Multiple sequence alignment - TraesCS2D01G373900

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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 TraesCS2D01G373900 chr2D 100.000 5578 0 0 1 5578 477268994 477274571 0.000000e+00 10301.0
1 TraesCS2D01G373900 chr2D 89.932 1460 140 3 3132 4585 477395483 477396941 0.000000e+00 1875.0
2 TraesCS2D01G373900 chr2D 82.229 619 59 31 885 1465 477393852 477394457 2.340000e-133 486.0
3 TraesCS2D01G373900 chr2D 86.000 400 47 6 2107 2501 477395078 477395473 2.400000e-113 420.0
4 TraesCS2D01G373900 chr2D 87.941 340 37 3 1120 1458 477264784 477264448 1.130000e-106 398.0
5 TraesCS2D01G373900 chr2D 82.937 252 38 5 1820 2069 477394763 477395011 7.270000e-54 222.0
6 TraesCS2D01G373900 chr2D 78.846 104 20 2 3962 4064 493004995 493004893 1.000000e-07 69.4
7 TraesCS2D01G373900 chr2B 93.918 3716 159 31 1820 5497 559307027 559310713 0.000000e+00 5548.0
8 TraesCS2D01G373900 chr2B 89.416 1455 146 8 3137 4585 559417441 559418893 0.000000e+00 1827.0
9 TraesCS2D01G373900 chr2B 93.198 985 53 8 544 1516 559305721 559306703 0.000000e+00 1435.0
10 TraesCS2D01G373900 chr2B 86.453 406 46 6 2100 2500 559417024 559417425 2.390000e-118 436.0
11 TraesCS2D01G373900 chr2B 80.357 616 76 26 885 1465 559415950 559416555 5.160000e-115 425.0
12 TraesCS2D01G373900 chr2B 89.968 309 31 0 1150 1458 559193246 559192938 3.130000e-107 399.0
13 TraesCS2D01G373900 chr2B 85.714 231 28 4 1850 2077 559416745 559416973 7.220000e-59 239.0
14 TraesCS2D01G373900 chr2B 78.571 140 12 6 1570 1709 559306833 559306954 5.990000e-10 76.8
15 TraesCS2D01G373900 chr2B 79.808 104 19 2 3962 4064 579572123 579572021 2.160000e-09 75.0
16 TraesCS2D01G373900 chr2A 93.133 3160 121 33 2359 5497 619756007 619759091 0.000000e+00 4545.0
17 TraesCS2D01G373900 chr2A 91.313 1531 102 19 1 1516 619753932 619755446 0.000000e+00 2061.0
18 TraesCS2D01G373900 chr2A 89.966 1465 142 4 3126 4585 619766539 619768003 0.000000e+00 1886.0
19 TraesCS2D01G373900 chr2A 91.049 324 29 0 1142 1465 619765217 619765540 6.630000e-119 438.0
20 TraesCS2D01G373900 chr2A 87.222 360 39 5 2107 2461 619766145 619766502 2.420000e-108 403.0
21 TraesCS2D01G373900 chr2A 87.311 331 40 2 1128 1458 619628329 619628001 1.470000e-100 377.0
22 TraesCS2D01G373900 chr2A 83.155 374 37 15 1670 2020 619755638 619756008 9.020000e-83 318.0
23 TraesCS2D01G373900 chr2A 83.908 261 35 6 1820 2077 619765830 619766086 5.580000e-60 243.0
24 TraesCS2D01G373900 chr2A 88.415 164 16 2 1569 1731 619755572 619755733 1.590000e-45 195.0
25 TraesCS2D01G373900 chr6D 84.058 276 41 3 1184 1458 304297162 304296889 4.290000e-66 263.0
26 TraesCS2D01G373900 chr3A 83.516 91 12 1 77 167 599782691 599782604 1.290000e-11 82.4
27 TraesCS2D01G373900 chr1B 88.406 69 7 1 113 181 307486484 307486417 1.290000e-11 82.4


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 TraesCS2D01G373900 chr2D 477268994 477274571 5577 False 10301.000000 10301 100.000000 1 5578 1 chr2D.!!$F1 5577
