Multiple sequence alignment - TraesCS3B01G420600

Loading Multiple Alignment...

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 TraesCS3B01G420600 chr3B 100.000 4079 0 0 1 4079 657652689 657648611 0.000000e+00 7533
1 TraesCS3B01G420600 chr3B 91.184 760 66 1 1 760 714521268 714520510 0.000000e+00 1031
2 TraesCS3B01G420600 chr3B 84.539 401 34 10 3181 3574 811123691 811124070 4.980000e-99 372
3 TraesCS3B01G420600 chr3B 85.915 284 25 7 3185 3461 727505627 727505352 5.160000e-74 289
4 TraesCS3B01G420600 chr3B 85.769 260 24 6 3243 3495 798486856 798486603 3.130000e-66 263
5 TraesCS3B01G420600 chr3A 90.912 3367 155 56 760 4079 637109860 637113122 0.000000e+00 4383
6 TraesCS3B01G420600 chr3D 93.361 2380 100 30 1722 4079 497603466 497601123 0.000000e+00 3467
7 TraesCS3B01G420600 chr3D 91.173 929 34 16 760 1660 497604394 497603486 0.000000e+00 1218
8 TraesCS3B01G420600 chr3D 90.933 761 66 3 1 759 610719747 610720506 0.000000e+00 1020
9 TraesCS3B01G420600 chr3D 90.670 761 66 5 1 759 500603934 500603177 0.000000e+00 1007
10 TraesCS3B01G420600 chr3D 84.788 401 34 13 3181 3574 40808779 40809159 1.070000e-100 377
11 TraesCS3B01G420600 chr3D 85.385 260 26 6 3243 3495 595030128 595029874 4.040000e-65 259
12 TraesCS3B01G420600 chr6D 92.084 758 56 4 3 759 292036194 292035440 0.000000e+00 1064
13 TraesCS3B01G420600 chr6D 91.207 762 63 4 1 760 67693922 67693163 0.000000e+00 1033
14 TraesCS3B01G420600 chr6D 85.532 470 48 10 3385 3842 77328119 77328580 1.330000e-129 473
15 TraesCS3B01G420600 chr6D 83.600 250 27 6 3185 3428 161304005 161303764 5.310000e-54 222
16 TraesCS3B01G420600 chr6B 92.091 746 56 3 1 745 420700755 420701498 0.000000e+00 1048
17 TraesCS3B01G420600 chr6B 85.386 479 52 11 3390 3854 570079807 570080281 7.930000e-132 481
18 TraesCS3B01G420600 chr6B 84.648 469 56 9 3398 3854 361271724 361271260 1.730000e-123 453
19 TraesCS3B01G420600 chr6B 84.342 479 53 12 3390 3854 308977356 308977826 2.240000e-122 449
20 TraesCS3B01G420600 chr5D 90.980 765 64 5 1 762 526658254 526659016 0.000000e+00 1026
21 TraesCS3B01G420600 chr7D 90.539 761 67 5 1 759 34179483 34178726 0.000000e+00 1002
22 TraesCS3B01G420600 chr5B 90.130 770 66 8 1 764 712176876 712177641 0.000000e+00 992
23 TraesCS3B01G420600 chr5B 86.593 455 47 7 3398 3842 176793543 176793093 1.320000e-134 490
24 TraesCS3B01G420600 chr5B 85.319 470 51 10 3398 3854 204615642 204615178 1.720000e-128 470
25 TraesCS3B01G420600 chr1D 87.049 471 44 9 3385 3842 348124690 348125156 2.170000e-142 516
26 TraesCS3B01G420600 chr1D 83.333 270 29 9 3142 3399 348124373 348124638 6.820000e-58 235
27 TraesCS3B01G420600 chr2D 85.744 484 49 10 3385 3854 244754490 244754967 1.020000e-135 494
28 TraesCS3B01G420600 chr2D 91.818 110 9 0 3183 3292 373852714 373852605 1.960000e-33 154
29 TraesCS3B01G420600 chr1B 86.141 469 49 9 3398 3854 177158825 177159289 3.660000e-135 492
30 TraesCS3B01G420600 chr1B 84.134 479 48 15 3390 3854 192674109 192674573 4.840000e-119 438
