Multiple sequence alignment - TraesCS2D01G568800

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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 TraesCS2D01G568800 chr2D 100.000 4348 0 0 1 4348 636737752 636733405 0.000000e+00 8030.0
1 TraesCS2D01G568800 chr2D 82.420 2025 304 27 1 2001 637380807 637378811 0.000000e+00 1720.0
2 TraesCS2D01G568800 chr2D 83.647 1804 263 19 37 1817 637021085 637019291 0.000000e+00 1668.0
3 TraesCS2D01G568800 chr2D 82.500 1840 244 37 1 1797 637340943 637339139 0.000000e+00 1543.0
4 TraesCS2D01G568800 chr2D 82.460 1642 256 24 3 1623 636795092 636793462 0.000000e+00 1408.0
5 TraesCS2D01G568800 chr2D 81.971 1370 200 30 1 1353 636930975 636929636 0.000000e+00 1118.0
6 TraesCS2D01G568800 chr2D 77.477 888 173 19 2095 2962 637338614 637337734 1.400000e-139 507.0
7 TraesCS2D01G568800 chr2D 82.590 471 70 7 2460 2920 636941827 636941359 5.240000e-109 405.0
8 TraesCS2D01G568800 chr2D 75.867 663 138 17 2183 2832 636793022 636792369 7.020000e-83 318.0
9 TraesCS2D01G568800 chr2D 80.592 304 52 6 2088 2388 636773413 636773114 1.220000e-55 228.0
10 TraesCS2D01G568800 chr2D 91.772 158 10 3 3515 3672 636941276 636941122 2.630000e-52 217.0
11 TraesCS2D01G568800 chr2D 87.719 57 4 2 3282 3338 636790575 636790522 3.630000e-06 63.9
12 TraesCS2D01G568800 chr2A 97.627 3961 58 14 1 3951 762771207 762775141 0.000000e+00 6761.0
13 TraesCS2D01G568800 chr2A 80.033 3015 485 77 2 2962 762891360 762894311 0.000000e+00 2124.0
14 TraesCS2D01G568800 chr2A 82.908 1843 276 25 1 1817 762686413 762688242 0.000000e+00 1622.0
15 TraesCS2D01G568800 chr2A 79.952 2065 341 44 1 2008 763019133 763021181 0.000000e+00 1452.0
16 TraesCS2D01G568800 chr2A 73.269 1545 309 56 1669 3161 762803533 762805025 1.830000e-128 470.0
17 TraesCS2D01G568800 chr2A 94.301 193 6 4 3935 4122 762775232 762775424 1.530000e-74 291.0
18 TraesCS2D01G568800 chr2A 84.000 125 10 6 4145 4261 762776059 762776181 1.280000e-20 111.0
19 TraesCS2D01G568800 chr2A 91.176 68 5 1 3572 3639 762762733 762762799 1.670000e-14 91.6
20 TraesCS2D01G568800 chr2B 85.530 2474 299 39 1 2451 774708003 774705566 0.000000e+00 2531.0
21 TraesCS2D01G568800 chr2B 81.962 1641 271 19 1 1623 794671842 794670209 0.000000e+00 1367.0
22 TraesCS2D01G568800 chr2B 85.294 238 15 10 3191 3414 774704822 774704591 1.220000e-55 228.0
23 TraesCS2D01G568800 chr2B 87.975 158 10 5 3783 3935 774704230 774704077 1.240000e-40 178.0
24 TraesCS2D01G568800 chr2B 79.795 292 22 18 3472 3752 774704494 774704229 1.240000e-40 178.0
25 TraesCS2D01G568800 chr2B 92.079 101 4 4 3573 3672 794560492 794560395 5.860000e-29 139.0
26 TraesCS2D01G568800 chr2B 96.154 52 2 0 3940 3991 774703896 774703845 7.750000e-13 86.1
27 TraesCS2D01G568800 chr7B 88.701 1363 151 3 1087 2449 746114949 746113590 0.000000e+00 1661.0
28 TraesCS2D01G568800 chr7B 88.701 1363 151 3 1087 2449 746117875 746116516 0.000000e+00 1661.0
29 TraesCS2D01G568800 chr7B 88.802 1286 141 3 1164 2449 746120724 746119442 0.000000e+00 1574.0
30 TraesCS2D01G568800 chr7B 92.176 818 32 10 2456 3251 746113547 746112740 0.000000e+00 1127.0
31 TraesCS2D01G568800 chr7B 88.522 758 84 3 1692 2449 746122659 746121905 0.000000e+00 915.0
