Multiple sequence alignment - TraesCS3A01G515300

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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 TraesCS3A01G515300 chr3A 100.000 5095 0 0 1 5095 733489931 733495025 0.000000e+00 9409
1 TraesCS3A01G515300 chr3A 84.430 623 81 6 2116 2723 12813858 12813237 2.630000e-167 599
2 TraesCS3A01G515300 chr3D 96.533 3288 95 10 1824 5095 603973771 603977055 0.000000e+00 5422
3 TraesCS3A01G515300 chr3D 89.394 1122 57 18 1 1109 603972127 603973199 0.000000e+00 1356
4 TraesCS3A01G515300 chr3D 93.431 685 44 1 4412 5095 610887154 610886470 0.000000e+00 1014
5 TraesCS3A01G515300 chr3D 89.312 552 30 15 1129 1676 603973249 603973775 0.000000e+00 665
6 TraesCS3A01G515300 chr3D 84.927 617 77 7 2115 2723 7591870 7592478 1.210000e-170 610
7 TraesCS3A01G515300 chr3B 92.636 3463 135 51 686 4071 811093124 811096543 0.000000e+00 4872
8 TraesCS3A01G515300 chr3B 82.709 1174 138 40 2141 3279 9915859 9917002 0.000000e+00 983
9 TraesCS3A01G515300 chr3B 92.958 213 15 0 1308 1520 9914557 9914769 1.380000e-80 311
10 TraesCS3A01G515300 chr3B 88.889 252 15 9 155 404 811090343 811090583 1.070000e-76 298
11 TraesCS3A01G515300 chr3B 81.967 305 31 12 4121 4412 811096560 811096853 2.370000e-58 237
12 TraesCS3A01G515300 chr3B 89.205 176 16 1 1 173 811090156 811090331 3.090000e-52 217
13 TraesCS3A01G515300 chr3B 92.593 108 5 2 474 580 811093001 811093106 8.840000e-33 152
14 TraesCS3A01G515300 chr1D 94.905 687 32 2 4412 5095 319517716 319517030 0.000000e+00 1072
15 TraesCS3A01G515300 chr5D 94.161 685 37 3 4414 5095 389374131 389374815 0.000000e+00 1040
16 TraesCS3A01G515300 chr7D 93.362 693 42 3 4407 5095 635693018 635692326 0.000000e+00 1022
17 TraesCS3A01G515300 chr7D 93.567 684 43 1 4413 5095 117521635 117520952 0.000000e+00 1018
18 TraesCS3A01G515300 chr7D 93.285 685 39 4 4413 5095 379328638 379327959 0.000000e+00 1003
19 TraesCS3A01G515300 chr4D 93.149 686 45 2 4412 5095 455275781 455276466 0.000000e+00 1005
20 TraesCS3A01G515300 chr4D 93.458 214 14 0 1308 1521 393635964 393636177 8.230000e-83 318
21 TraesCS3A01G515300 chr4D 93.333 210 14 0 1308 1517 28837078 28837287 1.380000e-80 311
22 TraesCS3A01G515300 chr2D 92.795 694 46 4 4405 5095 394919683 394918991 0.000000e+00 1002
23 TraesCS3A01G515300 chr4A 94.762 210 11 0 1308 1517 75215127 75214918 1.370000e-85 327
24 TraesCS3A01G515300 chr4A 94.286 210 12 0 1308 1517 574872618 574872409 6.360000e-84 322
25 TraesCS3A01G515300 chr4B 93.810 210 13 0 1308 1517 41010038 41010247 2.960000e-82 316
26 TraesCS3A01G515300 chr4B 92.991 214 15 0 1308 1521 483335245 483335032 3.830000e-81 313


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 TraesCS3A01G515300 chr3A 733489931 733495025 5094 False 9409.0 9409 100.000000 1 5095 1 chr3A.!!$F1 5094
1 TraesCS3A01G515300 chr3A 12813237 12813858 621 True 599.0 599 84.430000 2116 2723 1 chr3A.!!$R1 607
2 TraesCS3A01G515300 chr3D 603972127 603977055 4928 False 2481.0 5422 91.746333 1 5095 3 chr3D.!!$F2 5094
3 TraesCS3A01G515300 chr3D 610886470 610887154 684 True 1014.0 1014 93.431000 4412 5095 1 chr3D.!!$R1 683
