Multiple sequence alignment - TraesCS7D01G247200

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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 TraesCS7D01G247200 chr7D 100.000 4171 0 0 1 4171 217472948 217477118 0.000000e+00 7703
1 TraesCS7D01G247200 chr7D 100.000 249 0 0 4423 4671 217477370 217477618 1.180000e-125 460
2 TraesCS7D01G247200 chr7D 98.876 89 0 1 3916 4003 252284100 252284012 1.740000e-34 158
3 TraesCS7D01G247200 chr7A 93.904 3166 109 23 806 3921 230295668 230298799 0.000000e+00 4700
4 TraesCS7D01G247200 chr7A 95.000 200 10 0 4471 4670 230299152 230299351 9.760000e-82 315
5 TraesCS7D01G247200 chr7A 90.698 172 13 3 4002 4171 230298797 230298967 4.700000e-55 226
6 TraesCS7D01G247200 chr7B 94.795 1460 52 7 1851 3287 183308146 183306688 0.000000e+00 2254
7 TraesCS7D01G247200 chr7B 93.518 1049 43 7 819 1845 183309370 183308325 0.000000e+00 1537
8 TraesCS7D01G247200 chr7B 93.805 678 15 2 3270 3920 183306506 183305829 0.000000e+00 994
9 TraesCS7D01G247200 chr7B 96.000 200 8 0 4471 4670 183305475 183305276 4.510000e-85 326
10 TraesCS7D01G247200 chr7B 95.833 72 3 0 4002 4073 183305830 183305759 2.950000e-22 117
11 TraesCS7D01G247200 chr5B 91.624 788 63 2 1 788 661246339 661245555 0.000000e+00 1086
12 TraesCS7D01G247200 chr5B 96.809 94 3 0 3911 4004 449753550 449753643 1.740000e-34 158
13 TraesCS7D01G247200 chr3B 88.198 788 85 7 1 785 726613864 726614646 0.000000e+00 933
14 TraesCS7D01G247200 chr5A 87.863 791 88 7 1 788 529812010 529811225 0.000000e+00 922
15 TraesCS7D01G247200 chr1D 87.768 793 85 9 1 785 40574869 40575657 0.000000e+00 917
16 TraesCS7D01G247200 chr1D 98.876 89 0 1 3916 4003 295568406 295568318 1.740000e-34 158
17 TraesCS7D01G247200 chrUn 86.995 792 96 6 1 789 286753616 286754403 0.000000e+00 885
18 TraesCS7D01G247200 chrUn 86.995 792 96 6 1 789 296179920 296180707 0.000000e+00 885
19 TraesCS7D01G247200 chr4A 86.995 792 96 6 1 789 662322061 662322848 0.000000e+00 885
20 TraesCS7D01G247200 chr4A 93.333 105 6 1 3899 4003 123956163 123956060 2.250000e-33 154
21 TraesCS7D01G247200 chr2B 86.875 800 94 9 1 796 5134259 5135051 0.000000e+00 885
22 TraesCS7D01G247200 chr6B 86.852 791 99 4 1 789 648665614 648666401 0.000000e+00 880
23 TraesCS7D01G247200 chr6D 98.876 89 0 1 3916 4003 265667889 265667801 1.740000e-34 158
24 TraesCS7D01G247200 chr6D 97.753 89 1 1 3916 4003 283850991 283850903 8.100000e-33 152
25 TraesCS7D01G247200 chr2D 96.842 95 2 1 3914 4008 44481294 44481387 1.740000e-34 158
26 TraesCS7D01G247200 chr2D 97.701 87 2 0 3918 4004 296173761 296173675 2.910000e-32 150
27 TraesCS7D01G247200 chr3D 92.308 104 5 3 3906 4008 123309482 123309583 1.350000e-30 145


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 TraesCS7D01G247200 chr7D 217472948 217477618 4670 False 4081.5 7703 100.000000 1 4671 2 chr7D.!!$F1 4670
1 TraesCS7D01G247200 chr7A 230295668 230299351 3683 False 1747.0 4700 93.200667 806 4670 3 chr7A.!!$F1 3864
2 TraesCS7D01G247200 chr7B 183305276 183309370 4094 True 1045.6 2254 94.790200 819 4670 5 chr7B.!!$R1 3851
3 TraesCS7D01G247200 chr5B 661245555 661246339 784 True 1086.0 1086 91.624000 1 788 1 chr5B.!!$R1 787
