Multiple sequence alignment - TraesCS4A01G370500

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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 TraesCS4A01G370500 chr4A 100.000 5575 0 0 1 5575 642214722 642209148 0.000000e+00 10296.0
1 TraesCS4A01G370500 chr4A 89.916 833 36 22 3738 4570 686548215 686548999 0.000000e+00 1029.0
2 TraesCS4A01G370500 chr4A 91.813 342 16 5 5227 5567 686549485 686549815 3.040000e-127 466.0
3 TraesCS4A01G370500 chr4A 88.966 290 22 5 4946 5231 686549059 686549342 3.200000e-92 350.0
4 TraesCS4A01G370500 chr4A 100.000 41 0 0 3701 3741 686538532 686538572 5.990000e-10 76.8
5 TraesCS4A01G370500 chr7D 92.416 2123 100 30 510 2593 38179647 38181747 0.000000e+00 2972.0
6 TraesCS4A01G370500 chr7D 90.956 2145 104 36 2610 4710 38182517 38184615 0.000000e+00 2804.0
7 TraesCS4A01G370500 chr7D 84.797 467 37 18 4762 5224 38185176 38185612 6.630000e-119 438.0
8 TraesCS4A01G370500 chr7D 88.779 303 22 8 1 296 38178539 38178836 1.480000e-95 361.0
9 TraesCS4A01G370500 chr7D 85.271 129 11 6 317 444 38178822 38178943 5.860000e-25 126.0
10 TraesCS4A01G370500 chr7A 90.581 2134 105 44 512 2594 37703655 37705743 0.000000e+00 2739.0
11 TraesCS4A01G370500 chr7A 89.343 2130 109 45 2645 4700 37706431 37708516 0.000000e+00 2567.0
12 TraesCS4A01G370500 chr7A 85.806 465 36 14 4762 5225 37708858 37709293 3.040000e-127 466.0
13 TraesCS4A01G370500 chr7A 87.789 303 21 10 1 296 37701726 37702019 1.920000e-89 340.0
14 TraesCS4A01G370500 chr4B 79.870 308 31 20 5282 5570 478185705 478186000 4.410000e-46 196.0
15 TraesCS4A01G370500 chr4B 82.629 213 19 11 4627 4837 478184935 478185131 7.430000e-39 172.0


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 TraesCS4A01G370500 chr4A 642209148 642214722 5574 True 10296.0 10296 100.000000 1 5575 1 chr4A.!!$R1 5574
1 TraesCS4A01G370500 chr4A 686548215 686549815 1600 False 615.0 1029 90.231667 3738 5567 3 chr4A.!!$F2 1829
2 TraesCS4A01G370500 chr7D 38178539 38185612 7073 False 1340.2 2972 88.443800 1 5224 5 chr7D.!!$F1 5223
3 TraesCS4A01G370500 chr7A 37701726 37709293 7567 False 1528.0 2739 88.379750 1 5225 4 chr7A.!!$F1 5224

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
534 2415 0.107165 GGGGACATCCTCCTTTTCGG 60.107 60.0 0.00 0.00 39.39 4.30 F
665 2546 0.686441 CCCCTCCGTGTCTCCATACA 60.686 60.0 0.00 0.00 0.00 2.29 F
2465 4405 0.392461 GGCCTGGTCGCAATCAACTA 60.392 55.0 0.00 0.00 0.00 2.24 F
2585 4526 0.391661 GCCATGGACATGTCACTCGT 60.392 55.0 26.47 8.68 37.11 4.18 F
4337 7177 0.395686 CATGGAGATGGAGGACGCAT 59.604 55.0 0.00 0.00 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2366 4304 0.034896 GTGATGTGGGTTCGTGGTCT 59.965 55.000 0.00 0.00 0.00 3.85 R
2545 4486 1.032657 AGTCACTGGATCTCGGTCCG 61.033 60.000 4.39 4.39 41.35 4.79 R
4444 7286 0.107017 ACCCATGGATCCAAGAAGCG 60.107 55.000 20.67 5.84 0.00 4.68 R
4486 7330 1.587054 CTCGAACGGTCAAGCCTCT 59.413 57.895 0.00 0.00 34.25 3.69 R
5518 9089 3.632145 CACCAGCACCAGGGATATAAAAC 59.368 47.826 0.00 0.00 0.00 2.43 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
94 96 2.404789 CGCACCCACATCGCAATC 59.595 61.111 0.00 0.00 0.00 2.67
181 185 4.336713 GCCTTGGATTATGGTTCTCTTCAC 59.663 45.833 0.00 0.00 0.00 3.18
192 196 4.996758 TGGTTCTCTTCACACACACATATG 59.003 41.667 0.00 0.00 0.00 1.78
222 226 1.213296 AGGTGAACAAGGGTGTCACT 58.787 50.000 2.35 0.00 36.80 3.41
223 227 1.141053 AGGTGAACAAGGGTGTCACTC 59.859 52.381 2.35 0.00 36.80 3.51
230 234 3.347216 ACAAGGGTGTCACTCATAATGC 58.653 45.455 5.45 0.00 29.49 3.56
258 262 8.268605 TGTATAGATATGGGTGTAGTGCAAAAA 58.731 33.333 0.00 0.00 0.00 1.94
262 266 7.346471 AGATATGGGTGTAGTGCAAAAAGTAT 58.654 34.615 0.00 0.00 0.00 2.12
265 269 5.622180 TGGGTGTAGTGCAAAAAGTATGTA 58.378 37.500 0.00 0.00 0.00 2.29
266 270 5.470777 TGGGTGTAGTGCAAAAAGTATGTAC 59.529 40.000 0.00 0.00 0.00 2.90
268 272 6.348213 GGGTGTAGTGCAAAAAGTATGTACTG 60.348 42.308 7.40 0.00 36.50 2.74
272 276 6.072112 AGTGCAAAAAGTATGTACTGGTTG 57.928 37.500 0.00 9.86 36.50 3.77
275 279 7.041372 AGTGCAAAAAGTATGTACTGGTTGTAG 60.041 37.037 13.34 0.00 36.50 2.74
277 281 7.663905 TGCAAAAAGTATGTACTGGTTGTAGAT 59.336 33.333 13.34 0.00 38.47 1.98
331 335 7.874528 TGTGAGGTATATGTTATCATGAGCTTG 59.125 37.037 0.09 0.00 35.70 4.01
332 336 7.332926 GTGAGGTATATGTTATCATGAGCTTGG 59.667 40.741 0.09 0.00 35.70 3.61
365 369 2.831685 TCTTGAGCTCGCCTTTGTTA 57.168 45.000 9.64 0.00 0.00 2.41
367 371 2.299013 TCTTGAGCTCGCCTTTGTTAGA 59.701 45.455 9.64 0.00 0.00 2.10
370 374 2.806244 TGAGCTCGCCTTTGTTAGAAAC 59.194 45.455 9.64 0.00 0.00 2.78
379 383 5.049828 GCCTTTGTTAGAAACACAAATGCT 58.950 37.500 14.67 0.00 45.16 3.79
390 394 2.293399 ACACAAATGCTTCCTTCGAACC 59.707 45.455 0.00 0.00 0.00 3.62
392 396 2.955660 ACAAATGCTTCCTTCGAACCAA 59.044 40.909 0.00 0.00 0.00 3.67
394 398 3.923017 AATGCTTCCTTCGAACCAAAG 57.077 42.857 0.00 0.00 0.00 2.77
395 399 2.631160 TGCTTCCTTCGAACCAAAGA 57.369 45.000 11.61 0.00 0.00 2.52
399 403 3.253432 GCTTCCTTCGAACCAAAGAATGT 59.747 43.478 11.61 0.00 0.00 2.71
400 404 4.787598 CTTCCTTCGAACCAAAGAATGTG 58.212 43.478 0.00 0.00 0.00 3.21
401 405 3.815809 TCCTTCGAACCAAAGAATGTGT 58.184 40.909 0.00 0.00 0.00 3.72
