Multiple sequence alignment - TraesCS5D01G178900

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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 TraesCS5D01G178900 chr5D 100.000 6509 0 0 1 6509 278279742 278273234 0.000000e+00 12020.0
1 TraesCS5D01G178900 chr5D 98.837 86 1 0 4547 4632 369298297 369298382 3.140000e-33 154.0
2 TraesCS5D01G178900 chr5D 100.000 46 0 0 3990 4035 278275711 278275666 1.160000e-12 86.1
3 TraesCS5D01G178900 chr5D 100.000 46 0 0 4032 4077 278275753 278275708 1.160000e-12 86.1
4 TraesCS5D01G178900 chr5A 92.718 2307 73 25 1 2240 367599322 367597044 0.000000e+00 3241.0
5 TraesCS5D01G178900 chr5A 96.552 1653 24 4 2237 3887 367596942 367595321 0.000000e+00 2706.0
6 TraesCS5D01G178900 chr5A 92.023 1028 50 18 5095 6105 367594019 367593007 0.000000e+00 1415.0
7 TraesCS5D01G178900 chr5A 95.046 545 21 6 4525 5065 367595322 367594780 0.000000e+00 852.0
8 TraesCS5D01G178900 chr5A 95.738 305 11 2 6207 6509 367593008 367592704 2.110000e-134 490.0
9 TraesCS5D01G178900 chr5A 94.286 70 4 0 5055 5124 367594088 367594019 2.480000e-19 108.0
10 TraesCS5D01G178900 chr5A 90.476 42 2 1 2078 2119 367597312 367597273 3.000000e-03 54.7
11 TraesCS5D01G178900 chr5B 94.418 2114 88 18 1 2096 316369404 316367303 0.000000e+00 3223.0
12 TraesCS5D01G178900 chr5B 94.150 2000 59 19 2075 4035 316367287 316365307 0.000000e+00 2992.0
13 TraesCS5D01G178900 chr5B 92.785 1386 60 20 4630 6005 316364838 316363483 0.000000e+00 1969.0
14 TraesCS5D01G178900 chr5B 94.837 523 16 3 4033 4550 316365351 316364835 0.000000e+00 806.0
15 TraesCS5D01G178900 chr5B 96.296 297 7 2 6217 6509 316363054 316362758 9.810000e-133 484.0
16 TraesCS5D01G178900 chr5B 97.143 35 1 0 2076 2110 316367389 316367355 7.050000e-05 60.2
17 TraesCS5D01G178900 chr4D 98.864 88 1 0 4547 4634 453135312 453135399 2.430000e-34 158.0
18 TraesCS5D01G178900 chr3D 94.792 96 5 0 4546 4641 81366079 81366174 4.070000e-32 150.0
19 TraesCS5D01G178900 chr3D 95.699 93 3 1 4539 4631 338296404 338296495 1.460000e-31 148.0
20 TraesCS5D01G178900 chr3D 88.235 68 8 0 4669 4736 579575859 579575792 1.500000e-11 82.4
21 TraesCS5D01G178900 chr6D 95.652 92 4 0 4547 4638 168293839 168293748 1.460000e-31 148.0
22 TraesCS5D01G178900 chr2A 93.069 101 7 0 4537 4637 498099433 498099533 1.460000e-31 148.0
23 TraesCS5D01G178900 chr2D 96.591 88 3 0 4547 4634 53145727 53145814 5.260000e-31 147.0
24 TraesCS5D01G178900 chr4A 95.556 90 3 1 4543 4631 440964818 440964907 6.800000e-30 143.0
25 TraesCS5D01G178900 chr3A 89.189 74 4 4 4679 4750 721452086 721452015 8.990000e-14 89.8
26 TraesCS5D01G178900 chr1A 87.931 58 7 0 4640 4697 241320972 241321029 1.170000e-07 69.4
27 TraesCS5D01G178900 chr6B 90.244 41 4 0 4634 4674 600289586 600289626 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 TraesCS5D01G178900 chr5D 278273234 278279742 6508 True 12020.000000 12020 100.000000 1 6509 1 chr5D.!!$R1 6508
1 TraesCS5D01G178900 chr5A 367592704 367599322 6618 True 1266.671429 3241 93.834143 1 6509 7 chr5A.!!$R1 6508
2 TraesCS5D01G178900 chr5B 316362758 316369404 6646 True 1589.033333 3223 94.938167 1 6509 6 chr5B.!!$R1 6508

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
449 453 0.189822 ATCTAGCCTCCCCCTCAGAC 59.810 60.000 0.0 0.0 0.00 3.51 F
1021 1047 0.481128 GGTGAGTTCCTTTTCCCCCA 59.519 55.000 0.0 0.0 0.00 4.96 F
