Multiple sequence alignment - TraesCS1B01G040400

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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 TraesCS1B01G040400 chr1B 100.000 4531 0 0 1 4531 20018794 20014264 0.000000e+00 8368.0
1 TraesCS1B01G040400 chr1B 92.377 2322 148 13 2087 4390 20573552 20575862 0.000000e+00 3280.0
2 TraesCS1B01G040400 chr1B 84.602 1669 192 21 2751 4390 19439110 19437478 0.000000e+00 1598.0
3 TraesCS1B01G040400 chr1B 84.491 1670 193 21 2751 4390 19537746 19536113 0.000000e+00 1589.0
4 TraesCS1B01G040400 chr1B 85.522 1112 111 12 2751 3844 19340380 19339301 0.000000e+00 1116.0
5 TraesCS1B01G040400 chr1B 89.714 525 34 11 1060 1564 20571289 20571813 0.000000e+00 652.0
6 TraesCS1B01G040400 chr1B 91.553 438 37 0 2090 2527 19551241 19550804 5.010000e-169 604.0
7 TraesCS1B01G040400 chr1B 88.189 508 58 2 1584 2089 20571900 20572407 5.010000e-169 604.0
8 TraesCS1B01G040400 chr1B 91.196 443 39 0 2090 2532 19478161 19477719 1.800000e-168 603.0
9 TraesCS1B01G040400 chr1B 90.971 443 40 0 2090 2532 19379234 19378792 8.390000e-167 597.0
10 TraesCS1B01G040400 chr1B 79.627 697 101 21 1397 2089 19552935 19552276 3.190000e-126 462.0
11 TraesCS1B01G040400 chr1B 89.971 339 34 0 1060 1398 19553304 19552966 5.380000e-119 438.0
12 TraesCS1B01G040400 chr1B 90.520 327 31 0 2090 2416 19441226 19440900 2.500000e-117 433.0
13 TraesCS1B01G040400 chr1B 90.214 327 32 0 2090 2416 19342488 19342162 1.160000e-115 427.0
14 TraesCS1B01G040400 chr1B 93.061 245 16 1 2514 2758 19475450 19475207 1.550000e-94 357.0
15 TraesCS1B01G040400 chr1B 92.653 245 17 1 2514 2758 19539953 19539710 7.210000e-93 351.0
16 TraesCS1B01G040400 chr1B 92.245 245 18 1 2514 2758 19376523 19376280 3.360000e-91 346.0
17 TraesCS1B01G040400 chr1B 91.429 140 11 1 4388 4527 388261220 388261358 1.660000e-44 191.0
18 TraesCS1B01G040400 chr1B 91.429 140 11 1 4388 4527 528618635 528618773 1.660000e-44 191.0
19 TraesCS1B01G040400 chr1B 93.976 83 5 0 973 1055 20571029 20571111 4.760000e-25 126.0
20 TraesCS1B01G040400 chr1B 75.862 174 25 15 3908 4077 485301405 485301245 6.290000e-09 73.1
21 TraesCS1B01G040400 chr1D 94.363 2466 110 13 2087 4527 13703583 13701122 0.000000e+00 3757.0
22 TraesCS1B01G040400 chr1D 92.772 1771 106 9 2090 3841 13799241 13797474 0.000000e+00 2542.0
23 TraesCS1B01G040400 chr1D 92.520 508 35 3 1584 2089 13705285 13704779 0.000000e+00 725.0
24 TraesCS1B01G040400 chr1D 91.142 508 39 3 3885 4390 13797475 13796972 0.000000e+00 684.0
25 TraesCS1B01G040400 chr1D 87.033 509 63 3 1584 2089 13800949 13800441 5.090000e-159 571.0
26 TraesCS1B01G040400 chr1D 95.280 339 16 0 1060 1398 13705882 13705544 5.160000e-149 538.0
27 TraesCS1B01G040400 chr1D 92.920 339 24 0 1060 1398 13801947 13801609 1.130000e-135 494.0
28 TraesCS1B01G040400 chr1D 90.148 203 12 3 1385 1587 13705525 13705331 1.620000e-64 257.0
29 TraesCS1B01G040400 chr1D 92.958 142 10 0 1394 1535 13801581 13801440 1.650000e-49 207.0
30 TraesCS1B01G040400 chr1D 93.182 132 9 0 4396 4527 111433107 111433238 1.290000e-45 195.0
31 TraesCS1B01G040400 chr1D 94.262 122 7 0 4406 4527 37869606 37869485 2.150000e-43 187.0
32 TraesCS1B01G040400 chr1D 91.241 137 12 0 4391 4527 341414330 341414194 2.150000e-43 187.0
33 TraesCS1B01G040400 chr1D 97.802 91 2 0 974 1064 13706138 13706048 1.690000e-34 158.0
34 TraesCS1B01G040400 chr1D 90.217 92 7 2 974 1063 13802211 13802120 7.960000e-23 119.0
35 TraesCS1B01G040400 chr1A 89.985 2027 166 14 2090 4089 14745696 14743680 0.000000e+00 2584.0
36 TraesCS1B01G040400 chr1A 93.235 340 23 0 1060 1399 14747949 14747610 6.770000e-138 501.0
37 TraesCS1B01G040400 chr1A 90.780 141 13 0 4387 4527 342067822 342067682 5.980000e-44 189.0
