Multiple sequence alignment - TraesCS3B01G124300

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 TraesCS3B01G124300 chr3B 100.000 7912 0 0 1 7912 97745403 97737492 0.000000e+00 14611.0
1 TraesCS3B01G124300 chr3D 96.808 5514 126 15 5 5479 61576677 61571175 0.000000e+00 9162.0
2 TraesCS3B01G124300 chr3D 96.429 1876 44 9 5430 7282 61571150 61569275 0.000000e+00 3072.0
3 TraesCS3B01G124300 chr3D 94.398 357 8 4 7561 7912 61569184 61568835 9.030000e-149 538.0
4 TraesCS3B01G124300 chr3D 94.231 52 3 0 5968 6019 477906264 477906213 6.580000e-11 80.5
5 TraesCS3B01G124300 chr3A 96.810 5486 124 17 22 5486 69654100 69648645 0.000000e+00 9114.0
6 TraesCS3B01G124300 chr3A 97.257 1422 35 2 5543 6960 69648367 69646946 0.000000e+00 2407.0
7 TraesCS3B01G124300 chr3A 93.466 352 14 4 7568 7912 69642914 69642565 1.520000e-141 514.0
8 TraesCS3B01G124300 chr3A 92.357 314 9 9 6965 7264 69646910 69646598 4.390000e-117 433.0
9 TraesCS3B01G124300 chr3A 94.931 217 5 2 5488 5701 69648579 69648366 1.270000e-87 335.0
10 TraesCS3B01G124300 chr3A 97.059 34 1 0 7397 7430 562912855 562912888 3.080000e-04 58.4
11 TraesCS3B01G124300 chr4A 93.103 58 3 1 5955 6011 120379632 120379689 5.090000e-12 84.2
12 TraesCS3B01G124300 chr1D 86.250 80 7 1 5964 6039 458142836 458142915 5.090000e-12 84.2
13 TraesCS3B01G124300 chr1D 85.000 80 8 1 5967 6042 458142932 458142853 2.370000e-10 78.7
14 TraesCS3B01G124300 chr5B 92.453 53 4 0 5960 6012 65711619 65711671 8.510000e-10 76.8
15 TraesCS3B01G124300 chr5B 94.444 36 2 0 7398 7433 334071916 334071881 1.000000e-03 56.5
16 TraesCS3B01G124300 chr5A 85.507 69 8 2 5942 6010 42569301 42569367 3.960000e-08 71.3
17 TraesCS3B01G124300 chr2D 83.544 79 8 2 5966 6040 7074394 7074471 1.420000e-07 69.4
18 TraesCS3B01G124300 chr7A 85.294 68 5 3 5984 6050 83783509 83783572 1.840000e-06 65.8
19 TraesCS3B01G124300 chr6D 94.444 36 2 0 7398 7433 81654762 81654727 1.000000e-03 56.5
20 TraesCS3B01G124300 chr6D 100.000 28 0 0 7403 7430 112916680 112916707 1.400000e-02 52.8
21 TraesCS3B01G124300 chr2B 96.970 33 1 0 7398 7430 16263053 16263085 1.000000e-03 56.5
22 TraesCS3B01G124300 chr2B 96.970 33 1 0 7398 7430 765556363 765556395 1.000000e-03 56.5
23 TraesCS3B01G124300 chr1B 94.444 36 2 0 7398 7433 652480960 652480925 1.000000e-03 56.5
24 TraesCS3B01G124300 chr6A 94.286 35 2 0 7399 7433 600811448 600811414 4.000000e-03 54.7


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 TraesCS3B01G124300 chr3B 97737492 97745403 7911 True 14611.000000 14611 100.000000 1 7912 1 chr3B.!!$R1 7911
1 TraesCS3B01G124300 chr3D 61568835 61576677 7842 True 4257.333333 9162 95.878333 5 7912 3 chr3D.!!$R2 7907
2 TraesCS3B01G124300 chr3A 69642565 69654100 11535 True 2560.600000 9114 94.964200 22 7912 5 chr3A.!!$R1 7890

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
227 228 0.179225 CGAAGATTTGGTTGCGACGG 60.179 55.000 0.0 0.0 0.00 4.79 F
1023 1039 0.238553 GTCCAGCAAAAGGTTCTCGC 59.761 55.000 0.0 0.0 0.00 5.03 F
2223 2241 0.960364 ATTGCATCCGTTGAACCGCT 60.960 50.000 0.0 0.0 0.00 5.52 F
3408 3427 1.593006 GTCACATGCGATTAACCCTCG 59.407 52.381 0.0 0.0 39.11 4.63 F
