Multiple sequence alignment - TraesCS2D01G499500

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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 TraesCS2D01G499500 chr2D 100.000 5068 0 0 3590 8657 594541217 594536150 0.000000e+00 9359.0
1 TraesCS2D01G499500 chr2D 100.000 3109 0 0 1 3109 594544806 594541698 0.000000e+00 5742.0
2 TraesCS2D01G499500 chr2D 100.000 28 0 0 3599 3626 388833945 388833972 1.600000e-02 52.8
3 TraesCS2D01G499500 chr2B 95.891 3894 94 23 3590 7444 722083889 722080023 0.000000e+00 6244.0
4 TraesCS2D01G499500 chr2B 93.841 1656 61 13 1465 3108 722085638 722084012 0.000000e+00 2455.0
5 TraesCS2D01G499500 chr2B 92.746 772 41 8 1 763 722086965 722086200 0.000000e+00 1101.0
6 TraesCS2D01G499500 chr2B 89.123 616 43 11 7428 8036 722080011 722079413 0.000000e+00 745.0
7 TraesCS2D01G499500 chr2B 93.443 427 19 8 8237 8657 722027012 722026589 7.380000e-175 625.0
8 TraesCS2D01G499500 chr2B 85.822 529 21 20 792 1311 722086134 722085651 5.990000e-141 512.0
9 TraesCS2D01G499500 chr2B 88.626 211 17 5 8045 8249 722028229 722028020 5.190000e-62 250.0
10 TraesCS2D01G499500 chr2B 89.308 159 13 4 5951 6108 757065029 757065184 6.860000e-46 196.0
11 TraesCS2D01G499500 chr2B 89.375 160 9 6 5953 6108 497861526 497861371 2.470000e-45 195.0
12 TraesCS2D01G499500 chr2B 89.109 101 10 1 7196 7296 36434981 36434882 3.280000e-24 124.0
13 TraesCS2D01G499500 chr2A 92.118 1700 94 25 6981 8657 729160027 729158345 0.000000e+00 2361.0
14 TraesCS2D01G499500 chr2A 94.441 1511 56 11 1623 3106 729165598 729164089 0.000000e+00 2300.0
15 TraesCS2D01G499500 chr2A 95.169 1304 59 3 3599 4902 729163418 729162119 0.000000e+00 2056.0
16 TraesCS2D01G499500 chr2A 96.542 1041 33 1 4901 5941 729162004 729160967 0.000000e+00 1720.0
17 TraesCS2D01G499500 chr2A 93.678 949 31 10 6098 7036 729160965 729160036 0.000000e+00 1393.0
18 TraesCS2D01G499500 chr2A 92.308 780 37 8 1 763 729167361 729166588 0.000000e+00 1086.0
19 TraesCS2D01G499500 chr2A 89.302 860 41 21 792 1621 729166522 729165684 0.000000e+00 1031.0
20 TraesCS2D01G499500 chr2A 89.109 101 10 1 7196 7296 97566611 97566512 3.280000e-24 124.0
21 TraesCS2D01G499500 chr4B 86.774 310 33 6 5347 5649 578033383 578033075 1.080000e-88 339.0
22 TraesCS2D01G499500 chr1A 81.425 393 27 16 6097 6475 118275703 118276063 6.620000e-71 279.0
23 TraesCS2D01G499500 chr1A 91.791 134 10 1 3745 3878 118271174 118271306 1.480000e-42 185.0
24 TraesCS2D01G499500 chr1A 87.931 116 10 2 337 448 75388639 75388524 5.450000e-27 134.0
25 TraesCS2D01G499500 chr3D 91.617 167 10 2 5937 6101 120289835 120289999 2.430000e-55 228.0
26 TraesCS2D01G499500 chr3D 86.782 174 15 7 5943 6108 410990656 410990829 4.130000e-43 187.0
27 TraesCS2D01G499500 chr5A 91.358 162 9 4 5951 6109 577931146 577930987 5.260000e-52 217.0
28 TraesCS2D01G499500 chr5A 84.492 187 19 7 5953 6134 427828586 427828405 8.930000e-40 176.0
29 TraesCS2D01G499500 chr5A 89.655 116 8 2 337 448 245500908 245501023 2.520000e-30 145.0
30 TraesCS2D01G499500 chr5A 88.889 117 9 2 336 448 329387625 329387509 3.260000e-29 141.0
31 TraesCS2D01G499500 chr5D 90.123 162 11 4 5951 6109 458870282 458870123 1.140000e-48 206.0
32 TraesCS2D01G499500 chr5D 88.889 162 12 5 5951 6109 458874228 458874070 2.470000e-45 195.0
33 TraesCS2D01G499500 chr5D 100.000 29 0 0 3596 3624 42049814 42049842 4.000000e-03 54.7
