Multiple sequence alignment - TraesCS4D01G314800

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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 TraesCS4D01G314800 chr4D 100.000 4449 0 0 1 4449 480878232 480882680 0.000000e+00 8216.0
1 TraesCS4D01G314800 chr4D 100.000 508 0 0 4784 5291 480883015 480883522 0.000000e+00 939.0
2 TraesCS4D01G314800 chr5A 93.514 1881 89 18 2584 4449 662529735 662527873 0.000000e+00 2767.0
3 TraesCS4D01G314800 chr5A 89.059 1965 132 33 674 2580 662531705 662529766 0.000000e+00 2361.0
4 TraesCS4D01G314800 chr5A 86.514 697 61 21 1 677 662532414 662531731 0.000000e+00 736.0
5 TraesCS4D01G314800 chr5A 76.143 503 65 31 4784 5254 662527839 662527360 4.150000e-51 213.0
6 TraesCS4D01G314800 chr5A 76.628 261 46 11 1 255 429255337 429255588 4.300000e-26 130.0
7 TraesCS4D01G314800 chr4B 89.784 2036 112 48 1 1978 608965673 608967670 0.000000e+00 2519.0
8 TraesCS4D01G314800 chr4B 93.349 1308 62 13 3158 4449 608969281 608970579 0.000000e+00 1910.0
9 TraesCS4D01G314800 chr4B 93.408 622 32 7 1966 2580 608967716 608968335 0.000000e+00 913.0
10 TraesCS4D01G314800 chr4B 91.697 277 10 3 2584 2860 608968366 608968629 6.470000e-99 372.0
11 TraesCS4D01G314800 chr4B 97.895 190 4 0 2969 3158 608968971 608969160 3.950000e-86 329.0
12 TraesCS4D01G314800 chr4B 88.827 179 5 7 5092 5256 608971155 608971332 6.950000e-49 206.0
13 TraesCS4D01G314800 chr4B 94.643 112 6 0 2859 2970 608968743 608968854 1.960000e-39 174.0
14 TraesCS4D01G314800 chr4B 93.617 47 3 0 4981 5027 608970851 608970897 2.640000e-08 71.3
15 TraesCS4D01G314800 chr6A 80.000 275 35 16 1 265 592470027 592470291 9.050000e-43 185.0
16 TraesCS4D01G314800 chr4A 78.788 264 35 12 2 255 609184104 609183852 1.970000e-34 158.0
17 TraesCS4D01G314800 chr7A 78.277 267 36 18 9 264 393692107 393691852 9.180000e-33 152.0
18 TraesCS4D01G314800 chr1A 76.471 255 47 9 8 256 12309113 12309360 5.560000e-25 126.0
19 TraesCS4D01G314800 chr3A 76.378 254 47 10 8 255 99035573 99035327 2.000000e-24 124.0
20 TraesCS4D01G314800 chr2D 76.378 254 47 10 8 255 382165571 382165817 2.000000e-24 124.0


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 TraesCS4D01G314800 chr4D 480878232 480883522 5290 False 4577.5000 8216 100.0000 1 5291 2 chr4D.!!$F1 5290
1 TraesCS4D01G314800 chr5A 662527360 662532414 5054 True 1519.2500 2767 86.3075 1 5254 4 chr5A.!!$R1 5253
2 TraesCS4D01G314800 chr4B 608965673 608971332 5659 False 811.7875 2519 92.9025 1 5256 8 chr4B.!!$F1 5255

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
785 845 0.391130 CCCACGTGTCATGGAACGAT 60.391 55.0 22.38 8.48 42.32 3.73 F
1695 1777 1.043116 AGAATGTGATCGGCGAGGGA 61.043 55.0 17.22 0.00 0.00 4.20 F
2297 2492 0.395312 TCAAGGTGGAGGTCGAAACC 59.605 55.0 0.00 0.00 46.87 3.27 F
3428 4012 0.539051 ATCTTCACGAAGGGCTGGAG 59.461 55.0 6.94 0.00 38.88 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 2003 0.749454 ACTCTGGCCGATGGATTTGC 60.749 55.0 0.00 0.00 0.0 3.68 R
3096 3556 0.030638 CAAACCGGGTGCTCTGTTTG 59.969 55.0 6.32 0.39 0.0 2.93 R
3651 4235 0.452987 CGCCACATAGCTGCAACATT 59.547 50.0 1.02 0.00 0.0 2.71 R
5261 6124 0.108329 AGACGACGGGCATGGTTAAG 60.108 55.0 0.00 0.00 0.0 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 70 4.081862 TCCAACTAATCTCGACCGTCAAAT 60.082 41.667 0.00 0.00 0.00 2.32
76 81 3.703001 ACCGTCAAATGAGGTCAATCT 57.297 42.857 2.82 0.00 31.69 2.40
