Multiple sequence alignment - TraesCS7A01G006200

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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 TraesCS7A01G006200 chr7A 100.000 6838 0 0 1 6838 3006020 2999183 0.000000e+00 12628.0
1 TraesCS7A01G006200 chr7A 92.678 3032 176 21 3647 6648 2552793 2549778 0.000000e+00 4327.0
2 TraesCS7A01G006200 chr7A 91.803 2574 194 10 4080 6648 3381680 3384241 0.000000e+00 3568.0
3 TraesCS7A01G006200 chr7A 88.175 1869 168 29 2224 4063 3581485 3583329 0.000000e+00 2178.0
4 TraesCS7A01G006200 chr7A 90.774 1615 116 18 3647 5241 2849768 2848167 0.000000e+00 2126.0
5 TraesCS7A01G006200 chr7A 91.715 1038 82 2 1654 2690 3379597 3380631 0.000000e+00 1437.0
6 TraesCS7A01G006200 chr7A 89.796 1029 101 2 1663 2687 2554210 2553182 0.000000e+00 1315.0
7 TraesCS7A01G006200 chr7A 85.451 543 45 17 6107 6648 2848154 2847645 1.010000e-147 534.0
8 TraesCS7A01G006200 chr7A 81.132 424 33 22 3670 4063 3381206 3381612 5.190000e-76 296.0
9 TraesCS7A01G006200 chr7A 93.651 189 11 1 6650 6838 3384274 3384461 1.450000e-71 281.0
10 TraesCS7A01G006200 chr7A 90.426 94 9 0 6154 6247 13337640 13337547 2.590000e-24 124.0
11 TraesCS7A01G006200 chr7A 88.235 102 5 5 6646 6747 2549749 2549655 1.560000e-21 115.0
12 TraesCS7A01G006200 chr4A 94.090 2589 143 9 4065 6648 739808636 739811219 0.000000e+00 3925.0
13 TraesCS7A01G006200 chr4A 94.205 2554 137 9 4065 6614 740867702 740865156 0.000000e+00 3886.0
14 TraesCS7A01G006200 chr4A 93.429 2572 156 10 4079 6645 733927094 733924531 0.000000e+00 3801.0
15 TraesCS7A01G006200 chr4A 95.967 2306 87 2 428 2733 739804976 739807275 0.000000e+00 3738.0
16 TraesCS7A01G006200 chr4A 95.488 2305 83 8 431 2733 740870764 740868479 0.000000e+00 3661.0
17 TraesCS7A01G006200 chr4A 94.132 2386 125 8 4079 6454 739833365 739835745 0.000000e+00 3616.0
18 TraesCS7A01G006200 chr4A 81.957 1962 229 64 777 2690 739830485 739832369 0.000000e+00 1546.0
19 TraesCS7A01G006200 chr4A 91.368 1031 86 1 1661 2688 740063272 740062242 0.000000e+00 1408.0
20 TraesCS7A01G006200 chr4A 90.891 1032 90 2 1661 2688 742271668 742270637 0.000000e+00 1382.0
21 TraesCS7A01G006200 chr4A 86.906 947 66 17 2730 3664 739807333 739808233 0.000000e+00 1009.0
22 TraesCS7A01G006200 chr4A 91.435 432 30 4 7 432 740871239 740870809 2.750000e-163 586.0
23 TraesCS7A01G006200 chr4A 90.323 434 33 4 1 425 739804492 739804925 1.670000e-155 560.0
24 TraesCS7A01G006200 chr4A 89.773 352 32 3 3647 3994 739832890 739833241 1.350000e-121 448.0
25 TraesCS7A01G006200 chr4A 86.747 415 37 7 3647 4055 742270115 742269713 4.870000e-121 446.0
26 TraesCS7A01G006200 chr4A 89.266 354 35 2 3647 3997 740061720 740061367 2.260000e-119 440.0
27 TraesCS7A01G006200 chr4A 90.728 151 14 0 6498 6648 742078164 742078314 1.160000e-47 202.0
28 TraesCS7A01G006200 chr4A 86.667 135 9 4 2739 2864 740868411 740868277 2.570000e-29 141.0
29 TraesCS7A01G006200 chr4A 88.571 105 5 3 6643 6747 739811246 739811343 3.350000e-23 121.0
30 TraesCS7A01G006200 chr4A 87.255 102 6 1 6646 6747 733924500 733924406 7.250000e-20 110.0
