Multiple sequence alignment - TraesCS2A01G135300

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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 TraesCS2A01G135300 chr2A 100.000 3897 0 0 1 3897 81526025 81522129 0.000000e+00 7197.0
1 TraesCS2A01G135300 chr2A 93.085 1316 43 12 1 1303 81485358 81484078 0.000000e+00 1882.0
2 TraesCS2A01G135300 chr2A 80.754 1725 214 52 412 2087 81473847 81472192 0.000000e+00 1238.0
3 TraesCS2A01G135300 chr2A 87.563 796 83 9 2276 3062 81471340 81470552 0.000000e+00 907.0
4 TraesCS2A01G135300 chr2A 96.731 520 17 0 2326 2845 81479315 81478796 0.000000e+00 867.0
5 TraesCS2A01G135300 chr2A 92.870 547 28 5 3252 3794 81511641 81511102 0.000000e+00 784.0
6 TraesCS2A01G135300 chr2A 96.025 478 19 0 2842 3319 81477287 81476810 0.000000e+00 778.0
7 TraesCS2A01G135300 chr2A 88.013 634 59 9 3255 3881 81179189 81178566 0.000000e+00 734.0
8 TraesCS2A01G135300 chr2A 83.133 415 50 10 459 859 81512584 81512176 1.030000e-95 361.0
9 TraesCS2A01G135300 chr2A 94.937 158 5 2 3310 3464 81476020 81475863 1.080000e-60 244.0
10 TraesCS2A01G135300 chr2A 90.741 162 14 1 3082 3243 38343284 38343444 8.480000e-52 215.0
11 TraesCS2A01G135300 chr2A 95.327 107 5 0 3791 3897 81505291 81505185 1.860000e-38 171.0
12 TraesCS2A01G135300 chr2D 91.606 1918 128 17 1106 3010 80967658 80965761 0.000000e+00 2619.0
13 TraesCS2A01G135300 chr2D 93.141 1181 62 7 1686 2859 81017901 81016733 0.000000e+00 1714.0
14 TraesCS2A01G135300 chr2D 92.195 820 49 9 775 1593 81018851 81018046 0.000000e+00 1146.0
15 TraesCS2A01G135300 chr2D 87.250 800 87 8 2272 3062 81004644 81003851 0.000000e+00 898.0
16 TraesCS2A01G135300 chr2D 82.373 885 111 29 980 1850 580267121 580266268 0.000000e+00 728.0
17 TraesCS2A01G135300 chr2D 83.172 826 95 17 501 1302 81007234 81006429 0.000000e+00 715.0
18 TraesCS2A01G135300 chr2D 83.686 803 62 34 29 791 81019639 81018866 0.000000e+00 693.0
19 TraesCS2A01G135300 chr2D 82.716 729 96 20 1367 2087 81006392 81005686 4.280000e-174 621.0
20 TraesCS2A01G135300 chr2D 84.503 342 28 17 3252 3569 80758525 80758185 8.130000e-82 315.0
21 TraesCS2A01G135300 chr2D 80.142 423 62 15 1652 2064 81022815 81022405 2.940000e-76 296.0
22 TraesCS2A01G135300 chr2D 93.671 158 8 2 3723 3879 80757762 80757606 6.510000e-58 235.0
23 TraesCS2A01G135300 chr2D 96.667 60 2 0 531 590 80967822 80967763 2.480000e-17 100.0
24 TraesCS2A01G135300 chr2B 89.261 1313 71 33 1367 2626 132575344 132574049 0.000000e+00 1580.0
25 TraesCS2A01G135300 chr2B 87.707 846 47 26 1367 2173 132577430 132576603 0.000000e+00 933.0
26 TraesCS2A01G135300 chr2B 91.820 599 35 8 775 1371 132575962 132575376 0.000000e+00 822.0
27 TraesCS2A01G135300 chr2B 91.820 599 35 8 775 1371 132578048 132577462 0.000000e+00 822.0
28 TraesCS2A01G135300 chr2B 90.141 639 47 7 1706 2332 132508121 132507487 0.000000e+00 817.0
29 TraesCS2A01G135300 chr2B 79.916 1190 149 32 22 1164 132573016 132571870 0.000000e+00 791.0
30 TraesCS2A01G135300 chr2B 86.000 600 61 16 629 1224 132509294 132508714 4.280000e-174 621.0
31 TraesCS2A01G135300 chr2B 91.932 409 30 3 2654 3062 132574051 132573646 1.570000e-158 569.0
32 TraesCS2A01G135300 chr2B 90.160 437 38 3 312 748 132578695 132578264 7.310000e-157 564.0
