Multiple sequence alignment - TraesCS1B01G230100

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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 TraesCS1B01G230100 chr1B 100.000 2349 0 0 962 3310 413205855 413203507 0.000000e+00 4338
1 TraesCS1B01G230100 chr1B 100.000 623 0 0 1 623 413206816 413206194 0.000000e+00 1151
2 TraesCS1B01G230100 chr1B 94.118 170 7 3 1 168 619696709 619696541 4.240000e-64 255
3 TraesCS1B01G230100 chr1A 91.319 2304 104 39 962 3216 384776222 384773966 0.000000e+00 3059
4 TraesCS1B01G230100 chr1A 90.092 434 18 9 164 576 384778338 384777909 1.040000e-149 540
5 TraesCS1B01G230100 chr1A 95.050 101 5 0 3210 3310 384773926 384773826 3.420000e-35 159
6 TraesCS1B01G230100 chr1D 93.204 1133 47 11 1453 2576 305769212 305768101 0.000000e+00 1639
7 TraesCS1B01G230100 chr1D 96.950 459 11 2 984 1442 305769726 305769271 0.000000e+00 767
8 TraesCS1B01G230100 chr1D 91.376 487 14 9 165 623 305770339 305769853 2.780000e-180 641
9 TraesCS1B01G230100 chr1D 91.368 475 30 5 2648 3121 305768075 305767611 1.000000e-179 640
10 TraesCS1B01G230100 chr1D 97.030 101 3 0 3210 3310 305767518 305767418 1.580000e-38 171
11 TraesCS1B01G230100 chr7B 98.795 166 1 1 1 166 656511916 656511752 8.980000e-76 294
12 TraesCS1B01G230100 chr7B 98.171 164 3 0 1 164 548479933 548480096 1.500000e-73 287
13 TraesCS1B01G230100 chr7B 97.561 164 4 0 1 164 246380198 246380361 6.990000e-72 281
14 TraesCS1B01G230100 chr4A 98.780 164 2 0 1 164 655164251 655164414 3.230000e-75 292
15 TraesCS1B01G230100 chr4A 93.902 164 6 2 1 161 63013884 63014046 9.180000e-61 244
16 TraesCS1B01G230100 chr5A 98.780 164 1 1 1 164 672756141 672756303 1.160000e-74 291
17 TraesCS1B01G230100 chr3A 96.970 165 2 3 1 163 745271385 745271222 1.170000e-69 274
18 TraesCS1B01G230100 chr4B 93.373 166 7 2 1 166 663880342 663880181 3.300000e-60 243
19 TraesCS1B01G230100 chr6B 85.057 174 21 4 1983 2154 509259624 509259794 4.390000e-39 172
20 TraesCS1B01G230100 chr6D 86.164 159 20 2 1997 2154 315817043 315816886 1.580000e-38 171
21 TraesCS1B01G230100 chr2D 84.277 159 23 2 1997 2154 496637761 496637604 1.590000e-33 154


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 TraesCS1B01G230100 chr1B 413203507 413206816 3309 True 2744.500000 4338 100.000000 1 3310 2 chr1B.!!$R2 3309
1 TraesCS1B01G230100 chr1A 384773826 384778338 4512 True 1252.666667 3059 92.153667 164 3310 3 chr1A.!!$R1 3146
2 TraesCS1B01G230100 chr1D 305767418 305770339 2921 True 771.600000 1639 93.985600 165 3310 5 chr1D.!!$R1 3145


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
989 2560 0.250727 CAAGAAACTGGGGGAGCGAA 60.251 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2894 4551 0.108019 GGAACGCCGAGGGGAATTAT 59.892 55.0 13.32 0.0 34.06 1.28 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
23 24 5.913637 CATTGTAGCAGAGAAGCGAATATG 58.086 41.667 0.00 0.00 40.15 1.78
24 25 3.982475 TGTAGCAGAGAAGCGAATATGG 58.018 45.455 0.00 0.00 40.15 2.74
25 26 3.384789 TGTAGCAGAGAAGCGAATATGGT 59.615 43.478 0.00 0.00 40.15 3.55
26 27 4.583073 TGTAGCAGAGAAGCGAATATGGTA 59.417 41.667 0.00 0.00 40.15 3.25
27 28 4.250116 AGCAGAGAAGCGAATATGGTAG 57.750 45.455 0.00 0.00 40.15 3.18
