Multiple sequence alignment - TraesCS1A01G117500

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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 TraesCS1A01G117500 chr1A 100.000 7514 0 0 1 7514 124892820 124885307 0.000000e+00 13876
1 TraesCS1A01G117500 chr1D 97.769 4707 89 15 2054 6752 114358939 114354241 0.000000e+00 8096
2 TraesCS1A01G117500 chr1D 91.610 1335 47 24 50 1371 114360928 114359646 0.000000e+00 1784
3 TraesCS1A01G117500 chr1D 94.637 634 31 3 1426 2057 114359645 114359013 0.000000e+00 979
4 TraesCS1A01G117500 chr1D 87.147 389 32 7 6909 7281 114353785 114353399 6.970000e-115 425
5 TraesCS1A01G117500 chr1D 86.709 158 18 3 6806 6960 114353947 114353790 1.000000e-38 172
6 TraesCS1A01G117500 chr1B 97.749 2887 57 7 3890 6772 175418456 175415574 0.000000e+00 4964
7 TraesCS1A01G117500 chr1B 98.075 1818 33 2 2054 3870 175420391 175418575 0.000000e+00 3162
8 TraesCS1A01G117500 chr1B 90.019 2124 94 36 1 2057 175422536 175420464 0.000000e+00 2639
9 TraesCS1A01G117500 chr1B 86.514 393 30 10 6904 7290 175415355 175414980 1.950000e-110 411
10 TraesCS1A01G117500 chr1B 94.444 72 2 2 6806 6875 175415429 175415358 7.970000e-20 110
11 TraesCS1A01G117500 chr5A 95.376 173 5 3 7283 7454 702727960 702727790 9.610000e-69 272
12 TraesCS1A01G117500 chr5A 97.468 158 4 0 7290 7447 434410226 434410069 3.460000e-68 270
13 TraesCS1A01G117500 chr5A 97.468 158 4 0 7290 7447 494949330 494949173 3.460000e-68 270
14 TraesCS1A01G117500 chr7A 97.468 158 4 0 7290 7447 284010595 284010438 3.460000e-68 270
15 TraesCS1A01G117500 chr3A 97.468 158 4 0 7290 7447 199578448 199578291 3.460000e-68 270
16 TraesCS1A01G117500 chr3A 95.266 169 6 2 7290 7456 199571465 199571297 4.470000e-67 267
17 TraesCS1A01G117500 chr4A 97.452 157 4 0 7291 7447 502922238 502922394 1.240000e-67 268
18 TraesCS1A01G117500 chr4A 97.436 156 4 0 7292 7447 443174185 443174030 4.470000e-67 267
19 TraesCS1A01G117500 chr2A 94.118 170 8 2 7286 7454 578457040 578457208 2.690000e-64 257


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 TraesCS1A01G117500 chr1A 124885307 124892820 7513 True 13876.0 13876 100.0000 1 7514 1 chr1A.!!$R1 7513
1 TraesCS1A01G117500 chr1D 114353399 114360928 7529 True 2291.2 8096 91.5744 50 7281 5 chr1D.!!$R1 7231
2 TraesCS1A01G117500 chr1B 175414980 175422536 7556 True 2257.2 4964 93.3602 1 7290 5 chr1B.!!$R1 7289

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
491 528 0.460987 AGTCGTAATGGCAGCAGAGC 60.461 55.0 0.00 0.00 0.00 4.09 F
1840 1930 0.029834 GCCATCGCATAAGCTTGTGG 59.970 55.0 22.71 13.63 39.10 4.17 F
1962 2052 0.744281 TCGATAGGATGCTTGCGTCA 59.256 50.0 15.50 0.00 0.00 4.35 F
2706 2875 1.451449 TTTAGTCCCCCTTTCAGGCA 58.549 50.0 0.00 0.00 32.73 4.75 F
4531 4801 0.958382 TGCAACATTGGACGGTAGCC 60.958 55.0 0.00 0.00 0.00 3.93 F
5612 5883 1.064825 CAGTCCTGTGGGGGTACTTT 58.935 55.0 0.00 0.00 35.33 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2365 0.037419 TAGCACGTGAAGCATCAGCA 60.037 50.000 22.23 0.0 45.49 4.41 R
3483 3652 3.114606 TCCAGATGCAAACCCTATCAGA 58.885 45.455 0.00 0.0 0.00 3.27 R
4035 4305 9.520204 CCAAAATATATAGTGCTTTGAACAAGG 57.480 33.333 7.95 0.0 0.00 3.61 R
4665 4935 0.892755 CCATCACAGCAGGCACAATT 59.107 50.000 0.00 0.0 0.00 2.32 R
5752 6023 0.309922 CCAAGATGCATAAGGCTGCG 59.690 55.000 0.00 0.0 45.30 5.18 R
7213 7825 0.105964 ACAACCTCGCAGCAACACTA 59.894 50.000 0.00 0.0 0.00 2.74 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
30 31 7.647715 CCTTATTTTTGCCGATTTGTATGTAGG 59.352 37.037 0.00 0.00 0.00 3.18
45 46 3.235157 TGTAGGCTTGCATGAATTTGC 57.765 42.857 3.33 0.00 43.07 3.68
100 106 2.148768 GTTAGTTGTGAGGTTTCCCCG 58.851 52.381 0.00 0.00 38.74 5.73
123 129 4.256920 AGGTGATGTAGTCAGATTTGTGC 58.743 43.478 0.00 0.00 37.56 4.57
228 257 1.329906 CTGAATCAAGCAGCGTGGATC 59.670 52.381 8.59 7.73 0.00 3.36
247 276 4.821805 GGATCCTTCTGTTTGTTTCAGTCA 59.178 41.667 3.84 0.00 34.86 3.41
389 425 3.630204 CACGCGTGCAGTTCTTCT 58.370 55.556 28.16 0.00 0.00 2.85
390 426 1.202568 CACGCGTGCAGTTCTTCTG 59.797 57.895 28.16 0.00 46.12 3.02
449 485 2.452295 ATATGACATGGCTGCGAGAG 57.548 50.000 0.00 0.00 0.00 3.20
473 510 1.226491 CACCCCGTACGCTCGTAAG 60.226 63.158 10.49 6.09 31.86 2.34
474 511 1.675641 ACCCCGTACGCTCGTAAGT 60.676 57.895 10.49 0.00 39.48 2.24
475 512 1.063166 CCCCGTACGCTCGTAAGTC 59.937 63.158 10.49 0.00 39.48 3.01
476 513 1.297158 CCCGTACGCTCGTAAGTCG 60.297 63.158 10.49 8.63 41.41 4.18
477 514 1.421485 CCGTACGCTCGTAAGTCGT 59.579 57.895 10.49 1.98 45.59 4.34
478 515 0.645355 CCGTACGCTCGTAAGTCGTA 59.355 55.000 10.49 1.14 44.05 3.43
479 516 1.060553 CCGTACGCTCGTAAGTCGTAA 59.939 52.381 10.49 0.00 45.30 3.18
480 517 2.285834 CCGTACGCTCGTAAGTCGTAAT 60.286 50.000 10.49 0.00 45.30 1.89
