Multiple sequence alignment - TraesCS6A01G314300

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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 TraesCS6A01G314300 chr6A 100.000 5511 0 0 1 5511 550751185 550745675 0.000000e+00 10178.0
1 TraesCS6A01G314300 chr6D 96.762 4416 93 7 982 5395 404234478 404230111 0.000000e+00 7317.0
2 TraesCS6A01G314300 chr6D 87.111 450 22 19 548 983 404234946 404234519 1.390000e-130 477.0
3 TraesCS6A01G314300 chr6D 95.833 48 2 0 5422 5469 404229931 404229884 1.650000e-10 78.7
4 TraesCS6A01G314300 chrUn 95.594 2542 66 12 2853 5393 78928063 78930559 0.000000e+00 4032.0
5 TraesCS6A01G314300 chrUn 96.429 1876 54 6 982 2851 78926094 78927962 0.000000e+00 3081.0
6 TraesCS6A01G314300 chrUn 96.250 160 6 0 638 797 78925600 78925759 4.230000e-66 263.0
7 TraesCS6A01G314300 chrUn 93.893 131 5 3 530 660 338079151 338079024 1.570000e-45 195.0
8 TraesCS6A01G314300 chr1A 76.297 3008 642 58 1073 4052 3503803 3500839 0.000000e+00 1539.0
9 TraesCS6A01G314300 chr1A 75.839 2980 636 70 1106 4052 3491715 3488787 0.000000e+00 1437.0
10 TraesCS6A01G314300 chr1B 75.940 3005 658 53 1073 4052 4095641 4098605 0.000000e+00 1483.0
11 TraesCS6A01G314300 chr1B 75.882 2977 657 53 1097 4052 4114619 4117555 0.000000e+00 1463.0
12 TraesCS6A01G314300 chr1B 75.158 3003 682 51 1073 4052 3964621 3967582 0.000000e+00 1354.0
13 TraesCS6A01G314300 chr1B 76.032 2132 470 37 1940 4052 4560726 4558617 0.000000e+00 1068.0
14 TraesCS6A01G314300 chr1B 74.333 2513 591 40 1565 4052 4824040 4821557 0.000000e+00 1018.0
15 TraesCS6A01G314300 chr1B 71.277 1692 434 38 1538 3203 4534296 4532631 8.660000e-103 385.0
16 TraesCS6A01G314300 chr1B 74.124 885 207 18 1126 2005 4762268 4761401 4.090000e-91 346.0
17 TraesCS6A01G314300 chr1D 75.891 3003 657 55 1073 4052 621077 618119 0.000000e+00 1472.0
18 TraesCS6A01G314300 chr1D 87.736 530 60 5 1 528 22272173 22271647 1.010000e-171 614.0
19 TraesCS6A01G314300 chr1D 87.037 540 60 9 1 535 229604651 229605185 7.900000e-168 601.0
20 TraesCS6A01G314300 chr4D 90.395 531 44 7 1 528 336251820 336252346 0.000000e+00 691.0
21 TraesCS6A01G314300 chr4D 88.324 531 55 7 1 528 487201419 487201945 1.010000e-176 630.0
22 TraesCS6A01G314300 chr5D 89.623 530 49 6 1 528 2801478 2802003 0.000000e+00 669.0
23 TraesCS6A01G314300 chr7D 89.205 528 49 8 11 534 575585076 575584553 0.000000e+00 652.0
24 TraesCS6A01G314300 chr7D 87.992 533 56 7 1 528 4255825 4255296 1.690000e-174 623.0
25 TraesCS6A01G314300 chr5A 88.390 534 56 6 1 532 566042535 566042006 6.020000e-179 638.0
26 TraesCS6A01G314300 chr3D 87.266 534 54 13 16 542 43736624 43736098 1.020000e-166 597.0
27 TraesCS6A01G314300 chr6B 91.429 70 5 1 5399 5468 606305877 606305809 1.630000e-15 95.3


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 TraesCS6A01G314300 chr6A 550745675 550751185 5510 True 10178.000000 10178 100.000000 1 5511 1 chr6A.!!$R1 5510
1 TraesCS6A01G314300 chr6D 404229884 404234946 5062 True 2624.233333 7317 93.235333 548 5469 3 chr6D.!!$R1 4921
2 TraesCS6A01G314300 chrUn 78925600 78930559 4959 False 2458.666667 4032 96.091000 638 5393 3 chrUn.!!$F1 4755
