Multiple sequence alignment - TraesCS7B01G472900

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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 TraesCS7B01G472900 chr7B 100.000 4090 0 0 1 4090 728932698 728936787 0.000000e+00 7553.0
1 TraesCS7B01G472900 chr7B 87.898 942 84 11 1009 1944 704289557 704290474 0.000000e+00 1081.0
2 TraesCS7B01G472900 chr7B 85.917 987 118 8 965 1944 704547786 704548758 0.000000e+00 1033.0
3 TraesCS7B01G472900 chr7B 95.484 620 27 1 2496 3115 729217501 729218119 0.000000e+00 989.0
4 TraesCS7B01G472900 chr7B 85.910 951 105 10 1009 1944 704637530 704636594 0.000000e+00 987.0
5 TraesCS7B01G472900 chr7B 94.194 620 36 0 2496 3115 704290466 704291085 0.000000e+00 946.0
6 TraesCS7B01G472900 chr7B 86.829 782 100 2 1009 1787 704318243 704317462 0.000000e+00 870.0
7 TraesCS7B01G472900 chr7B 89.773 616 61 2 2496 3110 704548750 704549364 0.000000e+00 787.0
8 TraesCS7B01G472900 chr7B 89.951 607 58 1 2499 3102 704317356 704316750 0.000000e+00 780.0
9 TraesCS7B01G472900 chr7B 88.511 618 46 13 2 608 704626657 704627260 0.000000e+00 725.0
10 TraesCS7B01G472900 chr7B 81.413 538 85 10 3555 4089 425223040 425222515 3.780000e-115 425.0
11 TraesCS7B01G472900 chr7B 83.333 366 25 17 779 1130 704627993 704628336 5.140000e-79 305.0
12 TraesCS7B01G472900 chr7B 87.984 258 21 4 3138 3395 729218114 729218361 3.090000e-76 296.0
13 TraesCS7B01G472900 chr7B 87.013 231 24 3 340 570 704288040 704288264 5.250000e-64 255.0
14 TraesCS7B01G472900 chr7B 92.308 104 5 2 677 777 704627285 704627388 1.180000e-30 145.0
15 TraesCS7B01G472900 chr7D 93.881 1193 35 10 779 1944 627449486 627450667 0.000000e+00 1764.0
16 TraesCS7B01G472900 chr7D 95.556 900 24 2 2496 3395 627450659 627451542 0.000000e+00 1426.0
17 TraesCS7B01G472900 chr7D 91.429 805 33 16 1 777 627447187 627447983 0.000000e+00 1072.0
18 TraesCS7B01G472900 chr7D 86.943 942 105 6 1009 1944 613626252 613627181 0.000000e+00 1042.0
19 TraesCS7B01G472900 chr7D 86.379 903 105 8 1046 1944 613661554 613660666 0.000000e+00 970.0
20 TraesCS7B01G472900 chr7D 90.705 624 58 0 2496 3119 613627173 613627796 0.000000e+00 832.0
21 TraesCS7B01G472900 chr7D 91.126 586 52 0 2499 3084 613660671 613660086 0.000000e+00 795.0
22 TraesCS7B01G472900 chr7D 90.556 540 50 1 3551 4090 508346979 508346441 0.000000e+00 713.0
23 TraesCS7B01G472900 chr7D 89.266 531 43 8 64 592 613637148 613637666 0.000000e+00 652.0
24 TraesCS7B01G472900 chr7D 89.796 343 14 6 935 1256 613649380 613649722 1.760000e-113 420.0
25 TraesCS7B01G472900 chr7D 95.631 206 8 1 2296 2500 268833763 268833968 3.050000e-86 329.0
26 TraesCS7B01G472900 chr7D 93.082 159 11 0 434 592 613650463 613650621 2.460000e-57 233.0
27 TraesCS7B01G472900 chr7D 94.059 101 6 0 677 777 613637690 613637790 1.970000e-33 154.0
