Multiple sequence alignment - TraesCS2A01G341000

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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 TraesCS2A01G341000 chr2A 100.000 3802 0 0 1 3802 576660424 576656623 0.000000e+00 7022.0
1 TraesCS2A01G341000 chr2A 92.958 781 42 6 1 770 715831268 715832046 0.000000e+00 1125.0
2 TraesCS2A01G341000 chr2A 92.477 771 57 1 1 770 209646867 209646097 0.000000e+00 1101.0
3 TraesCS2A01G341000 chrUn 93.131 1878 84 17 776 2642 176723017 176721174 0.000000e+00 2712.0
4 TraesCS2A01G341000 chrUn 92.705 1878 97 11 776 2644 176757347 176755501 0.000000e+00 2673.0
5 TraesCS2A01G341000 chrUn 93.539 1006 44 7 1642 2642 407210360 407209371 0.000000e+00 1478.0
6 TraesCS2A01G341000 chrUn 93.658 946 44 2 1563 2507 326547643 326546713 0.000000e+00 1400.0
7 TraesCS2A01G341000 chrUn 93.658 946 44 2 1563 2507 328301739 328302669 0.000000e+00 1400.0
8 TraesCS2A01G341000 chrUn 90.956 387 24 5 917 1303 326548016 326547641 9.420000e-141 510.0
9 TraesCS2A01G341000 chrUn 90.956 387 24 5 917 1303 328301366 328301741 9.420000e-141 510.0
10 TraesCS2A01G341000 chrUn 80.503 477 72 14 3003 3467 114791351 114791818 2.810000e-91 346.0
11 TraesCS2A01G341000 chr3B 92.876 1881 93 11 773 2644 713802671 713804519 0.000000e+00 2693.0
12 TraesCS2A01G341000 chr3B 92.717 1881 97 14 773 2644 713870599 713872448 0.000000e+00 2678.0
13 TraesCS2A01G341000 chr3B 92.610 1881 98 16 773 2644 713836608 713838456 0.000000e+00 2665.0
14 TraesCS2A01G341000 chr3B 92.557 1881 99 15 773 2644 713767471 713769319 0.000000e+00 2660.0
15 TraesCS2A01G341000 chr3B 83.710 221 26 8 3591 3802 823581895 823581676 2.320000e-47 200.0
16 TraesCS2A01G341000 chr3A 94.599 1222 44 5 1425 2644 705932137 705930936 0.000000e+00 1871.0
17 TraesCS2A01G341000 chr3A 95.381 1169 40 6 2646 3802 705929350 705928184 0.000000e+00 1847.0
18 TraesCS2A01G341000 chr3A 93.478 782 40 1 1 771 606617095 606617876 0.000000e+00 1151.0
19 TraesCS2A01G341000 chr3A 92.692 780 45 2 2 770 688935739 688936517 0.000000e+00 1114.0
20 TraesCS2A01G341000 chr3A 92.318 781 49 1 1 770 108222152 108222932 0.000000e+00 1099.0
21 TraesCS2A01G341000 chr3A 91.818 660 38 8 788 1441 705933594 705932945 0.000000e+00 905.0
22 TraesCS2A01G341000 chr3A 84.722 216 25 8 3591 3801 750508129 750507917 3.850000e-50 209.0
23 TraesCS2A01G341000 chr4D 92.958 781 43 2 1 770 467771817 467771038 0.000000e+00 1127.0
24 TraesCS2A01G341000 chr4D 91.933 781 52 1 1 770 12064882 12064102 0.000000e+00 1083.0
25 TraesCS2A01G341000 chr7D 92.702 781 45 2 1 770 455881244 455882023 0.000000e+00 1116.0
26 TraesCS2A01G341000 chr7D 89.315 730 64 8 1 716 617776388 617775659 0.000000e+00 904.0
27 TraesCS2A01G341000 chr7D 81.342 477 68 15 3003 3467 52530973 52530506 6.000000e-98 368.0
28 TraesCS2A01G341000 chr1A 92.446 781 47 5 1 770 460855776 460856555 0.000000e+00 1105.0
