Multiple sequence alignment - TraesCS2D01G020700

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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 TraesCS2D01G020700 chr2D 100.000 3416 0 0 1 3416 9759495 9756080 0.000000e+00 6309.0
1 TraesCS2D01G020700 chr2D 81.770 1141 191 9 1322 2455 8671062 8672192 0.000000e+00 939.0
2 TraesCS2D01G020700 chr2D 79.590 1269 223 20 1222 2461 9371769 9373030 0.000000e+00 876.0
3 TraesCS2D01G020700 chr2D 83.046 348 42 9 887 1229 9642869 9643204 1.990000e-77 300.0
4 TraesCS2D01G020700 chr2D 83.492 315 39 7 924 1229 9588218 9588528 7.220000e-72 281.0
5 TraesCS2D01G020700 chr2D 77.411 394 73 13 847 1229 8686314 8686702 1.600000e-53 220.0
6 TraesCS2D01G020700 chr2D 77.041 196 28 11 495 683 9561624 9561809 2.810000e-16 97.1
7 TraesCS2D01G020700 chr2A 93.226 1609 76 12 1228 2830 9094222 9092641 0.000000e+00 2337.0
8 TraesCS2D01G020700 chr2A 97.094 1239 36 0 1222 2460 9983207 9984445 0.000000e+00 2089.0
9 TraesCS2D01G020700 chr2A 94.571 1234 37 13 1 1229 9981973 9983181 0.000000e+00 1881.0
10 TraesCS2D01G020700 chr2A 80.856 1238 221 11 1232 2458 8631230 8632462 0.000000e+00 959.0
11 TraesCS2D01G020700 chr2A 79.653 1268 223 21 1222 2461 8627679 8628939 0.000000e+00 880.0
12 TraesCS2D01G020700 chr2A 91.700 506 36 4 730 1229 9094759 9094254 0.000000e+00 697.0
13 TraesCS2D01G020700 chr2A 88.702 416 40 7 818 1229 9111300 9110888 5.090000e-138 501.0
14 TraesCS2D01G020700 chr2A 82.789 337 41 9 898 1229 8727216 8727540 5.580000e-73 285.0
15 TraesCS2D01G020700 chr2A 83.442 308 38 9 924 1222 8682649 8682952 1.210000e-69 274.0
16 TraesCS2D01G020700 chr2A 87.978 183 14 3 2666 2840 9984492 9984674 3.450000e-50 209.0
17 TraesCS2D01G020700 chr2A 98.077 104 2 0 3312 3415 9092639 9092536 7.530000e-42 182.0
18 TraesCS2D01G020700 chr2A 77.574 272 46 11 145 404 9108067 9107799 2.120000e-32 150.0
19 TraesCS2D01G020700 chr2B 92.532 1473 100 7 1222 2687 13068249 13066780 0.000000e+00 2102.0
20 TraesCS2D01G020700 chr2B 92.560 457 30 4 775 1229 13068729 13068275 0.000000e+00 652.0
21 TraesCS2D01G020700 chr2B 90.336 238 21 2 2468 2703 13064093 13063856 9.210000e-81 311.0
22 TraesCS2D01G020700 chr2B 93.694 111 7 0 2859 2969 13063366 13063256 2.110000e-37 167.0
23 TraesCS2D01G020700 chr2B 89.720 107 11 0 3309 3415 13060486 13060380 1.650000e-28 137.0
24 TraesCS2D01G020700 chr2B 77.220 259 33 11 531 765 13069288 13069032 9.950000e-26 128.0
25 TraesCS2D01G020700 chr2B 97.368 38 0 1 2981 3017 13063260 13063223 2.850000e-06 63.9
26 TraesCS2D01G020700 chrUn 79.124 1279 219 29 1225 2467 273231266 273230000 0.000000e+00 839.0
27 TraesCS2D01G020700 chrUn 79.183 1273 217 29 1222 2458 292878583 292879843 0.000000e+00 839.0


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 TraesCS2D01G020700 chr2D 9756080 9759495 3415 True 6309.0 6309 100.000000 1 3416 1 chr2D.!!$R1 3415
1 TraesCS2D01G020700 chr2D 8671062 8672192 1130 False 939.0 939 81.770000 1322 2455 1 chr2D.!!$F1 1133
2 TraesCS2D01G020700 chr2D 9371769 9373030 1261 False 876.0 876 79.590000 1222 2461 1 chr2D.!!$F3 1239
