Multiple sequence alignment - TraesCS1B01G196500

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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 TraesCS1B01G196500 chr1B 100.000 5826 0 0 1 5826 353940913 353946738 0.000000e+00 10759.0
1 TraesCS1B01G196500 chr1A 92.795 4025 148 42 1855 5799 341868926 341872888 0.000000e+00 5696.0
2 TraesCS1B01G196500 chr1A 95.701 977 37 5 884 1855 341867714 341868690 0.000000e+00 1567.0
3 TraesCS1B01G196500 chr1A 86.903 901 72 17 1 883 558722655 558721783 0.000000e+00 968.0
4 TraesCS1B01G196500 chr1D 89.731 2600 125 50 2180 4711 258983251 258980726 0.000000e+00 3192.0
5 TraesCS1B01G196500 chr1D 93.637 1383 66 14 884 2244 258984632 258983250 0.000000e+00 2047.0
6 TraesCS1B01G196500 chr1D 93.934 1121 45 13 4707 5826 258980661 258979563 0.000000e+00 1672.0
7 TraesCS1B01G196500 chr1D 84.715 929 89 29 1 883 316222138 316223059 0.000000e+00 880.0
8 TraesCS1B01G196500 chr1D 89.258 512 39 9 139 639 316577101 316577607 1.380000e-175 627.0
9 TraesCS1B01G196500 chr1D 90.698 43 2 1 173 215 473016904 473016944 8.160000e-04 56.5
10 TraesCS1B01G196500 chr7B 87.680 901 88 15 1 882 200374452 200375348 0.000000e+00 1027.0
11 TraesCS1B01G196500 chr7B 83.045 926 106 32 1 883 387099374 387098457 0.000000e+00 793.0
12 TraesCS1B01G196500 chr7B 82.101 676 81 21 1 637 434954375 434953701 5.140000e-150 542.0
13 TraesCS1B01G196500 chr7B 86.755 151 16 1 2379 2529 652931761 652931615 1.300000e-36 165.0
14 TraesCS1B01G196500 chr5A 86.743 875 84 18 1 855 1519576 1520438 0.000000e+00 944.0
15 TraesCS1B01G196500 chr5A 84.525 769 88 25 140 884 469444806 469445567 0.000000e+00 732.0
16 TraesCS1B01G196500 chr5A 80.000 325 61 4 1064 1386 685988676 685988998 2.710000e-58 237.0
17 TraesCS1B01G196500 chr5A 85.976 164 23 0 5583 5746 685996205 685996368 6.000000e-40 176.0
18 TraesCS1B01G196500 chr5A 91.935 124 10 0 5676 5799 342329246 342329369 2.160000e-39 174.0
19 TraesCS1B01G196500 chr3D 83.896 919 108 25 1 883 2504833 2503919 0.000000e+00 841.0
20 TraesCS1B01G196500 chr3D 78.172 536 85 20 376 883 496047589 496047058 4.380000e-81 313.0
21 TraesCS1B01G196500 chr3D 78.458 506 76 25 404 883 129354364 129354862 3.410000e-77 300.0
22 TraesCS1B01G196500 chr3A 83.312 791 101 25 111 883 679257005 679257782 0.000000e+00 701.0
23 TraesCS1B01G196500 chr3A 81.417 635 86 24 274 881 7867560 7868189 1.890000e-134 490.0
24 TraesCS1B01G196500 chr2B 84.793 651 65 20 1 621 210487803 210487157 1.780000e-174 623.0
25 TraesCS1B01G196500 chr2B 79.472 833 128 26 61 854 86535396 86536224 8.530000e-153 551.0
26 TraesCS1B01G196500 chr6D 84.532 556 58 14 1 542 69755553 69756094 5.170000e-145 525.0
27 TraesCS1B01G196500 chr6D 79.670 728 89 32 1 694 69830382 69831084 2.460000e-128 470.0
28 TraesCS1B01G196500 chr6D 82.292 384 40 19 294 651 72431840 72431459 2.040000e-79 307.0
29 TraesCS1B01G196500 chr6D 78.373 504 79 22 404 883 452927193 452927690 3.410000e-77 300.0
30 TraesCS1B01G196500 chr2D 78.854 506 76 23 404 884 81835595 81836094 4.380000e-81 313.0
31 TraesCS1B01G196500 chr7D 78.770 504 76 23 404 883 500980656 500980160 5.670000e-80 309.0
