Multiple sequence alignment - TraesCS6A01G281400

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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 TraesCS6A01G281400 chr6A 100.000 5718 0 0 1 5718 511290730 511285013 0.000000e+00 10560.0
1 TraesCS6A01G281400 chr4B 93.529 4219 172 33 581 4778 413486568 413482430 0.000000e+00 6185.0
2 TraesCS6A01G281400 chr4B 90.078 766 57 8 1 749 413487246 413486483 0.000000e+00 976.0
3 TraesCS6A01G281400 chr4B 90.723 733 34 16 4776 5496 413482307 413481597 0.000000e+00 946.0
4 TraesCS6A01G281400 chr4B 86.924 543 48 9 3822 4355 389751821 389751293 6.380000e-164 588.0
5 TraesCS6A01G281400 chr4B 92.511 227 17 0 5492 5718 413473017 413472791 5.520000e-85 326.0
6 TraesCS6A01G281400 chr4B 89.177 231 25 0 1937 2167 290783579 290783349 7.250000e-74 289.0
7 TraesCS6A01G281400 chr4B 93.069 101 3 1 5500 5596 54772476 54772376 1.660000e-30 145.0
8 TraesCS6A01G281400 chr4B 92.233 103 4 1 5500 5598 96977390 96977288 5.970000e-30 143.0
9 TraesCS6A01G281400 chr4B 91.781 73 6 0 4770 4842 551228437 551228365 1.010000e-17 102.0
10 TraesCS6A01G281400 chr1D 93.083 2212 105 22 1701 3892 174148775 174150958 0.000000e+00 3193.0
11 TraesCS6A01G281400 chr1D 93.344 616 25 4 498 1103 174147660 174148269 0.000000e+00 896.0
12 TraesCS6A01G281400 chr1D 88.725 541 41 7 3822 4350 104594658 104595190 1.340000e-180 643.0
13 TraesCS6A01G281400 chr1D 94.778 383 18 2 1292 1674 174148407 174148787 3.810000e-166 595.0
14 TraesCS6A01G281400 chr1D 86.432 199 26 1 3163 3361 452155127 452154930 3.470000e-52 217.0
15 TraesCS6A01G281400 chr1D 86.432 199 26 1 3163 3361 452156876 452156679 3.470000e-52 217.0
16 TraesCS6A01G281400 chr1D 86.432 199 26 1 3163 3361 452157752 452157555 3.470000e-52 217.0
17 TraesCS6A01G281400 chr5B 88.636 1408 117 22 3508 4884 392500976 392502371 0.000000e+00 1674.0
18 TraesCS6A01G281400 chr5B 88.491 530 37 10 2821 3334 392499134 392499655 2.260000e-173 619.0
19 TraesCS6A01G281400 chr5B 86.186 333 19 16 2554 2881 570953858 570954168 9.180000e-88 335.0
20 TraesCS6A01G281400 chr7B 91.644 1101 77 11 3615 4708 345990251 345991343 0.000000e+00 1509.0
21 TraesCS6A01G281400 chr7B 86.235 988 86 20 4712 5694 345991421 345992363 0.000000e+00 1026.0
22 TraesCS6A01G281400 chr7B 87.087 333 28 11 2554 2881 423436869 423436547 4.210000e-96 363.0
23 TraesCS6A01G281400 chr7B 92.746 193 9 3 2694 2881 732523858 732524050 2.030000e-69 274.0
24 TraesCS6A01G281400 chr7B 81.356 236 26 8 5441 5661 474541891 474541659 5.890000e-40 176.0
25 TraesCS6A01G281400 chr7B 93.204 103 3 2 5500 5598 191213897 191213795 1.280000e-31 148.0
26 TraesCS6A01G281400 chr7B 76.012 321 53 13 5418 5718 355608267 355607951 1.660000e-30 145.0
27 TraesCS6A01G281400 chr7B 84.810 79 12 0 5002 5080 710144503 710144425 4.750000e-11 80.5
28 TraesCS6A01G281400 chr2B 89.231 1105 77 15 3606 4708 135780517 135781581 0.000000e+00 1343.0
29 TraesCS6A01G281400 chr2B 86.614 1016 86 18 4708 5718 135781679 135782649 0.000000e+00 1077.0
30 TraesCS6A01G281400 chr2B 92.634 543 33 5 3579 4121 135776839 135777374 0.000000e+00 774.0
31 TraesCS6A01G281400 chr2B 85.886 333 32 11 2554 2881 300327881 300328203 1.970000e-89 340.0
32 TraesCS6A01G281400 chr2B 92.632 190 14 0 4519 4708 501729713 501729524 2.030000e-69 274.0
33 TraesCS6A01G281400 chr2B 82.323 198 10 9 4711 4908 501729285 501729113 1.280000e-31 148.0
34 TraesCS6A01G281400 chr2B 82.143 196 11 7 4711 4906 364327475 364327304 4.620000e-31 147.0
35 TraesCS6A01G281400 chr2B 77.358 106 18 3 4418 4518 262702294 262702398 2.230000e-04 58.4
36 TraesCS6A01G281400 chr3D 91.371 649 48 3 3604 4252 11428282 11427642 0.000000e+00 881.0
