Multiple sequence alignment - TraesCS2D01G524000

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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 TraesCS2D01G524000 chr2D 100.000 3219 0 0 1 3219 612533982 612537200 0.000000e+00 5945.0
1 TraesCS2D01G524000 chr2D 93.066 649 44 1 1302 1949 627914094 627913446 0.000000e+00 948.0
2 TraesCS2D01G524000 chr2D 87.317 615 56 10 665 1268 627914884 627914281 0.000000e+00 684.0
3 TraesCS2D01G524000 chr4A 95.905 2979 106 11 93 3065 563267623 563270591 0.000000e+00 4811.0
4 TraesCS2D01G524000 chr4A 95.298 1361 58 4 93 1452 563298598 563299953 0.000000e+00 2154.0
5 TraesCS2D01G524000 chr4A 97.901 905 19 0 1447 2351 563304227 563305131 0.000000e+00 1567.0
6 TraesCS2D01G524000 chr4A 93.962 679 28 3 2400 3065 563305417 563306095 0.000000e+00 1014.0
7 TraesCS2D01G524000 chr2A 91.859 651 50 3 1301 1949 758388920 758388271 0.000000e+00 905.0
8 TraesCS2D01G524000 chr2A 88.060 603 57 7 665 1254 758389715 758389115 0.000000e+00 701.0
9 TraesCS2D01G524000 chr2A 87.268 377 35 6 665 1030 758391182 758390808 4.970000e-113 418.0
10 TraesCS2D01G524000 chr2B 93.128 553 35 2 1400 1949 748367244 748367796 0.000000e+00 808.0
11 TraesCS2D01G524000 chr2B 92.252 555 37 3 1400 1949 770673490 770672937 0.000000e+00 782.0
12 TraesCS2D01G524000 chr2B 92.196 551 42 1 1400 1949 748216273 748216823 0.000000e+00 778.0
13 TraesCS2D01G524000 chr2B 89.525 611 56 7 665 1268 770674341 770673732 0.000000e+00 767.0
14 TraesCS2D01G524000 chr2B 88.760 605 55 6 673 1265 748366398 748367001 0.000000e+00 728.0
15 TraesCS2D01G524000 chr2B 86.964 606 65 7 673 1265 748215425 748216029 0.000000e+00 669.0
16 TraesCS2D01G524000 chr2B 91.667 72 5 1 1275 1346 770673576 770673646 7.350000e-17 99.0
17 TraesCS2D01G524000 chr2B 96.552 58 2 0 583 640 461526664 461526721 2.640000e-16 97.1
18 TraesCS2D01G524000 chr2B 95.082 61 2 1 583 642 461527092 461527152 9.510000e-16 95.3
19 TraesCS2D01G524000 chr2B 93.443 61 3 1 583 642 461538184 461538244 4.420000e-14 89.8
20 TraesCS2D01G524000 chr2B 91.379 58 3 2 1294 1351 748367189 748367244 9.570000e-11 78.7
21 TraesCS2D01G524000 chr3A 82.426 404 62 9 2615 3013 714337352 714337751 8.550000e-91 344.0
22 TraesCS2D01G524000 chr7D 84.181 354 50 6 2623 2971 339792785 339793137 3.980000e-89 339.0
23 TraesCS2D01G524000 chr7D 87.435 191 17 3 3029 3219 386851205 386851022 2.520000e-51 213.0
24 TraesCS2D01G524000 chr7D 92.241 116 9 0 3104 3219 339793288 339793403 7.140000e-37 165.0
25 TraesCS2D01G524000 chr7D 89.431 123 11 1 3096 3216 320156201 320156323 1.550000e-33 154.0
26 TraesCS2D01G524000 chr7D 94.737 57 3 0 586 642 629436002 629435946 4.420000e-14 89.8
27 TraesCS2D01G524000 chr1D 82.178 404 61 9 2619 3014 482904829 482905229 1.430000e-88 337.0
28 TraesCS2D01G524000 chr1D 82.323 396 61 8 2623 3013 292427806 292427415 5.150000e-88 335.0
29 TraesCS2D01G524000 chr1D 81.127 408 73 1 2623 3026 154056996 154057403 1.110000e-84 324.0
30 TraesCS2D01G524000 chr1D 91.304 115 10 0 3105 3219 251034471 251034357 1.200000e-34 158.0
31 TraesCS2D01G524000 chr1D 98.000 50 1 0 591 640 397389561 397389610 1.590000e-13 87.9
