Multiple sequence alignment - TraesCS1D01G200200

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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 TraesCS1D01G200200 chr1D 100.000 6006 0 0 1 6006 282959656 282953651 0.000000e+00 11092.0
1 TraesCS1D01G200200 chr1B 95.064 1722 62 14 2141 3847 384338766 384337053 0.000000e+00 2687.0
2 TraesCS1D01G200200 chr1B 94.246 1512 53 22 655 2143 384340353 384338853 0.000000e+00 2279.0
3 TraesCS1D01G200200 chr1B 92.093 1467 62 25 3889 5345 384337042 384335620 0.000000e+00 2017.0
4 TraesCS1D01G200200 chr1B 89.590 586 32 13 5345 5902 384335593 384335009 0.000000e+00 717.0
5 TraesCS1D01G200200 chr1B 78.000 600 79 31 135 691 384340944 384340355 1.610000e-85 327.0
6 TraesCS1D01G200200 chr1B 98.131 107 2 0 5898 6004 384303040 384302934 2.860000e-43 187.0
7 TraesCS1D01G200200 chr1A 90.558 1917 115 34 223 2085 354949160 354947256 0.000000e+00 2477.0
8 TraesCS1D01G200200 chr1A 89.704 1991 129 38 3304 5250 354945494 354943536 0.000000e+00 2471.0
9 TraesCS1D01G200200 chr1A 91.598 1452 79 19 2083 3523 354947210 354945791 0.000000e+00 1965.0
10 TraesCS1D01G200200 chr1A 87.059 680 64 14 5345 6006 354943476 354942803 0.000000e+00 747.0
11 TraesCS1D01G200200 chr1A 79.570 279 33 11 131 388 354949875 354949600 1.720000e-40 178.0
12 TraesCS1D01G200200 chr1A 90.588 85 5 2 3526 3607 354945663 354945579 6.360000e-20 110.0
13 TraesCS1D01G200200 chr1A 94.000 50 3 0 1 50 354949995 354949946 6.450000e-10 76.8
14 TraesCS1D01G200200 chr1A 91.304 46 4 0 131 176 354949204 354949159 5.030000e-06 63.9
15 TraesCS1D01G200200 chr1A 100.000 33 0 0 100 132 97730024 97730056 1.810000e-05 62.1
16 TraesCS1D01G200200 chr6A 100.000 28 0 0 105 132 323404490 323404463 1.100000e-02 52.8


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 TraesCS1D01G200200 chr1D 282953651 282959656 6005 True 11092.0000 11092 100.000000 1 6006 1 chr1D.!!$R1 6005
1 TraesCS1D01G200200 chr1B 384335009 384340944 5935 True 1605.4000 2687 89.798600 135 5902 5 chr1B.!!$R2 5767
2 TraesCS1D01G200200 chr1A 354942803 354949995 7192 True 1011.0875 2477 89.297625 1 6006 8 chr1A.!!$R1 6005

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
760 1496 0.179097 TTTGGCCAAAACGTGCTTCC 60.179 50.000 28.57 0.0 0.00 3.46 F
892 1651 0.790814 GGAAGGAAGAAGAACGCACG 59.209 55.000 0.00 0.0 0.00 5.34 F
1572 2343 2.025727 GATTCCGACGCCGACGAT 59.974 61.111 11.04 0.0 43.93 3.73 F
2366 3278 0.032912 TGCCATCCTCCCACTACGTA 60.033 55.000 0.00 0.0 0.00 3.57 F
3864 5316 0.254747 GCTGGCCCTACAATACACCA 59.745 55.000 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2922 0.827368 TTGTTTGCCTTCACCAACCC 59.173 50.000 0.00 0.00 0.00 4.11 R
2280 3191 1.066929 CAAAAAGGGGAGGATTTGCCG 60.067 52.381 0.00 0.00 43.43 5.69 R
