Multiple sequence alignment - TraesCS3D01G225700

Loading Multiple Alignment...

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 TraesCS3D01G225700 chr3D 100.000 6305 0 0 1 6305 307239643 307233339 0.000000e+00 11644.0
1 TraesCS3D01G225700 chr3D 85.113 309 14 6 3428 3705 210621184 210620877 2.880000e-73 287.0
2 TraesCS3D01G225700 chr3D 100.000 28 0 0 3868 3895 337526764 337526737 1.100000e-02 52.8
3 TraesCS3D01G225700 chr3B 94.556 3582 121 24 1205 4746 414014830 414018377 0.000000e+00 5467.0
4 TraesCS3D01G225700 chr3B 95.521 1228 33 7 1 1214 414013580 414014799 0.000000e+00 1943.0
5 TraesCS3D01G225700 chr3B 90.585 1009 48 20 4774 5758 414018433 414019418 0.000000e+00 1293.0
6 TraesCS3D01G225700 chr3B 95.181 249 12 0 6057 6305 414019890 414020138 1.650000e-105 394.0
7 TraesCS3D01G225700 chr3B 84.466 309 16 6 3428 3705 332929585 332929278 6.230000e-70 276.0
8 TraesCS3D01G225700 chr3B 93.789 161 10 0 5883 6043 414019469 414019629 6.320000e-60 243.0
9 TraesCS3D01G225700 chr3B 100.000 28 0 0 3868 3895 435292902 435292875 1.100000e-02 52.8
10 TraesCS3D01G225700 chr3A 93.586 1450 49 16 4097 5514 426862026 426863463 0.000000e+00 2122.0
11 TraesCS3D01G225700 chr3A 94.189 1325 42 10 1 1305 426858025 426859334 0.000000e+00 1988.0
12 TraesCS3D01G225700 chr3A 91.350 1422 76 10 2580 3964 426860564 426861975 0.000000e+00 1901.0
13 TraesCS3D01G225700 chr3A 91.003 1156 68 15 1286 2429 426859429 426860560 0.000000e+00 1526.0
14 TraesCS3D01G225700 chr3A 95.238 546 23 2 5513 6056 426863546 426864090 0.000000e+00 861.0
15 TraesCS3D01G225700 chr3A 97.189 249 5 1 6057 6305 426864117 426864363 2.720000e-113 420.0
16 TraesCS3D01G225700 chr3A 84.466 309 13 7 3428 3705 275291717 275292021 8.050000e-69 272.0
17 TraesCS3D01G225700 chr3A 100.000 28 0 0 3868 3895 455028763 455028736 1.100000e-02 52.8
18 TraesCS3D01G225700 chr7D 89.933 149 13 2 2430 2577 509926307 509926454 2.320000e-44 191.0
19 TraesCS3D01G225700 chr7D 88.350 103 12 0 5760 5862 484367011 484366909 2.390000e-24 124.0
20 TraesCS3D01G225700 chr1D 88.415 164 11 2 2430 2585 452344728 452344565 2.320000e-44 191.0
21 TraesCS3D01G225700 chr6B 87.135 171 14 5 2430 2594 469779924 469780092 3.000000e-43 187.0
22 TraesCS3D01G225700 chr2B 88.816 152 15 1 2430 2581 509573222 509573371 1.080000e-42 185.0
23 TraesCS3D01G225700 chr2B 88.742 151 16 1 2427 2577 151653682 151653831 3.880000e-42 183.0
24 TraesCS3D01G225700 chr2B 87.500 104 13 0 5760 5863 92976391 92976494 3.090000e-23 121.0
25 TraesCS3D01G225700 chr5A 90.000 140 14 0 2441 2580 151254782 151254643 1.400000e-41 182.0
26 TraesCS3D01G225700 chr4D 88.235 153 16 2 2429 2580 309696995 309696844 1.400000e-41 182.0
27 TraesCS3D01G225700 chr1A 88.194 144 16 1 2434 2577 443660827 443660969 3.020000e-38 171.0