4 TraesCS7D01G247200 chr3B 726613864 726614646 782 False 933.0 933 88.198000 1 785 1 chr3B.!!$F1 784
5 TraesCS7D01G247200 chr5A 529811225 529812010 785 True 922.0 922 87.863000 1 788 1 chr5A.!!$R1 787
6 TraesCS7D01G247200 chr1D 40574869 40575657 788 False 917.0 917 87.768000 1 785 1 chr1D.!!$F1 784
7 TraesCS7D01G247200 chrUn 286753616 286754403 787 False 885.0 885 86.995000 1 789 1 chrUn.!!$F1 788
8 TraesCS7D01G247200 chrUn 296179920 296180707 787 False 885.0 885 86.995000 1 789 1 chrUn.!!$F2 788
9 TraesCS7D01G247200 chr4A 662322061 662322848 787 False 885.0 885 86.995000 1 789 1 chr4A.!!$F1 788
10 TraesCS7D01G247200 chr2B 5134259 5135051 792 False 885.0 885 86.875000 1 796 1 chr2B.!!$F1 795
11 TraesCS7D01G247200 chr6B 648665614 648666401 787 False 880.0 880 86.852000 1 789 1 chr6B.!!$F1 788

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
728 738 0.537653 GAGGACAGCAGGGGAGTAAC 59.462 60.0 0.00 0.00 0.0 2.50 F
1009 1021 0.681243 GGAGGAAGCCATGGGTGAAC 60.681 60.0 19.09 10.81 0.0 3.18 F
1092 1104 0.774491 ACACACCCAACCCATACCCT 60.774 55.0 0.00 0.00 0.0 4.34 F
2933 3165 0.842635 ATCTCCTTGGATGGTGGCTC 59.157 55.0 0.00 0.00 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2638 2850 1.202200 TGTTTGTACAACCAACAGCGC 60.202 47.619 8.07 0.00 0.00 5.92 R
2933 3165 0.457509 CTCTACACTGGCGCTCACAG 60.458 60.000 7.64 9.17 41.64 3.66 R
3003 3235 3.498774 AGGTGCACAATCTGAGAAAGT 57.501 42.857 20.43 0.00 0.00 2.66 R
4000 4476 0.035820 TGGTCGGCCAACCAAGATAC 60.036 55.000 14.92 0.00 46.26 2.24 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
39 40 4.246712 TCTTTACCACTAGGGAGACGAT 57.753 45.455 0.00 0.00 41.15 3.73
70 71 6.549364 TCAAGGGTTTAGTGACATCAATGTTT 59.451 34.615 0.00 0.00 41.95 2.83
82 83 2.202566 TCAATGTTTACACGCACACGA 58.797 42.857 0.00 0.00 43.93 4.35
151 152 3.133003 ACTCCCCAACTGTCGATGATAAG 59.867 47.826 0.00 0.00 0.00 1.73
246 247 3.636153 ATGGAGAAGGGCTTAGTGAAC 57.364 47.619 0.00 0.00 0.00 3.18
339 340 1.208535 TCACCCAGACACGAAAACTGT 59.791 47.619 0.00 0.00 0.00 3.55
345 346 3.245284 CCAGACACGAAAACTGTAGTGTG 59.755 47.826 13.28 7.94 46.34 3.82
498 500 1.751162 CTCTTCCGGGAGCTCGTCT 60.751 63.158 4.24 0.00 0.00 4.18
522 524 0.812811 CCACGATCACATCCTGCAGG 60.813 60.000 27.87 27.87 0.00 4.85
525 527 0.873312 CGATCACATCCTGCAGGTCG 60.873 60.000 31.58 26.24 36.34 4.79
555 557 1.637553 AGTCCCAACTCTGCCATCATT 59.362 47.619 0.00 0.00 0.00 2.57
558 560 1.471119 CCAACTCTGCCATCATTGCT 58.529 50.000 0.00 0.00 0.00 3.91
573 575 2.347630 TGCTTCGAGTTCGGAGGAA 58.652 52.632 11.51 0.00 42.40 3.36
634 641 1.241315 CCCGTGGTTTCTTTCCGCAT 61.241 55.000 0.00 0.00 35.45 4.73
728 738 0.537653 GAGGACAGCAGGGGAGTAAC 59.462 60.000 0.00 0.00 0.00 2.50
789 799 2.427812 GGAACCCTAACGAGAGGAGAAG 59.572 54.545 8.68 0.00 39.15 2.85
790 800 1.476477 ACCCTAACGAGAGGAGAAGC 58.524 55.000 8.68 0.00 39.15 3.86
791 801 1.272536 ACCCTAACGAGAGGAGAAGCA 60.273 52.381 8.68 0.00 39.15 3.91
792 802 2.035632 CCCTAACGAGAGGAGAAGCAT 58.964 52.381 8.68 0.00 39.15 3.79
793 803 2.223923 CCCTAACGAGAGGAGAAGCATG 60.224 54.545 8.68 0.00 39.15 4.06