32 TraesCS2D01G524000 chr4D 81.934 393 64 4 2631 3018 21868081 21867691 3.100000e-85 326.0
33 TraesCS2D01G524000 chr4D 91.453 117 9 1 3104 3219 93092354 93092470 3.320000e-35 159.0
34 TraesCS2D01G524000 chr4D 94.915 59 1 2 586 643 457521409 457521352 1.230000e-14 91.6
35 TraesCS2D01G524000 chr4D 91.045 67 1 4 580 642 462830571 462830636 5.720000e-13 86.1
36 TraesCS2D01G524000 chr4D 96.000 50 2 0 591 640 417477952 417478001 7.400000e-12 82.4
37 TraesCS2D01G524000 chr7B 81.841 391 57 12 2633 3018 313195932 313196313 1.860000e-82 316.0
38 TraesCS2D01G524000 chr7B 93.103 58 2 2 583 640 334243996 334244051 2.060000e-12 84.2
39 TraesCS2D01G524000 chr5D 92.241 116 9 0 3104 3219 99758454 99758569 7.140000e-37 165.0
40 TraesCS2D01G524000 chr5A 92.241 116 9 0 3104 3219 281949185 281949070 7.140000e-37 165.0
41 TraesCS2D01G524000 chr5A 96.226 53 2 0 588 640 855341 855393 1.590000e-13 87.9
42 TraesCS2D01G524000 chr3D 92.174 115 7 2 3103 3217 353855803 353855691 9.240000e-36 161.0
43 TraesCS2D01G524000 chr3D 98.077 52 0 1 591 642 427036973 427036923 4.420000e-14 89.8
44 TraesCS2D01G524000 chr7A 91.379 116 10 0 3104 3219 101907471 101907356 3.320000e-35 159.0
45 TraesCS2D01G524000 chr6A 90.625 64 6 0 3029 3092 230848012 230848075 5.720000e-13 86.1


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 TraesCS2D01G524000 chr2D 612533982 612537200 3218 False 5945.000000 5945 100.000000 1 3219 1 chr2D.!!$F1 3218
1 TraesCS2D01G524000 chr2D 627913446 627914884 1438 True 816.000000 948 90.191500 665 1949 2 chr2D.!!$R1 1284
2 TraesCS2D01G524000 chr4A 563267623 563270591 2968 False 4811.000000 4811 95.905000 93 3065 1 chr4A.!!$F1 2972
3 TraesCS2D01G524000 chr4A 563298598 563299953 1355 False 2154.000000 2154 95.298000 93 1452 1 chr4A.!!$F2 1359
4 TraesCS2D01G524000 chr4A 563304227 563306095 1868 False 1290.500000 1567 95.931500 1447 3065 2 chr4A.!!$F3 1618
5 TraesCS2D01G524000 chr2A 758388271 758391182 2911 True 674.666667 905 89.062333 665 1949 3 chr2A.!!$R1 1284
6 TraesCS2D01G524000 chr2B 770672937 770674341 1404 True 774.500000 782 90.888500 665 1949 2 chr2B.!!$R1 1284
7 TraesCS2D01G524000 chr2B 748215425 748216823 1398 False 723.500000 778 89.580000 673 1949 2 chr2B.!!$F4 1276
8 TraesCS2D01G524000 chr2B 748366398 748367796 1398 False 538.233333 808 91.089000 673 1949 3 chr2B.!!$F5 1276
9 TraesCS2D01G524000 chr7D 339792785 339793403 618 False 252.000000 339 88.211000 2623 3219 2 chr7D.!!$F2 596

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
79 80 0.038599 TGTACACTCCGGCTCCAGTA 59.961 55.000 0.00 0.0 0.00 2.74 F
431 432 1.003112 TTGTACGACCCATGCCCAC 60.003 57.895 0.00 0.0 0.00 4.61 F
451 452 1.299089 GGTGCCGCAACACACTTTC 60.299 57.895 2.72 0.0 42.55 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1023 2506 0.458669 GCATGAGCAACCCCATGAAG 59.541 55.000 0.0 0.0 41.88 3.02 R
1321 2973 3.756963 ACGAAGGGCTTATCTTTTCCAAC 59.243 43.478 0.0 0.0 0.00 3.77 R
2218 3876 6.374417 AAGAGGTGAGTATGTGGTTGTATT 57.626 37.500 0.0 0.0 0.00 1.89 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
20 21 3.744238 GTTGGTGGTTGCAATTAGGTT 57.256 42.857 0.59 0.00 0.00 3.50
21 22 4.857509 GTTGGTGGTTGCAATTAGGTTA 57.142 40.909 0.59 0.00 0.00 2.85
