Multiple sequence alignment - TraesCS7A01G131800

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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 TraesCS7A01G131800 chr7A 100.000 6393 0 0 1 6393 85076883 85083275 0.000000e+00 11806.0
1 TraesCS7A01G131800 chr7A 85.437 103 7 3 4830 4925 8235998 8236099 4.080000e-17 100.0
2 TraesCS7A01G131800 chr7A 100.000 31 0 0 3509 3539 400867758 400867728 2.490000e-04 58.4
3 TraesCS7A01G131800 chr7A 94.286 35 0 2 3509 3543 246710887 246710919 1.200000e-02 52.8
4 TraesCS7A01G131800 chr7D 91.584 3541 159 60 1 3475 83094569 83098036 0.000000e+00 4759.0
5 TraesCS7A01G131800 chr7D 96.623 1362 41 3 4885 6241 83099372 83100733 0.000000e+00 2255.0
6 TraesCS7A01G131800 chr7D 96.122 1341 33 5 3537 4859 83098035 83099374 0.000000e+00 2170.0
7 TraesCS7A01G131800 chr7D 95.618 753 27 3 5007 5753 83346645 83347397 0.000000e+00 1203.0
8 TraesCS7A01G131800 chr7D 94.470 434 15 4 5967 6393 83348545 83348976 0.000000e+00 660.0
9 TraesCS7A01G131800 chr7D 93.467 199 11 1 5755 5951 83347561 83347759 1.740000e-75 294.0
10 TraesCS7A01G131800 chr7D 92.500 40 3 0 3467 3506 614282406 614282367 2.490000e-04 58.4
11 TraesCS7A01G131800 chr7D 94.286 35 0 2 3509 3543 234073725 234073757 1.200000e-02 52.8
12 TraesCS7A01G131800 chr7B 92.693 2614 106 37 924 3483 32470936 32473518 0.000000e+00 3690.0
13 TraesCS7A01G131800 chr7B 95.759 1462 37 7 4942 6393 32475184 32476630 0.000000e+00 2333.0
14 TraesCS7A01G131800 chr7B 96.161 1146 26 4 3537 4665 32473607 32474751 0.000000e+00 1857.0
15 TraesCS7A01G131800 chr7B 86.777 968 64 17 12 938 32469975 32470919 0.000000e+00 1020.0
16 TraesCS7A01G131800 chr7B 94.194 155 8 1 4726 4879 32475036 32475190 1.070000e-57 235.0
17 TraesCS7A01G131800 chr7B 89.412 85 5 3 4845 4928 105509169 105509088 3.150000e-18 104.0
18 TraesCS7A01G131800 chr7B 100.000 28 0 0 3516 3543 609144667 609144640 1.200000e-02 52.8
19 TraesCS7A01G131800 chr7B 100.000 28 0 0 3511 3538 645595403 645595430 1.200000e-02 52.8
20 TraesCS7A01G131800 chr3A 79.565 827 110 32 5147 5936 203414614 203413810 2.620000e-148 536.0
21 TraesCS7A01G131800 chr3D 83.692 558 62 19 5401 5947 165588448 165587909 3.440000e-137 499.0
22 TraesCS7A01G131800 chr3B 81.469 572 74 21 5390 5947 240805139 240804586 2.120000e-119 440.0
23 TraesCS7A01G131800 chr3B 82.452 473 43 15 243 695 433936941 433937393 1.680000e-100 377.0
24 TraesCS7A01G131800 chr3B 93.671 79 5 0 4841 4919 707431483 707431405 1.130000e-22 119.0
25 TraesCS7A01G131800 chr4D 91.765 85 3 1 4840 4920 322662591 322662507 1.460000e-21 115.0
26 TraesCS7A01G131800 chr4D 90.244 82 4 1 4842 4919 322662508 322662589 3.150000e-18 104.0
27 TraesCS7A01G131800 chr5A 90.123 81 6 1 4842 4922 401142948 401143026 3.150000e-18 104.0
28 TraesCS7A01G131800 chr5A 89.024 82 7 1 4838 4919 401143027 401142948 4.080000e-17 100.0
29 TraesCS7A01G131800 chr5A 94.286 35 0 2 3509 3543 559038257 559038289 1.200000e-02 52.8
30 TraesCS7A01G131800 chr2D 88.235 85 7 2 4835 4919 416856723 416856642 1.470000e-16 99.0
31 TraesCS7A01G131800 chr2D 100.000 28 0 0 3479 3506 359396457 359396484 1.200000e-02 52.8
32 TraesCS7A01G131800 chr4A 87.671 73 3 4 3474 3542 580896073 580896003 5.310000e-11 80.5
33 TraesCS7A01G131800 chr4A 84.615 65 1 4 3474 3538 617948956 617949011 8.950000e-04 56.5