3 TraesCS6A01G314300 chr1A 3500839 3503803 2964 True 1539.000000 1539 76.297000 1073 4052 1 chr1A.!!$R2 2979
4 TraesCS6A01G314300 chr1A 3488787 3491715 2928 True 1437.000000 1437 75.839000 1106 4052 1 chr1A.!!$R1 2946
5 TraesCS6A01G314300 chr1B 4095641 4098605 2964 False 1483.000000 1483 75.940000 1073 4052 1 chr1B.!!$F2 2979
6 TraesCS6A01G314300 chr1B 4114619 4117555 2936 False 1463.000000 1463 75.882000 1097 4052 1 chr1B.!!$F3 2955
7 TraesCS6A01G314300 chr1B 3964621 3967582 2961 False 1354.000000 1354 75.158000 1073 4052 1 chr1B.!!$F1 2979
8 TraesCS6A01G314300 chr1B 4558617 4560726 2109 True 1068.000000 1068 76.032000 1940 4052 1 chr1B.!!$R2 2112
9 TraesCS6A01G314300 chr1B 4821557 4824040 2483 True 1018.000000 1018 74.333000 1565 4052 1 chr1B.!!$R4 2487
10 TraesCS6A01G314300 chr1B 4532631 4534296 1665 True 385.000000 385 71.277000 1538 3203 1 chr1B.!!$R1 1665
11 TraesCS6A01G314300 chr1B 4761401 4762268 867 True 346.000000 346 74.124000 1126 2005 1 chr1B.!!$R3 879
12 TraesCS6A01G314300 chr1D 618119 621077 2958 True 1472.000000 1472 75.891000 1073 4052 1 chr1D.!!$R1 2979
13 TraesCS6A01G314300 chr1D 22271647 22272173 526 True 614.000000 614 87.736000 1 528 1 chr1D.!!$R2 527
14 TraesCS6A01G314300 chr1D 229604651 229605185 534 False 601.000000 601 87.037000 1 535 1 chr1D.!!$F1 534
15 TraesCS6A01G314300 chr4D 336251820 336252346 526 False 691.000000 691 90.395000 1 528 1 chr4D.!!$F1 527
16 TraesCS6A01G314300 chr4D 487201419 487201945 526 False 630.000000 630 88.324000 1 528 1 chr4D.!!$F2 527
17 TraesCS6A01G314300 chr5D 2801478 2802003 525 False 669.000000 669 89.623000 1 528 1 chr5D.!!$F1 527
18 TraesCS6A01G314300 chr7D 575584553 575585076 523 True 652.000000 652 89.205000 11 534 1 chr7D.!!$R2 523
19 TraesCS6A01G314300 chr7D 4255296 4255825 529 True 623.000000 623 87.992000 1 528 1 chr7D.!!$R1 527
20 TraesCS6A01G314300 chr5A 566042006 566042535 529 True 638.000000 638 88.390000 1 532 1 chr5A.!!$R1 531
21 TraesCS6A01G314300 chr3D 43736098 43736624 526 True 597.000000 597 87.266000 16 542 1 chr3D.!!$R1 526

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
823 934 0.107800 CAGTCTGTCATCCTGCCCTG 60.108 60.000 0.00 0.0 0.00 4.45 F
995 1172 0.465705 CATACCCCAGCACACGAGAT 59.534 55.000 0.00 0.0 0.00 2.75 F
1040 1217 1.002868 CCTCAACACCCCTGCTCTG 60.003 63.158 0.00 0.0 0.00 3.35 F
2228 2412 0.243636 GGCAATTTGGTGAACCTCCG 59.756 55.000 0.37 0.0 36.82 4.63 F
2444 2628 3.755628 TACCGGCGGCAGTCTCAC 61.756 66.667 28.71 0.0 0.00 3.51 F
3861 4153 4.342092 ACTGCCCTTATAAATGATGTTGCC 59.658 41.667 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2374 1.896755 GCCAATTTCCTGTGGGATGGT 60.897 52.381 5.44 0.00 39.98 3.55 R
2228 2412 5.613358 ATTCTCGTCCAAGAACAATGTTC 57.387 39.130 17.67 17.67 38.06 3.18 R
2444 2628 8.671921 ACATATTCAGAGACATTACAAAAGCTG 58.328 33.333 0.00 0.00 0.00 4.24 R
4092 4384 4.885325 GGAACCATAAAAGCGGATAAAGGA 59.115 41.667 0.00 0.00 0.00 3.36 R
4342 4634 1.534729 GCCGTTGGTCCAAGATTTCT 58.465 50.000 3.96 0.00 0.00 2.52 R
5491 5937 0.042131 TCCGAGGTACCCATCAAGGT 59.958 55.000 8.74 0.00 44.37 3.50 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
