Multiple sequence alignment - TraesCS6D01G143600

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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 TraesCS6D01G143600 chr6D 100.000 3594 0 0 1 3594 114223519 114227112 0.000000e+00 6637.0
1 TraesCS6D01G143600 chr6A 91.315 2349 135 31 741 3067 142772394 142774695 0.000000e+00 3144.0
2 TraesCS6D01G143600 chr6A 89.973 748 55 9 1 743 142771395 142772127 0.000000e+00 948.0
3 TraesCS6D01G143600 chr6A 86.944 360 32 5 3076 3428 142774802 142775153 1.210000e-104 390.0
4 TraesCS6D01G143600 chr6A 83.459 133 15 4 3423 3551 142776887 142777016 2.270000e-22 117.0
5 TraesCS6D01G143600 chr6A 89.412 85 9 0 3163 3247 499288347 499288431 1.360000e-19 108.0
6 TraesCS6D01G143600 chr6B 89.549 2172 149 36 961 3068 203893916 203896073 0.000000e+00 2682.0
7 TraesCS6D01G143600 chr6B 87.266 534 52 7 3064 3594 203896165 203896685 2.390000e-166 595.0
8 TraesCS6D01G143600 chr7B 76.190 1176 216 45 1414 2564 133707758 133706622 2.420000e-156 562.0
9 TraesCS6D01G143600 chr7B 73.975 707 144 36 1886 2572 153582469 153583155 2.140000e-62 250.0
10 TraesCS6D01G143600 chr7B 79.365 189 32 6 3062 3247 703957563 703957379 3.770000e-25 126.0
11 TraesCS6D01G143600 chr7D 76.231 1178 211 48 1414 2563 168297612 168296476 8.710000e-156 560.0
12 TraesCS6D01G143600 chr7D 74.270 1267 249 56 1340 2572 184500318 184501541 2.530000e-126 462.0
13 TraesCS6D01G143600 chr7D 73.370 1258 268 46 1347 2572 184523924 184522702 4.320000e-109 405.0
14 TraesCS6D01G143600 chr7A 76.166 1179 211 48 1414 2564 170613891 170612755 1.130000e-154 556.0
15 TraesCS6D01G143600 chr7A 74.483 1258 248 50 1347 2572 186097261 186096045 9.030000e-131 477.0
16 TraesCS6D01G143600 chr7A 73.618 1266 267 41 1339 2572 185975492 185976722 3.320000e-115 425.0
17 TraesCS6D01G143600 chr7A 79.817 436 74 12 1 426 46311442 46311011 4.510000e-79 305.0
18 TraesCS6D01G143600 chr7A 83.942 137 14 6 3119 3248 53003661 53003796 1.350000e-24 124.0
19 TraesCS6D01G143600 chr7A 100.000 29 0 0 3468 3496 699631345 699631373 2.000000e-03 54.7
20 TraesCS6D01G143600 chrUn 79.796 589 95 14 1414 1991 91795754 91795179 1.200000e-109 407.0
21 TraesCS6D01G143600 chr5B 82.469 405 61 7 1 400 375796045 375796444 2.660000e-91 346.0
22 TraesCS6D01G143600 chr5B 89.474 57 5 1 3449 3504 617807501 617807557 1.790000e-08 71.3
23 TraesCS6D01G143600 chr4A 82.134 403 66 3 1 400 578106528 578106129 1.240000e-89 340.0
24 TraesCS6D01G143600 chr4A 80.482 415 71 8 1 406 654897439 654897026 3.480000e-80 309.0
25 TraesCS6D01G143600 chr2B 80.974 431 67 9 2 419 20303385 20303813 9.620000e-86 327.0
26 TraesCS6D01G143600 chr5D 81.235 405 64 10 32 426 346874055 346874457 2.080000e-82 316.0
27 TraesCS6D01G143600 chr5D 84.058 138 16 3 3113 3245 324637442 324637306 1.050000e-25 128.0
28 TraesCS6D01G143600 chr5D 93.671 79 5 0 3169 3247 324637570 324637492 6.300000e-23 119.0
29 TraesCS6D01G143600 chr5D 100.000 29 0 0 3468 3496 475520443 475520415 2.000000e-03 54.7
30 TraesCS6D01G143600 chr3A 80.278 431 70 12 1 419 728255016 728254589 9.690000e-81 311.0
