Multiple sequence alignment - TraesCS2D01G046100

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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 TraesCS2D01G046100 chr2D 100.000 3685 0 0 1 3685 16887399 16883715 0.000000e+00 6806.0
1 TraesCS2D01G046100 chr2D 88.672 1386 103 19 1197 2566 16960418 16959071 0.000000e+00 1640.0
2 TraesCS2D01G046100 chr2D 86.720 1378 126 22 1 1338 16961808 16960448 0.000000e+00 1478.0
3 TraesCS2D01G046100 chr2D 81.368 1798 216 70 616 2347 16981817 16983561 0.000000e+00 1354.0
4 TraesCS2D01G046100 chr2D 85.506 959 91 23 1905 2851 16944388 16943466 0.000000e+00 957.0
5 TraesCS2D01G046100 chr2D 80.702 1083 143 32 1238 2294 16728924 16727882 0.000000e+00 782.0
6 TraesCS2D01G046100 chr2D 91.906 556 16 7 2693 3220 16878279 16877725 0.000000e+00 750.0
7 TraesCS2D01G046100 chr2D 84.288 751 59 23 2500 3220 16948066 16947345 0.000000e+00 678.0
8 TraesCS2D01G046100 chr2D 95.562 338 15 0 3215 3552 16867441 16867104 3.240000e-150 542.0
9 TraesCS2D01G046100 chr2D 81.588 554 70 19 2416 2964 16985424 16985950 2.630000e-116 429.0
10 TraesCS2D01G046100 chr2D 83.227 471 49 17 1152 1599 16895490 16895953 4.430000e-109 405.0
11 TraesCS2D01G046100 chr2D 84.701 268 34 5 3286 3552 16894666 16894405 1.020000e-65 261.0
12 TraesCS2D01G046100 chr2D 95.489 133 6 0 3553 3685 16867072 16866940 2.880000e-51 213.0
13 TraesCS2D01G046100 chr2D 95.385 130 6 0 3553 3682 16981304 16981175 1.340000e-49 207.0
14 TraesCS2D01G046100 chr2D 90.526 95 8 1 3131 3224 16947271 16947177 1.390000e-24 124.0
15 TraesCS2D01G046100 chr2D 88.421 95 9 2 3127 3220 16877654 16877561 3.010000e-21 113.0
16 TraesCS2D01G046100 chr2D 91.463 82 7 0 3018 3099 16984083 16984164 3.010000e-21 113.0
17 TraesCS2D01G046100 chr2D 83.562 73 10 2 3215 3287 621364782 621364712 2.370000e-07 67.6
18 TraesCS2D01G046100 chr2A 90.461 3124 199 47 1 3093 18492987 18496042 0.000000e+00 4026.0
19 TraesCS2D01G046100 chr2A 80.239 1842 228 76 586 2350 18469420 18467638 0.000000e+00 1260.0
20 TraesCS2D01G046100 chr2A 81.949 554 67 20 2416 2964 18465780 18465255 4.370000e-119 438.0
21 TraesCS2D01G046100 chr2A 80.522 498 65 20 34 514 64331669 64331187 1.630000e-93 353.0
22 TraesCS2D01G046100 chr2A 93.284 134 8 1 3553 3685 18469930 18470063 2.900000e-46 196.0
23 TraesCS2D01G046100 chr2A 87.000 100 12 1 3018 3117 18467119 18467021 1.080000e-20 111.0
24 TraesCS2D01G046100 chr2B 86.136 1933 175 44 1197 3110 28841889 28840031 0.000000e+00 1999.0
25 TraesCS2D01G046100 chr2B 81.807 2358 251 91 583 2880 28873588 28875827 0.000000e+00 1814.0
26 TraesCS2D01G046100 chr2B 85.166 1382 144 29 1 1340 28843279 28841917 0.000000e+00 1360.0
27 TraesCS2D01G046100 chr2B 77.086 1414 189 69 955 2294 28813919 28812567 0.000000e+00 691.0
28 TraesCS2D01G046100 chr2B 81.115 556 72 22 2416 2964 28877212 28877741 7.360000e-112 414.0
29 TraesCS2D01G046100 chr2B 92.565 269 20 0 3286 3554 28873378 28873110 1.610000e-103 387.0
30 TraesCS2D01G046100 chr2B 81.141 403 52 18 620 1001 28814317 28813918 5.980000e-78 302.0
31 TraesCS2D01G046100 chr2B 86.000 100 8 4 3126 3220 28839819 28839721 6.510000e-18 102.0
32 TraesCS2D01G046100 chr2B 89.024 82 9 0 3018 3099 28875867 28875948 6.510000e-18 102.0
