Multiple sequence alignment - TraesCS4B01G291300

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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 TraesCS4B01G291300 chr4B 100.000 2651 0 0 1 2651 576193950 576196600 0.000000e+00 4896
1 TraesCS4B01G291300 chr4B 81.443 485 74 14 993 1473 83337787 83338259 1.490000e-102 383
2 TraesCS4B01G291300 chr4B 80.730 493 71 18 997 1475 146017777 146017295 1.940000e-96 363
3 TraesCS4B01G291300 chr4B 80.567 494 70 19 997 1475 316988555 316989037 9.020000e-95 357
4 TraesCS4B01G291300 chr4B 91.089 101 9 0 1735 1835 201661382 201661282 1.280000e-28 137
5 TraesCS4B01G291300 chr4D 90.102 1667 109 38 460 2080 461212084 461213740 0.000000e+00 2113
6 TraesCS4B01G291300 chr4D 87.450 502 45 9 2117 2604 461213879 461214376 1.780000e-156 562
7 TraesCS4B01G291300 chr4D 88.128 438 38 2 4 440 461211570 461211994 2.350000e-140 508
8 TraesCS4B01G291300 chr4A 90.915 1420 70 25 692 2080 7408632 7407241 0.000000e+00 1853
9 TraesCS4B01G291300 chr7B 83.519 449 60 10 1029 1472 179639061 179638622 8.830000e-110 407
10 TraesCS4B01G291300 chr6B 82.697 445 64 9 1029 1469 19453033 19453468 1.490000e-102 383
11 TraesCS4B01G291300 chr6B 92.157 102 6 2 1735 1835 505324289 505324389 2.750000e-30 143
12 TraesCS4B01G291300 chr2B 78.431 408 49 20 1074 1475 663372743 663372369 2.050000e-56 230
13 TraesCS4B01G291300 chr5D 78.545 275 26 19 1614 1880 459348770 459348521 1.640000e-32 150
14 TraesCS4B01G291300 chr5D 92.157 102 6 2 1735 1835 249070655 249070555 2.750000e-30 143
15 TraesCS4B01G291300 chr2D 92.157 102 6 2 1735 1835 53042182 53042082 2.750000e-30 143
16 TraesCS4B01G291300 chr7D 91.176 102 7 2 1735 1835 2748720 2748620 1.280000e-28 137
17 TraesCS4B01G291300 chr7D 91.176 102 7 2 1735 1835 629749040 629748940 1.280000e-28 137


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 TraesCS4B01G291300 chr4B 576193950 576196600 2650 False 4896 4896 100.000 1 2651 1 chr4B.!!$F3 2650
1 TraesCS4B01G291300 chr4D 461211570 461214376 2806 False 1061 2113 88.560 4 2604 3 chr4D.!!$F1 2600
2 TraesCS4B01G291300 chr4A 7407241 7408632 1391 True 1853 1853 90.915 692 2080 1 chr4A.!!$R1 1388

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
204 205 0.036164 TATGCGGCAAGTTCCACTGT 59.964 50.0 6.82 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2186 1.072806 TGCACCTGATCTTGCTGAAGT 59.927 47.619 13.41 0.0 39.62 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
18 19 3.573569 CGAACAGTAACACCGACCA 57.426 52.632 0.00 0.00 0.00 4.02
19 20 1.415374 CGAACAGTAACACCGACCAG 58.585 55.000 0.00 0.00 0.00 4.00
20 21 1.269413 CGAACAGTAACACCGACCAGT 60.269 52.381 0.00 0.00 0.00 4.00
35 36 4.635765 CCGACCAGTGATTATTGTGAACAT 59.364 41.667 0.00 0.00 0.00 2.71
40 41 8.125978 ACCAGTGATTATTGTGAACATCATTT 57.874 30.769 0.00 0.00 0.00 2.32
41 42 8.587608 ACCAGTGATTATTGTGAACATCATTTT 58.412 29.630 0.00 0.00 0.00 1.82
54 55 7.379529 GTGAACATCATTTTCGAACAATGTCTT 59.620 33.333 21.58 15.11 33.91 3.01
98 99 4.670896 TTGATCCGACATATCAAGCAGA 57.329 40.909 0.00 0.00 38.19 4.26
142 143 5.439721 CCCTCCAATAGATTGTTCACATCA 58.560 41.667 1.78 0.00 36.06 3.07
143 144 5.887598 CCCTCCAATAGATTGTTCACATCAA 59.112 40.000 1.78 0.00 36.06 2.57
144 145 6.548622 CCCTCCAATAGATTGTTCACATCAAT 59.451 38.462 1.78 0.00 38.08 2.57