31 TraesCS6D01G143600 chr1D 80.535 411 69 6 1 400 74341976 74341566 4.510000e-79 305.0
32 TraesCS6D01G143600 chr1D 84.375 128 13 4 3113 3234 476752952 476752826 6.300000e-23 119.0
33 TraesCS6D01G143600 chr1D 79.825 114 14 7 3447 3559 308579486 308579591 1.380000e-09 75.0
34 TraesCS6D01G143600 chr4B 92.500 80 5 1 3170 3248 13999086 13999007 2.930000e-21 113.0
35 TraesCS6D01G143600 chr3D 89.831 59 6 0 3447 3505 514678659 514678601 3.850000e-10 76.8
36 TraesCS6D01G143600 chr3B 90.196 51 5 0 3447 3497 676965468 676965418 2.320000e-07 67.6


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 TraesCS6D01G143600 chr6D 114223519 114227112 3593 False 6637.00 6637 100.00000 1 3594 1 chr6D.!!$F1 3593
1 TraesCS6D01G143600 chr6A 142771395 142777016 5621 False 1149.75 3144 87.92275 1 3551 4 chr6A.!!$F2 3550
2 TraesCS6D01G143600 chr6B 203893916 203896685 2769 False 1638.50 2682 88.40750 961 3594 2 chr6B.!!$F1 2633
3 TraesCS6D01G143600 chr7B 133706622 133707758 1136 True 562.00 562 76.19000 1414 2564 1 chr7B.!!$R1 1150
4 TraesCS6D01G143600 chr7B 153582469 153583155 686 False 250.00 250 73.97500 1886 2572 1 chr7B.!!$F1 686
5 TraesCS6D01G143600 chr7D 168296476 168297612 1136 True 560.00 560 76.23100 1414 2563 1 chr7D.!!$R1 1149
6 TraesCS6D01G143600 chr7D 184500318 184501541 1223 False 462.00 462 74.27000 1340 2572 1 chr7D.!!$F1 1232
7 TraesCS6D01G143600 chr7D 184522702 184523924 1222 True 405.00 405 73.37000 1347 2572 1 chr7D.!!$R2 1225
8 TraesCS6D01G143600 chr7A 170612755 170613891 1136 True 556.00 556 76.16600 1414 2564 1 chr7A.!!$R2 1150
9 TraesCS6D01G143600 chr7A 186096045 186097261 1216 True 477.00 477 74.48300 1347 2572 1 chr7A.!!$R3 1225
10 TraesCS6D01G143600 chr7A 185975492 185976722 1230 False 425.00 425 73.61800 1339 2572 1 chr7A.!!$F2 1233
11 TraesCS6D01G143600 chrUn 91795179 91795754 575 True 407.00 407 79.79600 1414 1991 1 chrUn.!!$R1 577

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
472 476 0.030369 AGCGATTCGGCTAAGTACGG 59.970 55.0 8.34 0.00 42.62 4.02 F
596 600 0.108138 AGCATGTTCTCCGCACCTAC 60.108 55.0 0.00 0.00 0.00 3.18 F
835 1110 0.112008 GTACGCACAAACGTCGTGTC 60.112 55.0 16.67 9.83 44.43 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1741 0.029967 CTCTGAAGATAGCGCGCAGA 59.970 55.000 35.10 23.01 34.71 4.26 R
1845 2168 1.066918 ACGCGAACCTGAAGTCGTT 59.933 52.632 15.93 0.00 0.00 3.85 R
2732 3082 1.067974 TCCACTCCACACTTACACACG 59.932 52.381 0.00 0.00 0.00 4.49 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
19 20 0.680061 GCTAAGACCCCATAGGACCG 59.320 60.000 0.00 0.00 39.89 4.79
20 21 1.756690 GCTAAGACCCCATAGGACCGA 60.757 57.143 0.00 0.00 39.89 4.69
28 29 0.180171 CCATAGGACCGATGCACCAA 59.820 55.000 8.99 0.00 0.00 3.67
30 31 2.364632 CATAGGACCGATGCACCAAAA 58.635 47.619 1.26 0.00 0.00 2.44
43 44 2.327568 CACCAAAACATCAACCATCGC 58.672 47.619 0.00 0.00 0.00 4.58
45 46 1.616620 CAAAACATCAACCATCGCCG 58.383 50.000 0.00 0.00 0.00 6.46
51 52 1.262417 CATCAACCATCGCCGATGAAG 59.738 52.381 27.59 14.48 42.09 3.02
54 55 1.737236 CAACCATCGCCGATGAAGAAA 59.263 47.619 27.59 0.00 42.09 2.52
