Multiple sequence alignment - TraesCS1D01G291800

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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 TraesCS1D01G291800 chr1D 100.000 2564 0 0 1 2564 390672614 390670051 0.000000e+00 4735.0
1 TraesCS1D01G291800 chr1D 88.571 1050 80 20 774 1800 390677592 390678624 0.000000e+00 1238.0
2 TraesCS1D01G291800 chr1D 90.327 703 52 6 1873 2562 151431865 151432564 0.000000e+00 907.0
3 TraesCS1D01G291800 chr1D 89.784 695 57 8 1873 2562 56753934 56754619 0.000000e+00 878.0
4 TraesCS1D01G291800 chr1D 91.765 85 7 0 774 858 390677254 390677338 4.480000e-23 119.0
5 TraesCS1D01G291800 chr1B 90.057 1046 82 10 768 1805 523042851 523041820 0.000000e+00 1336.0
6 TraesCS1D01G291800 chr1B 90.376 852 66 8 954 1795 523144137 523144982 0.000000e+00 1105.0
7 TraesCS1D01G291800 chr1B 88.615 325 28 7 303 625 523138419 523138736 1.110000e-103 387.0
8 TraesCS1D01G291800 chr1B 86.103 331 25 7 308 631 523137003 523137319 1.140000e-88 337.0
9 TraesCS1D01G291800 chr1B 94.857 175 7 2 768 940 523139004 523139178 3.250000e-69 272.0
10 TraesCS1D01G291800 chr1B 94.737 38 1 1 821 858 523137481 523137517 9.910000e-05 58.4
11 TraesCS1D01G291800 chr1A 91.055 995 61 14 768 1743 488218959 488219944 0.000000e+00 1319.0
12 TraesCS1D01G291800 chr1A 93.485 307 15 3 1 302 488218444 488218750 3.890000e-123 451.0
13 TraesCS1D01G291800 chr1A 79.529 425 55 26 303 712 488218343 488218750 9.040000e-70 274.0
14 TraesCS1D01G291800 chr1A 87.671 219 14 9 501 708 488218780 488218996 2.550000e-60 243.0
15 TraesCS1D01G291800 chr1A 94.828 58 3 0 303 360 488218723 488218780 9.770000e-15 91.6
16 TraesCS1D01G291800 chr7D 90.617 746 52 10 1835 2564 78426607 78425864 0.000000e+00 974.0
17 TraesCS1D01G291800 chr7D 91.379 696 44 9 1882 2564 535735672 535734980 0.000000e+00 939.0
18 TraesCS1D01G291800 chr7D 88.527 706 43 12 1873 2564 575004542 575003861 0.000000e+00 821.0
19 TraesCS1D01G291800 chr5D 91.559 699 51 5 1873 2564 521710526 521709829 0.000000e+00 957.0
20 TraesCS1D01G291800 chr3D 91.218 706 45 10 1873 2564 400273186 400272484 0.000000e+00 944.0
21 TraesCS1D01G291800 chr3D 88.533 750 66 13 1828 2564 300923330 300924072 0.000000e+00 891.0
22 TraesCS1D01G291800 chrUn 90.000 700 56 9 1873 2564 69201343 69202036 0.000000e+00 893.0
23 TraesCS1D01G291800 chr2D 89.347 704 48 7 1873 2564 495043772 495043084 0.000000e+00 859.0
24 TraesCS1D01G291800 chr6D 90.199 653 48 8 1916 2564 414469892 414470532 0.000000e+00 837.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G291800 chr1D 390670051 390672614 2563 True 4735.00 4735 100.0000 1 2564 1 chr1D.!!$R1 2563
1 TraesCS1D01G291800 chr1D 151431865 151432564 699 False 907.00 907 90.3270 1873 2562 1 chr1D.!!$F2 689
2 TraesCS1D01G291800 chr1D 56753934 56754619 685 False 878.00 878 89.7840 1873 2562 1 chr1D.!!$F1 689
3 TraesCS1D01G291800 chr1D 390677254 390678624 1370 False 678.50 1238 90.1680 774 1800 2 chr1D.!!$F3 1026
4 TraesCS1D01G291800 chr1B 523041820 523042851 1031 True 1336.00 1336 90.0570 768 1805 1 chr1B.!!$R1 1037
5 TraesCS1D01G291800 chr1B 523144137 523144982 845 False 1105.00 1105 90.3760 954 1795 1 chr1B.!!$F1 841
6 TraesCS1D01G291800 chr1B 523137003 523139178 2175 False 263.60 387 91.0780 303 940 4 chr1B.!!$F2 637
7 TraesCS1D01G291800 chr1A 488218343 488219944 1601 False 475.72 1319 89.3136 1 1743 5 chr1A.!!$F1 1742
8 TraesCS1D01G291800 chr7D 78425864 78426607 743 True 974.00 974 90.6170 1835 2564 1 chr7D.!!$R1 729
9 TraesCS1D01G291800 chr7D 535734980 535735672 692 True 939.00 939 91.3790 1882 2564 1 chr7D.!!$R2 682
10 TraesCS1D01G291800 chr7D 575003861 575004542 681 True 821.00 821 88.5270 1873 2564 1 chr7D.!!$R3 691
