Multiple sequence alignment - TraesCS3B01G134100

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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 TraesCS3B01G134100 chr3B 100.000 3611 0 0 1 3611 116149942 116146332 0.000000e+00 6669.0
1 TraesCS3B01G134100 chr3B 98.611 72 1 0 2708 2779 116147195 116147124 1.050000e-25 128.0
2 TraesCS3B01G134100 chr3B 98.611 72 1 0 2748 2819 116147235 116147164 1.050000e-25 128.0
3 TraesCS3B01G134100 chr3B 93.827 81 3 1 3123 3201 116136309 116136229 1.760000e-23 121.0
4 TraesCS3B01G134100 chr3B 90.476 63 5 1 3178 3240 116136229 116136168 8.310000e-12 82.4
5 TraesCS3B01G134100 chr3B 96.875 32 1 0 2708 2739 116147155 116147124 2.000000e-03 54.7
6 TraesCS3B01G134100 chr3B 96.875 32 1 0 2788 2819 116147235 116147204 2.000000e-03 54.7
7 TraesCS3B01G134100 chr3D 92.054 3335 195 27 5 3301 70715446 70712144 0.000000e+00 4626.0
8 TraesCS3B01G134100 chr3D 93.515 293 15 3 3322 3611 70712088 70711797 1.990000e-117 433.0
9 TraesCS3B01G134100 chr3D 97.222 72 2 0 2708 2779 70712690 70712619 4.900000e-24 122.0
10 TraesCS3B01G134100 chr3D 88.889 72 6 1 2748 2819 70712728 70712659 1.790000e-13 87.9
11 TraesCS3B01G134100 chr3A 91.638 3157 201 24 5 3144 82395489 82392379 0.000000e+00 4309.0
12 TraesCS3B01G134100 chr3A 84.925 199 13 6 3184 3374 82392383 82392194 6.160000e-43 185.0
13 TraesCS3B01G134100 chr3A 100.000 72 0 0 2708 2779 82392751 82392680 2.260000e-27 134.0
14 TraesCS3B01G134100 chr3A 94.915 59 3 0 3404 3462 82351941 82351883 3.840000e-15 93.5
15 TraesCS3B01G134100 chr3A 100.000 32 0 0 2708 2739 82392711 82392680 3.890000e-05 60.2


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 TraesCS3B01G134100 chr3B 116146332 116149942 3610 True 1406.880 6669 98.19440 1 3611 5 chr3B.!!$R2 3610
1 TraesCS3B01G134100 chr3D 70711797 70715446 3649 True 1317.225 4626 92.92000 5 3611 4 chr3D.!!$R1 3606
2 TraesCS3B01G134100 chr3A 82392194 82395489 3295 True 1172.050 4309 94.14075 5 3374 4 chr3A.!!$R2 3369

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
517 545 0.458716 GTTCTGTCCCTAGTCGCAGC 60.459 60.0 0.00 0.0 0.00 5.25 F
1082 1124 0.117140 TTCTGCCTCTCCCTCTTCCA 59.883 55.0 0.00 0.0 0.00 3.53 F
1157 1199 0.984230 ATGCTTCCCTTCCTCGTGAA 59.016 50.0 0.00 0.0 0.00 3.18 F
1944 1986 0.111253 CTGGGAAGGACCTTGTTGCT 59.889 55.0 12.68 0.0 38.98 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 1404 0.036577 CAGAGTCTGCCACAAGGAGG 60.037 60.0 7.33 0.0 36.89 4.30 R
1938 1980 0.108377 ACGTGAGTGTGACAGCAACA 60.108 50.0 0.00 0.0 46.97 3.33 R
2010 2052 0.619832 TCTGCAGGGCCTTGATCTCT 60.620 55.0 20.85 0.0 0.00 3.10 R
3540 3626 0.110056 CACAAACAGATGCTGCCGTC 60.110 55.0 0.00 0.0 34.37 4.79 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
56 57 7.719871 AGAGTAAGAGTGCTACCATCTAAAA 57.280 36.000 0.00 0.00 0.00 1.52
57 58 7.777095 AGAGTAAGAGTGCTACCATCTAAAAG 58.223 38.462 0.00 0.00 0.00 2.27
60 66 8.688151 AGTAAGAGTGCTACCATCTAAAAGTAG 58.312 37.037 0.00 0.00 37.20 2.57
62 68 7.102847 AGAGTGCTACCATCTAAAAGTAGAC 57.897 40.000 0.00 0.00 39.20 2.59
68 74 8.904834 TGCTACCATCTAAAAGTAGACTAAGAG 58.095 37.037 0.00 0.00 39.20 2.85
78 84 8.866970 AAAAGTAGACTAAGAGTGCTACTAGT 57.133 34.615 0.00 0.00 37.77 2.57
