Multiple sequence alignment - TraesCS7D01G112700

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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 TraesCS7D01G112700 chr7D 100.000 3440 0 0 1 3440 68982588 68986027 0.000000e+00 6353.0
1 TraesCS7D01G112700 chr7D 94.000 900 20 9 731 1606 66416732 66415843 0.000000e+00 1332.0
2 TraesCS7D01G112700 chr7D 93.961 563 21 6 1604 2153 66415807 66415245 0.000000e+00 839.0
3 TraesCS7D01G112700 chr7D 85.954 655 30 22 2359 2974 66413268 66412637 0.000000e+00 643.0
4 TraesCS7D01G112700 chr7D 76.417 1217 177 60 821 2003 69055283 69056423 1.080000e-154 556.0
5 TraesCS7D01G112700 chr7D 82.540 441 58 12 842 1269 66548199 66547765 1.510000e-98 370.0
6 TraesCS7D01G112700 chr7D 75.908 606 98 37 915 1511 73367902 73368468 2.040000e-67 267.0
7 TraesCS7D01G112700 chr7D 85.039 254 11 4 2392 2625 68930308 68930554 2.060000e-57 233.0
8 TraesCS7D01G112700 chr7D 88.384 198 15 6 510 706 66440409 66440219 7.420000e-57 231.0
9 TraesCS7D01G112700 chr7D 73.819 783 114 52 823 1599 65814710 65814013 3.450000e-55 226.0
10 TraesCS7D01G112700 chr7D 91.525 118 9 1 2366 2483 69057112 69057228 9.880000e-36 161.0
11 TraesCS7D01G112700 chr7D 80.120 166 31 2 1436 1600 66547631 66547467 4.660000e-24 122.0
12 TraesCS7D01G112700 chr7D 89.474 95 7 2 2506 2600 66345839 66345748 2.170000e-22 117.0
13 TraesCS7D01G112700 chr7D 94.595 74 4 0 2258 2331 66415104 66415031 7.800000e-22 115.0
14 TraesCS7D01G112700 chr7D 84.694 98 8 6 2071 2165 66415036 66414943 1.310000e-14 91.6
15 TraesCS7D01G112700 chr7D 81.651 109 8 4 2257 2365 66414745 66414649 2.850000e-11 80.5
16 TraesCS7D01G112700 chr7A 92.822 1644 75 24 3 1606 70890898 70889258 0.000000e+00 2342.0
17 TraesCS7D01G112700 chr7A 90.095 1474 64 30 731 2165 74642366 74643796 0.000000e+00 1838.0
18 TraesCS7D01G112700 chr7A 92.389 565 22 11 2570 3130 70888156 70887609 0.000000e+00 785.0
19 TraesCS7D01G112700 chr7A 89.175 582 17 5 2785 3344 74644516 74645073 0.000000e+00 684.0
20 TraesCS7D01G112700 chr7A 97.113 381 11 0 1604 1984 70889213 70888833 0.000000e+00 643.0
21 TraesCS7D01G112700 chr7A 89.375 480 28 10 250 720 74641389 74641854 1.780000e-162 582.0
22 TraesCS7D01G112700 chr7A 89.096 376 20 5 2359 2713 74644120 74644495 6.770000e-122 448.0
23 TraesCS7D01G112700 chr7A 94.902 255 12 1 1 254 74615248 74615502 6.920000e-107 398.0
24 TraesCS7D01G112700 chr7A 76.777 788 123 36 823 1599 70238202 70237464 1.500000e-103 387.0
25 TraesCS7D01G112700 chr7A 81.797 434 60 11 843 1276 70767385 70766971 2.540000e-91 346.0
26 TraesCS7D01G112700 chr7A 79.950 404 51 14 1651 2050 71113977 71113600 1.570000e-68 270.0
27 TraesCS7D01G112700 chr7A 83.219 292 42 7 858 1144 70268006 70267717 9.470000e-66 261.0
28 TraesCS7D01G112700 chr7A 75.662 604 103 36 915 1511 77915149 77915715 9.470000e-66 261.0
29 TraesCS7D01G112700 chr7A 86.561 253 11 7 2395 2625 71112899 71112648 1.220000e-64 257.0
30 TraesCS7D01G112700 chr7A 96.732 153 2 1 3192 3344 70887602 70887453 5.700000e-63 252.0