28 29 2.734079 GCAGAGAAGCGAATATGGTAGC 59.266 50.000 0.00 0.00 0.00 3.58
29 30 2.983136 CAGAGAAGCGAATATGGTAGCG 59.017 50.000 0.00 0.00 34.34 4.26
30 31 2.029828 AGAGAAGCGAATATGGTAGCGG 60.030 50.000 0.00 0.00 34.34 5.52
31 32 1.961394 AGAAGCGAATATGGTAGCGGA 59.039 47.619 0.00 0.00 34.34 5.54
32 33 2.563179 AGAAGCGAATATGGTAGCGGAT 59.437 45.455 0.00 0.00 34.34 4.18
33 34 2.370281 AGCGAATATGGTAGCGGATG 57.630 50.000 0.00 0.00 34.34 3.51
34 35 1.066858 AGCGAATATGGTAGCGGATGG 60.067 52.381 0.00 0.00 34.34 3.51
35 36 1.359848 CGAATATGGTAGCGGATGGC 58.640 55.000 0.00 0.00 44.05 4.40
66 67 5.983540 AGCATAGCTTTAGTCTTAGCAAGT 58.016 37.500 0.00 0.00 39.85 3.16
67 68 6.045955 AGCATAGCTTTAGTCTTAGCAAGTC 58.954 40.000 0.00 0.00 39.85 3.01
68 69 6.045955 GCATAGCTTTAGTCTTAGCAAGTCT 58.954 40.000 0.00 0.00 39.85 3.24
69 70 6.019156 GCATAGCTTTAGTCTTAGCAAGTCTG 60.019 42.308 0.00 1.88 39.85 3.51
70 71 5.730296 AGCTTTAGTCTTAGCAAGTCTGA 57.270 39.130 8.76 0.00 39.85 3.27
71 72 6.102897 AGCTTTAGTCTTAGCAAGTCTGAA 57.897 37.500 8.76 0.00 39.85 3.02
72 73 6.525629 AGCTTTAGTCTTAGCAAGTCTGAAA 58.474 36.000 8.76 0.00 39.85 2.69
73 74 6.425417 AGCTTTAGTCTTAGCAAGTCTGAAAC 59.575 38.462 8.76 0.00 39.85 2.78
74 75 6.425417 GCTTTAGTCTTAGCAAGTCTGAAACT 59.575 38.462 0.00 0.00 41.10 2.66
76 77 7.948278 TTAGTCTTAGCAAGTCTGAAACTTC 57.052 36.000 0.00 0.00 45.28 3.01
77 78 4.985409 AGTCTTAGCAAGTCTGAAACTTCG 59.015 41.667 0.00 0.00 45.28 3.79
78 79 4.150804 GTCTTAGCAAGTCTGAAACTTCGG 59.849 45.833 0.00 0.00 45.28 4.30
79 80 2.910688 AGCAAGTCTGAAACTTCGGA 57.089 45.000 0.00 0.00 45.28 4.55
85 86 2.589798 TCTGAAACTTCGGACGTTGT 57.410 45.000 0.25 0.00 37.65 3.32
86 87 2.466846 TCTGAAACTTCGGACGTTGTC 58.533 47.619 0.25 2.62 37.65 3.18
94 95 2.739132 GGACGTTGTCCCGGACTT 59.261 61.111 18.54 0.51 46.19 3.01
95 96 1.070275 GGACGTTGTCCCGGACTTT 59.930 57.895 18.54 0.16 46.19 2.66
96 97 0.318120 GGACGTTGTCCCGGACTTTA 59.682 55.000 18.54 1.65 46.19 1.85
97 98 1.066645 GGACGTTGTCCCGGACTTTAT 60.067 52.381 18.54 2.17 46.19 1.40
98 99 2.613725 GGACGTTGTCCCGGACTTTATT 60.614 50.000 18.54 0.00 46.19 1.40
99 100 2.669924 GACGTTGTCCCGGACTTTATTC 59.330 50.000 18.54 5.30 33.15 1.75
100 101 2.301009 ACGTTGTCCCGGACTTTATTCT 59.699 45.455 18.54 0.00 33.15 2.40
101 102 2.671396 CGTTGTCCCGGACTTTATTCTG 59.329 50.000 18.54 0.00 33.15 3.02
102 103 2.396590 TGTCCCGGACTTTATTCTGC 57.603 50.000 18.54 0.00 33.15 4.26
103 104 1.626321 TGTCCCGGACTTTATTCTGCA 59.374 47.619 18.54 0.00 33.15 4.41
104 105 2.238646 TGTCCCGGACTTTATTCTGCAT 59.761 45.455 18.54 0.00 33.15 3.96
105 106 3.279434 GTCCCGGACTTTATTCTGCATT 58.721 45.455 10.59 0.00 0.00 3.56
106 107 3.312697 GTCCCGGACTTTATTCTGCATTC 59.687 47.826 10.59 0.00 0.00 2.67
107 108 3.199946 TCCCGGACTTTATTCTGCATTCT 59.800 43.478 0.73 0.00 0.00 2.40
108 109 3.947834 CCCGGACTTTATTCTGCATTCTT 59.052 43.478 0.73 0.00 0.00 2.52
109 110 5.104693 TCCCGGACTTTATTCTGCATTCTTA 60.105 40.000 0.73 0.00 0.00 2.10
110 111 5.765182 CCCGGACTTTATTCTGCATTCTTAT 59.235 40.000 0.73 0.00 0.00 1.73
111 112 6.293626 CCCGGACTTTATTCTGCATTCTTATG 60.294 42.308 0.73 0.00 34.76 1.90
112 113 6.260936 CCGGACTTTATTCTGCATTCTTATGT 59.739 38.462 0.00 0.00 34.12 2.29
113 114 7.441157 CCGGACTTTATTCTGCATTCTTATGTA 59.559 37.037 0.00 0.00 34.12 2.29
