Multiple sequence alignment - TraesCS4D01G357800

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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 TraesCS4D01G357800 chr4D 100.000 4928 0 0 1 4928 505993380 505988453 0.000000e+00 9101.0
1 TraesCS4D01G357800 chr5A 93.139 3644 188 25 2 3629 702142295 702138698 0.000000e+00 5288.0
2 TraesCS4D01G357800 chr5A 95.908 611 25 0 4318 4928 702137763 702137153 0.000000e+00 990.0
3 TraesCS4D01G357800 chr5A 88.828 546 16 7 3766 4266 702138306 702137761 3.240000e-176 628.0
4 TraesCS4D01G357800 chr5A 89.394 132 14 0 3638 3769 702138632 702138501 3.050000e-37 167.0
5 TraesCS4D01G357800 chr4B 90.310 3808 319 26 1 3769 661684632 661680836 0.000000e+00 4942.0
6 TraesCS4D01G357800 chr4B 91.279 2947 230 19 1 2926 661492220 661495160 0.000000e+00 3993.0
7 TraesCS4D01G357800 chr4B 92.792 874 45 2 2914 3769 661495190 661496063 0.000000e+00 1249.0
8 TraesCS4D01G357800 chr4B 93.137 612 23 4 4318 4928 661680117 661679524 0.000000e+00 880.0
9 TraesCS4D01G357800 chr4B 90.909 528 22 2 3765 4266 661680642 661680115 0.000000e+00 686.0
10 TraesCS4D01G357800 chr4B 89.513 534 23 6 3766 4266 661496258 661496791 0.000000e+00 645.0
11 TraesCS4D01G357800 chr4B 95.498 311 14 0 4618 4928 661497058 661497368 9.530000e-137 497.0
12 TraesCS4D01G357800 chr4B 94.361 266 11 3 4318 4579 661496789 661497054 5.940000e-109 405.0
13 TraesCS4D01G357800 chr4B 90.769 65 1 3 4264 4323 340684680 340684616 1.140000e-11 82.4
14 TraesCS4D01G357800 chrUn 78.682 1351 204 54 2328 3633 88950158 88951469 0.000000e+00 822.0
15 TraesCS4D01G357800 chrUn 78.698 1352 202 57 2328 3633 269543239 269541928 0.000000e+00 822.0
16 TraesCS4D01G357800 chrUn 77.558 1466 240 59 2213 3633 88958397 88959818 0.000000e+00 802.0
17 TraesCS4D01G357800 chrUn 77.698 417 49 25 3766 4146 88953766 88954174 1.070000e-51 215.0
18 TraesCS4D01G357800 chrUn 77.778 414 48 25 3769 4146 269539628 269539223 1.070000e-51 215.0
19 TraesCS4D01G357800 chrUn 77.458 417 49 26 3766 4146 88962159 88962566 1.800000e-49 207.0
20 TraesCS4D01G357800 chr7B 78.176 1338 231 34 2207 3504 746601411 746600095 0.000000e+00 797.0
21 TraesCS4D01G357800 chr7B 78.102 1338 232 34 2207 3504 746573103 746571787 0.000000e+00 791.0
22 TraesCS4D01G357800 chr7B 84.261 521 74 8 3107 3621 744679438 744678920 7.360000e-138 501.0
23 TraesCS4D01G357800 chr7B 81.328 241 37 5 3907 4142 744678478 744678241 6.510000e-44 189.0
24 TraesCS4D01G357800 chr7B 80.579 242 39 5 3907 4143 746224750 746224988 3.920000e-41 180.0
25 TraesCS4D01G357800 chr7B 82.143 140 23 2 4443 4581 746215743 746215881 8.670000e-23 119.0
26 TraesCS4D01G357800 chr1B 87.798 336 33 4 4354 4682 89696854 89696520 2.150000e-103 387.0
27 TraesCS4D01G357800 chr1B 81.431 517 49 14 3766 4245 89697383 89696877 3.600000e-101 379.0
28 TraesCS4D01G357800 chr1B 88.400 250 26 3 4664 4913 89696337 89696091 1.040000e-76 298.0
29 TraesCS4D01G357800 chr1B 88.406 69 5 2 4262 4327 596247429 596247361 4.090000e-11 80.5
30 TraesCS4D01G357800 chr7A 81.667 180 31 2 4404 4581 735053594 735053415 1.110000e-31 148.0
