Multiple sequence alignment - TraesCS7D01G324800

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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 TraesCS7D01G324800 chr7D 100.000 3662 0 0 1 3662 414494039 414490378 0.000000e+00 6763
1 TraesCS7D01G324800 chr7D 85.424 590 76 6 1 586 577180895 577181478 4.040000e-169 604
2 TraesCS7D01G324800 chr7A 91.582 1675 89 22 341 1998 476940741 476939102 0.000000e+00 2265
3 TraesCS7D01G324800 chr7A 93.497 815 29 11 2527 3323 476938233 476937425 0.000000e+00 1190
4 TraesCS7D01G324800 chr7A 83.386 319 37 11 2197 2511 476938729 476938423 7.740000e-72 281
5 TraesCS7D01G324800 chr7A 86.310 168 17 3 2021 2188 476939005 476938844 1.040000e-40 178
6 TraesCS7D01G324800 chr7A 86.420 162 19 2 3411 3570 476937338 476937178 1.350000e-39 174
7 TraesCS7D01G324800 chr7B 94.049 773 40 4 1236 2006 428928053 428927285 0.000000e+00 1168
8 TraesCS7D01G324800 chr7B 90.741 648 28 16 2527 3172 428926538 428925921 0.000000e+00 835
9 TraesCS7D01G324800 chr7B 93.011 558 8 8 699 1250 428928606 428928074 0.000000e+00 785
10 TraesCS7D01G324800 chr7B 82.294 497 57 19 2009 2500 428927210 428926740 5.700000e-108 401
11 TraesCS7D01G324800 chr7B 89.286 224 13 9 3349 3563 428922712 428922491 1.680000e-68 270
12 TraesCS7D01G324800 chr7B 84.348 115 8 5 3558 3662 428922126 428922012 1.800000e-18 104
13 TraesCS7D01G324800 chr5D 85.692 643 77 11 1 636 458001155 458000521 0.000000e+00 664
14 TraesCS7D01G324800 chr5D 88.288 555 52 8 1 548 497817668 497817120 0.000000e+00 652
15 TraesCS7D01G324800 chr2D 89.808 520 44 6 1 516 587269652 587269138 0.000000e+00 658
16 TraesCS7D01G324800 chr2D 86.102 590 71 7 1 585 479318648 479318065 3.100000e-175 625
17 TraesCS7D01G324800 chr2D 80.000 185 31 5 3354 3533 566268422 566268239 8.250000e-27 132
18 TraesCS7D01G324800 chr6A 89.205 528 47 6 1 523 115035552 115035030 0.000000e+00 651
19 TraesCS7D01G324800 chr6A 88.065 553 56 8 1 548 444709056 444708509 0.000000e+00 647
20 TraesCS7D01G324800 chr3B 89.251 521 45 7 1 516 182466681 182467195 3.080000e-180 641
21 TraesCS7D01G324800 chr5A 86.102 590 68 8 4 585 615294448 615293865 1.120000e-174 623
22 TraesCS7D01G324800 chr6B 83.158 190 25 5 3364 3549 694255289 694255475 2.260000e-37 167
23 TraesCS7D01G324800 chr6B 80.100 201 34 5 3338 3533 81010772 81010573 1.060000e-30 145
24 TraesCS7D01G324800 chr4B 80.000 235 33 9 3338 3565 101712692 101712919 1.050000e-35 161
25 TraesCS7D01G324800 chr2B 80.203 197 30 7 3379 3570 597000073 596999881 4.930000e-29 139
26 TraesCS7D01G324800 chr2B 78.818 203 35 6 3338 3533 465132922 465133123 2.970000e-26 130
27 TraesCS7D01G324800 chr1B 80.105 191 20 8 3353 3539 667386760 667386584 3.840000e-25 126


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 TraesCS7D01G324800 chr7D 414490378 414494039 3661 True 6763.000000 6763 100.000000 1 3662 1 chr7D.!!$R1 3661
1 TraesCS7D01G324800 chr7D 577180895 577181478 583 False 604.000000 604 85.424000 1 586 1 chr7D.!!$F1 585
2 TraesCS7D01G324800 chr7A 476937178 476940741 3563 True 817.600000 2265 88.239000 341 3570 5 chr7A.!!$R1 3229
3 TraesCS7D01G324800 chr7B 428922012 428928606 6594 True 593.833333 1168 88.954833 699 3662 6 chr7B.!!$R1 2963
4 TraesCS7D01G324800 chr5D 458000521 458001155 634 True 664.000000 664 85.692000 1 636 1 chr5D.!!$R1 635
5 TraesCS7D01G324800 chr5D 497817120 497817668 548 True 652.000000 652 88.288000 1 548 1 chr5D.!!$R2 547