31 TraesCS7A01G006200 chr4A 92.105 76 6 0 6641 6716 742267146 742267071 2.610000e-19 108.0
32 TraesCS7A01G006200 chr4A 93.750 64 4 0 2828 2891 742270392 742270329 5.640000e-16 97.1
33 TraesCS7A01G006200 chr4A 91.429 70 3 1 6650 6716 740864819 740864750 7.300000e-15 93.5
34 TraesCS7A01G006200 chr4A 90.625 64 6 0 2828 2891 733927837 733927774 1.220000e-12 86.1
35 TraesCS7A01G006200 chr4A 93.103 58 4 0 2828 2885 739832611 739832668 1.220000e-12 86.1
36 TraesCS7A01G006200 chr7D 89.408 3040 258 28 3627 6648 2429621 2432614 0.000000e+00 3771.0
37 TraesCS7A01G006200 chr7D 91.097 2662 183 29 3647 6281 3729844 3727210 0.000000e+00 3554.0
38 TraesCS7A01G006200 chr7D 92.535 2371 108 28 428 2788 3437321 3439632 0.000000e+00 3334.0
39 TraesCS7A01G006200 chr7D 93.420 2006 119 9 4079 6082 3699796 3701790 0.000000e+00 2961.0
40 TraesCS7A01G006200 chr7D 92.079 1616 115 6 1657 3260 3697386 3699000 0.000000e+00 2263.0
41 TraesCS7A01G006200 chr7D 87.549 763 54 19 3307 4063 3699002 3699729 0.000000e+00 845.0
42 TraesCS7A01G006200 chr7D 87.022 732 42 15 2936 3664 3439813 3440494 0.000000e+00 776.0
43 TraesCS7A01G006200 chr7D 92.857 434 25 2 1 428 3436843 3437276 5.820000e-175 625.0
44 TraesCS7A01G006200 chr7D 89.535 344 33 2 3651 3991 3583317 3583660 3.790000e-117 433.0
45 TraesCS7A01G006200 chr7D 87.619 105 6 3 6643 6747 3443558 3443655 1.560000e-21 115.0
46 TraesCS7A01G006200 chr7D 81.944 144 12 8 2782 2911 3439678 3439821 7.250000e-20 110.0
47 TraesCS7A01G006200 chr7D 90.789 76 7 0 6641 6716 3594518 3594593 1.210000e-17 102.0
48 TraesCS7A01G006200 chr7D 90.789 76 6 1 6642 6716 2432635 2432710 4.360000e-17 100.0
49 TraesCS7A01G006200 chr7D 92.188 64 5 0 2828 2891 3582960 3583023 2.630000e-14 91.6
50 TraesCS7A01G006200 chr6A 93.651 63 4 0 3301 3363 18036750 18036812 2.030000e-15 95.3


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 TraesCS7A01G006200 chr7A 2999183 3006020 6837 True 12628.000000 12628 100.000000 1 6838 1 chr7A.!!$R1 6837
1 TraesCS7A01G006200 chr7A 3581485 3583329 1844 False 2178.000000 2178 88.175000 2224 4063 1 chr7A.!!$F1 1839
2 TraesCS7A01G006200 chr7A 2549655 2554210 4555 True 1919.000000 4327 90.236333 1663 6747 3 chr7A.!!$R3 5084
3 TraesCS7A01G006200 chr7A 3379597 3384461 4864 False 1395.500000 3568 89.575250 1654 6838 4 chr7A.!!$F2 5184
4 TraesCS7A01G006200 chr7A 2847645 2849768 2123 True 1330.000000 2126 88.112500 3647 6648 2 chr7A.!!$R4 3001
5 TraesCS7A01G006200 chr4A 739804492 739811343 6851 False 1870.600000 3925 91.171400 1 6747 5 chr4A.!!$F2 6746
6 TraesCS7A01G006200 chr4A 740864750 740871239 6489 True 1673.500000 3886 91.844800 7 6716 5 chr4A.!!$R3 6709
7 TraesCS7A01G006200 chr4A 739830485 739835745 5260 False 1424.025000 3616 89.741250 777 6454 4 chr4A.!!$F3 5677
8 TraesCS7A01G006200 chr4A 733924406 733927837 3431 True 1332.366667 3801 90.436333 2828 6747 3 chr4A.!!$R1 3919
9 TraesCS7A01G006200 chr4A 740061367 740063272 1905 True 924.000000 1408 90.317000 1661 3997 2 chr4A.!!$R2 2336
10 TraesCS7A01G006200 chr4A 742267071 742271668 4597 True 508.275000 1382 90.873250 1661 6716 4 chr4A.!!$R4 5055
