Multiple sequence alignment - TraesCS5D01G303200

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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 TraesCS5D01G303200 chr5D 100.000 8210 0 0 1 8210 398895838 398904047 0.000000e+00 15162.0
1 TraesCS5D01G303200 chr5D 87.179 78 6 4 3699 3772 499865465 499865388 1.470000e-12 86.1
2 TraesCS5D01G303200 chr5D 100.000 32 0 0 3704 3735 28480034 28480003 8.900000e-05 60.2
3 TraesCS5D01G303200 chr5D 100.000 32 0 0 3704 3735 332447744 332447775 8.900000e-05 60.2
4 TraesCS5D01G303200 chr5B 96.503 5805 144 28 2410 8210 479194583 479200332 0.000000e+00 9540.0
5 TraesCS5D01G303200 chr5B 96.945 2095 53 7 330 2417 479192466 479194556 0.000000e+00 3504.0
6 TraesCS5D01G303200 chr5B 93.730 319 10 3 19 327 479192025 479192343 3.470000e-128 470.0
7 TraesCS5D01G303200 chr5A 89.943 2118 137 40 330 2409 503940895 503942974 0.000000e+00 2662.0
8 TraesCS5D01G303200 chr5A 92.689 1614 89 8 4817 6418 503945305 503946901 0.000000e+00 2300.0
9 TraesCS5D01G303200 chr5A 93.048 1050 44 12 2410 3447 503943006 503944038 0.000000e+00 1507.0
10 TraesCS5D01G303200 chr5A 82.707 1463 168 43 962 2393 109302745 109304153 0.000000e+00 1221.0
11 TraesCS5D01G303200 chr5A 86.143 1032 96 26 3851 4840 503944262 503945288 0.000000e+00 1070.0
12 TraesCS5D01G303200 chr5A 92.407 619 45 2 6663 7280 503947082 503947699 0.000000e+00 881.0
13 TraesCS5D01G303200 chr5A 83.714 657 67 15 7567 8205 503948183 503948817 1.190000e-162 584.0
14 TraesCS5D01G303200 chr5A 88.696 230 18 4 7322 7551 503947705 503947926 2.920000e-69 274.0
15 TraesCS5D01G303200 chr5A 82.353 340 21 13 4 330 503940402 503940715 8.170000e-65 259.0
16 TraesCS5D01G303200 chr5A 97.297 37 1 0 3699 3735 135141222 135141258 6.880000e-06 63.9
17 TraesCS5D01G303200 chr6D 84.522 2300 195 79 5343 7528 473234768 473237020 0.000000e+00 2126.0
18 TraesCS5D01G303200 chr6D 89.975 1197 100 17 2501 3685 473231937 473233125 0.000000e+00 1528.0
19 TraesCS5D01G303200 chr6D 88.949 1104 100 11 1082 2177 473230479 473231568 0.000000e+00 1343.0
20 TraesCS5D01G303200 chr6D 84.235 1072 120 18 4265 5294 473233616 473234680 0.000000e+00 998.0
21 TraesCS5D01G303200 chr6D 78.442 385 57 9 702 1061 473230028 473230411 2.310000e-55 228.0
22 TraesCS5D01G303200 chr6D 86.275 102 7 2 2413 2508 473231794 473231894 4.050000e-18 104.0
23 TraesCS5D01G303200 chr6A 84.284 2278 211 74 5351 7532 616757082 616754856 0.000000e+00 2087.0
24 TraesCS5D01G303200 chr6A 85.304 1531 151 30 706 2177 616761832 616760317 0.000000e+00 1513.0
25 TraesCS5D01G303200 chr6A 90.144 1177 94 17 2518 3685 616759856 616758693 0.000000e+00 1511.0
26 TraesCS5D01G303200 chr6A 83.898 1093 124 23 4255 5305 616758248 616757166 0.000000e+00 996.0
27 TraesCS5D01G303200 chr6A 88.249 417 42 6 3854 4266 616758696 616758283 7.400000e-135 492.0
