Multiple sequence alignment - TraesCS4B01G221500

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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 TraesCS4B01G221500 chr4B 100.000 3030 0 0 1 3030 465740936 465743965 0.000000e+00 5596
1 TraesCS4B01G221500 chr4B 81.310 931 136 26 1094 1993 531245777 531246700 0.000000e+00 721
2 TraesCS4B01G221500 chr4B 98.305 118 2 0 2913 3030 103432021 103432138 1.100000e-49 207
3 TraesCS4B01G221500 chr4D 93.130 2955 113 42 1 2901 379153905 379156823 0.000000e+00 4250
4 TraesCS4B01G221500 chr4D 81.847 931 131 26 1094 1993 433220627 433221550 0.000000e+00 749
5 TraesCS4B01G221500 chr4A 90.392 1863 92 41 350 2188 85893836 85892037 0.000000e+00 2368
6 TraesCS4B01G221500 chr4A 81.478 934 132 29 1094 1993 34669443 34670369 0.000000e+00 728
7 TraesCS4B01G221500 chr4A 81.753 696 51 29 2226 2901 85892045 85891406 2.080000e-141 512
8 TraesCS4B01G221500 chr4A 87.444 223 7 7 1 204 85895932 85895712 1.400000e-58 237
9 TraesCS4B01G221500 chr4A 88.750 160 12 4 201 354 85895552 85895393 1.110000e-44 191
10 TraesCS4B01G221500 chr5B 99.153 118 1 0 2913 3030 690047395 690047278 2.370000e-51 213
11 TraesCS4B01G221500 chr5B 97.458 118 3 0 2913 3030 575963434 575963317 5.120000e-48 202
12 TraesCS4B01G221500 chr6B 98.305 118 2 0 2913 3030 516867438 516867321 1.100000e-49 207
13 TraesCS4B01G221500 chr3D 98.305 118 2 0 2913 3030 497371799 497371916 1.100000e-49 207
14 TraesCS4B01G221500 chr3D 97.458 118 3 0 2913 3030 79506486 79506369 5.120000e-48 202
15 TraesCS4B01G221500 chr7D 97.458 118 3 0 2913 3030 557774293 557774410 5.120000e-48 202
16 TraesCS4B01G221500 chr6A 97.458 118 3 0 2913 3030 63114774 63114891 5.120000e-48 202
17 TraesCS4B01G221500 chr2B 97.458 118 3 0 2913 3030 747832127 747832244 5.120000e-48 202


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 TraesCS4B01G221500 chr4B 465740936 465743965 3029 False 5596 5596 100.00000 1 3030 1 chr4B.!!$F2 3029
1 TraesCS4B01G221500 chr4B 531245777 531246700 923 False 721 721 81.31000 1094 1993 1 chr4B.!!$F3 899
2 TraesCS4B01G221500 chr4D 379153905 379156823 2918 False 4250 4250 93.13000 1 2901 1 chr4D.!!$F1 2900
3 TraesCS4B01G221500 chr4D 433220627 433221550 923 False 749 749 81.84700 1094 1993 1 chr4D.!!$F2 899
4 TraesCS4B01G221500 chr4A 85891406 85895932 4526 True 827 2368 87.08475 1 2901 4 chr4A.!!$R1 2900
5 TraesCS4B01G221500 chr4A 34669443 34670369 926 False 728 728 81.47800 1094 1993 1 chr4A.!!$F1 899

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
394 2157 0.179094 CGCTCGCCTACCAACCATTA 60.179 55.0 0.0 0.0 0.0 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 3987 0.04109 GGAATGGCTTCAGGGGGAAA 59.959 55.0 0.0 0.0 34.44 3.13 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
112 126 6.510536 AGCTGATGAAGGTCAAAAAGAAAAG 58.489 36.000 0.00 0.00 27.29 2.27
134 149 3.428746 AAAAACTAACGTGTGCATGCA 57.571 38.095 18.46 18.46 0.00 3.96
206 229 6.548993 TGCCCAATGATGCATGTAAACTAATA 59.451 34.615 2.46 0.00 31.31 0.98
265 454 3.181495 CCCAACAAACTGCGTACTTTGAA 60.181 43.478 11.37 0.00 32.63 2.69
266 455 4.035017 CCAACAAACTGCGTACTTTGAAG 58.965 43.478 11.37 4.67 32.63 3.02
277 466 8.564574 ACTGCGTACTTTGAAGAAAATCAAATA 58.435 29.630 3.23 0.00 45.45 1.40
278 467 8.722342 TGCGTACTTTGAAGAAAATCAAATAC 57.278 30.769 3.23 7.29 45.45 1.89
