Multiple sequence alignment - TraesCS3D01G544700

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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 TraesCS3D01G544700 chr3D 100.000 3246 0 0 1 3246 614204918 614201673 0.000000e+00 5995.0
1 TraesCS3D01G544700 chr3D 100.000 2435 0 0 3591 6025 614201328 614198894 0.000000e+00 4497.0
2 TraesCS3D01G544700 chr3D 90.566 106 10 0 3132 3237 614201319 614201214 2.260000e-29 141.0
3 TraesCS3D01G544700 chr3D 90.566 106 10 0 3600 3705 614201787 614201682 2.260000e-29 141.0
4 TraesCS3D01G544700 chr3D 89.474 76 4 2 5138 5212 513387492 513387420 6.430000e-15 93.5
5 TraesCS3D01G544700 chr3D 85.227 88 10 2 5602 5687 85447128 85447042 2.990000e-13 87.9
6 TraesCS3D01G544700 chr3D 83.158 95 15 1 5603 5696 363272451 363272357 1.080000e-12 86.1
7 TraesCS3D01G544700 chr3D 100.000 32 0 0 5535 5566 486041212 486041243 6.520000e-05 60.2
8 TraesCS3D01G544700 chr3D 92.105 38 2 1 5505 5542 571378041 571378005 1.100000e-02 52.8
9 TraesCS3D01G544700 chr3A 97.983 1834 28 6 1395 3221 750503798 750501967 0.000000e+00 3173.0
10 TraesCS3D01G544700 chr3A 91.628 1959 82 18 3600 5512 750501882 750499960 0.000000e+00 2634.0
11 TraesCS3D01G544700 chr3A 97.496 1358 18 4 50 1398 750505176 750503826 0.000000e+00 2305.0
12 TraesCS3D01G544700 chr3A 89.202 213 19 3 5646 5857 750499494 750499285 4.630000e-66 263.0
13 TraesCS3D01G544700 chr3A 94.521 146 8 0 3101 3246 750501913 750501768 6.080000e-55 226.0
14 TraesCS3D01G544700 chr3A 94.444 126 7 0 3102 3227 750501999 750501874 1.710000e-45 195.0
15 TraesCS3D01G544700 chr3A 94.915 118 3 1 3597 3714 750501927 750501813 1.330000e-41 182.0
16 TraesCS3D01G544700 chr3A 92.742 124 6 3 3591 3714 750502020 750501900 6.210000e-40 176.0
17 TraesCS3D01G544700 chr3A 89.928 139 8 3 3102 3237 750501957 750501822 2.230000e-39 174.0
18 TraesCS3D01G544700 chr3A 88.112 143 8 3 3101 3237 750502048 750501909 1.740000e-35 161.0
19 TraesCS3D01G544700 chr3A 94.393 107 3 1 3611 3714 750502093 750501987 1.740000e-35 161.0
20 TraesCS3D01G544700 chr3A 92.174 115 6 2 3600 3714 750501969 750501858 6.250000e-35 159.0
21 TraesCS3D01G544700 chr3A 94.565 92 5 0 3144 3235 750502092 750502001 6.290000e-30 143.0
22 TraesCS3D01G544700 chr3A 98.305 59 1 0 3656 3714 750502093 750502035 2.970000e-18 104.0
23 TraesCS3D01G544700 chr3A 96.774 31 1 0 5505 5535 290445978 290445948 1.100000e-02 52.8
24 TraesCS3D01G544700 chr3B 94.984 1934 53 13 3600 5511 823575195 823573284 0.000000e+00 2994.0
25 TraesCS3D01G544700 chr3B 95.522 1809 63 8 1395 3187 823577566 823575760 0.000000e+00 2876.0
26 TraesCS3D01G544700 chr3B 89.696 1087 22 24 50 1116 823578840 823577824 0.000000e+00 1304.0
27 TraesCS3D01G544700 chr3B 91.648 443 24 9 5562 5994 823573284 823572845 8.640000e-168 601.0
28 TraesCS3D01G544700 chr3B 87.550 249 5 7 1156 1398 823577819 823577591 1.290000e-66 265.0