34 TraesCS2D01G499500 chr1D 78.623 276 21 15 344 615 334608055 334607814 1.950000e-31 148.0
35 TraesCS2D01G499500 chr1D 100.000 31 0 0 3595 3625 12291442 12291472 3.380000e-04 58.4
36 TraesCS2D01G499500 chr1D 100.000 31 0 0 3595 3625 160525366 160525396 3.380000e-04 58.4
37 TraesCS2D01G499500 chr1D 100.000 28 0 0 3599 3626 491802473 491802500 1.600000e-02 52.8
38 TraesCS2D01G499500 chr7A 90.991 111 6 2 336 442 217752719 217752829 7.000000e-31 147.0
39 TraesCS2D01G499500 chr4A 90.826 109 6 2 344 448 140710710 140710818 9.060000e-30 143.0
40 TraesCS2D01G499500 chr7D 88.889 117 9 3 336 448 366721428 366721312 3.260000e-29 141.0
41 TraesCS2D01G499500 chr5B 91.346 104 8 1 7193 7296 339622967 339623069 3.260000e-29 141.0
42 TraesCS2D01G499500 chr1B 89.524 105 9 2 7193 7296 666842032 666842135 1.960000e-26 132.0
43 TraesCS2D01G499500 chr6A 90.099 101 9 1 7196 7296 38873811 38873712 7.050000e-26 130.0
44 TraesCS2D01G499500 chr6A 100.000 28 0 0 3599 3626 189986591 189986618 1.600000e-02 52.8
45 TraesCS2D01G499500 chr6A 96.774 31 1 0 3595 3625 609587292 609587322 1.600000e-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 TraesCS2D01G499500 chr2D 594536150 594544806 8656 True 7550.500000 9359 100.000000 1 8657 2 chr2D.!!$R1 8656
1 TraesCS2D01G499500 chr2B 722079413 722086965 7552 True 2211.400000 6244 91.484600 1 8036 5 chr2B.!!$R4 8035
2 TraesCS2D01G499500 chr2B 722026589 722028229 1640 True 437.500000 625 91.034500 8045 8657 2 chr2B.!!$R3 612
3 TraesCS2D01G499500 chr2A 729158345 729167361 9016 True 1706.714286 2361 93.365429 1 8657 7 chr2A.!!$R2 8656
4 TraesCS2D01G499500 chr5D 458870123 458874228 4105 True 200.500000 206 89.506000 5951 6109 2 chr5D.!!$R1 158

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
873 935 0.036590 TTCCCCGGAAAGGTAAACCG 59.963 55.000 0.73 0.00 45.24 4.44 F
1674 1850 0.323451 CAAGGGCCTTCCAGTTACCC 60.323 60.000 17.86 0.00 41.17 3.69 F
1885 2079 0.178967 TTGGCTTCCAACATCAGGCA 60.179 50.000 0.00 0.00 38.75 4.75 F
2566 2779 3.763057 AGTACCCTTGGCTTAAACTTGG 58.237 45.455 0.00 0.00 0.00 3.61 F
3947 4391 0.732571 AACAGCAACAAGGTCACGTG 59.267 50.000 9.94 9.94 0.00 4.49 F
4613 5059 1.077265 CCAACCACCCTGATGCCTT 59.923 57.895 0.00 0.00 0.00 4.35 F
4828 5274 1.766494 ACATCCACCGTCCACGTATA 58.234 50.000 0.00 0.00 37.74 1.47 F
5834 6403 1.003349 AGTGCAGCTGCTCAGATCTTT 59.997 47.619 36.61 14.63 42.66 2.52 F
7329 8001 0.594284 GGCGACCGTGAGTATACTGC 60.594 60.000 10.90 5.34 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1865 1.202533 GGCGATCAATTTCGAGGGAGA 60.203 52.381 3.75 0.00 41.62 3.71 R
2500 2708 4.476297 TGGTAGTCCACAGAGTAAACAGA 58.524 43.478 0.00 0.00 39.03 3.41 R
3750 4194 0.544223 TGTGTAACTGCACAGGGTGT 59.456 50.000 2.21 0.00 43.54 4.16 R
4186 4632 4.383649 CAGACAAGCAATGTAATGTGTTGC 59.616 41.667 1.35 1.35 44.12 4.17 R
5779 6348 1.813513 AAGTGTCTGGCATGTGTAGC 58.186 50.000 0.00 0.00 0.00 3.58 R
5811 6380 2.435069 AGATCTGAGCAGCTGCACTTAT 59.565 45.455 38.24 27.00 45.16 1.73 R
6814 7412 3.064545 GCTGAACAAAGCAGGCTACATAG 59.935 47.826 0.00 0.00 43.01 2.23 R
7338 8010 1.295792 GAACAAGGTGTGCGAGTTCA 58.704 50.000 0.00 0.00 38.66 3.18 R
8176 8890 4.895297 CCAAGAATACATAAATGGGCTGGT 59.105 41.667 0.00 0.00 0.00 4.00 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
195 200 3.072944 CAGCCTGGAAAAGAAGTCAGAG 58.927 50.000 0.00 0.00 0.00 3.35
222 227 2.613474 CGGTAAGAACAACGAATCCCCA 60.613 50.000 0.00 0.00 0.00 4.96
