Multiple sequence alignment - TraesCS4D01G032700

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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 TraesCS4D01G032700 chr4D 100.000 3599 0 0 1 3599 14982675 14979077 0.000000e+00 6647.0
1 TraesCS4D01G032700 chr4D 88.966 145 14 2 482 626 64390632 64390490 1.030000e-40 178.0
2 TraesCS4D01G032700 chr4D 85.897 156 17 5 482 636 397390931 397390780 1.030000e-35 161.0
3 TraesCS4D01G032700 chr4B 88.796 2276 134 42 762 2977 24901620 24903834 0.000000e+00 2678.0
4 TraesCS4D01G032700 chr4B 97.496 639 15 1 2961 3599 24904270 24904907 0.000000e+00 1090.0
5 TraesCS4D01G032700 chr4B 91.866 418 28 3 2508 2925 24903857 24904268 2.410000e-161 579.0
6 TraesCS4D01G032700 chr4B 83.226 620 87 9 1 618 24895000 24895604 1.460000e-153 553.0
7 TraesCS4D01G032700 chr4B 85.920 348 48 1 1 348 24900803 24901149 1.580000e-98 370.0
8 TraesCS4D01G032700 chr4B 81.100 291 24 15 728 1001 24861639 24861915 1.690000e-48 204.0
9 TraesCS4D01G032700 chr4B 80.645 279 41 5 350 628 24901322 24901587 1.690000e-48 204.0
10 TraesCS4D01G032700 chr4B 85.279 197 14 6 762 955 24895644 24895828 4.740000e-44 189.0
11 TraesCS4D01G032700 chr4B 94.186 86 5 0 624 709 669101687 669101772 8.110000e-27 132.0
12 TraesCS4D01G032700 chr4B 97.143 35 1 0 701 735 594536875 594536841 3.880000e-05 60.2
13 TraesCS4D01G032700 chr3B 87.441 1903 148 32 1104 2977 452491431 452489591 0.000000e+00 2106.0
14 TraesCS4D01G032700 chr3B 97.809 639 13 1 2961 3599 452489119 452488482 0.000000e+00 1101.0
15 TraesCS4D01G032700 chr3B 93.095 420 21 3 2508 2925 452489534 452489121 3.070000e-170 608.0
16 TraesCS4D01G032700 chr3B 84.107 560 24 21 706 1228 452491904 452491373 6.990000e-132 481.0
17 TraesCS4D01G032700 chr4A 91.875 960 70 3 1357 2309 586447280 586448238 0.000000e+00 1334.0
18 TraesCS4D01G032700 chr4A 95.579 656 11 3 2961 3599 586449334 586449988 0.000000e+00 1035.0
19 TraesCS4D01G032700 chr4A 87.900 562 20 12 708 1222 586446591 586447151 5.110000e-173 617.0
20 TraesCS4D01G032700 chr4A 89.019 428 36 7 2509 2925 586448905 586449332 1.480000e-143 520.0
21 TraesCS4D01G032700 chr4A 83.397 524 66 13 2470 2977 586448330 586448848 1.960000e-127 466.0
22 TraesCS4D01G032700 chr4A 89.398 349 35 2 1 348 586445593 586445940 4.270000e-119 438.0
23 TraesCS4D01G032700 chr4A 86.897 145 17 2 482 626 533460153 533460011 1.030000e-35 161.0
24 TraesCS4D01G032700 chr4A 93.578 109 4 2 1220 1325 586447179 586447287 3.720000e-35 159.0
25 TraesCS4D01G032700 chr2B 83.267 251 35 5 482 728 15005409 15005656 1.300000e-54 224.0
26 TraesCS4D01G032700 chr2B 93.333 90 5 1 621 709 777636804 777636893 8.110000e-27 132.0
27 TraesCS4D01G032700 chr2B 94.737 38 2 0 698 735 153279227 153279264 3.880000e-05 60.2
28 TraesCS4D01G032700 chr2B 100.000 32 0 0 701 732 633576954 633576923 3.880000e-05 60.2
29 TraesCS4D01G032700 chr7B 88.276 145 15 1 482 626 106542867 106542725 4.780000e-39 172.0
30 TraesCS4D01G032700 chr2A 88.276 145 15 2 482 626 419206977 419206835 4.780000e-39 172.0
31 TraesCS4D01G032700 chr3A 87.162 148 15 2 479 626 21364621 21364478 7.990000e-37 165.0
32 TraesCS4D01G032700 chr3A 95.294 85 4 0 625 709 36857909 36857825 6.270000e-28 135.0