38 TraesCS1B01G040400 chr1A 86.957 92 10 2 974 1063 14748215 14748124 8.020000e-18 102.0
39 TraesCS1B01G040400 chr6B 95.850 988 26 5 1 974 659625588 659624602 0.000000e+00 1583.0
40 TraesCS1B01G040400 chr6B 91.115 574 35 5 407 974 27734172 27733609 0.000000e+00 763.0
41 TraesCS1B01G040400 chr6B 82.131 291 47 5 1795 2082 25268012 25268300 1.260000e-60 244.0
42 TraesCS1B01G040400 chr3B 95.556 990 29 5 1 976 770611953 770610965 0.000000e+00 1570.0
43 TraesCS1B01G040400 chr3B 95.450 989 30 5 1 975 780640898 780639911 0.000000e+00 1563.0
44 TraesCS1B01G040400 chr3B 77.143 140 28 3 3916 4053 737461273 737461410 1.350000e-10 78.7
45 TraesCS1B01G040400 chr3B 76.712 146 30 3 3909 4053 737496517 737496659 1.350000e-10 78.7
46 TraesCS1B01G040400 chr7B 95.344 988 30 6 1 974 740375574 740376559 0.000000e+00 1555.0
47 TraesCS1B01G040400 chr7B 90.476 147 13 1 4381 4527 558395703 558395848 4.630000e-45 193.0
48 TraesCS1B01G040400 chr7B 78.182 165 33 2 3908 4072 6092068 6092229 8.020000e-18 102.0
49 TraesCS1B01G040400 chr5B 95.238 987 33 4 1 974 540246710 540247695 0.000000e+00 1550.0
50 TraesCS1B01G040400 chr5B 89.547 574 52 7 407 974 673361398 673360827 0.000000e+00 721.0
51 TraesCS1B01G040400 chr2B 95.142 988 33 5 1 974 708216160 708215174 0.000000e+00 1544.0
52 TraesCS1B01G040400 chr2B 95.040 988 34 5 1 974 88888415 88887429 0.000000e+00 1539.0
53 TraesCS1B01G040400 chr2B 95.410 915 27 5 1 901 46853931 46853018 0.000000e+00 1443.0
54 TraesCS1B01G040400 chr4A 94.864 993 36 6 1 979 674297908 674296917 0.000000e+00 1537.0
55 TraesCS1B01G040400 chr4A 79.420 345 62 5 1745 2082 236159311 236159653 7.580000e-58 235.0
56 TraesCS1B01G040400 chr4A 82.353 85 14 1 3940 4024 683538307 683538224 6.290000e-09 73.1
57 TraesCS1B01G040400 chr4B 91.021 568 48 3 407 974 3793783 3793219 0.000000e+00 763.0
58 TraesCS1B01G040400 chr4B 92.806 139 10 0 4387 4525 66453528 66453390 7.690000e-48 202.0
59 TraesCS1B01G040400 chr4B 89.655 145 14 1 4375 4518 421500875 421501019 2.780000e-42 183.0
60 TraesCS1B01G040400 chr4B 76.667 330 72 5 1752 2079 482644302 482643976 1.300000e-40 178.0
61 TraesCS1B01G040400 chr7A 88.021 576 57 9 407 974 50304913 50305484 0.000000e+00 671.0
62 TraesCS1B01G040400 chr7A 93.023 43 3 0 4218 4260 403358549 403358591 3.780000e-06 63.9
63 TraesCS1B01G040400 chr3A 86.942 582 57 8 407 974 697121667 697122243 1.780000e-178 636.0
64 TraesCS1B01G040400 chr7D 83.160 576 85 10 407 974 558243158 558242587 2.420000e-142 516.0
65 TraesCS1B01G040400 chr7D 77.647 170 31 5 1915 2082 628692338 628692174 3.730000e-16 97.1
66 TraesCS1B01G040400 chr7D 76.786 112 17 4 3973 4084 626426749 626426647 2.000000e-03 54.7
67 TraesCS1B01G040400 chr5D 78.830 581 104 17 407 976 561107672 561107100 1.540000e-99 374.0
68 TraesCS1B01G040400 chr5D 78.621 580 107 15 407 976 561227597 561227025 7.160000e-98 368.0
69 TraesCS1B01G040400 chr5D 89.933 149 14 1 4381 4528 267829315 267829463 1.660000e-44 191.0
70 TraesCS1B01G040400 chr5D 82.524 206 31 5 1882 2085 111617917 111617715 4.660000e-40 176.0
71 TraesCS1B01G040400 chr5D 75.976 333 76 4 1751 2082 14608395 14608066 7.800000e-38 169.0
72 TraesCS1B01G040400 chr5D 80.342 117 19 4 1945 2059 340538421 340538535 8.080000e-13 86.1
73 TraesCS1B01G040400 chr5D 79.661 118 22 1 1942 2059 14608476 14608361 2.900000e-12 84.2
74 TraesCS1B01G040400 chr6A 78.886 341 57 7 1744 2082 22437073 22436746 2.740000e-52 217.0
75 TraesCS1B01G040400 chr6A 80.488 164 31 1 1914 2077 22437176 22437014 1.710000e-24 124.0
76 TraesCS1B01G040400 chr6D 90.066 151 15 0 4377 4527 215509049 215508899 3.580000e-46 196.0
77 TraesCS1B01G040400 chr6D 91.667 132 11 0 4389 4520 110612948 110613079 2.780000e-42 183.0