32 TraesCS2D01G568800 chr7B 91.846 650 24 9 2621 3251 746142450 746141811 0.000000e+00 880.0
33 TraesCS2D01G568800 chr7B 92.342 444 11 6 3267 3710 746141736 746141316 1.030000e-170 610.0
34 TraesCS2D01G568800 chr7B 91.536 319 8 5 3267 3585 746112665 746112366 5.200000e-114 422.0
35 TraesCS2D01G568800 chr7B 93.119 218 9 4 3935 4146 746141001 746140784 9.080000e-82 315.0
36 TraesCS2D01G568800 chr7B 95.161 124 6 0 2456 2579 746116473 746116350 3.430000e-46 196.0
37 TraesCS2D01G568800 chr7B 95.161 124 6 0 2456 2579 746119399 746119276 3.430000e-46 196.0
38 TraesCS2D01G568800 chr7B 94.355 124 7 0 2456 2579 746121862 746121739 1.600000e-44 191.0
39 TraesCS2D01G568800 chr7B 92.063 126 7 3 3805 3930 746141291 746141169 1.610000e-39 174.0
40 TraesCS2D01G568800 chr7B 84.298 121 7 8 4150 4261 746140276 746140159 1.650000e-19 108.0
41 TraesCS2D01G568800 chr6B 84.657 1675 221 27 1 1650 130302204 130303867 0.000000e+00 1637.0
42 TraesCS2D01G568800 chrUn 83.113 1818 271 18 8 1797 234394975 234396784 0.000000e+00 1624.0
43 TraesCS2D01G568800 chrUn 83.113 1818 271 18 8 1797 283150995 283152804 0.000000e+00 1624.0
44 TraesCS2D01G568800 chrUn 83.140 1815 270 18 11 1797 312596469 312594663 0.000000e+00 1624.0
45 TraesCS2D01G568800 chrUn 92.421 818 30 10 2456 3251 359504880 359504073 0.000000e+00 1138.0
46 TraesCS2D01G568800 chrUn 92.176 818 32 10 2456 3251 359483890 359483083 0.000000e+00 1127.0
47 TraesCS2D01G568800 chrUn 88.339 849 96 3 1601 2449 359484778 359483933 0.000000e+00 1016.0
48 TraesCS2D01G568800 chrUn 88.339 849 96 3 1601 2449 359505768 359504923 0.000000e+00 1016.0
49 TraesCS2D01G568800 chrUn 100.000 389 0 0 2788 3176 480126019 480125631 0.000000e+00 719.0
50 TraesCS2D01G568800 chrUn 77.370 1118 216 23 1882 2967 234396851 234397963 2.850000e-176 628.0
51 TraesCS2D01G568800 chrUn 89.919 248 6 5 3267 3514 359483008 359482780 7.070000e-78 302.0
52 TraesCS2D01G568800 chrUn 89.919 248 6 5 3267 3514 359503998 359503770 7.070000e-78 302.0
53 TraesCS2D01G568800 chr6D 84.436 1677 222 30 1 1650 58043451 58045115 0.000000e+00 1615.0
54 TraesCS2D01G568800 chr1B 80.458 2052 332 46 1 2008 626091501 626093527 0.000000e+00 1504.0


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 TraesCS2D01G568800 chr2D 636733405 636737752 4347 True 8030.000000 8030 100.000000 1 4348 1 chr2D.!!$R1 4347
1 TraesCS2D01G568800 chr2D 637378811 637380807 1996 True 1720.000000 1720 82.420000 1 2001 1 chr2D.!!$R5 2000
2 TraesCS2D01G568800 chr2D 637019291 637021085 1794 True 1668.000000 1668 83.647000 37 1817 1 chr2D.!!$R4 1780
3 TraesCS2D01G568800 chr2D 636929636 636930975 1339 True 1118.000000 1118 81.971000 1 1353 1 chr2D.!!$R3 1352
4 TraesCS2D01G568800 chr2D 637337734 637340943 3209 True 1025.000000 1543 79.988500 1 2962 2 chr2D.!!$R8 2961
5 TraesCS2D01G568800 chr2D 636790522 636795092 4570 True 596.633333 1408 82.015333 3 3338 3 chr2D.!!$R6 3335
6 TraesCS2D01G568800 chr2D 636941122 636941827 705 True 311.000000 405 87.181000 2460 3672 2 chr2D.!!$R7 1212
7 TraesCS2D01G568800 chr2A 762771207 762776181 4974 False 2387.666667 6761 91.976000 1 4261 3 chr2A.!!$F6 4260