3 TraesCS2D01G020700 chr2A 9981973 9984674 2701 False 1393.0 2089 93.214333 1 2840 3 chr2A.!!$F4 2839
4 TraesCS2D01G020700 chr2A 9092536 9094759 2223 True 1072.0 2337 94.334333 730 3415 3 chr2A.!!$R1 2685
5 TraesCS2D01G020700 chr2A 8627679 8632462 4783 False 919.5 959 80.254500 1222 2461 2 chr2A.!!$F3 1239
6 TraesCS2D01G020700 chr2A 9107799 9111300 3501 True 325.5 501 83.138000 145 1229 2 chr2A.!!$R2 1084
7 TraesCS2D01G020700 chr2B 13060380 13069288 8908 True 508.7 2102 90.490000 531 3415 7 chr2B.!!$R1 2884
8 TraesCS2D01G020700 chrUn 273230000 273231266 1266 True 839.0 839 79.124000 1225 2467 1 chrUn.!!$R1 1242
9 TraesCS2D01G020700 chrUn 292878583 292879843 1260 False 839.0 839 79.183000 1222 2458 1 chrUn.!!$F1 1236

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
229 230 0.250467 GGTCAAGCCTGAACTCTGCA 60.250 55.0 0.0 0.0 36.25 4.41 F
885 1209 0.318441 CACCCACTCGTCACAGTCAT 59.682 55.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 1539 1.227380 GAGCTCGGTACATGGCCTG 60.227 63.158 3.32 2.01 0.00 4.85 R
2562 6540 0.610232 AAGAGCAGGTGGTGGATTGC 60.610 55.000 0.00 0.00 36.83 3.56 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
32 33 0.613012 AAGCCTGGCATGTCTTTCCC 60.613 55.000 22.65 0.00 0.00 3.97
64 65 3.058914 GCACTTCTGCTAACAACGACATT 60.059 43.478 0.00 0.00 40.63 2.71
98 99 0.806868 TAGACTGTACAAGGCGGTCG 59.193 55.000 0.00 0.00 44.52 4.79
99 100 2.048503 ACTGTACAAGGCGGTCGC 60.049 61.111 6.83 6.83 41.06 5.19
100 101 3.179265 CTGTACAAGGCGGTCGCG 61.179 66.667 0.00 0.00 43.06 5.87
101 102 3.620300 CTGTACAAGGCGGTCGCGA 62.620 63.158 3.71 3.71 43.06 5.87
102 103 2.879462 GTACAAGGCGGTCGCGAG 60.879 66.667 10.24 0.00 43.06 5.03
103 104 3.057548 TACAAGGCGGTCGCGAGA 61.058 61.111 10.24 0.00 43.06 4.04
104 105 2.628696 TACAAGGCGGTCGCGAGAA 61.629 57.895 10.24 0.00 45.01 2.87
105 106 1.940883 TACAAGGCGGTCGCGAGAAT 61.941 55.000 10.24 0.00 45.01 2.40
106 107 2.202756 AAGGCGGTCGCGAGAATC 60.203 61.111 10.24 0.00 45.01 2.52
107 108 3.718210 AAGGCGGTCGCGAGAATCC 62.718 63.158 10.24 6.17 45.01 3.01
108 109 4.508128 GGCGGTCGCGAGAATCCA 62.508 66.667 10.24 0.00 45.01 3.41
109 110 2.956964 GCGGTCGCGAGAATCCAG 60.957 66.667 10.24 5.05 45.01 3.86
110 111 2.278857 CGGTCGCGAGAATCCAGG 60.279 66.667 10.24 0.00 45.01 4.45
111 112 2.586357 GGTCGCGAGAATCCAGGC 60.586 66.667 10.24 0.00 45.01 4.85
112 113 2.496817 GTCGCGAGAATCCAGGCT 59.503 61.111 10.24 0.00 45.01 4.58
113 114 1.590259 GTCGCGAGAATCCAGGCTC 60.590 63.158 10.24 0.00 45.01 4.70
114 115 1.754621 TCGCGAGAATCCAGGCTCT 60.755 57.895 3.71 0.00 37.03 4.09
115 116 1.591059 CGCGAGAATCCAGGCTCTG 60.591 63.158 0.00 0.00 0.00 3.35
116 117 1.886777 GCGAGAATCCAGGCTCTGC 60.887 63.158 0.00 0.00 0.00 4.26
117 118 1.591059 CGAGAATCCAGGCTCTGCG 60.591 63.158 0.00 0.00 0.00 5.18
138 139 2.346365 CCACTGCTGAGCTGCTCA 59.654 61.111 28.77 28.77 38.25 4.26
154 155 0.510359 CTCAGCACTGAAGTCGTTGC 59.490 55.000 1.42 0.00 39.39 4.17
191 192 5.676552 TCAGGTCAAGCAACACTTTTACTA 58.323 37.500 0.00 0.00 36.04 1.82
194 195 6.857964 CAGGTCAAGCAACACTTTTACTATTG 59.142 38.462 0.00 0.00 36.04 1.90
