Multiple sequence alignment - TraesCS4A01G353700

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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 TraesCS4A01G353700 chr4A 100.000 3216 0 0 1 3216 628621824 628625039 0.000000e+00 5939.0
1 TraesCS4A01G353700 chr4A 83.227 1413 167 37 854 2227 628635507 628636888 0.000000e+00 1232.0
2 TraesCS4A01G353700 chr4A 81.776 214 32 6 682 890 628635295 628635506 4.270000e-39 172.0
3 TraesCS4A01G353700 chr4A 90.323 93 7 2 2402 2493 628630174 628630083 1.570000e-23 121.0
4 TraesCS4A01G353700 chr4A 91.379 58 5 0 2428 2485 628642737 628642794 2.660000e-11 80.5
5 TraesCS4A01G353700 chr5B 95.650 1770 57 10 518 2286 681817456 681815706 0.000000e+00 2824.0
6 TraesCS4A01G353700 chr5B 83.583 1602 181 45 685 2227 681780115 681778537 0.000000e+00 1426.0
7 TraesCS4A01G353700 chr5B 88.393 448 39 7 90 527 681818270 681817826 7.900000e-146 527.0
8 TraesCS4A01G353700 chr5B 88.626 422 34 6 2280 2695 681815656 681815243 4.790000e-138 501.0
9 TraesCS4A01G353700 chr5B 86.589 343 34 7 2732 3062 681815238 681814896 5.070000e-98 368.0
10 TraesCS4A01G353700 chr5B 92.208 154 12 0 3062 3215 681793171 681793018 5.400000e-53 219.0
11 TraesCS4A01G353700 chr5B 93.407 91 5 1 1 91 681819099 681819010 2.010000e-27 134.0
12 TraesCS4A01G353700 chr5B 91.489 94 6 2 2399 2491 681789410 681789502 9.360000e-26 128.0
13 TraesCS4A01G353700 chr5B 91.489 94 6 2 2399 2491 681824812 681824904 9.360000e-26 128.0
14 TraesCS4A01G353700 chr5B 87.500 88 10 1 2404 2491 681777868 681777782 2.040000e-17 100.0
15 TraesCS4A01G353700 chr5D 95.259 1603 68 6 685 2282 539814656 539813057 0.000000e+00 2532.0
16 TraesCS4A01G353700 chr5D 84.763 1457 156 31 685 2085 539786451 539785005 0.000000e+00 1400.0
17 TraesCS4A01G353700 chr5D 90.024 421 32 6 2280 2695 539813003 539812588 1.310000e-148 536.0
18 TraesCS4A01G353700 chr5D 95.946 148 6 0 3068 3215 539812085 539811938 1.150000e-59 241.0
19 TraesCS4A01G353700 chr5D 90.960 177 15 1 2732 2907 539812583 539812407 1.490000e-58 237.0
20 TraesCS4A01G353700 chr5D 90.426 94 6 3 2399 2491 539793035 539793126 1.570000e-23 121.0
21 TraesCS4A01G353700 chr5D 84.091 88 13 1 2404 2491 539784069 539783983 2.060000e-12 84.2
22 TraesCS4A01G353700 chrUn 80.982 163 22 5 327 484 37078147 37078305 1.570000e-23 121.0
23 TraesCS4A01G353700 chr2D 81.373 102 14 3 202 299 3442136 3442236 9.570000e-11 78.7


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 TraesCS4A01G353700 chr4A 628621824 628625039 3215 False 5939.0 5939 100.00000 1 3216 1 chr4A.!!$F1 3215
1 TraesCS4A01G353700 chr4A 628635295 628636888 1593 False 702.0 1232 82.50150 682 2227 2 chr4A.!!$F3 1545
2 TraesCS4A01G353700 chr5B 681814896 681819099 4203 True 870.8 2824 90.53300 1 3062 5 chr5B.!!$R3 3061
3 TraesCS4A01G353700 chr5B 681777782 681780115 2333 True 763.0 1426 85.54150 685 2491 2 chr5B.!!$R2 1806
4 TraesCS4A01G353700 chr5D 539811938 539814656 2718 True 886.5 2532 93.04725 685 3215 4 chr5D.!!$R2 2530
5 TraesCS4A01G353700 chr5D 539783983 539786451 2468 True 742.1 1400 84.42700 685 2491 2 chr5D.!!$R1 1806

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