794 804 2.690497 CCTAACGAGAGGAGAAGCATGA 59.310 50.000 0.00 0.00 39.15 3.07
795 805 3.131223 CCTAACGAGAGGAGAAGCATGAA 59.869 47.826 0.00 0.00 39.15 2.57
796 806 3.685139 AACGAGAGGAGAAGCATGAAA 57.315 42.857 0.00 0.00 0.00 2.69
797 807 3.685139 ACGAGAGGAGAAGCATGAAAA 57.315 42.857 0.00 0.00 0.00 2.29
798 808 4.008074 ACGAGAGGAGAAGCATGAAAAA 57.992 40.909 0.00 0.00 0.00 1.94
823 833 1.335872 CGTTGATGTGGGCTTCCAAAC 60.336 52.381 0.00 0.00 43.12 2.93
876 886 0.986019 AATCCATACCACAGGCCCGA 60.986 55.000 0.00 0.00 0.00 5.14
899 909 1.607612 CCCAGTAACCCATCGGCTT 59.392 57.895 0.00 0.00 0.00 4.35
1009 1021 0.681243 GGAGGAAGCCATGGGTGAAC 60.681 60.000 19.09 10.81 0.00 3.18
1020 1032 2.671682 GGTGAACAGGGGGAGCTC 59.328 66.667 4.71 4.71 0.00 4.09
1092 1104 0.774491 ACACACCCAACCCATACCCT 60.774 55.000 0.00 0.00 0.00 4.34
1346 1358 2.296190 GGAGCCTTGGTTTTGTCGATTT 59.704 45.455 0.00 0.00 0.00 2.17
1362 1374 3.702548 TCGATTTGGATCCTCGGTTCTTA 59.297 43.478 18.63 0.00 33.38 2.10
1519 1531 3.904571 TGATGCAGACAAAATTGCTGAC 58.095 40.909 16.44 10.65 40.87 3.51
1663 1691 8.792830 ATTGCTAGTAAGAAAGCTGAAACATA 57.207 30.769 0.00 0.00 39.53 2.29
1710 1739 2.483876 TCAGCAGTGAAGGAGAAAACG 58.516 47.619 0.00 0.00 0.00 3.60
1733 1762 3.433343 TGCATCTTGAAATGTGGATGGT 58.567 40.909 0.00 0.00 36.88 3.55
1753 1782 8.126700 GGATGGTTTTATGGAGTTATGTTAACG 58.873 37.037 0.26 0.00 0.00 3.18
1774 1803 3.784883 CGCAGCTTAGCATCTATGAAC 57.215 47.619 7.07 0.00 0.00 3.18
1776 1805 3.557185 CGCAGCTTAGCATCTATGAACAA 59.443 43.478 7.07 0.00 0.00 2.83
1777 1806 4.212847 CGCAGCTTAGCATCTATGAACAAT 59.787 41.667 7.07 0.00 0.00 2.71
1778 1807 5.450171 GCAGCTTAGCATCTATGAACAATG 58.550 41.667 7.07 0.00 0.00 2.82
1784 1816 4.202441 AGCATCTATGAACAATGTCCACC 58.798 43.478 0.00 0.00 0.00 4.61
1798 1830 4.286297 TGTCCACCAATTTCCTCACTAG 57.714 45.455 0.00 0.00 0.00 2.57
1846 2054 5.039920 ACTGCTGCATCCAGAATACAATA 57.960 39.130 18.21 0.00 41.77 1.90
1847 2055 4.818546 ACTGCTGCATCCAGAATACAATAC 59.181 41.667 18.21 0.00 41.77 1.89
1848 2056 4.136796 TGCTGCATCCAGAATACAATACC 58.863 43.478 0.00 0.00 41.77 2.73
1955 2167 4.130118 CCAGTAGGTATGTGATTGCCTTC 58.870 47.826 0.00 0.00 32.90 3.46
1994 2206 5.705902 TGCATGCTGTATATCATGAAATGC 58.294 37.500 20.33 6.32 46.21 3.56
2059 2271 7.370383 GTTTTCTGAATGAATTGAAGTAGCCA 58.630 34.615 0.00 0.00 34.24 4.75
2079 2291 3.152341 CACACCCTGAGCTTGAAATCTT 58.848 45.455 0.00 0.00 0.00 2.40
2084 2296 3.691609 CCCTGAGCTTGAAATCTTGTACC 59.308 47.826 0.00 0.00 0.00 3.34
2087 2299 5.338381 CCTGAGCTTGAAATCTTGTACCCTA 60.338 44.000 0.00 0.00 0.00 3.53
2090 2302 7.857456 TGAGCTTGAAATCTTGTACCCTATTA 58.143 34.615 0.00 0.00 0.00 0.98
2187 2399 6.111382 GGGGTGAAGTTGATACTAGGTAAAC 58.889 44.000 0.00 0.00 33.17 2.01
2194 2406 9.583765 GAAGTTGATACTAGGTAAACACCTTAG 57.416 37.037 0.91 1.14 41.12 2.18
2211 2423 6.826741 ACACCTTAGCTGTTCTTTTTGAGTTA 59.173 34.615 0.00 0.00 0.00 2.24
2246 2458 1.170442 TGAATGCAGCATCTGTGTGG 58.830 50.000 8.77 0.00 33.43 4.17
2264 2476 6.054941 TGTGTGGGCTACTAATATGAATGTG 58.945 40.000 1.79 0.00 0.00 3.21
2343 2555 5.009110 TCGTCTGCACAAAATTAATGTGGAA 59.991 36.000 19.95 9.76 46.33 3.53