100 101 3.068691 CTTCCGCCCTCCACTCGA 61.069 66.667 0.00 0.00 0.00 4.04
116 117 2.024868 CGACGTTTGTCATGCCCGA 61.025 57.895 0.00 0.00 45.80 5.14
215 216 0.806868 ATCACGTACTTCTTCGGCGA 59.193 50.000 4.99 4.99 0.00 5.54
273 275 1.202592 GCGGGAGGAAAGGAGAGAATC 60.203 57.143 0.00 0.00 0.00 2.52
279 281 4.285863 GAGGAAAGGAGAGAATCAGAGGA 58.714 47.826 0.00 0.00 37.82 3.71
284 286 5.419239 AAGGAGAGAATCAGAGGAAAGTG 57.581 43.478 0.00 0.00 37.82 3.16
285 287 4.682563 AGGAGAGAATCAGAGGAAAGTGA 58.317 43.478 0.00 0.00 37.82 3.41
290 292 0.915364 ATCAGAGGAAAGTGAGGGGC 59.085 55.000 0.00 0.00 0.00 5.80
311 313 3.045492 GGCGGAAAGAAACGGCGA 61.045 61.111 16.62 0.00 45.38 5.54
469 476 1.582610 GCGACTGGGCCGAATTTTGA 61.583 55.000 0.00 0.00 0.00 2.69
470 477 0.878416 CGACTGGGCCGAATTTTGAA 59.122 50.000 0.00 0.00 0.00 2.69
491 498 0.247775 GTCGACACGGCAAAAACGTT 60.248 50.000 11.55 0.00 43.58 3.99
528 538 3.094062 GCCACGGCTGGAGATGCTA 62.094 63.158 0.00 0.00 40.55 3.49
535 545 2.352225 CGGCTGGAGATGCTATCAGTAC 60.352 54.545 0.00 0.00 0.00 2.73
536 546 2.896685 GGCTGGAGATGCTATCAGTACT 59.103 50.000 0.00 0.00 0.00 2.73
539 549 4.321156 GCTGGAGATGCTATCAGTACTCTG 60.321 50.000 0.00 0.00 42.54 3.35
540 550 3.571828 TGGAGATGCTATCAGTACTCTGC 59.428 47.826 0.00 0.00 41.10 4.26
541 551 3.826157 GGAGATGCTATCAGTACTCTGCT 59.174 47.826 0.00 0.00 41.10 4.24
542 552 4.280677 GGAGATGCTATCAGTACTCTGCTT 59.719 45.833 0.00 0.00 41.10 3.91
544 554 6.015856 GGAGATGCTATCAGTACTCTGCTTTA 60.016 42.308 0.00 0.00 41.10 1.85
545 555 6.744112 AGATGCTATCAGTACTCTGCTTTAC 58.256 40.000 0.00 0.00 41.10 2.01
546 556 5.263968 TGCTATCAGTACTCTGCTTTACC 57.736 43.478 0.00 0.00 41.10 2.85
547 557 4.709886 TGCTATCAGTACTCTGCTTTACCA 59.290 41.667 0.00 0.00 41.10 3.25
548 558 5.186992 TGCTATCAGTACTCTGCTTTACCAA 59.813 40.000 0.00 0.00 41.10 3.67
549 559 6.127054 TGCTATCAGTACTCTGCTTTACCAAT 60.127 38.462 0.00 0.00 41.10 3.16
550 560 6.422400 GCTATCAGTACTCTGCTTTACCAATC 59.578 42.308 0.00 0.00 41.10 2.67
551 561 4.744570 TCAGTACTCTGCTTTACCAATCG 58.255 43.478 0.00 0.00 41.10 3.34
581 591 3.084039 GTGGGCTGAGACAAATCAATCA 58.916 45.455 0.00 0.00 0.00 2.57
597 607 5.181690 TCAATCACCTTTAGTTTGTGCAC 57.818 39.130 10.75 10.75 0.00 4.57
603 613 3.569701 ACCTTTAGTTTGTGCACCTCATG 59.430 43.478 15.69 0.00 0.00 3.07
640 650 7.834068 TTAAGCTGTTGATGTCAGAAGATAC 57.166 36.000 0.00 0.00 35.20 2.24
643 653 4.678044 GCTGTTGATGTCAGAAGATACGGA 60.678 45.833 0.00 0.00 35.20 4.69
644 654 4.998788 TGTTGATGTCAGAAGATACGGAG 58.001 43.478 0.00 0.00 0.00 4.63
679 689 7.468922 TTGTTCAGATTACAGAATATCGCTG 57.531 36.000 4.49 4.49 39.26 5.18
695 705 3.459378 CTGGCGATGATGCGTTGGC 62.459 63.158 0.00 0.00 40.52 4.52
782 792 1.144057 GGCCTGGTGTATGAGGACG 59.856 63.158 0.00 0.00 0.00 4.79
823 934 0.107800 CAGTCTGTCATCCTGCCCTG 60.108 60.000 0.00 0.00 0.00 4.45
875 987 2.549754 CGCTCAACAAGTCAAGAACCAT 59.450 45.455 0.00 0.00 0.00 3.55
917 1034 0.744874 CTGATGGCCCTGCAATGAAG 59.255 55.000 0.00 0.00 0.00 3.02
945 1062 1.941812 CAACGGACAACTGCACTCC 59.058 57.895 0.00 0.00 0.00 3.85
946 1063 0.813610 CAACGGACAACTGCACTCCA 60.814 55.000 0.00 0.00 0.00 3.86
