Multiple sequence alignment - TraesCS2D01G155100

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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 TraesCS2D01G155100 chr2D 100.000 3047 0 0 1 3047 98709704 98706658 0.000000e+00 5627.0
1 TraesCS2D01G155100 chr2D 86.247 1476 162 26 741 2191 98673873 98672414 0.000000e+00 1563.0
2 TraesCS2D01G155100 chr2D 84.956 1356 160 21 857 2191 98668434 98667102 0.000000e+00 1334.0
3 TraesCS2D01G155100 chr2D 85.908 1256 137 17 903 2135 98659736 98658498 0.000000e+00 1303.0
4 TraesCS2D01G155100 chr2D 83.848 551 36 21 2442 2965 7173354 7172830 2.750000e-130 475.0
5 TraesCS2D01G155100 chr2D 78.824 595 55 38 10 566 98674494 98673933 4.870000e-88 335.0
6 TraesCS2D01G155100 chr2D 84.000 150 16 2 16 157 98662407 98662258 1.470000e-28 137.0
7 TraesCS2D01G155100 chr2D 82.237 152 15 9 143 292 98661585 98661444 1.480000e-23 121.0
8 TraesCS2D01G155100 chr2D 87.037 108 9 4 614 718 385149889 385149784 1.920000e-22 117.0
9 TraesCS2D01G155100 chr2B 95.708 1491 60 1 836 2326 150339410 150337924 0.000000e+00 2396.0
10 TraesCS2D01G155100 chr2B 95.814 1051 40 1 836 1886 150387775 150386729 0.000000e+00 1694.0
11 TraesCS2D01G155100 chr2B 86.395 1470 165 24 741 2191 150201585 150200132 0.000000e+00 1574.0
12 TraesCS2D01G155100 chr2B 86.043 1304 140 17 903 2191 150142102 150140826 0.000000e+00 1362.0
13 TraesCS2D01G155100 chr2B 85.896 1255 144 21 903 2135 150119194 150117951 0.000000e+00 1306.0
14 TraesCS2D01G155100 chr2B 95.516 446 19 1 1882 2326 150360659 150360214 0.000000e+00 712.0
15 TraesCS2D01G155100 chr2B 91.316 380 15 9 1 380 150340129 150339768 1.260000e-138 503.0
16 TraesCS2D01G155100 chr2B 84.549 466 59 12 2447 2907 34415105 34415562 1.670000e-122 449.0
17 TraesCS2D01G155100 chr2B 91.597 238 13 3 143 380 150388685 150388455 3.790000e-84 322.0
18 TraesCS2D01G155100 chr2B 89.474 247 11 7 392 625 150339712 150339468 6.390000e-77 298.0
19 TraesCS2D01G155100 chr2B 91.919 198 7 3 392 581 150388392 150388196 5.010000e-68 268.0
20 TraesCS2D01G155100 chr2B 83.103 290 26 12 16 292 150120399 150120120 3.040000e-60 243.0
21 TraesCS2D01G155100 chr2B 97.561 123 3 0 1 123 150394139 150394017 8.560000e-51 211.0
22 TraesCS2D01G155100 chr2A 86.325 1309 147 18 903 2191 97308660 97307364 0.000000e+00 1397.0
23 TraesCS2D01G155100 chr2A 84.926 1360 160 26 741 2080 97316578 97315244 0.000000e+00 1334.0
24 TraesCS2D01G155100 chr2A 80.763 603 53 32 10 566 97550350 97549765 2.190000e-111 412.0
25 TraesCS2D01G155100 chr2A 80.265 603 55 33 10 566 97317226 97316642 2.200000e-106 396.0
26 TraesCS2D01G155100 chr2A 82.818 291 28 11 14 292 97311431 97311151 1.090000e-59 241.0
27 TraesCS2D01G155100 chr6A 83.509 570 78 15 2442 3003 24429185 24429746 4.500000e-143 518.0
28 TraesCS2D01G155100 chr6A 78.906 640 72 27 2321 2950 585578065 585577479 2.870000e-100 375.0
29 TraesCS2D01G155100 chr3B 83.365 523 57 26 2442 2950 61529458 61528952 9.960000e-125 457.0
30 TraesCS2D01G155100 chr3B 89.691 97 8 1 624 718 531562165 531562261 4.130000e-24 122.0
31 TraesCS2D01G155100 chr3B 91.358 81 7 0 638 718 10669776 10669696 8.930000e-21 111.0
32 TraesCS2D01G155100 chr6B 78.811 656 63 32 2321 2952 662110194 662109591 3.710000e-99 372.0
33 TraesCS2D01G155100 chr4D 80.039 516 52 17 2442 2933 400890483 400889995 4.870000e-88 335.0
34 TraesCS2D01G155100 chr4D 87.879 99 10 1 622 718 11241029 11240931 6.900000e-22 115.0
35 TraesCS2D01G155100 chr4A 78.599 514 74 23 2442 2950 58679493 58679011 1.060000e-79 307.0
36 TraesCS2D01G155100 chr1D 82.692 312 39 14 2442 2746 86107620 86107923 2.330000e-66 263.0
37 TraesCS2D01G155100 chr5D 80.628 382 33 20 2327 2677 391785332 391785703 1.080000e-64 257.0