202 203 7.023575 GCAACACTTTTACTATTGTGGAGATG 58.976 38.462 0.00 0.00 35.02 2.90
229 230 0.250467 GGTCAAGCCTGAACTCTGCA 60.250 55.000 0.00 0.00 36.25 4.41
259 260 4.216257 AGAAGATGTGACAATTTCGGGTTG 59.784 41.667 0.00 0.00 0.00 3.77
370 371 6.422100 TGCGAGATTAATGAAGTATTGAGCTC 59.578 38.462 6.82 6.82 41.64 4.09
401 402 5.951148 TCATCATCACTGGCCAAGATTAAAA 59.049 36.000 15.74 5.05 0.00 1.52
402 403 6.436847 TCATCATCACTGGCCAAGATTAAAAA 59.563 34.615 15.74 3.08 0.00 1.94
457 458 9.929722 GTGAACATATATTTTCATGCTACGAAA 57.070 29.630 15.49 0.00 34.34 3.46
683 691 6.037610 CAGAGCCACTTTATTTGTCCATAGAC 59.962 42.308 0.00 0.00 43.83 2.59
707 732 2.422597 TGCCTACCAAGTTTGTCGATG 58.577 47.619 0.00 0.00 0.00 3.84
765 790 5.028549 ACCATAGTGGAGATCAACATCAC 57.971 43.478 2.45 0.00 40.96 3.06
791 1111 2.154462 ACCTGACCTTTGAAGAATGCG 58.846 47.619 0.00 0.00 0.00 4.73
850 1174 5.596836 AGCACAAAGGAGAAAATGACAAA 57.403 34.783 0.00 0.00 0.00 2.83
885 1209 0.318441 CACCCACTCGTCACAGTCAT 59.682 55.000 0.00 0.00 0.00 3.06
968 1294 7.341769 TGCCAGCCTATAAATTTGTCAATAAGT 59.658 33.333 0.00 0.00 0.00 2.24
1625 2013 3.089784 CGATGAAAGGGTTCGCGG 58.910 61.111 6.13 0.00 36.46 6.46
1684 2072 7.558444 ACAACCTTTTAAGAATACTTGACCACA 59.442 33.333 0.00 0.00 37.53 4.17
1776 2164 6.385033 GGAAAGGTTTCACTCATTTCTCATG 58.615 40.000 4.89 0.00 38.92 3.07
1944 2332 1.078759 CGACAGAACATCCACGGCTC 61.079 60.000 0.00 0.00 0.00 4.70
2078 2468 2.689983 GTTGCATATTGGACAAGGGGAG 59.310 50.000 0.00 0.00 0.00 4.30
2086 2476 1.363246 GGACAAGGGGAGAAGGTTCT 58.637 55.000 0.00 0.00 41.00 3.01
2340 6263 6.018832 CCCCGCATGAATCATTTGTTTATTTC 60.019 38.462 0.00 0.00 0.00 2.17
2363 6286 4.491676 GTTACAAGTCGTGCTCAGGATAA 58.508 43.478 0.00 0.00 0.00 1.75
2564 6542 7.112122 ACTTGTACATTTTATCAGATCCAGCA 58.888 34.615 0.00 0.00 0.00 4.41
2596 6574 4.271291 CCTGCTCTTTTTAGATAGCGAACC 59.729 45.833 0.00 0.00 37.80 3.62
2601 6579 4.628333 TCTTTTTAGATAGCGAACCAACGG 59.372 41.667 0.00 0.00 0.00 4.44
2606 9491 0.107897 ATAGCGAACCAACGGCATCA 60.108 50.000 0.00 0.00 0.00 3.07
2624 9509 3.245518 TCATCCAATGTGACAGTACCG 57.754 47.619 0.00 0.00 0.00 4.02
2797 9971 3.757248 CTAGGCGCCGGCATCCTTT 62.757 63.158 33.67 18.61 42.47 3.11
2845 10020 8.160521 TGATAAAATTTCAGAAACTGTCGGAA 57.839 30.769 0.00 0.00 38.48 4.30
2846 10021 8.073768 TGATAAAATTTCAGAAACTGTCGGAAC 58.926 33.333 0.00 0.00 39.74 3.62
2871 10355 8.933807 ACGAGCATCTGATGATAATGATTTAAG 58.066 33.333 21.30 0.77 0.00 1.85
2898 10382 7.387265 TGAGGTGTATATGGTGTGGATATTT 57.613 36.000 0.00 0.00 0.00 1.40
2906 10390 9.231297 GTATATGGTGTGGATATTTGCAGTAAT 57.769 33.333 0.00 0.00 0.00 1.89
2964 10448 0.318441 CACTCGTCCAGAAGCCAAGA 59.682 55.000 0.00 0.00 0.00 3.02
2965 10449 1.048601 ACTCGTCCAGAAGCCAAGAA 58.951 50.000 0.00 0.00 0.00 2.52
2966 10450 1.416401 ACTCGTCCAGAAGCCAAGAAA 59.584 47.619 0.00 0.00 0.00 2.52
2967 10451 1.801178 CTCGTCCAGAAGCCAAGAAAC 59.199 52.381 0.00 0.00 0.00 2.78
2968 10452 1.140052 TCGTCCAGAAGCCAAGAAACA 59.860 47.619 0.00 0.00 0.00 2.83
2969 10453 1.532868 CGTCCAGAAGCCAAGAAACAG 59.467 52.381 0.00 0.00 0.00 3.16
