Multiple sequence alignment - TraesCS1B01G462800

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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 TraesCS1B01G462800 chr1B 100.000 3229 0 0 1 3229 674932401 674935629 0.000000e+00 5963.0
1 TraesCS1B01G462800 chr1B 90.719 1293 84 14 1 1287 674818494 674819756 0.000000e+00 1690.0
2 TraesCS1B01G462800 chr1B 85.780 1301 138 27 417 1708 646774570 646775832 0.000000e+00 1334.0
3 TraesCS1B01G462800 chr1B 93.333 645 35 3 1 644 674892339 674892976 0.000000e+00 946.0
4 TraesCS1B01G462800 chr1B 90.698 645 30 15 1 644 675223522 675222907 0.000000e+00 832.0
5 TraesCS1B01G462800 chr1B 93.678 522 19 5 2293 2808 646776435 646776948 0.000000e+00 769.0
6 TraesCS1B01G462800 chr1B 91.788 548 35 6 1757 2294 646775940 646776487 0.000000e+00 754.0
7 TraesCS1B01G462800 chr1B 94.043 470 23 3 1 470 646684696 646685160 0.000000e+00 708.0
8 TraesCS1B01G462800 chr1B 83.851 322 32 10 2040 2346 675227532 675227216 4.080000e-74 289.0
9 TraesCS1B01G462800 chr1B 98.693 153 2 0 2293 2445 674894999 674895151 4.100000e-69 272.0
10 TraesCS1B01G462800 chr1B 98.077 156 3 0 2293 2448 675220898 675220743 4.100000e-69 272.0
11 TraesCS1B01G462800 chr1B 93.082 159 5 2 2293 2445 646687181 646687339 9.010000e-56 228.0
12 TraesCS1B01G462800 chr1B 78.626 262 35 14 2866 3111 646776946 646777202 1.550000e-33 154.0
13 TraesCS1B01G462800 chr1B 87.037 108 7 1 2197 2297 675311532 675311639 7.320000e-22 115.0
14 TraesCS1B01G462800 chr1B 96.552 58 2 0 2411 2468 674821320 674821377 2.650000e-16 97.1
15 TraesCS1B01G462800 chr1B 100.000 31 0 0 645 675 646773225 646773255 1.250000e-04 58.4
16 TraesCS1B01G462800 chr1D 95.152 1712 74 4 1 1708 484868977 484870683 0.000000e+00 2693.0
17 TraesCS1B01G462800 chr1D 84.719 1407 155 24 314 1708 466603453 466604811 0.000000e+00 1352.0
18 TraesCS1B01G462800 chr1D 95.582 679 19 2 2293 2961 466605385 466606062 0.000000e+00 1077.0
19 TraesCS1B01G462800 chr1D 93.344 646 27 7 1 644 484737185 484737816 0.000000e+00 941.0
20 TraesCS1B01G462800 chr1D 93.399 606 26 5 1699 2294 484870701 484871302 0.000000e+00 885.0
21 TraesCS1B01G462800 chr1D 92.739 606 26 6 1699 2294 466604838 466605435 0.000000e+00 859.0
22 TraesCS1B01G462800 chr1D 95.564 541 12 3 2293 2822 484871252 484871791 0.000000e+00 856.0
23 TraesCS1B01G462800 chr1D 92.016 501 30 7 69 563 484562356 484562852 0.000000e+00 695.0
24 TraesCS1B01G462800 chr1D 83.607 244 17 15 2965 3190 484871915 484872153 1.170000e-49 207.0
25 TraesCS1B01G462800 chr1D 93.860 114 7 0 2184 2297 484796760 484796873 4.280000e-39 172.0
26 TraesCS1B01G462800 chr1D 94.393 107 6 0 2184 2290 484566265 484566371 7.170000e-37 165.0
27 TraesCS1B01G462800 chr1D 82.692 156 17 4 2293 2448 485020395 485020540 2.610000e-26 130.0
28 TraesCS1B01G462800 chr1D 100.000 31 0 0 645 675 484868510 484868540 1.250000e-04 58.4
29 TraesCS1B01G462800 chr1A 93.953 645 28 6 1 644 581878233 581878867 0.000000e+00 965.0
