Multiple sequence alignment - TraesCS2D01G366800

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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 TraesCS2D01G366800 chr2D 100.000 4142 0 0 1 4142 471374628 471370487 0.000000e+00 7649.0
1 TraesCS2D01G366800 chr2D 85.906 745 60 17 444 1161 471451895 471451169 0.000000e+00 752.0
2 TraesCS2D01G366800 chr2D 87.143 630 52 14 2537 3145 471896166 471895545 0.000000e+00 688.0
3 TraesCS2D01G366800 chr2D 84.444 630 64 15 2540 3145 471448834 471448215 1.280000e-164 590.0
4 TraesCS2D01G366800 chr2D 84.322 472 54 12 1190 1654 471451169 471450711 1.060000e-120 444.0
5 TraesCS2D01G366800 chr2D 83.047 407 35 20 1276 1654 471896886 471896486 5.130000e-89 339.0
6 TraesCS2D01G366800 chr2D 93.976 166 10 0 1000 1165 471897075 471896910 6.870000e-63 252.0
7 TraesCS2D01G366800 chr2D 83.209 268 24 9 1888 2146 471450562 471450307 4.170000e-55 226.0
8 TraesCS2D01G366800 chr2D 81.429 210 17 13 611 815 471897451 471897259 7.170000e-33 152.0
9 TraesCS2D01G366800 chr2D 95.556 45 2 0 1 45 31358517 31358473 5.740000e-09 73.1
10 TraesCS2D01G366800 chr2D 95.455 44 2 0 1 44 254392800 254392757 2.070000e-08 71.3
11 TraesCS2D01G366800 chr2D 93.617 47 3 0 3 49 512550328 512550374 2.070000e-08 71.3
12 TraesCS2D01G366800 chr2A 90.947 1900 78 32 509 2363 613039283 613037433 0.000000e+00 2470.0
13 TraesCS2D01G366800 chr2A 91.409 1164 57 18 2537 3672 613037399 613036251 0.000000e+00 1555.0
14 TraesCS2D01G366800 chr2A 92.787 610 34 5 2537 3140 613273627 613273022 0.000000e+00 874.0
15 TraesCS2D01G366800 chr2A 86.435 634 57 14 2537 3145 613174226 613173597 0.000000e+00 667.0
16 TraesCS2D01G366800 chr2A 79.284 922 115 46 1251 2146 613274860 613273989 3.590000e-160 575.0
17 TraesCS2D01G366800 chr2A 88.636 440 24 10 733 1161 613176037 613175613 2.860000e-141 512.0
18 TraesCS2D01G366800 chr2A 84.783 506 43 18 677 1161 613275401 613274909 1.040000e-130 477.0
19 TraesCS2D01G366800 chr2A 87.651 413 32 7 501 906 613043447 613043847 2.920000e-126 462.0
20 TraesCS2D01G366800 chr2A 84.513 452 52 12 1190 1634 613175613 613175173 8.230000e-117 431.0
21 TraesCS2D01G366800 chr2A 84.322 472 39 13 3688 4142 613036266 613035813 2.960000e-116 429.0
22 TraesCS2D01G366800 chr2A 90.698 129 11 1 140 268 613177997 613177870 1.980000e-38 171.0
23 TraesCS2D01G366800 chr2B 88.403 1897 133 39 405 2230 550513170 550511290 0.000000e+00 2204.0
24 TraesCS2D01G366800 chr2B 86.310 1344 77 52 2223 3501 550511207 550509906 0.000000e+00 1363.0
25 TraesCS2D01G366800 chr2B 78.733 1815 210 106 699 2437 550998213 550996499 0.000000e+00 1051.0
26 TraesCS2D01G366800 chr2B 83.276 1154 123 28 42 1160 550721689 550720571 0.000000e+00 998.0
27 TraesCS2D01G366800 chr2B 84.473 1024 85 37 655 1654 550859516 550858543 0.000000e+00 942.0
28 TraesCS2D01G366800 chr2B 94.108 611 28 5 2537 3145 550857424 550856820 0.000000e+00 922.0
29 TraesCS2D01G366800 chr2B 87.200 625 55 14 2537 3145 550996495 550995880 0.000000e+00 688.0
30 TraesCS2D01G366800 chr2B 85.331 634 65 13 2536 3145 550719367 550718738 7.560000e-177 630.0
31 TraesCS2D01G366800 chr2B 89.462 465 37 9 1191 1650 550720569 550720112 9.980000e-161 577.0
32 TraesCS2D01G366800 chr2B 84.539 401 51 7 251 643 550861472 550861075 1.810000e-103 387.0
33 TraesCS2D01G366800 chr2B 79.671 487 62 26 1888 2363 550719860 550719400 2.400000e-82 316.0
34 TraesCS2D01G366800 chr2B 90.476 168 14 2 3506 3672 550485273 550485107 1.940000e-53 220.0
35 TraesCS2D01G366800 chr2B 80.228 263 30 12 3688 3936 550485123 550484869 1.180000e-40 178.0
36 TraesCS2D01G366800 chr2B 91.860 86 6 1 39 124 550861569 550861485 7.270000e-23 119.0
37 TraesCS2D01G366800 chr2B 84.034 119 13 5 4028 4142 550484829 550484713 4.380000e-20 110.0
38 TraesCS2D01G366800 chr6D 96.078 51 2 0 4012 4062 63325321 63325271 2.650000e-12 84.2
39 TraesCS2D01G366800 chr4B 96.078 51 2 0 4012 4062 76050424 76050474 2.650000e-12 84.2
40 TraesCS2D01G366800 chr3D 96.078 51 2 0 4012 4062 586500940 586500990 2.650000e-12 84.2
41 TraesCS2D01G366800 chr3D 88.889 54 4 1 3 56 415782562 415782511 9.610000e-07 65.8
42 TraesCS2D01G366800 chr3B 96.078 51 2 0 4012 4062 745291304 745291354 2.650000e-12 84.2