114 115 8.826710 CGGACTTTATTCTGCATTCTTATGTAA 58.173 33.333 0.00 0.00 34.12 2.41
124 125 8.347771 TCTGCATTCTTATGTAAATGATCTTGC 58.652 33.333 0.00 0.00 35.35 4.01
125 126 8.229253 TGCATTCTTATGTAAATGATCTTGCT 57.771 30.769 0.00 0.00 35.35 3.91
126 127 8.347771 TGCATTCTTATGTAAATGATCTTGCTC 58.652 33.333 0.00 0.00 35.35 4.26
127 128 8.566260 GCATTCTTATGTAAATGATCTTGCTCT 58.434 33.333 0.00 0.00 35.35 4.09
305 316 2.101185 CGACACTCGCGATCTGCT 59.899 61.111 10.36 0.00 43.27 4.24
461 487 0.910088 GACCCCCAGAGTTACCAGCT 60.910 60.000 0.00 0.00 0.00 4.24
465 491 1.078143 CCAGAGTTACCAGCTGCCC 60.078 63.158 8.66 0.00 0.00 5.36
466 492 1.679311 CAGAGTTACCAGCTGCCCA 59.321 57.895 8.66 0.00 0.00 5.36
468 494 0.545309 AGAGTTACCAGCTGCCCAGA 60.545 55.000 8.66 0.00 0.00 3.86
469 495 0.543749 GAGTTACCAGCTGCCCAGAT 59.456 55.000 8.66 0.00 0.00 2.90
470 496 0.995024 AGTTACCAGCTGCCCAGATT 59.005 50.000 8.66 0.00 0.00 2.40
587 2155 1.449601 CTCCCACCCACGAATTCCG 60.450 63.158 0.00 0.00 45.44 4.30
602 2173 0.541863 TTCCGCCATCCTCTCCTTTC 59.458 55.000 0.00 0.00 0.00 2.62
989 2560 0.250727 CAAGAAACTGGGGGAGCGAA 60.251 55.000 0.00 0.00 0.00 4.70
1138 2709 3.775654 GGGACGTGGAGGAGCAGG 61.776 72.222 0.00 0.00 0.00 4.85
1146 2720 1.002274 GGAGGAGCAGGAGGAGGAA 59.998 63.158 0.00 0.00 0.00 3.36
1148 2722 0.032615 GAGGAGCAGGAGGAGGAAGA 60.033 60.000 0.00 0.00 0.00 2.87
1149 2723 0.032217 AGGAGCAGGAGGAGGAAGAG 60.032 60.000 0.00 0.00 0.00 2.85
1150 2724 1.685355 GGAGCAGGAGGAGGAAGAGC 61.685 65.000 0.00 0.00 0.00 4.09
1159 2733 3.465871 GAGGAGGAAGAGCATGATCAAC 58.534 50.000 14.38 6.31 0.00 3.18
1160 2734 2.842496 AGGAGGAAGAGCATGATCAACA 59.158 45.455 14.38 0.00 0.00 3.33
1177 2751 0.759346 ACAAGAAGACGGCAAGGAGT 59.241 50.000 0.00 0.00 0.00 3.85
1442 3016 2.677337 TCGACGACATGTACGTATCCAA 59.323 45.455 18.75 5.29 43.97 3.53
1443 3017 3.313249 TCGACGACATGTACGTATCCAAT 59.687 43.478 18.75 0.61 43.97 3.16
1447 3021 3.734231 CGACATGTACGTATCCAATCCAC 59.266 47.826 0.00 0.00 0.00 4.02
1448 3022 4.689071 GACATGTACGTATCCAATCCACA 58.311 43.478 0.00 0.00 0.00 4.17
1450 3024 3.530265 TGTACGTATCCAATCCACACC 57.470 47.619 0.00 0.00 0.00 4.16
1451 3025 2.832733 TGTACGTATCCAATCCACACCA 59.167 45.455 0.00 0.00 0.00 4.17
1473 3095 5.704978 CCATCAAAATTTCGGTCCCAAATTT 59.295 36.000 12.62 12.62 42.59 1.82
1475 3097 7.389053 CCATCAAAATTTCGGTCCCAAATTTAA 59.611 33.333 17.17 10.86 40.81 1.52
1476 3098 7.716768 TCAAAATTTCGGTCCCAAATTTAAC 57.283 32.000 17.17 0.00 40.81 2.01
1478 3100 7.769044 TCAAAATTTCGGTCCCAAATTTAACAA 59.231 29.630 17.17 4.47 40.81 2.83
1479 3101 7.485418 AAATTTCGGTCCCAAATTTAACAAC 57.515 32.000 15.80 0.00 40.20 3.32
1545 3167 7.306953 CAGTAGGATTAAAGCGATCTACTACC 58.693 42.308 0.00 0.00 31.21 3.18
1548 3170 5.834204 AGGATTAAAGCGATCTACTACCACT 59.166 40.000 0.00 0.00 0.00 4.00
1549 3171 7.002879 AGGATTAAAGCGATCTACTACCACTA 58.997 38.462 0.00 0.00 0.00 2.74
1557 3179 6.430616 AGCGATCTACTACCACTAGATAAACC 59.569 42.308 0.00 0.00 32.14 3.27
1574 3196 6.542370 AGATAAACCGAACCATAATTGAGGTG 59.458 38.462 4.61 0.00 38.37 4.00
1584 3206 4.201910 CCATAATTGAGGTGGTTTAGTGCG 60.202 45.833 0.00 0.00 0.00 5.34
1589 3211 0.676782 AGGTGGTTTAGTGCGGCATC 60.677 55.000 5.72 0.00 0.00 3.91
