Multiple sequence alignment - TraesCS7B01G455400

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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 TraesCS7B01G455400 chr7B 100.000 3300 0 0 1 3300 716131644 716134943 0.000000e+00 6095.0
1 TraesCS7B01G455400 chr7B 90.778 553 42 2 1683 2226 716041889 716042441 0.000000e+00 730.0
2 TraesCS7B01G455400 chr7B 84.190 506 60 13 1111 1606 716041324 716041819 1.070000e-129 473.0
3 TraesCS7B01G455400 chr7B 90.278 144 7 1 1 137 427686153 427686296 7.270000e-42 182.0
4 TraesCS7B01G455400 chr7B 100.000 28 0 0 2399 2426 716134127 716134154 6.000000e-03 52.8
5 TraesCS7B01G455400 chr7D 94.407 1341 64 7 1065 2394 620475446 620476786 0.000000e+00 2050.0
6 TraesCS7B01G455400 chr7D 92.541 925 37 14 136 1046 620474482 620475388 0.000000e+00 1297.0
7 TraesCS7B01G455400 chr7D 89.821 560 47 3 1683 2232 620282138 620282697 0.000000e+00 710.0
8 TraesCS7B01G455400 chr7D 86.355 513 52 10 1109 1612 620281539 620282042 8.050000e-151 544.0
9 TraesCS7B01G455400 chr7D 91.034 145 6 1 1 138 594209301 594209157 4.350000e-44 189.0
10 TraesCS7B01G455400 chr7A 85.440 1147 121 26 1109 2226 714617905 714616776 0.000000e+00 1151.0
11 TraesCS7B01G455400 chr6B 90.089 787 69 2 138 916 718274614 718275399 0.000000e+00 1013.0
12 TraesCS7B01G455400 chr6B 83.969 917 89 34 2430 3300 277638219 277637315 0.000000e+00 826.0
13 TraesCS7B01G455400 chr6B 90.604 149 6 2 1 141 390039474 390039326 1.210000e-44 191.0
14 TraesCS7B01G455400 chr2D 84.825 916 91 24 2420 3300 188054355 188055257 0.000000e+00 878.0
15 TraesCS7B01G455400 chr2D 90.411 146 7 1 1 139 134535699 134535844 5.620000e-43 185.0
16 TraesCS7B01G455400 chr1D 85.106 893 82 34 2421 3300 256318282 256319136 0.000000e+00 865.0
17 TraesCS7B01G455400 chr1D 83.077 910 102 24 2421 3300 109131118 109132005 0.000000e+00 780.0
18 TraesCS7B01G455400 chr1D 86.455 347 22 11 2978 3300 476505179 476504834 1.130000e-94 357.0
19 TraesCS7B01G455400 chr2A 83.787 919 97 28 2420 3300 201015862 201016766 0.000000e+00 824.0
20 TraesCS7B01G455400 chr2A 83.260 908 112 17 2420 3300 200941936 200942830 0.000000e+00 798.0
21 TraesCS7B01G455400 chr2A 82.604 914 109 33 2421 3300 289834416 289835313 0.000000e+00 761.0
22 TraesCS7B01G455400 chr2A 89.130 138 9 1 1 132 138919556 138919419 2.040000e-37 167.0
23 TraesCS7B01G455400 chr5D 83.296 898 102 25 2435 3299 310807229 310806347 0.000000e+00 784.0
24 TraesCS7B01G455400 chr5D 87.614 549 37 19 2776 3299 429708017 429707475 2.820000e-170 608.0
25 TraesCS7B01G455400 chr5D 88.819 474 39 8 138 610 528220765 528221225 1.330000e-158 569.0
26 TraesCS7B01G455400 chr5D 89.116 147 9 1 1 140 517961238 517961092 3.380000e-40 176.0
27 TraesCS7B01G455400 chr3B 81.291 914 113 37 2420 3299 167258624 167257735 0.000000e+00 688.0
28 TraesCS7B01G455400 chr3D 80.748 909 99 37 2427 3300 411661992 411662859 9.980000e-180 640.0
29 TraesCS7B01G455400 chr3D 80.769 208 28 7 1243 1450 469805183 469804988 5.700000e-33 152.0
30 TraesCS7B01G455400 chr3D 79.500 200 30 6 1243 1442 493036731 493036543 7.430000e-27 132.0
31 TraesCS7B01G455400 chr1B 82.504 663 89 21 2427 3076 412922707 412922059 1.030000e-154 556.0
32 TraesCS7B01G455400 chr1B 87.919 149 11 2 1 142 228245701 228245849 5.660000e-38 169.0
33 TraesCS7B01G455400 chr6A 83.721 602 72 19 2434 3028 140752771 140753353 2.240000e-151 545.0
34 TraesCS7B01G455400 chr6A 88.591 149 9 2 1 141 284816299 284816447 1.220000e-39 174.0
