Multiple sequence alignment - TraesCS3D01G088300

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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 TraesCS3D01G088300 chr3D 100.000 5261 0 0 1 5261 45014435 45019695 0.000000e+00 9716.0
1 TraesCS3D01G088300 chr3D 70.660 3122 781 102 1169 4233 26586904 26583861 2.750000e-157 566.0
2 TraesCS3D01G088300 chr3D 75.219 343 65 14 3892 4233 26571673 26571996 1.530000e-30 145.0
3 TraesCS3D01G088300 chr3A 94.209 3799 186 10 573 4361 56762475 56766249 0.000000e+00 5766.0
4 TraesCS3D01G088300 chr3A 91.522 920 42 11 4358 5258 56771241 56772143 0.000000e+00 1234.0
5 TraesCS3D01G088300 chr3A 70.626 3132 773 110 1165 4233 36662437 36659390 7.700000e-153 551.0
6 TraesCS3D01G088300 chr3A 90.537 391 30 5 150 533 56762084 56762474 1.310000e-140 510.0
7 TraesCS3D01G088300 chr3B 89.457 920 78 9 4358 5261 70313192 70314108 0.000000e+00 1144.0
8 TraesCS3D01G088300 chr3B 84.421 674 66 19 1 653 70125812 70126467 1.240000e-175 627.0
9 TraesCS3D01G088300 chr3B 70.419 3127 790 104 1165 4233 44787359 44784310 4.670000e-145 525.0
10 TraesCS3D01G088300 chr3B 75.940 266 55 8 1165 1424 44760780 44761042 1.540000e-25 128.0
11 TraesCS3D01G088300 chr6B 70.544 2278 546 97 1997 4224 65089871 65087669 1.790000e-99 374.0
12 TraesCS3D01G088300 chr6B 71.115 1776 402 80 2498 4231 64688205 64686499 8.440000e-88 335.0
13 TraesCS3D01G088300 chr6D 70.669 1674 409 68 2444 4067 3613142 3611501 3.980000e-76 296.0
14 TraesCS3D01G088300 chrUn 69.859 2130 541 78 1973 4052 94837296 94839374 3.100000e-72 283.0
15 TraesCS3D01G088300 chrUn 71.955 1059 222 53 3185 4231 101629335 101630330 1.890000e-59 241.0
16 TraesCS3D01G088300 chr5A 76.106 452 108 0 3315 3766 688717478 688717929 2.450000e-58 237.0
17 TraesCS3D01G088300 chr5B 73.529 510 110 21 1165 1660 35548828 35548330 2.520000e-38 171.0
18 TraesCS3D01G088300 chr4B 74.870 386 75 11 3848 4231 650658725 650659090 7.050000e-34 156.0
19 TraesCS3D01G088300 chr7D 72.527 364 88 11 1289 1646 568631557 568631200 2.000000e-19 108.0
20 TraesCS3D01G088300 chr7B 78.659 164 33 2 1289 1451 624709624 624709462 2.000000e-19 108.0
21 TraesCS3D01G088300 chr7A 79.452 146 30 0 1289 1434 657420138 657419993 2.590000e-18 104.0
22 TraesCS3D01G088300 chr4A 71.302 338 86 9 1165 1495 657097234 657097567 5.650000e-10 76.8
23 TraesCS3D01G088300 chr4A 84.615 78 9 2 4365 4442 650290564 650290490 2.030000e-09 75.0
24 TraesCS3D01G088300 chr1B 70.874 412 98 16 1165 1564 2916205 2916606 5.650000e-10 76.8


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 TraesCS3D01G088300 chr3D 45014435 45019695 5260 False 9716 9716 100.000 1 5261 1 chr3D.!!$F2 5260
1 TraesCS3D01G088300 chr3D 26583861 26586904 3043 True 566 566 70.660 1169 4233 1 chr3D.!!$R1 3064
2 TraesCS3D01G088300 chr3A 56762084 56766249 4165 False 3138 5766 92.373 150 4361 2 chr3A.!!$F2 4211
3 TraesCS3D01G088300 chr3A 56771241 56772143 902 False 1234 1234 91.522 4358 5258 1 chr3A.!!$F1 900
4 TraesCS3D01G088300 chr3A 36659390 36662437 3047 True 551 551 70.626 1165 4233 1 chr3A.!!$R1 3068
5 TraesCS3D01G088300 chr3B 70313192 70314108 916 False 1144 1144 89.457 4358 5261 1 chr3B.!!$F3 903
6 TraesCS3D01G088300 chr3B 70125812 70126467 655 False 627 627 84.421 1 653 1 chr3B.!!$F2 652
7 TraesCS3D01G088300 chr3B 44784310 44787359 3049 True 525 525 70.419 1165 4233 1 chr3B.!!$R1 3068
