Multiple sequence alignment - TraesCS4D01G001800

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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 TraesCS4D01G001800 chr4D 100.000 2858 0 0 1 2858 1229749 1232606 0.000000e+00 5278.0
1 TraesCS4D01G001800 chr4A 91.919 1819 96 30 857 2642 603540704 603538904 0.000000e+00 2497.0
2 TraesCS4D01G001800 chr4A 92.642 530 26 5 1 519 603541540 603541013 0.000000e+00 750.0
3 TraesCS4D01G001800 chr4A 82.664 473 76 4 1204 1670 103068740 103069212 5.700000e-112 414.0
4 TraesCS4D01G001800 chr4A 79.894 189 10 11 555 740 603540933 603540770 2.330000e-21 113.0
5 TraesCS4D01G001800 chr4B 91.248 1634 63 38 559 2136 654246 652637 0.000000e+00 2152.0
6 TraesCS4D01G001800 chr4B 93.169 527 20 10 1 519 654844 654326 0.000000e+00 760.0
7 TraesCS4D01G001800 chr4B 90.439 387 31 4 2223 2605 652406 652022 3.290000e-139 505.0
8 TraesCS4D01G001800 chr6A 80.436 2341 226 114 338 2580 27772036 27774242 0.000000e+00 1572.0
9 TraesCS4D01G001800 chr6A 87.269 487 55 4 1180 1661 609176277 609176761 1.500000e-152 549.0
10 TraesCS4D01G001800 chr6A 83.636 110 5 4 88 184 27771773 27771882 1.090000e-14 91.6
11 TraesCS4D01G001800 chr6D 81.140 2105 152 127 109 2111 26350075 26352036 0.000000e+00 1461.0
12 TraesCS4D01G001800 chr6D 86.848 479 57 3 1189 1661 462422969 462423447 5.420000e-147 531.0
13 TraesCS4D01G001800 chr6B 87.887 1164 81 28 984 2130 48551814 48552934 0.000000e+00 1314.0
14 TraesCS4D01G001800 chr6B 87.064 487 56 4 1180 1661 704890658 704891142 6.960000e-151 544.0
15 TraesCS4D01G001800 chr6B 75.964 674 66 54 109 754 48550959 48551564 2.820000e-65 259.0


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 TraesCS4D01G001800 chr4D 1229749 1232606 2857 False 5278.0 5278 100.000000 1 2858 1 chr4D.!!$F1 2857
1 TraesCS4D01G001800 chr4A 603538904 603541540 2636 True 1120.0 2497 88.151667 1 2642 3 chr4A.!!$R1 2641
2 TraesCS4D01G001800 chr4B 652022 654844 2822 True 1139.0 2152 91.618667 1 2605 3 chr4B.!!$R1 2604
3 TraesCS4D01G001800 chr6A 27771773 27774242 2469 False 831.8 1572 82.036000 88 2580 2 chr6A.!!$F2 2492
4 TraesCS4D01G001800 chr6D 26350075 26352036 1961 False 1461.0 1461 81.140000 109 2111 1 chr6D.!!$F1 2002
5 TraesCS4D01G001800 chr6B 48550959 48552934 1975 False 786.5 1314 81.925500 109 2130 2 chr6B.!!$F2 2021

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
46 47 1.207570 TGCCAATCCACATTTGATGGC 59.792 47.619 13.24 13.24 37.13 4.40 F
1242 1513 1.228429 CCCGGGCTCCAAGAACAAA 60.228 57.895 8.08 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1996 1.832912 GGCCATCATCGGAGGAAGT 59.167 57.895 0.00 0.00 0.00 3.01 R
2794 3280 0.031994 AACAGCAATGTTGGGCGAAC 59.968 50.000 5.34 5.34 34.54 3.95 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
46 47 1.207570 TGCCAATCCACATTTGATGGC 59.792 47.619 13.24 13.24 37.13 4.40
267 285 7.053498 ACAAATGCCATGTACACATACTGATA 58.947 34.615 0.00 0.00 34.26 2.15
391 451 2.167900 ACTAGAAGGTACCCATCAACGC 59.832 50.000 8.74 0.00 0.00 4.84
423 485 2.832643 TGCATCCCTCCATGACAAAT 57.167 45.000 0.00 0.00 0.00 2.32
459 525 1.813513 GCAGCAAGCAAGTCTTCCTA 58.186 50.000 0.00 0.00 44.79 2.94
521 620 5.063204 CCCCATATATACAACACACACCAG 58.937 45.833 0.00 0.00 0.00 4.00
588 727 8.517062 AATTCTAGATCTTCCTGGTTTGATTG 57.483 34.615 0.00 0.00 0.00 2.67
590 729 4.664688 AGATCTTCCTGGTTTGATTGGT 57.335 40.909 0.00 0.00 0.00 3.67
618 757 1.447838 ATGGCGCACAAGGTACTCG 60.448 57.895 10.83 0.00 38.49 4.18