55 56 1.656652 ACCATCGCCGATGAAGAAAG 58.343 50.000 27.59 12.35 42.09 2.62
56 57 1.066143 ACCATCGCCGATGAAGAAAGT 60.066 47.619 27.59 12.99 42.09 2.66
57 58 1.594862 CCATCGCCGATGAAGAAAGTC 59.405 52.381 27.59 0.00 42.09 3.01
58 59 1.256376 CATCGCCGATGAAGAAAGTCG 59.744 52.381 22.11 0.00 42.09 4.18
59 60 0.242825 TCGCCGATGAAGAAAGTCGT 59.757 50.000 0.00 0.00 33.77 4.34
61 62 1.846782 CGCCGATGAAGAAAGTCGTAG 59.153 52.381 0.00 0.00 33.77 3.51
62 63 2.477357 CGCCGATGAAGAAAGTCGTAGA 60.477 50.000 0.00 0.00 33.77 2.59
63 64 3.707793 GCCGATGAAGAAAGTCGTAGAT 58.292 45.455 0.00 0.00 40.67 1.98
64 65 3.731717 GCCGATGAAGAAAGTCGTAGATC 59.268 47.826 0.00 0.00 40.67 2.75
105 106 1.463444 GACCCAAACGAAGACGAATGG 59.537 52.381 0.00 0.00 42.95 3.16
114 115 3.000041 CGAAGACGAATGGATCCAAACA 59.000 45.455 20.67 0.00 42.66 2.83
135 136 1.194781 ATCCACCGAAGACCAGCACT 61.195 55.000 0.00 0.00 0.00 4.40
155 156 1.249407 GACCTAATCCCGCGAGATCT 58.751 55.000 8.23 0.00 0.00 2.75
156 157 0.962489 ACCTAATCCCGCGAGATCTG 59.038 55.000 8.23 1.38 0.00 2.90
162 165 1.098129 TCCCGCGAGATCTGACAGAG 61.098 60.000 8.23 0.00 0.00 3.35
178 181 2.842462 AGACACCTCCACACGCCA 60.842 61.111 0.00 0.00 0.00 5.69
182 185 4.082523 ACCTCCACACGCCATCCG 62.083 66.667 0.00 0.00 44.21 4.18
187 190 2.173669 CCACACGCCATCCGATGAC 61.174 63.158 10.12 0.00 41.02 3.06
227 230 2.439507 GCAGGGATAGAATGTGGGAGAA 59.560 50.000 0.00 0.00 0.00 2.87
253 256 2.125326 CCACCGAGGGACATCGCTA 61.125 63.158 0.27 0.00 41.37 4.26
264 267 1.521457 CATCGCTACCGCCACACAT 60.521 57.895 0.00 0.00 0.00 3.21
288 292 3.956199 CCAACCATGATGCTGAACCTAAT 59.044 43.478 0.00 0.00 0.00 1.73
290 294 5.771666 CCAACCATGATGCTGAACCTAATAT 59.228 40.000 0.00 0.00 0.00 1.28
303 307 7.119709 TGAACCTAATATGAACGAGAATGGA 57.880 36.000 0.00 0.00 0.00 3.41
308 312 2.990066 ATGAACGAGAATGGAGTCCC 57.010 50.000 6.74 0.00 0.00 4.46
378 382 3.917760 GGAGATGGAGCGGACCGG 61.918 72.222 17.22 0.00 0.00 5.28
412 416 0.698818 GGAGGAGGGGAAAGCTTGAA 59.301 55.000 0.00 0.00 0.00 2.69
420 424 5.658634 GGAGGGGAAAGCTTGAAATCTTTAT 59.341 40.000 0.00 0.00 33.14 1.40
422 426 7.175347 AGGGGAAAGCTTGAAATCTTTATTC 57.825 36.000 0.00 0.00 33.14 1.75
472 476 0.030369 AGCGATTCGGCTAAGTACGG 59.970 55.000 8.34 0.00 42.62 4.02
566 570 7.924947 AGTTAAAATACAAGGTATCGGCTAGAC 59.075 37.037 0.00 0.00 0.00 2.59
587 591 2.698855 TGCCCTAAGAGCATGTTCTC 57.301 50.000 12.88 2.29 34.69 2.87
596 600 0.108138 AGCATGTTCTCCGCACCTAC 60.108 55.000 0.00 0.00 0.00 3.18
613 617 5.621781 GCACCTACGAGGCTTATAATCTACC 60.622 48.000 0.00 0.00 39.63 3.18
614 618 5.475909 CACCTACGAGGCTTATAATCTACCA 59.524 44.000 0.00 0.00 39.63 3.25
646 652 3.294214 CTCCTAATGAAAATGGCAGGCT 58.706 45.455 0.00 0.00 0.00 4.58
659 665 2.100584 TGGCAGGCTGTTACTTGTTTTG 59.899 45.455 17.16 0.00 0.00 2.44
662 668 4.429108 GCAGGCTGTTACTTGTTTTGAAA 58.571 39.130 17.16 0.00 0.00 2.69
666 672 5.580691 AGGCTGTTACTTGTTTTGAAAAAGC 59.419 36.000 0.00 0.00 0.00 3.51
688 694 6.996509 AGCCATGAAAAAGATACAACACATT 58.003 32.000 0.00 0.00 0.00 2.71
770 1045 1.465187 GGTTAGCCGCACGATTTTGTC 60.465 52.381 0.00 0.00 0.00 3.18