38 TraesCS2D01G155100 chr5D 75.038 665 93 42 2441 3047 528554228 528554877 1.090000e-59 241.0
39 TraesCS2D01G155100 chr5D 81.923 260 38 9 2442 2698 63615241 63615494 8.560000e-51 211.0
40 TraesCS2D01G155100 chr5D 73.836 623 89 44 2441 3007 24351112 24351716 2.410000e-41 180.0
41 TraesCS2D01G155100 chr5D 90.000 100 8 1 621 718 432046260 432046359 8.870000e-26 128.0
42 TraesCS2D01G155100 chr3D 79.231 390 58 12 2350 2724 550421867 550422248 1.810000e-62 250.0
43 TraesCS2D01G155100 chr3D 80.342 117 15 6 110 224 19840044 19840154 7.000000e-12 82.4
44 TraesCS2D01G155100 chr3D 87.500 64 6 2 2791 2853 440984814 440984752 4.210000e-09 73.1
45 TraesCS2D01G155100 chr6D 76.357 516 88 23 2475 2967 7473601 7473097 2.350000e-61 246.0
46 TraesCS2D01G155100 chr1A 82.061 262 36 11 2441 2697 316890479 316890734 2.380000e-51 213.0
47 TraesCS2D01G155100 chr1A 86.992 123 12 1 2327 2449 316890342 316890460 5.300000e-28 135.0
48 TraesCS2D01G155100 chr5A 73.286 700 130 37 2326 2988 637188692 637189371 1.430000e-48 204.0
49 TraesCS2D01G155100 chr4B 74.877 406 73 24 2527 2921 596340851 596340464 1.130000e-34 158.0
50 TraesCS2D01G155100 chr4B 85.455 110 13 2 611 718 590912438 590912546 8.930000e-21 111.0
51 TraesCS2D01G155100 chr4B 84.848 99 12 2 622 718 376150055 376150152 2.500000e-16 97.1
52 TraesCS2D01G155100 chrUn 88.618 123 12 2 2325 2447 448751397 448751517 6.810000e-32 148.0
53 TraesCS2D01G155100 chrUn 88.525 122 12 2 2326 2447 301082837 301082718 2.450000e-31 147.0
54 TraesCS2D01G155100 chr7B 87.395 119 15 0 2327 2445 718830503 718830621 1.470000e-28 137.0
55 TraesCS2D01G155100 chr5B 78.673 211 35 8 2515 2722 203038825 203038622 6.850000e-27 132.0
56 TraesCS2D01G155100 chr7A 74.622 331 62 17 2648 2966 170074579 170074259 3.190000e-25 126.0
57 TraesCS2D01G155100 chr1B 92.405 79 6 0 640 718 158499445 158499367 2.480000e-21 113.0
58 TraesCS2D01G155100 chr3A 86.598 97 11 1 624 718 743838191 743838095 4.150000e-19 106.0
59 TraesCS2D01G155100 chr3A 85.859 99 12 2 2351 2449 588543390 588543486 1.490000e-18 104.0


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 TraesCS2D01G155100 chr2D 98706658 98709704 3046 True 5627.000000 5627 100.000000 1 3047 1 chr2D.!!$R2 3046
1 TraesCS2D01G155100 chr2D 98667102 98674494 7392 True 1077.333333 1563 83.342333 10 2191 3 chr2D.!!$R5 2181
2 TraesCS2D01G155100 chr2D 98658498 98662407 3909 True 520.333333 1303 84.048333 16 2135 3 chr2D.!!$R4 2119
3 TraesCS2D01G155100 chr2D 7172830 7173354 524 True 475.000000 475 83.848000 2442 2965 1 chr2D.!!$R1 523
4 TraesCS2D01G155100 chr2B 150200132 150201585 1453 True 1574.000000 1574 86.395000 741 2191 1 chr2B.!!$R2 1450
5 TraesCS2D01G155100 chr2B 150140826 150142102 1276 True 1362.000000 1362 86.043000 903 2191 1 chr2B.!!$R1 1288
6 TraesCS2D01G155100 chr2B 150337924 150340129 2205 True 1065.666667 2396 92.166000 1 2326 3 chr2B.!!$R6 2325
7 TraesCS2D01G155100 chr2B 150117951 150120399 2448 True 774.500000 1306 84.499500 16 2135 2 chr2B.!!$R5 2119
8 TraesCS2D01G155100 chr2B 150386729 150388685 1956 True 761.333333 1694 93.110000 143 1886 3 chr2B.!!$R7 1743
9 TraesCS2D01G155100 chr2A 97307364 97317226 9862 True 842.000000 1397 83.583500 10 2191 4 chr2A.!!$R2 2181
10 TraesCS2D01G155100 chr2A 97549765 97550350 585 True 412.000000 412 80.763000 10 566 1 chr2A.!!$R1 556
11 TraesCS2D01G155100 chr6A 24429185 24429746 561 False 518.000000 518 83.509000 2442 3003 1 chr6A.!!$F1 561
12 TraesCS2D01G155100 chr6A 585577479 585578065 586 True 375.000000 375 78.906000 2321 2950 1 chr6A.!!$R1 629
13 TraesCS2D01G155100 chr3B 61528952 61529458 506 True 457.000000 457 83.365000 2442 2950 1 chr3B.!!$R2 508