37 TraesCS6A01G281400 chr3D 85.822 663 67 18 4244 4884 11426321 11425664 0.000000e+00 678.0
38 TraesCS6A01G281400 chr3D 86.988 561 44 13 2821 3361 11429033 11428482 6.340000e-169 604.0
39 TraesCS6A01G281400 chr1A 91.228 627 48 2 4086 4708 327381655 327381032 0.000000e+00 846.0
40 TraesCS6A01G281400 chr1A 90.909 627 50 2 4086 4708 335907801 335908424 0.000000e+00 835.0
41 TraesCS6A01G281400 chr1A 90.271 627 54 2 4086 4708 335874003 335874626 0.000000e+00 813.0
42 TraesCS6A01G281400 chr1A 87.234 564 59 10 1924 2480 538680149 538680706 1.050000e-176 630.0
43 TraesCS6A01G281400 chr1A 87.661 389 44 3 1098 1485 560194448 560194063 3.140000e-122 449.0
44 TraesCS6A01G281400 chr1A 90.968 155 13 1 949 1103 560194629 560194476 2.090000e-49 207.0
45 TraesCS6A01G281400 chr1A 95.789 95 4 0 4708 4802 335874859 335874953 2.760000e-33 154.0
46 TraesCS6A01G281400 chr1A 94.737 95 5 0 4708 4802 335908657 335908751 1.280000e-31 148.0
47 TraesCS6A01G281400 chr1A 82.143 196 11 7 4711 4906 327380795 327380624 4.620000e-31 147.0
48 TraesCS6A01G281400 chr5D 90.033 602 42 9 3105 3705 21305738 21306322 0.000000e+00 763.0
49 TraesCS6A01G281400 chr5D 88.432 389 41 3 1098 1485 15671058 15670673 3.120000e-127 466.0
50 TraesCS6A01G281400 chr5D 76.890 463 68 25 665 1103 15671533 15671086 5.760000e-55 226.0
51 TraesCS6A01G281400 chr3B 89.744 507 33 10 3105 3609 818404725 818405214 1.050000e-176 630.0
52 TraesCS6A01G281400 chr3B 89.315 496 36 8 3105 3599 29355921 29355442 1.760000e-169 606.0
53 TraesCS6A01G281400 chr3B 86.145 332 19 14 2554 2880 279515828 279515519 3.300000e-87 333.0
54 TraesCS6A01G281400 chr3B 89.610 231 22 2 1937 2167 505449365 505449137 5.600000e-75 292.0
55 TraesCS6A01G281400 chr3B 87.975 158 10 3 3822 3977 554039067 554039217 1.640000e-40 178.0
56 TraesCS6A01G281400 chr5A 87.590 556 40 12 3822 4355 580862919 580862371 8.140000e-173 617.0
57 TraesCS6A01G281400 chr5A 75.622 402 56 23 4908 5303 490849602 490849237 1.650000e-35 161.0
58 TraesCS6A01G281400 chr2D 89.119 386 38 3 1098 1482 102656743 102657125 1.440000e-130 477.0
59 TraesCS6A01G281400 chr2D 88.718 390 40 3 1098 1486 487948330 487947944 1.860000e-129 473.0
60 TraesCS6A01G281400 chr2D 88.601 386 40 3 1098 1482 102656235 102656617 3.120000e-127 466.0
61 TraesCS6A01G281400 chr2D 86.207 348 39 7 3370 3713 534959697 534960039 9.050000e-98 368.0
62 TraesCS6A01G281400 chr2D 77.223 461 70 21 665 1103 487948805 487948358 2.660000e-58 237.0
63 TraesCS6A01G281400 chr2D 78.177 417 58 16 4906 5303 258329048 258329450 9.580000e-58 235.0
64 TraesCS6A01G281400 chr2D 87.826 115 11 3 4772 4884 68465586 68465699 1.290000e-26 132.0
65 TraesCS6A01G281400 chrUn 88.432 389 41 3 1098 1485 390790916 390790531 3.120000e-127 466.0
66 TraesCS6A01G281400 chrUn 90.171 234 21 2 1934 2167 40465253 40465484 2.590000e-78 303.0
67 TraesCS6A01G281400 chrUn 90.476 231 20 2 1937 2167 319287330 319287102 2.590000e-78 303.0
68 TraesCS6A01G281400 chrUn 77.106 463 67 25 665 1103 390791391 390790944 1.240000e-56 231.0
69 TraesCS6A01G281400 chrUn 77.673 318 55 9 4982 5288 103387151 103387463 4.550000e-41 180.0
70 TraesCS6A01G281400 chrUn 97.561 41 1 0 5369 5409 53049123 53049083 2.860000e-08 71.3
71 TraesCS6A01G281400 chr2A 87.500 408 45 3 3366 3772 339108500 339108902 3.120000e-127 466.0
72 TraesCS6A01G281400 chr2A 87.255 408 46 3 3366 3772 325794435 325794033 1.450000e-125 460.0
73 TraesCS6A01G281400 chr2A 84.108 409 53 8 3370 3774 678194409 678194809 8.990000e-103 385.0
74 TraesCS6A01G281400 chr2A 92.784 194 9 3 2693 2881 300215008 300214815 5.640000e-70 276.0
