Multiple sequence alignment - TraesCS2D01G443000

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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 TraesCS2D01G443000 chr2D 100.000 5955 0 0 1 5955 553734187 553728233 0.000000e+00 10997
1 TraesCS2D01G443000 chr2D 98.387 124 2 0 2465 2588 553731601 553731478 1.000000e-52 219
2 TraesCS2D01G443000 chr2D 98.387 124 2 0 2587 2710 553731723 553731600 1.000000e-52 219
3 TraesCS2D01G443000 chr2A 95.399 2782 81 18 2727 5480 693896618 693893856 0.000000e+00 4385
4 TraesCS2D01G443000 chr2A 93.449 2244 45 31 88 2280 693899342 693897150 0.000000e+00 3236
5 TraesCS2D01G443000 chr2A 97.201 393 8 2 5564 5955 693893856 693893466 0.000000e+00 662
6 TraesCS2D01G443000 chr2A 97.846 325 7 0 2230 2554 693896942 693896618 4.030000e-156 562
7 TraesCS2D01G443000 chr2A 97.778 90 2 0 2587 2676 693896707 693896618 7.990000e-34 156
8 TraesCS2D01G443000 chr2B 94.270 2426 79 17 3133 5526 659534382 659531985 0.000000e+00 3655
9 TraesCS2D01G443000 chr2B 94.030 2211 50 20 1 2169 659537608 659535438 0.000000e+00 3277
10 TraesCS2D01G443000 chr2B 93.286 566 14 14 2587 3134 659535056 659534497 0.000000e+00 813
11 TraesCS2D01G443000 chr2B 96.618 414 9 2 2175 2588 659535341 659534933 0.000000e+00 682
12 TraesCS2D01G443000 chr2B 91.711 374 13 6 5547 5908 659531524 659531157 2.480000e-138 503
13 TraesCS2D01G443000 chr1D 87.582 153 18 1 4224 4375 283617844 283617996 6.130000e-40 176
14 TraesCS2D01G443000 chr1B 87.582 153 18 1 4224 4375 385296796 385296948 6.130000e-40 176
15 TraesCS2D01G443000 chr1A 87.582 153 18 1 4224 4375 355343728 355343880 6.130000e-40 176
16 TraesCS2D01G443000 chr6D 83.750 160 16 9 2369 2522 350514318 350514163 6.220000e-30 143
17 TraesCS2D01G443000 chr6B 83.750 160 16 9 2369 2522 529478098 529478253 6.220000e-30 143
18 TraesCS2D01G443000 chr6A 83.544 158 20 6 2369 2522 493341335 493341490 6.220000e-30 143
19 TraesCS2D01G443000 chr7B 76.957 230 38 12 3442 3668 600478525 600478742 3.770000e-22 117


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 TraesCS2D01G443000 chr2D 553728233 553734187 5954 True 3811.666667 10997 98.924667 1 5955 3 chr2D.!!$R1 5954
1 TraesCS2D01G443000 chr2A 693893466 693899342 5876 True 1800.200000 4385 96.334600 88 5955 5 chr2A.!!$R1 5867
2 TraesCS2D01G443000 chr2B 659531157 659537608 6451 True 1786.000000 3655 93.983000 1 5908 5 chr2B.!!$R1 5907

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
436 462 0.629596 TGTACCCCCTGATCTCGTCT 59.370 55.000 0.00 0.0 0.0 4.18 F
438 464 0.755698 TACCCCCTGATCTCGTCTGC 60.756 60.000 0.00 0.0 0.0 4.26 F
916 961 1.085893 GCTCTTCCTCTTGCTTGCTC 58.914 55.000 0.00 0.0 0.0 4.26 F
917 962 1.736612 CTCTTCCTCTTGCTTGCTCC 58.263 55.000 0.00 0.0 0.0 4.70 F
1296 1344 2.927056 GCCCCCGAATTCCTGGAT 59.073 61.111 9.69 0.0 0.0 3.41 F
2607 3032 0.175989 GGAGGAAGTACGGCCAGAAG 59.824 60.000 2.24 0.0 0.0 2.85 F
3087 3514 0.034574 GGGGGTGCACACATCACATA 60.035 55.000 22.94 0.0 28.8 2.29 F
