Multiple sequence alignment - TraesCS6B01G209100

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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 TraesCS6B01G209100 chr6B 100.000 5657 0 0 1 5657 274989727 274984071 0.000000e+00 10447
1 TraesCS6B01G209100 chr6B 85.294 136 16 2 651 786 215721492 215721361 2.750000e-28 137
2 TraesCS6B01G209100 chr6D 96.519 2557 69 11 1 2548 150782649 150785194 0.000000e+00 4211
3 TraesCS6B01G209100 chr6D 94.816 1871 39 15 3446 5290 150785220 150787058 0.000000e+00 2865
4 TraesCS6B01G209100 chr6D 91.375 371 15 8 5292 5654 150787134 150787495 5.090000e-135 492
5 TraesCS6B01G209100 chr6D 93.103 87 5 1 2743 2829 450890409 450890494 5.950000e-25 126
6 TraesCS6B01G209100 chr6A 94.537 2453 86 24 1 2435 193839693 193837271 0.000000e+00 3744
7 TraesCS6B01G209100 chr6A 96.159 1380 20 8 2831 4192 193836685 193835321 0.000000e+00 2224
8 TraesCS6B01G209100 chr6A 95.212 1274 30 15 4407 5654 193835233 193833965 0.000000e+00 1986
9 TraesCS6B01G209100 chr6A 95.556 270 9 1 2482 2748 193836953 193836684 4.050000e-116 429
10 TraesCS6B01G209100 chr6A 87.255 102 11 2 2740 2841 338118927 338119026 1.290000e-21 115
11 TraesCS6B01G209100 chr3A 87.500 136 13 2 651 786 66031327 66031458 2.730000e-33 154
12 TraesCS6B01G209100 chr7D 94.253 87 4 1 2744 2830 148114555 148114470 1.280000e-26 132
13 TraesCS6B01G209100 chr7B 90.426 94 8 1 2738 2831 551488107 551488199 7.700000e-24 122
14 TraesCS6B01G209100 chr7A 87.387 111 8 5 2740 2847 224600263 224600370 7.700000e-24 122
15 TraesCS6B01G209100 chr7A 88.235 102 11 1 2740 2841 664215807 664215707 2.770000e-23 121
16 TraesCS6B01G209100 chr5D 90.426 94 8 1 2737 2830 354874452 354874360 7.700000e-24 122
17 TraesCS6B01G209100 chr4A 88.235 102 10 2 2740 2841 507914721 507914820 2.770000e-23 121
18 TraesCS6B01G209100 chr4B 90.217 92 7 2 2740 2831 531091950 531092039 9.960000e-23 119


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 TraesCS6B01G209100 chr6B 274984071 274989727 5656 True 10447.000000 10447 100.000000 1 5657 1 chr6B.!!$R2 5656
1 TraesCS6B01G209100 chr6D 150782649 150787495 4846 False 2522.666667 4211 94.236667 1 5654 3 chr6D.!!$F2 5653
2 TraesCS6B01G209100 chr6A 193833965 193839693 5728 True 2095.750000 3744 95.366000 1 5654 4 chr6A.!!$R1 5653

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
969 987 0.341258 TCTGAAGATGCTCCTCCCCT 59.659 55.0 0.00 0.0 0.00 4.79 F
1965 1986 0.991920 TCTTCCCTGGGACAATGGTC 59.008 55.0 16.85 0.0 43.55 4.02 F
3287 3583 0.179018 GCCAGTCTGTCCAAACACCT 60.179 55.0 0.00 0.0 0.00 4.00 F
3296 3592 0.687920 TCCAAACACCTCGCCACATA 59.312 50.0 0.00 0.0 0.00 2.29 F
4305 4618 0.250553 TTTTCCGGTAGGTGCCACTG 60.251 55.0 0.00 0.0 39.05 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2815 3110 0.034283 ACTGACTACTCCCTCCGTCC 60.034 60.0 0.00 0.00 0.00 4.79 R
3471 3767 0.535780 TGAAGTTGAGGTGCTGGCAG 60.536 55.0 10.94 10.94 0.00 4.85 R
4285 4598 0.250597 AGTGGCACCTACCGGAAAAC 60.251 55.0 15.27 0.00 0.00 2.43 R
4361 4676 0.737715 CCAGCTGCGGTCTTGTACTC 60.738 60.0 8.66 0.00 0.00 2.59 R
5300 5705 0.400213 AAAGACGACAAGGGCATCCA 59.600 50.0 0.00 0.00 34.83 3.41 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
