Multiple sequence alignment - TraesCS3D01G507500

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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 TraesCS3D01G507500 chr3D 100.000 7842 0 0 1 7842 594004839 593996998 0.000000e+00 14482.0
1 TraesCS3D01G507500 chr3D 92.066 2735 139 44 889 3582 594190770 594193467 0.000000e+00 3777.0
2 TraesCS3D01G507500 chr3D 89.688 2880 210 38 3630 6461 594147362 594150202 0.000000e+00 3592.0
3 TraesCS3D01G507500 chr3D 89.729 1879 125 25 1748 3576 594489723 594487863 0.000000e+00 2338.0
4 TraesCS3D01G507500 chr3D 87.415 1478 110 36 897 2343 594144518 594145950 0.000000e+00 1629.0
5 TraesCS3D01G507500 chr3D 89.869 1293 96 17 3730 4998 594487491 594486210 0.000000e+00 1629.0
6 TraesCS3D01G507500 chr3D 97.851 884 18 1 6959 7842 9695127 9694245 0.000000e+00 1526.0
7 TraesCS3D01G507500 chr3D 97.851 884 17 2 6959 7842 505471102 505470221 0.000000e+00 1526.0
8 TraesCS3D01G507500 chr3D 90.564 1081 73 15 3630 4693 594193773 594194841 0.000000e+00 1404.0
9 TraesCS3D01G507500 chr3D 94.058 892 46 4 5608 6492 594195984 594196875 0.000000e+00 1347.0
10 TraesCS3D01G507500 chr3D 88.712 815 57 15 2353 3133 594146085 594146898 0.000000e+00 963.0
11 TraesCS3D01G507500 chr3D 87.883 685 78 5 106 789 594189670 594190350 0.000000e+00 800.0
12 TraesCS3D01G507500 chr3D 84.390 852 70 28 887 1703 594490551 594489728 0.000000e+00 778.0
13 TraesCS3D01G507500 chr3D 91.557 533 36 5 5044 5576 594195463 594195986 0.000000e+00 726.0
14 TraesCS3D01G507500 chr3D 85.213 656 86 9 175 826 594491825 594491177 0.000000e+00 664.0
15 TraesCS3D01G507500 chr3D 84.962 399 39 15 6570 6960 594196997 594197382 1.230000e-102 385.0
16 TraesCS3D01G507500 chr7A 95.133 6575 186 52 419 6964 92385402 92391871 0.000000e+00 10246.0
17 TraesCS3D01G507500 chr7A 92.758 359 20 2 1 359 92384693 92385045 1.510000e-141 514.0
18 TraesCS3D01G507500 chr3A 96.927 4849 97 18 1754 6576 724881599 724876777 0.000000e+00 8082.0
19 TraesCS3D01G507500 chr3A 92.668 832 41 14 891 1718 724882418 724881603 0.000000e+00 1181.0
20 TraesCS3D01G507500 chr3A 89.313 917 75 9 5349 6263 725069391 725068496 0.000000e+00 1129.0
21 TraesCS3D01G507500 chr3A 89.173 822 48 10 4 823 724883225 724882443 0.000000e+00 987.0
22 TraesCS3D01G507500 chr3A 88.830 761 44 12 4 762 724925061 724924340 0.000000e+00 896.0
23 TraesCS3D01G507500 chr3A 91.143 350 14 3 4994 5342 725069919 725069586 7.170000e-125 459.0
24 TraesCS3D01G507500 chr3A 85.971 278 22 13 6575 6849 724876515 724876252 1.670000e-71 281.0
25 TraesCS3D01G507500 chr3B 91.670 2761 139 40 890 3581 797446477 797449215 0.000000e+00 3740.0