28 TraesCS5D01G303200 chr6A 83.938 193 18 8 2222 2409 616760317 616760133 1.100000e-38 172.0
29 TraesCS5D01G303200 chr6A 97.222 36 1 0 3703 3738 25691350 25691315 2.470000e-05 62.1
30 TraesCS5D01G303200 chr6A 100.000 28 0 0 8084 8111 616754372 616754345 1.500000e-02 52.8
31 TraesCS5D01G303200 chr6B 85.021 2163 179 78 5343 7394 718642968 718645096 0.000000e+00 2065.0
32 TraesCS5D01G303200 chr6B 89.941 1193 96 13 2504 3685 718640189 718641368 0.000000e+00 1517.0
33 TraesCS5D01G303200 chr6B 89.321 1105 98 10 1082 2177 718638651 718639744 0.000000e+00 1369.0
34 TraesCS5D01G303200 chr6B 83.533 1087 131 20 4255 5302 718641813 718642890 0.000000e+00 972.0
35 TraesCS5D01G303200 chr6B 87.530 417 45 6 3854 4266 718641365 718641778 7.460000e-130 475.0
36 TraesCS5D01G303200 chr6B 86.538 312 29 7 6720 7021 669739974 669739666 1.710000e-86 331.0
37 TraesCS5D01G303200 chr6B 82.630 403 40 14 6630 7021 669686480 669686097 6.140000e-86 329.0
38 TraesCS5D01G303200 chr6B 82.203 354 45 10 7068 7417 669686077 669685738 1.040000e-73 289.0
39 TraesCS5D01G303200 chr6B 79.320 353 44 9 737 1061 718638228 718638579 3.860000e-53 220.0
40 TraesCS5D01G303200 chr6B 88.182 110 8 2 2413 2517 718639969 718640078 8.650000e-25 126.0
41 TraesCS5D01G303200 chr6B 80.451 133 19 4 7392 7524 718645211 718645336 2.440000e-15 95.3
42 TraesCS5D01G303200 chr1B 82.568 1480 171 46 962 2409 674639819 674638395 0.000000e+00 1223.0
43 TraesCS5D01G303200 chr1B 82.096 229 29 8 912 1134 545451911 545452133 1.410000e-42 185.0
44 TraesCS5D01G303200 chr2B 82.570 1463 171 43 962 2393 10670137 10671546 0.000000e+00 1212.0
45 TraesCS5D01G303200 chr2B 81.855 1466 176 45 962 2396 390973497 390972091 0.000000e+00 1151.0
46 TraesCS5D01G303200 chr2B 75.146 515 86 23 654 1136 736737720 736737216 3.880000e-48 204.0
47 TraesCS5D01G303200 chr2A 82.285 1479 176 44 962 2409 130176989 130175566 0.000000e+00 1201.0
48 TraesCS5D01G303200 chr2A 74.713 522 93 19 645 1134 537056919 537057433 6.500000e-46 196.0
49 TraesCS5D01G303200 chr2A 100.000 28 0 0 3749 3776 34328154 34328127 1.500000e-02 52.8
50 TraesCS5D01G303200 chr7B 76.117 515 78 28 654 1134 697783980 697783477 2.310000e-55 228.0
51 TraesCS5D01G303200 chr7B 95.238 42 1 1 3733 3774 28496288 28496328 1.910000e-06 65.8
52 TraesCS5D01G303200 chr4A 80.812 271 38 12 872 1134 696445616 696445880 5.030000e-47 200.0
53 TraesCS5D01G303200 chr4B 97.436 39 1 0 3698 3736 584940052 584940090 5.320000e-07 67.6
54 TraesCS5D01G303200 chr3D 100.000 32 0 0 3743 3774 82363899 82363868 8.900000e-05 60.2
55 TraesCS5D01G303200 chr1D 100.000 32 0 0 3704 3735 218898546 218898577 8.900000e-05 60.2
56 TraesCS5D01G303200 chr1D 96.970 33 0 1 3704 3735 47957707 47957675 4.000000e-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 TraesCS5D01G303200 chr5D 398895838 398904047 8209 False 15162.000000 15162 100.000000 1 8210 1 chr5D.!!$F2 8209