32 TraesCS1B01G196500 chr7D 78.614 505 78 22 404 883 394397025 394397524 2.040000e-79 307.0
33 TraesCS1B01G196500 chr4B 86.383 235 20 8 32 256 561898743 561898511 4.510000e-61 246.0
34 TraesCS1B01G196500 chr4B 79.876 323 61 4 1065 1385 646968311 646968631 3.510000e-57 233.0
35 TraesCS1B01G196500 chr4D 80.000 325 61 4 1064 1386 502571394 502571716 2.710000e-58 237.0
36 TraesCS1B01G196500 chr4D 91.129 124 11 0 5676 5799 217220527 217220650 1.000000e-37 169.0
37 TraesCS1B01G196500 chr4D 92.523 107 8 0 5676 5782 446595687 446595793 2.810000e-33 154.0
38 TraesCS1B01G196500 chr5B 78.176 307 61 6 580 883 265066640 265066337 2.140000e-44 191.0
39 TraesCS1B01G196500 chr5D 92.523 107 8 0 5676 5782 473055879 473055985 2.810000e-33 154.0


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 TraesCS1B01G196500 chr1B 353940913 353946738 5825 False 10759.000000 10759 100.000 1 5826 1 chr1B.!!$F1 5825
1 TraesCS1B01G196500 chr1A 341867714 341872888 5174 False 3631.500000 5696 94.248 884 5799 2 chr1A.!!$F1 4915
2 TraesCS1B01G196500 chr1A 558721783 558722655 872 True 968.000000 968 86.903 1 883 1 chr1A.!!$R1 882
3 TraesCS1B01G196500 chr1D 258979563 258984632 5069 True 2303.666667 3192 92.434 884 5826 3 chr1D.!!$R1 4942
4 TraesCS1B01G196500 chr1D 316222138 316223059 921 False 880.000000 880 84.715 1 883 1 chr1D.!!$F1 882
5 TraesCS1B01G196500 chr1D 316577101 316577607 506 False 627.000000 627 89.258 139 639 1 chr1D.!!$F2 500
6 TraesCS1B01G196500 chr7B 200374452 200375348 896 False 1027.000000 1027 87.680 1 882 1 chr7B.!!$F1 881
7 TraesCS1B01G196500 chr7B 387098457 387099374 917 True 793.000000 793 83.045 1 883 1 chr7B.!!$R1 882
8 TraesCS1B01G196500 chr7B 434953701 434954375 674 True 542.000000 542 82.101 1 637 1 chr7B.!!$R2 636
9 TraesCS1B01G196500 chr5A 1519576 1520438 862 False 944.000000 944 86.743 1 855 1 chr5A.!!$F1 854
10 TraesCS1B01G196500 chr5A 469444806 469445567 761 False 732.000000 732 84.525 140 884 1 chr5A.!!$F3 744
11 TraesCS1B01G196500 chr3D 2503919 2504833 914 True 841.000000 841 83.896 1 883 1 chr3D.!!$R1 882
12 TraesCS1B01G196500 chr3D 496047058 496047589 531 True 313.000000 313 78.172 376 883 1 chr3D.!!$R2 507
13 TraesCS1B01G196500 chr3A 679257005 679257782 777 False 701.000000 701 83.312 111 883 1 chr3A.!!$F2 772
14 TraesCS1B01G196500 chr3A 7867560 7868189 629 False 490.000000 490 81.417 274 881 1 chr3A.!!$F1 607
15 TraesCS1B01G196500 chr2B 210487157 210487803 646 True 623.000000 623 84.793 1 621 1 chr2B.!!$R1 620
16 TraesCS1B01G196500 chr2B 86535396 86536224 828 False 551.000000 551 79.472 61 854 1 chr2B.!!$F1 793
17 TraesCS1B01G196500 chr6D 69755553 69756094 541 False 525.000000 525 84.532 1 542 1 chr6D.!!$F1 541
18 TraesCS1B01G196500 chr6D 69830382 69831084 702 False 470.000000 470 79.670 1 694 1 chr6D.!!$F2 693

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
564 644 0.174617 GAGAAGAGGAGGAAGCCGTG 59.825 60.000 0.00 0.00 0.00 4.94 F
597 726 0.698198 TGTAACTGGGGTGGGTGGAA 60.698 55.000 0.00 0.00 0.00 3.53 F
1407 1556 1.067060 ACTTCGCTCCCTTTTGTTTGC 59.933 47.619 0.00 0.00 0.00 3.68 F
1903 2290 1.063492 AGGGATTCATGAAGCATGCCA 60.063 47.619 23.99 6.58 41.18 4.92 F