29 TraesCS2A01G341000 chr1A 82.058 379 55 6 1 367 278544181 278544558 1.030000e-80 311.0
30 TraesCS2A01G341000 chr1A 92.683 82 6 0 2658 2739 526909149 526909230 6.670000e-23 119.0
31 TraesCS2A01G341000 chr1A 87.356 87 6 4 2658 2739 472142129 472142215 1.120000e-15 95.3
32 TraesCS2A01G341000 chr5A 92.318 781 49 1 1 770 608644090 608644870 0.000000e+00 1099.0
33 TraesCS2A01G341000 chr6A 91.293 781 57 1 1 770 211309376 211308596 0.000000e+00 1055.0
34 TraesCS2A01G341000 chr1D 91.293 781 57 2 1 770 85854196 85853416 0.000000e+00 1055.0
35 TraesCS2A01G341000 chr1D 88.033 727 74 6 1 716 12792981 12793705 0.000000e+00 848.0
36 TraesCS2A01G341000 chr6D 91.165 781 57 5 1 770 65143269 65142490 0.000000e+00 1050.0
37 TraesCS2A01G341000 chr5D 88.721 727 69 6 1 716 214393278 214394002 0.000000e+00 876.0
38 TraesCS2A01G341000 chr2B 90.982 499 34 4 776 1274 43243365 43242878 0.000000e+00 662.0
39 TraesCS2A01G341000 chr2B 83.333 198 25 6 3588 3778 397907544 397907740 3.900000e-40 176.0
40 TraesCS2A01G341000 chr5B 88.471 425 43 4 2773 3192 5127238 5126815 3.390000e-140 508.0
41 TraesCS2A01G341000 chr1B 89.489 333 15 7 3387 3708 9159649 9159326 1.640000e-108 403.0
42 TraesCS2A01G341000 chr1B 84.103 195 23 6 3591 3778 37102316 37102123 8.390000e-42 182.0
43 TraesCS2A01G341000 chr1B 95.327 107 5 0 3696 3802 9156179 9156073 1.820000e-38 171.0
44 TraesCS2A01G341000 chr7B 91.739 230 19 0 2430 2659 641101051 641101280 1.700000e-83 320.0
45 TraesCS2A01G341000 chr3D 85.116 215 26 6 3591 3801 614207787 614207575 8.270000e-52 215.0


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 TraesCS2A01G341000 chr2A 576656623 576660424 3801 True 7022 7022 100.000000 1 3802 1 chr2A.!!$R2 3801
1 TraesCS2A01G341000 chr2A 715831268 715832046 778 False 1125 1125 92.958000 1 770 1 chr2A.!!$F1 769
2 TraesCS2A01G341000 chr2A 209646097 209646867 770 True 1101 1101 92.477000 1 770 1 chr2A.!!$R1 769
3 TraesCS2A01G341000 chrUn 176721174 176723017 1843 True 2712 2712 93.131000 776 2642 1 chrUn.!!$R1 1866
4 TraesCS2A01G341000 chrUn 176755501 176757347 1846 True 2673 2673 92.705000 776 2644 1 chrUn.!!$R2 1868
5 TraesCS2A01G341000 chrUn 407209371 407210360 989 True 1478 1478 93.539000 1642 2642 1 chrUn.!!$R3 1000
6 TraesCS2A01G341000 chrUn 326546713 326548016 1303 True 955 1400 92.307000 917 2507 2 chrUn.!!$R4 1590
7 TraesCS2A01G341000 chrUn 328301366 328302669 1303 False 955 1400 92.307000 917 2507 2 chrUn.!!$F2 1590
8 TraesCS2A01G341000 chr3B 713802671 713804519 1848 False 2693 2693 92.876000 773 2644 1 chr3B.!!$F2 1871
9 TraesCS2A01G341000 chr3B 713870599 713872448 1849 False 2678 2678 92.717000 773 2644 1 chr3B.!!$F4 1871
10 TraesCS2A01G341000 chr3B 713836608 713838456 1848 False 2665 2665 92.610000 773 2644 1 chr3B.!!$F3 1871
11 TraesCS2A01G341000 chr3B 713767471 713769319 1848 False 2660 2660 92.557000 773 2644 1 chr3B.!!$F1 1871