34 TraesCS7A01G131800 chr1D 95.238 42 2 0 3467 3508 389323949 389323990 4.140000e-07 67.6
35 TraesCS7A01G131800 chr1A 86.154 65 4 4 3475 3538 548893388 548893448 1.490000e-06 65.8
36 TraesCS7A01G131800 chr6A 97.059 34 1 0 3473 3506 562706296 562706329 2.490000e-04 58.4
37 TraesCS7A01G131800 chr1B 96.970 33 1 0 3474 3506 602170860 602170828 8.950000e-04 56.5


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 TraesCS7A01G131800 chr7A 85076883 85083275 6392 False 11806.000000 11806 100.000000 1 6393 1 chr7A.!!$F2 6392
1 TraesCS7A01G131800 chr7D 83094569 83100733 6164 False 3061.333333 4759 94.776333 1 6241 3 chr7D.!!$F2 6240
2 TraesCS7A01G131800 chr7D 83346645 83348976 2331 False 719.000000 1203 94.518333 5007 6393 3 chr7D.!!$F3 1386
3 TraesCS7A01G131800 chr7B 32469975 32476630 6655 False 1827.000000 3690 93.116800 12 6393 5 chr7B.!!$F2 6381
4 TraesCS7A01G131800 chr3A 203413810 203414614 804 True 536.000000 536 79.565000 5147 5936 1 chr3A.!!$R1 789
5 TraesCS7A01G131800 chr3D 165587909 165588448 539 True 499.000000 499 83.692000 5401 5947 1 chr3D.!!$R1 546
6 TraesCS7A01G131800 chr3B 240804586 240805139 553 True 440.000000 440 81.469000 5390 5947 1 chr3B.!!$R1 557

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
619 649 0.533755 CGCAGATGATGGGGAAGTCC 60.534 60.0 0.00 0.0 38.18 3.85 F
1355 1459 0.037326 CCTCTGACGCCTTGCTAACA 60.037 55.0 0.00 0.0 0.00 2.41 F
1556 1661 0.605319 TGCTTTCCTGTAACCCGCTG 60.605 55.0 0.00 0.0 0.00 5.18 F
3327 3457 0.801251 GAATGCTGCTCTTTGACGCT 59.199 50.0 0.00 0.0 0.00 5.07 F
3646 3822 0.972883 GACTTGCTGTCCAGTCCTCT 59.027 55.0 0.00 0.0 39.69 3.69 F
5228 5653 1.344953 AACTATGGATGCCTCCGCCA 61.345 55.0 3.39 0.0 45.37 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1661 0.691413 CCCAAGACCCCTAGGAGGAC 60.691 65.000 19.81 14.56 37.67 3.85 R
2486 2597 1.168714 CAGAAGGCTTGCTAACCACC 58.831 55.000 3.46 0.00 0.00 4.61 R
3403 3543 1.072173 ACCTGACTGTATGCAGCACAA 59.928 47.619 11.09 0.00 46.30 3.33 R
4682 4875 0.108662 CATGTGACACGCAGGCTCTA 60.109 55.000 0.22 0.00 0.00 2.43 R
5257 5682 0.601046 CGTTGCCTCTTCTGCAGACA 60.601 55.000 18.03 7.99 40.35 3.41 R
6331 7733 2.222027 GGTGACAAGTTTGTGGAGGAG 58.778 52.381 1.62 0.00 42.43 3.69 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
24 25 3.118905 AGAGAACAAGGAGCAGTTCAC 57.881 47.619 7.88 2.02 44.94 3.18
33 34 3.620488 AGGAGCAGTTCACAGAAACAAA 58.380 40.909 0.00 0.00 0.00 2.83
78 79 4.141981 TGTTTTCACATCCACTGCATGTTT 60.142 37.500 0.00 0.00 31.83 2.83
92 93 6.151985 CACTGCATGTTTAATTGTACCCCTAA 59.848 38.462 0.00 0.00 0.00 2.69
107 108 6.617784 TGTACCCCTAAACCATCTGATTGATA 59.382 38.462 0.00 0.00 33.36 2.15
127 134 8.635765 TTGATACCTTCTTTCTGTTTTGCTAT 57.364 30.769 0.00 0.00 0.00 2.97
128 135 8.268850 TGATACCTTCTTTCTGTTTTGCTATC 57.731 34.615 0.00 0.00 0.00 2.08
129 136 5.966742 ACCTTCTTTCTGTTTTGCTATCC 57.033 39.130 0.00 0.00 0.00 2.59
131 138 5.474876 ACCTTCTTTCTGTTTTGCTATCCAG 59.525 40.000 0.00 0.00 0.00 3.86
132 139 5.474876 CCTTCTTTCTGTTTTGCTATCCAGT 59.525 40.000 0.00 0.00 0.00 4.00
134 141 7.174946 CCTTCTTTCTGTTTTGCTATCCAGTTA 59.825 37.037 0.00 0.00 0.00 2.24
135 142 8.458573 TTCTTTCTGTTTTGCTATCCAGTTAA 57.541 30.769 0.00 0.00 0.00 2.01
136 143 7.871853 TCTTTCTGTTTTGCTATCCAGTTAAC 58.128 34.615 0.00 0.00 0.00 2.01