112 113 0.822944 GGCTACCCTCGAGGACTACC 60.823 65.000 33.39 22.81 39.89 3.18
359 360 6.258727 CGTAGCAATCCATTTGTCTTATGTCT 59.741 38.462 0.00 0.00 37.65 3.41
552 565 1.683441 CTCTTAGGGCCCGTTTGGT 59.317 57.895 18.44 0.00 36.04 3.67
693 706 2.045524 CCACTATCCCAGCACAGATCT 58.954 52.381 0.00 0.00 0.00 2.75
774 787 8.967918 GGGGTATCTTTCTTTTGCTTTACTATT 58.032 33.333 0.00 0.00 0.00 1.73
782 795 7.391148 TCTTTTGCTTTACTATTAAGCCAGG 57.609 36.000 0.00 0.00 45.73 4.45
969 987 0.341258 TCTGAAGATGCTCCTCCCCT 59.659 55.000 0.00 0.00 0.00 4.79
996 1014 5.017975 TCCCCACCCCTAAGGAAAATAAAAT 59.982 40.000 0.00 0.00 39.89 1.82
1040 1058 3.065786 AGCGAGCAAATATGTTCCACATG 59.934 43.478 0.00 0.00 39.53 3.21
1145 1163 9.503427 CAGAAGTTTCTCGTTTGTTAAATTTCT 57.497 29.630 0.00 0.00 37.98 2.52
1170 1188 4.192317 AGTGTTGGTTTCTCTGTCACTTC 58.808 43.478 0.00 0.00 31.95 3.01
1353 1371 5.705400 TCCTTTTTCTCCTTCCATTGTCTT 58.295 37.500 0.00 0.00 0.00 3.01
1463 1481 6.070824 TGGAATGCTAGACAGAAACAGATACA 60.071 38.462 0.00 0.00 0.00 2.29
1464 1482 6.478344 GGAATGCTAGACAGAAACAGATACAG 59.522 42.308 0.00 0.00 0.00 2.74
1465 1483 6.782082 ATGCTAGACAGAAACAGATACAGA 57.218 37.500 0.00 0.00 0.00 3.41
1466 1484 5.955488 TGCTAGACAGAAACAGATACAGAC 58.045 41.667 0.00 0.00 0.00 3.51
1467 1485 5.712446 TGCTAGACAGAAACAGATACAGACT 59.288 40.000 0.00 0.00 0.00 3.24
1480 1498 6.041637 ACAGATACAGACTTACAGACACCAAA 59.958 38.462 0.00 0.00 0.00 3.28
1482 1500 7.604164 CAGATACAGACTTACAGACACCAAAAT 59.396 37.037 0.00 0.00 0.00 1.82
1545 1566 6.024563 TGGAATGGATTCTATGGGCTTTTA 57.975 37.500 0.00 0.00 37.00 1.52
1582 1603 7.016361 AGTAAAAGACAGCAAAGTTAGTGTG 57.984 36.000 0.00 0.00 0.00 3.82
1791 1812 1.867233 CCTGTACATGCAGTATTCCGC 59.133 52.381 0.00 0.00 34.67 5.54
1839 1860 4.482386 CATCAAGTTCCACATTTGCTCAG 58.518 43.478 0.00 0.00 0.00 3.35
1910 1931 8.405418 ACATTCCTTATCGTAGATACAGCTTA 57.595 34.615 0.00 0.00 45.12 3.09
1918 1939 5.243954 ATCGTAGATACAGCTTATGGCTTCA 59.756 40.000 0.00 0.00 46.95 3.02
1948 1969 4.020128 GGTAGAAAAGAGGGTGATGTGTCT 60.020 45.833 0.00 0.00 0.00 3.41
1965 1986 0.991920 TCTTCCCTGGGACAATGGTC 59.008 55.000 16.85 0.00 43.55 4.02
2216 2237 3.765026 ACAAAAACTGCTGTTGGTTACG 58.235 40.909 9.95 0.43 36.39 3.18
2333 2354 1.550072 TGCTCCTTGCCCAATAAAAGC 59.450 47.619 0.00 0.00 42.00 3.51
2385 2406 9.739276 TGAAGATGTATAGTCCTTTTCATGTTT 57.261 29.630 0.00 0.00 0.00 2.83
2543 2835 9.665719 AAGTTTTATTTGAACTGTCAATGGTTT 57.334 25.926 0.00 0.00 43.29 3.27
2572 2867 9.810545 CTCCCTTGTTTGTGTTATTTAAAGAAA 57.189 29.630 0.00 0.00 0.00 2.52
2606 2901 4.323553 AGTGTGGTCTGAAACTAGTGTC 57.676 45.455 6.07 6.07 0.00 3.67
2675 2970 1.234821 GTGCCGATGTTGTCCTGAAA 58.765 50.000 0.00 0.00 0.00 2.69
2689 2984 8.328758 TGTTGTCCTGAAATTCCATATTACTCT 58.671 33.333 0.00 0.00 0.00 3.24
2704 2999 7.389053 CCATATTACTCTACTCTTGCCATTTCC 59.611 40.741 0.00 0.00 0.00 3.13
2753 3048 8.904099 AAGTTGAAAATATTATACTCCCTCCG 57.096 34.615 0.00 0.00 0.00 4.63
2754 3049 8.030913 AGTTGAAAATATTATACTCCCTCCGT 57.969 34.615 0.00 0.00 0.00 4.69
2755 3050 8.148999 AGTTGAAAATATTATACTCCCTCCGTC 58.851 37.037 0.00 0.00 0.00 4.79