31 TraesCS4D01G357800 chr7A 83.594 128 20 1 4796 4923 62482662 62482536 8.670000e-23 119.0
32 TraesCS4D01G357800 chr3D 84.483 116 16 2 4814 4928 71763022 71762908 4.030000e-21 113.0
33 TraesCS4D01G357800 chr3D 94.737 57 3 0 4264 4320 12253082 12253138 6.790000e-14 89.8
34 TraesCS4D01G357800 chr3A 83.333 114 16 3 4814 4926 585607578 585607689 8.730000e-18 102.0
35 TraesCS4D01G357800 chr5B 91.667 72 6 0 4818 4889 303583926 303583997 3.140000e-17 100.0
36 TraesCS4D01G357800 chr6D 96.491 57 1 1 4264 4320 455902771 455902716 5.250000e-15 93.5
37 TraesCS4D01G357800 chr6D 94.737 57 2 1 4265 4320 220391790 220391734 2.440000e-13 87.9
38 TraesCS4D01G357800 chr6D 93.333 60 2 2 4261 4320 436463252 436463309 2.440000e-13 87.9
39 TraesCS4D01G357800 chr3B 96.429 56 0 1 4265 4320 485387351 485387298 1.890000e-14 91.6
40 TraesCS4D01G357800 chr1D 93.220 59 1 1 4262 4320 10816051 10816106 3.160000e-12 84.2
41 TraesCS4D01G357800 chr7D 91.525 59 5 0 4814 4872 279743768 279743710 1.140000e-11 82.4
42 TraesCS4D01G357800 chr2A 90.769 65 1 2 4261 4320 755180130 755180194 1.140000e-11 82.4


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 TraesCS4D01G357800 chr4D 505988453 505993380 4927 True 9101.000000 9101 100.000000 1 4928 1 chr4D.!!$R1 4927
1 TraesCS4D01G357800 chr5A 702137153 702142295 5142 True 1768.250000 5288 91.817250 2 4928 4 chr5A.!!$R1 4926
2 TraesCS4D01G357800 chr4B 661679524 661684632 5108 True 2169.333333 4942 91.452000 1 4928 3 chr4B.!!$R2 4927
3 TraesCS4D01G357800 chr4B 661492220 661497368 5148 False 1357.800000 3993 92.688600 1 4928 5 chr4B.!!$F1 4927
4 TraesCS4D01G357800 chrUn 88950158 88954174 4016 False 518.500000 822 78.190000 2328 4146 2 chrUn.!!$F1 1818
5 TraesCS4D01G357800 chrUn 269539223 269543239 4016 True 518.500000 822 78.238000 2328 4146 2 chrUn.!!$R1 1818
6 TraesCS4D01G357800 chrUn 88958397 88962566 4169 False 504.500000 802 77.508000 2213 4146 2 chrUn.!!$F2 1933
7 TraesCS4D01G357800 chr7B 746600095 746601411 1316 True 797.000000 797 78.176000 2207 3504 1 chr7B.!!$R2 1297
8 TraesCS4D01G357800 chr7B 746571787 746573103 1316 True 791.000000 791 78.102000 2207 3504 1 chr7B.!!$R1 1297
9 TraesCS4D01G357800 chr7B 744678241 744679438 1197 True 345.000000 501 82.794500 3107 4142 2 chr7B.!!$R3 1035
10 TraesCS4D01G357800 chr1B 89696091 89697383 1292 True 354.666667 387 85.876333 3766 4913 3 chr1B.!!$R2 1147

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
70 71 1.168714 GGTGCCAGCTACTTCCTTTG 58.831 55.0 0.00 0.0 0.00 2.77 F
1465 1479 0.396435 TATTCGGAGCGGCCATCAAT 59.604 50.0 2.24 0.0 35.94 2.57 F
2047 2061 0.181350 ATGATGGCTTCTTCGGTCCC 59.819 55.0 1.86 0.0 0.00 4.46 F
3468 3566 0.106149 AGTTCCTGGTGTTGTCGTCC 59.894 55.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 1949 0.541392 AGCCCACTGCACATTATCGA 59.459 50.000 0.00 0.0 44.83 3.59 R
3202 3300 1.606668 GTTGCTCACGGTTTCAATGGA 59.393 47.619 0.00 0.0 0.00 3.41 R
3533 5617 0.474184 AGGATTGCCCTTGGGATACG 59.526 55.000 10.36 0.0 44.85 3.06 R
