Multiple sequence alignment - TraesCS3D01G255700

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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 TraesCS3D01G255700 chr3D 100.000 7062 0 0 1 7062 357159612 357152551 0.000000e+00 13042
1 TraesCS3D01G255700 chr2D 97.618 2645 48 2 1354 3986 106330060 106332701 0.000000e+00 4521
2 TraesCS3D01G255700 chr2D 97.431 2647 55 2 1354 3988 136424167 136426812 0.000000e+00 4499
3 TraesCS3D01G255700 chr7A 97.546 2649 50 4 1354 3990 109349318 109351963 0.000000e+00 4518
4 TraesCS3D01G255700 chr7A 96.553 2640 75 2 1354 3981 126385091 126387726 0.000000e+00 4357
5 TraesCS3D01G255700 chr3A 97.582 2647 47 3 1354 3986 217719974 217717331 0.000000e+00 4518
6 TraesCS3D01G255700 chr3A 96.141 2669 86 6 1336 3987 278308560 278311228 0.000000e+00 4342
7 TraesCS3D01G255700 chr3A 94.908 2278 101 4 1336 3600 84048769 84051044 0.000000e+00 3550
8 TraesCS3D01G255700 chr3A 94.315 2111 92 6 3990 6083 476659270 476657171 0.000000e+00 3208
9 TraesCS3D01G255700 chr3A 98.018 757 14 1 1 756 476661877 476661121 0.000000e+00 1314
10 TraesCS3D01G255700 chr3A 93.354 632 22 5 743 1354 476659885 476659254 0.000000e+00 917
11 TraesCS3D01G255700 chr3A 86.162 542 33 26 6444 6965 476569296 476568777 1.340000e-151 547
12 TraesCS3D01G255700 chr2A 97.539 2641 50 2 1354 3982 101857496 101854859 0.000000e+00 4503
13 TraesCS3D01G255700 chr2A 97.501 2641 51 2 1354 3982 421216642 421219279 0.000000e+00 4497
14 TraesCS3D01G255700 chr5D 97.393 2647 57 1 1354 3988 166629204 166631850 0.000000e+00 4495
15 TraesCS3D01G255700 chr5D 75.612 1878 341 83 4265 6076 27616411 27614585 0.000000e+00 822
16 TraesCS3D01G255700 chr4D 97.496 2636 53 3 1354 3977 484343784 484346418 0.000000e+00 4490
17 TraesCS3D01G255700 chr4D 90.964 166 15 0 983 1148 481370320 481370485 2.560000e-54 224
18 TraesCS3D01G255700 chr6A 97.393 2647 50 4 1354 3988 58017894 58015255 0.000000e+00 4488
19 TraesCS3D01G255700 chr6A 83.835 532 40 21 6458 6965 614938290 614937781 1.390000e-126 464
20 TraesCS3D01G255700 chr5A 96.774 2666 69 4 1336 3988 174598928 174601589 0.000000e+00 4431
21 TraesCS3D01G255700 chr5A 76.659 1281 224 46 4300 5544 18907751 18906510 2.150000e-179 640
22 TraesCS3D01G255700 chr3B 96.693 2661 75 2 1336 3983 547669288 547671948 0.000000e+00 4414
23 TraesCS3D01G255700 chr3B 96.331 2671 79 8 1336 3987 796797524 796800194 0.000000e+00 4372
24 TraesCS3D01G255700 chr3B 95.539 2645 86 2 1354 3986 411104679 411102055 0.000000e+00 4202
25 TraesCS3D01G255700 chr3B 93.176 1861 93 19 4634 6486 458409541 458407707 0.000000e+00 2702
26 TraesCS3D01G255700 chr3B 94.172 978 41 7 1 973 458439097 458438131 0.000000e+00 1476
27 TraesCS3D01G255700 chr3B 93.944 677 23 5 3990 4648 458417372 458416696 0.000000e+00 1007
28 TraesCS3D01G255700 chr3B 93.787 676 25 4 3990 4648 458437736 458437061 0.000000e+00 1000
29 TraesCS3D01G255700 chr3B 92.322 521 21 7 6548 7062 458407674 458407167 0.000000e+00 723
30 TraesCS3D01G255700 chr3B 94.307 404 21 2 950 1353 458417758 458417357 1.010000e-172 617
31 TraesCS3D01G255700 chr3B 93.812 404 23 2 950 1353 458438122 458437721 2.180000e-169 606
32 TraesCS3D01G255700 chr3B 90.634 331 16 6 647 973 458418086 458417767 6.550000e-115 425
33 TraesCS3D01G255700 chr4A 95.646 1355 46 2 1336 2677 311612980 311611626 0.000000e+00 2163
34 TraesCS3D01G255700 chrUn 94.376 978 39 7 1 973 391828454 391827488 0.000000e+00 1487
35 TraesCS3D01G255700 chrUn 93.750 656 24 6 4010 4648 463829886 463829231 0.000000e+00 968
36 TraesCS3D01G255700 chrUn 94.307 404 22 1 950 1353 391827479 391827077 1.010000e-172 617
