Multiple sequence alignment - TraesCS7B01G490800

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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 TraesCS7B01G490800 chr7B 100.000 4483 0 0 1365 5847 743968400 743972882 0.000000e+00 8279.0
1 TraesCS7B01G490800 chr7B 100.000 1233 0 0 1 1233 743967036 743968268 0.000000e+00 2278.0
2 TraesCS7B01G490800 chr7B 99.919 1233 1 0 1 1233 743921761 743922993 0.000000e+00 2272.0
3 TraesCS7B01G490800 chr7B 99.480 1153 6 0 1365 2517 743923023 743924175 0.000000e+00 2097.0
4 TraesCS7B01G490800 chr7B 99.422 1038 5 1 2867 3903 743924176 743925213 0.000000e+00 1882.0
5 TraesCS7B01G490800 chr7B 99.138 696 6 0 5015 5710 743925211 743925906 0.000000e+00 1253.0
6 TraesCS7B01G490800 chr7B 84.337 498 73 4 4996 5490 743874780 743875275 3.170000e-132 483.0
7 TraesCS7B01G490800 chr7B 84.137 498 73 6 4996 5490 743881278 743881772 1.470000e-130 477.0
8 TraesCS7B01G490800 chr7B 86.813 91 12 0 5375 5465 743916791 743916881 1.040000e-17 102.0
9 TraesCS7B01G490800 chr7B 86.813 91 12 0 5375 5465 743962069 743962159 1.040000e-17 102.0
10 TraesCS7B01G490800 chr7B 86.207 58 7 1 357 413 20100689 20100632 1.760000e-05 62.1
11 TraesCS7B01G490800 chrUn 96.156 4344 151 8 1377 5710 88855032 88850695 0.000000e+00 7083.0
12 TraesCS7B01G490800 chrUn 96.110 4344 152 9 1377 5710 88835142 88830806 0.000000e+00 7070.0
13 TraesCS7B01G490800 chrUn 96.002 1926 65 5 2523 4440 363858872 363860793 0.000000e+00 3120.0
14 TraesCS7B01G490800 chrUn 90.614 554 52 0 648 1201 88835788 88835235 0.000000e+00 736.0
15 TraesCS7B01G490800 chrUn 90.614 554 52 0 648 1201 88855678 88855125 0.000000e+00 736.0
16 TraesCS7B01G490800 chrUn 98.526 407 6 0 4442 4848 478039249 478039655 0.000000e+00 719.0
17 TraesCS7B01G490800 chrUn 97.872 141 3 0 5707 5847 47462967 47462827 1.630000e-60 244.0
18 TraesCS7B01G490800 chr7A 86.683 3214 348 38 1784 4961 735518535 735521704 0.000000e+00 3491.0
19 TraesCS7B01G490800 chr7A 89.744 390 40 0 669 1058 735511016 735511405 3.150000e-137 499.0
20 TraesCS7B01G490800 chr7A 78.138 494 89 12 4974 5465 735505525 735506001 4.430000e-76 296.0
21 TraesCS7B01G490800 chr7A 88.824 170 18 1 1 170 622865093 622865261 2.140000e-49 207.0
22 TraesCS7B01G490800 chr7A 90.769 65 6 0 5161 5225 735508543 735508607 2.900000e-13 87.9
23 TraesCS7B01G490800 chr7A 93.750 48 2 1 525 571 735510870 735510917 2.920000e-08 71.3
24 TraesCS7B01G490800 chr7A 87.273 55 6 1 354 407 79218183 79218237 1.760000e-05 62.1
25 TraesCS7B01G490800 chr2B 97.872 141 3 0 5707 5847 798814120 798813980 1.630000e-60 244.0
26 TraesCS7B01G490800 chr2B 97.163 141 4 0 5707 5847 7850979 7850839 7.570000e-59 239.0
27 TraesCS7B01G490800 chr2B 97.163 141 3 1 5707 5847 239466430 239466291 2.720000e-58 237.0
28 TraesCS7B01G490800 chr2B 88.824 170 18 1 1 170 702713442 702713610 2.140000e-49 207.0
29 TraesCS7B01G490800 chr5B 97.163 141 4 0 5707 5847 368789131 368788991 7.570000e-59 239.0
30 TraesCS7B01G490800 chr5B 96.454 141 5 0 5707 5847 64716233 64716373 3.520000e-57 233.0
31 TraesCS7B01G490800 chr5B 90.062 161 16 0 7 167 648261616 648261456 5.940000e-50 209.0
32 TraesCS7B01G490800 chr6A 96.454 141 5 0 5707 5847 490314952 490314812 3.520000e-57 233.0
33 TraesCS7B01G490800 chr6A 92.500 40 2 1 358 397 61895429 61895391 8.190000e-04 56.5
34 TraesCS7B01G490800 chr4A 96.454 141 5 0 5707 5847 697974242 697974102 3.520000e-57 233.0