28 TraesCS3D01G225700 chr1A 87.963 108 13 0 5756 5863 498162149 498162256 1.840000e-25 128.0
29 TraesCS3D01G225700 chr1A 91.667 60 4 1 2676 2735 536442633 536442691 1.460000e-11 82.4
30 TraesCS3D01G225700 chr7B 93.269 104 7 0 5760 5863 445020177 445020280 3.040000e-33 154.0
31 TraesCS3D01G225700 chr6D 88.462 104 12 0 5760 5863 128921726 128921623 6.640000e-25 126.0
32 TraesCS3D01G225700 chr6D 87.156 109 11 3 5756 5863 459064739 459064845 3.090000e-23 121.0
33 TraesCS3D01G225700 chr4A 87.736 106 9 4 5760 5863 615207132 615207235 3.090000e-23 121.0
34 TraesCS3D01G225700 chr4A 85.437 103 15 0 5760 5862 706248700 706248802 2.400000e-19 108.0


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 TraesCS3D01G225700 chr3D 307233339 307239643 6304 True 11644.000000 11644 100.000000 1 6305 1 chr3D.!!$R2 6304
1 TraesCS3D01G225700 chr3B 414013580 414020138 6558 False 1868.000000 5467 93.926400 1 6305 5 chr3B.!!$F1 6304
2 TraesCS3D01G225700 chr3A 426858025 426864363 6338 False 1469.666667 2122 93.759167 1 6305 6 chr3A.!!$F2 6304

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
103 104 0.907230 GTGTTGCTCTCCCTCTCCCT 60.907 60.000 0.00 0.0 0.00 4.20 F
105 106 1.002274 TTGCTCTCCCTCTCCCTCC 59.998 63.158 0.00 0.0 0.00 4.30 F
337 353 1.067706 TGTGATTGCTGCGGATTTTGG 60.068 47.619 0.00 0.0 0.00 3.28 F
541 564 1.399791 CTCCTGCTCCGAATTTTCTGC 59.600 52.381 0.00 0.0 0.00 4.26 F
1946 2141 1.800655 CGCAGTATCAGCAGGAGACAC 60.801 57.143 6.04 0.0 40.23 3.67 F
1964 2159 2.158623 ACACTGGAATGGCTGAAGTCAA 60.159 45.455 0.00 0.0 31.21 3.18 F
2998 3213 0.457851 AGCCTAGAAGCACTGCTACG 59.542 55.000 3.33 0.0 38.25 3.51 F
3101 3318 1.487976 TCTGGCCTTGAAGCTATCCTG 59.512 52.381 3.32 0.0 0.00 3.86 F
4916 5236 0.868406 GCACCTTTGAACTCCAGACG 59.132 55.000 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 2062 1.336887 GCAACACTTCGGCAGTAGAGA 60.337 52.381 0.0 0.0 32.76 3.10 R
1946 2141 2.787994 AGTTGACTTCAGCCATTCCAG 58.212 47.619 0.0 0.0 0.00 3.86 R
1964 2159 3.254166 GTCAGATTCACCATGCAACAAGT 59.746 43.478 0.0 0.0 0.00 3.16 R
2219 2415 5.309020 ACCACAATGCCAGATATGAGTCTAT 59.691 40.000 0.0 0.0 0.00 1.98 R
2844 3053 0.100325 TGCAGAAAACAACCACAGCG 59.900 50.000 0.0 0.0 0.00 5.18 R
3389 3612 0.790814 GAAGGAACTCGGTGCTTTCG 59.209 55.000 0.0 0.0 38.49 3.46 R
4134 4396 0.749049 GGGCTTGCAGGGATTGATTC 59.251 55.000 0.0 0.0 0.00 2.52 R
4925 5245 0.868406 GAAACACTGAGAACTGGGCG 59.132 55.000 0.0 0.0 0.00 6.13 R
6225 6895 1.183549 TTTCTAGGGCGAGGAGACAC 58.816 55.000 0.0 0.0 0.00 3.67 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
103 104 0.907230 GTGTTGCTCTCCCTCTCCCT 60.907 60.000 0.00 0.00 0.00 4.20
105 106 1.002274 TTGCTCTCCCTCTCCCTCC 59.998 63.158 0.00 0.00 0.00 4.30
111 112 2.015726 TCCCTCTCCCTCCCTCTCC 61.016 68.421 0.00 0.00 0.00 3.71