955 1072 3.108521 CTGCACTCCAGTACGACAC 57.891 57.895 0.00 0.00 36.79 3.67
956 1073 0.598562 CTGCACTCCAGTACGACACT 59.401 55.000 0.00 0.00 38.32 3.55
995 1172 0.465705 CATACCCCAGCACACGAGAT 59.534 55.000 0.00 0.00 0.00 2.75
1040 1217 1.002868 CCTCAACACCCCTGCTCTG 60.003 63.158 0.00 0.00 0.00 3.35
1070 1253 1.293924 CTCGTCTTGCCATCATGTCC 58.706 55.000 0.00 0.00 0.00 4.02
1161 1344 2.350522 CTCCTCCACTGGAAATCAACG 58.649 52.381 0.00 0.00 35.43 4.10
1311 1494 1.228184 CATCTCCCTGCCAGATGCC 60.228 63.158 0.00 0.00 40.61 4.40
1389 1572 7.923344 ACATATATCGATCTAGGCAACAATAGC 59.077 37.037 0.00 0.00 41.41 2.97
1479 1662 1.227380 GCTCAGAGGCCACATACCG 60.227 63.158 5.01 0.00 0.00 4.02
1584 1767 4.537015 GCAACCTGACAGTGTTGATTTAC 58.463 43.478 27.23 13.74 43.50 2.01
1623 1806 1.264749 TGGTCTCAGGTCCCATTCCG 61.265 60.000 0.00 0.00 0.00 4.30
1885 2068 6.327279 TGTTAAATGAACTCTCTCTCGTCA 57.673 37.500 0.00 0.00 38.98 4.35
2191 2374 7.122650 CCCTTTTTAGAAATCAGATAACAGGCA 59.877 37.037 0.00 0.00 0.00 4.75
2228 2412 0.243636 GGCAATTTGGTGAACCTCCG 59.756 55.000 0.37 0.00 36.82 4.63
2444 2628 3.755628 TACCGGCGGCAGTCTCAC 61.756 66.667 28.71 0.00 0.00 3.51
2886 3169 6.486993 AGTTGAGAAATTTAGGACACCTTGAC 59.513 38.462 0.00 0.00 34.61 3.18
3861 4153 4.342092 ACTGCCCTTATAAATGATGTTGCC 59.658 41.667 0.00 0.00 0.00 4.52
3950 4242 7.701539 ACAACATCCTGCTTGATACAAATTA 57.298 32.000 0.00 0.00 0.00 1.40
4078 4370 6.547510 AGATATGCCTCCCTTTGACATAAAAC 59.452 38.462 0.00 0.00 0.00 2.43
4142 4434 7.859325 AGCTTCTTGTTTACACTTTCTTGTA 57.141 32.000 0.00 0.00 0.00 2.41
4143 4435 7.920738 AGCTTCTTGTTTACACTTTCTTGTAG 58.079 34.615 0.00 0.00 33.50 2.74
4144 4436 6.633234 GCTTCTTGTTTACACTTTCTTGTAGC 59.367 38.462 0.00 0.00 33.50 3.58
4145 4437 7.618502 TTCTTGTTTACACTTTCTTGTAGCA 57.381 32.000 0.00 0.00 33.50 3.49
4146 4438 7.801716 TCTTGTTTACACTTTCTTGTAGCAT 57.198 32.000 0.00 0.00 33.50 3.79
4147 4439 8.896320 TCTTGTTTACACTTTCTTGTAGCATA 57.104 30.769 0.00 0.00 33.50 3.14
4148 4440 9.332502 TCTTGTTTACACTTTCTTGTAGCATAA 57.667 29.630 0.00 0.00 33.50 1.90
4336 4628 6.435591 CCTCATCAACAGAGCCATATACTCTA 59.564 42.308 7.04 0.00 42.62 2.43
4342 4634 7.342026 TCAACAGAGCCATATACTCTAGTCAAA 59.658 37.037 7.04 0.00 42.62 2.69
4365 4657 0.112412 ATCTTGGACCAACGGCCTTT 59.888 50.000 1.69 0.00 0.00 3.11
4410 4702 9.971922 AGAGAAAAACATAGTTTTCCAAATCAG 57.028 29.630 8.16 0.00 44.93 2.90
4527 4819 8.060813 TTCAGTGTGAAGACAACATGTTGTAGA 61.061 37.037 37.21 21.29 41.44 2.59
4580 4872 3.858135 TGGTAGGGATGATTACCTCTCC 58.142 50.000 2.74 0.00 40.01 3.71
4670 4962 2.897271 TCTGAGGCCAGGCATAAAAA 57.103 45.000 15.19 0.00 40.76 1.94
4700 4992 7.592533 CAGGTTTATCTCCAATAAATGCAATCG 59.407 37.037 0.00 0.00 0.00 3.34
4706 4998 5.647658 TCTCCAATAAATGCAATCGACACTT 59.352 36.000 0.00 0.00 0.00 3.16
4776 5068 7.275920 AGAGGTAATATGCAAGTTCCTTACTG 58.724 38.462 0.00 0.00 37.12 2.74
4848 5140 4.202441 GACCCTTGTGCATTCACTATGAT 58.798 43.478 0.00 0.00 43.49 2.45
5145 5438 2.833794 TGGACTGACTTTAGCACACAC 58.166 47.619 0.00 0.00 0.00 3.82
5148 5441 3.625764 GGACTGACTTTAGCACACACAAA 59.374 43.478 0.00 0.00 0.00 2.83
5226 5519 2.139917 GGCGTACAATTGTCAGTGACA 58.860 47.619 22.06 22.06 41.09 3.58