35 TraesCS7B01G490800 chr4A 89.571 163 17 0 1 163 542123123 542123285 2.140000e-49 207.0
36 TraesCS7B01G490800 chr4A 88.824 170 18 1 1 170 614962800 614962968 2.140000e-49 207.0
37 TraesCS7B01G490800 chr3A 96.454 141 5 0 5707 5847 714078687 714078827 3.520000e-57 233.0
38 TraesCS7B01G490800 chr6B 89.634 164 16 1 7 170 551808679 551808517 2.140000e-49 207.0
39 TraesCS7B01G490800 chr6B 88.824 170 18 1 1 170 686371131 686371299 2.140000e-49 207.0
40 TraesCS7B01G490800 chr5A 89.634 164 16 1 7 170 660883371 660883209 2.140000e-49 207.0
41 TraesCS7B01G490800 chr2A 97.297 37 1 0 354 390 79647735 79647771 4.890000e-06 63.9


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 TraesCS7B01G490800 chr7B 743967036 743972882 5846 False 5278.50 8279 100.00000 1 5847 2 chr7B.!!$F6 5846
1 TraesCS7B01G490800 chr7B 743921761 743925906 4145 False 1876.00 2272 99.48975 1 5710 4 chr7B.!!$F5 5709
2 TraesCS7B01G490800 chrUn 88850695 88855678 4983 True 3909.50 7083 93.38500 648 5710 2 chrUn.!!$R3 5062
3 TraesCS7B01G490800 chrUn 88830806 88835788 4982 True 3903.00 7070 93.36200 648 5710 2 chrUn.!!$R2 5062
4 TraesCS7B01G490800 chrUn 363858872 363860793 1921 False 3120.00 3120 96.00200 2523 4440 1 chrUn.!!$F1 1917
5 TraesCS7B01G490800 chr7A 735518535 735521704 3169 False 3491.00 3491 86.68300 1784 4961 1 chr7A.!!$F3 3177
6 TraesCS7B01G490800 chr7A 735505525 735511405 5880 False 238.55 499 88.10025 525 5465 4 chr7A.!!$F4 4940

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
888 5749 1.299976 GGTGGACACCCCTCATGAC 59.700 63.158 10.38 0.0 45.68 3.06 F
1729 6626 0.887933 GGCTCGCCTTTGGAATTTCA 59.112 50.000 0.00 0.0 0.00 2.69 F
2317 7214 3.721035 TGTATCATGAGACGGATGCTTG 58.279 45.455 15.31 0.0 0.00 4.01 F
4201 9143 3.314541 TTCAGGAGAGAACGGCTAAAC 57.685 47.619 0.00 0.0 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2682 7600 0.034767 CTGCTGGAGATGGCTTGGAA 60.035 55.000 0.00 0.00 0.00 3.53 R
2811 7729 6.730960 ATCCATGCAAAGTTTAAGCAAATG 57.269 33.333 4.88 0.93 42.15 2.32 R
4210 9152 0.943673 TCACAAATGCTGACACACCG 59.056 50.000 0.00 0.00 0.00 4.94 R
5773 10715 0.243636 GCCATCCAAACCGGTTGAAG 59.756 55.000 23.08 13.88 39.87 3.02 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
888 5749 1.299976 GGTGGACACCCCTCATGAC 59.700 63.158 10.38 0.00 45.68 3.06
1613 6510 9.968870 GTCCGTTCTATTAGAGATTCTGTTTAT 57.031 33.333 0.00 0.00 32.88 1.40
1729 6626 0.887933 GGCTCGCCTTTGGAATTTCA 59.112 50.000 0.00 0.00 0.00 2.69
2317 7214 3.721035 TGTATCATGAGACGGATGCTTG 58.279 45.455 15.31 0.00 0.00 4.01
2664 7582 9.109393 GACATAGTAATTAACATGCAGGAAAGA 57.891 33.333 4.84 0.00 0.00 2.52
2682 7600 8.046107 CAGGAAAGAGGAGAAAGAACAATATCT 58.954 37.037 0.00 0.00 0.00 1.98
2733 7651 7.229506 GCAATAGAAGTTCTGGTAAATGCCTAT 59.770 37.037 15.90 0.00 0.00 2.57
2797 7715 7.027161 GCACGACATAAATGAAATGGTTAGTT 58.973 34.615 0.00 0.00 0.00 2.24
3558 8479 6.652481 AGCAGGTTAATCATCTGATTTATCGG 59.348 38.462 10.47 4.72 41.64 4.18
3761 8683 6.815089 AGGTAAAAATTGCACATTTGACTGA 58.185 32.000 9.62 0.00 0.00 3.41
4067 9009 9.363401 ACCAAGTAGCCTTTAAAGTTTCTTATT 57.637 29.630 14.03 4.49 0.00 1.40
4166 9108 4.371786 TGCTCTCACTTGTAGTCTTGTTG 58.628 43.478 0.00 0.00 0.00 3.33
4201 9143 3.314541 TTCAGGAGAGAACGGCTAAAC 57.685 47.619 0.00 0.00 0.00 2.01
4210 9152 1.063027 GAACGGCTAAACGGGCATTAC 59.937 52.381 0.00 0.00 38.39 1.89
