Multiple sequence alignment - TraesCS7D01G009200

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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 TraesCS7D01G009200 chr7D 100.000 5021 0 0 1 5021 4427567 4422547 0.000000e+00 9273.0
1 TraesCS7D01G009200 chr7D 90.305 3208 237 42 925 4086 29405893 29402714 0.000000e+00 4133.0
2 TraesCS7D01G009200 chr7D 89.850 867 58 14 4122 4963 29402711 29401850 0.000000e+00 1086.0
3 TraesCS7D01G009200 chr7D 82.430 922 156 4 1829 2747 4503421 4502503 0.000000e+00 800.0
4 TraesCS7D01G009200 chr7D 79.791 955 181 10 1828 2775 4291490 4290541 0.000000e+00 684.0
5 TraesCS7D01G009200 chr7D 79.256 699 131 12 3336 4024 4412869 4412175 4.550000e-130 475.0
6 TraesCS7D01G009200 chr7D 77.930 657 122 14 3339 3979 4289587 4288938 6.100000e-104 388.0
7 TraesCS7D01G009200 chr7D 89.389 311 30 3 546 854 29406354 29406045 6.100000e-104 388.0
8 TraesCS7D01G009200 chr7D 77.560 664 125 15 3333 3979 29600190 29600846 3.670000e-101 379.0
9 TraesCS7D01G009200 chr7D 73.198 888 198 30 1846 2698 4201392 4200510 8.230000e-73 285.0
10 TraesCS7D01G009200 chr7D 84.831 178 27 0 1842 2019 4508522 4508345 3.990000e-41 180.0
11 TraesCS7D01G009200 chr7D 80.240 167 29 3 2848 3012 421873388 421873552 6.830000e-24 122.0
12 TraesCS7D01G009200 chr7D 91.250 80 7 0 1448 1527 4201779 4201700 5.310000e-20 110.0
13 TraesCS7D01G009200 chr7D 86.735 98 13 0 1429 1526 4793115 4793212 5.310000e-20 110.0
14 TraesCS7D01G009200 chr7D 95.238 42 2 0 508 549 531131573 531131614 3.240000e-07 67.6
15 TraesCS7D01G009200 chr7D 97.368 38 1 0 511 548 148359894 148359857 1.170000e-06 65.8
16 TraesCS7D01G009200 chr7D 91.304 46 4 0 511 556 561621902 561621857 4.200000e-06 63.9
17 TraesCS7D01G009200 chr4A 91.880 3793 202 38 558 4291 739128739 739132484 0.000000e+00 5201.0
18 TraesCS7D01G009200 chr4A 83.833 934 147 2 1842 2772 739079323 739080255 0.000000e+00 885.0
19 TraesCS7D01G009200 chr4A 79.562 959 184 11 1825 2775 739273606 739274560 0.000000e+00 675.0
20 TraesCS7D01G009200 chr4A 79.471 945 187 6 1846 2786 739152648 739153589 0.000000e+00 664.0
21 TraesCS7D01G009200 chr4A 93.350 406 19 4 4616 5021 739132497 739132894 1.200000e-165 593.0
22 TraesCS7D01G009200 chr4A 80.059 677 119 14 3333 3998 739153891 739154562 5.840000e-134 488.0
23 TraesCS7D01G009200 chr4A 94.220 173 10 0 546 718 739128285 739128457 1.070000e-66 265.0
24 TraesCS7D01G009200 chr4A 92.683 82 6 0 1445 1526 739310613 739310694 8.830000e-23 119.0
25 TraesCS7D01G009200 chr4A 87.755 98 12 0 1429 1526 738890283 738890186 1.140000e-21 115.0
26 TraesCS7D01G009200 chr4A 92.308 78 6 0 1448 1525 739079054 739079131 1.480000e-20 111.0
27 TraesCS7D01G009200 chr4A 90.361 83 8 0 1445 1527 739415743 739415825 5.310000e-20 110.0
28 TraesCS7D01G009200 chr7A 93.109 1959 92 17 852 2789 4255327 4253391 0.000000e+00 2830.0
29 TraesCS7D01G009200 chr7A 89.186 1794 138 30 1028 2784 29665494 29663720 0.000000e+00 2187.0
30 TraesCS7D01G009200 chr7A 91.092 1291 100 12 2807 4086 29663280 29661994 0.000000e+00 1733.0
31 TraesCS7D01G009200 chr7A 87.142 1361 131 20 2812 4155 4253320 4251987 0.000000e+00 1504.0
32 TraesCS7D01G009200 chr7A 89.273 867 63 14 4122 4963 29661991 29661130 0.000000e+00 1059.0
33 TraesCS7D01G009200 chr7A 82.260 947 163 4 1829 2772 4329867 4328923 0.000000e+00 813.0
34 TraesCS7D01G009200 chr7A 79.464 672 124 12 3336 3997 4206952 4206285 9.850000e-127 464.0
