Multiple sequence alignment - TraesCS7D01G078900

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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 TraesCS7D01G078900 chr7D 100.000 3022 0 0 1 3022 46672107 46669086 0.000000e+00 5581
1 TraesCS7D01G078900 chr7D 87.569 1094 109 12 1561 2637 46711921 46710838 0.000000e+00 1242
2 TraesCS7D01G078900 chr7D 80.545 1100 88 68 786 1838 46586883 46585863 0.000000e+00 730
3 TraesCS7D01G078900 chr7D 83.708 178 21 6 211 383 88171571 88171745 8.670000e-36 161
4 TraesCS7D01G078900 chr7D 86.486 111 12 1 1337 1444 46712108 46711998 5.290000e-23 119
5 TraesCS7D01G078900 chr7A 83.765 2279 233 66 785 2996 48715103 48717311 0.000000e+00 2032
6 TraesCS7D01G078900 chr7A 82.004 1567 174 65 856 2369 48583205 48584716 0.000000e+00 1232
7 TraesCS7D01G078900 chr7A 83.213 1108 127 30 1337 2420 48525972 48527044 0.000000e+00 961
8 TraesCS7D01G078900 chr7A 84.159 1029 81 41 783 1776 48755484 48756465 0.000000e+00 922
9 TraesCS7D01G078900 chr7A 88.554 332 24 4 545 862 48582585 48582916 1.020000e-104 390
10 TraesCS7D01G078900 chr7A 78.842 449 56 22 121 546 48581696 48582128 1.790000e-67 267
11 TraesCS7D01G078900 chr7A 86.179 246 24 4 2393 2637 48527125 48527361 1.070000e-64 257
12 TraesCS7D01G078900 chr7A 91.892 74 6 0 702 775 48714982 48715055 1.480000e-18 104
13 TraesCS7D01G078900 chr4A 85.384 1471 125 41 786 2238 660624250 660625648 0.000000e+00 1443
14 TraesCS7D01G078900 chr4A 84.800 875 103 12 1559 2420 660452661 660453518 0.000000e+00 852
15 TraesCS7D01G078900 chr4A 80.309 1102 110 58 786 1838 660653754 660654797 0.000000e+00 734
16 TraesCS7D01G078900 chr4A 82.709 561 57 19 19 546 660620430 660620983 2.120000e-126 462
17 TraesCS7D01G078900 chr4A 80.791 177 21 8 545 712 660621364 660621536 3.160000e-25 126
18 TraesCS7D01G078900 chr7B 86.628 172 16 6 214 383 113525836 113526002 1.850000e-42 183
19 TraesCS7D01G078900 chr6A 86.047 172 18 6 215 383 19178942 19179110 2.390000e-41 180
20 TraesCS7D01G078900 chr5D 86.047 172 18 6 214 383 6364099 6364266 2.390000e-41 180
21 TraesCS7D01G078900 chr5D 85.465 172 19 5 215 383 238777789 238777621 1.110000e-39 174
22 TraesCS7D01G078900 chr5D 80.435 184 28 3 983 1166 438973764 438973939 1.890000e-27 134
23 TraesCS7D01G078900 chr3A 85.549 173 18 7 215 383 59443677 59443508 1.110000e-39 174
24 TraesCS7D01G078900 chr2A 84.659 176 19 6 211 383 715399510 715399680 5.180000e-38 169
25 TraesCS7D01G078900 chr2A 88.235 136 12 3 250 383 21712124 21711991 3.120000e-35 159
26 TraesCS7D01G078900 chr4D 84.940 166 15 7 221 383 503812418 503812576 3.120000e-35 159
27 TraesCS7D01G078900 chr3B 92.857 98 7 0 1354 1451 191290526 191290623 3.140000e-30 143


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 TraesCS7D01G078900 chr7D 46669086 46672107 3021 True 5581.000000 5581 100.000000 1 3022 1 chr7D.!!$R2 3021
1 TraesCS7D01G078900 chr7D 46585863 46586883 1020 True 730.000000 730 80.545000 786 1838 1 chr7D.!!$R1 1052
2 TraesCS7D01G078900 chr7D 46710838 46712108 1270 True 680.500000 1242 87.027500 1337 2637 2 chr7D.!!$R3 1300
3 TraesCS7D01G078900 chr7A 48714982 48717311 2329 False 1068.000000 2032 87.828500 702 2996 2 chr7A.!!$F4 2294
4 TraesCS7D01G078900 chr7A 48755484 48756465 981 False 922.000000 922 84.159000 783 1776 1 chr7A.!!$F1 993
5 TraesCS7D01G078900 chr7A 48581696 48584716 3020 False 629.666667 1232 83.133333 121 2369 3 chr7A.!!$F3 2248