31 TraesCS3B01G420600 chr2B 84.760 479 55 10 3390 3854 407886791 407887265 7.990000e-127 464
32 TraesCS3B01G420600 chr5A 84.644 267 29 9 3142 3397 73840993 73841258 5.230000e-64 255
33 TraesCS3B01G420600 chr6A 89.610 154 14 2 3142 3294 568178717 568178565 1.160000e-45 195


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 TraesCS3B01G420600 chr3B 657648611 657652689 4078 True 7533.0 7533 100.000 1 4079 1 chr3B.!!$R1 4078
1 TraesCS3B01G420600 chr3B 714520510 714521268 758 True 1031.0 1031 91.184 1 760 1 chr3B.!!$R2 759
2 TraesCS3B01G420600 chr3A 637109860 637113122 3262 False 4383.0 4383 90.912 760 4079 1 chr3A.!!$F1 3319
3 TraesCS3B01G420600 chr3D 497601123 497604394 3271 True 2342.5 3467 92.267 760 4079 2 chr3D.!!$R3 3319
4 TraesCS3B01G420600 chr3D 610719747 610720506 759 False 1020.0 1020 90.933 1 759 1 chr3D.!!$F2 758
5 TraesCS3B01G420600 chr3D 500603177 500603934 757 True 1007.0 1007 90.670 1 759 1 chr3D.!!$R1 758
6 TraesCS3B01G420600 chr6D 292035440 292036194 754 True 1064.0 1064 92.084 3 759 1 chr6D.!!$R3 756
7 TraesCS3B01G420600 chr6D 67693163 67693922 759 True 1033.0 1033 91.207 1 760 1 chr6D.!!$R1 759
8 TraesCS3B01G420600 chr6B 420700755 420701498 743 False 1048.0 1048 92.091 1 745 1 chr6B.!!$F2 744
9 TraesCS3B01G420600 chr5D 526658254 526659016 762 False 1026.0 1026 90.980 1 762 1 chr5D.!!$F1 761
10 TraesCS3B01G420600 chr7D 34178726 34179483 757 True 1002.0 1002 90.539 1 759 1 chr7D.!!$R1 758
11 TraesCS3B01G420600 chr5B 712176876 712177641 765 False 992.0 992 90.130 1 764 1 chr5B.!!$F1 763
12 TraesCS3B01G420600 chr1D 348124373 348125156 783 False 375.5 516 85.191 3142 3842 2 chr1D.!!$F1 700

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
514 522 0.031043 CCGACCACTACACACAACGA 59.969 55.000 0.0 0.0 0.0 3.85 F
1468 1519 0.100146 CCTACCTCAGTACGTTCGGC 59.900 60.000 0.0 0.0 0.0 5.54 F
1470 1521 1.315257 TACCTCAGTACGTTCGGCCC 61.315 60.000 0.0 0.0 0.0 5.80 F
1777 1836 1.597742 TTCTCTTTGTGTGCTCTGCC 58.402 50.000 0.0 0.0 0.0 4.85 F
2507 2572 1.222936 GTGCCTCATCCTCCACCTG 59.777 63.158 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1537 0.336737 GAGGAACAGAGAGAGGGGGA 59.663 60.0 0.00 0.0 0.0 4.81 R
2303 2368 0.393537 CAGATGGTGGGGACTTCAGC 60.394 60.0 0.00 0.0 0.0 4.26 R
2507 2572 0.468226 TGACCTGATACGCCCCAATC 59.532 55.0 0.00 0.0 0.0 2.67 R
2592 2657 0.888285 AGTTCAGCTGCAAGGCTCAC 60.888 55.0 9.47 0.0 41.0 3.51 R
3858 4016 0.036164 CTGTGTCCGGGGTTTGATCA 59.964 55.0 0.00 0.0 0.0 2.92 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
32 33 3.151554 TCCCGTATGTATATGCACGAGT 58.848 45.455 5.57 0.00 36.53 4.18
87 88 1.694169 CATGACCCTAGCCCACCCT 60.694 63.158 0.00 0.00 0.00 4.34
121 122 4.189231 CGGTTTCCCAATCGAAATAGTCT 58.811 43.478 0.00 0.00 38.98 3.24
132 133 1.141053 GAAATAGTCTGCGGGGGTGAT 59.859 52.381 0.00 0.00 0.00 3.06
162 163 1.084289 CCGGAAAATGAGTTCGACCC 58.916 55.000 0.00 0.00 0.00 4.46
286 288 1.202651 CGGGTGAGTGGAGAAACAAGT 60.203 52.381 0.00 0.00 0.00 3.16
301 304 1.336609 ACAAGTAGGGACGAAGAACGC 60.337 52.381 0.00 0.00 46.94 4.84