4541 5108 0.667487 CAGCACAGTCACTACCACGG 60.667 60.000 0.00 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1353 1.656818 CGATTTTGGCCATGGCGTCT 61.657 55.0 29.90 12.74 43.06 4.18 R
1870 1941 2.239681 ATCCTCGGAACTTCCTCACT 57.760 50.0 6.25 0.00 33.30 3.41 R
2588 3013 0.175989 CTTCTGGCCGTACTTCCTCC 59.824 60.0 0.00 0.00 0.00 4.30 R
2589 3014 0.460459 GCTTCTGGCCGTACTTCCTC 60.460 60.0 0.00 0.00 34.27 3.71 R
2617 3042 0.617820 TACCTTGGGTGAGGAGAGCC 60.618 60.0 0.00 0.00 39.25 4.70 R
3735 4299 0.766131 TTTTCTACTCCCGGGTGCAA 59.234 50.0 22.86 9.24 0.00 4.08 R
4634 5201 0.833834 ACCTGCTGCAGTACTCCTGT 60.834 55.0 26.41 13.34 43.55 4.00 R
5562 6589 1.201424 TCTGCCATCTGAGCTGATGT 58.799 50.0 11.82 0.00 41.47 3.06 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
47 59 2.127708 ACAGTCAGGGTTTCCAGAAGT 58.872 47.619 0.00 0.00 34.83 3.01
182 197 1.962100 TGAGTTTTCACCATGCATGCA 59.038 42.857 25.04 25.04 0.00 3.96
185 200 2.093869 AGTTTTCACCATGCATGCATCC 60.094 45.455 30.07 10.33 33.90 3.51
329 344 2.678580 TCAGCGTCCGTCCATCCA 60.679 61.111 0.00 0.00 0.00 3.41
330 345 2.058001 TCAGCGTCCGTCCATCCAT 61.058 57.895 0.00 0.00 0.00 3.41
331 346 1.592669 CAGCGTCCGTCCATCCATC 60.593 63.158 0.00 0.00 0.00 3.51
332 347 2.280186 GCGTCCGTCCATCCATCC 60.280 66.667 0.00 0.00 0.00 3.51
387 411 4.323477 CCTTCCGCCCGTCCACAA 62.323 66.667 0.00 0.00 0.00 3.33
436 462 0.629596 TGTACCCCCTGATCTCGTCT 59.370 55.000 0.00 0.00 0.00 4.18
437 463 1.033574 GTACCCCCTGATCTCGTCTG 58.966 60.000 0.00 0.00 0.00 3.51
438 464 0.755698 TACCCCCTGATCTCGTCTGC 60.756 60.000 0.00 0.00 0.00 4.26
439 465 2.801631 CCCCCTGATCTCGTCTGCC 61.802 68.421 0.00 0.00 0.00 4.85
440 466 1.760086 CCCCTGATCTCGTCTGCCT 60.760 63.158 0.00 0.00 0.00 4.75
500 526 4.567537 CCAACTCAAGTTACCCATCCATCA 60.568 45.833 0.00 0.00 36.32 3.07
561 588 8.002459 TGGTGTAAAGAAAAGATAGTTCCCTTT 58.998 33.333 0.00 0.00 34.39 3.11
651 679 2.370445 ACATCCTGCTTCCCCTCCG 61.370 63.158 0.00 0.00 0.00 4.63
710 739 6.926272 ACGCACACAAATAACACCAAATAAAT 59.074 30.769 0.00 0.00 0.00 1.40
816 848 8.233868 CAGCGACACCTATATCATATATAGCTC 58.766 40.741 0.00 3.19 0.00 4.09
903 935 1.578206 GGTTGGCGGTGAAGCTCTTC 61.578 60.000 2.80 2.80 39.91 2.87
916 961 1.085893 GCTCTTCCTCTTGCTTGCTC 58.914 55.000 0.00 0.00 0.00 4.26
917 962 1.736612 CTCTTCCTCTTGCTTGCTCC 58.263 55.000 0.00 0.00 0.00 4.70
1182 1230 3.011517 ATGCTGTTCCCGCCTCCT 61.012 61.111 0.00 0.00 0.00 3.69
1183 1231 2.932130 GATGCTGTTCCCGCCTCCTC 62.932 65.000 0.00 0.00 0.00 3.71
1184 1232 4.475135 GCTGTTCCCGCCTCCTCC 62.475 72.222 0.00 0.00 0.00 4.30
1296 1344 2.927056 GCCCCCGAATTCCTGGAT 59.073 61.111 9.69 0.00 0.00 3.41
1870 1941 8.585018 TCACCATGAAGATATTATTAGAGCGAA 58.415 33.333 0.00 0.00 0.00 4.70
2065 2142 4.281657 TGTCATGTGCATCTAGACCTAGT 58.718 43.478 0.00 0.00 34.84 2.57
2267 2692 6.091123 ACATCGCGTGTTCTTATTAACTTC 57.909 37.500 5.77 0.00 38.01 3.01
2601 3026 3.814005 TCTTTATGGAGGAAGTACGGC 57.186 47.619 0.00 0.00 0.00 5.68