94 99 6.040391 GTCAATCTAATGACCTAGACTGCTCT 59.960 42.308 0.00 0.00 43.11 4.09
99 104 5.543507 AATGACCTAGACTGCTCTAATGG 57.456 43.478 0.00 0.00 0.00 3.16
100 105 3.982516 TGACCTAGACTGCTCTAATGGT 58.017 45.455 0.00 0.00 32.58 3.55
108 113 3.967886 GCTCTAATGGTGAGCGCTA 57.032 52.632 11.50 0.00 45.73 4.26
115 130 2.113860 ATGGTGAGCGCTAAACATGT 57.886 45.000 24.96 1.56 0.00 3.21
120 135 4.142708 TGGTGAGCGCTAAACATGTAATTG 60.143 41.667 8.95 0.00 0.00 2.32
125 140 8.070171 GTGAGCGCTAAACATGTAATTGATATT 58.930 33.333 11.50 0.00 0.00 1.28
126 141 8.620416 TGAGCGCTAAACATGTAATTGATATTT 58.380 29.630 11.50 0.00 0.00 1.40
153 169 9.729023 TGCCAAATATAAACGTCAGAATTAATG 57.271 29.630 0.00 0.00 0.00 1.90
212 231 5.119694 TCCACGTGCAATTAATATACTGCA 58.880 37.500 10.91 8.18 42.28 4.41
213 232 5.762711 TCCACGTGCAATTAATATACTGCAT 59.237 36.000 10.91 0.00 45.77 3.96
214 233 6.931840 TCCACGTGCAATTAATATACTGCATA 59.068 34.615 10.91 0.00 45.77 3.14
237 256 9.006839 CATACTAATATCAATGTGCATTCCACT 57.993 33.333 0.00 0.00 44.92 4.00
257 276 7.923888 TCCACTCGTACACATTTACTAGTATC 58.076 38.462 2.79 0.00 29.36 2.24
288 307 5.410132 TCACACAGTCCCATTAATTAACACG 59.590 40.000 0.00 0.00 0.00 4.49
365 384 2.486203 CGATGGGAACGATTTTGGAACA 59.514 45.455 0.00 0.00 0.00 3.18
386 405 3.601685 GGCACCCAACCACCAACG 61.602 66.667 0.00 0.00 0.00 4.10
403 422 6.212955 CACCAACGAACACAAATCCTATTTT 58.787 36.000 0.00 0.00 0.00 1.82
404 423 6.362283 CACCAACGAACACAAATCCTATTTTC 59.638 38.462 0.00 0.00 0.00 2.29
418 437 8.670521 AATCCTATTTTCAACAAAAGATCCCT 57.329 30.769 0.00 0.00 34.92 4.20
422 441 5.789643 TTTTCAACAAAAGATCCCTCCAG 57.210 39.130 0.00 0.00 0.00 3.86
428 447 4.723309 ACAAAAGATCCCTCCAGCATATC 58.277 43.478 0.00 0.00 0.00 1.63
485 507 3.405170 AAGCAAAAGACACAGACAACG 57.595 42.857 0.00 0.00 0.00 4.10
524 546 4.804868 TGCAAAAGGTGATTACATGCAT 57.195 36.364 0.00 0.00 0.00 3.96
526 548 4.220163 TGCAAAAGGTGATTACATGCATGA 59.780 37.500 32.75 12.33 0.00 3.07
527 549 5.105269 TGCAAAAGGTGATTACATGCATGAT 60.105 36.000 32.75 16.86 0.00 2.45
528 550 6.096564 TGCAAAAGGTGATTACATGCATGATA 59.903 34.615 32.75 19.14 0.00 2.15
530 552 7.043192 GCAAAAGGTGATTACATGCATGATAAC 60.043 37.037 32.75 18.57 0.00 1.89
572 601 9.561069 ACTATCATTGACAAAAGTTGAACTAGT 57.439 29.630 0.00 0.00 0.00 2.57
578 607 8.882415 TTGACAAAAGTTGAACTAGTAGTAGG 57.118 34.615 2.50 0.00 0.00 3.18
581 610 8.247666 ACAAAAGTTGAACTAGTAGTAGGAGT 57.752 34.615 2.50 0.00 0.00 3.85
723 783 4.431131 CTCTGGCCCCACCGCAAT 62.431 66.667 0.00 0.00 43.94 3.56
755 815 4.599500 ACTGCCCCTGGGTCCACT 62.599 66.667 12.71 0.00 37.65 4.00
785 845 0.391130 CCCACGTGTCATGGAACGAT 60.391 55.000 22.38 8.48 42.32 3.73
800 860 2.359850 GATGGCAACGGGCTGACA 60.360 61.111 0.00 0.00 44.01 3.58
1635 1717 3.868200 CTGGGGCCACTGGTTCACC 62.868 68.421 6.53 0.00 0.00 4.02
1695 1777 1.043116 AGAATGTGATCGGCGAGGGA 61.043 55.000 17.22 0.00 0.00 4.20
1787 1869 1.254954 AGGTAACCTCGTGACCTCAC 58.745 55.000 0.00 0.00 43.57 3.51
1821 1903 2.028020 TCCGCCTCTTCTTTCTCCTTTC 60.028 50.000 0.00 0.00 0.00 2.62
1888 1971 3.749064 GTGAGCGCTCGAGGGTCA 61.749 66.667 30.75 25.20 0.00 4.02
1918 2003 4.041723 GTGTTTTGGTCCGTTCATCAAAG 58.958 43.478 0.00 0.00 31.89 2.77
1977 2110 6.490566 AAAAATCTTGCAAGCAAATCCATC 57.509 33.333 21.99 0.00 35.33 3.51
1978 2111 3.814005 ATCTTGCAAGCAAATCCATCC 57.186 42.857 21.99 0.00 35.33 3.51