43 TraesCS2D01G366800 chr1B 96.078 51 2 0 4012 4062 148112163 148112113 2.650000e-12 84.2
44 TraesCS2D01G366800 chr1B 96.078 51 2 0 4012 4062 439014217 439014167 2.650000e-12 84.2
45 TraesCS2D01G366800 chr1A 96.078 51 2 0 4012 4062 60804947 60804997 2.650000e-12 84.2
46 TraesCS2D01G366800 chr1A 92.727 55 4 0 4008 4062 508627285 508627339 3.430000e-11 80.5
47 TraesCS2D01G366800 chr7D 97.619 42 1 0 1 42 536662798 536662757 5.740000e-09 73.1
48 TraesCS2D01G366800 chr7D 93.617 47 2 1 3 49 124397431 124397476 7.430000e-08 69.4
49 TraesCS2D01G366800 chr7D 89.474 57 3 3 3 59 410979703 410979650 7.430000e-08 69.4
50 TraesCS2D01G366800 chr4D 97.619 42 1 0 1 42 426949431 426949390 5.740000e-09 73.1
51 TraesCS2D01G366800 chr4D 97.297 37 1 0 4 40 129046991 129047027 3.460000e-06 63.9


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 TraesCS2D01G366800 chr2D 471370487 471374628 4141 True 7649.000000 7649 100.000000 1 4142 1 chr2D.!!$R3 4141
1 TraesCS2D01G366800 chr2D 471448215 471451895 3680 True 503.000000 752 84.470250 444 3145 4 chr2D.!!$R4 2701
2 TraesCS2D01G366800 chr2D 471895545 471897451 1906 True 357.750000 688 86.398750 611 3145 4 chr2D.!!$R5 2534
3 TraesCS2D01G366800 chr2A 613035813 613039283 3470 True 1484.666667 2470 88.892667 509 4142 3 chr2A.!!$R1 3633
4 TraesCS2D01G366800 chr2A 613273022 613275401 2379 True 642.000000 874 85.618000 677 3140 3 chr2A.!!$R3 2463
5 TraesCS2D01G366800 chr2A 613173597 613177997 4400 True 445.250000 667 87.570500 140 3145 4 chr2A.!!$R2 3005
6 TraesCS2D01G366800 chr2B 550509906 550513170 3264 True 1783.500000 2204 87.356500 405 3501 2 chr2B.!!$R2 3096
7 TraesCS2D01G366800 chr2B 550995880 550998213 2333 True 869.500000 1051 82.966500 699 3145 2 chr2B.!!$R5 2446
8 TraesCS2D01G366800 chr2B 550718738 550721689 2951 True 630.250000 998 84.435000 42 3145 4 chr2B.!!$R3 3103
9 TraesCS2D01G366800 chr2B 550856820 550861569 4749 True 592.500000 942 88.745000 39 3145 4 chr2B.!!$R4 3106

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
31 32 0.107361 GCTACCCGTGGCCATTTACT 60.107 55.000 9.72 0.0 0.00 2.24 F
37 38 0.390603 CGTGGCCATTTACTCCGACA 60.391 55.000 9.72 0.0 0.00 4.35 F
1205 4336 0.463833 CCGGAGAATTTCGAAGGGGG 60.464 60.000 0.00 0.0 0.00 5.40 F
1468 4626 0.975556 GTGGGGTGGGGGCTAAATTG 60.976 60.000 0.00 0.0 0.00 2.32 F
1472 4630 1.035385 GGTGGGGGCTAAATTGTCCG 61.035 60.000 0.00 0.0 31.23 4.79 F
1662 4864 2.968574 TCTCACCTTCTTCAGAGCAAGT 59.031 45.455 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 4630 0.529378 CTGAAGCCCTGCAATTCACC 59.471 55.000 0.00 0.0 0.00 4.02 R
1922 5236 2.520260 GGTCTCCATGCCCATGCC 60.520 66.667 2.75 0.0 37.49 4.40 R
2487 7595 0.536006 GGTCAGCACAGCCAAGAACT 60.536 55.000 0.00 0.0 0.00 3.01 R
2494 7606 0.610232 AATTCTGGGTCAGCACAGCC 60.610 55.000 0.00 0.0 45.49 4.85 R
2495 7607 0.807496 GAATTCTGGGTCAGCACAGC 59.193 55.000 0.00 0.0 45.49 4.40 R
3160 8318 0.835971 TTAGCCTGCTGTCTCACCCA 60.836 55.000 0.97 0.0 0.00 4.51 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
19 20 2.412421 GTAGTCGGTTATGCTACCCG 57.588 55.000 0.00 0.00 43.03 5.28
20 21 1.678101 GTAGTCGGTTATGCTACCCGT 59.322 52.381 0.00 0.00 42.30 5.28
21 22 0.458669 AGTCGGTTATGCTACCCGTG 59.541 55.000 0.00 0.00 42.30 4.94
22 23 0.529119 GTCGGTTATGCTACCCGTGG 60.529 60.000 0.00 0.00 42.30 4.94
23 24 1.885850 CGGTTATGCTACCCGTGGC 60.886 63.158 0.00 0.00 37.00 5.01
24 25 1.525306 GGTTATGCTACCCGTGGCC 60.525 63.158 0.00 0.00 36.12 5.36
25 26 1.222387 GTTATGCTACCCGTGGCCA 59.778 57.895 0.00 0.00 36.12 5.36
26 27 0.179029 GTTATGCTACCCGTGGCCAT 60.179 55.000 9.72 0.00 36.12 4.40
27 28 0.548989 TTATGCTACCCGTGGCCATT 59.451 50.000 9.72 0.00 36.12 3.16
28 29 0.548989 TATGCTACCCGTGGCCATTT 59.451 50.000 9.72 0.00 36.12 2.32
29 30 0.548989 ATGCTACCCGTGGCCATTTA 59.451 50.000 9.72 0.00 36.12 1.40
30 31 0.393267 TGCTACCCGTGGCCATTTAC 60.393 55.000 9.72 0.00 36.12 2.01
31 32 0.107361 GCTACCCGTGGCCATTTACT 60.107 55.000 9.72 0.00 0.00 2.24
32 33 1.949465 CTACCCGTGGCCATTTACTC 58.051 55.000 9.72 0.00 0.00 2.59
33 34 0.542805 TACCCGTGGCCATTTACTCC 59.457 55.000 9.72 0.00 0.00 3.85
34 35 1.817941 CCCGTGGCCATTTACTCCG 60.818 63.158 9.72 5.55 0.00 4.63