30 TraesCS1B01G462800 chr1A 93.032 531 25 3 2293 2822 581960245 581960764 0.000000e+00 765.0
31 TraesCS1B01G462800 chr1A 86.864 609 59 10 1699 2294 581959695 581960295 0.000000e+00 662.0
32 TraesCS1B01G462800 chr1A 93.494 415 20 5 1 410 581913959 581914371 7.660000e-171 610.0
33 TraesCS1B01G462800 chr1A 79.870 308 46 12 1991 2290 581880157 581880456 9.080000e-51 211.0
34 TraesCS1B01G462800 chr1A 83.265 245 18 15 2965 3191 581960893 581961132 1.520000e-48 204.0
35 TraesCS1B01G462800 chr1A 75.610 369 40 32 2411 2774 581880462 581880785 1.560000e-28 137.0
36 TraesCS1B01G462800 chr1A 90.291 103 9 1 2860 2962 581960756 581960857 2.020000e-27 134.0


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 TraesCS1B01G462800 chr1B 674932401 674935629 3228 False 5963.000000 5963 100.000000 1 3229 1 chr1B.!!$F1 3228
1 TraesCS1B01G462800 chr1B 674818494 674821377 2883 False 893.550000 1690 93.635500 1 2468 2 chr1B.!!$F5 2467
2 TraesCS1B01G462800 chr1B 646773225 646777202 3977 False 613.880000 1334 89.974400 417 3111 5 chr1B.!!$F4 2694
3 TraesCS1B01G462800 chr1B 674892339 674895151 2812 False 609.000000 946 96.013000 1 2445 2 chr1B.!!$F6 2444
4 TraesCS1B01G462800 chr1B 646684696 646687339 2643 False 468.000000 708 93.562500 1 2445 2 chr1B.!!$F3 2444
5 TraesCS1B01G462800 chr1B 675220743 675227532 6789 True 464.333333 832 90.875333 1 2448 3 chr1B.!!$R1 2447
6 TraesCS1B01G462800 chr1D 466603453 466606062 2609 False 1096.000000 1352 91.013333 314 2961 3 chr1D.!!$F4 2647
7 TraesCS1B01G462800 chr1D 484737185 484737816 631 False 941.000000 941 93.344000 1 644 1 chr1D.!!$F1 643
8 TraesCS1B01G462800 chr1D 484868510 484872153 3643 False 939.880000 2693 93.544400 1 3190 5 chr1D.!!$F6 3189
9 TraesCS1B01G462800 chr1D 484562356 484566371 4015 False 430.000000 695 93.204500 69 2290 2 chr1D.!!$F5 2221
10 TraesCS1B01G462800 chr1A 581959695 581961132 1437 False 441.250000 765 88.363000 1699 3191 4 chr1A.!!$F3 1492
11 TraesCS1B01G462800 chr1A 581878233 581880785 2552 False 437.666667 965 83.144333 1 2774 3 chr1A.!!$F2 2773

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
935 6440 1.131126 GTTTGATCGTGCATCCCACAG 59.869 52.381 0.0 0.0 44.91 3.66 F
1558 8089 1.002868 GCAGATGTGTCAGGGCTGT 60.003 57.895 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 8599 0.252479 CTTGGCAGAGGTCAGAGCAT 59.748 55.0 1.66 0.0 0.0 3.79 R
3195 10807 0.036010 AGCCATTGGAGGACTGAACG 60.036 55.0 6.95 0.0 0.0 3.95 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
49 4061 1.660607 CGTCGAATGCAGCATACAACT 59.339 47.619 8.75 0.00 0.00 3.16
400 4414 6.879962 TCTTTTGTTTGTTACCGTATTCTCG 58.120 36.000 0.00 0.00 0.00 4.04
624 5775 2.928801 TGAGTTCTTAGTTGCTGGCA 57.071 45.000 0.00 0.00 0.00 4.92
687 5838 2.612212 TCTGACGCTTGGAAACTTTGTC 59.388 45.455 0.00 0.00 0.00 3.18
794 6133 5.485620 TCTGATATCTAGTTGGATGCATGC 58.514 41.667 11.82 11.82 0.00 4.06
889 6231 5.047802 TGAATGCCTTCTTCAGAAATTGTCC 60.048 40.000 3.32 0.00 33.07 4.02
935 6440 1.131126 GTTTGATCGTGCATCCCACAG 59.869 52.381 0.00 0.00 44.91 3.66