2602 3027 2.433239 TCTTTATGGAGGAAGTACGGCC 59.567 50.000 0.00 0.00 0.00 6.13
2603 3028 1.868713 TTATGGAGGAAGTACGGCCA 58.131 50.000 2.24 4.24 0.00 5.36
2604 3029 1.410004 TATGGAGGAAGTACGGCCAG 58.590 55.000 2.24 0.00 31.23 4.85
2605 3030 0.325296 ATGGAGGAAGTACGGCCAGA 60.325 55.000 2.24 0.00 31.23 3.86
2606 3031 0.543410 TGGAGGAAGTACGGCCAGAA 60.543 55.000 2.24 0.00 0.00 3.02
2607 3032 0.175989 GGAGGAAGTACGGCCAGAAG 59.824 60.000 2.24 0.00 0.00 2.85
2608 3033 0.460459 GAGGAAGTACGGCCAGAAGC 60.460 60.000 2.24 0.00 42.60 3.86
2618 3043 3.410960 GCCAGAAGCCTATCAAGGG 57.589 57.895 0.00 0.00 43.87 3.95
2632 3057 2.538760 AGGGCTCTCCTCACCCAA 59.461 61.111 0.00 0.00 44.06 4.12
2633 3058 1.614824 AGGGCTCTCCTCACCCAAG 60.615 63.158 0.00 0.00 44.06 3.61
2634 3059 2.674220 GGGCTCTCCTCACCCAAGG 61.674 68.421 0.00 0.00 43.64 3.61
2635 3060 1.920835 GGCTCTCCTCACCCAAGGT 60.921 63.158 0.00 0.00 37.69 3.50
2636 3061 0.617820 GGCTCTCCTCACCCAAGGTA 60.618 60.000 0.00 0.00 37.69 3.08
2637 3062 1.501582 GCTCTCCTCACCCAAGGTAT 58.498 55.000 0.00 0.00 37.69 2.73
2638 3063 1.139853 GCTCTCCTCACCCAAGGTATG 59.860 57.143 0.00 0.00 37.69 2.39
2639 3064 2.472029 CTCTCCTCACCCAAGGTATGT 58.528 52.381 0.00 0.00 37.69 2.29
2640 3065 3.643237 CTCTCCTCACCCAAGGTATGTA 58.357 50.000 0.00 0.00 37.69 2.29
2641 3066 3.371965 TCTCCTCACCCAAGGTATGTAC 58.628 50.000 0.00 0.00 37.69 2.90
2642 3067 3.104512 CTCCTCACCCAAGGTATGTACA 58.895 50.000 0.00 0.00 37.69 2.90
2643 3068 3.711704 CTCCTCACCCAAGGTATGTACAT 59.288 47.826 13.93 13.93 37.69 2.29
2644 3069 4.886163 TCCTCACCCAAGGTATGTACATA 58.114 43.478 11.62 11.62 37.69 2.29
2645 3070 5.473273 TCCTCACCCAAGGTATGTACATAT 58.527 41.667 18.27 0.97 37.69 1.78
2646 3071 6.626238 TCCTCACCCAAGGTATGTACATATA 58.374 40.000 18.27 0.00 37.69 0.86
2647 3072 6.495872 TCCTCACCCAAGGTATGTACATATAC 59.504 42.308 18.27 14.01 37.69 1.47
2648 3073 6.497259 CCTCACCCAAGGTATGTACATATACT 59.503 42.308 18.27 15.82 32.11 2.12
2649 3074 7.672660 CCTCACCCAAGGTATGTACATATACTA 59.327 40.741 18.27 0.00 32.11 1.82
2650 3075 8.413309 TCACCCAAGGTATGTACATATACTAC 57.587 38.462 18.27 7.90 32.11 2.73
2651 3076 8.005976 TCACCCAAGGTATGTACATATACTACA 58.994 37.037 18.27 0.00 32.11 2.74
2652 3077 8.812972 CACCCAAGGTATGTACATATACTACAT 58.187 37.037 18.27 3.04 38.23 2.29
2653 3078 8.812972 ACCCAAGGTATGTACATATACTACATG 58.187 37.037 18.27 13.48 35.90 3.21
2654 3079 9.031537 CCCAAGGTATGTACATATACTACATGA 57.968 37.037 18.27 0.00 35.90 3.07
2801 3226 5.385617 CAAGTCGTTGACATCTTTTCATCC 58.614 41.667 0.00 0.00 35.46 3.51
2809 3236 8.853345 CGTTGACATCTTTTCATCCAATTAAAG 58.147 33.333 0.00 0.00 0.00 1.85
2873 3300 4.515361 AGGATGAAGCTTCTGAAGTGATG 58.485 43.478 26.09 0.00 0.00 3.07
3000 3427 8.429237 AATTGGAAGATAAACAAATGGGTACA 57.571 30.769 0.00 0.00 0.00 2.90
3086 3513 1.304381 GGGGGTGCACACATCACAT 60.304 57.895 22.94 0.00 28.80 3.21
3087 3514 0.034574 GGGGGTGCACACATCACATA 60.035 55.000 22.94 0.00 28.80 2.29
3088 3515 1.410083 GGGGGTGCACACATCACATAT 60.410 52.381 22.94 0.00 28.80 1.78
