Multiple sequence alignment - TraesCS7A01G141800

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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 TraesCS7A01G141800 chr7A 100.000 6145 0 0 1 6145 93071718 93077862 0.000000e+00 11348.0
1 TraesCS7A01G141800 chr7A 93.150 1270 81 5 2384 3651 192670772 192669507 0.000000e+00 1858.0
2 TraesCS7A01G141800 chr7A 85.227 1523 141 33 3701 5192 192669412 192667943 0.000000e+00 1489.0
3 TraesCS7A01G141800 chr7A 84.709 654 69 19 990 1624 192672668 192672027 5.230000e-175 625.0
4 TraesCS7A01G141800 chr7A 79.578 759 105 30 1103 1849 192818377 192817657 1.190000e-136 497.0
5 TraesCS7A01G141800 chr7A 87.097 186 23 1 2144 2328 192671088 192670903 6.240000e-50 209.0
6 TraesCS7A01G141800 chr7A 86.957 161 16 3 5269 5426 192667760 192667602 6.330000e-40 176.0
7 TraesCS7A01G141800 chr7A 80.000 235 23 15 1696 1927 192671860 192671647 1.070000e-32 152.0
8 TraesCS7A01G141800 chr7A 96.970 33 1 0 1604 1636 192817840 192817808 8.600000e-04 56.5
9 TraesCS7A01G141800 chr7B 93.214 2682 139 26 975 3638 43883170 43880514 0.000000e+00 3904.0
10 TraesCS7A01G141800 chr7B 91.288 1561 80 22 4630 6145 43879804 43878255 0.000000e+00 2078.0
11 TraesCS7A01G141800 chr7B 93.168 1288 81 7 2366 3651 327275896 327274614 0.000000e+00 1884.0
12 TraesCS7A01G141800 chr7B 85.649 1533 144 35 3701 5206 327274540 327273057 0.000000e+00 1543.0
13 TraesCS7A01G141800 chr7B 92.308 702 38 8 3796 4489 43880495 43879802 0.000000e+00 983.0
14 TraesCS7A01G141800 chr7B 79.693 1044 131 47 923 1927 327277485 327276484 0.000000e+00 678.0
15 TraesCS7A01G141800 chr7B 89.420 293 19 10 706 991 43883481 43883194 5.860000e-95 359.0
16 TraesCS7A01G141800 chr7B 96.602 206 7 0 4955 5160 43895903 43895698 5.900000e-90 342.0
17 TraesCS7A01G141800 chr7B 85.953 299 24 9 387 681 43884015 43883731 2.780000e-78 303.0
18 TraesCS7A01G141800 chr7B 84.980 253 34 4 1 252 43884261 43884012 2.840000e-63 254.0
19 TraesCS7A01G141800 chr7B 83.154 279 34 7 2054 2328 327276278 327276009 6.150000e-60 243.0
20 TraesCS7A01G141800 chr7B 85.845 219 14 7 5560 5768 327272384 327272173 3.730000e-52 217.0
21 TraesCS7A01G141800 chr7B 82.353 153 20 4 5269 5417 327272890 327272741 6.470000e-25 126.0
22 TraesCS7A01G141800 chr7D 92.691 2408 124 20 3782 6145 91392211 91389812 0.000000e+00 3424.0
23 TraesCS7A01G141800 chr7D 96.072 1273 47 2 2366 3638 91393480 91392211 0.000000e+00 2071.0
24 TraesCS7A01G141800 chr7D 93.401 1288 79 5 2366 3651 185139356 185138073 0.000000e+00 1903.0
25 TraesCS7A01G141800 chr7D 85.180 1525 153 36 3703 5206 185137994 185136522 0.000000e+00 1496.0
26 TraesCS7A01G141800 chr7D 86.585 1230 86 36 815 2005 91395514 91394325 0.000000e+00 1284.0
27 TraesCS7A01G141800 chr7D 81.679 977 106 40 975 1927 185140838 185139911 0.000000e+00 745.0
28 TraesCS7A01G141800 chr7D 85.455 550 69 7 3 546 91397388 91396844 4.160000e-156 562.0
29 TraesCS7A01G141800 chr7D 82.642 386 29 15 5411 5768 185136054 185135679 2.150000e-79 307.0
30 TraesCS7A01G141800 chr7D 87.273 275 22 3 2040 2314 91394210 91393949 1.000000e-77 302.0
31 TraesCS7A01G141800 chr7D 88.199 161 15 2 5269 5426 185136355 185136196 8.130000e-44 189.0
32 TraesCS7A01G141800 chr7D 88.889 108 11 1 2222 2328 185139576 185139469 1.390000e-26 132.0
33 TraesCS7A01G141800 chr4A 93.694 666 39 2 2925 3590 439068900 439068238 0.000000e+00 994.0
34 TraesCS7A01G141800 chr4A 95.055 182 9 0 3825 4006 439068241 439068060 2.800000e-73 287.0
35 TraesCS7A01G141800 chr4D 84.433 758 85 16 5411 6145 189583608 189584355 0.000000e+00 715.0


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 TraesCS7A01G141800 chr7A 93071718 93077862 6144 False 11348.000000 11348 100.000000 1 6145 1 chr7A.!!$F1 6144
1 TraesCS7A01G141800 chr7A 192667602 192672668 5066 True 751.500000 1858 86.190000 990 5426 6 chr7A.!!$R1 4436
2 TraesCS7A01G141800 chr7A 192817657 192818377 720 True 276.750000 497 88.274000 1103 1849 2 chr7A.!!$R2 746
3 TraesCS7A01G141800 chr7B 43878255 43884261 6006 True 1313.500000 3904 89.527167 1 6145 6 chr7B.!!$R2 6144
4 TraesCS7A01G141800 chr7B 327272173 327277485 5312 True 781.833333 1884 84.977000 923 5768 6 chr7B.!!$R3 4845
5 TraesCS7A01G141800 chr7D 91389812 91397388 7576 True 1528.600000 3424 89.615200 3 6145 5 chr7D.!!$R1 6142
6 TraesCS7A01G141800 chr7D 185135679 185140838 5159 True 795.333333 1903 86.665000 975 5768 6 chr7D.!!$R2 4793
7 TraesCS7A01G141800 chr4A 439068060 439068900 840 True 640.500000 994 94.374500 2925 4006 2 chr4A.!!$R1 1081