619 758 1.884075 ATGGCGCACAAGGTACTCGA 61.884 55.000 10.83 0.00 38.49 4.04
646 785 8.850860 TCATATATTTCCTCTCCATCTCCTAGA 58.149 37.037 0.00 0.00 0.00 2.43
650 789 6.538209 TTTCCTCTCCATCTCCTAGATACT 57.462 41.667 0.00 0.00 32.12 2.12
651 790 7.649702 TTTCCTCTCCATCTCCTAGATACTA 57.350 40.000 0.00 0.00 32.12 1.82
652 791 6.884472 TCCTCTCCATCTCCTAGATACTAG 57.116 45.833 0.00 0.00 32.12 2.57
653 792 6.576360 TCCTCTCCATCTCCTAGATACTAGA 58.424 44.000 0.00 0.00 32.12 2.43
655 794 7.347222 TCCTCTCCATCTCCTAGATACTAGATC 59.653 44.444 0.00 0.00 32.12 2.75
728 903 8.030692 TGCTCATGAAATCAAAAGATAACAAGG 58.969 33.333 0.00 0.00 0.00 3.61
729 904 8.246180 GCTCATGAAATCAAAAGATAACAAGGA 58.754 33.333 0.00 0.00 0.00 3.36
797 982 8.829612 TGTAAACAAGTATCTATCACATGCATG 58.170 33.333 25.09 25.09 0.00 4.06
806 991 3.720949 ATCACATGCATGTATGGTTGC 57.279 42.857 30.92 0.00 39.39 4.17
821 1009 2.884639 TGGTTGCTGCTAGTTTTCTTCC 59.115 45.455 0.00 0.00 0.00 3.46
826 1019 5.125100 TGCTGCTAGTTTTCTTCCATTTG 57.875 39.130 0.00 0.00 0.00 2.32
827 1020 4.826733 TGCTGCTAGTTTTCTTCCATTTGA 59.173 37.500 0.00 0.00 0.00 2.69
828 1021 5.477984 TGCTGCTAGTTTTCTTCCATTTGAT 59.522 36.000 0.00 0.00 0.00 2.57
829 1022 6.032717 GCTGCTAGTTTTCTTCCATTTGATC 58.967 40.000 0.00 0.00 0.00 2.92
830 1023 6.127786 GCTGCTAGTTTTCTTCCATTTGATCT 60.128 38.462 0.00 0.00 0.00 2.75
831 1024 7.383102 TGCTAGTTTTCTTCCATTTGATCTC 57.617 36.000 0.00 0.00 0.00 2.75
832 1025 7.170965 TGCTAGTTTTCTTCCATTTGATCTCT 58.829 34.615 0.00 0.00 0.00 3.10
833 1026 7.667219 TGCTAGTTTTCTTCCATTTGATCTCTT 59.333 33.333 0.00 0.00 0.00 2.85
834 1027 9.167311 GCTAGTTTTCTTCCATTTGATCTCTTA 57.833 33.333 0.00 0.00 0.00 2.10
890 1087 6.798482 TCATTTCATTTGTATGCAGATCCAC 58.202 36.000 0.00 0.00 0.00 4.02
958 1197 2.975489 AGCCACCAAGAAGAAGAAGAGA 59.025 45.455 0.00 0.00 0.00 3.10
1077 1333 4.279043 GCCGGCAACCACAACCAC 62.279 66.667 24.80 0.00 0.00 4.16
1130 1401 3.319198 GGTGGACGGGGAGAGCAA 61.319 66.667 0.00 0.00 0.00 3.91
1242 1513 1.228429 CCCGGGCTCCAAGAACAAA 60.228 57.895 8.08 0.00 0.00 2.83
1545 1816 3.138798 GTCTACCTCGCAGGCGGA 61.139 66.667 14.24 0.00 39.63 5.54
1677 1948 2.502492 CGCCGAGGAGGATCACCAT 61.502 63.158 10.13 0.00 45.00 3.55
1690 1961 3.381983 ACCATCAGCTCGACGCCA 61.382 61.111 3.66 0.00 40.39 5.69
1868 2139 2.516906 GCCCTACTAGCTACCTACCTG 58.483 57.143 0.00 0.00 0.00 4.00
1869 2140 2.516906 CCCTACTAGCTACCTACCTGC 58.483 57.143 0.00 0.00 0.00 4.85
1923 2204 1.658686 ATGTGTCGACCTCTCCGAGC 61.659 60.000 14.12 0.00 36.66 5.03
1924 2205 2.033602 TGTCGACCTCTCCGAGCA 59.966 61.111 14.12 0.00 36.66 4.26
1925 2206 1.378646 TGTCGACCTCTCCGAGCAT 60.379 57.895 14.12 0.00 36.66 3.79
2004 2313 3.580022 TGCATATACATCTAGCAGCTGGT 59.420 43.478 23.72 23.72 0.00 4.00
2005 2314 4.772100 TGCATATACATCTAGCAGCTGGTA 59.228 41.667 23.39 23.39 0.00 3.25
2006 2315 5.245977 TGCATATACATCTAGCAGCTGGTAA 59.754 40.000 24.70 16.22 0.00 2.85
2007 2316 6.070596 TGCATATACATCTAGCAGCTGGTAAT 60.071 38.462 24.70 17.19 0.00 1.89
2074 2388 7.719193 TCTGTGAAAAATCATCTGGAGTTACAA 59.281 33.333 0.00 0.00 31.51 2.41
2275 2753 3.456280 AGTTTGTTTCACGCAATTGCAT 58.544 36.364 28.77 12.92 42.21 3.96
2318 2800 7.040892 GCCTGACATTGCTGAGAAATATTGATA 60.041 37.037 0.00 0.00 0.00 2.15
2349 2831 4.940654 TCCACATTTCTCGCAATGATGTTA 59.059 37.500 8.32 0.00 37.55 2.41
2449 2931 9.242477 ACTTAAACTAAACTTTACTCGAGTCAC 57.758 33.333 23.89 0.00 0.00 3.67
