Multiple sequence alignment - TraesCS6A01G265500

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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 TraesCS6A01G265500 chr6A 100.000 6296 0 0 1 6296 490474250 490480545 0.000000e+00 11627.0
1 TraesCS6A01G265500 chr6A 100.000 1381 0 0 6537 7917 490480786 490482166 0.000000e+00 2551.0
2 TraesCS6A01G265500 chr6A 96.825 63 0 1 7784 7844 490481968 490482030 3.910000e-18 104.0
3 TraesCS6A01G265500 chr6A 96.825 63 0 1 7719 7781 490482033 490482093 3.910000e-18 104.0
4 TraesCS6A01G265500 chr6A 95.455 44 2 0 5905 5948 161105550 161105507 3.960000e-08 71.3
5 TraesCS6A01G265500 chr6D 96.423 4137 110 13 1 4115 352874207 352878327 0.000000e+00 6785.0
6 TraesCS6A01G265500 chr6D 95.464 1940 38 15 4227 6158 352878846 352880743 0.000000e+00 3049.0
7 TraesCS6A01G265500 chr6D 97.201 536 15 0 6586 7121 352880840 352881375 0.000000e+00 907.0
8 TraesCS6A01G265500 chr6D 94.375 320 14 2 7188 7505 352881376 352881693 9.230000e-134 488.0
9 TraesCS6A01G265500 chr6D 93.382 136 6 2 7784 7917 352881916 352882050 1.740000e-46 198.0
10 TraesCS6A01G265500 chr6D 94.792 96 5 0 7686 7781 352881883 352881978 4.950000e-32 150.0
11 TraesCS6A01G265500 chr6D 98.630 73 1 0 4114 4186 352878489 352878561 6.450000e-26 130.0
12 TraesCS6A01G265500 chr6D 96.970 33 1 0 7599 7631 422610453 422610421 1.000000e-03 56.5
13 TraesCS6A01G265500 chr6B 95.756 3252 105 11 1390 4622 526037480 526034243 0.000000e+00 5210.0
14 TraesCS6A01G265500 chr6B 95.731 1546 43 11 4621 6158 526034161 526032631 0.000000e+00 2468.0
15 TraesCS6A01G265500 chr6B 94.989 1397 47 10 8 1397 526038961 526037581 0.000000e+00 2170.0
16 TraesCS6A01G265500 chr6B 93.996 1066 49 9 6547 7602 526032454 526031394 0.000000e+00 1600.0
17 TraesCS6A01G265500 chr6B 91.203 557 36 7 7053 7602 525995965 525995415 0.000000e+00 745.0
18 TraesCS6A01G265500 chr6B 94.286 140 6 2 6158 6296 526032591 526032453 6.220000e-51 213.0
19 TraesCS6A01G265500 chr6B 91.736 121 8 2 7797 7917 525995154 525995036 4.910000e-37 167.0
20 TraesCS6A01G265500 chr6B 87.500 72 6 3 7599 7667 649824520 649824449 6.590000e-11 80.5
21 TraesCS6A01G265500 chr5D 87.143 70 7 2 7600 7667 388431047 388431116 2.370000e-10 78.7
22 TraesCS6A01G265500 chr4A 92.308 52 4 0 5905 5956 562284107 562284056 3.060000e-09 75.0
23 TraesCS6A01G265500 chr2B 92.308 52 4 0 5905 5956 657789203 657789254 3.060000e-09 75.0
24 TraesCS6A01G265500 chr2A 91.228 57 2 3 5895 5948 712316364 712316420 3.060000e-09 75.0
25 TraesCS6A01G265500 chr7D 92.308 52 2 2 5897 5948 236842961 236843010 1.100000e-08 73.1
26 TraesCS6A01G265500 chr3B 91.071 56 2 2 5905 5957 620673523 620673468 1.100000e-08 73.1
27 TraesCS6A01G265500 chr3B 97.561 41 1 0 7600 7640 752295104 752295144 3.960000e-08 71.3
28 TraesCS6A01G265500 chr3A 90.909 55 3 2 5895 5948 528595035 528595088 1.100000e-08 73.1
29 TraesCS6A01G265500 chr3D 100.000 36 0 0 7600 7635 39590571 39590606 5.130000e-07 67.6
30 TraesCS6A01G265500 chr5A 95.000 40 2 0 7601 7640 597741367 597741406 6.630000e-06 63.9
31 TraesCS6A01G265500 chr7B 97.222 36 1 0 7600 7635 672390724 672390689 2.390000e-05 62.1
32 TraesCS6A01G265500 chr1D 89.130 46 3 1 7613 7656 322910520 322910565 1.000000e-03 56.5


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 TraesCS6A01G265500 chr6A 490474250 490482166 7916 False 3596.500000 11627 98.412500 1 7917 4 chr6A.!!$F1 7916
1 TraesCS6A01G265500 chr6D 352874207 352882050 7843 False 1672.428571 6785 95.752429 1 7917 7 chr6D.!!$F1 7916
2 TraesCS6A01G265500 chr6B 526031394 526038961 7567 True 2332.200000 5210 94.951600 8 7602 5 chr6B.!!$R3 7594
3 TraesCS6A01G265500 chr6B 525995036 525995965 929 True 456.000000 745 91.469500 7053 7917 2 chr6B.!!$R2 864

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
320 323 0.035458 AGCCGGAGAAACAGACAAGG 59.965 55.000 5.05 0.0 0.00 3.61 F
425 428 0.897863 CACGATGCCTTTTTCCCCCA 60.898 55.000 0.00 0.0 0.00 4.96 F
1563 1684 0.178992 TGCTGGGCACTTAGCTGTTT 60.179 50.000 0.00 0.0 44.79 2.83 F
1564 1685 0.961753 GCTGGGCACTTAGCTGTTTT 59.038 50.000 0.00 0.0 44.79 2.43 F
1565 1686 1.341209 GCTGGGCACTTAGCTGTTTTT 59.659 47.619 0.00 0.0 44.79 1.94 F
1646 1767 1.819632 GGCCACACGATCATGGTCC 60.820 63.158 0.00 7.2 38.34 4.46 F
1724 1845 1.944709 CAAAGCGCAGGATCATCATCA 59.055 47.619 11.47 0.0 0.00 3.07 F
2885 3006 2.012673 GTCAGTGAGATTGTCATGGGC 58.987 52.381 0.00 0.0 37.56 5.36 F
4204 4503 1.545651 GGAAGGTGGAGTTGGAAGTGG 60.546 57.143 0.00 0.0 0.00 4.00 F
4488 5039 0.241749 TGCATGCTGCTAACTTGTGC 59.758 50.000 20.33 1.2 45.31 4.57 F