3291 3809 1.133199 TGGGCATTCCTGTTCTTTGGT 60.133 47.619 0.00 0.00 36.20 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1663 0.468226 GGTCATTGTAGCCCATCCGA 59.532 55.0 0.00 0.00 0.00 4.55 R
1608 1759 2.227388 CTGAACAACATGCTTGGAGGTC 59.773 50.0 4.44 4.83 0.00 3.85 R
3208 3726 1.024271 GGATAATGCCGCTTTGAGCA 58.976 50.0 1.86 0.00 42.58 4.26 R
3669 4211 0.740737 GTGCAAGTGACAAGCAAGGT 59.259 50.0 3.60 0.00 40.35 3.50 R
4843 5462 0.106708 GCTGGATAGTCGGCATTCCA 59.893 55.0 10.13 10.13 38.79 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
96 99 5.864418 ATCTACAATCAAAGCATGCCAAT 57.136 34.783 15.66 0.00 0.00 3.16
204 224 6.966632 GCAAAGCATTCTTGTCAATACGAATA 59.033 34.615 0.00 0.00 31.78 1.75
275 304 7.871853 ACATGTGTAAGGTTCATCTTAACAAC 58.128 34.615 0.00 0.00 31.85 3.32
477 535 3.141272 AGAAGGGAATCGGAGGAGAGTAT 59.859 47.826 0.00 0.00 0.00 2.12
506 564 8.331740 TCTAGAATGGATTGGTGAAGAAATTCT 58.668 33.333 0.00 0.00 37.07 2.40
537 606 4.450082 TCGTCAGATCCGAAGAATTTGA 57.550 40.909 0.00 0.00 0.00 2.69
542 611 6.279882 GTCAGATCCGAAGAATTTGAGAGAT 58.720 40.000 0.00 0.00 0.00 2.75
564 644 0.174617 GAGAAGAGGAGGAAGCCGTG 59.825 60.000 0.00 0.00 0.00 4.94
596 724 1.073629 TGTAACTGGGGTGGGTGGA 60.074 57.895 0.00 0.00 0.00 4.02
597 726 0.698198 TGTAACTGGGGTGGGTGGAA 60.698 55.000 0.00 0.00 0.00 3.53
646 783 4.838152 CGTGCAGCGCCTATGGGT 62.838 66.667 2.29 0.00 34.45 4.51
772 913 1.576421 GCGCTGCATAATAGGGTGC 59.424 57.895 0.00 0.00 41.61 5.01
812 953 1.132262 CACACAAAAACGGTCAGCTGT 59.868 47.619 14.67 0.00 35.32 4.40
816 957 1.132262 CAAAAACGGTCAGCTGTGTGT 59.868 47.619 14.67 7.61 33.83 3.72
876 1022 4.606961 GTCCACACGTCAAAATTGTCAAT 58.393 39.130 0.00 0.00 0.00 2.57
895 1041 4.709397 TCAATTTTGCCCGGATTTACAGAT 59.291 37.500 0.73 0.00 0.00 2.90
905 1051 3.118408 CGGATTTACAGATCAACCCCTCA 60.118 47.826 0.00 0.00 0.00 3.86
911 1057 2.982488 ACAGATCAACCCCTCAACTTCT 59.018 45.455 0.00 0.00 0.00 2.85
919 1065 2.637872 ACCCCTCAACTTCTCATTTCGA 59.362 45.455 0.00 0.00 0.00 3.71
925 1072 6.072508 CCCTCAACTTCTCATTTCGATTCAAA 60.073 38.462 0.00 0.00 0.00 2.69
931 1078 7.134815 ACTTCTCATTTCGATTCAAACAAGTG 58.865 34.615 0.00 0.00 0.00 3.16
932 1079 6.618287 TCTCATTTCGATTCAAACAAGTGT 57.382 33.333 0.00 0.00 0.00 3.55
1376 1524 2.427453 AGCTCAATGTCTACAGGGTACG 59.573 50.000 0.00 0.00 0.00 3.67
1407 1556 1.067060 ACTTCGCTCCCTTTTGTTTGC 59.933 47.619 0.00 0.00 0.00 3.68
1512 1663 8.088463 AGACCAATCTGATCAAAGAGAGTATT 57.912 34.615 0.00 0.00 32.29 1.89
1608 1759 2.508439 ACCCGCGATTACTGCACG 60.508 61.111 8.23 0.00 0.00 5.34
1614 1765 1.146358 GCGATTACTGCACGACCTCC 61.146 60.000 0.00 0.00 0.00 4.30
1902 2289 1.340248 CAGGGATTCATGAAGCATGCC 59.660 52.381 23.99 16.47 41.18 4.40
1903 2290 1.063492 AGGGATTCATGAAGCATGCCA 60.063 47.619 23.99 6.58 41.18 4.92
2129 2532 9.200817 CCCTTTTCAGGAAATCTGGATAATTTA 57.799 33.333 0.00 0.00 44.19 1.40
2192 2599 6.871492 TCTCACGACAAAACTCATTATGCTAA 59.129 34.615 0.00 0.00 0.00 3.09
2222 2692 4.199310 TCAATTTCTATTTCGGGCTGGAG 58.801 43.478 0.00 0.00 0.00 3.86
2243 2713 5.763698 GGAGATAAAGCCCAGTAATTGGTAC 59.236 44.000 0.00 0.00 46.25 3.34
2274 2747 7.823745 ACTTCTTTTGTGAAGAACCACATAT 57.176 32.000 10.68 0.00 45.31 1.78