8 TraesCS7A01G141800 chr4D 189583608 189584355 747 False 715.000000 715 84.433000 5411 6145 1 chr4D.!!$F1 734

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
186 188 0.037590 TCCAACAAGGACCCCGATTG 59.962 55.0 0.00 0.00 43.07 2.67 F
891 2188 0.041090 ATTTACAGGGGCCCAACTGG 59.959 55.0 27.72 10.94 39.00 4.00 F
2094 3722 0.719465 GACTACGATGGTTGGTTGCG 59.281 55.0 0.00 0.00 0.00 4.85 F
2882 5198 0.405585 TTCAGGGAAAAGCAGGGGAG 59.594 55.0 0.00 0.00 0.00 4.30 F
3676 5993 0.106419 TTTTTGCGGGGACAGGTTCT 60.106 50.0 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 2823 0.509499 CAACGCGCGGTAAAAAGAGA 59.491 50.0 35.22 0.00 0.00 3.10 R
2861 5177 0.113190 CCCCTGCTTTTCCCTGAAGT 59.887 55.0 0.00 0.00 0.00 3.01 R
3657 5974 0.106419 AGAACCTGTCCCCGCAAAAA 60.106 50.0 0.00 0.00 0.00 1.94 R
4419 6836 0.755698 GTCAGGGCGACAGGAGGATA 60.756 60.0 0.00 0.00 44.69 2.59 R
5157 7610 0.670546 TAACGGTCTGAGCTTGCAGC 60.671 55.0 5.23 0.47 42.84 5.25 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
48 50 4.142071 CCCTCATCGTCTCATCTTCTTTGA 60.142 45.833 0.00 0.00 0.00 2.69
49 51 5.414360 CCTCATCGTCTCATCTTCTTTGAA 58.586 41.667 0.00 0.00 0.00 2.69
72 74 2.202610 CTCGAGCGGATGCAACGA 60.203 61.111 16.97 8.36 46.23 3.85
78 80 2.452813 GCGGATGCAACGACGACAT 61.453 57.895 16.97 1.88 42.15 3.06
91 93 2.536365 GACGACATCGGCTATTGTGAA 58.464 47.619 6.21 0.00 45.57 3.18
99 101 0.308993 GGCTATTGTGAATCTGCGGC 59.691 55.000 0.00 0.00 0.00 6.53
101 103 1.290203 CTATTGTGAATCTGCGGCGT 58.710 50.000 9.37 0.00 0.00 5.68
142 144 0.804364 GCGGCATCACATCACTTTCA 59.196 50.000 0.00 0.00 0.00 2.69
185 187 2.470311 TCCAACAAGGACCCCGATT 58.530 52.632 0.00 0.00 43.07 3.34
186 188 0.037590 TCCAACAAGGACCCCGATTG 59.962 55.000 0.00 0.00 43.07 2.67
206 208 2.875933 TGTTGACCACCAAAGAATCGAC 59.124 45.455 0.00 0.00 36.36 4.20
207 209 2.875933 GTTGACCACCAAAGAATCGACA 59.124 45.455 0.00 0.00 36.36 4.35
210 212 1.142060 ACCACCAAAGAATCGACACCA 59.858 47.619 0.00 0.00 0.00 4.17
244 246 0.678048 AAGAACGCCAAGATGCTCCC 60.678 55.000 0.00 0.00 0.00 4.30
262 264 1.372087 CCAAAGAGCCTGTGATCGCC 61.372 60.000 3.31 0.00 30.37 5.54
263 265 0.674581 CAAAGAGCCTGTGATCGCCA 60.675 55.000 3.31 0.00 30.37 5.69
264 266 0.254178 AAAGAGCCTGTGATCGCCAT 59.746 50.000 3.31 0.00 30.37 4.40
294 296 2.665537 CTCTACGAGAAGCAAGCTTGTG 59.334 50.000 26.55 12.46 36.26 3.33
296 298 1.208614 CGAGAAGCAAGCTTGTGCC 59.791 57.895 26.55 15.36 46.14 5.01
297 299 1.233285 CGAGAAGCAAGCTTGTGCCT 61.233 55.000 26.55 19.36 46.14 4.75
298 300 0.520847 GAGAAGCAAGCTTGTGCCTC 59.479 55.000 26.55 22.68 46.14 4.70
312 314 2.684104 CCTCCTGACCCCTCGAGA 59.316 66.667 15.71 0.00 0.00 4.04
313 315 1.454847 CCTCCTGACCCCTCGAGAG 60.455 68.421 15.71 7.49 0.00 3.20
322 324 3.515611 CCTCGAGAGGGACCGAAG 58.484 66.667 15.71 0.00 44.87 3.79
367 369 3.746949 CTCTGATGGCCCTGGCGAC 62.747 68.421 0.00 0.00 43.06 5.19
376 378 3.834799 CCTGGCGACGTCCCCTAC 61.835 72.222 19.59 2.16 0.00 3.18
546 552 9.599866 TTTGTCCTATGTATGAACTATGTGAAG 57.400 33.333 0.00 0.00 0.00 3.02
548 554 9.416284 TGTCCTATGTATGAACTATGTGAAGTA 57.584 33.333 0.00 0.00 0.00 2.24
555 561 9.936759 TGTATGAACTATGTGAAGTATGTTGAA 57.063 29.630 0.00 0.00 0.00 2.69
558 564 8.846943 TGAACTATGTGAAGTATGTTGAATGT 57.153 30.769 0.00 0.00 0.00 2.71
559 565 8.720562 TGAACTATGTGAAGTATGTTGAATGTG 58.279 33.333 0.00 0.00 0.00 3.21
560 566 8.846943 AACTATGTGAAGTATGTTGAATGTGA 57.153 30.769 0.00 0.00 0.00 3.58
561 567 9.453572 AACTATGTGAAGTATGTTGAATGTGAT 57.546 29.630 0.00 0.00 0.00 3.06
562 568 8.886719 ACTATGTGAAGTATGTTGAATGTGATG 58.113 33.333 0.00 0.00 0.00 3.07
563 569 7.926674 ATGTGAAGTATGTTGAATGTGATGA 57.073 32.000 0.00 0.00 0.00 2.92
564 570 7.368480 TGTGAAGTATGTTGAATGTGATGAG 57.632 36.000 0.00 0.00 0.00 2.90
565 571 6.936335 TGTGAAGTATGTTGAATGTGATGAGT 59.064 34.615 0.00 0.00 0.00 3.41
569 575 6.111382 AGTATGTTGAATGTGATGAGTCCTG 58.889 40.000 0.00 0.00 0.00 3.86
576 582 3.599730 TGTGATGAGTCCTGTGTCATC 57.400 47.619 5.54 5.54 46.33 2.92
587 593 4.756642 GTCCTGTGTCATCTGTTTTGATCA 59.243 41.667 0.00 0.00 0.00 2.92
611 617 4.750460 CATGGCTTGCATGCATCC 57.250 55.556 23.37 24.17 34.04 3.51
613 619 2.495409 ATGGCTTGCATGCATCCGG 61.495 57.895 23.37 12.97 34.04 5.14
631 637 3.426836 GGAGGGGGTAAAGGGGGC 61.427 72.222 0.00 0.00 0.00 5.80
664 1325 3.265791 AGTCGGACAAATGATGCTCTTC 58.734 45.455 11.27 0.00 0.00 2.87
690 1569 9.559732 CATTAGGGAGACATGTATGTGATTTTA 57.440 33.333 0.00 0.00 41.95 1.52