35 36 1.219664 CCGTGGCCATTTACTCCGA 59.780 57.895 9.72 0.00 0.00 4.55
36 37 1.087771 CCGTGGCCATTTACTCCGAC 61.088 60.000 9.72 0.00 0.00 4.79
37 38 0.390603 CGTGGCCATTTACTCCGACA 60.391 55.000 9.72 0.00 0.00 4.35
84 85 7.068702 TCATTATGTTCCTAGCCCAATTCATT 58.931 34.615 0.00 0.00 0.00 2.57
91 92 5.579047 TCCTAGCCCAATTCATTTTGAAGA 58.421 37.500 0.00 0.00 40.05 2.87
94 95 7.016072 TCCTAGCCCAATTCATTTTGAAGAAAA 59.984 33.333 0.00 0.00 40.05 2.29
115 116 8.946085 AGAAAATGAAATATCACTGCGACTAAA 58.054 29.630 0.00 0.00 38.69 1.85
127 128 6.537301 TCACTGCGACTAAATATAAAAGTGGG 59.463 38.462 0.00 0.00 34.64 4.61
128 129 5.296035 ACTGCGACTAAATATAAAAGTGGGC 59.704 40.000 0.00 0.00 0.00 5.36
130 131 6.584488 TGCGACTAAATATAAAAGTGGGCTA 58.416 36.000 0.00 0.00 0.00 3.93
198 199 6.922957 TGAACATCACCTTTCTAACAAATTGC 59.077 34.615 0.00 0.00 0.00 3.56
245 248 5.289917 GCTTTTAAACTTGGTTTTCGCAGAA 59.710 36.000 0.99 0.00 45.90 3.02
274 1566 9.981114 CTTTTTATTGTAACTTGGTTTCCATCT 57.019 29.630 0.00 0.00 31.53 2.90
286 1578 6.834168 TGGTTTCCATCTGATACTTTTTCC 57.166 37.500 0.00 0.00 0.00 3.13
305 1597 6.478512 TTTCCTTTTTAAGTTGCCATCAGT 57.521 33.333 0.00 0.00 0.00 3.41
312 1604 5.689383 TTAAGTTGCCATCAGTCACTTTC 57.311 39.130 0.00 0.00 0.00 2.62
313 1605 3.498774 AGTTGCCATCAGTCACTTTCT 57.501 42.857 0.00 0.00 0.00 2.52
348 1642 3.386402 AGCAGTAGGGAAGCTCTACAATC 59.614 47.826 12.22 0.00 39.48 2.67
439 1735 9.672086 GTGCTAACAAGTAAATGAACACATTAA 57.328 29.630 0.00 0.00 34.38 1.40
498 1810 0.747852 GGTCACCTAGCTAGCTGTCC 59.252 60.000 27.68 14.81 0.00 4.02
552 1867 3.810386 GCTTACCTTCCATAGCTAACAGC 59.190 47.826 0.00 0.00 42.84 4.40
605 1923 5.193679 GCAGGACTTATAATTGGGTGTCTT 58.806 41.667 0.00 0.00 0.00 3.01
610 1928 6.318900 GGACTTATAATTGGGTGTCTTGAAGG 59.681 42.308 0.00 0.00 0.00 3.46
716 3602 7.148639 GCATTGCAGAAATTAATGGATATGCTG 60.149 37.037 3.15 3.49 33.24 4.41
717 3603 6.964807 TGCAGAAATTAATGGATATGCTGT 57.035 33.333 13.51 0.00 33.68 4.40
718 3604 6.973843 TGCAGAAATTAATGGATATGCTGTC 58.026 36.000 13.51 1.06 33.68 3.51
719 3605 6.774170 TGCAGAAATTAATGGATATGCTGTCT 59.226 34.615 13.51 0.00 33.68 3.41
720 3606 7.040892 TGCAGAAATTAATGGATATGCTGTCTC 60.041 37.037 13.51 0.00 33.68 3.36
721 3607 7.040892 GCAGAAATTAATGGATATGCTGTCTCA 60.041 37.037 7.94 0.00 0.00 3.27
722 3608 8.843262 CAGAAATTAATGGATATGCTGTCTCAA 58.157 33.333 0.00 0.00 0.00 3.02
810 3849 2.170166 GGCCAACAACTCATCATTGGA 58.830 47.619 0.00 0.00 43.66 3.53
1205 4336 0.463833 CCGGAGAATTTCGAAGGGGG 60.464 60.000 0.00 0.00 0.00 5.40
1220 4351 1.923148 AGGGGGATCGGACAGATTTTT 59.077 47.619 0.00 0.00 40.26 1.94
1308 4442 1.798735 CCGAGGCTCTGCAAATGTG 59.201 57.895 13.50 0.00 0.00 3.21
1468 4626 0.975556 GTGGGGTGGGGGCTAAATTG 60.976 60.000 0.00 0.00 0.00 2.32
1472 4630 1.035385 GGTGGGGGCTAAATTGTCCG 61.035 60.000 0.00 0.00 31.23 4.79
1650 4817 4.614535 GCACACATCACAATTCTCACCTTC 60.615 45.833 0.00 0.00 0.00 3.46
1652 4819 5.240183 CACACATCACAATTCTCACCTTCTT 59.760 40.000 0.00 0.00 0.00 2.52
1655 4822 5.704515 ACATCACAATTCTCACCTTCTTCAG 59.295 40.000 0.00 0.00 0.00 3.02
1656 4823 5.551305 TCACAATTCTCACCTTCTTCAGA 57.449 39.130 0.00 0.00 0.00 3.27
1662 4864 2.968574 TCTCACCTTCTTCAGAGCAAGT 59.031 45.455 0.00 0.00 0.00 3.16
1664 4866 4.774726 TCTCACCTTCTTCAGAGCAAGTAT 59.225 41.667 0.00 0.00 0.00 2.12
1672 4874 5.641709 TCTTCAGAGCAAGTATAACGTCAG 58.358 41.667 0.00 0.00 0.00 3.51
1894 5206 3.504520 GGGAAAGAAAACGTATTGCTGGA 59.495 43.478 0.00 0.00 0.00 3.86
1922 5236 5.535333 ACAAAAGGAAATGCTGATGTCTTG 58.465 37.500 0.00 0.00 0.00 3.02
1923 5237 4.796038 AAAGGAAATGCTGATGTCTTGG 57.204 40.909 0.00 0.00 0.00 3.61
2204 6060 5.476945 AGCTGGTTTTATCATTTCCGTTTCT 59.523 36.000 0.00 0.00 0.00 2.52
2335 6365 3.152341 GAGACCAATGGGCAATGATAGG 58.848 50.000 8.33 0.00 37.90 2.57
2363 6393 5.475909 ACAGATGCTTTGACATTGACAATCT 59.524 36.000 0.00 0.69 0.00 2.40
2410 6440 5.798132 TGCTACAAGTCTCTGACAATCATT 58.202 37.500 0.46 0.00 34.60 2.57
2437 7545 7.908827 TTATTTATTGGAGCGACTGTACAAA 57.091 32.000 0.00 0.00 0.00 2.83
2438 7546 8.500753 TTATTTATTGGAGCGACTGTACAAAT 57.499 30.769 0.00 0.00 0.00 2.32
2439 7547 9.602568 TTATTTATTGGAGCGACTGTACAAATA 57.397 29.630 0.00 0.00 0.00 1.40
