Multiple sequence alignment - TraesCS5B01G043500

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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 TraesCS5B01G043500 chr5B 100.000 2135 0 0 1 2135 48448628 48446494 0.000000e+00 3943
1 TraesCS5B01G043500 chr5B 96.693 635 20 1 1502 2135 48440301 48440935 0.000000e+00 1055
2 TraesCS5B01G043500 chr5B 96.220 635 23 1 1502 2135 48434175 48433541 0.000000e+00 1038
3 TraesCS5B01G043500 chr5B 92.663 368 26 1 1134 1501 196702036 196701670 1.450000e-146 529
4 TraesCS5B01G043500 chr5B 91.848 368 29 1 1134 1500 648195831 648195464 1.460000e-141 512
5 TraesCS5B01G043500 chr5B 94.694 245 13 0 101 345 256760637 256760393 4.300000e-102 381
6 TraesCS5B01G043500 chr5B 94.694 245 13 0 101 345 648196074 648195830 4.300000e-102 381
7 TraesCS5B01G043500 chr5B 93.548 248 15 1 99 346 663931460 663931214 3.350000e-98 368
8 TraesCS5B01G043500 chr5B 96.364 110 4 0 1 110 589479967 589479858 4.680000e-42 182
9 TraesCS5B01G043500 chr5B 99.000 100 1 0 1 100 645066288 645066189 1.680000e-41 180
10 TraesCS5B01G043500 chr5B 99.000 100 0 1 1 100 48475197 48475099 6.050000e-41 178
11 TraesCS5B01G043500 chr3B 96.546 637 21 1 1500 2135 535672216 535671580 0.000000e+00 1053
12 TraesCS5B01G043500 chr3B 96.063 635 24 1 1502 2135 535659970 535659336 0.000000e+00 1033
13 TraesCS5B01G043500 chr3B 92.098 367 29 0 1134 1500 103512276 103511910 3.140000e-143 518
14 TraesCS5B01G043500 chr3B 94.694 245 12 1 101 345 118613360 118613603 1.550000e-101 379
15 TraesCS5B01G043500 chr3B 93.878 245 15 0 101 345 103512519 103512275 9.310000e-99 370
16 TraesCS5B01G043500 chr6B 96.094 640 23 2 1498 2135 718582237 718581598 0.000000e+00 1042
17 TraesCS5B01G043500 chr6B 96.069 636 23 2 1502 2135 718570019 718569384 0.000000e+00 1035
18 TraesCS5B01G043500 chr6B 91.057 369 31 2 1134 1500 223558903 223559271 4.090000e-137 497
19 TraesCS5B01G043500 chr6B 98.039 102 2 0 1 102 460370672 460370571 6.050000e-41 178
20 TraesCS5B01G043500 chr6B 95.455 110 2 3 1 110 344149270 344149164 2.820000e-39 172
21 TraesCS5B01G043500 chr2B 96.063 635 24 1 1502 2135 171367539 171366905 0.000000e+00 1033
22 TraesCS5B01G043500 chr2B 95.906 635 25 1 1502 2135 171379782 171379148 0.000000e+00 1027
23 TraesCS5B01G043500 chr1B 95.775 639 25 2 1499 2135 421359440 421360078 0.000000e+00 1029
24 TraesCS5B01G043500 chr1B 93.733 367 23 0 1134 1500 478007814 478008180 3.100000e-153 551
25 TraesCS5B01G043500 chr1B 91.781 365 29 1 1134 1497 94525643 94526007 6.800000e-140 507
26 TraesCS5B01G043500 chr1B 94.239 243 14 0 103 345 116507091 116507333 2.590000e-99 372
27 TraesCS5B01G043500 chr1B 93.878 245 15 0 101 345 533608223 533608467 9.310000e-99 370
28 TraesCS5B01G043500 chr1B 99.000 100 1 0 1 100 648893382 648893481 1.680000e-41 180
29 TraesCS5B01G043500 chr4B 92.935 368 24 2 1134 1500 242977546 242977180 3.120000e-148 534
30 TraesCS5B01G043500 chr4B 92.120 368 28 1 1134 1500 436496064 436496431 3.140000e-143 518
31 TraesCS5B01G043500 chr4B 95.102 245 12 0 101 345 436495821 436496065 9.240000e-104 387
32 TraesCS5B01G043500 chr4B 94.286 245 14 0 101 345 193831966 193831722 2.000000e-100 375
