Multiple sequence alignment - TraesCS3A01G523600

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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 TraesCS3A01G523600 chr3A 100.000 5519 0 0 1 5519 739117258 739122776 0.000000e+00 10192
1 TraesCS3A01G523600 chr3A 100.000 40 0 0 2758 2797 739119978 739120017 2.130000e-09 75
2 TraesCS3A01G523600 chr3A 100.000 40 0 0 2721 2760 739120015 739120054 2.130000e-09 75
3 TraesCS3A01G523600 chr3D 94.718 2802 78 24 2758 5519 606860782 606863553 0.000000e+00 4290
4 TraesCS3A01G523600 chr3D 92.422 1953 81 25 844 2763 606858906 606860824 0.000000e+00 2724
5 TraesCS3A01G523600 chr3D 94.257 296 10 4 535 830 606858527 606858815 3.920000e-121 446
6 TraesCS3A01G523600 chr3D 94.466 253 4 6 286 538 606858260 606858502 1.120000e-101 381
7 TraesCS3A01G523600 chrUn 93.078 2817 120 22 2758 5519 42442465 42439669 0.000000e+00 4052
8 TraesCS3A01G523600 chrUn 93.445 1968 85 22 828 2763 42444378 42442423 0.000000e+00 2880
9 TraesCS3A01G523600 chrUn 93.242 1968 88 23 828 2763 327871685 327869731 0.000000e+00 2856
10 TraesCS3A01G523600 chrUn 93.498 446 16 5 78 522 42445232 42444799 0.000000e+00 651
11 TraesCS3A01G523600 chrUn 93.458 428 15 5 96 522 327872521 327872106 1.690000e-174 623
12 TraesCS3A01G523600 chrUn 93.919 296 11 4 535 830 327872055 327871767 1.820000e-119 440
13 TraesCS3A01G523600 chrUn 93.581 296 12 4 535 830 42444748 42444460 8.490000e-118 435
14 TraesCS3A01G523600 chrUn 92.424 132 2 2 2758 2881 327869773 327869642 1.220000e-41 182
15 TraesCS3A01G523600 chr5B 82.335 2004 251 55 835 2763 185218727 185220702 0.000000e+00 1644
16 TraesCS3A01G523600 chr5B 81.910 1183 133 39 3369 4523 185221248 185222377 0.000000e+00 924
17 TraesCS3A01G523600 chr5B 81.611 571 66 21 2762 3309 185220664 185221218 2.360000e-118 436
18 TraesCS3A01G523600 chr5D 85.244 1064 126 19 828 1881 173590704 173589662 0.000000e+00 1066
19 TraesCS3A01G523600 chr5D 81.065 1183 136 38 3369 4523 173588172 173587050 0.000000e+00 863
20 TraesCS3A01G523600 chr5D 82.888 935 115 29 1867 2763 173589645 173588718 0.000000e+00 798
21 TraesCS3A01G523600 chr5D 81.818 572 63 25 2762 3309 173588756 173588202 5.070000e-120 442
22 TraesCS3A01G523600 chr5A 84.507 1065 134 18 828 1881 194455215 194454171 0.000000e+00 1024
23 TraesCS3A01G523600 chr5A 81.350 1185 136 34 3369 4523 194452680 194451551 0.000000e+00 885
24 TraesCS3A01G523600 chr5A 82.265 936 120 28 1867 2763 194454154 194453226 0.000000e+00 767
25 TraesCS3A01G523600 chr5A 81.786 571 65 21 2762 3309 194453264 194452710 5.070000e-120 442


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 TraesCS3A01G523600 chr3A 739117258 739122776 5518 False 3447.333333 10192 100.00000 1 5519 3 chr3A.!!$F1 5518
1 TraesCS3A01G523600 chr3D 606858260 606863553 5293 False 1960.250000 4290 93.96575 286 5519 4 chr3D.!!$F1 5233
2 TraesCS3A01G523600 chrUn 42439669 42445232 5563 True 2004.500000 4052 93.40050 78 5519 4 chrUn.!!$R1 5441
3 TraesCS3A01G523600 chrUn 327869642 327872521 2879 True 1025.250000 2856 93.26075 96 2881 4 chrUn.!!$R2 2785
4 TraesCS3A01G523600 chr5B 185218727 185222377 3650 False 1001.333333 1644 81.95200 835 4523 3 chr5B.!!$F1 3688
5 TraesCS3A01G523600 chr5D 173587050 173590704 3654 True 792.250000 1066 82.75375 828 4523 4 chr5D.!!$R1 3695