2489 2974 2.884639 TCGATCGACATTGCTCATCCTA 59.115 45.455 15.15 0.00 0.00 2.94
2506 2991 7.451731 TCATCCTAGGGTTACATGAATTTCT 57.548 36.000 9.46 0.00 0.00 2.52
2508 2993 7.993183 TCATCCTAGGGTTACATGAATTTCTTC 59.007 37.037 9.46 0.00 0.00 2.87
2541 3026 6.989759 TCTAGCACAGTTTTGACAAGTTGATA 59.010 34.615 10.54 0.00 0.00 2.15
2567 3053 2.034687 AGTGCATGAGGTGGCCAC 59.965 61.111 28.57 28.57 0.00 5.01
2594 3080 4.007659 GGTCATTTCATCAGGTTTACGGT 58.992 43.478 0.00 0.00 0.00 4.83
2618 3104 1.691196 TTTGATTCGCATGATCCCCC 58.309 50.000 0.00 0.00 0.00 5.40
2622 3108 1.338020 GATTCGCATGATCCCCCAAAC 59.662 52.381 0.00 0.00 0.00 2.93
2623 3109 0.038890 TTCGCATGATCCCCCAAACA 59.961 50.000 0.00 0.00 0.00 2.83
2624 3110 0.258484 TCGCATGATCCCCCAAACAT 59.742 50.000 0.00 0.00 0.00 2.71
2625 3111 1.492599 TCGCATGATCCCCCAAACATA 59.507 47.619 0.00 0.00 0.00 2.29
2626 3112 1.881973 CGCATGATCCCCCAAACATAG 59.118 52.381 0.00 0.00 0.00 2.23
2627 3113 1.615392 GCATGATCCCCCAAACATAGC 59.385 52.381 0.00 0.00 0.00 2.97
2628 3114 2.948115 CATGATCCCCCAAACATAGCA 58.052 47.619 0.00 0.00 0.00 3.49
2630 3116 3.686227 TGATCCCCCAAACATAGCAAT 57.314 42.857 0.00 0.00 0.00 3.56
2631 3117 4.805140 TGATCCCCCAAACATAGCAATA 57.195 40.909 0.00 0.00 0.00 1.90
2632 3118 4.469657 TGATCCCCCAAACATAGCAATAC 58.530 43.478 0.00 0.00 0.00 1.89
2633 3119 4.079500 TGATCCCCCAAACATAGCAATACA 60.080 41.667 0.00 0.00 0.00 2.29
2634 3120 3.897239 TCCCCCAAACATAGCAATACAG 58.103 45.455 0.00 0.00 0.00 2.74
2635 3121 3.525609 TCCCCCAAACATAGCAATACAGA 59.474 43.478 0.00 0.00 0.00 3.41
2636 3122 4.017958 TCCCCCAAACATAGCAATACAGAA 60.018 41.667 0.00 0.00 0.00 3.02
2637 3123 4.895297 CCCCCAAACATAGCAATACAGAAT 59.105 41.667 0.00 0.00 0.00 2.40
2667 3153 8.948631 ACATGAGAACTAGGTACAATTACATG 57.051 34.615 0.00 0.00 37.06 3.21
2668 3154 8.540388 ACATGAGAACTAGGTACAATTACATGT 58.460 33.333 2.69 2.69 38.60 3.21
2669 3155 9.383519 CATGAGAACTAGGTACAATTACATGTT 57.616 33.333 2.30 0.00 34.75 2.71
2670 3156 9.959721 ATGAGAACTAGGTACAATTACATGTTT 57.040 29.630 2.30 0.00 34.75 2.83
2671 3157 9.787435 TGAGAACTAGGTACAATTACATGTTTT 57.213 29.630 2.30 0.00 34.75 2.43
2700 3186 5.559427 ACATGAATGTATAGCAAAACGCA 57.441 34.783 0.00 0.00 40.77 5.24
2701 3187 6.135290 ACATGAATGTATAGCAAAACGCAT 57.865 33.333 0.00 0.00 40.77 4.73
2702 3188 7.258022 ACATGAATGTATAGCAAAACGCATA 57.742 32.000 0.00 0.00 40.77 3.14
2703 3189 7.702386 ACATGAATGTATAGCAAAACGCATAA 58.298 30.769 0.00 0.00 40.77 1.90
2704 3190 8.352201 ACATGAATGTATAGCAAAACGCATAAT 58.648 29.630 0.00 0.00 40.77 1.28
2705 3191 9.184062 CATGAATGTATAGCAAAACGCATAATT 57.816 29.630 0.00 0.00 46.13 1.40
2706 3192 8.781067 TGAATGTATAGCAAAACGCATAATTC 57.219 30.769 0.00 0.00 46.13 2.17
2707 3193 7.860373 TGAATGTATAGCAAAACGCATAATTCC 59.140 33.333 0.00 0.00 46.13 3.01
2708 3194 5.743467 TGTATAGCAAAACGCATAATTCCG 58.257 37.500 0.00 0.00 46.13 4.30
2709 3195 4.893424 ATAGCAAAACGCATAATTCCGT 57.107 36.364 0.00 0.00 46.13 4.69
2710 3196 3.131240 AGCAAAACGCATAATTCCGTC 57.869 42.857 0.19 0.00 46.13 4.79
2711 3197 2.486203 AGCAAAACGCATAATTCCGTCA 59.514 40.909 0.19 0.00 46.13 4.35
2712 3198 2.592459 GCAAAACGCATAATTCCGTCAC 59.408 45.455 0.19 0.00 41.79 3.67
2713 3199 3.816091 CAAAACGCATAATTCCGTCACA 58.184 40.909 0.19 0.00 36.56 3.58
2714 3200 4.411327 CAAAACGCATAATTCCGTCACAT 58.589 39.130 0.19 0.00 36.56 3.21
2715 3201 3.673746 AACGCATAATTCCGTCACATG 57.326 42.857 0.00 0.00 36.56 3.21