3959 3978 2.568956 TGTCTTCTGTGGCAGCTTCTAT 59.431 45.455 0.0 0.0 0.00 1.98 F
5019 5038 4.446371 ACTATGCTGAACTAAGTGATGGC 58.554 43.478 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1823 1.488705 CCCCTGGCAGTACCTTCACA 61.489 60.000 14.43 0.00 40.22 3.58 R
2453 2471 0.107456 CCGTCCCTTCCCAGATGATG 59.893 60.000 0.00 0.00 0.00 3.07 R
3683 3702 1.610886 GCCCTTCCTCCTGTGTGTTAC 60.611 57.143 0.00 0.00 0.00 2.50 R
5277 5296 1.068588 TGCCACATAGATAGACGGCAC 59.931 52.381 0.00 0.00 44.27 5.01 R
5301 5320 3.756434 GTGCAAAACCAATAGCTGACCTA 59.244 43.478 0.00 0.00 0.00 3.08 R
6948 7293 0.175760 ATCAATCACCGAGGACCACG 59.824 55.000 4.11 4.11 0.00 4.94 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 2.327940 GCTCTCTCTCGCTCTCGC 59.672 66.667 0.00 0.00 35.26 5.03
18 19 2.180204 GCTCTCTCTCGCTCTCGCT 61.180 63.158 0.00 0.00 35.26 4.93
19 20 1.934463 CTCTCTCTCGCTCTCGCTC 59.066 63.158 0.00 0.00 35.26 5.03
20 21 1.821241 CTCTCTCTCGCTCTCGCTCG 61.821 65.000 0.00 0.00 35.26 5.03
21 22 3.506312 CTCTCTCGCTCTCGCTCGC 62.506 68.421 0.00 0.00 35.26 5.03
22 23 3.572539 CTCTCGCTCTCGCTCGCT 61.573 66.667 0.00 0.00 35.26 4.93
23 24 3.506312 CTCTCGCTCTCGCTCGCTC 62.506 68.421 0.00 0.00 35.26 5.03
24 25 4.936248 CTCGCTCTCGCTCGCTCG 62.936 72.222 0.00 0.00 35.26 5.03
65 66 4.131088 GGTCGCGTCTGGGAGGTC 62.131 72.222 5.77 0.00 37.78 3.85
68 69 4.803426 CGCGTCTGGGAGGTCTGC 62.803 72.222 0.00 0.00 0.00 4.26
122 123 1.666209 CGATGGGGAATTTTGCGGCT 61.666 55.000 0.00 0.00 0.00 5.52
156 157 5.715070 CACGTTTTAGATGGTCTCTTCTCT 58.285 41.667 0.00 0.00 35.28 3.10
168 169 4.584325 GGTCTCTTCTCTATGAGCAGATGT 59.416 45.833 0.00 0.00 32.23 3.06
225 226 1.461888 CGTCGAAGATTTGGTTGCGAC 60.462 52.381 0.00 0.00 43.10 5.19
227 228 0.179225 CGAAGATTTGGTTGCGACGG 60.179 55.000 0.00 0.00 0.00 4.79
228 229 0.454452 GAAGATTTGGTTGCGACGGC 60.454 55.000 0.00 0.00 40.52 5.68
360 361 1.894756 TTCCCTGGGTTGCGTTTCG 60.895 57.895 13.56 0.00 0.00 3.46
361 362 2.593436 CCCTGGGTTGCGTTTCGT 60.593 61.111 3.97 0.00 0.00 3.85
378 379 4.895224 TTCGTCTATCTGCTGTTACGAT 57.105 40.909 0.00 0.00 38.90 3.73
459 475 3.433615 AGCAATTCTCTTCTTCGTTTCCG 59.566 43.478 0.00 0.00 0.00 4.30
482 498 5.352569 CGGTCATGGATTAATTCTGCTATCC 59.647 44.000 0.00 0.00 37.62 2.59
596 612 1.126846 CAGTTCGTCGGACAATTCAGC 59.873 52.381 6.41 0.00 0.00 4.26
692 708 1.814248 GCCGGGTAGATTCCATGAACC 60.814 57.143 2.18 0.00 0.00 3.62
707 723 5.988561 TCCATGAACCTTTGTGTAAATTTGC 59.011 36.000 0.00 0.00 0.00 3.68
719 735 7.192148 TGTGTAAATTTGCGTAGTAACATGT 57.808 32.000 0.00 0.00 0.00 3.21
820 836 2.494870 TCGGTTCTTAAGTAGGTCTGGC 59.505 50.000 1.63 0.00 0.00 4.85
831 847 4.417437 AGTAGGTCTGGCTTGAACTCTTA 58.583 43.478 2.18 0.00 35.38 2.10
849 865 6.432581 ACTCTTAATTATGGTTTCCTTCCCC 58.567 40.000 0.00 0.00 0.00 4.81
860 876 1.414158 TCCTTCCCCGAAGCTGATAG 58.586 55.000 0.00 0.00 38.24 2.08
1023 1039 0.238553 GTCCAGCAAAAGGTTCTCGC 59.761 55.000 0.00 0.00 0.00 5.03
1125 1141 6.641474 ACTTAAAGTAAGACATAGCAGGACC 58.359 40.000 2.11 0.00 39.09 4.46
1143 1159 6.072618 GCAGGACCTGATGATAGATTCATTTG 60.073 42.308 26.25 0.00 45.29 2.32
1197 1213 7.341769 CACCACATTTCCCCATTCTTAAGATAA 59.658 37.037 5.89 0.00 0.00 1.75