279 468 7.532546 TGCGTACTTTGAAGAAAATCAAATACG 59.467 33.333 22.54 22.54 45.45 3.06
368 2131 4.056050 ACAACGTACCAGATGTTTGTCTC 58.944 43.478 0.00 0.00 34.92 3.36
392 2155 2.186903 CGCTCGCCTACCAACCAT 59.813 61.111 0.00 0.00 0.00 3.55
393 2156 1.449601 CGCTCGCCTACCAACCATT 60.450 57.895 0.00 0.00 0.00 3.16
394 2157 0.179094 CGCTCGCCTACCAACCATTA 60.179 55.000 0.00 0.00 0.00 1.90
395 2158 1.296727 GCTCGCCTACCAACCATTAC 58.703 55.000 0.00 0.00 0.00 1.89
396 2159 1.949465 CTCGCCTACCAACCATTACC 58.051 55.000 0.00 0.00 0.00 2.85
397 2160 1.208535 CTCGCCTACCAACCATTACCA 59.791 52.381 0.00 0.00 0.00 3.25
414 2177 2.305928 ACCAATGCAGCAGTACAAACA 58.694 42.857 0.00 0.00 0.00 2.83
483 2246 0.408309 TCTTCTGTCTTCTCCCCCGA 59.592 55.000 0.00 0.00 0.00 5.14
524 2287 2.114670 CATCACCGCCACATGACCC 61.115 63.158 0.00 0.00 0.00 4.46
549 2312 2.282462 CCCGCCACAAAAGCCTCT 60.282 61.111 0.00 0.00 0.00 3.69
587 2354 5.868801 GCAGCCAATATCTCTCTATCTTGAC 59.131 44.000 0.00 0.00 0.00 3.18
595 2362 6.982160 ATCTCTCTATCTTGACAAGCTGAT 57.018 37.500 10.50 2.25 0.00 2.90
655 2428 1.107538 CAGATCAGGGGCAAGCATGG 61.108 60.000 0.00 0.00 0.00 3.66
667 2440 0.962356 AAGCATGGCAAGTTCCCTCG 60.962 55.000 0.00 0.00 0.00 4.63
697 2471 4.080751 CCAGTTAAACCTTCCCTATCCGAA 60.081 45.833 0.00 0.00 0.00 4.30
698 2472 5.397559 CCAGTTAAACCTTCCCTATCCGAAT 60.398 44.000 0.00 0.00 0.00 3.34
699 2473 6.120220 CAGTTAAACCTTCCCTATCCGAATT 58.880 40.000 0.00 0.00 0.00 2.17
700 2474 6.602009 CAGTTAAACCTTCCCTATCCGAATTT 59.398 38.462 0.00 0.00 0.00 1.82
701 2475 7.122204 CAGTTAAACCTTCCCTATCCGAATTTT 59.878 37.037 0.00 0.00 0.00 1.82
702 2476 7.672660 AGTTAAACCTTCCCTATCCGAATTTTT 59.327 33.333 0.00 0.00 0.00 1.94
703 2477 6.525578 AAACCTTCCCTATCCGAATTTTTC 57.474 37.500 0.00 0.00 0.00 2.29
704 2478 4.533815 ACCTTCCCTATCCGAATTTTTCC 58.466 43.478 0.00 0.00 0.00 3.13
705 2479 4.017867 ACCTTCCCTATCCGAATTTTTCCA 60.018 41.667 0.00 0.00 0.00 3.53
706 2480 4.953579 CCTTCCCTATCCGAATTTTTCCAA 59.046 41.667 0.00 0.00 0.00 3.53
707 2481 5.067805 CCTTCCCTATCCGAATTTTTCCAAG 59.932 44.000 0.00 0.00 0.00 3.61
708 2482 3.951680 TCCCTATCCGAATTTTTCCAAGC 59.048 43.478 0.00 0.00 0.00 4.01
721 2495 1.201429 TCCAAGCTCCAACTCCCTCC 61.201 60.000 0.00 0.00 0.00 4.30
736 2510 3.248024 TCCCTCCTTTCTTCTACAAGCA 58.752 45.455 0.00 0.00 0.00 3.91
752 2526 1.103398 AGCAACAACTCCAGCACACC 61.103 55.000 0.00 0.00 0.00 4.16
754 2528 0.664761 CAACAACTCCAGCACACCAG 59.335 55.000 0.00 0.00 0.00 4.00
755 2529 1.103398 AACAACTCCAGCACACCAGC 61.103 55.000 0.00 0.00 0.00 4.85
756 2530 1.526686 CAACTCCAGCACACCAGCA 60.527 57.895 0.00 0.00 36.85 4.41
757 2531 0.892358 CAACTCCAGCACACCAGCAT 60.892 55.000 0.00 0.00 36.85 3.79
758 2532 0.607489 AACTCCAGCACACCAGCATC 60.607 55.000 0.00 0.00 36.85 3.91
759 2533 1.748122 CTCCAGCACACCAGCATCC 60.748 63.158 0.00 0.00 36.85 3.51
760 2534 2.034532 CCAGCACACCAGCATCCA 59.965 61.111 0.00 0.00 36.85 3.41
761 2535 1.379443 CCAGCACACCAGCATCCAT 60.379 57.895 0.00 0.00 36.85 3.41
762 2536 1.381928 CCAGCACACCAGCATCCATC 61.382 60.000 0.00 0.00 36.85 3.51
763 2537 1.077212 AGCACACCAGCATCCATCC 60.077 57.895 0.00 0.00 36.85 3.51
764 2538 1.378911 GCACACCAGCATCCATCCA 60.379 57.895 0.00 0.00 0.00 3.41
765 2539 0.754217 GCACACCAGCATCCATCCAT 60.754 55.000 0.00 0.00 0.00 3.41