115 116 3.039526 CTCCCTCCCTCTCCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
117 118 3.039526 CCCTCCCTCTCCCCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
337 353 1.067706 TGTGATTGCTGCGGATTTTGG 60.068 47.619 0.00 0.00 0.00 3.28
350 366 5.708230 TGCGGATTTTGGTTACTAATTGAGT 59.292 36.000 0.00 0.00 42.69 3.41
354 370 8.079809 CGGATTTTGGTTACTAATTGAGTTGTT 58.920 33.333 0.00 0.00 39.81 2.83
393 415 2.290705 CCGGGGTCAAACTTGAGGTATT 60.291 50.000 0.00 0.00 37.98 1.89
395 417 3.190535 CGGGGTCAAACTTGAGGTATTTG 59.809 47.826 0.00 0.00 37.98 2.32
541 564 1.399791 CTCCTGCTCCGAATTTTCTGC 59.600 52.381 0.00 0.00 0.00 4.26
598 621 3.671433 CGGGAAAGTGTGCATCTCAAATG 60.671 47.826 0.00 0.00 0.00 2.32
658 681 6.881602 GGTGGGATTAAATCTGTGGAGATATC 59.118 42.308 0.00 0.00 38.03 1.63
871 897 6.869206 TCCACTACACTAGCCTTTAGATTT 57.131 37.500 0.00 0.00 0.00 2.17
1059 1085 5.048083 GCAGGAGTTTCATACATTCCACAAA 60.048 40.000 0.00 0.00 0.00 2.83
1090 1116 2.376808 ACTGGAAGACTCGCAATCTG 57.623 50.000 0.00 0.00 37.43 2.90
1099 1125 5.843673 AGACTCGCAATCTGAAGAGATTA 57.156 39.130 0.00 0.00 45.57 1.75
1106 1132 5.332883 CGCAATCTGAAGAGATTACATTCCG 60.333 44.000 0.00 0.00 45.57 4.30
1262 1328 3.667282 CCTGCACTGTGGCTGCAC 61.667 66.667 10.21 0.00 39.76 4.57
1490 1675 7.717875 TGTTCCTTGTTGTACTTTTATACTGCT 59.282 33.333 0.00 0.00 0.00 4.24
1491 1676 9.211485 GTTCCTTGTTGTACTTTTATACTGCTA 57.789 33.333 0.00 0.00 0.00 3.49
1492 1677 9.953565 TTCCTTGTTGTACTTTTATACTGCTAT 57.046 29.630 0.00 0.00 0.00 2.97
1493 1678 9.953565 TCCTTGTTGTACTTTTATACTGCTATT 57.046 29.630 0.00 0.00 0.00 1.73
1543 1728 4.547671 ACCTCTTTATACTCTGGCTGCTA 58.452 43.478 0.00 0.00 0.00 3.49
1581 1767 6.868622 ACTGCTAAGTTCCAAGTCTATGTAG 58.131 40.000 0.00 0.00 30.14 2.74
1642 1828 3.068024 AGGTTGTTGCTTATGTTGTGTGG 59.932 43.478 0.00 0.00 0.00 4.17
1644 1830 4.429108 GTTGTTGCTTATGTTGTGTGGTT 58.571 39.130 0.00 0.00 0.00 3.67
1739 1925 7.826690 TGTTTTAGAAAGCCCAGATATTTCAC 58.173 34.615 0.00 0.00 35.79 3.18
1740 1926 7.093945 TGTTTTAGAAAGCCCAGATATTTCACC 60.094 37.037 0.00 0.00 35.79 4.02
1840 2034 2.342651 CGACAGTGAGTTCATAGTTGCG 59.657 50.000 0.00 0.00 0.00 4.85
1946 2141 1.800655 CGCAGTATCAGCAGGAGACAC 60.801 57.143 6.04 0.00 40.23 3.67
1964 2159 2.158623 ACACTGGAATGGCTGAAGTCAA 60.159 45.455 0.00 0.00 31.21 3.18
2182 2378 7.551974 TGATTTCCTCTATTTCTCAGAAGCAAG 59.448 37.037 0.00 0.00 0.00 4.01
2210 2406 9.525409 GCGTACTTAGGTTCATATCTTCTTTTA 57.475 33.333 0.00 0.00 0.00 1.52
2273 2469 5.128827 TGAAAAAGTATGCCGATCTAGGACT 59.871 40.000 0.00 0.00 0.00 3.85
2339 2535 7.341445 TGGTTTTACATCTTGTAGCAACTTT 57.659 32.000 9.70 0.00 33.92 2.66
2440 2636 5.895534 TCATGTTAATAAGTACTCCCTCCGT 59.104 40.000 0.00 0.00 0.00 4.69