11 TraesCS1D01G291800 chr5D 521709829 521710526 697 True 957.00 957 91.5590 1873 2564 1 chr5D.!!$R1 691
12 TraesCS1D01G291800 chr3D 400272484 400273186 702 True 944.00 944 91.2180 1873 2564 1 chr3D.!!$R1 691
13 TraesCS1D01G291800 chr3D 300923330 300924072 742 False 891.00 891 88.5330 1828 2564 1 chr3D.!!$F1 736
14 TraesCS1D01G291800 chrUn 69201343 69202036 693 False 893.00 893 90.0000 1873 2564 1 chrUn.!!$F1 691
15 TraesCS1D01G291800 chr2D 495043084 495043772 688 True 859.00 859 89.3470 1873 2564 1 chr2D.!!$R1 691
16 TraesCS1D01G291800 chr6D 414469892 414470532 640 False 837.00 837 90.1990 1916 2564 1 chr6D.!!$F1 648

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
519 1654 0.112218 TGCCACCCACTACTGCATTT 59.888 50.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 3971 1.213094 CGCTCTGGAACACGACGTTT 61.213 55.0 0.0 0.0 38.19 3.6 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
230 334 8.622948 GGGGGAGAAAAATATATACTCAAGTG 57.377 38.462 0.00 0.00 0.00 3.16
231 335 8.437575 GGGGGAGAAAAATATATACTCAAGTGA 58.562 37.037 0.00 0.00 0.00 3.41
233 337 8.994170 GGGAGAAAAATATATACTCAAGTGAGC 58.006 37.037 8.25 0.00 45.79 4.26
234 338 9.771534 GGAGAAAAATATATACTCAAGTGAGCT 57.228 33.333 8.25 0.00 45.79 4.09
248 352 5.972107 AAGTGAGCTTGATGTGCTTTAAT 57.028 34.783 0.00 0.00 41.30 1.40
249 353 5.972107 AGTGAGCTTGATGTGCTTTAATT 57.028 34.783 0.00 0.00 41.30 1.40
251 355 5.709164 AGTGAGCTTGATGTGCTTTAATTCT 59.291 36.000 0.00 0.00 41.30 2.40
252 356 6.026513 GTGAGCTTGATGTGCTTTAATTCTC 58.973 40.000 0.00 0.00 41.30 2.87
253 357 5.706833 TGAGCTTGATGTGCTTTAATTCTCA 59.293 36.000 0.00 0.00 41.30 3.27
255 359 7.094075 TGAGCTTGATGTGCTTTAATTCTCATT 60.094 33.333 0.00 0.00 41.30 2.57
257 361 8.742777 AGCTTGATGTGCTTTAATTCTCATTTA 58.257 29.630 0.00 0.00 37.52 1.40
258 362 9.017669 GCTTGATGTGCTTTAATTCTCATTTAG 57.982 33.333 0.00 0.00 0.00 1.85
274 378 8.712228 TCTCATTTAGATTAGAGATAGCCACA 57.288 34.615 0.00 0.00 32.57 4.17
275 379 8.580720 TCTCATTTAGATTAGAGATAGCCACAC 58.419 37.037 0.00 0.00 32.57 3.82
276 380 7.671302 TCATTTAGATTAGAGATAGCCACACC 58.329 38.462 0.00 0.00 0.00 4.16
277 381 7.290014 TCATTTAGATTAGAGATAGCCACACCA 59.710 37.037 0.00 0.00 0.00 4.17
278 382 7.432148 TTTAGATTAGAGATAGCCACACCAA 57.568 36.000 0.00 0.00 0.00 3.67
279 383 7.618019 TTAGATTAGAGATAGCCACACCAAT 57.382 36.000 0.00 0.00 0.00 3.16
282 386 8.034313 AGATTAGAGATAGCCACACCAATAAA 57.966 34.615 0.00 0.00 0.00 1.40
283 387 7.934120 AGATTAGAGATAGCCACACCAATAAAC 59.066 37.037 0.00 0.00 0.00 2.01
284 388 5.700402 AGAGATAGCCACACCAATAAACT 57.300 39.130 0.00 0.00 0.00 2.66
285 389 6.808321 AGAGATAGCCACACCAATAAACTA 57.192 37.500 0.00 0.00 0.00 2.24
286 390 7.195374 AGAGATAGCCACACCAATAAACTAA 57.805 36.000 0.00 0.00 0.00 2.24
287 391 7.806180 AGAGATAGCCACACCAATAAACTAAT 58.194 34.615 0.00 0.00 0.00 1.73
288 392 7.716998 AGAGATAGCCACACCAATAAACTAATG 59.283 37.037 0.00 0.00 0.00 1.90
289 393 4.718940 AGCCACACCAATAAACTAATGC 57.281 40.909 0.00 0.00 0.00 3.56
290 394 4.344104 AGCCACACCAATAAACTAATGCT 58.656 39.130 0.00 0.00 0.00 3.79
291 395 5.505780 AGCCACACCAATAAACTAATGCTA 58.494 37.500 0.00 0.00 0.00 3.49
292 396 5.357032 AGCCACACCAATAAACTAATGCTAC 59.643 40.000 0.00 0.00 0.00 3.58
293 397 5.124776 GCCACACCAATAAACTAATGCTACA 59.875 40.000 0.00 0.00 0.00 2.74
294 398 6.551736 CCACACCAATAAACTAATGCTACAC 58.448 40.000 0.00 0.00 0.00 2.90
295 399 6.150307 CCACACCAATAAACTAATGCTACACA 59.850 38.462 0.00 0.00 0.00 3.72
296 400 7.148086 CCACACCAATAAACTAATGCTACACAT 60.148 37.037 0.00 0.00 42.30 3.21
311 841 8.588290 ATGCTACACATTGATTACCCTTAAAA 57.412 30.769 0.00 0.00 34.40 1.52