33 TraesCS2D01G046100 chrUn 86.172 1186 117 29 1793 2968 361988638 361989786 0.000000e+00 1238.0
34 TraesCS2D01G046100 chrUn 76.571 1639 232 81 740 2277 373680789 373682376 0.000000e+00 760.0
35 TraesCS2D01G046100 chrUn 95.562 338 15 0 3215 3552 24227617 24227280 3.240000e-150 542.0
36 TraesCS2D01G046100 chrUn 77.852 596 76 32 746 1301 470129122 470128543 5.940000e-83 318.0
37 TraesCS2D01G046100 chrUn 95.489 133 6 0 3553 3685 24227248 24227116 2.880000e-51 213.0
38 TraesCS2D01G046100 chr7B 78.454 1759 193 92 621 2290 584224199 584225860 0.000000e+00 977.0
39 TraesCS2D01G046100 chr7B 78.947 494 82 11 38 514 624338234 624337746 2.140000e-82 316.0
40 TraesCS2D01G046100 chr7A 80.251 876 111 34 1307 2160 622806028 622806863 1.460000e-168 603.0
41 TraesCS2D01G046100 chr7A 80.091 879 119 30 1307 2160 622938712 622939559 1.460000e-168 603.0
42 TraesCS2D01G046100 chr7A 79.680 876 110 40 1307 2160 622819865 622820694 1.480000e-158 569.0
43 TraesCS2D01G046100 chr7A 76.937 1097 113 57 686 1722 622832991 622834007 2.560000e-136 496.0
44 TraesCS2D01G046100 chr6D 80.321 498 76 12 34 514 218127503 218127011 1.260000e-94 357.0
45 TraesCS2D01G046100 chr4B 80.000 510 81 11 22 514 620271391 620271896 1.260000e-94 357.0
46 TraesCS2D01G046100 chr4B 82.432 74 10 3 3215 3288 585824545 585824615 1.100000e-05 62.1
47 TraesCS2D01G046100 chr7D 81.591 440 72 8 11 444 568379502 568379938 4.530000e-94 355.0
48 TraesCS2D01G046100 chr7D 100.000 38 0 0 535 572 60523736 60523773 1.840000e-08 71.3
49 TraesCS2D01G046100 chr3D 81.141 403 69 6 23 423 20869039 20869436 2.140000e-82 316.0
50 TraesCS2D01G046100 chr3D 78.788 198 29 9 3346 3538 519176920 519176731 1.800000e-23 121.0
51 TraesCS2D01G046100 chr3D 100.000 38 0 0 535 572 87508678 87508715 1.840000e-08 71.3
52 TraesCS2D01G046100 chr6B 77.909 507 89 13 26 514 362876378 362876879 1.000000e-75 294.0
53 TraesCS2D01G046100 chr6B 97.561 41 1 0 535 575 698672187 698672147 1.840000e-08 71.3
54 TraesCS2D01G046100 chr3A 91.026 78 7 0 3220 3297 327124331 327124254 5.030000e-19 106.0
55 TraesCS2D01G046100 chr3A 89.474 76 6 2 3215 3290 706015220 706015147 1.090000e-15 95.3
56 TraesCS2D01G046100 chr3A 86.667 75 8 2 3213 3287 708069667 708069739 8.480000e-12 82.4
57 TraesCS2D01G046100 chr3A 86.111 72 8 2 3215 3286 127915104 127915173 3.950000e-10 76.8
58 TraesCS2D01G046100 chr4A 86.667 75 8 2 3213 3287 182121589 182121517 8.480000e-12 82.4
59 TraesCS2D01G046100 chr5D 97.561 41 1 0 535 575 271172233 271172193 1.840000e-08 71.3
60 TraesCS2D01G046100 chr4D 100.000 38 0 0 535 572 437128513 437128550 1.840000e-08 71.3
61 TraesCS2D01G046100 chr3B 97.561 41 1 0 535 575 468543128 468543088 1.840000e-08 71.3
62 TraesCS2D01G046100 chr3B 100.000 37 0 0 535 571 28659184 28659220 6.600000e-08 69.4
63 TraesCS2D01G046100 chr1B 97.561 41 1 0 535 575 674750415 674750375 1.840000e-08 71.3
64 TraesCS2D01G046100 chr1D 100.000 29 0 0 3553 3581 298280747 298280719 2.000000e-03 54.7


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 TraesCS2D01G046100 chr2D 16883715 16887399 3684 True 6806.000000 6806 100.000000 1 3685 1 chr2D.!!$R2 3684
1 TraesCS2D01G046100 chr2D 16959071 16961808 2737 True 1559.000000 1640 87.696000 1 2566 2 chr2D.!!$R9 2565