2367 2857 3.482436 TGACTGCGGGATTAAAAGTGTT 58.518 40.909 0.00 0.00 0.00 3.32
2699 3192 5.540719 AGGTACTAGGAATCTAGGATGCAAC 59.459 44.000 0.00 0.00 45.50 4.17
2723 3216 5.481105 TGCTGCAATTAATTTTCTCCCTTG 58.519 37.500 0.00 0.00 0.00 3.61
2765 3258 1.821216 TTTCTGCGGGATGAAGTTCC 58.179 50.000 0.00 0.00 34.83 3.62
2835 3328 3.030291 AGGAGCTCTGGTCTTCTACATG 58.970 50.000 14.64 0.00 0.00 3.21
2837 3330 3.640967 GGAGCTCTGGTCTTCTACATGAT 59.359 47.826 14.64 0.00 0.00 2.45
2886 3380 8.236585 AGCATATGAAATGTATGGTTGCTTAA 57.763 30.769 6.97 0.00 37.05 1.85
2902 3396 7.067615 TGGTTGCTTAATGAGTCTTGTTTTACA 59.932 33.333 0.00 0.00 0.00 2.41
2955 3449 8.449397 GCAGGATAATTTATAGCTCATTCACAG 58.551 37.037 0.00 0.00 0.00 3.66
3208 3726 5.422012 CCCAAAATAGTCATTTTAGCCTGGT 59.578 40.000 0.00 0.00 41.41 4.00
3291 3809 1.133199 TGGGCATTCCTGTTCTTTGGT 60.133 47.619 0.00 0.00 36.20 3.67
3392 3934 8.131100 CAGTTTCTGATTGTTGTAAGTGATGTT 58.869 33.333 0.00 0.00 32.44 2.71
3525 4067 3.890527 CCTCAGTTAGCTGGGCATT 57.109 52.632 6.75 0.00 41.82 3.56
3597 4139 9.337396 CTTTACAGTGGATGCCATAACTTTATA 57.663 33.333 0.00 0.00 35.28 0.98
3600 4142 4.997395 AGTGGATGCCATAACTTTATAGCG 59.003 41.667 0.00 0.00 35.28 4.26
3668 4210 6.758416 CACATCTAATAAGACAGCAGTTGCTA 59.242 38.462 6.27 0.00 41.68 3.49
3669 4211 7.278646 CACATCTAATAAGACAGCAGTTGCTAA 59.721 37.037 6.27 0.00 41.68 3.09
3740 4282 9.227777 GGATAAACTATAACAACTGAACCAACT 57.772 33.333 0.00 0.00 0.00 3.16
3754 4296 5.197451 TGAACCAACTAAAACCTGTCACAT 58.803 37.500 0.00 0.00 0.00 3.21
3761 4303 5.901552 ACTAAAACCTGTCACATTTTGGTG 58.098 37.500 5.16 0.00 36.18 4.17
3863 4405 4.254492 GAGATGTGTTGAACCTTCTACCC 58.746 47.826 0.00 0.00 33.02 3.69
3874 4416 2.213499 CCTTCTACCCGATGATGTTGC 58.787 52.381 0.00 0.00 0.00 4.17
4064 4611 1.133575 ACCTGCTGCTGGATATGCATT 60.134 47.619 29.14 4.05 39.86 3.56
4126 4673 4.694982 CACAAAGCCATCATACAGTACACA 59.305 41.667 0.00 0.00 0.00 3.72
4308 4855 4.703575 TGCAGAGCTAATTTGCTGATCTTT 59.296 37.500 19.20 0.00 44.17 2.52
4406 4953 4.065110 GGAACTTTCCAGCGTGCT 57.935 55.556 2.93 0.00 46.76 4.40
4420 4967 1.376942 GTGCTCTGCAGACTGGCAT 60.377 57.895 26.12 0.00 43.97 4.40
4480 5027 1.544691 GAACCTCCTCAAGCACGAGTA 59.455 52.381 0.00 0.00 0.00 2.59
4537 5084 2.136026 AGTTCTCCTTGGTTTGGACCT 58.864 47.619 0.00 0.00 46.66 3.85
4568 5115 8.963725 TGCATTGAGAGATTTTAGTGATGATTT 58.036 29.630 0.00 0.00 0.00 2.17
4691 5238 1.222115 GCACGTCTTTTGCGGAGACT 61.222 55.000 10.82 0.00 41.02 3.24
4748 5367 8.475331 TCATTTTGGAGTTTTCGTATAGACTC 57.525 34.615 0.00 0.00 38.19 3.36
4797 5416 2.278661 GTCTACTACAGCCGCGCC 60.279 66.667 0.00 0.00 0.00 6.53
4836 5455 7.969536 TTAAGAATTGCTGATAGTATGCTCC 57.030 36.000 0.00 0.00 0.00 4.70
4837 5456 5.822132 AGAATTGCTGATAGTATGCTCCT 57.178 39.130 0.00 0.00 0.00 3.69
4838 5457 5.792741 AGAATTGCTGATAGTATGCTCCTC 58.207 41.667 0.00 0.00 0.00 3.71
4840 5459 1.889170 TGCTGATAGTATGCTCCTCCG 59.111 52.381 0.00 0.00 0.00 4.63
4841 5460 2.163509 GCTGATAGTATGCTCCTCCGA 58.836 52.381 0.00 0.00 0.00 4.55
4842 5461 2.094957 GCTGATAGTATGCTCCTCCGAC 60.095 54.545 0.00 0.00 0.00 4.79
4843 5462 3.417101 CTGATAGTATGCTCCTCCGACT 58.583 50.000 0.00 0.00 0.00 4.18