145 146 7.069085 CCCTCCAATAGATTGTTCACATCAATT 59.931 37.037 1.78 0.00 35.94 2.32
146 147 8.133627 CCTCCAATAGATTGTTCACATCAATTC 58.866 37.037 1.78 0.00 35.94 2.17
147 148 8.812513 TCCAATAGATTGTTCACATCAATTCT 57.187 30.769 1.78 0.00 35.94 2.40
148 149 9.246670 TCCAATAGATTGTTCACATCAATTCTT 57.753 29.630 1.78 0.00 35.94 2.52
175 176 3.006859 AGTTACATGGAAAAGGCAAAGGC 59.993 43.478 0.00 0.00 40.13 4.35
178 179 0.890683 ATGGAAAAGGCAAAGGCTCG 59.109 50.000 0.00 0.00 37.50 5.03
190 191 1.788258 AAGGCTCGATCACATATGCG 58.212 50.000 1.58 0.00 0.00 4.73
198 199 2.348872 CGATCACATATGCGGCAAGTTC 60.349 50.000 6.82 1.47 0.00 3.01
204 205 0.036164 TATGCGGCAAGTTCCACTGT 59.964 50.000 6.82 0.00 0.00 3.55
222 223 3.003275 ACTGTTAACACTGAACAATGCGG 59.997 43.478 3.59 0.00 36.41 5.69
236 237 2.034999 GCGGATCAACCCCACCAA 59.965 61.111 0.00 0.00 34.64 3.67
237 238 1.379843 GCGGATCAACCCCACCAAT 60.380 57.895 0.00 0.00 34.64 3.16
247 248 3.652057 ACCCCACCAATACATCTTCAG 57.348 47.619 0.00 0.00 0.00 3.02
293 294 4.051922 GTCAGAACTCAACATTGACGACT 58.948 43.478 0.00 0.00 32.90 4.18
297 298 2.408050 ACTCAACATTGACGACTGCTC 58.592 47.619 0.00 0.00 32.90 4.26
298 299 2.036475 ACTCAACATTGACGACTGCTCT 59.964 45.455 0.00 0.00 32.90 4.09
315 316 2.872858 GCTCTGTCTTTGAAACCGAAGT 59.127 45.455 0.00 0.00 0.00 3.01
323 324 5.050295 GTCTTTGAAACCGAAGTAACTGAGG 60.050 44.000 0.00 0.00 0.00 3.86
341 342 0.107643 GGCTAGAATGGTCCTCCTGC 59.892 60.000 0.00 0.00 34.23 4.85
346 347 0.107459 GAATGGTCCTCCTGCTCACC 60.107 60.000 0.00 0.00 34.23 4.02
360 361 1.396653 CTCACCTGGGCCAATTGATC 58.603 55.000 15.25 0.00 0.00 2.92
372 373 3.760684 GCCAATTGATCTTCAGTTCAGGT 59.239 43.478 7.12 0.00 0.00 4.00
392 393 2.413453 GTCGAAACCTGCTCTCATGTTC 59.587 50.000 0.00 0.00 31.29 3.18
415 416 0.321298 GGCACTTGAAGCGGGAACTA 60.321 55.000 0.00 0.00 0.00 2.24
431 433 4.081087 GGGAACTACTGCTTGTATGAAGGA 60.081 45.833 0.00 0.00 0.00 3.36
443 473 8.965819 TGCTTGTATGAAGGAATTGCTTTAATA 58.034 29.630 13.87 11.65 0.00 0.98
444 474 9.237846 GCTTGTATGAAGGAATTGCTTTAATAC 57.762 33.333 24.34 24.34 0.00 1.89
498 570 5.731591 TGCTTAAGGCTAAAGTTAGAGACC 58.268 41.667 4.29 0.00 42.39 3.85
502 574 4.453177 AGGCTAAAGTTAGAGACCGTTC 57.547 45.455 2.18 0.00 32.47 3.95
503 575 3.830755 AGGCTAAAGTTAGAGACCGTTCA 59.169 43.478 2.18 0.00 32.47 3.18
522 594 6.347483 CCGTTCAAAGTTAGCCTCTTTAGTTC 60.347 42.308 0.00 0.00 34.35 3.01
523 595 6.202188 CGTTCAAAGTTAGCCTCTTTAGTTCA 59.798 38.462 0.00 0.00 34.35 3.18
550 622 7.773224 TGAGATAAAAAGTTTGTTGTCCAGAGA 59.227 33.333 0.00 0.00 0.00 3.10
551 623 8.519799 AGATAAAAAGTTTGTTGTCCAGAGAA 57.480 30.769 0.00 0.00 0.00 2.87
610 682 9.640952 AACACTATTAGTGGTTATATGGCAAAT 57.359 29.630 24.01 0.00 45.36 2.32
636 708 3.001168 GCACACATCGAACAACAAACAAC 60.001 43.478 0.00 0.00 0.00 3.32
642 714 4.335082 TCGAACAACAAACAACTGTCTG 57.665 40.909 0.00 0.00 0.00 3.51
657 729 0.534873 GTCTGGCTCTTCTCTGGACC 59.465 60.000 0.00 0.00 0.00 4.46
667 739 2.030027 TCTCTGGACCAGGTGATGTT 57.970 50.000 21.56 0.00 31.51 2.71
676 748 4.323485 GGACCAGGTGATGTTGTTGATCTA 60.323 45.833 0.00 0.00 0.00 1.98
678 750 6.408092 GGACCAGGTGATGTTGTTGATCTATA 60.408 42.308 0.00 0.00 0.00 1.31
679 751 7.141758 ACCAGGTGATGTTGTTGATCTATAT 57.858 36.000 0.00 0.00 0.00 0.86
683 755 5.164051 GGTGATGTTGTTGATCTATATCGCG 60.164 44.000 0.00 0.00 33.56 5.87