3089 3516 2.158682 GGGGGTGCACACATCACATATA 60.159 50.000 22.94 0.00 28.80 0.86
3090 3517 3.550820 GGGGTGCACACATCACATATAA 58.449 45.455 22.94 0.00 36.22 0.98
3091 3518 3.565482 GGGGTGCACACATCACATATAAG 59.435 47.826 22.94 0.00 36.22 1.73
3117 3544 9.722056 GTATAACAGAGAAATAATTTGTGCCAG 57.278 33.333 0.00 0.00 0.00 4.85
3263 3806 4.532916 TCAATAACAAGTAGCCCACCACTA 59.467 41.667 0.00 0.00 0.00 2.74
3474 4025 6.479660 TGAAAACAGCATCCAAAATTTCTGAC 59.520 34.615 8.76 0.79 0.00 3.51
3481 4032 6.484308 AGCATCCAAAATTTCTGACCTTTTTG 59.516 34.615 0.00 9.95 38.28 2.44
3482 4033 6.661669 CATCCAAAATTTCTGACCTTTTTGC 58.338 36.000 10.86 0.00 37.60 3.68
3534 4085 5.905181 GTGCTTGCAAAATTTCATCAACAAG 59.095 36.000 0.00 0.00 37.05 3.16
3536 4087 6.093771 TGCTTGCAAAATTTCATCAACAAGTT 59.906 30.769 0.00 0.00 36.51 2.66
3603 4158 5.348451 GTGCACAAAACTTTGAACTGTGATT 59.652 36.000 13.17 0.00 39.80 2.57
3604 4159 5.931146 TGCACAAAACTTTGAACTGTGATTT 59.069 32.000 9.12 0.00 39.80 2.17
3605 4160 6.426328 TGCACAAAACTTTGAACTGTGATTTT 59.574 30.769 9.12 0.00 39.80 1.82
3606 4161 6.737750 GCACAAAACTTTGAACTGTGATTTTG 59.262 34.615 9.12 0.00 39.80 2.44
3692 4247 8.958506 TCATACATTTGATCATGTTTGATGTCA 58.041 29.630 14.73 0.00 42.73 3.58
3705 4269 8.775527 CATGTTTGATGTCATGAAATTTTGGAA 58.224 29.630 0.00 0.00 42.52 3.53
3728 4292 9.271828 GGAATTTGTTTCATAGTGTTTTTCCAT 57.728 29.630 0.00 0.00 35.94 3.41
3735 4299 4.832266 TCATAGTGTTTTTCCATTGTGCCT 59.168 37.500 0.00 0.00 0.00 4.75
3792 4356 4.154942 AGTGCATTTTTCCCTGAACTGAT 58.845 39.130 0.00 0.00 29.79 2.90
3947 4514 8.996024 GCTCTTTAGCCCAAAATTTTGTAATA 57.004 30.769 25.25 13.73 43.40 0.98
3994 4561 3.773117 GCACGCAGCATTGTTACTT 57.227 47.368 0.00 0.00 44.79 2.24
3996 4563 1.729149 GCACGCAGCATTGTTACTTCC 60.729 52.381 0.00 0.00 44.79 3.46
4053 4620 4.918037 GGAGTGGACTTACTACGTACATG 58.082 47.826 0.00 0.00 35.12 3.21
4180 4747 7.040617 GCAAATGATGAAGGTACATGATGAGAT 60.041 37.037 0.00 0.00 0.00 2.75
4426 4993 3.640407 AGCGGCTCAGGCTCCAAA 61.640 61.111 0.00 0.00 35.37 3.28
4541 5108 0.667487 CAGCACAGTCACTACCACGG 60.667 60.000 0.00 0.00 0.00 4.94
4634 5201 0.610174 GAGAGCCATGGACACTGTGA 59.390 55.000 18.40 0.00 0.00 3.58
4678 5245 4.509756 CGTGAGCTCATGGACCAG 57.490 61.111 25.59 6.14 0.00 4.00
4786 5353 1.267574 TGGAGTCAGACCCCATGAGC 61.268 60.000 0.00 0.00 0.00 4.26
4942 5509 0.884704 GGAGCACGTTTGAGCAAGGA 60.885 55.000 0.00 0.00 33.73 3.36
5012 5587 4.629200 CACACTTGAGATCTCCAGCTAAAC 59.371 45.833 20.82 0.00 0.00 2.01
5061 5640 4.630940 GTCAGCAAGGAAGAAAGATGAGAG 59.369 45.833 0.00 0.00 0.00 3.20
5233 5812 6.821160 GGATCATCTATCTCTCGATACTGTCA 59.179 42.308 0.00 0.00 34.75 3.58
5244 5823 5.825151 TCTCGATACTGTCATCTTCATCTGT 59.175 40.000 0.00 0.00 0.00 3.41
5385 5971 4.944619 TGAGTGTGATAGATGGATGACC 57.055 45.455 0.00 0.00 0.00 4.02
5418 6004 2.038813 TCGGAGGGGATGTGAGCA 59.961 61.111 0.00 0.00 0.00 4.26
5515 6101 3.255642 CCACCATGACCACAGGTAAAAAG 59.744 47.826 0.00 0.00 35.25 2.27