8 TraesCS3D01G088300 chr6B 65087669 65089871 2202 True 374 374 70.544 1997 4224 1 chr6B.!!$R2 2227
9 TraesCS3D01G088300 chr6B 64686499 64688205 1706 True 335 335 71.115 2498 4231 1 chr6B.!!$R1 1733
10 TraesCS3D01G088300 chr6D 3611501 3613142 1641 True 296 296 70.669 2444 4067 1 chr6D.!!$R1 1623
11 TraesCS3D01G088300 chrUn 94837296 94839374 2078 False 283 283 69.859 1973 4052 1 chrUn.!!$F1 2079
12 TraesCS3D01G088300 chrUn 101629335 101630330 995 False 241 241 71.955 3185 4231 1 chrUn.!!$F2 1046

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
581 610 0.321919 AAGGCAGACGCACACATCAT 60.322 50.000 0.00 0.0 41.24 2.45 F
1113 1152 0.536687 ATGATGATGGAGCCGCCTTG 60.537 55.000 0.00 0.0 37.63 3.61 F
1929 1971 1.079681 CCAGTTTAGCGGCCACGTA 60.080 57.895 2.24 0.0 43.45 3.57 F
3522 3584 0.103026 CATGCAGTACGCTCAGCCTA 59.897 55.000 10.27 0.0 43.06 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 2358 0.108138 GTGAGGTTCCCGACAGATGG 60.108 60.0 0.00 0.00 0.00 3.51 R
2336 2380 1.084370 CGCGAGGATCCAGTTCAACC 61.084 60.0 15.82 0.00 0.00 3.77 R
3867 3959 0.251354 GTGAGGCAGCAGATCCTTCA 59.749 55.0 0.00 0.00 31.71 3.02 R
4356 4448 0.105593 TGAAGCTGAGCCGGATCATC 59.894 55.0 24.87 19.94 0.00 2.92 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
34 35 0.599991 TCAGCTAACCTGCACACACG 60.600 55.000 0.00 0.00 41.50 4.49
45 46 1.499502 CACACACGCACACACACAA 59.500 52.632 0.00 0.00 0.00 3.33
69 78 7.693969 AAAAACTTAGTTCAGATATGCAGCT 57.306 32.000 0.00 0.00 0.00 4.24
91 100 7.809331 CAGCTTTAAATGAAATACAAGCTCACA 59.191 33.333 1.25 0.00 36.10 3.58
102 111 2.880890 ACAAGCTCACAGTGGATCAAAC 59.119 45.455 0.00 0.00 0.00 2.93
104 113 3.498774 AGCTCACAGTGGATCAAACTT 57.501 42.857 0.00 0.00 0.00 2.66
113 122 4.278170 CAGTGGATCAAACTTAAGCCACAA 59.722 41.667 22.09 0.46 46.15 3.33
127 136 3.319755 AGCCACAATGATTTCGCAAAAG 58.680 40.909 0.00 0.00 0.00 2.27
128 137 3.059166 GCCACAATGATTTCGCAAAAGT 58.941 40.909 0.00 0.00 0.00 2.66
129 138 4.022416 AGCCACAATGATTTCGCAAAAGTA 60.022 37.500 0.00 0.00 0.00 2.24
131 140 5.348451 GCCACAATGATTTCGCAAAAGTAAT 59.652 36.000 0.00 0.00 0.00 1.89
134 143 9.086336 CCACAATGATTTCGCAAAAGTAATAAT 57.914 29.630 0.00 0.00 0.00 1.28
163 172 5.600484 ACATTGGTTAAATTCTGTGGGTTGA 59.400 36.000 0.00 0.00 0.00 3.18
213 222 1.352083 CAGGTCTTCACTTCTCCCCA 58.648 55.000 0.00 0.00 0.00 4.96
214 223 1.002544 CAGGTCTTCACTTCTCCCCAC 59.997 57.143 0.00 0.00 0.00 4.61
234 249 4.202050 CCACTTGGTCTGGTCTTGAAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
235 250 4.640201 CACTTGGTCTGGTCTTGAAAAAGA 59.360 41.667 0.00 0.00 0.00 2.52
236 251 5.125417 CACTTGGTCTGGTCTTGAAAAAGAA 59.875 40.000 0.00 0.00 0.00 2.52
250 265 9.634163 TCTTGAAAAAGAAAAGGTTAAGTCAAC 57.366 29.630 0.00 0.00 36.32 3.18
378 395 8.596271 TTACACAGAATTTACGATGACTTCAA 57.404 30.769 0.00 0.00 0.00 2.69
383 400 5.934625 AGAATTTACGATGACTTCAAGCAGT 59.065 36.000 0.00 0.00 0.00 4.40
410 427 0.806102 CTACCTCATGACCCGTTGCG 60.806 60.000 0.00 0.00 0.00 4.85
454 471 1.922447 TCAGCTCTCCCTCTCTCTCTT 59.078 52.381 0.00 0.00 0.00 2.85
469 488 4.557205 TCTCTCTTTTCGTACTTTGGAGC 58.443 43.478 0.00 0.00 0.00 4.70
499 518 1.770294 TCACAAACCTGGGGAACAAC 58.230 50.000 0.00 0.00 0.00 3.32
533 552 4.081420 ACTCTGTACTTGTGCAGGGATAAG 60.081 45.833 22.07 12.39 36.73 1.73