12 TraesCS2A01G341000 chr3A 705928184 705933594 5410 True 1541 1871 93.932667 788 3802 3 chr3A.!!$R2 3014
13 TraesCS2A01G341000 chr3A 606617095 606617876 781 False 1151 1151 93.478000 1 771 1 chr3A.!!$F2 770
14 TraesCS2A01G341000 chr3A 688935739 688936517 778 False 1114 1114 92.692000 2 770 1 chr3A.!!$F3 768
15 TraesCS2A01G341000 chr3A 108222152 108222932 780 False 1099 1099 92.318000 1 770 1 chr3A.!!$F1 769
16 TraesCS2A01G341000 chr4D 467771038 467771817 779 True 1127 1127 92.958000 1 770 1 chr4D.!!$R2 769
17 TraesCS2A01G341000 chr4D 12064102 12064882 780 True 1083 1083 91.933000 1 770 1 chr4D.!!$R1 769
18 TraesCS2A01G341000 chr7D 455881244 455882023 779 False 1116 1116 92.702000 1 770 1 chr7D.!!$F1 769
19 TraesCS2A01G341000 chr7D 617775659 617776388 729 True 904 904 89.315000 1 716 1 chr7D.!!$R2 715
20 TraesCS2A01G341000 chr1A 460855776 460856555 779 False 1105 1105 92.446000 1 770 1 chr1A.!!$F2 769
21 TraesCS2A01G341000 chr5A 608644090 608644870 780 False 1099 1099 92.318000 1 770 1 chr5A.!!$F1 769
22 TraesCS2A01G341000 chr6A 211308596 211309376 780 True 1055 1055 91.293000 1 770 1 chr6A.!!$R1 769
23 TraesCS2A01G341000 chr1D 85853416 85854196 780 True 1055 1055 91.293000 1 770 1 chr1D.!!$R1 769
24 TraesCS2A01G341000 chr1D 12792981 12793705 724 False 848 848 88.033000 1 716 1 chr1D.!!$F1 715
25 TraesCS2A01G341000 chr6D 65142490 65143269 779 True 1050 1050 91.165000 1 770 1 chr6D.!!$R1 769
26 TraesCS2A01G341000 chr5D 214393278 214394002 724 False 876 876 88.721000 1 716 1 chr5D.!!$F1 715
27 TraesCS2A01G341000 chr1B 9156073 9159649 3576 True 287 403 92.408000 3387 3802 2 chr1B.!!$R2 415

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
238 254 0.704076 AGTGTACATGGCCAATGGGT 59.296 50.000 10.96 8.83 40.94 4.51 F
334 350 1.135141 GGTGACACTTGCTTTGCAACA 60.135 47.619 0.00 0.00 43.99 3.33 F
1628 2474 0.175760 TGATCAACTCGCACCTAGCC 59.824 55.000 0.00 0.00 41.38 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 2474 0.438830 GCTACCTTCGTGTGCTTTCG 59.561 55.000 0.00 0.0 0.00 3.46 R
1639 2485 0.685097 TGGTGTGACCTGCTACCTTC 59.315 55.000 0.00 0.0 39.58 3.46 R
3289 5726 1.680207 ACTAAGGAGAACGTATCCCGC 59.320 52.381 14.46 0.0 41.42 6.13 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
107 119 3.116096 AGGCATGTCTAGTAGGTTGGA 57.884 47.619 0.00 0.00 0.00 3.53
162 174 5.510520 GGCAATAGAAGAATCTCACGAGGAT 60.511 44.000 0.00 0.00 37.10 3.24
189 201 7.048629 TGAACCAAGCTCAAACATGAATTAA 57.951 32.000 0.00 0.00 0.00 1.40
220 236 4.390909 GTGTTTGATTAGTGGTACGGGAAG 59.609 45.833 0.00 0.00 0.00 3.46
238 254 0.704076 AGTGTACATGGCCAATGGGT 59.296 50.000 10.96 8.83 40.94 4.51
273 289 4.400884 CCGAGGATGATCATCTACTAAGGG 59.599 50.000 29.85 18.16 37.92 3.95
294 310 3.859386 GGCACTATCTTGGAAAATTTGCG 59.141 43.478 0.00 0.00 0.00 4.85
313 329 2.886081 CGTCTCAAATGGAGGAGTCTG 58.114 52.381 0.00 0.00 44.19 3.51
