Multiple sequence alignment - TraesCS3D01G183700

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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 TraesCS3D01G183700 chr3D 100.000 6379 0 0 1 6379 168849712 168856090 0.000000e+00 11780.0
1 TraesCS3D01G183700 chr3D 90.795 239 20 1 3410 3646 350735151 350734913 1.030000e-82 318.0
2 TraesCS3D01G183700 chr3A 95.698 2441 55 13 664 3074 198494361 198491941 0.000000e+00 3880.0
3 TraesCS3D01G183700 chr3A 96.971 1684 34 4 3653 5319 198491470 198489787 0.000000e+00 2811.0
4 TraesCS3D01G183700 chr3A 89.362 658 58 10 1 652 198495084 198494433 0.000000e+00 817.0
5 TraesCS3D01G183700 chr3A 91.884 345 19 5 3072 3412 198491818 198491479 2.080000e-129 473.0
6 TraesCS3D01G183700 chr3A 91.379 174 15 0 3195 3368 609951132 609950959 8.270000e-59 239.0
7 TraesCS3D01G183700 chr3B 90.625 2464 108 35 666 3074 243937315 243939710 0.000000e+00 3157.0
8 TraesCS3D01G183700 chr3B 96.353 1700 35 7 3642 5319 243939928 243941622 0.000000e+00 2771.0
9 TraesCS3D01G183700 chr3B 89.034 611 61 4 1 607 243936371 243936979 0.000000e+00 752.0
10 TraesCS3D01G183700 chr3B 95.745 376 16 0 6004 6379 243944252 243944627 1.970000e-169 606.0
11 TraesCS3D01G183700 chr3B 95.455 44 2 0 3369 3412 243939889 243939932 3.190000e-08 71.3
12 TraesCS3D01G183700 chr1D 85.714 371 48 4 6007 6374 409094910 409094542 2.790000e-103 387.0
13 TraesCS3D01G183700 chr1D 88.333 240 25 2 3410 3646 409501711 409501472 1.050000e-72 285.0
14 TraesCS3D01G183700 chr1D 75.331 604 110 23 5417 6005 409095522 409094943 2.950000e-63 254.0
15 TraesCS3D01G183700 chr1A 84.169 379 55 4 6004 6379 372622127 372622503 4.700000e-96 363.0
16 TraesCS3D01G183700 chr1A 75.432 521 105 18 5502 6005 505288899 505288385 1.380000e-56 231.0
17 TraesCS3D01G183700 chr1A 77.898 371 67 11 6019 6379 273623062 273622697 3.870000e-52 217.0
18 TraesCS3D01G183700 chr1A 78.922 204 38 4 3 201 208884244 208884447 4.010000e-27 134.0
19 TraesCS3D01G183700 chr6B 92.469 239 12 4 3411 3646 276229253 276229488 2.850000e-88 337.0
20 TraesCS3D01G183700 chr6B 79.372 223 39 7 6160 6379 482566294 482566076 3.980000e-32 150.0
21 TraesCS3D01G183700 chr6B 86.179 123 15 1 3186 3308 713966775 713966895 1.440000e-26 132.0
22 TraesCS3D01G183700 chr6B 84.211 76 8 3 43 115 633870001 633870075 3.190000e-08 71.3
23 TraesCS3D01G183700 chr6D 91.213 239 16 4 3411 3646 151765571 151765807 2.870000e-83 320.0
24 TraesCS3D01G183700 chr5D 89.600 250 23 2 3407 3653 538171532 538171781 1.340000e-81 315.0
25 TraesCS3D01G183700 chr5D 88.477 243 22 5 3408 3646 118058217 118058457 8.090000e-74 289.0
26 TraesCS3D01G183700 chr5D 90.659 182 16 1 3187 3368 299073400 299073580 2.300000e-59 241.0
27 TraesCS3D01G183700 chr6A 89.167 240 22 3 3408 3644 614103075 614102837 4.840000e-76 296.0
28 TraesCS3D01G183700 chr2B 88.430 242 25 3 3408 3646 557731667 557731908 8.090000e-74 289.0
29 TraesCS3D01G183700 chr2B 92.899 169 11 1 3200 3368 316008030 316008197 1.780000e-60 244.0
30 TraesCS3D01G183700 chr2B 100.000 28 0 0 173 200 743411520 743411493 1.200000e-02 52.8
31 TraesCS3D01G183700 chr7B 88.017 242 26 3 3408 3646 414077422 414077181 3.760000e-72 283.0
32 TraesCS3D01G183700 chr7B 92.941 170 11 1 3199 3368 244640494 244640662 4.940000e-61 246.0
33 TraesCS3D01G183700 chr7B 85.227 88 10 3 369 454 539922938 539923024 3.170000e-13 87.9
34 TraesCS3D01G183700 chr2D 93.642 173 11 0 3196 3368 268894468 268894296 6.340000e-65 259.0
35 TraesCS3D01G183700 chr5B 93.064 173 12 0 3196 3368 573003719 573003547 2.950000e-63 254.0
36 TraesCS3D01G183700 chr5B 90.698 43 3 1 29 70 415814583 415814625 8.930000e-04 56.5
37 TraesCS3D01G183700 chr4A 93.064 173 12 0 3196 3368 584667429 584667601 2.950000e-63 254.0
38 TraesCS3D01G183700 chr4B 92.899 169 11 1 3200 3368 386210235 386210402 1.780000e-60 244.0
39 TraesCS3D01G183700 chr4B 84.239 184 23 4 3190 3373 22851756 22851933 2.360000e-39 174.0
40 TraesCS3D01G183700 chr7A 78.674 347 63 11 6038 6377 521899077 521899419 2.990000e-53 220.0
41 TraesCS3D01G183700 chr5A 87.912 91 11 0 6289 6379 128558894 128558984 2.430000e-19 108.0
42 TraesCS3D01G183700 chr5A 82.609 69 8 4 5 70 452990663 452990596 2.480000e-04 58.4
43 TraesCS3D01G183700 chr7D 86.000 100 12 2 356 454 511083114 511083212 8.750000e-19 106.0


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 TraesCS3D01G183700 chr3D 168849712 168856090 6378 False 11780.00 11780 100.00000 1 6379 1 chr3D.!!$F1 6378
1 TraesCS3D01G183700 chr3A 198489787 198495084 5297 True 1995.25 3880 93.47875 1 5319 4 chr3A.!!$R2 5318
2 TraesCS3D01G183700 chr3B 243936371 243944627 8256 False 1471.46 3157 93.44240 1 6379 5 chr3B.!!$F1 6378
3 TraesCS3D01G183700 chr1D 409094542 409095522 980 True 320.50 387 80.52250 5417 6374 2 chr1D.!!$R2 957
4 TraesCS3D01G183700 chr1A 505288385 505288899 514 True 231.00 231 75.43200 5502 6005 1 chr1A.!!$R2 503

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
353 355 0.526739 GAACTTGCCGGCGTTTGTTT 60.527 50.0 23.9 8.62 0.00 2.83 F