1 TraesCS5D01G303200 chr5B 479192025 479200332 8307 False 4504.666667 9540 95.726000 19 8210 3 chr5B.!!$F1 8191
2 TraesCS5D01G303200 chr5A 109302745 109304153 1408 False 1221.000000 1221 82.707000 962 2393 1 chr5A.!!$F1 1431
3 TraesCS5D01G303200 chr5A 503940402 503948817 8415 False 1192.125000 2662 88.624125 4 8205 8 chr5A.!!$F3 8201
4 TraesCS5D01G303200 chr6D 473230028 473237020 6992 False 1054.500000 2126 85.399667 702 7528 6 chr6D.!!$F1 6826
5 TraesCS5D01G303200 chr6A 616754345 616761832 7487 True 974.828571 2087 87.973857 706 8111 7 chr6A.!!$R2 7405
6 TraesCS5D01G303200 chr6B 718638228 718645336 7108 False 854.912500 2065 85.412375 737 7524 8 chr6B.!!$F1 6787
7 TraesCS5D01G303200 chr6B 669685738 669686480 742 True 309.000000 329 82.416500 6630 7417 2 chr6B.!!$R2 787
8 TraesCS5D01G303200 chr1B 674638395 674639819 1424 True 1223.000000 1223 82.568000 962 2409 1 chr1B.!!$R1 1447
9 TraesCS5D01G303200 chr2B 10670137 10671546 1409 False 1212.000000 1212 82.570000 962 2393 1 chr2B.!!$F1 1431
10 TraesCS5D01G303200 chr2B 390972091 390973497 1406 True 1151.000000 1151 81.855000 962 2396 1 chr2B.!!$R1 1434
11 TraesCS5D01G303200 chr2B 736737216 736737720 504 True 204.000000 204 75.146000 654 1136 1 chr2B.!!$R2 482
12 TraesCS5D01G303200 chr2A 130175566 130176989 1423 True 1201.000000 1201 82.285000 962 2409 1 chr2A.!!$R2 1447
13 TraesCS5D01G303200 chr7B 697783477 697783980 503 True 228.000000 228 76.117000 654 1134 1 chr7B.!!$R1 480

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
491 722 0.598065 GTCATGTGGTTTGTGGCTCC 59.402 55.000 0.00 0.00 0.00 4.70 F
990 1268 1.724082 GAGTGCTGACTCGCTTTTCTC 59.276 52.381 0.00 0.00 39.44 2.87 F
2232 2614 1.064825 TCCTCACCCCTTGACTTTCC 58.935 55.000 0.00 0.00 0.00 3.13 F
3546 4137 1.719780 CTAAAAGGTGTCGTGCTCGTC 59.280 52.381 8.17 3.14 38.33 4.20 F
3994 4594 0.308993 GCTGCAATTCGGATGCCTAC 59.691 55.000 0.00 0.00 43.16 3.18 F
4145 4764 1.686587 TGTCTTTCCTGCGAGAACTCA 59.313 47.619 2.78 0.00 0.00 3.41 F
5158 5962 2.265904 GGCAAGGTCCGTTGGGTTC 61.266 63.158 2.35 0.00 33.83 3.62 F
6660 7604 1.284657 CTTGCTCATGACCTAGTGCG 58.715 55.000 0.00 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 2007 0.036164 CCTCCACATGAAACCACGGA 59.964 55.000 0.00 0.0 0.00 4.69 R
2821 3411 3.119137 GGTTGCATTTGGTTCTGGGATAC 60.119 47.826 0.00 0.0 0.00 2.24 R
3590 4181 0.830648 CATCTTCGCCTTCCCACCTA 59.169 55.000 0.00 0.0 0.00 3.08 R
4419 5156 1.820519 TGCTGCAGCTAATTTTCAGGG 59.179 47.619 36.61 0.0 42.66 4.45 R
5368 6222 2.836372 TCCAGCACTCTGAATCTGACAT 59.164 45.455 0.00 0.0 42.95 3.06 R
5872 6744 4.665451 TGCATCAAAGAAAGATTCTGGGA 58.335 39.130 0.00 0.0 40.59 4.37 R
7026 8000 0.402504 ACCTACCAATTTGGGACGCA 59.597 50.000 19.39 0.0 43.37 5.24 R