4 TraesCS3A01G515300 chr3D 7591870 7592478 608 False 610.0 610 84.927000 2115 2723 1 chr3D.!!$F1 608
5 TraesCS3A01G515300 chr3B 811090156 811096853 6697 False 1155.2 4872 89.058000 1 4412 5 chr3B.!!$F2 4411
6 TraesCS3A01G515300 chr3B 9914557 9917002 2445 False 647.0 983 87.833500 1308 3279 2 chr3B.!!$F1 1971
7 TraesCS3A01G515300 chr1D 319517030 319517716 686 True 1072.0 1072 94.905000 4412 5095 1 chr1D.!!$R1 683
8 TraesCS3A01G515300 chr5D 389374131 389374815 684 False 1040.0 1040 94.161000 4414 5095 1 chr5D.!!$F1 681
9 TraesCS3A01G515300 chr7D 635692326 635693018 692 True 1022.0 1022 93.362000 4407 5095 1 chr7D.!!$R3 688
10 TraesCS3A01G515300 chr7D 117520952 117521635 683 True 1018.0 1018 93.567000 4413 5095 1 chr7D.!!$R1 682
11 TraesCS3A01G515300 chr7D 379327959 379328638 679 True 1003.0 1003 93.285000 4413 5095 1 chr7D.!!$R2 682
12 TraesCS3A01G515300 chr4D 455275781 455276466 685 False 1005.0 1005 93.149000 4412 5095 1 chr4D.!!$F3 683
13 TraesCS3A01G515300 chr2D 394918991 394919683 692 True 1002.0 1002 92.795000 4405 5095 1 chr2D.!!$R1 690

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
668 3060 0.035725 GTTGGGGTGGGTAGTGTAGC 60.036 60.000 0.00 0.0 0.00 3.58 F
1722 4608 0.037605 AGCCGGGTCGAACACTTTAG 60.038 55.000 0.00 0.0 0.00 1.85 F
2909 5922 0.456628 TGCCAATCCATGTTGATGCG 59.543 50.000 0.00 0.0 0.00 4.73 F
3683 6711 2.341543 CTGCACGAGCTGGACACT 59.658 61.111 1.44 0.0 42.74 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 4627 1.459592 GTCACCATACGAACAGTGTGC 59.540 52.381 0.0 0.0 40.16 4.57 R
3479 6507 1.301716 GGTGCTGTCCTTGAGCGAA 60.302 57.895 0.0 0.0 39.47 4.70 R
3954 6983 0.320683 CAGAACCACAGACCATGCGA 60.321 55.000 0.0 0.0 0.00 5.10 R
4568 7618 0.761187 GCCCAGACTATCAGCATCCA 59.239 55.000 0.0 0.0 0.00 3.41 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
22 23 2.314071 TTAAGAGGGTCCGAACCTGA 57.686 50.000 10.61 0.00 45.66 3.86
38 39 5.872617 CGAACCTGAGTAAATAATGTGTCCA 59.127 40.000 0.00 0.00 0.00 4.02
63 64 1.942657 CTTCCTGTTACCATCATGCCG 59.057 52.381 0.00 0.00 0.00 5.69
64 65 0.180171 TCCTGTTACCATCATGCCGG 59.820 55.000 0.00 0.00 0.00 6.13
66 67 0.819259 CTGTTACCATCATGCCGGGG 60.819 60.000 2.18 0.00 0.00 5.73
70 71 1.059584 TACCATCATGCCGGGGTCAT 61.060 55.000 2.18 0.00 34.88 3.06
73 74 0.466007 CATCATGCCGGGGTCATCAA 60.466 55.000 2.18 0.00 0.00 2.57
88 89 3.053077 TCATCAATTCGGGACCCCTTAT 58.947 45.455 4.46 0.00 0.00 1.73
240 275 4.488879 CACATTTTTAGCAGAAAGAGGCC 58.511 43.478 0.00 0.00 0.00 5.19
255 290 3.414700 GCCTTCACGAGTGCACCG 61.415 66.667 21.20 21.20 0.00 4.94
256 291 2.029073 CCTTCACGAGTGCACCGT 59.971 61.111 22.31 22.31 41.36 4.83
257 292 2.022129 CCTTCACGAGTGCACCGTC 61.022 63.158 24.30 12.25 38.29 4.79
258 293 1.299850 CTTCACGAGTGCACCGTCA 60.300 57.895 24.30 13.89 38.29 4.35
259 294 1.278172 CTTCACGAGTGCACCGTCAG 61.278 60.000 24.30 19.55 38.29 3.51
260 295 2.011741 TTCACGAGTGCACCGTCAGT 62.012 55.000 24.30 11.26 38.29 3.41
270 305 2.049433 CCGTCAGTGTCCACGTCC 60.049 66.667 2.65 0.00 34.06 4.79
