Multiple sequence alignment - TraesCS4A01G223000

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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 TraesCS4A01G223000 chr4A 100.000 2726 0 0 1 2726 530890468 530893193 0.000000e+00 5035.0
1 TraesCS4A01G223000 chr4A 90.634 331 20 10 1281 1604 531109706 531109380 1.940000e-116 429.0
2 TraesCS4A01G223000 chr4A 87.302 126 13 2 2055 2178 517011041 517011165 1.020000e-29 141.0
3 TraesCS4A01G223000 chr4A 89.744 78 8 0 1953 2030 530892497 530892420 1.730000e-17 100.0
4 TraesCS4A01G223000 chr4D 87.250 1200 81 26 829 1990 65173107 65171942 0.000000e+00 1303.0
5 TraesCS4A01G223000 chr4D 89.231 130 13 1 683 811 65173300 65173171 7.810000e-36 161.0
6 TraesCS4A01G223000 chr4B 90.984 854 37 19 1174 1999 95718758 95717917 0.000000e+00 1114.0
7 TraesCS4A01G223000 chr4B 81.607 473 43 23 683 1124 95719329 95718870 4.320000e-93 351.0
8 TraesCS4A01G223000 chr7A 93.886 687 31 7 1 676 114015568 114014882 0.000000e+00 1026.0
9 TraesCS4A01G223000 chr7A 93.501 677 39 2 1 672 609140237 609140913 0.000000e+00 1002.0
10 TraesCS4A01G223000 chr7A 93.255 682 36 6 1 672 114010091 114009410 0.000000e+00 996.0
11 TraesCS4A01G223000 chr7A 83.333 96 11 5 2180 2273 9052895 9052987 1.740000e-12 84.2
12 TraesCS4A01G223000 chr3A 93.833 681 33 4 1 672 69635353 69636033 0.000000e+00 1016.0
13 TraesCS4A01G223000 chr3A 93.548 682 38 3 1 676 721073236 721072555 0.000000e+00 1011.0
14 TraesCS4A01G223000 chr6A 93.450 687 33 9 1 676 52800046 52800731 0.000000e+00 1009.0
15 TraesCS4A01G223000 chr6A 84.946 93 13 1 2170 2262 426323146 426323055 2.890000e-15 93.5
16 TraesCS4A01G223000 chr1A 93.520 679 38 3 1 674 556963989 556963312 0.000000e+00 1005.0
17 TraesCS4A01G223000 chr1A 93.382 680 36 6 1 672 554215706 554215028 0.000000e+00 998.0
18 TraesCS4A01G223000 chr1A 89.189 148 13 2 2034 2178 103682575 103682428 6.000000e-42 182.0
19 TraesCS4A01G223000 chr1A 87.662 154 17 1 2027 2178 562776194 562776347 7.760000e-41 178.0
20 TraesCS4A01G223000 chr5A 93.353 677 40 2 1 672 352472285 352471609 0.000000e+00 996.0
21 TraesCS4A01G223000 chr1B 99.088 548 5 0 2179 2726 660000966 660000419 0.000000e+00 985.0
22 TraesCS4A01G223000 chr1B 86.535 557 47 19 2178 2721 348483951 348484492 3.020000e-164 588.0
23 TraesCS4A01G223000 chr1B 87.075 147 17 1 2034 2178 340474397 340474251 6.040000e-37 165.0
24 TraesCS4A01G223000 chr5D 85.230 501 63 7 1047 1546 116748173 116748663 3.130000e-139 505.0
25 TraesCS4A01G223000 chr5D 88.119 303 31 4 2425 2726 432481275 432481573 3.340000e-94 355.0
26 TraesCS4A01G223000 chr5B 81.859 441 50 17 949 1380 128471280 128471699 7.230000e-91 344.0
27 TraesCS4A01G223000 chr5B 87.755 147 16 1 2034 2178 671338771 671338625 1.300000e-38 171.0
28 TraesCS4A01G223000 chr5B 86.486 148 16 2 2033 2178 114431621 114431476 2.810000e-35 159.0
29 TraesCS4A01G223000 chr2B 86.601 306 33 4 2429 2726 670933307 670933612 5.630000e-87 331.0
30 TraesCS4A01G223000 chr2B 86.400 250 29 4 2179 2426 670933029 670933275 4.470000e-68 268.0
31 TraesCS4A01G223000 chr6D 88.048 251 24 6 2178 2426 12997467 12997713 2.650000e-75 292.0
