Multiple sequence alignment - TraesCS2D01G236700

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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 TraesCS2D01G236700 chr2D 100.000 6290 0 0 1 6290 234324734 234331023 0.000000e+00 11616.0
1 TraesCS2D01G236700 chr2D 89.444 180 13 6 410 585 605119738 605119915 8.210000e-54 222.0
2 TraesCS2D01G236700 chr2D 94.382 89 4 1 3321 3408 307490086 307490174 1.100000e-27 135.0
3 TraesCS2D01G236700 chr2A 97.465 3195 37 14 864 4017 235678012 235674821 0.000000e+00 5411.0
4 TraesCS2D01G236700 chr2A 96.201 2027 32 8 4292 6290 235674509 235672500 0.000000e+00 3275.0
5 TraesCS2D01G236700 chr2A 90.060 664 55 4 56 718 235711311 235710658 0.000000e+00 850.0
6 TraesCS2D01G236700 chr2A 79.845 516 85 14 43 551 203532154 203532657 6.000000e-95 359.0
7 TraesCS2D01G236700 chr2A 98.013 151 3 0 4140 4290 235674823 235674673 4.840000e-66 263.0
8 TraesCS2D01G236700 chr2B 97.607 1421 28 4 1906 3322 283015282 283016700 0.000000e+00 2431.0
9 TraesCS2D01G236700 chr2B 96.972 1255 33 5 4140 5391 283017248 283018500 0.000000e+00 2102.0
10 TraesCS2D01G236700 chr2B 93.981 1080 24 10 847 1913 283013455 283014506 0.000000e+00 1596.0
11 TraesCS2D01G236700 chr2B 98.148 540 9 1 3479 4017 283016711 283017250 0.000000e+00 941.0
12 TraesCS2D01G236700 chr2B 85.561 651 63 14 34 659 282957769 282958413 0.000000e+00 652.0
13 TraesCS2D01G236700 chr2B 97.908 239 5 0 5447 5685 283018500 283018738 1.260000e-111 414.0
14 TraesCS2D01G236700 chr2B 96.774 155 5 0 702 856 283012175 283012329 6.260000e-65 259.0
15 TraesCS2D01G236700 chr2B 93.333 90 4 2 3321 3409 159893128 159893216 1.420000e-26 132.0
16 TraesCS2D01G236700 chr2B 93.333 75 5 0 4737 4811 283017764 283017838 1.850000e-20 111.0
17 TraesCS2D01G236700 chr3D 85.616 584 82 2 5708 6290 32585894 32585312 4.170000e-171 612.0
18 TraesCS2D01G236700 chr6D 84.091 616 66 20 1 585 342480770 342480156 3.290000e-157 566.0
19 TraesCS2D01G236700 chr6D 95.775 142 5 1 4003 4144 435990649 435990509 1.760000e-55 228.0
20 TraesCS2D01G236700 chr6D 95.683 139 5 1 4016 4154 246340309 246340172 8.210000e-54 222.0
21 TraesCS2D01G236700 chr6D 95.349 86 2 2 3321 3405 101231575 101231491 1.100000e-27 135.0
22 TraesCS2D01G236700 chr1D 84.375 576 57 13 1 551 371540758 371541325 9.280000e-148 534.0
23 TraesCS2D01G236700 chr1D 98.438 128 2 0 4015 4142 469018685 469018558 6.340000e-55 226.0
24 TraesCS2D01G236700 chr1D 92.647 68 4 1 3414 3480 50710644 50710577 5.190000e-16 97.1
25 TraesCS2D01G236700 chr5B 83.170 511 72 9 43 551 454678815 454678317 7.430000e-124 455.0
26 TraesCS2D01G236700 chr5B 93.878 147 6 3 4001 4145 431076680 431076535 1.060000e-52 219.0
27 TraesCS2D01G236700 chr5D 79.964 554 88 22 51 589 486559675 486559130 2.750000e-103 387.0
28 TraesCS2D01G236700 chr5A 79.762 504 76 21 88 578 584589856 584590346 6.040000e-90 342.0
29 TraesCS2D01G236700 chr5A 93.333 90 5 1 3321 3409 494867305 494867394 1.420000e-26 132.0
30 TraesCS2D01G236700 chr7B 78.261 552 89 23 51 587 454647744 454648279 6.080000e-85 326.0
