Multiple sequence alignment - TraesCS2A01G203100

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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 TraesCS2A01G203100 chr2A 100.000 5698 0 0 303 6000 178461301 178466998 0.000000e+00 10523.0
1 TraesCS2A01G203100 chr2A 100.000 70 0 0 1 70 178460999 178461068 4.880000e-26 130.0
2 TraesCS2A01G203100 chr2A 93.182 44 2 1 562 604 314725060 314725017 5.020000e-06 63.9
3 TraesCS2A01G203100 chr2B 94.434 4366 163 31 838 5179 225816205 225820514 0.000000e+00 6643.0
4 TraesCS2A01G203100 chr2B 95.811 740 18 2 5261 6000 38354197 38354923 0.000000e+00 1182.0
5 TraesCS2A01G203100 chr2B 86.528 193 25 1 419 610 225815344 225815536 1.690000e-50 211.0
6 TraesCS2A01G203100 chr2B 82.805 221 21 6 616 821 225815618 225815836 1.330000e-41 182.0
7 TraesCS2A01G203100 chr2B 80.508 118 20 3 499 614 783707865 783707981 2.980000e-13 87.9
8 TraesCS2A01G203100 chr2B 96.970 33 1 0 679 711 675453960 675453928 8.400000e-04 56.5
9 TraesCS2A01G203100 chr2D 95.796 2260 75 15 819 3069 170814258 170812010 0.000000e+00 3629.0
10 TraesCS2A01G203100 chr2D 93.467 1791 68 17 3071 4848 170811855 170810101 0.000000e+00 2614.0
11 TraesCS2A01G203100 chr2D 92.945 326 17 5 5260 5583 557283404 557283725 2.530000e-128 470.0
12 TraesCS2A01G203100 chr2D 91.975 324 23 2 5261 5583 48383054 48383375 9.170000e-123 451.0
13 TraesCS2A01G203100 chr2D 91.975 324 23 2 5261 5583 151665996 151665675 9.170000e-123 451.0
14 TraesCS2A01G203100 chr2D 82.734 417 56 7 419 822 170817095 170816682 2.060000e-94 357.0
15 TraesCS2A01G203100 chr2D 81.982 111 17 3 505 613 579217098 579217207 2.300000e-14 91.6
16 TraesCS2A01G203100 chr2D 93.443 61 3 1 4887 4946 170810020 170810080 8.280000e-14 89.8
17 TraesCS2A01G203100 chr2D 85.294 68 10 0 5574 5641 621832756 621832689 3.000000e-08 71.3
18 TraesCS2A01G203100 chr2D 90.000 50 4 1 20 69 170817306 170817258 5.020000e-06 63.9
19 TraesCS2A01G203100 chr2D 93.023 43 2 1 26 68 429090115 429090156 1.810000e-05 62.1
20 TraesCS2A01G203100 chr6B 96.216 740 28 0 5261 6000 349457002 349457741 0.000000e+00 1212.0
21 TraesCS2A01G203100 chr7B 92.180 422 27 3 5584 6000 743729475 743729055 5.180000e-165 592.0
22 TraesCS2A01G203100 chr5A 87.972 424 40 7 5586 6000 602790463 602790042 1.940000e-134 490.0
23 TraesCS2A01G203100 chr5A 87.736 424 41 7 5586 6000 602814341 602813920 9.040000e-133 484.0
24 TraesCS2A01G203100 chr6D 92.308 325 21 3 5261 5583 28153592 28153270 5.480000e-125 459.0
25 TraesCS2A01G203100 chr6D 90.909 55 3 2 5584 5637 81043169 81043116 8.340000e-09 73.1
26 TraesCS2A01G203100 chr3B 91.975 324 22 3 5261 5583 814647633 814647313 9.170000e-123 451.0
27 TraesCS2A01G203100 chr7D 91.667 324 24 2 5261 5583 385865093 385865414 4.270000e-121 446.0
28 TraesCS2A01G203100 chr7D 90.116 344 23 10 5245 5583 294652012 294651675 2.570000e-118 436.0
29 TraesCS2A01G203100 chr7D 91.071 56 4 1 15 70 149104896 149104950 2.320000e-09 75.0
30 TraesCS2A01G203100 chr4A 90.000 340 24 8 5248 5583 742815482 742815149 1.190000e-116 431.0
31 TraesCS2A01G203100 chr7A 80.526 190 31 5 419 603 426584103 426584291 2.250000e-29 141.0
32 TraesCS2A01G203100 chr1B 89.535 86 9 0 3507 3592 562891665 562891580 6.360000e-20 110.0
33 TraesCS2A01G203100 chr1B 87.879 66 7 1 4 69 237368881 237368817 6.450000e-10 76.8
34 TraesCS2A01G203100 chr1A 89.535 86 9 0 3507 3592 513720180 513720095 6.360000e-20 110.0
35 TraesCS2A01G203100 chr1A 92.593 54 3 1 17 70 63003528 63003580 6.450000e-10 76.8
36 TraesCS2A01G203100 chr6A 80.000 110 17 5 505 611 190576309 190576416 6.450000e-10 76.8
37 TraesCS2A01G203100 chr5D 73.894 226 42 13 499 711 28956363 28956584 2.320000e-09 75.0
38 TraesCS2A01G203100 chr4D 79.279 111 18 5 504 611 439773674 439773782 8.340000e-09 73.1
39 TraesCS2A01G203100 chr3A 77.311 119 22 5 499 614 652575588 652575704 1.400000e-06 65.8
40 TraesCS2A01G203100 chr1D 100.000 31 0 0 40 70 63921299 63921329 2.340000e-04 58.4


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 TraesCS2A01G203100 chr2A 178460999 178466998 5999 False 5326.500000 10523 100.000000 1 6000 2 chr2A.!!$F1 5999
1 TraesCS2A01G203100 chr2B 225815344 225820514 5170 False 2345.333333 6643 87.922333 419 5179 3 chr2B.!!$F3 4760
2 TraesCS2A01G203100 chr2B 38354197 38354923 726 False 1182.000000 1182 95.811000 5261 6000 1 chr2B.!!$F1 739
3 TraesCS2A01G203100 chr2D 170810101 170817306 7205 True 1665.975000 3629 90.499250 20 4848 4 chr2D.!!$R3 4828
4 TraesCS2A01G203100 chr6B 349457002 349457741 739 False 1212.000000 1212 96.216000 5261 6000 1 chr6B.!!$F1 739