2 TraesCS2D01G046100 chr2D 16727882 16728924 1042 True 782.000000 782 80.702000 1238 2294 1 chr2D.!!$R1 1056
3 TraesCS2D01G046100 chr2D 16981817 16985950 4133 False 632.000000 1354 84.806333 616 3099 3 chr2D.!!$F2 2483
4 TraesCS2D01G046100 chr2D 16943466 16948066 4600 True 586.333333 957 86.773333 1905 3224 3 chr2D.!!$R8 1319
5 TraesCS2D01G046100 chr2D 16877561 16878279 718 True 431.500000 750 90.163500 2693 3220 2 chr2D.!!$R7 527
6 TraesCS2D01G046100 chr2D 16866940 16867441 501 True 377.500000 542 95.525500 3215 3685 2 chr2D.!!$R6 470
7 TraesCS2D01G046100 chr2A 18492987 18496042 3055 False 4026.000000 4026 90.461000 1 3093 1 chr2A.!!$F2 3092
8 TraesCS2D01G046100 chr2A 18465255 18469420 4165 True 603.000000 1260 83.062667 586 3117 3 chr2A.!!$R2 2531
9 TraesCS2D01G046100 chr2B 28839721 28843279 3558 True 1153.666667 1999 85.767333 1 3220 3 chr2B.!!$R3 3219
10 TraesCS2D01G046100 chr2B 28873588 28877741 4153 False 776.666667 1814 83.982000 583 3099 3 chr2B.!!$F1 2516
11 TraesCS2D01G046100 chr2B 28812567 28814317 1750 True 496.500000 691 79.113500 620 2294 2 chr2B.!!$R2 1674
12 TraesCS2D01G046100 chrUn 361988638 361989786 1148 False 1238.000000 1238 86.172000 1793 2968 1 chrUn.!!$F1 1175
13 TraesCS2D01G046100 chrUn 373680789 373682376 1587 False 760.000000 760 76.571000 740 2277 1 chrUn.!!$F2 1537
14 TraesCS2D01G046100 chrUn 24227116 24227617 501 True 377.500000 542 95.525500 3215 3685 2 chrUn.!!$R2 470
15 TraesCS2D01G046100 chrUn 470128543 470129122 579 True 318.000000 318 77.852000 746 1301 1 chrUn.!!$R1 555
16 TraesCS2D01G046100 chr7B 584224199 584225860 1661 False 977.000000 977 78.454000 621 2290 1 chr7B.!!$F1 1669
17 TraesCS2D01G046100 chr7A 622806028 622806863 835 False 603.000000 603 80.251000 1307 2160 1 chr7A.!!$F1 853
18 TraesCS2D01G046100 chr7A 622938712 622939559 847 False 603.000000 603 80.091000 1307 2160 1 chr7A.!!$F4 853
19 TraesCS2D01G046100 chr7A 622819865 622820694 829 False 569.000000 569 79.680000 1307 2160 1 chr7A.!!$F2 853
20 TraesCS2D01G046100 chr7A 622832991 622834007 1016 False 496.000000 496 76.937000 686 1722 1 chr7A.!!$F3 1036
21 TraesCS2D01G046100 chr4B 620271391 620271896 505 False 357.000000 357 80.000000 22 514 1 chr4B.!!$F2 492
22 TraesCS2D01G046100 chr6B 362876378 362876879 501 False 294.000000 294 77.909000 26 514 1 chr6B.!!$F1 488

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
274 283 2.060370 AAAAACCCTCCGTAGCCGA 58.940 52.632 0.0 0.0 35.63 5.54 F
2149 3942 0.470766 TGCTGGTGGTTCGTAGGTTT 59.529 50.000 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 3967 1.271379 CTGGAACACTGCATTGCACAT 59.729 47.619 7.38 0.0 33.79 3.21 R
3403 7506 0.035458 CCGTTCTTGGCTCTGGTCTT 59.965 55.000 0.00 0.0 0.00 3.01 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
274 283 2.060370 AAAAACCCTCCGTAGCCGA 58.940 52.632 0.00 0.00 35.63 5.54
361 371 2.240040 GTACGAAGCGAGTGTGTACAG 58.760 52.381 0.00 0.00 36.35 2.74
391 401 3.920231 ACCTGCAGATGAGAAGCATTA 57.080 42.857 17.39 0.00 37.34 1.90
447 471 2.443958 AGGGAGCAAAATAGGCCTTC 57.556 50.000 12.58 0.00 0.00 3.46
851 910 4.328983 GCGAATCATCCGTAGAAGTTTGAA 59.671 41.667 0.00 0.00 0.00 2.69
1427 1945 2.804090 GCGACGTGACGGACTTCC 60.804 66.667 10.66 0.00 0.00 3.46