4720 7356 1.072965 CCTTCTTGCAGGTCTCCTTGT 59.927 52.381 0.00 0.0 0.00 3.16 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
30 31 7.045868 CGTATGTTCGTTGTGCAATAATTGTAC 60.046 37.037 0.00 0.00 45.03 2.90
70 71 1.168714 GGTGCCAGCTACTTCCTTTG 58.831 55.000 0.00 0.00 0.00 2.77
347 350 2.399580 GTCTACCATGTCCTTAGGCCT 58.600 52.381 11.78 11.78 0.00 5.19
365 368 4.660303 AGGCCTACAATTCATAGACATGGA 59.340 41.667 1.29 0.00 32.61 3.41
372 375 3.497103 TTCATAGACATGGATGGCCTG 57.503 47.619 3.32 0.00 36.08 4.85
389 392 2.486982 GCCTGTATGCCATAGATGCAAG 59.513 50.000 4.59 0.00 42.92 4.01
439 451 1.215647 GTCTACAGACAGGGTGGCG 59.784 63.158 4.48 0.00 44.18 5.69
491 503 4.076394 GTCTACAAATGCAAGGGGTGTTA 58.924 43.478 0.00 0.00 0.00 2.41
501 513 3.243737 GCAAGGGGTGTTACTTTTTCCTG 60.244 47.826 0.00 0.00 0.00 3.86
505 517 2.035449 GGGTGTTACTTTTTCCTGTGCC 59.965 50.000 0.00 0.00 0.00 5.01
625 638 1.269569 CGGCATCGTAAGCAGTGGATA 60.270 52.381 0.00 0.00 37.18 2.59
745 758 2.091830 ACCACTCGTCCTCTATCCATGA 60.092 50.000 0.00 0.00 0.00 3.07
984 997 2.428530 GGGAAGTGAGGCCATTTCAATC 59.571 50.000 5.01 2.37 39.79 2.67
1064 1077 3.255642 GGAAGCAATTCTAGCAACACCAA 59.744 43.478 0.00 0.00 0.00 3.67
1071 1084 4.893424 TTCTAGCAACACCAACTTGAAC 57.107 40.909 0.00 0.00 0.00 3.18
1079 1092 5.277828 GCAACACCAACTTGAACTAGGTTAG 60.278 44.000 0.00 0.00 0.00 2.34
1217 1231 4.906618 TCCCAAAACTTCTACTCATCCAC 58.093 43.478 0.00 0.00 0.00 4.02
1282 1296 1.868713 AAATGGGCAATGGCATCTCA 58.131 45.000 9.51 0.00 43.71 3.27
1381 1395 4.012374 ACTCCTTCAAGTATGTGCCAATG 58.988 43.478 0.00 0.00 0.00 2.82
1436 1450 2.029918 GTGCTCTCATCAAAAACACCCC 60.030 50.000 0.00 0.00 0.00 4.95
1465 1479 0.396435 TATTCGGAGCGGCCATCAAT 59.604 50.000 2.24 0.00 35.94 2.57
1646 1660 2.030562 CATCCGGCACCGTATCCC 59.969 66.667 8.49 0.00 37.81 3.85
1718 1732 1.036707 CTCCTTCTCATCGTCCTCCC 58.963 60.000 0.00 0.00 0.00 4.30
1753 1767 2.341257 CGGGACAGTGTTTCTCATCTG 58.659 52.381 0.00 0.00 34.14 2.90
1768 1782 2.038426 TCATCTGATGGTTGAACACGGT 59.962 45.455 17.06 0.00 0.00 4.83
1906 1920 6.493166 TGAGGTGTCAAATATGGATTCCTTT 58.507 36.000 3.95 0.00 0.00 3.11
1909 1923 5.422012 GGTGTCAAATATGGATTCCTTTGGT 59.578 40.000 13.15 0.00 31.20 3.67
1917 1931 1.689258 GGATTCCTTTGGTGATGGGGG 60.689 57.143 0.00 0.00 0.00 5.40
2032 2046 3.551846 GGTGTTCGTGGGGATTTATGAT 58.448 45.455 0.00 0.00 0.00 2.45
2047 2061 0.181350 ATGATGGCTTCTTCGGTCCC 59.819 55.000 1.86 0.00 0.00 4.46
2086 2100 4.719369 GCGAACCTCCACGTCGCT 62.719 66.667 9.81 0.00 45.01 4.93
2170 2184 7.346471 CCAATTCTGGTAATCTCTTTTCCCTA 58.654 38.462 0.00 0.00 38.00 3.53
2293 2307 0.534412 CGATGCACCAGAGAGTCCTT 59.466 55.000 0.00 0.00 0.00 3.36
2304 2318 3.927481 GAGTCCTTGGGGCACTGGC 62.927 68.421 0.00 0.00 40.13 4.85
2398 2412 1.146041 GCTGATGGGGTCATGCGTA 59.854 57.895 0.00 0.00 35.97 4.42
2633 2671 9.388346 GTACACACTCTCTTAATTAGATCATCG 57.612 37.037 0.00 0.00 30.92 3.84
2669 2707 8.768955 TGCATTTATTTGTGTTTTGACCATTAC 58.231 29.630 0.00 0.00 0.00 1.89
2693 2731 3.290710 ACTTGTGCTTGTTGGAATCTGT 58.709 40.909 0.00 0.00 0.00 3.41