81 87 8.866970 AGTAGACTAAGAGTGCTACTAGTTTT 57.133 34.615 0.00 0.00 37.39 2.43
86 92 9.688592 GACTAAGAGTGCTACTAGTTTTAAACA 57.311 33.333 10.60 0.00 0.00 2.83
91 97 9.780186 AGAGTGCTACTAGTTTTAAACAAGATT 57.220 29.630 10.60 0.00 0.00 2.40
120 126 3.243771 GCTGTTACAGAGTACACACCACT 60.244 47.826 17.40 0.00 32.44 4.00
121 127 4.547532 CTGTTACAGAGTACACACCACTC 58.452 47.826 6.50 0.00 42.30 3.51
142 154 3.323979 TCTCTTTGGTGGTTCACTAGGAC 59.676 47.826 0.00 0.00 34.40 3.85
143 155 3.314693 TCTTTGGTGGTTCACTAGGACT 58.685 45.455 0.00 0.00 34.40 3.85
160 172 3.610911 GGACTCATCCCTTTGTTACAGG 58.389 50.000 0.00 0.00 39.39 4.00
177 189 2.307098 ACAGGCCTGCTAACAAGAGAAT 59.693 45.455 33.06 5.13 0.00 2.40
194 220 4.730657 GAGAATCTGCACAAGAAATGGTG 58.269 43.478 0.00 0.00 38.79 4.17
199 225 3.072330 TCTGCACAAGAAATGGTGGTCTA 59.928 43.478 0.00 0.00 35.58 2.59
212 238 9.574516 GAAATGGTGGTCTATATTTATTGGTCT 57.425 33.333 0.00 0.00 0.00 3.85
215 241 5.705905 GGTGGTCTATATTTATTGGTCTGCC 59.294 44.000 0.00 0.00 0.00 4.85
223 249 9.429359 CTATATTTATTGGTCTGCCAGAGTTAG 57.571 37.037 0.00 0.00 46.91 2.34
224 250 2.409948 ATTGGTCTGCCAGAGTTAGC 57.590 50.000 0.00 0.00 46.91 3.09
228 254 1.681793 GGTCTGCCAGAGTTAGCGATA 59.318 52.381 0.00 0.00 34.09 2.92
239 265 7.549488 GCCAGAGTTAGCGATATGGTTTATATT 59.451 37.037 0.49 0.00 32.09 1.28
262 290 4.623932 AGTGATTCAGCAGTTACTTGGA 57.376 40.909 0.00 0.00 0.00 3.53
268 296 3.273434 TCAGCAGTTACTTGGATGATGC 58.727 45.455 0.00 0.00 0.00 3.91
271 299 3.012518 GCAGTTACTTGGATGATGCACT 58.987 45.455 0.00 0.00 32.58 4.40
283 311 5.104817 TGGATGATGCACTCTGTCATAAGAA 60.105 40.000 0.00 0.00 33.03 2.52
285 313 7.157347 GGATGATGCACTCTGTCATAAGAATA 58.843 38.462 0.00 0.00 33.03 1.75
291 319 5.982516 GCACTCTGTCATAAGAATACTCCAG 59.017 44.000 0.00 0.00 0.00 3.86
318 346 4.407945 GGTTGCCCTTAGGTAATGTCTCTA 59.592 45.833 0.00 0.00 40.16 2.43
319 347 5.358090 GTTGCCCTTAGGTAATGTCTCTAC 58.642 45.833 0.00 0.00 40.16 2.59
337 365 6.760770 GTCTCTACTTAGGAAGCTAAGACGTA 59.239 42.308 0.00 0.00 38.76 3.57
349 377 3.250280 GCTAAGACGTATCGGTCTGATGA 59.750 47.826 4.27 0.00 46.21 2.92
357 385 4.492570 CGTATCGGTCTGATGAAAACAAGC 60.493 45.833 4.27 0.00 37.99 4.01
362 390 3.365767 GGTCTGATGAAAACAAGCAGCTC 60.366 47.826 0.00 0.00 0.00 4.09
363 391 3.251729 GTCTGATGAAAACAAGCAGCTCA 59.748 43.478 0.00 0.00 0.00 4.26
364 392 3.251729 TCTGATGAAAACAAGCAGCTCAC 59.748 43.478 0.00 0.00 0.00 3.51
411 439 6.209192 ACTGGCATCACAAAATTTACATGAGA 59.791 34.615 0.00 0.00 0.00 3.27
425 453 6.560003 TTACATGAGAGTAATCCCACACAT 57.440 37.500 0.00 0.00 0.00 3.21
448 476 0.755686 GGGTGTTTGCATGGGAAACA 59.244 50.000 11.24 11.24 40.23 2.83
454 482 4.756135 GTGTTTGCATGGGAAACAAATCAT 59.244 37.500 15.85 0.00 43.18 2.45
461 489 5.121142 GCATGGGAAACAAATCATTCAACAG 59.879 40.000 0.00 0.00 0.00 3.16
490 518 8.879342 AGGATTATGATCAGTTTTAAGACTCG 57.121 34.615 0.09 0.00 33.77 4.18
491 519 8.696374 AGGATTATGATCAGTTTTAAGACTCGA 58.304 33.333 0.09 0.00 33.77 4.04
499 527 8.608844 ATCAGTTTTAAGACTCGAAGAAATGT 57.391 30.769 0.00 0.00 34.09 2.71
504 532 8.336080 GTTTTAAGACTCGAAGAAATGTTCTGT 58.664 33.333 0.00 0.00 40.59 3.41
505 533 7.639162 TTAAGACTCGAAGAAATGTTCTGTC 57.361 36.000 0.00 0.00 40.59 3.51