8 TraesCS2D01G568800 chr2A 762891360 762894311 2951 False 2124.000000 2124 80.033000 2 2962 1 chr2A.!!$F4 2960
9 TraesCS2D01G568800 chr2A 762686413 762688242 1829 False 1622.000000 1622 82.908000 1 1817 1 chr2A.!!$F1 1816
10 TraesCS2D01G568800 chr2A 763019133 763021181 2048 False 1452.000000 1452 79.952000 1 2008 1 chr2A.!!$F5 2007
11 TraesCS2D01G568800 chr2A 762803533 762805025 1492 False 470.000000 470 73.269000 1669 3161 1 chr2A.!!$F3 1492
12 TraesCS2D01G568800 chr2B 794670209 794671842 1633 True 1367.000000 1367 81.962000 1 1623 1 chr2B.!!$R2 1622
13 TraesCS2D01G568800 chr2B 774703845 774708003 4158 True 640.220000 2531 86.949600 1 3991 5 chr2B.!!$R3 3990
14 TraesCS2D01G568800 chr7B 746112366 746122659 10293 True 882.555556 1661 91.457222 1087 3585 9 chr7B.!!$R1 2498
15 TraesCS2D01G568800 chr7B 746140159 746142450 2291 True 417.400000 880 90.733600 2621 4261 5 chr7B.!!$R2 1640
16 TraesCS2D01G568800 chr6B 130302204 130303867 1663 False 1637.000000 1637 84.657000 1 1650 1 chr6B.!!$F1 1649
17 TraesCS2D01G568800 chrUn 283150995 283152804 1809 False 1624.000000 1624 83.113000 8 1797 1 chrUn.!!$F1 1789
18 TraesCS2D01G568800 chrUn 312594663 312596469 1806 True 1624.000000 1624 83.140000 11 1797 1 chrUn.!!$R1 1786
19 TraesCS2D01G568800 chrUn 234394975 234397963 2988 False 1126.000000 1624 80.241500 8 2967 2 chrUn.!!$F2 2959
20 TraesCS2D01G568800 chrUn 359503770 359505768 1998 True 818.666667 1138 90.226333 1601 3514 3 chrUn.!!$R4 1913
21 TraesCS2D01G568800 chrUn 359482780 359484778 1998 True 815.000000 1127 90.144667 1601 3514 3 chrUn.!!$R3 1913
22 TraesCS2D01G568800 chr6D 58043451 58045115 1664 False 1615.000000 1615 84.436000 1 1650 1 chr6D.!!$F1 1649
23 TraesCS2D01G568800 chr1B 626091501 626093527 2026 False 1504.000000 1504 80.458000 1 2008 1 chr1B.!!$F1 2007

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
969 1004 9.502091 GGTTGAGCTATATGTATTTACCATTCA 57.498 33.333 0.00 0.0 0.00 2.57 F
1088 1123 0.606673 GAGCCTCAAGGTGGTGTTCC 60.607 60.000 0.00 0.0 37.57 3.62 F
1089 1124 1.603739 GCCTCAAGGTGGTGTTCCC 60.604 63.158 0.00 0.0 37.57 3.97 F
1090 1125 1.843421 CCTCAAGGTGGTGTTCCCA 59.157 57.895 0.00 0.0 42.51 4.37 F
2296 9291 2.231478 CAGTCCCTTAAGAAGCTCGACA 59.769 50.000 3.36 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 9291 4.338879 CAAAAGAGACCAGAATCCCACAT 58.661 43.478 0.00 0.0 0.0 3.21 R
3247 11460 2.611722 GCACGGCACCCAAATAAAACAT 60.612 45.455 0.00 0.0 0.0 2.71 R
3248 11461 1.269831 GCACGGCACCCAAATAAAACA 60.270 47.619 0.00 0.0 0.0 2.83 R
3249 11462 1.000394 AGCACGGCACCCAAATAAAAC 60.000 47.619 0.00 0.0 0.0 2.43 R
4264 14128 0.031111 AGGCTGCCACTCCCATACTA 60.031 55.000 22.65 0.0 0.0 1.82 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
969 1004 9.502091 GGTTGAGCTATATGTATTTACCATTCA 57.498 33.333 0.00 0.00 0.00 2.57
1088 1123 0.606673 GAGCCTCAAGGTGGTGTTCC 60.607 60.000 0.00 0.00 37.57 3.62
1089 1124 1.603739 GCCTCAAGGTGGTGTTCCC 60.604 63.158 0.00 0.00 37.57 3.97
1090 1125 1.843421 CCTCAAGGTGGTGTTCCCA 59.157 57.895 0.00 0.00 42.51 4.37
1596 8231 6.350780 CCAAGAAATGCAAGCTAGAAATTCCT 60.351 38.462 0.00 0.00 0.00 3.36
2154 9149 5.587388 ATGTACCAGGCATCAAGAAAATG 57.413 39.130 0.00 0.00 0.00 2.32
