Multiple sequence alignment - TraesCS1A01G440600

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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 TraesCS1A01G440600 chr1A 100.000 3545 0 0 1 3545 589501727 589498183 0.000000e+00 6547.0
1 TraesCS1A01G440600 chr1A 83.353 1706 249 23 1223 2917 589447063 589445382 0.000000e+00 1544.0
2 TraesCS1A01G440600 chr1A 82.528 1717 258 22 1215 2918 589478738 589477051 0.000000e+00 1471.0
3 TraesCS1A01G440600 chr1A 82.122 1706 277 16 1223 2918 589638351 589636664 0.000000e+00 1435.0
4 TraesCS1A01G440600 chr1A 83.344 1579 211 28 1215 2782 589454072 589452535 0.000000e+00 1411.0
5 TraesCS1A01G440600 chr1A 79.409 1185 214 22 126 1303 589448216 589447055 0.000000e+00 809.0
6 TraesCS1A01G440600 chr1A 79.005 1186 215 25 132 1303 589639508 589638343 0.000000e+00 780.0
7 TraesCS1A01G440600 chr1A 78.693 1178 208 32 132 1303 589479862 589478722 0.000000e+00 745.0
8 TraesCS1A01G440600 chr1A 78.708 991 175 25 132 1109 589510604 589509637 2.320000e-176 628.0
9 TraesCS1A01G440600 chr1A 96.328 354 13 0 2919 3272 589451894 589451541 1.830000e-162 582.0
10 TraesCS1A01G440600 chr1A 81.841 402 73 0 1215 1616 589517012 589516611 4.380000e-89 339.0
11 TraesCS1A01G440600 chr1A 94.845 194 9 1 3352 3545 589451541 589451349 5.750000e-78 302.0
12 TraesCS1A01G440600 chr1A 83.007 306 37 12 132 431 589475289 589474993 2.710000e-66 263.0
13 TraesCS1A01G440600 chr1A 83.590 195 7 7 2916 3088 589476746 589476555 3.660000e-35 159.0
14 TraesCS1A01G440600 chr1A 92.135 89 6 1 2916 3004 589445078 589444991 1.340000e-24 124.0
15 TraesCS1A01G440600 chr1B 89.908 2933 252 23 1 2917 683584516 683581612 0.000000e+00 3736.0
16 TraesCS1A01G440600 chr1B 83.863 2578 371 32 359 2918 683580373 683577823 0.000000e+00 2414.0
17 TraesCS1A01G440600 chr1B 93.229 192 8 2 3354 3545 683577172 683576986 9.690000e-71 278.0
18 TraesCS1A01G440600 chr1B 80.000 380 22 23 2916 3272 683577519 683577171 7.650000e-57 231.0
19 TraesCS1A01G440600 chr1B 86.022 186 16 2 3370 3545 683580927 683580742 1.300000e-44 191.0
20 TraesCS1A01G440600 chr1D 84.011 2927 397 48 22 2918 491640366 491637481 0.000000e+00 2747.0
21 TraesCS1A01G440600 chr1D 84.100 1717 239 23 1215 2916 491665696 491663999 0.000000e+00 1628.0
22 TraesCS1A01G440600 chr1D 82.528 1717 258 25 1216 2918 491688167 491686479 0.000000e+00 1471.0
23 TraesCS1A01G440600 chr1D 79.813 1179 214 16 132 1303 491697410 491696249 0.000000e+00 837.0
24 TraesCS1A01G440600 chr1D 79.209 1188 212 24 126 1299 491689394 491688228 0.000000e+00 793.0
25 TraesCS1A01G440600 chr1D 83.511 655 51 26 2916 3545 491637178 491636556 3.090000e-155 558.0
26 TraesCS1A01G440600 chr1D 84.615 286 39 4 52 333 491667113 491666829 2.690000e-71 279.0
27 TraesCS1A01G440600 chr5D 75.000 2824 609 70 132 2918 434473720 434476483 0.000000e+00 1214.0
28 TraesCS1A01G440600 chr5B 74.525 2634 574 74 132 2733 527248978 527251546 0.000000e+00 1057.0
