Multiple sequence alignment - TraesCS2B01G559800

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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 TraesCS2B01G559800 chr2B 100.000 2501 0 0 1 2501 753783504 753786004 0.000000e+00 4619.0
1 TraesCS2B01G559800 chr2B 95.931 934 37 1 1 934 753810256 753809324 0.000000e+00 1513.0
2 TraesCS2B01G559800 chr2B 88.835 824 77 8 1 809 44288313 44289136 0.000000e+00 998.0
3 TraesCS2B01G559800 chr2B 96.648 358 5 2 1930 2280 753809041 753808684 2.770000e-164 588.0
4 TraesCS2B01G559800 chr2B 84.601 526 38 19 1206 1721 753837840 753837348 1.350000e-132 483.0
5 TraesCS2B01G559800 chr2B 100.000 211 0 0 2291 2501 753808459 753808249 8.390000e-105 390.0
6 TraesCS2B01G559800 chr2B 81.373 306 32 10 1764 2053 773349069 773348773 2.500000e-55 226.0
7 TraesCS2B01G559800 chr2B 90.303 165 16 0 1241 1405 753987004 753987168 1.510000e-52 217.0
8 TraesCS2B01G559800 chr2B 89.697 165 17 0 1241 1405 753952585 753952749 7.010000e-51 211.0
9 TraesCS2B01G559800 chr2B 88.485 165 19 0 1241 1405 754001404 754001568 1.520000e-47 200.0
10 TraesCS2B01G559800 chr2B 88.535 157 12 3 1455 1611 753809322 753809172 4.250000e-43 185.0
11 TraesCS2B01G559800 chr2B 97.727 88 2 0 2414 2501 753940055 753939968 4.310000e-33 152.0
12 TraesCS2B01G559800 chr2B 100.000 28 0 0 2361 2388 753808462 753808435 4.000000e-03 52.8
13 TraesCS2B01G559800 chr6B 89.831 826 69 5 1 811 41852217 41853042 0.000000e+00 1046.0
14 TraesCS2B01G559800 chr6B 89.734 789 64 10 39 811 361860629 361861416 0.000000e+00 992.0
15 TraesCS2B01G559800 chr6B 80.757 317 29 18 1755 2050 4490740 4491045 4.190000e-53 219.0
16 TraesCS2B01G559800 chr6B 78.613 173 32 5 809 978 228975396 228975226 2.630000e-20 110.0
17 TraesCS2B01G559800 chr6B 90.278 72 6 1 2183 2254 4491759 4491829 2.650000e-15 93.5
18 TraesCS2B01G559800 chr7B 89.769 821 69 9 1 806 745881026 745881846 0.000000e+00 1037.0
19 TraesCS2B01G559800 chr7B 89.403 821 71 9 1 806 745918245 745919064 0.000000e+00 1020.0
20 TraesCS2B01G559800 chr7B 89.435 814 71 8 8 806 745857708 745858521 0.000000e+00 1013.0
21 TraesCS2B01G559800 chr7B 81.651 436 67 7 3 432 607174247 607173819 1.420000e-92 350.0
22 TraesCS2B01G559800 chr7B 82.310 407 59 5 3 402 11547649 11548049 8.570000e-90 340.0
23 TraesCS2B01G559800 chr7B 76.027 292 42 13 1751 2023 593407023 593407305 2.610000e-25 126.0
24 TraesCS2B01G559800 chr2D 89.614 828 68 8 1 811 508095716 508094890 0.000000e+00 1037.0
25 TraesCS2B01G559800 chr2D 85.962 520 40 22 1016 1508 617535927 617536440 2.200000e-145 525.0
26 TraesCS2B01G559800 chr2D 87.198 414 16 13 1718 2113 617523150 617523544 1.060000e-118 436.0
27 TraesCS2B01G559800 chr2D 88.393 336 25 8 1718 2053 617536719 617537040 2.330000e-105 392.0
28 TraesCS2B01G559800 chr2D 93.333 165 11 0 1241 1405 617957811 617957975 6.910000e-61 244.0
29 TraesCS2B01G559800 chr2D 79.467 375 31 12 1241 1611 617522644 617522976 9.000000e-55 224.0