5516 6102 2.890945 ACCATGACCACAGGTAAAAAGC 59.109 45.455 0.00 0.00 35.25 3.51
5517 6103 2.890311 CCATGACCACAGGTAAAAAGCA 59.110 45.455 0.00 0.00 35.25 3.91
5519 6105 4.298332 CATGACCACAGGTAAAAAGCAAC 58.702 43.478 0.00 0.00 35.25 4.17
5520 6106 3.626930 TGACCACAGGTAAAAAGCAACT 58.373 40.909 0.00 0.00 35.25 3.16
5521 6107 3.630312 TGACCACAGGTAAAAAGCAACTC 59.370 43.478 0.00 0.00 35.25 3.01
5522 6108 3.883489 GACCACAGGTAAAAAGCAACTCT 59.117 43.478 0.00 0.00 35.25 3.24
5523 6109 3.883489 ACCACAGGTAAAAAGCAACTCTC 59.117 43.478 0.00 0.00 32.11 3.20
5524 6110 4.137543 CCACAGGTAAAAAGCAACTCTCT 58.862 43.478 0.00 0.00 0.00 3.10
5525 6111 4.214332 CCACAGGTAAAAAGCAACTCTCTC 59.786 45.833 0.00 0.00 0.00 3.20
5526 6112 5.059833 CACAGGTAAAAAGCAACTCTCTCT 58.940 41.667 0.00 0.00 0.00 3.10
5527 6113 5.178438 CACAGGTAAAAAGCAACTCTCTCTC 59.822 44.000 0.00 0.00 0.00 3.20
5528 6114 5.071115 ACAGGTAAAAAGCAACTCTCTCTCT 59.929 40.000 0.00 0.00 0.00 3.10
5529 6115 5.637387 CAGGTAAAAAGCAACTCTCTCTCTC 59.363 44.000 0.00 0.00 0.00 3.20
5530 6116 5.542251 AGGTAAAAAGCAACTCTCTCTCTCT 59.458 40.000 0.00 0.00 0.00 3.10
5531 6117 5.867174 GGTAAAAAGCAACTCTCTCTCTCTC 59.133 44.000 0.00 0.00 0.00 3.20
5532 6118 5.806654 AAAAAGCAACTCTCTCTCTCTCT 57.193 39.130 0.00 0.00 0.00 3.10
5533 6119 5.391312 AAAAGCAACTCTCTCTCTCTCTC 57.609 43.478 0.00 0.00 0.00 3.20
5534 6120 4.307032 AAGCAACTCTCTCTCTCTCTCT 57.693 45.455 0.00 0.00 0.00 3.10
5535 6121 3.878778 AGCAACTCTCTCTCTCTCTCTC 58.121 50.000 0.00 0.00 0.00 3.20
5536 6122 3.521126 AGCAACTCTCTCTCTCTCTCTCT 59.479 47.826 0.00 0.00 0.00 3.10
5537 6123 3.873952 GCAACTCTCTCTCTCTCTCTCTC 59.126 52.174 0.00 0.00 0.00 3.20
5538 6124 4.383552 GCAACTCTCTCTCTCTCTCTCTCT 60.384 50.000 0.00 0.00 0.00 3.10
5539 6125 5.355596 CAACTCTCTCTCTCTCTCTCTCTC 58.644 50.000 0.00 0.00 0.00 3.20
5540 6126 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
5541 6127 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
5542 6128 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
5543 6129 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5544 6130 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5545 6131 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5554 6581 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5562 6589 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
5780 6819 5.583854 CCTCTGTTCTCCTGAATTGTACATG 59.416 44.000 0.00 0.00 34.40 3.21
5942 6981 1.625315 CACCTGCATATGCCCTAGCTA 59.375 52.381 24.54 3.35 41.18 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
304 319 0.039437 GACGGACGCTGACTTTCTCA 60.039 55.000 0.00 0.00 0.00 3.27
387 411 1.880027 GAGCGATGGCCGGATTATTTT 59.120 47.619 5.05 0.00 41.24 1.82
436 462 0.698238 AAGTATGTGAGGGCAAGGCA 59.302 50.000 0.00 0.00 0.00 4.75
437 463 1.065126 AGAAGTATGTGAGGGCAAGGC 60.065 52.381 0.00 0.00 0.00 4.35
438 464 3.356529 AAGAAGTATGTGAGGGCAAGG 57.643 47.619 0.00 0.00 0.00 3.61
439 465 6.375455 ACAATAAAGAAGTATGTGAGGGCAAG 59.625 38.462 0.00 0.00 0.00 4.01