29 TraesCS1A01G440600 chr5B 96.667 90 3 0 3271 3360 429615329 429615240 2.200000e-32 150.0
30 TraesCS1A01G440600 chr5B 90.000 110 7 4 3071 3177 477078549 477078441 4.770000e-29 139.0
31 TraesCS1A01G440600 chr5B 87.500 88 9 2 3088 3175 695728083 695728168 2.250000e-17 100.0
32 TraesCS1A01G440600 chr3B 97.727 88 2 0 3267 3354 71400375 71400462 6.130000e-33 152.0
33 TraesCS1A01G440600 chr6D 97.647 85 2 0 3271 3355 465043922 465043838 2.850000e-31 147.0
34 TraesCS1A01G440600 chr6D 96.512 86 3 0 3271 3356 142846313 142846398 3.690000e-30 143.0
35 TraesCS1A01G440600 chr6D 81.982 111 11 5 3070 3177 50742371 50742267 6.310000e-13 86.1
36 TraesCS1A01G440600 chr3D 96.512 86 3 0 3270 3355 13181987 13181902 3.690000e-30 143.0
37 TraesCS1A01G440600 chr4D 95.455 88 4 0 3268 3355 31895463 31895550 1.330000e-29 141.0
38 TraesCS1A01G440600 chr4D 95.455 88 4 0 3268 3355 492602149 492602236 1.330000e-29 141.0
39 TraesCS1A01G440600 chr2A 92.000 100 7 1 3256 3355 377798871 377798773 4.770000e-29 139.0
40 TraesCS1A01G440600 chr2A 80.833 120 13 7 3066 3177 510432997 510433114 6.310000e-13 86.1
41 TraesCS1A01G440600 chr2A 81.081 111 13 4 3071 3178 728548671 728548776 8.160000e-12 82.4
42 TraesCS1A01G440600 chr7D 95.714 70 3 0 3109 3178 470204859 470204790 2.890000e-21 113.0
43 TraesCS1A01G440600 chr2B 89.535 86 9 0 3108 3193 197957536 197957451 3.740000e-20 110.0
44 TraesCS1A01G440600 chr2D 89.412 85 9 0 3108 3192 139318513 139318429 1.350000e-19 108.0
45 TraesCS1A01G440600 chr2D 82.727 110 14 4 3071 3177 32984542 32984435 3.770000e-15 93.5
46 TraesCS1A01G440600 chr6B 85.185 108 9 6 3070 3171 579196387 579196493 1.740000e-18 104.0
47 TraesCS1A01G440600 chr6A 87.097 93 7 3 3071 3160 426258268 426258358 2.250000e-17 100.0


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 TraesCS1A01G440600 chr1A 589498183 589501727 3544 True 6547.000000 6547 100.000000 1 3545 1 chr1A.!!$R1 3544
1 TraesCS1A01G440600 chr1A 589636664 589639508 2844 True 1107.500000 1435 80.563500 132 2918 2 chr1A.!!$R6 2786
2 TraesCS1A01G440600 chr1A 589444991 589454072 9081 True 795.333333 1544 88.235667 126 3545 6 chr1A.!!$R4 3419
3 TraesCS1A01G440600 chr1A 589474993 589479862 4869 True 659.500000 1471 81.954500 132 3088 4 chr1A.!!$R5 2956
4 TraesCS1A01G440600 chr1A 589509637 589510604 967 True 628.000000 628 78.708000 132 1109 1 chr1A.!!$R2 977
5 TraesCS1A01G440600 chr1B 683576986 683584516 7530 True 1370.000000 3736 86.604400 1 3545 5 chr1B.!!$R1 3544
6 TraesCS1A01G440600 chr1D 491636556 491640366 3810 True 1652.500000 2747 83.761000 22 3545 2 chr1D.!!$R2 3523
7 TraesCS1A01G440600 chr1D 491686479 491689394 2915 True 1132.000000 1471 80.868500 126 2918 2 chr1D.!!$R4 2792
8 TraesCS1A01G440600 chr1D 491663999 491667113 3114 True 953.500000 1628 84.357500 52 2916 2 chr1D.!!$R3 2864