33 TraesCS5B01G043500 chr4B 93.631 157 10 0 783 939 308694033 308694189 3.540000e-58 235
34 TraesCS5B01G043500 chr7B 90.786 369 30 4 1134 1500 39366307 39366673 6.850000e-135 490
35 TraesCS5B01G043500 chr7B 93.860 114 3 4 1 113 98355646 98355536 3.640000e-38 169
36 TraesCS5B01G043500 chrUn 100.000 196 0 0 938 1133 465624034 465624229 1.560000e-96 363
37 TraesCS5B01G043500 chrUn 94.340 159 9 0 781 939 398477358 398477200 5.890000e-61 244
38 TraesCS5B01G043500 chrUn 93.082 159 11 0 781 939 327842139 327842297 1.270000e-57 233
39 TraesCS5B01G043500 chrUn 95.775 142 3 3 648 788 453774826 453774687 2.130000e-55 226
40 TraesCS5B01G043500 chrUn 96.850 127 4 0 340 466 261572414 261572540 1.660000e-51 213
41 TraesCS5B01G043500 chr6D 99.490 196 1 0 938 1133 431398745 431398550 7.250000e-95 357
42 TraesCS5B01G043500 chr6D 93.711 159 10 0 781 939 45517120 45517278 2.740000e-59 239
43 TraesCS5B01G043500 chr6D 95.070 142 5 2 648 788 431398389 431398249 2.760000e-54 222
44 TraesCS5B01G043500 chr2D 99.490 196 1 0 938 1133 628284392 628284197 7.250000e-95 357
45 TraesCS5B01G043500 chr2D 99.490 196 1 0 938 1133 628287646 628287451 7.250000e-95 357
46 TraesCS5B01G043500 chr2D 98.421 190 3 0 462 651 33932433 33932622 3.390000e-88 335
47 TraesCS5B01G043500 chr2D 98.421 190 3 0 462 651 630264426 630264237 3.390000e-88 335
48 TraesCS5B01G043500 chr2D 95.775 142 4 2 648 788 28725461 28725321 5.930000e-56 228
49 TraesCS5B01G043500 chr2D 95.775 142 4 2 648 788 628284036 628283896 5.930000e-56 228
50 TraesCS5B01G043500 chr2D 95.070 142 6 1 648 788 334224279 334224138 2.760000e-54 222
51 TraesCS5B01G043500 chr2D 97.581 124 3 0 343 466 245531762 245531639 1.660000e-51 213
52 TraesCS5B01G043500 chr2D 89.147 129 10 4 1 128 623922032 623921907 7.890000e-35 158
53 TraesCS5B01G043500 chr1D 99.490 196 1 0 938 1133 254488416 254488221 7.250000e-95 357
54 TraesCS5B01G043500 chr1D 99.490 196 1 0 938 1133 394176571 394176376 7.250000e-95 357
55 TraesCS5B01G043500 chr1D 98.947 190 2 0 462 651 180365309 180365498 7.300000e-90 340
56 TraesCS5B01G043500 chr1D 98.421 190 2 1 462 651 254473960 254473772 1.220000e-87 333
57 TraesCS5B01G043500 chr1D 93.711 159 10 0 781 939 254400561 254400403 2.740000e-59 239
58 TraesCS5B01G043500 chr1D 95.070 142 4 3 648 788 254488060 254487921 9.920000e-54 220
59 TraesCS5B01G043500 chr1D 96.774 124 4 0 343 466 254402802 254402679 7.720000e-50 207
60 TraesCS5B01G043500 chr5D 98.980 196 2 0 938 1133 329132995 329133190 3.370000e-93 351
61 TraesCS5B01G043500 chr5D 98.429 191 2 1 462 651 503328055 503327865 3.390000e-88 335
62 TraesCS5B01G043500 chr5D 96.954 197 5 1 455 651 432307823 432308018 1.580000e-86 329
63 TraesCS5B01G043500 chr5D 93.711 159 10 0 781 939 6186489 6186647 2.740000e-59 239
64 TraesCS5B01G043500 chr5D 93.711 159 10 0 781 939 503280676 503280518 2.740000e-59 239
65 TraesCS5B01G043500 chr5D 96.850 127 4 0 340 466 6184243 6184369 1.660000e-51 213
66 TraesCS5B01G043500 chr5D 96.774 124 4 0 343 466 167068637 167068514 7.720000e-50 207
67 TraesCS5B01G043500 chr5D 96.774 124 4 0 343 466 503283994 503283871 7.720000e-50 207
