Multiple sequence alignment - TraesCS5A01G167400

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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 TraesCS5A01G167400 chr5A 100.000 4457 0 0 1 4457 356479564 356475108 0.000000e+00 8231.0
1 TraesCS5A01G167400 chr5A 95.253 1285 46 8 1442 2714 619180104 619178823 0.000000e+00 2021.0
2 TraesCS5A01G167400 chr5A 94.380 1210 54 7 1517 2714 474914242 474913035 0.000000e+00 1845.0
3 TraesCS5A01G167400 chr5A 79.310 174 22 10 2551 2714 8516781 8516612 4.710000e-20 110.0
4 TraesCS5A01G167400 chr5A 84.416 77 4 3 2646 2714 474915997 474916073 8.000000e-08 69.4
5 TraesCS5A01G167400 chr5B 92.887 1434 60 15 3 1405 304607707 304606285 0.000000e+00 2045.0
6 TraesCS5A01G167400 chr5B 86.346 1311 113 35 1427 2725 338956418 338957674 0.000000e+00 1369.0
7 TraesCS5A01G167400 chr5B 92.880 941 45 8 2716 3649 304606264 304605339 0.000000e+00 1347.0
8 TraesCS5A01G167400 chr5B 94.093 237 14 0 4077 4313 304605022 304604786 1.180000e-95 361.0
9 TraesCS5A01G167400 chr5B 90.351 114 3 1 4352 4457 304604780 304604667 4.650000e-30 143.0
10 TraesCS5A01G167400 chr5B 83.212 137 14 7 3819 3952 641389326 641389196 2.820000e-22 117.0
11 TraesCS5A01G167400 chr5B 78.992 119 14 7 2616 2725 488188350 488188234 2.220000e-08 71.3
12 TraesCS5A01G167400 chr7A 94.926 1281 53 5 1444 2714 115499358 115498080 0.000000e+00 1995.0
13 TraesCS5A01G167400 chr4A 93.866 1288 65 7 1440 2714 598224530 598223244 0.000000e+00 1929.0
14 TraesCS5A01G167400 chr4A 93.781 1206 71 4 1443 2646 590152963 590151760 0.000000e+00 1808.0
15 TraesCS5A01G167400 chr4A 87.603 363 37 3 2361 2715 720085133 720084771 8.920000e-112 414.0
16 TraesCS5A01G167400 chr4A 83.721 86 12 2 3869 3954 734955011 734954928 3.700000e-11 80.5
17 TraesCS5A01G167400 chr5D 90.479 1439 63 31 1 1403 268884996 268883596 0.000000e+00 1831.0
18 TraesCS5A01G167400 chr5D 93.316 1167 50 12 2716 3879 268883573 268882432 0.000000e+00 1698.0
19 TraesCS5A01G167400 chr5D 90.216 603 48 5 2123 2714 442757924 442758526 0.000000e+00 776.0
20 TraesCS5A01G167400 chr5D 89.377 546 27 11 3912 4457 268882380 268881866 0.000000e+00 658.0
21 TraesCS5A01G167400 chr5D 89.000 300 32 1 1828 2127 442727773 442728071 1.960000e-98 370.0
22 TraesCS5A01G167400 chr4B 87.655 1288 116 22 1444 2719 44661603 44660347 0.000000e+00 1458.0
23 TraesCS5A01G167400 chr4B 87.345 1288 118 26 1444 2719 44472364 44471110 0.000000e+00 1434.0
24 TraesCS5A01G167400 chr3A 90.909 638 55 3 1727 2362 693176359 693175723 0.000000e+00 854.0
25 TraesCS5A01G167400 chr3D 90.767 639 56 3 1726 2362 556164412 556163775 0.000000e+00 850.0
26 TraesCS5A01G167400 chr3D 75.622 201 37 8 2536 2726 590376403 590376601 6.140000e-14 89.8
27 TraesCS5A01G167400 chr3B 90.781 640 54 5 1726 2362 739166036 739165399 0.000000e+00 850.0
28 TraesCS5A01G167400 chr7B 88.832 591 55 5 2146 2725 89778269 89777679 0.000000e+00 715.0
29 TraesCS5A01G167400 chr2D 92.908 423 28 2 1441 1862 513461758 513461337 8.190000e-172 614.0
30 TraesCS5A01G167400 chr1D 81.319 182 20 9 2545 2715 18948132 18947954 7.780000e-28 135.0
31 TraesCS5A01G167400 chr6A 79.429 175 24 8 2551 2715 101993387 101993559 3.640000e-21 113.0
32 TraesCS5A01G167400 chr2A 93.617 47 2 1 2676 2721 740934696 740934650 8.000000e-08 69.4
