Multiple sequence alignment - TraesCS7B01G391700

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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 TraesCS7B01G391700 chr7B 100.000 3668 0 0 1 3668 658172620 658176287 0.000000e+00 6774.0
1 TraesCS7B01G391700 chr7B 95.228 901 40 2 968 1868 658139326 658140223 0.000000e+00 1423.0
2 TraesCS7B01G391700 chr7B 94.505 546 30 0 1 546 567993858 567994403 0.000000e+00 843.0
3 TraesCS7B01G391700 chr7B 98.571 140 2 0 696 835 658131262 658131401 7.870000e-62 248.0
4 TraesCS7B01G391700 chr7B 91.667 144 4 1 837 972 658135851 658135994 3.740000e-45 193.0
5 TraesCS7B01G391700 chr7D 90.853 2777 169 40 802 3532 587102249 587104986 0.000000e+00 3642.0
6 TraesCS7B01G391700 chr7D 85.714 203 16 8 568 768 587102056 587102247 6.210000e-48 202.0
7 TraesCS7B01G391700 chr7A 91.283 2650 154 28 928 3532 678953356 678955973 0.000000e+00 3542.0
8 TraesCS7B01G391700 chr7A 94.017 117 7 0 756 872 678951291 678951407 1.050000e-40 178.0
9 TraesCS7B01G391700 chr7A 84.277 159 16 7 568 724 678951137 678951288 2.950000e-31 147.0
10 TraesCS7B01G391700 chr1D 85.476 2458 291 32 805 3228 366873700 366876125 0.000000e+00 2501.0
11 TraesCS7B01G391700 chr1A 85.151 2458 298 38 805 3228 465343538 465341114 0.000000e+00 2455.0
12 TraesCS7B01G391700 chr1A 79.219 640 101 18 2096 2716 465340726 465340100 2.040000e-112 416.0
13 TraesCS7B01G391700 chr1A 80.876 251 40 7 1169 1417 465344605 465344361 1.340000e-44 191.0
14 TraesCS7B01G391700 chr1A 92.593 81 5 1 730 809 465343679 465343599 8.320000e-22 115.0
15 TraesCS7B01G391700 chr1B 84.550 2479 299 40 805 3237 490723176 490720736 0.000000e+00 2379.0
16 TraesCS7B01G391700 chr1B 85.925 1087 133 13 994 2075 490446548 490447619 0.000000e+00 1142.0
17 TraesCS7B01G391700 chr1B 78.319 226 37 8 1197 1417 490724217 490723999 6.390000e-28 135.0
18 TraesCS7B01G391700 chr1B 92.593 81 5 1 730 809 490723318 490723238 8.320000e-22 115.0
19 TraesCS7B01G391700 chr5B 97.137 524 15 0 1 524 530709391 530709914 0.000000e+00 885.0
20 TraesCS7B01G391700 chr5B 95.903 537 22 0 1 537 677650829 677651365 0.000000e+00 870.0
21 TraesCS7B01G391700 chr5B 95.857 531 22 0 1 531 606280172 606279642 0.000000e+00 859.0
22 TraesCS7B01G391700 chr3B 95.788 546 23 0 1 546 685611870 685611325 0.000000e+00 881.0
23 TraesCS7B01G391700 chr3B 94.872 546 28 0 1 546 820524035 820524580 0.000000e+00 854.0
24 TraesCS7B01G391700 chr6B 95.580 543 22 2 4 546 478881121 478880581 0.000000e+00 869.0
25 TraesCS7B01G391700 chr6B 95.055 546 26 1 1 546 116328235 116328779 0.000000e+00 857.0
26 TraesCS7B01G391700 chr6B 95.660 530 23 0 1 530 51383918 51383389 0.000000e+00 852.0
27 TraesCS7B01G391700 chr2D 95.833 72 3 0 3565 3636 325242267 325242196 2.310000e-22 117.0
28 TraesCS7B01G391700 chr4B 80.153 131 18 6 2545 2675 74442814 74442936 1.400000e-14 91.6
29 TraesCS7B01G391700 chr4A 79.851 134 19 6 2545 2678 546297261 546297136 1.400000e-14 91.6
30 TraesCS7B01G391700 chr4D 79.389 131 19 6 2545 2675 50642875 50642997 6.530000e-13 86.1


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 TraesCS7B01G391700 chr7B 658172620 658176287 3667 False 6774.000000 6774 100.00000 1 3668 1 chr7B.!!$F3 3667
1 TraesCS7B01G391700 chr7B 567993858 567994403 545 False 843.000000 843 94.50500 1 546 1 chr7B.!!$F1 545
2 TraesCS7B01G391700 chr7B 658135851 658140223 4372 False 808.000000 1423 93.44750 837 1868 2 chr7B.!!$F4 1031
3 TraesCS7B01G391700 chr7D 587102056 587104986 2930 False 1922.000000 3642 88.28350 568 3532 2 chr7D.!!$F1 2964
