Multiple sequence alignment - TraesCS3D01G244700

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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 TraesCS3D01G244700 chr3D 100.000 2840 0 0 1 2840 339862833 339859994 0.000000e+00 5245.0
1 TraesCS3D01G244700 chr3D 81.833 600 45 24 1 549 482834046 482833460 2.010000e-121 446.0
2 TraesCS3D01G244700 chr3D 96.850 127 4 0 547 673 123898837 123898963 2.220000e-51 213.0
3 TraesCS3D01G244700 chr3D 94.203 69 4 0 2772 2840 2928768 2928700 3.870000e-19 106.0
4 TraesCS3D01G244700 chr3D 94.203 69 4 0 2772 2840 67728793 67728725 3.870000e-19 106.0
5 TraesCS3D01G244700 chr3D 88.889 81 9 0 2692 2772 225524815 225524895 1.800000e-17 100.0
6 TraesCS3D01G244700 chr3A 94.597 1925 57 22 672 2574 464896407 464898306 0.000000e+00 2935.0
7 TraesCS3D01G244700 chr3A 97.455 550 11 2 1 549 464895862 464896409 0.000000e+00 935.0
8 TraesCS3D01G244700 chr3A 95.489 266 11 1 2576 2840 464898363 464898628 9.410000e-115 424.0
9 TraesCS3D01G244700 chr3A 97.638 127 3 0 547 673 365363203 365363077 4.760000e-53 219.0
10 TraesCS3D01G244700 chr3A 94.118 68 4 0 2773 2840 79454861 79454794 1.390000e-18 104.0
11 TraesCS3D01G244700 chr3A 87.179 78 10 0 2695 2772 323102594 323102517 3.900000e-14 89.8
12 TraesCS3D01G244700 chr3B 93.679 1677 56 18 695 2341 438580916 438579260 0.000000e+00 2464.0
13 TraesCS3D01G244700 chr3B 89.236 576 32 7 1 549 438581592 438581020 0.000000e+00 693.0
14 TraesCS3D01G244700 chr3B 95.376 173 7 1 2591 2762 438578826 438578654 1.000000e-69 274.0
15 TraesCS3D01G244700 chr3B 92.754 69 5 0 2772 2840 114096216 114096284 1.800000e-17 100.0
16 TraesCS3D01G244700 chr4B 90.570 456 37 3 672 1125 22445597 22445146 1.460000e-167 599.0
17 TraesCS3D01G244700 chr4B 82.272 581 41 16 1 522 22446189 22445612 2.010000e-121 446.0
18 TraesCS3D01G244700 chr4B 100.000 39 0 0 1144 1182 22445148 22445110 3.920000e-09 73.1
19 TraesCS3D01G244700 chr2D 89.956 458 36 6 672 1125 601805651 601805200 1.470000e-162 582.0
20 TraesCS3D01G244700 chr2D 89.542 459 45 2 669 1125 564472375 564472832 1.900000e-161 579.0
21 TraesCS3D01G244700 chr2D 81.353 606 53 19 1 549 564471778 564472380 3.360000e-119 438.0
22 TraesCS3D01G244700 chr2D 87.255 408 21 14 1020 1416 43956494 43956107 1.210000e-118 436.0
23 TraesCS3D01G244700 chr2D 82.196 337 26 19 1 317 601806333 601806011 2.810000e-65 259.0
24 TraesCS3D01G244700 chr2D 97.638 127 3 0 547 673 376857748 376857622 4.760000e-53 219.0
25 TraesCS3D01G244700 chr2D 95.652 69 3 0 2772 2840 27826676 27826744 8.320000e-21 111.0
26 TraesCS3D01G244700 chr2D 86.667 75 10 0 680 754 43956562 43956488 1.810000e-12 84.2
27 TraesCS3D01G244700 chr2D 100.000 29 0 0 1144 1172 564472830 564472858 1.000000e-03 54.7
28 TraesCS3D01G244700 chr4A 87.821 468 47 5 663 1125 30779812 30780274 8.950000e-150 540.0
29 TraesCS3D01G244700 chr4A 81.032 601 47 26 1 549 30779238 30779823 1.570000e-112 416.0