440 466 6.245408 ACAATAAAGAAGTATGTGAGGGCAA 58.755 36.000 0.00 0.00 0.00 4.52
500 526 2.877168 GCAGCAGATCGAAATGGAGATT 59.123 45.455 0.00 0.00 0.00 2.40
561 588 0.107848 GCTAGTAGCGGCCAAGGAAA 60.108 55.000 6.36 0.00 0.00 3.13
651 679 0.328258 TGCAGAAAAGGAGGTAGGGC 59.672 55.000 0.00 0.00 0.00 5.19
688 717 9.379811 GCAAATTTATTTGGTGTTATTTGTGTG 57.620 29.630 14.97 0.00 45.44 3.82
816 848 3.126879 TGGCAAGCCGATTGAGCG 61.127 61.111 6.60 0.00 41.83 5.03
903 935 2.437359 CCGGGAGCAAGCAAGAGG 60.437 66.667 0.00 0.00 0.00 3.69
930 975 3.377172 GCCGATCTCTTCTCCTCTATAGC 59.623 52.174 0.00 0.00 0.00 2.97
966 1014 1.202592 GCAAGCTAGCTAGGGTTCTCC 60.203 57.143 19.70 3.65 0.00 3.71
1305 1353 1.656818 CGATTTTGGCCATGGCGTCT 61.657 55.000 29.90 12.74 43.06 4.18
1746 1812 7.951347 TTTCCCTTCGAAATCTACTACTACT 57.049 36.000 0.00 0.00 35.49 2.57
1794 1865 5.319931 CGAATTAAAGAGCAGCAGAAGAAC 58.680 41.667 0.00 0.00 0.00 3.01
1795 1866 4.142816 GCGAATTAAAGAGCAGCAGAAGAA 60.143 41.667 0.00 0.00 0.00 2.52
1856 1927 7.584122 ACTTCCTCACTTCGCTCTAATAATA 57.416 36.000 0.00 0.00 0.00 0.98
1870 1941 2.239681 ATCCTCGGAACTTCCTCACT 57.760 50.000 6.25 0.00 33.30 3.41
2132 2209 6.410540 TGGAAACTTTGCAACCAACTAAAAT 58.589 32.000 0.00 0.00 0.00 1.82
2267 2692 7.214467 ACAAACACCACAAAATAGGTATCAG 57.786 36.000 0.00 0.00 36.07 2.90
2575 3000 8.910944 GCCGTACTTCCTCCATAAAGATATATA 58.089 37.037 0.00 0.00 0.00 0.86
2576 3001 7.147707 GGCCGTACTTCCTCCATAAAGATATAT 60.148 40.741 0.00 0.00 0.00 0.86
2577 3002 6.154021 GGCCGTACTTCCTCCATAAAGATATA 59.846 42.308 0.00 0.00 0.00 0.86
2578 3003 5.046520 GGCCGTACTTCCTCCATAAAGATAT 60.047 44.000 0.00 0.00 0.00 1.63
2579 3004 4.282703 GGCCGTACTTCCTCCATAAAGATA 59.717 45.833 0.00 0.00 0.00 1.98
2580 3005 3.071167 GGCCGTACTTCCTCCATAAAGAT 59.929 47.826 0.00 0.00 0.00 2.40
2581 3006 2.433239 GGCCGTACTTCCTCCATAAAGA 59.567 50.000 0.00 0.00 0.00 2.52
2582 3007 2.169769 TGGCCGTACTTCCTCCATAAAG 59.830 50.000 0.00 0.00 0.00 1.85
2583 3008 2.169769 CTGGCCGTACTTCCTCCATAAA 59.830 50.000 0.00 0.00 0.00 1.40
2584 3009 1.760613 CTGGCCGTACTTCCTCCATAA 59.239 52.381 0.00 0.00 0.00 1.90
2585 3010 1.063492 TCTGGCCGTACTTCCTCCATA 60.063 52.381 0.00 0.00 0.00 2.74
2586 3011 0.325296 TCTGGCCGTACTTCCTCCAT 60.325 55.000 0.00 0.00 0.00 3.41
2587 3012 0.543410 TTCTGGCCGTACTTCCTCCA 60.543 55.000 0.00 0.00 0.00 3.86
2588 3013 0.175989 CTTCTGGCCGTACTTCCTCC 59.824 60.000 0.00 0.00 0.00 4.30
2589 3014 0.460459 GCTTCTGGCCGTACTTCCTC 60.460 60.000 0.00 0.00 34.27 3.71
2590 3015 1.597461 GCTTCTGGCCGTACTTCCT 59.403 57.895 0.00 0.00 34.27 3.36
2591 3016 4.203618 GCTTCTGGCCGTACTTCC 57.796 61.111 0.00 0.00 34.27 3.46
2600 3025 3.410960 CCCTTGATAGGCTTCTGGC 57.589 57.895 0.00 0.00 40.50 4.85
2616 3041 2.674220 CCTTGGGTGAGGAGAGCCC 61.674 68.421 0.00 0.00 39.25 5.19
2617 3042 0.617820 TACCTTGGGTGAGGAGAGCC 60.618 60.000 0.00 0.00 39.25 4.70
2618 3043 1.139853 CATACCTTGGGTGAGGAGAGC 59.860 57.143 0.00 0.00 39.25 4.09
2619 3044 2.472029 ACATACCTTGGGTGAGGAGAG 58.528 52.381 0.00 0.00 39.25 3.20