323 358 7.412853 AGCAATCATGTCTCGCTAAATAAAAG 58.587 34.615 0.00 0.00 0.00 2.27
376 416 3.078837 TGTGGGAATCTTTTAGGCGAAC 58.921 45.455 0.00 0.00 0.00 3.95
377 417 3.244770 TGTGGGAATCTTTTAGGCGAACT 60.245 43.478 0.00 0.00 0.00 3.01
378 418 3.756963 GTGGGAATCTTTTAGGCGAACTT 59.243 43.478 0.00 0.00 0.00 2.66
417 1780 6.594937 TCGGGTACTGTTGTTAAATAATGGTC 59.405 38.462 0.00 0.00 35.30 4.02
459 2846 4.450976 TGAAACCACATTCTATCCATCGG 58.549 43.478 0.00 0.00 0.00 4.18
460 2847 4.080582 TGAAACCACATTCTATCCATCGGT 60.081 41.667 0.00 0.00 0.00 4.69
471 2858 9.277783 CATTCTATCCATCGGTAAAAATCTTCT 57.722 33.333 0.00 0.00 0.00 2.85
472 2859 8.662781 TTCTATCCATCGGTAAAAATCTTCTG 57.337 34.615 0.00 0.00 0.00 3.02
476 2863 6.001460 TCCATCGGTAAAAATCTTCTGTGTT 58.999 36.000 0.00 0.00 0.00 3.32
479 2866 7.326063 CCATCGGTAAAAATCTTCTGTGTTTTC 59.674 37.037 0.00 0.00 0.00 2.29
510 2900 0.593128 GCTTTGATGAGTGCACCGTT 59.407 50.000 14.63 0.00 0.00 4.44
615 3005 3.152341 ACAAGATGAGAAGTTGGCTTGG 58.848 45.455 0.00 0.00 37.60 3.61
646 3036 2.475487 GCATCTTTTAGGTACGATCGGC 59.525 50.000 20.98 11.58 0.00 5.54
648 3038 1.066002 TCTTTTAGGTACGATCGGCGG 59.934 52.381 20.98 0.00 46.49 6.13
649 3039 0.102844 TTTTAGGTACGATCGGCGGG 59.897 55.000 20.98 0.00 46.49 6.13
650 3040 1.037030 TTTAGGTACGATCGGCGGGT 61.037 55.000 20.98 5.70 46.49 5.28
651 3041 1.037030 TTAGGTACGATCGGCGGGTT 61.037 55.000 20.98 0.00 46.49 4.11
652 3042 1.727511 TAGGTACGATCGGCGGGTTG 61.728 60.000 20.98 2.78 46.49 3.77
668 3060 0.035725 GTTGGGGTGGGTAGTGTAGC 60.036 60.000 0.00 0.00 0.00 3.58
669 3061 0.178885 TTGGGGTGGGTAGTGTAGCT 60.179 55.000 0.00 0.00 0.00 3.32
671 3063 0.616679 GGGGTGGGTAGTGTAGCTGA 60.617 60.000 0.00 0.00 0.00 4.26
672 3064 0.824759 GGGTGGGTAGTGTAGCTGAG 59.175 60.000 0.00 0.00 0.00 3.35
673 3065 1.618888 GGGTGGGTAGTGTAGCTGAGA 60.619 57.143 0.00 0.00 0.00 3.27
674 3066 1.751924 GGTGGGTAGTGTAGCTGAGAG 59.248 57.143 0.00 0.00 0.00 3.20
675 3067 1.135333 GTGGGTAGTGTAGCTGAGAGC 59.865 57.143 0.00 0.00 42.84 4.09
676 3068 0.747852 GGGTAGTGTAGCTGAGAGCC 59.252 60.000 0.00 0.00 43.77 4.70
677 3069 0.382515 GGTAGTGTAGCTGAGAGCCG 59.617 60.000 0.00 0.00 43.77 5.52
678 3070 0.382515 GTAGTGTAGCTGAGAGCCGG 59.617 60.000 0.00 0.00 43.77 6.13
679 3071 0.255033 TAGTGTAGCTGAGAGCCGGA 59.745 55.000 5.05 0.00 43.77 5.14
680 3072 1.034838 AGTGTAGCTGAGAGCCGGAG 61.035 60.000 5.05 0.00 43.77 4.63
681 3073 1.032657 GTGTAGCTGAGAGCCGGAGA 61.033 60.000 5.05 0.00 43.77 3.71
682 3074 0.106469 TGTAGCTGAGAGCCGGAGAT 60.106 55.000 5.05 0.00 43.77 2.75
683 3075 0.313672 GTAGCTGAGAGCCGGAGATG 59.686 60.000 5.05 0.00 43.77 2.90
684 3076 0.183731 TAGCTGAGAGCCGGAGATGA 59.816 55.000 5.05 0.00 43.77 2.92
685 3077 1.108727 AGCTGAGAGCCGGAGATGAG 61.109 60.000 5.05 0.00 43.77 2.90
686 3078 1.106351 GCTGAGAGCCGGAGATGAGA 61.106 60.000 5.05 0.00 34.48 3.27
687 3079 1.619654 CTGAGAGCCGGAGATGAGAT 58.380 55.000 5.05 0.00 0.00 2.75
762 3154 3.340034 AGAGCGTAGGAATCTATCTCCG 58.660 50.000 0.00 0.00 38.08 4.63
951 3352 2.515523 ATGGCGATGCTGACTGGC 60.516 61.111 0.00 0.00 0.00 4.85
952 3353 3.333899 ATGGCGATGCTGACTGGCA 62.334 57.895 0.00 0.00 46.63 4.92