28 TraesCS7B01G472900 chr7D 97.778 45 1 0 779 823 613638368 613638412 1.220000e-10 78.7
29 TraesCS7B01G472900 chr7A 87.177 1084 104 14 886 1944 705296892 705297965 0.000000e+00 1199.0
30 TraesCS7B01G472900 chr7A 85.499 931 116 9 1018 1944 705332647 705331732 0.000000e+00 953.0
31 TraesCS7B01G472900 chr7A 91.074 605 40 9 11 604 705295481 705296082 0.000000e+00 806.0
32 TraesCS7B01G472900 chr7A 87.681 690 80 2 2496 3183 705297957 705298643 0.000000e+00 798.0
33 TraesCS7B01G472900 chr7A 90.785 586 54 0 2499 3084 705331737 705331152 0.000000e+00 784.0
34 TraesCS7B01G472900 chr7A 94.059 101 6 0 677 777 705296108 705296208 1.970000e-33 154.0
35 TraesCS7B01G472900 chr7A 94.505 91 5 0 677 767 705307027 705307117 1.530000e-29 141.0
36 TraesCS7B01G472900 chr2B 98.221 562 7 3 1944 2504 698002964 698003523 0.000000e+00 979.0
37 TraesCS7B01G472900 chr2B 94.096 542 25 5 1945 2481 141155416 141155955 0.000000e+00 817.0
38 TraesCS7B01G472900 chr3A 94.444 558 24 5 1945 2497 77482911 77482356 0.000000e+00 852.0
39 TraesCS7B01G472900 chr5A 93.907 558 27 5 1944 2496 606545642 606546197 0.000000e+00 835.0
40 TraesCS7B01G472900 chr1B 92.572 552 39 2 1942 2492 67502278 67502828 0.000000e+00 791.0
41 TraesCS7B01G472900 chr6B 91.848 552 41 4 1948 2498 291257055 291256507 0.000000e+00 767.0
42 TraesCS7B01G472900 chr6B 88.148 540 63 1 3549 4088 493332325 493331787 3.450000e-180 641.0
43 TraesCS7B01G472900 chr6B 95.876 388 15 1 2109 2496 257598642 257599028 9.650000e-176 627.0
44 TraesCS7B01G472900 chr5B 89.051 548 57 3 3545 4090 74440196 74440742 0.000000e+00 676.0
45 TraesCS7B01G472900 chr5B 95.506 356 15 1 1945 2299 615700170 615700525 5.930000e-158 568.0
46 TraesCS7B01G472900 chrUn 92.308 416 27 3 1944 2354 117082499 117082084 1.640000e-163 586.0
47 TraesCS7B01G472900 chr2A 95.238 357 16 1 1944 2299 44026004 44025648 7.670000e-157 564.0
48 TraesCS7B01G472900 chr4A 84.794 559 46 16 1945 2497 515418108 515418633 3.620000e-145 525.0
49 TraesCS7B01G472900 chr3B 88.345 429 49 1 3662 4090 361747535 361747108 7.840000e-142 514.0
50 TraesCS7B01G472900 chr2D 78.559 583 82 33 14 579 575269072 575268516 1.090000e-90 344.0
51 TraesCS7B01G472900 chr2D 78.169 568 82 31 14 565 263422882 263422341 1.420000e-84 324.0
52 TraesCS7B01G472900 chr2D 82.090 201 25 7 14 207 118382184 118381988 1.180000e-35 161.0
53 TraesCS7B01G472900 chr4D 78.407 565 80 30 14 562 264462417 264462955 3.050000e-86 329.0
54 TraesCS7B01G472900 chr6A 77.465 568 86 31 14 565 526164027 526163486 6.640000e-78 302.0


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 TraesCS7B01G472900 chr7B 728932698 728936787 4089 False 7553.000000 7553 100.000000 1 4090 1 chr7B.!!$F1 4089
1 TraesCS7B01G472900 chr7B 704636594 704637530 936 True 987.000000 987 85.910000 1009 1944 1 chr7B.!!$R2 935