6 TraesCS7D01G078900 chr7A 48525972 48527361 1389 False 609.000000 961 84.696000 1337 2637 2 chr7A.!!$F2 1300
7 TraesCS7D01G078900 chr4A 660452661 660453518 857 False 852.000000 852 84.800000 1559 2420 1 chr4A.!!$F1 861
8 TraesCS7D01G078900 chr4A 660653754 660654797 1043 False 734.000000 734 80.309000 786 1838 1 chr4A.!!$F2 1052
9 TraesCS7D01G078900 chr4A 660620430 660625648 5218 False 677.000000 1443 82.961333 19 2238 3 chr4A.!!$F3 2219

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
806 4178 0.031616 GGAGAGGAGATCCACCACCT 60.032 60.0 0.92 0.0 38.89 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 5985 0.036294 CCCCAGAGACGGAGAAAACC 60.036 60.0 0.0 0.0 0.0 3.27 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
63 64 8.611051 AGTTAGTCCTTGATATCCAGTAGTTT 57.389 34.615 0.00 0.00 0.00 2.66
67 68 8.024145 AGTCCTTGATATCCAGTAGTTTTAGG 57.976 38.462 0.00 0.00 0.00 2.69
127 128 6.325919 TGACCAAAACATTGTAATCCAGAC 57.674 37.500 0.00 0.00 0.00 3.51
129 130 4.217550 ACCAAAACATTGTAATCCAGACCG 59.782 41.667 0.00 0.00 0.00 4.79
144 145 3.181506 CCAGACCGCAAGCTTTATCTTTC 60.182 47.826 0.00 0.00 0.00 2.62
149 150 3.366273 CCGCAAGCTTTATCTTTCAAGCA 60.366 43.478 0.00 0.00 46.70 3.91
244 270 0.535102 AGAAACCTTGTGTGAGGGCG 60.535 55.000 0.00 0.00 41.31 6.13
247 273 3.953775 CCTTGTGTGAGGGCGGGT 61.954 66.667 0.00 0.00 32.94 5.28
248 274 2.113139 CTTGTGTGAGGGCGGGTT 59.887 61.111 0.00 0.00 0.00 4.11
280 306 7.896811 TGCAGTTCATTAAGAAGAAGAGAGTA 58.103 34.615 0.00 0.00 36.78 2.59
310 336 0.986527 ATAAGGAAAACCGGACCCGT 59.013 50.000 9.46 4.14 37.81 5.28
324 350 3.368739 CGGACCCGTAAACCTAACATTCT 60.369 47.826 0.00 0.00 34.35 2.40
325 351 4.582869 GGACCCGTAAACCTAACATTCTT 58.417 43.478 0.00 0.00 0.00 2.52
328 354 3.692593 CCCGTAAACCTAACATTCTTGGG 59.307 47.826 0.00 0.00 0.00 4.12
361 387 7.558444 GGGAAAACCTAAAGAAAACCCAAAAAT 59.442 33.333 0.00 0.00 35.41 1.82
366 392 8.731275 ACCTAAAGAAAACCCAAAAATGAAAG 57.269 30.769 0.00 0.00 0.00 2.62
367 393 8.544622 ACCTAAAGAAAACCCAAAAATGAAAGA 58.455 29.630 0.00 0.00 0.00 2.52
438 480 4.398673 CGTAAGACTCCTTTGTACTAGGCT 59.601 45.833 9.09 0.00 43.02 4.58
444 486 4.263506 ACTCCTTTGTACTAGGCTGCAATT 60.264 41.667 0.50 0.00 32.59 2.32
458 500 2.573941 GCAATTGGAGAGTGCCATTC 57.426 50.000 7.72 0.00 43.27 2.67
463 505 0.616395 TGGAGAGTGCCATTCGGGTA 60.616 55.000 0.00 0.00 39.65 3.69
466 508 0.541863 AGAGTGCCATTCGGGTAAGG 59.458 55.000 0.00 0.00 39.65 2.69
506 548 5.412594 ACGTGTGAAATTAGACATCTGCAAT 59.587 36.000 0.00 0.00 0.00 3.56
510 553 6.433716 TGTGAAATTAGACATCTGCAATGGAA 59.566 34.615 11.76 5.35 0.00 3.53
532 575 4.577834 TTGGTTAGCTAAACAGCAAACC 57.422 40.909 22.71 13.26 40.08 3.27
539 582 3.758554 AGCTAAACAGCAAACCGATGAAT 59.241 39.130 0.00 0.00 34.21 2.57
598 1265 2.747855 CGGAACTGCTTGGAGCCC 60.748 66.667 0.00 0.00 41.51 5.19
683 1352 1.890979 GTGGCTGGCGATGATGAGG 60.891 63.158 0.00 0.00 0.00 3.86
684 1353 2.976903 GGCTGGCGATGATGAGGC 60.977 66.667 0.00 0.00 0.00 4.70
778 4112 4.519540 ATCGCCATTATTTACCCAATGC 57.480 40.909 0.00 0.00 32.00 3.56
803 4175 1.216678 GAGAGGAGAGGAGATCCACCA 59.783 57.143 0.92 0.00 39.47 4.17
806 4178 0.031616 GGAGAGGAGATCCACCACCT 60.032 60.000 0.92 0.00 38.89 4.00
924 4615 2.573009 AGATCATCACATCACCACCACA 59.427 45.455 0.00 0.00 0.00 4.17
940 4631 3.046087 CAGAGCACTGCCACCGTG 61.046 66.667 0.00 0.00 37.33 4.94
960 4652 1.280421 GCCATCATCCATCCTCTACCC 59.720 57.143 0.00 0.00 0.00 3.69