6 TraesCS7D01G324800 chr2D 587269138 587269652 514 True 658.000000 658 89.808000 1 516 1 chr2D.!!$R3 515
7 TraesCS7D01G324800 chr2D 479318065 479318648 583 True 625.000000 625 86.102000 1 585 1 chr2D.!!$R1 584
8 TraesCS7D01G324800 chr6A 115035030 115035552 522 True 651.000000 651 89.205000 1 523 1 chr6A.!!$R1 522
9 TraesCS7D01G324800 chr6A 444708509 444709056 547 True 647.000000 647 88.065000 1 548 1 chr6A.!!$R2 547
10 TraesCS7D01G324800 chr3B 182466681 182467195 514 False 641.000000 641 89.251000 1 516 1 chr3B.!!$F1 515
11 TraesCS7D01G324800 chr5A 615293865 615294448 583 True 623.000000 623 86.102000 4 585 1 chr5A.!!$R1 581

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
588 606 0.179192 TTCGTATTCGTGTCCGTCCG 60.179 55.0 0.0 0.0 38.33 4.79 F
1246 1272 0.326332 GTACTGCTAACCCCCTCCCT 60.326 60.0 0.0 0.0 0.00 4.20 F
2416 2666 0.396811 ACTGAAACCCCTGTTCCGAG 59.603 55.0 0.0 0.0 32.15 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 2954 0.250467 TCTCAGGAGCTGCCAAACAC 60.250 55.0 0.00 0.00 40.02 3.32 R
2556 2985 0.317269 CCGCTCTGCAACAAACACAG 60.317 55.0 0.00 0.00 0.00 3.66 R
3590 7447 0.320073 CAAACAAGGTGGCTGGCATG 60.320 55.0 7.33 4.37 0.00 4.06 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
39 41 3.141398 GTCAGCACCATCTCAAACTCAA 58.859 45.455 0.00 0.00 0.00 3.02
96 100 4.837972 AGAAGCAACTAGAAAGGATGTCC 58.162 43.478 0.00 0.00 0.00 4.02
200 206 5.824624 GGAGGTGATGACATATTGTGTGATT 59.175 40.000 0.00 0.00 42.36 2.57
384 396 7.711772 AGCTGAAAGAAGATCTGATTGAGTATG 59.288 37.037 0.00 0.00 34.07 2.39
385 397 7.710044 GCTGAAAGAAGATCTGATTGAGTATGA 59.290 37.037 0.00 0.00 34.07 2.15
386 398 9.767228 CTGAAAGAAGATCTGATTGAGTATGAT 57.233 33.333 0.00 0.00 34.07 2.45
404 416 2.983192 TGATCAGTGGGTGGTTAAAGGA 59.017 45.455 0.00 0.00 0.00 3.36
420 432 3.312736 AAGGAGACAACAATGTTGGGT 57.687 42.857 27.15 15.26 40.74 4.51
483 498 2.864343 GCGGCTATTTGAACGTCTGTAT 59.136 45.455 0.00 0.00 0.00 2.29
496 511 2.279741 GTCTGTATCCTTTGCATGCGA 58.720 47.619 14.09 8.74 0.00 5.10
523 538 7.961325 ATTTGATTGTGCGGACTTTAAAAAT 57.039 28.000 8.99 5.69 0.00 1.82
534 551 9.424319 TGCGGACTTTAAAAATATATGCAAAAA 57.576 25.926 0.00 0.00 0.00 1.94
567 585 3.789756 CGCTAATAACGTTGATGTCGTCT 59.210 43.478 11.99 0.00 40.69 4.18
576 594 4.682860 ACGTTGATGTCGTCTTTTCGTATT 59.317 37.500 0.00 0.00 36.85 1.89
586 604 3.058651 GTCTTTTCGTATTCGTGTCCGTC 59.941 47.826 0.00 0.00 38.33 4.79
587 605 1.981254 TTTCGTATTCGTGTCCGTCC 58.019 50.000 0.00 0.00 38.33 4.79
588 606 0.179192 TTCGTATTCGTGTCCGTCCG 60.179 55.000 0.00 0.00 38.33 4.79
589 607 1.135315 CGTATTCGTGTCCGTCCGT 59.865 57.895 0.00 0.00 35.01 4.69
590 608 1.129879 CGTATTCGTGTCCGTCCGTG 61.130 60.000 0.00 0.00 35.01 4.94
592 610 0.959867 TATTCGTGTCCGTCCGTGGA 60.960 55.000 0.00 0.00 35.04 4.02
598 616 2.987547 TCCGTCCGTGGACTGGTC 60.988 66.667 21.18 0.00 42.54 4.02
599 617 2.989824 CCGTCCGTGGACTGGTCT 60.990 66.667 16.51 0.00 42.54 3.85
605 623 0.393077 CCGTGGACTGGTCTTCTGTT 59.607 55.000 0.67 0.00 0.00 3.16
606 624 1.202651 CCGTGGACTGGTCTTCTGTTT 60.203 52.381 0.67 0.00 0.00 2.83
612 630 3.576648 GACTGGTCTTCTGTTTACGGAG 58.423 50.000 0.00 0.00 32.05 4.63
631 650 3.566553 GGAGGGATGGGGAGAAAATTTGT 60.567 47.826 0.00 0.00 0.00 2.83
644 663 2.496899 AATTTGTGGGTCGAGATGCT 57.503 45.000 0.00 0.00 0.00 3.79