2296 9291 2.231478 CAGTCCCTTAAGAAGCTCGACA 59.769 50.000 3.36 0.00 0.00 4.35
3247 11460 7.655328 CCATGTTTTGATAAAAGTTGCTAACCA 59.345 33.333 0.00 0.00 0.00 3.67
3248 11461 9.206870 CATGTTTTGATAAAAGTTGCTAACCAT 57.793 29.630 0.00 0.00 0.00 3.55
3249 11462 8.586570 TGTTTTGATAAAAGTTGCTAACCATG 57.413 30.769 0.00 0.00 0.00 3.66
3250 11463 8.200792 TGTTTTGATAAAAGTTGCTAACCATGT 58.799 29.630 0.00 0.00 0.00 3.21
3251 11464 9.040939 GTTTTGATAAAAGTTGCTAACCATGTT 57.959 29.630 0.00 0.00 0.00 2.71
3292 11789 0.034616 TTTGGGGAGCCAAATTTGCG 59.965 50.000 12.92 7.39 35.16 4.85
3461 12009 8.833231 ACGGTTCTATTCCATTAATCTGTATG 57.167 34.615 0.00 0.00 0.00 2.39
3462 12010 8.429641 ACGGTTCTATTCCATTAATCTGTATGT 58.570 33.333 0.00 0.00 0.00 2.29
3463 12011 9.923143 CGGTTCTATTCCATTAATCTGTATGTA 57.077 33.333 0.00 0.00 0.00 2.29
3778 12347 1.081094 TGAGCACAACATCTGCATCG 58.919 50.000 0.00 0.00 37.08 3.84
3779 12348 1.338011 TGAGCACAACATCTGCATCGA 60.338 47.619 0.00 0.00 37.08 3.59
3780 12349 1.938577 GAGCACAACATCTGCATCGAT 59.061 47.619 0.00 0.00 37.08 3.59
3781 12350 1.938577 AGCACAACATCTGCATCGATC 59.061 47.619 0.00 0.00 37.08 3.69
3789 12358 0.179092 TCTGCATCGATCTGCCTGTG 60.179 55.000 8.46 0.00 41.58 3.66
3820 12390 4.212716 ACCCCCTTGTTCTGTAGTTTTTC 58.787 43.478 0.00 0.00 0.00 2.29
3872 12443 3.701040 TGCTCTCTTTCTTTGCTGGTTTT 59.299 39.130 0.00 0.00 0.00 2.43
4036 12791 3.910627 AGTCCCTTGTGGTAGTTTCAGAT 59.089 43.478 0.00 0.00 34.77 2.90
4052 12807 8.237811 AGTTTCAGATTACAACCAAGTTGAAT 57.762 30.769 14.05 8.99 45.28 2.57
4053 12808 8.137437 AGTTTCAGATTACAACCAAGTTGAATG 58.863 33.333 14.05 5.42 45.28 2.67
4056 12811 4.220602 AGATTACAACCAAGTTGAATGGGC 59.779 41.667 14.05 0.00 45.28 5.36
4094 12853 6.980397 ACACATGATTTGAAGTTTCTGAAACC 59.020 34.615 25.22 14.12 42.34 3.27
4109 12869 4.082895 TCTGAAACCGAGAAGTACAGTAGC 60.083 45.833 0.00 0.00 0.00 3.58
4126 13480 0.804989 AGCAGCCTAACGTTTGATGC 59.195 50.000 24.46 24.46 0.00 3.91
4128 13482 1.075542 CAGCCTAACGTTTGATGCGA 58.924 50.000 5.91 0.00 0.00 5.10
4140 13494 1.660167 TGATGCGAGAATGGAGCTTG 58.340 50.000 0.00 0.00 0.00 4.01
4146 13500 1.065854 CGAGAATGGAGCTTGAAGGGT 60.066 52.381 0.00 0.00 0.00 4.34
4148 13502 3.369471 CGAGAATGGAGCTTGAAGGGTTA 60.369 47.826 0.00 0.00 0.00 2.85
4261 14125 6.680810 CAACATGTGACATTGGTTAGTTCAT 58.319 36.000 0.00 0.00 0.00 2.57
4262 14126 6.258230 ACATGTGACATTGGTTAGTTCATG 57.742 37.500 0.00 0.00 36.92 3.07
4263 14127 6.003326 ACATGTGACATTGGTTAGTTCATGA 58.997 36.000 0.00 0.00 35.74 3.07
4264 14128 6.660521 ACATGTGACATTGGTTAGTTCATGAT 59.339 34.615 0.00 0.00 35.74 2.45
4265 14129 7.828717 ACATGTGACATTGGTTAGTTCATGATA 59.171 33.333 0.00 0.00 35.74 2.15
4266 14130 7.848223 TGTGACATTGGTTAGTTCATGATAG 57.152 36.000 0.00 0.00 0.00 2.08
4267 14131 7.394016 TGTGACATTGGTTAGTTCATGATAGT 58.606 34.615 0.00 0.00 0.00 2.12
4268 14132 8.536175 TGTGACATTGGTTAGTTCATGATAGTA 58.464 33.333 0.00 0.00 0.00 1.82
4269 14133 9.547753 GTGACATTGGTTAGTTCATGATAGTAT 57.452 33.333 0.00 0.00 0.00 2.12
4270 14134 9.546428 TGACATTGGTTAGTTCATGATAGTATG 57.454 33.333 0.00 0.00 0.00 2.39
4271 14135 8.908786 ACATTGGTTAGTTCATGATAGTATGG 57.091 34.615 0.00 0.00 0.00 2.74
