Multiple sequence alignment - TraesCS3A01G196000

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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 TraesCS3A01G196000 chr3A 100.000 5872 0 0 1 5872 293069180 293063309 0.000000e+00 10844.0
1 TraesCS3A01G196000 chr3A 99.084 4150 33 2 1452 5600 356336807 356332662 0.000000e+00 7448.0
2 TraesCS3A01G196000 chr3A 98.963 4146 36 4 1454 5596 315816687 315820828 0.000000e+00 7411.0
3 TraesCS3A01G196000 chr3A 100.000 3249 0 0 6155 9403 293063026 293059778 0.000000e+00 6000.0
4 TraesCS3A01G196000 chr4B 98.746 4146 43 4 1454 5596 492520643 492516504 0.000000e+00 7360.0
5 TraesCS3A01G196000 chr3B 98.578 4149 51 6 1451 5596 692979821 692983964 0.000000e+00 7328.0
6 TraesCS3A01G196000 chr3B 98.552 4145 51 4 1454 5595 692989980 692994118 0.000000e+00 7313.0
7 TraesCS3A01G196000 chr3B 94.369 2131 100 10 6697 8824 324259139 324257026 0.000000e+00 3253.0
8 TraesCS3A01G196000 chr3B 89.051 822 42 25 60 837 324261748 324260931 0.000000e+00 976.0
9 TraesCS3A01G196000 chr3B 93.681 633 34 3 824 1450 324260631 324259999 0.000000e+00 942.0
10 TraesCS3A01G196000 chr3B 91.623 573 48 0 8826 9398 324256663 324256091 0.000000e+00 793.0
11 TraesCS3A01G196000 chr3B 92.857 406 28 1 6191 6595 324259757 324259352 1.050000e-163 588.0
12 TraesCS3A01G196000 chr3B 98.165 218 4 0 5608 5825 324259999 324259782 1.920000e-101 381.0
13 TraesCS3A01G196000 chr3B 100.000 30 0 0 8677 8706 775479200 775479229 1.000000e-03 56.5
14 TraesCS3A01G196000 chr4A 98.577 4146 49 6 1454 5596 396908648 396904510 0.000000e+00 7321.0
15 TraesCS3A01G196000 chr4A 98.408 4146 57 6 1454 5596 382961559 382957420 0.000000e+00 7282.0
16 TraesCS3A01G196000 chr2A 98.577 4145 45 7 1453 5596 754885323 754889454 0.000000e+00 7315.0
17 TraesCS3A01G196000 chr2B 98.456 4146 49 9 1456 5595 94858436 94862572 0.000000e+00 7287.0
18 TraesCS3A01G196000 chr3D 94.064 2645 143 11 6191 8825 219239400 219236760 0.000000e+00 4002.0
19 TraesCS3A01G196000 chr3D 91.241 1450 70 17 60 1454 219241120 219239673 0.000000e+00 1921.0
20 TraesCS3A01G196000 chr3D 94.241 573 33 0 8826 9398 219236394 219235822 0.000000e+00 876.0
21 TraesCS3A01G196000 chr3D 84.461 547 60 11 8862 9398 408334132 408333601 5.030000e-142 516.0
22 TraesCS3A01G196000 chr3D 99.251 267 2 0 5596 5862 219239678 219239412 5.110000e-132 483.0
23 TraesCS3A01G196000 chr7A 97.059 34 1 0 8672 8705 691410574 691410541 3.670000e-04 58.4
24 TraesCS3A01G196000 chr6B 100.000 30 0 0 8677 8706 658534595 658534624 1.000000e-03 56.5
25 TraesCS3A01G196000 chr6A 96.970 33 1 0 8669 8701 86386313 86386345 1.000000e-03 56.5


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 TraesCS3A01G196000 chr3A 293059778 293069180 9402 True 8422.0 10844 100.00000 1 9403 2 chr3A.!!$R2 9402
1 TraesCS3A01G196000 chr3A 356332662 356336807 4145 True 7448.0 7448 99.08400 1452 5600 1 chr3A.!!$R1 4148
2 TraesCS3A01G196000 chr3A 315816687 315820828 4141 False 7411.0 7411 98.96300 1454 5596 1 chr3A.!!$F1 4142
3 TraesCS3A01G196000 chr4B 492516504 492520643 4139 True 7360.0 7360 98.74600 1454 5596 1 chr4B.!!$R1 4142
4 TraesCS3A01G196000 chr3B 692979821 692983964 4143 False 7328.0 7328 98.57800 1451 5596 1 chr3B.!!$F1 4145
5 TraesCS3A01G196000 chr3B 692989980 692994118 4138 False 7313.0 7313 98.55200 1454 5595 1 chr3B.!!$F2 4141