26 TraesCS3D01G507500 chr3B 90.083 2773 130 50 891 3579 797751371 797748660 0.000000e+00 3463.0
27 TraesCS3D01G507500 chr3B 88.239 1726 136 26 3889 5576 797449892 797451588 0.000000e+00 2001.0
28 TraesCS3D01G507500 chr3B 91.680 1238 66 11 1829 3039 797129322 797130549 0.000000e+00 1681.0
29 TraesCS3D01G507500 chr3B 88.160 1402 116 24 3630 4998 797748342 797746958 0.000000e+00 1624.0
30 TraesCS3D01G507500 chr3B 88.906 1271 93 13 4994 6251 797728403 797727168 0.000000e+00 1522.0
31 TraesCS3D01G507500 chr3B 86.522 831 98 10 1 823 797444905 797445729 0.000000e+00 902.0
32 TraesCS3D01G507500 chr3B 88.400 750 42 16 6214 6945 797452056 797452778 0.000000e+00 861.0
33 TraesCS3D01G507500 chr3B 85.433 762 68 25 840 1583 797128593 797129329 0.000000e+00 752.0
34 TraesCS3D01G507500 chr3B 83.755 751 78 21 112 823 797752141 797751396 0.000000e+00 671.0
35 TraesCS3D01G507500 chr3B 91.845 466 33 4 5606 6067 797451584 797452048 0.000000e+00 645.0
36 TraesCS3D01G507500 chr3B 87.879 231 20 6 3630 3852 797449538 797449768 1.680000e-66 265.0
37 TraesCS3D01G507500 chr3B 83.026 271 41 3 6263 6528 797726047 797725777 2.830000e-59 241.0
38 TraesCS3D01G507500 chr3B 82.456 171 13 7 3225 3389 797130558 797130717 4.940000e-27 134.0
39 TraesCS3D01G507500 chrUn 89.744 1794 119 22 1832 3576 45794550 45792773 0.000000e+00 2233.0
40 TraesCS3D01G507500 chrUn 89.869 1293 96 17 3730 4998 45792401 45791120 0.000000e+00 1629.0
41 TraesCS3D01G507500 chrUn 97.686 389 9 0 2315 2703 480171108 480171496 0.000000e+00 669.0
42 TraesCS3D01G507500 chr7D 97.964 884 18 0 6959 7842 568588512 568587629 0.000000e+00 1533.0
43 TraesCS3D01G507500 chr5D 97.964 884 16 1 6959 7842 90204228 90205109 0.000000e+00 1531.0
44 TraesCS3D01G507500 chr5D 97.740 885 19 1 6959 7842 138166404 138167288 0.000000e+00 1522.0
45 TraesCS3D01G507500 chr5D 82.883 111 15 4 591 700 520912144 520912251 6.480000e-16 97.1
46 TraesCS3D01G507500 chr6D 97.961 883 16 2 6959 7841 142009813 142010693 0.000000e+00 1530.0
47 TraesCS3D01G507500 chr6D 97.851 884 16 1 6959 7842 101032949 101032069 0.000000e+00 1524.0
48 TraesCS3D01G507500 chr4D 97.738 884 19 1 6959 7842 11595511 11594629 0.000000e+00 1520.0
49 TraesCS3D01G507500 chr4D 97.738 884 19 1 6959 7842 289316199 289315317 0.000000e+00 1520.0
50 TraesCS3D01G507500 chr2A 79.429 350 48 11 6581 6930 526303826 526304151 7.920000e-55 226.0
51 TraesCS3D01G507500 chr2A 94.074 135 7 1 5490 5624 526302575 526302708 3.710000e-48 204.0
52 TraesCS3D01G507500 chr2A 90.226 133 13 0 5285 5417 526302435 526302567 2.910000e-39 174.0
53 TraesCS3D01G507500 chr1A 79.592 98 10 6 533 622 497272796 497272701 2.360000e-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 TraesCS3D01G507500 chr3D 593996998 594004839 7841 True 14482.000000 14482 100.000000 1 7842 1 chr3D.!!$R3 7841