2620 3045 2.642171 ACATACCTTGGGTGAGGAGA 57.358 50.000 0.00 0.00 39.25 3.71
2621 3046 3.104512 TGTACATACCTTGGGTGAGGAG 58.895 50.000 0.00 0.00 39.25 3.69
2622 3047 3.193395 TGTACATACCTTGGGTGAGGA 57.807 47.619 0.00 0.00 39.25 3.71
2623 3048 5.825593 ATATGTACATACCTTGGGTGAGG 57.174 43.478 17.69 0.00 42.75 3.86
2624 3049 7.540474 AGTATATGTACATACCTTGGGTGAG 57.460 40.000 17.69 0.00 33.56 3.51
2625 3050 8.005976 TGTAGTATATGTACATACCTTGGGTGA 58.994 37.037 17.69 0.00 33.56 4.02
2626 3051 8.185506 TGTAGTATATGTACATACCTTGGGTG 57.814 38.462 17.69 0.00 33.56 4.61
2627 3052 8.812972 CATGTAGTATATGTACATACCTTGGGT 58.187 37.037 17.69 3.15 38.75 4.51
2628 3053 9.031537 TCATGTAGTATATGTACATACCTTGGG 57.968 37.037 17.69 4.70 38.75 4.12
2801 3226 9.962759 GCAATGCTAGAAATGTTTCTTTAATTG 57.037 29.630 12.73 17.04 44.70 2.32
2809 3236 5.572211 TCGATGCAATGCTAGAAATGTTTC 58.428 37.500 6.82 0.00 37.45 2.78
2873 3300 7.277098 TGCGTGTAACCAAGATTATTTACTCTC 59.723 37.037 0.00 0.00 0.00 3.20
3000 3427 7.310113 CCGAGGGTTGATTTTCTAGCTAGATAT 60.310 40.741 23.81 18.85 31.40 1.63
3090 3517 9.461312 TGGCACAAATTATTTCTCTGTTATACT 57.539 29.630 0.00 0.00 31.92 2.12
3091 3518 9.722056 CTGGCACAAATTATTTCTCTGTTATAC 57.278 33.333 0.00 0.00 38.70 1.47
3172 3715 6.086222 GGCATGCTTAAATTATATGTGTCGG 58.914 40.000 18.92 0.00 0.00 4.79
3252 3795 1.765314 CAATCTAGCTAGTGGTGGGCT 59.235 52.381 20.10 0.00 39.74 5.19
3263 3806 5.190726 AGAAGGCCTTAAACTCAATCTAGCT 59.809 40.000 20.54 2.56 0.00 3.32
3334 3877 4.843728 TGACAGCTCCCTAAAATTGGTAG 58.156 43.478 0.00 0.00 0.00 3.18
3346 3889 5.880332 TGTTTGTAGATTTATGACAGCTCCC 59.120 40.000 0.00 0.00 0.00 4.30
3421 3971 1.826487 GGCACCACACCTTTCCGTT 60.826 57.895 0.00 0.00 0.00 4.44
3422 3972 1.412453 TAGGCACCACACCTTTCCGT 61.412 55.000 0.00 0.00 38.81 4.69
3474 4025 4.297510 TCATGTTTGATGTCGCAAAAAGG 58.702 39.130 0.00 0.00 39.26 3.11
3481 4032 6.636666 AAATTTGATCATGTTTGATGTCGC 57.363 33.333 0.00 0.00 42.73 5.19
3482 4033 9.505995 TCATAAATTTGATCATGTTTGATGTCG 57.494 29.630 13.26 0.00 42.73 4.35
3705 4269 9.612066 ACAATGGAAAAACACTATGAAACAAAT 57.388 25.926 0.00 0.00 0.00 2.32
3735 4299 0.766131 TTTTCTACTCCCGGGTGCAA 59.234 50.000 22.86 9.24 0.00 4.08
3792 4356 5.471797 TCAATCGATTAGGAAAAGTGCAACA 59.528 36.000 10.97 0.00 41.43 3.33
3831 4395 4.646945 TGTGAATGGGTCTGTCTAGATCTC 59.353 45.833 0.00 0.00 34.35 2.75
3924 4488 8.315482 GGGTATTACAAAATTTTGGGCTAAAGA 58.685 33.333 29.37 13.08 42.34 2.52
3937 4504 7.678171 ACCAAAATCTCCTGGGTATTACAAAAT 59.322 33.333 0.00 0.00 37.00 1.82
3947 4514 2.279173 AGCTACCAAAATCTCCTGGGT 58.721 47.619 0.00 0.00 37.00 4.51
3994 4561 5.596361 TGTCTGGTTTTTCATAAGCAAAGGA 59.404 36.000 0.00 0.00 35.35 3.36
3996 4563 6.507023 AGTGTCTGGTTTTTCATAAGCAAAG 58.493 36.000 0.00 0.00 35.35 2.77
4180 4747 5.723672 AGAACTTTGGTTAGACTCGATCA 57.276 39.130 0.00 0.00 35.58 2.92
4541 5108 2.743928 CACGGGAGAAGTGCTGGC 60.744 66.667 0.00 0.00 32.52 4.85
4634 5201 0.833834 ACCTGCTGCAGTACTCCTGT 60.834 55.000 26.41 13.34 43.55 4.00