2440 7548 6.897259 TTATTGGAGCGACTGTACAAATAC 57.103 37.500 0.00 0.00 0.00 1.89
2441 7549 3.945981 TGGAGCGACTGTACAAATACA 57.054 42.857 0.00 0.00 39.06 2.29
2442 7550 4.260139 TGGAGCGACTGTACAAATACAA 57.740 40.909 0.00 0.00 40.84 2.41
2446 7554 5.808540 GGAGCGACTGTACAAATACAATACA 59.191 40.000 0.00 0.00 40.84 2.29
2447 7555 6.311935 GGAGCGACTGTACAAATACAATACAA 59.688 38.462 0.00 0.00 40.84 2.41
2465 7573 8.832521 ACAATACAACGAGATTAAAACACAAGA 58.167 29.630 0.00 0.00 0.00 3.02
2492 7604 8.721133 AAAATAACCTGGGTTTGATTAGTTCT 57.279 30.769 10.42 0.00 39.31 3.01
2494 7606 7.703058 ATAACCTGGGTTTGATTAGTTCTTG 57.297 36.000 10.42 0.00 39.31 3.02
2495 7607 4.407365 ACCTGGGTTTGATTAGTTCTTGG 58.593 43.478 0.00 0.00 0.00 3.61
2498 7610 3.826157 TGGGTTTGATTAGTTCTTGGCTG 59.174 43.478 0.00 0.00 0.00 4.85
2507 7619 1.228245 TTCTTGGCTGTGCTGACCC 60.228 57.895 0.00 0.00 0.00 4.46
2509 7621 1.970114 CTTGGCTGTGCTGACCCAG 60.970 63.158 0.00 0.00 34.12 4.45
2512 7624 1.001641 GGCTGTGCTGACCCAGAAT 60.002 57.895 0.00 0.00 32.44 2.40
2513 7625 0.610232 GGCTGTGCTGACCCAGAATT 60.610 55.000 0.00 0.00 32.44 2.17
2514 7626 0.807496 GCTGTGCTGACCCAGAATTC 59.193 55.000 0.00 0.00 32.44 2.17
2516 7628 2.082231 CTGTGCTGACCCAGAATTCAG 58.918 52.381 8.44 0.00 41.96 3.02
2517 7629 1.699083 TGTGCTGACCCAGAATTCAGA 59.301 47.619 8.44 0.00 41.65 3.27
2518 7630 2.289882 TGTGCTGACCCAGAATTCAGAG 60.290 50.000 8.44 0.00 41.65 3.35
2521 7633 2.679349 GCTGACCCAGAATTCAGAGTCC 60.679 54.545 8.44 0.00 41.65 3.85
2523 7635 2.978978 TGACCCAGAATTCAGAGTCCAA 59.021 45.455 8.44 0.00 0.00 3.53
2524 7636 3.394274 TGACCCAGAATTCAGAGTCCAAA 59.606 43.478 8.44 0.00 0.00 3.28
2525 7637 4.043310 TGACCCAGAATTCAGAGTCCAAAT 59.957 41.667 8.44 0.00 0.00 2.32
2526 7638 5.003096 ACCCAGAATTCAGAGTCCAAATT 57.997 39.130 8.44 1.08 0.00 1.82
2527 7639 6.139679 ACCCAGAATTCAGAGTCCAAATTA 57.860 37.500 8.44 0.00 0.00 1.40
2528 7640 5.946377 ACCCAGAATTCAGAGTCCAAATTAC 59.054 40.000 8.44 0.00 0.00 1.89
2529 7641 5.358160 CCCAGAATTCAGAGTCCAAATTACC 59.642 44.000 8.44 0.00 0.00 2.85
2531 7643 6.317391 CCAGAATTCAGAGTCCAAATTACCTC 59.683 42.308 8.44 0.00 0.00 3.85
2532 7644 6.881065 CAGAATTCAGAGTCCAAATTACCTCA 59.119 38.462 8.44 0.00 0.00 3.86
2533 7645 7.555554 CAGAATTCAGAGTCCAAATTACCTCAT 59.444 37.037 8.44 0.00 0.00 2.90
2534 7646 7.555554 AGAATTCAGAGTCCAAATTACCTCATG 59.444 37.037 8.44 0.00 0.00 3.07
2559 7672 4.890158 TGCTTCTCTAACATGGTGAGAA 57.110 40.909 18.50 18.50 42.37 2.87
3251 8433 2.621526 AGGTGTTTGATTCGTTGTTCCC 59.378 45.455 0.00 0.00 0.00 3.97
3325 8507 3.497118 TCTTTTTGCGGATAATTGTGCG 58.503 40.909 11.67 11.67 35.93 5.34
3334 8516 3.789224 CGGATAATTGTGCGGTTTTAAGC 59.211 43.478 8.22 0.00 0.00 3.09
3337 8547 6.557110 GGATAATTGTGCGGTTTTAAGCTTA 58.443 36.000 0.86 0.86 0.00 3.09
3338 8548 6.691388 GGATAATTGTGCGGTTTTAAGCTTAG 59.309 38.462 6.24 0.00 0.00 2.18
3339 8549 2.981400 TGTGCGGTTTTAAGCTTAGC 57.019 45.000 6.24 6.97 0.00 3.09
3340 8550 1.195900 TGTGCGGTTTTAAGCTTAGCG 59.804 47.619 13.50 13.50 36.02 4.26
3341 8551 1.196127 GTGCGGTTTTAAGCTTAGCGT 59.804 47.619 17.64 0.00 35.43 5.07
3344 8554 2.412770 GCGGTTTTAAGCTTAGCGTGTA 59.587 45.455 17.64 0.00 35.43 2.90
3352 8562 4.500603 AAGCTTAGCGTGTATAGCGTAT 57.499 40.909 0.00 0.00 38.62 3.06
3376 8586 5.668558 AAGCGTTGATTTTCTTCGTAAGT 57.331 34.783 0.00 0.00 39.48 2.24
3377 8587 5.668558 AGCGTTGATTTTCTTCGTAAGTT 57.331 34.783 0.00 0.00 39.48 2.66
3380 8590 7.632721 AGCGTTGATTTTCTTCGTAAGTTTTA 58.367 30.769 0.00 0.00 39.48 1.52
3381 8591 8.124199 AGCGTTGATTTTCTTCGTAAGTTTTAA 58.876 29.630 0.00 0.00 39.48 1.52
3382 8592 8.407458 GCGTTGATTTTCTTCGTAAGTTTTAAG 58.593 33.333 0.00 0.00 39.48 1.85
3383 8593 8.407458 CGTTGATTTTCTTCGTAAGTTTTAAGC 58.593 33.333 0.00 0.00 39.48 3.09
3384 8594 9.447040 GTTGATTTTCTTCGTAAGTTTTAAGCT 57.553 29.630 0.00 0.00 39.48 3.74
3415 8625 0.612732 TGGTCCCGGAGAACGTGTAT 60.613 55.000 0.73 0.00 42.24 2.29
3416 8626 1.340893 TGGTCCCGGAGAACGTGTATA 60.341 52.381 0.73 0.00 42.24 1.47
3417 8627 1.066152 GGTCCCGGAGAACGTGTATAC 59.934 57.143 0.73 0.00 42.24 1.47
3506 8726 6.115446 GGTGTCTGAATTTCTACATCATGGA 58.885 40.000 9.48 0.00 0.00 3.41
3524 8744 2.701951 TGGAACCTCGAGTTGTTAAGGT 59.298 45.455 12.31 0.00 43.96 3.50