766 2540 1.315690 CACACCAGCATCCATCCATC 58.684 55.000 0.00 0.00 0.00 3.51
786 2564 2.790585 TCCATCCATCCATCCATCCAAA 59.209 45.455 0.00 0.00 0.00 3.28
791 2569 0.862554 ATCCATCCATCCAAAGGGGG 59.137 55.000 0.00 0.00 37.22 5.40
825 2615 0.326143 AAGAGGAGGAGGAAGAGGGC 60.326 60.000 0.00 0.00 0.00 5.19
898 2688 2.095372 GCGTATTGGCTAACAGGACAAC 59.905 50.000 0.00 0.00 37.01 3.32
964 2760 4.621832 GGACGACGAGAGAGGAGT 57.378 61.111 0.00 0.00 0.00 3.85
993 2789 3.333969 GCTAGCTAGCTTGCCGCG 61.334 66.667 32.67 12.86 45.62 6.46
994 2790 2.659897 CTAGCTAGCTTGCCGCGG 60.660 66.667 24.88 24.05 45.59 6.46
995 2791 3.138930 CTAGCTAGCTTGCCGCGGA 62.139 63.158 33.48 11.82 45.59 5.54
1281 3078 4.719369 GCCGTGCTCGACCTCGTT 62.719 66.667 10.21 0.00 40.80 3.85
1284 3081 3.173240 GTGCTCGACCTCGTTCGC 61.173 66.667 0.00 0.00 38.95 4.70
1713 3534 2.630317 GCCATCATCTTCGCGCTG 59.370 61.111 5.56 0.00 0.00 5.18
1737 3558 1.077501 CAGGATGGTGTGCCGGATT 60.078 57.895 5.05 0.00 37.67 3.01
1935 3756 1.128692 GTGTACAGATTCTTGGCGTGC 59.871 52.381 0.00 0.00 0.00 5.34
2134 3965 1.252215 TGCATGACACAATGGGCAGG 61.252 55.000 0.00 0.00 0.00 4.85
2135 3966 1.514087 CATGACACAATGGGCAGGC 59.486 57.895 0.00 0.00 0.00 4.85
2137 3968 0.542467 ATGACACAATGGGCAGGCAA 60.542 50.000 0.00 0.00 0.00 4.52
2138 3969 0.758310 TGACACAATGGGCAGGCAAA 60.758 50.000 0.00 0.00 0.00 3.68
2139 3970 0.392336 GACACAATGGGCAGGCAAAA 59.608 50.000 0.00 0.00 0.00 2.44
2140 3971 0.393820 ACACAATGGGCAGGCAAAAG 59.606 50.000 0.00 0.00 0.00 2.27
2153 3987 4.214758 GCAGGCAAAAGAATTCTGCAAAAT 59.785 37.500 17.06 0.00 46.92 1.82
2169 4007 2.573009 CAAAATTTCCCCCTGAAGCCAT 59.427 45.455 0.00 0.00 33.63 4.40
2203 4041 7.912056 TTTCTGTCGATGAATCTTCAGAAAT 57.088 32.000 21.68 0.00 42.15 2.17
2204 4042 7.531280 TTCTGTCGATGAATCTTCAGAAATC 57.469 36.000 16.90 0.00 41.08 2.17
2211 4050 4.665451 TGAATCTTCAGAAATCTGCCCAA 58.335 39.130 5.53 0.00 43.46 4.12
2245 4087 2.183478 TTCTGTCGGTCACATTGCAT 57.817 45.000 0.00 0.00 33.23 3.96
2403 4259 2.495084 GGGTTCAGAAAAGCGAAGAGT 58.505 47.619 0.00 0.00 0.00 3.24
2453 4309 1.115326 GCTTGTTCAGGGGCCTTTGT 61.115 55.000 0.84 0.00 0.00 2.83
2523 4379 0.465705 CTTGGAGGCTTCCTGCGATA 59.534 55.000 16.82 0.00 45.25 2.92
2608 4466 0.250467 GAGAGCAAGTGGTTGGAGCA 60.250 55.000 0.00 0.00 33.87 4.26
2617 4479 0.251297 TGGTTGGAGCATTCACCTGG 60.251 55.000 0.00 0.00 0.00 4.45
2690 4552 1.689813 TCACCGAGGACTGCAGTTTAA 59.310 47.619 22.65 0.00 0.00 1.52
2707 4569 6.146021 GCAGTTTAACAAAGAATTGGTCATGG 59.854 38.462 0.00 0.00 41.01 3.66
2709 4571 6.041979 AGTTTAACAAAGAATTGGTCATGGCT 59.958 34.615 0.00 0.00 41.01 4.75
2800 4667 3.772025 GTGGCCCTATGCATATAGTCTCT 59.228 47.826 6.92 0.00 43.89 3.10
2801 4668 4.956700 GTGGCCCTATGCATATAGTCTCTA 59.043 45.833 6.92 0.00 43.89 2.43
2901 4771 2.049959 CTCTCATCATCATCGTGCGAC 58.950 52.381 0.00 0.00 0.00 5.19
2902 4772 1.405105 TCTCATCATCATCGTGCGACA 59.595 47.619 0.00 0.00 0.00 4.35
2903 4773 2.035066 TCTCATCATCATCGTGCGACAT 59.965 45.455 0.00 0.00 0.00 3.06
2904 4774 2.798847 CTCATCATCATCGTGCGACATT 59.201 45.455 0.00 0.00 0.00 2.71
2905 4775 2.540931 TCATCATCATCGTGCGACATTG 59.459 45.455 0.00 0.00 0.00 2.82
2906 4776 0.652071 TCATCATCGTGCGACATTGC 59.348 50.000 0.00 0.00 0.00 3.56
2907 4777 0.652465 CATCATCGTGCGACATTGCG 60.652 55.000 0.00 0.00 37.81 4.85
