Multiple sequence alignment - TraesCS2A01G388800

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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 TraesCS2A01G388800 chr2A 100.000 7538 0 0 772 8309 636904004 636911541 0.000000e+00 13921.0
1 TraesCS2A01G388800 chr2A 100.000 264 0 0 1 264 636903233 636903496 9.690000e-134 488.0
2 TraesCS2A01G388800 chr2A 95.753 259 11 0 1198 1456 232387130 232387388 1.290000e-112 418.0
3 TraesCS2A01G388800 chr2A 100.000 86 0 0 8223 8308 690329336 690329421 8.630000e-35 159.0
4 TraesCS2A01G388800 chr2A 92.593 108 8 0 8118 8225 547791731 547791838 1.120000e-33 156.0
5 TraesCS2A01G388800 chr2A 91.071 112 9 1 8115 8225 547277238 547277349 5.200000e-32 150.0
6 TraesCS2A01G388800 chr2A 90.179 112 10 1 8115 8225 566977832 566977721 2.420000e-30 145.0
7 TraesCS2A01G388800 chr2D 97.712 7344 115 27 806 8117 491802220 491809542 0.000000e+00 12582.0
8 TraesCS2A01G388800 chr2D 96.970 264 5 1 1 264 491801534 491801794 2.750000e-119 440.0
9 TraesCS2A01G388800 chr2D 83.957 187 28 1 2690 2876 573233333 573233517 2.380000e-40 178.0
10 TraesCS2A01G388800 chr2D 94.643 112 4 2 8116 8225 377110840 377110729 1.110000e-38 172.0
11 TraesCS2A01G388800 chr2B 97.889 4594 80 8 778 5367 576084744 576089324 0.000000e+00 7930.0
12 TraesCS2A01G388800 chr2B 96.118 2653 77 11 5486 8117 576089730 576092377 0.000000e+00 4305.0
13 TraesCS2A01G388800 chr2B 94.298 228 7 1 1 222 576083926 576084153 2.220000e-90 344.0
14 TraesCS2A01G388800 chr2B 97.849 93 2 0 5366 5458 576089486 576089578 2.400000e-35 161.0
15 TraesCS2A01G388800 chr2B 82.353 187 32 1 2690 2876 689300273 689300458 2.400000e-35 161.0
16 TraesCS2A01G388800 chr2B 91.892 111 8 1 8116 8225 448580678 448580568 4.020000e-33 154.0
17 TraesCS2A01G388800 chr7B 87.356 609 55 11 3624 4218 584316865 584317465 0.000000e+00 678.0
18 TraesCS2A01G388800 chr7B 97.647 85 2 0 8223 8307 537828022 537827938 6.720000e-31 147.0
19 TraesCS2A01G388800 chr7A 95.402 261 12 0 1195 1455 595822975 595822715 4.640000e-112 416.0
20 TraesCS2A01G388800 chr7A 93.636 110 7 0 8116 8225 102566793 102566902 1.860000e-36 165.0
21 TraesCS2A01G388800 chr7A 83.929 112 11 6 8117 8225 667323316 667323423 5.310000e-17 100.0
22 TraesCS2A01G388800 chr6A 94.757 267 14 0 1189 1455 599623039 599623305 4.640000e-112 416.0
23 TraesCS2A01G388800 chr1A 94.697 264 13 1 1193 1455 533465019 533464756 7.760000e-110 409.0
24 TraesCS2A01G388800 chr1A 90.756 119 9 1 5457 5575 218526956 218526840 3.100000e-34 158.0
25 TraesCS2A01G388800 chr1A 100.000 85 0 0 8223 8307 511001594 511001510 3.100000e-34 158.0
26 TraesCS2A01G388800 chr4D 95.652 253 11 0 1203 1455 252186814 252187066 2.790000e-109 407.0
27 TraesCS2A01G388800 chr3B 93.750 272 14 2 1185 1456 144814327 144814595 1.000000e-108 405.0
28 TraesCS2A01G388800 chr3B 90.756 119 9 1 5457 5575 42630933 42630817 3.100000e-34 158.0
29 TraesCS2A01G388800 chr5A 94.922 256 12 1 1200 1455 477975540 477975286 4.670000e-107 399.0
30 TraesCS2A01G388800 chr5A 81.019 216 38 3 2677 2891 522059417 522059204 1.430000e-37 169.0