534 553 3.838317 TCTGTACTTGTGCAGGGATAAGT 59.162 43.478 16.45 7.92 37.21 2.24
568 597 3.041874 CTGCGAGAGTACAAGGCAG 57.958 57.895 11.88 11.88 44.19 4.85
581 610 0.321919 AAGGCAGACGCACACATCAT 60.322 50.000 0.00 0.00 41.24 2.45
595 624 3.054728 ACACATCATCACCACCGGAAATA 60.055 43.478 9.46 0.00 0.00 1.40
636 665 8.491045 AAATTATATATGAACTTTGGTGGGGG 57.509 34.615 0.00 0.00 0.00 5.40
646 675 3.580319 GGTGGGGGCAGGAACAGT 61.580 66.667 0.00 0.00 0.00 3.55
681 710 1.627864 AAAAATTGGTGCGGCCTACT 58.372 45.000 0.00 0.00 38.35 2.57
686 715 0.605319 TTGGTGCGGCCTACTTCAAG 60.605 55.000 0.00 0.00 38.35 3.02
712 741 2.099141 TGGCGAGAAGTTTCCTGATG 57.901 50.000 0.00 0.00 0.00 3.07
713 742 1.623311 TGGCGAGAAGTTTCCTGATGA 59.377 47.619 0.00 0.00 0.00 2.92
714 743 2.038426 TGGCGAGAAGTTTCCTGATGAA 59.962 45.455 0.00 0.00 0.00 2.57
715 744 3.274288 GGCGAGAAGTTTCCTGATGAAT 58.726 45.455 0.00 0.00 31.67 2.57
716 745 3.064545 GGCGAGAAGTTTCCTGATGAATG 59.935 47.826 0.00 0.00 31.67 2.67
717 746 3.064545 GCGAGAAGTTTCCTGATGAATGG 59.935 47.826 0.00 0.00 31.67 3.16
718 747 4.507710 CGAGAAGTTTCCTGATGAATGGA 58.492 43.478 0.00 0.00 31.67 3.41
719 748 5.121811 CGAGAAGTTTCCTGATGAATGGAT 58.878 41.667 0.00 0.00 31.67 3.41
720 749 5.587844 CGAGAAGTTTCCTGATGAATGGATT 59.412 40.000 0.00 0.00 31.67 3.01
721 750 6.457934 CGAGAAGTTTCCTGATGAATGGATTG 60.458 42.308 0.00 0.00 31.67 2.67
722 751 5.655532 AGAAGTTTCCTGATGAATGGATTGG 59.344 40.000 0.00 0.00 31.67 3.16
723 752 5.197224 AGTTTCCTGATGAATGGATTGGA 57.803 39.130 0.00 0.00 31.67 3.53
724 753 5.582953 AGTTTCCTGATGAATGGATTGGAA 58.417 37.500 0.00 0.00 31.67 3.53
725 754 6.018469 AGTTTCCTGATGAATGGATTGGAAA 58.982 36.000 0.00 0.00 39.03 3.13
726 755 6.497954 AGTTTCCTGATGAATGGATTGGAAAA 59.502 34.615 0.00 0.00 41.69 2.29
727 756 5.920193 TCCTGATGAATGGATTGGAAAAC 57.080 39.130 0.00 0.00 0.00 2.43
741 770 4.909696 TGGAAAACAATGTCGTGTCAAT 57.090 36.364 0.00 0.00 0.00 2.57
746 775 3.410631 ACAATGTCGTGTCAATACCCA 57.589 42.857 0.00 0.00 0.00 4.51
748 777 3.070748 CAATGTCGTGTCAATACCCACA 58.929 45.455 0.00 0.00 0.00 4.17
798 827 4.025061 CACTTTGAGACTTGAGAGCAACAG 60.025 45.833 0.00 0.00 0.00 3.16
806 835 4.517285 ACTTGAGAGCAACAGAAAGTGAA 58.483 39.130 0.00 0.00 0.00 3.18
810 839 2.609459 AGAGCAACAGAAAGTGAACACG 59.391 45.455 0.00 0.00 36.20 4.49
811 840 1.064060 AGCAACAGAAAGTGAACACGC 59.936 47.619 0.00 0.00 36.20 5.34
855 894 7.761651 ATGAAGTCAAAACTGAAGAAAAAGC 57.238 32.000 0.00 0.00 35.36 3.51
933 972 0.686769 ACCTGGGTTACTAGCCTCGG 60.687 60.000 0.00 0.00 42.60 4.63
1007 1046 1.017177 CGAACCGAAGAAATGGCCGA 61.017 55.000 0.00 0.00 0.00 5.54
1048 1087 3.820557 CTTTTGTTGTCCCTCCTCTTCA 58.179 45.455 0.00 0.00 0.00 3.02
1054 1093 1.000486 TCCCTCCTCTTCACCCTCG 60.000 63.158 0.00 0.00 0.00 4.63
1063 1102 2.678580 TCACCCTCGTGATCGCCA 60.679 61.111 0.00 0.00 44.20 5.69
1081 1120 2.738521 CGGCGAGGGACAGTGTTG 60.739 66.667 0.00 0.00 0.00 3.33
1091 1130 1.317613 GACAGTGTTGGCAACCATGA 58.682 50.000 28.16 10.70 31.53 3.07
1108 1147 2.467566 TGATGATGATGATGGAGCCG 57.532 50.000 0.00 0.00 0.00 5.52
1113 1152 0.536687 ATGATGATGGAGCCGCCTTG 60.537 55.000 0.00 0.00 37.63 3.61
1116 1155 2.439156 GATGGAGCCGCCTTGCTT 60.439 61.111 0.00 0.00 42.95 3.91
1136 1175 3.071874 TGCTTTCAAGGTGGGTATCAG 57.928 47.619 0.00 0.00 0.00 2.90
1140 1179 1.879575 TCAAGGTGGGTATCAGGAGG 58.120 55.000 0.00 0.00 0.00 4.30