481 518 2.705981 CGTACGCTCGTAAGTCGTAATG 59.294 50.000 0.52 2.21 45.30 1.90
482 519 2.184385 ACGCTCGTAAGTCGTAATGG 57.816 50.000 0.00 0.00 43.12 3.16
483 520 0.844503 CGCTCGTAAGTCGTAATGGC 59.155 55.000 0.00 0.00 40.80 4.40
484 521 1.796253 CGCTCGTAAGTCGTAATGGCA 60.796 52.381 0.00 0.00 40.80 4.92
485 522 1.852895 GCTCGTAAGTCGTAATGGCAG 59.147 52.381 0.00 0.00 40.80 4.85
486 523 1.852895 CTCGTAAGTCGTAATGGCAGC 59.147 52.381 0.00 0.00 40.80 5.25
487 524 1.202817 TCGTAAGTCGTAATGGCAGCA 59.797 47.619 0.00 0.00 40.80 4.41
488 525 1.588404 CGTAAGTCGTAATGGCAGCAG 59.412 52.381 0.00 0.00 34.52 4.24
489 526 2.734175 CGTAAGTCGTAATGGCAGCAGA 60.734 50.000 0.00 0.00 34.52 4.26
490 527 2.015736 AAGTCGTAATGGCAGCAGAG 57.984 50.000 0.00 0.00 0.00 3.35
491 528 0.460987 AGTCGTAATGGCAGCAGAGC 60.461 55.000 0.00 0.00 0.00 4.09
531 579 1.202734 CCCTGATTGCCATGTCTCGAT 60.203 52.381 0.00 0.00 0.00 3.59
532 580 2.037641 CCCTGATTGCCATGTCTCGATA 59.962 50.000 0.00 0.00 0.00 2.92
533 581 3.324117 CCTGATTGCCATGTCTCGATAG 58.676 50.000 0.00 0.00 0.00 2.08
534 582 3.244009 CCTGATTGCCATGTCTCGATAGT 60.244 47.826 0.00 0.00 37.40 2.12
535 583 3.982475 TGATTGCCATGTCTCGATAGTC 58.018 45.455 0.00 0.00 37.40 2.59
536 584 2.492019 TTGCCATGTCTCGATAGTCG 57.508 50.000 0.00 0.00 42.10 4.18
578 626 2.451167 CCTCGCGTACGTCTCGTCT 61.451 63.158 17.90 0.00 41.54 4.18
615 663 1.653609 CGTGCATCAAGTTTCGATCGA 59.346 47.619 15.15 15.15 0.00 3.59
767 820 2.044806 GATGTGGACCAGATCGGGGG 62.045 65.000 15.31 8.11 40.22 5.40
999 1052 0.961358 ACACTCGTCTTCTCTCCCCG 60.961 60.000 0.00 0.00 0.00 5.73
1053 1115 1.139498 TGCAGAGGAAATGGGTGGGA 61.139 55.000 0.00 0.00 0.00 4.37
1054 1116 0.039618 GCAGAGGAAATGGGTGGGAA 59.960 55.000 0.00 0.00 0.00 3.97
1055 1117 1.957113 GCAGAGGAAATGGGTGGGAAG 60.957 57.143 0.00 0.00 0.00 3.46
1056 1118 1.002857 AGAGGAAATGGGTGGGAAGG 58.997 55.000 0.00 0.00 0.00 3.46
1230 1292 2.754658 CCGCCTCGACCTGGTACT 60.755 66.667 0.00 0.00 0.00 2.73
1263 1325 2.174319 GCTCCGCTCCGTTCCAATC 61.174 63.158 0.00 0.00 0.00 2.67
1348 1421 3.064682 CCGTGCGGATATGTCAAATTTGA 59.935 43.478 16.91 16.91 37.50 2.69
1384 1462 4.512944 TCTGTCTGTTGCTCTTGTTGATTC 59.487 41.667 0.00 0.00 0.00 2.52
1395 1473 1.890876 TGTTGATTCAACTCGGGGTG 58.109 50.000 25.49 0.00 43.85 4.61
1399 1477 4.258543 GTTGATTCAACTCGGGGTGATTA 58.741 43.478 19.90 0.00 40.73 1.75
1401 1479 4.450976 TGATTCAACTCGGGGTGATTATG 58.549 43.478 2.49 0.00 0.00 1.90
1407 1485 2.542907 CGGGGTGATTATGTGCGCC 61.543 63.158 4.18 0.00 0.00 6.53
1420 1498 0.598065 GTGCGCCTGAAGGAAATGTT 59.402 50.000 4.18 0.00 37.39 2.71
1421 1499 1.000274 GTGCGCCTGAAGGAAATGTTT 60.000 47.619 4.18 0.00 37.39 2.83
1446 1524 4.970662 TGTAGCTCTTGAATTTGATGCC 57.029 40.909 0.00 0.00 0.00 4.40
1562 1652 5.415701 TCTGTAACATTTCTTTGGCCATCTC 59.584 40.000 6.09 0.00 0.00 2.75
1706 1796 2.997980 ACATGCATGATTTGTACCCGA 58.002 42.857 32.75 0.00 0.00 5.14
1787 1877 3.036819 AGCTTGCATACAGAGGAGATCA 58.963 45.455 0.00 0.00 0.00 2.92
1806 1896 2.756760 TCAGGCAGCTTGATTGATTTCC 59.243 45.455 2.39 0.00 0.00 3.13
1840 1930 0.029834 GCCATCGCATAAGCTTGTGG 59.970 55.000 22.71 13.63 39.10 4.17
1847 1937 3.809279 TCGCATAAGCTTGTGGTATCATG 59.191 43.478 22.71 10.64 39.10 3.07
1890 1980 3.508845 TTCCCTTTGCTATGGCCTATC 57.491 47.619 3.32 0.00 37.74 2.08
1891 1981 1.347707 TCCCTTTGCTATGGCCTATCG 59.652 52.381 3.32 0.00 37.74 2.92
1898 1988 3.161866 TGCTATGGCCTATCGTCACATA 58.838 45.455 3.32 0.00 37.74 2.29
1906 1996 5.411361 TGGCCTATCGTCACATAATATTTGC 59.589 40.000 3.32 0.00 0.00 3.68
1940 2030 3.826729 GGGGCTAGTTTCAAATGTCTGTT 59.173 43.478 0.00 0.00 0.00 3.16
1961 2051 1.132588 GTCGATAGGATGCTTGCGTC 58.867 55.000 6.29 6.29 0.00 5.19
1962 2052 0.744281 TCGATAGGATGCTTGCGTCA 59.256 50.000 15.50 0.00 0.00 4.35
1998 2088 4.220382 TGGTCCAAATGGTCTGCTTTAATG 59.780 41.667 0.00 0.00 36.34 1.90
2004 2094 3.350219 TGGTCTGCTTTAATGACCCTC 57.650 47.619 8.63 0.00 46.97 4.30
2005 2095 2.026262 TGGTCTGCTTTAATGACCCTCC 60.026 50.000 8.63 0.00 46.97 4.30
2006 2096 2.644676 GTCTGCTTTAATGACCCTCCC 58.355 52.381 0.00 0.00 0.00 4.30
2056 2224 2.288525 ACCCTCCCTTTTTGGCTATCT 58.711 47.619 0.00 0.00 0.00 1.98
2099 2267 4.217118 GGCATACCAAAGGCTATCATTCAG 59.783 45.833 0.00 0.00 35.26 3.02
2197 2365 3.007940 GGCCAACCTTGCTATTTCCTTTT 59.992 43.478 0.00 0.00 0.00 2.27
2265 2433 8.752766 AAATCTCAAGTTATGAAGCAACATTG 57.247 30.769 1.32 0.00 37.67 2.82
2391 2559 6.854496 TTTACGAGATGCTGTTTTACTTGT 57.146 33.333 0.00 0.00 0.00 3.16
2423 2591 9.291664 CGTCCAAAATAGAACTTCTAGTCTTAG 57.708 37.037 4.82 0.00 31.67 2.18
2494 2662 9.554395 TGAACAAGTAGTTTCAAATATGACTCA 57.446 29.630 0.00 0.00 41.51 3.41
2674 2843 2.977456 TGCCTTTGCACGCACGAT 60.977 55.556 0.00 0.00 44.23 3.73