2 TraesCS7B01G472900 chr7B 704547786 704549364 1578 False 910.000000 1033 87.845000 965 3110 2 chr7B.!!$F3 2145
3 TraesCS7B01G472900 chr7B 704316750 704318243 1493 True 825.000000 870 88.390000 1009 3102 2 chr7B.!!$R3 2093
4 TraesCS7B01G472900 chr7B 704288040 704291085 3045 False 760.666667 1081 89.701667 340 3115 3 chr7B.!!$F2 2775
5 TraesCS7B01G472900 chr7B 729217501 729218361 860 False 642.500000 989 91.734000 2496 3395 2 chr7B.!!$F5 899
6 TraesCS7B01G472900 chr7B 425222515 425223040 525 True 425.000000 425 81.413000 3555 4089 1 chr7B.!!$R1 534
7 TraesCS7B01G472900 chr7B 704626657 704628336 1679 False 391.666667 725 88.050667 2 1130 3 chr7B.!!$F4 1128
8 TraesCS7B01G472900 chr7D 627447187 627451542 4355 False 1420.666667 1764 93.622000 1 3395 3 chr7D.!!$F5 3394
9 TraesCS7B01G472900 chr7D 613626252 613627796 1544 False 937.000000 1042 88.824000 1009 3119 2 chr7D.!!$F2 2110
10 TraesCS7B01G472900 chr7D 613660086 613661554 1468 True 882.500000 970 88.752500 1046 3084 2 chr7D.!!$R2 2038
11 TraesCS7B01G472900 chr7D 508346441 508346979 538 True 713.000000 713 90.556000 3551 4090 1 chr7D.!!$R1 539
12 TraesCS7B01G472900 chr7D 613649380 613650621 1241 False 326.500000 420 91.439000 434 1256 2 chr7D.!!$F4 822
13 TraesCS7B01G472900 chr7D 613637148 613638412 1264 False 294.900000 652 93.701000 64 823 3 chr7D.!!$F3 759
14 TraesCS7B01G472900 chr7A 705331152 705332647 1495 True 868.500000 953 88.142000 1018 3084 2 chr7A.!!$R1 2066
15 TraesCS7B01G472900 chr7A 705295481 705298643 3162 False 739.250000 1199 89.997750 11 3183 4 chr7A.!!$F2 3172
16 TraesCS7B01G472900 chr2B 698002964 698003523 559 False 979.000000 979 98.221000 1944 2504 1 chr2B.!!$F2 560
17 TraesCS7B01G472900 chr2B 141155416 141155955 539 False 817.000000 817 94.096000 1945 2481 1 chr2B.!!$F1 536
18 TraesCS7B01G472900 chr3A 77482356 77482911 555 True 852.000000 852 94.444000 1945 2497 1 chr3A.!!$R1 552
19 TraesCS7B01G472900 chr5A 606545642 606546197 555 False 835.000000 835 93.907000 1944 2496 1 chr5A.!!$F1 552
20 TraesCS7B01G472900 chr1B 67502278 67502828 550 False 791.000000 791 92.572000 1942 2492 1 chr1B.!!$F1 550
21 TraesCS7B01G472900 chr6B 291256507 291257055 548 True 767.000000 767 91.848000 1948 2498 1 chr6B.!!$R1 550
22 TraesCS7B01G472900 chr6B 493331787 493332325 538 True 641.000000 641 88.148000 3549 4088 1 chr6B.!!$R2 539
23 TraesCS7B01G472900 chr5B 74440196 74440742 546 False 676.000000 676 89.051000 3545 4090 1 chr5B.!!$F1 545
24 TraesCS7B01G472900 chr4A 515418108 515418633 525 False 525.000000 525 84.794000 1945 2497 1 chr4A.!!$F1 552
25 TraesCS7B01G472900 chr2D 575268516 575269072 556 True 344.000000 344 78.559000 14 579 1 chr2D.!!$R3 565
26 TraesCS7B01G472900 chr2D 263422341 263422882 541 True 324.000000 324 78.169000 14 565 1 chr2D.!!$R2 551
27 TraesCS7B01G472900 chr4D 264462417 264462955 538 False 329.000000 329 78.407000 14 562 1 chr4D.!!$F1 548