22 23 5.203060 GTTGGTGGTTGCAATTAGGTTAA 57.797 39.130 0.59 0.00 0.00 2.01
23 24 5.602628 GTTGGTGGTTGCAATTAGGTTAAA 58.397 37.500 0.59 0.00 0.00 1.52
24 25 5.871396 TGGTGGTTGCAATTAGGTTAAAA 57.129 34.783 0.59 0.00 0.00 1.52
25 26 6.426646 TGGTGGTTGCAATTAGGTTAAAAT 57.573 33.333 0.59 0.00 0.00 1.82
26 27 7.540474 TGGTGGTTGCAATTAGGTTAAAATA 57.460 32.000 0.59 0.00 0.00 1.40
27 28 7.963532 TGGTGGTTGCAATTAGGTTAAAATAA 58.036 30.769 0.59 0.00 0.00 1.40
28 29 8.598041 TGGTGGTTGCAATTAGGTTAAAATAAT 58.402 29.630 0.59 0.00 0.00 1.28
29 30 8.878769 GGTGGTTGCAATTAGGTTAAAATAATG 58.121 33.333 0.59 0.00 0.00 1.90
30 31 9.646427 GTGGTTGCAATTAGGTTAAAATAATGA 57.354 29.630 0.59 0.00 0.00 2.57
31 32 9.646427 TGGTTGCAATTAGGTTAAAATAATGAC 57.354 29.630 0.59 0.00 0.00 3.06
32 33 9.646427 GGTTGCAATTAGGTTAAAATAATGACA 57.354 29.630 0.59 0.00 0.00 3.58
40 41 7.601705 AGGTTAAAATAATGACATGATGGGG 57.398 36.000 0.00 0.00 0.00 4.96
41 42 6.041979 AGGTTAAAATAATGACATGATGGGGC 59.958 38.462 0.00 0.00 0.00 5.80
42 43 4.961438 AAAATAATGACATGATGGGGCC 57.039 40.909 0.00 0.00 0.00 5.80
43 44 2.205022 ATAATGACATGATGGGGCCG 57.795 50.000 0.00 0.00 0.00 6.13
44 45 0.110295 TAATGACATGATGGGGCCGG 59.890 55.000 0.00 0.00 0.00 6.13
45 46 2.645394 AATGACATGATGGGGCCGGG 62.645 60.000 2.18 0.00 0.00 5.73
46 47 3.809013 GACATGATGGGGCCGGGT 61.809 66.667 2.18 0.00 0.00 5.28
47 48 2.367648 ACATGATGGGGCCGGGTA 60.368 61.111 2.18 0.00 0.00 3.69
48 49 2.113139 CATGATGGGGCCGGGTAC 59.887 66.667 2.18 0.00 0.00 3.34
49 50 2.367648 ATGATGGGGCCGGGTACA 60.368 61.111 2.18 0.00 0.00 2.90
50 51 2.004120 ATGATGGGGCCGGGTACAA 61.004 57.895 2.18 0.00 0.00 2.41
51 52 1.360393 ATGATGGGGCCGGGTACAAT 61.360 55.000 2.18 0.00 0.00 2.71
52 53 0.694783 TGATGGGGCCGGGTACAATA 60.695 55.000 2.18 0.00 0.00 1.90
53 54 0.696501 GATGGGGCCGGGTACAATAT 59.303 55.000 2.18 0.00 0.00 1.28
54 55 0.404040 ATGGGGCCGGGTACAATATG 59.596 55.000 2.18 0.00 0.00 1.78
55 56 0.694783 TGGGGCCGGGTACAATATGA 60.695 55.000 2.18 0.00 0.00 2.15
56 57 0.475044 GGGGCCGGGTACAATATGAA 59.525 55.000 2.18 0.00 0.00 2.57
57 58 1.544759 GGGGCCGGGTACAATATGAAG 60.545 57.143 2.18 0.00 0.00 3.02
58 59 1.142262 GGGCCGGGTACAATATGAAGT 59.858 52.381 2.18 0.00 0.00 3.01
59 60 2.369532 GGGCCGGGTACAATATGAAGTA 59.630 50.000 2.18 0.00 0.00 2.24
60 61 3.008704 GGGCCGGGTACAATATGAAGTAT 59.991 47.826 2.18 0.00 0.00 2.12
61 62 4.000988 GGCCGGGTACAATATGAAGTATG 58.999 47.826 2.18 0.00 0.00 2.39
62 63 4.504340 GGCCGGGTACAATATGAAGTATGT 60.504 45.833 2.18 0.00 0.00 2.29
63 64 5.279607 GGCCGGGTACAATATGAAGTATGTA 60.280 44.000 2.18 0.00 0.00 2.29
64 65 5.636543 GCCGGGTACAATATGAAGTATGTAC 59.363 44.000 2.18 6.41 32.49 2.90
65 66 6.739286 GCCGGGTACAATATGAAGTATGTACA 60.739 42.308 2.18 0.00 33.59 2.90
66 67 6.643770 CCGGGTACAATATGAAGTATGTACAC 59.356 42.308 14.58 11.00 33.59 2.90
67 68 7.431249 CGGGTACAATATGAAGTATGTACACT 58.569 38.462 13.38 0.00 33.39 3.55
68 69 7.594015 CGGGTACAATATGAAGTATGTACACTC 59.406 40.741 13.38 0.00 33.39 3.51
69 70 7.871463 GGGTACAATATGAAGTATGTACACTCC 59.129 40.741 14.58 5.49 33.12 3.85
70 71 7.594015 GGTACAATATGAAGTATGTACACTCCG 59.406 40.741 14.58 0.00 33.59 4.63