2418 2630 2.363172 GCCAGGAGGGGAGTCTCAC 61.363 68.421 1.47 0.00 37.04 3.51
2553 2765 4.130118 CCAAGTGTTCTAGTATGATGCCC 58.870 47.826 0.00 0.00 0.00 5.36
2573 2785 5.072736 TGCCCTATCAGATTCATGTCAGATT 59.927 40.000 0.00 0.00 0.00 2.40
2611 2823 7.655521 TCTATCTGTATTCCGGAAGAAGAAA 57.344 36.000 23.47 11.34 38.07 2.52
2698 2930 9.512435 CTTCAGGAAAATGCAAGATATTTACTG 57.488 33.333 13.81 13.81 35.82 2.74
2771 3003 5.528320 ACCTGAAATTTGCATTTTCACAAGG 59.472 36.000 16.96 17.69 37.97 3.61
2821 3053 4.000988 CCAAGTTGTCACTTTATAGCGGT 58.999 43.478 1.45 0.00 40.66 5.68
2850 3082 9.125026 GATAACCTGAAAACATGTATCCATTCT 57.875 33.333 0.00 0.00 0.00 2.40
2933 3165 0.842635 ATCTCCTTGGATGGTGGCTC 59.157 55.000 0.00 0.00 0.00 4.70
3003 3235 5.411831 ACTTGCTGATGTGAGATTGACTA 57.588 39.130 0.00 0.00 0.00 2.59
3206 3438 7.698506 TGATTCTTGCTCTGAAATTCTGATT 57.301 32.000 3.08 0.00 0.00 2.57
3257 3489 9.661187 CATCATCTAAAAGATCAATTTTCTCCG 57.339 33.333 0.00 0.00 31.32 4.63
3277 3708 7.362662 TCTCCGTTTACCGTATATATTGTCAC 58.637 38.462 0.00 0.00 33.66 3.67
3453 3920 8.635765 AAGTCATAAACTCCTTGCTGAATTAA 57.364 30.769 0.00 0.00 37.17 1.40
3464 3931 6.891908 TCCTTGCTGAATTAATTAGCCTCTTT 59.108 34.615 18.66 0.00 36.64 2.52
3551 4018 4.104102 TCCCTTTAGATGTTGTCAACAGGT 59.896 41.667 22.16 14.36 45.95 4.00
3571 4038 5.801947 CAGGTTCTTCTTGACAAAACAACAG 59.198 40.000 3.57 0.00 0.00 3.16
3695 4162 0.943673 TCATGTTGTGACTGCGTTGG 59.056 50.000 0.00 0.00 0.00 3.77
3815 4291 5.636903 AGTGCAGACCTCATATTTACCAT 57.363 39.130 0.00 0.00 0.00 3.55
3929 4405 6.749036 ATCTTTCAATATTACTCCCTCCGT 57.251 37.500 0.00 0.00 0.00 4.69
3930 4406 6.158023 TCTTTCAATATTACTCCCTCCGTC 57.842 41.667 0.00 0.00 0.00 4.79
3931 4407 4.950205 TTCAATATTACTCCCTCCGTCC 57.050 45.455 0.00 0.00 0.00 4.79
3932 4408 3.236896 TCAATATTACTCCCTCCGTCCC 58.763 50.000 0.00 0.00 0.00 4.46
3933 4409 2.969950 CAATATTACTCCCTCCGTCCCA 59.030 50.000 0.00 0.00 0.00 4.37
3934 4410 3.562108 ATATTACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
3935 4411 4.687262 ATATTACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
3936 4412 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
3937 4413 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
3938 4414 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
3939 4415 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3940 4416 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3941 4417 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3942 4418 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3943 4419 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3944 4420 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
3945 4421 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
3946 4422 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
3947 4423 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
3948 4424 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
3949 4425 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
3950 4426 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
3951 4427 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