4844 5463 3.149981 TGATAGTATGCTCCTCCGACTG 58.850 50.000 0.00 0.00 0.00 3.51
4845 5464 1.982660 TAGTATGCTCCTCCGACTGG 58.017 55.000 0.00 0.00 0.00 4.00
4846 5465 0.259065 AGTATGCTCCTCCGACTGGA 59.741 55.000 0.00 0.00 43.88 3.86
4847 5466 1.112113 GTATGCTCCTCCGACTGGAA 58.888 55.000 0.00 0.00 45.87 3.53
4848 5467 1.689273 GTATGCTCCTCCGACTGGAAT 59.311 52.381 0.00 0.00 45.87 3.01
4849 5468 0.467384 ATGCTCCTCCGACTGGAATG 59.533 55.000 0.00 0.00 45.87 2.67
4850 5469 1.522580 GCTCCTCCGACTGGAATGC 60.523 63.158 0.00 0.00 45.87 3.56
4851 5470 1.144936 CTCCTCCGACTGGAATGCC 59.855 63.158 0.00 0.00 45.87 4.40
4852 5471 2.202932 CCTCCGACTGGAATGCCG 60.203 66.667 0.00 0.00 45.87 5.69
4853 5472 2.721167 CCTCCGACTGGAATGCCGA 61.721 63.158 0.00 0.00 45.87 5.54
4854 5473 1.519455 CTCCGACTGGAATGCCGAC 60.519 63.158 0.00 0.00 45.87 4.79
4855 5474 1.949847 CTCCGACTGGAATGCCGACT 61.950 60.000 0.00 0.00 45.87 4.18
4856 5475 0.681887 TCCGACTGGAATGCCGACTA 60.682 55.000 0.00 0.00 42.85 2.59
4857 5476 0.389391 CCGACTGGAATGCCGACTAT 59.611 55.000 0.00 0.00 37.49 2.12
4858 5477 1.603172 CCGACTGGAATGCCGACTATC 60.603 57.143 0.00 0.00 37.49 2.08
4859 5478 1.603172 CGACTGGAATGCCGACTATCC 60.603 57.143 0.00 0.00 36.79 2.59
4860 5479 1.412710 GACTGGAATGCCGACTATCCA 59.587 52.381 0.00 0.00 39.57 3.41
4862 5481 0.106708 TGGAATGCCGACTATCCAGC 59.893 55.000 0.00 0.00 37.05 4.85
4863 5482 0.946221 GGAATGCCGACTATCCAGCG 60.946 60.000 0.00 0.00 32.08 5.18
4864 5483 0.946221 GAATGCCGACTATCCAGCGG 60.946 60.000 0.00 0.00 41.50 5.52
4913 5539 1.961277 ACTTGCTTTCGGTGCGGAG 60.961 57.895 0.00 0.00 0.00 4.63
4918 5544 0.521735 GCTTTCGGTGCGGAGAAAAT 59.478 50.000 2.75 0.00 36.14 1.82
4923 5549 5.473796 TTTCGGTGCGGAGAAAATAATAC 57.526 39.130 0.00 0.00 33.93 1.89
4976 5602 2.623878 TCTGCACCGACCAGTTTTTA 57.376 45.000 0.00 0.00 0.00 1.52
5100 5731 1.601759 GTCAGGCACATGCAGGTGT 60.602 57.895 29.89 11.00 44.36 4.16
5120 5751 5.701290 GGTGTAAGATTCAAGATATTCCCCG 59.299 44.000 0.00 0.00 0.00 5.73
5129 5760 6.509418 TCAAGATATTCCCCGTTTTTCAAG 57.491 37.500 0.00 0.00 0.00 3.02
5132 5763 4.948004 AGATATTCCCCGTTTTTCAAGTCC 59.052 41.667 0.00 0.00 0.00 3.85
5143 5774 4.364415 TTTTCAAGTCCAACAACCGAAG 57.636 40.909 0.00 0.00 0.00 3.79
5163 5794 7.005062 CGAAGGAAACAATCATCGAGTAAAT 57.995 36.000 0.00 0.00 39.75 1.40
5166 5797 6.414732 AGGAAACAATCATCGAGTAAATCCA 58.585 36.000 0.00 0.00 0.00 3.41
5181 5812 1.591768 ATCCAGGGGTGTAATCCGTT 58.408 50.000 0.00 0.00 0.00 4.44
5241 5877 1.082104 GCCTGTGCGGAAAAGAACG 60.082 57.895 0.00 0.00 33.16 3.95
5411 6047 2.253452 GCGCAGGACAACAGCAAG 59.747 61.111 0.30 0.00 0.00 4.01
5412 6048 2.253758 GCGCAGGACAACAGCAAGA 61.254 57.895 0.30 0.00 0.00 3.02
5435 6071 1.350193 CATCAGTCAACCGGAAGTCG 58.650 55.000 9.46 0.00 38.88 4.18
5448 6084 0.741915 GAAGTCGAGAGCCCACCTAG 59.258 60.000 0.00 0.00 0.00 3.02
5494 6130 2.112815 GCCGCTTTGCTTACCCGAT 61.113 57.895 0.00 0.00 0.00 4.18
5515 6151 3.775654 GACCAGGACCGAGGCCAG 61.776 72.222 5.01 0.00 0.00 4.85
5633 6269 1.139095 GAGCAGTACGAACCCGAGG 59.861 63.158 0.00 0.00 39.50 4.63
5702 6338 2.839632 AGGATGCCGATCGCCAGA 60.840 61.111 10.32 0.00 36.24 3.86
5725 6361 2.379634 CCGCGATCACGAACAGCAA 61.380 57.895 8.23 0.00 42.66 3.91