1759 2076 0.108615 CAGCCTCGTGTTTCCTCGAT 60.109 55.0 0.0 0.00 36.17 3.59 F
3337 3895 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.00 44.78 4.85 F
3647 4205 0.258194 ACCAGGACGGAGGTAGTAGG 59.742 60.0 0.0 0.00 36.07 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2590 0.777446 AGCTAAACCCCTTGCTTGGA 59.223 50.000 0.0 0.0 30.96 3.53 R
3628 4186 0.258194 CCTACTACCTCCGTCCTGGT 59.742 60.000 0.0 0.0 39.52 4.00 R
4807 5384 3.525537 AGATGCTAACCACGTTGATGAG 58.474 45.455 0.0 0.0 0.00 2.90 R
5438 7950 0.651031 GGACGCAAGCCGAAATCTAC 59.349 55.000 0.0 0.0 45.62 2.59 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
53 55 6.701400 ACTCACACAATTGGCAAGTTTTATTC 59.299 34.615 10.83 0.00 0.00 1.75
132 134 9.539825 TTTTAGCAATTATTGTTGATGTTGTGT 57.460 25.926 6.81 0.00 0.00 3.72
133 135 8.741101 TTAGCAATTATTGTTGATGTTGTGTC 57.259 30.769 6.81 0.00 0.00 3.67
146 148 7.742556 TGATGTTGTGTCATGATCAAGTTAA 57.257 32.000 13.86 4.60 0.00 2.01
151 153 7.281999 TGTTGTGTCATGATCAAGTTAACAAGA 59.718 33.333 8.61 5.44 0.00 3.02
160 162 7.223584 TGATCAAGTTAACAAGATCCAAGTCA 58.776 34.615 25.08 12.82 36.84 3.41
177 179 3.300388 AGTCATCCATAGTCACGGACAT 58.700 45.455 6.78 0.00 34.60 3.06
230 232 2.872842 GCACCAACTTACCCATACACGT 60.873 50.000 0.00 0.00 0.00 4.49
232 234 2.027837 ACCAACTTACCCATACACGTCC 60.028 50.000 0.00 0.00 0.00 4.79
238 240 1.660575 CCCATACACGTCCGATCGC 60.661 63.158 10.32 0.00 0.00 4.58
310 312 5.048364 GCTTTTTGTATGGGTGTGTGTATCA 60.048 40.000 0.00 0.00 0.00 2.15
325 327 4.202357 TGTGTATCAGTGCAGTTTCTTCCT 60.202 41.667 0.00 0.00 0.00 3.36
349 351 2.122167 TTGGAACTTGCCGGCGTTT 61.122 52.632 23.90 14.60 0.00 3.60
353 355 0.526739 GAACTTGCCGGCGTTTGTTT 60.527 50.000 23.90 8.62 0.00 2.83
457 461 3.078837 GCCCATTCGTAAAGAACCTCAA 58.921 45.455 0.00 0.00 42.39 3.02
464 468 6.613755 TTCGTAAAGAACCTCAAAAGGAAG 57.386 37.500 0.00 0.00 46.39 3.46
617 626 9.875675 TGTGTTTTTCAGAAAAGAAATGTTTTG 57.124 25.926 8.34 0.00 37.35 2.44
624 633 7.151308 TCAGAAAAGAAATGTTTTGTGTGTGT 58.849 30.769 11.07 0.00 40.10 3.72
646 655 7.334671 TGTGTAAATCAGTACAAACACACTTGA 59.665 33.333 13.15 0.00 41.48 3.02
652 661 4.808895 CAGTACAAACACACTTGAGCTGTA 59.191 41.667 0.00 0.00 32.45 2.74
654 663 2.607635 ACAAACACACTTGAGCTGTACG 59.392 45.455 0.00 0.00 0.00 3.67
656 665 0.939577 ACACACTTGAGCTGTACGCG 60.940 55.000 3.53 3.53 45.59 6.01
658 667 0.663568 ACACTTGAGCTGTACGCGTC 60.664 55.000 18.63 8.55 45.59 5.19
659 668 1.442184 ACTTGAGCTGTACGCGTCG 60.442 57.895 18.63 6.92 45.59 5.12
661 670 1.128724 CTTGAGCTGTACGCGTCGAG 61.129 60.000 18.63 14.45 45.59 4.04
925 1208 1.600916 AAGAGCAACACGGCTTCCC 60.601 57.895 0.00 0.00 45.99 3.97
926 1209 3.056328 GAGCAACACGGCTTCCCC 61.056 66.667 0.00 0.00 45.99 4.81
1005 1296 2.579657 CCACCTACCAGCACCACGA 61.580 63.158 0.00 0.00 0.00 4.35
1024 1315 5.692654 CCACGAAACGGAAATAAACCATTTT 59.307 36.000 0.00 0.00 36.96 1.82
1080 1371 1.166531 GCGCTCCTCTCTCTCTCTCC 61.167 65.000 0.00 0.00 0.00 3.71
1081 1372 0.469917 CGCTCCTCTCTCTCTCTCCT 59.530 60.000 0.00 0.00 0.00 3.69
1082 1373 1.541233 CGCTCCTCTCTCTCTCTCCTC 60.541 61.905 0.00 0.00 0.00 3.71
1083 1374 1.541233 GCTCCTCTCTCTCTCTCCTCG 60.541 61.905 0.00 0.00 0.00 4.63
1084 1375 1.070758 CTCCTCTCTCTCTCTCCTCGG 59.929 61.905 0.00 0.00 0.00 4.63
1280 1580 2.441750 AGCTTCCGATTGGGGCTAAATA 59.558 45.455 15.63 0.00 40.86 1.40
1483 1791 7.611213 ATTTTCCTTAGTTCACATCGTAAGG 57.389 36.000 0.00 0.00 42.01 2.69
1571 1888 9.601971 TTTACGTACTTCAAAATGAATTGTAGC 57.398 29.630 0.00 0.00 35.59 3.58
1572 1889 7.435068 ACGTACTTCAAAATGAATTGTAGCT 57.565 32.000 0.00 0.00 35.59 3.32
1629 1946 4.710324 TGGTATGTTCATCCCCGATTTAC 58.290 43.478 0.00 0.00 0.00 2.01
1725 2042 7.938140 TTTAACCTGATACCCAAGAAAGATG 57.062 36.000 0.00 0.00 0.00 2.90
1757 2074 0.319555 TTCAGCCTCGTGTTTCCTCG 60.320 55.000 0.00 0.00 0.00 4.63
1758 2075 1.176619 TCAGCCTCGTGTTTCCTCGA 61.177 55.000 0.00 0.00 35.51 4.04
1759 2076 0.108615 CAGCCTCGTGTTTCCTCGAT 60.109 55.000 0.00 0.00 36.17 3.59
1760 2077 0.608640 AGCCTCGTGTTTCCTCGATT 59.391 50.000 0.00 0.00 36.17 3.34
1761 2078 1.000145 GCCTCGTGTTTCCTCGATTC 59.000 55.000 0.00 0.00 36.17 2.52
1762 2079 1.404315 GCCTCGTGTTTCCTCGATTCT 60.404 52.381 0.00 0.00 36.17 2.40
1763 2080 2.531206 CCTCGTGTTTCCTCGATTCTC 58.469 52.381 0.00 0.00 36.17 2.87
1764 2081 2.177977 CTCGTGTTTCCTCGATTCTCG 58.822 52.381 0.00 0.00 42.10 4.04
2005 2326 3.942130 AATTTGTTAGCTTGCTCCCAC 57.058 42.857 0.00 0.00 0.00 4.61
2257 2578 4.553330 TCTTTCTGGATTGTAGGTCCAC 57.447 45.455 0.00 0.00 40.72 4.02
2863 3202 4.040339 GGGGTCAAATGTCAAAAACCTGAT 59.960 41.667 0.00 0.00 0.00 2.90
2878 3217 4.065321 ACCTGATAAGAAGATGGAAGCG 57.935 45.455 0.00 0.00 0.00 4.68
3057 3402 5.125417 GGACCACAAAATGAAGCTGCTTATA 59.875 40.000 15.95 8.06 0.00 0.98
3222 3780 1.678635 GGCAGCCTGGTGCATGTAA 60.679 57.895 21.31 0.00 45.93 2.41
3227 3785 1.369091 GCCTGGTGCATGTAACTCCG 61.369 60.000 0.00 0.00 40.77 4.63
3235 3793 0.447801 CATGTAACTCCGGCTTGCAC 59.552 55.000 0.00 0.00 0.00 4.57