31 TraesCS7D01G112700 chr7A 99.200 125 1 0 2359 2483 70888346 70888222 3.450000e-55 226.0
32 TraesCS7D01G112700 chr7A 93.043 115 7 1 2369 2483 74885353 74885466 2.120000e-37 167.0
33 TraesCS7D01G112700 chr7A 88.421 95 8 2 2506 2600 70765225 70765134 1.010000e-20 111.0
34 TraesCS7D01G112700 chr7A 82.569 109 7 8 2257 2365 70888470 70888374 6.120000e-13 86.1
35 TraesCS7D01G112700 chr7A 77.143 140 18 8 2031 2165 70888806 70888676 6.160000e-08 69.4
36 TraesCS7D01G112700 chr7B 95.619 662 26 1 948 1606 10559008 10559669 0.000000e+00 1059.0
37 TraesCS7D01G112700 chr7B 95.448 659 24 1 948 1606 7717616 7716964 0.000000e+00 1046.0
38 TraesCS7D01G112700 chr7B 89.946 557 26 10 1604 2153 10559714 10560247 0.000000e+00 691.0
39 TraesCS7D01G112700 chr7B 89.048 557 22 12 1604 2153 7716919 7716395 0.000000e+00 654.0
40 TraesCS7D01G112700 chr7B 84.021 751 47 30 2359 3098 10560629 10561317 0.000000e+00 654.0
41 TraesCS7D01G112700 chr7B 87.260 573 40 18 2359 2904 7715992 7715426 1.050000e-174 623.0
42 TraesCS7D01G112700 chr7B 89.459 370 13 16 2995 3344 139855166 139854803 8.760000e-121 444.0
43 TraesCS7D01G112700 chr7B 85.383 431 31 14 534 956 10558582 10558988 5.310000e-113 418.0
44 TraesCS7D01G112700 chr7B 81.109 487 60 15 843 1315 10581893 10582361 9.080000e-96 361.0
45 TraesCS7D01G112700 chr7B 81.250 416 58 15 841 1238 8448737 8448324 5.540000e-83 318.0
46 TraesCS7D01G112700 chr7B 75.700 679 101 40 821 1485 491084386 491083758 7.270000e-72 281.0
47 TraesCS7D01G112700 chr7B 89.778 225 11 1 732 956 7717848 7717636 9.400000e-71 278.0
48 TraesCS7D01G112700 chr7B 87.805 246 15 2 2395 2625 7730560 7730315 1.220000e-69 274.0
49 TraesCS7D01G112700 chr7B 81.538 325 52 7 1648 1971 10238266 10238583 9.470000e-66 261.0
50 TraesCS7D01G112700 chr7B 89.041 146 1 1 2198 2328 7716382 7716237 2.120000e-37 167.0
51 TraesCS7D01G112700 chr7B 88.356 146 2 1 2198 2328 10560260 10560405 9.880000e-36 161.0
52 TraesCS7D01G112700 chr7B 82.320 181 28 4 1428 1606 10061409 10061587 1.650000e-33 154.0
53 TraesCS7D01G112700 chr7B 95.455 44 2 0 2322 2365 10560558 10560601 1.710000e-08 71.3
54 TraesCS7D01G112700 chr7B 100.000 36 0 0 2330 2365 7716055 7716020 2.220000e-07 67.6
55 TraesCS7D01G112700 chr2B 78.967 813 112 30 796 1568 135794716 135795509 1.840000e-137 499.0
56 TraesCS7D01G112700 chr2B 77.339 759 130 25 859 1599 76517518 76516784 8.890000e-111 411.0
57 TraesCS7D01G112700 chr2B 80.473 338 55 9 1661 1996 135795661 135795989 7.370000e-62 248.0
58 TraesCS7D01G112700 chr2A 80.495 364 56 9 1639 1996 84749785 84750139 7.320000e-67 265.0
59 TraesCS7D01G112700 chr6D 91.275 149 10 3 789 937 411918527 411918382 2.090000e-47 200.0
60 TraesCS7D01G112700 chr2D 75.819 397 60 21 913 1278 33374210 33373819 5.900000e-38 169.0
61 TraesCS7D01G112700 chr6B 79.695 197 30 8 1184 1378 521450235 521450423 2.150000e-27 134.0


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 TraesCS7D01G112700 chr7D 68982588 68986027 3439 False 6353.000000 6353 100.000000 1 3440 1 chr7D.!!$F2 3439
1 TraesCS7D01G112700 chr7D 66412637 66416732 4095 True 516.850000 1332 89.142500 731 2974 6 chr7D.!!$R4 2243