2908 4778 1.765161 ATCATCGTGCGACATTGCGG 61.765 55.000 0.00 0.00 37.81 5.69
2909 4779 2.434185 ATCGTGCGACATTGCGGT 60.434 55.556 0.00 0.00 37.81 5.68
2910 4780 2.452813 ATCGTGCGACATTGCGGTC 61.453 57.895 0.00 0.00 37.81 4.79
2911 4781 3.410516 CGTGCGACATTGCGGTCA 61.411 61.111 0.00 0.00 37.66 4.02
2912 4782 2.173382 GTGCGACATTGCGGTCAC 59.827 61.111 0.00 0.00 37.66 3.67
2913 4783 2.030412 TGCGACATTGCGGTCACT 59.970 55.556 0.00 0.00 37.66 3.41
2914 4784 2.027073 TGCGACATTGCGGTCACTC 61.027 57.895 0.00 0.00 37.66 3.51
2915 4785 3.071459 GCGACATTGCGGTCACTCG 62.071 63.158 0.00 0.00 37.66 4.18
2922 4792 2.809601 GCGGTCACTCGCGACATT 60.810 61.111 3.71 0.00 46.23 2.71
2923 4793 3.071459 GCGGTCACTCGCGACATTG 62.071 63.158 3.71 2.59 46.23 2.82
2924 4794 2.778679 GGTCACTCGCGACATTGC 59.221 61.111 3.71 0.00 37.66 3.56
2954 4824 3.906660 GTCTGTCCGACAATGTGGA 57.093 52.632 2.19 0.00 42.37 4.02
2955 4825 2.386661 GTCTGTCCGACAATGTGGAT 57.613 50.000 2.19 0.00 42.37 3.41
2956 4826 2.002586 GTCTGTCCGACAATGTGGATG 58.997 52.381 2.19 5.27 42.37 3.51
2957 4827 1.623311 TCTGTCCGACAATGTGGATGT 59.377 47.619 2.19 0.00 36.48 3.06
2958 4828 2.038426 TCTGTCCGACAATGTGGATGTT 59.962 45.455 2.19 0.00 36.48 2.71
2959 4829 2.150390 TGTCCGACAATGTGGATGTTG 58.850 47.619 0.00 0.00 36.48 3.33
2960 4830 1.135689 GTCCGACAATGTGGATGTTGC 60.136 52.381 7.59 0.00 36.48 4.17
2961 4831 0.179192 CCGACAATGTGGATGTTGCG 60.179 55.000 0.00 0.00 31.94 4.85
2962 4832 0.794229 CGACAATGTGGATGTTGCGC 60.794 55.000 0.00 0.00 0.00 6.09
2963 4833 0.794229 GACAATGTGGATGTTGCGCG 60.794 55.000 0.00 0.00 0.00 6.86
2964 4834 1.233950 ACAATGTGGATGTTGCGCGA 61.234 50.000 12.10 0.00 0.00 5.87
2965 4835 0.794229 CAATGTGGATGTTGCGCGAC 60.794 55.000 21.27 21.27 0.00 5.19
2966 4836 0.955428 AATGTGGATGTTGCGCGACT 60.955 50.000 27.33 13.69 0.00 4.18
2967 4837 0.955428 ATGTGGATGTTGCGCGACTT 60.955 50.000 27.33 21.59 0.00 3.01
2968 4838 1.132640 GTGGATGTTGCGCGACTTC 59.867 57.895 27.42 27.42 0.00 3.01
2969 4839 1.005037 TGGATGTTGCGCGACTTCT 60.005 52.632 31.33 17.36 0.00 2.85
2970 4840 0.245266 TGGATGTTGCGCGACTTCTA 59.755 50.000 31.33 26.59 0.00 2.10
2971 4841 0.924090 GGATGTTGCGCGACTTCTAG 59.076 55.000 31.33 0.00 0.00 2.43
2972 4842 1.630148 GATGTTGCGCGACTTCTAGT 58.370 50.000 27.83 10.16 0.00 2.57
2973 4843 1.321743 GATGTTGCGCGACTTCTAGTG 59.678 52.381 27.83 0.00 0.00 2.74
2974 4844 0.031585 TGTTGCGCGACTTCTAGTGT 59.968 50.000 27.33 0.00 0.00 3.55
2975 4845 0.435008 GTTGCGCGACTTCTAGTGTG 59.565 55.000 20.81 0.00 0.00 3.82
2976 4846 0.666274 TTGCGCGACTTCTAGTGTGG 60.666 55.000 12.10 0.00 0.00 4.17
2977 4847 2.445438 GCGCGACTTCTAGTGTGGC 61.445 63.158 12.10 12.61 36.13 5.01
2978 4848 1.080772 CGCGACTTCTAGTGTGGCA 60.081 57.895 18.77 0.00 38.71 4.92
2979 4849 0.666274 CGCGACTTCTAGTGTGGCAA 60.666 55.000 18.77 0.00 38.71 4.52
2980 4850 0.790814 GCGACTTCTAGTGTGGCAAC 59.209 55.000 15.86 0.00 38.66 4.17
2981 4851 1.060713 CGACTTCTAGTGTGGCAACG 58.939 55.000 0.00 0.00 42.51 4.10
2982 4852 1.335597 CGACTTCTAGTGTGGCAACGA 60.336 52.381 0.00 0.00 42.51 3.85
2983 4853 2.671351 CGACTTCTAGTGTGGCAACGAT 60.671 50.000 0.00 0.00 42.51 3.73
2984 4854 2.668457 GACTTCTAGTGTGGCAACGATG 59.332 50.000 0.00 0.00 42.51 3.84
2985 4855 2.299013 ACTTCTAGTGTGGCAACGATGA 59.701 45.455 0.00 0.00 42.51 2.92
