Multiple sequence alignment - TraesCS4B01G310300

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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 TraesCS4B01G310300 chr4B 100.000 4018 0 0 1471 5488 600657854 600653837 0.000000e+00 7420.0
1 TraesCS4B01G310300 chr4B 100.000 1130 0 0 1 1130 600659324 600658195 0.000000e+00 2087.0
2 TraesCS4B01G310300 chr4D 92.718 4106 173 46 1471 5488 476306263 476302196 0.000000e+00 5810.0
3 TraesCS4B01G310300 chr4D 87.058 904 59 24 260 1129 476307170 476306291 0.000000e+00 968.0
4 TraesCS4B01G310300 chr4A 92.179 3516 144 47 1518 4933 683488167 683484683 0.000000e+00 4848.0
5 TraesCS4B01G310300 chr4A 87.755 735 49 20 412 1130 683488960 683488251 0.000000e+00 821.0
6 TraesCS4B01G310300 chr4A 85.106 564 37 21 4935 5485 683484633 683484104 2.910000e-147 532.0
7 TraesCS4B01G310300 chr4A 89.256 363 36 3 19 380 683489406 683489046 8.380000e-123 451.0
8 TraesCS4B01G310300 chr2D 79.689 2314 322 88 2276 4492 367504813 367502551 0.000000e+00 1533.0
9 TraesCS4B01G310300 chr2D 77.663 873 170 17 3142 4007 367921944 367922798 4.900000e-140 508.0
10 TraesCS4B01G310300 chr2D 94.372 231 13 0 1564 1794 367505464 367505234 6.760000e-94 355.0
11 TraesCS4B01G310300 chr2D 86.923 260 34 0 1891 2150 367505149 367504890 5.380000e-75 292.0
12 TraesCS4B01G310300 chr2D 78.070 228 48 2 4270 4496 367923052 367923278 5.730000e-30 143.0
13 TraesCS4B01G310300 chr2A 79.398 2325 322 89 2276 4492 497654768 497652493 0.000000e+00 1495.0
14 TraesCS4B01G310300 chr2A 76.119 1072 214 34 2949 4007 498042480 498043522 1.750000e-144 523.0
15 TraesCS4B01G310300 chr2A 93.103 232 16 0 1564 1795 497655429 497655198 1.890000e-89 340.0
16 TraesCS4B01G310300 chr2A 90.000 260 26 0 1891 2150 497655108 497654849 2.450000e-88 337.0
17 TraesCS4B01G310300 chr2A 76.754 228 51 2 4270 4496 498043776 498044002 5.770000e-25 126.0
18 TraesCS4B01G310300 chr2B 80.232 1897 262 73 2276 4097 436240278 436238420 0.000000e+00 1321.0
19 TraesCS4B01G310300 chr2B 78.146 874 164 20 3142 4007 436960280 436961134 1.050000e-146 531.0
20 TraesCS4B01G310300 chr2B 94.828 232 12 0 1564 1795 436240940 436240709 4.040000e-96 363.0
21 TraesCS4B01G310300 chr2B 89.231 260 28 0 1891 2150 436240618 436240359 5.300000e-85 326.0
22 TraesCS4B01G310300 chr2B 83.861 316 39 5 4186 4492 436238364 436238052 1.930000e-74 291.0
23 TraesCS4B01G310300 chr2B 77.193 228 50 2 4270 4496 436961388 436961614 1.240000e-26 132.0
24 TraesCS4B01G310300 chr6A 80.723 249 44 2 1548 1793 33542574 33542327 2.020000e-44 191.0
25 TraesCS4B01G310300 chr3B 100.000 28 0 0 4812 4839 237247044 237247017 1.000000e-02 52.8


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 TraesCS4B01G310300 chr4B 600653837 600659324 5487 True 4753.500000 7420 100.000000 1 5488 2 chr4B.!!$R1 5487
1 TraesCS4B01G310300 chr4D 476302196 476307170 4974 True 3389.000000 5810 89.888000 260 5488 2 chr4D.!!$R1 5228
2 TraesCS4B01G310300 chr4A 683484104 683489406 5302 True 1663.000000 4848 88.574000 19 5485 4 chr4A.!!$R1 5466
3 TraesCS4B01G310300 chr2D 367502551 367505464 2913 True 726.666667 1533 86.994667 1564 4492 3 chr2D.!!$R1 2928
4 TraesCS4B01G310300 chr2D 367921944 367923278 1334 False 325.500000 508 77.866500 3142 4496 2 chr2D.!!$F1 1354
5 TraesCS4B01G310300 chr2A 497652493 497655429 2936 True 724.000000 1495 87.500333 1564 4492 3 chr2A.!!$R1 2928
6 TraesCS4B01G310300 chr2A 498042480 498044002 1522 False 324.500000 523 76.436500 2949 4496 2 chr2A.!!$F1 1547