5818 6457 0.960364 TCCCTCGCTTGCCATTTGTC 60.960 55.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1282 0.894184 ACCGAGCGAGAAGTTCTCCA 60.894 55.000 24.01 0.0 40.34 3.86 R
1716 1837 1.071228 AGCTAATGCCGCTGATGATGA 59.929 47.619 0.00 0.0 40.80 2.92 R
3254 3388 0.448990 CACCATGATCACCAACTGCG 59.551 55.000 0.00 0.0 0.00 5.18 R
3326 3460 1.742831 GCATCGACTGGTGCCAAATTA 59.257 47.619 0.00 0.0 35.35 1.40 R
3549 3683 9.474313 AAATTATTTAGTTTCCAGATGCAGGTA 57.526 29.630 0.00 0.0 0.00 3.08 R
3593 3727 5.508567 TCCATGGCATCAAACTCAAAGATA 58.491 37.500 6.96 0.0 0.00 1.98 R
3710 3844 5.276773 CGCTAGCTCTGACAGATTTGATTTC 60.277 44.000 13.93 0.0 0.00 2.17 R
4438 4989 1.154197 CACATATCAGGCCAGCATCG 58.846 55.000 5.01 0.0 0.00 3.84 R
6037 6679 1.864711 CTGAAGCCGTTTCGTCTTTCA 59.135 47.619 0.00 0.0 38.71 2.69 R
6222 6905 2.682352 GGCCTCTGCAAATTCTCTTCTC 59.318 50.000 0.00 0.0 40.13 2.87 R
7545 8329 0.040058 ACAATCAGCATCAGGGCCAA 59.960 50.000 6.18 0.0 0.00 4.52 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
64 65 7.038659 CCACTTCTAGACATAAAAGGACTCTG 58.961 42.308 0.00 0.00 0.00 3.35
128 131 2.736682 GACCACCCGTTGCGAATCG 61.737 63.158 0.00 0.00 0.00 3.34
187 190 3.882025 GCAGCTGTGCCTGTACTC 58.118 61.111 16.64 0.00 44.72 2.59
188 191 2.097038 GCAGCTGTGCCTGTACTCG 61.097 63.158 16.64 0.00 44.72 4.18
189 192 1.586541 CAGCTGTGCCTGTACTCGA 59.413 57.895 5.25 0.00 0.00 4.04
190 193 0.457509 CAGCTGTGCCTGTACTCGAG 60.458 60.000 11.84 11.84 0.00 4.04
191 194 1.153745 GCTGTGCCTGTACTCGAGG 60.154 63.158 18.41 0.00 0.00 4.63
206 209 1.893062 GAGGCCTGCCCATGAAAAC 59.107 57.895 12.00 0.00 36.58 2.43
312 315 0.179158 GAGACGAGAGCCGGAGAAAC 60.179 60.000 5.05 0.00 43.93 2.78
320 323 0.035458 AGCCGGAGAAACAGACAAGG 59.965 55.000 5.05 0.00 0.00 3.61
419 422 4.549458 CATCAAGAACACGATGCCTTTTT 58.451 39.130 0.00 0.00 33.19 1.94
425 428 0.897863 CACGATGCCTTTTTCCCCCA 60.898 55.000 0.00 0.00 0.00 4.96
444 447 3.787001 CCCACCCCTCGCTTCCTC 61.787 72.222 0.00 0.00 0.00 3.71
489 493 1.211818 GAGATCTCGCGTCCATGTGC 61.212 60.000 7.04 0.00 0.00 4.57
498 502 4.358841 TCCATGTGCCCGGGGTTG 62.359 66.667 25.28 7.61 0.00 3.77
513 517 3.633065 CGGGGTTGTTTTCCTTTGACTTA 59.367 43.478 0.00 0.00 0.00 2.24
596 600 2.040278 CTCCCATCACTTGGTTTCCTCA 59.960 50.000 0.00 0.00 44.83 3.86
623 631 1.160137 GCCATTTCTCGTCTGCTTGT 58.840 50.000 0.00 0.00 0.00 3.16
637 645 5.332959 CGTCTGCTTGTTTCTTCTTCTTCTC 60.333 44.000 0.00 0.00 0.00 2.87
694 702 1.138661 CTGATCTGGTTCTCCTCCTGC 59.861 57.143 0.00 0.00 34.23 4.85
772 780 3.503363 GCCGATGTGCCTGTCAGC 61.503 66.667 0.00 0.00 0.00 4.26
780 788 2.195567 TGCCTGTCAGCCTTGTTGC 61.196 57.895 0.00 0.00 0.00 4.17
820 828 2.124695 GGGCGGGCGAGAAAGAAT 60.125 61.111 0.00 0.00 0.00 2.40
910 918 1.075896 TTGGTTCTTTTGGGGCGGT 60.076 52.632 0.00 0.00 0.00 5.68
1224 1232 2.103094 TGATGAAGACATGATCGGGACC 59.897 50.000 0.00 0.00 36.82 4.46
1274 1282 1.306141 TGGAGGATCTTCTGGCCGT 60.306 57.895 4.68 0.00 33.73 5.68
1293 1301 0.894184 TGGAGAACTTCTCGCTCGGT 60.894 55.000 11.85 0.00 44.28 4.69
1339 1347 1.490490 AGACCAAGAGTGACAAGGCAA 59.510 47.619 0.00 0.00 0.00 4.52
1342 1350 4.072131 GACCAAGAGTGACAAGGCAATTA 58.928 43.478 0.00 0.00 0.00 1.40
1360 1368 7.330700 AGGCAATTAATTGTGGTAATTGTTTCG 59.669 33.333 25.15 0.00 44.98 3.46
1368 1376 4.513692 TGTGGTAATTGTTTCGACTTCCAG 59.486 41.667 0.00 0.00 0.00 3.86
1397 1517 4.323417 TCTATTTGCTCATGGACGTTTGT 58.677 39.130 0.00 0.00 0.00 2.83
1398 1518 5.483811 TCTATTTGCTCATGGACGTTTGTA 58.516 37.500 0.00 0.00 0.00 2.41
1453 1574 8.158169 TGCATATGGATTCAGTATTTGACTTC 57.842 34.615 4.56 0.00 35.64 3.01
1556 1677 1.946768 GCGAAATATGCTGGGCACTTA 59.053 47.619 0.00 0.00 43.04 2.24
1563 1684 0.178992 TGCTGGGCACTTAGCTGTTT 60.179 50.000 0.00 0.00 44.79 2.83
1564 1685 0.961753 GCTGGGCACTTAGCTGTTTT 59.038 50.000 0.00 0.00 44.79 2.43
1565 1686 1.341209 GCTGGGCACTTAGCTGTTTTT 59.659 47.619 0.00 0.00 44.79 1.94
1646 1767 1.819632 GGCCACACGATCATGGTCC 60.820 63.158 0.00 7.20 38.34 4.46
1700 1821 5.713389 ACAGAAAGAGGATTCATTGCAATCA 59.287 36.000 9.53 0.00 34.84 2.57
1716 1837 2.119801 ATCAAGTCAAAGCGCAGGAT 57.880 45.000 11.47 0.00 0.00 3.24
1724 1845 1.944709 CAAAGCGCAGGATCATCATCA 59.055 47.619 11.47 0.00 0.00 3.07
1727 1848 2.151295 CGCAGGATCATCATCAGCG 58.849 57.895 1.70 1.70 43.83 5.18
1811 1932 4.934797 TGGAACTGAAATCCCTGAAGAT 57.065 40.909 0.00 0.00 36.04 2.40
2012 2133 3.929610 CCGAGGCTTTAGAAGAAGTTCAG 59.070 47.826 5.50 0.00 34.82 3.02
2062 2183 8.303876 TCCTTTAAGCCAAAATAGTGACATTTC 58.696 33.333 0.00 0.00 0.00 2.17