1327 1343 4.261489 GGATGAGCTGATGCACTTTTATGG 60.261 45.833 0.00 0.00 42.74 2.74
1585 1601 6.922247 ATCATGCATCTTCTACAGTTTCTG 57.078 37.500 0.00 0.00 37.52 3.02
1615 1631 4.324402 GCAAACCAAGACGATAATTTGCTG 59.676 41.667 11.22 0.00 45.25 4.41
1695 1713 1.527034 TCAGCCTGCAGTGATGTTTC 58.473 50.000 13.81 0.00 0.00 2.78
1696 1714 1.202794 TCAGCCTGCAGTGATGTTTCA 60.203 47.619 13.81 0.00 0.00 2.69
1805 1823 5.265989 AGACTTTCTTATCTCTTCCGGAGT 58.734 41.667 3.34 0.00 42.40 3.85
1972 1990 5.894393 TCTCTTTTTGGTTGGTTCCATAACA 59.106 36.000 0.00 0.00 37.34 2.41
1973 1991 6.553100 TCTCTTTTTGGTTGGTTCCATAACAT 59.447 34.615 0.00 0.00 37.34 2.71
2041 2059 5.537295 TCAGTTCTAGTGTTGCCTGTAAGTA 59.463 40.000 0.00 0.00 0.00 2.24
2176 2194 9.331282 GATGATTATTACTAACCTTGAGTGCTT 57.669 33.333 0.00 0.00 0.00 3.91
2213 2231 3.058016 AGTGACTTTTGACATTGCATCCG 60.058 43.478 0.00 0.00 0.00 4.18
2223 2241 0.960364 ATTGCATCCGTTGAACCGCT 60.960 50.000 0.00 0.00 0.00 5.52
2430 2448 1.704628 TGGCAGGAATCTCCAAGTCAA 59.295 47.619 0.00 0.00 39.61 3.18
2453 2471 7.604164 TCAAAGAGAAACTGATCAGATGGTTAC 59.396 37.037 29.27 12.82 0.00 2.50
2490 2508 1.803519 GAGACGTGGAGAAGCTGCG 60.804 63.158 0.00 0.00 0.00 5.18
2758 2777 8.143835 CAGTTTTACTTCCTTTGGACATCAATT 58.856 33.333 0.00 0.00 34.98 2.32
3122 3141 4.187694 AGAGCTTCTTTCTGGAATTAGCG 58.812 43.478 0.00 0.00 0.00 4.26
3256 3275 6.127535 CCAGTTCAGATGCATAGAAACCAAAT 60.128 38.462 13.78 0.00 0.00 2.32
3296 3315 3.181489 ACTCTAGCTTATTGTCCGAACCG 60.181 47.826 0.00 0.00 0.00 4.44
3408 3427 1.593006 GTCACATGCGATTAACCCTCG 59.407 52.381 0.00 0.00 39.11 4.63
3668 3687 4.474651 TGATCCAGGTACATGTGGAAAGAT 59.525 41.667 9.11 5.45 46.01 2.40
3683 3702 7.485810 TGTGGAAAGATAATTTCTGCATCATG 58.514 34.615 0.00 0.00 33.93 3.07
3959 3978 2.568956 TGTCTTCTGTGGCAGCTTCTAT 59.431 45.455 0.00 0.00 0.00 1.98
5004 5023 7.201496 CGACAAAACGTTAGGAAATACTATGCT 60.201 37.037 0.00 0.00 0.00 3.79
5019 5038 4.446371 ACTATGCTGAACTAAGTGATGGC 58.554 43.478 0.00 0.00 0.00 4.40
5277 5296 9.294030 GGCAATTAGACATTTAGAAATGAAGTG 57.706 33.333 19.31 13.59 46.72 3.16
5301 5320 3.306364 GCCGTCTATCTATGTGGCAGAAT 60.306 47.826 0.00 0.00 42.03 2.40
5314 5333 3.812053 GTGGCAGAATAGGTCAGCTATTG 59.188 47.826 13.93 2.68 38.74 1.90
5493 5674 8.320617 AGATGTGGTTTTAATACATGCCAATTT 58.679 29.630 0.00 0.00 35.35 1.82
5494 5675 9.593134 GATGTGGTTTTAATACATGCCAATTTA 57.407 29.630 0.00 0.00 35.35 1.40
5626 5970 9.643693 AAGAACAAGGTGAATGCTATATTTTTG 57.356 29.630 0.00 0.00 0.00 2.44
5981 6325 5.589452 AGCTAATATATACTCCTTCCGTCCG 59.411 44.000 0.00 0.00 0.00 4.79
6090 6434 4.666512 ACATCAAATACTGCTTGGTCCTT 58.333 39.130 0.00 0.00 0.00 3.36
6104 6448 5.582665 GCTTGGTCCTTGAACTGTTCTATAG 59.417 44.000 20.18 14.03 0.00 1.31
6253 6597 1.678970 GCCACCATTCCACCCACTC 60.679 63.158 0.00 0.00 0.00 3.51
6443 6787 1.893808 CTTCTGTGCAGCCACGGTT 60.894 57.895 0.00 0.00 46.30 4.44
6448 6792 1.210155 GTGCAGCCACGGTTTCATC 59.790 57.895 0.00 0.00 31.34 2.92
6710 7055 1.464997 GCTTCATCGTCCTTGTCCAAC 59.535 52.381 0.00 0.00 0.00 3.77
6711 7056 2.076863 CTTCATCGTCCTTGTCCAACC 58.923 52.381 0.00 0.00 0.00 3.77
