00 34.40 2.74
761 766 2.496070 TGGTCTGCTGGTGATACACTAC 59.504 50.000 0.00 0.00 34.40 2.73
762 767 2.479730 GGTCTGCTGGTGATACACTACG 60.480 54.545 0.00 0.00 34.40 3.51
763 768 1.749063 TCTGCTGGTGATACACTACGG 59.251 52.381 0.00 0.00 34.40 4.02
764 769 1.476891 CTGCTGGTGATACACTACGGT 59.523 52.381 0.00 0.00 34.40 4.83
765 770 2.686405 CTGCTGGTGATACACTACGGTA 59.314 50.000 0.00 0.00 34.40 4.02
766 771 2.424601 TGCTGGTGATACACTACGGTAC 59.575 50.000 0.00 0.00 34.40 3.34
767 772 2.424601 GCTGGTGATACACTACGGTACA 59.575 50.000 0.00 0.00 34.40 2.90
768 773 3.733077 GCTGGTGATACACTACGGTACAC 60.733 52.174 0.00 0.00 34.40 2.90
769 774 2.754552 TGGTGATACACTACGGTACACC 59.245 50.000 13.52 13.52 41.11 4.16
770 775 2.754552 GGTGATACACTACGGTACACCA 59.245 50.000 14.85 0.00 40.80 4.17
771 776 3.428045 GGTGATACACTACGGTACACCAC 60.428 52.174 14.85 0.00 40.80 4.16
772 777 2.754552 TGATACACTACGGTACACCACC 59.245 50.000 0.00 0.00 44.75 4.61
791 823 4.148838 CACCACCTAACAGAAAAATGGGA 58.851 43.478 0.00 0.00 0.00 4.37
877 909 5.128335 AGTGTCTGATCTGACAGATAATGCA 59.872 40.000 29.31 10.57 46.09 3.96
907 942 0.109132 CCAATGCAACGGAAGAAGGC 60.109 55.000 0.00 0.00 0.00 4.35
951 988 4.838152 AGCAATCCACCGCGCGAT 62.838 61.111 34.63 13.37 0.00 4.58
1137 1180 2.185494 GTACGACCCGAGGAGCGAT 61.185 63.158 9.77 0.00 44.57 4.58
1316 1368 2.589494 AGGTGCAGCTCTACCTCAG 58.411 57.895 13.85 0.00 43.69 3.35
1695 1927 2.042930 ATGGAGGAGGTCACCCCC 59.957 66.667 0.00 0.00 0.00 5.40
1829 2148 2.043411 CCACATGCAAAACGAAACGAG 58.957 47.619 0.00 0.00 0.00 4.18
1966 2285 2.467566 TTACTCTTTCCCGTTCCTGC 57.532 50.000 0.00 0.00 0.00 4.85
2079 2403 2.743838 CGTCGGCATACCCATAAAGGTT 60.744 50.000 0.00 0.00 41.58 3.50
2087 2411 5.067283 GCATACCCATAAAGGTTCGTGAAAT 59.933 40.000 0.00 0.00 41.58 2.17
2088 2412 6.725246 CATACCCATAAAGGTTCGTGAAATC 58.275 40.000 0.00 0.00 41.58 2.17
2092 2416 6.887545 ACCCATAAAGGTTCGTGAAATCATAA 59.112 34.615 0.00 0.00 36.44 1.90
2101 2446 6.907212 GGTTCGTGAAATCATAAGCATTACAG 59.093 38.462 0.00 0.00 30.46 2.74
2102 2447 6.048073 TCGTGAAATCATAAGCATTACAGC 57.952 37.500 0.00 0.00 30.46 4.40
2113 2458 7.718314 TCATAAGCATTACAGCAGATCTTGATT 59.282 33.333 1.35 0.00 36.85 2.57
2149 2666 6.751514 ACAAATTAATCAATGCGTCTGGTA 57.248 33.333 0.00 0.00 0.00 3.25
2195 2713 2.830370 GGCTCAGGCGAAATGGGG 60.830 66.667 0.00 0.00 39.81 4.96
2371 2890 6.303839 ACAACAAATTTAGCAGACTCCCTAA 58.696 36.000 0.00 0.00 0.00 2.69
2400 2921 3.119316 GGATCGACTATGCATCCTACCTG 60.119 52.174 0.19 0.00 34.31 4.00
2401 2922 3.223674 TCGACTATGCATCCTACCTGA 57.776 47.619 0.19 0.00 0.00 3.86