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
478 512 0.321653 GATTTGGTGCGGAGTCAGGT 60.322 55.000 0.00 0.0 0.0 4.00 F
1103 3931 0.336737 AGGAGGAGGAGGACGTGAAT 59.663 55.000 0.00 0.0 0.0 2.57 F
1598 4427 0.693049 ATCCCAGAAACGTTGCTCCT 59.307 50.000 5.58 0.0 0.0 3.69 F
3000 5839 1.079819 ACATCCTGTCGCCGAAGTG 60.080 57.895 0.00 0.0 0.0 3.16 F
4605 7608 2.092429 GGGTTATCCAGGTCAGCATTCA 60.092 50.000 0.00 0.0 35.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 4260 0.327924 CACCATAGTTGGACTGCCCA 59.672 55.000 0.00 0.00 46.92 5.36 R
3005 5844 1.135460 GGCTGTCAGCTGAAGAAATGC 60.135 52.381 20.19 15.15 41.99 3.56 R
3350 6342 2.266554 CGACATTCCAGAAGAGACAGC 58.733 52.381 0.00 0.00 0.00 4.40 R
4989 7995 0.808125 CTCTCAGGAGTCAGGACACG 59.192 60.000 1.84 0.00 35.03 4.49 R
5530 8551 0.896940 CAAGTGCATGTCCAAGGGCT 60.897 55.000 0.00 0.00 0.00 5.19 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
69 70 2.202756 CGCGCCTCCACTAACTCC 60.203 66.667 0.00 0.00 0.00 3.85
329 330 1.689273 GGATGAAGCCTACTCCATCGT 59.311 52.381 0.00 0.00 37.02 3.73
331 332 3.057174 GGATGAAGCCTACTCCATCGTAG 60.057 52.174 0.00 0.00 37.02 3.51
337 338 2.506444 CCTACTCCATCGTAGACCTCC 58.494 57.143 0.00 0.00 42.51 4.30
338 339 2.106857 CCTACTCCATCGTAGACCTCCT 59.893 54.545 0.00 0.00 42.51 3.69
339 340 2.830651 ACTCCATCGTAGACCTCCTT 57.169 50.000 0.00 0.00 42.51 3.36
365 366 3.053291 CGTTTAGGCCAGCCGCAA 61.053 61.111 5.01 0.00 41.95 4.85
367 368 2.114199 TTTAGGCCAGCCGCAACA 59.886 55.556 5.01 0.00 41.95 3.33
369 370 2.690653 TTTAGGCCAGCCGCAACAGT 62.691 55.000 5.01 0.00 41.95 3.55
378 379 4.655527 CGCAACAGTCGGAGAAGT 57.344 55.556 0.00 0.00 39.69 3.01
389 390 3.256136 AGTCGGAGAAGTTTCGATTCAGT 59.744 43.478 0.47 0.00 39.69 3.41
394 395 3.330267 AGAAGTTTCGATTCAGTGGCTC 58.670 45.455 0.47 0.00 0.00 4.70
475 509 1.234821 GTTGATTTGGTGCGGAGTCA 58.765 50.000 0.00 0.00 0.00 3.41
478 512 0.321653 GATTTGGTGCGGAGTCAGGT 60.322 55.000 0.00 0.00 0.00 4.00
520 554 4.941263 CGGAAGGGAAATGAATGACAGTTA 59.059 41.667 0.00 0.00 36.92 2.24
553 587 3.624410 GGGCGTCCGTATTTTTACATCTT 59.376 43.478 0.00 0.00 0.00 2.40
555 589 4.502558 GCGTCCGTATTTTTACATCTTCG 58.497 43.478 0.00 0.00 0.00 3.79
556 590 4.266029 GCGTCCGTATTTTTACATCTTCGA 59.734 41.667 0.00 0.00 0.00 3.71
561 595 6.643770 TCCGTATTTTTACATCTTCGATAGGC 59.356 38.462 0.00 0.00 0.00 3.93
611 646 3.565010 TTGTAGTTACATCTCCGGGAGGT 60.565 47.826 23.39 14.75 43.07 3.85
657 769 2.241176 TCTGTTGGAGAGGTGTTTTGGT 59.759 45.455 0.00 0.00 0.00 3.67
669 781 3.067601 GGTGTTTTGGTCCTCGAAAATGT 59.932 43.478 0.00 0.00 34.76 2.71
679 791 7.218614 TGGTCCTCGAAAATGTAAAAGTTAGA 58.781 34.615 0.00 0.00 0.00 2.10
822 949 2.102084 TCATCGAAATGAGAGCCAGAGG 59.898 50.000 0.00 0.00 36.98 3.69
824 951 0.826715 CGAAATGAGAGCCAGAGGGA 59.173 55.000 0.00 0.00 35.59 4.20
959 3787 3.479269 GTGCGTGCGCTCCTGTAC 61.479 66.667 17.49 1.44 42.51 2.90
968 3796 0.537188 CGCTCCTGTACCCATCTGTT 59.463 55.000 0.00 0.00 0.00 3.16
969 3797 1.754803 CGCTCCTGTACCCATCTGTTA 59.245 52.381 0.00 0.00 0.00 2.41
1103 3931 0.336737 AGGAGGAGGAGGACGTGAAT 59.663 55.000 0.00 0.00 0.00 2.57
1139 3967 2.192175 CAATCCCCTACCCACGCC 59.808 66.667 0.00 0.00 0.00 5.68
1147 3975 3.075641 TACCCACGCCACGCCATA 61.076 61.111 0.00 0.00 0.00 2.74
1399 4227 4.343814 CCTAACTGAAATTTGTGGGTGGTT 59.656 41.667 0.00 0.00 0.00 3.67
1415 4243 2.031120 TGGTTTCTTGGCAGGAACAAG 58.969 47.619 11.97 0.00 40.07 3.16
1474 4302 2.563942 GGCGCGTTTTACATGCCA 59.436 55.556 8.43 0.00 45.06 4.92
1485 4313 4.511786 TTTACATGCCAGTATGCCCTTA 57.488 40.909 0.00 0.00 31.97 2.69
1489 4317 3.458118 ACATGCCAGTATGCCCTTAGTTA 59.542 43.478 0.00 0.00 31.97 2.24
1595 4424 2.568623 AGAATCCCAGAAACGTTGCT 57.431 45.000 1.82 1.82 0.00 3.91
1598 4427 0.693049 ATCCCAGAAACGTTGCTCCT 59.307 50.000 5.58 0.00 0.00 3.69
1676 4505 3.963374 CAGTGGATATCCCTCTTGAGTCA 59.037 47.826 19.34 0.00 36.67 3.41
1692 4521 5.482163 TGAGTCATCAAAGGTATGTGTGA 57.518 39.130 0.00 0.00 30.61 3.58
1705 4534 4.155826 GGTATGTGTGATTGTGCAGCTTAA 59.844 41.667 0.00 0.00 0.00 1.85
1738 4567 4.439305 GCAAAATGCACCTATGAGAACA 57.561 40.909 0.00 0.00 44.26 3.18
1770 4599 2.959030 GGAAAATGATACCCAGGGCTTC 59.041 50.000 4.91 3.01 0.00 3.86
1883 4712 4.725556 AGGTACAATGCATATTTACGCG 57.274 40.909 3.53 3.53 0.00 6.01
1893 4722 7.751047 ATGCATATTTACGCGGTTATACTAG 57.249 36.000 12.47 0.00 0.00 2.57
1896 4725 6.021939 GCATATTTACGCGGTTATACTAGTCG 60.022 42.308 12.47 0.00 0.00 4.18
1901 4730 4.588278 ACGCGGTTATACTAGTCGTTAAC 58.412 43.478 12.47 6.69 0.00 2.01
1905 4734 6.258160 GCGGTTATACTAGTCGTTAACTTGA 58.742 40.000 16.55 0.00 39.55 3.02