1144 1183 2.445845 TGGGTATCAGGAGGGGCG 60.446 66.667 0.00 0.00 0.00 6.13
1162 1201 2.270527 GAAGCTCTGGCCCACTCC 59.729 66.667 0.00 0.00 39.73 3.85
1266 1308 4.804420 TCCTCCCATGGGCTCGCT 62.804 66.667 27.41 0.00 34.68 4.93
1271 1313 3.882326 CCATGGGCTCGCTGGGAT 61.882 66.667 2.85 0.00 0.00 3.85
1374 1416 2.436646 CTTGGCCGCCTTCATCGT 60.437 61.111 11.61 0.00 0.00 3.73
1396 1438 1.291588 CAGACGCTTGACCTGAGCT 59.708 57.895 0.00 0.00 37.99 4.09
1476 1518 2.617274 GGTCCTCGGCAGCAACAAC 61.617 63.158 0.00 0.00 0.00 3.32
1506 1548 4.779733 ATCCCGTCCAGCCTCGGT 62.780 66.667 0.00 0.00 44.51 4.69
1592 1634 1.374252 CGCTAGCCAACCTGTCGTT 60.374 57.895 9.66 0.00 33.90 3.85
1662 1704 3.627690 GGACTCAGAGGCCTCAGG 58.372 66.667 33.90 24.49 41.45 3.86
1675 1717 1.482954 CCTCAGGAGCATCTCTCACA 58.517 55.000 0.00 0.00 43.70 3.58
1742 1784 3.930336 TCTACAACCTGTCATTGCTGAG 58.070 45.455 0.00 0.00 30.18 3.35
1888 1930 1.429299 TCACCAACCTCTCCTCTCTCA 59.571 52.381 0.00 0.00 0.00 3.27
1929 1971 1.079681 CCAGTTTAGCGGCCACGTA 60.080 57.895 2.24 0.00 43.45 3.57
2028 2070 2.498167 GGATGGGAGTTCATGGATTCG 58.502 52.381 0.00 0.00 0.00 3.34
2125 2167 3.669122 CGTAAACCTCTCAACAAGTCTCG 59.331 47.826 0.00 0.00 0.00 4.04
2481 2528 6.453943 CAGAGAGATCTTCAAACTGTCTTCA 58.546 40.000 0.00 0.00 33.19 3.02
2590 2637 7.494952 GGTTGGTACTATCAGGAAATCAGTTAC 59.505 40.741 0.00 0.00 0.00 2.50
2597 2644 2.858344 CAGGAAATCAGTTACGCGGTAG 59.142 50.000 12.47 0.00 0.00 3.18
2683 2730 6.418057 TTGAAGGAAGCATACCAACAAATT 57.582 33.333 0.00 0.00 0.00 1.82
2894 2941 0.954452 CTGGAAGGTGAAGTGCCAAC 59.046 55.000 0.00 0.00 0.00 3.77
2897 2944 0.954452 GAAGGTGAAGTGCCAACTGG 59.046 55.000 0.00 0.00 36.51 4.00
2927 2974 8.818057 CGTCTTTAGAAACCTAACCTATGAATG 58.182 37.037 0.00 0.00 0.00 2.67
2932 2979 4.790718 AACCTAACCTATGAATGGGTCC 57.209 45.455 0.00 0.00 41.16 4.46
2934 2981 4.116113 ACCTAACCTATGAATGGGTCCAA 58.884 43.478 0.00 0.00 41.16 3.53
3055 3114 2.628178 CTCACAGTAACAGGGTCACTCA 59.372 50.000 0.00 0.00 0.00 3.41
3066 3125 3.027412 AGGGTCACTCATGCTACTAGTG 58.973 50.000 5.39 5.37 41.58 2.74
3272 3334 2.486191 CCTTGGATGATGAGGGTACAGC 60.486 54.545 0.00 0.00 0.00 4.40
3278 3340 4.502259 GGATGATGAGGGTACAGCTACAAG 60.502 50.000 0.00 0.00 0.00 3.16
3300 3362 1.002142 GTGGCCGTAAAGGTGTTTGAC 60.002 52.381 0.00 0.00 43.70 3.18
3462 3524 0.178981 AGCTCATGCCCAACAACAGT 60.179 50.000 0.00 0.00 40.80 3.55
3497 3559 3.475566 TCATCCTAAATCCCAAGAGCG 57.524 47.619 0.00 0.00 0.00 5.03
3522 3584 0.103026 CATGCAGTACGCTCAGCCTA 59.897 55.000 10.27 0.00 43.06 3.93
3630 3692 5.528690 TGATATCAAGCCAAGCAACATACTC 59.471 40.000 1.98 0.00 0.00 2.59
3639 3701 1.208052 AGCAACATACTCCTCGCACAT 59.792 47.619 0.00 0.00 0.00 3.21
3647 3709 1.284657 CTCCTCGCACATGACATGAC 58.715 55.000 22.19 11.97 0.00 3.06
3769 3831 2.565841 GCTACATTGCTCCAGGTTAGG 58.434 52.381 0.00 0.00 0.00 2.69
3770 3832 2.170607 GCTACATTGCTCCAGGTTAGGA 59.829 50.000 0.00 0.00 36.00 2.94
3771 3833 3.370527 GCTACATTGCTCCAGGTTAGGAA 60.371 47.826 0.00 0.00 37.20 3.36
3772 3834 3.073274 ACATTGCTCCAGGTTAGGAAC 57.927 47.619 0.00 0.00 37.20 3.62
3773 3835 2.375174 ACATTGCTCCAGGTTAGGAACA 59.625 45.455 0.00 0.00 37.20 3.18
3826 3918 6.759497 AGCCTGTTTCATGTTCCTAAATAC 57.241 37.500 0.00 0.00 0.00 1.89
3889 3981 0.031716 AGGATCTGCTGCCTCACCTA 60.032 55.000 0.00 0.00 0.00 3.08