2986 4856 2.363788 TCTAGTGTGGCAACGATGAC 57.636 50.000 0.00 0.00 42.51 3.06
2987 4857 0.992072 CTAGTGTGGCAACGATGACG 59.008 55.000 0.00 0.00 37.40 4.35
2988 4858 0.389296 TAGTGTGGCAACGATGACGG 60.389 55.000 0.00 0.00 44.46 4.79
2989 4859 3.047280 TGTGGCAACGATGACGGC 61.047 61.111 0.00 0.00 44.46 5.68
2990 4860 2.742372 GTGGCAACGATGACGGCT 60.742 61.111 0.00 0.00 44.46 5.52
2991 4861 2.031919 TGGCAACGATGACGGCTT 59.968 55.556 0.00 0.00 44.46 4.35
2992 4862 2.032634 TGGCAACGATGACGGCTTC 61.033 57.895 0.00 0.00 44.46 3.86
2993 4863 2.395690 GCAACGATGACGGCTTCG 59.604 61.111 23.52 23.52 44.46 3.79
2994 4864 2.092291 GCAACGATGACGGCTTCGA 61.092 57.895 30.64 0.00 42.36 3.71
2995 4865 1.991430 CAACGATGACGGCTTCGAG 59.009 57.895 30.64 18.75 42.36 4.04
2996 4866 1.805945 AACGATGACGGCTTCGAGC 60.806 57.895 30.64 0.00 42.36 5.03
2997 4867 3.315521 CGATGACGGCTTCGAGCG 61.316 66.667 21.05 0.00 43.62 5.03
2998 4868 2.102357 GATGACGGCTTCGAGCGA 59.898 61.111 0.00 0.00 43.62 4.93
2999 4869 1.516386 GATGACGGCTTCGAGCGAA 60.516 57.895 5.14 5.14 43.62 4.70
3006 4876 3.169198 CTTCGAGCGAAGTTGGGC 58.831 61.111 20.99 0.00 44.65 5.36
3007 4877 2.730672 CTTCGAGCGAAGTTGGGCG 61.731 63.158 20.99 0.00 44.65 6.13
3008 4878 4.735132 TCGAGCGAAGTTGGGCGG 62.735 66.667 0.00 0.00 0.00 6.13
3014 4884 3.741476 GAAGTTGGGCGGCTGCTG 61.741 66.667 18.85 3.55 42.25 4.41
3015 4885 4.269523 AAGTTGGGCGGCTGCTGA 62.270 61.111 18.85 0.54 42.25 4.26
3016 4886 4.711949 AGTTGGGCGGCTGCTGAG 62.712 66.667 18.85 0.00 42.25 3.35
3021 4891 4.112341 GGCGGCTGCTGAGCTTTG 62.112 66.667 18.85 0.00 45.44 2.77
3022 4892 4.112341 GCGGCTGCTGAGCTTTGG 62.112 66.667 13.72 0.00 45.44 3.28
3023 4893 2.670934 CGGCTGCTGAGCTTTGGT 60.671 61.111 5.83 0.00 45.44 3.67
3024 4894 1.375908 CGGCTGCTGAGCTTTGGTA 60.376 57.895 5.83 0.00 45.44 3.25
3025 4895 1.364626 CGGCTGCTGAGCTTTGGTAG 61.365 60.000 5.83 0.00 45.44 3.18
3026 4896 0.322008 GGCTGCTGAGCTTTGGTAGT 60.322 55.000 5.83 0.00 45.44 2.73
3027 4897 1.082690 GCTGCTGAGCTTTGGTAGTC 58.917 55.000 5.83 0.00 42.52 2.59
3028 4898 1.354040 CTGCTGAGCTTTGGTAGTCG 58.646 55.000 5.83 0.00 0.00 4.18
3029 4899 0.037326 TGCTGAGCTTTGGTAGTCGG 60.037 55.000 5.83 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 145 2.283298 CTACCTCGTCTTGCATTGCAT 58.717 47.619 12.95 0.00 38.76 3.96
131 146 1.725641 CTACCTCGTCTTGCATTGCA 58.274 50.000 7.38 7.38 36.47 4.08
132 147 0.375106 GCTACCTCGTCTTGCATTGC 59.625 55.000 0.46 0.46 0.00 3.56
133 148 2.015736 AGCTACCTCGTCTTGCATTG 57.984 50.000 0.00 0.00 0.00 2.82
134 149 3.024547 TCTAGCTACCTCGTCTTGCATT 58.975 45.455 0.00 0.00 0.00 3.56
164 179 1.201998 GGCATGCATGATTAGCGATCG 60.202 52.381 30.64 11.69 37.60 3.69
265 454 4.511826 GGGCTCGATCGTATTTGATTTTCT 59.488 41.667 15.94 0.00 0.00 2.52
266 455 4.319549 GGGGCTCGATCGTATTTGATTTTC 60.320 45.833 15.94 0.00 0.00 2.29
277 466 2.119484 TTTGTTGGGGGCTCGATCGT 62.119 55.000 15.94 0.00 0.00 3.73
278 467 1.376683 TTTGTTGGGGGCTCGATCG 60.377 57.895 9.36 9.36 0.00 3.69
279 468 0.322546 AGTTTGTTGGGGGCTCGATC 60.323 55.000 0.00 0.00 0.00 3.69
368 2131 4.253257 GTAGGCGAGCGAGGACGG 62.253 72.222 0.00 0.00 40.15 4.79
392 2155 3.885901 TGTTTGTACTGCTGCATTGGTAA 59.114 39.130 1.31 0.00 0.00 2.85
393 2156 3.481453 TGTTTGTACTGCTGCATTGGTA 58.519 40.909 1.31 0.00 0.00 3.25