320 1065 0.894835 GTTGTTGTATGGGCCCTTGG 59.105 55.0 25.7 0.0 0.0 3.61 F
1842 3045 0.031585 CCGTCGAGAACACTTCACCA 59.968 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 3221 0.105709 TGAGTCTGTCTGGTGACCCA 60.106 55.0 0.0 0.0 42.28 4.51 R
2859 4761 0.031414 GGTGGAGGGGGCTAAGAGTA 60.031 60.0 0.0 0.0 0.00 2.59 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
147 890 1.597742 CTAATTGGAGATGTGGCCGG 58.402 55.000 0.00 0.00 0.00 6.13
154 897 2.672996 GATGTGGCCGGTGTTGCT 60.673 61.111 1.90 0.00 0.00 3.91
160 903 1.302192 GGCCGGTGTTGCTACTTGA 60.302 57.895 1.90 0.00 0.00 3.02
164 907 1.798813 CCGGTGTTGCTACTTGAAGAC 59.201 52.381 0.00 0.00 0.00 3.01
165 908 2.479837 CGGTGTTGCTACTTGAAGACA 58.520 47.619 0.00 0.00 0.00 3.41
170 913 4.153117 GTGTTGCTACTTGAAGACAGGATG 59.847 45.833 0.00 0.00 46.00 3.51
177 920 5.341872 ACTTGAAGACAGGATGATGAGAG 57.658 43.478 0.00 0.00 39.69 3.20
200 943 1.302033 CTGCTGTCCAAGAACCGCT 60.302 57.895 0.00 0.00 31.47 5.52
203 946 1.019805 GCTGTCCAAGAACCGCTACC 61.020 60.000 0.00 0.00 0.00 3.18
233 976 1.876453 CTCACAAGTCACGAACGCCG 61.876 60.000 0.00 0.00 45.44 6.46
257 1000 2.755876 TCGCCCTCGATCAGCAGT 60.756 61.111 0.00 0.00 40.21 4.40
270 1013 1.771854 TCAGCAGTTGGTGGGAAACTA 59.228 47.619 11.01 0.00 43.23 2.24
286 1029 5.112686 GGAAACTAGTGATGAGTTGGCTAG 58.887 45.833 0.00 0.00 37.22 3.42
301 1044 1.605712 GGCTAGGTTAGGCTGTATGCG 60.606 57.143 0.00 0.00 46.78 4.73
320 1065 0.894835 GTTGTTGTATGGGCCCTTGG 59.105 55.000 25.70 0.00 0.00 3.61
333 1078 1.377725 CCTTGGATGCCTTGCGTCT 60.378 57.895 8.09 0.00 43.35 4.18
368 1115 2.045926 AGTGAGTTGGGCCGATGC 60.046 61.111 0.00 0.00 0.00 3.91
369 1116 2.359850 GTGAGTTGGGCCGATGCA 60.360 61.111 0.00 0.00 40.13 3.96
384 1131 2.203112 GCAGCGATGCCTGATGGA 60.203 61.111 16.30 0.00 34.77 3.41
394 1141 1.303799 GCCTGATGGACTGCTGTGTG 61.304 60.000 0.00 0.00 34.57 3.82
408 1155 2.794350 GCTGTGTGGTACATGCAAAAAC 59.206 45.455 0.00 0.00 44.52 2.43
409 1156 3.736433 GCTGTGTGGTACATGCAAAAACA 60.736 43.478 0.00 0.00 44.52 2.83
416 1163 6.183360 TGTGGTACATGCAAAAACACTACAAT 60.183 34.615 13.54 0.00 44.52 2.71
432 1179 8.722342 ACACTACAATGTTATTTTGTTTAGCG 57.278 30.769 0.00 0.00 38.26 4.26
443 1190 1.552226 TGTTTAGCGTCGGAATAGCG 58.448 50.000 0.00 0.00 35.78 4.26
454 1201 3.424529 GTCGGAATAGCGCAGTATAACAC 59.575 47.826 11.47 0.00 0.00 3.32
460 1207 6.033619 GGAATAGCGCAGTATAACACGAATAG 59.966 42.308 11.47 0.00 0.00 1.73
463 1210 2.160143 CGCAGTATAACACGAATAGCGC 60.160 50.000 0.00 0.00 46.04 5.92
465 1212 2.404029 CAGTATAACACGAATAGCGCCG 59.596 50.000 2.29 2.21 46.04 6.46
466 1213 2.033801 AGTATAACACGAATAGCGCCGT 59.966 45.455 2.29 3.03 46.04 5.68
489 1239 3.302286 GGCGAGCAAATTAGCTACGTAAC 60.302 47.826 0.00 0.00 46.75 2.50
500 1250 6.754702 TTAGCTACGTAACATGACTCTTCT 57.245 37.500 0.00 0.00 0.00 2.85
515 1265 5.006455 TGACTCTTCTAGACACGCTATAACG 59.994 44.000 0.00 0.00 39.50 3.18
518 1268 3.848846 TCTAGACACGCTATAACGTCG 57.151 47.619 0.00 0.00 46.34 5.12
613 1742 8.850156 GGCACCATGTACTTTGATATAAGAAAT 58.150 33.333 0.00 0.00 0.00 2.17
653 1782 3.694566 ACAGACAGAACCTTTTTGTGGTC 59.305 43.478 0.00 0.00 36.69 4.02
655 1784 1.404035 ACAGAACCTTTTTGTGGTCGC 59.596 47.619 0.00 0.00 36.69 5.19