68 TraesCS5B01G043500 chr1A 98.980 196 2 0 938 1133 554466314 554466509 3.370000e-93 351
69 TraesCS5B01G043500 chr1A 98.980 196 1 1 938 1133 256027445 256027639 1.210000e-92 350
70 TraesCS5B01G043500 chr3D 98.947 190 2 0 462 651 24163211 24163022 7.300000e-90 340
71 TraesCS5B01G043500 chr3D 96.774 124 4 0 343 466 598875498 598875375 7.720000e-50 207
72 TraesCS5B01G043500 chr3A 98.421 190 3 0 462 651 524025735 524025546 3.390000e-88 335
73 TraesCS5B01G043500 chr2A 97.884 189 4 0 463 651 419793322 419793134 5.680000e-86 327
74 TraesCS5B01G043500 chr2A 94.340 159 9 0 781 939 335836197 335836355 5.890000e-61 244
75 TraesCS5B01G043500 chr2A 95.775 142 5 1 648 788 276442720 276442861 5.930000e-56 228
76 TraesCS5B01G043500 chr2A 96.063 127 5 0 340 466 335833949 335834075 7.720000e-50 207
77 TraesCS5B01G043500 chr7D 94.340 159 9 0 781 939 231594273 231594115 5.890000e-61 244
78 TraesCS5B01G043500 chr5A 95.775 142 4 2 648 788 684323967 684323827 5.930000e-56 228
79 TraesCS5B01G043500 chr5A 96.063 127 5 0 340 466 607203383 607203509 7.720000e-50 207
80 TraesCS5B01G043500 chr6A 95.775 142 3 3 648 788 192821998 192821859 2.130000e-55 226
81 TraesCS5B01G043500 chr4A 98.039 102 2 0 1 102 677323243 677323142 6.050000e-41 178


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 TraesCS5B01G043500 chr5B 48446494 48448628 2134 True 3943.0 3943 100.000000 1 2135 1 chr5B.!!$R2 2134
1 TraesCS5B01G043500 chr5B 48440301 48440935 634 False 1055.0 1055 96.693000 1502 2135 1 chr5B.!!$F1 633
2 TraesCS5B01G043500 chr5B 48433541 48434175 634 True 1038.0 1038 96.220000 1502 2135 1 chr5B.!!$R1 633
3 TraesCS5B01G043500 chr5B 648195464 648196074 610 True 446.5 512 93.271000 101 1500 2 chr5B.!!$R9 1399
4 TraesCS5B01G043500 chr3B 535671580 535672216 636 True 1053.0 1053 96.546000 1500 2135 1 chr3B.!!$R2 635
5 TraesCS5B01G043500 chr3B 535659336 535659970 634 True 1033.0 1033 96.063000 1502 2135 1 chr3B.!!$R1 633
6 TraesCS5B01G043500 chr3B 103511910 103512519 609 True 444.0 518 92.988000 101 1500 2 chr3B.!!$R3 1399
7 TraesCS5B01G043500 chr6B 718581598 718582237 639 True 1042.0 1042 96.094000 1498 2135 1 chr6B.!!$R4 637
8 TraesCS5B01G043500 chr6B 718569384 718570019 635 True 1035.0 1035 96.069000 1502 2135 1 chr6B.!!$R3 633
9 TraesCS5B01G043500 chr2B 171366905 171367539 634 True 1033.0 1033 96.063000 1502 2135 1 chr2B.!!$R1 633
10 TraesCS5B01G043500 chr2B 171379148 171379782 634 True 1027.0 1027 95.906000 1502 2135 1 chr2B.!!$R2 633
11 TraesCS5B01G043500 chr1B 421359440 421360078 638 False 1029.0 1029 95.775000 1499 2135 1 chr1B.!!$F3 636
12 TraesCS5B01G043500 chr4B 436495821 436496431 610 False 452.5 518 93.611000 101 1500 2 chr4B.!!$F2 1399
13 TraesCS5B01G043500 chr2D 628283896 628287646 3750 True 314.0 357 98.251667 648 1133 3 chr2D.!!$R6 485
14 TraesCS5B01G043500 chr1D 254400403 254402802 2399 True 223.0 239 95.242500 343 939 2 chr1D.!!$R3 596
15 TraesCS5B01G043500 chr5D 6184243 6186647 2404 False 226.0 239 95.280500 340 939 2 chr5D.!!$F3 599
16 TraesCS5B01G043500 chr5D 503280518 503283994 3476 True 223.0 239 95.242500 343 939 2 chr5D.!!$R3 596