14 TraesCS2D01G155100 chr6B 662109591 662110194 603 True 372.000000 372 78.811000 2321 2952 1 chr6B.!!$R1 631
15 TraesCS2D01G155100 chr5D 528554228 528554877 649 False 241.000000 241 75.038000 2441 3047 1 chr5D.!!$F5 606
16 TraesCS2D01G155100 chr6D 7473097 7473601 504 True 246.000000 246 76.357000 2475 2967 1 chr6D.!!$R1 492
17 TraesCS2D01G155100 chr5A 637188692 637189371 679 False 204.000000 204 73.286000 2326 2988 1 chr5A.!!$F1 662

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
958 3350 0.105913 ATCCATCACCCATGCATGCA 60.106 50.0 25.04 25.04 0.0 3.96 F
1291 3698 0.038744 ATGTTGTCAAGGGAGCTGGG 59.961 55.0 0.00 0.00 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 12111 0.038166 TGGGCTCCGATTCTTGCTTT 59.962 50.0 0.00 0.0 0.00 3.51 R
2220 12420 0.800683 CGAAGGTGACGAATAGCGCA 60.801 55.0 11.47 0.0 46.04 6.09 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
75 94 2.001361 TAGGTCGCCGCTGTTAGCTC 62.001 60.000 0.00 0.00 39.60 4.09
108 130 7.661536 AGGAGTAGTGTGCAATAAATCTAGA 57.338 36.000 0.00 0.00 0.00 2.43
223 939 1.509370 CACCGACGACGACGAAGAG 60.509 63.158 20.63 6.71 42.66 2.85
305 1036 7.435784 GCTTCTAGGAGTACTTAGTGTTAATGC 59.564 40.741 0.00 0.00 0.00 3.56
309 1040 9.601217 CTAGGAGTACTTAGTGTTAATGCAATT 57.399 33.333 0.00 0.00 41.28 2.32
310 1041 8.268850 AGGAGTACTTAGTGTTAATGCAATTG 57.731 34.615 0.00 0.00 36.99 2.32
385 1250 3.551259 CAAGGGACATGCCTTACGT 57.449 52.632 4.15 0.00 36.66 3.57
387 1252 2.550978 CAAGGGACATGCCTTACGTAG 58.449 52.381 4.15 0.00 36.66 3.51
389 1254 0.106149 GGGACATGCCTTACGTAGGG 59.894 60.000 18.93 18.93 44.91 3.53
390 1255 0.106149 GGACATGCCTTACGTAGGGG 59.894 60.000 23.64 16.86 44.91 4.79
391 1256 0.828677 GACATGCCTTACGTAGGGGT 59.171 55.000 23.64 13.81 44.91 4.95
393 1258 1.758862 ACATGCCTTACGTAGGGGTAC 59.241 52.381 23.64 9.07 44.91 3.34
410 1325 3.996363 GGGTACGGTATGTTTTCGTTCTT 59.004 43.478 0.00 0.00 38.19 2.52
412 1327 5.637387 GGGTACGGTATGTTTTCGTTCTTTA 59.363 40.000 0.00 0.00 38.19 1.85
415 1330 8.868916 GGTACGGTATGTTTTCGTTCTTTATTA 58.131 33.333 0.00 0.00 38.19 0.98
488 1410 3.763897 AGTGCAATGTCAAAGGATTACCC 59.236 43.478 0.00 0.00 36.73 3.69
510 2195 1.503542 CTTCCAGTTCATGCGTGCC 59.496 57.895 0.00 0.00 0.00 5.01
575 2620 9.399403 GTGGAGAGAAAACAATTTGTTAATCTC 57.601 33.333 29.05 29.05 44.78 2.75
589 2949 0.254178 AATCTCGATGCCAGTTGCCT 59.746 50.000 0.00 0.00 40.16 4.75
590 2950 1.123077 ATCTCGATGCCAGTTGCCTA 58.877 50.000 0.00 0.00 40.16 3.93
627 3000 4.548991 CGTCAGTACGTATCTTTAGGCT 57.451 45.455 0.00 0.00 44.21 4.58
628 3001 4.280461 CGTCAGTACGTATCTTTAGGCTG 58.720 47.826 0.00 0.00 44.21 4.85
629 3002 4.608951 GTCAGTACGTATCTTTAGGCTGG 58.391 47.826 0.00 0.00 0.00 4.85
630 3003 3.067742 TCAGTACGTATCTTTAGGCTGGC 59.932 47.826 0.00 0.00 0.00 4.85
631 3004 2.364647 AGTACGTATCTTTAGGCTGGCC 59.635 50.000 3.00 3.00 0.00 5.36
632 3005 1.200519 ACGTATCTTTAGGCTGGCCA 58.799 50.000 14.39 4.71 38.92 5.36
633 3006 1.139058 ACGTATCTTTAGGCTGGCCAG 59.861 52.381 29.34 29.34 38.92 4.85
634 3007 1.139058 CGTATCTTTAGGCTGGCCAGT 59.861 52.381 32.81 17.61 38.92 4.00
635 3008 2.364324 CGTATCTTTAGGCTGGCCAGTA 59.636 50.000 32.81 16.49 38.92 2.74
636 3009 3.181469 CGTATCTTTAGGCTGGCCAGTAA 60.181 47.826 32.81 21.29 38.92 2.24
637 3010 3.567478 ATCTTTAGGCTGGCCAGTAAG 57.433 47.619 32.81 26.44 38.92 2.34
638 3011 1.559682 TCTTTAGGCTGGCCAGTAAGG 59.440 52.381 32.81 22.91 38.92 2.69
639 3012 0.623723 TTTAGGCTGGCCAGTAAGGG 59.376 55.000 32.81 8.97 38.92 3.95
640 3013 0.549169 TTAGGCTGGCCAGTAAGGGT 60.549 55.000 32.81 13.98 38.92 4.34
641 3014 0.340558 TAGGCTGGCCAGTAAGGGTA 59.659 55.000 32.81 13.03 38.92 3.69
642 3015 0.549169 AGGCTGGCCAGTAAGGGTAA 60.549 55.000 32.81 0.00 38.92 2.85