2575 3491 2.089201 CAACTGCATCCTCATCTGCAA 58.911 47.619 0.00 0.00 46.87 4.08 R
4201 5658 0.671251 TTTTTACCTGCTTGGCCACG 59.329 50.000 3.88 4.24 40.22 4.94 R
5289 6768 0.111089 CAAGTTCGTCGCTGTTGAGC 60.111 55.000 0.00 0.00 42.37 4.26 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
21 22 4.678509 GGCAACTCAATGTCGTAAATCA 57.321 40.909 0.00 0.00 0.00 2.57
22 23 5.041951 GGCAACTCAATGTCGTAAATCAA 57.958 39.130 0.00 0.00 0.00 2.57
23 24 5.457140 GGCAACTCAATGTCGTAAATCAAA 58.543 37.500 0.00 0.00 0.00 2.69
24 25 5.342259 GGCAACTCAATGTCGTAAATCAAAC 59.658 40.000 0.00 0.00 0.00 2.93
25 26 5.342259 GCAACTCAATGTCGTAAATCAAACC 59.658 40.000 0.00 0.00 0.00 3.27
26 27 5.277601 ACTCAATGTCGTAAATCAAACCG 57.722 39.130 0.00 0.00 0.00 4.44
27 28 4.073169 TCAATGTCGTAAATCAAACCGC 57.927 40.909 0.00 0.00 0.00 5.68
28 29 3.749088 TCAATGTCGTAAATCAAACCGCT 59.251 39.130 0.00 0.00 0.00 5.52
29 30 4.214545 TCAATGTCGTAAATCAAACCGCTT 59.785 37.500 0.00 0.00 0.00 4.68
30 31 5.408909 TCAATGTCGTAAATCAAACCGCTTA 59.591 36.000 0.00 0.00 0.00 3.09
31 32 5.866335 ATGTCGTAAATCAAACCGCTTAA 57.134 34.783 0.00 0.00 0.00 1.85
32 33 5.866335 TGTCGTAAATCAAACCGCTTAAT 57.134 34.783 0.00 0.00 0.00 1.40
33 34 5.623335 TGTCGTAAATCAAACCGCTTAATG 58.377 37.500 0.00 0.00 0.00 1.90
34 35 4.494410 GTCGTAAATCAAACCGCTTAATGC 59.506 41.667 0.00 0.00 38.57 3.56
35 36 4.154375 TCGTAAATCAAACCGCTTAATGCA 59.846 37.500 0.00 0.00 43.06 3.96
36 37 5.034152 CGTAAATCAAACCGCTTAATGCAT 58.966 37.500 0.00 0.00 43.06 3.96
37 38 5.171337 CGTAAATCAAACCGCTTAATGCATC 59.829 40.000 0.00 0.00 43.06 3.91
38 39 4.989279 AATCAAACCGCTTAATGCATCT 57.011 36.364 0.00 0.00 43.06 2.90
39 40 4.989279 ATCAAACCGCTTAATGCATCTT 57.011 36.364 0.00 0.00 43.06 2.40
40 41 4.355543 TCAAACCGCTTAATGCATCTTC 57.644 40.909 0.00 0.00 43.06 2.87
41 42 3.755905 TCAAACCGCTTAATGCATCTTCA 59.244 39.130 0.00 0.00 43.06 3.02
42 43 4.398988 TCAAACCGCTTAATGCATCTTCAT 59.601 37.500 0.00 0.00 43.06 2.57
43 44 5.588246 TCAAACCGCTTAATGCATCTTCATA 59.412 36.000 0.00 0.00 43.06 2.15
44 45 6.262944 TCAAACCGCTTAATGCATCTTCATAT 59.737 34.615 0.00 0.00 43.06 1.78
45 46 6.639632 AACCGCTTAATGCATCTTCATATT 57.360 33.333 0.00 0.00 43.06 1.28
46 47 7.744087 AACCGCTTAATGCATCTTCATATTA 57.256 32.000 0.00 0.00 43.06 0.98
47 48 7.928307 ACCGCTTAATGCATCTTCATATTAT 57.072 32.000 0.00 0.00 43.06 1.28
48 49 8.340618 ACCGCTTAATGCATCTTCATATTATT 57.659 30.769 0.00 0.00 43.06 1.40
49 50 8.454106 ACCGCTTAATGCATCTTCATATTATTC 58.546 33.333 0.00 0.00 43.06 1.75
50 51 7.912250 CCGCTTAATGCATCTTCATATTATTCC 59.088 37.037 0.00 0.00 43.06 3.01
51 52 8.671921 CGCTTAATGCATCTTCATATTATTCCT 58.328 33.333 0.00 0.00 43.06 3.36
74 75 4.782019 TCAAACCGCTTAATGCATCTTT 57.218 36.364 0.00 0.00 43.06 2.52
