Multiple sequence alignment - TraesCS2D01G445900

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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 TraesCS2D01G445900 chr2D 100.000 3115 0 0 1 3115 556266231 556269345 0.000000e+00 5753.0
1 TraesCS2D01G445900 chr2D 89.224 1494 145 11 821 2309 556350373 556351855 0.000000e+00 1853.0
2 TraesCS2D01G445900 chr2D 87.935 1235 118 14 1346 2553 556339260 556340490 0.000000e+00 1426.0
3 TraesCS2D01G445900 chr2D 83.643 1559 164 28 770 2302 556618903 556620396 0.000000e+00 1382.0
4 TraesCS2D01G445900 chr2D 83.032 1550 162 43 768 2302 556407818 556409281 0.000000e+00 1312.0
5 TraesCS2D01G445900 chr2D 81.000 1600 177 57 731 2302 556365228 556366728 0.000000e+00 1153.0
6 TraesCS2D01G445900 chr2D 88.825 519 39 8 983 1491 556318398 556318907 1.230000e-173 619.0
7 TraesCS2D01G445900 chr2D 81.497 481 72 12 1486 1963 556333284 556333750 2.270000e-101 379.0
8 TraesCS2D01G445900 chr2D 89.552 134 14 0 1984 2117 556333871 556334004 1.490000e-38 171.0
9 TraesCS2D01G445900 chr2D 95.161 62 3 0 10 71 109700406 109700467 7.110000e-17 99.0
10 TraesCS2D01G445900 chr2D 91.667 72 5 1 1 71 270480315 270480386 7.110000e-17 99.0
11 TraesCS2D01G445900 chr2A 93.589 2324 115 24 731 3026 695998844 696001161 0.000000e+00 3435.0
12 TraesCS2D01G445900 chr2A 88.036 1797 154 31 770 2553 696040231 696041979 0.000000e+00 2071.0
13 TraesCS2D01G445900 chr2A 89.411 1001 88 10 2045 3036 696001156 696002147 0.000000e+00 1245.0
14 TraesCS2D01G445900 chr2A 88.336 763 59 15 862 1597 696306895 696307654 0.000000e+00 889.0
15 TraesCS2D01G445900 chr2A 91.667 72 5 1 1 71 346210394 346210465 7.110000e-17 99.0
16 TraesCS2D01G445900 chr2B 89.683 1832 151 21 731 2533 663828700 663830522 0.000000e+00 2302.0
17 TraesCS2D01G445900 chr2B 83.804 1877 188 34 731 2553 663837741 663839555 0.000000e+00 1676.0
18 TraesCS2D01G445900 chr2B 82.228 1553 164 44 768 2302 663885801 663887259 0.000000e+00 1236.0
19 TraesCS2D01G445900 chr2B 84.061 985 147 5 1379 2357 663180828 663179848 0.000000e+00 941.0
20 TraesCS2D01G445900 chr2B 90.287 731 46 10 10 731 76899320 76900034 0.000000e+00 933.0
21 TraesCS2D01G445900 chr2B 90.278 72 6 1 1 71 8709865 8709936 3.310000e-15 93.5
22 TraesCS2D01G445900 chr3B 87.517 745 55 10 10 730 756308558 756309288 0.000000e+00 845.0
23 TraesCS2D01G445900 chr3B 80.607 428 70 10 2552 2973 23928779 23928359 5.010000e-83 318.0
24 TraesCS2D01G445900 chr3D 86.667 750 60 20 10 733 39859835 39859100 0.000000e+00 813.0
25 TraesCS2D01G445900 chr3D 89.189 629 54 6 10 638 39895871 39895257 0.000000e+00 791.0
26 TraesCS2D01G445900 chr3D 97.143 105 3 0 626 730 39895235 39895131 8.880000e-41 178.0
27 TraesCS2D01G445900 chr3D 92.537 67 4 1 10 76 609106251 609106316 9.200000e-16 95.3
28 TraesCS2D01G445900 chr6D 89.189 629 54 6 10 638 431858482 431857868 0.000000e+00 791.0
29 TraesCS2D01G445900 chr6D 97.143 105 3 0 626 730 431857852 431857748 8.880000e-41 178.0
30 TraesCS2D01G445900 chr6D 96.154 78 3 0 3038 3115 48142547 48142470 9.070000e-26 128.0
31 TraesCS2D01G445900 chr6D 92.754 69 3 1 10 76 389702363 389702295 7.110000e-17 99.0