6 TraesCS3A01G196000 chr3B 324256091 324261748 5657 True 1155.5 3253 93.29100 60 9398 6 chr3B.!!$R1 9338
7 TraesCS3A01G196000 chr4A 396904510 396908648 4138 True 7321.0 7321 98.57700 1454 5596 1 chr4A.!!$R2 4142
8 TraesCS3A01G196000 chr4A 382957420 382961559 4139 True 7282.0 7282 98.40800 1454 5596 1 chr4A.!!$R1 4142
9 TraesCS3A01G196000 chr2A 754885323 754889454 4131 False 7315.0 7315 98.57700 1453 5596 1 chr2A.!!$F1 4143
10 TraesCS3A01G196000 chr2B 94858436 94862572 4136 False 7287.0 7287 98.45600 1456 5595 1 chr2B.!!$F1 4139
11 TraesCS3A01G196000 chr3D 219235822 219241120 5298 True 1820.5 4002 94.69925 60 9398 4 chr3D.!!$R2 9338
12 TraesCS3A01G196000 chr3D 408333601 408334132 531 True 516.0 516 84.46100 8862 9398 1 chr3D.!!$R1 536

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
65 66 0.808060 TCGTGCGCTGACAGAAAACA 60.808 50.000 9.73 0.0 0.00 2.83 F
1223 1583 1.135257 CACAGCTACTCCTTCCGTCTG 60.135 57.143 0.00 0.0 0.00 3.51 F
1449 1815 1.061131 CGCAACTCGCAATTAGTCTGG 59.939 52.381 0.00 0.0 42.60 3.86 F
2160 2537 0.106719 CTCCTCTCCCTCGCTCTCTT 60.107 60.000 0.00 0.0 0.00 2.85 F
3689 4070 3.935203 CTGTCATTGCCACAGTAACTAGG 59.065 47.826 0.00 0.0 37.15 3.02 F
4212 4593 3.147595 CGGACTCCCTGCGGATGA 61.148 66.667 0.00 0.0 37.60 2.92 F
6183 6567 2.228103 ACACACTCTCGTGCTTATTCGA 59.772 45.455 0.00 0.0 45.10 3.71 F
7069 7572 0.249784 TGCGTGCAACATTGGCAATT 60.250 45.000 10.65 0.0 43.91 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1628 2.104963 GCTGGACCGAATTAATCCCTCT 59.895 50.000 0.00 0.00 0.00 3.69 R
2160 2537 2.646719 CGTTCGGACACGGGAGAA 59.353 61.111 0.00 0.00 41.39 2.87 R
2860 3239 3.991051 ACGCGTCAGTGACCCTGG 61.991 66.667 17.57 4.68 41.83 4.45 R
3689 4070 2.504367 ACACATGCTAGTGGGTTTCAC 58.496 47.619 12.54 0.00 46.39 3.18 R
4731 5115 0.321298 GAAGGGGTTGCAGCGTCTTA 60.321 55.000 6.92 0.00 0.00 2.10 R
6198 6582 5.338614 CGAGGACGTTTCAGTGTTTATTT 57.661 39.130 0.00 0.00 34.56 1.40 R
8102 8606 0.107268 AAAGTTAACAGGGGTCGCGT 59.893 50.000 5.77 0.00 0.00 6.01 R
8978 9874 0.036105 AATCAGTGCCTCGACATGCA 60.036 50.000 0.00 0.00 34.54 3.96 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
27 28 4.387343 CATGGCAGCCCCCTTGGT 62.387 66.667 9.64 0.00 36.04 3.67
28 29 4.066139 ATGGCAGCCCCCTTGGTC 62.066 66.667 9.64 0.00 36.04 4.02
32 33 4.722700 CAGCCCCCTTGGTCGTGG 62.723 72.222 0.00 0.00 36.04 4.94
34 35 4.717313 GCCCCCTTGGTCGTGGTC 62.717 72.222 0.00 0.00 36.04 4.02
35 36 4.388499 CCCCCTTGGTCGTGGTCG 62.388 72.222 0.00 0.00 38.55 4.79
36 37 3.622826 CCCCTTGGTCGTGGTCGT 61.623 66.667 0.00 0.00 38.33 4.34
37 38 2.048503 CCCTTGGTCGTGGTCGTC 60.049 66.667 0.00 0.00 38.33 4.20
38 39 2.732016 CCTTGGTCGTGGTCGTCA 59.268 61.111 0.00 0.00 38.33 4.35
39 40 1.068417 CCTTGGTCGTGGTCGTCAA 59.932 57.895 0.00 0.00 38.33 3.18
40 41 0.944311 CCTTGGTCGTGGTCGTCAAG 60.944 60.000 13.93 13.93 42.36 3.02
41 42 0.944311 CTTGGTCGTGGTCGTCAAGG 60.944 60.000 13.46 0.00 40.93 3.61
42 43 2.737376 GGTCGTGGTCGTCAAGGC 60.737 66.667 0.00 0.00 38.33 4.35
43 44 2.028484 GTCGTGGTCGTCAAGGCA 59.972 61.111 0.00 0.00 38.33 4.75
44 45 2.022129 GTCGTGGTCGTCAAGGCAG 61.022 63.158 0.00 0.00 38.33 4.85
45 46 2.738521 CGTGGTCGTCAAGGCAGG 60.739 66.667 0.00 0.00 0.00 4.85
46 47 2.426023 GTGGTCGTCAAGGCAGGT 59.574 61.111 0.00 0.00 0.00 4.00