84 85 9.722056 CCGCTTAATGCATCTTTATATTATTCC 57.278 33.333 0.00 0.00 43.06 3.01
103 108 6.824305 ATTCCTGAATGACTGTAGGTTTTG 57.176 37.500 0.00 0.00 0.00 2.44
115 120 8.794553 TGACTGTAGGTTTTGTTTTGTTTTCTA 58.205 29.630 0.00 0.00 0.00 2.10
120 125 5.575218 AGGTTTTGTTTTGTTTTCTACTGCG 59.425 36.000 0.00 0.00 0.00 5.18
132 137 1.156736 CTACTGCGTTTCCCAACAGG 58.843 55.000 0.00 0.00 34.40 4.00
133 138 0.470766 TACTGCGTTTCCCAACAGGT 59.529 50.000 0.00 0.00 36.75 4.00
189 214 1.201647 GCGCTGCCTATCGACCTAATA 59.798 52.381 0.00 0.00 0.00 0.98
237 281 1.592223 GTCGCACTACAGGCTCCTT 59.408 57.895 0.00 0.00 0.00 3.36
238 282 0.815734 GTCGCACTACAGGCTCCTTA 59.184 55.000 0.00 0.00 0.00 2.69
279 924 1.521906 CACCGTCGTCACACCCAAA 60.522 57.895 0.00 0.00 0.00 3.28
344 989 3.708220 GAGAGACCAGCCCGCGAAG 62.708 68.421 8.23 0.00 0.00 3.79
357 1002 2.338620 CGAAGGACCTGACACGCA 59.661 61.111 0.00 0.00 0.00 5.24
364 1009 2.214181 GACCTGACACGCACGAGGAT 62.214 60.000 0.00 0.00 0.00 3.24
430 1080 3.147595 CCTGACGATGGCGAGGGA 61.148 66.667 0.00 0.00 41.64 4.20
435 1085 2.356818 GACGATGGCGAGGGAAGGAG 62.357 65.000 0.00 0.00 41.64 3.69
440 1090 4.798682 GCGAGGGAAGGAGGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
457 1107 2.762459 AAGACCGGCGGCAGGATA 60.762 61.111 28.71 0.00 0.00 2.59
517 1179 2.363038 GTTACCCCAACAAACTTCCCAC 59.637 50.000 0.00 0.00 37.09 4.61
616 1284 1.172180 ACATGGGTGACACGCCTTTG 61.172 55.000 18.89 15.30 33.98 2.77
620 1288 1.966451 GGTGACACGCCTTTGAGGG 60.966 63.158 0.00 0.00 35.37 4.30
631 1299 3.234630 TTTGAGGGCGAGACGTGGG 62.235 63.158 0.00 0.00 0.00 4.61
633 1301 3.692406 GAGGGCGAGACGTGGGTT 61.692 66.667 0.00 0.00 0.00 4.11
634 1302 3.644399 GAGGGCGAGACGTGGGTTC 62.644 68.421 0.00 0.00 0.00 3.62
636 1304 2.029964 GGCGAGACGTGGGTTCAA 59.970 61.111 0.00 0.00 0.00 2.69
637 1305 2.027625 GGCGAGACGTGGGTTCAAG 61.028 63.158 0.00 0.00 0.00 3.02
638 1306 1.006571 GCGAGACGTGGGTTCAAGA 60.007 57.895 0.00 0.00 0.00 3.02
639 1307 0.389948 GCGAGACGTGGGTTCAAGAT 60.390 55.000 0.00 0.00 0.00 2.40
641 1309 1.336887 CGAGACGTGGGTTCAAGATGT 60.337 52.381 0.00 0.00 0.00 3.06
653 1344 6.550854 TGGGTTCAAGATGTCATTTTCTTTCT 59.449 34.615 0.00 0.00 29.85 2.52
721 1452 3.859961 CACGAGCATCCACAGTTTACTAG 59.140 47.826 0.00 0.00 0.00 2.57
726 1457 5.238583 AGCATCCACAGTTTACTAGTGTTC 58.761 41.667 5.39 0.00 38.37 3.18
760 1496 0.179097 TTTGGCCAAAACGTGCTTCC 60.179 50.000 28.57 0.00 0.00 3.46
772 1508 0.935898 GTGCTTCCGCTGATGAGATG 59.064 55.000 0.00 0.00 36.97 2.90
799 1541 3.808726 GCTGTTTGCATGAACCAATCAAA 59.191 39.130 0.00 0.00 42.54 2.69
885 1644 2.903784 TGGATCAACGGAAGGAAGAAGA 59.096 45.455 0.00 0.00 0.00 2.87
886 1645 3.326588 TGGATCAACGGAAGGAAGAAGAA 59.673 43.478 0.00 0.00 0.00 2.52