7 TraesCS4B01G310300 chr2B 436238052 436240940 2888 True 575.250000 1321 87.038000 1564 4492 4 chr2B.!!$R1 2928
8 TraesCS4B01G310300 chr2B 436960280 436961614 1334 False 331.500000 531 77.669500 3142 4496 2 chr2B.!!$F1 1354

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
39 40 0.023732 CGCATGCGTTCGAGTAAGTG 59.976 55.000 31.33 0.0 34.35 3.16 F
922 999 0.034896 TTCTTCCTCCAACACGAGCC 59.965 55.000 0.00 0.0 0.00 4.70 F
2469 2617 0.179001 TCATCTCGGTGGCGATCCTA 60.179 55.000 0.00 0.0 0.00 2.94 F
3600 3879 1.207089 TCGTGTTTGGCTCCATAGAGG 59.793 52.381 0.00 0.0 40.79 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 1998 0.041663 CAAACGTGCCACCTACAACG 60.042 55.000 0.00 0.00 0.00 4.10 R
2520 2668 1.556911 ACTGAGATGACCGGAGCAAAT 59.443 47.619 9.46 0.00 0.00 2.32 R
4340 4637 0.037590 ATGAGTTGGCTTTGGCGGTA 59.962 50.000 0.00 0.00 39.81 4.02 R
5146 5507 1.078143 GTAGCTCCCAGTGGGCAAG 60.078 63.158 24.75 17.62 43.94 4.01 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
18 19 3.050703 CGGTCATAGGTGCTCACAC 57.949 57.895 2.21 0.00 46.66 3.82
39 40 0.023732 CGCATGCGTTCGAGTAAGTG 59.976 55.000 31.33 0.00 34.35 3.16
50 51 5.003496 CGTTCGAGTAAGTGACATGTGTATG 59.997 44.000 1.15 0.00 40.24 2.39
60 61 2.610433 ACATGTGTATGTGAGCGTCTG 58.390 47.619 0.00 0.00 45.54 3.51
61 62 1.325640 CATGTGTATGTGAGCGTCTGC 59.674 52.381 0.00 0.00 43.24 4.26
71 72 2.468532 GCGTCTGCGTTTGTACCG 59.531 61.111 0.00 0.00 40.81 4.02
108 109 9.810545 CACTTTTACAAGGAAATCTAAACCAAA 57.189 29.630 0.00 0.00 33.82 3.28
123 124 8.876275 TCTAAACCAAATATATGACACCGTAC 57.124 34.615 0.00 0.00 0.00 3.67
139 140 0.531200 GTACGTGCTCCTGCCTTACT 59.469 55.000 0.00 0.00 38.71 2.24
157 158 6.040391 GCCTTACTGCAATTATCACCCAAATA 59.960 38.462 0.00 0.00 0.00 1.40
167 168 4.903045 ATCACCCAAATATAGTACCCCG 57.097 45.455 0.00 0.00 0.00 5.73
182 183 2.247358 ACCCCGCATGAAGTGAAATTT 58.753 42.857 0.00 0.00 0.00 1.82
242 243 9.880157 ATAGTTTTACTAGATGCCGAGTTTTAA 57.120 29.630 0.00 0.00 33.66 1.52
272 273 4.000988 CGACAGGCAAGTGTATTTTACCT 58.999 43.478 0.00 0.00 0.00 3.08
318 320 4.653868 TCGACTTATAAAACAAGCCCCAA 58.346 39.130 0.00 0.00 0.00 4.12
330 332 0.617820 AGCCCCAAGGTCATACGAGT 60.618 55.000 0.00 0.00 34.57 4.18
375 377 5.563842 GCATAAGCATAACTGAAGTCACAC 58.436 41.667 0.00 0.00 41.58 3.82
401 428 2.675889 GCCAAAACGATCCGGAGACTAA 60.676 50.000 11.34 0.00 0.00 2.24
415 442 2.979813 GAGACTAAACCGTCGCGTTAAA 59.020 45.455 5.77 0.00 38.90 1.52
424 451 3.740321 ACCGTCGCGTTAAATAAAGACAA 59.260 39.130 5.77 0.00 0.00 3.18
431 458 8.250445 GTCGCGTTAAATAAAGACAATATTTGC 58.750 33.333 5.77 0.00 35.28 3.68
440 467 5.866335 AAGACAATATTTGCCGACGTAAA 57.134 34.783 0.00 0.00 0.00 2.01
446 505 7.976826 ACAATATTTGCCGACGTAAATAAAGA 58.023 30.769 14.50 0.00 39.17 2.52
480 539 4.049186 GCTTACTCCATATGTACACACCG 58.951 47.826 0.00 0.00 0.00 4.94
486 545 5.597182 ACTCCATATGTACACACCGAAGTAT 59.403 40.000 0.00 0.00 0.00 2.12
513 575 4.506095 GGCAAGTAACCTACCTTGGAGAAA 60.506 45.833 0.00 0.00 0.00 2.52
515 577 5.181433 GCAAGTAACCTACCTTGGAGAAAAG 59.819 44.000 0.00 0.00 0.00 2.27
519 581 2.087646 CCTACCTTGGAGAAAAGCAGC 58.912 52.381 0.00 0.00 0.00 5.25
575 637 5.417580 TGGGATTTGTTTATCCGAGGAAAAG 59.582 40.000 0.00 0.00 44.22 2.27
595 657 2.627699 AGGTCAATGGACGCAAACAATT 59.372 40.909 0.00 0.00 45.28 2.32
596 658 2.986479 GGTCAATGGACGCAAACAATTC 59.014 45.455 0.00 0.00 45.28 2.17
611 678 1.739338 AATTCCGGCAACCGCAAACA 61.739 50.000 0.00 0.00 46.86 2.83