1555 2088 1.756538 CAAGGTGAGCAAACCAGGTTT 59.243 47.619 12.23 12.23 43.20 3.27
1657 2190 3.073735 CTCTGCGCCTCACCCTCT 61.074 66.667 4.18 0.00 0.00 3.69
2149 3942 0.470766 TGCTGGTGGTTCGTAGGTTT 59.529 50.000 0.00 0.00 0.00 3.27
2304 4099 0.458543 ACGCAATGAGCTAGTGTCCG 60.459 55.000 0.00 0.00 42.61 4.79
2306 4101 1.281899 GCAATGAGCTAGTGTCCGAC 58.718 55.000 0.00 0.00 41.15 4.79
2310 4108 4.744570 CAATGAGCTAGTGTCCGACTTAA 58.255 43.478 0.00 0.00 35.96 1.85
2312 4110 5.599999 ATGAGCTAGTGTCCGACTTAATT 57.400 39.130 0.00 0.00 35.96 1.40
2322 4120 8.019656 AGTGTCCGACTTAATTATTACCAGAT 57.980 34.615 0.00 0.00 0.00 2.90
2323 4121 8.142551 AGTGTCCGACTTAATTATTACCAGATC 58.857 37.037 0.00 0.00 0.00 2.75
2324 4122 7.114529 GTGTCCGACTTAATTATTACCAGATCG 59.885 40.741 0.00 0.00 0.00 3.69
2325 4123 6.585322 GTCCGACTTAATTATTACCAGATCGG 59.415 42.308 14.35 14.35 45.17 4.18
2342 4140 2.600790 TCGGTCTCAGGGAAAAGTGTA 58.399 47.619 0.00 0.00 0.00 2.90
2350 4148 4.894784 TCAGGGAAAAGTGTACTCACATC 58.105 43.478 0.00 0.00 46.01 3.06
2351 4149 4.346709 TCAGGGAAAAGTGTACTCACATCA 59.653 41.667 0.00 0.00 46.01 3.07
2352 4150 4.452455 CAGGGAAAAGTGTACTCACATCAC 59.548 45.833 0.00 0.00 46.01 3.06
2353 4151 4.102524 AGGGAAAAGTGTACTCACATCACA 59.897 41.667 0.00 0.00 46.01 3.58
2354 4152 4.452455 GGGAAAAGTGTACTCACATCACAG 59.548 45.833 0.00 0.00 46.01 3.66
2355 4153 4.083802 GGAAAAGTGTACTCACATCACAGC 60.084 45.833 0.00 0.00 46.01 4.40
2356 4154 3.751479 AAGTGTACTCACATCACAGCA 57.249 42.857 0.00 0.00 46.01 4.41
2357 4155 3.032017 AGTGTACTCACATCACAGCAC 57.968 47.619 0.00 0.00 46.01 4.40
2358 4156 2.365293 AGTGTACTCACATCACAGCACA 59.635 45.455 0.00 0.00 46.01 4.57
2359 4157 3.007290 AGTGTACTCACATCACAGCACAT 59.993 43.478 0.00 0.00 46.01 3.21
2361 4159 2.556144 ACTCACATCACAGCACATGT 57.444 45.000 0.00 0.00 45.43 3.21
2375 4173 5.068198 ACAGCACATGTTGAGAGATTTTGTT 59.932 36.000 4.54 0.00 39.96 2.83
2413 4214 1.993370 GCGAATGTATGGCTATCGTCC 59.007 52.381 0.00 0.00 36.01 4.79
2435 4236 3.482598 CGCTACTGAACAATTTGCTCTCG 60.483 47.826 0.00 0.00 0.00 4.04
2442 4243 6.016276 ACTGAACAATTTGCTCTCGGTTATTT 60.016 34.615 0.00 0.00 0.00 1.40
2443 4247 6.148948 TGAACAATTTGCTCTCGGTTATTTG 58.851 36.000 0.00 0.00 0.00 2.32
2444 4248 5.059404 ACAATTTGCTCTCGGTTATTTGG 57.941 39.130 0.00 0.00 0.00 3.28
2457 4261 8.102047 TCTCGGTTATTTGGTAATTCCTGTTTA 58.898 33.333 0.00 0.00 37.07 2.01
2461 4265 9.811995 GGTTATTTGGTAATTCCTGTTTAATCC 57.188 33.333 0.00 0.00 37.07 3.01
2517 4324 7.865820 TCAAGATAGATTTCTTCCTGGAACAT 58.134 34.615 4.68 0.00 33.23 2.71
2518 4325 7.772292 TCAAGATAGATTTCTTCCTGGAACATG 59.228 37.037 4.68 0.00 33.23 3.21
2519 4326 7.205515 AGATAGATTTCTTCCTGGAACATGT 57.794 36.000 4.68 0.00 38.20 3.21
2520 4327 8.324191 AGATAGATTTCTTCCTGGAACATGTA 57.676 34.615 4.68 2.02 38.20 2.29
2521 4328 8.207545 AGATAGATTTCTTCCTGGAACATGTAC 58.792 37.037 4.68 0.00 38.20 2.90
2591 4416 3.696548 GGAAGATTTCAGTTGGATGGACC 59.303 47.826 0.00 0.00 39.54 4.46
2617 4448 6.145338 TCTATTTCCACTCTTAACCTAGCG 57.855 41.667 0.00 0.00 0.00 4.26
2623 4454 3.693085 CCACTCTTAACCTAGCGACTGTA 59.307 47.826 0.00 0.00 0.00 2.74
2660 4492 5.587388 TTTCTTCAGGAATGCAATCCATC 57.413 39.130 22.75 1.22 42.27 3.51
