Multiple sequence alignment - TraesCS5A01G100000

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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 TraesCS5A01G100000 chr5A 100.000 3058 0 0 1 3058 143553947 143550890 0.000000e+00 5648
1 TraesCS5A01G100000 chr5A 80.822 511 92 4 2549 3056 279845504 279846011 2.210000e-106 396
2 TraesCS5A01G100000 chr5D 92.896 2548 109 26 1 2503 128566490 128563970 0.000000e+00 3637
3 TraesCS5A01G100000 chr2D 86.819 569 72 3 1048 1613 480181621 480181053 1.550000e-177 632
4 TraesCS5A01G100000 chr2D 86.140 570 74 5 1048 1613 480325483 480324915 7.250000e-171 610
5 TraesCS5A01G100000 chr2D 85.821 134 19 0 1698 1831 480324457 480324324 3.180000e-30 143
6 TraesCS5A01G100000 chr2D 84.328 134 21 0 1698 1831 480180549 480180416 6.880000e-27 132
7 TraesCS5A01G100000 chr2B 86.467 569 74 2 1048 1613 563046391 563045823 3.350000e-174 621
8 TraesCS5A01G100000 chr2B 86.092 568 74 5 1048 1611 563184907 563184341 9.380000e-170 606
9 TraesCS5A01G100000 chr2B 84.588 571 81 5 1048 1613 216708511 216709079 7.400000e-156 560
10 TraesCS5A01G100000 chr2B 85.075 134 20 0 1698 1831 563045282 563045149 1.480000e-28 137
11 TraesCS5A01G100000 chr2A 86.467 569 74 3 1048 1613 622748004 622747436 3.350000e-174 621
12 TraesCS5A01G100000 chr2A 86.467 569 74 3 1048 1613 622853692 622853124 3.350000e-174 621
13 TraesCS5A01G100000 chr2A 84.413 571 82 7 1048 1613 170602969 170603537 3.440000e-154 555
14 TraesCS5A01G100000 chr2A 80.512 508 91 6 2553 3056 151607197 151607700 1.720000e-102 383
15 TraesCS5A01G100000 chr2A 83.562 146 24 0 1698 1843 622746936 622746791 1.480000e-28 137
16 TraesCS5A01G100000 chr3A 83.107 515 77 8 2549 3057 683578712 683578202 7.730000e-126 460
17 TraesCS5A01G100000 chr7A 81.676 513 88 4 2549 3058 443814605 443815114 3.650000e-114 422
18 TraesCS5A01G100000 chr4A 81.225 506 91 2 2549 3051 546789235 546788731 3.670000e-109 405
19 TraesCS5A01G100000 chr4A 80.922 477 88 3 2582 3058 131065425 131065898 1.040000e-99 374
20 TraesCS5A01G100000 chr4A 79.884 517 94 8 2548 3058 413977592 413978104 1.340000e-98 370
21 TraesCS5A01G100000 chr4A 84.559 136 19 2 1698 1832 591862597 591862731 1.910000e-27 134
22 TraesCS5A01G100000 chr1A 81.299 508 87 6 2556 3058 123916686 123917190 3.670000e-109 405
23 TraesCS5A01G100000 chr1D 80.971 515 87 9 2549 3058 146875589 146875081 6.140000e-107 398


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 TraesCS5A01G100000 chr5A 143550890 143553947 3057 True 5648.0 5648 100.0000 1 3058 1 chr5A.!!$R1 3057
1 TraesCS5A01G100000 chr5A 279845504 279846011 507 False 396.0 396 80.8220 2549 3056 1 chr5A.!!$F1 507
2 TraesCS5A01G100000 chr5D 128563970 128566490 2520 True 3637.0 3637 92.8960 1 2503 1 chr5D.!!$R1 2502
3 TraesCS5A01G100000 chr2D 480180416 480181621 1205 True 382.0 632 85.5735 1048 1831 2 chr2D.!!$R1 783
4 TraesCS5A01G100000 chr2D 480324324 480325483 1159 True 376.5 610 85.9805 1048 1831 2 chr2D.!!$R2 783
5 TraesCS5A01G100000 chr2B 563184341 563184907 566 True 606.0 606 86.0920 1048 1611 1 chr2B.!!$R1 563
6 TraesCS5A01G100000 chr2B 216708511 216709079 568 False 560.0 560 84.5880 1048 1613 1 chr2B.!!$F1 565
7 TraesCS5A01G100000 chr2B 563045149 563046391 1242 True 379.0 621 85.7710 1048 1831 2 chr2B.!!$R2 783
8 TraesCS5A01G100000 chr2A 622853124 622853692 568 True 621.0 621 86.4670 1048 1613 1 chr2A.!!$R1 565
9 TraesCS5A01G100000 chr2A 170602969 170603537 568 False 555.0 555 84.4130 1048 1613 1 chr2A.!!$F2 565