11 TraesCS7A01G006200 chr7D 3727210 3729844 2634 True 3554.000000 3554 91.097000 3647 6281 1 chr7D.!!$R1 2634
12 TraesCS7A01G006200 chr7D 3697386 3701790 4404 False 2023.000000 2961 91.016000 1657 6082 3 chr7D.!!$F5 4425
13 TraesCS7A01G006200 chr7D 2429621 2432710 3089 False 1935.500000 3771 90.098500 3627 6716 2 chr7D.!!$F2 3089
14 TraesCS7A01G006200 chr7D 3436843 3443655 6812 False 992.000000 3334 88.395400 1 6747 5 chr7D.!!$F3 6746
15 TraesCS7A01G006200 chr7D 3582960 3583660 700 False 262.300000 433 90.861500 2828 3991 2 chr7D.!!$F4 1163

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
58 59 0.034896 CTGCTACCAACTGAACCGGT 59.965 55.0 0.00 0.00 36.79 5.28 F
276 277 0.179936 CATCTCTGGTCCTTGCCCTC 59.820 60.0 0.00 0.00 0.00 4.30 F
1558 1638 0.459585 CGATGGTGACCGTACCCTTG 60.460 60.0 0.00 0.00 40.09 3.61 F
2547 2672 0.317020 GTGAAGCGAGTTGTGCCAAC 60.317 55.0 9.31 9.31 0.00 3.77 F
3305 3904 0.452784 CACTAACGGCAGAAAAGCGC 60.453 55.0 0.00 0.00 34.64 5.92 F
3320 3919 0.508641 AGCGCGCATCGATTGATTAC 59.491 50.0 35.10 0.00 41.67 1.89 F
4795 5532 0.178990 GGCTGGAAGGGTTTGACAGT 60.179 55.0 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1105 1177 0.614812 GCCATGGCAAGGGAACAAAT 59.385 50.000 32.08 0.00 41.49 2.32 R
1974 2096 0.659427 TACCTCGTAGATTGCCGTCG 59.341 55.000 0.00 0.00 33.89 5.12 R
3248 3847 0.117541 TAGGCCACCCTTACTGGACA 59.882 55.000 5.01 0.00 39.64 4.02 R
4008 4685 0.107312 CCTTCGGAGGACTCGGTAGA 60.107 60.000 2.45 0.08 46.74 2.59 R
4721 5458 1.191535 ACGAATGGAATGGGAGTCGA 58.808 50.000 0.00 0.00 34.03 4.20 R
5136 5874 7.811282 TCCCTTATATTGAGCTTGTAAATGGA 58.189 34.615 0.00 0.00 0.00 3.41 R
6230 6983 0.528924 TGCATGCATCTGAAGGCAAC 59.471 50.000 18.46 7.49 46.57 4.17 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
58 59 0.034896 CTGCTACCAACTGAACCGGT 59.965 55.000 0.00 0.00 36.79 5.28
89 90 1.842381 CTCCACCGCCTTCTTTCCCT 61.842 60.000 0.00 0.00 0.00 4.20
113 114 1.293498 GGCGAGCTCCTTTGAGTCA 59.707 57.895 8.47 0.00 40.95 3.41
144 145 3.002348 GTCTTCTTGTTTCCACCAGTTCG 59.998 47.826 0.00 0.00 0.00 3.95
164 165 4.113815 CATCTGCCTGCCCGGGAA 62.114 66.667 29.31 15.24 30.11 3.97
191 192 2.219875 CCATCCATAGGCCTCCGCT 61.220 63.158 9.68 0.00 34.44 5.52
235 236 1.407258 CTGACTGCTAGTGCCTACTCC 59.593 57.143 0.00 0.00 38.36 3.85
244 245 3.075005 GCCTACTCCGTGGCCAGA 61.075 66.667 5.11 0.00 43.11 3.86
276 277 0.179936 CATCTCTGGTCCTTGCCCTC 59.820 60.000 0.00 0.00 0.00 4.30
327 334 5.760253 TGAGGGAAGATCGAATTAATCAAGC 59.240 40.000 0.00 0.00 0.00 4.01
428 441 6.263842 TCTTCAACATTGATTTCACAGCTCTT 59.736 34.615 0.00 0.00 37.00 2.85
477 535 7.944729 AATGAAGTTCATATTGTGGTTAGCT 57.055 32.000 18.56 0.00 35.76 3.32
497 558 3.002862 GCTGGACAGATCTACTAGTCGTG 59.997 52.174 0.00 0.00 31.98 4.35
554 615 6.915300 TCAGTGATTAAAATTTCACCACAACG 59.085 34.615 4.70 0.00 42.56 4.10
637 698 7.618964 CAAGAATTGTTTCATGTTCTGACTG 57.381 36.000 0.00 0.00 42.34 3.51
718 781 7.368480 TGGGTCTAGCGTTTTCTAAATTAAC 57.632 36.000 0.00 0.00 0.00 2.01