2731 2772 2.975489 AGAGGATCAAGGCCGAACATAT 59.025 45.455 0.00 0.00 37.82 1.78
2877 2928 2.486592 TGCATGTTCAAGCACATCTCTG 59.513 45.455 0.00 0.00 35.03 3.35
2892 2943 6.148480 GCACATCTCTGAGTGTAATGTTTCTT 59.852 38.462 4.32 0.00 38.02 2.52
2929 3024 7.784037 TGATGCCACTATGAAATTGCTAAATT 58.216 30.769 0.00 0.00 37.61 1.82
3052 3147 6.358974 TGAGATAAGTTGTTCACCTCATGA 57.641 37.500 0.00 0.00 34.65 3.07
3213 3311 7.846644 TGCAAATATGAAATCCATTGAAACC 57.153 32.000 0.00 0.00 36.71 3.27
3312 3410 6.433716 TCAATCTGCACACCTGATAATTCAAA 59.566 34.615 0.00 0.00 32.52 2.69
3323 3421 6.489361 ACCTGATAATTCAAAGGATGCTCATC 59.511 38.462 7.11 1.35 37.11 2.92
3468 3566 0.106149 AGTTCCTGGTGTTGTCGTCC 59.894 55.000 0.00 0.00 0.00 4.79
3533 5617 2.093764 AGGTAGAGATGTTCACAGCTGC 60.094 50.000 15.27 0.00 43.41 5.25
3568 5652 0.757512 TCCTGCTGAGCATCTCATCC 59.242 55.000 7.94 0.00 39.92 3.51
3623 5709 3.436496 GTGAGCAACACCTCTATACGTC 58.564 50.000 0.00 0.00 43.05 4.34
3641 5746 2.182014 GTCGCACACAAACCAGTTTTC 58.818 47.619 0.00 0.00 0.00 2.29
3713 5858 4.080129 ACCATGAACTGCTCAACATATCCT 60.080 41.667 0.00 0.00 37.67 3.24
3763 5908 3.119137 ACGTTTCCATCATCGTGATCTCA 60.119 43.478 0.00 0.00 34.28 3.27
3993 6390 5.403246 CCTATACATGACCGAGATTGCTAC 58.597 45.833 0.00 0.00 0.00 3.58
4015 6412 2.502142 TCCAGTACTAGAAGCCGACA 57.498 50.000 0.00 0.00 0.00 4.35
4032 6429 1.744368 CACATGCTTCTCTGCGCCT 60.744 57.895 4.18 0.00 35.36 5.52
4109 6511 8.761575 AAAAATTACACTCCAAGCACATAATG 57.238 30.769 0.00 0.00 0.00 1.90
4158 6561 7.388776 TCATAGACTATGCATACTGATTTTGGC 59.611 37.037 16.38 0.00 36.14 4.52
4221 6634 2.755952 ACAAAAGCCTCCTCACCTTT 57.244 45.000 0.00 0.00 0.00 3.11
4266 6679 7.896811 TGGTCCTATGACTCATATTCATGTAC 58.103 38.462 0.00 0.00 41.47 2.90
4267 6680 7.730332 TGGTCCTATGACTCATATTCATGTACT 59.270 37.037 0.00 0.00 41.47 2.73
4268 6681 8.247562 GGTCCTATGACTCATATTCATGTACTC 58.752 40.741 0.00 0.00 41.47 2.59
4269 6682 8.247562 GTCCTATGACTCATATTCATGTACTCC 58.752 40.741 0.00 0.00 38.53 3.85
4270 6683 7.397476 TCCTATGACTCATATTCATGTACTCCC 59.603 40.741 0.00 0.00 35.31 4.30
4271 6684 7.398618 CCTATGACTCATATTCATGTACTCCCT 59.601 40.741 0.00 0.00 35.31 4.20
4272 6685 6.656632 TGACTCATATTCATGTACTCCCTC 57.343 41.667 0.00 0.00 33.57 4.30
4273 6686 5.540337 TGACTCATATTCATGTACTCCCTCC 59.460 44.000 0.00 0.00 33.57 4.30
4274 6687 4.524714 ACTCATATTCATGTACTCCCTCCG 59.475 45.833 0.00 0.00 33.57 4.63
4275 6688 4.480115 TCATATTCATGTACTCCCTCCGT 58.520 43.478 0.00 0.00 33.57 4.69
4276 6689 4.899457 TCATATTCATGTACTCCCTCCGTT 59.101 41.667 0.00 0.00 33.57 4.44
4277 6690 3.821421 ATTCATGTACTCCCTCCGTTC 57.179 47.619 0.00 0.00 0.00 3.95
4278 6691 1.481871 TCATGTACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
4279 6692 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
4280 6693 1.553248 CATGTACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
4281 6694 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
4282 6695 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
4283 6696 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