512 540 4.865365 CGAAGAAATGTTCTGTCCCTAGTC 59.135 45.833 0.00 0.00 40.59 2.59
517 545 0.458716 GTTCTGTCCCTAGTCGCAGC 60.459 60.000 0.00 0.00 0.00 5.25
518 546 1.605058 TTCTGTCCCTAGTCGCAGCC 61.605 60.000 0.00 0.00 0.00 4.85
520 548 1.680522 CTGTCCCTAGTCGCAGCCAT 61.681 60.000 0.00 0.00 0.00 4.40
523 551 1.138266 GTCCCTAGTCGCAGCCATTTA 59.862 52.381 0.00 0.00 0.00 1.40
524 552 2.047061 TCCCTAGTCGCAGCCATTTAT 58.953 47.619 0.00 0.00 0.00 1.40
602 633 9.553064 ACTGCAAAATTAAATGGTTATTTGTGA 57.447 25.926 0.00 0.00 37.12 3.58
604 635 8.502387 TGCAAAATTAAATGGTTATTTGTGAGC 58.498 29.630 0.00 0.00 37.12 4.26
608 639 9.777297 AAATTAAATGGTTATTTGTGAGCAAGT 57.223 25.926 0.00 0.00 37.12 3.16
614 645 5.095490 GGTTATTTGTGAGCAAGTGCATAC 58.905 41.667 6.00 4.69 45.16 2.39
631 670 3.119849 GCATACAGTTGTGATGGGTCAAC 60.120 47.826 0.00 0.00 42.62 3.18
649 688 7.392113 TGGGTCAACGTTGATTTTCTATAATGT 59.608 33.333 31.81 0.00 39.73 2.71
650 689 7.696453 GGGTCAACGTTGATTTTCTATAATGTG 59.304 37.037 31.81 0.00 39.73 3.21
673 715 6.513991 GTGTATGTATTCGAAAACGTCAACAC 59.486 38.462 0.00 7.73 0.00 3.32
674 716 5.660629 ATGTATTCGAAAACGTCAACACA 57.339 34.783 0.00 0.00 0.00 3.72
686 728 3.928992 ACGTCAACACAGCTTATCTGATG 59.071 43.478 0.00 0.00 45.72 3.07
700 742 9.672673 AGCTTATCTGATGTGTTAATTAAGTGT 57.327 29.630 0.00 0.00 0.00 3.55
710 752 8.590719 TGTGTTAATTAAGTGTGTATCGACAA 57.409 30.769 0.00 0.00 37.31 3.18
761 803 3.254166 GGATGCTGAAGAAAGCTGTTTGA 59.746 43.478 0.00 0.00 43.90 2.69
772 814 4.965200 AAGCTGTTTGAGGTAGAAGACT 57.035 40.909 0.00 0.00 0.00 3.24
773 815 6.267928 AGAAAGCTGTTTGAGGTAGAAGACTA 59.732 38.462 0.00 0.00 0.00 2.59
774 816 6.420913 AAGCTGTTTGAGGTAGAAGACTAA 57.579 37.500 0.00 0.00 0.00 2.24
775 817 6.613153 AGCTGTTTGAGGTAGAAGACTAAT 57.387 37.500 0.00 0.00 0.00 1.73
776 818 6.402222 AGCTGTTTGAGGTAGAAGACTAATG 58.598 40.000 0.00 0.00 0.00 1.90
777 819 5.064071 GCTGTTTGAGGTAGAAGACTAATGC 59.936 44.000 0.00 0.00 0.00 3.56
778 820 6.360370 TGTTTGAGGTAGAAGACTAATGCT 57.640 37.500 0.00 0.00 0.00 3.79
779 821 7.476540 TGTTTGAGGTAGAAGACTAATGCTA 57.523 36.000 0.00 0.00 0.00 3.49
780 822 8.079211 TGTTTGAGGTAGAAGACTAATGCTAT 57.921 34.615 0.00 0.00 0.00 2.97
781 823 7.981789 TGTTTGAGGTAGAAGACTAATGCTATG 59.018 37.037 0.00 0.00 0.00 2.23
782 824 6.656632 TGAGGTAGAAGACTAATGCTATGG 57.343 41.667 0.00 0.00 0.00 2.74
783 825 5.011125 TGAGGTAGAAGACTAATGCTATGGC 59.989 44.000 0.00 0.00 39.26 4.40
804 846 4.998033 GGCCTCCAGAATTATAGCAGTTAC 59.002 45.833 0.00 0.00 0.00 2.50
807 849 6.712547 GCCTCCAGAATTATAGCAGTTACATT 59.287 38.462 0.00 0.00 0.00 2.71
828 870 8.213518 ACATTAGGACATATGAATGTTGTGAC 57.786 34.615 10.38 0.00 46.49 3.67
837 879 3.479489 TGAATGTTGTGACTCACTGCAT 58.521 40.909 10.54 10.81 35.11 3.96
851 893 2.166459 CACTGCATCCTAAACTCTCGGA 59.834 50.000 0.00 0.00 0.00 4.55
859 901 5.740290 TCCTAAACTCTCGGAAACTGATT 57.260 39.130 0.00 0.00 0.00 2.57
860 902 6.845758 TCCTAAACTCTCGGAAACTGATTA 57.154 37.500 0.00 0.00 0.00 1.75
916 958 8.880244 AGTTTCTGTATATATCAATACCAGCCA 58.120 33.333 0.00 0.00 32.36 4.75
928 970 5.356751 TCAATACCAGCCATACATTTGACAC 59.643 40.000 0.00 0.00 0.00 3.67
968 1010 2.678769 GCCTAAATTGCTGCATGCCTTT 60.679 45.455 16.68 9.44 42.00 3.11
1004 1046 5.048083 TCTCATAACTTTGTTCAACCATGGC 60.048 40.000 13.04 0.00 0.00 4.40