28 TraesCS7B01G472900 chr6A 526163486 526164027 541 True 302.000000 302 77.465000 14 565 1 chr6A.!!$R1 551

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
364 393 1.006086 TGTTAATCGCAGTGGCATCG 58.994 50.0 0.0 0.0 41.24 3.84 F
1846 4362 0.379669 GGATGTGCTTCTGGATTGCG 59.620 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 4497 0.679505 GGGTCGATGAATCCGGATCA 59.32 55.0 19.43 17.21 0.0 2.92 R
3431 6285 0.530211 CAGAGCGAGATGGAGGCAAG 60.53 60.0 0.00 0.00 0.0 4.01 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
20 21 2.115427 TGTCACAGTGGGAGACTTGAA 58.885 47.619 0.00 0.00 29.75 2.69
45 46 4.018415 ACCCAGGTTCATACTGTATTGCTT 60.018 41.667 0.00 0.00 34.16 3.91
55 56 4.970662 ACTGTATTGCTTTGTAGGCATG 57.029 40.909 0.00 0.00 39.54 4.06
66 70 5.750067 GCTTTGTAGGCATGTAATGGATTTG 59.250 40.000 0.00 0.00 46.86 2.32
74 81 5.299949 GCATGTAATGGATTTGGGGATTTC 58.700 41.667 0.00 0.00 46.86 2.17
130 137 3.520290 AATGTCTTGGATGCTGCAATG 57.480 42.857 6.36 0.00 0.00 2.82
177 184 1.039856 GGTTCAGCACCAACCAATGT 58.960 50.000 6.60 0.00 46.42 2.71
208 215 3.251016 TCATCTAGAGGTATGGCTGCT 57.749 47.619 4.02 0.00 0.00 4.24
209 216 2.896044 TCATCTAGAGGTATGGCTGCTG 59.104 50.000 4.02 0.00 0.00 4.41
335 364 8.589335 TCTTGTCTAACTCAAGTTGTTCATAC 57.411 34.615 5.66 0.00 41.78 2.39
364 393 1.006086 TGTTAATCGCAGTGGCATCG 58.994 50.000 0.00 0.00 41.24 3.84
581 611 6.421801 TGATGCATCTACTGTTGATTGATACG 59.578 38.462 26.32 0.00 0.00 3.06
582 612 5.660460 TGCATCTACTGTTGATTGATACGT 58.340 37.500 1.94 0.00 0.00 3.57
585 615 5.324784 TCTACTGTTGATTGATACGTGCT 57.675 39.130 0.00 0.00 0.00 4.40
755 883 6.303054 TCAAATGTTACTTCTGGGATGTTGA 58.697 36.000 0.00 0.00 0.00 3.18
823 2609 9.162764 CAATGATTGATCTGATGATGCATACTA 57.837 33.333 0.00 0.00 32.19 1.82
826 2612 7.817962 TGATTGATCTGATGATGCATACTACAG 59.182 37.037 0.00 7.67 32.19 2.74
837 2623 7.931275 TGATGCATACTACAGTACTGAACTAG 58.069 38.462 29.30 20.71 35.76 2.57
884 2731 4.537015 GCTATAACGAAAACATGGCATCC 58.463 43.478 0.00 0.00 0.00 3.51
982 2847 4.910456 CAGCTACATAAACTACGACCGATC 59.090 45.833 0.00 0.00 0.00 3.69
1083 2997 3.996124 AAGCTCAGGCGACGCAGT 61.996 61.111 23.09 4.98 44.37 4.40
1339 3843 1.156736 GAGGACCAACACCATCGTTG 58.843 55.000 0.00 0.00 44.78 4.10
1346 3850 1.568612 AACACCATCGTTGCGCTCAG 61.569 55.000 9.73 0.00 0.00 3.35
1842 4358 1.588239 TCCTGGATGTGCTTCTGGAT 58.412 50.000 0.00 0.00 0.00 3.41
1843 4359 1.918262 TCCTGGATGTGCTTCTGGATT 59.082 47.619 0.00 0.00 0.00 3.01
1844 4360 2.022195 CCTGGATGTGCTTCTGGATTG 58.978 52.381 0.00 0.00 0.00 2.67
1845 4361 1.404391 CTGGATGTGCTTCTGGATTGC 59.596 52.381 0.00 0.00 0.00 3.56
1846 4362 0.379669 GGATGTGCTTCTGGATTGCG 59.620 55.000 0.00 0.00 0.00 4.85
1847 4363 0.379669 GATGTGCTTCTGGATTGCGG 59.620 55.000 0.00 0.00 0.00 5.69