835 1110 0.112008 GTACGCACAAACGTCGTGTC 60.112 55.000 16.67 9.83 44.43 3.67
877 1152 6.623114 GCTGATCGTACGTGGAGACATATAAT 60.623 42.308 16.05 0.00 46.14 1.28
920 1195 9.521503 GAAGGCTGAGAAAAACCATTTTATATC 57.478 33.333 0.00 0.00 38.83 1.63
928 1203 9.449719 AGAAAAACCATTTTATATCAGTCGTCT 57.550 29.630 0.00 0.00 38.83 4.18
944 1219 3.013219 TCGTCTCAGGATGACAGAAGAG 58.987 50.000 0.00 0.00 42.56 2.85
1105 1381 1.209019 TCTGCCATTCCTTCTCTGCTC 59.791 52.381 0.00 0.00 0.00 4.26
1131 1407 4.856607 GCTCGTTCTCGCCCCTCG 62.857 72.222 0.00 0.00 40.15 4.63
1374 1679 3.706373 GCCCGTGCTCTCCTTCCA 61.706 66.667 0.00 0.00 33.53 3.53
1452 1757 1.586303 CGTCTGCGCGCTATCTTCA 60.586 57.895 33.29 8.98 0.00 3.02
1454 1759 0.248661 GTCTGCGCGCTATCTTCAGA 60.249 55.000 33.29 21.25 0.00 3.27
1589 1894 2.742372 CAGAAACTCGCCGTGGGG 60.742 66.667 0.00 0.00 0.00 4.96
1733 2056 3.059982 CCAGACTGCCCGTTGAGA 58.940 61.111 0.00 0.00 0.00 3.27
1736 2059 2.811317 GACTGCCCGTTGAGAGCG 60.811 66.667 0.00 0.00 0.00 5.03
1744 2067 2.258591 GTTGAGAGCGTGCTCCGA 59.741 61.111 17.76 7.13 43.70 4.55
1835 2158 3.733960 CTCACGGTCTCGCGGTCA 61.734 66.667 6.13 0.00 40.63 4.02
1862 2185 1.773496 GAACGACTTCAGGTTCGCG 59.227 57.895 0.00 0.00 33.93 5.87
1913 2248 1.524165 CTCGTCGGGAGTCCTCGAT 60.524 63.158 20.85 0.00 38.02 3.59
2420 2767 1.834263 CTCTACTTCAAGGACCCCAGG 59.166 57.143 0.00 0.00 0.00 4.45
2613 2960 4.051237 CAAATAAGGATCGATCGAGCACA 58.949 43.478 31.78 17.61 31.28 4.57
2614 2961 2.776312 TAAGGATCGATCGAGCACAC 57.224 50.000 31.78 16.58 31.28 3.82
2615 2962 0.248661 AAGGATCGATCGAGCACACG 60.249 55.000 31.78 0.00 31.28 4.49
2616 2963 2.296480 GGATCGATCGAGCACACGC 61.296 63.158 31.78 12.72 38.99 5.34
2617 2964 2.630714 GATCGATCGAGCACACGCG 61.631 63.158 27.18 3.53 45.49 6.01
2644 2993 1.523258 GCATGCTCATCGACCAGCT 60.523 57.895 11.37 2.42 36.53 4.24
2645 2994 1.773054 GCATGCTCATCGACCAGCTG 61.773 60.000 11.37 6.78 36.53 4.24
2660 3009 4.156622 CTGGCGTGCGTGCATCTG 62.157 66.667 0.00 0.00 36.28 2.90
2732 3082 8.779354 ATAAGACTGTCATAAAAGTGACCTTC 57.221 34.615 10.88 1.86 46.17 3.46
2754 3104 1.070134 TGTGTAAGTGTGGAGTGGAGC 59.930 52.381 0.00 0.00 0.00 4.70
2811 3161 2.390599 GCCGTCGCTGCAGATTTGA 61.391 57.895 20.43 6.08 0.00 2.69
2907 3277 5.664735 GCGTGAAGAGTGTTGACGTATAAAC 60.665 44.000 13.12 0.00 32.66 2.01
2929 3299 3.621558 GCTTAGCTCACCTTTACCCATT 58.378 45.455 0.00 0.00 0.00 3.16
2932 3302 5.396436 GCTTAGCTCACCTTTACCCATTAGA 60.396 44.000 0.00 0.00 0.00 2.10
2956 3326 9.391006 AGATTGAGTTTTTGTGTGAACTAGTTA 57.609 29.630 8.42 0.00 36.31 2.24
2976 3346 5.066893 AGTTAATGCATGCAGTTCTACATGG 59.933 40.000 27.14 0.00 43.13 3.66
2979 3349 3.949132 TGCATGCAGTTCTACATGGTAA 58.051 40.909 18.46 0.00 43.13 2.85
2980 3350 4.525996 TGCATGCAGTTCTACATGGTAAT 58.474 39.130 18.46 0.00 43.13 1.89
3001 3371 3.717707 TCGAGTCAAAAGGTCTTGAGTG 58.282 45.455 0.00 0.00 38.75 3.51
3008 3378 3.498774 AAAGGTCTTGAGTGCATGACT 57.501 42.857 0.00 0.00 44.34 3.41
3042 3412 1.070601 CATGGCTACATCGATCCCACA 59.929 52.381 0.00 0.00 34.35 4.17
3092 3560 2.092592 AGTTTTGAGTTCAAGACCCGGT 60.093 45.455 10.77 0.00 40.56 5.28