6 TraesCS3A01G523600 chr5A 194451551 194455215 3664 True 779.500000 1024 82.47700 828 4523 4 chr5A.!!$R1 3695

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
504 507 0.322648 GGCTGCCCTTTCTGCATTTT 59.677 50.000 7.66 0.00 38.22 1.82 F
1431 1569 0.112412 CCCACACAAAAGGTAGGGCT 59.888 55.000 0.00 0.00 37.25 5.19 F
2095 2271 1.003464 TGTGCTTCCTATGCTGCAGAA 59.997 47.619 20.43 7.68 36.03 3.02 F
3408 3655 0.747644 CCATTGGCGCCAGTGACATA 60.748 55.000 43.07 23.94 36.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1961 0.039708 GACTGCCAGCAAAGAAGTGC 60.040 55.000 0.00 0.0 45.28 4.40 R
2615 2832 1.183030 TCCAACGAGGTCGGATGTGT 61.183 55.000 4.13 0.0 44.95 3.72 R
4012 4272 1.884579 CATCTTGCAAGGAACACTGCT 59.115 47.619 25.73 0.0 0.00 4.24 R
4627 4902 1.139455 ACAACTCGAAAAAGGTCGGGA 59.861 47.619 0.78 0.0 44.57 5.14 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
26 27 4.715523 CCGCCCTTTCCGAGCCAA 62.716 66.667 0.00 0.00 0.00 4.52
27 28 3.127533 CGCCCTTTCCGAGCCAAG 61.128 66.667 0.00 0.00 0.00 3.61
28 29 2.351276 GCCCTTTCCGAGCCAAGA 59.649 61.111 0.00 0.00 0.00 3.02
29 30 1.303317 GCCCTTTCCGAGCCAAGAA 60.303 57.895 0.00 0.00 0.00 2.52
30 31 1.308783 GCCCTTTCCGAGCCAAGAAG 61.309 60.000 0.00 0.00 0.00 2.85
31 32 1.308783 CCCTTTCCGAGCCAAGAAGC 61.309 60.000 0.00 0.00 0.00 3.86
32 33 1.308783 CCTTTCCGAGCCAAGAAGCC 61.309 60.000 0.00 0.00 0.00 4.35
33 34 1.639298 CTTTCCGAGCCAAGAAGCCG 61.639 60.000 0.00 0.00 0.00 5.52
34 35 3.605749 TTCCGAGCCAAGAAGCCGG 62.606 63.158 0.00 0.00 43.58 6.13
58 59 4.803426 CTGCTCCCCGTCACGCTC 62.803 72.222 0.00 0.00 0.00 5.03
60 61 4.500116 GCTCCCCGTCACGCTCTC 62.500 72.222 0.00 0.00 0.00 3.20
61 62 4.180946 CTCCCCGTCACGCTCTCG 62.181 72.222 0.00 0.00 42.43 4.04
73 74 4.856607 CTCTCGGCGAACGGCTCC 62.857 72.222 12.13 0.00 44.45 4.70
152 153 1.712977 ATCGACGGCGGTACAGTCTC 61.713 60.000 12.58 0.00 40.88 3.36
243 244 0.685097 CCCGGTGAGTTCTTTCTCCA 59.315 55.000 0.00 0.00 33.93 3.86
247 248 2.035961 CGGTGAGTTCTTTCTCCACTCA 59.964 50.000 0.00 0.00 43.71 3.41
248 249 3.306364 CGGTGAGTTCTTTCTCCACTCAT 60.306 47.826 4.64 0.00 46.56 2.90
253 254 1.584724 TCTTTCTCCACTCATCCCCC 58.415 55.000 0.00 0.00 0.00 5.40
254 255 1.203428 TCTTTCTCCACTCATCCCCCA 60.203 52.381 0.00 0.00 0.00 4.96
255 256 1.849039 CTTTCTCCACTCATCCCCCAT 59.151 52.381 0.00 0.00 0.00 4.00
256 257 2.887454 TTCTCCACTCATCCCCCATA 57.113 50.000 0.00 0.00 0.00 2.74
257 258 2.405618 TCTCCACTCATCCCCCATAG 57.594 55.000 0.00 0.00 0.00 2.23
258 259 1.866269 TCTCCACTCATCCCCCATAGA 59.134 52.381 0.00 0.00 0.00 1.98
259 260 2.456340 TCTCCACTCATCCCCCATAGAT 59.544 50.000 0.00 0.00 0.00 1.98
260 261 2.570752 CTCCACTCATCCCCCATAGATG 59.429 54.545 0.00 0.00 42.08 2.90
261 262 1.004044 CCACTCATCCCCCATAGATGC 59.996 57.143 0.00 0.00 40.79 3.91
262 263 1.983691 CACTCATCCCCCATAGATGCT 59.016 52.381 0.00 0.00 40.79 3.79
263 264 3.176411 CACTCATCCCCCATAGATGCTA 58.824 50.000 0.00 0.00 40.79 3.49
309 310 3.740832 CCGAATTTGGGCTTTCTTGTTTC 59.259 43.478 3.45 0.00 0.00 2.78
504 507 0.322648 GGCTGCCCTTTCTGCATTTT 59.677 50.000 7.66 0.00 38.22 1.82
505 508 1.271001 GGCTGCCCTTTCTGCATTTTT 60.271 47.619 7.66 0.00 38.22 1.94
570 611 5.914085 ATAGATGCACATTTCTTCTACGC 57.086 39.130 0.00 0.00 0.00 4.42
575 616 2.333926 CACATTTCTTCTACGCGGTCA 58.666 47.619 12.47 0.00 0.00 4.02