685 704 1.229428 CGGCATCGGCATGAAAGTAT 58.771 50.000 0.00 0.00 43.71 2.12
686 705 2.224185 ACGGCATCGGCATGAAAGTATA 60.224 45.455 0.00 0.00 43.71 1.47
697 716 6.389906 GGCATGAAAGTATACAAAGCAAGTT 58.610 36.000 5.50 0.00 0.00 2.66
710 730 0.595095 GCAAGTTGTGAGAGCAAGGG 59.405 55.000 4.48 0.00 0.00 3.95
956 982 0.707616 AATTTCGATTCCCACCCCCA 59.292 50.000 0.00 0.00 0.00 4.96
989 1015 1.152839 GACCGAGGAGGAGGAGGAG 60.153 68.421 0.00 0.00 45.00 3.69
990 1016 2.197324 CCGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 45.00 4.30
991 1017 2.387772 CCGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 45.00 3.71
992 1018 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
993 1019 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
994 1020 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
995 1021 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
996 1022 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
997 1023 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1246 1272 0.326332 GTACTGCTAACCCCCTCCCT 60.326 60.000 0.00 0.00 0.00 4.20
1327 1385 2.584418 CTCTCAGCGGGATGTGCG 60.584 66.667 0.00 0.00 37.44 5.34
1367 1428 4.129380 TGAGATGTTGGGATAGAATTGCG 58.871 43.478 0.00 0.00 0.00 4.85
1633 1700 3.222354 GACGAGTTCGCCAGGGTGT 62.222 63.158 0.73 0.00 44.43 4.16
1671 1738 2.638363 GTTCTTCTCCAGTAACCCCAGT 59.362 50.000 0.00 0.00 0.00 4.00
1707 1774 1.913762 CCTCCGGGGTGAAGTCAGT 60.914 63.158 0.00 0.00 0.00 3.41
1713 1780 1.754745 GGGTGAAGTCAGTGAGGCA 59.245 57.895 0.00 0.00 0.00 4.75
1757 1824 5.957842 TTGGGACATTTCTGTTGTATGTC 57.042 39.130 0.00 0.00 44.60 3.06
1979 2047 6.767902 TGAAGAATGTCAAGCTTCTGTAAGTT 59.232 34.615 15.11 0.00 38.96 2.66
1991 2059 6.435904 AGCTTCTGTAAGTTCTACACATCTCT 59.564 38.462 0.00 0.00 34.99 3.10
1998 2066 8.904834 TGTAAGTTCTACACATCTCTATCTTCC 58.095 37.037 0.00 0.00 0.00 3.46
1999 2067 7.962995 AAGTTCTACACATCTCTATCTTCCA 57.037 36.000 0.00 0.00 0.00 3.53
2045 2187 8.520351 GTTTTTATAGTGTGCAAGTCCCTATTT 58.480 33.333 0.00 0.00 0.00 1.40
2052 2194 5.527582 GTGTGCAAGTCCCTATTTATACCAG 59.472 44.000 0.00 0.00 0.00 4.00
2096 2238 2.683211 ACAAAACCAGATTCCAGCCT 57.317 45.000 0.00 0.00 0.00 4.58
2100 2242 3.806949 AAACCAGATTCCAGCCTGTTA 57.193 42.857 0.00 0.00 0.00 2.41
2101 2243 3.356529 AACCAGATTCCAGCCTGTTAG 57.643 47.619 0.00 0.00 0.00 2.34
2115 2257 4.042187 AGCCTGTTAGAGTTTTCCATGTCT 59.958 41.667 0.00 0.00 0.00 3.41
2154 2296 4.561735 GGAAACTGTCATTTCCGAACAA 57.438 40.909 1.71 0.00 46.16 2.83
2161 2303 4.109050 TGTCATTTCCGAACAAAAGCAAC 58.891 39.130 0.00 0.00 0.00 4.17
2162 2304 4.142271 TGTCATTTCCGAACAAAAGCAACT 60.142 37.500 0.00 0.00 0.00 3.16
2163 2305 4.207019 GTCATTTCCGAACAAAAGCAACTG 59.793 41.667 0.00 0.00 0.00 3.16
2164 2306 3.859411 TTTCCGAACAAAAGCAACTGT 57.141 38.095 0.00 0.00 0.00 3.55
2165 2307 3.859411 TTCCGAACAAAAGCAACTGTT 57.141 38.095 0.00 0.00 38.46 3.16
2166 2308 4.966965 TTCCGAACAAAAGCAACTGTTA 57.033 36.364 0.00 0.00 35.93 2.41
2171 2313 5.229260 CCGAACAAAAGCAACTGTTAGTTTC 59.771 40.000 0.00 0.00 36.03 2.78
2191 2333 6.564709 TTTCATGAGAAACACAAGATGGAG 57.435 37.500 0.00 0.00 38.76 3.86
2192 2334 5.488262 TCATGAGAAACACAAGATGGAGA 57.512 39.130 0.00 0.00 0.00 3.71
2193 2335 5.868454 TCATGAGAAACACAAGATGGAGAA 58.132 37.500 0.00 0.00 0.00 2.87
2194 2336 6.298361 TCATGAGAAACACAAGATGGAGAAA 58.702 36.000 0.00 0.00 0.00 2.52