9 TraesCS1A01G440600 chr1D 491696249 491697410 1161 True 837.000000 837 79.813000 132 1303 1 chr1D.!!$R1 1171
10 TraesCS1A01G440600 chr5D 434473720 434476483 2763 False 1214.000000 1214 75.000000 132 2918 1 chr5D.!!$F1 2786
11 TraesCS1A01G440600 chr5B 527248978 527251546 2568 False 1057.000000 1057 74.525000 132 2733 1 chr5B.!!$F1 2601

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
552 6536 0.324738 TGGTAGAGTGCCTCCTCAGG 60.325 60.000 0.0 0.0 43.82 3.86 F
1238 7301 1.202687 CCAGTTGAGAGGTTCAGTGCA 60.203 52.381 0.0 0.0 37.07 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 7596 1.002624 GAACGGAGGCACCCAATGA 60.003 57.895 0.0 0.0 34.64 2.57 R
2785 12799 0.682852 CGTTGGTTGGTGGACCTCTA 59.317 55.000 0.0 0.0 40.47 2.43 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
72 74 1.973281 ATGGCTGCACCGAACAAGG 60.973 57.895 0.50 0.00 43.94 3.61
112 120 2.373836 TCCTAGCTACAGCCTCCTCTAG 59.626 54.545 0.00 0.00 43.38 2.43
115 123 1.104577 GCTACAGCCTCCTCTAGCGT 61.105 60.000 0.00 0.00 28.21 5.07
116 124 0.665835 CTACAGCCTCCTCTAGCGTG 59.334 60.000 0.00 0.00 0.00 5.34
120 128 0.547075 AGCCTCCTCTAGCGTGAGTA 59.453 55.000 7.92 0.00 32.50 2.59
121 129 0.948678 GCCTCCTCTAGCGTGAGTAG 59.051 60.000 7.92 2.43 32.50 2.57
122 130 1.747898 GCCTCCTCTAGCGTGAGTAGT 60.748 57.143 7.92 0.00 32.50 2.73
135 5867 4.143179 GCGTGAGTAGTGTAACATTCAACC 60.143 45.833 0.00 0.00 41.43 3.77
182 5914 1.299321 GCTGCTCTCCTTCAAGGCT 59.701 57.895 0.00 0.00 34.61 4.58
297 6041 3.112709 GCCACGTCGTGAAGCTCC 61.113 66.667 26.53 4.01 35.23 4.70
311 6055 2.125912 CTCCACCTCCGCAACGAG 60.126 66.667 0.00 0.00 0.00 4.18
316 6060 0.456221 CACCTCCGCAACGAGTATCT 59.544 55.000 0.00 0.00 0.00 1.98
317 6061 1.674441 CACCTCCGCAACGAGTATCTA 59.326 52.381 0.00 0.00 0.00 1.98
318 6062 2.293677 CACCTCCGCAACGAGTATCTAT 59.706 50.000 0.00 0.00 0.00 1.98
320 6064 3.383825 ACCTCCGCAACGAGTATCTATTT 59.616 43.478 0.00 0.00 0.00 1.40
321 6065 3.982058 CCTCCGCAACGAGTATCTATTTC 59.018 47.826 0.00 0.00 0.00 2.17
353 6218 7.271511 CAGAAGAGGATTATATATCTGGTGCC 58.728 42.308 0.00 0.00 31.50 5.01
354 6219 6.962311 AGAAGAGGATTATATATCTGGTGCCA 59.038 38.462 0.00 0.00 0.00 4.92
355 6220 7.626890 AGAAGAGGATTATATATCTGGTGCCAT 59.373 37.037 0.00 0.00 0.00 4.40
356 6221 7.372260 AGAGGATTATATATCTGGTGCCATC 57.628 40.000 0.00 0.00 0.00 3.51
406 6271 4.201990 GCAGGTATCTTCTTCATTGCTTGG 60.202 45.833 0.00 0.00 0.00 3.61
434 6414 5.449553 TCACATCTCAAGCATCTAGACCTA 58.550 41.667 0.00 0.00 0.00 3.08
440 6420 4.610333 TCAAGCATCTAGACCTAAGTGGA 58.390 43.478 0.00 0.00 39.71 4.02
519 6499 5.782845 AGTTTGACTTATCTCAACCTCTCCT 59.217 40.000 0.00 0.00 29.62 3.69
552 6536 0.324738 TGGTAGAGTGCCTCCTCAGG 60.325 60.000 0.00 0.00 43.82 3.86
578 6562 4.323562 GGCAACCTCTCTAAACTGGTACAT 60.324 45.833 0.00 0.00 38.20 2.29
581 6565 5.923733 ACCTCTCTAAACTGGTACATCTG 57.076 43.478 0.00 0.00 38.20 2.90
639 6629 8.749026 ATACTCGGACGATATATCTTGGTTAT 57.251 34.615 10.93 0.00 0.00 1.89