32 TraesCS2D01G445900 chr7B 89.198 611 52 4 10 620 126230266 126229670 0.000000e+00 769.0
33 TraesCS2D01G445900 chr7B 94.949 297 14 1 342 638 117217792 117218087 6.080000e-127 464.0
34 TraesCS2D01G445900 chr7B 94.613 297 15 1 342 638 117213670 117213375 2.830000e-125 459.0
35 TraesCS2D01G445900 chr7B 90.066 302 23 1 10 311 117214165 117213871 4.870000e-103 385.0
36 TraesCS2D01G445900 chr7B 90.066 302 23 1 10 311 117217029 117217323 4.870000e-103 385.0
37 TraesCS2D01G445900 chr7B 90.066 302 23 1 10 311 122773451 122773157 4.870000e-103 385.0
38 TraesCS2D01G445900 chr7B 97.196 107 3 0 626 732 126229512 126229406 6.860000e-42 182.0
39 TraesCS2D01G445900 chr7B 97.170 106 3 0 626 731 117218103 117218208 2.470000e-41 180.0
40 TraesCS2D01G445900 chr3A 89.858 424 17 6 342 740 26152974 26152552 3.560000e-144 521.0
41 TraesCS2D01G445900 chr6A 94.949 297 14 1 342 638 73783672 73783967 6.080000e-127 464.0
42 TraesCS2D01G445900 chr6A 90.066 302 23 1 10 311 73783269 73783563 4.870000e-103 385.0
43 TraesCS2D01G445900 chr6A 97.143 105 3 0 626 730 73784003 73784107 8.880000e-41 178.0
44 TraesCS2D01G445900 chr6A 95.161 62 3 0 10 71 272994955 272995016 7.110000e-17 99.0
45 TraesCS2D01G445900 chr1D 81.818 418 69 7 2562 2973 466395375 466395791 8.270000e-91 344.0
46 TraesCS2D01G445900 chr1D 96.203 79 3 0 3037 3115 6659324 6659246 2.520000e-26 130.0
47 TraesCS2D01G445900 chr1D 92.222 90 6 1 3027 3115 20818518 20818429 3.260000e-25 126.0
48 TraesCS2D01G445900 chr4A 81.308 428 63 11 2554 2973 491693199 491693617 6.440000e-87 331.0
49 TraesCS2D01G445900 chr4A 96.203 79 3 0 3037 3115 563286701 563286623 2.520000e-26 130.0
50 TraesCS2D01G445900 chr6B 80.796 427 73 7 2552 2973 598447365 598446943 3.000000e-85 326.0
51 TraesCS2D01G445900 chr5B 80.930 430 61 15 2553 2973 282702473 282702056 1.390000e-83 320.0
52 TraesCS2D01G445900 chr5A 80.425 424 72 9 2553 2965 426572106 426572529 2.330000e-81 313.0
53 TraesCS2D01G445900 chr5A 97.170 106 3 0 626 731 632255791 632255896 2.470000e-41 180.0
54 TraesCS2D01G445900 chr5A 95.122 82 4 0 3034 3115 492335518 492335437 2.520000e-26 130.0
55 TraesCS2D01G445900 chr1B 80.465 430 65 11 2553 2964 491703940 491703512 8.390000e-81 311.0
56 TraesCS2D01G445900 chr1A 75.926 324 64 10 1813 2130 459441787 459441472 1.500000e-33 154.0
57 TraesCS2D01G445900 chr5D 97.436 78 2 0 3038 3115 144353880 144353803 1.950000e-27 134.0
58 TraesCS2D01G445900 chrUn 96.203 79 3 0 3037 3115 28861748 28861826 2.520000e-26 130.0
59 TraesCS2D01G445900 chrUn 95.122 82 4 0 3034 3115 326893423 326893504 2.520000e-26 130.0
60 TraesCS2D01G445900 chr4D 93.976 83 5 0 3033 3115 488555838 488555920 3.260000e-25 126.0
61 TraesCS2D01G445900 chr4D 96.774 62 2 0 10 71 367720599 367720660 1.530000e-18 104.0


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 TraesCS2D01G445900 chr2D 556266231 556269345 3114 False 5753.000000 5753 100.000000 1 3115 1 chr2D.!!$F3 3114
1 TraesCS2D01G445900 chr2D 556350373 556351855 1482 False 1853.000000 1853 89.224000 821 2309 1 chr2D.!!$F6 1488
2 TraesCS2D01G445900 chr2D 556339260 556340490 1230 False 1426.000000 1426 87.935000 1346 2553 1 chr2D.!!$F5 1207