2205 2453 8.299570 ACACAAGATGGAGAAATTATGTGTTTC 58.700 33.333 2.64 0.00 45.48 2.78
2211 2459 7.441890 TGGAGAAATTATGTGTTTCGCTTAA 57.558 32.000 0.00 0.00 39.83 1.85
2223 2471 7.925993 TGTGTTTCGCTTAAAGAATATATGGG 58.074 34.615 0.00 0.00 0.00 4.00
2224 2472 7.012894 TGTGTTTCGCTTAAAGAATATATGGGG 59.987 37.037 0.00 0.00 0.00 4.96
2229 2477 8.335532 TCGCTTAAAGAATATATGGGGAAATG 57.664 34.615 0.00 0.00 0.00 2.32
2266 2514 4.283978 TGAATTACACTGTTCGGGTAAGGA 59.716 41.667 0.00 0.00 31.26 3.36
2271 2519 3.836562 ACACTGTTCGGGTAAGGAGTAAT 59.163 43.478 0.00 0.00 0.00 1.89
2286 2534 9.100554 GTAAGGAGTAATTTTAGAGGAGCTTTC 57.899 37.037 0.00 0.00 0.00 2.62
2297 2545 5.864628 AGAGGAGCTTTCGTAATTTCAAC 57.135 39.130 0.00 0.00 0.00 3.18
2319 2568 9.862371 TCAACTAAATTCTAGAGCTCTGTAAAG 57.138 33.333 26.78 15.34 0.00 1.85
2343 2593 0.631212 ACCCCTCATCCAAACATCCC 59.369 55.000 0.00 0.00 0.00 3.85
2348 2598 3.052944 CCCTCATCCAAACATCCCCTAAA 60.053 47.826 0.00 0.00 0.00 1.85
2352 2602 6.183361 CCTCATCCAAACATCCCCTAAATCTA 60.183 42.308 0.00 0.00 0.00 1.98
2354 2604 7.825709 TCATCCAAACATCCCCTAAATCTATT 58.174 34.615 0.00 0.00 0.00 1.73
2397 2647 3.814842 GTGGTGTGTCATGACTGAAATCA 59.185 43.478 25.55 12.28 31.85 2.57
2399 2649 4.067896 GGTGTGTCATGACTGAAATCACT 58.932 43.478 25.55 0.00 33.24 3.41
2416 2666 0.396811 ACTGAAACCCCTGTTCCGAG 59.603 55.000 0.00 0.00 32.15 4.63
2441 2691 5.464069 AGGAAACCCCTGTTCAACTAAATT 58.536 37.500 0.00 0.00 45.61 1.82
2443 2693 5.538813 GGAAACCCCTGTTCAACTAAATTCT 59.461 40.000 0.00 0.00 32.15 2.40
2444 2694 6.717997 GGAAACCCCTGTTCAACTAAATTCTA 59.282 38.462 0.00 0.00 32.15 2.10
2445 2695 7.094334 GGAAACCCCTGTTCAACTAAATTCTAG 60.094 40.741 0.00 0.00 32.15 2.43
2446 2696 6.697641 ACCCCTGTTCAACTAAATTCTAGA 57.302 37.500 0.00 0.00 0.00 2.43
2447 2697 6.712276 ACCCCTGTTCAACTAAATTCTAGAG 58.288 40.000 0.00 0.00 0.00 2.43
2448 2698 5.586643 CCCCTGTTCAACTAAATTCTAGAGC 59.413 44.000 0.00 0.00 0.00 4.09
2449 2699 6.410540 CCCTGTTCAACTAAATTCTAGAGCT 58.589 40.000 0.00 0.00 0.00 4.09
2450 2700 6.536941 CCCTGTTCAACTAAATTCTAGAGCTC 59.463 42.308 5.27 5.27 0.00 4.09
2451 2701 7.327214 CCTGTTCAACTAAATTCTAGAGCTCT 58.673 38.462 22.17 22.17 0.00 4.09
2452 2702 7.277539 CCTGTTCAACTAAATTCTAGAGCTCTG 59.722 40.741 26.78 15.63 0.00 3.35
2483 2735 1.690893 TGCAGCCAAGCAAAACCAATA 59.309 42.857 0.00 0.00 42.46 1.90
2500 2755 6.500589 ACCAATAGCTGTCTATAACACCAT 57.499 37.500 0.00 0.00 34.53 3.55
2506 2761 9.765795 AATAGCTGTCTATAACACCATAGTTTC 57.234 33.333 0.00 0.00 34.53 2.78
2521 2776 8.863049 CACCATAGTTTCATTTTTATGCACTTC 58.137 33.333 0.00 0.00 0.00 3.01
2525 2954 9.988350 ATAGTTTCATTTTTATGCACTTCTACG 57.012 29.630 0.00 0.00 0.00 3.51
2538 2967 1.461127 CTTCTACGTGTTTGGCAGCTC 59.539 52.381 0.00 0.00 0.00 4.09
2556 2985 4.153835 CAGCTCCTGAGATGTTTCTTGTTC 59.846 45.833 4.29 0.00 39.78 3.18
2585 3014 2.738521 CAGAGCGGTGTTGACGGG 60.739 66.667 0.00 0.00 0.00 5.28
2619 3048 5.102953 TGCTACTTTACCTGATCATTGCT 57.897 39.130 0.00 0.00 0.00 3.91
2666 3095 3.492383 CCATCGTGCAGATCATAGAACAC 59.508 47.826 0.00 0.00 37.52 3.32
2673 3102 4.892345 TGCAGATCATAGAACACTAGCTCT 59.108 41.667 0.00 0.00 0.00 4.09
2678 3107 6.488683 AGATCATAGAACACTAGCTCTACACC 59.511 42.308 0.00 0.00 0.00 4.16
2679 3108 5.756918 TCATAGAACACTAGCTCTACACCT 58.243 41.667 0.00 0.00 0.00 4.00
2680 3109 5.823570 TCATAGAACACTAGCTCTACACCTC 59.176 44.000 0.00 0.00 0.00 3.85
2910 3345 1.944024 TGCACTGGTTCGTCGAAATTT 59.056 42.857 9.70 0.00 0.00 1.82