2666 4498 5.319453 TCAGGAATGCAATCCATCTTATCC 58.681 41.667 22.75 3.06 42.27 2.59
2669 4501 1.896220 TGCAATCCATCTTATCCGGC 58.104 50.000 0.00 0.00 0.00 6.13
2675 4507 5.738909 CAATCCATCTTATCCGGCTAGAAT 58.261 41.667 0.00 0.00 0.00 2.40
2679 4511 5.306937 TCCATCTTATCCGGCTAGAATTTGA 59.693 40.000 0.00 0.00 0.00 2.69
2680 4512 6.013379 TCCATCTTATCCGGCTAGAATTTGAT 60.013 38.462 0.00 0.00 0.00 2.57
2681 4513 7.180229 TCCATCTTATCCGGCTAGAATTTGATA 59.820 37.037 0.00 0.00 0.00 2.15
2801 4638 0.461870 TGGATTCGCATTCCGTCTGG 60.462 55.000 0.00 0.00 35.94 3.86
2840 4679 7.291411 TCCTCTGCACTTCCTATCTTATTAC 57.709 40.000 0.00 0.00 0.00 1.89
2927 7030 3.181484 TGCAAACAGCCAGAATATGATGC 60.181 43.478 0.00 0.00 44.83 3.91
2943 7046 8.517062 AATATGATGCTGGATTTAAGATAGCC 57.483 34.615 0.00 0.00 33.60 3.93
2977 7080 7.894753 TGATAAATGGGCATTTCATTGTAGA 57.105 32.000 0.00 0.00 40.99 2.59
3021 7124 7.410120 TCTCTCTATGTCTAAAAGCATGACA 57.590 36.000 0.00 0.00 43.53 3.58
3028 7131 5.840715 TGTCTAAAAGCATGACATTTGCAA 58.159 33.333 0.00 0.00 42.62 4.08
3030 7133 6.421501 TGTCTAAAAGCATGACATTTGCAAAG 59.578 34.615 18.19 11.80 42.62 2.77
3055 7158 9.539825 AGTTATCTAATATGTCTGCTCAAACAG 57.460 33.333 0.00 0.00 39.12 3.16
3095 7198 9.647797 TTATTATTCACATGTACTGTTTCTCGT 57.352 29.630 0.00 0.00 35.29 4.18
3097 7200 9.647797 ATTATTCACATGTACTGTTTCTCGTAA 57.352 29.630 0.00 0.00 35.29 3.18
3098 7201 7.956420 ATTCACATGTACTGTTTCTCGTAAA 57.044 32.000 0.00 0.00 35.29 2.01
3099 7202 7.773864 TTCACATGTACTGTTTCTCGTAAAA 57.226 32.000 0.00 0.00 35.29 1.52
3100 7203 7.773864 TCACATGTACTGTTTCTCGTAAAAA 57.226 32.000 0.00 0.00 35.29 1.94
3101 7204 7.623770 TCACATGTACTGTTTCTCGTAAAAAC 58.376 34.615 0.00 0.00 35.29 2.43
3102 7205 7.493320 TCACATGTACTGTTTCTCGTAAAAACT 59.507 33.333 0.00 0.00 37.48 2.66
3103 7206 8.120465 CACATGTACTGTTTCTCGTAAAAACTT 58.880 33.333 0.00 2.86 37.48 2.66
3104 7207 8.120465 ACATGTACTGTTTCTCGTAAAAACTTG 58.880 33.333 0.00 0.00 37.48 3.16
3105 7208 7.599630 TGTACTGTTTCTCGTAAAAACTTGT 57.400 32.000 0.00 10.39 37.48 3.16
3106 7209 8.031848 TGTACTGTTTCTCGTAAAAACTTGTT 57.968 30.769 0.00 0.00 37.48 2.83
3107 7210 8.505625 TGTACTGTTTCTCGTAAAAACTTGTTT 58.494 29.630 0.00 0.00 37.48 2.83
3108 7211 7.790861 ACTGTTTCTCGTAAAAACTTGTTTG 57.209 32.000 0.00 0.00 37.48 2.93
3109 7212 7.364970 ACTGTTTCTCGTAAAAACTTGTTTGT 58.635 30.769 0.00 0.00 37.48 2.83
3110 7213 8.505625 ACTGTTTCTCGTAAAAACTTGTTTGTA 58.494 29.630 0.00 0.00 37.48 2.41
3111 7214 8.883789 TGTTTCTCGTAAAAACTTGTTTGTAG 57.116 30.769 0.00 0.00 37.48 2.74
3112 7215 7.482428 TGTTTCTCGTAAAAACTTGTTTGTAGC 59.518 33.333 0.00 0.00 37.48 3.58
3113 7216 6.913873 TCTCGTAAAAACTTGTTTGTAGCT 57.086 33.333 0.00 0.00 0.00 3.32
3114 7217 7.311364 TCTCGTAAAAACTTGTTTGTAGCTT 57.689 32.000 0.00 0.00 0.00 3.74
3115 7218 7.754625 TCTCGTAAAAACTTGTTTGTAGCTTT 58.245 30.769 0.00 0.00 0.00 3.51
3116 7219 8.881743 TCTCGTAAAAACTTGTTTGTAGCTTTA 58.118 29.630 0.00 0.00 0.00 1.85
3117 7220 9.155053 CTCGTAAAAACTTGTTTGTAGCTTTAG 57.845 33.333 0.00 0.00 0.00 1.85
3118 7221 8.124199 TCGTAAAAACTTGTTTGTAGCTTTAGG 58.876 33.333 0.00 1.08 0.00 2.69
3119 7222 7.911727 CGTAAAAACTTGTTTGTAGCTTTAGGT 59.088 33.333 0.00 0.00 0.00 3.08
3120 7223 9.577110 GTAAAAACTTGTTTGTAGCTTTAGGTT 57.423 29.630 0.00 0.00 0.00 3.50