33 TraesCS2A01G135300 chr2B 90.686 408 34 3 341 748 132576581 132576178 1.230000e-149 540.0
34 TraesCS2A01G135300 chr2B 93.913 345 19 2 1 344 132579052 132578709 1.600000e-143 520.0
35 TraesCS2A01G135300 chr2B 86.797 462 51 5 3252 3711 132505429 132504976 1.250000e-139 507.0
36 TraesCS2A01G135300 chr2B 81.468 545 65 17 1367 1900 132571633 132571114 7.790000e-112 414.0
37 TraesCS2A01G135300 chr2B 85.175 371 25 5 1220 1590 132508471 132508131 1.720000e-93 353.0
38 TraesCS2A01G135300 chr2B 88.716 257 21 8 3627 3881 132504876 132504626 1.360000e-79 307.0
39 TraesCS2A01G135300 chr2B 79.905 423 63 15 1652 2064 132582745 132582335 1.370000e-74 291.0
40 TraesCS2A01G135300 chr2B 95.092 163 8 0 531 693 132509457 132509295 1.390000e-64 257.0
41 TraesCS2A01G135300 chr2B 87.879 165 13 2 2853 3010 132507440 132507276 1.850000e-43 187.0
42 TraesCS2A01G135300 chr2B 94.643 56 3 0 2776 2831 132507492 132507437 1.930000e-13 87.9
43 TraesCS2A01G135300 chrUn 88.948 1321 74 32 1361 2626 318561007 318562310 0.000000e+00 1565.0
44 TraesCS2A01G135300 chrUn 91.820 599 35 8 775 1371 318560395 318560981 0.000000e+00 822.0
45 TraesCS2A01G135300 chrUn 91.932 409 30 3 2654 3062 318562308 318562713 1.570000e-158 569.0
46 TraesCS2A01G135300 chrUn 92.218 257 20 0 492 748 318559923 318560179 7.960000e-97 364.0
47 TraesCS2A01G135300 chr4B 93.511 262 9 4 531 791 281900703 281900449 2.200000e-102 383.0
48 TraesCS2A01G135300 chr4B 85.915 71 7 3 3191 3258 559842853 559842923 5.400000e-09 73.1
49 TraesCS2A01G135300 chr4B 85.246 61 5 3 3050 3108 4409316 4409374 4.200000e-05 60.2
50 TraesCS2A01G135300 chr6A 80.365 219 31 6 3051 3258 592204099 592204316 5.210000e-34 156.0
51 TraesCS2A01G135300 chr3B 92.308 104 8 0 2098 2201 519860758 519860655 8.720000e-32 148.0
52 TraesCS2A01G135300 chr3B 85.833 120 16 1 2098 2217 354001632 354001750 4.090000e-25 126.0
53 TraesCS2A01G135300 chr6D 84.286 140 16 4 3051 3186 445612840 445612977 8.790000e-27 132.0
54 TraesCS2A01G135300 chr3D 86.667 120 15 1 2098 2217 236634680 236634798 8.790000e-27 132.0
55 TraesCS2A01G135300 chr3D 88.732 71 8 0 3188 3258 367346430 367346500 1.930000e-13 87.9
56 TraesCS2A01G135300 chr1A 80.556 144 24 2 468 611 585389578 585389439 1.480000e-19 108.0
57 TraesCS2A01G135300 chr3A 80.153 131 22 3 3058 3186 429459548 429459676 1.150000e-15 95.3
58 TraesCS2A01G135300 chr5D 80.159 126 21 3 3062 3184 507141457 507141333 1.490000e-14 91.6
59 TraesCS2A01G135300 chr4A 87.143 70 9 0 3189 3258 539146000 539146069 3.230000e-11 80.5
60 TraesCS2A01G135300 chr7B 84.507 71 11 0 3191 3261 577224802 577224732 1.940000e-08 71.3
61 TraesCS2A01G135300 chr7B 91.489 47 4 0 3062 3108 730505206 730505160 9.040000e-07 65.8
62 TraesCS2A01G135300 chr4D 93.617 47 3 0 3062 3108 428951323 428951277 1.940000e-08 71.3
63 TraesCS2A01G135300 chr1D 84.722 72 10 1 3191 3261 302712344 302712273 1.940000e-08 71.3


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 TraesCS2A01G135300 chr2A 81522129 81526025 3896 True 7197.000000 7197 100.000000 1 3897 1 chr2A.!!$R4 3896
1 TraesCS2A01G135300 chr2A 81484078 81485358 1280 True 1882.000000 1882 93.085000 1 1303 1 chr2A.!!$R2 1302