7472 8573 0.319555 GCACAGCAGTTACTCGGTGA 60.320 55.000 16.37 0.0 34.74 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 3.869246 CGTGCTCGGAATTTTGTAGGTAT 59.131 43.478 0.00 0.00 0.00 2.73
123 124 3.625764 TGCTCGGAATTTTGTAGGTATGC 59.374 43.478 0.00 0.00 0.00 3.14
215 226 1.819632 CGTTGGTGGGAGCATAGGC 60.820 63.158 0.00 0.00 41.61 3.93
292 303 6.850555 TGCCCTGTTTTTCTTTTTCATTTTG 58.149 32.000 0.00 0.00 0.00 2.44
342 551 4.445385 CGCCTGGATGTTTTTCTTTCTTTG 59.555 41.667 0.00 0.00 0.00 2.77
347 556 8.413229 CCTGGATGTTTTTCTTTCTTTGTTCTA 58.587 33.333 0.00 0.00 0.00 2.10
410 625 2.839486 AAGAGCCATGAAACGACAGA 57.161 45.000 0.00 0.00 0.00 3.41
465 696 0.874390 TTTGCCGTGATCAGCTCAAC 59.126 50.000 8.27 0.00 35.07 3.18
491 722 0.598065 GTCATGTGGTTTGTGGCTCC 59.402 55.000 0.00 0.00 0.00 4.70
684 920 8.079809 TGGAAATTAAGCCTTCTTTTAGTTTCG 58.920 33.333 6.30 0.00 36.84 3.46
781 1034 4.166523 CTGCTGAAATCTGCACATTTCTG 58.833 43.478 22.72 22.23 44.12 3.02
899 1177 2.618053 ACAAGCTACTAACGGATGTGC 58.382 47.619 0.00 0.00 0.00 4.57
990 1268 1.724082 GAGTGCTGACTCGCTTTTCTC 59.276 52.381 0.00 0.00 39.44 2.87
1128 1476 7.369803 TGTCTTGATAACTTGATGCTTTCTC 57.630 36.000 0.00 0.00 0.00 2.87
1393 1755 3.824133 TCCAAATATGCCTGGATCACTG 58.176 45.455 0.00 0.00 36.79 3.66
1877 2251 3.117284 TCCAGCTTTAGGAAACTTGGGTT 60.117 43.478 0.00 0.00 43.67 4.11
2232 2614 1.064825 TCCTCACCCCTTGACTTTCC 58.935 55.000 0.00 0.00 0.00 3.13
2387 2785 7.388776 TGATGCTATAGTGTATTGCAGAATTCC 59.611 37.037 0.65 0.00 46.70 3.01
2401 2799 5.811613 TGCAGAATTCCTTTTTGAAAGTGTG 59.188 36.000 0.65 0.00 0.00 3.82
2704 3285 8.507249 AGAAGCATACAGTGTGTTATTTTCTTC 58.493 33.333 5.88 7.22 0.00 2.87
2976 3566 4.497291 TCCACAGGGACAATATGGTAAC 57.503 45.455 0.00 0.00 38.64 2.50
3116 3706 5.407407 ACCACGAGTTCAGTATTCAGAAT 57.593 39.130 0.20 0.20 0.00 2.40
3385 3975 8.552296 ACCCTGTCATAAAATCTTCTATCTGTT 58.448 33.333 0.00 0.00 0.00 3.16
3448 4038 4.502962 GGTGATCTTCTCCTCAAGTCAAG 58.497 47.826 0.00 0.00 0.00 3.02
3462 4052 6.360370 TCAAGTCAAGGAATGCTTACTACT 57.640 37.500 0.00 0.00 0.00 2.57
3546 4137 1.719780 CTAAAAGGTGTCGTGCTCGTC 59.280 52.381 8.17 3.14 38.33 4.20
3553 4144 4.753877 TCGTGCTCGTCGAAGCGG 62.754 66.667 8.17 0.00 45.54 5.52
3721 4319 5.486735 TTGGTACTCCCTTCGTATCAAAA 57.513 39.130 0.00 0.00 35.63 2.44
3774 4372 8.421784 TCTTATATTTTGGTGCAGAGGTAGTAG 58.578 37.037 0.00 0.00 0.00 2.57
3954 4554 9.893305 CAAACGACATTTAGATAAAAAGGTCTT 57.107 29.630 11.00 1.22 44.09 3.01
3994 4594 0.308993 GCTGCAATTCGGATGCCTAC 59.691 55.000 0.00 0.00 43.16 3.18
4033 4633 6.885918 CCCTAATTTTTGGCAAGAAATGGAAT 59.114 34.615 7.32 2.44 0.00 3.01
4036 4636 7.585579 AATTTTTGGCAAGAAATGGAATTGT 57.414 28.000 7.32 0.00 36.10 2.71
4037 4637 6.374565 TTTTTGGCAAGAAATGGAATTGTG 57.625 33.333 0.03 0.00 36.10 3.33