10 TraesCS5A01G100000 chr2A 151607197 151607700 503 False 383.0 383 80.5120 2553 3056 1 chr2A.!!$F1 503
11 TraesCS5A01G100000 chr2A 622746791 622748004 1213 True 379.0 621 85.0145 1048 1843 2 chr2A.!!$R2 795
12 TraesCS5A01G100000 chr3A 683578202 683578712 510 True 460.0 460 83.1070 2549 3057 1 chr3A.!!$R1 508
13 TraesCS5A01G100000 chr7A 443814605 443815114 509 False 422.0 422 81.6760 2549 3058 1 chr7A.!!$F1 509
14 TraesCS5A01G100000 chr4A 546788731 546789235 504 True 405.0 405 81.2250 2549 3051 1 chr4A.!!$R1 502
15 TraesCS5A01G100000 chr4A 413977592 413978104 512 False 370.0 370 79.8840 2548 3058 1 chr4A.!!$F2 510
16 TraesCS5A01G100000 chr1A 123916686 123917190 504 False 405.0 405 81.2990 2556 3058 1 chr1A.!!$F1 502
17 TraesCS5A01G100000 chr1D 146875081 146875589 508 True 398.0 398 80.9710 2549 3058 1 chr1D.!!$R1 509

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
210 211 0.165944 GTCGTTTTGATGGAGCACGG 59.834 55.0 0.0 0.0 0.0 4.94 F
874 910 0.178961 AACCTTCCTCTTGCCCCAAC 60.179 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 2495 0.325933 CACCCAGAAGATCCACTGCA 59.674 55.0 10.18 0.0 33.4 4.41 R
2512 3070 0.034477 GAGGCGAGGGGATTTTTCCA 60.034 55.0 0.00 0.0 0.0 3.53 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
28 29 5.239306 CCAACAGAGATTCTAGCAAACACAA 59.761 40.000 0.00 0.00 0.00 3.33
35 36 3.902261 TCTAGCAAACACAATGTGCAG 57.098 42.857 14.01 4.67 40.83 4.41
37 38 2.497107 AGCAAACACAATGTGCAGAC 57.503 45.000 14.01 1.13 40.83 3.51
115 116 3.450578 CGTAAGCAAATTAGCGAGGGTA 58.549 45.455 0.00 0.00 40.15 3.69
117 118 4.084537 CGTAAGCAAATTAGCGAGGGTATG 60.085 45.833 0.00 0.00 40.15 2.39
144 145 2.689646 GGCCTTATAGCGAAGGTGATC 58.310 52.381 14.24 0.00 46.73 2.92
146 147 2.927014 GCCTTATAGCGAAGGTGATCGG 60.927 54.545 14.24 0.00 46.73 4.18
157 158 3.634397 AGGTGATCGGACATTCAACAT 57.366 42.857 0.00 0.00 31.82 2.71
169 170 5.048504 GGACATTCAACATGAGTGACACAAT 60.049 40.000 8.59 0.00 36.36 2.71
173 174 6.638096 TTCAACATGAGTGACACAATGATT 57.362 33.333 21.53 12.40 0.00 2.57
179 180 7.365741 ACATGAGTGACACAATGATTCTTTTC 58.634 34.615 21.53 3.06 0.00 2.29
198 199 7.992008 TCTTTTCAAATAGGTCAAGTCGTTTT 58.008 30.769 0.00 0.00 0.00 2.43
210 211 0.165944 GTCGTTTTGATGGAGCACGG 59.834 55.000 0.00 0.00 0.00 4.94
257 258 6.591935 TCTATCAACCCATTGTGTAAGGATC 58.408 40.000 0.00 0.00 37.11 3.36
267 268 7.362920 CCCATTGTGTAAGGATCGATTTTCTTT 60.363 37.037 0.00 0.00 0.00 2.52
272 273 6.801862 GTGTAAGGATCGATTTTCTTTGTTGG 59.198 38.462 0.00 0.00 0.00 3.77
273 274 4.440839 AGGATCGATTTTCTTTGTTGGC 57.559 40.909 0.00 0.00 0.00 4.52
274 275 3.193479 AGGATCGATTTTCTTTGTTGGCC 59.807 43.478 0.00 0.00 0.00 5.36
275 276 3.193479 GGATCGATTTTCTTTGTTGGCCT 59.807 43.478 3.32 0.00 0.00 5.19
335 339 8.167605 TGTTTGAGTTTTGGGTTATCGATTTA 57.832 30.769 1.71 0.00 0.00 1.40
408 412 4.945543 TGATGACAATCAATGAGGAACTGG 59.054 41.667 0.00 0.00 38.39 4.00
431 435 4.479158 GGATATCCAATGGGTTTTAGGCA 58.521 43.478 17.34 0.00 35.64 4.75
463 467 9.178758 GGAAAGTAGATGATTGGTCATAAGTTT 57.821 33.333 0.00 0.00 44.96 2.66
511 516 2.084546 GTTGGCGCTACAAGAAATCCT 58.915 47.619 7.64 0.00 0.00 3.24
516 521 3.804873 GGCGCTACAAGAAATCCTCTAAG 59.195 47.826 7.64 0.00 32.46 2.18
519 524 5.581085 GCGCTACAAGAAATCCTCTAAGAAA 59.419 40.000 0.00 0.00 32.46 2.52
521 526 7.675170 GCGCTACAAGAAATCCTCTAAGAAAAG 60.675 40.741 0.00 0.00 32.46 2.27
526 537 8.432805 ACAAGAAATCCTCTAAGAAAAGTGAGA 58.567 33.333 0.00 0.00 32.46 3.27
535 546 7.821359 CCTCTAAGAAAAGTGAGACATCATGAA 59.179 37.037 0.00 0.00 37.87 2.57
563 574 0.970427 AAAATCCGGCGGCCAGAATT 60.970 50.000 23.83 12.78 0.00 2.17
