Multiple sequence alignment - TraesCS3A01G059100

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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 TraesCS3A01G059100 chr3A 100.000 3818 0 0 1 3818 35756074 35752257 0.000000e+00 7051.0
1 TraesCS3A01G059100 chr3A 89.683 1609 118 22 905 2493 35768445 35770025 0.000000e+00 2008.0
2 TraesCS3A01G059100 chr3A 94.496 963 44 5 2858 3818 35770367 35771322 0.000000e+00 1476.0
3 TraesCS3A01G059100 chr3A 77.296 392 71 17 15 396 686840990 686840607 8.310000e-52 215.0
4 TraesCS3A01G059100 chr3A 95.833 96 4 0 541 636 35768262 35768357 5.110000e-34 156.0
5 TraesCS3A01G059100 chr3B 83.469 3690 363 105 1 3551 43311847 43315428 0.000000e+00 3206.0
6 TraesCS3A01G059100 chr3B 87.607 1759 148 33 775 2493 43193037 43191309 0.000000e+00 1977.0
7 TraesCS3A01G059100 chr3B 86.784 1483 147 28 1047 2489 74176679 74178152 0.000000e+00 1607.0
8 TraesCS3A01G059100 chr3B 84.615 949 80 25 2812 3733 74178475 74179384 0.000000e+00 883.0
9 TraesCS3A01G059100 chr3B 88.383 637 61 10 1036 1671 74173600 74174224 0.000000e+00 754.0
10 TraesCS3A01G059100 chr3B 82.786 639 75 20 2811 3420 43190854 43190222 4.340000e-149 538.0
11 TraesCS3A01G059100 chr3B 93.238 281 18 1 2492 2771 74178193 74178473 2.740000e-111 412.0
12 TraesCS3A01G059100 chr3B 86.216 370 46 2 2495 2860 43191268 43190900 2.760000e-106 396.0
13 TraesCS3A01G059100 chr3B 82.500 360 20 13 654 980 74176200 74176549 3.760000e-70 276.0
14 TraesCS3A01G059100 chr3B 89.855 138 10 1 525 658 43193270 43193133 1.410000e-39 174.0
15 TraesCS3A01G059100 chr3B 80.620 129 12 8 814 942 74173403 74173518 1.890000e-13 87.9
16 TraesCS3A01G059100 chr3B 100.000 29 0 0 534 562 74176160 74176188 2.000000e-03 54.7
17 TraesCS3A01G059100 chr3D 84.044 2814 291 73 814 3551 26073126 26075857 0.000000e+00 2564.0
18 TraesCS3A01G059100 chr3D 93.926 1350 61 10 2484 3818 25984350 25983007 0.000000e+00 2019.0
19 TraesCS3A01G059100 chr3D 86.106 1749 171 39 775 2489 26019912 26018202 0.000000e+00 1818.0
20 TraesCS3A01G059100 chr3D 89.428 1277 111 12 1236 2489 25987839 25986564 0.000000e+00 1589.0
21 TraesCS3A01G059100 chr3D 86.287 1247 94 36 2495 3733 26018157 26016980 0.000000e+00 1284.0
22 TraesCS3A01G059100 chr3D 86.047 1247 97 32 2495 3733 25986519 25985342 0.000000e+00 1267.0
23 TraesCS3A01G059100 chr3D 86.010 579 62 8 1930 2489 25984954 25984376 1.520000e-168 603.0
24 TraesCS3A01G059100 chr3D 77.232 448 75 20 1 428 90777078 90777518 1.770000e-58 237.0
25 TraesCS3A01G059100 chr3D 91.379 116 6 1 525 636 26020143 26020028 5.110000e-34 156.0
26 TraesCS3A01G059100 chr3D 88.710 124 14 0 856 979 25988180 25988057 6.610000e-33 152.0
27 TraesCS3A01G059100 chr3D 100.000 34 0 0 725 758 25988299 25988266 3.180000e-06 63.9
28 TraesCS3A01G059100 chrUn 86.287 1247 94 36 2495 3733 321665205 321664028 0.000000e+00 1284.0
29 TraesCS3A01G059100 chrUn 89.637 193 16 2 2301 2489 321665442 321665250 3.810000e-60 243.0
30 TraesCS3A01G059100 chr2D 77.568 1217 217 40 1255 2431 17955199 17956399 0.000000e+00 684.0
31 TraesCS3A01G059100 chr2D 80.982 326 49 12 28 345 488062434 488062114 2.950000e-61 246.0
32 TraesCS3A01G059100 chr6D 76.145 830 146 36 1641 2431 395094826 395094010 4.630000e-104 388.0
33 TraesCS3A01G059100 chr2B 78.837 430 72 15 1 414 572551974 572551548 4.860000e-69 272.0
34 TraesCS3A01G059100 chr5A 78.605 430 60 23 1 404 123575698 123576121 4.890000e-64 255.0
35 TraesCS3A01G059100 chr4A 80.696 316 42 17 23 327 520202304 520202611 1.070000e-55 228.0