175 182 2.102420 CCCATAGATAGACACAACCGCA 59.898 50.000 0.00 0.00 0.00 5.69
212 219 2.226437 CCACACATGTAACCAAGCAGAC 59.774 50.000 0.00 0.00 0.00 3.51
213 220 2.226437 CACACATGTAACCAAGCAGACC 59.774 50.000 0.00 0.00 0.00 3.85
217 224 3.758554 ACATGTAACCAAGCAGACCAATC 59.241 43.478 0.00 0.00 0.00 2.67
235 242 2.432300 CCACCCCGAGCTACCGATT 61.432 63.158 0.00 0.00 0.00 3.34
236 243 1.520666 CACCCCGAGCTACCGATTT 59.479 57.895 0.00 0.00 0.00 2.17
280 287 1.399089 ACGTGGCAACTACAACAACAC 59.601 47.619 0.00 0.00 37.61 3.32
291 298 4.947388 ACTACAACAACACAACCAATCTGT 59.053 37.500 0.00 0.00 0.00 3.41
292 299 4.799564 ACAACAACACAACCAATCTGTT 57.200 36.364 0.00 0.00 0.00 3.16
295 302 4.637483 ACAACACAACCAATCTGTTCAG 57.363 40.909 0.00 0.00 0.00 3.02
303 310 1.466167 CCAATCTGTTCAGTTCAGCCG 59.534 52.381 0.00 0.00 33.48 5.52
425 452 2.322658 ACTCCCCAACGTAGAGACAAA 58.677 47.619 10.65 0.00 0.00 2.83
433 460 1.202440 ACGTAGAGACAAACAACCGCA 60.202 47.619 0.00 0.00 0.00 5.69
436 463 1.157870 AGAGACAAACAACCGCACCG 61.158 55.000 0.00 0.00 0.00 4.94
471 501 4.437959 CGCACAAAATCGCGCCGA 62.438 61.111 0.00 2.55 45.57 5.54
513 543 4.559386 GCGCGCGAATCGACAAGG 62.559 66.667 37.18 0.00 41.67 3.61
532 562 0.627451 GTAGGGTTAGGGTTTGGGGG 59.373 60.000 0.00 0.00 0.00 5.40
619 649 0.533755 CGCAGATGATGGGGAAGTCC 60.534 60.000 0.00 0.00 38.18 3.85
759 793 2.561922 CTCGATTCGATTAGACGACCG 58.438 52.381 9.54 0.00 41.97 4.79
793 827 1.134175 GGCTCTCTCTTTCTCGTCTGG 59.866 57.143 0.00 0.00 0.00 3.86
950 1032 3.259902 CGGCCCACTAGAGAAAGTTAAC 58.740 50.000 0.00 0.00 0.00 2.01
958 1040 1.891150 AGAGAAAGTTAACTCGGCCGA 59.109 47.619 29.03 29.03 38.08 5.54
1305 1409 4.689484 GCTCTCAGCTCAACTGCA 57.311 55.556 0.00 0.00 46.76 4.41
1343 1447 0.460987 CGATGAACCTGCCCTCTGAC 60.461 60.000 0.00 0.00 0.00 3.51
1352 1456 3.019003 GCCCTCTGACGCCTTGCTA 62.019 63.158 0.00 0.00 0.00 3.49
1355 1459 0.037326 CCTCTGACGCCTTGCTAACA 60.037 55.000 0.00 0.00 0.00 2.41
1356 1460 1.608025 CCTCTGACGCCTTGCTAACAA 60.608 52.381 0.00 0.00 0.00 2.83
1556 1661 0.605319 TGCTTTCCTGTAACCCGCTG 60.605 55.000 0.00 0.00 0.00 5.18
1632 1737 6.281405 ACCTTCATCGACAGGTATGAATAAC 58.719 40.000 10.41 0.00 41.97 1.89
1668 1773 6.909550 TTGCTCCTCTTATCTCCTATTCTC 57.090 41.667 0.00 0.00 0.00 2.87
1707 1812 3.788227 ACCTTCTGAGTTATGTTGGCA 57.212 42.857 0.00 0.00 0.00 4.92
1773 1878 8.147642 AGAAGTAGGCAAAATATTCTCATTCG 57.852 34.615 0.00 0.00 0.00 3.34
1798 1903 5.353394 TTTCAGGGTGTTAGCTATCGAAT 57.647 39.130 0.00 0.00 0.00 3.34
1861 1967 3.057033 ACTGCTCATCAGAAATTGGTTGC 60.057 43.478 0.00 0.00 45.72 4.17
1892 1998 1.529226 TTTAACAGTGACGGGGCATG 58.471 50.000 0.00 0.00 0.00 4.06
1946 2052 6.156949 TGTCTTAGATAATCCACCAAGAAGCT 59.843 38.462 0.00 0.00 0.00 3.74
2005 2111 0.804544 TGCCGTGCGTAAGATACTGC 60.805 55.000 0.00 0.00 43.02 4.40
2042 2148 5.130477 TCTTTGTATGGTTGTATCCCCTCTC 59.870 44.000 0.00 0.00 0.00 3.20
2046 2152 5.491078 TGTATGGTTGTATCCCCTCTCTTTT 59.509 40.000 0.00 0.00 0.00 2.27
2063 2169 4.602995 TCTTTTTGCGAATGTGGTTGTAC 58.397 39.130 0.00 0.00 0.00 2.90
2116 2227 2.941720 CTCTTGCAGATTTGAGGCTACC 59.058 50.000 0.00 0.00 0.00 3.18
2123 2234 4.250464 CAGATTTGAGGCTACCGTGTAAA 58.750 43.478 0.00 0.00 0.00 2.01
2433 2544 8.788409 TTTTGTTTTTGGCTTTTGTTAACAAG 57.212 26.923 19.72 11.46 35.99 3.16