2756 3051 7.001099 TGAAAATATTATACTCCCTCCGTCC 57.999 40.000 0.00 0.00 0.00 4.79
2757 3052 6.013984 TGAAAATATTATACTCCCTCCGTCCC 60.014 42.308 0.00 0.00 0.00 4.46
2758 3053 4.687262 ATATTATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
2759 3054 3.562108 ATTATACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
2760 3055 4.687262 ATTATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
2761 3056 4.474303 TTATACTCCCTCCGTCCCATAA 57.526 45.455 0.00 0.00 0.00 1.90
2762 3057 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2763 3058 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2764 3059 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2765 3060 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2766 3061 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2767 3062 3.386063 TCCCTCCGTCCCATAATGTAAA 58.614 45.455 0.00 0.00 0.00 2.01
2768 3063 3.781407 TCCCTCCGTCCCATAATGTAAAA 59.219 43.478 0.00 0.00 0.00 1.52
2769 3064 4.414182 TCCCTCCGTCCCATAATGTAAAAT 59.586 41.667 0.00 0.00 0.00 1.82
2770 3065 4.518970 CCCTCCGTCCCATAATGTAAAATG 59.481 45.833 0.00 0.00 0.00 2.32
2771 3066 5.130350 CCTCCGTCCCATAATGTAAAATGT 58.870 41.667 0.00 0.00 0.00 2.71
2772 3067 5.592688 CCTCCGTCCCATAATGTAAAATGTT 59.407 40.000 0.00 0.00 0.00 2.71
2773 3068 6.096282 CCTCCGTCCCATAATGTAAAATGTTT 59.904 38.462 0.00 0.00 0.00 2.83
2774 3069 7.363443 CCTCCGTCCCATAATGTAAAATGTTTT 60.363 37.037 0.00 0.00 0.00 2.43
2775 3070 7.897864 TCCGTCCCATAATGTAAAATGTTTTT 58.102 30.769 0.00 0.00 0.00 1.94
2805 3100 7.211966 ACTAGTGTAGTGTCAAAATACGTCT 57.788 36.000 0.00 0.00 37.69 4.18
2806 3101 7.655490 ACTAGTGTAGTGTCAAAATACGTCTT 58.345 34.615 0.00 0.00 37.69 3.01
2807 3102 8.786898 ACTAGTGTAGTGTCAAAATACGTCTTA 58.213 33.333 0.00 0.00 37.69 2.10
2808 3103 7.864307 AGTGTAGTGTCAAAATACGTCTTAC 57.136 36.000 0.00 0.00 0.00 2.34
2809 3104 7.428020 AGTGTAGTGTCAAAATACGTCTTACA 58.572 34.615 0.00 0.00 0.00 2.41
2810 3105 8.086522 AGTGTAGTGTCAAAATACGTCTTACAT 58.913 33.333 0.00 0.00 0.00 2.29
2811 3106 8.706035 GTGTAGTGTCAAAATACGTCTTACATT 58.294 33.333 0.00 0.00 0.00 2.71
2812 3107 9.911138 TGTAGTGTCAAAATACGTCTTACATTA 57.089 29.630 0.00 0.00 0.00 1.90
2815 3110 8.804743 AGTGTCAAAATACGTCTTACATTATCG 58.195 33.333 0.00 0.00 0.00 2.92
2816 3111 8.054236 GTGTCAAAATACGTCTTACATTATCGG 58.946 37.037 0.00 0.00 0.00 4.18
2817 3112 7.975058 TGTCAAAATACGTCTTACATTATCGGA 59.025 33.333 0.00 0.00 0.00 4.55
2818 3113 8.264632 GTCAAAATACGTCTTACATTATCGGAC 58.735 37.037 0.00 0.00 0.00 4.79
2821 3116 3.614159 CGTCTTACATTATCGGACGGA 57.386 47.619 0.00 0.00 43.69 4.69
2822 3117 3.552541 CGTCTTACATTATCGGACGGAG 58.447 50.000 0.00 0.00 43.69 4.63
2823 3118 3.608707 CGTCTTACATTATCGGACGGAGG 60.609 52.174 0.00 0.00 43.69 4.30
2824 3119 2.889045 TCTTACATTATCGGACGGAGGG 59.111 50.000 0.00 0.00 0.00 4.30
2825 3120 2.662535 TACATTATCGGACGGAGGGA 57.337 50.000 0.00 0.00 0.00 4.20
2826 3121 1.329256 ACATTATCGGACGGAGGGAG 58.671 55.000 0.00 0.00 0.00 4.30
2827 3122 1.329256 CATTATCGGACGGAGGGAGT 58.671 55.000 0.00 0.00 0.00 3.85
2828 3123 2.158564 ACATTATCGGACGGAGGGAGTA 60.159 50.000 0.00 0.00 0.00 2.59
2829 3124 2.267174 TTATCGGACGGAGGGAGTAG 57.733 55.000 0.00 0.00 0.00 2.57