656 1785 1.676006 CAGAACCTTTTTGTGGTCGCT 59.324 47.619 0.00 0.00 36.69 4.93
659 1788 4.693566 CAGAACCTTTTTGTGGTCGCTATA 59.306 41.667 0.00 0.00 36.69 1.31
939 2114 1.472662 CCTACCCTCCCATACGCCTG 61.473 65.000 0.00 0.00 0.00 4.85
1046 2222 2.026449 CCACTTGCTCCTCCTCAAAGAT 60.026 50.000 0.00 0.00 0.00 2.40
1146 2325 1.226746 CAACGAGACCCAAAGACCAC 58.773 55.000 0.00 0.00 0.00 4.16
1188 2367 0.520404 CGCAGCAAGAAGAGCAACAT 59.480 50.000 0.00 0.00 0.00 2.71
1229 2411 1.079336 CTCTACAGCAGCAGCAGCA 60.079 57.895 12.92 0.00 45.49 4.41
1230 2412 1.079336 TCTACAGCAGCAGCAGCAG 60.079 57.895 12.92 6.60 45.49 4.24
1355 2537 1.487976 GATCCACAGAGCCTCCATGAA 59.512 52.381 0.00 0.00 0.00 2.57
1509 2706 1.172180 ACCCATTTGCACACTCCACG 61.172 55.000 0.00 0.00 0.00 4.94
1511 2708 0.888736 CCATTTGCACACTCCACGGA 60.889 55.000 0.00 0.00 0.00 4.69
1605 2808 2.435805 TCCCATGGTTGATGCTCTAGAC 59.564 50.000 11.73 0.00 0.00 2.59
1665 2868 2.439156 AGCTTCCATGGCTTCGGC 60.439 61.111 6.96 6.50 36.56 5.54
1666 2869 3.880846 GCTTCCATGGCTTCGGCG 61.881 66.667 6.96 0.00 42.91 6.46
1667 2870 3.204827 CTTCCATGGCTTCGGCGG 61.205 66.667 6.96 0.00 42.91 6.13
1704 2907 2.622942 TGAAGATGCCAAGAACAACACC 59.377 45.455 0.00 0.00 0.00 4.16
1712 2915 2.875933 CCAAGAACAACACCGCTTCTAA 59.124 45.455 0.00 0.00 0.00 2.10
1842 3045 0.031585 CCGTCGAGAACACTTCACCA 59.968 55.000 0.00 0.00 0.00 4.17
1926 3129 1.212751 CATCGAGTGGAGCGACACA 59.787 57.895 14.70 0.00 43.72 3.72
2008 3247 1.332195 CCAGACAGACTCAGTGGACA 58.668 55.000 0.00 0.00 0.00 4.02
2062 3301 0.109226 CGAAGACGTCTCCTTCCCAC 60.109 60.000 20.33 2.76 37.36 4.61
2088 3327 1.535015 GCTAGCTAGACTGAGGCAACG 60.535 57.143 25.15 0.00 46.39 4.10
2089 3328 1.746220 CTAGCTAGACTGAGGCAACGT 59.254 52.381 16.15 0.00 46.39 3.99
2146 3389 7.270757 TGTTTAATAATCGGGGATGTTGATG 57.729 36.000 0.00 0.00 0.00 3.07
2167 3520 3.057946 TGTTTGGTTTTGGTTTTTGCAGC 60.058 39.130 0.00 0.00 0.00 5.25
2188 3541 3.106054 CATGGAGATAGGAGAGATGGGG 58.894 54.545 0.00 0.00 0.00 4.96
2295 4139 4.652881 TCTGTGCAGACTAGGATTGATGAT 59.347 41.667 0.00 0.00 31.41 2.45
2299 4143 6.105333 GTGCAGACTAGGATTGATGATATCC 58.895 44.000 0.00 0.00 41.59 2.59
2300 4144 5.105595 TGCAGACTAGGATTGATGATATCCG 60.106 44.000 0.00 0.00 45.09 4.18
2314 4158 5.391312 TGATATCCGATGACCATGTACTG 57.609 43.478 0.00 0.00 0.00 2.74
2326 4170 5.479027 TGACCATGTACTGCTACTTTACTGA 59.521 40.000 0.00 0.00 0.00 3.41
2345 4189 5.784177 ACTGAGTCCAAGTTATAGTGTGTG 58.216 41.667 0.00 0.00 0.00 3.82
2361 4205 6.515272 AGTGTGTGTTTTTCAGTCTGAAAT 57.485 33.333 24.98 7.49 44.75 2.17
2469 4364 2.566724 CCATGCAACACCTTAATTGGGT 59.433 45.455 0.00 0.00 37.59 4.51
2501 4399 5.011023 GGAGATGGTCAGGTTCATTGTTTTT 59.989 40.000 0.00 0.00 0.00 1.94
2534 4433 3.696051 GAGAAATATTTCAGCCACAGCCA 59.304 43.478 26.02 0.00 39.61 4.75
2535 4434 4.088634 AGAAATATTTCAGCCACAGCCAA 58.911 39.130 26.02 0.00 39.61 4.52
2553 4452 5.811613 CAGCCAAATTTCAGTTTGTCTTTGA 59.188 36.000 0.00 0.00 37.37 2.69
2630 4531 8.732746 AACATGTTTAAGTTCTTGTGTCTACT 57.267 30.769 4.92 0.00 0.00 2.57
2631 4532 9.826574 AACATGTTTAAGTTCTTGTGTCTACTA 57.173 29.630 4.92 0.00 0.00 1.82
2632 4533 9.998106 ACATGTTTAAGTTCTTGTGTCTACTAT 57.002 29.630 0.00 0.00 0.00 2.12