31 TraesCS2D01G236700 chr7B 97.059 34 1 0 3409 3442 501138826 501138859 2.450000e-04 58.4
32 TraesCS2D01G236700 chr4B 98.485 132 1 1 4016 4146 499756134 499756003 1.360000e-56 231.0
33 TraesCS2D01G236700 chr4B 93.333 90 5 1 3318 3406 91298311 91298400 1.420000e-26 132.0
34 TraesCS2D01G236700 chr4A 94.079 152 5 4 4015 4165 729151841 729151989 1.760000e-55 228.0
35 TraesCS2D01G236700 chr6B 93.919 148 8 1 4009 4155 67527521 67527374 8.210000e-54 222.0
36 TraesCS2D01G236700 chr3B 95.683 139 5 1 4016 4154 726607542 726607405 8.210000e-54 222.0
37 TraesCS2D01G236700 chr3A 96.183 131 5 0 4012 4142 642715812 642715942 1.370000e-51 215.0
38 TraesCS2D01G236700 chr7A 93.684 95 4 2 3317 3410 184126736 184126829 2.360000e-29 141.0
39 TraesCS2D01G236700 chr7D 93.407 91 4 2 3316 3405 81911043 81910954 3.960000e-27 134.0
40 TraesCS2D01G236700 chr6A 93.333 90 4 2 3317 3405 121888019 121887931 1.420000e-26 132.0
41 TraesCS2D01G236700 chr4D 84.810 79 11 1 3414 3491 416427864 416427786 1.880000e-10 78.7
42 TraesCS2D01G236700 chr1B 83.077 65 6 4 3406 3469 612940133 612940193 3.000000e-03 54.7


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 TraesCS2D01G236700 chr2D 234324734 234331023 6289 False 11616 11616 100.000000 1 6290 1 chr2D.!!$F1 6289
1 TraesCS2D01G236700 chr2A 235672500 235678012 5512 True 2983 5411 97.226333 864 6290 3 chr2A.!!$R2 5426
2 TraesCS2D01G236700 chr2A 235710658 235711311 653 True 850 850 90.060000 56 718 1 chr2A.!!$R1 662
3 TraesCS2D01G236700 chr2A 203532154 203532657 503 False 359 359 79.845000 43 551 1 chr2A.!!$F1 508
4 TraesCS2D01G236700 chr2B 283012175 283018738 6563 False 1122 2431 96.389000 702 5685 7 chr2B.!!$F3 4983
5 TraesCS2D01G236700 chr2B 282957769 282958413 644 False 652 652 85.561000 34 659 1 chr2B.!!$F2 625
6 TraesCS2D01G236700 chr3D 32585312 32585894 582 True 612 612 85.616000 5708 6290 1 chr3D.!!$R1 582
7 TraesCS2D01G236700 chr6D 342480156 342480770 614 True 566 566 84.091000 1 585 1 chr6D.!!$R3 584
8 TraesCS2D01G236700 chr1D 371540758 371541325 567 False 534 534 84.375000 1 551 1 chr1D.!!$F1 550
9 TraesCS2D01G236700 chr5D 486559130 486559675 545 True 387 387 79.964000 51 589 1 chr5D.!!$R1 538
10 TraesCS2D01G236700 chr7B 454647744 454648279 535 False 326 326 78.261000 51 587 1 chr7B.!!$F1 536

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
857 913 0.035247 GCACCATACCCGTTTACCCA 60.035 55.0 0.0 0.0 0.00 4.51 F
859 915 0.620030 ACCATACCCGTTTACCCACC 59.380 55.0 0.0 0.0 0.00 4.61 F
940 2129 0.654683 GCAGCAGCGGAATTAGACTG 59.345 55.0 0.0 0.0 0.00 3.51 F
943 2132 0.924090 GCAGCGGAATTAGACTGACG 59.076 55.0 5.5 0.0 31.67 4.35 F
3334 5347 0.978907 TTTGTTACTCCCTCCGTCCC 59.021 55.0 0.0 0.0 0.00 4.46 F
4028 6071 0.614134 AGTTGGTACTCCCTCCGTCC 60.614 60.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 4288 6.471146 ACCTGATAATATTCTGCTCCATCAC 58.529 40.000 0.00 0.00 0.00 3.06 R
2864 4874 8.623903 TGAATAACAGAGCATGGAATAATTGAC 58.376 33.333 0.00 0.00 0.00 3.18 R