1088 4797 1.754380 CTCACGTCCTCCACCACCAA 61.754 60.000 0.00 0.00 0.00 3.67
1098 4807 2.526873 ACCACCAACGCCTCCTCT 60.527 61.111 0.00 0.00 0.00 3.69
1206 4930 3.387091 TCGTACGGGCTGCACCAT 61.387 61.111 16.52 0.00 42.05 3.55
1347 5089 4.838486 GGCAGCGACGAGGACGAG 62.838 72.222 0.00 0.00 42.66 4.18
1456 5219 1.171308 CGTACGTCCCTTCTCCTTCA 58.829 55.000 7.22 0.00 0.00 3.02
1460 5242 0.905337 CGTCCCTTCTCCTTCACCCT 60.905 60.000 0.00 0.00 0.00 4.34
1462 5244 0.491823 TCCCTTCTCCTTCACCCTCA 59.508 55.000 0.00 0.00 0.00 3.86
1469 5262 2.034878 CTCCTTCACCCTCATCGATCA 58.965 52.381 0.00 0.00 0.00 2.92
1470 5263 2.432146 CTCCTTCACCCTCATCGATCAA 59.568 50.000 0.00 0.00 0.00 2.57
1471 5264 3.041211 TCCTTCACCCTCATCGATCAAT 58.959 45.455 0.00 0.00 0.00 2.57
1472 5265 3.070159 TCCTTCACCCTCATCGATCAATC 59.930 47.826 0.00 0.00 0.00 2.67
1484 5277 1.707632 GATCAATCGATCTGCCTCGG 58.292 55.000 0.00 0.00 44.10 4.63
1485 5278 0.320247 ATCAATCGATCTGCCTCGGC 60.320 55.000 0.00 0.00 39.13 5.54
1486 5279 1.958205 CAATCGATCTGCCTCGGCC 60.958 63.158 5.33 0.00 41.09 6.13
1487 5280 2.434843 AATCGATCTGCCTCGGCCA 61.435 57.895 2.24 0.00 41.09 5.36
1523 5316 5.061853 CCATGGATTCTTTGTGATCGATCT 58.938 41.667 25.02 3.06 0.00 2.75
1540 5370 3.402691 CTCATCGCGCTGACCGAGT 62.403 63.158 8.85 0.00 40.02 4.18
1577 5412 1.669115 GCAGAAGCAGAAGACGGCA 60.669 57.895 0.00 0.00 41.58 5.69
1716 5551 2.992114 ACCTCGCCGAGCAGAACT 60.992 61.111 9.01 0.00 0.00 3.01
1886 5730 2.747855 CCCAGCTTCTCCGCCAAC 60.748 66.667 0.00 0.00 0.00 3.77
1887 5731 2.348998 CCAGCTTCTCCGCCAACT 59.651 61.111 0.00 0.00 0.00 3.16
1916 5760 2.122280 ATGCCAATGCCAACCCCA 59.878 55.556 0.00 0.00 36.33 4.96
1958 5802 2.149578 CAGTTCTTCTGCAGGTTCAGG 58.850 52.381 15.13 0.00 37.36 3.86
1966 5810 2.879233 GCAGGTTCAGGGACACCGA 61.879 63.158 0.00 0.00 43.47 4.69
2026 5873 2.280186 GCCGGCCAGATAGAACGG 60.280 66.667 18.11 0.00 46.78 4.44
2028 5875 2.432300 CCGGCCAGATAGAACGGGT 61.432 63.158 2.24 0.00 40.79 5.28
2034 5881 3.830755 GGCCAGATAGAACGGGTTATCTA 59.169 47.826 0.00 0.00 35.44 1.98
2042 5889 3.949754 AGAACGGGTTATCTATGTGACGA 59.050 43.478 0.00 0.00 0.00 4.20
2089 5939 1.521580 AACAAAAATGGCGGCATTGG 58.478 45.000 34.37 27.05 0.00 3.16
2135 5985 9.185192 CAAGTTTAGCAGAAAGTTTAATCCTTG 57.815 33.333 2.36 0.00 0.00 3.61
2150 6002 2.326428 TCCTTGGTTTTCTCCGTCTCT 58.674 47.619 0.00 0.00 0.00 3.10
2151 6003 2.037251 TCCTTGGTTTTCTCCGTCTCTG 59.963 50.000 0.00 0.00 0.00 3.35
2152 6004 2.417719 CTTGGTTTTCTCCGTCTCTGG 58.582 52.381 0.00 0.00 0.00 3.86
2167 6021 4.262617 GTCTCTGGGGGAAATGTAAGTTC 58.737 47.826 0.00 0.00 40.82 3.01
2210 6072 2.408050 CGAATCGATGGATGAGTTCCC 58.592 52.381 0.00 0.00 44.77 3.97
2213 6075 1.143838 CGATGGATGAGTTCCCGCA 59.856 57.895 0.00 0.00 44.77 5.69
2317 6206 9.314321 GTAATAGTACAGCAACATGTTGAGTAT 57.686 33.333 36.65 24.37 42.93 2.12
2328 6225 7.312899 CAACATGTTGAGTATTTTTCTACCCC 58.687 38.462 30.69 0.00 42.93 4.95
2345 6242 2.026262 ACCCCGTCTTGCATAGATGTTT 60.026 45.455 13.53 0.58 38.08 2.83
2347 6244 2.285220 CCCGTCTTGCATAGATGTTTCG 59.715 50.000 13.53 7.58 38.08 3.46
2364 6261 2.786495 CGGTGGGCAGCGTAGATCT 61.786 63.158 0.00 0.00 46.01 2.75
2369 6266 0.885196 GGGCAGCGTAGATCTAGAGG 59.115 60.000 1.64 0.00 0.00 3.69
2375 6272 1.001158 GCGTAGATCTAGAGGTGGTGC 60.001 57.143 1.64 0.00 0.00 5.01
2380 6277 5.335269 CGTAGATCTAGAGGTGGTGCATTAG 60.335 48.000 1.64 0.00 0.00 1.73
2486 6492 6.150140 GTGACTTCTGCTTTAGATTGGTCATT 59.850 38.462 0.00 0.00 39.51 2.57