1038 1080 2.534042 TCCTTCTGTCCTACCCTGAG 57.466 55.000 0.00 0.00 0.00 3.35
1082 1124 0.117140 TTCTGCCTCTCCCTCTTCCA 59.883 55.000 0.00 0.00 0.00 3.53
1132 1174 1.966451 CCGGTGAACTGGCCTGTTC 60.966 63.158 35.92 35.92 44.60 3.18
1157 1199 0.984230 ATGCTTCCCTTCCTCGTGAA 59.016 50.000 0.00 0.00 0.00 3.18
1170 1212 3.192844 TCCTCGTGAAGAATCTGTACCAC 59.807 47.826 0.00 0.00 0.00 4.16
1182 1224 4.206477 TCTGTACCACATTCATGACAGG 57.794 45.455 0.00 0.00 35.96 4.00
1184 1226 2.026356 TGTACCACATTCATGACAGGGG 60.026 50.000 12.27 12.27 0.00 4.79
1200 1242 2.734591 GGCACCGATATGCTCCGA 59.265 61.111 6.29 0.00 45.38 4.55
1259 1301 2.373169 TCCTCAACATGAGCTTCTTGGT 59.627 45.455 0.00 0.00 42.98 3.67
1362 1404 6.714730 GATGTTTGACATCCTAGGTGATGGC 61.715 48.000 9.08 9.05 46.99 4.40
1383 1425 1.345741 CTCCTTGTGGCAGACTCTGAA 59.654 52.381 10.45 0.00 32.44 3.02
1852 1894 3.619733 GCTGTCCATGTACATGAACTGGA 60.620 47.826 32.72 21.73 41.20 3.86
1861 1903 3.744940 ACATGAACTGGACCATGGATT 57.255 42.857 21.47 4.19 43.16 3.01
1938 1980 1.149101 TCTTTGCTGGGAAGGACCTT 58.851 50.000 6.40 6.40 38.98 3.50
1944 1986 0.111253 CTGGGAAGGACCTTGTTGCT 59.889 55.000 12.68 0.00 38.98 3.91
1947 1989 1.239347 GGAAGGACCTTGTTGCTGTC 58.761 55.000 12.68 0.00 35.41 3.51
2034 2076 4.357279 AAGGCCCTGCAGAGCACC 62.357 66.667 22.55 13.52 33.79 5.01
2067 2109 2.829741 ACCTCTCTGTCTTTGAGTGC 57.170 50.000 0.00 0.00 33.59 4.40
2072 2114 1.789464 CTCTGTCTTTGAGTGCGACAC 59.211 52.381 2.28 2.28 34.32 3.67
2202 2244 3.420893 CATGTGTTTTAGGCTCTTCCCA 58.579 45.455 0.00 0.00 34.51 4.37
2421 2463 5.053978 ACAAGTTCCTGTCCTTCAATTCT 57.946 39.130 0.00 0.00 0.00 2.40
2469 2511 2.886523 CCTTGGTCTCAGCAACATGAAA 59.113 45.455 0.00 0.00 31.65 2.69
2470 2512 3.304928 CCTTGGTCTCAGCAACATGAAAC 60.305 47.826 0.00 0.00 31.65 2.78
2475 2517 0.592637 TCAGCAACATGAAACTGGCG 59.407 50.000 0.00 0.00 0.00 5.69
2620 2662 2.097142 GCAGCTGCTTGATCTTTACTGG 59.903 50.000 31.33 0.00 38.21 4.00
2645 2687 9.895138 GGTATCTGTTTTCTTACTTGGGTTATA 57.105 33.333 0.00 0.00 0.00 0.98
2738 2780 3.565307 AGTGTTGGAATTGTCACCATGT 58.435 40.909 0.00 0.00 36.02 3.21
2739 2781 4.724399 AGTGTTGGAATTGTCACCATGTA 58.276 39.130 0.00 0.00 36.02 2.29
2815 2857 2.156891 CGTAGTGTTGGAATTGTCACCG 59.843 50.000 0.00 0.00 0.00 4.94
2849 2891 9.220767 GGAACAGAATATTATAGTGATTGGTCC 57.779 37.037 0.00 0.00 0.00 4.46
2870 2912 6.092807 GGTCCTGTGATGATCTTTTGAGTTAC 59.907 42.308 0.00 0.00 0.00 2.50
2879 2921 9.552114 GATGATCTTTTGAGTTACTTTCATGTG 57.448 33.333 0.00 0.00 0.00 3.21
2946 2988 3.243002 GCATCTGCCTATCAAAAGTGCTC 60.243 47.826 0.00 0.00 34.31 4.26
3005 3047 0.550914 TCTTGGACCTGCACCTGTTT 59.449 50.000 0.00 0.00 0.00 2.83
3006 3048 1.064017 TCTTGGACCTGCACCTGTTTT 60.064 47.619 0.00 0.00 0.00 2.43
3070 3112 6.127786 GCTCATTTTGTTTCAGAGGCTATTCT 60.128 38.462 0.00 0.00 0.00 2.40
3112 3154 7.995463 TTGTTCGCTTTTAAAAGTAGCATTT 57.005 28.000 24.95 0.00 38.28 2.32
3170 3212 4.157289 GGTCGTCAGAGTGGTTACTTGATA 59.843 45.833 0.00 0.00 37.25 2.15
3216 3259 0.601311 GAAAGTGACGCTCCTGCAGT 60.601 55.000 13.81 0.00 39.64 4.40
3244 3287 8.311836 TGAGGAGTTTAATTTCGTCTCTGTTAT 58.688 33.333 9.44 0.00 0.00 1.89
3245 3288 9.152595 GAGGAGTTTAATTTCGTCTCTGTTATT 57.847 33.333 0.00 0.00 0.00 1.40