1979 2112 2.811410 TCTTGCAAGCAAATCCATCCT 58.189 42.857 21.99 0.00 35.33 3.24
1981 2114 3.579586 TCTTGCAAGCAAATCCATCCTTT 59.420 39.130 21.99 0.00 35.33 3.11
1982 2115 3.322211 TGCAAGCAAATCCATCCTTTG 57.678 42.857 0.00 0.00 36.81 2.77
2061 2227 4.360889 TGGATTGTGGGGCTCAATAAAAT 58.639 39.130 0.00 0.00 35.94 1.82
2065 2231 6.316140 GGATTGTGGGGCTCAATAAAATTTTC 59.684 38.462 6.72 0.00 35.94 2.29
2160 2332 5.940603 TTTTAAACACTGCACACATTTCG 57.059 34.783 0.00 0.00 0.00 3.46
2189 2361 1.885560 TTCGCCGTTCCATTTCTCAA 58.114 45.000 0.00 0.00 0.00 3.02
2297 2492 0.395312 TCAAGGTGGAGGTCGAAACC 59.605 55.000 0.00 0.00 46.87 3.27
2348 2543 2.798689 CTGCTCGGCTACTGCGTA 59.201 61.111 0.00 0.00 40.82 4.42
2366 2561 2.308690 GTAGAGGGTGCCTACAGGTAG 58.691 57.143 0.00 0.00 37.15 3.18
2580 2777 5.065346 GCTAAAGGGTAATGCTTCTTCACTC 59.935 44.000 0.00 0.00 0.00 3.51
2581 2778 4.640771 AAGGGTAATGCTTCTTCACTCA 57.359 40.909 0.00 0.00 0.00 3.41
2582 2779 4.213564 AGGGTAATGCTTCTTCACTCAG 57.786 45.455 0.00 0.00 0.00 3.35
2589 2813 2.067766 GCTTCTTCACTCAGAGTGCTG 58.932 52.381 23.94 17.93 45.54 4.41
2615 2839 9.620259 GTTTCTTGGACTATAATCTTCCTCATT 57.380 33.333 0.00 0.00 0.00 2.57
2631 2858 5.626142 TCCTCATTTTACAGTTTAGCACCA 58.374 37.500 0.00 0.00 0.00 4.17
2682 2909 2.739379 GCTAGGCTGTGACTGAAGAAAC 59.261 50.000 0.00 0.00 0.00 2.78
2696 2923 8.296713 TGACTGAAGAAACAAACCAAATATAGC 58.703 33.333 0.00 0.00 0.00 2.97
2885 3227 6.198650 TCTTGACATGCACATATTCCTTTG 57.801 37.500 0.00 0.00 0.00 2.77
2929 3271 4.685169 ACTGATTGCAACCTATGTTTCG 57.315 40.909 0.00 0.00 30.42 3.46
2942 3284 8.559536 CAACCTATGTTTCGCAGATATGTAAAT 58.440 33.333 0.00 0.00 35.04 1.40
3096 3556 2.094675 TCCTGCTGCCAGCTTTATTTC 58.905 47.619 18.96 0.00 42.97 2.17
3127 3587 3.435671 CACCCGGTTTGAGATAGTTTGAC 59.564 47.826 0.00 0.00 0.00 3.18
3154 3738 5.132985 TCTCCCTCTAGCACTCTAATGTAGT 59.867 44.000 0.00 0.00 0.00 2.73
3155 3739 6.329460 TCTCCCTCTAGCACTCTAATGTAGTA 59.671 42.308 0.00 0.00 0.00 1.82
3156 3740 6.297582 TCCCTCTAGCACTCTAATGTAGTAC 58.702 44.000 0.00 0.00 0.00 2.73
3189 3773 8.221801 TGTTAATATTTTGTTTAGCTTGCGTG 57.778 30.769 0.00 0.00 0.00 5.34
3195 3779 3.495670 TGTTTAGCTTGCGTGTGTTTT 57.504 38.095 0.00 0.00 0.00 2.43
3371 3955 7.126398 GCTGGATGTGATAGTAAAAATTCGTC 58.874 38.462 0.00 0.00 0.00 4.20
3391 3975 2.105821 TCACCTCTGACACCCGATTTTT 59.894 45.455 0.00 0.00 0.00 1.94
3397 3981 2.293122 CTGACACCCGATTTTTCTTGCA 59.707 45.455 0.00 0.00 0.00 4.08
3428 4012 0.539051 ATCTTCACGAAGGGCTGGAG 59.461 55.000 6.94 0.00 38.88 3.86
3580 4164 2.173143 TGGGAACTTTCGGGTTAGTGTT 59.827 45.455 0.00 0.00 0.00 3.32
3639 4223 7.293745 GTTGTTTGTATCTTGTCATGACTGAG 58.706 38.462 25.55 21.35 30.18 3.35
3646 4230 4.464008 TCTTGTCATGACTGAGCCTTTTT 58.536 39.130 25.55 0.00 30.18 1.94
3676 4260 1.886313 CAGCTATGTGGCGCCTGAG 60.886 63.158 29.70 19.08 37.29 3.35
3775 4359 8.110908 ACTGGTAGATCTCCTGTAGATTATACC 58.889 40.741 16.58 13.85 45.35 2.73
3796 4380 0.176910 GGTCAGCTGGAGAGGTAAGC 59.823 60.000 15.13 0.00 37.20 3.09
3848 4434 0.960364 TTCAGAAATGTGGAGGCGGC 60.960 55.000 0.00 0.00 0.00 6.53
3876 4462 9.573133 CCGATGAAGCTAAATTCTTGTATTTTT 57.427 29.630 0.00 0.00 0.00 1.94
3891 4477 8.912988 TCTTGTATTTTTCAGGTGAACTTGATT 58.087 29.630 0.00 0.00 31.87 2.57
3987 4573 2.203337 AAAGCACTGAAGCGGGCA 60.203 55.556 0.00 0.00 40.15 5.36
3993 4579 0.037326 CACTGAAGCGGGCACTTCTA 60.037 55.000 17.15 6.37 45.20 2.10