36 TraesCS3A01G059100 chr4A 86.022 93 6 6 355 445 501477994 501478081 4.060000e-15 93.5
37 TraesCS3A01G059100 chr4A 83.516 91 12 3 376 464 569852571 569852482 8.790000e-12 82.4
38 TraesCS3A01G059100 chr7A 80.192 313 52 8 23 327 513226147 513225837 3.840000e-55 226.0
39 TraesCS3A01G059100 chr2A 77.660 376 65 14 15 375 632602933 632602562 1.070000e-50 211.0
40 TraesCS3A01G059100 chr1B 79.608 255 33 15 98 338 74709314 74709065 8.490000e-37 165.0
41 TraesCS3A01G059100 chr1B 80.508 118 15 7 354 463 534236210 534236327 2.440000e-12 84.2
42 TraesCS3A01G059100 chr5D 83.696 92 12 3 354 442 544289864 544289955 2.440000e-12 84.2
43 TraesCS3A01G059100 chr4D 82.828 99 8 8 354 445 100834433 100834529 3.160000e-11 80.5


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 TraesCS3A01G059100 chr3A 35752257 35756074 3817 True 7051.000000 7051 100.000000 1 3818 1 chr3A.!!$R1 3817
1 TraesCS3A01G059100 chr3A 35768262 35771322 3060 False 1213.333333 2008 93.337333 541 3818 3 chr3A.!!$F1 3277
2 TraesCS3A01G059100 chr3B 43311847 43315428 3581 False 3206.000000 3206 83.469000 1 3551 1 chr3B.!!$F1 3550
3 TraesCS3A01G059100 chr3B 43190222 43193270 3048 True 771.250000 1977 86.616000 525 3420 4 chr3B.!!$R1 2895
4 TraesCS3A01G059100 chr3B 74173403 74179384 5981 False 582.085714 1607 88.020000 534 3733 7 chr3B.!!$F2 3199
5 TraesCS3A01G059100 chr3D 26073126 26075857 2731 False 2564.000000 2564 84.044000 814 3551 1 chr3D.!!$F1 2737
6 TraesCS3A01G059100 chr3D 26016980 26020143 3163 True 1086.000000 1818 87.924000 525 3733 3 chr3D.!!$R2 3208
7 TraesCS3A01G059100 chr3D 25983007 25988299 5292 True 948.983333 2019 90.686833 725 3818 6 chr3D.!!$R1 3093
8 TraesCS3A01G059100 chrUn 321664028 321665442 1414 True 763.500000 1284 87.962000 2301 3733 2 chrUn.!!$R1 1432
9 TraesCS3A01G059100 chr2D 17955199 17956399 1200 False 684.000000 684 77.568000 1255 2431 1 chr2D.!!$F1 1176
10 TraesCS3A01G059100 chr6D 395094010 395094826 816 True 388.000000 388 76.145000 1641 2431 1 chr6D.!!$R1 790

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
466 492 0.108756 GAGGTTGTAGTCTCCCGTGC 60.109 60.0 0.00 0.00 0.00 5.34 F
468 494 0.389948 GGTTGTAGTCTCCCGTGCTG 60.390 60.0 0.00 0.00 0.00 4.41 F
764 3077 0.526662 TTCTCTTCTTCGTCCTCGGC 59.473 55.0 0.00 0.00 37.69 5.54 F
1959 4473 0.378257 CAATGGGAGAAATCCACGCG 59.622 55.0 3.53 3.53 37.08 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 4400 0.106708 AGTGCAGTCCTCGAAAAGCA 59.893 50.0 0.00 0.0 0.00 3.91 R
1943 4457 0.672401 GAACGCGTGGATTTCTCCCA 60.672 55.0 14.98 0.0 41.29 4.37 R
2576 5148 0.399833 TGATTACCACACCAGCAGCA 59.600 50.0 0.00 0.0 0.00 4.41 R
3050 5733 1.095228 ATATTTGCCACGACCTGCCG 61.095 55.0 0.00 0.0 0.00 5.69 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
28 30 8.138712 ACATGGTCAACGTTTTATAAACACATT 58.861 29.630 0.00 0.00 0.00 2.71
29 31 8.973378 CATGGTCAACGTTTTATAAACACATTT 58.027 29.630 0.00 0.00 0.00 2.32
31 33 9.448294 TGGTCAACGTTTTATAAACACATTTAC 57.552 29.630 0.00 0.00 33.09 2.01
65 67 8.845413 ATGCTTTTTAATATTTTCCAAGTGCA 57.155 26.923 0.00 0.00 0.00 4.57
67 69 9.282569 TGCTTTTTAATATTTTCCAAGTGCAAT 57.717 25.926 0.00 0.00 0.00 3.56
81 83 7.026562 TCCAAGTGCAATATTAACATTTGTCG 58.973 34.615 17.32 8.87 31.34 4.35
372 378 9.003658 TCAAAAGTTTTTCAAATGCTTGGTTAA 57.996 25.926 0.00 0.00 33.01 2.01
373 379 9.060547 CAAAAGTTTTTCAAATGCTTGGTTAAC 57.939 29.630 0.00 0.00 33.01 2.01
374 380 7.913674 AAGTTTTTCAAATGCTTGGTTAACA 57.086 28.000 8.10 0.00 33.01 2.41
461 487 4.368565 AAAAAGGGAGGTTGTAGTCTCC 57.631 45.455 0.00 0.00 46.57 3.71