402 406 4.963373 TCCTTCGAACCAAAGAATGTGTA 58.037 39.130 0.00 0.00 0.00 2.90
403 407 4.994852 TCCTTCGAACCAAAGAATGTGTAG 59.005 41.667 0.00 0.00 0.00 2.74
404 408 4.378459 CCTTCGAACCAAAGAATGTGTAGC 60.378 45.833 0.00 0.00 0.00 3.58
405 409 4.002906 TCGAACCAAAGAATGTGTAGCT 57.997 40.909 0.00 0.00 0.00 3.32
406 410 4.385825 TCGAACCAAAGAATGTGTAGCTT 58.614 39.130 0.00 0.00 0.00 3.74
407 411 5.543714 TCGAACCAAAGAATGTGTAGCTTA 58.456 37.500 0.00 0.00 0.00 3.09
451 455 3.327148 CCTTGCTCGGCATCGATG 58.673 61.111 21.27 21.27 45.04 3.84
469 473 7.884668 CATCGATGCTTGGTATTGTTTTAAAC 58.115 34.615 13.37 0.20 0.00 2.01
470 474 6.971602 TCGATGCTTGGTATTGTTTTAAACA 58.028 32.000 6.41 6.41 40.21 2.83
514 2395 4.645136 TCTGTAACAATCGATACAGAGGCT 59.355 41.667 19.91 0.00 46.61 4.58
519 2400 0.188587 ATCGATACAGAGGCTGGGGA 59.811 55.000 0.00 0.00 35.51 4.81
534 2415 0.107165 GGGGACATCCTCCTTTTCGG 60.107 60.000 0.00 0.00 39.39 4.30
573 2454 4.390297 GCAGTTTGATCAGTAAGTCCACTC 59.610 45.833 0.00 0.00 0.00 3.51
656 2537 3.402681 CATCCTGCCCCTCCGTGT 61.403 66.667 0.00 0.00 0.00 4.49
665 2546 0.686441 CCCCTCCGTGTCTCCATACA 60.686 60.000 0.00 0.00 0.00 2.29
667 2548 1.553248 CCCTCCGTGTCTCCATACAAA 59.447 52.381 0.00 0.00 0.00 2.83
687 2569 4.033894 GCTACAGCGGCCACTATG 57.966 61.111 2.24 0.00 0.00 2.23
688 2570 2.247437 GCTACAGCGGCCACTATGC 61.247 63.158 2.24 0.00 0.00 3.14
894 2778 5.401550 CAAAGAGAAAGTGACAGCAACAAA 58.598 37.500 0.00 0.00 0.00 2.83
895 2779 4.889832 AGAGAAAGTGACAGCAACAAAG 57.110 40.909 0.00 0.00 0.00 2.77
896 2780 4.265073 AGAGAAAGTGACAGCAACAAAGT 58.735 39.130 0.00 0.00 0.00 2.66
897 2781 4.095483 AGAGAAAGTGACAGCAACAAAGTG 59.905 41.667 0.00 0.00 0.00 3.16
899 2783 3.764885 AAGTGACAGCAACAAAGTGTC 57.235 42.857 0.00 0.00 40.89 3.67
906 2790 1.444119 GCAACAAAGTGTCGCTCCCA 61.444 55.000 0.00 0.00 0.00 4.37
992 2876 4.704833 CACCACCCCAGCCAGACG 62.705 72.222 0.00 0.00 0.00 4.18
1017 2901 1.609208 ACCAAGTAGCAGTGGCAAAG 58.391 50.000 0.00 0.00 44.61 2.77
1027 2911 0.771127 AGTGGCAAAGCAAGGTCCTA 59.229 50.000 0.00 0.00 0.00 2.94
1030 2914 1.960689 TGGCAAAGCAAGGTCCTAAAC 59.039 47.619 0.00 0.00 0.00 2.01
1056 2940 4.771903 CCCCATCTCATCTCATCATCATC 58.228 47.826 0.00 0.00 0.00 2.92
1057 2941 4.225267 CCCCATCTCATCTCATCATCATCA 59.775 45.833 0.00 0.00 0.00 3.07
1058 2942 5.104318 CCCCATCTCATCTCATCATCATCAT 60.104 44.000 0.00 0.00 0.00 2.45
1059 2943 6.052360 CCCATCTCATCTCATCATCATCATC 58.948 44.000 0.00 0.00 0.00 2.92
1060 2944 6.352222 CCCATCTCATCTCATCATCATCATCA 60.352 42.308 0.00 0.00 0.00 3.07
1061 2945 7.278875 CCATCTCATCTCATCATCATCATCAT 58.721 38.462 0.00 0.00 0.00 2.45
1069 2953 7.266400 TCTCATCATCATCATCATAAGCTAGC 58.734 38.462 6.62 6.62 0.00 3.42
1154 3038 3.442977 AGGCACCTACTTCTACTTGTACG 59.557 47.826 0.00 0.00 0.00 3.67
1161 3045 2.546645 TTCTACTTGTACGCCGCCCG 62.547 60.000 0.00 0.00 44.21 6.13
1265 3149 1.296715 CAACCCCTTCCCTCTCGTG 59.703 63.158 0.00 0.00 0.00 4.35
1288 3172 4.418392 CTCAAGGTAATGTTTCATGCAGC 58.582 43.478 0.00 0.00 0.00 5.25
1289 3173 4.081406 TCAAGGTAATGTTTCATGCAGCT 58.919 39.130 0.00 0.00 0.00 4.24
1313 3220 1.423845 CCCGTGCGCATTCAGTTAC 59.576 57.895 15.91 0.00 0.00 2.50
1345 3255 1.813513 GATTGGTGGTGAGACTGTGG 58.186 55.000 0.00 0.00 0.00 4.17
1518 3428 2.764128 ATCAGCGGGATGTCGGGT 60.764 61.111 0.00 0.00 34.06 5.28
1920 3830 1.597302 CATCGGGCTGGAGATGCTG 60.597 63.158 0.00 0.00 37.94 4.41
2091 4001 1.069703 CACATGTTCGACAAGGTGCTG 60.070 52.381 0.00 0.00 33.12 4.41
2127 4037 3.048602 CGGCCCATCTACTACGGG 58.951 66.667 0.00 0.00 43.42 5.28
2231 4141 3.860125 CGCCAACGGTATGCCACG 61.860 66.667 0.00 0.00 34.97 4.94
2300 4230 5.413969 TCGCTTTATTTCTCATGATGCTG 57.586 39.130 0.00 0.00 0.00 4.41
2366 4304 1.402787 TCCATCACGCTGAGCTCATA 58.597 50.000 18.63 1.05 0.00 2.15
2367 4305 1.339291 TCCATCACGCTGAGCTCATAG 59.661 52.381 18.63 16.24 0.00 2.23
2373 4312 0.593518 CGCTGAGCTCATAGACCACG 60.594 60.000 18.63 8.77 0.00 4.94
2425 4364 2.238898 GCCAAGATGGTTAGTGTAGGGT 59.761 50.000 0.00 0.00 40.46 4.34
2426 4366 3.873910 CCAAGATGGTTAGTGTAGGGTG 58.126 50.000 0.00 0.00 31.35 4.61
2431 4371 2.966915 TGGTTAGTGTAGGGTGTCACT 58.033 47.619 2.35 0.00 45.21 3.41
2435 4375 5.011329 TGGTTAGTGTAGGGTGTCACTTAAG 59.989 44.000 0.00 0.00 43.39 1.85
2443 4383 2.488153 GGGTGTCACTTAAGATGCCAAC 59.512 50.000 10.09 2.74 0.00 3.77
2465 4405 0.392461 GGCCTGGTCGCAATCAACTA 60.392 55.000 0.00 0.00 0.00 2.24
2467 4407 1.331756 GCCTGGTCGCAATCAACTATG 59.668 52.381 0.00 0.00 0.00 2.23
2468 4408 2.632377 CCTGGTCGCAATCAACTATGT 58.368 47.619 0.00 0.00 0.00 2.29
2469 4409 3.792401 CCTGGTCGCAATCAACTATGTA 58.208 45.455 0.00 0.00 0.00 2.29
2470 4410 4.380531 CCTGGTCGCAATCAACTATGTAT 58.619 43.478 0.00 0.00 0.00 2.29
2471 4411 5.538118 CCTGGTCGCAATCAACTATGTATA 58.462 41.667 0.00 0.00 0.00 1.47
2472 4412 5.989168 CCTGGTCGCAATCAACTATGTATAA 59.011 40.000 0.00 0.00 0.00 0.98
2473 4413 6.073765 CCTGGTCGCAATCAACTATGTATAAC 60.074 42.308 0.00 0.00 0.00 1.89
2474 4414 5.460748 TGGTCGCAATCAACTATGTATAACG 59.539 40.000 0.00 0.00 0.00 3.18
2475 4415 5.461078 GGTCGCAATCAACTATGTATAACGT 59.539 40.000 0.00 0.00 0.00 3.99