1594 3216 1.064060 GGTTTAGTGCGGCATCATCAC 59.936 52.381 5.72 0.00 0.00 3.06
1599 3221 2.923121 AGTGCGGCATCATCACTTAAT 58.077 42.857 5.72 0.00 37.78 1.40
1605 3227 3.879295 CGGCATCATCACTTAATTGAGGT 59.121 43.478 7.26 0.00 0.00 3.85
1606 3228 4.260907 CGGCATCATCACTTAATTGAGGTG 60.261 45.833 7.26 6.55 0.00 4.00
1608 3230 4.641989 GCATCATCACTTAATTGAGGTGGT 59.358 41.667 7.26 0.00 0.00 4.16
1609 3231 5.822519 GCATCATCACTTAATTGAGGTGGTA 59.177 40.000 7.26 0.00 0.00 3.25
1610 3232 6.017605 GCATCATCACTTAATTGAGGTGGTAG 60.018 42.308 7.26 0.00 0.00 3.18
1811 3437 1.224592 CCAACCGGAGCCAAGCTAT 59.775 57.895 9.46 0.00 39.88 2.97
1849 3475 1.442857 GTCACGAGGACAGCTCACG 60.443 63.158 7.03 0.00 46.19 4.35
1870 3496 3.623060 CGGATGTCCAATTCGATGTCTTT 59.377 43.478 0.00 0.00 35.14 2.52
1917 3546 3.253230 GTCAAAACAAGCTTGCTGTTGT 58.747 40.909 26.27 6.49 37.10 3.32
1935 3564 0.713883 GTTGTTGATGCGTCGATCGT 59.286 50.000 15.94 0.00 42.13 3.73
2342 3979 4.624913 TCTTCCTCTCTCTCTCTCTCTCT 58.375 47.826 0.00 0.00 0.00 3.10
2505 4146 0.374758 CGGATTGAGATTGTGCGTGG 59.625 55.000 0.00 0.00 0.00 4.94
2546 4187 4.633175 AGATGCTGCTGATCTAATCTGTG 58.367 43.478 0.00 0.00 0.00 3.66
2547 4188 3.900966 TGCTGCTGATCTAATCTGTGT 57.099 42.857 0.00 0.00 0.00 3.72
2548 4189 3.790091 TGCTGCTGATCTAATCTGTGTC 58.210 45.455 0.00 0.00 0.00 3.67
2549 4190 3.196254 TGCTGCTGATCTAATCTGTGTCA 59.804 43.478 0.00 0.00 0.00 3.58
2550 4191 3.555139 GCTGCTGATCTAATCTGTGTCAC 59.445 47.826 0.00 0.00 0.00 3.67
2551 4192 4.680172 GCTGCTGATCTAATCTGTGTCACT 60.680 45.833 4.27 0.00 0.00 3.41
2565 4206 0.786581 GTCACTGTGCATGTGAGTCG 59.213 55.000 20.77 4.43 43.90 4.18
2603 4244 0.756442 TGCTTTGCTTGCCTCCTGTT 60.756 50.000 0.00 0.00 0.00 3.16
2633 4274 7.509546 TCTTTTCCTCTGCTCTTCTTTTTCTA 58.490 34.615 0.00 0.00 0.00 2.10
2637 4278 7.913674 TCCTCTGCTCTTCTTTTTCTATTTC 57.086 36.000 0.00 0.00 0.00 2.17
2678 4319 1.139455 CTATTCGCCGGGGAAAAGGTA 59.861 52.381 34.14 21.50 0.00 3.08
2879 4536 2.419990 GGCCATGGGTTTATTTGCTTCC 60.420 50.000 15.13 0.00 0.00 3.46
2885 4542 2.496070 GGGTTTATTTGCTTCCCAGGAC 59.504 50.000 0.00 0.00 38.15 3.85
2887 4544 3.193479 GGTTTATTTGCTTCCCAGGACAG 59.807 47.826 0.00 0.00 0.00 3.51
2894 4551 1.623811 GCTTCCCAGGACAGTGAGTAA 59.376 52.381 0.00 0.00 0.00 2.24
2926 4583 4.036977 GTTCCGAACGTGCAGGAA 57.963 55.556 14.38 13.69 41.28 3.36
2927 4584 2.313267 GTTCCGAACGTGCAGGAAA 58.687 52.632 17.76 4.19 44.56 3.13
2928 4585 0.872388 GTTCCGAACGTGCAGGAAAT 59.128 50.000 17.76 0.00 44.56 2.17
2929 4586 2.070783 GTTCCGAACGTGCAGGAAATA 58.929 47.619 17.76 0.00 44.56 1.40
2930 4587 2.004583 TCCGAACGTGCAGGAAATAG 57.995 50.000 14.38 0.00 0.00 1.73
2931 4588 1.006832 CCGAACGTGCAGGAAATAGG 58.993 55.000 14.38 5.07 0.00 2.57
2932 4589 1.404986 CCGAACGTGCAGGAAATAGGA 60.405 52.381 14.38 0.00 0.00 2.94
2933 4590 2.343101 CGAACGTGCAGGAAATAGGAA 58.657 47.619 14.38 0.00 0.00 3.36
3000 4659 2.037121 TGAATTGTCTCTGAGGCAACGA 59.963 45.455 25.38 10.51 43.26 3.85
3002 4661 1.040646 TTGTCTCTGAGGCAACGAGT 58.959 50.000 19.99 0.00 34.46 4.18
3063 4738 8.103305 TGACCAGAAATAGCTTAGTCAGAAATT 58.897 33.333 0.00 0.00 29.78 1.82
3064 4739 8.870075 ACCAGAAATAGCTTAGTCAGAAATTT 57.130 30.769 0.00 0.00 0.00 1.82