3098 3566 3.056107 TGAGTTCAAGACCCGGTTGATAG 60.056 47.826 6.80 0.00 33.95 2.08
3142 3610 3.385111 AGCCATTTTTGGTCCACGTTTAA 59.615 39.130 0.00 0.00 0.00 1.52
3165 3633 1.070786 GAGGGAGCCACACGTGAAA 59.929 57.895 25.01 0.00 0.00 2.69
3242 3716 3.595758 GGCTGGTGCGTGCAGTTT 61.596 61.111 0.00 0.00 40.82 2.66
3248 3722 1.472878 TGGTGCGTGCAGTTTTACAAA 59.527 42.857 0.00 0.00 0.00 2.83
3249 3723 2.116366 GGTGCGTGCAGTTTTACAAAG 58.884 47.619 0.00 0.00 0.00 2.77
3250 3724 2.116366 GTGCGTGCAGTTTTACAAAGG 58.884 47.619 0.00 0.00 0.00 3.11
3251 3725 1.066303 TGCGTGCAGTTTTACAAAGGG 59.934 47.619 0.00 0.00 0.00 3.95
3252 3726 1.066454 GCGTGCAGTTTTACAAAGGGT 59.934 47.619 0.00 0.00 0.00 4.34
3253 3727 2.857104 GCGTGCAGTTTTACAAAGGGTC 60.857 50.000 0.00 0.00 0.00 4.46
3264 3738 2.073776 ACAAAGGGTCAGGGGATCTTT 58.926 47.619 0.00 0.00 32.99 2.52
3281 3755 6.015350 GGGATCTTTATATGTTCTGTCGAGGA 60.015 42.308 0.00 0.00 0.00 3.71
3293 3767 3.057019 CTGTCGAGGAATTGTTTGTCGA 58.943 45.455 0.00 0.00 37.32 4.20
3322 3796 4.509970 TCGACACATAATTTATCTTGGGCG 59.490 41.667 0.00 0.00 0.00 6.13
3410 3885 9.918630 CAATTGATGAATAGAGTGGAAGTTTTT 57.081 29.630 0.00 0.00 0.00 1.94
3412 3887 8.924511 TTGATGAATAGAGTGGAAGTTTTTCT 57.075 30.769 0.00 0.00 33.68 2.52
3443 5657 6.346096 TGTATCTTGGGCACATAGAAAGTAC 58.654 40.000 0.00 0.00 0.00 2.73
3451 5665 5.066117 GGGCACATAGAAAGTACTTTTAGGC 59.934 44.000 21.40 17.19 32.11 3.93
3457 5671 8.329502 ACATAGAAAGTACTTTTAGGCCATCTT 58.670 33.333 21.40 0.00 32.11 2.40
3461 5675 7.890655 AGAAAGTACTTTTAGGCCATCTTCAAT 59.109 33.333 21.40 0.00 32.11 2.57
3463 5677 8.507524 AAGTACTTTTAGGCCATCTTCAATAC 57.492 34.615 5.01 0.00 0.00 1.89
3505 5719 4.367023 CCGTCCGCGAACAGGGAA 62.367 66.667 8.23 0.00 41.33 3.97
3506 5720 2.809601 CGTCCGCGAACAGGGAAG 60.810 66.667 8.23 0.00 41.33 3.46
3507 5721 2.654877 GTCCGCGAACAGGGAAGA 59.345 61.111 8.23 0.00 33.27 2.87
3508 5722 1.005394 GTCCGCGAACAGGGAAGAA 60.005 57.895 8.23 0.00 33.27 2.52
3509 5723 1.005394 TCCGCGAACAGGGAAGAAC 60.005 57.895 8.23 0.00 34.27 3.01
3510 5724 2.033194 CCGCGAACAGGGAAGAACC 61.033 63.158 8.23 0.00 38.08 3.62
3513 5727 0.250338 GCGAACAGGGAAGAACCAGT 60.250 55.000 0.00 0.00 41.20 4.00
3542 5764 3.717294 GGACATGGGTGCGGGAGT 61.717 66.667 0.00 0.00 0.00 3.85
3566 5789 1.459539 ATCTAAGCTAGGCCGGGCA 60.460 57.895 31.59 15.08 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.383943 TGCATCGGTCCTATGGGGT 60.384 57.895 5.58 0.00 36.25 4.95
11 12 2.290641 TGTTTTGGTGCATCGGTCCTAT 60.291 45.455 0.00 0.00 0.00 2.57
19 20 3.383620 TGGTTGATGTTTTGGTGCATC 57.616 42.857 0.00 0.00 41.19 3.91
20 21 3.614630 CGATGGTTGATGTTTTGGTGCAT 60.615 43.478 0.00 0.00 0.00 3.96
28 29 1.401552 CATCGGCGATGGTTGATGTTT 59.598 47.619 35.72 3.56 36.51 2.83
30 31 0.177836 TCATCGGCGATGGTTGATGT 59.822 50.000 39.82 9.05 40.15 3.06
43 44 3.969352 CGATCTACGACTTTCTTCATCGG 59.031 47.826 0.00 0.00 45.77 4.18
56 57 7.658261 ACATATTTGATCCTTTCGATCTACGA 58.342 34.615 0.00 0.00 46.65 3.43
57 58 7.875316 ACATATTTGATCCTTTCGATCTACG 57.125 36.000 1.77 0.00 46.65 3.51