3074 5084 4.023279 ACACATGTTAATGCAATCACGTGT 60.023 37.500 16.51 7.91 39.14 4.49 R
3338 5351 9.310716 ACTTTAGTACAAAGTTGAGTCACTTAC 57.689 33.333 14.04 0.00 37.18 2.34 R
4538 6744 4.040461 AGACCACCTGGATTATAATGACCG 59.960 45.833 1.78 0.00 38.94 4.79 R
5829 8065 1.735571 CTGGCATGGAAAATTGCTTGC 59.264 47.619 14.40 14.40 44.87 4.01 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
39 44 2.156774 CCTTATGGGGAGGGGAGCC 61.157 68.421 0.00 0.00 0.00 4.70
373 397 4.192317 GGATCTTGAAGACCGTATGCTTT 58.808 43.478 0.00 0.00 0.00 3.51
425 472 0.880278 CCATTCGCGGGATCGTCATT 60.880 55.000 6.13 0.00 38.89 2.57
517 567 1.933853 CGATCGTTGATCCAAACCCTC 59.066 52.381 7.03 0.00 35.83 4.30
551 601 3.992943 ATTGTTCCTGGGTGATCGTAA 57.007 42.857 0.00 0.00 0.00 3.18
630 686 2.664568 TGAGTTGTTCATAGTTACGCGC 59.335 45.455 5.73 0.00 0.00 6.86
631 687 2.664568 GAGTTGTTCATAGTTACGCGCA 59.335 45.455 5.73 0.00 0.00 6.09
636 692 5.037015 TGTTCATAGTTACGCGCAAAAAT 57.963 34.783 5.73 2.14 0.00 1.82
653 709 8.907685 GCGCAAAAATGTCTAGTTATTGTTTTA 58.092 29.630 0.30 0.00 0.00 1.52
722 778 8.262227 ACATGCATTTAAATCAGAACAATCCAT 58.738 29.630 0.00 0.00 0.00 3.41
735 791 1.672881 CAATCCATTTCCGAGCTGTCC 59.327 52.381 0.00 0.00 0.00 4.02
754 810 3.147595 TCCCAGTCTCCATCGCCG 61.148 66.667 0.00 0.00 0.00 6.46
762 818 3.214250 CTCCATCGCCGGTAGGAGC 62.214 68.421 16.73 0.00 40.98 4.70
856 912 1.091197 CGCACCATACCCGTTTACCC 61.091 60.000 0.00 0.00 0.00 3.69
857 913 0.035247 GCACCATACCCGTTTACCCA 60.035 55.000 0.00 0.00 0.00 4.51
858 914 1.741528 CACCATACCCGTTTACCCAC 58.258 55.000 0.00 0.00 0.00 4.61
859 915 0.620030 ACCATACCCGTTTACCCACC 59.380 55.000 0.00 0.00 0.00 4.61
924 2113 3.456798 CGAGAGCAAGACACGCAG 58.543 61.111 0.00 0.00 0.00 5.18
925 2114 2.724708 CGAGAGCAAGACACGCAGC 61.725 63.158 0.00 0.00 0.00 5.25
926 2115 1.665916 GAGAGCAAGACACGCAGCA 60.666 57.895 0.00 0.00 0.00 4.41
927 2116 1.624865 GAGAGCAAGACACGCAGCAG 61.625 60.000 0.00 0.00 0.00 4.24
928 2117 3.306134 GAGCAAGACACGCAGCAGC 62.306 63.158 0.00 0.00 37.42 5.25
939 2128 3.071580 GCAGCAGCGGAATTAGACT 57.928 52.632 0.00 0.00 0.00 3.24
940 2129 0.654683 GCAGCAGCGGAATTAGACTG 59.345 55.000 0.00 0.00 0.00 3.51
941 2130 1.740380 GCAGCAGCGGAATTAGACTGA 60.740 52.381 0.00 0.00 31.67 3.41
942 2131 1.929836 CAGCAGCGGAATTAGACTGAC 59.070 52.381 5.50 0.00 31.67 3.51
943 2132 0.924090 GCAGCGGAATTAGACTGACG 59.076 55.000 5.50 0.00 31.67 4.35
944 2133 1.469251 GCAGCGGAATTAGACTGACGA 60.469 52.381 5.50 0.00 31.67 4.20
945 2134 2.455032 CAGCGGAATTAGACTGACGAG 58.545 52.381 0.00 0.00 31.67 4.18
946 2135 1.201343 GCGGAATTAGACTGACGAGC 58.799 55.000 0.00 0.00 0.00 5.03
947 2136 1.841450 CGGAATTAGACTGACGAGCC 58.159 55.000 0.00 0.00 0.00 4.70
948 2137 1.536284 CGGAATTAGACTGACGAGCCC 60.536 57.143 0.00 0.00 0.00 5.19
971 2184 2.282180 GCCAAGCCAAGGGAACGA 60.282 61.111 0.00 0.00 0.00 3.85
1819 3045 3.181451 TGCTGTTGTTCTGTCCTTCTCAT 60.181 43.478 0.00 0.00 0.00 2.90
1841 3067 9.258826 CTCATCGATTCATTAGTTTTCATCTCT 57.741 33.333 0.00 0.00 0.00 3.10