71 72 6.513180 ACAATATGAAGTATGTACACTCCGG 58.487 40.000 0.00 0.00 0.00 5.14
72 73 2.953466 TGAAGTATGTACACTCCGGC 57.047 50.000 0.00 0.00 0.00 6.13
73 74 2.453521 TGAAGTATGTACACTCCGGCT 58.546 47.619 0.00 0.00 0.00 5.52
74 75 2.426024 TGAAGTATGTACACTCCGGCTC 59.574 50.000 0.00 0.00 0.00 4.70
75 76 1.400737 AGTATGTACACTCCGGCTCC 58.599 55.000 0.00 0.00 0.00 4.70
76 77 1.108776 GTATGTACACTCCGGCTCCA 58.891 55.000 0.00 0.00 0.00 3.86
77 78 1.067212 GTATGTACACTCCGGCTCCAG 59.933 57.143 0.00 0.00 0.00 3.86
78 79 0.614979 ATGTACACTCCGGCTCCAGT 60.615 55.000 0.00 0.00 0.00 4.00
79 80 0.038599 TGTACACTCCGGCTCCAGTA 59.961 55.000 0.00 0.00 0.00 2.74
80 81 1.341679 TGTACACTCCGGCTCCAGTAT 60.342 52.381 0.00 0.00 0.00 2.12
81 82 1.067212 GTACACTCCGGCTCCAGTATG 59.933 57.143 0.00 0.00 0.00 2.39
98 99 2.353607 GGGCGTCGATCGTAGCTG 60.354 66.667 26.64 11.94 42.13 4.24
135 136 3.118847 GCATTCATCTCTCACACTCCTGA 60.119 47.826 0.00 0.00 0.00 3.86
165 166 6.194235 AGCAAATAAAGTTCCCACCATGATA 58.806 36.000 0.00 0.00 0.00 2.15
167 168 7.014615 AGCAAATAAAGTTCCCACCATGATATC 59.985 37.037 0.00 0.00 0.00 1.63
171 172 4.543590 AGTTCCCACCATGATATCGATC 57.456 45.455 0.00 0.00 0.00 3.69
192 193 6.572182 ATCGATGAATCCCATCCAATATCT 57.428 37.500 0.00 0.00 46.98 1.98
234 235 1.696063 AAGGCGCATTGCATTCCTAT 58.304 45.000 6.46 1.27 46.23 2.57
244 245 1.273606 TGCATTCCTATCTAGAGGCGC 59.726 52.381 0.00 0.00 36.45 6.53
312 313 2.157640 AGACATGGTCTCTCCTCCAG 57.842 55.000 0.00 0.00 38.71 3.86
321 322 5.032846 TGGTCTCTCCTCCAGAAAACATAT 58.967 41.667 0.00 0.00 37.07 1.78
372 373 9.956720 CAGTTTTTCTTTTCTGATGAGTAACAT 57.043 29.630 0.00 0.00 42.47 2.71
431 432 1.003112 TTGTACGACCCATGCCCAC 60.003 57.895 0.00 0.00 0.00 4.61
451 452 1.299089 GGTGCCGCAACACACTTTC 60.299 57.895 2.72 0.00 42.55 2.62
489 490 5.287752 GTCCTACACACACGTACATTACATG 59.712 44.000 0.00 0.00 0.00 3.21
495 497 6.090763 ACACACACGTACATTACATGAATGAG 59.909 38.462 18.66 13.26 46.94 2.90
513 515 5.886960 ATGAGTGAACCAGCAAGTTTATC 57.113 39.130 0.00 0.00 0.00 1.75
557 559 1.308998 GCTAGCACACACCAAACACT 58.691 50.000 10.63 0.00 0.00 3.55
559 561 2.480419 GCTAGCACACACCAAACACTAG 59.520 50.000 10.63 0.00 0.00 2.57
560 562 2.710096 AGCACACACCAAACACTAGT 57.290 45.000 0.00 0.00 0.00 2.57
590 592 3.285484 CATGCATGCTTAACCCTCTTCT 58.715 45.455 20.33 0.00 0.00 2.85
591 593 3.439857 TGCATGCTTAACCCTCTTCTT 57.560 42.857 20.33 0.00 0.00 2.52
592 594 3.347216 TGCATGCTTAACCCTCTTCTTC 58.653 45.455 20.33 0.00 0.00 2.87
604 606 7.767250 AACCCTCTTCTTCTTAATGGAAAAG 57.233 36.000 0.00 0.00 0.00 2.27
633 635 3.631145 TGCTCTTGCATGTTCTTGAAC 57.369 42.857 6.56 6.56 45.31 3.18
637 639 4.805192 GCTCTTGCATGTTCTTGAACAAAA 59.195 37.500 18.31 12.50 39.41 2.44
667 669 6.376177 CACATACGTGCGTAAGATATCCTTA 58.624 40.000 12.82 0.00 36.06 2.69
884 2367 5.495640 AGAATTGATTCAAGACCACTCTCC 58.504 41.667 5.21 0.00 39.23 3.71
885 2368 5.250313 AGAATTGATTCAAGACCACTCTCCT 59.750 40.000 5.21 0.00 39.23 3.69
896 2379 2.224402 ACCACTCTCCTTGCTTGTTCTC 60.224 50.000 0.00 0.00 0.00 2.87
940 2423 7.311297 CCTGCCAATGTGAACTATATATACCCT 60.311 40.741 0.00 0.00 0.00 4.34
1023 2506 3.263261 GGGGATGAAGAAACTCTCGTTC 58.737 50.000 0.00 0.00 31.66 3.95