4002 4588 1.142097 GGCACTTCTAGTCGCCCTC 59.858 63.158 8.27 0.00 36.82 4.30
4008 4594 3.141488 CTAGTCGCCCTCCGCTGT 61.141 66.667 0.00 0.00 36.73 4.40
4088 4674 4.478371 GGACCTAAACCCCCGCGG 62.478 72.222 21.04 21.04 37.81 6.46
4146 4736 5.707931 TGCTATAATCTCTCATTCGCTCAG 58.292 41.667 0.00 0.00 0.00 3.35
4258 4848 4.271816 CGATGGAGGACGGGAGCG 62.272 72.222 0.00 0.00 0.00 5.03
4300 4890 3.181465 ACGGTACAGATGATGATGGGAAC 60.181 47.826 0.00 0.00 0.00 3.62
4317 4910 1.485032 AACGGCACAAGAACGACGAC 61.485 55.000 0.00 0.00 0.00 4.34
4339 4935 0.530650 CGAACCGGGACATGATCTGG 60.531 60.000 6.32 8.02 0.00 3.86
4354 4952 3.080765 TGGGTGTGCGGATCGGAT 61.081 61.111 4.16 0.00 0.00 4.18
4380 4979 4.083431 CCGCTTGCTAGATATGTACGTACT 60.083 45.833 25.12 13.70 0.00 2.73
4406 5009 4.013728 GGTACCATTAACCAAGCATGTCA 58.986 43.478 7.15 0.00 36.96 3.58
4853 5457 2.856032 CTCACTTGTTGAGCCGCG 59.144 61.111 0.00 0.00 45.51 6.46
4933 5539 1.139654 TGGCCATAGCTGACACTCATC 59.860 52.381 0.00 0.00 39.73 2.92
4934 5540 1.139654 GGCCATAGCTGACACTCATCA 59.860 52.381 0.00 0.00 39.73 3.07
4956 5562 6.878317 TCAGAGTCTTAATGATAACCCACTG 58.122 40.000 0.00 0.00 0.00 3.66
4962 5568 6.826741 GTCTTAATGATAACCCACTGGCTAAA 59.173 38.462 0.00 0.00 33.59 1.85
4974 5580 0.889994 TGGCTAAATGCAAGTGCTGG 59.110 50.000 4.69 0.00 45.15 4.85
4975 5581 1.176527 GGCTAAATGCAAGTGCTGGA 58.823 50.000 4.69 0.00 45.15 3.86
4976 5582 1.133790 GGCTAAATGCAAGTGCTGGAG 59.866 52.381 4.69 0.00 45.15 3.86
4978 5584 3.009723 GCTAAATGCAAGTGCTGGAGTA 58.990 45.455 4.69 0.00 42.66 2.59
4979 5585 3.064545 GCTAAATGCAAGTGCTGGAGTAG 59.935 47.826 4.69 1.37 42.66 2.57
4982 5588 3.981071 ATGCAAGTGCTGGAGTAGTTA 57.019 42.857 4.69 0.00 42.66 2.24
4983 5589 3.762407 TGCAAGTGCTGGAGTAGTTAA 57.238 42.857 4.69 0.00 42.66 2.01
4984 5590 4.286297 TGCAAGTGCTGGAGTAGTTAAT 57.714 40.909 4.69 0.00 42.66 1.40
4986 5592 3.623510 GCAAGTGCTGGAGTAGTTAATCC 59.376 47.826 0.00 0.00 40.67 3.01
4987 5593 4.624125 GCAAGTGCTGGAGTAGTTAATCCT 60.624 45.833 7.12 0.00 40.87 3.24
5029 5670 3.782656 ATGAGGCACTGATCATGCATA 57.217 42.857 22.88 13.36 45.27 3.14
5030 5671 3.782656 TGAGGCACTGATCATGCATAT 57.217 42.857 22.88 13.17 45.27 1.78
5031 5672 3.408634 TGAGGCACTGATCATGCATATG 58.591 45.455 22.88 0.00 45.27 1.78
5032 5673 2.160205 AGGCACTGATCATGCATATGC 58.840 47.619 21.09 21.09 45.27 3.14
5051 5692 2.882927 CATATGCATGCCTTGTTGCT 57.117 45.000 16.68 0.00 39.60 3.91
5052 5693 2.469826 CATATGCATGCCTTGTTGCTG 58.530 47.619 16.68 0.00 39.60 4.41
5053 5694 0.818938 TATGCATGCCTTGTTGCTGG 59.181 50.000 16.68 0.00 39.60 4.85
5090 5911 0.179156 GAGGTCACATGCCATTTGCG 60.179 55.000 0.00 0.00 45.60 4.85
5098 5941 3.248125 CACATGCCATTTGCGTTCTTTTT 59.752 39.130 0.00 0.00 45.60 1.94
5117 5964 5.892160 TTTTTCTCTGATGAAGATGCTGG 57.108 39.130 0.00 0.00 33.29 4.85
5157 6015 0.608035 ATCGTCGCCATTGGTTTGGT 60.608 50.000 4.26 0.00 39.11 3.67
5158 6016 0.820074 TCGTCGCCATTGGTTTGGTT 60.820 50.000 4.26 0.00 39.11 3.67
5159 6017 0.031449 CGTCGCCATTGGTTTGGTTT 59.969 50.000 4.26 0.00 39.11 3.27
5160 6018 1.496934 GTCGCCATTGGTTTGGTTTG 58.503 50.000 4.26 0.00 39.11 2.93
5161 6019 0.390860 TCGCCATTGGTTTGGTTTGG 59.609 50.000 4.26 0.00 39.11 3.28
5207 6065 2.705934 ATACCGCATCTGGCTGCTCG 62.706 60.000 0.00 0.00 40.06 5.03
5254 6117 2.032681 GGCTTCGCCTTGTCCTGT 59.967 61.111 0.00 0.00 46.69 4.00