35 TraesCS7B01G455400 chr4D 95.455 220 10 0 3080 3299 390831974 390832193 5.240000e-93 351.0
36 TraesCS7B01G455400 chr4D 95.413 218 10 0 3083 3300 448540621 448540404 6.780000e-92 348.0
37 TraesCS7B01G455400 chr4D 90.345 145 7 1 1 138 395403300 395403156 2.020000e-42 183.0
38 TraesCS7B01G455400 chr4D 85.294 102 13 2 1341 1441 502489013 502489113 1.620000e-18 104.0
39 TraesCS7B01G455400 chr2B 90.476 147 7 1 1 140 120234200 120234054 1.560000e-43 187.0
40 TraesCS7B01G455400 chr2B 86.207 145 13 1 1 138 556600150 556600006 2.050000e-32 150.0
41 TraesCS7B01G455400 chr2B 84.516 155 15 3 1 147 480456521 480456674 9.540000e-31 145.0
42 TraesCS7B01G455400 chr4B 89.655 145 8 1 1 138 302845522 302845666 9.410000e-41 178.0
43 TraesCS7B01G455400 chr6D 88.591 149 9 3 1 141 200865089 200864941 1.220000e-39 174.0
44 TraesCS7B01G455400 chr6D 87.857 140 13 4 1 137 95017074 95017212 9.480000e-36 161.0
45 TraesCS7B01G455400 chr4A 87.662 154 11 3 1 146 671653507 671653354 4.380000e-39 172.0
46 TraesCS7B01G455400 chr5A 85.149 101 15 0 1341 1441 685793483 685793583 1.620000e-18 104.0


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 TraesCS7B01G455400 chr7B 716131644 716134943 3299 False 3073.9 6095 100.000 1 3300 2 chr7B.!!$F3 3299
1 TraesCS7B01G455400 chr7B 716041324 716042441 1117 False 601.5 730 87.484 1111 2226 2 chr7B.!!$F2 1115
2 TraesCS7B01G455400 chr7D 620474482 620476786 2304 False 1673.5 2050 93.474 136 2394 2 chr7D.!!$F2 2258
3 TraesCS7B01G455400 chr7D 620281539 620282697 1158 False 627.0 710 88.088 1109 2232 2 chr7D.!!$F1 1123
4 TraesCS7B01G455400 chr7A 714616776 714617905 1129 True 1151.0 1151 85.440 1109 2226 1 chr7A.!!$R1 1117
5 TraesCS7B01G455400 chr6B 718274614 718275399 785 False 1013.0 1013 90.089 138 916 1 chr6B.!!$F1 778
6 TraesCS7B01G455400 chr6B 277637315 277638219 904 True 826.0 826 83.969 2430 3300 1 chr6B.!!$R1 870
7 TraesCS7B01G455400 chr2D 188054355 188055257 902 False 878.0 878 84.825 2420 3300 1 chr2D.!!$F2 880
8 TraesCS7B01G455400 chr1D 256318282 256319136 854 False 865.0 865 85.106 2421 3300 1 chr1D.!!$F2 879
9 TraesCS7B01G455400 chr1D 109131118 109132005 887 False 780.0 780 83.077 2421 3300 1 chr1D.!!$F1 879
10 TraesCS7B01G455400 chr2A 201015862 201016766 904 False 824.0 824 83.787 2420 3300 1 chr2A.!!$F2 880
11 TraesCS7B01G455400 chr2A 200941936 200942830 894 False 798.0 798 83.260 2420 3300 1 chr2A.!!$F1 880
12 TraesCS7B01G455400 chr2A 289834416 289835313 897 False 761.0 761 82.604 2421 3300 1 chr2A.!!$F3 879
13 TraesCS7B01G455400 chr5D 310806347 310807229 882 True 784.0 784 83.296 2435 3299 1 chr5D.!!$R1 864
14 TraesCS7B01G455400 chr5D 429707475 429708017 542 True 608.0 608 87.614 2776 3299 1 chr5D.!!$R2 523
15 TraesCS7B01G455400 chr3B 167257735 167258624 889 True 688.0 688 81.291 2420 3299 1 chr3B.!!$R1 879
16 TraesCS7B01G455400 chr3D 411661992 411662859 867 False 640.0 640 80.748 2427 3300 1 chr3D.!!$F1 873
17 TraesCS7B01G455400 chr1B 412922059 412922707 648 True 556.0 556 82.504 2427 3076 1 chr1B.!!$R1 649
18 TraesCS7B01G455400 chr6A 140752771 140753353 582 False 545.0 545 83.721 2434 3028 1 chr6A.!!$F1 594

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
86 87 0.179094 TCGGTCAAACTTGCACTCGT 60.179 50.0 0.00 0.00 0.00 4.18 F
967 976 0.308068 GATGAGCTCGCGTGCTAGTA 59.692 55.0 32.83 22.34 44.17 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 1080 0.966920 GGTCTTCAGAGGTCCGTCAA 59.033 55.0 0.0 0.0 0.00 3.18 R
