Multiple sequence alignment - TraesCS7D01G006800

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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 TraesCS7D01G006800 chr7D 100.000 4838 0 0 1 4838 3552868 3548031 0.000000e+00 8935.0
1 TraesCS7D01G006800 chr7D 92.915 3585 235 15 108 3682 2905032 2901457 0.000000e+00 5195.0
2 TraesCS7D01G006800 chr7D 86.110 2023 218 32 1064 3064 2687462 2685481 0.000000e+00 2121.0
3 TraesCS7D01G006800 chr7D 81.928 2562 387 59 1152 3682 4009761 4007245 0.000000e+00 2097.0
4 TraesCS7D01G006800 chr7D 83.633 1002 156 8 108 1105 2522573 2521576 0.000000e+00 935.0
5 TraesCS7D01G006800 chr7D 83.064 927 153 4 181 1105 3425076 3424152 0.000000e+00 839.0
6 TraesCS7D01G006800 chr7D 95.105 143 7 0 4532 4674 2900654 2900512 4.870000e-55 226.0
7 TraesCS7D01G006800 chr7D 97.260 73 2 0 2 74 2719793 2719721 1.830000e-24 124.0
8 TraesCS7D01G006800 chr7D 100.000 28 0 0 109 136 2687496 2687469 9.000000e-03 52.8
9 TraesCS7D01G006800 chr7A 92.495 3451 197 18 232 3678 3156012 3152620 0.000000e+00 4881.0
10 TraesCS7D01G006800 chr7A 81.380 3507 565 69 229 3682 3844174 3840703 0.000000e+00 2778.0
11 TraesCS7D01G006800 chr7A 95.559 1216 53 1 1649 2864 2685990 2684776 0.000000e+00 1945.0
12 TraesCS7D01G006800 chr7A 83.653 1927 272 23 1625 3515 2800550 2798631 0.000000e+00 1773.0
13 TraesCS7D01G006800 chr7A 95.252 1053 43 7 124 1171 2688527 2687477 0.000000e+00 1661.0
14 TraesCS7D01G006800 chr7A 84.707 1007 144 5 108 1112 2806019 2805021 0.000000e+00 998.0
15 TraesCS7D01G006800 chr7A 92.016 501 40 0 3056 3556 2684780 2684280 0.000000e+00 704.0
16 TraesCS7D01G006800 chr7A 88.643 361 37 4 1170 1528 2687442 2687084 2.070000e-118 436.0
17 TraesCS7D01G006800 chr7A 89.803 304 19 3 4546 4838 3152214 3151912 3.530000e-101 379.0
18 TraesCS7D01G006800 chr7A 87.460 311 14 9 4546 4838 2683504 2683201 7.760000e-88 335.0
19 TraesCS7D01G006800 chr7A 87.562 201 19 5 3899 4094 3152402 3152203 1.350000e-55 228.0
20 TraesCS7D01G006800 chr7A 96.396 111 4 0 1 111 3156372 3156262 2.970000e-42 183.0
21 TraesCS7D01G006800 chr7A 93.750 96 5 1 108 202 2688629 2688534 5.050000e-30 143.0
22 TraesCS7D01G006800 chr7A 95.238 84 4 0 108 191 3156093 3156010 3.040000e-27 134.0
23 TraesCS7D01G006800 chr4A 82.158 3503 525 69 232 3675 739605580 739609041 0.000000e+00 2915.0
24 TraesCS7D01G006800 chr4A 81.647 3400 555 53 232 3597 742161105 742157741 0.000000e+00 2758.0
25 TraesCS7D01G006800 chr4A 81.101 3016 476 61 704 3673 740494221 740497188 0.000000e+00 2326.0
26 TraesCS7D01G006800 chr4A 85.012 2035 273 26 1578 3597 742021129 742023146 0.000000e+00 2039.0
27 TraesCS7D01G006800 chr4A 82.425 2276 345 36 1341 3597 740122932 740120693 0.000000e+00 1936.0
28 TraesCS7D01G006800 chr4A 82.923 2114 294 39 1596 3673 739886359 739888441 0.000000e+00 1842.0
29 TraesCS7D01G006800 chr4A 82.255 2164 353 27 1528 3679 733805942 733808086 0.000000e+00 1840.0
30 TraesCS7D01G006800 chr4A 82.933 2039 313 27 1592 3615 741421960 741423978 0.000000e+00 1805.0
31 TraesCS7D01G006800 chr4A 82.335 1285 217 9 2402 3682 741505837 741504559 0.000000e+00 1107.0
32 TraesCS7D01G006800 chr4A 86.348 857 117 0 108 964 740442686 740441830 0.000000e+00 935.0