577 618 2.735134 ACATTTCTTCTACGCGGTCAAC 59.265 45.455 12.47 0.00 0.00 3.18
580 621 1.990799 TCTTCTACGCGGTCAACATG 58.009 50.000 12.47 0.00 0.00 3.21
581 622 1.542472 TCTTCTACGCGGTCAACATGA 59.458 47.619 12.47 0.00 0.00 3.07
582 623 2.165641 TCTTCTACGCGGTCAACATGAT 59.834 45.455 12.47 0.00 0.00 2.45
583 624 2.665649 TCTACGCGGTCAACATGATT 57.334 45.000 12.47 0.00 0.00 2.57
584 625 2.967362 TCTACGCGGTCAACATGATTT 58.033 42.857 12.47 0.00 0.00 2.17
585 626 3.331150 TCTACGCGGTCAACATGATTTT 58.669 40.909 12.47 0.00 0.00 1.82
586 627 2.611974 ACGCGGTCAACATGATTTTC 57.388 45.000 12.47 0.00 0.00 2.29
587 628 2.151202 ACGCGGTCAACATGATTTTCT 58.849 42.857 12.47 0.00 0.00 2.52
588 629 2.552315 ACGCGGTCAACATGATTTTCTT 59.448 40.909 12.47 0.00 0.00 2.52
589 630 3.749088 ACGCGGTCAACATGATTTTCTTA 59.251 39.130 12.47 0.00 0.00 2.10
595 636 6.585702 CGGTCAACATGATTTTCTTATTGCAA 59.414 34.615 0.00 0.00 0.00 4.08
677 718 8.414003 AGAAAGAACTACCTTTTCCACAATTTC 58.586 33.333 0.00 0.00 36.58 2.17
711 752 8.689061 ACAACGTCACCTGTATTCATATACTTA 58.311 33.333 0.00 0.00 37.97 2.24
1011 1136 1.188863 AGGCTTAAATGGCTGCAAGG 58.811 50.000 0.50 0.00 41.44 3.61
1142 1270 1.937899 CAGAACTGAACGAAAACCGGT 59.062 47.619 0.00 0.00 43.51 5.28
1279 1407 3.951306 TGTGCAAACTCGTTCAGAAATG 58.049 40.909 0.00 0.00 0.00 2.32
1375 1513 6.825213 TGATGATTACCTTTTCCTGATGTCAG 59.175 38.462 3.01 3.01 43.40 3.51
1431 1569 0.112412 CCCACACAAAAGGTAGGGCT 59.888 55.000 0.00 0.00 37.25 5.19
1437 1575 4.007659 ACACAAAAGGTAGGGCTAAATCG 58.992 43.478 0.00 0.00 0.00 3.34
1821 1961 5.766222 AGCTTCTCTTTGCTTGTAATGTTG 58.234 37.500 0.00 0.00 35.86 3.33
1893 2064 2.666272 TGGTCTTTATGTGGCCACAA 57.334 45.000 40.48 26.16 45.41 3.33
1906 2078 5.305585 TGTGGCCACAAAACTTAAAACAAA 58.694 33.333 36.10 6.71 38.56 2.83
1980 2153 9.855021 GCAGGTATTTATGTATTCTGTTTTGTT 57.145 29.630 0.00 0.00 0.00 2.83
2001 2177 4.240881 TGGGCAGCATCTAAAGAATCTT 57.759 40.909 0.00 0.00 0.00 2.40
2095 2271 1.003464 TGTGCTTCCTATGCTGCAGAA 59.997 47.619 20.43 7.68 36.03 3.02
2110 2286 5.355071 TGCTGCAGAAATATACAGAAACCTG 59.645 40.000 20.43 0.00 37.67 4.00
2133 2309 5.071653 TGATGGCTGCAGAGGTATGTTTATA 59.928 40.000 20.43 0.00 0.00 0.98
2138 2314 6.148480 GGCTGCAGAGGTATGTTTATATTCTG 59.852 42.308 20.43 0.00 36.93 3.02
2228 2404 7.682981 GCCTTATTAAGCTGGGAAGAATTTCAG 60.683 40.741 0.00 0.00 34.90 3.02
2248 2424 5.415221 TCAGTTTTGGATGTTTGTGTTTCC 58.585 37.500 0.00 0.00 0.00 3.13
2250 2426 5.874261 CAGTTTTGGATGTTTGTGTTTCCTT 59.126 36.000 0.00 0.00 0.00 3.36
2251 2427 6.035975 CAGTTTTGGATGTTTGTGTTTCCTTC 59.964 38.462 0.00 0.00 0.00 3.46
2252 2428 5.667539 TTTGGATGTTTGTGTTTCCTTCA 57.332 34.783 0.00 0.00 0.00 3.02
2253 2429 4.647424 TGGATGTTTGTGTTTCCTTCAC 57.353 40.909 0.00 0.00 36.48 3.18
2258 2449 7.721842 TGGATGTTTGTGTTTCCTTCACTATAA 59.278 33.333 0.00 0.00 36.83 0.98
2414 2608 6.007076 TGATTGGCTTGTTGAGGTTTGTATA 58.993 36.000 0.00 0.00 0.00 1.47
2415 2609 6.663093 TGATTGGCTTGTTGAGGTTTGTATAT 59.337 34.615 0.00 0.00 0.00 0.86
2462 2661 7.601886 TGCATAAATAGTCCAACCATGTTTTTG 59.398 33.333 0.00 0.00 0.00 2.44
2482 2686 7.514784 TTTTGAGACTGAACATCATCATTGT 57.485 32.000 0.00 0.00 0.00 2.71
2485 2689 5.640783 TGAGACTGAACATCATCATTGTCAC 59.359 40.000 0.00 0.00 30.66 3.67
2493 2697 6.187125 ACATCATCATTGTCACTTAACTGC 57.813 37.500 0.00 0.00 0.00 4.40
