Multiple sequence alignment - TraesCS1B01G099200

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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 TraesCS1B01G099200 chr1B 100.000 4200 0 0 1 4200 106793927 106789728 0.000000e+00 7757.0
1 TraesCS1B01G099200 chr1B 83.604 738 114 6 3465 4197 2327357 2328092 0.000000e+00 686.0
2 TraesCS1B01G099200 chr1B 79.972 724 128 16 3472 4187 576130139 576130853 6.220000e-143 518.0
3 TraesCS1B01G099200 chr1D 93.470 1945 79 20 1 1936 66188498 66186593 0.000000e+00 2844.0
4 TraesCS1B01G099200 chr1D 93.329 1484 61 14 1937 3391 66186487 66185013 0.000000e+00 2158.0
5 TraesCS1B01G099200 chr1D 83.070 697 100 15 3517 4200 2891437 2890746 5.970000e-173 617.0
6 TraesCS1B01G099200 chr1A 92.872 1487 58 19 1937 3391 64714318 64712848 0.000000e+00 2115.0
7 TraesCS1B01G099200 chr1A 92.105 1368 53 26 593 1938 64715792 64714458 0.000000e+00 1877.0
8 TraesCS1B01G099200 chr2B 81.656 785 131 11 3421 4200 443829745 443830521 1.270000e-179 640.0
9 TraesCS1B01G099200 chr3A 80.968 599 99 14 3518 4108 28884271 28884862 1.060000e-125 460.0
10 TraesCS1B01G099200 chr3A 80.000 295 39 11 2836 3116 700575348 700575636 2.560000e-47 200.0
11 TraesCS1B01G099200 chr6D 80.035 576 97 17 3634 4200 98281314 98280748 1.090000e-110 411.0
12 TraesCS1B01G099200 chr7B 82.796 465 73 7 3725 4187 701772634 701772175 3.910000e-110 409.0
13 TraesCS1B01G099200 chr3B 83.294 425 67 4 3765 4187 754957755 754957333 5.090000e-104 388.0
14 TraesCS1B01G099200 chr3B 81.469 286 39 6 2842 3116 756182649 756182367 5.470000e-54 222.0
15 TraesCS1B01G099200 chr3B 81.405 242 36 6 2836 3075 755042087 755042321 5.540000e-44 189.0
16 TraesCS1B01G099200 chr3B 80.097 206 30 3 2918 3115 754979572 754979774 4.380000e-30 143.0
17 TraesCS1B01G099200 chr3B 88.000 50 4 2 51 99 819889305 819889257 1.630000e-04 58.4
18 TraesCS1B01G099200 chr6B 80.710 451 64 14 3756 4184 79889790 79890239 3.130000e-86 329.0
19 TraesCS1B01G099200 chr3D 81.849 292 39 10 2836 3116 569546404 569546692 2.520000e-57 233.0
20 TraesCS1B01G099200 chr3D 83.122 237 33 7 2842 3075 567216944 567216712 4.260000e-50 209.0
21 TraesCS1B01G099200 chr7D 79.439 321 63 2 3523 3840 372961441 372961761 1.520000e-54 224.0
22 TraesCS1B01G099200 chrUn 81.185 287 37 10 2842 3116 41101741 41101460 9.150000e-52 215.0
23 TraesCS1B01G099200 chr5A 88.430 121 13 1 51 170 14375436 14375316 1.220000e-30 145.0


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 TraesCS1B01G099200 chr1B 106789728 106793927 4199 True 7757 7757 100.0000 1 4200 1 chr1B.!!$R1 4199
1 TraesCS1B01G099200 chr1B 2327357 2328092 735 False 686 686 83.6040 3465 4197 1 chr1B.!!$F1 732
2 TraesCS1B01G099200 chr1B 576130139 576130853 714 False 518 518 79.9720 3472 4187 1 chr1B.!!$F2 715
3 TraesCS1B01G099200 chr1D 66185013 66188498 3485 True 2501 2844 93.3995 1 3391 2 chr1D.!!$R2 3390
4 TraesCS1B01G099200 chr1D 2890746 2891437 691 True 617 617 83.0700 3517 4200 1 chr1D.!!$R1 683
5 TraesCS1B01G099200 chr1A 64712848 64715792 2944 True 1996 2115 92.4885 593 3391 2 chr1A.!!$R1 2798
6 TraesCS1B01G099200 chr2B 443829745 443830521 776 False 640 640 81.6560 3421 4200 1 chr2B.!!$F1 779