3952 4428 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
3953 4429 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
3954 4430 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3955 4431 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3965 4441 7.781548 AGAACGTTTTTGACATTAGTGTAGT 57.218 32.000 0.46 0.00 39.09 2.73
3966 4442 7.627340 AGAACGTTTTTGACATTAGTGTAGTG 58.373 34.615 0.46 0.00 39.09 2.74
3967 4443 6.913873 ACGTTTTTGACATTAGTGTAGTGT 57.086 33.333 0.00 0.00 39.09 3.55
3968 4444 8.422973 AACGTTTTTGACATTAGTGTAGTGTA 57.577 30.769 0.00 0.00 39.09 2.90
3969 4445 8.422973 ACGTTTTTGACATTAGTGTAGTGTAA 57.577 30.769 0.00 0.00 39.09 2.41
3970 4446 8.881743 ACGTTTTTGACATTAGTGTAGTGTAAA 58.118 29.630 0.00 0.00 39.09 2.01
3971 4447 9.705471 CGTTTTTGACATTAGTGTAGTGTAAAA 57.295 29.630 0.00 0.00 39.09 1.52
3994 4470 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
3995 4471 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
3996 4472 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
3997 4473 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
3998 4474 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
3999 4475 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
4000 4476 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4063 4539 5.742562 ACCATTTCCCTCCATAATAACCA 57.257 39.130 0.00 0.00 0.00 3.67
4069 4545 9.705103 CATTTCCCTCCATAATAACCATCATAT 57.295 33.333 0.00 0.00 0.00 1.78
4087 4563 7.284489 CCATCATATAGAGGCTAGAGAGGTAAC 59.716 44.444 0.00 0.00 0.00 2.50
4138 4616 7.746475 GCTATATGGATCGCTATTCAACAAAAC 59.254 37.037 0.00 0.00 0.00 2.43
4143 4621 5.743872 GGATCGCTATTCAACAAAACATTCC 59.256 40.000 0.00 0.00 0.00 3.01
4166 4644 1.777272 AGGCACTCAATATTCTCCCCC 59.223 52.381 0.00 0.00 0.00 5.40
4167 4645 1.777272 GGCACTCAATATTCTCCCCCT 59.223 52.381 0.00 0.00 0.00 4.79
4169 4647 2.224646 GCACTCAATATTCTCCCCCTCC 60.225 54.545 0.00 0.00 0.00 4.30
4170 4648 3.048600 CACTCAATATTCTCCCCCTCCA 58.951 50.000 0.00 0.00 0.00 3.86
4535 5055 1.227853 GTTGGCCTCGTGGAGTTGT 60.228 57.895 7.92 0.00 34.57 3.32
4538 5058 2.031163 GCCTCGTGGAGTTGTGCT 59.969 61.111 7.92 0.00 34.57 4.40
4648 5168 0.631753 AGTGGGAGAGAGGAATCGGA 59.368 55.000 0.00 0.00 0.00 4.55
4670 5190 3.507233 AGTGAACTTGAGCAGAGAGAGAG 59.493 47.826 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.105567 TGTCACTAAACCCTTGAAGAACA 57.894 39.130 0.00 0.00 0.00 3.18
82 83 4.082026 CAGGATTTTGAAGGGAATTTCGCT 60.082 41.667 9.98 9.98 41.77 4.93
151 152 5.012975 AGGATATTTCTCCAAGATCAGAGCC 59.987 44.000 0.00 0.00 35.13 4.70
188 189 3.386402 TGAGATGTGGGTGCGAATACATA 59.614 43.478 0.00 0.00 34.18 2.29
189 190 2.170397 TGAGATGTGGGTGCGAATACAT 59.830 45.455 0.00 0.00 36.54 2.29
196 197 1.238439 AAAGTTGAGATGTGGGTGCG 58.762 50.000 0.00 0.00 0.00 5.34
339 340 4.401022 TCGAGGAAAACCTCTACACACTA 58.599 43.478 13.27 0.00 34.91 2.74
345 346 2.561858 ACCACTCGAGGAAAACCTCTAC 59.438 50.000 18.41 0.00 34.91 2.59
498 500 2.677902 GCAGGATGTGATCGTGGAAGAA 60.678 50.000 8.03 0.00 43.40 2.52
522 524 2.053277 GGGACTCCAGGAGGACGAC 61.053 68.421 21.31 5.61 39.61 4.34
525 527 0.545548 AGTTGGGACTCCAGGAGGAC 60.546 60.000 21.31 13.51 45.04 3.85