4038 4638 4.686191 TTGGCAAGAAATGGAATTGTGT 57.314 36.364 0.00 0.00 36.10 3.72
4039 4639 5.798125 TTGGCAAGAAATGGAATTGTGTA 57.202 34.783 0.00 0.00 36.10 2.90
4040 4640 5.999205 TGGCAAGAAATGGAATTGTGTAT 57.001 34.783 0.00 0.00 36.10 2.29
4041 4641 6.357579 TGGCAAGAAATGGAATTGTGTATT 57.642 33.333 0.00 0.00 36.10 1.89
4042 4642 6.767456 TGGCAAGAAATGGAATTGTGTATTT 58.233 32.000 0.00 0.00 36.10 1.40
4043 4643 7.901029 TGGCAAGAAATGGAATTGTGTATTTA 58.099 30.769 0.00 0.00 36.10 1.40
4044 4644 8.538701 TGGCAAGAAATGGAATTGTGTATTTAT 58.461 29.630 0.00 0.00 36.10 1.40
4045 4645 9.382275 GGCAAGAAATGGAATTGTGTATTTATT 57.618 29.630 0.00 0.00 36.10 1.40
4049 4649 9.787532 AGAAATGGAATTGTGTATTTATTCGTG 57.212 29.630 0.00 0.00 36.10 4.35
4050 4650 9.781834 GAAATGGAATTGTGTATTTATTCGTGA 57.218 29.630 0.00 0.00 36.10 4.35
4051 4651 9.567848 AAATGGAATTGTGTATTTATTCGTGAC 57.432 29.630 0.00 0.00 36.10 3.67
4052 4652 7.674471 TGGAATTGTGTATTTATTCGTGACA 57.326 32.000 0.00 0.00 0.00 3.58
4145 4764 1.686587 TGTCTTTCCTGCGAGAACTCA 59.313 47.619 2.78 0.00 0.00 3.41
4228 4848 3.128589 CCTAACCCATCGTGTTTTCCATG 59.871 47.826 0.00 0.00 0.00 3.66
4251 4871 6.812998 TGGGTCCTACTCTTCATATAAAACG 58.187 40.000 0.00 0.00 0.00 3.60
4287 5015 5.052693 AGGTATGATTTGAGGCATAGCAA 57.947 39.130 12.65 0.00 43.98 3.91
4378 5112 7.147479 ACCATGGCAGTAAGTTAACTATGAGAT 60.147 37.037 13.04 0.00 0.00 2.75
4419 5156 5.248870 ACCAATATGGATCAAAAGAACGC 57.751 39.130 2.85 0.00 40.96 4.84
4480 5221 3.443681 CGAAGTTACCAATTTGGCCATCT 59.556 43.478 15.49 6.32 42.67 2.90
4521 5262 4.761739 CCTCAACTTTGGTAAGCATCTCAA 59.238 41.667 0.00 0.00 34.60 3.02
4866 5655 6.263168 ACCTTGGTAGTGTTTCTTCATTCTTG 59.737 38.462 0.00 0.00 0.00 3.02
4939 5737 2.525368 CTTCCTTTTTCCCCATTCCGT 58.475 47.619 0.00 0.00 0.00 4.69
4995 5795 3.812053 CAGGTAGCAGTTCAGATTATGGC 59.188 47.826 0.00 0.00 0.00 4.40
5118 5922 5.545658 TCTCCGAGCATTTATTTTGACAC 57.454 39.130 0.00 0.00 0.00 3.67
5158 5962 2.265904 GGCAAGGTCCGTTGGGTTC 61.266 63.158 2.35 0.00 33.83 3.62
5651 6508 4.511527 TCCTGATTTGTCATCTCTTGCTC 58.488 43.478 0.00 0.00 0.00 4.26
5919 6791 9.912634 CAGCCGGTTCATTTTATGATAAATATT 57.087 29.630 1.90 0.00 39.39 1.28
6041 6920 5.818857 TGTATTAGGTTCGGCCATTAGTTTC 59.181 40.000 2.24 0.00 40.61 2.78
6364 7250 5.280164 GCCCATTGACTGTCATGGATCTATA 60.280 44.000 26.73 7.80 36.31 1.31
6365 7251 6.577838 GCCCATTGACTGTCATGGATCTATAT 60.578 42.308 26.73 9.41 36.31 0.86
6371 7257 7.664758 TGACTGTCATGGATCTATATCACAAG 58.335 38.462 6.36 0.00 33.41 3.16
6612 7524 6.360370 TCAAACTGACTTGTAAGCTATCCT 57.640 37.500 0.00 0.00 0.00 3.24
6660 7604 1.284657 CTTGCTCATGACCTAGTGCG 58.715 55.000 0.00 0.00 0.00 5.34
6684 7629 2.627515 TCACAACTGAGCAGAGCTTT 57.372 45.000 4.21 0.00 39.88 3.51
6836 7781 3.308046 GGAGCCTCTCATCAAAACTCCTT 60.308 47.826 0.00 0.00 39.30 3.36