30 TraesCS3D01G244700 chr2B 87.905 463 44 7 669 1125 675715747 675716203 4.160000e-148 534.0
31 TraesCS3D01G244700 chr2B 87.257 463 36 11 669 1125 601737819 601738264 9.080000e-140 507.0
32 TraesCS3D01G244700 chr2B 80.905 597 54 23 1 549 675715168 675715752 1.570000e-112 416.0
33 TraesCS3D01G244700 chr2B 92.667 150 10 1 1 149 601734985 601735134 6.160000e-52 215.0
34 TraesCS3D01G244700 chr2B 90.123 81 8 0 2692 2772 113275026 113275106 3.870000e-19 106.0
35 TraesCS3D01G244700 chr6D 98.425 127 2 0 547 673 62116135 62116261 1.020000e-54 224.0
36 TraesCS3D01G244700 chr7D 96.970 132 4 0 543 674 403812033 403812164 3.680000e-54 222.0
37 TraesCS3D01G244700 chr7D 97.656 128 3 0 547 674 570160620 570160747 1.320000e-53 220.0
38 TraesCS3D01G244700 chr7D 96.875 128 4 0 547 674 411614185 411614058 6.160000e-52 215.0
39 TraesCS3D01G244700 chr7D 91.139 79 7 0 2693 2771 8735130 8735052 1.080000e-19 108.0
40 TraesCS3D01G244700 chr5D 96.850 127 4 0 547 673 395734437 395734311 2.220000e-51 213.0
41 TraesCS3D01G244700 chr2A 94.776 134 7 0 540 673 7724653 7724520 2.870000e-50 209.0
42 TraesCS3D01G244700 chr2A 91.358 81 7 0 2692 2772 73540767 73540847 8.320000e-21 111.0
43 TraesCS3D01G244700 chr2A 89.157 83 9 0 672 754 46318378 46318296 1.390000e-18 104.0
44 TraesCS3D01G244700 chr1D 80.556 180 25 6 1665 1841 469834438 469834610 2.300000e-26 130.0
45 TraesCS3D01G244700 chr1B 82.313 147 22 2 1698 1841 651544322 651544467 1.070000e-24 124.0
46 TraesCS3D01G244700 chr5B 97.101 69 2 0 2772 2840 406054099 406054031 1.790000e-22 117.0
47 TraesCS3D01G244700 chr7A 94.286 70 4 0 2771 2840 214321300 214321231 1.080000e-19 108.0
48 TraesCS3D01G244700 chr7A 90.000 80 8 0 2693 2772 616806955 616806876 1.390000e-18 104.0
49 TraesCS3D01G244700 chr6B 92.754 69 4 1 2772 2840 455134459 455134526 6.480000e-17 99.0
50 TraesCS3D01G244700 chr6B 88.000 75 9 0 2693 2767 51987049 51987123 3.900000e-14 89.8


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 TraesCS3D01G244700 chr3D 339859994 339862833 2839 True 5245.000000 5245 100.000000 1 2840 1 chr3D.!!$R3 2839
1 TraesCS3D01G244700 chr3D 482833460 482834046 586 True 446.000000 446 81.833000 1 549 1 chr3D.!!$R4 548
2 TraesCS3D01G244700 chr3A 464895862 464898628 2766 False 1431.333333 2935 95.847000 1 2840 3 chr3A.!!$F1 2839
3 TraesCS3D01G244700 chr3B 438578654 438581592 2938 True 1143.666667 2464 92.763667 1 2762 3 chr3B.!!$R1 2761
4 TraesCS3D01G244700 chr4B 22445110 22446189 1079 True 372.700000 599 90.947333 1 1182 3 chr4B.!!$R1 1181
5 TraesCS3D01G244700 chr2D 601805200 601806333 1133 True 420.500000 582 86.076000 1 1125 2 chr2D.!!$R3 1124
6 TraesCS3D01G244700 chr2D 564471778 564472858 1080 False 357.233333 579 90.298333 1 1172 3 chr2D.!!$F2 1171
7 TraesCS3D01G244700 chr4A 30779238 30780274 1036 False 478.000000 540 84.426500 1 1125 2 chr4A.!!$F1 1124
8 TraesCS3D01G244700 chr2B 675715168 675716203 1035 False 475.000000 534 84.405000 1 1125 2 chr2B.!!$F3 1124