47 48 1.668151 GTGGTCGTCAAGGCAGGTC 60.668 63.158 0.00 0.00 0.00 3.85
48 49 2.432628 GGTCGTCAAGGCAGGTCG 60.433 66.667 0.00 0.00 0.00 4.79
49 50 2.338984 GTCGTCAAGGCAGGTCGT 59.661 61.111 0.00 0.00 0.00 4.34
50 51 2.022129 GTCGTCAAGGCAGGTCGTG 61.022 63.158 0.00 0.00 0.00 4.35
65 66 0.808060 TCGTGCGCTGACAGAAAACA 60.808 50.000 9.73 0.00 0.00 2.83
73 74 3.291585 GCTGACAGAAAACATGAACACG 58.708 45.455 6.65 0.00 0.00 4.49
223 240 9.635404 ATTATTATTTTGTTTAGGATGGACGGA 57.365 29.630 0.00 0.00 0.00 4.69
225 242 3.773418 TTTGTTTAGGATGGACGGACA 57.227 42.857 0.00 0.00 0.00 4.02
335 377 3.431922 AACAGTTTCAGTTCGTCTCGA 57.568 42.857 0.00 0.00 0.00 4.04
512 555 9.634163 GGAAAAGAACGGACAACAAAATATATT 57.366 29.630 0.00 0.00 0.00 1.28
591 634 4.558178 TCGGTCGTTAGAGTGCAAAATTA 58.442 39.130 0.00 0.00 0.00 1.40
641 684 9.066892 ACAAATTTAACTGCAGAGTCAAGAATA 57.933 29.630 23.35 0.00 0.00 1.75
644 687 7.658179 TTTAACTGCAGAGTCAAGAATACAG 57.342 36.000 23.35 0.00 0.00 2.74
680 723 4.608774 ACGACCCTCCCCGTCACA 62.609 66.667 0.00 0.00 33.23 3.58
731 774 2.421424 GTGTCTGCTTGCCTCCATTAAG 59.579 50.000 0.00 0.00 0.00 1.85
748 793 1.442769 AAGTGTATGCCTTGTCGCTG 58.557 50.000 0.00 0.00 0.00 5.18
853 1211 9.472361 CTCTCTCTCTTCGCTACCTATATATAC 57.528 40.741 0.00 0.00 0.00 1.47
963 1323 2.917713 TTGAGAGAGAAGAGGAGGCT 57.082 50.000 0.00 0.00 0.00 4.58
1223 1583 1.135257 CACAGCTACTCCTTCCGTCTG 60.135 57.143 0.00 0.00 0.00 3.51
1235 1595 8.707796 ACTCCTTCCGTCTGATAATATAAGAA 57.292 34.615 0.00 0.00 0.00 2.52
1300 1662 1.407936 GTCCAGCTGCTGAGGAGATA 58.592 55.000 30.10 4.33 32.44 1.98
1326 1688 9.458727 AATCTATGAATGTGTTTCTCTTGTCAT 57.541 29.630 0.00 0.00 35.23 3.06
1353 1715 6.204882 ACCAAGAGCTTGTTTACATGAACTAC 59.795 38.462 0.00 0.00 38.85 2.73
1354 1716 6.204688 CCAAGAGCTTGTTTACATGAACTACA 59.795 38.462 0.00 0.00 38.85 2.74
1362 1726 9.599322 CTTGTTTACATGAACTACATTTCTGTC 57.401 33.333 0.00 0.00 37.07 3.51
1449 1815 1.061131 CGCAACTCGCAATTAGTCTGG 59.939 52.381 0.00 0.00 42.60 3.86
1450 1816 2.346803 GCAACTCGCAATTAGTCTGGA 58.653 47.619 0.00 0.00 41.79 3.86
1524 1890 7.503566 ACTCTTTCATCAGAAACTTGAAATGGA 59.496 33.333 0.00 0.00 38.76 3.41
2160 2537 0.106719 CTCCTCTCCCTCGCTCTCTT 60.107 60.000 0.00 0.00 0.00 2.85
3689 4070 3.935203 CTGTCATTGCCACAGTAACTAGG 59.065 47.826 0.00 0.00 37.15 3.02
4212 4593 3.147595 CGGACTCCCTGCGGATGA 61.148 66.667 0.00 0.00 37.60 2.92
5000 5384 9.871238 CTCTGAGCCTTAAATAAAGTACTTGTA 57.129 33.333 9.34 4.60 32.89 2.41
5029 5413 4.314961 AGTCATGTTGTGATGCTTCGTTA 58.685 39.130 0.00 0.00 39.48 3.18
5847 6231 4.157656 TCCTTCAAACAAACAACAGACAGG 59.842 41.667 0.00 0.00 0.00 4.00
6175 6559 3.511699 TGAATGATACACACTCTCGTGC 58.488 45.455 0.00 0.00 45.10 5.34
6176 6560 3.193479 TGAATGATACACACTCTCGTGCT 59.807 43.478 0.00 0.00 45.10 4.40
6177 6561 3.876274 ATGATACACACTCTCGTGCTT 57.124 42.857 0.00 0.00 45.10 3.91
6178 6562 4.983671 ATGATACACACTCTCGTGCTTA 57.016 40.909 0.00 0.00 45.10 3.09
6179 6563 4.983671 TGATACACACTCTCGTGCTTAT 57.016 40.909 0.00 0.00 45.10 1.73
6180 6564 5.324784 TGATACACACTCTCGTGCTTATT 57.675 39.130 0.00 0.00 45.10 1.40
6181 6565 5.340803 TGATACACACTCTCGTGCTTATTC 58.659 41.667 0.00 0.00 45.10 1.75
6182 6566 2.596452 ACACACTCTCGTGCTTATTCG 58.404 47.619 0.00 0.00 45.10 3.34
6183 6567 2.228103 ACACACTCTCGTGCTTATTCGA 59.772 45.455 0.00 0.00 45.10 3.71