1107 2590 1.509923 GGTGGCATTGCAAGAGAGC 59.490 57.895 11.39 6.36 0.00 4.09
1205 2690 2.833794 TCCATACACTATCTTTGGCGC 58.166 47.619 0.00 0.00 0.00 6.53
1270 2755 3.695830 TCCCCAATGACAACACTAGAC 57.304 47.619 0.00 0.00 0.00 2.59
1321 2973 1.137513 GTTCCGTGAGAAGGTGTTCG 58.862 55.000 0.00 0.00 37.79 3.95
2218 3876 0.696143 TTCCCCCGGCTGATCCATAA 60.696 55.000 0.00 0.00 34.01 1.90
2259 3917 8.733458 TCACCTCTTTAATATTGCATGCATATC 58.267 33.333 23.37 0.00 0.00 1.63
2471 4374 1.527034 TGCACTGAGCTTTGATGACC 58.473 50.000 0.00 0.00 45.94 4.02
2481 4384 3.953612 AGCTTTGATGACCTGTTCAAACA 59.046 39.130 0.00 0.00 37.03 2.83
2491 4394 2.746904 CCTGTTCAAACATGTGCGGATA 59.253 45.455 0.00 0.00 38.41 2.59
2539 4442 3.197766 TCTCATCCCGTGTTGCTCTTATT 59.802 43.478 0.00 0.00 0.00 1.40
2616 4519 0.476611 AGGGGCTTTCCAGAGGAAGT 60.477 55.000 0.00 0.00 43.06 3.01
2618 4521 1.633945 GGGGCTTTCCAGAGGAAGTAA 59.366 52.381 0.00 0.00 43.06 2.24
2629 4532 8.603898 TTCCAGAGGAAGTAATCACACTAATA 57.396 34.615 0.00 0.00 36.71 0.98
2714 4621 2.973419 TCGCAAACGGTATGGAAAAC 57.027 45.000 0.00 0.00 40.63 2.43
2736 4643 6.259550 ACTGTCTCCAATAAAATGAACTGC 57.740 37.500 0.00 0.00 0.00 4.40
2902 4810 5.006649 GCATACATGTCGCTCAAATGAACTA 59.993 40.000 0.00 0.00 0.00 2.24
2992 4901 4.260294 GGTCACTCGACTGAACTATCTACG 60.260 50.000 3.15 0.00 42.21 3.51
3066 4975 6.103997 AGACCGATAATAACACACACGATTT 58.896 36.000 0.00 0.00 0.00 2.17
3078 4987 5.351465 ACACACACGATTTCTGCTAATAAGG 59.649 40.000 0.00 0.00 0.00 2.69
3079 4988 4.332819 ACACACGATTTCTGCTAATAAGGC 59.667 41.667 0.00 0.00 0.00 4.35
3082 4991 3.555956 ACGATTTCTGCTAATAAGGCGTG 59.444 43.478 0.00 0.00 0.00 5.34
3091 5000 3.666902 GCTAATAAGGCGTGTGTGTTGTG 60.667 47.826 0.00 0.00 0.00 3.33
3092 5001 2.248280 ATAAGGCGTGTGTGTTGTGA 57.752 45.000 0.00 0.00 0.00 3.58
3093 5002 2.025589 TAAGGCGTGTGTGTTGTGAA 57.974 45.000 0.00 0.00 0.00 3.18
3116 5091 2.907910 ACGCTTGATGTGATTTGCTC 57.092 45.000 0.00 0.00 0.00 4.26
3120 5095 3.727079 CGCTTGATGTGATTTGCTCTGTC 60.727 47.826 0.00 0.00 0.00 3.51
3127 5102 1.875514 TGATTTGCTCTGTCTGCACAC 59.124 47.619 0.00 0.00 40.40 3.82
3128 5103 1.198637 GATTTGCTCTGTCTGCACACC 59.801 52.381 0.00 0.00 40.40 4.16
3140 5115 2.102084 TCTGCACACCATCTATGCTCTC 59.898 50.000 0.00 0.00 40.13 3.20
3142 5117 2.102084 TGCACACCATCTATGCTCTCTC 59.898 50.000 0.00 0.00 40.13 3.20
3156 5131 8.845227 TCTATGCTCTCTCTATAGAACAACAAG 58.155 37.037 3.57 0.00 32.20 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.744238 AACCTAATTGCAACCACCAAC 57.256 42.857 0.00 0.00 0.00 3.77
1 2 5.871396 TTTAACCTAATTGCAACCACCAA 57.129 34.783 0.00 0.00 0.00 3.67
2 3 5.871396 TTTTAACCTAATTGCAACCACCA 57.129 34.783 0.00 0.00 0.00 4.17
3 4 8.878769 CATTATTTTAACCTAATTGCAACCACC 58.121 33.333 0.00 0.00 0.00 4.61
4 5 9.646427 TCATTATTTTAACCTAATTGCAACCAC 57.354 29.630 0.00 0.00 0.00 4.16
5 6 9.646427 GTCATTATTTTAACCTAATTGCAACCA 57.354 29.630 0.00 0.00 0.00 3.67
6 7 9.646427 TGTCATTATTTTAACCTAATTGCAACC 57.354 29.630 0.00 0.00 0.00 3.77
14 15 9.142014 CCCCATCATGTCATTATTTTAACCTAA 57.858 33.333 0.00 0.00 0.00 2.69
15 16 7.232534 GCCCCATCATGTCATTATTTTAACCTA 59.767 37.037 0.00 0.00 0.00 3.08
16 17 6.041979 GCCCCATCATGTCATTATTTTAACCT 59.958 38.462 0.00 0.00 0.00 3.50