2964 3399 1.537202 GATGTGAACACTGAACAGGGC 59.463 52.381 3.83 0.00 34.48 5.19
2980 3415 5.405935 ACAGGGCATGTTTCCTTTTTATC 57.594 39.130 0.00 0.00 39.96 1.75
2981 3416 5.086621 ACAGGGCATGTTTCCTTTTTATCT 58.913 37.500 0.00 0.00 39.96 1.98
2984 3419 6.019108 AGGGCATGTTTCCTTTTTATCTTCT 58.981 36.000 0.00 0.00 0.00 2.85
3003 3438 4.836125 TCTTTTTGCTTACTCTGCTTGG 57.164 40.909 0.00 0.00 0.00 3.61
3004 3439 3.569701 TCTTTTTGCTTACTCTGCTTGGG 59.430 43.478 0.00 0.00 0.00 4.12
3005 3440 1.247567 TTTGCTTACTCTGCTTGGGC 58.752 50.000 0.00 0.00 39.26 5.36
3031 3469 5.824429 TGAGCAAATTGTCAGCTATATTGC 58.176 37.500 0.41 0.41 41.34 3.56
3244 5079 6.453791 GGCTTCGAACTTGTTTTTCTTTTGAC 60.454 38.462 0.00 0.00 0.00 3.18
3319 5641 6.652481 TGTGCAATATTATGGTTGGGTTTTTG 59.348 34.615 0.00 0.00 0.00 2.44
3347 5696 3.025262 CTCAGTTGTAGTACTCCCTCCC 58.975 54.545 0.00 0.00 0.00 4.30
3364 6838 4.266714 CCTCCCTTTATTTTTACTCCGCA 58.733 43.478 0.00 0.00 0.00 5.69
3398 6872 9.646427 TGTTTGAAGTTAAACTATGCAAACTTT 57.354 25.926 19.67 3.02 41.08 2.66
3584 7441 2.111384 TGCTGAAGGAGGGAGTACATC 58.889 52.381 0.00 0.00 0.00 3.06
3585 7442 2.111384 GCTGAAGGAGGGAGTACATCA 58.889 52.381 0.00 0.00 0.00 3.07
3590 7447 1.771255 AGGAGGGAGTACATCATTGCC 59.229 52.381 0.00 0.00 0.00 4.52
3623 7480 4.222810 ACCTTGTTTGAACTTTTGCCTCTT 59.777 37.500 0.00 0.00 0.00 2.85
3625 7482 6.071051 ACCTTGTTTGAACTTTTGCCTCTTTA 60.071 34.615 0.00 0.00 0.00 1.85
3628 7492 8.785329 TTGTTTGAACTTTTGCCTCTTTATTT 57.215 26.923 0.00 0.00 0.00 1.40
3654 7518 6.942532 TTTGCTCAAATATGTGAGGGTATC 57.057 37.500 21.96 7.58 44.43 2.24
3656 7520 5.614308 TGCTCAAATATGTGAGGGTATCTG 58.386 41.667 21.96 0.00 44.43 2.90
3659 7523 6.647067 GCTCAAATATGTGAGGGTATCTGTAC 59.353 42.308 21.96 0.50 44.43 2.90
3660 7524 6.745116 TCAAATATGTGAGGGTATCTGTACG 58.255 40.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.764890 TGGTGCTGACAAAGGTAGCT 59.235 50.000 0.00 0.00 38.25 3.32
96 100 2.089980 CAGAACTCCAAATGCCCTCTG 58.910 52.381 0.00 0.00 0.00 3.35
200 206 3.115554 CTCGACGATCATGTTGTGCATA 58.884 45.455 0.00 0.00 35.74 3.14
384 396 3.263425 TCTCCTTTAACCACCCACTGATC 59.737 47.826 0.00 0.00 0.00 2.92
385 397 3.009143 GTCTCCTTTAACCACCCACTGAT 59.991 47.826 0.00 0.00 0.00 2.90
386 398 2.370849 GTCTCCTTTAACCACCCACTGA 59.629 50.000 0.00 0.00 0.00 3.41
404 416 2.106566 TGCAACCCAACATTGTTGTCT 58.893 42.857 24.01 9.03 42.91 3.41
483 498 3.342719 TCAAATAGTCGCATGCAAAGGA 58.657 40.909 19.57 3.42 0.00 3.36
496 511 6.811253 TTAAAGTCCGCACAATCAAATAGT 57.189 33.333 0.00 0.00 0.00 2.12
534 551 3.181487 ACGTTATTAGCGTACATCCGGTT 60.181 43.478 0.00 0.00 41.06 4.44
545 562 3.789756 AGACGACATCAACGTTATTAGCG 59.210 43.478 0.00 5.50 43.97 4.26
548 565 6.363088 ACGAAAAGACGACATCAACGTTATTA 59.637 34.615 0.00 0.00 43.97 0.98
553 570 2.466846 ACGAAAAGACGACATCAACGT 58.533 42.857 0.00 0.00 46.58 3.99
567 585 2.327568 GGACGGACACGAATACGAAAA 58.672 47.619 2.34 0.00 44.60 2.29
586 604 0.393077 AACAGAAGACCAGTCCACGG 59.607 55.000 0.00 0.00 0.00 4.94
587 605 2.240493 AAACAGAAGACCAGTCCACG 57.760 50.000 0.00 0.00 0.00 4.94
588 606 3.057734 CGTAAACAGAAGACCAGTCCAC 58.942 50.000 0.00 0.00 0.00 4.02
589 607 2.036733 CCGTAAACAGAAGACCAGTCCA 59.963 50.000 0.00 0.00 0.00 4.02
590 608 2.298163 TCCGTAAACAGAAGACCAGTCC 59.702 50.000 0.00 0.00 0.00 3.85
592 610 2.299297 CCTCCGTAAACAGAAGACCAGT 59.701 50.000 0.00 0.00 0.00 4.00