2 TraesCS2A01G135300 chr2A 81470552 81479315 8763 True 806.800000 1238 91.202000 412 3464 5 chr2A.!!$R5 3052
3 TraesCS2A01G135300 chr2A 81178566 81179189 623 True 734.000000 734 88.013000 3255 3881 1 chr2A.!!$R1 626
4 TraesCS2A01G135300 chr2A 81511102 81512584 1482 True 572.500000 784 88.001500 459 3794 2 chr2A.!!$R6 3335
5 TraesCS2A01G135300 chr2D 80965761 80967822 2061 True 1359.500000 2619 94.136500 531 3010 2 chr2D.!!$R3 2479
6 TraesCS2A01G135300 chr2D 81016733 81022815 6082 True 962.250000 1714 87.291000 29 2859 4 chr2D.!!$R5 2830
7 TraesCS2A01G135300 chr2D 81003851 81007234 3383 True 744.666667 898 84.379333 501 3062 3 chr2D.!!$R4 2561
8 TraesCS2A01G135300 chr2D 580266268 580267121 853 True 728.000000 728 82.373000 980 1850 1 chr2D.!!$R1 870
9 TraesCS2A01G135300 chr2D 80757606 80758525 919 True 275.000000 315 89.087000 3252 3879 2 chr2D.!!$R2 627
10 TraesCS2A01G135300 chr2B 132571114 132582745 11631 True 713.272727 1580 88.053455 1 3062 11 chr2B.!!$R2 3061
11 TraesCS2A01G135300 chr2B 132504626 132509457 4831 True 392.112500 817 89.305375 531 3881 8 chr2B.!!$R1 3350
12 TraesCS2A01G135300 chrUn 318559923 318562713 2790 False 830.000000 1565 91.229500 492 3062 4 chrUn.!!$F1 2570

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
489 5557 0.183492 TGCTTCAAAGTCACCCTGCT 59.817 50.000 0.0 0.0 0.00 4.24 F
1152 6788 0.915872 TGGTCATGTGGGCTGATCCT 60.916 55.000 0.0 0.0 34.39 3.24 F
1824 9923 1.950909 TGTTCCCCAAATCGTTGACAC 59.049 47.619 0.0 0.0 36.83 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 7725 0.036010 ATGACAAACAGGGAGCTCCG 60.036 55.0 26.36 16.01 41.52 4.63 R
2268 11265 0.464554 GTACCTGCAGAGGATTGCCC 60.465 60.0 17.39 0.00 42.93 5.36 R
3467 15052 0.108992 GTACGGTCCATGAAGCACGA 60.109 55.0 0.00 0.00 0.00 4.35 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
473 5541 1.615392 GCCACACAATTCCTCTTTGCT 59.385 47.619 0.00 0.00 0.00 3.91
489 5557 0.183492 TGCTTCAAAGTCACCCTGCT 59.817 50.000 0.00 0.00 0.00 4.24
490 5558 1.322442 GCTTCAAAGTCACCCTGCTT 58.678 50.000 0.00 0.00 0.00 3.91
690 5836 6.867293 ACATTTGGTCTAGTCGTAAAGAGAAC 59.133 38.462 0.00 0.00 0.00 3.01
732 5881 9.429359 CTACTCAAATCTCACAATCTACAACTT 57.571 33.333 0.00 0.00 0.00 2.66
810 6350 5.242434 ACCTGTACATTCGTAGAAAATGCA 58.758 37.500 0.00 0.00 45.90 3.96
839 6379 3.130340 ACACACATTTGGTTGACTGGAAC 59.870 43.478 0.00 0.00 0.00 3.62
850 6390 7.135591 TGGTTGACTGGAACATCATCATATA 57.864 36.000 0.00 0.00 38.20 0.86
856 6396 9.387257 TGACTGGAACATCATCATATAATATGC 57.613 33.333 0.00 0.00 38.20 3.14
1152 6788 0.915872 TGGTCATGTGGGCTGATCCT 60.916 55.000 0.00 0.00 34.39 3.24
1171 6807 3.327404 TCCTTCCCGGCCCTCAAC 61.327 66.667 0.00 0.00 0.00 3.18
1172 6808 4.426313 CCTTCCCGGCCCTCAACC 62.426 72.222 0.00 0.00 0.00 3.77
1188 6827 2.125512 CCGCTCAAGAACCTCCCG 60.126 66.667 0.00 0.00 0.00 5.14
1211 6850 2.202623 CGAGACCTTCTTCGGCCG 60.203 66.667 22.12 22.12 0.00 6.13
1212 6851 2.971452 GAGACCTTCTTCGGCCGT 59.029 61.111 27.15 2.66 0.00 5.68
1292 7183 2.228138 ATGCACTGCCAAACTTGTTG 57.772 45.000 0.00 0.00 0.00 3.33
1315 7224 7.241042 TGAACTACTGTTAATCTTACTGCCT 57.759 36.000 0.00 0.00 36.39 4.75