17 TraesCS5B01G043500 chr2A 335833949 335836355 2406 False 225.5 244 95.201500 340 939 2 chr2A.!!$F2 599

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
902 5748 0.103208 ACTTCTGCGGTGATCGGATC 59.897 55.0 11.07 11.07 38.83 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 6800 0.250901 GTTGGTGGATGTGCTGGAGT 60.251 55.0 0.0 0.0 0.0 3.85 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 4.875561 GGTATGAAGATACAGTCCCCTC 57.124 50.000 0.00 0.00 36.85 4.30
22 23 4.484912 GGTATGAAGATACAGTCCCCTCT 58.515 47.826 0.00 0.00 36.85 3.69
24 25 4.551215 ATGAAGATACAGTCCCCTCTCT 57.449 45.455 0.00 0.00 0.00 3.10
26 27 3.529734 TGAAGATACAGTCCCCTCTCTCT 59.470 47.826 0.00 0.00 0.00 3.10
29 30 3.270960 AGATACAGTCCCCTCTCTCTTGT 59.729 47.826 0.00 0.00 0.00 3.16
30 31 2.407340 ACAGTCCCCTCTCTCTTGTT 57.593 50.000 0.00 0.00 0.00 2.83
31 32 1.974236 ACAGTCCCCTCTCTCTTGTTG 59.026 52.381 0.00 0.00 0.00 3.33
32 33 0.980423 AGTCCCCTCTCTCTTGTTGC 59.020 55.000 0.00 0.00 0.00 4.17
34 35 2.180276 GTCCCCTCTCTCTTGTTGCTA 58.820 52.381 0.00 0.00 0.00 3.49
35 36 2.167487 GTCCCCTCTCTCTTGTTGCTAG 59.833 54.545 0.00 0.00 0.00 3.42
36 37 2.043115 TCCCCTCTCTCTTGTTGCTAGA 59.957 50.000 0.00 0.00 0.00 2.43
37 38 2.834549 CCCCTCTCTCTTGTTGCTAGAA 59.165 50.000 0.00 0.00 0.00 2.10
38 39 3.454082 CCCCTCTCTCTTGTTGCTAGAAT 59.546 47.826 0.00 0.00 0.00 2.40
39 40 4.442753 CCCCTCTCTCTTGTTGCTAGAATC 60.443 50.000 0.00 0.00 0.00 2.52
40 41 4.405358 CCCTCTCTCTTGTTGCTAGAATCT 59.595 45.833 0.00 0.00 0.00 2.40
41 42 5.451798 CCCTCTCTCTTGTTGCTAGAATCTC 60.452 48.000 0.00 0.00 0.00 2.75
43 44 5.019470 TCTCTCTTGTTGCTAGAATCTCCA 58.981 41.667 0.00 0.00 0.00 3.86
44 45 5.660417 TCTCTCTTGTTGCTAGAATCTCCAT 59.340 40.000 0.00 0.00 0.00 3.41
45 46 6.836007 TCTCTCTTGTTGCTAGAATCTCCATA 59.164 38.462 0.00 0.00 0.00 2.74
46 47 7.014134 TCTCTCTTGTTGCTAGAATCTCCATAG 59.986 40.741 0.00 0.00 0.00 2.23
61 62 7.571071 ATCTCCATAGATTGATCTTGGTGAT 57.429 36.000 19.83 19.83 39.55 3.06
62 63 6.766429 TCTCCATAGATTGATCTTGGTGATG 58.234 40.000 15.48 7.45 38.32 3.07
63 64 5.311265 TCCATAGATTGATCTTGGTGATGC 58.689 41.667 15.48 0.00 38.32 3.91
64 65 4.153655 CCATAGATTGATCTTGGTGATGCG 59.846 45.833 0.00 0.00 38.32 4.73
65 66 3.272574 AGATTGATCTTGGTGATGCGT 57.727 42.857 0.00 0.00 35.14 5.24
66 67 4.406648 AGATTGATCTTGGTGATGCGTA 57.593 40.909 0.00 0.00 35.14 4.42
68 69 3.885724 TTGATCTTGGTGATGCGTAGA 57.114 42.857 0.00 0.00 35.14 2.59
70 71 4.200838 TGATCTTGGTGATGCGTAGAAA 57.799 40.909 0.00 0.00 35.14 2.52
71 72 4.574892 TGATCTTGGTGATGCGTAGAAAA 58.425 39.130 0.00 0.00 35.14 2.29
72 73 5.185454 TGATCTTGGTGATGCGTAGAAAAT 58.815 37.500 0.00 0.00 35.14 1.82
73 74 5.647658 TGATCTTGGTGATGCGTAGAAAATT 59.352 36.000 0.00 0.00 35.14 1.82
74 75 5.957842 TCTTGGTGATGCGTAGAAAATTT 57.042 34.783 0.00 0.00 0.00 1.82
75 76 6.325919 TCTTGGTGATGCGTAGAAAATTTT 57.674 33.333 2.28 2.28 0.00 1.82
76 77 6.148948 TCTTGGTGATGCGTAGAAAATTTTG 58.851 36.000 8.47 0.00 0.00 2.44
78 79 6.078202 TGGTGATGCGTAGAAAATTTTGAA 57.922 33.333 8.47 0.00 0.00 2.69
79 80 6.686630 TGGTGATGCGTAGAAAATTTTGAAT 58.313 32.000 8.47 0.00 0.00 2.57
80 81 7.151308 TGGTGATGCGTAGAAAATTTTGAATT 58.849 30.769 8.47 0.00 0.00 2.17