2716 3202 1.939934 ACGCATAATTCCGTCACATGG 59.060 47.619 0.00 0.00 31.00 3.66
2717 3203 1.334059 CGCATAATTCCGTCACATGGC 60.334 52.381 0.00 0.00 0.00 4.40
2718 3204 1.675483 GCATAATTCCGTCACATGGCA 59.325 47.619 0.00 0.00 0.00 4.92
2719 3205 2.541588 GCATAATTCCGTCACATGGCAC 60.542 50.000 0.00 0.00 0.00 5.01
2720 3206 1.364721 TAATTCCGTCACATGGCACG 58.635 50.000 10.82 10.82 35.72 5.34
2724 3210 4.697756 CGTCACATGGCACGGGGT 62.698 66.667 10.10 0.00 32.19 4.95
2725 3211 2.282180 GTCACATGGCACGGGGTT 60.282 61.111 0.00 0.00 0.00 4.11
2726 3212 1.901464 GTCACATGGCACGGGGTTT 60.901 57.895 0.00 0.00 0.00 3.27
2727 3213 1.900981 TCACATGGCACGGGGTTTG 60.901 57.895 0.00 0.00 0.00 2.93
2728 3214 2.197324 ACATGGCACGGGGTTTGT 59.803 55.556 0.00 0.00 0.00 2.83
2729 3215 2.199652 ACATGGCACGGGGTTTGTG 61.200 57.895 0.00 0.00 40.32 3.33
2730 3216 2.600173 ATGGCACGGGGTTTGTGG 60.600 61.111 0.00 0.00 37.80 4.17
2731 3217 3.444818 ATGGCACGGGGTTTGTGGT 62.445 57.895 0.00 0.00 37.80 4.16
2732 3218 3.601685 GGCACGGGGTTTGTGGTG 61.602 66.667 0.00 0.00 37.80 4.17
2733 3219 3.601685 GCACGGGGTTTGTGGTGG 61.602 66.667 0.00 0.00 37.80 4.61
2734 3220 2.124067 CACGGGGTTTGTGGTGGT 60.124 61.111 0.00 0.00 33.69 4.16
2735 3221 1.755008 CACGGGGTTTGTGGTGGTT 60.755 57.895 0.00 0.00 33.69 3.67
2736 3222 1.000612 ACGGGGTTTGTGGTGGTTT 59.999 52.632 0.00 0.00 0.00 3.27
2737 3223 0.615261 ACGGGGTTTGTGGTGGTTTT 60.615 50.000 0.00 0.00 0.00 2.43
2738 3224 0.179097 CGGGGTTTGTGGTGGTTTTG 60.179 55.000 0.00 0.00 0.00 2.44
2739 3225 0.906066 GGGGTTTGTGGTGGTTTTGT 59.094 50.000 0.00 0.00 0.00 2.83
2740 3226 1.406205 GGGGTTTGTGGTGGTTTTGTG 60.406 52.381 0.00 0.00 0.00 3.33
2741 3227 1.406205 GGGTTTGTGGTGGTTTTGTGG 60.406 52.381 0.00 0.00 0.00 4.17
2742 3228 1.550976 GGTTTGTGGTGGTTTTGTGGA 59.449 47.619 0.00 0.00 0.00 4.02
2743 3229 2.169561 GGTTTGTGGTGGTTTTGTGGAT 59.830 45.455 0.00 0.00 0.00 3.41
2744 3230 3.385111 GGTTTGTGGTGGTTTTGTGGATA 59.615 43.478 0.00 0.00 0.00 2.59
2745 3231 4.039852 GGTTTGTGGTGGTTTTGTGGATAT 59.960 41.667 0.00 0.00 0.00 1.63
2746 3232 5.227152 GTTTGTGGTGGTTTTGTGGATATC 58.773 41.667 0.00 0.00 0.00 1.63
2747 3233 4.380843 TGTGGTGGTTTTGTGGATATCT 57.619 40.909 2.05 0.00 0.00 1.98
2748 3234 4.735369 TGTGGTGGTTTTGTGGATATCTT 58.265 39.130 2.05 0.00 0.00 2.40
2749 3235 5.144100 TGTGGTGGTTTTGTGGATATCTTT 58.856 37.500 2.05 0.00 0.00 2.52
2750 3236 5.010516 TGTGGTGGTTTTGTGGATATCTTTG 59.989 40.000 2.05 0.00 0.00 2.77
2751 3237 5.010617 GTGGTGGTTTTGTGGATATCTTTGT 59.989 40.000 2.05 0.00 0.00 2.83
2752 3238 5.242838 TGGTGGTTTTGTGGATATCTTTGTC 59.757 40.000 2.05 0.00 0.00 3.18
2753 3239 5.390613 GTGGTTTTGTGGATATCTTTGTCG 58.609 41.667 2.05 0.00 0.00 4.35
2754 3240 5.048991 GTGGTTTTGTGGATATCTTTGTCGT 60.049 40.000 2.05 0.00 0.00 4.34
2755 3241 5.049060 TGGTTTTGTGGATATCTTTGTCGTG 60.049 40.000 2.05 0.00 0.00 4.35
2756 3242 5.180492 GGTTTTGTGGATATCTTTGTCGTGA 59.820 40.000 2.05 0.00 0.00 4.35
2757 3243 6.307155 GTTTTGTGGATATCTTTGTCGTGAG 58.693 40.000 2.05 0.00 0.00 3.51
2758 3244 4.123497 TGTGGATATCTTTGTCGTGAGG 57.877 45.455 2.05 0.00 0.00 3.86
2759 3245 3.767131 TGTGGATATCTTTGTCGTGAGGA 59.233 43.478 2.05 0.00 0.00 3.71
2760 3246 4.221924 TGTGGATATCTTTGTCGTGAGGAA 59.778 41.667 2.05 0.00 0.00 3.36
2761 3247 4.806247 GTGGATATCTTTGTCGTGAGGAAG 59.194 45.833 2.05 0.00 0.00 3.46
2762 3248 4.709886 TGGATATCTTTGTCGTGAGGAAGA 59.290 41.667 2.05 0.00 33.17 2.87
2763 3249 5.363868 TGGATATCTTTGTCGTGAGGAAGAT 59.636 40.000 2.05 10.62 40.73 2.40