2642 4543 5.880332 TCTTGTGTCTACTATGGAAATTGCC 59.120 40.000 0.00 0.00 0.00 4.52
2643 4544 4.188462 TGTGTCTACTATGGAAATTGCCG 58.812 43.478 0.00 0.00 0.00 5.69
2660 4561 2.933906 TGCCGAGATATTTTGACCGAAC 59.066 45.455 0.00 0.00 0.00 3.95
2661 4562 3.195661 GCCGAGATATTTTGACCGAACT 58.804 45.455 0.00 0.00 0.00 3.01
2702 4603 5.893897 AAGAAGCATCTTCTCCATTTCAC 57.106 39.130 9.26 0.00 42.26 3.18
2703 4604 5.176741 AGAAGCATCTTCTCCATTTCACT 57.823 39.130 3.43 0.00 29.15 3.41
2704 4605 5.184711 AGAAGCATCTTCTCCATTTCACTC 58.815 41.667 3.43 0.00 29.15 3.51
2705 4606 3.883669 AGCATCTTCTCCATTTCACTCC 58.116 45.455 0.00 0.00 0.00 3.85
2706 4607 2.948315 GCATCTTCTCCATTTCACTCCC 59.052 50.000 0.00 0.00 0.00 4.30
2707 4608 3.371380 GCATCTTCTCCATTTCACTCCCT 60.371 47.826 0.00 0.00 0.00 4.20
2708 4609 4.450053 CATCTTCTCCATTTCACTCCCTC 58.550 47.826 0.00 0.00 0.00 4.30
2709 4610 3.520696 TCTTCTCCATTTCACTCCCTCA 58.479 45.455 0.00 0.00 0.00 3.86
2710 4611 3.909995 TCTTCTCCATTTCACTCCCTCAA 59.090 43.478 0.00 0.00 0.00 3.02
2711 4612 4.350816 TCTTCTCCATTTCACTCCCTCAAA 59.649 41.667 0.00 0.00 0.00 2.69
2712 4613 4.934797 TCTCCATTTCACTCCCTCAAAT 57.065 40.909 0.00 0.00 0.00 2.32
2713 4614 6.215431 TCTTCTCCATTTCACTCCCTCAAATA 59.785 38.462 0.00 0.00 0.00 1.40
2714 4615 6.387192 TCTCCATTTCACTCCCTCAAATAA 57.613 37.500 0.00 0.00 0.00 1.40
2715 4616 6.418101 TCTCCATTTCACTCCCTCAAATAAG 58.582 40.000 0.00 0.00 0.00 1.73
2716 4617 6.215431 TCTCCATTTCACTCCCTCAAATAAGA 59.785 38.462 0.00 0.00 0.00 2.10
2717 4618 6.789268 TCCATTTCACTCCCTCAAATAAGAA 58.211 36.000 0.00 0.00 0.00 2.52
2718 4619 7.413446 TCCATTTCACTCCCTCAAATAAGAAT 58.587 34.615 0.00 0.00 0.00 2.40
2719 4620 8.556589 TCCATTTCACTCCCTCAAATAAGAATA 58.443 33.333 0.00 0.00 0.00 1.75
2720 4621 9.359653 CCATTTCACTCCCTCAAATAAGAATAT 57.640 33.333 0.00 0.00 0.00 1.28
2748 4649 0.393077 AGTTGGACGTTCCTGGTCTG 59.607 55.000 0.00 0.00 37.46 3.51
2757 4658 1.968493 GTTCCTGGTCTGTCTGTACCA 59.032 52.381 0.00 0.00 43.47 3.25
2786 4687 7.678947 TTTCTTTGAGATCCATCAAGAAGTC 57.321 36.000 9.24 0.00 40.16 3.01
2790 4691 6.808008 TTGAGATCCATCAAGAAGTCAAAC 57.192 37.500 0.00 0.00 34.31 2.93
2835 4737 2.936498 CCGTTAGGCAGACAACAATAGG 59.064 50.000 0.00 0.00 0.00 2.57
2836 4738 2.351726 CGTTAGGCAGACAACAATAGGC 59.648 50.000 0.00 0.00 0.00 3.93
2859 4761 3.199508 AGCTGCCTTAGAACATCATGACT 59.800 43.478 0.00 0.00 0.00 3.41
2876 4778 1.016415 ACTACTCTTAGCCCCCTCCA 58.984 55.000 0.00 0.00 0.00 3.86
2907 4809 2.554032 ACTCCGAAATTTGTCTGCCTTG 59.446 45.455 0.00 0.00 0.00 3.61
2917 4819 1.266718 TGTCTGCCTTGTCGCAATTTC 59.733 47.619 0.00 0.00 38.56 2.17
2921 4823 0.517316 GCCTTGTCGCAATTTCGAGT 59.483 50.000 0.00 0.00 39.34 4.18
2923 4825 2.069273 CCTTGTCGCAATTTCGAGTCT 58.931 47.619 0.00 0.00 39.34 3.24
2925 4827 2.148916 TGTCGCAATTTCGAGTCTGT 57.851 45.000 0.00 0.00 39.34 3.41
2931 4833 4.621460 TCGCAATTTCGAGTCTGTAAAGAG 59.379 41.667 0.00 0.00 34.09 2.85
2933 4835 5.443431 CGCAATTTCGAGTCTGTAAAGAGTC 60.443 44.000 7.61 7.61 35.50 3.36
2935 4837 4.516365 TTTCGAGTCTGTAAAGAGTCCC 57.484 45.455 11.51 0.00 35.43 4.46
2937 4839 2.041350 TCGAGTCTGTAAAGAGTCCCCT 59.959 50.000 11.51 0.00 35.43 4.79