33 TraesCS7D01G006800 chr4A 83.220 882 143 5 232 1110 741420769 741421648 0.000000e+00 804.0
34 TraesCS7D01G006800 chr4A 95.433 416 16 2 903 1315 740852617 740853032 0.000000e+00 660.0
35 TraesCS7D01G006800 chr4A 77.743 966 131 59 3899 4830 742157420 742156505 2.580000e-142 516.0
36 TraesCS7D01G006800 chr4A 83.163 196 26 6 107 295 740607097 740606902 6.440000e-39 172.0
37 TraesCS7D01G006800 chr4A 91.753 97 6 2 3668 3763 589084952 589084857 3.040000e-27 134.0
38 TraesCS7D01G006800 chr1D 83.776 1960 287 23 1561 3507 464795416 464797357 0.000000e+00 1829.0
39 TraesCS7D01G006800 chr1D 95.833 72 3 0 4536 4607 464798689 464798760 3.060000e-22 117.0
40 TraesCS7D01G006800 chr5B 95.556 90 4 0 3674 3763 655839914 655840003 1.400000e-30 145.0
41 TraesCS7D01G006800 chr6D 95.506 89 4 0 3677 3765 385917027 385916939 5.050000e-30 143.0
42 TraesCS7D01G006800 chr1B 92.784 97 6 1 3670 3765 112300999 112301095 6.530000e-29 139.0
43 TraesCS7D01G006800 chrUn 90.385 104 9 1 3661 3763 371558030 371558133 8.450000e-28 135.0
44 TraesCS7D01G006800 chrUn 90.385 104 9 1 3661 3763 371616837 371616940 8.450000e-28 135.0
45 TraesCS7D01G006800 chr5A 90.385 104 9 1 3661 3763 30009444 30009547 8.450000e-28 135.0
46 TraesCS7D01G006800 chr5A 90.385 104 9 1 3661 3763 30013533 30013636 8.450000e-28 135.0
47 TraesCS7D01G006800 chr5D 91.753 97 6 2 3668 3763 475843304 475843399 3.040000e-27 134.0


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 TraesCS7D01G006800 chr7D 3548031 3552868 4837 True 8935.000000 8935 100.000000 1 4838 1 chr7D.!!$R4 4837
1 TraesCS7D01G006800 chr7D 2900512 2905032 4520 True 2710.500000 5195 94.010000 108 4674 2 chr7D.!!$R7 4566
2 TraesCS7D01G006800 chr7D 4007245 4009761 2516 True 2097.000000 2097 81.928000 1152 3682 1 chr7D.!!$R5 2530
3 TraesCS7D01G006800 chr7D 2685481 2687496 2015 True 1086.900000 2121 93.055000 109 3064 2 chr7D.!!$R6 2955
4 TraesCS7D01G006800 chr7D 2521576 2522573 997 True 935.000000 935 83.633000 108 1105 1 chr7D.!!$R1 997
5 TraesCS7D01G006800 chr7D 3424152 3425076 924 True 839.000000 839 83.064000 181 1105 1 chr7D.!!$R3 924
6 TraesCS7D01G006800 chr7A 3840703 3844174 3471 True 2778.000000 2778 81.380000 229 3682 1 chr7A.!!$R3 3453
7 TraesCS7D01G006800 chr7A 2798631 2800550 1919 True 1773.000000 1773 83.653000 1625 3515 1 chr7A.!!$R1 1890
8 TraesCS7D01G006800 chr7A 3151912 3156372 4460 True 1161.000000 4881 92.298800 1 4838 5 chr7A.!!$R5 4837
9 TraesCS7D01G006800 chr7A 2805021 2806019 998 True 998.000000 998 84.707000 108 1112 1 chr7A.!!$R2 1004
10 TraesCS7D01G006800 chr7A 2683201 2688629 5428 True 870.666667 1945 92.113333 108 4838 6 chr7A.!!$R4 4730
11 TraesCS7D01G006800 chr4A 739605580 739609041 3461 False 2915.000000 2915 82.158000 232 3675 1 chr4A.!!$F2 3443
12 TraesCS7D01G006800 chr4A 740494221 740497188 2967 False 2326.000000 2326 81.101000 704 3673 1 chr4A.!!$F4 2969
13 TraesCS7D01G006800 chr4A 742021129 742023146 2017 False 2039.000000 2039 85.012000 1578 3597 1 chr4A.!!$F6 2019
14 TraesCS7D01G006800 chr4A 740120693 740122932 2239 True 1936.000000 1936 82.425000 1341 3597 1 chr4A.!!$R2 2256
15 TraesCS7D01G006800 chr4A 739886359 739888441 2082 False 1842.000000 1842 82.923000 1596 3673 1 chr4A.!!$F3 2077