3246 3289 9.152595 AGGAGTTTAATTTCGTCTCTGTTATTC 57.847 33.333 0.00 0.00 0.00 1.75
3247 3290 9.152595 GGAGTTTAATTTCGTCTCTGTTATTCT 57.847 33.333 0.00 0.00 0.00 2.40
3248 3291 9.959775 GAGTTTAATTTCGTCTCTGTTATTCTG 57.040 33.333 0.00 0.00 0.00 3.02
3249 3292 9.490379 AGTTTAATTTCGTCTCTGTTATTCTGT 57.510 29.630 0.00 0.00 0.00 3.41
3301 3344 8.682936 ATGATCCATCCAAAGTTCATAAGTAC 57.317 34.615 0.00 0.00 0.00 2.73
3302 3345 7.629157 TGATCCATCCAAAGTTCATAAGTACA 58.371 34.615 0.00 0.00 0.00 2.90
3303 3346 7.770433 TGATCCATCCAAAGTTCATAAGTACAG 59.230 37.037 0.00 0.00 0.00 2.74
3307 3350 7.822334 CCATCCAAAGTTCATAAGTACAGTACA 59.178 37.037 13.37 0.00 0.00 2.90
3308 3351 8.873830 CATCCAAAGTTCATAAGTACAGTACAG 58.126 37.037 13.37 0.50 0.00 2.74
3309 3352 7.959175 TCCAAAGTTCATAAGTACAGTACAGT 58.041 34.615 13.37 3.09 0.00 3.55
3310 3353 9.081204 TCCAAAGTTCATAAGTACAGTACAGTA 57.919 33.333 13.37 5.21 0.00 2.74
3311 3354 9.355215 CCAAAGTTCATAAGTACAGTACAGTAG 57.645 37.037 13.37 0.84 0.00 2.57
3312 3355 9.909644 CAAAGTTCATAAGTACAGTACAGTAGT 57.090 33.333 13.37 0.00 0.00 2.73
3354 3439 7.916914 TGCTTAAGATTTCTAAGTTGGGTAC 57.083 36.000 6.67 0.00 0.00 3.34
3381 3466 6.295349 GCTTGGTGATACTACAGCTATGGTAT 60.295 42.308 0.00 0.00 38.79 2.73
3382 3467 7.093902 GCTTGGTGATACTACAGCTATGGTATA 60.094 40.741 0.45 0.00 38.79 1.47
3383 3468 7.698506 TGGTGATACTACAGCTATGGTATAC 57.301 40.000 0.45 1.39 38.79 1.47
3393 3479 2.352814 GCTATGGTATACTGACAGGCCG 60.353 54.545 7.51 0.00 0.00 6.13
3451 3537 1.066143 CACTGACAGGGCCGATAGTTT 60.066 52.381 7.51 0.00 0.00 2.66
3462 3548 4.634443 GGGCCGATAGTTTCGCATATATTT 59.366 41.667 0.00 0.00 46.71 1.40
3463 3549 5.447279 GGGCCGATAGTTTCGCATATATTTG 60.447 44.000 0.00 0.00 46.71 2.32
3499 3585 2.948979 TGGGCACTTTTGACTTGTACTG 59.051 45.455 0.00 0.00 0.00 2.74
3533 3619 9.434420 CTGTAGATTGGAGAAATTAGGATGATC 57.566 37.037 0.00 0.00 0.00 2.92
3604 3690 9.055248 GTGACATAATCAGAAATTTCAAACTCG 57.945 33.333 19.99 5.60 38.28 4.18
3605 3691 8.998377 TGACATAATCAGAAATTTCAAACTCGA 58.002 29.630 19.99 6.87 31.91 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.864379 GCATACCAAATTGTAAAGGAGATGATG 59.136 37.037 0.00 0.00 0.00 3.07
1 2 7.781693 AGCATACCAAATTGTAAAGGAGATGAT 59.218 33.333 0.00 0.00 0.00 2.45
2 3 7.067372 CAGCATACCAAATTGTAAAGGAGATGA 59.933 37.037 0.00 0.00 0.00 2.92
3 4 7.198390 CAGCATACCAAATTGTAAAGGAGATG 58.802 38.462 0.00 0.00 0.00 2.90
20 21 5.285651 CACTCTTACTCTTAGCAGCATACC 58.714 45.833 0.00 0.00 0.00 2.73
56 57 8.866970 AAAACTAGTAGCACTCTTAGTCTACT 57.133 34.615 16.32 16.32 39.78 2.57
60 66 9.688592 TGTTTAAAACTAGTAGCACTCTTAGTC 57.311 33.333 0.00 0.00 0.00 2.59
83 89 9.167311 CTCTGTAACAGCCTTTATAATCTTGTT 57.833 33.333 0.00 8.95 0.00 2.83
86 92 9.819267 GTACTCTGTAACAGCCTTTATAATCTT 57.181 33.333 0.00 0.00 0.00 2.40
87 93 8.978472 TGTACTCTGTAACAGCCTTTATAATCT 58.022 33.333 0.00 0.00 0.00 2.40
89 95 8.537016 TGTGTACTCTGTAACAGCCTTTATAAT 58.463 33.333 0.00 0.00 0.00 1.28
91 97 7.318141 GTGTGTACTCTGTAACAGCCTTTATA 58.682 38.462 0.00 0.00 0.00 0.98
92 98 6.164176 GTGTGTACTCTGTAACAGCCTTTAT 58.836 40.000 0.00 0.00 0.00 1.40
93 99 5.510179 GGTGTGTACTCTGTAACAGCCTTTA 60.510 44.000 0.00 0.00 35.53 1.85
94 100 4.377897 GTGTGTACTCTGTAACAGCCTTT 58.622 43.478 0.00 0.00 0.00 3.11