312 842 8.410673 TGCTACACATTGATTACCCTTAAAAA 57.589 30.769 0.00 0.00 0.00 1.94
360 1495 8.319146 GCATTTATTGGGCTCTATAGGTTACTA 58.681 37.037 0.00 0.00 0.00 1.82
473 1608 1.813513 ACTACACTTGCATGACTGGC 58.186 50.000 6.60 0.00 0.00 4.85
476 1611 1.672030 CACTTGCATGACTGGCCGA 60.672 57.895 6.60 0.00 0.00 5.54
483 1618 2.587247 ATGACTGGCCGACTGTGCT 61.587 57.895 0.00 0.00 0.00 4.40
515 1650 1.002134 ACATGCCACCCACTACTGC 60.002 57.895 0.00 0.00 0.00 4.40
519 1654 0.112218 TGCCACCCACTACTGCATTT 59.888 50.000 0.00 0.00 0.00 2.32
521 1656 1.886222 GCCACCCACTACTGCATTTGA 60.886 52.381 0.00 0.00 0.00 2.69
522 1657 2.513753 CCACCCACTACTGCATTTGAA 58.486 47.619 0.00 0.00 0.00 2.69
686 2039 8.214364 AGTTCTCATTTAGATTTGAGATACCCC 58.786 37.037 3.69 0.00 45.66 4.95
687 2040 7.079451 TCTCATTTAGATTTGAGATACCCCC 57.921 40.000 0.00 0.00 42.52 5.40
688 2041 6.619437 TCTCATTTAGATTTGAGATACCCCCA 59.381 38.462 0.00 0.00 42.52 4.96
689 2042 7.128728 TCTCATTTAGATTTGAGATACCCCCAA 59.871 37.037 0.00 0.00 42.52 4.12
690 2043 7.647827 TCATTTAGATTTGAGATACCCCCAAA 58.352 34.615 0.00 0.00 34.76 3.28
691 2044 8.119246 TCATTTAGATTTGAGATACCCCCAAAA 58.881 33.333 0.00 0.00 34.08 2.44
692 2045 8.757877 CATTTAGATTTGAGATACCCCCAAAAA 58.242 33.333 0.00 0.00 34.08 1.94
693 2046 7.712204 TTAGATTTGAGATACCCCCAAAAAC 57.288 36.000 0.00 0.00 34.08 2.43
694 2047 5.903923 AGATTTGAGATACCCCCAAAAACT 58.096 37.500 0.00 0.00 34.08 2.66
695 2048 7.039722 AGATTTGAGATACCCCCAAAAACTA 57.960 36.000 0.00 0.00 34.08 2.24
696 2049 7.475299 AGATTTGAGATACCCCCAAAAACTAA 58.525 34.615 0.00 0.00 34.08 2.24
697 2050 8.122481 AGATTTGAGATACCCCCAAAAACTAAT 58.878 33.333 0.00 0.00 34.08 1.73
698 2051 7.475137 TTTGAGATACCCCCAAAAACTAATG 57.525 36.000 0.00 0.00 0.00 1.90
699 2052 4.953579 TGAGATACCCCCAAAAACTAATGC 59.046 41.667 0.00 0.00 0.00 3.56
700 2053 5.201243 GAGATACCCCCAAAAACTAATGCT 58.799 41.667 0.00 0.00 0.00 3.79
701 2054 6.069323 TGAGATACCCCCAAAAACTAATGCTA 60.069 38.462 0.00 0.00 0.00 3.49
702 2055 6.127101 AGATACCCCCAAAAACTAATGCTAC 58.873 40.000 0.00 0.00 0.00 3.58
703 2056 4.120946 ACCCCCAAAAACTAATGCTACA 57.879 40.909 0.00 0.00 0.00 2.74
704 2057 3.830178 ACCCCCAAAAACTAATGCTACAC 59.170 43.478 0.00 0.00 0.00 2.90
705 2058 3.829601 CCCCCAAAAACTAATGCTACACA 59.170 43.478 0.00 0.00 0.00 3.72
706 2059 4.466015 CCCCCAAAAACTAATGCTACACAT 59.534 41.667 0.00 0.00 42.30 3.21
747 2100 9.830975 ATAAGTGTGATTAATACTGTACATGCA 57.169 29.630 0.00 0.00 0.00 3.96
748 2101 7.776933 AGTGTGATTAATACTGTACATGCAG 57.223 36.000 0.00 0.00 41.92 4.41
749 2102 6.258727 AGTGTGATTAATACTGTACATGCAGC 59.741 38.462 0.00 0.00 39.96 5.25
750 2103 6.037062 GTGTGATTAATACTGTACATGCAGCA 59.963 38.462 0.00 0.00 39.96 4.41
751 2104 6.767423 TGTGATTAATACTGTACATGCAGCAT 59.233 34.615 0.52 0.52 39.96 3.79
752 2105 7.930865 TGTGATTAATACTGTACATGCAGCATA 59.069 33.333 7.82 0.00 39.96 3.14
753 2106 8.939929 GTGATTAATACTGTACATGCAGCATAT 58.060 33.333 7.82 0.00 39.96 1.78
754 2107 9.154847 TGATTAATACTGTACATGCAGCATATC 57.845 33.333 7.82 3.64 39.96 1.63
755 2108 9.376075 GATTAATACTGTACATGCAGCATATCT 57.624 33.333 7.82 0.00 39.96 1.98
756 2109 9.730705 ATTAATACTGTACATGCAGCATATCTT 57.269 29.630 7.82 0.00 39.96 2.40
757 2110 7.430992 AATACTGTACATGCAGCATATCTTG 57.569 36.000 7.82 0.00 39.96 3.02
758 2111 5.027293 ACTGTACATGCAGCATATCTTGA 57.973 39.130 7.82 0.00 39.96 3.02
759 2112 5.055144 ACTGTACATGCAGCATATCTTGAG 58.945 41.667 7.82 2.49 39.96 3.02
760 2113 5.163374 ACTGTACATGCAGCATATCTTGAGA 60.163 40.000 7.82 0.00 39.96 3.27
761 2114 5.861727 TGTACATGCAGCATATCTTGAGAT 58.138 37.500 7.82 0.00 38.51 2.75
762 2115 6.293698 TGTACATGCAGCATATCTTGAGATT 58.706 36.000 7.82 0.00 36.05 2.40