637 708 4.427312 GCCTCATTTGCTAACCAATCTTG 58.573 43.478 0.00 0.00 32.49 3.02
660 731 2.056481 GATCTGGTGGCAGCATTCGC 62.056 60.000 20.91 6.53 38.99 4.70
730 801 0.886563 AAGTGCTCATGAGGCTTTGC 59.113 50.000 23.89 9.99 0.00 3.68
767 838 6.600822 CCAATCATCACCCAGGTATGATAATC 59.399 42.308 15.84 0.00 38.97 1.75
840 913 1.762370 TGTCAACTCTCAGGAGCAACA 59.238 47.619 0.00 0.00 42.98 3.33
849 922 0.454600 CAGGAGCAACATCATGTGCC 59.545 55.000 8.15 1.06 0.00 5.01
850 923 1.028330 AGGAGCAACATCATGTGCCG 61.028 55.000 8.15 0.00 0.00 5.69
859 932 1.027357 ATCATGTGCCGGCTCAAATC 58.973 50.000 32.53 13.87 0.00 2.17
860 933 0.035152 TCATGTGCCGGCTCAAATCT 60.035 50.000 32.53 15.39 0.00 2.40
861 934 0.099968 CATGTGCCGGCTCAAATCTG 59.900 55.000 32.53 22.42 0.00 2.90
862 935 1.660560 ATGTGCCGGCTCAAATCTGC 61.661 55.000 32.53 9.81 0.00 4.26
863 936 2.033911 TGCCGGCTCAAATCTGCA 59.966 55.556 29.70 0.00 0.00 4.41
892 965 3.312697 CGCTCTATTTAAACAAGCCCTCC 59.687 47.826 10.87 0.00 0.00 4.30
893 966 3.312697 GCTCTATTTAAACAAGCCCTCCG 59.687 47.826 6.93 0.00 0.00 4.63
894 967 4.766375 CTCTATTTAAACAAGCCCTCCGA 58.234 43.478 0.00 0.00 0.00 4.55
895 968 5.367945 TCTATTTAAACAAGCCCTCCGAT 57.632 39.130 0.00 0.00 0.00 4.18
896 969 5.123227 TCTATTTAAACAAGCCCTCCGATG 58.877 41.667 0.00 0.00 0.00 3.84
897 970 1.459450 TTAAACAAGCCCTCCGATGC 58.541 50.000 0.00 0.00 0.00 3.91
898 971 0.618458 TAAACAAGCCCTCCGATGCT 59.382 50.000 0.00 0.00 40.17 3.79
899 972 0.678048 AAACAAGCCCTCCGATGCTC 60.678 55.000 0.00 0.00 36.66 4.26
900 973 1.841302 AACAAGCCCTCCGATGCTCA 61.841 55.000 0.00 0.00 36.66 4.26
901 974 1.147824 CAAGCCCTCCGATGCTCAT 59.852 57.895 0.00 0.00 36.66 2.90
917 990 3.006247 GCTCATCTTCTTCCTCCAACAC 58.994 50.000 0.00 0.00 0.00 3.32
922 999 0.034896 TTCTTCCTCCAACACGAGCC 59.965 55.000 0.00 0.00 0.00 4.70
947 1024 2.125350 GCTGCAGACCTTCTCCGG 60.125 66.667 20.43 0.00 0.00 5.14
948 1025 2.125350 CTGCAGACCTTCTCCGGC 60.125 66.667 8.42 0.00 0.00 6.13
949 1026 3.672295 CTGCAGACCTTCTCCGGCC 62.672 68.421 8.42 0.00 0.00 6.13
950 1027 4.821589 GCAGACCTTCTCCGGCCG 62.822 72.222 21.04 21.04 0.00 6.13
1532 1622 6.546772 GCAGTGAGTAGAGTACCCTACTTAAT 59.453 42.308 17.16 10.45 46.66 1.40
1853 1962 3.182152 AGTGTACCTACCTGCTGGATTT 58.818 45.455 17.64 0.00 37.04 2.17
1889 1998 1.303155 ACTGCTCTTCTTGCTGGCC 60.303 57.895 0.00 0.00 34.40 5.36
2096 2213 1.912043 CTCTTCACCCTCACCATCCTT 59.088 52.381 0.00 0.00 0.00 3.36
2132 2249 1.375396 CGGCGATGGAACCTTGACA 60.375 57.895 0.00 0.00 0.00 3.58
2141 2258 0.958822 GAACCTTGACACCCGCAATT 59.041 50.000 0.00 0.00 0.00 2.32
2184 2306 9.623000 TCAATCAATCATGTATCAAAGAGTCAT 57.377 29.630 0.00 0.00 0.00 3.06
2186 2308 8.618702 ATCAATCATGTATCAAAGAGTCATCC 57.381 34.615 0.00 0.00 0.00 3.51
2194 2316 8.195165 TGTATCAAAGAGTCATCCCCTATTAG 57.805 38.462 0.00 0.00 0.00 1.73
2200 2322 9.930693 CAAAGAGTCATCCCCTATTAGTTATAC 57.069 37.037 0.00 0.00 0.00 1.47
2202 2324 9.845214 AAGAGTCATCCCCTATTAGTTATACAT 57.155 33.333 0.00 0.00 0.00 2.29
2341 2478 3.947834 CCTGACCCAAAGTATGTGAATCC 59.052 47.826 0.00 0.00 0.00 3.01
2342 2479 4.567537 CCTGACCCAAAGTATGTGAATCCA 60.568 45.833 0.00 0.00 0.00 3.41
2343 2480 4.991776 TGACCCAAAGTATGTGAATCCAA 58.008 39.130 0.00 0.00 0.00 3.53
2344 2481 5.009631 TGACCCAAAGTATGTGAATCCAAG 58.990 41.667 0.00 0.00 0.00 3.61
2362 2499 5.600749 TCCAAGGAAGGAAGGATTAGTAGT 58.399 41.667 0.00 0.00 33.93 2.73
2469 2617 0.179001 TCATCTCGGTGGCGATCCTA 60.179 55.000 0.00 0.00 0.00 2.94