691 1570 8.958119 TTAGGGAGACATGTATGTGATTTTAC 57.042 34.615 0.00 0.00 41.95 2.01
700 1579 7.665559 ACATGTATGTGATTTTACCAGTCTTGT 59.334 33.333 0.00 0.00 40.03 3.16
736 1624 9.665719 TTTGTTATATATCATGTGAGTGTGTGT 57.334 29.630 0.00 0.00 0.00 3.72
791 1824 8.839310 AGACATGTATAAACTCATAAGATGGC 57.161 34.615 0.00 0.00 0.00 4.40
821 2115 5.921004 TTACGTTACACAGCCGTTTTATT 57.079 34.783 0.00 0.00 36.12 1.40
862 2156 1.824230 TGGATTCGGGAGGCAAAATTG 59.176 47.619 0.00 0.00 0.00 2.32
866 2160 4.524328 GGATTCGGGAGGCAAAATTGATAT 59.476 41.667 0.00 0.00 0.00 1.63
891 2188 0.041090 ATTTACAGGGGCCCAACTGG 59.959 55.000 27.72 10.94 39.00 4.00
894 2191 1.068943 TACAGGGGCCCAACTGGAAA 61.069 55.000 27.72 9.74 39.00 3.13
909 2206 1.027792 GGAAAATGCGCCTCCCGTTA 61.028 55.000 4.18 0.00 39.71 3.18
912 2209 0.743345 AAATGCGCCTCCCGTTAGAC 60.743 55.000 4.18 0.00 39.71 2.59
932 2230 0.815095 CCCCATTAAAGCAACGTCCC 59.185 55.000 0.00 0.00 0.00 4.46
965 2263 0.731514 CGACTAACTTCGGCTTCGCA 60.732 55.000 0.00 0.00 35.26 5.10
1014 2350 4.722700 GCCATGGCCACCACGTCT 62.723 66.667 27.24 0.00 35.80 4.18
1044 2380 4.813526 CACGGCTCCGACGACGAG 62.814 72.222 15.95 5.69 42.83 4.18
1053 2389 1.020333 CCGACGACGAGGAAGACTCT 61.020 60.000 9.28 0.00 44.33 3.24
1470 2818 1.798813 CAGTACAGGTTGGTTCGCTTC 59.201 52.381 0.00 0.00 0.00 3.86
1475 2823 2.222027 CAGGTTGGTTCGCTTCTTCTT 58.778 47.619 0.00 0.00 0.00 2.52
1478 2830 2.480802 GGTTGGTTCGCTTCTTCTTCTC 59.519 50.000 0.00 0.00 0.00 2.87
1512 2865 6.400940 GCGCGTTGTAGTTAATTACTGGTAAA 60.401 38.462 8.43 0.00 37.73 2.01
1527 2880 6.002653 ACTGGTAAATCAGTATTTCCCTCC 57.997 41.667 0.00 0.00 45.18 4.30
1532 2886 6.096423 GGTAAATCAGTATTTCCCTCCCAAAC 59.904 42.308 0.00 0.00 36.67 2.93
1554 2908 4.705023 ACAAACTGGTAAAGAACACAGCTT 59.295 37.500 0.00 0.00 32.60 3.74
1558 2912 5.865085 ACTGGTAAAGAACACAGCTTGATA 58.135 37.500 3.37 0.00 32.60 2.15
1566 2920 7.551035 AAGAACACAGCTTGATATCTGAATC 57.449 36.000 3.98 0.00 34.57 2.52
1576 2930 6.183360 GCTTGATATCTGAATCGCTTCCATAC 60.183 42.308 3.98 0.00 0.00 2.39
1578 2932 1.852942 TCTGAATCGCTTCCATACGC 58.147 50.000 0.00 0.00 0.00 4.42
1583 2937 1.571919 ATCGCTTCCATACGCTTCAC 58.428 50.000 0.00 0.00 0.00 3.18
1681 3081 1.822990 CCCTTGCTTGATGTGATGCTT 59.177 47.619 0.00 0.00 0.00 3.91
1697 3097 1.153745 CTTCGAGGGGAACTGCGAG 60.154 63.158 0.00 0.00 32.93 5.03
1709 3214 0.826715 ACTGCGAGCTACATCCATGT 59.173 50.000 0.00 0.00 44.48 3.21
1778 3283 9.413048 TCGTTTTGTTTTACTCTTTTGAATGTT 57.587 25.926 0.00 0.00 0.00 2.71
1790 3295 7.773690 ACTCTTTTGAATGTTAGTAACACACCT 59.226 33.333 17.79 3.48 45.50 4.00
1792 3297 7.771361 TCTTTTGAATGTTAGTAACACACCTCA 59.229 33.333 17.79 14.17 45.50 3.86
1795 3300 4.967084 ATGTTAGTAACACACCTCACCA 57.033 40.909 17.79 0.00 45.50 4.17
1796 3301 4.330944 TGTTAGTAACACACCTCACCAG 57.669 45.455 11.75 0.00 36.25 4.00
1818 3323 4.518590 AGTCATCATACTGATCTCTGACCG 59.481 45.833 0.00 0.00 34.77 4.79
1820 3325 5.470437 GTCATCATACTGATCTCTGACCGTA 59.530 44.000 0.00 0.00 34.28 4.02
1821 3326 5.470437 TCATCATACTGATCTCTGACCGTAC 59.530 44.000 0.00 0.00 34.28 3.67
1822 3327 5.037383 TCATACTGATCTCTGACCGTACT 57.963 43.478 0.00 0.00 0.00 2.73
1823 3328 4.816925 TCATACTGATCTCTGACCGTACTG 59.183 45.833 0.00 0.00 0.00 2.74
1824 3329 3.351794 ACTGATCTCTGACCGTACTGA 57.648 47.619 0.00 0.00 0.00 3.41
1838 3343 2.654056 CGTACTGAGATGATCGCATTCG 59.346 50.000 0.00 2.00 34.11 3.34
1862 3367 4.624882 CGAGGATTCTAGCATGTTAGCATC 59.375 45.833 16.99 16.99 36.85 3.91
1874 3379 5.848036 GCATGTTAGCATCGTTAATGTGATC 59.152 40.000 0.00 0.00 37.71 2.92
1913 3454 3.118884 GGATCCGTTGGTAGCTTAACTGA 60.119 47.826 0.00 0.00 0.00 3.41
1936 3477 3.991367 ACCTAATTCATGTACGGCTAGC 58.009 45.455 6.04 6.04 0.00 3.42
1970 3511 5.352569 CACTCCTTATTGAGGCAAGTACTTG 59.647 44.000 27.85 27.85 45.87 3.16
2033 3639 2.177394 TTTCGCTGCAATAGTGTGGA 57.823 45.000 0.00 0.00 38.11 4.02
2048 3676 5.241403 AGTGTGGACCTGATTGATTGTTA 57.759 39.130 0.00 0.00 0.00 2.41
2049 3677 5.003804 AGTGTGGACCTGATTGATTGTTAC 58.996 41.667 0.00 0.00 0.00 2.50
2077 3705 1.328986 GAAGCGGCATTAGCTCTTGAC 59.671 52.381 1.45 0.00 45.31 3.18
2094 3722 0.719465 GACTACGATGGTTGGTTGCG 59.281 55.000 0.00 0.00 0.00 4.85
2097 3725 1.009903 TACGATGGTTGGTTGCGACG 61.010 55.000 0.00 0.00 0.00 5.12
2116 4014 3.602483 ACGCAACTTCGGTTATGGTTAT 58.398 40.909 0.00 0.00 36.26 1.89
2117 4015 3.372822 ACGCAACTTCGGTTATGGTTATG 59.627 43.478 0.00 0.00 36.26 1.90