2394 2515 0.179062 AGGTGAAGGCATCATCGCTC 60.179 55.0 0.0 0.0 44.36 5.03 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
25 26 8.786826 ATGAAACTACTTTTCGTGATGGATAA 57.213 30.769 0.00 0.00 45.96 1.75
26 27 8.610248 TGAAACTACTTTTCGTGATGGATAAA 57.390 30.769 0.00 0.00 45.96 1.40
27 28 9.058174 TGAAACTACTTTTCGTGATGGATAAAA 57.942 29.630 0.00 0.00 45.96 1.52
29 30 9.840427 AAACTACTTTTCGTGATGGATAAAATG 57.160 29.630 0.00 0.00 0.00 2.32
30 31 8.786826 ACTACTTTTCGTGATGGATAAAATGA 57.213 30.769 0.00 0.00 0.00 2.57
31 32 9.396022 ACTACTTTTCGTGATGGATAAAATGAT 57.604 29.630 0.00 0.00 0.00 2.45
81 82 3.859411 AAAAACTCGGTCAAACTTGCA 57.141 38.095 0.00 0.00 0.00 4.08
82 83 2.844122 AAACTCGGTCAAACTTGCAC 57.156 45.000 0.00 0.00 0.00 4.57
83 84 2.038387 AACTCGGTCAAACTTGCACT 57.962 45.000 0.00 0.00 0.00 4.40
84 85 1.583054 ACTCGGTCAAACTTGCACTC 58.417 50.000 0.00 0.00 0.00 3.51
85 86 0.508641 CTCGGTCAAACTTGCACTCG 59.491 55.000 0.00 0.00 0.00 4.18
86 87 0.179094 TCGGTCAAACTTGCACTCGT 60.179 50.000 0.00 0.00 0.00 4.18
87 88 0.655733 CGGTCAAACTTGCACTCGTT 59.344 50.000 0.00 0.00 0.00 3.85
88 89 1.063469 CGGTCAAACTTGCACTCGTTT 59.937 47.619 0.00 0.00 33.92 3.60
89 90 2.450160 GGTCAAACTTGCACTCGTTTG 58.550 47.619 20.85 20.85 46.90 2.93
94 95 4.434713 AAACTTGCACTCGTTTGACTTT 57.565 36.364 7.04 0.00 32.55 2.66
95 96 4.434713 AACTTGCACTCGTTTGACTTTT 57.565 36.364 0.00 0.00 0.00 2.27
96 97 4.016113 ACTTGCACTCGTTTGACTTTTC 57.984 40.909 0.00 0.00 0.00 2.29
97 98 3.438781 ACTTGCACTCGTTTGACTTTTCA 59.561 39.130 0.00 0.00 0.00 2.69
98 99 4.083003 ACTTGCACTCGTTTGACTTTTCAA 60.083 37.500 0.00 0.00 40.14 2.69
132 133 7.091533 ACACCTTATATAAAGGAATGGAGGG 57.908 40.000 10.67 4.11 39.81 4.30
133 134 6.855061 ACACCTTATATAAAGGAATGGAGGGA 59.145 38.462 10.67 0.00 39.81 4.20
134 135 7.017651 ACACCTTATATAAAGGAATGGAGGGAG 59.982 40.741 10.67 3.30 39.81 4.30
197 198 3.265479 AGGTCCAAAAAGATCTCTCCCTG 59.735 47.826 0.00 0.00 0.00 4.45
359 368 3.403038 CTTCCTTCATATTGGGCTACCG 58.597 50.000 0.00 0.00 40.75 4.02
404 413 2.103771 TGTTGATCTAGAGGCTGCATCC 59.896 50.000 11.08 0.00 0.00 3.51
429 438 9.850628 CCGAATATCATTAATTTGATTCTGCAT 57.149 29.630 0.00 0.00 37.51 3.96
459 468 1.288127 GCTGCTGAAGTGGCCTTTG 59.712 57.895 3.32 0.00 0.00 2.77
460 469 1.174712 GCTGCTGAAGTGGCCTTTGA 61.175 55.000 3.32 0.00 0.00 2.69
487 496 2.143925 GCACCACACTTTGAGAGTACC 58.856 52.381 0.00 0.00 36.65 3.34
489 498 3.006537 GCACCACACTTTGAGAGTACCTA 59.993 47.826 0.00 0.00 36.65 3.08
830 839 0.798776 GATCGAACAAGCCACACTGG 59.201 55.000 0.00 0.00 41.55 4.00
879 888 8.060090 GCATACGATTGTAATTAACGTTAGCTT 58.940 33.333 8.23 8.90 38.18 3.74
934 943 2.666994 GGTGTAGCAGCTTTACTCGTTC 59.333 50.000 0.00 0.00 0.00 3.95
966 975 1.064946 GATGAGCTCGCGTGCTAGT 59.935 57.895 32.83 23.99 44.17 2.57
967 976 0.308068 GATGAGCTCGCGTGCTAGTA 59.692 55.000 32.83 22.34 44.17 1.82
968 977 0.955178 ATGAGCTCGCGTGCTAGTAT 59.045 50.000 32.83 23.38 44.17 2.12
969 978 1.589803 TGAGCTCGCGTGCTAGTATA 58.410 50.000 32.83 15.50 44.17 1.47
970 979 2.152016 TGAGCTCGCGTGCTAGTATAT 58.848 47.619 32.83 11.95 44.17 0.86
971 980 2.159824 TGAGCTCGCGTGCTAGTATATC 59.840 50.000 32.83 19.81 44.17 1.63
972 981 1.469308 AGCTCGCGTGCTAGTATATCC 59.531 52.381 31.99 0.48 42.10 2.59
973 982 1.469308 GCTCGCGTGCTAGTATATCCT 59.531 52.381 24.65 0.00 0.00 3.24
976 985 3.409570 TCGCGTGCTAGTATATCCTTCT 58.590 45.455 5.77 0.00 0.00 2.85
977 986 3.436015 TCGCGTGCTAGTATATCCTTCTC 59.564 47.826 5.77 0.00 0.00 2.87
978 987 3.188667 CGCGTGCTAGTATATCCTTCTCA 59.811 47.826 0.00 0.00 0.00 3.27