7 TraesCS1B01G099200 chr3A 28884271 28884862 591 False 460 460 80.9680 3518 4108 1 chr3A.!!$F1 590
8 TraesCS1B01G099200 chr6D 98280748 98281314 566 True 411 411 80.0350 3634 4200 1 chr6D.!!$R1 566

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
237 240 0.097674 CGCTGAAGCAAATTCCCTCG 59.902 55.0 2.79 0.0 42.21 4.63 F
1299 1313 0.030908 GATCTCAGCGTTAGGGTCGG 59.969 60.0 0.00 0.0 0.00 4.79 F
1617 1641 0.036765 TGCCTGCGAAAACCGATACT 60.037 50.0 0.00 0.0 41.76 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1824 0.318762 AAGCTGACGGTGAGGAAGAC 59.681 55.0 0.0 0.0 0.0 3.01 R
2255 2432 0.036765 TGTGCCGGTATGAGAACACC 60.037 55.0 1.9 0.0 0.0 4.16 R
3408 3614 0.318614 CCGGTGCGCAAACAATCTTT 60.319 50.0 14.0 0.0 0.0 2.52 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
125 126 1.597742 ACGTACGTGTAGGTGTCTGT 58.402 50.000 22.14 0.00 33.48 3.41
129 130 4.216257 ACGTACGTGTAGGTGTCTGTTTAT 59.784 41.667 22.14 0.00 33.48 1.40
176 179 4.802051 TGGCCCATCAAGGAGCGC 62.802 66.667 0.00 0.00 41.22 5.92
200 203 5.086104 AGGACTATTTCTCGCTTTAAGCA 57.914 39.130 17.51 3.59 42.58 3.91
237 240 0.097674 CGCTGAAGCAAATTCCCTCG 59.902 55.000 2.79 0.00 42.21 4.63
242 245 0.883833 AAGCAAATTCCCTCGCACTG 59.116 50.000 0.00 0.00 0.00 3.66
279 282 4.045783 GCCTGTTAGTGCGCTTTTAAAAA 58.954 39.130 9.73 0.00 0.00 1.94
304 307 4.895889 AGGGAAGAAGAAAAAGGTGGAAAG 59.104 41.667 0.00 0.00 0.00 2.62
308 311 3.638627 AGAAGAAAAAGGTGGAAAGCAGG 59.361 43.478 0.00 0.00 0.00 4.85
381 384 3.744660 ACATCAGGTTCTTGTTGACTCC 58.255 45.455 1.17 0.00 0.00 3.85
390 393 1.192146 TTGTTGACTCCTAGCCGCCT 61.192 55.000 0.00 0.00 0.00 5.52
404 407 1.205064 CGCCTGCGAAAGTGACTTG 59.795 57.895 5.43 0.00 42.83 3.16
410 413 1.860078 CGAAAGTGACTTGGGCGAC 59.140 57.895 0.00 0.00 0.00 5.19
444 447 2.295349 GGAGTCGGGCGTTCATAGATTA 59.705 50.000 0.00 0.00 0.00 1.75
447 450 3.572682 AGTCGGGCGTTCATAGATTATCA 59.427 43.478 0.00 0.00 0.00 2.15
454 457 3.428870 CGTTCATAGATTATCACGGGTGC 59.571 47.826 0.00 0.00 0.00 5.01
455 458 4.377021 GTTCATAGATTATCACGGGTGCA 58.623 43.478 0.00 0.00 0.00 4.57
465 468 1.621317 TCACGGGTGCAGATGAGTTTA 59.379 47.619 0.00 0.00 0.00 2.01
563 566 5.627135 TCTTAGGGGAACTTTGTAACTTGG 58.373 41.667 0.00 0.00 0.00 3.61
584 587 6.131544 TGGTAGAGAAGAAACAAAACAAGC 57.868 37.500 0.00 0.00 0.00 4.01
591 594 3.785486 AGAAACAAAACAAGCTTGGCTC 58.215 40.909 29.18 13.96 38.25 4.70
646 652 8.959705 AAGTAAGAGTACTTGCTACACTTTTT 57.040 30.769 0.00 0.00 46.64 1.94
719 726 1.219664 CCGACCCAACGAGGCAATA 59.780 57.895 0.00 0.00 35.39 1.90
720 727 0.391927 CCGACCCAACGAGGCAATAA 60.392 55.000 0.00 0.00 35.39 1.40
721 728 1.444836 CGACCCAACGAGGCAATAAA 58.555 50.000 0.00 0.00 35.39 1.40
724 731 1.173043 CCCAACGAGGCAATAAAGCA 58.827 50.000 0.00 0.00 35.83 3.91
725 732 1.750778 CCCAACGAGGCAATAAAGCAT 59.249 47.619 0.00 0.00 35.83 3.79
726 733 2.480073 CCCAACGAGGCAATAAAGCATG 60.480 50.000 0.00 0.00 35.83 4.06
727 734 2.187707 CAACGAGGCAATAAAGCATGC 58.812 47.619 10.51 10.51 41.82 4.06
728 735 0.378257 ACGAGGCAATAAAGCATGCG 59.622 50.000 13.01 0.00 43.47 4.73
765 774 0.878961 ACACGAGCAGTTTTCCCGAC 60.879 55.000 0.00 0.00 0.00 4.79
800 809 0.108520 TCCACGGCAAATCGTCCTAC 60.109 55.000 0.00 0.00 41.86 3.18