17 18 6.223120 GCCCCATCATGTCATTATTTTAACC 58.777 40.000 0.00 0.00 0.00 2.85
18 19 6.223120 GGCCCCATCATGTCATTATTTTAAC 58.777 40.000 0.00 0.00 0.00 2.01
19 20 5.010516 CGGCCCCATCATGTCATTATTTTAA 59.989 40.000 0.00 0.00 0.00 1.52
20 21 4.522405 CGGCCCCATCATGTCATTATTTTA 59.478 41.667 0.00 0.00 0.00 1.52
21 22 3.321682 CGGCCCCATCATGTCATTATTTT 59.678 43.478 0.00 0.00 0.00 1.82
22 23 2.892852 CGGCCCCATCATGTCATTATTT 59.107 45.455 0.00 0.00 0.00 1.40
23 24 2.517959 CGGCCCCATCATGTCATTATT 58.482 47.619 0.00 0.00 0.00 1.40
24 25 1.272092 CCGGCCCCATCATGTCATTAT 60.272 52.381 0.00 0.00 0.00 1.28
25 26 0.110295 CCGGCCCCATCATGTCATTA 59.890 55.000 0.00 0.00 0.00 1.90
26 27 1.152694 CCGGCCCCATCATGTCATT 60.153 57.895 0.00 0.00 0.00 2.57
27 28 2.517414 CCGGCCCCATCATGTCAT 59.483 61.111 0.00 0.00 0.00 3.06
28 29 3.807839 CCCGGCCCCATCATGTCA 61.808 66.667 0.00 0.00 0.00 3.58
29 30 2.448582 TACCCGGCCCCATCATGTC 61.449 63.158 0.00 0.00 0.00 3.06
30 31 2.367648 TACCCGGCCCCATCATGT 60.368 61.111 0.00 0.00 0.00 3.21
31 32 2.113139 GTACCCGGCCCCATCATG 59.887 66.667 0.00 0.00 0.00 3.07
32 33 1.360393 ATTGTACCCGGCCCCATCAT 61.360 55.000 0.00 0.00 0.00 2.45
33 34 0.694783 TATTGTACCCGGCCCCATCA 60.695 55.000 0.00 0.00 0.00 3.07
34 35 0.696501 ATATTGTACCCGGCCCCATC 59.303 55.000 0.00 0.00 0.00 3.51
35 36 0.404040 CATATTGTACCCGGCCCCAT 59.596 55.000 0.00 0.00 0.00 4.00
36 37 0.694783 TCATATTGTACCCGGCCCCA 60.695 55.000 0.00 0.00 0.00 4.96
37 38 0.475044 TTCATATTGTACCCGGCCCC 59.525 55.000 0.00 0.00 0.00 5.80
38 39 1.142262 ACTTCATATTGTACCCGGCCC 59.858 52.381 0.00 0.00 0.00 5.80
39 40 2.632987 ACTTCATATTGTACCCGGCC 57.367 50.000 0.00 0.00 0.00 6.13
40 41 4.638304 ACATACTTCATATTGTACCCGGC 58.362 43.478 0.00 0.00 0.00 6.13
41 42 6.643770 GTGTACATACTTCATATTGTACCCGG 59.356 42.308 0.00 0.00 32.46 5.73
42 43 7.431249 AGTGTACATACTTCATATTGTACCCG 58.569 38.462 0.00 0.00 32.46 5.28
43 44 7.871463 GGAGTGTACATACTTCATATTGTACCC 59.129 40.741 0.00 0.84 32.46 3.69
44 45 7.594015 CGGAGTGTACATACTTCATATTGTACC 59.406 40.741 0.00 3.55 32.46 3.34
45 46 7.594015 CCGGAGTGTACATACTTCATATTGTAC 59.406 40.741 0.00 6.28 33.21 2.90
46 47 7.654568 CCGGAGTGTACATACTTCATATTGTA 58.345 38.462 0.00 0.00 0.00 2.41
47 48 6.513180 CCGGAGTGTACATACTTCATATTGT 58.487 40.000 0.00 0.00 0.00 2.71
48 49 5.405571 GCCGGAGTGTACATACTTCATATTG 59.594 44.000 5.05 0.00 0.00 1.90
49 50 5.304614 AGCCGGAGTGTACATACTTCATATT 59.695 40.000 5.05 0.00 0.00 1.28
50 51 4.833380 AGCCGGAGTGTACATACTTCATAT 59.167 41.667 5.05 0.00 0.00 1.78
51 52 4.212716 AGCCGGAGTGTACATACTTCATA 58.787 43.478 5.05 0.00 0.00 2.15
52 53 3.031736 AGCCGGAGTGTACATACTTCAT 58.968 45.455 5.05 0.00 0.00 2.57
53 54 2.426024 GAGCCGGAGTGTACATACTTCA 59.574 50.000 5.05 0.00 0.00 3.02
54 55 2.223758 GGAGCCGGAGTGTACATACTTC 60.224 54.545 5.05 0.00 0.00 3.01
55 56 1.755380 GGAGCCGGAGTGTACATACTT 59.245 52.381 5.05 0.00 0.00 2.24
56 57 1.341679 TGGAGCCGGAGTGTACATACT 60.342 52.381 5.05 0.00 0.00 2.12
57 58 1.067212 CTGGAGCCGGAGTGTACATAC 59.933 57.143 5.05 0.00 0.00 2.39
58 59 1.341679 ACTGGAGCCGGAGTGTACATA 60.342 52.381 5.05 0.00 0.00 2.29
59 60 0.614979 ACTGGAGCCGGAGTGTACAT 60.615 55.000 5.05 0.00 0.00 2.29