9 TraesCS3D01G244700 chr2B 601734985 601738264 3279 False 361.000000 507 89.962000 1 1125 2 chr2B.!!$F2 1124

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
73 75 0.827368 GTGCCTTTGGTTTTGTGGGA 59.173 50.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 4610 0.178953 ACCACTTCCAGGCAGCAAAT 60.179 50.0 0.0 0.0 0.0 2.32 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
37 38 3.289702 GAAGTATTCATGTGCGACACG 57.710 47.619 0.00 0.00 46.62 4.49
73 75 0.827368 GTGCCTTTGGTTTTGTGGGA 59.173 50.000 0.00 0.00 0.00 4.37
183 186 6.072175 TGCTTTTTACTATCCGAATGCAGTTT 60.072 34.615 0.00 0.00 31.35 2.66
399 2737 1.535462 CCTTCAAGTTACTGGTTGCCG 59.465 52.381 0.00 0.00 0.00 5.69
548 2992 5.869344 GGCATTTTCCTTTGGTGAGAATTAC 59.131 40.000 0.00 0.00 0.00 1.89
549 2993 6.295292 GGCATTTTCCTTTGGTGAGAATTACT 60.295 38.462 0.00 0.00 0.00 2.24
550 2994 6.808704 GCATTTTCCTTTGGTGAGAATTACTC 59.191 38.462 0.00 0.00 45.11 2.59
551 2995 6.894339 TTTTCCTTTGGTGAGAATTACTCC 57.106 37.500 0.00 0.00 44.34 3.85
552 2996 4.569719 TCCTTTGGTGAGAATTACTCCC 57.430 45.455 0.00 0.00 44.34 4.30
553 2997 4.175962 TCCTTTGGTGAGAATTACTCCCT 58.824 43.478 0.00 0.00 44.34 4.20
554 2998 4.225267 TCCTTTGGTGAGAATTACTCCCTC 59.775 45.833 0.00 0.00 44.34 4.30
555 2999 4.518249 CTTTGGTGAGAATTACTCCCTCC 58.482 47.826 0.00 0.00 44.34 4.30
556 3000 2.108168 TGGTGAGAATTACTCCCTCCG 58.892 52.381 0.00 0.00 44.34 4.63
557 3001 2.108970 GGTGAGAATTACTCCCTCCGT 58.891 52.381 0.00 0.00 44.34 4.69
558 3002 2.500504 GGTGAGAATTACTCCCTCCGTT 59.499 50.000 0.00 0.00 44.34 4.44
559 3003 3.430513 GGTGAGAATTACTCCCTCCGTTC 60.431 52.174 0.00 0.00 44.34 3.95
560 3004 2.764572 TGAGAATTACTCCCTCCGTTCC 59.235 50.000 0.00 0.00 44.34 3.62
561 3005 2.764572 GAGAATTACTCCCTCCGTTCCA 59.235 50.000 0.00 0.00 39.53 3.53
562 3006 3.178865 AGAATTACTCCCTCCGTTCCAA 58.821 45.455 0.00 0.00 0.00 3.53
563 3007 3.585732 AGAATTACTCCCTCCGTTCCAAA 59.414 43.478 0.00 0.00 0.00 3.28
564 3008 4.227527 AGAATTACTCCCTCCGTTCCAAAT 59.772 41.667 0.00 0.00 0.00 2.32
565 3009 4.586306 ATTACTCCCTCCGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
566 3010 5.703730 ATTACTCCCTCCGTTCCAAATTA 57.296 39.130 0.00 0.00 0.00 1.40
567 3011 3.629142 ACTCCCTCCGTTCCAAATTAG 57.371 47.619 0.00 0.00 0.00 1.73
568 3012 2.910977 ACTCCCTCCGTTCCAAATTAGT 59.089 45.455 0.00 0.00 0.00 2.24
569 3013 3.329814 ACTCCCTCCGTTCCAAATTAGTT 59.670 43.478 0.00 0.00 0.00 2.24
570 3014 3.681593 TCCCTCCGTTCCAAATTAGTTG 58.318 45.455 0.00 0.00 36.94 3.16
571 3015 3.328343 TCCCTCCGTTCCAAATTAGTTGA 59.672 43.478 0.00 0.00 39.87 3.18
572 3016 3.439129 CCCTCCGTTCCAAATTAGTTGAC 59.561 47.826 0.00 0.00 39.87 3.18
573 3017 4.324267 CCTCCGTTCCAAATTAGTTGACT 58.676 43.478 0.00 0.00 39.87 3.41
574 3018 4.760204 CCTCCGTTCCAAATTAGTTGACTT 59.240 41.667 0.00 0.00 39.87 3.01
575 3019 5.334879 CCTCCGTTCCAAATTAGTTGACTTG 60.335 44.000 0.00 0.00 39.87 3.16