37 TraesCS3D01G255700 chr1B 93.855 830 33 4 1336 2151 558818902 558818077 0.000000e+00 1234
38 TraesCS3D01G255700 chr1B 80.352 341 33 15 6633 6940 1514393 1514054 1.980000e-55 228
39 TraesCS3D01G255700 chr4B 75.405 1854 346 71 4278 6071 87009368 87011171 0.000000e+00 797
40 TraesCS3D01G255700 chr6B 75.334 1873 349 74 4265 6076 594855863 594854043 0.000000e+00 795
41 TraesCS3D01G255700 chr7D 91.071 168 15 0 983 1150 484299073 484298906 1.980000e-55 228
42 TraesCS3D01G255700 chr5B 91.018 167 15 0 984 1150 112531589 112531423 7.130000e-55 226
43 TraesCS3D01G255700 chr1D 90.058 171 15 2 985 1154 469874871 469874702 3.320000e-53 220
44 TraesCS3D01G255700 chr1D 79.290 338 32 21 6649 6956 2164639 2164968 1.200000e-47 202
45 TraesCS3D01G255700 chr1A 90.361 166 16 0 983 1148 58290729 58290564 1.190000e-52 219


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 TraesCS3D01G255700 chr3D 357152551 357159612 7061 True 13042.000000 13042 100.000000 1 7062 1 chr3D.!!$R1 7061
1 TraesCS3D01G255700 chr2D 106330060 106332701 2641 False 4521.000000 4521 97.618000 1354 3986 1 chr2D.!!$F1 2632
2 TraesCS3D01G255700 chr2D 136424167 136426812 2645 False 4499.000000 4499 97.431000 1354 3988 1 chr2D.!!$F2 2634
3 TraesCS3D01G255700 chr7A 109349318 109351963 2645 False 4518.000000 4518 97.546000 1354 3990 1 chr7A.!!$F1 2636
4 TraesCS3D01G255700 chr7A 126385091 126387726 2635 False 4357.000000 4357 96.553000 1354 3981 1 chr7A.!!$F2 2627
5 TraesCS3D01G255700 chr3A 217717331 217719974 2643 True 4518.000000 4518 97.582000 1354 3986 1 chr3A.!!$R1 2632
6 TraesCS3D01G255700 chr3A 278308560 278311228 2668 False 4342.000000 4342 96.141000 1336 3987 1 chr3A.!!$F2 2651
7 TraesCS3D01G255700 chr3A 84048769 84051044 2275 False 3550.000000 3550 94.908000 1336 3600 1 chr3A.!!$F1 2264
8 TraesCS3D01G255700 chr3A 476657171 476661877 4706 True 1813.000000 3208 95.229000 1 6083 3 chr3A.!!$R3 6082
9 TraesCS3D01G255700 chr3A 476568777 476569296 519 True 547.000000 547 86.162000 6444 6965 1 chr3A.!!$R2 521
10 TraesCS3D01G255700 chr2A 101854859 101857496 2637 True 4503.000000 4503 97.539000 1354 3982 1 chr2A.!!$R1 2628
11 TraesCS3D01G255700 chr2A 421216642 421219279 2637 False 4497.000000 4497 97.501000 1354 3982 1 chr2A.!!$F1 2628
12 TraesCS3D01G255700 chr5D 166629204 166631850 2646 False 4495.000000 4495 97.393000 1354 3988 1 chr5D.!!$F1 2634
13 TraesCS3D01G255700 chr5D 27614585 27616411 1826 True 822.000000 822 75.612000 4265 6076 1 chr5D.!!$R1 1811
14 TraesCS3D01G255700 chr4D 484343784 484346418 2634 False 4490.000000 4490 97.496000 1354 3977 1 chr4D.!!$F2 2623
15 TraesCS3D01G255700 chr6A 58015255 58017894 2639 True 4488.000000 4488 97.393000 1354 3988 1 chr6A.!!$R1 2634
16 TraesCS3D01G255700 chr6A 614937781 614938290 509 True 464.000000 464 83.835000 6458 6965 1 chr6A.!!$R2 507
17 TraesCS3D01G255700 chr5A 174598928 174601589 2661 False 4431.000000 4431 96.774000 1336 3988 1 chr5A.!!$F1 2652
18 TraesCS3D01G255700 chr5A 18906510 18907751 1241 True 640.000000 640 76.659000 4300 5544 1 chr5A.!!$R1 1244
19 TraesCS3D01G255700 chr3B 547669288 547671948 2660 False 4414.000000 4414 96.693000 1336 3983 1 chr3B.!!$F1 2647
20 TraesCS3D01G255700 chr3B 796797524 796800194 2670 False 4372.000000 4372 96.331000 1336 3987 1 chr3B.!!$F2 2651
21 TraesCS3D01G255700 chr3B 411102055 411104679 2624 True 4202.000000 4202 95.539000 1354 3986 1 chr3B.!!$R1 2632
22 TraesCS3D01G255700 chr3B 458407167 458409541 2374 True 1712.500000 2702 92.749000 4634 7062 2 chr3B.!!$R2 2428
23 TraesCS3D01G255700 chr3B 458437061 458439097 2036 True 1027.333333 1476 93.923667 1 4648 3 chr3B.!!$R4 4647