2855 3150 6.095580 TCAGTATGCAACAAAAACCAGTAACA 59.904 34.615 0.00 0.00 34.76 2.41
3116 3411 1.833630 CACAAGGATAGCTCACCCTCA 59.166 52.381 0.00 0.00 0.00 3.86
3191 3486 2.439409 CTGCATCACCATTTCACCTCA 58.561 47.619 0.00 0.00 0.00 3.86
3192 3487 2.161855 TGCATCACCATTTCACCTCAC 58.838 47.619 0.00 0.00 0.00 3.51
3193 3488 2.161855 GCATCACCATTTCACCTCACA 58.838 47.619 0.00 0.00 0.00 3.58
3194 3489 2.557924 GCATCACCATTTCACCTCACAA 59.442 45.455 0.00 0.00 0.00 3.33
3195 3490 3.612479 GCATCACCATTTCACCTCACAAC 60.612 47.826 0.00 0.00 0.00 3.32
3196 3491 3.289407 TCACCATTTCACCTCACAACA 57.711 42.857 0.00 0.00 0.00 3.33
3197 3492 2.948979 TCACCATTTCACCTCACAACAC 59.051 45.455 0.00 0.00 0.00 3.32
3198 3493 2.951642 CACCATTTCACCTCACAACACT 59.048 45.455 0.00 0.00 0.00 3.55
3202 3497 4.578516 CCATTTCACCTCACAACACTACAA 59.421 41.667 0.00 0.00 0.00 2.41
3264 3560 6.028368 GCTTTTTCTTCGGTAATTAGCTTCC 58.972 40.000 12.54 0.00 0.00 3.46
3265 3561 6.127980 GCTTTTTCTTCGGTAATTAGCTTCCT 60.128 38.462 12.54 0.00 0.00 3.36
3275 3571 1.944177 TTAGCTTCCTCTGCCAGTCT 58.056 50.000 0.00 0.00 0.00 3.24
3287 3583 0.179018 GCCAGTCTGTCCAAACACCT 60.179 55.000 0.00 0.00 0.00 4.00
3296 3592 0.687920 TCCAAACACCTCGCCACATA 59.312 50.000 0.00 0.00 0.00 2.29
3327 3623 5.255397 TGGATTATGTTTCTTGACTGGGT 57.745 39.130 0.00 0.00 0.00 4.51
3359 3655 4.154942 AGATCAAACTTGGGCTTGTTCAT 58.845 39.130 0.00 0.00 0.00 2.57
3380 3676 8.651588 GTTCATGTGTGTTGTTTTTGTTATTCA 58.348 29.630 0.00 0.00 0.00 2.57
3408 3704 5.899547 TGATCATACCACCTTGTATCTGACT 59.100 40.000 0.00 0.00 28.98 3.41
3921 4234 1.001406 CACTGTCCTGTCCTGTCCTTC 59.999 57.143 0.00 0.00 0.00 3.46
3933 4246 2.025887 CCTGTCCTTCATTTGGGTAGCT 60.026 50.000 0.00 0.00 0.00 3.32
3934 4247 3.562176 CCTGTCCTTCATTTGGGTAGCTT 60.562 47.826 0.00 0.00 0.00 3.74
3935 4248 3.686016 TGTCCTTCATTTGGGTAGCTTC 58.314 45.455 0.00 0.00 0.00 3.86
3936 4249 3.073798 TGTCCTTCATTTGGGTAGCTTCA 59.926 43.478 0.00 0.00 0.00 3.02
3977 4290 7.272084 ACTTAACGTTAAACTATGCGTAGACAG 59.728 37.037 20.47 6.59 36.51 3.51
3978 4291 5.051891 ACGTTAAACTATGCGTAGACAGT 57.948 39.130 19.88 7.50 35.71 3.55
3979 4292 6.182039 ACGTTAAACTATGCGTAGACAGTA 57.818 37.500 19.88 3.31 35.71 2.74
3980 4293 6.253746 ACGTTAAACTATGCGTAGACAGTAG 58.746 40.000 19.88 8.81 35.71 2.57
3981 4294 6.092670 ACGTTAAACTATGCGTAGACAGTAGA 59.907 38.462 19.88 0.00 35.71 2.59
4095 4408 7.092137 TCGTTGCTTTGCTTCTAGTAGTATA 57.908 36.000 0.00 0.00 0.00 1.47
4246 4559 6.350629 TGTAAACAAGTAGGTACTCCCTTC 57.649 41.667 0.00 0.00 42.73 3.46
4253 4566 4.805744 AGTAGGTACTCCCTTCGATTCAT 58.194 43.478 0.00 0.00 42.73 2.57
4272 4585 8.583765 CGATTCATATTAATTGATGCATGCTTG 58.416 33.333 20.33 0.00 0.00 4.01
4292 4605 4.886247 TGGTACAACTTTGAGTTTTCCG 57.114 40.909 0.00 0.00 36.03 4.30
4305 4618 0.250553 TTTTCCGGTAGGTGCCACTG 60.251 55.000 0.00 0.00 39.05 3.66
4361 4676 5.812642 AGCAATTAGATGTAGGTCGTCTTTG 59.187 40.000 0.00 0.00 41.91 2.77
4362 4677 5.810587 GCAATTAGATGTAGGTCGTCTTTGA 59.189 40.000 0.00 0.00 41.91 2.69
4374 4689 1.719780 CGTCTTTGAGTACAAGACCGC 59.280 52.381 15.28 0.00 37.32 5.68
4402 4717 4.142093 GGCTGTTCCATGCATGTTCTTATT 60.142 41.667 24.58 0.00 34.01 1.40