4284 6697 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
4285 6698 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4286 6699 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4287 6700 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4288 6701 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4289 6702 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4290 6703 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
4291 6704 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
4292 6705 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
4293 6706 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
4294 6707 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
4295 6708 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
4296 6709 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
4297 6710 4.517952 TCCAAATTACTCGTCGTGGTTA 57.482 40.909 0.00 0.00 0.00 2.85
4298 6711 4.487948 TCCAAATTACTCGTCGTGGTTAG 58.512 43.478 0.00 0.00 0.00 2.34
4299 6712 4.022068 TCCAAATTACTCGTCGTGGTTAGT 60.022 41.667 0.00 0.00 0.00 2.24
4300 6713 5.182950 TCCAAATTACTCGTCGTGGTTAGTA 59.817 40.000 0.00 0.00 0.00 1.82
4301 6714 5.863397 CCAAATTACTCGTCGTGGTTAGTAA 59.137 40.000 6.09 6.09 38.43 2.24
4302 6715 6.532657 CCAAATTACTCGTCGTGGTTAGTAAT 59.467 38.462 9.35 9.35 43.52 1.89
4305 6718 6.932901 TTACTCGTCGTGGTTAGTAATTTG 57.067 37.500 0.00 0.00 31.30 2.32
4306 6719 4.240096 ACTCGTCGTGGTTAGTAATTTGG 58.760 43.478 0.00 0.00 0.00 3.28
4307 6720 4.022068 ACTCGTCGTGGTTAGTAATTTGGA 60.022 41.667 0.00 0.00 0.00 3.53
4308 6721 4.880759 TCGTCGTGGTTAGTAATTTGGAA 58.119 39.130 0.00 0.00 0.00 3.53
4309 6722 4.685628 TCGTCGTGGTTAGTAATTTGGAAC 59.314 41.667 0.00 0.00 0.00 3.62
4310 6723 4.433283 CGTCGTGGTTAGTAATTTGGAACG 60.433 45.833 0.00 0.00 0.00 3.95
4311 6724 3.995705 TCGTGGTTAGTAATTTGGAACGG 59.004 43.478 0.00 0.00 0.00 4.44
4312 6725 3.995705 CGTGGTTAGTAATTTGGAACGGA 59.004 43.478 0.00 0.00 0.00 4.69
4313 6726 4.092383 CGTGGTTAGTAATTTGGAACGGAG 59.908 45.833 0.00 0.00 0.00 4.63
4314 6727 4.393990 GTGGTTAGTAATTTGGAACGGAGG 59.606 45.833 0.00 0.00 0.00 4.30
4315 6728 3.943381 GGTTAGTAATTTGGAACGGAGGG 59.057 47.826 0.00 0.00 0.00 4.30
4316 6729 4.323715 GGTTAGTAATTTGGAACGGAGGGA 60.324 45.833 0.00 0.00 0.00 4.20
4317 6730 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
4318 6731 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
4319 6732 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
4320 6733 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
4321 6734 2.314071 TTTGGAACGGAGGGAGTAGA 57.686 50.000 0.00 0.00 0.00 2.59
4437 6854 6.417635 GCAACAATAACGATTATGTGGATTGG 59.582 38.462 0.00 0.00 33.50 3.16
4441 6858 4.771114 AACGATTATGTGGATTGGGAGA 57.229 40.909 0.00 0.00 0.00 3.71
4578 6996 6.183360 GCATACTTTAGCTGCAACCTCATTAA 60.183 38.462 1.02 0.00 35.96 1.40
4579 6997 7.469181 GCATACTTTAGCTGCAACCTCATTAAT 60.469 37.037 1.02 0.00 35.96 1.40
4580 6998 6.199937 ACTTTAGCTGCAACCTCATTAATG 57.800 37.500 9.29 9.29 0.00 1.90
4581 6999 5.126061 ACTTTAGCTGCAACCTCATTAATGG 59.874 40.000 15.36 2.97 0.00 3.16