31 TraesCS2A01G388800 chr5A 96.825 63 0 2 1457 1517 444942200 444942138 4.100000e-18 104.0
32 TraesCS2A01G388800 chr5A 95.161 62 3 0 1459 1520 354544142 354544081 1.910000e-16 99.0
33 TraesCS2A01G388800 chr5A 91.429 70 5 1 1463 1531 366235688 366235757 2.470000e-15 95.3
34 TraesCS2A01G388800 chr7D 90.378 291 24 3 4055 4344 540858154 540858441 6.090000e-101 379.0
35 TraesCS2A01G388800 chr7D 91.288 264 22 1 3624 3886 540857895 540858158 7.930000e-95 359.0
36 TraesCS2A01G388800 chr7D 92.661 109 8 0 8117 8225 124535083 124534975 3.100000e-34 158.0
37 TraesCS2A01G388800 chr1B 80.077 261 39 4 2615 2874 377191039 377191287 1.840000e-41 182.0
38 TraesCS2A01G388800 chr1B 97.647 85 2 0 8223 8307 662158779 662158863 6.720000e-31 147.0
39 TraesCS2A01G388800 chr1B 97.647 85 2 0 8223 8307 662161332 662161416 6.720000e-31 147.0
40 TraesCS2A01G388800 chr1B 90.526 95 7 2 8131 8225 328923239 328923331 3.150000e-24 124.0
41 TraesCS2A01G388800 chr6B 79.137 278 45 7 2619 2896 706113847 706114111 6.630000e-41 180.0
42 TraesCS2A01G388800 chr3D 84.324 185 26 3 2690 2874 567337018 567337199 2.380000e-40 178.0
43 TraesCS2A01G388800 chr3D 93.043 115 6 1 5459 5573 71517791 71517679 5.160000e-37 167.0
44 TraesCS2A01G388800 chr3D 91.597 119 8 1 5457 5575 426451974 426451858 6.670000e-36 163.0
45 TraesCS2A01G388800 chr4A 81.553 206 35 2 2690 2895 650324347 650324549 5.160000e-37 167.0
46 TraesCS2A01G388800 chr4A 98.824 85 1 0 8223 8307 82849270 82849186 1.440000e-32 152.0
47 TraesCS2A01G388800 chr4A 98.333 60 1 0 1459 1518 29026027 29026086 1.140000e-18 106.0
48 TraesCS2A01G388800 chr3A 91.597 119 8 1 5457 5575 34532564 34532448 6.670000e-36 163.0
49 TraesCS2A01G388800 chr3A 98.837 86 1 0 8223 8308 303756876 303756791 4.020000e-33 154.0
50 TraesCS2A01G388800 chr3A 98.305 59 0 1 1465 1522 509865353 509865411 1.480000e-17 102.0
51 TraesCS2A01G388800 chr3A 92.537 67 3 1 1456 1520 38393240 38393174 2.470000e-15 95.3
52 TraesCS2A01G388800 chr6D 89.916 119 10 1 5457 5575 304099337 304099453 1.440000e-32 152.0
53 TraesCS2A01G388800 chr5D 98.824 85 1 0 8223 8307 231356277 231356361 1.440000e-32 152.0
54 TraesCS2A01G388800 chr1D 89.916 119 10 1 5457 5575 175819951 175819835 1.440000e-32 152.0
55 TraesCS2A01G388800 chr5B 91.262 103 7 2 8209 8309 432174686 432174788 1.120000e-28 139.0
56 TraesCS2A01G388800 chr4B 93.750 64 4 0 1454 1517 544041840 544041903 6.860000e-16 97.1


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 TraesCS2A01G388800 chr2A 636903233 636911541 8308 False 7204.5 13921 100.0000 1 8309 2 chr2A.!!$F5 8308
1 TraesCS2A01G388800 chr2D 491801534 491809542 8008 False 6511.0 12582 97.3410 1 8117 2 chr2D.!!$F2 8116
2 TraesCS2A01G388800 chr2B 576083926 576092377 8451 False 3185.0 7930 96.5385 1 8117 4 chr2B.!!$F2 8116
3 TraesCS2A01G388800 chr7B 584316865 584317465 600 False 678.0 678 87.3560 3624 4218 1 chr7B.!!$F1 594
4 TraesCS2A01G388800 chr7D 540857895 540858441 546 False 369.0 379 90.8330 3624 4344 2 chr7D.!!$F1 720

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