2105 2226 7.850003 GCTGAACTATTGAGATCTTTTGAATCG 59.150 37.037 0.00 0.00 0.00 3.34
2660 2781 8.204903 AGAAGATCAAGCCTATTGATGTAGAT 57.795 34.615 7.77 0.00 39.08 1.98
2747 2868 7.510685 TGGAAGATAGCATTCCTATACTTCTGT 59.489 37.037 6.31 0.00 45.45 3.41
2885 3006 2.012673 GTCAGTGAGATTGTCATGGGC 58.987 52.381 0.00 0.00 37.56 5.36
2962 3083 5.385198 TCAGGCAAGAGAACAAAAAGGTAT 58.615 37.500 0.00 0.00 0.00 2.73
3077 3211 8.848474 AACCATGGCTATATCTAACATGTTAC 57.152 34.615 14.35 3.17 37.74 2.50
3233 3367 8.146479 TCTTGTAGACATGAATGTGATTATGC 57.854 34.615 0.00 0.00 41.95 3.14
3254 3388 4.101119 TGCTAGGCTAATAGTTTCCCTCAC 59.899 45.833 0.00 0.00 0.00 3.51
3549 3683 5.950023 AGAAAAGATGGAGCCATGTGATAT 58.050 37.500 6.76 0.00 36.70 1.63
3641 3775 6.293698 TGATCCTCCATCAGTTATGAATGTG 58.706 40.000 0.00 0.00 39.39 3.21
3710 3844 4.682860 GGACATGCTGAAATCAACTTTGTG 59.317 41.667 0.00 0.00 0.00 3.33
4190 4489 2.708861 GGAAATTGGGGTTTTGGAAGGT 59.291 45.455 0.00 0.00 0.00 3.50
4204 4503 1.545651 GGAAGGTGGAGTTGGAAGTGG 60.546 57.143 0.00 0.00 0.00 4.00
4211 4510 4.567747 GGTGGAGTTGGAAGTGGAACATAT 60.568 45.833 0.00 0.00 44.52 1.78
4214 4513 7.419750 GGTGGAGTTGGAAGTGGAACATATATA 60.420 40.741 0.00 0.00 44.52 0.86
4218 4517 8.554490 AGTTGGAAGTGGAACATATATAGAGT 57.446 34.615 0.00 0.00 44.52 3.24
4231 4774 9.427821 AACATATATAGAGTATCATGGGGAGAC 57.572 37.037 0.00 0.00 38.02 3.36
4488 5039 0.241749 TGCATGCTGCTAACTTGTGC 59.758 50.000 20.33 1.20 45.31 4.57
4495 5046 1.200716 CTGCTAACTTGTGCATGTGGG 59.799 52.381 0.00 0.00 38.59 4.61
4747 5381 9.632638 TTTTTCTTTCTATGGGAGGATATTGAG 57.367 33.333 0.00 0.00 0.00 3.02
4888 5522 5.628606 GCTGAAGTTTTCTCTGCAATCTTTC 59.371 40.000 0.00 0.00 0.00 2.62
4920 5554 4.040755 AGTGTGGCCAATAGGTAATCTCT 58.959 43.478 7.24 0.00 37.19 3.10
4965 5599 4.277423 GCTTTAGCTCCACTAACACCAAAA 59.723 41.667 0.00 0.00 40.63 2.44
5049 5683 4.770795 ACACATAGCACCTTGGACTATTC 58.229 43.478 0.00 0.00 0.00 1.75
5213 5848 1.274728 CTTCAGAGTGAGGACAGTGGG 59.725 57.143 0.00 0.00 0.00 4.61
5418 6053 1.343465 GAGGTGTTCGAAGGAGGTTCA 59.657 52.381 0.00 0.00 34.44 3.18
5493 6128 3.838244 TGGGAATCAGATAAACCCGAG 57.162 47.619 12.68 0.00 43.04 4.63
5818 6457 0.960364 TCCCTCGCTTGCCATTTGTC 60.960 55.000 0.00 0.00 0.00 3.18
6067 6709 2.029838 ACGGCTTCAGTGAATGATCC 57.970 50.000 5.91 5.00 37.89 3.36
6070 6712 2.096496 CGGCTTCAGTGAATGATCCAAC 59.904 50.000 5.91 0.00 37.89 3.77
6222 6905 0.747255 ACGACATCTCTTCCATCCGG 59.253 55.000 0.00 0.00 0.00 5.14
6236 6919 2.615912 CCATCCGGAGAAGAGAATTTGC 59.384 50.000 11.34 0.00 0.00 3.68
6239 6922 2.567169 TCCGGAGAAGAGAATTTGCAGA 59.433 45.455 0.00 0.00 0.00 4.26
6251 6934 4.823989 AGAATTTGCAGAGGCCATACATAC 59.176 41.667 5.01 0.00 40.13 2.39
6572 7255 2.372172 ACCTTTGTCATCCTTCTTCCGT 59.628 45.455 0.00 0.00 0.00 4.69
6581 7264 1.946768 TCCTTCTTCCGTTGCAACAAG 59.053 47.619 28.01 22.95 0.00 3.16
6597 7280 4.019174 CAACAAGCACCCTCCATCTTAAT 58.981 43.478 0.00 0.00 0.00 1.40
6604 7287 1.133699 CCCTCCATCTTAATGCAGCCA 60.134 52.381 0.00 0.00 0.00 4.75
6607 7290 4.401022 CCTCCATCTTAATGCAGCCAATA 58.599 43.478 0.00 0.00 0.00 1.90
6627 7310 0.961753 GCACCAAGTTCCTCCTTTGG 59.038 55.000 1.18 1.18 45.37 3.28
6714 7397 2.171659 TGACCTGTTCACCTAACTTGCA 59.828 45.455 0.00 0.00 38.99 4.08
6853 7536 3.997021 TCGAGAAGAATGTTCTTTCCAGC 59.003 43.478 9.20 0.00 46.84 4.85
6905 7588 0.321346 TGCATCCAAGCAACTCTCGA 59.679 50.000 0.00 0.00 42.46 4.04
7016 7699 6.883756 TGTACATACATTGCTTGATTGAAGGA 59.116 34.615 0.00 0.00 31.56 3.36
7160 7846 7.667043 TTTGGTGTACTGTATCTGATCAAAC 57.333 36.000 0.00 0.00 0.00 2.93
7161 7847 6.353404 TGGTGTACTGTATCTGATCAAACA 57.647 37.500 0.00 1.03 0.00 2.83
7182 7868 4.162888 ACATAGATCCAATCAGCACAGACA 59.837 41.667 0.00 0.00 0.00 3.41
7247 7933 6.237901 ACCAGTTATGATTTACACTGAAGCA 58.762 36.000 0.00 0.00 0.00 3.91
7249 7935 7.394359 ACCAGTTATGATTTACACTGAAGCAAT 59.606 33.333 0.00 0.00 0.00 3.56
7250 7936 8.246180 CCAGTTATGATTTACACTGAAGCAATT 58.754 33.333 0.00 0.00 0.00 2.32
7283 7969 7.459486 CAATTTGTTGATCTGTAGACAGTAGC 58.541 38.462 9.43 0.98 44.12 3.58
7285 7971 4.007659 TGTTGATCTGTAGACAGTAGCGA 58.992 43.478 9.43 0.00 44.12 4.93
7302 7988 8.577296 ACAGTAGCGATTGTCTTGTATACATAT 58.423 33.333 6.36 0.00 0.00 1.78
7324 8010 4.309933 TGATAGCAGTGTTGTTCTCTGTG 58.690 43.478 0.00 0.00 39.15 3.66
7340 8026 3.369400 TGCGTTGGAATTGGGCCG 61.369 61.111 0.00 0.00 0.00 6.13
7375 8061 5.761003 TGTTTCATTGATCACACACATGTC 58.239 37.500 0.00 0.00 36.72 3.06
7443 8135 9.661563 ATTGGATTTTTATGACACTAGACGTAA 57.338 29.630 0.00 0.00 0.00 3.18