33 TraesCS5A01G167400 chr1A 97.500 40 1 0 2676 2715 91102430 91102469 8.000000e-08 69.4


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 TraesCS5A01G167400 chr5A 356475108 356479564 4456 True 8231.000000 8231 100.000000 1 4457 1 chr5A.!!$R2 4456
1 TraesCS5A01G167400 chr5A 619178823 619180104 1281 True 2021.000000 2021 95.253000 1442 2714 1 chr5A.!!$R4 1272
2 TraesCS5A01G167400 chr5A 474913035 474914242 1207 True 1845.000000 1845 94.380000 1517 2714 1 chr5A.!!$R3 1197
3 TraesCS5A01G167400 chr5B 338956418 338957674 1256 False 1369.000000 1369 86.346000 1427 2725 1 chr5B.!!$F1 1298
4 TraesCS5A01G167400 chr5B 304604667 304607707 3040 True 974.000000 2045 92.552750 3 4457 4 chr5B.!!$R3 4454
5 TraesCS5A01G167400 chr7A 115498080 115499358 1278 True 1995.000000 1995 94.926000 1444 2714 1 chr7A.!!$R1 1270
6 TraesCS5A01G167400 chr4A 598223244 598224530 1286 True 1929.000000 1929 93.866000 1440 2714 1 chr4A.!!$R2 1274
7 TraesCS5A01G167400 chr4A 590151760 590152963 1203 True 1808.000000 1808 93.781000 1443 2646 1 chr4A.!!$R1 1203
8 TraesCS5A01G167400 chr5D 268881866 268884996 3130 True 1395.666667 1831 91.057333 1 4457 3 chr5D.!!$R1 4456
9 TraesCS5A01G167400 chr5D 442757924 442758526 602 False 776.000000 776 90.216000 2123 2714 1 chr5D.!!$F2 591
10 TraesCS5A01G167400 chr4B 44660347 44661603 1256 True 1458.000000 1458 87.655000 1444 2719 1 chr4B.!!$R2 1275
11 TraesCS5A01G167400 chr4B 44471110 44472364 1254 True 1434.000000 1434 87.345000 1444 2719 1 chr4B.!!$R1 1275
12 TraesCS5A01G167400 chr3A 693175723 693176359 636 True 854.000000 854 90.909000 1727 2362 1 chr3A.!!$R1 635
13 TraesCS5A01G167400 chr3D 556163775 556164412 637 True 850.000000 850 90.767000 1726 2362 1 chr3D.!!$R1 636
14 TraesCS5A01G167400 chr3B 739165399 739166036 637 True 850.000000 850 90.781000 1726 2362 1 chr3B.!!$R1 636
15 TraesCS5A01G167400 chr7B 89777679 89778269 590 True 715.000000 715 88.832000 2146 2725 1 chr7B.!!$R1 579

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
796 834 0.304098 CGAGCTCGGTCCTTAGTACG 59.696 60.0 28.40 0.0 35.37 3.67 F
1812 1880 0.107508 CGATGGCCAGGAACTCATGT 60.108 55.0 13.05 0.0 34.60 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2048 1.002403 TTATCCTCCTCCACCGCCA 59.998 57.895 0.00 0.00 0.0 5.69 R
3589 3683 0.027716 CGTACTGATCAGACCGGACG 59.972 60.000 29.27 21.89 0.0 4.79 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
186 187 3.447040 GCAAGCAGCAAGTGGGAA 58.553 55.556 0.00 0.00 44.79 3.97
189 190 0.529378 CAAGCAGCAAGTGGGAATCC 59.471 55.000 0.00 0.00 0.00 3.01
227 228 1.674962 GAGCAACATGAAGGAGATGGC 59.325 52.381 0.00 0.00 0.00 4.40
258 259 0.913451 AGGACCTGCTCTCATGGCTT 60.913 55.000 0.00 0.00 0.00 4.35
333 334 2.029844 GCCAGACGTGTTCTCCAGC 61.030 63.158 0.00 0.00 28.96 4.85
398 399 4.527583 GAGGAGCTGAGCGGCCAG 62.528 72.222 18.84 12.35 37.23 4.85
400 401 4.087892 GGAGCTGAGCGGCCAGAA 62.088 66.667 18.59 0.00 36.29 3.02
577 596 0.466007 TGCTTTGCTCCTGCTGTCAA 60.466 50.000 0.00 0.00 40.48 3.18
599 618 3.042887 CTGTTACAGTTGCCGCTTTTTC 58.957 45.455 3.88 0.00 0.00 2.29
600 619 2.685897 TGTTACAGTTGCCGCTTTTTCT 59.314 40.909 0.00 0.00 0.00 2.52
601 620 3.129638 TGTTACAGTTGCCGCTTTTTCTT 59.870 39.130 0.00 0.00 0.00 2.52
602 621 2.959507 ACAGTTGCCGCTTTTTCTTT 57.040 40.000 0.00 0.00 0.00 2.52