2970 10454 1.882623 GTCCAGAAGCCAAGAAACAGG 59.117 52.381 0.00 0.00 0.00 4.00
2971 10455 1.202927 TCCAGAAGCCAAGAAACAGGG 60.203 52.381 0.00 0.00 0.00 4.45
2972 10456 1.251251 CAGAAGCCAAGAAACAGGGG 58.749 55.000 0.00 0.00 0.00 4.79
2973 10457 0.113190 AGAAGCCAAGAAACAGGGGG 59.887 55.000 0.00 0.00 0.00 5.40
3014 10498 3.051081 AGGAAGACAGCTGCTAGTTTG 57.949 47.619 15.27 0.00 0.00 2.93
3035 11062 5.606348 TGGAATAGCAAACAAAACCAAGT 57.394 34.783 0.00 0.00 0.00 3.16
3036 11063 5.983540 TGGAATAGCAAACAAAACCAAGTT 58.016 33.333 0.00 0.00 0.00 2.66
3037 11064 5.814705 TGGAATAGCAAACAAAACCAAGTTG 59.185 36.000 0.00 0.00 0.00 3.16
3038 11065 5.815222 GGAATAGCAAACAAAACCAAGTTGT 59.185 36.000 1.45 0.00 40.92 3.32
3040 11067 3.249917 AGCAAACAAAACCAAGTTGTCG 58.750 40.909 1.45 0.00 38.24 4.35
3054 11081 5.388475 CCAAGTTGTCGATCGTCTAAAACTG 60.388 44.000 15.94 9.62 0.00 3.16
3063 11090 3.986277 TCGTCTAAAACTGACCAGAACC 58.014 45.455 3.76 0.00 0.00 3.62
3097 11124 6.743575 ACCAGAAAATACAGTACATTCAGC 57.256 37.500 0.00 0.00 0.00 4.26
3127 11154 5.063880 GCTAGACCTGAAACAAGAAGGAAA 58.936 41.667 0.00 0.00 34.97 3.13
3130 11157 5.694995 AGACCTGAAACAAGAAGGAAATCA 58.305 37.500 0.00 0.00 34.97 2.57
3137 13090 8.181904 TGAAACAAGAAGGAAATCATAAGCTT 57.818 30.769 3.48 3.48 0.00 3.74
3157 13110 8.877808 AAGCTTTATTTTTCTGAAGGAAACTG 57.122 30.769 0.00 0.00 42.80 3.16
3172 13125 2.751166 AACTGCTTGCTATGTCGACT 57.249 45.000 17.92 4.95 0.00 4.18
3177 13130 3.599343 TGCTTGCTATGTCGACTTGAAT 58.401 40.909 17.92 4.15 0.00 2.57
3178 13131 4.754322 TGCTTGCTATGTCGACTTGAATA 58.246 39.130 17.92 5.18 0.00 1.75
3218 13171 0.097674 GGCAATGCGCTCTGTTACAG 59.902 55.000 9.73 5.94 41.91 2.74
3222 13175 3.302740 GCAATGCGCTCTGTTACAGTATC 60.303 47.826 12.41 2.29 37.77 2.24
3223 13176 2.579207 TGCGCTCTGTTACAGTATCC 57.421 50.000 12.41 1.29 32.61 2.59
3226 13179 2.224066 GCGCTCTGTTACAGTATCCCAT 60.224 50.000 12.41 0.00 32.61 4.00
3227 13180 3.005472 GCGCTCTGTTACAGTATCCCATA 59.995 47.826 12.41 0.00 32.61 2.74
3228 13181 4.500887 GCGCTCTGTTACAGTATCCCATAA 60.501 45.833 12.41 0.00 32.61 1.90
3229 13182 4.982916 CGCTCTGTTACAGTATCCCATAAC 59.017 45.833 12.41 0.00 32.61 1.89
3230 13183 5.451381 CGCTCTGTTACAGTATCCCATAACA 60.451 44.000 12.41 0.00 36.40 2.41
3231 13184 5.753921 GCTCTGTTACAGTATCCCATAACAC 59.246 44.000 12.41 0.00 34.63 3.32
3232 13185 6.407074 GCTCTGTTACAGTATCCCATAACACT 60.407 42.308 12.41 0.00 34.63 3.55
3233 13186 7.201884 GCTCTGTTACAGTATCCCATAACACTA 60.202 40.741 12.41 0.00 34.63 2.74
3235 13188 6.812998 TGTTACAGTATCCCATAACACTAGC 58.187 40.000 0.00 0.00 33.67 3.42
3236 13189 6.610020 TGTTACAGTATCCCATAACACTAGCT 59.390 38.462 0.00 0.00 33.67 3.32
3237 13190 7.781219 TGTTACAGTATCCCATAACACTAGCTA 59.219 37.037 0.00 0.00 33.67 3.32
3238 13191 8.804204 GTTACAGTATCCCATAACACTAGCTAT 58.196 37.037 0.00 0.00 0.00 2.97
3240 13193 8.582657 ACAGTATCCCATAACACTAGCTATAG 57.417 38.462 0.00 0.00 34.96 1.31
3241 13194 7.122948 ACAGTATCCCATAACACTAGCTATAGC 59.877 40.741 17.33 17.33 42.49 2.97
3243 13196 5.723672 TCCCATAACACTAGCTATAGCAC 57.276 43.478 26.07 0.00 45.16 4.40