763 2116 7.444299 TGTACATGCAGCATATCTTGAGATTA 58.556 34.615 7.82 0.00 36.05 1.75
764 2117 7.933033 TGTACATGCAGCATATCTTGAGATTAA 59.067 33.333 7.82 0.00 36.05 1.40
765 2118 7.997773 ACATGCAGCATATCTTGAGATTAAT 57.002 32.000 7.82 0.00 36.05 1.40
766 2119 7.817641 ACATGCAGCATATCTTGAGATTAATG 58.182 34.615 7.82 0.00 36.05 1.90
767 2120 6.812879 TGCAGCATATCTTGAGATTAATGG 57.187 37.500 0.00 0.00 36.05 3.16
768 2121 6.536447 TGCAGCATATCTTGAGATTAATGGA 58.464 36.000 0.00 0.00 36.05 3.41
769 2122 6.653740 TGCAGCATATCTTGAGATTAATGGAG 59.346 38.462 0.00 0.00 36.05 3.86
770 2123 6.654161 GCAGCATATCTTGAGATTAATGGAGT 59.346 38.462 0.00 0.00 36.05 3.85
771 2124 7.821359 GCAGCATATCTTGAGATTAATGGAGTA 59.179 37.037 0.00 0.00 36.05 2.59
956 2664 4.143179 CGTCCTTTGTTCCTTTCGATACAC 60.143 45.833 0.00 0.00 0.00 2.90
961 2669 3.921677 TGTTCCTTTCGATACACAGGTC 58.078 45.455 0.00 0.00 0.00 3.85
963 2671 2.439409 TCCTTTCGATACACAGGTCGA 58.561 47.619 0.00 0.00 44.25 4.20
977 2685 1.270099 GTCGAAGAACGCGCATAGC 59.730 57.895 5.73 0.00 39.69 2.97
982 2690 2.028763 CGAAGAACGCGCATAGCTTTAA 59.971 45.455 5.73 0.00 45.59 1.52
1013 2722 3.242706 CGAGCAAACATGAAGAACACACA 60.243 43.478 0.00 0.00 0.00 3.72
1253 2965 2.125912 CCTCGAGTCGTGCAAGGG 60.126 66.667 13.12 3.19 0.00 3.95
1332 3044 1.877443 GTGATGTACCAAACCTGCGTT 59.123 47.619 0.00 0.00 0.00 4.84
1353 3065 2.885644 ATGTACGGCTTCGCGCAG 60.886 61.111 8.75 0.00 41.67 5.18
1387 3099 3.612247 ATGGAAGGCGCGCTCAAGT 62.612 57.895 32.29 11.67 0.00 3.16
1569 3281 6.189677 TCTTTTCCAAAATGGTAGTATGCG 57.810 37.500 0.00 0.00 39.03 4.73
1617 3333 5.232626 TGTCGATAATAATTCGGTGGAAACG 59.767 40.000 0.00 0.00 37.22 3.60
1622 3338 5.821516 AATAATTCGGTGGAAACGCAATA 57.178 34.783 0.00 0.00 44.70 1.90
1626 3343 4.603231 TTCGGTGGAAACGCAATAATAC 57.397 40.909 0.00 0.00 44.70 1.89
1627 3344 3.597255 TCGGTGGAAACGCAATAATACA 58.403 40.909 0.00 0.00 44.70 2.29
1628 3345 4.193090 TCGGTGGAAACGCAATAATACAT 58.807 39.130 0.00 0.00 44.70 2.29
1629 3346 4.034626 TCGGTGGAAACGCAATAATACATG 59.965 41.667 0.00 0.00 44.70 3.21
1630 3347 4.606961 GGTGGAAACGCAATAATACATGG 58.393 43.478 0.00 0.00 44.70 3.66
1631 3348 4.041723 GTGGAAACGCAATAATACATGGC 58.958 43.478 0.00 0.00 41.67 4.40
1632 3349 3.951037 TGGAAACGCAATAATACATGGCT 59.049 39.130 0.00 0.00 0.00 4.75
1633 3350 4.400884 TGGAAACGCAATAATACATGGCTT 59.599 37.500 0.00 0.00 0.00 4.35
1634 3351 5.590663 TGGAAACGCAATAATACATGGCTTA 59.409 36.000 0.00 0.00 0.00 3.09
1638 3355 4.518590 ACGCAATAATACATGGCTTATGCA 59.481 37.500 0.00 0.00 40.59 3.96
1648 3370 4.339247 ACATGGCTTATGCAGTGGTATTTC 59.661 41.667 0.00 0.00 40.59 2.17
1652 3374 4.214332 GGCTTATGCAGTGGTATTTCTAGC 59.786 45.833 2.72 0.00 41.91 3.42
1655 3390 3.266510 TGCAGTGGTATTTCTAGCTGG 57.733 47.619 0.00 0.00 0.00 4.85
1680 3415 6.239036 GCTAGATTTGGTTGAAAGGTGTTTCT 60.239 38.462 0.00 0.00 42.39 2.52
1681 3417 6.544928 AGATTTGGTTGAAAGGTGTTTCTT 57.455 33.333 0.01 0.00 42.39 2.52
1682 3418 6.946340 AGATTTGGTTGAAAGGTGTTTCTTT 58.054 32.000 0.01 0.00 42.39 2.52
1782 3529 7.433708 TTTATTTTTGATTCGACTCTGCTCA 57.566 32.000 4.29 0.00 0.00 4.26
1805 3552 6.493115 TCATATTTTGAACTGAGCTGGGAAAA 59.507 34.615 0.00 0.00 0.00 2.29
1806 3553 5.612725 ATTTTGAACTGAGCTGGGAAAAA 57.387 34.783 0.00 0.00 0.00 1.94
1807 3554 5.612725 TTTTGAACTGAGCTGGGAAAAAT 57.387 34.783 0.00 0.00 0.00 1.82
1808 3555 4.853924 TTGAACTGAGCTGGGAAAAATC 57.146 40.909 0.00 0.00 0.00 2.17
1809 3556 3.831323 TGAACTGAGCTGGGAAAAATCA 58.169 40.909 0.00 0.00 0.00 2.57
1810 3557 4.410099 TGAACTGAGCTGGGAAAAATCAT 58.590 39.130 0.00 0.00 0.00 2.45
1811 3558 4.219070 TGAACTGAGCTGGGAAAAATCATG 59.781 41.667 0.00 0.00 0.00 3.07