640 6630 7.463961 ACTCGGACGATATATCTTGGTTATT 57.536 36.000 10.93 0.00 0.00 1.40
667 6657 4.051922 CTCCGATGGCTACAACATCTTAC 58.948 47.826 0.00 0.00 41.91 2.34
672 6662 4.835284 TGGCTACAACATCTTACCATGA 57.165 40.909 0.00 0.00 0.00 3.07
676 6666 4.878397 GCTACAACATCTTACCATGAGCTT 59.122 41.667 0.00 0.00 0.00 3.74
750 6741 4.262121 CCAATTTGGTTGCACTGATTCTCA 60.262 41.667 7.31 0.00 36.46 3.27
769 6760 6.211587 TCTCAATGATTGTTGGCTTAATGG 57.788 37.500 4.93 0.00 0.00 3.16
782 6773 3.564225 GGCTTAATGGGAGTAATGTTCCG 59.436 47.826 0.00 0.00 35.48 4.30
790 6781 4.058817 GGGAGTAATGTTCCGTCATCATC 58.941 47.826 0.00 0.00 35.48 2.92
794 6785 5.111989 AGTAATGTTCCGTCATCATCTGTG 58.888 41.667 0.00 0.00 0.00 3.66
841 6832 4.693095 GGAGCTTGACCTCTCTTTTAACTG 59.307 45.833 0.00 0.00 32.43 3.16
842 6833 4.646572 AGCTTGACCTCTCTTTTAACTGG 58.353 43.478 0.00 0.00 0.00 4.00
980 6971 6.149474 CCTTGTTAGAGACACTTAACATTGGG 59.851 42.308 0.00 0.00 38.18 4.12
984 6975 7.390440 TGTTAGAGACACTTAACATTGGGATTG 59.610 37.037 0.00 0.00 32.00 2.67
1079 7070 5.447683 CCAACAACATCGACATGGACATAAG 60.448 44.000 0.00 0.00 33.82 1.73
1094 7085 8.811017 CATGGACATAAGAGAGGTAATAGACAT 58.189 37.037 0.00 0.00 0.00 3.06
1227 7218 2.499693 TGTCAGTGACAACCAGTTGAGA 59.500 45.455 23.55 0.00 42.93 3.27
1238 7301 1.202687 CCAGTTGAGAGGTTCAGTGCA 60.203 52.381 0.00 0.00 37.07 4.57
1242 7305 2.880890 GTTGAGAGGTTCAGTGCATGTT 59.119 45.455 0.00 0.00 37.07 2.71
1327 7534 9.049523 GTGTGATATCAGAAGATCATTTTGCTA 57.950 33.333 5.42 0.00 35.67 3.49
1335 7542 9.017509 TCAGAAGATCATTTTGCTAGTTTGATT 57.982 29.630 0.00 0.00 0.00 2.57
1482 7689 0.107945 GGCTTCGATGGCAGAAGAGT 60.108 55.000 17.76 0.00 45.78 3.24
1701 7908 7.055378 AGTTACCAACAACAATTGTGGTACTA 58.945 34.615 18.96 6.22 44.59 1.82
1754 7964 0.173481 TCAGATTTCCGAGCTCCACG 59.827 55.000 8.47 0.00 0.00 4.94
1784 7994 4.875536 GGTTGCAGTTCTGTTTTCCAATTT 59.124 37.500 1.78 0.00 0.00 1.82
1898 8108 1.743252 GTGGCCGGAAAGAGCTGAG 60.743 63.158 5.05 0.00 0.00 3.35
1925 8135 3.181479 CGTAACCCATCTAGCAGCAACTA 60.181 47.826 0.00 0.00 0.00 2.24
1929 8139 3.713764 ACCCATCTAGCAGCAACTATTCT 59.286 43.478 0.00 0.00 0.00 2.40
1950 8160 6.274157 TCTAGAGTCAAGTCAATGAGTTCC 57.726 41.667 0.00 0.00 33.17 3.62
2021 8231 4.985538 AGCAGATTTCCTTTGTTCCTACA 58.014 39.130 0.00 0.00 0.00 2.74
2046 8256 7.839680 ACAATGTCCAAGTCTTATTTTCCTT 57.160 32.000 0.00 0.00 0.00 3.36
2049 8259 6.877611 TGTCCAAGTCTTATTTTCCTTGAC 57.122 37.500 0.00 0.00 37.14 3.18
2063 8273 5.382664 TTCCTTGACCTAACTCAAAACCT 57.617 39.130 0.00 0.00 29.66 3.50
2069 8279 7.447238 CCTTGACCTAACTCAAAACCTATTCAA 59.553 37.037 0.00 0.00 29.66 2.69
2164 8374 3.599343 TCTGGTCACATTCCGATTGAAG 58.401 45.455 0.00 0.00 36.14 3.02
2264 8474 2.760092 ACTTGAAAGCTTTGACTGGCAA 59.240 40.909 18.30 12.01 33.88 4.52
2278 8488 3.209410 ACTGGCAATGCTACTGCTAATC 58.791 45.455 4.82 0.00 39.82 1.75