6298 6682 6.465894 CCTCCTTTTCTTTTCCTCTCAGGTTA 60.466 42.308 0.00 0.00 36.53 2.85
6305 6689 2.930109 TCCTCTCAGGTTAAGCTCCT 57.070 50.000 3.68 0.00 36.53 3.69
6485 6871 2.003301 GCTGCTAGTTCCAGTTAGCAC 58.997 52.381 2.32 0.00 45.26 4.40
6486 6872 2.612972 GCTGCTAGTTCCAGTTAGCACA 60.613 50.000 2.32 0.00 45.26 4.57
6498 6884 3.370978 CAGTTAGCACACTACCAAATCGG 59.629 47.826 0.00 0.00 42.50 4.18
6552 6938 9.981114 GGATCTTTTTAGAAGAAAATGACCAAA 57.019 29.630 0.00 0.00 0.00 3.28
6557 6943 8.491045 TTTTAGAAGAAAATGACCAAATCCCT 57.509 30.769 0.00 0.00 0.00 4.20
6673 7090 3.842923 CATCTCGCGGCCCAGAGT 61.843 66.667 18.31 6.68 36.03 3.24
6734 7235 7.584396 ACCTTCCTCCCTTTATTTTTCTCTA 57.416 36.000 0.00 0.00 0.00 2.43
6817 7318 7.971722 ACCACGTTATAATATTGGCAAACTTTC 59.028 33.333 3.01 0.00 0.00 2.62
6836 7337 6.962182 ACTTTCTGAGATATTTGGGATGTCA 58.038 36.000 0.00 0.00 0.00 3.58
6837 7338 7.580910 ACTTTCTGAGATATTTGGGATGTCAT 58.419 34.615 0.00 0.00 0.00 3.06
6997 7498 6.480320 ACTCAATTATGATGCTTTAGGTCGTC 59.520 38.462 0.00 0.00 34.37 4.20
7069 7572 0.249784 TGCGTGCAACATTGGCAATT 60.250 45.000 10.65 0.00 43.91 2.32
7102 7605 6.334989 CAAACCAGACATATGTAACGTAGGA 58.665 40.000 8.71 0.00 0.00 2.94
7121 7624 6.238293 CGTAGGACAGAGTTGACGTGATATAA 60.238 42.308 0.00 0.00 0.00 0.98
7242 7745 3.804036 CTGAACCAGGTGTTGTACTTCA 58.196 45.455 0.00 0.00 37.29 3.02
7268 7771 1.885388 CAAGTCCACAACGCCGACA 60.885 57.895 0.00 0.00 0.00 4.35
7301 7804 3.872603 AGCAACACACTCCCGGCA 61.873 61.111 0.00 0.00 0.00 5.69
7310 7813 1.074889 ACACTCCCGGCATTAACCTTT 59.925 47.619 0.00 0.00 0.00 3.11
7321 7824 2.279935 TTAACCTTTGTCATGGCGGT 57.720 45.000 0.00 0.00 0.00 5.68
7379 7882 2.506957 CGGGCAGGCCAAGGTTTTT 61.507 57.895 14.59 0.00 37.98 1.94
7553 8056 1.761784 GTCCTCATCATCCTCAGCTGT 59.238 52.381 14.67 0.00 0.00 4.40
7561 8064 0.684479 ATCCTCAGCTGTGTCGCCTA 60.684 55.000 14.67 0.00 0.00 3.93
7655 8159 1.417145 TGTTGGTGTAGGCGGTTAGTT 59.583 47.619 0.00 0.00 0.00 2.24
7656 8160 2.158784 TGTTGGTGTAGGCGGTTAGTTT 60.159 45.455 0.00 0.00 0.00 2.66
7692 8196 3.089284 TCTGTAGAGCAAGATGTCGGAA 58.911 45.455 0.00 0.00 0.00 4.30
7701 8205 3.866449 GCAAGATGTCGGAAAGGTTCTCT 60.866 47.826 0.00 0.00 0.00 3.10
7941 8445 4.508128 GCTCCGGGATCGCGTTCA 62.508 66.667 27.58 12.34 34.56 3.18
8021 8525 3.649277 GATGCTCGTGGTCGTGGCT 62.649 63.158 0.00 0.00 37.58 4.75
8084 8588 2.280524 TACCACTGCGCGCAAACT 60.281 55.556 35.50 17.39 0.00 2.66
8102 8606 2.031870 ACTACACACAGACACAGCTCA 58.968 47.619 0.00 0.00 0.00 4.26
8181 8685 1.404391 GTTCTTCCCTCATCGTCGCTA 59.596 52.381 0.00 0.00 0.00 4.26
8300 8804 0.694771 TGGAGCTCAACTGCAAGGAT 59.305 50.000 17.19 0.00 44.73 3.24
8315 8820 1.002624 GGATGCCAGGAACGGAACA 60.003 57.895 0.00 0.00 0.00 3.18
8370 8875 2.550830 AAGCACCAACTTGAGACGAT 57.449 45.000 0.00 0.00 0.00 3.73
8389 8894 2.260869 CCCAAACGGCACTGACTGG 61.261 63.158 0.00 0.00 0.00 4.00
8402 8907 1.827344 CTGACTGGTAGATGCTGGTGA 59.173 52.381 0.00 0.00 0.00 4.02
8542 9047 4.079212 AGAGAGGAGAAGTTAGAGCATCCT 60.079 45.833 0.00 0.00 39.85 3.24
8607 9112 8.371699 CCATTTTCTGGTAATTTTTAAGGGACA 58.628 33.333 0.00 0.00 40.49 4.02
8608 9113 9.942850 CATTTTCTGGTAATTTTTAAGGGACAT 57.057 29.630 0.00 0.00 0.00 3.06
8642 9147 3.778265 ACAAGCCCCTAAACACATCAAT 58.222 40.909 0.00 0.00 0.00 2.57
8649 9154 7.759607 AGCCCCTAAACACATCAATATAGAAT 58.240 34.615 0.00 0.00 0.00 2.40