2764 3250 5.923684 GGATATCTTTGTCGTGAGGAAGATC 59.076 44.000 2.05 0.00 39.07 2.75
2765 3251 3.594603 TCTTTGTCGTGAGGAAGATCC 57.405 47.619 0.00 0.00 36.58 3.36
2779 3265 5.143369 AGGAAGATCCTTTATTGGATTGCC 58.857 41.667 0.00 0.00 46.91 4.52
2780 3266 5.103344 AGGAAGATCCTTTATTGGATTGCCT 60.103 40.000 0.00 0.00 46.91 4.75
2781 3267 5.600069 GGAAGATCCTTTATTGGATTGCCTT 59.400 40.000 0.00 0.00 46.00 4.35
2782 3268 6.098838 GGAAGATCCTTTATTGGATTGCCTTT 59.901 38.462 0.00 0.00 46.00 3.11
2783 3269 7.365028 GGAAGATCCTTTATTGGATTGCCTTTT 60.365 37.037 0.00 0.00 46.00 2.27
2784 3270 7.500629 AGATCCTTTATTGGATTGCCTTTTT 57.499 32.000 0.00 0.00 46.00 1.94
2801 3287 1.228533 TTTTGTAAGACGGTTCGCCC 58.771 50.000 0.00 0.00 0.00 6.13
2802 3288 0.106335 TTTGTAAGACGGTTCGCCCA 59.894 50.000 0.00 0.00 0.00 5.36
2803 3289 0.106335 TTGTAAGACGGTTCGCCCAA 59.894 50.000 0.00 0.00 0.00 4.12
2804 3290 0.600782 TGTAAGACGGTTCGCCCAAC 60.601 55.000 0.00 0.00 0.00 3.77
2805 3291 0.600782 GTAAGACGGTTCGCCCAACA 60.601 55.000 0.00 0.00 36.61 3.33
2806 3292 0.322322 TAAGACGGTTCGCCCAACAT 59.678 50.000 0.00 0.00 36.61 2.71
2807 3293 0.536460 AAGACGGTTCGCCCAACATT 60.536 50.000 0.00 0.00 36.61 2.71
2808 3294 1.209127 GACGGTTCGCCCAACATTG 59.791 57.895 0.00 0.00 36.61 2.82
2809 3295 2.126502 CGGTTCGCCCAACATTGC 60.127 61.111 0.00 0.00 36.61 3.56
2810 3296 2.625823 CGGTTCGCCCAACATTGCT 61.626 57.895 0.00 0.00 36.61 3.91
2811 3297 1.080569 GGTTCGCCCAACATTGCTG 60.081 57.895 0.00 0.00 36.61 4.41
2812 3298 1.659794 GTTCGCCCAACATTGCTGT 59.340 52.632 0.00 0.00 37.12 4.40
2813 3299 0.031994 GTTCGCCCAACATTGCTGTT 59.968 50.000 0.00 0.00 46.54 3.16
2814 3300 1.268352 GTTCGCCCAACATTGCTGTTA 59.732 47.619 0.00 0.00 43.76 2.41
2815 3301 1.610363 TCGCCCAACATTGCTGTTAA 58.390 45.000 0.00 0.00 43.76 2.01
2816 3302 1.539388 TCGCCCAACATTGCTGTTAAG 59.461 47.619 0.00 0.00 43.76 1.85
2833 3319 3.834732 AGCTTCGCTTGGTATCGTT 57.165 47.368 0.00 0.00 33.89 3.85
2834 3320 2.953466 AGCTTCGCTTGGTATCGTTA 57.047 45.000 0.00 0.00 33.89 3.18
2835 3321 3.241067 AGCTTCGCTTGGTATCGTTAA 57.759 42.857 0.00 0.00 33.89 2.01
2836 3322 3.592059 AGCTTCGCTTGGTATCGTTAAA 58.408 40.909 0.00 0.00 33.89 1.52
2837 3323 4.189231 AGCTTCGCTTGGTATCGTTAAAT 58.811 39.130 0.00 0.00 33.89 1.40
2838 3324 5.353938 AGCTTCGCTTGGTATCGTTAAATA 58.646 37.500 0.00 0.00 33.89 1.40
2839 3325 5.989777 AGCTTCGCTTGGTATCGTTAAATAT 59.010 36.000 0.00 0.00 33.89 1.28
2840 3326 6.482308 AGCTTCGCTTGGTATCGTTAAATATT 59.518 34.615 0.00 0.00 33.89 1.28
2841 3327 6.790825 GCTTCGCTTGGTATCGTTAAATATTC 59.209 38.462 0.00 0.00 0.00 1.75
2842 3328 7.517734 GCTTCGCTTGGTATCGTTAAATATTCA 60.518 37.037 0.00 0.00 0.00 2.57
2843 3329 7.773864 TCGCTTGGTATCGTTAAATATTCAA 57.226 32.000 0.00 0.00 0.00 2.69
2844 3330 8.373048 TCGCTTGGTATCGTTAAATATTCAAT 57.627 30.769 0.00 0.00 0.00 2.57
2845 3331 9.478768 TCGCTTGGTATCGTTAAATATTCAATA 57.521 29.630 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.520492 ACTTAAAAATGAGTCACCCTGCTG 59.480 41.667 0.00 0.00 0.00 4.41
319 377 8.934507 AGCTAATTCACTTCACTACAGTTATC 57.065 34.615 0.00 0.00 0.00 1.75
326 386 4.636206 CCCCAAGCTAATTCACTTCACTAC 59.364 45.833 0.00 0.00 0.00 2.73
391 451 2.092753 AGGGATGCATGAGGTGTGTTAG 60.093 50.000 2.46 0.00 0.00 2.34
459 525 1.218450 GCTAGAGGGTAGAAGAGGGGT 59.782 57.143 0.00 0.00 0.00 4.95
521 620 0.675633 TGGCTGCTCCTTCTTTTTGC 59.324 50.000 0.00 0.00 35.26 3.68