2438 2549 5.916661 TTGGCTTTTGTTAACAAGTGGTA 57.083 34.783 19.72 3.47 37.15 3.25
2445 2556 7.854422 GCTTTTGTTAACAAGTGGTACTCTAAC 59.146 37.037 19.72 1.66 37.15 2.34
2486 2597 6.017192 TCCTGATTGTCTGTTGTGTTATGTTG 60.017 38.462 0.00 0.00 0.00 3.33
2555 2666 8.746052 AGCTTGCACCACTATATTTATGTTTA 57.254 30.769 0.00 0.00 0.00 2.01
2576 2687 7.550551 TGTTTATTTCATTTGCACTGGTTTTCA 59.449 29.630 0.00 0.00 0.00 2.69
2879 2991 9.276590 TCTAGTAAATCATGTTTCATGGCATAG 57.723 33.333 0.00 0.00 0.00 2.23
2888 3000 2.061509 TCATGGCATAGCAACAGCAT 57.938 45.000 0.00 0.00 0.00 3.79
2934 3046 9.783256 GAACTGTAGTTTTCACTGTAAACATTT 57.217 29.630 12.27 0.00 38.56 2.32
3018 3130 9.772973 ATTAAGTTACTCATCAAACACTACACA 57.227 29.630 0.00 0.00 0.00 3.72
3023 3135 8.395633 GTTACTCATCAAACACTACACAGTTTT 58.604 33.333 0.00 0.00 35.90 2.43
3117 3230 8.303156 AGATAGAGCATGCATTTACTACTGTAG 58.697 37.037 21.98 13.13 0.00 2.74
3136 3254 8.404107 ACTGTAGTTGTAAATTATTTGGCAGT 57.596 30.769 0.00 0.00 0.00 4.40
3154 3272 4.384208 GGCAGTAAATAGGATGGTCTGTGT 60.384 45.833 0.00 0.00 0.00 3.72
3155 3273 4.572389 GCAGTAAATAGGATGGTCTGTGTG 59.428 45.833 0.00 0.00 0.00 3.82
3156 3274 5.734720 CAGTAAATAGGATGGTCTGTGTGT 58.265 41.667 0.00 0.00 0.00 3.72
3157 3275 5.582269 CAGTAAATAGGATGGTCTGTGTGTG 59.418 44.000 0.00 0.00 0.00 3.82
3158 3276 2.698855 ATAGGATGGTCTGTGTGTGC 57.301 50.000 0.00 0.00 0.00 4.57
3159 3277 1.644509 TAGGATGGTCTGTGTGTGCT 58.355 50.000 0.00 0.00 0.00 4.40
3327 3457 0.801251 GAATGCTGCTCTTTGACGCT 59.199 50.000 0.00 0.00 0.00 5.07
3419 3559 3.251729 CCCATATTGTGCTGCATACAGTC 59.748 47.826 5.27 0.00 46.30 3.51
3483 3623 4.430908 GAGTGTAACAAATACTCCCTCCG 58.569 47.826 0.00 0.00 39.71 4.63
3485 3625 5.018809 AGTGTAACAAATACTCCCTCCGTA 58.981 41.667 0.00 0.00 41.43 4.02
3486 3626 5.481473 AGTGTAACAAATACTCCCTCCGTAA 59.519 40.000 0.00 0.00 41.43 3.18
3487 3627 6.155737 AGTGTAACAAATACTCCCTCCGTAAT 59.844 38.462 0.00 0.00 41.43 1.89
3488 3628 6.257193 GTGTAACAAATACTCCCTCCGTAATG 59.743 42.308 0.00 0.00 36.32 1.90
3491 3631 6.057321 ACAAATACTCCCTCCGTAATGAAA 57.943 37.500 0.00 0.00 0.00 2.69
3494 3634 8.437575 ACAAATACTCCCTCCGTAATGAAATAT 58.562 33.333 0.00 0.00 0.00 1.28
3495 3635 9.938280 CAAATACTCCCTCCGTAATGAAATATA 57.062 33.333 0.00 0.00 0.00 0.86
3498 3638 7.850935 ACTCCCTCCGTAATGAAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
3499 3639 7.897864 ACTCCCTCCGTAATGAAATATAAGAG 58.102 38.462 0.00 0.00 0.00 2.85
3500 3640 6.698380 TCCCTCCGTAATGAAATATAAGAGC 58.302 40.000 0.00 0.00 0.00 4.09
3501 3641 6.269077 TCCCTCCGTAATGAAATATAAGAGCA 59.731 38.462 0.00 0.00 0.00 4.26
3502 3642 7.038302 TCCCTCCGTAATGAAATATAAGAGCAT 60.038 37.037 0.00 0.00 0.00 3.79
3503 3643 7.607991 CCCTCCGTAATGAAATATAAGAGCATT 59.392 37.037 0.00 0.00 34.05 3.56
3504 3644 9.003658 CCTCCGTAATGAAATATAAGAGCATTT 57.996 33.333 0.00 0.00 32.13 2.32
3565 3740 9.635404 TTAGGAAGGAAATTTCACTTTTCTACA 57.365 29.630 19.49 11.95 34.29 2.74
3646 3822 0.972883 GACTTGCTGTCCAGTCCTCT 59.027 55.000 0.00 0.00 39.69 3.69
3654 3830 3.687125 CTGTCCAGTCCTCTGTGTACTA 58.313 50.000 0.00 0.00 39.82 1.82
3718 3894 2.480759 GCTGCAGCTCAAATAATGGGTG 60.481 50.000 31.33 0.00 38.21 4.61
3738 3914 2.364002 TGCAAGCGCCATATACTGTCTA 59.636 45.455 2.29 0.00 37.32 2.59
3898 4074 9.742144 ACAATGTAGGTTTTTGTACCATATGTA 57.258 29.630 1.24 0.00 40.82 2.29