60 61 0.038599 TACTGGAGCCGGAGTGTACA 59.961 55.000 5.05 0.00 0.00 2.90
61 62 1.067212 CATACTGGAGCCGGAGTGTAC 59.933 57.143 5.05 0.00 0.00 2.90
62 63 1.399714 CATACTGGAGCCGGAGTGTA 58.600 55.000 5.05 0.24 0.00 2.90
63 64 1.330655 CCATACTGGAGCCGGAGTGT 61.331 60.000 5.05 0.00 40.96 3.55
64 65 1.443407 CCATACTGGAGCCGGAGTG 59.557 63.158 5.05 0.64 40.96 3.51
65 66 1.762460 CCCATACTGGAGCCGGAGT 60.762 63.158 5.05 1.15 40.96 3.85
66 67 3.142393 CCCATACTGGAGCCGGAG 58.858 66.667 5.05 0.00 40.96 4.63
67 68 3.161450 GCCCATACTGGAGCCGGA 61.161 66.667 5.05 0.00 40.96 5.14
68 69 4.609018 CGCCCATACTGGAGCCGG 62.609 72.222 0.00 0.00 40.96 6.13
69 70 3.792053 GACGCCCATACTGGAGCCG 62.792 68.421 0.00 0.00 40.96 5.52
70 71 2.109181 GACGCCCATACTGGAGCC 59.891 66.667 0.00 0.00 40.96 4.70
71 72 2.088674 ATCGACGCCCATACTGGAGC 62.089 60.000 0.00 0.00 40.96 4.70
72 73 0.039074 GATCGACGCCCATACTGGAG 60.039 60.000 0.00 0.00 40.96 3.86
73 74 1.792118 CGATCGACGCCCATACTGGA 61.792 60.000 10.26 0.00 37.58 3.86
74 75 1.371758 CGATCGACGCCCATACTGG 60.372 63.158 10.26 0.00 37.25 4.00
75 76 0.589708 TACGATCGACGCCCATACTG 59.410 55.000 24.34 0.00 46.94 2.74
76 77 0.873054 CTACGATCGACGCCCATACT 59.127 55.000 24.34 0.00 46.94 2.12
77 78 0.728466 GCTACGATCGACGCCCATAC 60.728 60.000 24.34 0.00 46.94 2.39
78 79 0.887836 AGCTACGATCGACGCCCATA 60.888 55.000 24.34 0.19 46.94 2.74
79 80 2.194212 AGCTACGATCGACGCCCAT 61.194 57.895 24.34 5.07 46.94 4.00
80 81 2.827190 AGCTACGATCGACGCCCA 60.827 61.111 24.34 0.00 46.94 5.36
81 82 2.353607 CAGCTACGATCGACGCCC 60.354 66.667 24.34 5.08 46.94 6.13
82 83 2.353607 CCAGCTACGATCGACGCC 60.354 66.667 24.34 6.90 46.94 5.68
83 84 3.025176 GCCAGCTACGATCGACGC 61.025 66.667 24.34 21.78 46.94 5.19
85 86 0.030773 TGATGCCAGCTACGATCGAC 59.969 55.000 24.34 10.72 0.00 4.20
86 87 0.312102 CTGATGCCAGCTACGATCGA 59.688 55.000 24.34 4.52 33.07 3.59
87 88 2.806577 CTGATGCCAGCTACGATCG 58.193 57.895 14.88 14.88 33.07 3.69
98 99 1.872313 GAATGCACTCTAGCTGATGCC 59.128 52.381 0.00 0.00 40.80 4.40
135 136 3.509575 TGGGAACTTTATTTGCTCGCATT 59.490 39.130 0.00 0.00 0.00 3.56
192 193 5.576563 TTTTTGTTCCCTCACTCTCCATA 57.423 39.130 0.00 0.00 0.00 2.74
234 235 2.750237 TCGTGCAGCGCCTCTAGA 60.750 61.111 2.29 0.00 41.07 2.43
244 245 2.797156 GAGCTATAATGGTGTCGTGCAG 59.203 50.000 0.00 0.00 0.00 4.41
258 259 6.171213 CCTGAAGATGCATTCATGAGCTATA 58.829 40.000 0.00 0.00 38.47 1.31
321 322 9.466497 TGTGCATCAGTGTCATATATATAGAGA 57.534 33.333 0.00 0.00 0.00 3.10
346 347 9.956720 ATGTTACTCATCAGAAAAGAAAAACTG 57.043 29.630 0.00 0.00 29.76 3.16
372 373 0.325671 TGGTTGTTTGGGGCCTTTCA 60.326 50.000 0.84 0.00 0.00 2.69
442 443 0.756903 AGTACGGGCTGAAAGTGTGT 59.243 50.000 0.00 0.00 35.30 3.72
451 452 1.134560 GTAGGACTCAAGTACGGGCTG 59.865 57.143 0.00 0.00 33.01 4.85
489 490 4.574599 AAACTTGCTGGTTCACTCATTC 57.425 40.909 0.00 0.00 0.00 2.67
495 497 4.483476 AACGATAAACTTGCTGGTTCAC 57.517 40.909 0.00 0.00 0.00 3.18
513 515 2.223144 TCTCCGTGATTTCAGCAAAACG 59.777 45.455 0.00 0.00 0.00 3.60
579 581 8.665906 TCTTTTCCATTAAGAAGAAGAGGGTTA 58.334 33.333 0.00 0.00 0.00 2.85
590 592 6.591062 GCATTGCATGTCTTTTCCATTAAGAA 59.409 34.615 3.15 0.00 33.71 2.52