32 TraesCS4A01G223000 chr3D 86.454 251 30 4 2177 2426 11461870 11461623 3.460000e-69 272.0
33 TraesCS4A01G223000 chr3D 82.941 170 24 5 2178 2345 481217838 481218004 6.080000e-32 148.0
34 TraesCS4A01G223000 chr2D 86.986 146 16 2 2035 2178 63564673 63564529 7.810000e-36 161.0
35 TraesCS4A01G223000 chr3B 90.654 107 9 1 2070 2176 602242815 602242920 1.020000e-29 141.0
36 TraesCS4A01G223000 chr3B 82.432 148 22 3 2034 2178 825987965 825987819 2.850000e-25 126.0


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 TraesCS4A01G223000 chr4A 530890468 530893193 2725 False 5035.0 5035 100.0000 1 2726 1 chr4A.!!$F2 2725
1 TraesCS4A01G223000 chr4D 65171942 65173300 1358 True 732.0 1303 88.2405 683 1990 2 chr4D.!!$R1 1307
2 TraesCS4A01G223000 chr4B 95717917 95719329 1412 True 732.5 1114 86.2955 683 1999 2 chr4B.!!$R1 1316
3 TraesCS4A01G223000 chr7A 114014882 114015568 686 True 1026.0 1026 93.8860 1 676 1 chr7A.!!$R2 675
4 TraesCS4A01G223000 chr7A 609140237 609140913 676 False 1002.0 1002 93.5010 1 672 1 chr7A.!!$F2 671
5 TraesCS4A01G223000 chr7A 114009410 114010091 681 True 996.0 996 93.2550 1 672 1 chr7A.!!$R1 671
6 TraesCS4A01G223000 chr3A 69635353 69636033 680 False 1016.0 1016 93.8330 1 672 1 chr3A.!!$F1 671
7 TraesCS4A01G223000 chr3A 721072555 721073236 681 True 1011.0 1011 93.5480 1 676 1 chr3A.!!$R1 675
8 TraesCS4A01G223000 chr6A 52800046 52800731 685 False 1009.0 1009 93.4500 1 676 1 chr6A.!!$F1 675
9 TraesCS4A01G223000 chr1A 556963312 556963989 677 True 1005.0 1005 93.5200 1 674 1 chr1A.!!$R3 673
10 TraesCS4A01G223000 chr1A 554215028 554215706 678 True 998.0 998 93.3820 1 672 1 chr1A.!!$R2 671
11 TraesCS4A01G223000 chr5A 352471609 352472285 676 True 996.0 996 93.3530 1 672 1 chr5A.!!$R1 671
12 TraesCS4A01G223000 chr1B 660000419 660000966 547 True 985.0 985 99.0880 2179 2726 1 chr1B.!!$R2 547
13 TraesCS4A01G223000 chr1B 348483951 348484492 541 False 588.0 588 86.5350 2178 2721 1 chr1B.!!$F1 543
14 TraesCS4A01G223000 chr2B 670933029 670933612 583 False 299.5 331 86.5005 2179 2726 2 chr2B.!!$F1 547

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
880 943 0.246635 TTTAGCACGAGAGAGGGCAC 59.753 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2229 0.965439 CTCTAAGCCAGAGGATCCGG 59.035 60.0 5.98 2.6 46.21 5.14 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
77 78 1.256812 CAAAAACCTGATCGCCCCTT 58.743 50.000 0.00 0.00 0.00 3.95
159 160 3.788672 CGGAAGGAGGGATGGAAAG 57.211 57.895 0.00 0.00 0.00 2.62
214 215 2.602878 GTGAGAAACCATACGAAGCGA 58.397 47.619 0.00 0.00 0.00 4.93
229 230 3.134879 CGATGGCGGCTAGGGTAA 58.865 61.111 11.43 0.00 0.00 2.85
333 334 6.841443 TCGAAAACGGTTCAGTAATTAACA 57.159 33.333 0.00 0.00 0.00 2.41
412 413 0.898320 ACGTGCATAGCTCTGTCCTT 59.102 50.000 0.00 0.00 0.00 3.36
432 438 2.046314 CTCAATCCCGCAACCCGT 60.046 61.111 0.00 0.00 34.38 5.28
528 540 7.180408 AGTGGTAGAAGAGCTCACCTTATAAAA 59.820 37.037 17.77 0.00 32.04 1.52
567 579 1.990327 ACTTTCGGGGTGGGACTAAAT 59.010 47.619 0.00 0.00 0.00 1.40
606 618 5.495640 TCCACTCACATGTGTGCATAAATA 58.504 37.500 24.63 1.89 45.25 1.40