3925 4117 7.114754 CAGTTGGATTGGGATATGCATAGTAT 58.885 38.462 12.79 0.00 0.00 2.12
4293 4485 9.346725 GAGATTCTGGTTTGCTTTTAATACTTG 57.653 33.333 0.00 0.00 0.00 3.16
4585 4778 3.814842 CCAGTACAGATGTGCAGTGAAAA 59.185 43.478 3.89 0.00 32.87 2.29
4691 4884 2.094762 TCTTTTTCGGTAGAGCCTGC 57.905 50.000 0.00 0.00 34.25 4.85
4704 4897 1.965930 GCCTGCGTGTCACATGGAA 60.966 57.895 3.42 0.00 0.00 3.53
4843 5261 5.874261 GGTGCAGTGCCAAACAAAATAATAT 59.126 36.000 13.72 0.00 0.00 1.28
4851 5269 6.441924 TGCCAAACAAAATAATATTCCCTCCA 59.558 34.615 0.00 0.00 0.00 3.86
4856 5274 6.932753 ACAAAATAATATTCCCTCCATCCCA 58.067 36.000 0.00 0.00 0.00 4.37
4857 5275 7.369434 ACAAAATAATATTCCCTCCATCCCAA 58.631 34.615 0.00 0.00 0.00 4.12
4858 5276 7.848875 ACAAAATAATATTCCCTCCATCCCAAA 59.151 33.333 0.00 0.00 0.00 3.28
4859 5277 8.713036 CAAAATAATATTCCCTCCATCCCAAAA 58.287 33.333 0.00 0.00 0.00 2.44
4860 5278 9.464379 AAAATAATATTCCCTCCATCCCAAAAT 57.536 29.630 0.00 0.00 0.00 1.82
4863 5281 9.774071 ATAATATTCCCTCCATCCCAAAATAAG 57.226 33.333 0.00 0.00 0.00 1.73
4864 5282 4.965283 TTCCCTCCATCCCAAAATAAGT 57.035 40.909 0.00 0.00 0.00 2.24
4865 5283 4.249638 TCCCTCCATCCCAAAATAAGTG 57.750 45.455 0.00 0.00 0.00 3.16
4866 5284 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
4867 5285 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
4868 5286 3.627577 CCTCCATCCCAAAATAAGTGTCG 59.372 47.826 0.00 0.00 0.00 4.35
4869 5287 4.261801 CTCCATCCCAAAATAAGTGTCGT 58.738 43.478 0.00 0.00 0.00 4.34
4870 5288 4.658063 TCCATCCCAAAATAAGTGTCGTT 58.342 39.130 0.00 0.00 0.00 3.85
4871 5289 4.457603 TCCATCCCAAAATAAGTGTCGTTG 59.542 41.667 0.00 0.00 0.00 4.10
4872 5290 4.457603 CCATCCCAAAATAAGTGTCGTTGA 59.542 41.667 0.00 0.00 0.00 3.18
4873 5291 5.125417 CCATCCCAAAATAAGTGTCGTTGAT 59.875 40.000 0.00 0.00 0.00 2.57
4874 5292 6.350110 CCATCCCAAAATAAGTGTCGTTGATT 60.350 38.462 0.00 0.00 0.00 2.57
4875 5293 6.642707 TCCCAAAATAAGTGTCGTTGATTT 57.357 33.333 0.00 0.00 0.00 2.17
4876 5294 7.747155 TCCCAAAATAAGTGTCGTTGATTTA 57.253 32.000 0.00 0.00 0.00 1.40
4877 5295 7.812648 TCCCAAAATAAGTGTCGTTGATTTAG 58.187 34.615 0.00 0.00 0.00 1.85
4878 5296 7.446013 TCCCAAAATAAGTGTCGTTGATTTAGT 59.554 33.333 0.00 0.00 0.00 2.24
4879 5297 7.537306 CCCAAAATAAGTGTCGTTGATTTAGTG 59.463 37.037 0.00 0.00 0.00 2.74
4880 5298 8.073768 CCAAAATAAGTGTCGTTGATTTAGTGT 58.926 33.333 0.00 0.00 0.00 3.55
4883 5301 9.485206 AAATAAGTGTCGTTGATTTAGTGTACT 57.515 29.630 0.00 0.00 0.00 2.73
4899 5317 6.263516 AGTGTACTAAATCAGCGACACTTA 57.736 37.500 0.00 0.00 45.67 2.24
4906 5324 4.701956 AATCAGCGACACTTATTTTGGG 57.298 40.909 0.00 0.00 0.00 4.12
5228 5653 1.344953 AACTATGGATGCCTCCGCCA 61.345 55.000 3.39 0.00 45.37 5.69
5257 5682 2.632987 AACAGCCTTCCTTGTACGTT 57.367 45.000 0.00 0.00 0.00 3.99
5324 5758 0.321671 CGAGAAGGGCTTTCACTCCA 59.678 55.000 12.17 0.00 38.31 3.86
5550 5994 4.133078 GGATTGCTACCTCCAAAGATCTG 58.867 47.826 0.00 0.00 0.00 2.90
5697 6141 0.671781 CTGAAGTGAGGCGTTCCTGG 60.672 60.000 0.00 0.00 44.46 4.45
5742 6191 2.541556 GTTTCTAGCCGTCATGGAGAC 58.458 52.381 0.00 0.00 42.00 3.36
5804 6417 3.000322 GTCCAGCGAGAACATAACGAATG 60.000 47.826 0.00 0.00 41.74 2.67
5939 6562 7.376866 GTCATGCATCGTGTAATAAAAAGGATG 59.623 37.037 0.00 0.00 38.57 3.51
5997 7391 0.375454 TGTTTTCGCTGTTGTGTCCG 59.625 50.000 0.00 0.00 0.00 4.79