953 3354 3.503363 GGCGATGCTGACTGGCAC 61.503 66.667 0.00 0.00 45.36 5.01
954 3355 2.435586 GCGATGCTGACTGGCACT 60.436 61.111 0.00 0.00 45.36 4.40
955 3356 2.459442 GCGATGCTGACTGGCACTC 61.459 63.158 0.00 0.00 45.36 3.51
956 3357 1.217511 CGATGCTGACTGGCACTCT 59.782 57.895 0.00 0.00 45.36 3.24
957 3358 1.082679 CGATGCTGACTGGCACTCTG 61.083 60.000 0.00 0.00 45.36 3.35
958 3359 1.367599 GATGCTGACTGGCACTCTGC 61.368 60.000 15.58 15.58 45.36 4.26
967 3368 4.385405 GCACTCTGCCAGCGACCT 62.385 66.667 0.00 0.00 37.42 3.85
1100 3501 0.534412 CACCACCACAAGCACCAAAA 59.466 50.000 0.00 0.00 0.00 2.44
1117 3518 2.323939 AAAACACACACACACACACG 57.676 45.000 0.00 0.00 0.00 4.49
1119 3520 1.917782 AACACACACACACACACGCC 61.918 55.000 0.00 0.00 0.00 5.68
1120 3521 3.192230 ACACACACACACACGCCG 61.192 61.111 0.00 0.00 0.00 6.46
1121 3522 3.192230 CACACACACACACGCCGT 61.192 61.111 0.00 0.00 0.00 5.68
1152 3593 1.152881 GGTGGCCATGGTGATCTCC 60.153 63.158 9.72 6.88 0.00 3.71
1206 3647 1.064296 CACCTTCTCGTCGCGCTAT 59.936 57.895 5.56 0.00 0.00 2.97
1240 3681 2.334946 CCGAGGTGACGACCCGTAA 61.335 63.158 0.00 0.00 44.40 3.18
1252 3693 1.153309 CCCGTAAATCCGACCACCC 60.153 63.158 0.00 0.00 0.00 4.61
1253 3694 1.597989 CCGTAAATCCGACCACCCA 59.402 57.895 0.00 0.00 0.00 4.51
1254 3695 0.179468 CCGTAAATCCGACCACCCAT 59.821 55.000 0.00 0.00 0.00 4.00
1255 3696 1.407712 CCGTAAATCCGACCACCCATT 60.408 52.381 0.00 0.00 0.00 3.16
1257 3698 1.937899 GTAAATCCGACCACCCATTCG 59.062 52.381 0.00 0.00 34.93 3.34
1258 3699 0.616371 AAATCCGACCACCCATTCGA 59.384 50.000 0.00 0.00 37.43 3.71
1259 3700 0.837272 AATCCGACCACCCATTCGAT 59.163 50.000 0.00 0.00 37.43 3.59
1270 3713 1.298413 CATTCGATCGTCCGACGCT 60.298 57.895 16.24 6.51 42.21 5.07
1271 3714 1.298413 ATTCGATCGTCCGACGCTG 60.298 57.895 16.24 8.11 42.21 5.18
1272 3715 1.712018 ATTCGATCGTCCGACGCTGA 61.712 55.000 16.24 10.23 42.21 4.26
1287 3730 1.519246 CTGAGGCGAGCCATCTGAA 59.481 57.895 17.18 0.00 38.92 3.02
1288 3731 0.809241 CTGAGGCGAGCCATCTGAAC 60.809 60.000 17.18 0.00 38.92 3.18
1289 3732 1.880340 GAGGCGAGCCATCTGAACG 60.880 63.158 17.18 0.00 38.92 3.95
1296 3741 1.464997 GAGCCATCTGAACGGTGTTTC 59.535 52.381 0.00 0.00 0.00 2.78
1391 3836 3.918253 GATGCTGGACGGCAACCCA 62.918 63.158 10.18 0.00 45.68 4.51
1403 3848 3.175710 AACCCACGGCTGGACCTT 61.176 61.111 0.00 0.00 40.55 3.50
1469 3914 4.920999 TCATCATGGACTCCATCAACAAA 58.079 39.130 7.69 0.00 43.15 2.83
1554 4069 9.117145 GTTCACAACATGTTTATATGTTCACAG 57.883 33.333 8.77 0.00 45.49 3.66
1596 4482 7.380431 ACTAGTAGTAGTAAGAACAGCAGTG 57.620 40.000 8.55 0.00 37.76 3.66
1684 4570 4.088923 GTCACAATTGATGTCACATTTGCG 59.911 41.667 13.59 0.00 41.46 4.85
1693 4579 2.556189 TGTCACATTTGCGCCATTAGTT 59.444 40.909 4.18 0.00 0.00 2.24
1696 4582 3.119884 TCACATTTGCGCCATTAGTTCTG 60.120 43.478 4.18 0.00 0.00 3.02
1706 4592 5.273944 CGCCATTAGTTCTGAAATTAAGCC 58.726 41.667 0.00 0.00 0.00 4.35
1712 4598 2.018542 TCTGAAATTAAGCCGGGTCG 57.981 50.000 6.62 0.00 0.00 4.79
1722 4608 0.037605 AGCCGGGTCGAACACTTTAG 60.038 55.000 0.00 0.00 0.00 1.85