377 382 2.660552 CCGCCGTCGAACACAACT 60.661 61.111 0.00 0.00 38.10 3.16
498 506 0.945265 ACGAAATTCGAAACCGCCGA 60.945 50.000 22.92 0.00 43.74 5.54
506 514 1.005867 GAAACCGCCGACCACTACA 60.006 57.895 0.00 0.00 0.00 2.74
510 518 2.337170 CGCCGACCACTACACACA 59.663 61.111 0.00 0.00 0.00 3.72
514 522 0.031043 CCGACCACTACACACAACGA 59.969 55.000 0.00 0.00 0.00 3.85
562 570 2.103771 CTCTATGACATGTGGGTCCCAG 59.896 54.545 12.21 1.83 36.97 4.45
582 590 1.146358 AAGAGGTTTATCTCGCGCGC 61.146 55.000 27.95 23.91 38.71 6.86
603 611 4.812476 CGGCGCAATCGGACCAGA 62.812 66.667 10.83 0.00 35.95 3.86
852 861 1.334160 TTTACAGGTCAGAGTGCCGA 58.666 50.000 0.00 0.00 0.00 5.54
862 871 1.043816 AGAGTGCCGACCCTATCATG 58.956 55.000 0.00 0.00 0.00 3.07
885 899 2.269529 CGCCGGTTTAAAGCCCCAA 61.270 57.895 11.61 0.00 0.00 4.12
945 964 0.616371 CCGTCCTGGTGGGTTCATTA 59.384 55.000 0.00 0.00 36.25 1.90
1148 1194 4.771360 GTTTGTTTAACGGCTTTAGCGTA 58.229 39.130 0.00 0.00 43.26 4.42
1154 1200 0.730494 ACGGCTTTAGCGTACACGAC 60.730 55.000 5.84 0.00 43.26 4.34
1366 1417 0.520404 CGTGCGTCACCTACTACACT 59.480 55.000 4.73 0.00 33.13 3.55
1464 1515 2.092753 TCCGATCCTACCTCAGTACGTT 60.093 50.000 0.00 0.00 0.00 3.99
1465 1516 2.290093 CCGATCCTACCTCAGTACGTTC 59.710 54.545 0.00 0.00 0.00 3.95
1466 1517 2.033065 CGATCCTACCTCAGTACGTTCG 60.033 54.545 0.00 0.00 0.00 3.95
1467 1518 1.742761 TCCTACCTCAGTACGTTCGG 58.257 55.000 0.00 0.00 0.00 4.30
1468 1519 0.100146 CCTACCTCAGTACGTTCGGC 59.900 60.000 0.00 0.00 0.00 5.54
1469 1520 0.100146 CTACCTCAGTACGTTCGGCC 59.900 60.000 0.00 0.00 0.00 6.13
1470 1521 1.315257 TACCTCAGTACGTTCGGCCC 61.315 60.000 0.00 0.00 0.00 5.80
1471 1522 2.183555 CTCAGTACGTTCGGCCCC 59.816 66.667 0.00 0.00 0.00 5.80
1472 1523 3.366739 CTCAGTACGTTCGGCCCCC 62.367 68.421 0.00 0.00 0.00 5.40
1513 1564 1.734477 CTCTGTTCCTCCACACGCG 60.734 63.158 3.53 3.53 0.00 6.01
1522 1573 3.716006 CCACACGCGCACCAGAAG 61.716 66.667 5.73 0.00 0.00 2.85
1569 1622 1.687493 CCCAGGTCCCAGAGAGGTC 60.687 68.421 0.00 0.00 34.66 3.85
1635 1688 2.890474 GGCTACACCATCACCGCG 60.890 66.667 0.00 0.00 38.86 6.46
1666 1719 9.633962 TCAGCATGGTGTGAGTATCATCAAACT 62.634 40.741 23.35 0.00 43.00 2.66
1710 1763 5.129485 ACCTCCTCATCACGAATCAAACTAT 59.871 40.000 0.00 0.00 0.00 2.12
1711 1764 5.464722 CCTCCTCATCACGAATCAAACTATG 59.535 44.000 0.00 0.00 0.00 2.23
1713 1766 6.042777 TCCTCATCACGAATCAAACTATGAC 58.957 40.000 0.00 0.00 41.93 3.06
1715 1768 6.313658 CCTCATCACGAATCAAACTATGACAA 59.686 38.462 0.00 0.00 41.93 3.18
1716 1769 7.148423 CCTCATCACGAATCAAACTATGACAAA 60.148 37.037 0.00 0.00 41.93 2.83
1717 1770 8.267620 TCATCACGAATCAAACTATGACAAAT 57.732 30.769 0.00 0.00 41.93 2.32
1718 1771 8.729756 TCATCACGAATCAAACTATGACAAATT 58.270 29.630 0.00 0.00 41.93 1.82
1719 1772 9.345517 CATCACGAATCAAACTATGACAAATTT 57.654 29.630 0.00 0.00 41.93 1.82
1777 1836 1.597742 TTCTCTTTGTGTGCTCTGCC 58.402 50.000 0.00 0.00 0.00 4.85
1863 1922 2.821366 GGGACCGTGCTCATGCTG 60.821 66.667 0.00 0.00 40.48 4.41