318 334 1.630369 CAAATGGAGGAGTCTGGGTGA 59.370 52.381 0.00 0.00 0.00 4.02
334 350 1.135141 GGTGACACTTGCTTTGCAACA 60.135 47.619 0.00 0.00 43.99 3.33
356 372 8.735315 CAACATACCACACTGGACAAAAATATA 58.265 33.333 0.00 0.00 40.96 0.86
417 433 6.942576 GGGCTCAAATTTTATGGAGAGCTATA 59.057 38.462 19.42 0.00 45.66 1.31
458 474 4.059511 TGTGGCAAAAATTCAGCTCATTG 58.940 39.130 0.00 0.00 0.00 2.82
498 514 3.132289 ACTTCCTTCACAACAGTTCGAGA 59.868 43.478 0.00 0.00 0.00 4.04
593 609 8.139989 GCAATGATTTGGATAGTAAAGAATGCT 58.860 33.333 0.00 0.00 33.22 3.79
595 611 8.985315 ATGATTTGGATAGTAAAGAATGCTCA 57.015 30.769 0.00 0.00 0.00 4.26
665 682 7.434013 CACAACCTAGGACAAAAATTAACACAC 59.566 37.037 17.98 0.00 0.00 3.82
682 699 1.899814 ACACGGACATGACACATAGGT 59.100 47.619 0.00 0.00 0.00 3.08
697 714 7.179516 TGACACATAGGTAAAACTGATGAGGTA 59.820 37.037 0.00 0.00 0.00 3.08
702 719 2.770164 AAAACTGATGAGGTAGCGCT 57.230 45.000 17.26 17.26 0.00 5.92
712 729 2.496070 TGAGGTAGCGCTTTGTCATAGT 59.504 45.455 18.68 0.00 0.00 2.12
783 800 5.929278 TGGTCGTAATTGAAACCATTAACG 58.071 37.500 4.15 0.00 36.88 3.18
840 859 2.757099 GTTAGGGACGGGCGAGGA 60.757 66.667 0.00 0.00 0.00 3.71
940 960 1.178276 GCTCCTCTCCTCGTTTCTCA 58.822 55.000 0.00 0.00 0.00 3.27
981 1001 4.201122 GGCTGCAGAGGGATGGGG 62.201 72.222 20.43 0.00 0.00 4.96
982 1002 4.201122 GCTGCAGAGGGATGGGGG 62.201 72.222 20.43 0.00 0.00 5.40
983 1003 4.201122 CTGCAGAGGGATGGGGGC 62.201 72.222 8.42 0.00 0.00 5.80
1010 1030 4.431131 AAGCAGGATGGGTGGCCG 62.431 66.667 0.00 0.00 35.86 6.13
1135 1155 2.743928 CCAGCCTTCGGAGCACAC 60.744 66.667 0.00 0.00 0.00 3.82
1148 1168 2.358125 CACACGGGTGCGGATCAA 60.358 61.111 4.08 0.00 38.37 2.57
1149 1169 1.963855 CACACGGGTGCGGATCAAA 60.964 57.895 4.08 0.00 38.37 2.69
1179 1199 2.747855 CGGGCTTGTGAAGGAGCC 60.748 66.667 5.84 5.84 45.99 4.70
1183 1203 2.684843 GCTTGTGAAGGAGCCGCAG 61.685 63.158 0.00 0.00 0.00 5.18
1310 1330 3.907474 TGGAATCTACAGGACTTTCCACA 59.093 43.478 0.00 0.00 37.86 4.17
1320 1340 2.291741 GGACTTTCCACAAGTTCTGCTG 59.708 50.000 0.00 0.00 36.28 4.41
1350 1370 3.794911 AGCCCTCCTCAATTTGGAATTT 58.205 40.909 0.00 0.00 32.61 1.82
1492 2338 4.752101 GCAATAAGCGTGATTGGAGTAGAT 59.248 41.667 9.39 0.00 35.28 1.98
1504 2350 8.946085 GTGATTGGAGTAGATGATTTTTGTGTA 58.054 33.333 0.00 0.00 0.00 2.90
1506 2352 9.941664 GATTGGAGTAGATGATTTTTGTGTATG 57.058 33.333 0.00 0.00 0.00 2.39
1507 2353 7.320443 TGGAGTAGATGATTTTTGTGTATGC 57.680 36.000 0.00 0.00 0.00 3.14
1508 2354 6.883756 TGGAGTAGATGATTTTTGTGTATGCA 59.116 34.615 0.00 0.00 0.00 3.96
1509 2355 7.392953 TGGAGTAGATGATTTTTGTGTATGCAA 59.607 33.333 0.00 0.00 0.00 4.08
1510 2356 7.912250 GGAGTAGATGATTTTTGTGTATGCAAG 59.088 37.037 0.00 0.00 0.00 4.01
1628 2474 0.175760 TGATCAACTCGCACCTAGCC 59.824 55.000 0.00 0.00 41.38 3.93
1649 2495 1.461127 GAAAGCACACGAAGGTAGCAG 59.539 52.381 0.00 0.00 0.00 4.24
1673 2519 2.144738 ACCAGCCCGTACACAAGGT 61.145 57.895 0.00 0.00 0.00 3.50