81 82 7.655328 TGGTGATGCGTAGAAAATTTTGAATTT 59.345 29.630 8.47 0.00 0.00 1.82
82 83 8.162245 GGTGATGCGTAGAAAATTTTGAATTTC 58.838 33.333 8.47 0.00 36.11 2.17
83 84 8.915654 GTGATGCGTAGAAAATTTTGAATTTCT 58.084 29.630 8.47 0.48 45.29 2.52
84 85 8.914654 TGATGCGTAGAAAATTTTGAATTTCTG 58.085 29.630 8.47 0.00 43.67 3.02
85 86 7.104326 TGCGTAGAAAATTTTGAATTTCTGC 57.896 32.000 8.47 8.21 43.67 4.26
86 87 6.922957 TGCGTAGAAAATTTTGAATTTCTGCT 59.077 30.769 8.47 0.00 43.67 4.24
87 88 8.079203 TGCGTAGAAAATTTTGAATTTCTGCTA 58.921 29.630 8.47 0.00 43.67 3.49
89 90 8.567221 CGTAGAAAATTTTGAATTTCTGCTACG 58.433 33.333 22.91 22.91 43.67 3.51
90 91 9.394477 GTAGAAAATTTTGAATTTCTGCTACGT 57.606 29.630 8.47 0.00 43.67 3.57
91 92 8.871686 AGAAAATTTTGAATTTCTGCTACGTT 57.128 26.923 8.47 0.00 42.62 3.99
92 93 8.968242 AGAAAATTTTGAATTTCTGCTACGTTC 58.032 29.630 8.47 0.00 42.62 3.95
93 94 8.871686 AAAATTTTGAATTTCTGCTACGTTCT 57.128 26.923 1.75 0.00 0.00 3.01
95 96 5.607119 TTTGAATTTCTGCTACGTTCTCC 57.393 39.130 0.00 0.00 0.00 3.71
97 98 4.637276 TGAATTTCTGCTACGTTCTCCAA 58.363 39.130 0.00 0.00 0.00 3.53
98 99 4.451096 TGAATTTCTGCTACGTTCTCCAAC 59.549 41.667 0.00 0.00 0.00 3.77
99 100 3.462483 TTTCTGCTACGTTCTCCAACA 57.538 42.857 0.00 0.00 32.14 3.33
133 134 3.056891 GGGGAAGATAGCATCTCTTCTCG 60.057 52.174 17.22 0.00 46.70 4.04
143 144 3.064545 GCATCTCTTCTCGGTTGAATTGG 59.935 47.826 0.00 0.00 0.00 3.16
209 210 7.639113 TCTGCCGGTTCAGATAAAAATATTT 57.361 32.000 7.61 0.00 38.11 1.40
211 212 7.556275 TCTGCCGGTTCAGATAAAAATATTTCT 59.444 33.333 7.61 0.00 38.11 2.52
243 244 0.979665 CACTGGGCTCCTCTTGAAGA 59.020 55.000 0.00 0.00 0.00 2.87
368 369 5.862845 TGCTTCTTCTCTCTGATTCAAGTT 58.137 37.500 0.00 0.00 0.00 2.66
581 803 9.661187 GAGTTCTGTGATTAATCATTTGCTATG 57.339 33.333 20.65 6.16 39.30 2.23
582 804 9.182214 AGTTCTGTGATTAATCATTTGCTATGT 57.818 29.630 20.65 0.00 39.30 2.29
585 807 8.833493 TCTGTGATTAATCATTTGCTATGTCAG 58.167 33.333 20.65 16.98 39.30 3.51
586 808 8.510243 TGTGATTAATCATTTGCTATGTCAGT 57.490 30.769 20.65 0.00 39.30 3.41
595 817 9.794685 ATCATTTGCTATGTCAGTATCTATACG 57.205 33.333 0.00 0.00 38.28 3.06
597 819 8.854312 CATTTGCTATGTCAGTATCTATACGTG 58.146 37.037 0.00 0.00 38.28 4.49
600 822 7.937649 TGCTATGTCAGTATCTATACGTGTTT 58.062 34.615 0.00 0.00 38.28 2.83
601 823 9.059260 TGCTATGTCAGTATCTATACGTGTTTA 57.941 33.333 0.00 0.00 38.28 2.01
811 5498 3.511934 CGCTGCCCCTCTAGTAGATATTT 59.488 47.826 0.00 0.00 0.00 1.40
813 5500 5.185249 CGCTGCCCCTCTAGTAGATATTTAA 59.815 44.000 0.00 0.00 0.00 1.52
902 5748 0.103208 ACTTCTGCGGTGATCGGATC 59.897 55.000 11.07 11.07 38.83 3.36
1133 6109 6.334378 TGGTTCATATTCTGGATTGGGTTA 57.666 37.500 0.00 0.00 0.00 2.85
1147 6123 2.638325 TGGGTTAACTTGGATCCAGGA 58.362 47.619 29.15 8.48 0.00 3.86
1222 6198 3.365364 GCGACTGAGGGTTTTTCTCATTG 60.365 47.826 0.00 0.00 40.07 2.82
1228 6204 4.086457 GAGGGTTTTTCTCATTGGGCTTA 58.914 43.478 0.00 0.00 0.00 3.09
1241 6217 3.490890 GCTTAGGAGCGTGCCAAG 58.509 61.111 0.00 2.34 39.48 3.61
1352 6328 2.279582 AACTGTCTTCGGCATCGTAG 57.720 50.000 0.00 0.00 37.69 3.51
1412 6388 5.827797 TGATTTGCTAAGCCGGAGATAAAAT 59.172 36.000 5.05 3.23 0.00 1.82