924 1374 0.387622 CAGCAAAAGGTCGTGGCATG 60.388 55.000 0.00 0.0 0.00 4.06 F
1245 1695 1.180029 CAAAGGGGCAGATCCAACAG 58.820 55.000 0.00 0.0 36.21 3.16 F
2144 2598 2.498167 AGTGCTCAACTGATTGACACC 58.502 47.619 13.93 0.0 42.10 4.16 F
3389 3844 6.892658 AATGGTGCTGTTAACAAATGTCTA 57.107 33.333 10.03 0.0 0.00 2.59 F
4605 5074 3.369242 TGGGAATCATGCATCTTGTCA 57.631 42.857 0.00 0.0 0.00 3.58 F
5214 5683 0.610232 ATGGCTTCCACAGGAGTTGC 60.610 55.000 0.00 0.0 35.80 4.17 F
6389 7145 0.804989 AAGCTCAGCAATAACACCGC 59.195 50.000 0.00 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2657 5.091261 ACACCTATTGCAGAAGGAAGTAG 57.909 43.478 20.08 8.76 36.66 2.57 R
3203 3658 2.298729 GCATTTAAGTTTCCCAGTGCCA 59.701 45.455 0.00 0.00 0.00 4.92 R
3781 4236 5.175859 TCATTAGCTCCAGGAAAAACTACG 58.824 41.667 0.00 0.00 0.00 3.51 R
4736 5205 0.523072 GTCATGACTGCAATTGCCGT 59.477 50.000 25.05 25.05 41.16 5.68 R
5448 6080 0.823356 TTGAACCCAGGAGCAACTGC 60.823 55.000 2.41 0.00 42.49 4.40 R
6411 7167 1.067071 CGAAGGTCACAACTCCTACCC 60.067 57.143 0.00 0.00 33.27 3.69 R
8064 8834 0.109781 CGCCCACTGCATGTAACAAC 60.110 55.000 0.00 0.00 41.33 3.32 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
58 59 3.019564 ACCACTATCAGCAGAAAATGGC 58.980 45.455 5.99 0.00 0.00 4.40
167 177 0.989212 ACCACCACCACCACCAAGTA 60.989 55.000 0.00 0.00 0.00 2.24
170 180 1.060163 ACCACCACCACCAAGTAGCT 61.060 55.000 0.00 0.00 0.00 3.32
801 849 3.260100 CCCCCACCACCTCAAGCT 61.260 66.667 0.00 0.00 0.00 3.74
924 1374 0.387622 CAGCAAAAGGTCGTGGCATG 60.388 55.000 0.00 0.00 0.00 4.06
996 1446 1.871039 CACTGGGTGAAAGTTACACGG 59.129 52.381 0.00 0.00 38.90 4.94
1090 1540 7.644945 GCCAATATTTTTGCATTTAATTCAGCC 59.355 33.333 0.00 0.00 0.00 4.85
1245 1695 1.180029 CAAAGGGGCAGATCCAACAG 58.820 55.000 0.00 0.00 36.21 3.16
1456 1906 4.500127 TGCACGCACACATTTACTAGTAT 58.500 39.130 2.79 0.00 0.00 2.12
1536 1988 6.183360 GGAGTATATATCATGCTACAGTCGCA 60.183 42.308 1.61 1.61 42.25 5.10
2060 2514 9.883142 AAACCATTCTTGATTAAAACTGTTTCA 57.117 25.926 6.20 0.00 0.00 2.69
2081 2535 7.595311 TTCATGGTAATACGATATGCATGAC 57.405 36.000 10.16 2.04 0.00 3.06
2144 2598 2.498167 AGTGCTCAACTGATTGACACC 58.502 47.619 13.93 0.00 42.10 4.16
3068 3523 7.097192 ACATTAATAGATTCGGCGATGTACAT 58.903 34.615 11.76 8.43 0.00 2.29
3069 3524 6.944557 TTAATAGATTCGGCGATGTACATG 57.055 37.500 14.43 6.99 0.00 3.21
3389 3844 6.892658 AATGGTGCTGTTAACAAATGTCTA 57.107 33.333 10.03 0.00 0.00 2.59
3637 4092 8.671921 CATTTAGTATCTGATGCTGTTTTGTCT 58.328 33.333 17.09 0.00 0.00 3.41
3644 4099 7.509141 TCTGATGCTGTTTTGTCTTAATTCA 57.491 32.000 0.00 0.00 0.00 2.57
4075 4543 4.243270 ACACGTAGACTGGCTTAATGTTC 58.757 43.478 0.00 0.00 0.00 3.18
4417 4886 4.650588 AGATTCCTCTCAGTCCATCTTCAG 59.349 45.833 0.00 0.00 0.00 3.02
4605 5074 3.369242 TGGGAATCATGCATCTTGTCA 57.631 42.857 0.00 0.00 0.00 3.58
4826 5295 3.685139 TTCTTTCACGGATCAGCTCTT 57.315 42.857 0.00 0.00 0.00 2.85
5214 5683 0.610232 ATGGCTTCCACAGGAGTTGC 60.610 55.000 0.00 0.00 35.80 4.17