2194 4093 5.640218 ATTGTGAAATGTCAAGCGTTTTG 57.360 34.783 0.00 0.00 36.51 2.44
2241 4140 2.693267 TTTTGTTTCGGGTTTTGGGG 57.307 45.000 0.00 0.00 0.00 4.96
2251 4150 3.333082 TCGGGTTTTGGGGTTATTTAGGA 59.667 43.478 0.00 0.00 0.00 2.94
2309 4208 4.203226 TCATACAACCTCAAACACTGCAA 58.797 39.130 0.00 0.00 0.00 4.08
2314 4221 3.508744 ACCTCAAACACTGCAACTTTG 57.491 42.857 0.00 0.00 0.00 2.77
2360 4279 3.397955 AGTAAGATGGGAGTTTGGTTGGT 59.602 43.478 0.00 0.00 0.00 3.67
2382 4698 2.879026 GGAGTTTTCCTTGTCTGTCCAC 59.121 50.000 0.00 0.00 40.58 4.02
2404 4720 9.209048 TCCACTGTTATATATCCACTAACTTGT 57.791 33.333 0.00 0.00 0.00 3.16
2590 4906 7.607991 CAGTATTTCTGACTTCCTGTTTGGTAT 59.392 37.037 0.00 0.00 46.27 2.73
2618 4934 4.481930 TGATTTGCGGTTTAACTGTCTG 57.518 40.909 5.77 0.00 0.00 3.51
2831 5147 4.877378 TGCAGCTCTTCATGGAAAATTT 57.123 36.364 0.00 0.00 0.00 1.82
2861 5177 6.570692 TGTTTTTGCGAGGTTAATTTTACCA 58.429 32.000 7.29 0.00 38.16 3.25
2875 5191 4.929819 TTTTACCACTTCAGGGAAAAGC 57.070 40.909 0.00 0.00 44.53 3.51
2882 5198 0.405585 TTCAGGGAAAAGCAGGGGAG 59.594 55.000 0.00 0.00 0.00 4.30
2951 5267 2.238521 GAAACCCATGCTGTTCTTCCA 58.761 47.619 0.05 0.00 0.00 3.53
2957 5273 2.686915 CCATGCTGTTCTTCCAGGAATC 59.313 50.000 1.09 0.00 36.33 2.52
3338 5654 3.861113 CAGCGTATGCATTTCATTTTGCT 59.139 39.130 3.54 0.25 46.23 3.91
3643 5960 4.821805 CGTAATATTTGATGGGCAGGTTCT 59.178 41.667 0.00 0.00 0.00 3.01
3644 5961 5.299279 CGTAATATTTGATGGGCAGGTTCTT 59.701 40.000 0.00 0.00 0.00 2.52
3651 5968 2.806945 TGGGCAGGTTCTTTGATAGG 57.193 50.000 0.00 0.00 0.00 2.57
3652 5969 1.992557 TGGGCAGGTTCTTTGATAGGT 59.007 47.619 0.00 0.00 0.00 3.08
3653 5970 2.378547 TGGGCAGGTTCTTTGATAGGTT 59.621 45.455 0.00 0.00 0.00 3.50
3654 5971 3.181423 TGGGCAGGTTCTTTGATAGGTTT 60.181 43.478 0.00 0.00 0.00 3.27
3655 5972 3.832490 GGGCAGGTTCTTTGATAGGTTTT 59.168 43.478 0.00 0.00 0.00 2.43
3656 5973 4.283467 GGGCAGGTTCTTTGATAGGTTTTT 59.717 41.667 0.00 0.00 0.00 1.94
3674 5991 4.688770 TTTTTGCGGGGACAGGTT 57.311 50.000 0.00 0.00 0.00 3.50
3675 5992 2.421220 TTTTTGCGGGGACAGGTTC 58.579 52.632 0.00 0.00 0.00 3.62
3676 5993 0.106419 TTTTTGCGGGGACAGGTTCT 60.106 50.000 0.00 0.00 0.00 3.01
3677 5994 0.766131 TTTTGCGGGGACAGGTTCTA 59.234 50.000 0.00 0.00 0.00 2.10
3678 5995 0.988832 TTTGCGGGGACAGGTTCTAT 59.011 50.000 0.00 0.00 0.00 1.98
3679 5996 0.251916 TTGCGGGGACAGGTTCTATG 59.748 55.000 0.00 0.00 0.00 2.23
3680 5997 0.616395 TGCGGGGACAGGTTCTATGA 60.616 55.000 0.00 0.00 0.00 2.15
3681 5998 0.759346 GCGGGGACAGGTTCTATGAT 59.241 55.000 0.00 0.00 0.00 2.45
3682 5999 1.141053 GCGGGGACAGGTTCTATGATT 59.859 52.381 0.00 0.00 0.00 2.57
3683 6000 2.838736 CGGGGACAGGTTCTATGATTG 58.161 52.381 0.00 0.00 0.00 2.67
3692 6009 5.711976 ACAGGTTCTATGATTGTTGAAAGGG 59.288 40.000 0.00 0.00 0.00 3.95
3695 6012 7.393234 CAGGTTCTATGATTGTTGAAAGGGTAA 59.607 37.037 0.00 0.00 0.00 2.85
3700 6017 9.613428 TCTATGATTGTTGAAAGGGTAATACTG 57.387 33.333 0.00 0.00 0.00 2.74
3721 6119 9.745880 ATACTGTATATCTTAGGAAAACACACG 57.254 33.333 0.00 0.00 0.00 4.49
3737 6135 5.871465 ACACACGTAATTGCATATTGTGA 57.129 34.783 16.22 0.00 37.04 3.58
3738 6136 6.247727 ACACACGTAATTGCATATTGTGAA 57.752 33.333 16.22 0.00 37.04 3.18
3754 6152 8.739039 CATATTGTGAATAGAAGTTTGGGTGAA 58.261 33.333 0.00 0.00 0.00 3.18
3817 6225 6.013842 TGTACCTCTTATCACGATGCTATG 57.986 41.667 0.00 0.00 0.00 2.23
4057 6466 9.989296 ATATCAGTAGCTATTGGATAGAAGTCT 57.011 33.333 15.46 0.00 34.77 3.24
4070 6479 5.460419 GGATAGAAGTCTTGTACTGATTGCG 59.540 44.000 0.00 0.00 38.88 4.85
4071 6480 4.258702 AGAAGTCTTGTACTGATTGCGT 57.741 40.909 0.00 0.00 38.88 5.24
4072 6481 5.386958 AGAAGTCTTGTACTGATTGCGTA 57.613 39.130 0.00 0.00 38.88 4.42
4073 6482 5.967088 AGAAGTCTTGTACTGATTGCGTAT 58.033 37.500 0.00 0.00 38.88 3.06
4162 6571 2.814280 TGAAGACACTCGGAGGTTTC 57.186 50.000 10.23 7.78 0.00 2.78
4234 6643 0.171231 TTGAGTCTGTCATCCTCGCG 59.829 55.000 0.00 0.00 34.17 5.87
4262 6671 7.654116 GGTTTATAGAAGCAGTGAAGAGGTATC 59.346 40.741 0.00 0.00 0.00 2.24
4447 6864 0.598065 GTCGCCCTGACTGCATTTTT 59.402 50.000 0.00 0.00 44.58 1.94
4489 6914 9.282247 GATTATTTGTGCTTGAGTTGTAGAATG 57.718 33.333 0.00 0.00 0.00 2.67
4507 6932 7.895429 TGTAGAATGATCCCTTGAAAAATCCTT 59.105 33.333 0.00 0.00 0.00 3.36
4511 6936 4.463891 TGATCCCTTGAAAAATCCTTCTGC 59.536 41.667 0.00 0.00 0.00 4.26
4512 6937 4.118168 TCCCTTGAAAAATCCTTCTGCT 57.882 40.909 0.00 0.00 0.00 4.24
4579 7005 0.250467 GCCACTGAGCACTCCTTTCA 60.250 55.000 0.00 0.00 0.00 2.69