979 988 4.670478 CGCGTGCTAGTATATCCTTCTCAG 60.670 50.000 0.00 0.00 0.00 3.35
981 990 5.618195 GCGTGCTAGTATATCCTTCTCAGTC 60.618 48.000 0.00 0.00 0.00 3.51
984 993 6.150474 GTGCTAGTATATCCTTCTCAGTCCTC 59.850 46.154 0.00 0.00 0.00 3.71
985 994 5.353123 GCTAGTATATCCTTCTCAGTCCTCG 59.647 48.000 0.00 0.00 0.00 4.63
986 995 5.570205 AGTATATCCTTCTCAGTCCTCGA 57.430 43.478 0.00 0.00 0.00 4.04
987 996 5.556915 AGTATATCCTTCTCAGTCCTCGAG 58.443 45.833 5.13 5.13 0.00 4.04
989 998 2.116827 TCCTTCTCAGTCCTCGAGTC 57.883 55.000 12.31 4.21 0.00 3.36
991 1000 1.099689 CTTCTCAGTCCTCGAGTCCC 58.900 60.000 12.31 0.00 0.00 4.46
994 1003 1.662438 CTCAGTCCTCGAGTCCCAGC 61.662 65.000 12.31 0.00 0.00 4.85
999 1008 2.108425 AGTCCTCGAGTCCCAGCATATA 59.892 50.000 12.31 0.00 0.00 0.86
1000 1009 2.490115 GTCCTCGAGTCCCAGCATATAG 59.510 54.545 12.31 0.00 0.00 1.31
1046 1068 3.280295 AGAATGGATCAGAAGCTTGCTG 58.720 45.455 2.10 11.43 34.71 4.41
1047 1069 2.054232 ATGGATCAGAAGCTTGCTGG 57.946 50.000 19.31 2.57 34.20 4.85
1049 1071 1.712977 GGATCAGAAGCTTGCTGGCG 61.713 60.000 19.31 2.42 37.29 5.69
1050 1072 2.320339 GATCAGAAGCTTGCTGGCGC 62.320 60.000 19.31 0.00 37.29 6.53
1068 1129 4.778143 GGCGCCATTGACGGACCT 62.778 66.667 24.80 0.00 0.00 3.85
1076 1137 2.611518 CATTGACGGACCTCTGAAGAC 58.388 52.381 0.00 0.00 0.00 3.01
1081 1142 1.985116 GGACCTCTGAAGACCGGCT 60.985 63.158 0.00 0.00 0.00 5.52
1332 1393 3.519930 GAGGAGCCGGAGTCGTCC 61.520 72.222 5.05 1.95 39.88 4.79
1357 1418 4.070265 ACGTCCCCGGGATCTGGA 62.070 66.667 26.32 7.29 38.78 3.86
1485 1555 4.025858 GAGCAGCAGGTGAGCCCA 62.026 66.667 3.02 0.00 34.66 5.36
1524 1594 2.811317 CGCAAGGAGCTGACGTCC 60.811 66.667 14.12 0.00 42.61 4.79
1645 1715 2.096417 CGGAAACCGTTGCTTCAGTTAG 60.096 50.000 1.80 0.00 42.73 2.34
1660 1730 6.368243 GCTTCAGTTAGTACAGTAGGGTTTTC 59.632 42.308 0.00 0.00 0.00 2.29
1678 1749 2.507992 CTGCGCTCACTCCTTCCG 60.508 66.667 9.73 0.00 0.00 4.30
1755 1869 2.203056 CGGCGATGGCATGGAGAA 60.203 61.111 14.07 0.00 42.47 2.87
1783 1897 2.434185 TTCGCGCTGGATGTGGTC 60.434 61.111 5.56 0.00 0.00 4.02
1789 1903 2.573869 CTGGATGTGGTCGACGCT 59.426 61.111 9.92 0.00 0.00 5.07
2076 2190 3.740397 CGACCTGGTGGCGTACGA 61.740 66.667 21.65 0.00 36.63 3.43
2080 2194 4.111016 CTGGTGGCGTACGAGCGA 62.111 66.667 21.65 4.15 38.18 4.93
2212 2329 0.603065 GGTACACCGACTACCCGTTT 59.397 55.000 0.00 0.00 0.00 3.60
2244 2361 1.256635 GAGCTCGAATACTGCTTTCGC 59.743 52.381 0.00 0.00 44.20 4.70
2325 2442 1.818060 TCAAATGTCCATTTCGGCCAG 59.182 47.619 2.24 0.00 38.84 4.85
2326 2443 1.818060 CAAATGTCCATTTCGGCCAGA 59.182 47.619 2.24 0.00 38.84 3.86
2327 2444 2.428171 CAAATGTCCATTTCGGCCAGAT 59.572 45.455 2.24 0.00 38.84 2.90
2328 2445 1.972872 ATGTCCATTTCGGCCAGATC 58.027 50.000 2.24 0.00 33.14 2.75
2329 2446 0.461870 TGTCCATTTCGGCCAGATCG 60.462 55.000 2.24 0.00 33.14 3.69
2330 2447 0.179084 GTCCATTTCGGCCAGATCGA 60.179 55.000 2.24 0.00 34.62 3.59
2332 2449 1.140852 TCCATTTCGGCCAGATCGAAT 59.859 47.619 2.24 0.00 44.47 3.34
2342 2461 7.129109 TCGGCCAGATCGAATATTTTATTTC 57.871 36.000 2.24 0.00 33.42 2.17
2372 2491 5.932619 TCGAGATCCAAGGAATTTCACTA 57.067 39.130 0.00 0.00 0.00 2.74
2399 2520 9.684448 TTTTAAAAATATGACAACATTGAGCGA 57.316 25.926 0.00 0.00 37.87 4.93
2400 2521 9.853555 TTTAAAAATATGACAACATTGAGCGAT 57.146 25.926 0.00 0.00 37.87 4.58
2401 2522 7.745022 AAAAATATGACAACATTGAGCGATG 57.255 32.000 0.00 0.00 37.87 3.84
2402 2523 6.682423 AAATATGACAACATTGAGCGATGA 57.318 33.333 4.76 0.00 37.87 2.92