4786 5353 4.026744 TGTACTCCTTGGAGAAGATGAGG 58.973 47.826 22.10 0.00 0.00 3.86
4835 5402 2.191375 CTGGCCACCATGATCGCT 59.809 61.111 0.00 0.00 30.82 4.93
4942 5509 5.883115 GCCTCAAGTAATTTAGCCTCTCTTT 59.117 40.000 0.00 0.00 0.00 2.52
5012 5587 7.308589 CCTTGTGGTAGTTAATCTTCAAGGTTG 60.309 40.741 11.07 0.00 42.94 3.77
5233 5812 3.748083 ACACACAAGCACAGATGAAGAT 58.252 40.909 0.00 0.00 0.00 2.40
5244 5823 4.956085 TCTTAGCTAGAAACACACAAGCA 58.044 39.130 0.00 0.00 35.63 3.91
5385 5971 2.701780 CGAGGACGTGGGTCTCCTG 61.702 68.421 0.00 0.00 42.97 3.86
5515 6101 3.873952 GAGAGAGAGAGAGAGAGAGTTGC 59.126 52.174 0.00 0.00 0.00 4.17
5516 6102 5.128499 AGAGAGAGAGAGAGAGAGAGAGTTG 59.872 48.000 0.00 0.00 0.00 3.16
5517 6103 5.276440 AGAGAGAGAGAGAGAGAGAGAGTT 58.724 45.833 0.00 0.00 0.00 3.01
5519 6105 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5520 6106 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5521 6107 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5522 6108 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5523 6109 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5524 6110 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5525 6111 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5526 6112 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5527 6113 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5528 6114 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5529 6115 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5530 6116 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5531 6117 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5532 6118 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5533 6119 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5534 6120 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5535 6121 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5536 6122 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5537 6123 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5538 6124 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
5539 6125 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
5540 6126 4.646945 GTGAGAGAGAGAGAGAGAGAGAGA 59.353 50.000 0.00 0.00 0.00 3.10
5541 6127 4.403752 TGTGAGAGAGAGAGAGAGAGAGAG 59.596 50.000 0.00 0.00 0.00 3.20
5542 6128 4.352893 TGTGAGAGAGAGAGAGAGAGAGA 58.647 47.826 0.00 0.00 0.00 3.10
5543 6129 4.743057 TGTGAGAGAGAGAGAGAGAGAG 57.257 50.000 0.00 0.00 0.00 3.20
5544 6130 4.716287 TGATGTGAGAGAGAGAGAGAGAGA 59.284 45.833 0.00 0.00 0.00 3.10
5545 6131 5.027293 TGATGTGAGAGAGAGAGAGAGAG 57.973 47.826 0.00 0.00 0.00 3.20
5554 6581 3.362870 TCTGAGCTGATGTGAGAGAGA 57.637 47.619 0.00 0.00 0.00 3.10
5562 6589 1.201424 TCTGCCATCTGAGCTGATGT 58.799 50.000 11.82 0.00 41.47 3.06
5736 6763 7.173390 ACAGAGGAAGTAAATGCAGTACTTTTC 59.827 37.037 20.67 19.55 40.93 2.29


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

AutoCloner maintained by Alex Coulton.