1472 6449 6.925211 TGACATATGACTAGCTATAACTGGC 58.075 40.000 10.38 0.00 0.00 4.85
1612 6589 3.391382 GGTCCTCCGTGGTCCCTG 61.391 72.222 0.00 0.00 37.96 4.45
1822 6800 1.550130 GCTACCACCCTGTACCTGCA 61.550 60.000 0.00 0.00 0.00 4.41
1998 6976 1.852067 GCGACACAGACGGGCATTTT 61.852 55.000 0.00 0.00 0.00 1.82
2116 7094 2.856360 ACCTGTCGGTGACCCCTA 59.144 61.111 0.00 0.00 43.51 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.390387 AGAGAGGGGACTGTATCTTCATAC 58.610 45.833 0.00 0.00 44.43 2.39
2 3 5.636123 GAGAGAGGGGACTGTATCTTCATA 58.364 45.833 0.00 0.00 44.43 2.15
3 4 4.479158 GAGAGAGGGGACTGTATCTTCAT 58.521 47.826 0.00 0.00 44.43 2.57
4 5 3.904717 GAGAGAGGGGACTGTATCTTCA 58.095 50.000 0.00 0.00 44.43 3.02
8 9 3.637769 ACAAGAGAGAGGGGACTGTATC 58.362 50.000 0.00 0.00 44.43 2.24
9 10 3.767309 ACAAGAGAGAGGGGACTGTAT 57.233 47.619 0.00 0.00 44.43 2.29
10 11 3.165875 CAACAAGAGAGAGGGGACTGTA 58.834 50.000 0.00 0.00 44.43 2.74
11 12 1.974236 CAACAAGAGAGAGGGGACTGT 59.026 52.381 0.00 0.00 44.43 3.55
14 15 0.980423 AGCAACAAGAGAGAGGGGAC 59.020 55.000 0.00 0.00 0.00 4.46
16 17 2.461695 TCTAGCAACAAGAGAGAGGGG 58.538 52.381 0.00 0.00 0.00 4.79
17 18 4.405358 AGATTCTAGCAACAAGAGAGAGGG 59.595 45.833 0.00 0.00 0.00 4.30
18 19 5.451798 GGAGATTCTAGCAACAAGAGAGAGG 60.452 48.000 0.00 0.00 0.00 3.69
19 20 5.126869 TGGAGATTCTAGCAACAAGAGAGAG 59.873 44.000 0.00 0.00 0.00 3.20
20 21 5.019470 TGGAGATTCTAGCAACAAGAGAGA 58.981 41.667 0.00 0.00 0.00 3.10
21 22 5.336150 TGGAGATTCTAGCAACAAGAGAG 57.664 43.478 0.00 0.00 0.00 3.20
22 23 5.946942 ATGGAGATTCTAGCAACAAGAGA 57.053 39.130 0.00 0.00 0.00 3.10
24 25 7.609097 ATCTATGGAGATTCTAGCAACAAGA 57.391 36.000 0.00 0.00 39.56 3.02
36 37 7.883833 CATCACCAAGATCAATCTATGGAGATT 59.116 37.037 19.21 0.00 42.96 2.40
37 38 7.395617 CATCACCAAGATCAATCTATGGAGAT 58.604 38.462 19.34 18.46 40.83 2.75
38 39 6.743490 GCATCACCAAGATCAATCTATGGAGA 60.743 42.308 19.34 17.57 38.10 3.71
39 40 5.411977 GCATCACCAAGATCAATCTATGGAG 59.588 44.000 19.34 14.57 37.92 3.86
40 41 5.311265 GCATCACCAAGATCAATCTATGGA 58.689 41.667 19.34 6.96 37.92 3.41
41 42 4.153655 CGCATCACCAAGATCAATCTATGG 59.846 45.833 14.46 14.46 39.18 2.74
43 44 4.965814 ACGCATCACCAAGATCAATCTAT 58.034 39.130 0.00 0.00 35.76 1.98
44 45 4.406648 ACGCATCACCAAGATCAATCTA 57.593 40.909 0.00 0.00 35.76 1.98
45 46 3.272574 ACGCATCACCAAGATCAATCT 57.727 42.857 0.00 0.00 39.22 2.40
46 47 4.371786 TCTACGCATCACCAAGATCAATC 58.628 43.478 0.00 0.00 33.72 2.67
49 50 3.885724 TTCTACGCATCACCAAGATCA 57.114 42.857 0.00 0.00 33.72 2.92
50 51 5.741388 ATTTTCTACGCATCACCAAGATC 57.259 39.130 0.00 0.00 33.72 2.75
51 52 6.515272 AAATTTTCTACGCATCACCAAGAT 57.485 33.333 0.00 0.00 37.48 2.40
52 53 5.957842 AAATTTTCTACGCATCACCAAGA 57.042 34.783 0.00 0.00 0.00 3.02
53 54 6.148948 TCAAAATTTTCTACGCATCACCAAG 58.851 36.000 0.00 0.00 0.00 3.61
54 55 6.078202 TCAAAATTTTCTACGCATCACCAA 57.922 33.333 0.00 0.00 0.00 3.67
56 57 7.581011 AATTCAAAATTTTCTACGCATCACC 57.419 32.000 0.00 0.00 0.00 4.02
58 59 8.914654 CAGAAATTCAAAATTTTCTACGCATCA 58.085 29.630 0.00 0.00 39.53 3.07
59 60 7.894753 GCAGAAATTCAAAATTTTCTACGCATC 59.105 33.333 0.00 0.00 39.53 3.91
61 62 6.922957 AGCAGAAATTCAAAATTTTCTACGCA 59.077 30.769 0.00 0.00 39.53 5.24