690 762 5.949735 TGTTGATCTATATCGCGCTGATTA 58.050 37.500 17.38 10.19 38.57 1.75
705 777 6.301607 CGCGCTGATTATAATCTTGATGTTTG 59.698 38.462 22.77 6.95 36.39 2.93
776 856 3.152341 ACCATTCTGAAAAGTGCCTGAG 58.848 45.455 0.00 0.00 0.00 3.35
781 861 0.178992 TGAAAAGTGCCTGAGGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
783 863 1.073284 GAAAAGTGCCTGAGGTGGGTA 59.927 52.381 0.00 0.00 0.00 3.69
786 866 0.043334 AGTGCCTGAGGTGGGTATCT 59.957 55.000 0.00 0.00 0.00 1.98
812 892 0.959553 GATCCTTGATCCGACGGCTA 59.040 55.000 9.66 0.00 33.37 3.93
843 933 1.973281 CTTGGCCACCGCAAGTCAT 60.973 57.895 3.88 0.00 36.38 3.06
844 934 1.526575 CTTGGCCACCGCAAGTCATT 61.527 55.000 3.88 0.00 36.38 2.57
860 950 1.304134 ATTGAACCCGTGCCTTCCC 60.304 57.895 0.00 0.00 0.00 3.97
862 952 2.359975 GAACCCGTGCCTTCCCTG 60.360 66.667 0.00 0.00 0.00 4.45
921 1019 3.791973 GAGAATCGCATCGGGATAGAT 57.208 47.619 0.00 0.00 34.14 1.98
947 1054 0.624500 ATAGAAGAAGGGCAGGGGCA 60.625 55.000 0.00 0.00 43.71 5.36
948 1055 1.274703 TAGAAGAAGGGCAGGGGCAG 61.275 60.000 0.00 0.00 43.71 4.85
979 1090 2.012673 CAGAGGAAATCAAGAAGGCGG 58.987 52.381 0.00 0.00 0.00 6.13
983 1094 1.615919 GGAAATCAAGAAGGCGGGGAA 60.616 52.381 0.00 0.00 0.00 3.97
1119 1230 2.362632 AAGGAGGAGTACCGCGCT 60.363 61.111 5.56 0.00 41.83 5.92
1174 1285 1.736645 AACGACTGGTTCCGCATCG 60.737 57.895 0.00 7.37 31.79 3.84
1348 1459 1.741770 AAGGTCCGCAATCACGCTC 60.742 57.895 0.00 0.00 0.00 5.03
1349 1460 2.125512 GGTCCGCAATCACGCTCT 60.126 61.111 0.00 0.00 0.00 4.09
1405 1516 1.886542 GTGGGTTCTTGGTTGTGGATC 59.113 52.381 0.00 0.00 0.00 3.36
1476 1606 2.253452 GTGCACTTCAAGCCGCTG 59.747 61.111 10.32 0.00 0.00 5.18
1527 1657 3.443925 CACGCTCTCTGCCTCGGA 61.444 66.667 0.00 0.00 38.78 4.55
1569 1699 2.125106 GTGCCCATCCTGGTCGAC 60.125 66.667 7.13 7.13 35.17 4.20
1672 1802 4.590400 CTGCAAGACAGTTACAGTATGC 57.410 45.455 9.90 9.90 40.18 3.14
1777 1910 4.998033 GGACTAATAAGAGCCAGCAATACC 59.002 45.833 0.00 0.00 0.00 2.73
1800 1933 7.061054 ACCTATACTCTAGTTGTCATGTGCTA 58.939 38.462 0.00 0.00 0.00 3.49
1835 1969 4.942761 ATTTTGCTGATGAACTGGTTGT 57.057 36.364 0.00 0.00 0.00 3.32
1841 1975 4.341806 TGCTGATGAACTGGTTGTTGATTT 59.658 37.500 0.00 0.00 39.30 2.17
1866 2000 7.553334 TGAACTGTAGTTAGTTTGTCTGACTT 58.447 34.615 9.51 0.00 41.97 3.01
1910 2046 7.035840 AGTAGATTTGCATCCAACATTGATC 57.964 36.000 0.00 0.00 0.00 2.92
1915 2051 5.725325 TTGCATCCAACATTGATCTTCAA 57.275 34.783 0.00 0.00 41.09 2.69
1917 2053 5.472148 TGCATCCAACATTGATCTTCAAAC 58.528 37.500 0.00 0.00 40.12 2.93
1918 2054 5.010820 TGCATCCAACATTGATCTTCAAACA 59.989 36.000 0.00 0.00 40.12 2.83
1993 2132 6.547510 GCTGTTAATTTAGGATGGAACCTGAT 59.452 38.462 0.00 0.00 40.81 2.90
1995 2134 8.974060 TGTTAATTTAGGATGGAACCTGATAC 57.026 34.615 0.00 0.00 40.81 2.24
2003 2142 4.396166 GGATGGAACCTGATACTTGTGTTG 59.604 45.833 0.00 0.00 0.00 3.33
2004 2143 3.146066 TGGAACCTGATACTTGTGTTGC 58.854 45.455 0.00 0.00 0.00 4.17
2039 2178 5.291128 GTCTGTTTTCTGTCTCGACAAAGAA 59.709 40.000 1.02 0.16 41.33 2.52
2040 2179 6.018669 GTCTGTTTTCTGTCTCGACAAAGAAT 60.019 38.462 1.02 0.00 41.33 2.40
2049 2188 9.706691 TCTGTCTCGACAAAGAATAATAAAACT 57.293 29.630 1.02 0.00 41.33 2.66
2072 2211 1.816835 AGCAAGATCAGGTGCACAATG 59.183 47.619 20.43 16.53 43.42 2.82