2494 2698 5.706833 ACATCATCATTGTCACTTAACTGCA 59.293 36.000 0.00 0.00 0.00 4.41
2615 2832 5.721960 AGAGAGGAATAGAGTGCAAGGTTTA 59.278 40.000 0.00 0.00 0.00 2.01
2624 2841 2.147958 GTGCAAGGTTTACACATCCGA 58.852 47.619 0.00 0.00 34.43 4.55
2630 2847 1.067354 GGTTTACACATCCGACCTCGT 60.067 52.381 0.00 0.00 37.74 4.18
2763 2982 4.763793 AGAAGTTTGAATCAGTGGTGATGG 59.236 41.667 0.00 0.00 43.04 3.51
2764 2983 4.371624 AGTTTGAATCAGTGGTGATGGA 57.628 40.909 0.00 0.00 43.04 3.41
2765 2984 4.330250 AGTTTGAATCAGTGGTGATGGAG 58.670 43.478 0.00 0.00 43.04 3.86
2766 2985 3.354948 TTGAATCAGTGGTGATGGAGG 57.645 47.619 0.00 0.00 43.04 4.30
2768 2987 3.117745 TGAATCAGTGGTGATGGAGGAT 58.882 45.455 0.00 0.00 43.04 3.24
2769 2988 3.524789 TGAATCAGTGGTGATGGAGGATT 59.475 43.478 0.00 0.00 43.04 3.01
2770 2989 4.018141 TGAATCAGTGGTGATGGAGGATTT 60.018 41.667 0.00 0.00 43.04 2.17
2771 2990 4.598036 ATCAGTGGTGATGGAGGATTTT 57.402 40.909 0.00 0.00 42.19 1.82
2772 2991 5.715439 ATCAGTGGTGATGGAGGATTTTA 57.285 39.130 0.00 0.00 42.19 1.52
2773 2992 5.715439 TCAGTGGTGATGGAGGATTTTAT 57.285 39.130 0.00 0.00 0.00 1.40
2774 2993 6.823286 TCAGTGGTGATGGAGGATTTTATA 57.177 37.500 0.00 0.00 0.00 0.98
2775 2994 7.392766 TCAGTGGTGATGGAGGATTTTATAT 57.607 36.000 0.00 0.00 0.00 0.86
2776 2995 7.226441 TCAGTGGTGATGGAGGATTTTATATG 58.774 38.462 0.00 0.00 0.00 1.78
2777 2996 7.072328 TCAGTGGTGATGGAGGATTTTATATGA 59.928 37.037 0.00 0.00 0.00 2.15
2778 2997 7.389884 CAGTGGTGATGGAGGATTTTATATGAG 59.610 40.741 0.00 0.00 0.00 2.90
2779 2998 7.293299 AGTGGTGATGGAGGATTTTATATGAGA 59.707 37.037 0.00 0.00 0.00 3.27
2780 2999 7.939039 GTGGTGATGGAGGATTTTATATGAGAA 59.061 37.037 0.00 0.00 0.00 2.87
2781 3000 8.159447 TGGTGATGGAGGATTTTATATGAGAAG 58.841 37.037 0.00 0.00 0.00 2.85
2782 3001 8.160106 GGTGATGGAGGATTTTATATGAGAAGT 58.840 37.037 0.00 0.00 0.00 3.01
2783 3002 9.566432 GTGATGGAGGATTTTATATGAGAAGTT 57.434 33.333 0.00 0.00 0.00 2.66
2787 3006 9.973661 TGGAGGATTTTATATGAGAAGTTTGAA 57.026 29.630 0.00 0.00 0.00 2.69
2795 3014 9.739276 TTTATATGAGAAGTTTGAATCAGTGGT 57.261 29.630 0.00 0.00 0.00 4.16
2796 3015 5.954296 ATGAGAAGTTTGAATCAGTGGTG 57.046 39.130 0.00 0.00 0.00 4.17
2797 3016 4.780815 TGAGAAGTTTGAATCAGTGGTGT 58.219 39.130 0.00 0.00 0.00 4.16
2804 3023 2.269023 TGAATCAGTGGTGTCCATCCT 58.731 47.619 0.00 0.00 35.28 3.24
2937 3166 1.137872 CAGAGGCCCTGTGATAGTGAC 59.862 57.143 0.52 0.00 38.10 3.67
2978 3213 4.008330 CAGTGATCTTCAGCACCAGAAAT 58.992 43.478 0.00 0.00 35.67 2.17
3028 3265 3.876320 GGAAACCTGCATTTTCTTTTGCA 59.124 39.130 16.45 0.00 46.03 4.08
3100 3337 7.766278 TCATGACTTCTTAGCTTATGAAGTTCC 59.234 37.037 21.32 14.10 46.66 3.62
3170 3407 9.900710 CTGTACCTCACTGTATATCTTATTGAC 57.099 37.037 0.00 0.00 0.00 3.18
3408 3655 0.747644 CCATTGGCGCCAGTGACATA 60.748 55.000 43.07 23.94 36.00 2.29
3997 4257 4.278419 AGTTTCCTGAAATTTCACCCTTCG 59.722 41.667 16.91 6.35 32.90 3.79
4072 4332 0.463654 TGCCATGGGTTCGTATGAGC 60.464 55.000 15.13 0.00 0.00 4.26
4176 4446 6.151144 AGCATTACACCTCATACAAAAGTTCC 59.849 38.462 0.00 0.00 0.00 3.62
4230 4500 2.203394 CAGCAGGGCAACACCAGT 60.203 61.111 0.00 0.00 42.05 4.00
4312 4582 1.133976 ACCACTTGCTGCTTGAGTTCT 60.134 47.619 0.00 0.00 0.00 3.01
4317 4587 3.812053 ACTTGCTGCTTGAGTTCTGTAAG 59.188 43.478 0.00 0.00 32.93 2.34