603 622 3.245518 ACAGTTGCCGCTTTTTCTTTT 57.754 38.095 0.00 0.00 0.00 2.27
604 623 3.186909 ACAGTTGCCGCTTTTTCTTTTC 58.813 40.909 0.00 0.00 0.00 2.29
605 624 3.119137 ACAGTTGCCGCTTTTTCTTTTCT 60.119 39.130 0.00 0.00 0.00 2.52
645 664 0.884704 GTTTTCTGCTGTGGCTCGGA 60.885 55.000 0.00 0.00 39.59 4.55
647 666 0.884704 TTTCTGCTGTGGCTCGGAAC 60.885 55.000 0.00 0.00 39.59 3.62
651 670 1.292223 GCTGTGGCTCGGAACTGTA 59.708 57.895 0.00 0.00 35.22 2.74
681 716 3.077359 GAGTCTGGCATGTTTAGCTGTT 58.923 45.455 0.00 0.00 0.00 3.16
682 717 4.253685 GAGTCTGGCATGTTTAGCTGTTA 58.746 43.478 0.00 0.00 0.00 2.41
696 731 4.130286 AGCTGTTATAAGTGGCTGAGTC 57.870 45.455 6.12 0.00 31.68 3.36
714 749 1.226945 CGAATGAAATTGGCGGCCC 60.227 57.895 17.97 0.23 36.07 5.80
745 780 0.887933 ATTGAAAGCGCCACCGAAAT 59.112 45.000 2.29 0.00 36.29 2.17
776 814 5.539048 ACTACTAGTTGTTGGCTTGTAGTG 58.461 41.667 14.95 0.00 45.98 2.74
791 829 0.393402 TAGTGCGAGCTCGGTCCTTA 60.393 55.000 35.10 13.67 40.23 2.69
792 830 1.226717 GTGCGAGCTCGGTCCTTAG 60.227 63.158 35.10 7.44 40.23 2.18
793 831 1.677966 TGCGAGCTCGGTCCTTAGT 60.678 57.895 35.10 0.00 40.23 2.24
794 832 0.393402 TGCGAGCTCGGTCCTTAGTA 60.393 55.000 35.10 2.87 40.23 1.82
796 834 0.304098 CGAGCTCGGTCCTTAGTACG 59.696 60.000 28.40 0.00 35.37 3.67
797 835 1.377536 GAGCTCGGTCCTTAGTACGT 58.622 55.000 0.00 0.00 0.00 3.57
798 836 1.742268 GAGCTCGGTCCTTAGTACGTT 59.258 52.381 0.00 0.00 0.00 3.99
799 837 1.742268 AGCTCGGTCCTTAGTACGTTC 59.258 52.381 0.00 0.00 0.00 3.95
893 945 1.227089 CTCGGCTCATCCTTCACCG 60.227 63.158 0.00 0.00 45.15 4.94
969 1024 2.034317 TACATGTGCACGCAGCCAG 61.034 57.895 13.13 0.00 44.83 4.85
977 1043 4.996434 ACGCAGCCAGTGAGCACC 62.996 66.667 6.40 0.00 34.23 5.01
989 1055 1.734465 GTGAGCACCCGAGAATTTGAG 59.266 52.381 0.00 0.00 0.00 3.02
1029 1095 3.576356 CGACATGCCATGCCCGTC 61.576 66.667 4.17 0.00 0.00 4.79
1041 1107 2.261671 CCCGTCGTCTTGGTCCTG 59.738 66.667 0.00 0.00 0.00 3.86
1405 1471 2.680251 TCCCGGTAACCATGCATACTA 58.320 47.619 0.00 0.00 0.00 1.82
1406 1472 2.366266 TCCCGGTAACCATGCATACTAC 59.634 50.000 0.00 1.15 0.00 2.73
1407 1473 2.367567 CCCGGTAACCATGCATACTACT 59.632 50.000 0.00 0.00 0.00 2.57
1408 1474 3.554337 CCCGGTAACCATGCATACTACTC 60.554 52.174 0.00 0.00 0.00 2.59
1409 1475 3.554337 CCGGTAACCATGCATACTACTCC 60.554 52.174 0.00 0.00 0.00 3.85
1413 1479 4.844349 AACCATGCATACTACTCCAGTT 57.156 40.909 0.00 0.00 38.80 3.16
1414 1480 4.142609 ACCATGCATACTACTCCAGTTG 57.857 45.455 0.00 0.00 38.80 3.16
1415 1481 3.519510 ACCATGCATACTACTCCAGTTGT 59.480 43.478 0.00 0.00 38.80 3.32
1417 1483 4.572389 CCATGCATACTACTCCAGTTGTTC 59.428 45.833 0.00 0.00 38.80 3.18
1419 1485 5.073311 TGCATACTACTCCAGTTGTTCTC 57.927 43.478 0.00 0.00 38.80 2.87
1420 1486 4.526650 TGCATACTACTCCAGTTGTTCTCA 59.473 41.667 0.00 0.00 38.80 3.27
1421 1487 5.105752 GCATACTACTCCAGTTGTTCTCAG 58.894 45.833 0.00 0.00 38.80 3.35
1422 1488 3.669251 ACTACTCCAGTTGTTCTCAGC 57.331 47.619 0.00 0.00 31.59 4.26
1425 1491 2.042464 ACTCCAGTTGTTCTCAGCTCA 58.958 47.619 0.00 0.00 32.98 4.26
1426 1492 2.435805 ACTCCAGTTGTTCTCAGCTCAA 59.564 45.455 0.00 0.00 32.98 3.02
1427 1493 3.118261 ACTCCAGTTGTTCTCAGCTCAAA 60.118 43.478 0.00 0.00 32.98 2.69
1494 1560 2.445525 AGTTGGTGGTTCACATTACCCT 59.554 45.455 0.38 0.00 35.86 4.34