1926 1985 2.103042 GGAGCACATCACGTGGCTC 61.103 63.158 26.67 26.67 46.45 4.70
2168 2227 7.793948 TGGATGATGATGATTCAGATACTCT 57.206 36.000 0.00 0.00 34.73 3.24
2169 2228 8.203681 TGGATGATGATGATTCAGATACTCTT 57.796 34.615 0.00 0.00 34.73 2.85
2181 2240 9.528018 GATTCAGATACTCTTAACTTCCAGAAG 57.472 37.037 5.85 5.85 43.79 2.85
2200 2259 7.173218 TCCAGAAGTGATATGTTTGTTCAGAAC 59.827 37.037 6.32 6.32 0.00 3.01
2203 2262 8.153550 AGAAGTGATATGTTTGTTCAGAACTCT 58.846 33.333 14.51 1.53 0.00 3.24
2218 2277 5.615708 CAGAACTCTGAATTGAATGACACG 58.384 41.667 0.03 0.00 46.59 4.49
2219 2278 5.178252 CAGAACTCTGAATTGAATGACACGT 59.822 40.000 0.03 0.00 46.59 4.49
2220 2279 5.406780 AGAACTCTGAATTGAATGACACGTC 59.593 40.000 0.00 0.00 0.00 4.34
2221 2280 4.631131 ACTCTGAATTGAATGACACGTCA 58.369 39.130 1.71 1.71 44.59 4.35
2222 2281 5.056480 ACTCTGAATTGAATGACACGTCAA 58.944 37.500 3.61 5.99 43.58 3.18
2223 2282 5.702670 ACTCTGAATTGAATGACACGTCAAT 59.297 36.000 3.61 9.42 44.43 2.57
2230 2289 6.480524 TTGAATGACACGTCAATTAGGAAG 57.519 37.500 3.61 0.00 43.58 3.46
2231 2290 4.935205 TGAATGACACGTCAATTAGGAAGG 59.065 41.667 3.61 0.00 43.58 3.46
2232 2291 4.819105 ATGACACGTCAATTAGGAAGGA 57.181 40.909 3.61 0.00 43.58 3.36
2264 2323 5.674525 TCAGAATATTACTCCAAGTGGCAG 58.325 41.667 0.00 0.00 34.44 4.85
2267 2326 5.189736 AGAATATTACTCCAAGTGGCAGTGA 59.810 40.000 0.00 5.33 34.44 3.41
2269 2328 3.334583 TTACTCCAAGTGGCAGTGATC 57.665 47.619 0.00 0.00 34.44 2.92
2286 2346 6.347240 GCAGTGATCTTGTCAGTAACTTCTTG 60.347 42.308 0.00 0.00 38.45 3.02
2288 2348 5.698545 GTGATCTTGTCAGTAACTTCTTGCT 59.301 40.000 0.00 0.00 37.56 3.91
2303 2368 5.049405 ACTTCTTGCTTGTTTTCAGGATACG 60.049 40.000 0.00 0.00 46.39 3.06
2360 2425 4.284178 AGAAGGCAGCAATGTATGGAATT 58.716 39.130 0.00 0.00 0.00 2.17
2387 2452 4.040952 GCCACCACCATATTCTACATCTCT 59.959 45.833 0.00 0.00 0.00 3.10
2507 2572 1.222936 GTGCCTCATCCTCCACCTG 59.777 63.158 0.00 0.00 0.00 4.00
2516 2581 2.124570 CTCCACCTGATTGGGGCG 60.125 66.667 0.00 0.00 38.11 6.13
2541 2606 6.744175 ATCAGGTCAGTACATCTCAATCAT 57.256 37.500 0.00 0.00 0.00 2.45
2597 2662 1.069364 GCTGAACTGCTTGAAGTGAGC 60.069 52.381 0.00 0.00 40.53 4.26
2794 2859 2.885861 CGCCCTACAAGCTCGTCT 59.114 61.111 0.00 0.00 0.00 4.18
2823 2888 4.757657 ACCGTCATAGTTATTGCAACAACA 59.242 37.500 21.80 8.94 0.00 3.33
2844 2909 2.241941 AGTGGTGGCAATGATGATACCA 59.758 45.455 0.00 0.00 39.94 3.25
2892 2957 2.669569 GCGTTCAGCTTCTGGCCA 60.670 61.111 4.71 4.71 44.04 5.36
2898 2963 1.352083 TCAGCTTCTGGCCACTAACT 58.648 50.000 0.00 0.00 43.05 2.24
3093 3158 4.642885 GTCAGCTAGAGGATGTACAAGACT 59.357 45.833 0.00 0.00 32.48 3.24
3314 3383 6.650807 ACATGTGAAATAGGAAGTACTGTGTG 59.349 38.462 0.00 0.00 0.00 3.82
3315 3384 5.547465 TGTGAAATAGGAAGTACTGTGTGG 58.453 41.667 0.00 0.00 0.00 4.17
3318 3387 5.305902 TGAAATAGGAAGTACTGTGTGGACA 59.694 40.000 0.00 0.00 0.00 4.02
3319 3388 6.013725 TGAAATAGGAAGTACTGTGTGGACAT 60.014 38.462 0.00 0.00 0.00 3.06
3321 3390 2.076863 GGAAGTACTGTGTGGACATGC 58.923 52.381 0.00 0.00 0.00 4.06