29 TraesCS3D01G544700 chr3B 96.330 109 4 0 3597 3705 823575243 823575135 4.800000e-41 180.0
30 TraesCS3D01G544700 chr3B 87.919 149 9 5 3101 3240 823575229 823575081 3.740000e-37 167.0
31 TraesCS3D01G544700 chr3B 89.844 128 10 2 3120 3244 823575255 823575128 1.740000e-35 161.0
32 TraesCS3D01G544700 chr3B 88.496 113 1 6 3101 3201 823575184 823575072 6.340000e-25 126.0
33 TraesCS3D01G544700 chr3B 100.000 52 0 0 1 52 823578972 823578921 4.970000e-16 97.1
34 TraesCS3D01G544700 chr3B 86.207 87 11 1 5602 5687 135685089 135685003 6.430000e-15 93.5
35 TraesCS3D01G544700 chr3B 100.000 36 0 0 5535 5570 173097691 173097726 3.900000e-07 67.6
36 TraesCS3D01G544700 chrUn 100.000 384 0 0 1688 2071 480950117 480950500 0.000000e+00 710.0
37 TraesCS3D01G544700 chrUn 100.000 29 0 0 5504 5532 15963704 15963732 3.000000e-03 54.7
38 TraesCS3D01G544700 chr1D 91.589 107 8 1 990 1096 34622952 34623057 4.870000e-31 147.0
39 TraesCS3D01G544700 chr1D 86.364 88 11 1 5602 5688 358222552 358222639 1.790000e-15 95.3
40 TraesCS3D01G544700 chr1D 90.476 42 2 2 5501 5542 64326010 64325971 3.000000e-03 54.7
41 TraesCS3D01G544700 chr1D 90.476 42 2 2 5501 5542 96069577 96069616 3.000000e-03 54.7
42 TraesCS3D01G544700 chr1B 91.589 107 8 1 990 1096 52903636 52903741 4.870000e-31 147.0
43 TraesCS3D01G544700 chr1B 85.227 88 12 1 5602 5688 480973020 480972933 8.320000e-14 89.8
44 TraesCS3D01G544700 chr1B 93.220 59 3 1 5602 5659 59598414 59598472 1.080000e-12 86.1
45 TraesCS3D01G544700 chr1B 97.368 38 0 1 5535 5571 8913771 8913808 5.040000e-06 63.9
46 TraesCS3D01G544700 chr1B 100.000 32 0 0 5535 5566 41366318 41366287 6.520000e-05 60.2
47 TraesCS3D01G544700 chr1B 100.000 32 0 0 5535 5566 597430417 597430448 6.520000e-05 60.2
48 TraesCS3D01G544700 chr1A 90.909 99 9 0 998 1096 32896088 32896186 3.790000e-27 134.0
49 TraesCS3D01G544700 chr1A 100.000 32 0 0 5535 5566 372065895 372065926 6.520000e-05 60.2
50 TraesCS3D01G544700 chr2B 89.796 98 10 0 1000 1097 55881137 55881234 6.340000e-25 126.0
51 TraesCS3D01G544700 chr2A 89.691 97 10 0 1000 1096 36628193 36628289 2.280000e-24 124.0
52 TraesCS3D01G544700 chr2A 97.143 35 1 0 5535 5569 691662345 691662311 6.520000e-05 60.2
53 TraesCS3D01G544700 chr6A 88.776 98 11 0 1000 1097 76578628 76578725 2.950000e-23 121.0
54 TraesCS3D01G544700 chr2D 88.776 98 11 0 1000 1097 33718817 33718914 2.950000e-23 121.0
55 TraesCS3D01G544700 chr7A 85.106 94 13 1 5594 5686 247257075 247256982 1.790000e-15 95.3
56 TraesCS3D01G544700 chr5A 86.207 87 11 1 5602 5687 364712632 364712718 6.430000e-15 93.5
57 TraesCS3D01G544700 chr5D 100.000 34 0 0 5535 5568 512778704 512778737 5.040000e-06 63.9
58 TraesCS3D01G544700 chr5D 100.000 33 0 0 5535 5567 299393426 299393394 1.810000e-05 62.1
59 TraesCS3D01G544700 chr4B 92.857 42 2 1 5501 5542 172767695 172767735 6.520000e-05 60.2