1515 1581 5.396884 CCCTCTGATCTTTATTTCGGTTCCT 60.397 44.000 0.00 0.00 0.00 3.36
1524 1590 3.820195 ATTTCGGTTCCTTTTACCCCT 57.180 42.857 0.00 0.00 31.75 4.79
1534 1600 5.333566 TCCTTTTACCCCTTGAACAATCT 57.666 39.130 0.00 0.00 0.00 2.40
1581 1647 2.358898 GTGGTTTGTCTCAACATGCAGT 59.641 45.455 0.00 0.00 34.73 4.40
1652 1718 7.384115 CACGAGGATTAACTTAAGTGAAACAGA 59.616 37.037 9.34 0.00 41.43 3.41
1812 1880 0.107508 CGATGGCCAGGAACTCATGT 60.108 55.000 13.05 0.00 34.60 3.21
1820 1888 2.401766 GGAACTCATGTGCTGCGGG 61.402 63.158 0.00 0.00 0.00 6.13
1997 2065 1.760875 GTGGCGGTGGAGGAGGATA 60.761 63.158 0.00 0.00 0.00 2.59
2352 2434 2.564947 GGTGGATCTCAGTGAGTTCAGT 59.435 50.000 25.44 8.42 32.00 3.41
2453 2535 2.202919 CGTCATCCAGATGCGGCA 60.203 61.111 4.58 4.58 38.65 5.69
2534 2616 1.069090 GTCTCAACCCAGCGTGACA 59.931 57.895 0.00 0.00 0.00 3.58
2637 2719 6.884832 ACTGATTTTGTCCGGTATGAGATTA 58.115 36.000 0.00 0.00 0.00 1.75
2647 2729 4.775780 CCGGTATGAGATTATTCAGGGGTA 59.224 45.833 0.00 0.00 0.00 3.69
2707 2798 6.715264 ACTTTGTTCAGGGTAGTAAAATGGAG 59.285 38.462 0.00 0.00 0.00 3.86
2767 2858 3.461773 AGTCGGCGATGACCCTGG 61.462 66.667 14.79 0.00 39.77 4.45
2916 3007 1.295423 CTACCTGGTGTTCCCCGTG 59.705 63.158 10.23 0.00 0.00 4.94
2938 3029 2.820037 GCTACAGCTTCACCCCGC 60.820 66.667 0.00 0.00 38.21 6.13
3117 3208 2.435234 TACAACATGGCGGCCGTC 60.435 61.111 26.05 26.05 0.00 4.79
3270 3361 4.802051 TCGGCCCAAGGATGCTGC 62.802 66.667 0.00 0.00 33.81 5.25
3363 3454 1.467342 GCCGGCAAATACGTCTTCTTT 59.533 47.619 24.80 0.00 0.00 2.52
3411 3502 4.008933 AGGATGATAGCCGGCGCC 62.009 66.667 23.20 19.07 34.57 6.53
3417 3508 4.320456 ATAGCCGGCGCCATCCTG 62.320 66.667 28.98 9.56 34.57 3.86
3433 3527 2.033448 TGAATGCCACGTCCCACC 59.967 61.111 0.00 0.00 0.00 4.61
3489 3583 0.450583 TCGGACGTCAGATACACAGC 59.549 55.000 18.91 0.00 0.00 4.40
3493 3587 1.472878 GACGTCAGATACACAGCTCCA 59.527 52.381 11.55 0.00 0.00 3.86
3562 3656 2.544267 GTCTAGTGACCAACAACTGCAC 59.456 50.000 0.00 0.00 37.24 4.57
3602 3696 1.630148 CAACTTCGTCCGGTCTGATC 58.370 55.000 0.00 0.00 0.00 2.92
3622 3719 5.122869 TGATCAGTACGTGTCCAACTAGTAC 59.877 44.000 0.00 0.00 38.25 2.73
3623 3720 4.645535 TCAGTACGTGTCCAACTAGTACT 58.354 43.478 0.00 0.00 45.94 2.73
3624 3721 4.692625 TCAGTACGTGTCCAACTAGTACTC 59.307 45.833 0.00 0.00 44.02 2.59
3625 3722 4.006319 AGTACGTGTCCAACTAGTACTCC 58.994 47.826 0.00 0.00 42.79 3.85
3626 3723 3.151912 ACGTGTCCAACTAGTACTCCT 57.848 47.619 0.00 0.00 0.00 3.69
3627 3724 4.292186 ACGTGTCCAACTAGTACTCCTA 57.708 45.455 0.00 0.00 0.00 2.94
3628 3725 4.006319 ACGTGTCCAACTAGTACTCCTAC 58.994 47.826 0.00 0.00 0.00 3.18
3636 3733 6.377429 TCCAACTAGTACTCCTACATGAGTTG 59.623 42.308 17.98 17.98 42.92 3.16
3638 3735 4.645588 ACTAGTACTCCTACATGAGTTGGC 59.354 45.833 0.00 0.00 42.92 4.52
3649 3746 1.292223 GAGTTGGCTGCCGTGTAGA 59.708 57.895 14.98 0.00 0.00 2.59
3655 3752 0.531200 GGCTGCCGTGTAGAACTAGT 59.469 55.000 1.35 0.00 0.00 2.57
3656 3753 1.747355 GGCTGCCGTGTAGAACTAGTA 59.253 52.381 1.35 0.00 0.00 1.82
3764 3861 7.706607 AGTTGAAAAGCAATAAAGAAGAACACC 59.293 33.333 0.00 0.00 39.03 4.16
3801 3898 3.876914 CTGCTGGCTATTCAAATAACCGA 59.123 43.478 0.00 0.00 31.24 4.69
3802 3899 3.876914 TGCTGGCTATTCAAATAACCGAG 59.123 43.478 0.00 0.22 31.24 4.63
3803 3900 3.877508 GCTGGCTATTCAAATAACCGAGT 59.122 43.478 0.00 0.00 31.24 4.18