847 910 8.045507 TCTATTCTTGATCTGAACTTTCTGCAT 58.954 33.333 0.00 0.00 0.00 3.96
910 978 3.886505 TGAAGTTTGTGGTGGGTCATTAC 59.113 43.478 0.00 0.00 0.00 1.89
929 998 5.873179 TTACGAACAACCATGAAGATTCC 57.127 39.130 0.00 0.00 0.00 3.01
941 1010 2.964464 TGAAGATTCCTTTTGGCAAGCA 59.036 40.909 0.00 0.00 40.12 3.91
1019 1088 3.640407 GCCCTGGCCAGTGACTGA 61.640 66.667 30.63 0.00 32.44 3.41
1026 1095 1.911357 TGGCCAGTGACTGATCAAGAT 59.089 47.619 15.33 0.00 36.31 2.40
1094 1166 3.950395 CTCCCCATCTCCATTTTCTGTTC 59.050 47.826 0.00 0.00 0.00 3.18
1105 1177 7.234782 TCTCCATTTTCTGTTCTCTGGTAGTTA 59.765 37.037 0.00 0.00 0.00 2.24
1152 1225 4.105754 TGTTACCAACCAACCATCATCA 57.894 40.909 0.00 0.00 0.00 3.07
1488 1563 8.859090 AGGACAATTTGACATTCACAAGAATTA 58.141 29.630 2.79 0.00 42.46 1.40
1558 1638 0.459585 CGATGGTGACCGTACCCTTG 60.460 60.000 0.00 0.00 40.09 3.61
1755 1877 3.559171 GCCCAAGAGTACACTTTGATCCA 60.559 47.826 2.49 0.00 0.00 3.41
1974 2096 1.399440 TGCAAGATGCTCTTTCATCGC 59.601 47.619 3.78 0.00 45.57 4.58
2047 2169 1.195115 AGATTGCCGAGCTCAAGGTA 58.805 50.000 15.40 4.31 0.00 3.08
2434 2556 3.855689 ATTCTTGGTCAAATCAAGCCG 57.144 42.857 0.00 0.00 40.82 5.52
2510 2635 3.059352 TGGAGAAGAAAAGCCTAGTGC 57.941 47.619 0.00 0.00 41.71 4.40
2547 2672 0.317020 GTGAAGCGAGTTGTGCCAAC 60.317 55.000 9.31 9.31 0.00 3.77
2572 2697 2.281484 GGTCACAGGCCGCAAAGA 60.281 61.111 0.00 0.00 0.00 2.52
2597 2722 2.103042 GGCAGCACGCAGAGTAAGG 61.103 63.158 0.00 0.00 45.17 2.69
2747 3164 9.990360 TTAAGTATGTACACTGATGACTGAAAA 57.010 29.630 0.00 0.00 0.00 2.29
2805 3278 2.403252 ATGTAGTGGTGCCTTGCTAC 57.597 50.000 0.00 0.00 35.62 3.58
2810 3292 3.502123 AGTGGTGCCTTGCTACTAAAA 57.498 42.857 0.00 0.00 0.00 1.52
2812 3294 3.568430 AGTGGTGCCTTGCTACTAAAAAC 59.432 43.478 0.00 0.00 0.00 2.43
2903 3418 2.817258 AGCAAATTTAGTACCGCTGCAA 59.183 40.909 0.00 0.00 0.00 4.08
2909 3424 7.112984 GCAAATTTAGTACCGCTGCAAATATAC 59.887 37.037 0.00 0.00 0.00 1.47
3051 3572 7.975866 ACTATAAATTTGAATTTCTGCAGCG 57.024 32.000 9.47 0.00 39.24 5.18
3090 3683 6.315393 AGCAAGTAACATACTAAATTGGACCG 59.685 38.462 0.00 0.00 38.26 4.79
3143 3738 7.181361 TGTCCCTCCAATTCATAAAAAGATGA 58.819 34.615 0.00 0.00 33.96 2.92
3165 3760 6.068010 TGACAATTTGGACATAGGTCAGTTT 58.932 36.000 10.08 0.00 46.17 2.66
3176 3771 5.238650 ACATAGGTCAGTTTGTACTTGTTGC 59.761 40.000 0.00 0.00 30.26 4.17
3228 3824 2.683768 ACTCTTGGACTGTTGAGAGGT 58.316 47.619 15.59 4.44 39.88 3.85
3257 3856 6.516739 TGTTGTTGTGAAAATGTCCAGTAA 57.483 33.333 0.00 0.00 0.00 2.24
3269 3868 1.209747 GTCCAGTAAGGGTGGCCTAAG 59.790 57.143 3.32 0.00 38.24 2.18
3297 3896 5.048991 ACCTAAACATTTTCACTAACGGCAG 60.049 40.000 0.00 0.00 0.00 4.85
3305 3904 0.452784 CACTAACGGCAGAAAAGCGC 60.453 55.000 0.00 0.00 34.64 5.92
3320 3919 0.508641 AGCGCGCATCGATTGATTAC 59.491 50.000 35.10 0.00 41.67 1.89
3403 4003 2.360350 AATCGCCTGCCACCACTG 60.360 61.111 0.00 0.00 0.00 3.66
3447 4058 1.512926 AACTGACCTCACGCATGTTC 58.487 50.000 0.00 0.00 0.00 3.18
3504 4115 1.145803 GCCTGTTACACCAACGAGAC 58.854 55.000 0.00 0.00 40.26 3.36
3520 4131 6.313905 CCAACGAGACATAGCTCAAATTAACT 59.686 38.462 0.00 0.00 34.56 2.24