33 TraesCS4D01G032700 chr7D 81.915 188 28 5 479 664 619403984 619404167 1.730000e-33 154.0
34 TraesCS4D01G032700 chr6D 98.824 85 1 0 625 709 370690844 370690760 6.220000e-33 152.0
35 TraesCS4D01G032700 chr3D 90.625 96 9 0 621 716 584333720 584333625 1.050000e-25 128.0
36 TraesCS4D01G032700 chr7A 86.607 112 15 0 625 736 575100043 575099932 1.360000e-24 124.0
37 TraesCS4D01G032700 chr1D 91.209 91 8 0 619 709 481017021 481017111 1.360000e-24 124.0
38 TraesCS4D01G032700 chr2D 89.474 95 10 0 615 709 486498406 486498500 1.760000e-23 121.0
39 TraesCS4D01G032700 chr6A 97.143 35 1 0 701 735 367658794 367658828 3.880000e-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 TraesCS4D01G032700 chr4D 14979077 14982675 3598 True 6647.000000 6647 100.000000 1 3599 1 chr4D.!!$R1 3598
1 TraesCS4D01G032700 chr4B 24900803 24904907 4104 False 984.200000 2678 88.944600 1 3599 5 chr4B.!!$F4 3598
2 TraesCS4D01G032700 chr4B 24895000 24895828 828 False 371.000000 553 84.252500 1 955 2 chr4B.!!$F3 954
3 TraesCS4D01G032700 chr3B 452488482 452491904 3422 True 1074.000000 2106 90.613000 706 3599 4 chr3B.!!$R1 2893
4 TraesCS4D01G032700 chr4A 586445593 586449988 4395 False 652.714286 1334 90.106571 1 3599 7 chr4A.!!$F1 3598

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
966 1409 0.763035 ACCAGTAACGCCAGTCCTTT 59.237 50.0 0.0 0.0 0.0 3.11 F
1311 1837 0.036294 GGTATAATGAGAGGCCCCGC 60.036 60.0 0.0 0.0 0.0 6.13 F
1312 1838 0.389948 GTATAATGAGAGGCCCCGCG 60.390 60.0 0.0 0.0 0.0 6.46 F
1780 2318 0.462047 CGATTCGGAGAACAAGGGGG 60.462 60.0 0.0 0.0 45.9 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2619 0.179026 AGTAGGCGGATGCGAGTAGA 60.179 55.000 12.10 0.0 44.10 2.59 R
2357 2895 0.183492 TTGACCACTGCTGCTCCTTT 59.817 50.000 0.00 0.0 0.00 3.11 R
2441 2982 2.044252 ATGGCTTCTGCTGGGCTG 60.044 61.111 8.65 0.0 39.59 4.85 R
3313 4425 0.249489 GACGGTGATTCAGGGGATCG 60.249 60.000 0.00 0.0 0.00 3.69 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
29 31 1.578583 CTCCACCTTCGTCGTTTTGT 58.421 50.000 0.00 0.00 0.00 2.83
34 36 2.220133 CACCTTCGTCGTTTTGTGGTAG 59.780 50.000 0.00 0.00 0.00 3.18
46 48 4.991153 TTTGTGGTAGCAACATTCAACA 57.009 36.364 0.00 0.00 0.00 3.33
51 53 3.243704 TGGTAGCAACATTCAACAAAGCC 60.244 43.478 0.00 0.00 0.00 4.35
178 181 2.899339 GCAGATCAAGGGCCGCTC 60.899 66.667 0.00 0.00 0.00 5.03
217 220 3.507233 GGTCATTGATTGCTCTTGGTTGA 59.493 43.478 0.00 0.00 0.00 3.18
239 242 4.985538 AAAACCATGTTGTGACGGTAAA 57.014 36.364 0.00 0.00 0.00 2.01
247 250 5.421212 TGTTGTGACGGTAAATACAAACC 57.579 39.130 0.00 0.00 35.12 3.27
291 294 3.325201 GAGGGGATGCCCGTTCGTT 62.325 63.158 17.80 0.00 46.66 3.85
318 321 1.539712 GGGAGCGGTTTTCCTATACGG 60.540 57.143 0.00 0.00 37.95 4.02
348 351 7.603404 CCATTTAGAAAAGGCATCAATCAAACA 59.397 33.333 0.00 0.00 0.00 2.83
378 767 3.038417 GCACGTCGCAAGCTCACT 61.038 61.111 5.30 0.00 41.79 3.41
418 807 3.256631 GCGAATCCGGTATCTTAGGGTTA 59.743 47.826 0.00 0.00 36.06 2.85
420 809 5.225642 CGAATCCGGTATCTTAGGGTTAAC 58.774 45.833 0.00 0.00 0.00 2.01
468 857 1.839994 CCATGAGTAGACCACCACCAT 59.160 52.381 0.00 0.00 0.00 3.55