4272 14136 7.939039 ACATTGGTTAGTTCATGATAGTATGGG 59.061 37.037 0.00 0.00 0.00 4.00
4273 14137 7.684317 TTGGTTAGTTCATGATAGTATGGGA 57.316 36.000 0.00 0.00 0.00 4.37
4274 14138 7.303182 TGGTTAGTTCATGATAGTATGGGAG 57.697 40.000 0.00 0.00 0.00 4.30
4275 14139 6.844388 TGGTTAGTTCATGATAGTATGGGAGT 59.156 38.462 0.00 0.00 0.00 3.85
4276 14140 7.155328 GGTTAGTTCATGATAGTATGGGAGTG 58.845 42.308 0.00 0.00 0.00 3.51
4277 14141 5.815233 AGTTCATGATAGTATGGGAGTGG 57.185 43.478 0.00 0.00 0.00 4.00
4278 14142 4.040952 AGTTCATGATAGTATGGGAGTGGC 59.959 45.833 0.00 0.00 0.00 5.01
4279 14143 3.586429 TCATGATAGTATGGGAGTGGCA 58.414 45.455 0.00 0.00 0.00 4.92
4280 14144 3.580022 TCATGATAGTATGGGAGTGGCAG 59.420 47.826 0.00 0.00 0.00 4.85
4281 14145 1.694150 TGATAGTATGGGAGTGGCAGC 59.306 52.381 0.00 0.00 0.00 5.25
4282 14146 1.002544 GATAGTATGGGAGTGGCAGCC 59.997 57.143 3.66 3.66 0.00 4.85
4283 14147 0.031111 TAGTATGGGAGTGGCAGCCT 60.031 55.000 14.15 0.00 0.00 4.58
4284 14148 1.147153 GTATGGGAGTGGCAGCCTC 59.853 63.158 14.15 9.57 0.00 4.70
4285 14149 1.003442 TATGGGAGTGGCAGCCTCT 59.997 57.895 16.19 16.19 0.00 3.69
4286 14150 1.050988 TATGGGAGTGGCAGCCTCTC 61.051 60.000 28.71 28.71 41.71 3.20
4287 14151 3.005539 GGGAGTGGCAGCCTCTCA 61.006 66.667 34.19 5.47 43.52 3.27
4288 14152 2.373707 GGGAGTGGCAGCCTCTCAT 61.374 63.158 34.19 9.34 43.52 2.90
4289 14153 1.153208 GGAGTGGCAGCCTCTCATG 60.153 63.158 34.19 0.00 43.52 3.07
4290 14154 1.153208 GAGTGGCAGCCTCTCATGG 60.153 63.158 30.69 0.00 41.94 3.66
4291 14155 1.614525 AGTGGCAGCCTCTCATGGA 60.615 57.895 14.15 0.00 0.00 3.41
4292 14156 1.451028 GTGGCAGCCTCTCATGGAC 60.451 63.158 14.15 0.00 0.00 4.02
4293 14157 2.202987 GGCAGCCTCTCATGGACG 60.203 66.667 3.29 0.00 0.00 4.79
4294 14158 2.202987 GCAGCCTCTCATGGACGG 60.203 66.667 0.00 0.00 0.00 4.79
4295 14159 2.202987 CAGCCTCTCATGGACGGC 60.203 66.667 10.76 10.76 38.01 5.68
4296 14160 3.474570 AGCCTCTCATGGACGGCC 61.475 66.667 0.00 0.00 38.28 6.13
4310 14174 3.656045 GGCCAACCAACCGTCGTG 61.656 66.667 0.00 0.00 35.26 4.35
4311 14175 3.656045 GCCAACCAACCGTCGTGG 61.656 66.667 0.53 0.53 46.41 4.94
4312 14176 3.656045 CCAACCAACCGTCGTGGC 61.656 66.667 1.94 0.00 43.94 5.01
4313 14177 2.897846 CAACCAACCGTCGTGGCA 60.898 61.111 1.94 0.00 43.94 4.92
4314 14178 2.898343 AACCAACCGTCGTGGCAC 60.898 61.111 7.79 7.79 43.94 5.01
4315 14179 3.394635 AACCAACCGTCGTGGCACT 62.395 57.895 16.72 0.00 43.94 4.40
4316 14180 3.345808 CCAACCGTCGTGGCACTG 61.346 66.667 16.72 9.49 43.94 3.66
4317 14181 2.279851 CAACCGTCGTGGCACTGA 60.280 61.111 16.72 11.75 43.94 3.41
4318 14182 1.885388 CAACCGTCGTGGCACTGAA 60.885 57.895 16.72 0.00 43.94 3.02
4319 14183 1.070786 AACCGTCGTGGCACTGAAT 59.929 52.632 16.72 1.93 43.94 2.57
4320 14184 0.534203 AACCGTCGTGGCACTGAATT 60.534 50.000 16.72 7.37 43.94 2.17
4321 14185 0.534203 ACCGTCGTGGCACTGAATTT 60.534 50.000 16.72 0.09 43.94 1.82
4322 14186 1.270412 ACCGTCGTGGCACTGAATTTA 60.270 47.619 16.72 0.00 43.94 1.40
4323 14187 1.393539 CCGTCGTGGCACTGAATTTAG 59.606 52.381 16.72 0.00 0.00 1.85
4324 14188 1.393539 CGTCGTGGCACTGAATTTAGG 59.606 52.381 16.72 0.00 0.00 2.69
4325 14189 2.423577 GTCGTGGCACTGAATTTAGGT 58.576 47.619 16.72 0.00 0.00 3.08
4326 14190 2.159627 GTCGTGGCACTGAATTTAGGTG 59.840 50.000 16.72 2.67 0.00 4.00