2026 4860 4.276926 GGATCATCTTTGGTTGATGGCTAC 59.723 45.833 0.00 0.00 41.01 3.58
2046 4880 7.151976 GGCTACCTTTCAAATTCAGCTTTTTA 58.848 34.615 0.00 0.00 0.00 1.52
2051 4885 7.819415 ACCTTTCAAATTCAGCTTTTTATAGCC 59.181 33.333 0.00 0.00 42.20 3.93
2064 4898 6.238266 GCTTTTTATAGCCGCACACTGTATTA 60.238 38.462 0.00 0.00 35.06 0.98
2079 4913 7.011109 CACACTGTATTACTGGCACTATTTACC 59.989 40.741 5.80 0.00 0.00 2.85
2082 4916 8.639761 ACTGTATTACTGGCACTATTTACCTAG 58.360 37.037 5.80 0.00 0.00 3.02
2189 5023 2.612212 CAGCACGAGGTTAGTGTTTGTT 59.388 45.455 0.00 0.00 41.36 2.83
2275 5109 9.702494 ATTTTCTCTGGACAAAATGAAAGAATC 57.298 29.630 0.00 0.00 32.20 2.52
2325 5159 3.819564 ACAAGTATCCGCTAAGCATCA 57.180 42.857 0.00 0.00 0.00 3.07
2365 5199 6.318648 TGCTATAGCCAAGGTCTAAATTTGTG 59.681 38.462 21.84 0.00 41.18 3.33
2373 5207 5.869649 AGGTCTAAATTTGTGCCTTTTGT 57.130 34.783 0.00 0.00 0.00 2.83
2414 5248 7.124573 TCTCCTCTGCAAACAAAGCTATATA 57.875 36.000 0.00 0.00 0.00 0.86
2415 5249 7.739825 TCTCCTCTGCAAACAAAGCTATATAT 58.260 34.615 0.00 0.00 0.00 0.86
2584 5418 9.921637 TGTCACTTATTGTTTTCAAAAGAAACT 57.078 25.926 0.00 0.00 43.39 2.66
2638 5472 7.278875 AGCTAAACTTCTGATCCCTTATTCTG 58.721 38.462 0.00 0.00 0.00 3.02
2784 5618 3.907894 TTTGCGTCATTTCTTGGTACC 57.092 42.857 4.43 4.43 0.00 3.34
2825 5659 9.748708 CTTGAAATATTCCTGAAGTTTGTTGAA 57.251 29.630 0.00 0.00 0.00 2.69
2878 5712 4.162131 GGTGGCCAAACATTTTCTCCATAT 59.838 41.667 7.24 0.00 0.00 1.78
2885 5719 7.285401 GCCAAACATTTTCTCCATATCTTAGGA 59.715 37.037 0.00 0.00 0.00 2.94
3000 5839 1.079819 ACATCCTGTCGCCGAAGTG 60.080 57.895 0.00 0.00 0.00 3.16
3027 5866 2.574006 TTTCTTCAGCTGACAGCCAT 57.426 45.000 23.74 3.32 43.77 4.40
3132 6124 6.604735 AGGATGTACGTTAATTTGATCTGC 57.395 37.500 0.00 0.00 0.00 4.26
3174 6166 5.748592 CCTTAATGGCTTTAGAATGTACGC 58.251 41.667 0.00 0.00 0.00 4.42
3175 6167 5.527582 CCTTAATGGCTTTAGAATGTACGCT 59.472 40.000 0.00 0.00 0.00 5.07
3176 6168 6.704493 CCTTAATGGCTTTAGAATGTACGCTA 59.296 38.462 0.00 0.00 0.00 4.26
3177 6169 7.387948 CCTTAATGGCTTTAGAATGTACGCTAT 59.612 37.037 0.00 0.00 0.00 2.97
3178 6170 9.419297 CTTAATGGCTTTAGAATGTACGCTATA 57.581 33.333 0.00 0.00 0.00 1.31
3179 6171 9.938280 TTAATGGCTTTAGAATGTACGCTATAT 57.062 29.630 0.00 0.00 0.00 0.86
3180 6172 8.848474 AATGGCTTTAGAATGTACGCTATATT 57.152 30.769 0.00 0.00 0.00 1.28
3181 6173 8.848474 ATGGCTTTAGAATGTACGCTATATTT 57.152 30.769 0.00 0.00 0.00 1.40
3182 6174 8.306680 TGGCTTTAGAATGTACGCTATATTTC 57.693 34.615 0.00 0.00 0.00 2.17
3183 6175 8.148351 TGGCTTTAGAATGTACGCTATATTTCT 58.852 33.333 0.00 0.00 0.00 2.52
3184 6176 9.635520 GGCTTTAGAATGTACGCTATATTTCTA 57.364 33.333 0.00 0.00 0.00 2.10
3189 6181 8.467402 AGAATGTACGCTATATTTCTACATGC 57.533 34.615 0.00 0.00 30.25 4.06
3210 6202 6.783892 TGCCTGCATTTTATTTTCAAGTTC 57.216 33.333 0.00 0.00 0.00 3.01
3350 6342 4.892433 TGGCATTGAATAGGTTTGGTTTG 58.108 39.130 0.00 0.00 0.00 2.93
3409 6401 2.513738 TGGATCAAGGGGGAAGGTAATG 59.486 50.000 0.00 0.00 0.00 1.90
3415 6407 2.217776 AGGGGGAAGGTAATGCTCAAT 58.782 47.619 0.00 0.00 0.00 2.57
3593 6585 8.049721 GCCCTCTTTATAATGCTATGAGGTATT 58.950 37.037 0.00 0.00 38.24 1.89
3716 6712 2.526304 TGTGTTACAGGACTGACAGC 57.474 50.000 6.29 0.00 0.00 4.40
3813 6810 7.975058 TGGTTCATCTGCATAATGTTTAATGTG 59.025 33.333 8.57 0.00 0.00 3.21
3958 6955 7.846592 GCGTAAGTCTCTTGTTTGCTTATATTC 59.153 37.037 0.00 0.00 41.68 1.75
3962 6959 7.624549 AGTCTCTTGTTTGCTTATATTCAGGA 58.375 34.615 0.00 0.00 0.00 3.86
3984 6981 7.065563 CAGGAAATGACATTAGAAGACTGGAAG 59.934 40.741 0.00 0.00 42.29 3.46
4063 7060 3.553508 GGCAAGACAGTTGCATGAATTGT 60.554 43.478 11.56 1.30 46.58 2.71
4111 7111 8.229253 AGCATATTTCAATTTGTAGATGAGCA 57.771 30.769 10.73 0.00 0.00 4.26
4112 7112 8.857098 AGCATATTTCAATTTGTAGATGAGCAT 58.143 29.630 10.73 0.00 0.00 3.79
4113 7113 9.125906 GCATATTTCAATTTGTAGATGAGCATC 57.874 33.333 2.27 2.27 38.09 3.91
4134 7134 4.285020 TCATCATAGAAGTCAGCTCAGGT 58.715 43.478 0.00 0.00 0.00 4.00
4274 7274 6.624423 AGTGCTTCACTTTAAAATATGGCAG 58.376 36.000 0.00 0.29 42.59 4.85
4289 7289 2.387757 TGGCAGCCCAAAATATTCCTC 58.612 47.619 9.64 0.00 38.46 3.71
4324 7325 3.753797 GGAACTTCACCTGGACTGAATTC 59.246 47.826 0.00 0.00 0.00 2.17
4353 7354 5.947228 TCTGCTTGTGTAGAGGAATTTTG 57.053 39.130 0.00 0.00 31.41 2.44
4374 7375 2.868044 GCCGGCGATTGATCTTATCAGT 60.868 50.000 12.58 0.00 40.94 3.41
4415 7416 5.820947 GGGTAAGTACATGAACCTATGGTTG 59.179 44.000 6.72 0.00 46.95 3.77
4427 7428 4.492604 TGGTTGGCCAGCTAACAC 57.507 55.556 19.84 7.02 40.46 3.32
4470 7473 3.070878 TGAATCACCAGTGCAGTAGTCAA 59.929 43.478 0.00 0.00 0.00 3.18