5255 6118 2.035442 GGCTTCGCCTTGTCCTGTC 61.035 63.158 0.00 0.00 46.69 3.51
5256 6119 2.035442 GCTTCGCCTTGTCCTGTCC 61.035 63.158 0.00 0.00 0.00 4.02
5257 6120 1.674057 CTTCGCCTTGTCCTGTCCT 59.326 57.895 0.00 0.00 0.00 3.85
5258 6121 0.671781 CTTCGCCTTGTCCTGTCCTG 60.672 60.000 0.00 0.00 0.00 3.86
5259 6122 2.046892 CGCCTTGTCCTGTCCTGG 60.047 66.667 0.00 0.00 0.00 4.45
5260 6123 2.883828 CGCCTTGTCCTGTCCTGGT 61.884 63.158 0.00 0.00 0.00 4.00
5261 6124 1.003233 GCCTTGTCCTGTCCTGGTC 60.003 63.158 0.00 0.00 0.00 4.02
5262 6125 1.484444 GCCTTGTCCTGTCCTGGTCT 61.484 60.000 0.00 0.00 0.00 3.85
5263 6126 1.059913 CCTTGTCCTGTCCTGGTCTT 58.940 55.000 0.00 0.00 0.00 3.01
5264 6127 2.257207 CCTTGTCCTGTCCTGGTCTTA 58.743 52.381 0.00 0.00 0.00 2.10
5265 6128 2.637872 CCTTGTCCTGTCCTGGTCTTAA 59.362 50.000 0.00 0.00 0.00 1.85
5266 6129 3.557264 CCTTGTCCTGTCCTGGTCTTAAC 60.557 52.174 0.00 0.00 0.00 2.01
5267 6130 1.975680 TGTCCTGTCCTGGTCTTAACC 59.024 52.381 0.00 0.00 46.66 2.85
5276 6139 2.776659 GGTCTTAACCATGCCCGTC 58.223 57.895 0.00 0.00 45.68 4.79
5277 6140 1.087771 GGTCTTAACCATGCCCGTCG 61.088 60.000 0.00 0.00 45.68 5.12
5278 6141 0.390735 GTCTTAACCATGCCCGTCGT 60.391 55.000 0.00 0.00 0.00 4.34
5279 6142 0.108520 TCTTAACCATGCCCGTCGTC 60.109 55.000 0.00 0.00 0.00 4.20
5280 6143 0.108329 CTTAACCATGCCCGTCGTCT 60.108 55.000 0.00 0.00 0.00 4.18
5281 6144 0.322322 TTAACCATGCCCGTCGTCTT 59.678 50.000 0.00 0.00 0.00 3.01
5282 6145 0.322322 TAACCATGCCCGTCGTCTTT 59.678 50.000 0.00 0.00 0.00 2.52
5283 6146 0.322322 AACCATGCCCGTCGTCTTTA 59.678 50.000 0.00 0.00 0.00 1.85
5284 6147 0.390735 ACCATGCCCGTCGTCTTTAC 60.391 55.000 0.00 0.00 0.00 2.01
5285 6148 1.087771 CCATGCCCGTCGTCTTTACC 61.088 60.000 0.00 0.00 0.00 2.85
5286 6149 0.108329 CATGCCCGTCGTCTTTACCT 60.108 55.000 0.00 0.00 0.00 3.08
5287 6150 0.611714 ATGCCCGTCGTCTTTACCTT 59.388 50.000 0.00 0.00 0.00 3.50
5288 6151 0.393820 TGCCCGTCGTCTTTACCTTT 59.606 50.000 0.00 0.00 0.00 3.11
5289 6152 0.794473 GCCCGTCGTCTTTACCTTTG 59.206 55.000 0.00 0.00 0.00 2.77
5290 6153 0.794473 CCCGTCGTCTTTACCTTTGC 59.206 55.000 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 81 6.040955 CACCATTAGAGCAGTCTAGGTCATTA 59.959 42.308 0.00 0.00 33.49 1.90
94 99 3.605634 ACATGTTTAGCGCTCACCATTA 58.394 40.909 16.34 0.00 0.00 1.90
99 104 5.216566 TCAATTACATGTTTAGCGCTCAC 57.783 39.130 16.34 13.48 0.00 3.51
100 105 7.728847 ATATCAATTACATGTTTAGCGCTCA 57.271 32.000 16.34 6.43 0.00 4.26
120 135 9.944663 TCTGACGTTTATATTTGGCAAAATATC 57.055 29.630 20.16 8.56 42.71 1.63
153 169 8.507249 GGGTATCATCTGCTTGTTAATTATGTC 58.493 37.037 0.00 0.00 0.00 3.06
166 182 6.841755 GGATATTAGGTAGGGTATCATCTGCT 59.158 42.308 0.00 0.00 0.00 4.24
170 186 6.606395 ACGTGGATATTAGGTAGGGTATCATC 59.394 42.308 0.00 0.00 0.00 2.92
212 231 9.224267 GAGTGGAATGCACATTGATATTAGTAT 57.776 33.333 7.79 0.00 0.00 2.12
213 232 7.384932 CGAGTGGAATGCACATTGATATTAGTA 59.615 37.037 7.79 0.00 0.00 1.82
214 233 6.203530 CGAGTGGAATGCACATTGATATTAGT 59.796 38.462 7.79 0.00 0.00 2.24
283 302 3.560636 AGGAATATTGCTAGGCGTGTT 57.439 42.857 7.83 0.00 0.00 3.32
338 357 4.380444 CCAAAATCGTTCCCATCGTTGATT 60.380 41.667 0.00 0.00 0.00 2.57
350 369 4.798387 GTGCCATATGTTCCAAAATCGTTC 59.202 41.667 1.24 0.00 0.00 3.95
354 373 3.450457 TGGGTGCCATATGTTCCAAAATC 59.550 43.478 1.24 0.00 0.00 2.17
365 384 0.411452 TTGGTGGTTGGGTGCCATAT 59.589 50.000 0.00 0.00 38.40 1.78