1848 4364 1.660560 ATGTGCTTCTGGATTGCGGC 61.661 55.000 0.00 0.00 0.00 6.53
1849 4365 3.126879 TGCTTCTGGATTGCGGCG 61.127 61.111 0.51 0.51 0.00 6.46
1850 4366 3.880846 GCTTCTGGATTGCGGCGG 61.881 66.667 9.78 0.00 0.00 6.13
2879 5696 0.683504 GAGGGACGGACTTCCAGCTA 60.684 60.000 0.00 0.00 37.40 3.32
3095 5949 3.069872 TCGTGCCACCTCTGTAAGTAAAA 59.930 43.478 0.00 0.00 33.76 1.52
3197 6051 8.708742 TCAAAACTCATAGTACGATTCTTGTTG 58.291 33.333 0.00 0.00 0.00 3.33
3224 6078 1.815003 GCATCTTGTGGAAACTCCCTG 59.185 52.381 0.00 0.00 35.03 4.45
3317 6171 1.332375 CGCCCTCGTTCTTTCAAACAA 59.668 47.619 0.00 0.00 0.00 2.83
3359 6213 6.757897 AACTGTCAATTTCTCAACACTGAA 57.242 33.333 0.00 0.00 0.00 3.02
3376 6230 8.902540 AACACTGAAGTTGATTTATGTACTGA 57.097 30.769 0.00 0.00 0.00 3.41
3377 6231 9.507329 AACACTGAAGTTGATTTATGTACTGAT 57.493 29.630 0.00 0.00 0.00 2.90
3408 6262 8.974060 TTTAACATTACAACTCCTTCTGAACT 57.026 30.769 0.00 0.00 0.00 3.01
3409 6263 8.603242 TTAACATTACAACTCCTTCTGAACTC 57.397 34.615 0.00 0.00 0.00 3.01
3410 6264 5.552178 ACATTACAACTCCTTCTGAACTCC 58.448 41.667 0.00 0.00 0.00 3.85
3411 6265 5.308237 ACATTACAACTCCTTCTGAACTCCT 59.692 40.000 0.00 0.00 0.00 3.69
3412 6266 5.888982 TTACAACTCCTTCTGAACTCCTT 57.111 39.130 0.00 0.00 0.00 3.36
3413 6267 4.344359 ACAACTCCTTCTGAACTCCTTC 57.656 45.455 0.00 0.00 0.00 3.46
3414 6268 3.970640 ACAACTCCTTCTGAACTCCTTCT 59.029 43.478 0.00 0.00 0.00 2.85
3415 6269 4.202305 ACAACTCCTTCTGAACTCCTTCTG 60.202 45.833 0.00 0.00 0.00 3.02
3416 6270 3.850752 ACTCCTTCTGAACTCCTTCTGA 58.149 45.455 0.00 0.00 33.74 3.27
3433 6287 9.495572 CTCCTTCTGAGTTAAGTTTTGATACTT 57.504 33.333 0.00 0.00 37.88 2.24
3434 6288 9.273016 TCCTTCTGAGTTAAGTTTTGATACTTG 57.727 33.333 0.00 0.00 38.72 3.16
3435 6289 8.017946 CCTTCTGAGTTAAGTTTTGATACTTGC 58.982 37.037 0.00 0.00 38.72 4.01
3436 6290 7.435068 TCTGAGTTAAGTTTTGATACTTGCC 57.565 36.000 0.00 0.00 38.72 4.52
3437 6291 7.224297 TCTGAGTTAAGTTTTGATACTTGCCT 58.776 34.615 0.00 0.00 38.72 4.75
3438 6292 7.387948 TCTGAGTTAAGTTTTGATACTTGCCTC 59.612 37.037 0.00 0.00 38.72 4.70
3439 6293 6.430000 TGAGTTAAGTTTTGATACTTGCCTCC 59.570 38.462 0.00 0.00 38.72 4.30
3440 6294 6.303839 AGTTAAGTTTTGATACTTGCCTCCA 58.696 36.000 0.00 0.00 38.72 3.86
3441 6295 6.948309 AGTTAAGTTTTGATACTTGCCTCCAT 59.052 34.615 0.00 0.00 38.72 3.41
3442 6296 5.904362 AAGTTTTGATACTTGCCTCCATC 57.096 39.130 0.00 0.00 37.00 3.51
3443 6297 5.184892 AGTTTTGATACTTGCCTCCATCT 57.815 39.130 0.00 0.00 0.00 2.90
3444 6298 5.189180 AGTTTTGATACTTGCCTCCATCTC 58.811 41.667 0.00 0.00 0.00 2.75
3445 6299 3.459232 TTGATACTTGCCTCCATCTCG 57.541 47.619 0.00 0.00 0.00 4.04
3446 6300 1.069204 TGATACTTGCCTCCATCTCGC 59.931 52.381 0.00 0.00 0.00 5.03
3447 6301 1.342819 GATACTTGCCTCCATCTCGCT 59.657 52.381 0.00 0.00 0.00 4.93
3448 6302 0.747255 TACTTGCCTCCATCTCGCTC 59.253 55.000 0.00 0.00 0.00 5.03