569 708 4.664688 ACCAATCAAACCAGGAAGATCT 57.335 40.909 0.00 0.00 0.00 2.75
588 727 0.669932 TGCGCCATGAAATTGCAACC 60.670 50.000 4.18 0.00 34.03 3.77
590 729 0.033090 TGTGCGCCATGAAATTGCAA 59.967 45.000 4.18 0.00 34.03 4.08
618 757 8.551682 AGGAGATGGAGAGGAAATATATGATC 57.448 38.462 0.00 0.00 0.00 2.92
619 758 9.659135 CTAGGAGATGGAGAGGAAATATATGAT 57.341 37.037 0.00 0.00 0.00 2.45
646 785 6.601613 GGATCGATGAACCTGAGATCTAGTAT 59.398 42.308 0.54 0.00 38.15 2.12
649 788 4.157656 GGGATCGATGAACCTGAGATCTAG 59.842 50.000 0.54 0.00 38.15 2.43
650 789 4.082845 GGGATCGATGAACCTGAGATCTA 58.917 47.826 0.54 0.00 38.15 1.98
651 790 2.896685 GGGATCGATGAACCTGAGATCT 59.103 50.000 0.54 0.00 38.15 2.75
652 791 2.352225 CGGGATCGATGAACCTGAGATC 60.352 54.545 0.54 0.00 33.43 2.75
653 792 1.615883 CGGGATCGATGAACCTGAGAT 59.384 52.381 0.54 0.00 33.43 2.75
655 794 0.032678 CCGGGATCGATGAACCTGAG 59.967 60.000 0.54 0.00 33.43 3.35
728 903 1.683319 GGGGATTGGGAAACAGCTCTC 60.683 57.143 0.00 0.00 0.00 3.20
729 904 0.332972 GGGGATTGGGAAACAGCTCT 59.667 55.000 0.00 0.00 0.00 4.09
797 982 5.392057 GGAAGAAAACTAGCAGCAACCATAC 60.392 44.000 0.00 0.00 0.00 2.39
806 991 7.336427 AGAGATCAAATGGAAGAAAACTAGCAG 59.664 37.037 0.00 0.00 0.00 4.24
826 1019 9.897744 TTCATGTCAACACAAAATTAAGAGATC 57.102 29.630 0.00 0.00 35.64 2.75
827 1020 9.903682 CTTCATGTCAACACAAAATTAAGAGAT 57.096 29.630 0.00 0.00 35.64 2.75
828 1021 7.862372 GCTTCATGTCAACACAAAATTAAGAGA 59.138 33.333 0.00 0.00 35.64 3.10
829 1022 7.864379 AGCTTCATGTCAACACAAAATTAAGAG 59.136 33.333 0.00 0.00 35.64 2.85
830 1023 7.715657 AGCTTCATGTCAACACAAAATTAAGA 58.284 30.769 0.00 0.00 35.64 2.10
831 1024 7.935338 AGCTTCATGTCAACACAAAATTAAG 57.065 32.000 0.00 0.00 35.64 1.85
832 1025 8.196771 AGAAGCTTCATGTCAACACAAAATTAA 58.803 29.630 27.57 0.00 35.64 1.40
833 1026 7.715657 AGAAGCTTCATGTCAACACAAAATTA 58.284 30.769 27.57 0.00 35.64 1.40
834 1027 6.576185 AGAAGCTTCATGTCAACACAAAATT 58.424 32.000 27.57 0.00 35.64 1.82
835 1028 6.040166 AGAGAAGCTTCATGTCAACACAAAAT 59.960 34.615 27.57 1.23 35.64 1.82
890 1087 1.667724 GTCTTCTTCACCATGATGCCG 59.332 52.381 0.00 0.00 0.00 5.69
958 1197 4.978099 TCTGTGCTTCCTTTCTTGATCTT 58.022 39.130 0.00 0.00 0.00 2.40
1107 1378 4.257810 TCCCCGTCCACCTTGGGA 62.258 66.667 0.00 0.00 46.41 4.37
1242 1513 3.645268 GAAGATGGGCGGCTTGGGT 62.645 63.158 9.56 0.00 0.00 4.51
1725 1996 1.832912 GGCCATCATCGGAGGAAGT 59.167 57.895 0.00 0.00 0.00 3.01
1841 2112 2.055689 TAGCTAGTAGGGCGGCCGTA 62.056 60.000 28.70 16.93 34.52 4.02
1868 2139 3.129871 GTCCTGACTGATTGATGCTAGC 58.870 50.000 8.10 8.10 0.00 3.42
1869 2140 4.669206 AGTCCTGACTGATTGATGCTAG 57.331 45.455 0.00 0.00 40.75 3.42
2221 2586 1.635487 TCACCATTCCTTCTTCCCCTG 59.365 52.381 0.00 0.00 0.00 4.45
2251 2729 5.046529 TGCAATTGCGTGAAACAAACTATT 58.953 33.333 24.58 0.00 45.83 1.73
2256 2734 4.330894 TGAAATGCAATTGCGTGAAACAAA 59.669 33.333 25.23 4.82 45.83 2.83
2265 2743 1.652124 GCTCACTGAAATGCAATTGCG 59.348 47.619 24.58 12.05 45.83 4.85
2275 2753 1.141657 AGGCTCTTGTGCTCACTGAAA 59.858 47.619 1.47 0.00 0.00 2.69
2318 2800 5.389859 TGCGAGAAATGTGGAATTCATTT 57.610 34.783 7.93 5.59 44.67 2.32
2349 2831 5.453198 CCCAAGCAAAACTGGTTAATCTTGT 60.453 40.000 10.94 0.00 0.00 3.16
2424 2906 9.460906 AGTGACTCGAGTAAAGTTTAGTTTAAG 57.539 33.333 20.09 5.60 0.00 1.85
2489 2974 5.016831 GTGGGAAGAAATTCATGTAACCCT 58.983 41.667 0.00 0.00 36.20 4.34
2506 2991 3.788227 ACTGTGCTAGAAATGTGGGAA 57.212 42.857 0.00 0.00 0.00 3.97