3547 8767 1.226802 CGTGGAGGCTGATGTCTCG 60.227 63.158 0.00 0.00 45.33 4.04
3656 8883 6.713762 AAAACATTGACCTCACATCAAAGA 57.286 33.333 0.00 0.00 39.43 2.52
3657 8884 6.713762 AAACATTGACCTCACATCAAAGAA 57.286 33.333 0.00 0.00 39.43 2.52
3658 8885 6.713762 AACATTGACCTCACATCAAAGAAA 57.286 33.333 0.00 0.00 39.43 2.52
3659 8886 6.906157 ACATTGACCTCACATCAAAGAAAT 57.094 33.333 0.00 0.00 39.43 2.17
3660 8887 8.408043 AACATTGACCTCACATCAAAGAAATA 57.592 30.769 0.00 0.00 39.43 1.40
3661 8888 7.820648 ACATTGACCTCACATCAAAGAAATAC 58.179 34.615 0.00 0.00 39.43 1.89
3662 8889 7.448161 ACATTGACCTCACATCAAAGAAATACA 59.552 33.333 0.00 0.00 39.43 2.29
3663 8890 6.801539 TGACCTCACATCAAAGAAATACAC 57.198 37.500 0.00 0.00 0.00 2.90
3664 8891 6.295249 TGACCTCACATCAAAGAAATACACA 58.705 36.000 0.00 0.00 0.00 3.72
3665 8892 6.942005 TGACCTCACATCAAAGAAATACACAT 59.058 34.615 0.00 0.00 0.00 3.21
3666 8893 8.100164 TGACCTCACATCAAAGAAATACACATA 58.900 33.333 0.00 0.00 0.00 2.29
3667 8894 8.862325 ACCTCACATCAAAGAAATACACATAA 57.138 30.769 0.00 0.00 0.00 1.90
3668 8895 9.466497 ACCTCACATCAAAGAAATACACATAAT 57.534 29.630 0.00 0.00 0.00 1.28
3703 8930 7.381139 GGCGGGTGAAAAATACACATAATATTG 59.619 37.037 0.00 0.00 39.65 1.90
3749 8976 9.194972 TCATTAAATCATAAGGTGTTATTGGCA 57.805 29.630 0.00 0.00 0.00 4.92
3793 9021 3.264450 CCTCAAGGTTAGGTGTTCATCCT 59.736 47.826 0.00 0.00 38.91 3.24
3794 9022 4.263506 CCTCAAGGTTAGGTGTTCATCCTT 60.264 45.833 0.00 0.00 36.60 3.36
3797 9025 5.546499 TCAAGGTTAGGTGTTCATCCTTAGT 59.454 40.000 0.00 0.00 36.60 2.24
3831 9059 3.680777 TTTTGAATATCCCCCTCCCAC 57.319 47.619 0.00 0.00 0.00 4.61
3832 9060 2.605825 TTGAATATCCCCCTCCCACT 57.394 50.000 0.00 0.00 0.00 4.00
3833 9061 2.605825 TGAATATCCCCCTCCCACTT 57.394 50.000 0.00 0.00 0.00 3.16
3862 9090 9.974980 TTTTTACTAAAAGACCAATAAGGCAAG 57.025 29.630 0.00 0.00 43.14 4.01
3864 9092 9.528489 TTTACTAAAAGACCAATAAGGCAAGAT 57.472 29.630 0.00 0.00 43.14 2.40
3865 9093 7.396540 ACTAAAAGACCAATAAGGCAAGATG 57.603 36.000 0.00 0.00 43.14 2.90
3866 9094 4.725790 AAAGACCAATAAGGCAAGATGC 57.274 40.909 0.00 0.00 43.14 3.91
3880 9122 1.534729 AGATGCCGTTCCTGGTTTTC 58.465 50.000 0.00 0.00 0.00 2.29
3882 9124 0.112412 ATGCCGTTCCTGGTTTTCCT 59.888 50.000 0.00 0.00 41.38 3.36
3896 9138 0.672401 TTTCCTGGTCGAATCGGTGC 60.672 55.000 1.76 0.00 0.00 5.01
3927 9169 8.553696 GTCTCGTTTTTAAAACTATGGTCTCAA 58.446 33.333 16.96 0.00 0.00 3.02
3939 9181 1.374758 GTCTCAACAGACCTGGCCG 60.375 63.158 0.00 0.00 43.14 6.13
3973 9215 2.763651 GCCTAGGGCTAAACGTGTG 58.236 57.895 11.72 0.00 46.69 3.82
3975 9217 1.609841 GCCTAGGGCTAAACGTGTGTT 60.610 52.381 11.72 0.00 46.69 3.32
3977 9219 2.073816 CTAGGGCTAAACGTGTGTTGG 58.926 52.381 0.00 0.00 38.62 3.77
3978 9220 0.470766 AGGGCTAAACGTGTGTTGGA 59.529 50.000 0.00 0.00 38.62 3.53
3988 9230 0.390209 GTGTGTTGGAATGGCATGGC 60.390 55.000 13.29 13.29 0.00 4.40
4017 9259 1.080569 ACGTTTAGTACACGGGCCG 60.081 57.895 27.06 27.06 42.14 6.13
4068 9310 2.031919 CCAGGCACGGCACTACAA 59.968 61.111 0.00 0.00 0.00 2.41
4079 9321 2.870411 CGGCACTACAAGTAAATAGGCC 59.130 50.000 0.00 0.00 34.21 5.19
4107 9349 2.800736 CATGTTTAGCCCGCCAGC 59.199 61.111 0.00 0.00 0.00 4.85
4108 9350 2.824041 ATGTTTAGCCCGCCAGCG 60.824 61.111 4.75 4.75 38.01 5.18
4109 9351 3.622060 ATGTTTAGCCCGCCAGCGT 62.622 57.895 11.55 0.00 38.01 5.07
4131 9373 3.004629 TGCGCATTATTCAGCCTATTTGG 59.995 43.478 5.66 0.00 39.35 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.179029 ATGGCCACGGGTAGCATAAC 60.179 55.000 8.16 0.00 0.00 1.89
8 9 0.548989 AATGGCCACGGGTAGCATAA 59.451 50.000 8.16 0.00 0.00 1.90
9 10 0.548989 AAATGGCCACGGGTAGCATA 59.451 50.000 8.16 0.00 0.00 3.14
10 11 0.548989 TAAATGGCCACGGGTAGCAT 59.451 50.000 8.16 0.00 0.00 3.79
11 12 0.393267 GTAAATGGCCACGGGTAGCA 60.393 55.000 8.16 0.00 0.00 3.49
12 13 0.107361 AGTAAATGGCCACGGGTAGC 60.107 55.000 8.16 0.00 0.00 3.58
13 14 1.474498 GGAGTAAATGGCCACGGGTAG 60.474 57.143 8.16 0.00 0.00 3.18
14 15 0.542805 GGAGTAAATGGCCACGGGTA 59.457 55.000 8.16 0.00 0.00 3.69
15 16 1.301954 GGAGTAAATGGCCACGGGT 59.698 57.895 8.16 0.00 0.00 5.28
16 17 1.817941 CGGAGTAAATGGCCACGGG 60.818 63.158 8.16 0.00 0.00 5.28