4495 7498 2.751806 CCTGATGCCAAGGAGTTCTTTC 59.248 50.000 0.00 0.00 32.41 2.62
4546 7549 4.574013 GTGCAGATCTTCTACTTCATTGGG 59.426 45.833 0.00 0.00 0.00 4.12
4574 7577 2.610438 ATTTGCCCTGGAGTCATTGT 57.390 45.000 0.00 0.00 0.00 2.71
4605 7608 2.092429 GGGTTATCCAGGTCAGCATTCA 60.092 50.000 0.00 0.00 35.00 2.57
4616 7619 3.314635 GGTCAGCATTCAGATGATCAACC 59.685 47.826 0.00 0.00 45.61 3.77
4770 7776 2.286654 GCTATGAGAGCGGCATTTTGAC 60.287 50.000 1.45 0.00 42.62 3.18
4909 7915 3.748083 ACTGCTGTGATGAAGTGACATT 58.252 40.909 0.00 0.00 0.00 2.71
4931 7937 5.367945 TGTAGGACTTGTCCACTTTTCTT 57.632 39.130 20.36 1.53 0.00 2.52
4936 7942 3.473625 ACTTGTCCACTTTTCTTACCGG 58.526 45.455 0.00 0.00 0.00 5.28
4989 7995 3.102052 TCCGTCCTGAATATAAACGCC 57.898 47.619 0.00 0.00 32.26 5.68
4999 8005 2.282701 TATAAACGCCGTGTCCTGAC 57.717 50.000 0.00 0.00 0.00 3.51
5000 8006 0.606604 ATAAACGCCGTGTCCTGACT 59.393 50.000 0.00 0.00 0.00 3.41
5001 8007 0.038892 TAAACGCCGTGTCCTGACTC 60.039 55.000 0.00 0.00 0.00 3.36
5002 8008 2.710724 AAACGCCGTGTCCTGACTCC 62.711 60.000 0.00 0.00 0.00 3.85
5003 8009 3.374402 CGCCGTGTCCTGACTCCT 61.374 66.667 0.00 0.00 0.00 3.69
5004 8010 2.262915 GCCGTGTCCTGACTCCTG 59.737 66.667 0.00 0.00 0.00 3.86
5006 8012 1.886585 CCGTGTCCTGACTCCTGAG 59.113 63.158 0.00 0.00 0.00 3.35
5007 8013 0.609406 CCGTGTCCTGACTCCTGAGA 60.609 60.000 0.22 0.00 0.00 3.27
5008 8014 0.808125 CGTGTCCTGACTCCTGAGAG 59.192 60.000 0.22 0.00 46.36 3.20
5043 8049 3.637998 AGGTACCGTTGCGACTATATG 57.362 47.619 6.18 0.00 0.00 1.78
5050 8056 3.184379 CCGTTGCGACTATATGAATGGTG 59.816 47.826 1.84 0.00 0.00 4.17
5053 8059 2.368548 TGCGACTATATGAATGGTGCCT 59.631 45.455 0.00 0.00 0.00 4.75
5054 8060 3.576550 TGCGACTATATGAATGGTGCCTA 59.423 43.478 0.00 0.00 0.00 3.93
5061 8069 2.890808 TGAATGGTGCCTACGATCTC 57.109 50.000 0.00 0.00 0.00 2.75
5085 8093 4.560513 GCCTATTTGTTGCAGCTTTACCAA 60.561 41.667 1.17 0.00 0.00 3.67
5086 8094 5.723295 CCTATTTGTTGCAGCTTTACCAAT 58.277 37.500 1.17 0.00 0.00 3.16
5119 8128 5.353111 TCGGTTTAAAGAAAAAGCAAAGGG 58.647 37.500 0.00 0.00 36.81 3.95
5129 8138 2.595124 AAGCAAAGGGTTTTCCAACG 57.405 45.000 0.00 0.00 42.91 4.10
5170 8179 6.985059 GTGGTCTCACCTAATGGTAAGAATAC 59.015 42.308 0.00 0.00 42.00 1.89
5171 8180 6.183360 TGGTCTCACCTAATGGTAAGAATACG 60.183 42.308 0.00 0.00 42.00 3.06
5174 8183 5.210430 TCACCTAATGGTAAGAATACGGGA 58.790 41.667 0.00 0.00 46.60 5.14
5175 8184 5.662208 TCACCTAATGGTAAGAATACGGGAA 59.338 40.000 0.00 0.00 46.60 3.97
5178 8187 7.012044 CACCTAATGGTAAGAATACGGGAAAAG 59.988 40.741 0.00 0.00 46.60 2.27
5179 8188 5.830000 AATGGTAAGAATACGGGAAAAGC 57.170 39.130 0.00 0.00 32.51 3.51
5180 8189 4.563140 TGGTAAGAATACGGGAAAAGCT 57.437 40.909 0.00 0.00 32.51 3.74
5181 8190 4.913784 TGGTAAGAATACGGGAAAAGCTT 58.086 39.130 0.00 0.00 32.51 3.74
5182 8191 6.052405 TGGTAAGAATACGGGAAAAGCTTA 57.948 37.500 0.00 0.00 32.51 3.09
5183 8192 6.110707 TGGTAAGAATACGGGAAAAGCTTAG 58.889 40.000 0.00 0.00 32.51 2.18
5184 8193 5.526479 GGTAAGAATACGGGAAAAGCTTAGG 59.474 44.000 0.00 0.00 32.51 2.69
5185 8194 5.431179 AAGAATACGGGAAAAGCTTAGGA 57.569 39.130 0.00 0.00 0.00 2.94
5186 8195 5.431179 AGAATACGGGAAAAGCTTAGGAA 57.569 39.130 0.00 0.00 0.00 3.36
5187 8196 5.183969 AGAATACGGGAAAAGCTTAGGAAC 58.816 41.667 0.00 0.00 0.00 3.62
5188 8197 2.943036 ACGGGAAAAGCTTAGGAACA 57.057 45.000 0.00 0.00 0.00 3.18
5189 8198 2.779506 ACGGGAAAAGCTTAGGAACAG 58.220 47.619 0.00 0.00 0.00 3.16
5190 8199 1.468914 CGGGAAAAGCTTAGGAACAGC 59.531 52.381 0.00 0.00 37.56 4.40
5191 8200 2.514803 GGGAAAAGCTTAGGAACAGCA 58.485 47.619 0.00 0.00 39.99 4.41
5192 8201 2.489722 GGGAAAAGCTTAGGAACAGCAG 59.510 50.000 0.00 0.00 39.99 4.24
5193 8202 2.489722 GGAAAAGCTTAGGAACAGCAGG 59.510 50.000 0.00 0.00 39.99 4.85
5194 8203 1.539157 AAAGCTTAGGAACAGCAGGC 58.461 50.000 0.00 0.00 39.99 4.85
5195 8204 0.674895 AAGCTTAGGAACAGCAGGCG 60.675 55.000 0.00 0.00 39.99 5.52
5196 8205 1.376037 GCTTAGGAACAGCAGGCGT 60.376 57.895 0.00 0.00 37.22 5.68
5197 8206 1.362406 GCTTAGGAACAGCAGGCGTC 61.362 60.000 0.00 0.00 37.22 5.19
5198 8207 0.741221 CTTAGGAACAGCAGGCGTCC 60.741 60.000 4.22 4.22 0.00 4.79
5199 8208 2.501223 TTAGGAACAGCAGGCGTCCG 62.501 60.000 6.19 0.00 0.00 4.79
5219 8228 3.121030 GCCTTCAGCATGCGACGT 61.121 61.111 13.01 0.00 42.97 4.34
5220 8229 2.780643 CCTTCAGCATGCGACGTG 59.219 61.111 13.01 5.07 34.76 4.49
5221 8230 2.029288 CCTTCAGCATGCGACGTGT 61.029 57.895 13.01 0.00 34.76 4.49
5222 8231 1.131218 CTTCAGCATGCGACGTGTG 59.869 57.895 13.01 3.84 34.76 3.82
5223 8232 1.560004 CTTCAGCATGCGACGTGTGT 61.560 55.000 13.01 0.00 34.76 3.72