3065 4740 8.951243 ACCAGAAATAGCTTAGTCAGAAATTTC 58.049 33.333 10.33 10.33 36.40 2.17
3066 4741 8.950210 CCAGAAATAGCTTAGTCAGAAATTTCA 58.050 33.333 19.99 0.00 37.49 2.69
3067 4742 9.766277 CAGAAATAGCTTAGTCAGAAATTTCAC 57.234 33.333 19.99 10.33 37.49 3.18
3068 4743 9.732130 AGAAATAGCTTAGTCAGAAATTTCACT 57.268 29.630 19.99 16.52 37.49 3.41
3069 4744 9.766277 GAAATAGCTTAGTCAGAAATTTCACTG 57.234 33.333 19.99 10.56 36.30 3.66
3070 4745 7.856145 ATAGCTTAGTCAGAAATTTCACTGG 57.144 36.000 19.99 12.64 35.20 4.00
3071 4746 5.625150 AGCTTAGTCAGAAATTTCACTGGT 58.375 37.500 19.99 7.65 35.20 4.00
3072 4747 6.769512 AGCTTAGTCAGAAATTTCACTGGTA 58.230 36.000 19.99 2.68 35.20 3.25
3073 4748 6.651225 AGCTTAGTCAGAAATTTCACTGGTAC 59.349 38.462 19.99 6.16 35.20 3.34
3074 4749 6.426937 GCTTAGTCAGAAATTTCACTGGTACA 59.573 38.462 19.99 0.00 35.20 2.90
3075 4750 7.119846 GCTTAGTCAGAAATTTCACTGGTACAT 59.880 37.037 19.99 0.00 38.20 2.29
3076 4751 6.808008 AGTCAGAAATTTCACTGGTACATG 57.192 37.500 19.99 6.47 38.20 3.21
3077 4752 6.533730 AGTCAGAAATTTCACTGGTACATGA 58.466 36.000 19.99 8.61 38.20 3.07
3078 4753 7.170965 AGTCAGAAATTTCACTGGTACATGAT 58.829 34.615 19.99 0.89 38.20 2.45
3126 4801 4.630069 GCTTCTTCAGACGCCTTTTATACA 59.370 41.667 0.00 0.00 33.76 2.29
3132 4808 8.255206 TCTTCAGACGCCTTTTATACAGAATTA 58.745 33.333 0.00 0.00 0.00 1.40
3168 4844 5.474876 CAGAGTTTAGTTCCCTCTTTGCAAT 59.525 40.000 0.00 0.00 33.38 3.56
3225 4948 4.950050 AGAACACCACAAGAGACAAGTAG 58.050 43.478 0.00 0.00 0.00 2.57
3242 4965 5.009010 ACAAGTAGAAGTCCAATGCACAAAG 59.991 40.000 0.00 0.00 0.00 2.77
3263 4986 4.175962 AGGATGAGACCCTACAAGGAAAA 58.824 43.478 0.00 0.00 37.67 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.107182 CCATATTCGCTTCTCTGCTACAATG 60.107 44.000 0.00 0.00 0.00 2.82
1 2 4.993584 CCATATTCGCTTCTCTGCTACAAT 59.006 41.667 0.00 0.00 0.00 2.71
2 3 4.141937 ACCATATTCGCTTCTCTGCTACAA 60.142 41.667 0.00 0.00 0.00 2.41
3 4 3.384789 ACCATATTCGCTTCTCTGCTACA 59.615 43.478 0.00 0.00 0.00 2.74
4 5 3.983741 ACCATATTCGCTTCTCTGCTAC 58.016 45.455 0.00 0.00 0.00 3.58
5 6 4.321304 GCTACCATATTCGCTTCTCTGCTA 60.321 45.833 0.00 0.00 0.00 3.49
6 7 3.553922 GCTACCATATTCGCTTCTCTGCT 60.554 47.826 0.00 0.00 0.00 4.24
7 8 2.734079 GCTACCATATTCGCTTCTCTGC 59.266 50.000 0.00 0.00 0.00 4.26
8 9 2.983136 CGCTACCATATTCGCTTCTCTG 59.017 50.000 0.00 0.00 0.00 3.35
9 10 2.029828 CCGCTACCATATTCGCTTCTCT 60.030 50.000 0.00 0.00 0.00 3.10
10 11 2.030185 TCCGCTACCATATTCGCTTCTC 60.030 50.000 0.00 0.00 0.00 2.87
11 12 1.961394 TCCGCTACCATATTCGCTTCT 59.039 47.619 0.00 0.00 0.00 2.85
12 13 2.433868 TCCGCTACCATATTCGCTTC 57.566 50.000 0.00 0.00 0.00 3.86
13 14 2.612972 CCATCCGCTACCATATTCGCTT 60.613 50.000 0.00 0.00 0.00 4.68
14 15 1.066858 CCATCCGCTACCATATTCGCT 60.067 52.381 0.00 0.00 0.00 4.93
15 16 1.359848 CCATCCGCTACCATATTCGC 58.640 55.000 0.00 0.00 0.00 4.70
16 17 1.359848 GCCATCCGCTACCATATTCG 58.640 55.000 0.00 0.00 0.00 3.34
43 44 5.983540 ACTTGCTAAGACTAAAGCTATGCT 58.016 37.500 10.22 0.00 42.56 3.79
44 45 6.019156 CAGACTTGCTAAGACTAAAGCTATGC 60.019 42.308 10.22 0.00 39.53 3.14
45 46 7.261325 TCAGACTTGCTAAGACTAAAGCTATG 58.739 38.462 10.22 0.59 39.53 2.23
46 47 7.411486 TCAGACTTGCTAAGACTAAAGCTAT 57.589 36.000 10.22 0.00 39.53 2.97