60 TraesCS3D01G544700 chr5B 92.500 40 2 1 5503 5542 644543593 644543555 8.440000e-04 56.5
61 TraesCS3D01G544700 chr4A 92.500 40 2 1 5503 5542 153650862 153650824 8.440000e-04 56.5
62 TraesCS3D01G544700 chr4A 96.774 31 1 0 5505 5535 649803984 649803954 1.100000e-02 52.8


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 TraesCS3D01G544700 chr3D 614198894 614204918 6024 True 2693.500000 5995 95.283000 1 6025 4 chr3D.!!$R5 6024
1 TraesCS3D01G544700 chr3A 750499285 750505176 5891 True 718.285714 3173 93.600571 50 5857 14 chr3A.!!$R2 5807
2 TraesCS3D01G544700 chr3B 823572845 823578972 6127 True 877.110000 2994 92.198900 1 5994 10 chr3B.!!$R2 5993

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
883 1004 0.253207 TCCTCCCTCCCCCTTTCTTC 60.253 60.0 0.0 0.0 0.0 2.87 F
2360 2535 2.357569 GGCCCTCAAATCCTGTGAAGAT 60.358 50.0 0.0 0.0 0.0 2.40 F
3915 4332 0.105964 CGAGAAGGGGTGTGTTGACA 59.894 55.0 0.0 0.0 0.0 3.58 F
4067 4484 0.398318 AGAACCAGGAGTGCCTCAAC 59.602 55.0 0.0 0.0 44.8 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 2577 0.036952 CAGACTCGTCCAATGCCTGT 60.037 55.000 0.0 0.0 0.00 4.00 R
3983 4400 0.681564 CCAGGAGCGAGGTGTACTCT 60.682 60.000 0.0 0.0 44.33 3.24 R
4887 5307 1.701031 TTGGTCGGGAACAGGAAGCA 61.701 55.000 0.0 0.0 0.00 3.91 R
5389 5819 3.055963 TGGAATGGGAAAACATGATGTGC 60.056 43.478 0.0 0.0 0.00 4.57 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 1.052617 TACAGCACTACCCTGTTGCA 58.947 50.000 0.00 0.00 42.98 4.08
93 190 6.781014 TGTATAGGATTAGAGGTGGTTAGGTG 59.219 42.308 0.00 0.00 0.00 4.00
94 191 4.348020 AGGATTAGAGGTGGTTAGGTGA 57.652 45.455 0.00 0.00 0.00 4.02
95 192 4.695606 AGGATTAGAGGTGGTTAGGTGAA 58.304 43.478 0.00 0.00 0.00 3.18
96 193 5.098663 AGGATTAGAGGTGGTTAGGTGAAA 58.901 41.667 0.00 0.00 0.00 2.69
97 194 5.189934 AGGATTAGAGGTGGTTAGGTGAAAG 59.810 44.000 0.00 0.00 0.00 2.62
98 195 5.189145 GGATTAGAGGTGGTTAGGTGAAAGA 59.811 44.000 0.00 0.00 0.00 2.52
99 196 6.296259 GGATTAGAGGTGGTTAGGTGAAAGAA 60.296 42.308 0.00 0.00 0.00 2.52
100 197 6.697641 TTAGAGGTGGTTAGGTGAAAGAAT 57.302 37.500 0.00 0.00 0.00 2.40
101 198 4.911390 AGAGGTGGTTAGGTGAAAGAATG 58.089 43.478 0.00 0.00 0.00 2.67
102 199 4.010349 GAGGTGGTTAGGTGAAAGAATGG 58.990 47.826 0.00 0.00 0.00 3.16
103 200 2.492088 GGTGGTTAGGTGAAAGAATGGC 59.508 50.000 0.00 0.00 0.00 4.40
104 201 2.492088 GTGGTTAGGTGAAAGAATGGCC 59.508 50.000 0.00 0.00 0.00 5.36
105 202 2.378547 TGGTTAGGTGAAAGAATGGCCT 59.621 45.455 3.32 0.00 0.00 5.19
340 446 2.180432 GCATCTAGGAGCATGCATCA 57.820 50.000 21.98 0.52 44.18 3.07
481 594 7.536895 CTAATTATAGGAGCATGCATGAGAC 57.463 40.000 30.64 17.40 0.00 3.36
593 713 3.996363 TGTGTAGTGTGCTGCTAGAAATG 59.004 43.478 0.00 0.00 0.00 2.32
608 728 6.015519 TGCTAGAAATGTTAGGCATGTTTGTT 60.016 34.615 0.00 0.00 37.96 2.83
643 763 7.065120 TGACATGATTTTTGGAGGTTTGATT 57.935 32.000 0.00 0.00 0.00 2.57