887 1646 3.685272 GGATCAACGGAAGGAAGAAGAAC 59.315 47.826 0.00 0.00 0.00 3.01
892 1651 0.790814 GGAAGGAAGAAGAACGCACG 59.209 55.000 0.00 0.00 0.00 5.34
954 1713 3.056393 TCTCCCGAAAGCAAAGACGAATA 60.056 43.478 0.00 0.00 0.00 1.75
1491 2262 3.384532 GCCCCGGTCGTCCTTGTA 61.385 66.667 0.00 0.00 0.00 2.41
1504 2275 2.232941 GTCCTTGTACCGGAGACATTCA 59.767 50.000 9.46 0.00 0.00 2.57
1572 2343 2.025727 GATTCCGACGCCGACGAT 59.974 61.111 11.04 0.00 43.93 3.73
2076 2849 6.602009 AGGTACATAGCCTACCAAATTTCAAC 59.398 38.462 0.00 0.00 36.80 3.18
2101 2922 7.174946 ACTGTTTGTAGTATTCTGGGAAACATG 59.825 37.037 0.00 0.00 32.45 3.21
2232 3142 4.090057 GGCGAACGTCAGCTTGGC 62.090 66.667 13.64 0.00 0.00 4.52
2280 3191 2.140717 CAAGTTTACGTGGTGGGAGAC 58.859 52.381 0.00 0.00 0.00 3.36
2366 3278 0.032912 TGCCATCCTCCCACTACGTA 60.033 55.000 0.00 0.00 0.00 3.57
2384 3296 7.381139 CACTACGTAAAATTGCCAGTCAAAATT 59.619 33.333 0.00 0.00 38.34 1.82
2385 3297 6.523676 ACGTAAAATTGCCAGTCAAAATTG 57.476 33.333 0.00 0.00 38.34 2.32
2423 3335 4.680237 CCAGCTGACGGTCGCCAA 62.680 66.667 17.39 0.00 0.00 4.52
2575 3491 7.070696 ACCTTAAAGTTCAGCCTACCAATTTTT 59.929 33.333 0.00 0.00 0.00 1.94
2636 3552 8.562052 ACATTACAGACATGTATGTGCATATTG 58.438 33.333 31.12 20.07 41.49 1.90
2651 3567 5.351465 GTGCATATTGTAGATGGGATAACCG 59.649 44.000 0.00 0.00 44.64 4.44
2670 3586 6.462552 AACCGAGTAGGGATTAACTAGTTC 57.537 41.667 12.39 0.00 46.96 3.01
2674 3590 7.125356 ACCGAGTAGGGATTAACTAGTTCAAAT 59.875 37.037 12.39 7.37 46.96 2.32
2919 3835 8.391106 CCAACTGCTTGTAATATTCTGAGTAAC 58.609 37.037 0.00 0.00 0.00 2.50
3198 4114 6.482973 CACCTTGAATTTTGGCATTTGTAGTT 59.517 34.615 0.00 0.00 0.00 2.24
3287 4203 7.817418 ATTGACTTGCCTTTACTTAACTCAA 57.183 32.000 0.00 0.00 0.00 3.02
3452 4886 7.504924 TTTTTATACAACTCCCTTGTGTCTG 57.495 36.000 0.00 0.00 43.38 3.51
3583 5020 5.690464 AGGTAAACAGAATCAGCTCTCAT 57.310 39.130 0.00 0.00 0.00 2.90
3639 5088 7.335127 ACCATTCAGCCTGAATTACCTATAT 57.665 36.000 17.16 0.00 44.03 0.86
3648 5097 9.512748 AGCCTGAATTACCTATATTCTATCCAT 57.487 33.333 0.00 0.00 34.00 3.41
3741 5193 1.154225 GAAACGATGGCTGGTTGCG 60.154 57.895 0.00 0.00 44.05 4.85
3777 5229 6.258230 TGCTTACTTTGATTCAGATGGTTG 57.742 37.500 0.00 0.00 0.00 3.77
3847 5299 3.041211 TCAGGTATGCCTTCATGTAGCT 58.959 45.455 0.00 0.00 44.18 3.32
3851 5303 0.466922 ATGCCTTCATGTAGCTGGCC 60.467 55.000 6.53 0.00 42.62 5.36
3855 5307 1.202698 CCTTCATGTAGCTGGCCCTAC 60.203 57.143 11.20 11.20 38.50 3.18
3864 5316 0.254747 GCTGGCCCTACAATACACCA 59.745 55.000 0.00 0.00 0.00 4.17
3865 5317 2.017113 GCTGGCCCTACAATACACCAC 61.017 57.143 0.00 0.00 0.00 4.16
3866 5318 1.280710 CTGGCCCTACAATACACCACA 59.719 52.381 0.00 0.00 0.00 4.17
3867 5319 1.919654 TGGCCCTACAATACACCACAT 59.080 47.619 0.00 0.00 0.00 3.21