7509 8202 2.568956 ACCATGCTTGCTCTCTAACTGA 59.431 45.455 0.00 0.00 0.00 3.41
7559 8343 2.441532 CCCTTGGCCCTGATGCTG 60.442 66.667 0.00 0.00 0.00 4.41
7578 8362 0.391130 GATTGTGGCACGCTGAGGTA 60.391 55.000 13.77 0.00 40.97 3.08
7602 8386 1.066858 CGCATGTGTGACCTTCCTACT 60.067 52.381 0.00 0.00 0.00 2.57
7603 8387 2.622436 GCATGTGTGACCTTCCTACTC 58.378 52.381 0.00 0.00 0.00 2.59
7604 8388 2.678190 GCATGTGTGACCTTCCTACTCC 60.678 54.545 0.00 0.00 0.00 3.85
7606 8390 1.149288 TGTGTGACCTTCCTACTCCCT 59.851 52.381 0.00 0.00 0.00 4.20
7608 8392 2.234168 GTGTGACCTTCCTACTCCCTTC 59.766 54.545 0.00 0.00 0.00 3.46
7609 8393 2.158219 TGTGACCTTCCTACTCCCTTCA 60.158 50.000 0.00 0.00 0.00 3.02
7612 8396 3.012959 TGACCTTCCTACTCCCTTCATCT 59.987 47.826 0.00 0.00 0.00 2.90
7614 8398 3.012959 ACCTTCCTACTCCCTTCATCTCA 59.987 47.826 0.00 0.00 0.00 3.27
7615 8399 4.230455 CCTTCCTACTCCCTTCATCTCAT 58.770 47.826 0.00 0.00 0.00 2.90
7645 8437 9.950680 ATAAGAGCGTTTTTGATATTAATGGTG 57.049 29.630 0.00 0.00 0.00 4.17
7647 8439 8.500753 AGAGCGTTTTTGATATTAATGGTGTA 57.499 30.769 0.00 0.00 0.00 2.90
7648 8440 8.952278 AGAGCGTTTTTGATATTAATGGTGTAA 58.048 29.630 0.00 0.00 0.00 2.41
7649 8441 9.562583 GAGCGTTTTTGATATTAATGGTGTAAA 57.437 29.630 0.00 0.00 0.00 2.01
7650 8442 9.915629 AGCGTTTTTGATATTAATGGTGTAAAA 57.084 25.926 0.00 0.00 0.00 1.52
7706 8619 8.287807 GGAGTACCAAATAAACCATGTGCTGG 62.288 46.154 0.00 0.00 42.67 4.85
7724 8637 3.445096 GCTGGAACCATTACAAGCTCAAT 59.555 43.478 0.00 0.00 0.00 2.57
7753 8666 1.834263 CTCTCGGGAGTGGAATTCCTT 59.166 52.381 24.73 13.33 43.30 3.36
7757 8670 1.756430 GGGAGTGGAATTCCTTCAGC 58.244 55.000 24.73 13.05 43.30 4.26
7764 8677 6.013812 GGAGTGGAATTCCTTCAGCTATATCT 60.014 42.308 24.73 6.37 40.07 1.98
7765 8678 6.767456 AGTGGAATTCCTTCAGCTATATCTG 58.233 40.000 24.73 0.00 36.82 2.90
7766 8679 6.556495 AGTGGAATTCCTTCAGCTATATCTGA 59.444 38.462 24.73 2.11 40.99 3.27
7767 8680 6.873076 GTGGAATTCCTTCAGCTATATCTGAG 59.127 42.308 24.73 2.36 43.23 3.35
7768 8681 5.874261 GGAATTCCTTCAGCTATATCTGAGC 59.126 44.000 17.73 0.00 43.23 4.26
7769 8682 4.881019 TTCCTTCAGCTATATCTGAGCC 57.119 45.455 6.40 0.00 43.23 4.70
7770 8683 3.849527 TCCTTCAGCTATATCTGAGCCA 58.150 45.455 6.40 0.00 43.23 4.75
7771 8684 4.226384 TCCTTCAGCTATATCTGAGCCAA 58.774 43.478 6.40 0.00 43.23 4.52
7772 8685 4.655649 TCCTTCAGCTATATCTGAGCCAAA 59.344 41.667 6.40 0.00 43.23 3.28
7773 8686 5.130975 TCCTTCAGCTATATCTGAGCCAAAA 59.869 40.000 6.40 0.00 43.23 2.44
7774 8687 5.824624 CCTTCAGCTATATCTGAGCCAAAAA 59.175 40.000 6.40 0.00 43.23 1.94
7775 8688 6.489361 CCTTCAGCTATATCTGAGCCAAAAAT 59.511 38.462 6.40 0.00 43.23 1.82
7776 8689 6.872628 TCAGCTATATCTGAGCCAAAAATG 57.127 37.500 2.11 0.00 41.06 2.32
7777 8690 5.240183 TCAGCTATATCTGAGCCAAAAATGC 59.760 40.000 2.11 0.00 41.06 3.56
7778 8691 5.241064 CAGCTATATCTGAGCCAAAAATGCT 59.759 40.000 0.00 0.00 41.06 3.79
7779 8692 6.429078 CAGCTATATCTGAGCCAAAAATGCTA 59.571 38.462 0.00 0.00 41.06 3.49
7780 8693 6.654161 AGCTATATCTGAGCCAAAAATGCTAG 59.346 38.462 0.00 0.00 41.06 3.42
7781 8694 6.652481 GCTATATCTGAGCCAAAAATGCTAGA 59.348 38.462 0.00 0.00 39.69 2.43
7782 8695 6.874288 ATATCTGAGCCAAAAATGCTAGAC 57.126 37.500 0.00 0.00 39.69 2.59
7783 8696 3.002791 TCTGAGCCAAAAATGCTAGACG 58.997 45.455 0.00 0.00 39.69 4.18
7784 8697 1.468520 TGAGCCAAAAATGCTAGACGC 59.531 47.619 0.00 0.00 39.69 5.19
7785 8698 1.740025 GAGCCAAAAATGCTAGACGCT 59.260 47.619 0.00 0.00 39.69 5.07
7786 8699 1.740025 AGCCAAAAATGCTAGACGCTC 59.260 47.619 0.00 0.00 37.28 5.03
7787 8700 1.468520 GCCAAAAATGCTAGACGCTCA 59.531 47.619 0.00 0.00 40.11 4.26
7788 8701 2.095263 GCCAAAAATGCTAGACGCTCAA 60.095 45.455 0.00 0.00 40.11 3.02
7789 8702 3.428045 GCCAAAAATGCTAGACGCTCAAT 60.428 43.478 0.00 0.00 40.11 2.57
7790 8703 4.737054 CCAAAAATGCTAGACGCTCAATT 58.263 39.130 0.00 0.00 40.11 2.32
7791 8704 4.560035 CCAAAAATGCTAGACGCTCAATTG 59.440 41.667 0.00 0.00 40.11 2.32
7792 8705 4.361451 AAAATGCTAGACGCTCAATTGG 57.639 40.909 5.42 0.00 40.11 3.16
7793 8706 1.959042 ATGCTAGACGCTCAATTGGG 58.041 50.000 5.42 2.47 40.11 4.12
7794 8707 0.613260 TGCTAGACGCTCAATTGGGT 59.387 50.000 7.27 2.34 40.11 4.51
7795 8708 1.291132 GCTAGACGCTCAATTGGGTC 58.709 55.000 7.27 11.34 46.14 4.46
7796 8709 1.941325 CTAGACGCTCAATTGGGTCC 58.059 55.000 7.27 0.00 46.71 4.46
7797 8710 1.482593 CTAGACGCTCAATTGGGTCCT 59.517 52.381 7.27 4.53 46.71 3.85
7798 8711 0.250513 AGACGCTCAATTGGGTCCTC 59.749 55.000 7.27 0.00 46.71 3.71
7799 8712 0.250513 GACGCTCAATTGGGTCCTCT 59.749 55.000 7.27 0.00 41.94 3.69