2941 4843 0.824759 CTGTAAAGAGTCCCCTCCCG 59.175 60.000 0.00 0.00 38.58 5.14
2943 4845 1.688187 TAAAGAGTCCCCTCCCGCC 60.688 63.158 0.00 0.00 38.58 6.13
2944 4846 2.177529 TAAAGAGTCCCCTCCCGCCT 62.178 60.000 0.00 0.00 38.58 5.52
2945 4847 2.177529 AAAGAGTCCCCTCCCGCCTA 62.178 60.000 0.00 0.00 38.58 3.93
2946 4848 2.042230 GAGTCCCCTCCCGCCTAA 60.042 66.667 0.00 0.00 0.00 2.69
2947 4849 1.459730 GAGTCCCCTCCCGCCTAAT 60.460 63.158 0.00 0.00 0.00 1.73
2948 4850 1.004361 AGTCCCCTCCCGCCTAATT 59.996 57.895 0.00 0.00 0.00 1.40
2975 4889 4.061357 CATGCCATGCCATGATTTTGTA 57.939 40.909 11.15 0.00 44.12 2.41
2981 4895 4.501915 CCATGCCATGATTTTGTATCACCC 60.502 45.833 6.18 0.00 0.00 4.61
2988 4902 0.693622 TTTTGTATCACCCCGCCAGA 59.306 50.000 0.00 0.00 0.00 3.86
2994 4908 4.489771 CACCCCGCCAGATCCACC 62.490 72.222 0.00 0.00 0.00 4.61
3039 4953 0.246635 AGTCGGCTACAAGCGAATGT 59.753 50.000 0.00 0.00 43.62 2.71
3043 4957 1.095807 GGCTACAAGCGAATGTCCCC 61.096 60.000 0.00 0.00 43.62 4.81
3045 4959 0.810031 CTACAAGCGAATGTCCCCCG 60.810 60.000 0.00 0.00 34.75 5.73
3062 4976 1.210931 CGCCGTGGTCGTTCTAGAA 59.789 57.895 0.00 0.00 35.01 2.10
3063 4977 0.797249 CGCCGTGGTCGTTCTAGAAG 60.797 60.000 5.12 0.59 35.01 2.85
3064 4978 0.458025 GCCGTGGTCGTTCTAGAAGG 60.458 60.000 17.25 17.25 35.01 3.46
3065 4979 0.886563 CCGTGGTCGTTCTAGAAGGT 59.113 55.000 21.25 0.00 35.01 3.50
3066 4980 1.135460 CCGTGGTCGTTCTAGAAGGTC 60.135 57.143 21.25 16.66 35.01 3.85
3109 5172 4.885907 AGGACCATTCAGATTTGCATACAG 59.114 41.667 0.00 0.00 0.00 2.74
3116 5179 7.166970 CCATTCAGATTTGCATACAGAATTTCG 59.833 37.037 0.00 0.00 0.00 3.46
3127 5190 1.071605 AGAATTTCGCACGTCTGAGC 58.928 50.000 0.00 0.00 0.00 4.26
3165 5228 4.090761 TGGATATGTCAAGGATCTTGGC 57.909 45.455 5.41 5.41 0.00 4.52
3186 5249 5.045213 TGGCCATGAAGTATAAGAAGGTTCA 60.045 40.000 0.00 0.00 0.00 3.18
3189 5252 6.205658 GCCATGAAGTATAAGAAGGTTCATCC 59.794 42.308 0.00 0.00 36.04 3.51
3215 5278 4.765339 AGCATTTGGTAGAAGGGTGTAAAC 59.235 41.667 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.067821 GAGGTCATGTTAGAGCCCTCG 59.932 57.143 0.00 0.00 36.71 4.63
34 35 1.067821 CGAGGTCATGTTAGAGCCCTC 59.932 57.143 0.00 0.00 36.71 4.30
35 36 1.115467 CGAGGTCATGTTAGAGCCCT 58.885 55.000 0.00 0.00 36.71 5.19
37 38 0.530870 GGCGAGGTCATGTTAGAGCC 60.531 60.000 8.07 8.07 36.71 4.70
38 39 0.872021 CGGCGAGGTCATGTTAGAGC 60.872 60.000 0.00 0.00 36.31 4.09
84 85 2.910688 AGGAGTATACATGCCCAACG 57.089 50.000 5.50 0.00 0.00 4.10
91 92 8.450578 TTCCTTGCAAATTAGGAGTATACATG 57.549 34.615 5.50 0.00 0.00 3.21
92 93 9.646522 ATTTCCTTGCAAATTAGGAGTATACAT 57.353 29.630 5.50 0.00 0.00 2.29
93 94 8.902806 CATTTCCTTGCAAATTAGGAGTATACA 58.097 33.333 5.50 0.00 0.00 2.29
94 95 8.352942 CCATTTCCTTGCAAATTAGGAGTATAC 58.647 37.037 0.00 0.00 0.00 1.47
145 888 2.476619 CTGTCTTCAAGTAGCAACACCG 59.523 50.000 0.00 0.00 0.00 4.94
147 890 3.728845 TCCTGTCTTCAAGTAGCAACAC 58.271 45.455 0.00 0.00 0.00 3.32
154 897 5.362143 CCTCTCATCATCCTGTCTTCAAGTA 59.638 44.000 0.00 0.00 0.00 2.24
160 903 2.435069 CAGCCTCTCATCATCCTGTCTT 59.565 50.000 0.00 0.00 0.00 3.01
164 907 0.759959 AGCAGCCTCTCATCATCCTG 59.240 55.000 0.00 0.00 0.00 3.86