3 TraesCS2D01G445900 chr2D 556618903 556620396 1493 False 1382.000000 1382 83.643000 770 2302 1 chr2D.!!$F9 1532
4 TraesCS2D01G445900 chr2D 556407818 556409281 1463 False 1312.000000 1312 83.032000 768 2302 1 chr2D.!!$F8 1534
5 TraesCS2D01G445900 chr2D 556365228 556366728 1500 False 1153.000000 1153 81.000000 731 2302 1 chr2D.!!$F7 1571
6 TraesCS2D01G445900 chr2D 556318398 556318907 509 False 619.000000 619 88.825000 983 1491 1 chr2D.!!$F4 508
7 TraesCS2D01G445900 chr2D 556333284 556334004 720 False 275.000000 379 85.524500 1486 2117 2 chr2D.!!$F10 631
8 TraesCS2D01G445900 chr2A 695998844 696002147 3303 False 2340.000000 3435 91.500000 731 3036 2 chr2A.!!$F4 2305
9 TraesCS2D01G445900 chr2A 696040231 696041979 1748 False 2071.000000 2071 88.036000 770 2553 1 chr2A.!!$F2 1783
10 TraesCS2D01G445900 chr2A 696306895 696307654 759 False 889.000000 889 88.336000 862 1597 1 chr2A.!!$F3 735
11 TraesCS2D01G445900 chr2B 663828700 663830522 1822 False 2302.000000 2302 89.683000 731 2533 1 chr2B.!!$F3 1802
12 TraesCS2D01G445900 chr2B 663837741 663839555 1814 False 1676.000000 1676 83.804000 731 2553 1 chr2B.!!$F4 1822
13 TraesCS2D01G445900 chr2B 663885801 663887259 1458 False 1236.000000 1236 82.228000 768 2302 1 chr2B.!!$F5 1534
14 TraesCS2D01G445900 chr2B 663179848 663180828 980 True 941.000000 941 84.061000 1379 2357 1 chr2B.!!$R1 978
15 TraesCS2D01G445900 chr2B 76899320 76900034 714 False 933.000000 933 90.287000 10 731 1 chr2B.!!$F2 721
16 TraesCS2D01G445900 chr3B 756308558 756309288 730 False 845.000000 845 87.517000 10 730 1 chr3B.!!$F1 720
17 TraesCS2D01G445900 chr3D 39859100 39859835 735 True 813.000000 813 86.667000 10 733 1 chr3D.!!$R1 723
18 TraesCS2D01G445900 chr3D 39895131 39895871 740 True 484.500000 791 93.166000 10 730 2 chr3D.!!$R2 720
19 TraesCS2D01G445900 chr6D 431857748 431858482 734 True 484.500000 791 93.166000 10 730 2 chr6D.!!$R3 720
20 TraesCS2D01G445900 chr7B 126229406 126230266 860 True 475.500000 769 93.197000 10 732 2 chr7B.!!$R3 722
21 TraesCS2D01G445900 chr7B 117213375 117214165 790 True 422.000000 459 92.339500 10 638 2 chr7B.!!$R2 628
22 TraesCS2D01G445900 chr7B 117217029 117218208 1179 False 343.000000 464 94.061667 10 731 3 chr7B.!!$F1 721
23 TraesCS2D01G445900 chr6A 73783269 73784107 838 False 342.333333 464 94.052667 10 730 3 chr6A.!!$F2 720

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
493 945 0.034616 GGAGGAATCAGGAGCATCGG 59.965 60.000 0.00 0.0 34.37 4.18 F
622 1216 2.365582 CCGTAGCTGGCCTATGTTTTT 58.634 47.619 3.32 0.0 32.20 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 2488 1.438651 CGTTTGCTGCAGCTAGGTTA 58.561 50.000 36.61 15.23 42.66 2.85 R
2464 3394 2.889852 GACACCTTAGGTCCATTCGTC 58.110 52.381 0.00 0.89 31.02 4.20 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
48 49 3.939454 TTGAGGGACAAACTTGGGACAAG 60.939 47.826 7.41 7.41 38.59 3.16
65 66 2.224113 ACAAGCTTTTTCGTACGGAGGA 60.224 45.455 16.52 0.00 0.00 3.71
79 80 8.450578 TCGTACGGAGGAAGTATCTTTTAATA 57.549 34.615 16.52 0.00 0.00 0.98
80 81 9.071276 TCGTACGGAGGAAGTATCTTTTAATAT 57.929 33.333 16.52 0.00 0.00 1.28
325 326 2.950172 AAGCTGCCGTAAACGCACG 61.950 57.895 0.00 0.00 41.59 5.34