2461 2657 9.333724 CTCCGTTTCTAAATATAAGCCCTTTTA 57.666 33.333 0.00 0.00 0.00 1.52
2480 2687 7.499232 CCCTTTTAGAGATTTCAATACGGATGT 59.501 37.037 0.00 0.00 0.00 3.06
2555 2762 4.760204 CCACGTTGGAATCTCTAAAAAGGT 59.240 41.667 0.00 0.00 40.96 3.50
2577 2784 6.387807 AGGTTTATATTTAGGAACGGAGGGAA 59.612 38.462 0.00 0.00 0.00 3.97
2578 2785 7.073343 AGGTTTATATTTAGGAACGGAGGGAAT 59.927 37.037 0.00 0.00 0.00 3.01
2590 2797 8.541234 AGGAACGGAGGGAATAATATCTTATTC 58.459 37.037 12.82 12.82 46.69 1.75
2807 3016 6.206634 TGAAGTGATGAAACCATAACAGTTCC 59.793 38.462 0.00 0.00 37.08 3.62
2844 3053 6.210584 TGGAAATAACAAACCCATTCTCCTTC 59.789 38.462 0.00 0.00 0.00 3.46
2998 3213 0.457851 AGCCTAGAAGCACTGCTACG 59.542 55.000 3.33 0.00 38.25 3.51
3040 3256 9.851686 ATTCTGCAGTATGGATTATTCAACTAA 57.148 29.630 14.67 0.00 34.26 2.24
3095 3312 1.562942 TCATCATCTGGCCTTGAAGCT 59.437 47.619 3.32 0.00 0.00 3.74
3101 3318 1.487976 TCTGGCCTTGAAGCTATCCTG 59.512 52.381 3.32 0.00 0.00 3.86
3200 3420 9.237846 CTTTCAACTCTTCCAATGTTTTAAGTC 57.762 33.333 0.00 0.00 0.00 3.01
3275 3498 7.768582 TCCAGTGTTGTATTGGACTATATGTTG 59.231 37.037 0.00 0.00 39.97 3.33
3276 3499 7.409697 CAGTGTTGTATTGGACTATATGTTGC 58.590 38.462 0.00 0.00 0.00 4.17
3277 3500 7.280876 CAGTGTTGTATTGGACTATATGTTGCT 59.719 37.037 0.00 0.00 0.00 3.91
3278 3501 7.495934 AGTGTTGTATTGGACTATATGTTGCTC 59.504 37.037 0.00 0.00 0.00 4.26
3279 3502 7.279981 GTGTTGTATTGGACTATATGTTGCTCA 59.720 37.037 0.00 0.00 0.00 4.26
3281 3504 8.338259 GTTGTATTGGACTATATGTTGCTCAAG 58.662 37.037 0.00 0.00 0.00 3.02
3365 3588 3.118482 TCTGAATGTGCTGATCTTCTCCC 60.118 47.826 0.00 0.00 0.00 4.30
3479 3702 2.827921 GCAAGTTTGGGATGTTCTGGAT 59.172 45.455 0.00 0.00 0.00 3.41
3775 3998 6.877855 CAGGATGTGATAGGAATTGAGTATGG 59.122 42.308 0.00 0.00 0.00 2.74
3970 4220 7.539712 TCTAGTAATTGTGACTTAAGCATGC 57.460 36.000 10.51 10.51 0.00 4.06
4001 4251 5.296151 TGTCTGCTCAGGGATTTATAAGG 57.704 43.478 0.00 0.00 0.00 2.69
4002 4252 4.721776 TGTCTGCTCAGGGATTTATAAGGT 59.278 41.667 0.00 0.00 0.00 3.50
4119 4381 5.013599 AGGGGATTTGATTATGCTCTCCTAC 59.986 44.000 0.00 0.00 35.02 3.18
4240 4502 7.009540 CAGTTCACTGTGAATGGTTTTCTTTTC 59.990 37.037 24.44 8.35 38.79 2.29
4254 4516 4.712122 TTCTTTTCCTTTGTGGTGTCAC 57.288 40.909 0.00 0.00 43.87 3.67
4270 4533 7.233689 GTGGTGTCACAAATTTTCAGTTTTTC 58.766 34.615 5.12 0.00 43.13 2.29
4288 4551 8.225107 CAGTTTTTCATTTTAGGTCATGCATTG 58.775 33.333 0.00 0.00 0.00 2.82
4351 4614 7.815549 TGTCAACATTCTTACTACGATTGCTAA 59.184 33.333 0.00 0.00 0.00 3.09
4420 4685 5.126545 CCATTCAACATTGGATCACTGTGAT 59.873 40.000 22.45 22.45 40.34 3.06
4615 4880 3.208594 TGATGGGAAATTGATCTCGCAG 58.791 45.455 5.81 0.00 37.84 5.18
4621 4886 3.494626 GGAAATTGATCTCGCAGCGAATA 59.505 43.478 20.04 10.52 34.74 1.75
4678 4943 7.335422 AGCTATACAAAAGACCTGACAATTCTG 59.665 37.037 0.00 0.00 0.00 3.02