2508 2993 4.278170 TCAAAACTGTGCTAGAAATGTGGG 59.722 41.667 0.00 0.00 0.00 4.61
2567 3053 2.426522 ACCTGATGAAATGACCACACG 58.573 47.619 0.00 0.00 0.00 4.49
2594 3080 3.381272 GGGATCATGCGAATCAAAAAGGA 59.619 43.478 0.00 0.00 0.00 3.36
2642 3128 8.540388 ACATGTAATTGTACCTAGTTCTCATGT 58.460 33.333 0.00 0.00 37.00 3.21
2643 3129 8.948631 ACATGTAATTGTACCTAGTTCTCATG 57.051 34.615 0.00 0.00 35.45 3.07
2644 3130 9.959721 AAACATGTAATTGTACCTAGTTCTCAT 57.040 29.630 0.00 0.00 0.00 2.90
2645 3131 9.787435 AAAACATGTAATTGTACCTAGTTCTCA 57.213 29.630 0.00 0.00 0.00 3.27
2675 3161 8.371770 TGCGTTTTGCTATACATTCATGTATA 57.628 30.769 15.72 15.72 46.47 1.47
2676 3162 7.258022 TGCGTTTTGCTATACATTCATGTAT 57.742 32.000 15.21 15.21 46.83 2.29
2677 3163 6.670077 TGCGTTTTGCTATACATTCATGTA 57.330 33.333 2.13 2.13 45.01 2.29
2678 3164 5.559427 TGCGTTTTGCTATACATTCATGT 57.441 34.783 0.00 0.00 46.63 3.21
2679 3165 8.732413 ATTATGCGTTTTGCTATACATTCATG 57.268 30.769 0.00 0.00 46.63 3.07
2680 3166 9.398170 GAATTATGCGTTTTGCTATACATTCAT 57.602 29.630 0.00 0.00 46.63 2.57
2681 3167 7.860373 GGAATTATGCGTTTTGCTATACATTCA 59.140 33.333 0.00 0.00 46.63 2.57
2682 3168 7.059488 CGGAATTATGCGTTTTGCTATACATTC 59.941 37.037 0.00 0.00 46.63 2.67
2683 3169 6.855914 CGGAATTATGCGTTTTGCTATACATT 59.144 34.615 0.00 0.00 46.63 2.71
2684 3170 6.370593 CGGAATTATGCGTTTTGCTATACAT 58.629 36.000 0.00 0.00 46.63 2.29
2685 3171 5.743467 CGGAATTATGCGTTTTGCTATACA 58.257 37.500 0.00 0.00 46.63 2.29
2697 3183 1.334059 GCCATGTGACGGAATTATGCG 60.334 52.381 0.00 0.00 46.87 4.73
2698 3184 1.675483 TGCCATGTGACGGAATTATGC 59.325 47.619 0.00 0.00 0.00 3.14
2699 3185 2.286359 CGTGCCATGTGACGGAATTATG 60.286 50.000 5.97 0.00 31.84 1.90
2700 3186 1.939934 CGTGCCATGTGACGGAATTAT 59.060 47.619 5.97 0.00 31.84 1.28
2701 3187 1.364721 CGTGCCATGTGACGGAATTA 58.635 50.000 5.97 0.00 31.84 1.40
2702 3188 2.170738 CGTGCCATGTGACGGAATT 58.829 52.632 5.97 0.00 31.84 2.17
2703 3189 3.889227 CGTGCCATGTGACGGAAT 58.111 55.556 5.97 0.00 31.84 3.01
2707 3193 4.697756 ACCCCGTGCCATGTGACG 62.698 66.667 6.74 6.74 35.31 4.35
2708 3194 1.901464 AAACCCCGTGCCATGTGAC 60.901 57.895 0.00 0.00 0.00 3.67
2709 3195 1.900981 CAAACCCCGTGCCATGTGA 60.901 57.895 0.00 0.00 0.00 3.58
2710 3196 2.199652 ACAAACCCCGTGCCATGTG 61.200 57.895 0.00 0.00 0.00 3.21
2711 3197 2.197324 ACAAACCCCGTGCCATGT 59.803 55.556 0.00 0.00 0.00 3.21
2712 3198 2.650196 CACAAACCCCGTGCCATG 59.350 61.111 0.00 0.00 0.00 3.66
2713 3199 2.600173 CCACAAACCCCGTGCCAT 60.600 61.111 0.00 0.00 32.85 4.40
2714 3200 4.130554 ACCACAAACCCCGTGCCA 62.131 61.111 0.00 0.00 32.85 4.92
2715 3201 3.601685 CACCACAAACCCCGTGCC 61.602 66.667 0.00 0.00 32.85 5.01
2716 3202 3.601685 CCACCACAAACCCCGTGC 61.602 66.667 0.00 0.00 32.85 5.34
2717 3203 1.324005 AAACCACCACAAACCCCGTG 61.324 55.000 0.00 0.00 0.00 4.94
2718 3204 0.615261 AAAACCACCACAAACCCCGT 60.615 50.000 0.00 0.00 0.00 5.28
2719 3205 0.179097 CAAAACCACCACAAACCCCG 60.179 55.000 0.00 0.00 0.00 5.73
2720 3206 0.906066 ACAAAACCACCACAAACCCC 59.094 50.000 0.00 0.00 0.00 4.95
2721 3207 1.406205 CCACAAAACCACCACAAACCC 60.406 52.381 0.00 0.00 0.00 4.11
2722 3208 1.550976 TCCACAAAACCACCACAAACC 59.449 47.619 0.00 0.00 0.00 3.27
2723 3209 3.535280 ATCCACAAAACCACCACAAAC 57.465 42.857 0.00 0.00 0.00 2.93
2724 3210 5.144100 AGATATCCACAAAACCACCACAAA 58.856 37.500 0.00 0.00 0.00 2.83