3322 3391 2.289694 GGAAGTACTGTGTGGACATGCT 60.290 50.000 0.00 0.00 0.00 3.79
3323 3392 2.462456 AGTACTGTGTGGACATGCTG 57.538 50.000 0.00 0.00 0.00 4.41
3324 3393 0.798776 GTACTGTGTGGACATGCTGC 59.201 55.000 0.00 0.00 0.00 5.25
3332 3408 2.229543 TGTGGACATGCTGCTTTTGATC 59.770 45.455 0.00 0.00 0.00 2.92
3360 3436 4.192317 GAGCCCATTCAAAGTAGTCGAAT 58.808 43.478 0.00 0.00 0.00 3.34
3477 3622 7.174772 TGAATTTATACAGAAACTGCTGCAGAA 59.825 33.333 34.28 15.02 39.51 3.02
3481 3626 2.754552 ACAGAAACTGCTGCAGAAACAA 59.245 40.909 34.28 0.00 39.51 2.83
3564 3711 3.194542 ACTTGCTTCCAGCTCACTAGTAG 59.805 47.826 0.00 0.00 42.97 2.57
3578 3734 9.280174 AGCTCACTAGTAGTACATTCTAATCTC 57.720 37.037 1.57 0.00 0.00 2.75
3700 3856 2.304761 TGTTCTTTGCCCTCCGAATACT 59.695 45.455 0.00 0.00 0.00 2.12
3736 3892 7.384660 TCAATGTCAATAAGCATTTTCACAACC 59.615 33.333 0.00 0.00 33.55 3.77
3747 3903 2.370281 TTCACAACCTCTCTCATCGC 57.630 50.000 0.00 0.00 0.00 4.58
3770 3926 2.498726 GCTCAGAAGGGGCTCGAG 59.501 66.667 8.45 8.45 0.00 4.04
3781 3937 1.536284 GGGGCTCGAGTAATTCAGACG 60.536 57.143 15.13 0.00 0.00 4.18
3793 3950 4.361451 AATTCAGACGATGGCAATGTTC 57.639 40.909 0.00 0.00 0.00 3.18
3843 4001 1.064654 GCTGCCGGCTTTTAGATCAAG 59.935 52.381 29.70 13.44 38.06 3.02
3850 4008 2.009774 GCTTTTAGATCAAGCCGCTGA 58.990 47.619 5.20 0.00 40.79 4.26
3858 4016 2.472695 TCAAGCCGCTGAAGTTATGT 57.527 45.000 0.00 0.00 0.00 2.29
3869 4027 4.142381 GCTGAAGTTATGTGATCAAACCCC 60.142 45.833 0.00 0.00 0.00 4.95
3940 4098 1.986378 CACTAAGAAACTCTGACGGCG 59.014 52.381 4.80 4.80 0.00 6.46
3944 4102 1.204312 GAAACTCTGACGGCGCAAC 59.796 57.895 10.83 0.00 0.00 4.17
3952 4110 2.432628 ACGGCGCAACACTAGAGC 60.433 61.111 10.83 0.00 0.00 4.09
3956 4114 0.460987 GGCGCAACACTAGAGCTCAT 60.461 55.000 17.77 3.63 0.00 2.90
3965 4123 4.085733 ACACTAGAGCTCATGTCACTCTT 58.914 43.478 17.77 0.00 41.03 2.85
3971 4129 4.527816 AGAGCTCATGTCACTCTTTTCTCT 59.472 41.667 17.77 0.00 37.50 3.10
3978 4136 3.181465 TGTCACTCTTTTCTCTCGCCTTT 60.181 43.478 0.00 0.00 0.00 3.11
3994 4152 4.345257 TCGCCTTTAGAGAATATGGAAGCT 59.655 41.667 0.00 0.00 0.00 3.74
4017 4175 4.405036 TCTGCAGTTCAGAGATAAGCTGAT 59.595 41.667 14.67 0.00 46.34 2.90
4027 4185 7.487484 TCAGAGATAAGCTGATGTAAGACTTG 58.513 38.462 0.00 0.00 37.46 3.16
4036 4194 6.817641 AGCTGATGTAAGACTTGAATCTTCAG 59.182 38.462 0.00 9.44 39.65 3.02
4041 4199 5.928839 TGTAAGACTTGAATCTTCAGACTGC 59.071 40.000 0.00 0.00 39.65 4.40
4057 4215 7.661536 TCAGACTGCTATCTTTAAGGTGTAT 57.338 36.000 0.00 0.00 0.00 2.29
4058 4216 8.079211 TCAGACTGCTATCTTTAAGGTGTATT 57.921 34.615 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.364324 GGGGAGAACTCGTGCATATACA 59.636 50.000 0.00 0.00 0.00 2.29
32 33 0.393808 GCGTTGCAATAGGGGGAGAA 60.394 55.000 0.59 0.00 0.00 2.87
121 122 2.668632 GTTGAGATCACCCCCGCA 59.331 61.111 0.00 0.00 0.00 5.69
132 133 0.323629 ATTTTCCGGCGAGGTTGAGA 59.676 50.000 9.30 0.00 41.99 3.27
162 163 3.152400 CGAGGTCGGGGTTAGGGG 61.152 72.222 0.00 0.00 35.37 4.79