1 TraesCS2D01G373900 chr2D 477393852 477396941 3089 False 750.750000 1875 85.274500 885 4585 4 chr2D.!!$F2 3700
2 TraesCS2D01G373900 chr2B 559305721 559310713 4992 False 2353.266667 5548 88.562333 544 5497 3 chr2B.!!$F1 4953
3 TraesCS2D01G373900 chr2B 559415950 559418893 2943 False 731.750000 1827 85.485000 885 4585 4 chr2B.!!$F2 3700
4 TraesCS2D01G373900 chr2A 619753932 619759091 5159 False 1779.750000 4545 89.004000 1 5497 4 chr2A.!!$F1 5496
5 TraesCS2D01G373900 chr2A 619765217 619768003 2786 False 742.500000 1886 88.036250 1142 4585 4 chr2A.!!$F2 3443

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
216 217 0.102481 GATGTAAAGCGCGGGAGAGA 59.898 55.0 8.83 0.00 0.00 3.10 F
217 218 0.753262 ATGTAAAGCGCGGGAGAGAT 59.247 50.0 8.83 0.00 0.00 2.75 F
1476 1546 0.806868 ATTCTTGTGGCAGCACATCG 59.193 50.0 0.00 0.00 34.76 3.84 F
1480 1550 1.360931 TTGTGGCAGCACATCGATCG 61.361 55.0 9.36 9.36 34.76 3.69 F
2570 2929 0.107831 TCCAACAACTCGGGAAGTGG 59.892 55.0 0.00 0.00 38.58 4.00 F
2742 3109 0.036306 AACTGAACCTGGGCCTTACG 59.964 55.0 4.53 0.00 0.00 3.18 F
3354 3727 0.255033 GGGGTATTTGGTTCTCGGCT 59.745 55.0 0.00 0.00 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2328 1.074405 AGCCCAATGAAGCTGACAAGA 59.926 47.619 0.00 0.00 38.11 3.02 R
2091 2418 5.336150 TGGTTAAAATGGTATGCACATGG 57.664 39.130 0.00 0.00 0.00 3.66 R
2291 2650 0.248458 ACGACGCAAACCAAAGCAAG 60.248 50.000 0.00 0.00 0.00 4.01 R
2664 3023 0.586319 CCCAATATGCAAGGTACGCG 59.414 55.000 3.53 3.53 0.00 6.01 R
3601 3980 1.915141 AGCTGCAGTACCATTGCTTT 58.085 45.000 16.64 0.00 42.02 3.51 R
4541 4920 2.655090 TGAAAGCATCCACCTTGTCA 57.345 45.000 0.00 0.00 0.00 3.58 R
4805 5189 0.604780 CAACTCCTGCCACACTCCTG 60.605 60.000 0.00 0.00 0.00 3.86 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
21 22 0.577269 GTTACATAGCGCGGCTTCAG 59.423 55.000 8.83 2.07 40.44 3.02
47 48 4.082523 GCTACGTGCTCTGGGCCA 62.083 66.667 5.85 5.85 40.92 5.36
57 58 1.030457 CTCTGGGCCAAGATGAATGC 58.970 55.000 11.26 0.00 0.00 3.56
59 60 0.749091 CTGGGCCAAGATGAATGCGA 60.749 55.000 8.04 0.00 0.00 5.10
89 90 3.518998 CGAGGCCCGAGATGTCGT 61.519 66.667 11.66 0.00 45.30 4.34
100 101 2.126463 ATGTCGTGTCGGTCAGCG 60.126 61.111 0.00 0.00 0.00 5.18
121 122 4.778415 CGCTCCTGTCCGGTCACG 62.778 72.222 0.00 0.00 40.55 4.35
126 127 3.403057 CTGTCCGGTCACGTTGCG 61.403 66.667 0.00 0.00 38.78 4.85
138 139 2.082366 CGTTGCGTGGCTTCAATGC 61.082 57.895 0.00 0.00 0.00 3.56
156 157 2.728180 CGGCCGCTACATGCTCTA 59.272 61.111 14.67 0.00 40.11 2.43
200 201 2.872557 CAGCACGTGCCTTGGATG 59.127 61.111 35.51 22.36 43.38 3.51
206 207 1.135689 CACGTGCCTTGGATGTAAAGC 60.136 52.381 0.82 0.00 0.00 3.51
209 210 1.062525 GCCTTGGATGTAAAGCGCG 59.937 57.895 0.00 0.00 0.00 6.86
210 211 1.721487 CCTTGGATGTAAAGCGCGG 59.279 57.895 8.83 0.00 0.00 6.46
216 217 0.102481 GATGTAAAGCGCGGGAGAGA 59.898 55.000 8.83 0.00 0.00 3.10
217 218 0.753262 ATGTAAAGCGCGGGAGAGAT 59.247 50.000 8.83 0.00 0.00 2.75