4336 4606 2.440409 AGCAGAACACCACATGAATCC 58.560 47.619 0.00 0.00 0.00 3.01
4440 4711 3.912496 TGTGTAGCCAATATGCTGTCT 57.088 42.857 0.00 0.00 42.77 3.41
4462 4733 2.182791 CGATGCCTGTGTCGCTCT 59.817 61.111 0.00 0.00 0.00 4.09
4463 4734 1.446792 CGATGCCTGTGTCGCTCTT 60.447 57.895 0.00 0.00 0.00 2.85
4464 4735 1.416813 CGATGCCTGTGTCGCTCTTC 61.417 60.000 0.00 0.00 0.00 2.87
4626 4901 5.533154 TCCGATCTGGTTGTGTTGTTATTTT 59.467 36.000 3.97 0.00 39.52 1.82
4627 4902 6.039941 TCCGATCTGGTTGTGTTGTTATTTTT 59.960 34.615 3.97 0.00 39.52 1.94
4645 4921 2.625695 TTCCCGACCTTTTTCGAGTT 57.374 45.000 0.00 0.00 41.78 3.01
4865 5148 3.020274 AGTGCTCGCTCTTGAGATTAGA 58.980 45.455 1.30 0.00 38.28 2.10
5007 5295 3.186909 GCTGAACACAAGGGTTTGTTTC 58.813 45.455 0.00 0.91 45.01 2.78
5013 5305 7.262048 TGAACACAAGGGTTTGTTTCTTTATC 58.738 34.615 0.00 0.00 45.01 1.75
5024 5316 8.325282 GGTTTGTTTCTTTATCGTTTCCTTTTG 58.675 33.333 0.00 0.00 0.00 2.44
5048 5342 3.198068 TGCGATGAGATGAAACTAAGCC 58.802 45.455 0.00 0.00 0.00 4.35
5081 5375 4.322801 CCAATCTTTCGTACTCCCTCTGTT 60.323 45.833 0.00 0.00 0.00 3.16
5085 5379 3.655276 TTCGTACTCCCTCTGTTGTTC 57.345 47.619 0.00 0.00 0.00 3.18
5134 5433 4.873746 TTTGAGACAGAGGGAGTAGTTG 57.126 45.455 0.00 0.00 0.00 3.16
5144 5443 4.162509 AGAGGGAGTAGTTGACTTTATGCC 59.837 45.833 0.00 0.00 39.06 4.40
5221 5521 6.371825 GGAAGTCATTTTCAGTCCGTAGAAAT 59.628 38.462 0.00 0.00 0.00 2.17
5222 5522 7.548075 GGAAGTCATTTTCAGTCCGTAGAAATA 59.452 37.037 0.00 0.00 0.00 1.40
5223 5523 8.480643 AAGTCATTTTCAGTCCGTAGAAATAG 57.519 34.615 0.00 0.00 0.00 1.73
5253 5576 4.893524 GGTTTAGAATTTGGGGATCGGAAT 59.106 41.667 0.00 0.00 0.00 3.01
5464 5789 3.111098 CCACGTTACGCCAGTAGTATTC 58.889 50.000 4.09 0.00 33.87 1.75
5470 5795 5.220931 CGTTACGCCAGTAGTATTCTAAGGT 60.221 44.000 0.00 0.00 33.87 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.308783 GCTTCTTGGCTCGGAAAGGG 61.309 60.000 0.00 0.00 0.00 3.95
13 14 1.308783 GGCTTCTTGGCTCGGAAAGG 61.309 60.000 0.00 0.00 38.32 3.11
14 15 1.639298 CGGCTTCTTGGCTCGGAAAG 61.639 60.000 0.00 0.00 39.32 2.62
15 16 1.671054 CGGCTTCTTGGCTCGGAAA 60.671 57.895 0.00 0.00 39.32 3.13
16 17 2.047274 CGGCTTCTTGGCTCGGAA 60.047 61.111 0.00 0.00 39.32 4.30
17 18 4.082523 CCGGCTTCTTGGCTCGGA 62.083 66.667 9.52 0.00 43.47 4.55
41 42 4.803426 GAGCGTGACGGGGAGCAG 62.803 72.222 7.25 0.00 0.00 4.24
43 44 4.500116 GAGAGCGTGACGGGGAGC 62.500 72.222 7.25 0.00 0.00 4.70
44 45 4.180946 CGAGAGCGTGACGGGGAG 62.181 72.222 7.25 0.00 0.00 4.30
56 57 4.856607 GGAGCCGTTCGCCGAGAG 62.857 72.222 0.00 0.00 39.56 3.20
144 145 3.255149 GGAACGACCAAGAAGAGACTGTA 59.745 47.826 0.00 0.00 38.79 2.74
152 153 1.983972 CGAGAGGAACGACCAAGAAG 58.016 55.000 0.00 0.00 42.04 2.85
243 244 2.429933 AGCATCTATGGGGGATGAGT 57.570 50.000 7.73 0.00 42.02 3.41
247 248 3.811152 AGGATAGCATCTATGGGGGAT 57.189 47.619 0.00 0.00 0.00 3.85
248 249 3.454858 GAAGGATAGCATCTATGGGGGA 58.545 50.000 0.00 0.00 0.00 4.81
253 254 3.931468 CGCAAGGAAGGATAGCATCTATG 59.069 47.826 0.00 0.00 0.00 2.23
254 255 3.618507 GCGCAAGGAAGGATAGCATCTAT 60.619 47.826 0.30 0.00 38.28 1.98
255 256 2.289072 GCGCAAGGAAGGATAGCATCTA 60.289 50.000 0.30 0.00 38.28 1.98
256 257 1.542108 GCGCAAGGAAGGATAGCATCT 60.542 52.381 0.30 0.00 38.28 2.90
257 258 0.871057 GCGCAAGGAAGGATAGCATC 59.129 55.000 0.30 0.00 38.28 3.91
