Multiple sequence alignment - TraesCS4A01G183400

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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 TraesCS4A01G183400 chr4A 100.000 7498 0 0 1 7498 460896370 460903867 0.000000e+00 13847.0
1 TraesCS4A01G183400 chr4A 88.332 1337 132 10 4061 5395 359894177 359895491 0.000000e+00 1583.0
2 TraesCS4A01G183400 chr4A 86.235 247 15 9 3959 4205 666478191 666478418 4.490000e-62 250.0
3 TraesCS4A01G183400 chr4D 95.435 7557 171 75 1 7498 115940743 115933302 0.000000e+00 11884.0
4 TraesCS4A01G183400 chr4B 93.893 7205 214 97 1 7098 176259324 176266409 0.000000e+00 10659.0
5 TraesCS4A01G183400 chr4B 95.500 400 10 3 7097 7496 176266570 176266961 3.820000e-177 632.0
6 TraesCS4A01G183400 chr2B 93.728 1116 61 4 4143 5257 637454265 637453158 0.000000e+00 1664.0
7 TraesCS4A01G183400 chr2B 90.659 728 41 11 3959 4686 615568610 615567910 0.000000e+00 942.0
8 TraesCS4A01G183400 chr2B 92.374 577 43 1 4682 5257 615558840 615558264 0.000000e+00 821.0
9 TraesCS4A01G183400 chr2B 85.000 200 11 8 3959 4158 637456786 637456606 1.280000e-42 185.0
10 TraesCS4A01G183400 chr6D 92.224 643 45 3 4654 5296 429405238 429404601 0.000000e+00 905.0
11 TraesCS4A01G183400 chr2D 88.102 353 18 12 4823 5174 582155554 582155225 1.520000e-106 398.0
12 TraesCS4A01G183400 chr7B 92.683 82 6 0 4630 4711 156919399 156919318 1.320000e-22 119.0
13 TraesCS4A01G183400 chr5B 96.825 63 2 0 4298 4360 533442047 533441985 1.030000e-18 106.0
14 TraesCS4A01G183400 chr3A 95.238 63 3 0 4632 4694 157997652 157997590 4.790000e-17 100.0
15 TraesCS4A01G183400 chr3A 97.222 36 1 0 1538 1573 623053203 623053168 2.260000e-05 62.1
16 TraesCS4A01G183400 chr1D 95.238 63 3 0 4298 4360 4550588 4550526 4.790000e-17 100.0
17 TraesCS4A01G183400 chr1D 97.619 42 1 0 4574 4615 484187322 484187363 1.040000e-08 73.1
18 TraesCS4A01G183400 chr1D 100.000 28 0 0 2910 2937 494143074 494143101 1.400000e-02 52.8
19 TraesCS4A01G183400 chr3B 93.651 63 4 0 4298 4360 751098190 751098128 2.230000e-15 95.3
20 TraesCS4A01G183400 chr3B 93.182 44 2 1 1531 1573 640067439 640067396 6.280000e-06 63.9
21 TraesCS4A01G183400 chr3D 97.619 42 1 0 4574 4615 33322996 33323037 1.040000e-08 73.1
22 TraesCS4A01G183400 chr3D 91.667 48 3 1 1527 1573 479619473 479619426 1.750000e-06 65.8
23 TraesCS4A01G183400 chr2A 100.000 28 0 0 2905 2932 770410565 770410538 1.400000e-02 52.8


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 TraesCS4A01G183400 chr4A 460896370 460903867 7497 False 13847.0 13847 100.0000 1 7498 1 chr4A.!!$F2 7497
1 TraesCS4A01G183400 chr4A 359894177 359895491 1314 False 1583.0 1583 88.3320 4061 5395 1 chr4A.!!$F1 1334
2 TraesCS4A01G183400 chr4D 115933302 115940743 7441 True 11884.0 11884 95.4350 1 7498 1 chr4D.!!$R1 7497
3 TraesCS4A01G183400 chr4B 176259324 176266961 7637 False 5645.5 10659 94.6965 1 7496 2 chr4B.!!$F1 7495
4 TraesCS4A01G183400 chr2B 615567910 615568610 700 True 942.0 942 90.6590 3959 4686 1 chr2B.!!$R2 727
5 TraesCS4A01G183400 chr2B 637453158 637456786 3628 True 924.5 1664 89.3640 3959 5257 2 chr2B.!!$R3 1298
6 TraesCS4A01G183400 chr2B 615558264 615558840 576 True 821.0 821 92.3740 4682 5257 1 chr2B.!!$R1 575