2 TraesCS7D01G112700 chr7D 69055283 69057228 1945 False 358.500000 556 83.971000 821 2483 2 chr7D.!!$F4 1662
3 TraesCS7D01G112700 chr7D 73367902 73368468 566 False 267.000000 267 75.908000 915 1511 1 chr7D.!!$F3 596
4 TraesCS7D01G112700 chr7D 66547467 66548199 732 True 246.000000 370 81.330000 842 1600 2 chr7D.!!$R5 758
5 TraesCS7D01G112700 chr7D 65814013 65814710 697 True 226.000000 226 73.819000 823 1599 1 chr7D.!!$R1 776
6 TraesCS7D01G112700 chr7A 74641389 74645073 3684 False 888.000000 1838 89.435250 250 3344 4 chr7A.!!$F4 3094
7 TraesCS7D01G112700 chr7A 70887453 70890898 3445 True 629.071429 2342 91.138286 3 3344 7 chr7A.!!$R4 3341
8 TraesCS7D01G112700 chr7A 70237464 70238202 738 True 387.000000 387 76.777000 823 1599 1 chr7A.!!$R1 776
9 TraesCS7D01G112700 chr7A 71112648 71113977 1329 True 263.500000 270 83.255500 1651 2625 2 chr7A.!!$R5 974
10 TraesCS7D01G112700 chr7A 77915149 77915715 566 False 261.000000 261 75.662000 915 1511 1 chr7A.!!$F3 596
11 TraesCS7D01G112700 chr7A 70765134 70767385 2251 True 228.500000 346 85.109000 843 2600 2 chr7A.!!$R3 1757
12 TraesCS7D01G112700 chr7B 10558582 10561317 2735 False 509.050000 1059 89.796667 534 3098 6 chr7B.!!$F4 2564
13 TraesCS7D01G112700 chr7B 7715426 7717848 2422 True 472.600000 1046 91.762500 732 2904 6 chr7B.!!$R5 2172
14 TraesCS7D01G112700 chr7B 491083758 491084386 628 True 281.000000 281 75.700000 821 1485 1 chr7B.!!$R4 664
15 TraesCS7D01G112700 chr2B 76516784 76517518 734 True 411.000000 411 77.339000 859 1599 1 chr2B.!!$R1 740
16 TraesCS7D01G112700 chr2B 135794716 135795989 1273 False 373.500000 499 79.720000 796 1996 2 chr2B.!!$F1 1200

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
113 116 0.405198 TGGCACCACCATCAACATCT 59.595 50.0 0.00 0.0 46.36 2.90 F
1159 1803 0.611896 GTACCACCAGGGCAATGCTT 60.612 55.0 4.82 0.0 42.05 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2856 0.767060 AAAGGGACACGGAGAGGGTT 60.767 55.0 0.0 0.0 35.98 4.11 R
2500 6150 0.105039 GGAACCCCTATCTCACTGCG 59.895 60.0 0.0 0.0 0.00 5.18 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 27 1.202348 GGAAAAATTGCCCTCCTCACG 59.798 52.381 0.00 0.00 0.00 4.35
50 52 2.028112 CCAACGAGGAAGAAGACCATGA 60.028 50.000 0.00 0.00 41.22 3.07
55 57 1.280421 AGGAAGAAGACCATGAGTGCC 59.720 52.381 0.00 0.00 0.00 5.01
113 116 0.405198 TGGCACCACCATCAACATCT 59.595 50.000 0.00 0.00 46.36 2.90
135 138 8.535592 CATCTTAAAACTACGATGAGTAAGCAG 58.464 37.037 0.00 0.00 36.29 4.24
151 154 1.745087 AGCAGCATTAACCATCCAACG 59.255 47.619 0.00 0.00 0.00 4.10
178 181 4.803098 AAGTCGTTAATCTACTGCACCT 57.197 40.909 0.00 0.00 0.00 4.00
179 182 5.909621 AAGTCGTTAATCTACTGCACCTA 57.090 39.130 0.00 0.00 0.00 3.08
183 186 7.328737 AGTCGTTAATCTACTGCACCTAAAAT 58.671 34.615 0.00 0.00 0.00 1.82
271 274 2.430921 CTCACGCCACGAGGACAC 60.431 66.667 1.86 0.00 36.89 3.67
348 354 1.144936 CATCAGGAGTTCCTCGGCC 59.855 63.158 0.00 0.00 46.65 6.13
367 373 2.826428 CCCCATGTGTCAGAATAGTCG 58.174 52.381 0.00 0.00 0.00 4.18