1 TraesCS3D01G507500 chr3D 594144518 594150202 5684 False 2061.333333 3592 88.605000 897 6461 3 chr3D.!!$F1 5564
2 TraesCS3D01G507500 chr3D 9694245 9695127 882 True 1526.000000 1526 97.851000 6959 7842 1 chr3D.!!$R1 883
3 TraesCS3D01G507500 chr3D 505470221 505471102 881 True 1526.000000 1526 97.851000 6959 7842 1 chr3D.!!$R2 883
4 TraesCS3D01G507500 chr3D 594189670 594197382 7712 False 1406.500000 3777 90.181667 106 6960 6 chr3D.!!$F2 6854
5 TraesCS3D01G507500 chr3D 594486210 594491825 5615 True 1352.250000 2338 87.300250 175 4998 4 chr3D.!!$R4 4823
6 TraesCS3D01G507500 chr7A 92384693 92391871 7178 False 5380.000000 10246 93.945500 1 6964 2 chr7A.!!$F1 6963
7 TraesCS3D01G507500 chr3A 724876252 724883225 6973 True 2632.750000 8082 91.184750 4 6849 4 chr3A.!!$R2 6845
8 TraesCS3D01G507500 chr3A 724924340 724925061 721 True 896.000000 896 88.830000 4 762 1 chr3A.!!$R1 758
9 TraesCS3D01G507500 chr3A 725068496 725069919 1423 True 794.000000 1129 90.228000 4994 6263 2 chr3A.!!$R3 1269
10 TraesCS3D01G507500 chr3B 797746958 797752141 5183 True 1919.333333 3463 87.332667 112 4998 3 chr3B.!!$R2 4886
11 TraesCS3D01G507500 chr3B 797444905 797452778 7873 False 1402.333333 3740 89.092500 1 6945 6 chr3B.!!$F2 6944
12 TraesCS3D01G507500 chr3B 797725777 797728403 2626 True 881.500000 1522 85.966000 4994 6528 2 chr3B.!!$R1 1534
13 TraesCS3D01G507500 chr3B 797128593 797130717 2124 False 855.666667 1681 86.523000 840 3389 3 chr3B.!!$F1 2549
14 TraesCS3D01G507500 chrUn 45791120 45794550 3430 True 1931.000000 2233 89.806500 1832 4998 2 chrUn.!!$R1 3166
15 TraesCS3D01G507500 chr7D 568587629 568588512 883 True 1533.000000 1533 97.964000 6959 7842 1 chr7D.!!$R1 883
16 TraesCS3D01G507500 chr5D 90204228 90205109 881 False 1531.000000 1531 97.964000 6959 7842 1 chr5D.!!$F1 883
17 TraesCS3D01G507500 chr5D 138166404 138167288 884 False 1522.000000 1522 97.740000 6959 7842 1 chr5D.!!$F2 883
18 TraesCS3D01G507500 chr6D 142009813 142010693 880 False 1530.000000 1530 97.961000 6959 7841 1 chr6D.!!$F1 882
19 TraesCS3D01G507500 chr6D 101032069 101032949 880 True 1524.000000 1524 97.851000 6959 7842 1 chr6D.!!$R1 883
20 TraesCS3D01G507500 chr4D 11594629 11595511 882 True 1520.000000 1520 97.738000 6959 7842 1 chr4D.!!$R1 883
21 TraesCS3D01G507500 chr4D 289315317 289316199 882 True 1520.000000 1520 97.738000 6959 7842 1 chr4D.!!$R2 883
22 TraesCS3D01G507500 chr2A 526302435 526304151 1716 False 201.333333 226 87.909667 5285 6930 3 chr2A.!!$F1 1645

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