5782 6418 2.159142 ACGTCGGAAGTGTCAGAAACTT 60.159 45.455 5.59 5.59 40.54 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.360607 CCTTTTAGTTTGTACCGATTGTAGGTG 60.361 40.741 0.00 0.00 42.83 4.00
27 28 6.652062 CCTTTTAGTTTGTACCGATTGTAGGT 59.348 38.462 0.00 0.00 45.28 3.08
179 195 4.722194 TCGTATTGACAAGAATGCTTTGC 58.278 39.130 0.00 0.00 30.14 3.68
256 285 7.392418 ACCTAGGTTGTTAAGATGAACCTTAC 58.608 38.462 9.21 0.00 45.94 2.34
462 520 6.442541 TCTAGAAGATACTCTCCTCCGATT 57.557 41.667 0.00 0.00 0.00 3.34
477 535 6.874278 TCTTCACCAATCCATTCTAGAAGA 57.126 37.500 11.53 4.14 38.22 2.87
485 543 5.126061 CCGAGAATTTCTTCACCAATCCATT 59.874 40.000 0.00 0.00 33.56 3.16
506 564 1.136305 GGATCTGACGATTTGGTCCGA 59.864 52.381 0.00 0.00 36.07 4.55
537 606 4.447762 GCTTCCTCCTCTTCTCCTATCTCT 60.448 50.000 0.00 0.00 0.00 3.10
542 611 1.410365 CGGCTTCCTCCTCTTCTCCTA 60.410 57.143 0.00 0.00 0.00 2.94
564 644 2.023223 TTACAGAAACGACGCGCCC 61.023 57.895 5.73 0.00 0.00 6.13
596 724 4.162690 CCGCGCCTAGCCCTCTTT 62.163 66.667 0.00 0.00 44.76 2.52
646 783 2.147958 CCTGTAAAGTGCAACGCCTAA 58.852 47.619 0.00 0.00 45.86 2.69
789 930 0.591236 CTGACCGTTTTTGTGTGGCG 60.591 55.000 0.00 0.00 0.00 5.69
790 931 0.869880 GCTGACCGTTTTTGTGTGGC 60.870 55.000 0.00 0.00 0.00 5.01
793 934 1.132262 CACAGCTGACCGTTTTTGTGT 59.868 47.619 23.35 0.00 33.21 3.72
794 935 1.132262 ACACAGCTGACCGTTTTTGTG 59.868 47.619 23.35 7.31 41.12 3.33
796 937 1.132262 ACACACAGCTGACCGTTTTTG 59.868 47.619 23.35 8.00 0.00 2.44
797 938 1.459450 ACACACAGCTGACCGTTTTT 58.541 45.000 23.35 0.00 0.00 1.94
876 1022 3.691575 TGATCTGTAAATCCGGGCAAAA 58.308 40.909 0.00 0.00 0.00 2.44
895 1041 4.398319 GAAATGAGAAGTTGAGGGGTTGA 58.602 43.478 0.00 0.00 0.00 3.18
905 1051 7.645340 CACTTGTTTGAATCGAAATGAGAAGTT 59.355 33.333 0.00 0.00 0.00 2.66
911 1057 6.485313 AGGTACACTTGTTTGAATCGAAATGA 59.515 34.615 0.00 0.00 0.00 2.57
919 1065 7.036220 CGAGATAGAGGTACACTTGTTTGAAT 58.964 38.462 0.00 0.00 0.00 2.57
925 1072 2.688958 GGCGAGATAGAGGTACACTTGT 59.311 50.000 0.00 0.00 0.00 3.16
931 1078 0.512085 CGACGGCGAGATAGAGGTAC 59.488 60.000 16.62 0.00 40.82 3.34
932 1079 1.226686 GCGACGGCGAGATAGAGGTA 61.227 60.000 18.90 0.00 40.82 3.08
1140 1288 1.133216 CACTTCTCCGCGATGAAGAGA 59.867 52.381 32.00 22.10 41.38 3.10
1376 1524 2.082231 GGAGCGAAGTTTAGGGTTTCC 58.918 52.381 0.00 0.00 0.00 3.13
1407 1556 0.517316 GCGACAGTGCAACCCTAAAG 59.483 55.000 0.00 0.00 37.80 1.85
1465 1616 6.372659 GTCTGCAGGTAGAATGATTTCAGAAA 59.627 38.462 15.13 0.00 34.08 2.52
1512 1663 0.468226 GGTCATTGTAGCCCATCCGA 59.532 55.000 0.00 0.00 0.00 4.55
1608 1759 2.227388 CTGAACAACATGCTTGGAGGTC 59.773 50.000 4.44 4.83 0.00 3.85
1614 1765 2.984471 GCACATCTGAACAACATGCTTG 59.016 45.455 0.00 0.00 30.83 4.01
1671 1822 7.534282 TGACATAATTTGACACGTGCATAAAT 58.466 30.769 17.22 16.02 0.00 1.40
1902 2289 9.533253 AGTTCAAAGTTCCAACAGATTAAATTG 57.467 29.630 0.00 0.00 0.00 2.32
1903 2290 9.533253 CAGTTCAAAGTTCCAACAGATTAAATT 57.467 29.630 0.00 0.00 0.00 1.82
2072 2462 9.102757 ACAAACTGACAAACATAGCAGATATAG 57.897 33.333 0.00 0.00 32.86 1.31
2075 2465 7.744087 AACAAACTGACAAACATAGCAGATA 57.256 32.000 0.00 0.00 32.86 1.98