2403 2524 6.872628 AATATGACAACATTGAGCGATGAT 57.127 33.333 4.76 0.00 37.87 2.45
2404 2525 4.547406 ATGACAACATTGAGCGATGATG 57.453 40.909 4.76 5.70 36.31 3.07
2405 2526 2.096335 TGACAACATTGAGCGATGATGC 59.904 45.455 4.76 1.56 34.32 3.91
2406 2527 1.402968 ACAACATTGAGCGATGATGCC 59.597 47.619 4.76 0.00 34.32 4.40
2407 2528 1.674441 CAACATTGAGCGATGATGCCT 59.326 47.619 4.76 0.00 34.65 4.75
2408 2529 2.048444 ACATTGAGCGATGATGCCTT 57.952 45.000 4.76 0.00 34.65 4.35
2409 2530 1.945394 ACATTGAGCGATGATGCCTTC 59.055 47.619 4.76 0.00 34.65 3.46
2410 2531 1.944709 CATTGAGCGATGATGCCTTCA 59.055 47.619 0.00 0.00 39.12 3.02
2411 2532 1.372582 TTGAGCGATGATGCCTTCAC 58.627 50.000 0.00 0.00 37.11 3.18
2412 2533 0.462581 TGAGCGATGATGCCTTCACC 60.463 55.000 0.00 0.00 37.11 4.02
2413 2534 0.179062 GAGCGATGATGCCTTCACCT 60.179 55.000 0.00 0.00 37.11 4.00
2414 2535 0.179062 AGCGATGATGCCTTCACCTC 60.179 55.000 0.00 0.00 37.11 3.85
2415 2536 1.162800 GCGATGATGCCTTCACCTCC 61.163 60.000 0.00 0.00 37.11 4.30
2416 2537 0.467384 CGATGATGCCTTCACCTCCT 59.533 55.000 0.00 0.00 37.11 3.69
2417 2538 1.134280 CGATGATGCCTTCACCTCCTT 60.134 52.381 0.00 0.00 37.11 3.36
2418 2539 2.295885 GATGATGCCTTCACCTCCTTG 58.704 52.381 0.00 0.00 37.11 3.61
2424 2545 1.213926 GCCTTCACCTCCTTGATCCAT 59.786 52.381 0.00 0.00 0.00 3.41
2425 2546 2.357569 GCCTTCACCTCCTTGATCCATT 60.358 50.000 0.00 0.00 0.00 3.16
2428 2549 5.509498 CCTTCACCTCCTTGATCCATTAAA 58.491 41.667 0.00 0.00 0.00 1.52
2509 2632 1.213926 GCCTTCACCTCCTTGATCCAT 59.786 52.381 0.00 0.00 0.00 3.41
2529 2652 1.186200 TGAGCGATGGTGAAGTAGCT 58.814 50.000 0.00 0.00 37.69 3.32
2530 2653 2.375146 TGAGCGATGGTGAAGTAGCTA 58.625 47.619 0.00 0.00 34.85 3.32
2531 2654 2.359214 TGAGCGATGGTGAAGTAGCTAG 59.641 50.000 0.00 0.00 34.85 3.42
2532 2655 2.359531 GAGCGATGGTGAAGTAGCTAGT 59.640 50.000 0.00 0.00 34.85 2.57
2629 2766 4.221041 CCTAACGAAGAAGGAGAGGAACTT 59.779 45.833 0.00 0.00 36.03 2.66
2638 2775 1.557371 GGAGAGGAACTTTGAGGGAGG 59.443 57.143 0.00 0.00 41.55 4.30
2730 2879 4.752594 GGTGGGGTGCCCTAGGGA 62.753 72.222 33.21 13.92 45.70 4.20
2874 3039 3.065787 GCTGAGGTGATGGGGGCAT 62.066 63.158 0.00 0.00 0.00 4.40
3007 3186 2.148768 GAACACTTCCGGAATCCGTTT 58.851 47.619 19.21 6.85 46.80 3.60
3073 3252 1.391933 CCTCGTCATGTCCGGGATCA 61.392 60.000 0.00 0.54 0.00 2.92
3076 3255 0.108377 CGTCATGTCCGGGATCACAA 60.108 55.000 0.00 0.00 0.00 3.33
3140 3342 2.288579 CGTTAAGTGTGTAGACCCTGCA 60.289 50.000 0.00 0.00 0.00 4.41
3245 3447 9.967346 TTCCTACATATTCTACGAAGATCTTTG 57.033 33.333 19.46 19.46 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.610248 TTTATCCATCACGAAAAGTAGTTTCA 57.390 30.769 0.00 0.00 45.15 2.69
3 4 9.840427 CATTTTATCCATCACGAAAAGTAGTTT 57.160 29.630 0.00 0.00 0.00 2.66
4 5 9.226606 TCATTTTATCCATCACGAAAAGTAGTT 57.773 29.630 0.00 0.00 0.00 2.24
5 6 8.786826 TCATTTTATCCATCACGAAAAGTAGT 57.213 30.769 0.00 0.00 0.00 2.73
61 62 3.192633 AGTGCAAGTTTGACCGAGTTTTT 59.807 39.130 0.00 0.00 0.00 1.94
62 63 2.752903 AGTGCAAGTTTGACCGAGTTTT 59.247 40.909 0.00 0.00 0.00 2.43
63 64 2.354821 GAGTGCAAGTTTGACCGAGTTT 59.645 45.455 0.00 0.00 0.00 2.66
64 65 1.940613 GAGTGCAAGTTTGACCGAGTT 59.059 47.619 0.00 0.00 0.00 3.01
65 66 1.583054 GAGTGCAAGTTTGACCGAGT 58.417 50.000 0.00 0.00 0.00 4.18
66 67 0.508641 CGAGTGCAAGTTTGACCGAG 59.491 55.000 0.00 0.00 0.00 4.63
67 68 0.179094 ACGAGTGCAAGTTTGACCGA 60.179 50.000 0.00 0.00 0.00 4.69
68 69 0.655733 AACGAGTGCAAGTTTGACCG 59.344 50.000 0.00 0.00 0.00 4.79