2155 4164 7.144722 TGATTGATTAGGACACATGTTCAAC 57.855 36.000 8.60 5.08 0.00 3.18
2278 4288 1.081892 CATGACTCAACTGAAGGGCG 58.918 55.000 0.00 0.00 0.00 6.13
3074 5084 5.880332 AGACTGCTGTAAAACTGAAACTTGA 59.120 36.000 0.00 0.00 0.00 3.02
3190 5200 6.641474 TGTATTGTCCACCATATTTGTACGA 58.359 36.000 0.00 0.00 0.00 3.43
3235 5245 5.733620 ATGTGCTTGGTTCATTCTTTGAT 57.266 34.783 0.00 0.00 33.34 2.57
3334 5347 0.978907 TTTGTTACTCCCTCCGTCCC 59.021 55.000 0.00 0.00 0.00 4.46
3407 5432 1.961133 TTGGGACGGAGGGAGTATTT 58.039 50.000 0.00 0.00 0.00 1.40
3408 5433 2.852714 TGGGACGGAGGGAGTATTTA 57.147 50.000 0.00 0.00 0.00 1.40
3409 5434 3.119009 TGGGACGGAGGGAGTATTTAA 57.881 47.619 0.00 0.00 0.00 1.52
3410 5435 2.767960 TGGGACGGAGGGAGTATTTAAC 59.232 50.000 0.00 0.00 0.00 2.01
3569 5611 2.054453 GGAATCCCCAGCTGCAACC 61.054 63.158 8.66 1.66 34.14 3.77
4017 6060 7.277319 GCTTGTACTATGTCCTTTAGTTGGTAC 59.723 40.741 0.00 0.00 32.35 3.34
4018 6061 8.426569 TTGTACTATGTCCTTTAGTTGGTACT 57.573 34.615 0.00 0.00 38.44 2.73
4019 6062 8.059798 TGTACTATGTCCTTTAGTTGGTACTC 57.940 38.462 0.00 0.00 35.78 2.59
4020 6063 6.541934 ACTATGTCCTTTAGTTGGTACTCC 57.458 41.667 0.00 0.00 35.78 3.85
4021 6064 4.838904 ATGTCCTTTAGTTGGTACTCCC 57.161 45.455 0.00 0.00 35.78 4.30
4022 6065 3.865571 TGTCCTTTAGTTGGTACTCCCT 58.134 45.455 0.00 0.00 35.78 4.20
4023 6066 3.836562 TGTCCTTTAGTTGGTACTCCCTC 59.163 47.826 0.00 0.00 35.78 4.30
4024 6067 3.197333 GTCCTTTAGTTGGTACTCCCTCC 59.803 52.174 0.00 0.00 35.78 4.30
4025 6068 2.167900 CCTTTAGTTGGTACTCCCTCCG 59.832 54.545 0.00 0.00 35.78 4.63
4026 6069 2.610438 TTAGTTGGTACTCCCTCCGT 57.390 50.000 0.00 0.00 35.78 4.69
4027 6070 2.134789 TAGTTGGTACTCCCTCCGTC 57.865 55.000 0.00 0.00 35.78 4.79
4028 6071 0.614134 AGTTGGTACTCCCTCCGTCC 60.614 60.000 0.00 0.00 0.00 4.79
4029 6072 1.305549 TTGGTACTCCCTCCGTCCC 60.306 63.158 0.00 0.00 0.00 4.46
4030 6073 2.096707 TTGGTACTCCCTCCGTCCCA 62.097 60.000 0.00 0.00 0.00 4.37
4031 6074 1.305549 GGTACTCCCTCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
4032 6075 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
4033 6076 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
4034 6077 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4035 6078 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4036 6079 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4037 6080 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4038 6081 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4039 6082 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
4040 6083 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
4041 6084 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
4042 6085 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
4043 6086 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
4044 6087 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
4045 6088 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
4046 6089 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