6722 7067 4.680237 TCCAACCACGCGCAGGAG 62.680 66.667 23.14 14.58 0.00 3.69
6919 7264 2.481441 TCTGGCAATGTAGTCCCAGAT 58.519 47.619 4.23 0.00 46.50 2.90
6944 7289 4.035102 GGCACACCCAGGGTCCTC 62.035 72.222 8.79 0.00 31.02 3.71
6946 7291 3.706373 CACACCCAGGGTCCTCCG 61.706 72.222 8.79 0.00 41.52 4.63
6947 7292 3.923645 ACACCCAGGGTCCTCCGA 61.924 66.667 8.79 0.00 41.52 4.55
6948 7293 3.391382 CACCCAGGGTCCTCCGAC 61.391 72.222 8.79 0.00 41.52 4.79
6951 7296 3.760035 CCAGGGTCCTCCGACGTG 61.760 72.222 0.00 0.00 40.17 4.49
6953 7298 4.296729 AGGGTCCTCCGACGTGGT 62.297 66.667 0.00 0.00 40.17 4.16
6956 7301 2.675772 GTCCTCCGACGTGGTCCT 60.676 66.667 0.00 0.00 39.52 3.85
6957 7302 2.360852 TCCTCCGACGTGGTCCTC 60.361 66.667 0.00 0.00 39.52 3.71
6958 7303 3.812019 CCTCCGACGTGGTCCTCG 61.812 72.222 11.71 11.71 39.52 4.63
6962 7307 3.359523 CGACGTGGTCCTCGGTGA 61.360 66.667 17.11 0.00 0.00 4.02
7069 7446 3.605486 GCTTAGAAATGCAGCGTTTTGAG 59.395 43.478 13.93 12.29 0.00 3.02
7211 7590 7.482169 ACTCACAGGAACAATAAGAGATACA 57.518 36.000 0.00 0.00 0.00 2.29
7264 7655 3.126171 TCGGACGGCTGAATTTTGTTATG 59.874 43.478 0.00 0.00 0.00 1.90
7270 7661 4.165779 GGCTGAATTTTGTTATGACGGTG 58.834 43.478 0.00 0.00 0.00 4.94
7282 7673 1.816074 TGACGGTGTTGCTAAATCCC 58.184 50.000 0.00 0.00 0.00 3.85
7287 7678 2.790433 GGTGTTGCTAAATCCCACTCA 58.210 47.619 0.00 0.00 0.00 3.41
7288 7679 2.488153 GGTGTTGCTAAATCCCACTCAC 59.512 50.000 0.00 0.00 0.00 3.51
7290 7681 3.189287 GTGTTGCTAAATCCCACTCACAG 59.811 47.826 0.00 0.00 0.00 3.66
7291 7682 3.181445 TGTTGCTAAATCCCACTCACAGT 60.181 43.478 0.00 0.00 0.00 3.55
7292 7683 4.041075 TGTTGCTAAATCCCACTCACAGTA 59.959 41.667 0.00 0.00 0.00 2.74
7294 7685 3.187700 GCTAAATCCCACTCACAGTACG 58.812 50.000 0.00 0.00 0.00 3.67
7295 7686 3.368116 GCTAAATCCCACTCACAGTACGT 60.368 47.826 0.00 0.00 0.00 3.57
7296 7687 4.142315 GCTAAATCCCACTCACAGTACGTA 60.142 45.833 0.00 0.00 0.00 3.57
7297 7688 4.451629 AAATCCCACTCACAGTACGTAG 57.548 45.455 0.00 0.00 0.00 3.51
7301 7692 2.352421 CCCACTCACAGTACGTAGTTGG 60.352 54.545 10.06 10.06 37.78 3.77
7320 7734 4.193826 TGGCTGTCTTGAGATCTTACAC 57.806 45.455 0.00 0.00 0.00 2.90
7321 7735 3.578282 TGGCTGTCTTGAGATCTTACACA 59.422 43.478 0.00 0.00 0.00 3.72
7322 7736 4.180057 GGCTGTCTTGAGATCTTACACAG 58.820 47.826 16.28 16.28 0.00 3.66
7323 7737 4.081972 GGCTGTCTTGAGATCTTACACAGA 60.082 45.833 21.54 6.62 35.33 3.41
7324 7738 5.101628 GCTGTCTTGAGATCTTACACAGAG 58.898 45.833 21.54 4.06 33.87 3.35
7326 7740 6.260870 TGTCTTGAGATCTTACACAGAGAC 57.739 41.667 0.00 3.09 33.87 3.36
7327 7741 5.184096 TGTCTTGAGATCTTACACAGAGACC 59.816 44.000 11.62 0.00 33.87 3.85
7329 7743 5.417266 TCTTGAGATCTTACACAGAGACCTG 59.583 44.000 0.00 0.00 45.76 4.00
7342 7756 5.756195 CAGAGACCTGTGTGATTTTTCAA 57.244 39.130 0.00 0.00 35.70 2.69
7343 7757 5.755813 CAGAGACCTGTGTGATTTTTCAAG 58.244 41.667 0.00 0.00 35.70 3.02
7344 7758 5.297776 CAGAGACCTGTGTGATTTTTCAAGT 59.702 40.000 0.00 0.00 35.70 3.16
7345 7759 5.888161 AGAGACCTGTGTGATTTTTCAAGTT 59.112 36.000 0.00 0.00 0.00 2.66
7346 7760 6.038714 AGAGACCTGTGTGATTTTTCAAGTTC 59.961 38.462 0.00 0.00 0.00 3.01