1697 2543 1.270839 GGGCTTGCTGTAGTCTTGACA 60.271 52.381 3.49 0.00 0.00 3.58
1701 2547 3.058639 GCTTGCTGTAGTCTTGACAAAGG 60.059 47.826 3.49 0.00 33.90 3.11
1710 2556 2.806244 GTCTTGACAAAGGCATGTACGT 59.194 45.455 0.00 0.00 37.97 3.57
1718 2564 0.385751 AGGCATGTACGTGGAGATCG 59.614 55.000 16.68 0.00 0.00 3.69
1745 2591 4.526650 TGGTTGATAGCTACTGTTGTCTCA 59.473 41.667 0.00 0.00 0.00 3.27
1746 2592 5.011635 TGGTTGATAGCTACTGTTGTCTCAA 59.988 40.000 0.00 0.00 0.00 3.02
1805 2651 5.838529 TCAGTCTATGACAAAAGTTCACGA 58.161 37.500 0.00 0.00 34.60 4.35
1833 2679 5.582665 GCTACTGAAGAAATCAATCGACCTT 59.417 40.000 0.00 0.00 37.67 3.50
2008 2854 7.164230 ACGAGAATACAGAGATTTCTTGACT 57.836 36.000 6.23 0.00 35.39 3.41
2012 2858 7.684529 AGAATACAGAGATTTCTTGACTGGTT 58.315 34.615 0.00 0.00 33.57 3.67
2065 2911 5.355071 CAGAATAGTGCATCTTTTGGCAGTA 59.645 40.000 3.92 3.92 46.51 2.74
2193 3039 9.817809 CTCAAAACTTGGTTATAGCTCTGTATA 57.182 33.333 0.00 0.00 0.00 1.47
2231 3077 6.089417 GGCAACTATATGTGCTTTTTGTTCAC 59.911 38.462 7.49 0.00 0.00 3.18
2388 3236 7.011499 TGTTAACAGTACCACCATAATCAGT 57.989 36.000 3.59 0.00 0.00 3.41
2389 3237 6.876789 TGTTAACAGTACCACCATAATCAGTG 59.123 38.462 3.59 0.00 0.00 3.66
2394 3242 1.027357 CCACCATAATCAGTGGCTGC 58.973 55.000 0.00 0.00 46.55 5.25
2395 3243 0.659427 CACCATAATCAGTGGCTGCG 59.341 55.000 0.00 0.00 40.49 5.18
2396 3244 0.253044 ACCATAATCAGTGGCTGCGT 59.747 50.000 0.00 0.00 40.49 5.24
2397 3245 1.340017 ACCATAATCAGTGGCTGCGTT 60.340 47.619 0.00 0.00 40.49 4.84
2398 3246 1.331756 CCATAATCAGTGGCTGCGTTC 59.668 52.381 0.00 0.00 0.00 3.95
2399 3247 2.009051 CATAATCAGTGGCTGCGTTCA 58.991 47.619 0.00 0.00 0.00 3.18
2400 3248 2.401583 TAATCAGTGGCTGCGTTCAT 57.598 45.000 0.00 0.00 0.00 2.57
2401 3249 0.806868 AATCAGTGGCTGCGTTCATG 59.193 50.000 0.00 0.00 0.00 3.07
2402 3250 1.028330 ATCAGTGGCTGCGTTCATGG 61.028 55.000 0.00 0.00 0.00 3.66
2424 3272 2.358193 ATATTCACCAGCGCGGCGTA 62.358 55.000 24.46 5.89 39.03 4.42
2644 3496 3.146066 TGTGATGTCAGGTTTTAGCCAC 58.854 45.455 0.00 0.00 0.00 5.01
2773 5209 1.201647 GTCGTACCTAGCAGACAAGCA 59.798 52.381 0.00 0.00 36.85 3.91
2874 5310 4.386652 CCAATTGCTTGCTGTACATTTGAC 59.613 41.667 0.00 0.00 30.18 3.18
2885 5321 8.105097 TGCTGTACATTTGACTAAATAAAGCA 57.895 30.769 0.00 5.56 35.89 3.91
2984 5421 8.561738 TGGACAATAAAGAGACAAGGTATTTC 57.438 34.615 0.00 0.00 0.00 2.17
3047 5484 6.687105 GCATAAATACGGTTGAAGCTTTACTG 59.313 38.462 15.91 15.91 0.00 2.74
3055 5492 6.373216 ACGGTTGAAGCTTTACTGCAATATTA 59.627 34.615 16.92 0.00 46.01 0.98
3107 5544 8.246180 TCAAGATTGAGCACCTCATTATTTTTC 58.754 33.333 0.00 0.00 40.39 2.29
3220 5657 6.500684 ACTGCAGTGTAAATATGGTTGAAG 57.499 37.500 20.97 0.00 0.00 3.02
3223 5660 6.176896 TGCAGTGTAAATATGGTTGAAGCTA 58.823 36.000 0.00 0.00 0.00 3.32
3228 5665 6.912591 GTGTAAATATGGTTGAAGCTATGTGC 59.087 38.462 0.00 0.00 43.29 4.57