610 622 4.525996 TCACATGTGTGCATAAATAGGCT 58.474 39.130 24.63 0.00 45.25 4.58
676 688 3.443681 ACTAGCAAAATTCCAACATCCCG 59.556 43.478 0.00 0.00 0.00 5.14
677 689 2.524306 AGCAAAATTCCAACATCCCGA 58.476 42.857 0.00 0.00 0.00 5.14
678 690 3.099141 AGCAAAATTCCAACATCCCGAT 58.901 40.909 0.00 0.00 0.00 4.18
679 691 4.277476 AGCAAAATTCCAACATCCCGATA 58.723 39.130 0.00 0.00 0.00 2.92
680 692 4.339247 AGCAAAATTCCAACATCCCGATAG 59.661 41.667 0.00 0.00 0.00 2.08
727 739 2.278596 CGTCGGTATGCACGGAGG 60.279 66.667 0.00 0.00 34.96 4.30
742 754 3.562973 CACGGAGGATGATTTCATTCCAG 59.437 47.826 10.44 6.75 34.46 3.86
750 763 4.771590 TGATTTCATTCCAGACTTGTGC 57.228 40.909 0.00 0.00 0.00 4.57
751 764 3.189080 TGATTTCATTCCAGACTTGTGCG 59.811 43.478 0.00 0.00 0.00 5.34
767 780 1.226717 GCGCGTACTCTCCTGAAGG 60.227 63.158 8.43 0.00 0.00 3.46
783 796 8.487028 TCTCCTGAAGGTAGAAGGAAATTAATC 58.513 37.037 0.00 0.00 39.59 1.75
786 799 7.283354 CCTGAAGGTAGAAGGAAATTAATCCAC 59.717 40.741 0.00 0.00 42.27 4.02
793 806 5.527582 AGAAGGAAATTAATCCACGGATTCG 59.472 40.000 14.55 0.00 43.04 3.34
796 809 5.058490 GGAAATTAATCCACGGATTCGGTA 58.942 41.667 14.55 0.00 43.04 4.02
800 813 1.784358 ATCCACGGATTCGGTAGGAA 58.216 50.000 8.32 0.00 38.62 3.36
808 858 5.176958 CACGGATTCGGTAGGAAATGATTAC 59.823 44.000 0.00 0.00 38.36 1.89
876 939 2.860735 CGGAATTTTAGCACGAGAGAGG 59.139 50.000 0.00 0.00 0.00 3.69
880 943 0.246635 TTTAGCACGAGAGAGGGCAC 59.753 55.000 0.00 0.00 0.00 5.01
881 944 0.898326 TTAGCACGAGAGAGGGCACA 60.898 55.000 0.00 0.00 0.00 4.57
882 945 0.684479 TAGCACGAGAGAGGGCACAT 60.684 55.000 0.00 0.00 0.00 3.21
883 946 1.812922 GCACGAGAGAGGGCACATG 60.813 63.158 0.00 0.00 0.00 3.21
911 979 5.467063 GGAAGGAGATTATAAACGGAAGCAG 59.533 44.000 0.00 0.00 0.00 4.24
920 988 1.507141 AACGGAAGCAGCAAACTCGG 61.507 55.000 0.00 0.00 0.00 4.63
927 995 0.811616 GCAGCAAACTCGGGATCGAT 60.812 55.000 0.00 0.00 45.04 3.59
934 1002 4.929808 GCAAACTCGGGATCGATGTATATT 59.070 41.667 0.54 0.00 45.04 1.28
947 1028 5.005971 TCGATGTATATTCGATCGATACGCA 59.994 40.000 20.18 14.28 42.20 5.24
982 1064 4.141620 CCACAGGCCTATATAATAGCTGGG 60.142 50.000 3.98 0.00 0.00 4.45
983 1065 3.456277 ACAGGCCTATATAATAGCTGGGC 59.544 47.826 3.98 0.00 39.92 5.36
984 1066 4.014273 AGGCCTATATAATAGCTGGGCT 57.986 45.455 1.29 5.79 44.00 5.19
985 1067 3.713764 AGGCCTATATAATAGCTGGGCTG 59.286 47.826 1.29 0.00 46.38 4.85
986 1068 3.181450 GGCCTATATAATAGCTGGGCTGG 60.181 52.174 0.00 0.00 40.10 4.85
1024 1107 4.363991 ACATCAAAGCTTCTCCTGAACT 57.636 40.909 0.00 0.00 0.00 3.01
1026 1109 6.059787 ACATCAAAGCTTCTCCTGAACTAT 57.940 37.500 0.00 0.00 0.00 2.12
1027 1110 7.187824 ACATCAAAGCTTCTCCTGAACTATA 57.812 36.000 0.00 0.00 0.00 1.31
1028 1111 7.044798 ACATCAAAGCTTCTCCTGAACTATAC 58.955 38.462 0.00 0.00 0.00 1.47
1029 1112 5.978814 TCAAAGCTTCTCCTGAACTATACC 58.021 41.667 0.00 0.00 0.00 2.73
1030 1113 5.721960 TCAAAGCTTCTCCTGAACTATACCT 59.278 40.000 0.00 0.00 0.00 3.08
1044 1127 7.328737 TGAACTATACCTTTGTTCTTAGCTCC 58.671 38.462 0.00 0.00 40.27 4.70
1107 1190 2.417924 CGTTGCAGCTCTTCTCCATACT 60.418 50.000 0.00 0.00 0.00 2.12