8670 9175 7.675062 AGAATATCTCTCCATACGCTTTCATT 58.325 34.615 0.00 0.00 0.00 2.57
8675 9180 7.482654 TCTCTCCATACGCTTTCATTATTTG 57.517 36.000 0.00 0.00 0.00 2.32
8701 9206 5.013183 ACTCCTAATGAAGCAGTTGGTAGTT 59.987 40.000 0.00 0.00 0.00 2.24
8739 9260 1.155390 TCTGACCTCCCACCTTCGT 59.845 57.895 0.00 0.00 0.00 3.85
8740 9261 0.898789 TCTGACCTCCCACCTTCGTC 60.899 60.000 0.00 0.00 0.00 4.20
8741 9262 0.900647 CTGACCTCCCACCTTCGTCT 60.901 60.000 0.00 0.00 0.00 4.18
8742 9263 1.185618 TGACCTCCCACCTTCGTCTG 61.186 60.000 0.00 0.00 0.00 3.51
8743 9264 0.898789 GACCTCCCACCTTCGTCTGA 60.899 60.000 0.00 0.00 0.00 3.27
8744 9265 0.252284 ACCTCCCACCTTCGTCTGAT 60.252 55.000 0.00 0.00 0.00 2.90
8745 9266 0.905357 CCTCCCACCTTCGTCTGATT 59.095 55.000 0.00 0.00 0.00 2.57
8746 9267 1.279271 CCTCCCACCTTCGTCTGATTT 59.721 52.381 0.00 0.00 0.00 2.17
8747 9268 2.290323 CCTCCCACCTTCGTCTGATTTT 60.290 50.000 0.00 0.00 0.00 1.82
8748 9269 3.412386 CTCCCACCTTCGTCTGATTTTT 58.588 45.455 0.00 0.00 0.00 1.94
8777 9298 5.060506 TCTGCTTATTTTCGTTTCACCTCA 58.939 37.500 0.00 0.00 0.00 3.86
8794 9315 2.289072 CCTCACACCAACATCTTCTCGT 60.289 50.000 0.00 0.00 0.00 4.18
8946 9842 4.473520 CCTCCCCGCGTTGCAGAT 62.474 66.667 4.92 0.00 0.00 2.90
9223 10119 1.604915 GCCTCCCCTTCTCTGTTCC 59.395 63.158 0.00 0.00 0.00 3.62
9289 10185 2.443394 CGGAGGATTGGGCTAGCCA 61.443 63.158 34.09 16.44 37.98 4.75
9290 10186 1.772819 CGGAGGATTGGGCTAGCCAT 61.773 60.000 34.09 20.68 37.98 4.40
9398 10294 5.758296 GGACTTTAGATGAACACAGACACAA 59.242 40.000 0.00 0.00 0.00 3.33
9399 10295 6.292919 GGACTTTAGATGAACACAGACACAAC 60.293 42.308 0.00 0.00 0.00 3.32
9400 10296 5.527582 ACTTTAGATGAACACAGACACAACC 59.472 40.000 0.00 0.00 0.00 3.77
9401 10297 3.845781 AGATGAACACAGACACAACCT 57.154 42.857 0.00 0.00 0.00 3.50
9402 10298 4.156455 AGATGAACACAGACACAACCTT 57.844 40.909 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.387343 ACCAAGGGGGCTGCCATG 62.387 66.667 22.05 12.82 42.05 3.66
11 12 4.066139 GACCAAGGGGGCTGCCAT 62.066 66.667 22.05 2.37 40.08 4.40
15 16 4.722700 CCACGACCAAGGGGGCTG 62.723 72.222 0.00 0.00 41.63 4.85
17 18 4.717313 GACCACGACCAAGGGGGC 62.717 72.222 0.00 0.00 39.55 5.80
18 19 4.388499 CGACCACGACCAAGGGGG 62.388 72.222 0.00 0.00 39.55 5.40
19 20 3.584868 GACGACCACGACCAAGGGG 62.585 68.421 0.00 0.00 42.66 4.79
20 21 2.048503 GACGACCACGACCAAGGG 60.049 66.667 0.00 0.00 42.66 3.95
21 22 0.944311 CTTGACGACCACGACCAAGG 60.944 60.000 1.54 0.00 42.75 3.61
22 23 0.944311 CCTTGACGACCACGACCAAG 60.944 60.000 15.65 15.65 44.16 3.61
23 24 1.068417 CCTTGACGACCACGACCAA 59.932 57.895 0.00 0.00 42.66 3.67
24 25 2.732016 CCTTGACGACCACGACCA 59.268 61.111 0.00 0.00 42.66 4.02
25 26 2.737376 GCCTTGACGACCACGACC 60.737 66.667 0.00 0.00 42.66 4.79
26 27 2.022129 CTGCCTTGACGACCACGAC 61.022 63.158 0.00 0.00 42.66 4.34
27 28 2.338620 CTGCCTTGACGACCACGA 59.661 61.111 0.00 0.00 42.66 4.35
28 29 2.738521 CCTGCCTTGACGACCACG 60.739 66.667 0.00 0.00 45.75 4.94
29 30 1.668151 GACCTGCCTTGACGACCAC 60.668 63.158 0.00 0.00 0.00 4.16
30 31 2.741092 GACCTGCCTTGACGACCA 59.259 61.111 0.00 0.00 0.00 4.02
31 32 2.432628 CGACCTGCCTTGACGACC 60.433 66.667 0.00 0.00 0.00 4.79
32 33 2.022129 CACGACCTGCCTTGACGAC 61.022 63.158 0.00 0.00 0.00 4.34
33 34 2.338620 CACGACCTGCCTTGACGA 59.661 61.111 0.00 0.00 0.00 4.20