2361 8574 7.885399 GGTATGGGAATGTCTAATGATAGCTTT 59.115 37.037 0.00 0.00 0.00 3.51
2389 8602 2.360801 GTGACAAAAGGGCAAGTGCTTA 59.639 45.455 2.85 0.00 41.70 3.09
2493 8706 2.840651 CTCCCTTGGTGGTCTCATAAGT 59.159 50.000 0.00 0.00 0.00 2.24
2494 8707 3.256704 TCCCTTGGTGGTCTCATAAGTT 58.743 45.455 0.00 0.00 0.00 2.66
2495 8708 3.655777 TCCCTTGGTGGTCTCATAAGTTT 59.344 43.478 0.00 0.00 0.00 2.66
2496 8709 3.758554 CCCTTGGTGGTCTCATAAGTTTG 59.241 47.826 0.00 0.00 0.00 2.93
2497 8710 4.506625 CCCTTGGTGGTCTCATAAGTTTGA 60.507 45.833 0.00 0.00 0.00 2.69
2498 8711 5.256474 CCTTGGTGGTCTCATAAGTTTGAT 58.744 41.667 0.00 0.00 0.00 2.57
2499 8712 5.355350 CCTTGGTGGTCTCATAAGTTTGATC 59.645 44.000 0.00 0.00 0.00 2.92
2617 12631 0.326927 GTGGTGAAATTCCTCGGGGA 59.673 55.000 0.00 0.00 40.36 4.81
2782 12796 1.135315 CCAGTTCCAATGCAATGTCCG 60.135 52.381 0.21 0.00 0.00 4.79
2783 12797 0.527565 AGTTCCAATGCAATGTCCGC 59.472 50.000 0.21 0.00 0.00 5.54
2784 12798 0.458370 GTTCCAATGCAATGTCCGCC 60.458 55.000 0.21 0.00 0.00 6.13
2785 12799 0.611618 TTCCAATGCAATGTCCGCCT 60.612 50.000 0.21 0.00 0.00 5.52
2786 12800 0.254462 TCCAATGCAATGTCCGCCTA 59.746 50.000 0.21 0.00 0.00 3.93
2787 12801 0.664761 CCAATGCAATGTCCGCCTAG 59.335 55.000 0.21 0.00 0.00 3.02
2788 12802 1.667236 CAATGCAATGTCCGCCTAGA 58.333 50.000 0.00 0.00 0.00 2.43
2794 12820 0.325296 AATGTCCGCCTAGAGGTCCA 60.325 55.000 0.00 0.00 37.57 4.02
2817 12855 2.621055 CAACCAACGGAGATCCAACAAA 59.379 45.455 0.00 0.00 35.14 2.83
2823 12861 2.878406 ACGGAGATCCAACAAAGTTGTG 59.122 45.455 8.83 1.65 41.31 3.33
2840 12878 4.065088 GTTGTGTGAAGATGGCTTGTCTA 58.935 43.478 0.00 0.00 33.61 2.59
2851 12889 7.105241 AGATGGCTTGTCTAAAATGGATTTC 57.895 36.000 0.00 0.00 32.27 2.17
2999 13344 6.698766 CCATTGCTTGCTTAGATGGTTATTTC 59.301 38.462 0.00 0.00 0.00 2.17
3020 13385 4.558178 TCGGATTTTGCTGAAGTACGTTA 58.442 39.130 0.00 0.00 33.43 3.18
3032 13397 9.439500 TGCTGAAGTACGTTATTATTACCTTTT 57.561 29.630 0.00 0.00 0.00 2.27
3081 13449 2.832733 ACTTGTTAGGTACTCCCTCTGC 59.167 50.000 0.00 0.00 44.81 4.26
3105 13476 8.388103 TGCTAAGAATAAAAGCGTTTAGATCAC 58.612 33.333 16.97 8.47 39.14 3.06
3117 13488 8.942338 AGCGTTTAGATCACTGAAATATAACA 57.058 30.769 0.00 0.00 0.00 2.41
3118 13489 9.035607 AGCGTTTAGATCACTGAAATATAACAG 57.964 33.333 0.00 7.30 39.65 3.16
3120 13491 8.817100 CGTTTAGATCACTGAAATATAACAGCA 58.183 33.333 0.00 0.00 37.61 4.41
3172 13543 8.855804 ACACTCTTATATTTCTTTAGGGAGGA 57.144 34.615 0.00 0.00 0.00 3.71
3184 13555 7.808279 TCTTTAGGGAGGAAGTAGAATTCAA 57.192 36.000 8.44 0.00 0.00 2.69
3251 13622 9.631257 TTGTATTGGTGATCATCAATGATAAGT 57.369 29.630 34.48 16.70 46.84 2.24
3259 13630 7.924412 GTGATCATCAATGATAAGTGGCAAAAT 59.076 33.333 0.00 0.00 46.84 1.82
3283 13793 4.957327 AGTTATCAACTACTCCCTCTGTCC 59.043 45.833 0.00 0.00 40.69 4.02
3296 13806 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
3302 13812 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