394 2157 2.305928 TGTTTGTACTGCTGCATTGGT 58.694 42.857 1.31 0.00 0.00 3.67
395 2158 3.367992 TTGTTTGTACTGCTGCATTGG 57.632 42.857 1.31 0.00 0.00 3.16
396 2159 4.362279 ACTTTGTTTGTACTGCTGCATTG 58.638 39.130 1.31 0.00 0.00 2.82
397 2160 4.097741 TGACTTTGTTTGTACTGCTGCATT 59.902 37.500 1.31 0.00 0.00 3.56
414 2177 4.152647 GGAGGGAAGGATTGTTTGACTTT 58.847 43.478 0.00 0.00 0.00 2.66
483 2246 1.228552 GCTGTCATGGTGGTTGGGT 60.229 57.895 0.00 0.00 0.00 4.51
587 2354 8.453320 TCGCCATTATTAAATGATATCAGCTTG 58.547 33.333 11.78 0.98 44.50 4.01
595 2362 5.121611 CGCACCTCGCCATTATTAAATGATA 59.878 40.000 0.00 0.00 42.02 2.15
655 2428 2.436824 GGCTCCGAGGGAACTTGC 60.437 66.667 0.00 0.00 44.43 4.01
667 2440 2.618302 GGAAGGTTTAACTGGAGGCTCC 60.618 54.545 26.95 26.95 36.96 4.70
697 2471 2.899900 GGGAGTTGGAGCTTGGAAAAAT 59.100 45.455 0.00 0.00 0.00 1.82
698 2472 2.091333 AGGGAGTTGGAGCTTGGAAAAA 60.091 45.455 0.00 0.00 0.00 1.94
699 2473 1.499007 AGGGAGTTGGAGCTTGGAAAA 59.501 47.619 0.00 0.00 0.00 2.29
700 2474 1.073923 GAGGGAGTTGGAGCTTGGAAA 59.926 52.381 0.00 0.00 0.00 3.13
701 2475 0.693049 GAGGGAGTTGGAGCTTGGAA 59.307 55.000 0.00 0.00 0.00 3.53
702 2476 1.201429 GGAGGGAGTTGGAGCTTGGA 61.201 60.000 0.00 0.00 0.00 3.53
703 2477 1.204113 AGGAGGGAGTTGGAGCTTGG 61.204 60.000 0.00 0.00 0.00 3.61
704 2478 0.695347 AAGGAGGGAGTTGGAGCTTG 59.305 55.000 0.00 0.00 0.00 4.01
705 2479 1.352687 GAAAGGAGGGAGTTGGAGCTT 59.647 52.381 0.00 0.00 0.00 3.74
706 2480 0.988063 GAAAGGAGGGAGTTGGAGCT 59.012 55.000 0.00 0.00 0.00 4.09
707 2481 0.988063 AGAAAGGAGGGAGTTGGAGC 59.012 55.000 0.00 0.00 0.00 4.70
708 2482 2.909662 AGAAGAAAGGAGGGAGTTGGAG 59.090 50.000 0.00 0.00 0.00 3.86
721 2495 5.296780 TGGAGTTGTTGCTTGTAGAAGAAAG 59.703 40.000 3.33 0.00 26.10 2.62
736 2510 1.103398 GCTGGTGTGCTGGAGTTGTT 61.103 55.000 0.00 0.00 0.00 2.83
752 2526 1.074889 TGGATGGATGGATGGATGCTG 59.925 52.381 0.00 0.00 0.00 4.41
754 2528 2.376109 GATGGATGGATGGATGGATGC 58.624 52.381 0.00 0.00 0.00 3.91
755 2529 2.310647 TGGATGGATGGATGGATGGATG 59.689 50.000 0.00 0.00 0.00 3.51
756 2530 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
757 2531 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
758 2532 2.357881 GGATGGATGGATGGATGGATGG 60.358 54.545 0.00 0.00 0.00 3.51
759 2533 2.310647 TGGATGGATGGATGGATGGATG 59.689 50.000 0.00 0.00 0.00 3.51
760 2534 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
761 2535 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
762 2536 2.357881 GGATGGATGGATGGATGGATGG 60.358 54.545 0.00 0.00 0.00 3.51
763 2537 2.310647 TGGATGGATGGATGGATGGATG 59.689 50.000 0.00 0.00 0.00 3.51
764 2538 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
765 2539 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
766 2540 2.984435 TTGGATGGATGGATGGATGG 57.016 50.000 0.00 0.00 0.00 3.51
791 2569 2.910977 TCCTCTTACACCCCTTTTCTCC 59.089 50.000 0.00 0.00 0.00 3.71
799 2577 0.338814 TCCTCCTCCTCTTACACCCC 59.661 60.000 0.00 0.00 0.00 4.95
898 2688 0.390472 GCTCCTTGGTCCTCGACTTG 60.390 60.000 0.00 0.00 32.47 3.16
993 2789 1.269569 TGATCATACGACATGGCGTCC 60.270 52.381 33.41 15.74 44.39 4.79
994 2790 2.054363 CTGATCATACGACATGGCGTC 58.946 52.381 33.41 16.81 44.39 5.19
1713 3534 2.042831 GCACACCATCCTGGAGCAC 61.043 63.158 1.52 0.00 40.96 4.40