3909 4001 6.534634 ACCTATTGGTGATGTTTATAGCCTC 58.465 40.000 0.00 0.00 46.51 4.70
3959 4051 1.070786 GAAGCCCCACAGACGACAA 59.929 57.895 0.00 0.00 0.00 3.18
3994 4086 6.558009 TCACTGAATCTGCATAAATTTGCTC 58.442 36.000 0.00 0.00 43.18 4.26
4029 4121 7.346751 TCCAAATAAAGTCATGGAAATAGCC 57.653 36.000 0.00 0.00 38.95 3.93
4073 4165 2.357009 CAGAGGCAAATGATACAGGTGC 59.643 50.000 0.00 0.00 34.42 5.01
4077 4169 1.747355 GCAAATGATACAGGTGCAGCT 59.253 47.619 13.85 13.85 35.28 4.24
4242 4334 5.514274 ACCTTATATTTGCCAATTCACCG 57.486 39.130 0.00 0.00 0.00 4.94
4255 4347 4.987285 CCAATTCACCGATACATCAGAGAG 59.013 45.833 0.00 0.00 0.00 3.20
4295 4387 8.354426 TGCAATGATATCCAACTAATGAACATG 58.646 33.333 0.00 0.00 0.00 3.21
4337 4429 1.061131 CAGTTTGTAGCGGCGAAGATG 59.939 52.381 12.98 0.00 0.00 2.90
4356 4448 9.199184 CGAAGATGATATTTCTTTGTTAACACG 57.801 33.333 8.07 2.71 33.65 4.49
4382 4474 1.599047 GGCTCAGCTTCAGGCACTA 59.401 57.895 10.41 0.00 44.79 2.74
4443 4535 5.884792 CCTTTAATTCCTCAGCTCAAGATGT 59.115 40.000 0.00 0.00 32.47 3.06
4462 4554 8.671028 CAAGATGTCATGTTAGTGATTCATCAA 58.329 33.333 0.00 0.00 38.75 2.57
4465 4557 7.144722 TGTCATGTTAGTGATTCATCAAACC 57.855 36.000 0.00 0.00 38.75 3.27
4626 4740 5.684704 TGTCCAAGTCAAGTCTGAAAATCT 58.315 37.500 0.00 0.00 31.88 2.40
4672 4788 8.803235 GGTAACCAATAAATAATTCCCAGGATC 58.197 37.037 0.00 0.00 0.00 3.36
4676 4792 9.533831 ACCAATAAATAATTCCCAGGATCATAC 57.466 33.333 0.00 0.00 0.00 2.39
4751 4867 1.063027 CGCGACTCAGAATGTACCGTA 59.937 52.381 0.00 0.00 37.40 4.02
4768 4884 3.705043 CGTACACGGGCTAAATACTCT 57.295 47.619 0.00 0.00 35.37 3.24
4811 4927 4.865925 CGTGACCGGAACTAACAAATATGA 59.134 41.667 9.46 0.00 0.00 2.15
4860 4976 5.239525 AGAGATGACAAGTTACCAAAACTGC 59.760 40.000 0.00 0.00 0.00 4.40
4881 4997 4.038763 TGCAAGCTGTAACAGTAGTGTAGT 59.961 41.667 3.00 0.00 35.08 2.73
4915 5031 1.620819 AGAACAGCTACACCAGGACTG 59.379 52.381 0.00 0.00 0.00 3.51
4926 5042 1.901085 CAGGACTGGAGTGCCCTAC 59.099 63.158 0.00 0.00 37.04 3.18
5046 5163 1.023502 CCGCCATTATGTGACATGCA 58.976 50.000 8.61 0.00 0.00 3.96
5053 5170 5.813672 GCCATTATGTGACATGCAAAAGATT 59.186 36.000 8.61 0.00 0.00 2.40
5129 5246 4.691216 GCTATAGAATGGAGTAAAAGCCCG 59.309 45.833 3.21 0.00 0.00 6.13
5141 5258 2.851263 AAAGCCCGACTATGTGTTCA 57.149 45.000 0.00 0.00 0.00 3.18
5195 5312 7.996385 ACCTCAAAATTTCCACCTAATTATCG 58.004 34.615 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.862123 CGTGTGTGCAGGTTAGCTG 59.138 57.895 7.10 7.10 34.99 4.24
45 46 7.693969 AGCTGCATATCTGAACTAAGTTTTT 57.306 32.000 1.02 0.00 0.00 1.94
54 63 8.915871 TTTCATTTAAAGCTGCATATCTGAAC 57.084 30.769 1.02 0.00 0.00 3.18
69 78 8.081633 CCACTGTGAGCTTGTATTTCATTTAAA 58.918 33.333 9.86 0.00 0.00 1.52
91 100 4.098914 TGTGGCTTAAGTTTGATCCACT 57.901 40.909 21.11 0.00 43.10 4.00
102 111 4.095410 TGCGAAATCATTGTGGCTTAAG 57.905 40.909 0.00 0.00 0.00 1.85
104 113 4.511617 TTTGCGAAATCATTGTGGCTTA 57.488 36.364 0.00 0.00 0.00 3.09
138 147 5.467035 ACCCACAGAATTTAACCAATGTG 57.533 39.130 0.00 0.00 38.17 3.21
213 222 4.855340 TCTTTTTCAAGACCAGACCAAGT 58.145 39.130 0.00 0.00 33.80 3.16
214 223 5.835113 TTCTTTTTCAAGACCAGACCAAG 57.165 39.130 0.00 0.00 38.86 3.61
335 352 8.508800 CTGTGTAAGACAGTAAAAGTGTAGAG 57.491 38.462 0.00 0.00 46.30 2.43
378 395 6.463614 GGTCATGAGGTAGATCATTTACTGCT 60.464 42.308 0.00 0.00 37.84 4.24