5297 5590 5.087323 TCCTCTCAGTTATTCCAGTTCTGT 58.913 41.667 0.00 0.00 0.00 3.41
5301 5594 7.297936 TCTCAGTTATTCCAGTTCTGTGTAA 57.702 36.000 0.00 0.00 0.00 2.41
5399 5692 8.846423 ATTATTGTATCCCCAATTTAACACCA 57.154 30.769 0.00 0.00 36.48 4.17
5400 5693 5.986501 TTGTATCCCCAATTTAACACCAC 57.013 39.130 0.00 0.00 0.00 4.16
5401 5694 4.345854 TGTATCCCCAATTTAACACCACC 58.654 43.478 0.00 0.00 0.00 4.61
5402 5695 2.312424 TCCCCAATTTAACACCACCC 57.688 50.000 0.00 0.00 0.00 4.61
5403 5696 1.203199 TCCCCAATTTAACACCACCCC 60.203 52.381 0.00 0.00 0.00 4.95
5404 5697 1.203250 CCCCAATTTAACACCACCCCT 60.203 52.381 0.00 0.00 0.00 4.79
5405 5698 2.176045 CCCAATTTAACACCACCCCTC 58.824 52.381 0.00 0.00 0.00 4.30
5406 5699 2.225267 CCCAATTTAACACCACCCCTCT 60.225 50.000 0.00 0.00 0.00 3.69
5407 5700 3.089284 CCAATTTAACACCACCCCTCTC 58.911 50.000 0.00 0.00 0.00 3.20
5408 5701 3.089284 CAATTTAACACCACCCCTCTCC 58.911 50.000 0.00 0.00 0.00 3.71
5409 5702 1.822425 TTTAACACCACCCCTCTCCA 58.178 50.000 0.00 0.00 0.00 3.86
5410 5703 1.061546 TTAACACCACCCCTCTCCAC 58.938 55.000 0.00 0.00 0.00 4.02
5411 5704 0.838987 TAACACCACCCCTCTCCACC 60.839 60.000 0.00 0.00 0.00 4.61
5412 5705 3.330720 CACCACCCCTCTCCACCC 61.331 72.222 0.00 0.00 0.00 4.61
5413 5706 3.542602 ACCACCCCTCTCCACCCT 61.543 66.667 0.00 0.00 0.00 4.34
5414 5707 2.204151 CCACCCCTCTCCACCCTT 60.204 66.667 0.00 0.00 0.00 3.95
5415 5708 2.301738 CCACCCCTCTCCACCCTTC 61.302 68.421 0.00 0.00 0.00 3.46
5416 5709 1.229658 CACCCCTCTCCACCCTTCT 60.230 63.158 0.00 0.00 0.00 2.85
5417 5710 1.229658 ACCCCTCTCCACCCTTCTG 60.230 63.158 0.00 0.00 0.00 3.02
5418 5711 1.997874 CCCCTCTCCACCCTTCTGG 60.998 68.421 0.00 0.00 41.37 3.86
5439 5885 9.875691 TTCTGGTCGATATTTGATCCTATAATG 57.124 33.333 0.00 0.00 0.00 1.90
5475 5921 1.688772 CCTTGATGGGCAGAAGGATG 58.311 55.000 0.00 0.00 38.93 3.51
5476 5922 1.688772 CTTGATGGGCAGAAGGATGG 58.311 55.000 0.00 0.00 0.00 3.51
5477 5923 0.259647 TTGATGGGCAGAAGGATGGG 59.740 55.000 0.00 0.00 0.00 4.00
5478 5924 1.530183 GATGGGCAGAAGGATGGGC 60.530 63.158 0.00 0.00 0.00 5.36
5479 5925 2.288642 GATGGGCAGAAGGATGGGCA 62.289 60.000 0.00 0.00 0.00 5.36
5480 5926 2.123982 GGGCAGAAGGATGGGCAG 60.124 66.667 0.00 0.00 0.00 4.85
5481 5927 2.683465 GGGCAGAAGGATGGGCAGA 61.683 63.158 0.00 0.00 0.00 4.26
5482 5928 1.304282 GGCAGAAGGATGGGCAGAA 59.696 57.895 0.00 0.00 0.00 3.02
5483 5929 0.750911 GGCAGAAGGATGGGCAGAAG 60.751 60.000 0.00 0.00 0.00 2.85
5484 5930 0.750911 GCAGAAGGATGGGCAGAAGG 60.751 60.000 0.00 0.00 0.00 3.46
5485 5931 0.914644 CAGAAGGATGGGCAGAAGGA 59.085 55.000 0.00 0.00 0.00 3.36
5486 5932 1.493871 CAGAAGGATGGGCAGAAGGAT 59.506 52.381 0.00 0.00 0.00 3.24
5487 5933 1.493871 AGAAGGATGGGCAGAAGGATG 59.506 52.381 0.00 0.00 0.00 3.51
5488 5934 0.554792 AAGGATGGGCAGAAGGATGG 59.445 55.000 0.00 0.00 0.00 3.51
5489 5935 1.152368 GGATGGGCAGAAGGATGGG 59.848 63.158 0.00 0.00 0.00 4.00
5490 5936 1.649271 GGATGGGCAGAAGGATGGGT 61.649 60.000 0.00 0.00 0.00 4.51
5491 5937 1.140312 GATGGGCAGAAGGATGGGTA 58.860 55.000 0.00 0.00 0.00 3.69