3804 3901 4.260784 GCTGGCTATTCAAATAACCGAGTG 60.261 45.833 0.00 0.00 31.24 3.51
3805 3902 3.625764 TGGCTATTCAAATAACCGAGTGC 59.374 43.478 0.00 0.00 31.24 4.40
3818 3915 2.514592 AGTGCTGCGTGTTGCTGT 60.515 55.556 0.00 0.00 46.63 4.40
3899 4027 1.000396 GGATCAGGTGGCCAGCTTT 60.000 57.895 34.41 24.11 36.98 3.51
3900 4028 1.318158 GGATCAGGTGGCCAGCTTTG 61.318 60.000 34.41 24.46 36.98 2.77
3901 4029 0.610232 GATCAGGTGGCCAGCTTTGT 60.610 55.000 34.41 22.11 36.98 2.83
3902 4030 0.698238 ATCAGGTGGCCAGCTTTGTA 59.302 50.000 34.41 19.78 36.98 2.41
3903 4031 0.250727 TCAGGTGGCCAGCTTTGTAC 60.251 55.000 34.41 5.88 36.98 2.90
3904 4032 0.250901 CAGGTGGCCAGCTTTGTACT 60.251 55.000 34.41 9.95 36.98 2.73
3905 4033 1.003118 CAGGTGGCCAGCTTTGTACTA 59.997 52.381 34.41 0.00 36.98 1.82
3906 4034 1.003233 AGGTGGCCAGCTTTGTACTAC 59.997 52.381 31.61 1.90 35.28 2.73
3907 4035 1.076332 GTGGCCAGCTTTGTACTACG 58.924 55.000 5.11 0.00 0.00 3.51
3908 4036 0.036765 TGGCCAGCTTTGTACTACGG 60.037 55.000 0.00 0.00 0.00 4.02
3909 4037 0.036671 GGCCAGCTTTGTACTACGGT 60.037 55.000 0.00 0.00 0.00 4.83
3910 4038 1.076332 GCCAGCTTTGTACTACGGTG 58.924 55.000 6.12 6.12 0.00 4.94
3911 4039 1.076332 CCAGCTTTGTACTACGGTGC 58.924 55.000 7.33 0.00 0.00 5.01
3912 4040 1.606994 CCAGCTTTGTACTACGGTGCA 60.607 52.381 7.33 0.00 36.33 4.57
3913 4041 1.459592 CAGCTTTGTACTACGGTGCAC 59.540 52.381 8.80 8.80 37.76 4.57
3914 4042 0.794473 GCTTTGTACTACGGTGCACC 59.206 55.000 26.78 26.78 37.76 5.01
3915 4043 1.607251 GCTTTGTACTACGGTGCACCT 60.607 52.381 32.28 21.25 37.76 4.00
3916 4044 2.066262 CTTTGTACTACGGTGCACCTG 58.934 52.381 32.28 26.14 37.76 4.00
3930 4058 3.357079 CCTGGACGCACAAGCACC 61.357 66.667 0.00 0.00 42.27 5.01
3957 4085 3.004419 CGAGTTCAGTCAGTGAGTTGGTA 59.996 47.826 0.00 0.00 36.21 3.25
3964 4092 1.677576 TCAGTGAGTTGGTACGTCGTT 59.322 47.619 1.78 0.00 0.00 3.85
3983 4111 2.582728 TGTCGGTAGTTGTTGTCGTT 57.417 45.000 0.00 0.00 0.00 3.85
4001 4129 0.387622 TTGGAAAGTACTCGGCGTCG 60.388 55.000 1.15 1.15 37.82 5.12
4002 4130 1.211190 GGAAAGTACTCGGCGTCGT 59.789 57.895 10.18 8.33 37.69 4.34
4003 4131 0.796113 GGAAAGTACTCGGCGTCGTC 60.796 60.000 10.18 0.00 37.69 4.20
4044 4172 0.433492 CGAACGAAACAGTGTAGCGG 59.567 55.000 18.21 3.11 0.00 5.52
4112 4338 3.442100 GATGGTTGCTAGCAATTTCAGC 58.558 45.455 31.46 25.52 38.28 4.26
4191 4417 0.464036 CCGGTGTAAGCTGGCTGATA 59.536 55.000 0.00 0.00 0.00 2.15
4198 4424 2.133281 AAGCTGGCTGATATGCACAA 57.867 45.000 0.00 0.00 34.04 3.33
4225 4451 7.169813 GGAAAAAGTTAAGGCACTCTTGATTTG 59.830 37.037 0.00 0.00 38.49 2.32
4277 4503 0.036010 GCTTCTGCAGCTTCCACCTA 60.036 55.000 9.47 0.00 46.27 3.08
4313 4539 7.293828 ACCATGATGAAGAGAGTGAGTATCTA 58.706 38.462 0.00 0.00 34.92 1.98
4314 4540 7.949565 ACCATGATGAAGAGAGTGAGTATCTAT 59.050 37.037 0.00 0.00 34.92 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 187 3.012518 CAGCCTTTCTTTCATCGTGGAT 58.987 45.455 0.00 0.00 0.00 3.41
189 190 2.159599 GCTCAGCCTTTCTTTCATCGTG 60.160 50.000 0.00 0.00 0.00 4.35
227 228 1.473434 GCAGGTCCTTTGATAGTCCCG 60.473 57.143 0.00 0.00 0.00 5.14
269 270 1.396301 CCTGCAAATCTTCAGACGAGC 59.604 52.381 0.00 0.00 32.26 5.03
333 334 2.612604 TCATCACATTTCGTGTACCCG 58.387 47.619 0.00 0.00 46.44 5.28
398 399 2.614057 CACAAACAGTGGAGTGGAGTTC 59.386 50.000 0.00 0.00 44.69 3.01