4639 7067 7.545265 GCTGAACCATGATGCAAATTAAAGTTA 59.455 33.333 0.00 0.00 0.00 2.24
4664 7092 8.644374 AAATTACCAAAGCCTACTCACAATTA 57.356 30.769 0.00 0.00 0.00 1.40
4711 7143 5.180492 CACTTTATCCGGTGAAGTTAAAGCA 59.820 40.000 14.23 0.00 34.71 3.91
4784 7216 2.700897 AGAAGTACTGAAGCTGGTGTGT 59.299 45.455 0.00 0.00 0.00 3.72
4796 7228 2.503331 CTGGTGTGTGACCTTTATGCA 58.497 47.619 0.00 0.00 46.32 3.96
4847 7279 7.030165 GGACATATCGGAATGTAGACTATGTG 58.970 42.308 3.91 0.00 40.17 3.21
4917 7353 7.558137 CACACAATTGCAATTTCAGTTCTTAC 58.442 34.615 21.95 0.00 0.00 2.34
4966 7411 4.020396 CCTGATGCTATGCTCCTCTGTATT 60.020 45.833 0.00 0.00 0.00 1.89
5099 7544 0.607489 GCATGCAATCGGAGGCCTAT 60.607 55.000 14.21 0.00 33.74 2.57
5157 7610 5.359194 ACCAACATAGACCTACCATTCTG 57.641 43.478 0.00 0.00 0.00 3.02
5192 7645 4.632153 ACCGTTAGGCAAGAAGCTATATG 58.368 43.478 0.00 0.00 44.79 1.78
5233 7813 4.137543 ACCCAACAGAGTGAGTCAAAATC 58.862 43.478 0.00 0.00 0.00 2.17
5241 7821 6.480320 ACAGAGTGAGTCAAAATCAAGTGTAC 59.520 38.462 0.00 0.00 0.00 2.90
5248 7828 9.337396 TGAGTCAAAATCAAGTGTACAATAAGT 57.663 29.630 0.00 0.00 0.00 2.24
5338 7932 2.798283 CAGACTTTGTTTTGGCAGCATG 59.202 45.455 0.00 0.00 40.87 4.06
5389 7986 8.798859 AAATTCTGTAGCTACAATGTCTGATT 57.201 30.769 25.95 12.54 35.50 2.57
5418 8015 1.001706 CTCTTCGGTCACGTGACAAGA 60.002 52.381 40.51 35.95 46.47 3.02
5427 8182 3.182572 GTCACGTGACAAGACTTGATGTC 59.817 47.826 37.16 10.25 44.84 3.06
5478 8233 3.960571 AGCTGAAATGCCTAACACTGAT 58.039 40.909 0.00 0.00 0.00 2.90
5548 8322 5.235516 CGATAACTGGTGTAAAACTGGAGT 58.764 41.667 0.00 0.00 0.00 3.85
5551 8325 7.148689 CGATAACTGGTGTAAAACTGGAGTTAC 60.149 40.741 0.00 0.00 37.25 2.50
5573 8384 6.078202 ACTGACAGATCACTAATACATCCG 57.922 41.667 10.08 0.00 0.00 4.18
5576 8387 3.898123 ACAGATCACTAATACATCCGGCT 59.102 43.478 0.00 0.00 0.00 5.52
5621 8434 7.639039 ACAATACGGCACACATAAATCATAAG 58.361 34.615 0.00 0.00 0.00 1.73
5656 8472 7.727181 AGAGCTAGAGTACAAAAGAGACAAAA 58.273 34.615 0.00 0.00 0.00 2.44
5862 8687 2.162208 TCGAATTGTGAAGGAATGCTGC 59.838 45.455 0.00 0.00 0.00 5.25
5952 8783 5.419542 TCATCTTTACTTCCAAGGTCATCG 58.580 41.667 0.00 0.00 0.00 3.84
5972 8803 2.350388 CGAAACCAACCAACCGATCAAG 60.350 50.000 0.00 0.00 0.00 3.02
6015 8846 4.811908 ACAAAAGTACCGCAAAAACACTT 58.188 34.783 0.00 0.00 0.00 3.16
6051 8882 6.039717 ACCCTCGATTAAATTTGACATGATGG 59.960 38.462 0.00 1.69 0.00 3.51
6053 8884 5.509771 TCGATTAAATTTGACATGATGGCG 58.490 37.500 0.00 0.00 0.00 5.69
6129 8960 7.720957 TGGAATAGGTAGAATCCATGAACAATG 59.279 37.037 0.00 0.00 37.05 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.623167 CACGTTCAAAGAAGATGAGACGAT 59.377 41.667 13.78 0.00 36.14 3.73
48 50 3.760035 ATCCGCTCGAGCCACGTT 61.760 61.111 30.66 11.13 43.13 3.99
49 51 4.498520 CATCCGCTCGAGCCACGT 62.499 66.667 30.66 12.24 43.13 4.49
72 74 2.665649 TTCACAATAGCCGATGTCGT 57.334 45.000 1.44 0.00 37.74 4.34
78 80 1.570813 CGCAGATTCACAATAGCCGA 58.429 50.000 0.00 0.00 0.00 5.54
81 83 0.041839 CGCCGCAGATTCACAATAGC 60.042 55.000 0.00 0.00 0.00 2.97
112 114 0.462581 TGATGCCGCTAGCTTTGAGG 60.463 55.000 13.93 7.21 44.23 3.86
117 119 0.178767 TGATGTGATGCCGCTAGCTT 59.821 50.000 13.93 0.00 44.23 3.74
142 144 3.560251 AACACCCGCACTGGAGCT 61.560 61.111 0.00 0.00 42.00 4.09
185 187 2.875933 GTCGATTCTTTGGTGGTCAACA 59.124 45.455 0.00 0.00 34.67 3.33
186 188 2.875933 TGTCGATTCTTTGGTGGTCAAC 59.124 45.455 0.00 0.00 34.67 3.18
244 246 0.674581 TGGCGATCACAGGCTCTTTG 60.675 55.000 0.00 0.00 35.01 2.77
262 264 3.598678 TCGTAGAGTTGACGCGATG 57.401 52.632 15.93 0.00 40.14 3.84
275 277 1.127582 GCACAAGCTTGCTTCTCGTAG 59.872 52.381 26.27 6.28 39.59 3.51
276 278 1.148310 GCACAAGCTTGCTTCTCGTA 58.852 50.000 26.27 0.00 39.59 3.43
294 296 3.151022 CTCGAGGGGTCAGGAGGC 61.151 72.222 3.91 0.00 0.00 4.70
296 298 1.454847 CCTCTCGAGGGGTCAGGAG 60.455 68.421 24.17 5.10 44.87 3.69
297 299 2.684104 CCTCTCGAGGGGTCAGGA 59.316 66.667 24.17 0.00 44.87 3.86
312 314 0.702902 TGAGTAGTCCTTCGGTCCCT 59.297 55.000 0.00 0.00 0.00 4.20
313 315 1.104630 CTGAGTAGTCCTTCGGTCCC 58.895 60.000 0.00 0.00 0.00 4.46
332 334 2.126031 GGCGTCCTTGGACTCGTC 60.126 66.667 16.60 3.66 0.00 4.20
334 336 2.182030 GAGGCGTCCTTGGACTCG 59.818 66.667 16.60 6.75 31.76 4.18
337 339 0.460987 CATCAGAGGCGTCCTTGGAC 60.461 60.000 9.62 9.62 31.76 4.02
348 350 4.559063 CGCCAGGGCCATCAGAGG 62.559 72.222 6.18 0.00 37.98 3.69
373 375 4.194720 AGCTCGAAGGCGGCGTAG 62.195 66.667 9.37 0.00 38.28 3.51