5230 5699 6.375455 CAGGAGTTGCTAGTTGGATTGTAAAT 59.625 38.462 0.00 0.00 0.00 1.40
5466 6117 1.228245 GCAGTTGCTCCTGGGTTCA 60.228 57.895 0.00 0.00 38.21 3.18
5516 6272 2.107552 GGGGTATGGCTTGCCTTGTATA 59.892 50.000 13.18 0.00 0.00 1.47
5517 6273 3.435890 GGGGTATGGCTTGCCTTGTATAA 60.436 47.826 13.18 0.00 0.00 0.98
6104 6860 3.329225 TCCCCAGACATTCAATGTGTACA 59.671 43.478 8.05 0.00 45.03 2.90
6289 7045 7.229306 TCAGAACATAAAGTCAAAGAATGTGCT 59.771 33.333 0.00 0.00 36.98 4.40
6389 7145 0.804989 AAGCTCAGCAATAACACCGC 59.195 50.000 0.00 0.00 0.00 5.68
6441 7197 1.305046 TGACCTTCGGGGACTCCTC 60.305 63.158 2.52 0.00 40.03 3.71
6458 7214 3.668447 TCCTCAACTCTAAAGCAAGCAG 58.332 45.455 0.00 0.00 0.00 4.24
6917 7676 3.674997 TCGCACTAGCAGAAGGAAAAAT 58.325 40.909 0.00 0.00 42.27 1.82
6986 7745 4.119136 GGTCCAAACATTTTGTTGTCCAG 58.881 43.478 0.00 0.00 40.14 3.86
7375 8134 2.042831 GGAGCTGCCGCAGAATGTT 61.043 57.895 24.80 3.20 39.31 2.71
7376 8135 0.744414 GGAGCTGCCGCAGAATGTTA 60.744 55.000 24.80 0.00 39.31 2.41
7476 8235 4.695993 TGGCTGCGCGTCATCCAA 62.696 61.111 19.00 7.27 37.98 3.53
7705 8467 4.876652 GCTGCTTTTAGTGGCTGC 57.123 55.556 0.00 0.00 43.58 5.25
7760 8522 0.796312 CAAATACGCAGGTTGCTCGT 59.204 50.000 0.00 0.00 42.25 4.18
7769 8531 1.299089 GGTTGCTCGTGGTTTGCAC 60.299 57.895 0.00 0.00 36.37 4.57
7937 8700 4.374399 CTCAAGTGGAAGCAAAGCAAAAT 58.626 39.130 0.00 0.00 0.00 1.82
7938 8701 5.528043 TCAAGTGGAAGCAAAGCAAAATA 57.472 34.783 0.00 0.00 0.00 1.40
7997 8761 4.215109 ACAAGTAGACTGGTGCCATTTTT 58.785 39.130 0.00 0.00 0.00 1.94
8002 8766 1.069049 GACTGGTGCCATTTTTGCAGT 59.931 47.619 0.00 0.00 39.87 4.40
8004 8768 0.532417 TGGTGCCATTTTTGCAGTGC 60.532 50.000 8.58 8.58 39.87 4.40
8041 8811 3.181474 ACGAAGCTCCTACAAGGCTTATC 60.181 47.826 0.00 0.00 44.81 1.75
8064 8834 8.746922 ATCGTGCCTTTATGCAATTATTATTG 57.253 30.769 0.00 0.00 44.11 1.90
8067 8837 8.268052 CGTGCCTTTATGCAATTATTATTGTTG 58.732 33.333 6.33 0.00 44.11 3.33
8080 8857 9.585099 AATTATTATTGTTGTTACATGCAGTGG 57.415 29.630 0.00 0.00 33.44 4.00
8109 8886 1.556911 AGGATGTGTCTGGTGCTAAGG 59.443 52.381 0.00 0.00 0.00 2.69
8175 8952 4.896562 TCAAATAAGCACAGTTACGTCG 57.103 40.909 0.00 0.00 0.00 5.12
8176 8953 4.300803 TCAAATAAGCACAGTTACGTCGT 58.699 39.130 2.21 2.21 0.00 4.34
8177 8954 4.746115 TCAAATAAGCACAGTTACGTCGTT 59.254 37.500 1.78 0.00 0.00 3.85
8178 8955 4.898328 AATAAGCACAGTTACGTCGTTC 57.102 40.909 1.78 0.00 0.00 3.95
8179 8956 2.212869 AAGCACAGTTACGTCGTTCA 57.787 45.000 1.78 0.00 0.00 3.18
8180 8957 2.433868 AGCACAGTTACGTCGTTCAT 57.566 45.000 1.78 0.00 0.00 2.57
8181 8958 2.058798 AGCACAGTTACGTCGTTCATG 58.941 47.619 1.78 2.49 0.00 3.07
8182 8959 2.055838 GCACAGTTACGTCGTTCATGA 58.944 47.619 1.78 0.00 0.00 3.07
8183 8960 2.090658 GCACAGTTACGTCGTTCATGAG 59.909 50.000 1.78 0.09 0.00 2.90
8184 8961 3.561503 CACAGTTACGTCGTTCATGAGA 58.438 45.455 1.78 0.00 0.00 3.27
8185 8962 4.166523 CACAGTTACGTCGTTCATGAGAT 58.833 43.478 1.78 0.00 0.00 2.75
8186 8963 5.329493 CACAGTTACGTCGTTCATGAGATA 58.671 41.667 1.78 0.00 0.00 1.98
8187 8964 5.971792 CACAGTTACGTCGTTCATGAGATAT 59.028 40.000 1.78 0.00 0.00 1.63