2706 2875 1.451449 TTTAGTCCCCCTTTCAGGCA 58.549 50.000 0.00 0.00 32.73 4.75
3046 3215 8.352942 CAAGAACTTTAGGTCAGTAGCATTTTT 58.647 33.333 0.00 0.00 0.00 1.94
4035 4305 7.867403 TCAGGTTTTTCTTATTGAAGATTGTGC 59.133 33.333 0.00 0.00 41.40 4.57
4099 4369 2.674852 TGGTAGACGCTTACTCACTACG 59.325 50.000 0.00 0.00 35.66 3.51
4210 4480 7.770897 GGGTATATATTAATGGTCTGCTTGGAG 59.229 40.741 0.00 0.00 0.00 3.86
4325 4595 8.896744 CATGTAGTACATTTGATCAACCAATCT 58.103 33.333 13.25 7.18 36.53 2.40
4344 4614 6.255887 CCAATCTTCTCCACGTACAAACTATC 59.744 42.308 0.00 0.00 0.00 2.08
4478 4748 1.208293 CTTCAGGTGTTCCTAGGAGGC 59.792 57.143 12.26 9.82 43.07 4.70
4531 4801 0.958382 TGCAACATTGGACGGTAGCC 60.958 55.000 0.00 0.00 0.00 3.93
4544 4814 3.377573 ACGGTAGCCAAGGTAATAAGGA 58.622 45.455 0.00 0.00 0.00 3.36
4585 4855 7.765819 CAGGATCAAACAGTAGATATGTCACAA 59.234 37.037 0.00 0.00 0.00 3.33
4665 4935 4.141711 CCTCTAGCCTACATACTTTTGGCA 60.142 45.833 0.00 0.00 45.42 4.92
4740 5010 1.348696 TCACAGATGGCTCAGCAGAAA 59.651 47.619 0.00 0.00 0.00 2.52
4884 5154 8.728337 TGAAGATCTTATCTGTGAATTCCAAG 57.272 34.615 8.25 0.52 40.13 3.61
4975 5246 1.651987 TAGAAATGCTACGCAGGTGC 58.348 50.000 0.00 0.00 43.65 5.01
5291 5562 3.924686 CGTAAGTAGTCACTCGCCAAAAT 59.075 43.478 0.00 0.00 32.29 1.82
5612 5883 1.064825 CAGTCCTGTGGGGGTACTTT 58.935 55.000 0.00 0.00 35.33 2.66
5679 5950 3.186409 GCGCTTACAACTTCTGTTCATCA 59.814 43.478 0.00 0.00 39.64 3.07
5752 6023 7.760794 TGTTCATTTCTTTCCATCATATGCAAC 59.239 33.333 0.00 0.00 0.00 4.17
5767 6038 0.593263 GCAACGCAGCCTTATGCATC 60.593 55.000 0.19 0.00 46.87 3.91
5995 6266 1.552792 CCGCTCCTCTTCTTCTTCCTT 59.447 52.381 0.00 0.00 0.00 3.36
6016 6287 2.367894 TGTCATCATCAGGGAGCATCTC 59.632 50.000 0.00 0.00 33.92 2.75
6031 6302 2.875317 GCATCTCCTCCCGAAATTCTTC 59.125 50.000 0.00 0.00 0.00 2.87
6097 6368 4.699522 GAGGGGGTGCACCGTGAC 62.700 72.222 29.08 18.18 41.60 3.67
6147 6422 1.468520 CACTCCCGGTTGCATTTACTG 59.531 52.381 0.00 0.00 0.00 2.74
6246 6521 2.545742 CGAATCCATCACACGAGGCATA 60.546 50.000 0.00 0.00 0.00 3.14
6307 6582 1.658673 ACGACTCACCGTGGAGAAC 59.341 57.895 7.49 1.56 41.70 3.01
6650 6927 0.179094 ACGTCGAGGAAACTGTGCAA 60.179 50.000 12.85 0.00 44.43 4.08
6671 6948 4.081030 CAAGTGCCAGTCGCTGCG 62.081 66.667 17.25 17.25 38.78 5.18
6687 6964 2.919043 CGGGGGAGAAATGGGGAG 59.081 66.667 0.00 0.00 0.00 4.30
6774 7053 0.032815 GGCGAGGGAGCAATCTACTC 59.967 60.000 0.00 0.00 39.27 2.59
6809 7324 7.982371 AGTATTATGTTTGTAGTACAGACGC 57.018 36.000 16.63 4.60 36.14 5.19
6810 7325 7.541162 AGTATTATGTTTGTAGTACAGACGCA 58.459 34.615 16.63 9.18 36.14 5.24
6811 7326 6.887376 ATTATGTTTGTAGTACAGACGCAG 57.113 37.500 16.63 0.00 36.14 5.18
6812 7327 2.400399 TGTTTGTAGTACAGACGCAGC 58.600 47.619 16.63 0.18 36.14 5.25
6813 7328 2.035449 TGTTTGTAGTACAGACGCAGCT 59.965 45.455 16.63 0.00 36.14 4.24
6814 7329 2.631418 TTGTAGTACAGACGCAGCTC 57.369 50.000 2.68 0.00 0.00 4.09
6826 7367 3.195825 AGACGCAGCTCCTAGTTTTATGT 59.804 43.478 0.00 0.00 0.00 2.29
6894 7435 1.587613 GCACGATGAGAGTCCTCGC 60.588 63.158 7.14 0.00 42.33 5.03
6897 7438 1.297967 CGATGAGAGTCCTCGCGTG 60.298 63.158 5.77 2.75 42.33 5.34
6917 7458 2.580276 GCCCGTGAACCGTCCATA 59.420 61.111 0.00 0.00 33.66 2.74
6931 7472 3.266254 CCGTCCATACCCTCTCCTATCTA 59.734 52.174 0.00 0.00 0.00 1.98
6986 7582 1.005340 GTGCTCAGGCTTCTCATTCG 58.995 55.000 0.00 0.00 39.59 3.34
7002 7598 6.220201 TCTCATTCGTGTCACATCTAAAACA 58.780 36.000 3.42 0.00 0.00 2.83
7141 7752 0.608640 AGGTCCAAGTACTTCTGCGG 59.391 55.000 4.77 4.19 0.00 5.69
7157 7768 2.911143 GGAGCGGGGTGATGATGT 59.089 61.111 0.00 0.00 0.00 3.06
7190 7801 4.942090 CACGATTGGTGTTGGTGC 57.058 55.556 0.00 0.00 41.89 5.01
7191 7802 1.082169 CACGATTGGTGTTGGTGCG 60.082 57.895 0.00 0.00 41.89 5.34
7193 7804 2.258013 CGATTGGTGTTGGTGCGGT 61.258 57.895 0.00 0.00 0.00 5.68
7195 7806 0.039527 GATTGGTGTTGGTGCGGTTC 60.040 55.000 0.00 0.00 0.00 3.62
7213 7825 3.077359 GTTCTGTGCTTCTGCTATGGTT 58.923 45.455 0.00 0.00 40.48 3.67
7256 7868 1.588674 CTACGACAAAGTTGCACCCA 58.411 50.000 0.00 0.00 0.00 4.51
7269 7881 4.082523 ACCCACGAGGCGACCATG 62.083 66.667 0.00 0.00 40.58 3.66
7270 7882 4.838152 CCCACGAGGCGACCATGG 62.838 72.222 11.19 11.19 0.00 3.66
7290 7902 4.913126 CTGGAACCAGCTACGACC 57.087 61.111 7.95 0.00 37.24 4.79
7291 7903 1.972198 CTGGAACCAGCTACGACCA 59.028 57.895 7.95 0.00 37.24 4.02
7292 7904 0.108615 CTGGAACCAGCTACGACCAG 60.109 60.000 7.95 12.46 38.77 4.00
7293 7905 0.830444 TGGAACCAGCTACGACCAGT 60.830 55.000 0.00 0.00 0.00 4.00
7294 7906 0.389948 GGAACCAGCTACGACCAGTG 60.390 60.000 0.00 0.00 0.00 3.66
7295 7907 0.389948 GAACCAGCTACGACCAGTGG 60.390 60.000 7.91 7.91 0.00 4.00
7300 7912 2.490217 CTACGACCAGTGGCGGAG 59.510 66.667 23.62 21.57 30.06 4.63