555 557 0.038526 GTTCCTCCGAACTCGAAGCA 60.039 55.000 0.00 0.00 44.29 3.91
558 560 1.969862 GGGTTCCTCCGAACTCGAA 59.030 57.895 0.00 0.00 46.46 3.71
594 596 2.935201 GCAAGAGATATGATCGATGGCC 59.065 50.000 0.54 0.00 0.00 5.36
606 608 1.906574 AGAAACCACGGGCAAGAGATA 59.093 47.619 0.00 0.00 0.00 1.98
728 738 2.249692 GGCTCCTCCGTAGAGATCG 58.750 63.158 0.00 0.00 43.39 3.69
795 805 0.678950 CCCACATCAACGGCCTTTTT 59.321 50.000 0.00 0.00 0.00 1.94
796 806 1.815817 GCCCACATCAACGGCCTTTT 61.816 55.000 0.00 0.00 36.63 2.27
797 807 2.275380 GCCCACATCAACGGCCTTT 61.275 57.895 0.00 0.00 36.63 3.11
798 808 2.676471 GCCCACATCAACGGCCTT 60.676 61.111 0.00 0.00 36.63 4.35
799 809 3.210012 AAGCCCACATCAACGGCCT 62.210 57.895 0.00 0.00 44.13 5.19
800 810 2.676471 AAGCCCACATCAACGGCC 60.676 61.111 0.00 0.00 44.13 6.13
801 811 2.700773 GGAAGCCCACATCAACGGC 61.701 63.158 0.00 0.00 43.35 5.68
802 812 0.893270 TTGGAAGCCCACATCAACGG 60.893 55.000 0.00 0.00 43.41 4.44
803 813 0.958091 TTTGGAAGCCCACATCAACG 59.042 50.000 0.00 0.00 43.41 4.10
804 814 1.335872 CGTTTGGAAGCCCACATCAAC 60.336 52.381 0.00 0.00 43.41 3.18
805 815 0.958091 CGTTTGGAAGCCCACATCAA 59.042 50.000 0.00 0.00 43.41 2.57
806 816 1.523154 GCGTTTGGAAGCCCACATCA 61.523 55.000 0.00 0.00 43.41 3.07
807 817 1.212751 GCGTTTGGAAGCCCACATC 59.787 57.895 0.00 0.00 43.41 3.06
808 818 1.228552 AGCGTTTGGAAGCCCACAT 60.229 52.632 0.00 0.00 43.41 3.21
809 819 1.896660 GAGCGTTTGGAAGCCCACA 60.897 57.895 0.00 0.00 43.41 4.17
810 820 1.244019 ATGAGCGTTTGGAAGCCCAC 61.244 55.000 0.00 0.00 43.41 4.61
811 821 1.074775 ATGAGCGTTTGGAAGCCCA 59.925 52.632 0.00 0.00 41.64 5.36
876 886 1.120530 CGATGGGTTACTGGGCTAGT 58.879 55.000 9.01 9.01 43.56 2.57
899 909 2.881491 ATCAGGGGAATCAGGGGCCA 62.881 60.000 4.39 0.00 0.00 5.36
1075 1087 0.178843 AGAGGGTATGGGTTGGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
1123 1135 2.423898 GGCGAGGAGGACGGATGAA 61.424 63.158 0.00 0.00 0.00 2.57
1326 1338 3.308530 CAAATCGACAAAACCAAGGCTC 58.691 45.455 0.00 0.00 0.00 4.70
1346 1358 5.630415 ATCATTTAAGAACCGAGGATCCA 57.370 39.130 15.82 0.00 0.00 3.41
1362 1374 6.949352 AGAAGACACACAACTGAATCATTT 57.051 33.333 0.00 0.00 0.00 2.32
1519 1531 7.821359 TCACTGAAGATCTTGAAAAGGATACAG 59.179 37.037 14.00 11.67 46.24 2.74
1663 1691 6.493458 AGGAAAGGTAATGTAAATGCAACACT 59.507 34.615 0.00 0.00 0.00 3.55
1710 1739 4.178540 CCATCCACATTTCAAGATGCAAC 58.821 43.478 0.00 0.00 35.78 4.17
1733 1762 5.121925 TGCGCGTTAACATAACTCCATAAAA 59.878 36.000 8.43 0.00 0.00 1.52
1753 1782 1.788258 TCATAGATGCTAAGCTGCGC 58.212 50.000 0.00 0.00 35.36 6.09
1771 1800 4.280677 TGAGGAAATTGGTGGACATTGTTC 59.719 41.667 0.00 0.00 0.00 3.18
1772 1801 4.039124 GTGAGGAAATTGGTGGACATTGTT 59.961 41.667 0.00 0.00 0.00 2.83
1773 1802 3.573967 GTGAGGAAATTGGTGGACATTGT 59.426 43.478 0.00 0.00 0.00 2.71
1774 1803 3.828451 AGTGAGGAAATTGGTGGACATTG 59.172 43.478 0.00 0.00 0.00 2.82
1776 1805 3.814504 AGTGAGGAAATTGGTGGACAT 57.185 42.857 0.00 0.00 0.00 3.06
1777 1806 4.286297 CTAGTGAGGAAATTGGTGGACA 57.714 45.455 0.00 0.00 0.00 4.02
1798 1830 4.990426 ACTAAAATTTTGACATGCTGCACC 59.010 37.500 13.76 0.00 0.00 5.01