8188 8965 6.472486 CACAGTTACGTCGTTCATGAGATATT 59.528 38.462 1.78 0.00 0.00 1.28
8189 8966 6.691818 ACAGTTACGTCGTTCATGAGATATTC 59.308 38.462 1.78 0.00 0.00 1.75
8190 8967 6.691388 CAGTTACGTCGTTCATGAGATATTCA 59.309 38.462 1.78 0.00 40.85 2.57
8191 8968 6.913132 AGTTACGTCGTTCATGAGATATTCAG 59.087 38.462 1.78 0.00 39.68 3.02
8192 8969 5.250235 ACGTCGTTCATGAGATATTCAGT 57.750 39.130 0.00 0.00 39.68 3.41
8193 8970 6.373186 ACGTCGTTCATGAGATATTCAGTA 57.627 37.500 0.00 0.00 39.68 2.74
8194 8971 6.792326 ACGTCGTTCATGAGATATTCAGTAA 58.208 36.000 0.00 0.00 39.68 2.24
8195 8972 6.913132 ACGTCGTTCATGAGATATTCAGTAAG 59.087 38.462 0.00 0.00 39.68 2.34
8196 8973 7.132863 CGTCGTTCATGAGATATTCAGTAAGA 58.867 38.462 0.00 0.00 39.68 2.10
8197 8974 7.644157 CGTCGTTCATGAGATATTCAGTAAGAA 59.356 37.037 0.00 0.00 39.68 2.52
8198 8975 9.302345 GTCGTTCATGAGATATTCAGTAAGAAA 57.698 33.333 0.00 0.00 40.22 2.52
8199 8976 9.869757 TCGTTCATGAGATATTCAGTAAGAAAA 57.130 29.630 0.00 0.00 40.22 2.29
8212 8989 9.927081 ATTCAGTAAGAAAATAAGGGTGATCAT 57.073 29.630 0.00 0.00 40.22 2.45
8213 8990 8.964476 TCAGTAAGAAAATAAGGGTGATCATC 57.036 34.615 0.00 0.00 0.00 2.92
8214 8991 8.772250 TCAGTAAGAAAATAAGGGTGATCATCT 58.228 33.333 5.82 0.72 0.00 2.90
8217 8994 9.274206 GTAAGAAAATAAGGGTGATCATCTACC 57.726 37.037 5.82 3.42 36.21 3.18
8227 9004 5.552178 GGTGATCATCTACCCAATTACTCC 58.448 45.833 0.00 0.00 0.00 3.85
8228 9005 5.513267 GGTGATCATCTACCCAATTACTCCC 60.513 48.000 0.00 0.00 0.00 4.30
8229 9006 5.308237 GTGATCATCTACCCAATTACTCCCT 59.692 44.000 0.00 0.00 0.00 4.20
8230 9007 5.544176 TGATCATCTACCCAATTACTCCCTC 59.456 44.000 0.00 0.00 0.00 4.30
8231 9008 5.157770 TCATCTACCCAATTACTCCCTCT 57.842 43.478 0.00 0.00 0.00 3.69
8232 9009 4.901849 TCATCTACCCAATTACTCCCTCTG 59.098 45.833 0.00 0.00 0.00 3.35
8233 9010 4.348020 TCTACCCAATTACTCCCTCTGT 57.652 45.455 0.00 0.00 0.00 3.41
8234 9011 5.476950 TCTACCCAATTACTCCCTCTGTA 57.523 43.478 0.00 0.00 0.00 2.74
8235 9012 5.845734 TCTACCCAATTACTCCCTCTGTAA 58.154 41.667 0.00 0.00 34.87 2.41
8236 9013 6.266080 TCTACCCAATTACTCCCTCTGTAAA 58.734 40.000 0.00 0.00 34.20 2.01
8237 9014 5.175388 ACCCAATTACTCCCTCTGTAAAC 57.825 43.478 0.00 0.00 34.20 2.01
8238 9015 4.600111 ACCCAATTACTCCCTCTGTAAACA 59.400 41.667 0.00 0.00 34.20 2.83
8239 9016 5.073965 ACCCAATTACTCCCTCTGTAAACAA 59.926 40.000 0.00 0.00 34.20 2.83
8240 9017 6.007703 CCCAATTACTCCCTCTGTAAACAAA 58.992 40.000 0.00 0.00 34.20 2.83
8241 9018 6.663523 CCCAATTACTCCCTCTGTAAACAAAT 59.336 38.462 0.00 0.00 34.20 2.32
8242 9019 7.832187 CCCAATTACTCCCTCTGTAAACAAATA 59.168 37.037 0.00 0.00 34.20 1.40
8243 9020 9.408648 CCAATTACTCCCTCTGTAAACAAATAT 57.591 33.333 0.00 0.00 34.20 1.28
8249 9026 7.988028 ACTCCCTCTGTAAACAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
8250 9027 6.984474 TCCCTCTGTAAACAAATATAAGAGCG 59.016 38.462 0.00 0.00 0.00 5.03
8251 9028 6.761714 CCCTCTGTAAACAAATATAAGAGCGT 59.238 38.462 0.00 0.00 0.00 5.07
8252 9029 7.280205 CCCTCTGTAAACAAATATAAGAGCGTT 59.720 37.037 0.00 0.00 0.00 4.84