47 48 6.835819 TCAGACTTGCTAAGACTAAAGCTA 57.164 37.500 10.22 3.38 39.53 3.32
48 49 5.730296 TCAGACTTGCTAAGACTAAAGCT 57.270 39.130 10.22 0.00 39.53 3.74
49 50 6.425417 AGTTTCAGACTTGCTAAGACTAAAGC 59.575 38.462 3.33 3.33 33.92 3.51
50 51 7.954788 AGTTTCAGACTTGCTAAGACTAAAG 57.045 36.000 3.37 0.00 33.92 1.85
64 65 2.159142 ACAACGTCCGAAGTTTCAGACT 60.159 45.455 6.65 0.00 41.47 3.24
65 66 2.199236 ACAACGTCCGAAGTTTCAGAC 58.801 47.619 0.00 0.00 32.58 3.51
66 67 2.466846 GACAACGTCCGAAGTTTCAGA 58.533 47.619 0.00 0.00 0.00 3.27
67 68 1.525619 GGACAACGTCCGAAGTTTCAG 59.474 52.381 0.00 0.00 43.14 3.02
68 69 1.574134 GGACAACGTCCGAAGTTTCA 58.426 50.000 0.00 0.00 43.14 2.69
78 79 2.375173 ATAAAGTCCGGGACAACGTC 57.625 50.000 27.87 0.67 34.60 4.34
79 80 2.301009 AGAATAAAGTCCGGGACAACGT 59.699 45.455 27.87 12.51 34.60 3.99
80 81 2.671396 CAGAATAAAGTCCGGGACAACG 59.329 50.000 27.87 4.73 34.60 4.10
81 82 2.418976 GCAGAATAAAGTCCGGGACAAC 59.581 50.000 27.87 12.15 34.60 3.32
82 83 2.039216 TGCAGAATAAAGTCCGGGACAA 59.961 45.455 27.87 13.78 34.60 3.18
83 84 1.626321 TGCAGAATAAAGTCCGGGACA 59.374 47.619 27.87 9.04 34.60 4.02
84 85 2.396590 TGCAGAATAAAGTCCGGGAC 57.603 50.000 19.61 19.61 0.00 4.46
85 86 3.199946 AGAATGCAGAATAAAGTCCGGGA 59.800 43.478 0.00 0.00 0.00 5.14
86 87 3.545703 AGAATGCAGAATAAAGTCCGGG 58.454 45.455 0.00 0.00 0.00 5.73
87 88 6.260936 ACATAAGAATGCAGAATAAAGTCCGG 59.739 38.462 0.00 0.00 36.50 5.14
88 89 7.251704 ACATAAGAATGCAGAATAAAGTCCG 57.748 36.000 0.00 0.00 36.50 4.79
98 99 8.347771 GCAAGATCATTTACATAAGAATGCAGA 58.652 33.333 0.00 0.00 36.50 4.26
99 100 8.350722 AGCAAGATCATTTACATAAGAATGCAG 58.649 33.333 0.00 0.00 36.50 4.41
100 101 8.229253 AGCAAGATCATTTACATAAGAATGCA 57.771 30.769 0.00 0.00 36.50 3.96
101 102 8.566260 AGAGCAAGATCATTTACATAAGAATGC 58.434 33.333 0.00 0.00 36.50 3.56
160 161 3.677976 CGGGCGTAGTATCTCCAGTTTTT 60.678 47.826 0.00 0.00 0.00 1.94
161 162 2.159142 CGGGCGTAGTATCTCCAGTTTT 60.159 50.000 0.00 0.00 0.00 2.43
162 163 1.407979 CGGGCGTAGTATCTCCAGTTT 59.592 52.381 0.00 0.00 0.00 2.66
305 316 0.244450 CGGTGACCACGCCTTAACTA 59.756 55.000 1.11 0.00 43.77 2.24
384 399 2.937689 ATGACAGCAGGCCCCAGT 60.938 61.111 0.00 0.00 0.00 4.00
461 487 0.825425 TGCGGTGAAAAATCTGGGCA 60.825 50.000 0.00 0.00 0.00 5.36
587 2155 1.884926 CGCGAAAGGAGAGGATGGC 60.885 63.158 0.00 0.00 0.00 4.40
602 2173 1.203313 GGAAAGTGAAACGGACGCG 59.797 57.895 3.53 3.53 45.86 6.01
967 2538 1.770324 CTCCCCCAGTTTCTTGGCT 59.230 57.895 0.00 0.00 36.88 4.75
1138 2709 3.118482 TGTTGATCATGCTCTTCCTCCTC 60.118 47.826 0.00 0.00 0.00 3.71
1146 2720 3.931468 CGTCTTCTTGTTGATCATGCTCT 59.069 43.478 0.00 0.00 0.00 4.09
1148 2722 3.005554 CCGTCTTCTTGTTGATCATGCT 58.994 45.455 0.00 0.00 0.00 3.79
1149 2723 2.476854 GCCGTCTTCTTGTTGATCATGC 60.477 50.000 0.00 0.00 0.00 4.06
1150 2724 2.743664 TGCCGTCTTCTTGTTGATCATG 59.256 45.455 0.00 0.00 0.00 3.07
1159 2733 1.433534 GACTCCTTGCCGTCTTCTTG 58.566 55.000 0.00 0.00 0.00 3.02
1160 2734 0.038159 CGACTCCTTGCCGTCTTCTT 60.038 55.000 0.00 0.00 0.00 2.52
1177 2751 1.616872 TTCGTCATCGTCGTCGTCGA 61.617 55.000 16.35 16.35 41.45 4.20
1189 2763 2.611518 CGCCTTCTTCTTCTTCGTCAT 58.388 47.619 0.00 0.00 0.00 3.06