469 921 4.334837 GCTAGCTAGCTCAAGCCG 57.665 61.111 33.71 5.19 45.62 5.52
489 941 1.556911 GTTCAGGAGGAATCAGGAGCA 59.443 52.381 0.00 0.00 37.93 4.26
493 945 0.034616 GGAGGAATCAGGAGCATCGG 59.965 60.000 0.00 0.00 34.37 4.18
533 985 7.464273 TGCATCTCCATACATTTATTCAGGAT 58.536 34.615 0.00 0.00 0.00 3.24
598 1050 5.261216 AGTACTTGGAAATGGTAATGTGGG 58.739 41.667 0.00 0.00 0.00 4.61
622 1216 2.365582 CCGTAGCTGGCCTATGTTTTT 58.634 47.619 3.32 0.00 32.20 1.94
644 1276 2.481289 TCTCTCTCTCTCTGAACGCA 57.519 50.000 0.00 0.00 0.00 5.24
747 1379 3.748048 CACTGGACATAGACAAACTGTGG 59.252 47.826 0.00 0.00 41.11 4.17
819 1463 3.114616 CCTCGCGTGCCTTGTCAG 61.115 66.667 5.77 0.00 0.00 3.51
1369 2080 2.629656 CCAGCTGGACCTTTTGCCG 61.630 63.158 29.88 0.00 37.39 5.69
1395 2119 7.484035 AGTTGTTAGTCTTGAAATGACACTC 57.516 36.000 0.00 0.00 42.90 3.51
1535 2266 3.986006 GGCGTCGACCCAGTGACA 61.986 66.667 10.58 0.00 34.78 3.58
1733 2488 2.517875 GCCAGCGGCCTCATCATT 60.518 61.111 0.00 0.00 44.06 2.57
1850 2611 0.179018 ACCTCTGCAACACCTCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
2166 3053 9.537848 GTGTTGTGTATAATAGTTTTGTACAGC 57.462 33.333 3.72 0.00 0.00 4.40
2167 3054 9.496873 TGTTGTGTATAATAGTTTTGTACAGCT 57.503 29.630 3.72 0.00 0.00 4.24
2204 3092 6.678568 AGAGGTGTAGATGGGATGATAAAG 57.321 41.667 0.00 0.00 0.00 1.85
2290 3215 7.395772 TGAAGGTTGTCCATTGCTGATTTAATA 59.604 33.333 0.00 0.00 35.89 0.98
2464 3394 7.118390 GCTTACACATCCCATGTTAGCTAATAG 59.882 40.741 9.88 2.84 45.04 1.73
2557 3490 9.856488 GGTAGGGAAACTATCTTTTCATTTTTC 57.144 33.333 0.00 0.00 37.24 2.29
2560 3493 9.987272 AGGGAAACTATCTTTTCATTTTTCTTG 57.013 29.630 0.00 0.00 37.24 3.02
2600 3534 8.706492 TTATTGGCTCAAAATGAAGCATAAAG 57.294 30.769 0.00 0.00 0.00 1.85
2649 3584 2.611473 CGGCCTCTGCATAGTTAGGATG 60.611 54.545 0.00 0.00 40.13 3.51
2683 3618 2.865551 CCAACTCACACATGCAAAAACC 59.134 45.455 0.00 0.00 0.00 3.27
2730 3665 1.206578 CCACAACTTTGCGTAGGCG 59.793 57.895 2.53 0.00 44.10 5.52
2749 3684 3.680458 GGCGAGAAAACAAACCAAAACAA 59.320 39.130 0.00 0.00 0.00 2.83
2775 3710 3.484547 GCGGTCGGCAAACTACGG 61.485 66.667 0.00 0.00 42.87 4.02
2799 3734 0.802494 GGCCATATCCGCATAAACCG 59.198 55.000 0.00 0.00 0.00 4.44
2823 3758 1.393539 GATGACACCAAATGGACGACG 59.606 52.381 6.42 0.00 38.94 5.12
2826 3761 0.105224 ACACCAAATGGACGACGACA 59.895 50.000 6.42 0.00 38.94 4.35
2838 3773 3.370978 GGACGACGACATCATTCAACAAT 59.629 43.478 0.00 0.00 0.00 2.71
2842 3777 4.949691 CGACGACATCATTCAACAATAACG 59.050 41.667 0.00 0.00 0.00 3.18
2889 3824 0.456221 GTCGTCGTCACCAGATCCAT 59.544 55.000 0.00 0.00 0.00 3.41
2915 3850 4.202567 ACAAGGCCAGAATCTAGGTTTTCA 60.203 41.667 5.01 0.00 0.00 2.69
2977 3912 6.389830 TCAACAAGGTAAGAACGTACTACA 57.610 37.500 0.00 0.00 0.00 2.74
3039 4950 2.496817 CCTGGAGGCGCTAGTCAC 59.503 66.667 7.64 0.00 0.00 3.67
3040 4951 2.055042 CCTGGAGGCGCTAGTCACT 61.055 63.158 7.64 0.00 0.00 3.41
3041 4952 1.608717 CCTGGAGGCGCTAGTCACTT 61.609 60.000 7.64 0.00 0.00 3.16
3042 4953 0.459237 CTGGAGGCGCTAGTCACTTG 60.459 60.000 7.64 0.00 0.00 3.16
3043 4954 1.185618 TGGAGGCGCTAGTCACTTGT 61.186 55.000 7.64 0.00 0.00 3.16