7800 8713 0.250513 ACGCTCAATTGGGTCCTCTC 59.749 55.000 7.27 0.00 0.00 3.20
7801 8714 0.807667 CGCTCAATTGGGTCCTCTCG 60.808 60.000 7.27 0.00 0.00 4.04
7802 8715 0.462759 GCTCAATTGGGTCCTCTCGG 60.463 60.000 7.27 0.00 0.00 4.63
7803 8716 0.179000 CTCAATTGGGTCCTCTCGGG 59.821 60.000 5.42 0.00 0.00 5.14
7804 8717 0.252513 TCAATTGGGTCCTCTCGGGA 60.253 55.000 5.42 0.00 42.77 5.14
7805 8718 0.179000 CAATTGGGTCCTCTCGGGAG 59.821 60.000 4.93 4.93 46.10 4.30
7806 8719 0.252742 AATTGGGTCCTCTCGGGAGT 60.253 55.000 12.26 0.00 46.10 3.85
7807 8720 0.978146 ATTGGGTCCTCTCGGGAGTG 60.978 60.000 12.26 2.83 46.10 3.51
7808 8721 2.760385 GGGTCCTCTCGGGAGTGG 60.760 72.222 12.26 9.91 46.10 4.00
7809 8722 2.359404 GGTCCTCTCGGGAGTGGA 59.641 66.667 12.26 13.88 46.10 4.02
7812 8725 3.711849 TCCTCTCGGGAGTGGAATT 57.288 52.632 12.26 0.00 45.11 2.17
7813 8726 1.486211 TCCTCTCGGGAGTGGAATTC 58.514 55.000 12.26 0.00 45.11 2.17
7814 8727 0.466124 CCTCTCGGGAGTGGAATTCC 59.534 60.000 18.17 18.17 42.98 3.01
7815 8728 1.490574 CTCTCGGGAGTGGAATTCCT 58.509 55.000 24.73 5.96 43.30 3.36
7816 8729 1.834263 CTCTCGGGAGTGGAATTCCTT 59.166 52.381 24.73 13.33 43.30 3.36
7817 8730 1.831736 TCTCGGGAGTGGAATTCCTTC 59.168 52.381 24.73 20.12 43.30 3.46
7818 8731 1.555075 CTCGGGAGTGGAATTCCTTCA 59.445 52.381 24.73 2.19 43.30 3.02
7819 8732 1.555075 TCGGGAGTGGAATTCCTTCAG 59.445 52.381 24.73 17.53 43.30 3.02
7820 8733 1.756430 GGGAGTGGAATTCCTTCAGC 58.244 55.000 24.73 13.05 43.30 4.26
7821 8734 1.283321 GGGAGTGGAATTCCTTCAGCT 59.717 52.381 24.73 14.13 43.30 4.24
7822 8735 2.505819 GGGAGTGGAATTCCTTCAGCTA 59.494 50.000 24.73 0.00 43.30 3.32
7823 8736 3.137360 GGGAGTGGAATTCCTTCAGCTAT 59.863 47.826 24.73 2.52 43.30 2.97
7824 8737 4.348168 GGGAGTGGAATTCCTTCAGCTATA 59.652 45.833 24.73 0.00 43.30 1.31
7825 8738 5.013599 GGGAGTGGAATTCCTTCAGCTATAT 59.986 44.000 24.73 1.64 43.30 0.86
7826 8739 6.169800 GGAGTGGAATTCCTTCAGCTATATC 58.830 44.000 24.73 9.50 40.07 1.63
7827 8740 6.013812 GGAGTGGAATTCCTTCAGCTATATCT 60.014 42.308 24.73 6.37 40.07 1.98
7907 8820 2.483014 TCCCACTAATCAAACCACCG 57.517 50.000 0.00 0.00 0.00 4.94
7910 8823 0.446222 CACTAATCAAACCACCGCCG 59.554 55.000 0.00 0.00 0.00 6.46
7911 8824 0.035739 ACTAATCAAACCACCGCCGT 59.964 50.000 0.00 0.00 0.00 5.68
7913 8826 2.289569 ACTAATCAAACCACCGCCGTAA 60.290 45.455 0.00 0.00 0.00 3.18
7916 8829 2.281692 AAACCACCGCCGTAACCC 60.282 61.111 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.837093 TCCCCTCTTGTTATGTTGTAGG 57.163 45.455 0.00 0.00 0.00 3.18
47 48 4.042187 AGGCAACAGAGTCCTTTTATGTCT 59.958 41.667 0.00 0.00 41.41 3.41
64 65 1.478105 CCCTCCTGCAATTTAGGCAAC 59.522 52.381 1.34 0.00 41.39 4.17
128 131 5.724328 TGGTAAGAGACATGTCAGACAATC 58.276 41.667 27.02 14.52 0.00 2.67
180 183 2.496817 GGCAGGCCTCGAGTACAG 59.503 66.667 12.31 1.72 0.00 2.74
181 184 3.075005 GGGCAGGCCTCGAGTACA 61.075 66.667 12.31 0.00 36.10 2.90
183 186 2.041922 ATGGGCAGGCCTCGAGTA 60.042 61.111 15.38 0.00 36.10 2.59
184 187 3.790437 CATGGGCAGGCCTCGAGT 61.790 66.667 15.38 0.00 36.10 4.18
185 188 2.541547 TTTCATGGGCAGGCCTCGAG 62.542 60.000 15.38 5.13 36.10 4.04
186 189 2.135903 TTTTCATGGGCAGGCCTCGA 62.136 55.000 15.38 7.70 36.10 4.04
187 190 1.678635 TTTTCATGGGCAGGCCTCG 60.679 57.895 15.38 5.21 36.10 4.63
188 191 1.607801 GGTTTTCATGGGCAGGCCTC 61.608 60.000 15.38 0.00 36.10 4.70
189 192 1.610379 GGTTTTCATGGGCAGGCCT 60.610 57.895 15.38 0.00 36.10 5.19
190 193 2.659063 GGGTTTTCATGGGCAGGCC 61.659 63.158 5.91 5.91 0.00 5.19
191 194 1.266867 ATGGGTTTTCATGGGCAGGC 61.267 55.000 0.00 0.00 0.00 4.85
192 195 0.826062 GATGGGTTTTCATGGGCAGG 59.174 55.000 0.00 0.00 0.00 4.85
193 196 1.205417 GTGATGGGTTTTCATGGGCAG 59.795 52.381 0.00 0.00 0.00 4.85
194 197 1.265236 GTGATGGGTTTTCATGGGCA 58.735 50.000 0.00 0.00 0.00 5.36
278 281 0.735287 GTCTCCCCGCGTTTGTAGTC 60.735 60.000 4.92 0.00 0.00 2.59
281 284 2.203972 CTCGTCTCCCCGCGTTTGTA 62.204 60.000 4.92 0.00 0.00 2.41
312 315 0.390472 GGGTCTCTTCGCCTTGTCTG 60.390 60.000 0.00 0.00 0.00 3.51
320 323 2.125633 GGTTCGGGGTCTCTTCGC 60.126 66.667 0.00 0.00 0.00 4.70
419 422 4.448340 GAGGGGTGGGATGGGGGA 62.448 72.222 0.00 0.00 0.00 4.81
425 428 3.090532 GGAAGCGAGGGGTGGGAT 61.091 66.667 0.00 0.00 0.00 3.85
444 447 0.240945 GACACACAAGCGAAATGGGG 59.759 55.000 0.00 0.00 0.00 4.96
489 493 0.391228 CAAAGGAAAACAACCCCGGG 59.609 55.000 15.80 15.80 0.00 5.73
498 502 6.811954 TGGTTGGATTAAGTCAAAGGAAAAC 58.188 36.000 0.00 0.00 0.00 2.43
513 517 2.637165 AGTCCTCTTCCTGGTTGGATT 58.363 47.619 0.00 0.00 45.68 3.01