165 908 0.759959 CAGCAGCCTCTCATCATCCT 59.240 55.000 0.00 0.00 0.00 3.24
170 913 0.810823 GACAGCAGCAGCCTCTCATC 60.811 60.000 0.00 0.00 43.56 2.92
177 920 1.601759 TTCTTGGACAGCAGCAGCC 60.602 57.895 0.00 0.00 43.56 4.85
200 943 3.057548 TGAGCGAAGACGGCGGTA 61.058 61.111 13.24 0.00 39.81 4.02
203 946 2.720758 CTTGTGAGCGAAGACGGCG 61.721 63.158 4.80 4.80 40.15 6.46
249 992 1.145738 AGTTTCCCACCAACTGCTGAT 59.854 47.619 0.00 0.00 33.04 2.90
257 1000 3.650942 ACTCATCACTAGTTTCCCACCAA 59.349 43.478 0.00 0.00 0.00 3.67
270 1013 3.452627 CCTAACCTAGCCAACTCATCACT 59.547 47.826 0.00 0.00 0.00 3.41
286 1029 1.734163 ACAACGCATACAGCCTAACC 58.266 50.000 0.00 0.00 41.38 2.85
301 1044 0.894835 CCAAGGGCCCATACAACAAC 59.105 55.000 27.56 0.00 0.00 3.32
333 1078 3.329225 TCACTCTCACTCTCTCTCTTCCA 59.671 47.826 0.00 0.00 0.00 3.53
368 1115 1.145598 AGTCCATCAGGCATCGCTG 59.854 57.895 0.00 0.00 33.74 5.18
369 1116 1.145598 CAGTCCATCAGGCATCGCT 59.854 57.895 0.00 0.00 33.74 4.93
384 1131 0.108396 TGCATGTACCACACAGCAGT 59.892 50.000 0.00 0.00 41.51 4.40
394 1141 6.212955 ACATTGTAGTGTTTTTGCATGTACC 58.787 36.000 0.00 0.00 0.00 3.34
408 1155 8.722342 ACGCTAAACAAAATAACATTGTAGTG 57.278 30.769 0.00 0.00 39.98 2.74
409 1156 7.742963 CGACGCTAAACAAAATAACATTGTAGT 59.257 33.333 0.00 0.00 39.98 2.73
416 1163 5.670149 TTCCGACGCTAAACAAAATAACA 57.330 34.783 0.00 0.00 0.00 2.41
432 1179 3.424529 GTGTTATACTGCGCTATTCCGAC 59.575 47.826 9.73 0.00 0.00 4.79
443 1190 2.155155 GGCGCTATTCGTGTTATACTGC 59.845 50.000 7.64 0.00 41.07 4.40
445 1192 2.033801 ACGGCGCTATTCGTGTTATACT 59.966 45.455 6.90 0.00 41.07 2.12
446 1193 2.388121 ACGGCGCTATTCGTGTTATAC 58.612 47.619 6.90 0.00 41.07 1.47
462 1209 1.062525 CTAATTTGCTCGCCACGGC 59.937 57.895 0.00 0.00 37.85 5.68
463 1210 1.062525 GCTAATTTGCTCGCCACGG 59.937 57.895 4.53 0.00 0.00 4.94
465 1212 1.004927 CGTAGCTAATTTGCTCGCCAC 60.005 52.381 17.74 9.64 42.97 5.01
466 1213 1.286501 CGTAGCTAATTTGCTCGCCA 58.713 50.000 17.74 0.00 42.97 5.69
467 1214 1.287425 ACGTAGCTAATTTGCTCGCC 58.713 50.000 17.74 6.82 42.97 5.54
469 1216 5.231357 TCATGTTACGTAGCTAATTTGCTCG 59.769 40.000 17.74 20.25 42.97 5.03
471 1218 6.106673 AGTCATGTTACGTAGCTAATTTGCT 58.893 36.000 18.24 18.24 46.11 3.91
472 1219 6.255887 AGAGTCATGTTACGTAGCTAATTTGC 59.744 38.462 10.88 3.49 0.00 3.68
473 1220 7.757097 AGAGTCATGTTACGTAGCTAATTTG 57.243 36.000 10.88 1.84 0.00 2.32
489 1239 3.773860 AGCGTGTCTAGAAGAGTCATG 57.226 47.619 0.00 0.00 34.44 3.07
500 1250 3.447742 TCTCGACGTTATAGCGTGTCTA 58.552 45.455 19.72 0.00 45.79 2.59
515 1265 3.242248 ACAAAATAGCGCGTTATCTCGAC 59.758 43.478 16.05 0.00 0.00 4.20
518 1268 4.893795 ACAACAAAATAGCGCGTTATCTC 58.106 39.130 16.05 0.00 0.00 2.75
584 1713 5.835113 ATATCAAAGTACATGGTGCCAAC 57.165 39.130 0.00 0.00 0.00 3.77
627 1756 7.231467 ACCACAAAAAGGTTCTGTCTGTATAT 58.769 34.615 0.00 0.00 35.33 0.86
635 1764 1.404035 GCGACCACAAAAAGGTTCTGT 59.596 47.619 0.00 0.00 40.09 3.41
939 2114 3.412386 TCTTTCTTGCTAAGGGAACAGC 58.588 45.455 0.00 0.00 38.31 4.40
1046 2222 4.201950 GCTCTTCTTGCTTTCTGTTGTTGA 60.202 41.667 0.00 0.00 0.00 3.18
1146 2325 2.053865 GGTGCCCATGGTGATGTGG 61.054 63.158 11.73 0.00 35.22 4.17
1229 2411 0.820891 CACCTGCTTCTTGTGTGGCT 60.821 55.000 0.00 0.00 0.00 4.75