78 TraesCS1B01G040400 chr6D 91.667 132 11 0 4396 4527 198909538 198909669 2.780000e-42 183.0
79 TraesCS1B01G040400 chr6D 93.496 123 8 0 4405 4527 200761678 200761800 2.780000e-42 183.0
80 TraesCS1B01G040400 chr6D 90.580 138 13 0 4390 4527 267180390 267180527 2.780000e-42 183.0
81 TraesCS1B01G040400 chr6D 93.496 123 8 0 4405 4527 300722875 300722997 2.780000e-42 183.0
82 TraesCS1B01G040400 chr6D 93.496 123 8 0 4405 4527 408954319 408954441 2.780000e-42 183.0
83 TraesCS1B01G040400 chr6D 90.580 138 11 2 4391 4528 105641583 105641718 1.000000e-41 182.0
84 TraesCS1B01G040400 chr6D 90.511 137 13 0 4391 4527 139076882 139077018 1.000000e-41 182.0
85 TraesCS1B01G040400 chr6D 90.511 137 13 0 4391 4527 197409591 197409455 1.000000e-41 182.0
86 TraesCS1B01G040400 chr6D 90.511 137 13 0 4391 4527 229204066 229203930 1.000000e-41 182.0
87 TraesCS1B01G040400 chr6D 90.511 137 13 0 4391 4527 290892342 290892206 1.000000e-41 182.0
88 TraesCS1B01G040400 chr6D 90.580 138 12 1 4391 4527 307611051 307611188 1.000000e-41 182.0
89 TraesCS1B01G040400 chr6D 89.510 143 14 1 4386 4527 386401936 386401794 3.600000e-41 180.0
90 TraesCS1B01G040400 chr6D 88.079 151 16 1 4377 4527 309837315 309837463 1.300000e-40 178.0
91 TraesCS1B01G040400 chr2A 92.647 136 10 0 4391 4526 272274704 272274569 3.580000e-46 196.0
92 TraesCS1B01G040400 chr4D 92.029 138 10 1 4391 4527 287473784 287473647 4.630000e-45 193.0
93 TraesCS1B01G040400 chr4D 91.971 137 11 0 4391 4527 333237047 333237183 4.630000e-45 193.0
94 TraesCS1B01G040400 chr4D 91.304 138 11 1 4391 4527 316602397 316602260 2.150000e-43 187.0
95 TraesCS1B01G040400 chr4D 90.647 139 12 1 4390 4527 361405478 361405340 2.780000e-42 183.0
96 TraesCS1B01G040400 chr4D 89.583 144 14 1 4385 4527 339833660 339833517 1.000000e-41 182.0
97 TraesCS1B01G040400 chr4D 77.703 148 27 4 3943 4087 93349389 93349245 8.080000e-13 86.1
98 TraesCS1B01G040400 chr2D 91.971 137 11 0 4391 4527 121259336 121259472 4.630000e-45 193.0
99 TraesCS1B01G040400 chr2D 90.909 143 12 1 4386 4527 614475077 614475219 1.660000e-44 191.0
100 TraesCS1B01G040400 chr2D 89.796 147 14 1 4382 4527 593592898 593592752 2.150000e-43 187.0
101 TraesCS1B01G040400 chrUn 91.870 123 10 0 4405 4527 28037586 28037708 6.030000e-39 172.0
102 TraesCS1B01G040400 chrUn 89.130 138 15 0 4390 4527 104491187 104491324 6.030000e-39 172.0
103 TraesCS1B01G040400 chrUn 91.200 125 11 0 4403 4527 98978470 98978346 2.170000e-38 171.0
104 TraesCS1B01G040400 chrUn 88.652 141 15 1 4388 4528 121087930 121088069 2.170000e-38 171.0
105 TraesCS1B01G040400 chrUn 90.152 132 12 1 4391 4522 364468782 364468652 2.170000e-38 171.0
106 TraesCS1B01G040400 chrUn 91.736 121 10 0 4407 4527 131694477 131694597 7.800000e-38 169.0
107 TraesCS1B01G040400 chrUn 91.057 123 11 0 4405 4527 68639271 68639149 2.800000e-37 167.0
108 TraesCS1B01G040400 chrUn 90.400 125 12 0 4403 4527 4473594 4473470 1.010000e-36 165.0
109 TraesCS1B01G040400 chrUn 87.943 141 16 1 4391 4531 118857145 118857006 1.010000e-36 165.0
110 TraesCS1B01G040400 chrUn 88.321 137 16 0 4391 4527 285140163 285140299 1.010000e-36 165.0


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 TraesCS1B01G040400 chr1B 20014264 20018794 4530 True 8368.000000 8368 100.000000 1 4531 1 chr1B.!!$R1 4530
1 TraesCS1B01G040400 chr1B 20571029 20575862 4833 False 1165.500000 3280 91.064000 973 4390 4 chr1B.!!$F3 3417
2 TraesCS1B01G040400 chr1B 19437478 19441226 3748 True 1015.500000 1598 87.561000 2090 4390 2 chr1B.!!$R5 2300
3 TraesCS1B01G040400 chr1B 19536113 19539953 3840 True 970.000000 1589 88.572000 2514 4390 2 chr1B.!!$R7 1876