955 6525 4.190001 CAGCATGCATCCTATCTCATACC 58.810 47.826 21.98 0.00 0.00 2.73
1069 6657 1.301423 TGAGTACGTGCAAAACCACC 58.699 50.000 6.38 0.00 32.10 4.61
1104 6692 5.211201 TGACATGAACCTGATCTATCCAGA 58.789 41.667 0.00 0.00 33.65 3.86
1157 6782 9.469807 TTTGCTAATTGTTTTGTTATGTACAGG 57.530 29.630 0.33 0.00 38.19 4.00
1244 6869 6.292596 GCGAGAACATCTTGGATAATGAAGAC 60.293 42.308 0.00 0.00 31.09 3.01
1306 6972 2.590291 TGCCGCTCAAACGCTTCA 60.590 55.556 0.00 0.00 0.00 3.02
1526 8057 3.476295 ACTGTTGCTTGTTGATATGCG 57.524 42.857 0.00 0.00 0.00 4.73
1558 8089 1.002868 GCAGATGTGTCAGGGCTGT 60.003 57.895 0.00 0.00 0.00 4.40
1577 8111 1.893808 CTTGCCTTGCTGTGACCGT 60.894 57.895 0.00 0.00 0.00 4.83
1724 8580 6.015027 TCTTCTTTAGAGAGCACACTACAC 57.985 41.667 0.00 0.00 32.44 2.90
1737 8593 4.112634 CACACTACACTCATGAATACCGG 58.887 47.826 0.00 0.00 0.00 5.28
1739 8595 4.112634 CACTACACTCATGAATACCGGTG 58.887 47.826 19.93 8.52 0.00 4.94
1740 8596 2.691409 ACACTCATGAATACCGGTGG 57.309 50.000 19.93 0.00 0.00 4.61
1741 8597 2.184533 ACACTCATGAATACCGGTGGA 58.815 47.619 19.93 0.00 0.00 4.02
1742 8598 2.569853 ACACTCATGAATACCGGTGGAA 59.430 45.455 19.93 0.00 0.00 3.53
1743 8599 3.008594 ACACTCATGAATACCGGTGGAAA 59.991 43.478 19.93 0.00 0.00 3.13
1810 9128 4.329545 TGCCAAGGAGTCCACCGC 62.330 66.667 12.86 9.58 34.73 5.68
2012 9476 7.169982 CACTCACTCGTGTAATTTTCTCTCTTT 59.830 37.037 0.00 0.00 0.00 2.52
2036 9500 4.623002 TCTGCGTTTATGTACACAACAGA 58.377 39.130 16.32 9.97 42.70 3.41
2082 9546 0.173708 GTCAAGGGAGTACTCGCAGG 59.826 60.000 33.61 25.78 43.96 4.85
2229 9730 1.002033 CTGCTCCTTTTGTGCAGTGAC 60.002 52.381 7.80 0.00 46.23 3.67
2235 9736 0.376852 TTTTGTGCAGTGACGACAGC 59.623 50.000 0.00 0.00 35.23 4.40
2243 9744 1.300931 GTGACGACAGCAGGCTTCA 60.301 57.895 0.00 0.00 0.00 3.02
2244 9745 1.005748 TGACGACAGCAGGCTTCAG 60.006 57.895 0.00 0.00 0.00 3.02
2245 9746 1.290324 GACGACAGCAGGCTTCAGA 59.710 57.895 0.00 0.00 0.00 3.27
2246 9747 1.005630 ACGACAGCAGGCTTCAGAC 60.006 57.895 0.00 0.00 0.00 3.51
2247 9748 1.005748 CGACAGCAGGCTTCAGACA 60.006 57.895 0.00 0.00 0.00 3.41
2248 9749 0.390866 CGACAGCAGGCTTCAGACAT 60.391 55.000 0.00 0.00 0.00 3.06
2249 9750 1.134995 CGACAGCAGGCTTCAGACATA 60.135 52.381 0.00 0.00 0.00 2.29
2250 9751 2.548875 GACAGCAGGCTTCAGACATAG 58.451 52.381 0.00 0.00 0.00 2.23
2251 9752 1.297664 CAGCAGGCTTCAGACATAGC 58.702 55.000 0.00 0.00 36.66 2.97
2252 9753 0.907486 AGCAGGCTTCAGACATAGCA 59.093 50.000 0.00 0.00 39.15 3.49
2253 9754 1.134461 AGCAGGCTTCAGACATAGCAG 60.134 52.381 0.00 0.00 39.15 4.24
2254 9755 1.134580 GCAGGCTTCAGACATAGCAGA 60.135 52.381 0.00 0.00 39.15 4.26
2255 9756 2.823984 CAGGCTTCAGACATAGCAGAG 58.176 52.381 0.00 0.00 39.15 3.35
2256 9757 1.138661 AGGCTTCAGACATAGCAGAGC 59.861 52.381 0.00 0.00 39.15 4.09
2257 9758 1.134580 GGCTTCAGACATAGCAGAGCA 60.135 52.381 0.00 0.00 39.15 4.26
2258 9759 2.485124 GGCTTCAGACATAGCAGAGCAT 60.485 50.000 0.00 0.00 39.15 3.79
2259 9760 2.544686 GCTTCAGACATAGCAGAGCATG 59.455 50.000 0.00 0.00 37.35 4.06