2562 2710 1.425066 TGGTTCCTTCTGATTGCTGGT 59.575 47.619 0.00 0.00 0.00 4.00
2565 2713 4.263905 TGGTTCCTTCTGATTGCTGGTATT 60.264 41.667 0.00 0.00 0.00 1.89
2583 2731 4.099881 GGTATTGGGATGTACAACCTCGTA 59.900 45.833 20.31 8.87 0.00 3.43
2586 2734 2.756760 TGGGATGTACAACCTCGTAGTC 59.243 50.000 20.31 4.09 0.00 2.59
2593 2741 5.195185 TGTACAACCTCGTAGTCCATGATA 58.805 41.667 0.00 0.00 0.00 2.15
2604 2752 4.592485 AGTCCATGATATCGGTGTTCTC 57.408 45.455 0.00 0.00 0.00 2.87
2613 2761 2.434774 GGTGTTCTCCGGGCCTTT 59.565 61.111 0.84 0.00 0.00 3.11
2652 2800 4.724279 ACAGTACTTCCAAAGGAATGGT 57.276 40.909 4.58 0.00 41.61 3.55
2682 2830 1.318576 GGGTTTCACTTGGTGGAGTG 58.681 55.000 0.00 0.00 46.58 3.51
2703 2851 4.997395 GTGATCTTGTGTGTCACAGGTAAT 59.003 41.667 5.74 0.00 45.39 1.89
2704 2852 5.470098 GTGATCTTGTGTGTCACAGGTAATT 59.530 40.000 5.74 0.00 45.39 1.40
2710 2858 6.366315 TGTGTGTCACAGGTAATTAACAAC 57.634 37.500 5.74 0.00 39.62 3.32
2711 2859 5.297278 TGTGTGTCACAGGTAATTAACAACC 59.703 40.000 5.74 0.00 39.62 3.77
2735 2893 5.751243 TTCTAACTGAAAAGACCTTGTGC 57.249 39.130 0.00 0.00 0.00 4.57
2747 2905 4.591399 TTGTGCTGCCTGCCTGCT 62.591 61.111 0.00 0.00 42.00 4.24
2773 2941 4.226427 AGGCTGCAATGACTAATCTGAA 57.774 40.909 0.50 0.00 0.00 3.02
2778 2946 6.405065 GGCTGCAATGACTAATCTGAAATGAA 60.405 38.462 0.50 0.00 0.00 2.57
2779 2947 7.201145 GCTGCAATGACTAATCTGAAATGAAT 58.799 34.615 0.00 0.00 0.00 2.57
2780 2948 7.705325 GCTGCAATGACTAATCTGAAATGAATT 59.295 33.333 0.00 0.00 0.00 2.17
2781 2949 9.234384 CTGCAATGACTAATCTGAAATGAATTC 57.766 33.333 0.00 0.00 38.60 2.17
2782 2950 8.741841 TGCAATGACTAATCTGAAATGAATTCA 58.258 29.630 11.26 11.26 45.71 2.57
2893 3085 6.877611 TCTTTCGGAAGTAAGCATTCTTTT 57.122 33.333 2.72 0.00 38.25 2.27
2906 3098 4.637977 AGCATTCTTTTCCTAGCTACAAGC 59.362 41.667 0.00 0.00 42.84 4.01
2907 3099 7.798114 TAAGCATTCTTTTCCTAGCTACAAGCT 60.798 37.037 6.66 6.66 42.97 3.74
2925 3117 4.708726 AGCTAAAACAGAACCATGCATC 57.291 40.909 0.00 0.00 0.00 3.91
2937 3154 2.504585 ACCATGCATCTCACAGATCAGT 59.495 45.455 0.00 0.00 31.32 3.41
2944 3161 4.694509 GCATCTCACAGATCAGTTTCAACT 59.305 41.667 0.00 0.00 34.19 3.16
2945 3162 5.180868 GCATCTCACAGATCAGTTTCAACTT 59.819 40.000 0.00 0.00 32.48 2.66
2946 3163 6.293845 GCATCTCACAGATCAGTTTCAACTTT 60.294 38.462 0.00 0.00 32.48 2.66
2960 3177 3.681593 TCAACTTTATCTTGTTCCCGGG 58.318 45.455 16.85 16.85 0.00 5.73
3009 3226 2.289565 GCTTACCTGAGGAAATTCCCG 58.710 52.381 4.99 0.00 37.19 5.14
3407 3657 1.873591 CGGGCATGCTTATGGTAAGTC 59.126 52.381 18.92 0.00 0.00 3.01
3408 3658 2.230660 GGGCATGCTTATGGTAAGTCC 58.769 52.381 18.92 1.21 0.00 3.85
3409 3659 2.158608 GGGCATGCTTATGGTAAGTCCT 60.159 50.000 18.92 0.00 37.07 3.85
3600 3879 1.207089 TCGTGTTTGGCTCCATAGAGG 59.793 52.381 0.00 0.00 40.79 3.69
3602 3881 2.615493 CGTGTTTGGCTCCATAGAGGTT 60.615 50.000 0.00 0.00 40.79 3.50
3756 4035 3.699538 TCACATCGTGCCTACTAGTGAAT 59.300 43.478 5.39 0.00 32.98 2.57
3908 4187 6.127563 CCATCTTCATGTTCATGTCCATCAAA 60.128 38.462 11.73 0.00 0.00 2.69
4056 4335 1.425066 AGTTTGTGGCCTTCCTCATGA 59.575 47.619 3.32 0.00 35.94 3.07
4118 4403 2.289072 ACACAACGAAGTGGAGGAGATG 60.289 50.000 14.48 0.00 45.00 2.90
4340 4637 1.311059 GATGGGGGAGGCCAATGTT 59.689 57.895 5.01 0.00 0.00 2.71
4561 4859 4.444733 CCATGTCATTCTGGCTGTATGGTA 60.445 45.833 10.27 2.23 31.19 3.25
4562 4860 4.406648 TGTCATTCTGGCTGTATGGTAG 57.593 45.455 10.27 0.00 0.00 3.18
4563 4861 3.134623 TGTCATTCTGGCTGTATGGTAGG 59.865 47.826 10.27 0.00 0.00 3.18