1887 3708 1.137825 GACGCAGAGGAAGACGAGG 59.862 63.158 0.00 0.00 0.00 4.63
2131 3962 5.934935 ATTTTGCAGAATTCTTTTGCCTG 57.065 34.783 4.86 0.00 37.03 4.85
2134 3965 6.144854 GGGAAATTTTGCAGAATTCTTTTGC 58.855 36.000 14.91 8.22 38.30 3.68
2135 3966 6.294120 GGGGGAAATTTTGCAGAATTCTTTTG 60.294 38.462 14.91 0.00 0.00 2.44
2137 3968 5.073554 AGGGGGAAATTTTGCAGAATTCTTT 59.926 36.000 14.91 1.53 0.00 2.52
2138 3969 4.598807 AGGGGGAAATTTTGCAGAATTCTT 59.401 37.500 14.91 1.41 0.00 2.52
2139 3970 4.019950 CAGGGGGAAATTTTGCAGAATTCT 60.020 41.667 14.91 0.88 0.00 2.40
2140 3971 4.020307 TCAGGGGGAAATTTTGCAGAATTC 60.020 41.667 14.91 8.96 0.00 2.17
2153 3987 0.041090 GGAATGGCTTCAGGGGGAAA 59.959 55.000 0.00 0.00 34.44 3.13
2169 4007 4.956085 TCATCGACAGAAAAACAGAGGAA 58.044 39.130 0.00 0.00 0.00 3.36
2203 4041 4.870636 AGATATGGAAAATGTTGGGCAGA 58.129 39.130 0.00 0.00 0.00 4.26
2204 4042 5.603170 AAGATATGGAAAATGTTGGGCAG 57.397 39.130 0.00 0.00 0.00 4.85
2211 4050 6.180472 ACCGACAGAAAGATATGGAAAATGT 58.820 36.000 0.00 0.00 0.00 2.71
2254 4096 3.084786 AGCCTTTTCTTTCCTGATTCGG 58.915 45.455 0.00 0.00 0.00 4.30
2255 4097 3.503748 ACAGCCTTTTCTTTCCTGATTCG 59.496 43.478 0.00 0.00 0.00 3.34
2256 4098 5.707764 AGTACAGCCTTTTCTTTCCTGATTC 59.292 40.000 0.00 0.00 0.00 2.52
2257 4099 5.474876 CAGTACAGCCTTTTCTTTCCTGATT 59.525 40.000 0.00 0.00 0.00 2.57
2258 4100 5.006386 CAGTACAGCCTTTTCTTTCCTGAT 58.994 41.667 0.00 0.00 0.00 2.90
2260 4102 3.057946 GCAGTACAGCCTTTTCTTTCCTG 60.058 47.826 0.00 0.00 0.00 3.86
2261 4103 3.149981 GCAGTACAGCCTTTTCTTTCCT 58.850 45.455 0.00 0.00 0.00 3.36
2262 4104 2.884639 TGCAGTACAGCCTTTTCTTTCC 59.115 45.455 7.87 0.00 0.00 3.13
2403 4259 4.677584 GACATTGTTGTTGCTGGTTTGTA 58.322 39.130 0.00 0.00 35.79 2.41
2428 4284 1.398958 GCCCCTGAACAAGCCAACAA 61.399 55.000 0.00 0.00 0.00 2.83
2453 4309 1.069596 CATCGCCCGATCACCATGA 59.930 57.895 0.00 0.00 31.62 3.07
2523 4379 4.141620 ACTCAAGTGGAACAACTGTCAGAT 60.142 41.667 6.91 0.00 44.16 2.90
2583 4441 2.023673 CAACCACTTGCTCTCAAACCA 58.976 47.619 0.00 0.00 0.00 3.67
2690 4552 2.489329 CGAGCCATGACCAATTCTTTGT 59.511 45.455 0.00 0.00 0.00 2.83
2800 4667 7.164230 ACCAAGTCAAACACTTTGTTTCATA 57.836 32.000 1.25 0.00 46.61 2.15
2801 4668 6.036577 ACCAAGTCAAACACTTTGTTTCAT 57.963 33.333 1.25 0.00 46.61 2.57
2906 4776 3.071459 GCAATGTCGCGAGTGACCG 62.071 63.158 10.24 0.00 38.11 4.79
2907 4777 2.778679 GCAATGTCGCGAGTGACC 59.221 61.111 10.24 0.00 38.11 4.02
2937 4807 1.623311 ACATCCACATTGTCGGACAGA 59.377 47.619 11.14 5.27 33.05 3.41
2938 4808 2.099141 ACATCCACATTGTCGGACAG 57.901 50.000 11.14 3.42 33.05 3.51
2939 4809 2.150390 CAACATCCACATTGTCGGACA 58.850 47.619 6.76 6.76 33.05 4.02
2940 4810 1.135689 GCAACATCCACATTGTCGGAC 60.136 52.381 0.00 0.00 33.05 4.79
2941 4811 1.164411 GCAACATCCACATTGTCGGA 58.836 50.000 9.45 9.45 35.27 4.55
2942 4812 0.179192 CGCAACATCCACATTGTCGG 60.179 55.000 0.00 0.00 0.00 4.79
2943 4813 0.794229 GCGCAACATCCACATTGTCG 60.794 55.000 0.30 0.00 0.00 4.35
2944 4814 0.794229 CGCGCAACATCCACATTGTC 60.794 55.000 8.75 0.00 0.00 3.18
2945 4815 1.209898 CGCGCAACATCCACATTGT 59.790 52.632 8.75 0.00 0.00 2.71
2946 4816 0.794229 GTCGCGCAACATCCACATTG 60.794 55.000 8.75 0.00 0.00 2.82
2947 4817 0.955428 AGTCGCGCAACATCCACATT 60.955 50.000 8.75 0.00 0.00 2.71
2948 4818 0.955428 AAGTCGCGCAACATCCACAT 60.955 50.000 8.75 0.00 0.00 3.21