4274 9216 7.198390 CACACCATATCTTTTCCTTATTGCTG 58.802 38.462 0.00 0.00 0.00 4.41
4294 9236 3.462982 TGTATTACCTGGTGCAATAGCG 58.537 45.455 10.23 0.00 46.23 4.26
4303 9245 2.100252 TGGTGCAATAGCGTACTACCTC 59.900 50.000 0.00 0.00 46.23 3.85
4648 9590 7.119846 ACAATAACTGGTGAAGAAGTGATAAGC 59.880 37.037 0.00 0.00 0.00 3.09
4943 9885 8.939201 ACGGTGATATATCAGATTCATCATTC 57.061 34.615 15.83 0.00 37.51 2.67
4989 9931 0.458669 GGCGAGGACCGATGACTAAA 59.541 55.000 0.00 0.00 41.76 1.85
4993 9935 3.782046 CGAGGACCGATGACTAAACATT 58.218 45.455 0.00 0.00 41.76 2.71
5008 9950 5.784906 ACTAAACATTGGGGTCAATTCCATT 59.215 36.000 0.00 0.00 41.29 3.16
5025 9967 0.183492 ATTGCACCAGTGTGACACCT 59.817 50.000 12.81 0.00 45.76 4.00
5037 9979 3.258372 GTGTGACACCTTCTACCTGATCA 59.742 47.826 3.92 0.00 0.00 2.92
5526 10468 7.190871 CGATCATGACAAAATGATGTTGATCA 58.809 34.615 17.42 3.14 45.27 2.92
5715 10657 9.845740 TTTCAAATTATCTTATTCTCCGATGGA 57.154 29.630 0.00 0.00 0.00 3.41
5723 10665 3.554342 CTCCGATGGAGGCCAGGG 61.554 72.222 5.01 0.00 45.43 4.45
5724 10666 4.088351 TCCGATGGAGGCCAGGGA 62.088 66.667 5.01 0.00 37.61 4.20
5725 10667 3.554342 CCGATGGAGGCCAGGGAG 61.554 72.222 5.01 0.00 36.75 4.30
5726 10668 4.247380 CGATGGAGGCCAGGGAGC 62.247 72.222 5.01 0.00 36.75 4.70
5727 10669 3.092511 GATGGAGGCCAGGGAGCA 61.093 66.667 5.01 0.00 36.75 4.26
5728 10670 2.369291 ATGGAGGCCAGGGAGCAT 60.369 61.111 5.01 0.00 36.75 3.79
5729 10671 2.004408 GATGGAGGCCAGGGAGCATT 62.004 60.000 5.01 0.00 36.75 3.56
5730 10672 1.587522 ATGGAGGCCAGGGAGCATTT 61.588 55.000 5.01 0.00 36.75 2.32
5731 10673 1.755783 GGAGGCCAGGGAGCATTTG 60.756 63.158 5.01 0.00 0.00 2.32
5732 10674 1.755783 GAGGCCAGGGAGCATTTGG 60.756 63.158 5.01 0.00 35.06 3.28
5733 10675 2.037847 GGCCAGGGAGCATTTGGT 59.962 61.111 0.00 0.00 34.43 3.67
5734 10676 1.610379 GGCCAGGGAGCATTTGGTT 60.610 57.895 0.00 0.00 34.43 3.67
5735 10677 0.324275 GGCCAGGGAGCATTTGGTTA 60.324 55.000 0.00 0.00 34.43 2.85
5736 10678 0.817654 GCCAGGGAGCATTTGGTTAC 59.182 55.000 0.00 0.00 34.43 2.50
5737 10679 1.616994 GCCAGGGAGCATTTGGTTACT 60.617 52.381 0.00 0.00 34.43 2.24
5738 10680 2.094675 CCAGGGAGCATTTGGTTACTG 58.905 52.381 7.32 7.32 32.88 2.74
5739 10681 2.290896 CCAGGGAGCATTTGGTTACTGA 60.291 50.000 12.98 0.00 34.05 3.41
5740 10682 3.012518 CAGGGAGCATTTGGTTACTGAG 58.987 50.000 8.17 0.00 34.05 3.35
5741 10683 2.644798 AGGGAGCATTTGGTTACTGAGT 59.355 45.455 0.00 0.00 0.00 3.41
5742 10684 3.010420 GGGAGCATTTGGTTACTGAGTC 58.990 50.000 0.00 0.00 0.00 3.36
5743 10685 3.307762 GGGAGCATTTGGTTACTGAGTCT 60.308 47.826 0.00 0.00 0.00 3.24
5744 10686 4.081087 GGGAGCATTTGGTTACTGAGTCTA 60.081 45.833 0.00 0.00 0.00 2.59
5745 10687 5.396884 GGGAGCATTTGGTTACTGAGTCTAT 60.397 44.000 0.00 0.00 0.00 1.98
5746 10688 5.755861 GGAGCATTTGGTTACTGAGTCTATC 59.244 44.000 0.00 0.00 0.00 2.08
5747 10689 5.675538 AGCATTTGGTTACTGAGTCTATCC 58.324 41.667 0.00 0.00 0.00 2.59
5748 10690 4.508124 GCATTTGGTTACTGAGTCTATCCG 59.492 45.833 0.00 0.00 0.00 4.18
5749 10691 5.661458 CATTTGGTTACTGAGTCTATCCGT 58.339 41.667 0.00 0.00 0.00 4.69
5750 10692 5.733620 TTTGGTTACTGAGTCTATCCGTT 57.266 39.130 0.00 0.00 0.00 4.44
5751 10693 4.713824 TGGTTACTGAGTCTATCCGTTG 57.286 45.455 0.00 0.00 0.00 4.10
5752 10694 4.338012 TGGTTACTGAGTCTATCCGTTGA 58.662 43.478 0.00 0.00 0.00 3.18
5753 10695 4.398358 TGGTTACTGAGTCTATCCGTTGAG 59.602 45.833 0.00 0.00 0.00 3.02