24 TraesCS3D01G255700 chr3B 458416696 458418086 1390 True 683.000000 1007 92.961667 647 4648 3 chr3B.!!$R3 4001
25 TraesCS3D01G255700 chr4A 311611626 311612980 1354 True 2163.000000 2163 95.646000 1336 2677 1 chr4A.!!$R1 1341
26 TraesCS3D01G255700 chrUn 391827077 391828454 1377 True 1052.000000 1487 94.341500 1 1353 2 chrUn.!!$R2 1352
27 TraesCS3D01G255700 chrUn 463829231 463829886 655 True 968.000000 968 93.750000 4010 4648 1 chrUn.!!$R1 638
28 TraesCS3D01G255700 chr1B 558818077 558818902 825 True 1234.000000 1234 93.855000 1336 2151 1 chr1B.!!$R2 815
29 TraesCS3D01G255700 chr4B 87009368 87011171 1803 False 797.000000 797 75.405000 4278 6071 1 chr4B.!!$F1 1793
30 TraesCS3D01G255700 chr6B 594854043 594855863 1820 True 795.000000 795 75.334000 4265 6076 1 chr6B.!!$R1 1811

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
205 206 0.529378 GGGCCTGCATGTCTTTTCAG 59.471 55.000 0.84 0.00 0.00 3.02 F
1543 2843 0.106066 CATGGGGGCTTTGGCTATGA 60.106 55.000 0.00 0.00 38.73 2.15 F
1864 3165 1.381327 TCAAGGGGGAGGTAGCTCG 60.381 63.158 15.43 1.18 0.00 5.03 F
2536 3837 1.295746 GGAAAGGTCTCGGGGACAC 59.704 63.158 10.69 0.00 46.16 3.67 F
3492 4799 1.080025 AAGTTCTACAGGACGGCGC 60.080 57.895 6.90 0.00 0.00 6.53 F
3765 5074 1.626654 AAAGCGTGCGGAGAATGTCG 61.627 55.000 0.00 0.00 0.00 4.35 F
5349 6716 1.200092 AGAGCTGCTGGAGAGGCTTT 61.200 55.000 7.01 0.00 35.01 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 3385 1.279496 TGTTGCCTGCACTCCTATCT 58.721 50.000 0.00 0.00 0.00 1.98 R
2418 3719 1.284408 GGATTCGCCGCACAAAACA 59.716 52.632 0.00 0.00 0.00 2.83 R
3492 4799 1.434555 TACAACATTGCGGGTCGAAG 58.565 50.000 0.00 0.00 0.00 3.79 R
3998 5307 0.257039 CATAGGCCCCTGCTCTGTTT 59.743 55.000 0.00 0.00 37.74 2.83 R
5338 6705 1.133513 TGAAAGCCAAAAGCCTCTCCA 60.134 47.619 0.00 0.00 45.47 3.86 R
5739 7115 0.318441 TGCTTCAGGTGACTCGAAGG 59.682 55.000 13.58 0.77 41.67 3.46 R
6200 7585 0.325296 ATGAGGGGCTACACGAGGAA 60.325 55.000 0.00 0.00 0.00 3.36 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
104 105 9.860650 TTGGTTGAGGTATATAATAAGCATTGT 57.139 29.630 0.00 0.00 0.00 2.71
205 206 0.529378 GGGCCTGCATGTCTTTTCAG 59.471 55.000 0.84 0.00 0.00 3.02
256 257 6.952358 TCTACTGGTCAGGTCACTACTAATTT 59.048 38.462 2.87 0.00 0.00 1.82
448 449 4.328169 GGTAAAGCTTCATTGCATTTCAGC 59.672 41.667 0.00 0.00 34.99 4.26
561 562 3.019564 GCAGCCAGGTCAGTTGAATTAT 58.980 45.455 0.00 0.00 0.00 1.28
666 668 8.630917 TGAAGTTAACCTACTCATACTCATAGC 58.369 37.037 0.88 0.00 0.00 2.97
667 669 8.534954 AAGTTAACCTACTCATACTCATAGCA 57.465 34.615 0.88 0.00 0.00 3.49
883 2136 4.686972 TCTAGATCTTTCCATGCAGTTCG 58.313 43.478 0.00 0.00 0.00 3.95
923 2176 6.593770 ACAAGTTTGAAGTTTCCATTTGTTCC 59.406 34.615 0.00 0.00 0.00 3.62
1086 2373 2.034607 CCGGAAAAGAAAACGGCCA 58.965 52.632 2.24 0.00 39.85 5.36
1117 2404 7.876582 AGGTCTGTATCTTTTACAGGTGTAAAC 59.123 37.037 13.61 5.11 46.48 2.01
1166 2453 5.065914 GCCCTAATATTGTGAGATGAGCAA 58.934 41.667 0.00 0.00 0.00 3.91
1258 2545 9.971922 TCTCTTTTCTTGAATCCAAAAGAAATC 57.028 29.630 10.42 0.00 46.36 2.17
1543 2843 0.106066 CATGGGGGCTTTGGCTATGA 60.106 55.000 0.00 0.00 38.73 2.15
1864 3165 1.381327 TCAAGGGGGAGGTAGCTCG 60.381 63.158 15.43 1.18 0.00 5.03
2034 3335 3.122480 ACCTGGTGGTGGAATGATGATA 58.878 45.455 0.00 0.00 46.51 2.15
2043 3344 5.608015 TGGTGGAATGATGATATCCAGAAGA 59.392 40.000 0.00 0.00 43.59 2.87
2074 3375 5.862845 AGAGAAGAAAGATTGCTTCAGACA 58.137 37.500 14.37 0.00 42.21 3.41
2084 3385 6.136857 AGATTGCTTCAGACACCTATACCTA 58.863 40.000 0.00 0.00 0.00 3.08
2110 3411 2.548875 GAGTGCAGGCAACATAGAGAG 58.451 52.381 0.00 0.00 41.41 3.20
2370 3671 4.263905 ACAAGCTGTTCAATGGGGAGAATA 60.264 41.667 0.00 0.00 0.00 1.75