8253 9030 8.665685 CCTCTGTAAACAAATATAAGAGCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
8261 9038 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
8268 9045 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
8269 9046 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
8302 9079 8.738645 ATGCTCTTATAAAAGTTTACAGAGGG 57.261 34.615 16.49 5.38 35.69 4.30
8303 9080 7.913789 TGCTCTTATAAAAGTTTACAGAGGGA 58.086 34.615 16.49 4.34 35.69 4.20
8304 9081 8.041323 TGCTCTTATAAAAGTTTACAGAGGGAG 58.959 37.037 16.49 0.00 35.69 4.30
8305 9082 8.041919 GCTCTTATAAAAGTTTACAGAGGGAGT 58.958 37.037 16.49 0.00 35.69 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.258982 GCCGAGATAGCATGTTTGTCG 59.741 52.381 0.00 0.00 0.00 4.35
143 144 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
144 145 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
145 146 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
167 177 2.099756 GTGAGAAAACAGGTTTGCAGCT 59.900 45.455 5.71 0.00 30.40 4.24
170 180 2.165437 GTGGTGAGAAAACAGGTTTGCA 59.835 45.455 5.71 0.00 30.40 4.08
801 849 1.286553 ACAGTTCCAGGTGGTTTTGGA 59.713 47.619 0.00 0.00 41.59 3.53
924 1374 1.459450 TACTTTGAAGCGCCAATCCC 58.541 50.000 2.29 0.00 0.00 3.85
996 1446 1.471684 CAGAGACTTCCTTGCATTGCC 59.528 52.381 6.12 0.00 0.00 4.52
1245 1695 1.571919 CTGATTTGACGGACGGGATC 58.428 55.000 0.00 0.00 0.00 3.36
1506 1958 6.741724 TGTAGCATGATATATACTCCCTCCA 58.258 40.000 0.00 0.00 0.00 3.86
1908 2360 6.501781 AGAAGCACAAGAATGAAAGTTCAAG 58.498 36.000 0.00 0.00 41.13 3.02
2060 2514 7.976175 CAGTAGTCATGCATATCGTATTACCAT 59.024 37.037 0.00 0.00 0.00 3.55
2202 2657 5.091261 ACACCTATTGCAGAAGGAAGTAG 57.909 43.478 20.08 8.76 36.66 2.57
2236 2691 7.226720 TGCGAGAGAGAAAACTATTCAAAAGTT 59.773 33.333 0.00 0.00 38.82 2.66
2856 3311 7.225341 CAGCTCAACAATGTAGTGCATATAGAA 59.775 37.037 0.00 0.00 36.67 2.10
3068 3523 7.280876 GTGTATGGAAGATGTTAGCAAGATTCA 59.719 37.037 0.00 0.00 0.00 2.57
3069 3524 7.497249 AGTGTATGGAAGATGTTAGCAAGATTC 59.503 37.037 0.00 0.00 0.00 2.52
3161 3616 7.363880 CCTAATGTTAGACCACTGTATGAGTGT 60.364 40.741 1.42 0.00 40.63 3.55
3203 3658 2.298729 GCATTTAAGTTTCCCAGTGCCA 59.701 45.455 0.00 0.00 0.00 4.92
3389 3844 8.329502 AGGAACACTAAAAAGTATCAGGCTAAT 58.670 33.333 0.00 0.00 0.00 1.73
3644 4099 6.139671 TGAGCTCATAGAGGAAAAGGATAGT 58.860 40.000 13.74 0.00 0.00 2.12
3781 4236 5.175859 TCATTAGCTCCAGGAAAAACTACG 58.824 41.667 0.00 0.00 0.00 3.51
4075 4543 5.471456 AGACTCTTTCACCTGCACAAAATAG 59.529 40.000 0.00 0.00 0.00 1.73
4236 4705 1.024271 GCAGAACCTGTTCAGCACAA 58.976 50.000 18.77 0.00 46.87 3.33
4736 5205 0.523072 GTCATGACTGCAATTGCCGT 59.477 50.000 25.05 25.05 41.16 5.68
5214 5683 7.094205 ACTGGCAGAAATTTACAATCCAACTAG 60.094 37.037 23.66 0.00 0.00 2.57
5230 5699 2.574006 ATGCAGAGAACTGGCAGAAA 57.426 45.000 23.66 0.00 43.62 2.52
5448 6080 0.823356 TTGAACCCAGGAGCAACTGC 60.823 55.000 2.41 0.00 42.49 4.40
5466 6117 3.612247 AATGCAGAGAGGCCGCGTT 62.612 57.895 4.92 0.51 0.00 4.84
6018 6774 3.141398 GTGTCATTTCTTGTCCTGAGCA 58.859 45.455 0.00 0.00 0.00 4.26