2725 3211 4.735369 AGATATCCACAAAACCACCACAA 58.265 39.130 0.00 0.00 0.00 3.33
2726 3212 4.380843 AGATATCCACAAAACCACCACA 57.619 40.909 0.00 0.00 0.00 4.17
2727 3213 5.010617 ACAAAGATATCCACAAAACCACCAC 59.989 40.000 0.00 0.00 0.00 4.16
2728 3214 5.144100 ACAAAGATATCCACAAAACCACCA 58.856 37.500 0.00 0.00 0.00 4.17
2729 3215 5.619086 CGACAAAGATATCCACAAAACCACC 60.619 44.000 0.00 0.00 0.00 4.61
2730 3216 5.048991 ACGACAAAGATATCCACAAAACCAC 60.049 40.000 0.00 0.00 0.00 4.16
2731 3217 5.049060 CACGACAAAGATATCCACAAAACCA 60.049 40.000 0.00 0.00 0.00 3.67
2732 3218 5.180492 TCACGACAAAGATATCCACAAAACC 59.820 40.000 0.00 0.00 0.00 3.27
2733 3219 6.236017 TCACGACAAAGATATCCACAAAAC 57.764 37.500 0.00 0.00 0.00 2.43
2734 3220 5.411361 CCTCACGACAAAGATATCCACAAAA 59.589 40.000 0.00 0.00 0.00 2.44
2735 3221 4.935205 CCTCACGACAAAGATATCCACAAA 59.065 41.667 0.00 0.00 0.00 2.83
2736 3222 4.221924 TCCTCACGACAAAGATATCCACAA 59.778 41.667 0.00 0.00 0.00 3.33
2737 3223 3.767131 TCCTCACGACAAAGATATCCACA 59.233 43.478 0.00 0.00 0.00 4.17
2738 3224 4.386867 TCCTCACGACAAAGATATCCAC 57.613 45.455 0.00 0.00 0.00 4.02
2739 3225 4.709886 TCTTCCTCACGACAAAGATATCCA 59.290 41.667 0.00 0.00 0.00 3.41
2740 3226 5.263968 TCTTCCTCACGACAAAGATATCC 57.736 43.478 0.00 0.00 0.00 2.59
2741 3227 5.923684 GGATCTTCCTCACGACAAAGATATC 59.076 44.000 0.00 0.00 38.30 1.63
2742 3228 5.600484 AGGATCTTCCTCACGACAAAGATAT 59.400 40.000 0.00 0.00 45.66 1.63
2743 3229 4.956700 AGGATCTTCCTCACGACAAAGATA 59.043 41.667 0.00 0.00 45.66 1.98
2744 3230 3.772025 AGGATCTTCCTCACGACAAAGAT 59.228 43.478 0.00 0.00 45.66 2.40
2745 3231 3.165875 AGGATCTTCCTCACGACAAAGA 58.834 45.455 0.00 0.00 45.66 2.52
2746 3232 3.601443 AGGATCTTCCTCACGACAAAG 57.399 47.619 0.00 0.00 45.66 2.77
2781 3267 1.603326 GGGCGAACCGTCTTACAAAAA 59.397 47.619 0.00 0.00 36.48 1.94
2782 3268 1.228533 GGGCGAACCGTCTTACAAAA 58.771 50.000 0.00 0.00 36.48 2.44
2783 3269 0.106335 TGGGCGAACCGTCTTACAAA 59.894 50.000 0.00 0.00 44.64 2.83
2784 3270 0.106335 TTGGGCGAACCGTCTTACAA 59.894 50.000 0.00 0.00 44.64 2.41
2785 3271 0.600782 GTTGGGCGAACCGTCTTACA 60.601 55.000 0.30 0.00 44.64 2.41
2786 3272 0.600782 TGTTGGGCGAACCGTCTTAC 60.601 55.000 9.96 0.00 44.64 2.34
2787 3273 0.322322 ATGTTGGGCGAACCGTCTTA 59.678 50.000 9.96 0.00 44.64 2.10
2788 3274 0.536460 AATGTTGGGCGAACCGTCTT 60.536 50.000 9.96 0.00 44.64 3.01
2789 3275 1.072505 AATGTTGGGCGAACCGTCT 59.927 52.632 9.96 0.00 44.64 4.18
2790 3276 1.209127 CAATGTTGGGCGAACCGTC 59.791 57.895 9.96 0.00 44.64 4.79
2791 3277 2.914908 GCAATGTTGGGCGAACCGT 61.915 57.895 9.96 0.00 44.64 4.83
2792 3278 2.126502 GCAATGTTGGGCGAACCG 60.127 61.111 9.96 0.05 44.64 4.44
2793 3279 1.080569 CAGCAATGTTGGGCGAACC 60.081 57.895 9.96 0.00 40.81 3.62
2794 3280 0.031994 AACAGCAATGTTGGGCGAAC 59.968 50.000 5.34 5.34 34.54 3.95
2795 3281 1.610363 TAACAGCAATGTTGGGCGAA 58.390 45.000 1.55 0.00 33.59 4.70
2796 3282 1.539388 CTTAACAGCAATGTTGGGCGA 59.461 47.619 1.55 0.00 33.59 5.54
2797 3283 1.981254 CTTAACAGCAATGTTGGGCG 58.019 50.000 1.55 0.00 33.59 6.13
2798 3284 1.713597 GCTTAACAGCAATGTTGGGC 58.286 50.000 1.55 4.61 46.49 5.36
2817 3303 7.847487 TGAATATTTAACGATACCAAGCGAAG 58.153 34.615 0.00 0.00 38.08 3.79
2818 3304 7.773864 TGAATATTTAACGATACCAAGCGAA 57.226 32.000 0.00 0.00 38.08 4.70
2819 3305 7.773864 TTGAATATTTAACGATACCAAGCGA 57.226 32.000 0.00 0.00 38.08 4.93


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

AutoCloner maintained by Alex Coulton.