4 TraesCS1B01G040400 chr1B 19339301 19342488 3187 True 771.500000 1116 87.868000 2090 3844 2 chr1B.!!$R3 1754
5 TraesCS1B01G040400 chr1B 19550804 19553304 2500 True 501.333333 604 87.050333 1060 2527 3 chr1B.!!$R8 1467
6 TraesCS1B01G040400 chr1B 19475207 19478161 2954 True 480.000000 603 92.128500 2090 2758 2 chr1B.!!$R6 668
7 TraesCS1B01G040400 chr1B 19376280 19379234 2954 True 471.500000 597 91.608000 2090 2758 2 chr1B.!!$R4 668
8 TraesCS1B01G040400 chr1D 13701122 13706138 5016 True 1087.000000 3757 94.022600 974 4527 5 chr1D.!!$R3 3553
9 TraesCS1B01G040400 chr1D 13796972 13802211 5239 True 769.500000 2542 91.173667 974 4390 6 chr1D.!!$R4 3416
10 TraesCS1B01G040400 chr1A 14743680 14748215 4535 True 1062.333333 2584 90.059000 974 4089 3 chr1A.!!$R2 3115
11 TraesCS1B01G040400 chr6B 659624602 659625588 986 True 1583.000000 1583 95.850000 1 974 1 chr6B.!!$R2 973
12 TraesCS1B01G040400 chr6B 27733609 27734172 563 True 763.000000 763 91.115000 407 974 1 chr6B.!!$R1 567
13 TraesCS1B01G040400 chr3B 770610965 770611953 988 True 1570.000000 1570 95.556000 1 976 1 chr3B.!!$R1 975
14 TraesCS1B01G040400 chr3B 780639911 780640898 987 True 1563.000000 1563 95.450000 1 975 1 chr3B.!!$R2 974
15 TraesCS1B01G040400 chr7B 740375574 740376559 985 False 1555.000000 1555 95.344000 1 974 1 chr7B.!!$F3 973
16 TraesCS1B01G040400 chr5B 540246710 540247695 985 False 1550.000000 1550 95.238000 1 974 1 chr5B.!!$F1 973
17 TraesCS1B01G040400 chr5B 673360827 673361398 571 True 721.000000 721 89.547000 407 974 1 chr5B.!!$R1 567
18 TraesCS1B01G040400 chr2B 708215174 708216160 986 True 1544.000000 1544 95.142000 1 974 1 chr2B.!!$R3 973
19 TraesCS1B01G040400 chr2B 88887429 88888415 986 True 1539.000000 1539 95.040000 1 974 1 chr2B.!!$R2 973
20 TraesCS1B01G040400 chr2B 46853018 46853931 913 True 1443.000000 1443 95.410000 1 901 1 chr2B.!!$R1 900
21 TraesCS1B01G040400 chr4A 674296917 674297908 991 True 1537.000000 1537 94.864000 1 979 1 chr4A.!!$R1 978
22 TraesCS1B01G040400 chr4B 3793219 3793783 564 True 763.000000 763 91.021000 407 974 1 chr4B.!!$R1 567
23 TraesCS1B01G040400 chr7A 50304913 50305484 571 False 671.000000 671 88.021000 407 974 1 chr7A.!!$F1 567
24 TraesCS1B01G040400 chr3A 697121667 697122243 576 False 636.000000 636 86.942000 407 974 1 chr3A.!!$F1 567
25 TraesCS1B01G040400 chr7D 558242587 558243158 571 True 516.000000 516 83.160000 407 974 1 chr7D.!!$R1 567
26 TraesCS1B01G040400 chr5D 561107100 561107672 572 True 374.000000 374 78.830000 407 976 1 chr5D.!!$R2 569
27 TraesCS1B01G040400 chr5D 561227025 561227597 572 True 368.000000 368 78.621000 407 976 1 chr5D.!!$R3 569

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
911 933 0.695122 CCCCCTATTGGTCCCGGTTA 60.695 60.0 0.00 0.00 0.00 2.85 F
1057 1084 0.247460 AGCTACGAATGACTGCTGCA 59.753 50.0 0.88 0.88 32.32 4.41 F
1937 2657 0.393077 CAAGAACCAGACACTCGGGT 59.607 55.0 0.00 0.00 46.89 5.28 F
2082 2802 0.249120 TCTCCGATGCACACCGAAAT 59.751 50.0 6.56 0.00 0.00 2.17 F
2084 2804 0.321210 TCCGATGCACACCGAAATGT 60.321 50.0 6.56 0.00 0.00 2.71 F
3428 9678 0.547954 AGGGTGGGAAGGAGAGAACC 60.548 60.0 0.00 0.00 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2530 0.179111 GTCCATCGGCATCTGTTCGA 60.179 55.000 0.0 0.0 37.33 3.71 R
2059 2779 0.248661 CGGTGTGCATCGGAGAGTAG 60.249 60.000 0.0 0.0 43.63 2.57 R
2864 9107 0.846693 ACTTTTGAGGGGCTGTCTGT 59.153 50.000 0.0 0.0 0.00 3.41 R
2986 9234 0.998669 ACGTTTTGCTTTGTTGCAGC 59.001 45.000 0.0 0.0 44.27 5.25 R
3449 9699 1.209504 CTGAAACCCGATTCCCTAGCA 59.790 52.381 0.0 0.0 0.00 3.49 R
4298 10629 0.179111 CCTATTGAGCTTCGTCGCCA 60.179 55.000 0.0 0.0 0.00 5.69 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