2260 9761 3.740452 GCTTCAGACATAGCAGAGCATGA 60.740 47.826 0.00 0.00 37.35 3.07
2261 9762 4.633175 CTTCAGACATAGCAGAGCATGAT 58.367 43.478 0.00 0.00 0.00 2.45
2262 9763 3.991367 TCAGACATAGCAGAGCATGATG 58.009 45.455 0.00 0.00 0.00 3.07
2263 9764 2.480802 CAGACATAGCAGAGCATGATGC 59.519 50.000 9.89 9.89 45.46 3.91
2275 9776 3.411415 GCATGATGCAAGTCACCTTAC 57.589 47.619 13.36 0.00 44.26 2.34
2276 9777 2.749076 GCATGATGCAAGTCACCTTACA 59.251 45.455 13.36 0.00 44.26 2.41
2277 9778 3.379372 GCATGATGCAAGTCACCTTACAT 59.621 43.478 13.36 0.00 44.26 2.29
2278 9779 4.576053 GCATGATGCAAGTCACCTTACATA 59.424 41.667 13.36 0.00 44.26 2.29
2279 9780 5.504665 GCATGATGCAAGTCACCTTACATAC 60.505 44.000 13.36 0.00 44.26 2.39
2280 9781 5.420725 TGATGCAAGTCACCTTACATACT 57.579 39.130 0.00 0.00 35.29 2.12
2281 9782 5.804639 TGATGCAAGTCACCTTACATACTT 58.195 37.500 0.00 0.00 35.29 2.24
2282 9783 6.941857 TGATGCAAGTCACCTTACATACTTA 58.058 36.000 0.00 0.00 35.29 2.24
2283 9784 6.816640 TGATGCAAGTCACCTTACATACTTAC 59.183 38.462 0.00 0.00 35.29 2.34
2284 9785 5.484715 TGCAAGTCACCTTACATACTTACC 58.515 41.667 0.00 0.00 31.20 2.85
2285 9786 5.012251 TGCAAGTCACCTTACATACTTACCA 59.988 40.000 0.00 0.00 31.20 3.25
2286 9787 6.113411 GCAAGTCACCTTACATACTTACCAT 58.887 40.000 0.00 0.00 31.20 3.55
2287 9788 6.258068 GCAAGTCACCTTACATACTTACCATC 59.742 42.308 0.00 0.00 31.20 3.51
2288 9789 6.481434 AGTCACCTTACATACTTACCATCC 57.519 41.667 0.00 0.00 0.00 3.51
2289 9790 6.203072 AGTCACCTTACATACTTACCATCCT 58.797 40.000 0.00 0.00 0.00 3.24
2290 9791 6.324254 AGTCACCTTACATACTTACCATCCTC 59.676 42.308 0.00 0.00 0.00 3.71
2291 9792 6.097839 GTCACCTTACATACTTACCATCCTCA 59.902 42.308 0.00 0.00 0.00 3.86
2544 10084 1.693627 AGGAATATCAGTCGGCGTCT 58.306 50.000 6.85 3.06 0.00 4.18
2900 10440 1.542544 GACAAATCGCATGCAAGCTC 58.457 50.000 19.57 0.00 0.00 4.09
2922 10462 2.856222 ACTCTGAAGGAGGCAAAACAG 58.144 47.619 0.00 0.00 45.83 3.16
2926 10466 5.221925 ACTCTGAAGGAGGCAAAACAGATTA 60.222 40.000 0.00 0.00 45.83 1.75
2927 10467 5.248640 TCTGAAGGAGGCAAAACAGATTAG 58.751 41.667 0.00 0.00 31.02 1.73
2935 10475 4.393062 AGGCAAAACAGATTAGTGATGTCG 59.607 41.667 0.00 0.00 0.00 4.35
2962 10502 1.132262 TCGATGCCGCAATTCTTTTCC 59.868 47.619 0.00 0.00 35.37 3.13
2985 10566 5.455392 CATTTTCTGCAGTAGAGTTGGTTG 58.545 41.667 14.67 0.00 36.61 3.77
2997 10578 0.532115 GTTGGTTGGCTTGCCCTATG 59.468 55.000 9.35 0.00 0.00 2.23
3003 10584 3.508840 GCTTGCCCTATGCGCGTT 61.509 61.111 7.78 0.00 45.60 4.84
3005 10586 2.046796 TTGCCCTATGCGCGTTCA 60.047 55.556 7.78 0.00 45.60 3.18
3006 10587 2.309764 CTTGCCCTATGCGCGTTCAC 62.310 60.000 7.78 0.00 45.60 3.18
3007 10588 3.573491 GCCCTATGCGCGTTCACC 61.573 66.667 7.78 0.00 0.00 4.02
3008 10589 2.186903 CCCTATGCGCGTTCACCT 59.813 61.111 7.78 0.00 0.00 4.00
3014 10595 0.810031 ATGCGCGTTCACCTACCATC 60.810 55.000 8.43 0.00 0.00 3.51
3117 10729 9.534565 GATGATGCAAGATACTCACTAACTAAA 57.465 33.333 0.00 0.00 0.00 1.85
3118 10730 9.890629 ATGATGCAAGATACTCACTAACTAAAA 57.109 29.630 0.00 0.00 0.00 1.52