464 490 2.973148 GGAGGTTGTAGTCTCCCGT 58.027 57.895 0.00 0.00 42.72 5.28
465 491 0.531200 GGAGGTTGTAGTCTCCCGTG 59.469 60.000 0.00 0.00 42.72 4.94
466 492 0.108756 GAGGTTGTAGTCTCCCGTGC 60.109 60.000 0.00 0.00 0.00 5.34
468 494 0.389948 GGTTGTAGTCTCCCGTGCTG 60.390 60.000 0.00 0.00 0.00 4.41
470 496 2.167398 TTGTAGTCTCCCGTGCTGCC 62.167 60.000 0.00 0.00 0.00 4.85
471 497 3.075005 TAGTCTCCCGTGCTGCCC 61.075 66.667 0.00 0.00 0.00 5.36
472 498 3.897681 TAGTCTCCCGTGCTGCCCA 62.898 63.158 0.00 0.00 0.00 5.36
473 499 4.101448 GTCTCCCGTGCTGCCCAT 62.101 66.667 0.00 0.00 0.00 4.00
474 500 3.785859 TCTCCCGTGCTGCCCATC 61.786 66.667 0.00 0.00 0.00 3.51
475 501 3.790437 CTCCCGTGCTGCCCATCT 61.790 66.667 0.00 0.00 0.00 2.90
476 502 3.746949 CTCCCGTGCTGCCCATCTC 62.747 68.421 0.00 0.00 0.00 2.75
478 504 3.790437 CCGTGCTGCCCATCTCCT 61.790 66.667 0.00 0.00 0.00 3.69
480 506 2.191641 GTGCTGCCCATCTCCTCC 59.808 66.667 0.00 0.00 0.00 4.30
482 508 3.092511 GCTGCCCATCTCCTCCCA 61.093 66.667 0.00 0.00 0.00 4.37
483 509 2.459086 GCTGCCCATCTCCTCCCAT 61.459 63.158 0.00 0.00 0.00 4.00
484 510 1.130054 GCTGCCCATCTCCTCCCATA 61.130 60.000 0.00 0.00 0.00 2.74
485 511 0.982704 CTGCCCATCTCCTCCCATAG 59.017 60.000 0.00 0.00 0.00 2.23
486 512 0.567687 TGCCCATCTCCTCCCATAGA 59.432 55.000 0.00 0.00 0.00 1.98
487 513 1.274712 GCCCATCTCCTCCCATAGAG 58.725 60.000 0.00 0.00 42.83 2.43
495 521 4.533124 TCCCATAGAGGCGCCCGA 62.533 66.667 26.15 11.73 35.39 5.14
496 522 3.546543 CCCATAGAGGCGCCCGAA 61.547 66.667 26.15 9.05 35.39 4.30
497 523 2.029666 CCATAGAGGCGCCCGAAG 59.970 66.667 26.15 9.82 0.00 3.79
498 524 2.498941 CCATAGAGGCGCCCGAAGA 61.499 63.158 26.15 4.44 0.00 2.87
500 526 2.203771 ATAGAGGCGCCCGAAGAGG 61.204 63.158 26.15 0.00 40.63 3.69
509 535 2.669240 CCGAAGAGGGGGTTGGAC 59.331 66.667 0.00 0.00 35.97 4.02
510 536 2.669240 CGAAGAGGGGGTTGGACC 59.331 66.667 0.00 0.00 37.60 4.46
511 537 2.669240 GAAGAGGGGGTTGGACCG 59.331 66.667 0.00 0.00 39.83 4.79
512 538 2.122099 AAGAGGGGGTTGGACCGT 60.122 61.111 0.00 0.00 39.83 4.83
514 540 2.033602 GAGGGGGTTGGACCGTTG 59.966 66.667 0.00 0.00 39.83 4.10
515 541 3.562732 GAGGGGGTTGGACCGTTGG 62.563 68.421 0.00 0.00 39.83 3.77
517 543 2.033602 GGGGTTGGACCGTTGGAG 59.966 66.667 0.00 0.00 39.83 3.86
518 544 2.671963 GGGTTGGACCGTTGGAGC 60.672 66.667 0.00 0.00 39.83 4.70
519 545 3.047877 GGTTGGACCGTTGGAGCG 61.048 66.667 0.00 0.00 0.00 5.03
520 546 3.723348 GTTGGACCGTTGGAGCGC 61.723 66.667 0.00 0.00 0.00 5.92
590 2844 4.812476 CCAATCGAGCGGCGGTGA 62.812 66.667 19.47 14.87 41.33 4.02
760 3073 2.234908 CCACCATTCTCTTCTTCGTCCT 59.765 50.000 0.00 0.00 0.00 3.85
761 3074 3.516615 CACCATTCTCTTCTTCGTCCTC 58.483 50.000 0.00 0.00 0.00 3.71
763 3076 2.480416 CCATTCTCTTCTTCGTCCTCGG 60.480 54.545 0.00 0.00 37.69 4.63
764 3077 0.526662 TTCTCTTCTTCGTCCTCGGC 59.473 55.000 0.00 0.00 37.69 5.54
765 3078 1.226435 CTCTTCTTCGTCCTCGGCG 60.226 63.158 0.00 0.00 37.69 6.46
767 3080 3.626680 CTTCTTCGTCCTCGGCGCA 62.627 63.158 10.83 0.00 37.69 6.09
769 3082 2.884087 TTCTTCGTCCTCGGCGCATC 62.884 60.000 10.83 0.00 37.69 3.91
770 3083 3.417275 CTTCGTCCTCGGCGCATCT 62.417 63.158 10.83 0.00 37.69 2.90
838 3178 3.689161 TGGCAATCATAGTTCGTGGAAAG 59.311 43.478 0.00 0.00 0.00 2.62
839 3179 3.487544 GGCAATCATAGTTCGTGGAAAGC 60.488 47.826 0.00 0.00 0.00 3.51
840 3180 3.126858 GCAATCATAGTTCGTGGAAAGCA 59.873 43.478 0.00 0.00 0.00 3.91
841 3181 4.379394 GCAATCATAGTTCGTGGAAAGCAA 60.379 41.667 0.00 0.00 0.00 3.91
883 3224 3.119495 CGGAATTCCTTCACCAATCAACC 60.119 47.826 22.05 0.00 32.70 3.77