62 63 7.338440 AGCAGAAATTCAAAATTTTCTACGC 57.662 32.000 0.00 0.00 39.53 4.42
63 64 8.567221 CGTAGCAGAAATTCAAAATTTTCTACG 58.433 33.333 19.51 19.51 39.53 3.51
64 65 9.394477 ACGTAGCAGAAATTCAAAATTTTCTAC 57.606 29.630 0.00 5.68 39.53 2.59
65 66 9.959749 AACGTAGCAGAAATTCAAAATTTTCTA 57.040 25.926 0.00 0.00 39.53 2.10
66 67 8.871686 AACGTAGCAGAAATTCAAAATTTTCT 57.128 26.923 0.00 0.00 41.61 2.52
68 69 8.871686 AGAACGTAGCAGAAATTCAAAATTTT 57.128 26.923 0.00 0.00 0.00 1.82
70 71 7.084486 GGAGAACGTAGCAGAAATTCAAAATT 58.916 34.615 0.00 0.00 0.00 1.82
71 72 6.206634 TGGAGAACGTAGCAGAAATTCAAAAT 59.793 34.615 0.00 0.00 0.00 1.82
72 73 5.529430 TGGAGAACGTAGCAGAAATTCAAAA 59.471 36.000 0.00 0.00 0.00 2.44
73 74 5.060506 TGGAGAACGTAGCAGAAATTCAAA 58.939 37.500 0.00 0.00 0.00 2.69
74 75 4.637276 TGGAGAACGTAGCAGAAATTCAA 58.363 39.130 0.00 0.00 0.00 2.69
75 76 4.265904 TGGAGAACGTAGCAGAAATTCA 57.734 40.909 0.00 0.00 0.00 2.57
76 77 4.451096 TGTTGGAGAACGTAGCAGAAATTC 59.549 41.667 0.00 0.00 34.49 2.17
78 79 4.002906 TGTTGGAGAACGTAGCAGAAAT 57.997 40.909 0.00 0.00 34.49 2.17
79 80 3.462483 TGTTGGAGAACGTAGCAGAAA 57.538 42.857 0.00 0.00 34.49 2.52
80 81 3.390135 CTTGTTGGAGAACGTAGCAGAA 58.610 45.455 0.00 0.00 34.49 3.02
81 82 2.288825 CCTTGTTGGAGAACGTAGCAGA 60.289 50.000 0.00 0.00 38.35 4.26
82 83 2.069273 CCTTGTTGGAGAACGTAGCAG 58.931 52.381 0.00 0.00 38.35 4.24
83 84 1.414919 ACCTTGTTGGAGAACGTAGCA 59.585 47.619 0.00 0.00 39.71 3.49
84 85 1.798813 CACCTTGTTGGAGAACGTAGC 59.201 52.381 0.00 0.00 39.71 3.58
85 86 3.318017 CTCACCTTGTTGGAGAACGTAG 58.682 50.000 0.00 0.00 39.71 3.51
86 87 2.547218 GCTCACCTTGTTGGAGAACGTA 60.547 50.000 0.00 0.00 39.71 3.57
87 88 1.810412 GCTCACCTTGTTGGAGAACGT 60.810 52.381 0.00 0.00 39.71 3.99
89 90 1.967319 TGCTCACCTTGTTGGAGAAC 58.033 50.000 0.00 0.00 39.71 3.01
90 91 2.957402 ATGCTCACCTTGTTGGAGAA 57.043 45.000 0.00 0.00 39.71 2.87
91 92 2.237143 CCTATGCTCACCTTGTTGGAGA 59.763 50.000 0.00 0.00 39.71 3.71
92 93 2.636830 CCTATGCTCACCTTGTTGGAG 58.363 52.381 0.00 0.00 39.71 3.86
93 94 1.281867 CCCTATGCTCACCTTGTTGGA 59.718 52.381 0.00 0.00 39.71 3.53
95 96 1.281867 TCCCCTATGCTCACCTTGTTG 59.718 52.381 0.00 0.00 0.00 3.33
97 98 1.561542 CTTCCCCTATGCTCACCTTGT 59.438 52.381 0.00 0.00 0.00 3.16
98 99 1.839994 TCTTCCCCTATGCTCACCTTG 59.160 52.381 0.00 0.00 0.00 3.61
99 100 2.270434 TCTTCCCCTATGCTCACCTT 57.730 50.000 0.00 0.00 0.00 3.50
133 134 2.348104 GCGGGGTCCCAATTCAACC 61.348 63.158 10.98 0.00 35.37 3.77
143 144 0.392595 CTTAGAACTTGGCGGGGTCC 60.393 60.000 0.00 0.00 0.00 4.46
211 212 2.092429 AGCCCAGTGTTGAACTCTTCAA 60.092 45.455 0.00 0.00 46.68 2.69
552 774 9.399797 AGCAAATGATTAATCACAGAACTCATA 57.600 29.630 20.19 0.00 40.03 2.15
553 775 8.289939 AGCAAATGATTAATCACAGAACTCAT 57.710 30.769 20.19 0.00 40.03 2.90
554 776 7.692460 AGCAAATGATTAATCACAGAACTCA 57.308 32.000 20.19 0.00 40.03 3.41
555 777 9.661187 CATAGCAAATGATTAATCACAGAACTC 57.339 33.333 20.19 6.54 40.03 3.01
557 779 9.443283 GACATAGCAAATGATTAATCACAGAAC 57.557 33.333 20.19 9.27 40.03 3.01
559 781 8.735692 TGACATAGCAAATGATTAATCACAGA 57.264 30.769 20.19 3.92 40.03 3.41