686 806 0.542467 TTCAACAGCCCCATGCATGT 60.542 50.000 24.58 4.09 44.83 3.21
761 881 1.808945 CCATCACTTCCACTGCACTTC 59.191 52.381 0.00 0.00 0.00 3.01
883 1004 0.253207 TCCTCCCTCCCCCTTTCTTC 60.253 60.000 0.00 0.00 0.00 2.87
1403 1565 6.114187 TGATCAGTGTTAGTTCCATTCTGT 57.886 37.500 0.00 0.00 0.00 3.41
2243 2418 6.903534 AGTACTGGGATCTTGAGAAGGAAATA 59.096 38.462 0.00 0.00 0.00 1.40
2256 2431 6.039047 TGAGAAGGAAATAAATGAGATGCAGC 59.961 38.462 0.00 0.00 0.00 5.25
2257 2432 5.889853 AGAAGGAAATAAATGAGATGCAGCA 59.110 36.000 4.07 0.00 0.00 4.41
2360 2535 2.357569 GGCCCTCAAATCCTGTGAAGAT 60.358 50.000 0.00 0.00 0.00 2.40
2543 2718 1.319541 CGGAGATGGGAGACGTGTAT 58.680 55.000 0.00 0.00 0.00 2.29
2974 3149 0.322277 CCTGGTTCTGCTGCTCACAT 60.322 55.000 0.00 0.00 0.00 3.21
3009 3184 3.394836 AGGAAGCACCGCCTCCTC 61.395 66.667 0.10 0.00 45.30 3.71
3011 3186 4.821589 GAAGCACCGCCTCCTCCG 62.822 72.222 0.00 0.00 0.00 4.63
3057 3232 3.326836 CTCCACCTGAGGAAGAAGAAC 57.673 52.381 4.99 0.00 37.20 3.01
3142 3317 1.078356 CTGGAGATGCTGCTGCTGT 60.078 57.895 17.00 5.48 40.48 4.40
3169 3347 1.529010 CCCAACAAGCCAGCACTGA 60.529 57.895 0.00 0.00 0.00 3.41
3223 3416 3.200593 CAGCACTGGAGATGCCGC 61.201 66.667 0.00 0.00 44.53 6.53
3224 3417 4.479993 AGCACTGGAGATGCCGCC 62.480 66.667 0.00 0.00 44.53 6.13
3629 3914 0.111253 CTCCTCAACCCCAACAAGCT 59.889 55.000 0.00 0.00 0.00 3.74
3729 4146 2.519302 AAGCTGCTGCACCGGTTT 60.519 55.556 18.42 0.00 42.74 3.27
3865 4282 0.109086 CGCCACATCTCTTCTGACGT 60.109 55.000 0.00 0.00 0.00 4.34
3869 4286 3.854666 CCACATCTCTTCTGACGTTGAT 58.145 45.455 0.00 0.00 0.00 2.57
3872 4289 5.107824 CACATCTCTTCTGACGTTGATGAT 58.892 41.667 18.30 0.00 36.25 2.45
3905 4322 2.736826 GGAGAAGGGCGAGAAGGGG 61.737 68.421 0.00 0.00 0.00 4.79
3915 4332 0.105964 CGAGAAGGGGTGTGTTGACA 59.894 55.000 0.00 0.00 0.00 3.58
4067 4484 0.398318 AGAACCAGGAGTGCCTCAAC 59.602 55.000 0.00 0.00 44.80 3.18
4111 4528 4.521536 TTATCGGAGAGAAGGAGAAGGA 57.478 45.455 0.00 0.00 43.63 3.36
4112 4529 2.428544 TCGGAGAGAAGGAGAAGGAG 57.571 55.000 0.00 0.00 0.00 3.69
4113 4530 1.916874 TCGGAGAGAAGGAGAAGGAGA 59.083 52.381 0.00 0.00 0.00 3.71
4586 5003 2.634777 GAGGAGATCTCGACGGCG 59.365 66.667 16.46 2.87 39.35 6.46
4801 5221 1.111277 GTCAAGCTCTCCTCCTCCTC 58.889 60.000 0.00 0.00 0.00 3.71
5072 5501 9.231297 GCAGGGATATGTCATTTAGCTTAATTA 57.769 33.333 0.00 0.00 0.00 1.40
5260 5690 3.630312 TGTCAGGAAACAAACCTACTTGC 59.370 43.478 0.00 0.00 35.84 4.01
5306 5736 8.023021 TGAGTGATGTGCTTATCTAGGTTATT 57.977 34.615 0.00 0.00 0.00 1.40
5309 5739 7.653713 AGTGATGTGCTTATCTAGGTTATTTCG 59.346 37.037 0.00 0.00 0.00 3.46
5313 5743 9.640963 ATGTGCTTATCTAGGTTATTTCGATAC 57.359 33.333 0.00 0.00 0.00 2.24
5337 5767 8.502161 ACGACAAATTTTTACTTGATAGCAAC 57.498 30.769 0.00 0.00 0.00 4.17
5388 5818 6.401394 TGTGACCTCTGAGATCAATGTAAAG 58.599 40.000 2.59 0.00 0.00 1.85