2476 4416 6.638063 GGTCGCAATCAACTATGTATAACGTA 59.362 38.462 0.00 0.00 0.00 3.57
2477 4417 7.149015 GGTCGCAATCAACTATGTATAACGTAG 60.149 40.741 5.03 5.03 42.07 3.51
2479 4419 8.558700 TCGCAATCAACTATGTATAACGTAGTA 58.441 33.333 11.31 0.00 46.90 1.82
2545 4486 2.056577 GTTCGGTACACAGTGTAGTGC 58.943 52.381 14.03 2.59 43.23 4.40
2585 4526 0.391661 GCCATGGACATGTCACTCGT 60.392 55.000 26.47 8.68 37.11 4.18
2594 4535 4.295870 GACATGTCACTCGTGAACAGTAA 58.704 43.478 21.07 0.00 41.85 2.24
2596 4537 4.037565 ACATGTCACTCGTGAACAGTAAGA 59.962 41.667 0.64 0.00 41.85 2.10
2600 4541 5.220381 GTCACTCGTGAACAGTAAGATGAA 58.780 41.667 0.64 0.00 41.85 2.57
2602 4543 6.200286 GTCACTCGTGAACAGTAAGATGAAAA 59.800 38.462 0.64 0.00 41.85 2.29
2603 4544 6.929049 TCACTCGTGAACAGTAAGATGAAAAT 59.071 34.615 0.00 0.00 36.53 1.82
2604 4545 7.011773 CACTCGTGAACAGTAAGATGAAAATG 58.988 38.462 0.00 0.00 0.00 2.32
2629 5349 5.951747 CCCCAAAGAATCTAACCATCTGAAA 59.048 40.000 0.00 0.00 0.00 2.69
2630 5350 6.127619 CCCCAAAGAATCTAACCATCTGAAAC 60.128 42.308 0.00 0.00 0.00 2.78
2631 5351 6.660949 CCCAAAGAATCTAACCATCTGAAACT 59.339 38.462 0.00 0.00 0.00 2.66
2633 5353 9.231297 CCAAAGAATCTAACCATCTGAAACTAA 57.769 33.333 0.00 0.00 0.00 2.24
2635 5355 8.499403 AAGAATCTAACCATCTGAAACTAAGC 57.501 34.615 0.00 0.00 0.00 3.09
2636 5356 7.856415 AGAATCTAACCATCTGAAACTAAGCT 58.144 34.615 0.00 0.00 0.00 3.74
2637 5357 7.984617 AGAATCTAACCATCTGAAACTAAGCTC 59.015 37.037 0.00 0.00 0.00 4.09
2638 5358 6.605471 TCTAACCATCTGAAACTAAGCTCA 57.395 37.500 0.00 0.00 0.00 4.26
2639 5359 6.634805 TCTAACCATCTGAAACTAAGCTCAG 58.365 40.000 0.00 0.00 40.42 3.35
2641 5361 5.234466 ACCATCTGAAACTAAGCTCAGTT 57.766 39.130 0.00 0.00 40.49 3.16
2642 5362 5.241662 ACCATCTGAAACTAAGCTCAGTTC 58.758 41.667 1.79 0.00 37.78 3.01
2643 5363 5.221722 ACCATCTGAAACTAAGCTCAGTTCA 60.222 40.000 1.79 2.56 37.78 3.18
2644 5364 5.879223 CCATCTGAAACTAAGCTCAGTTCAT 59.121 40.000 1.79 0.00 37.78 2.57
2645 5365 6.036953 CCATCTGAAACTAAGCTCAGTTCATC 59.963 42.308 1.79 0.00 37.78 2.92
2647 5367 6.705302 TCTGAAACTAAGCTCAGTTCATCAT 58.295 36.000 1.79 0.00 37.78 2.45
2648 5368 6.592994 TCTGAAACTAAGCTCAGTTCATCATG 59.407 38.462 1.79 0.00 37.78 3.07
2649 5369 5.645067 TGAAACTAAGCTCAGTTCATCATGG 59.355 40.000 1.79 0.00 37.78 3.66
2650 5370 5.426689 AACTAAGCTCAGTTCATCATGGA 57.573 39.130 0.00 0.00 33.41 3.41
2677 5422 9.965824 AATAATATAAATACAGTTGGTTGCAGC 57.034 29.630 0.00 0.00 0.00 5.25
2715 5460 2.032030 CAGTTGTTCGGCTAACCACTTG 60.032 50.000 5.97 0.40 40.25 3.16
2808 5561 9.465985 TTTTTCGATTAAAGGGATTACACAAAC 57.534 29.630 0.00 0.00 0.00 2.93
2812 5565 8.630917 TCGATTAAAGGGATTACACAAACAAAA 58.369 29.630 0.00 0.00 0.00 2.44
2813 5566 8.696175 CGATTAAAGGGATTACACAAACAAAAC 58.304 33.333 0.00 0.00 0.00 2.43
3000 5802 1.954362 ATCGGCAGCCACTGAGAGAC 61.954 60.000 13.30 0.00 32.44 3.36
3036 5842 2.672908 AATGGCGACGTACGATCGGG 62.673 60.000 28.29 10.65 45.77 5.14
3066 5872 3.628646 ATGGAGCTGTTGGGTCGCC 62.629 63.158 0.00 0.00 42.80 5.54
3067 5873 4.021925 GGAGCTGTTGGGTCGCCT 62.022 66.667 0.00 0.00 42.80 5.52
3142 5951 1.678635 AATCATGGCCACCACCACG 60.679 57.895 8.16 0.00 44.17 4.94
3143 5952 3.643595 ATCATGGCCACCACCACGG 62.644 63.158 8.16 0.00 44.17 4.94
3185 5996 1.709994 ATTCCCTCCTCCATTCCGGC 61.710 60.000 0.00 0.00 33.14 6.13
3189 6000 3.740128 CTCCTCCATTCCGGCCACG 62.740 68.421 2.24 0.00 40.55 4.94
3252 6074 3.373130 CGCTGATCATCACTGTGAATTGT 59.627 43.478 15.31 1.47 0.00 2.71
3253 6075 4.659088 GCTGATCATCACTGTGAATTGTG 58.341 43.478 15.31 8.60 35.68 3.33
3256 6078 4.393990 TGATCATCACTGTGAATTGTGCTC 59.606 41.667 15.31 9.80 34.49 4.26
3406 6228 2.697229 CTGGACATATGCTCCAGTGAGA 59.303 50.000 28.44 10.51 46.91 3.27
3483 6323 4.373116 TGCGCCCAGTTCTCGGTC 62.373 66.667 4.18 0.00 0.00 4.79
3552 6392 1.817099 CCGCATCTTCCAGGTGCTC 60.817 63.158 7.39 0.00 36.74 4.26
3558 6398 1.739562 CTTCCAGGTGCTCAGCGTC 60.740 63.158 0.00 0.00 0.00 5.19
3756 6596 3.140225 CTCCTCCTACTTCGCCGCC 62.140 68.421 0.00 0.00 0.00 6.13
4119 6959 4.112341 GGCGTCTACGACTGCGGT 62.112 66.667 6.71 0.00 45.57 5.68
4325 7165 3.473647 CTCAGCCGCCCATGGAGA 61.474 66.667 15.22 0.19 0.00 3.71
4326 7166 2.769621 TCAGCCGCCCATGGAGAT 60.770 61.111 15.22 0.00 0.00 2.75
4327 7167 2.593725 CAGCCGCCCATGGAGATG 60.594 66.667 15.22 6.79 0.00 2.90
4335 7175 4.766970 CATGGAGATGGAGGACGC 57.233 61.111 0.00 0.00 0.00 5.19
4336 7176 1.825341 CATGGAGATGGAGGACGCA 59.175 57.895 0.00 0.00 0.00 5.24
4337 7177 0.395686 CATGGAGATGGAGGACGCAT 59.604 55.000 0.00 0.00 0.00 4.73
4338 7178 1.620323 CATGGAGATGGAGGACGCATA 59.380 52.381 0.00 0.00 0.00 3.14
4339 7179 1.788229 TGGAGATGGAGGACGCATAA 58.212 50.000 0.00 0.00 0.00 1.90
4406 7248 1.815421 CTGAAGATTGACCGGCCGG 60.815 63.158 42.17 42.17 42.03 6.13
4467 7311 4.327680 GCTTCTTGGATCCATGGGTATAC 58.672 47.826 23.54 0.00 0.00 1.47
4486 7330 2.388735 ACTCTATTGCGATCCAGACCA 58.611 47.619 0.00 0.00 0.00 4.02
4663 7536 4.800471 GTGGAACAAAAGAGAAAACTGCAG 59.200 41.667 13.48 13.48 44.16 4.41
4696 7569 2.490903 GAGCACCATGATCAACTTTGCT 59.509 45.455 18.92 18.92 41.43 3.91