403 422 2.108075 TGCTGGAGGGATCTTTTGTTGA 59.892 45.455 0.00 0.00 0.00 3.18
404 423 2.517959 TGCTGGAGGGATCTTTTGTTG 58.482 47.619 0.00 0.00 0.00 3.33
418 437 2.779430 ACCACTTGGATGATATGCTGGA 59.221 45.455 1.14 0.00 38.94 3.86
422 441 6.569226 GCTTTATCACCACTTGGATGATATGC 60.569 42.308 15.44 16.65 35.73 3.14
428 447 3.758023 TGTGCTTTATCACCACTTGGATG 59.242 43.478 1.14 0.00 38.94 3.51
485 507 5.421212 TTGCAACATTTCATTTTTGCCTC 57.579 34.783 0.00 0.00 43.04 4.70
671 702 9.793259 GATATGGTTTTGGGATCAGTCTTTATA 57.207 33.333 0.00 0.00 0.00 0.98
677 708 3.815401 CGGATATGGTTTTGGGATCAGTC 59.185 47.826 0.00 0.00 0.00 3.51
678 709 3.435026 CCGGATATGGTTTTGGGATCAGT 60.435 47.826 0.00 0.00 0.00 3.41
679 710 3.149196 CCGGATATGGTTTTGGGATCAG 58.851 50.000 0.00 0.00 0.00 2.90
680 711 2.751479 GCCGGATATGGTTTTGGGATCA 60.751 50.000 5.05 0.00 0.00 2.92
778 838 3.810896 GCCCGTTGCCATCGTTCC 61.811 66.667 0.00 0.00 0.00 3.62
785 845 2.046009 TACTTGTCAGCCCGTTGCCA 62.046 55.000 0.00 0.00 42.71 4.92
800 860 3.625745 CAGGGTTCTGCCGTTACTT 57.374 52.632 0.00 0.00 38.44 2.24
1015 1082 3.714001 CAGCAGCAGCCTCCTCCA 61.714 66.667 0.00 0.00 43.56 3.86
1101 1168 0.033504 ACAGCCACGTGTTGAGGTAG 59.966 55.000 20.16 2.52 0.00 3.18
1617 1699 2.282462 GTGAACCAGTGGCCCCAG 60.282 66.667 9.78 0.00 0.00 4.45
1695 1777 2.835764 TCTGTAAACAATCCCGTAGCCT 59.164 45.455 0.00 0.00 0.00 4.58
1888 1971 4.729227 ACGGACCAAAACACAGAAATTT 57.271 36.364 0.00 0.00 0.00 1.82
1918 2003 0.749454 ACTCTGGCCGATGGATTTGC 60.749 55.000 0.00 0.00 0.00 3.68
1973 2106 3.508793 ACAAGTTCATCAGCAAAGGATGG 59.491 43.478 0.00 0.00 41.89 3.51
1975 2108 4.219288 GGAACAAGTTCATCAGCAAAGGAT 59.781 41.667 14.25 0.00 41.20 3.24
1976 2109 3.569701 GGAACAAGTTCATCAGCAAAGGA 59.430 43.478 14.25 0.00 41.20 3.36
1977 2110 3.318839 TGGAACAAGTTCATCAGCAAAGG 59.681 43.478 14.25 0.00 41.20 3.11
1978 2111 4.037208 ACTGGAACAAGTTCATCAGCAAAG 59.963 41.667 14.25 2.40 41.20 2.77
1979 2112 3.953612 ACTGGAACAAGTTCATCAGCAAA 59.046 39.130 14.25 0.00 41.20 3.68
1981 2114 3.213206 ACTGGAACAAGTTCATCAGCA 57.787 42.857 14.25 2.72 41.20 4.41
1982 2115 4.574599 AAACTGGAACAAGTTCATCAGC 57.425 40.909 14.25 0.00 41.20 4.26
2061 2227 9.541143 GGGTGAATGAAGAAAGTAATTTGAAAA 57.459 29.630 0.00 0.00 0.00 2.29
2065 2231 8.115490 AGAGGGTGAATGAAGAAAGTAATTTG 57.885 34.615 0.00 0.00 0.00 2.32
2074 2240 5.065914 CACAGAAAGAGGGTGAATGAAGAA 58.934 41.667 0.00 0.00 34.52 2.52
2077 2249 4.136796 CACACAGAAAGAGGGTGAATGAA 58.863 43.478 0.00 0.00 36.42 2.57
2086 2258 1.004044 AGATGGGCACACAGAAAGAGG 59.996 52.381 0.00 0.00 0.00 3.69
2175 2347 4.261801 AGTATGGGTTGAGAAATGGAACG 58.738 43.478 0.00 0.00 0.00 3.95
2189 2361 6.565974 ACATGGATATCAGAGTAGTATGGGT 58.434 40.000 4.83 0.00 0.00 4.51
2238 2413 1.830279 CTGATGCAAAAGCAGGGAGA 58.170 50.000 0.00 0.00 38.71 3.71
2348 2543 1.008403 TCTACCTGTAGGCACCCTCT 58.992 55.000 4.58 0.00 39.32 3.69
2366 2561 4.097437 TGAGGAAGAGATTGCAATGCATTC 59.903 41.667 18.59 19.02 38.76 2.67
2580 2777 2.843701 AGTCCAAGAAACAGCACTCTG 58.156 47.619 0.00 0.00 45.71 3.35
2581 2778 4.899352 ATAGTCCAAGAAACAGCACTCT 57.101 40.909 0.00 0.00 0.00 3.24
2582 2779 7.044798 AGATTATAGTCCAAGAAACAGCACTC 58.955 38.462 0.00 0.00 0.00 3.51
2589 2813 9.620259 AATGAGGAAGATTATAGTCCAAGAAAC 57.380 33.333 0.00 0.00 33.57 2.78
2615 2839 9.899661 ATATACAGATTGGTGCTAAACTGTAAA 57.100 29.630 17.21 4.05 44.01 2.01