7301 7913 2.034532 TACGACCAGTGGCGGAGA 59.965 61.111 23.62 10.56 0.00 3.71
7302 7914 2.267681 CTACGACCAGTGGCGGAGAC 62.268 65.000 25.29 5.10 36.02 3.36
7340 7952 2.606751 GCTATAGCCCCAGGTCTAGA 57.393 55.000 14.13 0.00 34.31 2.43
7341 7953 2.890814 GCTATAGCCCCAGGTCTAGAA 58.109 52.381 14.13 0.00 34.31 2.10
7342 7954 3.240302 GCTATAGCCCCAGGTCTAGAAA 58.760 50.000 14.13 0.00 34.31 2.52
7343 7955 3.007074 GCTATAGCCCCAGGTCTAGAAAC 59.993 52.174 14.13 0.00 34.31 2.78
7344 7956 2.634639 TAGCCCCAGGTCTAGAAACA 57.365 50.000 0.00 0.00 0.00 2.83
7345 7957 1.742308 AGCCCCAGGTCTAGAAACAA 58.258 50.000 0.00 0.00 0.00 2.83
7346 7958 1.351350 AGCCCCAGGTCTAGAAACAAC 59.649 52.381 0.00 0.00 0.00 3.32
7347 7959 1.351350 GCCCCAGGTCTAGAAACAACT 59.649 52.381 0.00 0.00 0.00 3.16
7348 7960 2.224793 GCCCCAGGTCTAGAAACAACTT 60.225 50.000 0.00 0.00 0.00 2.66
7349 7961 3.676093 CCCCAGGTCTAGAAACAACTTC 58.324 50.000 0.00 0.00 0.00 3.01
7350 7962 3.559384 CCCCAGGTCTAGAAACAACTTCC 60.559 52.174 0.00 0.00 34.21 3.46
7351 7963 3.328050 CCCAGGTCTAGAAACAACTTCCT 59.672 47.826 0.00 0.00 34.21 3.36
7352 7964 4.202472 CCCAGGTCTAGAAACAACTTCCTT 60.202 45.833 0.00 0.00 34.21 3.36
7353 7965 5.377478 CCAGGTCTAGAAACAACTTCCTTT 58.623 41.667 0.00 0.00 34.21 3.11
7354 7966 6.465321 CCCAGGTCTAGAAACAACTTCCTTTA 60.465 42.308 0.00 0.00 34.21 1.85
7355 7967 7.168905 CCAGGTCTAGAAACAACTTCCTTTAT 58.831 38.462 0.00 0.00 34.21 1.40
7356 7968 8.319146 CCAGGTCTAGAAACAACTTCCTTTATA 58.681 37.037 0.00 0.00 34.21 0.98
7357 7969 9.720769 CAGGTCTAGAAACAACTTCCTTTATAA 57.279 33.333 0.00 0.00 34.21 0.98
7368 7980 9.860898 ACAACTTCCTTTATAATTTCTTCATGC 57.139 29.630 0.00 0.00 0.00 4.06
7369 7981 9.859427 CAACTTCCTTTATAATTTCTTCATGCA 57.141 29.630 0.00 0.00 0.00 3.96
7373 7985 8.931385 TCCTTTATAATTTCTTCATGCAAAGC 57.069 30.769 0.00 0.00 0.00 3.51
7374 7986 8.530311 TCCTTTATAATTTCTTCATGCAAAGCA 58.470 29.630 0.00 0.00 44.86 3.91
7392 8004 9.709495 TGCAAAGCATAGAAAATCATAAAAGTT 57.291 25.926 0.00 0.00 31.71 2.66
7413 8025 7.308782 AGTTTATCACTTAACATAGCACAGC 57.691 36.000 0.00 0.00 27.32 4.40
7414 8026 6.316390 AGTTTATCACTTAACATAGCACAGCC 59.684 38.462 0.00 0.00 27.32 4.85
7415 8027 2.985896 TCACTTAACATAGCACAGCCC 58.014 47.619 0.00 0.00 0.00 5.19
7416 8028 2.017049 CACTTAACATAGCACAGCCCC 58.983 52.381 0.00 0.00 0.00 5.80
7417 8029 1.633432 ACTTAACATAGCACAGCCCCA 59.367 47.619 0.00 0.00 0.00 4.96
7418 8030 2.292267 CTTAACATAGCACAGCCCCAG 58.708 52.381 0.00 0.00 0.00 4.45
7419 8031 0.546122 TAACATAGCACAGCCCCAGG 59.454 55.000 0.00 0.00 0.00 4.45
7436 8048 0.671251 AGGCGTAGTCTGCATCTAGC 59.329 55.000 0.00 0.24 46.61 3.42
7437 8049 0.671251 GGCGTAGTCTGCATCTAGCT 59.329 55.000 0.00 0.00 45.94 3.32
7438 8050 1.335506 GGCGTAGTCTGCATCTAGCTC 60.336 57.143 0.00 0.00 45.94 4.09
7439 8051 1.335506 GCGTAGTCTGCATCTAGCTCC 60.336 57.143 0.00 0.00 45.94 4.70
7440 8052 1.069568 CGTAGTCTGCATCTAGCTCCG 60.070 57.143 0.00 0.00 45.94 4.63
7441 8053 0.955178 TAGTCTGCATCTAGCTCCGC 59.045 55.000 0.00 0.00 45.94 5.54
7442 8054 1.300542 GTCTGCATCTAGCTCCGCC 60.301 63.158 0.00 0.00 45.94 6.13
7443 8055 1.758122 TCTGCATCTAGCTCCGCCA 60.758 57.895 0.00 0.00 45.94 5.69
7444 8056 1.593750 CTGCATCTAGCTCCGCCAC 60.594 63.158 0.00 0.00 45.94 5.01
7445 8057 2.025767 CTGCATCTAGCTCCGCCACT 62.026 60.000 0.00 0.00 45.94 4.00
7446 8058 1.593750 GCATCTAGCTCCGCCACTG 60.594 63.158 0.00 0.00 41.15 3.66
7447 8059 1.068753 CATCTAGCTCCGCCACTGG 59.931 63.158 0.00 0.00 0.00 4.00
7448 8060 2.801631 ATCTAGCTCCGCCACTGGC 61.802 63.158 10.35 10.35 46.75 4.85
7459 8071 1.571919 GCCACTGGCTACGACTAATG 58.428 55.000 13.28 0.00 46.69 1.90
7460 8072 1.571919 CCACTGGCTACGACTAATGC 58.428 55.000 0.00 0.00 0.00 3.56
7461 8073 1.137086 CCACTGGCTACGACTAATGCT 59.863 52.381 0.00 0.00 0.00 3.79
7462 8074 2.361119 CCACTGGCTACGACTAATGCTA 59.639 50.000 0.00 0.00 0.00 3.49
7463 8075 3.372954 CACTGGCTACGACTAATGCTAC 58.627 50.000 0.00 0.00 0.00 3.58
7464 8076 2.033049 ACTGGCTACGACTAATGCTACG 59.967 50.000 0.00 0.00 0.00 3.51
7465 8077 2.289820 CTGGCTACGACTAATGCTACGA 59.710 50.000 0.00 0.00 0.00 3.43
7466 8078 2.882761 TGGCTACGACTAATGCTACGAT 59.117 45.455 0.00 0.00 0.00 3.73
7467 8079 3.058432 TGGCTACGACTAATGCTACGATC 60.058 47.826 0.00 0.00 0.00 3.69
7468 8080 3.154489 GCTACGACTAATGCTACGATCG 58.846 50.000 14.88 14.88 35.74 3.69
7469 8081 2.033793 ACGACTAATGCTACGATCGC 57.966 50.000 16.60 0.00 32.95 4.58
7470 8082 0.968503 CGACTAATGCTACGATCGCG 59.031 55.000 16.60 7.89 44.79 5.87
7471 8083 1.328439 GACTAATGCTACGATCGCGG 58.672 55.000 16.60 9.32 43.17 6.46
7472 8084 0.666913 ACTAATGCTACGATCGCGGT 59.333 50.000 16.60 0.00 43.17 5.68
7473 8085 1.066605 ACTAATGCTACGATCGCGGTT 59.933 47.619 16.60 6.08 43.17 4.44
7474 8086 2.291465 ACTAATGCTACGATCGCGGTTA 59.709 45.455 16.60 6.90 43.17 2.85