2440 2961 7.012138 TGTCAGTCACTTATATTCTAGACCGTC 59.988 40.741 0.00 0.00 0.00 4.79
2445 2966 8.231837 GTCACTTATATTCTAGACCGTCTGATC 58.768 40.741 11.52 0.00 0.00 2.92
2451 2972 5.759506 TTCTAGACCGTCTGATCTTCATC 57.240 43.478 11.52 0.00 0.00 2.92
2452 2973 4.138290 TCTAGACCGTCTGATCTTCATCC 58.862 47.826 11.52 0.00 0.00 3.51
2455 2976 3.118956 AGACCGTCTGATCTTCATCCAAC 60.119 47.826 0.00 0.00 0.00 3.77
2457 2978 2.159240 CCGTCTGATCTTCATCCAACGA 60.159 50.000 0.00 0.00 37.80 3.85
2462 2983 3.588955 TGATCTTCATCCAACGACTGTG 58.411 45.455 0.00 0.00 0.00 3.66
2465 2986 3.390135 TCTTCATCCAACGACTGTGAAC 58.610 45.455 0.00 0.00 0.00 3.18
2470 2991 1.754803 TCCAACGACTGTGAACAGACT 59.245 47.619 17.11 0.00 46.59 3.24
2475 2997 3.703420 ACGACTGTGAACAGACTTACAC 58.297 45.455 17.11 0.00 46.59 2.90
2484 3006 6.102663 GTGAACAGACTTACACTGCTCATAT 58.897 40.000 0.00 0.00 40.73 1.78
2494 3016 4.511527 ACACTGCTCATATTCAACCTCTG 58.488 43.478 0.00 0.00 0.00 3.35
2505 3027 7.944554 TCATATTCAACCTCTGGTTTCTTCTTT 59.055 33.333 0.00 0.00 44.33 2.52
2510 3032 3.073209 ACCTCTGGTTTCTTCTTTCTCCC 59.927 47.826 0.00 0.00 27.29 4.30
2511 3033 3.330267 CTCTGGTTTCTTCTTTCTCCCG 58.670 50.000 0.00 0.00 0.00 5.14
2519 3041 0.245539 TTCTTTCTCCCGTGTAGCCG 59.754 55.000 0.00 0.00 0.00 5.52
2520 3042 0.896940 TCTTTCTCCCGTGTAGCCGT 60.897 55.000 0.00 0.00 0.00 5.68
2522 3044 1.180456 TTTCTCCCGTGTAGCCGTCA 61.180 55.000 0.00 0.00 0.00 4.35
2525 3047 4.814294 CCCGTGTAGCCGTCAGCC 62.814 72.222 0.00 0.00 45.47 4.85
2569 3091 3.087253 CCCCATGGCCGGTGTCTA 61.087 66.667 6.09 0.00 0.00 2.59
2572 3094 2.586079 CATGGCCGGTGTCTAGCG 60.586 66.667 1.90 0.00 46.68 4.26
2608 3130 0.105401 CCCTTCCCTCTACCTCTCCC 60.105 65.000 0.00 0.00 0.00 4.30
2614 3136 2.043248 TCTACCTCTCCCCACCGC 60.043 66.667 0.00 0.00 0.00 5.68
2615 3137 3.155167 CTACCTCTCCCCACCGCC 61.155 72.222 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.308458 CGAACAGCCCACGGTCCA 62.308 66.667 0.00 0.00 0.00 4.02
6 7 3.041940 CACGAACAGCCCACGGTC 61.042 66.667 0.00 0.00 0.00 4.79
7 8 4.619227 CCACGAACAGCCCACGGT 62.619 66.667 0.00 0.00 0.00 4.83
8 9 4.308458 TCCACGAACAGCCCACGG 62.308 66.667 0.00 0.00 0.00 4.94
9 10 3.041940 GTCCACGAACAGCCCACG 61.042 66.667 0.00 0.00 0.00 4.94
10 11 1.668151 GAGTCCACGAACAGCCCAC 60.668 63.158 0.00 0.00 0.00 4.61
11 12 2.741092 GAGTCCACGAACAGCCCA 59.259 61.111 0.00 0.00 0.00 5.36
12 13 2.432628 CGAGTCCACGAACAGCCC 60.433 66.667 0.00 0.00 35.09 5.19
13 14 2.432628 CCGAGTCCACGAACAGCC 60.433 66.667 0.00 0.00 35.09 4.85
14 15 1.733399 GACCGAGTCCACGAACAGC 60.733 63.158 0.00 0.00 35.09 4.40