383 400 4.899457 ACGGGTCATGAGGTAGATCATTTA 59.101 41.667 0.00 0.00 37.84 1.40
454 471 4.214758 GCCTTTAAGCTCCAAAGTACGAAA 59.785 41.667 15.75 0.00 32.23 3.46
469 488 4.559153 CCAGGTTTGTGAATGCCTTTAAG 58.441 43.478 0.00 0.00 0.00 1.85
543 562 4.058817 CCTTGTACTCTCGCAGACTTTTT 58.941 43.478 0.00 0.00 0.00 1.94
544 563 3.654414 CCTTGTACTCTCGCAGACTTTT 58.346 45.455 0.00 0.00 0.00 2.27
545 564 2.610727 GCCTTGTACTCTCGCAGACTTT 60.611 50.000 0.00 0.00 0.00 2.66
548 577 0.243907 TGCCTTGTACTCTCGCAGAC 59.756 55.000 0.00 0.00 0.00 3.51
557 586 0.600255 GTGTGCGTCTGCCTTGTACT 60.600 55.000 0.00 0.00 41.78 2.73
568 597 0.443869 GTGGTGATGATGTGTGCGTC 59.556 55.000 0.00 0.00 0.00 5.19
581 610 3.754323 GTGTTCATTATTTCCGGTGGTGA 59.246 43.478 0.00 0.00 0.00 4.02
595 624 0.881118 ATTTCCAGCGCGTGTTCATT 59.119 45.000 8.43 0.00 0.00 2.57
662 691 1.627864 AGTAGGCCGCACCAATTTTT 58.372 45.000 0.00 0.00 43.14 1.94
666 695 0.037590 TTGAAGTAGGCCGCACCAAT 59.962 50.000 0.00 0.00 43.14 3.16
674 703 3.129462 GCCATTTTCTCTTGAAGTAGGCC 59.871 47.826 0.00 0.00 37.67 5.19
675 704 3.181506 CGCCATTTTCTCTTGAAGTAGGC 60.182 47.826 0.00 0.00 38.93 3.93
681 710 4.389374 ACTTCTCGCCATTTTCTCTTGAA 58.611 39.130 0.00 0.00 0.00 2.69
686 715 3.753797 AGGAAACTTCTCGCCATTTTCTC 59.246 43.478 0.00 0.00 37.44 2.87
712 741 5.345741 CACGACATTGTTTTCCAATCCATTC 59.654 40.000 0.00 0.00 41.93 2.67
713 742 5.221422 ACACGACATTGTTTTCCAATCCATT 60.221 36.000 0.00 0.00 41.93 3.16
714 743 4.280677 ACACGACATTGTTTTCCAATCCAT 59.719 37.500 0.00 0.00 41.93 3.41
715 744 3.634448 ACACGACATTGTTTTCCAATCCA 59.366 39.130 0.00 0.00 41.93 3.41
716 745 4.226761 GACACGACATTGTTTTCCAATCC 58.773 43.478 0.00 0.00 41.93 3.01
717 746 4.854399 TGACACGACATTGTTTTCCAATC 58.146 39.130 0.00 0.00 41.93 2.67
718 747 4.909696 TGACACGACATTGTTTTCCAAT 57.090 36.364 0.00 0.00 44.73 3.16
719 748 4.703645 TTGACACGACATTGTTTTCCAA 57.296 36.364 0.00 0.00 37.49 3.53
720 749 4.909696 ATTGACACGACATTGTTTTCCA 57.090 36.364 0.00 0.00 0.00 3.53
721 750 5.151389 GGTATTGACACGACATTGTTTTCC 58.849 41.667 0.00 0.00 0.00 3.13
722 751 5.151389 GGGTATTGACACGACATTGTTTTC 58.849 41.667 0.00 0.00 0.00 2.29
723 752 4.580995 TGGGTATTGACACGACATTGTTTT 59.419 37.500 0.00 0.00 0.00 2.43
724 753 4.023536 GTGGGTATTGACACGACATTGTTT 60.024 41.667 0.00 0.00 0.00 2.83
725 754 3.500680 GTGGGTATTGACACGACATTGTT 59.499 43.478 0.00 0.00 0.00 2.83
726 755 3.071479 GTGGGTATTGACACGACATTGT 58.929 45.455 0.00 0.00 0.00 2.71
727 756 3.070748 TGTGGGTATTGACACGACATTG 58.929 45.455 0.00 0.00 40.39 2.82
732 761 3.686916 TCAATGTGGGTATTGACACGA 57.313 42.857 0.00 0.00 40.95 4.35
741 770 5.538053 TGAAGCAAAAGATTCAATGTGGGTA 59.462 36.000 0.00 0.00 32.66 3.69
746 775 7.437267 CACTTTCTGAAGCAAAAGATTCAATGT 59.563 33.333 2.14 0.00 35.14 2.71
748 777 6.927381 CCACTTTCTGAAGCAAAAGATTCAAT 59.073 34.615 2.14 0.00 35.14 2.57
798 827 3.060473 GTGTCACTAGCGTGTTCACTTTC 60.060 47.826 0.00 0.00 41.89 2.62
806 835 1.537638 CTCTCTGTGTCACTAGCGTGT 59.462 52.381 4.27 0.00 41.89 4.49
810 839 2.163509 TGTCCTCTCTGTGTCACTAGC 58.836 52.381 4.27 0.00 0.00 3.42
811 840 4.460731 TCATTGTCCTCTCTGTGTCACTAG 59.539 45.833 4.27 2.28 0.00 2.57
855 894 2.301296 TCACTTTCTTCCTCTCTGCCTG 59.699 50.000 0.00 0.00 0.00 4.85
1013 1052 1.530655 AAAAGCAACCTCACGGGGG 60.531 57.895 0.00 0.00 40.03 5.40