3284 3842 1.066716 TGCAGCCTTTCCATGCATTTC 60.067 47.619 0.00 0.00 44.56 2.17
3337 3895 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
3421 3979 8.937207 AATATCAGTTCTATTACTACCTCCGT 57.063 34.615 0.00 0.00 0.00 4.69
3422 3980 6.880942 ATCAGTTCTATTACTACCTCCGTC 57.119 41.667 0.00 0.00 0.00 4.79
3423 3981 5.128919 TCAGTTCTATTACTACCTCCGTCC 58.871 45.833 0.00 0.00 0.00 4.79
3424 3982 5.104193 TCAGTTCTATTACTACCTCCGTCCT 60.104 44.000 0.00 0.00 0.00 3.85
3425 3983 5.008811 CAGTTCTATTACTACCTCCGTCCTG 59.991 48.000 0.00 0.00 0.00 3.86
3426 3984 4.096190 TCTATTACTACCTCCGTCCTGG 57.904 50.000 0.00 0.00 40.09 4.45
3427 3985 2.842645 ATTACTACCTCCGTCCTGGT 57.157 50.000 0.00 0.00 39.52 4.00
3428 3986 2.610438 TTACTACCTCCGTCCTGGTT 57.390 50.000 0.00 0.00 39.52 3.67
3429 3987 2.610438 TACTACCTCCGTCCTGGTTT 57.390 50.000 0.00 0.00 39.52 3.27
3430 3988 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
3431 3989 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
3432 3990 3.447950 ACTACCTCCGTCCTGGTTTATT 58.552 45.455 0.00 0.00 39.52 1.40
3433 3991 2.781681 ACCTCCGTCCTGGTTTATTG 57.218 50.000 0.00 0.00 39.52 1.90
3434 3992 1.280998 ACCTCCGTCCTGGTTTATTGG 59.719 52.381 0.00 0.00 39.52 3.16
3435 3993 1.280998 CCTCCGTCCTGGTTTATTGGT 59.719 52.381 0.00 0.00 39.52 3.67
3436 3994 2.629051 CTCCGTCCTGGTTTATTGGTC 58.371 52.381 0.00 0.00 39.52 4.02
3437 3995 1.279846 TCCGTCCTGGTTTATTGGTCC 59.720 52.381 0.00 0.00 39.52 4.46
3438 3996 1.680860 CCGTCCTGGTTTATTGGTCCC 60.681 57.143 0.00 0.00 0.00 4.46
3439 3997 1.280998 CGTCCTGGTTTATTGGTCCCT 59.719 52.381 0.00 0.00 0.00 4.20
3440 3998 2.290705 CGTCCTGGTTTATTGGTCCCTT 60.291 50.000 0.00 0.00 0.00 3.95
3441 3999 3.353557 GTCCTGGTTTATTGGTCCCTTC 58.646 50.000 0.00 0.00 0.00 3.46
3442 4000 2.026636 TCCTGGTTTATTGGTCCCTTCG 60.027 50.000 0.00 0.00 0.00 3.79
3443 4001 2.290705 CCTGGTTTATTGGTCCCTTCGT 60.291 50.000 0.00 0.00 0.00 3.85
3444 4002 3.054948 CCTGGTTTATTGGTCCCTTCGTA 60.055 47.826 0.00 0.00 0.00 3.43
3445 4003 4.384868 CCTGGTTTATTGGTCCCTTCGTAT 60.385 45.833 0.00 0.00 0.00 3.06
3446 4004 5.182169 TGGTTTATTGGTCCCTTCGTATT 57.818 39.130 0.00 0.00 0.00 1.89
3447 4005 4.944930 TGGTTTATTGGTCCCTTCGTATTG 59.055 41.667 0.00 0.00 0.00 1.90
3448 4006 4.945543 GGTTTATTGGTCCCTTCGTATTGT 59.054 41.667 0.00 0.00 0.00 2.71
3449 4007 5.163693 GGTTTATTGGTCCCTTCGTATTGTG 60.164 44.000 0.00 0.00 0.00 3.33
3450 4008 3.713826 ATTGGTCCCTTCGTATTGTGT 57.286 42.857 0.00 0.00 0.00 3.72
3451 4009 2.754946 TGGTCCCTTCGTATTGTGTC 57.245 50.000 0.00 0.00 0.00 3.67
3452 4010 1.972075 TGGTCCCTTCGTATTGTGTCA 59.028 47.619 0.00 0.00 0.00 3.58
3453 4011 2.369203 TGGTCCCTTCGTATTGTGTCAA 59.631 45.455 0.00 0.00 0.00 3.18
3454 4012 3.181453 TGGTCCCTTCGTATTGTGTCAAA 60.181 43.478 0.00 0.00 0.00 2.69
3455 4013 4.007659 GGTCCCTTCGTATTGTGTCAAAT 58.992 43.478 0.00 0.00 0.00 2.32
3456 4014 4.457949 GGTCCCTTCGTATTGTGTCAAATT 59.542 41.667 0.00 0.00 0.00 1.82
3457 4015 5.048294 GGTCCCTTCGTATTGTGTCAAATTT 60.048 40.000 0.00 0.00 0.00 1.82
3458 4016 6.443792 GTCCCTTCGTATTGTGTCAAATTTT 58.556 36.000 0.00 0.00 0.00 1.82
3459 4017 6.362283 GTCCCTTCGTATTGTGTCAAATTTTG 59.638 38.462 2.59 2.59 0.00 2.44
3460 4018 6.263392 TCCCTTCGTATTGTGTCAAATTTTGA 59.737 34.615 7.74 7.74 37.33 2.69
3461 4019 7.040062 TCCCTTCGTATTGTGTCAAATTTTGAT 60.040 33.333 14.54 1.78 42.47 2.57
3462 4020 7.273381 CCCTTCGTATTGTGTCAAATTTTGATC 59.727 37.037 14.54 11.31 42.47 2.92
3463 4021 7.807433 CCTTCGTATTGTGTCAAATTTTGATCA 59.193 33.333 14.54 13.38 42.47 2.92
3464 4022 9.345517 CTTCGTATTGTGTCAAATTTTGATCAT 57.654 29.630 14.54 7.53 42.47 2.45
3534 4092 8.706492 TCGTTGGATTCGTATTTAAACATAGT 57.294 30.769 0.00 0.00 0.00 2.12
3535 4093 9.153721 TCGTTGGATTCGTATTTAAACATAGTT 57.846 29.630 0.00 0.00 0.00 2.24
3536 4094 9.763465 CGTTGGATTCGTATTTAAACATAGTTT 57.237 29.630 0.51 0.51 0.00 2.66
3573 4131 6.922247 TTTTTGTGACATGCATTGACATTT 57.078 29.167 0.00 0.00 32.72 2.32
3574 4132 6.922247 TTTTGTGACATGCATTGACATTTT 57.078 29.167 0.00 0.00 32.72 1.82
3575 4133 5.908916 TTGTGACATGCATTGACATTTTG 57.091 34.783 0.00 0.00 32.72 2.44
3576 4134 4.946445 TGTGACATGCATTGACATTTTGT 58.054 34.783 0.00 0.00 32.72 2.83
3577 4135 5.358090 TGTGACATGCATTGACATTTTGTT 58.642 33.333 0.00 0.00 32.72 2.83
3578 4136 6.510536 TGTGACATGCATTGACATTTTGTTA 58.489 32.000 0.00 0.00 32.72 2.41
3579 4137 6.641723 TGTGACATGCATTGACATTTTGTTAG 59.358 34.615 0.00 0.00 32.72 2.34
3580 4138 6.642131 GTGACATGCATTGACATTTTGTTAGT 59.358 34.615 0.00 0.00 32.72 2.24
3581 4139 7.169645 GTGACATGCATTGACATTTTGTTAGTT 59.830 33.333 0.00 0.00 32.72 2.24
3582 4140 8.355913 TGACATGCATTGACATTTTGTTAGTTA 58.644 29.630 0.00 0.00 0.00 2.24
3583 4141 9.190858 GACATGCATTGACATTTTGTTAGTTAA 57.809 29.630 0.00 0.00 0.00 2.01
3584 4142 9.539825 ACATGCATTGACATTTTGTTAGTTAAA 57.460 25.926 0.00 0.00 0.00 1.52
3587 4145 9.593134 TGCATTGACATTTTGTTAGTTAAAACT 57.407 25.926 0.39 0.39 42.91 2.66
3588 4146 9.848172 GCATTGACATTTTGTTAGTTAAAACTG 57.152 29.630 5.62 0.00 40.07 3.16