500 889 2.442236 TACTCCCTCCGTCCGTAAAT 57.558 50.000 0.00 0.00 0.00 1.40
505 894 4.895297 ACTCCCTCCGTCCGTAAATATAAA 59.105 41.667 0.00 0.00 0.00 1.40
508 897 5.047092 TCCCTCCGTCCGTAAATATAAATCC 60.047 44.000 0.00 0.00 0.00 3.01
509 898 5.046807 CCCTCCGTCCGTAAATATAAATCCT 60.047 44.000 0.00 0.00 0.00 3.24
510 899 6.461640 CCTCCGTCCGTAAATATAAATCCTT 58.538 40.000 0.00 0.00 0.00 3.36
511 900 6.932960 CCTCCGTCCGTAAATATAAATCCTTT 59.067 38.462 0.00 0.00 0.00 3.11
512 901 7.443272 CCTCCGTCCGTAAATATAAATCCTTTT 59.557 37.037 0.00 0.00 0.00 2.27
513 902 9.480053 CTCCGTCCGTAAATATAAATCCTTTTA 57.520 33.333 0.00 0.00 0.00 1.52
552 945 7.384439 TGAATTACATACGGAGCAAAATGAA 57.616 32.000 0.00 0.00 0.00 2.57
604 997 5.403897 ACATTCGTATGTAGCCGATTTTG 57.596 39.130 5.81 0.00 43.12 2.44
611 1004 6.200286 TCGTATGTAGCCGATTTTGAAATCTC 59.800 38.462 12.98 6.30 41.99 2.75
639 1033 7.912056 AAAAACTTATACTCCCTCCGTAAAC 57.088 36.000 0.00 0.00 0.00 2.01
640 1034 6.864151 AAACTTATACTCCCTCCGTAAACT 57.136 37.500 0.00 0.00 0.00 2.66
641 1035 7.961326 AAACTTATACTCCCTCCGTAAACTA 57.039 36.000 0.00 0.00 0.00 2.24
642 1036 7.961326 AACTTATACTCCCTCCGTAAACTAA 57.039 36.000 0.00 0.00 0.00 2.24
643 1037 8.544687 AACTTATACTCCCTCCGTAAACTAAT 57.455 34.615 0.00 0.00 0.00 1.73
644 1038 7.949434 ACTTATACTCCCTCCGTAAACTAATG 58.051 38.462 0.00 0.00 0.00 1.90
645 1039 7.562821 ACTTATACTCCCTCCGTAAACTAATGT 59.437 37.037 0.00 0.00 0.00 2.71
646 1040 8.995027 TTATACTCCCTCCGTAAACTAATGTA 57.005 34.615 0.00 0.00 0.00 2.29
647 1041 7.902920 ATACTCCCTCCGTAAACTAATGTAA 57.097 36.000 0.00 0.00 0.00 2.41
648 1042 6.218108 ACTCCCTCCGTAAACTAATGTAAG 57.782 41.667 0.00 0.00 0.00 2.34
649 1043 5.954150 ACTCCCTCCGTAAACTAATGTAAGA 59.046 40.000 0.00 0.00 0.00 2.10
650 1044 6.096564 ACTCCCTCCGTAAACTAATGTAAGAG 59.903 42.308 0.00 0.00 0.00 2.85
651 1045 5.048507 CCCTCCGTAAACTAATGTAAGAGC 58.951 45.833 0.00 0.00 0.00 4.09
652 1046 4.738740 CCTCCGTAAACTAATGTAAGAGCG 59.261 45.833 0.00 0.00 0.00 5.03
653 1047 5.314923 TCCGTAAACTAATGTAAGAGCGT 57.685 39.130 0.00 0.00 0.00 5.07
654 1048 5.713025 TCCGTAAACTAATGTAAGAGCGTT 58.287 37.500 0.00 0.00 0.00 4.84
655 1049 6.158598 TCCGTAAACTAATGTAAGAGCGTTT 58.841 36.000 0.00 0.00 0.00 3.60
656 1050 7.312154 TCCGTAAACTAATGTAAGAGCGTTTA 58.688 34.615 0.00 0.00 0.00 2.01
657 1051 7.485913 TCCGTAAACTAATGTAAGAGCGTTTAG 59.514 37.037 0.00 0.00 30.36 1.85
658 1052 7.485913 CCGTAAACTAATGTAAGAGCGTTTAGA 59.514 37.037 0.00 0.00 30.36 2.10
659 1053 9.017669 CGTAAACTAATGTAAGAGCGTTTAGAT 57.982 33.333 0.00 0.00 30.36 1.98
661 1055 8.997621 AAACTAATGTAAGAGCGTTTAGATCA 57.002 30.769 0.00 0.00 37.82 2.92
662 1056 7.988904 ACTAATGTAAGAGCGTTTAGATCAC 57.011 36.000 0.00 0.00 37.82 3.06
663 1057 7.773149 ACTAATGTAAGAGCGTTTAGATCACT 58.227 34.615 0.00 0.00 37.82 3.41
664 1058 8.900781 ACTAATGTAAGAGCGTTTAGATCACTA 58.099 33.333 0.00 0.00 37.82 2.74
665 1059 7.988904 AATGTAAGAGCGTTTAGATCACTAC 57.011 36.000 0.00 0.00 37.82 2.73
666 1060 6.754702 TGTAAGAGCGTTTAGATCACTACT 57.245 37.500 0.00 0.00 37.82 2.57
667 1061 7.154435 TGTAAGAGCGTTTAGATCACTACTT 57.846 36.000 0.00 0.00 37.82 2.24
668 1062 7.249147 TGTAAGAGCGTTTAGATCACTACTTC 58.751 38.462 0.00 0.00 37.82 3.01