62 63 9.057089 GGTCTTTACATATTTGATCCTTTCGAT 57.943 33.333 0.00 0.00 0.00 3.59
63 64 7.497909 GGGTCTTTACATATTTGATCCTTTCGA 59.502 37.037 0.00 0.00 0.00 3.71
64 65 7.282224 TGGGTCTTTACATATTTGATCCTTTCG 59.718 37.037 0.00 0.00 0.00 3.46
85 86 1.463444 CCATTCGTCTTCGTTTGGGTC 59.537 52.381 0.00 0.00 36.93 4.46
105 106 2.691409 TCGGTGGATCTGTTTGGATC 57.309 50.000 0.00 0.00 40.78 3.36
114 115 0.904865 TGCTGGTCTTCGGTGGATCT 60.905 55.000 0.00 0.00 0.00 2.75
135 136 0.959553 GATCTCGCGGGATTAGGTCA 59.040 55.000 24.71 0.00 0.00 4.02
155 156 1.040646 GTGTGGAGGTGTCTCTGTCA 58.959 55.000 0.00 0.00 39.86 3.58
156 157 0.039074 CGTGTGGAGGTGTCTCTGTC 60.039 60.000 0.00 0.00 39.86 3.51
162 165 1.741770 GATGGCGTGTGGAGGTGTC 60.742 63.158 0.00 0.00 0.00 3.67
178 181 1.283181 GCGTCTAGCGTCATCGGAT 59.717 57.895 8.08 0.00 43.66 4.18
200 203 0.035458 CATTCTATCCCTGCCCCGAC 59.965 60.000 0.00 0.00 0.00 4.79
210 213 8.341892 GGAATAATTTCTCCCACATTCTATCC 57.658 38.462 0.00 0.00 32.16 2.59
251 254 1.024579 GTTGGGATGTGTGGCGGTAG 61.025 60.000 0.00 0.00 0.00 3.18
253 256 2.282180 GTTGGGATGTGTGGCGGT 60.282 61.111 0.00 0.00 0.00 5.68
264 267 1.616725 GGTTCAGCATCATGGTTGGGA 60.617 52.381 0.00 0.00 0.00 4.37
288 292 3.643237 AGGGACTCCATTCTCGTTCATA 58.357 45.455 0.00 0.00 34.83 2.15
290 294 1.938585 AGGGACTCCATTCTCGTTCA 58.061 50.000 0.00 0.00 34.83 3.18
323 327 4.452733 GGTGCGGAGAACCTCGGG 62.453 72.222 0.00 0.00 34.66 5.14
383 387 3.775654 CCTCCTCCTGACGGTGCC 61.776 72.222 0.00 0.00 0.00 5.01
386 390 2.396651 TTTCCCCTCCTCCTGACGGT 62.397 60.000 0.00 0.00 0.00 4.83
390 394 0.178861 AAGCTTTCCCCTCCTCCTGA 60.179 55.000 0.00 0.00 0.00 3.86
401 405 6.033937 GCACGAATAAAGATTTCAAGCTTTCC 59.966 38.462 6.07 0.00 42.94 3.13
412 416 8.749354 AGAAAATTTAGGGCACGAATAAAGATT 58.251 29.630 0.00 0.00 0.00 2.40
420 424 5.776173 TCAAAGAAAATTTAGGGCACGAA 57.224 34.783 0.00 0.00 0.00 3.85
422 426 5.528870 ACTTCAAAGAAAATTTAGGGCACG 58.471 37.500 0.00 0.00 0.00 5.34
472 476 4.911514 TTTTGAGGAGTTAAACAGTGGC 57.088 40.909 0.00 0.00 0.00 5.01
538 542 6.053650 AGCCGATACCTTGTATTTTAACTCC 58.946 40.000 0.00 0.00 0.00 3.85
587 591 0.956633 TATAAGCCTCGTAGGTGCGG 59.043 55.000 3.38 0.00 37.80 5.69
596 600 6.601613 AGAGAGATGGTAGATTATAAGCCTCG 59.398 42.308 0.00 0.00 0.00 4.63
613 617 9.695526 CATTTTCATTAGGAGTAGAGAGAGATG 57.304 37.037 0.00 0.00 0.00 2.90
614 618 8.869109 CCATTTTCATTAGGAGTAGAGAGAGAT 58.131 37.037 0.00 0.00 0.00 2.75
628 634 4.460948 AACAGCCTGCCATTTTCATTAG 57.539 40.909 0.00 0.00 0.00 1.73
646 652 7.099764 TCATGGCTTTTTCAAAACAAGTAACA 58.900 30.769 0.00 0.00 0.00 2.41
659 665 8.275632 GTGTTGTATCTTTTTCATGGCTTTTTC 58.724 33.333 0.00 0.00 0.00 2.29
662 668 6.815089 TGTGTTGTATCTTTTTCATGGCTTT 58.185 32.000 0.00 0.00 0.00 3.51
688 694 9.027202 TGTGAAAGACGGGTATATATGCTTATA 57.973 33.333 0.62 2.11 0.00 0.98
770 1045 3.407657 GCTTCCAGCAGAGCGATG 58.592 61.111 0.00 0.00 41.89 3.84
835 1110 2.662150 GCCCAAAGCTCGTACGTAG 58.338 57.895 16.05 12.17 38.99 3.51
877 1152 2.483876 CTTCTGCGTGGTTTCTCTTGA 58.516 47.619 0.00 0.00 0.00 3.02
920 1195 2.087646 TCTGTCATCCTGAGACGACTG 58.912 52.381 0.00 0.00 38.83 3.51