576 3020 5.369833 TCCGTTCCAAATTAGTTGACTTGA 58.630 37.500 0.00 0.00 39.87 3.02
577 3021 5.823570 TCCGTTCCAAATTAGTTGACTTGAA 59.176 36.000 0.00 0.00 39.87 2.69
578 3022 6.488683 TCCGTTCCAAATTAGTTGACTTGAAT 59.511 34.615 0.00 0.00 39.87 2.57
579 3023 7.013846 TCCGTTCCAAATTAGTTGACTTGAATT 59.986 33.333 0.00 0.00 39.87 2.17
580 3024 7.651704 CCGTTCCAAATTAGTTGACTTGAATTT 59.348 33.333 0.00 0.00 39.87 1.82
581 3025 8.479280 CGTTCCAAATTAGTTGACTTGAATTTG 58.521 33.333 17.35 17.35 43.82 2.32
582 3026 9.313118 GTTCCAAATTAGTTGACTTGAATTTGT 57.687 29.630 20.10 0.00 43.18 2.83
583 3027 9.528018 TTCCAAATTAGTTGACTTGAATTTGTC 57.472 29.630 20.10 0.00 43.18 3.18
584 3028 8.912988 TCCAAATTAGTTGACTTGAATTTGTCT 58.087 29.630 20.10 0.00 43.18 3.41
592 3036 8.504005 AGTTGACTTGAATTTGTCTAAATACGG 58.496 33.333 8.09 0.00 35.50 4.02
593 3037 8.500773 GTTGACTTGAATTTGTCTAAATACGGA 58.499 33.333 8.09 0.00 35.50 4.69
594 3038 8.786826 TGACTTGAATTTGTCTAAATACGGAT 57.213 30.769 8.09 0.00 35.50 4.18
595 3039 8.664798 TGACTTGAATTTGTCTAAATACGGATG 58.335 33.333 8.09 0.00 35.50 3.51
596 3040 8.561738 ACTTGAATTTGTCTAAATACGGATGT 57.438 30.769 0.00 0.00 35.50 3.06
597 3041 9.661563 ACTTGAATTTGTCTAAATACGGATGTA 57.338 29.630 0.00 0.00 35.50 2.29
615 3059 8.910944 ACGGATGTATCTATACTTGTTTAGTGT 58.089 33.333 2.07 0.00 37.73 3.55
616 3060 9.395707 CGGATGTATCTATACTTGTTTAGTGTC 57.604 37.037 2.07 0.00 37.73 3.67
628 3072 8.462143 ACTTGTTTAGTGTCTACATACATTCG 57.538 34.615 0.00 0.00 35.19 3.34
629 3073 8.086522 ACTTGTTTAGTGTCTACATACATTCGT 58.913 33.333 0.00 0.00 35.19 3.85
630 3074 7.806149 TGTTTAGTGTCTACATACATTCGTG 57.194 36.000 0.00 0.00 0.00 4.35
631 3075 7.372714 TGTTTAGTGTCTACATACATTCGTGT 58.627 34.615 0.00 0.00 0.00 4.49
632 3076 7.539710 TGTTTAGTGTCTACATACATTCGTGTC 59.460 37.037 0.00 0.00 0.00 3.67
633 3077 5.899120 AGTGTCTACATACATTCGTGTCT 57.101 39.130 0.00 0.00 0.00 3.41
634 3078 6.997239 AGTGTCTACATACATTCGTGTCTA 57.003 37.500 0.00 0.00 0.00 2.59
635 3079 7.017498 AGTGTCTACATACATTCGTGTCTAG 57.983 40.000 0.00 0.00 0.00 2.43
636 3080 6.822170 AGTGTCTACATACATTCGTGTCTAGA 59.178 38.462 0.00 0.00 0.00 2.43
637 3081 7.499563 AGTGTCTACATACATTCGTGTCTAGAT 59.500 37.037 0.00 0.00 0.00 1.98
638 3082 8.771766 GTGTCTACATACATTCGTGTCTAGATA 58.228 37.037 0.00 0.00 0.00 1.98
639 3083 9.333724 TGTCTACATACATTCGTGTCTAGATAA 57.666 33.333 0.00 0.00 0.00 1.75
647 3091 7.963532 ACATTCGTGTCTAGATAAATATGGGT 58.036 34.615 0.00 0.00 0.00 4.51
648 3092 8.088981 ACATTCGTGTCTAGATAAATATGGGTC 58.911 37.037 0.00 0.00 0.00 4.46
649 3093 7.591421 TTCGTGTCTAGATAAATATGGGTCA 57.409 36.000 0.00 0.00 0.00 4.02
650 3094 7.591421 TCGTGTCTAGATAAATATGGGTCAA 57.409 36.000 0.00 0.00 0.00 3.18
651 3095 7.658261 TCGTGTCTAGATAAATATGGGTCAAG 58.342 38.462 0.00 0.00 0.00 3.02
652 3096 7.287005 TCGTGTCTAGATAAATATGGGTCAAGT 59.713 37.037 0.00 0.00 0.00 3.16
653 3097 8.573885 CGTGTCTAGATAAATATGGGTCAAGTA 58.426 37.037 0.00 0.00 0.00 2.24