643 3016 0.393944 GGCTGGCCAGTAAGGGTAAC 60.394 60.000 32.81 13.25 38.09 2.50
644 3017 0.326927 GCTGGCCAGTAAGGGTAACA 59.673 55.000 32.81 0.00 38.09 2.41
645 3018 1.064685 GCTGGCCAGTAAGGGTAACAT 60.065 52.381 32.81 0.00 38.09 2.71
646 3019 2.171870 GCTGGCCAGTAAGGGTAACATA 59.828 50.000 32.81 0.00 38.09 2.29
647 3020 3.371166 GCTGGCCAGTAAGGGTAACATAA 60.371 47.826 32.81 0.00 38.09 1.90
648 3021 4.451900 CTGGCCAGTAAGGGTAACATAAG 58.548 47.826 25.53 0.00 38.09 1.73
649 3022 3.847780 TGGCCAGTAAGGGTAACATAAGT 59.152 43.478 0.00 0.00 38.09 2.24
650 3023 5.031495 TGGCCAGTAAGGGTAACATAAGTA 58.969 41.667 0.00 0.00 38.09 2.24
651 3024 5.488203 TGGCCAGTAAGGGTAACATAAGTAA 59.512 40.000 0.00 0.00 38.09 2.24
652 3025 6.159046 TGGCCAGTAAGGGTAACATAAGTAAT 59.841 38.462 0.00 0.00 38.09 1.89
653 3026 7.347748 TGGCCAGTAAGGGTAACATAAGTAATA 59.652 37.037 0.00 0.00 38.09 0.98
654 3027 8.380867 GGCCAGTAAGGGTAACATAAGTAATAT 58.619 37.037 0.00 0.00 38.09 1.28
655 3028 9.433153 GCCAGTAAGGGTAACATAAGTAATATC 57.567 37.037 0.00 0.00 38.09 1.63
672 3045 8.268850 AGTAATATCATGTATTTGGGATTCGC 57.731 34.615 0.00 0.00 0.00 4.70
673 3046 7.882791 AGTAATATCATGTATTTGGGATTCGCA 59.117 33.333 0.00 0.00 0.00 5.10
674 3047 7.523293 AATATCATGTATTTGGGATTCGCAA 57.477 32.000 11.71 11.71 34.59 4.85
675 3048 5.850557 ATCATGTATTTGGGATTCGCAAA 57.149 34.783 25.27 25.27 46.88 3.68
676 3049 4.992688 TCATGTATTTGGGATTCGCAAAC 58.007 39.130 25.49 17.41 45.99 2.93
677 3050 4.460731 TCATGTATTTGGGATTCGCAAACA 59.539 37.500 25.49 21.41 45.99 2.83
678 3051 5.126869 TCATGTATTTGGGATTCGCAAACAT 59.873 36.000 25.49 22.38 45.99 2.71
679 3052 4.742417 TGTATTTGGGATTCGCAAACATG 58.258 39.130 25.49 0.00 45.99 3.21
680 3053 2.077413 TTTGGGATTCGCAAACATGC 57.923 45.000 21.02 0.00 40.41 4.06
681 3054 1.255882 TTGGGATTCGCAAACATGCT 58.744 45.000 13.18 0.00 33.52 3.79
682 3055 1.255882 TGGGATTCGCAAACATGCTT 58.744 45.000 0.20 0.00 0.00 3.91
683 3056 2.441410 TGGGATTCGCAAACATGCTTA 58.559 42.857 0.20 0.00 0.00 3.09
684 3057 3.023119 TGGGATTCGCAAACATGCTTAT 58.977 40.909 0.20 0.00 0.00 1.73
685 3058 4.203226 TGGGATTCGCAAACATGCTTATA 58.797 39.130 0.20 0.00 0.00 0.98
686 3059 4.826733 TGGGATTCGCAAACATGCTTATAT 59.173 37.500 0.20 0.00 0.00 0.86
687 3060 5.156355 GGGATTCGCAAACATGCTTATATG 58.844 41.667 0.00 0.00 0.00 1.78
688 3061 5.048782 GGGATTCGCAAACATGCTTATATGA 60.049 40.000 0.00 0.00 0.00 2.15
689 3062 5.853282 GGATTCGCAAACATGCTTATATGAC 59.147 40.000 0.00 0.00 0.00 3.06
690 3063 5.809719 TTCGCAAACATGCTTATATGACA 57.190 34.783 0.00 0.00 0.00 3.58
691 3064 5.408204 TCGCAAACATGCTTATATGACAG 57.592 39.130 0.00 0.00 0.00 3.51
692 3065 4.273235 TCGCAAACATGCTTATATGACAGG 59.727 41.667 0.00 0.00 0.00 4.00
693 3066 4.293415 GCAAACATGCTTATATGACAGGC 58.707 43.478 0.00 0.00 0.00 4.85
694 3067 4.202040 GCAAACATGCTTATATGACAGGCA 60.202 41.667 0.00 0.00 37.32 4.75
695 3068 5.679382 GCAAACATGCTTATATGACAGGCAA 60.679 40.000 0.00 0.00 36.49 4.52
696 3069 6.509656 CAAACATGCTTATATGACAGGCAAT 58.490 36.000 0.00 0.00 36.49 3.56
697 3070 6.720112 AACATGCTTATATGACAGGCAATT 57.280 33.333 0.00 0.00 36.49 2.32
698 3071 7.822161 AACATGCTTATATGACAGGCAATTA 57.178 32.000 0.00 0.00 36.49 1.40
699 3072 7.822161 ACATGCTTATATGACAGGCAATTAA 57.178 32.000 0.00 0.00 36.49 1.40
700 3073 8.236585 ACATGCTTATATGACAGGCAATTAAA 57.763 30.769 0.00 0.00 36.49 1.52
701 3074 8.694540 ACATGCTTATATGACAGGCAATTAAAA 58.305 29.630 0.00 0.00 36.49 1.52
702 3075 9.531942 CATGCTTATATGACAGGCAATTAAAAA 57.468 29.630 0.00 0.00 36.49 1.94
722 3095 6.943899 AAAAAGAGAGAGATGGTTACTCCT 57.056 37.500 0.00 0.00 35.27 3.69
723 3096 6.538945 AAAAGAGAGAGATGGTTACTCCTC 57.461 41.667 0.00 0.00 35.27 3.71
724 3097 4.871871 AGAGAGAGATGGTTACTCCTCA 57.128 45.455 0.00 0.00 35.85 3.86