3244 13197 5.144832 TCCCATAACACTAGCTATAGCACA 58.855 41.667 26.07 12.55 45.16 4.57
3245 13198 5.780282 TCCCATAACACTAGCTATAGCACAT 59.220 40.000 26.07 8.78 45.16 3.21
3246 13199 6.270000 TCCCATAACACTAGCTATAGCACATT 59.730 38.462 26.07 14.30 45.16 2.71
3247 13200 6.591834 CCCATAACACTAGCTATAGCACATTC 59.408 42.308 26.07 0.00 45.16 2.67
3248 13201 7.154656 CCATAACACTAGCTATAGCACATTCA 58.845 38.462 26.07 6.42 45.16 2.57
3249 13202 7.657354 CCATAACACTAGCTATAGCACATTCAA 59.343 37.037 26.07 7.51 45.16 2.69
3250 13203 8.706936 CATAACACTAGCTATAGCACATTCAAG 58.293 37.037 26.07 12.87 45.16 3.02
3252 13205 6.276847 ACACTAGCTATAGCACATTCAAGAC 58.723 40.000 26.07 0.00 45.16 3.01
3253 13206 5.694006 CACTAGCTATAGCACATTCAAGACC 59.306 44.000 26.07 0.00 45.16 3.85
3256 13209 4.406972 AGCTATAGCACATTCAAGACCTGA 59.593 41.667 26.07 0.00 45.16 3.86
3257 13210 4.509600 GCTATAGCACATTCAAGACCTGAC 59.490 45.833 20.01 0.00 41.59 3.51
3258 13211 2.936919 AGCACATTCAAGACCTGACA 57.063 45.000 0.00 0.00 32.21 3.58
3259 13212 3.213206 AGCACATTCAAGACCTGACAA 57.787 42.857 0.00 0.00 32.21 3.18
3260 13213 3.759581 AGCACATTCAAGACCTGACAAT 58.240 40.909 0.00 0.00 32.21 2.71
3261 13214 4.910195 AGCACATTCAAGACCTGACAATA 58.090 39.130 0.00 0.00 32.21 1.90
3262 13215 5.503927 AGCACATTCAAGACCTGACAATAT 58.496 37.500 0.00 0.00 32.21 1.28
3263 13216 5.948162 AGCACATTCAAGACCTGACAATATT 59.052 36.000 0.00 0.00 32.21 1.28
3264 13217 6.032094 GCACATTCAAGACCTGACAATATTG 58.968 40.000 14.01 14.01 32.21 1.90
3265 13218 6.558009 CACATTCAAGACCTGACAATATTGG 58.442 40.000 19.37 4.29 32.21 3.16
3266 13219 6.375174 CACATTCAAGACCTGACAATATTGGA 59.625 38.462 19.37 4.99 32.21 3.53
3268 13221 5.102953 TCAAGACCTGACAATATTGGAGG 57.897 43.478 24.27 24.27 37.72 4.30
3269 13222 4.536090 TCAAGACCTGACAATATTGGAGGT 59.464 41.667 28.60 28.60 43.66 3.85
3272 13225 4.222124 ACCTGACAATATTGGAGGTCAC 57.778 45.455 25.24 8.84 39.55 3.67
3274 13227 4.289672 ACCTGACAATATTGGAGGTCACTT 59.710 41.667 25.24 10.81 39.55 3.16
3275 13228 4.878397 CCTGACAATATTGGAGGTCACTTC 59.122 45.833 19.37 5.36 35.51 3.01
3276 13229 4.843728 TGACAATATTGGAGGTCACTTCC 58.156 43.478 19.37 0.00 35.51 3.46
3277 13230 3.871594 GACAATATTGGAGGTCACTTCCG 59.128 47.826 19.37 0.00 0.00 4.30
3281 13234 0.105964 TTGGAGGTCACTTCCGTGTG 59.894 55.000 0.74 0.00 41.89 3.82
3282 13235 0.757561 TGGAGGTCACTTCCGTGTGA 60.758 55.000 0.74 0.00 43.72 3.58
3289 13242 2.223377 GTCACTTCCGTGTGAAATCCAC 59.777 50.000 5.02 0.00 46.77 4.02
3415 13368 2.426024 TGAGTCTGGTTGCTATACGGAC 59.574 50.000 6.65 6.65 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.613012 GGGAAAGACATGCCAGGCTT 60.613 55.000 14.15 2.78 0.00 4.35
32 33 2.097038 CAGAAGTGCGCTCCTTCCG 61.097 63.158 26.24 17.89 39.29 4.30
89 90 2.202756 GATTCTCGCGACCGCCTT 60.203 61.111 3.71 0.00 37.98 4.35
98 99 1.886777 GCAGAGCCTGGATTCTCGC 60.887 63.158 0.00 3.11 34.66 5.03
99 100 1.591059 CGCAGAGCCTGGATTCTCG 60.591 63.158 0.00 2.62 34.66 4.04
100 101 1.227497 CCGCAGAGCCTGGATTCTC 60.227 63.158 0.00 0.00 31.21 2.87
101 102 1.992277 ACCGCAGAGCCTGGATTCT 60.992 57.895 0.00 0.00 31.21 2.40
102 103 1.817099 CACCGCAGAGCCTGGATTC 60.817 63.158 0.00 0.00 31.21 2.52