6918 7871 7.446106 AGGTACTTACATTGGGTGAATATCA 57.554 36.000 0.00 0.00 27.25 2.15
7026 8000 1.450360 AAAGGCCAAGTCTCCCTTCT 58.550 50.000 5.01 0.00 37.97 2.85
7062 8036 5.777732 TGGTAGGTGAAATTTTGCTTGGTAT 59.222 36.000 0.00 0.00 0.00 2.73
7064 8038 5.806654 AGGTGAAATTTTGCTTGGTATGT 57.193 34.783 0.00 0.00 0.00 2.29
7066 8040 6.591001 AGGTGAAATTTTGCTTGGTATGTTT 58.409 32.000 0.00 0.00 0.00 2.83
7137 8117 5.247862 TCATCTCACTGTTGTATGCAATGT 58.752 37.500 0.00 0.00 36.92 2.71
7438 8539 0.605319 GGTCCTTGAATGCGTGTGGA 60.605 55.000 0.00 0.00 0.00 4.02
7452 8553 1.466167 GTGTGGATGAGCATGTGACAC 59.534 52.381 0.00 0.00 0.00 3.67
7453 8554 1.072015 TGTGGATGAGCATGTGACACA 59.928 47.619 11.41 11.41 35.29 3.72
7472 8573 0.035881 ACACACACATGCTGCTAGCT 59.964 50.000 17.23 0.00 42.97 3.32
7633 8980 1.294041 TGGACATTATCACCAGGGCA 58.706 50.000 0.00 0.00 0.00 5.36
7634 8981 1.852309 TGGACATTATCACCAGGGCAT 59.148 47.619 0.00 0.00 0.00 4.40
7635 8982 2.244510 TGGACATTATCACCAGGGCATT 59.755 45.455 0.00 0.00 0.00 3.56
7636 8983 3.299503 GGACATTATCACCAGGGCATTT 58.700 45.455 0.00 0.00 0.00 2.32
7708 9059 0.036952 CAGGTGGACGAGTGCTTGAT 60.037 55.000 0.00 0.00 0.00 2.57
7710 9061 1.899814 AGGTGGACGAGTGCTTGATTA 59.100 47.619 0.00 0.00 0.00 1.75
7736 9087 1.662044 CAGCCAACCAAGCACTTCC 59.338 57.895 0.00 0.00 0.00 3.46
7778 9132 9.578439 AGATAGTATGTTAACGTTGTAGTTTCC 57.422 33.333 11.99 0.00 35.70 3.13
7820 9174 1.830836 GGAAACCTCGAGGATCCCC 59.169 63.158 37.69 24.38 38.15 4.81
7822 9176 2.646117 GAAACCTCGAGGATCCCCGC 62.646 65.000 37.69 14.65 38.94 6.13
7939 9304 8.872845 CCATTTATTTCCACTTATGTTTTGAGC 58.127 33.333 0.00 0.00 0.00 4.26
7943 9308 4.944962 TCCACTTATGTTTTGAGCGATG 57.055 40.909 0.00 0.00 0.00 3.84
7946 9311 5.935206 TCCACTTATGTTTTGAGCGATGTAA 59.065 36.000 0.00 0.00 0.00 2.41
7949 9314 7.413988 CCACTTATGTTTTGAGCGATGTAATCA 60.414 37.037 0.00 0.00 45.97 2.57
8039 9414 2.564771 TGGGATGCAATTCGACTGATC 58.435 47.619 0.00 0.00 0.00 2.92
8129 9535 1.447945 GCTGCTGAAGGAGGAGAAAC 58.552 55.000 0.78 0.00 42.77 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 4.752879 GCGGGGCGAGTAGTTGCA 62.753 66.667 11.95 0.00 34.26 4.08
143 144 0.678684 TGCAGGCATGATCTGTGGTG 60.679 55.000 0.62 0.00 34.89 4.17
145 146 2.265589 TATGCAGGCATGATCTGTGG 57.734 50.000 16.61 0.00 37.82 4.17
383 598 4.023536 TCGTTTCATGGCTCTTTTAACCAC 60.024 41.667 0.00 0.00 35.99 4.16
451 666 3.084579 GCGGTTGAGCTGATCACG 58.915 61.111 0.00 0.00 37.77 4.35
465 696 0.518636 CAAACCACATGACTGAGCGG 59.481 55.000 0.00 0.00 0.00 5.52
653 889 6.493189 AAAGAAGGCTTAATTTCCAACCAA 57.507 33.333 0.00 0.00 32.98 3.67
684 920 0.875908 TGCCGATAATGCTCGAGTGC 60.876 55.000 15.13 1.33 41.12 4.40
781 1034 4.932200 CCAAGGATCAAGTCAGAACAGTAC 59.068 45.833 0.00 0.00 0.00 2.73