5754 10696 4.639310 GGTTACTGAGTCTATCCGTTGAGA 59.361 45.833 0.00 0.00 0.00 3.27
5755 10697 5.220892 GGTTACTGAGTCTATCCGTTGAGAG 60.221 48.000 0.00 0.00 0.00 3.20
5756 10698 4.223556 ACTGAGTCTATCCGTTGAGAGA 57.776 45.455 0.00 0.00 36.52 3.10
5757 10699 4.787551 ACTGAGTCTATCCGTTGAGAGAT 58.212 43.478 0.00 0.00 40.71 2.75
5758 10700 4.578516 ACTGAGTCTATCCGTTGAGAGATG 59.421 45.833 0.00 0.00 40.71 2.90
5759 10701 3.885901 TGAGTCTATCCGTTGAGAGATGG 59.114 47.826 0.00 0.00 40.71 3.51
5760 10702 3.886505 GAGTCTATCCGTTGAGAGATGGT 59.113 47.826 0.00 0.00 40.71 3.55
5761 10703 4.282496 AGTCTATCCGTTGAGAGATGGTT 58.718 43.478 0.00 0.00 40.71 3.67
5762 10704 4.098654 AGTCTATCCGTTGAGAGATGGTTG 59.901 45.833 0.00 0.00 40.71 3.77
5763 10705 2.029838 ATCCGTTGAGAGATGGTTGC 57.970 50.000 0.00 0.00 0.00 4.17
5764 10706 0.976641 TCCGTTGAGAGATGGTTGCT 59.023 50.000 0.00 0.00 0.00 3.91
5765 10707 1.066858 TCCGTTGAGAGATGGTTGCTC 60.067 52.381 0.00 0.00 0.00 4.26
5766 10708 0.994995 CGTTGAGAGATGGTTGCTCG 59.005 55.000 0.00 0.00 37.46 5.03
5767 10709 1.363744 GTTGAGAGATGGTTGCTCGG 58.636 55.000 0.00 0.00 37.46 4.63
5768 10710 0.250234 TTGAGAGATGGTTGCTCGGG 59.750 55.000 0.00 0.00 37.46 5.14
5769 10711 0.614697 TGAGAGATGGTTGCTCGGGA 60.615 55.000 0.00 0.00 37.46 5.14
5770 10712 0.755686 GAGAGATGGTTGCTCGGGAT 59.244 55.000 0.00 0.00 37.46 3.85
5771 10713 1.964223 GAGAGATGGTTGCTCGGGATA 59.036 52.381 0.00 0.00 37.46 2.59
5772 10714 2.564947 GAGAGATGGTTGCTCGGGATAT 59.435 50.000 0.00 0.00 37.46 1.63
5773 10715 2.564947 AGAGATGGTTGCTCGGGATATC 59.435 50.000 0.00 0.00 37.46 1.63
5774 10716 2.564947 GAGATGGTTGCTCGGGATATCT 59.435 50.000 2.05 0.00 0.00 1.98
5775 10717 2.975489 AGATGGTTGCTCGGGATATCTT 59.025 45.455 2.05 0.00 0.00 2.40
5776 10718 2.910688 TGGTTGCTCGGGATATCTTC 57.089 50.000 2.05 0.00 0.00 2.87
5777 10719 2.115427 TGGTTGCTCGGGATATCTTCA 58.885 47.619 2.05 0.00 0.00 3.02
5778 10720 2.503765 TGGTTGCTCGGGATATCTTCAA 59.496 45.455 2.05 0.00 0.00 2.69
5779 10721 2.872858 GGTTGCTCGGGATATCTTCAAC 59.127 50.000 2.05 9.29 33.61 3.18
5780 10722 2.872858 GTTGCTCGGGATATCTTCAACC 59.127 50.000 2.05 0.00 0.00 3.77
5781 10723 1.068588 TGCTCGGGATATCTTCAACCG 59.931 52.381 10.16 10.16 45.52 4.44
5782 10724 1.605712 GCTCGGGATATCTTCAACCGG 60.606 57.143 14.77 0.00 44.36 5.28
5783 10725 1.687123 CTCGGGATATCTTCAACCGGT 59.313 52.381 0.00 0.00 44.36 5.28
5784 10726 2.102588 CTCGGGATATCTTCAACCGGTT 59.897 50.000 15.86 15.86 44.36 4.44
5785 10727 2.502538 TCGGGATATCTTCAACCGGTTT 59.497 45.455 19.55 5.23 44.36 3.27
5786 10728 2.612212 CGGGATATCTTCAACCGGTTTG 59.388 50.000 19.55 13.53 40.79 2.93
5787 10729 2.949644 GGGATATCTTCAACCGGTTTGG 59.050 50.000 19.55 7.84 46.41 3.28
5788 10730 3.371166 GGGATATCTTCAACCGGTTTGGA 60.371 47.826 19.55 15.86 42.00 3.53
5789 10731 4.461198 GGATATCTTCAACCGGTTTGGAT 58.539 43.478 19.55 21.16 42.00 3.41
5790 10732 4.275936 GGATATCTTCAACCGGTTTGGATG 59.724 45.833 19.55 14.79 41.73 3.51
5791 10733 1.904287 TCTTCAACCGGTTTGGATGG 58.096 50.000 19.55 5.30 40.78 3.51
5792 10734 0.243636 CTTCAACCGGTTTGGATGGC 59.756 55.000 19.55 0.00 40.78 4.40
5793 10735 1.519751 TTCAACCGGTTTGGATGGCG 61.520 55.000 19.55 3.62 40.78 5.69
5794 10736 2.675075 AACCGGTTTGGATGGCGG 60.675 61.111 15.86 0.00 42.00 6.13
5795 10737 3.501040 AACCGGTTTGGATGGCGGT 62.501 57.895 15.86 0.00 42.00 5.68
5796 10738 3.131478 CCGGTTTGGATGGCGGTC 61.131 66.667 0.00 0.00 42.00 4.79