669 1063 5.899120 AGAGCGTTTAGATCACTACTTCA 57.101 39.130 0.00 0.00 37.82 3.02
670 1064 5.885881 AGAGCGTTTAGATCACTACTTCAG 58.114 41.667 0.00 0.00 37.82 3.02
671 1065 5.416326 AGAGCGTTTAGATCACTACTTCAGT 59.584 40.000 0.00 0.00 37.82 3.41
672 1066 6.598457 AGAGCGTTTAGATCACTACTTCAGTA 59.402 38.462 0.00 0.00 37.82 2.74
673 1067 7.120873 AGAGCGTTTAGATCACTACTTCAGTAA 59.879 37.037 0.00 0.00 37.82 2.24
674 1068 7.773149 AGCGTTTAGATCACTACTTCAGTAAT 58.227 34.615 0.00 0.00 34.98 1.89
675 1069 7.916450 AGCGTTTAGATCACTACTTCAGTAATC 59.084 37.037 0.00 0.00 34.98 1.75
676 1070 7.916450 GCGTTTAGATCACTACTTCAGTAATCT 59.084 37.037 0.00 5.42 34.98 2.40
718 1112 8.487028 AGTTTACAGAGGGAGTATTTAGGAATG 58.513 37.037 0.00 0.00 0.00 2.67
720 1114 5.538877 ACAGAGGGAGTATTTAGGAATGGA 58.461 41.667 0.00 0.00 0.00 3.41
721 1115 5.604650 ACAGAGGGAGTATTTAGGAATGGAG 59.395 44.000 0.00 0.00 0.00 3.86
966 1409 0.763035 ACCAGTAACGCCAGTCCTTT 59.237 50.000 0.00 0.00 0.00 3.11
967 1410 1.270678 ACCAGTAACGCCAGTCCTTTC 60.271 52.381 0.00 0.00 0.00 2.62
1309 1835 2.621070 TCAGGTATAATGAGAGGCCCC 58.379 52.381 0.00 0.00 0.00 5.80
1310 1836 1.276421 CAGGTATAATGAGAGGCCCCG 59.724 57.143 0.00 0.00 0.00 5.73
1311 1837 0.036294 GGTATAATGAGAGGCCCCGC 60.036 60.000 0.00 0.00 0.00 6.13
1312 1838 0.389948 GTATAATGAGAGGCCCCGCG 60.390 60.000 0.00 0.00 0.00 6.46
1313 1839 1.541310 TATAATGAGAGGCCCCGCGG 61.541 60.000 21.04 21.04 0.00 6.46
1314 1840 3.906400 TATAATGAGAGGCCCCGCGGA 62.906 57.143 30.73 3.37 0.00 5.54
1532 2070 2.104331 CGAGATTGCTACCGGCGT 59.896 61.111 6.01 0.00 45.43 5.68
1580 2118 2.228711 CCTCTGGATGTCAGGGCAT 58.771 57.895 0.00 0.00 42.63 4.40
1780 2318 0.462047 CGATTCGGAGAACAAGGGGG 60.462 60.000 0.00 0.00 45.90 5.40
1965 2503 1.916777 GAACGGGAGGAGGGACCAA 60.917 63.158 0.00 0.00 42.04 3.67
2007 2545 4.143333 CGCGGTCGGAGGAATGGT 62.143 66.667 0.00 0.00 0.00 3.55
2046 2584 3.778075 TCTGGGAAGTAAAATCCGATGGA 59.222 43.478 0.00 0.00 37.87 3.41
2081 2619 2.125225 GGAGGTGGAGGGGAAGGT 59.875 66.667 0.00 0.00 0.00 3.50
2083 2621 1.081277 GAGGTGGAGGGGAAGGTCT 59.919 63.158 0.00 0.00 0.00 3.85
2097 2635 2.491022 GGTCTACTCGCATCCGCCT 61.491 63.158 0.00 0.00 33.11 5.52
2273 2811 4.043310 TGATCAAGGAATGAACAGGAAGGT 59.957 41.667 0.00 0.00 42.54 3.50
2402 2940 2.225343 TGAACCAGGAGGCAAATTCCAT 60.225 45.455 0.00 0.00 39.06 3.41
2441 2982 1.086634 GTTGTGGAGATGAGAGCCGC 61.087 60.000 0.00 0.00 0.00 6.53
2646 3187 1.133637 TGGTAACATGTGCCAGTGGTT 60.134 47.619 15.89 0.00 46.17 3.67
2733 3828 0.038343 TTTGCGGGCTTTGAGATTGC 60.038 50.000 0.00 0.00 0.00 3.56
2749 3844 2.996249 TTGCCAAATTGGTTTGCTGA 57.004 40.000 14.17 0.00 42.66 4.26
2821 3916 7.781548 AAATTCCTGCTGCAATTAAATCATC 57.218 32.000 3.02 0.00 0.00 2.92
2899 3994 3.071312 ACAAAAAGGCATGGAATTGCAGA 59.929 39.130 5.69 0.00 44.59 4.26
2925 4020 7.918076 TGAGGATGGTGAACTAGAATTAACTT 58.082 34.615 0.00 0.00 0.00 2.66
2926 4021 7.824289 TGAGGATGGTGAACTAGAATTAACTTG 59.176 37.037 0.00 0.00 0.00 3.16
2927 4022 7.690256 AGGATGGTGAACTAGAATTAACTTGT 58.310 34.615 0.00 0.00 0.00 3.16
2928 4023 8.822805 AGGATGGTGAACTAGAATTAACTTGTA 58.177 33.333 0.00 0.00 0.00 2.41
2929 4024 9.614792 GGATGGTGAACTAGAATTAACTTGTAT 57.385 33.333 0.00 0.00 0.00 2.29