529 533 3.909258 TTCGCACGGCTCGAAGTCC 62.909 63.158 1.50 0.00 40.49 3.85
596 600 3.937706 CAGACGAGAAATGGCAAGAAGAT 59.062 43.478 0.00 0.00 0.00 2.40
623 631 1.003233 GGGGGCGAGAAGAAGAAGAAA 59.997 52.381 0.00 0.00 0.00 2.52
694 702 2.184322 CCTGGATGTGGACGGACG 59.816 66.667 0.00 0.00 0.00 4.79
772 780 1.535204 ATCCCGGCAAAGCAACAAGG 61.535 55.000 0.00 0.00 0.00 3.61
780 788 0.450184 CGTTACCAATCCCGGCAAAG 59.550 55.000 0.00 0.00 0.00 2.77
820 828 3.006752 GTGGCAAATCAAACTCCCATCAA 59.993 43.478 0.00 0.00 0.00 2.57
910 918 1.422024 TCTCCCGATCCCAAACAAACA 59.578 47.619 0.00 0.00 0.00 2.83
976 984 2.045926 CGGGGAACTTGCCTCAGG 60.046 66.667 0.00 0.00 0.00 3.86
990 998 3.854669 AGCCTCATCTTCGCCGGG 61.855 66.667 2.18 0.00 0.00 5.73
991 999 2.587194 CAGCCTCATCTTCGCCGG 60.587 66.667 0.00 0.00 0.00 6.13
1224 1232 1.153289 CTGGCCCAGGAAGTCATCG 60.153 63.158 1.63 0.00 0.00 3.84
1274 1282 0.894184 ACCGAGCGAGAAGTTCTCCA 60.894 55.000 24.01 0.00 40.34 3.86
1339 1347 9.620660 GAAGTCGAAACAATTACCACAATTAAT 57.379 29.630 0.00 0.00 0.00 1.40
1342 1350 6.039941 TGGAAGTCGAAACAATTACCACAATT 59.960 34.615 0.00 0.00 0.00 2.32
1368 1376 6.024049 CGTCCATGAGCAAATAGAGAAAAAC 58.976 40.000 0.00 0.00 0.00 2.43
1417 1537 7.816031 ACTGAATCCATATGCAAAAAGACAAAG 59.184 33.333 0.00 0.00 0.00 2.77
1453 1574 5.778161 TGACTACATGCTGTAATTTCACG 57.222 39.130 0.00 0.00 31.67 4.35
1564 1685 6.761731 CAGGATGCAACGAAATAACAAAAA 57.238 33.333 0.00 0.00 0.00 1.94
1646 1767 5.349817 AGTTAGTTCAGTTGCAAGATCATCG 59.650 40.000 0.00 0.00 0.00 3.84
1686 1807 5.220154 CGCTTTGACTTGATTGCAATGAATC 60.220 40.000 18.59 13.84 32.68 2.52
1700 1821 2.012673 GATGATCCTGCGCTTTGACTT 58.987 47.619 9.73 0.00 0.00 3.01
1716 1837 1.071228 AGCTAATGCCGCTGATGATGA 59.929 47.619 0.00 0.00 40.80 2.92
1724 1845 3.475566 TCTTCATAAGCTAATGCCGCT 57.524 42.857 0.00 0.00 40.80 5.52
1727 1848 7.168804 GCTTCATTTTCTTCATAAGCTAATGCC 59.831 37.037 0.00 0.00 40.80 4.40
1811 1932 1.872952 CTCACTTCGCCACATTTGTCA 59.127 47.619 0.00 0.00 0.00 3.58
2012 2133 1.541147 TCAAATACTGCTGGTGCTTGC 59.459 47.619 0.00 0.00 40.48 4.01
2062 2183 7.375106 AGTTCAGCAAATGTAATCTCTGAAG 57.625 36.000 3.10 0.00 36.89 3.02
2660 2781 3.007723 GCTCCTTATCTGATCCAGCATCA 59.992 47.826 0.00 0.00 39.39 3.07
2747 2868 4.654262 AGAGAGGACAAGACACCAAAGTTA 59.346 41.667 0.00 0.00 0.00 2.24
2865 2986 2.012673 GCCCATGACAATCTCACTGAC 58.987 52.381 0.00 0.00 0.00 3.51
2885 3006 2.420022 CACCTGAAGAAACAATAGCCCG 59.580 50.000 0.00 0.00 0.00 6.13
2962 3083 6.717540 TGATGAGAAGATAAAAACGGGGAAAA 59.282 34.615 0.00 0.00 0.00 2.29
3004 3125 3.560025 CCAAAGAGGTTCAGGTACATGCT 60.560 47.826 1.79 0.00 0.00 3.79
3145 3279 7.284716 GGTATTTACCCATAAGTTTCCTTGAGG 59.715 40.741 0.00 0.00 40.53 3.86
3233 3367 4.796618 GCGTGAGGGAAACTATTAGCCTAG 60.797 50.000 0.00 0.00 0.00 3.02
3254 3388 0.448990 CACCATGATCACCAACTGCG 59.551 55.000 0.00 0.00 0.00 5.18
3326 3460 1.742831 GCATCGACTGGTGCCAAATTA 59.257 47.619 0.00 0.00 35.35 1.40
3549 3683 9.474313 AAATTATTTAGTTTCCAGATGCAGGTA 57.526 29.630 0.00 0.00 0.00 3.08
3593 3727 5.508567 TCCATGGCATCAAACTCAAAGATA 58.491 37.500 6.96 0.00 0.00 1.98
3641 3775 7.218228 TGGTCCATCAAAATCATATACATGC 57.782 36.000 0.00 0.00 31.73 4.06
3710 3844 5.276773 CGCTAGCTCTGACAGATTTGATTTC 60.277 44.000 13.93 0.00 0.00 2.17
4190 4489 4.927267 ATATGTTCCACTTCCAACTCCA 57.073 40.909 0.00 0.00 0.00 3.86
4204 4503 9.647918 TCTCCCCATGATACTCTATATATGTTC 57.352 37.037 0.00 0.00 0.00 3.18
4214 4513 7.713518 TCAATATAGTCTCCCCATGATACTCT 58.286 38.462 0.00 0.00 33.00 3.24
4218 4517 9.566331 AAGAATCAATATAGTCTCCCCATGATA 57.434 33.333 0.00 0.00 0.00 2.15
4299 4850 4.543590 TCAGAGAAGTTCAAGCCTTAGG 57.456 45.455 5.50 0.00 0.00 2.69
4301 4852 6.114187 TGAATCAGAGAAGTTCAAGCCTTA 57.886 37.500 5.50 0.00 0.00 2.69
4302 4853 4.978099 TGAATCAGAGAAGTTCAAGCCTT 58.022 39.130 5.50 0.00 0.00 4.35
4303 4854 4.630644 TGAATCAGAGAAGTTCAAGCCT 57.369 40.909 5.50 0.00 0.00 4.58
4304 4855 6.991531 AGATATGAATCAGAGAAGTTCAAGCC 59.008 38.462 5.50 0.00 35.70 4.35
4305 4856 8.436046 AAGATATGAATCAGAGAAGTTCAAGC 57.564 34.615 5.50 0.00 35.70 4.01
4307 4858 9.823647 GGTAAGATATGAATCAGAGAAGTTCAA 57.176 33.333 5.50 0.00 35.70 2.69
4308 4859 8.424918 GGGTAAGATATGAATCAGAGAAGTTCA 58.575 37.037 5.50 0.00 36.42 3.18
4430 4981 2.083774 CAGGCCAGCATCGTTTTAAGA 58.916 47.619 5.01 0.00 0.00 2.10
4431 4982 2.083774 TCAGGCCAGCATCGTTTTAAG 58.916 47.619 5.01 0.00 0.00 1.85
4438 4989 1.154197 CACATATCAGGCCAGCATCG 58.846 55.000 5.01 0.00 0.00 3.84
4488 5039 6.828273 TCATAGTTGATAAAAGGTCCCACATG 59.172 38.462 0.00 0.00 0.00 3.21