1190 2764 1.336887 CCGCCTTCTTCTTCTTCGTCA 60.337 52.381 0.00 0.00 0.00 4.35
1191 2765 1.336980 ACCGCCTTCTTCTTCTTCGTC 60.337 52.381 0.00 0.00 0.00 4.20
1192 2766 0.680061 ACCGCCTTCTTCTTCTTCGT 59.320 50.000 0.00 0.00 0.00 3.85
1299 2873 1.261938 TGTAGGCCACCACGTAGCAT 61.262 55.000 5.01 0.00 0.00 3.79
1442 3016 3.831911 ACCGAAATTTTGATGGTGTGGAT 59.168 39.130 7.02 0.00 0.00 3.41
1443 3017 3.226777 ACCGAAATTTTGATGGTGTGGA 58.773 40.909 7.02 0.00 0.00 4.02
1447 3021 2.560542 TGGGACCGAAATTTTGATGGTG 59.439 45.455 7.02 0.00 31.86 4.17
1448 3022 2.883026 TGGGACCGAAATTTTGATGGT 58.117 42.857 7.02 6.08 35.14 3.55
1450 3024 6.799926 AAATTTGGGACCGAAATTTTGATG 57.200 33.333 25.75 0.00 39.05 3.07
1451 3025 7.934120 TGTTAAATTTGGGACCGAAATTTTGAT 59.066 29.630 32.06 18.26 41.23 2.57
1473 3095 5.816258 TGTAATTCGGTGTCTGTTGTTGTTA 59.184 36.000 0.00 0.00 0.00 2.41
1475 3097 4.034742 GTGTAATTCGGTGTCTGTTGTTGT 59.965 41.667 0.00 0.00 0.00 3.32
1476 3098 4.523813 GTGTAATTCGGTGTCTGTTGTTG 58.476 43.478 0.00 0.00 0.00 3.33
1478 3100 3.135994 GGTGTAATTCGGTGTCTGTTGT 58.864 45.455 0.00 0.00 0.00 3.32
1479 3101 3.135225 TGGTGTAATTCGGTGTCTGTTG 58.865 45.455 0.00 0.00 0.00 3.33
1545 3167 8.657074 TCAATTATGGTTCGGTTTATCTAGTG 57.343 34.615 0.00 0.00 0.00 2.74
1548 3170 7.713507 CACCTCAATTATGGTTCGGTTTATCTA 59.286 37.037 0.00 0.00 33.75 1.98
1549 3171 6.542370 CACCTCAATTATGGTTCGGTTTATCT 59.458 38.462 0.00 0.00 33.75 1.98
1574 3196 1.064060 GTGATGATGCCGCACTAAACC 59.936 52.381 0.00 0.00 0.00 3.27
1584 3206 4.037208 CCACCTCAATTAAGTGATGATGCC 59.963 45.833 13.92 0.00 33.21 4.40
1589 3211 9.613428 TTAATCTACCACCTCAATTAAGTGATG 57.387 33.333 6.00 6.36 33.21 3.07
1599 3221 6.061022 TGCAGATTTAATCTACCACCTCAA 57.939 37.500 7.18 0.00 37.58 3.02
1605 3227 5.692115 TGGACTGCAGATTTAATCTACCA 57.308 39.130 23.35 9.25 37.58 3.25
1606 3228 7.420800 CAATTGGACTGCAGATTTAATCTACC 58.579 38.462 23.35 7.11 37.58 3.18
1608 3230 6.547141 CCCAATTGGACTGCAGATTTAATCTA 59.453 38.462 26.60 0.53 35.92 1.98
1609 3231 5.361857 CCCAATTGGACTGCAGATTTAATCT 59.638 40.000 26.60 0.99 37.49 2.40
1610 3232 5.594926 CCCAATTGGACTGCAGATTTAATC 58.405 41.667 26.60 5.91 37.39 1.75
1811 3437 1.678728 CCAGCTAGAAACGGCAATGGA 60.679 52.381 0.00 0.00 0.00 3.41
1849 3475 4.731773 GCAAAGACATCGAATTGGACATCC 60.732 45.833 0.00 0.00 0.00 3.51
1870 3496 2.203408 TGAATTGCGGTGGTGGCA 60.203 55.556 0.00 0.00 38.93 4.92
1917 3546 0.713329 CACGATCGACGCATCAACAA 59.287 50.000 24.34 0.00 46.94 2.83
1969 3598 5.920840 TCACAACAAACAAACATTCGTCAAA 59.079 32.000 0.00 0.00 0.00 2.69
2264 3901 4.641645 TGGCAGCCGGACTTGGTG 62.642 66.667 5.05 0.00 0.00 4.17
2302 3939 1.507974 GAGCCCGATCGATCAGACGA 61.508 60.000 24.40 0.00 46.04 4.20
2505 4146 2.742053 TCTCAGCTCGTTAAACAATGGC 59.258 45.455 0.00 0.00 0.00 4.40
2534 4175 4.498241 TGCACAGTGACACAGATTAGATC 58.502 43.478 4.15 0.00 0.00 2.75
2546 4187 0.786581 CGACTCACATGCACAGTGAC 59.213 55.000 17.23 9.69 40.80 3.67
2547 4188 0.945743 GCGACTCACATGCACAGTGA 60.946 55.000 19.28 19.28 43.23 3.41
2548 4189 1.223417 TGCGACTCACATGCACAGTG 61.223 55.000 13.47 13.47 38.32 3.66
2549 4190 0.947660 CTGCGACTCACATGCACAGT 60.948 55.000 0.00 0.00 34.42 3.55
2550 4191 1.785951 CTGCGACTCACATGCACAG 59.214 57.895 0.00 0.00 34.42 3.66