225 230 4.814771 GGTAAGAACAACGAATCCCCATAG 59.185 45.833 0.00 0.00 0.00 2.23
226 231 3.560636 AGAACAACGAATCCCCATAGG 57.439 47.619 0.00 0.00 0.00 2.57
272 282 1.831652 AACCTGTCCTTCCAGAGCCG 61.832 60.000 0.00 0.00 34.23 5.52
389 399 0.674895 ACCTGCTTGAATCCTGACGC 60.675 55.000 0.00 0.00 0.00 5.19
428 438 3.308014 AAGCAGGCCACGAGAGAGC 62.308 63.158 5.01 0.00 0.00 4.09
493 503 3.003763 GGAGTGGAGGAAGGCCGT 61.004 66.667 0.00 0.00 39.96 5.68
666 687 3.787001 GGGGGAGAAGGGAGCACG 61.787 72.222 0.00 0.00 0.00 5.34
763 788 4.043200 GGCTTGTTGGGCTGCGTC 62.043 66.667 0.00 0.00 0.00 5.19
764 789 4.389576 GCTTGTTGGGCTGCGTCG 62.390 66.667 0.00 0.00 0.00 5.12
768 793 2.356553 GTTGGGCTGCGTCGTGTA 60.357 61.111 0.00 0.00 0.00 2.90
769 794 2.048597 TTGGGCTGCGTCGTGTAG 60.049 61.111 0.00 0.00 0.00 2.74
770 795 3.583276 TTGGGCTGCGTCGTGTAGG 62.583 63.158 0.00 0.00 0.00 3.18
778 803 2.663196 GTCGTGTAGGCAGGCCTT 59.337 61.111 19.37 2.83 45.70 4.35
779 804 1.895238 GTCGTGTAGGCAGGCCTTA 59.105 57.895 19.37 5.50 45.70 2.69
780 805 0.459759 GTCGTGTAGGCAGGCCTTAC 60.460 60.000 19.37 16.09 45.70 2.34
781 806 0.901114 TCGTGTAGGCAGGCCTTACA 60.901 55.000 19.37 16.31 45.70 2.41
784 809 0.902531 TGTAGGCAGGCCTTACAGTC 59.097 55.000 19.37 0.00 45.70 3.51
786 811 0.902531 TAGGCAGGCCTTACAGTCAC 59.097 55.000 19.37 0.00 45.70 3.67
788 813 1.741770 GCAGGCCTTACAGTCACGG 60.742 63.158 0.00 0.00 0.00 4.94
789 814 1.079127 CAGGCCTTACAGTCACGGG 60.079 63.158 0.00 0.00 0.00 5.28
790 815 2.436115 GGCCTTACAGTCACGGGC 60.436 66.667 0.00 0.00 41.80 6.13
863 925 0.689745 ATCACGAGGATTCCCCGGAA 60.690 55.000 11.54 0.00 40.87 4.30
865 927 0.462047 CACGAGGATTCCCCGGAAAG 60.462 60.000 11.54 0.00 40.87 2.62
867 929 1.623542 CGAGGATTCCCCGGAAAGGT 61.624 60.000 0.73 0.00 40.87 3.50
870 932 2.240414 GAGGATTCCCCGGAAAGGTAAA 59.760 50.000 0.73 0.00 40.87 2.01
871 933 2.025605 AGGATTCCCCGGAAAGGTAAAC 60.026 50.000 0.73 0.00 40.87 2.01
872 934 2.372264 GATTCCCCGGAAAGGTAAACC 58.628 52.381 0.73 0.00 37.69 3.27
873 935 0.036590 TTCCCCGGAAAGGTAAACCG 59.963 55.000 0.73 0.00 45.24 4.44
878 940 2.463592 GGAAAGGTAAACCGAGGCG 58.536 57.895 0.00 0.00 42.08 5.52
1029 1100 4.812476 CACCGCAATCTCGCCCGA 62.812 66.667 0.00 0.00 0.00 5.14
1060 1132 3.330720 CCGCCAAGGTCCCCTCTT 61.331 66.667 0.00 0.00 30.89 2.85
1061 1133 2.269241 CGCCAAGGTCCCCTCTTC 59.731 66.667 0.00 0.00 30.89 2.87
1063 1135 1.925972 GCCAAGGTCCCCTCTTCCT 60.926 63.158 0.00 0.00 30.89 3.36
1064 1136 1.916206 GCCAAGGTCCCCTCTTCCTC 61.916 65.000 0.00 0.00 30.89 3.71
1150 1222 1.378762 CCGGTTGGATTCTGTGGGT 59.621 57.895 0.00 0.00 37.49 4.51
1152 1224 1.586154 CGGTTGGATTCTGTGGGTGC 61.586 60.000 0.00 0.00 0.00 5.01
1177 1255 1.923204 GCTGACTAGCTCGTTCATGTG 59.077 52.381 0.00 0.00 46.57 3.21
1290 1368 3.149196 GGTGAGTTCTCCTTTTGCATCA 58.851 45.455 0.00 0.00 0.00 3.07
1295 1373 4.154942 AGTTCTCCTTTTGCATCATGGTT 58.845 39.130 0.00 0.00 0.00 3.67
1334 1412 1.761198 TCAGCTCATGTGCTCTATGCT 59.239 47.619 19.00 2.13 41.98 3.79
1335 1413 2.961062 TCAGCTCATGTGCTCTATGCTA 59.039 45.455 19.00 0.00 41.98 3.49
1336 1414 3.005578 TCAGCTCATGTGCTCTATGCTAG 59.994 47.826 19.00 6.26 41.98 3.42
1337 1415 2.964464 AGCTCATGTGCTCTATGCTAGT 59.036 45.455 16.33 0.00 39.34 2.57
1338 1416 3.058450 GCTCATGTGCTCTATGCTAGTG 58.942 50.000 12.42 0.00 43.37 2.74
1344 1434 4.023980 TGTGCTCTATGCTAGTGGTTAGT 58.976 43.478 0.00 0.00 43.37 2.24
1379 1469 2.592574 GATGCTGCAGCCGCCATA 60.593 61.111 34.64 16.51 41.18 2.74