4604 4904 2.191400 AGAGGATATGTGTGTGTGCCT 58.809 47.619 0.00 0.00 0.00 4.75
4704 5004 6.823689 TCTGAGCTGAATATAAGGGTGTTTTC 59.176 38.462 0.00 0.00 0.00 2.29
4833 5134 0.322456 TGGTGGAGCCAGGATTTTCG 60.322 55.000 0.00 0.00 43.61 3.46
4856 5157 5.391950 CGACATGAATGTGGGGAGTTAAAAG 60.392 44.000 0.00 0.00 41.95 2.27
4859 5160 6.725834 ACATGAATGTGGGGAGTTAAAAGAAT 59.274 34.615 0.00 0.00 40.03 2.40
4908 5211 9.345517 CATGAAGATTCACAATTAACGACAATT 57.654 29.630 0.00 0.00 40.49 2.32
4988 5342 6.206634 AGTTACATCGCAAAATCAAGGAGAAA 59.793 34.615 0.00 0.00 0.00 2.52
5146 5507 3.409026 TTTCACCTTGCTCCTTCTCTC 57.591 47.619 0.00 0.00 0.00 3.20
5178 5539 1.011595 AGCTACTCCTTCCTCCCTCA 58.988 55.000 0.00 0.00 0.00 3.86
5188 5549 0.322456 TCCTCCCTCAACCAAATGCG 60.322 55.000 0.00 0.00 0.00 4.73
5216 5577 2.618709 AGAAAAGGTTGCTGAAACTCGG 59.381 45.455 0.00 0.00 38.92 4.63
5217 5578 2.341846 AAAGGTTGCTGAAACTCGGA 57.658 45.000 0.00 0.00 38.92 4.55
5219 5580 2.568623 AGGTTGCTGAAACTCGGATT 57.431 45.000 0.00 0.00 38.92 3.01
5221 5582 2.151202 GGTTGCTGAAACTCGGATTGA 58.849 47.619 0.00 0.00 38.92 2.57
5222 5583 2.095718 GGTTGCTGAAACTCGGATTGAC 60.096 50.000 0.00 0.00 38.92 3.18
5225 5586 3.476552 TGCTGAAACTCGGATTGACTTT 58.523 40.909 0.00 0.00 0.00 2.66
5226 5587 3.882888 TGCTGAAACTCGGATTGACTTTT 59.117 39.130 0.00 0.00 0.00 2.27
5227 5588 5.060506 TGCTGAAACTCGGATTGACTTTTA 58.939 37.500 0.00 0.00 0.00 1.52
5228 5589 5.705441 TGCTGAAACTCGGATTGACTTTTAT 59.295 36.000 0.00 0.00 0.00 1.40
5263 5626 4.202295 GGCAGACAGATCAATAGATGTGGA 60.202 45.833 7.41 0.00 46.69 4.02
5273 5636 5.715921 TCAATAGATGTGGATCACCCTCTA 58.284 41.667 0.00 8.72 34.52 2.43
5280 5643 4.104086 TGTGGATCACCCTCTATTCTTGT 58.896 43.478 0.00 0.00 32.73 3.16
5282 5645 4.878397 GTGGATCACCCTCTATTCTTGTTG 59.122 45.833 0.00 0.00 35.38 3.33
5284 5647 4.164221 GGATCACCCTCTATTCTTGTTGGA 59.836 45.833 0.00 0.00 0.00 3.53
5285 5648 4.826274 TCACCCTCTATTCTTGTTGGAG 57.174 45.455 0.00 0.00 0.00 3.86
5286 5649 4.425772 TCACCCTCTATTCTTGTTGGAGA 58.574 43.478 0.00 0.00 0.00 3.71
5319 5688 9.315363 AGAAACCTAGAAGAAGATTAGAAGACA 57.685 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.413767 CGCGTGTGAGCACCTATGAC 61.414 60.000 0.00 0.00 42.39 3.06
3 4 1.153842 CGCGTGTGAGCACCTATGA 60.154 57.895 0.00 0.00 42.39 2.15
4 5 2.802667 GCGCGTGTGAGCACCTATG 61.803 63.158 8.43 0.00 42.39 2.23
5 6 2.509336 GCGCGTGTGAGCACCTAT 60.509 61.111 8.43 0.00 42.39 2.57
6 7 3.984749 TGCGCGTGTGAGCACCTA 61.985 61.111 8.43 0.00 46.37 3.08
19 20 1.013323 CTTACTCGAACGCATGCGC 60.013 57.895 38.15 22.56 44.19 6.09
20 21 0.023732 CACTTACTCGAACGCATGCG 59.976 55.000 36.79 36.79 46.03 4.73
21 22 1.059264 GTCACTTACTCGAACGCATGC 59.941 52.381 7.91 7.91 0.00 4.06
26 27 3.305964 ACACATGTCACTTACTCGAACG 58.694 45.455 0.00 0.00 0.00 3.95
31 32 5.289675 GCTCACATACACATGTCACTTACTC 59.710 44.000 0.00 0.00 43.73 2.59
39 40 2.600420 CAGACGCTCACATACACATGTC 59.400 50.000 0.00 0.00 43.73 3.06
50 51 0.161024 GTACAAACGCAGACGCTCAC 59.839 55.000 0.00 0.00 45.53 3.51
54 55 1.824272 AACGGTACAAACGCAGACGC 61.824 55.000 0.00 0.00 45.53 5.19
80 81 8.626526 TGGTTTAGATTTCCTTGTAAAAGTGAC 58.373 33.333 0.00 0.00 0.00 3.67
123 124 2.103042 GCAGTAAGGCAGGAGCACG 61.103 63.158 0.00 0.00 44.61 5.34
139 140 7.668052 GGGTACTATATTTGGGTGATAATTGCA 59.332 37.037 0.00 0.00 0.00 4.08
157 158 2.394632 TCACTTCATGCGGGGTACTAT 58.605 47.619 0.00 0.00 0.00 2.12
242 243 2.037251 ACACTTGCCTGTCGTCAATACT 59.963 45.455 0.00 0.00 0.00 2.12