374 376 4.189188 GAGCTCGAAGGCGGCGTA 62.189 66.667 9.37 0.00 38.28 4.42
386 388 1.380524 TCGTAGTGGTAGCAGAGCTC 58.619 55.000 5.27 5.27 40.44 4.09
455 457 9.293404 ACACATTATACCACTACGACATACTAT 57.707 33.333 0.00 0.00 0.00 2.12
465 467 5.642063 AGCACACAACACATTATACCACTAC 59.358 40.000 0.00 0.00 0.00 2.73
543 549 6.820656 AGGACTCATCACATTCAACATACTTC 59.179 38.462 0.00 0.00 0.00 3.01
546 552 5.877012 ACAGGACTCATCACATTCAACATAC 59.123 40.000 0.00 0.00 0.00 2.39
548 554 4.698780 CACAGGACTCATCACATTCAACAT 59.301 41.667 0.00 0.00 0.00 2.71
551 557 4.202346 TGACACAGGACTCATCACATTCAA 60.202 41.667 0.00 0.00 0.00 2.69
553 559 3.930336 TGACACAGGACTCATCACATTC 58.070 45.455 0.00 0.00 0.00 2.67
554 560 4.224594 AGATGACACAGGACTCATCACATT 59.775 41.667 9.65 0.00 43.63 2.71
555 561 3.773667 AGATGACACAGGACTCATCACAT 59.226 43.478 9.65 0.00 43.63 3.21
556 562 3.056322 CAGATGACACAGGACTCATCACA 60.056 47.826 9.65 0.00 43.63 3.58
557 563 3.056250 ACAGATGACACAGGACTCATCAC 60.056 47.826 9.65 0.00 43.63 3.06
558 564 3.168292 ACAGATGACACAGGACTCATCA 58.832 45.455 9.65 0.00 43.63 3.07
559 565 3.883830 ACAGATGACACAGGACTCATC 57.116 47.619 0.00 0.00 42.16 2.92
560 566 4.630644 AAACAGATGACACAGGACTCAT 57.369 40.909 0.00 0.00 0.00 2.90
561 567 4.129380 CAAAACAGATGACACAGGACTCA 58.871 43.478 0.00 0.00 0.00 3.41
562 568 4.380531 TCAAAACAGATGACACAGGACTC 58.619 43.478 0.00 0.00 0.00 3.36
563 569 4.422073 TCAAAACAGATGACACAGGACT 57.578 40.909 0.00 0.00 0.00 3.85
564 570 4.756642 TGATCAAAACAGATGACACAGGAC 59.243 41.667 0.00 0.00 0.00 3.85
565 571 4.971939 TGATCAAAACAGATGACACAGGA 58.028 39.130 0.00 0.00 0.00 3.86
569 575 6.129009 GCAACATTGATCAAAACAGATGACAC 60.129 38.462 13.09 0.00 0.00 3.67
576 582 4.142988 GCCATGCAACATTGATCAAAACAG 60.143 41.667 13.09 5.70 0.00 3.16
610 616 3.094498 CCTTTACCCCCTCCCCGG 61.094 72.222 0.00 0.00 0.00 5.73
611 617 3.094498 CCCTTTACCCCCTCCCCG 61.094 72.222 0.00 0.00 0.00 5.73
613 619 2.698788 CCCCCTTTACCCCCTCCC 60.699 72.222 0.00 0.00 0.00 4.30
631 637 0.602905 GTCCGACTCAACAAGGGTGG 60.603 60.000 0.00 0.00 0.00 4.61
643 1100 3.265791 GAAGAGCATCATTTGTCCGACT 58.734 45.455 0.00 0.00 37.82 4.18
664 1325 8.455903 AAAATCACATACATGTCTCCCTAATG 57.544 34.615 0.00 0.76 39.39 1.90
690 1569 7.404671 ACAAAGATTAAAACACAAGACTGGT 57.595 32.000 0.00 0.00 0.00 4.00
691 1570 9.965824 ATAACAAAGATTAAAACACAAGACTGG 57.034 29.630 0.00 0.00 0.00 4.00
791 1824 2.900046 GCTGTGTAACGTAAAATGCACG 59.100 45.455 0.00 0.00 42.39 5.34
821 2115 6.387465 TCCACGTGTTCACATGTTTTTAAAA 58.613 32.000 15.65 0.00 43.01 1.52
862 2156 5.193679 GGGCCCCTGTAAATATGTGATATC 58.806 45.833 12.23 0.00 0.00 1.63
866 2160 2.209758 TGGGCCCCTGTAAATATGTGA 58.790 47.619 22.27 0.00 0.00 3.58
891 2188 0.377203 CTAACGGGAGGCGCATTTTC 59.623 55.000 10.83 0.27 0.00 2.29
894 2191 1.153429 GTCTAACGGGAGGCGCATT 60.153 57.895 10.83 0.00 0.00 3.56
909 2206 1.074889 ACGTTGCTTTAATGGGGGTCT 59.925 47.619 0.00 0.00 0.00 3.85
912 2209 0.815095 GGACGTTGCTTTAATGGGGG 59.185 55.000 0.00 0.00 0.00 5.40
932 2230 0.387112 TAGTCGGTGCCGTTACGTTG 60.387 55.000 10.60 0.00 40.74 4.10
965 2263 0.850100 TGAGGTGTTGGTGTGGGAAT 59.150 50.000 0.00 0.00 0.00 3.01
1042 2378 1.728672 CCGGCGTAGAGTCTTCCTC 59.271 63.158 6.01 0.00 40.80 3.71
1043 2379 2.416432 GCCGGCGTAGAGTCTTCCT 61.416 63.158 12.58 0.00 0.00 3.36
1044 2380 2.104530 GCCGGCGTAGAGTCTTCC 59.895 66.667 12.58 0.00 0.00 3.46
1470 2818 2.472397 CGCGCGGTAAAAAGAGAAGAAG 60.472 50.000 24.84 0.00 0.00 2.85
1475 2823 0.509499 CAACGCGCGGTAAAAAGAGA 59.491 50.000 35.22 0.00 0.00 3.10
1478 2830 1.192980 ACTACAACGCGCGGTAAAAAG 59.807 47.619 35.22 23.09 0.00 2.27
1512 2865 4.946160 TGTTTGGGAGGGAAATACTGAT 57.054 40.909 0.00 0.00 0.00 2.90
1519 2872 2.292587 ACCAGTTTGTTTGGGAGGGAAA 60.293 45.455 0.00 0.00 40.11 3.13
1527 2880 5.715070 TGTGTTCTTTACCAGTTTGTTTGG 58.285 37.500 0.00 0.00 41.60 3.28
1532 2886 4.900635 AGCTGTGTTCTTTACCAGTTTG 57.099 40.909 0.00 0.00 31.53 2.93
1554 2908 5.402398 CGTATGGAAGCGATTCAGATATCA 58.598 41.667 16.24 2.94 0.00 2.15
1558 2912 2.036475 AGCGTATGGAAGCGATTCAGAT 59.964 45.455 16.24 8.89 38.61 2.90
1566 2920 1.004610 CATGTGAAGCGTATGGAAGCG 60.005 52.381 0.00 0.00 38.61 4.68
1576 2930 1.176527 AACAATCCCCATGTGAAGCG 58.823 50.000 0.00 0.00 0.00 4.68
1578 2932 3.379372 CAGCTAACAATCCCCATGTGAAG 59.621 47.826 0.00 0.00 0.00 3.02
1583 2937 2.026641 CACCAGCTAACAATCCCCATG 58.973 52.381 0.00 0.00 0.00 3.66
1681 3081 2.831894 TAGCTCGCAGTTCCCCTCGA 62.832 60.000 0.00 0.00 0.00 4.04