30 TraesCS2B01G559800 chr2D 87.709 179 18 3 2324 2501 617538167 617538342 3.260000e-49 206.0
31 TraesCS2B01G559800 chr2D 88.462 130 3 2 2055 2184 617537495 617537612 2.000000e-31 147.0
32 TraesCS2B01G559800 chr2D 94.118 85 5 0 2417 2501 617637378 617637462 2.020000e-26 130.0
33 TraesCS2B01G559800 chr2D 94.118 85 5 0 2417 2501 617915943 617915859 2.020000e-26 130.0
34 TraesCS2B01G559800 chr2D 92.593 54 4 0 1186 1239 587111820 587111767 7.420000e-11 78.7
35 TraesCS2B01G559800 chr2D 100.000 41 0 0 977 1017 617535862 617535902 2.670000e-10 76.8
36 TraesCS2B01G559800 chr2D 85.185 54 8 0 1186 1239 618074268 618074321 3.480000e-04 56.5
37 TraesCS2B01G559800 chr3D 84.668 737 95 12 91 810 12460394 12459659 0.000000e+00 719.0
38 TraesCS2B01G559800 chr3D 82.099 162 23 5 810 968 394193636 394193478 1.560000e-27 134.0
39 TraesCS2B01G559800 chr3D 97.297 74 2 0 2428 2501 925642 925569 2.610000e-25 126.0
40 TraesCS2B01G559800 chr3D 100.000 66 0 0 2436 2501 11753072 11753137 3.380000e-24 122.0
41 TraesCS2B01G559800 chr3D 93.827 81 3 2 2423 2501 687576 687656 1.220000e-23 121.0
42 TraesCS2B01G559800 chr3D 81.343 134 21 4 830 961 418784914 418784783 3.400000e-19 106.0
43 TraesCS2B01G559800 chr2A 84.161 745 103 9 82 811 195327753 195328497 0.000000e+00 708.0
44 TraesCS2B01G559800 chr2A 87.681 552 38 18 1012 1549 748198611 748199146 1.270000e-172 616.0
45 TraesCS2B01G559800 chr2A 89.773 264 18 3 1718 1981 748199425 748199679 1.850000e-86 329.0
46 TraesCS2B01G559800 chr2A 90.909 165 15 0 1241 1405 748537966 748538130 3.240000e-54 222.0
47 TraesCS2B01G559800 chr2A 95.522 134 6 0 2050 2183 748199950 748200083 5.420000e-52 215.0
48 TraesCS2B01G559800 chr2A 85.549 173 13 7 810 978 748198268 748198432 1.190000e-38 171.0
49 TraesCS2B01G559800 chr2A 83.978 181 23 6 2324 2501 748203393 748203570 4.280000e-38 169.0
50 TraesCS2B01G559800 chr2A 87.755 147 9 2 1259 1405 748698252 748698389 1.990000e-36 163.0
51 TraesCS2B01G559800 chr2A 82.313 147 11 5 1259 1405 748535138 748535269 2.030000e-21 113.0
52 TraesCS2B01G559800 chr2A 95.122 41 2 0 977 1017 748198548 748198588 5.770000e-07 65.8
53 TraesCS2B01G559800 chr5D 82.688 439 58 8 3 432 437049570 437049999 8.450000e-100 374.0
54 TraesCS2B01G559800 chr7A 81.481 432 66 9 3 432 36361817 36361398 2.380000e-90 342.0
55 TraesCS2B01G559800 chr7A 80.838 167 18 1 1897 2049 634900318 634900484 4.370000e-23 119.0
56 TraesCS2B01G559800 chr7A 94.737 38 2 0 2211 2248 41045483 41045520 2.690000e-05 60.2
57 TraesCS2B01G559800 chr4A 81.439 431 68 10 3 432 420033647 420033228 2.380000e-90 342.0
58 TraesCS2B01G559800 chr4A 84.298 121 14 4 859 978 45469639 45469755 2.030000e-21 113.0
59 TraesCS2B01G559800 chr6D 81.388 317 31 13 1755 2053 2102720 2102414 1.500000e-57 233.0
60 TraesCS2B01G559800 chr6D 96.053 76 3 0 2426 2501 379851151 379851226 9.390000e-25 124.0