1726 4612 3.181487 GCCGGGTCGAACACTTTAGTATA 60.181 47.826 2.18 0.00 0.00 1.47
1728 4614 4.354587 CGGGTCGAACACTTTAGTATACC 58.645 47.826 1.31 0.00 0.00 2.73
1775 4661 1.003839 GTGACGTCCTGGCATCCAA 60.004 57.895 14.12 0.00 30.80 3.53
1809 4698 1.419762 TGGGCTTGACTTGACTTGCTA 59.580 47.619 0.00 0.00 0.00 3.49
1956 4910 7.275999 CACGTATGTTGTGTTACACATATACCA 59.724 37.037 27.76 18.15 44.16 3.25
2227 5209 3.419943 TGCTCACTTATTCAATGCACCA 58.580 40.909 0.00 0.00 0.00 4.17
2359 5341 1.676006 GGGAAGCCATATGACAAACCG 59.324 52.381 3.65 0.00 0.00 4.44
2441 5447 4.586884 TGGTTTTTACCACAGTGTGTACA 58.413 39.130 21.48 3.70 34.33 2.90
2484 5497 7.259088 ACCTCTCTCATGTTAATAGGTTTGT 57.741 36.000 0.00 0.00 31.95 2.83
2815 5828 9.817809 TGAATTAGTGATGGATACTGACTAAAC 57.182 33.333 0.00 0.00 36.49 2.01
2909 5922 0.456628 TGCCAATCCATGTTGATGCG 59.543 50.000 0.00 0.00 0.00 4.73
3128 6141 4.037923 CAGCCCACATTTACACTGAACTTT 59.962 41.667 0.00 0.00 0.00 2.66
3178 6201 4.008330 AGTTGAGCATGAATCCTCTGTTG 58.992 43.478 0.00 0.00 0.00 3.33
3211 6239 7.987750 TTCAACAACTTAAGTACATGCCATA 57.012 32.000 8.92 0.00 0.00 2.74
3479 6507 2.511600 GTGCCATTAGTCGCCGCT 60.512 61.111 0.00 0.00 0.00 5.52
3683 6711 2.341543 CTGCACGAGCTGGACACT 59.658 61.111 1.44 0.00 42.74 3.55
3830 6858 4.038642 TGCATGTCCCTGGTAAAGAAAAAC 59.961 41.667 0.00 0.00 0.00 2.43
3833 6861 5.845391 TGTCCCTGGTAAAGAAAAACAAG 57.155 39.130 0.00 0.00 0.00 3.16
3954 6983 4.464244 TGTCAGCTTGCTAGAGATTAGTGT 59.536 41.667 0.00 0.00 0.00 3.55
3959 6988 4.615949 CTTGCTAGAGATTAGTGTCGCAT 58.384 43.478 0.00 0.00 0.00 4.73
3999 7028 0.039764 ACAGGACACCTCTCGATGGA 59.960 55.000 11.00 0.00 0.00 3.41
4062 7098 3.641437 ATGTTACGTGTTTGCTGCATT 57.359 38.095 1.84 0.00 0.00 3.56
4071 7107 4.146961 CGTGTTTGCTGCATTCTTTAGTTG 59.853 41.667 1.84 0.00 0.00 3.16
4074 7110 3.287312 TGCTGCATTCTTTAGTTGTGC 57.713 42.857 0.00 0.00 36.39 4.57
4245 7289 5.105228 CCCCATAAGCAGAATTCAAACATGT 60.105 40.000 8.44 0.00 0.00 3.21
4326 7370 6.974622 CCTATCAAATCAACACAATAACTGGC 59.025 38.462 0.00 0.00 0.00 4.85
4380 7427 5.560722 AAGGGAAAATGTAAAACCCCAAG 57.439 39.130 0.00 0.00 41.26 3.61
4568 7618 5.279206 CGCTACTCCTATCCAGTTGATGAAT 60.279 44.000 0.00 0.00 34.76 2.57
4611 7661 1.045407 TACCAAACAGACCTCGCAGT 58.955 50.000 0.00 0.00 0.00 4.40
4772 7822 4.793731 CAGTGTTGTACTACTGCATCTACG 59.206 45.833 8.88 0.00 37.60 3.51
4856 7906 1.377072 CATCATCACACGCCCACCA 60.377 57.895 0.00 0.00 0.00 4.17
4939 7989 1.534235 ACCACCTCACGCCTCTTCT 60.534 57.895 0.00 0.00 0.00 2.85
5038 8088 0.396695 TAGGATTTCTCCCGGAGCGT 60.397 55.000 9.87 0.27 43.21 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.045072 ACACATTATTTACTCAGGTTCGGA 57.955 37.500 0.00 0.00 0.00 4.55
63 64 0.465642 GGTCCCGAATTGATGACCCC 60.466 60.000 5.83 0.00 41.14 4.95
64 65 3.095922 GGTCCCGAATTGATGACCC 57.904 57.895 5.83 0.00 41.14 4.46
66 67 0.546598 AGGGGTCCCGAATTGATGAC 59.453 55.000 0.48 0.00 41.95 3.06
70 71 1.772453 GGATAAGGGGTCCCGAATTGA 59.228 52.381 0.48 0.00 41.95 2.57
73 74 0.105349 TCGGATAAGGGGTCCCGAAT 60.105 55.000 0.48 0.00 46.63 3.34