2505 6511 4.399303 TCATTTAGCAAAAGAAGCTAGGCC 59.601 41.667 0.00 0.00 44.57 5.19
2519 6525 5.986501 AGCTAGGCCATTAGTATACTCAC 57.013 43.478 9.12 0.00 0.00 3.51
2530 6536 7.283127 CCATTAGTATACTCACCATTGCACTTT 59.717 37.037 9.12 0.00 0.00 2.66
2534 6540 2.233271 ACTCACCATTGCACTTTCCTG 58.767 47.619 0.00 0.00 0.00 3.86
2539 6545 3.556775 CACCATTGCACTTTCCTGTTTTG 59.443 43.478 0.00 0.00 0.00 2.44
2540 6546 3.132925 CCATTGCACTTTCCTGTTTTGG 58.867 45.455 0.00 0.00 0.00 3.28
2551 6557 2.105649 TCCTGTTTTGGGGGCAAATTTC 59.894 45.455 0.00 0.00 0.00 2.17
2575 6585 5.313712 CCAAGTCCAAGTAACATGTTAGGT 58.686 41.667 18.56 6.57 0.00 3.08
2576 6586 5.181245 CCAAGTCCAAGTAACATGTTAGGTG 59.819 44.000 18.56 17.32 0.00 4.00
2577 6587 5.562298 AGTCCAAGTAACATGTTAGGTGT 57.438 39.130 18.56 6.10 0.00 4.16
2578 6588 6.675413 AGTCCAAGTAACATGTTAGGTGTA 57.325 37.500 18.56 4.34 0.00 2.90
2616 6626 7.432869 TCATTTTGGTTGTTCAGGTATTTCAG 58.567 34.615 0.00 0.00 0.00 3.02
2627 6637 4.213270 TCAGGTATTTCAGCTTGTCGTTTG 59.787 41.667 0.00 0.00 30.72 2.93
2639 6654 6.356977 CAGCTTGTCGTTTGTATGTGTTTAAG 59.643 38.462 0.00 0.00 0.00 1.85
2686 6701 7.398332 AGAGAAACAAAAAGCCTATCATGGATT 59.602 33.333 0.00 0.00 37.30 3.01
2692 6707 9.646522 ACAAAAAGCCTATCATGGATTATAACT 57.353 29.630 0.00 0.00 34.26 2.24
2693 6708 9.903682 CAAAAAGCCTATCATGGATTATAACTG 57.096 33.333 0.00 0.00 34.26 3.16
2694 6709 8.641498 AAAAGCCTATCATGGATTATAACTGG 57.359 34.615 0.00 0.00 34.26 4.00
2697 6712 5.573502 GCCTATCATGGATTATAACTGGGCA 60.574 44.000 0.00 0.00 34.27 5.36
2733 6748 9.125026 ACATATAGGTTTCAAGGAATCATGAAC 57.875 33.333 0.00 0.00 35.42 3.18
2744 6760 8.377034 TCAAGGAATCATGAACAAAATGGATTT 58.623 29.630 0.00 0.00 0.00 2.17
2754 6770 5.314923 ACAAAATGGATTTCATGTCGAGG 57.685 39.130 0.00 0.00 35.99 4.63
2755 6771 5.009631 ACAAAATGGATTTCATGTCGAGGA 58.990 37.500 0.00 0.00 35.99 3.71
2756 6772 5.653769 ACAAAATGGATTTCATGTCGAGGAT 59.346 36.000 0.00 0.00 35.99 3.24
2758 6774 3.198409 TGGATTTCATGTCGAGGATGG 57.802 47.619 4.86 0.00 0.00 3.51
2759 6775 2.771372 TGGATTTCATGTCGAGGATGGA 59.229 45.455 4.86 0.00 0.00 3.41
2760 6776 3.392285 TGGATTTCATGTCGAGGATGGAT 59.608 43.478 4.86 1.01 0.00 3.41
2761 6777 4.592778 TGGATTTCATGTCGAGGATGGATA 59.407 41.667 4.86 0.00 0.00 2.59
2762 6778 5.249163 TGGATTTCATGTCGAGGATGGATAT 59.751 40.000 4.86 0.00 0.00 1.63
2763 6779 6.440328 TGGATTTCATGTCGAGGATGGATATA 59.560 38.462 4.86 0.00 0.00 0.86
2764 6780 7.038373 TGGATTTCATGTCGAGGATGGATATAA 60.038 37.037 4.86 0.00 0.00 0.98
2765 6781 7.824289 GGATTTCATGTCGAGGATGGATATAAA 59.176 37.037 4.86 0.00 0.00 1.40
2793 6809 8.504812 ACATAATATGTGTGTGATTTAGCACA 57.495 30.769 4.93 0.00 43.20 4.57
2813 6829 4.810491 CACACAAAAGGATTTCTTTGTGGG 59.190 41.667 23.85 19.19 44.30 4.61
2818 6834 8.028938 CACAAAAGGATTTCTTTGTGGGTATAG 58.971 37.037 16.26 0.00 44.30 1.31
2819 6835 6.775594 AAAGGATTTCTTTGTGGGTATAGC 57.224 37.500 0.00 0.00 43.50 2.97
2884 6915 5.397142 AAGAAAACAATCCTCTTCATGGC 57.603 39.130 0.00 0.00 0.00 4.40
2887 6918 3.726557 AACAATCCTCTTCATGGCTGA 57.273 42.857 0.00 0.00 0.00 4.26
2934 6965 6.256539 CGATTATATACATTCTCGCCAGCAAT 59.743 38.462 0.00 0.00 0.00 3.56
2936 6967 2.689553 TACATTCTCGCCAGCAATCA 57.310 45.000 0.00 0.00 0.00 2.57
2940 6971 0.674581 TTCTCGCCAGCAATCACCAG 60.675 55.000 0.00 0.00 0.00 4.00
2945 6976 0.961019 GCCAGCAATCACCAGTTTCA 59.039 50.000 0.00 0.00 0.00 2.69
2949 6980 1.610522 AGCAATCACCAGTTTCAGCAC 59.389 47.619 0.00 0.00 0.00 4.40