1201 1228 1.004745 GGGCTGTGAATCTTCCTTCCA 59.995 52.381 0.0 0.0 0.00 3.53 F
2935 3149 0.318869 ACGACAACCGACAACGCATA 60.319 50.000 0.0 0.0 41.76 3.14 F
4443 4675 1.419922 GCTGCGGTACATGAACACG 59.580 57.895 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 1553 0.995803 AGGAAAGGCCCCTCTTCTTC 59.004 55.000 0.00 0.00 37.37 2.87 R
1913 1951 6.072508 TGGAAACAGATACTGATTTCTTGTGC 60.073 38.462 5.76 0.00 34.82 4.57 R
3192 3406 1.774254 TCCCTGCCTCTTTTCAAGTCA 59.226 47.619 0.00 0.00 0.00 3.41 R
4481 4713 1.982395 CAGGTGTCTACGCCCCTGA 60.982 63.158 9.06 0.00 45.97 3.86 R
5514 6493 0.397941 TAGGGCATATGCAGGCTGTC 59.602 55.000 28.07 9.46 44.36 3.51 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
62 63 1.000896 GCTAAAGGCCAGCTTCCCA 60.001 57.895 5.01 0.00 36.07 4.37
104 105 3.302347 CTTCACCTCGAGCGGCCTT 62.302 63.158 6.99 0.00 0.00 4.35
125 126 1.028130 TGTTTGCCGCAATGACAAGA 58.972 45.000 6.64 0.00 0.00 3.02
347 351 4.213482 CACACAAAAGCTAACAGGTCTACC 59.787 45.833 0.00 0.00 0.00 3.18
449 453 0.189822 ATCTAGCCTCCCCCTCAGAC 59.810 60.000 0.00 0.00 0.00 3.51
759 783 0.679505 CAGAGACAAGTCGGGTTCCA 59.320 55.000 0.00 0.00 34.09 3.53
807 831 2.983791 CCCAGCAGGCCCAATTTG 59.016 61.111 0.00 0.00 0.00 2.32
833 858 4.958897 CCGGGGGTCCAAAACGCA 62.959 66.667 0.00 0.00 42.43 5.24
848 873 4.803426 GCACCCTCGCCTCGTCTG 62.803 72.222 0.00 0.00 0.00 3.51
1018 1044 2.171003 CCATGGTGAGTTCCTTTTCCC 58.829 52.381 2.57 0.00 0.00 3.97
1021 1047 0.481128 GGTGAGTTCCTTTTCCCCCA 59.519 55.000 0.00 0.00 0.00 4.96
1022 1048 1.617322 GTGAGTTCCTTTTCCCCCAC 58.383 55.000 0.00 0.00 0.00 4.61
1048 1075 3.259425 CTTCAGCCTTGCGCACCAC 62.259 63.158 11.12 1.16 41.38 4.16
1050 1077 3.289834 CAGCCTTGCGCACCACTT 61.290 61.111 11.12 0.00 41.38 3.16
1076 1103 3.521765 AATTTGGTCGGGGCAGCCA 62.522 57.895 15.19 0.00 0.00 4.75
1122 1149 1.430369 AAGTGAAGCCCCCTCTTGCT 61.430 55.000 0.00 0.00 40.17 3.91
1132 1159 1.226717 CCTCTTGCTCGCGAGGTAC 60.227 63.158 35.10 20.30 41.49 3.34
1150 1177 5.586877 AGGTACTTGGGTTATACACTGAGA 58.413 41.667 0.00 0.00 27.25 3.27
1183 1210 2.537401 GAGAAGTCGGTACATTTCGGG 58.463 52.381 0.00 0.00 0.00 5.14
1201 1228 1.004745 GGGCTGTGAATCTTCCTTCCA 59.995 52.381 0.00 0.00 0.00 3.53
1216 1243 3.460340 TCCTTCCAACACTAGGTTTTCCA 59.540 43.478 0.00 0.00 43.73 3.53
1242 1269 2.896801 GCTGCCGGCCATCGTATTG 61.897 63.158 26.77 3.67 37.11 1.90
1408 1440 2.770699 GGACTACATTCCCTACGACG 57.229 55.000 0.00 0.00 0.00 5.12
1423 1455 1.135803 ACGACGAATTTGGAATTGCGG 60.136 47.619 0.00 0.00 0.00 5.69
1436 1468 3.308530 GAATTGCGGTGACCTTTTCTTG 58.691 45.455 0.00 0.00 0.00 3.02
1437 1469 1.757682 TTGCGGTGACCTTTTCTTGT 58.242 45.000 0.00 0.00 0.00 3.16
1438 1470 2.623878 TGCGGTGACCTTTTCTTGTA 57.376 45.000 0.00 0.00 0.00 2.41
1439 1471 2.215196 TGCGGTGACCTTTTCTTGTAC 58.785 47.619 0.00 0.00 0.00 2.90
1440 1472 2.158871 TGCGGTGACCTTTTCTTGTACT 60.159 45.455 0.00 0.00 0.00 2.73
1510 1546 5.357257 AGCTGATTATTTTCCGTATCGTGT 58.643 37.500 0.00 0.00 0.00 4.49
1517 1553 5.691508 ATTTTCCGTATCGTGTTTAGTCG 57.308 39.130 0.00 0.00 0.00 4.18
1744 1780 5.241506 TGTGGAAGTTTTAGCTTGAAGATGG 59.758 40.000 0.00 0.00 0.00 3.51
1799 1835 5.656416 ACTTTGGAAAGTTGGTGATTGAAGA 59.344 36.000 0.00 0.00 46.52 2.87
1856 1892 2.030805 GCAGTTCATTCCTGTTTTCGCT 60.031 45.455 0.00 0.00 32.41 4.93