7 TraesCS4A01G183400 chr6D 429404601 429405238 637 True 905.0 905 92.2240 4654 5296 1 chr6D.!!$R1 642

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
57 58 0.165079 CGCGCGATTGGTTAAGTTGT 59.835 50.000 28.94 0.00 0.00 3.32 F
1380 1428 0.102481 CTTCATGCTTCATGCCTGCC 59.898 55.000 2.12 0.00 41.18 4.85 F
2579 2699 0.745486 CGGATCATCACCAGCAGCAA 60.745 55.000 0.00 0.00 0.00 3.91 F
2585 2705 0.824595 ATCACCAGCAGCAACAGCAA 60.825 50.000 0.00 0.00 0.00 3.91 F
3192 3325 1.138036 CACTGCCATTGGTGATGCG 59.862 57.895 4.26 0.00 35.69 4.73 F
4496 7004 1.860240 ACCCCAGTATCAGCTCTCCTA 59.140 52.381 0.00 0.00 0.00 2.94 F
5271 7792 1.227205 CTCTCGGCAAGCTGGCTAG 60.227 63.158 14.08 11.14 41.25 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1996 1.015609 TGGTCCATGGGGTAGAGAGA 58.984 55.000 13.02 0.00 34.93 3.10 R
2585 2705 0.254178 CTACCATCCCTTGCTGCTGT 59.746 55.000 0.00 0.00 0.00 4.40 R
3667 3805 2.094545 GGAAGAACAATGTGTCCATGGC 60.095 50.000 6.96 2.72 0.00 4.40 R
4515 7023 2.166907 AACCAAATTCCCACCACACA 57.833 45.000 0.00 0.00 0.00 3.72 R
4516 7024 3.892588 TCTTAACCAAATTCCCACCACAC 59.107 43.478 0.00 0.00 0.00 3.82 R
6086 8610 1.062428 AGGAGGGTGGTCGATTCCATA 60.062 52.381 0.00 0.00 39.81 2.74 R
7076 9616 1.893801 AGGTACTAGCGTGCTTGAACT 59.106 47.619 10.19 2.65 36.02 3.01 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
57 58 0.165079 CGCGCGATTGGTTAAGTTGT 59.835 50.000 28.94 0.00 0.00 3.32
58 59 1.390803 CGCGCGATTGGTTAAGTTGTA 59.609 47.619 28.94 0.00 0.00 2.41
93 94 2.696707 AGACGGTGTCAAGGTCTAAACA 59.303 45.455 5.47 0.00 39.14 2.83
119 120 2.377628 TAAGATGGTCATCGCCCGCC 62.378 60.000 5.43 0.00 42.48 6.13
170 171 6.650390 ACAAAGCACAAATTTTCTTCAACAGT 59.350 30.769 0.00 0.00 0.00 3.55
171 172 6.651755 AAGCACAAATTTTCTTCAACAGTG 57.348 33.333 0.00 0.00 0.00 3.66
264 282 1.688772 CCTTTGGAGCATGGATGGAG 58.311 55.000 0.00 0.00 0.00 3.86
267 285 3.359033 CTTTGGAGCATGGATGGAGAAA 58.641 45.455 0.00 0.00 0.00 2.52
271 289 3.212685 GGAGCATGGATGGAGAAAAGAG 58.787 50.000 0.00 0.00 0.00 2.85
272 290 3.118112 GGAGCATGGATGGAGAAAAGAGA 60.118 47.826 0.00 0.00 0.00 3.10
273 291 4.521146 GAGCATGGATGGAGAAAAGAGAA 58.479 43.478 0.00 0.00 0.00 2.87
274 292 4.525024 AGCATGGATGGAGAAAAGAGAAG 58.475 43.478 0.00 0.00 0.00 2.85
291 309 0.980423 AAGAGAGAAGGGCTGGACAC 59.020 55.000 0.00 0.00 0.00 3.67
392 410 0.396974 CAGTCAGGGAGAGGGAGAGG 60.397 65.000 0.00 0.00 0.00 3.69
393 411 1.075600 GTCAGGGAGAGGGAGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
394 412 1.230650 TCAGGGAGAGGGAGAGGGA 60.231 63.158 0.00 0.00 0.00 4.20
395 413 1.232792 CAGGGAGAGGGAGAGGGAG 59.767 68.421 0.00 0.00 0.00 4.30
396 414 1.087725 AGGGAGAGGGAGAGGGAGA 59.912 63.158 0.00 0.00 0.00 3.71
397 415 0.998945 AGGGAGAGGGAGAGGGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
625 657 2.644992 CCACAAGGCAGGCGAAAC 59.355 61.111 0.00 0.00 0.00 2.78
630 662 0.886490 CAAGGCAGGCGAAACAGAGT 60.886 55.000 0.00 0.00 0.00 3.24
862 894 6.721704 TGCTGAGGTAGATATATAGGCATG 57.278 41.667 0.00 0.00 0.00 4.06
863 895 5.600069 TGCTGAGGTAGATATATAGGCATGG 59.400 44.000 0.00 0.00 0.00 3.66
1023 1055 2.033141 GAGGCCAGCAGCAGTTCA 59.967 61.111 5.01 0.00 46.50 3.18
1044 1076 3.402681 CATCCGAGGCACAGGGGT 61.403 66.667 0.00 0.00 0.00 4.95
1154 1186 0.390472 GAGCAACCTCTTCTGTCCCG 60.390 60.000 0.00 0.00 35.16 5.14