402 412 0.038310 CCAGACACCTTTTCCTCCCC 59.962 60.000 0.00 0.0 0.00 4.81 F
1270 2739 0.106868 CTAAACCCCGGACCCAATCC 60.107 60.000 0.73 0.0 45.20 3.01 F
2765 4465 0.394565 AGAGTAATCTGGCCGCATCC 59.605 55.000 0.00 0.0 0.00 3.51 F
3391 5132 0.320050 TATGGTGCGACAGTTGCTGA 59.680 50.000 14.20 0.0 35.18 4.26 F
3817 5984 2.044758 ACACGAAAGGACAAGGGTACT 58.955 47.619 0.00 0.0 41.07 2.73 F
4369 6649 3.477530 AGTGCTGGACCTTTTTCTACAC 58.522 45.455 0.00 0.0 0.00 2.90 F
5372 8243 3.646946 TGATTCATGTAGCATCGCTCTC 58.353 45.455 0.00 0.0 40.44 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 3112 0.613853 AGTACCCTGCAGACGCCTAA 60.614 55.000 17.39 0.00 37.32 2.69 R
3056 4781 0.602638 TGACATCCACGTGTTCTGGC 60.603 55.000 15.65 11.16 31.16 4.85 R
3817 5984 0.038251 CAGTAGGCGTGCTGACTTCA 60.038 55.000 18.22 0.00 38.63 3.02 R
4554 6843 4.716784 TGAGCTCACCAGGATGTAAGTTAT 59.283 41.667 13.74 0.00 0.00 1.89 R
5624 8495 4.889409 TCAGCAGGGAATGGATAATCAAAC 59.111 41.667 0.00 0.00 0.00 2.93 R
6025 8902 1.148157 CGTTATCAGCCTGTCCAGCG 61.148 60.000 0.00 0.00 34.64 5.18 R
7226 12219 0.250684 ACACATCGGATGGTGTTGCA 60.251 50.000 21.19 0.00 45.39 4.08 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
65 66 2.859165 ACGTGTCCCATTGATGAACT 57.141 45.000 0.00 0.00 0.00 3.01
67 68 1.739466 CGTGTCCCATTGATGAACTGG 59.261 52.381 0.00 0.00 0.00 4.00
124 132 1.001406 GAGAGGCGATGTGATAAGGGG 59.999 57.143 0.00 0.00 0.00 4.79
126 134 1.056700 AGGCGATGTGATAAGGGGCT 61.057 55.000 0.00 0.00 0.00 5.19
151 159 1.008424 CCGGGACATCATCGACGAG 60.008 63.158 3.01 0.00 32.01 4.18
169 177 2.543031 CGAGTGGTTGAGTTTCGACTCA 60.543 50.000 5.21 5.21 44.15 3.41
284 292 3.948473 TGTTTGAGGGAACGTTTTCATGA 59.052 39.130 0.46 0.00 32.80 3.07
368 376 6.959639 TTTGTTAAACCTCAGCTTCTTGAT 57.040 33.333 0.00 0.00 0.00 2.57
369 377 6.959639 TTGTTAAACCTCAGCTTCTTGATT 57.040 33.333 0.00 0.00 0.00 2.57
391 399 0.820871 TTTTGTTGGCACCAGACACC 59.179 50.000 0.00 0.00 27.28 4.16
399 409 1.239347 GCACCAGACACCTTTTCCTC 58.761 55.000 0.00 0.00 0.00 3.71
402 412 0.038310 CCAGACACCTTTTCCTCCCC 59.962 60.000 0.00 0.00 0.00 4.81
403 413 0.771127 CAGACACCTTTTCCTCCCCA 59.229 55.000 0.00 0.00 0.00 4.96
407 418 1.388217 ACCTTTTCCTCCCCACCCA 60.388 57.895 0.00 0.00 0.00 4.51
425 730 2.140792 AAGCGCGATATGGGGAGGT 61.141 57.895 12.10 0.00 0.00 3.85
428 733 2.265904 CGCGATATGGGGAGGTCGA 61.266 63.158 0.00 0.00 36.25 4.20
547 852 5.136392 ACCTCACTATCTATCTTAGGGGTGT 59.864 44.000 0.00 0.00 0.00 4.16
549 854 5.394738 TCACTATCTATCTTAGGGGTGTGG 58.605 45.833 0.00 0.00 0.00 4.17
589 901 1.640428 ATTGTTCATCGATGCGACGT 58.360 45.000 20.81 10.92 39.18 4.34
626 938 4.980805 GGTGGCCAGCAACGACGA 62.981 66.667 29.70 0.00 0.00 4.20