34 35 3.414700 GCACGACCTGCCTTGACG 61.415 66.667 0.00 0.00 40.42 4.35
35 36 3.414700 CGCACGACCTGCCTTGAC 61.415 66.667 0.00 0.00 43.84 3.18
42 43 3.108289 CTGTCAGCGCACGACCTG 61.108 66.667 22.47 13.83 32.15 4.00
43 44 2.363711 TTTCTGTCAGCGCACGACCT 62.364 55.000 22.47 0.00 32.15 3.85
44 45 1.495584 TTTTCTGTCAGCGCACGACC 61.496 55.000 22.47 9.14 32.15 4.79
45 46 0.383124 GTTTTCTGTCAGCGCACGAC 60.383 55.000 19.69 19.69 0.00 4.34
46 47 0.808060 TGTTTTCTGTCAGCGCACGA 60.808 50.000 11.47 1.91 0.00 4.35
47 48 0.235665 ATGTTTTCTGTCAGCGCACG 59.764 50.000 11.47 0.00 0.00 5.34
48 49 1.264020 TCATGTTTTCTGTCAGCGCAC 59.736 47.619 11.47 0.00 0.00 5.34
49 50 1.592064 TCATGTTTTCTGTCAGCGCA 58.408 45.000 11.47 0.00 0.00 6.09
50 51 2.286950 TGTTCATGTTTTCTGTCAGCGC 60.287 45.455 0.00 0.00 0.00 5.92
51 52 3.291585 GTGTTCATGTTTTCTGTCAGCG 58.708 45.455 0.00 0.00 0.00 5.18
52 53 3.002246 TCGTGTTCATGTTTTCTGTCAGC 59.998 43.478 0.00 0.00 0.00 4.26
53 54 4.794248 TCGTGTTCATGTTTTCTGTCAG 57.206 40.909 0.00 0.00 0.00 3.51
54 55 5.448496 CCTTTCGTGTTCATGTTTTCTGTCA 60.448 40.000 0.00 0.00 0.00 3.58
55 56 4.970003 CCTTTCGTGTTCATGTTTTCTGTC 59.030 41.667 0.00 0.00 0.00 3.51
56 57 4.638421 TCCTTTCGTGTTCATGTTTTCTGT 59.362 37.500 0.00 0.00 0.00 3.41
57 58 5.168526 TCCTTTCGTGTTCATGTTTTCTG 57.831 39.130 0.00 0.00 0.00 3.02
58 59 6.391227 AATCCTTTCGTGTTCATGTTTTCT 57.609 33.333 0.00 0.00 0.00 2.52
65 66 5.766150 TCACAAAATCCTTTCGTGTTCAT 57.234 34.783 0.00 0.00 31.28 2.57
73 74 7.174946 TCAGTCCACTAATCACAAAATCCTTTC 59.825 37.037 0.00 0.00 0.00 2.62
223 240 6.474427 CGTTATCATTACATTAGACCACGTGT 59.526 38.462 15.65 2.26 0.00 4.49
225 242 5.981315 CCGTTATCATTACATTAGACCACGT 59.019 40.000 0.00 0.00 0.00 4.49
235 252 5.238650 GCTTACTTGCCCGTTATCATTACAT 59.761 40.000 0.00 0.00 0.00 2.29
349 392 4.492791 TTATCGTTCGTCAGAGTTGTGA 57.507 40.909 0.00 0.00 0.00 3.58
480 523 3.176552 TGTCCGTTCTTTTCCGTGTTA 57.823 42.857 0.00 0.00 0.00 2.41
591 634 1.342174 CTCATGGCTGGTTTGCTGTTT 59.658 47.619 0.00 0.00 0.00 2.83
641 684 2.348104 TACGATCCTGGCGTGCTGT 61.348 57.895 9.23 0.00 42.62 4.40
644 687 2.585247 GGTACGATCCTGGCGTGC 60.585 66.667 9.23 7.79 42.62 5.34
680 723 2.434428 CAAGCTTGGAGACAGCTGAAT 58.566 47.619 23.35 8.07 44.54 2.57
731 774 1.394917 CTTCAGCGACAAGGCATACAC 59.605 52.381 0.00 0.00 34.64 2.90
748 793 3.120025 GCTACTCCAGAAGCAAAAGCTTC 60.120 47.826 19.47 19.47 44.51 3.86
769 814 1.539827 ACGTGGCAATAACAGAAAGGC 59.460 47.619 0.00 0.00 0.00 4.35
853 1211 1.819928 TGGAATGGGATGTTCGTGTG 58.180 50.000 0.00 0.00 0.00 3.82
932 1292 7.723616 CCTCTTCTCTCTCAATTCCTGATACTA 59.276 40.741 0.00 0.00 32.14 1.82
963 1323 7.597288 TTAGAGATCGATCCCAACTTAATCA 57.403 36.000 21.66 0.00 0.00 2.57
1017 1377 2.363276 ACCATGGCGACGGTAGGA 60.363 61.111 13.04 0.00 32.31 2.94
1190 1550 4.636249 AGTAGCTGTGAAGCCATATAAGC 58.364 43.478 0.00 0.00 34.90 3.09
1248 1608 6.334296 TCCCTCTGTCCCATGATATAAGAAT 58.666 40.000 0.00 0.00 0.00 2.40
1249 1611 5.726560 TCCCTCTGTCCCATGATATAAGAA 58.273 41.667 0.00 0.00 0.00 2.52
1258 1620 4.067896 CGAATTAATCCCTCTGTCCCATG 58.932 47.826 0.00 0.00 0.00 3.66
1266 1628 2.104963 GCTGGACCGAATTAATCCCTCT 59.895 50.000 0.00 0.00 0.00 3.69
1300 1662 8.853077 TGACAAGAGAAACACATTCATAGATT 57.147 30.769 0.00 0.00 40.72 2.40
1326 1688 4.713553 TCATGTAAACAAGCTCTTGGTGA 58.286 39.130 13.48 0.00 40.05 4.02