3122 7225 9.496873 AAAAACTTGTTTGTAGCTTTAGGTTTT 57.503 25.926 0.00 0.00 35.58 2.43
3161 7264 7.219484 ACGAGAAATTTCATTGGATCAAACT 57.781 32.000 19.99 0.00 0.00 2.66
3162 7265 7.308435 ACGAGAAATTTCATTGGATCAAACTC 58.692 34.615 19.99 3.50 0.00 3.01
3163 7266 6.749118 CGAGAAATTTCATTGGATCAAACTCC 59.251 38.462 19.99 0.00 35.74 3.85
3164 7267 6.939622 AGAAATTTCATTGGATCAAACTCCC 58.060 36.000 19.99 0.00 34.12 4.30
3165 7268 6.727697 AGAAATTTCATTGGATCAAACTCCCT 59.272 34.615 19.99 0.00 34.12 4.20
3166 7269 7.895429 AGAAATTTCATTGGATCAAACTCCCTA 59.105 33.333 19.99 0.00 34.12 3.53
3167 7270 8.613922 AAATTTCATTGGATCAAACTCCCTAT 57.386 30.769 0.00 0.00 34.12 2.57
3168 7271 9.713684 AAATTTCATTGGATCAAACTCCCTATA 57.286 29.630 0.00 0.00 34.12 1.31
3169 7272 9.887862 AATTTCATTGGATCAAACTCCCTATAT 57.112 29.630 0.00 0.00 34.12 0.86
3204 7307 9.161629 TCATCGTATGATTAGTCAAATGTTTGT 57.838 29.630 5.48 0.00 38.01 2.83
3247 7350 7.524717 ACCAAATCCCACTATAATATGTTGC 57.475 36.000 0.00 0.00 0.00 4.17
3281 7384 1.967319 ACAATGTGCGGGGTATCATC 58.033 50.000 0.00 0.00 0.00 2.92
3325 7428 1.675483 AGATGACACAAACGCAAGCAA 59.325 42.857 0.00 0.00 45.62 3.91
3366 7469 1.485895 GCAGAGAGAGAAGGGATGCTT 59.514 52.381 0.00 0.00 0.00 3.91
3389 7492 3.554129 GGCCCAAACAAAGGATACAACAC 60.554 47.826 0.00 0.00 41.41 3.32
3403 7506 6.156256 AGGATACAACACAGCTAAACCTATCA 59.844 38.462 0.00 0.00 41.41 2.15
3442 7545 3.686016 GGCAATACTGAACCAGGAAGAA 58.314 45.455 0.00 0.00 35.51 2.52
3448 7551 6.783708 ATACTGAACCAGGAAGAAGACTAG 57.216 41.667 0.00 0.00 35.51 2.57
3449 7552 3.259625 ACTGAACCAGGAAGAAGACTAGC 59.740 47.826 0.00 0.00 35.51 3.42
3466 7569 2.758089 GCATCGCCAGAGCCAACAG 61.758 63.158 0.00 0.00 34.57 3.16
3505 7608 2.632377 TCAAAGATAGCGCCTTCAAGG 58.368 47.619 2.29 0.00 38.80 3.61
3575 7709 1.980772 AACTGAAGGCCATGGCAGC 60.981 57.895 36.56 24.31 44.11 5.25
3632 7766 2.742589 GGCAAGCTTTGAGGTGTACTAC 59.257 50.000 0.00 0.00 0.00 2.73
3640 7774 0.459078 GAGGTGTACTACGAAGGGCC 59.541 60.000 0.00 0.00 0.00 5.80
3641 7775 0.251922 AGGTGTACTACGAAGGGCCA 60.252 55.000 6.18 0.00 0.00 5.36
3677 7811 1.131126 CAATCACAAGGTGGATGCGAC 59.869 52.381 0.00 0.00 33.87 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 237 0.929244 ATGGGAGGCAGCATAACCTT 59.071 50.000 0.00 0.00 36.05 3.50
261 269 3.429925 GTAGTCGGCTACGGAGGG 58.570 66.667 12.08 0.00 38.30 4.30
274 283 0.242017 GTGTACGCGGTTGGAGTAGT 59.758 55.000 12.47 0.00 31.22 2.73
361 371 4.094887 TCTCATCTGCAGGTTATTTTTCGC 59.905 41.667 15.13 0.00 0.00 4.70
851 910 2.056906 GATGCCCATCCTACGGCCTT 62.057 60.000 0.00 0.00 45.07 4.35
896 969 6.231211 ACCTGATGTGACTTAATTTCTCGTT 58.769 36.000 0.00 0.00 0.00 3.85
923 998 1.300311 TGGTACGAACAGCACACCG 60.300 57.895 0.00 0.00 31.64 4.94
924 999 1.226030 GGTGGTACGAACAGCACACC 61.226 60.000 16.25 0.00 46.34 4.16
925 1000 0.249741 AGGTGGTACGAACAGCACAC 60.250 55.000 16.25 0.00 46.34 3.82
1148 1302 2.488355 CTTTCATGGCCGCTGCTG 59.512 61.111 0.00 0.00 37.74 4.41
1150 1304 3.056313 GACCTTTCATGGCCGCTGC 62.056 63.158 0.00 0.00 0.00 5.25
1427 1945 2.154798 TTGACGGTTCTCAGGCGGAG 62.155 60.000 8.46 8.46 45.49 4.63
2174 3967 1.271379 CTGGAACACTGCATTGCACAT 59.729 47.619 7.38 0.00 33.79 3.21