61 TraesCS2B01G559800 chr6D 100.000 66 0 0 2436 2501 17887727 17887792 3.380000e-24 122.0
62 TraesCS2B01G559800 chr6D 100.000 66 0 0 2436 2501 17998730 17998795 3.380000e-24 122.0
63 TraesCS2B01G559800 chr6D 90.278 72 6 1 2183 2254 2101756 2101686 2.650000e-15 93.5
64 TraesCS2B01G559800 chr6A 81.046 306 28 14 1764 2050 796451 796745 1.510000e-52 217.0
65 TraesCS2B01G559800 chr6A 96.053 76 3 0 2426 2501 520853855 520853780 9.390000e-25 124.0
66 TraesCS2B01G559800 chr6A 85.000 120 14 4 860 978 169514925 169514809 4.370000e-23 119.0
67 TraesCS2B01G559800 chr6A 90.278 72 6 1 2183 2254 797294 797364 2.650000e-15 93.5
68 TraesCS2B01G559800 chr1A 98.630 73 1 0 2429 2501 12109068 12108996 2.020000e-26 130.0
69 TraesCS2B01G559800 chr1A 98.630 73 1 0 2429 2501 12171165 12171237 2.020000e-26 130.0
70 TraesCS2B01G559800 chr4D 100.000 66 0 0 2436 2501 323354308 323354243 3.380000e-24 122.0
71 TraesCS2B01G559800 chr4D 100.000 65 0 0 2437 2501 427324459 427324523 1.220000e-23 121.0
72 TraesCS2B01G559800 chr4D 98.462 65 1 0 2437 2501 427022654 427022718 5.650000e-22 115.0
73 TraesCS2B01G559800 chr4D 96.923 65 2 0 2437 2501 428393646 428393582 2.630000e-20 110.0
74 TraesCS2B01G559800 chr4D 94.915 59 3 0 2437 2495 426903308 426903366 2.650000e-15 93.5
75 TraesCS2B01G559800 chr1D 95.946 74 3 0 2428 2501 9875610 9875683 1.220000e-23 121.0
76 TraesCS2B01G559800 chr1D 92.771 83 5 1 2420 2501 10397507 10397425 4.370000e-23 119.0
77 TraesCS2B01G559800 chr1D 95.890 73 3 0 2429 2501 10443619 10443691 4.370000e-23 119.0
78 TraesCS2B01G559800 chr1D 98.485 66 1 0 2436 2501 9877922 9877987 1.570000e-22 117.0
79 TraesCS2B01G559800 chr1D 95.833 72 3 0 2430 2501 10539742 10539813 1.570000e-22 117.0
80 TraesCS2B01G559800 chr1D 82.836 134 17 5 839 969 343883060 343883190 5.650000e-22 115.0
81 TraesCS2B01G559800 chr1D 98.438 64 1 0 2438 2501 181034043 181033980 2.030000e-21 113.0
82 TraesCS2B01G559800 chr5B 83.607 122 17 3 858 978 553946931 553946812 7.310000e-21 111.0
83 TraesCS2B01G559800 chrUn 96.923 65 0 2 2437 2501 308783253 308783315 9.460000e-20 108.0
84 TraesCS2B01G559800 chrUn 95.455 66 3 0 2436 2501 34255868 34255803 3.400000e-19 106.0
85 TraesCS2B01G559800 chrUn 93.056 72 5 0 2430 2501 421624017 421624088 3.400000e-19 106.0
86 TraesCS2B01G559800 chrUn 98.214 56 0 1 2438 2493 149848655 149848709 2.050000e-16 97.1
87 TraesCS2B01G559800 chrUn 100.000 49 0 0 2453 2501 439645434 439645482 9.530000e-15 91.6
88 TraesCS2B01G559800 chrUn 100.000 48 0 0 2454 2501 190549562 190549609 3.430000e-14 89.8
89 TraesCS2B01G559800 chrUn 100.000 42 0 0 2459 2500 269143003 269143044 7.420000e-11 78.7
90 TraesCS2B01G559800 chrUn 100.000 40 0 0 2461 2500 5967640 5967679 9.590000e-10 75.0
91 TraesCS2B01G559800 chrUn 100.000 40 0 0 2461 2500 192074426 192074387 9.590000e-10 75.0


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 TraesCS2B01G559800 chr2B 753783504 753786004 2500 False 4619.000000 4619 100.000000 1 2501 1 chr2B.!!$F2 2500