2413 3714 2.632996 ACGACTCCTTTGATGAGACCAA 59.367 45.455 0.00 0.00 33.95 3.67
2418 3719 4.202503 ACTCCTTTGATGAGACCAACATGT 60.203 41.667 0.00 0.00 33.95 3.21
2463 3764 2.834549 TCTGAGGTCAAGGAGGCTTTAG 59.165 50.000 0.00 0.00 0.00 1.85
2536 3837 1.295746 GGAAAGGTCTCGGGGACAC 59.704 63.158 10.69 0.00 46.16 3.67
3012 4314 3.251487 TCGAACAAGTGATGTCGACACTA 59.749 43.478 22.71 10.10 46.01 2.74
3261 4565 2.760634 AACCGAGTACATGATGTGCA 57.239 45.000 15.78 0.00 35.34 4.57
3367 4674 1.380785 CAATGCTGCAGGGGGATGT 60.381 57.895 17.12 0.00 0.00 3.06
3492 4799 1.080025 AAGTTCTACAGGACGGCGC 60.080 57.895 6.90 0.00 0.00 6.53
3642 4951 9.859152 TCTGGAATGATGATATACGAGATAGAT 57.141 33.333 0.00 0.00 0.00 1.98
3765 5074 1.626654 AAAGCGTGCGGAGAATGTCG 61.627 55.000 0.00 0.00 0.00 4.35
3857 5166 3.969976 TCACCAAAGAGCTAGCTATGGAT 59.030 43.478 33.71 21.79 32.26 3.41
3935 5244 4.362677 TCTTATGGGTTTCACCTCTAGCT 58.637 43.478 0.00 0.00 38.64 3.32
3988 5297 5.109210 TGTTGTTGTTGTTGTTGTTGTTGA 58.891 33.333 0.00 0.00 0.00 3.18
3989 5298 5.755375 TGTTGTTGTTGTTGTTGTTGTTGAT 59.245 32.000 0.00 0.00 0.00 2.57
3990 5299 6.074088 TGTTGTTGTTGTTGTTGTTGTTGATC 60.074 34.615 0.00 0.00 0.00 2.92
3991 5300 5.532557 TGTTGTTGTTGTTGTTGTTGATCA 58.467 33.333 0.00 0.00 0.00 2.92
3992 5301 5.985530 TGTTGTTGTTGTTGTTGTTGATCAA 59.014 32.000 3.38 3.38 0.00 2.57
3993 5302 6.479990 TGTTGTTGTTGTTGTTGTTGATCAAA 59.520 30.769 10.35 0.00 37.81 2.69
3994 5303 7.011389 TGTTGTTGTTGTTGTTGTTGATCAAAA 59.989 29.630 10.35 0.76 37.81 2.44
3995 5304 7.664082 TGTTGTTGTTGTTGTTGATCAAAAT 57.336 28.000 10.35 0.00 37.81 1.82
3996 5305 7.516481 TGTTGTTGTTGTTGTTGATCAAAATG 58.484 30.769 10.35 0.00 37.81 2.32
3997 5306 7.386025 TGTTGTTGTTGTTGTTGATCAAAATGA 59.614 29.630 10.35 0.00 37.81 2.57
3998 5307 7.895975 TGTTGTTGTTGTTGATCAAAATGAA 57.104 28.000 10.35 0.00 37.81 2.57
3999 5308 8.315391 TGTTGTTGTTGTTGATCAAAATGAAA 57.685 26.923 10.35 0.00 37.81 2.69
4000 5309 8.777413 TGTTGTTGTTGTTGATCAAAATGAAAA 58.223 25.926 10.35 0.00 37.81 2.29
4001 5310 9.049974 GTTGTTGTTGTTGATCAAAATGAAAAC 57.950 29.630 10.35 10.53 37.81 2.43
4002 5311 8.315391 TGTTGTTGTTGATCAAAATGAAAACA 57.685 26.923 10.35 12.75 36.13 2.83
4003 5312 8.441608 TGTTGTTGTTGATCAAAATGAAAACAG 58.558 29.630 10.35 0.00 37.88 3.16
4004 5313 8.655092 GTTGTTGTTGATCAAAATGAAAACAGA 58.345 29.630 10.35 3.96 37.88 3.41
4005 5314 8.410030 TGTTGTTGATCAAAATGAAAACAGAG 57.590 30.769 10.35 0.00 37.88 3.35
4020 5329 1.768077 AGAGCAGGGGCCTATGGTC 60.768 63.158 24.52 24.52 42.77 4.02
4539 5875 5.831702 ATCTGATCAATGCTTTGGACTTC 57.168 39.130 11.99 5.78 33.44 3.01
4563 5899 2.198827 TGCACCAGGACAACTAATGG 57.801 50.000 0.00 0.00 38.83 3.16
4774 6113 7.608761 ACTGAAAAGTACTCAGGTGTTTTTGTA 59.391 33.333 13.43 0.00 43.88 2.41
4775 6114 8.338072 TGAAAAGTACTCAGGTGTTTTTGTAA 57.662 30.769 0.00 0.00 0.00 2.41
4776 6115 8.794553 TGAAAAGTACTCAGGTGTTTTTGTAAA 58.205 29.630 0.00 0.00 0.00 2.01
4777 6116 9.628746 GAAAAGTACTCAGGTGTTTTTGTAAAA 57.371 29.630 0.00 0.00 0.00 1.52
4778 6117 9.984190 AAAAGTACTCAGGTGTTTTTGTAAAAA 57.016 25.926 0.00 0.00 35.67 1.94
4780 6119 9.797556 AAGTACTCAGGTGTTTTTGTAAAAATC 57.202 29.630 0.00 3.61 39.75 2.17
4781 6120 9.185680 AGTACTCAGGTGTTTTTGTAAAAATCT 57.814 29.630 5.88 2.88 39.75 2.40
4782 6121 9.797556 GTACTCAGGTGTTTTTGTAAAAATCTT 57.202 29.630 5.88 0.00 39.75 2.40
4783 6122 8.926715 ACTCAGGTGTTTTTGTAAAAATCTTC 57.073 30.769 5.88 0.00 39.75 2.87
5053 6417 3.701205 ATGGGATATCATAGTTGCGCA 57.299 42.857 5.66 5.66 0.00 6.09
5112 6476 4.911514 ACGTTAATGCATAAATGGGTCC 57.088 40.909 0.00 0.00 0.00 4.46
5251 6618 4.408182 AAGTAATGCTTAGCGACCATCT 57.592 40.909 0.00 0.00 35.27 2.90