1317 7226 8.809066 TGAACTACTGTTAATCTTACTGCCTAA 58.191 33.333 0.00 0.00 36.39 2.69
1318 7227 9.819267 GAACTACTGTTAATCTTACTGCCTAAT 57.181 33.333 0.00 0.00 36.39 1.73
1351 7260 9.747898 GAGAAAGAGAGGGAGATAGATTACATA 57.252 37.037 0.00 0.00 0.00 2.29
1604 7564 6.465439 GCAAGGGTAGGTTGCTAATTAAAT 57.535 37.500 0.58 0.00 45.67 1.40
1656 7666 7.661437 AGAAAGCACTGTGATTATGTTCAAGTA 59.339 33.333 12.10 0.00 0.00 2.24
1673 7683 9.391006 TGTTCAAGTAATTTACCTGATCATACC 57.609 33.333 12.02 0.28 29.94 2.73
1674 7684 9.614792 GTTCAAGTAATTTACCTGATCATACCT 57.385 33.333 8.34 0.00 29.94 3.08
1677 7687 9.193133 CAAGTAATTTACCTGATCATACCTACG 57.807 37.037 0.00 0.00 0.00 3.51
1681 7691 2.928334 ACCTGATCATACCTACGTCGT 58.072 47.619 2.21 2.21 0.00 4.34
1712 7725 3.010420 GGACAAGGTACTGATTGCTTCC 58.990 50.000 0.00 0.00 40.86 3.46
1769 9868 3.902881 ATGACTACAGGAGCTTCCTTG 57.097 47.619 2.32 0.00 46.91 3.61
1824 9923 1.950909 TGTTCCCCAAATCGTTGACAC 59.049 47.619 0.00 0.00 36.83 3.67
1870 9978 5.819379 ACTATGTTGTGCACAGAATAGATGG 59.181 40.000 34.65 23.41 39.40 3.51
1974 10087 9.692749 CAATACTTGTCTATCTTATCGCCTTAA 57.307 33.333 0.00 0.00 0.00 1.85
1975 10088 9.694137 AATACTTGTCTATCTTATCGCCTTAAC 57.306 33.333 0.00 0.00 0.00 2.01
1978 10091 8.258708 ACTTGTCTATCTTATCGCCTTAACTTT 58.741 33.333 0.00 0.00 0.00 2.66
2019 10139 2.290641 GTCGCCATGACCATATCCAAAC 59.709 50.000 0.00 0.00 42.04 2.93
2129 10255 5.519927 GGTGTCAATGTTTTTCTCCACAAAG 59.480 40.000 0.00 0.00 0.00 2.77
2252 11249 4.988540 TGCTAACACTTGTGTATGACTCAC 59.011 41.667 6.84 0.00 36.48 3.51
2284 11281 1.751927 GTGGGCAATCCTCTGCAGG 60.752 63.158 15.13 4.45 44.52 4.85
2532 11529 2.601067 TACCGACCCGTCCTTGCA 60.601 61.111 0.00 0.00 0.00 4.08
2572 11572 3.552890 GCATTTTGGTGAGTTGGTCCTTC 60.553 47.826 0.00 0.00 0.00 3.46
2592 11598 7.499563 GTCCTTCCTGATTAATTTAGGTCTTCC 59.500 40.741 15.40 4.08 33.30 3.46
2676 11682 0.601046 CTCGCAGGACTGAACAGCAA 60.601 55.000 3.00 0.00 0.00 3.91
2737 11743 6.779117 TCCTTATAACTACGACTTCAACTCG 58.221 40.000 0.00 0.00 37.17 4.18
2747 11753 2.436087 CTTCAACTCGGAGTGCGGGT 62.436 60.000 12.12 2.67 0.00 5.28
2900 11909 2.645730 TGTTGCACGCCCATAATTTC 57.354 45.000 0.00 0.00 0.00 2.17
2949 11958 9.778741 TGTGTACTAGAGTTGAAAATTCAGATT 57.221 29.630 0.00 0.00 38.61 2.40
2977 11988 6.385033 GGGCATGCATAAATTTATGTCTCTC 58.615 40.000 29.73 17.96 41.92 3.20
3028 12046 3.756933 AACTAAACTAGCGGGACAACA 57.243 42.857 0.00 0.00 0.00 3.33
3075 12093 9.653287 TTTAATACATATTAGAAGGGATGAGCG 57.347 33.333 0.00 0.00 30.57 5.03
3076 12094 3.931578 ACATATTAGAAGGGATGAGCGC 58.068 45.455 0.00 0.00 0.00 5.92
3077 12095 2.724977 TATTAGAAGGGATGAGCGCG 57.275 50.000 0.00 0.00 34.07 6.86
3079 12097 1.676678 TTAGAAGGGATGAGCGCGCT 61.677 55.000 37.28 37.28 34.07 5.92
3080 12098 1.676678 TAGAAGGGATGAGCGCGCTT 61.677 55.000 36.87 21.70 40.63 4.68
3083 12101 4.543084 GGGATGAGCGCGCTTTGC 62.543 66.667 36.87 28.29 41.47 3.68
3085 12103 2.277120 GATGAGCGCGCTTTGCTG 60.277 61.111 36.87 0.00 44.18 4.41
3086 12104 4.471726 ATGAGCGCGCTTTGCTGC 62.472 61.111 36.87 21.55 44.18 5.25
3095 13340 2.723746 CTTTGCTGCGCTGTTGGT 59.276 55.556 16.05 0.00 0.00 3.67
3101 13346 1.433064 CTGCGCTGTTGGTGTTGTT 59.567 52.632 9.73 0.00 0.00 2.83