96 102 2.299297 GGTGTGTACTCTGTAACAGCCT 59.701 50.000 0.00 0.00 35.53 4.58
97 103 2.036733 TGGTGTGTACTCTGTAACAGCC 59.963 50.000 8.06 2.58 39.64 4.85
98 104 3.057734 GTGGTGTGTACTCTGTAACAGC 58.942 50.000 4.51 4.51 40.52 4.40
99 105 4.547532 GAGTGGTGTGTACTCTGTAACAG 58.452 47.826 0.00 0.00 41.00 3.16
100 106 4.579454 GAGTGGTGTGTACTCTGTAACA 57.421 45.455 0.00 0.00 41.00 2.41
120 126 3.323979 GTCCTAGTGAACCACCAAAGAGA 59.676 47.826 0.00 0.00 34.49 3.10
121 127 3.325135 AGTCCTAGTGAACCACCAAAGAG 59.675 47.826 0.00 0.00 34.49 2.85
142 154 2.025887 AGGCCTGTAACAAAGGGATGAG 60.026 50.000 3.11 0.00 35.17 2.90
143 155 1.992557 AGGCCTGTAACAAAGGGATGA 59.007 47.619 3.11 0.00 35.17 2.92
160 172 2.354199 GCAGATTCTCTTGTTAGCAGGC 59.646 50.000 0.00 0.00 0.00 4.85
177 189 2.158623 AGACCACCATTTCTTGTGCAGA 60.159 45.455 0.00 0.00 0.00 4.26
185 197 9.574516 GACCAATAAATATAGACCACCATTTCT 57.425 33.333 0.00 0.00 0.00 2.52
212 238 2.039418 ACCATATCGCTAACTCTGGCA 58.961 47.619 0.00 0.00 0.00 4.92
228 254 9.632638 ACTGCTGAATCACTAAATATAAACCAT 57.367 29.630 0.00 0.00 0.00 3.55
239 265 6.109156 TCCAAGTAACTGCTGAATCACTAA 57.891 37.500 0.00 0.00 0.00 2.24
243 269 5.164620 TCATCCAAGTAACTGCTGAATCA 57.835 39.130 0.00 0.00 0.00 2.57
262 290 7.733969 AGTATTCTTATGACAGAGTGCATCAT 58.266 34.615 5.18 5.18 36.95 2.45
268 296 5.982516 GCTGGAGTATTCTTATGACAGAGTG 59.017 44.000 0.00 0.00 0.00 3.51
271 299 6.407412 CCTTGCTGGAGTATTCTTATGACAGA 60.407 42.308 0.00 0.00 38.35 3.41
318 346 4.275443 CCGATACGTCTTAGCTTCCTAAGT 59.725 45.833 0.00 0.00 46.87 2.24
337 365 3.411446 TGCTTGTTTTCATCAGACCGAT 58.589 40.909 0.00 0.00 33.27 4.18
349 377 1.683385 GGGAAGTGAGCTGCTTGTTTT 59.317 47.619 2.53 0.00 0.00 2.43
357 385 0.676151 GGCAAGAGGGAAGTGAGCTG 60.676 60.000 0.00 0.00 0.00 4.24
362 390 1.672356 CCGTGGCAAGAGGGAAGTG 60.672 63.158 0.76 0.00 0.00 3.16
363 391 2.750350 CCGTGGCAAGAGGGAAGT 59.250 61.111 0.76 0.00 0.00 3.01
425 453 1.500474 TCCCATGCAAACACCCAAAA 58.500 45.000 0.00 0.00 0.00 2.44
471 499 8.833231 TTTCTTCGAGTCTTAAAACTGATCAT 57.167 30.769 0.00 0.00 0.00 2.45
472 500 8.712363 CATTTCTTCGAGTCTTAAAACTGATCA 58.288 33.333 0.00 0.00 0.00 2.92
482 510 6.157211 GGACAGAACATTTCTTCGAGTCTTA 58.843 40.000 0.00 0.00 38.11 2.10
486 514 3.325135 AGGGACAGAACATTTCTTCGAGT 59.675 43.478 0.00 0.00 38.11 4.18
487 515 3.931578 AGGGACAGAACATTTCTTCGAG 58.068 45.455 0.00 0.00 38.11 4.04
489 517 4.822026 ACTAGGGACAGAACATTTCTTCG 58.178 43.478 0.00 0.00 38.11 3.79
490 518 4.865365 CGACTAGGGACAGAACATTTCTTC 59.135 45.833 0.00 0.00 38.11 2.87
491 519 4.822026 CGACTAGGGACAGAACATTTCTT 58.178 43.478 0.00 0.00 38.11 2.52
499 527 1.605058 GGCTGCGACTAGGGACAGAA 61.605 60.000 11.12 0.00 31.67 3.02
504 532 1.491668 TAAATGGCTGCGACTAGGGA 58.508 50.000 0.00 0.00 0.00 4.20
505 533 2.146342 CATAAATGGCTGCGACTAGGG 58.854 52.381 0.00 0.00 0.00 3.53
524 552 9.661954 AGATCTGTATAATCCTCTTTTAGACCA 57.338 33.333 0.00 0.00 0.00 4.02
597 628 2.849942 ACTGTATGCACTTGCTCACAA 58.150 42.857 2.33 0.00 42.66 3.33
602 633 2.849942 TCACAACTGTATGCACTTGCT 58.150 42.857 2.33 0.00 42.66 3.91
604 635 3.119743 CCCATCACAACTGTATGCACTTG 60.120 47.826 0.00 2.48 0.00 3.16
608 639 2.039613 TGACCCATCACAACTGTATGCA 59.960 45.455 0.00 0.00 0.00 3.96