3044 4955 0.815734 GGAGGCGCTAGTCACTTGTA 59.184 55.000 7.64 0.00 0.00 2.41
3045 4956 1.202313 GGAGGCGCTAGTCACTTGTAG 60.202 57.143 7.64 0.00 0.00 2.74
3046 4957 1.743958 GAGGCGCTAGTCACTTGTAGA 59.256 52.381 7.64 0.00 0.00 2.59
3047 4958 2.163815 GAGGCGCTAGTCACTTGTAGAA 59.836 50.000 7.64 0.00 0.00 2.10
3048 4959 2.561419 AGGCGCTAGTCACTTGTAGAAA 59.439 45.455 7.64 0.00 0.00 2.52
3049 4960 3.006537 AGGCGCTAGTCACTTGTAGAAAA 59.993 43.478 7.64 0.00 0.00 2.29
3050 4961 3.123116 GGCGCTAGTCACTTGTAGAAAAC 59.877 47.826 7.64 0.00 0.00 2.43
3051 4962 3.739300 GCGCTAGTCACTTGTAGAAAACA 59.261 43.478 0.00 0.00 35.88 2.83
3052 4963 4.143305 GCGCTAGTCACTTGTAGAAAACAG 60.143 45.833 0.00 0.00 39.87 3.16
3053 4964 4.386049 CGCTAGTCACTTGTAGAAAACAGG 59.614 45.833 0.00 0.00 39.87 4.00
3054 4965 4.691216 GCTAGTCACTTGTAGAAAACAGGG 59.309 45.833 0.00 0.00 39.44 4.45
3055 4966 3.477530 AGTCACTTGTAGAAAACAGGGC 58.522 45.455 0.00 0.00 39.44 5.19
3056 4967 3.136626 AGTCACTTGTAGAAAACAGGGCT 59.863 43.478 0.00 0.00 39.44 5.19
3057 4968 3.883489 GTCACTTGTAGAAAACAGGGCTT 59.117 43.478 0.00 0.00 39.44 4.35
3058 4969 4.338400 GTCACTTGTAGAAAACAGGGCTTT 59.662 41.667 0.00 0.00 39.44 3.51
3059 4970 4.338118 TCACTTGTAGAAAACAGGGCTTTG 59.662 41.667 0.00 0.00 39.44 2.77
3060 4971 3.636764 ACTTGTAGAAAACAGGGCTTTGG 59.363 43.478 0.00 0.00 39.44 3.28
3061 4972 3.306472 TGTAGAAAACAGGGCTTTGGT 57.694 42.857 0.00 0.00 33.01 3.67
3062 4973 3.637769 TGTAGAAAACAGGGCTTTGGTT 58.362 40.909 0.00 0.00 33.01 3.67
3063 4974 3.634910 TGTAGAAAACAGGGCTTTGGTTC 59.365 43.478 0.00 0.00 33.01 3.62
3064 4975 1.681264 AGAAAACAGGGCTTTGGTTCG 59.319 47.619 0.00 0.00 0.00 3.95
3065 4976 0.750249 AAAACAGGGCTTTGGTTCGG 59.250 50.000 0.00 0.00 0.00 4.30
3066 4977 1.112916 AAACAGGGCTTTGGTTCGGG 61.113 55.000 0.00 0.00 0.00 5.14
3067 4978 3.373565 CAGGGCTTTGGTTCGGGC 61.374 66.667 0.00 0.00 0.00 6.13
3068 4979 4.678743 AGGGCTTTGGTTCGGGCC 62.679 66.667 0.00 0.00 44.57 5.80
3069 4980 4.678743 GGGCTTTGGTTCGGGCCT 62.679 66.667 0.84 0.00 43.62 5.19
3070 4981 3.373565 GGCTTTGGTTCGGGCCTG 61.374 66.667 4.71 4.71 41.20 4.85
3071 4982 3.373565 GCTTTGGTTCGGGCCTGG 61.374 66.667 12.87 0.00 0.00 4.45
3072 4983 3.373565 CTTTGGTTCGGGCCTGGC 61.374 66.667 12.87 11.05 0.00 4.85
3083 4994 2.520260 GCCTGGCCAGCCCATTAG 60.520 66.667 28.39 12.86 44.33 1.73
3084 4995 2.520260 CCTGGCCAGCCCATTAGC 60.520 66.667 28.39 0.00 44.33 3.09
3085 4996 2.520260 CTGGCCAGCCCATTAGCC 60.520 66.667 22.33 0.00 44.33 3.93
3086 4997 4.141876 TGGCCAGCCCATTAGCCC 62.142 66.667 0.00 0.00 45.14 5.19
3087 4998 4.922215 GGCCAGCCCATTAGCCCC 62.922 72.222 0.00 0.00 39.60 5.80
3089 5000 4.586235 CCAGCCCATTAGCCCCGG 62.586 72.222 0.00 0.00 0.00 5.73
3090 5001 3.809013 CAGCCCATTAGCCCCGGT 61.809 66.667 0.00 0.00 0.00 5.28
3091 5002 3.489513 AGCCCATTAGCCCCGGTC 61.490 66.667 0.00 0.00 0.00 4.79
3092 5003 4.581093 GCCCATTAGCCCCGGTCC 62.581 72.222 0.00 0.00 0.00 4.46
3093 5004 3.093835 CCCATTAGCCCCGGTCCA 61.094 66.667 0.00 0.00 0.00 4.02
3094 5005 2.510906 CCATTAGCCCCGGTCCAG 59.489 66.667 0.00 0.00 0.00 3.86
3095 5006 2.375345 CCATTAGCCCCGGTCCAGT 61.375 63.158 0.00 0.00 0.00 4.00
3096 5007 1.146263 CATTAGCCCCGGTCCAGTC 59.854 63.158 0.00 0.00 0.00 3.51