815 824 4.304537 GTCCTACTTAACTGGACGATCC 57.695 50.000 0.00 0.00 40.44 3.36
937 946 4.787260 AAAGGAAGAGTTACCGAGAGAC 57.213 45.455 0.00 0.00 0.00 3.36
989 998 5.352643 AGAATAAATTATAACCGCACGGC 57.647 39.130 9.43 0.00 39.32 5.68
1014 1025 6.667848 CCAAGAACAAGGGAGGGTAAATAAAT 59.332 38.462 0.00 0.00 0.00 1.40
1069 1080 5.039333 CGATCTGATTTCCTTTTCCAATGC 58.961 41.667 0.00 0.00 0.00 3.56
1111 1122 0.757188 CCTAGGTCCATCGAGCAGGT 60.757 60.000 0.00 0.00 39.06 4.00
1112 1123 1.115467 CTAGGTCCATCGAGCAGGTT 58.885 55.000 0.00 0.00 39.06 3.50
1135 1146 4.603989 TCTTGCATGATCTCTCTCCATC 57.396 45.455 0.00 0.00 0.00 3.51
1137 1148 4.039366 TCTTGCATGATCTCTCTCCATCTG 59.961 45.833 0.00 0.00 0.00 2.90
1203 1214 2.279582 ACGACTTGTCTAATCTGCCG 57.720 50.000 0.00 0.00 0.00 5.69
1228 1239 4.747108 AGCAGAATGTAGATAATGCGTGTC 59.253 41.667 4.26 0.00 39.31 3.67
1297 1311 2.500509 CTGATCTCAGCGTTAGGGTC 57.499 55.000 0.00 0.00 37.15 4.46
1298 1312 0.738975 TGATCTCAGCGTTAGGGTCG 59.261 55.000 0.00 0.00 0.00 4.79
1299 1313 0.030908 GATCTCAGCGTTAGGGTCGG 59.969 60.000 0.00 0.00 0.00 4.79
1300 1314 0.683504 ATCTCAGCGTTAGGGTCGGT 60.684 55.000 0.00 0.00 39.57 4.69
1433 1447 2.648059 CTCCTGGAAAAGATTGGCGAT 58.352 47.619 0.00 0.00 0.00 4.58
1506 1526 1.061485 GGACGACGACAAGAAGAAGC 58.939 55.000 0.00 0.00 0.00 3.86
1571 1591 3.353836 CACAACGTCCTTGGCGGG 61.354 66.667 0.00 0.00 33.75 6.13
1589 1610 1.532604 GGGGCAAAGGTAGTGCAACC 61.533 60.000 0.00 0.00 44.07 3.77
1604 1628 0.458669 CAACCATGGAGAATGCCTGC 59.541 55.000 21.47 0.00 34.67 4.85
1615 1639 1.668751 GAATGCCTGCGAAAACCGATA 59.331 47.619 0.00 0.00 41.76 2.92
1616 1640 1.014352 ATGCCTGCGAAAACCGATAC 58.986 50.000 0.00 0.00 41.76 2.24
1617 1641 0.036765 TGCCTGCGAAAACCGATACT 60.037 50.000 0.00 0.00 41.76 2.12
1618 1642 0.651031 GCCTGCGAAAACCGATACTC 59.349 55.000 0.00 0.00 41.76 2.59
1619 1643 1.739371 GCCTGCGAAAACCGATACTCT 60.739 52.381 0.00 0.00 41.76 3.24
1620 1644 2.480759 GCCTGCGAAAACCGATACTCTA 60.481 50.000 0.00 0.00 41.76 2.43
1663 1691 9.855021 GATAATTACTAATGCCTTGTGTTTTGT 57.145 29.630 0.00 0.00 0.00 2.83
1796 1824 1.088340 CCTCTGCCACTTGCTCATCG 61.088 60.000 0.00 0.00 42.00 3.84
1831 1859 1.300620 CTTCGTCTGGTCCAACGCA 60.301 57.895 16.87 9.17 38.72 5.24
1857 1885 2.232452 CCTTCATCAACAGGTCTCGTCT 59.768 50.000 0.00 0.00 0.00 4.18
1858 1886 3.506810 CTTCATCAACAGGTCTCGTCTC 58.493 50.000 0.00 0.00 0.00 3.36
1859 1887 1.468914 TCATCAACAGGTCTCGTCTCG 59.531 52.381 0.00 0.00 0.00 4.04
1860 1888 1.200252 CATCAACAGGTCTCGTCTCGT 59.800 52.381 0.00 0.00 0.00 4.18
1861 1889 0.873054 TCAACAGGTCTCGTCTCGTC 59.127 55.000 0.00 0.00 0.00 4.20
1864 1892 1.015085 ACAGGTCTCGTCTCGTCTCG 61.015 60.000 0.00 0.00 0.00 4.04
1868 1896 1.447489 TCTCGTCTCGTCTCGTCCC 60.447 63.158 0.00 0.00 0.00 4.46
1887 1915 1.245732 CCTGCTTCTTTTGCTCTGCT 58.754 50.000 0.00 0.00 0.00 4.24
1929 1957 5.499139 TCTTCTGTGTGCTTTGTTTTAGG 57.501 39.130 0.00 0.00 0.00 2.69
1936 1964 7.119699 TCTGTGTGCTTTGTTTTAGGATAGATG 59.880 37.037 0.00 0.00 0.00 2.90
1937 1965 6.939730 TGTGTGCTTTGTTTTAGGATAGATGA 59.060 34.615 0.00 0.00 0.00 2.92
1939 1967 7.750903 GTGTGCTTTGTTTTAGGATAGATGAAC 59.249 37.037 0.00 0.00 0.00 3.18
1940 1968 7.446931 TGTGCTTTGTTTTAGGATAGATGAACA 59.553 33.333 0.00 0.00 0.00 3.18