885 3226 1.904287 TTCCTTCACCAATCAACCGG 58.096 50.000 0.00 0.00 0.00 5.28
954 3301 3.827898 CTCGGAGTCGGGGTGAGC 61.828 72.222 0.00 0.00 36.95 4.26
980 3327 3.065786 CGGCCGGCGATCTATAAGTATAA 59.934 47.826 22.54 0.00 0.00 0.98
983 3330 4.595116 CCGGCGATCTATAAGTATAACCG 58.405 47.826 9.30 0.00 36.74 4.44
989 3336 5.067023 CGATCTATAAGTATAACCGGGACCC 59.933 48.000 6.32 0.00 0.00 4.46
990 3337 4.677182 TCTATAAGTATAACCGGGACCCC 58.323 47.826 6.32 0.00 0.00 4.95
1012 3359 4.435970 TGCCCTCGGTCCGCTCTA 62.436 66.667 6.34 0.00 0.00 2.43
1014 3361 2.806237 CCCTCGGTCCGCTCTAAC 59.194 66.667 6.34 0.00 0.00 2.34
1024 3371 1.277842 TCCGCTCTAACCAAGATTGCA 59.722 47.619 0.00 0.00 32.41 4.08
1026 3373 2.684881 CCGCTCTAACCAAGATTGCAAT 59.315 45.455 12.83 12.83 32.41 3.56
1031 3378 6.393171 GCTCTAACCAAGATTGCAATTTTCT 58.607 36.000 14.33 4.11 32.41 2.52
1032 3379 6.870439 GCTCTAACCAAGATTGCAATTTTCTT 59.130 34.615 14.33 10.60 32.41 2.52
1033 3380 7.148689 GCTCTAACCAAGATTGCAATTTTCTTG 60.149 37.037 24.77 24.77 43.75 3.02
1043 3459 3.071312 TGCAATTTTCTTGCCCAACAGAT 59.929 39.130 7.42 0.00 44.32 2.90
1046 3462 5.413499 CAATTTTCTTGCCCAACAGATAGG 58.587 41.667 0.00 0.00 0.00 2.57
1073 3544 3.204526 CTCTGCTTTAAGCCATGGAGAG 58.795 50.000 18.40 14.35 41.51 3.20
1085 3559 2.632028 CCATGGAGAGCTGTAGCATAGT 59.368 50.000 5.56 0.00 45.16 2.12
1086 3560 3.829026 CCATGGAGAGCTGTAGCATAGTA 59.171 47.826 5.56 0.00 45.16 1.82
1087 3561 4.082300 CCATGGAGAGCTGTAGCATAGTAG 60.082 50.000 5.56 0.00 45.16 2.57
1098 3572 6.286240 TGTAGCATAGTAGCCAGGATAATG 57.714 41.667 0.00 0.00 34.23 1.90
1099 3573 4.833478 AGCATAGTAGCCAGGATAATGG 57.167 45.455 0.00 0.00 43.72 3.16
1109 3583 2.895404 CCAGGATAATGGGATTGCAAGG 59.105 50.000 4.94 0.00 36.64 3.61
1153 3627 6.909550 AGTTGTGTTCTCTAGTCTTCAGAT 57.090 37.500 0.00 0.00 0.00 2.90
1154 3628 6.919721 AGTTGTGTTCTCTAGTCTTCAGATC 58.080 40.000 0.00 0.00 0.00 2.75
1164 3638 2.026449 AGTCTTCAGATCTTTGCCCAGG 60.026 50.000 0.00 0.00 0.00 4.45
1165 3639 1.101331 CTTCAGATCTTTGCCCAGGC 58.899 55.000 0.38 0.38 42.35 4.85
1166 3640 0.700564 TTCAGATCTTTGCCCAGGCT 59.299 50.000 10.58 0.00 42.51 4.58
1185 3668 3.113514 GCTGCTAGGCTTCCCTCCC 62.114 68.421 0.00 0.00 41.75 4.30
1186 3669 1.690633 CTGCTAGGCTTCCCTCCCA 60.691 63.158 0.00 0.00 41.75 4.37
1187 3670 1.690633 TGCTAGGCTTCCCTCCCAG 60.691 63.158 0.00 0.00 41.75 4.45
1188 3671 3.113514 GCTAGGCTTCCCTCCCAGC 62.114 68.421 0.00 0.00 41.75 4.85
1189 3672 1.383803 CTAGGCTTCCCTCCCAGCT 60.384 63.158 0.00 0.00 41.75 4.24
1190 3673 1.383248 TAGGCTTCCCTCCCAGCTC 60.383 63.158 0.00 0.00 41.75 4.09
1191 3674 2.181523 TAGGCTTCCCTCCCAGCTCA 62.182 60.000 0.00 0.00 41.75 4.26
1192 3675 2.606587 GGCTTCCCTCCCAGCTCAA 61.607 63.158 0.00 0.00 36.20 3.02
1196 3679 0.914644 TTCCCTCCCAGCTCAATCAG 59.085 55.000 0.00 0.00 0.00 2.90
1205 3688 4.021916 CCCAGCTCAATCAGGAAATTCTT 58.978 43.478 0.00 0.00 0.00 2.52
1212 3695 6.183360 GCTCAATCAGGAAATTCTTCAGAGAC 60.183 42.308 0.00 0.00 32.75 3.36
1213 3696 6.176183 TCAATCAGGAAATTCTTCAGAGACC 58.824 40.000 0.00 0.00 32.75 3.85
1317 3821 1.969064 CGCTCTCGAGATCCCCGAT 60.969 63.158 17.03 0.00 38.10 4.18
1416 3920 2.281761 CAGACGCCTTGCCTGGTT 60.282 61.111 0.00 0.00 0.00 3.67
1444 3948 6.210984 CACCTCTGAATCTGATCCTGATGATA 59.789 42.308 0.00 0.00 32.41 2.15
1476 3980 2.044848 AGCCTCGCCGAGAAGAGA 60.045 61.111 17.19 0.00 36.65 3.10
1624 4128 1.558756 AGATTGCTCTCCCTTCAGTGG 59.441 52.381 0.00 0.00 0.00 4.00
1626 4130 1.130054 TTGCTCTCCCTTCAGTGGCT 61.130 55.000 0.00 0.00 0.00 4.75