35 TraesCS7D01G009200 chr7A 77.795 662 126 13 3333 3979 4068370 4067715 6.100000e-104 388.0
36 TraesCS7D01G009200 chr7A 89.032 310 33 1 546 854 29667946 29667637 2.840000e-102 383.0
37 TraesCS7D01G009200 chr7A 93.902 82 5 0 1445 1526 4016872 4016791 1.900000e-24 124.0
38 TraesCS7D01G009200 chr7A 89.000 100 11 0 1429 1528 4070358 4070259 1.900000e-24 124.0
39 TraesCS7D01G009200 chr7A 87.755 98 12 0 1429 1526 4625654 4625751 1.140000e-21 115.0
40 TraesCS7D01G009200 chr7A 87.654 81 10 0 3164 3244 565350174 565350094 1.490000e-15 95.3
41 TraesCS7D01G009200 chr5D 99.018 509 5 0 1 509 559443393 559443901 0.000000e+00 913.0
42 TraesCS7D01G009200 chr5D 98.821 509 6 0 1 509 11230541 11231049 0.000000e+00 907.0
43 TraesCS7D01G009200 chr5D 98.821 509 6 0 1 509 181308533 181309041 0.000000e+00 907.0
44 TraesCS7D01G009200 chr5D 93.478 46 2 1 508 552 525266109 525266154 3.240000e-07 67.6
45 TraesCS7D01G009200 chr6D 98.821 509 6 0 1 509 45998816 45999324 0.000000e+00 907.0
46 TraesCS7D01G009200 chr6D 98.821 509 6 0 1 509 378394110 378393602 0.000000e+00 907.0
47 TraesCS7D01G009200 chr6D 85.714 63 5 3 511 571 448617468 448617408 4.200000e-06 63.9
48 TraesCS7D01G009200 chr3D 98.821 509 6 0 1 509 8704749 8705257 0.000000e+00 907.0
49 TraesCS7D01G009200 chr3D 98.821 509 6 0 1 509 33904408 33903900 0.000000e+00 907.0
50 TraesCS7D01G009200 chr3D 95.122 41 2 0 508 548 608277847 608277887 1.170000e-06 65.8
51 TraesCS7D01G009200 chr1D 98.821 509 6 0 1 509 6594835 6595343 0.000000e+00 907.0
52 TraesCS7D01G009200 chr1D 98.821 509 6 0 1 509 415785339 415784831 0.000000e+00 907.0
53 TraesCS7D01G009200 chr1D 89.157 83 9 0 3164 3246 51912620 51912538 2.470000e-18 104.0
54 TraesCS7D01G009200 chr1D 95.122 41 2 0 508 548 38805529 38805569 1.170000e-06 65.8
55 TraesCS7D01G009200 chr6B 85.294 136 16 3 2848 2981 537553841 537553974 2.440000e-28 137.0
56 TraesCS7D01G009200 chr7B 82.581 155 23 3 2848 3000 44939554 44939706 3.150000e-27 134.0
57 TraesCS7D01G009200 chr2D 81.707 164 26 3 2851 3012 241662043 241661882 3.150000e-27 134.0
58 TraesCS7D01G009200 chr2D 97.368 38 1 0 511 548 624273070 624273033 1.170000e-06 65.8
59 TraesCS7D01G009200 chr2D 97.368 38 1 0 511 548 635890299 635890262 1.170000e-06 65.8
60 TraesCS7D01G009200 chr3B 82.895 152 20 3 2848 2995 328715444 328715593 1.130000e-26 132.0
61 TraesCS7D01G009200 chr2B 89.157 83 9 0 3164 3246 716361233 716361315 2.470000e-18 104.0
62 TraesCS7D01G009200 chr2B 89.796 49 5 0 1873 1921 711321066 711321018 4.200000e-06 63.9


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 TraesCS7D01G009200 chr7D 4422547 4427567 5020 True 9273.000000 9273 100.00000 1 5021 1 chr7D.!!$R2 5020
1 TraesCS7D01G009200 chr7D 29401850 29406354 4504 True 1869.000000 4133 89.84800 546 4963 3 chr7D.!!$R9 4417
2 TraesCS7D01G009200 chr7D 4502503 4503421 918 True 800.000000 800 82.43000 1829 2747 1 chr7D.!!$R3 918
3 TraesCS7D01G009200 chr7D 4288938 4291490 2552 True 536.000000 684 78.86050 1828 3979 2 chr7D.!!$R8 2151
4 TraesCS7D01G009200 chr7D 4412175 4412869 694 True 475.000000 475 79.25600 3336 4024 1 chr7D.!!$R1 688
5 TraesCS7D01G009200 chr7D 29600190 29600846 656 False 379.000000 379 77.56000 3333 3979 1 chr7D.!!$F2 646
6 TraesCS7D01G009200 chr4A 739128285 739132894 4609 False 2019.666667 5201 93.15000 546 5021 3 chr4A.!!$F5 4475
7 TraesCS7D01G009200 chr4A 739273606 739274560 954 False 675.000000 675 79.56200 1825 2775 1 chr4A.!!$F1 950