1943 2116 9.129209 GCTTTGTTTTAGGATAGATGAACAAAC 57.871 33.333 7.79 0.00 40.17 2.93
1971 2144 3.689161 TGCCGTTAGATTCACCTTCATTG 59.311 43.478 0.00 0.00 0.00 2.82
1986 2159 4.625311 CCTTCATTGTTTGGCCGTTAATTC 59.375 41.667 0.00 0.00 0.00 2.17
2099 2272 1.856629 ATCTGAAACCCAATGCCTGG 58.143 50.000 0.00 0.00 45.97 4.45
2101 2274 0.604578 CTGAAACCCAATGCCTGGTG 59.395 55.000 0.00 0.00 44.76 4.17
2188 2361 6.349033 CCGGAAAAGACCTTAAAACATACCTG 60.349 42.308 0.00 0.00 0.00 4.00
2239 2412 6.659824 TCTTTCTGTTACCTTTCTTCTGGTT 58.340 36.000 0.00 0.00 37.74 3.67
2255 2432 5.295431 TCTGGTTCAACTTATTTGATGCG 57.705 39.130 0.00 0.00 43.99 4.73
2282 2459 3.876914 TCTCATACCGGCACAATTCATTC 59.123 43.478 0.00 0.00 0.00 2.67
2293 2470 2.926200 ACAATTCATTCTCTCGCAGTCG 59.074 45.455 0.00 0.00 0.00 4.18
2378 2555 6.980416 ACACTAGTAAGCCCCTTTCTATAG 57.020 41.667 0.00 0.00 0.00 1.31
2379 2556 6.442091 ACACTAGTAAGCCCCTTTCTATAGT 58.558 40.000 0.00 0.00 0.00 2.12
2380 2557 7.589993 ACACTAGTAAGCCCCTTTCTATAGTA 58.410 38.462 0.00 0.00 0.00 1.82
2381 2558 8.063770 ACACTAGTAAGCCCCTTTCTATAGTAA 58.936 37.037 0.00 0.00 0.00 2.24
2382 2559 9.091220 CACTAGTAAGCCCCTTTCTATAGTAAT 57.909 37.037 0.00 0.00 0.00 1.89
2383 2560 9.671862 ACTAGTAAGCCCCTTTCTATAGTAATT 57.328 33.333 0.00 0.00 0.00 1.40
2386 2563 9.671862 AGTAAGCCCCTTTCTATAGTAATTAGT 57.328 33.333 0.00 0.00 0.00 2.24
2389 2566 8.120140 AGCCCCTTTCTATAGTAATTAGTACG 57.880 38.462 2.05 0.00 37.81 3.67
2390 2567 7.946776 AGCCCCTTTCTATAGTAATTAGTACGA 59.053 37.037 2.05 0.61 37.81 3.43
2391 2568 8.579863 GCCCCTTTCTATAGTAATTAGTACGAA 58.420 37.037 2.05 6.11 37.81 3.85
2392 2569 9.905171 CCCCTTTCTATAGTAATTAGTACGAAC 57.095 37.037 2.05 0.00 37.81 3.95
2434 2611 7.712797 TCTGAAAGCGTCTGATGTATGTTATA 58.287 34.615 0.00 0.00 29.86 0.98
2438 2615 9.119329 GAAAGCGTCTGATGTATGTTATACTAG 57.881 37.037 0.00 0.00 0.00 2.57
2440 2617 8.167605 AGCGTCTGATGTATGTTATACTAGTT 57.832 34.615 0.00 0.00 0.00 2.24
2441 2618 9.281371 AGCGTCTGATGTATGTTATACTAGTTA 57.719 33.333 0.00 0.00 0.00 2.24
2861 3062 0.303493 GCTTTGAAGCGTTCGACACA 59.697 50.000 0.00 0.00 42.88 3.72
2906 3107 3.935203 AGCACATCAACCAAATAGTCTCG 59.065 43.478 0.00 0.00 0.00 4.04
3253 3454 5.240183 TGTGATCCGTGCCTACTATAGTTAC 59.760 44.000 11.40 5.16 0.00 2.50
3295 3496 6.126409 ACTTTAGGTGTTCATCAAACTTGGA 58.874 36.000 0.00 0.00 38.76 3.53
3314 3515 4.651778 TGGAAGTTGGGACATCAGTTTAG 58.348 43.478 0.00 0.00 39.30 1.85
3327 3528 4.868450 TCAGTTTAGTTGAACACGTTGG 57.132 40.909 0.00 0.00 31.94 3.77
3374 3580 7.517614 TTTTGAGCAGTAATACCATGTTCAA 57.482 32.000 7.49 7.49 40.77 2.69
3375 3581 7.517614 TTTGAGCAGTAATACCATGTTCAAA 57.482 32.000 15.37 15.37 45.62 2.69
3384 3590 1.953686 ACCATGTTCAAACCCAGTTCG 59.046 47.619 0.00 0.00 0.00 3.95
3391 3597 1.152963 AAACCCAGTTCGTGCAGCT 60.153 52.632 0.00 0.00 0.00 4.24
3392 3598 0.107831 AAACCCAGTTCGTGCAGCTA 59.892 50.000 0.00 0.00 0.00 3.32
3393 3599 0.324943 AACCCAGTTCGTGCAGCTAT 59.675 50.000 0.00 0.00 0.00 2.97
3394 3600 0.324943 ACCCAGTTCGTGCAGCTATT 59.675 50.000 0.00 0.00 0.00 1.73
3395 3601 1.271379 ACCCAGTTCGTGCAGCTATTT 60.271 47.619 0.00 0.00 0.00 1.40
3396 3602 1.398390 CCCAGTTCGTGCAGCTATTTC 59.602 52.381 0.00 0.00 0.00 2.17