1015 1054 0.744281 AACAAAAGCAACCTCACGGG 59.256 50.000 0.00 0.00 41.89 5.28
1034 1073 0.252284 GAGGGTGAAGAGGAGGGACA 60.252 60.000 0.00 0.00 0.00 4.02
1063 1102 3.231736 AACACTGTCCCTCGCCGT 61.232 61.111 0.00 0.00 0.00 5.68
1081 1120 3.056821 CCATCATCATCATCATGGTTGCC 60.057 47.826 0.00 0.00 32.49 4.52
1091 1130 0.322277 GGCGGCTCCATCATCATCAT 60.322 55.000 0.00 0.00 34.01 2.45
1116 1155 2.290896 CCTGATACCCACCTTGAAAGCA 60.291 50.000 0.00 0.00 0.00 3.91
1127 1166 2.445845 CGCCCCTCCTGATACCCA 60.446 66.667 0.00 0.00 0.00 4.51
1136 1175 4.168291 CAGAGCTTCCGCCCCTCC 62.168 72.222 0.00 0.00 36.60 4.30
1144 1183 2.270527 GAGTGGGCCAGAGCTTCC 59.729 66.667 6.40 0.00 39.73 3.46
1162 1201 3.782244 GCTGCTGTTCCACGAGCG 61.782 66.667 0.00 0.00 38.09 5.03
1167 1206 2.912624 GCTGGTGCTGCTGTTCCAC 61.913 63.158 0.00 0.00 36.03 4.02
1256 1298 4.575973 GCATCCCAGCGAGCCCAT 62.576 66.667 0.00 0.00 0.00 4.00
1305 1347 2.651361 CTCAGGTTGAGCGTCCGT 59.349 61.111 0.00 0.00 37.72 4.69
1374 1416 0.539669 TCAGGTCAAGCGTCTGGAGA 60.540 55.000 0.00 0.00 0.00 3.71
1396 1438 1.674441 CGTGCCGGAGAGTGAGTTATA 59.326 52.381 5.05 0.00 0.00 0.98
1506 1548 3.901222 TCTTCAGGTTGGTCAGTGTATCA 59.099 43.478 0.00 0.00 0.00 2.15
1569 1611 3.382832 AGGTTGGCTAGCGACGCT 61.383 61.111 27.45 27.45 43.41 5.07
1578 1620 1.071471 CAGGAACGACAGGTTGGCT 59.929 57.895 0.00 0.00 39.50 4.75
1592 1634 0.532573 GAGATCGAGGTGTTGCAGGA 59.467 55.000 0.00 0.00 0.00 3.86
1651 1693 0.760189 GAGATGCTCCTGAGGCCTCT 60.760 60.000 32.28 11.42 37.38 3.69
1660 1702 2.064434 TCGATGTGAGAGATGCTCCT 57.936 50.000 0.00 0.00 43.26 3.69
1662 1704 3.503363 AGAGATCGATGTGAGAGATGCTC 59.497 47.826 0.54 0.00 44.21 4.26
1675 1717 3.258225 CGTTTGCGGAGAGATCGAT 57.742 52.632 0.00 0.00 0.00 3.59
1742 1784 1.301293 CCCTCAACCTGAAGGCTCC 59.699 63.158 0.00 0.00 39.32 4.70
1888 1930 2.281761 CCCAAGGCGAAGTGCTGT 60.282 61.111 0.00 0.00 45.43 4.40
2125 2167 7.435068 TGTTGTAGCCTATGAAAAACTTCTC 57.565 36.000 0.00 0.00 0.00 2.87
2234 2276 2.242926 TCCCGATGCTCTCTGGAATAG 58.757 52.381 0.00 0.00 34.62 1.73
2314 2358 0.108138 GTGAGGTTCCCGACAGATGG 60.108 60.000 0.00 0.00 0.00 3.51
2336 2380 1.084370 CGCGAGGATCCAGTTCAACC 61.084 60.000 15.82 0.00 0.00 3.77
2349 2393 3.739300 CCAGGTTATTATTGTACGCGAGG 59.261 47.826 15.93 0.00 0.00 4.63
2481 2528 8.596781 ATGACAGGTCTAGTTGTATAGAAAGT 57.403 34.615 0.65 0.00 33.66 2.66
2597 2644 6.210078 CAACTCGAGATACTTTCAGGTATCC 58.790 44.000 21.68 3.40 45.29 2.59
2683 2730 5.044476 TGGTGAGCCCCTTTATATTCTTCAA 60.044 40.000 0.00 0.00 0.00 2.69
2894 2941 1.450025 GTTTCTAAAGACGCCCCCAG 58.550 55.000 0.00 0.00 0.00 4.45
2897 2944 3.005554 GTTAGGTTTCTAAAGACGCCCC 58.994 50.000 0.00 0.00 37.24 5.80
2927 2974 3.503800 ACTTACTGTTTCCTTGGACCC 57.496 47.619 0.00 0.00 0.00 4.46
2932 2979 4.398044 ACCACACAACTTACTGTTTCCTTG 59.602 41.667 0.00 0.00 36.63 3.61
2934 2981 3.945285 CACCACACAACTTACTGTTTCCT 59.055 43.478 0.00 0.00 36.63 3.36
3272 3334 2.073816 CCTTTACGGCCACACTTGTAG 58.926 52.381 2.24 0.00 0.00 2.74
3278 3340 1.026584 AAACACCTTTACGGCCACAC 58.973 50.000 2.24 0.00 35.61 3.82
3300 3362 2.659428 GAAGATCCTGATTGTTGGGGG 58.341 52.381 0.00 0.00 0.00 5.40
3462 3524 1.759445 GGATGAAGCCAGCTGTCTAGA 59.241 52.381 13.81 0.00 0.00 2.43
3497 3559 2.897350 GCGTACTGCATGGAGCCC 60.897 66.667 14.95 3.89 45.45 5.19