1976 2014 7.610305 CCATTAATACCTGAACCTACAACTGTT 59.390 37.037 0.00 0.00 0.00 3.16
2034 2072 9.117183 CAGAGTTTAGGTTAAAGTTGTAGGTTT 57.883 33.333 0.00 0.00 31.78 3.27
2165 2258 3.187022 TCATCGTGCTTTGATGAACTGTG 59.813 43.478 11.84 0.00 46.77 3.66
2188 2294 7.985184 TGTGTTCAGTGTACTTAAAGTCTCATT 59.015 33.333 1.38 0.00 0.00 2.57
2935 3149 0.318869 ACGACAACCGACAACGCATA 60.319 50.000 0.00 0.00 41.76 3.14
3061 3275 8.331022 CACTTTCGTATCCTTGTTGATCATTAG 58.669 37.037 0.00 0.00 0.00 1.73
3085 3299 7.669427 AGATGTTAGAATAGAGATTCAGGCTG 58.331 38.462 8.58 8.58 43.51 4.85
3276 3490 4.505922 GCAAGAAGGATGTAGATCAACTCG 59.494 45.833 1.87 0.00 0.00 4.18
3514 3728 7.000472 TGAGATCCATCATTCCTCATTTTACC 59.000 38.462 0.00 0.00 0.00 2.85
3567 3781 5.863965 TGTTTTGATACATCACTCTGACCA 58.136 37.500 0.00 0.00 36.36 4.02
3760 3974 1.869767 CGGCTTGCCTATCATCACTTC 59.130 52.381 10.12 0.00 0.00 3.01
3773 3987 7.437565 CCTATCATCACTTCGGCTAATATCATG 59.562 40.741 0.00 0.00 0.00 3.07
3934 4161 4.139786 TGGAAAATAGAGAGATGGCATGC 58.860 43.478 9.90 9.90 0.00 4.06
3959 4186 3.045601 ACTTGACTTCTTGGGTCGATG 57.954 47.619 0.00 0.00 36.58 3.84
3962 4189 3.587797 TGACTTCTTGGGTCGATGTAC 57.412 47.619 0.00 0.00 36.58 2.90
4003 4230 1.624336 AGCATTGCTTGAAGCTTGGA 58.376 45.000 18.94 2.36 42.97 3.53
4004 4231 1.965643 AGCATTGCTTGAAGCTTGGAA 59.034 42.857 18.94 4.38 42.97 3.53
4005 4232 2.029290 AGCATTGCTTGAAGCTTGGAAG 60.029 45.455 18.94 7.08 42.97 3.46
4006 4233 2.029649 GCATTGCTTGAAGCTTGGAAGA 60.030 45.455 18.94 0.00 42.97 2.87
4007 4234 3.553508 GCATTGCTTGAAGCTTGGAAGAA 60.554 43.478 18.94 2.46 42.97 2.52
4008 4235 4.817517 CATTGCTTGAAGCTTGGAAGAAT 58.182 39.130 18.94 4.86 42.97 2.40
4009 4236 4.510038 TTGCTTGAAGCTTGGAAGAATC 57.490 40.909 18.94 0.00 42.97 2.52
4010 4237 3.489355 TGCTTGAAGCTTGGAAGAATCA 58.511 40.909 18.94 0.00 42.97 2.57
4011 4238 3.890756 TGCTTGAAGCTTGGAAGAATCAA 59.109 39.130 18.94 0.00 42.97 2.57
4012 4239 4.233005 GCTTGAAGCTTGGAAGAATCAAC 58.767 43.478 10.44 0.00 38.45 3.18
4013 4240 4.261741 GCTTGAAGCTTGGAAGAATCAACA 60.262 41.667 10.44 0.00 38.45 3.33
4014 4241 5.443185 TTGAAGCTTGGAAGAATCAACAG 57.557 39.130 2.10 0.00 31.55 3.16
4015 4242 4.464008 TGAAGCTTGGAAGAATCAACAGT 58.536 39.130 2.10 0.00 0.00 3.55
4016 4243 4.889409 TGAAGCTTGGAAGAATCAACAGTT 59.111 37.500 2.10 0.00 0.00 3.16
4017 4244 5.360714 TGAAGCTTGGAAGAATCAACAGTTT 59.639 36.000 2.10 0.00 0.00 2.66
4018 4245 5.192327 AGCTTGGAAGAATCAACAGTTTG 57.808 39.130 0.00 0.00 0.00 2.93
4019 4246 4.646492 AGCTTGGAAGAATCAACAGTTTGT 59.354 37.500 0.00 0.00 34.02 2.83
4020 4247 5.827797 AGCTTGGAAGAATCAACAGTTTGTA 59.172 36.000 0.00 0.00 34.02 2.41
4021 4248 6.016777 AGCTTGGAAGAATCAACAGTTTGTAG 60.017 38.462 0.00 0.00 34.02 2.74
4022 4249 6.238759 GCTTGGAAGAATCAACAGTTTGTAGT 60.239 38.462 0.00 0.00 34.02 2.73
4023 4250 7.639113 TTGGAAGAATCAACAGTTTGTAGTT 57.361 32.000 0.00 0.00 34.02 2.24
4024 4251 8.740123 TTGGAAGAATCAACAGTTTGTAGTTA 57.260 30.769 0.00 0.00 34.02 2.24
4025 4252 8.378172 TGGAAGAATCAACAGTTTGTAGTTAG 57.622 34.615 0.00 0.00 34.02 2.34
4026 4253 7.990886 TGGAAGAATCAACAGTTTGTAGTTAGT 59.009 33.333 0.00 0.00 34.02 2.24
4027 4254 9.485206 GGAAGAATCAACAGTTTGTAGTTAGTA 57.515 33.333 0.00 0.00 34.02 1.82
4033 4260 8.306680 TCAACAGTTTGTAGTTAGTAGAATGC 57.693 34.615 0.00 0.00 34.02 3.56