1 TraesCS2B01G559800 chr2B 44288313 44289136 823 False 998.000000 998 88.835000 1 809 1 chr2B.!!$F1 808
2 TraesCS2B01G559800 chr2B 753808249 753810256 2007 True 545.760000 1513 96.222800 1 2501 5 chr2B.!!$R4 2500
3 TraesCS2B01G559800 chr6B 41852217 41853042 825 False 1046.000000 1046 89.831000 1 811 1 chr6B.!!$F1 810
4 TraesCS2B01G559800 chr6B 361860629 361861416 787 False 992.000000 992 89.734000 39 811 1 chr6B.!!$F2 772
5 TraesCS2B01G559800 chr7B 745881026 745881846 820 False 1037.000000 1037 89.769000 1 806 1 chr7B.!!$F4 805
6 TraesCS2B01G559800 chr7B 745918245 745919064 819 False 1020.000000 1020 89.403000 1 806 1 chr7B.!!$F5 805
7 TraesCS2B01G559800 chr7B 745857708 745858521 813 False 1013.000000 1013 89.435000 8 806 1 chr7B.!!$F3 798
8 TraesCS2B01G559800 chr2D 508094890 508095716 826 True 1037.000000 1037 89.614000 1 811 1 chr2D.!!$R1 810
9 TraesCS2B01G559800 chr2D 617522644 617523544 900 False 330.000000 436 83.332500 1241 2113 2 chr2D.!!$F4 872
10 TraesCS2B01G559800 chr2D 617535862 617538342 2480 False 269.360000 525 90.105200 977 2501 5 chr2D.!!$F5 1524
11 TraesCS2B01G559800 chr3D 12459659 12460394 735 True 719.000000 719 84.668000 91 810 1 chr3D.!!$R2 719
12 TraesCS2B01G559800 chr2A 195327753 195328497 744 False 708.000000 708 84.161000 82 811 1 chr2A.!!$F1 729
13 TraesCS2B01G559800 chr2A 748198268 748203570 5302 False 260.966667 616 89.604167 810 2501 6 chr2A.!!$F3 1691

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
415 440 0.976641 AGAAGGCCAACGATGTCTGA 59.023 50.0 5.01 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2338 0.111061 TGGCAACCTCTGTTCTGCAT 59.889 50.0 0.0 0.0 30.42 3.96 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
37 38 4.241590 TCGTTTTAGAGTTTGCTACGGA 57.758 40.909 0.00 0.00 0.00 4.69
232 235 4.375406 GGGTCTCCCAGATCGGAA 57.625 61.111 5.32 0.00 44.65 4.30
373 398 1.996798 CCCTGGAGATTAGCCGTCTA 58.003 55.000 0.00 0.00 0.00 2.59
379 404 3.704566 TGGAGATTAGCCGTCTAATGTGT 59.295 43.478 2.97 0.00 43.55 3.72
402 427 4.742201 TGGACTCGCGCAGAAGGC 62.742 66.667 8.75 3.03 39.90 4.35
415 440 0.976641 AGAAGGCCAACGATGTCTGA 59.023 50.000 5.01 0.00 0.00 3.27
635 667 3.369052 CGAGGTCTGTTTGGTATTAGGCA 60.369 47.826 0.00 0.00 0.00 4.75
936 975 8.677300 GCTTCATAAATAAAGTTGTCATCTCCA 58.323 33.333 0.00 0.00 0.00 3.86
938 977 9.958180 TTCATAAATAAAGTTGTCATCTCCAGA 57.042 29.630 0.00 0.00 0.00 3.86
1049 1259 0.904649 TCCCATCGACACAAGCATCT 59.095 50.000 0.00 0.00 0.00 2.90
1051 1261 2.159099 TCCCATCGACACAAGCATCTAC 60.159 50.000 0.00 0.00 0.00 2.59
1052 1262 2.418609 CCCATCGACACAAGCATCTACA 60.419 50.000 0.00 0.00 0.00 2.74
1053 1263 3.261580 CCATCGACACAAGCATCTACAA 58.738 45.455 0.00 0.00 0.00 2.41
1055 1265 4.154015 CCATCGACACAAGCATCTACAAAA 59.846 41.667 0.00 0.00 0.00 2.44
1057 1267 5.530519 TCGACACAAGCATCTACAAAATC 57.469 39.130 0.00 0.00 0.00 2.17