3590 4205 8.910944 AGGAACTATGTATTGTATCACTAACGT 58.089 33.333 0.00 0.00 36.02 3.99
3591 4206 8.965172 GGAACTATGTATTGTATCACTAACGTG 58.035 37.037 0.00 0.00 42.59 4.49
3625 4242 3.853355 AATTGGGCAGATCTAGGTGAG 57.147 47.619 0.00 0.00 0.00 3.51
3649 4267 3.173599 CGACATTGGTGTGATGCATTTC 58.826 45.455 0.00 0.00 39.09 2.17
3667 4311 7.587629 TGCATTTCTTTCTCACTTGTATGAAG 58.412 34.615 0.00 0.00 0.00 3.02
3704 4349 8.621532 AGCACATTTCTTCTCACTTGTATTTA 57.378 30.769 0.00 0.00 0.00 1.40
3740 4389 4.376146 GCAGGTATCTCCTCTTGATTGAC 58.624 47.826 0.00 0.00 46.24 3.18
3806 4455 6.265577 GTTGCCACATGATAATACAAAGGAC 58.734 40.000 0.00 0.00 0.00 3.85
3909 4586 5.648092 ACAGTTAATGTTCTAAGTGATGCCC 59.352 40.000 5.43 0.00 39.96 5.36
3998 4675 6.054295 GGATACAAGATCTCAAGCTGATGTT 58.946 40.000 0.00 0.00 0.00 2.71
3999 4676 6.202570 GGATACAAGATCTCAAGCTGATGTTC 59.797 42.308 0.00 0.00 0.00 3.18
4000 4677 4.260170 ACAAGATCTCAAGCTGATGTTCC 58.740 43.478 0.00 0.00 0.00 3.62
4001 4678 4.019501 ACAAGATCTCAAGCTGATGTTCCT 60.020 41.667 0.00 0.00 0.00 3.36
4002 4679 5.188555 ACAAGATCTCAAGCTGATGTTCCTA 59.811 40.000 0.00 0.00 0.00 2.94
4003 4680 5.534207 AGATCTCAAGCTGATGTTCCTAG 57.466 43.478 0.00 0.00 0.00 3.02
4004 4681 4.961730 AGATCTCAAGCTGATGTTCCTAGT 59.038 41.667 0.00 0.00 0.00 2.57
4005 4682 4.462508 TCTCAAGCTGATGTTCCTAGTG 57.537 45.455 0.00 0.00 0.00 2.74
4006 4683 3.834813 TCTCAAGCTGATGTTCCTAGTGT 59.165 43.478 0.00 0.00 0.00 3.55
4007 4684 4.284490 TCTCAAGCTGATGTTCCTAGTGTT 59.716 41.667 0.00 0.00 0.00 3.32
4008 4685 4.973168 TCAAGCTGATGTTCCTAGTGTTT 58.027 39.130 0.00 0.00 0.00 2.83
4009 4686 4.997395 TCAAGCTGATGTTCCTAGTGTTTC 59.003 41.667 0.00 0.00 0.00 2.78
4045 4722 5.847304 CGAAGGAGATGGAACTGATAATCA 58.153 41.667 0.00 0.00 0.00 2.57
4067 4744 2.094854 GCCTTCAGCTCATGTTCAAAGG 60.095 50.000 10.34 10.34 38.99 3.11
4094 4822 2.108425 GGTTGGGGAGAAAGAAGAGGTT 59.892 50.000 0.00 0.00 0.00 3.50
4098 4826 4.435137 TGGGGAGAAAGAAGAGGTTCATA 58.565 43.478 0.00 0.00 34.82 2.15
4099 4827 5.039645 TGGGGAGAAAGAAGAGGTTCATAT 58.960 41.667 0.00 0.00 34.82 1.78
4172 4900 3.673484 CTTGTGGCCTGCAACCCG 61.673 66.667 3.32 0.00 0.00 5.28
4206 4935 5.183904 AGTGATCATTGGAGTAAAGTTTGCC 59.816 40.000 0.00 0.00 0.00 4.52
4430 5159 3.312404 TGCAGAGGAAGTTGCAGAC 57.688 52.632 0.00 0.00 44.72 3.51
4682 5419 4.159321 TCAACAAAAGGCATGAACTTGTCA 59.841 37.500 0.00 0.00 41.67 3.58
4795 5532 0.178990 GGCTGGAAGGGTTTGACAGT 60.179 55.000 0.00 0.00 0.00 3.55
5390 6134 0.034059 AGCTGACCCTTTCTGTGACG 59.966 55.000 0.00 0.00 0.00 4.35
5545 6289 4.349048 CAGGGAGATCATTATTCCACCTGA 59.651 45.833 0.00 0.00 44.26 3.86
5573 6317 3.005897 TCAAGAGTCTAAAGCTGCTTCGT 59.994 43.478 16.28 3.41 0.00 3.85
5726 6470 2.344950 CAAGAGGTGCATCTCAGTGTC 58.655 52.381 28.21 1.27 36.30 3.67
5831 6575 3.193267 GCAAGTGGCCAAAGATAATCACA 59.807 43.478 7.24 0.00 36.11 3.58
5853 6597 6.018098 CACAGAGTGAAGAGATTGGAATATGC 60.018 42.308 0.00 0.00 35.23 3.14
5873 6617 4.075682 TGCCACATTATCTTTCGGTTGAA 58.924 39.130 0.00 0.00 0.00 2.69