6289 7045 4.082787 GCTAGCAGAACATTTTGTAAGCCA 60.083 41.667 10.63 0.00 0.00 4.75
6389 7145 1.734477 CCAGAGTTCGGACTGTGCG 60.734 63.158 15.49 15.86 43.75 5.34
6411 7167 1.067071 CGAAGGTCACAACTCCTACCC 60.067 57.143 0.00 0.00 33.27 3.69
6441 7197 4.934001 TCAGATCTGCTTGCTTTAGAGTTG 59.066 41.667 18.36 0.00 0.00 3.16
6917 7676 6.831868 GGATTAGGGGCAATACTTTGAAGTTA 59.168 38.462 1.20 0.00 40.37 2.24
6986 7745 3.367932 TCGATTCGAAGAAATGCACTGTC 59.632 43.478 6.24 0.00 45.90 3.51
7307 8066 3.198853 GGCTTAGAAATGTCCTCACTCCT 59.801 47.826 0.00 0.00 0.00 3.69
7375 8134 1.250328 CGGGCTCCGGTGTATGTATA 58.750 55.000 0.00 0.00 44.15 1.47
7376 8135 2.046938 CGGGCTCCGGTGTATGTAT 58.953 57.895 0.00 0.00 44.15 2.29
7705 8467 5.619132 AGCATGAAAAATAAATCCCAGGG 57.381 39.130 0.00 0.00 0.00 4.45
7760 8522 0.948678 GTTCCTTAGCGTGCAAACCA 59.051 50.000 0.00 0.00 0.00 3.67
7769 8531 3.626028 AGCACAAAAAGTTCCTTAGCG 57.374 42.857 0.00 0.00 0.00 4.26
7980 8744 2.557924 CTGCAAAAATGGCACCAGTCTA 59.442 45.455 0.00 0.00 36.11 2.59
8004 8768 4.191485 CGTTAACTGGCTCGCGCG 62.191 66.667 26.76 26.76 36.88 6.86
8041 8811 7.928908 ACAATAATAATTGCATAAAGGCACG 57.071 32.000 0.00 0.00 45.41 5.34
8064 8834 0.109781 CGCCCACTGCATGTAACAAC 60.110 55.000 0.00 0.00 41.33 3.32
8067 8837 2.485122 GCGCCCACTGCATGTAAC 59.515 61.111 0.00 0.00 41.33 2.50
8080 8857 2.045926 ACACATCCTTCAGGCGCC 60.046 61.111 21.89 21.89 34.44 6.53
8149 8926 8.114290 CGACGTAACTGTGCTTATTTGATTAAT 58.886 33.333 0.00 0.00 0.00 1.40
8150 8927 7.116662 ACGACGTAACTGTGCTTATTTGATTAA 59.883 33.333 0.00 0.00 0.00 1.40
8151 8928 6.587226 ACGACGTAACTGTGCTTATTTGATTA 59.413 34.615 0.00 0.00 0.00 1.75
8152 8929 5.407387 ACGACGTAACTGTGCTTATTTGATT 59.593 36.000 0.00 0.00 0.00 2.57
8153 8930 4.927425 ACGACGTAACTGTGCTTATTTGAT 59.073 37.500 0.00 0.00 0.00 2.57
8154 8931 4.300803 ACGACGTAACTGTGCTTATTTGA 58.699 39.130 0.00 0.00 0.00 2.69
8155 8932 4.640805 ACGACGTAACTGTGCTTATTTG 57.359 40.909 0.00 0.00 0.00 2.32
8156 8933 4.746115 TGAACGACGTAACTGTGCTTATTT 59.254 37.500 0.00 0.00 0.00 1.40
8157 8934 4.300803 TGAACGACGTAACTGTGCTTATT 58.699 39.130 0.00 0.00 0.00 1.40
8158 8935 3.904571 TGAACGACGTAACTGTGCTTAT 58.095 40.909 0.00 0.00 0.00 1.73
8159 8936 3.352554 TGAACGACGTAACTGTGCTTA 57.647 42.857 0.00 0.00 0.00 3.09
8160 8937 2.212869 TGAACGACGTAACTGTGCTT 57.787 45.000 0.00 0.00 0.00 3.91
8161 8938 2.058798 CATGAACGACGTAACTGTGCT 58.941 47.619 0.00 0.00 0.00 4.40
8162 8939 2.055838 TCATGAACGACGTAACTGTGC 58.944 47.619 0.00 0.00 0.00 4.57
8163 8940 3.561503 TCTCATGAACGACGTAACTGTG 58.438 45.455 0.00 0.49 0.00 3.66
8164 8941 3.909776 TCTCATGAACGACGTAACTGT 57.090 42.857 0.00 0.00 0.00 3.55
8165 8942 6.691388 TGAATATCTCATGAACGACGTAACTG 59.309 38.462 0.00 0.00 0.00 3.16
8166 8943 6.792326 TGAATATCTCATGAACGACGTAACT 58.208 36.000 0.00 0.00 0.00 2.24
8167 8944 6.691818 ACTGAATATCTCATGAACGACGTAAC 59.308 38.462 0.00 0.00 32.14 2.50
8168 8945 6.792326 ACTGAATATCTCATGAACGACGTAA 58.208 36.000 0.00 0.00 32.14 3.18
8169 8946 6.373186 ACTGAATATCTCATGAACGACGTA 57.627 37.500 0.00 0.00 32.14 3.57