4403 4718 5.039333 GCTGTTCCATGCATGTTCTTATTC 58.961 41.667 24.58 7.26 0.00 1.75
4404 4719 5.581126 TGTTCCATGCATGTTCTTATTCC 57.419 39.130 24.58 3.51 0.00 3.01
4405 4720 4.402155 TGTTCCATGCATGTTCTTATTCCC 59.598 41.667 24.58 2.18 0.00 3.97
4931 5256 6.594159 CAGTTCGAGTTATGTAACCCAAAGAT 59.406 38.462 0.00 0.00 36.88 2.40
5249 5581 2.726691 CTCGCGGCGACACGAAAAT 61.727 57.895 22.69 0.00 45.33 1.82
5290 5683 0.392461 GCTAAAGACATGCCCCGTCA 60.392 55.000 0.00 0.00 35.77 4.35
5291 5684 1.747206 GCTAAAGACATGCCCCGTCAT 60.747 52.381 0.00 0.00 35.77 3.06
5292 5685 2.484770 GCTAAAGACATGCCCCGTCATA 60.485 50.000 0.00 0.00 35.77 2.15
5293 5686 2.332063 AAAGACATGCCCCGTCATAG 57.668 50.000 0.00 0.00 35.77 2.23
5294 5687 1.204146 AAGACATGCCCCGTCATAGT 58.796 50.000 0.00 0.00 35.77 2.12
5300 5705 0.034574 TGCCCCGTCATAGTTGCATT 60.035 50.000 0.00 0.00 0.00 3.56
5331 5736 1.737793 GTCGTCTTTTACCATGGCCAG 59.262 52.381 13.05 0.00 0.00 4.85
5385 5790 4.069232 CGGCCAGGTGCGAGAGAA 62.069 66.667 2.24 0.00 42.61 2.87
5387 5792 2.817396 GCCAGGTGCGAGAGAAGC 60.817 66.667 0.00 0.00 37.43 3.86
5469 5875 1.056700 AGGTCCAGCGGATTGGCTAT 61.057 55.000 0.67 0.00 42.53 2.97
5492 5898 3.930012 CTCCCGGCGAGATTCCCC 61.930 72.222 9.30 0.00 41.63 4.81
5493 5899 4.789173 TCCCGGCGAGATTCCCCA 62.789 66.667 9.30 0.00 0.00 4.96
5500 5915 1.485066 GGCGAGATTCCCCACTTCTTA 59.515 52.381 0.00 0.00 0.00 2.10
5502 5917 2.431057 GCGAGATTCCCCACTTCTTAGA 59.569 50.000 0.00 0.00 0.00 2.10
5599 6015 4.202151 CCTTTGGTTTCCTTGTCTCTTTGG 60.202 45.833 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 7.816513 TGAAGATAGACTGAAATCAACAGAGTG 59.183 37.037 0.00 0.00 38.55 3.51
507 519 4.020928 ACGATAACACACCCTTGTCATGTA 60.021 41.667 0.00 0.00 31.66 2.29
693 706 5.221722 GGACATGATCAATAGAACCTGGCTA 60.222 44.000 0.00 0.00 0.00 3.93
774 787 1.643868 CGTCATTTGCGCCTGGCTTA 61.644 55.000 17.92 2.04 44.05 3.09
782 795 5.494863 AACTTTAAAATCGTCATTTGCGC 57.505 34.783 0.00 0.00 32.18 6.09
864 881 9.774742 GACAAGTTGTCATTTGGAATATAAGAC 57.225 33.333 27.37 0.00 46.22 3.01
969 987 0.423956 TTCCTTAGGGGTGGGGATGA 59.576 55.000 0.00 0.00 36.25 2.92
1002 1020 6.106877 TGCTCGCTTAATAACTCACATTTC 57.893 37.500 0.00 0.00 0.00 2.17
1007 1025 7.630924 ACATATTTGCTCGCTTAATAACTCAC 58.369 34.615 0.00 0.00 0.00 3.51
1040 1058 6.012658 TGAAGGACTGATGCACATAAAAAC 57.987 37.500 0.00 0.00 0.00 2.43
1145 1163 4.649674 AGTGACAGAGAAACCAACACTAGA 59.350 41.667 0.00 0.00 35.77 2.43
1239 1257 9.320352 ACCAATAATACCGGAATTTTAAAATGC 57.680 29.630 9.46 12.02 0.00 3.56
1269 1287 7.595875 TCAACATGATGTGCAAGTGATAAAAAG 59.404 33.333 0.00 0.00 0.00 2.27
1353 1371 4.682787 CAGTAGCACCGAGTGAATATTCA 58.317 43.478 14.23 14.23 35.23 2.57
1463 1481 8.918202 TCATTTATTTTGGTGTCTGTAAGTCT 57.082 30.769 0.00 0.00 33.76 3.24
1464 1482 9.959749 TTTCATTTATTTTGGTGTCTGTAAGTC 57.040 29.630 0.00 0.00 33.76 3.01
1507 1525 3.510753 CCATTCCAACCAACATCACATCA 59.489 43.478 0.00 0.00 0.00 3.07
1545 1566 9.177608 TGCTGTCTTTTACTAGCAATAATTGAT 57.822 29.630 0.00 0.00 38.46 2.57
1582 1603 5.182001 AGGCAATTCACATCGCTATTATTCC 59.818 40.000 0.00 0.00 0.00 3.01
1769 1790 3.803715 GCGGAATACTGCATGTACAGGAT 60.804 47.826 12.53 0.00 43.34 3.24