5252 6619 3.722147 AGTAATGCTTAGCGACCATCTG 58.278 45.455 0.00 0.00 0.00 2.90
5338 6705 3.129792 GTAGCGAAACAGAGCTGCT 57.870 52.632 0.00 0.00 44.32 4.24
5349 6716 1.200092 AGAGCTGCTGGAGAGGCTTT 61.200 55.000 7.01 0.00 35.01 3.51
5402 6769 4.695455 CGAATATCATATTTGCGGAAGGGT 59.305 41.667 0.00 0.00 0.00 4.34
5547 6914 2.228822 AGCAGGTATTCGTTTTGCCAAG 59.771 45.455 0.00 0.00 35.44 3.61
5560 6929 5.957796 CGTTTTGCCAAGTTAATCGACTATC 59.042 40.000 0.00 0.00 0.00 2.08
5563 6934 4.945246 TGCCAAGTTAATCGACTATCCTC 58.055 43.478 0.00 0.00 0.00 3.71
5572 6943 2.595238 TCGACTATCCTCCCTTTAGCC 58.405 52.381 0.00 0.00 0.00 3.93
5574 6945 2.297597 CGACTATCCTCCCTTTAGCCAG 59.702 54.545 0.00 0.00 0.00 4.85
5755 7131 1.118965 TGCCCTTCGAGTCACCTGAA 61.119 55.000 0.00 0.00 0.00 3.02
5757 7133 0.390472 CCCTTCGAGTCACCTGAAGC 60.390 60.000 1.81 0.00 38.19 3.86
5818 7194 2.738213 AAAGGCACAGGCTGTCGAGG 62.738 60.000 19.13 7.82 38.81 4.63
5948 7330 1.080907 TCCCCTCTGGATGCTGACA 59.919 57.895 0.00 0.00 38.61 3.58
5971 7353 3.398406 TGACAGTGAATCGCTTTGCTTA 58.602 40.909 0.00 0.00 0.00 3.09
5974 7356 3.062639 ACAGTGAATCGCTTTGCTTATCG 59.937 43.478 0.00 0.00 0.00 2.92
5975 7357 3.062639 CAGTGAATCGCTTTGCTTATCGT 59.937 43.478 0.00 0.00 0.00 3.73
6026 7408 0.529337 CATAGTGCTGCAGAGGTCGG 60.529 60.000 20.43 0.00 0.00 4.79
6028 7410 4.687215 GTGCTGCAGAGGTCGGCA 62.687 66.667 20.43 3.74 44.34 5.69
6089 7471 2.464582 GGACTCCCCAGTTCCAAGT 58.535 57.895 0.00 0.00 30.63 3.16
6090 7472 0.036875 GGACTCCCCAGTTCCAAGTG 59.963 60.000 0.00 0.00 30.63 3.16
6091 7473 0.765510 GACTCCCCAGTTCCAAGTGT 59.234 55.000 0.00 0.00 30.63 3.55
6092 7474 1.143073 GACTCCCCAGTTCCAAGTGTT 59.857 52.381 0.00 0.00 30.63 3.32
6093 7475 2.370849 GACTCCCCAGTTCCAAGTGTTA 59.629 50.000 0.00 0.00 30.63 2.41
6096 7478 2.714250 TCCCCAGTTCCAAGTGTTACAT 59.286 45.455 0.00 0.00 0.00 2.29
6107 7489 5.071788 TCCAAGTGTTACATCCAGTTCTTCT 59.928 40.000 0.00 0.00 0.00 2.85
6132 7514 1.961277 GCAGTAGTGTGCGCCTGTT 60.961 57.895 4.18 0.00 32.74 3.16
6134 7516 0.880278 CAGTAGTGTGCGCCTGTTGT 60.880 55.000 4.18 0.00 0.00 3.32
6142 7524 1.725164 GTGCGCCTGTTGTTAGTAGAC 59.275 52.381 4.18 0.00 0.00 2.59
6170 7555 0.032952 TAGTCTGCGGCGAAACAAGT 59.967 50.000 12.98 0.00 0.00 3.16
6212 7597 1.993370 GTGACATGTTCCTCGTGTAGC 59.007 52.381 0.00 0.00 45.10 3.58
6225 7610 2.174210 TCGTGTAGCCCCTCATAGTACT 59.826 50.000 0.00 0.00 0.00 2.73
6226 7611 2.293677 CGTGTAGCCCCTCATAGTACTG 59.706 54.545 5.39 0.00 0.00 2.74
6227 7612 2.036089 GTGTAGCCCCTCATAGTACTGC 59.964 54.545 5.39 0.00 0.00 4.40
6228 7613 2.091278 TGTAGCCCCTCATAGTACTGCT 60.091 50.000 5.39 6.25 0.00 4.24
6229 7614 3.139584 TGTAGCCCCTCATAGTACTGCTA 59.860 47.826 5.39 5.20 0.00 3.49
6230 7615 2.883026 AGCCCCTCATAGTACTGCTAG 58.117 52.381 5.39 0.00 32.45 3.42
6242 7627 5.041191 AGTACTGCTAGGCAATAAAGCAT 57.959 39.130 0.00 0.00 44.69 3.79
6255 7640 9.236006 AGGCAATAAAGCATATATCGAGATTTT 57.764 29.630 0.00 0.00 35.83 1.82
6283 7669 2.371841 TGATAAATACTCCGCCATGGCT 59.628 45.455 33.07 17.87 39.32 4.75
6345 7731 3.025262 ACCGCCAACTTAACTGGAAAAA 58.975 40.909 3.43 0.00 35.85 1.94
6375 7761 1.729881 CCAAGGCATAGCTTTCGGC 59.270 57.895 0.00 0.00 42.19 5.54
6696 8128 2.018086 AGGAGGAGGAGGAGAGGGG 61.018 68.421 0.00 0.00 0.00 4.79
6802 8234 2.005971 CCTCAAGGTGCGTAGTAACC 57.994 55.000 0.00 0.00 36.77 2.85
6803 8235 1.625616 CTCAAGGTGCGTAGTAACCG 58.374 55.000 0.00 0.00 40.51 4.44
6840 8272 1.219124 GATGCTGACGGCTCCTGAA 59.781 57.895 7.96 0.00 42.39 3.02
6853 8285 1.667724 CTCCTGAATTAACTGCGCTGG 59.332 52.381 18.98 9.22 0.00 4.85
6880 8314 0.251165 TGGGTTTCTACAGGCCAAGC 60.251 55.000 5.01 0.00 0.00 4.01