5389 5819 5.814705 GTGACCTCTGAGATCAATGTAAAGG 59.185 44.000 2.59 0.00 0.00 3.11
5406 5844 2.307496 AGGCACATCATGTTTTCCCA 57.693 45.000 0.00 0.00 0.00 4.37
5488 5966 8.870160 TTCTTGGATCATTTTAGTGTTGTTTG 57.130 30.769 0.00 0.00 0.00 2.93
5516 5994 9.268282 TCTTAGAACATTTACTTGATACTCCCT 57.732 33.333 0.00 0.00 0.00 4.20
5517 5995 9.535878 CTTAGAACATTTACTTGATACTCCCTC 57.464 37.037 0.00 0.00 0.00 4.30
5518 5996 7.741554 AGAACATTTACTTGATACTCCCTCT 57.258 36.000 0.00 0.00 0.00 3.69
5519 5997 7.560368 AGAACATTTACTTGATACTCCCTCTG 58.440 38.462 0.00 0.00 0.00 3.35
5520 5998 6.875972 ACATTTACTTGATACTCCCTCTGT 57.124 37.500 0.00 0.00 0.00 3.41
5521 5999 7.973048 ACATTTACTTGATACTCCCTCTGTA 57.027 36.000 0.00 0.00 0.00 2.74
5522 6000 8.375493 ACATTTACTTGATACTCCCTCTGTAA 57.625 34.615 0.00 0.00 0.00 2.41
5523 6001 8.822805 ACATTTACTTGATACTCCCTCTGTAAA 58.177 33.333 0.00 0.00 34.57 2.01
5524 6002 9.099454 CATTTACTTGATACTCCCTCTGTAAAC 57.901 37.037 0.00 0.00 33.45 2.01
5525 6003 8.431910 TTTACTTGATACTCCCTCTGTAAACT 57.568 34.615 0.00 0.00 0.00 2.66
5526 6004 9.537852 TTTACTTGATACTCCCTCTGTAAACTA 57.462 33.333 0.00 0.00 0.00 2.24
5527 6005 9.537852 TTACTTGATACTCCCTCTGTAAACTAA 57.462 33.333 0.00 0.00 0.00 2.24
5528 6006 8.611051 ACTTGATACTCCCTCTGTAAACTAAT 57.389 34.615 0.00 0.00 0.00 1.73
5529 6007 9.710818 ACTTGATACTCCCTCTGTAAACTAATA 57.289 33.333 0.00 0.00 0.00 0.98
5535 6013 8.757982 ACTCCCTCTGTAAACTAATATACGAA 57.242 34.615 0.00 0.00 0.00 3.85
5536 6014 8.628280 ACTCCCTCTGTAAACTAATATACGAAC 58.372 37.037 0.00 0.00 0.00 3.95
5537 6015 7.642669 TCCCTCTGTAAACTAATATACGAACG 58.357 38.462 0.00 0.00 0.00 3.95
5538 6016 6.361748 CCCTCTGTAAACTAATATACGAACGC 59.638 42.308 0.00 0.00 0.00 4.84
5539 6017 7.137426 CCTCTGTAAACTAATATACGAACGCT 58.863 38.462 0.00 0.00 0.00 5.07
5540 6018 7.646922 CCTCTGTAAACTAATATACGAACGCTT 59.353 37.037 0.00 0.00 0.00 4.68
5541 6019 8.915871 TCTGTAAACTAATATACGAACGCTTT 57.084 30.769 0.00 0.00 0.00 3.51
5542 6020 9.357652 TCTGTAAACTAATATACGAACGCTTTT 57.642 29.630 0.00 0.00 0.00 2.27
5557 6035 9.316730 ACGAACGCTTTTATATTAGTTTATGGA 57.683 29.630 0.00 0.00 0.00 3.41
5558 6036 9.793245 CGAACGCTTTTATATTAGTTTATGGAG 57.207 33.333 0.00 0.00 0.00 3.86
5560 6038 8.617290 ACGCTTTTATATTAGTTTATGGAGGG 57.383 34.615 0.00 0.00 0.00 4.30
5620 6413 5.011840 ACTTGGTACTCCCTCTGTAAACTTC 59.988 44.000 0.00 0.00 0.00 3.01
5758 6580 9.950680 TTGTGTAATCTCAGACAAATTTTCTTC 57.049 29.630 0.00 0.00 29.60 2.87
5776 6598 5.405935 TCTTCATGTATAGTGCTGTGTGT 57.594 39.130 0.00 0.00 0.00 3.72
5819 6641 9.093970 TGATACATAGTGTTGTAATTTTCTCCG 57.906 33.333 0.00 0.00 35.80 4.63
5825 6647 6.001460 AGTGTTGTAATTTTCTCCGGATGAA 58.999 36.000 3.57 8.48 0.00 2.57
5969 6791 3.455177 ACCTCTGTGCAGATCATCATCTT 59.545 43.478 2.06 0.00 37.25 2.40
5971 6793 4.882427 CCTCTGTGCAGATCATCATCTTTT 59.118 41.667 2.06 0.00 37.25 2.27