569 580 3.508840 GCGGCCAGAATTGTCCGG 61.509 66.667 2.24 0.00 41.96 5.14
579 590 5.072741 CCAGAATTGTCCGGGATATGAAAT 58.927 41.667 0.00 0.00 0.00 2.17
582 593 5.536161 AGAATTGTCCGGGATATGAAATTGG 59.464 40.000 0.00 0.00 0.00 3.16
584 595 4.722526 TGTCCGGGATATGAAATTGGAT 57.277 40.909 0.00 0.00 0.00 3.41
587 598 3.397618 TCCGGGATATGAAATTGGATGGT 59.602 43.478 0.00 0.00 0.00 3.55
589 600 4.218417 CCGGGATATGAAATTGGATGGTTC 59.782 45.833 0.00 0.00 0.00 3.62
600 611 1.751351 TGGATGGTTCAAAACGTTGCA 59.249 42.857 0.00 0.00 34.50 4.08
601 612 2.223688 TGGATGGTTCAAAACGTTGCAG 60.224 45.455 0.00 0.00 34.50 4.41
602 613 1.786579 GATGGTTCAAAACGTTGCAGC 59.213 47.619 0.00 0.00 34.50 5.25
604 615 1.202245 TGGTTCAAAACGTTGCAGCTC 60.202 47.619 0.00 0.00 34.50 4.09
605 616 1.065551 GGTTCAAAACGTTGCAGCTCT 59.934 47.619 0.00 0.00 34.50 4.09
606 617 2.111756 GTTCAAAACGTTGCAGCTCTG 58.888 47.619 0.00 0.00 34.50 3.35
607 618 1.378531 TCAAAACGTTGCAGCTCTGT 58.621 45.000 0.00 0.00 34.50 3.41
608 619 1.063912 TCAAAACGTTGCAGCTCTGTG 59.936 47.619 0.00 0.00 34.50 3.66
609 620 1.063912 CAAAACGTTGCAGCTCTGTGA 59.936 47.619 0.00 0.00 0.00 3.58
610 621 0.940126 AAACGTTGCAGCTCTGTGAG 59.060 50.000 0.00 0.00 0.00 3.51
611 622 0.882042 AACGTTGCAGCTCTGTGAGG 60.882 55.000 0.00 0.00 0.00 3.86
612 623 2.031516 CGTTGCAGCTCTGTGAGGG 61.032 63.158 0.00 0.00 0.00 4.30
613 624 1.072159 GTTGCAGCTCTGTGAGGGT 59.928 57.895 0.00 0.00 0.00 4.34
614 625 0.536006 GTTGCAGCTCTGTGAGGGTT 60.536 55.000 0.00 0.00 0.00 4.11
615 626 1.055849 TTGCAGCTCTGTGAGGGTTA 58.944 50.000 0.00 0.00 0.00 2.85
616 627 1.055849 TGCAGCTCTGTGAGGGTTAA 58.944 50.000 0.00 0.00 0.00 2.01
617 628 1.419762 TGCAGCTCTGTGAGGGTTAAA 59.580 47.619 0.00 0.00 0.00 1.52
622 633 4.580580 CAGCTCTGTGAGGGTTAAAACTTT 59.419 41.667 0.00 0.00 0.00 2.66
635 646 7.396339 AGGGTTAAAACTTTAAAGGATGCCTAG 59.604 37.037 19.14 0.00 34.71 3.02
646 657 3.733337 AGGATGCCTAGCTGTAAATTCG 58.267 45.455 0.00 0.00 28.47 3.34
700 711 8.372521 GCGTAAATAAATGTTGGAAATTGACTG 58.627 33.333 0.00 0.00 0.00 3.51
744 776 1.425412 AGTATGAACACGCGTCAACC 58.575 50.000 9.86 0.00 0.00 3.77
766 798 2.887152 CCAGAAAAGGAAACACCCTCTG 59.113 50.000 0.00 0.00 38.76 3.35
874 910 0.178961 AACCTTCCTCTTGCCCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
887 923 0.902984 CCCCAACAGGCTTAAACCCC 60.903 60.000 0.00 0.00 0.00 4.95
898 934 5.704053 CAGGCTTAAACCCCTATAAATACCG 59.296 44.000 0.00 0.00 0.00 4.02
900 936 4.456911 GCTTAAACCCCTATAAATACCGCC 59.543 45.833 0.00 0.00 0.00 6.13
902 938 1.720781 ACCCCTATAAATACCGCCGT 58.279 50.000 0.00 0.00 0.00 5.68
914 950 0.952010 ACCGCCGTTCATAACCACAC 60.952 55.000 0.00 0.00 0.00 3.82
915 951 1.418367 CGCCGTTCATAACCACACG 59.582 57.895 0.00 0.00 0.00 4.49
937 973 3.417101 AGACCACAACACAAACACAAGA 58.583 40.909 0.00 0.00 0.00 3.02
938 974 3.823873 AGACCACAACACAAACACAAGAA 59.176 39.130 0.00 0.00 0.00 2.52
939 975 4.462483 AGACCACAACACAAACACAAGAAT 59.538 37.500 0.00 0.00 0.00 2.40
940 976 5.047377 AGACCACAACACAAACACAAGAATT 60.047 36.000 0.00 0.00 0.00 2.17
941 977 6.151985 AGACCACAACACAAACACAAGAATTA 59.848 34.615 0.00 0.00 0.00 1.40
942 978 6.096695 ACCACAACACAAACACAAGAATTAC 58.903 36.000 0.00 0.00 0.00 1.89
943 979 5.518487 CCACAACACAAACACAAGAATTACC 59.482 40.000 0.00 0.00 0.00 2.85
944 980 6.329496 CACAACACAAACACAAGAATTACCT 58.671 36.000 0.00 0.00 0.00 3.08
969 1005 2.764269 AGTAGCCTTGCTTCCATCCTA 58.236 47.619 0.00 0.00 40.44 2.94
991 1027 4.455606 AGAGTTCCAAGAAAACCACAGAG 58.544 43.478 0.00 0.00 0.00 3.35