82 83 0.244994 CGGCAGATCTCGGATAAGGG 59.755 60.000 0.00 0.00 0.00 3.95
240 275 1.278172 CTGACGGTGCACTCGTGAAG 61.278 60.000 29.47 22.81 41.22 3.02
255 290 1.660575 CACGGACGTGGACACTGAC 60.661 63.158 16.46 0.00 42.00 3.51
256 291 2.725641 CACGGACGTGGACACTGA 59.274 61.111 16.46 0.00 42.00 3.41
270 305 7.325097 GGTTTATGGACAAAAATCTTACACACG 59.675 37.037 0.00 0.00 0.00 4.49
336 376 4.136796 CACAAACCACCTTCTCATCTTCA 58.863 43.478 0.00 0.00 0.00 3.02
376 416 1.024579 CCGACCAATCCCACCGAAAG 61.025 60.000 0.00 0.00 0.00 2.62
377 417 1.003112 CCGACCAATCCCACCGAAA 60.003 57.895 0.00 0.00 0.00 3.46
378 418 2.666207 CCGACCAATCCCACCGAA 59.334 61.111 0.00 0.00 0.00 4.30
381 422 1.222661 GTACCCGACCAATCCCACC 59.777 63.158 0.00 0.00 0.00 4.61
451 2838 6.180472 ACACAGAAGATTTTTACCGATGGAT 58.820 36.000 0.00 0.00 0.00 3.41
459 2846 6.811954 TGGGGAAAACACAGAAGATTTTTAC 58.188 36.000 0.00 0.00 0.00 2.01
460 2847 7.425224 TTGGGGAAAACACAGAAGATTTTTA 57.575 32.000 0.00 0.00 31.29 1.52
476 2863 2.840651 TCAAAGCCTTGTTTTGGGGAAA 59.159 40.909 4.04 0.00 35.13 3.13
479 2866 2.368221 TCATCAAAGCCTTGTTTTGGGG 59.632 45.455 4.04 0.00 35.13 4.96
576 2966 5.651303 TCTTGTTGCTCCCTATAGGCTATA 58.349 41.667 13.85 13.39 34.51 1.31
577 2967 4.493618 TCTTGTTGCTCCCTATAGGCTAT 58.506 43.478 13.85 12.41 34.51 2.97
578 2968 3.923648 TCTTGTTGCTCCCTATAGGCTA 58.076 45.455 13.85 0.00 34.51 3.93
579 2969 2.764269 TCTTGTTGCTCCCTATAGGCT 58.236 47.619 13.85 0.00 34.51 4.58
580 2970 3.071602 TCATCTTGTTGCTCCCTATAGGC 59.928 47.826 13.85 2.84 34.51 3.93
581 2971 4.590647 TCTCATCTTGTTGCTCCCTATAGG 59.409 45.833 12.27 12.27 0.00 2.57
582 2972 5.798125 TCTCATCTTGTTGCTCCCTATAG 57.202 43.478 0.00 0.00 0.00 1.31
615 3005 1.478105 CTAAAAGATGCCCACAAGCCC 59.522 52.381 0.00 0.00 0.00 5.19
646 3036 2.931649 ACTACCCACCCCAACCCG 60.932 66.667 0.00 0.00 0.00 5.28
647 3037 0.841594 TACACTACCCACCCCAACCC 60.842 60.000 0.00 0.00 0.00 4.11
648 3038 0.616891 CTACACTACCCACCCCAACC 59.383 60.000 0.00 0.00 0.00 3.77
649 3039 0.035725 GCTACACTACCCACCCCAAC 60.036 60.000 0.00 0.00 0.00 3.77
650 3040 0.178885 AGCTACACTACCCACCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
651 3041 0.907704 CAGCTACACTACCCACCCCA 60.908 60.000 0.00 0.00 0.00 4.96
652 3042 0.616679 TCAGCTACACTACCCACCCC 60.617 60.000 0.00 0.00 0.00 4.95
668 3060 1.619654 ATCTCATCTCCGGCTCTCAG 58.380 55.000 0.00 0.00 0.00 3.35
669 3061 2.959465 TATCTCATCTCCGGCTCTCA 57.041 50.000 0.00 0.00 0.00 3.27
671 3063 3.448093 TCATATCTCATCTCCGGCTCT 57.552 47.619 0.00 0.00 0.00 4.09
672 3064 3.737663 GCATCATATCTCATCTCCGGCTC 60.738 52.174 0.00 0.00 0.00 4.70
673 3065 2.168106 GCATCATATCTCATCTCCGGCT 59.832 50.000 0.00 0.00 0.00 5.52
674 3066 2.168106 AGCATCATATCTCATCTCCGGC 59.832 50.000 0.00 0.00 0.00 6.13
675 3067 3.700539 AGAGCATCATATCTCATCTCCGG 59.299 47.826 0.00 0.00 37.82 5.14
676 3068 4.987408 AGAGCATCATATCTCATCTCCG 57.013 45.455 0.00 0.00 37.82 4.63
677 3069 6.372103 CCAAAAGAGCATCATATCTCATCTCC 59.628 42.308 0.00 0.00 37.82 3.71
678 3070 6.935771 ACCAAAAGAGCATCATATCTCATCTC 59.064 38.462 0.00 0.00 37.82 2.75