2952 6983 0.478072 ATCACCAGTTTCAGCACCCA 59.522 50.000 0.00 0.00 0.00 4.51
2964 6995 2.040330 GCACCCACATGCTTCACAA 58.960 52.632 0.00 0.00 42.62 3.33
2965 6996 0.038892 GCACCCACATGCTTCACAAG 60.039 55.000 0.00 0.00 42.62 3.16
2966 6997 1.321474 CACCCACATGCTTCACAAGT 58.679 50.000 0.00 0.00 0.00 3.16
2967 6998 1.267806 CACCCACATGCTTCACAAGTC 59.732 52.381 0.00 0.00 0.00 3.01
2968 6999 1.133823 ACCCACATGCTTCACAAGTCA 60.134 47.619 0.00 0.00 0.00 3.41
2969 7000 2.165167 CCCACATGCTTCACAAGTCAT 58.835 47.619 0.00 0.00 0.00 3.06
2974 7008 4.915667 CACATGCTTCACAAGTCATCTTTG 59.084 41.667 0.00 0.00 0.00 2.77
2975 7009 4.022589 ACATGCTTCACAAGTCATCTTTGG 60.023 41.667 0.00 0.00 0.00 3.28
2984 7018 4.956075 ACAAGTCATCTTTGGTTTTGGTCT 59.044 37.500 0.00 0.00 0.00 3.85
2985 7019 5.422012 ACAAGTCATCTTTGGTTTTGGTCTT 59.578 36.000 0.00 0.00 0.00 3.01
2996 7030 4.405358 TGGTTTTGGTCTTTCTGCAAGATT 59.595 37.500 0.00 0.00 46.36 2.40
2997 7031 4.746611 GGTTTTGGTCTTTCTGCAAGATTG 59.253 41.667 0.00 0.00 46.36 2.67
2998 7032 5.351458 GTTTTGGTCTTTCTGCAAGATTGT 58.649 37.500 0.00 0.00 46.36 2.71
2999 7033 4.836125 TTGGTCTTTCTGCAAGATTGTC 57.164 40.909 0.00 0.00 46.36 3.18
3000 7034 3.149196 TGGTCTTTCTGCAAGATTGTCC 58.851 45.455 0.00 0.00 46.36 4.02
3001 7035 3.149196 GGTCTTTCTGCAAGATTGTCCA 58.851 45.455 0.00 0.00 46.36 4.02
3002 7036 3.760684 GGTCTTTCTGCAAGATTGTCCAT 59.239 43.478 0.00 0.00 46.36 3.41
3003 7037 4.219288 GGTCTTTCTGCAAGATTGTCCATT 59.781 41.667 0.00 0.00 46.36 3.16
3004 7038 5.279156 GGTCTTTCTGCAAGATTGTCCATTT 60.279 40.000 0.00 0.00 46.36 2.32
3005 7039 6.218746 GTCTTTCTGCAAGATTGTCCATTTT 58.781 36.000 0.00 0.00 46.36 1.82
3006 7040 6.703165 GTCTTTCTGCAAGATTGTCCATTTTT 59.297 34.615 0.00 0.00 46.36 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 5.771165 GGTGTATCTTCCAAAACAACCCTAA 59.229 40.000 0.00 0.00 0.00 2.69
67 68 5.068591 ACAAGGTGTATCTTCCAAAACAACC 59.931 40.000 0.00 0.00 29.60 3.77
127 128 3.174375 GCTTGAAAGATAAAGCTTGCGG 58.826 45.455 0.00 0.00 44.33 5.69
149 150 2.158696 GCAGAGTATGGAGCAATCCCTT 60.159 50.000 0.00 0.00 0.00 3.95
216 242 6.350110 CCTCACACAAGGTTTCTCAAAAGAAA 60.350 38.462 0.00 0.00 46.72 2.52
217 243 5.125417 CCTCACACAAGGTTTCTCAAAAGAA 59.875 40.000 0.00 0.00 39.78 2.52
218 244 4.640201 CCTCACACAAGGTTTCTCAAAAGA 59.360 41.667 0.00 0.00 0.00 2.52
219 245 4.202050 CCCTCACACAAGGTTTCTCAAAAG 60.202 45.833 0.00 0.00 34.34 2.27
233 259 4.263572 CCAACCCGCCCTCACACA 62.264 66.667 0.00 0.00 0.00 3.72
244 270 0.467290 TGAACTGCAGGAACCAACCC 60.467 55.000 19.93 0.00 0.00 4.11
247 273 4.724399 TCTTAATGAACTGCAGGAACCAA 58.276 39.130 19.93 3.86 0.00 3.67
248 274 4.365514 TCTTAATGAACTGCAGGAACCA 57.634 40.909 19.93 10.14 0.00 3.67
259 285 9.308318 GGACATACTCTCTTCTTCTTAATGAAC 57.692 37.037 0.00 0.00 0.00 3.18
280 306 6.753107 CGGTTTTCCTTATAAACTGGACAT 57.247 37.500 0.00 0.00 37.92 3.06
310 336 7.832187 CCTGATTACCCAAGAATGTTAGGTTTA 59.168 37.037 0.00 0.00 31.89 2.01
324 350 5.602291 TTAGGTTTTCCCTGATTACCCAA 57.398 39.130 0.00 0.00 45.81 4.12
325 351 5.313772 TCTTTAGGTTTTCCCTGATTACCCA 59.686 40.000 0.00 0.00 45.81 4.51
328 354 8.086522 GGTTTTCTTTAGGTTTTCCCTGATTAC 58.913 37.037 0.00 0.00 45.81 1.89
370 396 9.740710 AGTAGCACTTATAATTCTTGTTTTCCT 57.259 29.630 0.00 0.00 0.00 3.36
389 430 9.543018 GAAAATGAAACAATGTAGTAGTAGCAC 57.457 33.333 0.00 0.00 0.00 4.40
432 474 2.286872 CACTCTCCAATTGCAGCCTAG 58.713 52.381 0.00 0.00 0.00 3.02