1380 1470 1.970114 GATGCTGCAGCCGCCATAT 60.970 57.895 34.64 20.67 41.18 1.78
1382 1472 2.903855 GCTGCAGCCGCCATATGT 60.904 61.111 28.76 0.00 37.32 2.29
1395 1485 3.189287 CGCCATATGTAATTTGCTCTCCC 59.811 47.826 1.24 0.00 0.00 4.30
1402 1492 2.891191 AATTTGCTCTCCCCGGTTTA 57.109 45.000 0.00 0.00 0.00 2.01
1403 1493 2.420058 ATTTGCTCTCCCCGGTTTAG 57.580 50.000 0.00 0.00 0.00 1.85
1606 1698 5.407502 TGTAGACCATTCGTGTGATAAGTG 58.592 41.667 0.00 0.00 0.00 3.16
1607 1699 4.801330 AGACCATTCGTGTGATAAGTGA 57.199 40.909 0.00 0.00 0.00 3.41
1621 1713 8.734386 GTGTGATAAGTGATTTTCTCCTTCATT 58.266 33.333 0.00 0.00 0.00 2.57
1650 1826 8.322091 AGTATAGTTGTGATAAGTTCAAGCCTT 58.678 33.333 0.00 0.00 35.70 4.35
1672 1848 2.160205 GTTCAAGGGCCTTCCAGTTAC 58.840 52.381 17.86 4.64 38.24 2.50
1674 1850 0.323451 CAAGGGCCTTCCAGTTACCC 60.323 60.000 17.86 0.00 41.17 3.69
1675 1851 0.774491 AAGGGCCTTCCAGTTACCCA 60.774 55.000 14.48 0.00 43.47 4.51
1689 1865 5.073144 CCAGTTACCCAGTATACCATGGAAT 59.927 44.000 21.47 0.00 39.02 3.01
1707 1890 3.743396 GGAATCTCCCTCGAAATTGATCG 59.257 47.826 0.00 0.00 44.04 3.69
1845 2035 2.881513 TGCATCGAGTGGCTTTGTTTAA 59.118 40.909 7.82 0.00 0.00 1.52
1877 2071 4.306600 CTGTAACCATTTTGGCTTCCAAC 58.693 43.478 0.00 0.00 43.82 3.77
1878 2072 3.706594 TGTAACCATTTTGGCTTCCAACA 59.293 39.130 0.00 0.00 43.82 3.33
1879 2073 4.346418 TGTAACCATTTTGGCTTCCAACAT 59.654 37.500 0.00 0.00 43.82 2.71
1880 2074 3.683365 ACCATTTTGGCTTCCAACATC 57.317 42.857 0.00 0.00 43.82 3.06
1884 2078 0.968405 TTTGGCTTCCAACATCAGGC 59.032 50.000 0.00 0.00 43.82 4.85
1885 2079 0.178967 TTGGCTTCCAACATCAGGCA 60.179 50.000 0.00 0.00 38.75 4.75
2105 2309 5.049405 GCTGCCACTGCGTTAGAATAATAAT 60.049 40.000 0.00 0.00 41.78 1.28
2481 2689 4.653868 TCTACGAAAGGTATGCCCAAAAA 58.346 39.130 0.00 0.00 34.66 1.94
2566 2779 3.763057 AGTACCCTTGGCTTAAACTTGG 58.237 45.455 0.00 0.00 0.00 3.61
2776 2989 6.677913 AGACAGTATTTTAATTGTGTGCACC 58.322 36.000 15.69 6.37 0.00 5.01
3102 3315 5.944007 AGCGACCATTACCTTAAAAGTTGAT 59.056 36.000 0.00 0.00 0.00 2.57
3947 4391 0.732571 AACAGCAACAAGGTCACGTG 59.267 50.000 9.94 9.94 0.00 4.49
4120 4566 8.579705 AAGAAGTTCTTTGAGCATGTTTTGCAG 61.580 37.037 12.50 0.00 43.41 4.41
4345 4791 5.254115 ACTTTCTTTATAAGGGTCACCAGC 58.746 41.667 0.00 0.00 40.13 4.85
4554 5000 4.261614 GGTCGTATCATATGTCAGCACTGA 60.262 45.833 1.90 0.00 37.24 3.41
4613 5059 1.077265 CCAACCACCCTGATGCCTT 59.923 57.895 0.00 0.00 0.00 4.35
4793 5239 7.201875 CCCTAATTTTGTTACCAACTTGAGTGT 60.202 37.037 0.00 0.00 0.00 3.55
4828 5274 1.766494 ACATCCACCGTCCACGTATA 58.234 50.000 0.00 0.00 37.74 1.47
4836 5282 2.097466 ACCGTCCACGTATAGTTTACCG 59.903 50.000 0.00 0.00 37.74 4.02
4865 5311 5.470777 TCGTTGTCCTGTTTTAATGGGTAAG 59.529 40.000 0.00 0.00 0.00 2.34
4876 5322 8.005976 TGTTTTAATGGGTAAGTAGGGAGTTTT 58.994 33.333 0.00 0.00 0.00 2.43
5042 5604 4.469657 TGCTGTCTACTTCCATTTTGGTT 58.530 39.130 0.00 0.00 39.03 3.67
5087 5649 7.451731 AGTTAAACCCTCCATATCTTCATCA 57.548 36.000 0.00 0.00 0.00 3.07
5088 5650 8.050316 AGTTAAACCCTCCATATCTTCATCAT 57.950 34.615 0.00 0.00 0.00 2.45
5715 6283 6.265304 AGGTAAGTCTGATTTAGAACTCCCT 58.735 40.000 0.00 0.00 37.12 4.20
5811 6380 5.592282 TGCCAGACACTTTCAAAACAGATTA 59.408 36.000 0.00 0.00 0.00 1.75
5834 6403 1.003349 AGTGCAGCTGCTCAGATCTTT 59.997 47.619 36.61 14.63 42.66 2.52
5919 6488 3.207265 TGTAAGCCTCTTGAACAAGCA 57.793 42.857 9.38 0.00 38.28 3.91