253 254 2.034221 GGGCCAGGGTTGTCAGAC 59.966 66.667 4.39 0.00 0.00 3.51
256 257 2.743718 CCAGGGTTGTCAGACGCT 59.256 61.111 0.00 0.00 42.74 5.07
259 260 0.868406 CAGGGTTGTCAGACGCTTTC 59.132 55.000 0.00 0.00 40.38 2.62
279 280 2.110213 GTGGCAGTGGTTCGGACA 59.890 61.111 0.00 0.00 0.00 4.02
311 312 3.306433 CCCCCTGGTTTATTTTCGGTTTG 60.306 47.826 0.00 0.00 0.00 2.93
357 359 5.241949 ACAGAATGGATCGATACAGTACCTC 59.758 44.000 16.93 7.30 43.62 3.85
362 364 3.304525 GGATCGATACAGTACCTCGTTGG 60.305 52.174 1.67 0.00 42.93 3.77
372 374 4.062991 AGTACCTCGTTGGATGACAAAAC 58.937 43.478 4.38 0.00 41.58 2.43
374 376 3.486383 ACCTCGTTGGATGACAAAACAT 58.514 40.909 4.38 0.00 41.58 2.71
377 379 4.261572 CCTCGTTGGATGACAAAACATGTT 60.262 41.667 4.92 4.92 41.58 2.71
381 383 4.852134 TGGATGACAAAACATGTTCTGG 57.148 40.909 16.03 9.24 44.12 3.86
382 384 4.468713 TGGATGACAAAACATGTTCTGGA 58.531 39.130 16.03 2.90 44.12 3.86
383 385 4.278170 TGGATGACAAAACATGTTCTGGAC 59.722 41.667 16.03 9.91 44.12 4.02
412 425 1.835494 GGAGGTTTGAGCCCTTAACC 58.165 55.000 0.00 0.00 41.27 2.85
546 559 5.479306 AGTATAACCTACGCAATGCCTATG 58.521 41.667 0.00 0.00 0.00 2.23
550 563 1.344438 CCTACGCAATGCCTATGGAGA 59.656 52.381 0.00 0.00 0.00 3.71
626 639 2.631418 TCGACGAGAAGGTTGCTTAG 57.369 50.000 0.00 0.00 0.00 2.18
627 640 1.201647 TCGACGAGAAGGTTGCTTAGG 59.798 52.381 0.00 0.00 0.00 2.69
644 660 4.514401 CTTAGGCAGAAAGAATAACCCGT 58.486 43.478 0.00 0.00 0.00 5.28
677 694 4.453478 ACACATCAATAATAGCAGATGCCG 59.547 41.667 0.14 0.00 41.08 5.69
694 711 3.261580 TGCCGACTATGTCAAATGTGAG 58.738 45.455 0.00 0.00 33.27 3.51
698 715 5.446473 GCCGACTATGTCAAATGTGAGAAAG 60.446 44.000 0.00 0.00 33.27 2.62
715 732 2.105006 AAGCTGTACACCAGATGCAG 57.895 50.000 5.46 0.00 44.49 4.41
772 789 4.817517 ACATTTAGGAACAGAGGTACGTG 58.182 43.478 0.00 0.00 0.00 4.49
776 793 3.097342 AGGAACAGAGGTACGTGGTAT 57.903 47.619 0.00 0.00 0.00 2.73
956 977 1.533547 GGCTACCTCGACGTAGAAAGC 60.534 57.143 21.24 14.77 38.41 3.51
986 1007 1.736645 GTGCGCCGTTCTCTTGCTA 60.737 57.895 4.18 0.00 0.00 3.49
991 1012 1.079503 GCCGTTCTCTTGCTAGGTTG 58.920 55.000 0.00 0.00 0.00 3.77
1423 1493 1.913262 ACCGTCATCCAGACCTGCA 60.913 57.895 0.00 0.00 44.66 4.41
1473 1543 1.885887 GGTAATTCTTGTGGCAGCACA 59.114 47.619 0.00 0.00 0.00 4.57
1476 1546 0.806868 ATTCTTGTGGCAGCACATCG 59.193 50.000 0.00 0.00 34.76 3.84
1480 1550 1.360931 TTGTGGCAGCACATCGATCG 61.361 55.000 9.36 9.36 34.76 3.69
1481 1551 2.202919 TGGCAGCACATCGATCGG 60.203 61.111 16.41 2.12 0.00 4.18
1535 1747 5.545588 ACTGGCATGCTCATACATACTAAG 58.454 41.667 18.92 1.14 0.00 2.18
1536 1748 4.898320 TGGCATGCTCATACATACTAAGG 58.102 43.478 18.92 0.00 0.00 2.69
1537 1749 4.592778 TGGCATGCTCATACATACTAAGGA 59.407 41.667 18.92 0.00 0.00 3.36
1568 1791 5.459505 AGGCTCATACATACTAAGTCACCT 58.540 41.667 0.00 0.00 0.00 4.00
1641 1905 5.660460 CCACAATAGGGAAATTGTAAAGCC 58.340 41.667 2.17 0.00 45.92 4.35
1662 1926 9.553064 AAAGCCTGTTAGATATTTCTACATGAG 57.447 33.333 0.00 0.00 34.15 2.90