69 70 2.844122 AAACGAGTGCAAGTTTGACC 57.156 45.000 13.25 0.00 38.90 4.02
73 74 4.434713 AAAGTCAAACGAGTGCAAGTTT 57.565 36.364 9.52 9.52 40.74 2.66
74 75 4.083003 TGAAAAGTCAAACGAGTGCAAGTT 60.083 37.500 0.00 0.00 0.00 2.66
75 76 3.438781 TGAAAAGTCAAACGAGTGCAAGT 59.561 39.130 0.00 0.00 0.00 3.16
76 77 4.014847 TGAAAAGTCAAACGAGTGCAAG 57.985 40.909 0.00 0.00 0.00 4.01
77 78 4.427096 TTGAAAAGTCAAACGAGTGCAA 57.573 36.364 0.00 0.00 40.87 4.08
78 79 4.427096 TTTGAAAAGTCAAACGAGTGCA 57.573 36.364 0.00 0.00 46.48 4.57
106 107 8.836735 CCCTCCATTCCTTTATATAAGGTGTAT 58.163 37.037 4.13 4.58 38.55 2.29
107 108 8.020253 TCCCTCCATTCCTTTATATAAGGTGTA 58.980 37.037 4.13 3.09 38.55 2.90
108 109 6.855061 TCCCTCCATTCCTTTATATAAGGTGT 59.145 38.462 4.13 2.81 38.55 4.16
109 110 7.017651 ACTCCCTCCATTCCTTTATATAAGGTG 59.982 40.741 4.13 0.00 38.55 4.00
110 111 7.089566 ACTCCCTCCATTCCTTTATATAAGGT 58.910 38.462 4.13 0.00 38.55 3.50
111 112 7.575499 ACTCCCTCCATTCCTTTATATAAGG 57.425 40.000 0.00 0.00 38.78 2.69
115 116 8.759782 CGTAATACTCCCTCCATTCCTTTATAT 58.240 37.037 0.00 0.00 0.00 0.86
116 117 7.179694 CCGTAATACTCCCTCCATTCCTTTATA 59.820 40.741 0.00 0.00 0.00 0.98
117 118 6.013639 CCGTAATACTCCCTCCATTCCTTTAT 60.014 42.308 0.00 0.00 0.00 1.40
118 119 5.306160 CCGTAATACTCCCTCCATTCCTTTA 59.694 44.000 0.00 0.00 0.00 1.85
119 120 4.102681 CCGTAATACTCCCTCCATTCCTTT 59.897 45.833 0.00 0.00 0.00 3.11
120 121 3.646637 CCGTAATACTCCCTCCATTCCTT 59.353 47.826 0.00 0.00 0.00 3.36
121 122 3.116862 TCCGTAATACTCCCTCCATTCCT 60.117 47.826 0.00 0.00 0.00 3.36
122 123 3.236896 TCCGTAATACTCCCTCCATTCC 58.763 50.000 0.00 0.00 0.00 3.01
123 124 4.344390 ACTTCCGTAATACTCCCTCCATTC 59.656 45.833 0.00 0.00 0.00 2.67
124 125 4.296056 ACTTCCGTAATACTCCCTCCATT 58.704 43.478 0.00 0.00 0.00 3.16
125 126 3.924922 ACTTCCGTAATACTCCCTCCAT 58.075 45.455 0.00 0.00 0.00 3.41
126 127 3.393426 ACTTCCGTAATACTCCCTCCA 57.607 47.619 0.00 0.00 0.00 3.86
127 128 4.892345 ACTTACTTCCGTAATACTCCCTCC 59.108 45.833 0.00 0.00 35.23 4.30
128 129 5.591877 TCACTTACTTCCGTAATACTCCCTC 59.408 44.000 0.00 0.00 35.23 4.30
129 130 5.513233 TCACTTACTTCCGTAATACTCCCT 58.487 41.667 0.00 0.00 35.23 4.20
130 131 5.841957 TCACTTACTTCCGTAATACTCCC 57.158 43.478 0.00 0.00 35.23 4.30
131 132 9.978044 ATTTATCACTTACTTCCGTAATACTCC 57.022 33.333 0.00 0.00 35.23 3.85
178 179 3.264450 GTCCAGGGAGAGATCTTTTTGGA 59.736 47.826 0.00 4.02 31.18 3.53
214 215 6.326323 AGAGGAGGAGAAGAAATAGGATTGTC 59.674 42.308 0.00 0.00 0.00 3.18
376 385 4.037446 CAGCCTCTAGATCAACAGGACTAC 59.963 50.000 7.80 0.00 0.00 2.73
429 438 2.845363 TCAGCAGCAACTTGATCAGA 57.155 45.000 0.00 0.00 0.00 3.27
459 468 3.843999 TCAAAGTGTGGTGCAAAAAGTC 58.156 40.909 0.00 0.00 0.00 3.01
460 469 3.509575 TCTCAAAGTGTGGTGCAAAAAGT 59.490 39.130 0.00 0.00 0.00 2.66
487 496 4.740268 TGTACGCACTAACCATCTTGTAG 58.260 43.478 0.00 0.00 0.00 2.74
489 498 3.671008 TGTACGCACTAACCATCTTGT 57.329 42.857 0.00 0.00 0.00 3.16
645 654 5.115480 TCATAGTTTTAGCGATCATGCACA 58.885 37.500 0.00 0.00 37.31 4.57
699 708 0.598065 GAATGGTGCGCTTTGTTCCT 59.402 50.000 9.73 0.00 0.00 3.36
922 931 3.246619 CTCCTGTCTGAACGAGTAAAGC 58.753 50.000 0.00 0.00 0.00 3.51
934 943 2.008329 GCTCATCTTTGCTCCTGTCTG 58.992 52.381 0.00 0.00 0.00 3.51
966 975 5.513441 GGACTCGAGGACTGAGAAGGATATA 60.513 48.000 18.41 0.00 36.93 0.86
967 976 4.394729 GACTCGAGGACTGAGAAGGATAT 58.605 47.826 18.41 0.00 36.93 1.63
968 977 3.433882 GGACTCGAGGACTGAGAAGGATA 60.434 52.174 18.41 0.00 36.93 2.59