433 475 1.679944 GCACTCTCCAATTGCAGCCTA 60.680 52.381 0.00 0.00 36.22 3.93
434 476 0.964358 GCACTCTCCAATTGCAGCCT 60.964 55.000 0.00 0.00 36.22 4.58
438 480 1.820519 GAATGGCACTCTCCAATTGCA 59.179 47.619 0.00 0.00 39.96 4.08
444 486 0.616395 TACCCGAATGGCACTCTCCA 60.616 55.000 0.00 0.00 40.97 3.86
455 497 8.419442 CAAACTAGTATTACTCCTTACCCGAAT 58.581 37.037 0.00 0.00 0.00 3.34
458 500 7.199078 GTCAAACTAGTATTACTCCTTACCCG 58.801 42.308 0.00 0.00 0.00 5.28
463 505 7.040201 TCACACGTCAAACTAGTATTACTCCTT 60.040 37.037 0.00 0.00 0.00 3.36
466 508 8.511465 TTTCACACGTCAAACTAGTATTACTC 57.489 34.615 0.00 0.00 0.00 2.59
526 569 3.853671 GTGTGATCAATTCATCGGTTTGC 59.146 43.478 0.00 0.00 36.54 3.68
532 575 2.929398 TGGTCGTGTGATCAATTCATCG 59.071 45.455 0.00 0.00 36.54 3.84
539 582 2.613026 AGTTGTGGTCGTGTGATCAA 57.387 45.000 0.00 0.00 36.87 2.57
584 1246 2.282745 GCTGGGCTCCAAGCAGTT 60.283 61.111 10.36 0.00 44.75 3.16
598 1265 2.837291 CTCCCTCCCTCTCGGCTG 60.837 72.222 0.00 0.00 0.00 4.85
710 1392 6.855763 ATTAATTGGCTGTGAATGAAAGGA 57.144 33.333 0.00 0.00 0.00 3.36
778 4112 0.178992 ATCTCCTCTCCTCTCCGCAG 60.179 60.000 0.00 0.00 0.00 5.18
803 4175 0.620410 TGTTCGATGATGGGGGAGGT 60.620 55.000 0.00 0.00 0.00 3.85
806 4178 0.982852 AGCTGTTCGATGATGGGGGA 60.983 55.000 0.00 0.00 0.00 4.81
850 4224 3.244911 TGGGCTATAAATAAGGCAGAGGC 60.245 47.826 0.00 0.00 41.11 4.70
940 4631 1.280421 GGGTAGAGGATGGATGATGGC 59.720 57.143 0.00 0.00 0.00 4.40
960 4652 0.665835 CCGATCTGAGAACTCTCCGG 59.334 60.000 0.00 0.00 42.20 5.14
1147 4871 4.104417 GACGACGGAGCTGAGCGT 62.104 66.667 0.00 0.00 37.97 5.07
1180 4904 3.061260 GCCCGTACGACTCCTGGTC 62.061 68.421 18.76 1.13 41.28 4.02
1181 4905 3.066814 GCCCGTACGACTCCTGGT 61.067 66.667 18.76 0.00 0.00 4.00
1182 4906 2.754658 AGCCCGTACGACTCCTGG 60.755 66.667 18.76 9.31 0.00 4.45
1206 4930 2.045708 CCGCTGCTGGTTGGCATAA 61.046 57.895 0.00 0.00 41.63 1.90
1272 5002 1.227497 CCTCTTGATGCCTCCGCTC 60.227 63.158 0.00 0.00 35.36 5.03
1283 5013 3.011517 GCTCCAGGCCCCTCTTGA 61.012 66.667 0.00 0.00 34.27 3.02
1469 5262 2.423446 GGCCGAGGCAGATCGATT 59.577 61.111 16.65 0.00 45.56 3.34
1470 5263 2.839632 TGGCCGAGGCAGATCGAT 60.840 61.111 16.65 0.00 45.56 3.59
1471 5264 3.838271 GTGGCCGAGGCAGATCGA 61.838 66.667 16.65 0.00 45.56 3.59
1473 5266 4.148825 ACGTGGCCGAGGCAGATC 62.149 66.667 16.65 0.00 44.11 2.75
1474 5267 4.457496 CACGTGGCCGAGGCAGAT 62.457 66.667 16.65 0.00 44.11 2.90
1480 5273 3.041940 GAACACCACGTGGCCGAG 61.042 66.667 34.26 22.50 37.94 4.63
1481 5274 4.953868 CGAACACCACGTGGCCGA 62.954 66.667 34.26 0.00 37.94 5.54
1483 5276 3.343421 GACGAACACCACGTGGCC 61.343 66.667 34.26 18.88 43.97 5.36
1484 5277 3.343421 GGACGAACACCACGTGGC 61.343 66.667 34.26 16.84 43.97 5.01
1485 5278 1.301401 ATGGACGAACACCACGTGG 60.301 57.895 32.83 32.83 43.97 4.94
1486 5279 1.565156 CCATGGACGAACACCACGTG 61.565 60.000 5.56 9.08 43.97 4.49
1487 5280 1.301401 CCATGGACGAACACCACGT 60.301 57.895 5.56 0.00 46.58 4.49
1523 5316 2.486636 AAACTCGGTCAGCGCGATGA 62.487 55.000 25.05 25.05 0.00 2.92
1540 5370 6.698008 TCTGCAGATTGTCAAGAAAGAAAA 57.302 33.333 13.74 0.00 0.00 2.29
1677 5512 2.177531 GCACCAGCGCTTCATGTG 59.822 61.111 7.50 14.23 0.00 3.21
1700 5535 2.507992 CAGTTCTGCTCGGCGAGG 60.508 66.667 35.03 21.15 0.00 4.63
1716 5551 3.452786 CTCCTTCTCGAGGCGGCA 61.453 66.667 13.56 3.37 45.87 5.69
1950 5794 0.763223 ACTTCGGTGTCCCTGAACCT 60.763 55.000 0.00 0.00 34.06 3.50