8 TraesCS7D01G009200 chr4A 739152648 739154562 1914 False 576.000000 664 79.76500 1846 3998 2 chr4A.!!$F6 2152
9 TraesCS7D01G009200 chr4A 739079054 739080255 1201 False 498.000000 885 88.07050 1448 2772 2 chr4A.!!$F4 1324
10 TraesCS7D01G009200 chr7A 4251987 4255327 3340 True 2167.000000 2830 90.12550 852 4155 2 chr7A.!!$R6 3303
11 TraesCS7D01G009200 chr7A 29661130 29667946 6816 True 1340.500000 2187 89.64575 546 4963 4 chr7A.!!$R7 4417
12 TraesCS7D01G009200 chr7A 4328923 4329867 944 True 813.000000 813 82.26000 1829 2772 1 chr7A.!!$R3 943
13 TraesCS7D01G009200 chr7A 4206285 4206952 667 True 464.000000 464 79.46400 3336 3997 1 chr7A.!!$R2 661
14 TraesCS7D01G009200 chr7A 4067715 4070358 2643 True 256.000000 388 83.39750 1429 3979 2 chr7A.!!$R5 2550
15 TraesCS7D01G009200 chr5D 559443393 559443901 508 False 913.000000 913 99.01800 1 509 1 chr5D.!!$F4 508
16 TraesCS7D01G009200 chr5D 11230541 11231049 508 False 907.000000 907 98.82100 1 509 1 chr5D.!!$F1 508
17 TraesCS7D01G009200 chr5D 181308533 181309041 508 False 907.000000 907 98.82100 1 509 1 chr5D.!!$F2 508
18 TraesCS7D01G009200 chr6D 45998816 45999324 508 False 907.000000 907 98.82100 1 509 1 chr6D.!!$F1 508
19 TraesCS7D01G009200 chr6D 378393602 378394110 508 True 907.000000 907 98.82100 1 509 1 chr6D.!!$R1 508
20 TraesCS7D01G009200 chr3D 8704749 8705257 508 False 907.000000 907 98.82100 1 509 1 chr3D.!!$F1 508
21 TraesCS7D01G009200 chr3D 33903900 33904408 508 True 907.000000 907 98.82100 1 509 1 chr3D.!!$R1 508
22 TraesCS7D01G009200 chr1D 6594835 6595343 508 False 907.000000 907 98.82100 1 509 1 chr1D.!!$F1 508
23 TraesCS7D01G009200 chr1D 415784831 415785339 508 True 907.000000 907 98.82100 1 509 1 chr1D.!!$R2 508

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
527 528 0.777446 TTATGGGGGCCTATGGAAGC 59.223 55.000 0.84 0.00 0.00 3.86 F
741 1186 1.195222 CACACCACGTCATGACATGTG 59.805 52.381 25.74 25.74 33.18 3.21 F
1748 4266 0.179156 CATGCAGATCCAAACGGTGC 60.179 55.000 0.00 0.00 34.62 5.01 F
1756 4278 1.009903 TCCAAACGGTGCGTACGATG 61.010 55.000 21.65 7.19 39.99 3.84 F
3557 7247 1.899437 ATCGCATCCCACAACGAGGT 61.899 55.000 0.00 0.00 38.04 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 3887 1.052124 ATCGCCGATTTCCCCTACCA 61.052 55.000 0.00 0.0 0.00 3.25 R
1954 4496 1.296715 GTAGGTGGTGCCAGTGGAG 59.703 63.158 15.20 0.0 40.61 3.86 R
3557 7247 0.457853 GCAGTTGTAGCCGATGTCGA 60.458 55.000 3.62 0.0 43.02 4.20 R
3753 7452 3.663176 CTGCCCACCACACGCTTG 61.663 66.667 0.00 0.0 0.00 4.01 R
4539 8252 0.104855 CCGATCAGAATCTGGGCGAA 59.895 55.000 20.84 0.0 33.11 4.70 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
241 242 6.953743 CCATATACAACTTCGAACAAGTTTCG 59.046 38.462 0.00 0.00 38.32 3.46
392 393 1.807981 CCGCAAGTTATCCGTCGCA 60.808 57.895 0.00 0.00 0.00 5.10
509 510 8.107095 TGCTTATCCACATTAACTAACCTTCTT 58.893 33.333 0.00 0.00 0.00 2.52
510 511 9.609346 GCTTATCCACATTAACTAACCTTCTTA 57.391 33.333 0.00 0.00 0.00 2.10
513 514 8.980481 ATCCACATTAACTAACCTTCTTATGG 57.020 34.615 0.00 0.00 0.00 2.74
514 515 7.343357 TCCACATTAACTAACCTTCTTATGGG 58.657 38.462 0.00 0.00 0.00 4.00
515 516 6.546034 CCACATTAACTAACCTTCTTATGGGG 59.454 42.308 0.00 0.00 0.00 4.96
516 517 6.546034 CACATTAACTAACCTTCTTATGGGGG 59.454 42.308 0.00 0.00 0.00 5.40
517 518 3.664551 AACTAACCTTCTTATGGGGGC 57.335 47.619 0.00 0.00 0.00 5.80
518 519 1.850998 ACTAACCTTCTTATGGGGGCC 59.149 52.381 0.00 0.00 0.00 5.80
519 520 2.136026 CTAACCTTCTTATGGGGGCCT 58.864 52.381 0.84 0.00 0.00 5.19