1058 1268 4.391830 TCGACACAAGCATCTACAAAATCC 59.608 41.667 0.00 0.00 0.00 3.01
1060 1270 4.406456 ACACAAGCATCTACAAAATCCCA 58.594 39.130 0.00 0.00 0.00 4.37
1061 1271 4.832266 ACACAAGCATCTACAAAATCCCAA 59.168 37.500 0.00 0.00 0.00 4.12
1062 1272 5.481473 ACACAAGCATCTACAAAATCCCAAT 59.519 36.000 0.00 0.00 0.00 3.16
1063 1273 6.014327 ACACAAGCATCTACAAAATCCCAATT 60.014 34.615 0.00 0.00 0.00 2.32
1064 1274 6.532657 CACAAGCATCTACAAAATCCCAATTC 59.467 38.462 0.00 0.00 0.00 2.17
1065 1275 5.859205 AGCATCTACAAAATCCCAATTCC 57.141 39.130 0.00 0.00 0.00 3.01
1068 1279 5.221322 GCATCTACAAAATCCCAATTCCTCC 60.221 44.000 0.00 0.00 0.00 4.30
1130 1374 1.202687 TCACACAGTTCAGGGCTTCAG 60.203 52.381 0.00 0.00 0.00 3.02
1131 1375 0.109342 ACACAGTTCAGGGCTTCAGG 59.891 55.000 0.00 0.00 0.00 3.86
1132 1376 0.109342 CACAGTTCAGGGCTTCAGGT 59.891 55.000 0.00 0.00 0.00 4.00
1133 1377 0.846693 ACAGTTCAGGGCTTCAGGTT 59.153 50.000 0.00 0.00 0.00 3.50
1134 1378 1.202818 ACAGTTCAGGGCTTCAGGTTC 60.203 52.381 0.00 0.00 0.00 3.62
1275 1519 4.043200 GCCAAGGCCAACGTCAGC 62.043 66.667 5.01 1.27 34.56 4.26
1412 1656 0.626916 GGCCCCAATTAGTACCACCA 59.373 55.000 0.00 0.00 0.00 4.17
1414 1658 1.683938 GCCCCAATTAGTACCACCACC 60.684 57.143 0.00 0.00 0.00 4.61
1449 1699 7.889073 TCTTCTAGTTCTAGCCTCTGTTAGAAA 59.111 37.037 2.31 0.00 43.24 2.52
1450 1700 7.393841 TCTAGTTCTAGCCTCTGTTAGAAAC 57.606 40.000 2.31 0.00 43.24 2.78
1451 1701 5.408880 AGTTCTAGCCTCTGTTAGAAACC 57.591 43.478 1.26 0.00 43.24 3.27
1452 1702 5.088026 AGTTCTAGCCTCTGTTAGAAACCT 58.912 41.667 1.26 0.00 43.24 3.50
1466 1721 2.307098 AGAAACCTCTAGCAACAGCCAT 59.693 45.455 0.00 0.00 0.00 4.40
1514 1774 4.660771 CCCTCCTGATTGTAAATACTCCCT 59.339 45.833 0.00 0.00 0.00 4.20
1534 1869 6.540083 TCCCTAGTATGTATCAGTCGATGAA 58.460 40.000 0.00 0.00 42.53 2.57
1553 1888 8.504005 TCGATGAAGATGATGATGATGAAATTG 58.496 33.333 0.00 0.00 0.00 2.32
1555 1890 7.582667 TGAAGATGATGATGATGAAATTGCT 57.417 32.000 0.00 0.00 0.00 3.91
1611 1968 3.628769 GGGGTTTACATTGCCCTCCAATA 60.629 47.826 0.00 0.00 42.15 1.90
1621 1990 3.691575 TGCCCTCCAATATTCGTTTCAA 58.308 40.909 0.00 0.00 0.00 2.69
1622 1991 4.277476 TGCCCTCCAATATTCGTTTCAAT 58.723 39.130 0.00 0.00 0.00 2.57
1625 1994 6.106003 GCCCTCCAATATTCGTTTCAATTTT 58.894 36.000 0.00 0.00 0.00 1.82
1647 2016 3.806949 TTTGGAATACCCTGCTTGAGT 57.193 42.857 0.00 0.00 35.38 3.41
1648 2017 3.806949 TTGGAATACCCTGCTTGAGTT 57.193 42.857 0.00 0.00 35.38 3.01
1649 2018 3.350219 TGGAATACCCTGCTTGAGTTC 57.650 47.619 0.00 0.00 35.38 3.01
1650 2019 2.642311 TGGAATACCCTGCTTGAGTTCA 59.358 45.455 0.00 0.00 35.38 3.18
1651 2020 3.010420 GGAATACCCTGCTTGAGTTCAC 58.990 50.000 0.00 0.00 0.00 3.18
1652 2021 3.559171 GGAATACCCTGCTTGAGTTCACA 60.559 47.826 0.00 0.00 0.00 3.58
1653 2022 3.788227 ATACCCTGCTTGAGTTCACAA 57.212 42.857 0.00 0.00 0.00 3.33
1654 2023 2.664402 ACCCTGCTTGAGTTCACAAT 57.336 45.000 0.00 0.00 0.00 2.71