1065 1101 1.305623 GGACTACTCCGACCCTCCA 59.694 63.158 0.00 0.00 0.00 3.86
1572 1611 2.600769 ACCGTCTTCTCCGCCACT 60.601 61.111 0.00 0.00 0.00 4.00
1613 1652 2.218037 GACTCCCACGTCCCGGTAAC 62.218 65.000 0.00 0.00 0.00 2.50
1614 1653 2.996734 TCCCACGTCCCGGTAACC 60.997 66.667 0.00 0.00 0.00 2.85
1669 1895 1.148157 CTATCGCCTTGGCACACTCG 61.148 60.000 12.45 0.00 39.29 4.18
1678 1904 3.440173 CCTTGGCACACTCGTTTTGATAT 59.560 43.478 0.00 0.00 39.29 1.63
1685 1911 6.183360 GGCACACTCGTTTTGATATATGTTGA 60.183 38.462 0.00 0.00 0.00 3.18
1903 2451 5.484958 GCAAGAATTTTAGTGTCGATCGAG 58.515 41.667 20.09 2.32 0.00 4.04
1920 2468 1.155042 GAGCTTGCCTGAACTGACAG 58.845 55.000 0.00 0.00 37.61 3.51
1929 2482 2.620115 CCTGAACTGACAGTGCATTGTT 59.380 45.455 16.89 0.00 32.25 2.83
1935 2488 3.181497 ACTGACAGTGCATTGTTGTTCAC 60.181 43.478 16.63 3.04 0.00 3.18
1942 2495 2.957680 TGCATTGTTGTTCACCTGTGAT 59.042 40.909 0.03 0.00 39.64 3.06
2006 2559 2.184579 GCGCTCTACCACCAGACC 59.815 66.667 0.00 0.00 0.00 3.85
2018 2571 4.899239 CAGACCATCCTCCGCGCC 62.899 72.222 0.00 0.00 0.00 6.53
2045 2598 2.444256 GGGCTATGGCTCCTTCCGT 61.444 63.158 0.00 0.00 38.73 4.69
2068 2621 4.350441 CGCCTAGCTAGCTCGCCC 62.350 72.222 23.26 7.73 0.00 6.13
2070 2623 2.731374 CCTAGCTAGCTCGCCCAC 59.269 66.667 23.26 0.00 0.00 4.61
2076 2629 3.161450 TAGCTCGCCCACCCATCC 61.161 66.667 0.00 0.00 0.00 3.51
2104 2657 6.700352 CCAAAATTGGCATCTTTCTCCTTAA 58.300 36.000 0.00 0.00 42.21 1.85
2105 2658 6.591448 CCAAAATTGGCATCTTTCTCCTTAAC 59.409 38.462 0.00 0.00 42.21 2.01
2170 2723 3.350219 AGTGAAGTGTCCTTGTGTGTT 57.650 42.857 0.00 0.00 0.00 3.32
2200 2753 4.213270 TCCGATTGAAGCAGTTGTAACTTG 59.787 41.667 0.00 0.00 37.08 3.16
2422 2980 2.771372 ACTGACTGTTTTGGGCCAAAAT 59.229 40.909 38.50 26.95 43.66 1.82
2429 2987 5.012561 ACTGTTTTGGGCCAAAATAATGCTA 59.987 36.000 38.50 17.98 43.66 3.49
2490 3048 4.778143 ATTGGGGCGACGCTGGAC 62.778 66.667 20.77 8.11 45.02 4.02
2504 3062 4.736896 GGACACTGGCCGACCGAC 62.737 72.222 0.00 0.00 39.70 4.79
2505 3063 4.736896 GACACTGGCCGACCGACC 62.737 72.222 0.00 0.00 39.70 4.79
2509 3067 4.873129 CTGGCCGACCGACCGATG 62.873 72.222 0.00 0.00 39.70 3.84
2512 3070 4.891727 GCCGACCGACCGATGCAT 62.892 66.667 0.00 0.00 0.00 3.96
2513 3071 2.961721 CCGACCGACCGATGCATG 60.962 66.667 2.46 0.00 0.00 4.06
2514 3072 2.961721 CGACCGACCGATGCATGG 60.962 66.667 2.46 8.85 0.00 3.66
2515 3073 2.499205 GACCGACCGATGCATGGA 59.501 61.111 18.41 0.00 0.00 3.41
2516 3074 1.153449 GACCGACCGATGCATGGAA 60.153 57.895 18.41 0.00 0.00 3.53
2517 3075 0.742990 GACCGACCGATGCATGGAAA 60.743 55.000 18.41 0.00 0.00 3.13
2518 3076 0.322098 ACCGACCGATGCATGGAAAA 60.322 50.000 18.41 0.00 0.00 2.29
2519 3077 0.808125 CCGACCGATGCATGGAAAAA 59.192 50.000 18.41 0.00 0.00 1.94
2520 3078 1.405105 CCGACCGATGCATGGAAAAAT 59.595 47.619 18.41 0.04 0.00 1.82
2521 3079 2.541588 CCGACCGATGCATGGAAAAATC 60.542 50.000 18.41 7.19 0.00 2.17
2522 3080 2.541588 CGACCGATGCATGGAAAAATCC 60.542 50.000 18.41 0.00 0.00 3.01
2523 3081 1.756538 ACCGATGCATGGAAAAATCCC 59.243 47.619 18.41 0.00 0.00 3.85
2524 3082 1.069049 CCGATGCATGGAAAAATCCCC 59.931 52.381 10.66 0.00 0.00 4.81
2525 3083 2.034124 CGATGCATGGAAAAATCCCCT 58.966 47.619 2.46 0.00 0.00 4.79
2526 3084 2.035066 CGATGCATGGAAAAATCCCCTC 59.965 50.000 2.46 0.00 0.00 4.30
2527 3085 1.473258 TGCATGGAAAAATCCCCTCG 58.527 50.000 0.00 0.00 0.00 4.63
2528 3086 0.103026 GCATGGAAAAATCCCCTCGC 59.897 55.000 0.00 0.00 0.00 5.03
2529 3087 0.746659 CATGGAAAAATCCCCTCGCC 59.253 55.000 0.00 0.00 0.00 5.54
2530 3088 0.631212 ATGGAAAAATCCCCTCGCCT 59.369 50.000 0.00 0.00 0.00 5.52