593 611 2.353803 CCCTCCGTAAACAGAAGACCAG 60.354 54.545 0.00 0.00 0.00 4.00
595 613 1.897802 TCCCTCCGTAAACAGAAGACC 59.102 52.381 0.00 0.00 0.00 3.85
596 614 3.522553 CATCCCTCCGTAAACAGAAGAC 58.477 50.000 0.00 0.00 0.00 3.01
597 615 2.500098 CCATCCCTCCGTAAACAGAAGA 59.500 50.000 0.00 0.00 0.00 2.87
598 616 2.420129 CCCATCCCTCCGTAAACAGAAG 60.420 54.545 0.00 0.00 0.00 2.85
599 617 1.557832 CCCATCCCTCCGTAAACAGAA 59.442 52.381 0.00 0.00 0.00 3.02
605 623 0.340558 TTCTCCCCATCCCTCCGTAA 59.659 55.000 0.00 0.00 0.00 3.18
606 624 0.340558 TTTCTCCCCATCCCTCCGTA 59.659 55.000 0.00 0.00 0.00 4.02
612 630 2.501316 CCACAAATTTTCTCCCCATCCC 59.499 50.000 0.00 0.00 0.00 3.85
644 663 3.312421 GTGCTGTCTGTTTGCTTGTTAGA 59.688 43.478 0.00 0.00 0.00 2.10
656 675 2.433145 CGATGCCGTGCTGTCTGT 60.433 61.111 0.00 0.00 0.00 3.41
657 676 3.190849 CCGATGCCGTGCTGTCTG 61.191 66.667 0.00 0.00 0.00 3.51
685 704 3.540617 TGCTCTCACAACTTGCTTTGTA 58.459 40.909 0.00 0.00 37.62 2.41
686 705 2.368439 TGCTCTCACAACTTGCTTTGT 58.632 42.857 0.00 0.00 40.46 2.83
697 716 1.434188 TTTCCTCCCTTGCTCTCACA 58.566 50.000 0.00 0.00 0.00 3.58
710 730 5.177511 CGCCCAATTTTCTTTCTTTTTCCTC 59.822 40.000 0.00 0.00 0.00 3.71
749 769 6.410337 CGTCGACTACCGTTTTCTATTCTAAG 59.590 42.308 14.70 0.00 39.75 2.18
928 954 2.427095 GGGAATCGAAATTGGAACTGGG 59.573 50.000 0.00 0.00 0.00 4.45
989 1015 1.535202 ATCGCCATCCTCCTCCTCC 60.535 63.158 0.00 0.00 0.00 4.30
990 1016 1.872197 CGATCGCCATCCTCCTCCTC 61.872 65.000 0.26 0.00 0.00 3.71
991 1017 1.905843 CGATCGCCATCCTCCTCCT 60.906 63.158 0.26 0.00 0.00 3.69
992 1018 2.203771 ACGATCGCCATCCTCCTCC 61.204 63.158 16.60 0.00 0.00 4.30
993 1019 1.006805 CACGATCGCCATCCTCCTC 60.007 63.158 16.60 0.00 0.00 3.71
994 1020 0.467474 TACACGATCGCCATCCTCCT 60.467 55.000 16.60 0.00 0.00 3.69
995 1021 0.318784 GTACACGATCGCCATCCTCC 60.319 60.000 16.60 0.00 0.00 4.30
996 1022 0.660595 CGTACACGATCGCCATCCTC 60.661 60.000 16.60 0.00 43.02 3.71
997 1023 1.359117 CGTACACGATCGCCATCCT 59.641 57.895 16.60 0.00 43.02 3.24
1246 1272 4.263550 ACTGACTAACTAGAGGCTGAGTGA 60.264 45.833 0.00 0.00 0.00 3.41
1327 1385 2.076100 TCAGATCACGTCATGTTTGCC 58.924 47.619 0.00 0.00 0.00 4.52
1367 1428 4.023193 ACTGTCCATGATGAACCGAAAAAC 60.023 41.667 0.00 0.00 0.00 2.43
1698 1765 2.037251 GGTACTTGCCTCACTGACTTCA 59.963 50.000 0.00 0.00 0.00 3.02
1707 1774 1.204704 CATCTCGTGGTACTTGCCTCA 59.795 52.381 0.00 0.00 0.00 3.86
1713 1780 1.001974 TGCAAGCATCTCGTGGTACTT 59.998 47.619 0.00 0.00 37.63 2.24
1757 1824 2.014068 GCCCAGCACTGCTAACTAAGG 61.014 57.143 2.39 0.00 36.40 2.69
2007 2075 9.341899 GCACACTATAAAAACCATTGTAGAAAG 57.658 33.333 0.00 0.00 30.96 2.62
2009 2077 8.397575 TGCACACTATAAAAACCATTGTAGAA 57.602 30.769 0.00 0.00 30.96 2.10
2011 2079 8.296713 ACTTGCACACTATAAAAACCATTGTAG 58.703 33.333 0.00 0.00 32.22 2.74
2013 2081 7.049799 ACTTGCACACTATAAAAACCATTGT 57.950 32.000 0.00 0.00 0.00 2.71
2014 2082 6.586082 GGACTTGCACACTATAAAAACCATTG 59.414 38.462 0.00 0.00 0.00 2.82
2015 2083 6.295067 GGGACTTGCACACTATAAAAACCATT 60.295 38.462 0.00 0.00 0.00 3.16
2016 2084 5.185056 GGGACTTGCACACTATAAAAACCAT 59.815 40.000 0.00 0.00 0.00 3.55
2018 2086 4.765339 AGGGACTTGCACACTATAAAAACC 59.235 41.667 0.00 0.00 27.25 3.27
2019 2087 5.959618 AGGGACTTGCACACTATAAAAAC 57.040 39.130 0.00 0.00 27.25 2.43
2026 2168 6.384595 TGGTATAAATAGGGACTTGCACACTA 59.615 38.462 0.00 0.00 41.75 2.74