520 521 2.296943 AACCTTCTTATGGGGGCCTA 57.703 50.000 0.84 0.00 0.00 3.93
521 522 2.533018 ACCTTCTTATGGGGGCCTAT 57.467 50.000 0.84 0.79 0.00 2.57
522 523 2.065799 ACCTTCTTATGGGGGCCTATG 58.934 52.381 0.84 0.00 0.00 2.23
523 524 1.355720 CCTTCTTATGGGGGCCTATGG 59.644 57.143 0.84 0.00 0.00 2.74
524 525 2.348472 CTTCTTATGGGGGCCTATGGA 58.652 52.381 0.84 0.00 0.00 3.41
525 526 2.523841 TCTTATGGGGGCCTATGGAA 57.476 50.000 0.84 0.00 0.00 3.53
526 527 2.348472 TCTTATGGGGGCCTATGGAAG 58.652 52.381 0.84 1.66 0.00 3.46
527 528 0.777446 TTATGGGGGCCTATGGAAGC 59.223 55.000 0.84 0.00 0.00 3.86
531 532 1.772156 GGGGCCTATGGAAGCCTCT 60.772 63.158 0.84 0.00 46.82 3.69
532 533 1.356494 GGGGCCTATGGAAGCCTCTT 61.356 60.000 0.84 0.00 46.82 2.85
533 534 2.884666 GGGGCCTATGGAAGCCTCTTT 61.885 57.143 0.84 0.00 46.82 2.52
534 535 2.443958 GGCCTATGGAAGCCTCTTTT 57.556 50.000 0.00 0.00 46.14 2.27
535 536 2.739943 GGCCTATGGAAGCCTCTTTTT 58.260 47.619 0.00 0.00 46.14 1.94
536 537 2.690497 GGCCTATGGAAGCCTCTTTTTC 59.310 50.000 0.00 0.00 46.14 2.29
537 538 3.625853 GCCTATGGAAGCCTCTTTTTCT 58.374 45.455 0.00 0.00 0.00 2.52
538 539 4.385310 GGCCTATGGAAGCCTCTTTTTCTA 60.385 45.833 0.00 0.00 46.14 2.10
539 540 4.576873 GCCTATGGAAGCCTCTTTTTCTAC 59.423 45.833 0.00 0.00 0.00 2.59
540 541 5.630304 GCCTATGGAAGCCTCTTTTTCTACT 60.630 44.000 0.00 0.00 0.00 2.57
541 542 6.408206 GCCTATGGAAGCCTCTTTTTCTACTA 60.408 42.308 0.00 0.00 0.00 1.82
542 543 7.213678 CCTATGGAAGCCTCTTTTTCTACTAG 58.786 42.308 0.00 0.00 0.00 2.57
543 544 6.628644 ATGGAAGCCTCTTTTTCTACTAGT 57.371 37.500 0.00 0.00 0.00 2.57
544 545 5.794894 TGGAAGCCTCTTTTTCTACTAGTG 58.205 41.667 5.39 0.00 0.00 2.74
614 615 5.935789 GTGACCTTTTAGGCATGTTGTACTA 59.064 40.000 0.00 0.00 39.63 1.82
625 626 7.882179 AGGCATGTTGTACTAAAACTTTTAGG 58.118 34.615 20.55 7.39 0.00 2.69
669 670 6.594284 TCATTTATTCAGACTGAAGATGCG 57.406 37.500 21.78 11.06 40.05 4.73
702 703 6.647067 TCTTCTTAAGTCAGTTTGAGCTAAGC 59.353 38.462 1.63 0.00 0.00 3.09
741 1186 1.195222 CACACCACGTCATGACATGTG 59.805 52.381 25.74 25.74 33.18 3.21
748 1193 3.854240 CACGTCATGACATGTGTAGTCTC 59.146 47.826 24.93 0.00 36.94 3.36
750 1195 4.941873 ACGTCATGACATGTGTAGTCTCTA 59.058 41.667 24.93 0.00 36.94 2.43
778 1223 8.599624 AATTGTGATGAAATTTATCCCTGACT 57.400 30.769 0.00 0.00 0.00 3.41
781 1226 8.908786 TGTGATGAAATTTATCCCTGACTATC 57.091 34.615 0.00 0.00 0.00 2.08
800 1245 8.088365 TGACTATCATGATAAGGATTGTTACCG 58.912 37.037 16.08 3.11 31.34 4.02
805 1250 7.981142 TCATGATAAGGATTGTTACCGTTTTC 58.019 34.615 0.00 0.00 0.00 2.29
914 1406 9.202273 GTGTTAATTTGGAGCATTGAATGTTAA 57.798 29.630 7.05 0.00 0.00 2.01
932 1493 7.640597 ATGTTAAGCCTAAAATTGGTACTCC 57.359 36.000 0.00 0.00 0.00 3.85
933 1494 6.544650 TGTTAAGCCTAAAATTGGTACTCCA 58.455 36.000 0.00 0.00 42.66 3.86
1010 1578 8.753497 ATCTTTTGGATTAAGATGGGTCTAAC 57.247 34.615 0.00 0.00 40.04 2.34
1023 1593 4.138290 TGGGTCTAACTTCATTCGCAAAA 58.862 39.130 0.00 0.00 0.00 2.44
1055 3518 9.347240 AGATGGGTCTAAATTAATGATTCAGTG 57.653 33.333 0.00 0.00 31.36 3.66
1059 3522 8.837389 GGGTCTAAATTAATGATTCAGTGGTAC 58.163 37.037 0.00 0.00 0.00 3.34
1109 3572 3.717400 AAGAGATAAATCGCGCTCTCA 57.283 42.857 20.17 0.00 36.76 3.27
1125 3588 4.747108 CGCTCTCAAAGACTCAAGAAAGAA 59.253 41.667 0.00 0.00 0.00 2.52
1126 3589 5.235186 CGCTCTCAAAGACTCAAGAAAGAAA 59.765 40.000 0.00 0.00 0.00 2.52
1127 3590 6.563753 CGCTCTCAAAGACTCAAGAAAGAAAG 60.564 42.308 0.00 0.00 0.00 2.62