636 980 0.452184 GCAACGACGATGGAGAGAGA 59.548 55.000 0.00 0.00 0.00 3.10
964 2389 1.005556 CCCCATTCCCCACCTCCTA 59.994 63.158 0.00 0.00 0.00 2.94
1270 2739 0.106868 CTAAACCCCGGACCCAATCC 60.107 60.000 0.73 0.00 45.20 3.01
1381 2859 5.983720 TGATTACGAGCTGTTAATCCTAAGC 59.016 40.000 16.25 0.00 35.86 3.09
1471 2953 0.534203 TGTTTGTTCCGACTCAGGCC 60.534 55.000 0.00 0.00 0.00 5.19
1620 3103 4.830046 TGGGCTTGTTTTGTGCTATAAAGA 59.170 37.500 0.00 0.00 0.00 2.52
1629 3112 1.141858 GTGCTATAAAGAGGGCAGGCT 59.858 52.381 0.00 0.00 35.29 4.58
1649 3132 0.613853 TAGGCGTCTGCAGGGTACTT 60.614 55.000 15.13 0.43 45.35 2.24
1650 3133 1.741770 GGCGTCTGCAGGGTACTTG 60.742 63.158 15.13 0.00 45.35 3.16
1766 3265 4.515191 TGACCATCACTTTTGTCAGCTAAC 59.485 41.667 0.00 0.00 33.09 2.34
1767 3266 4.718961 ACCATCACTTTTGTCAGCTAACT 58.281 39.130 0.00 0.00 0.00 2.24
1769 3268 5.009010 ACCATCACTTTTGTCAGCTAACTTG 59.991 40.000 0.00 0.00 0.00 3.16
1771 3270 4.523083 TCACTTTTGTCAGCTAACTTGGT 58.477 39.130 0.00 0.00 0.00 3.67
1799 3298 1.069765 ACAGTGTGAGGACTTGCCG 59.930 57.895 0.00 0.00 43.43 5.69
1943 3445 3.820467 TGACAACAATAACAGAAGGCCAG 59.180 43.478 5.01 0.00 0.00 4.85
1963 3465 0.538584 CTGCATGGCTACAGGTCAGA 59.461 55.000 0.00 0.00 35.83 3.27
2384 4050 2.957402 AGAAGGTGACATTTGCCTCA 57.043 45.000 0.00 0.00 0.00 3.86
2478 4144 2.492025 AGGAATGTCTATGGGGCTTCA 58.508 47.619 0.00 0.00 0.00 3.02
2765 4465 0.394565 AGAGTAATCTGGCCGCATCC 59.605 55.000 0.00 0.00 0.00 3.51
3056 4781 7.099120 TCATATACATGTCCATCAATCTTCCG 58.901 38.462 0.00 0.00 33.57 4.30
3151 4882 4.154737 TCCAACATCTCTGCGATTTTTCAG 59.845 41.667 0.00 0.00 0.00 3.02
3315 5056 7.218773 CAGGTTATTCATTTGTTCATGCTTACG 59.781 37.037 0.00 0.00 0.00 3.18
3334 5075 6.805271 GCTTACGTAAACTCACAGATACTTGA 59.195 38.462 9.68 0.00 0.00 3.02
3360 5101 6.992123 TCTGTTATTGTTGTGTCTCATGACTT 59.008 34.615 0.00 0.00 43.29 3.01
3391 5132 0.320050 TATGGTGCGACAGTTGCTGA 59.680 50.000 14.20 0.00 35.18 4.26
3466 5215 8.709386 CAGTGTATCTGTTCAAAAGCTACTAT 57.291 34.615 0.00 0.00 39.17 2.12
3817 5984 2.044758 ACACGAAAGGACAAGGGTACT 58.955 47.619 0.00 0.00 41.07 2.73
4369 6649 3.477530 AGTGCTGGACCTTTTTCTACAC 58.522 45.455 0.00 0.00 0.00 2.90
4416 6696 6.928348 TTTGAAGAAGGGAGTACAGTGATA 57.072 37.500 0.00 0.00 0.00 2.15
4417 6697 7.496346 TTTGAAGAAGGGAGTACAGTGATAT 57.504 36.000 0.00 0.00 0.00 1.63
4554 6843 9.330063 CCATGAGCTTGTTACAGAAATAGATTA 57.670 33.333 0.00 0.00 0.00 1.75
4763 7054 9.886132 ATGTGGTAAATGTTAGGTAAACTCTAG 57.114 33.333 0.00 0.00 38.99 2.43
4782 7419 7.437748 ACTCTAGGCATTACATTGATGACTAC 58.562 38.462 0.00 0.00 41.02 2.73
4867 7539 9.326413 CATATTTCTTTGAAGGTAACCGATACT 57.674 33.333 0.00 0.00 34.74 2.12