6049 7443 5.239525 ACTTCTCTGTGGAATTTTGTAGCAC 59.760 40.000 0.00 0.00 0.00 4.40
6055 7449 3.126343 GTGGAATTTTGTAGCACGGTAGG 59.874 47.826 0.00 0.00 0.00 3.18
6331 7733 0.310854 CAGTTCCTTTTGTGTCGGGC 59.689 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.805099 CTGTGAACTGCTCCTTGTTCTC 59.195 50.000 0.00 0.00 41.99 2.87
78 79 6.894735 TCAGATGGTTTAGGGGTACAATTA 57.105 37.500 0.00 0.00 0.00 1.40
92 93 7.555554 CAGAAAGAAGGTATCAATCAGATGGTT 59.444 37.037 0.00 0.00 37.57 3.67
107 108 5.385198 TGGATAGCAAAACAGAAAGAAGGT 58.615 37.500 0.00 0.00 0.00 3.50
131 138 9.169592 TGGGTAAATTAGATGTAAGCAGTTAAC 57.830 33.333 0.00 0.00 0.00 2.01
132 139 9.914834 ATGGGTAAATTAGATGTAAGCAGTTAA 57.085 29.630 0.00 0.00 0.00 2.01
134 141 9.561069 CTATGGGTAAATTAGATGTAAGCAGTT 57.439 33.333 0.00 0.00 0.00 3.16
135 142 8.934697 TCTATGGGTAAATTAGATGTAAGCAGT 58.065 33.333 0.00 0.00 0.00 4.40
136 143 9.950496 ATCTATGGGTAAATTAGATGTAAGCAG 57.050 33.333 0.00 0.00 0.00 4.24
166 173 2.107041 TACCTGTCCCTGCGGTTGTG 62.107 60.000 0.00 0.00 32.36 3.33
212 219 1.146263 GTAGCTCGGGGTGGATTGG 59.854 63.158 0.00 0.00 0.00 3.16
213 220 1.146263 GGTAGCTCGGGGTGGATTG 59.854 63.158 0.00 0.00 0.00 2.67
217 224 1.968050 AAATCGGTAGCTCGGGGTGG 61.968 60.000 0.00 0.00 0.00 4.61
252 259 3.997762 TGTAGTTGCCACGTTGTAGAAT 58.002 40.909 0.00 0.00 0.00 2.40
280 287 3.304928 GGCTGAACTGAACAGATTGGTTG 60.305 47.826 8.87 0.00 37.54 3.77
291 298 4.996976 GCTCTCGGCTGAACTGAA 57.003 55.556 0.00 0.00 38.06 3.02
474 504 4.641645 TTGCTGGTCCGGCTGTGG 62.642 66.667 23.33 0.00 36.58 4.17
476 506 4.643387 GGTTGCTGGTCCGGCTGT 62.643 66.667 23.33 0.00 36.58 4.40
498 528 1.480219 CCTACCTTGTCGATTCGCGC 61.480 60.000 0.00 0.00 40.61 6.86
513 543 0.627451 CCCCCAAACCCTAACCCTAC 59.373 60.000 0.00 0.00 0.00 3.18
701 734 3.062500 CTTCTCGCTCTCGCTGCCT 62.063 63.158 0.00 0.00 35.26 4.75
857 899 3.446570 CGGTCGGGCCTACGTCTT 61.447 66.667 0.84 0.00 34.25 3.01
858 900 4.415150 TCGGTCGGGCCTACGTCT 62.415 66.667 0.84 0.00 34.25 4.18
859 901 4.185059 GTCGGTCGGGCCTACGTC 62.185 72.222 0.84 0.00 34.25 4.34
922 973 0.179081 CTCTAGTGGGCCGCTAAACC 60.179 60.000 25.81 0.00 0.00 3.27
974 1056 3.753434 AGCTCGACACCTCTGCCG 61.753 66.667 0.00 0.00 0.00 5.69
976 1058 2.813042 GCAGCTCGACACCTCTGC 60.813 66.667 0.00 0.00 43.95 4.26
977 1059 2.505777 CGCAGCTCGACACCTCTG 60.506 66.667 0.00 0.00 41.67 3.35
1204 1308 2.031163 CGGGAGGGAATCGGCATC 59.969 66.667 0.00 0.00 0.00 3.91
1319 1423 2.586792 GGCAGGTTCATCGAGCCT 59.413 61.111 2.55 0.00 43.95 4.58
1343 1447 1.206578 CCACGTTGTTAGCAAGGCG 59.793 57.895 11.32 6.38 42.36 5.52
1352 1456 2.902423 TTCTGGCCTGCCACGTTGTT 62.902 55.000 6.80 0.00 41.89 2.83
1355 1459 2.281761 CTTCTGGCCTGCCACGTT 60.282 61.111 6.80 0.00 41.89 3.99
1356 1460 2.738213 CTTCTTCTGGCCTGCCACGT 62.738 60.000 6.80 0.00 41.89 4.49
1371 1475 1.388065 CGATGACCGGGAGAGCTTCT 61.388 60.000 6.32 0.00 33.91 2.85
1510 1615 3.247173 GTCAGTGACAGCAAGAAGAAGTG 59.753 47.826 18.54 0.00 32.09 3.16
1556 1661 0.691413 CCCAAGACCCCTAGGAGGAC 60.691 65.000 19.81 14.56 37.67 3.85
1632 1737 1.897802 AGGAGCAAAGCAAATCCCAAG 59.102 47.619 0.00 0.00 31.86 3.61
1679 1784 7.278868 CCAACATAACTCAGAAGGTAGATTGAC 59.721 40.741 0.00 0.00 30.35 3.18
1681 1786 6.037610 GCCAACATAACTCAGAAGGTAGATTG 59.962 42.308 0.00 0.00 0.00 2.67