4327 14191 1.468520 CGTGGCACTGAATTTAGGTGG 59.531 52.381 16.72 0.00 0.00 4.61
4328 14192 1.818674 GTGGCACTGAATTTAGGTGGG 59.181 52.381 11.13 0.00 0.00 4.61
4329 14193 1.707989 TGGCACTGAATTTAGGTGGGA 59.292 47.619 1.95 0.00 0.00 4.37
4330 14194 2.109128 TGGCACTGAATTTAGGTGGGAA 59.891 45.455 1.95 0.00 0.00 3.97
4331 14195 3.245586 TGGCACTGAATTTAGGTGGGAAT 60.246 43.478 1.95 0.00 0.00 3.01
4332 14196 3.769300 GGCACTGAATTTAGGTGGGAATT 59.231 43.478 1.95 0.00 0.00 2.17
4333 14197 4.953579 GGCACTGAATTTAGGTGGGAATTA 59.046 41.667 1.95 0.00 0.00 1.40
4334 14198 5.067805 GGCACTGAATTTAGGTGGGAATTAG 59.932 44.000 1.95 0.00 0.00 1.73
4335 14199 5.885912 GCACTGAATTTAGGTGGGAATTAGA 59.114 40.000 1.95 0.00 0.00 2.10
4336 14200 6.547510 GCACTGAATTTAGGTGGGAATTAGAT 59.452 38.462 1.95 0.00 0.00 1.98
4337 14201 7.469181 GCACTGAATTTAGGTGGGAATTAGATG 60.469 40.741 1.95 0.00 0.00 2.90
4338 14202 7.557719 CACTGAATTTAGGTGGGAATTAGATGT 59.442 37.037 1.95 0.00 0.00 3.06
4339 14203 7.775561 ACTGAATTTAGGTGGGAATTAGATGTC 59.224 37.037 1.95 0.00 0.00 3.06
4340 14204 7.872138 TGAATTTAGGTGGGAATTAGATGTCT 58.128 34.615 0.00 0.00 0.00 3.41
4341 14205 7.993183 TGAATTTAGGTGGGAATTAGATGTCTC 59.007 37.037 0.00 0.00 0.00 3.36
4342 14206 6.884472 TTTAGGTGGGAATTAGATGTCTCA 57.116 37.500 0.00 0.00 0.00 3.27
4343 14207 7.451731 TTTAGGTGGGAATTAGATGTCTCAT 57.548 36.000 0.00 0.00 0.00 2.90
4344 14208 5.559148 AGGTGGGAATTAGATGTCTCATC 57.441 43.478 1.98 1.98 0.00 2.92
4345 14209 4.349342 AGGTGGGAATTAGATGTCTCATCC 59.651 45.833 6.18 0.00 0.00 3.51
4346 14210 4.505742 GGTGGGAATTAGATGTCTCATCCC 60.506 50.000 15.51 15.51 40.16 3.85
4347 14211 3.324846 TGGGAATTAGATGTCTCATCCCG 59.675 47.826 16.51 0.00 41.45 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
733 768 2.099141 TTCCTCAGATCCAAACGCAG 57.901 50.000 0.00 0.00 0.00 5.18
1088 1123 2.821378 TGACAGCCAACATCTTGAATGG 59.179 45.455 0.00 0.00 33.32 3.16
1089 1124 3.504906 ACTGACAGCCAACATCTTGAATG 59.495 43.478 1.25 0.00 0.00 2.67
1090 1125 3.759581 ACTGACAGCCAACATCTTGAAT 58.240 40.909 1.25 0.00 0.00 2.57
1162 7790 2.223112 GCAGCAAGTCATGGATTACGTG 60.223 50.000 0.00 0.00 37.44 4.49
1596 8231 3.013921 GGTCAACTTCACAAAGTCACCA 58.986 45.455 11.68 0.00 45.07 4.17
2154 9149 8.623903 TCTAACATCTTGCAATTGATAATCACC 58.376 33.333 10.34 0.00 0.00 4.02
2296 9291 4.338879 CAAAAGAGACCAGAATCCCACAT 58.661 43.478 0.00 0.00 0.00 3.21
3247 11460 2.611722 GCACGGCACCCAAATAAAACAT 60.612 45.455 0.00 0.00 0.00 2.71
3248 11461 1.269831 GCACGGCACCCAAATAAAACA 60.270 47.619 0.00 0.00 0.00 2.83
3249 11462 1.000394 AGCACGGCACCCAAATAAAAC 60.000 47.619 0.00 0.00 0.00 2.43
3250 11463 1.333177 AGCACGGCACCCAAATAAAA 58.667 45.000 0.00 0.00 0.00 1.52
3251 11464 1.333177 AAGCACGGCACCCAAATAAA 58.667 45.000 0.00 0.00 0.00 1.40
3254 11467 1.555967 ATAAAGCACGGCACCCAAAT 58.444 45.000 0.00 0.00 0.00 2.32
3256 11469 1.000283 CAAATAAAGCACGGCACCCAA 60.000 47.619 0.00 0.00 0.00 4.12
3292 11789 7.257722 TGAAGAAGAAAACATGGTCAGAAAAC 58.742 34.615 0.00 0.00 0.00 2.43
3778 12347 3.375299 GGTAAATCACACACAGGCAGATC 59.625 47.826 0.00 0.00 0.00 2.75
3779 12348 3.347216 GGTAAATCACACACAGGCAGAT 58.653 45.455 0.00 0.00 0.00 2.90