663 3107 6.693315 ATATGGGTCAAGTAATTTGGAACG 57.307 37.500 0.00 0.00 37.39 3.95
664 3108 3.150767 TGGGTCAAGTAATTTGGAACGG 58.849 45.455 0.00 0.00 37.39 4.44
665 3109 3.181442 TGGGTCAAGTAATTTGGAACGGA 60.181 43.478 0.00 0.00 37.39 4.69
666 3110 3.439129 GGGTCAAGTAATTTGGAACGGAG 59.561 47.826 0.00 0.00 37.39 4.63
667 3111 3.439129 GGTCAAGTAATTTGGAACGGAGG 59.561 47.826 0.00 0.00 37.39 4.30
668 3112 3.439129 GTCAAGTAATTTGGAACGGAGGG 59.561 47.826 0.00 0.00 37.39 4.30
669 3113 3.328343 TCAAGTAATTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 37.39 4.20
670 3114 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
671 3115 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
672 3116 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
725 3255 3.439476 CCCTTCTGTTTCTCTTGCATCAG 59.561 47.826 0.00 0.00 0.00 2.90
847 3378 7.168219 AGGTCAGCAATCTATGAAACACTTAA 58.832 34.615 0.00 0.00 0.00 1.85
960 3493 8.659925 TTTGATGATTGTGCACTAAACATTTT 57.340 26.923 19.41 1.72 0.00 1.82
1873 4415 2.281761 CTGGGTGTGTCCTGTGCC 60.282 66.667 0.00 0.00 36.25 5.01
1915 4457 7.491696 GGATTTCGTTCTGTAGTTGCTACTATT 59.508 37.037 11.20 0.00 39.01 1.73
1957 4499 6.681729 TCCTGTAATTTAGGTGACTTCACT 57.318 37.500 9.20 0.00 45.73 3.41
1958 4500 7.074653 TCCTGTAATTTAGGTGACTTCACTT 57.925 36.000 9.20 4.34 45.73 3.16
1967 4510 5.104259 AGGTGACTTCACTTTGAGACTTT 57.896 39.130 9.20 0.00 45.73 2.66
1989 4532 2.847327 ATTGTCACTAGTGTGCTGCT 57.153 45.000 21.99 1.74 43.49 4.24
1993 4536 0.605083 TCACTAGTGTGCTGCTGGAG 59.395 55.000 21.99 0.00 43.49 3.86
2047 4595 7.928873 TCCTACTAGTTTCCCATTTTTCTGAT 58.071 34.615 0.00 0.00 0.00 2.90
2062 4610 3.701205 TCTGATGCTGGCTGTTCTAAA 57.299 42.857 0.00 0.00 0.00 1.85
2084 4632 2.674380 CTGCCTGGAAGTGGTGCC 60.674 66.667 0.00 0.00 0.00 5.01
2236 4805 4.980805 GTTCCCTGCGACGCCACA 62.981 66.667 18.69 0.00 0.00 4.17
2334 4905 9.130661 TCTAAAAAGATTTGGAGTGATTGACAA 57.869 29.630 0.00 0.00 31.87 3.18
2335 4906 9.185192 CTAAAAAGATTTGGAGTGATTGACAAC 57.815 33.333 0.00 0.00 0.00 3.32
2336 4907 6.966534 AAAGATTTGGAGTGATTGACAACT 57.033 33.333 0.00 0.00 0.00 3.16
2337 4908 8.463930 AAAAGATTTGGAGTGATTGACAACTA 57.536 30.769 0.00 0.00 0.00 2.24
2338 4909 8.641498 AAAGATTTGGAGTGATTGACAACTAT 57.359 30.769 0.00 0.00 0.00 2.12
2339 4910 7.621428 AGATTTGGAGTGATTGACAACTATG 57.379 36.000 0.00 0.00 0.00 2.23
2340 4911 5.627499 TTTGGAGTGATTGACAACTATGC 57.373 39.130 0.00 0.00 0.00 3.14
2348 4919 6.372659 AGTGATTGACAACTATGCTTAACCTG 59.627 38.462 0.00 0.00 0.00 4.00
2362 4936 1.045407 AACCTGGCACGTAGAGAACA 58.955 50.000 0.00 0.00 0.00 3.18
2376 4950 5.773680 CGTAGAGAACATCTATTTAGGGGGA 59.226 44.000 0.00 0.00 42.50 4.81
2379 4953 7.800300 AGAGAACATCTATTTAGGGGGATAC 57.200 40.000 0.00 0.00 36.10 2.24
2410 4990 3.319137 AAAGAAGATAGCACAGACGCA 57.681 42.857 0.00 0.00 0.00 5.24
2416 4996 6.051717 AGAAGATAGCACAGACGCATAATTT 58.948 36.000 0.00 0.00 0.00 1.82