1655 2024 2.233271 ACCCTGCTTGAGTTCACAATG 58.767 47.619 0.00 0.00 0.00 2.82
1656 2025 1.068055 CCCTGCTTGAGTTCACAATGC 60.068 52.381 0.00 0.00 0.00 3.56
1657 2026 1.884579 CCTGCTTGAGTTCACAATGCT 59.115 47.619 0.00 0.00 0.00 3.79
1658 2027 2.095364 CCTGCTTGAGTTCACAATGCTC 60.095 50.000 0.00 0.00 0.00 4.26
1666 2035 1.532868 GTTCACAATGCTCTGCTTCGT 59.467 47.619 0.00 0.00 0.00 3.85
1677 2051 0.583438 CTGCTTCGTGTTGGTCACAG 59.417 55.000 0.00 0.00 46.44 3.66
1688 2062 2.808543 GTTGGTCACAGTTAAGCTCTGG 59.191 50.000 5.94 0.00 37.25 3.86
1707 2081 1.741401 CCGTTGCTCCATTCGCTGA 60.741 57.895 0.00 0.00 0.00 4.26
1728 2176 2.456119 CGATGGGCAGACAAGTCGC 61.456 63.158 7.99 7.99 34.09 5.19
1741 2189 2.231964 ACAAGTCGCGGTATTGGAAGTA 59.768 45.455 6.13 0.00 0.00 2.24
1807 2261 9.520515 TGCTAGAATATATACTGACATCTCACA 57.479 33.333 0.00 0.00 0.00 3.58
1817 2271 2.114616 GACATCTCACATCTCCCTGGT 58.885 52.381 0.00 0.00 0.00 4.00
1848 2306 8.985315 AGAAAGATAATATTGCCATGACTTCA 57.015 30.769 0.00 0.00 0.00 3.02
1880 2338 0.687757 ATAACCCAGCGCCTCTCTGA 60.688 55.000 2.29 0.00 33.54 3.27
1881 2339 0.687757 TAACCCAGCGCCTCTCTGAT 60.688 55.000 2.29 0.00 33.54 2.90
1891 2349 1.206610 GCCTCTCTGATGCAGAACAGA 59.793 52.381 16.31 16.31 40.18 3.41
2263 6338 3.002371 CCCCCTTCCTCCTCTTGC 58.998 66.667 0.00 0.00 0.00 4.01
2280 6355 1.702182 TGCCAAATGAAGCTGACCAA 58.298 45.000 0.00 0.00 0.00 3.67
2281 6356 2.037901 TGCCAAATGAAGCTGACCAAA 58.962 42.857 0.00 0.00 0.00 3.28
2282 6357 2.633967 TGCCAAATGAAGCTGACCAAAT 59.366 40.909 0.00 0.00 0.00 2.32
2286 6361 4.927425 CCAAATGAAGCTGACCAAATGAAG 59.073 41.667 0.00 0.00 0.00 3.02
2289 6364 2.555325 TGAAGCTGACCAAATGAAGCTG 59.445 45.455 0.00 0.00 45.04 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.825085 ACTCTAAAACGATGCCCTGAAAAA 59.175 37.500 0.00 0.00 0.00 1.94
6 7 4.015872 ACTCTAAAACGATGCCCTGAAA 57.984 40.909 0.00 0.00 0.00 2.69
37 38 0.985490 GGCCTCTCTGGTCCCTTCAT 60.985 60.000 0.00 0.00 38.35 2.57
232 235 3.505480 GAGGGAAAGCCATCATCATCT 57.495 47.619 0.00 0.00 44.29 2.90
373 398 2.283298 GCGAGTCCATCATCACACATT 58.717 47.619 0.00 0.00 0.00 2.71
379 404 1.227060 CTGCGCGAGTCCATCATCA 60.227 57.895 12.10 0.00 0.00 3.07
402 427 1.655597 CATGACGTCAGACATCGTTGG 59.344 52.381 24.41 0.00 40.39 3.77
415 440 4.735132 CCGACGCCACCATGACGT 62.735 66.667 0.00 0.00 43.83 4.34
478 509 2.283101 GCCACCTGCCACCAATCA 60.283 61.111 0.00 0.00 0.00 2.57
604 636 0.250901 AACAGACCTCGCAGCCAAAT 60.251 50.000 0.00 0.00 0.00 2.32
635 667 0.978146 AAGGGGCGCTGATAGTCTGT 60.978 55.000 7.64 0.00 0.00 3.41
866 902 4.898861 TGGCAAGTTTCAGGATTTTTAGGT 59.101 37.500 0.00 0.00 0.00 3.08
958 997 5.519927 CAGGAAATTTTGCTCTGACGTTTTT 59.480 36.000 0.00 0.00 0.00 1.94
959 998 5.043248 CAGGAAATTTTGCTCTGACGTTTT 58.957 37.500 0.00 0.00 0.00 2.43
970 1009 4.084589 CGCTGGTTTTACAGGAAATTTTGC 60.085 41.667 0.00 0.00 38.90 3.68
972 1011 4.055360 GCGCTGGTTTTACAGGAAATTTT 58.945 39.130 0.00 0.00 38.90 1.82