1846 2054 6.143915 ACCAAGTACTATCTCATATGGTGGT 58.856 40.000 10.16 6.28 38.44 4.16
1847 2055 6.672266 ACCAAGTACTATCTCATATGGTGG 57.328 41.667 10.16 5.70 38.44 4.61
1848 2056 8.637196 TCTACCAAGTACTATCTCATATGGTG 57.363 38.462 17.88 10.27 40.02 4.17
1955 2167 3.181397 CATGCAATTTAAGTCAAGCCGG 58.819 45.455 0.00 0.00 0.00 6.13
1994 2206 8.644318 AGCTTACAATGTTATTACTACTTCCG 57.356 34.615 0.00 0.00 0.00 4.30
2033 2245 6.524586 GGCTACTTCAATTCATTCAGAAAACG 59.475 38.462 0.00 0.00 40.22 3.60
2059 2271 3.152341 CAAGATTTCAAGCTCAGGGTGT 58.848 45.455 0.00 0.00 0.00 4.16
2187 2399 5.757850 ACTCAAAAAGAACAGCTAAGGTG 57.242 39.130 0.00 0.00 37.06 4.00
2194 2406 4.911514 TGGGTAACTCAAAAAGAACAGC 57.088 40.909 0.00 0.00 0.00 4.40
2211 2423 5.862845 TGCATTCAAATAAAACACATGGGT 58.137 33.333 0.00 0.00 0.00 4.51
2343 2555 9.277783 CAGCTAACAATATATTCTACAGCCTTT 57.722 33.333 11.48 0.00 0.00 3.11
2418 2630 2.533266 AATACATACTCTGCCCAGCG 57.467 50.000 0.00 0.00 0.00 5.18
2470 2682 7.876582 ACAAAATTACAGTTCTACTCAGGTACC 59.123 37.037 2.73 2.73 0.00 3.34
2638 2850 1.202200 TGTTTGTACAACCAACAGCGC 60.202 47.619 8.07 0.00 0.00 5.92
2821 3053 7.629157 TGGATACATGTTTTCAGGTTATCTGA 58.371 34.615 2.30 0.00 46.86 3.27
2933 3165 0.457509 CTCTACACTGGCGCTCACAG 60.458 60.000 7.64 9.17 41.64 3.66
3003 3235 3.498774 AGGTGCACAATCTGAGAAAGT 57.501 42.857 20.43 0.00 0.00 2.66
3214 3446 5.669447 AGATGATGGGAGTTAGAAGTTGGAT 59.331 40.000 0.00 0.00 0.00 3.41
3277 3708 4.942852 TGTCCTGCCAATGTAAAAAGTTG 58.057 39.130 0.00 0.00 0.00 3.16
3453 3920 4.021104 GCCCTGTTTTTGAAAGAGGCTAAT 60.021 41.667 10.24 0.00 0.00 1.73
3464 3931 5.299148 CATCAATGAAAGCCCTGTTTTTGA 58.701 37.500 0.00 0.00 0.00 2.69
3551 4018 7.174253 ACACTACTGTTGTTTTGTCAAGAAGAA 59.826 33.333 0.00 0.00 0.00 2.52
3695 4162 2.807045 CTCGTGCTGACCTGACGC 60.807 66.667 0.00 0.00 33.11 5.19
3815 4291 2.649531 AACCAAGTGTCCGGATTTCA 57.350 45.000 7.81 0.00 0.00 2.69
3915 4391 4.474303 TTATGGGACGGAGGGAGTAATA 57.526 45.455 0.00 0.00 0.00 0.98
3918 4394 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3919 4395 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
3920 4396 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3921 4397 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
3922 4398 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
3923 4399 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
3924 4400 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
3925 4401 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
3926 4402 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
3927 4403 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
3928 4404 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3929 4405 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3939 4415 9.316730 ACTACACTAATGTCAAAAACGTTCTTA 57.683 29.630 0.00 0.00 40.48 2.10
3940 4416 8.120465 CACTACACTAATGTCAAAAACGTTCTT 58.880 33.333 0.00 0.00 40.48 2.52
3941 4417 7.279313 ACACTACACTAATGTCAAAAACGTTCT 59.721 33.333 0.00 0.00 40.48 3.01
3942 4418 7.404203 ACACTACACTAATGTCAAAAACGTTC 58.596 34.615 0.00 0.00 40.48 3.95