928 1203 1.198713 GGGCTCTTCTGTCATCCTGA 58.801 55.000 0.00 0.00 0.00 3.86
944 1219 1.337387 CTTGTCCTACGTAGCTAGGGC 59.663 57.143 17.41 8.47 36.76 5.19
1053 1329 5.675323 GCTTGTGGTATTTCGATGGTAAACC 60.675 44.000 0.00 0.00 0.00 3.27
1055 1331 5.004448 TGCTTGTGGTATTTCGATGGTAAA 58.996 37.500 0.00 0.00 0.00 2.01
1105 1381 1.075425 CGAGAACGAGCAGGCAGAAG 61.075 60.000 0.00 0.00 42.66 2.85
1131 1407 1.076923 TGGGAGGAGCTACCGAGAC 60.077 63.158 0.00 0.00 37.26 3.36
1389 1694 1.134946 GCCGGCAGATAACATGCTTTT 59.865 47.619 24.80 0.00 43.35 2.27
1436 1741 0.029967 CTCTGAAGATAGCGCGCAGA 59.970 55.000 35.10 23.01 34.71 4.26
1446 1751 1.398692 GGCTCCGACTCTCTGAAGAT 58.601 55.000 0.00 0.00 0.00 2.40
1452 1757 2.124487 CTCCGGCTCCGACTCTCT 60.124 66.667 10.28 0.00 42.83 3.10
1454 1759 3.729489 TCCTCCGGCTCCGACTCT 61.729 66.667 10.28 0.00 42.83 3.24
1613 1918 2.203195 TTGCACTGGAGCAGCGTT 60.203 55.556 0.00 0.00 46.54 4.84
1744 2067 2.788191 GAACGTGCAGCTACTGGGCT 62.788 60.000 0.00 0.00 44.10 5.19
1751 2074 3.691342 AGGGCGAACGTGCAGCTA 61.691 61.111 9.65 0.00 36.28 3.32
1791 2114 3.400590 GACGACGGTGGCGTTGAC 61.401 66.667 0.00 0.00 42.77 3.18
1835 2158 3.628280 GAAGTCGTTCGCGGAGGCT 62.628 63.158 6.13 1.35 41.70 4.58
1837 2160 1.801913 CTGAAGTCGTTCGCGGAGG 60.802 63.158 6.13 2.47 41.70 4.30
1839 2162 2.079020 AACCTGAAGTCGTTCGCGGA 62.079 55.000 6.13 0.00 41.70 5.54
1845 2168 1.066918 ACGCGAACCTGAAGTCGTT 59.933 52.632 15.93 0.00 0.00 3.85
1862 2185 3.512516 GCGCCCATCTCCAAGCAC 61.513 66.667 0.00 0.00 0.00 4.40
1882 2208 2.257676 ACGAGCTTTCCGTCGTCC 59.742 61.111 0.00 0.00 46.17 4.79
1892 2227 2.035940 AGGACTCCCGACGAGCTT 59.964 61.111 0.00 0.00 43.01 3.74
2420 2767 3.774702 GCCACGCCGAAGACGTTC 61.775 66.667 0.00 0.00 42.96 3.95
2509 2856 1.548719 CGTAGACCACCTCCATGTTGA 59.451 52.381 0.00 0.00 0.00 3.18
2618 2965 3.273748 GATGAGCATGCTACGCGCG 62.274 63.158 30.96 30.96 43.27 6.86
2663 3012 3.556543 AAACTTGCATGCGCGGGTG 62.557 57.895 14.09 2.52 42.97 4.61
2664 3013 3.294493 AAACTTGCATGCGCGGGT 61.294 55.556 14.09 6.04 42.97 5.28
2675 3024 7.917505 ACTACTTGAAGATTTGAAGCAAACTTG 59.082 33.333 0.00 0.00 36.13 3.16
2676 3025 7.917505 CACTACTTGAAGATTTGAAGCAAACTT 59.082 33.333 0.00 0.00 36.13 2.66
2677 3026 7.420800 CACTACTTGAAGATTTGAAGCAAACT 58.579 34.615 0.00 0.00 36.13 2.66
2678 3027 6.638468 CCACTACTTGAAGATTTGAAGCAAAC 59.362 38.462 0.00 0.00 36.13 2.93
2679 3028 6.545666 TCCACTACTTGAAGATTTGAAGCAAA 59.454 34.615 0.00 0.00 37.75 3.68
2729 3078 2.794910 CACTCCACACTTACACACGAAG 59.205 50.000 0.00 0.00 0.00 3.79
2732 3082 1.067974 TCCACTCCACACTTACACACG 59.932 52.381 0.00 0.00 0.00 4.49
2754 3104 4.441415 GCTTATTCGTCCGTGTGAAGATAG 59.559 45.833 0.00 0.00 31.33 2.08
2795 3145 2.532531 AAATCAAATCTGCAGCGACG 57.467 45.000 9.47 0.00 0.00 5.12
2877 3228 0.304705 AACACTCTTCACGCGCAAAG 59.695 50.000 5.73 10.62 0.00 2.77
2881 3232 1.201825 GTCAACACTCTTCACGCGC 59.798 57.895 5.73 0.00 0.00 6.86
2907 3277 1.066430 TGGGTAAAGGTGAGCTAAGCG 60.066 52.381 0.00 0.00 0.00 4.68
2929 3299 8.958119 ACTAGTTCACACAAAAACTCAATCTA 57.042 30.769 0.00 0.00 37.02 1.98