2073 2212 1.542915 GCAAGATCAGGTGCACAATGT 59.457 47.619 20.43 4.58 40.58 2.71
2075 2214 3.553508 GCAAGATCAGGTGCACAATGTTT 60.554 43.478 20.43 8.85 40.58 2.83
2102 2253 6.387127 TGCCTTACCTATACTATCCAGGAAA 58.613 40.000 0.00 0.00 33.44 3.13
2119 2270 9.713684 ATCCAGGAAATATTAAAATGACTTGGA 57.286 29.630 0.00 0.00 0.00 3.53
2121 2272 9.754382 CCAGGAAATATTAAAATGACTTGGATG 57.246 33.333 0.00 0.00 0.00 3.51
2230 2472 8.370940 TGGTTGAATTGTTGCCTTTTATATTGA 58.629 29.630 0.00 0.00 0.00 2.57
2259 2501 1.462616 TTCATGATTGGAACAGCGGG 58.537 50.000 0.00 0.00 42.39 6.13
2261 2503 1.212688 TCATGATTGGAACAGCGGGAT 59.787 47.619 0.00 0.00 42.39 3.85
2285 2527 4.706035 TGACTTACGGGTTGTTGTGTTAT 58.294 39.130 0.00 0.00 0.00 1.89
2286 2528 5.851720 TGACTTACGGGTTGTTGTGTTATA 58.148 37.500 0.00 0.00 0.00 0.98
2294 2536 6.935771 ACGGGTTGTTGTGTTATAACTTCATA 59.064 34.615 16.33 6.13 0.00 2.15
2323 2565 9.733556 TTCTTGGTGCTATACTTTATTTTGAGA 57.266 29.630 0.00 0.00 0.00 3.27
2327 2569 9.162764 TGGTGCTATACTTTATTTTGAGAGAAC 57.837 33.333 0.00 0.00 0.00 3.01
2358 2603 9.947669 GATTTCATTGATTCATAGGAGAGTTTG 57.052 33.333 0.00 0.00 0.00 2.93
2367 2612 4.159321 TCATAGGAGAGTTTGCAGAGTCAG 59.841 45.833 14.03 0.00 0.00 3.51
2376 2621 2.908688 TGCAGAGTCAGCAACTACAA 57.091 45.000 7.88 0.00 38.74 2.41
2379 2624 3.561310 TGCAGAGTCAGCAACTACAAAAG 59.439 43.478 7.88 0.00 38.74 2.27
2393 2638 5.552178 ACTACAAAAGGACCAATCTCTGTC 58.448 41.667 0.00 0.00 0.00 3.51
2401 2646 1.208052 ACCAATCTCTGTCCGGACATG 59.792 52.381 36.21 28.63 41.01 3.21
2410 2655 4.047125 CCGGACATGCCCCAACCT 62.047 66.667 0.00 0.00 0.00 3.50
2417 2662 1.624813 ACATGCCCCAACCTGAAATTG 59.375 47.619 0.00 0.00 0.00 2.32
2422 2667 3.906846 TGCCCCAACCTGAAATTGTTAAT 59.093 39.130 0.00 0.00 0.00 1.40
2424 2669 5.046950 TGCCCCAACCTGAAATTGTTAATAC 60.047 40.000 0.00 0.00 0.00 1.89
2426 2671 6.627287 GCCCCAACCTGAAATTGTTAATACTC 60.627 42.308 0.00 0.00 0.00 2.59
2427 2672 6.663523 CCCCAACCTGAAATTGTTAATACTCT 59.336 38.462 0.00 0.00 0.00 3.24
2456 2710 0.809385 CAAGCTCATGAGTTGCCTGG 59.191 55.000 23.38 6.35 0.00 4.45
2465 2719 3.857157 TGAGTTGCCTGGTTAAACTCT 57.143 42.857 25.45 7.13 46.44 3.24
2489 2743 9.416284 TCTACCAATTTTAGAAACTTTGAACCT 57.584 29.630 0.00 0.00 0.00 3.50
2502 2756 9.356433 GAAACTTTGAACCTATACAGAGTAGAC 57.644 37.037 0.00 0.00 32.57 2.59
2504 2758 8.653036 ACTTTGAACCTATACAGAGTAGACTT 57.347 34.615 0.00 0.00 31.43 3.01
2534 2788 5.307716 TGTTGATCTCTCCATATGTATGCCA 59.692 40.000 1.24 0.00 32.40 4.92
2536 2790 3.942130 TCTCTCCATATGTATGCCACG 57.058 47.619 1.24 0.00 32.40 4.94
2565 2820 7.093552 TGGAAACATTTTGGTCTTTCTTTCTGA 60.094 33.333 0.00 0.00 33.40 3.27
2577 2832 5.829924 TCTTTCTTTCTGATTGCTTCCACTT 59.170 36.000 0.00 0.00 0.00 3.16
2585 2840 0.179032 TTGCTTCCACTTCAGCCGAA 60.179 50.000 0.00 0.00 34.91 4.30
2595 2850 4.038042 CCACTTCAGCCGAACTATCAGATA 59.962 45.833 0.00 0.00 0.00 1.98
2598 2853 3.562182 TCAGCCGAACTATCAGATACCA 58.438 45.455 0.00 0.00 0.00 3.25
2604 2859 7.063898 CAGCCGAACTATCAGATACCAATATTG 59.936 40.741 8.58 8.58 0.00 1.90
2605 2860 6.183360 GCCGAACTATCAGATACCAATATTGC 60.183 42.308 10.11 0.00 0.00 3.56
2606 2861 7.099764 CCGAACTATCAGATACCAATATTGCT 58.900 38.462 10.11 0.00 0.00 3.91
2607 2862 7.604164 CCGAACTATCAGATACCAATATTGCTT 59.396 37.037 10.11 1.74 0.00 3.91
2608 2863 8.651588 CGAACTATCAGATACCAATATTGCTTC 58.348 37.037 10.11 6.23 0.00 3.86