4 TraesCS7B01G391700 chr7A 678951137 678955973 4836 False 1289.000000 3542 89.85900 568 3532 3 chr7A.!!$F1 2964
5 TraesCS7B01G391700 chr1D 366873700 366876125 2425 False 2501.000000 2501 85.47600 805 3228 1 chr1D.!!$F1 2423
6 TraesCS7B01G391700 chr1A 465340100 465344605 4505 True 794.250000 2455 84.45975 730 3228 4 chr1A.!!$R1 2498
7 TraesCS7B01G391700 chr1B 490446548 490447619 1071 False 1142.000000 1142 85.92500 994 2075 1 chr1B.!!$F1 1081
8 TraesCS7B01G391700 chr1B 490720736 490724217 3481 True 876.333333 2379 85.15400 730 3237 3 chr1B.!!$R1 2507
9 TraesCS7B01G391700 chr5B 530709391 530709914 523 False 885.000000 885 97.13700 1 524 1 chr5B.!!$F1 523
10 TraesCS7B01G391700 chr5B 677650829 677651365 536 False 870.000000 870 95.90300 1 537 1 chr5B.!!$F2 536
11 TraesCS7B01G391700 chr5B 606279642 606280172 530 True 859.000000 859 95.85700 1 531 1 chr5B.!!$R1 530
12 TraesCS7B01G391700 chr3B 685611325 685611870 545 True 881.000000 881 95.78800 1 546 1 chr3B.!!$R1 545
13 TraesCS7B01G391700 chr3B 820524035 820524580 545 False 854.000000 854 94.87200 1 546 1 chr3B.!!$F1 545
14 TraesCS7B01G391700 chr6B 478880581 478881121 540 True 869.000000 869 95.58000 4 546 1 chr6B.!!$R2 542
15 TraesCS7B01G391700 chr6B 116328235 116328779 544 False 857.000000 857 95.05500 1 546 1 chr6B.!!$F1 545
16 TraesCS7B01G391700 chr6B 51383389 51383918 529 True 852.000000 852 95.66000 1 530 1 chr6B.!!$R1 529

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
558 559 0.035881 CAGATGCGTATCCCTGCCAT 59.964 55.0 10.09 0.0 33.64 4.40 F
560 561 0.250467 GATGCGTATCCCTGCCATGT 60.250 55.0 1.49 0.0 0.00 3.21 F
909 2752 0.390603 GCACTGGCCATACACGTACA 60.391 55.0 5.51 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 7798 1.456287 GTTGGACAGGAACAGCCCT 59.544 57.895 0.0 0.0 37.37 5.19 R
2651 8237 3.838271 ATCATCGCCGACCGCACT 61.838 61.111 0.0 0.0 37.30 4.40 R
2948 8537 0.982673 CGCCGTTGTAGTCGAAGAAG 59.017 55.000 0.0 0.0 39.69 2.85 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
142 143 1.933181 CGCCGCAGATGAAGAATAACA 59.067 47.619 0.00 0.00 0.00 2.41
170 171 4.391830 TCAGAAAAATCCAATCCGAAGACG 59.608 41.667 0.00 0.00 39.43 4.18
203 204 1.726892 CGAACAACGACGAGATCCGAA 60.727 52.381 0.00 0.00 45.77 4.30
347 348 1.535896 CGTCTCGTCTTCCTGAACAGA 59.464 52.381 3.19 0.00 0.00 3.41
375 376 5.774498 AACCCTAGCAAAACTGAAAGAAG 57.226 39.130 0.00 0.00 37.43 2.85
546 547 2.286294 GCTACAAAGGATGACAGATGCG 59.714 50.000 0.00 0.00 0.00 4.73
547 548 2.479566 ACAAAGGATGACAGATGCGT 57.520 45.000 0.00 0.00 0.00 5.24
548 549 3.610040 ACAAAGGATGACAGATGCGTA 57.390 42.857 0.00 0.00 0.00 4.42
549 550 4.142609 ACAAAGGATGACAGATGCGTAT 57.857 40.909 0.00 0.00 0.00 3.06
550 551 4.122776 ACAAAGGATGACAGATGCGTATC 58.877 43.478 5.22 5.22 0.00 2.24
551 552 3.393089 AAGGATGACAGATGCGTATCC 57.607 47.619 10.09 0.00 38.03 2.59
552 553 1.620819 AGGATGACAGATGCGTATCCC 59.379 52.381 10.09 3.15 38.42 3.85
553 554 1.620819 GGATGACAGATGCGTATCCCT 59.379 52.381 10.09 0.00 33.64 4.20
554 555 2.611473 GGATGACAGATGCGTATCCCTG 60.611 54.545 10.09 5.59 33.64 4.45
555 556 0.104855 TGACAGATGCGTATCCCTGC 59.895 55.000 10.09 0.00 33.64 4.85
556 557 0.601311 GACAGATGCGTATCCCTGCC 60.601 60.000 10.09 0.00 33.64 4.85
558 559 0.035881 CAGATGCGTATCCCTGCCAT 59.964 55.000 10.09 0.00 33.64 4.40
559 560 0.035881 AGATGCGTATCCCTGCCATG 59.964 55.000 10.09 0.00 33.64 3.66
560 561 0.250467 GATGCGTATCCCTGCCATGT 60.250 55.000 1.49 0.00 0.00 3.21
561 562 0.250467 ATGCGTATCCCTGCCATGTC 60.250 55.000 0.00 0.00 0.00 3.06
562 563 1.337384 TGCGTATCCCTGCCATGTCT 61.337 55.000 0.00 0.00 0.00 3.41