400 401 2.332063 CACAAACAGTGGAGTGGAGT 57.668 50.000 0.00 0.00 44.69 3.85
599 618 1.911057 AGCGAAAAGGGGGAGAAAAG 58.089 50.000 0.00 0.00 0.00 2.27
600 619 1.960689 CAAGCGAAAAGGGGGAGAAAA 59.039 47.619 0.00 0.00 0.00 2.29
601 620 1.616159 CAAGCGAAAAGGGGGAGAAA 58.384 50.000 0.00 0.00 0.00 2.52
602 621 0.893727 GCAAGCGAAAAGGGGGAGAA 60.894 55.000 0.00 0.00 0.00 2.87
603 622 1.303317 GCAAGCGAAAAGGGGGAGA 60.303 57.895 0.00 0.00 0.00 3.71
604 623 2.690778 CGCAAGCGAAAAGGGGGAG 61.691 63.158 9.11 0.00 42.83 4.30
605 624 2.671619 CGCAAGCGAAAAGGGGGA 60.672 61.111 9.11 0.00 42.83 4.81
645 664 7.520451 TGCCAGACTCGTATATTATACAGTT 57.480 36.000 12.99 0.00 0.00 3.16
647 666 7.539436 ACATGCCAGACTCGTATATTATACAG 58.461 38.462 12.99 11.13 0.00 2.74
651 670 7.545965 GCTAAACATGCCAGACTCGTATATTAT 59.454 37.037 0.00 0.00 0.00 1.28
681 716 5.592104 TTCATTCGACTCAGCCACTTATA 57.408 39.130 0.00 0.00 0.00 0.98
682 717 4.471904 TTCATTCGACTCAGCCACTTAT 57.528 40.909 0.00 0.00 0.00 1.73
696 731 1.226945 GGGCCGCCAATTTCATTCG 60.227 57.895 12.58 0.00 0.00 3.34
714 749 1.727857 GCTTTCAATACGTGCAACCCG 60.728 52.381 0.00 0.00 0.00 5.28
745 780 8.564574 CAAGCCAACAACTAGTAGTTAATCAAA 58.435 33.333 15.13 0.00 36.03 2.69
776 814 0.029167 GTACTAAGGACCGAGCTCGC 59.971 60.000 30.49 17.47 38.18 5.03
796 834 5.869888 ACTTCAGAGATTCGTTACATGGAAC 59.130 40.000 11.06 11.06 0.00 3.62
797 835 5.869344 CACTTCAGAGATTCGTTACATGGAA 59.131 40.000 0.00 0.00 0.00 3.53
798 836 5.410924 CACTTCAGAGATTCGTTACATGGA 58.589 41.667 0.00 0.00 0.00 3.41
799 837 4.033358 GCACTTCAGAGATTCGTTACATGG 59.967 45.833 0.00 0.00 0.00 3.66
847 898 1.301558 CATCCATCTCTGAGGCGGC 60.302 63.158 0.00 0.00 0.00 6.53
893 945 4.368391 CCGCTAGGCATGGTGATC 57.632 61.111 0.00 0.00 0.00 2.92
926 978 4.037684 ACCGAGCGTAAGATTTATAGTGCT 59.962 41.667 0.00 0.00 43.02 4.40
969 1024 1.734465 CTCAAATTCTCGGGTGCTCAC 59.266 52.381 0.00 0.00 0.00 3.51
977 1043 5.171476 TGTTTCTCTAGCTCAAATTCTCGG 58.829 41.667 0.00 0.00 0.00 4.63
989 1055 4.681744 CAGAGAGGACATGTTTCTCTAGC 58.318 47.826 28.78 18.99 44.30 3.42
1029 1095 3.958147 ATGCGCCAGGACCAAGACG 62.958 63.158 4.18 0.00 0.00 4.18
1131 1197 0.678366 AGTTGTTGTTGCCGGTGTCA 60.678 50.000 1.90 0.00 0.00 3.58
1224 1290 2.044946 AGGCGGCCATTGGAGAAC 60.045 61.111 23.09 0.00 0.00 3.01
1405 1471 2.042464 TGAGCTGAGAACAACTGGAGT 58.958 47.619 0.00 0.00 0.00 3.85
1406 1472 2.827800 TGAGCTGAGAACAACTGGAG 57.172 50.000 0.00 0.00 0.00 3.86
1407 1473 3.558931 TTTGAGCTGAGAACAACTGGA 57.441 42.857 0.00 0.00 0.00 3.86
1408 1474 4.637483 TTTTTGAGCTGAGAACAACTGG 57.363 40.909 0.00 0.00 0.00 4.00
1446 1512 8.561738 TGTTCAGGATAGTAAAATGGACTTTC 57.438 34.615 0.00 0.00 0.00 2.62
1463 1529 2.818751 ACCACCAACTTTGTTCAGGA 57.181 45.000 0.00 0.00 0.00 3.86
1494 1560 7.996098 AAAAGGAACCGAAATAAAGATCAGA 57.004 32.000 0.00 0.00 0.00 3.27
1515 1581 6.183360 GGTTTGAGATTGTTCAAGGGGTAAAA 60.183 38.462 0.00 0.00 38.25 1.52
1524 1590 3.546724 TGTCCGGTTTGAGATTGTTCAA 58.453 40.909 0.00 0.00 35.38 2.69
1534 1600 1.682740 GGGTCTTTTGTCCGGTTTGA 58.317 50.000 0.00 0.00 0.00 2.69
1581 1647 0.608856 ATTGACCAGCGCCACATCAA 60.609 50.000 2.29 10.15 34.03 2.57
1652 1718 8.616799 TTCCTAATTAACCATGGGCTAATTTT 57.383 30.769 26.54 14.86 0.00 1.82
1868 1936 4.624117 CTATTCCCGCGCGCTCGA 62.624 66.667 30.48 20.75 38.10 4.04