2045 2187 3.719871 TCTGGAGGTGCTTTCTGGTATA 58.280 45.455 0.00 0.00 0.00 1.47
2071 2213 5.297029 GGCTGGAATCTGGTTTTGTAGATAC 59.703 44.000 0.00 0.00 33.49 2.24
2077 2219 2.242043 CAGGCTGGAATCTGGTTTTGT 58.758 47.619 6.61 0.00 0.00 2.83
2080 2222 2.683211 AACAGGCTGGAATCTGGTTT 57.317 45.000 20.34 0.00 35.47 3.27
2096 2238 5.306937 TCTGGAGACATGGAAAACTCTAACA 59.693 40.000 0.00 0.00 41.51 2.41
2100 2242 5.013495 TGAATCTGGAGACATGGAAAACTCT 59.987 40.000 0.00 0.00 41.51 3.24
2101 2243 5.248640 TGAATCTGGAGACATGGAAAACTC 58.751 41.667 0.00 0.00 41.51 3.01
2148 2290 5.797934 TGAAACTAACAGTTGCTTTTGTTCG 59.202 36.000 0.00 2.05 38.66 3.95
2154 2296 6.942532 TCTCATGAAACTAACAGTTGCTTT 57.057 33.333 0.00 0.00 38.66 3.51
2171 2313 6.564709 TTTCTCCATCTTGTGTTTCTCATG 57.435 37.500 0.00 0.00 0.00 3.07
2180 2322 7.482743 CGAAACACATAATTTCTCCATCTTGTG 59.517 37.037 0.00 0.00 39.20 3.33
2181 2323 7.530010 CGAAACACATAATTTCTCCATCTTGT 58.470 34.615 0.00 0.00 34.50 3.16
2188 2330 8.234546 TCTTTAAGCGAAACACATAATTTCTCC 58.765 33.333 0.00 0.00 34.50 3.71
2189 2331 9.607285 TTCTTTAAGCGAAACACATAATTTCTC 57.393 29.630 0.00 0.00 34.50 2.87
2202 2450 8.754991 TTTCCCCATATATTCTTTAAGCGAAA 57.245 30.769 0.00 0.00 0.00 3.46
2205 2453 8.335532 TCATTTCCCCATATATTCTTTAAGCG 57.664 34.615 0.00 0.00 0.00 4.68
2244 2492 4.824289 TCCTTACCCGAACAGTGTAATTC 58.176 43.478 0.00 0.00 0.00 2.17
2266 2514 9.668497 AATTACGAAAGCTCCTCTAAAATTACT 57.332 29.630 0.00 0.00 0.00 2.24
2271 2519 7.972832 TGAAATTACGAAAGCTCCTCTAAAA 57.027 32.000 0.00 0.00 0.00 1.52
2294 2542 9.862371 TCTTTACAGAGCTCTAGAATTTAGTTG 57.138 33.333 17.75 2.60 0.00 3.16
2319 2568 4.584743 GGATGTTTGGATGAGGGGTATTTC 59.415 45.833 0.00 0.00 0.00 2.17
2362 2612 5.919755 TGACACACCACACTAACTTAATCA 58.080 37.500 0.00 0.00 0.00 2.57
2364 2614 6.426937 GTCATGACACACCACACTAACTTAAT 59.573 38.462 21.07 0.00 0.00 1.40
2397 2647 0.396811 CTCGGAACAGGGGTTTCAGT 59.603 55.000 0.00 0.00 37.36 3.41
2399 2649 1.621814 CTACTCGGAACAGGGGTTTCA 59.378 52.381 0.00 0.00 37.36 2.69
2416 2666 3.503800 AGTTGAACAGGGGTTTCCTAC 57.496 47.619 0.00 0.00 46.12 3.18
2424 2674 5.586643 GCTCTAGAATTTAGTTGAACAGGGG 59.413 44.000 0.00 0.00 0.00 4.79
2426 2676 7.277539 CAGAGCTCTAGAATTTAGTTGAACAGG 59.722 40.741 17.75 0.00 0.00 4.00
2427 2677 7.816995 ACAGAGCTCTAGAATTTAGTTGAACAG 59.183 37.037 17.75 0.00 0.00 3.16
2428 2678 7.671302 ACAGAGCTCTAGAATTTAGTTGAACA 58.329 34.615 17.75 0.00 0.00 3.18
2429 2679 9.810545 ATACAGAGCTCTAGAATTTAGTTGAAC 57.189 33.333 17.75 0.00 0.00 3.18
2431 2681 9.809096 CAATACAGAGCTCTAGAATTTAGTTGA 57.191 33.333 17.75 0.00 0.00 3.18
2432 2682 9.039870 CCAATACAGAGCTCTAGAATTTAGTTG 57.960 37.037 17.75 10.60 0.00 3.16
2433 2683 7.713073 GCCAATACAGAGCTCTAGAATTTAGTT 59.287 37.037 17.75 0.00 0.00 2.24
2435 2685 7.212976 TGCCAATACAGAGCTCTAGAATTTAG 58.787 38.462 17.75 3.73 0.00 1.85
2437 2687 5.994250 TGCCAATACAGAGCTCTAGAATTT 58.006 37.500 17.75 3.45 0.00 1.82
2438 2688 5.620738 TGCCAATACAGAGCTCTAGAATT 57.379 39.130 17.75 13.03 0.00 2.17
2441 2691 4.026744 ACTTGCCAATACAGAGCTCTAGA 58.973 43.478 17.75 7.62 0.00 2.43
2443 2693 3.679917 GCACTTGCCAATACAGAGCTCTA 60.680 47.826 17.75 1.39 34.31 2.43
2444 2694 2.938756 GCACTTGCCAATACAGAGCTCT 60.939 50.000 11.45 11.45 34.31 4.09
2445 2695 1.399791 GCACTTGCCAATACAGAGCTC 59.600 52.381 5.27 5.27 34.31 4.09