725 3098 4.532834 AGAGAGAGATGGTTACTCCTCAC 58.467 47.826 0.00 0.00 35.85 3.51
726 3099 4.229582 AGAGAGAGATGGTTACTCCTCACT 59.770 45.833 0.00 0.00 35.85 3.41
727 3100 5.430417 AGAGAGAGATGGTTACTCCTCACTA 59.570 44.000 0.00 0.00 35.85 2.74
728 3101 6.102615 AGAGAGAGATGGTTACTCCTCACTAT 59.897 42.308 0.00 0.00 35.85 2.12
729 3102 6.068010 AGAGAGATGGTTACTCCTCACTATG 58.932 44.000 0.00 0.00 35.27 2.23
730 3103 6.019656 AGAGATGGTTACTCCTCACTATGA 57.980 41.667 0.00 0.00 35.27 2.15
731 3104 6.619464 AGAGATGGTTACTCCTCACTATGAT 58.381 40.000 0.00 0.00 35.27 2.45
732 3105 6.719370 AGAGATGGTTACTCCTCACTATGATC 59.281 42.308 0.00 0.00 35.27 2.92
733 3106 6.377080 AGATGGTTACTCCTCACTATGATCA 58.623 40.000 0.00 0.00 37.07 2.92
734 3107 6.493115 AGATGGTTACTCCTCACTATGATCAG 59.507 42.308 0.09 0.00 37.07 2.90
735 3108 4.342378 TGGTTACTCCTCACTATGATCAGC 59.658 45.833 0.09 0.00 37.07 4.26
736 3109 4.262249 GGTTACTCCTCACTATGATCAGCC 60.262 50.000 0.09 0.00 0.00 4.85
737 3110 3.326946 ACTCCTCACTATGATCAGCCT 57.673 47.619 0.09 0.00 0.00 4.58
738 3111 3.652055 ACTCCTCACTATGATCAGCCTT 58.348 45.455 0.09 0.00 0.00 4.35
739 3112 4.809193 ACTCCTCACTATGATCAGCCTTA 58.191 43.478 0.09 0.00 0.00 2.69
740 3113 4.832266 ACTCCTCACTATGATCAGCCTTAG 59.168 45.833 0.09 0.30 0.00 2.18
741 3114 5.066913 TCCTCACTATGATCAGCCTTAGA 57.933 43.478 0.09 0.00 0.00 2.10
742 3115 4.830046 TCCTCACTATGATCAGCCTTAGAC 59.170 45.833 0.09 0.00 0.00 2.59
743 3116 4.586421 CCTCACTATGATCAGCCTTAGACA 59.414 45.833 0.09 0.00 0.00 3.41
744 3117 5.508825 CCTCACTATGATCAGCCTTAGACAC 60.509 48.000 0.09 0.00 0.00 3.67
745 3118 5.204292 TCACTATGATCAGCCTTAGACACT 58.796 41.667 0.09 0.00 0.00 3.55
749 3122 4.462508 TGATCAGCCTTAGACACTTCTG 57.537 45.455 0.00 0.00 32.75 3.02
766 3139 1.005748 TGCAGCTGACCAGTTCTCG 60.006 57.895 20.43 0.00 0.00 4.04
780 3153 4.868734 CCAGTTCTCGTCAACTAATTACCC 59.131 45.833 2.13 0.00 34.70 3.69
786 3161 8.601476 GTTCTCGTCAACTAATTACCCATTAAG 58.399 37.037 0.00 0.00 0.00 1.85
787 3162 7.844009 TCTCGTCAACTAATTACCCATTAAGT 58.156 34.615 0.00 0.00 0.00 2.24
826 3207 2.427812 TGGTTGATCGATGCATGCATTT 59.572 40.909 32.60 20.61 36.70 2.32
827 3208 3.119065 TGGTTGATCGATGCATGCATTTT 60.119 39.130 32.60 20.27 36.70 1.82
846 3234 2.753055 TAGTCAACCGTGCATGCTAA 57.247 45.000 20.33 0.00 0.00 3.09
864 3252 5.566623 TGCTAACGTACGTGATTAGAGAAG 58.433 41.667 23.57 9.15 0.00 2.85
884 3272 3.786635 AGTTGTCATCGGATCACTAAGC 58.213 45.455 0.00 0.00 0.00 3.09
955 3347 2.109304 TCATCATCCATCACCCATGCAT 59.891 45.455 0.00 0.00 0.00 3.96
956 3348 1.989706 TCATCCATCACCCATGCATG 58.010 50.000 20.19 20.19 0.00 4.06
957 3349 0.317160 CATCCATCACCCATGCATGC 59.683 55.000 21.69 11.82 0.00 4.06
958 3350 0.105913 ATCCATCACCCATGCATGCA 60.106 50.000 25.04 25.04 0.00 3.96
977 3372 3.699538 TGCACGGCCTCCACTATATATAG 59.300 47.826 16.73 16.73 36.46 1.31
995 3390 2.111043 CCACGCAACCCTGTCTGT 59.889 61.111 0.00 0.00 0.00 3.41
1278 3685 9.699410 TGGAGATTCCAATAAGAATTATGTTGT 57.301 29.630 0.00 0.00 45.00 3.32
1291 3698 0.038744 ATGTTGTCAAGGGAGCTGGG 59.961 55.000 0.00 0.00 0.00 4.45
1479 11648 0.106708 GCAGATGGGTCAAGCGGATA 59.893 55.000 0.00 0.00 0.00 2.59
1516 11685 0.600255 CCGGCGAAGGATATGGTGAC 60.600 60.000 9.30 0.00 0.00 3.67
1969 12161 0.036875 AGCCCAACACCACTTCTAGC 59.963 55.000 0.00 0.00 0.00 3.42
2098 12293 9.262358 CTAAATAGTTTAGTGGAGCAATCTACC 57.738 37.037 2.14 0.00 38.21 3.18
2108 12303 4.941263 TGGAGCAATCTACCAACATGTAAC 59.059 41.667 0.00 0.00 0.00 2.50
2118 12313 3.453353 ACCAACATGTAACCGCTACCTAT 59.547 43.478 0.00 0.00 0.00 2.57
2119 12314 4.650588 ACCAACATGTAACCGCTACCTATA 59.349 41.667 0.00 0.00 0.00 1.31
2234 12434 0.739813 AGGGTTGCGCTATTCGTCAC 60.740 55.000 9.73 0.00 41.07 3.67