6068 6650 9.121658 TCTATATACATCCGTATGTGAATCTCC 57.878 37.037 3.56 0.00 45.99 3.71
6221 6819 3.500448 TGTGTTTATGACTTCCAGCCA 57.500 42.857 0.00 0.00 0.00 4.75
6242 6840 5.105997 GCCATTGATTCTGCTTAGTTCAAGT 60.106 40.000 0.00 0.00 36.55 3.16
6380 6978 7.327975 TGATGACAGATACTTTGTTTCGGTAT 58.672 34.615 0.00 0.00 0.00 2.73
6381 6979 8.471609 TGATGACAGATACTTTGTTTCGGTATA 58.528 33.333 0.00 0.00 0.00 1.47
6472 7070 6.366340 TGGTTTGGTATTAGAACAAGTGGAA 58.634 36.000 0.00 0.00 0.00 3.53
6578 7176 1.811941 GCTTGCCTACCTGCTATGGAC 60.812 57.143 0.00 0.00 0.00 4.02
6608 7206 2.290896 TGGCTCACCAGGAAACATTAGG 60.291 50.000 0.00 0.00 42.67 2.69
6728 7326 7.946655 TGATACCAAGAGAATTATTGTAGCG 57.053 36.000 0.00 0.00 0.00 4.26
6752 7350 8.274939 GCGACTACTACTATGTGTTCTAACTAG 58.725 40.741 0.00 0.00 0.00 2.57
6836 7436 1.238439 TGTAGCCTGCTTTGTTCAGC 58.762 50.000 0.00 0.00 40.55 4.26
7136 7807 9.674824 GCATCTAATATGACCTGAAAATTGAAG 57.325 33.333 0.00 0.00 0.00 3.02
7200 7871 7.699812 GCTGTTTATTTATTCTCCTTCTGCTTG 59.300 37.037 0.00 0.00 0.00 4.01
7329 8001 0.594284 GGCGACCGTGAGTATACTGC 60.594 60.000 10.90 5.34 0.00 4.40
7338 8010 5.105064 ACCGTGAGTATACTGCCACTATTTT 60.105 40.000 10.90 0.00 0.00 1.82
7344 8016 7.764443 TGAGTATACTGCCACTATTTTGAACTC 59.236 37.037 10.90 0.00 0.00 3.01
7386 8058 6.631971 TGCTCATTTCACACTACAATCAAA 57.368 33.333 0.00 0.00 0.00 2.69
7417 8090 6.822667 ATTGAGATGCAATAAAGTGTCACA 57.177 33.333 5.62 0.00 45.16 3.58
7419 8092 6.432162 ATTGAGATGCAATAAAGTGTCACACT 59.568 34.615 3.98 3.98 44.91 3.55
7435 8136 3.117794 CACACTGTTGGAAATGTGCAAG 58.882 45.455 0.00 0.00 35.52 4.01
7443 8144 5.163322 TGTTGGAAATGTGCAAGGAGAATTT 60.163 36.000 0.00 0.00 35.52 1.82
7445 8146 6.662865 TGGAAATGTGCAAGGAGAATTTAA 57.337 33.333 0.00 0.00 0.00 1.52
7542 8248 4.059511 CAATTTTCTGCACATTTCCTGCA 58.940 39.130 0.00 0.00 42.42 4.41
7565 8271 6.472808 GCATTCTGAGATTGCATTTTTCTCTC 59.527 38.462 20.71 8.21 38.36 3.20
7571 8277 7.341030 TGAGATTGCATTTTTCTCTCCTGATA 58.659 34.615 14.00 0.00 37.40 2.15
7870 8577 5.073280 ACTTAATAATAAGGGCCCTCTCCAC 59.927 44.000 28.84 0.00 42.39 4.02
7876 8583 1.979155 GGGCCCTCTCCACTTTTGC 60.979 63.158 17.04 0.00 0.00 3.68
7962 8670 3.381949 GACATATCTCGCTGTGTAACCC 58.618 50.000 0.00 0.00 34.36 4.11
7983 8691 4.589908 CCCCCTTGCTATATGTGTATTCC 58.410 47.826 0.00 0.00 0.00 3.01
7984 8692 4.289672 CCCCCTTGCTATATGTGTATTCCT 59.710 45.833 0.00 0.00 0.00 3.36
7986 8694 6.306987 CCCCTTGCTATATGTGTATTCCTTT 58.693 40.000 0.00 0.00 0.00 3.11
7989 8697 9.349713 CCCTTGCTATATGTGTATTCCTTTAAA 57.650 33.333 0.00 0.00 0.00 1.52
8020 8728 4.322499 GGATAAAGGTTGGTCGTTCTCTGA 60.322 45.833 0.00 0.00 0.00 3.27
8032 8740 4.032558 GTCGTTCTCTGAAAAACTTGTCGT 59.967 41.667 2.37 0.00 0.00 4.34
8038 8746 2.798283 CTGAAAAACTTGTCGTCGCCTA 59.202 45.455 0.00 0.00 0.00 3.93
8040 8748 3.185594 TGAAAAACTTGTCGTCGCCTATG 59.814 43.478 0.00 0.00 0.00 2.23
8052 8760 0.603569 CGCCTATGCCGTAGAATCCT 59.396 55.000 0.00 0.00 31.71 3.24
8081 8789 7.553504 TGATCTAAATATAACCCTAGCTGCA 57.446 36.000 1.02 0.00 0.00 4.41
8082 8790 7.973402 TGATCTAAATATAACCCTAGCTGCAA 58.027 34.615 1.02 0.00 0.00 4.08
8101 8809 4.086457 GCAACCATCCTTTCCTTTCCTAA 58.914 43.478 0.00 0.00 0.00 2.69
8117 8825 1.272425 CCTAATGTGGGGAACAGGCAA 60.272 52.381 0.00 0.00 43.64 4.52
8118 8826 2.624029 CCTAATGTGGGGAACAGGCAAT 60.624 50.000 0.00 0.00 43.64 3.56