1639 4143 2.025981 TCAGTGGCTACCATTGAGCATT 60.026 45.455 7.65 0.00 43.59 3.56
1691 4195 5.354767 TGTCTGCAAGTATGAGATGTCATC 58.645 41.667 8.90 4.52 42.80 2.92
1702 4206 1.002366 GATGTCATCGCACACTGGAC 58.998 55.000 0.00 0.00 0.00 4.02
1882 4393 2.014010 TAAGTGGACCTGGTTACCGT 57.986 50.000 0.00 0.00 0.00 4.83
1889 4400 2.027469 GGACCTGGTTACCGTCTCATTT 60.027 50.000 0.00 0.00 0.00 2.32
1890 4401 3.000727 GACCTGGTTACCGTCTCATTTG 58.999 50.000 0.00 0.00 0.00 2.32
1895 4406 3.886505 TGGTTACCGTCTCATTTGCTTTT 59.113 39.130 0.00 0.00 0.00 2.27
1935 4446 4.330250 AGGATGGCATATTGTATGCAGTC 58.670 43.478 19.92 16.14 46.21 3.51
1943 4457 7.231115 TGGCATATTGTATGCAGTCAATACAAT 59.769 33.333 20.57 20.57 46.75 2.71
1951 4465 4.661222 TGCAGTCAATACAATGGGAGAAA 58.339 39.130 0.00 0.00 0.00 2.52
1959 4473 0.378257 CAATGGGAGAAATCCACGCG 59.622 55.000 3.53 3.53 37.08 6.01
1989 4503 1.460497 TGGCCCTGTGGTCACTGTA 60.460 57.895 0.00 0.00 42.76 2.74
2129 4658 6.328641 TGAGTACTGGAAGACTACAGAAAC 57.671 41.667 0.00 10.02 38.09 2.78
2170 4699 5.314923 TGCTCTGTGGAATAAAATTGAGC 57.685 39.130 0.00 0.00 43.90 4.26
2174 4703 6.969473 GCTCTGTGGAATAAAATTGAGCTAAC 59.031 38.462 0.00 0.00 41.42 2.34
2185 4714 5.473066 AATTGAGCTAACCAATTGCTTGT 57.527 34.783 10.22 0.00 41.20 3.16
2214 4743 7.826690 ACCATGTGTTATTTCTTGGTCATAAC 58.173 34.615 0.00 0.00 37.48 1.89
2241 4770 2.102757 ACTATGCCTCAGTGCTGATGAG 59.897 50.000 8.34 6.46 43.15 2.90
2299 4828 9.839817 TTACCGATGATAATTTTCTATGGACAA 57.160 29.630 7.47 0.00 0.00 3.18
2304 4833 7.288810 TGATAATTTTCTATGGACAATGGGC 57.711 36.000 0.00 0.00 0.00 5.36
2351 4880 8.930846 ATGGGAATTCTTAACTTGGATGATAG 57.069 34.615 5.23 0.00 0.00 2.08
2423 4955 7.939039 TCCAATGTGGATTATTCCTGATCTTAC 59.061 37.037 5.31 0.00 42.67 2.34
2468 5001 2.880890 GAGCCAACAACTGTGAAGTGAT 59.119 45.455 0.00 0.00 0.00 3.06
2472 5005 3.251729 CCAACAACTGTGAAGTGATCTGG 59.748 47.826 0.00 0.00 0.00 3.86
2513 5085 0.470833 AGAGGTCCTGTCTGTGCTGT 60.471 55.000 0.00 0.00 0.00 4.40
2527 5099 2.697751 TGTGCTGTAAAAATGGCCTGTT 59.302 40.909 3.32 0.00 0.00 3.16
2576 5148 6.072064 CCTTTTCTGCTCAGTCTTTTGATGAT 60.072 38.462 0.00 0.00 0.00 2.45
2624 5197 9.884465 GATAATATATGCAGGTGTTTTCAGAAC 57.116 33.333 0.00 0.00 0.00 3.01
2724 5297 9.463443 GTTTGCTCAAATACTGTACAGATTTTT 57.537 29.630 29.30 19.56 32.36 1.94
2846 5519 4.093998 AGAGCTCTTTGTTGTATCATTGCG 59.906 41.667 11.45 0.00 0.00 4.85
2941 5621 9.740239 TGTAGTTTTAGAACCATAAGCGTATAG 57.260 33.333 0.00 0.00 36.39 1.31
2942 5622 7.710766 AGTTTTAGAACCATAAGCGTATAGC 57.289 36.000 0.00 0.00 40.52 2.97
2943 5623 7.270047 AGTTTTAGAACCATAAGCGTATAGCA 58.730 34.615 0.00 0.00 41.79 3.49
2944 5624 7.931948 AGTTTTAGAACCATAAGCGTATAGCAT 59.068 33.333 0.00 0.00 41.79 3.79
3050 5733 4.242602 GGTAGCCACCAATCAGCC 57.757 61.111 0.00 0.00 45.04 4.85
3133 8032 2.837291 GCCAAACCTGCCACACCA 60.837 61.111 0.00 0.00 0.00 4.17
3146 8045 1.873591 CCACACCAAACAGCTACTGAC 59.126 52.381 0.78 0.00 35.18 3.51
3233 8157 5.187186 GGAGAGATGTGTAGGGAGTAAAACA 59.813 44.000 0.00 0.00 0.00 2.83
3259 8184 6.233434 TGCTAGTTCAATTTCTCACATCAGT 58.767 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.028926 TGTGTTTATAAAACGTTGACCATGT 57.971 32.000 0.00 0.00 0.00 3.21
39 41 9.935241 TGCACTTGGAAAATATTAAAAAGCATA 57.065 25.926 0.00 0.00 0.00 3.14
40 42 8.845413 TGCACTTGGAAAATATTAAAAAGCAT 57.155 26.923 0.00 0.00 0.00 3.79
41 43 8.668510 TTGCACTTGGAAAATATTAAAAAGCA 57.331 26.923 0.00 0.00 0.00 3.91
61 63 9.497030 TGTATTCGACAAATGTTAATATTGCAC 57.503 29.630 0.00 0.00 34.15 4.57