3943 4419 7.311364 ACACTACACTAATGTCAAAAACGTT 57.689 32.000 0.00 0.00 40.48 3.99
3944 4420 6.913873 ACACTACACTAATGTCAAAAACGT 57.086 33.333 0.00 0.00 40.48 3.99
3945 4421 9.705471 TTTTACACTACACTAATGTCAAAAACG 57.295 29.630 0.00 0.00 40.48 3.60
3969 4445 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
3970 4446 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
3971 4447 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
3972 4448 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
3973 4449 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
3974 4450 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
3975 4451 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
3976 4452 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
3977 4453 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3978 4454 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3979 4455 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3980 4456 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3981 4457 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3982 4458 4.294168 AGATACTCCCTCCGTCCCATAATA 59.706 45.833 0.00 0.00 0.00 0.98
3983 4459 3.077695 AGATACTCCCTCCGTCCCATAAT 59.922 47.826 0.00 0.00 0.00 1.28
3984 4460 2.449730 AGATACTCCCTCCGTCCCATAA 59.550 50.000 0.00 0.00 0.00 1.90
3985 4461 2.071372 AGATACTCCCTCCGTCCCATA 58.929 52.381 0.00 0.00 0.00 2.74
3986 4462 0.861155 AGATACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
3987 4463 0.635009 AAGATACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
3988 4464 1.041437 CAAGATACTCCCTCCGTCCC 58.959 60.000 0.00 0.00 0.00 4.46
3989 4465 1.041437 CCAAGATACTCCCTCCGTCC 58.959 60.000 0.00 0.00 0.00 4.79
3990 4466 1.777941 ACCAAGATACTCCCTCCGTC 58.222 55.000 0.00 0.00 0.00 4.79
3991 4467 1.831736 CAACCAAGATACTCCCTCCGT 59.168 52.381 0.00 0.00 0.00 4.69
3992 4468 1.139058 CCAACCAAGATACTCCCTCCG 59.861 57.143 0.00 0.00 0.00 4.63
3993 4469 1.134068 GCCAACCAAGATACTCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
3994 4470 1.134068 GGCCAACCAAGATACTCCCTC 60.134 57.143 0.00 0.00 35.26 4.30
3995 4471 0.919710 GGCCAACCAAGATACTCCCT 59.080 55.000 0.00 0.00 35.26 4.20
3996 4472 0.463833 CGGCCAACCAAGATACTCCC 60.464 60.000 2.24 0.00 34.57 4.30
3997 4473 0.539986 TCGGCCAACCAAGATACTCC 59.460 55.000 2.24 0.00 34.57 3.85
3998 4474 1.653151 GTCGGCCAACCAAGATACTC 58.347 55.000 2.24 0.00 34.57 2.59
3999 4475 0.252197 GGTCGGCCAACCAAGATACT 59.748 55.000 8.40 0.00 39.27 2.12
4000 4476 0.035820 TGGTCGGCCAACCAAGATAC 60.036 55.000 14.92 0.00 46.26 2.24
4063 4539 7.934313 TGTTACCTCTCTAGCCTCTATATGAT 58.066 38.462 0.00 0.00 0.00 2.45
4116 4594 6.993786 TGTTTTGTTGAATAGCGATCCATA 57.006 33.333 0.00 0.00 0.00 2.74
4138 4616 4.818546 AGAATATTGAGTGCCTTCGGAATG 59.181 41.667 0.00 0.00 0.00 2.67
4143 4621 3.134458 GGGAGAATATTGAGTGCCTTCG 58.866 50.000 0.00 0.00 0.00 3.79
4447 4925 1.819632 CGGGATGGGTAGCAGCAAC 60.820 63.158 0.00 0.00 0.00 4.17
4467 4945 2.353109 GCAGCAAAATGAAGGGGAGAAC 60.353 50.000 0.00 0.00 0.00 3.01
4648 5168 3.495331 TCTCTCTCTGCTCAAGTTCACT 58.505 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.