7475 8087 1.767289 AATGCTACGATCGCGGTTAG 58.233 50.000 16.60 10.45 43.17 2.34
7476 8088 0.663568 ATGCTACGATCGCGGTTAGC 60.664 55.000 21.93 21.93 40.48 3.09
7492 8104 3.542742 GCGCGTGCTAGAACCGAC 61.543 66.667 15.02 4.07 38.39 4.79
7493 8105 3.238241 CGCGTGCTAGAACCGACG 61.238 66.667 0.00 0.00 34.93 5.12
7494 8106 2.126580 GCGTGCTAGAACCGACGT 60.127 61.111 0.00 0.00 34.32 4.34
7495 8107 1.731969 GCGTGCTAGAACCGACGTT 60.732 57.895 0.00 0.00 34.32 3.99
7496 8108 1.941476 GCGTGCTAGAACCGACGTTG 61.941 60.000 0.00 0.00 34.32 4.10
7497 8109 0.386352 CGTGCTAGAACCGACGTTGA 60.386 55.000 3.74 0.00 30.30 3.18
7498 8110 1.058404 GTGCTAGAACCGACGTTGAC 58.942 55.000 3.74 0.00 30.30 3.18
7499 8111 0.386352 TGCTAGAACCGACGTTGACG 60.386 55.000 3.74 1.41 46.33 4.35
7500 8112 0.110056 GCTAGAACCGACGTTGACGA 60.110 55.000 10.87 0.00 43.02 4.20
7501 8113 1.664016 GCTAGAACCGACGTTGACGAA 60.664 52.381 10.87 0.00 43.02 3.85
7502 8114 2.860062 CTAGAACCGACGTTGACGAAT 58.140 47.619 10.87 0.00 43.02 3.34
7503 8115 1.415374 AGAACCGACGTTGACGAATG 58.585 50.000 10.87 0.56 43.02 2.67
7504 8116 0.179258 GAACCGACGTTGACGAATGC 60.179 55.000 10.87 0.00 43.02 3.56
7505 8117 0.599204 AACCGACGTTGACGAATGCT 60.599 50.000 10.87 0.00 43.02 3.79
7506 8118 1.282248 ACCGACGTTGACGAATGCTG 61.282 55.000 10.87 0.00 43.02 4.41
7507 8119 1.416049 CGACGTTGACGAATGCTGG 59.584 57.895 10.87 0.00 43.02 4.85
7508 8120 1.787847 GACGTTGACGAATGCTGGG 59.212 57.895 10.87 0.00 43.02 4.45
7509 8121 0.669318 GACGTTGACGAATGCTGGGA 60.669 55.000 10.87 0.00 43.02 4.37
7510 8122 0.949105 ACGTTGACGAATGCTGGGAC 60.949 55.000 10.87 0.00 43.02 4.46
7511 8123 1.635663 CGTTGACGAATGCTGGGACC 61.636 60.000 0.00 0.00 43.02 4.46
7512 8124 0.605319 GTTGACGAATGCTGGGACCA 60.605 55.000 0.00 0.00 0.00 4.02
7513 8125 0.605319 TTGACGAATGCTGGGACCAC 60.605 55.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.127031 AGCCTACATACAAATCGGCAAAAAT 59.873 36.000 0.00 0.00 39.91 1.82
9 10 4.461081 AGCCTACATACAAATCGGCAAAAA 59.539 37.500 0.00 0.00 39.91 1.94
30 31 0.717224 CCACGCAAATTCATGCAAGC 59.283 50.000 0.00 0.00 46.76 4.01
45 46 6.456853 CGTGCCATAATATATTCATTCCCACG 60.457 42.308 0.00 10.48 34.81 4.94
100 106 4.331168 GCACAAATCTGACTACATCACCTC 59.669 45.833 0.00 0.00 32.37 3.85
123 129 2.196776 GCCACATGGGAGATGGGG 59.803 66.667 0.00 0.00 45.25 4.96
228 257 4.199310 TCCTGACTGAAACAAACAGAAGG 58.801 43.478 0.00 0.00 40.47 3.46
247 276 4.816385 CCGTAACAATAGCAATCACATCCT 59.184 41.667 0.00 0.00 0.00 3.24
386 422 4.158394 GGAGCATGGTTTTATCAAGCAGAA 59.842 41.667 0.00 0.00 32.07 3.02
387 423 3.696051 GGAGCATGGTTTTATCAAGCAGA 59.304 43.478 0.00 0.00 32.07 4.26
388 424 3.181483 GGGAGCATGGTTTTATCAAGCAG 60.181 47.826 0.00 0.00 32.07 4.24
389 425 2.760092 GGGAGCATGGTTTTATCAAGCA 59.240 45.455 0.00 0.00 32.07 3.91
390 426 2.760092 TGGGAGCATGGTTTTATCAAGC 59.240 45.455 0.00 0.00 0.00 4.01
391 427 5.105228 ACAATGGGAGCATGGTTTTATCAAG 60.105 40.000 0.00 0.00 0.00 3.02
473 510 2.009888 GCTCTGCTGCCATTACGAC 58.990 57.895 0.00 0.00 0.00 4.34
474 511 4.521075 GCTCTGCTGCCATTACGA 57.479 55.556 0.00 0.00 0.00 3.43
486 523 3.207669 GCGATTGGGCAGGCTCTG 61.208 66.667 0.00 0.00 34.12 3.35
487 524 4.496336 GGCGATTGGGCAGGCTCT 62.496 66.667 0.00 0.00 41.77 4.09
491 528 4.528039 ATGGGGCGATTGGGCAGG 62.528 66.667 0.00 0.00 44.56 4.85
492 529 2.019897 GAAATGGGGCGATTGGGCAG 62.020 60.000 0.00 0.00 44.56 4.85
493 530 2.038651 AAATGGGGCGATTGGGCA 59.961 55.556 0.00 0.00 44.56 5.36
494 531 2.796193 GGAAATGGGGCGATTGGGC 61.796 63.158 0.00 0.00 41.35 5.36
495 532 2.133641 GGGAAATGGGGCGATTGGG 61.134 63.158 0.00 0.00 0.00 4.12
496 533 1.076044 AGGGAAATGGGGCGATTGG 60.076 57.895 0.00 0.00 0.00 3.16
531 579 0.106167 ACCAGCTGGCCTATCGACTA 60.106 55.000 33.06 0.00 39.32 2.59
532 580 1.381872 ACCAGCTGGCCTATCGACT 60.382 57.895 33.06 6.80 39.32 4.18
533 581 1.227380 CACCAGCTGGCCTATCGAC 60.227 63.158 33.06 0.00 39.32 4.20
534 582 2.434843 CCACCAGCTGGCCTATCGA 61.435 63.158 33.06 0.00 39.32 3.59
535 583 2.109799 CCACCAGCTGGCCTATCG 59.890 66.667 33.06 13.54 39.32 2.92
536 584 2.378634 ACCCACCAGCTGGCCTATC 61.379 63.158 33.06 0.00 39.01 2.08
537 585 2.286425 ACCCACCAGCTGGCCTAT 60.286 61.111 33.06 13.53 39.01 2.57
578 626 2.619646 GCACGTTTCCCTTCCAAACTTA 59.380 45.455 0.00 0.00 32.46 2.24
912 965 3.186817 TGAAAATAGTAAACGTGGTGCCG 59.813 43.478 0.00 0.00 0.00 5.69
985 1038 1.736586 CCATCGGGGAGAGAAGACG 59.263 63.158 0.00 0.00 40.01 4.18
1053 1115 1.145738 TGCAGCCTTCTTTCCTTCCTT 59.854 47.619 0.00 0.00 0.00 3.36
1054 1116 0.773644 TGCAGCCTTCTTTCCTTCCT 59.226 50.000 0.00 0.00 0.00 3.36
1055 1117 1.270826 GTTGCAGCCTTCTTTCCTTCC 59.729 52.381 0.00 0.00 0.00 3.46
1056 1118 1.270826 GGTTGCAGCCTTCTTTCCTTC 59.729 52.381 13.08 0.00 0.00 3.46