1839 1860 0.390340 TGCAGAAGATCACACTCGGC 60.390 55.000 0.00 0.00 0.00 5.54
1910 1931 5.441718 TTTCTACCTGATTCTGAAGCCAT 57.558 39.130 2.88 0.00 0.00 4.40
1918 1939 5.094387 TCACCCTCTTTTCTACCTGATTCT 58.906 41.667 0.00 0.00 0.00 2.40
1948 1969 0.698238 CAGACCATTGTCCCAGGGAA 59.302 55.000 10.89 0.00 42.81 3.97
2216 2237 4.003648 AGGCACAGCTGTAATTTGAGTAC 58.996 43.478 21.20 3.23 0.00 2.73
2282 2303 6.946340 TGCTAGAGACATCTAATGGTTTCAA 58.054 36.000 0.00 0.00 37.58 2.69
2333 2354 2.746904 TGATTCGCACTGTTGGGTAATG 59.253 45.455 0.00 0.00 37.00 1.90
2385 2406 8.409371 TGATGCAACTAACATTTCACAAACTAA 58.591 29.630 0.00 0.00 0.00 2.24
2386 2407 7.935520 TGATGCAACTAACATTTCACAAACTA 58.064 30.769 0.00 0.00 0.00 2.24
2572 2867 5.071788 TCAGACCACACTTTTAGTCAAGGAT 59.928 40.000 0.00 0.00 0.00 3.24
2574 2869 4.703897 TCAGACCACACTTTTAGTCAAGG 58.296 43.478 0.00 0.00 0.00 3.61
2575 2870 6.316390 AGTTTCAGACCACACTTTTAGTCAAG 59.684 38.462 0.00 0.00 0.00 3.02
2606 2901 6.038161 TGCTAATGGATAAATGGAAGTGTTCG 59.962 38.462 0.00 0.00 0.00 3.95
2675 2970 7.618019 TGGCAAGAGTAGAGTAATATGGAAT 57.382 36.000 0.00 0.00 0.00 3.01
2689 2984 1.992557 AGGTGGGAAATGGCAAGAGTA 59.007 47.619 0.00 0.00 0.00 2.59
2704 2999 0.529378 GCATCCAGAAGCAAAGGTGG 59.471 55.000 0.00 0.00 0.00 4.61
2745 3040 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2746 3041 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2747 3042 3.849563 TTTACATTATGGGACGGAGGG 57.150 47.619 0.00 0.00 0.00 4.30
2748 3043 5.130350 ACATTTTACATTATGGGACGGAGG 58.870 41.667 0.00 0.00 0.00 4.30
2749 3044 6.693315 AACATTTTACATTATGGGACGGAG 57.307 37.500 0.00 0.00 0.00 4.63
2750 3045 7.469537 AAAACATTTTACATTATGGGACGGA 57.530 32.000 0.00 0.00 0.00 4.69
2781 3076 7.211966 AGACGTATTTTGACACTACACTAGT 57.788 36.000 0.00 0.00 40.28 2.57
2782 3077 9.059485 GTAAGACGTATTTTGACACTACACTAG 57.941 37.037 0.00 0.00 0.00 2.57
2783 3078 8.567104 TGTAAGACGTATTTTGACACTACACTA 58.433 33.333 0.00 0.00 0.00 2.74
2784 3079 7.428020 TGTAAGACGTATTTTGACACTACACT 58.572 34.615 0.00 0.00 0.00 3.55
2785 3080 7.627585 TGTAAGACGTATTTTGACACTACAC 57.372 36.000 0.00 0.00 0.00 2.90
2786 3081 8.821147 AATGTAAGACGTATTTTGACACTACA 57.179 30.769 0.00 0.00 0.00 2.74
2789 3084 8.804743 CGATAATGTAAGACGTATTTTGACACT 58.195 33.333 0.00 0.00 0.00 3.55
2790 3085 8.054236 CCGATAATGTAAGACGTATTTTGACAC 58.946 37.037 0.00 0.00 0.00 3.67
2791 3086 7.975058 TCCGATAATGTAAGACGTATTTTGACA 59.025 33.333 0.00 0.00 0.00 3.58
2792 3087 8.264632 GTCCGATAATGTAAGACGTATTTTGAC 58.735 37.037 0.00 0.00 0.00 3.18
2793 3088 7.166307 CGTCCGATAATGTAAGACGTATTTTGA 59.834 37.037 0.00 0.00 43.89 2.69
2794 3089 7.271539 CGTCCGATAATGTAAGACGTATTTTG 58.728 38.462 0.00 0.00 43.89 2.44
2795 3090 6.418819 CCGTCCGATAATGTAAGACGTATTTT 59.581 38.462 0.00 0.00 46.62 1.82
2796 3091 5.916883 CCGTCCGATAATGTAAGACGTATTT 59.083 40.000 0.00 0.00 46.62 1.40
2797 3092 5.239306 TCCGTCCGATAATGTAAGACGTATT 59.761 40.000 0.00 0.00 46.62 1.89
2798 3093 4.756642 TCCGTCCGATAATGTAAGACGTAT 59.243 41.667 9.63 0.00 46.62 3.06
2799 3094 4.126437 TCCGTCCGATAATGTAAGACGTA 58.874 43.478 9.63 0.00 46.62 3.57
2800 3095 2.945008 TCCGTCCGATAATGTAAGACGT 59.055 45.455 9.63 0.00 46.62 4.34