4703 7576 5.882557 ACCATGATCAACTTTGCTTACTAGG 59.117 40.000 0.00 0.00 0.00 3.02
4704 7577 5.220931 CCATGATCAACTTTGCTTACTAGGC 60.221 44.000 0.00 0.00 0.00 3.93
4705 7578 5.165961 TGATCAACTTTGCTTACTAGGCT 57.834 39.130 0.00 0.00 0.00 4.58
4707 7580 6.106673 TGATCAACTTTGCTTACTAGGCTAC 58.893 40.000 0.00 0.00 0.00 3.58
4708 7581 5.740290 TCAACTTTGCTTACTAGGCTACT 57.260 39.130 0.00 0.00 0.00 2.57
4710 7583 6.628185 TCAACTTTGCTTACTAGGCTACTAC 58.372 40.000 0.00 0.00 0.00 2.73
4711 7584 5.246145 ACTTTGCTTACTAGGCTACTACG 57.754 43.478 0.00 0.00 0.00 3.51
4715 7588 3.804325 TGCTTACTAGGCTACTACGTACG 59.196 47.826 15.01 15.01 0.00 3.67
4717 7590 4.982916 GCTTACTAGGCTACTACGTACGTA 59.017 45.833 25.41 25.41 0.00 3.57
4738 7611 1.202687 GCTGCCTGCTATACACATCCA 60.203 52.381 0.00 0.00 38.95 3.41
4739 7612 2.763933 CTGCCTGCTATACACATCCAG 58.236 52.381 0.00 0.00 0.00 3.86
4740 7613 2.366590 CTGCCTGCTATACACATCCAGA 59.633 50.000 0.00 0.00 0.00 3.86
4741 7614 2.974794 TGCCTGCTATACACATCCAGAT 59.025 45.455 0.00 0.00 0.00 2.90
4743 7616 4.021104 TGCCTGCTATACACATCCAGATAC 60.021 45.833 0.00 0.00 0.00 2.24
4744 7617 4.621747 GCCTGCTATACACATCCAGATACC 60.622 50.000 0.00 0.00 0.00 2.73
4747 7620 6.286240 TGCTATACACATCCAGATACCATC 57.714 41.667 0.00 0.00 0.00 3.51
4748 7621 6.019108 TGCTATACACATCCAGATACCATCT 58.981 40.000 0.00 0.00 41.15 2.90
4749 7622 6.498303 TGCTATACACATCCAGATACCATCTT 59.502 38.462 0.00 0.00 37.58 2.40
4750 7623 7.038659 GCTATACACATCCAGATACCATCTTC 58.961 42.308 0.00 0.00 37.58 2.87
4753 7626 5.431765 ACACATCCAGATACCATCTTCAAC 58.568 41.667 0.00 0.00 37.58 3.18
4754 7627 5.045651 ACACATCCAGATACCATCTTCAACA 60.046 40.000 0.00 0.00 37.58 3.33
4755 7628 5.882000 CACATCCAGATACCATCTTCAACAA 59.118 40.000 0.00 0.00 37.58 2.83
4760 7633 5.583854 CCAGATACCATCTTCAACAACTCAG 59.416 44.000 0.00 0.00 37.58 3.35
4763 8177 7.224362 CAGATACCATCTTCAACAACTCAGATC 59.776 40.741 0.00 0.00 37.58 2.75
4822 8237 4.455533 TGTGTTACTTGTCAGATCAATGCC 59.544 41.667 0.00 0.00 0.00 4.40
4831 8246 2.586079 ATCAATGCCTCGTCGCCG 60.586 61.111 0.00 0.00 0.00 6.46
4850 8265 1.404843 GTCTCCTATTCCTGTCGCCT 58.595 55.000 0.00 0.00 0.00 5.52
4864 8279 3.490890 GCCTCTGCGTTCACATCC 58.509 61.111 0.00 0.00 0.00 3.51
4869 8284 0.601057 TCTGCGTTCACATCCGAGAA 59.399 50.000 0.00 0.00 0.00 2.87
4873 8288 3.381045 TGCGTTCACATCCGAGAATATC 58.619 45.455 0.00 0.00 0.00 1.63
4879 8294 2.735663 CACATCCGAGAATATCTGCTGC 59.264 50.000 0.00 0.00 0.00 5.25
4880 8295 2.289320 ACATCCGAGAATATCTGCTGCC 60.289 50.000 0.00 0.00 0.00 4.85
4882 8297 0.668706 CCGAGAATATCTGCTGCCGG 60.669 60.000 0.00 0.00 0.00 6.13
4894 8309 4.693532 TGCCGGAGCAGTTAAGTG 57.306 55.556 5.05 5.89 46.52 3.16
4902 8317 3.192844 CGGAGCAGTTAAGTGGTAAGAGA 59.807 47.826 14.73 0.00 0.00 3.10
4916 8331 6.879458 AGTGGTAAGAGAAACATATTGGTGAC 59.121 38.462 0.00 0.00 0.00 3.67
4920 8335 7.064728 GGTAAGAGAAACATATTGGTGACTCAC 59.935 40.741 0.00 0.00 0.00 3.51
4921 8336 6.365970 AGAGAAACATATTGGTGACTCACT 57.634 37.500 9.08 0.00 34.40 3.41
4922 8337 6.773638 AGAGAAACATATTGGTGACTCACTT 58.226 36.000 9.08 0.00 34.40 3.16
4923 8338 6.652481 AGAGAAACATATTGGTGACTCACTTG 59.348 38.462 9.08 3.06 34.40 3.16
4924 8339 6.299141 AGAAACATATTGGTGACTCACTTGT 58.701 36.000 9.08 3.59 34.40 3.16
4925 8340 5.947228 AACATATTGGTGACTCACTTGTG 57.053 39.130 9.08 6.00 34.40 3.33
4926 8341 4.973168 ACATATTGGTGACTCACTTGTGT 58.027 39.130 9.08 6.53 34.40 3.72
4927 8342 4.756642 ACATATTGGTGACTCACTTGTGTG 59.243 41.667 9.08 6.13 45.07 3.82
4950 8365 0.734889 CAACGGAATCCTGATGTGGC 59.265 55.000 0.00 0.00 0.00 5.01
4979 8394 5.675684 AAACCAGAAAGAAACAACCATGT 57.324 34.783 0.00 0.00 43.14 3.21
5046 8464 3.248266 GCATTTGCTTGCTTGGTAGAAG 58.752 45.455 0.00 0.00 39.57 2.85
5047 8465 3.305608 GCATTTGCTTGCTTGGTAGAAGT 60.306 43.478 0.00 0.00 39.57 3.01
5048 8466 4.082787 GCATTTGCTTGCTTGGTAGAAGTA 60.083 41.667 0.00 0.00 39.57 2.24
5049 8467 5.634896 CATTTGCTTGCTTGGTAGAAGTAG 58.365 41.667 0.00 0.00 0.00 2.57
5050 8468 4.617253 TTGCTTGCTTGGTAGAAGTAGA 57.383 40.909 0.00 0.00 0.00 2.59
5051 8469 4.617253 TGCTTGCTTGGTAGAAGTAGAA 57.383 40.909 0.00 0.00 0.00 2.10
5054 8472 4.390297 GCTTGCTTGGTAGAAGTAGAACAG 59.610 45.833 0.00 0.00 0.00 3.16
5085 8504 1.649664 GCTGTAGGCATGTGAGACAG 58.350 55.000 12.17 12.17 40.39 3.51
5087 8506 2.738000 GCTGTAGGCATGTGAGACAGAG 60.738 54.545 17.72 0.00 39.94 3.35
5124 8543 8.289618 TGAGCTCAAAGTAAATGTCACAATAAC 58.710 33.333 15.67 0.00 0.00 1.89
5176 8597 4.965062 TCTTCGTCGTCAATTTTAATGGC 58.035 39.130 0.00 0.00 0.00 4.40
5235 8805 9.582431 CTTCTTTATGTGGTCGATTAGTAGAAA 57.418 33.333 0.00 0.00 0.00 2.52
5240 8810 7.772332 ATGTGGTCGATTAGTAGAAATTGTC 57.228 36.000 0.00 0.00 0.00 3.18
5274 8844 8.986929 ATTATTCCTCCTAAAATTGTCTGAGG 57.013 34.615 6.93 6.93 40.57 3.86
5332 8902 6.992664 AGCACTAGACTAGATTCCAATGAT 57.007 37.500 16.55 0.00 0.00 2.45
5347 8917 9.458727 GATTCCAATGATCCATGTATATCAAGT 57.541 33.333 6.70 0.00 35.82 3.16
5357 8927 7.896811 TCCATGTATATCAAGTAGCCACTTAG 58.103 38.462 0.00 0.00 43.30 2.18
5358 8928 7.509318 TCCATGTATATCAAGTAGCCACTTAGT 59.491 37.037 0.00 0.00 43.30 2.24
5359 8929 8.803235 CCATGTATATCAAGTAGCCACTTAGTA 58.197 37.037 0.00 0.00 43.30 1.82