286 288 1.651240 CTCCGCGTTCTTCGTCCCTA 61.651 60.000 4.92 0.00 42.13 3.53
370 375 1.234615 CCAAATCCGCCGAGTTGTGT 61.235 55.000 12.87 0.00 41.43 3.72
377 382 2.435234 CGGTTCCAAATCCGCCGA 60.435 61.111 0.00 0.00 44.57 5.54
498 506 4.595762 ATTAGTCGTTGTGTGTAGTGGT 57.404 40.909 0.00 0.00 0.00 4.16
506 514 2.602878 CCAGCGTATTAGTCGTTGTGT 58.397 47.619 0.00 0.00 37.71 3.72
510 518 1.477553 TCCCCAGCGTATTAGTCGTT 58.522 50.000 0.00 0.00 0.00 3.85
514 522 2.167900 GTCAGTTCCCCAGCGTATTAGT 59.832 50.000 0.00 0.00 0.00 2.24
562 570 0.847035 CGCGCGAGATAAACCTCTTC 59.153 55.000 28.94 0.00 0.00 2.87
747 756 4.378046 CGACTCATTAAACCCAAAACCTCG 60.378 45.833 0.00 0.00 0.00 4.63
813 822 1.303236 CACCGGCATTCCAGGTTCA 60.303 57.895 0.00 0.00 37.23 3.18
852 861 1.810606 CGGCGCTCTCATGATAGGGT 61.811 60.000 21.27 0.00 0.00 4.34
862 871 1.424240 GCTTTAAACCGGCGCTCTC 59.576 57.895 7.64 0.00 0.00 3.20
938 952 1.647084 GGCGGATGCGGTAATGAAC 59.353 57.895 9.20 0.00 44.10 3.18
951 970 4.779733 GGGAGTCAGAGGGGCGGA 62.780 72.222 0.00 0.00 0.00 5.54
1085 1116 0.991920 AAAAATCGAGAGGAGGGGCA 59.008 50.000 0.00 0.00 0.00 5.36
1148 1194 1.486211 CCCAGGAGGAATAGTCGTGT 58.514 55.000 0.00 0.00 38.24 4.49
1154 1200 1.062121 TCCAGTCCCCAGGAGGAATAG 60.062 57.143 0.00 0.00 37.78 1.73
1206 1256 2.098443 GTCCCTGCAACGAACAAGAAAA 59.902 45.455 0.00 0.00 0.00 2.29
1210 1260 1.569493 CGTCCCTGCAACGAACAAG 59.431 57.895 3.31 0.00 42.62 3.16
1478 1529 2.692741 GAGAGGGGGAGGGGTTGG 60.693 72.222 0.00 0.00 0.00 3.77
1479 1530 1.690985 GAGAGAGGGGGAGGGGTTG 60.691 68.421 0.00 0.00 0.00 3.77
1480 1531 1.869452 AGAGAGAGGGGGAGGGGTT 60.869 63.158 0.00 0.00 0.00 4.11
1481 1532 2.204705 AGAGAGAGGGGGAGGGGT 60.205 66.667 0.00 0.00 0.00 4.95
1482 1533 2.188215 AACAGAGAGAGGGGGAGGGG 62.188 65.000 0.00 0.00 0.00 4.79
1483 1534 0.689412 GAACAGAGAGAGGGGGAGGG 60.689 65.000 0.00 0.00 0.00 4.30
1486 1537 0.336737 GAGGAACAGAGAGAGGGGGA 59.663 60.000 0.00 0.00 0.00 4.81
1490 1541 1.548269 GTGTGGAGGAACAGAGAGAGG 59.452 57.143 0.00 0.00 0.00 3.69
1492 1543 1.248486 CGTGTGGAGGAACAGAGAGA 58.752 55.000 0.00 0.00 0.00 3.10
1494 1545 1.666011 GCGTGTGGAGGAACAGAGA 59.334 57.895 0.00 0.00 0.00 3.10
1525 1576 2.158475 AGTTTCAGGCATTGGGTTGAGA 60.158 45.455 0.00 0.00 0.00 3.27
1526 1577 2.242043 AGTTTCAGGCATTGGGTTGAG 58.758 47.619 0.00 0.00 0.00 3.02
1666 1719 5.205056 AGGTGGACTGAATTTTGGTTGTTA 58.795 37.500 0.00 0.00 0.00 2.41
1710 1763 9.473007 TGTCCCTGAATGATAATAAATTTGTCA 57.527 29.630 0.00 0.85 0.00 3.58
1713 1766 9.199982 GCATGTCCCTGAATGATAATAAATTTG 57.800 33.333 0.00 0.00 0.00 2.32
1715 1768 8.582437 CAGCATGTCCCTGAATGATAATAAATT 58.418 33.333 0.00 0.00 32.03 1.82
1716 1769 7.946219 TCAGCATGTCCCTGAATGATAATAAAT 59.054 33.333 0.00 0.00 36.46 1.40
1717 1770 7.289310 TCAGCATGTCCCTGAATGATAATAAA 58.711 34.615 0.00 0.00 36.46 1.40
1718 1771 6.840527 TCAGCATGTCCCTGAATGATAATAA 58.159 36.000 0.00 0.00 36.46 1.40
1719 1772 6.438186 TCAGCATGTCCCTGAATGATAATA 57.562 37.500 0.00 0.00 36.46 0.98