15 16 1.442184 CGACCGAGTCCACGAACAG 60.442 63.158 0.00 0.00 35.09 3.16
16 17 2.121564 GACGACCGAGTCCACGAACA 62.122 60.000 0.00 0.00 35.22 3.18
17 18 1.441682 GACGACCGAGTCCACGAAC 60.442 63.158 0.00 0.00 35.22 3.95
18 19 2.949106 GACGACCGAGTCCACGAA 59.051 61.111 0.00 0.00 35.22 3.85
24 25 0.731994 GAGTTAGGGACGACCGAGTC 59.268 60.000 0.00 0.00 46.96 3.36
25 26 0.037303 TGAGTTAGGGACGACCGAGT 59.963 55.000 0.00 0.00 46.96 4.18
26 27 0.733729 CTGAGTTAGGGACGACCGAG 59.266 60.000 0.00 0.00 46.96 4.63
27 28 0.037303 ACTGAGTTAGGGACGACCGA 59.963 55.000 0.00 0.00 46.96 4.69
28 29 0.886563 AACTGAGTTAGGGACGACCG 59.113 55.000 0.00 0.00 46.96 4.79
29 30 1.891150 TGAACTGAGTTAGGGACGACC 59.109 52.381 0.00 0.00 40.67 4.79
30 31 2.557490 AGTGAACTGAGTTAGGGACGAC 59.443 50.000 0.00 0.00 0.00 4.34
31 32 2.818432 GAGTGAACTGAGTTAGGGACGA 59.182 50.000 0.00 0.00 0.00 4.20
32 33 2.557056 TGAGTGAACTGAGTTAGGGACG 59.443 50.000 0.00 0.00 0.00 4.79
33 34 3.574826 AGTGAGTGAACTGAGTTAGGGAC 59.425 47.826 0.00 0.00 0.00 4.46
34 35 3.827302 GAGTGAGTGAACTGAGTTAGGGA 59.173 47.826 0.00 0.00 0.00 4.20
86 88 2.088423 AGCAGTACAGAGAGAGGAACG 58.912 52.381 0.00 0.00 0.00 3.95
101 105 4.162690 GGGATCGCCGGAAGCAGT 62.163 66.667 5.05 0.00 44.04 4.40
143 147 1.681327 GGCACCTACTCTCCCGACA 60.681 63.158 0.00 0.00 0.00 4.35
283 287 2.501128 CATGGAGTCGATGCCGGT 59.499 61.111 1.90 0.00 36.24 5.28
286 290 1.890979 CAGCCATGGAGTCGATGCC 60.891 63.158 18.40 0.00 0.00 4.40
318 322 4.384208 GCATAGGTTGAGGCCTTCTTCTTA 60.384 45.833 6.77 0.00 39.94 2.10
387 391 8.589338 AGCAAATAGAGGATAAACGAGTCATAT 58.411 33.333 0.00 0.00 0.00 1.78
399 403 5.985530 CACATGAACGAGCAAATAGAGGATA 59.014 40.000 0.00 0.00 0.00 2.59
404 408 4.571984 CCATCACATGAACGAGCAAATAGA 59.428 41.667 0.00 0.00 0.00 1.98
439 443 4.817517 AGAACCGAAACATCTACGAACAT 58.182 39.130 0.00 0.00 0.00 2.71
445 449 7.256286 ACAGTACATAGAACCGAAACATCTAC 58.744 38.462 0.00 0.00 0.00 2.59
474 478 3.319405 ACCGATACCTAAGCATGTGAGAG 59.681 47.826 0.00 0.00 0.00 3.20
475 479 3.296854 ACCGATACCTAAGCATGTGAGA 58.703 45.455 0.00 0.00 0.00 3.27
501 505 5.070001 AGCATGGTAAATACGGTATGCATT 58.930 37.500 3.54 1.78 39.23 3.56
517 521 6.186957 TCCATGAATAAACAGTAAGCATGGT 58.813 36.000 15.93 0.00 46.91 3.55
552 556 9.758651 ACTGTTGAAAATATTACCACTTTTTCC 57.241 29.630 0.00 0.00 37.30 3.13
571 575 4.400251 CGTACCTATTGGACCTACTGTTGA 59.600 45.833 0.00 0.00 37.04 3.18
581 585 1.274596 CGTGCACGTACCTATTGGAC 58.725 55.000 30.50 0.00 34.14 4.02
600 604 1.665735 CGTGTGTAGCCAAATTGCACC 60.666 52.381 0.00 0.00 31.22 5.01
601 605 1.265635 TCGTGTGTAGCCAAATTGCAC 59.734 47.619 0.00 0.00 0.00 4.57