2531 3089 0.034477 TGGAAAAATCCCCTCGCCTC 60.034 55.000 0.00 0.00 0.00 4.70
2532 3090 0.256177 GGAAAAATCCCCTCGCCTCT 59.744 55.000 0.00 0.00 0.00 3.69
2533 3091 1.383523 GAAAAATCCCCTCGCCTCTG 58.616 55.000 0.00 0.00 0.00 3.35
2534 3092 0.681243 AAAAATCCCCTCGCCTCTGC 60.681 55.000 0.00 0.00 0.00 4.26
2535 3093 2.558380 AAAATCCCCTCGCCTCTGCC 62.558 60.000 0.00 0.00 0.00 4.85
2536 3094 4.804420 ATCCCCTCGCCTCTGCCA 62.804 66.667 0.00 0.00 0.00 4.92
2539 3097 4.767255 CCCTCGCCTCTGCCACAC 62.767 72.222 0.00 0.00 0.00 3.82
2540 3098 4.007644 CCTCGCCTCTGCCACACA 62.008 66.667 0.00 0.00 0.00 3.72
2541 3099 2.740055 CTCGCCTCTGCCACACAC 60.740 66.667 0.00 0.00 0.00 3.82
2542 3100 3.519973 CTCGCCTCTGCCACACACA 62.520 63.158 0.00 0.00 0.00 3.72
2543 3101 3.349006 CGCCTCTGCCACACACAC 61.349 66.667 0.00 0.00 0.00 3.82
2544 3102 3.349006 GCCTCTGCCACACACACG 61.349 66.667 0.00 0.00 0.00 4.49
2545 3103 2.421314 CCTCTGCCACACACACGA 59.579 61.111 0.00 0.00 0.00 4.35
2546 3104 1.956170 CCTCTGCCACACACACGAC 60.956 63.158 0.00 0.00 0.00 4.34
2585 3148 1.814772 CTAGCCTCATCAGCTCCCCG 61.815 65.000 0.00 0.00 41.83 5.73
2641 3204 0.898789 ACACCTCCAGGACGAACGAT 60.899 55.000 0.00 0.00 38.94 3.73
2686 3249 2.711922 CGGTCGGCTGCTAAGAGGT 61.712 63.158 0.00 0.00 0.00 3.85
2691 3254 1.002134 GGCTGCTAAGAGGTGGCAA 60.002 57.895 0.00 0.00 35.49 4.52
2713 3276 0.966875 TACCAGAAGGCGGCTACGAA 60.967 55.000 13.71 0.00 43.17 3.85
2717 3281 1.444895 GAAGGCGGCTACGAAACGA 60.445 57.895 13.71 0.00 44.60 3.85
2727 3291 2.240040 CTACGAAACGACCGACTTCTG 58.760 52.381 0.00 0.00 0.00 3.02
2761 3325 0.670162 ATGCGCTCAAAGTTTGCACT 59.330 45.000 9.73 0.00 38.54 4.40
2765 3329 1.331756 CGCTCAAAGTTTGCACTCACT 59.668 47.619 10.90 0.00 30.45 3.41
2775 3339 5.539048 AGTTTGCACTCACTTAACTACGAT 58.461 37.500 0.00 0.00 0.00 3.73
2789 3353 3.822192 CGATGAGACGGGGCGTGA 61.822 66.667 0.00 0.00 41.37 4.35
2798 3362 2.927580 CGGGGCGTGACTACAGTGT 61.928 63.158 0.00 0.00 0.00 3.55
2804 3368 1.741706 GCGTGACTACAGTGTAGCCTA 59.258 52.381 26.79 12.69 0.00 3.93
2916 3481 4.081142 CCTGTGACATCACCTACCACATAA 60.081 45.833 9.48 0.00 45.88 1.90
2922 3487 1.754803 TCACCTACCACATAAGGAGCG 59.245 52.381 0.00 0.00 36.66 5.03
2923 3488 1.120530 ACCTACCACATAAGGAGCGG 58.879 55.000 0.00 0.00 36.66 5.52
2994 3559 3.717294 GGCAAGCCCCGAGAAGGA 61.717 66.667 0.00 0.00 45.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 5.118664 CGTCATACATACCCTCGCTAATTTG 59.881 44.000 0.00 0.00 0.00 2.32
109 110 1.339097 AGGCCGTCATACATACCCTC 58.661 55.000 0.00 0.00 0.00 4.30
115 116 2.823747 TCGCTATAAGGCCGTCATACAT 59.176 45.455 0.00 0.00 0.00 2.29
117 118 3.243336 CTTCGCTATAAGGCCGTCATAC 58.757 50.000 0.00 0.00 0.00 2.39
144 145 3.066380 TGTCACTCATGTTGAATGTCCG 58.934 45.455 0.00 0.00 0.00 4.79
146 147 5.422666 TTGTGTCACTCATGTTGAATGTC 57.577 39.130 4.27 0.00 0.00 3.06
157 158 6.940831 TGAAAAGAATCATTGTGTCACTCA 57.059 33.333 4.27 0.00 0.00 3.41
169 170 7.444183 ACGACTTGACCTATTTGAAAAGAATCA 59.556 33.333 0.00 0.00 0.00 2.57
173 174 7.562454 AAACGACTTGACCTATTTGAAAAGA 57.438 32.000 0.00 0.00 0.00 2.52
179 180 6.072728 TCCATCAAAACGACTTGACCTATTTG 60.073 38.462 6.17 0.00 38.12 2.32
198 199 1.199615 TCATTACCCGTGCTCCATCA 58.800 50.000 0.00 0.00 0.00 3.07
244 245 8.110860 ACAAAGAAAATCGATCCTTACACAAT 57.889 30.769 0.00 0.00 0.00 2.71
257 258 2.061028 GCAGGCCAACAAAGAAAATCG 58.939 47.619 5.01 0.00 0.00 3.34
286 290 4.904241 AGCTAATGATCATAGTTGGCTCC 58.096 43.478 9.04 0.00 35.15 4.70
335 339 8.321353 TGGTACTTACTCAGAATGTTGATGATT 58.679 33.333 0.00 0.00 37.40 2.57