65 66 3.378427 TCTTGTGATCATCGACGACATCT 59.622 43.478 15.95 0.00 0.00 2.90
195 197 4.434520 GTTGGAATTTCCGGTTCAACAAA 58.565 39.130 10.79 0.00 40.17 2.83
203 205 2.038033 TCCGGTTCAACAAACTCCTAGG 59.962 50.000 0.82 0.82 38.02 3.02
468 470 1.153901 GATCGACGGCGGTGAAGAA 60.154 57.895 12.58 0.00 38.28 2.52
513 515 6.292919 CCGCTAAACCTAGACAAATATTGAGC 60.293 42.308 0.00 0.00 0.00 4.26
520 522 8.579850 ACCTAGACAAATATTGAGCAAAATGA 57.420 30.769 0.00 0.00 0.00 2.57
551 553 2.039084 GTGGAGCTTGGAGAGGAGAAAA 59.961 50.000 0.00 0.00 0.00 2.29
566 568 3.683340 GGAGAAAACTTAAGTAGTGCGGG 59.317 47.826 8.92 0.00 37.12 6.13
688 709 2.686405 CTGCTCGCGGGGTATATATGTA 59.314 50.000 8.71 0.00 0.00 2.29
833 854 1.489230 ACCAAAAGGTCCAGACGAACT 59.511 47.619 0.00 0.00 41.77 3.01
911 933 0.695122 CCCCCTATTGGTCCCGGTTA 60.695 60.000 0.00 0.00 0.00 2.85
1055 1082 2.860735 GGTAAGCTACGAATGACTGCTG 59.139 50.000 0.00 0.00 33.96 4.41
1056 1083 1.363744 AAGCTACGAATGACTGCTGC 58.636 50.000 0.00 0.00 33.96 5.25
1057 1084 0.247460 AGCTACGAATGACTGCTGCA 59.753 50.000 0.88 0.88 32.32 4.41
1058 1085 1.078709 GCTACGAATGACTGCTGCAA 58.921 50.000 3.02 0.00 0.00 4.08
1140 1344 2.281208 CGGGAGGCGGACAAACAA 60.281 61.111 0.00 0.00 0.00 2.83
1211 1415 3.387947 CGGCTACTCGGGGTGGTT 61.388 66.667 0.00 0.00 0.00 3.67
1289 1493 1.079819 CAGGTTCGACGATGTGGCT 60.080 57.895 0.00 0.00 0.00 4.75
1298 1502 2.029288 CGATGTGGCTGTGCTCGTT 61.029 57.895 0.00 0.00 0.00 3.85
1434 1670 3.513912 TGGTCTCGTCACCTTGTGAATAT 59.486 43.478 0.00 0.00 44.49 1.28
1470 1706 8.492748 CGCTTTCTCTATAAACTTTTACACACA 58.507 33.333 0.00 0.00 0.00 3.72
1513 1749 3.618690 AGCACACTCTCCTAACCATTC 57.381 47.619 0.00 0.00 0.00 2.67
1563 1813 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1567 1817 2.161211 CACACACACACACACACATGAA 59.839 45.455 0.00 0.00 0.00 2.57
1603 1906 3.303189 AGTGCCCCACTCTCATCG 58.697 61.111 0.00 0.00 41.21 3.84
1629 1932 4.389374 CAGTCTTTTGTGATGTAGTGGGT 58.611 43.478 0.00 0.00 0.00 4.51
1653 1956 2.698274 TCTGCTTGTAGTGGAGTGTTCA 59.302 45.455 0.00 0.00 0.00 3.18
1720 2023 2.583143 GTCCTGGGTTGCTAACAAGTT 58.417 47.619 0.00 0.00 36.16 2.66
1725 2443 4.382577 CCTGGGTTGCTAACAAGTTGTTTT 60.383 41.667 25.35 6.00 41.45 2.43
1747 2465 2.687566 CCGTTCCTAGCCCCAGGT 60.688 66.667 0.00 0.00 36.99 4.00
1764 2482 1.133792 AGGTCAGTCTTTTGGGGTGTG 60.134 52.381 0.00 0.00 0.00 3.82
1766 2484 0.467290 TCAGTCTTTTGGGGTGTGGC 60.467 55.000 0.00 0.00 0.00 5.01
1786 2504 2.479901 GCGGGTTCTCTGCTAGTAGTTC 60.480 54.545 7.77 0.00 44.20 3.01
1790 2508 4.948621 GGGTTCTCTGCTAGTAGTTCAGTA 59.051 45.833 7.77 0.00 0.00 2.74
1799 2517 5.594317 TGCTAGTAGTTCAGTATCTGATGCA 59.406 40.000 8.45 0.00 40.39 3.96
1810 2528 1.960417 TCTGATGCACACCGAAAACA 58.040 45.000 0.00 0.00 0.00 2.83
1812 2530 2.884012 TCTGATGCACACCGAAAACATT 59.116 40.909 0.00 0.00 0.00 2.71
1848 2566 4.486503 CTGGGAGCTGAGCCTGGC 62.487 72.222 11.65 11.65 0.00 4.85
1937 2657 0.393077 CAAGAACCAGACACTCGGGT 59.607 55.000 0.00 0.00 46.89 5.28
2040 2760 2.414161 GGCTCGTGTTTTGGAATGTAGC 60.414 50.000 0.00 0.00 0.00 3.58
2059 2779 0.383949 CGGGCTCTCTGCTTCTAGTC 59.616 60.000 0.00 0.00 42.39 2.59
2060 2780 1.775385 GGGCTCTCTGCTTCTAGTCT 58.225 55.000 0.00 0.00 42.39 3.24
2082 2802 0.249120 TCTCCGATGCACACCGAAAT 59.751 50.000 6.56 0.00 0.00 2.17
2083 2803 0.374758 CTCCGATGCACACCGAAATG 59.625 55.000 6.56 0.00 0.00 2.32
2084 2804 0.321210 TCCGATGCACACCGAAATGT 60.321 50.000 6.56 0.00 0.00 2.71
2100 4053 4.149221 CGAAATGTTTGAGTACGTGCTGTA 59.851 41.667 12.07 0.00 0.00 2.74
2190 4143 8.547967 AATTTCTACTAGAAAAAGCATCGACA 57.452 30.769 13.98 0.00 46.08 4.35
2196 4149 6.170506 ACTAGAAAAAGCATCGACACCAATA 58.829 36.000 0.00 0.00 0.00 1.90