1812 3559 3.771216 ACTGAGCTGGGAAAAATCATGT 58.229 40.909 0.00 0.00 0.00 3.21
1813 3560 3.508793 ACTGAGCTGGGAAAAATCATGTG 59.491 43.478 0.00 0.00 0.00 3.21
1814 3561 3.760151 CTGAGCTGGGAAAAATCATGTGA 59.240 43.478 0.00 0.00 0.00 3.58
1815 3562 3.507233 TGAGCTGGGAAAAATCATGTGAC 59.493 43.478 0.00 0.00 0.00 3.67
1816 3563 3.499338 AGCTGGGAAAAATCATGTGACA 58.501 40.909 0.00 0.00 0.00 3.58
1817 3564 3.256631 AGCTGGGAAAAATCATGTGACAC 59.743 43.478 0.00 0.00 0.00 3.67
1818 3565 3.005684 GCTGGGAAAAATCATGTGACACA 59.994 43.478 11.41 11.41 0.00 3.72
1819 3566 4.322198 GCTGGGAAAAATCATGTGACACAT 60.322 41.667 15.48 15.48 39.91 3.21
1832 3579 5.878332 TGTGACACATGTGGTAATCAATC 57.122 39.130 28.64 14.99 34.19 2.67
1855 3602 3.842925 GAGCAACTCCAACGGGCCA 62.843 63.158 4.39 0.00 0.00 5.36
1857 3604 3.039134 CAACTCCAACGGGCCAAC 58.961 61.111 4.39 0.00 0.00 3.77
1859 3606 2.763645 AACTCCAACGGGCCAACCT 61.764 57.895 4.39 0.00 36.97 3.50
1867 3614 1.078001 CGGGCCAACCTAAACGGAT 60.078 57.895 4.39 0.00 36.97 4.18
1868 3615 1.373590 CGGGCCAACCTAAACGGATG 61.374 60.000 4.39 0.00 36.97 3.51
1890 3648 3.305539 GGTGTTTTTATCCGTTTGGGTCC 60.306 47.826 0.00 0.00 37.00 4.46
1979 3737 3.907894 TTTTGACGGCGCTAGAAAAAT 57.092 38.095 6.90 0.00 0.00 1.82
2072 3839 1.969589 GTCCCCGCGTCCACATTTT 60.970 57.895 4.92 0.00 0.00 1.82
2297 4080 4.824515 CCTCCTCCTCGGCCTCGT 62.825 72.222 0.00 0.00 37.69 4.18
2314 4097 2.036414 TGCTGCTCCTCCTCGAGT 59.964 61.111 12.31 0.00 32.11 4.18
2329 4112 2.854214 GAGTTCGCGCTCGAGCATG 61.854 63.158 34.69 25.70 46.36 4.06
2493 4276 4.227134 CTCGATGGGGGACGGCTG 62.227 72.222 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 196 1.002134 AGTAGTGGGTGGCATGTGC 60.002 57.895 0.00 0.00 41.14 4.57
226 330 5.972107 ATTAAAGCACATCAAGCTCACTT 57.028 34.783 0.00 0.00 42.53 3.16
227 331 5.709164 AGAATTAAAGCACATCAAGCTCACT 59.291 36.000 0.00 0.00 42.53 3.41
228 332 5.947443 AGAATTAAAGCACATCAAGCTCAC 58.053 37.500 0.00 0.00 42.53 3.51
229 333 5.706833 TGAGAATTAAAGCACATCAAGCTCA 59.293 36.000 0.00 0.00 42.53 4.26
230 334 6.187125 TGAGAATTAAAGCACATCAAGCTC 57.813 37.500 0.00 0.00 42.53 4.09
231 335 6.770746 ATGAGAATTAAAGCACATCAAGCT 57.229 33.333 0.00 0.00 45.97 3.74
232 336 7.823149 AAATGAGAATTAAAGCACATCAAGC 57.177 32.000 0.00 0.00 0.00 4.01
248 352 9.147732 TGTGGCTATCTCTAATCTAAATGAGAA 57.852 33.333 0.00 0.00 38.77 2.87
249 353 8.580720 GTGTGGCTATCTCTAATCTAAATGAGA 58.419 37.037 0.00 0.00 39.47 3.27
251 355 7.290014 TGGTGTGGCTATCTCTAATCTAAATGA 59.710 37.037 0.00 0.00 0.00 2.57
252 356 7.445121 TGGTGTGGCTATCTCTAATCTAAATG 58.555 38.462 0.00 0.00 0.00 2.32
253 357 7.618019 TGGTGTGGCTATCTCTAATCTAAAT 57.382 36.000 0.00 0.00 0.00 1.40
255 359 7.618019 ATTGGTGTGGCTATCTCTAATCTAA 57.382 36.000 0.00 0.00 0.00 2.10
257 361 7.618019 TTATTGGTGTGGCTATCTCTAATCT 57.382 36.000 0.00 0.00 0.00 2.40
258 362 7.934120 AGTTTATTGGTGTGGCTATCTCTAATC 59.066 37.037 0.00 0.00 0.00 1.75
259 363 7.806180 AGTTTATTGGTGTGGCTATCTCTAAT 58.194 34.615 0.00 0.00 0.00 1.73
261 365 6.808321 AGTTTATTGGTGTGGCTATCTCTA 57.192 37.500 0.00 0.00 0.00 2.43
262 366 5.700402 AGTTTATTGGTGTGGCTATCTCT 57.300 39.130 0.00 0.00 0.00 3.10
263 367 7.520614 GCATTAGTTTATTGGTGTGGCTATCTC 60.521 40.741 0.00 0.00 0.00 2.75
265 369 6.263168 AGCATTAGTTTATTGGTGTGGCTATC 59.737 38.462 0.00 0.00 0.00 2.08
266 370 6.129179 AGCATTAGTTTATTGGTGTGGCTAT 58.871 36.000 0.00 0.00 0.00 2.97
267 371 5.505780 AGCATTAGTTTATTGGTGTGGCTA 58.494 37.500 0.00 0.00 0.00 3.93
268 372 4.344104 AGCATTAGTTTATTGGTGTGGCT 58.656 39.130 0.00 0.00 0.00 4.75
269 373 4.718940 AGCATTAGTTTATTGGTGTGGC 57.281 40.909 0.00 0.00 0.00 5.01