4047 6090 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
4048 6091 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
4049 6092 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4050 6093 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
4051 6094 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
4052 6095 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
4053 6096 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
4061 6104 9.137459 TCTTGTCTTAGATTTGTCTAGATAGGG 57.863 37.037 0.00 0.00 0.00 3.53
4062 6105 9.137459 CTTGTCTTAGATTTGTCTAGATAGGGA 57.863 37.037 0.00 0.00 0.00 4.20
4063 6106 9.661954 TTGTCTTAGATTTGTCTAGATAGGGAT 57.338 33.333 0.00 0.00 0.00 3.85
4064 6107 9.083422 TGTCTTAGATTTGTCTAGATAGGGATG 57.917 37.037 0.00 0.00 0.00 3.51
4065 6108 9.084533 GTCTTAGATTTGTCTAGATAGGGATGT 57.915 37.037 0.00 0.00 0.00 3.06
4097 6140 7.539712 ACTAAAATGTGACTTGATACATCCG 57.460 36.000 0.00 0.00 36.56 4.18
4098 6141 7.103641 ACTAAAATGTGACTTGATACATCCGT 58.896 34.615 0.00 0.00 36.56 4.69
4099 6142 8.255206 ACTAAAATGTGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 36.56 4.02
4100 6143 9.261180 CTAAAATGTGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
4116 6159 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
4117 6160 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
4118 6161 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
4119 6162 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
4120 6163 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
4121 6164 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
4129 6172 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
4130 6173 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4131 6174 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
4132 6175 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
4133 6176 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
4134 6177 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
4135 6178 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
4136 6179 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
4137 6180 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
4138 6181 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4139 6182 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4140 6183 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
4141 6184 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4156 6199 8.437575 ACGGAGGGAGTATTTAATTAATGTGAT 58.562 33.333 0.00 0.00 0.00 3.06
4193 6236 9.612620 GACAATGTCAACTAAAGTTATCCTTTG 57.387 33.333 8.74 4.57 36.96 2.77
4538 6744 6.363357 GTCTTTGGTCTGTGTCATATTTTTGC 59.637 38.462 0.00 0.00 0.00 3.68
5327 7534 7.724287 ACTCGTACTAGTAGATATCACACTCA 58.276 38.462 11.94 0.00 0.00 3.41
5796 8032 5.130477 AGGCGGAGGTAAAGAATATCTTCAA 59.870 40.000 0.00 0.00 35.27 2.69
5826 8062 6.981762 TTTTAATGCCATCATTGCGATTTT 57.018 29.167 1.17 0.00 42.50 1.82
5829 8065 3.153676 TGCCATCATTGCGATTTTCAG 57.846 42.857 0.00 0.00 29.21 3.02