857 1119 5.635700 TGTAAATTAAAGGACAAATTGCGCC 59.364 36.000 4.18 0.00 0.00 6.53
899 1177 2.167075 GCCAATCTGAAACAGGAATGGG 59.833 50.000 14.69 5.54 33.15 4.00
990 1268 3.672511 GCAAGCCAGACATTGATGACAAG 60.673 47.826 0.00 0.00 39.46 3.16
1128 1476 3.826157 TGTTAAGATTTGACTGCCAAGGG 59.174 43.478 0.00 0.00 35.94 3.95
1393 1755 1.444895 CGCAGCATTCCTTTGTGCC 60.445 57.895 0.00 0.00 42.20 5.01
1633 2007 0.036164 CCTCCACATGAAACCACGGA 59.964 55.000 0.00 0.00 0.00 4.69
1827 2201 3.896888 TGACATGCCAGGAACAGAATTTT 59.103 39.130 0.00 0.00 0.00 1.82
2387 2785 9.450807 CCTAAATAGTGTCACACTTTCAAAAAG 57.549 33.333 17.55 5.21 42.59 2.27
2401 2799 6.819397 AAAAGTTGGCTCCTAAATAGTGTC 57.181 37.500 0.00 0.00 0.00 3.67
2821 3411 3.119137 GGTTGCATTTGGTTCTGGGATAC 60.119 47.826 0.00 0.00 0.00 2.24
3016 3606 5.698741 TTAGAGAGATTGGCCAAGAATCA 57.301 39.130 24.94 0.00 33.03 2.57
3116 3706 0.887933 GCAAAGCCGGGAAATCTTCA 59.112 50.000 2.18 0.00 0.00 3.02
3546 4137 3.303132 GGTGTGCTATAAATTCCGCTTCG 60.303 47.826 0.00 0.00 0.00 3.79
3553 4144 8.755696 TCACAAAAATGGTGTGCTATAAATTC 57.244 30.769 0.00 0.00 44.92 2.17
3590 4181 0.830648 CATCTTCGCCTTCCCACCTA 59.169 55.000 0.00 0.00 0.00 3.08
3662 4260 6.017440 TGAGATATTTTTCTAAATTCCCGCGG 60.017 38.462 21.04 21.04 35.61 6.46
3746 4344 5.815581 ACCTCTGCACCAAAATATAAGACA 58.184 37.500 0.00 0.00 0.00 3.41
3994 4594 7.812669 CCAAAAATTAGGGCTACTTGTTACTTG 59.187 37.037 0.00 0.00 0.00 3.16
4033 4633 7.279090 CCCTACATGTCACGAATAAATACACAA 59.721 37.037 0.00 0.00 0.00 3.33
4036 4636 5.756347 GCCCTACATGTCACGAATAAATACA 59.244 40.000 0.00 0.00 0.00 2.29
4037 4637 5.756347 TGCCCTACATGTCACGAATAAATAC 59.244 40.000 0.00 0.00 0.00 1.89
4038 4638 5.919755 TGCCCTACATGTCACGAATAAATA 58.080 37.500 0.00 0.00 0.00 1.40
4039 4639 4.776349 TGCCCTACATGTCACGAATAAAT 58.224 39.130 0.00 0.00 0.00 1.40
4040 4640 4.209307 TGCCCTACATGTCACGAATAAA 57.791 40.909 0.00 0.00 0.00 1.40
4041 4641 3.897141 TGCCCTACATGTCACGAATAA 57.103 42.857 0.00 0.00 0.00 1.40
4042 4642 3.897141 TTGCCCTACATGTCACGAATA 57.103 42.857 0.00 0.00 0.00 1.75
4043 4643 2.779755 TTGCCCTACATGTCACGAAT 57.220 45.000 0.00 0.00 0.00 3.34
4044 4644 2.290008 ACATTGCCCTACATGTCACGAA 60.290 45.455 0.00 0.00 0.00 3.85
4045 4645 1.277842 ACATTGCCCTACATGTCACGA 59.722 47.619 0.00 0.00 0.00 4.35
4046 4646 1.737838 ACATTGCCCTACATGTCACG 58.262 50.000 0.00 0.00 0.00 4.35
4047 4647 5.820423 TGTATTACATTGCCCTACATGTCAC 59.180 40.000 0.00 0.00 0.00 3.67
4048 4648 5.820423 GTGTATTACATTGCCCTACATGTCA 59.180 40.000 0.00 0.00 0.00 3.58
4049 4649 5.820423 TGTGTATTACATTGCCCTACATGTC 59.180 40.000 0.00 0.00 33.42 3.06
4050 4650 5.750524 TGTGTATTACATTGCCCTACATGT 58.249 37.500 2.69 2.69 33.42 3.21
4051 4651 6.542005 TCTTGTGTATTACATTGCCCTACATG 59.458 38.462 0.00 0.00 39.48 3.21
4052 4652 6.658849 TCTTGTGTATTACATTGCCCTACAT 58.341 36.000 0.00 0.00 39.48 2.29