17 18 1.087771 GTCGGAGTAAATGGCCACGG 61.088 60.000 8.16 0.00 0.00 4.94
18 19 0.390603 TGTCGGAGTAAATGGCCACG 60.391 55.000 8.16 5.22 0.00 4.94
19 20 1.816074 TTGTCGGAGTAAATGGCCAC 58.184 50.000 8.16 0.00 0.00 5.01
20 21 2.364632 CATTGTCGGAGTAAATGGCCA 58.635 47.619 8.56 8.56 31.40 5.36
21 22 1.676006 CCATTGTCGGAGTAAATGGCC 59.324 52.381 11.82 0.00 41.63 5.36
24 25 4.442706 AGCTACCATTGTCGGAGTAAATG 58.557 43.478 0.00 0.00 33.53 2.32
25 26 4.755266 AGCTACCATTGTCGGAGTAAAT 57.245 40.909 0.00 0.00 0.00 1.40
26 27 4.546829 AAGCTACCATTGTCGGAGTAAA 57.453 40.909 0.00 0.00 0.00 2.01
27 28 4.546829 AAAGCTACCATTGTCGGAGTAA 57.453 40.909 0.00 0.00 0.00 2.24
28 29 4.250464 CAAAAGCTACCATTGTCGGAGTA 58.750 43.478 0.00 0.00 0.00 2.59
29 30 3.074412 CAAAAGCTACCATTGTCGGAGT 58.926 45.455 0.00 0.00 0.00 3.85
30 31 2.159517 GCAAAAGCTACCATTGTCGGAG 60.160 50.000 0.00 0.00 0.00 4.63
31 32 1.810151 GCAAAAGCTACCATTGTCGGA 59.190 47.619 0.00 0.00 0.00 4.55
32 33 1.539388 TGCAAAAGCTACCATTGTCGG 59.461 47.619 0.00 0.00 0.00 4.79
33 34 2.987413 TGCAAAAGCTACCATTGTCG 57.013 45.000 0.00 0.00 0.00 4.35
34 35 6.563422 TCATAATGCAAAAGCTACCATTGTC 58.437 36.000 0.00 2.32 0.00 3.18
35 36 6.528537 TCATAATGCAAAAGCTACCATTGT 57.471 33.333 0.00 3.09 0.00 2.71
36 37 7.204604 TGATCATAATGCAAAAGCTACCATTG 58.795 34.615 0.00 4.83 0.00 2.82
37 38 7.350744 TGATCATAATGCAAAAGCTACCATT 57.649 32.000 0.00 0.00 0.00 3.16
84 85 8.296000 TCGCAGTGATATTTCATTTTCTTCAAA 58.704 29.630 0.00 0.00 33.56 2.69
105 106 5.527582 AGCCCACTTTTATATTTAGTCGCAG 59.472 40.000 0.00 0.00 0.00 5.18
108 109 9.754382 TTAGTAGCCCACTTTTATATTTAGTCG 57.246 33.333 0.00 0.00 38.80 4.18
230 231 6.588348 AAAAAGAATTCTGCGAAAACCAAG 57.412 33.333 9.17 0.00 0.00 3.61
240 243 9.476202 ACCAAGTTACAATAAAAAGAATTCTGC 57.524 29.630 9.17 0.00 0.00 4.26
274 1566 8.478877 TGGCAACTTAAAAAGGAAAAAGTATCA 58.521 29.630 0.00 0.00 32.09 2.15
286 1578 6.076981 AGTGACTGATGGCAACTTAAAAAG 57.923 37.500 0.00 0.00 37.61 2.27
292 1584 3.825328 AGAAAGTGACTGATGGCAACTT 58.175 40.909 0.00 0.00 37.61 2.66
305 1597 8.928448 ACTGCTTCCATAATCTATAGAAAGTGA 58.072 33.333 6.52 0.00 0.00 3.41
312 1604 7.962995 TCCCTACTGCTTCCATAATCTATAG 57.037 40.000 0.00 0.00 0.00 1.31
313 1605 7.093289 GCTTCCCTACTGCTTCCATAATCTATA 60.093 40.741 0.00 0.00 0.00 1.31
378 1673 9.794685 GGAACAATCAAAGAGAAATAAGATTCC 57.205 33.333 0.00 0.00 0.00 3.01
457 1761 0.039617 TGTAATTGCGTGGCTTGCAC 60.040 50.000 3.73 0.00 43.10 4.57
498 1810 9.533253 ACAATTTTAGTTGATCTTTGTTTCAGG 57.467 29.630 0.00 0.00 33.37 3.86
552 1867 6.765989 TGTGTCCTTTAATAATTCTCCATCCG 59.234 38.462 0.00 0.00 0.00 4.18
605 1923 7.889873 TTGTAGAAAGAAAAATCCACCTTCA 57.110 32.000 0.00 0.00 0.00 3.02
610 1928 9.143631 CATGGAATTGTAGAAAGAAAAATCCAC 57.856 33.333 0.00 0.00 0.00 4.02
716 3602 7.251704 TCACAAACTCTTTGAGATTTGAGAC 57.748 36.000 19.20 0.00 43.26 3.36
717 3603 7.716560 TGATCACAAACTCTTTGAGATTTGAGA 59.283 33.333 19.20 17.56 46.25 3.27
718 3604 7.802251 GTGATCACAAACTCTTTGAGATTTGAG 59.198 37.037 21.07 14.76 46.25 3.02
719 3605 7.500227 AGTGATCACAAACTCTTTGAGATTTGA 59.500 33.333 27.02 12.60 46.25 2.69
720 3606 7.646314 AGTGATCACAAACTCTTTGAGATTTG 58.354 34.615 27.02 10.13 46.25 2.32
721 3607 7.814264 AGTGATCACAAACTCTTTGAGATTT 57.186 32.000 27.02 0.00 46.25 2.17
722 3608 8.908786 TTAGTGATCACAAACTCTTTGAGATT 57.091 30.769 27.02 3.65 46.25 2.40
810 3849 5.699097 GCTCTCCGTGAGACTTTATAGAT 57.301 43.478 6.83 0.00 45.39 1.98
1188 4319 2.807108 CGATCCCCCTTCGAAATTCTCC 60.807 54.545 0.00 0.00 38.88 3.71
1205 4336 6.370166 AGACAAGAAGAAAAATCTGTCCGATC 59.630 38.462 0.00 0.00 31.28 3.69
1220 4351 3.797039 CGGGAATGCATAGACAAGAAGA 58.203 45.455 0.00 0.00 0.00 2.87
1308 4442 4.821589 CTTCCCACGAGCCGAGGC 62.822 72.222 5.89 5.89 36.35 4.70
1468 4626 2.700773 GCCCTGCAATTCACCGGAC 61.701 63.158 9.46 0.00 0.00 4.79
1472 4630 0.529378 CTGAAGCCCTGCAATTCACC 59.471 55.000 0.00 0.00 0.00 4.02
1650 4817 4.266502 GCTGACGTTATACTTGCTCTGAAG 59.733 45.833 0.00 0.00 0.00 3.02
1652 4819 3.444034 AGCTGACGTTATACTTGCTCTGA 59.556 43.478 0.00 0.00 0.00 3.27
1655 4822 3.770666 TCAGCTGACGTTATACTTGCTC 58.229 45.455 13.74 0.00 0.00 4.26
1656 4823 3.868757 TCAGCTGACGTTATACTTGCT 57.131 42.857 13.74 0.00 0.00 3.91