4582 7000 1.753073 AGCTGCAACCTCATTAATGGC 59.247 47.619 15.36 10.57 0.00 4.40
4583 7001 1.202452 GCTGCAACCTCATTAATGGCC 60.202 52.381 15.36 0.00 0.00 5.36
4584 7002 1.066002 CTGCAACCTCATTAATGGCCG 59.934 52.381 15.36 5.82 0.00 6.13
4585 7003 0.385390 GCAACCTCATTAATGGCCGG 59.615 55.000 15.36 14.58 0.00 6.13
4586 7004 0.385390 CAACCTCATTAATGGCCGGC 59.615 55.000 21.18 21.18 0.00 6.13
4587 7005 0.033601 AACCTCATTAATGGCCGGCA 60.034 50.000 30.85 15.30 0.00 5.69
4588 7006 0.751643 ACCTCATTAATGGCCGGCAC 60.752 55.000 30.85 18.39 0.00 5.01
4589 7007 0.751277 CCTCATTAATGGCCGGCACA 60.751 55.000 30.85 23.70 0.00 4.57
4720 7356 8.908903 TGCTTGTAGAATAAAAGGAAACAAGAA 58.091 29.630 14.56 3.09 43.01 2.52
4747 7383 0.185901 ACCTGCAAGAAGGGCAAGAA 59.814 50.000 0.00 0.00 42.11 2.52
4812 7448 4.390909 ACGGAAATGACAAATCTTACGGTC 59.609 41.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.716507 CATACCTTAGTACAATTATTGCACAAC 57.283 33.333 10.48 2.56 29.15 3.32
30 31 6.403636 GCACCACAAAATCAGTCATACCTTAG 60.404 42.308 0.00 0.00 0.00 2.18
70 71 8.903820 GGAATATATTATGGTAAAGCATCCACC 58.096 37.037 0.00 0.00 36.50 4.61
159 160 8.814235 GCATTTCAAGAACCTATGATCAATTTG 58.186 33.333 0.00 0.00 0.00 2.32
307 310 1.995484 CCATAGAGGCATGCGTTATCG 59.005 52.381 15.04 4.31 40.37 2.92
347 350 5.073554 AGGCCATCCATGTCTATGAATTGTA 59.926 40.000 5.01 0.00 36.36 2.41
372 375 2.440409 CCCCTTGCATCTATGGCATAC 58.560 52.381 2.32 0.00 41.58 2.39
405 410 4.018490 TGTAGACACCGAGTTGCCTATAA 58.982 43.478 0.00 0.00 0.00 0.98
406 411 3.623703 TGTAGACACCGAGTTGCCTATA 58.376 45.455 0.00 0.00 0.00 1.31
407 412 2.427453 CTGTAGACACCGAGTTGCCTAT 59.573 50.000 0.00 0.00 0.00 2.57
458 470 3.857010 GCATTTGTAGACACCAAGTTGCC 60.857 47.826 0.00 0.00 31.74 4.52
491 503 0.822121 GACCCGGCACAGGAAAAAGT 60.822 55.000 0.00 0.00 0.00 2.66
501 513 0.392998 ATTCTCATGTGACCCGGCAC 60.393 55.000 0.00 0.00 39.22 5.01
505 517 4.194640 AGATTCAATTCTCATGTGACCCG 58.805 43.478 0.00 0.00 0.00 5.28
549 562 8.585471 ACCAATCTTCAATAAATGAGACATGT 57.415 30.769 0.00 0.00 39.77 3.21
625 638 1.953559 CGACGGGGTCAATGAATGAT 58.046 50.000 0.00 0.00 40.97 2.45
745 758 2.630098 ACGTGCTATCTACATCAGGCAT 59.370 45.455 0.00 0.00 32.38 4.40
984 997 0.698238 TGTGGAGGAGTTTGGGATGG 59.302 55.000 0.00 0.00 0.00 3.51
1064 1077 6.096564 CGATTACCCTCTAACCTAGTTCAAGT 59.903 42.308 0.00 0.00 0.00 3.16
1071 1084 4.583489 TGCTTCGATTACCCTCTAACCTAG 59.417 45.833 0.00 0.00 0.00 3.02
1079 1092 3.064134 GCTTTCTTGCTTCGATTACCCTC 59.936 47.826 0.00 0.00 0.00 4.30
1139 1152 2.762535 ATAGTTGGAGTTGGGTGACG 57.237 50.000 0.00 0.00 0.00 4.35
1318 1332 1.305297 TGGGTCCGATGAGACAGCT 60.305 57.895 0.00 0.00 38.59 4.24
1436 1450 3.376540 CCGCTCCGAATAAAGAGAAGAG 58.623 50.000 0.00 0.00 31.43 2.85
1465 1479 0.608856 ATGATGTCGCTTGGTTGGCA 60.609 50.000 0.00 0.00 0.00 4.92
1579 1593 0.770557 TAGTTGGTTGGGCCTGGACT 60.771 55.000 4.53 4.56 38.35 3.85
1627 1641 1.006102 GGATACGGTGCCGGATGAG 60.006 63.158 13.69 0.00 43.85 2.90
1646 1660 1.833630 TGACAGCTGGTTGGAGATAGG 59.166 52.381 19.93 0.00 0.00 2.57