7347 7761 5.888161 AGACCTGTGTGATTTTTCAAGTTCT 59.112 36.000 0.00 0.00 0.00 3.01
7348 7762 6.378280 AGACCTGTGTGATTTTTCAAGTTCTT 59.622 34.615 0.00 0.00 0.00 2.52
7349 7763 6.935167 ACCTGTGTGATTTTTCAAGTTCTTT 58.065 32.000 0.00 0.00 0.00 2.52
7350 7764 7.386059 ACCTGTGTGATTTTTCAAGTTCTTTT 58.614 30.769 0.00 0.00 0.00 2.27
7351 7765 7.545615 ACCTGTGTGATTTTTCAAGTTCTTTTC 59.454 33.333 0.00 0.00 0.00 2.29
7352 7766 7.761249 CCTGTGTGATTTTTCAAGTTCTTTTCT 59.239 33.333 0.00 0.00 0.00 2.52
7353 7767 9.143631 CTGTGTGATTTTTCAAGTTCTTTTCTT 57.856 29.630 0.00 0.00 0.00 2.52
7401 7992 3.961480 AACATGATGGTGTCTCGAGAA 57.039 42.857 18.55 0.99 0.00 2.87
7414 8005 6.036191 GGTGTCTCGAGAATTGGTTAAATCTC 59.964 42.308 18.55 0.00 0.00 2.75
7421 8012 7.117812 TCGAGAATTGGTTAAATCTCAGTTGAC 59.882 37.037 6.08 0.00 0.00 3.18
7423 8014 8.103948 AGAATTGGTTAAATCTCAGTTGACTG 57.896 34.615 4.77 4.77 45.08 3.51
7433 8035 1.143305 CAGTTGACTGAGACCTTGCG 58.857 55.000 5.19 0.00 46.59 4.85
7435 8037 0.880278 GTTGACTGAGACCTTGCGCA 60.880 55.000 5.66 5.66 0.00 6.09
7453 8055 3.488047 GCGCAATTGCATCTCAGTGTATT 60.488 43.478 28.77 0.00 42.21 1.89
7454 8056 4.033019 CGCAATTGCATCTCAGTGTATTG 58.967 43.478 28.77 4.63 42.21 1.90
7455 8057 4.437794 CGCAATTGCATCTCAGTGTATTGT 60.438 41.667 28.77 0.00 42.21 2.71
7501 8103 3.932545 CGCAGCTATCCAGAGAAGTAT 57.067 47.619 0.00 0.00 0.00 2.12
7503 8105 3.366883 CGCAGCTATCCAGAGAAGTATCC 60.367 52.174 0.00 0.00 0.00 2.59
7504 8106 3.366883 GCAGCTATCCAGAGAAGTATCCG 60.367 52.174 0.00 0.00 0.00 4.18
7505 8107 3.823873 CAGCTATCCAGAGAAGTATCCGT 59.176 47.826 0.00 0.00 0.00 4.69
7507 8109 3.120130 GCTATCCAGAGAAGTATCCGTCG 60.120 52.174 0.00 0.00 0.00 5.12
7508 8110 2.414994 TCCAGAGAAGTATCCGTCGT 57.585 50.000 0.00 0.00 0.00 4.34
7509 8111 3.548745 TCCAGAGAAGTATCCGTCGTA 57.451 47.619 0.00 0.00 0.00 3.43
7510 8112 3.201290 TCCAGAGAAGTATCCGTCGTAC 58.799 50.000 0.00 0.00 0.00 3.67
7515 8117 2.424956 AGAAGTATCCGTCGTACCCAAC 59.575 50.000 0.00 0.00 0.00 3.77
7539 8141 6.486993 ACAACATAAGAAAACTCAAGGACTCC 59.513 38.462 0.00 0.00 0.00 3.85
7540 8142 5.238583 ACATAAGAAAACTCAAGGACTCCG 58.761 41.667 0.00 0.00 0.00 4.63
7543 8145 5.485209 AAGAAAACTCAAGGACTCCGTAT 57.515 39.130 0.00 0.00 0.00 3.06
7548 9953 4.920640 ACTCAAGGACTCCGTATGTATG 57.079 45.455 0.00 0.00 0.00 2.39
7627 11425 5.664457 TCTGTCTGCCTAATTCACTGTATG 58.336 41.667 0.00 0.00 0.00 2.39
7663 11469 4.862641 ATTCCCTGTGCCTATTACACTT 57.137 40.909 0.00 0.00 38.86 3.16
7693 11500 6.610075 ATCCAAAATCTTGCAACTGGTAAT 57.390 33.333 0.00 0.00 0.00 1.89
7735 11542 7.543947 TGTTTCTATTCATCTGTGCTGTATG 57.456 36.000 0.00 0.00 0.00 2.39
7736 11543 7.105588 TGTTTCTATTCATCTGTGCTGTATGT 58.894 34.615 0.00 0.00 0.00 2.29
7737 11544 8.257306 TGTTTCTATTCATCTGTGCTGTATGTA 58.743 33.333 0.00 0.00 0.00 2.29
7738 11545 9.265901 GTTTCTATTCATCTGTGCTGTATGTAT 57.734 33.333 0.00 0.00 0.00 2.29
7766 11575 7.336427 TGAATGTACATTGATCATGTTAGTGCA 59.664 33.333 25.42 8.97 44.40 4.57
7819 11628 1.767681 GTCATCTCCCTCCATCTTGCT 59.232 52.381 0.00 0.00 0.00 3.91
7820 11629 1.767088 TCATCTCCCTCCATCTTGCTG 59.233 52.381 0.00 0.00 0.00 4.41