1128 3591 6.481644 GCTCTCAAAGACTCAAGAAAGAAAGA 59.518 38.462 0.00 0.00 0.00 2.52
1129 3592 7.011857 GCTCTCAAAGACTCAAGAAAGAAAGAA 59.988 37.037 0.00 0.00 0.00 2.52
1157 3620 5.277393 GGTCGAAAACTTTCCTCTTCAGTTC 60.277 44.000 0.00 0.00 33.68 3.01
1359 3831 2.699768 CGACGTGGTTAGCCCGGTA 61.700 63.158 0.00 0.00 35.15 4.02
1590 4073 2.305927 CCTATATGTTCTTCCCCGGCAT 59.694 50.000 0.00 0.00 0.00 4.40
1748 4266 0.179156 CATGCAGATCCAAACGGTGC 60.179 55.000 0.00 0.00 34.62 5.01
1756 4278 1.009903 TCCAAACGGTGCGTACGATG 61.010 55.000 21.65 7.19 39.99 3.84
1768 4290 5.332355 GGTGCGTACGATGATTATCACTTTC 60.332 44.000 21.65 0.00 32.67 2.62
1807 4336 6.258947 TGTCGTCTCTCTGTATGTCTATCAAG 59.741 42.308 0.00 0.00 0.00 3.02
1811 4340 5.830457 TCTCTCTGTATGTCTATCAAGTGGG 59.170 44.000 0.00 0.00 0.00 4.61
1932 4474 2.438434 GGCAACATCTCGTGGGGG 60.438 66.667 0.00 0.00 0.00 5.40
2495 5043 2.093658 ACTACTACGCATTGGGAAGGTG 60.094 50.000 7.82 0.00 0.00 4.00
2502 5050 3.254024 ATTGGGAAGGTGCGACGCT 62.254 57.895 22.08 0.00 0.00 5.07
2512 5060 4.059459 GCGACGCTGTGACCAACG 62.059 66.667 13.73 0.00 36.28 4.10
2548 5096 3.473147 CCAGAAGCAGATGTGGGAG 57.527 57.895 0.00 0.00 30.30 4.30
2823 6005 4.381566 GCGATTGTTAACTTGCATTCGTTT 59.618 37.500 7.22 0.00 39.30 3.60
2951 6403 8.638873 TGTTTATTCATCTCAGTCCGTATGTAT 58.361 33.333 0.00 0.00 0.00 2.29
3097 6555 9.429359 TCTGAGAAGATCAAATCTAACTCAAAC 57.571 33.333 18.38 3.21 44.31 2.93
3290 6972 2.952310 GCCATCATGGTTAAGGGACTTC 59.048 50.000 5.31 0.00 42.73 3.01
3458 7148 2.596777 TGGCATCACCATCGGCAT 59.403 55.556 0.00 0.00 46.36 4.40
3557 7247 1.899437 ATCGCATCCCACAACGAGGT 61.899 55.000 0.00 0.00 38.04 3.85
3753 7452 2.617274 GCTGGCCAGGAACGTTGTC 61.617 63.158 33.46 10.16 0.00 3.18
4093 7796 2.017782 TGTCAGACGGATCTAGTCAGC 58.982 52.381 18.92 11.28 40.84 4.26
4109 7812 2.089201 TCAGCAGCACATTCATGGAAG 58.911 47.619 0.00 0.00 0.00 3.46
4119 7823 5.104374 CACATTCATGGAAGGGAAAAATCG 58.896 41.667 0.00 0.00 0.00 3.34
4172 7876 7.621426 GCAGCAGATCATAATATTTTGCATTGC 60.621 37.037 0.46 0.46 32.79 3.56
4212 7916 0.677288 CAGTACACGAGTCCAACCCA 59.323 55.000 0.00 0.00 0.00 4.51
4291 7995 4.439123 CGCTCTTCTCAAAAAGCAAAACTC 59.561 41.667 0.00 0.00 34.39 3.01
4292 7996 4.742167 GCTCTTCTCAAAAAGCAAAACTCC 59.258 41.667 0.00 0.00 34.86 3.85
4293 7997 4.920376 TCTTCTCAAAAAGCAAAACTCCG 58.080 39.130 0.00 0.00 0.00 4.63
4324 8037 2.911926 AAGCTGAAGTGGAGCCCCC 61.912 63.158 0.00 0.00 37.12 5.40
4346 8059 4.878397 CCTCACCTGTATGTCAATCCTTTC 59.122 45.833 0.00 0.00 0.00 2.62
4347 8060 5.338708 CCTCACCTGTATGTCAATCCTTTCT 60.339 44.000 0.00 0.00 0.00 2.52
4362 8075 6.749923 ATCCTTTCTCATTTCTTTTCCGAG 57.250 37.500 0.00 0.00 0.00 4.63
4385 8098 4.627900 GCAGTTTCTGAGCTAGAGGTTTAC 59.372 45.833 0.00 0.00 36.61 2.01
4425 8138 2.159407 GGCTTTTCTGCAAGATCTCTGC 60.159 50.000 17.68 17.68 46.36 4.26
4436 8149 5.235831 TGCAAGATCTCTGCGATTATTTCAG 59.764 40.000 18.64 0.00 30.84 3.02
4449 8162 7.147863 TGCGATTATTTCAGTACCTACAACCTA 60.148 37.037 0.00 0.00 0.00 3.08
4460 8173 8.353684 CAGTACCTACAACCTACAGATCAATAG 58.646 40.741 0.00 0.00 0.00 1.73
4464 8177 5.263968 ACAACCTACAGATCAATAGGACG 57.736 43.478 22.71 16.28 40.53 4.79
4469 8182 7.925043 ACCTACAGATCAATAGGACGTATAG 57.075 40.000 22.71 1.62 40.53 1.31
4473 8186 5.416326 ACAGATCAATAGGACGTATAGGAGC 59.584 44.000 0.00 0.00 0.00 4.70
4477 8190 5.004448 TCAATAGGACGTATAGGAGCTCTG 58.996 45.833 14.64 0.00 0.00 3.35
4478 8191 4.644163 ATAGGACGTATAGGAGCTCTGT 57.356 45.455 14.64 3.93 0.00 3.41