1120 1203 2.365617 CTCCATACTGGTACGCAAGGAT 59.634 50.000 0.00 0.00 39.70 3.24
1124 1207 4.690748 CCATACTGGTACGCAAGGATAATG 59.309 45.833 0.00 0.00 35.06 1.90
1125 1208 3.906720 ACTGGTACGCAAGGATAATGT 57.093 42.857 0.00 0.00 46.39 2.71
1127 1210 5.347620 ACTGGTACGCAAGGATAATGTAA 57.652 39.130 0.00 0.00 46.39 2.41
1130 1213 7.152645 ACTGGTACGCAAGGATAATGTAATAG 58.847 38.462 0.00 0.00 46.39 1.73
1132 1288 7.375834 TGGTACGCAAGGATAATGTAATAGAG 58.624 38.462 0.00 0.00 46.39 2.43
1135 1291 9.557338 GTACGCAAGGATAATGTAATAGAGTAG 57.443 37.037 0.00 0.00 46.39 2.57
1145 1301 3.940852 TGTAATAGAGTAGTTCGCCGTCA 59.059 43.478 0.00 0.00 0.00 4.35
1191 1347 4.497006 CCTTGGATCTTACGTAGTACCGTG 60.497 50.000 7.34 0.00 45.76 4.94
1386 1542 0.325296 AGGTGAAGGCGGTGATCCTA 60.325 55.000 0.00 0.00 32.65 2.94
1392 1548 0.324368 AGGCGGTGATCCTAGACACA 60.324 55.000 13.51 0.00 38.57 3.72
1403 1559 3.516586 TCCTAGACACAACCAAGATCCA 58.483 45.455 0.00 0.00 0.00 3.41
1410 1566 1.093159 CAACCAAGATCCAGCTGCTC 58.907 55.000 8.66 7.32 0.00 4.26
1568 1724 1.405105 CACGGTCCAGGCCAATATTTG 59.595 52.381 5.01 0.00 0.00 2.32
1569 1725 1.005450 ACGGTCCAGGCCAATATTTGT 59.995 47.619 5.01 0.00 0.00 2.83
1570 1726 2.099405 CGGTCCAGGCCAATATTTGTT 58.901 47.619 5.01 0.00 0.00 2.83
1571 1727 2.159254 CGGTCCAGGCCAATATTTGTTG 60.159 50.000 5.01 0.00 0.00 3.33
1572 1728 2.831526 GGTCCAGGCCAATATTTGTTGT 59.168 45.455 5.01 0.00 0.00 3.32
1573 1729 3.260632 GGTCCAGGCCAATATTTGTTGTT 59.739 43.478 5.01 0.00 0.00 2.83
1574 1730 4.262851 GGTCCAGGCCAATATTTGTTGTTT 60.263 41.667 5.01 0.00 0.00 2.83
1575 1731 5.304778 GTCCAGGCCAATATTTGTTGTTTT 58.695 37.500 5.01 0.00 0.00 2.43
1693 1849 2.776536 CCTCCATTCTTCATGTCCCTCT 59.223 50.000 0.00 0.00 0.00 3.69
1697 1853 4.164221 TCCATTCTTCATGTCCCTCTTACC 59.836 45.833 0.00 0.00 0.00 2.85
1698 1854 4.080356 CCATTCTTCATGTCCCTCTTACCA 60.080 45.833 0.00 0.00 0.00 3.25
1708 1868 5.636123 TGTCCCTCTTACCAAAGCAATTAA 58.364 37.500 0.00 0.00 32.36 1.40
1709 1869 5.710099 TGTCCCTCTTACCAAAGCAATTAAG 59.290 40.000 0.00 0.00 32.36 1.85
1710 1870 5.710567 GTCCCTCTTACCAAAGCAATTAAGT 59.289 40.000 0.00 0.00 32.36 2.24
1711 1871 5.944007 TCCCTCTTACCAAAGCAATTAAGTC 59.056 40.000 0.00 0.00 32.36 3.01
1768 1945 9.622004 CTGATATCATTTACAGGATGAAAATGC 57.378 33.333 5.72 0.00 39.69 3.56
1794 1982 0.037697 ATGCACGCGAAAGAGTACCA 60.038 50.000 15.93 0.00 44.22 3.25
1937 2129 9.672086 GTGTAAATTTTGCATAGTGAAACAGTA 57.328 29.630 3.20 0.00 41.43 2.74
2049 2241 3.610669 CGGAGCCGGATCCTCTGG 61.611 72.222 34.42 16.75 45.82 3.86
2055 2247 3.133437 CCGGATCCTCTGGCTTAGA 57.867 57.895 10.75 0.00 35.89 2.10
2066 2258 4.287766 TCTGGCTTAGAGAAGGGAAAAC 57.712 45.455 0.00 0.00 32.84 2.43
2067 2259 3.003480 CTGGCTTAGAGAAGGGAAAACG 58.997 50.000 0.00 0.00 32.84 3.60
2068 2260 2.635915 TGGCTTAGAGAAGGGAAAACGA 59.364 45.455 0.00 0.00 32.84 3.85
2069 2261 3.263425 TGGCTTAGAGAAGGGAAAACGAT 59.737 43.478 0.00 0.00 32.84 3.73
2070 2262 3.623510 GGCTTAGAGAAGGGAAAACGATG 59.376 47.826 0.00 0.00 32.84 3.84
2071 2263 3.064134 GCTTAGAGAAGGGAAAACGATGC 59.936 47.826 0.00 0.00 32.84 3.91
2072 2264 4.508662 CTTAGAGAAGGGAAAACGATGCT 58.491 43.478 0.00 0.00 0.00 3.79