564 565 1.276421 GCGTATCCCTGCCATGTCTAT 59.724 52.381 0.00 0.00 0.00 1.98
565 566 2.496070 GCGTATCCCTGCCATGTCTATA 59.504 50.000 0.00 0.00 0.00 1.31
568 569 4.220821 CGTATCCCTGCCATGTCTATAACT 59.779 45.833 0.00 0.00 0.00 2.24
569 570 4.899352 ATCCCTGCCATGTCTATAACTC 57.101 45.455 0.00 0.00 0.00 3.01
570 571 2.972713 TCCCTGCCATGTCTATAACTCC 59.027 50.000 0.00 0.00 0.00 3.85
574 575 3.743521 TGCCATGTCTATAACTCCATGC 58.256 45.455 0.00 0.00 34.69 4.06
592 593 1.202687 TGCTCAACTTGTCCACTGGAG 60.203 52.381 0.00 0.00 29.39 3.86
597 598 2.348411 ACTTGTCCACTGGAGTTTGG 57.652 50.000 0.00 0.00 29.39 3.28
607 608 5.104277 TCCACTGGAGTTTGGTCTCTTAAAA 60.104 40.000 0.00 0.00 35.11 1.52
609 610 6.294176 CCACTGGAGTTTGGTCTCTTAAAATG 60.294 42.308 0.00 0.00 35.11 2.32
637 638 2.094659 CGGCCTGACACTACGCTTG 61.095 63.158 0.00 0.00 0.00 4.01
659 660 4.022935 TGCCAGTGATGAACTTCAACATTC 60.023 41.667 5.15 0.00 36.83 2.67
752 971 3.817084 TGCTTAATGGTAGCTGCATGATC 59.183 43.478 3.61 0.00 39.38 2.92
892 1889 0.539669 TGAGTCCGACTCCAAGAGCA 60.540 55.000 23.01 3.23 44.44 4.26
904 2747 1.089920 CAAGAGCACTGGCCATACAC 58.910 55.000 5.51 0.00 42.56 2.90
909 2752 0.390603 GCACTGGCCATACACGTACA 60.391 55.000 5.51 0.00 0.00 2.90
986 6528 0.590195 CCGGCGCTCTACTTACGTAT 59.410 55.000 7.64 0.00 0.00 3.06
1201 6755 2.159476 GCGGACATGTTCTACGTCTACA 60.159 50.000 0.00 0.00 0.00 2.74
1209 6763 1.527034 TCTACGTCTACAACCACGCT 58.473 50.000 0.00 0.00 39.73 5.07
1347 6901 3.069318 GAGTTCCTCGGCCTCGGT 61.069 66.667 0.00 0.00 36.95 4.69
1697 7254 2.577059 CTTCTTCGGCTACGGGCA 59.423 61.111 5.12 0.00 44.01 5.36
1861 7418 1.908066 CTTCAACGGCCGGCAGTTAC 61.908 60.000 38.31 16.71 33.36 2.50
1878 7435 4.052229 CACGAAGACCCCGTCGCT 62.052 66.667 0.00 0.00 45.79 4.93
1947 7504 3.841758 GGTAACGACGGGCCGGAT 61.842 66.667 31.78 10.45 0.00 4.18
2055 7612 2.430367 GAGGGCACGACCTTGGTT 59.570 61.111 0.00 0.00 42.10 3.67
2088 7645 3.948719 GCCGGAACCCCACACAGA 61.949 66.667 5.05 0.00 0.00 3.41
2406 7966 2.426023 GTGGTGGACACGAAGCCT 59.574 61.111 0.00 0.00 40.85 4.58
2506 8066 4.212913 GCTCGCTCATCCTCGCCA 62.213 66.667 0.00 0.00 0.00 5.69
2507 8067 2.733301 CTCGCTCATCCTCGCCAT 59.267 61.111 0.00 0.00 0.00 4.40
2744 8330 1.008424 CATCGAGTACGCAGCCGAT 60.008 57.895 0.00 0.00 41.72 4.18
2758 8347 4.630785 CGATCCGCTCGCGATGGT 62.631 66.667 22.36 12.73 41.14 3.55
2813 8402 3.755628 GGCCTGGTCTACGACGCA 61.756 66.667 0.00 0.00 32.65 5.24
2831 8420 0.108329 CAGGGCCGAACGACTACATT 60.108 55.000 0.00 0.00 0.00 2.71
2933 8522 3.793801 GCGCGACTCTTGATCTCAACTAT 60.794 47.826 12.10 0.00 0.00 2.12
2948 8537 0.030369 ACTATCCGTCGTTCATCGCC 59.970 55.000 0.00 0.00 39.67 5.54
2988 8577 1.446272 GAGAAGACGTTCGCCAGGG 60.446 63.158 0.00 0.00 37.79 4.45
3107 8696 1.667830 CGGGAAGCACGAGAAGCAA 60.668 57.895 0.00 0.00 0.00 3.91
3119 8708 2.352030 CGAGAAGCAAAGGTACACGGTA 60.352 50.000 0.00 0.00 0.00 4.02
3139 8728 3.628982 GGTTCGGGTTGGGGACGA 61.629 66.667 0.00 0.00 34.47 4.20
3248 8837 1.000233 CGTCGGCGAACTTTTCTCGA 61.000 55.000 12.92 0.00 41.33 4.04
3281 8942 0.721718 GCGTGCACAGATCCAACTAC 59.278 55.000 18.64 0.00 0.00 2.73
3308 8969 5.830991 ACCATACGCCAATACATTATGGTTT 59.169 36.000 5.87 0.00 46.76 3.27
3309 8970 6.999272 ACCATACGCCAATACATTATGGTTTA 59.001 34.615 5.87 0.00 46.76 2.01
3310 8971 7.668052 ACCATACGCCAATACATTATGGTTTAT 59.332 33.333 5.87 0.00 46.76 1.40
3311 8972 7.967854 CCATACGCCAATACATTATGGTTTATG 59.032 37.037 0.00 0.00 39.00 1.90
3313 8974 6.065374 ACGCCAATACATTATGGTTTATGGA 58.935 36.000 0.00 0.00 39.00 3.41
3314 8975 6.206634 ACGCCAATACATTATGGTTTATGGAG 59.793 38.462 0.00 2.72 39.00 3.86