3102 13347 0.866906 CTGCGCTGTTGGTGTTGTTG 60.867 55.000 9.73 0.00 0.00 3.33
3103 13348 1.588667 GCGCTGTTGGTGTTGTTGG 60.589 57.895 0.00 0.00 0.00 3.77
3104 13349 1.065600 CGCTGTTGGTGTTGTTGGG 59.934 57.895 0.00 0.00 0.00 4.12
3106 13351 0.534873 GCTGTTGGTGTTGTTGGGTT 59.465 50.000 0.00 0.00 0.00 4.11
3107 13352 1.066502 GCTGTTGGTGTTGTTGGGTTT 60.067 47.619 0.00 0.00 0.00 3.27
3108 13353 2.614229 GCTGTTGGTGTTGTTGGGTTTT 60.614 45.455 0.00 0.00 0.00 2.43
3110 13355 2.263945 GTTGGTGTTGTTGGGTTTTCG 58.736 47.619 0.00 0.00 0.00 3.46
3111 13356 1.546961 TGGTGTTGTTGGGTTTTCGT 58.453 45.000 0.00 0.00 0.00 3.85
3112 13357 2.719739 TGGTGTTGTTGGGTTTTCGTA 58.280 42.857 0.00 0.00 0.00 3.43
3113 13358 3.087031 TGGTGTTGTTGGGTTTTCGTAA 58.913 40.909 0.00 0.00 0.00 3.18
3114 13359 3.700038 TGGTGTTGTTGGGTTTTCGTAAT 59.300 39.130 0.00 0.00 0.00 1.89
3115 13360 4.202030 TGGTGTTGTTGGGTTTTCGTAATC 60.202 41.667 0.00 0.00 0.00 1.75
3116 13361 4.202030 GGTGTTGTTGGGTTTTCGTAATCA 60.202 41.667 0.00 0.00 0.00 2.57
3121 13513 8.195436 TGTTGTTGGGTTTTCGTAATCATTTTA 58.805 29.630 0.00 0.00 0.00 1.52
3122 13514 8.481641 GTTGTTGGGTTTTCGTAATCATTTTAC 58.518 33.333 0.00 0.00 0.00 2.01
3124 13516 8.077386 TGTTGGGTTTTCGTAATCATTTTACTC 58.923 33.333 0.00 0.00 0.00 2.59
3125 13517 7.989416 TGGGTTTTCGTAATCATTTTACTCT 57.011 32.000 0.00 0.00 0.00 3.24
3126 13518 9.504708 TTGGGTTTTCGTAATCATTTTACTCTA 57.495 29.630 0.00 0.00 0.00 2.43
3133 13525 9.817809 TTCGTAATCATTTTACTCTATCTGCTT 57.182 29.630 0.00 0.00 0.00 3.91
3135 13527 9.249457 CGTAATCATTTTACTCTATCTGCTTCA 57.751 33.333 0.00 0.00 0.00 3.02
3147 13539 9.890629 ACTCTATCTGCTTCAAAATATTGTGTA 57.109 29.630 5.52 0.00 37.79 2.90
3193 13711 7.102847 ACTTTTTAAGTTTGACCGGAAATCA 57.897 32.000 9.46 0.00 39.04 2.57
3197 13715 9.685828 TTTTTAAGTTTGACCGGAAATCATTAG 57.314 29.630 9.46 0.00 0.00 1.73
3199 13717 8.801882 TTAAGTTTGACCGGAAATCATTAGAT 57.198 30.769 9.46 0.00 35.53 1.98
3200 13718 7.703058 AAGTTTGACCGGAAATCATTAGATT 57.297 32.000 9.46 0.00 46.20 2.40
3202 13720 6.884295 AGTTTGACCGGAAATCATTAGATTCA 59.116 34.615 9.46 0.00 43.52 2.57
3204 13722 7.496529 TTGACCGGAAATCATTAGATTCATC 57.503 36.000 9.46 0.00 43.52 2.92
3205 13723 6.591001 TGACCGGAAATCATTAGATTCATCA 58.409 36.000 9.46 0.00 43.52 3.07
3206 13724 7.226441 TGACCGGAAATCATTAGATTCATCAT 58.774 34.615 9.46 0.00 43.52 2.45
3207 13725 7.173735 TGACCGGAAATCATTAGATTCATCATG 59.826 37.037 9.46 0.00 43.52 3.07
3208 13726 7.226441 ACCGGAAATCATTAGATTCATCATGA 58.774 34.615 9.46 0.00 43.52 3.07
3209 13727 7.720957 ACCGGAAATCATTAGATTCATCATGAA 59.279 33.333 9.46 1.59 43.52 2.57
3222 13740 9.595823 AGATTCATCATGAATTGAATTTCCAAC 57.404 29.630 20.31 10.30 46.20 3.77
3223 13741 9.595823 GATTCATCATGAATTGAATTTCCAACT 57.404 29.630 20.31 2.73 46.20 3.16
3225 13743 8.991243 TCATCATGAATTGAATTTCCAACTTC 57.009 30.769 0.00 0.00 38.03 3.01
3227 13745 9.431887 CATCATGAATTGAATTTCCAACTTCTT 57.568 29.630 0.00 0.00 38.03 2.52
3229 13747 9.480053 TCATGAATTGAATTTCCAACTTCTTTC 57.520 29.630 0.00 0.00 0.00 2.62
3230 13748 9.485206 CATGAATTGAATTTCCAACTTCTTTCT 57.515 29.630 0.00 0.00 0.00 2.52
3250 13920 9.529325 TCTTTCTATTTAGTATTGTGGATGTCG 57.471 33.333 0.00 0.00 0.00 4.35