1230 1292 3.003173 AGCCTTACCAGCAGCGGA 61.003 61.111 9.87 0.00 0.00 5.54
1263 1325 1.690219 CGAGGTGAGGGGATTGAGGG 61.690 65.000 0.00 0.00 0.00 4.30
1348 1421 1.947642 GACAGAAACACGGACGCGT 60.948 57.895 13.85 13.85 0.00 6.01
1358 1431 4.094887 TCAACAAGAGCAACAGACAGAAAC 59.905 41.667 0.00 0.00 0.00 2.78
1362 1440 4.274214 TGAATCAACAAGAGCAACAGACAG 59.726 41.667 0.00 0.00 0.00 3.51
1384 1462 1.670811 GCACATAATCACCCCGAGTTG 59.329 52.381 0.00 0.00 0.00 3.16
1395 1473 1.953559 TCCTTCAGGCGCACATAATC 58.046 50.000 10.83 0.00 34.44 1.75
1399 1477 0.813184 CATTTCCTTCAGGCGCACAT 59.187 50.000 10.83 0.00 34.44 3.21
1401 1479 0.598065 AACATTTCCTTCAGGCGCAC 59.402 50.000 10.83 0.00 34.44 5.34
1420 1498 6.405065 GCATCAAATTCAAGAGCTACATGGAA 60.405 38.462 0.00 0.00 0.00 3.53
1421 1499 5.066893 GCATCAAATTCAAGAGCTACATGGA 59.933 40.000 0.00 0.00 0.00 3.41
1423 1501 5.279384 GGCATCAAATTCAAGAGCTACATG 58.721 41.667 0.00 0.00 0.00 3.21
1424 1502 4.036027 CGGCATCAAATTCAAGAGCTACAT 59.964 41.667 0.00 0.00 0.00 2.29
1426 1504 3.375299 ACGGCATCAAATTCAAGAGCTAC 59.625 43.478 0.00 0.00 0.00 3.58
1427 1505 3.609853 ACGGCATCAAATTCAAGAGCTA 58.390 40.909 0.00 0.00 0.00 3.32
1428 1506 2.440409 ACGGCATCAAATTCAAGAGCT 58.560 42.857 0.00 0.00 0.00 4.09
1429 1507 2.927553 ACGGCATCAAATTCAAGAGC 57.072 45.000 0.00 0.00 0.00 4.09
1430 1508 4.944962 TGTACGGCATCAAATTCAAGAG 57.055 40.909 0.00 0.00 0.00 2.85
1431 1509 4.699735 ACATGTACGGCATCAAATTCAAGA 59.300 37.500 0.00 0.00 35.19 3.02
1432 1510 4.985413 ACATGTACGGCATCAAATTCAAG 58.015 39.130 0.00 0.00 35.19 3.02
1433 1511 5.384063 AACATGTACGGCATCAAATTCAA 57.616 34.783 0.00 0.00 35.19 2.69
1434 1512 5.384063 AAACATGTACGGCATCAAATTCA 57.616 34.783 0.00 0.00 35.19 2.57
1435 1513 6.704512 AAAAACATGTACGGCATCAAATTC 57.295 33.333 0.00 0.00 35.19 2.17
1633 1723 6.072112 AGTGAAATGACGCTACAATTTTGT 57.928 33.333 1.08 1.08 44.86 2.83
1773 1863 1.969923 GCTGCCTGATCTCCTCTGTAT 59.030 52.381 0.00 0.00 0.00 2.29
1787 1877 3.097342 AGGAAATCAATCAAGCTGCCT 57.903 42.857 0.00 0.00 0.00 4.75
1806 1896 1.607628 GATGGCCATGCTCTGCTTAAG 59.392 52.381 26.56 0.00 0.00 1.85
1869 1959 3.747388 CGATAGGCCATAGCAAAGGGAAA 60.747 47.826 5.01 0.00 42.56 3.13
1890 1980 3.218453 TGGGGGCAAATATTATGTGACG 58.782 45.455 0.00 0.00 0.00 4.35
1891 1981 3.005791 GCTGGGGGCAAATATTATGTGAC 59.994 47.826 0.00 0.00 41.35 3.67
1898 1988 1.839354 CAAAGGCTGGGGGCAAATATT 59.161 47.619 0.00 0.00 44.01 1.28
1940 2030 0.249447 CGCAAGCATCCTATCGACCA 60.249 55.000 0.00 0.00 0.00 4.02
1962 2052 1.289160 TGGACCAGCTGAATTAGGCT 58.711 50.000 17.39 0.00 39.60 4.58
2021 2112 3.562182 GGAGGGTTTTCAACTTTCAGGA 58.438 45.455 0.00 0.00 0.00 3.86
2056 2224 5.575157 TGCCCAGTATCCTTCATTTAACAA 58.425 37.500 0.00 0.00 0.00 2.83
2153 2321 2.803956 CAATTTGGCTTGCCTCTGTTTG 59.196 45.455 13.18 6.19 0.00 2.93
2197 2365 0.037419 TAGCACGTGAAGCATCAGCA 60.037 50.000 22.23 0.00 45.49 4.41
2265 2433 2.158755 ACAGAGCTGCATTACCCCATAC 60.159 50.000 1.02 0.00 0.00 2.39
2391 2559 3.482436 AGTTCTATTTTGGACGCCACAA 58.518 40.909 0.00 0.00 30.78 3.33
2515 2683 6.716934 TTTCAACAATACTTAGGTTTGGCA 57.283 33.333 0.00 0.00 0.00 4.92
2666 2835 6.844696 AAAACATAATCAGATATCGTGCGT 57.155 33.333 0.00 0.00 0.00 5.24
2674 2843 7.947782 AGGGGGACTAAAACATAATCAGATA 57.052 36.000 0.00 0.00 0.00 1.98
2706 2875 9.831682 TTAAATAGGGTTTTCTTAGGTTCCATT 57.168 29.630 0.00 0.00 0.00 3.16
2902 3071 3.780294 AGGTGCCAATATCCTGACAGTAA 59.220 43.478 0.93 0.00 0.00 2.24
3483 3652 3.114606 TCCAGATGCAAACCCTATCAGA 58.885 45.455 0.00 0.00 0.00 3.27
4035 4305 9.520204 CCAAAATATATAGTGCTTTGAACAAGG 57.480 33.333 7.95 0.00 0.00 3.61
4099 4369 2.644992 CTGCGGAAAACAGGCCAC 59.355 61.111 5.01 0.00 0.00 5.01
4210 4480 5.649831 AGAGCAGTCCCATTGAAAAGATAAC 59.350 40.000 0.00 0.00 0.00 1.89
4325 4595 5.350365 GCATTGATAGTTTGTACGTGGAGAA 59.650 40.000 0.00 0.00 0.00 2.87
4344 4614 5.922544 CCTGAAAGTTTTACCTGAAGCATTG 59.077 40.000 0.00 0.00 0.00 2.82
4478 4748 1.609208 CAAGGAAGTGGGGTGAACAG 58.391 55.000 0.00 0.00 0.00 3.16
4544 4814 7.454380 TGTTTGATCCTGGATCCAAGTAAAATT 59.546 33.333 28.99 0.00 38.20 1.82
4585 4855 6.066690 CCCATCAGGATTATGAGTTCACATT 58.933 40.000 0.00 0.00 38.24 2.71
4665 4935 0.892755 CCATCACAGCAGGCACAATT 59.107 50.000 0.00 0.00 0.00 2.32
4740 5010 7.123355 TGATGGGTTTTTCAAATTGAACTCT 57.877 32.000 8.06 0.00 35.89 3.24
4884 5154 9.516314 AACAGTTTTTCTATTTTCTGTAAGCAC 57.484 29.630 0.00 0.00 35.53 4.40
5752 6023 0.309922 CCAAGATGCATAAGGCTGCG 59.690 55.000 0.00 0.00 45.30 5.18
5767 6038 4.002982 TGAATGAACCGAATGAGACCAAG 58.997 43.478 0.00 0.00 0.00 3.61
5995 6266 2.367894 GAGATGCTCCCTGATGATGACA 59.632 50.000 0.00 0.00 0.00 3.58
6097 6368 2.497675 CCATACCTCTGGTATCGATGGG 59.502 54.545 8.54 3.34 44.67 4.00