1353 1715 7.171678 ACGAGAAGGTAAAAGAAGACAGAAATG 59.828 37.037 0.00 0.00 0.00 2.32
1354 1716 7.171678 CACGAGAAGGTAAAAGAAGACAGAAAT 59.828 37.037 0.00 0.00 0.00 2.17
1362 1726 5.236478 TCTTTGCACGAGAAGGTAAAAGAAG 59.764 40.000 0.00 0.00 32.92 2.85
1449 1815 2.761208 ACTAGCTAGGGTGTGACACATC 59.239 50.000 24.35 11.38 35.86 3.06
1450 1816 2.761208 GACTAGCTAGGGTGTGACACAT 59.239 50.000 24.35 7.95 35.86 3.21
1524 1890 5.634118 TGATTCTGAGGGTTTCACAAATCT 58.366 37.500 0.00 0.00 35.66 2.40
2160 2537 2.646719 CGTTCGGACACGGGAGAA 59.353 61.111 0.00 0.00 41.39 2.87
2858 3237 4.394712 GCGTCAGTGACCCTGGGG 62.395 72.222 18.88 7.87 41.83 4.96
2859 3238 4.742201 CGCGTCAGTGACCCTGGG 62.742 72.222 17.57 12.28 41.83 4.45
2860 3239 3.991051 ACGCGTCAGTGACCCTGG 61.991 66.667 17.57 4.68 41.83 4.45
3689 4070 2.504367 ACACATGCTAGTGGGTTTCAC 58.496 47.619 12.54 0.00 46.39 3.18
4212 4593 4.881850 CAGGTTTATCGCCTATTCAGGTTT 59.118 41.667 0.00 0.00 44.68 3.27
4731 5115 0.321298 GAAGGGGTTGCAGCGTCTTA 60.321 55.000 6.92 0.00 0.00 2.10
4800 5184 1.344953 ACAAGCTCAGGGTCACCACA 61.345 55.000 0.00 0.00 40.13 4.17
5000 5384 4.115516 GCATCACAACATGACTCTACGAT 58.884 43.478 0.00 0.00 41.24 3.73
5702 6086 8.929487 AGAGGAAAAGAATATCTGGGTTAGTAG 58.071 37.037 0.00 0.00 0.00 2.57
6198 6582 5.338614 CGAGGACGTTTCAGTGTTTATTT 57.661 39.130 0.00 0.00 34.56 1.40
6298 6682 2.283145 AGTGCACAAATCAGGAGCTT 57.717 45.000 21.04 0.00 0.00 3.74
6443 6829 7.698130 GCAGCACTATAAACTCTTTGGTTAATG 59.302 37.037 0.00 0.00 30.81 1.90
6541 6927 2.833943 GAGCCAGGGATTTGGTCATTTT 59.166 45.455 0.00 0.00 40.49 1.82
6545 6931 1.139498 TGGAGCCAGGGATTTGGTCA 61.139 55.000 0.00 0.00 40.49 4.02
6617 7033 1.103987 TTGTTGCACTTTAGCCCGCA 61.104 50.000 0.00 0.00 0.00 5.69
6621 7037 5.538067 TTTGTTTTTGTTGCACTTTAGCC 57.462 34.783 0.00 0.00 0.00 3.93
6673 7090 4.362677 ACATTTAGTCTTCCTCCTGGCTA 58.637 43.478 0.00 0.00 0.00 3.93
6741 7242 5.001232 ACACCTCTACGCAAACAATAATGT 58.999 37.500 0.00 0.00 43.14 2.71
6804 7305 7.325694 CCAAATATCTCAGAAAGTTTGCCAAT 58.674 34.615 0.00 0.00 0.00 3.16
6817 7318 6.996879 AGTTGATGACATCCCAAATATCTCAG 59.003 38.462 12.90 0.00 0.00 3.35
6836 7337 5.176741 AGAAGAAATGAGGCAGAGTTGAT 57.823 39.130 0.00 0.00 0.00 2.57
6837 7338 4.630644 AGAAGAAATGAGGCAGAGTTGA 57.369 40.909 0.00 0.00 0.00 3.18
7069 7572 5.301551 ACATATGTCTGGTTTGCACTTCAAA 59.698 36.000 1.41 0.00 42.01 2.69
7102 7605 6.873997 TGGAATTATATCACGTCAACTCTGT 58.126 36.000 0.00 0.00 0.00 3.41
7121 7624 5.249163 TCACGGAAGATGATGGATATGGAAT 59.751 40.000 0.00 0.00 0.00 3.01
7242 7745 0.251341 GTTGTGGACTTGAGCCCCAT 60.251 55.000 0.00 0.00 31.94 4.00
7301 7804 2.752903 GACCGCCATGACAAAGGTTAAT 59.247 45.455 0.00 0.00 35.00 1.40
7310 7813 2.994995 AGGACGACCGCCATGACA 60.995 61.111 0.00 0.00 41.83 3.58
7321 7824 2.095461 CTGTCTCCATCTTGAGGACGA 58.905 52.381 0.00 0.00 33.04 4.20
7487 7990 2.355837 GGAAGTGCTGTCGCGTCA 60.356 61.111 5.77 5.79 39.65 4.35
7529 8032 2.027385 CTGAGGATGATGAGGACGTCA 58.973 52.381 18.91 0.00 44.59 4.35
7561 8064 1.613630 AGGATGAACCAGACGGCCT 60.614 57.895 0.00 0.00 42.04 5.19
7594 8097 3.228188 AGCTTGGTCTTGGTGAAATGA 57.772 42.857 0.00 0.00 0.00 2.57
7655 8159 6.701841 GCTCTACAGATCGACCATTATCAAAA 59.298 38.462 0.00 0.00 0.00 2.44
7656 8160 6.183360 TGCTCTACAGATCGACCATTATCAAA 60.183 38.462 0.00 0.00 0.00 2.69