2609 2864 8.854614 AACTATCAGATACCAATATTGCTTCC 57.145 34.615 10.11 0.00 0.00 3.46
2610 2865 7.977818 ACTATCAGATACCAATATTGCTTCCA 58.022 34.615 10.11 0.00 0.00 3.53
2611 2866 7.880195 ACTATCAGATACCAATATTGCTTCCAC 59.120 37.037 10.11 0.00 0.00 4.02
2612 2867 6.252599 TCAGATACCAATATTGCTTCCACT 57.747 37.500 10.11 1.93 0.00 4.00
2613 2868 6.662755 TCAGATACCAATATTGCTTCCACTT 58.337 36.000 10.11 0.00 0.00 3.16
2614 2869 6.767902 TCAGATACCAATATTGCTTCCACTTC 59.232 38.462 10.11 0.00 0.00 3.01
2615 2870 6.543465 CAGATACCAATATTGCTTCCACTTCA 59.457 38.462 10.11 0.00 0.00 3.02
2616 2871 6.769822 AGATACCAATATTGCTTCCACTTCAG 59.230 38.462 10.11 0.00 0.00 3.02
2617 2872 3.445096 ACCAATATTGCTTCCACTTCAGC 59.555 43.478 10.11 0.00 36.49 4.26
2618 2873 3.181483 CCAATATTGCTTCCACTTCAGCC 60.181 47.826 10.11 0.00 34.91 4.85
2619 2874 1.737838 TATTGCTTCCACTTCAGCCG 58.262 50.000 0.00 0.00 34.91 5.52
2620 2875 0.036732 ATTGCTTCCACTTCAGCCGA 59.963 50.000 0.00 0.00 34.91 5.54
2621 2876 0.179032 TTGCTTCCACTTCAGCCGAA 60.179 50.000 0.00 0.00 34.91 4.30
2622 2877 0.884704 TGCTTCCACTTCAGCCGAAC 60.885 55.000 0.00 0.00 34.91 3.95
2623 2878 0.884704 GCTTCCACTTCAGCCGAACA 60.885 55.000 0.00 0.00 0.00 3.18
2624 2879 1.593196 CTTCCACTTCAGCCGAACAA 58.407 50.000 0.00 0.00 0.00 2.83
2625 2880 1.532868 CTTCCACTTCAGCCGAACAAG 59.467 52.381 0.00 0.00 0.00 3.16
2626 2881 0.250295 TCCACTTCAGCCGAACAAGG 60.250 55.000 0.00 0.00 0.00 3.61
2635 2890 3.159298 CCGAACAAGGCATACTGCT 57.841 52.632 0.00 0.00 44.28 4.24
2636 2891 1.009829 CCGAACAAGGCATACTGCTC 58.990 55.000 0.00 0.00 44.28 4.26
2637 2892 0.647410 CGAACAAGGCATACTGCTCG 59.353 55.000 0.00 0.00 44.28 5.03
2638 2893 1.735700 CGAACAAGGCATACTGCTCGA 60.736 52.381 0.00 0.00 44.28 4.04
2639 2894 1.929836 GAACAAGGCATACTGCTCGAG 59.070 52.381 8.45 8.45 44.28 4.04
2640 2895 0.460987 ACAAGGCATACTGCTCGAGC 60.461 55.000 30.42 30.42 44.28 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.269413 ACTGGTCGGTGTTACTGTTCG 60.269 52.381 0.00 0.00 0.00 3.95
1 2 2.132762 CACTGGTCGGTGTTACTGTTC 58.867 52.381 1.96 0.00 33.04 3.18
2 3 1.758280 TCACTGGTCGGTGTTACTGTT 59.242 47.619 9.44 0.00 38.28 3.16
14 15 6.741992 TGATGTTCACAATAATCACTGGTC 57.258 37.500 0.00 0.00 0.00 4.02
15 16 7.707624 AATGATGTTCACAATAATCACTGGT 57.292 32.000 0.00 0.00 32.18 4.00
18 19 8.729756 TCGAAAATGATGTTCACAATAATCACT 58.270 29.630 0.00 0.00 32.18 3.41
19 20 8.894409 TCGAAAATGATGTTCACAATAATCAC 57.106 30.769 0.00 0.00 32.18 3.06
20 21 9.340695 GTTCGAAAATGATGTTCACAATAATCA 57.659 29.630 0.00 0.00 33.80 2.57
35 36 5.507149 CCACCAAGACATTGTTCGAAAATGA 60.507 40.000 25.90 1.94 38.21 2.57
40 41 3.201353 TCCACCAAGACATTGTTCGAA 57.799 42.857 0.00 0.00 34.39 3.71
41 42 2.920724 TCCACCAAGACATTGTTCGA 57.079 45.000 0.00 0.00 34.39 3.71
91 92 5.004061 CGTTTATCATGCACATTTCTGCTTG 59.996 40.000 0.00 0.00 41.47 4.01
93 94 4.665212 CGTTTATCATGCACATTTCTGCT 58.335 39.130 0.00 0.00 38.07 4.24
94 95 3.241322 GCGTTTATCATGCACATTTCTGC 59.759 43.478 0.00 0.00 37.36 4.26
96 97 3.683989 CGCGTTTATCATGCACATTTCT 58.316 40.909 0.00 0.00 37.23 2.52
98 99 2.184448 GCGCGTTTATCATGCACATTT 58.816 42.857 8.43 0.00 37.23 2.32
143 144 8.903820 GCCTTTTCCATGTAACTACATAAGAAT 58.096 33.333 12.04 0.00 44.57 2.40
144 145 7.885922 TGCCTTTTCCATGTAACTACATAAGAA 59.114 33.333 2.10 6.31 44.57 2.52