1155 1187 1.122019 AGCAACCTCTTCTGTCCCGT 61.122 55.000 0.00 0.00 0.00 5.28
1177 1209 3.009695 TCTCTCTCTCCCTCTTTCTCGTT 59.990 47.826 0.00 0.00 0.00 3.85
1249 1296 6.385843 TGGAAAACAATAACCATGATGAACG 58.614 36.000 0.00 0.00 0.00 3.95
1340 1388 3.242739 GCGTATTGCCTTGTATGGAGTTG 60.243 47.826 0.00 0.00 37.76 3.16
1377 1425 2.753452 CTGTTCTTCATGCTTCATGCCT 59.247 45.455 2.12 0.00 41.18 4.75
1378 1426 2.490509 TGTTCTTCATGCTTCATGCCTG 59.509 45.455 2.12 0.00 41.18 4.85
1379 1427 1.100510 TCTTCATGCTTCATGCCTGC 58.899 50.000 2.12 0.00 41.18 4.85
1380 1428 0.102481 CTTCATGCTTCATGCCTGCC 59.898 55.000 2.12 0.00 41.18 4.85
1481 1544 3.638160 GGTGATGGCAATGTAATGGTGAT 59.362 43.478 0.00 0.00 0.00 3.06
1482 1545 4.500205 GGTGATGGCAATGTAATGGTGATG 60.500 45.833 0.00 0.00 0.00 3.07
1483 1546 4.338964 GTGATGGCAATGTAATGGTGATGA 59.661 41.667 0.00 0.00 0.00 2.92
1528 1591 2.896443 CAAGACGGAGGAGGAGGC 59.104 66.667 0.00 0.00 0.00 4.70
1529 1592 1.984570 CAAGACGGAGGAGGAGGCA 60.985 63.158 0.00 0.00 0.00 4.75
1530 1593 1.684049 AAGACGGAGGAGGAGGCAG 60.684 63.158 0.00 0.00 0.00 4.85
1531 1594 3.844090 GACGGAGGAGGAGGCAGC 61.844 72.222 0.00 0.00 0.00 5.25
1671 1743 0.961753 TCCACGGATCATCCTCATCG 59.038 55.000 1.10 0.00 33.30 3.84
1732 1804 2.029623 ACGTACACACAACACCTCTCT 58.970 47.619 0.00 0.00 0.00 3.10
1733 1805 2.034305 ACGTACACACAACACCTCTCTC 59.966 50.000 0.00 0.00 0.00 3.20
1734 1806 2.293677 CGTACACACAACACCTCTCTCT 59.706 50.000 0.00 0.00 0.00 3.10
1735 1807 3.609644 CGTACACACAACACCTCTCTCTC 60.610 52.174 0.00 0.00 0.00 3.20
1881 1974 2.090760 TGTGTGTGTGTTGCTTGTGAT 58.909 42.857 0.00 0.00 0.00 3.06
1882 1975 3.274288 TGTGTGTGTGTTGCTTGTGATA 58.726 40.909 0.00 0.00 0.00 2.15
1895 1988 3.181470 GCTTGTGATACCCTTCTCTCTCC 60.181 52.174 0.00 0.00 0.00 3.71
1896 1989 3.033659 TGTGATACCCTTCTCTCTCCC 57.966 52.381 0.00 0.00 0.00 4.30
1897 1990 2.587777 TGTGATACCCTTCTCTCTCCCT 59.412 50.000 0.00 0.00 0.00 4.20
1898 1991 3.227614 GTGATACCCTTCTCTCTCCCTC 58.772 54.545 0.00 0.00 0.00 4.30
1899 1992 3.117284 GTGATACCCTTCTCTCTCCCTCT 60.117 52.174 0.00 0.00 0.00 3.69
1900 1993 3.139397 TGATACCCTTCTCTCTCCCTCTC 59.861 52.174 0.00 0.00 0.00 3.20
1901 1994 1.693799 ACCCTTCTCTCTCCCTCTCT 58.306 55.000 0.00 0.00 0.00 3.10
1902 1995 1.569072 ACCCTTCTCTCTCCCTCTCTC 59.431 57.143 0.00 0.00 0.00 3.20
1903 1996 1.852965 CCCTTCTCTCTCCCTCTCTCT 59.147 57.143 0.00 0.00 0.00 3.10
1904 1997 2.158608 CCCTTCTCTCTCCCTCTCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
1905 1998 2.780010 CCTTCTCTCTCCCTCTCTCTCT 59.220 54.545 0.00 0.00 0.00 3.10
1906 1999 3.181450 CCTTCTCTCTCCCTCTCTCTCTC 60.181 56.522 0.00 0.00 0.00 3.20
1907 2000 3.421394 TCTCTCTCCCTCTCTCTCTCT 57.579 52.381 0.00 0.00 0.00 3.10
1908 2001 3.309296 TCTCTCTCCCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
2152 2253 3.557207 CAGCCTTTGCACTTCACAC 57.443 52.632 0.00 0.00 41.13 3.82
2160 2261 1.709578 TGCACTTCACACCTCTCTCT 58.290 50.000 0.00 0.00 0.00 3.10
2161 2262 1.615883 TGCACTTCACACCTCTCTCTC 59.384 52.381 0.00 0.00 0.00 3.20
2179 2285 2.098614 CTCTCTCTCTGCTGTTGCCTA 58.901 52.381 0.00 0.00 38.71 3.93
2242 2348 2.125106 GCAGCCTTCCCCAGTACG 60.125 66.667 0.00 0.00 0.00 3.67
2402 2522 4.325204 CGTACGTACTGCAGCAAAAAGATA 59.675 41.667 22.55 0.00 0.00 1.98