5224 8233 1.157257 TTCAGCATGCGACGTGTGTT 61.157 50.000 13.01 0.00 34.76 3.32
5225 8234 1.154599 CAGCATGCGACGTGTGTTC 60.155 57.895 13.01 0.00 0.00 3.18
5226 8235 2.173382 GCATGCGACGTGTGTTCC 59.827 61.111 0.00 0.00 0.00 3.62
5227 8236 2.469847 CATGCGACGTGTGTTCCG 59.530 61.111 0.00 0.00 0.00 4.30
5228 8237 2.028484 ATGCGACGTGTGTTCCGT 59.972 55.556 0.00 0.00 42.06 4.69
5229 8238 2.307309 ATGCGACGTGTGTTCCGTG 61.307 57.895 0.00 0.00 38.92 4.94
5230 8239 2.958016 GCGACGTGTGTTCCGTGT 60.958 61.111 0.00 0.00 38.92 4.49
5231 8240 2.917901 CGACGTGTGTTCCGTGTG 59.082 61.111 0.00 0.00 38.92 3.82
5232 8241 1.874915 CGACGTGTGTTCCGTGTGT 60.875 57.895 0.00 0.00 38.92 3.72
5233 8242 1.634225 GACGTGTGTTCCGTGTGTG 59.366 57.895 0.00 0.00 38.92 3.82
5234 8243 1.758319 GACGTGTGTTCCGTGTGTGG 61.758 60.000 0.00 0.00 38.92 4.17
5235 8244 2.713154 GTGTGTTCCGTGTGTGGC 59.287 61.111 0.00 0.00 0.00 5.01
5236 8245 2.515057 TGTGTTCCGTGTGTGGCC 60.515 61.111 0.00 0.00 0.00 5.36
5237 8246 3.645975 GTGTTCCGTGTGTGGCCG 61.646 66.667 0.00 0.00 0.00 6.13
5238 8247 4.920112 TGTTCCGTGTGTGGCCGG 62.920 66.667 0.00 0.00 45.55 6.13
5252 8261 4.431131 CCGGGGCCACTGCATCTT 62.431 66.667 1.96 0.00 40.13 2.40
5253 8262 2.361610 CGGGGCCACTGCATCTTT 60.362 61.111 1.96 0.00 40.13 2.52
5254 8263 1.077787 CGGGGCCACTGCATCTTTA 60.078 57.895 1.96 0.00 40.13 1.85
5255 8264 1.376609 CGGGGCCACTGCATCTTTAC 61.377 60.000 1.96 0.00 40.13 2.01
5256 8265 1.037579 GGGGCCACTGCATCTTTACC 61.038 60.000 4.39 0.00 40.13 2.85
5257 8266 1.376609 GGGCCACTGCATCTTTACCG 61.377 60.000 4.39 0.00 40.13 4.02
5258 8267 0.676782 GGCCACTGCATCTTTACCGT 60.677 55.000 0.00 0.00 40.13 4.83
5259 8268 1.406341 GGCCACTGCATCTTTACCGTA 60.406 52.381 0.00 0.00 40.13 4.02
5309 8318 0.392193 AGACCGAGAGCAAGCCAATG 60.392 55.000 0.00 0.00 0.00 2.82
5364 8373 8.343168 ACACGGAAGGAACATATGAAAATAAA 57.657 30.769 10.38 0.00 0.00 1.40
5436 8445 6.795144 ACATAAGATCCAAAATGATGCCAA 57.205 33.333 0.00 0.00 0.00 4.52
5785 8806 8.688747 ATGCTAAGCAAAGCTATTTAGAGATT 57.311 30.769 11.10 0.00 43.62 2.40
5809 8830 9.878667 ATTCATCATGTAAATTGCTTTGATCAA 57.121 25.926 3.38 3.38 0.00 2.57
5841 8862 4.750598 TGTTACACAAAGCTACATACGCAA 59.249 37.500 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
329 330 5.985753 AACGCCTTCCTCAAGGAGGTCTA 62.986 52.174 11.78 0.00 45.96 2.59
331 332 3.053576 AACGCCTTCCTCAAGGAGGTC 62.054 57.143 11.78 0.00 45.96 3.85
337 338 1.087501 GCCTAAACGCCTTCCTCAAG 58.912 55.000 0.00 0.00 0.00 3.02
338 339 0.322187 GGCCTAAACGCCTTCCTCAA 60.322 55.000 0.00 0.00 46.10 3.02
339 340 1.298667 GGCCTAAACGCCTTCCTCA 59.701 57.895 0.00 0.00 46.10 3.86
365 366 3.005472 TGAATCGAAACTTCTCCGACTGT 59.995 43.478 0.00 0.00 35.02 3.55
367 368 3.256136 ACTGAATCGAAACTTCTCCGACT 59.744 43.478 0.00 0.00 35.02 4.18
369 370 3.575630 CACTGAATCGAAACTTCTCCGA 58.424 45.455 0.00 0.00 36.72 4.55
378 379 0.391130 CCGGAGCCACTGAATCGAAA 60.391 55.000 0.00 0.00 0.00 3.46
458 492 0.321564 CCTGACTCCGCACCAAATCA 60.322 55.000 0.00 0.00 0.00 2.57
490 524 3.310860 ATTTCCCTTCCGCGCGACT 62.311 57.895 34.63 0.00 0.00 4.18
508 542 3.411446 CCAACTGCCTAACTGTCATTCA 58.589 45.455 0.00 0.00 0.00 2.57
536 570 6.643770 GCCTATCGAAGATGTAAAAATACGGA 59.356 38.462 0.00 0.00 45.12 4.69
540 574 6.751157 TCCGCCTATCGAAGATGTAAAAATA 58.249 36.000 0.00 0.00 45.12 1.40
553 587 4.866508 AATTTACATCTCCGCCTATCGA 57.133 40.909 0.00 0.00 41.67 3.59
555 589 4.515191 TGCAAATTTACATCTCCGCCTATC 59.485 41.667 0.00 0.00 0.00 2.08
556 590 4.275936 GTGCAAATTTACATCTCCGCCTAT 59.724 41.667 0.00 0.00 0.00 2.57
561 595 2.791158 GCGGTGCAAATTTACATCTCCG 60.791 50.000 12.37 12.37 38.67 4.63
629 740 5.505181 ACACCTCTCCAACAGATGTATTT 57.495 39.130 0.00 0.00 29.40 1.40
630 741 5.505181 AACACCTCTCCAACAGATGTATT 57.495 39.130 0.00 0.00 29.40 1.89
631 742 5.505181 AAACACCTCTCCAACAGATGTAT 57.495 39.130 0.00 0.00 29.40 2.29
699 811 3.045634 ACCGTCCATCCATCTCCAATAA 58.954 45.455 0.00 0.00 0.00 1.40
817 944 4.150897 TCGGTTTATTTGGATCCCTCTG 57.849 45.455 9.90 0.00 0.00 3.35
959 3787 1.146263 GTCCCGGCTAACAGATGGG 59.854 63.158 0.00 0.00 41.43 4.00
968 3796 3.837578 GACGATGAGTCCCGGCTA 58.162 61.111 0.00 0.00 43.95 3.93
1139 3967 4.021104 TGGGATAAAGAGAGATATGGCGTG 60.021 45.833 0.00 0.00 0.00 5.34
1147 3975 3.008485 GGCGGAATGGGATAAAGAGAGAT 59.992 47.826 0.00 0.00 0.00 2.75
1223 4051 3.911155 GAACGCAAGCGAACGCCTG 62.911 63.158 22.30 13.88 43.17 4.85
1399 4227 1.795170 GCGCTTGTTCCTGCCAAGAA 61.795 55.000 0.00 0.00 41.44 2.52
1432 4260 0.327924 CACCATAGTTGGACTGCCCA 59.672 55.000 0.00 0.00 46.92 5.36