1697 3097 7.744087 TTACCAATTGATACATGGATGTAGC 57.256 36.000 7.12 7.89 46.66 3.58
1709 3214 6.882140 ACCGACAGTCAAATTACCAATTGATA 59.118 34.615 7.12 0.00 0.00 2.15
1778 3283 3.568443 TGACTGGTGAGGTGTGTTACTA 58.432 45.455 0.00 0.00 0.00 1.82
1780 3285 2.902705 TGACTGGTGAGGTGTGTTAC 57.097 50.000 0.00 0.00 0.00 2.50
1815 3320 1.389555 TGCGATCATCTCAGTACGGT 58.610 50.000 0.00 0.00 0.00 4.83
1817 3322 2.654056 CGAATGCGATCATCTCAGTACG 59.346 50.000 0.00 0.00 40.82 3.67
1818 3323 2.406691 GCGAATGCGATCATCTCAGTAC 59.593 50.000 0.00 0.00 40.82 2.73
1820 3325 1.495878 GCGAATGCGATCATCTCAGT 58.504 50.000 0.00 0.00 40.82 3.41
1838 3343 2.734079 GCTAACATGCTAGAATCCTCGC 59.266 50.000 7.34 0.00 0.00 5.03
1862 3367 4.091945 CCACACTCACAGATCACATTAACG 59.908 45.833 0.00 0.00 0.00 3.18
1874 3379 1.601759 CCAAGCCCCACACTCACAG 60.602 63.158 0.00 0.00 0.00 3.66
1913 3454 4.814771 GCTAGCCGTACATGAATTAGGTTT 59.185 41.667 2.29 0.00 0.00 3.27
1970 3511 5.048364 AGAGTCACTGTCACTCATAAGTCAC 60.048 44.000 14.34 0.00 42.51 3.67
2033 3639 6.878923 TCTTTCATCGTAACAATCAATCAGGT 59.121 34.615 0.00 0.00 0.00 4.00
2048 3676 1.453155 AATGCCGCTTCTTTCATCGT 58.547 45.000 0.00 0.00 0.00 3.73
2049 3677 2.600792 GCTAATGCCGCTTCTTTCATCG 60.601 50.000 0.00 0.00 0.00 3.84
2077 3705 0.719465 GTCGCAACCAACCATCGTAG 59.281 55.000 0.00 0.00 0.00 3.51
2094 3722 1.435577 ACCATAACCGAAGTTGCGTC 58.564 50.000 0.00 0.00 36.68 5.19
2097 3725 4.957759 ACATAACCATAACCGAAGTTGC 57.042 40.909 0.00 0.00 36.68 4.17
2116 4014 3.839490 AGGCAATCAAATGAATCCCAACA 59.161 39.130 0.00 0.00 0.00 3.33
2117 4015 4.476628 AGGCAATCAAATGAATCCCAAC 57.523 40.909 0.00 0.00 0.00 3.77
2241 4140 9.448438 TCCACATGCATGTATATCCTAAATAAC 57.552 33.333 30.92 0.00 39.39 1.89
2251 4150 5.448654 ACCAAACTCCACATGCATGTATAT 58.551 37.500 30.92 14.58 39.39 0.86
2309 4208 5.397360 AGGGAAATTCCAGAATCACAAAGT 58.603 37.500 14.68 0.00 38.64 2.66
2356 4275 3.287222 CAGACAAGGAAAACTCCACCAA 58.713 45.455 0.00 0.00 0.00 3.67
2360 4279 2.507886 TGGACAGACAAGGAAAACTCCA 59.492 45.455 0.00 0.00 0.00 3.86
2382 4698 9.197694 GCAGACAAGTTAGTGGATATATAACAG 57.802 37.037 0.00 0.00 32.92 3.16
2576 4892 9.492973 AAATCAATCAAAATACCAAACAGGAAG 57.507 29.630 0.00 0.00 41.22 3.46
2590 4906 6.758886 ACAGTTAAACCGCAAATCAATCAAAA 59.241 30.769 0.00 0.00 0.00 2.44
2671 4987 6.667007 AGCAACAAACAGAAATGAAAAAGG 57.333 33.333 0.00 0.00 0.00 3.11
2831 5147 1.961793 ACCTCGCAAAAACAGTAGCA 58.038 45.000 0.00 0.00 0.00 3.49
2861 5177 0.113190 CCCCTGCTTTTCCCTGAAGT 59.887 55.000 0.00 0.00 0.00 3.01
2882 5198 0.743097 GAATTCCCATGTCAGCAGGC 59.257 55.000 0.00 0.00 0.00 4.85
2951 5267 5.061853 CCACAATCATTGATCTCGATTCCT 58.938 41.667 3.79 0.00 0.00 3.36
2957 5273 2.032550 GTGCCCACAATCATTGATCTCG 59.967 50.000 3.79 0.00 0.00 4.04
3065 5381 3.333189 CCATCTCGCGCCACATCG 61.333 66.667 0.00 0.00 0.00 3.84
3290 5606 5.643379 CCAACATAGGCATTAGTTTGTGT 57.357 39.130 0.00 0.00 0.00 3.72
3338 5654 7.849160 AGTACATATCTACCAGATACGCTCTA 58.151 38.462 0.00 0.00 39.76 2.43
3539 5855 8.978539 TCTCCTTCGAATGTTTGAAATATATCG 58.021 33.333 0.00 10.47 30.57 2.92
3657 5974 0.106419 AGAACCTGTCCCCGCAAAAA 60.106 50.000 0.00 0.00 0.00 1.94
3658 5975 0.766131 TAGAACCTGTCCCCGCAAAA 59.234 50.000 0.00 0.00 0.00 2.44
3659 5976 0.988832 ATAGAACCTGTCCCCGCAAA 59.011 50.000 0.00 0.00 0.00 3.68
3660 5977 0.251916 CATAGAACCTGTCCCCGCAA 59.748 55.000 0.00 0.00 0.00 4.85
3661 5978 0.616395 TCATAGAACCTGTCCCCGCA 60.616 55.000 0.00 0.00 0.00 5.69
3662 5979 0.759346 ATCATAGAACCTGTCCCCGC 59.241 55.000 0.00 0.00 0.00 6.13
3663 5980 2.170607 ACAATCATAGAACCTGTCCCCG 59.829 50.000 0.00 0.00 0.00 5.73
3664 5981 3.933861 ACAATCATAGAACCTGTCCCC 57.066 47.619 0.00 0.00 0.00 4.81
3665 5982 4.843728 TCAACAATCATAGAACCTGTCCC 58.156 43.478 0.00 0.00 0.00 4.46
3666 5983 6.127897 CCTTTCAACAATCATAGAACCTGTCC 60.128 42.308 0.00 0.00 0.00 4.02
3667 5984 6.127897 CCCTTTCAACAATCATAGAACCTGTC 60.128 42.308 0.00 0.00 0.00 3.51
3668 5985 5.711976 CCCTTTCAACAATCATAGAACCTGT 59.288 40.000 0.00 0.00 0.00 4.00
3669 5986 5.711976 ACCCTTTCAACAATCATAGAACCTG 59.288 40.000 0.00 0.00 0.00 4.00
3670 5987 5.892348 ACCCTTTCAACAATCATAGAACCT 58.108 37.500 0.00 0.00 0.00 3.50
3671 5988 7.696992 TTACCCTTTCAACAATCATAGAACC 57.303 36.000 0.00 0.00 0.00 3.62
3674 5991 9.613428 CAGTATTACCCTTTCAACAATCATAGA 57.387 33.333 0.00 0.00 0.00 1.98
3675 5992 9.396022 ACAGTATTACCCTTTCAACAATCATAG 57.604 33.333 0.00 0.00 0.00 2.23
3677 5994 9.920946 ATACAGTATTACCCTTTCAACAATCAT 57.079 29.630 0.00 0.00 0.00 2.45