3097 5008 1.306654 ATTAGCCCCGGTCCAGTCA 60.307 57.895 0.00 0.00 0.00 3.41
3098 5009 1.623542 ATTAGCCCCGGTCCAGTCAC 61.624 60.000 0.00 0.00 0.00 3.67
3101 5012 3.307906 CCCCGGTCCAGTCACGAA 61.308 66.667 0.00 0.00 0.00 3.85
3102 5013 2.048503 CCCGGTCCAGTCACGAAC 60.049 66.667 0.00 0.00 0.00 3.95
3103 5014 2.048503 CCGGTCCAGTCACGAACC 60.049 66.667 0.00 0.00 0.00 3.62
3105 5016 2.048503 GGTCCAGTCACGAACCGG 60.049 66.667 0.00 0.00 0.00 5.28
3106 5017 2.048503 GTCCAGTCACGAACCGGG 60.049 66.667 6.32 0.00 0.00 5.73
3107 5018 2.203523 TCCAGTCACGAACCGGGA 60.204 61.111 6.32 0.00 36.75 5.14
3112 5023 2.605295 TCACGAACCGGGACCCAT 60.605 61.111 12.15 0.00 32.99 4.00
3113 5024 2.435938 CACGAACCGGGACCCATG 60.436 66.667 12.15 3.12 28.17 3.66
3114 5025 3.712907 ACGAACCGGGACCCATGG 61.713 66.667 12.15 4.14 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.454260 TGGATGTATCTAGCACATAGTAGTG 57.546 40.000 9.10 0.00 42.37 2.74
3 4 9.088987 TCAAATGGATGTATCTAGCACATAGTA 57.911 33.333 9.10 1.87 36.76 1.82
4 5 7.966812 TCAAATGGATGTATCTAGCACATAGT 58.033 34.615 9.10 0.00 36.76 2.12
5 6 7.548427 CCTCAAATGGATGTATCTAGCACATAG 59.452 40.741 9.10 3.30 36.76 2.23
6 7 7.389232 CCTCAAATGGATGTATCTAGCACATA 58.611 38.462 9.10 0.00 36.76 2.29
7 8 6.236409 CCTCAAATGGATGTATCTAGCACAT 58.764 40.000 8.93 8.93 39.31 3.21
8 9 5.455183 CCCTCAAATGGATGTATCTAGCACA 60.455 44.000 0.22 0.22 0.00 4.57
12 13 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
23 24 3.005791 GTCCCAAGTTTGTCCCTCAAATG 59.994 47.826 0.00 0.00 45.88 2.32
48 49 2.410939 ACTTCCTCCGTACGAAAAAGC 58.589 47.619 18.76 0.00 0.00 3.51
79 80 5.624159 TCACTCCAATTGAGAGTTTCACAT 58.376 37.500 20.41 2.56 41.87 3.21
80 81 5.034852 TCACTCCAATTGAGAGTTTCACA 57.965 39.130 20.41 6.27 41.87 3.58
117 118 9.237846 GCTTATATTAATGCTTGAACTGGAAAC 57.762 33.333 0.00 0.00 0.00 2.78
141 142 3.625649 TTTTTGCTTTCTGGGTTTGCT 57.374 38.095 0.00 0.00 0.00 3.91
184 185 6.655003 TGGTTTGAATAAGCTTAACTGAGAGG 59.345 38.462 10.85 0.00 0.00 3.69
216 217 9.748708 TCTTTCCAAGTATGTTCTCAATTTTTG 57.251 29.630 0.00 0.00 0.00 2.44
279 280 4.760047 GCAGGTGCACCGACCGAT 62.760 66.667 29.68 8.90 41.35 4.18
302 303 1.291877 CGTTTACGGCAGCTTGAGCT 61.292 55.000 0.00 0.00 43.67 4.09
337 338 3.706373 CAGGGTGTCGGGGTCCTG 61.706 72.222 0.00 0.00 40.46 3.86
463 915 1.339055 TGATTCCTCCTGAACGGCTTG 60.339 52.381 0.00 0.00 35.31 4.01
464 916 0.984230 TGATTCCTCCTGAACGGCTT 59.016 50.000 0.00 0.00 35.31 4.35
469 921 1.556911 TGCTCCTGATTCCTCCTGAAC 59.443 52.381 0.00 0.00 35.31 3.18
489 941 3.118629 TGCAACTTATTCTGAGCTCCGAT 60.119 43.478 12.15 5.08 0.00 4.18
493 945 4.511082 GGAGATGCAACTTATTCTGAGCTC 59.489 45.833 6.82 6.82 0.00 4.09
526 978 3.614150 CGTTCTCAACTTCCGATCCTGAA 60.614 47.826 0.00 0.00 0.00 3.02
533 985 2.671351 GCTGATCGTTCTCAACTTCCGA 60.671 50.000 0.00 0.00 0.00 4.55
568 1020 4.151883 ACCATTTCCAAGTACTTGCACAT 58.848 39.130 27.05 11.01 39.16 3.21
622 1216 3.570125 TGCGTTCAGAGAGAGAGAGAAAA 59.430 43.478 0.00 0.00 0.00 2.29
624 1218 2.784347 TGCGTTCAGAGAGAGAGAGAA 58.216 47.619 0.00 0.00 0.00 2.87
655 1287 1.152819 CCACCATCAGCCCATGAGG 60.153 63.158 0.00 0.00 42.53 3.86