2949 4819 1.565156 GAAGTCGCGCAACATCCACA 61.565 55.000 8.75 0.00 0.00 4.17
2950 4820 1.132640 GAAGTCGCGCAACATCCAC 59.867 57.895 8.75 0.00 0.00 4.02
2951 4821 0.245266 TAGAAGTCGCGCAACATCCA 59.755 50.000 8.75 0.00 0.00 3.41
2952 4822 0.924090 CTAGAAGTCGCGCAACATCC 59.076 55.000 8.75 0.00 0.00 3.51
2953 4823 1.321743 CACTAGAAGTCGCGCAACATC 59.678 52.381 8.75 0.58 0.00 3.06
2954 4824 1.336887 ACACTAGAAGTCGCGCAACAT 60.337 47.619 8.75 0.00 0.00 2.71
2955 4825 0.031585 ACACTAGAAGTCGCGCAACA 59.968 50.000 8.75 0.00 0.00 3.33
2956 4826 0.435008 CACACTAGAAGTCGCGCAAC 59.565 55.000 8.75 0.00 0.00 4.17
2957 4827 0.666274 CCACACTAGAAGTCGCGCAA 60.666 55.000 8.75 0.00 0.00 4.85
2958 4828 1.080772 CCACACTAGAAGTCGCGCA 60.081 57.895 8.75 0.00 0.00 6.09
2959 4829 2.445438 GCCACACTAGAAGTCGCGC 61.445 63.158 0.00 0.00 0.00 6.86
2960 4830 0.666274 TTGCCACACTAGAAGTCGCG 60.666 55.000 0.00 0.00 0.00 5.87
2961 4831 0.790814 GTTGCCACACTAGAAGTCGC 59.209 55.000 0.00 0.00 0.00 5.19
2962 4832 1.060713 CGTTGCCACACTAGAAGTCG 58.939 55.000 0.00 0.00 0.00 4.18
2963 4833 2.433868 TCGTTGCCACACTAGAAGTC 57.566 50.000 0.00 0.00 0.00 3.01
2964 4834 2.299013 TCATCGTTGCCACACTAGAAGT 59.701 45.455 0.00 0.00 0.00 3.01
2965 4835 2.668457 GTCATCGTTGCCACACTAGAAG 59.332 50.000 0.00 0.00 0.00 2.85
2966 4836 2.683968 GTCATCGTTGCCACACTAGAA 58.316 47.619 0.00 0.00 0.00 2.10
2967 4837 1.402325 CGTCATCGTTGCCACACTAGA 60.402 52.381 0.00 0.00 0.00 2.43
2968 4838 0.992072 CGTCATCGTTGCCACACTAG 59.008 55.000 0.00 0.00 0.00 2.57
2969 4839 0.389296 CCGTCATCGTTGCCACACTA 60.389 55.000 0.00 0.00 35.01 2.74
2970 4840 1.667830 CCGTCATCGTTGCCACACT 60.668 57.895 0.00 0.00 35.01 3.55
2971 4841 2.860293 CCGTCATCGTTGCCACAC 59.140 61.111 0.00 0.00 35.01 3.82
2972 4842 3.047280 GCCGTCATCGTTGCCACA 61.047 61.111 0.00 0.00 35.01 4.17
2973 4843 2.240612 GAAGCCGTCATCGTTGCCAC 62.241 60.000 0.00 0.00 35.01 5.01
2974 4844 2.031919 AAGCCGTCATCGTTGCCA 59.968 55.556 0.00 0.00 35.01 4.92
2975 4845 2.785258 GAAGCCGTCATCGTTGCC 59.215 61.111 0.00 0.00 35.01 4.52
2976 4846 2.014093 CTCGAAGCCGTCATCGTTGC 62.014 60.000 0.00 0.00 39.91 4.17
2977 4847 1.991430 CTCGAAGCCGTCATCGTTG 59.009 57.895 0.00 0.00 39.91 4.10
2978 4848 1.805945 GCTCGAAGCCGTCATCGTT 60.806 57.895 0.00 0.00 39.91 3.85
2979 4849 2.202623 GCTCGAAGCCGTCATCGT 60.203 61.111 0.00 0.00 39.91 3.73
2980 4850 3.315521 CGCTCGAAGCCGTCATCG 61.316 66.667 0.00 0.00 38.18 3.84
2981 4851 1.475441 CTTCGCTCGAAGCCGTCATC 61.475 60.000 17.45 0.00 43.95 2.92
2982 4852 1.517257 CTTCGCTCGAAGCCGTCAT 60.517 57.895 17.45 0.00 43.95 3.06
2983 4853 2.126463 CTTCGCTCGAAGCCGTCA 60.126 61.111 17.45 0.00 43.95 4.35
2990 4860 2.736995 CGCCCAACTTCGCTCGAA 60.737 61.111 4.58 4.58 0.00 3.71
2991 4861 4.735132 CCGCCCAACTTCGCTCGA 62.735 66.667 0.00 0.00 0.00 4.04
2997 4867 3.741476 CAGCAGCCGCCCAACTTC 61.741 66.667 0.00 0.00 39.83 3.01
2998 4868 4.269523 TCAGCAGCCGCCCAACTT 62.270 61.111 0.00 0.00 39.83 2.66
2999 4869 4.711949 CTCAGCAGCCGCCCAACT 62.712 66.667 0.00 0.00 39.83 3.16
3009 4879 1.354040 CGACTACCAAAGCTCAGCAG 58.646 55.000 0.00 0.00 0.00 4.24
3010 4880 0.037326 CCGACTACCAAAGCTCAGCA 60.037 55.000 0.00 0.00 0.00 4.41
3011 4881 2.755929 CCGACTACCAAAGCTCAGC 58.244 57.895 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.