1714 1978 9.665719 TTCTACATGAATATGTCAAGCTTGTTA 57.334 29.630 25.19 15.74 44.00 2.41
1715 1979 9.317936 TCTACATGAATATGTCAAGCTTGTTAG 57.682 33.333 25.19 6.72 44.00 2.34
1716 1980 9.317936 CTACATGAATATGTCAAGCTTGTTAGA 57.682 33.333 25.19 13.34 44.00 2.10
1717 1981 8.743085 ACATGAATATGTCAAGCTTGTTAGAT 57.257 30.769 25.19 13.65 44.00 1.98
1718 1982 9.836864 ACATGAATATGTCAAGCTTGTTAGATA 57.163 29.630 25.19 15.28 44.00 1.98
1726 1990 8.407457 TGTCAAGCTTGTTAGATATTTCTACG 57.593 34.615 25.19 0.00 34.15 3.51
1727 1991 8.248253 TGTCAAGCTTGTTAGATATTTCTACGA 58.752 33.333 25.19 0.00 34.15 3.43
1728 1992 9.250624 GTCAAGCTTGTTAGATATTTCTACGAT 57.749 33.333 25.19 0.00 34.15 3.73
1790 2068 9.065871 CCTTAACTATTTGCGAAATTCTCTTTG 57.934 33.333 0.00 0.00 32.38 2.77
1792 2070 6.817765 ACTATTTGCGAAATTCTCTTTGGA 57.182 33.333 0.00 0.00 32.38 3.53
1796 2074 3.218453 TGCGAAATTCTCTTTGGAACCA 58.782 40.909 0.00 0.00 0.00 3.67
1974 2298 9.713684 AATAACCCTCAAAATATCAAGAATCCA 57.286 29.630 0.00 0.00 0.00 3.41
2001 2325 5.893255 TCTTGGATGGATAATTGGTTTCCTG 59.107 40.000 0.00 0.00 0.00 3.86
2004 2328 4.651045 GGATGGATAATTGGTTTCCTGCTT 59.349 41.667 0.00 0.00 0.00 3.91
2037 2361 3.073798 TCATTGGGCTCTTTGGTCTTGTA 59.926 43.478 0.00 0.00 0.00 2.41
2069 2395 9.620259 GAGGAAGGTAAAATCATTCTATGTTCT 57.380 33.333 0.00 0.00 0.00 3.01
2070 2396 9.401058 AGGAAGGTAAAATCATTCTATGTTCTG 57.599 33.333 0.00 0.00 0.00 3.02
2126 2485 7.151976 ACCATTTTAACCAAATTAGCACTGTC 58.848 34.615 0.00 0.00 32.24 3.51
2278 2637 3.623960 AGCTAGTCAGATCTGTACACGAC 59.376 47.826 21.92 11.71 0.00 4.34
2291 2650 0.165511 ACACGACGAGCTTACGAGTC 59.834 55.000 0.00 6.26 37.03 3.36
2342 2701 3.319122 AGCAAGTAAAGAAACTGGGCTTG 59.681 43.478 0.00 0.00 37.55 4.01
2469 2828 6.464222 CAGAACAGGTAAAGATTGTAGACCA 58.536 40.000 0.00 0.00 32.28 4.02
2479 2838 5.121380 AGATTGTAGACCATGCAAAGGAT 57.879 39.130 14.81 6.05 37.05 3.24
2484 2843 3.446442 AGACCATGCAAAGGATGTCTT 57.554 42.857 14.81 0.00 37.28 3.01
2570 2929 0.107831 TCCAACAACTCGGGAAGTGG 59.892 55.000 0.00 0.00 38.58 4.00
2587 2946 6.168389 GGAAGTGGTCGATTTAGGAAGTAAA 58.832 40.000 0.00 0.00 35.03 2.01
2588 2947 6.822170 GGAAGTGGTCGATTTAGGAAGTAAAT 59.178 38.462 0.00 0.00 42.96 1.40
2589 2948 7.983484 GGAAGTGGTCGATTTAGGAAGTAAATA 59.017 37.037 0.00 0.00 40.77 1.40
2590 2949 9.374838 GAAGTGGTCGATTTAGGAAGTAAATAA 57.625 33.333 0.00 0.00 40.77 1.40
2591 2950 9.729281 AAGTGGTCGATTTAGGAAGTAAATAAA 57.271 29.630 0.00 0.00 40.77 1.40
2592 2951 9.159364 AGTGGTCGATTTAGGAAGTAAATAAAC 57.841 33.333 0.00 0.00 40.77 2.01
2593 2952 8.938906 GTGGTCGATTTAGGAAGTAAATAAACA 58.061 33.333 0.00 0.00 40.77 2.83
2616 2975 5.007332 CACGTTTAGTTGTTCAGTTAAGGCT 59.993 40.000 0.00 0.00 0.00 4.58
2634 2993 4.508662 AGGCTAAAACTGATTCGGAAGAG 58.491 43.478 0.00 0.00 43.69 2.85
2742 3109 0.036306 AACTGAACCTGGGCCTTACG 59.964 55.000 4.53 0.00 0.00 3.18
2804 3171 7.995463 TGTTTTGTTTATAAAGCAGGTCAAC 57.005 32.000 0.00 3.90 0.00 3.18