3780 12349 2.552155 GGGTAAATCACACACAGGCAGA 60.552 50.000 0.00 0.00 0.00 4.26
3781 12350 1.812571 GGGTAAATCACACACAGGCAG 59.187 52.381 0.00 0.00 0.00 4.85
3789 12358 3.506067 CAGAACAAGGGGGTAAATCACAC 59.494 47.826 0.00 0.00 0.00 3.82
3820 12390 3.951775 ACCACAGACAGAGCTAAGAAG 57.048 47.619 0.00 0.00 0.00 2.85
3872 12443 3.272285 TGGGAGAAACAGAGAGATAGGGA 59.728 47.826 0.00 0.00 0.00 4.20
4018 12773 6.072673 GGTTGTAATCTGAAACTACCACAAGG 60.073 42.308 16.48 0.00 40.06 3.61
4036 12791 2.630580 GGCCCATTCAACTTGGTTGTAA 59.369 45.455 9.71 4.68 43.23 2.41
4052 12807 2.451493 TCCTTCCCACAAGGCCCA 60.451 61.111 0.00 0.00 37.34 5.36
4053 12808 2.035783 GTCCTTCCCACAAGGCCC 59.964 66.667 0.00 0.00 37.34 5.80
4056 12811 1.073763 TCATGTGTCCTTCCCACAAGG 59.926 52.381 0.00 0.00 45.20 3.61
4094 12853 1.746220 AGGCTGCTACTGTACTTCTCG 59.254 52.381 0.00 0.00 0.00 4.04
4109 12869 1.061131 CTCGCATCAAACGTTAGGCTG 59.939 52.381 0.00 0.06 0.00 4.85
4126 13480 1.065854 ACCCTTCAAGCTCCATTCTCG 60.066 52.381 0.00 0.00 0.00 4.04
4128 13482 3.846588 TCTAACCCTTCAAGCTCCATTCT 59.153 43.478 0.00 0.00 0.00 2.40
4140 13494 4.287552 TCTGGTCCTACATCTAACCCTTC 58.712 47.826 0.00 0.00 0.00 3.46
4146 13500 4.030913 CCCAGTTCTGGTCCTACATCTAA 58.969 47.826 16.33 0.00 0.00 2.10
4148 13502 2.472029 CCCAGTTCTGGTCCTACATCT 58.528 52.381 16.33 0.00 0.00 2.90
4189 14047 0.039074 CAGGATGTCGGAGGCGTATC 60.039 60.000 0.00 0.00 28.88 2.24
4190 14048 2.041976 CAGGATGTCGGAGGCGTAT 58.958 57.895 0.00 0.00 28.88 3.06
4191 14049 3.521605 CAGGATGTCGGAGGCGTA 58.478 61.111 0.00 0.00 28.88 4.42
4261 14125 1.694150 GCTGCCACTCCCATACTATCA 59.306 52.381 0.00 0.00 0.00 2.15
4262 14126 1.002544 GGCTGCCACTCCCATACTATC 59.997 57.143 15.17 0.00 0.00 2.08
4263 14127 1.059913 GGCTGCCACTCCCATACTAT 58.940 55.000 15.17 0.00 0.00 2.12
4264 14128 0.031111 AGGCTGCCACTCCCATACTA 60.031 55.000 22.65 0.00 0.00 1.82
4265 14129 1.307343 AGGCTGCCACTCCCATACT 60.307 57.895 22.65 0.00 0.00 2.12
4266 14130 1.147153 GAGGCTGCCACTCCCATAC 59.853 63.158 22.65 0.00 0.00 2.39
4267 14131 1.003442 AGAGGCTGCCACTCCCATA 59.997 57.895 22.65 0.00 35.58 2.74
4268 14132 2.285969 AGAGGCTGCCACTCCCAT 60.286 61.111 22.65 0.00 35.58 4.00
4269 14133 3.005539 GAGAGGCTGCCACTCCCA 61.006 66.667 28.94 0.00 35.66 4.37
4270 14134 2.373707 ATGAGAGGCTGCCACTCCC 61.374 63.158 33.43 17.79 39.85 4.30
4271 14135 1.153208 CATGAGAGGCTGCCACTCC 60.153 63.158 33.43 20.51 39.85 3.85
4272 14136 1.153208 CCATGAGAGGCTGCCACTC 60.153 63.158 31.30 31.30 40.74 3.51
4273 14137 1.614525 TCCATGAGAGGCTGCCACT 60.615 57.895 22.65 20.68 0.00 4.00
4274 14138 1.451028 GTCCATGAGAGGCTGCCAC 60.451 63.158 22.65 15.46 0.00 5.01
4275 14139 2.993008 GTCCATGAGAGGCTGCCA 59.007 61.111 22.65 0.00 0.00 4.92
4276 14140 2.202987 CGTCCATGAGAGGCTGCC 60.203 66.667 11.65 11.65 0.00 4.85
4277 14141 2.202987 CCGTCCATGAGAGGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
4278 14142 2.202987 GCCGTCCATGAGAGGCTG 60.203 66.667 15.06 0.00 45.67 4.85
4281 14145 1.450312 GTTGGCCGTCCATGAGAGG 60.450 63.158 0.00 0.00 43.05 3.69
4282 14146 1.450312 GGTTGGCCGTCCATGAGAG 60.450 63.158 10.62 0.00 43.05 3.20
4283 14147 1.773856 TTGGTTGGCCGTCCATGAGA 61.774 55.000 17.51 2.40 43.05 3.27