16 TraesCS7D01G006800 chr4A 733805942 733808086 2144 False 1840.000000 1840 82.255000 1528 3679 1 chr4A.!!$F1 2151
17 TraesCS7D01G006800 chr4A 742156505 742161105 4600 True 1637.000000 2758 79.695000 232 4830 2 chr4A.!!$R6 4598
18 TraesCS7D01G006800 chr4A 741420769 741423978 3209 False 1304.500000 1805 83.076500 232 3615 2 chr4A.!!$F7 3383
19 TraesCS7D01G006800 chr4A 741504559 741505837 1278 True 1107.000000 1107 82.335000 2402 3682 1 chr4A.!!$R5 1280
20 TraesCS7D01G006800 chr4A 740441830 740442686 856 True 935.000000 935 86.348000 108 964 1 chr4A.!!$R3 856
21 TraesCS7D01G006800 chr1D 464795416 464798760 3344 False 973.000000 1829 89.804500 1561 4607 2 chr1D.!!$F1 3046

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
337 598 1.668419 ACAAACTGCAGAGAAGCGTT 58.332 45.000 23.35 0.0 37.31 4.84 F
1230 1535 0.532573 AGATAGTGTCACACCTGCGG 59.467 55.000 3.66 0.0 34.49 5.69 F
1232 1537 0.973632 ATAGTGTCACACCTGCGGAA 59.026 50.000 3.66 0.0 34.49 4.30 F
1643 2014 1.607628 GCTGACATTCATGCATCCTCC 59.392 52.381 0.00 0.0 0.00 4.30 F
2875 4339 0.820891 AATGCCATGCTGGATCGGAC 60.821 55.000 6.40 0.0 40.96 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1390 1729 1.278637 GGGCGAACGTTCAACAGTG 59.721 57.895 26.71 11.18 0.00 3.66 R
2369 3830 1.134371 TGTCATGGACACGACAACCAA 60.134 47.619 0.00 0.00 39.14 3.67 R
2511 3972 2.162681 GATGTGCTAGCCAAAGGTTGT 58.837 47.619 13.29 0.00 0.00 3.32 R
3556 5036 2.010817 CACGCTTTGCCGTTTCAGC 61.011 57.895 0.00 0.00 39.83 4.26 R
4503 6464 0.030501 CCCCTCCCCCTACATACACA 60.031 60.000 0.00 0.00 0.00 3.72 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
202 463 3.431912 CACTCGTTCCATCATCACGAAAA 59.568 43.478 0.00 0.00 42.10 2.29
203 464 4.093408 CACTCGTTCCATCATCACGAAAAT 59.907 41.667 0.00 0.00 42.10 1.82
212 473 8.292444 TCCATCATCACGAAAATAAAGGAAAT 57.708 30.769 0.00 0.00 0.00 2.17
337 598 1.668419 ACAAACTGCAGAGAAGCGTT 58.332 45.000 23.35 0.00 37.31 4.84
427 688 3.461773 CCACGGGACCAGCTCGAT 61.462 66.667 0.00 0.00 45.56 3.59
565 826 6.015688 ACATGCTCAAACAACTCATGAAGAAT 60.016 34.615 0.00 0.00 38.23 2.40
577 838 3.072330 TCATGAAGAATATGGGCGGCTTA 59.928 43.478 9.56 1.44 0.00 3.09
836 1097 3.820467 TGATGTGTCCAAGCAACTAAAGG 59.180 43.478 0.00 0.00 0.00 3.11
837 1098 1.953686 TGTGTCCAAGCAACTAAAGGC 59.046 47.619 0.00 0.00 0.00 4.35
1147 1415 6.491714 AGGTAGCTGATTGATGAACTATGT 57.508 37.500 0.00 0.00 0.00 2.29
1148 1416 6.893583 AGGTAGCTGATTGATGAACTATGTT 58.106 36.000 0.00 0.00 0.00 2.71
1217 1522 4.948062 AGTAAAAGGGGGCAAAGATAGT 57.052 40.909 0.00 0.00 0.00 2.12
1230 1535 0.532573 AGATAGTGTCACACCTGCGG 59.467 55.000 3.66 0.00 34.49 5.69
1232 1537 0.973632 ATAGTGTCACACCTGCGGAA 59.026 50.000 3.66 0.00 34.49 4.30
1390 1729 3.017442 GCTATTCTTTGGGTTGGGACTC 58.983 50.000 0.00 0.00 0.00 3.36
1486 1835 8.324306 TCTGAAAGATGAAAGTATCTGGATTGT 58.676 33.333 0.00 0.00 38.67 2.71
1519 1869 8.689251 TGTTAATCAGAAATAGAGTTCTCGTG 57.311 34.615 0.00 0.00 35.63 4.35
1643 2014 1.607628 GCTGACATTCATGCATCCTCC 59.392 52.381 0.00 0.00 0.00 4.30
2221 3658 6.069331 CCTGAAGATCATCTGATTGGGAAAT 58.931 40.000 6.42 0.00 34.37 2.17
2437 3898 7.650834 TTGTCAAAGGAAGAAAAGTTTGTTG 57.349 32.000 0.00 0.00 32.74 3.33
2511 3972 3.382546 GGCTAGTTGTTCATCGTAGGGTA 59.617 47.826 0.00 0.00 0.00 3.69