5797 10739 2.359354 CGGTTTGGATGGCGGTCA 60.359 61.111 0.00 0.00 0.00 4.02
5798 10740 1.748879 CGGTTTGGATGGCGGTCAT 60.749 57.895 0.00 0.00 39.13 3.06
5799 10741 1.809207 GGTTTGGATGGCGGTCATG 59.191 57.895 0.00 0.00 35.97 3.07
5800 10742 0.965363 GGTTTGGATGGCGGTCATGT 60.965 55.000 0.00 0.00 35.97 3.21
5801 10743 1.680555 GGTTTGGATGGCGGTCATGTA 60.681 52.381 0.00 0.00 35.97 2.29
5802 10744 2.088423 GTTTGGATGGCGGTCATGTAA 58.912 47.619 0.00 0.00 35.97 2.41
5803 10745 2.687935 GTTTGGATGGCGGTCATGTAAT 59.312 45.455 0.00 0.00 35.97 1.89
5804 10746 3.847671 TTGGATGGCGGTCATGTAATA 57.152 42.857 0.00 0.00 35.97 0.98
5805 10747 3.401033 TGGATGGCGGTCATGTAATAG 57.599 47.619 0.00 0.00 35.97 1.73
5806 10748 2.038426 TGGATGGCGGTCATGTAATAGG 59.962 50.000 0.00 0.00 35.97 2.57
5807 10749 2.301870 GGATGGCGGTCATGTAATAGGA 59.698 50.000 0.00 0.00 35.97 2.94
5808 10750 3.055094 GGATGGCGGTCATGTAATAGGAT 60.055 47.826 0.00 0.00 35.97 3.24
5809 10751 4.161565 GGATGGCGGTCATGTAATAGGATA 59.838 45.833 0.00 0.00 35.97 2.59
5810 10752 4.801330 TGGCGGTCATGTAATAGGATAG 57.199 45.455 0.00 0.00 0.00 2.08
5811 10753 3.513912 TGGCGGTCATGTAATAGGATAGG 59.486 47.826 0.00 0.00 0.00 2.57
5812 10754 3.522553 GCGGTCATGTAATAGGATAGGC 58.477 50.000 0.00 0.00 0.00 3.93
5813 10755 3.056107 GCGGTCATGTAATAGGATAGGCA 60.056 47.826 0.00 0.00 0.00 4.75
5814 10756 4.562757 GCGGTCATGTAATAGGATAGGCAA 60.563 45.833 0.00 0.00 0.00 4.52
5815 10757 5.734720 CGGTCATGTAATAGGATAGGCAAT 58.265 41.667 0.00 0.00 0.00 3.56
5816 10758 6.173339 CGGTCATGTAATAGGATAGGCAATT 58.827 40.000 0.00 0.00 0.00 2.32
5817 10759 7.327975 CGGTCATGTAATAGGATAGGCAATTA 58.672 38.462 0.00 0.00 0.00 1.40
5818 10760 7.492669 CGGTCATGTAATAGGATAGGCAATTAG 59.507 40.741 0.00 0.00 0.00 1.73
5819 10761 8.322091 GGTCATGTAATAGGATAGGCAATTAGT 58.678 37.037 0.00 0.00 0.00 2.24
5820 10762 9.726438 GTCATGTAATAGGATAGGCAATTAGTT 57.274 33.333 0.00 0.00 0.00 2.24
5828 10770 7.075851 AGGATAGGCAATTAGTTTACCTACC 57.924 40.000 0.00 0.00 35.88 3.18
5829 10771 6.850231 AGGATAGGCAATTAGTTTACCTACCT 59.150 38.462 0.00 0.00 35.88 3.08
5830 10772 7.350124 AGGATAGGCAATTAGTTTACCTACCTT 59.650 37.037 0.00 0.00 35.88 3.50
5831 10773 7.660617 GGATAGGCAATTAGTTTACCTACCTTC 59.339 40.741 0.00 0.00 35.88 3.46
5832 10774 6.638021 AGGCAATTAGTTTACCTACCTTCT 57.362 37.500 0.00 0.00 0.00 2.85
5833 10775 7.029053 AGGCAATTAGTTTACCTACCTTCTT 57.971 36.000 0.00 0.00 0.00 2.52
5834 10776 7.467650 AGGCAATTAGTTTACCTACCTTCTTT 58.532 34.615 0.00 0.00 0.00 2.52
5835 10777 8.608598 AGGCAATTAGTTTACCTACCTTCTTTA 58.391 33.333 0.00 0.00 0.00 1.85
5836 10778 8.890718 GGCAATTAGTTTACCTACCTTCTTTAG 58.109 37.037 0.00 0.00 0.00 1.85
5837 10779 8.396390 GCAATTAGTTTACCTACCTTCTTTAGC 58.604 37.037 0.00 0.00 0.00 3.09
5838 10780 8.890718 CAATTAGTTTACCTACCTTCTTTAGCC 58.109 37.037 0.00 0.00 0.00 3.93
5839 10781 7.557875 TTAGTTTACCTACCTTCTTTAGCCA 57.442 36.000 0.00 0.00 0.00 4.75
5840 10782 6.051179 AGTTTACCTACCTTCTTTAGCCAG 57.949 41.667 0.00 0.00 0.00 4.85
5841 10783 4.482952 TTACCTACCTTCTTTAGCCAGC 57.517 45.455 0.00 0.00 0.00 4.85
5842 10784 1.560146 ACCTACCTTCTTTAGCCAGCC 59.440 52.381 0.00 0.00 0.00 4.85
5843 10785 1.473434 CCTACCTTCTTTAGCCAGCCG 60.473 57.143 0.00 0.00 0.00 5.52
5844 10786 0.539986 TACCTTCTTTAGCCAGCCGG 59.460 55.000 0.00 0.00 0.00 6.13
5845 10787 1.299976 CCTTCTTTAGCCAGCCGGT 59.700 57.895 1.90 0.00 33.28 5.28