2931 4026 9.959721 ATGGTGAACTAGAATTAACTTGTATGT 57.040 29.630 0.00 0.00 0.00 2.29
2932 4027 9.214957 TGGTGAACTAGAATTAACTTGTATGTG 57.785 33.333 0.00 0.00 0.00 3.21
2933 4028 8.175716 GGTGAACTAGAATTAACTTGTATGTGC 58.824 37.037 0.00 0.00 0.00 4.57
2934 4029 8.717821 GTGAACTAGAATTAACTTGTATGTGCA 58.282 33.333 0.00 0.00 0.00 4.57
2935 4030 9.278978 TGAACTAGAATTAACTTGTATGTGCAA 57.721 29.630 0.00 0.00 0.00 4.08
2938 4033 8.184192 ACTAGAATTAACTTGTATGTGCAATGC 58.816 33.333 0.00 0.00 0.00 3.56
2939 4034 6.923012 AGAATTAACTTGTATGTGCAATGCA 58.077 32.000 2.72 2.72 35.60 3.96
2940 4035 7.549839 AGAATTAACTTGTATGTGCAATGCAT 58.450 30.769 12.38 0.00 41.91 3.96
2941 4036 8.036575 AGAATTAACTTGTATGTGCAATGCATT 58.963 29.630 12.38 5.99 41.91 3.56
2942 4037 8.550710 AATTAACTTGTATGTGCAATGCATTT 57.449 26.923 12.38 4.57 41.91 2.32
2943 4038 7.579589 TTAACTTGTATGTGCAATGCATTTC 57.420 32.000 12.38 5.52 41.91 2.17
2944 4039 5.136816 ACTTGTATGTGCAATGCATTTCA 57.863 34.783 12.38 8.69 41.91 2.69
2945 4040 4.925054 ACTTGTATGTGCAATGCATTTCAC 59.075 37.500 28.35 28.35 41.91 3.18
2946 4041 4.787260 TGTATGTGCAATGCATTTCACT 57.213 36.364 32.32 22.98 41.91 3.41
2947 4042 4.487019 TGTATGTGCAATGCATTTCACTG 58.513 39.130 32.32 15.57 41.91 3.66
2948 4043 3.945981 ATGTGCAATGCATTTCACTGA 57.054 38.095 32.32 19.77 41.91 3.41
2949 4044 3.945981 TGTGCAATGCATTTCACTGAT 57.054 38.095 32.32 0.72 41.91 2.90
2950 4045 3.840468 TGTGCAATGCATTTCACTGATC 58.160 40.909 32.32 14.37 41.91 2.92
2951 4046 3.508402 TGTGCAATGCATTTCACTGATCT 59.492 39.130 32.32 0.00 41.91 2.75
2952 4047 4.021807 TGTGCAATGCATTTCACTGATCTT 60.022 37.500 32.32 0.00 41.91 2.40
2953 4048 4.927425 GTGCAATGCATTTCACTGATCTTT 59.073 37.500 27.95 0.00 41.91 2.52
2954 4049 4.926832 TGCAATGCATTTCACTGATCTTTG 59.073 37.500 9.83 0.00 31.71 2.77
2955 4050 4.927425 GCAATGCATTTCACTGATCTTTGT 59.073 37.500 9.83 0.00 0.00 2.83
2956 4051 5.163992 GCAATGCATTTCACTGATCTTTGTG 60.164 40.000 9.83 1.16 35.68 3.33
2957 4052 5.970317 ATGCATTTCACTGATCTTTGTGA 57.030 34.783 10.96 10.96 40.86 3.58
3313 4425 9.212641 ACATCACATATTGCTTCATATACTGAC 57.787 33.333 0.00 0.00 32.17 3.51
3348 4460 4.161001 TCACCGTCTAATTTCTACTTCCCC 59.839 45.833 0.00 0.00 0.00 4.81
3411 4523 4.262506 GGGAAGTACCTGCTCATACCATAC 60.263 50.000 0.00 0.00 38.98 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 3.243704 GGCTTTGTTGAATGTTGCTACCA 60.244 43.478 0.00 0.00 0.00 3.25
34 36 1.139163 CCGGCTTTGTTGAATGTTGC 58.861 50.000 0.00 0.00 0.00 4.17
68 70 0.739813 ATCTAGTTCCCGTGCGCAAC 60.740 55.000 14.00 6.31 0.00 4.17
75 77 5.799978 ATATCCCTCTATCTAGTTCCCGT 57.200 43.478 0.00 0.00 0.00 5.28
146 149 1.302832 CTGCCACAGTCCTTGGTCC 60.303 63.158 0.00 0.00 36.40 4.46
151 154 1.004044 CCTTGATCTGCCACAGTCCTT 59.996 52.381 0.00 0.00 32.61 3.36
156 159 1.751927 GGCCCTTGATCTGCCACAG 60.752 63.158 10.09 0.00 44.70 3.66
175 178 1.794222 CGTTCCGTTTCCATGGAGC 59.206 57.895 15.53 11.13 39.44 4.70
178 181 2.478746 CGCGTTCCGTTTCCATGG 59.521 61.111 4.97 4.97 0.00 3.66
196 199 4.771590 TCAACCAAGAGCAATCAATGAC 57.228 40.909 0.00 0.00 0.00 3.06
217 220 4.985538 TTACCGTCACAACATGGTTTTT 57.014 36.364 0.00 0.00 35.93 1.94