1958 5802 0.727122 CGTACGTCACTTCGGTGTCC 60.727 60.000 7.22 0.00 45.46 4.02
1966 5810 3.621892 GAGCCGCCGTACGTCACTT 62.622 63.158 15.21 0.00 41.42 3.16
1996 5843 2.429930 CCGGCTTGACCACCTTGA 59.570 61.111 0.00 0.00 39.03 3.02
2026 5873 2.223641 TGGCGTCGTCACATAGATAACC 60.224 50.000 0.00 0.00 0.00 2.85
2028 5875 3.316868 TCATGGCGTCGTCACATAGATAA 59.683 43.478 0.00 0.00 0.00 1.75
2034 5881 0.175531 TGATCATGGCGTCGTCACAT 59.824 50.000 0.00 0.00 0.00 3.21
2089 5939 4.027572 TGCTTAAGTTTGTGAGTTGTGC 57.972 40.909 4.02 0.00 0.00 4.57
2135 5985 0.036294 CCCCAGAGACGGAGAAAACC 60.036 60.000 0.00 0.00 0.00 3.27
2150 6002 7.898636 AGAATTAATGAACTTACATTTCCCCCA 59.101 33.333 0.00 0.00 40.36 4.96
2151 6003 8.306313 AGAATTAATGAACTTACATTTCCCCC 57.694 34.615 0.00 0.00 40.36 5.40
2167 6021 5.685511 CGGCCCGAAATTGTTAGAATTAATG 59.314 40.000 0.00 0.00 0.00 1.90
2185 6039 2.029288 CATCCATCGATTCGGCCCG 61.029 63.158 6.18 0.00 0.00 6.13
2251 6118 8.068892 AGTTCCTCGTATGAATTAGTTTCTCT 57.931 34.615 0.00 0.00 35.23 3.10
2269 6150 9.654663 ATTACTCAACATGTTAGTAAGTTCCTC 57.345 33.333 26.46 0.00 38.66 3.71
2302 6186 6.806739 GGGTAGAAAAATACTCAACATGTTGC 59.193 38.462 29.84 14.64 40.24 4.17
2317 6206 2.642154 TGCAAGACGGGGTAGAAAAA 57.358 45.000 0.00 0.00 0.00 1.94
2328 6225 2.930040 ACCGAAACATCTATGCAAGACG 59.070 45.455 0.00 0.00 36.93 4.18
2345 6242 2.758327 ATCTACGCTGCCCACCGA 60.758 61.111 0.00 0.00 0.00 4.69
2347 6244 0.315568 CTAGATCTACGCTGCCCACC 59.684 60.000 0.00 0.00 0.00 4.61
2364 6261 5.763355 AGTAGTACTAATGCACCACCTCTA 58.237 41.667 3.61 0.00 0.00 2.43
2369 6266 5.721232 AGTCAAGTAGTACTAATGCACCAC 58.279 41.667 3.61 2.11 0.00 4.16
2380 6277 6.979465 ACCAAGTCAAGTAGTCAAGTAGTAC 58.021 40.000 0.00 0.00 34.64 2.73
2457 6463 5.106396 CCAATCTAAAGCAGAAGTCACCTTG 60.106 44.000 0.00 0.00 36.67 3.61
2486 6492 3.433306 TGGCCTAGCTTCTTTTGCTAA 57.567 42.857 3.32 0.00 41.70 3.09
2505 6511 7.792374 AAGTGCAATGGTGAGTATACTAATG 57.208 36.000 5.09 0.00 0.00 1.90
2519 6525 3.132925 CCAAAACAGGAAAGTGCAATGG 58.867 45.455 0.00 0.00 0.00 3.16
2530 6536 1.813102 AATTTGCCCCCAAAACAGGA 58.187 45.000 0.00 0.00 43.58 3.86
2534 6540 1.143889 TGGGAAATTTGCCCCCAAAAC 59.856 47.619 24.21 0.00 46.40 2.43
2539 6545 0.613260 GACTTGGGAAATTTGCCCCC 59.387 55.000 24.21 15.22 45.40 5.40
2540 6546 0.613260 GGACTTGGGAAATTTGCCCC 59.387 55.000 24.21 15.91 45.40 5.80
2551 6557 4.700213 CCTAACATGTTACTTGGACTTGGG 59.300 45.833 14.35 6.52 0.00 4.12
2575 6585 4.508551 AAATGAGGAGACCATGCATACA 57.491 40.909 0.00 0.00 0.00 2.29
2576 6586 4.037208 CCAAAATGAGGAGACCATGCATAC 59.963 45.833 0.00 0.00 0.00 2.39
2577 6587 4.209538 CCAAAATGAGGAGACCATGCATA 58.790 43.478 0.00 0.00 0.00 3.14
2578 6588 3.028850 CCAAAATGAGGAGACCATGCAT 58.971 45.455 0.00 0.00 0.00 3.96
2616 6626 6.423862 TCTTAAACACATACAAACGACAAGC 58.576 36.000 0.00 0.00 0.00 4.01
2667 6682 9.903682 CAGTTATAATCCATGATAGGCTTTTTG 57.096 33.333 0.00 0.00 0.00 2.44
2674 6689 6.065976 TGCCCAGTTATAATCCATGATAGG 57.934 41.667 0.00 0.00 0.00 2.57
2690 6705 7.170965 CCTATATGTATGATTTTCTGCCCAGT 58.829 38.462 0.00 0.00 0.00 4.00
2691 6706 7.170965 ACCTATATGTATGATTTTCTGCCCAG 58.829 38.462 0.00 0.00 0.00 4.45
2692 6707 7.090319 ACCTATATGTATGATTTTCTGCCCA 57.910 36.000 0.00 0.00 0.00 5.36
2693 6708 8.409358 AAACCTATATGTATGATTTTCTGCCC 57.591 34.615 0.00 0.00 0.00 5.36
2694 6709 9.066892 TGAAACCTATATGTATGATTTTCTGCC 57.933 33.333 0.00 0.00 0.00 4.85
2712 6727 7.831691 TTTGTTCATGATTCCTTGAAACCTA 57.168 32.000 0.00 0.00 37.92 3.08