407 413 1.594862 GCGACACATAGAACATGAGGC 59.405 52.381 0.00 0.00 0.00 4.70
411 417 2.027192 ACACATAGAACATGAGGCGGTT 60.027 45.455 0.00 0.00 0.00 4.44
426 432 2.357952 GGCGGTTATCAATTTCCCTGTC 59.642 50.000 0.00 0.00 0.00 3.51
437 443 6.234177 TCAATTTCCCTGTCTTTCTCTCTTC 58.766 40.000 0.00 0.00 0.00 2.87
457 463 0.623723 TCTCCCATGGTGGTTAAGGC 59.376 55.000 11.73 0.00 35.17 4.35
622 633 8.383318 TGAATTTTTATCTAGAGGCATAGCAC 57.617 34.615 0.00 0.00 0.00 4.40
713 752 5.619625 AGCTGAGAAACATAGCAGTTTTC 57.380 39.130 0.00 0.00 41.48 2.29
748 1287 4.655963 AGTCATAGCAGTTTGTTGTGGAT 58.344 39.130 0.00 0.00 0.00 3.41
754 1293 7.498900 TCATAGCAGTTTGTTGTGGATATTAGG 59.501 37.037 0.00 0.00 0.00 2.69
1159 1803 0.611896 GTACCACCAGGGCAATGCTT 60.612 55.000 4.82 0.00 42.05 3.91
1827 2691 1.070289 GTGTTCGACCTGAGGGAAACT 59.930 52.381 2.38 0.00 36.25 2.66
1986 2856 2.668632 GGGACGCCAGGTGAATGA 59.331 61.111 7.13 0.00 0.00 2.57
1987 2857 1.002624 GGGACGCCAGGTGAATGAA 60.003 57.895 7.13 0.00 0.00 2.57
1996 2866 0.905357 AGGTGAATGAACCCTCTCCG 59.095 55.000 0.00 0.00 41.54 4.63
2013 2889 1.626321 TCCGTGTCCCTTTGCAAGATA 59.374 47.619 0.00 0.00 0.00 1.98
2056 2949 6.127366 TGCCATGATCTTTTGGGTTCTATTTC 60.127 38.462 0.00 0.00 33.40 2.17
2066 2976 5.255397 TGGGTTCTATTTCAATGGTCTGT 57.745 39.130 0.00 0.00 0.00 3.41
2073 2985 1.795768 TTCAATGGTCTGTCTCGTGC 58.204 50.000 0.00 0.00 0.00 5.34
2095 3007 6.197096 GTGCTGAAAAACAGTGTACTGAATTG 59.803 38.462 18.18 3.55 46.59 2.32
2173 3917 4.022935 ACTGTTGTATTTGCTCCATGTGTG 60.023 41.667 0.00 0.00 0.00 3.82
2175 3919 1.818060 TGTATTTGCTCCATGTGTGGC 59.182 47.619 0.00 0.00 45.63 5.01
2178 3922 0.895100 TTTGCTCCATGTGTGGCCTC 60.895 55.000 3.32 0.00 45.63 4.70
2191 3935 1.200760 TGGCCTCAAGCTTAGCTGGA 61.201 55.000 11.23 11.23 39.62 3.86
2199 3943 5.420725 TCAAGCTTAGCTGGATGTTAGAA 57.579 39.130 7.77 0.00 39.62 2.10
2201 3945 3.786635 AGCTTAGCTGGATGTTAGAACG 58.213 45.455 5.70 0.00 37.57 3.95
2242 4058 7.335422 AGTTCAGCTTCACATAGAAAATACTGG 59.665 37.037 0.00 0.00 35.40 4.00
2285 4115 4.764823 ACGAAAATTCAGCTTGTATCCCAA 59.235 37.500 0.00 0.00 0.00 4.12
2289 4121 5.405935 AATTCAGCTTGTATCCCAAAACC 57.594 39.130 0.00 0.00 31.20 3.27
2290 4122 3.517296 TCAGCTTGTATCCCAAAACCA 57.483 42.857 0.00 0.00 31.20 3.67
2291 4123 4.046286 TCAGCTTGTATCCCAAAACCAT 57.954 40.909 0.00 0.00 31.20 3.55
2325 4450 4.430137 AGTTTCTGCATGCACATTACAG 57.570 40.909 18.46 5.29 0.00 2.74
2500 6150 3.963383 TCAACCGTCTCAAAGCTTTTC 57.037 42.857 9.53 0.00 0.00 2.29
2519 6170 0.105039 CGCAGTGAGATAGGGGTTCC 59.895 60.000 0.00 0.00 0.00 3.62
2773 6458 4.267690 GTGTTGCCACTTAAAAGTTTCAGC 59.732 41.667 0.00 0.00 37.08 4.26
2776 6461 2.364002 GCCACTTAAAAGTTTCAGCCCA 59.636 45.455 0.00 0.00 37.08 5.36
2777 6462 3.181470 GCCACTTAAAAGTTTCAGCCCAA 60.181 43.478 0.00 0.00 37.08 4.12
2778 6463 4.503123 GCCACTTAAAAGTTTCAGCCCAAT 60.503 41.667 0.00 0.00 37.08 3.16
2779 6464 5.610398 CCACTTAAAAGTTTCAGCCCAATT 58.390 37.500 0.00 0.00 37.08 2.32
2780 6465 6.054941 CCACTTAAAAGTTTCAGCCCAATTT 58.945 36.000 0.00 0.00 37.08 1.82