272 376 7.938140 ATGTGTAGCATTAGTTTATTGGTGT 57.062 32.000 0.00 0.00 33.14 4.16
274 378 8.574251 TCAATGTGTAGCATTAGTTTATTGGT 57.426 30.769 0.00 0.00 45.33 3.67
279 383 9.116067 GGGTAATCAATGTGTAGCATTAGTTTA 57.884 33.333 0.00 0.00 45.33 2.01
282 386 6.900194 AGGGTAATCAATGTGTAGCATTAGT 58.100 36.000 0.00 0.00 45.33 2.24
283 387 7.807977 AAGGGTAATCAATGTGTAGCATTAG 57.192 36.000 0.00 0.00 45.33 1.73
284 388 9.688091 TTTAAGGGTAATCAATGTGTAGCATTA 57.312 29.630 0.00 0.00 45.33 1.90
286 390 8.588290 TTTTAAGGGTAATCAATGTGTAGCAT 57.412 30.769 0.00 0.00 40.03 3.79
287 391 8.410673 TTTTTAAGGGTAATCAATGTGTAGCA 57.589 30.769 0.00 0.00 0.00 3.49
311 841 8.830201 TGCTTAAAATCAATGTGTAGCATTTT 57.170 26.923 0.00 0.00 44.82 1.82
430 1565 7.853929 AGTTACACGCGGCATAAAAATAAATAG 59.146 33.333 12.47 0.00 0.00 1.73
443 1578 4.248402 GTGTAGTTACACGCGGCA 57.752 55.556 12.47 0.00 45.87 5.69
483 1618 2.039613 TGGCATGTGGACATACTGTTGA 59.960 45.455 0.00 0.00 34.26 3.18
548 1683 9.893305 CCCATTTTACGTTATATTCTTGATTCC 57.107 33.333 0.00 0.00 0.00 3.01
549 1684 9.893305 CCCCATTTTACGTTATATTCTTGATTC 57.107 33.333 0.00 0.00 0.00 2.52
597 1735 9.120538 GTACATATTTATCTTTCCTGCTTCCAA 57.879 33.333 0.00 0.00 0.00 3.53
676 2029 4.953579 GCATTAGTTTTTGGGGGTATCTCA 59.046 41.667 0.00 0.00 0.00 3.27
683 2036 3.829601 TGTGTAGCATTAGTTTTTGGGGG 59.170 43.478 0.00 0.00 0.00 5.40
684 2037 5.659440 ATGTGTAGCATTAGTTTTTGGGG 57.341 39.130 0.00 0.00 33.14 4.96
685 2038 9.651913 AATTAATGTGTAGCATTAGTTTTTGGG 57.348 29.630 0.00 0.00 46.88 4.12
687 2040 9.956797 GCAATTAATGTGTAGCATTAGTTTTTG 57.043 29.630 5.41 7.04 46.88 2.44
688 2041 9.927668 AGCAATTAATGTGTAGCATTAGTTTTT 57.072 25.926 5.41 0.00 46.88 1.94
689 2042 9.573133 GAGCAATTAATGTGTAGCATTAGTTTT 57.427 29.630 5.41 0.00 46.88 2.43
690 2043 8.739039 TGAGCAATTAATGTGTAGCATTAGTTT 58.261 29.630 5.41 0.72 46.88 2.66
691 2044 8.279970 TGAGCAATTAATGTGTAGCATTAGTT 57.720 30.769 0.00 0.00 46.88 2.24
692 2045 7.864108 TGAGCAATTAATGTGTAGCATTAGT 57.136 32.000 0.00 0.00 46.88 2.24
693 2046 9.571810 TTTTGAGCAATTAATGTGTAGCATTAG 57.428 29.630 0.00 0.00 46.88 1.73
721 2074 9.830975 TGCATGTACAGTATTAATCACACTTAT 57.169 29.630 0.33 0.00 0.00 1.73
722 2075 9.313118 CTGCATGTACAGTATTAATCACACTTA 57.687 33.333 0.33 0.00 32.78 2.24
723 2076 7.201644 GCTGCATGTACAGTATTAATCACACTT 60.202 37.037 0.33 0.00 39.96 3.16
724 2077 6.258727 GCTGCATGTACAGTATTAATCACACT 59.741 38.462 0.33 0.00 39.96 3.55
725 2078 6.037062 TGCTGCATGTACAGTATTAATCACAC 59.963 38.462 0.00 0.00 39.96 3.82
726 2079 6.112058 TGCTGCATGTACAGTATTAATCACA 58.888 36.000 0.00 0.00 39.96 3.58
727 2080 6.603237 TGCTGCATGTACAGTATTAATCAC 57.397 37.500 0.00 0.00 39.96 3.06
728 2081 9.154847 GATATGCTGCATGTACAGTATTAATCA 57.845 33.333 24.59 0.00 39.60 2.57
729 2082 9.376075 AGATATGCTGCATGTACAGTATTAATC 57.624 33.333 24.59 13.93 39.60 1.75
730 2083 9.730705 AAGATATGCTGCATGTACAGTATTAAT 57.269 29.630 24.59 5.65 39.60 1.40
731 2084 8.992073 CAAGATATGCTGCATGTACAGTATTAA 58.008 33.333 24.59 0.47 39.60 1.40
732 2085 8.367156 TCAAGATATGCTGCATGTACAGTATTA 58.633 33.333 24.59 1.02 39.60 0.98
733 2086 7.219322 TCAAGATATGCTGCATGTACAGTATT 58.781 34.615 24.59 5.77 39.60 1.89
734 2087 6.762333 TCAAGATATGCTGCATGTACAGTAT 58.238 36.000 24.59 8.39 44.02 2.12
735 2088 6.040842 TCTCAAGATATGCTGCATGTACAGTA 59.959 38.462 24.59 3.33 39.96 2.74
736 2089 5.027293 TCAAGATATGCTGCATGTACAGT 57.973 39.130 24.59 0.00 39.96 3.55
737 2090 5.295152 TCTCAAGATATGCTGCATGTACAG 58.705 41.667 24.59 12.24 40.80 2.74
738 2091 5.280654 TCTCAAGATATGCTGCATGTACA 57.719 39.130 24.59 5.29 0.00 2.90
739 2092 6.798315 AATCTCAAGATATGCTGCATGTAC 57.202 37.500 24.59 14.66 33.73 2.90