3304 13814 8.441312 TGTCCCATAATATAAGAACGTTTTCC 57.559 34.615 0.46 0.00 31.28 3.13
3305 13815 8.047911 TGTCCCATAATATAAGAACGTTTTCCA 58.952 33.333 0.46 0.00 31.28 3.53
3306 13816 8.895737 GTCCCATAATATAAGAACGTTTTCCAA 58.104 33.333 0.46 0.00 31.28 3.53
3308 13818 9.511144 CCCATAATATAAGAACGTTTTCCAAAC 57.489 33.333 0.46 0.00 31.28 2.93
3317 13827 6.665465 AGAACGTTTTCCAAACTATGTTAGC 58.335 36.000 0.46 0.00 31.28 3.09
3318 13828 6.485648 AGAACGTTTTCCAAACTATGTTAGCT 59.514 34.615 0.46 0.00 31.28 3.32
3320 13830 6.435428 ACGTTTTCCAAACTATGTTAGCTTG 58.565 36.000 0.00 0.00 32.96 4.01
3328 13838 6.915843 CCAAACTATGTTAGCTTGAAAAACGT 59.084 34.615 0.00 0.00 34.61 3.99
3502 14014 0.326143 AACCAACAAGGGGGCAAAGT 60.326 50.000 0.00 0.00 43.89 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.719871 AGCTGATAAGTACTTCCTTAGACAA 57.280 36.000 12.39 0.00 30.84 3.18
72 74 7.396055 AGCTAGGATGATGATTAGGAAGAGTAC 59.604 40.741 0.00 0.00 0.00 2.73
112 120 4.143179 GGTTGAATGTTACACTACTCACGC 60.143 45.833 0.00 0.00 0.00 5.34
115 123 4.281435 TCCGGTTGAATGTTACACTACTCA 59.719 41.667 0.00 0.00 0.00 3.41
116 124 4.813027 TCCGGTTGAATGTTACACTACTC 58.187 43.478 0.00 0.00 0.00 2.59
120 128 2.038557 AGCTCCGGTTGAATGTTACACT 59.961 45.455 0.00 0.00 0.00 3.55
121 129 2.159627 CAGCTCCGGTTGAATGTTACAC 59.840 50.000 0.00 0.00 0.00 2.90
122 130 2.422597 CAGCTCCGGTTGAATGTTACA 58.577 47.619 0.00 0.00 0.00 2.41
182 5914 4.408821 GGGTCGCCTGTGATGCCA 62.409 66.667 0.00 0.00 0.00 4.92
290 6034 2.035442 GTTGCGGAGGTGGAGCTTC 61.035 63.158 0.00 0.00 0.00 3.86
297 6041 0.456221 AGATACTCGTTGCGGAGGTG 59.544 55.000 4.56 0.00 38.39 4.00
311 6055 8.432805 TCCTCTTCTGGAAATGGAAATAGATAC 58.567 37.037 0.00 0.00 32.39 2.24
342 6086 0.687354 GGGTCGATGGCACCAGATAT 59.313 55.000 0.00 0.00 35.35 1.63
349 6214 0.741221 GTCTTCAGGGTCGATGGCAC 60.741 60.000 0.00 0.00 0.00 5.01
351 6216 1.153349 GGTCTTCAGGGTCGATGGC 60.153 63.158 0.00 0.00 0.00 4.40
353 6218 0.898320 AGTGGTCTTCAGGGTCGATG 59.102 55.000 0.00 0.00 0.00 3.84
354 6219 1.187087 GAGTGGTCTTCAGGGTCGAT 58.813 55.000 0.00 0.00 0.00 3.59
355 6220 1.241990 CGAGTGGTCTTCAGGGTCGA 61.242 60.000 0.00 0.00 0.00 4.20
356 6221 1.213013 CGAGTGGTCTTCAGGGTCG 59.787 63.158 0.00 0.00 0.00 4.79
406 6271 4.389890 AGATGCTTGAGATGTGAGAGAC 57.610 45.455 0.00 0.00 0.00 3.36
434 6414 4.770795 CTCCGAGGACAATATTTCCACTT 58.229 43.478 14.95 0.56 35.33 3.16
440 6420 2.771943 TCCAGCTCCGAGGACAATATTT 59.228 45.455 0.00 0.00 0.00 1.40
519 6499 5.417580 GCACTCTACCATGAAAACCCATTTA 59.582 40.000 0.00 0.00 0.00 1.40
552 6536 3.261137 ACCAGTTTAGAGAGGTTGCCTAC 59.739 47.826 0.00 0.00 31.76 3.18
566 6550 5.719563 TCTCATGTCCAGATGTACCAGTTTA 59.280 40.000 0.00 0.00 0.00 2.01
610 6597 8.675504 ACCAAGATATATCGTCCGAGTATAAAG 58.324 37.037 7.08 0.00 0.00 1.85
639 6629 6.437477 AGATGTTGTAGCCATCGGAGATATAA 59.563 38.462 0.00 0.00 45.12 0.98
640 6630 5.952347 AGATGTTGTAGCCATCGGAGATATA 59.048 40.000 0.00 0.00 45.12 0.86