591 593 6.071221 AGCATTGCATGTCTTTTCCATTAAGA 60.071 34.615 11.91 0.00 0.00 2.10
592 594 6.103997 AGCATTGCATGTCTTTTCCATTAAG 58.896 36.000 11.91 0.00 0.00 1.85
646 648 6.183360 GGGATAAGGATATCTTACGCACGTAT 60.183 42.308 3.43 0.00 40.40 3.06
654 656 7.124448 ACATTCTCGGGGATAAGGATATCTTAC 59.876 40.741 2.05 0.00 40.40 2.34
667 669 4.829388 TGGGACATTCTCGGGGAT 57.171 55.556 0.00 0.00 0.00 3.85
884 2367 1.458827 GACGAGCAGAGAACAAGCAAG 59.541 52.381 0.00 0.00 0.00 4.01
885 2368 1.502231 GACGAGCAGAGAACAAGCAA 58.498 50.000 0.00 0.00 0.00 3.91
896 2379 2.028130 AGGTAATGAGAGGACGAGCAG 58.972 52.381 0.00 0.00 0.00 4.24
940 2423 7.908827 TTGTGGCTAACGATTTATTGAGTTA 57.091 32.000 0.00 0.00 0.00 2.24
1023 2506 0.458669 GCATGAGCAACCCCATGAAG 59.541 55.000 0.00 0.00 41.88 3.02
1107 2590 2.464865 GATGTGGCTACGCTAGTCTTG 58.535 52.381 0.00 0.00 0.00 3.02
1205 2690 3.311871 GCTCTTGTACATGCCATCTTCAG 59.688 47.826 0.00 0.00 0.00 3.02
1270 2755 6.457257 CCGGGTTTTAGGTTAAACATATGTCG 60.457 42.308 9.23 3.01 39.27 4.35
1321 2973 3.756963 ACGAAGGGCTTATCTTTTCCAAC 59.243 43.478 0.00 0.00 0.00 3.77
2218 3876 6.374417 AAGAGGTGAGTATGTGGTTGTATT 57.626 37.500 0.00 0.00 0.00 1.89
2471 4374 2.995466 ATCCGCACATGTTTGAACAG 57.005 45.000 0.00 0.00 43.04 3.16
2481 4384 2.758423 GGGTTTTCCTTTATCCGCACAT 59.242 45.455 0.00 0.00 40.46 3.21
2491 4394 5.313506 ACATCTCTTAGAGGGGTTTTCCTTT 59.686 40.000 9.58 0.00 37.25 3.11
2584 4487 1.228184 GCCCCTGGCTGATCATCTG 60.228 63.158 0.00 0.00 46.69 2.90
2616 4519 7.120923 GGACCTTCCTGTATTAGTGTGATTA 57.879 40.000 0.00 0.00 32.53 1.75
2618 4521 5.615925 GGACCTTCCTGTATTAGTGTGAT 57.384 43.478 0.00 0.00 32.53 3.06
2714 4621 5.106555 ACGCAGTTCATTTTATTGGAGACAG 60.107 40.000 0.00 0.00 37.78 3.51
2736 4643 4.939399 TGGATCAGCCATCACACG 57.061 55.556 0.00 0.00 43.33 4.49
2758 4665 5.635280 CACACAACTCTTATCTGAATCGTGT 59.365 40.000 0.00 0.00 34.41 4.49
2761 4668 5.445142 GCACACACAACTCTTATCTGAATCG 60.445 44.000 0.00 0.00 0.00 3.34
2902 4810 5.996513 TGTGTTATTTTGGCTCATTGCAAAT 59.003 32.000 1.71 0.00 45.15 2.32
3066 4975 2.028476 ACACACACGCCTTATTAGCAGA 60.028 45.455 0.00 0.00 0.00 4.26
3078 4987 1.646726 GTTTGTTCACAACACACACGC 59.353 47.619 1.65 0.00 40.76 5.34
3079 4988 1.901869 CGTTTGTTCACAACACACACG 59.098 47.619 6.51 0.00 41.04 4.49
3082 4991 2.256445 AGCGTTTGTTCACAACACAC 57.744 45.000 0.00 0.00 41.97 3.82
3091 5000 4.375305 GCAAATCACATCAAGCGTTTGTTC 60.375 41.667 11.93 0.00 35.73 3.18
3092 5001 3.490526 GCAAATCACATCAAGCGTTTGTT 59.509 39.130 11.93 0.49 35.73 2.83
3093 5002 3.052036 GCAAATCACATCAAGCGTTTGT 58.948 40.909 11.93 0.00 35.73 2.83
3098 5007 2.161012 ACAGAGCAAATCACATCAAGCG 59.839 45.455 0.00 0.00 0.00 4.68
3116 5091 1.938577 GCATAGATGGTGTGCAGACAG 59.061 52.381 16.68 0.00 42.69 3.51
3120 5095 2.102757 AGAGAGCATAGATGGTGTGCAG 59.897 50.000 0.00 0.00 45.50 4.41
3127 5102 7.936496 TGTTCTATAGAGAGAGCATAGATGG 57.064 40.000 2.02 0.00 32.41 3.51
3128 5103 8.791675 TGTTGTTCTATAGAGAGAGCATAGATG 58.208 37.037 2.02 0.00 36.67 2.90
3171 5146 9.757859 GTTTAATTTGGTTATGCAATCATGTTG 57.242 29.630 0.00 0.00 34.22 3.33


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

AutoCloner maintained by Alex Coulton.