2446 2696 1.271543 TGCACTTGCCAATACAGAGCT 60.272 47.619 0.00 0.00 41.18 4.09
2447 2697 1.131883 CTGCACTTGCCAATACAGAGC 59.868 52.381 0.00 0.00 41.18 4.09
2448 2698 1.131883 GCTGCACTTGCCAATACAGAG 59.868 52.381 0.00 0.00 41.18 3.35
2449 2699 1.167851 GCTGCACTTGCCAATACAGA 58.832 50.000 0.00 0.00 41.18 3.41
2450 2700 3.708195 GCTGCACTTGCCAATACAG 57.292 52.632 0.00 0.00 41.18 2.74
2500 2755 8.995220 ACGTAGAAGTGCATAAAAATGAAACTA 58.005 29.630 0.00 0.00 0.00 2.24
2506 2761 7.148983 CCAAACACGTAGAAGTGCATAAAAATG 60.149 37.037 0.00 0.00 45.45 2.32
2511 2766 3.187637 GCCAAACACGTAGAAGTGCATAA 59.812 43.478 0.00 0.00 45.45 1.90
2513 2768 1.535462 GCCAAACACGTAGAAGTGCAT 59.465 47.619 0.00 0.00 45.45 3.96
2515 2770 0.941542 TGCCAAACACGTAGAAGTGC 59.058 50.000 0.00 0.00 45.45 4.40
2516 2771 1.069906 GCTGCCAAACACGTAGAAGTG 60.070 52.381 0.00 0.00 46.83 3.16
2521 2776 0.320771 AGGAGCTGCCAAACACGTAG 60.321 55.000 0.00 0.00 40.02 3.51
2525 2954 0.250467 TCTCAGGAGCTGCCAAACAC 60.250 55.000 0.00 0.00 40.02 3.32
2538 2967 4.818546 ACACAGAACAAGAAACATCTCAGG 59.181 41.667 0.00 0.00 0.00 3.86
2556 2985 0.317269 CCGCTCTGCAACAAACACAG 60.317 55.000 0.00 0.00 0.00 3.66
2585 3014 1.826385 AAGTAGCAGCACAATGACCC 58.174 50.000 0.00 0.00 0.00 4.46
2619 3048 1.626356 ATAGGCCTCCGCAGAAAGCA 61.626 55.000 9.68 0.00 46.13 3.91
2666 3095 5.073428 TCATGTATGGAGGTGTAGAGCTAG 58.927 45.833 0.00 0.00 0.00 3.42
2673 3102 4.719273 TGGAACATCATGTATGGAGGTGTA 59.281 41.667 0.00 0.00 40.16 2.90
2678 3107 5.007039 CGAACTTGGAACATCATGTATGGAG 59.993 44.000 0.00 0.00 40.16 3.86
2679 3108 4.875536 CGAACTTGGAACATCATGTATGGA 59.124 41.667 0.00 0.00 40.16 3.41
2680 3109 4.035558 CCGAACTTGGAACATCATGTATGG 59.964 45.833 0.00 0.00 40.16 2.74
2910 3345 8.849543 AAAGGGAGGTACTATACATCAGTAAA 57.150 34.615 3.38 0.00 41.55 2.01
2964 3399 9.868389 GCAAAAAGAAGATAAAAAGGAAACATG 57.132 29.630 0.00 0.00 0.00 3.21
2977 3412 7.094634 CCAAGCAGAGTAAGCAAAAAGAAGATA 60.095 37.037 0.00 0.00 0.00 1.98
2978 3413 6.294397 CCAAGCAGAGTAAGCAAAAAGAAGAT 60.294 38.462 0.00 0.00 0.00 2.40
2979 3414 5.009010 CCAAGCAGAGTAAGCAAAAAGAAGA 59.991 40.000 0.00 0.00 0.00 2.87
2980 3415 5.218139 CCAAGCAGAGTAAGCAAAAAGAAG 58.782 41.667 0.00 0.00 0.00 2.85
2981 3416 4.037923 CCCAAGCAGAGTAAGCAAAAAGAA 59.962 41.667 0.00 0.00 0.00 2.52
2984 3419 2.035832 GCCCAAGCAGAGTAAGCAAAAA 59.964 45.455 0.00 0.00 39.53 1.94
3003 3438 1.689959 CTGACAATTTGCTCAACGCC 58.310 50.000 0.00 0.00 38.05 5.68
3004 3439 1.055338 GCTGACAATTTGCTCAACGC 58.945 50.000 0.00 0.00 39.77 4.84
3005 3440 2.693797 AGCTGACAATTTGCTCAACG 57.306 45.000 0.00 0.00 30.41 4.10
3031 3469 2.489329 ACTGCTTCCAAAACATCCATCG 59.511 45.455 0.00 0.00 0.00 3.84
3224 5059 7.326063 AGTTCAGTCAAAAGAAAAACAAGTTCG 59.674 33.333 0.00 0.00 0.00 3.95
3244 5079 1.208614 GCCTTGCGCTTCAGTTCAG 59.791 57.895 9.73 0.00 0.00 3.02
3319 5641 6.433716 AGGGAGTACTACAACTGAGTAAACTC 59.566 42.308 7.57 3.08 43.15 3.01
3551 7037 9.166222 TCCCTCCTTCAGCATATAAAACTTATA 57.834 33.333 0.00 0.00 0.00 0.98
3556 7042 5.685728 ACTCCCTCCTTCAGCATATAAAAC 58.314 41.667 0.00 0.00 0.00 2.43
3584 7441 2.185867 GTGGCTGGCATGGCAATG 59.814 61.111 23.47 13.51 44.02 2.82
3585 7442 3.078836 GGTGGCTGGCATGGCAAT 61.079 61.111 23.47 0.00 44.02 3.56
3590 7447 0.320073 CAAACAAGGTGGCTGGCATG 60.320 55.000 7.33 4.37 0.00 4.06
3637 7501 5.405571 GCGTACAGATACCCTCACATATTTG 59.594 44.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.