2236 12436 0.739813 GGTTGCGCTATTCGTCACCT 60.740 55.000 9.73 0.00 38.54 4.00
2239 12439 0.800683 TGCGCTATTCGTCACCTTCG 60.801 55.000 9.73 0.00 41.07 3.79
2278 12478 3.495983 CCTTACACCAACCATCTCACACA 60.496 47.826 0.00 0.00 0.00 3.72
2288 12488 4.464008 ACCATCTCACACAGTCACAATTT 58.536 39.130 0.00 0.00 0.00 1.82
2866 16367 7.647715 TCAAGGAATGTTCGAGAATTTGAAAAC 59.352 33.333 0.00 0.00 0.00 2.43
2938 18039 8.871742 TTTTTCAAAACAATGTTCACGAATTG 57.128 26.923 0.00 0.00 39.26 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 94 3.767673 TGCACACTACTCCTAGGGTTTAG 59.232 47.826 9.46 9.48 34.01 1.85
108 130 1.654954 CGACGACGGAGAGGGTTGAT 61.655 60.000 0.00 0.00 35.72 2.57
305 1036 8.017373 CCTAATCGTAATAAGGTGCATCAATTG 58.983 37.037 0.00 0.00 0.00 2.32
309 1040 6.169557 ACCTAATCGTAATAAGGTGCATCA 57.830 37.500 0.00 0.00 40.83 3.07
336 1102 7.687941 ATTACCAACAGAAAATGACTAGTGG 57.312 36.000 0.00 0.00 0.00 4.00
367 1232 2.550978 CTACGTAAGGCATGTCCCTTG 58.449 52.381 13.26 2.46 44.68 3.61
371 1236 0.106149 CCCCTACGTAAGGCATGTCC 59.894 60.000 4.56 0.00 45.03 4.02
380 1245 3.290948 ACATACCGTACCCCTACGTAA 57.709 47.619 0.00 0.00 43.69 3.18
381 1246 3.290948 AACATACCGTACCCCTACGTA 57.709 47.619 0.00 0.00 43.69 3.57
382 1247 2.143876 AACATACCGTACCCCTACGT 57.856 50.000 0.00 0.00 43.69 3.57
384 1249 3.119137 ACGAAAACATACCGTACCCCTAC 60.119 47.826 0.00 0.00 34.52 3.18
385 1250 3.096092 ACGAAAACATACCGTACCCCTA 58.904 45.455 0.00 0.00 34.52 3.53
387 1252 2.385013 ACGAAAACATACCGTACCCC 57.615 50.000 0.00 0.00 34.52 4.95
388 1253 3.588955 AGAACGAAAACATACCGTACCC 58.411 45.455 0.00 0.00 35.28 3.69
389 1254 5.596268 AAAGAACGAAAACATACCGTACC 57.404 39.130 0.00 0.00 35.28 3.34
410 1325 7.604549 TGAACACCGCGGATCTATAATAATAA 58.395 34.615 35.90 4.05 0.00 1.40
412 1327 6.032956 TGAACACCGCGGATCTATAATAAT 57.967 37.500 35.90 0.00 0.00 1.28
415 1330 4.021456 TCATGAACACCGCGGATCTATAAT 60.021 41.667 35.90 13.12 0.00 1.28
488 1410 2.753966 CGCATGAACTGGAAGCCGG 61.754 63.158 0.00 0.00 37.60 6.13
510 2195 4.142138 ACCTGAGTTGCCTTTACTCGATAG 60.142 45.833 0.00 0.00 43.90 2.08
531 2244 5.710099 TCTCCACCACATGAAATTAAGAACC 59.290 40.000 0.00 0.00 0.00 3.62
589 2949 4.095932 ACTGACGCATCGTTGAGATTACTA 59.904 41.667 4.14 0.00 41.37 1.82
590 2950 3.119459 ACTGACGCATCGTTGAGATTACT 60.119 43.478 4.14 0.00 41.37 2.24
622 2995 0.340558 TACCCTTACTGGCCAGCCTA 59.659 55.000 33.06 15.93 36.94 3.93
625 2998 0.326927 TGTTACCCTTACTGGCCAGC 59.673 55.000 33.06 13.27 0.00 4.85
627 3000 3.847780 ACTTATGTTACCCTTACTGGCCA 59.152 43.478 4.71 4.71 0.00 5.36
628 3001 4.498894 ACTTATGTTACCCTTACTGGCC 57.501 45.455 0.00 0.00 0.00 5.36
629 3002 9.433153 GATATTACTTATGTTACCCTTACTGGC 57.567 37.037 0.00 0.00 0.00 4.85
646 3019 8.730680 GCGAATCCCAAATACATGATATTACTT 58.269 33.333 0.00 0.00 0.00 2.24
647 3020 7.882791 TGCGAATCCCAAATACATGATATTACT 59.117 33.333 0.00 0.00 0.00 2.24
648 3021 8.039603 TGCGAATCCCAAATACATGATATTAC 57.960 34.615 0.00 0.00 0.00 1.89
649 3022 8.628630 TTGCGAATCCCAAATACATGATATTA 57.371 30.769 0.00 0.00 0.00 0.98
650 3023 7.523293 TTGCGAATCCCAAATACATGATATT 57.477 32.000 0.00 0.00 0.00 1.28
651 3024 7.014134 TGTTTGCGAATCCCAAATACATGATAT 59.986 33.333 0.00 0.00 34.99 1.63
652 3025 6.319911 TGTTTGCGAATCCCAAATACATGATA 59.680 34.615 0.00 0.00 34.99 2.15
653 3026 5.126869 TGTTTGCGAATCCCAAATACATGAT 59.873 36.000 0.00 0.00 34.99 2.45
654 3027 4.460731 TGTTTGCGAATCCCAAATACATGA 59.539 37.500 0.00 0.00 34.99 3.07
655 3028 4.742417 TGTTTGCGAATCCCAAATACATG 58.258 39.130 0.00 0.00 34.99 3.21
656 3029 5.350633 CATGTTTGCGAATCCCAAATACAT 58.649 37.500 0.00 0.00 34.99 2.29
657 3030 4.742417 CATGTTTGCGAATCCCAAATACA 58.258 39.130 0.00 0.00 34.99 2.29