1720 1773 5.314718 TCAGCATGTCCCTGAATGATAAT 57.685 39.130 0.00 0.00 36.46 1.28
1777 1836 1.144565 CTCCTGATCGCACTTCGCAG 61.145 60.000 0.00 0.00 42.60 5.18
1848 1907 3.503363 GCCAGCATGAGCACGGTC 61.503 66.667 0.00 0.00 45.49 4.79
1863 1922 3.901797 CTGGACCACGGTGAAGGCC 62.902 68.421 10.28 5.99 0.00 5.19
2016 2075 4.899239 CCTGCGATCCTGCCGTCC 62.899 72.222 0.00 0.00 0.00 4.79
2124 2183 3.558746 CCATGCCTACCTGGATCTCAATC 60.559 52.174 0.00 0.00 38.35 2.67
2172 2231 7.388776 TCTGAACAAACATATCACTTCTGGAAG 59.611 37.037 8.59 8.59 43.79 3.46
2173 2232 7.223584 TCTGAACAAACATATCACTTCTGGAA 58.776 34.615 0.00 0.00 0.00 3.53
2200 2259 5.596268 TTGACGTGTCATTCAATTCAGAG 57.404 39.130 3.14 0.00 39.64 3.35
2203 2262 6.652900 TCCTAATTGACGTGTCATTCAATTCA 59.347 34.615 20.50 11.50 45.24 2.57
2206 2265 6.094048 CCTTCCTAATTGACGTGTCATTCAAT 59.906 38.462 3.14 6.76 42.95 2.57
2207 2266 5.411361 CCTTCCTAATTGACGTGTCATTCAA 59.589 40.000 3.14 3.12 39.64 2.69
2208 2267 4.935205 CCTTCCTAATTGACGTGTCATTCA 59.065 41.667 3.14 0.00 39.64 2.57
2209 2268 5.175859 TCCTTCCTAATTGACGTGTCATTC 58.824 41.667 3.14 0.00 39.64 2.67
2210 2269 5.160607 TCCTTCCTAATTGACGTGTCATT 57.839 39.130 3.14 0.00 39.64 2.57
2214 2273 6.264518 ACAAAAATCCTTCCTAATTGACGTGT 59.735 34.615 0.00 0.00 0.00 4.49
2215 2274 6.677913 ACAAAAATCCTTCCTAATTGACGTG 58.322 36.000 0.00 0.00 0.00 4.49
2216 2275 6.894339 ACAAAAATCCTTCCTAATTGACGT 57.106 33.333 0.00 0.00 0.00 4.34
2217 2276 7.865385 TGAAACAAAAATCCTTCCTAATTGACG 59.135 33.333 0.00 0.00 0.00 4.35
2218 2277 9.196552 CTGAAACAAAAATCCTTCCTAATTGAC 57.803 33.333 0.00 0.00 0.00 3.18
2219 2278 9.142014 TCTGAAACAAAAATCCTTCCTAATTGA 57.858 29.630 0.00 0.00 0.00 2.57
2220 2279 9.762933 TTCTGAAACAAAAATCCTTCCTAATTG 57.237 29.630 0.00 0.00 0.00 2.32
2247 2306 4.716784 AGATCACTGCCACTTGGAGTAATA 59.283 41.667 0.00 0.00 37.39 0.98
2264 2323 5.698545 AGCAAGAAGTTACTGACAAGATCAC 59.301 40.000 0.00 0.00 32.37 3.06
2267 2326 6.058183 ACAAGCAAGAAGTTACTGACAAGAT 58.942 36.000 0.00 0.00 0.00 2.40
2269 2328 5.741388 ACAAGCAAGAAGTTACTGACAAG 57.259 39.130 0.00 0.00 0.00 3.16
2286 2346 2.742053 TCAGCGTATCCTGAAAACAAGC 59.258 45.455 0.00 0.00 38.81 4.01
2303 2368 0.393537 CAGATGGTGGGGACTTCAGC 60.394 60.000 0.00 0.00 0.00 4.26
2360 2425 1.595311 AGAATATGGTGGTGGCTCCA 58.405 50.000 3.73 3.73 45.01 3.86
2507 2572 0.468226 TGACCTGATACGCCCCAATC 59.532 55.000 0.00 0.00 0.00 2.67
2516 2581 7.043961 TGATTGAGATGTACTGACCTGATAC 57.956 40.000 0.00 0.00 0.00 2.24
2553 2618 7.929785 AGCTTTTCAAATTTATGGGATATGCAG 59.070 33.333 0.00 0.00 0.00 4.41
2561 2626 6.128472 GCAGTTCAGCTTTTCAAATTTATGGG 60.128 38.462 0.00 0.00 0.00 4.00
2592 2657 0.888285 AGTTCAGCTGCAAGGCTCAC 60.888 55.000 9.47 0.00 41.00 3.51
2616 2681 7.203218 AGGAAAACATTTTAGTTCAAGCTGTC 58.797 34.615 0.00 0.00 0.00 3.51
2623 2688 7.495901 TGCATTGAGGAAAACATTTTAGTTCA 58.504 30.769 0.00 0.00 0.00 3.18
2794 2859 4.142204 TGCAATAACTATGACGGTCCGTAA 60.142 41.667 18.88 11.25 41.37 3.18
2823 2888 2.241941 TGGTATCATCATTGCCACCACT 59.758 45.455 0.00 0.00 33.83 4.00