4987 7660 5.818136 TGAATGCCTGCAACTACTAAATC 57.182 39.130 0.00 0.00 0.00 2.17
5283 7958 5.907207 TCTTGTAGGTGATAGAACAGATGC 58.093 41.667 0.00 0.00 0.00 3.91
5343 8026 5.592104 TCTTGATTCTTGTGATACGGCTA 57.408 39.130 0.00 0.00 0.00 3.93
5372 8243 3.646946 TGATTCATGTAGCATCGCTCTC 58.353 45.455 0.00 0.00 40.44 3.20
6025 8902 9.440773 AAGAAAAATAAAGATTCCATGGAAAGC 57.559 29.630 30.28 23.45 37.69 3.51
6122 9002 6.974622 CCCATTAAAGTGCATGAAGAACATAC 59.025 38.462 0.00 0.00 37.46 2.39
6138 9018 8.615878 AAGAACATACATGCTTAGTGTTACAA 57.384 30.769 0.00 0.00 33.55 2.41
6170 9050 1.002366 CAGAATCCGCAGTTTCTCCG 58.998 55.000 0.00 0.00 31.06 4.63
6704 11684 3.273080 CTGGCTTCAAGCGCAACCC 62.273 63.158 11.47 1.04 43.62 4.11
6723 11703 4.389374 ACCCACTAGAACTGTGTGAAATG 58.611 43.478 0.00 0.00 33.95 2.32
6726 11706 4.067896 CACTAGAACTGTGTGAAATGCCT 58.932 43.478 0.00 0.00 33.95 4.75
6727 11707 4.516698 CACTAGAACTGTGTGAAATGCCTT 59.483 41.667 0.00 0.00 33.95 4.35
6728 11708 5.009010 CACTAGAACTGTGTGAAATGCCTTT 59.991 40.000 0.00 0.00 33.95 3.11
6735 11721 5.812127 ACTGTGTGAAATGCCTTTCTTTTTC 59.188 36.000 14.42 3.55 41.18 2.29
6920 11907 1.285950 GACGCCTTTGCTTGTTCCC 59.714 57.895 0.00 0.00 34.43 3.97
6964 11955 1.021202 CGGTGCCACTGTTTTCTTGA 58.979 50.000 0.00 0.00 0.00 3.02
6969 11960 4.875536 GGTGCCACTGTTTTCTTGAAATTT 59.124 37.500 0.00 0.00 0.00 1.82
7055 12046 5.577835 TCAACGTCAGGAAAATGTTCTTTG 58.422 37.500 0.00 0.00 33.92 2.77
7062 12053 5.811613 TCAGGAAAATGTTCTTTGTTTGCAG 59.188 36.000 0.00 0.00 33.92 4.41
7076 12067 1.198094 TTGCAGAATCTGTCCGGGGA 61.198 55.000 12.29 0.00 33.43 4.81
7226 12219 8.938906 GCATGTAATTCATCAAACTTTTTCCAT 58.061 29.630 0.00 0.00 34.09 3.41
7261 12254 5.334879 CCGATGTGTGTACGATCATCAGATA 60.335 44.000 17.57 0.00 37.21 1.98
7318 12311 1.065926 GTGCCATGTCATCTGTCTGGA 60.066 52.381 0.00 0.00 0.00 3.86
7417 12410 3.511934 GTCTGTGTCTTCTCACCCATACT 59.488 47.826 0.00 0.00 37.51 2.12
7783 12776 2.697751 CAGATTCCTCCATCTCCTCGTT 59.302 50.000 0.00 0.00 30.50 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 111 1.688735 CCCTTATCACATCGCCTCTCA 59.311 52.381 0.00 0.00 0.00 3.27
169 177 1.129058 AGGTTCTGTTCCGACCAACT 58.871 50.000 0.00 0.00 35.89 3.16
284 292 7.661027 ACCATTGTTTGCAATTTATAAAGCAGT 59.339 29.630 0.00 3.54 42.91 4.40
387 395 1.726192 GGGTGGGGAGGAAAAGGTGT 61.726 60.000 0.00 0.00 0.00 4.16
391 399 0.900182 GCTTGGGTGGGGAGGAAAAG 60.900 60.000 0.00 0.00 0.00 2.27
399 409 3.476031 ATATCGCGCTTGGGTGGGG 62.476 63.158 5.56 0.00 36.69 4.96
402 412 2.253758 CCCATATCGCGCTTGGGTG 61.254 63.158 24.34 8.96 44.30 4.61
403 413 2.111043 CCCATATCGCGCTTGGGT 59.889 61.111 24.34 0.00 44.30 4.51
407 418 2.100879 GACCTCCCCATATCGCGCTT 62.101 60.000 5.56 0.00 0.00 4.68