6944 8378 4.791411 GCGCAAGTTTCAGGTACATTTTCA 60.791 41.667 0.30 0.00 41.68 2.69
6945 8379 4.911610 CGCAAGTTTCAGGTACATTTTCAG 59.088 41.667 0.00 0.00 0.00 3.02
6956 8390 4.518970 GGTACATTTTCAGGCTTCTGTTCA 59.481 41.667 0.00 0.00 39.45 3.18
6975 8409 2.438385 AATTGCGTCGTGTGTTCCGC 62.438 55.000 0.00 0.00 45.92 5.54
7021 8455 1.815003 AGGAATGCAGAGCGGAAAAAG 59.185 47.619 0.00 0.00 0.00 2.27
7022 8456 1.812571 GGAATGCAGAGCGGAAAAAGA 59.187 47.619 0.00 0.00 0.00 2.52
7023 8457 2.228822 GGAATGCAGAGCGGAAAAAGAA 59.771 45.455 0.00 0.00 0.00 2.52
7024 8458 3.496155 GAATGCAGAGCGGAAAAAGAAG 58.504 45.455 0.00 0.00 0.00 2.85
7027 8461 2.549754 TGCAGAGCGGAAAAAGAAGAAG 59.450 45.455 0.00 0.00 0.00 2.85
7053 8487 5.649970 TTTTCCCTCTGGTAGTTTGGTTA 57.350 39.130 0.00 0.00 0.00 2.85
7058 8492 5.073965 TCCCTCTGGTAGTTTGGTTACATTT 59.926 40.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
256 257 1.106944 TGACGAGACTGGTGCTGACA 61.107 55.000 0.00 0.00 0.00 3.58
491 492 2.618053 CCACGATAAACCTGTCACCTC 58.382 52.381 0.00 0.00 0.00 3.85
561 562 3.307410 CCTGTACCTAAACAGTGCCATGA 60.307 47.826 0.00 0.00 44.45 3.07
666 668 6.615088 ACTAGTCAAAATGCAAAGCTACATG 58.385 36.000 0.00 0.00 0.00 3.21
667 669 6.824305 ACTAGTCAAAATGCAAAGCTACAT 57.176 33.333 0.00 0.00 0.00 2.29
799 2050 8.895932 AAAAATATAGACAGAAAATGCACGAC 57.104 30.769 0.00 0.00 0.00 4.34
883 2136 6.801575 TCAAACTTGTACTTTGGGTCAATTC 58.198 36.000 6.31 0.00 30.78 2.17
1086 2373 7.607991 CACCTGTAAAAGATACAGACCTCAATT 59.392 37.037 15.31 0.00 45.69 2.32
1117 2404 1.523515 TCGATTGTCGTTTTCCACACG 59.476 47.619 0.00 0.00 41.35 4.49
1136 2423 5.869579 TCTCACAATATTAGGGCCTGATTC 58.130 41.667 18.53 0.00 0.00 2.52
1543 2843 5.486775 TCTTCTCCTTCTTGATTCCTGATGT 59.513 40.000 0.00 0.00 0.00 3.06
1864 3165 2.269241 CCCTCTCCTTGAACGCCC 59.731 66.667 0.00 0.00 0.00 6.13
2034 3335 7.411486 TCTTCTCTTTAATCGTCTTCTGGAT 57.589 36.000 0.00 0.00 0.00 3.41
2043 3344 7.913674 AGCAATCTTTCTTCTCTTTAATCGT 57.086 32.000 0.00 0.00 0.00 3.73
2074 3375 5.281297 CCTGCACTCCTATCTAGGTATAGGT 60.281 48.000 14.27 0.00 45.98 3.08
2084 3385 1.279496 TGTTGCCTGCACTCCTATCT 58.721 50.000 0.00 0.00 0.00 1.98
2098 3399 5.053145 CCATCTTGTACCTCTCTATGTTGC 58.947 45.833 0.00 0.00 0.00 4.17
2110 3411 2.280628 CCTTCTTCGCCATCTTGTACC 58.719 52.381 0.00 0.00 0.00 3.34
2312 3613 4.322273 CGCCATCTATGCTTAATCTCCTCA 60.322 45.833 0.00 0.00 0.00 3.86
2413 3714 1.299014 CGCCGCACAAAACACATGT 60.299 52.632 0.00 0.00 0.00 3.21
2418 3719 1.284408 GGATTCGCCGCACAAAACA 59.716 52.632 0.00 0.00 0.00 2.83
2463 3764 2.757314 CCTTGCCTCCTTTCATCCTTTC 59.243 50.000 0.00 0.00 0.00 2.62
2536 3837 3.660501 TGGTTAGCCATACTATCGCTG 57.339 47.619 0.00 0.00 40.46 5.18
3012 4314 6.555360 AGTCCTATCTTAATCGGGAAGTCATT 59.445 38.462 0.00 0.00 0.00 2.57
3261 4565 5.711036 CCTCACACCTAGTAGTACTGAAACT 59.289 44.000 13.29 3.69 0.00 2.66
3367 4674 5.192927 GGTTCACATCTTCATCAATACCCA 58.807 41.667 0.00 0.00 0.00 4.51
3492 4799 1.434555 TACAACATTGCGGGTCGAAG 58.565 50.000 0.00 0.00 0.00 3.79
3642 4951 2.685106 TCAATTGGTGCTACCCCAAA 57.315 45.000 5.42 0.00 44.70 3.28
3765 5074 1.829096 GTCTACCCCGCCCTCTCTC 60.829 68.421 0.00 0.00 0.00 3.20
3857 5166 2.221299 AAGCTTCCACGCACCCCTA 61.221 57.895 0.00 0.00 0.00 3.53
3988 5297 4.020839 CCCCTGCTCTGTTTTCATTTTGAT 60.021 41.667 0.00 0.00 0.00 2.57
3989 5298 3.321682 CCCCTGCTCTGTTTTCATTTTGA 59.678 43.478 0.00 0.00 0.00 2.69
3990 5299 3.656559 CCCCTGCTCTGTTTTCATTTTG 58.343 45.455 0.00 0.00 0.00 2.44
3991 5300 2.037641 GCCCCTGCTCTGTTTTCATTTT 59.962 45.455 0.00 0.00 33.53 1.82
3992 5301 1.620323 GCCCCTGCTCTGTTTTCATTT 59.380 47.619 0.00 0.00 33.53 2.32