7821 11630 0.473326 ATCTCCCTCCATCTTGCTGC 59.527 55.000 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.936248 CGAGCGAGCGAGCGAGAG 62.936 72.222 1.41 0.00 43.00 3.20
86 87 1.656875 CGCATCTTCTCCGAGAGCG 60.657 63.158 13.37 13.37 37.15 5.03
122 123 3.787785 TCTAAAACGTGCAAGTCACAGA 58.212 40.909 5.55 5.97 45.92 3.41
168 169 2.196997 ATCCAAGCGGCCTAAGCACA 62.197 55.000 0.00 0.00 42.56 4.57
360 361 5.502544 GCCAAAATCGTAACAGCAGATAGAC 60.503 44.000 0.00 0.00 0.00 2.59
361 362 4.570772 GCCAAAATCGTAACAGCAGATAGA 59.429 41.667 0.00 0.00 0.00 1.98
378 379 2.869192 GCGACAAAAATCCAAGCCAAAA 59.131 40.909 0.00 0.00 0.00 2.44
459 475 6.240894 TGGATAGCAGAATTAATCCATGACC 58.759 40.000 0.00 0.00 42.25 4.02
482 498 4.677378 CGAGTTAGATAAGATCCGCAAGTG 59.323 45.833 0.00 0.00 0.00 3.16
596 612 1.779025 CGCATCCAAATCCGCCAGAG 61.779 60.000 0.00 0.00 0.00 3.35
692 708 8.626576 CATGTTACTACGCAAATTTACACAAAG 58.373 33.333 0.00 0.00 0.00 2.77
707 723 7.260558 TGAATCTCCTAGACATGTTACTACG 57.739 40.000 0.00 0.00 0.00 3.51
719 735 5.775195 TCACACAGACTTTGAATCTCCTAGA 59.225 40.000 0.00 0.00 0.00 2.43
831 847 4.278310 CTTCGGGGAAGGAAACCATAATT 58.722 43.478 0.00 0.00 36.16 1.40
860 876 0.960364 TCAGATTTGGGCAACGAGGC 60.960 55.000 0.00 0.00 43.27 4.70
1023 1039 8.815141 TTTTTATTGTGATCTTGTGGATTGTG 57.185 30.769 0.00 0.00 34.33 3.33
1143 1159 1.836383 CTACAACTACCGGTCATCGC 58.164 55.000 12.40 0.00 37.59 4.58
1303 1319 1.760192 AAAGTGCATCAGCTCATCCC 58.240 50.000 0.00 0.00 42.74 3.85
1615 1631 7.573968 ATTTAATAATGCCCTGTTCTCTGTC 57.426 36.000 0.00 0.00 0.00 3.51
1695 1713 8.810427 GCCAATTTAAACAATGATCATAGTGTG 58.190 33.333 9.04 6.09 0.00 3.82
1696 1714 8.530311 TGCCAATTTAAACAATGATCATAGTGT 58.470 29.630 9.04 7.94 0.00 3.55
1805 1823 1.488705 CCCCTGGCAGTACCTTCACA 61.489 60.000 14.43 0.00 40.22 3.58
2002 2020 8.037758 CACTAGAACTGAACTATGAAGAACCAT 58.962 37.037 0.00 0.00 0.00 3.55
2041 2059 4.463186 GCCCTCCTTACAGTATCATATCGT 59.537 45.833 0.00 0.00 0.00 3.73
2089 2107 6.540551 TGCACTTAGTTGACTGTACATTTCAA 59.459 34.615 13.48 13.48 0.00 2.69
2176 2194 8.647796 TCAAAAGTCACTCCAGAAGTTAAGATA 58.352 33.333 0.00 0.00 35.45 1.98
2223 2241 3.832490 TCAGAGCCTACTAAGTGCAAAGA 59.168 43.478 0.00 0.00 0.00 2.52
2360 2378 6.014584 TGCTAGTCAAATTCAGAAGTAGGTCA 60.015 38.462 0.00 0.00 0.00 4.02
2406 2424 1.280133 CTTGGAGATTCCTGCCAGTGA 59.720 52.381 0.00 0.00 37.46 3.41
2430 2448 7.009179 TGTAACCATCTGATCAGTTTCTCTT 57.991 36.000 21.92 9.67 0.00 2.85
2453 2471 0.107456 CCGTCCCTTCCCAGATGATG 59.893 60.000 0.00 0.00 0.00 3.07
2490 2508 2.064014 GCTGCATTCTCTTTTTGCCAC 58.936 47.619 0.00 0.00 35.51 5.01
2630 2648 8.315391 ACTATCAAAACTACGTTTAAGGGAAC 57.685 34.615 0.00 0.00 34.43 3.62
2758 2777 7.004555 TCTCTTCATTAGCCTTGTTTGTAGA 57.995 36.000 0.00 0.00 0.00 2.59
2928 2947 1.739466 TCGTCCATGCTTTGCTGAATC 59.261 47.619 0.00 0.00 0.00 2.52
3122 3141 3.305361 CACGACTCACATGACACATGATC 59.695 47.826 16.86 0.00 0.00 2.92
3256 3275 6.990349 GCTAGAGTGGTTGCCATACTATTTTA 59.010 38.462 0.00 0.00 35.28 1.52
3668 3687 7.361971 CCTGTGTGTTACATGATGCAGAAATTA 60.362 37.037 0.00 0.00 38.92 1.40
3683 3702 1.610886 GCCCTTCCTCCTGTGTGTTAC 60.611 57.143 0.00 0.00 0.00 2.50