75 TraesCS6A01G281400 chr2A 78.139 462 64 25 665 1103 30042150 30042597 5.680000e-65 259.0
76 TraesCS6A01G281400 chr2A 83.088 136 15 5 5348 5481 332068380 332068509 3.620000e-22 117.0
77 TraesCS6A01G281400 chr7D 87.824 386 43 3 1098 1482 608428644 608429026 3.140000e-122 449.0
78 TraesCS6A01G281400 chr7D 82.596 339 24 13 2808 3118 175872093 175872424 3.400000e-67 267.0
79 TraesCS6A01G281400 chr7D 77.609 460 66 25 665 1101 608428169 608428614 1.590000e-60 244.0
80 TraesCS6A01G281400 chr1B 86.618 411 46 5 2000 2402 611329866 611329457 4.060000e-121 446.0
81 TraesCS6A01G281400 chr1B 85.535 159 19 1 5447 5601 221270852 221270694 4.580000e-36 163.0
82 TraesCS6A01G281400 chr1B 77.551 147 23 7 665 804 542932236 542932379 4.750000e-11 80.5
83 TraesCS6A01G281400 chr6B 87.679 349 35 6 4955 5303 224216374 224216714 3.210000e-107 399.0
84 TraesCS6A01G281400 chr6B 90.301 299 23 4 2588 2881 369657011 369656714 2.500000e-103 387.0
85 TraesCS6A01G281400 chr6B 79.412 408 56 16 4907 5302 503880461 503880070 4.390000e-66 263.0
86 TraesCS6A01G281400 chr6B 81.553 206 13 8 4708 4913 224216197 224216377 4.620000e-31 147.0
87 TraesCS6A01G281400 chr4D 78.681 455 64 20 669 1103 82744651 82744210 7.300000e-69 272.0
88 TraesCS6A01G281400 chr7A 92.268 194 10 3 2693 2881 240669895 240669702 2.630000e-68 270.0
89 TraesCS6A01G281400 chr4A 92.268 194 10 3 2693 2881 284248371 284248178 2.630000e-68 270.0
90 TraesCS6A01G281400 chr4A 84.456 193 21 5 1713 1898 145344677 145344487 1.270000e-41 182.0
91 TraesCS6A01G281400 chr4A 75.835 389 55 19 4908 5293 299611513 299611161 1.650000e-35 161.0


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 TraesCS6A01G281400 chr6A 511285013 511290730 5717 True 10560.000000 10560 100.000000 1 5718 1 chr6A.!!$R1 5717
1 TraesCS6A01G281400 chr4B 413481597 413487246 5649 True 2702.333333 6185 91.443333 1 5496 3 chr4B.!!$R7 5495
2 TraesCS6A01G281400 chr4B 389751293 389751821 528 True 588.000000 588 86.924000 3822 4355 1 chr4B.!!$R4 533
3 TraesCS6A01G281400 chr1D 174147660 174150958 3298 False 1561.333333 3193 93.735000 498 3892 3 chr1D.!!$F2 3394
4 TraesCS6A01G281400 chr1D 104594658 104595190 532 False 643.000000 643 88.725000 3822 4350 1 chr1D.!!$F1 528
5 TraesCS6A01G281400 chr1D 452154930 452157752 2822 True 217.000000 217 86.432000 3163 3361 3 chr1D.!!$R1 198
6 TraesCS6A01G281400 chr5B 392499134 392502371 3237 False 1146.500000 1674 88.563500 2821 4884 2 chr5B.!!$F2 2063
7 TraesCS6A01G281400 chr7B 345990251 345992363 2112 False 1267.500000 1509 88.939500 3615 5694 2 chr7B.!!$F2 2079
8 TraesCS6A01G281400 chr2B 135776839 135782649 5810 False 1064.666667 1343 89.493000 3579 5718 3 chr2B.!!$F3 2139
9 TraesCS6A01G281400 chr2B 501729113 501729713 600 True 211.000000 274 87.477500 4519 4908 2 chr2B.!!$R2 389
10 TraesCS6A01G281400 chr3D 11425664 11429033 3369 True 721.000000 881 88.060333 2821 4884 3 chr3D.!!$R1 2063
11 TraesCS6A01G281400 chr1A 538680149 538680706 557 False 630.000000 630 87.234000 1924 2480 1 chr1A.!!$F1 556
12 TraesCS6A01G281400 chr1A 327380624 327381655 1031 True 496.500000 846 86.685500 4086 4906 2 chr1A.!!$R1 820
13 TraesCS6A01G281400 chr1A 335907801 335908751 950 False 491.500000 835 92.823000 4086 4802 2 chr1A.!!$F3 716
14 TraesCS6A01G281400 chr1A 335874003 335874953 950 False 483.500000 813 93.030000 4086 4802 2 chr1A.!!$F2 716
15 TraesCS6A01G281400 chr1A 560194063 560194629 566 True 328.000000 449 89.314500 949 1485 2 chr1A.!!$R2 536
16 TraesCS6A01G281400 chr5D 21305738 21306322 584 False 763.000000 763 90.033000 3105 3705 1 chr5D.!!$F1 600