5972 6794 6.053650 CCTCTGTGCAGATCATCATCTTTTA 58.946 40.000 2.06 0.00 37.25 1.52
5973 6795 6.541278 CCTCTGTGCAGATCATCATCTTTTAA 59.459 38.462 2.06 0.00 37.25 1.52
5974 6796 7.312657 TCTGTGCAGATCATCATCTTTTAAC 57.687 36.000 0.00 0.00 37.25 2.01
5977 6804 7.884257 TGTGCAGATCATCATCTTTTAACAAA 58.116 30.769 0.00 0.00 37.25 2.83
5999 6826 9.541884 ACAAATTACATAAACAGGAATAAGGGT 57.458 29.630 0.00 0.00 0.00 4.34
6005 6832 8.519799 ACATAAACAGGAATAAGGGTTACATG 57.480 34.615 0.00 0.00 0.00 3.21
6006 6833 8.333235 ACATAAACAGGAATAAGGGTTACATGA 58.667 33.333 0.00 0.00 0.00 3.07
6007 6834 9.354673 CATAAACAGGAATAAGGGTTACATGAT 57.645 33.333 0.00 0.00 0.00 2.45
6008 6835 7.881775 AAACAGGAATAAGGGTTACATGATC 57.118 36.000 0.00 0.00 0.00 2.92
6009 6836 6.831664 ACAGGAATAAGGGTTACATGATCT 57.168 37.500 0.00 0.00 0.00 2.75
6010 6837 7.213178 ACAGGAATAAGGGTTACATGATCTT 57.787 36.000 0.00 0.00 0.00 2.40
6011 6838 7.643123 ACAGGAATAAGGGTTACATGATCTTT 58.357 34.615 0.00 0.00 0.00 2.52
6012 6839 8.116026 ACAGGAATAAGGGTTACATGATCTTTT 58.884 33.333 0.00 0.00 0.00 2.27
6013 6840 9.627123 CAGGAATAAGGGTTACATGATCTTTTA 57.373 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.906720 ATACAAGTGGAACCGTATGCT 57.093 42.857 0.00 0.0 35.39 3.79
96 193 9.700831 AGAAAGTTAATATACAAAGGCCATTCT 57.299 29.630 5.01 0.0 0.00 2.40
340 446 7.823745 TTTTTAGCCATCTCTTTTCTGAACT 57.176 32.000 0.00 0.0 0.00 3.01
481 594 1.592669 CTGGCAATCCTACGCTCCG 60.593 63.158 0.00 0.0 0.00 4.63
593 713 5.493809 TCCTAGGTAACAAACATGCCTAAC 58.506 41.667 9.08 0.0 35.17 2.34
608 728 8.112822 TCCAAAAATCATGTCAATTCCTAGGTA 58.887 33.333 9.08 0.0 0.00 3.08
686 806 4.912586 TCCGGATGGTAATCAACTTTTCA 58.087 39.130 0.00 0.0 34.17 2.69
761 881 1.376543 AGAACGCATGCAGAAGGATG 58.623 50.000 19.57 0.5 45.39 3.51
826 947 4.261489 GCTGATAGCCAAGTCCATTCATTG 60.261 45.833 0.00 0.0 34.48 2.82
883 1004 3.142174 GACAAGTGGGAGGTGAAAAGAG 58.858 50.000 0.00 0.0 0.00 2.85
1026 1151 0.980754 TCGCCCACCACCATGAGTAT 60.981 55.000 0.00 0.0 0.00 2.12
1138 1263 7.927629 CCGAAAATTCCCATTTGACATATTCAT 59.072 33.333 0.00 0.0 32.57 2.57
1148 1273 6.815089 TCCATAATCCGAAAATTCCCATTTG 58.185 36.000 0.00 0.0 32.57 2.32
1241 1366 7.669304 TGTCAATTTTGAGATGGGACTAATTCA 59.331 33.333 0.00 0.0 37.98 2.57
1478 1645 5.482908 ACAGTTTCGAGACTTCATGCTATT 58.517 37.500 5.76 0.0 0.00 1.73
2256 2431 2.600470 TGGAAGTGGCAAGCTTTTTG 57.400 45.000 0.00 0.0 0.00 2.44
2257 2432 2.765699 TCTTGGAAGTGGCAAGCTTTTT 59.234 40.909 0.00 0.0 0.00 1.94
2360 2535 5.069318 TGTTCTTGCAATCTGACAATGGTA 58.931 37.500 0.00 0.0 0.00 3.25
2399 2574 1.197721 GACTCGTCCAATGCCTGTTTG 59.802 52.381 0.00 0.0 0.00 2.93
2402 2577 0.036952 CAGACTCGTCCAATGCCTGT 60.037 55.000 0.00 0.0 0.00 4.00
2543 2718 0.321919 GCTCACCCAGCTTCACATGA 60.322 55.000 0.00 0.0 45.83 3.07
3011 3186 2.509916 CTCTGGCTGGATGGCTCC 59.490 66.667 0.00 0.0 42.45 4.70