4120 4739 4.214332 AGTTCTCGCAGGAAAGACAAATTC 59.786 41.667 0.00 0.00 0.00 2.17
4228 4848 6.700520 CACGTTTTATATGAAGAGTAGGACCC 59.299 42.308 0.00 0.00 0.00 4.46
4287 5015 1.272480 GGCTTAACCACCTCCCAATGT 60.272 52.381 0.00 0.00 38.86 2.71
4378 5112 4.789977 CACACGGTGGGTCATGAA 57.210 55.556 13.48 0.00 0.00 2.57
4419 5156 1.820519 TGCTGCAGCTAATTTTCAGGG 59.179 47.619 36.61 0.00 42.66 4.45
4480 5221 3.194861 GAGGAGTAAATGTATGTGCGCA 58.805 45.455 5.66 5.66 0.00 6.09
4521 5262 3.595173 GGGCACAAGAAAACAAACAGTT 58.405 40.909 0.00 0.00 43.89 3.16
4771 5520 2.037902 TGCACGTGGAAAGAATAGGTCA 59.962 45.455 18.88 0.00 0.00 4.02
4866 5655 7.661968 ACTTCAGGAAAGAATTAAAAAGCCTC 58.338 34.615 0.00 0.00 38.44 4.70
4995 5795 5.003160 TGTTCCTTGTGATGTAACTCCATG 58.997 41.667 0.00 0.00 0.00 3.66
5118 5922 5.445939 GCCATCTGTGTAAGTGTTCATAACG 60.446 44.000 0.00 0.00 0.00 3.18
5158 5962 6.177610 TGGTTGGTAGCTACTTCCTAAATTG 58.822 40.000 22.74 0.00 0.00 2.32
5368 6222 2.836372 TCCAGCACTCTGAATCTGACAT 59.164 45.455 0.00 0.00 42.95 3.06
5651 6508 5.391950 CCAACGTTGTCAAATCTATTCCCAG 60.392 44.000 25.63 1.50 0.00 4.45
5872 6744 4.665451 TGCATCAAAGAAAGATTCTGGGA 58.335 39.130 0.00 0.00 40.59 4.37
5919 6791 5.392595 GCACCAAGACAGAACTTGTTACAAA 60.393 40.000 0.00 0.00 43.72 2.83
6181 7067 1.083209 CCGCATGCATGACGATTCG 60.083 57.895 31.35 23.07 32.02 3.34
6379 7266 8.966868 GGAAGATGAATAAATCCACAAGGTTAA 58.033 33.333 0.00 0.00 35.89 2.01
6660 7604 1.463831 CTCTGCTCAGTTGTGATGTGC 59.536 52.381 0.00 0.00 37.60 4.57
6836 7781 4.202461 GGCATAAGACCCCTGTTCATATGA 60.202 45.833 0.00 0.00 0.00 2.15
7026 8000 0.402504 ACCTACCAATTTGGGACGCA 59.597 50.000 19.39 0.00 43.37 5.24
7166 8146 5.967088 TCATGTACAAGAAAGCTAGAGTCC 58.033 41.667 0.00 0.00 0.00 3.85
7429 8530 1.003476 ACATGCTCATCCACACGCA 60.003 52.632 0.00 0.00 36.75 5.24
7452 8553 0.167470 GCTAGCAGCATGTGTGTGTG 59.833 55.000 10.63 0.00 41.89 3.82
7453 8554 0.035881 AGCTAGCAGCATGTGTGTGT 59.964 50.000 18.83 0.00 45.56 3.72
7472 8573 0.319555 GCACAGCAGTTACTCGGTGA 60.320 55.000 16.37 0.00 34.74 4.02
7736 9087 4.324267 ACTATCTTTCCAACCAAGAACCG 58.676 43.478 0.00 0.00 33.94 4.44
7778 9132 6.366877 CCCACTTTTCAGCAATGAGTTTAATG 59.633 38.462 0.00 0.00 0.00 1.90
7820 9174 6.142798 GGATTGTCAAATACATAAATGCAGCG 59.857 38.462 0.00 0.00 38.10 5.18
7822 9176 7.650504 CAGGGATTGTCAAATACATAAATGCAG 59.349 37.037 0.00 0.00 38.10 4.41
7939 9304 6.834959 ATTAGCAGAACAGTGATTACATCG 57.165 37.500 0.00 0.00 0.00 3.84
7946 9311 8.969260 TCAATCATTATTAGCAGAACAGTGAT 57.031 30.769 0.00 0.00 0.00 3.06
7949 9314 9.399797 TCATTCAATCATTATTAGCAGAACAGT 57.600 29.630 0.00 0.00 0.00 3.55
8039 9414 2.738521 CCTGCGTCAACCCAGTCG 60.739 66.667 0.00 0.00 0.00 4.18
8164 9575 6.364976 GCTAGGTAAAAAGTTTAACGACGGTA 59.635 38.462 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.