5492 5938 0.846693 ATGGGCAGAAGGATGGGTAC 59.153 55.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 1.305219 CCATCGGGCATGACAAACGT 61.305 55.000 0.00 0.00 33.80 3.99
144 145 4.087892 GCCCAGCCGAAGCAGAGA 62.088 66.667 0.00 0.00 43.56 3.10
215 216 2.927856 TCCCAGTCACCGCCATGT 60.928 61.111 0.00 0.00 0.00 3.21
273 275 1.078848 CGCCCCTCACTTTCCTCTG 60.079 63.158 0.00 0.00 0.00 3.35
279 281 4.035102 GCCCTCGCCCCTCACTTT 62.035 66.667 0.00 0.00 0.00 2.66
290 292 2.388232 CCGTTTCTTTCCGCCCTCG 61.388 63.158 0.00 0.00 0.00 4.63
299 301 1.797025 CCTCTTCTCGCCGTTTCTTT 58.203 50.000 0.00 0.00 0.00 2.52
311 313 1.459450 GTGAGTCGAGAGCCTCTTCT 58.541 55.000 0.00 0.00 0.00 2.85
345 347 2.203294 ACAAGCGAAAAGGGGCGT 60.203 55.556 0.00 0.00 0.00 5.68
346 348 2.255252 CACAAGCGAAAAGGGGCG 59.745 61.111 0.00 0.00 0.00 6.13
347 352 2.049156 GCACAAGCGAAAAGGGGC 60.049 61.111 0.00 0.00 0.00 5.80
348 353 2.650778 GGCACAAGCGAAAAGGGG 59.349 61.111 0.00 0.00 43.41 4.79
469 476 0.247775 GTTTTTGCCGTGTCGACGTT 60.248 50.000 11.62 0.00 44.54 3.99
470 477 1.349282 GTTTTTGCCGTGTCGACGT 59.651 52.632 11.62 0.00 44.54 4.34
491 498 2.525592 CCAACAAGCCCTCCCCAA 59.474 61.111 0.00 0.00 0.00 4.12
513 523 0.678395 CTGATAGCATCTCCAGCCGT 59.322 55.000 0.00 0.00 0.00 5.68
528 538 5.105310 ACGATTGGTAAAGCAGAGTACTGAT 60.105 40.000 0.00 0.00 46.03 2.90
535 545 5.651530 TCTAAGACGATTGGTAAAGCAGAG 58.348 41.667 0.00 0.00 0.00 3.35
536 546 5.394224 CCTCTAAGACGATTGGTAAAGCAGA 60.394 44.000 0.00 0.00 0.00 4.26
539 549 4.567159 CACCTCTAAGACGATTGGTAAAGC 59.433 45.833 0.00 0.00 0.00 3.51
540 550 5.109903 CCACCTCTAAGACGATTGGTAAAG 58.890 45.833 0.00 0.00 0.00 1.85
541 551 4.081309 CCCACCTCTAAGACGATTGGTAAA 60.081 45.833 0.00 0.00 0.00 2.01
542 552 3.449737 CCCACCTCTAAGACGATTGGTAA 59.550 47.826 0.00 0.00 0.00 2.85
544 554 1.831736 CCCACCTCTAAGACGATTGGT 59.168 52.381 0.00 0.00 0.00 3.67
545 555 1.473434 GCCCACCTCTAAGACGATTGG 60.473 57.143 0.00 0.00 0.00 3.16
546 556 1.482593 AGCCCACCTCTAAGACGATTG 59.517 52.381 0.00 0.00 0.00 2.67
547 557 1.482593 CAGCCCACCTCTAAGACGATT 59.517 52.381 0.00 0.00 0.00 3.34
548 558 1.115467 CAGCCCACCTCTAAGACGAT 58.885 55.000 0.00 0.00 0.00 3.73
549 559 0.039180 TCAGCCCACCTCTAAGACGA 59.961 55.000 0.00 0.00 0.00 4.20
550 560 0.457851 CTCAGCCCACCTCTAAGACG 59.542 60.000 0.00 0.00 0.00 4.18
551 561 1.478916 GTCTCAGCCCACCTCTAAGAC 59.521 57.143 0.00 0.00 0.00 3.01
581 591 3.290948 TGAGGTGCACAAACTAAAGGT 57.709 42.857 20.43 0.00 0.00 3.50
603 613 5.412594 TCAACAGCTTAATCTGTCCAATGAC 59.587 40.000 12.12 0.00 45.77 3.06
640 650 8.873215 AATCTGAACAAATATGTACTACTCCG 57.127 34.615 0.00 0.00 39.40 4.63
679 689 4.256090 GGCCAACGCATCATCGCC 62.256 66.667 0.00 0.00 36.38 5.54
782 792 5.217393 TGATAGTGGCATTTATACGACGAC 58.783 41.667 0.00 0.00 0.00 4.34
798 808 3.715495 GCAGGATGACAGACTGATAGTG 58.285 50.000 10.08 0.17 39.69 2.74
823 934 1.080025 CCCGTCTCCCTCGTTTGAC 60.080 63.158 0.00 0.00 0.00 3.18
917 1034 2.435059 GTCCGTTGCTCTCAGGGC 60.435 66.667 0.00 0.00 0.00 5.19
945 1062 5.752892 ATATGTGGAGTAGTGTCGTACTG 57.247 43.478 5.54 0.00 40.65 2.74
946 1063 7.201767 GGTTAATATGTGGAGTAGTGTCGTACT 60.202 40.741 0.00 1.17 43.56 2.73
951 1068 5.454329 GGGGGTTAATATGTGGAGTAGTGTC 60.454 48.000 0.00 0.00 0.00 3.67