4034 4261 8.148351 TCAACAGTTTGTAGTTAGTAGAATGCT 58.852 33.333 0.00 0.00 34.02 3.79
4035 4262 8.774586 CAACAGTTTGTAGTTAGTAGAATGCTT 58.225 33.333 0.00 0.00 29.76 3.91
4036 4263 8.311650 ACAGTTTGTAGTTAGTAGAATGCTTG 57.688 34.615 0.00 0.00 29.76 4.01
4037 4264 8.148351 ACAGTTTGTAGTTAGTAGAATGCTTGA 58.852 33.333 0.00 0.00 29.76 3.02
4038 4265 8.988934 CAGTTTGTAGTTAGTAGAATGCTTGAA 58.011 33.333 0.00 0.00 29.76 2.69
4039 4266 9.209175 AGTTTGTAGTTAGTAGAATGCTTGAAG 57.791 33.333 0.00 0.00 29.76 3.02
4040 4267 7.596749 TTGTAGTTAGTAGAATGCTTGAAGC 57.403 36.000 10.84 10.84 42.82 3.86
4351 4583 8.652810 TTCTTCTTGTTAACTACCTACACAAC 57.347 34.615 7.22 0.00 0.00 3.32
4359 4591 2.288640 ACTACCTACACAACGTTCTGGC 60.289 50.000 8.46 0.00 0.00 4.85
4373 4605 3.604772 CGTTCTGGCACTCTTTCTTTTCG 60.605 47.826 0.00 0.00 0.00 3.46
4375 4607 4.330944 TCTGGCACTCTTTCTTTTCGTA 57.669 40.909 0.00 0.00 0.00 3.43
4376 4608 4.699637 TCTGGCACTCTTTCTTTTCGTAA 58.300 39.130 0.00 0.00 0.00 3.18
4443 4675 1.419922 GCTGCGGTACATGAACACG 59.580 57.895 0.00 0.00 0.00 4.49
4509 4741 3.082548 CGTAGACACCTGAGAAGAGGAA 58.917 50.000 0.00 0.00 36.51 3.36
4555 4787 3.010696 TGTCACTGTCATCTACTCCCTCT 59.989 47.826 0.00 0.00 0.00 3.69
4619 4851 9.639563 TGTCAAAAATGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
4726 4958 4.711846 AGCTGTGACACTTACTATGGATCA 59.288 41.667 7.20 0.00 0.00 2.92
4770 5002 9.643693 CACATATTTACAAAGGAATTTGCTCTT 57.356 29.630 0.79 0.00 35.42 2.85
5021 5255 4.242475 TCTACGTGAGGCATTGTGTTTAG 58.758 43.478 0.00 0.00 0.00 1.85
5023 5257 2.806244 ACGTGAGGCATTGTGTTTAGAC 59.194 45.455 0.00 0.00 0.00 2.59
5057 5291 3.578688 CTTGCCCACTTAATTGTGAAGC 58.421 45.455 0.00 1.89 40.12 3.86
5101 6039 1.135972 CACCGTATGTGTTCAGCTTGC 60.136 52.381 0.00 0.00 40.26 4.01
5144 6112 4.860022 ACTAAGAGTAAAATGGCATGCCT 58.140 39.130 35.53 19.28 36.94 4.75
5226 6194 4.826274 AGTTTGTGCTTGCTAGGAGATA 57.174 40.909 0.00 0.00 0.00 1.98
5308 6276 8.623310 TTGATTGATTGATTTGATTGATGTCG 57.377 30.769 0.00 0.00 0.00 4.35
5377 6348 2.339712 GCGTGGGCTTGTTTGCAT 59.660 55.556 0.00 0.00 35.83 3.96
5450 6429 2.039084 ACCGGTTCTGCTTTCTTCTGAT 59.961 45.455 0.00 0.00 0.00 2.90
5514 6493 3.969899 TGAGTATCTGCAGTAATGCTCG 58.030 45.455 20.82 7.64 37.41 5.03
5549 6528 1.265095 CCCTATTGCATCATCGTGTGC 59.735 52.381 0.00 0.00 41.61 4.57
5632 6612 2.479389 CCGTACCGTCGGCTATTTAACA 60.479 50.000 12.28 0.00 43.96 2.41
5675 6655 9.442033 CATTATTGCACATGTTCTGTTATGTAG 57.558 33.333 0.00 0.00 35.86 2.74
5680 6660 5.063944 GCACATGTTCTGTTATGTAGAGGTG 59.936 44.000 0.00 0.00 35.86 4.00
5790 6770 4.942852 AGATTAGCAATCTGACGAGGAAG 58.057 43.478 9.65 0.00 46.16 3.46
5792 6772 4.801330 TTAGCAATCTGACGAGGAAGAA 57.199 40.909 0.00 0.00 0.00 2.52
5793 6773 3.685139 AGCAATCTGACGAGGAAGAAA 57.315 42.857 0.00 0.00 0.00 2.52
5821 6803 9.045745 AGAAGGATCTGAAATAAGAAGAGACTT 57.954 33.333 0.00 0.00 33.59 3.01
5823 6805 8.144862 AGGATCTGAAATAAGAAGAGACTTGT 57.855 34.615 0.00 0.00 0.00 3.16
5885 6867 5.730296 GCACAGGCCTCTCTTATATTCTA 57.270 43.478 0.00 0.00 0.00 2.10
5886 6868 5.719173 GCACAGGCCTCTCTTATATTCTAG 58.281 45.833 0.00 0.00 0.00 2.43
5887 6869 5.245075 GCACAGGCCTCTCTTATATTCTAGT 59.755 44.000 0.00 0.00 0.00 2.57
5888 6870 6.434652 GCACAGGCCTCTCTTATATTCTAGTA 59.565 42.308 0.00 0.00 0.00 1.82
5889 6871 7.123547 GCACAGGCCTCTCTTATATTCTAGTAT 59.876 40.741 0.00 0.00 0.00 2.12