5360 8930 9.627395 CATGTATATCAAGTAGCCACTTAGTAC 57.373 37.037 0.00 0.40 43.30 2.73
5361 8931 8.991783 TGTATATCAAGTAGCCACTTAGTACT 57.008 34.615 0.00 0.00 43.30 2.73
5432 9003 2.696506 TGTGCTCTTCTTCAGATGCAG 58.303 47.619 0.00 0.00 36.75 4.41
5439 9010 4.564041 TCTTCTTCAGATGCAGAACAGAC 58.436 43.478 0.00 0.00 0.00 3.51
5455 9026 3.458189 ACAGACAAAGGTTCAGAGTTCG 58.542 45.455 0.00 0.00 0.00 3.95
5463 9034 5.674933 AAGGTTCAGAGTTCGAACATTTC 57.325 39.130 28.78 17.85 42.79 2.17
5464 9035 4.962155 AGGTTCAGAGTTCGAACATTTCT 58.038 39.130 28.78 19.72 43.70 2.52
5465 9036 4.991687 AGGTTCAGAGTTCGAACATTTCTC 59.008 41.667 28.78 17.16 43.70 2.87
5466 9037 4.991687 GGTTCAGAGTTCGAACATTTCTCT 59.008 41.667 28.78 19.03 43.70 3.10
5467 9038 5.467063 GGTTCAGAGTTCGAACATTTCTCTT 59.533 40.000 28.78 6.59 43.70 2.85
5468 9039 6.346999 GGTTCAGAGTTCGAACATTTCTCTTC 60.347 42.308 28.78 15.10 43.70 2.87
5469 9040 5.230942 TCAGAGTTCGAACATTTCTCTTCC 58.769 41.667 28.78 0.00 33.92 3.46
5470 9041 4.991056 CAGAGTTCGAACATTTCTCTTCCA 59.009 41.667 28.78 0.00 33.92 3.53
5471 9042 5.466728 CAGAGTTCGAACATTTCTCTTCCAA 59.533 40.000 28.78 0.00 33.92 3.53
5472 9043 5.467063 AGAGTTCGAACATTTCTCTTCCAAC 59.533 40.000 28.78 0.00 32.52 3.77
5473 9044 5.123227 AGTTCGAACATTTCTCTTCCAACA 58.877 37.500 28.78 0.00 0.00 3.33
5474 9045 5.765182 AGTTCGAACATTTCTCTTCCAACAT 59.235 36.000 28.78 0.00 0.00 2.71
5475 9046 5.611796 TCGAACATTTCTCTTCCAACATG 57.388 39.130 0.00 0.00 0.00 3.21
5476 9047 5.063204 TCGAACATTTCTCTTCCAACATGT 58.937 37.500 0.00 0.00 0.00 3.21
5518 9089 5.431765 ACTGCTTATAAACCACTCATCCAG 58.568 41.667 0.00 0.00 0.00 3.86
5567 9138 8.278482 CATTTGCTGCTTATAAATTACAGAGC 57.722 34.615 0.00 0.00 0.00 4.09
5568 9139 5.657470 TGCTGCTTATAAATTACAGAGCG 57.343 39.130 0.00 0.00 33.03 5.03
5569 9140 4.024893 TGCTGCTTATAAATTACAGAGCGC 60.025 41.667 0.00 0.00 33.03 5.92
5570 9141 4.692135 CTGCTTATAAATTACAGAGCGCG 58.308 43.478 0.00 0.00 33.03 6.86
5571 9142 3.059868 TGCTTATAAATTACAGAGCGCGC 60.060 43.478 26.66 26.66 33.03 6.86
5572 9143 3.184581 GCTTATAAATTACAGAGCGCGCT 59.815 43.478 37.28 37.28 0.00 5.92
5573 9144 4.384846 GCTTATAAATTACAGAGCGCGCTA 59.615 41.667 36.69 19.60 0.00 4.26
5574 9145 5.107607 GCTTATAAATTACAGAGCGCGCTAA 60.108 40.000 36.69 25.15 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.827284 TCTCACACGCTGATATCCATCTTA 59.173 41.667 0.00 0.00 31.93 2.10
59 61 2.946329 TGCGCTCTGACCAAAAACTAAA 59.054 40.909 9.73 0.00 0.00 1.85
142 146 8.537728 AATCCAAGGCTGTGATAATGAATAAA 57.462 30.769 0.00 0.00 0.00 1.40
144 148 9.234827 CATAATCCAAGGCTGTGATAATGAATA 57.765 33.333 0.00 0.00 0.00 1.75
158 162 4.336713 GTGAAGAGAACCATAATCCAAGGC 59.663 45.833 0.00 0.00 0.00 4.35
192 196 4.141779 CCCTTGTTCACCTACCTATGGTAC 60.142 50.000 0.00 0.00 37.09 3.34
222 226 8.825774 ACACCCATATCTATACAAGCATTATGA 58.174 33.333 0.00 0.00 0.00 2.15
230 234 6.993079 TGCACTACACCCATATCTATACAAG 58.007 40.000 0.00 0.00 0.00 3.16
302 306 9.056005 GCTCATGATAACATATACCTCACAAAA 57.944 33.333 0.00 0.00 35.09 2.44
303 307 8.432013 AGCTCATGATAACATATACCTCACAAA 58.568 33.333 0.00 0.00 35.09 2.83
304 308 7.966812 AGCTCATGATAACATATACCTCACAA 58.033 34.615 0.00 0.00 35.09 3.33
305 309 7.544804 AGCTCATGATAACATATACCTCACA 57.455 36.000 0.00 0.00 35.09 3.58
306 310 7.332926 CCAAGCTCATGATAACATATACCTCAC 59.667 40.741 0.00 0.00 35.09 3.51
307 311 7.016563 ACCAAGCTCATGATAACATATACCTCA 59.983 37.037 0.00 0.00 35.09 3.86
308 312 7.332926 CACCAAGCTCATGATAACATATACCTC 59.667 40.741 0.00 0.00 35.09 3.85
309 313 7.164122 CACCAAGCTCATGATAACATATACCT 58.836 38.462 0.00 0.00 35.09 3.08
310 314 6.128172 GCACCAAGCTCATGATAACATATACC 60.128 42.308 0.00 0.00 41.15 2.73
311 315 6.427853 TGCACCAAGCTCATGATAACATATAC 59.572 38.462 0.00 0.00 45.94 1.47
312 316 6.532826 TGCACCAAGCTCATGATAACATATA 58.467 36.000 0.00 0.00 45.94 0.86
313 317 5.379187 TGCACCAAGCTCATGATAACATAT 58.621 37.500 0.00 0.00 45.94 1.78
314 318 4.779696 TGCACCAAGCTCATGATAACATA 58.220 39.130 0.00 0.00 45.94 2.29
315 319 3.623703 TGCACCAAGCTCATGATAACAT 58.376 40.909 0.00 0.00 45.94 2.71
316 320 3.011818 CTGCACCAAGCTCATGATAACA 58.988 45.455 0.00 0.00 45.94 2.41
317 321 2.357009 CCTGCACCAAGCTCATGATAAC 59.643 50.000 0.00 0.00 45.94 1.89
318 322 2.239402 TCCTGCACCAAGCTCATGATAA 59.761 45.455 0.00 0.00 45.94 1.75
331 335 3.127721 GCTCAAGAAACTTATCCTGCACC 59.872 47.826 0.00 0.00 0.00 5.01
332 336 4.006319 AGCTCAAGAAACTTATCCTGCAC 58.994 43.478 0.00 0.00 0.00 4.57
365 369 3.882888 TCGAAGGAAGCATTTGTGTTTCT 59.117 39.130 5.27 0.00 31.15 2.52
367 371 4.359706 GTTCGAAGGAAGCATTTGTGTTT 58.640 39.130 0.00 0.00 31.49 2.83
379 383 4.204012 ACACATTCTTTGGTTCGAAGGAA 58.796 39.130 0.00 0.00 0.00 3.36
403 407 6.089954 GGATTCACAAAAGACAAGCAATAAGC 59.910 38.462 0.00 0.00 46.19 3.09
404 408 6.306356 CGGATTCACAAAAGACAAGCAATAAG 59.694 38.462 0.00 0.00 0.00 1.73
405 409 6.148948 CGGATTCACAAAAGACAAGCAATAA 58.851 36.000 0.00 0.00 0.00 1.40
406 410 5.335583 CCGGATTCACAAAAGACAAGCAATA 60.336 40.000 0.00 0.00 0.00 1.90
407 411 4.549458 CGGATTCACAAAAGACAAGCAAT 58.451 39.130 0.00 0.00 0.00 3.56