2796 4260 5.885912 TGGAAATAGCATAAGTGAACTTCCC 59.114 40.000 0.00 0.00 37.40 3.97
2857 4321 9.684448 TGAACATTAGCGAAACAAATATTGAAA 57.316 25.926 0.00 0.00 0.00 2.69
2875 4339 0.820891 AATGCCATGCTGGATCGGAC 60.821 55.000 6.40 0.00 40.96 4.79
2928 4392 5.539955 AGGAAAAGTTGGTATGCACTCAAAT 59.460 36.000 0.00 0.00 0.00 2.32
3205 4679 4.559862 ACGATCAATCCCTCAGTTCTTT 57.440 40.909 0.00 0.00 0.00 2.52
3210 4684 5.060427 TCAATCCCTCAGTTCTTTCCAAA 57.940 39.130 0.00 0.00 0.00 3.28
3423 4903 3.136443 TGCCGGTCCTTGAATATCTTGAT 59.864 43.478 1.90 0.00 0.00 2.57
3456 4936 2.623416 AGCACATGCCAATGATGATGAG 59.377 45.455 0.00 0.00 43.38 2.90
3556 5036 1.009078 TGCGGATTTCGAGAATGCTG 58.991 50.000 9.05 5.49 42.43 4.41
3557 5037 0.316524 GCGGATTTCGAGAATGCTGC 60.317 55.000 0.00 0.00 42.43 5.25
3558 5038 1.293924 CGGATTTCGAGAATGCTGCT 58.706 50.000 0.00 0.00 42.43 4.24
3652 5397 1.829222 GGATTGGAGTCGGAGGTAACA 59.171 52.381 0.00 0.00 41.41 2.41
3688 5433 5.531122 TTTATTCATCAGTACTCCCTCCG 57.469 43.478 0.00 0.00 0.00 4.63
3689 5434 1.112113 TTCATCAGTACTCCCTCCGC 58.888 55.000 0.00 0.00 0.00 5.54
3690 5435 0.033503 TCATCAGTACTCCCTCCGCA 60.034 55.000 0.00 0.00 0.00 5.69
3691 5436 0.824109 CATCAGTACTCCCTCCGCAA 59.176 55.000 0.00 0.00 0.00 4.85
3692 5437 1.207089 CATCAGTACTCCCTCCGCAAA 59.793 52.381 0.00 0.00 0.00 3.68
3693 5438 0.606604 TCAGTACTCCCTCCGCAAAC 59.393 55.000 0.00 0.00 0.00 2.93
3694 5439 0.608640 CAGTACTCCCTCCGCAAACT 59.391 55.000 0.00 0.00 0.00 2.66
3695 5440 1.822990 CAGTACTCCCTCCGCAAACTA 59.177 52.381 0.00 0.00 0.00 2.24
3696 5441 2.232941 CAGTACTCCCTCCGCAAACTAA 59.767 50.000 0.00 0.00 0.00 2.24
3697 5442 3.105283 AGTACTCCCTCCGCAAACTAAT 58.895 45.455 0.00 0.00 0.00 1.73
3698 5443 4.098960 CAGTACTCCCTCCGCAAACTAATA 59.901 45.833 0.00 0.00 0.00 0.98
3699 5444 4.900054 AGTACTCCCTCCGCAAACTAATAT 59.100 41.667 0.00 0.00 0.00 1.28
3700 5445 6.015688 CAGTACTCCCTCCGCAAACTAATATA 60.016 42.308 0.00 0.00 0.00 0.86
3701 5446 5.881923 ACTCCCTCCGCAAACTAATATAA 57.118 39.130 0.00 0.00 0.00 0.98
3702 5447 5.855045 ACTCCCTCCGCAAACTAATATAAG 58.145 41.667 0.00 0.00 0.00 1.73
3703 5448 5.601313 ACTCCCTCCGCAAACTAATATAAGA 59.399 40.000 0.00 0.00 0.00 2.10
3704 5449 6.097915 TCCCTCCGCAAACTAATATAAGAG 57.902 41.667 0.00 0.00 0.00 2.85
3705 5450 5.601313 TCCCTCCGCAAACTAATATAAGAGT 59.399 40.000 0.00 0.00 0.00 3.24
3706 5451 5.696724 CCCTCCGCAAACTAATATAAGAGTG 59.303 44.000 0.00 0.00 0.00 3.51
3707 5452 6.281405 CCTCCGCAAACTAATATAAGAGTGT 58.719 40.000 0.00 0.00 0.00 3.55
3708 5453 6.201044 CCTCCGCAAACTAATATAAGAGTGTG 59.799 42.308 4.03 4.03 34.52 3.82
3709 5454 6.636705 TCCGCAAACTAATATAAGAGTGTGT 58.363 36.000 8.58 0.00 34.00 3.72
3710 5455 7.774134 TCCGCAAACTAATATAAGAGTGTGTA 58.226 34.615 8.58 0.00 34.00 2.90
3711 5456 7.919091 TCCGCAAACTAATATAAGAGTGTGTAG 59.081 37.037 8.58 4.81 34.00 2.74
3712 5457 7.919091 CCGCAAACTAATATAAGAGTGTGTAGA 59.081 37.037 8.58 0.00 34.00 2.59
3713 5458 9.464714 CGCAAACTAATATAAGAGTGTGTAGAT 57.535 33.333 8.58 0.00 34.00 1.98
3757 5502 9.930693 AAACACTCTTCTATTAGTTTACAGAGG 57.069 33.333 0.00 0.00 32.21 3.69
3758 5503 8.068892 ACACTCTTCTATTAGTTTACAGAGGG 57.931 38.462 0.00 0.00 36.55 4.30
3763 5508 9.986157 TCTTCTATTAGTTTACAGAGGGAGTAA 57.014 33.333 0.00 0.00 0.00 2.24