813 1449 3.057526 CGTACTCCATGACAGACTGACAA 60.058 47.826 10.08 0.00 0.00 3.18
819 1463 1.816835 TGGTCGTACTCCATGACAGAC 59.183 52.381 0.00 0.00 43.88 3.51
967 1632 3.809905 TCTCGATACAAGCTCTGCTAGA 58.190 45.455 0.00 0.00 38.25 2.43
1032 1708 3.062466 GGCCCTTTCTTCACGCCC 61.062 66.667 0.00 0.00 33.30 6.13
1292 1977 2.673368 GCTATGTGTGTGGAGTAGTTGC 59.327 50.000 0.00 0.00 0.00 4.17
1338 2046 2.108075 TCCAGCTGGAGGAAATTGACAA 59.892 45.455 32.00 4.40 39.78 3.18
1369 2080 8.366671 AGTGTCATTTCAAGACTAACAACTAC 57.633 34.615 0.00 0.00 36.94 2.73
1395 2119 9.781834 AACGTACAACAATAATTTATCCATGTG 57.218 29.630 0.00 0.00 0.00 3.21
1535 2266 2.360852 GGTGGCAGCTGCTGATGT 60.361 61.111 35.82 0.00 41.70 3.06
1731 2486 2.420022 CGTTTGCTGCAGCTAGGTTAAT 59.580 45.455 36.61 0.00 42.66 1.40
1732 2487 1.804151 CGTTTGCTGCAGCTAGGTTAA 59.196 47.619 36.61 20.31 42.66 2.01
1733 2488 1.438651 CGTTTGCTGCAGCTAGGTTA 58.561 50.000 36.61 15.23 42.66 2.85
2166 3053 8.642935 TCTACACCTCTATGATGGATCTAAAG 57.357 38.462 0.00 0.00 0.00 1.85
2167 3054 9.029368 CATCTACACCTCTATGATGGATCTAAA 57.971 37.037 0.00 0.00 33.12 1.85
2204 3092 4.024725 ACACACAAACAAATCAATGCATGC 60.025 37.500 11.82 11.82 0.00 4.06
2431 3361 4.079787 ACATGGGATGTGTAAGCCAGTATT 60.080 41.667 0.00 0.00 43.01 1.89
2464 3394 2.889852 GACACCTTAGGTCCATTCGTC 58.110 52.381 0.00 0.89 31.02 4.20
2557 3490 9.211485 AGCCAATAAAATTCATCTTTTGTCAAG 57.789 29.630 0.00 0.00 31.15 3.02
2558 3491 9.206870 GAGCCAATAAAATTCATCTTTTGTCAA 57.793 29.630 0.00 0.00 31.15 3.18
2560 3493 8.761575 TGAGCCAATAAAATTCATCTTTTGTC 57.238 30.769 0.00 0.00 31.15 3.18
2627 3562 0.034059 CCTAACTATGCAGAGGCCGG 59.966 60.000 13.85 0.00 40.13 6.13
2649 3584 0.865639 GAGTTGGCGTTGTTGTGTGC 60.866 55.000 0.00 0.00 0.00 4.57
2656 3591 0.662619 CATGTGTGAGTTGGCGTTGT 59.337 50.000 0.00 0.00 0.00 3.32
2683 3618 3.117794 TGACTTTGTTAGTTGTCGTCCG 58.882 45.455 0.00 0.00 37.17 4.79
2730 3665 7.826260 TCTGATTGTTTTGGTTTGTTTTCTC 57.174 32.000 0.00 0.00 0.00 2.87
2749 3684 2.419198 GCCGACCGCAGATCTGAT 59.581 61.111 27.04 10.52 37.47 2.90
2768 3703 3.306502 CGGATATGGCCATTACCGTAGTT 60.307 47.826 34.72 12.73 34.68 2.24
2774 3709 2.128771 ATGCGGATATGGCCATTACC 57.871 50.000 26.37 24.22 0.00 2.85
2775 3710 4.142469 GGTTTATGCGGATATGGCCATTAC 60.142 45.833 26.37 17.58 0.00 1.89
2799 3734 4.034048 GTCGTCCATTTGGTGTCATCATAC 59.966 45.833 0.00 0.00 36.34 2.39
2823 3758 5.235305 AGGCGTTATTGTTGAATGATGTC 57.765 39.130 0.00 0.00 0.00 3.06
2826 3761 5.895636 TGAAGGCGTTATTGTTGAATGAT 57.104 34.783 0.00 0.00 0.00 2.45
2838 3773 1.338769 GCTCCCTTCTTGAAGGCGTTA 60.339 52.381 20.71 7.54 38.63 3.18
2842 3777 1.021920 GTCGCTCCCTTCTTGAAGGC 61.022 60.000 20.71 10.77 38.63 4.35
2871 3806 0.738975 GATGGATCTGGTGACGACGA 59.261 55.000 0.00 0.00 0.00 4.20
2889 3824 1.839994 CCTAGATTCTGGCCTTGTGGA 59.160 52.381 3.32 0.00 34.57 4.02
2915 3850 3.265221 TGCTCAGATTGATTCTTCAGGGT 59.735 43.478 0.00 0.00 32.27 4.34
2965 3900 1.637553 TCCCCTCCTGTAGTACGTTCT 59.362 52.381 0.00 0.00 0.00 3.01
2977 3912 1.074623 CAGGATCTGCTCCCCTCCT 60.075 63.158 0.00 0.00 46.27 3.69
3036 4947 3.857157 AGCCCTGTTTTCTACAAGTGA 57.143 42.857 0.00 0.00 36.02 3.41