413 417 1.546773 CCCCCGGATTCACAAAAGACA 60.547 52.381 0.73 0.00 0.00 3.41
447 451 7.630470 TTGTTTAAAACAATACCAAGCATCG 57.370 32.000 0.00 0.00 45.79 3.84
484 488 9.599866 TCTGTATCGATTGTTACAGAAAATCAT 57.400 29.630 23.23 0.00 46.66 2.45
485 489 8.996024 TCTGTATCGATTGTTACAGAAAATCA 57.004 30.769 23.23 7.36 46.66 2.57
492 496 4.742167 CAGCCTCTGTATCGATTGTTACAG 59.258 45.833 19.28 19.28 44.42 2.74
493 497 4.441495 CCAGCCTCTGTATCGATTGTTACA 60.441 45.833 1.71 0.19 0.00 2.41
495 499 3.069586 CCCAGCCTCTGTATCGATTGTTA 59.930 47.826 1.71 0.00 0.00 2.41
496 500 2.158900 CCCAGCCTCTGTATCGATTGTT 60.159 50.000 1.71 0.00 0.00 2.83
498 502 1.270518 CCCCAGCCTCTGTATCGATTG 60.271 57.143 1.71 0.00 0.00 2.67
499 503 1.051812 CCCCAGCCTCTGTATCGATT 58.948 55.000 1.71 0.00 0.00 3.34
500 504 0.188587 TCCCCAGCCTCTGTATCGAT 59.811 55.000 2.16 2.16 0.00 3.59
501 505 0.755698 GTCCCCAGCCTCTGTATCGA 60.756 60.000 0.00 0.00 0.00 3.59
503 507 1.346068 GATGTCCCCAGCCTCTGTATC 59.654 57.143 0.00 0.00 0.00 2.24
504 508 1.428869 GATGTCCCCAGCCTCTGTAT 58.571 55.000 0.00 0.00 0.00 2.29
505 509 0.691078 GGATGTCCCCAGCCTCTGTA 60.691 60.000 0.00 0.00 44.01 2.74
507 511 2.914289 GGATGTCCCCAGCCTCTG 59.086 66.667 0.00 0.00 44.01 3.35
543 2424 6.476378 ACTTACTGATCAAACTGCATAGGTT 58.524 36.000 0.00 0.00 32.95 3.50
544 2425 6.054860 ACTTACTGATCAAACTGCATAGGT 57.945 37.500 0.00 0.00 0.00 3.08
562 2443 3.738281 CGGACATGATGGAGTGGACTTAC 60.738 52.174 0.00 0.00 0.00 2.34
573 2454 2.292267 CCTTTCCTTCGGACATGATGG 58.708 52.381 0.00 0.00 35.15 3.51
656 2537 3.676049 CGCTGTAGCTGTTTGTATGGAGA 60.676 47.826 0.00 0.00 39.32 3.71
665 2546 1.966451 GTGGCCGCTGTAGCTGTTT 60.966 57.895 9.68 0.00 39.32 2.83
667 2548 1.330655 ATAGTGGCCGCTGTAGCTGT 61.331 55.000 29.26 1.95 39.32 4.40
678 2559 1.878088 CAGATGTCATGCATAGTGGCC 59.122 52.381 0.00 0.00 38.06 5.36
687 2569 5.886960 AAGGAAGTTTACAGATGTCATGC 57.113 39.130 0.00 0.00 0.00 4.06
688 2570 7.173907 AGTGAAAGGAAGTTTACAGATGTCATG 59.826 37.037 0.00 0.00 0.00 3.07
894 2778 3.023949 GCCTCATGGGAGCGACACT 62.024 63.158 0.00 0.00 39.96 3.55
895 2779 2.512515 GCCTCATGGGAGCGACAC 60.513 66.667 0.00 0.00 39.96 3.67
896 2780 3.785859 GGCCTCATGGGAGCGACA 61.786 66.667 0.00 0.00 39.96 4.35
897 2781 3.474570 AGGCCTCATGGGAGCGAC 61.475 66.667 0.00 0.00 39.96 5.19
899 2783 3.457625 CTCAGGCCTCATGGGAGCG 62.458 68.421 0.00 0.00 39.96 5.03
992 2876 2.742589 GCCACTGCTACTTGGTTAACTC 59.257 50.000 5.42 0.00 35.09 3.01
1027 2911 2.309755 TGAGATGAGATGGGGCAAGTTT 59.690 45.455 0.00 0.00 0.00 2.66
1030 2914 2.105993 TGATGAGATGAGATGGGGCAAG 59.894 50.000 0.00 0.00 0.00 4.01
1069 2953 7.063898 CCATGGCGATCTTCTTTGTATATAGTG 59.936 40.741 0.00 0.00 0.00 2.74
1120 3004 2.271944 AGGTGCCTCCTTGTGTTTAC 57.728 50.000 0.00 0.00 45.67 2.01
1161 3045 2.426122 GAAGGGTTGCTGTTGCTGCC 62.426 60.000 0.00 0.00 40.48 4.85
1251 3135 1.544825 TTGAGCACGAGAGGGAAGGG 61.545 60.000 0.00 0.00 35.60 3.95
1265 3149 4.418392 CTGCATGAAACATTACCTTGAGC 58.582 43.478 0.00 0.00 0.00 4.26
1296 3180 0.370273 GAGTAACTGAATGCGCACGG 59.630 55.000 14.90 9.10 0.00 4.94
1457 3367 3.431725 CCGCCGCCTTGTTCTTCC 61.432 66.667 0.00 0.00 0.00 3.46
1530 3440 3.933722 ATCGCCAGCATCTCCCCG 61.934 66.667 0.00 0.00 0.00 5.73
2231 4141 4.699522 GGTGGGGTGGAGTCGTGC 62.700 72.222 0.00 0.00 0.00 5.34
2366 4304 0.034896 GTGATGTGGGTTCGTGGTCT 59.965 55.000 0.00 0.00 0.00 3.85
2367 4305 0.034896 AGTGATGTGGGTTCGTGGTC 59.965 55.000 0.00 0.00 0.00 4.02
2373 4312 5.253330 TGGATTTTAGAGTGATGTGGGTTC 58.747 41.667 0.00 0.00 0.00 3.62
2408 4347 3.514309 GTGACACCCTACACTAACCATCT 59.486 47.826 0.00 0.00 34.65 2.90
2425 4364 2.790433 GGGTTGGCATCTTAAGTGACA 58.210 47.619 8.87 8.87 31.41 3.58
2426 4366 1.737793 CGGGTTGGCATCTTAAGTGAC 59.262 52.381 1.63 3.33 0.00 3.67
2545 4486 1.032657 AGTCACTGGATCTCGGTCCG 61.033 60.000 4.39 4.39 41.35 4.79
2585 4526 4.462483 GGGGCATTTTCATCTTACTGTTCA 59.538 41.667 0.00 0.00 0.00 3.18
2594 4535 5.028131 AGATTCTTTGGGGCATTTTCATCT 58.972 37.500 0.00 0.00 0.00 2.90
2596 4537 6.352137 GGTTAGATTCTTTGGGGCATTTTCAT 60.352 38.462 0.00 0.00 0.00 2.57
2600 4541 4.424842 TGGTTAGATTCTTTGGGGCATTT 58.575 39.130 0.00 0.00 0.00 2.32
2602 4543 3.756082 TGGTTAGATTCTTTGGGGCAT 57.244 42.857 0.00 0.00 0.00 4.40
2603 4544 3.269381 AGATGGTTAGATTCTTTGGGGCA 59.731 43.478 0.00 0.00 0.00 5.36
2604 4545 3.633986 CAGATGGTTAGATTCTTTGGGGC 59.366 47.826 0.00 0.00 0.00 5.80
2629 5349 5.426689 TTCCATGATGAACTGAGCTTAGT 57.573 39.130 5.11 5.11 0.00 2.24
2630 5350 6.939132 ATTTCCATGATGAACTGAGCTTAG 57.061 37.500 3.53 3.53 0.00 2.18
2631 5351 8.985315 ATTATTTCCATGATGAACTGAGCTTA 57.015 30.769 0.00 0.00 0.00 3.09
2670 5415 3.044059 GCGGATCAGGTGCTGCAAC 62.044 63.158 10.28 10.28 0.00 4.17
2671 5416 2.747460 GCGGATCAGGTGCTGCAA 60.747 61.111 2.77 0.00 0.00 4.08
2672 5417 3.549900 TTGCGGATCAGGTGCTGCA 62.550 57.895 0.00 0.00 0.00 4.41
2673 5418 2.747460 TTGCGGATCAGGTGCTGC 60.747 61.111 0.00 0.00 0.00 5.25
2674 5419 2.743752 CGTTGCGGATCAGGTGCTG 61.744 63.158 0.00 0.00 0.00 4.41
2675 5420 2.434884 CGTTGCGGATCAGGTGCT 60.435 61.111 0.00 0.00 0.00 4.40
2676 5421 2.434185 TCGTTGCGGATCAGGTGC 60.434 61.111 0.00 0.00 0.00 5.01