3436 9104 8.911965 AGATATACATACATAGATGTCCTGCAG 58.088 37.037 6.78 6.78 40.54 4.41
3491 9373 7.472334 ACTATGATTTCACTTTGGCAGAATT 57.528 32.000 0.00 0.00 0.00 2.17
3509 9391 1.714794 TTTTGTGCCACACCAAAACG 58.285 45.000 0.00 0.00 32.73 3.60
3517 9399 1.456705 ACACCAAAACGCCACCCAT 60.457 52.632 0.00 0.00 0.00 4.00
3518 9400 1.045911 ACACCAAAACGCCACCCATT 61.046 50.000 0.00 0.00 0.00 3.16
3532 9414 1.768870 ACCCATTATTGTCCTCCTCCG 59.231 52.381 0.00 0.00 0.00 4.63
3533 9415 1.543429 CCCATTATTGTCCTCCTCCGC 60.543 57.143 0.00 0.00 0.00 5.54
3534 9416 1.543429 CCATTATTGTCCTCCTCCGCC 60.543 57.143 0.00 0.00 0.00 6.13
3535 9417 0.393077 ATTATTGTCCTCCTCCGCCG 59.607 55.000 0.00 0.00 0.00 6.46
3536 9418 2.306255 TTATTGTCCTCCTCCGCCGC 62.306 60.000 0.00 0.00 0.00 6.53
3551 9433 3.777925 CGCCGAGGCAACGTTGAG 61.778 66.667 31.62 17.40 46.39 3.02
3552 9434 2.357034 GCCGAGGCAACGTTGAGA 60.357 61.111 31.62 0.00 46.39 3.27
3554 9436 1.503818 GCCGAGGCAACGTTGAGAAA 61.504 55.000 31.62 0.00 46.39 2.52
3555 9437 0.941542 CCGAGGCAACGTTGAGAAAA 59.058 50.000 31.62 0.00 46.39 2.29
3556 9438 1.535462 CCGAGGCAACGTTGAGAAAAT 59.465 47.619 31.62 9.49 46.39 1.82
3557 9439 2.574322 CGAGGCAACGTTGAGAAAATG 58.426 47.619 31.62 9.77 46.39 2.32
3558 9440 2.665519 CGAGGCAACGTTGAGAAAATGG 60.666 50.000 31.62 7.70 46.39 3.16
3559 9441 1.613437 AGGCAACGTTGAGAAAATGGG 59.387 47.619 31.62 1.26 46.39 4.00
3561 9443 2.554893 GGCAACGTTGAGAAAATGGGTA 59.445 45.455 31.62 0.00 0.00 3.69
3564 9446 4.261447 GCAACGTTGAGAAAATGGGTACTT 60.261 41.667 31.62 0.00 0.00 2.24
3565 9447 5.212194 CAACGTTGAGAAAATGGGTACTTG 58.788 41.667 23.90 0.00 0.00 3.16
3566 9448 4.710324 ACGTTGAGAAAATGGGTACTTGA 58.290 39.130 0.00 0.00 0.00 3.02
3567 9449 5.313712 ACGTTGAGAAAATGGGTACTTGAT 58.686 37.500 0.00 0.00 0.00 2.57
3568 9450 5.181245 ACGTTGAGAAAATGGGTACTTGATG 59.819 40.000 0.00 0.00 0.00 3.07
3569 9451 5.411361 CGTTGAGAAAATGGGTACTTGATGA 59.589 40.000 0.00 0.00 0.00 2.92
3570 9452 6.072728 CGTTGAGAAAATGGGTACTTGATGAA 60.073 38.462 0.00 0.00 0.00 2.57
3572 9454 5.415701 TGAGAAAATGGGTACTTGATGAAGC 59.584 40.000 0.00 0.00 31.68 3.86
3573 9455 5.324409 AGAAAATGGGTACTTGATGAAGCA 58.676 37.500 0.00 0.00 31.68 3.91
3575 9457 7.118723 AGAAAATGGGTACTTGATGAAGCATA 58.881 34.615 0.00 0.00 31.68 3.14
3576 9458 6.699575 AAATGGGTACTTGATGAAGCATAC 57.300 37.500 0.00 0.00 31.68 2.39
3577 9459 4.150897 TGGGTACTTGATGAAGCATACC 57.849 45.455 3.89 3.89 33.12 2.73
3578 9460 3.118038 TGGGTACTTGATGAAGCATACCC 60.118 47.826 18.38 18.38 44.39 3.69
3579 9461 3.136626 GGGTACTTGATGAAGCATACCCT 59.863 47.826 18.09 0.00 42.59 4.34
3581 9463 5.298347 GGTACTTGATGAAGCATACCCTAC 58.702 45.833 1.63 0.00 29.92 3.18
3582 9464 4.423625 ACTTGATGAAGCATACCCTACC 57.576 45.455 0.00 0.00 31.68 3.18
3583 9465 3.780294 ACTTGATGAAGCATACCCTACCA 59.220 43.478 0.00 0.00 31.68 3.25
3584 9466 3.838244 TGATGAAGCATACCCTACCAC 57.162 47.619 0.00 0.00 0.00 4.16
3585 9467 3.111484 TGATGAAGCATACCCTACCACA 58.889 45.455 0.00 0.00 0.00 4.17
3586 9468 3.521531 TGATGAAGCATACCCTACCACAA 59.478 43.478 0.00 0.00 0.00 3.33
3587 9469 4.018870 TGATGAAGCATACCCTACCACAAA 60.019 41.667 0.00 0.00 0.00 2.83
3589 9471 3.073209 TGAAGCATACCCTACCACAAACA 59.927 43.478 0.00 0.00 0.00 2.83
3590 9472 4.263727 TGAAGCATACCCTACCACAAACAT 60.264 41.667 0.00 0.00 0.00 2.71
3592 9474 2.099098 GCATACCCTACCACAAACATGC 59.901 50.000 0.00 0.00 0.00 4.06
3593 9475 2.500392 TACCCTACCACAAACATGCC 57.500 50.000 0.00 0.00 0.00 4.40
3594 9476 0.251608 ACCCTACCACAAACATGCCC 60.252 55.000 0.00 0.00 0.00 5.36