2228 4182 4.585162 ACGAGTTCATAAGGGATCAGGTAG 59.415 45.833 0.00 0.00 0.00 3.18
2261 4215 1.859302 TCCAGCAAAACCAAACACCT 58.141 45.000 0.00 0.00 0.00 4.00
2308 4262 7.199766 TCCTTGTTTTTGTATTGCAACTGTAG 58.800 34.615 0.00 0.00 36.72 2.74
2327 4282 4.997395 TGTAGTCTCTTCTTTTGCATGGAC 59.003 41.667 0.00 0.00 0.00 4.02
2396 4351 9.230122 TGTTGAGTTATTTCATCTATGCTTTCA 57.770 29.630 0.00 0.00 0.00 2.69
2610 6853 8.619146 TCAAAACCTTGTAGATACGTTATACG 57.381 34.615 0.00 0.00 39.51 3.06
2809 9052 2.224744 TGCCCTTGTGCAGAACTAATCA 60.225 45.455 0.00 0.00 36.04 2.57
2864 9107 3.361174 TGCGATGTCGGACAGTGA 58.639 55.556 16.84 0.00 40.23 3.41
2871 9114 0.668535 TGTCGGACAGTGACAGACAG 59.331 55.000 20.39 0.00 41.20 3.51
2893 9136 1.071699 CCCTCAAAAGTCCTGACGGAA 59.928 52.381 0.00 0.00 42.08 4.30
2911 9154 3.623060 CGGAAAACCACACTCCTCATATG 59.377 47.826 0.00 0.00 0.00 1.78
2986 9234 2.030007 ACACCAATTCAACAATCCAGCG 60.030 45.455 0.00 0.00 0.00 5.18
3046 9295 7.993101 TCAAACATGCCAAAATTGAATTCAAA 58.007 26.923 23.91 6.94 39.55 2.69
3077 9326 7.693951 GTGTACAATAGTGAATCTGCAATGTTC 59.306 37.037 0.00 0.00 0.00 3.18
3279 9529 8.806146 ACAATGACTGCATAAAGGTTCTAAAAT 58.194 29.630 0.00 0.00 33.44 1.82
3285 9535 8.748412 ACTGCATAAAGGTTCTAAAATATTGCA 58.252 29.630 0.00 0.00 0.00 4.08
3346 9596 0.685097 TTTGTCTTGCCGGCTACTCT 59.315 50.000 29.70 0.00 0.00 3.24
3359 9609 3.622630 GGCTACTCTAGAGGTGACAAGA 58.377 50.000 23.50 0.00 0.00 3.02
3428 9678 0.547954 AGGGTGGGAAGGAGAGAACC 60.548 60.000 0.00 0.00 0.00 3.62
3449 9699 2.289002 CGTGCAAGAGTTTCTGAAGCTT 59.711 45.455 8.19 0.00 0.00 3.74
3500 9750 5.782893 TCCAGTCAACTTACATTTTTGGG 57.217 39.130 0.00 0.00 0.00 4.12
3527 9777 3.644966 TGGGCTCTCGAATTTACCAAT 57.355 42.857 0.00 0.00 0.00 3.16
3805 10071 8.130671 AGGTACATAAAAGCACAGAGTAGTTA 57.869 34.615 0.00 0.00 0.00 2.24
3818 10087 7.118390 GCACAGAGTAGTTATTCACAATGTCTT 59.882 37.037 0.00 0.00 0.00 3.01
3991 10313 2.293955 CACACAATGAGCACACATCCAA 59.706 45.455 0.00 0.00 0.00 3.53
4150 10480 0.390860 GGCGTGACCTCAGATAGCAT 59.609 55.000 0.00 0.00 34.51 3.79
4177 10507 0.760945 CCCCTCAAGAGTCCCGCTAT 60.761 60.000 0.00 0.00 0.00 2.97
4189 10519 2.428171 GTCCCGCTATACAACCACACTA 59.572 50.000 0.00 0.00 0.00 2.74
4204 10534 6.677781 ACCACACTATTCATATCAAAACCG 57.322 37.500 0.00 0.00 0.00 4.44
4303 10634 2.499693 TGAGTGATAGGAAACATGGCGA 59.500 45.455 0.00 0.00 0.00 5.54
4340 10671 1.657804 GGAGGAAGAAGTTGGGAGGA 58.342 55.000 0.00 0.00 0.00 3.71
4394 10726 3.370633 GGGAAGGATTAGGACAACCACTC 60.371 52.174 0.00 0.00 38.94 3.51
4395 10727 3.522553 GAAGGATTAGGACAACCACTCG 58.477 50.000 0.00 0.00 38.94 4.18
4400 10732 4.142004 GGATTAGGACAACCACTCGTACAT 60.142 45.833 0.00 0.00 38.94 2.29
4401 10733 4.877378 TTAGGACAACCACTCGTACATT 57.123 40.909 0.00 0.00 38.94 2.71
4413 10745 5.279006 CCACTCGTACATTGAGGTGCTATAT 60.279 44.000 0.00 0.00 37.79 0.86
4417 10749 7.176865 ACTCGTACATTGAGGTGCTATATACAT 59.823 37.037 0.00 0.00 37.79 2.29
4437 10769 2.443887 GGTTTTTAACCCCTTTCCGC 57.556 50.000 0.00 0.00 46.12 5.54
4438 10770 1.336148 GGTTTTTAACCCCTTTCCGCG 60.336 52.381 0.00 0.00 46.12 6.46
4439 10771 1.608109 GTTTTTAACCCCTTTCCGCGA 59.392 47.619 8.23 0.00 0.00 5.87
4440 10772 1.237533 TTTTAACCCCTTTCCGCGAC 58.762 50.000 8.23 0.00 0.00 5.19
4442 10774 1.814772 TTAACCCCTTTCCGCGACGA 61.815 55.000 8.23 0.00 0.00 4.20
4508 10840 1.147376 CCACACGACCCAGAAACCA 59.853 57.895 0.00 0.00 0.00 3.67
4522 10854 0.474184 AAACCATCAGGGATAGGCCG 59.526 55.000 0.00 0.00 41.15 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.954202 ACAAGATCAAGATGGATGCAATGT 59.046 37.500 0.00 0.00 0.00 2.71
203 205 9.698617 GACCAACGTGACATAGATTTTATTTAC 57.301 33.333 0.00 0.00 0.00 2.01