3397 3603 1.398390 CCAGTTCGTGCAGCTATTTCC 59.602 52.381 0.00 0.00 0.00 3.13
3398 3604 2.350522 CAGTTCGTGCAGCTATTTCCT 58.649 47.619 0.00 0.00 0.00 3.36
3399 3605 2.349886 CAGTTCGTGCAGCTATTTCCTC 59.650 50.000 0.00 0.00 0.00 3.71
3400 3606 2.234908 AGTTCGTGCAGCTATTTCCTCT 59.765 45.455 0.00 0.00 0.00 3.69
3401 3607 3.003480 GTTCGTGCAGCTATTTCCTCTT 58.997 45.455 0.00 0.00 0.00 2.85
3402 3608 3.334583 TCGTGCAGCTATTTCCTCTTT 57.665 42.857 0.00 0.00 0.00 2.52
3403 3609 3.674997 TCGTGCAGCTATTTCCTCTTTT 58.325 40.909 0.00 0.00 0.00 2.27
3404 3610 3.436704 TCGTGCAGCTATTTCCTCTTTTG 59.563 43.478 0.00 0.00 0.00 2.44
3405 3611 3.505836 GTGCAGCTATTTCCTCTTTTGC 58.494 45.455 0.00 0.00 0.00 3.68
3406 3612 3.192212 GTGCAGCTATTTCCTCTTTTGCT 59.808 43.478 0.00 0.00 0.00 3.91
3407 3613 3.192001 TGCAGCTATTTCCTCTTTTGCTG 59.808 43.478 0.00 0.00 46.11 4.41
3408 3614 3.441572 GCAGCTATTTCCTCTTTTGCTGA 59.558 43.478 14.95 0.00 46.23 4.26
3409 3615 4.082571 GCAGCTATTTCCTCTTTTGCTGAA 60.083 41.667 14.95 0.00 46.23 3.02
3410 3616 5.565439 GCAGCTATTTCCTCTTTTGCTGAAA 60.565 40.000 14.95 0.00 46.23 2.69
3411 3617 6.091437 CAGCTATTTCCTCTTTTGCTGAAAG 58.909 40.000 6.24 6.76 46.23 2.62
3461 3667 2.514824 GCCACCAGCGAAGGATCC 60.515 66.667 2.48 2.48 0.00 3.36
3463 3669 2.190578 CACCAGCGAAGGATCCCC 59.809 66.667 8.55 0.00 0.00 4.81
3548 3755 1.981636 CAGCAAGTCTCCTCAGCCT 59.018 57.895 0.00 0.00 0.00 4.58
3559 3766 1.664017 CTCAGCCTGCGATCGGATG 60.664 63.158 18.30 12.60 39.23 3.51
3601 3808 1.076777 CCGGATCAAGGGCATTGGT 60.077 57.895 12.41 4.27 39.54 3.67
3714 3932 1.075482 CAATGGGCCACACCTCAGT 59.925 57.895 9.28 0.00 39.10 3.41
3729 3950 0.960861 TCAGTCCGTCGTGCATCTCT 60.961 55.000 0.00 0.00 0.00 3.10
3730 3951 0.524392 CAGTCCGTCGTGCATCTCTC 60.524 60.000 0.00 0.00 0.00 3.20
3832 4053 1.680989 TGTCCATCTCCTTCGCCGA 60.681 57.895 0.00 0.00 0.00 5.54
3853 4074 1.228429 GTGGTTGGCTGGCTGGTTA 60.228 57.895 2.00 0.00 0.00 2.85
3854 4075 0.825840 GTGGTTGGCTGGCTGGTTAA 60.826 55.000 2.00 0.00 0.00 2.01
3855 4076 0.825840 TGGTTGGCTGGCTGGTTAAC 60.826 55.000 2.00 0.00 0.00 2.01
3874 4095 1.953138 GCATCTCGCATCCAGTCCG 60.953 63.158 0.00 0.00 41.79 4.79
3900 4123 0.753262 GAGTGGGGATGCGATACTGT 59.247 55.000 0.00 0.00 0.00 3.55
3969 4192 4.206088 GTTTTCGCGTCGTTATCTTGTTT 58.794 39.130 5.77 0.00 0.00 2.83
3999 4222 1.080772 CACTGCAGCTACCGTCGAA 60.081 57.895 15.27 0.00 0.00 3.71
4027 4250 3.672295 CTGCTCCGGCTGAGAACCC 62.672 68.421 10.34 0.00 44.42 4.11
4030 4253 2.203788 TCCGGCTGAGAACCCAGT 60.204 61.111 0.00 0.00 36.57 4.00
4072 4295 2.162681 GATGGCAGTGCTTTAGGTGTT 58.837 47.619 16.11 0.00 0.00 3.32
4104 4327 1.604147 GGGGCCATCGTTTTTGGAGG 61.604 60.000 4.39 0.00 36.26 4.30
4110 4333 2.154462 CATCGTTTTTGGAGGAGCTGT 58.846 47.619 0.00 0.00 0.00 4.40
4119 4342 1.145819 GAGGAGCTGTCAGATGGGC 59.854 63.158 3.32 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.758327 AGGTCGGCCATGCGACTA 60.758 61.111 20.39 0.00 37.19 2.59
53 54 2.095718 CCAACGCTTCTACTTTGGCTTC 60.096 50.000 0.00 0.00 32.89 3.86
54 55 1.880027 CCAACGCTTCTACTTTGGCTT 59.120 47.619 0.00 0.00 32.89 4.35
109 110 6.747125 TCAAATAAACAGACACCTACACGTA 58.253 36.000 0.00 0.00 0.00 3.57