258 259 0.882042 CGCGCAAGGAAGGATAGCAT 60.882 55.000 8.75 0.00 38.28 3.79
259 260 1.521457 CGCGCAAGGAAGGATAGCA 60.521 57.895 8.75 0.00 38.28 3.49
260 261 2.886782 GCGCGCAAGGAAGGATAGC 61.887 63.158 29.10 0.00 38.28 2.97
261 262 2.247437 GGCGCGCAAGGAAGGATAG 61.247 63.158 34.42 0.00 38.28 2.08
262 263 2.203015 GGCGCGCAAGGAAGGATA 60.203 61.111 34.42 0.00 38.28 2.59
309 310 5.928976 AGAAAACCCAAATCCTTTTCTTGG 58.071 37.500 0.00 0.00 39.95 3.61
467 469 3.376859 CAGCCGCCATCAAACTTAATACA 59.623 43.478 0.00 0.00 0.00 2.29
468 470 3.792124 GCAGCCGCCATCAAACTTAATAC 60.792 47.826 0.00 0.00 0.00 1.89
504 507 6.361433 TCATGTCCTTCAGGTAAGTGAAAAA 58.639 36.000 0.00 0.00 36.01 1.94
505 508 5.935945 TCATGTCCTTCAGGTAAGTGAAAA 58.064 37.500 0.00 0.00 36.01 2.29
565 606 3.370978 AGAAAATCATGTTGACCGCGTAG 59.629 43.478 4.92 0.00 0.00 3.51
570 611 6.092092 TGCAATAAGAAAATCATGTTGACCG 58.908 36.000 0.00 0.00 0.00 4.79
575 616 9.146984 CATGTCTTGCAATAAGAAAATCATGTT 57.853 29.630 0.00 0.00 29.64 2.71
577 618 8.592155 CACATGTCTTGCAATAAGAAAATCATG 58.408 33.333 0.00 6.63 35.21 3.07
580 621 7.092716 ACCACATGTCTTGCAATAAGAAAATC 58.907 34.615 0.00 0.00 0.00 2.17
581 622 6.996509 ACCACATGTCTTGCAATAAGAAAAT 58.003 32.000 0.00 0.00 0.00 1.82
582 623 6.403866 ACCACATGTCTTGCAATAAGAAAA 57.596 33.333 0.00 0.00 0.00 2.29
583 624 6.714810 ACTACCACATGTCTTGCAATAAGAAA 59.285 34.615 0.00 0.00 0.00 2.52
584 625 6.149308 CACTACCACATGTCTTGCAATAAGAA 59.851 38.462 0.00 0.00 0.00 2.52
585 626 5.643348 CACTACCACATGTCTTGCAATAAGA 59.357 40.000 0.00 0.00 0.00 2.10
586 627 5.163723 CCACTACCACATGTCTTGCAATAAG 60.164 44.000 0.00 0.00 0.00 1.73
587 628 4.699735 CCACTACCACATGTCTTGCAATAA 59.300 41.667 0.00 0.00 0.00 1.40
588 629 4.019771 TCCACTACCACATGTCTTGCAATA 60.020 41.667 0.00 0.00 0.00 1.90
589 630 3.084039 CCACTACCACATGTCTTGCAAT 58.916 45.455 0.00 0.00 0.00 3.56
595 636 4.431416 TTGTTTCCACTACCACATGTCT 57.569 40.909 0.00 0.00 0.00 3.41
677 718 4.091453 ACAGGTGACGTTGTTCTTTTTG 57.909 40.909 0.00 0.00 0.00 2.44
711 752 6.260870 AGATGCACGACTCGAATTATATCT 57.739 37.500 5.20 3.21 0.00 1.98
856 981 4.023792 TGAAACATCATGCAACACTCTGTC 60.024 41.667 0.00 0.00 0.00 3.51
1083 1208 3.558674 AGGCACTCCAAATCTTCCG 57.441 52.632 0.00 0.00 33.74 4.30
1142 1270 2.803956 CGTTTCGCCTTTCCTTTAGTCA 59.196 45.455 0.00 0.00 0.00 3.41
1279 1407 0.321122 AGCTTAGTCACAGCAGTGCC 60.321 55.000 12.58 0.00 45.49 5.01
1431 1569 5.458452 CACTGCTTGTTTTTGCTTCGATTTA 59.542 36.000 0.00 0.00 0.00 1.40
1437 1575 1.256117 CGCACTGCTTGTTTTTGCTTC 59.744 47.619 0.00 0.00 0.00 3.86
1783 1923 2.365617 AGAAGCTCCGAACAGTTTCTCA 59.634 45.455 0.00 0.00 39.09 3.27
1821 1961 0.039708 GACTGCCAGCAAAGAAGTGC 60.040 55.000 0.00 0.00 45.28 4.40
1882 2053 5.091261 TGTTTTAAGTTTTGTGGCCACAT 57.909 34.783 37.97 25.08 41.52 3.21
1923 2095 3.508793 CAGGAATGCTCAGTGGACAAAAT 59.491 43.478 0.00 0.00 0.00 1.82
1958 2131 9.083080 GCCCAACAAAACAGAATACATAAATAC 57.917 33.333 0.00 0.00 0.00 1.89
1980 2153 3.939740 AGATTCTTTAGATGCTGCCCA 57.060 42.857 0.00 0.00 0.00 5.36
2001 2177 5.491078 ACATAGTCCCCTGGAACAAAGATAA 59.509 40.000 0.00 0.00 38.70 1.75
2095 2271 4.823989 GCAGCCATCAGGTTTCTGTATATT 59.176 41.667 0.00 0.00 41.59 1.28
2110 2286 2.338577 AACATACCTCTGCAGCCATC 57.661 50.000 9.47 0.00 0.00 3.51
2133 2309 4.534103 AGCTCTTCCCTTCTACAACAGAAT 59.466 41.667 0.00 0.00 42.44 2.40