289 290 9.285770 GGGCTTGTTTTATAAGTCGATAAAAAG 57.714 33.333 3.84 1.58 40.93 2.27
318 320 5.417894 TGTGAATTCACTACTCGTATGACCT 59.582 40.000 32.57 0.00 46.55 3.85
330 332 2.779755 ATGCCGGTGTGAATTCACTA 57.220 45.000 32.57 19.57 46.55 2.74
368 370 0.932399 GTTTTGGCGTACGTGTGACT 59.068 50.000 17.90 0.00 0.00 3.41
375 377 1.342473 CGGATCGTTTTGGCGTACG 59.658 57.895 11.84 11.84 39.03 3.67
401 428 3.740321 TGTCTTTATTTAACGCGACGGTT 59.260 39.130 15.93 0.00 0.00 4.44
415 442 7.542534 TTACGTCGGCAAATATTGTCTTTAT 57.457 32.000 0.00 0.00 31.77 1.40
424 451 7.542534 TGTCTTTATTTACGTCGGCAAATAT 57.457 32.000 12.34 0.00 0.00 1.28
460 519 5.419788 ACTTCGGTGTGTACATATGGAGTAA 59.580 40.000 7.80 0.00 0.00 2.24
480 539 6.015603 AGGTAGGTTACTTGCCGATATACTTC 60.016 42.308 0.00 0.00 0.00 3.01
486 545 3.133362 CCAAGGTAGGTTACTTGCCGATA 59.867 47.826 0.00 0.00 42.01 2.92
513 575 5.611128 TTAATCAGATCAGAGAGCTGCTT 57.389 39.130 2.53 6.95 44.52 3.91
515 577 6.864360 ATTTTAATCAGATCAGAGAGCTGC 57.136 37.500 7.36 0.00 44.52 5.25
519 581 7.930325 TGGTGCTATTTTAATCAGATCAGAGAG 59.070 37.037 0.00 0.00 0.00 3.20
566 628 1.732259 CGTCCATTGACCTTTTCCTCG 59.268 52.381 0.00 0.00 38.32 4.63
575 637 2.723124 ATTGTTTGCGTCCATTGACC 57.277 45.000 0.00 0.00 38.32 4.02
611 678 1.635487 TGGTTAGCAAATGAGGCCTCT 59.365 47.619 32.28 15.91 0.00 3.69
637 708 0.745845 ATGCTGCCACCAGATCGAAC 60.746 55.000 0.00 0.00 41.77 3.95
670 741 1.260825 TCATGTTCACGCGCGTAAAAA 59.739 42.857 37.24 24.99 0.00 1.94
730 801 6.096705 TGGGTGATGATTGGTGCTATTTTAAG 59.903 38.462 0.00 0.00 0.00 1.85
747 818 6.213397 TGGTAGATTATCATACCTGGGTGATG 59.787 42.308 20.48 11.46 41.74 3.07
784 855 4.394712 GAGGTGGCACTGACCGGG 62.395 72.222 18.45 0.00 38.64 5.73
785 856 3.177194 TTGAGGTGGCACTGACCGG 62.177 63.158 18.45 0.00 38.64 5.28
840 913 1.027357 GATTTGAGCCGGCACATGAT 58.973 50.000 31.54 23.66 0.00 2.45
849 922 1.136147 GCAGTGCAGATTTGAGCCG 59.864 57.895 11.09 0.00 0.00 5.52
850 923 0.109412 GTGCAGTGCAGATTTGAGCC 60.109 55.000 20.42 0.00 40.08 4.70
859 932 0.742281 AATAGAGCGGTGCAGTGCAG 60.742 55.000 20.42 9.23 40.08 4.41
860 933 0.321564 AAATAGAGCGGTGCAGTGCA 60.322 50.000 15.37 15.37 35.60 4.57
861 934 1.651987 TAAATAGAGCGGTGCAGTGC 58.348 50.000 8.58 8.58 0.00 4.40
862 935 3.435327 TGTTTAAATAGAGCGGTGCAGTG 59.565 43.478 0.00 0.00 0.00 3.66
863 936 3.670625 TGTTTAAATAGAGCGGTGCAGT 58.329 40.909 0.00 0.00 0.00 4.40
892 965 2.102084 TGGAGGAAGAAGATGAGCATCG 59.898 50.000 4.93 0.00 42.48 3.84
893 966 3.834489 TGGAGGAAGAAGATGAGCATC 57.166 47.619 2.27 2.27 38.09 3.91
894 967 3.265221 TGTTGGAGGAAGAAGATGAGCAT 59.735 43.478 0.00 0.00 0.00 3.79
895 968 2.639347 TGTTGGAGGAAGAAGATGAGCA 59.361 45.455 0.00 0.00 0.00 4.26
896 969 3.006247 GTGTTGGAGGAAGAAGATGAGC 58.994 50.000 0.00 0.00 0.00 4.26
897 970 3.056536 TCGTGTTGGAGGAAGAAGATGAG 60.057 47.826 0.00 0.00 0.00 2.90
898 971 2.897326 TCGTGTTGGAGGAAGAAGATGA 59.103 45.455 0.00 0.00 0.00 2.92
899 972 3.257393 CTCGTGTTGGAGGAAGAAGATG 58.743 50.000 0.00 0.00 0.00 2.90
900 973 2.354203 GCTCGTGTTGGAGGAAGAAGAT 60.354 50.000 0.00 0.00 34.56 2.40
901 974 1.000955 GCTCGTGTTGGAGGAAGAAGA 59.999 52.381 0.00 0.00 34.56 2.87
958 1035 4.541020 GCAGTTTTGCTCCGAAGC 57.459 55.556 0.00 0.00 46.95 3.86
988 1065 0.041238 ACCGACATCTCCTTCAGGGA 59.959 55.000 0.00 0.00 42.77 4.20
1532 1622 2.981350 GCGGTCGCCCAAAGGAAA 60.981 61.111 3.73 0.00 33.47 3.13
1547 1637 6.480981 TCACCTGCATATATATCATTCATGCG 59.519 38.462 11.10 7.25 43.84 4.73