145 146 7.398829 TGCCTTTTCCATGTAACTACATAAGA 58.601 34.615 2.10 0.91 44.57 2.10
146 147 7.624360 TGCCTTTTCCATGTAACTACATAAG 57.376 36.000 2.10 3.38 44.57 1.73
147 148 8.410673 TTTGCCTTTTCCATGTAACTACATAA 57.589 30.769 2.10 0.00 44.57 1.90
148 149 7.122055 CCTTTGCCTTTTCCATGTAACTACATA 59.878 37.037 2.10 0.00 44.57 2.29
150 151 5.242838 CCTTTGCCTTTTCCATGTAACTACA 59.757 40.000 0.00 0.00 40.98 2.74
151 152 5.709966 CCTTTGCCTTTTCCATGTAACTAC 58.290 41.667 0.00 0.00 0.00 2.73
152 153 4.219725 GCCTTTGCCTTTTCCATGTAACTA 59.780 41.667 0.00 0.00 0.00 2.24
153 154 3.006859 GCCTTTGCCTTTTCCATGTAACT 59.993 43.478 0.00 0.00 0.00 2.24
154 155 3.006859 AGCCTTTGCCTTTTCCATGTAAC 59.993 43.478 0.00 0.00 38.69 2.50
175 176 1.458445 CTTGCCGCATATGTGATCGAG 59.542 52.381 17.89 12.95 0.00 4.04
178 179 2.031682 GGAACTTGCCGCATATGTGATC 60.032 50.000 17.89 9.29 0.00 2.92
198 199 4.290155 GCATTGTTCAGTGTTAACAGTGG 58.710 43.478 32.85 21.03 45.06 4.00
204 205 4.068599 TGATCCGCATTGTTCAGTGTTAA 58.931 39.130 0.00 0.00 0.00 2.01
222 223 4.170468 AGATGTATTGGTGGGGTTGATC 57.830 45.455 0.00 0.00 0.00 2.92
236 237 1.212935 GGGTGGCCACTGAAGATGTAT 59.787 52.381 33.91 0.00 0.00 2.29
237 238 0.618458 GGGTGGCCACTGAAGATGTA 59.382 55.000 33.91 0.00 0.00 2.29
261 262 1.226746 GAGTTCTGACCAACCAACCG 58.773 55.000 0.00 0.00 0.00 4.44
293 294 2.613026 TCGGTTTCAAAGACAGAGCA 57.387 45.000 0.00 0.00 0.00 4.26
297 298 5.522460 TCAGTTACTTCGGTTTCAAAGACAG 59.478 40.000 0.00 0.00 0.00 3.51
298 299 5.421277 TCAGTTACTTCGGTTTCAAAGACA 58.579 37.500 0.00 0.00 0.00 3.41
315 316 3.961408 GAGGACCATTCTAGCCTCAGTTA 59.039 47.826 0.00 0.00 44.91 2.24
323 324 1.069978 GAGCAGGAGGACCATTCTAGC 59.930 57.143 0.00 0.00 38.94 3.42
341 342 1.064166 AGATCAATTGGCCCAGGTGAG 60.064 52.381 5.42 0.00 0.00 3.51
346 347 2.731572 ACTGAAGATCAATTGGCCCAG 58.268 47.619 5.42 10.44 0.00 4.45
360 361 3.113260 AGGTTTCGACCTGAACTGAAG 57.887 47.619 0.00 0.00 38.98 3.02
372 373 2.839486 AACATGAGAGCAGGTTTCGA 57.161 45.000 0.00 0.00 45.77 3.71
392 393 2.680913 CCCGCTTCAAGTGCCGAAG 61.681 63.158 0.00 0.00 42.31 3.79
415 416 4.338879 AGCAATTCCTTCATACAAGCAGT 58.661 39.130 0.00 0.00 0.00 4.40
443 473 3.442977 GCTCCAAGCAATCTGATTCAAGT 59.557 43.478 0.00 0.00 41.89 3.16
444 474 3.695060 AGCTCCAAGCAATCTGATTCAAG 59.305 43.478 0.00 0.00 45.56 3.02
446 476 3.361281 AGCTCCAAGCAATCTGATTCA 57.639 42.857 0.00 0.00 45.56 2.57
457 487 2.229784 AGCATGTTAACAAGCTCCAAGC 59.770 45.455 27.80 14.24 46.47 4.01
498 570 6.202188 TGAACTAAAGAGGCTAACTTTGAACG 59.798 38.462 10.52 0.00 37.96 3.95
502 574 7.604164 TCTCATGAACTAAAGAGGCTAACTTTG 59.396 37.037 10.52 4.75 37.96 2.77
503 575 7.680730 TCTCATGAACTAAAGAGGCTAACTTT 58.319 34.615 6.46 6.46 40.13 2.66
522 594 8.352201 TCTGGACAACAAACTTTTTATCTCATG 58.648 33.333 0.00 0.00 0.00 3.07
523 595 8.463930 TCTGGACAACAAACTTTTTATCTCAT 57.536 30.769 0.00 0.00 0.00 2.90
610 682 4.820284 TTGTTGTTCGATGTGTGCATAA 57.180 36.364 0.00 0.00 35.07 1.90
615 687 4.262743 CAGTTGTTTGTTGTTCGATGTGTG 59.737 41.667 0.00 0.00 0.00 3.82
636 708 1.204467 GTCCAGAGAAGAGCCAGACAG 59.796 57.143 0.00 0.00 0.00 3.51
642 714 0.907230 ACCTGGTCCAGAGAAGAGCC 60.907 60.000 21.23 0.00 32.44 4.70
657 729 6.128715 GCGATATAGATCAACAACATCACCTG 60.129 42.308 0.00 0.00 31.78 4.00
667 739 3.915437 TCAGCGCGATATAGATCAACA 57.085 42.857 12.10 0.00 31.78 3.33