17 TraesCS6A01G281400 chr5D 15670673 15671533 860 True 346.000000 466 82.661000 665 1485 2 chr5D.!!$R1 820
18 TraesCS6A01G281400 chr5A 580862371 580862919 548 True 617.000000 617 87.590000 3822 4355 1 chr5A.!!$R2 533
19 TraesCS6A01G281400 chr2D 102656235 102657125 890 False 471.500000 477 88.860000 1098 1482 2 chr2D.!!$F4 384
20 TraesCS6A01G281400 chr2D 487947944 487948805 861 True 355.000000 473 82.970500 665 1486 2 chr2D.!!$R1 821
21 TraesCS6A01G281400 chrUn 390790531 390791391 860 True 348.500000 466 82.769000 665 1485 2 chrUn.!!$R3 820
22 TraesCS6A01G281400 chr7D 608428169 608429026 857 False 346.500000 449 82.716500 665 1482 2 chr7D.!!$F2 817
23 TraesCS6A01G281400 chr6B 224216197 224216714 517 False 273.000000 399 84.616000 4708 5303 2 chr6B.!!$F1 595

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
864 971 0.250510 TGTCATGCCCGTTGTTGCTA 60.251 50.0 0.0 0.0 0.0 3.49 F
1710 1893 2.172483 ATCTCGCACCACCACTCCAC 62.172 60.0 0.0 0.0 0.0 4.02 F
2644 2835 0.034059 ACCTGCAGCAGACTGTACAC 59.966 55.0 24.9 0.0 46.3 2.90 F
3835 8497 0.472044 TTGTTGTCCTGGCTGTGCTA 59.528 50.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 2044 0.036577 GTCACTGGCTCACTGCATCT 60.037 55.000 0.00 0.0 45.15 2.90 R
2759 2951 1.211949 GGCCTAACACCTCATTGCCTA 59.788 52.381 0.00 0.0 34.61 3.93 R
3973 8648 2.107552 ACAAAAGTAGGCCTAGCACCAA 59.892 45.455 14.38 0.0 0.00 3.67 R
5308 11977 0.112606 CGCTCCTAGGGGTCTATCCA 59.887 60.000 11.24 0.0 38.11 3.41 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
20 21 3.492545 GCGCATTCGTGGCCGTTA 61.493 61.111 0.30 0.00 38.14 3.18
54 55 9.574458 TTTGACTTTGTTTTTGATCGTTTGATA 57.426 25.926 0.00 0.00 34.09 2.15
170 171 1.134007 TCCCGTGTCCGCTAGAGATTA 60.134 52.381 0.00 0.00 0.00 1.75
185 186 1.066143 AGATTAGCCAACCACTCCGTG 60.066 52.381 0.00 0.00 0.00 4.94
211 212 2.811317 GAGCTTGACGGGCACTCG 60.811 66.667 0.00 0.00 0.00 4.18
338 353 3.077556 CCCTCCACTCCCTCCACG 61.078 72.222 0.00 0.00 0.00 4.94
356 371 3.237741 CCGCCTCCTCCCATCTCC 61.238 72.222 0.00 0.00 0.00 3.71
385 400 2.419198 CTCCCAAGCGAGGATCCG 59.581 66.667 5.98 0.00 31.48 4.18
392 407 3.224324 GCGAGGATCCGGCACCTA 61.224 66.667 21.50 0.00 36.57 3.08
435 450 1.117749 TCCTCATCCTGGATCCTGCG 61.118 60.000 14.23 7.01 0.00 5.18
438 453 3.564218 ATCCTGGATCCTGCGGGC 61.564 66.667 14.23 0.00 33.78 6.13
439 454 4.804420 TCCTGGATCCTGCGGGCT 62.804 66.667 14.23 0.00 33.78 5.19
442 457 1.070445 CTGGATCCTGCGGGCTAAG 59.930 63.158 14.23 0.00 0.00 2.18
444 459 2.281139 GATCCTGCGGGCTAAGGC 60.281 66.667 6.73 0.00 33.25 4.35
445 460 4.241555 ATCCTGCGGGCTAAGGCG 62.242 66.667 6.73 0.00 39.81 5.52
474 489 3.612247 GAGGCAAGCTTCTCCGGCA 62.612 63.158 10.16 0.00 0.00 5.69
500 515 0.539669 GCAACCTACAGGCAAAGGGT 60.540 55.000 0.00 0.00 39.32 4.34
854 961 1.074775 TTGGGTCAGTGTCATGCCC 59.925 57.895 0.00 0.00 37.17 5.36
856 963 2.347490 GGTCAGTGTCATGCCCGT 59.653 61.111 0.00 0.00 0.00 5.28
864 971 0.250510 TGTCATGCCCGTTGTTGCTA 60.251 50.000 0.00 0.00 0.00 3.49
890 997 4.013728 AGCACTTTACACAAGTCAACCAA 58.986 39.130 0.00 0.00 0.00 3.67
927 1034 4.467795 TGTTAGCACTAGGAGAAGAGCATT 59.532 41.667 0.00 0.00 35.77 3.56
1120 1300 7.609760 TTTGTCGTGTAAATGCTCATATTCT 57.390 32.000 0.00 0.00 0.00 2.40
1130 1310 9.638300 GTAAATGCTCATATTCTGTTAAGTTCG 57.362 33.333 0.00 0.00 0.00 3.95
1149 1329 5.121768 AGTTCGTGTGTATAAATCAACTGGC 59.878 40.000 0.00 0.00 0.00 4.85
1156 1336 5.648092 GTGTATAAATCAACTGGCCTGAAGT 59.352 40.000 17.64 1.85 0.00 3.01
1325 1508 7.367285 TGTTGCTATTATTTCAGTTTGTGGAC 58.633 34.615 0.00 0.00 0.00 4.02
1425 1608 5.166398 TCACATGATCGCTAGAAGCATATG 58.834 41.667 0.00 0.00 42.58 1.78