5874 6618 4.520874 TGCCACATTATCTTTCGGTTGAAA 59.479 37.500 0.00 0.00 41.69 2.69
5921 6665 5.907866 ATAATTAAGTGGGGGTTGTTTCG 57.092 39.130 0.00 0.00 0.00 3.46
6024 6768 3.195610 ACTGCTGAATCCGTCACTCATTA 59.804 43.478 0.00 0.00 31.13 1.90
6033 6777 8.826710 TGAATCCGTCACTCATTATTGTAATTC 58.173 33.333 0.00 0.00 0.00 2.17
6189 6936 5.012664 AGTCACATGGTTCAGTTGGTGTATA 59.987 40.000 0.00 0.00 0.00 1.47
6230 6983 3.263425 TGCTGGAGTTTTAGGAAGGTAGG 59.737 47.826 0.00 0.00 0.00 3.18
6298 7062 0.323629 TACCAGGAACTCCCGCTTTG 59.676 55.000 0.00 0.00 40.87 2.77
6506 7403 9.507329 AATGCATATAAGTTCAATACTACCAGG 57.493 33.333 0.00 0.00 35.54 4.45
6538 7436 4.953667 TGAAATTTTGGCTGTGCATACAA 58.046 34.783 0.00 0.00 36.14 2.41
6640 7540 1.990160 AACAAACCAGGAGCGTGGGA 61.990 55.000 13.17 0.00 42.54 4.37
6648 7548 0.682855 AGGAGCGTGGGAGAGAGAAG 60.683 60.000 0.00 0.00 0.00 2.85
6657 7858 3.454082 GTGGGAGAGAGAAGGAATGATGT 59.546 47.826 0.00 0.00 0.00 3.06
6794 7998 9.913310 TTCCCAAAGAAAAGGAACATTTTATTT 57.087 25.926 10.09 10.09 41.66 1.40
6818 8022 6.553953 GGGAACAAACCCCAAATGTATATT 57.446 37.500 0.00 0.00 43.81 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.485066 GCGGTGGAGAAATTAGGAGGA 59.515 52.381 0.00 0.00 0.00 3.71
89 90 1.167851 CAAAGGAGCTCGCCAATCAA 58.832 50.000 7.83 0.00 0.00 2.57
113 114 3.433740 GGAAACAAGAAGACACTGGGAGT 60.434 47.826 0.00 0.00 0.00 3.85
144 145 4.864334 CCGGGCAGGCAGATGGAC 62.864 72.222 0.00 0.00 0.00 4.02
164 165 1.441729 CTATGGATGGCGTGGTCGT 59.558 57.895 0.00 0.00 39.49 4.34
166 167 1.598130 GCCTATGGATGGCGTGGTC 60.598 63.158 0.00 0.00 41.03 4.02
235 236 2.047844 CCTGTGACTCTGGCCACG 60.048 66.667 0.00 0.00 36.15 4.94
303 304 5.760253 GCTTGATTAATTCGATCTTCCCTCA 59.240 40.000 0.00 0.00 0.00 3.86
327 334 2.658325 GCAACAAACAAGAAGCTATGCG 59.342 45.455 0.00 0.00 0.00 4.73
477 535 4.482952 TCACGACTAGTAGATCTGTCCA 57.517 45.455 10.22 0.00 0.00 4.02
554 615 4.519540 AACATGGCAATTGGTACTGTTC 57.480 40.909 7.72 0.00 0.00 3.18
718 781 5.817296 TCATTCCATAAATCGTGGTGAGAAG 59.183 40.000 0.00 0.00 37.96 2.85
785 848 0.768221 TCCCACCTCCTCAGCAGTTT 60.768 55.000 0.00 0.00 0.00 2.66
910 978 5.376854 AAAGGAATCTTCATGGTTGTTCG 57.623 39.130 0.00 0.00 31.82 3.95
929 998 0.249996 CCAACCCTGCTTGCCAAAAG 60.250 55.000 0.00 0.00 0.00 2.27
1019 1088 6.567602 AGCTGGTTACTAAGGAATCTTGAT 57.432 37.500 0.00 0.00 34.59 2.57
1026 1095 6.013206 TGGACAATAAGCTGGTTACTAAGGAA 60.013 38.462 0.81 0.00 0.00 3.36
1094 1166 5.123979 GCAAGGGAACAAATAACTACCAGAG 59.876 44.000 0.00 0.00 0.00 3.35
1105 1177 0.614812 GCCATGGCAAGGGAACAAAT 59.385 50.000 32.08 0.00 41.49 2.32
1202 1275 7.852971 ACTGAATGGCATTTTCCAATTTATG 57.147 32.000 14.93 0.00 39.96 1.90
1488 1563 8.654094 TCCACATGTCTAATCAGATCATGTAAT 58.346 33.333 12.77 0.00 43.68 1.89
1755 1877 2.842462 TGTCACTGCGGACACCCT 60.842 61.111 0.00 0.00 42.56 4.34
1974 2096 0.659427 TACCTCGTAGATTGCCGTCG 59.341 55.000 0.00 0.00 33.89 5.12
2047 2169 0.810648 CAGCAATGTATTGTGCCCGT 59.189 50.000 6.48 0.00 41.88 5.28
2434 2556 6.404074 CCTTTGGCTTGATTTGACTATCTGTC 60.404 42.308 0.00 0.00 45.54 3.51