3591 4149 8.918961 TGACATTTTGTTAGTTAAAACTGTGG 57.081 30.769 5.62 0.00 40.07 4.17
3592 4150 8.524487 TGACATTTTGTTAGTTAAAACTGTGGT 58.476 29.630 5.62 0.00 40.07 4.16
3593 4151 8.920509 ACATTTTGTTAGTTAAAACTGTGGTC 57.079 30.769 5.62 0.00 40.07 4.02
3594 4152 8.524487 ACATTTTGTTAGTTAAAACTGTGGTCA 58.476 29.630 5.62 0.00 40.07 4.02
3595 4153 9.360093 CATTTTGTTAGTTAAAACTGTGGTCAA 57.640 29.630 5.62 2.13 40.07 3.18
3596 4154 9.930693 ATTTTGTTAGTTAAAACTGTGGTCAAA 57.069 25.926 5.62 6.98 40.07 2.69
3597 4155 9.760077 TTTTGTTAGTTAAAACTGTGGTCAAAA 57.240 25.926 5.62 11.21 40.07 2.44
3598 4156 9.930693 TTTGTTAGTTAAAACTGTGGTCAAAAT 57.069 25.926 5.62 0.00 40.07 1.82
3599 4157 9.930693 TTGTTAGTTAAAACTGTGGTCAAAATT 57.069 25.926 5.62 0.00 40.07 1.82
3600 4158 9.930693 TGTTAGTTAAAACTGTGGTCAAAATTT 57.069 25.926 5.62 0.00 40.07 1.82
3603 4161 8.474006 AGTTAAAACTGTGGTCAAAATTTGAC 57.526 30.769 25.84 25.84 46.99 3.18
3617 4175 8.870160 TCAAAATTTGACACTGAATACAAAGG 57.130 30.769 4.03 0.00 36.07 3.11
3618 4176 7.925483 TCAAAATTTGACACTGAATACAAAGGG 59.075 33.333 4.03 0.00 36.07 3.95
3619 4177 5.982890 ATTTGACACTGAATACAAAGGGG 57.017 39.130 0.00 0.00 36.07 4.79
3620 4178 4.715534 TTGACACTGAATACAAAGGGGA 57.284 40.909 0.00 0.00 0.00 4.81
3621 4179 4.015872 TGACACTGAATACAAAGGGGAC 57.984 45.455 0.00 0.00 0.00 4.46
3623 4181 4.841813 TGACACTGAATACAAAGGGGACTA 59.158 41.667 0.00 0.00 42.68 2.59
3624 4182 5.308497 TGACACTGAATACAAAGGGGACTAA 59.692 40.000 0.00 0.00 42.68 2.24
3625 4183 6.012858 TGACACTGAATACAAAGGGGACTAAT 60.013 38.462 0.00 0.00 42.68 1.73
3626 4184 7.181305 TGACACTGAATACAAAGGGGACTAATA 59.819 37.037 0.00 0.00 42.68 0.98
3627 4185 7.924541 ACACTGAATACAAAGGGGACTAATAA 58.075 34.615 0.00 0.00 42.68 1.40
3628 4186 8.387813 ACACTGAATACAAAGGGGACTAATAAA 58.612 33.333 0.00 0.00 42.68 1.40
3629 4187 8.674607 CACTGAATACAAAGGGGACTAATAAAC 58.325 37.037 0.00 0.00 42.68 2.01
3630 4188 7.832685 ACTGAATACAAAGGGGACTAATAAACC 59.167 37.037 0.00 0.00 42.68 3.27
3631 4189 7.700846 TGAATACAAAGGGGACTAATAAACCA 58.299 34.615 0.00 0.00 42.68 3.67
3632 4190 7.832187 TGAATACAAAGGGGACTAATAAACCAG 59.168 37.037 0.00 0.00 42.68 4.00
3633 4191 4.930696 ACAAAGGGGACTAATAAACCAGG 58.069 43.478 0.00 0.00 42.68 4.45
3634 4192 4.604490 ACAAAGGGGACTAATAAACCAGGA 59.396 41.667 0.00 0.00 42.68 3.86
3635 4193 4.857130 AAGGGGACTAATAAACCAGGAC 57.143 45.455 0.00 0.00 42.68 3.85
3636 4194 2.770232 AGGGGACTAATAAACCAGGACG 59.230 50.000 0.00 0.00 40.61 4.79
3637 4195 2.158856 GGGGACTAATAAACCAGGACGG 60.159 54.545 0.00 0.00 42.50 4.79
3638 4196 2.767960 GGGACTAATAAACCAGGACGGA 59.232 50.000 0.00 0.00 38.63 4.69
3639 4197 3.181468 GGGACTAATAAACCAGGACGGAG 60.181 52.174 0.00 0.00 38.63 4.63
3640 4198 3.181468 GGACTAATAAACCAGGACGGAGG 60.181 52.174 0.00 0.00 38.63 4.30
3641 4199 3.447950 ACTAATAAACCAGGACGGAGGT 58.552 45.455 0.00 0.00 40.61 3.85
3642 4200 4.613437 ACTAATAAACCAGGACGGAGGTA 58.387 43.478 0.00 0.00 37.07 3.08
3643 4201 4.648307 ACTAATAAACCAGGACGGAGGTAG 59.352 45.833 0.00 0.00 37.07 3.18
3644 4202 2.610438 TAAACCAGGACGGAGGTAGT 57.390 50.000 0.00 0.00 37.07 2.73
3645 4203 2.610438 AAACCAGGACGGAGGTAGTA 57.390 50.000 0.00 0.00 37.07 1.82
3646 4204 2.140839 AACCAGGACGGAGGTAGTAG 57.859 55.000 0.00 0.00 37.07 2.57
3647 4205 0.258194 ACCAGGACGGAGGTAGTAGG 59.742 60.000 0.00 0.00 36.07 3.18
3648 4206 0.258194 CCAGGACGGAGGTAGTAGGT 59.742 60.000 0.00 0.00 36.56 3.08
3649 4207 1.492176 CCAGGACGGAGGTAGTAGGTA 59.508 57.143 0.00 0.00 36.56 3.08
3650 4208 2.107901 CCAGGACGGAGGTAGTAGGTAT 59.892 54.545 0.00 0.00 36.56 2.73
3651 4209 3.410508 CAGGACGGAGGTAGTAGGTATC 58.589 54.545 0.00 0.00 0.00 2.24
3974 4548 3.385111 CACCCCTAGTATCCAGAACAGAC 59.615 52.174 0.00 0.00 0.00 3.51
4074 4648 0.955178 ATGTAGGCAGATCTCGGACG 59.045 55.000 0.00 0.00 0.00 4.79
4153 4727 2.025155 GAGTTCCATGCTCTCGACCTA 58.975 52.381 0.00 0.00 0.00 3.08
4385 4959 6.261381 TGTGTTCAAAGCTATTAAAGGAACGT 59.739 34.615 0.00 0.00 36.77 3.99
4474 5048 7.172532 TGCAAACTGTTTGGATAGTACTACTTG 59.827 37.037 28.61 4.70 40.94 3.16
4481 5055 6.452494 TTGGATAGTACTACTTGTGAGAGC 57.548 41.667 4.31 0.00 0.00 4.09
4643 5220 3.450457 AGCACAAGAGAAGTATGAGGGAG 59.550 47.826 0.00 0.00 0.00 4.30
4807 5384 3.576118 TGGAGAGAATAGCCAGCTACATC 59.424 47.826 0.51 4.08 0.00 3.06
5015 5593 7.968405 GGTACTATTCATTAAAGCACACTTTGG 59.032 37.037 1.40 0.00 45.72 3.28
5273 5851 3.144506 CATGAGTGTTTGGAGACTGCTT 58.855 45.455 0.00 0.00 28.00 3.91
5319 5897 8.807118 AGATGCAGGAGTTCGAATATAAATAGA 58.193 33.333 0.00 0.00 0.00 1.98
5320 5898 8.764524 ATGCAGGAGTTCGAATATAAATAGAC 57.235 34.615 0.00 0.00 0.00 2.59
5321 5899 7.722363 TGCAGGAGTTCGAATATAAATAGACA 58.278 34.615 0.00 0.00 0.00 3.41
5322 5900 8.367911 TGCAGGAGTTCGAATATAAATAGACAT 58.632 33.333 0.00 0.00 0.00 3.06
5323 5901 9.856488 GCAGGAGTTCGAATATAAATAGACATA 57.144 33.333 0.00 0.00 0.00 2.29
5397 7909 8.747666 CATTTCTAGAACGAGTATTAGAGCAAC 58.252 37.037 4.18 0.00 0.00 4.17
5416 7928 4.233789 CAACTCTAGCAGATCCGCTAATC 58.766 47.826 11.69 0.00 43.68 1.75