3522 3584 2.964310 AATGTCCAGCCGCTGAGCT 61.964 57.895 22.35 0.60 46.45 4.09
3630 3692 1.004595 CAGTCATGTCATGTGCGAGG 58.995 55.000 12.54 0.70 0.00 4.63
3639 3701 0.936600 CAACACGTGCAGTCATGTCA 59.063 50.000 17.22 0.00 40.28 3.58
3647 3709 2.605338 CCAAAATCTCCAACACGTGCAG 60.605 50.000 17.22 8.25 0.00 4.41
3772 3834 8.683774 GCAAAGAAAATAATGCAACAATGTTTG 58.316 29.630 0.00 0.00 38.63 2.93
3773 3835 8.623030 AGCAAAGAAAATAATGCAACAATGTTT 58.377 25.926 0.00 0.00 41.18 2.83
3826 3918 4.790878 CAGCCATGATTGATCATTAACCG 58.209 43.478 3.78 0.00 44.70 4.44
3867 3959 0.251354 GTGAGGCAGCAGATCCTTCA 59.749 55.000 0.00 0.00 31.71 3.02
3889 3981 4.141482 ACCGAGGCTATAAACATCACCAAT 60.141 41.667 0.00 0.00 0.00 3.16
3909 4001 5.991328 ACATCTCAAGCAACAATATACCG 57.009 39.130 0.00 0.00 0.00 4.02
3959 4051 4.276926 GCAGATTCAGTGAACCTTTGAACT 59.723 41.667 7.96 0.00 34.04 3.01
3994 4086 1.750193 TTATTTGGAAGAGCGGCCTG 58.250 50.000 0.00 0.00 0.00 4.85
4073 4165 3.046087 CAGTGCCGGTGTCAGCTG 61.046 66.667 7.63 7.63 0.00 4.24
4077 4169 2.591429 CTTGCAGTGCCGGTGTCA 60.591 61.111 13.72 0.00 0.00 3.58
4242 4334 6.648725 GGGTGCTTTATTCTCTCTGATGTATC 59.351 42.308 0.00 0.00 0.00 2.24
4278 4370 9.959721 AAGTAACTACATGTTCATTAGTTGGAT 57.040 29.630 17.40 4.46 39.89 3.41
4279 4371 9.214957 CAAGTAACTACATGTTCATTAGTTGGA 57.785 33.333 21.94 6.51 39.89 3.53
4280 4372 9.214957 TCAAGTAACTACATGTTCATTAGTTGG 57.785 33.333 25.24 16.01 39.89 3.77
4282 4374 8.936864 GCTCAAGTAACTACATGTTCATTAGTT 58.063 33.333 13.85 13.85 39.89 2.24
4283 4375 8.094548 TGCTCAAGTAACTACATGTTCATTAGT 58.905 33.333 2.30 0.00 39.89 2.24
4337 4429 9.651718 GGATCATCGTGTTAACAAAGAAATATC 57.348 33.333 10.51 14.65 0.00 1.63
4356 4448 0.105593 TGAAGCTGAGCCGGATCATC 59.894 55.000 24.87 19.94 0.00 2.92
4382 4474 4.316823 TCTGGAGGGTGGCGAGGT 62.317 66.667 0.00 0.00 0.00 3.85
4385 4477 2.997315 CAGTCTGGAGGGTGGCGA 60.997 66.667 0.00 0.00 0.00 5.54
4387 4479 0.912486 ATAACAGTCTGGAGGGTGGC 59.088 55.000 4.53 0.00 0.00 5.01
4443 4535 5.163764 GCGGTTTGATGAATCACTAACATGA 60.164 40.000 0.00 0.00 36.36 3.07
4462 4554 1.077716 GAGGGGCTTACATGCGGTT 60.078 57.895 0.00 0.00 0.00 4.44
4465 4557 1.149174 ATGGAGGGGCTTACATGCG 59.851 57.895 0.00 0.00 0.00 4.73
4538 4634 6.122277 GGGAATTGTTGGAGATCATCTTGTA 58.878 40.000 0.00 0.00 0.00 2.41
4626 4740 4.232091 ACCCTTTTTCTCTAGTCTGGTCA 58.768 43.478 0.00 0.00 0.00 4.02
4695 4811 9.656323 ACTAGACTACAATAGGTTGGATATTCA 57.344 33.333 0.00 0.00 39.70 2.57
4751 4867 2.167900 GACCAGAGTATTTAGCCCGTGT 59.832 50.000 0.00 0.00 0.00 4.49
4860 4976 5.859114 CAGACTACACTACTGTTACAGCTTG 59.141 44.000 12.80 9.29 34.37 4.01
4881 4997 3.389329 AGCTGTTCTTGAGTTCTTCCAGA 59.611 43.478 0.00 0.00 0.00 3.86
4915 5031 2.152016 GTTCTTGTTGTAGGGCACTCC 58.848 52.381 0.00 0.00 0.00 3.85
4926 5042 3.799281 TTTCCAGCTTGGTTCTTGTTG 57.201 42.857 0.00 0.00 39.03 3.33
5104 5221 5.456186 GGGCTTTTACTCCATTCTATAGCCA 60.456 44.000 0.00 0.00 45.67 4.75
5129 5246 8.375608 AGCAGATTCATTATGAACACATAGTC 57.624 34.615 10.02 2.40 39.45 2.59
5195 5312 8.583765 GGCAACGACTGTAATTCATTTTAATTC 58.416 33.333 0.00 0.00 31.63 2.17
5210 5327 1.768684 ATCCTGTGGGCAACGACTGT 61.769 55.000 0.00 0.00 46.80 3.55
5215 5332 1.883275 TGTTTTATCCTGTGGGCAACG 59.117 47.619 0.00 0.00 37.60 4.10


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

AutoCloner maintained by Alex Coulton.