2073 2265 5.661458 CTTAGAGAAGGGAAAACGATGCTA 58.339 41.667 0.00 0.00 0.00 3.49
2074 2266 4.762289 AGAGAAGGGAAAACGATGCTAT 57.238 40.909 0.00 0.00 0.00 2.97
2075 2267 5.871396 AGAGAAGGGAAAACGATGCTATA 57.129 39.130 0.00 0.00 0.00 1.31
2076 2268 5.848406 AGAGAAGGGAAAACGATGCTATAG 58.152 41.667 0.00 0.00 0.00 1.31
2077 2269 5.364157 AGAGAAGGGAAAACGATGCTATAGT 59.636 40.000 0.84 0.00 0.00 2.12
2078 2270 5.360591 AGAAGGGAAAACGATGCTATAGTG 58.639 41.667 0.84 0.00 0.00 2.74
2079 2271 3.467803 AGGGAAAACGATGCTATAGTGC 58.532 45.455 0.84 0.00 0.00 4.40
2080 2272 3.134804 AGGGAAAACGATGCTATAGTGCT 59.865 43.478 0.84 0.00 0.00 4.40
2081 2273 3.877508 GGGAAAACGATGCTATAGTGCTT 59.122 43.478 0.84 0.00 0.00 3.91
2082 2274 4.260784 GGGAAAACGATGCTATAGTGCTTG 60.261 45.833 0.84 0.00 0.00 4.01
2083 2275 4.332819 GGAAAACGATGCTATAGTGCTTGT 59.667 41.667 0.84 0.00 0.00 3.16
2084 2276 5.470845 AAAACGATGCTATAGTGCTTGTC 57.529 39.130 0.84 0.00 0.00 3.18
2085 2277 4.392921 AACGATGCTATAGTGCTTGTCT 57.607 40.909 0.84 0.00 0.00 3.41
2086 2278 5.515797 AACGATGCTATAGTGCTTGTCTA 57.484 39.130 0.84 0.00 0.00 2.59
2087 2279 5.114785 ACGATGCTATAGTGCTTGTCTAG 57.885 43.478 0.84 0.00 0.00 2.43
2088 2280 4.580995 ACGATGCTATAGTGCTTGTCTAGT 59.419 41.667 0.84 0.00 0.00 2.57
2089 2281 4.914504 CGATGCTATAGTGCTTGTCTAGTG 59.085 45.833 0.84 0.00 0.00 2.74
2090 2282 5.506483 CGATGCTATAGTGCTTGTCTAGTGT 60.506 44.000 0.84 0.00 0.00 3.55
2091 2283 6.293462 CGATGCTATAGTGCTTGTCTAGTGTA 60.293 42.308 0.84 0.00 0.00 2.90
2092 2284 6.769134 TGCTATAGTGCTTGTCTAGTGTAA 57.231 37.500 0.84 0.00 0.00 2.41
2093 2285 7.165460 TGCTATAGTGCTTGTCTAGTGTAAA 57.835 36.000 0.84 0.00 0.00 2.01
2094 2286 7.608153 TGCTATAGTGCTTGTCTAGTGTAAAA 58.392 34.615 0.84 0.00 0.00 1.52
2095 2287 8.258007 TGCTATAGTGCTTGTCTAGTGTAAAAT 58.742 33.333 0.84 0.00 0.00 1.82
2096 2288 8.543774 GCTATAGTGCTTGTCTAGTGTAAAATG 58.456 37.037 0.84 0.00 0.00 2.32
2097 2289 9.803315 CTATAGTGCTTGTCTAGTGTAAAATGA 57.197 33.333 0.00 0.00 0.00 2.57
2099 2291 7.426929 AGTGCTTGTCTAGTGTAAAATGAAG 57.573 36.000 0.00 0.00 0.00 3.02
2100 2292 7.217200 AGTGCTTGTCTAGTGTAAAATGAAGA 58.783 34.615 0.00 0.00 0.00 2.87
2101 2293 7.715249 AGTGCTTGTCTAGTGTAAAATGAAGAA 59.285 33.333 0.00 0.00 0.00 2.52
2102 2294 8.012241 GTGCTTGTCTAGTGTAAAATGAAGAAG 58.988 37.037 0.00 0.00 0.00 2.85
2103 2295 7.931407 TGCTTGTCTAGTGTAAAATGAAGAAGA 59.069 33.333 0.00 0.00 0.00 2.87
2104 2296 8.774586 GCTTGTCTAGTGTAAAATGAAGAAGAA 58.225 33.333 0.00 0.00 0.00 2.52
2200 2392 0.252103 TTCTGCTTCGGTAGACCCCT 60.252 55.000 0.00 0.00 36.46 4.79
2217 2409 3.071892 ACCCCTCTTAAACACATGAACGA 59.928 43.478 0.00 0.00 0.00 3.85
2355 2548 1.248101 TTCTCATCCGCGGTGAGTGA 61.248 55.000 35.32 27.63 42.82 3.41
2608 2835 1.495951 GCAACCGACGACAATCACC 59.504 57.895 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.100510 CTCGTGATCCTGTACGGGAA 58.899 55.000 27.07 9.35 43.15 3.97
157 158 2.985847 GCCGCCAAGCAAGTCCTT 60.986 61.111 0.00 0.00 0.00 3.36
214 215 1.145377 CGTTTACCCTAGCCGCCAT 59.855 57.895 0.00 0.00 0.00 4.40
366 367 8.259411 TGTCTATATTTTTGCTGCATGGAAAAT 58.741 29.630 20.72 20.72 43.60 1.82