4535 8248 7.628769 ACATATGCAATAACATCACTTGACA 57.371 32.000 1.58 0.00 29.06 3.58
4536 8249 8.229253 ACATATGCAATAACATCACTTGACAT 57.771 30.769 1.58 0.00 29.06 3.06
4537 8250 8.689061 ACATATGCAATAACATCACTTGACATT 58.311 29.630 1.58 0.00 29.06 2.71
4538 8251 9.524106 CATATGCAATAACATCACTTGACATTT 57.476 29.630 0.00 0.00 29.06 2.32
4541 8254 8.296799 TGCAATAACATCACTTGACATTTTTC 57.703 30.769 0.00 0.00 0.00 2.29
4566 8282 4.754114 CCCAGATTCTGATCGGAATTTCTC 59.246 45.833 26.73 16.82 36.24 2.87
4568 8284 5.819379 CCAGATTCTGATCGGAATTTCTCAA 59.181 40.000 26.73 1.13 36.24 3.02
4575 8294 7.885297 TCTGATCGGAATTTCTCAATTTTGTT 58.115 30.769 0.39 0.00 32.35 2.83
4649 8368 5.051891 AGAATGATACAACTTGCTTGCAC 57.948 39.130 0.00 0.00 32.41 4.57
4683 8409 6.959639 TTTTGAGGCATCTAAACTTCAACT 57.040 33.333 3.90 0.00 0.00 3.16
4748 8474 5.518487 CGTTTTCTGTGCATGTTTAAACCTT 59.482 36.000 15.59 0.63 0.00 3.50
4821 8547 8.908786 TTTTTCCTTGCTATCTACCATATCAG 57.091 34.615 0.00 0.00 0.00 2.90
4845 8571 3.126831 GCGATACTCCCTCTGTTTCATG 58.873 50.000 0.00 0.00 0.00 3.07
4846 8572 3.430929 GCGATACTCCCTCTGTTTCATGT 60.431 47.826 0.00 0.00 0.00 3.21
4856 8582 6.212589 TCCCTCTGTTTCATGTATAAGTCACA 59.787 38.462 0.00 0.00 0.00 3.58
4941 8670 8.806429 AGTTTGGGTTGAAAATTTGAAAATCT 57.194 26.923 0.00 0.00 0.00 2.40
4976 8705 6.538945 TTGTACATATCTACAAGCAGGTGA 57.461 37.500 0.00 0.00 32.72 4.02
4982 8711 8.668510 ACATATCTACAAGCAGGTGATAAAAG 57.331 34.615 0.00 0.00 0.00 2.27
4986 8715 0.811281 AAGCAGGTGATAAAAGCGGC 59.189 50.000 0.00 0.00 38.75 6.53
5001 8730 9.516314 GATAAAAGCGGCAGTAAAATAATTTCT 57.484 29.630 1.45 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 242 8.723942 AGAAATTTATATGCATACCCGAGATC 57.276 34.615 8.99 3.14 0.00 2.75
392 393 0.667487 CATCGGATAGCGTGCGGAAT 60.667 55.000 6.26 0.00 42.48 3.01
509 510 1.140134 GGCTTCCATAGGCCCCCATA 61.140 60.000 0.00 0.00 43.40 2.74
510 511 2.473365 GGCTTCCATAGGCCCCCAT 61.473 63.158 0.00 0.00 43.40 4.00
511 512 3.103213 GGCTTCCATAGGCCCCCA 61.103 66.667 0.00 0.00 43.40 4.96
517 518 5.995446 AGTAGAAAAAGAGGCTTCCATAGG 58.005 41.667 0.00 0.00 0.00 2.57
518 519 7.708752 CACTAGTAGAAAAAGAGGCTTCCATAG 59.291 40.741 3.59 0.00 0.00 2.23
519 520 7.180408 ACACTAGTAGAAAAAGAGGCTTCCATA 59.820 37.037 3.59 0.00 0.00 2.74
520 521 6.013293 ACACTAGTAGAAAAAGAGGCTTCCAT 60.013 38.462 3.59 0.00 0.00 3.41
521 522 5.307196 ACACTAGTAGAAAAAGAGGCTTCCA 59.693 40.000 3.59 0.00 0.00 3.53
522 523 5.795972 ACACTAGTAGAAAAAGAGGCTTCC 58.204 41.667 3.59 0.00 0.00 3.46
523 524 6.347806 GCAACACTAGTAGAAAAAGAGGCTTC 60.348 42.308 3.59 0.00 0.00 3.86
524 525 5.470437 GCAACACTAGTAGAAAAAGAGGCTT 59.530 40.000 3.59 0.00 0.00 4.35
525 526 4.998033 GCAACACTAGTAGAAAAAGAGGCT 59.002 41.667 3.59 0.00 0.00 4.58
526 527 4.154375 GGCAACACTAGTAGAAAAAGAGGC 59.846 45.833 3.59 0.00 0.00 4.70
527 528 5.305585 TGGCAACACTAGTAGAAAAAGAGG 58.694 41.667 3.59 0.00 46.17 3.69
544 545 7.977904 TCGATGATGATATGATAAATGGCAAC 58.022 34.615 0.00 0.00 0.00 4.17
647 648 5.203370 GCGCATCTTCAGTCTGAATAAATG 58.797 41.667 15.60 17.79 35.59 2.32
669 670 6.734104 AACTGACTTAAGAAGATGATGTGC 57.266 37.500 10.09 0.00 0.00 4.57
682 683 3.432252 GCGCTTAGCTCAAACTGACTTAA 59.568 43.478 0.00 0.00 44.04 1.85
702 703 1.729517 TGGTCACATTGTTCATACGCG 59.270 47.619 3.53 3.53 0.00 6.01
765 1210 9.566331 TCCTTATCATGATAGTCAGGGATAAAT 57.434 33.333 23.14 0.00 36.76 1.40
771 1216 7.013823 ACAATCCTTATCATGATAGTCAGGG 57.986 40.000 23.14 16.94 0.00 4.45