392 394 6.313164 GGTGAGCCTCTTACTTGTATGTTTAC 59.687 42.308 0.00 0.00 0.00 2.01
513 515 4.797275 GCTCCACCTCCAAACTTCATTTTG 60.797 45.833 0.00 0.00 36.40 2.44
520 522 1.479389 CCAAGCTCCACCTCCAAACTT 60.479 52.381 0.00 0.00 0.00 2.66
551 553 1.002773 CCCAACCCGCACTACTTAAGT 59.997 52.381 13.68 13.68 39.81 2.24
688 709 1.890510 GTTCAAGCCACGAACCGGT 60.891 57.895 0.00 0.00 37.40 5.28
897 919 3.717392 TCAATCCATAACCGGGACCAATA 59.283 43.478 6.32 0.00 37.23 1.90
911 933 4.386761 CCCATTAGTCCTGGTTCAATCCAT 60.387 45.833 0.00 0.00 36.84 3.41
942 964 4.066139 GGGGCAATGGTCCAGGCT 62.066 66.667 15.66 0.00 42.08 4.58
997 1019 2.758979 CCTGGTCCGTAGTGAACATAGT 59.241 50.000 0.00 0.00 30.08 2.12
1139 1343 2.086869 CCATGCGTCCTCTTGAATGTT 58.913 47.619 0.00 0.00 0.00 2.71
1140 1344 1.679944 CCCATGCGTCCTCTTGAATGT 60.680 52.381 0.00 0.00 0.00 2.71
1211 1415 1.604308 CTGCACCATGGCCTTGTCA 60.604 57.895 13.04 10.53 0.00 3.58
1272 1476 1.079819 CAGCCACATCGTCGAACCT 60.080 57.895 0.00 0.00 0.00 3.50
1289 1493 0.943673 CACCAACATCAACGAGCACA 59.056 50.000 0.00 0.00 0.00 4.57
1298 1502 2.983030 GTGCCGCCACCAACATCA 60.983 61.111 0.00 0.00 35.92 3.07
1434 1670 2.472695 AGAGAAAGCGCACATTACCA 57.527 45.000 11.47 0.00 0.00 3.25
1470 1706 8.589338 TGCTAAGAGAGAAAGAGTAAATGAGTT 58.411 33.333 0.00 0.00 0.00 3.01
1513 1749 5.245751 AGAGAGAGAGAGAGAGAGAGCATAG 59.754 48.000 0.00 0.00 0.00 2.23
1600 1903 0.602638 TCACAAAAGACTGGCGCGAT 60.603 50.000 12.10 0.00 0.00 4.58
1603 1906 0.593128 ACATCACAAAAGACTGGCGC 59.407 50.000 0.00 0.00 0.00 6.53
1629 1932 2.965831 ACACTCCACTACAAGCAGAGAA 59.034 45.455 0.00 0.00 0.00 2.87
1653 1956 4.322385 GCGTTTTCGGTGCGCCTT 62.322 61.111 15.69 0.00 44.67 4.35
1701 2004 2.092103 ACAACTTGTTAGCAACCCAGGA 60.092 45.455 0.00 0.00 0.00 3.86
1720 2023 2.354403 GGCTAGGAACGGCTCTAAAACA 60.354 50.000 0.00 0.00 33.21 2.83
1725 2443 1.457079 GGGGCTAGGAACGGCTCTA 60.457 63.158 0.00 0.00 33.52 2.43
1747 2465 0.467290 GCCACACCCCAAAAGACTGA 60.467 55.000 0.00 0.00 0.00 3.41
1764 2482 0.386113 CTACTAGCAGAGAACCCGCC 59.614 60.000 0.00 0.00 0.00 6.13
1766 2484 2.753452 TGAACTACTAGCAGAGAACCCG 59.247 50.000 0.00 0.00 0.00 5.28
1786 2504 2.584492 TCGGTGTGCATCAGATACTG 57.416 50.000 0.00 0.00 0.00 2.74
1790 2508 2.503331 TGTTTTCGGTGTGCATCAGAT 58.497 42.857 0.00 0.00 0.00 2.90
1810 2528 1.138859 TCCATCGGCATCTGTTCGAAT 59.861 47.619 0.00 0.00 36.49 3.34
1812 2530 0.179111 GTCCATCGGCATCTGTTCGA 60.179 55.000 0.00 0.00 37.33 3.71
1848 2566 4.811557 GCTCTAATACCACTTGTTAGCAGG 59.188 45.833 0.00 0.00 0.00 4.85
1937 2657 5.493809 GTGGGACTAAAGTTATTGGCACTA 58.506 41.667 0.00 0.00 0.00 2.74
2006 2726 2.705821 CGAGCCTGAGGAGAGCGTT 61.706 63.158 0.65 0.00 0.00 4.84
2059 2779 0.248661 CGGTGTGCATCGGAGAGTAG 60.249 60.000 0.00 0.00 43.63 2.57
2060 2780 0.678684 TCGGTGTGCATCGGAGAGTA 60.679 55.000 4.96 0.00 43.63 2.59
2190 4143 7.687941 ATGAACTCGTGAGAAAAATATTGGT 57.312 32.000 3.44 0.00 41.32 3.67
2196 4149 6.472887 TCCCTTATGAACTCGTGAGAAAAAT 58.527 36.000 3.44 0.00 41.32 1.82
2228 4182 7.011857 TGGTTTTGCTGGATAACAACATTTTTC 59.988 33.333 5.06 0.00 0.00 2.29
2261 4215 7.509546 AGGAAAGACAAAAGAGTTGAGTGATA 58.490 34.615 0.00 0.00 0.00 2.15
2308 4262 2.808543 ACGTCCATGCAAAAGAAGAGAC 59.191 45.455 0.00 0.00 0.00 3.36
2327 4282 7.582435 AAGATCTAAATGTACAGTCACAACG 57.418 36.000 0.33 0.00 30.84 4.10
2379 4334 8.693120 ATCTCACATGAAAGCATAGATGAAAT 57.307 30.769 0.00 0.00 30.11 2.17
2396 4351 9.979578 CTAGCTAAGTTCTCAATTATCTCACAT 57.020 33.333 0.00 0.00 0.00 3.21
2691 6936 6.128553 CGAATGCATTGTTTGTCAGTAGTAGT 60.129 38.462 18.59 0.00 0.00 2.73
2758 7003 6.486993 CCTTAATTGCTTGGACCCTAGATAAC 59.513 42.308 1.73 0.00 0.00 1.89
2809 9052 8.974060 TCTTAGTAAGAGAAAACATGTGGTTT 57.026 30.769 8.59 0.00 40.99 3.27