1894 5206 5.070847 ACATCAGCATTTCCTTTTGTTTCCT 59.929 36.000 0.00 0.00 0.00 3.36
1922 5236 2.520260 GGTCTCCATGCCCATGCC 60.520 66.667 2.75 0.00 37.49 4.40
1923 5237 2.903855 CGGTCTCCATGCCCATGC 60.904 66.667 2.75 0.00 37.49 4.06
1954 5268 3.499737 CAGGCGTCGGCATCAACC 61.500 66.667 21.79 0.00 42.47 3.77
2204 6060 8.251026 CAGTACTAACTATGATCAAGGACACAA 58.749 37.037 8.98 0.00 33.48 3.33
2335 6365 5.048782 TGTCAATGTCAAAGCATCTGTTACC 60.049 40.000 0.00 0.00 0.00 2.85
2363 6393 3.259374 CAGCTACAAGTCTTCTCCCTTCA 59.741 47.826 0.00 0.00 0.00 3.02
2410 6440 6.874664 TGTACAGTCGCTCCAATAAATAAACA 59.125 34.615 0.00 0.00 0.00 2.83
2412 6442 7.908827 TTGTACAGTCGCTCCAATAAATAAA 57.091 32.000 0.00 0.00 0.00 1.40
2439 7547 8.832521 TCTTGTGTTTTAATCTCGTTGTATTGT 58.167 29.630 0.00 0.00 0.00 2.71
2440 7548 9.658475 TTCTTGTGTTTTAATCTCGTTGTATTG 57.342 29.630 0.00 0.00 0.00 1.90
2476 7584 3.826157 CAGCCAAGAACTAATCAAACCCA 59.174 43.478 0.00 0.00 0.00 4.51
2480 7588 4.022935 CAGCACAGCCAAGAACTAATCAAA 60.023 41.667 0.00 0.00 0.00 2.69
2481 7589 3.503363 CAGCACAGCCAAGAACTAATCAA 59.497 43.478 0.00 0.00 0.00 2.57
2483 7591 3.126000 GTCAGCACAGCCAAGAACTAATC 59.874 47.826 0.00 0.00 0.00 1.75
2484 7592 3.077359 GTCAGCACAGCCAAGAACTAAT 58.923 45.455 0.00 0.00 0.00 1.73
2485 7593 2.494059 GTCAGCACAGCCAAGAACTAA 58.506 47.619 0.00 0.00 0.00 2.24
2486 7594 1.270839 GGTCAGCACAGCCAAGAACTA 60.271 52.381 0.00 0.00 0.00 2.24
2487 7595 0.536006 GGTCAGCACAGCCAAGAACT 60.536 55.000 0.00 0.00 0.00 3.01
2488 7596 1.518903 GGGTCAGCACAGCCAAGAAC 61.519 60.000 0.00 0.00 33.76 3.01
2492 7604 1.993701 TTCTGGGTCAGCACAGCCAA 61.994 55.000 7.21 0.00 45.49 4.52
2494 7606 0.610232 AATTCTGGGTCAGCACAGCC 60.610 55.000 0.00 0.00 45.49 4.85
2495 7607 0.807496 GAATTCTGGGTCAGCACAGC 59.193 55.000 0.00 0.00 45.49 4.40
2498 7610 2.289945 ACTCTGAATTCTGGGTCAGCAC 60.290 50.000 11.78 0.00 40.93 4.40
2507 7619 6.881065 TGAGGTAATTTGGACTCTGAATTCTG 59.119 38.462 7.05 6.50 0.00 3.02
2509 7621 7.201767 CCATGAGGTAATTTGGACTCTGAATTC 60.202 40.741 0.00 0.00 0.00 2.17
2512 7624 5.500234 CCATGAGGTAATTTGGACTCTGAA 58.500 41.667 0.00 0.00 0.00 3.02
2513 7625 5.102953 CCATGAGGTAATTTGGACTCTGA 57.897 43.478 0.00 0.00 0.00 3.27
2528 7640 4.326826 TGTTAGAGAAGCAAACCATGAGG 58.673 43.478 0.00 0.00 42.21 3.86
2529 7641 5.163683 CCATGTTAGAGAAGCAAACCATGAG 60.164 44.000 0.00 0.00 0.00 2.90
2531 7643 4.460382 ACCATGTTAGAGAAGCAAACCATG 59.540 41.667 0.00 0.00 0.00 3.66
2532 7644 4.460382 CACCATGTTAGAGAAGCAAACCAT 59.540 41.667 0.00 0.00 0.00 3.55
2533 7645 3.820467 CACCATGTTAGAGAAGCAAACCA 59.180 43.478 0.00 0.00 0.00 3.67
2534 7646 4.072131 TCACCATGTTAGAGAAGCAAACC 58.928 43.478 0.00 0.00 0.00 3.27
2571 7686 1.107114 CTATCTGAGACCACCTGCGT 58.893 55.000 0.00 0.00 0.00 5.24
3157 8315 2.047844 CTGCTGTCTCACCCACGG 60.048 66.667 0.00 0.00 0.00 4.94
3160 8318 0.835971 TTAGCCTGCTGTCTCACCCA 60.836 55.000 0.97 0.00 0.00 4.51
3251 8433 2.744787 GGCACGATGATTTACAGCAG 57.255 50.000 0.00 0.00 34.21 4.24
3298 8480 7.625553 CACAATTATCCGCAAAAAGAACAAAA 58.374 30.769 0.00 0.00 0.00 2.44
3302 8484 4.201485 CGCACAATTATCCGCAAAAAGAAC 60.201 41.667 0.00 0.00 0.00 3.01
3325 8507 5.555818 CGCTATACACGCTAAGCTTAAAACC 60.556 44.000 7.74 0.00 32.73 3.27
3334 8516 5.002282 CGCTTTATACGCTATACACGCTAAG 59.998 44.000 0.00 0.00 0.00 2.18
3337 8547 3.231965 CGCTTTATACGCTATACACGCT 58.768 45.455 0.00 0.00 0.00 5.07
3338 8548 2.975851 ACGCTTTATACGCTATACACGC 59.024 45.455 0.00 0.00 0.00 5.34
3339 8549 4.671964 TCAACGCTTTATACGCTATACACG 59.328 41.667 0.00 0.00 0.00 4.49
3340 8550 6.686130 ATCAACGCTTTATACGCTATACAC 57.314 37.500 0.00 0.00 0.00 2.90
3341 8551 7.703298 AAATCAACGCTTTATACGCTATACA 57.297 32.000 0.00 0.00 0.00 2.29
3344 8554 7.478520 AGAAAATCAACGCTTTATACGCTAT 57.521 32.000 0.00 0.00 0.00 2.97
3352 8562 7.181143 ACTTACGAAGAAAATCAACGCTTTA 57.819 32.000 0.00 0.00 0.00 1.85
3376 8586 1.280998 AGAGCGGGGCTAAGCTTAAAA 59.719 47.619 7.74 0.00 44.69 1.52
3377 8587 0.909623 AGAGCGGGGCTAAGCTTAAA 59.090 50.000 7.74 0.00 44.69 1.52
3380 8590 2.586792 CAGAGCGGGGCTAAGCTT 59.413 61.111 3.48 3.48 44.69 3.74
3382 8592 3.741830 GACCAGAGCGGGGCTAAGC 62.742 68.421 0.00 0.00 39.88 3.09