2510 2635 5.855395 GCTTCACTGAGCTTTTAATGTCTTG 59.145 40.000 0.00 0.00 39.57 3.02
2547 2672 2.125753 GCCTGTGACCAGAGAGCG 60.126 66.667 0.00 0.00 41.50 5.03
2572 2697 0.961857 TCTGCGTGCTGCCATCATTT 60.962 50.000 0.00 0.00 45.60 2.32
2597 2722 5.957842 TGGTCATGGTTCATTGTTTCTAC 57.042 39.130 0.00 0.00 0.00 2.59
2737 3091 8.923270 TCTTAAAAACTCCCATTTTTCAGTCAT 58.077 29.630 0.00 0.00 40.18 3.06
2775 3195 5.188948 AGGCACCACTACATACATAACTTCA 59.811 40.000 0.00 0.00 0.00 3.02
2776 3196 5.671493 AGGCACCACTACATACATAACTTC 58.329 41.667 0.00 0.00 0.00 3.01
2969 3487 5.279356 GCACCCAAGTTAAGTACTAGACTGT 60.279 44.000 10.75 3.94 38.87 3.55
3051 3572 3.443099 ACTTGCTGCCTTTTTCTCAAC 57.557 42.857 0.00 0.00 0.00 3.18
3119 3714 7.122650 TGTCATCTTTTTATGAATTGGAGGGAC 59.877 37.037 0.00 0.00 37.61 4.46
3143 3738 5.833131 ACAAACTGACCTATGTCCAAATTGT 59.167 36.000 0.00 0.74 41.01 2.71
3165 3760 3.188667 TCAACACAAACGCAACAAGTACA 59.811 39.130 0.00 0.00 0.00 2.90
3248 3847 0.117541 TAGGCCACCCTTACTGGACA 59.882 55.000 5.01 0.00 39.64 4.02
3269 3868 5.466819 GTTAGTGAAAATGTTTAGGTGGGC 58.533 41.667 0.00 0.00 0.00 5.36
3275 3874 6.236017 TCTGCCGTTAGTGAAAATGTTTAG 57.764 37.500 0.00 0.00 0.00 1.85
3277 3876 5.508200 TTCTGCCGTTAGTGAAAATGTTT 57.492 34.783 0.00 0.00 0.00 2.83
3297 3896 0.247655 TCAATCGATGCGCGCTTTTC 60.248 50.000 33.29 23.25 40.61 2.29
3305 3904 5.387855 GCTCTTACTGTAATCAATCGATGCG 60.388 44.000 0.00 0.00 30.13 4.73
3320 3919 5.149977 GCTTTTGCTTAACTGCTCTTACTG 58.850 41.667 0.00 0.00 43.35 2.74
3430 4030 1.800805 AAGAACATGCGTGAGGTCAG 58.199 50.000 14.17 0.00 0.00 3.51
3558 4173 9.601217 GTGATACAATACATAGTTCCTCACTTT 57.399 33.333 0.00 0.00 36.88 2.66
3560 4175 8.540507 AGTGATACAATACATAGTTCCTCACT 57.459 34.615 0.00 0.00 39.87 3.41
3625 4242 0.454957 GCATCACACCAATGTCGTGC 60.455 55.000 0.00 0.00 36.72 5.34
3667 4311 9.709600 GAGAAGAAATGTGCTAGCTTATTTAAC 57.290 33.333 21.53 16.79 0.00 2.01
3704 4349 5.147767 AGATACCTGCCAAGAAAAAGGTTT 58.852 37.500 0.00 0.00 40.14 3.27
3740 4389 5.805486 CCATGTTTCTACGGACCATATATCG 59.195 44.000 0.00 0.00 0.00 2.92
3909 4586 5.649395 TCTGATGAAATAGGCTTTTGGAGTG 59.351 40.000 0.00 0.00 0.00 3.51
3945 4622 1.538687 CCTTCTTTGCTGCTTGGGGG 61.539 60.000 0.00 0.00 0.00 5.40
3994 4671 4.771054 ACTCGGTAGAAACACTAGGAACAT 59.229 41.667 0.00 0.00 0.00 2.71
3998 4675 3.009916 AGGACTCGGTAGAAACACTAGGA 59.990 47.826 0.00 0.00 0.00 2.94
3999 4676 3.354467 AGGACTCGGTAGAAACACTAGG 58.646 50.000 0.00 0.00 0.00 3.02
4000 4677 3.377798 GGAGGACTCGGTAGAAACACTAG 59.622 52.174 0.00 0.00 0.00 2.57
4001 4678 3.350833 GGAGGACTCGGTAGAAACACTA 58.649 50.000 0.00 0.00 0.00 2.74
4002 4679 2.169330 GGAGGACTCGGTAGAAACACT 58.831 52.381 0.00 0.00 0.00 3.55
4003 4680 1.135460 CGGAGGACTCGGTAGAAACAC 60.135 57.143 0.00 0.00 0.00 3.32
4004 4681 1.171308 CGGAGGACTCGGTAGAAACA 58.829 55.000 0.00 0.00 0.00 2.83
4005 4682 1.457346 TCGGAGGACTCGGTAGAAAC 58.543 55.000 6.76 0.00 0.00 2.78
4006 4683 2.089980 CTTCGGAGGACTCGGTAGAAA 58.910 52.381 7.45 0.00 32.01 2.52
4007 4684 1.681166 CCTTCGGAGGACTCGGTAGAA 60.681 57.143 2.45 6.56 46.74 2.10