8146 8860 0.162507 CTCTTTGCGACACAGAAGCG 59.837 55.000 0.00 0.00 0.00 4.68
8186 8900 2.361610 CAAGCGGACCAGCCCATT 60.362 61.111 4.93 0.00 38.01 3.16
8192 8906 1.476110 GCGGACCAGCCCATTTATGTA 60.476 52.381 0.00 0.00 0.00 2.29
8201 8915 5.598005 CCAGCCCATTTATGTATTCTTGGAA 59.402 40.000 0.00 0.00 0.00 3.53
8222 8936 5.278512 GGAAACTTCTCTAAGCAGTTTTGGG 60.279 44.000 6.26 0.00 40.15 4.12
8230 8944 6.379988 TCTCTAAGCAGTTTTGGGAAGTTTTT 59.620 34.615 0.00 0.00 0.00 1.94
8238 8952 6.873605 CAGTTTTGGGAAGTTTTTATGGATCC 59.126 38.462 4.20 4.20 0.00 3.36
8258 9991 5.943349 TCCGGTATTAGAAGTTTCCATCA 57.057 39.130 0.00 0.00 0.00 3.07
8365 10102 9.506018 CCCCTTTTCTTCATTTTTCAAATACAT 57.494 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 200 2.963432 TCGTTGTTCTTACCGGATTCC 58.037 47.619 9.46 0.00 0.00 3.01
222 227 2.089925 AGCTCAGTCCATTACCCCCTAT 60.090 50.000 0.00 0.00 0.00 2.57
225 230 0.470341 GAGCTCAGTCCATTACCCCC 59.530 60.000 9.40 0.00 0.00 5.40
226 231 0.470341 GGAGCTCAGTCCATTACCCC 59.530 60.000 17.19 0.00 36.51 4.95
764 789 3.993488 TGACTGTAAGGCCTGCCTACAC 61.993 54.545 5.69 12.75 46.74 2.90
768 793 1.679898 GTGACTGTAAGGCCTGCCT 59.320 57.895 5.69 4.45 46.74 4.75
769 794 1.741770 CGTGACTGTAAGGCCTGCC 60.742 63.158 5.69 0.00 46.74 4.85
770 795 1.741770 CCGTGACTGTAAGGCCTGC 60.742 63.158 5.69 2.70 46.74 4.85
771 796 1.079127 CCCGTGACTGTAAGGCCTG 60.079 63.158 5.69 0.00 46.74 4.85
772 797 2.955881 GCCCGTGACTGTAAGGCCT 61.956 63.158 0.00 0.00 46.74 5.19
773 798 2.436115 GCCCGTGACTGTAAGGCC 60.436 66.667 0.00 0.00 46.74 5.19
776 801 2.125673 CCGGCCCGTGACTGTAAG 60.126 66.667 0.85 0.00 42.29 2.34
777 802 3.697747 CCCGGCCCGTGACTGTAA 61.698 66.667 0.85 0.00 0.00 2.41
788 813 4.620937 GGAAGATACGGCCCGGCC 62.621 72.222 19.64 19.64 46.75 6.13
789 814 4.620937 GGGAAGATACGGCCCGGC 62.621 72.222 8.57 0.00 31.06 6.13
790 815 2.842936 AGGGAAGATACGGCCCGG 60.843 66.667 8.57 0.00 46.68 5.73
847 909 1.623542 CCTTTCCGGGGAATCCTCGT 61.624 60.000 21.21 0.00 33.79 4.18
858 920 1.022982 GCCTCGGTTTACCTTTCCGG 61.023 60.000 0.00 0.00 43.75 5.14
859 921 1.356527 CGCCTCGGTTTACCTTTCCG 61.357 60.000 0.00 0.00 44.76 4.30
860 922 1.022982 CCGCCTCGGTTTACCTTTCC 61.023 60.000 0.00 0.00 42.73 3.13
993 1061 4.435436 ACGAGCTTCATCGCGGCA 62.435 61.111 6.13 0.00 46.60 5.69
1060 1132 3.036959 GAGGGGAGAGGGGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
1061 1133 4.179599 GGAGGGGAGAGGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1133 1205 1.586154 GCACCCACAGAATCCAACCG 61.586 60.000 0.00 0.00 0.00 4.44
1137 1209 2.350895 CCGCACCCACAGAATCCA 59.649 61.111 0.00 0.00 0.00 3.41
1140 1212 2.360350 CAGCCGCACCCACAGAAT 60.360 61.111 0.00 0.00 0.00 2.40
1170 1242 1.898094 AGCTGCGCAACCACATGAA 60.898 52.632 13.05 0.00 0.00 2.57
1290 1368 8.097662 TGAACCAAAAAGTAAAACAAGAACCAT 58.902 29.630 0.00 0.00 0.00 3.55
1295 1373 6.930731 AGCTGAACCAAAAAGTAAAACAAGA 58.069 32.000 0.00 0.00 0.00 3.02
1344 1434 0.406750 TCCACCAGAGGACTCGGTTA 59.593 55.000 11.36 3.48 35.45 2.85
1354 1444 2.113433 GCTGCAGCATCCACCAGAG 61.113 63.158 33.36 0.00 41.59 3.35
1379 1469 1.564348 ACCGGGGAGAGCAAATTACAT 59.436 47.619 6.32 0.00 0.00 2.29
1380 1470 0.988832 ACCGGGGAGAGCAAATTACA 59.011 50.000 6.32 0.00 0.00 2.41
1382 1472 2.891191 AAACCGGGGAGAGCAAATTA 57.109 45.000 6.32 0.00 0.00 1.40
1395 1485 3.670627 GCAATCAGAAAGTGCTAAACCGG 60.671 47.826 0.00 0.00 35.36 5.28
1403 1493 5.762045 TCAAAACTAGCAATCAGAAAGTGC 58.238 37.500 0.00 0.00 38.59 4.40