3880 5332 3.784338 ACACCACATTTGCTCTTGTTTG 58.216 40.909 0.00 0.00 0.00 2.93
3882 5334 3.798337 CACCACATTTGCTCTTGTTTGTC 59.202 43.478 0.00 0.00 0.00 3.18
3883 5335 3.446873 ACCACATTTGCTCTTGTTTGTCA 59.553 39.130 0.00 0.00 0.00 3.58
3884 5336 3.798337 CCACATTTGCTCTTGTTTGTCAC 59.202 43.478 0.00 0.00 0.00 3.67
3886 5338 4.501559 CACATTTGCTCTTGTTTGTCACAG 59.498 41.667 0.00 0.00 36.48 3.66
3895 5351 2.940147 TGTTTGTCACAGTTGTGCAAC 58.060 42.857 16.21 6.94 45.25 4.17
3985 5442 1.541588 GTCCAGCACCCTGAAATTGTC 59.458 52.381 0.00 0.00 41.77 3.18
4010 5467 3.874543 TGTTGCTGTGACATCGTAAGTTT 59.125 39.130 0.00 0.00 39.48 2.66
4013 5470 3.740832 TGCTGTGACATCGTAAGTTTGAG 59.259 43.478 0.00 0.00 39.48 3.02
4015 5472 4.143305 GCTGTGACATCGTAAGTTTGAGAC 60.143 45.833 0.00 0.00 39.48 3.36
4017 5474 3.364023 GTGACATCGTAAGTTTGAGACCG 59.636 47.826 0.00 0.00 39.48 4.79
4018 5475 3.005050 TGACATCGTAAGTTTGAGACCGT 59.995 43.478 0.00 0.00 39.48 4.83
4020 5477 5.125100 ACATCGTAAGTTTGAGACCGTTA 57.875 39.130 0.00 0.00 39.48 3.18
4021 5478 5.159209 ACATCGTAAGTTTGAGACCGTTAG 58.841 41.667 0.00 0.00 39.48 2.34
4022 5479 4.836125 TCGTAAGTTTGAGACCGTTAGT 57.164 40.909 0.00 0.00 39.48 2.24
4023 5480 5.186996 TCGTAAGTTTGAGACCGTTAGTT 57.813 39.130 0.00 0.00 39.48 2.24
4024 5481 6.312399 TCGTAAGTTTGAGACCGTTAGTTA 57.688 37.500 0.00 0.00 39.48 2.24
4025 5482 6.373779 TCGTAAGTTTGAGACCGTTAGTTAG 58.626 40.000 0.00 0.00 39.48 2.34
4027 5484 6.522510 CGTAAGTTTGAGACCGTTAGTTAGAG 59.477 42.308 0.00 0.00 0.00 2.43
4028 5485 6.645790 AAGTTTGAGACCGTTAGTTAGAGA 57.354 37.500 0.00 0.00 0.00 3.10
4029 5486 6.645790 AGTTTGAGACCGTTAGTTAGAGAA 57.354 37.500 0.00 0.00 0.00 2.87
4030 5487 7.229581 AGTTTGAGACCGTTAGTTAGAGAAT 57.770 36.000 0.00 0.00 0.00 2.40
4031 5488 8.345724 AGTTTGAGACCGTTAGTTAGAGAATA 57.654 34.615 0.00 0.00 0.00 1.75
4032 5489 8.242739 AGTTTGAGACCGTTAGTTAGAGAATAC 58.757 37.037 0.00 0.00 0.00 1.89
4033 5490 7.934855 TTGAGACCGTTAGTTAGAGAATACT 57.065 36.000 0.00 0.00 0.00 2.12
4034 5491 7.551035 TGAGACCGTTAGTTAGAGAATACTC 57.449 40.000 0.00 0.00 42.90 2.59
4043 5500 9.312146 GTTAGTTAGAGAATACTCGTATTACGC 57.688 37.037 11.33 0.00 46.64 4.42
4061 5518 3.740115 ACGCTGGTTGAACTTATCTGTT 58.260 40.909 0.00 0.00 0.00 3.16
4076 5533 3.159213 TCTGTTGGCATGGAACTGAAT 57.841 42.857 0.00 0.00 30.88 2.57
4201 5658 2.738846 CTGTGTGCAAGTGATGGAGTAC 59.261 50.000 0.00 0.00 0.00 2.73
4235 5692 6.250819 CAGGTAAAAAGATGCTACGACATTG 58.749 40.000 0.00 0.00 0.00 2.82
4236 5693 5.028375 GGTAAAAAGATGCTACGACATTGC 58.972 41.667 0.00 0.00 0.00 3.56
4237 5694 4.764679 AAAAAGATGCTACGACATTGCA 57.235 36.364 0.00 0.00 43.40 4.08
4238 5695 3.747099 AAAGATGCTACGACATTGCAC 57.253 42.857 0.00 0.00 42.02 4.57