2874 3241 5.263599 TCAGCCAATTGTTCATAAGGTGAT 58.736 37.500 4.43 0.00 36.54 3.06
2875 3242 6.422333 TCAGCCAATTGTTCATAAGGTGATA 58.578 36.000 4.43 0.00 36.54 2.15
2876 3243 6.543465 TCAGCCAATTGTTCATAAGGTGATAG 59.457 38.462 4.43 0.00 36.54 2.08
3351 3724 4.332828 AGAAAAGGGGTATTTGGTTCTCG 58.667 43.478 0.00 0.00 0.00 4.04
3354 3727 0.255033 GGGGTATTTGGTTCTCGGCT 59.745 55.000 0.00 0.00 0.00 5.52
3575 3954 2.189342 CACAAGAAGAGTAGCGCTAGC 58.811 52.381 19.48 13.21 45.58 3.42
3601 3980 5.878669 CACTTCCAATCTCTGATGATGAACA 59.121 40.000 0.00 0.00 0.00 3.18
3605 3984 5.356190 TCCAATCTCTGATGATGAACAAAGC 59.644 40.000 0.00 0.00 0.00 3.51
4541 4920 5.511386 AGTTTCTGTCAAGAGGGATGAAT 57.489 39.130 0.00 0.00 32.79 2.57
4592 4971 8.432805 ACATTATCGTAGAATCTTCAGGGAAAT 58.567 33.333 0.00 0.00 43.58 2.17
4597 4976 4.516652 AGAATCTTCAGGGAAATGGAGG 57.483 45.455 0.00 0.00 0.00 4.30
4601 4980 2.840651 TCTTCAGGGAAATGGAGGAGTC 59.159 50.000 0.00 0.00 0.00 3.36
4638 5017 2.947652 AGATTCAGATTGATGCCAACCG 59.052 45.455 0.00 0.00 34.72 4.44
4804 5188 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
4805 5189 1.136565 GTGTGTGTGTGTGTGTGGC 59.863 57.895 0.00 0.00 0.00 5.01
4806 5190 1.302832 TGTGTGTGTGTGTGTGGCA 60.303 52.632 0.00 0.00 0.00 4.92
4808 5192 1.748500 TGTGTGTGTGTGTGGCAGG 60.749 57.895 0.00 0.00 0.00 4.85
4880 5283 5.463286 CAATGCTGCATACAAGAACAGAAA 58.537 37.500 16.58 0.00 31.67 2.52
4899 5306 7.989826 ACAGAAAATAGCAGGCTAATAGTTTG 58.010 34.615 4.94 3.49 31.73 2.93
4943 5350 5.331876 ACTGAGAAGATTGCCAGTAGTAC 57.668 43.478 0.00 0.00 38.02 2.73
4957 5364 5.970023 GCCAGTAGTACTAAACATACTCGTG 59.030 44.000 3.61 0.00 34.66 4.35
4979 5386 8.281194 TCGTGTTTTGCAATTATAAGTACGAAA 58.719 29.630 0.00 0.00 33.49 3.46
4980 5387 9.057365 CGTGTTTTGCAATTATAAGTACGAAAT 57.943 29.630 0.00 0.00 0.00 2.17
5119 5530 2.120718 AGGTCACGGCCTCTCCTT 59.879 61.111 0.00 0.00 32.39 3.36
5120 5531 1.985116 AGGTCACGGCCTCTCCTTC 60.985 63.158 0.00 0.00 32.39 3.46
5121 5532 1.985116 GGTCACGGCCTCTCCTTCT 60.985 63.158 0.00 0.00 0.00 2.85
5122 5533 1.216710 GTCACGGCCTCTCCTTCTG 59.783 63.158 0.00 0.00 0.00 3.02
5246 5657 1.364171 CTCTCCTGTATTCCGGGCG 59.636 63.158 0.00 0.00 39.73 6.13
5442 5871 2.223688 CCACCAAAAGTTGCACGAATCA 60.224 45.455 0.00 0.00 0.00 2.57
5573 6002 3.924144 CTTCAAGAGGAGACAAGTCTGG 58.076 50.000 7.57 0.00 40.61 3.86
5574 6003 2.251818 TCAAGAGGAGACAAGTCTGGG 58.748 52.381 7.57 0.00 40.61 4.45
5575 6004 0.980423 AAGAGGAGACAAGTCTGGGC 59.020 55.000 7.57 0.00 40.61 5.36
5576 6005 0.116143 AGAGGAGACAAGTCTGGGCT 59.884 55.000 7.57 0.00 40.61 5.19
5577 6006 0.534873 GAGGAGACAAGTCTGGGCTC 59.465 60.000 7.57 0.68 40.61 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.749091 TCGCATTCATCTTGGCCCAG 60.749 55.000 0.00 0.00 0.00 4.45
45 46 3.883779 CGTGTCGCATTCATCTTGG 57.116 52.632 0.00 0.00 0.00 3.61
105 106 3.222354 AACGTGACCGGACAGGAGC 62.222 63.158 28.51 7.78 45.00 4.70
110 111 4.210093 ACGCAACGTGACCGGACA 62.210 61.111 9.46 5.04 39.18 4.02