679 3071 6.711194 CACCAAAAGAGCATCATATCTCATCT 59.289 38.462 0.00 0.00 37.82 2.90
680 3072 6.709397 TCACCAAAAGAGCATCATATCTCATC 59.291 38.462 0.00 0.00 37.82 2.92
681 3073 6.598503 TCACCAAAAGAGCATCATATCTCAT 58.401 36.000 0.00 0.00 37.82 2.90
682 3074 5.993055 TCACCAAAAGAGCATCATATCTCA 58.007 37.500 0.00 0.00 37.82 3.27
683 3075 6.317140 TGTTCACCAAAAGAGCATCATATCTC 59.683 38.462 0.00 0.00 37.82 2.75
684 3076 6.182627 TGTTCACCAAAAGAGCATCATATCT 58.817 36.000 0.00 0.00 37.82 1.98
685 3077 6.441093 TGTTCACCAAAAGAGCATCATATC 57.559 37.500 0.00 0.00 37.82 1.63
686 3078 5.163581 GCTGTTCACCAAAAGAGCATCATAT 60.164 40.000 1.39 0.00 43.15 1.78
687 3079 4.156556 GCTGTTCACCAAAAGAGCATCATA 59.843 41.667 1.39 0.00 43.15 2.15
762 3154 7.038659 TGCCATTTGTTAGTGTTTATTATGCC 58.961 34.615 0.00 0.00 0.00 4.40
865 3257 1.172812 AAAGGAAGCAAGGTGTCGGC 61.173 55.000 0.00 0.00 0.00 5.54
866 3258 1.001378 CAAAAGGAAGCAAGGTGTCGG 60.001 52.381 0.00 0.00 0.00 4.79
868 3260 1.269778 GCCAAAAGGAAGCAAGGTGTC 60.270 52.381 0.00 0.00 0.00 3.67
869 3261 0.752658 GCCAAAAGGAAGCAAGGTGT 59.247 50.000 0.00 0.00 0.00 4.16
951 3352 2.433838 CAGGTCGCTGGCAGAGTG 60.434 66.667 20.86 5.77 0.00 3.51
952 3353 4.385405 GCAGGTCGCTGGCAGAGT 62.385 66.667 20.86 0.00 37.77 3.24
967 3368 2.666190 GAGTTGTGCAGCTCGGCA 60.666 61.111 0.00 0.00 42.53 5.69
975 3376 1.150536 GGGAAGGTGGAGTTGTGCA 59.849 57.895 0.00 0.00 0.00 4.57
1100 3501 1.499949 GCGTGTGTGTGTGTGTGTT 59.500 52.632 0.00 0.00 0.00 3.32
1136 3577 1.619057 TGGGAGATCACCATGGCCA 60.619 57.895 13.04 8.56 31.83 5.36
1138 3579 0.179034 GAGTGGGAGATCACCATGGC 60.179 60.000 13.04 0.00 40.70 4.40
1218 3659 2.675772 GGTCGTCACCTCGGGAGT 60.676 66.667 0.00 0.00 40.00 3.85
1240 3681 0.837272 ATCGAATGGGTGGTCGGATT 59.163 50.000 0.00 0.00 37.84 3.01
1252 3693 1.298413 AGCGTCGGACGATCGAATG 60.298 57.895 32.48 10.40 46.05 2.67
1253 3694 1.298413 CAGCGTCGGACGATCGAAT 60.298 57.895 32.48 0.00 46.05 3.34
1254 3695 2.099638 CAGCGTCGGACGATCGAA 59.900 61.111 32.48 0.86 46.05 3.71
1255 3696 2.810012 CTCAGCGTCGGACGATCGA 61.810 63.158 32.48 22.81 46.05 3.59
1257 3698 2.024871 CCTCAGCGTCGGACGATC 59.975 66.667 32.48 16.44 46.05 3.69
1258 3699 4.194720 GCCTCAGCGTCGGACGAT 62.195 66.667 32.48 25.13 46.05 3.73
1270 3713 1.219124 GTTCAGATGGCTCGCCTCA 59.781 57.895 9.65 0.00 36.94 3.86
1271 3714 1.880340 CGTTCAGATGGCTCGCCTC 60.880 63.158 9.65 4.62 36.94 4.70
1272 3715 2.185350 CGTTCAGATGGCTCGCCT 59.815 61.111 9.65 0.00 36.94 5.52
1281 3724 1.880027 GGCAAGAAACACCGTTCAGAT 59.120 47.619 0.00 0.00 0.00 2.90
1287 3730 0.034896 ATCGAGGCAAGAAACACCGT 59.965 50.000 0.00 0.00 0.00 4.83
1288 3731 0.721718 GATCGAGGCAAGAAACACCG 59.278 55.000 0.00 0.00 0.00 4.94
1289 3732 1.734465 CTGATCGAGGCAAGAAACACC 59.266 52.381 0.00 0.00 0.00 4.16
1391 3836 4.681978 GACGCAAGGTCCAGCCGT 62.682 66.667 0.00 0.00 43.70 5.68
1403 3848 2.028484 GTGGTGACGAAGGACGCA 59.972 61.111 0.00 0.00 46.94 5.24
1588 4472 8.154856 TCTTAGAAGTTAAATTACCACTGCTGT 58.845 33.333 3.34 0.00 28.65 4.40
1684 4570 5.273944 CGGCTTAATTTCAGAACTAATGGC 58.726 41.667 0.00 0.00 0.00 4.40