2677 5422 1.354337 CTGTCGTTGCGGATCAGGTG 61.354 60.000 0.00 0.00 0.00 4.00
2715 5460 7.047271 TGGCATTATTTTATCTTTTTCTGGCC 58.953 34.615 0.00 0.00 34.88 5.36
2873 5637 4.522789 CAGGAAAAGGGGAGAAATCGAAAA 59.477 41.667 0.00 0.00 0.00 2.29
3036 5842 0.600557 AGCTCCATCCATCGATCGAC 59.399 55.000 22.06 4.09 0.00 4.20
3046 5852 1.450312 CGACCCAACAGCTCCATCC 60.450 63.158 0.00 0.00 0.00 3.51
3079 5887 1.304217 TGTCCGTGTCCCTCTCTCC 60.304 63.158 0.00 0.00 0.00 3.71
3185 5996 3.345808 CGGGCACTGTGTTCGTGG 61.346 66.667 9.86 0.00 33.10 4.94
3189 6000 3.330275 GTGTCGGGCACTGTGTTC 58.670 61.111 5.29 2.43 44.41 3.18
3252 6074 0.835276 AGATACCTGCATGCAGAGCA 59.165 50.000 42.21 27.90 46.30 4.26
3253 6075 1.602851 CAAGATACCTGCATGCAGAGC 59.397 52.381 42.21 28.51 46.30 4.09
3256 6078 0.666913 GGCAAGATACCTGCATGCAG 59.333 55.000 35.88 35.88 43.26 4.41
3354 6176 4.236416 GCAATGTGGCGCGCGTAT 62.236 61.111 32.35 16.00 0.00 3.06
3438 6278 1.668101 CCGTCCACTCCACTCTAGCC 61.668 65.000 0.00 0.00 0.00 3.93
3618 6458 2.200899 GAGAAGAAGAAGATGAGCGCC 58.799 52.381 2.29 0.00 0.00 6.53
3858 6698 1.820481 GACGACGAGGAGGGAGAGG 60.820 68.421 0.00 0.00 0.00 3.69
3957 6797 3.771160 ATGGTGACGACGGAGGCC 61.771 66.667 0.00 0.00 0.00 5.19
4325 7165 2.172505 TGGATGTTTATGCGTCCTCCAT 59.827 45.455 5.99 0.00 43.25 3.41
4326 7166 1.557371 TGGATGTTTATGCGTCCTCCA 59.443 47.619 5.99 0.00 43.25 3.86
4327 7167 1.940613 GTGGATGTTTATGCGTCCTCC 59.059 52.381 5.99 0.00 43.25 4.30
4329 7169 1.280710 TGGTGGATGTTTATGCGTCCT 59.719 47.619 5.99 0.00 43.25 3.85
4330 7170 1.745232 TGGTGGATGTTTATGCGTCC 58.255 50.000 0.00 0.00 43.17 4.79
4334 7174 2.954318 AGCTCATGGTGGATGTTTATGC 59.046 45.455 0.00 0.00 33.29 3.14
4335 7175 4.214971 GCTAGCTCATGGTGGATGTTTATG 59.785 45.833 7.70 0.00 33.29 1.90
4336 7176 4.103785 AGCTAGCTCATGGTGGATGTTTAT 59.896 41.667 12.68 0.00 33.29 1.40
4337 7177 3.455910 AGCTAGCTCATGGTGGATGTTTA 59.544 43.478 12.68 0.00 33.29 2.01
4338 7178 2.240667 AGCTAGCTCATGGTGGATGTTT 59.759 45.455 12.68 0.00 33.29 2.83
4339 7179 1.842562 AGCTAGCTCATGGTGGATGTT 59.157 47.619 12.68 0.00 33.29 2.71
4444 7286 0.107017 ACCCATGGATCCAAGAAGCG 60.107 55.000 20.67 5.84 0.00 4.68
4450 7292 6.296432 GCAATAGAGTATACCCATGGATCCAA 60.296 42.308 20.67 1.11 0.00 3.53
4451 7293 5.189736 GCAATAGAGTATACCCATGGATCCA 59.810 44.000 18.88 18.88 0.00 3.41
4467 7311 2.625314 TCTGGTCTGGATCGCAATAGAG 59.375 50.000 0.00 0.00 0.00 2.43
4486 7330 1.587054 CTCGAACGGTCAAGCCTCT 59.413 57.895 0.00 0.00 34.25 3.69
4515 7362 2.611225 ATCCTCTGTTCCATTCTCGC 57.389 50.000 0.00 0.00 0.00 5.03
4522 7369 4.016444 GCCATTAACAATCCTCTGTTCCA 58.984 43.478 0.00 0.00 40.08 3.53
4601 7474 6.924060 GCCTGTAAAATCGATACAGTACAGAT 59.076 38.462 24.73 0.00 45.63 2.90
4675 7548 2.490903 AGCAAAGTTGATCATGGTGCTC 59.509 45.455 14.51 0.00 36.11 4.26
4708 7581 1.430632 GCAGGCAGCTACGTACGTA 59.569 57.895 25.41 25.41 41.15 3.57
4718 7591 1.202687 TGGATGTGTATAGCAGGCAGC 60.203 52.381 0.00 0.00 46.19 5.25
4719 7592 2.366590 TCTGGATGTGTATAGCAGGCAG 59.633 50.000 0.00 0.00 0.00 4.85
4720 7593 2.397597 TCTGGATGTGTATAGCAGGCA 58.602 47.619 0.00 0.00 0.00 4.75
4721 7594 3.692257 ATCTGGATGTGTATAGCAGGC 57.308 47.619 0.00 0.00 0.00 4.85
4722 7595 4.528206 TGGTATCTGGATGTGTATAGCAGG 59.472 45.833 0.00 0.00 30.96 4.85
4734 7607 6.070021 TGAGTTGTTGAAGATGGTATCTGGAT 60.070 38.462 0.00 0.00 40.13 3.41
4735 7608 5.248248 TGAGTTGTTGAAGATGGTATCTGGA 59.752 40.000 0.00 0.00 40.13 3.86
4736 7609 5.491070 TGAGTTGTTGAAGATGGTATCTGG 58.509 41.667 0.00 0.00 40.13 3.86
4738 7611 6.611613 TCTGAGTTGTTGAAGATGGTATCT 57.388 37.500 0.00 0.00 42.61 1.98
4739 7612 7.044181 TGATCTGAGTTGTTGAAGATGGTATC 58.956 38.462 0.00 0.00 29.59 2.24
4740 7613 6.950842 TGATCTGAGTTGTTGAAGATGGTAT 58.049 36.000 0.00 0.00 29.59 2.73
4741 7614 6.358974 TGATCTGAGTTGTTGAAGATGGTA 57.641 37.500 0.00 0.00 29.59 3.25
4743 7616 6.552629 CATTGATCTGAGTTGTTGAAGATGG 58.447 40.000 0.00 0.00 29.59 3.51
4744 7617 6.028368 GCATTGATCTGAGTTGTTGAAGATG 58.972 40.000 0.00 0.00 29.59 2.90
4747 7620 5.048921 AGTGCATTGATCTGAGTTGTTGAAG 60.049 40.000 0.00 0.00 0.00 3.02
4748 7621 4.823442 AGTGCATTGATCTGAGTTGTTGAA 59.177 37.500 0.00 0.00 0.00 2.69
4749 7622 4.214758 CAGTGCATTGATCTGAGTTGTTGA 59.785 41.667 2.46 0.00 0.00 3.18
4750 7623 4.473199 CAGTGCATTGATCTGAGTTGTTG 58.527 43.478 2.46 0.00 0.00 3.33
4753 7626 2.747989 AGCAGTGCATTGATCTGAGTTG 59.252 45.455 19.20 0.00 0.00 3.16
4754 7627 3.069079 AGCAGTGCATTGATCTGAGTT 57.931 42.857 19.20 0.00 0.00 3.01
4755 7628 2.783609 AGCAGTGCATTGATCTGAGT 57.216 45.000 19.20 0.00 0.00 3.41
4760 7633 8.112099 CACTTTTAATAAGCAGTGCATTGATC 57.888 34.615 19.20 0.00 30.79 2.92
4831 8246 1.338655 GAGGCGACAGGAATAGGAGAC 59.661 57.143 0.00 0.00 0.00 3.36
4850 8265 0.601057 TTCTCGGATGTGAACGCAGA 59.399 50.000 0.00 0.00 0.00 4.26
4861 8276 1.067283 CGGCAGCAGATATTCTCGGAT 60.067 52.381 0.00 0.00 0.00 4.18
4864 8279 0.315251 TCCGGCAGCAGATATTCTCG 59.685 55.000 0.00 0.00 0.00 4.04
4879 8294 2.232941 TCTTACCACTTAACTGCTCCGG 59.767 50.000 0.00 0.00 0.00 5.14
4880 8295 3.192844 TCTCTTACCACTTAACTGCTCCG 59.807 47.826 0.00 0.00 0.00 4.63
4882 8297 5.989777 TGTTTCTCTTACCACTTAACTGCTC 59.010 40.000 0.00 0.00 0.00 4.26