2864 9107 0.846693 ACTTTTGAGGGGCTGTCTGT 59.153 50.000 0.00 0.00 0.00 3.41
2871 9114 0.955919 CGTCAGGACTTTTGAGGGGC 60.956 60.000 0.00 0.00 0.00 5.80
2893 9136 5.476945 GGTTTTCATATGAGGAGTGTGGTTT 59.523 40.000 5.39 0.00 0.00 3.27
2911 9154 4.344104 TCTCCATGGAATTGAGGGTTTTC 58.656 43.478 17.00 0.00 36.78 2.29
2986 9234 0.998669 ACGTTTTGCTTTGTTGCAGC 59.001 45.000 0.00 0.00 44.27 5.25
3046 9295 5.577164 GCAGATTCACTATTGTACACGAACT 59.423 40.000 0.00 0.00 0.00 3.01
3077 9326 7.703621 AGAATGTTCTTTGTTTGTCACAATGAG 59.296 33.333 0.00 0.00 45.48 2.90
3285 9535 2.298163 CCTTGTCTGGCAAAGCTTGATT 59.702 45.455 0.00 0.00 36.53 2.57
3346 9596 1.273606 GTGCTGCTCTTGTCACCTCTA 59.726 52.381 0.00 0.00 0.00 2.43
3359 9609 5.251764 AGAATGTAGAGATTTTGTGCTGCT 58.748 37.500 0.00 0.00 0.00 4.24
3428 9678 1.869767 AGCTTCAGAAACTCTTGCACG 59.130 47.619 0.00 0.00 0.00 5.34
3449 9699 1.209504 CTGAAACCCGATTCCCTAGCA 59.790 52.381 0.00 0.00 0.00 3.49
3500 9750 4.505313 AAATTCGAGAGCCCAAAAGTTC 57.495 40.909 0.00 0.00 0.00 3.01
3527 9777 8.719560 TGTACATAAAATGCGATGGTTACTAA 57.280 30.769 0.00 0.00 0.00 2.24
3550 9800 6.429078 CACATTATCAATAGTAGCCAGCATGT 59.571 38.462 0.00 0.00 0.00 3.21
3726 9992 8.937207 AATACACCTAGAATACCTCGATAACT 57.063 34.615 0.00 0.00 0.00 2.24
3768 10034 6.072893 GCTTTTATGTACCTCTTCACGGAAAA 60.073 38.462 0.00 0.00 0.00 2.29
3771 10037 4.020928 TGCTTTTATGTACCTCTTCACGGA 60.021 41.667 0.00 0.00 0.00 4.69
3805 10071 4.220602 GGGCCAAAGTAAGACATTGTGAAT 59.779 41.667 4.39 0.00 0.00 2.57
3920 10242 9.344772 TGAGCTTACAAACTCAAACCTTTATTA 57.655 29.630 0.00 0.00 39.89 0.98
3931 10253 6.936335 TGATTCATCTTGAGCTTACAAACTCA 59.064 34.615 0.00 0.00 41.06 3.41
3991 10313 5.069251 GTGTGCATCCTAACTATGTAGAGGT 59.931 44.000 0.00 0.00 0.00 3.85
4150 10480 2.910977 GGACTCTTGAGGGGTTTTCCTA 59.089 50.000 2.55 0.00 37.25 2.94
4177 10507 8.952278 GGTTTTGATATGAATAGTGTGGTTGTA 58.048 33.333 0.00 0.00 0.00 2.41
4189 10519 9.304731 CATGAATTTGACGGTTTTGATATGAAT 57.695 29.630 0.00 0.00 0.00 2.57
4204 10534 5.151632 GCATGGATTTGCATGAATTTGAC 57.848 39.130 15.21 0.00 42.31 3.18
4260 10590 5.408909 TCATTGTGCTTTGTTGCATTATTGG 59.591 36.000 0.00 0.00 45.23 3.16
4279 10609 4.260907 CGCCATGTTTCCTATCACTCATTG 60.261 45.833 0.00 0.00 0.00 2.82
4298 10629 0.179111 CCTATTGAGCTTCGTCGCCA 60.179 55.000 0.00 0.00 0.00 5.69
4340 10671 1.390565 CTCCTATCCGTTCGTGGAGT 58.609 55.000 0.00 0.00 42.45 3.85
4394 10726 6.531594 CCATGTATATAGCACCTCAATGTACG 59.468 42.308 0.00 0.00 0.00 3.67
4395 10727 7.386851 ACCATGTATATAGCACCTCAATGTAC 58.613 38.462 0.00 0.00 0.00 2.90
4400 10732 9.688091 TTAAAAACCATGTATATAGCACCTCAA 57.312 29.630 0.00 0.00 0.00 3.02
4401 10733 9.116067 GTTAAAAACCATGTATATAGCACCTCA 57.884 33.333 0.00 0.00 0.00 3.86
4430 10762 0.179225 CCAAATGTCGTCGCGGAAAG 60.179 55.000 6.13 0.00 0.00 2.62
4433 10765 1.005984 TTCCAAATGTCGTCGCGGA 60.006 52.632 6.13 0.00 0.00 5.54
4434 10766 1.131826 GTTCCAAATGTCGTCGCGG 59.868 57.895 6.13 0.00 0.00 6.46
4435 10767 1.131826 GGTTCCAAATGTCGTCGCG 59.868 57.895 0.00 0.00 0.00 5.87
4436 10768 1.131826 CGGTTCCAAATGTCGTCGC 59.868 57.895 0.00 0.00 0.00 5.19
4437 10769 0.437295 GACGGTTCCAAATGTCGTCG 59.563 55.000 0.00 0.00 40.22 5.12
4438 10770 0.437295 CGACGGTTCCAAATGTCGTC 59.563 55.000 5.52 0.00 46.56 4.20
4439 10771 2.524300 CGACGGTTCCAAATGTCGT 58.476 52.632 5.52 0.00 46.56 4.34
4442 10774 0.820074 TTGGCGACGGTTCCAAATGT 60.820 50.000 11.70 0.00 39.22 2.71
4483 10815 2.346365 GGGTCGTGTGGGAAGGAC 59.654 66.667 0.00 0.00 34.86 3.85
4508 10840 0.784495 TAGGACGGCCTATCCCTGAT 59.216 55.000 14.85 3.97 44.74 2.90


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

AutoCloner maintained by Alex Coulton.