740 2093 8.943002 CATTAATCTCAAGATATGCTGCATGTA 58.057 33.333 24.59 6.47 33.73 2.29
741 2094 7.094334 CCATTAATCTCAAGATATGCTGCATGT 60.094 37.037 24.59 18.53 33.73 3.21
742 2095 7.120726 TCCATTAATCTCAAGATATGCTGCATG 59.879 37.037 24.59 9.56 33.73 4.06
743 2096 7.173032 TCCATTAATCTCAAGATATGCTGCAT 58.827 34.615 20.18 20.18 33.73 3.96
744 2097 6.536447 TCCATTAATCTCAAGATATGCTGCA 58.464 36.000 4.13 4.13 33.73 4.41
745 2098 6.654161 ACTCCATTAATCTCAAGATATGCTGC 59.346 38.462 0.00 0.00 33.73 5.25
746 2099 9.149225 GTACTCCATTAATCTCAAGATATGCTG 57.851 37.037 0.00 0.00 33.73 4.41
747 2100 9.099071 AGTACTCCATTAATCTCAAGATATGCT 57.901 33.333 0.00 0.00 33.73 3.79
751 2104 9.026121 GGCTAGTACTCCATTAATCTCAAGATA 57.974 37.037 0.00 0.00 33.73 1.98
752 2105 7.510685 TGGCTAGTACTCCATTAATCTCAAGAT 59.489 37.037 0.00 0.00 36.07 2.40
753 2106 6.839134 TGGCTAGTACTCCATTAATCTCAAGA 59.161 38.462 0.00 0.00 0.00 3.02
754 2107 6.926272 GTGGCTAGTACTCCATTAATCTCAAG 59.074 42.308 0.00 0.00 34.47 3.02
755 2108 6.382859 TGTGGCTAGTACTCCATTAATCTCAA 59.617 38.462 0.00 0.00 34.47 3.02
756 2109 5.897250 TGTGGCTAGTACTCCATTAATCTCA 59.103 40.000 0.00 0.00 34.47 3.27
757 2110 6.217294 GTGTGGCTAGTACTCCATTAATCTC 58.783 44.000 0.00 0.00 34.47 2.75
758 2111 5.070580 GGTGTGGCTAGTACTCCATTAATCT 59.929 44.000 0.00 0.00 34.47 2.40
759 2112 5.298347 GGTGTGGCTAGTACTCCATTAATC 58.702 45.833 0.00 0.00 34.47 1.75
760 2113 4.102681 GGGTGTGGCTAGTACTCCATTAAT 59.897 45.833 16.71 0.00 34.28 1.40
761 2114 3.453353 GGGTGTGGCTAGTACTCCATTAA 59.547 47.826 16.71 0.00 34.28 1.40
762 2115 3.036091 GGGTGTGGCTAGTACTCCATTA 58.964 50.000 16.71 0.00 34.28 1.90
763 2116 1.838077 GGGTGTGGCTAGTACTCCATT 59.162 52.381 16.71 0.00 34.28 3.16
764 2117 1.273609 TGGGTGTGGCTAGTACTCCAT 60.274 52.381 16.71 0.00 34.28 3.41
765 2118 0.115547 TGGGTGTGGCTAGTACTCCA 59.884 55.000 16.71 0.00 34.28 3.86
766 2119 1.272807 TTGGGTGTGGCTAGTACTCC 58.727 55.000 0.00 0.00 0.00 3.85
767 2120 3.412237 TTTTGGGTGTGGCTAGTACTC 57.588 47.619 0.00 0.00 0.00 2.59
768 2121 3.137728 AGTTTTTGGGTGTGGCTAGTACT 59.862 43.478 0.00 0.00 0.00 2.73
769 2122 3.483421 AGTTTTTGGGTGTGGCTAGTAC 58.517 45.455 0.00 0.00 0.00 2.73
770 2123 3.868619 AGTTTTTGGGTGTGGCTAGTA 57.131 42.857 0.00 0.00 0.00 1.82
771 2124 2.748209 AGTTTTTGGGTGTGGCTAGT 57.252 45.000 0.00 0.00 0.00 2.57
956 2664 0.800683 TATGCGCGTTCTTCGACCTG 60.801 55.000 7.78 0.00 42.86 4.00
961 2669 0.370273 AAAGCTATGCGCGTTCTTCG 59.630 50.000 7.78 0.00 45.59 3.79
963 2671 3.187637 TGTTTAAAGCTATGCGCGTTCTT 59.812 39.130 7.78 9.22 45.59 2.52
977 2685 6.228273 TGTTTGCTCGATCTCTGTTTAAAG 57.772 37.500 0.00 0.00 0.00 1.85
982 2690 3.930336 TCATGTTTGCTCGATCTCTGTT 58.070 40.909 0.00 0.00 0.00 3.16
1013 2722 2.107750 CGAGGGCGCAGATGATGT 59.892 61.111 10.83 0.00 0.00 3.06
1299 3011 3.771160 ATCACCCGCACGTCCTCC 61.771 66.667 0.00 0.00 0.00 4.30
1313 3025 1.876799 CAACGCAGGTTTGGTACATCA 59.123 47.619 0.00 0.00 39.30 3.07
1315 3027 1.877443 GTCAACGCAGGTTTGGTACAT 59.123 47.619 0.00 0.00 39.30 2.29
1433 3145 2.885113 CGCAGTGATCCACCGAGA 59.115 61.111 0.00 0.00 34.49 4.04
1569 3281 3.287867 AATCCACATCTCCACATCCAC 57.712 47.619 0.00 0.00 0.00 4.02
1617 3333 5.860182 CACTGCATAAGCCATGTATTATTGC 59.140 40.000 0.00 4.02 41.13 3.56
1622 3338 3.902218 ACCACTGCATAAGCCATGTATT 58.098 40.909 0.00 0.00 41.13 1.89
1626 3343 4.581824 AGAAATACCACTGCATAAGCCATG 59.418 41.667 0.00 0.00 41.13 3.66
1627 3344 4.796606 AGAAATACCACTGCATAAGCCAT 58.203 39.130 0.00 0.00 41.13 4.40
1628 3345 4.235079 AGAAATACCACTGCATAAGCCA 57.765 40.909 0.00 0.00 41.13 4.75
1629 3346 4.214332 GCTAGAAATACCACTGCATAAGCC 59.786 45.833 0.00 0.00 41.13 4.35