3119 10731 9.719355 TGATGCAAGATACTCACTAACTAAAAA 57.281 29.630 0.00 0.00 0.00 1.94
3157 10769 4.792704 GCAAACGACATCCACAATTCAAGT 60.793 41.667 0.00 0.00 0.00 3.16
3191 10803 5.877012 TCAAACAAGAGATGCCTACAAGATC 59.123 40.000 0.00 0.00 0.00 2.75
3192 10804 5.690464 AACAAGAGATGCCTACAAGATCT 57.310 39.130 0.00 0.00 0.00 2.75
3193 10805 5.690464 ACAAGAGATGCCTACAAGATCTT 57.310 39.130 0.88 0.88 0.00 2.40
3194 10806 5.669477 ACAAGAGATGCCTACAAGATCTTC 58.331 41.667 4.57 0.00 0.00 2.87
3195 10807 4.953940 AGAGATGCCTACAAGATCTTCC 57.046 45.455 4.57 0.00 0.00 3.46
3196 10808 3.320541 AGAGATGCCTACAAGATCTTCCG 59.679 47.826 4.57 0.00 0.00 4.30
3197 10809 3.034635 AGATGCCTACAAGATCTTCCGT 58.965 45.455 4.57 4.29 0.00 4.69
3198 10810 3.452627 AGATGCCTACAAGATCTTCCGTT 59.547 43.478 4.57 0.00 0.00 4.44
3199 10811 3.247006 TGCCTACAAGATCTTCCGTTC 57.753 47.619 4.57 0.00 0.00 3.95
3200 10812 2.565391 TGCCTACAAGATCTTCCGTTCA 59.435 45.455 4.57 0.00 0.00 3.18
3201 10813 3.190874 GCCTACAAGATCTTCCGTTCAG 58.809 50.000 4.57 0.00 0.00 3.02
3202 10814 3.368531 GCCTACAAGATCTTCCGTTCAGT 60.369 47.826 4.57 1.24 0.00 3.41
3203 10815 4.425520 CCTACAAGATCTTCCGTTCAGTC 58.574 47.826 4.57 0.00 0.00 3.51
3204 10816 3.320673 ACAAGATCTTCCGTTCAGTCC 57.679 47.619 4.57 0.00 0.00 3.85
3205 10817 2.900546 ACAAGATCTTCCGTTCAGTCCT 59.099 45.455 4.57 0.00 0.00 3.85
3206 10818 3.056465 ACAAGATCTTCCGTTCAGTCCTC 60.056 47.826 4.57 0.00 0.00 3.71
3207 10819 2.104170 AGATCTTCCGTTCAGTCCTCC 58.896 52.381 0.00 0.00 0.00 4.30
3208 10820 1.825474 GATCTTCCGTTCAGTCCTCCA 59.175 52.381 0.00 0.00 0.00 3.86
3209 10821 1.712056 TCTTCCGTTCAGTCCTCCAA 58.288 50.000 0.00 0.00 0.00 3.53
3210 10822 2.257207 TCTTCCGTTCAGTCCTCCAAT 58.743 47.619 0.00 0.00 0.00 3.16
3211 10823 2.028112 TCTTCCGTTCAGTCCTCCAATG 60.028 50.000 0.00 0.00 0.00 2.82
3212 10824 0.613260 TCCGTTCAGTCCTCCAATGG 59.387 55.000 0.00 0.00 0.00 3.16
3213 10825 1.026718 CCGTTCAGTCCTCCAATGGC 61.027 60.000 0.00 0.00 0.00 4.40
3214 10826 0.036010 CGTTCAGTCCTCCAATGGCT 60.036 55.000 0.00 0.00 0.00 4.75
3215 10827 1.743996 GTTCAGTCCTCCAATGGCTC 58.256 55.000 0.00 0.00 0.00 4.70
3216 10828 1.003580 GTTCAGTCCTCCAATGGCTCA 59.996 52.381 0.00 0.00 0.00 4.26
3217 10829 0.907486 TCAGTCCTCCAATGGCTCAG 59.093 55.000 0.00 0.00 0.00 3.35
3218 10830 0.907486 CAGTCCTCCAATGGCTCAGA 59.093 55.000 0.00 0.00 0.00 3.27
3219 10831 1.489649 CAGTCCTCCAATGGCTCAGAT 59.510 52.381 0.00 0.00 0.00 2.90
3220 10832 1.489649 AGTCCTCCAATGGCTCAGATG 59.510 52.381 0.00 0.00 0.00 2.90
3221 10833 0.182061 TCCTCCAATGGCTCAGATGC 59.818 55.000 0.00 0.00 0.00 3.91
3222 10834 0.183014 CCTCCAATGGCTCAGATGCT 59.817 55.000 0.00 0.00 0.00 3.79
3223 10835 1.595466 CTCCAATGGCTCAGATGCTC 58.405 55.000 0.00 0.00 0.00 4.26
3224 10836 1.141254 CTCCAATGGCTCAGATGCTCT 59.859 52.381 0.00 0.00 0.00 4.09
3225 10837 1.140452 TCCAATGGCTCAGATGCTCTC 59.860 52.381 0.00 0.00 0.00 3.20
3226 10838 1.218763 CAATGGCTCAGATGCTCTCG 58.781 55.000 0.00 0.00 0.00 4.04