2802 3097 3.305199 CCCTCCGTCCGATAATGTAAGAC 60.305 52.174 0.00 0.00 0.00 3.01
2803 3098 2.889045 CCCTCCGTCCGATAATGTAAGA 59.111 50.000 0.00 0.00 0.00 2.10
2804 3099 2.889045 TCCCTCCGTCCGATAATGTAAG 59.111 50.000 0.00 0.00 0.00 2.34
2805 3100 2.889045 CTCCCTCCGTCCGATAATGTAA 59.111 50.000 0.00 0.00 0.00 2.41
2806 3101 2.158564 ACTCCCTCCGTCCGATAATGTA 60.159 50.000 0.00 0.00 0.00 2.29
2807 3102 1.329256 CTCCCTCCGTCCGATAATGT 58.671 55.000 0.00 0.00 0.00 2.71
2808 3103 1.329256 ACTCCCTCCGTCCGATAATG 58.671 55.000 0.00 0.00 0.00 1.90
2809 3104 2.107901 ACTACTCCCTCCGTCCGATAAT 59.892 50.000 0.00 0.00 0.00 1.28
2810 3105 1.492176 ACTACTCCCTCCGTCCGATAA 59.508 52.381 0.00 0.00 0.00 1.75
2811 3106 1.071385 GACTACTCCCTCCGTCCGATA 59.929 57.143 0.00 0.00 0.00 2.92
2812 3107 0.179023 GACTACTCCCTCCGTCCGAT 60.179 60.000 0.00 0.00 0.00 4.18
2813 3108 1.222936 GACTACTCCCTCCGTCCGA 59.777 63.158 0.00 0.00 0.00 4.55
2814 3109 1.077930 TGACTACTCCCTCCGTCCG 60.078 63.158 0.00 0.00 0.00 4.79
2815 3110 0.034283 ACTGACTACTCCCTCCGTCC 60.034 60.000 0.00 0.00 0.00 4.79
2816 3111 2.706339 TACTGACTACTCCCTCCGTC 57.294 55.000 0.00 0.00 0.00 4.79
2817 3112 2.933573 CATACTGACTACTCCCTCCGT 58.066 52.381 0.00 0.00 0.00 4.69
2818 3113 1.609555 GCATACTGACTACTCCCTCCG 59.390 57.143 0.00 0.00 0.00 4.63
2819 3114 2.667470 TGCATACTGACTACTCCCTCC 58.333 52.381 0.00 0.00 0.00 4.30
2820 3115 3.447586 TGTTGCATACTGACTACTCCCTC 59.552 47.826 0.00 0.00 0.00 4.30
2821 3116 3.441101 TGTTGCATACTGACTACTCCCT 58.559 45.455 0.00 0.00 0.00 4.20
2822 3117 3.887621 TGTTGCATACTGACTACTCCC 57.112 47.619 0.00 0.00 0.00 4.30
2823 3118 6.371389 GTTTTTGTTGCATACTGACTACTCC 58.629 40.000 0.00 0.00 0.00 3.85
2824 3119 6.017440 TGGTTTTTGTTGCATACTGACTACTC 60.017 38.462 0.00 0.00 0.00 2.59
2825 3120 5.825679 TGGTTTTTGTTGCATACTGACTACT 59.174 36.000 0.00 0.00 0.00 2.57
2826 3121 6.067263 TGGTTTTTGTTGCATACTGACTAC 57.933 37.500 0.00 0.00 0.00 2.73
2827 3122 5.825679 ACTGGTTTTTGTTGCATACTGACTA 59.174 36.000 0.00 0.00 0.00 2.59
2828 3123 4.644685 ACTGGTTTTTGTTGCATACTGACT 59.355 37.500 0.00 0.00 0.00 3.41
2829 3124 4.932146 ACTGGTTTTTGTTGCATACTGAC 58.068 39.130 0.00 0.00 0.00 3.51
2855 3150 6.015519 TGTGCTTAGGAAATTTAACATGCACT 60.016 34.615 24.70 6.54 44.72 4.40
3116 3411 1.075601 TTGGAGGGGATGCTGAAACT 58.924 50.000 0.00 0.00 0.00 2.66
3191 3486 5.918608 AGATGAGAAGTGTTGTAGTGTTGT 58.081 37.500 0.00 0.00 0.00 3.32
3192 3487 6.293081 CCAAGATGAGAAGTGTTGTAGTGTTG 60.293 42.308 0.00 0.00 0.00 3.33
3193 3488 5.760253 CCAAGATGAGAAGTGTTGTAGTGTT 59.240 40.000 0.00 0.00 0.00 3.32
3194 3489 5.070446 TCCAAGATGAGAAGTGTTGTAGTGT 59.930 40.000 0.00 0.00 0.00 3.55
3195 3490 5.541845 TCCAAGATGAGAAGTGTTGTAGTG 58.458 41.667 0.00 0.00 0.00 2.74
3196 3491 5.788450 CTCCAAGATGAGAAGTGTTGTAGT 58.212 41.667 0.00 0.00 34.11 2.73
3197 3492 4.629200 GCTCCAAGATGAGAAGTGTTGTAG 59.371 45.833 0.00 0.00 34.11 2.74
3198 3493 4.284490 AGCTCCAAGATGAGAAGTGTTGTA 59.716 41.667 0.00 0.00 34.11 2.41
3202 3497 2.902486 TGAGCTCCAAGATGAGAAGTGT 59.098 45.455 12.15 0.00 34.11 3.55
3264 3560 1.202687 TGTTTGGACAGACTGGCAGAG 60.203 52.381 23.66 12.80 0.00 3.35