3024 3199 1.222936 GTGGAGGTGGATGGCTCTG 59.777 63.158 0.00 0.0 0.00 3.35
3057 3232 6.049149 TCTCTTCTTCTACCTGTTGTTTGTG 58.951 40.000 0.00 0.0 0.00 3.33
3142 3317 0.469144 GGCTTGTTGGGGTTGAGGAA 60.469 55.000 0.00 0.0 0.00 3.36
3169 3347 0.894184 AACAGCAGCAGCAGCATCTT 60.894 50.000 12.92 0.0 45.49 2.40
3629 3914 1.202615 GCAGCATCATCTCCAGTGCTA 60.203 52.381 0.00 0.0 45.42 3.49
3729 4146 0.963355 GCCCCTGTTTTCGCCACATA 60.963 55.000 0.00 0.0 0.00 2.29
3865 4282 4.703575 CCTTTTGCTCCTCAGAATCATCAA 59.296 41.667 0.00 0.0 0.00 2.57
3869 4286 3.584406 TCTCCTTTTGCTCCTCAGAATCA 59.416 43.478 0.00 0.0 0.00 2.57
3872 4289 3.244700 CCTTCTCCTTTTGCTCCTCAGAA 60.245 47.826 0.00 0.0 0.00 3.02
3905 4322 1.217001 TCATGTCGCTGTCAACACAC 58.783 50.000 0.00 0.0 0.00 3.82
3915 4332 1.882912 TGCAGTTTCTTCATGTCGCT 58.117 45.000 0.00 0.0 0.00 4.93
3917 4334 3.666374 GCTCTTGCAGTTTCTTCATGTCG 60.666 47.826 0.00 0.0 39.41 4.35
3983 4400 0.681564 CCAGGAGCGAGGTGTACTCT 60.682 60.000 0.00 0.0 44.33 3.24
4067 4484 2.653448 CGCAGCGACCTGATCTCG 60.653 66.667 9.98 0.0 41.77 4.04
4108 4525 1.290732 CCCTCTCCTTCTCCTTCTCCT 59.709 57.143 0.00 0.0 0.00 3.69
4109 4526 1.289530 TCCCTCTCCTTCTCCTTCTCC 59.710 57.143 0.00 0.0 0.00 3.71
4110 4527 2.243736 TCTCCCTCTCCTTCTCCTTCTC 59.756 54.545 0.00 0.0 0.00 2.87
4111 4528 2.244769 CTCTCCCTCTCCTTCTCCTTCT 59.755 54.545 0.00 0.0 0.00 2.85
4112 4529 2.666317 CTCTCCCTCTCCTTCTCCTTC 58.334 57.143 0.00 0.0 0.00 3.46
4113 4530 1.290732 CCTCTCCCTCTCCTTCTCCTT 59.709 57.143 0.00 0.0 0.00 3.36
4586 5003 1.142748 CTCCGTGTCCATCTCCAGC 59.857 63.158 0.00 0.0 0.00 4.85
4887 5307 1.701031 TTGGTCGGGAACAGGAAGCA 61.701 55.000 0.00 0.0 0.00 3.91
5072 5501 6.808321 TGTATCCCATCTGCTAGTTAGTTT 57.192 37.500 0.00 0.0 0.00 2.66
5282 5712 8.894768 AAATAACCTAGATAAGCACATCACTC 57.105 34.615 0.00 0.0 0.00 3.51
5287 5717 9.640963 GTATCGAAATAACCTAGATAAGCACAT 57.359 33.333 0.00 0.0 0.00 3.21
5309 5739 9.982291 TGCTATCAAGTAAAAATTTGTCGTATC 57.018 29.630 0.00 0.0 0.00 2.24
5313 5743 8.728088 AGTTGCTATCAAGTAAAAATTTGTCG 57.272 30.769 0.00 0.0 34.26 4.35
5342 5772 9.249053 TCACATTGCCCTAGAAAACAAAATATA 57.751 29.630 0.00 0.0 0.00 0.86
5367 5797 4.813697 GCCTTTACATTGATCTCAGAGGTC 59.186 45.833 3.40 3.4 0.00 3.85
5388 5818 3.524541 GAATGGGAAAACATGATGTGCC 58.475 45.455 0.00 0.0 0.00 5.01
5389 5819 3.055963 TGGAATGGGAAAACATGATGTGC 60.056 43.478 0.00 0.0 0.00 4.57
5406 5844 5.416952 GTGTCCTGACAGATGAAAATGGAAT 59.583 40.000 3.32 0.0 42.74 3.01
5498 5976 9.099454 GTTTACAGAGGGAGTATCAAGTAAATG 57.901 37.037 0.00 0.0 34.70 2.32
5510 5988 8.628280 GTTCGTATATTAGTTTACAGAGGGAGT 58.372 37.037 0.00 0.0 0.00 3.85
5511 5989 7.802251 CGTTCGTATATTAGTTTACAGAGGGAG 59.198 40.741 0.00 0.0 0.00 4.30
5512 5990 7.642669 CGTTCGTATATTAGTTTACAGAGGGA 58.357 38.462 0.00 0.0 0.00 4.20
5513 5991 6.361748 GCGTTCGTATATTAGTTTACAGAGGG 59.638 42.308 0.00 0.0 0.00 4.30