2138 2314 4.545208 AGAAGCTCTTCCCTTCTACAAC 57.455 45.455 6.04 0.00 45.24 3.32
2180 2356 8.995027 AGGCATGTAACATATGAGGAATTTAA 57.005 30.769 10.38 0.00 0.00 1.52
2195 2371 5.130350 TCCCAGCTTAATAAGGCATGTAAC 58.870 41.667 1.88 0.00 0.00 2.50
2228 2404 5.872070 TGAAGGAAACACAAACATCCAAAAC 59.128 36.000 0.00 0.00 34.30 2.43
2282 2476 8.097038 GGAGTAACATGAGCATATAAGATGGAA 58.903 37.037 0.00 0.00 0.00 3.53
2448 2642 4.916983 TCAGTCTCAAAAACATGGTTGG 57.083 40.909 0.00 0.00 0.00 3.77
2462 2661 5.873712 AGTGACAATGATGATGTTCAGTCTC 59.126 40.000 0.00 0.00 0.00 3.36
2482 2686 6.935741 ATGTAAAGTTGTGCAGTTAAGTGA 57.064 33.333 14.64 0.00 0.00 3.41
2485 2689 9.677567 ATTTGTATGTAAAGTTGTGCAGTTAAG 57.322 29.630 0.00 0.00 0.00 1.85
2615 2832 1.183030 TCCAACGAGGTCGGATGTGT 61.183 55.000 4.13 0.00 44.95 3.72
2624 2841 4.023980 TGATCTATTGAGTCCAACGAGGT 58.976 43.478 0.00 0.00 39.02 3.85
2665 2882 3.880047 TGAATAACTACGTGGACAGGG 57.120 47.619 5.70 0.00 0.00 4.45
2671 2888 6.373216 TGAAAGGGAAATGAATAACTACGTGG 59.627 38.462 0.00 0.00 0.00 4.94
2711 2930 5.456921 AAATCCTCCATCACTAACACCAT 57.543 39.130 0.00 0.00 0.00 3.55
2769 2988 9.739276 ACCACTGATTCAAACTTCTCATATAAA 57.261 29.630 0.00 0.00 0.00 1.40
2770 2989 9.166173 CACCACTGATTCAAACTTCTCATATAA 57.834 33.333 0.00 0.00 0.00 0.98
2771 2990 8.321353 ACACCACTGATTCAAACTTCTCATATA 58.679 33.333 0.00 0.00 0.00 0.86
2772 2991 7.170965 ACACCACTGATTCAAACTTCTCATAT 58.829 34.615 0.00 0.00 0.00 1.78
2773 2992 6.533730 ACACCACTGATTCAAACTTCTCATA 58.466 36.000 0.00 0.00 0.00 2.15
2774 2993 5.380043 ACACCACTGATTCAAACTTCTCAT 58.620 37.500 0.00 0.00 0.00 2.90
2775 2994 4.780815 ACACCACTGATTCAAACTTCTCA 58.219 39.130 0.00 0.00 0.00 3.27
2776 2995 4.214332 GGACACCACTGATTCAAACTTCTC 59.786 45.833 0.00 0.00 0.00 2.87
2777 2996 4.137543 GGACACCACTGATTCAAACTTCT 58.862 43.478 0.00 0.00 0.00 2.85
2778 2997 3.882888 TGGACACCACTGATTCAAACTTC 59.117 43.478 0.00 0.00 0.00 3.01
2779 2998 3.897239 TGGACACCACTGATTCAAACTT 58.103 40.909 0.00 0.00 0.00 2.66
2780 2999 3.576078 TGGACACCACTGATTCAAACT 57.424 42.857 0.00 0.00 0.00 2.66
2781 3000 3.191371 GGATGGACACCACTGATTCAAAC 59.809 47.826 0.00 0.00 35.80 2.93
2782 3001 3.074390 AGGATGGACACCACTGATTCAAA 59.926 43.478 0.00 0.00 35.80 2.69
2783 3002 2.644299 AGGATGGACACCACTGATTCAA 59.356 45.455 0.00 0.00 35.80 2.69
2784 3003 2.269023 AGGATGGACACCACTGATTCA 58.731 47.619 0.00 0.00 35.80 2.57
2785 3004 3.356529 AAGGATGGACACCACTGATTC 57.643 47.619 0.00 0.00 35.80 2.52
2786 3005 3.331889 AGAAAGGATGGACACCACTGATT 59.668 43.478 0.00 0.00 35.80 2.57
2787 3006 2.915604 AGAAAGGATGGACACCACTGAT 59.084 45.455 0.00 0.00 35.80 2.90
2788 3007 2.338809 AGAAAGGATGGACACCACTGA 58.661 47.619 0.00 0.00 35.80 3.41
2789 3008 2.867109 AGAAAGGATGGACACCACTG 57.133 50.000 0.00 0.00 35.80 3.66
2790 3009 3.884037 AAAGAAAGGATGGACACCACT 57.116 42.857 0.00 0.00 35.80 4.00
2791 3010 4.620982 CAAAAAGAAAGGATGGACACCAC 58.379 43.478 0.00 0.00 35.80 4.16
2792 3011 3.069443 GCAAAAAGAAAGGATGGACACCA 59.931 43.478 0.00 0.00 38.19 4.17
2793 3012 3.069443 TGCAAAAAGAAAGGATGGACACC 59.931 43.478 0.00 0.00 0.00 4.16
2794 3013 4.051237 GTGCAAAAAGAAAGGATGGACAC 58.949 43.478 0.00 0.00 33.26 3.67
2795 3014 3.069443 GGTGCAAAAAGAAAGGATGGACA 59.931 43.478 0.00 0.00 34.50 4.02
2796 3015 3.069443 TGGTGCAAAAAGAAAGGATGGAC 59.931 43.478 0.00 0.00 0.00 4.02