670 675 8.857216 GTGCAATAATTGAGATCTTTCAAACAG 58.143 33.333 0.00 0.00 40.21 3.16
717 722 2.765250 AAGGTGGCGTACTGTGCTCG 62.765 60.000 0.00 0.00 0.00 5.03
732 737 0.773644 ACCAGCAGACCATGAAAGGT 59.226 50.000 0.00 0.00 46.82 3.50
739 744 2.191400 AGTGTATCACCAGCAGACCAT 58.809 47.619 0.00 0.00 34.49 3.55
763 768 3.756933 TTCTGTTAGGTGGTGGTGTAC 57.243 47.619 0.00 0.00 0.00 2.90
764 769 4.774660 TTTTCTGTTAGGTGGTGGTGTA 57.225 40.909 0.00 0.00 0.00 2.90
765 770 3.655615 TTTTCTGTTAGGTGGTGGTGT 57.344 42.857 0.00 0.00 0.00 4.16
766 771 4.261994 CCATTTTTCTGTTAGGTGGTGGTG 60.262 45.833 0.00 0.00 0.00 4.17
767 772 3.895041 CCATTTTTCTGTTAGGTGGTGGT 59.105 43.478 0.00 0.00 0.00 4.16
768 773 3.258123 CCCATTTTTCTGTTAGGTGGTGG 59.742 47.826 0.00 0.00 0.00 4.61
769 774 4.148838 TCCCATTTTTCTGTTAGGTGGTG 58.851 43.478 0.00 0.00 0.00 4.17
770 775 4.105697 TCTCCCATTTTTCTGTTAGGTGGT 59.894 41.667 0.00 0.00 0.00 4.16
771 776 4.459337 GTCTCCCATTTTTCTGTTAGGTGG 59.541 45.833 0.00 0.00 0.00 4.61
772 777 5.070001 TGTCTCCCATTTTTCTGTTAGGTG 58.930 41.667 0.00 0.00 0.00 4.00
773 778 5.319043 TGTCTCCCATTTTTCTGTTAGGT 57.681 39.130 0.00 0.00 0.00 3.08
774 779 5.358160 GGATGTCTCCCATTTTTCTGTTAGG 59.642 44.000 0.00 0.00 35.28 2.69
775 780 6.442513 GGATGTCTCCCATTTTTCTGTTAG 57.557 41.667 0.00 0.00 35.28 2.34
791 823 1.069823 GCATGAGTCGATGGGATGTCT 59.930 52.381 0.00 0.00 0.00 3.41
877 909 3.367292 CCGTTGCATTGGCTCTTTTATGT 60.367 43.478 0.00 0.00 41.91 2.29
907 942 3.699484 CTCCGATCGCGCATGCTG 61.699 66.667 17.13 10.56 39.65 4.41
951 988 1.553248 ACCATGTCGATTCTCGGGAAA 59.447 47.619 0.00 0.00 40.88 3.13
1003 1046 0.596577 GCTCCGATCACGCATACCTA 59.403 55.000 0.00 0.00 38.29 3.08
1208 1254 3.035173 TTCTCCCTGGCGCTGATGG 62.035 63.158 7.64 3.18 0.00 3.51
1316 1368 4.719369 ACGCGTCGCAGAAGTCCC 62.719 66.667 18.75 0.00 39.69 4.46
1473 1579 1.805945 CTGCGAGTAGTGGCCGTTC 60.806 63.158 0.00 0.00 0.00 3.95
1798 2104 3.001902 GCATGTGGAGACCGACCGA 62.002 63.158 0.00 0.00 0.00 4.69
1829 2148 1.084289 GCTTTCCATGTACGGGTCAC 58.916 55.000 3.59 0.00 0.00 3.67
2079 2403 5.584251 TGCTGTAATGCTTATGATTTCACGA 59.416 36.000 0.00 0.00 0.00 4.35
2087 2411 6.585416 TCAAGATCTGCTGTAATGCTTATGA 58.415 36.000 0.00 0.00 0.00 2.15
2088 2412 6.856135 TCAAGATCTGCTGTAATGCTTATG 57.144 37.500 0.00 0.00 0.00 1.90
2092 2416 7.330454 CGTATAATCAAGATCTGCTGTAATGCT 59.670 37.037 0.00 0.00 0.00 3.79
2101 2446 7.709269 TTTGGTACGTATAATCAAGATCTGC 57.291 36.000 0.00 0.00 0.00 4.26
2102 2447 9.093970 TGTTTTGGTACGTATAATCAAGATCTG 57.906 33.333 0.00 0.00 0.00 2.90