352 356 9.640963 GATGAACCTACATATCATGGTACTTAC 57.359 37.037 0.00 0.00 34.10 2.34
400 404 2.718609 CCATTGGATATCCCCAGTTCCT 59.281 50.000 19.34 0.00 37.53 3.36
408 412 3.832490 GCCTAAAACCCATTGGATATCCC 59.168 47.826 19.34 1.87 34.81 3.85
431 435 5.892348 ACCAATCATCTACTTTCCCTTGTT 58.108 37.500 0.00 0.00 0.00 2.83
511 516 9.559732 TTTTCATGATGTCTCACTTTTCTTAGA 57.440 29.630 0.00 0.00 33.22 2.10
535 546 2.205911 CCGCCGGATTTTTGTGTTTTT 58.794 42.857 5.05 0.00 0.00 1.94
549 560 3.508840 GACAATTCTGGCCGCCGG 61.509 66.667 12.53 12.53 0.00 6.13
550 561 3.508840 GGACAATTCTGGCCGCCG 61.509 66.667 4.58 0.00 42.40 6.46
563 574 4.397420 CATCCAATTTCATATCCCGGACA 58.603 43.478 0.73 0.00 0.00 4.02
569 580 7.222611 CGTTTTGAACCATCCAATTTCATATCC 59.777 37.037 0.00 0.00 0.00 2.59
579 590 2.166459 TGCAACGTTTTGAACCATCCAA 59.834 40.909 0.00 0.00 34.24 3.53
582 593 1.786579 GCTGCAACGTTTTGAACCATC 59.213 47.619 0.00 0.00 34.24 3.51
584 595 0.814457 AGCTGCAACGTTTTGAACCA 59.186 45.000 0.00 0.00 34.24 3.67
587 598 1.742831 ACAGAGCTGCAACGTTTTGAA 59.257 42.857 0.00 0.00 34.24 2.69
589 600 1.063912 TCACAGAGCTGCAACGTTTTG 59.936 47.619 0.00 0.00 35.62 2.44
600 611 4.439253 AAGTTTTAACCCTCACAGAGCT 57.561 40.909 0.00 0.00 0.00 4.09
601 612 6.628919 TTAAAGTTTTAACCCTCACAGAGC 57.371 37.500 0.00 0.00 0.00 4.09
602 613 7.501225 TCCTTTAAAGTTTTAACCCTCACAGAG 59.499 37.037 14.03 0.00 32.77 3.35
604 615 7.576861 TCCTTTAAAGTTTTAACCCTCACAG 57.423 36.000 14.03 0.00 32.77 3.66
605 616 7.470841 GCATCCTTTAAAGTTTTAACCCTCACA 60.471 37.037 14.03 0.00 32.77 3.58
606 617 6.866770 GCATCCTTTAAAGTTTTAACCCTCAC 59.133 38.462 14.03 0.00 32.77 3.51
607 618 6.014925 GGCATCCTTTAAAGTTTTAACCCTCA 60.015 38.462 14.03 0.00 32.77 3.86
608 619 6.210784 AGGCATCCTTTAAAGTTTTAACCCTC 59.789 38.462 14.03 0.00 32.77 4.30
609 620 6.082031 AGGCATCCTTTAAAGTTTTAACCCT 58.918 36.000 14.03 7.16 32.77 4.34
610 621 6.354794 AGGCATCCTTTAAAGTTTTAACCC 57.645 37.500 14.03 5.24 32.77 4.11
611 622 7.033791 GCTAGGCATCCTTTAAAGTTTTAACC 58.966 38.462 14.03 7.58 34.61 2.85
612 623 7.755373 CAGCTAGGCATCCTTTAAAGTTTTAAC 59.245 37.037 14.03 0.60 34.61 2.01
613 624 7.450323 ACAGCTAGGCATCCTTTAAAGTTTTAA 59.550 33.333 14.03 0.00 34.61 1.52
614 625 6.946009 ACAGCTAGGCATCCTTTAAAGTTTTA 59.054 34.615 14.03 0.00 34.61 1.52
615 626 5.775195 ACAGCTAGGCATCCTTTAAAGTTTT 59.225 36.000 14.03 0.00 34.61 2.43
616 627 5.325239 ACAGCTAGGCATCCTTTAAAGTTT 58.675 37.500 14.03 0.00 34.61 2.66
617 628 4.923415 ACAGCTAGGCATCCTTTAAAGTT 58.077 39.130 14.03 0.00 34.61 2.66
622 633 5.758296 CGAATTTACAGCTAGGCATCCTTTA 59.242 40.000 0.00 0.00 34.61 1.85
693 704 1.599047 CTGGCCTCGTCCAGTCAAT 59.401 57.895 3.32 0.00 46.59 2.57
700 711 0.250513 ATTCTGTTCTGGCCTCGTCC 59.749 55.000 3.32 0.00 0.00 4.79
744 776 2.158460 AGAGGGTGTTTCCTTTTCTGGG 60.158 50.000 0.00 0.00 37.25 4.45
766 798 2.686915 ACGTGACCTAGCCTGTATACAC 59.313 50.000 0.08 0.00 0.00 2.90
784 816 5.897050 TGCTTAATTTTGGAAAGTTGACGT 58.103 33.333 0.00 0.00 0.00 4.34
843 876 6.882678 GCAAGAGGAAGGTTTAAGTTGGTATA 59.117 38.462 0.00 0.00 0.00 1.47
874 910 5.704053 CGGTATTTATAGGGGTTTAAGCCTG 59.296 44.000 13.14 0.00 35.71 4.85
887 923 5.927689 TGGTTATGAACGGCGGTATTTATAG 59.072 40.000 13.24 0.00 0.00 1.31
898 934 0.719465 CTCGTGTGGTTATGAACGGC 59.281 55.000 0.00 0.00 36.70 5.68
900 936 1.990563 GGTCTCGTGTGGTTATGAACG 59.009 52.381 0.00 0.00 37.38 3.95
902 938 2.365941 TGTGGTCTCGTGTGGTTATGAA 59.634 45.455 0.00 0.00 0.00 2.57
914 950 1.735018 TGTGTTTGTGTTGTGGTCTCG 59.265 47.619 0.00 0.00 0.00 4.04