171 174 1.855360 CGAGAAATAGTCCTTGCGCTC 59.145 52.381 9.73 0.00 0.00 5.03
176 179 5.351465 TGCTTAAAGCGAGAAATAGTCCTTG 59.649 40.000 0.00 0.00 46.26 3.61
200 203 1.506493 CGAGACAAGAAGCAGCACTT 58.494 50.000 0.00 0.00 42.98 3.16
237 240 1.586541 GGCCCAAAAGCTACAGTGC 59.413 57.895 0.00 0.00 0.00 4.40
242 245 3.449227 GGCCGGCCCAAAAGCTAC 61.449 66.667 36.64 5.01 0.00 3.58
279 282 4.878968 TCCACCTTTTTCTTCTTCCCTTT 58.121 39.130 0.00 0.00 0.00 3.11
282 285 4.501571 GCTTTCCACCTTTTTCTTCTTCCC 60.502 45.833 0.00 0.00 0.00 3.97
284 287 5.262588 TGCTTTCCACCTTTTTCTTCTTC 57.737 39.130 0.00 0.00 0.00 2.87
285 288 4.100035 CCTGCTTTCCACCTTTTTCTTCTT 59.900 41.667 0.00 0.00 0.00 2.52
352 355 3.068590 ACAAGAACCTGATGTTGGCTTTG 59.931 43.478 0.00 0.00 37.29 2.77
381 384 2.125512 ACTTTCGCAGGCGGCTAG 60.126 61.111 12.74 7.78 41.67 3.42
390 393 2.250939 CGCCCAAGTCACTTTCGCA 61.251 57.895 6.45 0.00 0.00 5.10
422 425 1.067582 CTATGAACGCCCGACTCCC 59.932 63.158 0.00 0.00 0.00 4.30
444 447 0.615331 AACTCATCTGCACCCGTGAT 59.385 50.000 0.00 0.00 0.00 3.06
447 450 1.066143 CCTAAACTCATCTGCACCCGT 60.066 52.381 0.00 0.00 0.00 5.28
454 457 4.747108 CGATTAGGTGCCTAAACTCATCTG 59.253 45.833 13.91 2.07 41.21 2.90
455 458 4.740934 GCGATTAGGTGCCTAAACTCATCT 60.741 45.833 13.91 0.00 41.21 2.90
522 525 8.568794 CCCCTAAGAAAAGAAAGTTAGAAAGTG 58.431 37.037 0.00 0.00 0.00 3.16
523 526 8.500238 TCCCCTAAGAAAAGAAAGTTAGAAAGT 58.500 33.333 0.00 0.00 0.00 2.66
528 531 8.693120 AAGTTCCCCTAAGAAAAGAAAGTTAG 57.307 34.615 0.00 0.00 0.00 2.34
563 566 6.693113 CCAAGCTTGTTTTGTTTCTTCTCTAC 59.307 38.462 24.35 0.00 0.00 2.59
584 587 7.440523 AGTTGATAGTTTAAGTTGAGCCAAG 57.559 36.000 0.00 0.00 0.00 3.61
724 731 1.738346 TAGTGAGCCTCGCATCGCAT 61.738 55.000 8.17 0.00 0.00 4.73
725 732 2.414785 TAGTGAGCCTCGCATCGCA 61.415 57.895 8.17 0.00 0.00 5.10
726 733 1.946650 GTAGTGAGCCTCGCATCGC 60.947 63.158 8.17 0.00 0.00 4.58
727 734 1.299468 GGTAGTGAGCCTCGCATCG 60.299 63.158 8.17 0.00 0.00 3.84
728 735 0.528684 GTGGTAGTGAGCCTCGCATC 60.529 60.000 8.17 0.00 0.00 3.91
815 824 0.935196 GGGACGCTATTTAACGCCTG 59.065 55.000 0.00 0.00 0.00 4.85
937 946 2.767496 CCTCCCCTGCCTCCTCTG 60.767 72.222 0.00 0.00 0.00 3.35
989 998 3.518992 TTTACCCTCCCTTGTTCTTGG 57.481 47.619 0.00 0.00 0.00 3.61
1069 1080 4.884164 GGAACCCAAAGATCAAGGATAGTG 59.116 45.833 0.00 0.00 0.00 2.74
1111 1122 5.169992 TGGAGAGAGATCATGCAAGAAAA 57.830 39.130 0.00 0.00 0.00 2.29
1112 1123 4.831674 TGGAGAGAGATCATGCAAGAAA 57.168 40.909 0.00 0.00 0.00 2.52
1203 1214 5.235186 ACACGCATTATCTACATTCTGCTTC 59.765 40.000 0.00 0.00 0.00 3.86
1228 1239 3.737774 ACATGATGCGAATGACATCTACG 59.262 43.478 0.00 0.00 43.53 3.51
1297 1311 4.439305 AATGAATCACATCCAACAACCG 57.561 40.909 0.00 0.00 38.38 4.44
1298 1312 5.343249 GCTAATGAATCACATCCAACAACC 58.657 41.667 0.00 0.00 38.38 3.77
1299 1313 5.126061 AGGCTAATGAATCACATCCAACAAC 59.874 40.000 0.00 0.00 38.38 3.32
1300 1314 5.263599 AGGCTAATGAATCACATCCAACAA 58.736 37.500 0.00 0.00 38.38 2.83
1433 1447 2.028876 TGGATCTTGTCGCCGATCTTA 58.971 47.619 0.00 0.00 36.97 2.10
1503 1523 3.620488 TCTTCTTGGATTTATGCGGCTT 58.380 40.909 0.00 0.00 0.00 4.35
1504 1524 3.281727 TCTTCTTGGATTTATGCGGCT 57.718 42.857 0.00 0.00 0.00 5.52