3597 9479 0.608035 CTACCACAAACATGCCCGGT 60.608 55.000 0.00 0.00 0.00 5.28
3598 9480 0.691332 TACCACAAACATGCCCGGTA 59.309 50.000 0.00 0.00 0.00 4.02
3600 9482 1.282447 ACCACAAACATGCCCGGTATA 59.718 47.619 0.00 0.00 0.00 1.47
3601 9483 1.673920 CCACAAACATGCCCGGTATAC 59.326 52.381 0.00 0.00 0.00 1.47
3602 9484 2.360844 CACAAACATGCCCGGTATACA 58.639 47.619 5.01 0.00 0.00 2.29
3604 9486 3.013921 ACAAACATGCCCGGTATACAAG 58.986 45.455 5.01 0.00 0.00 3.16
3607 9489 1.834896 ACATGCCCGGTATACAAGTCA 59.165 47.619 5.01 0.00 0.00 3.41
3608 9490 2.210116 CATGCCCGGTATACAAGTCAC 58.790 52.381 5.01 0.00 0.00 3.67
3611 9493 0.819582 CCCGGTATACAAGTCACGGT 59.180 55.000 12.88 0.00 39.68 4.83
3612 9494 1.470285 CCCGGTATACAAGTCACGGTG 60.470 57.143 12.88 0.56 39.68 4.94
3614 9496 2.094597 CCGGTATACAAGTCACGGTGAA 60.095 50.000 13.23 0.00 36.78 3.18
3615 9497 3.429822 CCGGTATACAAGTCACGGTGAAT 60.430 47.826 13.23 9.14 36.78 2.57
3617 9499 4.736793 CGGTATACAAGTCACGGTGAATAC 59.263 45.833 13.23 15.16 0.00 1.89
3618 9500 5.653507 GGTATACAAGTCACGGTGAATACA 58.346 41.667 21.98 9.49 0.00 2.29
3619 9501 5.517770 GGTATACAAGTCACGGTGAATACAC 59.482 44.000 21.98 9.52 45.27 2.90
3631 9513 3.331150 GTGAATACACCGGTCAATGACA 58.669 45.455 15.86 3.12 40.74 3.58
3633 9515 4.000325 TGAATACACCGGTCAATGACAAG 59.000 43.478 15.86 7.95 33.68 3.16
3635 9517 0.250727 ACACCGGTCAATGACAAGGG 60.251 55.000 23.81 18.84 36.63 3.95
3636 9518 0.036164 CACCGGTCAATGACAAGGGA 59.964 55.000 23.81 0.00 36.63 4.20
3639 9521 1.553248 CCGGTCAATGACAAGGGACTA 59.447 52.381 15.86 0.00 38.49 2.59
3640 9522 2.618053 CGGTCAATGACAAGGGACTAC 58.382 52.381 15.86 0.00 38.49 2.73
3641 9523 2.028476 CGGTCAATGACAAGGGACTACA 60.028 50.000 15.86 0.00 38.49 2.74
3643 9525 3.600388 GTCAATGACAAGGGACTACAGG 58.400 50.000 8.74 0.00 38.49 4.00
3644 9526 2.027192 TCAATGACAAGGGACTACAGGC 60.027 50.000 0.00 0.00 38.49 4.85
3647 9529 0.108756 GACAAGGGACTACAGGCGAC 60.109 60.000 0.00 0.00 38.49 5.19
3648 9530 0.542232 ACAAGGGACTACAGGCGACT 60.542 55.000 0.00 0.00 38.49 4.18
3649 9531 1.272313 ACAAGGGACTACAGGCGACTA 60.272 52.381 0.00 0.00 38.49 2.59
3650 9532 2.032620 CAAGGGACTACAGGCGACTAT 58.967 52.381 0.00 0.00 38.49 2.12
3651 9533 1.693627 AGGGACTACAGGCGACTATG 58.306 55.000 0.00 0.00 35.01 2.23
3652 9534 0.674534 GGGACTACAGGCGACTATGG 59.325 60.000 0.00 0.00 40.21 2.74
3653 9535 0.032267 GGACTACAGGCGACTATGGC 59.968 60.000 0.00 0.00 40.21 4.40
3654 9536 0.317938 GACTACAGGCGACTATGGCG 60.318 60.000 0.00 0.00 40.21 5.69
3655 9537 1.007271 CTACAGGCGACTATGGCGG 60.007 63.158 0.00 0.00 40.21 6.13
3662 9544 3.104766 GACTATGGCGGTCGTCGA 58.895 61.111 0.00 0.00 42.43 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.102554 CAACAAGTTGTGCCCGACA 58.897 52.632 9.79 0.00 35.92 4.35
69 70 2.203972 TTAGCACGACGACTTCCCGG 62.204 60.000 0.00 0.00 0.00 5.73
142 143 8.213679 TCTTCGGATTGGATTTTTCTGATCTAT 58.786 33.333 0.00 0.00 0.00 1.98
170 171 1.122849 TTGTTCGTCTACGTTCGTGC 58.877 50.000 8.14 0.00 40.80 5.34
203 204 5.126067 CGGATCTATCTTTGGTGGATTTGT 58.874 41.667 0.00 0.00 0.00 2.83
347 348 4.020543 TCAGTTTTGCTAGGGTTTGTGTT 58.979 39.130 0.00 0.00 0.00 3.32
375 376 1.063616 GAGGGCTCCGTTTTTAATCGC 59.936 52.381 0.00 0.00 0.00 4.58
447 448 3.394836 GCAGGTCCGCCTCCTCTT 61.395 66.667 0.00 0.00 44.97 2.85
546 547 5.337652 GGAGTTATAGACATGGCAGGGATAC 60.338 48.000 0.00 0.00 0.00 2.24
547 548 4.777896 GGAGTTATAGACATGGCAGGGATA 59.222 45.833 0.00 0.00 0.00 2.59
548 549 3.584848 GGAGTTATAGACATGGCAGGGAT 59.415 47.826 0.00 0.00 0.00 3.85
549 550 2.972713 GGAGTTATAGACATGGCAGGGA 59.027 50.000 0.00 0.00 0.00 4.20