5851 8087 3.869065 CAAGCAATTTTCCATGCCAGAT 58.131 40.909 0.00 0.00 43.57 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.993509 TTGGCTCCCCTCCCCATAAG 60.994 60.000 0.00 0.00 0.00 1.73
24 25 0.772124 GATTGGCTCCCCTCCCCATA 60.772 60.000 0.00 0.00 0.00 2.74
25 26 2.046855 ATTGGCTCCCCTCCCCAT 59.953 61.111 0.00 0.00 0.00 4.00
27 28 2.638025 TAGGATTGGCTCCCCTCCCC 62.638 65.000 0.00 0.00 46.27 4.81
29 30 0.400670 ACTAGGATTGGCTCCCCTCC 60.401 60.000 0.00 0.00 46.27 4.30
31 32 0.695803 CCACTAGGATTGGCTCCCCT 60.696 60.000 0.00 0.00 46.27 4.79
36 41 0.695803 CTCCCCCACTAGGATTGGCT 60.696 60.000 0.00 0.00 38.24 4.75
39 44 1.344496 ACTCCTCCCCCACTAGGATTG 60.344 57.143 0.00 0.00 41.06 2.67
373 397 4.284490 AGCACAATCTCTCTACTTGGTTGA 59.716 41.667 0.00 0.00 0.00 3.18
425 472 0.251297 TGGAGTCCCTCGAACCGTTA 60.251 55.000 6.74 0.00 0.00 3.18
517 567 6.150641 CCCAGGAACAATATGAAGATGCATAG 59.849 42.308 0.00 0.00 34.50 2.23
711 767 3.012518 CAGCTCGGAAATGGATTGTTCT 58.987 45.455 0.00 0.00 0.00 3.01
722 778 2.654877 GGACGGACAGCTCGGAAA 59.345 61.111 0.00 0.00 0.00 3.13
735 791 2.105128 GCGATGGAGACTGGGACG 59.895 66.667 0.00 0.00 0.00 4.79
754 810 1.028868 ACGTACTCGGTGCTCCTACC 61.029 60.000 2.85 0.00 41.85 3.18
762 818 1.061799 GTACACGCACGTACTCGGTG 61.062 60.000 0.00 5.77 38.96 4.94
856 912 2.758009 TCGTTCGTAAGGAAAAGGGTG 58.242 47.619 0.00 0.00 36.14 4.61
857 913 3.473923 TTCGTTCGTAAGGAAAAGGGT 57.526 42.857 0.00 0.00 36.14 4.34
858 914 3.811497 AGTTTCGTTCGTAAGGAAAAGGG 59.189 43.478 13.26 0.00 44.04 3.95
859 915 4.769215 CAGTTTCGTTCGTAAGGAAAAGG 58.231 43.478 13.26 7.90 44.04 3.11
923 2112 1.469940 CGTCAGTCTAATTCCGCTGCT 60.470 52.381 0.00 0.00 0.00 4.24
924 2113 0.924090 CGTCAGTCTAATTCCGCTGC 59.076 55.000 0.00 0.00 0.00 5.25
925 2114 2.455032 CTCGTCAGTCTAATTCCGCTG 58.545 52.381 0.00 0.00 0.00 5.18
926 2115 1.202313 GCTCGTCAGTCTAATTCCGCT 60.202 52.381 0.00 0.00 0.00 5.52
927 2116 1.201343 GCTCGTCAGTCTAATTCCGC 58.799 55.000 0.00 0.00 0.00 5.54
928 2117 1.536284 GGGCTCGTCAGTCTAATTCCG 60.536 57.143 0.00 0.00 0.00 4.30
929 2118 1.202545 GGGGCTCGTCAGTCTAATTCC 60.203 57.143 0.00 0.00 0.00 3.01
930 2119 1.480954 TGGGGCTCGTCAGTCTAATTC 59.519 52.381 0.00 0.00 0.00 2.17
931 2120 1.482593 CTGGGGCTCGTCAGTCTAATT 59.517 52.381 0.00 0.00 0.00 1.40
932 2121 1.115467 CTGGGGCTCGTCAGTCTAAT 58.885 55.000 0.00 0.00 0.00 1.73
933 2122 0.039180 TCTGGGGCTCGTCAGTCTAA 59.961 55.000 0.00 0.00 33.13 2.10
934 2123 0.039180 TTCTGGGGCTCGTCAGTCTA 59.961 55.000 0.00 0.00 33.13 2.59
935 2124 1.228894 TTCTGGGGCTCGTCAGTCT 60.229 57.895 0.00 0.00 33.13 3.24
936 2125 1.216710 CTTCTGGGGCTCGTCAGTC 59.783 63.158 0.00 0.00 33.13 3.51
937 2126 2.948720 GCTTCTGGGGCTCGTCAGT 61.949 63.158 0.00 0.00 33.13 3.41
938 2127 2.125350 GCTTCTGGGGCTCGTCAG 60.125 66.667 0.00 0.00 0.00 3.51
939 2128 3.706373 GGCTTCTGGGGCTCGTCA 61.706 66.667 0.00 0.00 0.00 4.35
940 2129 3.254024 TTGGCTTCTGGGGCTCGTC 62.254 63.158 0.00 0.00 0.00 4.20
941 2130 3.249189 TTGGCTTCTGGGGCTCGT 61.249 61.111 0.00 0.00 0.00 4.18
942 2131 2.437359 CTTGGCTTCTGGGGCTCG 60.437 66.667 0.00 0.00 0.00 5.03