976 1112 0.465705 ATCTCGTGTGCTGGGGTATG 59.534 55.000 0.00 0.00 0.00 2.39
977 1113 0.753262 GATCTCGTGTGCTGGGGTAT 59.247 55.000 0.00 0.00 0.00 2.73
978 1114 1.327690 GGATCTCGTGTGCTGGGGTA 61.328 60.000 0.00 0.00 0.00 3.69
979 1115 2.660064 GGATCTCGTGTGCTGGGGT 61.660 63.158 0.00 0.00 0.00 4.95
995 1172 2.690786 GCATTTTGCTTTGCATCTGGA 58.309 42.857 0.00 0.00 40.96 3.86
1040 1217 1.003233 AAGACGAGGAGGCAAAGGC 60.003 57.895 0.00 0.00 40.13 4.35
1070 1253 1.630244 CGCTCGTTGCAAGAGAAGGG 61.630 60.000 22.30 12.53 43.06 3.95
1101 1284 1.486310 AGTGATATGCCACCATGACGT 59.514 47.619 0.00 0.00 37.76 4.34
1161 1344 4.410743 GCTGCTGGGTTTGCGAGC 62.411 66.667 0.00 0.00 0.00 5.03
1219 1402 3.357079 CGTCCAGTTGCACAGGCC 61.357 66.667 0.00 0.00 40.13 5.19
1223 1406 2.463589 GATCCCCGTCCAGTTGCACA 62.464 60.000 0.00 0.00 0.00 4.57
1283 1466 2.187946 GGGAGATGCTGGTCACGG 59.812 66.667 0.00 0.00 0.00 4.94
1311 1494 2.420568 AAGCTTGCCATGGATGCCG 61.421 57.895 18.40 0.00 0.00 5.69
1479 1662 2.202623 AGTTCGCCGATCTCGTGC 60.203 61.111 0.00 1.53 37.74 5.34
1584 1767 3.195396 CCATGGTTTGGTGGATAACAAGG 59.805 47.826 2.57 0.00 40.99 3.61
1623 1806 3.057456 TGACAAGCCTCTCTAACTCGTTC 60.057 47.826 0.00 0.00 0.00 3.95
1787 1970 2.298163 AGTTGAAGGAATTGCAGCTTGG 59.702 45.455 0.00 0.00 0.00 3.61
1885 2068 6.466812 GGATGGAACCTGTGATTTGATTTTT 58.533 36.000 0.00 0.00 0.00 1.94
2191 2374 1.896755 GCCAATTTCCTGTGGGATGGT 60.897 52.381 5.44 0.00 39.98 3.55
2228 2412 5.613358 ATTCTCGTCCAAGAACAATGTTC 57.387 39.130 17.67 17.67 38.06 3.18
2444 2628 8.671921 ACATATTCAGAGACATTACAAAAGCTG 58.328 33.333 0.00 0.00 0.00 4.24
3882 4174 8.861086 TGAATTATAGGAGGACTACAGTCATTC 58.139 37.037 11.31 3.01 46.47 2.67
3950 4242 7.349598 ACCAAAATCTGAGACATAAGCCTTAT 58.650 34.615 0.00 0.00 0.00 1.73
4078 4370 8.527810 AGCGGATAAAGGAAGAGATAGAAATAG 58.472 37.037 0.00 0.00 0.00 1.73
4092 4384 4.885325 GGAACCATAAAAGCGGATAAAGGA 59.115 41.667 0.00 0.00 0.00 3.36
4158 4450 7.118971 GGATCAGCATTAGAAGTCAATGGATAC 59.881 40.741 0.00 0.00 34.58 2.24
4159 4451 7.016957 AGGATCAGCATTAGAAGTCAATGGATA 59.983 37.037 0.00 0.00 34.58 2.59
4160 4452 6.002704 GGATCAGCATTAGAAGTCAATGGAT 58.997 40.000 0.00 0.00 34.58 3.41
4161 4453 5.131642 AGGATCAGCATTAGAAGTCAATGGA 59.868 40.000 0.00 0.00 34.58 3.41
4336 4628 4.275936 CGTTGGTCCAAGATTTCTTTGACT 59.724 41.667 18.52 0.00 43.85 3.41
4342 4634 1.534729 GCCGTTGGTCCAAGATTTCT 58.465 50.000 3.96 0.00 0.00 2.52
4365 4657 6.109156 TCTCTTCTATTGTTGTTGGTGCTA 57.891 37.500 0.00 0.00 0.00 3.49
4527 4819 5.877012 GCATCCCATAGTTCATCGAATGTAT 59.123 40.000 0.00 0.00 0.00 2.29
4580 4872 8.888332 TGTATTGCTATTCATTACAACAAACG 57.112 30.769 0.00 0.00 38.10 3.60
4670 4962 7.147689 TGCATTTATTGGAGATAAACCTGCATT 60.148 33.333 12.29 0.00 35.92 3.56
4700 4992 8.487176 CAATGGTTTAAAAATGCACTAAGTGTC 58.513 33.333 0.00 0.00 35.75 3.67
4766 5058 4.879545 TCAACCACTTGTTCAGTAAGGAAC 59.120 41.667 0.00 0.00 45.75 3.62
4776 5068 6.612306 GTGGAAGATATTCAACCACTTGTTC 58.388 40.000 0.00 0.00 44.91 3.18
4848 5140 2.806818 TCGGCTGCGTTATACAACAAAA 59.193 40.909 0.00 0.00 34.05 2.44
4860 5152 0.527817 GTAAGCTACATCGGCTGCGT 60.528 55.000 0.00 0.00 40.19 5.24