2474 5054 4.322057 ACTCTTCTACCAATTTGCCCAT 57.678 40.909 0.00 0.00 0.00 4.00
2539 5279 4.679373 TGCAAGAATCTCCTACCTCATC 57.321 45.455 0.00 0.00 0.00 2.92
2540 5280 3.389329 TGCAAGAATCTCCTACCTCATCC 59.611 47.826 0.00 0.00 0.00 3.51
2541 5281 3.645687 GCAAGAATCTCCTACCTCATCCT 59.354 47.826 0.00 0.00 0.00 3.24
2542 5282 4.102367 GCAAGAATCTCCTACCTCATCCTT 59.898 45.833 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.684305 AGGCACAAACAAAGCAACTTTTC 59.316 39.130 0.00 0.00 30.60 2.29
208 2508 6.443792 ACAGGGTTACAATGTTTTTCGAATC 58.556 36.000 0.00 0.00 0.00 2.52
423 2864 5.895216 ATAATAGCACGCCGTACTTTTAC 57.105 39.130 0.00 0.00 0.00 2.01
548 2992 3.629142 ACTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
549 2993 3.328343 TCAACTAATTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 35.69 4.20
550 2994 3.439129 GTCAACTAATTTGGAACGGAGGG 59.561 47.826 0.00 0.00 35.69 4.30
551 2995 4.324267 AGTCAACTAATTTGGAACGGAGG 58.676 43.478 0.00 0.00 35.69 4.30
552 2996 5.468746 TCAAGTCAACTAATTTGGAACGGAG 59.531 40.000 0.00 0.00 35.69 4.63
553 2997 5.369833 TCAAGTCAACTAATTTGGAACGGA 58.630 37.500 0.00 0.00 35.69 4.69
554 2998 5.682943 TCAAGTCAACTAATTTGGAACGG 57.317 39.130 0.00 0.00 35.69 4.44
555 2999 8.479280 CAAATTCAAGTCAACTAATTTGGAACG 58.521 33.333 16.45 0.00 41.93 3.95
556 3000 9.313118 ACAAATTCAAGTCAACTAATTTGGAAC 57.687 29.630 22.68 0.00 46.31 3.62
557 3001 9.528018 GACAAATTCAAGTCAACTAATTTGGAA 57.472 29.630 22.68 7.42 46.31 3.53
558 3002 8.912988 AGACAAATTCAAGTCAACTAATTTGGA 58.087 29.630 22.68 1.26 46.31 3.53
566 3010 8.504005 CCGTATTTAGACAAATTCAAGTCAACT 58.496 33.333 7.95 0.00 37.23 3.16
567 3011 8.500773 TCCGTATTTAGACAAATTCAAGTCAAC 58.499 33.333 7.95 0.00 37.23 3.18
568 3012 8.610248 TCCGTATTTAGACAAATTCAAGTCAA 57.390 30.769 7.95 0.00 37.23 3.18
569 3013 8.664798 CATCCGTATTTAGACAAATTCAAGTCA 58.335 33.333 7.95 0.00 37.23 3.41
570 3014 8.665685 ACATCCGTATTTAGACAAATTCAAGTC 58.334 33.333 0.00 0.00 35.88 3.01
571 3015 8.561738 ACATCCGTATTTAGACAAATTCAAGT 57.438 30.769 0.00 0.00 35.88 3.16
589 3033 8.910944 ACACTAAACAAGTATAGATACATCCGT 58.089 33.333 2.66 0.00 35.76 4.69
590 3034 9.395707 GACACTAAACAAGTATAGATACATCCG 57.604 37.037 2.66 0.00 35.76 4.18
602 3046 9.563898 CGAATGTATGTAGACACTAAACAAGTA 57.436 33.333 0.00 0.00 35.76 2.24
603 3047 8.086522 ACGAATGTATGTAGACACTAAACAAGT 58.913 33.333 0.00 0.00 39.81 3.16
604 3048 8.373256 CACGAATGTATGTAGACACTAAACAAG 58.627 37.037 0.00 0.00 30.52 3.16
605 3049 7.868922 ACACGAATGTATGTAGACACTAAACAA 59.131 33.333 0.00 0.00 37.26 2.83
606 3050 7.372714 ACACGAATGTATGTAGACACTAAACA 58.627 34.615 0.00 0.00 37.26 2.83
607 3051 7.754027 AGACACGAATGTATGTAGACACTAAAC 59.246 37.037 0.00 0.00 39.95 2.01
608 3052 7.823665 AGACACGAATGTATGTAGACACTAAA 58.176 34.615 0.00 0.00 39.95 1.85
609 3053 7.387119 AGACACGAATGTATGTAGACACTAA 57.613 36.000 0.00 0.00 39.95 2.24
610 3054 6.997239 AGACACGAATGTATGTAGACACTA 57.003 37.500 0.00 0.00 39.95 2.74