3383 8593 2.501610 GACCAGAGCGGGGCTAAG 59.498 66.667 0.00 0.00 39.88 2.18
3384 8594 3.081409 GGACCAGAGCGGGGCTAA 61.081 66.667 0.00 0.00 39.88 3.09
3415 8625 7.286087 TCTGCCCTCGTTATTATTTCTGTAGTA 59.714 37.037 0.00 0.00 0.00 1.82
3416 8626 6.097839 TCTGCCCTCGTTATTATTTCTGTAGT 59.902 38.462 0.00 0.00 0.00 2.73
3417 8627 6.513180 TCTGCCCTCGTTATTATTTCTGTAG 58.487 40.000 0.00 0.00 0.00 2.74
3506 8726 5.536260 GAAGTACCTTAACAACTCGAGGTT 58.464 41.667 18.41 14.20 42.30 3.50
3524 8744 1.476891 GACATCAGCCTCCACGAAGTA 59.523 52.381 0.00 0.00 41.61 2.24
3567 8787 2.357517 CGACAGGCTCAGCGGTTT 60.358 61.111 0.00 0.00 0.00 3.27
3577 8797 3.873361 GGTAAATACCTTAACCGACAGGC 59.127 47.826 2.27 0.00 43.10 4.85
3578 8798 4.114794 CGGTAAATACCTTAACCGACAGG 58.885 47.826 6.92 0.00 44.25 4.00
3628 8855 8.641499 TTGATGTGAGGTCAATGTTTTAAAAC 57.359 30.769 21.66 21.66 33.96 2.43
3632 8859 7.815840 TCTTTGATGTGAGGTCAATGTTTTA 57.184 32.000 0.00 0.00 35.68 1.52
3637 8864 7.752239 GTGTATTTCTTTGATGTGAGGTCAATG 59.248 37.037 0.00 0.00 35.68 2.82
3638 8865 7.448161 TGTGTATTTCTTTGATGTGAGGTCAAT 59.552 33.333 0.00 0.00 35.68 2.57
3672 8899 4.120589 GTGTATTTTTCACCCGCCAAAAA 58.879 39.130 0.00 0.00 36.25 1.94
3673 8900 3.132289 TGTGTATTTTTCACCCGCCAAAA 59.868 39.130 0.00 0.00 35.25 2.44
3674 8901 2.693591 TGTGTATTTTTCACCCGCCAAA 59.306 40.909 0.00 0.00 35.25 3.28
3675 8902 2.307768 TGTGTATTTTTCACCCGCCAA 58.692 42.857 0.00 0.00 35.25 4.52
3676 8903 1.982660 TGTGTATTTTTCACCCGCCA 58.017 45.000 0.00 0.00 35.25 5.69
3677 8904 4.705337 TTATGTGTATTTTTCACCCGCC 57.295 40.909 0.00 0.00 35.25 6.13
3678 8905 7.381139 CCAATATTATGTGTATTTTTCACCCGC 59.619 37.037 0.00 0.00 35.25 6.13
3679 8906 8.625651 TCCAATATTATGTGTATTTTTCACCCG 58.374 33.333 0.00 0.00 35.25 5.28
3723 8950 9.194972 TGCCAATAACACCTTATGATTTAATGA 57.805 29.630 0.00 0.00 0.00 2.57
3724 8951 9.985730 ATGCCAATAACACCTTATGATTTAATG 57.014 29.630 0.00 0.00 0.00 1.90
3727 8954 9.860650 ACTATGCCAATAACACCTTATGATTTA 57.139 29.630 0.00 0.00 0.00 1.40
3728 8955 8.766994 ACTATGCCAATAACACCTTATGATTT 57.233 30.769 0.00 0.00 0.00 2.17
3729 8956 8.632679 CAACTATGCCAATAACACCTTATGATT 58.367 33.333 0.00 0.00 0.00 2.57
3730 8957 7.231317 CCAACTATGCCAATAACACCTTATGAT 59.769 37.037 0.00 0.00 0.00 2.45
3741 8968 6.665680 ACACCAATAACCAACTATGCCAATAA 59.334 34.615 0.00 0.00 0.00 1.40
3815 9043 3.973472 AAAAGTGGGAGGGGGATATTC 57.027 47.619 0.00 0.00 0.00 1.75
3858 9086 1.244019 AACCAGGAACGGCATCTTGC 61.244 55.000 0.00 0.00 44.08 4.01
3860 9088 1.886542 GAAAACCAGGAACGGCATCTT 59.113 47.619 0.00 0.00 0.00 2.40
3861 9089 1.534729 GAAAACCAGGAACGGCATCT 58.465 50.000 0.00 0.00 0.00 2.90
3862 9090 0.526211 GGAAAACCAGGAACGGCATC 59.474 55.000 0.00 0.00 0.00 3.91
3864 9092 0.821711 CAGGAAAACCAGGAACGGCA 60.822 55.000 0.00 0.00 0.00 5.69
3865 9093 1.524008 CCAGGAAAACCAGGAACGGC 61.524 60.000 0.00 0.00 0.00 5.68
3866 9094 0.179001 ACCAGGAAAACCAGGAACGG 60.179 55.000 4.77 0.00 0.00 4.44
3867 9095 1.235724 GACCAGGAAAACCAGGAACG 58.764 55.000 4.77 0.00 0.00 3.95
3880 9122 1.519455 GAGCACCGATTCGACCAGG 60.519 63.158 7.83 0.00 0.00 4.45
3882 9124 2.577059 GGAGCACCGATTCGACCA 59.423 61.111 7.83 0.00 0.00 4.02
3896 9138 6.401796 CCATAGTTTTAAAAACGAGACCGGAG 60.402 42.308 9.46 0.00 40.78 4.63
3905 9147 8.339714 TCTGTTGAGACCATAGTTTTAAAAACG 58.660 33.333 1.31 0.00 0.00 3.60
3969 9211 0.390209 GCCATGCCATTCCAACACAC 60.390 55.000 0.00 0.00 0.00 3.82
3992 9234 1.336148 CGTGTACTAAACGTGCCCTCA 60.336 52.381 0.00 0.00 36.31 3.86
3996 9238 1.629345 GCCCGTGTACTAAACGTGCC 61.629 60.000 1.14 0.00 38.28 5.01
4065 9307 1.557832 TGAGCCGGCCTATTTACTTGT 59.442 47.619 26.15 0.00 0.00 3.16
4068 9310 0.468648 GGTGAGCCGGCCTATTTACT 59.531 55.000 26.15 0.00 0.00 2.24
4107 9349 1.217001 TAGGCTGAATAATGCGCACG 58.783 50.000 14.90 0.00 0.00 5.34
4108 9350 3.904136 AATAGGCTGAATAATGCGCAC 57.096 42.857 14.90 0.00 0.00 5.34
4109 9351 3.004629 CCAAATAGGCTGAATAATGCGCA 59.995 43.478 14.96 14.96 0.00 6.09
4111 9353 4.836125 ACCAAATAGGCTGAATAATGCG 57.164 40.909 0.00 0.00 43.14 4.73
4113 9355 8.658609 CAAAACAACCAAATAGGCTGAATAATG 58.341 33.333 0.00 0.00 43.14 1.90


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

AutoCloner maintained by Alex Coulton.