1718 1732 0.688487 TCCCGGTGACTAACAAAGGG 59.312 55.000 0.00 0.00 43.91 3.95
1753 1767 1.169661 TGGCACCGTGTTCAACCATC 61.170 55.000 0.00 0.00 0.00 3.51
1824 1838 2.298158 GAAATCGAGCCTGGAGCCGA 62.298 60.000 0.00 2.73 45.47 5.54
1909 1923 3.399181 GAGCGGTGACCCCCATCA 61.399 66.667 0.00 0.00 0.00 3.07
1935 1949 0.541392 AGCCCACTGCACATTATCGA 59.459 50.000 0.00 0.00 44.83 3.59
2032 2046 2.602267 TCGGGACCGAAGAAGCCA 60.602 61.111 11.57 0.00 46.01 4.75
2047 2061 1.009900 GAGGTAGTCGGTCGCATCG 60.010 63.158 0.00 0.00 0.00 3.84
2154 2168 6.263392 GCCTCCATTTAGGGAAAAGAGATTAC 59.737 42.308 0.00 0.00 36.27 1.89
2304 2318 3.393970 TCTCCCTCAGCGCCCAAG 61.394 66.667 2.29 0.00 0.00 3.61
2398 2412 2.158842 GCCCTTCATCAGCATCACTAGT 60.159 50.000 0.00 0.00 0.00 2.57
2669 2707 5.009010 ACAGATTCCAACAAGCACAAGTTAG 59.991 40.000 0.00 0.00 0.00 2.34
2693 2731 2.693591 CCTCTTTACCTCCTGTATCGCA 59.306 50.000 0.00 0.00 0.00 5.10
2892 2943 9.533831 TTCATAGTGGCATCATAATAGTCTAGA 57.466 33.333 0.00 0.00 0.00 2.43
3052 3147 9.740710 GTATATGAATGAATTAAAGGGCCTACT 57.259 33.333 6.41 0.00 0.00 2.57
3202 3300 1.606668 GTTGCTCACGGTTTCAATGGA 59.393 47.619 0.00 0.00 0.00 3.41
3276 3374 4.157289 GTGTGCAGATTGACATTTCAGGAT 59.843 41.667 0.00 0.00 31.71 3.24
3312 3410 3.950395 GCCAAGTAAAAGATGAGCATCCT 59.050 43.478 6.84 0.00 38.58 3.24
3323 3421 3.383761 CACTTTGGCTGCCAAGTAAAAG 58.616 45.455 30.63 26.03 44.84 2.27
3365 3463 4.035558 TGCCGATGTAATCAATCTTGAAGC 59.964 41.667 0.00 0.00 45.97 3.86
3468 3566 4.926238 GTGAAATACTGATAGAGCCCATCG 59.074 45.833 0.00 0.00 0.00 3.84
3533 5617 0.474184 AGGATTGCCCTTGGGATACG 59.526 55.000 10.36 0.00 44.85 3.06
3621 5707 2.159435 AGAAAACTGGTTTGTGTGCGAC 60.159 45.455 0.00 0.00 32.36 5.19
3623 5709 2.159448 TCAGAAAACTGGTTTGTGTGCG 60.159 45.455 14.05 0.00 40.52 5.34
3641 5746 4.768145 TGCGAAGTTACGAACAATTTCAG 58.232 39.130 0.00 0.00 35.09 3.02
3713 5858 3.294214 GGTACCTCCTCCTTTCGTCATA 58.706 50.000 4.06 0.00 0.00 2.15
3763 5908 2.563620 TCATGGTGCATGTGCTTTGAAT 59.436 40.909 6.55 0.00 41.98 2.57
3993 6390 3.130516 TGTCGGCTTCTAGTACTGGAATG 59.869 47.826 20.47 15.26 29.71 2.67
4015 6412 1.002868 AAGGCGCAGAGAAGCATGT 60.003 52.632 10.83 0.00 34.54 3.21
4109 6511 4.574599 AGGAAAACTGAATGTGAACTGC 57.425 40.909 0.00 0.00 0.00 4.40
4158 6561 3.869065 TGTTTAGGCTATGTTTCTCCCG 58.131 45.455 0.00 0.00 0.00 5.14
4203 6614 1.615392 CCAAAGGTGAGGAGGCTTTTG 59.385 52.381 0.00 0.00 0.00 2.44
4221 6634 2.754552 CAAGAGCCGAATTGGATTTCCA 59.245 45.455 0.00 0.00 45.94 3.53
4266 6679 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4267 6680 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4268 6681 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4269 6682 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4270 6683 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4271 6684 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
4272 6685 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
4273 6686 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