915 951 3.438781 TCTTGTGTTTGTGTTGTGGTCTC 59.561 43.478 0.00 0.00 0.00 3.36
958 994 3.452627 TCTTGGAACTCTAGGATGGAAGC 59.547 47.826 0.00 0.00 0.00 3.86
969 1005 4.080299 ACTCTGTGGTTTTCTTGGAACTCT 60.080 41.667 0.00 0.00 0.00 3.24
991 1027 4.341487 ACCTCTTTGCCCATTTAACCTAC 58.659 43.478 0.00 0.00 0.00 3.18
1242 1281 2.335011 CACGCGATGCCGAGGATA 59.665 61.111 15.93 0.00 39.94 2.59
1497 1536 1.526917 CCCCGTACCGACCGAGTAT 60.527 63.158 0.00 0.00 0.00 2.12
1614 1653 4.025401 GACAGGTTTGTGCGGCCG 62.025 66.667 24.05 24.05 37.76 6.13
1615 1654 2.594592 AGACAGGTTTGTGCGGCC 60.595 61.111 0.00 0.00 37.76 6.13
1616 1655 2.617274 GGAGACAGGTTTGTGCGGC 61.617 63.158 0.00 0.00 37.76 6.53
1678 1904 5.937540 ACACCTTCGTTCATCAATCAACATA 59.062 36.000 0.00 0.00 0.00 2.29
1685 1911 2.228822 GCCAACACCTTCGTTCATCAAT 59.771 45.455 0.00 0.00 0.00 2.57
1694 2242 3.423154 GAGGCGCCAACACCTTCG 61.423 66.667 31.54 0.00 36.05 3.79
1716 2264 2.433664 AACACCGCGAACCCGATC 60.434 61.111 8.23 0.00 38.22 3.69
1903 2451 0.590195 CACTGTCAGTTCAGGCAAGC 59.410 55.000 1.67 0.00 39.48 4.01
1920 2468 2.098934 TCACAGGTGAACAACAATGCAC 59.901 45.455 0.00 0.00 36.53 4.57
1942 2495 0.325933 CACCCAGAAGATCCACTGCA 59.674 55.000 10.18 0.00 33.40 4.41
2045 2598 0.669077 GAGCTAGCTAGGCGTTGCTA 59.331 55.000 19.38 18.89 40.35 3.49
2068 2621 2.353605 CCAATTTTGGTTCGGATGGGTG 60.354 50.000 0.95 0.00 43.43 4.61
2070 2623 2.671130 CCAATTTTGGTTCGGATGGG 57.329 50.000 0.95 0.00 43.43 4.00
2104 2657 4.589908 ACTTCACAGTGGACTGAAAAAGT 58.410 39.130 13.74 14.30 46.59 2.66
2105 2658 4.878397 AGACTTCACAGTGGACTGAAAAAG 59.122 41.667 13.74 13.78 46.59 2.27
2170 2723 0.882484 TGCTTCAATCGGACGCACAA 60.882 50.000 0.00 0.00 44.82 3.33
2200 2753 2.691011 TGAACCAAAAAGTACACAGGCC 59.309 45.455 0.00 0.00 0.00 5.19
2262 2816 8.687824 TCAAACAAGTGAATTTGTCTTTTCTC 57.312 30.769 0.00 0.00 40.24 2.87
2263 2817 9.657419 AATCAAACAAGTGAATTTGTCTTTTCT 57.343 25.926 0.00 0.00 40.24 2.52
2380 2938 7.950496 GTCAGTGTAACACAAAACGATCTAATC 59.050 37.037 0.00 0.00 41.43 1.75
2422 2980 8.668510 TTTTGGCACTTTCATTTTTAGCATTA 57.331 26.923 0.00 0.00 0.00 1.90
2459 3017 4.461781 TCGCCCCAATTTAAAACCGATTTA 59.538 37.500 0.00 0.00 32.27 1.40
2503 3061 1.756538 GGGATTTTTCCATGCATCGGT 59.243 47.619 12.89 0.00 0.00 4.69
2504 3062 1.069049 GGGGATTTTTCCATGCATCGG 59.931 52.381 0.00 2.19 0.00 4.18
2505 3063 2.034124 AGGGGATTTTTCCATGCATCG 58.966 47.619 0.00 0.00 0.00 3.84
2506 3064 2.035066 CGAGGGGATTTTTCCATGCATC 59.965 50.000 0.00 0.00 0.00 3.91
2507 3065 2.034124 CGAGGGGATTTTTCCATGCAT 58.966 47.619 0.00 0.00 0.00 3.96
2508 3066 1.473258 CGAGGGGATTTTTCCATGCA 58.527 50.000 0.00 0.00 0.00 3.96
2509 3067 0.103026 GCGAGGGGATTTTTCCATGC 59.897 55.000 0.00 0.00 0.00 4.06
2510 3068 0.746659 GGCGAGGGGATTTTTCCATG 59.253 55.000 0.00 0.00 0.00 3.66
2511 3069 0.631212 AGGCGAGGGGATTTTTCCAT 59.369 50.000 0.00 0.00 0.00 3.41
2512 3070 0.034477 GAGGCGAGGGGATTTTTCCA 60.034 55.000 0.00 0.00 0.00 3.53
2513 3071 0.256177 AGAGGCGAGGGGATTTTTCC 59.744 55.000 0.00 0.00 0.00 3.13
2514 3072 1.383523 CAGAGGCGAGGGGATTTTTC 58.616 55.000 0.00 0.00 0.00 2.29
2515 3073 0.681243 GCAGAGGCGAGGGGATTTTT 60.681 55.000 0.00 0.00 0.00 1.94
2516 3074 1.077429 GCAGAGGCGAGGGGATTTT 60.077 57.895 0.00 0.00 0.00 1.82
2517 3075 2.592308 GCAGAGGCGAGGGGATTT 59.408 61.111 0.00 0.00 0.00 2.17
2518 3076 3.483869 GGCAGAGGCGAGGGGATT 61.484 66.667 0.00 0.00 42.47 3.01
2519 3077 4.804420 TGGCAGAGGCGAGGGGAT 62.804 66.667 0.00 0.00 42.47 3.85
2522 3080 4.767255 GTGTGGCAGAGGCGAGGG 62.767 72.222 0.00 0.00 42.47 4.30