343 349 7.821846 ACCAAGCATTTGAAAAACTTTTGAGTA 59.178 29.630 0.00 0.00 36.36 2.59
348 354 8.787852 TGTTAACCAAGCATTTGAAAAACTTTT 58.212 25.926 2.48 0.00 36.36 2.27
440 466 4.368565 GGAGACTACAACCTCCCTTTTT 57.631 45.455 0.00 0.00 42.35 1.94
446 472 0.531200 CACGGGAGACTACAACCTCC 59.469 60.000 0.00 0.00 46.29 4.30
447 473 0.108756 GCACGGGAGACTACAACCTC 60.109 60.000 0.00 0.00 0.00 3.85
448 474 0.542232 AGCACGGGAGACTACAACCT 60.542 55.000 0.00 0.00 0.00 3.50
450 476 1.014564 GCAGCACGGGAGACTACAAC 61.015 60.000 0.00 0.00 0.00 3.32
451 477 1.292223 GCAGCACGGGAGACTACAA 59.708 57.895 0.00 0.00 0.00 2.41
452 478 2.646175 GGCAGCACGGGAGACTACA 61.646 63.158 0.00 0.00 0.00 2.74
454 480 3.075005 GGGCAGCACGGGAGACTA 61.075 66.667 0.00 0.00 0.00 2.59
457 483 3.785859 GATGGGCAGCACGGGAGA 61.786 66.667 0.00 0.00 0.00 3.71
461 487 3.746949 GAGGAGATGGGCAGCACGG 62.747 68.421 0.00 0.00 0.00 4.94
462 488 2.202987 GAGGAGATGGGCAGCACG 60.203 66.667 0.00 0.00 0.00 5.34
463 489 2.191641 GGAGGAGATGGGCAGCAC 59.808 66.667 0.00 0.00 0.00 4.40
464 490 3.092511 GGGAGGAGATGGGCAGCA 61.093 66.667 0.00 0.00 0.00 4.41
465 491 1.130054 TATGGGAGGAGATGGGCAGC 61.130 60.000 0.00 0.00 0.00 5.25
466 492 0.982704 CTATGGGAGGAGATGGGCAG 59.017 60.000 0.00 0.00 0.00 4.85
468 494 1.274712 CTCTATGGGAGGAGATGGGC 58.725 60.000 0.00 0.00 38.35 5.36
478 504 4.533124 TCGGGCGCCTCTATGGGA 62.533 66.667 28.56 9.46 36.00 4.37
480 506 2.029666 CTTCGGGCGCCTCTATGG 59.970 66.667 28.56 9.00 39.35 2.74
482 508 2.203771 CCTCTTCGGGCGCCTCTAT 61.204 63.158 28.56 0.00 0.00 1.98
483 509 2.833582 CCTCTTCGGGCGCCTCTA 60.834 66.667 28.56 9.29 0.00 2.43
492 518 2.669240 GTCCAACCCCCTCTTCGG 59.331 66.667 0.00 0.00 0.00 4.30
493 519 2.669240 GGTCCAACCCCCTCTTCG 59.331 66.667 0.00 0.00 30.04 3.79
495 521 1.772979 AACGGTCCAACCCCCTCTT 60.773 57.895 0.00 0.00 33.75 2.85
496 522 2.122099 AACGGTCCAACCCCCTCT 60.122 61.111 0.00 0.00 33.75 3.69
497 523 2.033602 CAACGGTCCAACCCCCTC 59.966 66.667 0.00 0.00 33.75 4.30
498 524 3.576259 CCAACGGTCCAACCCCCT 61.576 66.667 0.00 0.00 33.75 4.79
500 526 2.033602 CTCCAACGGTCCAACCCC 59.966 66.667 0.00 0.00 33.75 4.95
501 527 2.671963 GCTCCAACGGTCCAACCC 60.672 66.667 0.00 0.00 33.75 4.11
502 528 3.047877 CGCTCCAACGGTCCAACC 61.048 66.667 0.00 0.00 34.05 3.77
503 529 3.723348 GCGCTCCAACGGTCCAAC 61.723 66.667 0.00 0.00 0.00 3.77
590 2844 2.678934 TGCTCGCCGGAGTAACCT 60.679 61.111 5.05 0.00 42.53 3.50
666 2920 0.244994 CCCGCCTCTCGATTGGATAG 59.755 60.000 7.88 0.00 41.67 2.08
812 3152 0.583438 CGAACTATGATTGCCAGCGG 59.417 55.000 0.00 0.00 0.00 5.52
819 3159 4.944962 TGCTTTCCACGAACTATGATTG 57.055 40.909 0.00 0.00 0.00 2.67
825 3165 5.529430 TCTGATTTTTGCTTTCCACGAACTA 59.471 36.000 0.00 0.00 0.00 2.24
838 3178 1.512694 CCCCCGCTCTGATTTTTGC 59.487 57.895 0.00 0.00 0.00 3.68
883 3224 4.700213 ACACTGAAATTATTTGGACTCCCG 59.300 41.667 0.00 0.00 34.29 5.14
885 3226 6.208599 TGGAACACTGAAATTATTTGGACTCC 59.791 38.462 0.00 0.00 0.00 3.85
996 3343 3.145551 TTAGAGCGGACCGAGGGC 61.146 66.667 20.50 0.00 0.00 5.19
997 3344 2.783288 GGTTAGAGCGGACCGAGGG 61.783 68.421 20.50 0.00 0.00 4.30
998 3345 1.601419 TTGGTTAGAGCGGACCGAGG 61.601 60.000 20.50 0.00 38.81 4.63
999 3346 0.179134 CTTGGTTAGAGCGGACCGAG 60.179 60.000 20.50 0.00 40.18 4.63
1000 3347 0.609957 TCTTGGTTAGAGCGGACCGA 60.610 55.000 20.50 0.00 38.81 4.69
1001 3348 0.460311 ATCTTGGTTAGAGCGGACCG 59.540 55.000 10.29 10.29 38.81 4.79
1002 3349 2.280628 CAATCTTGGTTAGAGCGGACC 58.719 52.381 0.00 0.00 36.02 4.46
1003 3350 1.666189 GCAATCTTGGTTAGAGCGGAC 59.334 52.381 0.00 0.00 36.02 4.79