614 645 1.593196 ACGTTGACCCATCACAACTG 58.407 50.000 0.00 0.00 42.53 3.16
621 652 4.766404 AGAAAATCAACGTTGACCCATC 57.234 40.909 31.87 24.40 40.49 3.51
623 655 7.392113 ACATTATAGAAAATCAACGTTGACCCA 59.608 33.333 31.87 11.57 40.49 4.51
660 702 5.050363 TCAGATAAGCTGTGTTGACGTTTTC 60.050 40.000 0.00 0.00 45.14 2.29
663 705 3.990092 TCAGATAAGCTGTGTTGACGTT 58.010 40.909 0.00 0.00 45.14 3.99
665 707 3.928992 ACATCAGATAAGCTGTGTTGACG 59.071 43.478 0.00 0.00 45.14 4.35
673 715 9.926751 CACTTAATTAACACATCAGATAAGCTG 57.073 33.333 0.00 0.00 46.31 4.24
674 716 9.672673 ACACTTAATTAACACATCAGATAAGCT 57.327 29.630 0.00 0.00 0.00 3.74
686 728 8.706035 ACTTGTCGATACACACTTAATTAACAC 58.294 33.333 0.00 0.00 34.61 3.32
700 742 9.557061 ACTAGACATTCTATACTTGTCGATACA 57.443 33.333 0.00 0.00 43.49 2.29
704 746 8.734218 AGAACTAGACATTCTATACTTGTCGA 57.266 34.615 0.00 0.00 43.49 4.20
705 747 9.440784 GAAGAACTAGACATTCTATACTTGTCG 57.559 37.037 0.00 0.00 43.49 4.35
739 781 3.254166 TCAAACAGCTTTCTTCAGCATCC 59.746 43.478 0.00 0.00 42.84 3.51
761 803 4.284746 GGCCATAGCATTAGTCTTCTACCT 59.715 45.833 0.00 0.00 42.56 3.08
772 814 4.729552 AATTCTGGAGGCCATAGCATTA 57.270 40.909 5.01 0.00 42.56 1.90
773 815 3.607490 AATTCTGGAGGCCATAGCATT 57.393 42.857 5.01 0.00 42.56 3.56
774 816 4.942363 ATAATTCTGGAGGCCATAGCAT 57.058 40.909 5.01 0.00 42.56 3.79
775 817 4.323792 GCTATAATTCTGGAGGCCATAGCA 60.324 45.833 16.80 0.00 42.56 3.49
776 818 4.195416 GCTATAATTCTGGAGGCCATAGC 58.805 47.826 5.01 7.87 30.83 2.97
777 819 5.046014 ACTGCTATAATTCTGGAGGCCATAG 60.046 44.000 5.01 0.65 30.82 2.23
778 820 4.846367 ACTGCTATAATTCTGGAGGCCATA 59.154 41.667 5.01 0.00 30.82 2.74
779 821 3.654806 ACTGCTATAATTCTGGAGGCCAT 59.345 43.478 5.01 0.00 30.82 4.40
780 822 3.048600 ACTGCTATAATTCTGGAGGCCA 58.951 45.455 5.01 0.00 0.00 5.36
781 823 3.778954 ACTGCTATAATTCTGGAGGCC 57.221 47.619 0.00 0.00 0.00 5.19
782 824 5.611374 TGTAACTGCTATAATTCTGGAGGC 58.389 41.667 0.00 0.00 0.00 4.70
783 825 9.429359 CTAATGTAACTGCTATAATTCTGGAGG 57.571 37.037 0.00 0.00 0.00 4.30
804 846 8.442632 AGTCACAACATTCATATGTCCTAATG 57.557 34.615 11.41 11.41 44.14 1.90
807 849 7.041721 GTGAGTCACAACATTCATATGTCCTA 58.958 38.462 18.54 0.00 44.14 2.94
828 870 3.443037 CGAGAGTTTAGGATGCAGTGAG 58.557 50.000 0.00 0.00 0.00 3.51
837 879 5.740290 AATCAGTTTCCGAGAGTTTAGGA 57.260 39.130 0.00 0.00 0.00 2.94
851 893 3.135895 CCCGTGGGATAGGTAATCAGTTT 59.864 47.826 0.00 0.00 36.20 2.66
916 958 2.493278 GCCTTGCCAGTGTCAAATGTAT 59.507 45.455 0.00 0.00 0.00 2.29
918 960 0.675633 GCCTTGCCAGTGTCAAATGT 59.324 50.000 0.00 0.00 0.00 2.71
928 970 0.316204 CTTCACCTTTGCCTTGCCAG 59.684 55.000 0.00 0.00 0.00 4.85
968 1010 5.441718 AAGTTATGAGATGCAGAGGGAAA 57.558 39.130 0.00 0.00 0.00 3.13
1082 1124 2.426023 GGCAGTGTCGGACAAGGT 59.574 61.111 13.23 0.00 0.00 3.50
1170 1212 1.378882 CGGTGCCCCTGTCATGAATG 61.379 60.000 0.00 0.00 0.00 2.67
1182 1224 2.357517 CGGAGCATATCGGTGCCC 60.358 66.667 5.03 5.65 46.19 5.36
1184 1226 0.387878 CTCTCGGAGCATATCGGTGC 60.388 60.000 0.00 0.96 45.38 5.01
1362 1404 0.036577 CAGAGTCTGCCACAAGGAGG 60.037 60.000 7.33 0.00 36.89 4.30
1374 1416 2.938428 ACTCCCAGGATTCAGAGTCT 57.062 50.000 0.00 0.00 34.53 3.24