5441 7953 9.627123 TCTAAATATTTTTGTGGGATCCTGTAG 57.373 33.333 12.58 0.00 0.00 2.74
5566 8094 4.821589 CTTCCACTCGCCGCCCTC 62.822 72.222 0.00 0.00 0.00 4.30
5583 8111 4.489771 CGATCTTGCCGGCCCCTT 62.490 66.667 26.77 6.33 0.00 3.95
5585 8113 3.338250 ATCTTGCCGGCCCCTTGA 61.338 61.111 26.77 14.74 0.00 3.02
5586 8114 3.645268 ATCTTGCCGGCCCCTTGAC 62.645 63.158 26.77 0.00 0.00 3.18
5593 8121 3.379445 GGCCCCTTGACGTCTCGA 61.379 66.667 17.92 1.92 0.00 4.04
5632 8160 1.299926 CACTATGGAGTACCCGCGC 60.300 63.158 0.00 0.00 37.93 6.86
5667 8195 4.596585 CCCCCAACCGTGCCACTT 62.597 66.667 0.00 0.00 0.00 3.16
5709 8246 4.622456 GTTGCCGTGCCAACACCG 62.622 66.667 6.11 0.00 44.40 4.94
5718 8255 2.029073 CCAACACCGTCTGTCGCT 59.971 61.111 0.00 0.00 38.35 4.93
5796 8333 1.448013 GCCGCCTTCTTCTAACGCT 60.448 57.895 0.00 0.00 0.00 5.07
5800 8337 1.469251 CGCCTTCTTCTAACGCTGCTA 60.469 52.381 0.00 0.00 0.00 3.49
5811 8348 2.800541 CGCTGCTATGCTCCCTCCA 61.801 63.158 0.00 0.00 0.00 3.86
5900 8452 3.009714 GGGCCCGAGGAAGAAGGT 61.010 66.667 5.69 0.00 0.00 3.50
5902 8454 2.593956 GGCCCGAGGAAGAAGGTGT 61.594 63.158 0.00 0.00 0.00 4.16
5914 8466 0.951040 GAAGGTGTCCACGGCTTGAG 60.951 60.000 0.00 0.00 0.00 3.02
5942 8494 1.271840 CCTCCACCCCCTTCGATCAA 61.272 60.000 0.00 0.00 0.00 2.57
5973 8525 2.982130 GATCCGGTCCACTGCACT 59.018 61.111 0.00 0.00 0.00 4.40
5982 8534 2.338015 CCACTGCACTGACCATGCC 61.338 63.158 0.00 0.00 42.69 4.40
6027 8613 6.621613 GTTATCTTTGGTTGGACTTTGGATC 58.378 40.000 0.00 0.00 0.00 3.36
6043 8629 5.539582 TTGGATCGTTTCCTTATGTTTCG 57.460 39.130 8.30 0.00 45.68 3.46
6083 8671 7.066284 GGAGCAAACATTCACTCAACATATACT 59.934 37.037 0.00 0.00 0.00 2.12
6101 8689 3.425162 ACTGAAATGTTGGAGGAGACC 57.575 47.619 0.00 0.00 0.00 3.85
6120 8708 1.598130 GCGGTGGACTTGAGTGCTT 60.598 57.895 4.31 0.00 37.28 3.91
6122 8710 1.284982 CGGTGGACTTGAGTGCTTCG 61.285 60.000 4.31 4.50 37.28 3.79
6219 8807 1.992277 GAGGAGCTTGAGGAGGCCA 60.992 63.158 5.01 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.101585 TGTGTGAGTGTCTGAGGATTCTTT 59.898 41.667 0.00 0.00 0.00 2.52
22 23 2.221169 GCCAATTGTGTGAGTGTCTGA 58.779 47.619 4.43 0.00 0.00 3.27
25 26 2.358898 ACTTGCCAATTGTGTGAGTGTC 59.641 45.455 4.43 0.00 0.00 3.67
26 27 2.378038 ACTTGCCAATTGTGTGAGTGT 58.622 42.857 4.43 0.00 0.00 3.55
53 55 6.147821 ACGGATCTTGACAACTTCAACTAATG 59.852 38.462 0.00 0.00 39.45 1.90
69 71 9.490663 CTTAATTTTGTTAGCTAACGGATCTTG 57.509 33.333 27.07 12.72 39.00 3.02
132 134 7.884877 ACTTGGATCTTGTTAACTTGATCATGA 59.115 33.333 26.70 0.00 37.60 3.07
133 135 8.048534 ACTTGGATCTTGTTAACTTGATCATG 57.951 34.615 26.70 20.89 37.60 3.07
146 148 5.426509 TGACTATGGATGACTTGGATCTTGT 59.573 40.000 0.00 0.00 0.00 3.16
151 153 3.070159 CCGTGACTATGGATGACTTGGAT 59.930 47.826 0.00 0.00 34.72 3.41
160 162 1.070758 GCCATGTCCGTGACTATGGAT 59.929 52.381 23.33 4.82 43.67 3.41
177 179 8.691797 GTTGGGTTAAATCTATTCAAATAGCCA 58.308 33.333 5.11 0.00 38.57 4.75
205 207 2.675658 ATGGGTAAGTTGGTGCACTT 57.324 45.000 17.98 5.50 40.28 3.16
230 232 1.827394 CCTTTTAGGGGCGATCGGA 59.173 57.895 18.30 0.00 0.00 4.55
232 234 3.732470 GCCTTTTAGGGGCGATCG 58.268 61.111 11.69 11.69 40.19 3.69
290 292 5.000591 CACTGATACACACACCCATACAAA 58.999 41.667 0.00 0.00 0.00 2.83
344 346 1.269051 CCCCACTCAAGAAACAAACGC 60.269 52.381 0.00 0.00 0.00 4.84
349 351 2.818751 ACAACCCCACTCAAGAAACA 57.181 45.000 0.00 0.00 0.00 2.83
353 355 2.976185 TCACATACAACCCCACTCAAGA 59.024 45.455 0.00 0.00 0.00 3.02
431 435 2.937149 GTTCTTTACGAATGGGCTCTCC 59.063 50.000 0.00 0.00 33.45 3.71
444 448 6.296803 TCTCCTTCCTTTTGAGGTTCTTTAC 58.703 40.000 0.00 0.00 0.00 2.01
457 461 9.862149 TTTCAATACTAGTTTTCTCCTTCCTTT 57.138 29.630 0.00 0.00 0.00 3.11
464 468 9.968743 CATTACGTTTCAATACTAGTTTTCTCC 57.031 33.333 0.00 0.00 0.00 3.71
594 603 9.877137 ACACAAAACATTTCTTTTCTGAAAAAC 57.123 25.926 15.67 0.00 39.08 2.43
600 609 7.350110 ACACACACAAAACATTTCTTTTCTG 57.650 32.000 0.00 0.00 0.00 3.02
624 633 6.765989 AGCTCAAGTGTGTTTGTACTGATTTA 59.234 34.615 0.00 0.00 0.00 1.40
629 638 3.623060 ACAGCTCAAGTGTGTTTGTACTG 59.377 43.478 0.00 0.00 37.71 2.74
646 655 1.154263 GAACTCGACGCGTACAGCT 60.154 57.895 13.97 1.36 45.59 4.24
656 665 2.355481 AACGGCCGTGAACTCGAC 60.355 61.111 34.95 0.00 0.00 4.20
658 667 1.952133 TTGAACGGCCGTGAACTCG 60.952 57.895 34.95 1.49 0.00 4.18
659 668 1.155424 TGTTGAACGGCCGTGAACTC 61.155 55.000 35.14 28.38 0.00 3.01
661 670 1.278637 CTGTTGAACGGCCGTGAAC 59.721 57.895 34.95 33.08 0.00 3.18
821 1104 2.365582 GTGCCGGAGATGTTTTGGTAT 58.634 47.619 5.05 0.00 0.00 2.73
994 1285 1.440938 TTTCCGTTTCGTGGTGCTGG 61.441 55.000 0.00 0.00 0.00 4.85
1024 1315 0.178955 TGGGTACGAAGACTGGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
1080 1371 1.188871 GGGGAATAGGAGGAGCCGAG 61.189 65.000 0.00 0.00 43.43 4.63
1081 1372 1.152312 GGGGAATAGGAGGAGCCGA 60.152 63.158 0.00 0.00 43.43 5.54
1082 1373 2.217745 GGGGGAATAGGAGGAGCCG 61.218 68.421 0.00 0.00 43.43 5.52