1049 1259 3.020984 GCGGAGGAATTGGGATTTTGTA 58.979 45.455 0.00 0.00 0.00 2.41
1051 1261 1.136891 GGCGGAGGAATTGGGATTTTG 59.863 52.381 0.00 0.00 0.00 2.44
1052 1262 1.485124 GGCGGAGGAATTGGGATTTT 58.515 50.000 0.00 0.00 0.00 1.82
1053 1263 0.397114 GGGCGGAGGAATTGGGATTT 60.397 55.000 0.00 0.00 0.00 2.17
1055 1265 1.580066 TTGGGCGGAGGAATTGGGAT 61.580 55.000 0.00 0.00 0.00 3.85
1057 1267 0.687427 AATTGGGCGGAGGAATTGGG 60.687 55.000 0.00 0.00 0.00 4.12
1058 1268 0.746659 GAATTGGGCGGAGGAATTGG 59.253 55.000 0.00 0.00 0.00 3.16
1060 1270 0.631212 AGGAATTGGGCGGAGGAATT 59.369 50.000 0.00 0.00 0.00 2.17
1061 1271 0.183731 GAGGAATTGGGCGGAGGAAT 59.816 55.000 0.00 0.00 0.00 3.01
1062 1272 1.607612 GAGGAATTGGGCGGAGGAA 59.392 57.895 0.00 0.00 0.00 3.36
1063 1273 2.375345 GGAGGAATTGGGCGGAGGA 61.375 63.158 0.00 0.00 0.00 3.71
1064 1274 2.193248 GGAGGAATTGGGCGGAGG 59.807 66.667 0.00 0.00 0.00 4.30
1065 1275 2.203070 CGGAGGAATTGGGCGGAG 60.203 66.667 0.00 0.00 0.00 4.63
1085 1296 3.056107 TCCGTGAGTCTGGATTTTGTAGG 60.056 47.826 1.06 0.00 0.00 3.18
1130 1374 2.234908 ACTGTACTGATCTGCCTGAACC 59.765 50.000 6.77 0.00 0.00 3.62
1131 1375 3.601443 ACTGTACTGATCTGCCTGAAC 57.399 47.619 6.77 0.00 0.00 3.18
1132 1376 4.563580 GGAAACTGTACTGATCTGCCTGAA 60.564 45.833 6.77 0.00 0.00 3.02
1133 1377 3.055819 GGAAACTGTACTGATCTGCCTGA 60.056 47.826 6.77 0.00 0.00 3.86
1134 1378 3.265791 GGAAACTGTACTGATCTGCCTG 58.734 50.000 6.77 0.00 0.00 4.85
1239 1483 3.944250 CTTGGCTGCCCGGTGGATT 62.944 63.158 17.53 0.00 0.00 3.01
1353 1597 2.039624 GTCCTCAGCCCCTCCTCA 59.960 66.667 0.00 0.00 0.00 3.86
1395 1639 1.920351 AGGTGGTGGTACTAATTGGGG 59.080 52.381 0.00 0.00 0.00 4.96
1412 1656 7.056006 GCTAGAACTAGAAGAAGGTACTAGGT 58.944 42.308 12.33 0.00 38.20 3.08
1414 1658 7.284820 AGGCTAGAACTAGAAGAAGGTACTAG 58.715 42.308 12.33 0.00 39.32 2.57
1449 1699 0.393537 GCATGGCTGTTGCTAGAGGT 60.394 55.000 0.00 0.00 39.59 3.85
1450 1700 1.099879 GGCATGGCTGTTGCTAGAGG 61.100 60.000 12.86 0.00 40.03 3.69
1451 1701 1.434622 CGGCATGGCTGTTGCTAGAG 61.435 60.000 18.09 0.00 40.03 2.43
1452 1702 1.450134 CGGCATGGCTGTTGCTAGA 60.450 57.895 18.09 0.00 40.03 2.43
1514 1774 8.848474 TCATCTTCATCGACTGATACATACTA 57.152 34.615 0.00 0.00 32.72 1.82
1526 1786 7.417496 TTTCATCATCATCATCTTCATCGAC 57.583 36.000 0.00 0.00 0.00 4.20
1534 1869 6.294231 GCAGAGCAATTTCATCATCATCATCT 60.294 38.462 0.00 0.00 0.00 2.90
1555 1890 1.881973 GGCATTGTGAACTCAAGCAGA 59.118 47.619 0.00 0.00 0.00 4.26
1585 1942 2.536066 AGGGCAATGTAAACCCCTTTC 58.464 47.619 0.00 0.00 45.49 2.62
1625 1994 4.479158 ACTCAAGCAGGGTATTCCAAAAA 58.521 39.130 0.00 0.00 38.24 1.94
1638 2007 2.812591 AGAGCATTGTGAACTCAAGCAG 59.187 45.455 0.00 0.00 32.71 4.24
1640 2009 2.667724 GCAGAGCATTGTGAACTCAAGC 60.668 50.000 0.00 0.00 32.71 4.01
1641 2010 2.812591 AGCAGAGCATTGTGAACTCAAG 59.187 45.455 0.00 0.00 32.71 3.02
1642 2011 2.854963 AGCAGAGCATTGTGAACTCAA 58.145 42.857 0.00 0.00 32.71 3.02