3449 6303 0.975040 ACTTGCCTCCATCTCGCTCT 60.975 55.000 0.00 0.00 0.00 4.09
3450 6304 0.530211 CTTGCCTCCATCTCGCTCTG 60.530 60.000 0.00 0.00 0.00 3.35
3451 6305 0.972471 TTGCCTCCATCTCGCTCTGA 60.972 55.000 0.00 0.00 0.00 3.27
3452 6306 1.363443 GCCTCCATCTCGCTCTGAG 59.637 63.158 0.00 0.00 46.72 3.35
3453 6307 1.363443 CCTCCATCTCGCTCTGAGC 59.637 63.158 19.53 19.53 44.86 4.26
3454 6308 1.363443 CTCCATCTCGCTCTGAGCC 59.637 63.158 22.97 6.56 44.86 4.70
3455 6309 2.027314 CCATCTCGCTCTGAGCCG 59.973 66.667 22.97 17.41 44.86 5.52
3456 6310 2.657944 CATCTCGCTCTGAGCCGC 60.658 66.667 22.97 0.45 44.86 6.53
3457 6311 2.832661 ATCTCGCTCTGAGCCGCT 60.833 61.111 22.97 4.29 44.86 5.52
3458 6312 3.136345 ATCTCGCTCTGAGCCGCTG 62.136 63.158 22.97 9.76 44.86 5.18
3459 6313 3.819920 CTCGCTCTGAGCCGCTGA 61.820 66.667 22.97 13.39 38.18 4.26
3460 6314 3.754740 CTCGCTCTGAGCCGCTGAG 62.755 68.421 22.97 18.39 43.29 3.35
3463 6317 2.202770 CTCTGAGCCGCTGAGCTG 60.203 66.667 1.78 0.00 45.15 4.24
3464 6318 4.447989 TCTGAGCCGCTGAGCTGC 62.448 66.667 13.14 13.14 45.15 5.25
3465 6319 4.754667 CTGAGCCGCTGAGCTGCA 62.755 66.667 22.39 2.18 45.15 4.41
3617 6474 4.436998 CACTCCGGTCCTGGCGTC 62.437 72.222 0.00 0.00 0.00 5.19
3651 6508 0.623617 GCCCCTTCCCTTCTCCCTTA 60.624 60.000 0.00 0.00 0.00 2.69
3656 6513 2.552367 CTTCCCTTCTCCCTTAGGTGT 58.448 52.381 0.00 0.00 0.00 4.16
3727 6584 2.336809 CAGCCTATCGTCTCGGGC 59.663 66.667 0.00 0.00 44.38 6.13
3747 6604 4.083862 GGGGCTTTCGGAGTCGCT 62.084 66.667 2.10 0.00 39.63 4.93
3910 6767 3.630013 TTCGCTGCAGGCAGGTCT 61.630 61.111 21.63 0.00 43.77 3.85
3925 6782 2.981909 TCTGGACCTCGTTCGCGT 60.982 61.111 5.77 0.00 42.11 6.01
3970 6827 2.755469 GTGGTACCGGCGGACCTA 60.755 66.667 35.78 20.47 36.62 3.08
3994 6851 2.564947 TGGCCTGTGTTTCAAGTGTTTT 59.435 40.909 3.32 0.00 0.00 2.43
3995 6852 3.007398 TGGCCTGTGTTTCAAGTGTTTTT 59.993 39.130 3.32 0.00 0.00 1.94
4029 6886 2.487265 GGAGGGAAGACTGCACTTTTCA 60.487 50.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.705023 GCAATACAGTATGAACCTGGGTTT 59.295 41.667 6.46 0.00 39.69 3.27
45 46 4.648762 CCCAAATCCATTACATGCCTACAA 59.351 41.667 0.00 0.00 0.00 2.41
55 56 7.069950 AGCTAAAGAAATCCCCAAATCCATTAC 59.930 37.037 0.00 0.00 0.00 1.89
66 70 4.514401 TCGAAGAAGCTAAAGAAATCCCC 58.486 43.478 0.00 0.00 0.00 4.81
130 137 4.037327 GCCAAATAATCCTTGAAGCCTCTC 59.963 45.833 0.00 0.00 0.00 3.20
208 215 9.134734 GGTTTAATTTTGAGCAATATTCGTTCA 57.865 29.630 2.85 0.00 0.00 3.18
209 216 9.353999 AGGTTTAATTTTGAGCAATATTCGTTC 57.646 29.630 2.85 0.00 0.00 3.95
335 364 4.725280 CACTGCGATTAACAATCATTGACG 59.275 41.667 3.79 3.33 37.78 4.35
364 393 0.830648 TCTTCATCACCGGGACATCC 59.169 55.000 6.32 0.00 0.00 3.51
585 615 9.923143 CGGGAGTATGTCATAATTATTAACAGA 57.077 33.333 13.23 8.13 0.00 3.41
662 695 3.137544 TGTCAATGTACCACTCCCTGTTT 59.862 43.478 0.00 0.00 0.00 2.83