1693 4579 1.551430 TCGACCCGGCTTAATTTCAGA 59.449 47.619 0.00 0.00 0.00 3.27
1696 4582 2.078392 TGTTCGACCCGGCTTAATTTC 58.922 47.619 0.00 0.00 0.00 2.17
1706 4592 4.142403 TGGTATACTAAAGTGTTCGACCCG 60.142 45.833 2.25 0.00 0.00 5.28
1722 4608 7.114811 CAGTGTGCAATTTTTGACTTGGTATAC 59.885 37.037 0.00 0.00 0.00 1.47
1726 4612 4.183101 CAGTGTGCAATTTTTGACTTGGT 58.817 39.130 0.00 0.00 0.00 3.67
1728 4614 5.499017 CGAACAGTGTGCAATTTTTGACTTG 60.499 40.000 1.23 0.00 0.00 3.16
1741 4627 1.459592 GTCACCATACGAACAGTGTGC 59.540 52.381 0.00 0.00 40.16 4.57
1775 4661 1.607467 GCCCATGTGGAAACAGCCT 60.607 57.895 0.00 0.00 44.46 4.58
1809 4698 6.126796 ACCAAGGGACATTTTGAACAATTTCT 60.127 34.615 0.00 0.00 32.36 2.52
1956 4910 5.759506 ATATGTCGACGAAGAGAGAATGT 57.240 39.130 11.62 0.00 0.00 2.71
2227 5209 7.227512 CCAATAGCTTTCTCATCCTCGTTTATT 59.772 37.037 0.00 0.00 0.00 1.40
2359 5341 5.288804 ACATTTGCACCAGTAACAATGTTC 58.711 37.500 0.22 0.00 0.00 3.18
2441 5447 5.014228 AGAGGTTACAAGAGGCACCTTTAAT 59.986 40.000 0.00 0.00 39.90 1.40
2484 5497 9.253832 TCAAAATATCTAGCAAATTTCTCCCAA 57.746 29.630 0.00 0.00 0.00 4.12
2815 5828 9.462174 TTTCATTGCTATACTTCAACAAAACAG 57.538 29.630 0.00 0.00 0.00 3.16
2872 5885 3.221771 GGCACATTCCACCTGCATTATA 58.778 45.455 0.00 0.00 32.20 0.98
2909 5922 2.300437 AGCGATAAATCCTCCACTAGCC 59.700 50.000 0.00 0.00 0.00 3.93
3128 6141 8.792633 CAGAACAATTAATACTGACCTTTGGAA 58.207 33.333 0.00 0.00 0.00 3.53
3178 6201 5.754778 ACTTAAGTTGTTGAAACGGCATAC 58.245 37.500 1.12 0.00 0.00 2.39
3211 6239 1.342174 CTGGCTTGCACCTGAACAAAT 59.658 47.619 0.00 0.00 0.00 2.32
3479 6507 1.301716 GGTGCTGTCCTTGAGCGAA 60.302 57.895 0.00 0.00 39.47 4.70
3850 6878 2.467826 GCGTCTGAGCATGCCCTTC 61.468 63.158 15.66 6.25 37.05 3.46
3926 6955 0.686789 TCTAGCAAGCTGACAGGCAA 59.313 50.000 4.53 0.00 34.17 4.52
3954 6983 0.320683 CAGAACCACAGACCATGCGA 60.321 55.000 0.00 0.00 0.00 5.10
3959 6988 2.394632 ACTGTACAGAACCACAGACCA 58.605 47.619 29.30 0.00 43.99 4.02
3999 7028 7.040961 AGCAAACAACAAATACGTACATAACCT 60.041 33.333 0.00 0.00 0.00 3.50
4062 7098 5.213891 TCATCTCAGTGCACAACTAAAGA 57.786 39.130 21.04 11.74 36.83 2.52
4071 7107 4.633126 ACATGTACAATCATCTCAGTGCAC 59.367 41.667 9.40 9.40 29.75 4.57
4074 7110 4.034858 GCCACATGTACAATCATCTCAGTG 59.965 45.833 0.00 0.00 0.00 3.66
4245 7289 7.434307 GCTACTGAACTAATCTTTACGTGCATA 59.566 37.037 0.00 0.00 0.00 3.14
4326 7370 2.582728 TCCAGTTGTTGCAAAAGCAG 57.417 45.000 0.00 0.00 0.00 4.24
4355 7399 5.931294 TGGGGTTTTACATTTTCCCTTTTC 58.069 37.500 0.00 0.00 38.31 2.29
4485 7534 7.931407 ACTGTTGTATGACTTTGTAAGATGTCA 59.069 33.333 0.00 0.00 42.50 3.58
4486 7535 8.311650 ACTGTTGTATGACTTTGTAAGATGTC 57.688 34.615 0.00 0.00 0.00 3.06
4542 7592 3.833732 TCAACTGGATAGGAGTAGCGAT 58.166 45.455 0.00 0.00 0.00 4.58
4568 7618 0.761187 GCCCAGACTATCAGCATCCA 59.239 55.000 0.00 0.00 0.00 3.41
4611 7661 6.070767 CCTCAGGTCTTAGATGTTAGGTTTGA 60.071 42.308 0.00 0.00 0.00 2.69
4772 7822 2.820037 GCAGCTAGACCGGGCAAC 60.820 66.667 11.69 0.00 0.00 4.17
5038 8088 1.132453 CTATCGTCAACCTGCTCGTGA 59.868 52.381 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.