3959 3978 6.288294 ACAGCATGAAGACAAGTACAACTAA 58.712 36.000 0.00 0.00 39.69 2.24
4126 4145 6.097554 ATTGATAACAAATGGACGCCCAATTA 59.902 34.615 0.00 0.00 40.82 1.40
4232 4251 3.118592 ACTGCCATTAGACTAACTGGAGC 60.119 47.826 19.59 10.39 0.00 4.70
4612 4631 3.128349 GTGAACACTTGCGAGTTAGGAA 58.872 45.455 3.02 0.00 32.54 3.36
5004 5023 2.076100 CGCAAGCCATCACTTAGTTCA 58.924 47.619 0.00 0.00 0.00 3.18
5019 5038 2.280628 GTTGGTAGAGAATCCCGCAAG 58.719 52.381 0.00 0.00 33.66 4.01
5229 5248 7.941919 TGCCAACAAAATGTAACAAGTATACA 58.058 30.769 5.50 0.00 37.64 2.29
5250 5269 9.023962 ACTTCATTTCTAAATGTCTAATTGCCA 57.976 29.630 13.58 0.00 44.66 4.92
5272 5291 4.045104 CACATAGATAGACGGCACACTTC 58.955 47.826 0.00 0.00 0.00 3.01
5277 5296 1.068588 TGCCACATAGATAGACGGCAC 59.931 52.381 0.00 0.00 44.27 5.01
5301 5320 3.756434 GTGCAAAACCAATAGCTGACCTA 59.244 43.478 0.00 0.00 0.00 3.08
5314 5333 4.578928 TCTTCCTTTCTACAGTGCAAAACC 59.421 41.667 0.00 0.00 0.00 3.27
5626 5970 5.648092 AGTTCAGTTATGCATTTCTGGGTAC 59.352 40.000 21.95 18.08 0.00 3.34
6028 6372 1.002315 CCCCTTCCCAAATTGCTTGTG 59.998 52.381 0.00 0.00 32.65 3.33
6946 7291 0.736325 CAATCACCGAGGACCACGTC 60.736 60.000 10.51 0.00 0.00 4.34
6947 7292 1.183030 TCAATCACCGAGGACCACGT 61.183 55.000 10.51 0.00 0.00 4.49
6948 7293 0.175760 ATCAATCACCGAGGACCACG 59.824 55.000 4.11 4.11 0.00 4.94
6949 7294 2.093447 AGAATCAATCACCGAGGACCAC 60.093 50.000 0.00 0.00 0.00 4.16
6950 7295 2.093500 CAGAATCAATCACCGAGGACCA 60.093 50.000 0.00 0.00 0.00 4.02
6951 7296 2.555199 CAGAATCAATCACCGAGGACC 58.445 52.381 0.00 0.00 0.00 4.46
6953 7298 1.486310 CCCAGAATCAATCACCGAGGA 59.514 52.381 0.00 0.00 0.00 3.71
6956 7301 1.905894 TCACCCAGAATCAATCACCGA 59.094 47.619 0.00 0.00 0.00 4.69
6957 7302 2.009774 GTCACCCAGAATCAATCACCG 58.990 52.381 0.00 0.00 0.00 4.94
6958 7303 3.356529 AGTCACCCAGAATCAATCACC 57.643 47.619 0.00 0.00 0.00 4.02
6960 7305 5.222027 TGGTAAAGTCACCCAGAATCAATCA 60.222 40.000 0.00 0.00 37.84 2.57
6962 7307 5.255397 TGGTAAAGTCACCCAGAATCAAT 57.745 39.130 0.00 0.00 37.84 2.57
7069 7446 7.391786 CAACACATCTATGCTACGTTTTCTAC 58.608 38.462 0.00 0.00 0.00 2.59
7230 7616 1.741145 GCCGTCCGAATTTGTATTGGT 59.259 47.619 0.00 0.00 0.00 3.67
7231 7617 2.014128 AGCCGTCCGAATTTGTATTGG 58.986 47.619 0.00 0.00 0.00 3.16
7264 7655 1.467342 GTGGGATTTAGCAACACCGTC 59.533 52.381 0.00 0.00 0.00 4.79
7270 7661 3.412386 ACTGTGAGTGGGATTTAGCAAC 58.588 45.455 0.00 0.00 0.00 4.17
7282 7673 2.030185 AGCCAACTACGTACTGTGAGTG 60.030 50.000 0.00 0.00 0.00 3.51
7287 7678 2.236766 AGACAGCCAACTACGTACTGT 58.763 47.619 13.73 13.73 43.93 3.55
7288 7679 2.987149 CAAGACAGCCAACTACGTACTG 59.013 50.000 8.21 8.21 0.00 2.74
7290 7681 3.057736 TCTCAAGACAGCCAACTACGTAC 60.058 47.826 0.00 0.00 0.00 3.67
7291 7682 3.151554 TCTCAAGACAGCCAACTACGTA 58.848 45.455 0.00 0.00 0.00 3.57
7292 7683 1.961394 TCTCAAGACAGCCAACTACGT 59.039 47.619 0.00 0.00 0.00 3.57
7294 7685 4.464069 AGATCTCAAGACAGCCAACTAC 57.536 45.455 0.00 0.00 0.00 2.73
7295 7686 5.480422 TGTAAGATCTCAAGACAGCCAACTA 59.520 40.000 0.00 0.00 0.00 2.24
7296 7687 4.284490 TGTAAGATCTCAAGACAGCCAACT 59.716 41.667 0.00 0.00 0.00 3.16