673 706 5.581085 GGTTGTGATCTACTGTCAATGTACC 59.419 44.000 0.00 0.00 0.00 3.34
823 2609 6.239396 TCAGCTAAGACTAGTTCAGTACTGT 58.761 40.000 21.99 6.25 37.72 3.55
826 2612 7.323049 TCATCAGCTAAGACTAGTTCAGTAC 57.677 40.000 0.00 0.00 37.72 2.73
837 2623 6.364706 CCGTCTAAATCATCATCAGCTAAGAC 59.635 42.308 0.00 0.00 0.00 3.01
843 2629 3.397482 AGCCGTCTAAATCATCATCAGC 58.603 45.455 0.00 0.00 0.00 4.26
982 2847 1.679680 CATGGCTATGGCTTGGAACAG 59.320 52.381 1.33 0.00 38.73 3.16
1083 2997 0.899019 TCACGCCACCATACTGCTTA 59.101 50.000 0.00 0.00 0.00 3.09
1384 3888 2.426023 GACACGGCTCCAGTGGTT 59.574 61.111 9.54 0.00 43.41 3.67
1757 4267 2.884087 TTTCTCCTCGATGACGCCGC 62.884 60.000 0.00 0.00 39.58 6.53
1938 4454 1.027357 TTCCGGCTACTATGGTCGAC 58.973 55.000 7.13 7.13 0.00 4.20
1939 4455 1.406539 GTTTCCGGCTACTATGGTCGA 59.593 52.381 0.00 0.00 0.00 4.20
1940 4456 1.849097 GTTTCCGGCTACTATGGTCG 58.151 55.000 0.00 0.00 0.00 4.79
1981 4497 0.679505 GGGTCGATGAATCCGGATCA 59.320 55.000 19.43 17.21 0.00 2.92
2062 4583 2.125832 TGAATCGACGAACCGGCC 60.126 61.111 0.00 0.00 0.00 6.13
2710 5351 1.078214 TCGTACCCGAGGACGTGAT 60.078 57.895 0.28 0.00 38.40 3.06
3095 5949 3.480505 TGATCGATCTCCACATGCAAT 57.519 42.857 25.02 0.00 0.00 3.56
3163 6017 8.462143 TCGTACTATGAGTTTTGAGACAAATC 57.538 34.615 0.00 0.00 0.00 2.17
3197 6051 3.251004 AGTTTCCACAAGATGCGAAACTC 59.749 43.478 15.13 0.01 45.67 3.01
3224 6078 1.404315 CGGAGGGAGCACTACTTCAAC 60.404 57.143 0.00 0.00 0.00 3.18
3317 6171 7.823745 ACAGTTTAGAACCAGAAATTGTCAT 57.176 32.000 0.00 0.00 32.04 3.06
3395 6249 3.831911 CTCAGAAGGAGTTCAGAAGGAGT 59.168 47.826 0.00 0.00 38.90 3.85
3396 6250 4.454728 CTCAGAAGGAGTTCAGAAGGAG 57.545 50.000 0.00 0.00 38.90 3.69
3407 6261 9.495572 AAGTATCAAAACTTAACTCAGAAGGAG 57.504 33.333 0.00 0.00 42.43 3.69
3408 6262 9.273016 CAAGTATCAAAACTTAACTCAGAAGGA 57.727 33.333 0.00 0.00 37.61 3.36
3409 6263 8.017946 GCAAGTATCAAAACTTAACTCAGAAGG 58.982 37.037 0.00 0.00 37.61 3.46
3410 6264 8.017946 GGCAAGTATCAAAACTTAACTCAGAAG 58.982 37.037 0.00 0.00 37.61 2.85
3411 6265 7.719633 AGGCAAGTATCAAAACTTAACTCAGAA 59.280 33.333 0.00 0.00 37.61 3.02
3412 6266 7.224297 AGGCAAGTATCAAAACTTAACTCAGA 58.776 34.615 0.00 0.00 37.61 3.27
3413 6267 7.361286 GGAGGCAAGTATCAAAACTTAACTCAG 60.361 40.741 15.58 0.00 40.08 3.35
3414 6268 6.430000 GGAGGCAAGTATCAAAACTTAACTCA 59.570 38.462 15.58 0.00 40.08 3.41
3415 6269 6.430000 TGGAGGCAAGTATCAAAACTTAACTC 59.570 38.462 9.55 9.55 37.61 3.01
3416 6270 6.303839 TGGAGGCAAGTATCAAAACTTAACT 58.696 36.000 0.00 0.00 37.61 2.24
3417 6271 6.569179 TGGAGGCAAGTATCAAAACTTAAC 57.431 37.500 0.00 0.00 37.61 2.01
3418 6272 7.175104 AGATGGAGGCAAGTATCAAAACTTAA 58.825 34.615 0.00 0.00 37.61 1.85
3419 6273 6.721318 AGATGGAGGCAAGTATCAAAACTTA 58.279 36.000 0.00 0.00 37.61 2.24