611 3055 5.899120 AGACACGAATGTATGTAGACACT 57.101 39.130 0.00 0.00 39.95 3.55
612 3056 7.012959 TCTAGACACGAATGTATGTAGACAC 57.987 40.000 0.00 0.00 39.95 3.67
613 3057 7.803279 ATCTAGACACGAATGTATGTAGACA 57.197 36.000 0.00 0.00 39.95 3.41
621 3065 9.085645 ACCCATATTTATCTAGACACGAATGTA 57.914 33.333 0.00 0.00 39.95 2.29
622 3066 7.963532 ACCCATATTTATCTAGACACGAATGT 58.036 34.615 0.00 0.00 43.71 2.71
623 3067 8.088365 TGACCCATATTTATCTAGACACGAATG 58.912 37.037 0.00 0.00 0.00 2.67
624 3068 8.190326 TGACCCATATTTATCTAGACACGAAT 57.810 34.615 0.00 0.00 0.00 3.34
625 3069 7.591421 TGACCCATATTTATCTAGACACGAA 57.409 36.000 0.00 0.00 0.00 3.85
626 3070 7.287005 ACTTGACCCATATTTATCTAGACACGA 59.713 37.037 0.00 0.00 0.00 4.35
627 3071 7.434492 ACTTGACCCATATTTATCTAGACACG 58.566 38.462 0.00 0.00 0.00 4.49
637 3081 8.679100 CGTTCCAAATTACTTGACCCATATTTA 58.321 33.333 0.00 0.00 37.17 1.40
638 3082 7.363443 CCGTTCCAAATTACTTGACCCATATTT 60.363 37.037 0.00 0.00 37.17 1.40
639 3083 6.096282 CCGTTCCAAATTACTTGACCCATATT 59.904 38.462 0.00 0.00 37.17 1.28
640 3084 5.592688 CCGTTCCAAATTACTTGACCCATAT 59.407 40.000 0.00 0.00 37.17 1.78
641 3085 4.944930 CCGTTCCAAATTACTTGACCCATA 59.055 41.667 0.00 0.00 37.17 2.74
642 3086 3.761752 CCGTTCCAAATTACTTGACCCAT 59.238 43.478 0.00 0.00 37.17 4.00
643 3087 3.150767 CCGTTCCAAATTACTTGACCCA 58.849 45.455 0.00 0.00 37.17 4.51
644 3088 3.414269 TCCGTTCCAAATTACTTGACCC 58.586 45.455 0.00 0.00 37.17 4.46
645 3089 3.439129 CCTCCGTTCCAAATTACTTGACC 59.561 47.826 0.00 0.00 37.17 4.02
646 3090 3.439129 CCCTCCGTTCCAAATTACTTGAC 59.561 47.826 0.00 0.00 37.17 3.18
647 3091 3.328343 TCCCTCCGTTCCAAATTACTTGA 59.672 43.478 0.00 0.00 37.17 3.02
648 3092 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
649 3093 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
650 3094 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
651 3095 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
652 3096 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
653 3097 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
654 3098 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
655 3099 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
656 3100 1.553248 CATGTACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
657 3101 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
658 3102 0.464452 CCATGTACTCCCTCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
659 3103 0.464452 CCCATGTACTCCCTCCGTTC 59.536 60.000 0.00 0.00 0.00 3.95
660 3104 0.252558 ACCCATGTACTCCCTCCGTT 60.253 55.000 0.00 0.00 0.00 4.44
661 3105 0.252558 AACCCATGTACTCCCTCCGT 60.253 55.000 0.00 0.00 0.00 4.69
662 3106 1.687123 CTAACCCATGTACTCCCTCCG 59.313 57.143 0.00 0.00 0.00 4.63
663 3107 3.042059 TCTAACCCATGTACTCCCTCC 57.958 52.381 0.00 0.00 0.00 4.30
664 3108 4.902448 AGATTCTAACCCATGTACTCCCTC 59.098 45.833 0.00 0.00 0.00 4.30