1083 1374 0.838554 GAGGGGGAATAGGAGGAGCC 60.839 65.000 0.00 0.00 0.00 4.70
1084 1375 0.838554 GGAGGGGGAATAGGAGGAGC 60.839 65.000 0.00 0.00 0.00 4.70
1280 1580 0.784495 TACCTCGAGCCTATGGGGAT 59.216 55.000 6.99 0.00 37.23 3.85
1368 1669 4.624024 AGTCGTCGATTCTTCGCAAAAATA 59.376 37.500 0.00 0.00 45.10 1.40
1391 1699 4.303282 GTGCAAAATTTTCTCCGCCTAAA 58.697 39.130 0.00 0.00 0.00 1.85
1466 1774 6.594788 ACTAACCCTTACGATGTGAACTAA 57.405 37.500 0.00 0.00 0.00 2.24
1483 1791 7.096353 GCAGTTTCCGTCAAAAATTAACTAACC 60.096 37.037 0.00 0.00 0.00 2.85
1571 1888 9.436957 AACAATGTAAAAGATAGACCTGTGTAG 57.563 33.333 0.00 0.00 0.00 2.74
1572 1889 9.214957 CAACAATGTAAAAGATAGACCTGTGTA 57.785 33.333 0.00 0.00 0.00 2.90
1629 1946 5.587388 ATGACTGCATTTCCCAACAATAG 57.413 39.130 0.00 0.00 0.00 1.73
1725 2042 2.860735 GAGGCTGAATGACACGTATGAC 59.139 50.000 0.00 0.00 0.00 3.06
1757 2074 8.820933 TGTATGTGAAATCAAGAATCGAGAATC 58.179 33.333 0.00 0.00 0.00 2.52
1758 2075 8.607459 GTGTATGTGAAATCAAGAATCGAGAAT 58.393 33.333 0.00 0.00 0.00 2.40
1759 2076 7.602265 TGTGTATGTGAAATCAAGAATCGAGAA 59.398 33.333 0.00 0.00 0.00 2.87
1760 2077 7.096551 TGTGTATGTGAAATCAAGAATCGAGA 58.903 34.615 0.00 0.00 0.00 4.04
1761 2078 7.294676 TGTGTATGTGAAATCAAGAATCGAG 57.705 36.000 0.00 0.00 0.00 4.04
1762 2079 7.848223 ATGTGTATGTGAAATCAAGAATCGA 57.152 32.000 0.00 0.00 0.00 3.59
1763 2080 9.642312 CTTATGTGTATGTGAAATCAAGAATCG 57.358 33.333 0.00 0.00 0.00 3.34
1793 2110 6.818354 GTTGTGTGCAATGTGAGAGCATCTA 61.818 44.000 0.00 0.00 40.83 1.98
2005 2326 4.868171 TGCCACTAAGCTATTTACTTCACG 59.132 41.667 0.00 0.00 0.00 4.35
2164 2485 8.946085 TGAAGTTAAAGAAATGATACGCTTCAT 58.054 29.630 0.00 0.00 37.96 2.57
2165 2486 8.227791 GTGAAGTTAAAGAAATGATACGCTTCA 58.772 33.333 0.00 0.00 37.05 3.02
2166 2487 8.227791 TGTGAAGTTAAAGAAATGATACGCTTC 58.772 33.333 0.00 0.00 0.00 3.86
2167 2488 8.094798 TGTGAAGTTAAAGAAATGATACGCTT 57.905 30.769 0.00 0.00 0.00 4.68
2168 2489 7.667043 TGTGAAGTTAAAGAAATGATACGCT 57.333 32.000 0.00 0.00 0.00 5.07
2169 2490 8.722342 TTTGTGAAGTTAAAGAAATGATACGC 57.278 30.769 0.00 0.00 0.00 4.42
2198 2519 6.014584 AGGGGTCCAAATTTAATTGTCACTTC 60.015 38.462 0.00 0.00 0.00 3.01
2269 2590 0.777446 AGCTAAACCCCTTGCTTGGA 59.223 50.000 0.00 0.00 30.96 3.53
2878 3217 1.269051 CCAGCTTTGGAACGTTTGGAC 60.269 52.381 0.46 0.00 0.00 4.02
2986 3331 8.916062 TCACCAACTATTGAGACCGTAAATATA 58.084 33.333 0.00 0.00 0.00 0.86
3138 3694 4.908966 AAAAGAATGTAAGCGCATTTGC 57.091 36.364 11.47 0.00 38.98 3.68
3211 3769 1.376683 GCCGGAGTTACATGCACCA 60.377 57.895 5.05 0.00 0.00 4.17
3222 3780 4.335647 CCCTGTGCAAGCCGGAGT 62.336 66.667 5.05 0.00 0.00 3.85
3227 3785 4.329545 TCGGACCCTGTGCAAGCC 62.330 66.667 0.00 0.00 0.00 4.35
3235 3793 1.302511 CCAAAGTGGTCGGACCCTG 60.303 63.158 23.81 14.77 37.50 4.45
3284 3842 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
3353 3911 0.258774 TATGAAAGGGGAGCCTTGGC 59.741 55.000 2.97 2.97 0.00 4.52
3412 3970 3.431766 CCAATAAACCAGGACGGAGGTAG 60.432 52.174 0.00 0.00 37.07 3.18
3413 3971 2.502538 CCAATAAACCAGGACGGAGGTA 59.497 50.000 0.00 0.00 37.07 3.08
3414 3972 1.280998 CCAATAAACCAGGACGGAGGT 59.719 52.381 0.00 0.00 40.61 3.85
3415 3973 1.280998 ACCAATAAACCAGGACGGAGG 59.719 52.381 0.00 0.00 38.63 4.30
3416 3974 2.629051 GACCAATAAACCAGGACGGAG 58.371 52.381 0.00 0.00 38.63 4.63
3417 3975 1.279846 GGACCAATAAACCAGGACGGA 59.720 52.381 0.00 0.00 38.63 4.69
3418 3976 1.680860 GGGACCAATAAACCAGGACGG 60.681 57.143 0.00 0.00 42.50 4.79
3419 3977 1.280998 AGGGACCAATAAACCAGGACG 59.719 52.381 0.00 0.00 0.00 4.79
3420 3978 3.353557 GAAGGGACCAATAAACCAGGAC 58.646 50.000 0.00 0.00 0.00 3.85
3421 3979 2.026636 CGAAGGGACCAATAAACCAGGA 60.027 50.000 0.00 0.00 0.00 3.86
3422 3980 2.290705 ACGAAGGGACCAATAAACCAGG 60.291 50.000 0.00 0.00 0.00 4.45
3423 3981 3.067684 ACGAAGGGACCAATAAACCAG 57.932 47.619 0.00 0.00 0.00 4.00
3424 3982 4.847990 ATACGAAGGGACCAATAAACCA 57.152 40.909 0.00 0.00 0.00 3.67
3425 3983 4.945543 ACAATACGAAGGGACCAATAAACC 59.054 41.667 0.00 0.00 0.00 3.27
3426 3984 5.413523 ACACAATACGAAGGGACCAATAAAC 59.586 40.000 0.00 0.00 0.00 2.01
3427 3985 5.562635 ACACAATACGAAGGGACCAATAAA 58.437 37.500 0.00 0.00 0.00 1.40
3428 3986 5.168647 ACACAATACGAAGGGACCAATAA 57.831 39.130 0.00 0.00 0.00 1.40
3429 3987 4.223255 TGACACAATACGAAGGGACCAATA 59.777 41.667 0.00 0.00 0.00 1.90
3430 3988 3.008594 TGACACAATACGAAGGGACCAAT 59.991 43.478 0.00 0.00 0.00 3.16
3431 3989 2.369203 TGACACAATACGAAGGGACCAA 59.631 45.455 0.00 0.00 0.00 3.67
3432 3990 1.972075 TGACACAATACGAAGGGACCA 59.028 47.619 0.00 0.00 0.00 4.02
3433 3991 2.754946 TGACACAATACGAAGGGACC 57.245 50.000 0.00 0.00 0.00 4.46
3434 3992 5.622770 AATTTGACACAATACGAAGGGAC 57.377 39.130 0.00 0.00 0.00 4.46
3435 3993 6.263392 TCAAAATTTGACACAATACGAAGGGA 59.737 34.615 4.03 0.00 34.08 4.20
3436 3994 6.442952 TCAAAATTTGACACAATACGAAGGG 58.557 36.000 4.03 0.00 34.08 3.95
3437 3995 7.807433 TGATCAAAATTTGACACAATACGAAGG 59.193 33.333 10.91 0.00 43.48 3.46
3438 3996 8.726650 TGATCAAAATTTGACACAATACGAAG 57.273 30.769 10.91 0.00 43.48 3.79