5846 10788 0.322546 CCTTCTTTAGCCAGCCGGTT 60.323 55.000 1.90 0.00 33.28 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
888 5749 2.398036 GTTATGAACACGCCGCCG 59.602 61.111 0.00 0.00 41.14 6.46
1613 6510 4.461198 TGATCGAGACAGCTCCTATTACA 58.539 43.478 0.00 0.00 37.91 2.41
1618 6515 3.291584 ACATTGATCGAGACAGCTCCTA 58.708 45.455 0.00 0.00 37.91 2.94
2655 7573 3.744660 TGTTCTTTCTCCTCTTTCCTGC 58.255 45.455 0.00 0.00 0.00 4.85
2664 7582 6.601217 GCTTGGAAGATATTGTTCTTTCTCCT 59.399 38.462 0.00 0.00 36.10 3.69
2682 7600 0.034767 CTGCTGGAGATGGCTTGGAA 60.035 55.000 0.00 0.00 0.00 3.53
2733 7651 8.686334 GCATTTTCAGAAGTATTGGAGGATTTA 58.314 33.333 0.00 0.00 0.00 1.40
2804 7722 8.885494 TGCAAAGTTTAAGCAAATGAAATACT 57.115 26.923 0.00 0.00 34.97 2.12
2811 7729 6.730960 ATCCATGCAAAGTTTAAGCAAATG 57.269 33.333 4.88 0.93 42.15 2.32
3918 8848 7.792508 CGTACTAAGTTTCAAAAGTAACAGCTG 59.207 37.037 13.48 13.48 0.00 4.24
4067 9009 4.654262 ACTCCTCACCTCAAGTAGTGAAAA 59.346 41.667 0.00 0.00 42.19 2.29
4201 9143 1.358725 CTGACACACCGTAATGCCCG 61.359 60.000 0.00 0.00 0.00 6.13
4210 9152 0.943673 TCACAAATGCTGACACACCG 59.056 50.000 0.00 0.00 0.00 4.94
4274 9216 3.463944 ACGCTATTGCACCAGGTAATAC 58.536 45.455 0.00 0.00 39.64 1.89
4303 9245 7.316544 GTCTACTCTTCTCTTTAGACCAGAG 57.683 44.000 8.13 8.13 40.42 3.35
4583 9525 6.197364 TGTGTTGTTTTCGAATACCAAACT 57.803 33.333 14.89 0.00 32.58 2.66
4648 9590 6.624423 CCCCATTTCTGTCTCAAATAACTTG 58.376 40.000 0.00 0.00 36.25 3.16
4920 9862 9.887629 ACAGAATGATGAATCTGATATATCACC 57.112 33.333 11.49 11.39 44.64 4.02
4943 9885 2.424601 TCGGGGTCTCATAACGTTACAG 59.575 50.000 10.81 9.75 0.00 2.74
4949 9891 2.596904 AATGTCGGGGTCTCATAACG 57.403 50.000 0.00 0.00 0.00 3.18
5008 9950 0.463654 GAAGGTGTCACACTGGTGCA 60.464 55.000 8.12 0.00 44.87 4.57
5025 9967 8.996651 TCACTGTTATAGATGATCAGGTAGAA 57.003 34.615 0.09 0.00 0.00 2.10
5526 10468 5.016173 TCAAACCAATCTTTTCCGATGGAT 58.984 37.500 0.00 0.00 0.00 3.41
5710 10652 2.004408 AATGCTCCCTGGCCTCCATC 62.004 60.000 3.32 0.00 30.82 3.51
5711 10653 1.587522 AAATGCTCCCTGGCCTCCAT 61.588 55.000 3.32 0.00 30.82 3.41
5712 10654 2.240918 AAATGCTCCCTGGCCTCCA 61.241 57.895 3.32 0.00 0.00 3.86
5713 10655 1.755783 CAAATGCTCCCTGGCCTCC 60.756 63.158 3.32 0.00 0.00 4.30
5714 10656 1.755783 CCAAATGCTCCCTGGCCTC 60.756 63.158 3.32 0.00 0.00 4.70
5715 10657 2.097978 AACCAAATGCTCCCTGGCCT 62.098 55.000 3.32 0.00 33.19 5.19
5716 10658 0.324275 TAACCAAATGCTCCCTGGCC 60.324 55.000 0.00 0.00 33.19 5.36
5717 10659 0.817654 GTAACCAAATGCTCCCTGGC 59.182 55.000 0.00 0.00 33.19 4.85
5718 10660 2.094675 CAGTAACCAAATGCTCCCTGG 58.905 52.381 0.00 0.00 36.24 4.45
5719 10661 3.012518 CTCAGTAACCAAATGCTCCCTG 58.987 50.000 0.00 0.00 0.00 4.45
5720 10662 2.644798 ACTCAGTAACCAAATGCTCCCT 59.355 45.455 0.00 0.00 0.00 4.20
5721 10663 3.010420 GACTCAGTAACCAAATGCTCCC 58.990 50.000 0.00 0.00 0.00 4.30
5722 10664 3.944087 AGACTCAGTAACCAAATGCTCC 58.056 45.455 0.00 0.00 0.00 4.70
5723 10665 5.755861 GGATAGACTCAGTAACCAAATGCTC 59.244 44.000 0.00 0.00 0.00 4.26
5724 10666 5.675538 GGATAGACTCAGTAACCAAATGCT 58.324 41.667 0.00 0.00 0.00 3.79
5725 10667 4.508124 CGGATAGACTCAGTAACCAAATGC 59.492 45.833 0.00 0.00 0.00 3.56
5726 10668 5.661458 ACGGATAGACTCAGTAACCAAATG 58.339 41.667 0.00 0.00 29.85 2.32
5727 10669 5.934402 ACGGATAGACTCAGTAACCAAAT 57.066 39.130 0.00 0.00 29.85 2.32
5728 10670 5.244402 TCAACGGATAGACTCAGTAACCAAA 59.756 40.000 0.00 0.00 31.55 3.28