665 3109 4.656112 CAGATTCTAACCCATGTACTCCCT 59.344 45.833 0.00 0.00 0.00 4.20
666 3110 4.202367 CCAGATTCTAACCCATGTACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
667 3111 4.743955 GCCAGATTCTAACCCATGTACTCC 60.744 50.000 0.00 0.00 0.00 3.85
668 3112 4.141711 TGCCAGATTCTAACCCATGTACTC 60.142 45.833 0.00 0.00 0.00 2.59
669 3113 3.780294 TGCCAGATTCTAACCCATGTACT 59.220 43.478 0.00 0.00 0.00 2.73
670 3114 4.150897 TGCCAGATTCTAACCCATGTAC 57.849 45.455 0.00 0.00 0.00 2.90
671 3115 6.702449 ATATGCCAGATTCTAACCCATGTA 57.298 37.500 0.00 0.00 0.00 2.29
672 3116 3.959495 ATGCCAGATTCTAACCCATGT 57.041 42.857 0.00 0.00 0.00 3.21
879 3410 6.722129 AGGCTCTCAGTCTTTAAAAGAGTAGA 59.278 38.462 12.99 3.53 39.12 2.59
960 3493 1.133945 TGACCACAAGCCTGCAAAGTA 60.134 47.619 0.00 0.00 0.00 2.24
1257 3793 1.532868 CCAAACTTGCTCAGTTCCTCG 59.467 52.381 2.76 0.00 45.77 4.63
1395 3931 7.773690 ACAATTATTAGGCGACCAGAGTAAAAT 59.226 33.333 0.00 0.00 0.00 1.82
1831 4373 1.343465 CAGTGGTCACCCTTACTTCGT 59.657 52.381 0.00 0.00 0.00 3.85
1915 4457 5.360714 ACAGGAACAGAAAAGCAAATCAAGA 59.639 36.000 0.00 0.00 0.00 3.02
1957 4499 9.391006 ACACTAGTGACAATTTAAAGTCTCAAA 57.609 29.630 29.30 0.00 35.81 2.69
1958 4500 8.958119 ACACTAGTGACAATTTAAAGTCTCAA 57.042 30.769 29.30 0.00 35.81 3.02
1989 4532 7.033791 CGAAGTAGCTAAAATGTAAGTCTCCA 58.966 38.462 0.00 0.00 0.00 3.86
1993 4536 8.463456 AGTTCGAAGTAGCTAAAATGTAAGTC 57.537 34.615 2.97 0.00 0.00 3.01
2047 4595 2.892852 AGCAAATTTAGAACAGCCAGCA 59.107 40.909 0.00 0.00 0.00 4.41
2062 4610 0.178953 ACCACTTCCAGGCAGCAAAT 60.179 50.000 0.00 0.00 0.00 2.32
2236 4805 2.416162 GCCGTCGATCAAGAGAGAAACT 60.416 50.000 0.00 0.00 0.00 2.66
2334 4905 1.278127 ACGTGCCAGGTTAAGCATAGT 59.722 47.619 7.52 0.83 41.86 2.12
2335 4906 2.024176 ACGTGCCAGGTTAAGCATAG 57.976 50.000 7.52 0.25 41.86 2.23
2336 4907 2.761767 TCTACGTGCCAGGTTAAGCATA 59.238 45.455 7.52 0.00 41.86 3.14
2337 4908 1.553248 TCTACGTGCCAGGTTAAGCAT 59.447 47.619 7.52 0.00 41.86 3.79
2338 4909 0.970640 TCTACGTGCCAGGTTAAGCA 59.029 50.000 7.52 0.00 36.44 3.91
2339 4910 1.203994 TCTCTACGTGCCAGGTTAAGC 59.796 52.381 0.00 0.00 0.00 3.09
2340 4911 3.251571 GTTCTCTACGTGCCAGGTTAAG 58.748 50.000 0.00 0.00 0.00 1.85
2348 4919 5.921408 CCTAAATAGATGTTCTCTACGTGCC 59.079 44.000 0.00 0.00 39.28 5.01
2400 4978 2.529151 CCCAAAATTATGCGTCTGTGC 58.471 47.619 0.00 0.00 0.00 4.57
2401 4979 2.094803 TGCCCAAAATTATGCGTCTGTG 60.095 45.455 0.00 0.00 0.00 3.66
2402 4980 2.166829 TGCCCAAAATTATGCGTCTGT 58.833 42.857 0.00 0.00 0.00 3.41
2403 4981 2.937469 TGCCCAAAATTATGCGTCTG 57.063 45.000 0.00 0.00 0.00 3.51
2404 4982 4.470334 AAATGCCCAAAATTATGCGTCT 57.530 36.364 0.00 0.00 0.00 4.18
2474 5054 7.913674 AAGAACTTTGTTGTTAAATTGCCAA 57.086 28.000 0.00 0.00 0.00 4.52
2490 5070 8.992073 GCATGTAAATTCCATTGAAAGAACTTT 58.008 29.630 0.00 0.00 33.32 2.66
2675 5478 7.389607 GGAGGTAGTAACATTGCACTCTTTAAA 59.610 37.037 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.