3280 5717 7.119846 GTGTGGTAAATATAGATTGAGCATCCC 59.880 40.741 2.75 0.00 36.51 3.85
3281 5718 7.168219 GTGGTAAATATAGATTGAGCATCCCA 58.832 38.462 2.75 0.00 36.51 4.37
3289 5726 5.531122 AGATTGAGCATCCCATTCATTTG 57.469 39.130 0.00 0.00 31.20 2.32
3297 5734 2.582052 TCCCATTCATTTGCGGGATAC 58.418 47.619 0.00 0.00 42.94 2.24
3301 5738 3.548014 CCATTCATTTGCGGGATACGTTC 60.548 47.826 0.00 0.00 46.52 3.95
3407 5844 5.105752 CAGTGATGGTAGCTTTACTCAGTC 58.894 45.833 0.00 0.00 0.00 3.51
3416 5853 7.981789 TGGTAGCTTTACTCAGTCTGAATATTG 59.018 37.037 3.67 0.00 0.00 1.90
3468 5905 3.312421 TCTTTTGTGTTGCCTCTCTTTCG 59.688 43.478 0.00 0.00 0.00 3.46
3574 6021 1.391485 CGGAAGTGCTCGATTGTCTTG 59.609 52.381 0.00 0.00 0.00 3.02
3596 6043 9.601217 TCTTGTAAGCTAGAATTCTTATGGTTC 57.399 33.333 14.36 10.20 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 119 1.078823 TGACACCTATCAGGGGAGTGT 59.921 52.381 0.37 0.00 43.10 3.55
162 174 6.647334 TTCATGTTTGAGCTTGGTTCAATA 57.353 33.333 0.00 0.00 33.23 1.90
220 236 1.102978 GACCCATTGGCCATGTACAC 58.897 55.000 6.09 0.00 33.59 2.90
238 254 0.984230 ATCCTCGGCCAAAACTCAGA 59.016 50.000 2.24 0.00 0.00 3.27
273 289 4.485163 ACGCAAATTTTCCAAGATAGTGC 58.515 39.130 0.00 0.00 0.00 4.40
294 310 2.093235 CCCAGACTCCTCCATTTGAGAC 60.093 54.545 0.00 0.00 44.42 3.36
313 329 0.459489 TTGCAAAGCAAGTGTCACCC 59.541 50.000 0.00 0.00 43.99 4.61
356 372 3.023119 TGTGAGTGTGGCTTCAACATTT 58.977 40.909 0.00 0.00 0.00 2.32
417 433 8.985315 TGCCACATCTTCTATATTCTCAAATT 57.015 30.769 0.00 0.00 0.00 1.82
458 474 2.541466 AGTACTGGCTAGGCATATCCC 58.459 52.381 20.56 6.47 34.51 3.85
498 514 7.484324 CGGCAAATTTTCAAAGTTTTTGTTCAT 59.516 29.630 1.92 0.00 31.56 2.57
514 530 5.245075 TGGTAAATCTTCCTCGGCAAATTTT 59.755 36.000 0.00 0.00 0.00 1.82
593 609 4.416848 TCCCAAAATTCCCCCAAAAATTGA 59.583 37.500 0.00 0.00 0.00 2.57
595 611 5.409590 TTCCCAAAATTCCCCCAAAAATT 57.590 34.783 0.00 0.00 0.00 1.82
650 667 5.974751 GTCATGTCCGTGTGTTAATTTTTGT 59.025 36.000 0.00 0.00 0.00 2.83
665 682 5.063438 CAGTTTTACCTATGTGTCATGTCCG 59.937 44.000 0.00 0.00 0.00 4.79
682 699 3.887621 AGCGCTACCTCATCAGTTTTA 57.112 42.857 8.99 0.00 0.00 1.52
697 714 8.141909 TGATACTTATTACTATGACAAAGCGCT 58.858 33.333 2.64 2.64 0.00 5.92
712 729 7.713073 TGAACGTGGATGCATTGATACTTATTA 59.287 33.333 0.00 0.00 0.00 0.98
771 788 0.519792 GCGCGACCGTTAATGGTTTC 60.520 55.000 20.35 13.49 44.01 2.78
772 789 1.229315 TGCGCGACCGTTAATGGTTT 61.229 50.000 20.35 0.00 44.01 3.27
773 790 1.229315 TTGCGCGACCGTTAATGGTT 61.229 50.000 20.35 4.76 44.01 3.67
801 818 1.517361 CACGTGGCATAGCTCCTCA 59.483 57.895 7.95 0.00 0.00 3.86
840 859 6.976934 TTTTCCCAGCTATCTGTTTTTCTT 57.023 33.333 0.00 0.00 38.66 2.52
866 886 4.384647 GGAGGTGTTATCTGGCTGATCTTT 60.385 45.833 10.36 0.00 36.65 2.52
869 889 2.224402 GGGAGGTGTTATCTGGCTGATC 60.224 54.545 10.36 0.00 36.65 2.92
873 893 0.044855 AGGGGAGGTGTTATCTGGCT 59.955 55.000 0.00 0.00 0.00 4.75