1465 1648 4.154015 TGGTTGCTTTCTTATCGACACATG 59.846 41.667 0.00 0.00 0.00 3.21
1508 1691 3.241067 TGTACCTTTGTGATCGTAGCC 57.759 47.619 0.00 0.00 0.00 3.93
1509 1692 2.563620 TGTACCTTTGTGATCGTAGCCA 59.436 45.455 0.00 0.00 0.00 4.75
1618 1801 5.443185 ACAAACCTGATCAAACACATGAG 57.557 39.130 0.00 0.00 31.76 2.90
1647 1830 2.238144 TCCTCTGAAAGCTCCATCTTGG 59.762 50.000 0.00 0.00 39.43 3.61
1692 1875 4.202264 CCAGCTATACTTCCCGACTTTGAT 60.202 45.833 0.00 0.00 0.00 2.57
1710 1893 2.172483 ATCTCGCACCACCACTCCAC 62.172 60.000 0.00 0.00 0.00 4.02
1711 1894 3.883744 CTCGCACCACCACTCCACC 62.884 68.421 0.00 0.00 0.00 4.61
1740 1923 6.098124 AGTGAAATGAACCTTGATTTGAACCA 59.902 34.615 0.00 0.00 0.00 3.67
1861 2044 3.521937 AGGGCATTAACTGTAGGTAAGCA 59.478 43.478 10.85 0.00 0.00 3.91
1922 2105 1.683917 TGTGGGTGGTTATTGTTGCAC 59.316 47.619 0.00 0.00 0.00 4.57
2187 2375 8.409371 TCATAACATGTGCAACTTTTTACTTCA 58.591 29.630 0.00 0.00 38.04 3.02
2267 2455 6.465948 TGCATGGCTTTTTGAGAATAAATGT 58.534 32.000 0.00 0.00 0.00 2.71
2366 2557 5.643379 TTTCAGTTTATTCTGGACATGCC 57.357 39.130 0.00 0.00 36.25 4.40
2475 2666 9.712305 CAATCTTTTACCCCTATACATAGACAG 57.288 37.037 0.00 0.00 32.05 3.51
2521 2712 3.368427 GCCTTCCTTTGGTGGCTAATTTC 60.368 47.826 12.98 0.00 39.09 2.17
2603 2794 6.495181 AGACCAATGATATTCTGACCTACGAT 59.505 38.462 0.00 0.00 0.00 3.73
2644 2835 0.034059 ACCTGCAGCAGACTGTACAC 59.966 55.000 24.90 0.00 46.30 2.90
2650 2841 2.720758 GCAGACTGTACACGCAGCG 61.721 63.158 14.82 14.82 39.96 5.18
2735 2927 4.397103 GCATCTGATTCCAACACATCAAGA 59.603 41.667 0.00 0.00 0.00 3.02
2743 2935 2.681848 CCAACACATCAAGATGAGCTCC 59.318 50.000 16.39 0.00 41.20 4.70
2759 2951 8.722422 AGATGAGCTCCCTCTTTTATTATTCTT 58.278 33.333 12.15 0.00 38.93 2.52
2804 3001 8.785946 CCCAATCTTTTTATTTGTTGCTTTGAT 58.214 29.630 0.00 0.00 0.00 2.57
2810 3007 8.715191 TTTTTATTTGTTGCTTTGATGAGTGT 57.285 26.923 0.00 0.00 0.00 3.55
3064 3279 7.607607 TGTGAATGGAATATGGACTGCATATAC 59.392 37.037 3.66 1.99 0.00 1.47
3104 3324 3.070018 GCATCCGGAGATTGGATTACAG 58.930 50.000 11.34 0.00 43.76 2.74
3232 3453 6.455360 TTCAAGTCTCAACTCAAGCAAAAT 57.545 33.333 0.00 0.00 33.48 1.82
3345 3566 3.380954 TCATGTGTTTGTCATGTGCTTGT 59.619 39.130 5.94 0.00 42.03 3.16
3355 3576 4.114794 GTCATGTGCTTGTTTCTGCTTTT 58.885 39.130 0.00 0.00 0.00 2.27
3361 3582 2.604462 GCTTGTTTCTGCTTTTGGTGTG 59.396 45.455 0.00 0.00 0.00 3.82
3368 3589 2.159254 TCTGCTTTTGGTGTGTGCTTTC 60.159 45.455 0.00 0.00 0.00 2.62
3381 4487 6.183360 GGTGTGTGCTTTCCTATCTAATGTTC 60.183 42.308 0.00 0.00 0.00 3.18
3483 4590 7.715249 TGACCTTCTTATTATACATGCAGGTTC 59.285 37.037 10.25 0.00 32.11 3.62
3505 4612 2.304092 TGATACTGAGGTTATCGGCGT 58.696 47.619 6.85 0.00 37.90 5.68
3741 8403 9.701098 ACGAATTTACTAACTATCAGTTCACAA 57.299 29.630 0.00 0.00 39.51 3.33
3835 8497 0.472044 TTGTTGTCCTGGCTGTGCTA 59.528 50.000 0.00 0.00 0.00 3.49
3973 8648 8.437274 TGGTATAATTTGGTGGGTGTATTTTT 57.563 30.769 0.00 0.00 0.00 1.94
4138 8820 5.200483 AGCTAAAAATACATTGGCTGGCTA 58.800 37.500 2.00 0.00 42.15 3.93
4573 10615 4.374843 TTTATCTTCCTGCGCGTAACTA 57.625 40.909 8.43 0.00 0.00 2.24
4649 10691 0.767375 AGCTGGTGTCCACATGTTCT 59.233 50.000 0.00 0.00 0.00 3.01
4900 11340 2.678336 GCCCACAAGAGGTCTTTTATCG 59.322 50.000 0.00 0.00 33.11 2.92
4917 11357 1.740296 CGTCGGGGCTTGTTACAGG 60.740 63.158 0.00 0.00 0.00 4.00
4929 11369 4.437930 GCTTGTTACAGGCATGATCAGTTC 60.438 45.833 14.55 0.00 36.46 3.01
5268 11937 9.911788 AGATTTGGAAGATGACATAAACTACAT 57.088 29.630 0.00 0.00 0.00 2.29
5303 11972 5.468540 TTGTATGATTCTGGATAGACCCG 57.531 43.478 0.00 0.00 38.00 5.28
5304 11973 4.736473 TGTATGATTCTGGATAGACCCGA 58.264 43.478 0.00 0.00 38.00 5.14