239 242 1.063912 CGTGCATGCATCGGTTTGTAT 59.936 47.619 25.64 0.00 0.00 2.29
247 250 2.816360 CTGGTCCGTGCATGCATCG 61.816 63.158 25.64 25.68 0.00 3.84
291 294 0.035439 GAAAACCGCTCCCAGATCCA 60.035 55.000 0.00 0.00 0.00 3.41
348 351 1.644786 GACGTGCAATAAAGGCGCCT 61.645 55.000 27.08 27.08 38.50 5.52
370 759 5.047306 GGCTTTTATAAAACCCAGTGAGCTT 60.047 40.000 14.82 0.00 0.00 3.74
378 767 1.473278 CGCGGGCTTTTATAAAACCCA 59.527 47.619 28.81 7.80 38.25 4.51
397 786 5.225642 GTTAACCCTAAGATACCGGATTCG 58.774 45.833 9.46 0.00 0.00 3.34
405 794 5.595952 TCCCTCTTCGTTAACCCTAAGATAC 59.404 44.000 11.15 0.00 0.00 2.24
418 807 0.818296 CATCCTCGTCCCTCTTCGTT 59.182 55.000 0.00 0.00 0.00 3.85
420 809 0.665835 CTCATCCTCGTCCCTCTTCG 59.334 60.000 0.00 0.00 0.00 3.79
457 846 0.958876 GGAAACCGATGGTGGTGGTC 60.959 60.000 0.00 0.00 42.89 4.02
468 857 3.708121 GGAGGGAGTATTTAGGAAACCGA 59.292 47.826 0.00 0.00 0.00 4.69
524 917 9.897744 CATTTTGCTCCGTATGTAATTCATATT 57.102 29.630 0.00 0.00 40.54 1.28
530 923 7.995289 TCATTCATTTTGCTCCGTATGTAATT 58.005 30.769 0.00 0.00 0.00 1.40
620 1014 7.949434 ACATTAGTTTACGGAGGGAGTATAAG 58.051 38.462 0.00 0.00 0.00 1.73
628 1022 5.048507 GCTCTTACATTAGTTTACGGAGGG 58.951 45.833 0.00 0.00 0.00 4.30
629 1023 4.738740 CGCTCTTACATTAGTTTACGGAGG 59.261 45.833 0.00 0.00 0.00 4.30
630 1024 5.338365 ACGCTCTTACATTAGTTTACGGAG 58.662 41.667 0.00 0.00 0.00 4.63
631 1025 5.314923 ACGCTCTTACATTAGTTTACGGA 57.685 39.130 0.00 0.00 0.00 4.69
632 1026 6.399204 AAACGCTCTTACATTAGTTTACGG 57.601 37.500 0.00 0.00 31.14 4.02
633 1027 8.385789 TCTAAACGCTCTTACATTAGTTTACG 57.614 34.615 0.00 0.00 34.29 3.18
636 1030 8.870879 GTGATCTAAACGCTCTTACATTAGTTT 58.129 33.333 0.00 0.00 36.11 2.66
637 1031 8.251721 AGTGATCTAAACGCTCTTACATTAGTT 58.748 33.333 0.00 0.00 0.00 2.24
638 1032 7.773149 AGTGATCTAAACGCTCTTACATTAGT 58.227 34.615 0.00 0.00 0.00 2.24
639 1033 9.171701 GTAGTGATCTAAACGCTCTTACATTAG 57.828 37.037 0.00 0.00 0.00 1.73
640 1034 8.900781 AGTAGTGATCTAAACGCTCTTACATTA 58.099 33.333 0.00 0.00 0.00 1.90
641 1035 7.773149 AGTAGTGATCTAAACGCTCTTACATT 58.227 34.615 0.00 0.00 0.00 2.71
642 1036 7.336161 AGTAGTGATCTAAACGCTCTTACAT 57.664 36.000 0.00 0.00 0.00 2.29
643 1037 6.754702 AGTAGTGATCTAAACGCTCTTACA 57.245 37.500 0.00 0.00 0.00 2.41
644 1038 7.249147 TGAAGTAGTGATCTAAACGCTCTTAC 58.751 38.462 0.00 0.00 0.00 2.34
645 1039 7.120873 ACTGAAGTAGTGATCTAAACGCTCTTA 59.879 37.037 0.00 0.00 38.49 2.10
646 1040 6.071840 ACTGAAGTAGTGATCTAAACGCTCTT 60.072 38.462 0.00 0.00 38.49 2.85
647 1041 5.416326 ACTGAAGTAGTGATCTAAACGCTCT 59.584 40.000 0.00 0.00 38.49 4.09
648 1042 5.642686 ACTGAAGTAGTGATCTAAACGCTC 58.357 41.667 0.00 0.00 38.49 5.03
649 1043 5.646577 ACTGAAGTAGTGATCTAAACGCT 57.353 39.130 0.00 0.00 38.49 5.07
650 1044 7.988904 ATTACTGAAGTAGTGATCTAAACGC 57.011 36.000 0.00 0.00 40.65 4.84
689 1083 9.725206 TCCTAAATACTCCCTCTGTAAACTATT 57.275 33.333 0.00 0.00 0.00 1.73
690 1084 9.725206 TTCCTAAATACTCCCTCTGTAAACTAT 57.275 33.333 0.00 0.00 0.00 2.12
691 1085 9.725206 ATTCCTAAATACTCCCTCTGTAAACTA 57.275 33.333 0.00 0.00 0.00 2.24
692 1086 8.487028 CATTCCTAAATACTCCCTCTGTAAACT 58.513 37.037 0.00 0.00 0.00 2.66