2403 2523 4.663636 ACGTACTGCAGCAAAAAGATAC 57.336 40.909 15.27 5.22 0.00 2.24
2404 2524 4.315803 ACGTACTGCAGCAAAAAGATACT 58.684 39.130 15.27 0.00 0.00 2.12
2405 2525 4.152402 ACGTACTGCAGCAAAAAGATACTG 59.848 41.667 15.27 5.60 0.00 2.74
2406 2526 4.152402 CGTACTGCAGCAAAAAGATACTGT 59.848 41.667 15.27 0.00 32.65 3.55
2407 2527 5.347635 CGTACTGCAGCAAAAAGATACTGTA 59.652 40.000 15.27 0.00 32.65 2.74
2449 2569 4.335315 TGCACCTAAAACTGTTCTTCACTG 59.665 41.667 0.00 0.00 0.00 3.66
2456 2576 5.490139 AAACTGTTCTTCACTGATGTGTG 57.510 39.130 0.00 0.00 44.14 3.82
2481 2601 2.158971 ACATGTGTTTGTTTTCTGGGCC 60.159 45.455 0.00 0.00 0.00 5.80
2579 2699 0.745486 CGGATCATCACCAGCAGCAA 60.745 55.000 0.00 0.00 0.00 3.91
2585 2705 0.824595 ATCACCAGCAGCAACAGCAA 60.825 50.000 0.00 0.00 0.00 3.91
2777 2898 4.260620 GCGTGTCTTTGTTCTTTGCTTCTA 60.261 41.667 0.00 0.00 0.00 2.10
2805 2926 1.303074 CCCTGGCCATCATCATCCG 60.303 63.158 5.51 0.00 0.00 4.18
2815 2936 3.443329 CCATCATCATCCGTCTCTCCTAG 59.557 52.174 0.00 0.00 0.00 3.02
2817 2938 4.171878 TCATCATCCGTCTCTCCTAGTT 57.828 45.455 0.00 0.00 0.00 2.24
2829 2953 7.177216 CCGTCTCTCCTAGTTCTAGAGTAGATA 59.823 44.444 11.18 0.38 38.32 1.98
2936 3064 9.978044 CAAGAAAGAAAGAAAGAAAGAATCCAT 57.022 29.630 0.00 0.00 0.00 3.41
2999 3127 3.373438 CCCAAGATCTCCAATCCCAACAT 60.373 47.826 0.00 0.00 0.00 2.71
3158 3291 1.347062 AGATTAGAGCCTAGCTGCCC 58.653 55.000 0.00 0.00 39.88 5.36
3167 3300 1.826921 CTAGCTGCCCTGCCATTGG 60.827 63.158 0.00 0.00 0.00 3.16
3192 3325 1.138036 CACTGCCATTGGTGATGCG 59.862 57.895 4.26 0.00 35.69 4.73
3227 3360 8.571336 CAAGGGATCATTCTTACAATATTGTCC 58.429 37.037 24.00 14.91 42.35 4.02
3278 3413 2.036346 GGATGCTTGAATAATGCCACCC 59.964 50.000 0.00 0.00 0.00 4.61
3401 3536 5.706916 AGCAAGACAAAATCTTATGCACTG 58.293 37.500 0.00 0.00 46.52 3.66
3519 3657 4.741676 CACACCATCAGAAAAGAAAAGCAC 59.258 41.667 0.00 0.00 0.00 4.40
3521 3659 3.004734 ACCATCAGAAAAGAAAAGCACGG 59.995 43.478 0.00 0.00 0.00 4.94
3588 3726 5.461032 GGTTTCCACCAAATGTACATTGA 57.539 39.130 21.46 11.13 43.61 2.57
3632 3770 2.680312 AACGTGCATGCAGTAGAGAT 57.320 45.000 23.41 3.31 0.00 2.75
3644 3782 9.891828 GCATGCAGTAGAGATCATACTATATAC 57.108 37.037 14.21 0.00 32.24 1.47
3667 3805 7.005062 ACTACTAAGTATTTGCTTGATTGCG 57.995 36.000 0.00 0.00 32.84 4.85
3718 3856 6.717540 CCCAGCTCTATCATACTAGTAGTGTT 59.282 42.308 13.29 5.30 0.00 3.32
3759 3897 7.013178 TGTGTCAACTGATTGCTTCTTATTGAA 59.987 33.333 0.00 0.00 35.63 2.69
3800 3938 5.238432 GCAATGTCGTGACCCATATATTTGA 59.762 40.000 0.00 0.00 0.00 2.69
3801 3939 6.566564 GCAATGTCGTGACCCATATATTTGAG 60.567 42.308 0.00 0.00 0.00 3.02
3957 4095 4.034510 CGAAATCTATGTTCCTGGAGCAAC 59.965 45.833 17.35 3.64 0.00 4.17
4149 6643 7.064060 CAATGAATTTGCCAAGTTATTGACC 57.936 36.000 9.07 0.00 36.54 4.02
4296 6804 2.098117 GCTAATTCACCATGTGCACCTC 59.902 50.000 15.69 0.00 32.98 3.85
4496 7004 1.860240 ACCCCAGTATCAGCTCTCCTA 59.140 52.381 0.00 0.00 0.00 2.94
4512 7020 5.777802 CTCTCCTACGCATTCACTGATTAT 58.222 41.667 0.00 0.00 0.00 1.28
4515 7023 7.896811 TCTCCTACGCATTCACTGATTATAAT 58.103 34.615 0.00 0.00 0.00 1.28
4516 7024 7.814587 TCTCCTACGCATTCACTGATTATAATG 59.185 37.037 1.78 0.00 33.45 1.90