3817 5564 5.007682 CACGATCTCCTTTTTCCCCTTTTA 58.992 41.667 0.00 0.00 0.00 1.52
3836 5583 7.396055 CCCTTTTACAGATTCCCAAACTGATTA 59.604 37.037 0.00 0.00 35.85 1.75
3838 5585 9.626045 CTTTTACAGATTCCCAAACTGATTAAC 57.374 33.333 0.00 0.00 35.85 2.01
3856 5618 6.491062 TGATTAACCTAAGCTAGCCGTGTATA 59.509 38.462 12.13 0.00 0.00 1.47
3864 5626 2.352814 GCTAGCCGTGTATATCCACCTG 60.353 54.545 2.29 0.00 31.47 4.00
3867 5629 0.756294 CCGTGTATATCCACCTGCCA 59.244 55.000 0.00 0.00 31.47 4.92
3880 5642 1.985159 ACCTGCCAGAATCAAGGTACA 59.015 47.619 0.00 0.00 0.00 2.90
3886 5648 3.545703 CCAGAATCAAGGTACATCCACC 58.454 50.000 0.00 0.00 39.02 4.61
3894 5656 0.618458 GGTACATCCACCTGCCAGAA 59.382 55.000 0.00 0.00 35.55 3.02
3897 5801 0.257039 ACATCCACCTGCCAGAATCC 59.743 55.000 0.00 0.00 0.00 3.01
3921 5825 7.119699 TCCAGAGTAAATAACAGCAATTGTCAG 59.880 37.037 7.40 0.00 39.73 3.51
3964 5871 1.398832 CCAATATGCATGCACGCTACG 60.399 52.381 25.37 9.51 0.00 3.51
4020 5938 7.498900 CCATGCACTCCACTTATATGTTTTCTA 59.501 37.037 0.00 0.00 0.00 2.10
4064 5984 1.526575 AAGCATCACCAAACCAGCCG 61.527 55.000 0.00 0.00 0.00 5.52
4077 5998 2.671963 AGCCGCGGGGAAAGAAAC 60.672 61.111 29.38 6.37 34.06 2.78
4089 6010 4.254492 GGGAAAGAAACGATAGCAAGAGT 58.746 43.478 0.00 0.00 42.67 3.24
4093 6014 6.147985 GGAAAGAAACGATAGCAAGAGTCTTT 59.852 38.462 1.56 0.00 36.92 2.52
4203 6137 9.786105 AAATTTAAAAATGACACAAAGGCAAAG 57.214 25.926 0.00 0.00 39.98 2.77
4206 6140 6.421377 AAAAATGACACAAAGGCAAAGAAC 57.579 33.333 0.00 0.00 39.98 3.01
4208 6142 3.781079 TGACACAAAGGCAAAGAACAG 57.219 42.857 0.00 0.00 26.55 3.16
4209 6143 3.088532 TGACACAAAGGCAAAGAACAGT 58.911 40.909 0.00 0.00 26.55 3.55
4210 6144 3.119531 TGACACAAAGGCAAAGAACAGTG 60.120 43.478 0.00 0.00 26.55 3.66
4211 6145 3.088532 ACACAAAGGCAAAGAACAGTGA 58.911 40.909 0.00 0.00 0.00 3.41
4285 6230 7.531716 TGGTTGTTTTACTGTCTTTTGTAGTG 58.468 34.615 0.00 0.00 0.00 2.74
4306 6251 7.951530 AGTGCAGGAAAATGAAATAACAAAG 57.048 32.000 0.00 0.00 0.00 2.77
4310 6255 7.071414 GCAGGAAAATGAAATAACAAAGCAAC 58.929 34.615 0.00 0.00 0.00 4.17
4331 6276 5.767816 ACATTGTTTACTTTGTGGAGTCC 57.232 39.130 0.73 0.73 0.00 3.85
4355 6306 6.094061 CAGTAGTCTGTTGCTAGGTTACTTC 58.906 44.000 0.00 0.00 36.97 3.01
4405 6358 2.020720 TCTCGTGCCATTTTGTGTGTT 58.979 42.857 0.00 0.00 0.00 3.32
4415 6368 4.450419 CCATTTTGTGTGTTTGTGTGTGTT 59.550 37.500 0.00 0.00 0.00 3.32
4418 6371 2.398498 TGTGTGTTTGTGTGTGTTTGC 58.602 42.857 0.00 0.00 0.00 3.68
4420 6373 0.988439 GTGTTTGTGTGTGTTTGCGG 59.012 50.000 0.00 0.00 0.00 5.69
4438 6395 2.794631 GCGGTGTTTGTCTGTCCTTTTG 60.795 50.000 0.00 0.00 0.00 2.44
4448 6405 5.432645 TGTCTGTCCTTTTGTGTGTATTGA 58.567 37.500 0.00 0.00 0.00 2.57
4467 6424 8.318412 TGTATTGATTAAGACTTAACAGGCAGA 58.682 33.333 9.82 0.00 0.00 4.26
4475 6432 3.815401 GACTTAACAGGCAGATGTGTGTT 59.185 43.478 4.58 4.58 37.00 3.32
4500 6461 7.820044 TTTATGTTCCTTGTTTTTGTGTGTC 57.180 32.000 0.00 0.00 0.00 3.67
4501 6462 5.659440 ATGTTCCTTGTTTTTGTGTGTCT 57.341 34.783 0.00 0.00 0.00 3.41
4502 6463 5.054390 TGTTCCTTGTTTTTGTGTGTCTC 57.946 39.130 0.00 0.00 0.00 3.36
4503 6464 4.764823 TGTTCCTTGTTTTTGTGTGTCTCT 59.235 37.500 0.00 0.00 0.00 3.10