4008 4685 0.107312 CCTTCGGAGGACTCGGTAGA 60.107 60.000 2.45 0.08 46.74 2.59
4009 4686 2.406205 CCTTCGGAGGACTCGGTAG 58.594 63.158 2.45 6.65 46.74 3.18
4056 4733 3.553508 CCAACCTTGCTCCTTTGAACATG 60.554 47.826 0.00 0.00 0.00 3.21
4063 4740 0.113190 CTCCCCAACCTTGCTCCTTT 59.887 55.000 0.00 0.00 0.00 3.11
4067 4744 1.073923 TCTTTCTCCCCAACCTTGCTC 59.926 52.381 0.00 0.00 0.00 4.26
4094 4822 9.506018 CCGCAATATTTCCATATATCCATATGA 57.494 33.333 3.65 0.00 44.70 2.15
4098 4826 6.070656 CCCCGCAATATTTCCATATATCCAT 58.929 40.000 0.00 0.00 0.00 3.41
4099 4827 5.445069 CCCCGCAATATTTCCATATATCCA 58.555 41.667 0.00 0.00 0.00 3.41
4127 4855 1.367346 TGGTGACTATGGCCAAAGGA 58.633 50.000 10.96 0.00 0.00 3.36
4172 4900 5.125100 TCCAATGATCACTCTGTTTTTGC 57.875 39.130 0.00 0.00 0.00 3.68
4179 4908 7.524912 CAAACTTTACTCCAATGATCACTCTG 58.475 38.462 0.00 0.00 0.00 3.35
4206 4935 5.163683 CCACTTGCTCTGGAAATAATGACTG 60.164 44.000 0.00 0.00 0.00 3.51
4430 5159 7.584108 TGCTTACAAGTTGATTGAAGTATGTG 58.416 34.615 10.54 0.00 41.83 3.21
4658 5395 5.163426 TGACAAGTTCATGCCTTTTGTTGAT 60.163 36.000 6.29 0.00 32.58 2.57
4721 5458 1.191535 ACGAATGGAATGGGAGTCGA 58.808 50.000 0.00 0.00 34.03 4.20
5136 5874 7.811282 TCCCTTATATTGAGCTTGTAAATGGA 58.189 34.615 0.00 0.00 0.00 3.41
5390 6134 4.817517 TGAAAGTATCAGTCCGAAGAACC 58.182 43.478 0.00 0.00 33.04 3.62
5545 6289 4.940654 GCAGCTTTAGACTCTTGAATCCTT 59.059 41.667 0.00 0.00 0.00 3.36
5573 6317 1.408702 GGCACCAGAGTTGCAAAGAAA 59.591 47.619 0.00 0.00 0.00 2.52
5726 6470 5.440685 GTTATTTCATCCGCTTGATTACCG 58.559 41.667 0.00 0.00 0.00 4.02
5831 6575 5.131642 TGGCATATTCCAATCTCTTCACTCT 59.868 40.000 0.00 0.00 32.18 3.24
5853 6597 6.920758 TGTTTTTCAACCGAAAGATAATGTGG 59.079 34.615 0.00 0.00 42.00 4.17
5873 6617 6.183360 ACAACACGTACCAGATGATTTGTTTT 60.183 34.615 0.00 0.00 0.00 2.43
5874 6618 5.298276 ACAACACGTACCAGATGATTTGTTT 59.702 36.000 0.00 0.00 0.00 2.83
5921 6665 1.618640 GAAGGCGACGCAGACTTGAC 61.619 60.000 23.09 0.83 0.00 3.18
6158 6905 4.256920 ACTGAACCATGTGACTGCTATTC 58.743 43.478 0.00 0.00 0.00 1.75
6189 6936 1.072965 CACTTTGGGCAAGAGACCTCT 59.927 52.381 0.00 0.00 46.30 3.69
6230 6983 0.528924 TGCATGCATCTGAAGGCAAC 59.471 50.000 18.46 7.49 46.57 4.17
6298 7062 6.403333 TCGCTAAGACAATCAAACATGTAC 57.597 37.500 0.00 0.00 0.00 2.90
6332 7221 5.735070 GCATTGATATACAAAACGGGGGTTC 60.735 44.000 0.00 0.00 42.03 3.62
6506 7403 6.742264 CACAGCCAAAATTTCAAAAACTGTTC 59.258 34.615 0.00 0.00 33.82 3.18
6538 7436 5.241728 GCTCTCTGAAACCTTACATTTTGGT 59.758 40.000 0.00 0.00 35.29 3.67
6605 7505 6.303839 TGGTTTGTTCTTTAGATTAGCACCT 58.696 36.000 0.00 0.00 0.00 4.00
6617 7517 1.676006 CACGCTCCTGGTTTGTTCTTT 59.324 47.619 0.00 0.00 0.00 2.52
6640 7540 5.248020 ACACTTCACATCATTCCTTCTCTCT 59.752 40.000 0.00 0.00 0.00 3.10
6648 7548 6.108687 TCATACTGACACTTCACATCATTCC 58.891 40.000 0.00 0.00 0.00 3.01
6657 7858 4.752146 CAGCAGATCATACTGACACTTCA 58.248 43.478 0.00 0.00 39.94 3.02
6751 7955 5.606348 TGGGAACAAACAAGCTTTAATGT 57.394 34.783 0.00 0.00 37.44 2.71


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

AutoCloner maintained by Alex Coulton.