2797 3016 3.069443 GTGGTGCAAAAAGAAAGGATGGA 59.931 43.478 0.00 0.00 0.00 3.41
2804 3023 5.293079 GCAACTTATGTGGTGCAAAAAGAAA 59.707 36.000 5.15 0.00 32.06 2.52
2937 3166 4.497251 CACTGTCATCGTATTCTGACTTCG 59.503 45.833 4.53 0.00 41.83 3.79
2978 3213 6.036577 TGCATGTGAGAAATGTAGAGTACA 57.963 37.500 0.00 0.00 43.80 2.90
3028 3265 4.038271 TGAACAGGGATCTTGATTTGCT 57.962 40.909 5.03 0.00 0.00 3.91
3100 3337 3.415212 TCCTCAGAAACCTGCAAAGATG 58.585 45.455 0.00 0.00 0.00 2.90
3708 3958 8.546083 AATAAGATCTGTCTAGTCATCCTGTT 57.454 34.615 0.00 0.00 33.30 3.16
4012 4272 1.884579 CATCTTGCAAGGAACACTGCT 59.115 47.619 25.73 0.00 0.00 4.24
4132 4402 2.159310 GCTCGAGAGTACAGTTCTGCAT 60.159 50.000 18.75 0.00 0.00 3.96
4176 4446 2.090658 GCGTACGCATCCTTGAATATCG 59.909 50.000 33.90 0.00 41.49 2.92
4312 4582 3.483808 TCATGTGGTGTTCTGCTTACA 57.516 42.857 0.00 0.00 0.00 2.41
4317 4587 2.440409 AGGATTCATGTGGTGTTCTGC 58.560 47.619 0.00 0.00 0.00 4.26
4336 4606 4.241590 TGTATGGCTTGCACAGAAAAAG 57.758 40.909 0.00 0.00 0.00 2.27
4459 4730 4.405358 AGCTTGTCTATGGAAGAGGAAGAG 59.595 45.833 0.00 0.00 33.88 2.85
4460 4731 4.357325 AGCTTGTCTATGGAAGAGGAAGA 58.643 43.478 0.00 0.00 33.88 2.87
4461 4732 4.751767 AGCTTGTCTATGGAAGAGGAAG 57.248 45.455 0.00 0.00 33.88 3.46
4462 4733 5.394224 CGTTAGCTTGTCTATGGAAGAGGAA 60.394 44.000 0.00 0.00 33.88 3.36
4463 4734 4.098044 CGTTAGCTTGTCTATGGAAGAGGA 59.902 45.833 0.00 0.00 33.88 3.71
4464 4735 4.363999 CGTTAGCTTGTCTATGGAAGAGG 58.636 47.826 0.00 0.00 33.88 3.69
4564 4837 3.853355 AGGGGATGCTACAAGATCTTG 57.147 47.619 29.74 29.74 45.58 3.02
4626 4901 2.215196 CAACTCGAAAAAGGTCGGGAA 58.785 47.619 0.78 0.00 44.57 3.97
4627 4902 1.139455 ACAACTCGAAAAAGGTCGGGA 59.861 47.619 0.78 0.00 44.57 5.14
4865 5148 2.965831 TGGACTCACTACAGTTGCTCTT 59.034 45.455 0.00 0.00 0.00 2.85
5007 5295 5.683743 TCGCAAACAAAAGGAAACGATAAAG 59.316 36.000 0.00 0.00 0.00 1.85
5013 5305 3.367607 TCATCGCAAACAAAAGGAAACG 58.632 40.909 0.00 0.00 0.00 3.60
5024 5316 5.024555 GCTTAGTTTCATCTCATCGCAAAC 58.975 41.667 0.00 0.00 0.00 2.93
5048 5342 3.070018 ACGAAAGATTGGCTCTTCACTG 58.930 45.455 0.00 0.00 43.60 3.66
5081 5375 6.518493 ACGTTCTTTTGACACTATAGGAACA 58.482 36.000 4.43 0.00 33.67 3.18
5085 5379 7.008086 CGTAAGACGTTCTTTTGACACTATAGG 59.992 40.741 4.43 0.00 37.89 2.57
5111 5405 4.875561 ACTACTCCCTCTGTCTCAAAAC 57.124 45.455 0.00 0.00 0.00 2.43
5120 5419 5.112686 GCATAAAGTCAACTACTCCCTCTG 58.887 45.833 0.00 0.00 37.50 3.35
5134 5433 9.678941 GGTTATTAAAGCTTATGGCATAAAGTC 57.321 33.333 19.68 12.04 44.79 3.01
5174 5474 7.945033 TCCATTTTATTTGCTCAACTGAAAC 57.055 32.000 0.00 0.00 0.00 2.78
5213 5513 2.493713 ACCAGAGCGCTATTTCTACG 57.506 50.000 11.50 0.00 0.00 3.51
5221 5521 3.938963 CCAAATTCTAAACCAGAGCGCTA 59.061 43.478 11.50 0.00 33.83 4.26
5222 5522 2.749621 CCAAATTCTAAACCAGAGCGCT 59.250 45.455 11.27 11.27 33.83 5.92
5223 5523 2.159379 CCCAAATTCTAAACCAGAGCGC 60.159 50.000 0.00 0.00 33.83 5.92
5253 5576 6.707440 TTACAAAAATCAGTTGCCTCTGAA 57.293 33.333 11.03 0.00 45.65 3.02
5381 5705 2.930040 CGTCACTTTGTGTCAGTTGACT 59.070 45.455 12.97 0.00 44.99 3.41
5443 5768 2.857592 ATACTACTGGCGTAACGTGG 57.142 50.000 0.00 0.00 0.00 4.94
5470 5795 8.260818 TGGGTTCAAAACTTCAAATCAAACATA 58.739 29.630 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.