3508 4066 9.321562 ACTATGTTTAAATACGAATCCAACGAT 57.678 29.630 0.00 0.00 34.70 3.73
3509 4067 8.706492 ACTATGTTTAAATACGAATCCAACGA 57.294 30.769 0.00 0.00 34.70 3.85
3510 4068 9.763465 AAACTATGTTTAAATACGAATCCAACG 57.237 29.630 0.00 0.00 0.00 4.10
3550 4108 6.922247 AAATGTCAATGCATGTCACAAAAA 57.078 29.167 0.00 0.00 29.85 1.94
3551 4109 6.315642 ACAAAATGTCAATGCATGTCACAAAA 59.684 30.769 0.00 0.00 29.85 2.44
3552 4110 5.816258 ACAAAATGTCAATGCATGTCACAAA 59.184 32.000 0.00 0.00 29.85 2.83
3553 4111 5.358090 ACAAAATGTCAATGCATGTCACAA 58.642 33.333 0.00 0.00 29.85 3.33
3554 4112 4.946445 ACAAAATGTCAATGCATGTCACA 58.054 34.783 0.00 3.88 29.85 3.58
3555 4113 5.910637 AACAAAATGTCAATGCATGTCAC 57.089 34.783 0.00 0.00 29.85 3.67
3556 4114 6.747125 ACTAACAAAATGTCAATGCATGTCA 58.253 32.000 0.00 0.14 0.00 3.58
3557 4115 7.642071 AACTAACAAAATGTCAATGCATGTC 57.358 32.000 0.00 0.00 0.00 3.06
3558 4116 9.539825 TTTAACTAACAAAATGTCAATGCATGT 57.460 25.926 0.00 0.00 0.00 3.21
3561 4119 9.593134 AGTTTTAACTAACAAAATGTCAATGCA 57.407 25.926 0.00 0.00 37.52 3.96
3562 4120 9.848172 CAGTTTTAACTAACAAAATGTCAATGC 57.152 29.630 0.00 0.00 37.08 3.56
3565 4123 9.360093 CCACAGTTTTAACTAACAAAATGTCAA 57.640 29.630 0.00 0.00 37.08 3.18
3566 4124 8.524487 ACCACAGTTTTAACTAACAAAATGTCA 58.476 29.630 0.00 0.00 37.08 3.58
3567 4125 8.920509 ACCACAGTTTTAACTAACAAAATGTC 57.079 30.769 0.00 0.00 37.08 3.06
3568 4126 8.524487 TGACCACAGTTTTAACTAACAAAATGT 58.476 29.630 0.00 0.00 37.08 2.71
3569 4127 8.918961 TGACCACAGTTTTAACTAACAAAATG 57.081 30.769 0.00 0.00 37.08 2.32
3570 4128 9.930693 TTTGACCACAGTTTTAACTAACAAAAT 57.069 25.926 0.00 0.00 37.08 1.82
3571 4129 9.760077 TTTTGACCACAGTTTTAACTAACAAAA 57.240 25.926 0.00 0.00 37.08 2.44
3572 4130 9.930693 ATTTTGACCACAGTTTTAACTAACAAA 57.069 25.926 0.00 0.00 37.08 2.83
3573 4131 9.930693 AATTTTGACCACAGTTTTAACTAACAA 57.069 25.926 0.00 0.00 37.08 2.83
3574 4132 9.930693 AAATTTTGACCACAGTTTTAACTAACA 57.069 25.926 0.00 0.00 37.08 2.41
3592 4150 7.925483 CCCTTTGTATTCAGTGTCAAATTTTGA 59.075 33.333 7.74 7.74 37.33 2.69
3593 4151 7.171337 CCCCTTTGTATTCAGTGTCAAATTTTG 59.829 37.037 2.59 2.59 31.08 2.44
3594 4152 7.070571 TCCCCTTTGTATTCAGTGTCAAATTTT 59.929 33.333 0.00 0.00 31.08 1.82
3595 4153 6.553100 TCCCCTTTGTATTCAGTGTCAAATTT 59.447 34.615 0.00 0.00 31.08 1.82
3596 4154 6.015434 GTCCCCTTTGTATTCAGTGTCAAATT 60.015 38.462 0.00 0.00 31.08 1.82
3597 4155 5.476945 GTCCCCTTTGTATTCAGTGTCAAAT 59.523 40.000 0.00 0.00 31.08 2.32
3598 4156 4.825085 GTCCCCTTTGTATTCAGTGTCAAA 59.175 41.667 0.00 0.00 0.00 2.69
3599 4157 4.104102 AGTCCCCTTTGTATTCAGTGTCAA 59.896 41.667 0.00 0.00 0.00 3.18
3600 4158 3.650942 AGTCCCCTTTGTATTCAGTGTCA 59.349 43.478 0.00 0.00 0.00 3.58
3601 4159 4.287766 AGTCCCCTTTGTATTCAGTGTC 57.712 45.455 0.00 0.00 0.00 3.67
3602 4160 5.836024 TTAGTCCCCTTTGTATTCAGTGT 57.164 39.130 0.00 0.00 0.00 3.55
3603 4161 8.674607 GTTTATTAGTCCCCTTTGTATTCAGTG 58.325 37.037 0.00 0.00 0.00 3.66
3604 4162 7.832685 GGTTTATTAGTCCCCTTTGTATTCAGT 59.167 37.037 0.00 0.00 0.00 3.41
3605 4163 7.832187 TGGTTTATTAGTCCCCTTTGTATTCAG 59.168 37.037 0.00 0.00 0.00 3.02
3606 4164 7.700846 TGGTTTATTAGTCCCCTTTGTATTCA 58.299 34.615 0.00 0.00 0.00 2.57
3607 4165 7.284716 CCTGGTTTATTAGTCCCCTTTGTATTC 59.715 40.741 0.00 0.00 0.00 1.75
3608 4166 7.036425 TCCTGGTTTATTAGTCCCCTTTGTATT 60.036 37.037 0.00 0.00 0.00 1.89
3609 4167 6.449041 TCCTGGTTTATTAGTCCCCTTTGTAT 59.551 38.462 0.00 0.00 0.00 2.29
3610 4168 5.791664 TCCTGGTTTATTAGTCCCCTTTGTA 59.208 40.000 0.00 0.00 0.00 2.41
3611 4169 4.604490 TCCTGGTTTATTAGTCCCCTTTGT 59.396 41.667 0.00 0.00 0.00 2.83
3612 4170 4.948004 GTCCTGGTTTATTAGTCCCCTTTG 59.052 45.833 0.00 0.00 0.00 2.77
3613 4171 4.324022 CGTCCTGGTTTATTAGTCCCCTTT 60.324 45.833 0.00 0.00 0.00 3.11
3614 4172 3.199289 CGTCCTGGTTTATTAGTCCCCTT 59.801 47.826 0.00 0.00 0.00 3.95
3615 4173 2.770232 CGTCCTGGTTTATTAGTCCCCT 59.230 50.000 0.00 0.00 0.00 4.79
3616 4174 2.158856 CCGTCCTGGTTTATTAGTCCCC 60.159 54.545 0.00 0.00 0.00 4.81
3617 4175 2.767960 TCCGTCCTGGTTTATTAGTCCC 59.232 50.000 0.00 0.00 39.52 4.46
3618 4176 3.181468 CCTCCGTCCTGGTTTATTAGTCC 60.181 52.174 0.00 0.00 39.52 3.85
3619 4177 3.450096 ACCTCCGTCCTGGTTTATTAGTC 59.550 47.826 0.00 0.00 39.52 2.59
3620 4178 3.447950 ACCTCCGTCCTGGTTTATTAGT 58.552 45.455 0.00 0.00 39.52 2.24
3621 4179 4.648307 ACTACCTCCGTCCTGGTTTATTAG 59.352 45.833 0.00 0.00 39.52 1.73
3622 4180 4.613437 ACTACCTCCGTCCTGGTTTATTA 58.387 43.478 0.00 0.00 39.52 0.98
3623 4181 3.447950 ACTACCTCCGTCCTGGTTTATT 58.552 45.455 0.00 0.00 39.52 1.40
3624 4182 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
3625 4183 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
3626 4184 2.454538 CTACTACCTCCGTCCTGGTTT 58.545 52.381 0.00 0.00 39.52 3.27
3627 4185 1.341778 CCTACTACCTCCGTCCTGGTT 60.342 57.143 0.00 0.00 39.52 3.67
3628 4186 0.258194 CCTACTACCTCCGTCCTGGT 59.742 60.000 0.00 0.00 39.52 4.00
3629 4187 0.258194 ACCTACTACCTCCGTCCTGG 59.742 60.000 0.00 0.00 40.09 4.45