676 748 7.708322 ACATCAAGATTATAATCAGCGCGATAT 59.292 33.333 24.00 0.00 37.89 1.63
678 750 5.871524 ACATCAAGATTATAATCAGCGCGAT 59.128 36.000 24.00 0.00 37.89 4.58
679 751 5.230182 ACATCAAGATTATAATCAGCGCGA 58.770 37.500 24.00 13.78 37.89 5.87
683 755 8.551205 TCGTCAAACATCAAGATTATAATCAGC 58.449 33.333 24.00 1.82 37.89 4.26
747 827 6.446318 GCACTTTTCAGAATGGTATTCACAA 58.554 36.000 4.56 0.00 36.16 3.33
754 834 4.326826 CTCAGGCACTTTTCAGAATGGTA 58.673 43.478 0.00 0.00 34.60 3.25
756 836 2.490903 CCTCAGGCACTTTTCAGAATGG 59.509 50.000 0.00 0.00 34.60 3.16
766 846 0.912486 GATACCCACCTCAGGCACTT 59.088 55.000 0.00 0.00 34.60 3.16
776 856 2.106684 GGATCCAAGGAAGATACCCACC 59.893 54.545 6.95 0.00 0.00 4.61
812 892 3.148084 CCAAGTCAGGGGTGACGT 58.852 61.111 0.00 0.00 43.15 4.34
843 933 2.114411 GGGAAGGCACGGGTTCAA 59.886 61.111 0.00 0.00 0.00 2.69
844 934 2.852075 AGGGAAGGCACGGGTTCA 60.852 61.111 0.00 0.00 0.00 3.18
879 975 1.160137 GACTGCTTGGATTTCACGCT 58.840 50.000 0.00 0.00 40.76 5.07
921 1019 4.163427 CCTGCCCTTCTTCTATGGATCTA 58.837 47.826 0.00 0.00 0.00 1.98
952 1059 0.740868 TTGATTTCCTCTGCTCCGCG 60.741 55.000 0.00 0.00 0.00 6.46
979 1090 2.026301 CGCTCCGACGATCTTCCC 59.974 66.667 0.00 0.00 34.06 3.97
1119 1230 1.101635 CGGAGGTGTAGGCGATGAGA 61.102 60.000 0.00 0.00 0.00 3.27
1405 1516 2.478370 GCATCCATGTCCAACAATCACG 60.478 50.000 0.00 0.00 0.00 4.35
1569 1699 2.046023 TGCTTCACCATGCCCGAG 60.046 61.111 0.00 0.00 0.00 4.63
1685 1815 2.054363 CTGTAACTGTCACTGTCAGCG 58.946 52.381 0.00 0.00 36.50 5.18
1777 1910 8.160521 AGTAGCACATGACAACTAGAGTATAG 57.839 38.462 0.00 0.00 0.00 1.31
1835 1969 9.391006 AGACAAACTAACTACAGTTCAAATCAA 57.609 29.630 0.00 0.00 37.78 2.57
1841 1975 7.108841 AGTCAGACAAACTAACTACAGTTCA 57.891 36.000 2.66 0.00 37.78 3.18
1866 2000 4.827692 ACTACTTCGATGCACACCAAATA 58.172 39.130 0.00 0.00 0.00 1.40
1915 2051 9.949174 GAGGCAATTAATTTGTTCAAATTTGTT 57.051 25.926 22.60 16.24 37.65 2.83
1917 2053 7.745594 CGGAGGCAATTAATTTGTTCAAATTTG 59.254 33.333 22.60 12.15 37.65 2.32
1918 2054 7.572910 GCGGAGGCAATTAATTTGTTCAAATTT 60.573 33.333 22.60 8.48 39.62 1.82
1993 2132 5.398176 CTTCTGTTAACGCAACACAAGTA 57.602 39.130 0.26 0.00 42.29 2.24
1995 2134 4.034048 AGACTTCTGTTAACGCAACACAAG 59.966 41.667 13.42 13.42 44.34 3.16
2039 2178 8.680903 CACCTGATCTTGCTGAAGTTTTATTAT 58.319 33.333 0.00 0.00 0.00 1.28
2040 2179 7.362056 GCACCTGATCTTGCTGAAGTTTTATTA 60.362 37.037 7.13 0.00 35.74 0.98
2045 2184 2.555757 GCACCTGATCTTGCTGAAGTTT 59.444 45.455 7.13 0.00 35.74 2.66
2047 2186 1.072806 TGCACCTGATCTTGCTGAAGT 59.927 47.619 13.41 0.00 39.62 3.01
2049 2188 1.202794 TGTGCACCTGATCTTGCTGAA 60.203 47.619 15.69 0.00 39.62 3.02
2075 2214 6.847567 TCCTGGATAGTATAGGTAAGGCAAAA 59.152 38.462 0.00 0.00 33.30 2.44
2110 2261 5.129320 TGCTACAGTCATACATCCAAGTCAT 59.871 40.000 0.00 0.00 0.00 3.06
2112 2263 4.806247 GTGCTACAGTCATACATCCAAGTC 59.194 45.833 0.00 0.00 0.00 3.01
2114 2265 4.807834 CAGTGCTACAGTCATACATCCAAG 59.192 45.833 0.00 0.00 0.00 3.61
2116 2267 3.430790 GCAGTGCTACAGTCATACATCCA 60.431 47.826 8.18 0.00 0.00 3.41
2117 2268 3.126831 GCAGTGCTACAGTCATACATCC 58.873 50.000 8.18 0.00 0.00 3.51
2118 2269 4.052159 AGCAGTGCTACAGTCATACATC 57.948 45.455 18.11 0.00 36.99 3.06
2187 2429 4.753107 TCAACCAGTTTTAGGTTTCTAGCG 59.247 41.667 0.00 0.00 46.85 4.26