103 104 2.270205 CACCGCAGAGCCTGGATT 59.730 61.111 0.00 0.00 31.21 3.01
104 105 4.479993 GCACCGCAGAGCCTGGAT 62.480 66.667 0.00 0.00 31.21 3.41
111 112 4.694233 AGCAGTGGCACCGCAGAG 62.694 66.667 26.19 6.09 44.61 3.35
112 113 4.994471 CAGCAGTGGCACCGCAGA 62.994 66.667 26.19 0.00 44.61 4.26
113 114 4.994471 TCAGCAGTGGCACCGCAG 62.994 66.667 26.19 19.06 44.61 5.18
114 115 4.994471 CTCAGCAGTGGCACCGCA 62.994 66.667 26.19 7.13 44.61 5.69
116 117 4.694233 AGCTCAGCAGTGGCACCG 62.694 66.667 15.27 4.97 44.61 4.94
117 118 3.054503 CAGCTCAGCAGTGGCACC 61.055 66.667 15.27 0.00 44.61 5.01
138 139 0.940126 CAAGCAACGACTTCAGTGCT 59.060 50.000 0.00 0.00 0.00 4.40
191 192 6.505048 TGACCTGATATTCATCTCCACAAT 57.495 37.500 0.00 0.00 31.93 2.71
194 195 4.754114 GCTTGACCTGATATTCATCTCCAC 59.246 45.833 0.00 0.00 31.93 4.02
229 230 7.086376 CGAAATTGTCACATCTTCTGGATTTT 58.914 34.615 0.00 0.00 31.27 1.82
259 260 6.311690 GGTCTATTTGTGCTAGTTCAGTCTTC 59.688 42.308 0.00 0.00 0.00 2.87
401 402 6.016777 CACTCAAGGAAAAGATGTGCTACTTT 60.017 38.462 0.00 0.00 37.85 2.66
402 403 5.471456 CACTCAAGGAAAAGATGTGCTACTT 59.529 40.000 0.00 0.00 0.00 2.24
405 406 5.227569 TCACTCAAGGAAAAGATGTGCTA 57.772 39.130 0.00 0.00 0.00 3.49
407 408 4.456911 TCATCACTCAAGGAAAAGATGTGC 59.543 41.667 0.00 0.00 35.56 4.57
408 409 5.704515 ACTCATCACTCAAGGAAAAGATGTG 59.295 40.000 0.00 0.00 35.56 3.21
409 410 5.704515 CACTCATCACTCAAGGAAAAGATGT 59.295 40.000 0.00 0.00 35.56 3.06
410 411 5.936372 TCACTCATCACTCAAGGAAAAGATG 59.064 40.000 0.00 0.00 35.42 2.90
411 412 6.119240 TCACTCATCACTCAAGGAAAAGAT 57.881 37.500 0.00 0.00 0.00 2.40
412 413 5.551305 TCACTCATCACTCAAGGAAAAGA 57.449 39.130 0.00 0.00 0.00 2.52
413 414 5.528690 TGTTCACTCATCACTCAAGGAAAAG 59.471 40.000 0.00 0.00 0.00 2.27
515 516 2.349886 GACAAGCCAACTATTCGAGCAG 59.650 50.000 0.00 0.00 0.00 4.24
683 691 2.032030 CGACAAACTTGGTAGGCAACAG 60.032 50.000 0.00 0.00 41.41 3.16
707 732 2.715046 TCATCAGATGCAACTTGGACC 58.285 47.619 5.41 0.00 0.00 4.46
1213 1539 1.227380 GAGCTCGGTACATGGCCTG 60.227 63.158 3.32 2.01 0.00 4.85
1624 2012 2.933056 GCAATATAGAGGAGAAGCGCCC 60.933 54.545 2.29 0.00 0.00 6.13
1625 2013 2.289072 TGCAATATAGAGGAGAAGCGCC 60.289 50.000 2.29 0.00 0.00 6.53
1684 2072 5.669447 ACATCATCCCTTTCATAGTCCTTCT 59.331 40.000 0.00 0.00 0.00 2.85
1776 2164 1.453155 TGCTTCCTCTTCCAATTCGC 58.547 50.000 0.00 0.00 0.00 4.70
1944 2332 1.950828 ATTCATCTGCGAGCTGAAGG 58.049 50.000 8.64 5.05 34.35 3.46
2086 2476 7.938140 CATACATGGAGAGGTTCCTTTTAAA 57.062 36.000 0.00 0.00 46.92 1.52
2340 6263 1.060713 CCTGAGCACGACTTGTAACG 58.939 55.000 0.00 0.00 0.00 3.18
2461 6409 7.447374 TGAACACATCCGTTTATTCTGAATT 57.553 32.000 8.38 0.00 0.00 2.17
2509 6487 8.089597 TGGTACGTTAACTGAAATCATTAGTGA 58.910 33.333 3.71 0.00 39.04 3.41
2510 6488 8.246908 TGGTACGTTAACTGAAATCATTAGTG 57.753 34.615 3.71 0.00 0.00 2.74
2522 6500 8.296799 TGTACAAGTTTATGGTACGTTAACTG 57.703 34.615 3.71 0.09 40.10 3.16
2562 6540 0.610232 AAGAGCAGGTGGTGGATTGC 60.610 55.000 0.00 0.00 36.83 3.56
2564 6542 2.683211 AAAAGAGCAGGTGGTGGATT 57.317 45.000 0.00 0.00 0.00 3.01