6120 6391 0.951040 GCAACCGGGAGTGACAGAAG 60.951 60.000 6.32 0.00 0.00 2.85
6147 6422 3.242543 CCGCACATGAGACTAAAAGATGC 60.243 47.826 0.00 0.00 0.00 3.91
6246 6521 5.483583 GGCAGTATATTCAGAGGGATCTTCT 59.516 44.000 0.00 0.00 0.00 2.85
6403 6678 2.215196 GTCAAGTTTCGGCACAAGGTA 58.785 47.619 0.00 0.00 0.00 3.08
6433 6708 4.122046 GAGTTCAGCTGCCAAAACAAAAT 58.878 39.130 9.47 0.00 0.00 1.82
6434 6709 3.195396 AGAGTTCAGCTGCCAAAACAAAA 59.805 39.130 9.47 0.00 0.00 2.44
6650 6927 2.358003 GCGACTGGCACTTGCTCT 60.358 61.111 0.38 0.00 42.87 4.09
6671 6948 0.710588 AAACTCCCCATTTCTCCCCC 59.289 55.000 0.00 0.00 0.00 5.40
6687 6964 3.521308 CTCGCGCACCCACACAAAC 62.521 63.158 8.75 0.00 0.00 2.93
6784 7063 8.676401 TGCGTCTGTACTACAAACATAATACTA 58.324 33.333 0.00 0.00 0.00 1.82
6805 7320 3.522553 ACATAAAACTAGGAGCTGCGTC 58.477 45.455 0.00 0.00 0.00 5.19
6806 7321 3.611766 ACATAAAACTAGGAGCTGCGT 57.388 42.857 0.00 0.00 0.00 5.24
6807 7322 5.005779 CACTTACATAAAACTAGGAGCTGCG 59.994 44.000 0.00 0.00 0.00 5.18
6808 7323 6.106673 TCACTTACATAAAACTAGGAGCTGC 58.893 40.000 0.00 0.00 0.00 5.25
6809 7324 8.723942 AATCACTTACATAAAACTAGGAGCTG 57.276 34.615 0.00 0.00 0.00 4.24
6810 7325 8.540388 TGAATCACTTACATAAAACTAGGAGCT 58.460 33.333 0.00 0.00 0.00 4.09
6811 7326 8.718102 TGAATCACTTACATAAAACTAGGAGC 57.282 34.615 0.00 0.00 0.00 4.70
6826 7367 1.002201 TCGGCCGGTTTGAATCACTTA 59.998 47.619 27.83 0.00 0.00 2.24
6882 7423 3.062466 CCCACGCGAGGACTCTCA 61.062 66.667 24.92 0.00 39.95 3.27
6917 7458 3.574826 GCGTGAAATAGATAGGAGAGGGT 59.425 47.826 0.00 0.00 0.00 4.34
6931 7472 1.490693 CGGATAGCTGCGCGTGAAAT 61.491 55.000 8.43 0.00 0.00 2.17
6986 7582 3.488310 ACGACGTGTTTTAGATGTGACAC 59.512 43.478 0.00 0.00 39.11 3.67
7002 7598 4.047059 CGGGTGTGGCTACGACGT 62.047 66.667 5.52 5.52 0.00 4.34
7141 7752 0.811616 GACACATCATCACCCCGCTC 60.812 60.000 0.00 0.00 0.00 5.03
7180 7791 1.822186 ACAGAACCGCACCAACACC 60.822 57.895 0.00 0.00 0.00 4.16
7182 7793 2.477176 GCACAGAACCGCACCAACA 61.477 57.895 0.00 0.00 0.00 3.33
7183 7794 1.724582 AAGCACAGAACCGCACCAAC 61.725 55.000 0.00 0.00 0.00 3.77
7184 7795 1.444119 GAAGCACAGAACCGCACCAA 61.444 55.000 0.00 0.00 0.00 3.67
7185 7796 1.891919 GAAGCACAGAACCGCACCA 60.892 57.895 0.00 0.00 0.00 4.17
7186 7797 1.598130 AGAAGCACAGAACCGCACC 60.598 57.895 0.00 0.00 0.00 5.01
7188 7799 2.253758 GCAGAAGCACAGAACCGCA 61.254 57.895 0.00 0.00 41.58 5.69
7189 7800 0.670546 TAGCAGAAGCACAGAACCGC 60.671 55.000 0.00 0.00 45.49 5.68
7190 7801 1.662629 CATAGCAGAAGCACAGAACCG 59.337 52.381 0.00 0.00 45.49 4.44
7191 7802 2.012673 CCATAGCAGAAGCACAGAACC 58.987 52.381 0.00 0.00 45.49 3.62
7193 7804 3.423539 AACCATAGCAGAAGCACAGAA 57.576 42.857 0.00 0.00 45.49 3.02
7195 7806 3.620374 CACTAACCATAGCAGAAGCACAG 59.380 47.826 0.00 0.00 45.49 3.66
7213 7825 0.105964 ACAACCTCGCAGCAACACTA 59.894 50.000 0.00 0.00 0.00 2.74
7256 7868 4.760047 GCACCATGGTCGCCTCGT 62.760 66.667 16.53 0.00 0.00 4.18
7290 7902 4.767255 GGCCTGTCTCCGCCACTG 62.767 72.222 0.00 0.00 45.01 3.66
7321 7933 2.606751 TCTAGACCTGGGGCTATAGC 57.393 55.000 16.78 16.78 41.14 2.97
7322 7934 4.223953 TGTTTCTAGACCTGGGGCTATAG 58.776 47.826 2.29 0.00 0.00 1.31
7323 7935 4.274794 TGTTTCTAGACCTGGGGCTATA 57.725 45.455 2.29 0.00 0.00 1.31
7324 7936 3.130734 TGTTTCTAGACCTGGGGCTAT 57.869 47.619 2.29 0.00 0.00 2.97
7325 7937 2.570302 GTTGTTTCTAGACCTGGGGCTA 59.430 50.000 1.90 1.90 0.00 3.93
7326 7938 1.351350 GTTGTTTCTAGACCTGGGGCT 59.649 52.381 0.00 0.00 0.00 5.19
7327 7939 1.351350 AGTTGTTTCTAGACCTGGGGC 59.649 52.381 0.00 0.00 0.00 5.80
7328 7940 3.559384 GGAAGTTGTTTCTAGACCTGGGG 60.559 52.174 0.00 0.00 36.03 4.96
7329 7941 3.328050 AGGAAGTTGTTTCTAGACCTGGG 59.672 47.826 0.00 0.00 36.03 4.45
7330 7942 4.625607 AGGAAGTTGTTTCTAGACCTGG 57.374 45.455 0.00 0.00 36.03 4.45
7331 7943 9.720769 TTATAAAGGAAGTTGTTTCTAGACCTG 57.279 33.333 0.00 0.00 36.03 4.00
7342 7954 9.860898 GCATGAAGAAATTATAAAGGAAGTTGT 57.139 29.630 0.00 0.00 0.00 3.32
7343 7955 9.859427 TGCATGAAGAAATTATAAAGGAAGTTG 57.141 29.630 0.00 0.00 0.00 3.16
7347 7959 9.369904 GCTTTGCATGAAGAAATTATAAAGGAA 57.630 29.630 0.00 0.00 0.00 3.36
7348 7960 8.530311 TGCTTTGCATGAAGAAATTATAAAGGA 58.470 29.630 0.00 0.00 31.71 3.36
7349 7961 8.706492 TGCTTTGCATGAAGAAATTATAAAGG 57.294 30.769 0.00 0.00 31.71 3.11
7366 7978 9.709495 AACTTTTATGATTTTCTATGCTTTGCA 57.291 25.926 0.00 0.00 44.86 4.08
7389 8001 6.316390 GGCTGTGCTATGTTAAGTGATAAACT 59.684 38.462 0.00 0.00 42.60 2.66
7390 8002 6.458342 GGGCTGTGCTATGTTAAGTGATAAAC 60.458 42.308 0.00 0.00 0.00 2.01
7391 8003 5.588648 GGGCTGTGCTATGTTAAGTGATAAA 59.411 40.000 0.00 0.00 0.00 1.40
7392 8004 5.123227 GGGCTGTGCTATGTTAAGTGATAA 58.877 41.667 0.00 0.00 0.00 1.75
7393 8005 4.444306 GGGGCTGTGCTATGTTAAGTGATA 60.444 45.833 0.00 0.00 0.00 2.15