2781 6466 6.018016 CCACTTAAAAGTTTCAGCCCAATTTG 60.018 38.462 0.00 0.00 37.08 2.32
2782 6467 5.527214 ACTTAAAAGTTTCAGCCCAATTTGC 59.473 36.000 0.00 0.00 35.21 3.68
2783 6468 3.843893 AAAGTTTCAGCCCAATTTGCT 57.156 38.095 0.00 0.00 40.41 3.91
2896 6583 4.625800 GCCGAAGCCTGAGAATGT 57.374 55.556 0.00 0.00 0.00 2.71
3084 6787 0.467290 ACAAATGACGCCCAACACCT 60.467 50.000 0.00 0.00 0.00 4.00
3149 6852 2.604914 CTGCTACGTTGTTCATGGCTAG 59.395 50.000 0.00 0.00 0.00 3.42
3189 6910 9.755064 AAACGAATCTCTAAAAATCATACAACG 57.245 29.630 0.00 0.00 0.00 4.10
3236 6957 2.562635 TCGTCTCCCTTATGACTCTCG 58.437 52.381 0.00 0.00 0.00 4.04
3355 7076 7.678947 GGTGATCCCTTCATAAGTTATGATG 57.321 40.000 23.01 22.93 44.06 3.07
3356 7077 6.150140 GGTGATCCCTTCATAAGTTATGATGC 59.850 42.308 23.01 13.73 44.06 3.91
3357 7078 6.712095 GTGATCCCTTCATAAGTTATGATGCA 59.288 38.462 23.01 15.60 44.06 3.96
3358 7079 6.938596 TGATCCCTTCATAAGTTATGATGCAG 59.061 38.462 23.01 17.52 44.06 4.41
3359 7080 5.065914 TCCCTTCATAAGTTATGATGCAGC 58.934 41.667 23.01 0.00 44.06 5.25
3360 7081 5.068636 CCCTTCATAAGTTATGATGCAGCT 58.931 41.667 23.01 0.00 44.06 4.24
3361 7082 5.048921 CCCTTCATAAGTTATGATGCAGCTG 60.049 44.000 23.01 10.11 44.06 4.24
3362 7083 5.530171 CCTTCATAAGTTATGATGCAGCTGT 59.470 40.000 23.01 0.00 44.06 4.40
3363 7084 6.039047 CCTTCATAAGTTATGATGCAGCTGTT 59.961 38.462 23.01 2.94 44.06 3.16
3364 7085 6.367686 TCATAAGTTATGATGCAGCTGTTG 57.632 37.500 19.51 0.00 40.09 3.33
3365 7086 5.297527 TCATAAGTTATGATGCAGCTGTTGG 59.702 40.000 19.51 0.00 40.09 3.77
3366 7087 3.077484 AGTTATGATGCAGCTGTTGGT 57.923 42.857 16.64 0.00 0.00 3.67
3367 7088 3.012518 AGTTATGATGCAGCTGTTGGTC 58.987 45.455 16.64 8.94 0.00 4.02
3368 7089 1.655484 TATGATGCAGCTGTTGGTCG 58.345 50.000 16.64 0.00 0.00 4.79
3369 7090 1.651240 ATGATGCAGCTGTTGGTCGC 61.651 55.000 16.64 0.00 0.00 5.19
3370 7091 3.044059 GATGCAGCTGTTGGTCGCC 62.044 63.158 16.64 0.00 0.00 5.54
3371 7092 3.557903 ATGCAGCTGTTGGTCGCCT 62.558 57.895 16.64 0.00 0.00 5.52
3372 7093 2.047274 GCAGCTGTTGGTCGCCTA 60.047 61.111 16.64 0.00 0.00 3.93
3373 7094 2.103042 GCAGCTGTTGGTCGCCTAG 61.103 63.158 16.64 0.00 0.00 3.02
3374 7095 2.103042 CAGCTGTTGGTCGCCTAGC 61.103 63.158 5.25 0.00 34.71 3.42
3386 7107 4.181010 CCTAGCGCACAGGCCCAT 62.181 66.667 11.47 0.00 36.38 4.00
3387 7108 2.898840 CTAGCGCACAGGCCCATG 60.899 66.667 11.47 0.00 36.38 3.66
3392 7113 2.677524 GCACAGGCCCATGCTCAA 60.678 61.111 19.27 0.00 38.84 3.02
3393 7114 2.707849 GCACAGGCCCATGCTCAAG 61.708 63.158 19.27 0.00 38.84 3.02
3394 7115 2.362120 ACAGGCCCATGCTCAAGC 60.362 61.111 0.00 0.00 42.50 4.01
3395 7116 3.145551 CAGGCCCATGCTCAAGCC 61.146 66.667 0.00 0.00 46.13 4.35
3397 7118 3.145551 GGCCCATGCTCAAGCCTG 61.146 66.667 0.00 0.00 42.34 4.85
3398 7119 2.044650 GCCCATGCTCAAGCCTGA 60.045 61.111 8.61 0.00 38.67 3.86
3399 7120 1.679977 GCCCATGCTCAAGCCTGAA 60.680 57.895 8.61 0.00 38.67 3.02
3400 7121 1.664321 GCCCATGCTCAAGCCTGAAG 61.664 60.000 8.61 2.00 38.67 3.02
3401 7122 1.035932 CCCATGCTCAAGCCTGAAGG 61.036 60.000 8.61 0.00 38.67 3.46