1548 1638 7.520131 GCTCACCTGCATATATATCATTCATGC 60.520 40.741 9.53 9.53 41.81 4.06
1549 1639 7.715686 AGCTCACCTGCATATATATCATTCATG 59.284 37.037 0.00 0.00 34.99 3.07
1550 1640 7.715686 CAGCTCACCTGCATATATATCATTCAT 59.284 37.037 0.00 0.00 34.21 2.57
1551 1641 7.046033 CAGCTCACCTGCATATATATCATTCA 58.954 38.462 0.00 0.00 34.21 2.57
1552 1642 6.482641 CCAGCTCACCTGCATATATATCATTC 59.517 42.308 0.00 0.00 40.36 2.67
1554 1644 5.163227 CCCAGCTCACCTGCATATATATCAT 60.163 44.000 0.00 0.00 40.36 2.45
1805 1896 5.400552 TGATGGAATGATTGGGGTCATAA 57.599 39.130 0.00 0.00 37.85 1.90
1807 1898 3.977489 TGATGGAATGATTGGGGTCAT 57.023 42.857 0.00 0.00 40.44 3.06
1808 1899 3.754219 TTGATGGAATGATTGGGGTCA 57.246 42.857 0.00 0.00 0.00 4.02
1809 1900 5.619132 AATTTGATGGAATGATTGGGGTC 57.381 39.130 0.00 0.00 0.00 4.46
1814 1919 8.906867 AGGTACACTAATTTGATGGAATGATTG 58.093 33.333 0.00 0.00 0.00 2.67
1816 1921 9.561069 GTAGGTACACTAATTTGATGGAATGAT 57.439 33.333 0.00 0.00 32.37 2.45
1818 1923 7.993183 AGGTAGGTACACTAATTTGATGGAATG 59.007 37.037 0.00 0.00 32.37 2.67
1853 1962 1.072806 AGTGTGCAATCCAGCTTCAGA 59.927 47.619 0.00 0.00 34.99 3.27
1889 1998 0.041663 CAAACGTGCCACCTACAACG 60.042 55.000 0.00 0.00 0.00 4.10
2132 2249 3.080300 TGATTACCAGAAATTGCGGGT 57.920 42.857 13.29 13.29 39.67 5.28
2325 2462 5.126061 CCTTCCTTGGATTCACATACTTTGG 59.874 44.000 0.00 0.00 0.00 3.28
2341 2478 8.759782 TCTTAACTACTAATCCTTCCTTCCTTG 58.240 37.037 0.00 0.00 0.00 3.61
2342 2479 8.912614 TCTTAACTACTAATCCTTCCTTCCTT 57.087 34.615 0.00 0.00 0.00 3.36
2343 2480 8.912614 TTCTTAACTACTAATCCTTCCTTCCT 57.087 34.615 0.00 0.00 0.00 3.36
2344 2481 8.760735 ACTTCTTAACTACTAATCCTTCCTTCC 58.239 37.037 0.00 0.00 0.00 3.46
2469 2617 1.833630 TGGACCGAGAAGAGCATGAAT 59.166 47.619 0.00 0.00 0.00 2.57
2520 2668 1.556911 ACTGAGATGACCGGAGCAAAT 59.443 47.619 9.46 0.00 0.00 2.32
2562 2710 4.957954 ACTACGAGGTTGTACATCCCAATA 59.042 41.667 17.65 8.00 0.00 1.90
2565 2713 2.756760 GACTACGAGGTTGTACATCCCA 59.243 50.000 17.65 2.58 0.00 4.37
2583 2731 3.322254 GGAGAACACCGATATCATGGACT 59.678 47.826 3.12 4.64 0.00 3.85
2604 2752 2.781681 ATATCGGATTAAAGGCCCGG 57.218 50.000 0.00 0.00 43.16 5.73
2641 2789 4.210331 CATCCCTCCTTACCATTCCTTTG 58.790 47.826 0.00 0.00 0.00 2.77
2652 2800 2.929301 AGTGAAACCCATCCCTCCTTA 58.071 47.619 0.00 0.00 37.80 2.69
2682 2830 7.172532 TGTTAATTACCTGTGACACACAAGATC 59.827 37.037 3.56 0.00 44.08 2.75
2703 2851 8.680001 GGTCTTTTCAGTTAGAAAGGTTGTTAA 58.320 33.333 0.00 0.00 46.24 2.01
2704 2852 8.050930 AGGTCTTTTCAGTTAGAAAGGTTGTTA 58.949 33.333 0.00 0.00 46.24 2.41
2710 2858 6.729187 CACAAGGTCTTTTCAGTTAGAAAGG 58.271 40.000 0.00 0.00 46.24 3.11
2711 2859 6.038714 AGCACAAGGTCTTTTCAGTTAGAAAG 59.961 38.462 0.00 0.00 46.24 2.62
2735 2893 3.282745 CTTGCAAGCAGGCAGGCAG 62.283 63.158 14.65 0.00 45.88 4.85
2751 2909 4.226427 TCAGATTAGTCATTGCAGCCTT 57.774 40.909 0.00 0.00 0.00 4.35
2773 2941 5.244402 TCTGTGCCTGTCATTTGAATTCATT 59.756 36.000 9.40 0.00 0.00 2.57
2778 2946 3.508793 CCTTCTGTGCCTGTCATTTGAAT 59.491 43.478 0.00 0.00 0.00 2.57
2779 2947 2.886523 CCTTCTGTGCCTGTCATTTGAA 59.113 45.455 0.00 0.00 0.00 2.69
2780 2948 2.158623 ACCTTCTGTGCCTGTCATTTGA 60.159 45.455 0.00 0.00 0.00 2.69
2781 2949 2.233271 ACCTTCTGTGCCTGTCATTTG 58.767 47.619 0.00 0.00 0.00 2.32
2782 2950 2.664402 ACCTTCTGTGCCTGTCATTT 57.336 45.000 0.00 0.00 0.00 2.32
2783 2951 3.009473 ACATACCTTCTGTGCCTGTCATT 59.991 43.478 0.00 0.00 0.00 2.57
2786 2973 2.770164 ACATACCTTCTGTGCCTGTC 57.230 50.000 0.00 0.00 0.00 3.51