7394 8006 3.545703 GGGCTGTGCTATGTTAAGTGAT 58.454 45.455 0.00 0.00 0.00 3.06
7395 8007 2.355716 GGGGCTGTGCTATGTTAAGTGA 60.356 50.000 0.00 0.00 0.00 3.41
7396 8008 2.017049 GGGGCTGTGCTATGTTAAGTG 58.983 52.381 0.00 0.00 0.00 3.16
7397 8009 1.633432 TGGGGCTGTGCTATGTTAAGT 59.367 47.619 0.00 0.00 0.00 2.24
7398 8010 2.292267 CTGGGGCTGTGCTATGTTAAG 58.708 52.381 0.00 0.00 0.00 1.85
7399 8011 1.064758 CCTGGGGCTGTGCTATGTTAA 60.065 52.381 0.00 0.00 0.00 2.01
7400 8012 0.546122 CCTGGGGCTGTGCTATGTTA 59.454 55.000 0.00 0.00 0.00 2.41
7401 8013 1.304282 CCTGGGGCTGTGCTATGTT 59.696 57.895 0.00 0.00 0.00 2.71
7402 8014 3.001514 CCTGGGGCTGTGCTATGT 58.998 61.111 0.00 0.00 0.00 2.29
7403 8015 2.517875 GCCTGGGGCTGTGCTATG 60.518 66.667 0.80 0.00 46.69 2.23
7412 8024 4.840005 GCAGACTACGCCTGGGGC 62.840 72.222 11.10 0.00 46.75 5.80
7413 8025 2.650813 GATGCAGACTACGCCTGGGG 62.651 65.000 9.49 9.49 32.51 4.96
7414 8026 1.227380 GATGCAGACTACGCCTGGG 60.227 63.158 0.00 0.00 32.51 4.45
7415 8027 1.000827 CTAGATGCAGACTACGCCTGG 60.001 57.143 0.00 0.00 32.51 4.45
7416 8028 1.601663 GCTAGATGCAGACTACGCCTG 60.602 57.143 0.00 0.00 42.31 4.85
7417 8029 0.671251 GCTAGATGCAGACTACGCCT 59.329 55.000 0.00 0.00 42.31 5.52
7418 8030 0.671251 AGCTAGATGCAGACTACGCC 59.329 55.000 0.00 0.00 45.94 5.68
7419 8031 1.335506 GGAGCTAGATGCAGACTACGC 60.336 57.143 0.00 5.09 45.94 4.42
7420 8032 1.069568 CGGAGCTAGATGCAGACTACG 60.070 57.143 0.00 0.00 45.94 3.51
7421 8033 2.697431 CGGAGCTAGATGCAGACTAC 57.303 55.000 0.00 0.00 45.94 2.73
7441 8053 1.137086 AGCATTAGTCGTAGCCAGTGG 59.863 52.381 4.20 4.20 0.00 4.00
7442 8054 2.586258 AGCATTAGTCGTAGCCAGTG 57.414 50.000 0.00 0.00 0.00 3.66
7443 8055 2.033049 CGTAGCATTAGTCGTAGCCAGT 59.967 50.000 0.00 0.00 0.00 4.00
7444 8056 2.289820 TCGTAGCATTAGTCGTAGCCAG 59.710 50.000 0.00 0.00 0.00 4.85
7445 8057 2.291365 TCGTAGCATTAGTCGTAGCCA 58.709 47.619 0.00 0.00 0.00 4.75
7446 8058 3.490399 GATCGTAGCATTAGTCGTAGCC 58.510 50.000 0.00 0.00 0.00 3.93
7447 8059 3.154489 CGATCGTAGCATTAGTCGTAGC 58.846 50.000 7.03 0.00 0.00 3.58
7448 8060 3.154489 GCGATCGTAGCATTAGTCGTAG 58.846 50.000 17.81 0.00 34.19 3.51
7449 8061 2.410646 CGCGATCGTAGCATTAGTCGTA 60.411 50.000 17.81 0.00 34.19 3.43
7450 8062 1.659491 CGCGATCGTAGCATTAGTCGT 60.659 52.381 17.81 0.00 34.19 4.34
7451 8063 0.968503 CGCGATCGTAGCATTAGTCG 59.031 55.000 17.81 3.49 34.19 4.18
7452 8064 1.328439 CCGCGATCGTAGCATTAGTC 58.672 55.000 17.81 0.00 34.19 2.59
7453 8065 0.666913 ACCGCGATCGTAGCATTAGT 59.333 50.000 17.81 1.89 34.19 2.24
7454 8066 1.767289 AACCGCGATCGTAGCATTAG 58.233 50.000 17.81 1.30 34.19 1.73
7455 8067 2.919387 GCTAACCGCGATCGTAGCATTA 60.919 50.000 23.12 14.45 39.00 1.90
7456 8068 1.767289 CTAACCGCGATCGTAGCATT 58.233 50.000 17.81 10.36 34.19 3.56
7457 8069 0.663568 GCTAACCGCGATCGTAGCAT 60.664 55.000 23.12 8.59 39.00 3.79
7458 8070 1.298863 GCTAACCGCGATCGTAGCA 60.299 57.895 23.12 4.94 39.00 3.49
7459 8071 3.523720 GCTAACCGCGATCGTAGC 58.476 61.111 17.81 17.09 34.62 3.58
7475 8087 3.542742 GTCGGTTCTAGCACGCGC 61.543 66.667 5.73 0.00 38.99 6.86
7476 8088 3.238241 CGTCGGTTCTAGCACGCG 61.238 66.667 3.53 3.53 0.00 6.01
7477 8089 1.731969 AACGTCGGTTCTAGCACGC 60.732 57.895 0.00 0.00 35.64 5.34
7478 8090 0.386352 TCAACGTCGGTTCTAGCACG 60.386 55.000 0.00 0.00 38.24 5.34
7479 8091 1.058404 GTCAACGTCGGTTCTAGCAC 58.942 55.000 0.00 0.00 32.98 4.40
7480 8092 0.386352 CGTCAACGTCGGTTCTAGCA 60.386 55.000 0.00 0.00 32.98 3.49
7481 8093 0.110056 TCGTCAACGTCGGTTCTAGC 60.110 55.000 2.09 0.00 40.80 3.42
7482 8094 2.320805 TTCGTCAACGTCGGTTCTAG 57.679 50.000 2.09 0.00 40.80 2.43
7483 8095 2.587956 CATTCGTCAACGTCGGTTCTA 58.412 47.619 2.09 0.00 40.80 2.10
7484 8096 1.415374 CATTCGTCAACGTCGGTTCT 58.585 50.000 2.09 0.00 40.80 3.01
7485 8097 0.179258 GCATTCGTCAACGTCGGTTC 60.179 55.000 2.09 0.00 40.80 3.62
7486 8098 0.599204 AGCATTCGTCAACGTCGGTT 60.599 50.000 2.09 0.00 40.80 4.44
7487 8099 1.006571 AGCATTCGTCAACGTCGGT 60.007 52.632 2.09 0.00 40.80 4.69
7488 8100 1.416049 CAGCATTCGTCAACGTCGG 59.584 57.895 2.09 0.00 40.80 4.79
7489 8101 1.416049 CCAGCATTCGTCAACGTCG 59.584 57.895 2.09 0.00 40.80 5.12
7490 8102 0.669318 TCCCAGCATTCGTCAACGTC 60.669 55.000 2.09 0.00 40.80 4.34
7491 8103 0.949105 GTCCCAGCATTCGTCAACGT 60.949 55.000 2.09 0.00 40.80 3.99
7492 8104 1.635663 GGTCCCAGCATTCGTCAACG 61.636 60.000 0.00 0.00 41.45 4.10
7493 8105 0.605319 TGGTCCCAGCATTCGTCAAC 60.605 55.000 0.00 0.00 0.00 3.18
7494 8106 0.605319 GTGGTCCCAGCATTCGTCAA 60.605 55.000 0.00 0.00 0.00 3.18
7495 8107 1.003839 GTGGTCCCAGCATTCGTCA 60.004 57.895 0.00 0.00 0.00 4.35
7496 8108 3.890674 GTGGTCCCAGCATTCGTC 58.109 61.111 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.