4932 7449 5.163513 ACGAAATCAACTGCCATTTTCATC 58.836 37.500 0.00 0.00 0.00 2.92
4977 7494 5.710099 GGTTCATTTGATAGTTCAGGAACCA 59.290 40.000 19.91 0.00 46.06 3.67
5222 7743 2.357009 TCTCTTAGCGACGATACCAACC 59.643 50.000 0.00 0.00 0.00 3.77
5269 7790 4.774503 GCTCTCGGCAAGCTGGCT 62.775 66.667 14.08 0.00 41.25 4.75
5271 7792 1.227205 CTCTCGGCAAGCTGGCTAG 60.227 63.158 14.08 11.14 41.25 3.42
5331 7852 4.444720 GTCACTACTCTTCAAACTTGACCG 59.555 45.833 0.00 0.00 36.83 4.79
5358 7879 7.588497 ATGTCAGTGTATGCTAGACTATTCA 57.412 36.000 0.00 0.00 30.30 2.57
5518 8039 7.937394 ACTAACTGTGCCAAGAATAAGTAAACT 59.063 33.333 0.00 0.00 0.00 2.66
5547 8068 9.933723 TTAAACCTCATAAGTACTTCCACTAAC 57.066 33.333 12.39 0.00 0.00 2.34
5610 8131 7.807977 ATCTATCCACAATTCGCAAGTTATT 57.192 32.000 0.00 0.00 39.48 1.40
5641 8162 9.883142 TTTTAAACTTCATTTGTTCATCTGGTT 57.117 25.926 0.00 0.00 0.00 3.67
5691 8212 1.608590 GCTGTGAGTTTTAGCTGCCAA 59.391 47.619 0.00 0.00 34.70 4.52
5924 8445 4.593206 ACAATTCTTACCTCTGTCCTGTGA 59.407 41.667 0.00 0.00 0.00 3.58
6086 8610 3.389329 CCAGATGTGCCCTACTAATCAGT 59.611 47.826 0.00 0.00 38.91 3.41
6219 8743 5.050023 GGTGTGCAGAAAAAGAACTAGAGAC 60.050 44.000 0.00 0.00 0.00 3.36
6260 8784 2.645838 GGATGCTTTCAGCTATCCCA 57.354 50.000 12.58 0.00 42.97 4.37
6323 8847 5.983540 TGCCAACTAACCATTTTCTGTTTT 58.016 33.333 0.00 0.00 0.00 2.43
6651 9175 3.368236 GGAGAACTTGTCAGAATGCGTAC 59.632 47.826 0.00 0.00 34.76 3.67
6712 9236 3.423539 TCCTGGAGTGAGAACAAATGG 57.576 47.619 0.00 0.00 0.00 3.16
6950 9490 3.294806 TTAGGAGGGAACAAAGGGGTA 57.705 47.619 0.00 0.00 0.00 3.69
6951 9491 2.143231 AGGAGGGAACAAAGGGGTAA 57.857 50.000 0.00 0.00 0.00 2.85
6952 9492 2.655914 AGGAGGGAACAAAGGGGTAAT 58.344 47.619 0.00 0.00 0.00 1.89
6954 9494 3.404769 AGGAGGGAACAAAGGGGTAATTT 59.595 43.478 0.00 0.00 0.00 1.82
6955 9495 3.767673 GGAGGGAACAAAGGGGTAATTTC 59.232 47.826 0.00 0.00 0.00 2.17
6956 9496 4.510386 GGAGGGAACAAAGGGGTAATTTCT 60.510 45.833 0.00 0.00 0.00 2.52
6957 9497 5.281349 GGAGGGAACAAAGGGGTAATTTCTA 60.281 44.000 0.00 0.00 0.00 2.10
7086 9626 6.539649 TTTACATCTGTACAGTTCAAGCAC 57.460 37.500 21.99 0.00 0.00 4.40
7147 9849 7.284489 TGTCATTTGAAGTTAAACCTTGCTACT 59.716 33.333 0.00 0.00 0.00 2.57
7148 9850 7.803659 GTCATTTGAAGTTAAACCTTGCTACTC 59.196 37.037 0.00 0.00 0.00 2.59
7149 9851 6.628919 TTTGAAGTTAAACCTTGCTACTCC 57.371 37.500 0.00 0.00 0.00 3.85
7150 9852 5.562298 TGAAGTTAAACCTTGCTACTCCT 57.438 39.130 0.00 0.00 0.00 3.69
7151 9853 6.675413 TGAAGTTAAACCTTGCTACTCCTA 57.325 37.500 0.00 0.00 0.00 2.94
7152 9854 6.461640 TGAAGTTAAACCTTGCTACTCCTAC 58.538 40.000 0.00 0.00 0.00 3.18
7230 9932 8.330466 TCCATTATAAACCAAAGTGTACACTG 57.670 34.615 28.55 18.30 41.58 3.66
7304 10006 6.907748 CACACATACATTGAACAAACACGTAA 59.092 34.615 0.00 0.00 0.00 3.18
7421 10123 6.702449 AGAATGGCATGGTATTCCTATACA 57.298 37.500 0.00 0.00 38.71 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 8.776376 TGACACCGTCTACATACGATTATATA 57.224 34.615 0.00 0.00 45.68 0.86
58 59 7.677454 TGACACCGTCTACATACGATTATAT 57.323 36.000 0.00 0.00 45.68 0.86
93 94 2.039084 GCGATGACCATCTTAATCCCCT 59.961 50.000 8.20 0.00 35.72 4.79
119 120 2.218759 CGGCCATTTTTCTACTCGATCG 59.781 50.000 9.36 9.36 0.00 3.69
120 121 3.454375 TCGGCCATTTTTCTACTCGATC 58.546 45.455 2.24 0.00 0.00 3.69