3412 7133 4.452733 CTGAAGGCCCGACCCGAC 62.453 72.222 0.00 0.00 40.58 4.79
3417 7138 4.801624 GGCCCGACCCGACGTAAC 62.802 72.222 0.00 0.00 0.00 2.50
3421 7142 4.107051 CGACCCGACGTAACGCCT 62.107 66.667 0.00 0.00 0.00 5.52
3422 7143 2.505557 GACCCGACGTAACGCCTG 60.506 66.667 0.00 0.00 0.00 4.85
3423 7144 2.981560 GACCCGACGTAACGCCTGA 61.982 63.158 0.00 0.00 0.00 3.86
3424 7145 2.259204 CCCGACGTAACGCCTGAA 59.741 61.111 0.00 0.00 0.00 3.02
3425 7146 1.804326 CCCGACGTAACGCCTGAAG 60.804 63.158 0.00 0.00 0.00 3.02
3426 7147 2.442188 CCGACGTAACGCCTGAAGC 61.442 63.158 0.00 0.00 38.52 3.86
3427 7148 1.731613 CGACGTAACGCCTGAAGCA 60.732 57.895 0.00 0.00 44.04 3.91
3428 7149 1.279527 CGACGTAACGCCTGAAGCAA 61.280 55.000 0.00 0.00 44.04 3.91
3429 7150 0.863144 GACGTAACGCCTGAAGCAAA 59.137 50.000 0.00 0.00 44.04 3.68
3430 7151 1.463444 GACGTAACGCCTGAAGCAAAT 59.537 47.619 0.00 0.00 44.04 2.32
3431 7152 2.669434 GACGTAACGCCTGAAGCAAATA 59.331 45.455 0.00 0.00 44.04 1.40
3432 7153 3.068560 ACGTAACGCCTGAAGCAAATAA 58.931 40.909 0.00 0.00 44.04 1.40
3433 7154 3.124636 ACGTAACGCCTGAAGCAAATAAG 59.875 43.478 0.00 0.00 44.04 1.73
3434 7155 2.636768 AACGCCTGAAGCAAATAAGC 57.363 45.000 0.00 0.00 44.04 3.09
3435 7156 0.811281 ACGCCTGAAGCAAATAAGCC 59.189 50.000 0.00 0.00 44.04 4.35
3436 7157 0.101219 CGCCTGAAGCAAATAAGCCC 59.899 55.000 0.00 0.00 44.04 5.19
3437 7158 1.185315 GCCTGAAGCAAATAAGCCCA 58.815 50.000 0.00 0.00 42.97 5.36
3438 7159 1.135721 GCCTGAAGCAAATAAGCCCAG 59.864 52.381 0.00 0.00 42.97 4.45
3439 7160 1.135721 CCTGAAGCAAATAAGCCCAGC 59.864 52.381 0.00 0.00 35.61 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.108662 GGAGGGCAATTTTTCCAGCG 60.109 55.000 0.00 0.00 0.00 5.18
25 27 0.608640 TCTTCTTCCTCGTTGGCTCC 59.391 55.000 0.00 0.00 35.26 4.70
50 52 4.525487 ACTCATGTTTCATCATTTGGCACT 59.475 37.500 0.00 0.00 0.00 4.40
55 57 8.291740 TGTCTTGTACTCATGTTTCATCATTTG 58.708 33.333 0.00 0.00 0.00 2.32
107 110 8.870879 GCTTACTCATCGTAGTTTTAAGATGTT 58.129 33.333 9.27 3.23 42.66 2.71
113 116 6.160684 TGCTGCTTACTCATCGTAGTTTTAA 58.839 36.000 0.00 0.00 0.00 1.52
135 138 3.840890 TGTTCGTTGGATGGTTAATGC 57.159 42.857 0.00 0.00 0.00 3.56
151 154 7.254017 GGTGCAGTAGATTAACGACTTATGTTC 60.254 40.741 0.00 0.00 32.40 3.18
211 214 1.205655 CACATCCTGTCATGGAGTCGT 59.794 52.381 0.00 0.00 39.78 4.34
214 217 5.458595 TCTATACACATCCTGTCATGGAGT 58.541 41.667 0.00 0.00 39.78 3.85
271 274 7.277319 GTCAACTTTAAGTATCCTTTCTACGGG 59.723 40.741 0.00 0.00 31.89 5.28
306 309 9.754382 ATGATTGTTTTTCATGTAGATTATGGC 57.246 29.630 0.00 0.00 32.67 4.40
348 354 3.190079 CACGACTATTCTGACACATGGG 58.810 50.000 0.00 0.00 0.00 4.00
367 373 0.678048 GTTGGTGCCCTCATCTCCAC 60.678 60.000 0.00 0.00 0.00 4.02
407 413 5.648092 AGAAAGACAGGGAAATTGATAACCG 59.352 40.000 0.00 0.00 0.00 4.44
411 417 7.502060 AGAGAGAAAGACAGGGAAATTGATA 57.498 36.000 0.00 0.00 0.00 2.15
426 432 3.774216 ACCATGGGAGAGAAGAGAGAAAG 59.226 47.826 18.09 0.00 0.00 2.62
437 443 1.408822 GCCTTAACCACCATGGGAGAG 60.409 57.143 18.09 3.80 43.37 3.20