5890 6872 9.688091 CACAGGCCTCTCTTATATTCTAGTATA 57.312 37.037 0.00 0.00 0.00 1.47
5922 6904 4.715713 GTTCCCGAATAGAAATAGGCCTT 58.284 43.478 12.58 0.00 0.00 4.35
5941 6923 5.008118 GGCCTTTCTCTCCAATATTCTTTCG 59.992 44.000 0.00 0.00 0.00 3.46
5963 6945 1.078214 CCTGGCCGCAAGAATCTGA 60.078 57.895 0.00 0.00 43.02 3.27
5993 6975 4.325741 TCTTTTGCGTTGTTGTCATGTTTG 59.674 37.500 0.00 0.00 0.00 2.93
5994 6976 1.554392 TGCGTTGTTGTCATGTTTGC 58.446 45.000 0.00 0.00 0.00 3.68
5995 6977 1.133982 TGCGTTGTTGTCATGTTTGCT 59.866 42.857 0.00 0.00 0.00 3.91
5996 6978 1.780860 GCGTTGTTGTCATGTTTGCTC 59.219 47.619 0.00 0.00 0.00 4.26
6035 7063 9.517868 TCTAAGGCTACATTAGGAGTAGTATTC 57.482 37.037 0.00 0.00 40.76 1.75
6038 7066 8.866970 AGGCTACATTAGGAGTAGTATTCTAC 57.133 38.462 1.43 1.43 44.79 2.59
6135 7217 2.218603 CACGTGAGGGCTTAGTTTGTT 58.781 47.619 10.90 0.00 0.00 2.83
6161 7243 5.419542 TGCTGTTGTAAGCTATGGTCTAAG 58.580 41.667 0.00 0.00 43.90 2.18
6205 7297 3.368236 GGTTCTTCGTAAGCACAGTCATC 59.632 47.826 0.00 0.00 37.18 2.92
6386 7591 2.159043 ACATCAGGAAGATACTGCACGG 60.159 50.000 0.00 0.00 34.43 4.94
6399 7604 2.144362 GCACGGTTTTGCAAGCATC 58.856 52.632 0.00 0.00 42.49 3.91
6408 7613 2.314323 TTGCAAGCATCGCAGATAGA 57.686 45.000 0.00 0.00 45.12 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.692406 GGCTCGGTCTTGTCGGGT 61.692 66.667 0.00 0.00 0.00 5.28
104 105 2.159184 TCTTGTCATTGCGGCAAACAAA 60.159 40.909 24.79 16.56 28.21 2.83
125 126 2.397413 CTGTCAACCCCAAGACGCCT 62.397 60.000 0.00 0.00 37.58 5.52
187 188 1.376037 GACAAGGAGAAGCCCGTGG 60.376 63.158 0.00 0.00 39.52 4.94
188 189 1.376037 GGACAAGGAGAAGCCCGTG 60.376 63.158 0.00 0.00 40.74 4.94
189 190 1.536662 AGGACAAGGAGAAGCCCGT 60.537 57.895 0.00 0.00 37.37 5.28
347 351 8.013378 GGTTTATTTCGGTGGATTATATGTTCG 58.987 37.037 0.00 0.00 0.00 3.95
391 395 7.606456 GGAAGTAAATAAATAGGGATGATCGCA 59.394 37.037 12.18 0.00 0.00 5.10
795 819 0.819582 CTGCCTACAAATTGGGCCTG 59.180 55.000 4.53 0.00 44.71 4.85
797 821 1.960040 GCCTGCCTACAAATTGGGCC 61.960 60.000 10.08 0.00 44.71 5.80
833 858 3.881019 TTCCAGACGAGGCGAGGGT 62.881 63.158 0.00 0.00 0.00 4.34
848 873 0.040692 GTCGGTTTCGGTTTGCTTCC 60.041 55.000 0.00 0.00 36.95 3.46
1018 1044 3.090765 CTGAAGGAAGGGGGTGGG 58.909 66.667 0.00 0.00 0.00 4.61
1021 1047 1.466186 AAGGCTGAAGGAAGGGGGT 60.466 57.895 0.00 0.00 0.00 4.95
1022 1048 1.000396 CAAGGCTGAAGGAAGGGGG 60.000 63.158 0.00 0.00 0.00 5.40
1048 1075 1.154035 GACCAAATTCGGCGGCAAG 60.154 57.895 10.53 0.00 0.00 4.01
1050 1077 3.427425 CGACCAAATTCGGCGGCA 61.427 61.111 10.53 0.00 35.26 5.69
1106 1133 2.959484 CGAGCAAGAGGGGGCTTCA 61.959 63.158 0.00 0.00 41.22 3.02
1111 1138 4.521062 CTCGCGAGCAAGAGGGGG 62.521 72.222 25.07 0.00 0.00 5.40
1122 1149 1.477553 ATAACCCAAGTACCTCGCGA 58.522 50.000 9.26 9.26 0.00 5.87
1132 1159 6.287589 AGACTTCTCAGTGTATAACCCAAG 57.712 41.667 0.00 0.00 31.22 3.61
1140 1167 7.836685 TCTCCAATCTAAGACTTCTCAGTGTAT 59.163 37.037 0.00 0.00 31.22 2.29
1150 1177 4.773149 ACCGACTTCTCCAATCTAAGACTT 59.227 41.667 0.00 0.00 0.00 3.01
1183 1210 3.057946 GTGTTGGAAGGAAGATTCACAGC 60.058 47.826 0.00 0.00 0.00 4.40
1201 1228 5.123344 GCGTGATAATGGAAAACCTAGTGTT 59.877 40.000 0.00 0.00 39.43 3.32
1216 1243 2.591715 GGCCGGCAGCGTGATAAT 60.592 61.111 30.85 0.00 45.17 1.28