2866 3056 6.846350 AGAATGCTTACTTCCGAAAGAAATG 58.154 36.000 0.00 0.00 36.30 2.32
2870 3060 6.072673 GGAAAAGAATGCTTACTTCCGAAAGA 60.073 38.462 1.75 0.00 33.59 2.52
2884 3076 4.914540 GCTTGTAGCTAGGAAAAGAATGC 58.085 43.478 0.00 0.00 38.45 3.56
2906 3098 5.181811 TGTGAGATGCATGGTTCTGTTTTAG 59.818 40.000 2.46 0.00 0.00 1.85
2907 3099 5.069318 TGTGAGATGCATGGTTCTGTTTTA 58.931 37.500 2.46 0.00 0.00 1.52
2909 3101 3.489355 TGTGAGATGCATGGTTCTGTTT 58.511 40.909 2.46 0.00 0.00 2.83
2925 3117 8.545229 AGATAAAGTTGAAACTGATCTGTGAG 57.455 34.615 15.19 0.00 39.33 3.51
2937 3154 4.521256 CCCGGGAACAAGATAAAGTTGAAA 59.479 41.667 18.48 0.00 0.00 2.69
2944 3161 1.004979 CACCCCCGGGAACAAGATAAA 59.995 52.381 26.32 0.00 38.96 1.40
2945 3162 0.621609 CACCCCCGGGAACAAGATAA 59.378 55.000 26.32 0.00 38.96 1.75
2946 3163 1.276140 CCACCCCCGGGAACAAGATA 61.276 60.000 26.32 0.00 38.96 1.98
2960 3177 2.159382 CAATGTAACACAGTCCCACCC 58.841 52.381 0.00 0.00 0.00 4.61
3009 3226 0.818040 AGGTGTTTGCCACGTTCTCC 60.818 55.000 0.00 0.00 45.52 3.71
3407 3657 8.298854 TCATCAAACACAAATCATTGAAGTAGG 58.701 33.333 0.00 0.00 38.94 3.18
3408 3658 9.850628 ATCATCAAACACAAATCATTGAAGTAG 57.149 29.630 0.00 0.00 38.94 2.57
3409 3659 9.844790 GATCATCAAACACAAATCATTGAAGTA 57.155 29.630 0.00 0.00 38.94 2.24
3600 3879 7.502895 TGACAGTATGGAAGAGAGGTAGATAAC 59.497 40.741 0.00 0.00 43.62 1.89
3602 3881 7.150447 TGACAGTATGGAAGAGAGGTAGATA 57.850 40.000 0.00 0.00 43.62 1.98
3756 4035 0.389025 TTCTCGAGCAGCACTGTCAA 59.611 50.000 7.81 0.00 0.00 3.18
3797 4076 1.001269 GTACAAGAGGCCAACCCCC 60.001 63.158 5.01 0.00 36.11 5.40
3908 4187 2.217038 ACGTGAGATGGGCAGGTGT 61.217 57.895 0.00 0.00 33.60 4.16
4056 4335 4.346730 TGAATGAACATCTTGAGCCCATT 58.653 39.130 0.00 0.00 0.00 3.16
4118 4403 2.676163 AAACCTCACCACCAGCGGTC 62.676 60.000 0.00 0.00 37.07 4.79
4340 4637 0.037590 ATGAGTTGGCTTTGGCGGTA 59.962 50.000 0.00 0.00 39.81 4.02
4544 4842 3.389329 ACTCCTACCATACAGCCAGAATG 59.611 47.826 0.00 0.00 0.00 2.67
4561 4859 2.496470 CGCCCTTCAAAGTAGTACTCCT 59.504 50.000 2.58 0.00 0.00 3.69
4562 4860 2.494870 TCGCCCTTCAAAGTAGTACTCC 59.505 50.000 2.58 0.00 0.00 3.85
4563 4861 3.863142 TCGCCCTTCAAAGTAGTACTC 57.137 47.619 2.58 0.00 0.00 2.59
4833 5134 5.710099 TCTTTTAACTCCCCACATTCATGTC 59.290 40.000 0.00 0.00 39.39 3.06
4947 5301 5.073311 TGTAACTCAACTACAGGAGATGC 57.927 43.478 0.00 0.00 35.17 3.91
4988 5342 6.884836 GGGGATTGTAGAGTTAACTTGTGATT 59.115 38.462 10.02 0.00 0.00 2.57
5064 5418 6.293790 GCCTGGTTACTTTTCTTGAACGTTAT 60.294 38.462 0.00 0.00 0.00 1.89
5146 5507 1.078143 GTAGCTCCCAGTGGGCAAG 60.078 63.158 24.75 17.62 43.94 4.01
5162 5523 1.435563 TGGTTGAGGGAGGAAGGAGTA 59.564 52.381 0.00 0.00 0.00 2.59
5188 5549 3.981211 TCAGCAACCTTTTCTGCAATTC 58.019 40.909 0.00 0.00 41.17 2.17
5216 5577 7.852516 CCGTAGGCTTCTAATAAAAGTCAATC 58.147 38.462 0.00 0.00 46.14 2.67
5217 5578 7.787725 CCGTAGGCTTCTAATAAAAGTCAAT 57.212 36.000 0.00 0.00 46.14 2.57
5263 5626 5.032846 TCTCCAACAAGAATAGAGGGTGAT 58.967 41.667 0.00 0.00 0.00 3.06
5273 5636 7.928167 GGTTTCTGAATTTTCTCCAACAAGAAT 59.072 33.333 0.00 0.00 35.30 2.40
5280 5643 8.217799 TCTTCTAGGTTTCTGAATTTTCTCCAA 58.782 33.333 0.00 0.00 0.00 3.53
5282 5645 8.622948 TTCTTCTAGGTTTCTGAATTTTCTCC 57.377 34.615 0.00 0.00 0.00 3.71
5316 5685 3.406361 CGGCGTCTGCTGTGTGTC 61.406 66.667 0.00 0.00 42.79 3.67


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

AutoCloner maintained by Alex Coulton.