4239 5696 2.385013 AGATGCTACGACATTGCACA 57.615 45.000 0.00 0.00 42.02 4.57
4283 5740 4.002316 CTCTTCTGCTTCCTTCCTTGAAG 58.998 47.826 0.00 0.00 41.70 3.02
4297 5757 2.926200 CCTTGAAGCTGACGTGTCATAG 59.074 50.000 2.72 0.00 39.13 2.23
4444 5919 1.080230 CCTGTCCTGACTCGCTGTG 60.080 63.158 0.00 0.00 0.00 3.66
4573 6048 2.040278 TCCCCCATCTCTTTGTTGACTG 59.960 50.000 0.00 0.00 0.00 3.51
4591 6066 2.009774 CTGACCAATCGAACCCATGAC 58.990 52.381 0.00 0.00 0.00 3.06
4647 6122 2.125350 GAGCTCGGCTGTTCCTGG 60.125 66.667 0.00 0.00 39.88 4.45
4870 6348 2.410939 GTGTCCCCGTACAAGAAAGTC 58.589 52.381 0.00 0.00 0.00 3.01
4981 6459 1.745141 GCTGCTTCCCGTTCAGATCAT 60.745 52.381 0.00 0.00 0.00 2.45
4993 6471 3.281727 TCAGATCATACCAAACCCAGC 57.718 47.619 0.00 0.00 0.00 4.85
5057 6535 5.449177 GGATGAAGTACATGTTTTAGCTGCC 60.449 44.000 2.30 0.00 39.56 4.85
5059 6537 1.737793 AGTACATGTTTTAGCTGCCGC 59.262 47.619 2.30 0.00 0.00 6.53
5112 6591 1.103398 GGGATTGGGATTGCTCGTGG 61.103 60.000 0.00 0.00 0.00 4.94
5158 6637 1.475751 GCTCCCATAGGATGTGTGTGG 60.476 57.143 0.00 0.00 42.93 4.17
5161 6640 2.123589 CCCATAGGATGTGTGTGGGTA 58.876 52.381 0.58 0.00 43.61 3.69
5179 6658 4.080807 TGGGTACGTCAATGGAATACATGT 60.081 41.667 2.69 2.69 40.44 3.21
5180 6659 4.510340 GGGTACGTCAATGGAATACATGTC 59.490 45.833 0.00 0.00 40.44 3.06
5192 6671 4.806247 GGAATACATGTCTCTGTGTGCTAC 59.194 45.833 0.00 0.00 0.00 3.58
5201 6680 5.586643 TGTCTCTGTGTGCTACTATAGTCTG 59.413 44.000 9.12 5.10 0.00 3.51
5253 6732 4.022413 TGGAACACCATTTCGTATCCAA 57.978 40.909 0.00 0.00 32.84 3.53
5256 6735 4.142469 GGAACACCATTTCGTATCCAAAGG 60.142 45.833 0.00 0.00 0.00 3.11
5264 6743 2.343101 TCGTATCCAAAGGTGAAAGCG 58.657 47.619 0.00 0.00 40.95 4.68
5281 6760 6.636850 GTGAAAGCGTTTGTCATGAACTTTAT 59.363 34.615 0.00 0.00 0.00 1.40
5289 6768 7.482743 CGTTTGTCATGAACTTTATTGATCAGG 59.517 37.037 0.00 0.00 0.00 3.86
5290 6769 6.441093 TGTCATGAACTTTATTGATCAGGC 57.559 37.500 0.00 0.00 0.00 4.85
5294 6773 6.885918 TCATGAACTTTATTGATCAGGCTCAA 59.114 34.615 0.00 0.00 39.35 3.02
5316 6795 0.442699 GCGACGAACTTGGGTCATTC 59.557 55.000 0.00 0.00 32.74 2.67
5339 6818 2.806608 TGTTGAAGGTGTCGTCTACC 57.193 50.000 0.00 0.00 38.52 3.18
5387 6893 4.124351 GGTCGGACATGGCGACGA 62.124 66.667 10.76 6.63 33.92 4.20
5391 6897 2.186903 GGACATGGCGACGATGGT 59.813 61.111 0.00 0.00 0.00 3.55
5399 6905 2.047274 CGACGATGGTGCAAGGGT 60.047 61.111 0.00 0.00 0.00 4.34
5411 6917 3.056821 GGTGCAAGGGTGTTTATTCCTTC 60.057 47.826 0.00 0.00 38.70 3.46
5420 6926 5.154222 GGTGTTTATTCCTTCTTGAAAGCG 58.846 41.667 0.00 0.00 0.00 4.68
5427 6933 3.013921 TCCTTCTTGAAAGCGTTGTTGT 58.986 40.909 0.00 0.00 0.00 3.32
5431 6937 3.753842 TCTTGAAAGCGTTGTTGTGAAC 58.246 40.909 0.00 0.00 0.00 3.18