121 122 3.536956 TCGGCCATTTTTCTACTCGAT 57.463 42.857 2.24 0.00 0.00 3.59
122 123 3.118920 TGATCGGCCATTTTTCTACTCGA 60.119 43.478 2.24 0.00 0.00 4.04
123 124 3.194861 TGATCGGCCATTTTTCTACTCG 58.805 45.455 2.24 0.00 0.00 4.18
170 171 6.257849 GTGAGAACGTATCCATTCTTTATGCA 59.742 38.462 0.00 0.00 35.29 3.96
171 172 6.562270 CGTGAGAACGTATCCATTCTTTATGC 60.562 42.308 0.00 0.00 35.29 3.14
264 282 4.252878 CAGCCCTTCTCTCTTCTCTTTTC 58.747 47.826 0.00 0.00 0.00 2.29
267 285 2.187100 CCAGCCCTTCTCTCTTCTCTT 58.813 52.381 0.00 0.00 0.00 2.85
271 289 1.066502 GTGTCCAGCCCTTCTCTCTTC 60.067 57.143 0.00 0.00 0.00 2.87
272 290 0.980423 GTGTCCAGCCCTTCTCTCTT 59.020 55.000 0.00 0.00 0.00 2.85
273 291 1.254284 CGTGTCCAGCCCTTCTCTCT 61.254 60.000 0.00 0.00 0.00 3.10
274 292 1.216710 CGTGTCCAGCCCTTCTCTC 59.783 63.158 0.00 0.00 0.00 3.20
291 309 4.804608 TTATTTTATGCGTCCATGTCCG 57.195 40.909 0.00 0.00 32.85 4.79
392 410 3.378399 GAAGCCACCCTCGCTCTCC 62.378 68.421 0.00 0.00 34.84 3.71
393 411 1.893919 AAGAAGCCACCCTCGCTCTC 61.894 60.000 0.00 0.00 34.84 3.20
394 412 1.915769 AAGAAGCCACCCTCGCTCT 60.916 57.895 0.00 0.00 34.84 4.09
395 413 1.743252 CAAGAAGCCACCCTCGCTC 60.743 63.158 0.00 0.00 34.84 5.03
396 414 2.217038 TCAAGAAGCCACCCTCGCT 61.217 57.895 0.00 0.00 38.53 4.93
397 415 2.035442 GTCAAGAAGCCACCCTCGC 61.035 63.158 0.00 0.00 0.00 5.03
638 670 4.548451 TCTTGTCTTGATGCATCTGACT 57.452 40.909 32.41 5.17 34.55 3.41
795 827 2.146342 AGAGGATGCAGACAAACAACG 58.854 47.619 0.00 0.00 0.00 4.10
1044 1076 1.126488 GCACATGATGAGGAGGAGGA 58.874 55.000 0.00 0.00 0.00 3.71
1154 1186 2.943033 CGAGAAAGAGGGAGAGAGAGAC 59.057 54.545 0.00 0.00 0.00 3.36
1155 1187 2.574369 ACGAGAAAGAGGGAGAGAGAGA 59.426 50.000 0.00 0.00 0.00 3.10
1177 1209 4.855715 TGACAGACAAAACAAAACCACA 57.144 36.364 0.00 0.00 0.00 4.17
1249 1296 6.973229 AATCTTGAAAAATAAGTGCATGCC 57.027 33.333 16.68 6.65 0.00 4.40
1377 1425 2.261361 CACACAGGATCGACGGCA 59.739 61.111 0.00 0.00 0.00 5.69
1378 1426 3.188786 GCACACAGGATCGACGGC 61.189 66.667 0.00 0.00 0.00 5.68
1379 1427 2.880879 CGCACACAGGATCGACGG 60.881 66.667 0.00 0.00 0.00 4.79
1380 1428 2.126463 ACGCACACAGGATCGACG 60.126 61.111 0.00 0.00 0.00 5.12
1481 1544 2.253154 CGCACGTACAGACCGTCA 59.747 61.111 0.40 0.00 36.17 4.35
1482 1545 2.078914 CACGCACGTACAGACCGTC 61.079 63.158 0.00 0.00 36.17 4.79
1483 1546 2.050714 CACGCACGTACAGACCGT 60.051 61.111 0.00 0.00 39.52 4.83
1596 1668 3.186390 GAAATCATCCTGCCGCCGC 62.186 63.158 0.00 0.00 0.00 6.53
1597 1669 2.885676 CGAAATCATCCTGCCGCCG 61.886 63.158 0.00 0.00 0.00 6.46
1598 1670 3.025619 CGAAATCATCCTGCCGCC 58.974 61.111 0.00 0.00 0.00 6.13
1732 1804 2.637872 GGCTAGGCTAGAGAGAGAGAGA 59.362 54.545 25.37 0.00 0.00 3.10
1733 1805 2.371841 TGGCTAGGCTAGAGAGAGAGAG 59.628 54.545 25.37 0.00 0.00 3.20
1734 1806 2.413601 TGGCTAGGCTAGAGAGAGAGA 58.586 52.381 25.37 0.00 0.00 3.10
1735 1807 2.949177 TGGCTAGGCTAGAGAGAGAG 57.051 55.000 25.37 0.00 0.00 3.20
1881 1974 2.781174 GAGAGAGGGAGAGAGAAGGGTA 59.219 54.545 0.00 0.00 0.00 3.69
1882 1975 1.569072 GAGAGAGGGAGAGAGAAGGGT 59.431 57.143 0.00 0.00 0.00 4.34
1895 1988 2.131854 TGGGGTAGAGAGAGAGAGAGG 58.868 57.143 0.00 0.00 0.00 3.69
1896 1989 3.498481 CCATGGGGTAGAGAGAGAGAGAG 60.498 56.522 2.85 0.00 0.00 3.20