658 3031 3.551485 GCATGTTTGCGAATCCCAAATAC 59.449 43.478 0.00 0.00 39.49 1.89
659 3032 3.779759 GCATGTTTGCGAATCCCAAATA 58.220 40.909 0.00 0.00 39.49 1.40
660 3033 2.620242 GCATGTTTGCGAATCCCAAAT 58.380 42.857 0.00 0.00 39.49 2.32
661 3034 2.077413 GCATGTTTGCGAATCCCAAA 57.923 45.000 0.00 0.00 39.49 3.28
662 3035 3.810579 GCATGTTTGCGAATCCCAA 57.189 47.368 0.00 0.00 39.49 4.12
672 3045 5.503662 TGCCTGTCATATAAGCATGTTTG 57.496 39.130 4.89 0.00 0.00 2.93
673 3046 6.720112 ATTGCCTGTCATATAAGCATGTTT 57.280 33.333 0.00 0.00 32.67 2.83
674 3047 6.720112 AATTGCCTGTCATATAAGCATGTT 57.280 33.333 0.00 0.00 32.67 2.71
675 3048 7.822161 TTAATTGCCTGTCATATAAGCATGT 57.178 32.000 0.00 0.00 32.67 3.21
676 3049 9.531942 TTTTTAATTGCCTGTCATATAAGCATG 57.468 29.630 0.00 0.00 32.67 4.06
699 3072 6.498651 TGAGGAGTAACCATCTCTCTCTTTTT 59.501 38.462 0.00 0.00 42.04 1.94
700 3073 6.019748 TGAGGAGTAACCATCTCTCTCTTTT 58.980 40.000 0.00 0.00 42.04 2.27
701 3074 5.420739 GTGAGGAGTAACCATCTCTCTCTTT 59.579 44.000 0.00 0.00 42.04 2.52
702 3075 4.953579 GTGAGGAGTAACCATCTCTCTCTT 59.046 45.833 0.00 0.00 42.04 2.85
703 3076 4.229582 AGTGAGGAGTAACCATCTCTCTCT 59.770 45.833 0.00 0.00 42.04 3.10
704 3077 4.532834 AGTGAGGAGTAACCATCTCTCTC 58.467 47.826 0.00 0.00 42.04 3.20
705 3078 4.601406 AGTGAGGAGTAACCATCTCTCT 57.399 45.455 0.00 0.00 42.04 3.10
706 3079 6.065374 TCATAGTGAGGAGTAACCATCTCTC 58.935 44.000 0.00 0.00 42.04 3.20
707 3080 6.019656 TCATAGTGAGGAGTAACCATCTCT 57.980 41.667 0.00 0.00 42.04 3.10
708 3081 6.491745 TGATCATAGTGAGGAGTAACCATCTC 59.508 42.308 0.00 0.00 42.04 2.75
709 3082 6.377080 TGATCATAGTGAGGAGTAACCATCT 58.623 40.000 0.00 0.00 42.04 2.90
710 3083 6.656632 TGATCATAGTGAGGAGTAACCATC 57.343 41.667 0.00 0.00 42.04 3.51
711 3084 5.011533 GCTGATCATAGTGAGGAGTAACCAT 59.988 44.000 0.00 0.00 42.04 3.55
712 3085 4.342378 GCTGATCATAGTGAGGAGTAACCA 59.658 45.833 0.00 0.00 42.04 3.67
713 3086 4.262249 GGCTGATCATAGTGAGGAGTAACC 60.262 50.000 0.00 0.00 39.35 2.85
714 3087 4.586841 AGGCTGATCATAGTGAGGAGTAAC 59.413 45.833 0.00 0.00 0.00 2.50
715 3088 4.809193 AGGCTGATCATAGTGAGGAGTAA 58.191 43.478 0.00 0.00 0.00 2.24
716 3089 4.461450 AGGCTGATCATAGTGAGGAGTA 57.539 45.455 0.00 0.00 0.00 2.59
717 3090 3.326946 AGGCTGATCATAGTGAGGAGT 57.673 47.619 0.00 0.00 0.00 3.85
718 3091 5.048083 GTCTAAGGCTGATCATAGTGAGGAG 60.048 48.000 0.00 0.00 0.00 3.69
719 3092 4.830046 GTCTAAGGCTGATCATAGTGAGGA 59.170 45.833 0.00 0.00 0.00 3.71
720 3093 4.586421 TGTCTAAGGCTGATCATAGTGAGG 59.414 45.833 0.00 0.00 0.00 3.86
721 3094 5.301551 AGTGTCTAAGGCTGATCATAGTGAG 59.698 44.000 0.00 0.00 0.00 3.51
722 3095 5.204292 AGTGTCTAAGGCTGATCATAGTGA 58.796 41.667 0.00 0.00 0.00 3.41
723 3096 5.528043 AGTGTCTAAGGCTGATCATAGTG 57.472 43.478 0.00 0.00 0.00 2.74
724 3097 5.896678 AGAAGTGTCTAAGGCTGATCATAGT 59.103 40.000 0.00 0.00 29.93 2.12
725 3098 6.215121 CAGAAGTGTCTAAGGCTGATCATAG 58.785 44.000 0.00 0.00 30.85 2.23
726 3099 5.452496 GCAGAAGTGTCTAAGGCTGATCATA 60.452 44.000 0.00 0.00 30.85 2.15
727 3100 4.682859 GCAGAAGTGTCTAAGGCTGATCAT 60.683 45.833 0.00 0.00 30.85 2.45
728 3101 3.368843 GCAGAAGTGTCTAAGGCTGATCA 60.369 47.826 0.00 0.00 30.85 2.92
729 3102 3.194062 GCAGAAGTGTCTAAGGCTGATC 58.806 50.000 0.00 0.00 30.85 2.92
730 3103 2.568956 TGCAGAAGTGTCTAAGGCTGAT 59.431 45.455 0.00 0.00 30.85 2.90
731 3104 1.970640 TGCAGAAGTGTCTAAGGCTGA 59.029 47.619 0.00 0.00 30.85 4.26
732 3105 2.344950 CTGCAGAAGTGTCTAAGGCTG 58.655 52.381 8.42 0.00 30.85 4.85
733 3106 1.338579 GCTGCAGAAGTGTCTAAGGCT 60.339 52.381 20.43 0.00 30.85 4.58
734 3107 1.082690 GCTGCAGAAGTGTCTAAGGC 58.917 55.000 20.43 0.00 30.85 4.35
735 3108 2.028658 TCAGCTGCAGAAGTGTCTAAGG 60.029 50.000 20.43 0.00 30.85 2.69