969 978 2.650322 GACTCGAGGACTGAGAAGGAT 58.350 52.381 18.41 0.00 36.93 3.24
970 979 1.340211 GGACTCGAGGACTGAGAAGGA 60.340 57.143 18.41 0.00 36.93 3.36
971 980 1.099689 GGACTCGAGGACTGAGAAGG 58.900 60.000 18.41 0.00 36.93 3.46
972 981 1.099689 GGGACTCGAGGACTGAGAAG 58.900 60.000 18.41 0.00 36.93 2.85
973 982 0.404426 TGGGACTCGAGGACTGAGAA 59.596 55.000 18.41 0.00 36.93 2.87
976 985 1.679305 GCTGGGACTCGAGGACTGA 60.679 63.158 18.41 0.00 0.00 3.41
977 986 1.326213 ATGCTGGGACTCGAGGACTG 61.326 60.000 18.41 10.95 0.00 3.51
978 987 0.259065 TATGCTGGGACTCGAGGACT 59.741 55.000 18.41 0.00 0.00 3.85
979 988 1.333177 ATATGCTGGGACTCGAGGAC 58.667 55.000 18.41 10.24 0.00 3.85
981 990 2.520069 ACTATATGCTGGGACTCGAGG 58.480 52.381 18.41 0.00 0.00 4.63
987 996 9.095065 CGGTTAAAATATACTATATGCTGGGAC 57.905 37.037 0.00 0.00 0.00 4.46
989 998 7.551262 TGCGGTTAAAATATACTATATGCTGGG 59.449 37.037 0.00 0.00 0.00 4.45
991 1000 8.388103 GGTGCGGTTAAAATATACTATATGCTG 58.612 37.037 0.00 0.00 0.00 4.41
999 1008 6.270064 GCAAATGGTGCGGTTAAAATATACT 58.730 36.000 0.00 0.00 45.10 2.12
1000 1009 6.505039 GCAAATGGTGCGGTTAAAATATAC 57.495 37.500 0.00 0.00 45.10 1.47
1052 1074 3.195698 GAGGTCCGTCAATGGCGC 61.196 66.667 0.00 0.00 0.00 6.53
1053 1075 1.811266 CAGAGGTCCGTCAATGGCG 60.811 63.158 0.00 0.00 0.00 5.69
1055 1077 1.550524 TCTTCAGAGGTCCGTCAATGG 59.449 52.381 0.00 0.00 0.00 3.16
1058 1080 0.966920 GGTCTTCAGAGGTCCGTCAA 59.033 55.000 0.00 0.00 0.00 3.18
1059 1081 1.241990 CGGTCTTCAGAGGTCCGTCA 61.242 60.000 9.62 0.00 36.66 4.35
1060 1082 1.507174 CGGTCTTCAGAGGTCCGTC 59.493 63.158 9.62 0.00 36.66 4.79
1061 1083 1.977544 CCGGTCTTCAGAGGTCCGT 60.978 63.158 15.29 0.00 38.29 4.69
1062 1084 2.885861 CCGGTCTTCAGAGGTCCG 59.114 66.667 10.67 10.67 39.03 4.79
1068 1129 3.706373 GCCCAGCCGGTCTTCAGA 61.706 66.667 1.90 0.00 0.00 3.27
1081 1142 3.772853 AAACAGTGCTGCGAGCCCA 62.773 57.895 5.82 0.00 41.51 5.36
1342 1403 3.537874 CGTCCAGATCCCGGGGAC 61.538 72.222 23.50 18.35 46.01 4.46
1485 1555 1.153745 GCCGTCGAAGCTCATCTGT 60.154 57.895 0.00 0.00 0.00 3.41
1645 1715 2.344025 CGCAGGAAAACCCTACTGTAC 58.656 52.381 0.00 0.00 45.60 2.90
1660 1730 2.125350 GGAAGGAGTGAGCGCAGG 60.125 66.667 11.47 0.00 0.00 4.85
1744 1852 2.350895 CACCGGTTCTCCATGCCA 59.649 61.111 2.97 0.00 0.00 4.92
1789 1903 3.770040 CCGATCTCCCGCACCACA 61.770 66.667 0.00 0.00 0.00 4.17
2076 2190 2.867855 TTCGCCAGGAACAGTCGCT 61.868 57.895 0.00 0.00 0.00 4.93
2275 2392 7.603404 CACCATTGGATCATTGTTTATTGTGTT 59.397 33.333 10.37 0.00 0.00 3.32
2287 2404 3.104519 TGAAGCCACCATTGGATCATT 57.895 42.857 10.37 0.00 42.27 2.57
2294 2411 2.299582 TGGACATTTGAAGCCACCATTG 59.700 45.455 0.00 0.00 0.00 2.82
2327 2444 9.240159 TCGATCGAGTTGAAATAAAATATTCGA 57.760 29.630 15.15 0.00 38.65 3.71
2328 2445 9.504713 CTCGATCGAGTTGAAATAAAATATTCG 57.495 33.333 32.23 5.21 37.47 3.34
2332 2449 9.193133 GGATCTCGATCGAGTTGAAATAAAATA 57.807 33.333 36.68 18.38 42.49 1.40
2342 2461 2.359214 TCCTTGGATCTCGATCGAGTTG 59.641 50.000 36.68 20.17 42.49 3.16
2380 2501 6.665465 CATCATCGCTCAATGTTGTCATATT 58.335 36.000 0.00 0.00 33.49 1.28
2382 2503 4.024641 GCATCATCGCTCAATGTTGTCATA 60.025 41.667 0.00 0.00 33.49 2.15
2388 2509 2.048444 AGGCATCATCGCTCAATGTT 57.952 45.000 0.00 0.00 0.00 2.71
2394 2515 0.179062 AGGTGAAGGCATCATCGCTC 60.179 55.000 0.00 0.00 44.36 5.03
2395 2516 0.179062 GAGGTGAAGGCATCATCGCT 60.179 55.000 0.00 0.00 44.36 4.93
2396 2517 1.162800 GGAGGTGAAGGCATCATCGC 61.163 60.000 0.00 0.00 44.36 4.58