3251 13921 9.529325 CTTTCTATTTAGTATTGTGGATGTCGA 57.471 33.333 0.00 0.00 0.00 4.20
3271 13949 8.867112 TGTCGATATTTTAGGTACAAGATGAC 57.133 34.615 0.00 0.00 0.00 3.06
3467 15052 1.676014 CGAGGCTCGGAGAAAACCAAT 60.676 52.381 28.52 0.00 36.00 3.16
3525 15110 0.314935 ATGTGGCGAGCTTTGTTTGG 59.685 50.000 0.00 0.00 0.00 3.28
3570 15155 4.870426 AGAACGTGGATGACAATGATGTAC 59.130 41.667 0.00 0.00 40.74 2.90
3571 15156 3.186909 ACGTGGATGACAATGATGTACG 58.813 45.455 0.00 0.00 40.74 3.67
3620 15294 9.681062 CTAGACCCAATTAAAGGTTAGAATTGA 57.319 33.333 7.88 0.00 41.16 2.57
3622 15296 9.374711 AGACCCAATTAAAGGTTAGAATTGAAA 57.625 29.630 7.88 0.00 41.16 2.69
3673 15347 2.635714 GTTTAGTTGGATACCACCCCG 58.364 52.381 0.00 0.00 30.78 5.73
3748 15610 1.738099 CACACTCACAGCTACCGCC 60.738 63.158 0.00 0.00 36.60 6.13
3798 16181 3.304525 GCGTCGGCTATGATAGTACAAGT 60.305 47.826 0.92 0.00 35.83 3.16
3799 16182 4.219802 CGTCGGCTATGATAGTACAAGTG 58.780 47.826 0.92 0.00 0.00 3.16
3800 16183 4.024302 CGTCGGCTATGATAGTACAAGTGA 60.024 45.833 0.92 0.00 0.00 3.41
3802 16185 5.859114 GTCGGCTATGATAGTACAAGTGATG 59.141 44.000 0.92 0.00 0.00 3.07
3847 16230 0.908198 TGGCTTGCCACAAGGTTTTT 59.092 45.000 10.65 0.00 37.19 1.94
3881 16264 5.876651 AGACCTGCTATTATCACATGTGA 57.123 39.130 29.67 29.67 44.59 3.58
3884 16267 3.742882 CCTGCTATTATCACATGTGACCG 59.257 47.826 30.09 16.63 43.11 4.79
3885 16268 3.130633 TGCTATTATCACATGTGACCGC 58.869 45.455 30.09 24.18 43.11 5.68
3887 16270 3.809832 GCTATTATCACATGTGACCGCTT 59.190 43.478 30.09 16.58 43.11 4.68
3888 16271 4.988540 GCTATTATCACATGTGACCGCTTA 59.011 41.667 30.09 15.53 43.11 3.09
3889 16272 5.119279 GCTATTATCACATGTGACCGCTTAG 59.881 44.000 30.09 23.09 43.11 2.18
3891 16274 0.320050 TCACATGTGACCGCTTAGCA 59.680 50.000 24.56 0.00 34.14 3.49
3892 16275 0.723414 CACATGTGACCGCTTAGCAG 59.277 55.000 21.64 0.00 0.00 4.24
3895 16278 1.129251 CATGTGACCGCTTAGCAGTTG 59.871 52.381 4.70 0.00 0.00 3.16
3896 16279 0.105964 TGTGACCGCTTAGCAGTTGT 59.894 50.000 4.70 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 3708 5.594724 AATTTGCCACAATTTGTCATTCG 57.405 34.783 0.00 0.00 0.00 3.34
672 5818 5.048154 ACCCAAGTTCTCTTTACGACTAGAC 60.048 44.000 0.00 0.00 0.00 2.59
690 5836 3.195610 TGAGTAGTGACTATGCACCCAAG 59.804 47.826 0.00 0.00 39.59 3.61
856 6396 7.591426 GGCAAAGAGAAGGTTAATTATAATGCG 59.409 37.037 0.00 0.00 0.00 4.73
938 6488 1.440618 TCCTGCTTGTTAGTTGGGGA 58.559 50.000 0.00 0.00 0.00 4.81
947 6497 1.818642 CTAGCTGCTTCCTGCTTGTT 58.181 50.000 7.79 0.00 42.73 2.83
1171 6807 1.601419 TACGGGAGGTTCTTGAGCGG 61.601 60.000 0.00 0.00 0.00 5.52
1172 6808 0.458025 GTACGGGAGGTTCTTGAGCG 60.458 60.000 0.00 0.00 0.00 5.03
1173 6809 0.458025 CGTACGGGAGGTTCTTGAGC 60.458 60.000 7.57 0.00 0.00 4.26
1188 6827 0.522915 CGAAGAAGGTCTCGCCGTAC 60.523 60.000 0.00 0.00 43.70 3.67
1241 7127 0.036952 ACCGATGAAGTCCAGCACAG 60.037 55.000 0.00 0.00 0.00 3.66
1292 7183 9.819267 ATTAGGCAGTAAGATTAACAGTAGTTC 57.181 33.333 0.00 0.00 39.15 3.01
1309 7218 7.690256 TCTCTTTCTCCTTTTAATTAGGCAGT 58.310 34.615 0.00 0.00 32.59 4.40
1315 7224 8.680820 TCTCCCTCTCTTTCTCCTTTTAATTA 57.319 34.615 0.00 0.00 0.00 1.40
1317 7226 7.763564 ATCTCCCTCTCTTTCTCCTTTTAAT 57.236 36.000 0.00 0.00 0.00 1.40