5305 11974 5.333581 TGTATGATTCTGGATAGACCCGAT 58.666 41.667 0.00 0.00 38.00 4.18
5306 11975 5.419155 TGTATGATTCTGGATAGACCCGATC 59.581 44.000 0.00 0.00 38.00 3.69
5307 11976 3.165875 TGATTCTGGATAGACCCGATCC 58.834 50.000 0.00 0.00 42.90 3.36
5308 11977 3.181417 TGATTCTGGATAGACCCGATCCT 60.181 47.826 7.44 0.00 43.00 3.24
5309 11978 2.294449 TCTGGATAGACCCGATCCTG 57.706 55.000 7.44 7.02 43.00 3.86
5310 11979 1.203063 TCTGGATAGACCCGATCCTGG 60.203 57.143 11.04 0.00 43.00 4.45
5311 11980 0.857675 TGGATAGACCCGATCCTGGA 59.142 55.000 0.00 0.00 43.00 3.86
5312 11981 1.433199 TGGATAGACCCGATCCTGGAT 59.567 52.381 9.42 9.42 43.00 3.41
5313 11982 2.652857 TGGATAGACCCGATCCTGGATA 59.347 50.000 9.66 0.00 43.00 2.59
5314 11983 3.292460 GGATAGACCCGATCCTGGATAG 58.708 54.545 9.66 9.62 39.94 2.08
5315 11984 3.053544 GGATAGACCCGATCCTGGATAGA 60.054 52.174 17.19 0.00 39.94 1.98
5316 11985 2.296073 AGACCCGATCCTGGATAGAC 57.704 55.000 17.19 8.79 0.00 2.59
5317 11986 1.203075 AGACCCGATCCTGGATAGACC 60.203 57.143 17.19 6.64 39.54 3.85
5318 11987 0.178929 ACCCGATCCTGGATAGACCC 60.179 60.000 17.19 0.64 38.00 4.46
5325 11994 2.074579 TCCTGGATAGACCCCTAGGAG 58.925 57.143 11.48 0.00 38.00 3.69
5343 12012 2.872858 GGAGCGGAAACAACATAGATCC 59.127 50.000 0.00 0.00 0.00 3.36
5498 12170 0.343372 TCCCCTAGAGGCCTGACAAT 59.657 55.000 12.00 0.00 0.00 2.71
5543 12215 1.016130 GTGAGGTCAGGTGCGACATG 61.016 60.000 0.00 0.00 37.66 3.21
5566 12238 2.592032 TTGGTGGCAGCTCGATCCA 61.592 57.895 18.53 2.11 0.00 3.41
5568 12240 2.581354 GTGGCAGCTCGATCCACT 59.419 61.111 14.94 0.00 45.04 4.00
5569 12241 1.520342 GTGGCAGCTCGATCCACTC 60.520 63.158 14.94 0.00 45.04 3.51
5570 12242 2.107953 GGCAGCTCGATCCACTCC 59.892 66.667 0.00 0.00 0.00 3.85
5571 12243 2.430610 GGCAGCTCGATCCACTCCT 61.431 63.158 0.00 0.00 0.00 3.69
5572 12244 1.227205 GCAGCTCGATCCACTCCTG 60.227 63.158 0.00 0.00 0.00 3.86
5573 12245 1.440893 CAGCTCGATCCACTCCTGG 59.559 63.158 0.00 0.00 39.23 4.45
5597 12269 2.553247 CCTTCTTCTTCCACTTCCCCAC 60.553 54.545 0.00 0.00 0.00 4.61
5598 12270 1.064825 TCTTCTTCCACTTCCCCACC 58.935 55.000 0.00 0.00 0.00 4.61
5601 12273 2.448931 TTCCACTTCCCCACCGGT 60.449 61.111 0.00 0.00 0.00 5.28
5603 12275 3.566210 CCACTTCCCCACCGGTGT 61.566 66.667 31.80 10.72 0.00 4.16
5616 12288 2.203153 GGTGTGGTCGCACAGGTT 60.203 61.111 15.27 0.00 40.89 3.50
5639 12311 1.686325 GGCGCCTTGATCCACTCCTA 61.686 60.000 22.15 0.00 0.00 2.94
5640 12312 0.530870 GCGCCTTGATCCACTCCTAC 60.531 60.000 0.00 0.00 0.00 3.18
5649 12321 5.403558 TGATCCACTCCTACATCCTTCTA 57.596 43.478 0.00 0.00 0.00 2.10
5663 12335 1.279271 CCTTCTACCACTTCCCCACTG 59.721 57.143 0.00 0.00 0.00 3.66
5668 12340 1.056660 ACCACTTCCCCACTGTGTAG 58.943 55.000 7.08 0.00 0.00 2.74
5678 12352 2.030412 CTGTGTAGCACCGCACCA 59.970 61.111 0.00 0.00 34.94 4.17
5698 12372 0.257039 GTGAGGGAGCATGGGATTGT 59.743 55.000 0.00 0.00 0.00 2.71
5699 12373 1.002069 TGAGGGAGCATGGGATTGTT 58.998 50.000 0.00 0.00 0.00 2.83
5705 12379 2.495866 CATGGGATTGTTGGCGGC 59.504 61.111 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.305925 GATCAAAAACAAAGTCAAAGTTGATCT 57.694 29.630 13.22 0.00 43.24 2.75
192 193 3.575351 GAGTGCCCGTCAAGCTCGT 62.575 63.158 0.00 0.00 0.00 4.18
338 353 3.934962 GAGATGGGAGGAGGCGGC 61.935 72.222 0.00 0.00 0.00 6.53
356 371 2.849120 CTTGGGAGCTGCCTCGTCAG 62.849 65.000 25.93 9.37 39.06 3.51
385 400 1.221021 GGCAGTGTAGGTAGGTGCC 59.779 63.158 0.00 0.00 46.49 5.01
392 407 2.657237 GACAGCGGCAGTGTAGGT 59.343 61.111 1.67 0.00 0.00 3.08
435 450 3.787001 AGCCTCACGCCTTAGCCC 61.787 66.667 0.00 0.00 38.78 5.19
438 453 2.887568 CGCAGCCTCACGCCTTAG 60.888 66.667 0.00 0.00 38.78 2.18