943 2132 2.753446 GCTTGGCTTCTGGGGCTC 60.753 66.667 0.00 0.00 0.00 4.70
944 2133 4.372999 GGCTTGGCTTCTGGGGCT 62.373 66.667 0.00 0.00 0.00 5.19
945 2134 4.684134 TGGCTTGGCTTCTGGGGC 62.684 66.667 0.00 0.00 0.00 5.80
946 2135 1.980772 CTTGGCTTGGCTTCTGGGG 60.981 63.158 0.00 0.00 0.00 4.96
947 2136 1.980772 CCTTGGCTTGGCTTCTGGG 60.981 63.158 0.00 0.00 0.00 4.45
948 2137 1.980772 CCCTTGGCTTGGCTTCTGG 60.981 63.158 0.00 0.00 0.00 3.86
1458 2680 3.069289 ACGAATTCGGACTAAACCCAAC 58.931 45.455 29.79 0.00 44.95 3.77
1819 3045 7.331026 ACCAGAGATGAAAACTAATGAATCGA 58.669 34.615 0.00 0.00 0.00 3.59
2278 4288 6.471146 ACCTGATAATATTCTGCTCCATCAC 58.529 40.000 0.00 0.00 0.00 3.06
2864 4874 8.623903 TGAATAACAGAGCATGGAATAATTGAC 58.376 33.333 0.00 0.00 0.00 3.18
3074 5084 4.023279 ACACATGTTAATGCAATCACGTGT 60.023 37.500 16.51 7.91 39.14 4.49
3338 5351 9.310716 ACTTTAGTACAAAGTTGAGTCACTTAC 57.689 33.333 14.04 0.00 37.18 2.34
3342 5355 9.310716 ACTAACTTTAGTACAAAGTTGAGTCAC 57.689 33.333 27.85 0.00 46.41 3.67
3569 5611 2.667536 ACAAGAGCACGCCAGCAG 60.668 61.111 0.00 0.00 36.85 4.24
3696 5738 4.334759 CAGACTACCAATGATGCCAGAAAG 59.665 45.833 0.00 0.00 0.00 2.62
3844 5886 2.125673 CCAGCACGGGGAAGTACG 60.126 66.667 0.00 0.00 0.00 3.67
4017 6060 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4018 6061 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4019 6062 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
4020 6063 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
4021 6064 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
4022 6065 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
4023 6066 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
4024 6067 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
4025 6068 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
4026 6069 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4027 6070 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
4035 6078 9.137459 CCCTATCTAGACAAATCTAAGACAAGA 57.863 37.037 0.00 0.00 36.98 3.02
4036 6079 9.137459 TCCCTATCTAGACAAATCTAAGACAAG 57.863 37.037 0.00 0.00 36.98 3.16
4037 6080 9.661954 ATCCCTATCTAGACAAATCTAAGACAA 57.338 33.333 0.00 0.00 36.98 3.18
4038 6081 9.083422 CATCCCTATCTAGACAAATCTAAGACA 57.917 37.037 0.00 0.00 36.98 3.41
4039 6082 9.084533 ACATCCCTATCTAGACAAATCTAAGAC 57.915 37.037 0.00 0.00 36.98 3.01
4071 6114 9.261180 CGGATGTATCAAGTCACATTTTAGTAT 57.739 33.333 0.00 0.00 35.55 2.12
4072 6115 8.255206 ACGGATGTATCAAGTCACATTTTAGTA 58.745 33.333 0.00 0.00 35.55 1.82
4073 6116 7.103641 ACGGATGTATCAAGTCACATTTTAGT 58.896 34.615 0.00 0.00 35.55 2.24
4074 6117 7.539712 ACGGATGTATCAAGTCACATTTTAG 57.460 36.000 0.00 0.00 35.55 1.85
4090 6133 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
4091 6134 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
4092 6135 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
4093 6136 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