1318 7227 8.123130 TCTATCTCCCTCTCTTTCTCCTTTTAA 58.877 37.037 0.00 0.00 0.00 1.52
1362 7314 0.171231 GGCTGGAAAATGAAGCGACC 59.829 55.000 0.00 0.00 37.83 4.79
1365 7317 0.521291 TTCGGCTGGAAAATGAAGCG 59.479 50.000 0.00 0.00 37.83 4.68
1604 7564 8.106462 TGAAAATGGTGTGATTAAGGACTGATA 58.894 33.333 0.00 0.00 0.00 2.15
1622 7589 4.572985 TCACAGTGCTTTCTGAAAATGG 57.427 40.909 4.18 0.00 38.63 3.16
1656 7666 6.040166 ACGACGTAGGTATGATCAGGTAAATT 59.960 38.462 0.00 0.00 0.00 1.82
1673 7683 0.861866 CCTGCACATCGACGACGTAG 60.862 60.000 0.00 0.00 40.69 3.51
1674 7684 1.135939 CCTGCACATCGACGACGTA 59.864 57.895 0.00 0.00 40.69 3.57
1675 7685 2.126463 CCTGCACATCGACGACGT 60.126 61.111 0.00 0.00 40.69 4.34
1676 7686 2.152699 GTCCTGCACATCGACGACG 61.153 63.158 0.00 0.00 41.26 5.12
1677 7687 0.666274 TTGTCCTGCACATCGACGAC 60.666 55.000 0.00 0.00 33.90 4.34
1681 7691 1.067142 GTACCTTGTCCTGCACATCGA 60.067 52.381 0.00 0.00 33.90 3.59
1712 7725 0.036010 ATGACAAACAGGGAGCTCCG 60.036 55.000 26.36 16.01 41.52 4.63
1824 9923 1.055040 CTCTAGGCCTTGGGAGATGG 58.945 60.000 12.58 0.00 0.00 3.51
1870 9978 7.178451 TGGGAATTAAAGGAAGAATGGACTTTC 59.822 37.037 0.00 0.00 35.11 2.62
1974 10087 6.990349 ACGCAACCAGCATATAGTATAAAAGT 59.010 34.615 0.00 0.00 46.13 2.66
1975 10088 7.421530 ACGCAACCAGCATATAGTATAAAAG 57.578 36.000 0.00 0.00 46.13 2.27
1978 10091 5.158494 CGACGCAACCAGCATATAGTATAA 58.842 41.667 0.00 0.00 46.13 0.98
1981 10094 2.860971 GCGACGCAACCAGCATATAGTA 60.861 50.000 16.42 0.00 46.13 1.82
1982 10095 1.852942 CGACGCAACCAGCATATAGT 58.147 50.000 0.00 0.00 46.13 2.12
2106 10232 6.099341 ACTTTGTGGAGAAAAACATTGACAC 58.901 36.000 0.00 0.00 0.00 3.67
2129 10255 8.507470 GTCAAATCTCATAAACTTTGACCAAC 57.493 34.615 13.37 0.00 45.88 3.77
2226 11192 6.540551 TGAGTCATACACAAGTGTTAGCAAAA 59.459 34.615 11.50 0.00 41.83 2.44
2252 11249 2.905075 TGCCCACTCATCAGTTTATCG 58.095 47.619 0.00 0.00 0.00 2.92
2268 11265 0.464554 GTACCTGCAGAGGATTGCCC 60.465 60.000 17.39 0.00 42.93 5.36
2532 11529 2.789409 GCCCCGGCATATCTAGAAAT 57.211 50.000 0.00 0.00 41.49 2.17
2572 11572 5.123227 TGCGGAAGACCTAAATTAATCAGG 58.877 41.667 12.44 12.44 35.45 3.86
2592 11598 6.801377 TGATGCTACTTTAATTTTGAACTGCG 59.199 34.615 0.00 0.00 0.00 5.18
2676 11682 0.694444 ACAGGTGAGGAGGGTTGTGT 60.694 55.000 0.00 0.00 0.00 3.72
2737 11743 4.162690 CCTAGCCACCCGCACTCC 62.163 72.222 0.00 0.00 41.38 3.85
2747 11753 2.290287 ACGCCATCACACCTAGCCA 61.290 57.895 0.00 0.00 0.00 4.75
2751 11757 1.375396 GCACACGCCATCACACCTA 60.375 57.895 0.00 0.00 0.00 3.08
2752 11758 2.669569 GCACACGCCATCACACCT 60.670 61.111 0.00 0.00 0.00 4.00
2900 11909 4.394729 TGTGTTTTAGGCCAGTAGGAAAG 58.605 43.478 5.01 0.00 36.89 2.62
2949 11958 4.340666 ACATAAATTTATGCATGCCCGTGA 59.659 37.500 29.73 0.00 43.30 4.35
2977 11988 8.025445 GGATAATTGCTTCAAGCCAATACATAG 58.975 37.037 7.01 0.00 41.51 2.23
3028 12046 1.098869 TCAACCACACAAATGCACGT 58.901 45.000 0.00 0.00 0.00 4.49
3062 12080 2.527951 AAAGCGCGCTCATCCCTTCT 62.528 55.000 36.57 12.91 0.00 2.85
3063 12081 2.109126 AAAGCGCGCTCATCCCTTC 61.109 57.895 36.57 0.00 0.00 3.46
3065 12083 2.821366 CAAAGCGCGCTCATCCCT 60.821 61.111 36.57 15.57 0.00 4.20
3066 12084 4.543084 GCAAAGCGCGCTCATCCC 62.543 66.667 36.57 17.05 0.00 3.85