121 122 3.846754 GCATTGAAGCCACGCAAC 58.153 55.556 0.00 0.00 0.00 4.17
178 179 2.980233 AAGGCACGTGCTGCTTCC 60.980 61.111 36.84 20.82 46.25 3.46
187 188 1.165270 GCTTTACATCCAAGGCACGT 58.835 50.000 0.00 0.00 31.29 4.49
193 194 0.742990 TCCCGCGCTTTACATCCAAG 60.743 55.000 5.56 0.00 0.00 3.61
200 201 0.876342 CCATCTCTCCCGCGCTTTAC 60.876 60.000 5.56 0.00 0.00 2.01
206 207 3.610669 CCTCCCATCTCTCCCGCG 61.611 72.222 0.00 0.00 0.00 6.46
209 210 0.990818 AAAGCCCTCCCATCTCTCCC 60.991 60.000 0.00 0.00 0.00 4.30
210 211 0.922626 AAAAGCCCTCCCATCTCTCC 59.077 55.000 0.00 0.00 0.00 3.71
256 257 2.515057 AACCACTGCCACGCGAAA 60.515 55.556 15.93 0.00 0.00 3.46
287 288 1.618616 CCGAAAATAAACCAGGGGGCT 60.619 52.381 0.00 0.00 37.90 5.19
288 289 0.821517 CCGAAAATAAACCAGGGGGC 59.178 55.000 0.00 0.00 37.90 5.80
335 337 4.456222 CGAGGTACTGTATCGATCCATTCT 59.544 45.833 0.00 0.00 41.55 2.40
353 355 2.925724 TGTTTTGTCATCCAACGAGGT 58.074 42.857 0.00 0.00 39.02 3.85
357 359 4.676471 CAGAACATGTTTTGTCATCCAACG 59.324 41.667 18.50 0.00 37.68 4.10
362 364 4.466828 CGTCCAGAACATGTTTTGTCATC 58.533 43.478 23.19 11.84 37.68 2.92
372 374 0.729116 GACCATGCGTCCAGAACATG 59.271 55.000 0.00 0.00 40.67 3.21
374 376 4.693532 GACCATGCGTCCAGAACA 57.306 55.556 3.65 0.00 35.23 3.18
381 383 2.798148 AAACCTCCGGACCATGCGTC 62.798 60.000 0.00 5.94 41.15 5.19
382 384 2.890766 AAACCTCCGGACCATGCGT 61.891 57.895 0.00 0.00 0.00 5.24
383 385 2.046314 AAACCTCCGGACCATGCG 60.046 61.111 0.00 0.00 0.00 4.73
402 415 6.444171 ACTCTATCTTAAAGTGGTTAAGGGCT 59.556 38.462 6.12 0.00 46.05 5.19
484 497 9.704098 GTGATTAACTAGTTTTATTGCTAGTGC 57.296 33.333 14.49 0.00 44.84 4.40
530 543 1.344438 TCTCCATAGGCATTGCGTAGG 59.656 52.381 15.43 14.83 32.49 3.18
531 544 2.802816 GTTCTCCATAGGCATTGCGTAG 59.197 50.000 15.43 5.12 32.49 3.51
546 559 3.300013 CCCAGACTCGGGTTCTCC 58.700 66.667 0.00 0.00 41.83 3.71
626 639 2.987232 AGACGGGTTATTCTTTCTGCC 58.013 47.619 0.00 0.00 0.00 4.85
627 640 5.447413 GCTTAAGACGGGTTATTCTTTCTGC 60.447 44.000 6.67 0.00 33.96 4.26
644 660 7.986889 TGCTATTATTGATGTGTCTGCTTAAGA 59.013 33.333 6.67 0.00 0.00 2.10
677 694 6.148480 ACAGCTTTCTCACATTTGACATAGTC 59.852 38.462 0.00 0.00 0.00 2.59
698 715 3.884496 GCATCTGCATCTGGTGTACAGC 61.884 54.545 18.10 18.10 43.13 4.40
715 732 2.608090 GAGGGCGTAGTTTGTAAGCATC 59.392 50.000 0.00 0.00 0.00 3.91
772 789 4.094442 CGCCTTCTGGTTTTGACTTATACC 59.906 45.833 0.00 0.00 35.27 2.73
776 793 3.135994 GACGCCTTCTGGTTTTGACTTA 58.864 45.455 0.00 0.00 35.27 2.24
807 824 4.467084 AACGATGGCCCGCGTGAT 62.467 61.111 18.95 3.62 41.06 3.06
890 907 3.128068 CGGAGCCTTTGGTTGGTTTATAC 59.872 47.826 0.00 0.00 0.00 1.47
939 956 2.611292 GCTAGCTTTCTACGTCGAGGTA 59.389 50.000 16.44 16.44 0.00 3.08
947 964 0.098376 ACGGACGCTAGCTTTCTACG 59.902 55.000 13.93 10.84 0.00 3.51
981 1002 1.603455 GTGCCTGCCAACCTAGCAA 60.603 57.895 0.00 0.00 40.35 3.91
986 1007 2.283388 CCATGTGCCTGCCAACCT 60.283 61.111 0.00 0.00 0.00 3.50
1473 1543 1.129326 GAATCGCGAAACCGATCGAT 58.871 50.000 18.66 0.00 46.29 3.59