2523 3081 4.007644 TGTGTGGCAGAGGCGAGG 62.008 66.667 0.00 0.00 42.47 4.63
2524 3082 2.740055 GTGTGTGGCAGAGGCGAG 60.740 66.667 0.00 0.00 42.47 5.03
2525 3083 3.545574 TGTGTGTGGCAGAGGCGA 61.546 61.111 0.00 0.00 42.47 5.54
2526 3084 3.349006 GTGTGTGTGGCAGAGGCG 61.349 66.667 0.00 0.00 42.47 5.52
2527 3085 3.349006 CGTGTGTGTGGCAGAGGC 61.349 66.667 0.00 0.00 40.13 4.70
2528 3086 1.956170 GTCGTGTGTGTGGCAGAGG 60.956 63.158 0.00 0.00 0.00 3.69
2529 3087 0.530650 AAGTCGTGTGTGTGGCAGAG 60.531 55.000 0.00 0.00 0.00 3.35
2530 3088 0.809636 CAAGTCGTGTGTGTGGCAGA 60.810 55.000 0.00 0.00 0.00 4.26
2531 3089 1.089481 ACAAGTCGTGTGTGTGGCAG 61.089 55.000 0.00 0.00 39.72 4.85
2532 3090 0.675208 AACAAGTCGTGTGTGTGGCA 60.675 50.000 0.00 0.00 40.60 4.92
2533 3091 0.248054 CAACAAGTCGTGTGTGTGGC 60.248 55.000 0.00 0.00 40.60 5.01
2534 3092 0.376852 CCAACAAGTCGTGTGTGTGG 59.623 55.000 0.00 0.00 40.60 4.17
2535 3093 1.327460 CTCCAACAAGTCGTGTGTGTG 59.673 52.381 0.00 0.00 40.60 3.82
2536 3094 1.066430 ACTCCAACAAGTCGTGTGTGT 60.066 47.619 0.00 0.00 40.60 3.72
2537 3095 1.651987 ACTCCAACAAGTCGTGTGTG 58.348 50.000 0.00 0.00 40.60 3.82
2538 3096 3.530265 TTACTCCAACAAGTCGTGTGT 57.470 42.857 0.00 0.00 40.60 3.72
2539 3097 4.509970 TCATTTACTCCAACAAGTCGTGTG 59.490 41.667 0.00 0.00 40.60 3.82
2540 3098 4.510340 GTCATTTACTCCAACAAGTCGTGT 59.490 41.667 0.00 0.00 44.64 4.49
2541 3099 4.084013 GGTCATTTACTCCAACAAGTCGTG 60.084 45.833 0.00 0.00 0.00 4.35
2542 3100 4.062991 GGTCATTTACTCCAACAAGTCGT 58.937 43.478 0.00 0.00 0.00 4.34
2543 3101 4.062293 TGGTCATTTACTCCAACAAGTCG 58.938 43.478 0.00 0.00 0.00 4.18
2544 3102 5.063880 AGTGGTCATTTACTCCAACAAGTC 58.936 41.667 0.00 0.00 32.82 3.01
2545 3103 5.048846 AGTGGTCATTTACTCCAACAAGT 57.951 39.130 0.00 0.00 32.82 3.16
2546 3104 5.122396 GCTAGTGGTCATTTACTCCAACAAG 59.878 44.000 0.00 0.00 32.82 3.16
2585 3148 2.943033 CCCCGATGTCTTGAAATACCAC 59.057 50.000 0.00 0.00 0.00 4.16
2618 3181 0.178973 TTCGTCCTGGAGGTGTGAGA 60.179 55.000 15.40 0.00 36.34 3.27
2681 3244 3.562176 CCTTCTGGTATTTTGCCACCTCT 60.562 47.826 0.00 0.00 35.73 3.69
2682 3245 2.755103 CCTTCTGGTATTTTGCCACCTC 59.245 50.000 0.00 0.00 35.73 3.85
2686 3249 1.173043 CGCCTTCTGGTATTTTGCCA 58.827 50.000 0.00 0.00 35.27 4.92
2691 3254 1.472728 CGTAGCCGCCTTCTGGTATTT 60.473 52.381 0.00 0.00 35.27 1.40
2713 3276 1.006102 CTGCCAGAAGTCGGTCGTT 60.006 57.895 0.00 0.00 0.00 3.85
2717 3281 4.379243 CGCCTGCCAGAAGTCGGT 62.379 66.667 0.00 0.00 0.00 4.69
2738 3302 1.069022 GCAAACTTTGAGCGCATGAGA 60.069 47.619 11.47 0.00 0.00 3.27
2746 3310 3.427161 AAGTGAGTGCAAACTTTGAGC 57.573 42.857 5.65 0.00 32.75 4.26
2761 3325 3.376234 CCCGTCTCATCGTAGTTAAGTGA 59.624 47.826 0.00 0.00 0.00 3.41
2765 3329 1.406539 GCCCCGTCTCATCGTAGTTAA 59.593 52.381 0.00 0.00 0.00 2.01
2775 3339 2.034532 TAGTCACGCCCCGTCTCA 59.965 61.111 0.00 0.00 38.32 3.27
2789 3353 2.454538 GGTGGTAGGCTACACTGTAGT 58.545 52.381 24.96 2.06 37.72 2.73
2798 3362 0.761702 GATTCGGGGGTGGTAGGCTA 60.762 60.000 0.00 0.00 0.00 3.93
2804 3368 3.015145 CCCAGATTCGGGGGTGGT 61.015 66.667 13.66 0.00 43.21 4.16
2870 3435 3.454573 TGGCTACAGTACCCCGCG 61.455 66.667 0.00 0.00 0.00 6.46
2933 3498 2.461110 GCCATACCGACAAGCCGTG 61.461 63.158 0.00 0.00 0.00 4.94
2983 3548 1.990060 TCTTGCCTCCTTCTCGGGG 60.990 63.158 0.00 0.00 0.00 5.73
2987 3552 1.201429 TGGGGTCTTGCCTCCTTCTC 61.201 60.000 0.00 0.00 36.72 2.87
2994 3559 3.655211 CCTGCTGGGGTCTTGCCT 61.655 66.667 0.71 0.00 37.43 4.75


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

AutoCloner maintained by Alex Coulton.