550 551 2.705658 TGGAGTTATAGACATGGCAGGG 59.294 50.000 0.00 0.00 0.00 4.45
551 552 4.321718 CATGGAGTTATAGACATGGCAGG 58.678 47.826 0.00 0.00 37.61 4.85
552 553 3.750130 GCATGGAGTTATAGACATGGCAG 59.250 47.826 0.00 0.00 40.66 4.85
553 554 3.392285 AGCATGGAGTTATAGACATGGCA 59.608 43.478 0.00 0.00 40.66 4.92
554 555 3.999663 GAGCATGGAGTTATAGACATGGC 59.000 47.826 0.00 0.00 40.66 4.40
555 556 5.219343 TGAGCATGGAGTTATAGACATGG 57.781 43.478 0.00 0.00 40.66 3.66
556 557 6.286758 AGTTGAGCATGGAGTTATAGACATG 58.713 40.000 0.00 0.00 42.61 3.21
558 559 5.939764 AGTTGAGCATGGAGTTATAGACA 57.060 39.130 0.00 0.00 0.00 3.41
559 560 6.109359 ACAAGTTGAGCATGGAGTTATAGAC 58.891 40.000 10.54 0.00 0.00 2.59
560 561 6.299805 ACAAGTTGAGCATGGAGTTATAGA 57.700 37.500 10.54 0.00 0.00 1.98
561 562 5.525378 GGACAAGTTGAGCATGGAGTTATAG 59.475 44.000 10.54 0.00 0.00 1.31
562 563 5.045942 TGGACAAGTTGAGCATGGAGTTATA 60.046 40.000 10.54 0.00 0.00 0.98
564 565 3.072330 TGGACAAGTTGAGCATGGAGTTA 59.928 43.478 10.54 0.00 0.00 2.24
565 566 2.158623 TGGACAAGTTGAGCATGGAGTT 60.159 45.455 10.54 0.00 0.00 3.01
568 569 1.421268 AGTGGACAAGTTGAGCATGGA 59.579 47.619 10.54 0.00 0.00 3.41
569 570 1.538512 CAGTGGACAAGTTGAGCATGG 59.461 52.381 10.54 0.00 0.00 3.66
570 571 1.538512 CCAGTGGACAAGTTGAGCATG 59.461 52.381 10.54 1.79 0.00 4.06
574 575 2.918712 ACTCCAGTGGACAAGTTGAG 57.081 50.000 8.12 0.00 0.00 3.02
592 593 8.410912 ACAAGTTACCATTTTAAGAGACCAAAC 58.589 33.333 0.00 0.00 0.00 2.93
597 598 6.620089 GCCGACAAGTTACCATTTTAAGAGAC 60.620 42.308 0.00 0.00 0.00 3.36
607 608 0.981183 TCAGGCCGACAAGTTACCAT 59.019 50.000 0.00 0.00 0.00 3.55
609 610 2.836944 GTCAGGCCGACAAGTTACC 58.163 57.895 18.80 0.00 44.69 2.85
637 638 4.217118 AGAATGTTGAAGTTCATCACTGGC 59.783 41.667 16.87 8.28 35.12 4.85
677 679 1.535462 GGCACGCACAACAACTAGAAT 59.465 47.619 0.00 0.00 0.00 2.40
678 680 0.941542 GGCACGCACAACAACTAGAA 59.058 50.000 0.00 0.00 0.00 2.10
680 682 1.574428 GGGCACGCACAACAACTAG 59.426 57.895 0.00 0.00 0.00 2.57
683 685 3.114647 TTCGGGCACGCACAACAAC 62.115 57.895 1.67 0.00 40.69 3.32
684 686 2.824489 TTCGGGCACGCACAACAA 60.824 55.556 1.67 0.00 40.69 2.83
752 971 3.326747 GCTTACAAGCGTATGATAGGGG 58.673 50.000 0.00 0.00 42.88 4.79
892 1889 2.101917 GGTATGTACGTGTATGGCCAGT 59.898 50.000 13.05 5.58 0.00 4.00
904 2747 2.278989 CGGGCGTGGGTATGTACG 60.279 66.667 0.00 0.00 42.79 3.67
986 6528 1.004785 CCACATTGTGCGACGTACGA 61.005 55.000 24.41 8.52 45.77 3.43
1201 6755 3.124921 GCCGTGCATAGCGTGGTT 61.125 61.111 0.00 0.00 0.00 3.67
1614 7171 3.382832 CCGTGGCCTTCCGAGTCT 61.383 66.667 3.32 0.00 34.14 3.24
1731 7288 2.032071 GCCTTGTACACCGCCACT 59.968 61.111 0.00 0.00 0.00 4.00
1861 7418 2.001361 ATAGCGACGGGGTCTTCGTG 62.001 60.000 0.00 0.00 41.22 4.35
1915 7472 1.546589 TTACCGGCCGAGGTTGACAT 61.547 55.000 30.73 1.22 43.00 3.06
2040 7597 2.983592 CCAACCAAGGTCGTGCCC 60.984 66.667 0.00 0.00 38.26 5.36
2238 7798 1.456287 GTTGGACAGGAACAGCCCT 59.544 57.895 0.00 0.00 37.37 5.19
2651 8237 3.838271 ATCATCGCCGACCGCACT 61.838 61.111 0.00 0.00 37.30 4.40
2744 8330 4.492160 GACACCATCGCGAGCGGA 62.492 66.667 28.51 0.08 40.25 5.54
2758 8347 4.077184 GGTCGATGTGGCCGGACA 62.077 66.667 5.41 5.41 0.00 4.02
2813 8402 1.477553 TAATGTAGTCGTTCGGCCCT 58.522 50.000 0.00 0.00 0.00 5.19
2820 8409 5.348724 CACACATGAGCTTAATGTAGTCGTT 59.651 40.000 13.77 0.00 36.10 3.85
2918 8507 3.945921 ACGACGGATAGTTGAGATCAAGA 59.054 43.478 0.00 0.00 37.67 3.02
2921 8510 3.692593 TGAACGACGGATAGTTGAGATCA 59.307 43.478 0.00 0.00 37.67 2.92
2948 8537 0.982673 CGCCGTTGTAGTCGAAGAAG 59.017 55.000 0.00 0.00 39.69 2.85