3630 4188 3.181447 TGATACCTACTACCTCCGTCCTG 60.181 52.174 0.00 0.00 0.00 3.86
3631 4189 3.051581 TGATACCTACTACCTCCGTCCT 58.948 50.000 0.00 0.00 0.00 3.85
3632 4190 3.498774 TGATACCTACTACCTCCGTCC 57.501 52.381 0.00 0.00 0.00 4.79
3633 4191 5.533903 TGAATTGATACCTACTACCTCCGTC 59.466 44.000 0.00 0.00 0.00 4.79
3634 4192 5.452255 TGAATTGATACCTACTACCTCCGT 58.548 41.667 0.00 0.00 0.00 4.69
3635 4193 6.401047 TTGAATTGATACCTACTACCTCCG 57.599 41.667 0.00 0.00 0.00 4.63
3636 4194 7.793036 AGTTTGAATTGATACCTACTACCTCC 58.207 38.462 0.00 0.00 0.00 4.30
3637 4195 9.315525 GAAGTTTGAATTGATACCTACTACCTC 57.684 37.037 0.00 0.00 0.00 3.85
3638 4196 8.822805 TGAAGTTTGAATTGATACCTACTACCT 58.177 33.333 0.00 0.00 0.00 3.08
3639 4197 8.880750 GTGAAGTTTGAATTGATACCTACTACC 58.119 37.037 0.00 0.00 0.00 3.18
3640 4198 9.654663 AGTGAAGTTTGAATTGATACCTACTAC 57.345 33.333 0.00 0.00 0.00 2.73
3645 4203 9.793259 TCTTTAGTGAAGTTTGAATTGATACCT 57.207 29.630 0.00 0.00 36.70 3.08
3974 4548 2.752030 TGACACCTAGAGGATGAAGGG 58.248 52.381 1.60 0.00 38.94 3.95
4031 4605 0.738975 GATGTCCAGGTGATCGACGA 59.261 55.000 0.00 0.00 0.00 4.20
4074 4648 2.172293 ACTTGAGAGATGGGATCTTGCC 59.828 50.000 0.00 0.00 40.38 4.52
4153 4727 5.398353 CCTCCTCCAAATGGATCATTACTGT 60.398 44.000 1.93 0.00 44.46 3.55
4385 4959 4.652881 AGATCATGAGCACTCCATGTAGAA 59.347 41.667 14.38 0.00 41.45 2.10
4474 5048 5.132897 AGGATCATATTTCTCGCTCTCAC 57.867 43.478 0.00 0.00 0.00 3.51
4481 5055 5.046735 AGGACATGGAGGATCATATTTCTCG 60.047 44.000 0.00 0.00 36.25 4.04
4615 5189 6.096141 CCTCATACTTCTCTTGTGCTTAGAGA 59.904 42.308 8.35 8.35 44.75 3.10
4807 5384 3.525537 AGATGCTAACCACGTTGATGAG 58.474 45.455 0.00 0.00 0.00 2.90
5015 5593 4.826556 AGTCTCACTAGATTTGTTCAGCC 58.173 43.478 0.00 0.00 33.30 4.85
5179 5757 9.530129 CTGACAAATAACGATTACAAAAGAGAC 57.470 33.333 0.00 0.00 0.00 3.36
5273 5851 6.820656 GCATCTTTCAGTCTGAAATCCTTCTA 59.179 38.462 24.69 4.16 44.37 2.10
5358 7870 8.630037 TCGTTCTAGAAATGCATAGACAGATTA 58.370 33.333 6.78 0.00 0.00 1.75
5372 7884 8.688151 AGTTGCTCTAATACTCGTTCTAGAAAT 58.312 33.333 6.78 0.00 0.00 2.17
5416 7928 9.627123 TCTACAGGATCCCACAAAAATATTTAG 57.373 33.333 8.55 0.25 0.00 1.85
5438 7950 0.651031 GGACGCAAGCCGAAATCTAC 59.349 55.000 0.00 0.00 45.62 2.59
5441 7953 1.134694 GTGGACGCAAGCCGAAATC 59.865 57.895 0.00 0.00 45.62 2.17
5482 7994 2.730550 ATCAGCAAAAAGAAAGCCGG 57.269 45.000 0.00 0.00 0.00 6.13
5484 7996 4.021632 AGAGGAATCAGCAAAAAGAAAGCC 60.022 41.667 0.00 0.00 0.00 4.35
5485 7997 5.131594 AGAGGAATCAGCAAAAAGAAAGC 57.868 39.130 0.00 0.00 0.00 3.51
5487 7999 6.378280 GGGATAGAGGAATCAGCAAAAAGAAA 59.622 38.462 0.00 0.00 0.00 2.52
5488 8000 5.888161 GGGATAGAGGAATCAGCAAAAAGAA 59.112 40.000 0.00 0.00 0.00 2.52
5542 8070 2.035442 GGCGAGTGGAAGCAGGAAC 61.035 63.158 0.00 0.00 34.54 3.62
5564 8092 4.918201 GGGGCCGGCAAGATCGAG 62.918 72.222 30.85 0.00 0.00 4.04
5566 8094 4.489771 AAGGGGCCGGCAAGATCG 62.490 66.667 30.85 0.00 0.00 3.69
5567 8095 2.830370 CAAGGGGCCGGCAAGATC 60.830 66.667 30.85 10.33 0.00 2.75
5574 8102 4.452733 GAGACGTCAAGGGGCCGG 62.453 72.222 19.50 0.00 0.00 6.13
5575 8103 4.796231 CGAGACGTCAAGGGGCCG 62.796 72.222 19.50 5.44 0.00 6.13
5611 8139 1.682451 GCGGGTACTCCATAGTGGCA 61.682 60.000 0.00 0.00 37.47 4.92
5615 8143 2.496291 GGCGCGGGTACTCCATAGT 61.496 63.158 8.83 0.00 39.91 2.12
5650 8178 4.596585 AAGTGGCACGGTTGGGGG 62.597 66.667 12.71 0.00 0.00 5.40
5699 8236 2.279851 CGACAGACGGTGTTGGCA 60.280 61.111 0.00 0.00 40.56 4.92
5709 8246 0.804156 GCTTGGAGCTAGCGACAGAC 60.804 60.000 9.55 4.91 38.45 3.51
5718 8255 1.447838 CCGCTTTCGCTTGGAGCTA 60.448 57.895 0.00 0.00 39.60 3.32
5790 8327 0.389391 GAGGGAGCATAGCAGCGTTA 59.611 55.000 0.00 0.00 40.15 3.18
5796 8333 0.543277 CAACTGGAGGGAGCATAGCA 59.457 55.000 0.00 0.00 0.00 3.49
5800 8337 1.136329 ACCACAACTGGAGGGAGCAT 61.136 55.000 0.00 0.00 40.55 3.79
5811 8348 4.681978 GAGCCGGCGACCACAACT 62.682 66.667 23.20 0.00 0.00 3.16
5876 8413 0.464554 CTTCCTCGGGCCCTTTGATC 60.465 60.000 22.43 0.00 0.00 2.92
5919 8471 3.412408 GAAGGGGGTGGAGGAGCC 61.412 72.222 0.00 0.00 42.09 4.70
5920 8472 3.787001 CGAAGGGGGTGGAGGAGC 61.787 72.222 0.00 0.00 0.00 4.70
5935 8487 1.209504 GGGGAAGACATGGTTGATCGA 59.790 52.381 0.00 0.00 0.00 3.59
5942 8494 1.686325 CGGATCGGGGAAGACATGGT 61.686 60.000 0.00 0.00 0.00 3.55
5973 8525 0.394938 ACACGTTGTAGGCATGGTCA 59.605 50.000 0.00 0.00 0.00 4.02
5982 8534 4.828704 ACGTTTCATTGAACACGTTGTAG 58.171 39.130 22.42 6.97 36.62 2.74
6005 8557 4.941263 CGATCCAAAGTCCAACCAAAGATA 59.059 41.667 0.00 0.00 0.00 1.98
6027 8613 2.733026 ACGACCGAAACATAAGGAAACG 59.267 45.455 0.00 0.00 0.00 3.60
6043 8629 3.363341 TTGCTCCAAAATTCAACGACC 57.637 42.857 0.00 0.00 0.00 4.79
6083 8671 1.610624 GCGGTCTCCTCCAACATTTCA 60.611 52.381 0.00 0.00 0.00 2.69
6101 8689 3.414700 GCACTCAAGTCCACCGCG 61.415 66.667 0.00 0.00 0.00 6.46
6219 8807 2.028112 TGTCTTGGCTAGCATCGAACTT 60.028 45.455 18.24 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.