1230 2412 0.819259 TCACCTGCTTCTTGTGTGGC 60.819 55.000 0.00 0.00 0.00 5.01
1231 2413 1.233019 CTCACCTGCTTCTTGTGTGG 58.767 55.000 0.00 0.00 0.00 4.17
1355 2537 2.354343 GCTGCTCCTTGGCTTCCT 59.646 61.111 0.00 0.00 0.00 3.36
1509 2706 4.893424 TGAGCAACTACTGTTTGTTTCC 57.107 40.909 0.00 0.00 33.52 3.13
1674 2877 0.111061 TGGCATCTTCACCAGCAACT 59.889 50.000 0.00 0.00 0.00 3.16
1683 2886 2.622942 GGTGTTGTTCTTGGCATCTTCA 59.377 45.455 0.00 0.00 0.00 3.02
1704 2907 4.116238 GAGGATCAAAGGAGTTAGAAGCG 58.884 47.826 0.00 0.00 33.17 4.68
1712 2915 1.273324 ACGGAGGAGGATCAAAGGAGT 60.273 52.381 0.00 0.00 36.25 3.85
1842 3045 3.075005 AGCACCCGGTGTAGCGAT 61.075 61.111 18.95 0.00 35.75 4.58
1926 3129 2.426023 GACGTGGCCAGGTTCAGT 59.574 61.111 30.36 12.43 0.00 3.41
1982 3221 0.105709 TGAGTCTGTCTGGTGACCCA 60.106 55.000 0.00 0.00 42.28 4.51
1985 3224 1.000283 CCACTGAGTCTGTCTGGTGAC 60.000 57.143 0.00 0.00 43.20 3.67
2008 3247 2.532532 CCAGATGCATCCCCGGGAT 61.533 63.158 26.32 13.83 44.21 3.85
2062 3301 2.550606 CCTCAGTCTAGCTAGCTTACCG 59.449 54.545 24.88 13.88 0.00 4.02
2088 3327 9.563898 GCACCTTAATTTTGGTATAACAACTAC 57.436 33.333 1.72 0.00 34.79 2.73
2089 3328 9.298250 TGCACCTTAATTTTGGTATAACAACTA 57.702 29.630 1.72 0.00 34.79 2.24
2134 3377 4.064388 CAAAACCAAACATCAACATCCCC 58.936 43.478 0.00 0.00 0.00 4.81
2146 3389 3.057946 TGCTGCAAAAACCAAAACCAAAC 60.058 39.130 0.00 0.00 0.00 2.93
2167 3520 3.106054 CCCCATCTCTCCTATCTCCATG 58.894 54.545 0.00 0.00 0.00 3.66
2188 3541 2.435693 CCACTCCTCGTCCCATCCC 61.436 68.421 0.00 0.00 0.00 3.85
2295 4139 3.230976 AGCAGTACATGGTCATCGGATA 58.769 45.455 0.00 0.00 33.17 2.59
2299 4143 3.717400 AGTAGCAGTACATGGTCATCG 57.283 47.619 0.00 0.00 40.89 3.84
2300 4144 6.477033 CAGTAAAGTAGCAGTACATGGTCATC 59.523 42.308 0.00 0.00 40.89 2.92
2314 4158 8.468399 ACTATAACTTGGACTCAGTAAAGTAGC 58.532 37.037 5.92 0.00 32.69 3.58
2326 4170 7.554835 TGAAAAACACACACTATAACTTGGACT 59.445 33.333 0.00 0.00 0.00 3.85
2361 4205 5.748152 GGCTACGACCAATACGTGTTTTATA 59.252 40.000 0.00 0.00 43.73 0.98
2414 4309 1.938926 GCAGCTCACACTTCTCTGGTC 60.939 57.143 0.00 0.00 0.00 4.02
2416 4311 0.034476 TGCAGCTCACACTTCTCTGG 59.966 55.000 0.00 0.00 0.00 3.86
2469 4364 1.685180 CCTGACCATCTCCTCGTACCA 60.685 57.143 0.00 0.00 0.00 3.25
2470 4365 1.033574 CCTGACCATCTCCTCGTACC 58.966 60.000 0.00 0.00 0.00 3.34
2501 4399 8.730680 GGCTGAAATATTTCTCAACTGAAAGTA 58.269 33.333 24.77 3.46 41.72 2.24
2534 4433 5.043248 CGGCTCAAAGACAAACTGAAATTT 58.957 37.500 0.00 0.00 0.00 1.82
2535 4434 4.338118 TCGGCTCAAAGACAAACTGAAATT 59.662 37.500 0.00 0.00 0.00 1.82
2553 4452 1.886542 GAATGTTTTGGTCCTTCGGCT 59.113 47.619 0.00 0.00 0.00 5.52
2603 4502 6.715464 AGACACAAGAACTTAAACATGTTCG 58.285 36.000 12.39 6.27 44.95 3.95
2604 4505 8.827677 AGTAGACACAAGAACTTAAACATGTTC 58.172 33.333 12.39 0.00 41.84 3.18
2630 4531 7.255451 GGTCAAAATATCTCGGCAATTTCCATA 60.255 37.037 0.00 0.00 0.00 2.74
2631 4532 6.461509 GGTCAAAATATCTCGGCAATTTCCAT 60.462 38.462 0.00 0.00 0.00 3.41
2632 4533 5.163561 GGTCAAAATATCTCGGCAATTTCCA 60.164 40.000 0.00 0.00 0.00 3.53
2714 4615 9.909644 GAACGTCCAACTACATATGTATATTCT 57.090 33.333 15.81 0.00 0.00 2.40