1505 1525 3.793465 GCTTCTTCTTGGATTTATGCGGC 60.793 47.826 0.00 0.00 0.00 6.53
1506 1526 3.378112 TGCTTCTTCTTGGATTTATGCGG 59.622 43.478 0.00 0.00 0.00 5.69
1571 1591 0.825840 TGGTTGCACTACCTTTGCCC 60.826 55.000 8.97 0.00 39.39 5.36
1589 1610 1.097232 TTTCGCAGGCATTCTCCATG 58.903 50.000 0.00 0.00 35.73 3.66
1604 1628 6.075519 CGTTTCATCTAGAGTATCGGTTTTCG 60.076 42.308 0.00 0.00 42.67 3.46
1615 1639 3.193691 CAGGTGTCCGTTTCATCTAGAGT 59.806 47.826 0.00 0.00 0.00 3.24
1616 1640 3.444034 TCAGGTGTCCGTTTCATCTAGAG 59.556 47.826 0.00 0.00 0.00 2.43
1617 1641 3.427573 TCAGGTGTCCGTTTCATCTAGA 58.572 45.455 0.00 0.00 0.00 2.43
1618 1642 3.868757 TCAGGTGTCCGTTTCATCTAG 57.131 47.619 0.00 0.00 0.00 2.43
1619 1643 5.925506 TTATCAGGTGTCCGTTTCATCTA 57.074 39.130 0.00 0.00 0.00 1.98
1620 1644 4.819105 TTATCAGGTGTCCGTTTCATCT 57.181 40.909 0.00 0.00 0.00 2.90
1663 1691 2.845363 TCACAAGATCAGCAGCTGAA 57.155 45.000 28.78 12.69 44.04 3.02
1796 1824 0.318762 AAGCTGACGGTGAGGAAGAC 59.681 55.000 0.00 0.00 0.00 3.01
1831 1859 2.575279 AGACCTGTTGATGAAGGATGCT 59.425 45.455 0.00 0.00 37.01 3.79
1857 1885 2.282958 AAGCAGGGGACGAGACGA 60.283 61.111 0.00 0.00 0.00 4.20
1858 1886 1.878656 AAGAAGCAGGGGACGAGACG 61.879 60.000 0.00 0.00 0.00 4.18
1859 1887 0.321996 AAAGAAGCAGGGGACGAGAC 59.678 55.000 0.00 0.00 0.00 3.36
1860 1888 1.056660 AAAAGAAGCAGGGGACGAGA 58.943 50.000 0.00 0.00 0.00 4.04
1861 1889 1.160137 CAAAAGAAGCAGGGGACGAG 58.840 55.000 0.00 0.00 0.00 4.18
1864 1892 0.884514 GAGCAAAAGAAGCAGGGGAC 59.115 55.000 0.00 0.00 0.00 4.46
1868 1896 1.245732 AGCAGAGCAAAAGAAGCAGG 58.754 50.000 0.00 0.00 0.00 4.85
1887 1915 2.178106 GAGGGGAGTAGAGGAGGATGAA 59.822 54.545 0.00 0.00 0.00 2.57
1929 1957 8.311650 ACGGCATATTAGTTTGTTCATCTATC 57.688 34.615 0.00 0.00 0.00 2.08
1936 1964 8.609176 TGAATCTAACGGCATATTAGTTTGTTC 58.391 33.333 0.00 0.00 32.46 3.18
1937 1965 8.395633 GTGAATCTAACGGCATATTAGTTTGTT 58.604 33.333 0.00 0.00 32.46 2.83
1939 1967 7.226720 AGGTGAATCTAACGGCATATTAGTTTG 59.773 37.037 0.00 0.00 32.46 2.93
1940 1968 7.280356 AGGTGAATCTAACGGCATATTAGTTT 58.720 34.615 0.00 0.00 32.46 2.66
1943 2116 6.929049 TGAAGGTGAATCTAACGGCATATTAG 59.071 38.462 0.00 0.00 0.00 1.73
1971 2144 8.497554 TGTATATAATCGAATTAACGGCCAAAC 58.502 33.333 2.24 0.00 0.00 2.93
2188 2361 0.444260 GCGCAACTCAGCTTACCTTC 59.556 55.000 0.30 0.00 0.00 3.46
2197 2370 0.445436 GAACAGATGGCGCAACTCAG 59.555 55.000 10.83 1.65 0.00 3.35
2255 2432 0.036765 TGTGCCGGTATGAGAACACC 60.037 55.000 1.90 0.00 0.00 4.16
2293 2470 3.922171 ATGAACCAGAGGACTCCAATC 57.078 47.619 0.00 0.00 0.00 2.67
2392 2569 9.907576 CGCTTTCAGAAGACACTAATAAATTAG 57.092 33.333 7.96 7.96 39.23 1.73
2454 2631 7.545615 GGAATGGCCATTTAGTTTTCAAAGTAG 59.454 37.037 31.13 0.00 36.34 2.57
2581 2771 9.577110 TCTCAACTTATGATTTTTGATGCAATC 57.423 29.630 0.00 0.00 39.89 2.67
2861 3062 3.821600 GAGCTGCAGATGAAATGATGGAT 59.178 43.478 20.43 0.00 0.00 3.41
2906 3107 0.881796 GGCAGCAGAGGTAACCAAAC 59.118 55.000 0.00 0.00 37.17 2.93
2968 3169 3.861276 TTTCCGATGCTTTAGAGTCGA 57.139 42.857 0.00 0.00 36.25 4.20
3141 3342 7.041098 GCCTAAGTGGTTCCATATCATAAAGTG 60.041 40.741 0.00 0.00 38.35 3.16
3161 3362 4.836825 TCAGAACTTCAGAATGGCCTAAG 58.163 43.478 3.32 0.79 36.16 2.18