693 1087 7.715686 CCATTCCTAAATACTCCCTCTGTAAAC 59.284 40.741 0.00 0.00 0.00 2.01
694 1088 7.626084 TCCATTCCTAAATACTCCCTCTGTAAA 59.374 37.037 0.00 0.00 0.00 2.01
695 1089 7.136885 TCCATTCCTAAATACTCCCTCTGTAA 58.863 38.462 0.00 0.00 0.00 2.41
696 1090 6.689561 TCCATTCCTAAATACTCCCTCTGTA 58.310 40.000 0.00 0.00 0.00 2.74
697 1091 5.538877 TCCATTCCTAAATACTCCCTCTGT 58.461 41.667 0.00 0.00 0.00 3.41
698 1092 5.012561 CCTCCATTCCTAAATACTCCCTCTG 59.987 48.000 0.00 0.00 0.00 3.35
699 1093 5.158889 CCTCCATTCCTAAATACTCCCTCT 58.841 45.833 0.00 0.00 0.00 3.69
700 1094 4.287326 CCCTCCATTCCTAAATACTCCCTC 59.713 50.000 0.00 0.00 0.00 4.30
701 1095 4.077387 TCCCTCCATTCCTAAATACTCCCT 60.077 45.833 0.00 0.00 0.00 4.20
702 1096 4.240323 TCCCTCCATTCCTAAATACTCCC 58.760 47.826 0.00 0.00 0.00 4.30
703 1097 4.908481 ACTCCCTCCATTCCTAAATACTCC 59.092 45.833 0.00 0.00 0.00 3.85
704 1098 6.783482 ACTACTCCCTCCATTCCTAAATACTC 59.217 42.308 0.00 0.00 0.00 2.59
718 1112 4.906060 ACCATGGTATTTACTACTCCCTCC 59.094 45.833 18.10 0.00 0.00 4.30
720 1114 4.906060 GGACCATGGTATTTACTACTCCCT 59.094 45.833 19.80 0.00 0.00 4.20
721 1115 4.657039 TGGACCATGGTATTTACTACTCCC 59.343 45.833 19.80 10.61 0.00 4.30
1258 1781 2.266055 CGAGGAGGTGCCCTTCAC 59.734 66.667 2.73 0.00 44.90 3.18
1493 2025 2.631580 GGGTCGCCGGCAATCAAAA 61.632 57.895 28.98 0.00 0.00 2.44
1520 2058 2.740826 GCTTGACGCCGGTAGCAA 60.741 61.111 1.90 4.03 44.04 3.91
1532 2070 1.990060 CTCTTCTCCCCCGGCTTGA 60.990 63.158 0.00 0.00 0.00 3.02
1541 2079 0.182299 CTCCCCATTGCTCTTCTCCC 59.818 60.000 0.00 0.00 0.00 4.30
1580 2118 2.350895 CACTCGTCCCCAATGCCA 59.649 61.111 0.00 0.00 0.00 4.92
1659 2197 3.562176 CCTTCTTCCCCTTGTGCTTGTAT 60.562 47.826 0.00 0.00 0.00 2.29
1754 2292 1.538512 TGTTCTCCGAATCGACGACTT 59.461 47.619 3.36 0.00 35.09 3.01
1780 2318 2.887783 TCTGATTACTCGATCCAGCCTC 59.112 50.000 0.00 0.00 0.00 4.70
1938 2476 2.267642 CTCCCGTTCGGCCAATCA 59.732 61.111 2.24 0.00 0.00 2.57
1995 2533 0.830648 GACCATCACCATTCCTCCGA 59.169 55.000 0.00 0.00 0.00 4.55
2046 2584 2.118294 GGCTGCTTTCCCCCAAGT 59.882 61.111 0.00 0.00 0.00 3.16
2081 2619 0.179026 AGTAGGCGGATGCGAGTAGA 60.179 55.000 12.10 0.00 44.10 2.59
2083 2621 0.464916 TCAGTAGGCGGATGCGAGTA 60.465 55.000 12.10 0.00 44.10 2.59
2097 2635 0.681175 TGTTGCTGCTGCTCTCAGTA 59.319 50.000 17.00 0.00 42.29 2.74
2149 2687 4.309933 CCAAAGTCCTCAAATTTTGCCTC 58.690 43.478 4.19 0.00 31.03 4.70
2208 2746 2.267006 CTGTCAGCAGCCGGATGT 59.733 61.111 22.68 5.18 35.77 3.06
2273 2811 2.986019 TCCCCAAAGTCCTCAGATTTGA 59.014 45.455 0.00 0.00 36.28 2.69
2311 2849 2.202851 CGGCTGCGCTCTCATCTT 60.203 61.111 9.73 0.00 0.00 2.40
2357 2895 0.183492 TTGACCACTGCTGCTCCTTT 59.817 50.000 0.00 0.00 0.00 3.11
2441 2982 2.044252 ATGGCTTCTGCTGGGCTG 60.044 61.111 8.65 0.00 39.59 4.85
2488 3029 2.282391 GCTGTGACCACCATGGCA 60.282 61.111 13.04 0.00 42.67 4.92
2492 3033 2.665000 CTCGGCTGTGACCACCAT 59.335 61.111 0.00 0.00 0.00 3.55
2646 3187 6.899393 AGCACCTTCATTACTTGAAAATCA 57.101 33.333 0.00 0.00 43.64 2.57
2690 3776 2.949177 ACATGGACACCTTTGCACTA 57.051 45.000 0.00 0.00 0.00 2.74
2697 3792 2.817839 GCAAACCCTACATGGACACCTT 60.818 50.000 0.00 0.00 38.35 3.50