2715 4616 9.136952 GGAACGTCCAACTACATATGTATATTC 57.863 37.037 15.81 10.11 36.28 1.75
2716 4617 8.867097 AGGAACGTCCAACTACATATGTATATT 58.133 33.333 15.81 10.61 39.61 1.28
2717 4618 8.304596 CAGGAACGTCCAACTACATATGTATAT 58.695 37.037 15.81 5.13 39.61 0.86
2718 4619 7.255695 CCAGGAACGTCCAACTACATATGTATA 60.256 40.741 15.81 0.00 39.61 1.47
2719 4620 6.462487 CCAGGAACGTCCAACTACATATGTAT 60.462 42.308 15.81 0.00 39.61 2.29
2720 4621 5.163488 CCAGGAACGTCCAACTACATATGTA 60.163 44.000 14.75 14.75 39.61 2.29
2721 4622 4.382685 CCAGGAACGTCCAACTACATATGT 60.383 45.833 13.93 13.93 39.61 2.29
2722 4623 4.119862 CCAGGAACGTCCAACTACATATG 58.880 47.826 0.00 0.00 39.61 1.78
2723 4624 3.773119 ACCAGGAACGTCCAACTACATAT 59.227 43.478 0.00 0.00 39.61 1.78
2724 4625 3.167485 ACCAGGAACGTCCAACTACATA 58.833 45.455 0.00 0.00 39.61 2.29
2725 4626 1.975680 ACCAGGAACGTCCAACTACAT 59.024 47.619 0.00 0.00 39.61 2.29
2726 4627 1.342174 GACCAGGAACGTCCAACTACA 59.658 52.381 0.00 0.00 39.61 2.74
2727 4628 1.617357 AGACCAGGAACGTCCAACTAC 59.383 52.381 0.00 0.00 39.61 2.73
2728 4629 1.616865 CAGACCAGGAACGTCCAACTA 59.383 52.381 0.00 0.00 39.61 2.24
2729 4630 0.393077 CAGACCAGGAACGTCCAACT 59.607 55.000 0.00 0.00 39.61 3.16
2730 4631 0.106149 ACAGACCAGGAACGTCCAAC 59.894 55.000 0.00 0.00 39.61 3.77
2748 4649 7.672983 TCTCAAAGAAATTGATGGTACAGAC 57.327 36.000 0.00 0.00 46.62 3.51
2757 4658 8.818622 TCTTGATGGATCTCAAAGAAATTGAT 57.181 30.769 0.00 0.00 46.62 2.57
2781 4682 6.517605 AGGTCTCTTTGACTAGTTTGACTTC 58.482 40.000 0.00 0.00 44.74 3.01
2790 4691 7.362229 CGGGCTATATAAGGTCTCTTTGACTAG 60.362 44.444 0.00 0.00 44.74 2.57
2835 4737 1.742761 TGATGTTCTAAGGCAGCTGC 58.257 50.000 30.88 30.88 41.14 5.25
2836 4738 3.311871 GTCATGATGTTCTAAGGCAGCTG 59.688 47.826 10.11 10.11 0.00 4.24
2859 4761 0.031414 GGTGGAGGGGGCTAAGAGTA 60.031 60.000 0.00 0.00 0.00 2.59
2876 4778 2.951229 ATTTCGGAGTTGACAAGGGT 57.049 45.000 0.00 0.00 0.00 4.34
2907 4809 4.384846 TCTTTACAGACTCGAAATTGCGAC 59.615 41.667 3.83 0.00 36.17 5.19
2917 4819 2.448453 AGGGGACTCTTTACAGACTCG 58.552 52.381 0.00 0.00 32.90 4.18
2931 4833 0.257905 AAAATTAGGCGGGAGGGGAC 59.742 55.000 0.00 0.00 0.00 4.46
2933 4835 3.607871 AAAAATTAGGCGGGAGGGG 57.392 52.632 0.00 0.00 0.00 4.79
2975 4889 2.366837 TGGATCTGGCGGGGTGAT 60.367 61.111 0.00 0.00 0.00 3.06
2981 4895 3.866582 GAGGGGTGGATCTGGCGG 61.867 72.222 0.00 0.00 0.00 6.13
2988 4902 1.997874 GCTGGTCAGAGGGGTGGAT 60.998 63.158 1.65 0.00 0.00 3.41
2994 4908 1.302832 GTTGTGGCTGGTCAGAGGG 60.303 63.158 1.65 0.00 0.00 4.30
3043 4957 2.202570 CTAGAACGACCACGGCGG 60.203 66.667 13.24 0.00 44.46 6.13
3045 4959 0.458025 CCTTCTAGAACGACCACGGC 60.458 60.000 0.00 0.00 44.46 5.68
3109 5172 1.059835 GAGCTCAGACGTGCGAAATTC 59.940 52.381 9.40 0.00 36.73 2.17
3116 5179 0.591236 GATCTCGAGCTCAGACGTGC 60.591 60.000 15.40 0.00 0.00 5.34
3127 5190 3.808466 TCCATGTGAAAGGATCTCGAG 57.192 47.619 5.93 5.93 0.00 4.04
3165 5228 7.736447 GGATGAACCTTCTTATACTTCATGG 57.264 40.000 0.00 0.00 32.85 3.66
3186 5249 3.117738 CCCTTCTACCAAATGCTCAGGAT 60.118 47.826 0.00 0.00 0.00 3.24
3189 5252 3.012518 CACCCTTCTACCAAATGCTCAG 58.987 50.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.