1264 1291 5.591643 ACGCTAAACTGAATTATATGGCG 57.408 39.130 0.00 0.00 43.55 5.69
1408 1440 2.231235 AGGTCACCGCAATTCCAAATTC 59.769 45.455 0.00 0.00 0.00 2.17
1423 1455 6.128526 GCAGATACAGTACAAGAAAAGGTCAC 60.129 42.308 0.00 0.00 0.00 3.67
1436 1468 7.721286 ATAAAGATGCTTGCAGATACAGTAC 57.279 36.000 0.87 0.00 0.00 2.73
1438 1470 9.429359 GTATATAAAGATGCTTGCAGATACAGT 57.571 33.333 0.87 0.00 0.00 3.55
1439 1471 9.650539 AGTATATAAAGATGCTTGCAGATACAG 57.349 33.333 0.87 0.00 0.00 2.74
1440 1472 9.428097 CAGTATATAAAGATGCTTGCAGATACA 57.572 33.333 0.87 0.00 0.00 2.29
1510 1546 1.553704 GGCCCCTCTTCTTCGACTAAA 59.446 52.381 0.00 0.00 0.00 1.85
1517 1553 0.995803 AGGAAAGGCCCCTCTTCTTC 59.004 55.000 0.00 0.00 37.37 2.87
1799 1835 4.070716 GCATCTGGCATATCACTAGCTTT 58.929 43.478 0.00 0.00 43.97 3.51
1913 1951 6.072508 TGGAAACAGATACTGATTTCTTGTGC 60.073 38.462 5.76 0.00 34.82 4.57
2165 2258 8.589335 TGAATGAGACTTTAAGTACACTGAAC 57.411 34.615 0.00 0.00 0.00 3.18
2251 2465 8.902540 AAACATATTGAACAGTCTACACAGAA 57.097 30.769 0.00 0.00 30.85 3.02
2935 3149 7.442364 CAGGTGATGGACTTAATTCGTATCATT 59.558 37.037 11.72 4.89 0.00 2.57
3040 3254 7.726216 ACATCTAATGATCAACAAGGATACGA 58.274 34.615 0.00 0.00 46.39 3.43
3061 3275 7.665690 TCAGCCTGAATCTCTATTCTAACATC 58.334 38.462 0.00 0.00 41.83 3.06
3192 3406 1.774254 TCCCTGCCTCTTTTCAAGTCA 59.226 47.619 0.00 0.00 0.00 3.41
3514 3728 2.259204 CAAGTGCCAACGCCCATG 59.741 61.111 0.00 0.00 0.00 3.66
3760 3974 7.642669 AGTTTCATTCAACATGATATTAGCCG 58.357 34.615 0.00 0.00 0.00 5.52
3773 3987 7.420800 AGATGTTGTCTGAAGTTTCATTCAAC 58.579 34.615 21.51 21.51 43.09 3.18
3918 4145 4.592351 AGTAACAGCATGCCATCTCTCTAT 59.408 41.667 15.66 0.00 42.53 1.98
3934 4161 3.741344 CGACCCAAGAAGTCAAGTAACAG 59.259 47.826 0.00 0.00 33.70 3.16
3959 4186 5.811399 TGAATCATTGGTTCCAATCGTAC 57.189 39.130 13.38 7.45 34.80 3.67
3962 4189 5.916883 GCTTATGAATCATTGGTTCCAATCG 59.083 40.000 13.38 9.82 34.80 3.34
3968 4195 6.520792 GCAATGCTTATGAATCATTGGTTC 57.479 37.500 14.30 2.56 44.20 3.62
3989 4216 3.489355 TGATTCTTCCAAGCTTCAAGCA 58.511 40.909 13.10 0.00 45.56 3.91
3998 4225 7.264373 ACTACAAACTGTTGATTCTTCCAAG 57.736 36.000 0.00 0.00 38.20 3.61
3999 4226 7.639113 AACTACAAACTGTTGATTCTTCCAA 57.361 32.000 0.00 0.00 38.20 3.53
4000 4227 7.990886 ACTAACTACAAACTGTTGATTCTTCCA 59.009 33.333 0.00 0.00 38.20 3.53
4001 4228 8.379457 ACTAACTACAAACTGTTGATTCTTCC 57.621 34.615 0.00 0.00 38.20 3.46
4007 4234 8.936864 GCATTCTACTAACTACAAACTGTTGAT 58.063 33.333 0.00 0.00 38.20 2.57
4008 4235 8.148351 AGCATTCTACTAACTACAAACTGTTGA 58.852 33.333 0.00 0.00 38.20 3.18
4009 4236 8.311650 AGCATTCTACTAACTACAAACTGTTG 57.688 34.615 0.00 0.00 40.84 3.33
4010 4237 8.774586 CAAGCATTCTACTAACTACAAACTGTT 58.225 33.333 0.00 0.00 0.00 3.16
4011 4238 8.148351 TCAAGCATTCTACTAACTACAAACTGT 58.852 33.333 0.00 0.00 0.00 3.55
4012 4239 8.534333 TCAAGCATTCTACTAACTACAAACTG 57.466 34.615 0.00 0.00 0.00 3.16
4013 4240 9.209175 CTTCAAGCATTCTACTAACTACAAACT 57.791 33.333 0.00 0.00 0.00 2.66
4014 4241 7.958025 GCTTCAAGCATTCTACTAACTACAAAC 59.042 37.037 3.89 0.00 41.89 2.93
4015 4242 7.878127 AGCTTCAAGCATTCTACTAACTACAAA 59.122 33.333 13.10 0.00 45.56 2.83
4016 4243 7.386851 AGCTTCAAGCATTCTACTAACTACAA 58.613 34.615 13.10 0.00 45.56 2.41
4017 4244 6.936279 AGCTTCAAGCATTCTACTAACTACA 58.064 36.000 13.10 0.00 45.56 2.74