2596 6574 1.744522 TCACATTGGATGATGCCGTTG 59.255 47.619 0.00 0.00 0.00 4.10
2601 6579 3.313526 GGTACTGTCACATTGGATGATGC 59.686 47.826 0.00 0.00 0.00 3.91
2606 9491 2.832129 AGTCGGTACTGTCACATTGGAT 59.168 45.455 0.64 0.00 33.57 3.41
2624 9509 6.205270 GCTAGTGATAGTAAGGAGTGGTAGTC 59.795 46.154 0.00 0.00 0.00 2.59
2797 9971 2.363306 TTTTCTGCTTTCAGCCTGGA 57.637 45.000 0.00 0.00 41.51 3.86
2840 10015 1.102978 TCATCAGATGCTCGTTCCGA 58.897 50.000 5.41 0.00 0.00 4.55
2841 10016 2.145958 ATCATCAGATGCTCGTTCCG 57.854 50.000 5.41 0.00 31.91 4.30
2845 10020 8.837788 TTAAATCATTATCATCAGATGCTCGT 57.162 30.769 5.41 0.00 35.67 4.18
2846 10021 8.933807 ACTTAAATCATTATCATCAGATGCTCG 58.066 33.333 5.41 0.00 35.67 5.03
2871 10355 4.839121 TCCACACCATATACACCTCAAAC 58.161 43.478 0.00 0.00 0.00 2.93
2882 10366 9.979897 ATATTACTGCAAATATCCACACCATAT 57.020 29.630 0.00 0.00 27.97 1.78
2883 10367 9.448438 GATATTACTGCAAATATCCACACCATA 57.552 33.333 15.80 0.00 40.59 2.74
2898 10382 3.455910 AGGAGGCTGTTGATATTACTGCA 59.544 43.478 16.79 0.00 40.80 4.41
2906 10390 1.833630 CAGGTCAGGAGGCTGTTGATA 59.166 52.381 0.00 0.00 0.00 2.15
2936 10420 1.107114 CTGGACGAGTGCTAGGATGT 58.893 55.000 0.00 0.00 0.00 3.06
2942 10426 0.898326 TGGCTTCTGGACGAGTGCTA 60.898 55.000 0.00 0.00 0.00 3.49
2971 10455 4.776349 ACAAGAAATTGTTTTTGTCCCCC 58.224 39.130 0.00 0.00 0.00 5.40
2972 10456 5.989168 CCTACAAGAAATTGTTTTTGTCCCC 59.011 40.000 0.00 0.00 35.55 4.81
2973 10457 6.811954 TCCTACAAGAAATTGTTTTTGTCCC 58.188 36.000 0.00 0.00 35.55 4.46
2974 10458 8.194769 TCTTCCTACAAGAAATTGTTTTTGTCC 58.805 33.333 0.00 0.00 35.55 4.02
2975 10459 9.020813 GTCTTCCTACAAGAAATTGTTTTTGTC 57.979 33.333 0.00 0.00 35.55 3.18
2976 10460 8.527810 TGTCTTCCTACAAGAAATTGTTTTTGT 58.472 29.630 0.00 1.68 37.51 2.83
2977 10461 8.925161 TGTCTTCCTACAAGAAATTGTTTTTG 57.075 30.769 0.00 0.00 36.44 2.44
2978 10462 7.706607 GCTGTCTTCCTACAAGAAATTGTTTTT 59.293 33.333 0.00 0.00 36.44 1.94
2979 10463 7.068716 AGCTGTCTTCCTACAAGAAATTGTTTT 59.931 33.333 0.00 0.00 36.44 2.43
3014 10498 5.815222 ACAACTTGGTTTTGTTTGCTATTCC 59.185 36.000 0.00 0.00 33.23 3.01
3025 11052 3.247648 AGACGATCGACAACTTGGTTTTG 59.752 43.478 24.34 0.00 0.00 2.44
3035 11062 4.232221 GGTCAGTTTTAGACGATCGACAA 58.768 43.478 24.34 9.31 36.87 3.18
3036 11063 3.253921 TGGTCAGTTTTAGACGATCGACA 59.746 43.478 24.34 2.80 36.87 4.35
3037 11064 3.829948 TGGTCAGTTTTAGACGATCGAC 58.170 45.455 24.34 16.66 36.87 4.20
3038 11065 3.754850 TCTGGTCAGTTTTAGACGATCGA 59.245 43.478 24.34 0.00 36.87 3.59
3040 11067 4.626172 GGTTCTGGTCAGTTTTAGACGATC 59.374 45.833 0.00 0.00 36.87 3.69
3054 11081 1.003718 CCACCCTTCGGTTCTGGTC 60.004 63.158 0.00 0.00 42.04 4.02
3063 11090 1.975660 TTTTCTGGTTCCACCCTTCG 58.024 50.000 0.00 0.00 37.50 3.79
3068 11095 5.310451 TGTACTGTATTTTCTGGTTCCACC 58.690 41.667 0.00 0.00 39.22 4.61
3112 11139 7.765695 AGCTTATGATTTCCTTCTTGTTTCA 57.234 32.000 0.00 0.00 0.00 2.69
3137 13090 6.701400 GCAAGCAGTTTCCTTCAGAAAAATAA 59.299 34.615 0.00 0.00 45.93 1.40
3139 13092 5.052481 GCAAGCAGTTTCCTTCAGAAAAAT 58.948 37.500 0.00 0.00 45.93 1.82