4495 5046 9.383519 TGAGATGTTCATAGTTGATAAAAGGTC 57.616 33.333 0.00 0.00 0.00 3.85
4747 5381 1.692411 GGGGAATTGCCTGTATGTCC 58.308 55.000 16.31 0.00 36.66 4.02
4888 5522 1.093972 TGGCCACACTAAATGATGCG 58.906 50.000 0.00 0.00 31.70 4.73
4965 5599 7.991460 GGTTGCTATAGGTAAACCTTTGAGTAT 59.009 37.037 7.04 0.00 46.09 2.12
4991 5625 0.107456 ATTGATGGTCTAGGCTGGCG 59.893 55.000 0.00 0.00 0.00 5.69
5213 5848 5.174943 GGAATCGTCAACACCAACAAAAATC 59.825 40.000 0.00 0.00 0.00 2.17
5314 5949 7.288810 AGTTCATCATAAGCAGTTCCAAAAA 57.711 32.000 0.00 0.00 0.00 1.94
5418 6053 5.705397 TCTCCATGACTTTCATCTCCAAT 57.295 39.130 0.00 0.00 34.28 3.16
5870 6509 8.898761 GGATTTCAACAAACCCACTTAAAATTT 58.101 29.630 0.00 0.00 0.00 1.82
5872 6511 6.995686 GGGATTTCAACAAACCCACTTAAAAT 59.004 34.615 0.00 0.00 34.95 1.82
5873 6512 6.157123 AGGGATTTCAACAAACCCACTTAAAA 59.843 34.615 0.00 0.00 36.23 1.52
5874 6513 5.663556 AGGGATTTCAACAAACCCACTTAAA 59.336 36.000 0.00 0.00 36.23 1.52
5875 6514 5.069781 CAGGGATTTCAACAAACCCACTTAA 59.930 40.000 0.00 0.00 36.23 1.85
5876 6515 4.586841 CAGGGATTTCAACAAACCCACTTA 59.413 41.667 0.00 0.00 36.23 2.24
5877 6516 3.387699 CAGGGATTTCAACAAACCCACTT 59.612 43.478 0.00 0.00 36.23 3.16
5878 6517 2.965147 CAGGGATTTCAACAAACCCACT 59.035 45.455 0.00 0.00 36.23 4.00
5879 6518 2.698274 ACAGGGATTTCAACAAACCCAC 59.302 45.455 0.00 0.00 36.23 4.61
5880 6519 3.039252 ACAGGGATTTCAACAAACCCA 57.961 42.857 0.00 0.00 36.23 4.51
5881 6520 4.770010 TCATACAGGGATTTCAACAAACCC 59.230 41.667 0.00 0.00 35.00 4.11
5882 6521 5.622233 GCTCATACAGGGATTTCAACAAACC 60.622 44.000 0.00 0.00 0.00 3.27
6019 6661 7.542025 GTCTTTCAAACCAGCAGATGATATTT 58.458 34.615 0.00 0.00 0.00 1.40
6021 6663 5.295292 CGTCTTTCAAACCAGCAGATGATAT 59.705 40.000 0.00 0.00 0.00 1.63
6022 6664 4.631377 CGTCTTTCAAACCAGCAGATGATA 59.369 41.667 0.00 0.00 0.00 2.15
6023 6665 3.438087 CGTCTTTCAAACCAGCAGATGAT 59.562 43.478 0.00 0.00 0.00 2.45
6024 6666 2.807967 CGTCTTTCAAACCAGCAGATGA 59.192 45.455 0.00 0.00 0.00 2.92
6025 6667 2.807967 TCGTCTTTCAAACCAGCAGATG 59.192 45.455 0.00 0.00 0.00 2.90
6026 6668 3.126001 TCGTCTTTCAAACCAGCAGAT 57.874 42.857 0.00 0.00 0.00 2.90
6037 6679 1.864711 CTGAAGCCGTTTCGTCTTTCA 59.135 47.619 0.00 0.00 38.71 2.69
6222 6905 2.682352 GGCCTCTGCAAATTCTCTTCTC 59.318 50.000 0.00 0.00 40.13 2.87
6236 6919 3.482156 AGCTTGTATGTATGGCCTCTG 57.518 47.619 3.32 0.00 0.00 3.35
6239 6922 5.505780 TGTTTTAGCTTGTATGTATGGCCT 58.494 37.500 3.32 0.00 0.00 5.19
6536 7219 5.738619 ACAAAGGTGTCCTTCTTTTGTTT 57.261 34.783 1.36 0.00 43.92 2.83
6581 7264 1.952296 CTGCATTAAGATGGAGGGTGC 59.048 52.381 0.00 0.00 45.07 5.01
6597 7280 0.251297 ACTTGGTGCTATTGGCTGCA 60.251 50.000 0.50 0.00 42.39 4.41
6604 7287 4.082125 CAAAGGAGGAACTTGGTGCTATT 58.918 43.478 0.00 0.00 41.55 1.73
6607 7290 1.479389 CCAAAGGAGGAACTTGGTGCT 60.479 52.381 0.00 0.00 41.55 4.40
6714 7397 8.681486 TTGATACTTTATATGAAGCTGCACAT 57.319 30.769 0.00 14.46 0.00 3.21
6853 7536 1.410517 TCCTTTAGGCGAGCAGATGAG 59.589 52.381 0.00 0.00 34.44 2.90
6905 7588 5.874093 GGATGAATGATCCTATCTGGTGTT 58.126 41.667 0.00 0.00 46.77 3.32
7160 7846 4.700700 TGTCTGTGCTGATTGGATCTATG 58.299 43.478 0.00 0.00 0.00 2.23
7161 7847 4.743045 GCTGTCTGTGCTGATTGGATCTAT 60.743 45.833 0.00 0.00 0.00 1.98
7182 7868 1.251251 GTCTGGTCCAAATTGCTGCT 58.749 50.000 0.00 0.00 0.00 4.24
7247 7933 3.818180 TCAACAAATTGCAGGCCAAATT 58.182 36.364 5.01 5.32 36.92 1.82
7249 7935 2.996249 TCAACAAATTGCAGGCCAAA 57.004 40.000 5.01 0.00 36.92 3.28
7250 7936 2.633967 AGATCAACAAATTGCAGGCCAA 59.366 40.909 5.01 0.00 35.63 4.52
7283 7969 9.573133 TGCTATCATATGTATACAAGACAATCG 57.427 33.333 10.14 0.00 0.00 3.34
7302 7988 4.309933 CACAGAGAACAACACTGCTATCA 58.690 43.478 0.00 0.00 40.05 2.15
7324 8010 4.794439 GCGGCCCAATTCCAACGC 62.794 66.667 0.00 0.00 40.19 4.84
7340 8026 3.569701 TCAATGAAACAGGGAGTTGAAGC 59.430 43.478 0.00 0.00 41.19 3.86
7509 8202 1.349688 TGGCCAGAAGATTACAACCGT 59.650 47.619 0.00 0.00 0.00 4.83
7539 8323 1.214305 AGCATCAGGGCCAAGGGTTA 61.214 55.000 6.18 0.00 0.00 2.85
7540 8324 2.037847 GCATCAGGGCCAAGGGTT 59.962 61.111 6.18 0.00 0.00 4.11
7542 8326 2.294170 ATCAGCATCAGGGCCAAGGG 62.294 60.000 6.18 0.00 0.00 3.95
7545 8329 0.040058 ACAATCAGCATCAGGGCCAA 59.960 50.000 6.18 0.00 0.00 4.52
7559 8343 0.391130 TACCTCAGCGTGCCACAATC 60.391 55.000 0.00 0.00 0.00 2.67
7578 8362 1.453155 GAAGGTCACACATGCGGATT 58.547 50.000 0.00 0.00 0.00 3.01
7602 8386 7.397476 ACGCTCTTATATTATGAGATGAAGGGA 59.603 37.037 0.00 0.00 33.20 4.20
7603 8387 7.551585 ACGCTCTTATATTATGAGATGAAGGG 58.448 38.462 0.00 0.21 33.20 3.95