1980 2048 1.002403 TTATCCTCCTCCACCGCCA 59.998 57.895 0.00 0.00 0.00 5.69
1997 2065 4.379243 CACCGCGCTCAGGGAGTT 62.379 66.667 5.56 0.00 34.27 3.01
2173 2241 2.126965 CACGACCTCACCGACGTC 60.127 66.667 5.18 5.18 36.86 4.34
2174 2242 3.667282 CCACGACCTCACCGACGT 61.667 66.667 0.00 0.00 39.53 4.34
2177 2245 2.675423 CCTCCACGACCTCACCGA 60.675 66.667 0.00 0.00 0.00 4.69
2352 2434 2.592993 CCTCTCCCTTCCCGCACAA 61.593 63.158 0.00 0.00 0.00 3.33
2435 2517 2.202932 GCCGCATCTGGATGACGT 60.203 61.111 13.96 0.00 41.20 4.34
2534 2616 2.604686 TGCAGGCGAGTCTCCCTT 60.605 61.111 7.05 0.00 0.00 3.95
2637 2719 4.376225 TCGGTTCTTTTTACCCCTGAAT 57.624 40.909 0.00 0.00 31.75 2.57
2647 2729 7.232737 ACCCTGATCTTTATTTCGGTTCTTTTT 59.767 33.333 0.00 0.00 0.00 1.94
2728 2819 3.689161 TGCGTCCATCCAATTCAACTTAG 59.311 43.478 0.00 0.00 0.00 2.18
2729 2820 3.680490 TGCGTCCATCCAATTCAACTTA 58.320 40.909 0.00 0.00 0.00 2.24
2916 3007 1.222113 GGTGAAGCTGTAGCCCCTC 59.778 63.158 0.00 0.00 43.38 4.30
3096 3187 3.427425 GCCGCCATGTTGTACGCA 61.427 61.111 0.00 0.00 0.00 5.24
3117 3208 2.670934 AGCCTGCGGTTGAAGCTG 60.671 61.111 0.00 0.00 35.28 4.24
3363 3454 4.124351 GACGGATGGACGGCGTCA 62.124 66.667 37.13 24.67 38.39 4.35
3411 3502 1.097547 GGGACGTGGCATTCAGGATG 61.098 60.000 0.00 0.00 38.85 3.51
3417 3508 2.750237 GGGTGGGACGTGGCATTC 60.750 66.667 0.00 0.00 0.00 2.67
3452 3546 0.647925 GAATTCGGAGAAGCGTCAGC 59.352 55.000 1.61 0.00 45.90 4.26
3489 3583 3.882444 TCTGCTTCCATCATTCTTGGAG 58.118 45.455 0.00 0.00 43.87 3.86
3527 3621 8.205131 TGGTCACTAGACTTTTTACTTGTTTC 57.795 34.615 0.00 0.00 44.36 2.78
3562 3656 2.486592 GGGTTTACTTCCAACATCGTGG 59.513 50.000 0.00 0.00 40.33 4.94
3587 3681 1.741706 GTACTGATCAGACCGGACGAA 59.258 52.381 29.27 0.00 0.00 3.85
3588 3682 1.376543 GTACTGATCAGACCGGACGA 58.623 55.000 29.27 4.52 0.00 4.20
3589 3683 0.027716 CGTACTGATCAGACCGGACG 59.972 60.000 29.27 21.89 0.00 4.79
3602 3696 4.142730 GGAGTACTAGTTGGACACGTACTG 60.143 50.000 0.00 0.00 36.87 2.74
3622 3719 1.661341 GCAGCCAACTCATGTAGGAG 58.339 55.000 0.00 0.00 40.79 3.69
3623 3720 0.253044 GGCAGCCAACTCATGTAGGA 59.747 55.000 6.55 0.00 0.00 2.94
3624 3721 1.091771 CGGCAGCCAACTCATGTAGG 61.092 60.000 13.30 0.00 0.00 3.18
3625 3722 0.391661 ACGGCAGCCAACTCATGTAG 60.392 55.000 13.30 0.00 0.00 2.74
3626 3723 0.673333 CACGGCAGCCAACTCATGTA 60.673 55.000 13.30 0.00 0.00 2.29
3627 3724 1.968017 CACGGCAGCCAACTCATGT 60.968 57.895 13.30 0.00 0.00 3.21
3628 3725 0.673333 TACACGGCAGCCAACTCATG 60.673 55.000 13.30 1.85 0.00 3.07
3636 3733 0.531200 ACTAGTTCTACACGGCAGCC 59.469 55.000 0.00 0.00 0.00 4.85
3638 3735 5.706369 AGGATATACTAGTTCTACACGGCAG 59.294 44.000 0.00 0.00 0.00 4.85
3704 3801 2.046604 GGGGACTTGCACGGGTAC 60.047 66.667 0.00 0.00 0.00 3.34
3790 3887 1.075542 CGCAGCACTCGGTTATTTGA 58.924 50.000 0.00 0.00 0.00 2.69
3801 3898 2.514592 ACAGCAACACGCAGCACT 60.515 55.556 0.00 0.00 46.13 4.40
3802 3899 2.051882 GACAGCAACACGCAGCAC 60.052 61.111 0.00 0.00 46.13 4.40
3803 3900 3.279116 GGACAGCAACACGCAGCA 61.279 61.111 0.00 0.00 46.13 4.41
3804 3901 2.974698 AGGACAGCAACACGCAGC 60.975 61.111 0.00 0.00 46.13 5.25
3805 3902 2.941333 CAGGACAGCAACACGCAG 59.059 61.111 0.00 0.00 46.13 5.18
3818 3915 1.478510 GCACTAGCACTTCTAGCAGGA 59.521 52.381 0.00 0.00 46.93 3.86