1630 3347 5.049818 CAGCTAGAAATACCACTGCATAAGC 60.050 44.000 0.00 0.00 42.57 3.09
1631 3348 5.468072 CCAGCTAGAAATACCACTGCATAAG 59.532 44.000 0.00 0.00 0.00 1.73
1632 3349 5.368145 CCAGCTAGAAATACCACTGCATAA 58.632 41.667 0.00 0.00 0.00 1.90
1633 3350 4.743651 GCCAGCTAGAAATACCACTGCATA 60.744 45.833 0.00 0.00 0.00 3.14
1634 3351 3.813443 CCAGCTAGAAATACCACTGCAT 58.187 45.455 0.00 0.00 0.00 3.96
1638 3355 4.946478 CTAGCCAGCTAGAAATACCACT 57.054 45.455 19.80 0.00 46.56 4.00
1648 3370 4.142609 TCAACCAAATCTAGCCAGCTAG 57.857 45.455 18.68 18.68 45.38 3.42
1652 3374 4.082125 ACCTTTCAACCAAATCTAGCCAG 58.918 43.478 0.00 0.00 0.00 4.85
1655 3390 5.453567 AACACCTTTCAACCAAATCTAGC 57.546 39.130 0.00 0.00 0.00 3.42
1752 3499 9.055248 CAGAGTCGAATCAAAAATAAATGTGAC 57.945 33.333 16.10 0.00 0.00 3.67
1782 3529 6.916360 TTTTCCCAGCTCAGTTCAAAATAT 57.084 33.333 0.00 0.00 0.00 1.28
1809 3556 5.357878 GGATTGATTACCACATGTGTCACAT 59.642 40.000 23.79 12.87 39.91 3.21
1810 3557 4.699735 GGATTGATTACCACATGTGTCACA 59.300 41.667 23.79 8.40 0.00 3.58
1811 3558 4.943705 AGGATTGATTACCACATGTGTCAC 59.056 41.667 23.79 9.88 0.00 3.67
1812 3559 5.178096 AGGATTGATTACCACATGTGTCA 57.822 39.130 23.79 17.32 0.00 3.58
1813 3560 7.047891 TCTTAGGATTGATTACCACATGTGTC 58.952 38.462 23.79 14.99 0.00 3.67
1814 3561 6.957631 TCTTAGGATTGATTACCACATGTGT 58.042 36.000 23.79 14.29 0.00 3.72
1815 3562 6.017605 GCTCTTAGGATTGATTACCACATGTG 60.018 42.308 19.31 19.31 0.00 3.21
1816 3563 6.058183 GCTCTTAGGATTGATTACCACATGT 58.942 40.000 0.00 0.00 0.00 3.21
1817 3564 6.057533 TGCTCTTAGGATTGATTACCACATG 58.942 40.000 0.00 0.00 0.00 3.21
1818 3565 6.252599 TGCTCTTAGGATTGATTACCACAT 57.747 37.500 0.00 0.00 0.00 3.21
1819 3566 5.692115 TGCTCTTAGGATTGATTACCACA 57.308 39.130 0.00 0.00 0.00 4.17
1820 3567 6.116126 AGTTGCTCTTAGGATTGATTACCAC 58.884 40.000 0.00 0.00 0.00 4.16
1821 3568 6.313519 AGTTGCTCTTAGGATTGATTACCA 57.686 37.500 0.00 0.00 0.00 3.25
1822 3569 5.760743 GGAGTTGCTCTTAGGATTGATTACC 59.239 44.000 0.00 0.00 0.00 2.85
1823 3570 6.349300 TGGAGTTGCTCTTAGGATTGATTAC 58.651 40.000 0.00 0.00 0.00 1.89
1824 3571 6.560003 TGGAGTTGCTCTTAGGATTGATTA 57.440 37.500 0.00 0.00 0.00 1.75
1825 3572 5.441718 TGGAGTTGCTCTTAGGATTGATT 57.558 39.130 0.00 0.00 0.00 2.57
1826 3573 5.189180 GTTGGAGTTGCTCTTAGGATTGAT 58.811 41.667 0.00 0.00 0.00 2.57
1827 3574 4.579869 GTTGGAGTTGCTCTTAGGATTGA 58.420 43.478 0.00 0.00 0.00 2.57
1828 3575 3.372206 CGTTGGAGTTGCTCTTAGGATTG 59.628 47.826 0.00 0.00 0.00 2.67
1829 3576 3.600388 CGTTGGAGTTGCTCTTAGGATT 58.400 45.455 0.00 0.00 0.00 3.01
1830 3577 2.093447 CCGTTGGAGTTGCTCTTAGGAT 60.093 50.000 0.00 0.00 0.00 3.24
1831 3578 1.275291 CCGTTGGAGTTGCTCTTAGGA 59.725 52.381 0.00 0.00 0.00 2.94
1832 3579 1.676014 CCCGTTGGAGTTGCTCTTAGG 60.676 57.143 0.00 0.00 0.00 2.69
1855 3602 6.071784 GGATAAAAACACCATCCGTTTAGGTT 60.072 38.462 0.00 0.00 41.99 3.50
1857 3604 5.886992 GGATAAAAACACCATCCGTTTAGG 58.113 41.667 0.00 0.00 35.57 2.69
1867 3614 3.297736 ACCCAAACGGATAAAAACACCA 58.702 40.909 0.00 0.00 34.64 4.17
1868 3615 3.305539 GGACCCAAACGGATAAAAACACC 60.306 47.826 0.00 0.00 34.64 4.16
1870 3617 2.553172 CGGACCCAAACGGATAAAAACA 59.447 45.455 0.00 0.00 34.64 2.83
2058 3825 2.346099 AAATGAAAATGTGGACGCGG 57.654 45.000 12.47 0.00 0.00 6.46
2088 3860 3.744426 CCACCTCGTAGTTTAGGTTGTTG 59.256 47.826 0.00 0.00 43.77 3.33
2189 3971 1.213094 CGCTCTGGAACACGACGTTT 61.213 55.000 0.00 0.00 38.19 3.60
2194 3976 3.493830 AACGCGCTCTGGAACACGA 62.494 57.895 5.73 0.00 0.00 4.35
2297 4080 1.599606 GAACTCGAGGAGGAGCAGCA 61.600 60.000 18.41 0.00 37.57 4.41


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

AutoCloner maintained by Alex Coulton.