3265 3561 0.836606 TGTTTGGACAGACTGGCAGA 59.163 50.000 23.66 0.00 0.00 4.26
3275 3571 1.525077 GTGGCGAGGTGTTTGGACA 60.525 57.895 0.00 0.00 0.00 4.02
3287 3583 3.157881 TCCAACCAAAAATATGTGGCGA 58.842 40.909 0.00 0.00 38.58 5.54
3296 3592 9.271828 GTCAAGAAACATAATCCAACCAAAAAT 57.728 29.630 0.00 0.00 0.00 1.82
3327 3623 4.082190 CCCAAGTTTGATCTAGTGTCTCGA 60.082 45.833 0.00 0.00 0.00 4.04
3359 3655 8.491152 CAAACTGAATAACAAAAACAACACACA 58.509 29.630 0.00 0.00 0.00 3.72
3380 3676 7.050377 CAGATACAAGGTGGTATGATCAAACT 58.950 38.462 0.00 0.00 34.22 2.66
3408 3704 3.363627 TGCAATGCCAAATGGATAGTCA 58.636 40.909 1.53 0.00 37.39 3.41
3471 3767 0.535780 TGAAGTTGAGGTGCTGGCAG 60.536 55.000 10.94 10.94 0.00 4.85
3599 3895 0.996762 ACCAAAGGAGGAACCACCCA 60.997 55.000 3.81 0.00 42.04 4.51
3921 4234 5.587388 ACATGAATGAAGCTACCCAAATG 57.413 39.130 0.00 0.00 0.00 2.32
3933 4246 9.701098 ACGTTAAGTCTTAACTACATGAATGAA 57.299 29.630 25.68 0.00 42.53 2.57
3934 4247 9.701098 AACGTTAAGTCTTAACTACATGAATGA 57.299 29.630 25.68 0.00 42.53 2.57
4095 4408 4.497516 AGTGGCAGGGACAGAAGATATAT 58.502 43.478 0.00 0.00 0.00 0.86
4162 4475 4.554723 GCTACTTGTTTTCTCGTGCATTGT 60.555 41.667 0.00 0.00 0.00 2.71
4203 4516 9.410556 GTTTACATTACAAGCATGATCAGTTTT 57.589 29.630 0.09 0.00 0.00 2.43
4204 4517 8.575589 TGTTTACATTACAAGCATGATCAGTTT 58.424 29.630 0.09 0.00 0.00 2.66
4246 4559 8.583765 CAAGCATGCATCAATTAATATGAATCG 58.416 33.333 21.98 0.00 0.00 3.34
4253 4566 7.579761 TGTACCAAGCATGCATCAATTAATA 57.420 32.000 21.98 0.00 0.00 0.98
4272 4585 3.628942 ACCGGAAAACTCAAAGTTGTACC 59.371 43.478 9.46 0.00 38.66 3.34
4285 4598 0.250597 AGTGGCACCTACCGGAAAAC 60.251 55.000 15.27 0.00 0.00 2.43
4287 4600 1.122632 TCAGTGGCACCTACCGGAAA 61.123 55.000 15.27 0.00 0.00 3.13
4292 4605 2.264794 CGGTCAGTGGCACCTACC 59.735 66.667 22.71 22.71 0.00 3.18
4313 4626 8.966194 GCTTATCTACTAATTAAACGACAGTCC 58.034 37.037 0.00 0.00 0.00 3.85
4342 4657 6.656270 TGTACTCAAAGACGACCTACATCTAA 59.344 38.462 0.00 0.00 0.00 2.10
4361 4676 0.737715 CCAGCTGCGGTCTTGTACTC 60.738 60.000 8.66 0.00 0.00 2.59
4362 4677 1.293498 CCAGCTGCGGTCTTGTACT 59.707 57.895 8.66 0.00 0.00 2.73
4402 4717 5.385509 GCACAAAGCAAAATACTTAGGGA 57.614 39.130 0.00 0.00 44.79 4.20
4931 5256 8.615211 CAATAATACTTCTGAAGCAAGCATACA 58.385 33.333 17.00 0.00 0.00 2.29
4973 5299 5.001232 AGCTTAACAGGAATTTAAGACGCA 58.999 37.500 6.12 0.00 38.36 5.24
5267 5599 1.839424 GGGGCATGTCTTTAGCTTGT 58.161 50.000 0.00 0.00 0.00 3.16
5300 5705 0.400213 AAAGACGACAAGGGCATCCA 59.600 50.000 0.00 0.00 34.83 3.41
5331 5736 2.751259 CAGGTGCATATGGATATGGCAC 59.249 50.000 17.18 17.18 41.54 5.01
5385 5790 2.690778 GCGATGCTTTTGACCGGCT 61.691 57.895 0.00 0.00 0.00 5.52
5387 5792 1.425428 GAGCGATGCTTTTGACCGG 59.575 57.895 0.00 0.00 39.88 5.28
5492 5898 5.461032 AGGGCGAGATAATCTAAGAAGTG 57.539 43.478 0.00 0.00 0.00 3.16
5493 5899 4.216687 CGAGGGCGAGATAATCTAAGAAGT 59.783 45.833 0.00 0.00 40.82 3.01
5500 5915 0.540830 AGGCGAGGGCGAGATAATCT 60.541 55.000 0.00 0.00 41.24 2.40
5502 5917 1.867919 CGAGGCGAGGGCGAGATAAT 61.868 60.000 0.00 0.00 41.24 1.28
5599 6015 7.062371 CGATAAAAGCCATGCATACTACTACTC 59.938 40.741 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.