4743 5008 6.435904 CCACAGGTAACATTCCTTCCAAAATA 59.564 38.462 0.00 0.00 41.41 1.40
4744 5009 7.312899 CACAGGTAACATTCCTTCCAAAATAC 58.687 38.462 0.00 0.00 41.41 1.89
4745 5010 7.176690 CACAGGTAACATTCCTTCCAAAATACT 59.823 37.037 0.00 0.00 41.41 2.12
4746 5011 7.393515 ACAGGTAACATTCCTTCCAAAATACTC 59.606 37.037 0.00 0.00 41.41 2.59
4747 5012 6.890268 AGGTAACATTCCTTCCAAAATACTCC 59.110 38.462 0.00 0.00 41.41 3.85
4760 5025 8.519799 TCCAAAATACTCCATGTTTTATCTCC 57.480 34.615 0.00 0.00 31.05 3.71
4785 5083 4.946157 CAGGCAGATATGTTTCTCCTTTGT 59.054 41.667 0.00 0.00 0.00 2.83
4844 5142 3.128764 TGTCCACTGTATAGAAGTGCGAG 59.871 47.826 9.19 0.00 43.06 5.03
4847 5145 3.367607 CACTGTATAGAAGTGCGAGCTC 58.632 50.000 2.73 2.73 38.72 4.09
4904 5224 2.597510 GGCGGGTTCAGCACCTTT 60.598 61.111 0.00 0.00 46.38 3.11
4914 5234 1.768275 TCAGCACCTTTGAACTCCAGA 59.232 47.619 0.00 0.00 0.00 3.86
4916 5236 0.868406 GCACCTTTGAACTCCAGACG 59.132 55.000 0.00 0.00 0.00 4.18
4917 5237 1.512926 CACCTTTGAACTCCAGACGG 58.487 55.000 0.00 0.00 0.00 4.79
4946 5266 2.147150 GCCCAGTTCTCAGTGTTTCTC 58.853 52.381 0.00 0.00 0.00 2.87
4949 5269 3.556004 CCCAGTTCTCAGTGTTTCTCCTC 60.556 52.174 0.00 0.00 0.00 3.71
4951 5271 4.202305 CCAGTTCTCAGTGTTTCTCCTCTT 60.202 45.833 0.00 0.00 0.00 2.85
4960 5280 6.882140 TCAGTGTTTCTCCTCTTTGTTTGTAA 59.118 34.615 0.00 0.00 0.00 2.41
4970 5290 9.971922 CTCCTCTTTGTTTGTAATTTTCAATCT 57.028 29.630 0.00 0.00 0.00 2.40
5034 5355 8.084073 TCTAGTTGCTTCCTTTTGAATCAAATG 58.916 33.333 9.41 11.40 39.90 2.32
5059 5380 4.252971 ACTTTTAACAGCTAGAGTCGCA 57.747 40.909 0.00 0.00 0.00 5.10
5109 5430 7.879677 CCTGAACACTCTTATGGATGCATTATA 59.120 37.037 4.56 0.34 0.00 0.98
5110 5431 9.445878 CTGAACACTCTTATGGATGCATTATAT 57.554 33.333 4.56 0.00 0.00 0.86
5111 5432 9.797642 TGAACACTCTTATGGATGCATTATATT 57.202 29.630 4.56 0.00 0.00 1.28
5163 5484 3.009723 CCAGTTGCAAGTCGATAATGGT 58.990 45.455 3.08 0.00 0.00 3.55
5175 5496 7.235935 AGTCGATAATGGTATCCCGATAAAA 57.764 36.000 0.00 0.00 33.74 1.52
5187 5508 4.340617 TCCCGATAAAAAGCTGGTTTGAT 58.659 39.130 5.50 2.94 0.00 2.57
5349 5676 3.715097 GAGCCTGAGCCTGCCACT 61.715 66.667 0.00 0.00 41.25 4.00
5625 6041 6.890268 ACCTACACAAAATTCTCCCTAAATCC 59.110 38.462 0.00 0.00 0.00 3.01
5708 6124 2.268762 TGCTTTGGAGTATGTGTGCA 57.731 45.000 0.00 0.00 0.00 4.57
5713 6129 3.694043 TTGGAGTATGTGTGCAGCTAA 57.306 42.857 0.00 0.00 0.00 3.09
5734 6157 1.115467 AGTGGGATAAGACTGCCTCG 58.885 55.000 0.00 0.00 0.00 4.63
5790 6213 9.865321 ATTTGATAAATGTCACTTGAATTCTGG 57.135 29.630 7.05 2.08 0.00 3.86
5798 6221 2.749076 CACTTGAATTCTGGCGATTCCA 59.251 45.455 7.05 0.00 44.18 3.53
5841 6264 6.628185 TGCAAACTTTGAAAAATGCCATTTT 58.372 28.000 9.57 9.57 43.83 1.82