1004 3351 1.277842 TGCAATCTTGGTTAGAGCGGA 59.722 47.619 0.00 0.00 36.02 5.54
1005 3352 1.737838 TGCAATCTTGGTTAGAGCGG 58.262 50.000 0.00 0.00 36.02 5.52
1006 3353 4.361451 AATTGCAATCTTGGTTAGAGCG 57.639 40.909 13.38 0.00 36.02 5.03
1007 3354 6.393171 AGAAAATTGCAATCTTGGTTAGAGC 58.607 36.000 13.38 0.00 36.02 4.09
1012 3359 4.516321 GGCAAGAAAATTGCAATCTTGGTT 59.484 37.500 29.17 13.41 46.38 3.67
1014 3361 3.437741 GGGCAAGAAAATTGCAATCTTGG 59.562 43.478 29.17 17.76 46.38 3.61
1024 3371 4.081476 GCCTATCTGTTGGGCAAGAAAATT 60.081 41.667 8.09 0.00 44.69 1.82
1026 3373 2.825532 GCCTATCTGTTGGGCAAGAAAA 59.174 45.455 8.09 0.00 44.69 2.29
1033 3380 0.457443 GCAAAGCCTATCTGTTGGGC 59.543 55.000 5.06 5.06 45.57 5.36
1043 3459 2.749621 GCTTAAAGCAGAGCAAAGCCTA 59.250 45.455 10.63 0.00 41.89 3.93
1046 3462 1.270550 TGGCTTAAAGCAGAGCAAAGC 59.729 47.619 12.37 12.37 44.75 3.51
1047 3463 3.508762 CATGGCTTAAAGCAGAGCAAAG 58.491 45.455 0.00 0.00 44.75 2.77
1048 3464 2.231964 CCATGGCTTAAAGCAGAGCAAA 59.768 45.455 0.00 0.00 44.75 3.68
1049 3465 1.820519 CCATGGCTTAAAGCAGAGCAA 59.179 47.619 0.00 0.00 44.75 3.91
1050 3466 1.004628 TCCATGGCTTAAAGCAGAGCA 59.995 47.619 6.96 0.00 44.75 4.26
1073 3544 1.964223 TCCTGGCTACTATGCTACAGC 59.036 52.381 0.00 0.00 42.50 4.40
1085 3559 2.715880 TGCAATCCCATTATCCTGGCTA 59.284 45.455 0.00 0.00 34.77 3.93
1086 3560 1.500303 TGCAATCCCATTATCCTGGCT 59.500 47.619 0.00 0.00 34.77 4.75
1087 3561 1.999648 TGCAATCCCATTATCCTGGC 58.000 50.000 0.00 0.00 34.77 4.85
1098 3572 0.474184 TAGCTAGGCCTTGCAATCCC 59.526 55.000 35.33 10.17 33.84 3.85
1099 3573 2.157738 CATAGCTAGGCCTTGCAATCC 58.842 52.381 35.33 10.87 33.84 3.01
1109 3583 0.319641 GTGCCGGTACATAGCTAGGC 60.320 60.000 18.66 8.85 44.38 3.93
1137 3611 5.105146 GGGCAAAGATCTGAAGACTAGAGAA 60.105 44.000 0.00 0.00 0.00 2.87
1153 3627 2.282674 CAGCAGCCTGGGCAAAGA 60.283 61.111 14.39 0.00 44.88 2.52
1154 3628 4.065281 GCAGCAGCCTGGGCAAAG 62.065 66.667 14.39 4.57 44.88 2.77
1164 3638 2.515757 GGGAAGCCTAGCAGCAGC 60.516 66.667 0.00 0.00 42.56 5.25
1165 3639 1.145819 GAGGGAAGCCTAGCAGCAG 59.854 63.158 0.00 0.00 34.23 4.24
1166 3640 2.370445 GGAGGGAAGCCTAGCAGCA 61.370 63.158 0.00 0.00 34.23 4.41
1185 3668 5.646793 TCTGAAGAATTTCCTGATTGAGCTG 59.353 40.000 0.00 0.00 32.09 4.24
1186 3669 5.813383 TCTGAAGAATTTCCTGATTGAGCT 58.187 37.500 0.00 0.00 32.09 4.09
1187 3670 5.879223 TCTCTGAAGAATTTCCTGATTGAGC 59.121 40.000 0.00 0.00 32.09 4.26
1188 3671 6.315891 GGTCTCTGAAGAATTTCCTGATTGAG 59.684 42.308 0.00 0.00 31.93 3.02
1189 3672 6.176183 GGTCTCTGAAGAATTTCCTGATTGA 58.824 40.000 0.00 0.00 31.93 2.57
1190 3673 5.942236 TGGTCTCTGAAGAATTTCCTGATTG 59.058 40.000 0.00 0.00 31.93 2.67
1191 3674 6.131972 TGGTCTCTGAAGAATTTCCTGATT 57.868 37.500 0.00 0.00 31.93 2.57
1192 3675 5.768980 TGGTCTCTGAAGAATTTCCTGAT 57.231 39.130 0.00 0.00 31.93 2.90
1196 3679 5.474876 ACATGTTGGTCTCTGAAGAATTTCC 59.525 40.000 0.00 0.00 31.93 3.13
1282 3786 2.289002 GAGCGGCAAAGATAACCATCAG 59.711 50.000 1.45 0.00 33.21 2.90
1416 3920 5.272402 TCAGGATCAGATTCAGAGGTGTAA 58.728 41.667 0.00 0.00 0.00 2.41
1444 3948 2.093447 CGAGGCTGTAGAGGGACAAAAT 60.093 50.000 0.00 0.00 0.00 1.82
1476 3980 3.679083 GCGGCAGAGTTAACTTGTAGGAT 60.679 47.826 10.02 0.00 0.00 3.24
1624 4128 3.442100 GCTTCAAATGCTCAATGGTAGC 58.558 45.455 0.00 0.00 40.50 3.58
1626 4130 2.760092 GGGCTTCAAATGCTCAATGGTA 59.240 45.455 0.00 0.00 0.00 3.25
1639 4143 4.279982 TGCTCATCAAATATGGGCTTCAA 58.720 39.130 10.89 0.00 45.35 2.69
1702 4206 1.134818 TGGATTACGGCTACTGCACAG 60.135 52.381 0.00 0.00 41.91 3.66