425 730 1.612676 TCTTCTCCAACGAGGTTCGA 58.387 50.000 5.38 0.00 43.74 3.71
428 733 1.416401 TGCTTCTTCTCCAACGAGGTT 59.584 47.619 0.00 0.00 39.02 3.50
436 741 1.072331 GGACAGGTTGCTTCTTCTCCA 59.928 52.381 0.00 0.00 0.00 3.86
520 825 5.482175 CCCCTAAGATAGATAGTGAGGTTGG 59.518 48.000 0.00 0.00 0.00 3.77
589 901 1.645402 GCCCCAGCCATCCCTCTAAA 61.645 60.000 0.00 0.00 0.00 1.85
626 938 3.316501 CCTTCCCTCAATCTCTCTCCAT 58.683 50.000 0.00 0.00 0.00 3.41
636 980 3.420482 CCCCGCCCTTCCCTCAAT 61.420 66.667 0.00 0.00 0.00 2.57
1270 2739 3.429580 GGGTTGAGGGGATGGGGG 61.430 72.222 0.00 0.00 0.00 5.40
1381 2859 3.195002 CACATGGCCCTGTACGCG 61.195 66.667 13.78 3.53 0.00 6.01
1531 3014 4.081406 AGCACTAACAATCTCAAATGGCA 58.919 39.130 0.00 0.00 0.00 4.92
1568 3051 8.626526 TCGTAGTATCATAGACAACTAAATGCA 58.373 33.333 0.00 0.00 32.04 3.96
1620 3103 3.787001 GACGCCTAAGCCTGCCCT 61.787 66.667 0.00 0.00 34.57 5.19
1629 3112 0.613853 AGTACCCTGCAGACGCCTAA 60.614 55.000 17.39 0.00 37.32 2.69
1649 3132 7.667635 TCAAATACCCAACAATCAATACTGTCA 59.332 33.333 0.00 0.00 0.00 3.58
1650 3133 8.050778 TCAAATACCCAACAATCAATACTGTC 57.949 34.615 0.00 0.00 0.00 3.51
1734 3233 4.942761 AAAGTGATGGTCAACAATGCTT 57.057 36.364 0.00 0.00 0.00 3.91
1766 3265 4.157656 TCACACTGTGAAAGGAAAACCAAG 59.842 41.667 15.86 0.00 39.78 3.61
1767 3266 4.082845 TCACACTGTGAAAGGAAAACCAA 58.917 39.130 15.86 0.00 39.78 3.67
1769 3268 3.066760 CCTCACACTGTGAAAGGAAAACC 59.933 47.826 20.91 0.00 42.26 3.27
1771 3270 3.945285 GTCCTCACACTGTGAAAGGAAAA 59.055 43.478 26.01 11.06 42.26 2.29
1799 3298 8.172352 AGGTAGTATGTCTCTCACACAATATC 57.828 38.462 0.00 0.00 38.04 1.63
1943 3445 1.078214 TGACCTGTAGCCATGCAGC 60.078 57.895 0.00 0.00 37.79 5.25
1963 3465 7.373493 CAGAAAGATTTAAAGTTGCTCATGGT 58.627 34.615 0.00 0.00 0.00 3.55
2022 3533 5.788450 AGAAACTCTGAGAGTACAACATGG 58.212 41.667 16.52 0.00 42.59 3.66
2136 3663 6.934083 TCGCAATACATATCCAATAGAGCAAA 59.066 34.615 0.00 0.00 0.00 3.68
2384 4050 1.485480 CTCCATGCTGTGACAGAGGAT 59.515 52.381 18.18 0.34 31.71 3.24
2478 4144 3.961480 TCCATCAGATCACGAACAACT 57.039 42.857 0.00 0.00 0.00 3.16
2623 4289 6.753107 GGCTCTAAAAATTTACTAGTGCCA 57.247 37.500 28.07 7.04 45.37 4.92
2693 4370 3.701205 TCTACATGGGCATCGCAATAT 57.299 42.857 0.00 0.00 0.00 1.28
3056 4781 0.602638 TGACATCCACGTGTTCTGGC 60.603 55.000 15.65 11.16 31.16 4.85
3170 4901 4.090761 TGCAAGACAGAAGGAATCACTT 57.909 40.909 0.00 0.00 0.00 3.16
3334 5075 7.369803 GTCATGAGACACAACAATAACAGAT 57.630 36.000 0.00 0.00 44.34 2.90
3817 5984 0.038251 CAGTAGGCGTGCTGACTTCA 60.038 55.000 18.22 0.00 38.63 3.02
3886 6079 8.138074 AGTAATGTGATGTAGCAGTATAGTGTG 58.862 37.037 9.30 0.00 0.00 3.82