3695 6012 9.745880 CGTGTGTTTTCCTAAGATATACAGTAT 57.254 33.333 0.00 0.00 0.00 2.12
3702 6019 8.395633 GCAATTACGTGTGTTTTCCTAAGATAT 58.604 33.333 0.00 0.00 0.00 1.63
3704 6021 6.205853 TGCAATTACGTGTGTTTTCCTAAGAT 59.794 34.615 0.00 0.00 0.00 2.40
3706 6023 5.753744 TGCAATTACGTGTGTTTTCCTAAG 58.246 37.500 0.00 0.00 0.00 2.18
3708 6025 5.950758 ATGCAATTACGTGTGTTTTCCTA 57.049 34.783 0.00 0.00 0.00 2.94
3710 6027 6.584563 ACAATATGCAATTACGTGTGTTTTCC 59.415 34.615 0.00 0.00 0.00 3.13
3715 6032 5.871465 TCACAATATGCAATTACGTGTGT 57.129 34.783 0.00 0.00 36.96 3.72
3727 6125 6.974622 CACCCAAACTTCTATTCACAATATGC 59.025 38.462 0.00 0.00 0.00 3.14
3817 6225 5.283457 AGATCTCCAGCAACCTACAATAC 57.717 43.478 0.00 0.00 0.00 1.89
4057 6466 9.459640 GAGAGTTTATATACGCAATCAGTACAA 57.540 33.333 0.00 0.00 0.00 2.41
4070 6479 9.270640 TCGGTACTGAGAAGAGAGTTTATATAC 57.729 37.037 0.00 0.00 0.00 1.47
4071 6480 9.842775 TTCGGTACTGAGAAGAGAGTTTATATA 57.157 33.333 4.23 0.00 0.00 0.86
4072 6481 8.623030 GTTCGGTACTGAGAAGAGAGTTTATAT 58.377 37.037 4.23 0.00 0.00 0.86
4073 6482 7.609146 TGTTCGGTACTGAGAAGAGAGTTTATA 59.391 37.037 4.23 0.00 0.00 0.98
4162 6571 1.227999 AACATCTGTTCCACGCACCG 61.228 55.000 0.00 0.00 31.64 4.94
4234 6643 6.045955 CCTCTTCACTGCTTCTATAAACCTC 58.954 44.000 0.00 0.00 0.00 3.85
4262 6671 1.331138 TCAGGTAACGGCACAAAAACG 59.669 47.619 0.00 0.00 46.39 3.60
4387 6804 3.510388 TCACCGATAGCAAGTCTCAAG 57.490 47.619 0.00 0.00 0.00 3.02
4416 6833 1.001406 CAGGGCGACAGGAGGATATTC 59.999 57.143 0.00 0.00 0.00 1.75
4419 6836 0.755698 GTCAGGGCGACAGGAGGATA 60.756 60.000 0.00 0.00 44.69 2.59
4447 6864 2.979814 AATCATGATCGACGGGTTGA 57.020 45.000 9.06 0.00 0.00 3.18
4489 6914 4.708909 AGCAGAAGGATTTTTCAAGGGATC 59.291 41.667 0.00 0.00 0.00 3.36
4507 6932 4.235079 ACAATATACAAAGGGCAGCAGA 57.765 40.909 0.00 0.00 0.00 4.26
4511 6936 9.561069 AGAACTATAACAATATACAAAGGGCAG 57.439 33.333 0.00 0.00 0.00 4.85
4512 6937 9.555727 GAGAACTATAACAATATACAAAGGGCA 57.444 33.333 0.00 0.00 0.00 5.36
4579 7005 4.574674 TGAGGATAATGGCTCAAACACT 57.425 40.909 0.00 0.00 0.00 3.55
4639 7067 7.539034 AATTGTGAGTAGGCTTTGGTAATTT 57.461 32.000 0.00 0.00 0.00 1.82
4642 7070 7.455058 TCTTAATTGTGAGTAGGCTTTGGTAA 58.545 34.615 0.00 0.00 0.00 2.85
4664 7092 2.561478 AGGGTTACGCACAACATCTT 57.439 45.000 1.60 0.00 0.00 2.40
4763 7195 2.700897 ACACACCAGCTTCAGTACTTCT 59.299 45.455 0.00 0.00 0.00 2.85
4784 7216 4.724399 TCCTTTCAAGTGCATAAAGGTCA 58.276 39.130 21.95 9.65 46.17 4.02
4796 7228 5.310409 TGTCTTTCCAGATCCTTTCAAGT 57.690 39.130 0.00 0.00 0.00 3.16
4847 7279 1.955663 CTTGGCTTTGTTTGGCGCC 60.956 57.895 22.73 22.73 42.78 6.53
4917 7353 2.551071 GGTTCTGGTTCTGGTCTGAAGG 60.551 54.545 0.00 0.00 0.00 3.46
4966 7411 4.454678 CAGTTTATGGATAGCCTGCAAGA 58.545 43.478 0.00 0.00 34.07 3.02
5027 7472 2.151295 GAAGGCGTCGACAAGTTCC 58.849 57.895 17.16 7.90 0.00 3.62
5099 7544 2.536066 ACACCCTGTGTATACTGAGCA 58.464 47.619 4.17 0.00 45.56 4.26
5157 7610 0.670546 TAACGGTCTGAGCTTGCAGC 60.671 55.000 5.23 0.47 42.84 5.25
5192 7645 9.787435 TGTTGGGTATATGATATAAGTTTGTCC 57.213 33.333 0.00 0.00 0.00 4.02
5219 7799 6.844696 TGTACACTTGATTTTGACTCACTC 57.155 37.500 0.00 0.00 0.00 3.51
5338 7932 5.528690 TCACATATGAGCTTTATTCACAGCC 59.471 40.000 10.38 0.00 36.62 4.85
5389 7986 5.587443 TCACGTGACCGAAGAGAGATAATTA 59.413 40.000 15.76 0.00 37.88 1.40
5418 8015 3.256631 GCATTTCCCTTGTGACATCAAGT 59.743 43.478 13.29 0.00 42.01 3.16
5427 8182 2.205022 TCTCTGGCATTTCCCTTGTG 57.795 50.000 0.00 0.00 0.00 3.33
5429 8184 3.008835 TCATCTCTGGCATTTCCCTTG 57.991 47.619 0.00 0.00 0.00 3.61
5430 8185 3.744940 TTCATCTCTGGCATTTCCCTT 57.255 42.857 0.00 0.00 0.00 3.95
5525 8280 5.235516 ACTCCAGTTTTACACCAGTTATCG 58.764 41.667 0.00 0.00 0.00 2.92
5551 8325 5.465051 CCGGATGTATTAGTGATCTGTCAG 58.535 45.833 0.00 0.00 34.36 3.51
5573 8384 1.801178 CGAACAAGAGAACTGGAAGCC 59.199 52.381 0.00 0.00 37.60 4.35
5576 8387 5.462530 TGTATCGAACAAGAGAACTGGAA 57.537 39.130 0.00 0.00 34.29 3.53
5621 8434 2.371306 ACTCTAGCTCTCGGAAGTTCC 58.629 52.381 12.27 12.27 0.00 3.62
5862 8687 9.522804 GGTAGAGATACTGTTAACTTCTTCATG 57.477 37.037 7.22 0.00 0.00 3.07
5952 8783 2.882137 TCTTGATCGGTTGGTTGGTTTC 59.118 45.455 0.00 0.00 0.00 2.78
5972 8803 5.437060 TGTATTTCAGGAAGGGTATTGCTC 58.563 41.667 0.00 0.00 0.00 4.26
6051 8882 9.090692 TGTTTTGTACTCTTTATTCCTATACGC 57.909 33.333 0.00 0.00 0.00 4.42


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

AutoCloner maintained by Alex Coulton.