1643 2012 2.556144 AGCAGAGCATTGTGAACTCA 57.444 45.000 0.00 0.00 32.71 3.41
1644 2013 2.159734 CGAAGCAGAGCATTGTGAACTC 60.160 50.000 0.00 0.00 0.00 3.01
1645 2014 1.802960 CGAAGCAGAGCATTGTGAACT 59.197 47.619 0.00 0.00 0.00 3.01
1646 2015 1.532868 ACGAAGCAGAGCATTGTGAAC 59.467 47.619 0.00 0.00 0.00 3.18
1647 2016 1.532437 CACGAAGCAGAGCATTGTGAA 59.468 47.619 8.48 0.00 42.17 3.18
1648 2017 1.150827 CACGAAGCAGAGCATTGTGA 58.849 50.000 8.48 0.00 42.17 3.58
1649 2018 0.870393 ACACGAAGCAGAGCATTGTG 59.130 50.000 11.73 11.73 44.24 3.33
1650 2019 1.265095 CAACACGAAGCAGAGCATTGT 59.735 47.619 0.00 0.00 0.00 2.71
1651 2020 1.400629 CCAACACGAAGCAGAGCATTG 60.401 52.381 0.00 0.00 0.00 2.82
1652 2021 0.877071 CCAACACGAAGCAGAGCATT 59.123 50.000 0.00 0.00 0.00 3.56
1653 2022 0.250467 ACCAACACGAAGCAGAGCAT 60.250 50.000 0.00 0.00 0.00 3.79
1654 2023 0.880278 GACCAACACGAAGCAGAGCA 60.880 55.000 0.00 0.00 0.00 4.26
1655 2024 0.880278 TGACCAACACGAAGCAGAGC 60.880 55.000 0.00 0.00 0.00 4.09
1656 2025 0.861837 GTGACCAACACGAAGCAGAG 59.138 55.000 0.00 0.00 39.78 3.35
1657 2026 2.986311 GTGACCAACACGAAGCAGA 58.014 52.632 0.00 0.00 39.78 4.26
1666 2035 3.466836 CAGAGCTTAACTGTGACCAACA 58.533 45.455 0.00 0.00 42.26 3.33
1677 2051 0.955919 AGCAACGGCCAGAGCTTAAC 60.956 55.000 2.24 0.00 42.56 2.01
1688 2062 3.127533 AGCGAATGGAGCAACGGC 61.128 61.111 0.00 0.00 41.61 5.68
1707 2081 1.740380 CGACTTGTCTGCCCATCGAAT 60.740 52.381 0.00 0.00 0.00 3.34
1728 2176 4.379082 GCAGTGGTTTTACTTCCAATACCG 60.379 45.833 0.00 0.00 33.60 4.02
1781 2230 9.520515 TGTGAGATGTCAGTATATATTCTAGCA 57.479 33.333 0.00 0.00 31.53 3.49
1804 2258 4.286297 TCTAACAAACCAGGGAGATGTG 57.714 45.455 0.00 0.00 0.00 3.21
1805 2259 4.993705 TTCTAACAAACCAGGGAGATGT 57.006 40.909 0.00 0.00 0.00 3.06
1806 2260 5.560724 TCTTTCTAACAAACCAGGGAGATG 58.439 41.667 0.00 0.00 0.00 2.90
1807 2261 5.843019 TCTTTCTAACAAACCAGGGAGAT 57.157 39.130 0.00 0.00 0.00 2.75
1808 2262 5.843019 ATCTTTCTAACAAACCAGGGAGA 57.157 39.130 0.00 0.00 0.00 3.71
1809 2263 9.853177 ATATTATCTTTCTAACAAACCAGGGAG 57.147 33.333 0.00 0.00 0.00 4.30
1848 2306 5.739358 GCGCTGGGTTATAAGTACAGAAGAT 60.739 44.000 0.00 0.00 0.00 2.40
1880 2338 0.111061 TGGCAACCTCTGTTCTGCAT 59.889 50.000 0.00 0.00 30.42 3.96
1881 2339 0.819259 GTGGCAACCTCTGTTCTGCA 60.819 55.000 0.00 0.00 30.42 4.41
2263 6338 4.524316 TCATTTGGTCAGCTTCATTTGG 57.476 40.909 0.00 0.00 0.00 3.28
2280 6355 4.038271 TCAACCTTCCATCAGCTTCATT 57.962 40.909 0.00 0.00 0.00 2.57
2281 6356 3.726557 TCAACCTTCCATCAGCTTCAT 57.273 42.857 0.00 0.00 0.00 2.57
2282 6357 3.726557 ATCAACCTTCCATCAGCTTCA 57.273 42.857 0.00 0.00 0.00 3.02
2286 6361 3.056322 AGCAAAATCAACCTTCCATCAGC 60.056 43.478 0.00 0.00 0.00 4.26
2288 6363 3.896888 ACAGCAAAATCAACCTTCCATCA 59.103 39.130 0.00 0.00 0.00 3.07
2289 6364 4.525912 ACAGCAAAATCAACCTTCCATC 57.474 40.909 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.