1474 4302 5.366768 TGAGCAGAATAACTAAGGGCATACT 59.633 40.000 0.00 0.00 0.00 2.12
1485 4313 3.689347 TGCAATGGTGAGCAGAATAACT 58.311 40.909 0.00 0.00 35.51 2.24
1489 4317 3.369052 CCAAATGCAATGGTGAGCAGAAT 60.369 43.478 12.56 0.00 44.94 2.40
1595 4424 4.806571 CGCGAATTCGAGGAAGGA 57.193 55.556 31.01 0.00 43.02 3.36
1676 4505 4.766373 TGCACAATCACACATACCTTTGAT 59.234 37.500 0.00 0.00 0.00 2.57
1692 4521 4.021719 ACTGCAAAGATTAAGCTGCACAAT 60.022 37.500 3.76 0.00 39.77 2.71
1738 4567 6.122964 GGGTATCATTTTCCTTCTAGCTGTT 58.877 40.000 0.00 0.00 0.00 3.16
1770 4599 6.183360 GCATTCAGAAAGCACACATTAATTGG 60.183 38.462 5.47 0.00 0.00 3.16
1883 4712 9.709600 GTAGTCAAGTTAACGACTAGTATAACC 57.290 37.037 18.24 6.55 43.53 2.85
2013 4847 3.517296 TTGAAAGGTAGCCATCAACCA 57.483 42.857 6.03 0.00 38.30 3.67
2026 4860 8.189709 GGCTATAAAAAGCTGAATTTGAAAGG 57.810 34.615 0.00 0.00 42.37 3.11
2046 4880 3.492656 CCAGTAATACAGTGTGCGGCTAT 60.493 47.826 5.88 0.00 0.00 2.97
2051 4885 1.393539 GTGCCAGTAATACAGTGTGCG 59.606 52.381 5.88 0.00 30.57 5.34
2064 4898 4.275810 TCGACTAGGTAAATAGTGCCAGT 58.724 43.478 0.00 0.00 36.13 4.00
2079 4913 4.116747 ACTTTTGGCTCAGATCGACTAG 57.883 45.455 0.00 0.00 0.00 2.57
2082 4916 4.489679 AAAACTTTTGGCTCAGATCGAC 57.510 40.909 0.00 0.00 0.00 4.20
2275 5109 9.607285 GTTGTTTTACAAGTCCATTACTGTATG 57.393 33.333 0.00 0.00 39.00 2.39
2314 5148 3.515630 TCTGAACTTCTGATGCTTAGCG 58.484 45.455 0.00 0.00 0.00 4.26
2325 5159 6.126940 TGGCTATAGCAAGATTCTGAACTTCT 60.127 38.462 25.53 0.00 44.36 2.85
2443 5277 9.841295 ATATTAAAGTGTCATTACCGGTTACAT 57.159 29.630 15.04 0.00 0.00 2.29
2485 5319 5.611796 TGTACAACTTGATGATGTTCAGC 57.388 39.130 0.00 0.00 33.62 4.26
2611 5445 8.993424 AGAATAAGGGATCAGAAGTTTAGCTAA 58.007 33.333 0.86 0.86 0.00 3.09
2841 5675 3.251484 TGGCCACCATCCCATTTAAAAA 58.749 40.909 0.00 0.00 0.00 1.94
2845 5679 2.183679 GTTTGGCCACCATCCCATTTA 58.816 47.619 3.88 0.00 31.53 1.40
3000 5839 3.189910 TGTCAGCTGAAGAAATGCATGTC 59.810 43.478 20.19 9.00 0.00 3.06
3005 5844 1.135460 GGCTGTCAGCTGAAGAAATGC 60.135 52.381 20.19 15.15 41.99 3.56
3027 5866 7.229306 CCTCTGCCAATTTATTTGACTATGCTA 59.771 37.037 0.00 0.00 37.53 3.49
3085 6077 6.964807 AATCTTGATAAATGCAGGCATGTA 57.035 33.333 7.64 7.08 36.68 2.29
3168 6160 6.156519 CAGGCATGTAGAAATATAGCGTACA 58.843 40.000 0.00 0.00 0.00 2.90
3169 6161 5.062308 GCAGGCATGTAGAAATATAGCGTAC 59.938 44.000 0.00 0.00 0.00 3.67
3170 6162 5.168569 GCAGGCATGTAGAAATATAGCGTA 58.831 41.667 0.00 0.00 0.00 4.42
3171 6163 3.997021 GCAGGCATGTAGAAATATAGCGT 59.003 43.478 0.00 0.00 0.00 5.07
3172 6164 3.996363 TGCAGGCATGTAGAAATATAGCG 59.004 43.478 0.00 0.00 0.00 4.26
3173 6165 6.506500 AATGCAGGCATGTAGAAATATAGC 57.493 37.500 7.64 0.00 36.68 2.97
3178 6170 9.101655 GAAAATAAAATGCAGGCATGTAGAAAT 57.898 29.630 7.64 0.00 36.68 2.17
3179 6171 8.093307 TGAAAATAAAATGCAGGCATGTAGAAA 58.907 29.630 7.64 0.00 36.68 2.52
3180 6172 7.609960 TGAAAATAAAATGCAGGCATGTAGAA 58.390 30.769 7.64 0.00 36.68 2.10
3181 6173 7.167924 TGAAAATAAAATGCAGGCATGTAGA 57.832 32.000 7.64 0.00 36.68 2.59
3182 6174 7.546667 ACTTGAAAATAAAATGCAGGCATGTAG 59.453 33.333 7.64 0.00 36.68 2.74
3183 6175 7.385267 ACTTGAAAATAAAATGCAGGCATGTA 58.615 30.769 7.64 0.00 36.68 2.29
3184 6176 6.232692 ACTTGAAAATAAAATGCAGGCATGT 58.767 32.000 7.64 0.00 36.68 3.21
3185 6177 6.730960 ACTTGAAAATAAAATGCAGGCATG 57.269 33.333 7.64 0.00 36.68 4.06
3186 6178 7.163441 AGAACTTGAAAATAAAATGCAGGCAT 58.837 30.769 0.00 0.00 38.46 4.40
3187 6179 6.523840 AGAACTTGAAAATAAAATGCAGGCA 58.476 32.000 0.00 0.00 0.00 4.75
3188 6180 8.598075 CATAGAACTTGAAAATAAAATGCAGGC 58.402 33.333 0.00 0.00 0.00 4.85
3189 6181 9.859427 TCATAGAACTTGAAAATAAAATGCAGG 57.141 29.630 0.00 0.00 0.00 4.85
3288 6280 3.541996 TGCTGATATGCGAAGAAGGAA 57.458 42.857 0.00 0.00 35.36 3.36
3297 6289 5.453587 GCTTTCTTAGTTTTGCTGATATGCG 59.546 40.000 0.00 0.00 35.36 4.73
3350 6342 2.266554 CGACATTCCAGAAGAGACAGC 58.733 52.381 0.00 0.00 0.00 4.40
3409 6401 2.353109 GGAACAGCAAAAGGGATTGAGC 60.353 50.000 0.00 0.00 31.84 4.26
3415 6407 2.291540 CCATAGGGAACAGCAAAAGGGA 60.292 50.000 0.00 0.00 35.59 4.20
3618 6614 4.844085 TCCAGGAGAAACAAGGAGATGTAA 59.156 41.667 0.00 0.00 32.02 2.41
3630 6626 6.488344 ACAGAGAAAGAAAATCCAGGAGAAAC 59.512 38.462 0.00 0.00 0.00 2.78
3716 6712 2.399396 ACAATCCAAACTTCAACGCG 57.601 45.000 3.53 3.53 0.00 6.01
3788 6784 7.975616 ACACATTAAACATTATGCAGATGAACC 59.024 33.333 17.04 0.00 0.00 3.62
3907 6904 0.886490 ACTTGCCCTCAAAGACAGCG 60.886 55.000 0.00 0.00 0.00 5.18
3958 6955 6.409704 TCCAGTCTTCTAATGTCATTTCCTG 58.590 40.000 2.79 2.15 0.00 3.86