3227 10839 0.106335 AATGGCTCAGATGCTCTCGG 59.894 55.000 0.00 0.00 0.00 4.63
3228 10840 0.758310 ATGGCTCAGATGCTCTCGGA 60.758 55.000 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 4061 1.813786 GGCCAGCATTTTACACCGTAA 59.186 47.619 0.00 0.00 0.00 3.18
354 4368 3.195396 AGTTGGCGGCATCATTAACAATT 59.805 39.130 20.58 0.00 0.00 2.32
365 4379 1.039856 AACAAAAGAGTTGGCGGCAT 58.960 45.000 14.32 0.00 0.00 4.40
410 4424 6.538945 ACAAACAAAACAGTTGGTAGGATT 57.461 33.333 0.00 0.00 33.97 3.01
411 4425 6.538945 AACAAACAAAACAGTTGGTAGGAT 57.461 33.333 0.00 0.00 34.63 3.24
412 4426 5.986501 AACAAACAAAACAGTTGGTAGGA 57.013 34.783 0.00 0.00 34.63 2.94
413 4427 5.746721 GCTAACAAACAAAACAGTTGGTAGG 59.253 40.000 9.15 0.00 34.63 3.18
414 4428 5.454232 CGCTAACAAACAAAACAGTTGGTAG 59.546 40.000 3.82 3.82 34.63 3.18
459 4475 6.808008 TGCTCAGAAACTAAGAAAATCAGG 57.192 37.500 0.00 0.00 0.00 3.86
624 5775 1.200716 CAGCAAGCATTCACGAACCAT 59.799 47.619 0.00 0.00 0.00 3.55
687 5838 5.894807 AGATTTTTCAATCCGCATTACAGG 58.105 37.500 0.00 0.00 39.95 4.00
889 6231 5.049198 TGCTCAGAAAACTTATGTTCAGCTG 60.049 40.000 7.63 7.63 34.96 4.24
935 6440 3.193263 CGGTATGAGATAGGATGCATGC 58.807 50.000 11.82 11.82 0.00 4.06
955 6525 4.212636 TGCAATGAGAATATGAGATGCACG 59.787 41.667 0.00 0.00 37.61 5.34
1069 6657 6.924612 TCAGGTTCATGTCATTTGAATTGTTG 59.075 34.615 0.00 0.00 35.68 3.33
1111 6703 4.927267 AACTGGTTGGATGGATCAGTTA 57.073 40.909 5.37 0.00 43.95 2.24
1208 6833 0.669619 TGTTCTCGCACTTACCACGA 59.330 50.000 0.00 0.00 0.00 4.35
1244 6869 2.094894 AGCAAATTTCTCTGCGATCGTG 59.905 45.455 17.81 10.27 43.51 4.35
1306 6972 2.743718 CCACAACAGAGCCCGAGT 59.256 61.111 0.00 0.00 0.00 4.18
1558 8089 1.597854 CGGTCACAGCAAGGCAAGA 60.598 57.895 0.00 0.00 0.00 3.02
1724 8580 3.003689 GCATTTCCACCGGTATTCATGAG 59.996 47.826 6.87 0.00 0.00 2.90
1737 8593 2.354259 CAGAGGTCAGAGCATTTCCAC 58.646 52.381 1.66 0.00 0.00 4.02
1739 8595 1.377536 GCAGAGGTCAGAGCATTTCC 58.622 55.000 1.66 0.00 0.00 3.13
1740 8596 1.339438 TGGCAGAGGTCAGAGCATTTC 60.339 52.381 1.66 0.00 0.00 2.17
1741 8597 0.694771 TGGCAGAGGTCAGAGCATTT 59.305 50.000 1.66 0.00 0.00 2.32
1742 8598 0.694771 TTGGCAGAGGTCAGAGCATT 59.305 50.000 1.66 0.00 0.00 3.56
1743 8599 0.252479 CTTGGCAGAGGTCAGAGCAT 59.748 55.000 1.66 0.00 0.00 3.79
1810 9128 1.067915 CGGTTTGGCATTTACACCCAG 60.068 52.381 0.00 0.00 0.00 4.45
2012 9476 5.524281 TCTGTTGTGTACATAAACGCAGAAA 59.476 36.000 16.62 2.10 40.68 2.52
2229 9730 0.390866 ATGTCTGAAGCCTGCTGTCG 60.391 55.000 0.00 0.00 0.00 4.35
2235 9736 2.823984 CTCTGCTATGTCTGAAGCCTG 58.176 52.381 0.00 0.00 37.97 4.85
2243 9744 2.104281 TGCATCATGCTCTGCTATGTCT 59.896 45.455 11.84 0.00 45.31 3.41
2244 9745 2.490991 TGCATCATGCTCTGCTATGTC 58.509 47.619 11.84 0.00 45.31 3.06
2245 9746 2.632987 TGCATCATGCTCTGCTATGT 57.367 45.000 11.84 0.00 45.31 2.29
2246 9747 2.879026 ACTTGCATCATGCTCTGCTATG 59.121 45.455 11.84 0.00 45.31 2.23
2247 9748 3.139850 GACTTGCATCATGCTCTGCTAT 58.860 45.455 11.84 0.00 45.31 2.97