3083 12101 0.866906 CAACAACACCAACAGCGCAG 60.867 55.000 11.47 3.33 0.00 5.18
3085 12103 1.588667 CCAACAACACCAACAGCGC 60.589 57.895 0.00 0.00 0.00 5.92
3086 12104 1.065600 CCCAACAACACCAACAGCG 59.934 57.895 0.00 0.00 0.00 5.18
3087 12105 0.534873 AACCCAACAACACCAACAGC 59.465 50.000 0.00 0.00 0.00 4.40
3095 13340 5.776173 ATGATTACGAAAACCCAACAACA 57.224 34.783 0.00 0.00 0.00 3.33
3101 13346 7.989416 AGAGTAAAATGATTACGAAAACCCA 57.011 32.000 0.00 0.00 0.00 4.51
3106 13351 9.817809 AGCAGATAGAGTAAAATGATTACGAAA 57.182 29.630 0.00 0.00 0.00 3.46
3107 13352 9.817809 AAGCAGATAGAGTAAAATGATTACGAA 57.182 29.630 0.00 0.00 0.00 3.85
3108 13353 9.464714 GAAGCAGATAGAGTAAAATGATTACGA 57.535 33.333 0.00 0.00 0.00 3.43
3121 13513 8.798859 ACACAATATTTTGAAGCAGATAGAGT 57.201 30.769 8.57 0.00 36.64 3.24
3171 13689 9.685828 CTAATGATTTCCGGTCAAACTTAAAAA 57.314 29.630 0.00 0.00 0.00 1.94
3178 13696 7.083875 TGAATCTAATGATTTCCGGTCAAAC 57.916 36.000 0.00 0.00 42.43 2.93
3182 13700 7.388776 TCATGATGAATCTAATGATTTCCGGTC 59.611 37.037 0.00 0.00 42.43 4.79
3197 13715 9.595823 AGTTGGAAATTCAATTCATGATGAATC 57.404 29.630 19.89 12.17 45.57 2.52
3199 13717 9.426837 GAAGTTGGAAATTCAATTCATGATGAA 57.573 29.630 10.65 10.65 41.09 2.57
3200 13718 8.809066 AGAAGTTGGAAATTCAATTCATGATGA 58.191 29.630 0.00 0.00 38.03 2.92
3204 13722 9.485206 AGAAAGAAGTTGGAAATTCAATTCATG 57.515 29.630 14.78 0.00 31.38 3.07
3225 13743 9.529325 TCGACATCCACAATACTAAATAGAAAG 57.471 33.333 0.00 0.00 0.00 2.62
3241 13911 7.924412 TCTTGTACCTAAAATATCGACATCCAC 59.076 37.037 0.00 0.00 0.00 4.02
3243 13913 8.926710 CATCTTGTACCTAAAATATCGACATCC 58.073 37.037 0.00 0.00 0.00 3.51
3249 13919 8.833231 ATGGTCATCTTGTACCTAAAATATCG 57.167 34.615 0.00 0.00 36.67 2.92
3429 15014 4.776743 CCTCGTCACATGTTTTTCTTCTG 58.223 43.478 0.00 0.00 0.00 3.02
3431 15016 3.251004 AGCCTCGTCACATGTTTTTCTTC 59.749 43.478 0.00 0.00 0.00 2.87
3467 15052 0.108992 GTACGGTCCATGAAGCACGA 60.109 55.000 0.00 0.00 0.00 4.35
3525 15110 3.444034 TGGTGCGAGCATCTATATCCTAC 59.556 47.826 9.88 0.00 0.00 3.18
3570 15155 5.559417 GCCCATTTATTCCAACACGTATACG 60.559 44.000 23.24 23.24 46.33 3.06
3571 15156 5.529800 AGCCCATTTATTCCAACACGTATAC 59.470 40.000 0.00 0.00 0.00 1.47
3609 15283 9.573133 CCACATGACTTATTTTCAATTCTAACC 57.427 33.333 0.00 0.00 0.00 2.85
3620 15294 4.772100 CCTTCCACCCACATGACTTATTTT 59.228 41.667 0.00 0.00 0.00 1.82
3622 15296 3.877735 GCCTTCCACCCACATGACTTATT 60.878 47.826 0.00 0.00 0.00 1.40
3673 15347 0.396139 TGATCTTTGCCATCCCTGCC 60.396 55.000 0.00 0.00 0.00 4.85
3748 15610 2.503895 AGTTTCTTGCCTCATCCCTG 57.496 50.000 0.00 0.00 0.00 4.45
3798 16181 2.237143 AGCACCTCCGAATCTTTCATCA 59.763 45.455 0.00 0.00 0.00 3.07
3799 16182 2.911484 AGCACCTCCGAATCTTTCATC 58.089 47.619 0.00 0.00 0.00 2.92
3800 16183 4.487714 TTAGCACCTCCGAATCTTTCAT 57.512 40.909 0.00 0.00 0.00 2.57
3802 16185 4.437524 GCTTTTAGCACCTCCGAATCTTTC 60.438 45.833 0.00 0.00 41.89 2.62
3832 16215 0.908198 AGGCAAAAACCTTGTGGCAA 59.092 45.000 5.97 0.00 36.28 4.52
3847 16230 3.249189 AGGTCTTCGGCCAAGGCA 61.249 61.111 13.87 0.00 38.64 4.75


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

AutoCloner maintained by Alex Coulton.