5856 6279 4.650545 CCATTTTCAGTGGCATTTTTCG 57.349 40.909 0.00 0.00 0.00 3.46
5857 6280 4.305769 CCATTTTCAGTGGCATTTTTCGA 58.694 39.130 0.00 0.00 0.00 3.71
5860 6283 4.647424 TTTCAGTGGCATTTTTCGAAGT 57.353 36.364 0.00 0.00 0.00 3.01
5862 6285 3.476552 TCAGTGGCATTTTTCGAAGTCT 58.523 40.909 0.00 0.00 0.00 3.24
5866 6289 5.003804 AGTGGCATTTTTCGAAGTCTACAT 58.996 37.500 0.00 0.00 0.00 2.29
5929 6352 3.195041 TGAAGCGTTCTCTTCACCG 57.805 52.632 2.43 0.00 45.21 4.94
6028 6451 1.372004 GCAACATTGCGCTTCAGCA 60.372 52.632 9.73 0.00 45.11 4.41
6050 6473 2.945668 AGCTAAGATGAAATTGCCGTCC 59.054 45.455 0.00 0.00 0.00 4.79
6120 6790 2.566952 GTGGCAATTATCACCTGCAC 57.433 50.000 0.00 0.00 37.83 4.57
6225 6895 2.812658 AGCATTCCTTCCTTTCCCTTG 58.187 47.619 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 0.996762 GAGAGAGAGGGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
105 106 0.478507 GAGAGAGAGAGGGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
111 112 1.402787 GCAAGAGAGAGAGAGAGGGG 58.597 60.000 0.00 0.00 0.00 4.79
115 116 1.987704 GCGCGCAAGAGAGAGAGAGA 61.988 60.000 29.10 0.00 40.82 3.10
117 118 1.590610 AAGCGCGCAAGAGAGAGAGA 61.591 55.000 35.10 0.00 40.82 3.10
291 307 7.011669 ACGGAAAATAAAAGTCAGAGAACGAAA 59.988 33.333 0.00 0.00 0.00 3.46
337 353 6.921307 CCAACCCAAACAACTCAATTAGTAAC 59.079 38.462 0.00 0.00 37.50 2.50
350 366 1.234529 CCCTCCCCAACCCAAACAA 59.765 57.895 0.00 0.00 0.00 2.83
406 428 8.024145 AGCTGAAGCAACCTAAATACTAGTAT 57.976 34.615 9.71 9.71 45.16 2.12
415 438 2.294233 CAGCAAGCTGAAGCAACCTAAA 59.706 45.455 16.75 0.00 46.30 1.85
420 443 1.484356 CAACAGCAAGCTGAAGCAAC 58.516 50.000 27.17 0.00 46.30 4.17
424 447 2.338381 AGCCAACAGCAAGCTGAAG 58.662 52.632 27.17 17.57 46.30 3.02
541 564 4.300803 CGCCATGATCCATGTTATTTTGG 58.699 43.478 0.00 0.00 39.94 3.28
598 621 7.027778 ACAAACACCAACTTCATTTCTAGAC 57.972 36.000 0.00 0.00 0.00 2.59
658 681 1.667724 CAAGCAGCCTCCGATAAACTG 59.332 52.381 0.00 0.00 0.00 3.16
729 752 6.183360 CGCCTATATAGTTCTCTAGCTGAAGG 60.183 46.154 8.92 0.00 0.00 3.46
1059 1085 5.552178 GAGTCTTCCAGTATTTCAGTGGTT 58.448 41.667 0.00 0.00 46.58 3.67
1090 1116 4.328983 TGTTTCGCGGAATGTAATCTCTTC 59.671 41.667 1.59 0.00 0.00 2.87
1167 1193 6.394025 AGTCTAACCAAGTAGATCGGAATC 57.606 41.667 0.00 0.00 32.81 2.52
1262 1328 7.915293 TCTGAAAGAGTCACTACTTCTCTAG 57.085 40.000 0.00 0.00 38.67 2.43
1377 1562 3.503363 TGATGTTCAGTCACCTGCAATTC 59.497 43.478 0.00 0.00 38.66 2.17
1444 1629 5.352643 ACAAAAACTACCTTCCGATTTCG 57.647 39.130 0.00 0.00 39.44 3.46
1491 1676 8.588472 TGCTAGATACACTCATGCAGTATAAAT 58.412 33.333 0.00 0.00 32.21 1.40
1492 1677 7.951591 TGCTAGATACACTCATGCAGTATAAA 58.048 34.615 0.00 0.00 32.21 1.40
1493 1678 7.524717 TGCTAGATACACTCATGCAGTATAA 57.475 36.000 0.00 0.00 32.21 0.98