439 454 4.451150 CCGCAGCCTCACGCCTTA 62.451 66.667 0.00 0.00 38.78 2.69
474 489 3.717294 CTGTAGGTTGCCCCCGCT 61.717 66.667 0.00 0.00 35.36 5.52
483 498 1.145571 TCACCCTTTGCCTGTAGGTT 58.854 50.000 0.00 0.00 37.57 3.50
514 529 0.466372 ATCTCCCGCAGATCGAGTCA 60.466 55.000 0.00 0.00 37.24 3.41
517 532 4.336713 TCATATTATCTCCCGCAGATCGAG 59.663 45.833 0.00 0.00 41.39 4.04
864 971 3.213506 TGACTTGTGTAAAGTGCTGCAT 58.786 40.909 5.27 0.00 0.00 3.96
890 997 5.564550 AGTGCTAACAGAGATTGAATTGGT 58.435 37.500 0.00 0.00 0.00 3.67
927 1034 1.145738 AGGGGCTCTTCTCTTTTGCAA 59.854 47.619 0.00 0.00 0.00 4.08
1120 1300 9.263538 AGTTGATTTATACACACGAACTTAACA 57.736 29.630 0.00 0.00 0.00 2.41
1130 1310 4.941263 TCAGGCCAGTTGATTTATACACAC 59.059 41.667 5.01 0.00 0.00 3.82
1149 1329 1.667236 TTCACAGCACACACTTCAGG 58.333 50.000 0.00 0.00 0.00 3.86
1156 1336 2.929641 TCAGGAAATTCACAGCACACA 58.070 42.857 0.00 0.00 0.00 3.72
1325 1508 2.704464 TGCTGGAATCACATCCTCTG 57.296 50.000 0.00 0.00 40.35 3.35
1425 1608 4.202050 GCAACCATCATTGTGGATACCTTC 60.202 45.833 10.89 0.00 42.02 3.46
1487 1670 3.196901 TGGCTACGATCACAAAGGTACAT 59.803 43.478 0.00 0.00 0.00 2.29
1508 1691 6.748333 AACTACACATTGAGATGGATTGTG 57.252 37.500 0.00 0.00 42.53 3.33
1509 1692 7.120285 CAGAAACTACACATTGAGATGGATTGT 59.880 37.037 0.00 0.00 37.60 2.71
1618 1801 1.134848 AGCTTTCAGAGGAGATGCGTC 60.135 52.381 0.00 0.00 0.00 5.19
1647 1830 4.304939 GTGGTGGTGTAGTGTTTAGAGAC 58.695 47.826 0.00 0.00 0.00 3.36
1692 1875 2.523168 TGGAGTGGTGGTGCGAGA 60.523 61.111 0.00 0.00 0.00 4.04
1710 1893 2.886523 TCAAGGTTCATTTCACTGCTGG 59.113 45.455 0.00 0.00 0.00 4.85
1711 1894 4.778534 ATCAAGGTTCATTTCACTGCTG 57.221 40.909 0.00 0.00 0.00 4.41
1792 1975 4.021544 TGGCTCGCAATACATTTCCTTTTT 60.022 37.500 0.00 0.00 0.00 1.94
1861 2044 0.036577 GTCACTGGCTCACTGCATCT 60.037 55.000 0.00 0.00 45.15 2.90
2066 2251 1.635487 ACTATGGGGCACACACTGAAT 59.365 47.619 0.00 0.00 0.00 2.57
2187 2375 2.501316 TGGCACTGTACTACATGCTCAT 59.499 45.455 16.50 0.00 34.95 2.90
2267 2455 7.595819 ATTAGGGAACAAAGAAACATTGTGA 57.404 32.000 0.00 0.00 39.98 3.58
2366 2557 7.477494 TCATGAGAACTATGTTGCATCAAATG 58.523 34.615 0.75 0.00 0.00 2.32
2475 2666 8.565416 GGCCTTACTAACCACATCATTAAATAC 58.435 37.037 0.00 0.00 0.00 1.89
2594 2785 1.742768 CCCAGCCTCATCGTAGGTC 59.257 63.158 0.00 0.00 39.02 3.85
2759 2951 1.211949 GGCCTAACACCTCATTGCCTA 59.788 52.381 0.00 0.00 34.61 3.93
2804 3001 3.274095 TCCACAACATGACAACACTCA 57.726 42.857 0.00 0.00 0.00 3.41
2810 3007 2.382882 TGCCTTTCCACAACATGACAA 58.617 42.857 0.00 0.00 0.00 3.18
2966 3180 4.523943 TGCCACTTATCAGCAGAACAAAAT 59.476 37.500 0.00 0.00 31.65 1.82
2990 3205 4.918810 TTCAAGCAGGTCTTTTCTTTCC 57.081 40.909 0.00 0.00 31.27 3.13
3078 3298 2.368439 TCCAATCTCCGGATGCAAAAG 58.632 47.619 3.57 0.00 31.75 2.27
3104 3324 5.700832 TCTGTGTACACAAACATGAGGAATC 59.299 40.000 27.66 0.00 41.33 2.52
3188 3409 1.374947 GGCAGCCTTCACACCTACA 59.625 57.895 3.29 0.00 0.00 2.74
3244 3465 5.979517 CAGATGCTACATCGACAGAACAATA 59.020 40.000 2.12 0.00 0.00 1.90
3251 3472 3.314913 AGTCTCAGATGCTACATCGACAG 59.685 47.826 13.12 6.87 0.00 3.51
3345 3566 1.824230 AGCACACACCAAAAGCAGAAA 59.176 42.857 0.00 0.00 0.00 2.52
3355 3576 4.901197 TTAGATAGGAAAGCACACACCA 57.099 40.909 0.00 0.00 0.00 4.17
3361 3582 7.984617 AGAAGAGAACATTAGATAGGAAAGCAC 59.015 37.037 0.00 0.00 0.00 4.40
3368 3589 8.729805 AAAGCAAGAAGAGAACATTAGATAGG 57.270 34.615 0.00 0.00 0.00 2.57
3381 4487 5.638783 CAGCTATTCCAAAAGCAAGAAGAG 58.361 41.667 0.00 0.00 41.32 2.85
3483 4590 3.245797 CGCCGATAACCTCAGTATCATG 58.754 50.000 0.00 0.00 0.00 3.07