4274 6687 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
4275 6688 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
4276 6689 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
4277 6690 4.240096 ACTAACCACGACGAGTAATTTGG 58.760 43.478 0.00 0.00 0.00 3.28
4278 6691 6.932901 TTACTAACCACGACGAGTAATTTG 57.067 37.500 0.00 0.00 31.18 2.32
4281 6694 6.532657 CCAAATTACTAACCACGACGAGTAAT 59.467 38.462 0.00 7.42 43.58 1.89
4282 6695 5.863397 CCAAATTACTAACCACGACGAGTAA 59.137 40.000 0.00 5.19 38.41 2.24
4283 6696 5.182950 TCCAAATTACTAACCACGACGAGTA 59.817 40.000 0.00 0.00 0.00 2.59
4284 6697 4.022068 TCCAAATTACTAACCACGACGAGT 60.022 41.667 0.00 0.00 0.00 4.18
4285 6698 4.487948 TCCAAATTACTAACCACGACGAG 58.512 43.478 0.00 0.00 0.00 4.18
4286 6699 4.517952 TCCAAATTACTAACCACGACGA 57.482 40.909 0.00 0.00 0.00 4.20
4287 6700 4.433283 CGTTCCAAATTACTAACCACGACG 60.433 45.833 0.00 0.00 0.00 5.12
4288 6701 4.143052 CCGTTCCAAATTACTAACCACGAC 60.143 45.833 0.00 0.00 0.00 4.34
4289 6702 3.995705 CCGTTCCAAATTACTAACCACGA 59.004 43.478 0.00 0.00 0.00 4.35
4290 6703 3.995705 TCCGTTCCAAATTACTAACCACG 59.004 43.478 0.00 0.00 0.00 4.94
4291 6704 4.393990 CCTCCGTTCCAAATTACTAACCAC 59.606 45.833 0.00 0.00 0.00 4.16
4292 6705 4.566070 CCCTCCGTTCCAAATTACTAACCA 60.566 45.833 0.00 0.00 0.00 3.67
4293 6706 3.943381 CCCTCCGTTCCAAATTACTAACC 59.057 47.826 0.00 0.00 0.00 2.85
4294 6707 4.835678 TCCCTCCGTTCCAAATTACTAAC 58.164 43.478 0.00 0.00 0.00 2.34
4295 6708 4.533311 ACTCCCTCCGTTCCAAATTACTAA 59.467 41.667 0.00 0.00 0.00 2.24
4296 6709 4.098894 ACTCCCTCCGTTCCAAATTACTA 58.901 43.478 0.00 0.00 0.00 1.82
4297 6710 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4298 6711 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4299 6712 4.355549 TCTACTCCCTCCGTTCCAAATTA 58.644 43.478 0.00 0.00 0.00 1.40
4300 6713 3.178865 TCTACTCCCTCCGTTCCAAATT 58.821 45.455 0.00 0.00 0.00 1.82
4301 6714 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
4302 6715 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
4303 6716 2.108168 CATCTACTCCCTCCGTTCCAA 58.892 52.381 0.00 0.00 0.00 3.53
4304 6717 1.286849 TCATCTACTCCCTCCGTTCCA 59.713 52.381 0.00 0.00 0.00 3.53
4305 6718 2.068834 TCATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
4306 6719 4.467198 TTTTCATCTACTCCCTCCGTTC 57.533 45.455 0.00 0.00 0.00 3.95
4307 6720 4.903045 TTTTTCATCTACTCCCTCCGTT 57.097 40.909 0.00 0.00 0.00 4.44
4437 6854 5.552870 TTGAGCCCTTATATGTCTTCTCC 57.447 43.478 0.00 0.00 0.00 3.71
4586 7004 3.457610 AAGAAAATGGTGCAGGTTGTG 57.542 42.857 0.00 0.00 0.00 3.33
4587 7005 4.162131 AGAAAAGAAAATGGTGCAGGTTGT 59.838 37.500 0.00 0.00 0.00 3.32
4588 7006 4.696455 AGAAAAGAAAATGGTGCAGGTTG 58.304 39.130 0.00 0.00 0.00 3.77
4589 7007 4.405358 TGAGAAAAGAAAATGGTGCAGGTT 59.595 37.500 0.00 0.00 0.00 3.50
4720 7356 1.072965 CCTTCTTGCAGGTCTCCTTGT 59.927 52.381 0.00 0.00 0.00 3.16
4747 7383 3.242284 CGTTTGATTTCATCGCACGGTAT 60.242 43.478 0.00 0.00 35.12 2.73
4756 7392 3.181510 CGTCCCTTCCGTTTGATTTCATC 60.182 47.826 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.