2844 2909 1.359848 CTAGCACCGCGTTGAAGAAT 58.640 50.000 8.22 0.00 0.00 2.40
2892 2957 5.338137 GCTTATGGGGAAGTACACAGTTAGT 60.338 44.000 0.00 0.00 0.00 2.24
2898 2963 3.884895 CATGCTTATGGGGAAGTACACA 58.115 45.455 0.00 0.00 0.00 3.72
3093 3158 6.170506 ACAGATTCAACCGCTATTCTACAAA 58.829 36.000 0.00 0.00 0.00 2.83
3314 3383 3.581024 TTGATCAAAAGCAGCATGTCC 57.419 42.857 5.45 0.00 39.31 4.02
3315 3384 4.264614 CGATTTGATCAAAAGCAGCATGTC 59.735 41.667 23.91 12.57 33.64 3.06
3318 3387 4.669318 CTCGATTTGATCAAAAGCAGCAT 58.331 39.130 23.91 6.44 33.64 3.79
3319 3388 3.671433 GCTCGATTTGATCAAAAGCAGCA 60.671 43.478 27.10 7.21 37.80 4.41
3321 3390 3.432782 GGCTCGATTTGATCAAAAGCAG 58.567 45.455 30.33 22.78 34.85 4.24
3322 3391 2.164219 GGGCTCGATTTGATCAAAAGCA 59.836 45.455 30.33 16.31 34.85 3.91
3323 3392 2.164219 TGGGCTCGATTTGATCAAAAGC 59.836 45.455 25.31 25.31 33.31 3.51
3324 3393 4.644103 ATGGGCTCGATTTGATCAAAAG 57.356 40.909 23.91 19.59 33.56 2.27
3332 3408 3.855689 ACTTTGAATGGGCTCGATTTG 57.144 42.857 0.00 0.00 0.00 2.32
3360 3436 3.328382 AACATAGCAGCGTAGTCCAAA 57.672 42.857 0.00 0.00 0.00 3.28
3477 3622 3.450904 TGGTAGCCTCATAGGTCTTGTT 58.549 45.455 0.00 0.00 37.80 2.83
3481 3626 2.158385 CCTCTGGTAGCCTCATAGGTCT 60.158 54.545 0.00 0.00 37.80 3.85
3564 3711 9.127277 ACTCTGAAGTAGGAGATTAGAATGTAC 57.873 37.037 0.00 0.00 32.59 2.90
3578 3734 3.733337 AGCAACAACACTCTGAAGTAGG 58.267 45.455 0.00 0.00 33.25 3.18
3700 3856 8.791327 TGCTTATTGACATTGATTCTACTTCA 57.209 30.769 0.00 0.00 0.00 3.02
3736 3892 2.329690 CGACCGGCGATGAGAGAG 59.670 66.667 9.30 0.00 44.57 3.20
3747 3903 4.148825 CCCCTTCTGAGCGACCGG 62.149 72.222 0.00 0.00 0.00 5.28
3770 3926 4.882671 ACATTGCCATCGTCTGAATTAC 57.117 40.909 0.00 0.00 0.00 1.89
3781 3937 4.525912 AAAGGTCTTGAACATTGCCATC 57.474 40.909 0.00 0.00 30.97 3.51
3824 3982 1.064654 GCTTGATCTAAAAGCCGGCAG 59.935 52.381 31.54 17.75 43.45 4.85
3843 4001 2.279741 TGATCACATAACTTCAGCGGC 58.720 47.619 0.00 0.00 0.00 6.53
3845 4003 4.437390 GGGTTTGATCACATAACTTCAGCG 60.437 45.833 8.31 0.00 0.00 5.18
3850 4008 3.009695 TCCGGGGTTTGATCACATAACTT 59.990 43.478 0.00 0.00 0.00 2.66
3858 4016 0.036164 CTGTGTCCGGGGTTTGATCA 59.964 55.000 0.00 0.00 0.00 2.92
3869 4027 1.597663 GTGAACTGGAAACTGTGTCCG 59.402 52.381 12.27 9.40 42.21 4.79
3940 4098 2.670414 GTGACATGAGCTCTAGTGTTGC 59.330 50.000 16.19 9.86 0.00 4.17
3944 4102 4.717233 AAGAGTGACATGAGCTCTAGTG 57.283 45.455 16.19 13.20 38.50 2.74
3952 4110 3.611986 GCGAGAGAAAAGAGTGACATGAG 59.388 47.826 0.00 0.00 0.00 2.90
3956 4114 1.964223 AGGCGAGAGAAAAGAGTGACA 59.036 47.619 0.00 0.00 0.00 3.58
3971 4129 4.345257 AGCTTCCATATTCTCTAAAGGCGA 59.655 41.667 0.00 0.00 0.00 5.54
3978 4136 4.898265 ACTGCAGAGCTTCCATATTCTCTA 59.102 41.667 23.35 0.00 34.45 2.43
4017 4175 5.928839 GCAGTCTGAAGATTCAAGTCTTACA 59.071 40.000 3.32 0.00 38.51 2.41
4027 4185 7.984617 ACCTTAAAGATAGCAGTCTGAAGATTC 59.015 37.037 3.32 0.00 29.69 2.52


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

AutoCloner maintained by Alex Coulton.