1494 1679 7.709149 ATGCTAGATACACTCATGCAGTATA 57.291 36.000 0.00 0.00 34.79 1.47
1495 1680 6.602410 ATGCTAGATACACTCATGCAGTAT 57.398 37.500 0.00 0.00 34.79 2.12
1496 1681 6.410942 AATGCTAGATACACTCATGCAGTA 57.589 37.500 0.00 0.00 34.79 2.74
1497 1682 4.952071 ATGCTAGATACACTCATGCAGT 57.048 40.909 0.00 0.00 34.79 4.40
1498 1683 6.146837 GGTTAATGCTAGATACACTCATGCAG 59.853 42.308 0.00 0.00 34.79 4.41
1499 1684 5.991606 GGTTAATGCTAGATACACTCATGCA 59.008 40.000 0.00 0.00 35.37 3.96
1500 1685 6.226787 AGGTTAATGCTAGATACACTCATGC 58.773 40.000 0.00 0.00 0.00 4.06
1501 1686 7.665690 AGAGGTTAATGCTAGATACACTCATG 58.334 38.462 0.00 0.00 0.00 3.07
1543 1728 8.565416 GGAACTTAGCAGTAGTGTTTATTGTTT 58.435 33.333 0.00 0.00 30.68 2.83
1581 1767 8.515414 AGTATTTCATTTCTACAGAAGGTTTGC 58.485 33.333 0.00 0.00 35.21 3.68
1739 1925 9.363763 CATATGCATATCCTAATTATAGAGCGG 57.636 37.037 16.46 0.00 0.00 5.52
1868 2062 1.336887 GCAACACTTCGGCAGTAGAGA 60.337 52.381 0.00 0.00 32.76 3.10
1946 2141 2.787994 AGTTGACTTCAGCCATTCCAG 58.212 47.619 0.00 0.00 0.00 3.86
1964 2159 3.254166 GTCAGATTCACCATGCAACAAGT 59.746 43.478 0.00 0.00 0.00 3.16
2182 2378 6.505272 AGAAGATATGAACCTAAGTACGCAC 58.495 40.000 0.00 0.00 0.00 5.34
2210 2406 7.125356 TGCCAGATATGAGTCTATGCATTATCT 59.875 37.037 3.54 6.75 33.12 1.98
2219 2415 5.309020 ACCACAATGCCAGATATGAGTCTAT 59.691 40.000 0.00 0.00 0.00 1.98
2273 2469 6.000246 TGATAATCCTTACAACTGGCATGA 58.000 37.500 0.00 0.00 0.00 3.07
2564 2771 8.450780 AATAAGATATTATTCCCTCCGTTCCT 57.549 34.615 0.00 0.00 0.00 3.36
2765 2974 5.298276 TCACTTCAACCAATGTTACAGGTTC 59.702 40.000 6.11 0.00 43.43 3.62
2807 3016 0.251916 TATTTCCAGCCCCAGTCACG 59.748 55.000 0.00 0.00 0.00 4.35
2844 3053 0.100325 TGCAGAAAACAACCACAGCG 59.900 50.000 0.00 0.00 0.00 5.18
2998 3213 7.978982 ACTGCAGAATTCATAACTTGACATAC 58.021 34.615 23.35 0.00 32.84 2.39
3095 3312 6.613679 TGTACATTGGATTAGGTGTCAGGATA 59.386 38.462 0.00 0.00 0.00 2.59
3101 3318 5.730550 TCACTGTACATTGGATTAGGTGTC 58.269 41.667 12.73 0.00 0.00 3.67
3389 3612 0.790814 GAAGGAACTCGGTGCTTTCG 59.209 55.000 0.00 0.00 38.49 3.46
3479 3702 9.667107 TCAGAAAAACTTTCTGAGAAGTAGAAA 57.333 29.630 22.01 0.00 46.95 2.52
3775 3998 6.597280 ACCTCTAGAATGAAGCTTTTCATCAC 59.403 38.462 12.29 5.81 40.51 3.06
4134 4396 0.749049 GGGCTTGCAGGGATTGATTC 59.251 55.000 0.00 0.00 0.00 2.52
4270 4533 3.117794 CGCCAATGCATGACCTAAAATG 58.882 45.455 0.00 0.00 37.32 2.32
4288 4551 2.658285 CAATGCTGAAGATAATGCGCC 58.342 47.619 4.18 0.00 0.00 6.53
4369 4633 7.280428 ACAAGAGTCTCTGCATATGAAAATGAG 59.720 37.037 6.97 0.00 0.00 2.90
4370 4634 7.108194 ACAAGAGTCTCTGCATATGAAAATGA 58.892 34.615 6.97 0.00 0.00 2.57
4621 4886 9.454859 TCAGAGAATATACATGACTCACGATAT 57.545 33.333 0.00 0.00 0.00 1.63
4633 4898 5.758790 AGCTGCCATCAGAGAATATACAT 57.241 39.130 0.00 0.00 42.95 2.29