1882 4393 3.748048 CAGTCCTCGAAAAGCAAATGAGA 59.252 43.478 0.00 0.00 0.00 3.27
1889 4400 0.106708 AGTGCAGTCCTCGAAAAGCA 59.893 50.000 0.00 0.00 0.00 3.91
1890 4401 1.230324 AAGTGCAGTCCTCGAAAAGC 58.770 50.000 0.00 0.00 0.00 3.51
1895 4406 1.272490 CCTTGTAAGTGCAGTCCTCGA 59.728 52.381 0.00 0.00 0.00 4.04
1935 4446 4.498009 GCGTGGATTTCTCCCATTGTATTG 60.498 45.833 0.00 0.00 41.29 1.90
1943 4457 0.672401 GAACGCGTGGATTTCTCCCA 60.672 55.000 14.98 0.00 41.29 4.37
1951 4465 1.404391 ACTAAGATCGAACGCGTGGAT 59.596 47.619 21.65 21.65 38.98 3.41
1959 4473 1.207329 ACAGGGCCACTAAGATCGAAC 59.793 52.381 6.18 0.00 0.00 3.95
1989 4503 6.462628 GCTCAGGTACCCTTATAATCGTCTTT 60.463 42.308 8.74 0.00 0.00 2.52
2105 4634 6.722129 AGTTTCTGTAGTCTTCCAGTACTCAT 59.278 38.462 0.00 0.00 32.61 2.90
2129 4658 9.053840 ACAGAGCATCAATCTCACATATTTTAG 57.946 33.333 0.00 0.00 37.82 1.85
2170 4699 3.317711 TGGTCACACAAGCAATTGGTTAG 59.682 43.478 21.61 18.42 33.98 2.34
2174 4703 2.036217 ACATGGTCACACAAGCAATTGG 59.964 45.455 7.72 0.00 0.00 3.16
2185 4714 5.136828 ACCAAGAAATAACACATGGTCACA 58.863 37.500 0.00 0.00 36.47 3.58
2214 4743 2.632028 AGCACTGAGGCATAGTGATAGG 59.368 50.000 20.73 0.00 46.52 2.57
2241 4770 2.698855 TTGCCTTGAGAGCAGGATAC 57.301 50.000 0.00 0.00 42.17 2.24
2299 4828 5.649395 CACGATGATTATTCTTATGGCCCAT 59.351 40.000 0.00 0.00 0.00 4.00
2304 4833 9.049523 CCCATATCACGATGATTATTCTTATGG 57.950 37.037 5.94 9.70 38.26 2.74
2351 4880 1.073897 ACAAGTTCCTCCCTGCTGC 59.926 57.895 0.00 0.00 0.00 5.25
2423 4955 1.033746 AGCCCATCGCCACATCTTTG 61.034 55.000 0.00 0.00 38.78 2.77
2479 5012 5.014858 AGGACCTCTGTCGAGTTAATTGTA 58.985 41.667 0.00 0.00 42.73 2.41
2513 5085 3.181423 ACTCCCTCAACAGGCCATTTTTA 60.181 43.478 5.01 0.00 38.72 1.52
2527 5099 1.351076 TGATGTTGAGCACTCCCTCA 58.649 50.000 0.00 0.00 39.94 3.86
2576 5148 0.399833 TGATTACCACACCAGCAGCA 59.600 50.000 0.00 0.00 0.00 4.41
2624 5197 4.063998 TGATTCCGTCTTCTCCATGATG 57.936 45.455 0.00 0.00 0.00 3.07
2767 5341 7.444183 ACACTGTTATATTGCTGTAACAACACT 59.556 33.333 0.00 0.00 38.15 3.55
2831 5504 3.563508 CTTGTGCGCAATGATACAACAA 58.436 40.909 14.00 7.96 33.65 2.83
2900 5573 4.974645 AACTACAACCAGATCCTTGTGA 57.025 40.909 10.03 0.00 32.77 3.58
2941 5621 4.390603 TGTAAATCGTGTGGTTCAGTATGC 59.609 41.667 0.00 0.00 34.76 3.14
2942 5622 6.147164 ACTTGTAAATCGTGTGGTTCAGTATG 59.853 38.462 0.00 0.00 37.54 2.39
2943 5623 6.228258 ACTTGTAAATCGTGTGGTTCAGTAT 58.772 36.000 0.00 0.00 0.00 2.12
2944 5624 5.603596 ACTTGTAAATCGTGTGGTTCAGTA 58.396 37.500 0.00 0.00 0.00 2.74
2945 5625 4.448210 ACTTGTAAATCGTGTGGTTCAGT 58.552 39.130 0.00 0.00 0.00 3.41
2946 5626 5.418310 AACTTGTAAATCGTGTGGTTCAG 57.582 39.130 0.00 0.00 0.00 3.02
2947 5627 5.821516 AAACTTGTAAATCGTGTGGTTCA 57.178 34.783 0.00 0.00 0.00 3.18
2948 5628 8.497554 TGTATAAACTTGTAAATCGTGTGGTTC 58.502 33.333 0.00 0.00 0.00 3.62
2949 5629 8.380743 TGTATAAACTTGTAAATCGTGTGGTT 57.619 30.769 0.00 0.00 0.00 3.67
2950 5630 7.360607 GCTGTATAAACTTGTAAATCGTGTGGT 60.361 37.037 0.00 0.00 0.00 4.16
3050 5733 1.095228 ATATTTGCCACGACCTGCCG 61.095 55.000 0.00 0.00 0.00 5.69
3133 8032 5.308825 ACAAGCATAAGTCAGTAGCTGTTT 58.691 37.500 0.00 0.00 35.42 2.83
3233 8157 7.392673 ACTGATGTGAGAAATTGAACTAGCATT 59.607 33.333 0.00 0.00 0.00 3.56
3259 8184 1.271934 CAAATGGGATTGTTCGCACCA 59.728 47.619 0.00 0.00 46.24 4.17
3498 8447 8.788325 TTTATCATTCCATCTCATATCTGCAG 57.212 34.615 7.63 7.63 0.00 4.41


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

AutoCloner maintained by Alex Coulton.