2733 3828 4.448732 GCTAAGTTCAGCAAACCAATTTGG 59.551 41.667 14.02 14.02 44.64 3.28
2749 3844 4.860022 ACCAATCTGGCAATAGCTAAGTT 58.140 39.130 0.00 0.00 42.67 2.66
2790 3885 2.715046 TGCAGCAGGAATTTACAGAGG 58.285 47.619 0.00 0.00 0.00 3.69
2798 3893 6.880484 TGATGATTTAATTGCAGCAGGAATT 58.120 32.000 12.90 12.90 45.93 2.17
2848 3943 4.218417 CGATCTGTTTGGAACCCAAGAATT 59.782 41.667 0.00 0.00 44.84 2.17
2899 3994 8.095452 AGTTAATTCTAGTTCACCATCCTCAT 57.905 34.615 0.00 0.00 0.00 2.90
2925 4020 4.217983 TCAGTGAAATGCATTGCACATACA 59.782 37.500 39.43 23.26 46.59 2.29
2926 4021 4.735985 TCAGTGAAATGCATTGCACATAC 58.264 39.130 39.43 21.43 46.59 2.39
2927 4022 5.358725 AGATCAGTGAAATGCATTGCACATA 59.641 36.000 39.43 30.05 46.59 2.29
2928 4023 3.945981 TCAGTGAAATGCATTGCACAT 57.054 38.095 39.43 26.49 46.59 3.21
2929 4024 3.508402 AGATCAGTGAAATGCATTGCACA 59.492 39.130 39.43 26.63 46.59 4.57
2930 4025 4.106029 AGATCAGTGAAATGCATTGCAC 57.894 40.909 34.53 34.53 44.92 4.57
2931 4026 4.794278 AAGATCAGTGAAATGCATTGCA 57.206 36.364 16.56 16.56 44.86 4.08
2932 4027 4.927425 ACAAAGATCAGTGAAATGCATTGC 59.073 37.500 13.82 12.24 34.50 3.56
2933 4028 6.153756 TCACAAAGATCAGTGAAATGCATTG 58.846 36.000 13.82 0.11 41.42 2.82
2934 4029 6.335471 TCACAAAGATCAGTGAAATGCATT 57.665 33.333 5.99 5.99 41.42 3.56
2935 4030 5.970317 TCACAAAGATCAGTGAAATGCAT 57.030 34.783 11.68 0.00 41.42 3.96
2942 4037 9.119418 TCAGTAAATTTTCACAAAGATCAGTGA 57.881 29.630 10.45 10.45 42.55 3.41
2943 4038 9.173939 GTCAGTAAATTTTCACAAAGATCAGTG 57.826 33.333 0.00 0.86 37.10 3.66
2944 4039 9.125026 AGTCAGTAAATTTTCACAAAGATCAGT 57.875 29.630 0.00 0.00 0.00 3.41
2945 4040 9.390795 CAGTCAGTAAATTTTCACAAAGATCAG 57.609 33.333 0.00 0.00 0.00 2.90
2946 4041 9.119418 TCAGTCAGTAAATTTTCACAAAGATCA 57.881 29.630 0.00 0.00 0.00 2.92
2948 4043 9.903682 CATCAGTCAGTAAATTTTCACAAAGAT 57.096 29.630 0.00 0.00 0.00 2.40
2949 4044 7.862372 GCATCAGTCAGTAAATTTTCACAAAGA 59.138 33.333 0.00 0.00 0.00 2.52
2950 4045 7.648908 TGCATCAGTCAGTAAATTTTCACAAAG 59.351 33.333 0.00 0.00 0.00 2.77
2951 4046 7.487484 TGCATCAGTCAGTAAATTTTCACAAA 58.513 30.769 0.00 0.00 0.00 2.83
2952 4047 7.036996 TGCATCAGTCAGTAAATTTTCACAA 57.963 32.000 0.00 0.00 0.00 3.33
2953 4048 6.631971 TGCATCAGTCAGTAAATTTTCACA 57.368 33.333 0.00 0.00 0.00 3.58
2954 4049 7.086376 ACATGCATCAGTCAGTAAATTTTCAC 58.914 34.615 0.00 0.00 0.00 3.18
2955 4050 7.218228 ACATGCATCAGTCAGTAAATTTTCA 57.782 32.000 0.00 0.00 0.00 2.69
2956 4051 8.524870 AAACATGCATCAGTCAGTAAATTTTC 57.475 30.769 0.00 0.00 0.00 2.29
2957 4052 7.599998 GGAAACATGCATCAGTCAGTAAATTTT 59.400 33.333 0.00 0.00 0.00 1.82
2958 4053 7.039504 AGGAAACATGCATCAGTCAGTAAATTT 60.040 33.333 0.00 0.00 0.00 1.82
2959 4054 6.435277 AGGAAACATGCATCAGTCAGTAAATT 59.565 34.615 0.00 0.00 0.00 1.82
3302 4414 4.382386 TCAGGGGATCGTCAGTATATGA 57.618 45.455 0.00 0.00 34.79 2.15
3313 4425 0.249489 GACGGTGATTCAGGGGATCG 60.249 60.000 0.00 0.00 0.00 3.69
3348 4460 2.125552 TGCGAGGATGAAGCGGTG 60.126 61.111 0.00 0.00 0.00 4.94
3411 4523 1.598601 GAGGAGTTCTACGCTCTACCG 59.401 57.143 0.00 0.00 33.73 4.02


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

AutoCloner maintained by Alex Coulton.