5729 10671 4.768448 TCAACGGATAGACTCAGTAACCAA 59.232 41.667 0.00 0.00 31.55 3.67
5730 10672 4.338012 TCAACGGATAGACTCAGTAACCA 58.662 43.478 0.00 0.00 31.55 3.67
5731 10673 4.639310 TCTCAACGGATAGACTCAGTAACC 59.361 45.833 0.00 0.00 31.55 2.85
5732 10674 5.585445 TCTCTCAACGGATAGACTCAGTAAC 59.415 44.000 0.00 0.00 31.55 2.50
5733 10675 5.742063 TCTCTCAACGGATAGACTCAGTAA 58.258 41.667 0.00 0.00 31.55 2.24
5734 10676 5.354842 TCTCTCAACGGATAGACTCAGTA 57.645 43.478 0.00 0.00 31.55 2.74
5735 10677 4.223556 TCTCTCAACGGATAGACTCAGT 57.776 45.455 0.00 0.00 33.34 3.41
5736 10678 4.023279 CCATCTCTCAACGGATAGACTCAG 60.023 50.000 0.00 0.00 30.10 3.35
5737 10679 3.885901 CCATCTCTCAACGGATAGACTCA 59.114 47.826 0.00 0.00 30.10 3.41
5738 10680 3.886505 ACCATCTCTCAACGGATAGACTC 59.113 47.826 0.00 0.00 30.10 3.36
5739 10681 3.904717 ACCATCTCTCAACGGATAGACT 58.095 45.455 0.00 0.00 30.10 3.24
5740 10682 4.363999 CAACCATCTCTCAACGGATAGAC 58.636 47.826 0.00 0.00 30.10 2.59
5741 10683 3.181475 GCAACCATCTCTCAACGGATAGA 60.181 47.826 0.00 0.00 31.69 1.98
5742 10684 3.126831 GCAACCATCTCTCAACGGATAG 58.873 50.000 0.00 0.00 0.00 2.08
5743 10685 2.766263 AGCAACCATCTCTCAACGGATA 59.234 45.455 0.00 0.00 0.00 2.59
5744 10686 1.556911 AGCAACCATCTCTCAACGGAT 59.443 47.619 0.00 0.00 0.00 4.18
5745 10687 0.976641 AGCAACCATCTCTCAACGGA 59.023 50.000 0.00 0.00 0.00 4.69
5746 10688 1.363744 GAGCAACCATCTCTCAACGG 58.636 55.000 0.00 0.00 0.00 4.44
5747 10689 0.994995 CGAGCAACCATCTCTCAACG 59.005 55.000 0.00 0.00 0.00 4.10
5748 10690 1.363744 CCGAGCAACCATCTCTCAAC 58.636 55.000 0.00 0.00 0.00 3.18
5749 10691 0.250234 CCCGAGCAACCATCTCTCAA 59.750 55.000 0.00 0.00 0.00 3.02
5750 10692 0.614697 TCCCGAGCAACCATCTCTCA 60.615 55.000 0.00 0.00 0.00 3.27
5751 10693 0.755686 ATCCCGAGCAACCATCTCTC 59.244 55.000 0.00 0.00 0.00 3.20
5752 10694 2.088104 TATCCCGAGCAACCATCTCT 57.912 50.000 0.00 0.00 0.00 3.10
5753 10695 2.564947 AGATATCCCGAGCAACCATCTC 59.435 50.000 0.00 0.00 0.00 2.75
5754 10696 2.614259 AGATATCCCGAGCAACCATCT 58.386 47.619 0.00 0.00 0.00 2.90
5755 10697 3.244215 TGAAGATATCCCGAGCAACCATC 60.244 47.826 0.00 0.00 0.00 3.51
5756 10698 2.705658 TGAAGATATCCCGAGCAACCAT 59.294 45.455 0.00 0.00 0.00 3.55
5757 10699 2.115427 TGAAGATATCCCGAGCAACCA 58.885 47.619 0.00 0.00 0.00 3.67
5758 10700 2.872858 GTTGAAGATATCCCGAGCAACC 59.127 50.000 0.00 0.00 0.00 3.77
5759 10701 2.872858 GGTTGAAGATATCCCGAGCAAC 59.127 50.000 0.00 7.06 34.88 4.17
5760 10702 2.483013 CGGTTGAAGATATCCCGAGCAA 60.483 50.000 10.76 1.53 41.08 3.91
5761 10703 1.068588 CGGTTGAAGATATCCCGAGCA 59.931 52.381 10.76 0.00 41.08 4.26
5762 10704 1.605712 CCGGTTGAAGATATCCCGAGC 60.606 57.143 16.17 9.53 41.08 5.03
5763 10705 1.687123 ACCGGTTGAAGATATCCCGAG 59.313 52.381 16.17 10.10 41.08 4.63
5764 10706 1.784358 ACCGGTTGAAGATATCCCGA 58.216 50.000 16.17 0.00 41.08 5.14
5765 10707 2.612212 CAAACCGGTTGAAGATATCCCG 59.388 50.000 23.08 9.61 39.87 5.14
5766 10708 2.949644 CCAAACCGGTTGAAGATATCCC 59.050 50.000 23.08 0.00 39.87 3.85
5767 10709 3.881220 TCCAAACCGGTTGAAGATATCC 58.119 45.455 23.08 0.00 39.87 2.59
5768 10710 4.275936 CCATCCAAACCGGTTGAAGATATC 59.724 45.833 23.08 0.00 39.87 1.63
5769 10711 4.207165 CCATCCAAACCGGTTGAAGATAT 58.793 43.478 23.08 6.33 39.87 1.63
5770 10712 3.616219 CCATCCAAACCGGTTGAAGATA 58.384 45.455 23.08 4.03 39.87 1.98
5771 10713 2.446435 CCATCCAAACCGGTTGAAGAT 58.554 47.619 23.08 19.33 39.87 2.40