2257 2499 2.786777 ACAACCCGTAAGTCAAATCCC 58.213 47.619 0.00 0.00 0.00 3.85
2259 2501 4.035909 ACACAACAACCCGTAAGTCAAATC 59.964 41.667 0.00 0.00 0.00 2.17
2261 2503 3.345414 ACACAACAACCCGTAAGTCAAA 58.655 40.909 0.00 0.00 0.00 2.69
2286 2528 9.686683 AGTATAGCACCAAGAAATTATGAAGTT 57.313 29.630 0.00 0.00 0.00 2.66
2299 2541 9.383519 TCTCTCAAAATAAAGTATAGCACCAAG 57.616 33.333 0.00 0.00 0.00 3.61
2315 2557 8.521176 CAATGAAATCCTCTGTTCTCTCAAAAT 58.479 33.333 0.00 0.00 0.00 1.82
2323 2565 9.339850 CTATGAATCAATGAAATCCTCTGTTCT 57.660 33.333 0.00 0.00 0.00 3.01
2327 2569 8.155510 TCTCCTATGAATCAATGAAATCCTCTG 58.844 37.037 0.00 0.00 0.00 3.35
2333 2575 8.411683 GCAAACTCTCCTATGAATCAATGAAAT 58.588 33.333 0.00 0.00 0.00 2.17
2358 2603 3.058639 CCTTTTGTAGTTGCTGACTCTGC 60.059 47.826 1.04 1.04 39.86 4.26
2367 2612 4.762251 AGAGATTGGTCCTTTTGTAGTTGC 59.238 41.667 0.00 0.00 0.00 4.17
2370 2615 5.552178 GACAGAGATTGGTCCTTTTGTAGT 58.448 41.667 0.00 0.00 0.00 2.73
2393 2638 4.047125 AGGTTGGGGCATGTCCGG 62.047 66.667 10.95 0.00 34.94 5.14
2394 2639 2.751436 CAGGTTGGGGCATGTCCG 60.751 66.667 10.95 0.00 34.94 4.79
2401 2646 4.551702 ATTAACAATTTCAGGTTGGGGC 57.448 40.909 0.00 0.00 0.00 5.80
2417 2662 6.819146 AGCTTGCCAAGTTAGAGAGTATTAAC 59.181 38.462 6.28 0.00 0.00 2.01
2422 2667 3.832490 TGAGCTTGCCAAGTTAGAGAGTA 59.168 43.478 6.28 0.00 0.00 2.59
2424 2669 3.325293 TGAGCTTGCCAAGTTAGAGAG 57.675 47.619 6.28 0.00 0.00 3.20
2426 2671 3.603532 TCATGAGCTTGCCAAGTTAGAG 58.396 45.455 6.28 0.00 0.00 2.43
2427 2672 3.008375 ACTCATGAGCTTGCCAAGTTAGA 59.992 43.478 22.83 0.00 0.00 2.10
2489 2743 9.916360 TCAACATCCTTAAGTCTACTCTGTATA 57.084 33.333 0.97 0.00 0.00 1.47
2492 2746 7.617723 AGATCAACATCCTTAAGTCTACTCTGT 59.382 37.037 0.97 0.00 0.00 3.41
2502 2756 8.373981 ACATATGGAGAGATCAACATCCTTAAG 58.626 37.037 7.80 0.00 32.79 1.85
2504 2758 7.862274 ACATATGGAGAGATCAACATCCTTA 57.138 36.000 7.80 0.23 32.79 2.69
2534 2788 3.496331 AGACCAAAATGTTTCCATCCGT 58.504 40.909 0.00 0.00 0.00 4.69
2536 2790 6.101650 AGAAAGACCAAAATGTTTCCATCC 57.898 37.500 0.00 0.00 33.43 3.51
2545 2800 6.927381 AGCAATCAGAAAGAAAGACCAAAATG 59.073 34.615 0.00 0.00 0.00 2.32
2546 2801 7.059202 AGCAATCAGAAAGAAAGACCAAAAT 57.941 32.000 0.00 0.00 0.00 1.82
2565 2820 0.036732 TCGGCTGAAGTGGAAGCAAT 59.963 50.000 0.00 0.00 41.36 3.56
2577 2832 3.562182 TGGTATCTGATAGTTCGGCTGA 58.438 45.455 0.00 0.00 0.00 4.26
2585 2840 7.880195 GTGGAAGCAATATTGGTATCTGATAGT 59.120 37.037 19.84 1.66 38.04 2.12
2595 2850 3.445096 GCTGAAGTGGAAGCAATATTGGT 59.555 43.478 14.31 14.31 41.27 3.67
2598 2853 2.684881 CGGCTGAAGTGGAAGCAATATT 59.315 45.455 0.00 0.00 41.36 1.28
2604 2859 0.884704 TGTTCGGCTGAAGTGGAAGC 60.885 55.000 8.61 0.00 38.76 3.86
2605 2860 1.532868 CTTGTTCGGCTGAAGTGGAAG 59.467 52.381 8.61 5.19 33.98 3.46
2606 2861 1.593196 CTTGTTCGGCTGAAGTGGAA 58.407 50.000 8.61 0.00 33.98 3.53
2607 2862 0.250295 CCTTGTTCGGCTGAAGTGGA 60.250 55.000 8.61 0.00 33.98 4.02
2608 2863 1.856265 GCCTTGTTCGGCTGAAGTGG 61.856 60.000 8.61 11.90 46.63 4.00
2609 2864 1.576421 GCCTTGTTCGGCTGAAGTG 59.424 57.895 8.61 1.76 46.63 3.16
2610 2865 4.065110 GCCTTGTTCGGCTGAAGT 57.935 55.556 8.61 0.00 46.63 3.01


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

AutoCloner maintained by Alex Coulton.