940 960 2.364448 GGAGGAAGAGGCGGAGGT 60.364 66.667 0.00 0.00 0.00 3.85
983 1003 3.307089 ATCCTGCTTGCCCCCTTGG 62.307 63.158 0.00 0.00 37.09 3.61
1010 1030 2.755103 AGATCCGGCAAAGAAATCAACC 59.245 45.455 0.00 0.00 0.00 3.77
1012 1032 3.016736 GGAGATCCGGCAAAGAAATCAA 58.983 45.455 0.00 0.00 0.00 2.57
1074 1094 3.068881 CCGGAGTTGAAGAGGGCA 58.931 61.111 0.00 0.00 0.00 5.36
1076 1096 1.078848 CAGCCGGAGTTGAAGAGGG 60.079 63.158 5.05 0.00 0.00 4.30
1135 1155 3.508840 GCCTTTGATCCGCACCCG 61.509 66.667 0.00 0.00 0.00 5.28
1144 1164 0.606401 CGTCCACCACTGCCTTTGAT 60.606 55.000 0.00 0.00 0.00 2.57
1145 1165 1.227823 CGTCCACCACTGCCTTTGA 60.228 57.895 0.00 0.00 0.00 2.69
1146 1166 2.260869 CCGTCCACCACTGCCTTTG 61.261 63.158 0.00 0.00 0.00 2.77
1147 1167 2.113139 CCGTCCACCACTGCCTTT 59.887 61.111 0.00 0.00 0.00 3.11
1148 1168 3.953775 CCCGTCCACCACTGCCTT 61.954 66.667 0.00 0.00 0.00 4.35
1167 1187 2.032528 CCTGCGGCTCCTTCACAA 59.967 61.111 0.00 0.00 0.00 3.33
1197 1217 3.092511 ATGCGGCCTGGATGTCCT 61.093 61.111 0.00 0.00 36.82 3.85
1310 1330 4.072839 GGCTAACCTTAACAGCAGAACTT 58.927 43.478 0.00 0.00 37.02 2.66
1443 2289 8.391106 CAAAAACTAATTCCTCTACTCCAATCG 58.609 37.037 0.00 0.00 0.00 3.34
1492 2338 4.597404 TGCCTTGCATACACAAAAATCA 57.403 36.364 0.00 0.00 31.71 2.57
1504 2350 2.951101 GCCTTGCCTTGCCTTGCAT 61.951 57.895 0.00 0.00 38.76 3.96
1506 2352 3.167822 TTGCCTTGCCTTGCCTTGC 62.168 57.895 0.00 0.00 0.00 4.01
1507 2353 1.005394 CTTGCCTTGCCTTGCCTTG 60.005 57.895 0.00 0.00 0.00 3.61
1508 2354 2.875804 GCTTGCCTTGCCTTGCCTT 61.876 57.895 0.00 0.00 0.00 4.35
1509 2355 3.308705 GCTTGCCTTGCCTTGCCT 61.309 61.111 0.00 0.00 0.00 4.75
1510 2356 4.383861 GGCTTGCCTTGCCTTGCC 62.384 66.667 4.11 0.00 46.38 4.52
1628 2474 0.438830 GCTACCTTCGTGTGCTTTCG 59.561 55.000 0.00 0.00 0.00 3.46
1639 2485 0.685097 TGGTGTGACCTGCTACCTTC 59.315 55.000 0.00 0.00 39.58 3.46
1649 2495 2.047560 GTACGGGCTGGTGTGACC 60.048 66.667 0.00 0.00 39.22 4.02
1673 2519 3.605749 GACTACAGCAAGCCCGGCA 62.606 63.158 13.15 0.00 0.00 5.69
1697 2543 2.738643 CGATCTCCACGTACATGCCTTT 60.739 50.000 0.00 0.00 0.00 3.11
1701 2547 1.215655 GCCGATCTCCACGTACATGC 61.216 60.000 0.00 0.00 0.00 4.06
1710 2556 0.911769 ATCAACCAAGCCGATCTCCA 59.088 50.000 0.00 0.00 0.00 3.86
1718 2564 3.268023 ACAGTAGCTATCAACCAAGCC 57.732 47.619 0.00 0.00 39.64 4.35
1745 2591 4.223923 CCACCCAGTTAAGAGAGATCTGTT 59.776 45.833 0.00 0.00 33.74 3.16
1746 2592 3.772025 CCACCCAGTTAAGAGAGATCTGT 59.228 47.826 0.00 0.00 0.00 3.41
1750 2596 3.707102 GCTACCACCCAGTTAAGAGAGAT 59.293 47.826 0.00 0.00 0.00 2.75
1805 2651 6.091441 GTCGATTGATTTCTTCAGTAGCTTGT 59.909 38.462 0.00 0.00 35.27 3.16
1833 2679 1.003580 CCAAAGCTAGCCAACAGAGGA 59.996 52.381 12.13 0.00 0.00 3.71
1918 2764 5.464389 AGTGTTTATTCGTGTACTTCCACAC 59.536 40.000 0.00 0.00 44.37 3.82
1935 2781 4.261405 CCTTGTTCCAATCGCAAGTGTTTA 60.261 41.667 0.00 0.00 38.24 2.01