2551 4192 2.319841 GCTGCGACTCACATGCACA 61.320 57.895 0.00 0.00 34.42 4.57
2603 4244 5.440610 AGAAGAGCAGAGGAAAAGAAACAA 58.559 37.500 0.00 0.00 0.00 2.83
2696 4337 0.389025 CCACGATGTCCGATCCATCA 59.611 55.000 10.02 0.00 38.90 3.07
2721 4362 1.339055 CCGCTTGTTCTCCAATCTCCA 60.339 52.381 0.00 0.00 31.20 3.86
2813 4470 3.450817 TGAGGCGAATTCTGTCCTAATGA 59.549 43.478 3.52 0.00 0.00 2.57
2814 4471 3.557595 GTGAGGCGAATTCTGTCCTAATG 59.442 47.826 3.52 0.00 0.00 1.90
2815 4472 3.432326 GGTGAGGCGAATTCTGTCCTAAT 60.432 47.826 3.52 0.00 0.00 1.73
2818 4475 0.250513 GGTGAGGCGAATTCTGTCCT 59.749 55.000 3.52 7.14 0.00 3.85
2824 4481 0.657840 CATTCCGGTGAGGCGAATTC 59.342 55.000 0.00 0.00 40.77 2.17
2879 4536 5.368989 GGGAATTATTACTCACTGTCCTGG 58.631 45.833 0.00 0.00 0.00 4.45
2885 4542 4.632153 CCGAGGGGAATTATTACTCACTG 58.368 47.826 0.00 0.00 34.06 3.66
2887 4544 3.400255 GCCGAGGGGAATTATTACTCAC 58.600 50.000 0.00 0.00 34.06 3.51
2894 4551 0.108019 GGAACGCCGAGGGGAATTAT 59.892 55.000 13.32 0.00 34.06 1.28
2926 4583 8.489489 TCTGCTCATAAATTCAGAGTTCCTATT 58.511 33.333 0.00 0.00 32.43 1.73
2927 4584 8.027524 TCTGCTCATAAATTCAGAGTTCCTAT 57.972 34.615 0.00 0.00 32.43 2.57
2928 4585 7.423844 TCTGCTCATAAATTCAGAGTTCCTA 57.576 36.000 0.00 0.00 32.43 2.94
2929 4586 6.305272 TCTGCTCATAAATTCAGAGTTCCT 57.695 37.500 0.00 0.00 32.43 3.36
2930 4587 6.601741 CTCTGCTCATAAATTCAGAGTTCC 57.398 41.667 10.12 0.00 44.43 3.62
2983 4640 1.040646 ACTCGTTGCCTCAGAGACAA 58.959 50.000 0.00 0.00 36.03 3.18
2985 4642 1.000163 TCAACTCGTTGCCTCAGAGAC 60.000 52.381 0.00 0.00 40.24 3.36
2986 4643 1.328279 TCAACTCGTTGCCTCAGAGA 58.672 50.000 0.00 0.00 40.24 3.10
2987 4644 2.154854 TTCAACTCGTTGCCTCAGAG 57.845 50.000 4.95 0.00 40.24 3.35
2988 4645 2.158957 AGTTTCAACTCGTTGCCTCAGA 60.159 45.455 4.95 0.00 40.24 3.27
2989 4646 2.032549 CAGTTTCAACTCGTTGCCTCAG 60.033 50.000 4.95 0.00 40.24 3.35
3047 4706 6.769512 ACCAGTGAAATTTCTGACTAAGCTA 58.230 36.000 18.64 0.00 34.02 3.32
3063 4738 7.607607 GCATGGATTATATCATGTACCAGTGAA 59.392 37.037 0.00 0.00 41.83 3.18
3064 4739 7.038088 AGCATGGATTATATCATGTACCAGTGA 60.038 37.037 0.00 0.00 41.83 3.41
3065 4740 7.108194 AGCATGGATTATATCATGTACCAGTG 58.892 38.462 0.00 0.00 41.83 3.66
3066 4741 7.262990 AGCATGGATTATATCATGTACCAGT 57.737 36.000 0.00 0.00 41.83 4.00
3067 4742 9.671279 TTTAGCATGGATTATATCATGTACCAG 57.329 33.333 0.00 0.00 41.83 4.00
3070 4745 9.994432 GCTTTTAGCATGGATTATATCATGTAC 57.006 33.333 0.00 0.00 41.89 2.90
3141 4817 5.049336 GCAAAGAGGGAACTAAACTCTGAAC 60.049 44.000 0.00 0.00 44.43 3.18
3149 4825 5.136828 TGTCATTGCAAAGAGGGAACTAAA 58.863 37.500 1.71 0.00 44.43 1.85
3151 4827 4.365514 TGTCATTGCAAAGAGGGAACTA 57.634 40.909 1.71 0.00 44.43 2.24
3182 4858 3.536158 TTTCGCAGAAGTTGTGTATGC 57.464 42.857 1.56 0.00 45.90 3.14
3191 4867 2.354821 GTGGTGTTCTTTTCGCAGAAGT 59.645 45.455 0.00 0.00 45.90 3.01
3225 4948 3.507233 TCATCCTTTGTGCATTGGACTTC 59.493 43.478 9.80 0.00 0.00 3.01
3242 4965 4.518249 CTTTTCCTTGTAGGGTCTCATCC 58.482 47.826 0.00 0.00 35.59 3.51
3263 4986 3.854669 CCGAAGATGCTCGCCCCT 61.855 66.667 0.00 0.00 37.51 4.79



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

AutoCloner maintained by Alex Coulton.