4505 6466 4.331968 TCCTTGTTTTTGTGTGTCTCTGT 58.668 39.130 0.00 0.00 0.00 3.41
4508 6469 5.123186 CCTTGTTTTTGTGTGTCTCTGTGTA 59.877 40.000 0.00 0.00 0.00 2.90
4512 6473 6.819146 TGTTTTTGTGTGTCTCTGTGTATGTA 59.181 34.615 0.00 0.00 0.00 2.29
4513 6474 7.011016 TGTTTTTGTGTGTCTCTGTGTATGTAG 59.989 37.037 0.00 0.00 0.00 2.74
4515 6476 3.509967 TGTGTGTCTCTGTGTATGTAGGG 59.490 47.826 0.00 0.00 0.00 3.53
4516 6477 3.096852 TGTGTCTCTGTGTATGTAGGGG 58.903 50.000 0.00 0.00 0.00 4.79
4517 6478 2.431057 GTGTCTCTGTGTATGTAGGGGG 59.569 54.545 0.00 0.00 0.00 5.40
4518 6479 2.313643 TGTCTCTGTGTATGTAGGGGGA 59.686 50.000 0.00 0.00 0.00 4.81
4519 6480 2.959707 GTCTCTGTGTATGTAGGGGGAG 59.040 54.545 0.00 0.00 0.00 4.30
4520 6481 2.091278 TCTCTGTGTATGTAGGGGGAGG 60.091 54.545 0.00 0.00 0.00 4.30
4521 6482 1.062428 TCTGTGTATGTAGGGGGAGGG 60.062 57.143 0.00 0.00 0.00 4.30
4522 6483 0.030501 TGTGTATGTAGGGGGAGGGG 60.031 60.000 0.00 0.00 0.00 4.79
4599 6876 1.925972 GAAGGAGGAGGGGCCAAGT 60.926 63.158 4.39 0.00 40.02 3.16
4631 6908 7.081349 TCGTGAAATGTCAAACCATTAATGTC 58.919 34.615 14.25 2.17 34.01 3.06
4632 6909 6.860539 CGTGAAATGTCAAACCATTAATGTCA 59.139 34.615 14.25 4.63 34.01 3.58
4741 7035 7.661437 TGACCATATATAGTTTCCTGTTCATGC 59.339 37.037 0.00 0.00 0.00 4.06
4784 7078 1.110442 TGGTGGTTCAAGTTTGGCTG 58.890 50.000 0.00 0.00 0.00 4.85
4791 7092 1.691196 TCAAGTTTGGCTGAGTTGGG 58.309 50.000 7.90 0.00 0.00 4.12
4793 7094 2.031120 CAAGTTTGGCTGAGTTGGGAA 58.969 47.619 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.073311 TCCATCAGAGAACCTTTTACTCG 57.927 43.478 0.00 0.00 36.03 4.18
60 61 5.220835 CCTGCAGAACATATAACGCAAATCA 60.221 40.000 17.39 0.00 0.00 2.57
166 340 1.065345 ACGAGTGGCTAGCTAGAGTGA 60.065 52.381 25.15 1.21 0.00 3.41
212 473 4.323104 GCTGGGTTTTTGGGTGCAATAATA 60.323 41.667 0.00 0.00 0.00 0.98
337 598 8.409358 TCTCGAGATGTTTGATATCATCCTTA 57.591 34.615 12.08 0.00 40.63 2.69
427 688 1.815408 GCCCAGAGCTTGACTTGTTCA 60.815 52.381 0.00 0.00 38.99 3.18
565 826 0.840617 TGGTGAATAAGCCGCCCATA 59.159 50.000 0.00 0.00 33.41 2.74
577 838 4.279671 TGGCGTTTCATAAACTTGGTGAAT 59.720 37.500 1.49 0.00 39.23 2.57
628 889 1.623811 GCCTCCTGAACACTGACCTTA 59.376 52.381 0.00 0.00 0.00 2.69
836 1097 6.377327 TCCGAATCCAAAAATAGAGATTGC 57.623 37.500 0.00 0.00 0.00 3.56
837 1098 6.514048 GCCTCCGAATCCAAAAATAGAGATTG 60.514 42.308 0.00 0.00 0.00 2.67
1390 1729 1.278637 GGGCGAACGTTCAACAGTG 59.721 57.895 26.71 11.18 0.00 3.66
1519 1869 3.737850 CAGAGGCTGATCCAGTTTATCC 58.262 50.000 0.00 0.00 37.29 2.59
1554 1905 1.501604 GGAGGGGTACAGGAGAGAGAT 59.498 57.143 0.00 0.00 0.00 2.75
2221 3658 6.653320 GCGACCCATTTCCATATCAAACTATA 59.347 38.462 0.00 0.00 0.00 1.31
2368 3829 1.944024 GTCATGGACACGACAACCAAA 59.056 47.619 0.00 0.00 37.24 3.28
2369 3830 1.134371 TGTCATGGACACGACAACCAA 60.134 47.619 0.00 0.00 39.14 3.67
2437 3898 3.053455 GCTCGTCACTATCCAATACAGC 58.947 50.000 0.00 0.00 0.00 4.40
2511 3972 2.162681 GATGTGCTAGCCAAAGGTTGT 58.837 47.619 13.29 0.00 0.00 3.32
2719 4183 3.652057 TCCTATTTCCTTTGGGAGCTG 57.348 47.619 0.00 0.00 43.29 4.24
2796 4260 8.832521 AGTTGACTTAGTAGATGAATACTCTCG 58.167 37.037 0.00 0.00 37.24 4.04
2875 4339 7.307278 GCATAGCTCTTCTAGACATGTCAAATG 60.307 40.741 27.02 13.09 0.00 2.32