4891 8306 6.879458 GTCACCAATATGTTTCTCTTACCACT 59.121 38.462 0.00 0.00 0.00 4.00
4892 8307 6.879458 AGTCACCAATATGTTTCTCTTACCAC 59.121 38.462 0.00 0.00 0.00 4.16
4893 8308 7.016153 AGTCACCAATATGTTTCTCTTACCA 57.984 36.000 0.00 0.00 0.00 3.25
4894 8309 7.064728 GTGAGTCACCAATATGTTTCTCTTACC 59.935 40.741 12.54 0.00 0.00 2.85
4902 8317 5.827797 ACACAAGTGAGTCACCAATATGTTT 59.172 36.000 19.71 7.84 34.49 2.83
4920 8335 3.315191 AGGATTCCGTTGTTTCACACAAG 59.685 43.478 0.00 0.00 46.49 3.16
4921 8336 3.066064 CAGGATTCCGTTGTTTCACACAA 59.934 43.478 0.00 0.00 43.55 3.33
4922 8337 2.616376 CAGGATTCCGTTGTTTCACACA 59.384 45.455 0.00 0.00 0.00 3.72
4923 8338 2.875933 TCAGGATTCCGTTGTTTCACAC 59.124 45.455 0.00 0.00 0.00 3.82
4924 8339 3.201353 TCAGGATTCCGTTGTTTCACA 57.799 42.857 0.00 0.00 0.00 3.58
4925 8340 3.502211 ACATCAGGATTCCGTTGTTTCAC 59.498 43.478 0.00 0.00 0.00 3.18
4926 8341 3.501828 CACATCAGGATTCCGTTGTTTCA 59.498 43.478 0.00 0.00 0.00 2.69
4927 8342 3.119849 CCACATCAGGATTCCGTTGTTTC 60.120 47.826 0.00 0.00 0.00 2.78
4928 8343 2.819608 CCACATCAGGATTCCGTTGTTT 59.180 45.455 0.00 0.00 0.00 2.83
4929 8344 2.436417 CCACATCAGGATTCCGTTGTT 58.564 47.619 0.00 0.00 0.00 2.83
4930 8345 1.950484 GCCACATCAGGATTCCGTTGT 60.950 52.381 0.00 0.04 0.00 3.32
4931 8346 0.734889 GCCACATCAGGATTCCGTTG 59.265 55.000 0.00 0.00 0.00 4.10
4932 8347 0.394352 GGCCACATCAGGATTCCGTT 60.394 55.000 0.00 0.00 0.00 4.44
4933 8348 1.224592 GGCCACATCAGGATTCCGT 59.775 57.895 0.00 0.00 0.00 4.69
4934 8349 0.179009 ATGGCCACATCAGGATTCCG 60.179 55.000 8.16 0.00 29.20 4.30
4935 8350 3.835810 ATGGCCACATCAGGATTCC 57.164 52.632 8.16 0.00 29.20 3.01
4950 8365 6.923508 GGTTGTTTCTTTCTGGTTTAAGATGG 59.076 38.462 0.00 0.00 31.00 3.51
5046 8464 2.352960 GCCAACATAGCAGCTGTTCTAC 59.647 50.000 16.64 0.00 34.69 2.59
5047 8465 2.237143 AGCCAACATAGCAGCTGTTCTA 59.763 45.455 16.64 9.52 34.69 2.10
5048 8466 1.004044 AGCCAACATAGCAGCTGTTCT 59.996 47.619 16.64 7.36 34.69 3.01
5049 8467 1.131883 CAGCCAACATAGCAGCTGTTC 59.868 52.381 16.64 0.00 46.00 3.18
5050 8468 1.171308 CAGCCAACATAGCAGCTGTT 58.829 50.000 16.64 12.62 46.00 3.16
5051 8469 2.864114 CAGCCAACATAGCAGCTGT 58.136 52.632 16.64 4.79 46.00 4.40
5054 8472 1.303309 CCTACAGCCAACATAGCAGC 58.697 55.000 0.00 0.00 0.00 5.25
5085 8504 7.138692 ACTTTGAGCTCATGTATTGTTTCTC 57.861 36.000 19.04 0.00 0.00 2.87
5087 8506 9.846248 ATTTACTTTGAGCTCATGTATTGTTTC 57.154 29.630 19.04 0.00 0.00 2.78
5124 8543 8.481974 TTGGCAAGATGACAATATTTCATTTG 57.518 30.769 0.00 15.02 41.15 2.32
5254 8824 5.683876 CTCCTCAGACAATTTTAGGAGGA 57.316 43.478 8.52 12.60 46.37 3.71
5269 8839 6.877855 TCTCAACTGAATTGATTTCTCCTCAG 59.122 38.462 0.00 0.00 46.37 3.35
5274 8844 9.059485 CGATTTTCTCAACTGAATTGATTTCTC 57.941 33.333 0.00 0.00 46.37 2.87
5299 8869 5.110598 TCTAGTCTAGTGCTTCTACTCACG 58.889 45.833 6.77 0.00 38.19 4.35
5302 8872 6.768861 TGGAATCTAGTCTAGTGCTTCTACTC 59.231 42.308 6.77 0.00 32.19 2.59
5332 8902 6.747414 AAGTGGCTACTTGATATACATGGA 57.253 37.500 15.40 0.00 45.17 3.41
5347 8917 5.748402 TGCTAGTACAGTACTAAGTGGCTA 58.252 41.667 19.11 8.84 40.49 3.93
5357 8927 6.939132 TCTGAAGGTATGCTAGTACAGTAC 57.061 41.667 2.05 2.05 0.00 2.73
5358 8928 6.016192 GCATCTGAAGGTATGCTAGTACAGTA 60.016 42.308 0.00 0.00 44.08 2.74
5359 8929 5.221342 GCATCTGAAGGTATGCTAGTACAGT 60.221 44.000 0.00 0.00 44.08 3.55
5360 8930 5.221322 TGCATCTGAAGGTATGCTAGTACAG 60.221 44.000 8.57 0.00 46.87 2.74
5361 8931 4.649218 TGCATCTGAAGGTATGCTAGTACA 59.351 41.667 8.57 0.00 46.87 2.90
5421 8992 4.083431 CCTTTGTCTGTTCTGCATCTGAAG 60.083 45.833 0.00 0.00 0.00 3.02
5432 9003 4.025647 CGAACTCTGAACCTTTGTCTGTTC 60.026 45.833 0.00 0.00 40.94 3.18
5439 9010 5.424121 AATGTTCGAACTCTGAACCTTTG 57.576 39.130 27.32 0.00 43.95 2.77
5455 9026 7.820648 ACATACATGTTGGAAGAGAAATGTTC 58.179 34.615 2.30 0.00 37.90 3.18
5463 9034 6.017605 GGAATGCTACATACATGTTGGAAGAG 60.018 42.308 2.30 0.00 41.97 2.85
5464 9035 5.822519 GGAATGCTACATACATGTTGGAAGA 59.177 40.000 2.30 0.00 41.97 2.87
5465 9036 5.824624 AGGAATGCTACATACATGTTGGAAG 59.175 40.000 2.30 6.08 41.97 3.46
5466 9037 5.754782 AGGAATGCTACATACATGTTGGAA 58.245 37.500 2.30 0.00 41.97 3.53
5467 9038 5.372343 AGGAATGCTACATACATGTTGGA 57.628 39.130 2.30 0.29 41.97 3.53
5468 9039 5.589855 TGAAGGAATGCTACATACATGTTGG 59.410 40.000 2.30 0.00 41.97 3.77
5469 9040 6.682423 TGAAGGAATGCTACATACATGTTG 57.318 37.500 2.30 5.06 41.97 3.33
5470 9041 7.886629 ATTGAAGGAATGCTACATACATGTT 57.113 32.000 2.30 0.00 41.97 2.71
5471 9042 8.213679 AGTATTGAAGGAATGCTACATACATGT 58.786 33.333 2.69 2.69 44.48 3.21
5472 9043 8.501580 CAGTATTGAAGGAATGCTACATACATG 58.498 37.037 0.00 0.00 34.99 3.21
5473 9044 7.173907 GCAGTATTGAAGGAATGCTACATACAT 59.826 37.037 0.00 0.00 34.99 2.29
5474 9045 6.483307 GCAGTATTGAAGGAATGCTACATACA 59.517 38.462 0.00 0.00 34.99 2.29
5475 9046 6.708054 AGCAGTATTGAAGGAATGCTACATAC 59.292 38.462 3.42 0.00 41.90 2.39
5476 9047 6.830912 AGCAGTATTGAAGGAATGCTACATA 58.169 36.000 3.42 0.00 41.90 2.29
5518 9089 3.632145 CACCAGCACCAGGGATATAAAAC 59.368 47.826 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.