412 413 2.361104 GGTTGCGGGATTGAGCCA 60.361 61.111 0.00 0.00 0.00 4.75
450 461 3.223589 GCTCCTCCTCCTCGCTCC 61.224 72.222 0.00 0.00 0.00 4.70
471 483 3.808834 TGAGAAGAGGAGACCTACACA 57.191 47.619 0.00 0.00 31.76 3.72
528 540 6.487299 AAAGTTGAGAGAGAGTTACACCTT 57.513 37.500 0.00 0.00 0.00 3.50
534 546 3.510360 CCCCGAAAGTTGAGAGAGAGTTA 59.490 47.826 0.00 0.00 0.00 2.24
567 579 4.040339 TGAGTGGAGTGAGTGATGCTAAAA 59.960 41.667 0.00 0.00 0.00 1.52
649 661 4.662278 TGTTGGAATTTTGCTAGTAGGCT 58.338 39.130 0.00 0.00 0.00 4.58
727 739 5.338365 GCACAAGTCTGGAATGAAATCATC 58.662 41.667 0.00 0.00 35.10 2.92
742 754 1.071567 GGAGAGTACGCGCACAAGTC 61.072 60.000 12.80 4.82 0.00 3.01
750 763 1.331138 CTACCTTCAGGAGAGTACGCG 59.669 57.143 3.53 3.53 38.94 6.01
751 764 2.641305 TCTACCTTCAGGAGAGTACGC 58.359 52.381 0.00 0.00 38.94 4.42
767 780 7.307219 CGAATCCGTGGATTAATTTCCTTCTAC 60.307 40.741 13.92 0.00 43.98 2.59
783 796 2.159014 TCATTTCCTACCGAATCCGTGG 60.159 50.000 0.00 0.00 0.00 4.94
786 799 5.539048 AGTAATCATTTCCTACCGAATCCG 58.461 41.667 0.00 0.00 0.00 4.18
808 858 9.708222 CCAAGTATATTTTGATCTCAACGAAAG 57.292 33.333 0.00 0.00 35.28 2.62
827 877 9.632638 AATGATATGCAGTTTCTTACCAAGTAT 57.367 29.630 0.00 0.00 0.00 2.12
847 910 7.204604 TCTCGTGCTAAAATTCCGTAATGATA 58.795 34.615 0.00 0.00 0.00 2.15
876 939 0.394762 TCTCCTTCCATGCATGTGCC 60.395 55.000 24.58 0.00 41.18 5.01
880 943 6.348786 CCGTTTATAATCTCCTTCCATGCATG 60.349 42.308 20.19 20.19 0.00 4.06
881 944 5.707298 CCGTTTATAATCTCCTTCCATGCAT 59.293 40.000 0.00 0.00 0.00 3.96
882 945 5.063204 CCGTTTATAATCTCCTTCCATGCA 58.937 41.667 0.00 0.00 0.00 3.96
883 946 5.305585 TCCGTTTATAATCTCCTTCCATGC 58.694 41.667 0.00 0.00 0.00 4.06
927 995 5.541098 ACTGCGTATCGATCGAATATACA 57.459 39.130 23.50 15.11 0.00 2.29
934 1002 3.181537 CGTACATACTGCGTATCGATCGA 60.182 47.826 21.86 21.86 0.00 3.59
939 1007 2.231693 GCTCGTACATACTGCGTATCG 58.768 52.381 0.00 1.76 0.00 2.92
941 1009 1.951602 TGGCTCGTACATACTGCGTAT 59.048 47.619 0.00 0.00 0.00 3.06
944 1012 0.179148 TGTGGCTCGTACATACTGCG 60.179 55.000 0.00 0.00 0.00 5.18
945 1026 1.560923 CTGTGGCTCGTACATACTGC 58.439 55.000 0.00 0.00 0.00 4.40
947 1028 0.460311 GCCTGTGGCTCGTACATACT 59.540 55.000 0.73 0.00 46.69 2.12
983 1065 3.444742 TGTTATGAAGATTGCTTGGCCAG 59.555 43.478 5.11 1.08 33.61 4.85
984 1066 3.429492 TGTTATGAAGATTGCTTGGCCA 58.571 40.909 0.00 0.00 33.61 5.36
985 1067 4.098349 TGATGTTATGAAGATTGCTTGGCC 59.902 41.667 0.00 0.00 33.61 5.36
986 1068 5.252969 TGATGTTATGAAGATTGCTTGGC 57.747 39.130 0.00 0.00 33.61 4.52
1024 1107 6.407074 GCTGAGGAGCTAAGAACAAAGGTATA 60.407 42.308 0.00 0.00 42.52 1.47
1026 1109 4.322801 GCTGAGGAGCTAAGAACAAAGGTA 60.323 45.833 0.00 0.00 42.52 3.08
1027 1110 3.558109 GCTGAGGAGCTAAGAACAAAGGT 60.558 47.826 0.00 0.00 42.52 3.50
1028 1111 3.006247 GCTGAGGAGCTAAGAACAAAGG 58.994 50.000 0.00 0.00 42.52 3.11
1029 1112 3.006247 GGCTGAGGAGCTAAGAACAAAG 58.994 50.000 0.00 0.00 45.44 2.77
1030 1113 2.371841 TGGCTGAGGAGCTAAGAACAAA 59.628 45.455 0.00 0.00 45.44 2.83
1044 1127 0.325933 TCTTGGACACCATGGCTGAG 59.674 55.000 13.04 1.76 31.53 3.35