4121 6395 1.400494 CATACCTTACGGCAACAAGGC 59.600 52.381 8.84 0.00 42.18 4.35
4188 6462 7.112122 ACAGATGACCAAATAAGACAGCATAA 58.888 34.615 0.00 0.00 0.00 1.90
4189 6463 6.653020 ACAGATGACCAAATAAGACAGCATA 58.347 36.000 0.00 0.00 0.00 3.14
4241 6515 7.468636 AGGTACTTAGTGCACAATTTGATGCA 61.469 38.462 21.04 17.11 43.54 3.96
4369 6649 9.603921 AAATAGAATTTATGAATTGGCAACCAG 57.396 29.630 0.00 0.00 35.65 4.00
4554 6843 4.716784 TGAGCTCACCAGGATGTAAGTTAT 59.283 41.667 13.74 0.00 0.00 1.89
4763 7054 7.928706 AGTAAGAGTAGTCATCAATGTAATGCC 59.071 37.037 0.00 0.00 0.00 4.40
4782 7419 8.133024 AGATATAAGGCATGGAAGAGTAAGAG 57.867 38.462 0.00 0.00 0.00 2.85
4987 7660 6.183360 TGCAATATTTGGAAGAGGTGCTTATG 60.183 38.462 0.00 0.00 36.83 1.90
5343 8026 5.176406 CGATGCTACATGAATCAAACGATCT 59.824 40.000 0.00 0.00 29.77 2.75
5372 8243 5.798934 GCAAACAAGCACTATCTTCATCAAG 59.201 40.000 0.00 0.00 0.00 3.02
5624 8495 4.889409 TCAGCAGGGAATGGATAATCAAAC 59.111 41.667 0.00 0.00 0.00 2.93
5760 8635 8.655970 GGAAATGGAATTCCGAAACAATTTAAG 58.344 33.333 19.57 0.00 39.54 1.85
6025 8902 1.148157 CGTTATCAGCCTGTCCAGCG 61.148 60.000 0.00 0.00 34.64 5.18
6122 9002 6.757010 CCTACTAGGTTGTAACACTAAGCATG 59.243 42.308 0.00 0.00 0.00 4.06
6704 11684 4.067896 AGGCATTTCACACAGTTCTAGTG 58.932 43.478 0.00 0.00 42.56 2.74
6723 11703 7.429630 GCGTCATCTATAAAGAAAAAGAAAGGC 59.570 37.037 0.00 0.00 34.73 4.35
6726 11706 7.461107 CCGCGTCATCTATAAAGAAAAAGAAA 58.539 34.615 4.92 0.00 34.73 2.52
6727 11707 6.456449 GCCGCGTCATCTATAAAGAAAAAGAA 60.456 38.462 4.92 0.00 34.73 2.52
6728 11708 5.006358 GCCGCGTCATCTATAAAGAAAAAGA 59.994 40.000 4.92 0.00 34.73 2.52
6735 11721 3.317150 TGATGCCGCGTCATCTATAAAG 58.683 45.455 27.87 0.00 42.44 1.85
6920 11907 2.125912 CGCAAGTCCGTCCCAGAG 60.126 66.667 0.00 0.00 0.00 3.35
6964 11955 2.352715 GCAGCCGCTTAAGGACAAATTT 60.353 45.455 4.29 0.00 34.30 1.82
6969 11960 1.026182 CATGCAGCCGCTTAAGGACA 61.026 55.000 4.29 0.00 39.64 4.02
7006 11997 2.770904 GGGCCCAACTATCCGGGA 60.771 66.667 19.95 0.00 46.34 5.14
7055 12046 0.804989 CCCGGACAGATTCTGCAAAC 59.195 55.000 13.64 3.41 34.37 2.93
7062 12053 1.382695 TCCCTCCCCGGACAGATTC 60.383 63.158 0.73 0.00 33.16 2.52
7076 12067 3.251484 TGTCTTTCCACTCAATCTCCCT 58.749 45.455 0.00 0.00 0.00 4.20
7183 12176 1.878775 GCTGACAAAGCGGCAGATT 59.121 52.632 1.45 0.00 43.45 2.40
7226 12219 0.250684 ACACATCGGATGGTGTTGCA 60.251 50.000 21.19 0.00 45.39 4.08
7261 12254 1.414181 CCGAACTAGATGCAGATGGGT 59.586 52.381 0.00 0.00 0.00 4.51
7783 12776 0.039165 CGATGATGCTCGGGATTCGA 60.039 55.000 0.00 0.00 46.77 3.71


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

AutoCloner maintained by Alex Coulton.