5772 10714 1.904287 CCATCCAAACCGGTTGAAGA 58.096 50.000 23.08 17.89 39.87 2.87
5773 10715 0.243636 GCCATCCAAACCGGTTGAAG 59.756 55.000 23.08 13.88 39.87 3.02
5774 10716 1.519751 CGCCATCCAAACCGGTTGAA 61.520 55.000 23.08 9.90 39.87 2.69
5775 10717 1.969064 CGCCATCCAAACCGGTTGA 60.969 57.895 23.08 15.50 39.87 3.18
5776 10718 2.566010 CGCCATCCAAACCGGTTG 59.434 61.111 23.08 14.70 36.94 3.77
5777 10719 2.675075 CCGCCATCCAAACCGGTT 60.675 61.111 15.86 15.86 36.18 4.44
5779 10721 3.131478 GACCGCCATCCAAACCGG 61.131 66.667 0.00 0.00 45.80 5.28
5780 10722 1.748879 ATGACCGCCATCCAAACCG 60.749 57.895 0.00 0.00 0.00 4.44
5781 10723 0.965363 ACATGACCGCCATCCAAACC 60.965 55.000 0.00 0.00 31.94 3.27
5782 10724 1.745232 TACATGACCGCCATCCAAAC 58.255 50.000 0.00 0.00 31.94 2.93
5783 10725 2.498644 TTACATGACCGCCATCCAAA 57.501 45.000 0.00 0.00 31.94 3.28
5784 10726 2.727123 ATTACATGACCGCCATCCAA 57.273 45.000 0.00 0.00 31.94 3.53
5785 10727 2.038426 CCTATTACATGACCGCCATCCA 59.962 50.000 0.00 0.00 31.94 3.41
5786 10728 2.301870 TCCTATTACATGACCGCCATCC 59.698 50.000 0.00 0.00 31.94 3.51
5787 10729 3.678056 TCCTATTACATGACCGCCATC 57.322 47.619 0.00 0.00 31.94 3.51
5788 10730 4.162320 CCTATCCTATTACATGACCGCCAT 59.838 45.833 0.00 0.00 35.44 4.40
5789 10731 3.513912 CCTATCCTATTACATGACCGCCA 59.486 47.826 0.00 0.00 0.00 5.69
5790 10732 3.679083 GCCTATCCTATTACATGACCGCC 60.679 52.174 0.00 0.00 0.00 6.13
5791 10733 3.056107 TGCCTATCCTATTACATGACCGC 60.056 47.826 0.00 0.00 0.00 5.68
5792 10734 4.801330 TGCCTATCCTATTACATGACCG 57.199 45.455 0.00 0.00 0.00 4.79
5793 10735 8.322091 ACTAATTGCCTATCCTATTACATGACC 58.678 37.037 0.00 0.00 0.00 4.02
5794 10736 9.726438 AACTAATTGCCTATCCTATTACATGAC 57.274 33.333 0.00 0.00 0.00 3.06
5810 10752 7.698506 AAAGAAGGTAGGTAAACTAATTGCC 57.301 36.000 0.00 0.00 43.60 4.52
5811 10753 8.396390 GCTAAAGAAGGTAGGTAAACTAATTGC 58.604 37.037 0.00 0.00 32.37 3.56
5812 10754 8.890718 GGCTAAAGAAGGTAGGTAAACTAATTG 58.109 37.037 0.00 0.00 32.37 2.32
5813 10755 8.608598 TGGCTAAAGAAGGTAGGTAAACTAATT 58.391 33.333 0.00 0.00 32.37 1.40
5814 10756 8.154420 TGGCTAAAGAAGGTAGGTAAACTAAT 57.846 34.615 0.00 0.00 32.37 1.73
5815 10757 7.557875 TGGCTAAAGAAGGTAGGTAAACTAA 57.442 36.000 0.00 0.00 32.37 2.24
5816 10758 6.351626 GCTGGCTAAAGAAGGTAGGTAAACTA 60.352 42.308 0.00 0.00 0.00 2.24
5817 10759 5.571047 GCTGGCTAAAGAAGGTAGGTAAACT 60.571 44.000 0.00 0.00 0.00 2.66
5818 10760 4.634883 GCTGGCTAAAGAAGGTAGGTAAAC 59.365 45.833 0.00 0.00 0.00 2.01
5819 10761 4.324022 GGCTGGCTAAAGAAGGTAGGTAAA 60.324 45.833 0.00 0.00 0.00 2.01
5820 10762 3.199289 GGCTGGCTAAAGAAGGTAGGTAA 59.801 47.826 0.00 0.00 0.00 2.85
5821 10763 2.770232 GGCTGGCTAAAGAAGGTAGGTA 59.230 50.000 0.00 0.00 0.00 3.08
5822 10764 1.560146 GGCTGGCTAAAGAAGGTAGGT 59.440 52.381 0.00 0.00 0.00 3.08
5823 10765 1.473434 CGGCTGGCTAAAGAAGGTAGG 60.473 57.143 0.00 0.00 0.00 3.18
5824 10766 1.473434 CCGGCTGGCTAAAGAAGGTAG 60.473 57.143 0.00 0.00 0.00 3.18
5825 10767 0.539986 CCGGCTGGCTAAAGAAGGTA 59.460 55.000 0.00 0.00 0.00 3.08
5826 10768 1.299976 CCGGCTGGCTAAAGAAGGT 59.700 57.895 0.00 0.00 0.00 3.50
5827 10769 0.322546 AACCGGCTGGCTAAAGAAGG 60.323 55.000 12.89 0.00 39.70 3.46
5828 10770 3.249687 AACCGGCTGGCTAAAGAAG 57.750 52.632 12.89 0.00 39.70 2.85


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

AutoCloner maintained by Alex Coulton.