3073 8662 2.690778 CCGCTAAACACCAGCCTGC 61.691 63.158 0.00 0.00 35.53 4.85
3087 8676 2.262915 CTTCTCGTGCTTCCCGCT 59.737 61.111 0.00 0.00 40.11 5.52
3107 8696 1.270550 CGAACCACTACCGTGTACCTT 59.729 52.381 0.00 0.00 39.55 3.50
3119 8708 2.448931 TCCCCAACCCGAACCACT 60.449 61.111 0.00 0.00 0.00 4.00
3139 8728 2.179424 ACTACCTCGGGGATTATCTGGT 59.821 50.000 9.33 0.00 36.25 4.00
3248 8837 0.670546 GCACGCGCATATCCTATGGT 60.671 55.000 5.73 0.00 38.36 3.55
3281 8942 5.122239 CCATAATGTATTGGCGTATGGTCAG 59.878 44.000 0.00 0.00 0.00 3.51
3414 9082 6.924913 ACTGCAGGACATCTATGTATGTAT 57.075 37.500 19.93 0.00 41.95 2.29
3415 9083 8.306761 CAATACTGCAGGACATCTATGTATGTA 58.693 37.037 19.93 0.00 41.95 2.29
3416 9084 6.924913 ATACTGCAGGACATCTATGTATGT 57.075 37.500 19.93 0.00 41.95 2.29
3436 9104 4.424061 TGCAAAGTGTCTGATGCAATAC 57.576 40.909 0.68 0.00 45.04 1.89
3471 9353 6.258287 CACAAAATTCTGCCAAAGTGAAATCA 59.742 34.615 0.00 0.00 0.00 2.57
3491 9373 0.737715 GCGTTTTGGTGTGGCACAAA 60.738 50.000 23.90 11.54 44.16 2.83
3509 9391 1.215423 AGGAGGACAATAATGGGTGGC 59.785 52.381 0.00 0.00 0.00 5.01
3517 9399 1.820581 CGGCGGAGGAGGACAATAA 59.179 57.895 0.00 0.00 0.00 1.40
3518 9400 2.792947 GCGGCGGAGGAGGACAATA 61.793 63.158 9.78 0.00 0.00 1.90
3534 9416 3.777925 CTCAACGTTGCCTCGGCG 61.778 66.667 23.47 0.00 45.51 6.46
3535 9417 1.503818 TTTCTCAACGTTGCCTCGGC 61.504 55.000 23.47 0.00 42.35 5.54
3536 9418 0.941542 TTTTCTCAACGTTGCCTCGG 59.058 50.000 23.47 10.31 34.94 4.63
3539 9421 1.613437 CCCATTTTCTCAACGTTGCCT 59.387 47.619 23.47 1.26 0.00 4.75
3541 9423 2.793278 ACCCATTTTCTCAACGTTGC 57.207 45.000 23.47 0.00 0.00 4.17
3542 9424 5.008217 TCAAGTACCCATTTTCTCAACGTTG 59.992 40.000 22.35 22.35 0.00 4.10
3543 9425 5.127491 TCAAGTACCCATTTTCTCAACGTT 58.873 37.500 0.00 0.00 0.00 3.99
3544 9426 4.710324 TCAAGTACCCATTTTCTCAACGT 58.290 39.130 0.00 0.00 0.00 3.99
3545 9427 5.411361 TCATCAAGTACCCATTTTCTCAACG 59.589 40.000 0.00 0.00 0.00 4.10
3547 9429 6.071952 GCTTCATCAAGTACCCATTTTCTCAA 60.072 38.462 0.00 0.00 31.45 3.02
3548 9430 5.415701 GCTTCATCAAGTACCCATTTTCTCA 59.584 40.000 0.00 0.00 31.45 3.27
3549 9431 5.415701 TGCTTCATCAAGTACCCATTTTCTC 59.584 40.000 0.00 0.00 31.45 2.87
3550 9432 5.324409 TGCTTCATCAAGTACCCATTTTCT 58.676 37.500 0.00 0.00 31.45 2.52
3551 9433 5.643379 TGCTTCATCAAGTACCCATTTTC 57.357 39.130 0.00 0.00 31.45 2.29
3552 9434 6.096846 GGTATGCTTCATCAAGTACCCATTTT 59.903 38.462 0.00 0.00 30.10 1.82
3554 9436 5.133221 GGTATGCTTCATCAAGTACCCATT 58.867 41.667 0.00 0.00 30.10 3.16
3555 9437 4.446311 GGGTATGCTTCATCAAGTACCCAT 60.446 45.833 9.53 0.00 44.24 4.00
3556 9438 3.118038 GGGTATGCTTCATCAAGTACCCA 60.118 47.826 9.53 0.00 44.24 4.51
3557 9439 3.136626 AGGGTATGCTTCATCAAGTACCC 59.863 47.826 7.00 7.00 44.72 3.69
3558 9440 4.423625 AGGGTATGCTTCATCAAGTACC 57.576 45.455 0.00 0.00 33.34 3.34
3559 9441 5.163343 TGGTAGGGTATGCTTCATCAAGTAC 60.163 44.000 0.00 0.00 31.45 2.73
3561 9443 3.780294 TGGTAGGGTATGCTTCATCAAGT 59.220 43.478 0.00 0.00 31.45 3.16
3564 9446 3.111484 TGTGGTAGGGTATGCTTCATCA 58.889 45.455 0.00 0.00 0.00 3.07
3565 9447 3.838244 TGTGGTAGGGTATGCTTCATC 57.162 47.619 0.00 0.00 0.00 2.92
3566 9448 4.263727 TGTTTGTGGTAGGGTATGCTTCAT 60.264 41.667 0.00 0.00 0.00 2.57
3567 9449 3.073209 TGTTTGTGGTAGGGTATGCTTCA 59.927 43.478 0.00 0.00 0.00 3.02
3568 9450 3.681593 TGTTTGTGGTAGGGTATGCTTC 58.318 45.455 0.00 0.00 0.00 3.86
3569 9451 3.799432 TGTTTGTGGTAGGGTATGCTT 57.201 42.857 0.00 0.00 0.00 3.91
3570 9452 3.620488 CATGTTTGTGGTAGGGTATGCT 58.380 45.455 0.00 0.00 0.00 3.79