8170 8947 5.250235 ACTGAATATCTCATGAACGACGT 57.750 39.130 0.00 0.00 32.14 4.34
8171 8948 7.132863 TCTTACTGAATATCTCATGAACGACG 58.867 38.462 0.00 0.00 32.14 5.12
8172 8949 8.858003 TTCTTACTGAATATCTCATGAACGAC 57.142 34.615 0.00 0.00 32.14 4.34
8173 8950 9.869757 TTTTCTTACTGAATATCTCATGAACGA 57.130 29.630 0.00 0.00 34.24 3.85
8186 8963 9.927081 ATGATCACCCTTATTTTCTTACTGAAT 57.073 29.630 0.00 0.00 34.24 2.57
8187 8964 9.396022 GATGATCACCCTTATTTTCTTACTGAA 57.604 33.333 0.00 0.00 0.00 3.02
8188 8965 8.772250 AGATGATCACCCTTATTTTCTTACTGA 58.228 33.333 0.00 0.00 0.00 3.41
8189 8966 8.970859 AGATGATCACCCTTATTTTCTTACTG 57.029 34.615 0.00 0.00 0.00 2.74
8191 8968 9.274206 GGTAGATGATCACCCTTATTTTCTTAC 57.726 37.037 0.00 0.00 0.00 2.34
8204 8981 5.513267 GGGAGTAATTGGGTAGATGATCACC 60.513 48.000 0.00 0.00 0.00 4.02
8205 8982 5.308237 AGGGAGTAATTGGGTAGATGATCAC 59.692 44.000 0.00 0.00 0.00 3.06
8206 8983 5.476983 AGGGAGTAATTGGGTAGATGATCA 58.523 41.667 0.00 0.00 0.00 2.92
8207 8984 5.782845 AGAGGGAGTAATTGGGTAGATGATC 59.217 44.000 0.00 0.00 0.00 2.92
8208 8985 5.545723 CAGAGGGAGTAATTGGGTAGATGAT 59.454 44.000 0.00 0.00 0.00 2.45
8209 8986 4.901849 CAGAGGGAGTAATTGGGTAGATGA 59.098 45.833 0.00 0.00 0.00 2.92
8210 8987 4.656112 ACAGAGGGAGTAATTGGGTAGATG 59.344 45.833 0.00 0.00 0.00 2.90
8211 8988 4.897051 ACAGAGGGAGTAATTGGGTAGAT 58.103 43.478 0.00 0.00 0.00 1.98
8212 8989 4.348020 ACAGAGGGAGTAATTGGGTAGA 57.652 45.455 0.00 0.00 0.00 2.59
8213 8990 6.070424 TGTTTACAGAGGGAGTAATTGGGTAG 60.070 42.308 0.00 0.00 32.07 3.18
8214 8991 5.786457 TGTTTACAGAGGGAGTAATTGGGTA 59.214 40.000 0.00 0.00 32.07 3.69
8215 8992 4.600111 TGTTTACAGAGGGAGTAATTGGGT 59.400 41.667 0.00 0.00 32.07 4.51
8216 8993 5.174037 TGTTTACAGAGGGAGTAATTGGG 57.826 43.478 0.00 0.00 32.07 4.12
8217 8994 7.703058 ATTTGTTTACAGAGGGAGTAATTGG 57.297 36.000 0.00 0.00 32.07 3.16
8223 9000 7.988028 GCTCTTATATTTGTTTACAGAGGGAGT 59.012 37.037 0.00 0.00 0.00 3.85
8224 9001 7.169982 CGCTCTTATATTTGTTTACAGAGGGAG 59.830 40.741 4.76 0.00 36.40 4.30
8225 9002 6.984474 CGCTCTTATATTTGTTTACAGAGGGA 59.016 38.462 4.76 0.00 36.40 4.20
8226 9003 6.761714 ACGCTCTTATATTTGTTTACAGAGGG 59.238 38.462 8.36 8.36 38.95 4.30
8227 9004 7.772332 ACGCTCTTATATTTGTTTACAGAGG 57.228 36.000 0.00 0.00 0.00 3.69
8235 9012 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
8242 9019 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
8243 9020 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
8244 9021 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
8245 9022 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
8276 9053 9.178758 CCCTCTGTAAACTTTTATAAGAGCATT 57.821 33.333 13.76 2.32 36.27 3.56
8277 9054 8.548877 TCCCTCTGTAAACTTTTATAAGAGCAT 58.451 33.333 13.76 0.00 36.27 3.79
8278 9055 7.913789 TCCCTCTGTAAACTTTTATAAGAGCA 58.086 34.615 13.76 0.00 36.27 4.26
8279 9056 8.041919 ACTCCCTCTGTAAACTTTTATAAGAGC 58.958 37.037 13.76 0.00 36.27 4.09


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

AutoCloner maintained by Alex Coulton.