5514 5992 7.137426 AGCGTTCGTATATTAGTTTACAGAGG 58.863 38.462 0.00 0.0 0.00 3.69
5515 5993 8.557869 AAGCGTTCGTATATTAGTTTACAGAG 57.442 34.615 0.00 0.0 0.00 3.35
5516 5994 8.915871 AAAGCGTTCGTATATTAGTTTACAGA 57.084 30.769 0.00 0.0 0.00 3.41
5531 6009 9.316730 TCCATAAACTAATATAAAAGCGTTCGT 57.683 29.630 0.00 0.0 0.00 3.85
5532 6010 9.793245 CTCCATAAACTAATATAAAAGCGTTCG 57.207 33.333 0.00 0.0 0.00 3.95
5534 6012 9.063615 CCCTCCATAAACTAATATAAAAGCGTT 57.936 33.333 0.00 0.0 0.00 4.84
5535 6013 8.434392 TCCCTCCATAAACTAATATAAAAGCGT 58.566 33.333 0.00 0.0 0.00 5.07
5536 6014 8.842358 TCCCTCCATAAACTAATATAAAAGCG 57.158 34.615 0.00 0.0 0.00 4.68
5537 6015 9.794719 ACTCCCTCCATAAACTAATATAAAAGC 57.205 33.333 0.00 0.0 0.00 3.51
5547 6025 9.275572 ACTAAAATGTACTCCCTCCATAAACTA 57.724 33.333 0.00 0.0 0.00 2.24
5548 6026 8.047310 CACTAAAATGTACTCCCTCCATAAACT 58.953 37.037 0.00 0.0 0.00 2.66
5549 6027 7.827729 ACACTAAAATGTACTCCCTCCATAAAC 59.172 37.037 0.00 0.0 0.00 2.01
5550 6028 7.924541 ACACTAAAATGTACTCCCTCCATAAA 58.075 34.615 0.00 0.0 0.00 1.40
5551 6029 7.504926 ACACTAAAATGTACTCCCTCCATAA 57.495 36.000 0.00 0.0 0.00 1.90
5552 6030 7.842743 ACTACACTAAAATGTACTCCCTCCATA 59.157 37.037 0.00 0.0 33.85 2.74
5553 6031 6.672657 ACTACACTAAAATGTACTCCCTCCAT 59.327 38.462 0.00 0.0 33.85 3.41
5554 6032 6.021030 ACTACACTAAAATGTACTCCCTCCA 58.979 40.000 0.00 0.0 33.85 3.86
5555 6033 6.070938 ACACTACACTAAAATGTACTCCCTCC 60.071 42.308 0.00 0.0 33.85 4.30
5556 6034 6.932947 ACACTACACTAAAATGTACTCCCTC 58.067 40.000 0.00 0.0 33.85 4.30
5557 6035 6.930068 ACACTACACTAAAATGTACTCCCT 57.070 37.500 0.00 0.0 33.85 4.20
5558 6036 7.277319 GCTTACACTACACTAAAATGTACTCCC 59.723 40.741 0.00 0.0 33.85 4.30
5559 6037 8.033626 AGCTTACACTACACTAAAATGTACTCC 58.966 37.037 0.00 0.0 33.85 3.85
5560 6038 8.983307 AGCTTACACTACACTAAAATGTACTC 57.017 34.615 0.00 0.0 33.85 2.59
5728 6550 6.560253 ATTTGTCTGAGATTACACAACACC 57.440 37.500 0.00 0.0 0.00 4.16
5758 6580 5.639082 TCAAGAACACACAGCACTATACATG 59.361 40.000 0.00 0.0 0.00 3.21
5923 6745 7.425606 GTCTTGTTTATGTCACAATTTGGTCT 58.574 34.615 0.78 0.0 33.67 3.85
5924 6746 6.640907 GGTCTTGTTTATGTCACAATTTGGTC 59.359 38.462 0.78 0.0 33.67 4.02
5925 6747 6.323739 AGGTCTTGTTTATGTCACAATTTGGT 59.676 34.615 0.78 0.0 33.67 3.67
5927 6749 7.592533 CAGAGGTCTTGTTTATGTCACAATTTG 59.407 37.037 0.00 0.0 33.67 2.32
5929 6751 6.772716 ACAGAGGTCTTGTTTATGTCACAATT 59.227 34.615 0.00 0.0 33.67 2.32
5930 6752 6.205464 CACAGAGGTCTTGTTTATGTCACAAT 59.795 38.462 0.00 0.0 33.67 2.71
5939 6761 4.040339 TGATCTGCACAGAGGTCTTGTTTA 59.960 41.667 6.50 0.0 41.33 2.01
5973 6795 9.541884 ACCCTTATTCCTGTTTATGTAATTTGT 57.458 29.630 0.00 0.0 0.00 2.83
5980 6807 8.333235 TCATGTAACCCTTATTCCTGTTTATGT 58.667 33.333 0.00 0.0 0.00 2.29


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

AutoCloner maintained by Alex Coulton.