2140 2546 7.613551 AGGACGAGGGAATACATATTTACTT 57.386 36.000 0.00 0.00 0.00 2.24
2192 2599 9.965902 AGCCCGAAATAGAAATTGATATATCTT 57.034 29.630 13.79 0.09 0.00 2.40
2243 2713 6.459710 GGTTCTTCACAAAAGAAGTTGGTAGG 60.460 42.308 0.65 0.00 44.18 3.18
2367 2857 5.661759 GTCTCTATAAACTTCAGAAGGGGGA 59.338 44.000 14.90 3.48 0.00 4.81
2699 3192 5.334724 AGGGAGAAAATTAATTGCAGCAG 57.665 39.130 0.39 0.00 0.00 4.24
2811 3304 2.909504 AGAAGACCAGAGCTCCTACA 57.090 50.000 10.93 0.00 0.00 2.74
2835 3328 4.453480 TCACCCAAAATCCCCATCTATC 57.547 45.455 0.00 0.00 0.00 2.08
2837 3330 4.898014 ATTCACCCAAAATCCCCATCTA 57.102 40.909 0.00 0.00 0.00 1.98
2886 3380 9.003658 CCTCTAAACATGTAAAACAAGACTCAT 57.996 33.333 0.00 0.00 0.00 2.90
2902 3396 4.405680 TGACATCACGATCCCTCTAAACAT 59.594 41.667 0.00 0.00 0.00 2.71
2955 3449 8.090214 TGGACCAACTGTATACTACTAAAACAC 58.910 37.037 4.17 0.00 0.00 3.32
3006 3500 7.027874 TGAACTGGGAGTAAATTTGGAGTAT 57.972 36.000 0.00 0.00 0.00 2.12
3161 3678 2.364002 CCCCGAACTTCCATTTTTGTGT 59.636 45.455 0.00 0.00 0.00 3.72
3208 3726 1.024271 GGATAATGCCGCTTTGAGCA 58.976 50.000 1.86 0.00 42.58 4.26
3313 3831 9.569167 CATCATCATTTATATCATTGGCTTCAC 57.431 33.333 0.00 0.00 0.00 3.18
3367 3885 7.807977 ACATCACTTACAACAATCAGAAACT 57.192 32.000 0.00 0.00 0.00 2.66
3400 3942 8.150945 ACTGAAGTATGCTCTCTTTCAAGTTTA 58.849 33.333 0.00 0.00 0.00 2.01
3401 3943 6.995091 ACTGAAGTATGCTCTCTTTCAAGTTT 59.005 34.615 0.00 0.00 0.00 2.66
3415 3957 7.364522 TGACTAATGAACAACTGAAGTATGC 57.635 36.000 0.00 0.00 0.00 3.14
3525 4067 3.680786 CACAGGGTGCTCGACGGA 61.681 66.667 0.00 0.00 0.00 4.69
3559 4101 3.149196 CACTGTAAAGAGTGGGCAACAT 58.851 45.455 0.00 0.00 39.85 2.71
3597 4139 8.055279 TCTCTTTTCAAATTCATAATTCCGCT 57.945 30.769 0.00 0.00 0.00 5.52
3600 4142 9.794685 GACCTCTCTTTTCAAATTCATAATTCC 57.205 33.333 0.00 0.00 0.00 3.01
3668 4210 1.134946 GTGCAAGTGACAAGCAAGGTT 59.865 47.619 3.60 0.00 40.35 3.50
3669 4211 0.740737 GTGCAAGTGACAAGCAAGGT 59.259 50.000 3.60 0.00 40.35 3.50
3740 4282 4.712337 ACCACCAAAATGTGACAGGTTTTA 59.288 37.500 0.00 0.00 38.55 1.52
3754 4296 6.834451 TCCTTATTAGACAACAACCACCAAAA 59.166 34.615 0.00 0.00 0.00 2.44
3982 4529 3.052036 GCGGCTGGTATTAATTGCAATG 58.948 45.455 13.82 0.00 0.00 2.82
3985 4532 2.051334 AGCGGCTGGTATTAATTGCA 57.949 45.000 0.00 0.00 0.00 4.08
4071 4618 6.418226 GTCCTTGTACAGAGTTTCTATATGCG 59.582 42.308 0.00 0.00 0.00 4.73
4126 4673 7.752638 TGAGATCAACAGATATGAATGGGAAT 58.247 34.615 0.00 0.00 0.00 3.01
4308 4855 8.682710 AGCCTGCATATAAATTAAAGAAACGAA 58.317 29.630 0.00 0.00 0.00 3.85
4406 4953 0.689055 ACTCAATGCCAGTCTGCAGA 59.311 50.000 13.74 13.74 45.93 4.26
4420 4967 4.103153 ACTTGACATCCCTCTCAAACTCAA 59.897 41.667 0.00 0.00 0.00 3.02
4466 5013 0.737715 GGCTGTACTCGTGCTTGAGG 60.738 60.000 9.97 0.00 40.39 3.86
4531 5078 0.325933 CTCAATGCACCTCAGGTCCA 59.674 55.000 0.00 0.00 31.02 4.02
4534 5081 1.649321 TCTCTCAATGCACCTCAGGT 58.351 50.000 0.00 0.00 35.62 4.00
4537 5084 5.645067 CACTAAAATCTCTCAATGCACCTCA 59.355 40.000 0.00 0.00 0.00 3.86
4647 5194 8.571336 GCATGGCAGAAGTTATATTATCTTTGT 58.429 33.333 0.00 0.00 0.00 2.83
4664 5211 0.592637 CAAAAGACGTGCATGGCAGA 59.407 50.000 15.74 0.00 40.08 4.26