549 558 4.699257 AGCTCTCCTTTCATGCTTTACAAG 59.301 41.667 0.00 0.00 0.00 3.16
551 560 4.292186 AGCTCTCCTTTCATGCTTTACA 57.708 40.909 0.00 0.00 0.00 2.41
600 609 8.986929 AAAGTGCTATGCCTCTAGATAAAAAT 57.013 30.769 0.00 0.00 0.00 1.82
606 617 5.994668 GCTAAAAAGTGCTATGCCTCTAGAT 59.005 40.000 0.00 0.00 0.00 1.98
719 758 4.973168 ACAAACTGCTATGACTCCTCAAA 58.027 39.130 0.00 0.00 0.00 2.69
722 799 4.153117 CACAACAAACTGCTATGACTCCTC 59.847 45.833 0.00 0.00 0.00 3.71
723 800 4.067896 CACAACAAACTGCTATGACTCCT 58.932 43.478 0.00 0.00 0.00 3.69
725 802 4.065088 TCCACAACAAACTGCTATGACTC 58.935 43.478 0.00 0.00 0.00 3.36
726 803 4.085357 TCCACAACAAACTGCTATGACT 57.915 40.909 0.00 0.00 0.00 3.41
727 804 6.683974 ATATCCACAACAAACTGCTATGAC 57.316 37.500 0.00 0.00 0.00 3.06
748 1287 2.889045 AGTTAGATCCGCACGCCTAATA 59.111 45.455 0.00 0.00 0.00 0.98
754 1293 0.844503 CGTAAGTTAGATCCGCACGC 59.155 55.000 0.00 0.00 0.00 5.34
1984 2854 1.911766 GGGACACGGAGAGGGTTCA 60.912 63.158 0.00 0.00 35.98 3.18
1986 2856 0.767060 AAAGGGACACGGAGAGGGTT 60.767 55.000 0.00 0.00 35.98 4.11
1987 2857 1.152096 AAAGGGACACGGAGAGGGT 60.152 57.895 0.00 0.00 40.76 4.34
2056 2949 1.073964 CAGCACGAGACAGACCATTG 58.926 55.000 0.00 0.00 0.00 2.82
2095 3007 6.093633 AGTGAACTGTTTTTCAGACTGTAACC 59.906 38.462 1.59 0.00 46.27 2.85
2173 3917 0.182299 ATCCAGCTAAGCTTGAGGCC 59.818 55.000 9.86 0.00 43.05 5.19
2175 3919 2.706339 ACATCCAGCTAAGCTTGAGG 57.294 50.000 9.86 5.62 37.94 3.86
2178 3922 4.033358 CGTTCTAACATCCAGCTAAGCTTG 59.967 45.833 9.86 0.01 36.40 4.01
2191 3935 6.207810 TGATTTGGGCTTTTACGTTCTAACAT 59.792 34.615 0.00 0.00 0.00 2.71
2199 3943 3.886505 TGAACTGATTTGGGCTTTTACGT 59.113 39.130 0.00 0.00 0.00 3.57
2201 3945 4.021981 AGCTGAACTGATTTGGGCTTTTAC 60.022 41.667 0.00 0.00 0.00 2.01
2263 4093 4.963276 TGGGATACAAGCTGAATTTTCG 57.037 40.909 0.00 0.00 39.74 3.46
2289 4121 9.027129 CATGCAGAAACTAATTTCCATGTAATG 57.973 33.333 7.38 1.31 44.66 1.90
2290 4122 7.707893 GCATGCAGAAACTAATTTCCATGTAAT 59.292 33.333 14.21 0.00 44.66 1.89
2291 4123 7.035004 GCATGCAGAAACTAATTTCCATGTAA 58.965 34.615 14.21 0.00 44.66 2.41
2325 4450 5.181690 TGATGTACAAAACCTGAAAGCAC 57.818 39.130 0.00 0.00 0.00 4.40
2500 6150 0.105039 GGAACCCCTATCTCACTGCG 59.895 60.000 0.00 0.00 0.00 5.18
2519 6170 2.192624 CAACAACTTCTGGGTTTTGCG 58.807 47.619 0.00 0.00 0.00 4.85
2780 6465 9.618890 AAATTCAATCTCTGCTATAGTTTAGCA 57.381 29.630 13.69 13.69 47.00 3.49
2799 6484 9.434420 ACTCTGAATGTGAAAACAAAAATTCAA 57.566 25.926 0.00 0.00 37.31 2.69
2807 6492 6.374053 TGAACTCACTCTGAATGTGAAAACAA 59.626 34.615 2.04 0.00 42.85 2.83
2950 6653 6.046593 GCCACATACTGTACTGCAAACTATA 58.953 40.000 0.00 0.00 0.00 1.31
3084 6787 2.883888 GCTAAAATGGCCTCAACCCTCA 60.884 50.000 3.32 0.00 0.00 3.86
3149 6852 1.512926 TCGTTTCAGGCTTGCTCTTC 58.487 50.000 0.00 0.00 0.00 2.87
3189 6910 3.312697 GTCGGCCAAGAATTATGGAGTTC 59.687 47.826 12.76 0.00 40.56 3.01
3218 6939 2.619646 GTCCGAGAGTCATAAGGGAGAC 59.380 54.545 0.00 0.00 35.02 3.36
3219 6940 2.241430 TGTCCGAGAGTCATAAGGGAGA 59.759 50.000 0.00 0.00 0.00 3.71