3993 5302 1.260544 GCCCCTGCTCTGTTTTCATT 58.739 50.000 0.00 0.00 33.53 2.57
3994 5303 0.613012 GGCCCCTGCTCTGTTTTCAT 60.613 55.000 0.00 0.00 37.74 2.57
3995 5304 1.228552 GGCCCCTGCTCTGTTTTCA 60.229 57.895 0.00 0.00 37.74 2.69
3996 5305 0.328258 TAGGCCCCTGCTCTGTTTTC 59.672 55.000 0.00 0.00 37.74 2.29
3997 5306 1.002857 ATAGGCCCCTGCTCTGTTTT 58.997 50.000 0.00 0.00 37.74 2.43
3998 5307 0.257039 CATAGGCCCCTGCTCTGTTT 59.743 55.000 0.00 0.00 37.74 2.83
3999 5308 1.639635 CCATAGGCCCCTGCTCTGTT 61.640 60.000 0.00 0.00 37.74 3.16
4000 5309 2.074948 CCATAGGCCCCTGCTCTGT 61.075 63.158 0.00 0.00 37.74 3.41
4001 5310 2.049627 GACCATAGGCCCCTGCTCTG 62.050 65.000 0.00 0.00 37.74 3.35
4002 5311 1.768077 GACCATAGGCCCCTGCTCT 60.768 63.158 0.00 0.00 37.74 4.09
4003 5312 1.635817 TTGACCATAGGCCCCTGCTC 61.636 60.000 0.00 0.00 37.74 4.26
4004 5313 1.214305 TTTGACCATAGGCCCCTGCT 61.214 55.000 0.00 0.00 37.74 4.24
4005 5314 0.324275 TTTTGACCATAGGCCCCTGC 60.324 55.000 0.00 0.00 0.00 4.85
4471 5805 6.474140 TTGCATATGCCAATCAGAAAGAAT 57.526 33.333 24.54 0.00 41.18 2.40
4539 5875 1.331214 AGTTGTCCTGGTGCAATTGG 58.669 50.000 7.72 0.00 0.00 3.16
4563 5899 3.408634 ACCTACAACATACCACAGCAAC 58.591 45.455 0.00 0.00 0.00 4.17
5019 6383 5.654209 TGATATCCCATAAGATCAGTCCTCG 59.346 44.000 0.00 0.00 0.00 4.63
5053 6417 3.568007 TGCGGATTTCTTTAGCACTTGTT 59.432 39.130 0.00 0.00 32.43 2.83
5112 6476 5.821470 ACTGATCATATGAAAGCAGACTTGG 59.179 40.000 26.84 11.03 35.85 3.61
5172 6539 2.981784 AGCTGGCCTTGGATATCATGTA 59.018 45.455 3.32 0.00 0.00 2.29
5251 6618 1.951209 TCCACCAGGAGAATACTGCA 58.049 50.000 0.00 0.00 39.61 4.41
5338 6705 1.133513 TGAAAGCCAAAAGCCTCTCCA 60.134 47.619 0.00 0.00 45.47 3.86
5349 6716 1.481772 AGCAGCAAAAGTGAAAGCCAA 59.518 42.857 0.00 0.00 0.00 4.52
5402 6769 2.028476 CCACCGGTTGTCATTAGAGACA 60.028 50.000 2.97 0.00 46.12 3.41
5547 6914 6.157904 GCTAAAGGGAGGATAGTCGATTAAC 58.842 44.000 0.00 0.00 0.00 2.01
5560 6929 2.437413 GTGAAACTGGCTAAAGGGAGG 58.563 52.381 0.00 0.00 0.00 4.30
5574 6945 6.877611 TTTATGTCCTTTCAGGAGTGAAAC 57.122 37.500 0.00 0.00 46.90 2.78
5739 7115 0.318441 TGCTTCAGGTGACTCGAAGG 59.682 55.000 13.58 0.77 41.67 3.46
5755 7131 4.711949 CTCCCGCACAAGGCTGCT 62.712 66.667 0.00 0.00 41.67 4.24
5770 7146 1.067582 CGTATCAGGAACCCCGCTC 59.932 63.158 0.00 0.00 37.58 5.03
5778 7154 0.325296 AGCTGGGACCGTATCAGGAA 60.325 55.000 0.00 0.00 34.73 3.36
5784 7160 0.541863 CCTTTCAGCTGGGACCGTAT 59.458 55.000 15.13 0.00 0.00 3.06
5909 7285 2.471255 CCGTCATGGTGAAGAAGGC 58.529 57.895 0.00 0.00 0.00 4.35
5948 7330 2.816087 AGCAAAGCGATTCACTGTCATT 59.184 40.909 0.00 0.00 0.00 2.57
5974 7356 0.818040 AAAGTGGAACGGCAGGTGAC 60.818 55.000 0.00 0.00 45.86 3.67
5975 7357 0.817634 CAAAGTGGAACGGCAGGTGA 60.818 55.000 0.00 0.00 45.86 4.02
6028 7410 4.070552 GAGAGCAGGAACGCCGGT 62.071 66.667 1.90 0.00 39.96 5.28
6083 7465 4.974645 AGAACTGGATGTAACACTTGGA 57.025 40.909 0.00 0.00 0.00 3.53
6084 7466 5.308825 AGAAGAACTGGATGTAACACTTGG 58.691 41.667 0.00 0.00 0.00 3.61
6085 7467 6.073003 GGAAGAAGAACTGGATGTAACACTTG 60.073 42.308 0.00 0.00 0.00 3.16
6086 7468 5.998363 GGAAGAAGAACTGGATGTAACACTT 59.002 40.000 0.00 0.00 0.00 3.16
6087 7469 5.308237 AGGAAGAAGAACTGGATGTAACACT 59.692 40.000 0.00 0.00 0.00 3.55
6088 7470 5.552178 AGGAAGAAGAACTGGATGTAACAC 58.448 41.667 0.00 0.00 0.00 3.32
6089 7471 5.825593 AGGAAGAAGAACTGGATGTAACA 57.174 39.130 0.00 0.00 0.00 2.41
6090 7472 6.568653 GCAAAGGAAGAAGAACTGGATGTAAC 60.569 42.308 0.00 0.00 0.00 2.50
6091 7473 5.473504 GCAAAGGAAGAAGAACTGGATGTAA 59.526 40.000 0.00 0.00 0.00 2.41
6092 7474 5.003804 GCAAAGGAAGAAGAACTGGATGTA 58.996 41.667 0.00 0.00 0.00 2.29