2248 9749 2.093341 TGACTTGCATCATGCTCTGCTA 60.093 45.455 11.84 7.25 45.31 3.49
2249 9750 1.339727 TGACTTGCATCATGCTCTGCT 60.340 47.619 11.84 0.00 45.31 4.24
2250 9751 1.092348 TGACTTGCATCATGCTCTGC 58.908 50.000 11.84 7.53 45.31 4.26
2251 9752 1.400846 GGTGACTTGCATCATGCTCTG 59.599 52.381 11.84 3.46 45.31 3.35
2252 9753 1.281287 AGGTGACTTGCATCATGCTCT 59.719 47.619 11.84 0.00 45.31 4.09
2253 9754 1.747709 AGGTGACTTGCATCATGCTC 58.252 50.000 11.84 0.32 45.31 4.26
2254 9755 3.972368 AGGTGACTTGCATCATGCT 57.028 47.368 11.84 0.00 45.31 3.79
2266 9767 6.097839 TGAGGATGGTAAGTATGTAAGGTGAC 59.902 42.308 0.00 0.00 0.00 3.67
2267 9768 6.199376 TGAGGATGGTAAGTATGTAAGGTGA 58.801 40.000 0.00 0.00 0.00 4.02
2268 9769 6.479972 TGAGGATGGTAAGTATGTAAGGTG 57.520 41.667 0.00 0.00 0.00 4.00
2269 9770 6.901300 TCTTGAGGATGGTAAGTATGTAAGGT 59.099 38.462 0.00 0.00 0.00 3.50
2270 9771 7.147724 TGTCTTGAGGATGGTAAGTATGTAAGG 60.148 40.741 0.00 0.00 0.00 2.69
2271 9772 7.782049 TGTCTTGAGGATGGTAAGTATGTAAG 58.218 38.462 0.00 0.00 0.00 2.34
2272 9773 7.727578 TGTCTTGAGGATGGTAAGTATGTAA 57.272 36.000 0.00 0.00 0.00 2.41
2273 9774 7.914427 ATGTCTTGAGGATGGTAAGTATGTA 57.086 36.000 0.00 0.00 0.00 2.29
2274 9775 6.814954 ATGTCTTGAGGATGGTAAGTATGT 57.185 37.500 0.00 0.00 0.00 2.29
2275 9776 7.155328 GGTATGTCTTGAGGATGGTAAGTATG 58.845 42.308 0.00 0.00 0.00 2.39
2276 9777 6.844388 TGGTATGTCTTGAGGATGGTAAGTAT 59.156 38.462 0.00 0.00 0.00 2.12
2277 9778 6.199376 TGGTATGTCTTGAGGATGGTAAGTA 58.801 40.000 0.00 0.00 0.00 2.24
2278 9779 5.030147 TGGTATGTCTTGAGGATGGTAAGT 58.970 41.667 0.00 0.00 0.00 2.24
2279 9780 5.363868 TCTGGTATGTCTTGAGGATGGTAAG 59.636 44.000 0.00 0.00 0.00 2.34
2280 9781 5.277250 TCTGGTATGTCTTGAGGATGGTAA 58.723 41.667 0.00 0.00 0.00 2.85
2281 9782 4.878968 TCTGGTATGTCTTGAGGATGGTA 58.121 43.478 0.00 0.00 0.00 3.25
2282 9783 3.708631 CTCTGGTATGTCTTGAGGATGGT 59.291 47.826 0.00 0.00 0.00 3.55
2283 9784 3.494048 GCTCTGGTATGTCTTGAGGATGG 60.494 52.174 0.00 0.00 0.00 3.51
2284 9785 3.133542 TGCTCTGGTATGTCTTGAGGATG 59.866 47.826 0.00 0.00 0.00 3.51
2285 9786 3.378512 TGCTCTGGTATGTCTTGAGGAT 58.621 45.455 0.00 0.00 0.00 3.24
2286 9787 2.820178 TGCTCTGGTATGTCTTGAGGA 58.180 47.619 0.00 0.00 0.00 3.71
2287 9788 3.133542 TCATGCTCTGGTATGTCTTGAGG 59.866 47.826 0.00 0.00 36.98 3.86
2288 9789 4.397481 TCATGCTCTGGTATGTCTTGAG 57.603 45.455 0.00 0.00 36.98 3.02
2289 9790 4.700700 CATCATGCTCTGGTATGTCTTGA 58.299 43.478 0.00 0.00 36.98 3.02
2290 9791 3.250280 GCATCATGCTCTGGTATGTCTTG 59.750 47.826 1.02 0.00 40.96 3.02
2291 9792 3.118149 TGCATCATGCTCTGGTATGTCTT 60.118 43.478 11.84 0.00 45.31 3.01
2544 10084 0.315886 CCAGGCACGCGGTATGTATA 59.684 55.000 12.47 0.00 0.00 1.47
2646 10186 5.128499 ACATTGGGTTTCAAACACTCATCAA 59.872 36.000 3.69 0.00 39.05 2.57
2652 10192 6.208599 CCATACTACATTGGGTTTCAAACACT 59.791 38.462 3.69 0.00 39.05 3.55
2900 10440 3.999663 CTGTTTTGCCTCCTTCAGAGTAG 59.000 47.826 0.00 0.00 41.47 2.57
2935 10475 2.693797 ATTGCGGCATCGATCAATTC 57.306 45.000 2.28 0.00 39.00 2.17