736 3109 2.992543 GTCAGCTGCAGAAGTGTCTAAG 59.007 50.000 20.43 0.00 30.85 2.18
737 3110 2.289072 GGTCAGCTGCAGAAGTGTCTAA 60.289 50.000 20.43 0.00 30.85 2.10
738 3111 1.273606 GGTCAGCTGCAGAAGTGTCTA 59.726 52.381 20.43 0.00 30.85 2.59
739 3112 0.034616 GGTCAGCTGCAGAAGTGTCT 59.965 55.000 20.43 0.00 32.85 3.41
740 3113 0.250038 TGGTCAGCTGCAGAAGTGTC 60.250 55.000 20.43 8.72 0.00 3.67
741 3114 0.250209 CTGGTCAGCTGCAGAAGTGT 60.250 55.000 20.43 0.00 0.00 3.55
742 3115 0.250209 ACTGGTCAGCTGCAGAAGTG 60.250 55.000 23.21 11.35 0.00 3.16
743 3116 0.471617 AACTGGTCAGCTGCAGAAGT 59.528 50.000 23.21 14.49 0.00 3.01
744 3117 1.155042 GAACTGGTCAGCTGCAGAAG 58.845 55.000 23.21 8.85 0.00 2.85
745 3118 0.761187 AGAACTGGTCAGCTGCAGAA 59.239 50.000 23.21 0.00 0.00 3.02
749 3122 1.005630 ACGAGAACTGGTCAGCTGC 60.006 57.895 9.47 4.04 0.00 5.25
791 3166 9.860898 CATCGATCAACCAAATCTCTACATATA 57.139 33.333 0.00 0.00 0.00 0.86
797 3172 5.022282 TGCATCGATCAACCAAATCTCTA 57.978 39.130 0.00 0.00 0.00 2.43
807 3182 5.276270 ACTAAAATGCATGCATCGATCAAC 58.724 37.500 32.25 0.00 35.31 3.18
826 3207 2.739913 GTTAGCATGCACGGTTGACTAA 59.260 45.455 21.98 3.24 0.00 2.24
827 3208 2.343101 GTTAGCATGCACGGTTGACTA 58.657 47.619 21.98 0.00 0.00 2.59
846 3234 5.049198 TGACAACTTCTCTAATCACGTACGT 60.049 40.000 16.72 16.72 0.00 3.57
864 3252 2.866762 GGCTTAGTGATCCGATGACAAC 59.133 50.000 0.62 0.00 0.00 3.32
884 3272 0.030638 CGCTTTGGGTTGTGAACTGG 59.969 55.000 0.00 0.00 0.00 4.00
955 3347 2.003937 TATATAGTGGAGGCCGTGCA 57.996 50.000 0.00 0.00 0.00 4.57
956 3348 3.491104 GCTATATATAGTGGAGGCCGTGC 60.491 52.174 18.81 0.10 32.96 5.34
957 3349 3.068307 GGCTATATATAGTGGAGGCCGTG 59.932 52.174 18.81 0.00 32.96 4.94
958 3350 3.297736 GGCTATATATAGTGGAGGCCGT 58.702 50.000 18.81 0.00 32.96 5.68
977 3372 3.357079 CAGACAGGGTTGCGTGGC 61.357 66.667 0.00 0.00 0.00 5.01
995 3390 4.338118 GTGAGATGAGTTGGGTGTTGAAAA 59.662 41.667 0.00 0.00 0.00 2.29
1273 3680 1.455849 CCCAGCTCCCTTGACAACA 59.544 57.895 0.00 0.00 0.00 3.33
1278 3685 2.285668 CTCCCCCAGCTCCCTTGA 60.286 66.667 0.00 0.00 0.00 3.02
1291 3698 1.612739 ACCGTTTCCTCCTCCTCCC 60.613 63.158 0.00 0.00 0.00 4.30
1479 11648 3.112205 GCACCATCTCCGGCTCCAT 62.112 63.158 0.00 0.00 0.00 3.41
1597 11772 3.659089 ATTTCCTCCGTCACCGCCG 62.659 63.158 0.00 0.00 0.00 6.46
1936 12111 0.038166 TGGGCTCCGATTCTTGCTTT 59.962 50.000 0.00 0.00 0.00 3.51
2098 12293 7.724305 ATTTATAGGTAGCGGTTACATGTTG 57.276 36.000 2.30 0.00 33.73 3.33
2218 12418 1.060698 GAAGGTGACGAATAGCGCAAC 59.939 52.381 11.47 0.00 46.04 4.17
2220 12420 0.800683 CGAAGGTGACGAATAGCGCA 60.801 55.000 11.47 0.00 46.04 6.09
2266 12466 3.777106 ATTGTGACTGTGTGAGATGGT 57.223 42.857 0.00 0.00 0.00 3.55
2288 12488 9.039870 CCACATGCTTTTGTTTCTTATGTTTTA 57.960 29.630 0.00 0.00 0.00 1.52
2308 12508 3.622630 TCCCGTAATTTTACCCCACATG 58.377 45.455 0.00 0.00 0.00 3.21
2367 12567 4.261781 GTAGGGAGGGTACGCGCG 62.262 72.222 30.96 30.96 34.59 6.86
2391 12591 4.181010 CCATGAGGGAGCGGTGGG 62.181 72.222 0.00 0.00 40.01 4.61
2467 12686 9.558648 GACATTTTTGCAACTTTTTCTGAAATT 57.441 25.926 0.00 0.00 0.00 1.82
2679 13235 6.907206 AGTTTGTGAACATTGTTCCAAATG 57.093 33.333 28.67 6.21 42.21 2.32
2912 18013 8.987729 CAATTCGTGAACATTGTTTTGAAAAAG 58.012 29.630 3.08 1.01 0.00 2.27
2919 18020 6.414408 TTTGCAATTCGTGAACATTGTTTT 57.586 29.167 0.00 0.00 33.58 2.43
2921 18022 6.414408 TTTTTGCAATTCGTGAACATTGTT 57.586 29.167 0.00 0.63 33.58 2.83
2948 18049 9.856803 GCGAACAAATTTTCTTAAATTGCTAAA 57.143 25.926 0.00 0.00 41.83 1.85
2951 18132 7.475771 TGCGAACAAATTTTCTTAAATTGCT 57.524 28.000 0.00 0.00 41.83 3.91


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

AutoCloner maintained by Alex Coulton.