643 6633 2.968574 AGATGTTGTAGCCATCGGAGAT 59.031 45.455 0.00 0.00 45.12 2.75
652 6642 3.561725 GCTCATGGTAAGATGTTGTAGCC 59.438 47.826 0.00 0.00 0.00 3.93
667 6657 1.137675 TGAGGTCGATGAAGCTCATGG 59.862 52.381 1.92 3.37 45.98 3.66
672 6662 1.140589 CGCTGAGGTCGATGAAGCT 59.859 57.895 9.63 0.00 0.00 3.74
676 6666 1.377366 GACTCCGCTGAGGTCGATGA 61.377 60.000 10.11 0.00 43.29 2.92
750 6741 5.025453 ACTCCCATTAAGCCAACAATCATT 58.975 37.500 0.00 0.00 0.00 2.57
769 6760 4.747108 CAGATGATGACGGAACATTACTCC 59.253 45.833 0.00 0.00 0.00 3.85
782 6773 3.558505 GTTGTGTTGCACAGATGATGAC 58.441 45.455 2.17 0.00 45.39 3.06
790 6781 2.682856 ACTGTAAGGTTGTGTTGCACAG 59.317 45.455 2.17 0.00 41.76 3.66
794 6785 4.095782 TCAAGAACTGTAAGGTTGTGTTGC 59.904 41.667 0.00 0.00 39.30 4.17
841 6832 2.743928 CAGCCGGACTGCAGAACC 60.744 66.667 23.35 20.79 40.19 3.62
1079 7070 9.091220 AGTTGGGTATTATGTCTATTACCTCTC 57.909 37.037 0.00 0.00 35.53 3.20
1094 7085 6.442541 TCTTCCAAGAACAGTTGGGTATTA 57.557 37.500 2.88 0.00 46.24 0.98
1227 7218 2.936919 TCTCAACATGCACTGAACCT 57.063 45.000 0.00 0.00 0.00 3.50
1238 7301 4.018490 TGTAAGCATGCCAATCTCAACAT 58.982 39.130 15.66 0.00 0.00 2.71
1242 7305 5.664294 AATTTGTAAGCATGCCAATCTCA 57.336 34.783 15.66 2.85 0.00 3.27
1327 7534 8.034804 GTCAATGGCCTGTAAATTAATCAAACT 58.965 33.333 3.32 0.00 0.00 2.66
1335 7542 8.271458 TGAGATAAGTCAATGGCCTGTAAATTA 58.729 33.333 3.32 0.00 0.00 1.40
1342 7549 4.412796 TCTGAGATAAGTCAATGGCCTG 57.587 45.455 3.32 0.00 0.00 4.85
1345 7552 9.674824 CAAATTATTCTGAGATAAGTCAATGGC 57.325 33.333 0.00 0.00 0.00 4.40
1389 7596 1.002624 GAACGGAGGCACCCAATGA 60.003 57.895 0.00 0.00 34.64 2.57
1482 7689 9.839817 TTGTTTGAAATATCAAGGATACGGATA 57.160 29.630 0.00 0.00 45.82 2.59
1701 7908 9.347240 CCATTTAAAGAGTTCATGGATATGTCT 57.653 33.333 0.00 0.00 37.20 3.41
1784 7994 3.911260 TGTTGGAATAGCCCCGGATATTA 59.089 43.478 0.73 0.00 36.91 0.98
1875 8085 1.982073 GCTCTTTCCGGCCACAATCG 61.982 60.000 2.24 0.00 0.00 3.34
1898 8108 1.296727 GCTAGATGGGTTACGTTGCC 58.703 55.000 0.00 0.00 0.00 4.52
1925 8135 7.180051 AGGAACTCATTGACTTGACTCTAGAAT 59.820 37.037 0.00 0.00 0.00 2.40
1929 8139 6.267699 TGAAGGAACTCATTGACTTGACTCTA 59.732 38.462 0.00 0.00 38.49 2.43
1950 8160 9.050601 AGAAGAGTAGTGATTTTCAAACTGAAG 57.949 33.333 0.09 0.00 37.70 3.02
2021 8231 7.839680 AGGAAAATAAGACTTGGACATTGTT 57.160 32.000 0.00 0.00 0.00 2.83
2046 8256 6.425721 CGTTGAATAGGTTTTGAGTTAGGTCA 59.574 38.462 0.00 0.00 0.00 4.02
2049 8259 5.935789 TCCGTTGAATAGGTTTTGAGTTAGG 59.064 40.000 0.00 0.00 0.00 2.69
2264 8474 7.166851 AGCTATTGAATGATTAGCAGTAGCAT 58.833 34.615 17.43 6.14 44.97 3.79
2364 8577 1.110442 CTTGCCCTTTTGTCACCACA 58.890 50.000 0.00 0.00 0.00 4.17
2372 8585 3.733443 ACTTAAGCACTTGCCCTTTTG 57.267 42.857 1.29 0.00 43.38 2.44
2617 12631 7.743749 AGCTCAGGTATGTCAAATCTGATAAT 58.256 34.615 0.00 0.00 34.50 1.28