2722 6737 8.726870 ATGAAATCCATTTTGTTCATGATTCC 57.273 30.769 0.00 0.00 38.84 3.01
2728 6743 6.923012 TCGACATGAAATCCATTTTGTTCAT 58.077 32.000 0.00 0.00 40.47 2.57
2729 6744 6.324561 TCGACATGAAATCCATTTTGTTCA 57.675 33.333 0.00 0.00 34.68 3.18
2730 6745 5.801947 CCTCGACATGAAATCCATTTTGTTC 59.198 40.000 0.00 0.00 31.94 3.18
2731 6746 5.476599 TCCTCGACATGAAATCCATTTTGTT 59.523 36.000 0.00 0.00 31.94 2.83
2732 6747 5.009631 TCCTCGACATGAAATCCATTTTGT 58.990 37.500 0.00 0.00 31.94 2.83
2733 6748 5.565592 TCCTCGACATGAAATCCATTTTG 57.434 39.130 0.00 0.00 31.94 2.44
2744 6760 6.929049 GTGTTTTATATCCATCCTCGACATGA 59.071 38.462 0.00 0.00 0.00 3.07
2782 6798 7.288810 AGAAATCCTTTTGTGTGCTAAATCA 57.711 32.000 0.00 0.00 0.00 2.57
2783 6799 8.490355 CAAAGAAATCCTTTTGTGTGCTAAATC 58.510 33.333 0.00 0.00 42.13 2.17
2792 6808 5.022282 ACCCACAAAGAAATCCTTTTGTG 57.978 39.130 18.26 18.26 42.13 3.33
2793 6809 6.994421 ATACCCACAAAGAAATCCTTTTGT 57.006 33.333 0.00 0.00 42.13 2.83
2794 6810 7.035612 GCTATACCCACAAAGAAATCCTTTTG 58.964 38.462 0.00 0.00 42.13 2.44
2802 6818 5.650703 GCTTAAGGCTATACCCACAAAGAAA 59.349 40.000 4.29 0.00 40.58 2.52
2818 6834 4.878397 AGTATGTCACATCAAGCTTAAGGC 59.122 41.667 0.00 0.00 42.19 4.35
2819 6835 6.992063 AAGTATGTCACATCAAGCTTAAGG 57.008 37.500 0.00 0.00 0.00 2.69
2894 6925 2.254546 AATCGCAATCGCTATGGGAA 57.745 45.000 5.95 0.00 42.10 3.97
2895 6926 3.610040 ATAATCGCAATCGCTATGGGA 57.390 42.857 4.66 4.66 42.84 4.37
2896 6927 5.983118 TGTATATAATCGCAATCGCTATGGG 59.017 40.000 0.00 0.00 35.30 4.00
2897 6928 7.643528 ATGTATATAATCGCAATCGCTATGG 57.356 36.000 0.00 0.00 35.30 2.74
2898 6929 8.972349 AGAATGTATATAATCGCAATCGCTATG 58.028 33.333 0.00 0.00 35.30 2.23
2899 6930 9.186323 GAGAATGTATATAATCGCAATCGCTAT 57.814 33.333 0.00 0.00 35.30 2.97
2900 6931 7.376072 CGAGAATGTATATAATCGCAATCGCTA 59.624 37.037 0.00 0.00 35.30 4.26
2901 6932 6.197282 CGAGAATGTATATAATCGCAATCGCT 59.803 38.462 0.00 0.00 35.30 4.93
2902 6933 6.340202 CGAGAATGTATATAATCGCAATCGC 58.660 40.000 0.00 0.00 35.26 4.58
2909 6940 5.102313 TGCTGGCGAGAATGTATATAATCG 58.898 41.667 0.00 2.95 0.00 3.34
2920 6951 0.035152 TGGTGATTGCTGGCGAGAAT 60.035 50.000 0.00 0.00 0.00 2.40
2928 6959 1.610038 TGCTGAAACTGGTGATTGCTG 59.390 47.619 0.00 0.00 0.00 4.41
2934 6965 0.465460 GTGGGTGCTGAAACTGGTGA 60.465 55.000 0.00 0.00 0.00 4.02
2936 6967 0.185901 ATGTGGGTGCTGAAACTGGT 59.814 50.000 0.00 0.00 0.00 4.00
2940 6971 4.972591 GCATGTGGGTGCTGAAAC 57.027 55.556 0.00 0.00 41.82 2.78
2949 6980 1.608055 TGACTTGTGAAGCATGTGGG 58.392 50.000 0.00 0.00 35.88 4.61
2952 6983 4.022589 CCAAAGATGACTTGTGAAGCATGT 60.023 41.667 0.00 0.00 38.06 3.21
2958 6989 5.186797 ACCAAAACCAAAGATGACTTGTGAA 59.813 36.000 0.00 0.00 36.39 3.18
2960 6991 5.009854 ACCAAAACCAAAGATGACTTGTG 57.990 39.130 0.00 0.00 36.39 3.33
2961 6992 4.956075 AGACCAAAACCAAAGATGACTTGT 59.044 37.500 0.00 0.00 36.39 3.16
2964 6995 5.893824 AGAAAGACCAAAACCAAAGATGACT 59.106 36.000 0.00 0.00 0.00 3.41
2965 6996 5.979517 CAGAAAGACCAAAACCAAAGATGAC 59.020 40.000 0.00 0.00 0.00 3.06
2966 6997 5.451798 GCAGAAAGACCAAAACCAAAGATGA 60.452 40.000 0.00 0.00 0.00 2.92
2967 6998 4.746611 GCAGAAAGACCAAAACCAAAGATG 59.253 41.667 0.00 0.00 0.00 2.90
2968 6999 4.405358 TGCAGAAAGACCAAAACCAAAGAT 59.595 37.500 0.00 0.00 0.00 2.40
2969 7000 3.766591 TGCAGAAAGACCAAAACCAAAGA 59.233 39.130 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.