3505 4612 6.721208 AGGAATTAATTCAGTTTGCAGGAGAA 59.279 34.615 25.55 0.00 38.53 2.87
3835 8497 3.679389 CAGTGCATTACCAGAAGGAAGT 58.321 45.455 0.00 0.00 38.69 3.01
3973 8648 2.107552 ACAAAAGTAGGCCTAGCACCAA 59.892 45.455 14.38 0.00 0.00 3.67
4138 8820 4.457257 GCTTTCTGCCAAACTAAGAGACAT 59.543 41.667 0.00 0.00 35.15 3.06
4573 10615 5.358160 GGTATTTTCAGCAAGGCTAGACATT 59.642 40.000 0.00 0.00 36.40 2.71
4900 11340 2.038837 GCCTGTAACAAGCCCCGAC 61.039 63.158 0.00 0.00 0.00 4.79
5234 11903 7.764141 TGTCATCTTCCAAATCTCAATTTCA 57.236 32.000 0.00 0.00 32.69 2.69
5303 11972 2.655407 TCCTAGGGGTCTATCCAGGATC 59.345 54.545 4.75 0.00 38.11 3.36
5304 11973 2.657459 CTCCTAGGGGTCTATCCAGGAT 59.343 54.545 9.46 7.27 38.11 3.24
5305 11974 2.074579 CTCCTAGGGGTCTATCCAGGA 58.925 57.143 9.46 0.00 38.11 3.86
5306 11975 1.551329 GCTCCTAGGGGTCTATCCAGG 60.551 61.905 11.24 0.00 38.11 4.45
5307 11976 1.888826 CGCTCCTAGGGGTCTATCCAG 60.889 61.905 11.24 0.00 38.11 3.86
5308 11977 0.112606 CGCTCCTAGGGGTCTATCCA 59.887 60.000 11.24 0.00 38.11 3.41
5309 11978 0.612453 CCGCTCCTAGGGGTCTATCC 60.612 65.000 11.24 0.00 42.78 2.59
5310 11979 2.964343 CCGCTCCTAGGGGTCTATC 58.036 63.158 11.24 0.00 42.78 2.08
5317 11986 0.323629 TGTTGTTTCCGCTCCTAGGG 59.676 55.000 9.46 0.44 0.00 3.53
5318 11987 2.403252 ATGTTGTTTCCGCTCCTAGG 57.597 50.000 0.82 0.82 0.00 3.02
5325 11994 3.270877 ACAGGATCTATGTTGTTTCCGC 58.729 45.455 0.00 0.00 0.00 5.54
5427 12098 3.243805 TGAACCCATGTGCACATTGAAAG 60.244 43.478 29.48 17.28 33.61 2.62
5498 12170 2.283676 GTGACCCTCTCCCGTCCA 60.284 66.667 0.00 0.00 0.00 4.02
5519 12191 4.742201 CACCTGACCTCACCGGCG 62.742 72.222 0.00 0.00 35.61 6.46
5525 12197 1.293179 CATGTCGCACCTGACCTCA 59.707 57.895 0.00 0.00 38.11 3.86
5526 12198 1.448540 CCATGTCGCACCTGACCTC 60.449 63.158 0.00 0.00 38.11 3.85
5533 12205 2.625823 CCAACCACCATGTCGCACC 61.626 63.158 0.00 0.00 0.00 5.01
5543 12215 2.985847 GAGCTGCCACCAACCACC 60.986 66.667 0.00 0.00 0.00 4.61
5566 12238 3.111484 GGAAGAAGAAGGATCCAGGAGT 58.889 50.000 15.82 0.00 32.08 3.85
5567 12239 3.110705 TGGAAGAAGAAGGATCCAGGAG 58.889 50.000 15.82 0.00 37.05 3.69
5568 12240 2.840651 GTGGAAGAAGAAGGATCCAGGA 59.159 50.000 15.82 0.00 42.35 3.86
5569 12241 2.843113 AGTGGAAGAAGAAGGATCCAGG 59.157 50.000 15.82 0.00 42.35 4.45
5570 12242 4.512484 GAAGTGGAAGAAGAAGGATCCAG 58.488 47.826 15.82 0.00 42.35 3.86
5571 12243 3.264450 GGAAGTGGAAGAAGAAGGATCCA 59.736 47.826 15.82 0.00 39.57 3.41
5572 12244 3.371059 GGGAAGTGGAAGAAGAAGGATCC 60.371 52.174 2.48 2.48 0.00 3.36
5573 12245 3.371059 GGGGAAGTGGAAGAAGAAGGATC 60.371 52.174 0.00 0.00 0.00 3.36
5574 12246 2.578480 GGGGAAGTGGAAGAAGAAGGAT 59.422 50.000 0.00 0.00 0.00 3.24
5575 12247 1.985895 GGGGAAGTGGAAGAAGAAGGA 59.014 52.381 0.00 0.00 0.00 3.36
5576 12248 1.705186 TGGGGAAGTGGAAGAAGAAGG 59.295 52.381 0.00 0.00 0.00 3.46
5577 12249 2.553247 GGTGGGGAAGTGGAAGAAGAAG 60.553 54.545 0.00 0.00 0.00 2.85
5598 12270 4.602259 ACCTGTGCGACCACACCG 62.602 66.667 0.00 0.00 46.51 4.94
5603 12275 1.302431 CCATCAACCTGTGCGACCA 60.302 57.895 0.00 0.00 0.00 4.02
5608 12280 4.120331 GGCGCCATCAACCTGTGC 62.120 66.667 24.80 0.00 34.86 4.57
5616 12288 1.451927 GTGGATCAAGGCGCCATCA 60.452 57.895 31.54 1.94 33.66 3.07
5639 12311 2.197465 GGGGAAGTGGTAGAAGGATGT 58.803 52.381 0.00 0.00 0.00 3.06
5640 12312 2.092914 GTGGGGAAGTGGTAGAAGGATG 60.093 54.545 0.00 0.00 0.00 3.51
5649 12321 1.056660 CTACACAGTGGGGAAGTGGT 58.943 55.000 5.31 0.00 37.58 4.16
5663 12335 2.030562 ACTGGTGCGGTGCTACAC 59.969 61.111 0.00 0.00 36.03 2.90
5678 12352 0.549950 CAATCCCATGCTCCCTCACT 59.450 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.