2951 10491 8.084073 TCTACTGCAGAAAATGGAAAAGAATTG 58.916 33.333 23.35 0.00 0.00 2.32
2952 10492 8.181904 TCTACTGCAGAAAATGGAAAAGAATT 57.818 30.769 23.35 0.00 0.00 2.17
2962 10502 5.455392 CAACCAACTCTACTGCAGAAAATG 58.545 41.667 23.35 10.88 31.12 2.32
2997 10578 1.153628 AGATGGTAGGTGAACGCGC 60.154 57.895 5.73 0.00 0.00 6.86
3014 10595 0.792640 CTGAACGCTTACTGCACCAG 59.207 55.000 0.00 0.00 43.06 4.00
3117 10729 7.543172 TGTCGTTTGCGTCTTTACTATCTATTT 59.457 33.333 0.00 0.00 39.49 1.40
3118 10730 7.031372 TGTCGTTTGCGTCTTTACTATCTATT 58.969 34.615 0.00 0.00 39.49 1.73
3119 10731 6.558009 TGTCGTTTGCGTCTTTACTATCTAT 58.442 36.000 0.00 0.00 39.49 1.98
3120 10732 5.941733 TGTCGTTTGCGTCTTTACTATCTA 58.058 37.500 0.00 0.00 39.49 1.98
3121 10733 4.801891 TGTCGTTTGCGTCTTTACTATCT 58.198 39.130 0.00 0.00 39.49 1.98
3122 10734 5.276254 GGATGTCGTTTGCGTCTTTACTATC 60.276 44.000 0.00 0.00 39.49 2.08
3123 10735 4.565564 GGATGTCGTTTGCGTCTTTACTAT 59.434 41.667 0.00 0.00 39.49 2.12
3124 10736 3.922240 GGATGTCGTTTGCGTCTTTACTA 59.078 43.478 0.00 0.00 39.49 1.82
3125 10737 2.735134 GGATGTCGTTTGCGTCTTTACT 59.265 45.455 0.00 0.00 39.49 2.24
3126 10738 2.477375 TGGATGTCGTTTGCGTCTTTAC 59.523 45.455 0.00 0.00 39.49 2.01
3127 10739 2.477375 GTGGATGTCGTTTGCGTCTTTA 59.523 45.455 0.00 0.00 39.49 1.85
3128 10740 1.263217 GTGGATGTCGTTTGCGTCTTT 59.737 47.619 0.00 0.00 39.49 2.52
3129 10741 0.865769 GTGGATGTCGTTTGCGTCTT 59.134 50.000 0.00 0.00 39.49 3.01
3130 10742 0.249699 TGTGGATGTCGTTTGCGTCT 60.250 50.000 0.00 0.00 39.49 4.18
3131 10743 0.584396 TTGTGGATGTCGTTTGCGTC 59.416 50.000 0.00 0.00 39.49 5.19
3140 10752 4.213270 TCGAACACTTGAATTGTGGATGTC 59.787 41.667 0.00 0.00 39.52 3.06
3157 10769 3.727726 TCTCTTGTTTGATGCTCGAACA 58.272 40.909 12.32 12.32 46.05 3.18
3191 10803 2.350522 CATTGGAGGACTGAACGGAAG 58.649 52.381 0.00 0.00 0.00 3.46
3192 10804 1.003118 CCATTGGAGGACTGAACGGAA 59.997 52.381 0.00 0.00 0.00 4.30
3193 10805 0.613260 CCATTGGAGGACTGAACGGA 59.387 55.000 0.00 0.00 0.00 4.69
3194 10806 1.026718 GCCATTGGAGGACTGAACGG 61.027 60.000 6.95 0.00 0.00 4.44
3195 10807 0.036010 AGCCATTGGAGGACTGAACG 60.036 55.000 6.95 0.00 0.00 3.95
3196 10808 1.003580 TGAGCCATTGGAGGACTGAAC 59.996 52.381 6.95 0.00 0.00 3.18
3197 10809 1.280133 CTGAGCCATTGGAGGACTGAA 59.720 52.381 6.95 0.00 0.00 3.02
3198 10810 0.907486 CTGAGCCATTGGAGGACTGA 59.093 55.000 6.95 0.00 0.00 3.41
3199 10811 0.907486 TCTGAGCCATTGGAGGACTG 59.093 55.000 6.95 0.00 0.00 3.51
3200 10812 1.489649 CATCTGAGCCATTGGAGGACT 59.510 52.381 6.95 0.00 0.00 3.85
3201 10813 1.964552 CATCTGAGCCATTGGAGGAC 58.035 55.000 6.95 0.00 0.00 3.85
3202 10814 0.182061 GCATCTGAGCCATTGGAGGA 59.818 55.000 6.95 0.00 0.00 3.71
3203 10815 0.183014 AGCATCTGAGCCATTGGAGG 59.817 55.000 6.95 0.00 34.23 4.30
3204 10816 1.595466 GAGCATCTGAGCCATTGGAG 58.405 55.000 6.95 0.00 34.23 3.86
3205 10817 3.794737 GAGCATCTGAGCCATTGGA 57.205 52.632 6.95 0.00 34.23 3.53


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

AutoCloner maintained by Alex Coulton.