3572 9454 2.687935 GGCATGTTTGTGGTAGGGTATG 59.312 50.000 0.00 0.00 0.00 2.39
3573 9455 2.357777 GGGCATGTTTGTGGTAGGGTAT 60.358 50.000 0.00 0.00 0.00 2.73
3575 9457 0.251608 GGGCATGTTTGTGGTAGGGT 60.252 55.000 0.00 0.00 0.00 4.34
3576 9458 1.312371 CGGGCATGTTTGTGGTAGGG 61.312 60.000 0.00 0.00 0.00 3.53
3577 9459 1.312371 CCGGGCATGTTTGTGGTAGG 61.312 60.000 0.00 0.00 0.00 3.18
3578 9460 0.608035 ACCGGGCATGTTTGTGGTAG 60.608 55.000 6.32 0.00 0.00 3.18
3579 9461 0.691332 TACCGGGCATGTTTGTGGTA 59.309 50.000 6.32 0.00 0.00 3.25
3581 9463 1.673920 GTATACCGGGCATGTTTGTGG 59.326 52.381 6.32 0.00 0.00 4.17
3582 9464 2.360844 TGTATACCGGGCATGTTTGTG 58.639 47.619 6.32 0.00 0.00 3.33
3583 9465 2.791347 TGTATACCGGGCATGTTTGT 57.209 45.000 6.32 0.00 0.00 2.83
3584 9466 3.013921 ACTTGTATACCGGGCATGTTTG 58.986 45.455 6.32 0.00 0.00 2.93
3585 9467 3.275999 GACTTGTATACCGGGCATGTTT 58.724 45.455 6.32 0.00 0.00 2.83
3586 9468 2.237643 TGACTTGTATACCGGGCATGTT 59.762 45.455 6.32 0.00 0.00 2.71
3587 9469 1.834896 TGACTTGTATACCGGGCATGT 59.165 47.619 6.32 7.55 0.00 3.21
3589 9471 1.202486 CGTGACTTGTATACCGGGCAT 60.202 52.381 6.32 0.34 0.00 4.40
3590 9472 0.173935 CGTGACTTGTATACCGGGCA 59.826 55.000 6.32 0.00 0.00 5.36
3592 9474 0.819582 ACCGTGACTTGTATACCGGG 59.180 55.000 16.85 0.00 39.68 5.73
3593 9475 1.473677 TCACCGTGACTTGTATACCGG 59.526 52.381 12.62 12.62 41.09 5.28
3594 9476 2.925578 TCACCGTGACTTGTATACCG 57.074 50.000 0.00 0.00 0.00 4.02
3611 9493 3.686916 TGTCATTGACCGGTGTATTCA 57.313 42.857 14.63 0.00 0.00 2.57
3612 9494 3.374058 CCTTGTCATTGACCGGTGTATTC 59.626 47.826 14.63 0.00 0.00 1.75
3614 9496 2.355716 CCCTTGTCATTGACCGGTGTAT 60.356 50.000 14.63 1.00 0.00 2.29
3615 9497 1.002659 CCCTTGTCATTGACCGGTGTA 59.997 52.381 14.63 0.00 0.00 2.90
3617 9499 0.036164 TCCCTTGTCATTGACCGGTG 59.964 55.000 14.63 0.00 0.00 4.94
3618 9500 0.036306 GTCCCTTGTCATTGACCGGT 59.964 55.000 6.92 6.92 0.00 5.28
3619 9501 0.324943 AGTCCCTTGTCATTGACCGG 59.675 55.000 14.05 13.33 0.00 5.28
3620 9502 2.028476 TGTAGTCCCTTGTCATTGACCG 60.028 50.000 14.05 5.43 0.00 4.79
3621 9503 3.600388 CTGTAGTCCCTTGTCATTGACC 58.400 50.000 14.05 0.00 0.00 4.02
3622 9504 3.600388 CCTGTAGTCCCTTGTCATTGAC 58.400 50.000 9.93 9.93 0.00 3.18
3623 9505 2.027192 GCCTGTAGTCCCTTGTCATTGA 60.027 50.000 0.00 0.00 0.00 2.57
3625 9507 1.066143 CGCCTGTAGTCCCTTGTCATT 60.066 52.381 0.00 0.00 0.00 2.57
3626 9508 0.537188 CGCCTGTAGTCCCTTGTCAT 59.463 55.000 0.00 0.00 0.00 3.06
3627 9509 0.541063 TCGCCTGTAGTCCCTTGTCA 60.541 55.000 0.00 0.00 0.00 3.58
3628 9510 0.108756 GTCGCCTGTAGTCCCTTGTC 60.109 60.000 0.00 0.00 0.00 3.18
3630 9512 1.471119 TAGTCGCCTGTAGTCCCTTG 58.529 55.000 0.00 0.00 0.00 3.61
3631 9513 2.032620 CATAGTCGCCTGTAGTCCCTT 58.967 52.381 0.00 0.00 0.00 3.95
3633 9515 0.674534 CCATAGTCGCCTGTAGTCCC 59.325 60.000 0.00 0.00 0.00 4.46
3635 9517 0.317938 CGCCATAGTCGCCTGTAGTC 60.318 60.000 0.00 0.00 0.00 2.59
3636 9518 1.734137 CGCCATAGTCGCCTGTAGT 59.266 57.895 0.00 0.00 0.00 2.73
3638 9520 1.731433 GACCGCCATAGTCGCCTGTA 61.731 60.000 0.00 0.00 0.00 2.74
3639 9521 3.075005 ACCGCCATAGTCGCCTGT 61.075 61.111 0.00 0.00 0.00 4.00
3640 9522 2.279517 GACCGCCATAGTCGCCTG 60.280 66.667 0.00 0.00 0.00 4.85
3647 9529 0.457166 TTTGTCGACGACCGCCATAG 60.457 55.000 24.33 0.00 38.37 2.23
3648 9530 0.457166 CTTTGTCGACGACCGCCATA 60.457 55.000 24.33 2.31 38.37 2.74
3649 9531 1.736645 CTTTGTCGACGACCGCCAT 60.737 57.895 24.33 0.00 38.37 4.40
3650 9532 2.355363 CTTTGTCGACGACCGCCA 60.355 61.111 24.33 3.56 38.37 5.69


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

AutoCloner maintained by Alex Coulton.