2166 2684 1.153745 CTGAGCCTCGAAGAACCGG 60.154 63.158 0.00 0.00 34.09 5.28
2167 2685 1.153745 CCTGAGCCTCGAAGAACCG 60.154 63.158 0.00 0.00 34.09 4.44
2354 2873 6.418946 CCTCTTTTTAGGGAGTCTGCTAAAT 58.581 40.000 0.00 0.00 32.55 1.40
2371 2890 4.503991 GGATGCATAGTCGATCCCTCTTTT 60.504 45.833 0.00 0.00 31.01 2.27
2381 2902 3.223674 TCAGGTAGGATGCATAGTCGA 57.776 47.619 0.00 0.00 0.00 4.20
2407 2928 7.432869 AGAATATAAGTGACTGACAGATGCTC 58.567 38.462 10.08 0.00 0.00 4.26
2409 2930 8.572185 TCTAGAATATAAGTGACTGACAGATGC 58.428 37.037 10.08 0.00 0.00 3.91
2411 2932 9.073475 GGTCTAGAATATAAGTGACTGACAGAT 57.927 37.037 10.08 0.00 0.00 2.90
2415 2936 7.227116 AGACGGTCTAGAATATAAGTGACTGAC 59.773 40.741 9.33 0.00 35.51 3.51
2440 2961 3.615937 CACAGTCGTTGGATGAAGATCAG 59.384 47.826 0.00 0.00 0.00 2.90
2445 2966 3.130633 TGTTCACAGTCGTTGGATGAAG 58.869 45.455 0.00 0.00 30.25 3.02
2451 2972 2.225068 AGTCTGTTCACAGTCGTTGG 57.775 50.000 6.84 0.00 44.12 3.77
2452 2973 4.026804 GTGTAAGTCTGTTCACAGTCGTTG 60.027 45.833 6.84 0.00 44.12 4.10
2455 2976 3.731216 CAGTGTAAGTCTGTTCACAGTCG 59.269 47.826 6.84 0.00 44.12 4.18
2457 2978 3.133003 AGCAGTGTAAGTCTGTTCACAGT 59.867 43.478 6.84 0.00 44.12 3.55
2462 2983 6.813649 TGAATATGAGCAGTGTAAGTCTGTTC 59.186 38.462 0.00 0.00 41.31 3.18
2465 2986 6.036517 GGTTGAATATGAGCAGTGTAAGTCTG 59.963 42.308 0.00 0.00 36.18 3.51
2470 2991 6.108687 CAGAGGTTGAATATGAGCAGTGTAA 58.891 40.000 0.00 0.00 0.00 2.41
2475 2997 4.148128 ACCAGAGGTTGAATATGAGCAG 57.852 45.455 0.00 0.00 27.29 4.24
2484 3006 5.755849 AGAAAGAAGAAACCAGAGGTTGAA 58.244 37.500 1.62 0.00 46.20 2.69
2494 3016 2.847441 ACACGGGAGAAAGAAGAAACC 58.153 47.619 0.00 0.00 0.00 3.27
2505 3027 2.034532 TGACGGCTACACGGGAGA 59.965 61.111 0.00 0.00 38.39 3.71
2510 3032 2.507102 CTGGCTGACGGCTACACG 60.507 66.667 6.16 0.00 41.46 4.49
2556 3078 4.530857 GCGCTAGACACCGGCCAT 62.531 66.667 0.00 0.00 0.00 4.40
2584 3106 2.042230 GTAGAGGGAAGGGCGGGA 60.042 66.667 0.00 0.00 0.00 5.14
2590 3112 0.105401 GGGGAGAGGTAGAGGGAAGG 60.105 65.000 0.00 0.00 0.00 3.46
2592 3114 0.338814 GTGGGGAGAGGTAGAGGGAA 59.661 60.000 0.00 0.00 0.00 3.97
2614 3136 1.665679 CTTAGCATGGCTAACACACGG 59.334 52.381 6.58 0.00 44.75 4.94
2615 3137 1.062587 GCTTAGCATGGCTAACACACG 59.937 52.381 6.58 0.00 44.75 4.49
2616 3138 2.352960 GAGCTTAGCATGGCTAACACAC 59.647 50.000 7.07 0.00 44.75 3.82
2617 3139 2.027285 TGAGCTTAGCATGGCTAACACA 60.027 45.455 7.07 6.59 44.75 3.72
3237 3840 2.595558 TGAGCATCATGGACGTCCT 58.404 52.632 33.39 17.38 42.56 3.85


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

AutoCloner maintained by Alex Coulton.