2008 2854 8.648698 TTAGGAAATCAAGATGAATTCAACCA 57.351 30.769 13.09 0.00 37.87 3.67
2012 2858 9.519191 TCACTTTAGGAAATCAAGATGAATTCA 57.481 29.630 11.26 11.26 37.87 2.57
2193 3039 4.736611 ATAGTTGCCAAGGATCCATGAT 57.263 40.909 18.56 0.00 0.00 2.45
2194 3040 5.073554 ACATATAGTTGCCAAGGATCCATGA 59.926 40.000 18.56 0.00 0.00 3.07
2308 3156 3.484524 GCCCATGCTTATTGCGATG 57.515 52.632 0.00 0.00 46.63 3.84
2388 3236 2.549169 TATGCCCATGAACGCAGCCA 62.549 55.000 0.00 0.00 38.64 4.75
2389 3237 1.174712 ATATGCCCATGAACGCAGCC 61.175 55.000 0.00 0.00 38.64 4.85
2390 3238 0.670162 AATATGCCCATGAACGCAGC 59.330 50.000 0.00 0.00 38.64 5.25
2391 3239 1.948834 TGAATATGCCCATGAACGCAG 59.051 47.619 0.00 0.00 38.64 5.18
2392 3240 1.675483 GTGAATATGCCCATGAACGCA 59.325 47.619 0.00 0.00 39.79 5.24
2393 3241 1.001378 GGTGAATATGCCCATGAACGC 60.001 52.381 0.00 0.00 0.00 4.84
2394 3242 2.291465 CTGGTGAATATGCCCATGAACG 59.709 50.000 0.00 0.00 0.00 3.95
2395 3243 2.035066 GCTGGTGAATATGCCCATGAAC 59.965 50.000 0.00 0.00 0.00 3.18
2396 3244 2.309613 GCTGGTGAATATGCCCATGAA 58.690 47.619 0.00 0.00 0.00 2.57
2397 3245 1.815021 CGCTGGTGAATATGCCCATGA 60.815 52.381 0.00 0.00 0.00 3.07
2398 3246 0.594602 CGCTGGTGAATATGCCCATG 59.405 55.000 0.00 0.00 0.00 3.66
2399 3247 1.174712 GCGCTGGTGAATATGCCCAT 61.175 55.000 0.00 0.00 0.00 4.00
2400 3248 1.823470 GCGCTGGTGAATATGCCCA 60.823 57.895 0.00 0.00 0.00 5.36
2401 3249 2.896801 CGCGCTGGTGAATATGCCC 61.897 63.158 5.56 0.00 0.00 5.36
2402 3250 2.633657 CGCGCTGGTGAATATGCC 59.366 61.111 5.56 0.00 0.00 4.40
2857 5293 8.964420 TTTATTTAGTCAAATGTACAGCAAGC 57.036 30.769 0.33 0.00 35.88 4.01
3020 5457 6.995511 AAAGCTTCAACCGTATTTATGCTA 57.004 33.333 0.00 0.00 0.00 3.49
3022 5459 6.687105 CAGTAAAGCTTCAACCGTATTTATGC 59.313 38.462 0.00 0.00 0.00 3.14
3055 5492 6.649155 TCACCACACATATATGTTACAGCTT 58.351 36.000 15.85 0.00 39.39 3.74
3107 5544 7.721286 AGAAATTGCATCGTCCTAATCTAAG 57.279 36.000 0.00 0.00 0.00 2.18
3123 5560 8.037166 AGGAACTCAATGGATTAAAGAAATTGC 58.963 33.333 0.00 0.00 0.00 3.56
3176 5613 7.816995 TGCAGTTGTCGTATATATATGCATGAA 59.183 33.333 10.16 0.00 36.33 2.57
3200 5637 5.567138 AGCTTCAACCATATTTACACTGC 57.433 39.130 0.00 0.00 0.00 4.40
3261 5698 9.543231 AATGAATGGGATGCTCAATCTATATTT 57.457 29.630 0.00 0.00 35.43 1.40
3280 5717 3.312421 AGAACGTATCCCGCAAATGAATG 59.688 43.478 0.00 0.00 41.42 2.67
3281 5718 3.541632 AGAACGTATCCCGCAAATGAAT 58.458 40.909 0.00 0.00 41.42 2.57
3289 5726 1.680207 ACTAAGGAGAACGTATCCCGC 59.320 52.381 14.46 0.00 41.42 6.13
3297 5734 4.457834 ACTCAATGGACTAAGGAGAACG 57.542 45.455 0.00 0.00 0.00 3.95
3416 5853 6.651975 TGGAAGAACCTACTAAGCTATAGC 57.348 41.667 17.33 17.33 39.86 2.97
3574 6021 8.966069 AAGGAACCATAAGAATTCTAGCTTAC 57.034 34.615 8.75 0.00 30.17 2.34
3596 6043 4.099419 ACAAAACAAGCCCAGTAAGAAAGG 59.901 41.667 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.