1403 1445 2.883574 CAAAGATTTGCATCGCCACAT 58.116 42.857 0.00 0.00 34.17 3.21
1806 1848 1.304381 TCCCTGGCATTGCTTGGTC 60.304 57.895 8.82 0.00 0.00 4.02
1852 1894 1.567649 ACTCATGCTGGAATCCATGGT 59.432 47.619 12.58 0.00 39.36 3.55
1861 1903 1.078637 GCTGCTCACTCATGCTGGA 60.079 57.895 0.00 0.00 0.00 3.86
1938 1980 0.108377 ACGTGAGTGTGACAGCAACA 60.108 50.000 0.00 0.00 46.97 3.33
2010 2052 0.619832 TCTGCAGGGCCTTGATCTCT 60.620 55.000 20.85 0.00 0.00 3.10
2034 2076 1.379044 GAGGTTCCCTGGCCATGTG 60.379 63.158 5.51 0.00 31.76 3.21
2072 2114 1.069090 TAAATAGCAGGCCGGAGCG 59.931 57.895 5.05 0.00 41.24 5.03
2202 2244 2.363795 TCCTCGAATGGGGTCGCT 60.364 61.111 0.00 0.00 40.88 4.93
2469 2511 3.984193 GATGGAAGCAGCCGCCAGT 62.984 63.158 9.50 0.00 39.83 4.00
2470 2512 3.207669 GATGGAAGCAGCCGCCAG 61.208 66.667 9.50 0.00 39.83 4.85
2475 2517 4.392940 AGTTGTATATGATGGAAGCAGCC 58.607 43.478 0.00 0.00 32.93 4.85
2645 2687 8.070171 GCATTTAGTTCTGTTCAATACGCATAT 58.930 33.333 0.00 0.00 0.00 1.78
2655 2697 6.003326 TGGATTCTGCATTTAGTTCTGTTCA 58.997 36.000 0.00 0.00 0.00 3.18
2702 2744 9.661563 AATTCCAACACTACGAACAGATTATAA 57.338 29.630 0.00 0.00 0.00 0.98
2714 2756 3.135225 TGGTGACAATTCCAACACTACG 58.865 45.455 0.00 0.00 37.44 3.51
2738 2780 6.263516 ACACTACGAACAGATAGCTTGTTA 57.736 37.500 2.29 0.00 0.00 2.41
2739 2781 5.135508 ACACTACGAACAGATAGCTTGTT 57.864 39.130 1.89 1.89 0.00 2.83
2815 2857 8.993121 CACTATAATATTCTGTTCCCATGACAC 58.007 37.037 0.00 0.00 0.00 3.67
2849 2891 8.777413 TGAAAGTAACTCAAAAGATCATCACAG 58.223 33.333 0.00 0.00 0.00 3.66
2870 2912 7.821595 ACATGCATACAATTTCACATGAAAG 57.178 32.000 12.30 3.25 45.87 2.62
2908 2950 5.991606 GGCAGATGCACATAAGATACAGTAA 59.008 40.000 7.19 0.00 44.36 2.24
3040 3082 4.083110 CCTCTGAAACAAAATGAGCGTCAT 60.083 41.667 0.00 0.00 39.09 3.06
3070 3112 8.028354 AGCGAACAAAACATATGATCATTTGAA 58.972 29.630 26.67 5.81 35.52 2.69
3112 3154 2.361992 CATGAGCAGGGGCAAGCA 60.362 61.111 0.00 0.00 44.61 3.91
3216 3259 6.015350 ACAGAGACGAAATTAAACTCCTCAGA 60.015 38.462 0.00 0.00 0.00 3.27
3247 3290 7.595819 AATGGAAATCTGTTCTGGTTTAACA 57.404 32.000 0.00 0.00 35.61 2.41
3248 3291 7.384932 CCAAATGGAAATCTGTTCTGGTTTAAC 59.615 37.037 0.00 0.00 37.39 2.01
3249 3292 7.288852 TCCAAATGGAAATCTGTTCTGGTTTAA 59.711 33.333 0.00 0.00 42.18 1.52
3250 3293 6.780031 TCCAAATGGAAATCTGTTCTGGTTTA 59.220 34.615 0.00 0.00 42.18 2.01
3251 3294 5.602145 TCCAAATGGAAATCTGTTCTGGTTT 59.398 36.000 0.00 0.00 42.18 3.27
3354 3439 3.533606 AGCTGTAGTATCACCAAGCTG 57.466 47.619 0.00 0.00 0.00 4.24
3393 3479 0.886563 ATGCAGAAAGCTTGCCTGAC 59.113 50.000 24.87 18.04 45.94 3.51
3417 3503 2.084546 GTCAGTGTACCAAATGGAGCC 58.915 52.381 6.42 0.00 38.94 4.70
3462 3548 7.582909 AAGTGCCCAAATATATATCCCTACA 57.417 36.000 0.00 0.00 0.00 2.74
3463 3549 8.739972 CAAAAGTGCCCAAATATATATCCCTAC 58.260 37.037 0.00 0.00 0.00 3.18
3499 3585 3.375699 TCTCCAATCTACAGTCCCTTCC 58.624 50.000 0.00 0.00 0.00 3.46
3533 3619 2.580470 GATGCTGCCGTCGATGTCG 61.580 63.158 3.52 0.00 41.45 4.35
3540 3626 0.110056 CACAAACAGATGCTGCCGTC 60.110 55.000 0.00 0.00 34.37 4.79
3542 3628 1.443194 GCACAAACAGATGCTGCCG 60.443 57.895 0.00 0.00 38.84 5.69


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

AutoCloner maintained by Alex Coulton.