3037 4948 4.499696 CCAAAGCCCTGTTTTCTACAAGTG 60.500 45.833 0.00 0.00 36.02 3.16
3038 4949 3.636764 CCAAAGCCCTGTTTTCTACAAGT 59.363 43.478 0.00 0.00 36.02 3.16
3039 4950 3.636764 ACCAAAGCCCTGTTTTCTACAAG 59.363 43.478 0.00 0.00 36.02 3.16
3040 4951 3.637769 ACCAAAGCCCTGTTTTCTACAA 58.362 40.909 0.00 0.00 36.02 2.41
3041 4952 3.306472 ACCAAAGCCCTGTTTTCTACA 57.694 42.857 0.00 0.00 34.95 2.74
3042 4953 3.304458 CGAACCAAAGCCCTGTTTTCTAC 60.304 47.826 0.00 0.00 0.00 2.59
3043 4954 2.882137 CGAACCAAAGCCCTGTTTTCTA 59.118 45.455 0.00 0.00 0.00 2.10
3044 4955 1.681264 CGAACCAAAGCCCTGTTTTCT 59.319 47.619 0.00 0.00 0.00 2.52
3045 4956 1.269569 CCGAACCAAAGCCCTGTTTTC 60.270 52.381 0.00 0.00 0.00 2.29
3046 4957 0.750249 CCGAACCAAAGCCCTGTTTT 59.250 50.000 0.00 0.00 0.00 2.43
3047 4958 1.112916 CCCGAACCAAAGCCCTGTTT 61.113 55.000 0.00 0.00 0.00 2.83
3048 4959 1.530655 CCCGAACCAAAGCCCTGTT 60.531 57.895 0.00 0.00 0.00 3.16
3049 4960 2.115266 CCCGAACCAAAGCCCTGT 59.885 61.111 0.00 0.00 0.00 4.00
3050 4961 3.373565 GCCCGAACCAAAGCCCTG 61.374 66.667 0.00 0.00 0.00 4.45
3051 4962 4.678743 GGCCCGAACCAAAGCCCT 62.679 66.667 0.00 0.00 39.60 5.19
3053 4964 3.373565 CAGGCCCGAACCAAAGCC 61.374 66.667 0.00 0.00 46.13 4.35
3054 4965 3.373565 CCAGGCCCGAACCAAAGC 61.374 66.667 0.00 0.00 0.00 3.51
3055 4966 3.373565 GCCAGGCCCGAACCAAAG 61.374 66.667 0.00 0.00 0.00 2.77
3056 4967 4.986708 GGCCAGGCCCGAACCAAA 62.987 66.667 21.62 0.00 44.06 3.28
3067 4978 2.520260 GCTAATGGGCTGGCCAGG 60.520 66.667 33.46 19.56 37.98 4.45
3068 4979 2.520260 GGCTAATGGGCTGGCCAG 60.520 66.667 29.34 29.34 43.59 4.85
3069 4980 4.141876 GGGCTAATGGGCTGGCCA 62.142 66.667 26.08 26.08 45.68 5.36
3070 4981 4.922215 GGGGCTAATGGGCTGGCC 62.922 72.222 14.23 14.23 44.43 5.36
3072 4983 4.586235 CCGGGGCTAATGGGCTGG 62.586 72.222 0.00 0.00 40.65 4.85
3073 4984 3.774599 GACCGGGGCTAATGGGCTG 62.775 68.421 6.32 0.00 40.65 4.85
3074 4985 3.489513 GACCGGGGCTAATGGGCT 61.490 66.667 6.32 0.00 40.65 5.19
3075 4986 4.581093 GGACCGGGGCTAATGGGC 62.581 72.222 6.32 0.00 40.05 5.36
3076 4987 3.093835 TGGACCGGGGCTAATGGG 61.094 66.667 6.32 0.00 0.00 4.00
3077 4988 2.325393 GACTGGACCGGGGCTAATGG 62.325 65.000 6.32 0.00 0.00 3.16
3078 4989 1.146263 GACTGGACCGGGGCTAATG 59.854 63.158 6.32 0.00 0.00 1.90
3079 4990 1.306654 TGACTGGACCGGGGCTAAT 60.307 57.895 6.32 0.00 0.00 1.73
3080 4991 2.120940 TGACTGGACCGGGGCTAA 59.879 61.111 6.32 0.00 0.00 3.09
3081 4992 2.682494 GTGACTGGACCGGGGCTA 60.682 66.667 6.32 0.00 0.00 3.93
3084 4995 3.307906 TTCGTGACTGGACCGGGG 61.308 66.667 6.32 0.00 0.00 5.73
3085 4996 2.048503 GTTCGTGACTGGACCGGG 60.049 66.667 6.32 0.00 0.00 5.73
3086 4997 2.048503 GGTTCGTGACTGGACCGG 60.049 66.667 0.00 0.00 0.00 5.28
3092 5003 2.048503 GGTCCCGGTTCGTGACTG 60.049 66.667 0.00 0.00 34.89 3.51
3093 5004 3.308705 GGGTCCCGGTTCGTGACT 61.309 66.667 0.00 0.00 34.89 3.41
3094 5005 2.951101 ATGGGTCCCGGTTCGTGAC 61.951 63.158 2.65 0.00 33.83 3.67
3095 5006 2.605295 ATGGGTCCCGGTTCGTGA 60.605 61.111 2.65 0.00 0.00 4.35
3096 5007 2.435938 CATGGGTCCCGGTTCGTG 60.436 66.667 2.65 0.00 0.00 4.35
3097 5008 3.712907 CCATGGGTCCCGGTTCGT 61.713 66.667 2.85 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.