4678 4943 0.961753 CTTTTGCCAAGTGGACTCCC 59.038 55.000 0.18 0.00 37.39 4.30
4743 5008 4.848357 CCTGTGGAGATAAAACATGGAGT 58.152 43.478 0.00 0.00 0.00 3.85
4744 5009 3.629398 GCCTGTGGAGATAAAACATGGAG 59.371 47.826 0.00 0.00 0.00 3.86
4745 5010 3.010027 TGCCTGTGGAGATAAAACATGGA 59.990 43.478 0.00 0.00 0.00 3.41
4746 5011 3.355378 TGCCTGTGGAGATAAAACATGG 58.645 45.455 0.00 0.00 0.00 3.66
4747 5012 4.264253 TCTGCCTGTGGAGATAAAACATG 58.736 43.478 0.00 0.00 0.00 3.21
4760 5025 4.148128 AGGAGAAACATATCTGCCTGTG 57.852 45.455 0.00 0.00 38.43 3.66
4785 5083 1.704070 TCCCCCTTTAGCCAACGTTTA 59.296 47.619 0.00 0.00 0.00 2.01
4824 5122 2.099263 GCTCGCACTTCTATACAGTGGA 59.901 50.000 8.70 0.00 41.81 4.02
4873 5171 2.124983 CGCCCAGCTGCACTGTAT 60.125 61.111 8.66 0.00 45.68 2.29
4874 5172 4.393155 CCGCCCAGCTGCACTGTA 62.393 66.667 8.66 0.00 45.68 2.74
4916 5236 3.741830 GAACTGGGCGCTAGCTCCC 62.742 68.421 32.17 32.17 45.20 4.30
4917 5237 2.202946 GAACTGGGCGCTAGCTCC 60.203 66.667 15.70 15.70 45.20 4.70
4925 5245 0.868406 GAAACACTGAGAACTGGGCG 59.132 55.000 0.00 0.00 0.00 6.13
4970 5290 9.929180 CACATGCCTAGAAAATATAGCTACTAA 57.071 33.333 0.00 0.00 0.00 2.24
4984 5304 0.983467 TGCAGGTCACATGCCTAGAA 59.017 50.000 12.77 0.00 43.18 2.10
5034 5355 6.072098 GCGACTCTAGCTGTTAAAAGTTTTC 58.928 40.000 3.60 0.00 0.00 2.29
5059 5380 1.980765 TGTGAAGCCCTCATGAAGAGT 59.019 47.619 0.00 0.00 43.12 3.24
5163 5484 5.502079 TCAAACCAGCTTTTTATCGGGATA 58.498 37.500 0.00 0.00 0.00 2.59
5175 5496 0.609131 CGGGGTCATCAAACCAGCTT 60.609 55.000 0.00 0.00 41.40 3.74
5349 5676 0.969149 AGATGGAGTTCGCTGACACA 59.031 50.000 0.00 0.00 0.00 3.72
5625 6041 5.050490 CGATTGTTCTACAACCAGGATAGG 58.950 45.833 0.00 0.00 41.40 2.57
5708 6124 4.518249 GCAGTCTTATCCCACTTTTAGCT 58.482 43.478 0.00 0.00 0.00 3.32
5713 6129 2.093447 CGAGGCAGTCTTATCCCACTTT 60.093 50.000 0.00 0.00 0.00 2.66
5790 6213 2.349886 CAGTAGCACTTCTTGGAATCGC 59.650 50.000 0.00 0.00 0.00 4.58
5841 6264 3.476552 AGACTTCGAAAAATGCCACTGA 58.523 40.909 0.00 0.00 0.00 3.41
5856 6279 5.602978 TCCCTCCATTCCTAATGTAGACTTC 59.397 44.000 0.00 0.00 37.18 3.01
5857 6280 5.538877 TCCCTCCATTCCTAATGTAGACTT 58.461 41.667 0.00 0.00 37.18 3.01
5860 6283 5.157770 ACTCCCTCCATTCCTAATGTAGA 57.842 43.478 0.00 0.00 37.18 2.59
5862 6285 6.289482 TCTACTCCCTCCATTCCTAATGTA 57.711 41.667 0.00 0.00 37.18 2.29
5866 6289 6.798544 TCTATCTACTCCCTCCATTCCTAA 57.201 41.667 0.00 0.00 0.00 2.69
6021 6444 5.515626 GCAATTTCATCTTAGCTTGCTGAAG 59.484 40.000 5.26 5.65 36.83 3.02
6028 6451 3.378427 GGACGGCAATTTCATCTTAGCTT 59.622 43.478 0.00 0.00 0.00 3.74
6067 6737 6.478512 AATCAGTGGCTTCTGGTTTTAAAA 57.521 33.333 0.00 0.00 35.55 1.52
6225 6895 1.183549 TTTCTAGGGCGAGGAGACAC 58.816 55.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.