1621 1713 9.582431 GCTTGAACTTATCACAACTATACTACA 57.418 33.333 0.00 0.00 37.92 2.74
1650 1826 0.555769 ACTGGAAGGCCCTTGAACAA 59.444 50.000 0.00 0.00 39.30 2.83
1666 1842 5.623956 TTCCATGGTATACTGGGTAACTG 57.376 43.478 12.58 0.00 33.13 3.16
1672 1848 3.264450 GGGAGATTCCATGGTATACTGGG 59.736 52.174 12.58 6.52 38.64 4.45
1674 1850 4.081972 CGAGGGAGATTCCATGGTATACTG 60.082 50.000 12.58 0.00 38.64 2.74
1675 1851 4.090090 CGAGGGAGATTCCATGGTATACT 58.910 47.826 12.58 7.27 38.64 2.12
1689 1865 1.202533 GGCGATCAATTTCGAGGGAGA 60.203 52.381 3.75 0.00 41.62 3.71
1707 1890 3.304057 CCTGAAAACGAACAGAAGAAGGC 60.304 47.826 0.00 0.00 36.38 4.35
1877 2071 1.575244 AACGACGATGATGCCTGATG 58.425 50.000 0.00 0.00 0.00 3.07
1878 2072 3.005791 TCATAACGACGATGATGCCTGAT 59.994 43.478 0.00 0.00 0.00 2.90
1879 2073 2.360801 TCATAACGACGATGATGCCTGA 59.639 45.455 0.00 0.00 0.00 3.86
1880 2074 2.472861 GTCATAACGACGATGATGCCTG 59.527 50.000 0.00 0.00 35.81 4.85
1884 2078 1.452025 GCGGTCATAACGACGATGATG 59.548 52.381 0.00 1.95 46.42 3.07
1885 2079 1.767289 GCGGTCATAACGACGATGAT 58.233 50.000 0.00 0.00 46.42 2.45
2105 2309 1.313772 TTTGCAAGGAAAGCGCTACA 58.686 45.000 12.05 0.00 33.85 2.74
2500 2708 4.476297 TGGTAGTCCACAGAGTAAACAGA 58.524 43.478 0.00 0.00 39.03 3.41
2566 2779 9.822185 AGCCATATCCAAAATTAAAACTGATTC 57.178 29.630 0.00 0.00 0.00 2.52
2586 2799 8.494433 AGTACCATTTAGATTTTCAGAGCCATA 58.506 33.333 0.00 0.00 0.00 2.74
2776 2989 5.127845 TGCAGTAGGATCTGAAGAGGTTTAG 59.872 44.000 0.00 0.00 37.61 1.85
2842 3055 6.447084 ACCTTCTCCCAATAAGGAATAAGTGA 59.553 38.462 8.06 0.00 44.27 3.41
2992 3205 6.571605 TCATGAGAGAATCAGACAAGCTTAG 58.428 40.000 0.00 0.00 42.53 2.18
3750 4194 0.544223 TGTGTAACTGCACAGGGTGT 59.456 50.000 2.21 0.00 43.54 4.16
3947 4391 4.467198 TCCTAGGAATCGAGGTTTCAAC 57.533 45.455 9.71 0.00 37.13 3.18
4035 4479 8.948631 TCAGTAGCAAATAGATAAGACAAAGG 57.051 34.615 0.00 0.00 0.00 3.11
4120 4566 9.722056 CTTTGAACAGATTATTATGTGCTTACC 57.278 33.333 0.00 0.00 0.00 2.85
4186 4632 4.383649 CAGACAAGCAATGTAATGTGTTGC 59.616 41.667 1.35 1.35 44.12 4.17
4187 4633 4.383649 GCAGACAAGCAATGTAATGTGTTG 59.616 41.667 0.00 0.00 44.12 3.33
4345 4791 8.647143 AACATTGTTTAAGATGTTTTCACAGG 57.353 30.769 0.00 0.00 42.18 4.00
4392 4838 9.844790 GAAATTGATTTAACATCACATGACAGA 57.155 29.630 0.00 0.00 0.00 3.41
4554 5000 7.477494 GCGTTACCACCTTATAAACAATGAAT 58.523 34.615 0.00 0.00 0.00 2.57
4585 5031 2.730094 GTGGTTGGTGCTTGCCTG 59.270 61.111 0.00 0.00 0.00 4.85
4613 5059 1.070134 CTATGCCCGCTTTAGGTGCTA 59.930 52.381 0.00 0.00 0.00 3.49
4836 5282 5.440685 CATTAAAACAGGACAACGAGTGAC 58.559 41.667 0.00 0.00 0.00 3.67
4865 5311 7.093858 ACTGTATGTACTCAGAAAACTCCCTAC 60.094 40.741 15.93 0.00 35.84 3.18
4906 5468 9.546428 CATGATAATTTGACCATACTACACTGA 57.454 33.333 0.00 0.00 0.00 3.41
4979 5541 3.923017 ACAAGTGTAGATGGCAAAAGC 57.077 42.857 0.00 0.00 0.00 3.51
5779 6348 1.813513 AAGTGTCTGGCATGTGTAGC 58.186 50.000 0.00 0.00 0.00 3.58
5811 6380 2.435069 AGATCTGAGCAGCTGCACTTAT 59.565 45.455 38.24 27.00 45.16 1.73
5919 6488 6.127479 TGTCAAAAGCCATCAGTTACAAGTTT 60.127 34.615 0.00 0.00 0.00 2.66
6050 6621 6.316140 TCTTTTTGGAGATTCACATACGGATG 59.684 38.462 5.94 5.94 39.16 3.51
6121 6703 5.123820 TGGTCAACATCTAAGCAATAGCAAC 59.876 40.000 0.00 0.00 45.49 4.17
6123 6705 4.842574 TGGTCAACATCTAAGCAATAGCA 58.157 39.130 0.00 0.00 45.49 3.49
6124 6706 5.297776 ACATGGTCAACATCTAAGCAATAGC 59.702 40.000 0.00 0.00 37.84 2.97