2290 4085 5.599999 AATTAAGTCGGACACTAGCTCAT 57.400 39.130 11.27 0.00 32.30 2.90
2295 4090 8.627403 TCTGGTAATAATTAAGTCGGACACTAG 58.373 37.037 11.27 4.02 32.30 2.57
2296 4091 8.523915 TCTGGTAATAATTAAGTCGGACACTA 57.476 34.615 11.27 0.00 32.30 2.74
2322 4120 1.420430 ACACTTTTCCCTGAGACCGA 58.580 50.000 0.00 0.00 0.00 4.69
2323 4121 2.299297 AGTACACTTTTCCCTGAGACCG 59.701 50.000 0.00 0.00 0.00 4.79
2324 4122 3.323979 TGAGTACACTTTTCCCTGAGACC 59.676 47.826 0.00 0.00 0.00 3.85
2325 4123 4.202223 TGTGAGTACACTTTTCCCTGAGAC 60.202 45.833 0.00 0.00 46.07 3.36
2342 4140 2.551032 CAACATGTGCTGTGATGTGAGT 59.449 45.455 0.00 0.00 38.39 3.41
2350 4148 4.761235 AAATCTCTCAACATGTGCTGTG 57.239 40.909 0.00 0.00 38.39 3.66
2351 4149 4.581824 ACAAAATCTCTCAACATGTGCTGT 59.418 37.500 0.00 0.00 40.84 4.40
2352 4150 5.117355 ACAAAATCTCTCAACATGTGCTG 57.883 39.130 0.00 0.00 0.00 4.41
2353 4151 5.779529 AACAAAATCTCTCAACATGTGCT 57.220 34.783 0.00 0.00 0.00 4.40
2354 4152 5.750067 ACAAACAAAATCTCTCAACATGTGC 59.250 36.000 0.00 0.00 0.00 4.57
2355 4153 7.760131 AACAAACAAAATCTCTCAACATGTG 57.240 32.000 0.00 0.00 0.00 3.21
2361 4159 9.796120 ACGAAATAAACAAACAAAATCTCTCAA 57.204 25.926 0.00 0.00 0.00 3.02
2413 4214 3.482598 CGAGAGCAAATTGTTCAGTAGCG 60.483 47.826 12.17 4.24 29.40 4.26
2435 4236 9.811995 GGATTAAACAGGAATTACCAAATAACC 57.188 33.333 0.00 0.00 42.04 2.85
2442 4243 9.016438 GTTTACAGGATTAAACAGGAATTACCA 57.984 33.333 1.73 0.00 40.34 3.25
2443 4247 8.464404 GGTTTACAGGATTAAACAGGAATTACC 58.536 37.037 7.77 0.00 41.76 2.85
2444 4248 9.239551 AGGTTTACAGGATTAAACAGGAATTAC 57.760 33.333 7.77 0.00 41.76 1.89
2487 4294 8.043710 TCCAGGAAGAAATCTATCTTGAGAAAC 58.956 37.037 0.00 0.00 39.70 2.78
2499 4306 6.176183 CAGTACATGTTCCAGGAAGAAATCT 58.824 40.000 2.30 0.00 0.00 2.40
2517 4324 6.207221 TGACGAAGGTTCTGTTATACAGTACA 59.793 38.462 15.34 0.00 44.89 2.90
2518 4325 6.615088 TGACGAAGGTTCTGTTATACAGTAC 58.385 40.000 6.71 7.26 46.03 2.73
2519 4326 6.822667 TGACGAAGGTTCTGTTATACAGTA 57.177 37.500 6.71 0.00 46.03 2.74
2520 4327 5.717078 TGACGAAGGTTCTGTTATACAGT 57.283 39.130 6.71 0.00 46.03 3.55
2591 4416 7.169982 CGCTAGGTTAAGAGTGGAAATAGAATG 59.830 40.741 0.00 0.00 0.00 2.67
2733 4566 7.872993 CACGCGGGATATATCATAAGGATTAAT 59.127 37.037 12.47 0.00 37.44 1.40
2881 4720 8.177663 GCACTGGTCGATCATATATAAAAATGG 58.822 37.037 0.00 0.00 0.00 3.16
2894 4733 1.511850 CTGTTTGCACTGGTCGATCA 58.488 50.000 0.00 0.00 0.00 2.92
3008 7111 6.774354 ACTTTGCAAATGTCATGCTTTTAG 57.226 33.333 13.23 0.00 44.14 1.85
3009 7112 8.830201 ATAACTTTGCAAATGTCATGCTTTTA 57.170 26.923 13.23 1.26 44.14 1.52
3010 7113 7.658575 AGATAACTTTGCAAATGTCATGCTTTT 59.341 29.630 13.23 0.00 44.14 2.27
3011 7114 7.156673 AGATAACTTTGCAAATGTCATGCTTT 58.843 30.769 13.23 0.00 44.14 3.51
3012 7115 6.694447 AGATAACTTTGCAAATGTCATGCTT 58.306 32.000 13.23 0.45 44.14 3.91
3013 7116 6.276832 AGATAACTTTGCAAATGTCATGCT 57.723 33.333 13.23 2.19 44.14 3.79
3014 7117 8.638685 ATTAGATAACTTTGCAAATGTCATGC 57.361 30.769 13.23 0.00 44.08 4.06
3021 7124 9.956720 GCAGACATATTAGATAACTTTGCAAAT 57.043 29.630 13.23 0.89 0.00 2.32
3028 7131 9.890629 TGTTTGAGCAGACATATTAGATAACTT 57.109 29.630 0.00 0.00 0.00 2.66
3030 7133 9.319143 ACTGTTTGAGCAGACATATTAGATAAC 57.681 33.333 1.73 0.00 39.62 1.89