2782 12796 1.198759 TGGTTGGTGGACCTCTAGGC 61.199 60.000 0.00 0.00 40.47 3.93
2783 12797 1.003233 GTTGGTTGGTGGACCTCTAGG 59.997 57.143 0.00 0.00 40.47 3.02
2784 12798 1.337823 CGTTGGTTGGTGGACCTCTAG 60.338 57.143 0.00 0.00 40.47 2.43
2785 12799 0.682852 CGTTGGTTGGTGGACCTCTA 59.317 55.000 0.00 0.00 40.47 2.43
2786 12800 1.450211 CGTTGGTTGGTGGACCTCT 59.550 57.895 0.00 0.00 40.47 3.69
2787 12801 1.599797 CCGTTGGTTGGTGGACCTC 60.600 63.158 0.00 0.00 40.47 3.85
2788 12802 2.052047 CTCCGTTGGTTGGTGGACCT 62.052 60.000 0.00 0.00 40.47 3.85
2794 12820 0.768622 TTGGATCTCCGTTGGTTGGT 59.231 50.000 0.00 0.00 39.43 3.67
2817 12855 2.880890 GACAAGCCATCTTCACACAACT 59.119 45.455 0.00 0.00 0.00 3.16
2823 12861 5.415701 TCCATTTTAGACAAGCCATCTTCAC 59.584 40.000 0.00 0.00 0.00 3.18
2851 12889 6.475596 AAGCCAATAATTGATCCAAGAAGG 57.524 37.500 0.00 0.00 39.47 3.46
2931 13276 7.769044 GTGGCATAAGAAATCCAAGTAGTTCTA 59.231 37.037 0.00 0.00 30.24 2.10
2999 13344 3.806316 AACGTACTTCAGCAAAATCCG 57.194 42.857 0.00 0.00 0.00 4.18
3032 13397 4.548451 TGCATGGAAATACATTTTGCCA 57.452 36.364 0.00 0.00 32.75 4.92
3069 13437 6.480651 GCTTTTATTCTTAGCAGAGGGAGTAC 59.519 42.308 0.00 0.00 35.05 2.73
3081 13449 9.907576 CAGTGATCTAAACGCTTTTATTCTTAG 57.092 33.333 0.00 0.00 0.00 2.18
3145 13516 9.907229 CCTCCCTAAAGAAATATAAGAGTGTTT 57.093 33.333 0.00 0.00 0.00 2.83
3146 13517 9.280456 TCCTCCCTAAAGAAATATAAGAGTGTT 57.720 33.333 0.00 0.00 0.00 3.32
3147 13518 8.855804 TCCTCCCTAAAGAAATATAAGAGTGT 57.144 34.615 0.00 0.00 0.00 3.55
3148 13519 9.771534 CTTCCTCCCTAAAGAAATATAAGAGTG 57.228 37.037 0.00 0.00 0.00 3.51
3149 13520 9.508721 ACTTCCTCCCTAAAGAAATATAAGAGT 57.491 33.333 0.00 0.00 0.00 3.24
3166 13537 7.176690 TGTTTTCATTGAATTCTACTTCCTCCC 59.823 37.037 7.05 0.00 0.00 4.30
3225 13596 9.631257 ACTTATCATTGATGATCACCAATACAA 57.369 29.630 15.13 8.44 43.72 2.41
3251 13622 6.826741 GGGAGTAGTTGATAACTATTTTGCCA 59.173 38.462 4.89 0.00 45.05 4.92
3259 13630 6.127793 GGACAGAGGGAGTAGTTGATAACTA 58.872 44.000 0.00 0.00 42.81 2.24
3296 13806 6.261381 TCAAGCTAACATAGTTTGGAAAACGT 59.739 34.615 12.15 0.00 44.16 3.99
3302 13812 7.136119 CGTTTTTCAAGCTAACATAGTTTGGA 58.864 34.615 12.15 3.22 44.16 3.53
3304 13814 7.908193 ACGTTTTTCAAGCTAACATAGTTTG 57.092 32.000 7.42 7.42 45.01 2.93
3305 13815 8.403236 AGAACGTTTTTCAAGCTAACATAGTTT 58.597 29.630 0.46 0.00 0.00 2.66
3306 13816 7.927048 AGAACGTTTTTCAAGCTAACATAGTT 58.073 30.769 0.46 0.00 0.00 2.24
3320 13830 9.931210 CTGTCCCATAATATAAGAACGTTTTTC 57.069 33.333 7.42 0.00 0.00 2.29
3328 13838 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
3345 13855 3.121929 TGCCTCTGAAATACTCCCTCT 57.878 47.619 0.00 0.00 0.00 3.69
3477 13989 1.974957 GCCCCCTTGTTGGTTGTAATT 59.025 47.619 0.00 0.00 0.00 1.40
3502 14014 7.284261 TGAATTTGTTTGACAAGTAGATGACCA 59.716 33.333 0.00 0.00 39.53 4.02


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

AutoCloner maintained by Alex Coulton.