5104 5397 5.104859 TCCATTTTGTTGCCATGCTAATCAT 60.105 36.000 0.00 0.00 35.31 2.45
5133 5426 7.538575 AGCCTATATTTTTGTGTGTGCTAAAG 58.461 34.615 0.00 0.00 0.00 1.85
5199 5492 3.729966 TGACAATTGTACGCCTGTGTTA 58.270 40.909 11.95 0.00 0.00 2.41
5216 5509 4.541973 ACAGATAGCAATGTCACTGACA 57.458 40.909 14.26 14.26 46.90 3.58
5250 5543 1.771255 ACAAGCTAGCTAGGGGAATGG 59.229 52.381 19.70 2.11 0.00 3.16
5314 5607 8.732746 AGTACACAAAGAGATAACAAAACTGT 57.267 30.769 0.00 0.00 0.00 3.55
5379 5672 4.345854 GGTGGTGTTAAATTGGGGATACA 58.654 43.478 0.00 0.00 39.74 2.29
5395 5688 3.330720 GGGTGGAGAGGGGTGGTG 61.331 72.222 0.00 0.00 0.00 4.17
5397 5690 2.204151 AAGGGTGGAGAGGGGTGG 60.204 66.667 0.00 0.00 0.00 4.61
5398 5691 1.229658 AGAAGGGTGGAGAGGGGTG 60.230 63.158 0.00 0.00 0.00 4.61
5399 5692 1.229658 CAGAAGGGTGGAGAGGGGT 60.230 63.158 0.00 0.00 0.00 4.95
5400 5693 1.997874 CCAGAAGGGTGGAGAGGGG 60.998 68.421 0.00 0.00 40.44 4.79
5401 5694 3.732938 CCAGAAGGGTGGAGAGGG 58.267 66.667 0.00 0.00 40.44 4.30
5410 5703 4.040952 AGGATCAAATATCGACCAGAAGGG 59.959 45.833 0.00 0.00 44.81 3.95
5411 5704 5.220710 AGGATCAAATATCGACCAGAAGG 57.779 43.478 0.00 0.00 42.21 3.46
5413 5706 9.875691 CATTATAGGATCAAATATCGACCAGAA 57.124 33.333 0.00 0.00 0.00 3.02
5414 5707 9.255029 TCATTATAGGATCAAATATCGACCAGA 57.745 33.333 0.00 0.00 0.00 3.86
5415 5708 9.875691 TTCATTATAGGATCAAATATCGACCAG 57.124 33.333 0.00 0.00 0.00 4.00
5416 5709 9.875691 CTTCATTATAGGATCAAATATCGACCA 57.124 33.333 0.00 0.00 0.00 4.02
5438 5884 2.057922 AGGCAAACTTCCTCCTCTTCA 58.942 47.619 0.00 0.00 0.00 3.02
5439 5885 2.816672 CAAGGCAAACTTCCTCCTCTTC 59.183 50.000 0.00 0.00 37.29 2.87
5469 5915 0.554792 CCATCCTTCTGCCCATCCTT 59.445 55.000 0.00 0.00 0.00 3.36
5470 5916 1.358830 CCCATCCTTCTGCCCATCCT 61.359 60.000 0.00 0.00 0.00 3.24
5471 5917 1.152368 CCCATCCTTCTGCCCATCC 59.848 63.158 0.00 0.00 0.00 3.51
5472 5918 1.140312 TACCCATCCTTCTGCCCATC 58.860 55.000 0.00 0.00 0.00 3.51
5473 5919 0.846693 GTACCCATCCTTCTGCCCAT 59.153 55.000 0.00 0.00 0.00 4.00
5474 5920 1.279025 GGTACCCATCCTTCTGCCCA 61.279 60.000 0.00 0.00 0.00 5.36
5475 5921 0.988678 AGGTACCCATCCTTCTGCCC 60.989 60.000 8.74 0.00 30.18 5.36
5476 5922 0.919710 AAGGTACCCATCCTTCTGCC 59.080 55.000 8.74 0.00 40.80 4.85
5477 5923 1.559682 TCAAGGTACCCATCCTTCTGC 59.440 52.381 8.74 0.00 42.57 4.26
5478 5924 3.434167 CCATCAAGGTACCCATCCTTCTG 60.434 52.174 8.74 0.00 42.57 3.02
5479 5925 2.780010 CCATCAAGGTACCCATCCTTCT 59.220 50.000 8.74 0.00 42.57 2.85
5480 5926 2.158608 CCCATCAAGGTACCCATCCTTC 60.159 54.545 8.74 0.00 42.57 3.46
5481 5927 1.852965 CCCATCAAGGTACCCATCCTT 59.147 52.381 8.74 0.00 44.93 3.36
5482 5928 1.275002 ACCCATCAAGGTACCCATCCT 60.275 52.381 8.74 0.00 38.79 3.24
5483 5929 1.222567 ACCCATCAAGGTACCCATCC 58.777 55.000 8.74 0.00 38.79 3.51
5490 5936 1.288633 TCCGAGGTACCCATCAAGGTA 59.711 52.381 8.74 0.00 41.58 3.08
5491 5937 0.042131 TCCGAGGTACCCATCAAGGT 59.958 55.000 8.74 0.00 44.37 3.50
5492 5938 2.910579 TCCGAGGTACCCATCAAGG 58.089 57.895 8.74 3.50 37.03 3.61


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

AutoCloner maintained by Alex Coulton.