5452 6958 4.205587 ACGAGGTCGATTTAGTCATAGGT 58.794 43.478 6.35 0.00 43.02 3.08
5458 6964 6.817140 AGGTCGATTTAGTCATAGGTGTTTTC 59.183 38.462 0.00 0.00 0.00 2.29
5462 6968 8.932791 TCGATTTAGTCATAGGTGTTTTCTTTC 58.067 33.333 0.00 0.00 0.00 2.62
5537 7044 0.108585 TGTGGTTCTTCTGGAGGCAC 59.891 55.000 0.00 0.00 0.00 5.01
5547 7054 2.351276 GGAGGCACCAACGTGGAT 59.649 61.111 10.46 0.00 40.96 3.41
5570 7077 2.742053 TGCTAAAATGGAACTCGAGTGC 59.258 45.455 20.85 18.26 0.00 4.40
5786 7321 4.998788 TCTGGAGAGAACGTGAATATGTG 58.001 43.478 0.00 0.00 0.00 3.21
5826 7361 5.259832 TGTGCATCTGAAAATGACACAAA 57.740 34.783 0.00 0.00 38.99 2.83
5905 7440 8.443160 CGAATGTTTCTTATGAAGCTAACAAGA 58.557 33.333 6.73 0.00 36.80 3.02
5916 7451 4.530710 AGCTAACAAGAATGGACACGTA 57.469 40.909 0.00 0.00 0.00 3.57
5919 7454 4.563184 GCTAACAAGAATGGACACGTAGAG 59.437 45.833 0.00 0.00 0.00 2.43
5925 7460 3.350219 AATGGACACGTAGAGCCATTT 57.650 42.857 14.10 3.76 46.05 2.32
5937 7472 3.520187 GCCATTTCTTTGGGCACTG 57.480 52.632 0.00 0.00 46.92 3.66
5941 7476 2.496871 CCATTTCTTTGGGCACTGCATA 59.503 45.455 2.82 0.00 32.80 3.14
5945 7480 2.093890 TCTTTGGGCACTGCATATGTG 58.906 47.619 4.29 0.37 38.36 3.21
5951 7486 0.527113 GCACTGCATATGTGTGGCAA 59.473 50.000 22.83 0.00 37.06 4.52
5969 7504 2.455557 CAAAGGGTTATGGGCACATCA 58.544 47.619 3.67 0.00 38.53 3.07
5982 7519 1.002366 CACATCACGCCTAGAGCAAC 58.998 55.000 0.00 0.00 44.04 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.991758 GCATTAAGCGGTTTGATTTACG 57.008 40.909 4.64 0.00 0.00 3.18
35 36 9.167311 GCGGTTTGATAGGAATAATATGAAGAT 57.833 33.333 0.00 0.00 0.00 2.40
36 37 8.375506 AGCGGTTTGATAGGAATAATATGAAGA 58.624 33.333 0.00 0.00 0.00 2.87
37 38 8.553459 AGCGGTTTGATAGGAATAATATGAAG 57.447 34.615 0.00 0.00 0.00 3.02
38 39 8.918202 AAGCGGTTTGATAGGAATAATATGAA 57.082 30.769 0.00 0.00 0.00 2.57
42 43 8.726988 GCATTAAGCGGTTTGATAGGAATAATA 58.273 33.333 4.64 0.00 0.00 0.98
43 44 7.593825 GCATTAAGCGGTTTGATAGGAATAAT 58.406 34.615 4.64 0.00 0.00 1.28
44 45 6.966021 GCATTAAGCGGTTTGATAGGAATAA 58.034 36.000 4.64 0.00 0.00 1.40
45 46 6.554334 GCATTAAGCGGTTTGATAGGAATA 57.446 37.500 4.64 0.00 0.00 1.75
46 47 5.438761 GCATTAAGCGGTTTGATAGGAAT 57.561 39.130 4.64 0.00 0.00 3.01
47 48 4.893424 GCATTAAGCGGTTTGATAGGAA 57.107 40.909 4.64 0.00 0.00 3.36
84 85 7.257722 ACAAAACAAAACCTACAGTCATTCAG 58.742 34.615 0.00 0.00 0.00 3.02
91 92 8.799367 AGTAGAAAACAAAACAAAACCTACAGT 58.201 29.630 0.00 0.00 0.00 3.55
93 94 7.542824 GCAGTAGAAAACAAAACAAAACCTACA 59.457 33.333 0.00 0.00 0.00 2.74
95 96 6.748198 CGCAGTAGAAAACAAAACAAAACCTA 59.252 34.615 0.00 0.00 0.00 3.08
96 97 5.575218 CGCAGTAGAAAACAAAACAAAACCT 59.425 36.000 0.00 0.00 0.00 3.50
103 108 4.501559 GGGAAACGCAGTAGAAAACAAAAC 59.498 41.667 0.00 0.00 45.00 2.43