7692 8196 1.192146 TGTAGGGCGCAGAGAACCTT 61.192 55.000 10.83 0.00 34.59 3.50
7701 8205 4.697756 GTGCTGGTGTAGGGCGCA 62.698 66.667 10.83 0.00 36.61 6.09
7767 8271 2.994995 ACGCTCCGGTCCATGACA 60.995 61.111 0.00 0.00 33.68 3.58
7830 8334 3.243301 GGATGGATGAGCTTACGACGTAA 60.243 47.826 18.74 18.74 0.00 3.18
7871 8375 5.543405 TCAGGAAAACATGGTTGGATCAATT 59.457 36.000 0.00 0.00 0.00 2.32
7941 8445 2.357034 GCACCACGACATGACCGT 60.357 61.111 0.00 5.86 41.36 4.83
8084 8588 1.269051 CGTGAGCTGTGTCTGTGTGTA 60.269 52.381 0.00 0.00 0.00 2.90
8102 8606 0.107268 AAAGTTAACAGGGGTCGCGT 59.893 50.000 5.77 0.00 0.00 6.01
8181 8685 3.627237 CCCCAAAGCACCATATACAACCT 60.627 47.826 0.00 0.00 0.00 3.50
8300 8804 2.112297 GGTGTTCCGTTCCTGGCA 59.888 61.111 0.00 0.00 0.00 4.92
8370 8875 1.227823 CAGTCAGTGCCGTTTGGGA 60.228 57.895 0.00 0.00 38.47 4.37
8389 8894 1.001974 TGTGTGGTCACCAGCATCTAC 59.998 52.381 0.00 0.00 43.26 2.59
8402 8907 3.595758 GCCTTGCGCTTGTGTGGT 61.596 61.111 9.73 0.00 0.00 4.16
8513 9018 6.071616 TGCTCTAACTTCTCCTCTCTCTTTTC 60.072 42.308 0.00 0.00 0.00 2.29
8607 9112 4.017126 GGGGCTTGTAGCAAAGTAGAAAT 58.983 43.478 0.67 0.00 44.75 2.17
8608 9113 3.073946 AGGGGCTTGTAGCAAAGTAGAAA 59.926 43.478 0.67 0.00 44.75 2.52
8642 9147 9.462606 TGAAAGCGTATGGAGAGATATTCTATA 57.537 33.333 0.00 0.00 35.87 1.31
8649 9154 9.208022 CAAATAATGAAAGCGTATGGAGAGATA 57.792 33.333 0.00 0.00 0.00 1.98
8723 9229 1.155390 AGACGAAGGTGGGAGGTCA 59.845 57.895 0.00 0.00 0.00 4.02
8745 9266 9.180678 GAAACGAAAATAAGCAGATGAGAAAAA 57.819 29.630 0.00 0.00 0.00 1.94
8746 9267 8.349245 TGAAACGAAAATAAGCAGATGAGAAAA 58.651 29.630 0.00 0.00 0.00 2.29
8747 9268 7.803189 GTGAAACGAAAATAAGCAGATGAGAAA 59.197 33.333 0.00 0.00 0.00 2.52
8748 9269 7.298122 GTGAAACGAAAATAAGCAGATGAGAA 58.702 34.615 0.00 0.00 0.00 2.87
8749 9270 6.128282 GGTGAAACGAAAATAAGCAGATGAGA 60.128 38.462 0.00 0.00 38.12 3.27
8750 9271 6.024049 GGTGAAACGAAAATAAGCAGATGAG 58.976 40.000 0.00 0.00 38.12 2.90
8751 9272 5.705441 AGGTGAAACGAAAATAAGCAGATGA 59.295 36.000 0.00 0.00 38.12 2.92
8752 9273 5.942872 AGGTGAAACGAAAATAAGCAGATG 58.057 37.500 0.00 0.00 38.12 2.90
8753 9274 5.705441 TGAGGTGAAACGAAAATAAGCAGAT 59.295 36.000 0.00 0.00 38.12 2.90
8777 9298 2.910688 ACACGAGAAGATGTTGGTGT 57.089 45.000 0.00 0.00 34.10 4.16
8939 9835 4.365111 AAGGGCCGGCATCTGCAA 62.365 61.111 30.85 0.00 44.36 4.08
8940 9836 4.802051 GAAGGGCCGGCATCTGCA 62.802 66.667 30.85 0.00 44.36 4.41
8946 9842 2.038975 AGTAGAGAAGGGCCGGCA 59.961 61.111 30.85 0.51 0.00 5.69
8978 9874 0.036105 AATCAGTGCCTCGACATGCA 60.036 50.000 0.00 0.00 34.54 3.96
9008 9904 2.655073 ATCGGTGATGGTGCGGTGA 61.655 57.895 0.00 0.00 0.00 4.02
9052 9948 1.153229 GATTGGGGTGTAGGCGTCC 60.153 63.158 0.00 0.00 0.00 4.79
9109 10005 0.460459 TGTGCAAAGTCGGTTGTCGA 60.460 50.000 0.00 0.00 46.77 4.20
9272 10168 3.660724 TGGCTAGCCCAATCCTCC 58.339 61.111 30.81 2.95 41.82 4.30
9289 10185 4.637387 AGCTGCTAGATAGAATGCCAAT 57.363 40.909 0.00 0.00 0.00 3.16
9290 10186 4.132336 CAAGCTGCTAGATAGAATGCCAA 58.868 43.478 0.90 0.00 0.00 4.52
9295 10191 4.653341 ACTCCACAAGCTGCTAGATAGAAT 59.347 41.667 0.90 0.00 0.00 2.40
9298 10194 4.118410 CAACTCCACAAGCTGCTAGATAG 58.882 47.826 0.90 0.00 0.00 2.08
9351 10247 0.601576 TGTCCCACGATGAAACCACG 60.602 55.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.