3962 6959 6.240894 TGCTTCCAGTCTTCTAATGTCATTT 58.759 36.000 2.79 0.00 0.00 2.32
4035 7032 1.001974 TGCAACTGTCTTGCCGATACT 59.998 47.619 2.30 0.00 44.32 2.12
4111 7111 4.900652 ACCTGAGCTGACTTCTATGATGAT 59.099 41.667 0.00 0.00 0.00 2.45
4112 7112 4.099113 CACCTGAGCTGACTTCTATGATGA 59.901 45.833 0.00 0.00 0.00 2.92
4113 7113 4.370049 CACCTGAGCTGACTTCTATGATG 58.630 47.826 0.00 0.00 0.00 3.07
4126 7126 1.404717 CGATAACTGTGCACCTGAGCT 60.405 52.381 15.69 0.00 34.99 4.09
4134 7134 2.401583 AATCAGGCGATAACTGTGCA 57.598 45.000 0.00 0.00 37.25 4.57
4219 7219 5.636965 CGTATGGAAGGATGAATAGAAGCAG 59.363 44.000 0.00 0.00 0.00 4.24
4251 7251 5.289434 GCTGCCATATTTTAAAGTGAAGCAC 59.711 40.000 13.58 0.00 34.10 4.40
4274 7274 6.828785 ACATATATCCGAGGAATATTTTGGGC 59.171 38.462 0.00 0.00 0.00 5.36
4289 7289 6.017934 CAGGTGAAGTTCCAAACATATATCCG 60.018 42.308 0.00 0.00 0.00 4.18
4324 7325 7.672983 TTCCTCTACACAAGCAGAAAAATAG 57.327 36.000 0.00 0.00 0.00 1.73
4353 7354 1.728971 CTGATAAGATCAATCGCCGGC 59.271 52.381 19.07 19.07 39.11 6.13
4374 7375 1.985159 ACCCCAACTAGAGCATTCACA 59.015 47.619 0.00 0.00 0.00 3.58
4415 7416 2.990066 AGACATAGTGTTAGCTGGCC 57.010 50.000 0.00 0.00 0.00 5.36
4461 7464 4.264253 TGGCATCAGGAATTTGACTACTG 58.736 43.478 0.00 0.00 0.00 2.74
4463 7466 4.096984 CCTTGGCATCAGGAATTTGACTAC 59.903 45.833 0.00 0.00 0.00 2.73
4470 7473 3.011032 AGAACTCCTTGGCATCAGGAATT 59.989 43.478 9.15 5.57 0.00 2.17
4495 7498 3.018856 TGCATCAATTACTTGGCCAGAG 58.981 45.455 5.11 9.46 32.95 3.35
4546 7549 3.769300 ACTCCAGGGCAAATAATCCAAAC 59.231 43.478 0.00 0.00 0.00 2.93
4605 7608 5.995282 TGTAAAACAGAACGGTTGATCATCT 59.005 36.000 0.00 0.00 0.00 2.90
4770 7776 5.148651 TCATCATCTGAGATATGTGGCAG 57.851 43.478 0.00 0.00 0.00 4.85
4931 7937 4.212716 ACTGCACATTCTCTATACCGGTA 58.787 43.478 18.46 18.46 0.00 4.02
4936 7942 9.151471 TCTGTAAAAACTGCACATTCTCTATAC 57.849 33.333 0.00 0.00 0.00 1.47
4989 7995 0.808125 CTCTCAGGAGTCAGGACACG 59.192 60.000 1.84 0.00 35.03 4.49
4999 8005 5.455872 TGTTAATACCCCTACTCTCAGGAG 58.544 45.833 0.00 0.00 44.62 3.69
5000 8006 5.476950 TGTTAATACCCCTACTCTCAGGA 57.523 43.478 0.00 0.00 38.00 3.86
5001 8007 5.070580 CCTTGTTAATACCCCTACTCTCAGG 59.929 48.000 0.00 0.00 35.26 3.86
5002 8008 5.661759 ACCTTGTTAATACCCCTACTCTCAG 59.338 44.000 0.00 0.00 0.00 3.35
5003 8009 5.596763 ACCTTGTTAATACCCCTACTCTCA 58.403 41.667 0.00 0.00 0.00 3.27
5004 8010 6.041409 GGTACCTTGTTAATACCCCTACTCTC 59.959 46.154 4.06 0.00 33.54 3.20
5006 8012 5.221322 CGGTACCTTGTTAATACCCCTACTC 60.221 48.000 10.90 0.00 35.85 2.59
5007 8013 4.651045 CGGTACCTTGTTAATACCCCTACT 59.349 45.833 10.90 0.00 35.85 2.57
5008 8014 4.405680 ACGGTACCTTGTTAATACCCCTAC 59.594 45.833 10.90 0.00 35.85 3.18
5009 8015 4.619679 ACGGTACCTTGTTAATACCCCTA 58.380 43.478 10.90 0.00 35.85 3.53
5010 8016 3.453868 ACGGTACCTTGTTAATACCCCT 58.546 45.455 10.90 0.00 35.85 4.79
5011 8017 3.912496 ACGGTACCTTGTTAATACCCC 57.088 47.619 10.90 0.00 35.85 4.95
5012 8018 3.374988 GCAACGGTACCTTGTTAATACCC 59.625 47.826 19.06 3.62 35.85 3.69
5043 8049 1.772182 CGAGATCGTAGGCACCATTC 58.228 55.000 0.00 0.00 34.11 2.67
5050 8056 2.288273 ACAAATAGGCGAGATCGTAGGC 60.288 50.000 3.94 4.08 42.22 3.93
5053 8059 3.120792 GCAACAAATAGGCGAGATCGTA 58.879 45.455 3.94 0.00 42.22 3.43
5054 8060 1.933853 GCAACAAATAGGCGAGATCGT 59.066 47.619 3.94 0.00 42.22 3.73
5061 8069 2.352503 AAAGCTGCAACAAATAGGCG 57.647 45.000 1.02 0.00 0.00 5.52
5112 8120 0.462375 ACCGTTGGAAAACCCTTTGC 59.538 50.000 0.00 0.00 35.38 3.68
5119 8128 5.224888 GGAAAATTCCTACCGTTGGAAAAC 58.775 41.667 16.84 9.32 45.38 2.43
5129 8138 7.794203 GTGAGACCACATGGAAAATTCCTACC 61.794 46.154 13.09 0.00 43.90 3.18
5170 8179 1.468914 GCTGTTCCTAAGCTTTTCCCG 59.531 52.381 3.20 0.00 37.69 5.14
5171 8180 2.489722 CTGCTGTTCCTAAGCTTTTCCC 59.510 50.000 3.20 0.00 41.42 3.97
5174 8183 1.889170 GCCTGCTGTTCCTAAGCTTTT 59.111 47.619 3.20 0.00 41.42 2.27
5175 8184 1.539157 GCCTGCTGTTCCTAAGCTTT 58.461 50.000 3.20 0.00 41.42 3.51
5178 8187 1.362406 GACGCCTGCTGTTCCTAAGC 61.362 60.000 0.00 0.00 41.22 3.09
5179 8188 0.741221 GGACGCCTGCTGTTCCTAAG 60.741 60.000 0.00 0.00 0.00 2.18
5180 8189 1.295423 GGACGCCTGCTGTTCCTAA 59.705 57.895 0.00 0.00 0.00 2.69
5181 8190 2.978824 GGACGCCTGCTGTTCCTA 59.021 61.111 0.00 0.00 0.00 2.94
5182 8191 4.379243 CGGACGCCTGCTGTTCCT 62.379 66.667 0.00 0.00 0.00 3.36
5202 8211 3.121030 ACGTCGCATGCTGAAGGC 61.121 61.111 17.13 0.00 42.22 4.35
5203 8212 2.029288 ACACGTCGCATGCTGAAGG 61.029 57.895 17.13 11.93 0.00 3.46
5204 8213 1.131218 CACACGTCGCATGCTGAAG 59.869 57.895 17.13 17.78 0.00 3.02
5205 8214 1.157257 AACACACGTCGCATGCTGAA 61.157 50.000 17.13 0.00 0.00 3.02