4748 5367 3.483196 CGACAGCACACAAACTTCAAATG 59.517 43.478 0.00 0.00 0.00 2.32
4797 5416 8.025445 AGCAATTCTTAATTTCTTGTACTGCAG 58.975 33.333 13.48 13.48 0.00 4.41
4833 5452 1.144936 GGCATTCCAGTCGGAGGAG 59.855 63.158 0.00 0.00 44.10 3.69
4836 5455 1.519455 GTCGGCATTCCAGTCGGAG 60.519 63.158 0.00 0.00 44.10 4.63
4837 5456 0.681887 TAGTCGGCATTCCAGTCGGA 60.682 55.000 0.00 0.00 40.60 4.55
4838 5457 0.389391 ATAGTCGGCATTCCAGTCGG 59.611 55.000 0.00 0.00 37.20 4.79
4840 5459 1.412710 TGGATAGTCGGCATTCCAGTC 59.587 52.381 6.84 0.00 33.40 3.51
4841 5460 1.414181 CTGGATAGTCGGCATTCCAGT 59.586 52.381 23.07 0.00 46.64 4.00
4842 5461 2.160822 CTGGATAGTCGGCATTCCAG 57.839 55.000 19.72 19.72 46.66 3.86
4843 5462 0.106708 GCTGGATAGTCGGCATTCCA 59.893 55.000 10.13 10.13 38.79 3.53
4844 5463 0.946221 CGCTGGATAGTCGGCATTCC 60.946 60.000 1.57 1.57 38.88 3.01
4845 5464 0.946221 CCGCTGGATAGTCGGCATTC 60.946 60.000 0.00 0.00 38.88 2.67
4846 5465 1.069765 CCGCTGGATAGTCGGCATT 59.930 57.895 0.00 0.00 38.88 3.56
4847 5466 1.188219 ATCCGCTGGATAGTCGGCAT 61.188 55.000 8.11 0.00 41.16 4.40
4848 5467 1.806461 GATCCGCTGGATAGTCGGCA 61.806 60.000 9.60 0.00 43.27 5.69
4849 5468 1.080434 GATCCGCTGGATAGTCGGC 60.080 63.158 9.60 0.00 43.27 5.54
4850 5469 1.210413 CGATCCGCTGGATAGTCGG 59.790 63.158 9.60 0.00 43.27 4.79
4851 5470 4.849336 CGATCCGCTGGATAGTCG 57.151 61.111 9.60 7.21 43.27 4.18
4862 5481 1.298157 TTCACAGCCAAAGCGATCCG 61.298 55.000 0.00 0.00 46.67 4.18
4863 5482 0.881118 TTTCACAGCCAAAGCGATCC 59.119 50.000 0.00 0.00 46.67 3.36
4864 5483 2.162208 TGATTTCACAGCCAAAGCGATC 59.838 45.455 0.00 0.00 46.67 3.69
4875 5501 6.529125 GCAAGTGGTAATGAATGATTTCACAG 59.471 38.462 0.00 0.00 44.36 3.66
4923 5549 7.156876 TGGCTTCATGTAGGAAATGTTTTAG 57.843 36.000 1.21 0.00 0.00 1.85
4976 5602 4.038271 TGAGATTCCACAAAGCCAAGAT 57.962 40.909 0.00 0.00 0.00 2.40
5100 5731 8.817092 AAAAACGGGGAATATCTTGAATCTTA 57.183 30.769 0.00 0.00 0.00 2.10
5120 5751 4.099380 TCGGTTGTTGGACTTGAAAAAC 57.901 40.909 0.00 0.00 0.00 2.43
5129 5760 2.018515 TGTTTCCTTCGGTTGTTGGAC 58.981 47.619 0.00 0.00 0.00 4.02
5132 5763 4.300189 TGATTGTTTCCTTCGGTTGTTG 57.700 40.909 0.00 0.00 0.00 3.33
5143 5774 6.238484 CCTGGATTTACTCGATGATTGTTTCC 60.238 42.308 0.00 0.00 0.00 3.13
5163 5794 2.250921 TAACGGATTACACCCCTGGA 57.749 50.000 0.00 0.00 0.00 3.86
5166 5797 5.088730 TGCTATATAACGGATTACACCCCT 58.911 41.667 0.00 0.00 0.00 4.79
5411 6047 0.037326 TCCGGTTGACTGATGCTGTC 60.037 55.000 0.00 0.00 33.83 3.51
5412 6048 0.396435 TTCCGGTTGACTGATGCTGT 59.604 50.000 0.00 0.00 0.00 4.40
5435 6071 1.478916 GTTGAGTCTAGGTGGGCTCTC 59.521 57.143 0.00 0.00 0.00 3.20
5448 6084 5.537188 ACATCTCTCTTGTTGAGTTGAGTC 58.463 41.667 8.28 0.00 43.13 3.36
5494 6130 2.675423 CCTCGGTCCTGGTCGTCA 60.675 66.667 10.69 0.00 0.00 4.35
5621 6257 0.967380 GGTTCCTCCTCGGGTTCGTA 60.967 60.000 0.00 0.00 37.69 3.43
5633 6269 1.295746 GTTCCTCACGGGGTTCCTC 59.704 63.158 0.00 0.00 35.33 3.71
5702 6338 0.389296 TGTTCGTGATCGCGGTCAAT 60.389 50.000 26.00 0.00 36.96 2.57
5782 6418 3.563808 CAGTTGGTTCTGAAAATCCGTCA 59.436 43.478 0.00 0.00 37.61 4.35


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

AutoCloner maintained by Alex Coulton.