1707 1812 5.543020 TCTCAGATAGACAGATGGCATGATT 59.457 40.000 3.81 0.00 0.00 2.57
1715 1820 8.819015 CAGATTTGTTTCTCAGATAGACAGATG 58.181 37.037 0.00 0.00 32.51 2.90
1773 1878 3.309954 CGATAGCTAACACCCTGAAAAGC 59.690 47.826 0.00 0.00 0.00 3.51
1798 1903 5.298276 ACTTTTATCAAGCAAAGTGACCGAA 59.702 36.000 0.00 0.00 40.87 4.30
1861 1967 8.388103 CCCGTCACTGTTAAATACTTGAAATAG 58.612 37.037 0.00 0.00 0.00 1.73
1946 2052 6.934645 ACTTCACTTTCGATCTTCCAATGTAA 59.065 34.615 0.00 0.00 0.00 2.41
2042 2148 3.733727 GGTACAACCACATTCGCAAAAAG 59.266 43.478 0.00 0.00 38.42 2.27
2046 2152 1.240256 GGGTACAACCACATTCGCAA 58.760 50.000 0.00 0.00 41.02 4.85
2063 2169 8.485578 TGCCATAAATACTATTTAAAAGGGGG 57.514 34.615 5.52 3.37 0.00 5.40
2162 2273 8.421784 TGATGATGTTCTACCACCTTAATAGAC 58.578 37.037 0.00 0.00 0.00 2.59
2433 2544 7.376615 ACATTGTGAAGTAGTTAGAGTACCAC 58.623 38.462 0.00 0.00 0.00 4.16
2438 2549 9.036980 AGGATTACATTGTGAAGTAGTTAGAGT 57.963 33.333 0.00 0.00 0.00 3.24
2445 2556 8.498054 ACAATCAGGATTACATTGTGAAGTAG 57.502 34.615 0.00 0.00 38.92 2.57
2486 2597 1.168714 CAGAAGGCTTGCTAACCACC 58.831 55.000 3.46 0.00 0.00 4.61
2555 2666 6.766944 TCAATGAAAACCAGTGCAAATGAAAT 59.233 30.769 1.78 0.00 40.40 2.17
2607 2718 3.397482 CACCAGATATAAGAGGCTGCAC 58.603 50.000 0.50 0.00 0.00 4.57
2694 2806 9.677567 GCAAATGAAGACAAAAATACTAAGTCA 57.322 29.630 0.00 0.00 0.00 3.41
2709 2821 5.618056 TCAAGACATCAGCAAATGAAGAC 57.382 39.130 5.45 0.00 42.53 3.01
2711 2823 7.759465 ACTATTCAAGACATCAGCAAATGAAG 58.241 34.615 5.45 0.00 42.53 3.02
2831 2943 2.265589 ACTTACCAACCCCAAGAACG 57.734 50.000 0.00 0.00 0.00 3.95
2867 2979 2.169330 TGCTGTTGCTATGCCATGAAA 58.831 42.857 0.00 0.00 40.48 2.69
2888 3000 5.939883 AGTTCATATTTCAACTGCTGCAGTA 59.060 36.000 33.11 19.41 44.62 2.74
2934 3046 1.340889 GGTACGCATACATACCCGGAA 59.659 52.381 0.73 0.00 35.71 4.30
3032 3144 9.537192 CTACATTGTAGTCACCCGATAAATAAA 57.463 33.333 14.52 0.00 0.00 1.40
3084 3197 9.790344 AGTAAATGCATGCTCTATCTAGAAAAT 57.210 29.630 20.33 0.00 0.00 1.82
3136 3254 4.225042 AGCACACACAGACCATCCTATTTA 59.775 41.667 0.00 0.00 0.00 1.40
3154 3272 9.453572 AAGAAGATATGAAGTCAATTAAGCACA 57.546 29.630 0.00 0.00 0.00 4.57
3403 3543 1.072173 ACCTGACTGTATGCAGCACAA 59.928 47.619 11.09 0.00 46.30 3.33
3419 3559 8.395633 GGTATTACAAGTAGCAAATAACACCTG 58.604 37.037 0.00 0.00 0.00 4.00
3518 3658 9.280456 TCCTAATTACTCCCTCTGTAAAGAAAT 57.720 33.333 0.00 0.00 34.20 2.17
3519 3659 8.674925 TCCTAATTACTCCCTCTGTAAAGAAA 57.325 34.615 0.00 0.00 34.20 2.52
3521 3661 7.344871 CCTTCCTAATTACTCCCTCTGTAAAGA 59.655 40.741 0.00 0.00 34.20 2.52
3524 3664 6.748969 TCCTTCCTAATTACTCCCTCTGTAA 58.251 40.000 0.00 0.00 34.87 2.41
3525 3665 6.351317 TCCTTCCTAATTACTCCCTCTGTA 57.649 41.667 0.00 0.00 0.00 2.74
3527 3667 6.561519 TTTCCTTCCTAATTACTCCCTCTG 57.438 41.667 0.00 0.00 0.00 3.35
3528 3668 7.773099 AATTTCCTTCCTAATTACTCCCTCT 57.227 36.000 0.00 0.00 0.00 3.69
3529 3669 8.053355 TGAAATTTCCTTCCTAATTACTCCCTC 58.947 37.037 15.48 0.00 0.00 4.30
3532 3672 8.809468 AGTGAAATTTCCTTCCTAATTACTCC 57.191 34.615 15.48 0.00 0.00 3.85
3562 3737 8.092687 CACATATTCATGGATGACTCTCATGTA 58.907 37.037 0.00 0.00 39.25 2.29
3565 3740 5.938710 GCACATATTCATGGATGACTCTCAT 59.061 40.000 0.00 0.00 36.32 2.90
3646 3822 7.935520 TCATGTTCAAAATTTGCTAGTACACA 58.064 30.769 0.00 0.00 0.00 3.72