3840 3937 3.846360 ACGTGAAGAGTACCAGTTATGC 58.154 45.455 0.00 0.00 0.00 3.14
3841 3938 4.082408 TGGACGTGAAGAGTACCAGTTATG 60.082 45.833 0.00 0.00 0.00 1.90
3842 3939 4.084287 TGGACGTGAAGAGTACCAGTTAT 58.916 43.478 0.00 0.00 0.00 1.89
3848 3945 0.601558 TGCTGGACGTGAAGAGTACC 59.398 55.000 0.00 0.00 0.00 3.34
3854 3951 1.734465 GATCCTTTGCTGGACGTGAAG 59.266 52.381 0.00 0.00 39.17 3.02
3899 4027 0.540133 TCCAGGTGCACCGTAGTACA 60.540 55.000 29.68 8.31 42.08 2.90
3900 4028 0.108945 GTCCAGGTGCACCGTAGTAC 60.109 60.000 29.68 19.54 42.08 2.73
3901 4029 1.588824 CGTCCAGGTGCACCGTAGTA 61.589 60.000 29.68 12.35 42.08 1.82
3902 4030 2.927580 CGTCCAGGTGCACCGTAGT 61.928 63.158 29.68 10.15 42.08 2.73
3903 4031 2.126071 CGTCCAGGTGCACCGTAG 60.126 66.667 29.68 22.12 42.08 3.51
3904 4032 4.367023 GCGTCCAGGTGCACCGTA 62.367 66.667 29.68 16.39 42.08 4.02
3909 4037 2.591429 CTTGTGCGTCCAGGTGCA 60.591 61.111 5.18 5.18 39.13 4.57
3910 4038 4.030452 GCTTGTGCGTCCAGGTGC 62.030 66.667 0.00 0.00 0.00 5.01
3911 4039 2.591429 TGCTTGTGCGTCCAGGTG 60.591 61.111 0.00 0.00 43.34 4.00
3912 4040 2.591715 GTGCTTGTGCGTCCAGGT 60.592 61.111 0.00 0.00 43.34 4.00
3913 4041 3.357079 GGTGCTTGTGCGTCCAGG 61.357 66.667 0.00 0.00 43.34 4.45
3914 4042 2.281070 AGGTGCTTGTGCGTCCAG 60.281 61.111 0.00 0.00 43.34 3.86
3915 4043 2.280797 GAGGTGCTTGTGCGTCCA 60.281 61.111 0.00 0.00 43.34 4.02
3916 4044 3.414700 CGAGGTGCTTGTGCGTCC 61.415 66.667 0.00 0.00 43.34 4.79
3930 4058 1.531578 TCACTGACTGAACTCGACGAG 59.468 52.381 22.97 22.97 35.52 4.18
3957 4085 0.381801 ACAACTACCGACAACGACGT 59.618 50.000 0.00 0.00 42.66 4.34
3964 4092 2.195096 CAACGACAACAACTACCGACA 58.805 47.619 0.00 0.00 0.00 4.35
3983 4111 1.210931 CGACGCCGAGTACTTTCCA 59.789 57.895 0.00 0.00 38.22 3.53
4001 4129 1.373371 GTGTTGGTACGGTCCCGAC 60.373 63.158 13.54 3.27 42.83 4.79
4002 4130 1.831726 TGTGTTGGTACGGTCCCGA 60.832 57.895 13.54 0.00 42.83 5.14
4003 4131 1.665599 GTGTGTTGGTACGGTCCCG 60.666 63.158 3.76 3.76 46.03 5.14
4009 4137 1.384409 GTTCGATCGTGTGTTGGTACG 59.616 52.381 15.94 0.00 41.38 3.67
4011 4139 1.266446 TCGTTCGATCGTGTGTTGGTA 59.734 47.619 15.94 0.00 0.00 3.25
4044 4172 0.107165 ATCTAGAAAGCCCGGTTGCC 60.107 55.000 0.00 0.00 0.00 4.52
4050 4178 2.315246 GCTGCATCTAGAAAGCCCG 58.685 57.895 15.45 9.27 0.00 6.13
4112 4338 1.651240 CGATTTGCTGCTGGGTCTGG 61.651 60.000 0.00 0.00 0.00 3.86
4191 4417 4.100808 TGCCTTAACTTTTTCCTTGTGCAT 59.899 37.500 0.00 0.00 0.00 3.96
4198 4424 5.445964 TCAAGAGTGCCTTAACTTTTTCCT 58.554 37.500 0.00 0.00 32.86 3.36
4225 4451 2.749776 GAGCTTTCCTCTTAGGATCGC 58.250 52.381 0.00 3.10 45.34 4.58
4245 4471 2.747855 GAAGCGGCTGGGGACAAG 60.748 66.667 1.81 0.00 42.06 3.16
4277 4503 0.463295 CATCATGGTCGAAGCTGGCT 60.463 55.000 0.00 0.00 0.00 4.75
4316 4542 9.431887 GTTGTGACTTGTTAAGATGGAAGTATA 57.568 33.333 0.00 0.00 0.00 1.47
4317 4543 7.390718 GGTTGTGACTTGTTAAGATGGAAGTAT 59.609 37.037 0.00 0.00 0.00 2.12
4324 4550 5.120208 CCTACGGTTGTGACTTGTTAAGATG 59.880 44.000 0.00 0.00 0.00 2.90
4327 4553 3.185797 GCCTACGGTTGTGACTTGTTAAG 59.814 47.826 0.00 0.00 0.00 1.85
4334 4560 0.320697 GGAAGCCTACGGTTGTGACT 59.679 55.000 0.00 0.00 0.00 3.41
4375 4601 1.021390 AAGAGCATGAACGCTTCCGG 61.021 55.000 0.00 0.00 44.01 5.14


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

AutoCloner maintained by Alex Coulton.