2619 2846 8.887036 TGTATATACAGATTGGTGCTAAACTG 57.113 34.615 11.62 4.53 36.76 3.16
2660 2887 0.898320 TCTTCAGTCACAGCCTAGCC 59.102 55.000 0.00 0.00 0.00 3.93
2696 2923 9.565213 CTTCCAAGAAACTAAAATGCTAATGAG 57.435 33.333 0.00 0.00 0.00 2.90
2885 3227 7.810759 CAGTTGTCTCTTTCTCTAACCTCTTAC 59.189 40.741 0.00 0.00 0.00 2.34
2942 3284 6.481976 CAGAATGAAACGCCAGTACCATAATA 59.518 38.462 0.00 0.00 39.69 0.98
2954 3296 1.806542 TCAGAAGCAGAATGAAACGCC 59.193 47.619 0.00 0.00 39.69 5.68
3096 3556 0.030638 CAAACCGGGTGCTCTGTTTG 59.969 55.000 6.32 0.39 0.00 2.93
3127 3587 1.757682 AGAGTGCTAGAGGGAGAACG 58.242 55.000 0.00 0.00 29.26 3.95
3299 3883 5.736951 TTAAGCAAACCACTGGCAATAAT 57.263 34.783 0.00 0.00 0.00 1.28
3300 3884 5.163405 TGTTTAAGCAAACCACTGGCAATAA 60.163 36.000 0.00 0.00 42.88 1.40
3301 3885 4.342378 TGTTTAAGCAAACCACTGGCAATA 59.658 37.500 0.00 0.00 42.88 1.90
3371 3955 2.185004 AAAATCGGGTGTCAGAGGTG 57.815 50.000 0.00 0.00 0.00 4.00
3391 3975 3.573229 AGGCCAGCCTGTGCAAGA 61.573 61.111 11.21 0.00 46.22 3.02
3440 4024 0.522626 TAGATTTGACGTCGCGGTGA 59.477 50.000 11.62 0.00 0.00 4.02
3580 4164 6.590234 TCACTGAGCACTAAAAGACTATCA 57.410 37.500 0.00 0.00 0.00 2.15
3646 4230 4.142403 GCCACATAGCTGCAACATTAAGAA 60.142 41.667 1.02 0.00 0.00 2.52
3647 4231 3.378112 GCCACATAGCTGCAACATTAAGA 59.622 43.478 1.02 0.00 0.00 2.10
3651 4235 0.452987 CGCCACATAGCTGCAACATT 59.547 50.000 1.02 0.00 0.00 2.71
3676 4260 2.125269 ATTCCGGTGCTGGCGTAC 60.125 61.111 0.00 0.00 0.00 3.67
3775 4359 1.480137 CTTACCTCTCCAGCTGACCTG 59.520 57.143 17.39 0.00 41.41 4.00
3804 4388 6.327279 AGAAACTACTAAAAATGGGCACAC 57.673 37.500 0.00 0.00 0.00 3.82
3806 4390 7.923878 TGAAAAGAAACTACTAAAAATGGGCAC 59.076 33.333 0.00 0.00 0.00 5.01
3848 4434 3.947834 ACAAGAATTTAGCTTCATCGGGG 59.052 43.478 0.00 0.00 0.00 5.73
3876 4462 3.743521 CCACTCAATCAAGTTCACCTGA 58.256 45.455 0.00 0.00 0.00 3.86
3891 4477 1.421268 ACCATGTTCTTCAGCCACTCA 59.579 47.619 0.00 0.00 0.00 3.41
3987 4573 2.416432 GCGGAGGGCGACTAGAAGT 61.416 63.158 0.00 0.00 0.00 3.01
4088 4674 2.098770 AGTAGGAAGGAACATACGTCGC 59.901 50.000 0.00 0.00 33.21 5.19
4089 4675 5.469421 AGATAGTAGGAAGGAACATACGTCG 59.531 44.000 0.00 0.00 33.21 5.12
4090 4676 6.485984 TGAGATAGTAGGAAGGAACATACGTC 59.514 42.308 0.00 0.00 33.21 4.34
4258 4848 2.472049 GTTCTCGCGCTTGCTCAC 59.528 61.111 5.56 0.00 36.08 3.51
4300 4890 2.844146 GTCGTCGTTCTTGTGCCG 59.156 61.111 0.00 0.00 0.00 5.69
4317 4910 3.733344 ATCATGTCCCGGTTCGGCG 62.733 63.158 0.00 0.00 46.86 6.46
4339 4935 2.823829 GCAATCCGATCCGCACACC 61.824 63.158 0.00 0.00 0.00 4.16
4359 4957 6.519078 CGTAAGTACGTACATATCTAGCAAGC 59.481 42.308 26.55 4.32 44.13 4.01
4380 4979 4.283363 TGCTTGGTTAATGGTACCGTAA 57.717 40.909 7.15 5.40 38.55 3.18
4805 5408 4.400884 AGAACTGTCATAGAACGATGCTCT 59.599 41.667 0.00 0.00 0.00 4.09
4864 5468 4.586235 ACACCACACCAGCAGGCC 62.586 66.667 0.00 0.00 39.06 5.19
4865 5469 2.519302 AACACCACACCAGCAGGC 60.519 61.111 0.00 0.00 39.06 4.85
4866 5470 0.466189 AAGAACACCACACCAGCAGG 60.466 55.000 0.00 0.00 42.21 4.85
4875 5479 3.309954 GTCACAAGTCAGAAGAACACCAC 59.690 47.826 0.00 0.00 0.00 4.16
4916 5522 3.979948 CTCTGATGAGTGTCAGCTATGG 58.020 50.000 0.00 0.00 44.15 2.74
4933 5539 6.051717 CCAGTGGGTTATCATTAAGACTCTG 58.948 44.000 0.00 0.00 0.00 3.35
4934 5540 5.396884 GCCAGTGGGTTATCATTAAGACTCT 60.397 44.000 12.15 0.00 36.17 3.24