3157 13110 5.718649 TTATTCAAGTCGACATAGCAAGC 57.281 39.130 19.50 0.00 0.00 4.01
3199 13152 2.541612 ACTGTAACAGAGCGCATTGCC 61.542 52.381 11.47 0.00 38.59 4.52
3218 13171 7.093902 TGTGCTATAGCTAGTGTTATGGGATAC 60.094 40.741 24.61 9.53 42.66 2.24
3222 13175 5.468540 TGTGCTATAGCTAGTGTTATGGG 57.531 43.478 24.61 0.00 42.66 4.00
3223 13176 7.154656 TGAATGTGCTATAGCTAGTGTTATGG 58.845 38.462 24.61 0.00 42.66 2.74
3226 13179 7.921214 GTCTTGAATGTGCTATAGCTAGTGTTA 59.079 37.037 24.61 0.21 42.66 2.41
3227 13180 6.758886 GTCTTGAATGTGCTATAGCTAGTGTT 59.241 38.462 24.61 12.36 42.66 3.32
3228 13181 6.276847 GTCTTGAATGTGCTATAGCTAGTGT 58.723 40.000 24.61 7.18 42.66 3.55
3229 13182 5.694006 GGTCTTGAATGTGCTATAGCTAGTG 59.306 44.000 24.61 7.76 42.66 2.74
3230 13183 5.600484 AGGTCTTGAATGTGCTATAGCTAGT 59.400 40.000 24.61 13.33 42.66 2.57
3231 13184 5.925397 CAGGTCTTGAATGTGCTATAGCTAG 59.075 44.000 24.61 10.60 42.66 3.42
3232 13185 5.598417 TCAGGTCTTGAATGTGCTATAGCTA 59.402 40.000 24.61 14.41 35.83 3.32
3233 13186 4.406972 TCAGGTCTTGAATGTGCTATAGCT 59.593 41.667 24.61 5.05 35.83 3.32
3235 13188 5.664457 TGTCAGGTCTTGAATGTGCTATAG 58.336 41.667 0.00 0.00 37.61 1.31
3236 13189 5.675684 TGTCAGGTCTTGAATGTGCTATA 57.324 39.130 0.00 0.00 37.61 1.31
3237 13190 4.558226 TGTCAGGTCTTGAATGTGCTAT 57.442 40.909 0.00 0.00 37.61 2.97
3238 13191 4.350368 TTGTCAGGTCTTGAATGTGCTA 57.650 40.909 0.00 0.00 37.61 3.49
3240 13193 5.824904 ATATTGTCAGGTCTTGAATGTGC 57.175 39.130 0.00 0.00 37.61 4.57
3241 13194 6.375174 TCCAATATTGTCAGGTCTTGAATGTG 59.625 38.462 14.25 0.00 37.61 3.21
3243 13196 6.039047 CCTCCAATATTGTCAGGTCTTGAATG 59.961 42.308 17.31 0.00 37.61 2.67
3244 13197 6.125029 CCTCCAATATTGTCAGGTCTTGAAT 58.875 40.000 17.31 0.00 37.61 2.57
3245 13198 5.014123 ACCTCCAATATTGTCAGGTCTTGAA 59.986 40.000 22.40 0.00 35.67 2.69
3246 13199 4.536090 ACCTCCAATATTGTCAGGTCTTGA 59.464 41.667 22.40 7.48 35.67 3.02
3247 13200 4.848357 ACCTCCAATATTGTCAGGTCTTG 58.152 43.478 22.40 4.08 35.67 3.02
3248 13201 4.536090 TGACCTCCAATATTGTCAGGTCTT 59.464 41.667 35.85 19.70 46.50 3.01
3249 13202 4.080863 GTGACCTCCAATATTGTCAGGTCT 60.081 45.833 35.85 20.17 46.50 3.85
3250 13203 4.080863 AGTGACCTCCAATATTGTCAGGTC 60.081 45.833 33.31 33.31 46.53 3.85
3252 13205 4.494091 AGTGACCTCCAATATTGTCAGG 57.506 45.455 21.42 21.42 38.32 3.86
3253 13206 4.878397 GGAAGTGACCTCCAATATTGTCAG 59.122 45.833 14.25 9.21 38.32 3.51
3256 13209 3.263425 ACGGAAGTGACCTCCAATATTGT 59.737 43.478 14.25 0.00 46.97 2.71
3257 13210 3.873910 ACGGAAGTGACCTCCAATATTG 58.126 45.455 8.58 8.58 46.97 1.90
3277 13230 2.392933 TTTTCGCGTGGATTTCACAC 57.607 45.000 5.77 0.00 46.36 3.82
3298 13251 7.280205 CCCATATTAGACGCTTTTTCTGTTAGT 59.720 37.037 0.00 0.00 0.00 2.24
3299 13252 7.630924 CCCATATTAGACGCTTTTTCTGTTAG 58.369 38.462 0.00 0.00 0.00 2.34
3300 13253 6.037830 GCCCATATTAGACGCTTTTTCTGTTA 59.962 38.462 0.00 0.00 0.00 2.41
3301 13254 5.163652 GCCCATATTAGACGCTTTTTCTGTT 60.164 40.000 0.00 0.00 0.00 3.16
3307 13260 3.886123 ACAGCCCATATTAGACGCTTTT 58.114 40.909 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.