2928 4392 3.630312 GCTTACCCAGTTCTGTCACAAAA 59.370 43.478 0.00 0.00 0.00 2.44
3205 4679 5.319043 AGTTGTAAATGGGAGAGTTTGGA 57.681 39.130 0.00 0.00 0.00 3.53
3556 5036 2.010817 CACGCTTTGCCGTTTCAGC 61.011 57.895 0.00 0.00 39.83 4.26
3557 5037 2.010817 GCACGCTTTGCCGTTTCAG 61.011 57.895 0.00 0.00 46.63 3.02
3558 5038 2.025441 GCACGCTTTGCCGTTTCA 59.975 55.556 0.00 0.00 46.63 2.69
3576 5319 3.006110 CAGTTGGGAAGCACATCAATTGT 59.994 43.478 5.13 0.00 39.91 2.71
3682 5427 5.696724 CACTCTTATATTAGTTTGCGGAGGG 59.303 44.000 0.00 0.00 0.00 4.30
3683 5428 6.201044 CACACTCTTATATTAGTTTGCGGAGG 59.799 42.308 0.00 0.00 0.00 4.30
3684 5429 6.757010 ACACACTCTTATATTAGTTTGCGGAG 59.243 38.462 0.00 0.00 28.57 4.63
3685 5430 6.636705 ACACACTCTTATATTAGTTTGCGGA 58.363 36.000 0.00 0.00 28.57 5.54
3686 5431 6.903883 ACACACTCTTATATTAGTTTGCGG 57.096 37.500 0.00 0.00 28.57 5.69
3687 5432 8.851960 TCTACACACTCTTATATTAGTTTGCG 57.148 34.615 0.00 0.00 28.57 4.85
3731 5476 9.930693 CCTCTGTAAACTAATAGAAGAGTGTTT 57.069 33.333 0.00 0.00 0.00 2.83
3732 5477 8.532819 CCCTCTGTAAACTAATAGAAGAGTGTT 58.467 37.037 0.00 0.00 0.00 3.32
3733 5478 7.894364 TCCCTCTGTAAACTAATAGAAGAGTGT 59.106 37.037 0.00 0.00 0.00 3.55
3734 5479 8.294954 TCCCTCTGTAAACTAATAGAAGAGTG 57.705 38.462 0.00 0.00 0.00 3.51
3735 5480 8.117312 ACTCCCTCTGTAAACTAATAGAAGAGT 58.883 37.037 0.00 0.00 32.44 3.24
3736 5481 8.528044 ACTCCCTCTGTAAACTAATAGAAGAG 57.472 38.462 0.00 0.00 0.00 2.85
3737 5482 9.986157 TTACTCCCTCTGTAAACTAATAGAAGA 57.014 33.333 0.00 0.00 0.00 2.87
3740 5485 9.931698 TCATTACTCCCTCTGTAAACTAATAGA 57.068 33.333 0.00 0.00 34.20 1.98
3743 5488 9.440761 AGATCATTACTCCCTCTGTAAACTAAT 57.559 33.333 0.00 0.00 34.20 1.73
3744 5489 8.840200 AGATCATTACTCCCTCTGTAAACTAA 57.160 34.615 0.00 0.00 34.20 2.24
3745 5490 7.506261 GGAGATCATTACTCCCTCTGTAAACTA 59.494 40.741 0.00 0.00 45.64 2.24
3746 5491 6.325286 GGAGATCATTACTCCCTCTGTAAACT 59.675 42.308 0.00 0.00 45.64 2.66
3747 5492 6.517605 GGAGATCATTACTCCCTCTGTAAAC 58.482 44.000 0.00 0.00 45.64 2.01
3748 5493 6.732896 GGAGATCATTACTCCCTCTGTAAA 57.267 41.667 0.00 0.00 45.64 2.01
3758 5503 4.040217 AGCTGTCCATGGAGATCATTACTC 59.960 45.833 16.81 0.00 32.92 2.59
3763 5508 2.302445 GCTAGCTGTCCATGGAGATCAT 59.698 50.000 16.81 5.29 36.31 2.45
3764 5509 1.690893 GCTAGCTGTCCATGGAGATCA 59.309 52.381 16.81 9.14 0.00 2.92
3817 5564 5.892348 AGGTTAATCAGTTTGGGAATCTGT 58.108 37.500 0.00 0.00 0.00 3.41
3836 5583 4.220163 GGATATACACGGCTAGCTTAGGTT 59.780 45.833 15.72 0.00 0.00 3.50
3838 5585 3.762288 TGGATATACACGGCTAGCTTAGG 59.238 47.826 15.72 4.75 0.00 2.69
3856 5618 1.064166 CCTTGATTCTGGCAGGTGGAT 60.064 52.381 15.73 4.07 0.00 3.41
3864 5626 2.945668 GTGGATGTACCTTGATTCTGGC 59.054 50.000 0.00 0.00 39.86 4.85
3880 5642 0.549950 CTGGATTCTGGCAGGTGGAT 59.450 55.000 15.73 4.07 0.00 3.41
3886 5648 6.115446 TGTTATTTACTCTGGATTCTGGCAG 58.885 40.000 8.58 8.58 0.00 4.85
3888 5650 5.008118 GCTGTTATTTACTCTGGATTCTGGC 59.992 44.000 0.00 0.00 0.00 4.85
3891 5653 8.680903 CAATTGCTGTTATTTACTCTGGATTCT 58.319 33.333 0.00 0.00 0.00 2.40
3894 5656 7.611467 TGACAATTGCTGTTATTTACTCTGGAT 59.389 33.333 5.05 0.00 38.84 3.41
3897 5801 7.810658 ACTGACAATTGCTGTTATTTACTCTG 58.189 34.615 5.05 0.00 38.84 3.35
3921 5825 9.691362 TTGGTAATTGCTTCTTTTTCTATTGAC 57.309 29.630 0.00 0.00 0.00 3.18