4018 4245 7.201565 CCAAGCTTCAAGCATTCTACTAACTAC 60.202 40.741 13.10 0.00 45.56 2.73
4019 4246 6.818644 CCAAGCTTCAAGCATTCTACTAACTA 59.181 38.462 13.10 0.00 45.56 2.24
4020 4247 5.645497 CCAAGCTTCAAGCATTCTACTAACT 59.355 40.000 13.10 0.00 45.56 2.24
4021 4248 5.643777 TCCAAGCTTCAAGCATTCTACTAAC 59.356 40.000 13.10 0.00 45.56 2.34
4022 4249 5.804639 TCCAAGCTTCAAGCATTCTACTAA 58.195 37.500 13.10 0.00 45.56 2.24
4023 4250 5.420725 TCCAAGCTTCAAGCATTCTACTA 57.579 39.130 13.10 0.00 45.56 1.82
4024 4251 4.292186 TCCAAGCTTCAAGCATTCTACT 57.708 40.909 13.10 0.00 45.56 2.57
4025 4252 4.697352 TCTTCCAAGCTTCAAGCATTCTAC 59.303 41.667 13.10 0.00 45.56 2.59
4026 4253 4.910195 TCTTCCAAGCTTCAAGCATTCTA 58.090 39.130 13.10 0.00 45.56 2.10
4027 4254 3.759581 TCTTCCAAGCTTCAAGCATTCT 58.240 40.909 13.10 0.00 45.56 2.40
4028 4255 4.510038 TTCTTCCAAGCTTCAAGCATTC 57.490 40.909 13.10 0.00 45.56 2.67
4029 4256 4.525487 TGATTCTTCCAAGCTTCAAGCATT 59.475 37.500 13.10 0.00 45.56 3.56
4030 4257 4.084287 TGATTCTTCCAAGCTTCAAGCAT 58.916 39.130 13.10 0.00 45.56 3.79
4031 4258 3.489355 TGATTCTTCCAAGCTTCAAGCA 58.511 40.909 13.10 0.00 45.56 3.91
4032 4259 4.233005 GTTGATTCTTCCAAGCTTCAAGC 58.767 43.478 0.00 0.00 42.84 4.01
4033 4260 5.009410 ACTGTTGATTCTTCCAAGCTTCAAG 59.991 40.000 0.00 1.85 31.73 3.02
4034 4261 4.889409 ACTGTTGATTCTTCCAAGCTTCAA 59.111 37.500 0.00 0.00 0.00 2.69
4035 4262 4.464008 ACTGTTGATTCTTCCAAGCTTCA 58.536 39.130 0.00 0.00 0.00 3.02
4036 4263 5.444663 AACTGTTGATTCTTCCAAGCTTC 57.555 39.130 0.00 0.00 0.00 3.86
4037 4264 5.127682 ACAAACTGTTGATTCTTCCAAGCTT 59.872 36.000 0.00 0.00 38.20 3.74
4038 4265 4.646492 ACAAACTGTTGATTCTTCCAAGCT 59.354 37.500 0.00 0.00 38.20 3.74
4039 4266 4.936891 ACAAACTGTTGATTCTTCCAAGC 58.063 39.130 0.00 0.00 38.20 4.01
4040 4267 7.264373 ACTACAAACTGTTGATTCTTCCAAG 57.736 36.000 0.00 0.00 38.20 3.61
4191 4419 2.678336 GAGGCGGGTGATCTTAAGTTTG 59.322 50.000 1.63 0.00 0.00 2.93
4207 4435 9.750125 TGCTAATATAGTAATATCAATGAGGCG 57.250 33.333 0.00 0.00 0.00 5.52
4243 4471 8.574251 AATAAAGGTTTACTGTACATGCATGA 57.426 30.769 32.75 13.72 0.00 3.07
4310 4538 6.260936 ACAAGAAGAAATATATTGGCTGACCG 59.739 38.462 0.00 0.00 39.70 4.79
4351 4583 3.604772 CGAAAAGAAAGAGTGCCAGAACG 60.605 47.826 0.00 0.00 0.00 3.95
4386 4618 7.495934 GCATAACCATCATGTTACACTCTTAGT 59.504 37.037 0.00 0.00 33.78 2.24
4388 4620 7.495606 CAGCATAACCATCATGTTACACTCTTA 59.504 37.037 0.00 0.00 33.78 2.10
4389 4621 6.317140 CAGCATAACCATCATGTTACACTCTT 59.683 38.462 0.00 0.00 33.78 2.85
4390 4622 5.819379 CAGCATAACCATCATGTTACACTCT 59.181 40.000 0.00 0.00 33.78 3.24
4391 4623 5.817296 TCAGCATAACCATCATGTTACACTC 59.183 40.000 0.00 0.00 33.78 3.51
4392 4624 5.744171 TCAGCATAACCATCATGTTACACT 58.256 37.500 0.00 0.00 33.78 3.55
4393 4625 6.624352 ATCAGCATAACCATCATGTTACAC 57.376 37.500 0.00 0.00 33.78 2.90
4481 4713 1.982395 CAGGTGTCTACGCCCCTGA 60.982 63.158 9.06 0.00 45.97 3.86
4488 4720 2.712709 TCCTCTTCTCAGGTGTCTACG 58.287 52.381 0.00 0.00 34.76 3.51
4509 4741 4.431131 CAATGGAGGCTGCCCCGT 62.431 66.667 16.57 14.59 39.21 5.28
4601 4833 5.129485 CCTCCGTCCCATAATATAAGAGCAT 59.871 44.000 0.00 0.00 0.00 3.79
4602 4834 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
4619 4851 7.757941 GAGTATTAATTAGTACTCCCTCCGT 57.242 40.000 26.31 4.96 38.71 4.69