1476 1546 1.556564 TGAGAATCGCGAAACCGATC 58.443 50.000 15.24 6.53 46.29 3.69
1480 1550 2.961522 TGTTTGAGAATCGCGAAACC 57.038 45.000 15.24 5.15 38.61 3.27
1481 1551 4.463209 TCAATGTTTGAGAATCGCGAAAC 58.537 39.130 15.24 12.73 38.61 2.78
1546 1758 5.793030 AGGTGACTTAGTATGTATGAGCC 57.207 43.478 0.00 0.00 37.44 4.70
1585 1849 4.158394 TCTGTAATTCAATCTGGCCTTTGC 59.842 41.667 3.32 0.00 0.00 3.68
1598 1862 4.081642 GTGGGCTGTAGAGTCTGTAATTCA 60.082 45.833 1.86 0.00 0.00 2.57
1655 1919 7.555965 ACAAGCTTGACATATGTACTCATGTA 58.444 34.615 32.50 0.01 35.55 2.29
1662 1926 5.880054 ACCAACAAGCTTGACATATGTAC 57.120 39.130 32.50 3.48 0.00 2.90
1666 1930 8.353423 AGAAATAACCAACAAGCTTGACATAT 57.647 30.769 32.50 17.87 0.00 1.78
1667 1931 7.759489 AGAAATAACCAACAAGCTTGACATA 57.241 32.000 32.50 16.58 0.00 2.29
1756 2020 8.652810 TTTCGCAAATAGTTAAGGTACCTATC 57.347 34.615 16.67 8.74 0.00 2.08
1762 2026 9.444600 AAGAGAATTTCGCAAATAGTTAAGGTA 57.555 29.630 2.95 0.00 0.00 3.08
1843 2167 3.040655 TCGTGAAATAGGGATCCTGGA 57.959 47.619 12.58 0.00 34.61 3.86
1974 2298 6.324770 GGAAACCAATTATCCATCCAAGATGT 59.675 38.462 4.04 0.00 33.30 3.06
2001 2325 2.094854 CCCAATGAAGCTGACAAGAAGC 60.095 50.000 0.00 0.00 41.15 3.86
2004 2328 1.074405 AGCCCAATGAAGCTGACAAGA 59.926 47.619 0.00 0.00 38.11 3.02
2069 2395 9.806203 CATGGTTGCTTGAGAAAATAAATATCA 57.194 29.630 0.00 0.00 0.00 2.15
2070 2396 9.807649 ACATGGTTGCTTGAGAAAATAAATATC 57.192 29.630 0.00 0.00 0.00 1.63
2091 2418 5.336150 TGGTTAAAATGGTATGCACATGG 57.664 39.130 0.00 0.00 0.00 3.66
2101 2457 7.061566 ACAGTGCTAATTTGGTTAAAATGGT 57.938 32.000 0.00 0.00 38.52 3.55
2126 2485 5.382618 TGTAGTCGATGATCATGATCTGG 57.617 43.478 30.65 20.79 38.60 3.86
2278 2637 1.983972 AAGCAAGACTCGTAAGCTCG 58.016 50.000 0.00 0.00 33.83 5.03
2291 2650 0.248458 ACGACGCAAACCAAAGCAAG 60.248 50.000 0.00 0.00 0.00 4.01
2342 2701 1.789506 AGAAGCTGAGCACGAAGAAC 58.210 50.000 7.39 0.00 0.00 3.01
2469 2828 4.025040 TGACTGAAGACATCCTTTGCAT 57.975 40.909 0.00 0.00 34.68 3.96
2479 2838 6.828273 TCTTTGGAGAAATTTGACTGAAGACA 59.172 34.615 0.00 0.00 0.00 3.41
2484 2843 6.356556 TCACTCTTTGGAGAAATTTGACTGA 58.643 36.000 0.00 0.00 41.86 3.41
2570 2929 8.650714 ACGTGTTTATTTACTTCCTAAATCGAC 58.349 33.333 0.00 0.00 36.58 4.20
2587 2946 9.925268 CTTAACTGAACAACTAAACGTGTTTAT 57.075 29.630 5.71 0.00 34.86 1.40
2588 2947 8.389603 CCTTAACTGAACAACTAAACGTGTTTA 58.610 33.333 5.20 5.20 34.23 2.01
2589 2948 7.245604 CCTTAACTGAACAACTAAACGTGTTT 58.754 34.615 3.21 3.21 36.63 2.83
2590 2949 6.676213 GCCTTAACTGAACAACTAAACGTGTT 60.676 38.462 0.00 0.00 0.00 3.32
2591 2950 5.220719 GCCTTAACTGAACAACTAAACGTGT 60.221 40.000 0.00 0.00 0.00 4.49
2592 2951 5.007332 AGCCTTAACTGAACAACTAAACGTG 59.993 40.000 0.00 0.00 0.00 4.49
2593 2952 5.121105 AGCCTTAACTGAACAACTAAACGT 58.879 37.500 0.00 0.00 0.00 3.99
2616 2975 7.811117 TTTTTCCTCTTCCGAATCAGTTTTA 57.189 32.000 0.00 0.00 0.00 1.52
2664 3023 0.586319 CCCAATATGCAAGGTACGCG 59.414 55.000 3.53 3.53 0.00 6.01