3949 5856 2.432206 TATACGTAGCGTGCATGCAT 57.568 45.000 31.36 18.12 41.39 3.96
4020 5938 6.611642 TCCAGCCTACAGATATGAAGTAACTT 59.388 38.462 0.00 0.00 0.00 2.66
4034 5954 1.661341 GTGATGCTTCCAGCCTACAG 58.339 55.000 0.00 0.00 41.51 2.74
4058 5978 4.715523 TTCTTTCCCCGCGGCTGG 62.716 66.667 22.85 17.71 0.00 4.85
4064 5984 0.656259 GCTATCGTTTCTTTCCCCGC 59.344 55.000 0.00 0.00 0.00 6.13
4068 5988 5.172205 AGACTCTTGCTATCGTTTCTTTCC 58.828 41.667 0.00 0.00 0.00 3.13
4077 5998 4.386049 ACAAACGAAAGACTCTTGCTATCG 59.614 41.667 8.44 8.44 35.16 2.92
4093 6014 8.077386 GGACAATAAATAAGACCAAACAAACGA 58.923 33.333 0.00 0.00 0.00 3.85
4156 6084 2.931325 TGCTGCAAAAGAAAGCAAAGTG 59.069 40.909 0.00 0.00 43.65 3.16
4173 6105 7.376601 GCCTTTGTGTCATTTTTAAATTTGCTG 59.623 33.333 0.00 0.00 0.00 4.41
4189 6123 3.128589 TCACTGTTCTTTGCCTTTGTGTC 59.871 43.478 0.00 0.00 0.00 3.67
4206 6140 6.377327 AGAAAACATACCAAACAGTCACTG 57.623 37.500 2.22 2.22 37.52 3.66
4208 6142 7.544217 ACAAAAGAAAACATACCAAACAGTCAC 59.456 33.333 0.00 0.00 0.00 3.67
4209 6143 7.607250 ACAAAAGAAAACATACCAAACAGTCA 58.393 30.769 0.00 0.00 0.00 3.41
4210 6144 9.233232 CTACAAAAGAAAACATACCAAACAGTC 57.767 33.333 0.00 0.00 0.00 3.51
4211 6145 7.704899 GCTACAAAAGAAAACATACCAAACAGT 59.295 33.333 0.00 0.00 0.00 3.55
4285 6230 6.783892 TGCTTTGTTATTTCATTTTCCTGC 57.216 33.333 0.00 0.00 0.00 4.85
4306 6251 5.348164 ACTCCACAAAGTAAACAATGTTGC 58.652 37.500 0.00 0.00 0.00 4.17
4310 6255 5.299279 ACTGGACTCCACAAAGTAAACAATG 59.701 40.000 0.00 0.00 0.00 2.82
4405 6358 0.598562 AACACCGCAAACACACACAA 59.401 45.000 0.00 0.00 0.00 3.33
4415 6368 0.107410 AGGACAGACAAACACCGCAA 60.107 50.000 0.00 0.00 0.00 4.85
4418 6371 2.422127 ACAAAAGGACAGACAAACACCG 59.578 45.455 0.00 0.00 0.00 4.94
4420 6373 4.165779 CACACAAAAGGACAGACAAACAC 58.834 43.478 0.00 0.00 0.00 3.32
4438 6395 8.175716 GCCTGTTAAGTCTTAATCAATACACAC 58.824 37.037 8.27 0.00 0.00 3.82
4448 6405 6.372659 CACACATCTGCCTGTTAAGTCTTAAT 59.627 38.462 8.27 0.00 0.00 1.40
4458 6415 5.068987 ACATAAAAACACACATCTGCCTGTT 59.931 36.000 0.00 0.00 0.00 3.16
4460 6417 5.125100 ACATAAAAACACACATCTGCCTG 57.875 39.130 0.00 0.00 0.00 4.85
4467 6424 8.785329 AAAACAAGGAACATAAAAACACACAT 57.215 26.923 0.00 0.00 0.00 3.21
4475 6432 8.091449 AGACACACAAAAACAAGGAACATAAAA 58.909 29.630 0.00 0.00 0.00 1.52
4500 6461 2.320781 CCTCCCCCTACATACACAGAG 58.679 57.143 0.00 0.00 0.00 3.35
4501 6462 1.062428 CCCTCCCCCTACATACACAGA 60.062 57.143 0.00 0.00 0.00 3.41
4502 6463 1.424638 CCCTCCCCCTACATACACAG 58.575 60.000 0.00 0.00 0.00 3.66
4503 6464 0.030501 CCCCTCCCCCTACATACACA 60.031 60.000 0.00 0.00 0.00 3.72
4505 6466 1.635631 CCCCCTCCCCCTACATACA 59.364 63.158 0.00 0.00 0.00 2.29
4599 6876 7.731882 TGGTTTGACATTTCACGAGTTTATA 57.268 32.000 0.00 0.00 0.00 0.98
4695 6979 4.703575 GTCAGCCACGATGGTATATACCTA 59.296 45.833 28.12 17.04 46.58 3.08
4697 6981 3.368116 GGTCAGCCACGATGGTATATACC 60.368 52.174 22.97 22.97 40.46 2.73
4714 6998 9.212641 CATGAACAGGAAACTATATATGGTCAG 57.787 37.037 1.78 0.00 37.75 3.51
4757 7051 6.287525 CCAAACTTGAACCACCATATTTTGT 58.712 36.000 0.00 0.00 0.00 2.83
4784 7078 2.222227 AGCTTCCCAATTCCCAACTC 57.778 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.