1055 1138 0.615331 GAGGATGCAGGTCTTGGACA 59.385 55.000 0.00 0.00 33.68 4.02
1107 1190 7.014905 ACTCTATTACATTATCCTTGCGTACCA 59.985 37.037 0.00 0.00 0.00 3.25
1120 1203 6.260714 TGACGGCGAACTACTCTATTACATTA 59.739 38.462 16.62 0.00 0.00 1.90
1124 1207 4.201851 TGTGACGGCGAACTACTCTATTAC 60.202 45.833 16.62 0.00 0.00 1.89
1125 1208 3.940852 TGTGACGGCGAACTACTCTATTA 59.059 43.478 16.62 0.00 0.00 0.98
1127 1210 2.355132 CTGTGACGGCGAACTACTCTAT 59.645 50.000 16.62 0.00 0.00 1.98
1130 1213 0.240411 ACTGTGACGGCGAACTACTC 59.760 55.000 16.62 0.00 0.00 2.59
1132 1288 1.494824 AAACTGTGACGGCGAACTAC 58.505 50.000 16.62 7.27 0.00 2.73
1135 1291 2.477375 TGATTAAACTGTGACGGCGAAC 59.523 45.455 16.62 12.42 0.00 3.95
1145 1301 5.692204 GGATCGATCGATGTGATTAAACTGT 59.308 40.000 33.86 6.57 37.47 3.55
1386 1542 1.701847 AGCTGGATCTTGGTTGTGTCT 59.298 47.619 0.00 0.00 0.00 3.41
1392 1548 0.694771 TGAGCAGCTGGATCTTGGTT 59.305 50.000 17.12 0.00 31.67 3.67
1403 1559 3.710722 CCTCCCGGTTGAGCAGCT 61.711 66.667 0.00 0.00 0.00 4.24
1503 1659 2.429610 GGCGTTATAGAGGGTGAAGTCA 59.570 50.000 0.00 0.00 0.00 3.41
1594 1750 2.750166 TGCGGGCATTCGATAAAAGAAA 59.250 40.909 0.00 0.00 0.00 2.52
1636 1792 0.593128 ACAGAAAGGAACATGCGCAC 59.407 50.000 14.90 0.00 0.00 5.34
1642 1798 7.884877 TGAGAAATGATACACAGAAAGGAACAT 59.115 33.333 0.00 0.00 0.00 2.71
1693 1849 6.377146 GGATGGAGACTTAATTGCTTTGGTAA 59.623 38.462 0.00 0.00 0.00 2.85
1697 1853 4.706476 TGGGATGGAGACTTAATTGCTTTG 59.294 41.667 0.00 0.00 0.00 2.77
1698 1854 4.934356 TGGGATGGAGACTTAATTGCTTT 58.066 39.130 0.00 0.00 0.00 3.51
1708 1868 3.852578 ACCAGTTTATTGGGATGGAGACT 59.147 43.478 0.00 0.00 42.76 3.24
1709 1869 4.236527 ACCAGTTTATTGGGATGGAGAC 57.763 45.455 0.00 0.00 42.76 3.36
1710 1870 6.069088 ACAATACCAGTTTATTGGGATGGAGA 60.069 38.462 0.00 0.00 41.07 3.71
1711 1871 6.039717 CACAATACCAGTTTATTGGGATGGAG 59.960 42.308 0.00 0.00 43.08 3.86
1909 2100 9.248291 CTGTTTCACTATGCAAAATTTACACTT 57.752 29.630 0.00 0.00 0.00 3.16
2031 2223 4.292178 CAGAGGATCCGGCTCCGC 62.292 72.222 19.20 19.20 40.46 5.54
2032 2224 3.610669 CCAGAGGATCCGGCTCCG 61.611 72.222 18.42 4.78 40.46 4.63
2033 2225 3.934962 GCCAGAGGATCCGGCTCC 61.935 72.222 16.90 16.90 42.78 4.70
2036 2228 1.115930 TCTAAGCCAGAGGATCCGGC 61.116 60.000 18.67 18.67 46.62 6.13
2037 2229 0.965439 CTCTAAGCCAGAGGATCCGG 59.035 60.000 5.98 2.60 46.21 5.14
2045 2237 3.306780 CGTTTTCCCTTCTCTAAGCCAGA 60.307 47.826 0.00 0.00 0.00 3.86
2046 2238 3.003480 CGTTTTCCCTTCTCTAAGCCAG 58.997 50.000 0.00 0.00 0.00 4.85
2047 2239 2.635915 TCGTTTTCCCTTCTCTAAGCCA 59.364 45.455 0.00 0.00 0.00 4.75
2048 2240 3.329929 TCGTTTTCCCTTCTCTAAGCC 57.670 47.619 0.00 0.00 0.00 4.35
2049 2241 3.064134 GCATCGTTTTCCCTTCTCTAAGC 59.936 47.826 0.00 0.00 0.00 3.09
2050 2242 4.508662 AGCATCGTTTTCCCTTCTCTAAG 58.491 43.478 0.00 0.00 0.00 2.18
2051 2243 4.553330 AGCATCGTTTTCCCTTCTCTAA 57.447 40.909 0.00 0.00 0.00 2.10
2052 2244 5.871396 ATAGCATCGTTTTCCCTTCTCTA 57.129 39.130 0.00 0.00 0.00 2.43
2053 2245 4.762289 ATAGCATCGTTTTCCCTTCTCT 57.238 40.909 0.00 0.00 0.00 3.10
2054 2246 5.463724 CACTATAGCATCGTTTTCCCTTCTC 59.536 44.000 0.00 0.00 0.00 2.87