3075 7178 7.773864 TTTTACGAGAAACAGTACATGTGAA 57.226 32.000 9.11 0.00 43.00 3.18
3079 7182 8.120465 ACAAGTTTTTACGAGAAACAGTACATG 58.880 33.333 12.75 0.00 38.99 3.21
3085 7188 7.790861 ACAAACAAGTTTTTACGAGAAACAG 57.209 32.000 12.75 8.66 38.99 3.16
3093 7196 7.911727 ACCTAAAGCTACAAACAAGTTTTTACG 59.088 33.333 0.00 0.00 31.11 3.18
3094 7197 9.577110 AACCTAAAGCTACAAACAAGTTTTTAC 57.423 29.630 0.00 0.00 31.11 2.01
3096 7199 9.496873 AAAACCTAAAGCTACAAACAAGTTTTT 57.503 25.926 0.00 0.00 31.64 1.94
3135 7238 8.960591 AGTTTGATCCAATGAAATTTCTCGTAT 58.039 29.630 18.64 6.55 31.22 3.06
3136 7239 8.335532 AGTTTGATCCAATGAAATTTCTCGTA 57.664 30.769 18.64 0.00 31.22 3.43
3137 7240 7.219484 AGTTTGATCCAATGAAATTTCTCGT 57.781 32.000 18.64 3.02 31.22 4.18
3138 7241 6.749118 GGAGTTTGATCCAATGAAATTTCTCG 59.251 38.462 18.64 7.29 39.34 4.04
3139 7242 7.038048 GGGAGTTTGATCCAATGAAATTTCTC 58.962 38.462 18.64 7.67 41.52 2.87
3140 7243 6.727697 AGGGAGTTTGATCCAATGAAATTTCT 59.272 34.615 18.64 2.40 41.52 2.52
3141 7244 6.939622 AGGGAGTTTGATCCAATGAAATTTC 58.060 36.000 11.41 11.41 41.52 2.17
3142 7245 6.940430 AGGGAGTTTGATCCAATGAAATTT 57.060 33.333 0.00 0.00 41.52 1.82
3143 7246 9.887862 ATATAGGGAGTTTGATCCAATGAAATT 57.112 29.630 0.00 0.00 41.52 1.82
3178 7281 9.161629 ACAAACATTTGACTAATCATACGATGA 57.838 29.630 11.24 0.00 41.06 2.92
3181 7284 9.425577 TGTACAAACATTTGACTAATCATACGA 57.574 29.630 11.24 0.00 40.55 3.43
3191 7294 9.825972 CGAATAGATTTGTACAAACATTTGACT 57.174 29.630 22.78 14.30 40.55 3.41
3192 7295 9.820229 TCGAATAGATTTGTACAAACATTTGAC 57.180 29.630 22.78 10.92 40.55 3.18
3199 7302 9.698617 GGTTGTATCGAATAGATTTGTACAAAC 57.301 33.333 22.78 15.84 40.66 2.93
3200 7303 9.438228 TGGTTGTATCGAATAGATTTGTACAAA 57.562 29.630 22.58 22.58 40.66 2.83
3201 7304 9.438228 TTGGTTGTATCGAATAGATTTGTACAA 57.562 29.630 3.59 3.59 40.66 2.41
3202 7305 9.438228 TTTGGTTGTATCGAATAGATTTGTACA 57.562 29.630 0.00 0.00 40.66 2.90
3205 7308 8.621286 GGATTTGGTTGTATCGAATAGATTTGT 58.379 33.333 0.00 0.00 40.66 2.83
3206 7309 8.076178 GGGATTTGGTTGTATCGAATAGATTTG 58.924 37.037 0.00 0.00 40.66 2.32
3247 7350 1.124658 CATTGTTGCGGCAATGTTTCG 59.875 47.619 19.53 2.34 46.24 3.46
3306 7409 2.118228 TTGCTTGCGTTTGTGTCATC 57.882 45.000 0.00 0.00 0.00 2.92
3325 7428 3.555586 GCTCCAAGCACCATTTTCACATT 60.556 43.478 0.00 0.00 41.89 2.71
3348 7451 2.117865 CCAAGCATCCCTTCTCTCTCT 58.882 52.381 0.00 0.00 0.00 3.10
3366 7469 2.630580 GTTGTATCCTTTGTTTGGGCCA 59.369 45.455 0.00 0.00 0.00 5.36
3389 7492 5.344743 TCTGGTCTTGATAGGTTTAGCTG 57.655 43.478 0.00 0.00 0.00 4.24
3403 7506 0.035458 CCGTTCTTGGCTCTGGTCTT 59.965 55.000 0.00 0.00 0.00 3.01
3442 7545 1.739049 GCTCTGGCGATGCTAGTCT 59.261 57.895 2.07 0.00 38.31 3.24
3448 7551 2.747460 TGTTGGCTCTGGCGATGC 60.747 61.111 0.00 0.00 39.81 3.91
3449 7552 2.758089 GCTGTTGGCTCTGGCGATG 61.758 63.158 0.00 0.00 39.81 3.84
3473 7576 1.645034 ATCTTTGATCGCTCGTGGTG 58.355 50.000 0.00 0.00 0.00 4.17
3505 7608 1.532921 CGTCTCAGCATCGTCTTCCTC 60.533 57.143 0.00 0.00 0.00 3.71
3591 7725 1.134610 CCTTTTGCCAGATCCAATGCC 60.135 52.381 0.00 0.00 0.00 4.40
3632 7766 2.032528 TTCACAGCTGGCCCTTCG 59.967 61.111 19.93 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.