1897 1990 2.445145 CCATGGGGTAGAGAGAGAGAGA 59.555 54.545 2.85 0.00 0.00 3.10
1898 1991 2.445145 TCCATGGGGTAGAGAGAGAGAG 59.555 54.545 13.02 0.00 34.93 3.20
1899 1992 2.175931 GTCCATGGGGTAGAGAGAGAGA 59.824 54.545 13.02 0.00 34.93 3.10
1900 1993 2.593026 GTCCATGGGGTAGAGAGAGAG 58.407 57.143 13.02 0.00 34.93 3.20
1901 1994 1.218196 GGTCCATGGGGTAGAGAGAGA 59.782 57.143 13.02 0.00 34.93 3.10
1902 1995 1.062886 TGGTCCATGGGGTAGAGAGAG 60.063 57.143 13.02 0.00 34.93 3.20
1903 1996 1.015609 TGGTCCATGGGGTAGAGAGA 58.984 55.000 13.02 0.00 34.93 3.10
1904 1997 1.696336 CATGGTCCATGGGGTAGAGAG 59.304 57.143 22.45 0.00 38.11 3.20
1905 1998 1.806496 CATGGTCCATGGGGTAGAGA 58.194 55.000 22.45 0.00 38.11 3.10
2151 2252 2.092753 CAGCAGAGAGAGAGAGAGAGGT 60.093 54.545 0.00 0.00 0.00 3.85
2152 2253 2.092753 ACAGCAGAGAGAGAGAGAGAGG 60.093 54.545 0.00 0.00 0.00 3.69
2160 2261 2.222227 TAGGCAACAGCAGAGAGAGA 57.778 50.000 0.00 0.00 41.41 3.10
2161 2262 3.196463 CAATAGGCAACAGCAGAGAGAG 58.804 50.000 0.00 0.00 41.41 3.20
2179 2285 3.211865 AGATCAAGACATGCATCGCAAT 58.788 40.909 0.00 0.00 43.62 3.56
2242 2348 1.808133 GCTGTAGCAGTATCAGCCACC 60.808 57.143 5.25 0.00 45.76 4.61
2402 2522 8.237267 GCAAAATGCTTGTAGTAATTCTACAGT 58.763 33.333 13.71 0.00 45.17 3.55
2403 2523 8.606727 GCAAAATGCTTGTAGTAATTCTACAG 57.393 34.615 13.71 10.81 45.17 2.74
2405 2525 7.484959 GGTGCAAAATGCTTGTAGTAATTCTAC 59.515 37.037 3.78 7.65 45.31 2.59
2406 2526 7.393234 AGGTGCAAAATGCTTGTAGTAATTCTA 59.607 33.333 3.78 0.00 45.31 2.10
2407 2527 6.209391 AGGTGCAAAATGCTTGTAGTAATTCT 59.791 34.615 3.78 0.00 45.31 2.40
2449 2569 8.795786 AAAACAAACACATGTATACACACATC 57.204 30.769 7.96 0.00 37.02 3.06
2456 2576 5.861787 GCCCAGAAAACAAACACATGTATAC 59.138 40.000 0.00 0.00 32.02 1.47
2481 2601 1.542915 CACATTTGAACCCTCCTGCTG 59.457 52.381 0.00 0.00 0.00 4.41
2579 2699 2.198287 CCCTTGCTGCTGTTGCTGT 61.198 57.895 0.00 0.00 39.81 4.40
2585 2705 0.254178 CTACCATCCCTTGCTGCTGT 59.746 55.000 0.00 0.00 0.00 4.40
2777 2898 1.217057 ATGGCCAGGGGAGAATGTGT 61.217 55.000 13.05 0.00 0.00 3.72
2805 2926 8.033626 GCTATCTACTCTAGAACTAGGAGAGAC 58.966 44.444 15.89 0.48 39.29 3.36
2815 2936 5.646360 CCAGGCTAGCTATCTACTCTAGAAC 59.354 48.000 15.72 0.00 38.50 3.01
2817 2938 4.847512 ACCAGGCTAGCTATCTACTCTAGA 59.152 45.833 15.72 0.00 39.50 2.43
2829 2953 2.262774 GACATGGCACCAGGCTAGCT 62.263 60.000 15.72 0.00 44.01 3.32
2936 3064 1.839747 ACACCCTGCCTCAACCGTA 60.840 57.895 0.00 0.00 0.00 4.02
3021 3154 8.846211 TGTTTCTATAGGTCCAAACAAGAAAAG 58.154 33.333 12.59 0.00 36.14 2.27
3031 3164 8.114102 TCTCTAGACTTGTTTCTATAGGTCCAA 58.886 37.037 0.00 0.06 0.00 3.53
3049 3182 5.047188 GCTATTCCAACAAGCTCTCTAGAC 58.953 45.833 0.00 0.00 33.40 2.59
3167 3300 1.448893 CCAATGGCAGTGGCAATGC 60.449 57.895 29.99 29.99 42.43 3.56
3192 3325 6.432403 AAGAATGATCCCTTGTCTCCTATC 57.568 41.667 0.00 0.00 0.00 2.08
3227 3360 1.168714 GGCCACAGTTTCTTGCTAGG 58.831 55.000 0.00 0.00 0.00 3.02
3278 3413 2.613977 CCTAAAGCAGACACTGACCCAG 60.614 54.545 2.81 0.00 37.52 4.45
3401 3536 8.612619 TGAGAAAGAAGCGTGGATTAATTAATC 58.387 33.333 24.27 24.27 40.96 1.75
3542 3680 3.181487 CCCACTCCAACAACAGACAAAAG 60.181 47.826 0.00 0.00 0.00 2.27
3644 3782 5.904080 GCGCAATCAAGCAAATACTTAGTAG 59.096 40.000 0.30 0.00 0.00 2.57