4770 5002 2.036098 CAGCTGACCCAATGGCCA 59.964 61.111 8.56 8.56 33.59 5.36
5021 5255 1.871126 GCAAGCAGCTTTGAGGGGTC 61.871 60.000 4.38 0.00 41.15 4.46
5023 5257 2.643232 GGCAAGCAGCTTTGAGGGG 61.643 63.158 4.38 0.00 44.79 4.79
5057 5291 2.355209 GGAGCTCTACTGGACAAAAGGG 60.355 54.545 14.64 0.00 0.00 3.95
5149 6117 3.081804 GTCCTATTTGATTATGCCCGGG 58.918 50.000 19.09 19.09 0.00 5.73
5152 6120 4.469657 TGGTGTCCTATTTGATTATGCCC 58.530 43.478 0.00 0.00 0.00 5.36
5251 6219 7.158697 TCTATCTTCACCTTCGAAACATTCAA 58.841 34.615 0.00 0.00 0.00 2.69
5252 6220 6.697395 TCTATCTTCACCTTCGAAACATTCA 58.303 36.000 0.00 0.00 0.00 2.57
5253 6221 6.814146 ACTCTATCTTCACCTTCGAAACATTC 59.186 38.462 0.00 0.00 0.00 2.67
5254 6222 6.702329 ACTCTATCTTCACCTTCGAAACATT 58.298 36.000 0.00 0.00 0.00 2.71
5255 6223 6.287589 ACTCTATCTTCACCTTCGAAACAT 57.712 37.500 0.00 0.00 0.00 2.71
5308 6276 9.309796 CAAACTTTATTAGTAGTTGTTACGTGC 57.690 33.333 0.00 0.00 35.54 5.34
5377 6348 5.013808 ACATGATGATATGGATTGCTGAGGA 59.986 40.000 0.00 0.00 32.32 3.71
5450 6429 5.529430 ACCTGAAATTTCACGACAATACACA 59.471 36.000 16.91 0.00 32.90 3.72
5514 6493 0.397941 TAGGGCATATGCAGGCTGTC 59.602 55.000 28.07 9.46 44.36 3.51
5549 6528 1.080230 CACGTGCTGAGGGAGACTG 60.080 63.158 0.82 0.00 0.00 3.51
5655 6635 5.178061 CCTCTACATAACAGAACATGTGCA 58.822 41.667 6.60 0.00 43.00 4.57
5675 6655 0.833287 TAGGCAAGGCATCTCACCTC 59.167 55.000 0.00 0.00 36.14 3.85
5680 6660 3.484407 ACAATGATAGGCAAGGCATCTC 58.516 45.455 0.00 0.00 0.00 2.75
5793 6773 9.665719 GTCTCTTCTTATTTCAGATCCTTCTTT 57.334 33.333 0.00 0.00 0.00 2.52
5880 6862 6.210984 GGGAACGTCCTCCATTATACTAGAAT 59.789 42.308 8.50 0.00 37.20 2.40
5881 6863 5.537674 GGGAACGTCCTCCATTATACTAGAA 59.462 44.000 8.50 0.00 37.20 2.10
5883 6865 5.388408 GGGAACGTCCTCCATTATACTAG 57.612 47.826 8.50 0.00 37.20 2.57
5922 6904 4.876107 GGTGCGAAAGAATATTGGAGAGAA 59.124 41.667 0.00 0.00 0.00 2.87
5963 6945 5.406780 TGACAACAACGCAAAAGACAAAATT 59.593 32.000 0.00 0.00 0.00 1.82
5993 6975 4.565962 GCCTTAGAAAACTAGTAACCGAGC 59.434 45.833 0.00 0.00 0.00 5.03
5994 6976 5.963594 AGCCTTAGAAAACTAGTAACCGAG 58.036 41.667 0.00 0.00 0.00 4.63
5995 6977 5.990120 AGCCTTAGAAAACTAGTAACCGA 57.010 39.130 0.00 0.00 0.00 4.69
5996 6978 6.624423 TGTAGCCTTAGAAAACTAGTAACCG 58.376 40.000 0.00 0.00 0.00 4.44
6035 7063 3.574354 AGGTACTCCCTCCTAACGTAG 57.426 52.381 0.00 0.00 40.71 3.51
6070 7141 3.078097 TGGTCACAACAATGGATAACGG 58.922 45.455 0.00 0.00 0.00 4.44
6083 7165 4.098914 ACTAAGCCTCAAATGGTCACAA 57.901 40.909 0.00 0.00 0.00 3.33
6117 7199 2.218603 ACAACAAACTAAGCCCTCACG 58.781 47.619 0.00 0.00 0.00 4.35
6121 7203 2.362077 CAGCAACAACAAACTAAGCCCT 59.638 45.455 0.00 0.00 0.00 5.19
6123 7205 3.436700 ACAGCAACAACAAACTAAGCC 57.563 42.857 0.00 0.00 0.00 4.35
6131 7213 5.507149 CCATAGCTTACAACAGCAACAACAA 60.507 40.000 0.00 0.00 42.84 2.83
6135 7217 3.750371 ACCATAGCTTACAACAGCAACA 58.250 40.909 0.00 0.00 42.84 3.33
6176 7258 2.806244 TGCTTACGAAGAACCAGCTTTC 59.194 45.455 0.00 0.00 0.00 2.62
6386 7591 1.986698 ATCTGCGATGCTTGCAAAAC 58.013 45.000 0.00 0.00 42.70 2.43
6399 7604 1.920574 CACGGTCTTTGTCTATCTGCG 59.079 52.381 0.00 0.00 0.00 5.18
6408 7613 2.038426 TCCATCATGACACGGTCTTTGT 59.962 45.455 0.00 0.00 33.15 2.83


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

AutoCloner maintained by Alex Coulton.