3253 3454 2.424557 AGTCTGAGCAAGAGCAACATG 58.575 47.619 0.00 0.00 45.49 3.21
3295 3496 5.690865 TCAACTAAACTGATGTCCCAACTT 58.309 37.500 0.00 0.00 0.00 2.66
3314 3515 3.963383 ATTCAGACCAACGTGTTCAAC 57.037 42.857 0.00 0.00 0.00 3.18
3374 3580 0.324943 ATAGCTGCACGAACTGGGTT 59.675 50.000 1.02 0.00 0.00 4.11
3375 3581 0.324943 AATAGCTGCACGAACTGGGT 59.675 50.000 1.02 0.00 0.00 4.51
3384 3590 3.192212 AGCAAAAGAGGAAATAGCTGCAC 59.808 43.478 1.02 0.00 0.00 4.57
3399 3605 4.754332 CGCAAACAATCTTTCAGCAAAAG 58.246 39.130 5.48 5.48 44.89 2.27
3400 3606 3.001127 GCGCAAACAATCTTTCAGCAAAA 59.999 39.130 0.30 0.00 0.00 2.44
3401 3607 2.539274 GCGCAAACAATCTTTCAGCAAA 59.461 40.909 0.30 0.00 0.00 3.68
3402 3608 2.126467 GCGCAAACAATCTTTCAGCAA 58.874 42.857 0.30 0.00 0.00 3.91
3403 3609 1.066757 TGCGCAAACAATCTTTCAGCA 59.933 42.857 8.16 0.00 0.00 4.41
3404 3610 1.453148 GTGCGCAAACAATCTTTCAGC 59.547 47.619 14.00 0.00 0.00 4.26
3405 3611 2.053627 GGTGCGCAAACAATCTTTCAG 58.946 47.619 14.00 0.00 0.00 3.02
3406 3612 1.599171 CGGTGCGCAAACAATCTTTCA 60.599 47.619 14.00 0.00 0.00 2.69
3407 3613 1.052287 CGGTGCGCAAACAATCTTTC 58.948 50.000 14.00 0.00 0.00 2.62
3408 3614 0.318614 CCGGTGCGCAAACAATCTTT 60.319 50.000 14.00 0.00 0.00 2.52
3409 3615 1.285641 CCGGTGCGCAAACAATCTT 59.714 52.632 14.00 0.00 0.00 2.40
3410 3616 2.625823 CCCGGTGCGCAAACAATCT 61.626 57.895 14.00 0.00 0.00 2.40
3411 3617 2.126502 CCCGGTGCGCAAACAATC 60.127 61.111 14.00 0.00 0.00 2.67
3412 3618 3.679738 CCCCGGTGCGCAAACAAT 61.680 61.111 14.00 0.00 0.00 2.71
3443 3649 2.268920 GATCCTTCGCTGGTGGCA 59.731 61.111 0.00 0.00 41.91 4.92
3447 3653 1.694169 ATGGGGATCCTTCGCTGGT 60.694 57.895 12.58 0.00 35.26 4.00
3451 3657 2.432123 GGGATGGGGATCCTTCGC 59.568 66.667 12.58 10.85 40.86 4.70
3452 3658 2.529744 GGGGGATGGGGATCCTTCG 61.530 68.421 12.58 0.00 40.54 3.79
3453 3659 3.594355 GGGGGATGGGGATCCTTC 58.406 66.667 12.58 6.53 40.54 3.46
3489 3696 2.359850 CTTAGCCTGCAACGCCCA 60.360 61.111 1.91 0.00 0.00 5.36
3531 3738 1.981636 CAGGCTGAGGAGACTTGCT 59.018 57.895 9.42 0.00 44.43 3.91
3536 3743 1.067250 GATCGCAGGCTGAGGAGAC 59.933 63.158 20.86 9.02 0.00 3.36
3548 3755 2.186644 CACCCACATCCGATCGCA 59.813 61.111 10.32 0.00 0.00 5.10
3699 3912 3.249189 GGACTGAGGTGTGGCCCA 61.249 66.667 0.00 0.00 38.26 5.36
3714 3932 1.378646 AGGAGAGATGCACGACGGA 60.379 57.895 0.00 0.00 0.00 4.69
3761 3982 0.968901 TCCTCGTGTTGCGGGTCTAT 60.969 55.000 0.00 0.00 40.01 1.98
3809 4030 0.898320 CGAAGGAGATGGACACCACT 59.102 55.000 0.00 0.00 35.80 4.00
3816 4037 1.816537 CTTCGGCGAAGGAGATGGA 59.183 57.895 35.50 6.85 36.16 3.41
3832 4053 2.203538 CAGCCAGCCAACCACCTT 60.204 61.111 0.00 0.00 0.00 3.50
3874 4095 4.530857 CATCCCCACTCGACGCCC 62.531 72.222 0.00 0.00 0.00 6.13
3969 4192 0.671472 CTGCAGTGGCGATGTCTTCA 60.671 55.000 5.25 0.00 45.35 3.02
4018 4241 2.660064 CCCGGGACTGGGTTCTCAG 61.660 68.421 18.48 0.00 44.76 3.35
4089 4312 1.470098 CAGCTCCTCCAAAAACGATGG 59.530 52.381 0.00 0.00 39.41 3.51
4104 4327 1.227205 CTCGCCCATCTGACAGCTC 60.227 63.158 0.00 0.00 0.00 4.09
4110 4333 0.247460 CACTTGTCTCGCCCATCTGA 59.753 55.000 0.00 0.00 0.00 3.27
4119 4342 1.734477 CGCTCCACCACTTGTCTCG 60.734 63.158 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.