7297 7688 4.390297 GTGTAAGATCTCAAGACAGCCAAC 59.610 45.833 0.00 0.00 0.00 3.77
7298 7689 4.040339 TGTGTAAGATCTCAAGACAGCCAA 59.960 41.667 0.00 0.00 0.00 4.52
7301 7692 5.065704 TCTGTGTAAGATCTCAAGACAGC 57.934 43.478 21.46 9.60 31.42 4.40
7320 7734 5.297776 ACTTGAAAAATCACACAGGTCTCTG 59.702 40.000 0.00 0.00 46.10 3.35
7321 7735 5.440610 ACTTGAAAAATCACACAGGTCTCT 58.559 37.500 0.00 0.00 0.00 3.10
7322 7736 5.757850 ACTTGAAAAATCACACAGGTCTC 57.242 39.130 0.00 0.00 0.00 3.36
7323 7737 5.888161 AGAACTTGAAAAATCACACAGGTCT 59.112 36.000 0.00 0.00 0.00 3.85
7324 7738 6.136541 AGAACTTGAAAAATCACACAGGTC 57.863 37.500 0.00 0.00 0.00 3.85
7326 7740 7.761249 AGAAAAGAACTTGAAAAATCACACAGG 59.239 33.333 0.00 0.00 0.00 4.00
7327 7741 8.693542 AGAAAAGAACTTGAAAAATCACACAG 57.306 30.769 0.00 0.00 0.00 3.66
7377 7791 4.462834 TCTCGAGACACCATCATGTTTAGT 59.537 41.667 12.08 0.00 31.24 2.24
7390 7804 6.590292 TGAGATTTAACCAATTCTCGAGACAC 59.410 38.462 16.36 0.00 41.18 3.67
7414 8005 1.143305 CGCAAGGTCTCAGTCAACTG 58.857 55.000 3.69 3.69 45.08 3.16
7421 8012 0.455633 GCAATTGCGCAAGGTCTCAG 60.456 55.000 28.62 12.81 38.28 3.35
7423 8014 0.171903 ATGCAATTGCGCAAGGTCTC 59.828 50.000 28.62 14.89 46.87 3.36
7433 8035 4.796830 CACAATACACTGAGATGCAATTGC 59.203 41.667 23.69 23.69 42.50 3.56
7435 8037 5.474532 ACACACAATACACTGAGATGCAATT 59.525 36.000 0.00 0.00 0.00 2.32
7453 8055 5.753438 GTCACTCTGAATTTCAGTACACACA 59.247 40.000 22.44 4.35 44.58 3.72
7454 8056 5.753438 TGTCACTCTGAATTTCAGTACACAC 59.247 40.000 22.44 14.92 44.58 3.82
7455 8057 5.912892 TGTCACTCTGAATTTCAGTACACA 58.087 37.500 22.44 17.53 44.58 3.72
7480 8082 0.103937 ACTTCTCTGGATAGCTGCGC 59.896 55.000 0.00 0.00 0.00 6.09
7482 8084 3.366883 CGGATACTTCTCTGGATAGCTGC 60.367 52.174 0.00 0.00 0.00 5.25
7493 8095 2.292267 TGGGTACGACGGATACTTCTC 58.708 52.381 0.00 0.00 31.42 2.87
7501 8103 0.680618 ATGTTGTTGGGTACGACGGA 59.319 50.000 0.00 0.00 43.08 4.69
7503 8105 3.577667 TCTTATGTTGTTGGGTACGACG 58.422 45.455 0.00 0.00 43.08 5.12
7504 8106 5.927954 TTTCTTATGTTGTTGGGTACGAC 57.072 39.130 0.00 0.00 40.93 4.34
7505 8107 6.056884 AGTTTTCTTATGTTGTTGGGTACGA 58.943 36.000 0.00 0.00 0.00 3.43
7507 8109 7.266922 TGAGTTTTCTTATGTTGTTGGGTAC 57.733 36.000 0.00 0.00 0.00 3.34
7508 8110 7.013846 CCTTGAGTTTTCTTATGTTGTTGGGTA 59.986 37.037 0.00 0.00 0.00 3.69
7509 8111 6.183360 CCTTGAGTTTTCTTATGTTGTTGGGT 60.183 38.462 0.00 0.00 0.00 4.51
7510 8112 6.040391 TCCTTGAGTTTTCTTATGTTGTTGGG 59.960 38.462 0.00 0.00 0.00 4.12
7515 8117 6.347725 CGGAGTCCTTGAGTTTTCTTATGTTG 60.348 42.308 7.77 0.00 0.00 3.33
7539 8141 7.090808 AGGCAGTGAACATATACATACATACG 58.909 38.462 0.00 0.00 0.00 3.06
7540 8142 9.355215 GTAGGCAGTGAACATATACATACATAC 57.645 37.037 0.00 0.00 0.00 2.39
7543 8145 6.239487 GGGTAGGCAGTGAACATATACATACA 60.239 42.308 0.00 0.00 0.00 2.29
7548 9953 4.682778 TGGGTAGGCAGTGAACATATAC 57.317 45.455 0.00 0.00 0.00 1.47
7627 11425 7.255139 GGCACAGGGAATACAGAATATGTTTAC 60.255 40.741 0.00 0.00 39.96 2.01
7663 11469 7.552687 CCAGTTGCAAGATTTTGGATAGTAGTA 59.447 37.037 0.00 0.00 34.44 1.82


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

AutoCloner maintained by Alex Coulton.