2952 3322 6.127810 CATGTAGAACTGCATGCATTAACT 57.872 37.500 22.97 19.11 44.29 2.24
2976 3346 5.927115 ACTCAAGACCTTTTGACTCGATTAC 59.073 40.000 0.00 0.00 33.71 1.89
2979 3349 4.310769 CACTCAAGACCTTTTGACTCGAT 58.689 43.478 0.00 0.00 33.71 3.59
2980 3350 3.717707 CACTCAAGACCTTTTGACTCGA 58.282 45.455 0.00 0.00 33.71 4.04
3001 3371 0.108138 AGGCGTTGGTAGAGTCATGC 60.108 55.000 0.00 0.00 0.00 4.06
3068 3438 4.142249 CCGGGTCTTGAACTCAAAACTTTT 60.142 41.667 0.00 0.00 35.15 2.27
3069 3439 3.380320 CCGGGTCTTGAACTCAAAACTTT 59.620 43.478 0.00 0.00 35.15 2.66
3074 3542 2.092861 TCAACCGGGTCTTGAACTCAAA 60.093 45.455 6.32 0.00 35.15 2.69
3125 3593 4.942483 TCAGACTTAAACGTGGACCAAAAA 59.058 37.500 0.00 0.00 0.00 1.94
3142 3610 2.279069 CGTGTGGCTCCCTCAGACT 61.279 63.158 0.00 0.00 0.00 3.24
3165 3633 4.755123 GGCTAGGCATTTATACGTCAACAT 59.245 41.667 12.16 0.00 0.00 2.71
3220 3688 2.668212 GCACGCACCAGCCAGTTA 60.668 61.111 0.00 0.00 37.52 2.24
3242 3716 2.929301 AGATCCCCTGACCCTTTGTAA 58.071 47.619 0.00 0.00 0.00 2.41
3248 3722 4.844348 ACATATAAAGATCCCCTGACCCT 58.156 43.478 0.00 0.00 0.00 4.34
3249 3723 5.310857 AGAACATATAAAGATCCCCTGACCC 59.689 44.000 0.00 0.00 0.00 4.46
3250 3724 6.183361 ACAGAACATATAAAGATCCCCTGACC 60.183 42.308 0.00 0.00 0.00 4.02
3251 3725 6.831976 ACAGAACATATAAAGATCCCCTGAC 58.168 40.000 0.00 0.00 0.00 3.51
3252 3726 6.239317 CGACAGAACATATAAAGATCCCCTGA 60.239 42.308 0.00 0.00 0.00 3.86
3253 3727 5.928839 CGACAGAACATATAAAGATCCCCTG 59.071 44.000 0.00 0.00 0.00 4.45
3264 3738 7.822334 ACAAACAATTCCTCGACAGAACATATA 59.178 33.333 0.00 0.00 0.00 0.86
3308 3782 3.088532 TCTTGTGCGCCCAAGATAAATT 58.911 40.909 28.05 0.00 44.39 1.82
3311 3785 3.946604 TCTTGTGCGCCCAAGATAA 57.053 47.368 28.05 9.61 44.39 1.75
3322 3796 3.686726 CAGGTTCTTAGACCATCTTGTGC 59.313 47.826 0.00 0.00 42.35 4.57
3329 3803 9.533831 AAAATTACATTCAGGTTCTTAGACCAT 57.466 29.630 0.00 0.00 42.35 3.55
3436 5650 7.448748 TTGAAGATGGCCTAAAAGTACTTTC 57.551 36.000 20.78 8.57 31.45 2.62
3443 5657 6.382869 CCAGTATTGAAGATGGCCTAAAAG 57.617 41.667 3.32 0.00 0.00 2.27
3451 5665 1.597742 CGGGCCAGTATTGAAGATGG 58.402 55.000 4.39 0.00 35.84 3.51
3457 5671 0.963355 GGTTTGCGGGCCAGTATTGA 60.963 55.000 4.39 0.00 0.00 2.57
3461 5675 4.708386 CCGGTTTGCGGGCCAGTA 62.708 66.667 4.39 0.00 0.00 2.74
3504 5718 1.507140 TGGACTGGTCACTGGTTCTT 58.493 50.000 3.10 0.00 0.00 2.52
3505 5719 1.349026 CATGGACTGGTCACTGGTTCT 59.651 52.381 3.10 0.00 0.00 3.01
3506 5720 1.611673 CCATGGACTGGTCACTGGTTC 60.612 57.143 5.56 0.00 40.49 3.62
3507 5721 0.401738 CCATGGACTGGTCACTGGTT 59.598 55.000 5.56 0.00 40.49 3.67
3508 5722 0.473694 TCCATGGACTGGTCACTGGT 60.474 55.000 11.44 0.00 46.08 4.00
3509 5723 0.036010 GTCCATGGACTGGTCACTGG 60.036 60.000 33.47 11.92 46.08 4.00
3510 5724 0.686789 TGTCCATGGACTGGTCACTG 59.313 55.000 37.92 0.00 46.08 3.66
3542 5764 2.050269 GCCTAGCTTAGATGGCCGA 58.950 57.895 0.00 0.00 39.49 5.54
3551 5773 1.054406 AATCTGCCCGGCCTAGCTTA 61.054 55.000 7.03 3.83 0.00 3.09
3566 5789 7.414222 AAATCATCTGGTTTGCATGTAATCT 57.586 32.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.