2397 2518 0.467384 AGGAGGTGAAGGCATCATCG 59.533 55.000 0.00 0.00 44.36 3.84
2398 2519 2.092753 TCAAGGAGGTGAAGGCATCATC 60.093 50.000 0.00 0.00 40.97 2.92
2399 2520 1.918262 TCAAGGAGGTGAAGGCATCAT 59.082 47.619 0.00 0.00 40.97 2.45
2400 2521 1.361204 TCAAGGAGGTGAAGGCATCA 58.639 50.000 0.00 0.00 35.05 3.07
2401 2522 2.570135 GATCAAGGAGGTGAAGGCATC 58.430 52.381 0.00 0.00 0.00 3.91
2402 2523 1.213926 GGATCAAGGAGGTGAAGGCAT 59.786 52.381 0.00 0.00 0.00 4.40
2403 2524 0.620556 GGATCAAGGAGGTGAAGGCA 59.379 55.000 0.00 0.00 0.00 4.75
2404 2525 0.620556 TGGATCAAGGAGGTGAAGGC 59.379 55.000 0.00 0.00 0.00 4.35
2405 2526 3.659183 AATGGATCAAGGAGGTGAAGG 57.341 47.619 0.00 0.00 0.00 3.46
2406 2527 6.264067 GGATTTAATGGATCAAGGAGGTGAAG 59.736 42.308 0.00 0.00 0.00 3.02
2407 2528 6.129179 GGATTTAATGGATCAAGGAGGTGAA 58.871 40.000 0.00 0.00 0.00 3.18
2408 2529 5.399038 GGGATTTAATGGATCAAGGAGGTGA 60.399 44.000 0.00 0.00 0.00 4.02
2409 2530 4.829492 GGGATTTAATGGATCAAGGAGGTG 59.171 45.833 0.00 0.00 0.00 4.00
2410 2531 4.446311 CGGGATTTAATGGATCAAGGAGGT 60.446 45.833 0.00 0.00 0.00 3.85
2411 2532 4.074970 CGGGATTTAATGGATCAAGGAGG 58.925 47.826 0.00 0.00 0.00 4.30
2412 2533 4.973168 TCGGGATTTAATGGATCAAGGAG 58.027 43.478 0.00 0.00 0.00 3.69
2413 2534 5.073008 TGATCGGGATTTAATGGATCAAGGA 59.927 40.000 9.17 0.00 40.17 3.36
2414 2535 5.316167 TGATCGGGATTTAATGGATCAAGG 58.684 41.667 9.17 0.00 40.17 3.61
2415 2536 6.882610 TTGATCGGGATTTAATGGATCAAG 57.117 37.500 15.47 0.00 44.61 3.02
2416 2537 6.262944 CACTTGATCGGGATTTAATGGATCAA 59.737 38.462 17.11 17.11 46.23 2.57
2417 2538 5.764686 CACTTGATCGGGATTTAATGGATCA 59.235 40.000 0.00 8.10 41.07 2.92
2418 2539 5.765182 ACACTTGATCGGGATTTAATGGATC 59.235 40.000 0.00 0.00 35.29 3.36
2424 2545 4.459390 TCGACACTTGATCGGGATTTAA 57.541 40.909 0.00 0.00 40.05 1.52
2425 2546 4.178540 GTTCGACACTTGATCGGGATTTA 58.821 43.478 0.00 0.00 40.05 1.40
2428 2549 1.469251 CGTTCGACACTTGATCGGGAT 60.469 52.381 0.00 0.00 40.05 3.85
2509 2632 1.550524 AGCTACTTCACCATCGCTCAA 59.449 47.619 0.00 0.00 0.00 3.02
2529 2652 1.749634 GCCGGAGAACTTGAGCTACTA 59.250 52.381 5.05 0.00 0.00 1.82
2530 2653 0.533032 GCCGGAGAACTTGAGCTACT 59.467 55.000 5.05 0.00 0.00 2.57
2531 2654 0.246635 TGCCGGAGAACTTGAGCTAC 59.753 55.000 5.05 0.00 0.00 3.58
2532 2655 0.532573 CTGCCGGAGAACTTGAGCTA 59.467 55.000 5.05 0.00 0.00 3.32
2538 2661 0.674895 GTCATGCTGCCGGAGAACTT 60.675 55.000 5.05 0.00 0.00 2.66
2629 2766 2.614013 GCCCTTCCCCTCCCTCAA 60.614 66.667 0.00 0.00 0.00 3.02
2705 2848 4.048470 GCACCCCACCCCTCCTTC 62.048 72.222 0.00 0.00 0.00 3.46
2819 2981 1.839296 GAGGGGCCCACCTAGCTAG 60.839 68.421 27.72 14.20 42.10 3.42
2820 2982 2.285868 GAGGGGCCCACCTAGCTA 59.714 66.667 27.72 0.00 42.10 3.32
2821 2983 4.825679 GGAGGGGCCCACCTAGCT 62.826 72.222 29.75 10.40 42.10 3.32
2895 3062 4.766632 GCCAAGGGAAGGGGGCAG 62.767 72.222 0.00 0.00 45.70 4.85
3031 3210 2.108168 CTCCGGAATGGTCCAGAGTTA 58.892 52.381 5.23 0.00 45.26 2.24
3033 3212 2.596776 CTCCGGAATGGTCCAGAGT 58.403 57.895 5.23 0.00 45.26 3.24
3053 3232 2.088674 GATCCCGGACATGACGAGGG 62.089 65.000 16.97 16.97 43.32 4.30
3073 3252 8.677148 AGTTGAGTTATTGTGTTAGTCATTGT 57.323 30.769 0.00 0.00 0.00 2.71
3140 3342 5.769662 TCATGTCTGCATAGTTTTTGAACCT 59.230 36.000 0.00 0.00 33.30 3.50
3148 3350 3.195610 TCTCGGTCATGTCTGCATAGTTT 59.804 43.478 0.00 0.00 33.30 2.66


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

AutoCloner maintained by Alex Coulton.