5206 8215 1.556591 GAACACACGTCGCATGCTGA 61.557 55.000 17.13 11.96 0.00 4.26
5207 8216 1.154599 GAACACACGTCGCATGCTG 60.155 57.895 17.13 9.68 0.00 4.41
5208 8217 2.317609 GGAACACACGTCGCATGCT 61.318 57.895 17.13 0.00 0.00 3.79
5209 8218 2.173382 GGAACACACGTCGCATGC 59.827 61.111 7.91 7.91 0.00 4.06
5210 8219 2.307309 ACGGAACACACGTCGCATG 61.307 57.895 0.00 0.00 41.25 4.06
5211 8220 2.028484 ACGGAACACACGTCGCAT 59.972 55.556 0.00 0.00 41.25 4.73
5212 8221 2.957489 CACGGAACACACGTCGCA 60.957 61.111 0.00 0.00 43.58 5.10
5213 8222 2.958016 ACACGGAACACACGTCGC 60.958 61.111 0.00 0.00 43.58 5.19
5214 8223 1.874915 ACACACGGAACACACGTCG 60.875 57.895 0.00 0.00 43.58 5.12
5215 8224 1.634225 CACACACGGAACACACGTC 59.366 57.895 0.00 0.00 43.58 4.34
5216 8225 1.812093 CCACACACGGAACACACGT 60.812 57.895 0.00 0.00 46.82 4.49
5217 8226 3.010767 CCACACACGGAACACACG 58.989 61.111 0.00 0.00 37.36 4.49
5218 8227 2.713154 GCCACACACGGAACACAC 59.287 61.111 0.00 0.00 0.00 3.82
5219 8228 2.515057 GGCCACACACGGAACACA 60.515 61.111 0.00 0.00 0.00 3.72
5220 8229 3.645975 CGGCCACACACGGAACAC 61.646 66.667 2.24 0.00 0.00 3.32
5235 8244 2.550699 TAAAGATGCAGTGGCCCCGG 62.551 60.000 0.00 0.00 40.13 5.73
5236 8245 1.077787 TAAAGATGCAGTGGCCCCG 60.078 57.895 0.00 0.00 40.13 5.73
5237 8246 1.037579 GGTAAAGATGCAGTGGCCCC 61.038 60.000 0.00 0.00 40.13 5.80
5238 8247 1.376609 CGGTAAAGATGCAGTGGCCC 61.377 60.000 0.00 0.00 40.13 5.80
5239 8248 0.676782 ACGGTAAAGATGCAGTGGCC 60.677 55.000 0.00 0.00 40.13 5.36
5240 8249 2.018542 TACGGTAAAGATGCAGTGGC 57.981 50.000 0.00 0.00 41.68 5.01
5241 8250 3.596214 AGTTACGGTAAAGATGCAGTGG 58.404 45.455 1.47 0.00 0.00 4.00
5242 8251 5.647589 TCTAGTTACGGTAAAGATGCAGTG 58.352 41.667 1.47 0.00 0.00 3.66
5243 8252 5.909621 TCTAGTTACGGTAAAGATGCAGT 57.090 39.130 1.47 0.00 0.00 4.40
5244 8253 6.418226 GTCATCTAGTTACGGTAAAGATGCAG 59.582 42.308 24.68 11.70 42.04 4.41
5245 8254 6.270815 GTCATCTAGTTACGGTAAAGATGCA 58.729 40.000 24.68 16.44 42.04 3.96
5246 8255 5.690857 GGTCATCTAGTTACGGTAAAGATGC 59.309 44.000 24.68 20.76 42.04 3.91
5247 8256 6.214399 GGGTCATCTAGTTACGGTAAAGATG 58.786 44.000 24.05 24.05 43.11 2.90
5248 8257 5.009410 CGGGTCATCTAGTTACGGTAAAGAT 59.991 44.000 1.47 5.80 0.00 2.40
5249 8258 4.336433 CGGGTCATCTAGTTACGGTAAAGA 59.664 45.833 1.47 3.61 0.00 2.52
5250 8259 4.096984 ACGGGTCATCTAGTTACGGTAAAG 59.903 45.833 1.47 0.00 0.00 1.85
5251 8260 4.016444 ACGGGTCATCTAGTTACGGTAAA 58.984 43.478 1.47 0.00 0.00 2.01
5252 8261 3.620488 ACGGGTCATCTAGTTACGGTAA 58.380 45.455 0.00 0.00 0.00 2.85
5253 8262 3.281727 ACGGGTCATCTAGTTACGGTA 57.718 47.619 0.00 0.00 0.00 4.02
5254 8263 2.134789 ACGGGTCATCTAGTTACGGT 57.865 50.000 0.00 0.00 0.00 4.83
5255 8264 2.805845 CAACGGGTCATCTAGTTACGG 58.194 52.381 0.00 0.00 0.00 4.02
5256 8265 2.190981 GCAACGGGTCATCTAGTTACG 58.809 52.381 0.00 0.00 0.00 3.18
5257 8266 2.190981 CGCAACGGGTCATCTAGTTAC 58.809 52.381 0.00 0.00 0.00 2.50
5258 8267 1.470285 GCGCAACGGGTCATCTAGTTA 60.470 52.381 0.30 0.00 0.00 2.24
5259 8268 0.739813 GCGCAACGGGTCATCTAGTT 60.740 55.000 0.30 0.00 0.00 2.24
5292 8301 0.254178 ATCATTGGCTTGCTCTCGGT 59.746 50.000 0.00 0.00 0.00 4.69
5309 8318 8.804743 CATATTTTGATGCACACTCTTTCAATC 58.195 33.333 0.00 0.00 0.00 2.67
5462 8471 9.740239 CCTTTGCTACGTAACTTGATATTACTA 57.260 33.333 0.00 0.00 31.53 1.82
5463 8472 8.472413 TCCTTTGCTACGTAACTTGATATTACT 58.528 33.333 0.00 0.00 31.53 2.24
5464 8473 8.538039 GTCCTTTGCTACGTAACTTGATATTAC 58.462 37.037 0.00 0.00 0.00 1.89
5465 8474 8.472413 AGTCCTTTGCTACGTAACTTGATATTA 58.528 33.333 0.00 0.00 0.00 0.98
5466 8475 7.328737 AGTCCTTTGCTACGTAACTTGATATT 58.671 34.615 0.00 0.00 0.00 1.28
5467 8476 6.875076 AGTCCTTTGCTACGTAACTTGATAT 58.125 36.000 0.00 0.00 0.00 1.63
5468 8477 6.276832 AGTCCTTTGCTACGTAACTTGATA 57.723 37.500 0.00 0.00 0.00 2.15
5469 8478 5.148651 AGTCCTTTGCTACGTAACTTGAT 57.851 39.130 0.00 0.00 0.00 2.57
5470 8479 4.595762 AGTCCTTTGCTACGTAACTTGA 57.404 40.909 0.00 0.00 0.00 3.02
5471 8480 5.345202 CAGTAGTCCTTTGCTACGTAACTTG 59.655 44.000 0.00 0.00 42.49 3.16
5472 8481 5.010415 ACAGTAGTCCTTTGCTACGTAACTT 59.990 40.000 0.00 0.00 42.49 2.66
5530 8551 0.896940 CAAGTGCATGTCCAAGGGCT 60.897 55.000 0.00 0.00 0.00 5.19
5653 8674 7.816945 TTTAAAGAATACCGGTCTCTAAACG 57.183 36.000 12.40 0.00 0.00 3.60
5785 8806 7.760794 GGTTGATCAAAGCAATTTACATGATGA 59.239 33.333 10.35 0.00 36.25 2.92
5841 8862 3.894759 AGCAACCTACATGATGCATCTT 58.105 40.909 26.32 18.05 41.18 2.40


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

AutoCloner maintained by Alex Coulton.