7604 8388 8.994429 AACGCTCTTATATTATGAGATGAAGG 57.006 34.615 0.00 0.00 33.20 3.46
7664 8456 8.425237 TGGTACTCCATTCGTTCCATAATATA 57.575 34.615 0.00 0.00 39.03 0.86
7667 8459 5.623956 TGGTACTCCATTCGTTCCATAAT 57.376 39.130 0.00 0.00 39.03 1.28
7668 8460 5.423704 TTGGTACTCCATTCGTTCCATAA 57.576 39.130 0.00 0.00 43.91 1.90
7669 8461 5.423704 TTTGGTACTCCATTCGTTCCATA 57.576 39.130 0.00 0.00 43.91 2.74
7671 8463 3.773418 TTTGGTACTCCATTCGTTCCA 57.227 42.857 0.00 0.00 43.91 3.53
7672 8464 6.403964 GGTTTATTTGGTACTCCATTCGTTCC 60.404 42.308 0.00 0.00 43.91 3.62
7676 8468 6.094881 ACATGGTTTATTTGGTACTCCATTCG 59.905 38.462 0.00 0.00 43.91 3.34
7677 8469 7.257722 CACATGGTTTATTTGGTACTCCATTC 58.742 38.462 0.00 0.00 43.91 2.67
7680 8472 4.461081 GCACATGGTTTATTTGGTACTCCA 59.539 41.667 0.00 0.00 42.66 3.86
7706 8619 4.220602 ACCCAATTGAGCTTGTAATGGTTC 59.779 41.667 7.12 0.00 0.00 3.62
7724 8637 1.000486 CTCCCGAGAGAGGACCCAA 60.000 63.158 0.00 0.00 43.39 4.12
7753 8666 5.240183 GCATTTTTGGCTCAGATATAGCTGA 59.760 40.000 19.10 19.10 42.31 4.26
7757 8670 7.148672 CGTCTAGCATTTTTGGCTCAGATATAG 60.149 40.741 0.00 0.00 42.62 1.31
7777 8690 1.482593 AGGACCCAATTGAGCGTCTAG 59.517 52.381 7.12 0.00 0.00 2.43
7778 8691 1.480954 GAGGACCCAATTGAGCGTCTA 59.519 52.381 7.12 0.00 0.00 2.59
7779 8692 0.250513 GAGGACCCAATTGAGCGTCT 59.749 55.000 7.12 0.00 0.00 4.18
7780 8693 0.250513 AGAGGACCCAATTGAGCGTC 59.749 55.000 7.12 9.10 0.00 5.19
7781 8694 0.250513 GAGAGGACCCAATTGAGCGT 59.749 55.000 7.12 0.00 0.00 5.07
7782 8695 0.807667 CGAGAGGACCCAATTGAGCG 60.808 60.000 7.12 0.00 0.00 5.03
7783 8696 3.071580 CGAGAGGACCCAATTGAGC 57.928 57.895 7.12 0.00 0.00 4.26
7793 8706 4.116173 GGAATTCCACTCCCGAGAGGAC 62.116 59.091 20.04 0.65 45.66 3.85
7794 8707 1.965318 GGAATTCCACTCCCGAGAGGA 60.965 57.143 20.04 6.77 45.70 3.71
7795 8708 0.466124 GGAATTCCACTCCCGAGAGG 59.534 60.000 20.04 2.03 45.11 3.69
7796 8709 1.490574 AGGAATTCCACTCCCGAGAG 58.509 55.000 26.22 0.00 46.36 3.20
7797 8710 1.831736 GAAGGAATTCCACTCCCGAGA 59.168 52.381 26.22 0.00 38.89 4.04
7798 8711 1.555075 TGAAGGAATTCCACTCCCGAG 59.445 52.381 26.22 0.00 38.89 4.63
7799 8712 1.555075 CTGAAGGAATTCCACTCCCGA 59.445 52.381 26.22 6.18 38.89 5.14
7800 8713 2.014068 GCTGAAGGAATTCCACTCCCG 61.014 57.143 26.22 15.07 38.89 5.14
7801 8714 1.283321 AGCTGAAGGAATTCCACTCCC 59.717 52.381 26.22 14.28 38.89 4.30
7802 8715 2.797177 AGCTGAAGGAATTCCACTCC 57.203 50.000 26.22 11.94 38.89 3.85
7803 8716 6.873076 CAGATATAGCTGAAGGAATTCCACTC 59.127 42.308 26.22 20.54 38.14 3.51
7804 8717 6.556495 TCAGATATAGCTGAAGGAATTCCACT 59.444 38.462 26.22 12.84 41.65 4.00
7805 8718 6.763355 TCAGATATAGCTGAAGGAATTCCAC 58.237 40.000 26.22 18.70 41.65 4.02
7806 8719 6.519721 GCTCAGATATAGCTGAAGGAATTCCA 60.520 42.308 26.22 5.01 43.75 3.53
7807 8720 5.874261 GCTCAGATATAGCTGAAGGAATTCC 59.126 44.000 20.45 17.31 43.75 3.01
7808 8721 5.874261 GGCTCAGATATAGCTGAAGGAATTC 59.126 44.000 20.45 0.00 43.75 2.17
7809 8722 5.309020 TGGCTCAGATATAGCTGAAGGAATT 59.691 40.000 20.45 0.00 43.75 2.17
7810 8723 4.842948 TGGCTCAGATATAGCTGAAGGAAT 59.157 41.667 20.45 0.00 43.75 3.01
7811 8724 4.226384 TGGCTCAGATATAGCTGAAGGAA 58.774 43.478 20.45 5.40 43.75 3.36
7812 8725 3.849527 TGGCTCAGATATAGCTGAAGGA 58.150 45.455 20.45 5.45 43.75 3.36
7813 8726 4.613925 TTGGCTCAGATATAGCTGAAGG 57.386 45.455 20.45 11.68 43.75 3.46
7814 8727 6.932356 TTTTTGGCTCAGATATAGCTGAAG 57.068 37.500 20.45 15.09 43.75 3.02
7815 8728 6.238842 GCATTTTTGGCTCAGATATAGCTGAA 60.239 38.462 20.45 4.56 43.75 3.02
7816 8729 5.240183 GCATTTTTGGCTCAGATATAGCTGA 59.760 40.000 19.10 19.10 42.31 4.26
7817 8730 5.241064 AGCATTTTTGGCTCAGATATAGCTG 59.759 40.000 11.87 11.87 36.81 4.24
7818 8731 5.383476 AGCATTTTTGGCTCAGATATAGCT 58.617 37.500 0.00 0.00 36.81 3.32
7819 8732 5.702349 AGCATTTTTGGCTCAGATATAGC 57.298 39.130 0.00 0.00 36.81 2.97
7820 8733 6.128063 GCCTAGCATTTTTGGCTCAGATATAG 60.128 42.308 0.00 0.00 42.62 1.31
7821 8734 5.707298 GCCTAGCATTTTTGGCTCAGATATA 59.293 40.000 0.00 0.00 42.62 0.86
7822 8735 4.522022 GCCTAGCATTTTTGGCTCAGATAT 59.478 41.667 0.00 0.00 42.62 1.63
7823 8736 3.885297 GCCTAGCATTTTTGGCTCAGATA 59.115 43.478 0.00 0.00 42.62 1.98
7824 8737 2.692041 GCCTAGCATTTTTGGCTCAGAT 59.308 45.455 0.00 0.00 42.62 2.90
7825 8738 2.094675 GCCTAGCATTTTTGGCTCAGA 58.905 47.619 0.00 0.00 42.62 3.27
7826 8739 2.573941 GCCTAGCATTTTTGGCTCAG 57.426 50.000 0.00 0.00 42.62 3.35
7866 8779 8.986991 TGGGAAAGGTAATTACGTAGGTTTATA 58.013 33.333 11.01 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.