2055 2247 5.360591 CACTATAGCATCGTTTTCCCTTCT 58.639 41.667 0.00 0.00 0.00 2.85
2056 2248 4.024809 GCACTATAGCATCGTTTTCCCTTC 60.025 45.833 0.00 0.00 0.00 3.46
2057 2249 3.877508 GCACTATAGCATCGTTTTCCCTT 59.122 43.478 0.00 0.00 0.00 3.95
2058 2250 3.134804 AGCACTATAGCATCGTTTTCCCT 59.865 43.478 0.00 0.00 36.85 4.20
2059 2251 3.467803 AGCACTATAGCATCGTTTTCCC 58.532 45.455 0.00 0.00 36.85 3.97
2060 2252 4.332819 ACAAGCACTATAGCATCGTTTTCC 59.667 41.667 0.00 0.00 36.85 3.13
2061 2253 5.292101 AGACAAGCACTATAGCATCGTTTTC 59.708 40.000 0.00 0.00 36.85 2.29
2062 2254 5.178797 AGACAAGCACTATAGCATCGTTTT 58.821 37.500 0.00 0.00 36.85 2.43
2063 2255 4.759782 AGACAAGCACTATAGCATCGTTT 58.240 39.130 0.00 0.00 36.85 3.60
2064 2256 4.392921 AGACAAGCACTATAGCATCGTT 57.607 40.909 0.00 0.00 36.85 3.85
2065 2257 4.580995 ACTAGACAAGCACTATAGCATCGT 59.419 41.667 0.00 0.00 36.85 3.73
2066 2258 4.914504 CACTAGACAAGCACTATAGCATCG 59.085 45.833 0.00 0.00 36.85 3.84
2067 2259 5.837437 ACACTAGACAAGCACTATAGCATC 58.163 41.667 0.00 0.00 36.85 3.91
2068 2260 5.860941 ACACTAGACAAGCACTATAGCAT 57.139 39.130 0.00 0.00 36.85 3.79
2069 2261 6.769134 TTACACTAGACAAGCACTATAGCA 57.231 37.500 0.00 0.00 36.85 3.49
2070 2262 8.543774 CATTTTACACTAGACAAGCACTATAGC 58.456 37.037 0.00 0.00 0.00 2.97
2071 2263 9.803315 TCATTTTACACTAGACAAGCACTATAG 57.197 33.333 0.00 0.00 0.00 1.31
2073 2265 9.155975 CTTCATTTTACACTAGACAAGCACTAT 57.844 33.333 0.00 0.00 0.00 2.12
2074 2266 8.364894 TCTTCATTTTACACTAGACAAGCACTA 58.635 33.333 0.00 0.00 0.00 2.74
2075 2267 7.217200 TCTTCATTTTACACTAGACAAGCACT 58.783 34.615 0.00 0.00 0.00 4.40
2076 2268 7.421530 TCTTCATTTTACACTAGACAAGCAC 57.578 36.000 0.00 0.00 0.00 4.40
2077 2269 7.931407 TCTTCTTCATTTTACACTAGACAAGCA 59.069 33.333 0.00 0.00 0.00 3.91
2078 2270 8.311650 TCTTCTTCATTTTACACTAGACAAGC 57.688 34.615 0.00 0.00 0.00 4.01
2164 2356 9.993881 CGAAGCAGAAGTGTAAAATTAATTTTG 57.006 29.630 28.45 15.41 40.00 2.44
2165 2357 9.191995 CCGAAGCAGAAGTGTAAAATTAATTTT 57.808 29.630 25.18 25.18 42.21 1.82
2166 2358 8.357402 ACCGAAGCAGAAGTGTAAAATTAATTT 58.643 29.630 7.64 7.64 34.92 1.82
2167 2359 7.882179 ACCGAAGCAGAAGTGTAAAATTAATT 58.118 30.769 0.00 0.00 0.00 1.40
2168 2360 7.448748 ACCGAAGCAGAAGTGTAAAATTAAT 57.551 32.000 0.00 0.00 0.00 1.40
2169 2361 6.870971 ACCGAAGCAGAAGTGTAAAATTAA 57.129 33.333 0.00 0.00 0.00 1.40
2170 2362 7.330208 GTCTACCGAAGCAGAAGTGTAAAATTA 59.670 37.037 0.00 0.00 0.00 1.40
2171 2363 6.147328 GTCTACCGAAGCAGAAGTGTAAAATT 59.853 38.462 0.00 0.00 0.00 1.82
2172 2364 5.638234 GTCTACCGAAGCAGAAGTGTAAAAT 59.362 40.000 0.00 0.00 0.00 1.82
2173 2365 4.986659 GTCTACCGAAGCAGAAGTGTAAAA 59.013 41.667 0.00 0.00 0.00 1.52
2174 2366 4.553323 GTCTACCGAAGCAGAAGTGTAAA 58.447 43.478 0.00 0.00 0.00 2.01
2175 2367 3.057033 GGTCTACCGAAGCAGAAGTGTAA 60.057 47.826 0.00 0.00 0.00 2.41
2176 2368 2.490903 GGTCTACCGAAGCAGAAGTGTA 59.509 50.000 0.00 0.00 0.00 2.90
2217 2409 7.808279 TGAAGGGGTATCGGATAATCTAAAT 57.192 36.000 0.00 0.00 0.00 1.40
2608 2835 1.741706 CAGCAGGCAAAGGATGTAGTG 59.258 52.381 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.