6125 6707 6.932356 ACATGGTCAACATCTAAGCAATAG 57.068 37.500 0.00 0.00 37.84 1.73
6126 6708 9.489084 GTATACATGGTCAACATCTAAGCAATA 57.511 33.333 0.00 0.00 37.84 1.90
6127 6709 7.992608 TGTATACATGGTCAACATCTAAGCAAT 59.007 33.333 0.08 0.00 37.84 3.56
6215 6813 3.285484 ACTAAGCAGAATCAATGGCTGG 58.715 45.455 0.00 0.00 36.58 4.85
6508 7106 3.556775 ACATTGCACAGTTTTGTTGCATC 59.443 39.130 0.00 0.00 39.40 3.91
6539 7137 4.903045 AGCAAGCTTAACTAACCTACCA 57.097 40.909 0.00 0.00 0.00 3.25
6624 7222 7.795859 ACCAATATTTCAGAATTTGCAAAACG 58.204 30.769 17.19 5.14 0.00 3.60
6814 7412 3.064545 GCTGAACAAAGCAGGCTACATAG 59.935 47.826 0.00 0.00 43.01 2.23
6974 7575 8.088365 ACTAACAAAATGAACTATTGAAAGGGC 58.912 33.333 0.00 0.00 0.00 5.19
7136 7807 3.631145 TTGCAACTCATGAACTTCTGC 57.369 42.857 0.00 2.31 0.00 4.26
7200 7871 4.296265 CCGTGTTCCTACAAGGGC 57.704 61.111 2.82 0.00 46.38 5.19
7329 8001 3.364964 GGTGTGCGAGTTCAAAATAGTGG 60.365 47.826 0.00 0.00 0.00 4.00
7338 8010 1.295792 GAACAAGGTGTGCGAGTTCA 58.704 50.000 0.00 0.00 38.66 3.18
7344 8016 2.916716 GCAATTATGAACAAGGTGTGCG 59.083 45.455 0.00 0.00 0.00 5.34
7417 8090 2.624838 CTCCTTGCACATTTCCAACAGT 59.375 45.455 0.00 0.00 0.00 3.55
7419 8092 2.942804 TCTCCTTGCACATTTCCAACA 58.057 42.857 0.00 0.00 0.00 3.33
7542 8248 6.890814 AGGAGAGAAAAATGCAATCTCAGAAT 59.109 34.615 18.45 4.20 41.60 2.40
7565 8271 6.038356 GCCAATTCTGTTCAAACATATCAGG 58.962 40.000 0.00 0.00 38.41 3.86
7571 8277 2.035704 TGCGCCAATTCTGTTCAAACAT 59.964 40.909 4.18 0.00 38.41 2.71
7796 8503 7.625828 AGCTAACCATTTACAACAAGGATAC 57.374 36.000 0.00 0.00 0.00 2.24
7870 8577 2.517959 TCCACATCTCAAGGGCAAAAG 58.482 47.619 0.00 0.00 0.00 2.27
7876 8583 1.211212 TCAGCATCCACATCTCAAGGG 59.789 52.381 0.00 0.00 0.00 3.95
7962 8670 5.505181 AGGAATACACATATAGCAAGGGG 57.495 43.478 0.00 0.00 0.00 4.79
7983 8691 9.855021 CCAACCTTTATCCAGTAATGTTTAAAG 57.145 33.333 11.92 11.92 0.00 1.85
7984 8692 9.369672 ACCAACCTTTATCCAGTAATGTTTAAA 57.630 29.630 0.00 0.00 0.00 1.52
7986 8694 7.334921 CGACCAACCTTTATCCAGTAATGTTTA 59.665 37.037 0.00 0.00 0.00 2.01
7989 8697 5.183228 CGACCAACCTTTATCCAGTAATGT 58.817 41.667 0.00 0.00 0.00 2.71
7990 8698 5.183228 ACGACCAACCTTTATCCAGTAATG 58.817 41.667 0.00 0.00 0.00 1.90
7991 8699 5.431179 ACGACCAACCTTTATCCAGTAAT 57.569 39.130 0.00 0.00 0.00 1.89
8020 8728 2.095919 GCATAGGCGACGACAAGTTTTT 60.096 45.455 2.19 0.00 0.00 1.94
8038 8746 5.305644 AGATCAACTAAGGATTCTACGGCAT 59.694 40.000 0.00 0.00 0.00 4.40
8040 8748 5.203060 AGATCAACTAAGGATTCTACGGC 57.797 43.478 0.00 0.00 0.00 5.68
8081 8789 5.716703 CACATTAGGAAAGGAAAGGATGGTT 59.283 40.000 0.00 0.00 0.00 3.67
8082 8790 5.264395 CACATTAGGAAAGGAAAGGATGGT 58.736 41.667 0.00 0.00 0.00 3.55
8101 8809 1.922447 TCTATTGCCTGTTCCCCACAT 59.078 47.619 0.00 0.00 33.76 3.21
8176 8890 4.895297 CCAAGAATACATAAATGGGCTGGT 59.105 41.667 0.00 0.00 0.00 4.00
8192 8906 6.538263 ACTGCTTAGAGAAGTTTCCAAGAAT 58.462 36.000 0.00 0.00 26.37 2.40
8201 8915 5.048846 TCCCAAAACTGCTTAGAGAAGTT 57.951 39.130 0.00 0.00 45.91 2.66
8222 8936 8.897872 TCTAATACCGGATCCATAAAAACTTC 57.102 34.615 9.46 0.00 0.00 3.01
8230 8944 6.555738 TGGAAACTTCTAATACCGGATCCATA 59.444 38.462 9.46 3.71 0.00 2.74
8238 8952 5.360591 AGCTGATGGAAACTTCTAATACCG 58.639 41.667 0.00 0.00 35.62 4.02
8365 10102 5.860941 TGTATTTGAAGAAAAAGCCCACA 57.139 34.783 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.