3667 3805 2.094545 GGAAGAACAATGTGTCCATGGC 60.095 50.000 6.96 2.72 0.00 4.40
3718 3856 5.764686 AGTTGACACATCATGCTCACTTAAA 59.235 36.000 0.00 0.00 33.85 1.52
3759 3897 9.113838 ACGACATTGCATATTAGAAGAAGAATT 57.886 29.630 0.00 0.00 0.00 2.17
3957 4095 3.058450 TCTCAAAACCAAATGCATTGCG 58.942 40.909 13.82 8.54 37.73 4.85
4149 6643 7.595130 CACATGATGGATAATTCAGATGCAAAG 59.405 37.037 0.00 0.00 0.00 2.77
4296 6804 9.608617 GAGTGATTTTTGTGATCATATATGCAG 57.391 33.333 7.92 0.00 36.07 4.41
4496 7004 6.238456 CCACACATTATAATCAGTGAATGCGT 60.238 38.462 20.52 0.00 35.97 5.24
4512 7020 3.850752 ACCAAATTCCCACCACACATTA 58.149 40.909 0.00 0.00 0.00 1.90
4515 7023 2.166907 AACCAAATTCCCACCACACA 57.833 45.000 0.00 0.00 0.00 3.72
4516 7024 3.892588 TCTTAACCAAATTCCCACCACAC 59.107 43.478 0.00 0.00 0.00 3.82
4861 7377 7.462571 TGCTAATGTTCAGTGTAGTTAGAGA 57.537 36.000 9.73 0.00 0.00 3.10
4922 7439 8.442632 TGCTAGAAACTATGAGATGAAAATGG 57.557 34.615 0.00 0.00 0.00 3.16
4977 7494 4.647424 TCGAGAGTTTGTTTGGCAATTT 57.353 36.364 0.00 0.00 36.89 1.82
5222 7743 2.123982 GCCCATGAAGCTCCCCAG 60.124 66.667 0.00 0.00 0.00 4.45
5331 7852 9.400638 GAATAGTCTAGCATACACTGACATAAC 57.599 37.037 0.00 0.00 0.00 1.89
5373 7894 4.337763 CGCTTCATTGCTCATCTACAAAC 58.662 43.478 0.00 0.00 0.00 2.93
5518 8039 9.856162 AGTGGAAGTACTTATGAGGTTTAAAAA 57.144 29.630 8.42 0.00 0.00 1.94
5691 8212 5.627182 ACATGCCTCAGTGATCTTATTCT 57.373 39.130 0.00 0.00 0.00 2.40
6086 8610 1.062428 AGGAGGGTGGTCGATTCCATA 60.062 52.381 0.00 0.00 39.81 2.74
6219 8743 4.359706 CCAGGAAAAAGTGAAAGAAACCG 58.640 43.478 0.00 0.00 0.00 4.44
6260 8784 3.009584 CCTAGGGAAAAGAAACAGAGGCT 59.990 47.826 0.00 0.00 0.00 4.58
6323 8847 4.263727 TGAACCTATGCTTCTTTTAGGCCA 60.264 41.667 5.01 0.00 36.72 5.36
6651 9175 7.041576 TGACTCAAGAAAATCTGATGACAGTTG 60.042 37.037 0.00 0.00 43.81 3.16
6712 9236 4.762289 ATAATGAACTCTGGGTGTCCTC 57.238 45.455 0.00 0.00 0.00 3.71
6950 9490 7.448469 AGGTTTGTGTACTCATGCTTAGAAATT 59.552 33.333 0.00 0.00 0.00 1.82
6951 9491 6.942576 AGGTTTGTGTACTCATGCTTAGAAAT 59.057 34.615 0.00 0.00 0.00 2.17
6952 9492 6.204688 CAGGTTTGTGTACTCATGCTTAGAAA 59.795 38.462 0.00 0.00 0.00 2.52
6954 9494 5.221641 ACAGGTTTGTGTACTCATGCTTAGA 60.222 40.000 0.00 0.00 35.83 2.10
6955 9495 4.997395 ACAGGTTTGTGTACTCATGCTTAG 59.003 41.667 0.00 0.00 35.83 2.18
6956 9496 4.968259 ACAGGTTTGTGTACTCATGCTTA 58.032 39.130 0.00 0.00 35.83 3.09
6957 9497 3.820557 ACAGGTTTGTGTACTCATGCTT 58.179 40.909 0.00 0.00 35.83 3.91
7018 9558 2.283298 ACTCAACAGCAGTGTGTGAAG 58.717 47.619 2.04 4.67 36.84 3.02
7020 9560 2.401583 AACTCAACAGCAGTGTGTGA 57.598 45.000 2.04 0.00 36.84 3.58
7076 9616 1.893801 AGGTACTAGCGTGCTTGAACT 59.106 47.619 10.19 2.65 36.02 3.01
7147 9849 7.517614 TTATCTGTGTTGCAAAATTGTAGGA 57.482 32.000 0.00 0.00 0.00 2.94
7148 9850 9.507280 CTATTATCTGTGTTGCAAAATTGTAGG 57.493 33.333 0.00 0.00 0.00 3.18
7151 9853 9.979578 TTTCTATTATCTGTGTTGCAAAATTGT 57.020 25.926 0.00 0.00 0.00 2.71
7230 9932 2.536803 CACAGCAAAATCAGTGTTGTGC 59.463 45.455 8.17 10.77 46.48 4.57
7340 10042 9.542318 TGTGTGACACAAGGAAATCCTCCATTA 62.542 40.741 17.13 0.00 42.28 1.90
7421 10123 7.539034 ACCAAAACAGAGTAAAGCCATATTT 57.461 32.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.