560 782 8.618677 ACTGACATAGCAAATGATTAATCACAG 58.381 33.333 20.19 18.35 40.03 3.66
569 791 9.794685 CGTATAGATACTGACATAGCAAATGAT 57.205 33.333 6.11 0.00 0.00 2.45
572 794 8.577296 ACACGTATAGATACTGACATAGCAAAT 58.423 33.333 0.00 0.00 0.00 2.32
573 795 7.937649 ACACGTATAGATACTGACATAGCAAA 58.062 34.615 0.00 0.00 0.00 3.68
607 829 9.287818 AGAAAGAGGGGTTTTATACCTTATACA 57.712 33.333 0.00 0.00 46.86 2.29
608 830 9.775854 GAGAAAGAGGGGTTTTATACCTTATAC 57.224 37.037 0.00 0.00 46.86 1.47
609 831 9.739737 AGAGAAAGAGGGGTTTTATACCTTATA 57.260 33.333 0.00 0.00 46.86 0.98
610 832 8.640033 AGAGAAAGAGGGGTTTTATACCTTAT 57.360 34.615 0.00 0.00 46.86 1.73
613 835 8.640033 ATTAGAGAAAGAGGGGTTTTATACCT 57.360 34.615 0.00 0.00 46.86 3.08
641 863 8.046107 CCTTGAGTGATCTCCTTTTCTAATTCT 58.954 37.037 0.00 0.00 39.75 2.40
643 865 7.922382 TCCTTGAGTGATCTCCTTTTCTAATT 58.078 34.615 0.00 0.00 39.75 1.40
645 867 6.935240 TCCTTGAGTGATCTCCTTTTCTAA 57.065 37.500 0.00 0.00 39.75 2.10
646 868 6.098982 GGATCCTTGAGTGATCTCCTTTTCTA 59.901 42.308 3.84 0.00 38.89 2.10
647 869 5.104569 GGATCCTTGAGTGATCTCCTTTTCT 60.105 44.000 3.84 0.00 38.89 2.52
648 870 5.122519 GGATCCTTGAGTGATCTCCTTTTC 58.877 45.833 3.84 0.00 38.89 2.29
649 871 4.537688 TGGATCCTTGAGTGATCTCCTTTT 59.462 41.667 14.23 0.00 38.89 2.27
650 872 4.107072 TGGATCCTTGAGTGATCTCCTTT 58.893 43.478 14.23 0.00 38.89 3.11
651 873 3.729108 TGGATCCTTGAGTGATCTCCTT 58.271 45.455 14.23 0.00 38.89 3.36
652 874 3.411454 TGGATCCTTGAGTGATCTCCT 57.589 47.619 14.23 0.00 38.89 3.69
653 875 4.703379 ATTGGATCCTTGAGTGATCTCC 57.297 45.455 14.23 0.00 38.89 3.71
811 5498 1.108776 ACAGGCTCGCGAATACCTTA 58.891 50.000 19.26 0.00 0.00 2.69
813 5500 0.249398 AAACAGGCTCGCGAATACCT 59.751 50.000 16.85 16.85 0.00 3.08
868 5714 4.021894 CGCAGAAGTAGGGATAATAGCACT 60.022 45.833 0.00 0.00 0.00 4.40
1071 6047 3.848272 AAACCAATCACAGCAATACCG 57.152 42.857 0.00 0.00 0.00 4.02
1133 6109 1.912043 CTCACCTCCTGGATCCAAGTT 59.088 52.381 17.00 0.00 37.04 2.66
1147 6123 2.529389 AACCGGGGCTTCTCACCT 60.529 61.111 6.32 0.00 0.00 4.00
1210 6186 4.380973 GCTCCTAAGCCCAATGAGAAAAAC 60.381 45.833 0.00 0.00 43.10 2.43
1222 6198 3.622060 TTGGCACGCTCCTAAGCCC 62.622 63.158 0.00 0.00 46.34 5.19
1228 6204 4.711949 CTGCCTTGGCACGCTCCT 62.712 66.667 10.65 0.00 0.00 3.69
1235 6211 2.496871 CAAAATATGTCCTGCCTTGGCA 59.503 45.455 14.10 14.10 0.00 4.92
1241 6217 2.951642 TGCTAGCAAAATATGTCCTGCC 59.048 45.455 16.84 0.00 35.33 4.85
1352 6328 6.582636 CCATATTTCTTTTAGGCTTTTCCCC 58.417 40.000 0.00 0.00 34.51 4.81
1412 6388 4.617253 AGCCGCCAATATATACTGTGAA 57.383 40.909 0.00 0.00 0.00 3.18
1472 6449 2.202690 TCACGGCGGCTTACATCG 60.203 61.111 13.24 0.00 0.00 3.84
1486 6463 3.367932 CACCGACACATCAGTATTGTCAC 59.632 47.826 0.00 0.00 39.77 3.67
1612 6589 3.319122 ACTTTGTTCTTGAATGGCTCCAC 59.681 43.478 0.00 0.00 0.00 4.02
1688 6666 2.163211 GCAAGTTCCTTGAGATGCCTTC 59.837 50.000 8.11 0.00 43.42 3.46
1822 6800 0.250901 GTTGGTGGATGTGCTGGAGT 60.251 55.000 0.00 0.00 0.00 3.85
1998 6976 1.306296 GGCAGGGGACAAAGGCATA 59.694 57.895 0.00 0.00 0.00 3.14
2058 7036 1.256812 AATGGAAAAGGAGTTGCGGG 58.743 50.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.