3654 3830 9.846248 GTAGACTTATCATGTTCAAAATTTGCT 57.154 29.630 0.00 0.00 0.00 3.91
3718 3894 1.871080 AGACAGTATATGGCGCTTGC 58.129 50.000 7.64 0.00 44.27 4.01
3898 4074 3.979911 TGCATATCCCAATCCAACTGTT 58.020 40.909 0.00 0.00 0.00 3.16
4293 4485 1.620819 TCAGTGTTCTGAAGCCCTCTC 59.379 52.381 0.00 0.00 46.17 3.20
4585 4778 3.514309 ACTAGAGGGTGCTCGTTAAATGT 59.486 43.478 0.00 0.00 0.00 2.71
4682 4875 0.108662 CATGTGACACGCAGGCTCTA 60.109 55.000 0.22 0.00 0.00 2.43
4691 4884 0.959867 TGGCCATTCCATGTGACACG 60.960 55.000 0.00 0.00 40.72 4.49
4793 5210 5.063880 TGTTTTCAGGAAACTAGAGAAGCC 58.936 41.667 5.88 0.00 46.25 4.35
4843 5261 4.045334 ACACTTATTTTGGGATGGAGGGAA 59.955 41.667 0.00 0.00 0.00 3.97
4851 5269 6.834168 AATCAACGACACTTATTTTGGGAT 57.166 33.333 0.00 0.00 0.00 3.85
4857 5275 9.485206 AGTACACTAAATCAACGACACTTATTT 57.515 29.630 0.00 0.00 0.00 1.40
4860 5278 9.964303 TTTAGTACACTAAATCAACGACACTTA 57.036 29.630 9.90 0.00 41.85 2.24
4861 5279 8.876275 TTTAGTACACTAAATCAACGACACTT 57.124 30.769 9.90 0.00 41.85 3.16
4873 5291 6.684686 AGTGTCGCTGATTTAGTACACTAAA 58.315 36.000 15.02 15.02 45.57 1.85
4874 5292 6.263516 AGTGTCGCTGATTTAGTACACTAA 57.736 37.500 13.35 0.00 45.57 2.24
4875 5293 5.892160 AGTGTCGCTGATTTAGTACACTA 57.108 39.130 13.35 0.00 45.57 2.74
4876 5294 4.785511 AGTGTCGCTGATTTAGTACACT 57.214 40.909 10.74 10.74 44.12 3.55
4877 5295 7.521509 AATAAGTGTCGCTGATTTAGTACAC 57.478 36.000 0.00 0.00 41.63 2.90
4878 5296 8.440059 CAAAATAAGTGTCGCTGATTTAGTACA 58.560 33.333 8.84 0.00 37.29 2.90
4879 5297 7.903431 CCAAAATAAGTGTCGCTGATTTAGTAC 59.097 37.037 8.84 0.00 37.29 2.73
4880 5298 7.065324 CCCAAAATAAGTGTCGCTGATTTAGTA 59.935 37.037 8.84 0.00 37.29 1.82
4881 5299 6.128007 CCCAAAATAAGTGTCGCTGATTTAGT 60.128 38.462 8.84 0.00 37.29 2.24
4882 5300 6.093495 TCCCAAAATAAGTGTCGCTGATTTAG 59.907 38.462 8.84 4.74 37.29 1.85
4883 5301 5.941058 TCCCAAAATAAGTGTCGCTGATTTA 59.059 36.000 8.84 0.00 37.29 1.40
4887 5305 3.071479 GTCCCAAAATAAGTGTCGCTGA 58.929 45.455 0.00 0.00 0.00 4.26
4899 5317 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4906 5324 4.522114 ACTAGTTTAGTACTCCCTCCGTC 58.478 47.826 0.00 0.00 37.23 4.79
5228 5653 3.185455 AGGAAGGCTGTTTATCTGAGGT 58.815 45.455 0.00 0.00 0.00 3.85
5257 5682 0.601046 CGTTGCCTCTTCTGCAGACA 60.601 55.000 18.03 7.99 40.35 3.41
5324 5758 0.902531 CCACCGACTATGTCCTTGGT 59.097 55.000 0.00 0.00 30.66 3.67
5550 5994 4.557205 CAGTGTCTTACTACAACTCCACC 58.443 47.826 0.00 0.00 37.60 4.61
5804 6417 3.807538 CAGCACCACATGAGCGCC 61.808 66.667 2.29 0.00 0.00 6.53
5837 6459 6.771267 CCACTAAGGAGTCCAAACTTTTTAGT 59.229 38.462 12.86 11.38 41.10 2.24
5882 6504 2.200899 ACTCAAATTTTTGTGGCACGC 58.799 42.857 13.77 0.00 39.18 5.34
5911 6533 7.120579 TCCTTTTTATTACACGATGCATGACTT 59.879 33.333 2.46 0.00 0.00 3.01
5939 6562 8.635877 ATGTTAGTCTATTCACGACAGAAATC 57.364 34.615 0.00 0.00 33.89 2.17
5997 7391 8.414003 AGGAAACCTACAAGAAATTTTTGAGAC 58.586 33.333 15.45 0.00 28.47 3.36
6055 7449 5.588240 TGAATGTATCGACATGGTGAGTAC 58.412 41.667 0.00 0.00 45.93 2.73
6292 7688 2.490115 TGTTACCGATTGCCACCAATTC 59.510 45.455 0.00 0.00 41.60 2.17
6331 7733 2.222027 GGTGACAAGTTTGTGGAGGAG 58.778 52.381 1.62 0.00 42.43 3.69


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

AutoCloner maintained by Alex Coulton.