3420 6274 5.574188 AGATGGAGGCAAGTATCAAAACTT 58.426 37.500 0.00 0.00 40.33 2.66
3421 6275 5.184892 AGATGGAGGCAAGTATCAAAACT 57.815 39.130 0.00 0.00 0.00 2.66
3422 6276 4.034510 CGAGATGGAGGCAAGTATCAAAAC 59.965 45.833 0.00 0.00 0.00 2.43
3423 6277 4.191544 CGAGATGGAGGCAAGTATCAAAA 58.808 43.478 0.00 0.00 0.00 2.44
3424 6278 3.797039 CGAGATGGAGGCAAGTATCAAA 58.203 45.455 0.00 0.00 0.00 2.69
3425 6279 2.483714 GCGAGATGGAGGCAAGTATCAA 60.484 50.000 0.00 0.00 0.00 2.57
3426 6280 1.069204 GCGAGATGGAGGCAAGTATCA 59.931 52.381 0.00 0.00 0.00 2.15
3427 6281 1.342819 AGCGAGATGGAGGCAAGTATC 59.657 52.381 0.00 0.00 0.00 2.24
3428 6282 1.342819 GAGCGAGATGGAGGCAAGTAT 59.657 52.381 0.00 0.00 0.00 2.12
3429 6283 0.747255 GAGCGAGATGGAGGCAAGTA 59.253 55.000 0.00 0.00 0.00 2.24
3430 6284 0.975040 AGAGCGAGATGGAGGCAAGT 60.975 55.000 0.00 0.00 0.00 3.16
3431 6285 0.530211 CAGAGCGAGATGGAGGCAAG 60.530 60.000 0.00 0.00 0.00 4.01
3432 6286 0.972471 TCAGAGCGAGATGGAGGCAA 60.972 55.000 0.00 0.00 0.00 4.52
3433 6287 1.380380 TCAGAGCGAGATGGAGGCA 60.380 57.895 0.00 0.00 0.00 4.75
3434 6288 1.363443 CTCAGAGCGAGATGGAGGC 59.637 63.158 0.00 0.00 45.45 4.70
3435 6289 1.363443 GCTCAGAGCGAGATGGAGG 59.637 63.158 6.67 0.00 45.45 4.30
3436 6290 1.363443 GGCTCAGAGCGAGATGGAG 59.637 63.158 16.47 0.00 45.45 3.86
3437 6291 2.484928 CGGCTCAGAGCGAGATGGA 61.485 63.158 16.47 0.00 45.45 3.41
3438 6292 2.027314 CGGCTCAGAGCGAGATGG 59.973 66.667 16.47 0.00 45.45 3.51
3439 6293 2.657944 GCGGCTCAGAGCGAGATG 60.658 66.667 16.47 4.80 45.45 2.90
3440 6294 2.832661 AGCGGCTCAGAGCGAGAT 60.833 61.111 16.47 8.80 45.45 2.75
3441 6295 3.819920 CAGCGGCTCAGAGCGAGA 61.820 66.667 16.47 0.00 45.45 4.04
3442 6296 3.754740 CTCAGCGGCTCAGAGCGAG 62.755 68.421 16.47 12.69 43.62 5.03
3443 6297 3.819920 CTCAGCGGCTCAGAGCGA 61.820 66.667 16.47 6.92 43.62 4.93
3446 6300 2.202770 CAGCTCAGCGGCTCAGAG 60.203 66.667 4.61 9.03 41.00 3.35
3447 6301 4.447989 GCAGCTCAGCGGCTCAGA 62.448 66.667 15.28 0.00 45.50 3.27
3727 6584 2.269241 GACTCCGAAAGCCCCAGG 59.731 66.667 0.00 0.00 0.00 4.45
3736 6593 1.379977 AGATCCCAGCGACTCCGAA 60.380 57.895 0.00 0.00 38.22 4.30
3747 6604 2.685017 ACGAGCCAGCAGATCCCA 60.685 61.111 0.00 0.00 0.00 4.37
3910 6767 2.049802 GAACGCGAACGAGGTCCA 60.050 61.111 15.93 0.00 43.93 4.02
3919 6776 2.025418 GGAAGAAGGCGAACGCGAA 61.025 57.895 15.93 0.00 43.06 4.70
3925 6782 2.656069 CGGGGAGGAAGAAGGCGAA 61.656 63.158 0.00 0.00 0.00 4.70
3954 6811 0.977108 AAATAGGTCCGCCGGTACCA 60.977 55.000 21.42 11.30 38.30 3.25
3970 6827 2.765699 ACACTTGAAACACAGGCCAAAT 59.234 40.909 5.01 0.00 0.00 2.32
3994 6851 3.089874 CTCCGATGCCCCTCCCAA 61.090 66.667 0.00 0.00 0.00 4.12
4029 6886 3.397439 AGCGGATGCACAGAGGCT 61.397 61.111 0.00 0.00 46.23 4.58


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

AutoCloner maintained by Alex Coulton.