4094 6137 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
4095 6138 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
4103 6146 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
4104 6147 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
4105 6148 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
4106 6149 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
4107 6150 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4108 6151 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
4109 6152 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
4110 6153 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
4111 6154 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
4112 6155 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
4113 6156 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
4114 6157 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
4115 6158 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
4116 6159 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
4117 6160 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
4118 6161 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4119 6162 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4120 6163 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4121 6164 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4122 6165 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4123 6166 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4124 6167 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
4125 6168 1.961133 AAATACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
4126 6169 2.852714 TAAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
4127 6170 4.701651 AATTAAATACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
4128 6171 7.172703 CACATTAATTAAATACTCCCTCCGTCC 59.827 40.741 1.21 0.00 0.00 4.79
4129 6172 7.929785 TCACATTAATTAAATACTCCCTCCGTC 59.070 37.037 1.21 0.00 0.00 4.79
4130 6173 7.798071 TCACATTAATTAAATACTCCCTCCGT 58.202 34.615 1.21 0.00 0.00 4.69
4131 6174 8.848474 ATCACATTAATTAAATACTCCCTCCG 57.152 34.615 1.21 0.00 0.00 4.63
4156 6199 5.674525 AGTTGACATTGTCTTTCACTCAGA 58.325 37.500 17.26 0.00 33.15 3.27
4193 6236 5.067805 CCATAAAATGTCCTACTTCTTGGGC 59.932 44.000 0.00 0.00 0.00 5.36
4538 6744 4.040461 AGACCACCTGGATTATAATGACCG 59.960 45.833 1.78 0.00 38.94 4.79
4595 6801 4.320861 CCAACCATTTCGTGCAGTTTATGA 60.321 41.667 0.00 0.00 0.00 2.15
4827 7033 7.455641 TTTTTCTCATTATCTGCGGGTTTAA 57.544 32.000 0.00 0.00 0.00 1.52
5327 7534 5.105310 ACAATCGCAGACTAAAGACTACCAT 60.105 40.000 0.00 0.00 42.51 3.55
5416 7624 4.398044 CAGATACACGTTGCCCCTTTTATT 59.602 41.667 0.00 0.00 0.00 1.40
5796 8032 7.280428 TCGCAATGATGGCATTAAAATTGATTT 59.720 29.630 20.69 0.00 42.66 2.17
5826 8062 2.613474 GGCATGGAAAATTGCTTGCTGA 60.613 45.455 19.55 0.00 44.93 4.26
5829 8065 1.735571 CTGGCATGGAAAATTGCTTGC 59.264 47.619 14.40 14.40 44.87 4.01
5899 8136 2.245159 TGTGTGAGGAAGCTTGTCTG 57.755 50.000 2.10 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.