778 1223 9.621629 AAAACGGTAACAATCCTTATCATGATA 57.378 29.630 11.49 11.49 0.00 2.15
781 1226 7.067008 AGGAAAACGGTAACAATCCTTATCATG 59.933 37.037 0.00 0.00 33.61 3.07
800 1245 4.489249 TCGCCGATCGAGGAAAAC 57.511 55.556 18.66 0.00 43.16 2.43
848 1294 3.963428 AATACAGTTGACGAGAGCCTT 57.037 42.857 0.00 0.00 0.00 4.35
857 1349 7.875971 AGAGATCCAAACAAAATACAGTTGAC 58.124 34.615 0.00 0.00 0.00 3.18
932 1493 5.740569 GCACATGCATACAACAGACTTTATG 59.259 40.000 0.00 0.00 41.59 1.90
933 1494 5.163622 GGCACATGCATACAACAGACTTTAT 60.164 40.000 0.00 0.00 44.36 1.40
1055 3518 0.101939 CGAGGCTAAGGAACGGTACC 59.898 60.000 0.16 0.16 0.00 3.34
1059 3522 2.202892 GCCGAGGCTAAGGAACGG 60.203 66.667 12.15 8.99 45.26 4.44
1083 3546 8.841300 TGAGAGCGCGATTTATCTCTTATATAT 58.159 33.333 12.10 0.00 39.15 0.86
1084 3547 8.209917 TGAGAGCGCGATTTATCTCTTATATA 57.790 34.615 12.10 0.09 39.15 0.86
1085 3548 7.089770 TGAGAGCGCGATTTATCTCTTATAT 57.910 36.000 12.10 0.00 39.15 0.86
1086 3549 6.496338 TGAGAGCGCGATTTATCTCTTATA 57.504 37.500 12.10 0.00 39.15 0.98
1087 3550 5.378292 TGAGAGCGCGATTTATCTCTTAT 57.622 39.130 12.10 0.00 39.15 1.73
1088 3551 4.830826 TGAGAGCGCGATTTATCTCTTA 57.169 40.909 12.10 4.80 39.15 2.10
1089 3552 3.717400 TGAGAGCGCGATTTATCTCTT 57.283 42.857 12.10 0.00 39.15 2.85
1090 3553 3.717400 TTGAGAGCGCGATTTATCTCT 57.283 42.857 12.10 11.29 39.15 3.10
1091 3554 4.045104 TCTTTGAGAGCGCGATTTATCTC 58.955 43.478 12.10 13.87 38.91 2.75
1092 3555 3.799420 GTCTTTGAGAGCGCGATTTATCT 59.201 43.478 12.10 3.87 0.00 1.98
1093 3556 3.799420 AGTCTTTGAGAGCGCGATTTATC 59.201 43.478 12.10 3.98 0.00 1.75
1109 3572 5.297029 CGGGTTCTTTCTTTCTTGAGTCTTT 59.703 40.000 0.00 0.00 0.00 2.52
1125 3588 2.336945 AAGTTTTCGACCGGGTTCTT 57.663 45.000 6.32 0.00 0.00 2.52
1126 3589 2.216046 GAAAGTTTTCGACCGGGTTCT 58.784 47.619 6.32 0.00 0.00 3.01
1127 3590 1.265095 GGAAAGTTTTCGACCGGGTTC 59.735 52.381 6.32 0.00 38.06 3.62
1128 3591 1.134007 AGGAAAGTTTTCGACCGGGTT 60.134 47.619 6.32 0.00 38.06 4.11
1129 3592 0.471191 AGGAAAGTTTTCGACCGGGT 59.529 50.000 6.32 0.00 38.06 5.28
1157 3620 0.179137 TGACTTCATCGCCGCTACAG 60.179 55.000 0.00 0.00 0.00 2.74
1415 3887 1.052124 ATCGCCGATTTCCCCTACCA 61.052 55.000 0.00 0.00 0.00 3.25
1485 3957 1.301623 CGGCTGGAAATGGTACCCA 59.698 57.895 10.07 0.00 38.19 4.51
1590 4073 2.439409 TCCTCCAAACATAGTCGTCGA 58.561 47.619 0.00 0.00 0.00 4.20
1748 4266 7.382488 AGGATTGAAAGTGATAATCATCGTACG 59.618 37.037 9.53 9.53 33.57 3.67
1756 4278 7.930865 AGCTAGTGAGGATTGAAAGTGATAATC 59.069 37.037 0.00 0.00 0.00 1.75
1768 4290 2.425312 AGACGACAGCTAGTGAGGATTG 59.575 50.000 0.00 0.00 0.00 2.67
1807 4336 1.961277 CAGCACGTGTCCTTCCCAC 60.961 63.158 18.38 0.00 0.00 4.61
1811 4340 4.391830 TCAATTAATCAGCACGTGTCCTTC 59.608 41.667 18.38 0.00 0.00 3.46
1954 4496 1.296715 GTAGGTGGTGCCAGTGGAG 59.703 63.158 15.20 0.00 40.61 3.86
2495 5043 4.059459 CGTTGGTCACAGCGTCGC 62.059 66.667 9.80 9.80 44.78 5.19
2502 5050 1.958715 CGTCCATGCGTTGGTCACA 60.959 57.895 5.49 0.00 46.52 3.58
2548 5096 2.223665 CCCAATCGTACCTTAGTCCGAC 60.224 54.545 0.00 0.00 37.16 4.79
2805 5570 8.388319 GCATAATAAACGAATGCAAGTTAACA 57.612 30.769 8.61 0.00 44.27 2.41
3048 6502 6.059787 AGAGCCTAATGTTGAAATGAGTCT 57.940 37.500 0.00 0.00 0.00 3.24
3097 6555 7.039270 TGATGGAAATGCTCAATTTGAATCTG 58.961 34.615 0.01 0.00 38.64 2.90
3290 6972 7.278875 AGAGAGTTCATTAATTCAAGCTAGGG 58.721 38.462 0.00 0.00 0.00 3.53
3458 7148 3.327404 GGGGGAAGACGGAGCCAA 61.327 66.667 0.00 0.00 0.00 4.52