6093 7475 3.823304 GCAAAGGAAGAAGAACTGGATGT 59.177 43.478 0.00 0.00 0.00 3.06
6096 7478 3.117888 ACTGCAAAGGAAGAAGAACTGGA 60.118 43.478 0.00 0.00 0.00 3.86
6107 7489 1.225855 CGCACACTACTGCAAAGGAA 58.774 50.000 0.00 0.00 36.94 3.36
6132 7514 3.504906 ACTACAAGCAGCGTCTACTAACA 59.495 43.478 0.00 0.00 0.00 2.41
6134 7516 4.008330 AGACTACAAGCAGCGTCTACTAA 58.992 43.478 0.00 0.00 35.15 2.24
6142 7524 2.447887 CCGCAGACTACAAGCAGCG 61.448 63.158 0.00 0.00 44.24 5.18
6170 7555 7.604927 GTCACCATACTGTTACTTAAATCCACA 59.395 37.037 0.00 0.00 0.00 4.17
6200 7585 0.325296 ATGAGGGGCTACACGAGGAA 60.325 55.000 0.00 0.00 0.00 3.36
6212 7597 1.896465 GCCTAGCAGTACTATGAGGGG 59.104 57.143 14.72 6.41 0.00 4.79
6226 7611 6.980978 TCTCGATATATGCTTTATTGCCTAGC 59.019 38.462 0.00 0.00 35.50 3.42
6227 7612 9.539825 AATCTCGATATATGCTTTATTGCCTAG 57.460 33.333 0.00 0.00 0.00 3.02
6228 7613 9.890629 AAATCTCGATATATGCTTTATTGCCTA 57.109 29.630 0.00 0.00 0.00 3.93
6229 7614 8.798859 AAATCTCGATATATGCTTTATTGCCT 57.201 30.769 0.00 0.00 0.00 4.75
6230 7615 9.846248 AAAAATCTCGATATATGCTTTATTGCC 57.154 29.630 0.00 0.00 0.00 4.52
6255 7640 7.390440 CCATGGCGGAGTATTTATCATAAGAAA 59.610 37.037 0.00 0.00 36.56 2.52
6295 7681 4.424711 AATGACGGGGGCGTGCAT 62.425 61.111 0.00 0.00 0.00 3.96
6298 7684 4.096003 AGGAATGACGGGGGCGTG 62.096 66.667 0.00 0.00 0.00 5.34
6299 7685 3.782443 GAGGAATGACGGGGGCGT 61.782 66.667 0.00 0.00 0.00 5.68
6300 7686 4.891727 CGAGGAATGACGGGGGCG 62.892 72.222 0.00 0.00 0.00 6.13
6301 7687 3.467226 TCGAGGAATGACGGGGGC 61.467 66.667 0.00 0.00 0.00 5.80
6302 7688 2.499685 GTCGAGGAATGACGGGGG 59.500 66.667 0.00 0.00 0.00 5.40
6307 7693 1.810030 GTGGCCGTCGAGGAATGAC 60.810 63.158 6.70 0.00 45.00 3.06
6308 7694 2.577059 GTGGCCGTCGAGGAATGA 59.423 61.111 6.70 0.00 45.00 2.57
6375 7761 2.459934 GCAAAACAGAAAGTTCCCGTG 58.540 47.619 0.00 0.00 40.26 4.94
6556 7970 1.523938 GTAGCTAGGGCAAAGGGCG 60.524 63.158 0.00 0.00 46.16 6.13
6683 8115 2.445654 CAGCCCCCTCTCCTCCTC 60.446 72.222 0.00 0.00 0.00 3.71
6684 8116 4.814041 GCAGCCCCCTCTCCTCCT 62.814 72.222 0.00 0.00 0.00 3.69
6696 8128 2.109126 GTCCTTCACCATCGCAGCC 61.109 63.158 0.00 0.00 0.00 4.85
6797 8229 2.128035 CGCTCATCAAGGATCGGTTAC 58.872 52.381 0.00 0.00 0.00 2.50
6799 8231 0.824109 TCGCTCATCAAGGATCGGTT 59.176 50.000 0.00 0.00 0.00 4.44
6801 8233 1.707632 GATCGCTCATCAAGGATCGG 58.292 55.000 0.00 0.00 0.00 4.18
6802 8234 1.334994 CGATCGCTCATCAAGGATCG 58.665 55.000 0.26 7.72 42.88 3.69
6803 8235 1.270826 TCCGATCGCTCATCAAGGATC 59.729 52.381 10.32 0.00 32.57 3.36
6840 8272 0.744414 ACATCGCCAGCGCAGTTAAT 60.744 50.000 11.47 0.00 39.59 1.40
6853 8285 2.161609 CCTGTAGAAACCCAAACATCGC 59.838 50.000 0.00 0.00 0.00 4.58
6880 8314 3.467803 GATTCTTATCCGGGTGAACCAG 58.532 50.000 0.00 0.00 40.22 4.00
6944 8378 1.537202 GACGCAATTGAACAGAAGCCT 59.463 47.619 10.34 0.00 0.00 4.58
6945 8379 1.725931 CGACGCAATTGAACAGAAGCC 60.726 52.381 10.34 0.00 0.00 4.35
6956 8390 1.567537 CGGAACACACGACGCAATT 59.432 52.632 0.00 0.00 0.00 2.32
6979 8413 3.458118 TGAATCCAGTAACAGGGGTATGG 59.542 47.826 0.00 0.00 0.00 2.74
6981 8415 3.716872 CCTGAATCCAGTAACAGGGGTAT 59.283 47.826 0.00 0.00 44.04 2.73
7021 8455 5.172687 ACCAGAGGGAAAATCTCTTCTTC 57.827 43.478 0.00 0.00 39.36 2.87
7022 8456 5.788014 ACTACCAGAGGGAAAATCTCTTCTT 59.212 40.000 0.00 0.00 39.36 2.52
7023 8457 5.346270 ACTACCAGAGGGAAAATCTCTTCT 58.654 41.667 0.00 0.00 39.36 2.85
7024 8458 5.685520 ACTACCAGAGGGAAAATCTCTTC 57.314 43.478 0.00 0.00 39.36 2.87
7027 8461 4.944317 CCAAACTACCAGAGGGAAAATCTC 59.056 45.833 0.00 0.00 38.05 2.75


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

AutoCloner maintained by Alex Coulton.