4284 14148 1.303236 TTGGTTGGCCGTCCATGAG 60.303 57.895 17.51 0.00 43.05 2.90
4285 14149 1.602323 GTTGGTTGGCCGTCCATGA 60.602 57.895 17.51 3.38 43.05 3.07
4286 14150 2.635443 GGTTGGTTGGCCGTCCATG 61.635 63.158 17.51 0.00 43.05 3.66
4287 14151 2.282887 GGTTGGTTGGCCGTCCAT 60.283 61.111 17.51 0.00 43.05 3.41
4288 14152 4.939368 CGGTTGGTTGGCCGTCCA 62.939 66.667 13.68 13.68 42.73 4.02
4293 14157 3.656045 CACGACGGTTGGTTGGCC 61.656 66.667 0.00 0.00 34.03 5.36
4294 14158 3.656045 CCACGACGGTTGGTTGGC 61.656 66.667 0.00 0.00 34.03 4.52
4295 14159 3.656045 GCCACGACGGTTGGTTGG 61.656 66.667 0.00 0.69 36.97 3.77
4296 14160 2.897846 TGCCACGACGGTTGGTTG 60.898 61.111 0.00 0.00 36.97 3.77
4297 14161 2.898343 GTGCCACGACGGTTGGTT 60.898 61.111 0.00 0.00 36.97 3.67
4298 14162 3.857038 AGTGCCACGACGGTTGGT 61.857 61.111 0.00 0.00 36.97 3.67
4299 14163 3.345808 CAGTGCCACGACGGTTGG 61.346 66.667 0.00 0.00 36.97 3.77
4300 14164 1.227999 ATTCAGTGCCACGACGGTTG 61.228 55.000 0.00 0.00 36.97 3.77
4301 14165 0.534203 AATTCAGTGCCACGACGGTT 60.534 50.000 0.00 0.00 36.97 4.44
4302 14166 0.534203 AAATTCAGTGCCACGACGGT 60.534 50.000 0.00 0.00 36.97 4.83
4303 14167 1.393539 CTAAATTCAGTGCCACGACGG 59.606 52.381 0.00 0.00 38.11 4.79
4304 14168 1.393539 CCTAAATTCAGTGCCACGACG 59.606 52.381 0.00 0.00 0.00 5.12
4305 14169 2.159627 CACCTAAATTCAGTGCCACGAC 59.840 50.000 0.00 0.00 0.00 4.34
4306 14170 2.422597 CACCTAAATTCAGTGCCACGA 58.577 47.619 0.00 0.00 0.00 4.35
4307 14171 1.468520 CCACCTAAATTCAGTGCCACG 59.531 52.381 0.00 0.00 0.00 4.94
4308 14172 1.818674 CCCACCTAAATTCAGTGCCAC 59.181 52.381 0.00 0.00 0.00 5.01
4309 14173 1.707989 TCCCACCTAAATTCAGTGCCA 59.292 47.619 0.00 0.00 0.00 4.92
4310 14174 2.507407 TCCCACCTAAATTCAGTGCC 57.493 50.000 0.00 0.00 0.00 5.01
4311 14175 5.885912 TCTAATTCCCACCTAAATTCAGTGC 59.114 40.000 0.00 0.00 0.00 4.40
4312 14176 7.557719 ACATCTAATTCCCACCTAAATTCAGTG 59.442 37.037 0.00 0.00 0.00 3.66
4313 14177 7.643123 ACATCTAATTCCCACCTAAATTCAGT 58.357 34.615 0.00 0.00 0.00 3.41
4314 14178 7.995488 AGACATCTAATTCCCACCTAAATTCAG 59.005 37.037 0.00 0.00 0.00 3.02
4315 14179 7.872138 AGACATCTAATTCCCACCTAAATTCA 58.128 34.615 0.00 0.00 0.00 2.57
4316 14180 7.993183 TGAGACATCTAATTCCCACCTAAATTC 59.007 37.037 0.00 0.00 0.00 2.17
4317 14181 7.872138 TGAGACATCTAATTCCCACCTAAATT 58.128 34.615 0.00 0.00 0.00 1.82
4318 14182 7.451731 TGAGACATCTAATTCCCACCTAAAT 57.548 36.000 0.00 0.00 0.00 1.40
4319 14183 6.884472 TGAGACATCTAATTCCCACCTAAA 57.116 37.500 0.00 0.00 0.00 1.85
4320 14184 6.043243 GGATGAGACATCTAATTCCCACCTAA 59.957 42.308 10.78 0.00 0.00 2.69
4321 14185 5.544176 GGATGAGACATCTAATTCCCACCTA 59.456 44.000 10.78 0.00 0.00 3.08
4322 14186 4.349342 GGATGAGACATCTAATTCCCACCT 59.651 45.833 10.78 0.00 0.00 4.00
4323 14187 4.505742 GGGATGAGACATCTAATTCCCACC 60.506 50.000 14.27 0.00 37.93 4.61
4324 14188 4.646572 GGGATGAGACATCTAATTCCCAC 58.353 47.826 14.27 0.00 37.93 4.61
4325 14189 3.324846 CGGGATGAGACATCTAATTCCCA 59.675 47.826 17.27 0.00 37.91 4.37
4326 14190 3.931578 CGGGATGAGACATCTAATTCCC 58.068 50.000 10.78 11.01 29.56 3.97


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

AutoCloner maintained by Alex Coulton.