2708 3073 3.040147 TCAGTTTCGTCTGCTTTAGGG 57.960 47.619 0.00 0.00 35.63 3.53
2764 3131 6.389830 ACAAAACAATGTGCATTCTAGTGA 57.610 33.333 0.00 0.00 30.82 3.41
2815 3182 9.462174 AAACAATTAACCATATCATTGCGTATG 57.538 29.630 0.00 0.00 35.45 2.39
2874 3241 9.298250 AGGCTCGAGAAGACATAAATAATACTA 57.702 33.333 18.75 0.00 34.25 1.82
2875 3242 8.085296 CAGGCTCGAGAAGACATAAATAATACT 58.915 37.037 18.75 0.00 34.25 2.12
2876 3243 7.329717 CCAGGCTCGAGAAGACATAAATAATAC 59.670 40.741 18.75 0.00 34.25 1.89
2998 3369 2.002586 AGCGTGCACACAATTAGCTAG 58.997 47.619 18.64 0.00 0.00 3.42
3351 3724 4.280677 AGACTAGTATCAGCAAGATCAGCC 59.719 45.833 0.00 0.00 38.19 4.85
3354 3727 6.458888 CGTGAAGACTAGTATCAGCAAGATCA 60.459 42.308 10.32 0.00 38.19 2.92
3470 3849 4.318332 CGAGAATCAAGGCAATGGCTATA 58.682 43.478 10.45 1.21 37.50 1.31
3575 3954 5.425630 TCATCATCAGAGATTGGAAGTGTG 58.574 41.667 0.00 0.00 0.00 3.82
3601 3980 1.915141 AGCTGCAGTACCATTGCTTT 58.085 45.000 16.64 0.00 42.02 3.51
3605 3984 6.254373 CGTATGATATAGCTGCAGTACCATTG 59.746 42.308 16.64 0.00 0.00 2.82
4541 4920 2.655090 TGAAAGCATCCACCTTGTCA 57.345 45.000 0.00 0.00 0.00 3.58
4592 4971 4.777366 TGATTCATAACTGTGACTCCTCCA 59.223 41.667 0.00 0.00 29.53 3.86
4597 4976 8.939929 TGAATCTTTGATTCATAACTGTGACTC 58.060 33.333 16.18 0.00 33.55 3.36
4638 5017 7.425606 ACAGGACAAATGTAAATTTCACAGAC 58.574 34.615 0.00 0.00 0.00 3.51
4773 5157 1.535028 CACACACACACACACACACTT 59.465 47.619 0.00 0.00 0.00 3.16
4804 5188 2.046507 CTCCTGCCACACTCCTGC 60.047 66.667 0.00 0.00 0.00 4.85
4805 5189 0.604780 CAACTCCTGCCACACTCCTG 60.605 60.000 0.00 0.00 0.00 3.86
4806 5190 1.757306 CAACTCCTGCCACACTCCT 59.243 57.895 0.00 0.00 0.00 3.69
4808 5192 3.660621 GCAACTCCTGCCACACTC 58.339 61.111 0.00 0.00 46.13 3.51
4915 5322 6.749923 ACTGGCAATCTTCTCAGTAAATTC 57.250 37.500 0.00 0.00 38.52 2.17
4979 5386 9.988350 CGTACTAATTGCAAAAGAAGAATACAT 57.012 29.630 16.60 0.00 0.00 2.29
4980 5387 9.210329 TCGTACTAATTGCAAAAGAAGAATACA 57.790 29.630 16.60 1.24 0.00 2.29
5105 5516 2.650116 GCAGAAGGAGAGGCCGTGA 61.650 63.158 0.00 0.00 43.43 4.35
5117 5528 4.441695 TCGCGGCAGAGGCAGAAG 62.442 66.667 6.13 0.00 43.71 2.85
5118 5529 4.742201 GTCGCGGCAGAGGCAGAA 62.742 66.667 5.47 0.00 43.71 3.02
5226 5637 1.759459 GCCCGGAATACAGGAGAGGG 61.759 65.000 0.73 0.00 40.27 4.30
5552 5981 3.306641 CCCAGACTTGTCTCCTCTTGAAG 60.307 52.174 0.00 0.00 0.00 3.02
5553 5982 2.634940 CCCAGACTTGTCTCCTCTTGAA 59.365 50.000 0.00 0.00 0.00 2.69
5554 5983 2.251818 CCCAGACTTGTCTCCTCTTGA 58.748 52.381 0.00 0.00 0.00 3.02
5555 5984 1.338579 GCCCAGACTTGTCTCCTCTTG 60.339 57.143 0.00 0.00 0.00 3.02
5556 5985 0.980423 GCCCAGACTTGTCTCCTCTT 59.020 55.000 0.00 0.00 0.00 2.85
5557 5986 0.116143 AGCCCAGACTTGTCTCCTCT 59.884 55.000 0.00 0.00 0.00 3.69
5558 5987 0.534873 GAGCCCAGACTTGTCTCCTC 59.465 60.000 0.00 4.13 0.00 3.71
5559 5988 2.677508 GAGCCCAGACTTGTCTCCT 58.322 57.895 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.