4935 5541 4.816925 GCCAGTGGGTTATCATTAAGACTC 59.183 45.833 12.15 0.00 36.17 3.36
4956 5562 1.133790 CTCCAGCACTTGCATTTAGCC 59.866 52.381 3.62 0.00 44.83 3.93
4962 5568 2.867109 AACTACTCCAGCACTTGCAT 57.133 45.000 3.62 0.00 45.16 3.96
4971 5577 7.016072 AGGAATCATGAGGATTAACTACTCCAG 59.984 40.741 0.09 0.00 46.17 3.86
4974 5580 7.158021 CCAGGAATCATGAGGATTAACTACTC 58.842 42.308 0.09 0.00 46.17 2.59
4975 5581 6.465035 GCCAGGAATCATGAGGATTAACTACT 60.465 42.308 0.09 0.00 46.17 2.57
4976 5582 5.703130 GCCAGGAATCATGAGGATTAACTAC 59.297 44.000 0.09 0.00 46.17 2.73
4978 5584 4.166725 TGCCAGGAATCATGAGGATTAACT 59.833 41.667 0.09 0.00 46.17 2.24
4979 5585 4.276926 GTGCCAGGAATCATGAGGATTAAC 59.723 45.833 0.09 0.00 46.17 2.01
4983 5589 2.133520 AGTGCCAGGAATCATGAGGAT 58.866 47.619 0.09 0.00 38.05 3.24
4984 5590 1.211212 CAGTGCCAGGAATCATGAGGA 59.789 52.381 0.09 0.00 0.00 3.71
4986 5592 1.211212 TCCAGTGCCAGGAATCATGAG 59.789 52.381 0.09 0.00 30.71 2.90
4987 5593 1.288188 TCCAGTGCCAGGAATCATGA 58.712 50.000 0.00 0.00 30.71 3.07
5032 5673 2.469826 CAGCAACAAGGCATGCATATG 58.530 47.619 21.36 16.55 44.95 1.78
5033 5674 1.411246 CCAGCAACAAGGCATGCATAT 59.589 47.619 21.36 0.94 44.95 1.78
5035 5676 1.594833 CCAGCAACAAGGCATGCAT 59.405 52.632 21.36 10.32 44.95 3.96
5054 5695 4.654904 CACGTGCGTGCAGTGCAG 62.655 66.667 20.42 13.74 44.21 4.41
5056 5697 4.360027 CTCACGTGCGTGCAGTGC 62.360 66.667 18.54 8.58 45.04 4.40
5057 5698 3.705638 CCTCACGTGCGTGCAGTG 61.706 66.667 18.54 14.29 45.04 3.66
5058 5699 4.221422 ACCTCACGTGCGTGCAGT 62.221 61.111 18.54 14.68 45.04 4.40
5098 5941 2.237893 TGCCAGCATCTTCATCAGAGAA 59.762 45.455 0.00 0.00 33.87 2.87
5129 5976 3.303329 CCAATGGCGACGATGATAAACAG 60.303 47.826 0.00 0.00 0.00 3.16
5141 5988 1.496934 CAAACCAAACCAATGGCGAC 58.503 50.000 0.00 0.00 44.75 5.19
5157 6015 2.547642 CCAAAAAGAGCATTCGGCCAAA 60.548 45.455 2.24 0.00 46.50 3.28
5158 6016 1.000731 CCAAAAAGAGCATTCGGCCAA 59.999 47.619 2.24 0.00 46.50 4.52
5159 6017 0.602562 CCAAAAAGAGCATTCGGCCA 59.397 50.000 2.24 0.00 46.50 5.36
5160 6018 0.737367 GCCAAAAAGAGCATTCGGCC 60.737 55.000 0.00 0.00 46.50 6.13
5161 6019 0.737367 GGCCAAAAAGAGCATTCGGC 60.737 55.000 0.00 0.00 45.30 5.54
5207 6065 0.320683 GGCCCAAATGCTGTTTCACC 60.321 55.000 0.00 0.00 0.00 4.02
5258 6121 1.087771 CGACGGGCATGGTTAAGACC 61.088 60.000 0.00 0.00 46.71 3.85
5259 6122 0.390735 ACGACGGGCATGGTTAAGAC 60.391 55.000 0.00 0.00 0.00 3.01
5260 6123 0.108520 GACGACGGGCATGGTTAAGA 60.109 55.000 0.00 0.00 0.00 2.10
5261 6124 0.108329 AGACGACGGGCATGGTTAAG 60.108 55.000 0.00 0.00 0.00 1.85
5262 6125 0.322322 AAGACGACGGGCATGGTTAA 59.678 50.000 0.00 0.00 0.00 2.01
5263 6126 0.322322 AAAGACGACGGGCATGGTTA 59.678 50.000 0.00 0.00 0.00 2.85
5264 6127 0.322322 TAAAGACGACGGGCATGGTT 59.678 50.000 0.00 0.00 0.00 3.67
5265 6128 0.390735 GTAAAGACGACGGGCATGGT 60.391 55.000 0.00 0.00 0.00 3.55
5266 6129 1.087771 GGTAAAGACGACGGGCATGG 61.088 60.000 0.00 0.00 0.00 3.66
5267 6130 0.108329 AGGTAAAGACGACGGGCATG 60.108 55.000 0.00 0.00 0.00 4.06
5268 6131 0.611714 AAGGTAAAGACGACGGGCAT 59.388 50.000 0.00 0.00 0.00 4.40
5269 6132 0.393820 AAAGGTAAAGACGACGGGCA 59.606 50.000 0.00 0.00 0.00 5.36
5270 6133 0.794473 CAAAGGTAAAGACGACGGGC 59.206 55.000 0.00 0.00 0.00 6.13
5271 6134 0.794473 GCAAAGGTAAAGACGACGGG 59.206 55.000 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.