3220 6941 2.621055 CTGTCCGAGAGTCATAAGGGAG 59.379 54.545 0.00 0.00 0.00 4.30
3236 6957 5.240403 AGCTTCAAATTTCTTCTGACTGTCC 59.760 40.000 5.17 0.00 0.00 4.02
3344 7065 4.588899 ACCAACAGCTGCATCATAACTTA 58.411 39.130 15.27 0.00 0.00 2.24
3345 7066 3.424703 ACCAACAGCTGCATCATAACTT 58.575 40.909 15.27 0.00 0.00 2.66
3346 7067 3.012518 GACCAACAGCTGCATCATAACT 58.987 45.455 15.27 0.00 0.00 2.24
3347 7068 2.223112 CGACCAACAGCTGCATCATAAC 60.223 50.000 15.27 0.00 0.00 1.89
3348 7069 2.009051 CGACCAACAGCTGCATCATAA 58.991 47.619 15.27 0.00 0.00 1.90
3349 7070 1.655484 CGACCAACAGCTGCATCATA 58.345 50.000 15.27 0.00 0.00 2.15
3350 7071 1.651240 GCGACCAACAGCTGCATCAT 61.651 55.000 15.27 0.00 0.00 2.45
3351 7072 2.327343 GCGACCAACAGCTGCATCA 61.327 57.895 15.27 0.00 0.00 3.07
3352 7073 2.482374 GCGACCAACAGCTGCATC 59.518 61.111 15.27 5.34 0.00 3.91
3353 7074 2.184020 TAGGCGACCAACAGCTGCAT 62.184 55.000 15.27 0.00 0.00 3.96
3354 7075 2.786539 CTAGGCGACCAACAGCTGCA 62.787 60.000 15.27 0.00 0.00 4.41
3355 7076 2.047274 TAGGCGACCAACAGCTGC 60.047 61.111 15.27 0.00 0.00 5.25
3356 7077 2.103042 GCTAGGCGACCAACAGCTG 61.103 63.158 13.48 13.48 0.00 4.24
3357 7078 2.266055 GCTAGGCGACCAACAGCT 59.734 61.111 0.00 0.00 0.00 4.24
3375 7096 2.677524 TTGAGCATGGGCCTGTGC 60.678 61.111 21.72 21.72 42.56 4.57
3376 7097 2.707849 GCTTGAGCATGGGCCTGTG 61.708 63.158 4.53 5.00 42.56 3.66
3377 7098 2.362120 GCTTGAGCATGGGCCTGT 60.362 61.111 4.53 0.00 42.56 4.00
3378 7099 3.145551 GGCTTGAGCATGGGCCTG 61.146 66.667 4.53 1.41 44.36 4.85
3395 7116 4.452733 GTCGGGTCGGGCCTTCAG 62.453 72.222 0.84 0.00 37.43 3.02
3400 7121 4.801624 GTTACGTCGGGTCGGGCC 62.802 72.222 0.00 0.00 34.94 5.80
3404 7125 4.107051 AGGCGTTACGTCGGGTCG 62.107 66.667 6.63 0.00 36.23 4.79
3405 7126 2.476534 TTCAGGCGTTACGTCGGGTC 62.477 60.000 9.75 0.00 36.23 4.46
3406 7127 2.482296 CTTCAGGCGTTACGTCGGGT 62.482 60.000 9.75 0.00 36.23 5.28
3407 7128 1.804326 CTTCAGGCGTTACGTCGGG 60.804 63.158 9.75 3.73 36.23 5.14
3408 7129 2.442188 GCTTCAGGCGTTACGTCGG 61.442 63.158 6.63 4.63 36.23 4.79
3409 7130 1.279527 TTGCTTCAGGCGTTACGTCG 61.280 55.000 6.63 0.56 45.43 5.12
3410 7131 0.863144 TTTGCTTCAGGCGTTACGTC 59.137 50.000 0.00 0.00 45.43 4.34
3411 7132 1.519408 ATTTGCTTCAGGCGTTACGT 58.481 45.000 6.63 0.00 45.43 3.57
3412 7133 3.670203 CTTATTTGCTTCAGGCGTTACG 58.330 45.455 0.00 0.00 45.43 3.18
3413 7134 3.426323 GCTTATTTGCTTCAGGCGTTAC 58.574 45.455 0.00 0.00 45.43 2.50
3414 7135 2.422127 GGCTTATTTGCTTCAGGCGTTA 59.578 45.455 0.00 0.00 45.43 3.18
3415 7136 1.202348 GGCTTATTTGCTTCAGGCGTT 59.798 47.619 0.00 0.00 45.43 4.84
3416 7137 0.811281 GGCTTATTTGCTTCAGGCGT 59.189 50.000 0.00 0.00 45.43 5.68
3417 7138 0.101219 GGGCTTATTTGCTTCAGGCG 59.899 55.000 0.00 0.00 45.43 5.52
3418 7139 1.135721 CTGGGCTTATTTGCTTCAGGC 59.864 52.381 0.00 0.00 42.22 4.85
3419 7140 1.135721 GCTGGGCTTATTTGCTTCAGG 59.864 52.381 0.00 0.00 36.02 3.86
3420 7141 2.573941 GCTGGGCTTATTTGCTTCAG 57.426 50.000 0.00 0.00 37.31 3.02


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

AutoCloner maintained by Alex Coulton.