3557 7247 0.457853 GCAGTTGTAGCCGATGTCGA 60.458 55.000 3.62 0.00 43.02 4.20
3753 7452 3.663176 CTGCCCACCACACGCTTG 61.663 66.667 0.00 0.00 0.00 4.01
4093 7796 2.133281 TCCCTTCCATGAATGTGCTG 57.867 50.000 0.00 0.00 0.00 4.41
4109 7812 4.621034 CAGTAACAATGTGCGATTTTTCCC 59.379 41.667 0.00 0.00 0.00 3.97
4119 7823 2.159787 CGAGCAGACAGTAACAATGTGC 60.160 50.000 0.00 0.00 0.00 4.57
4212 7916 0.620700 AGTTTCCGGCCTCACCCTAT 60.621 55.000 0.00 0.00 33.26 2.57
4324 8037 5.738909 AGAAAGGATTGACATACAGGTGAG 58.261 41.667 0.00 0.00 0.00 3.51
4346 8059 4.756084 AACTGCTCGGAAAAGAAATGAG 57.244 40.909 0.00 0.00 0.00 2.90
4347 8060 4.821805 AGAAACTGCTCGGAAAAGAAATGA 59.178 37.500 0.00 0.00 0.00 2.57
4362 8075 3.326836 AACCTCTAGCTCAGAAACTGC 57.673 47.619 0.00 0.00 31.12 4.40
4385 8098 4.067896 AGCCAACTTGAGTTACACATGAG 58.932 43.478 0.00 0.00 36.32 2.90
4425 8138 8.192774 TGTAGGTTGTAGGTACTGAAATAATCG 58.807 37.037 0.00 0.00 41.52 3.34
4436 8149 7.504911 TCCTATTGATCTGTAGGTTGTAGGTAC 59.495 40.741 17.86 0.00 38.84 3.34
4449 8162 5.416326 GCTCCTATACGTCCTATTGATCTGT 59.584 44.000 0.00 0.00 0.00 3.41
4460 8173 5.708877 ATAAACAGAGCTCCTATACGTCC 57.291 43.478 10.93 0.00 0.00 4.79
4464 8177 7.553881 TGCAAAATAAACAGAGCTCCTATAC 57.446 36.000 10.93 0.00 0.00 1.47
4469 8182 6.194796 TGTATGCAAAATAAACAGAGCTCC 57.805 37.500 10.93 0.00 0.00 4.70
4517 8230 7.439490 CGAAAAATGTCAAGTGATGTTATTGC 58.561 34.615 0.00 0.00 0.00 3.56
4519 8232 6.586082 GGCGAAAAATGTCAAGTGATGTTATT 59.414 34.615 0.00 0.00 0.00 1.40
4526 8239 2.293122 CTGGGCGAAAAATGTCAAGTGA 59.707 45.455 0.00 0.00 0.00 3.41
4527 8240 2.293122 TCTGGGCGAAAAATGTCAAGTG 59.707 45.455 0.00 0.00 0.00 3.16
4528 8241 2.582052 TCTGGGCGAAAAATGTCAAGT 58.418 42.857 0.00 0.00 0.00 3.16
4530 8243 3.826157 AGAATCTGGGCGAAAAATGTCAA 59.174 39.130 0.00 0.00 0.00 3.18
4531 8244 3.191162 CAGAATCTGGGCGAAAAATGTCA 59.809 43.478 1.53 0.00 0.00 3.58
4532 8245 3.440173 TCAGAATCTGGGCGAAAAATGTC 59.560 43.478 10.71 0.00 31.51 3.06
4533 8246 3.420893 TCAGAATCTGGGCGAAAAATGT 58.579 40.909 10.71 0.00 31.51 2.71
4534 8247 4.604976 GATCAGAATCTGGGCGAAAAATG 58.395 43.478 10.71 0.00 31.51 2.32
4535 8248 3.313526 CGATCAGAATCTGGGCGAAAAAT 59.686 43.478 16.45 0.00 33.11 1.82
4536 8249 2.677836 CGATCAGAATCTGGGCGAAAAA 59.322 45.455 16.45 0.00 33.11 1.94
4537 8250 2.279741 CGATCAGAATCTGGGCGAAAA 58.720 47.619 16.45 0.00 33.11 2.29
4538 8251 1.473257 CCGATCAGAATCTGGGCGAAA 60.473 52.381 20.84 0.00 33.11 3.46
4539 8252 0.104855 CCGATCAGAATCTGGGCGAA 59.895 55.000 20.84 0.00 33.11 4.70
4541 8254 0.104855 TTCCGATCAGAATCTGGGCG 59.895 55.000 10.71 13.39 31.51 6.13
4568 8284 9.337091 GCGTGTCTTGTATAATGTAAACAAAAT 57.663 29.630 0.00 0.00 33.05 1.82
4575 8294 4.996344 TCCGCGTGTCTTGTATAATGTAA 58.004 39.130 4.92 0.00 0.00 2.41
4586 8305 2.572191 TCGATATTTCCGCGTGTCTT 57.428 45.000 4.92 0.00 0.00 3.01
4683 8409 1.879380 CCGATTGAAGGTGCAAGTTGA 59.121 47.619 7.16 0.00 0.00 3.18
4748 8474 7.600375 GTCATCACAGAGAAAAATAGACACTGA 59.400 37.037 0.00 0.00 0.00 3.41
4845 8571 7.391148 ACCATGTCCAAAATGTGACTTATAC 57.609 36.000 0.00 0.00 32.67 1.47
4846 8572 8.415950 AAACCATGTCCAAAATGTGACTTATA 57.584 30.769 0.00 0.00 32.67 0.98
4856 8582 5.867903 TTGACTGAAACCATGTCCAAAAT 57.132 34.783 0.00 0.00 0.00 1.82
4963 8692 3.063997 CCGCTTTTATCACCTGCTTGTAG 59.936 47.826 0.00 0.00 0.00 2.74
4982 8711 9.595357 GTAAGATAGAAATTATTTTACTGCCGC 57.405 33.333 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.