115 120 0.470766 TACCTGTTGGGAAACGCAGT 59.529 50.000 0.00 0.00 40.46 4.40
120 125 1.073284 TGGCTCTACCTGTTGGGAAAC 59.927 52.381 0.00 0.00 40.22 2.78
132 137 1.227380 CCGATGGCTGTGGCTCTAC 60.227 63.158 0.00 0.00 38.73 2.59
133 138 3.094062 GCCGATGGCTGTGGCTCTA 62.094 63.158 0.00 0.00 46.69 2.43
189 214 3.849951 CCTAGGCGTGGCGACCAT 61.850 66.667 0.00 0.00 34.11 3.55
227 271 1.258445 CGGTGGACTAAGGAGCCTGT 61.258 60.000 0.00 0.00 0.00 4.00
255 299 4.295119 GTGACGACGGTGCCCTGT 62.295 66.667 0.00 0.00 0.00 4.00
339 984 3.112709 GCGTGTCAGGTCCTTCGC 61.113 66.667 10.32 10.32 37.17 4.70
344 989 2.430921 CTCGTGCGTGTCAGGTCC 60.431 66.667 0.00 0.00 32.68 4.46
346 991 2.276116 ATCCTCGTGCGTGTCAGGT 61.276 57.895 0.00 0.00 32.68 4.00
349 994 2.432456 GCATCCTCGTGCGTGTCA 60.432 61.111 0.00 0.00 35.10 3.58
357 1002 4.115199 GGGGGCTTGCATCCTCGT 62.115 66.667 5.62 0.00 0.00 4.18
387 1032 2.406616 CCCAGGCAATTCCCGTTCG 61.407 63.158 0.00 0.00 34.51 3.95
417 1067 2.363795 TCCTTCCCTCGCCATCGT 60.364 61.111 0.00 0.00 36.96 3.73
420 1070 2.770048 CCCTCCTTCCCTCGCCAT 60.770 66.667 0.00 0.00 0.00 4.40
430 1080 2.285442 CCGGTCTTCCCCCTCCTT 60.285 66.667 0.00 0.00 0.00 3.36
440 1090 2.140792 ATATCCTGCCGCCGGTCTT 61.141 57.895 4.45 0.00 0.00 3.01
482 1132 2.686106 TAACGCCCTCCCCCTCAC 60.686 66.667 0.00 0.00 0.00 3.51
483 1133 2.686106 GTAACGCCCTCCCCCTCA 60.686 66.667 0.00 0.00 0.00 3.86
517 1179 5.633830 AACATTGGCTTACATTGTCTCTG 57.366 39.130 0.00 0.00 41.43 3.35
559 1221 1.163554 CTCTGAGCTCACCCTTTTGC 58.836 55.000 13.74 0.00 0.00 3.68
560 1222 1.072965 ACCTCTGAGCTCACCCTTTTG 59.927 52.381 13.74 0.85 0.00 2.44
616 1284 3.644399 GAACCCACGTCTCGCCCTC 62.644 68.421 0.00 0.00 0.00 4.30
620 1288 0.389948 ATCTTGAACCCACGTCTCGC 60.390 55.000 0.00 0.00 0.00 5.03
631 1299 9.688592 ATTCAGAAAGAAAATGACATCTTGAAC 57.311 29.630 0.00 0.00 40.22 3.18
636 1304 9.688592 GACAAATTCAGAAAGAAAATGACATCT 57.311 29.630 0.00 0.00 40.22 2.90
637 1305 9.467258 TGACAAATTCAGAAAGAAAATGACATC 57.533 29.630 0.00 0.00 40.22 3.06
638 1306 9.820725 TTGACAAATTCAGAAAGAAAATGACAT 57.179 25.926 0.00 0.00 40.22 3.06
639 1307 9.650539 TTTGACAAATTCAGAAAGAAAATGACA 57.349 25.926 0.00 0.00 40.22 3.58
641 1309 9.650539 TGTTTGACAAATTCAGAAAGAAAATGA 57.349 25.926 3.49 0.00 40.22 2.57
653 1344 9.979578 AATAGCTTTACATGTTTGACAAATTCA 57.020 25.926 2.30 0.00 0.00 2.57
741 1477 0.179097 GGAAGCACGTTTTGGCCAAA 60.179 50.000 27.13 27.13 0.00 3.28
760 1496 1.953138 GCCGTCCATCTCATCAGCG 60.953 63.158 0.00 0.00 0.00 5.18
772 1508 0.387239 GTTCATGCAAACAGCCGTCC 60.387 55.000 0.00 0.00 44.83 4.79
799 1541 2.672996 ATGCGGTTCGGCTTTGCT 60.673 55.556 4.22 0.00 0.00 3.91
849 1591 2.575125 ATCCACGCTCTGCTCTGCTG 62.575 60.000 0.00 0.00 0.00 4.41
954 1713 5.415221 GCTGTGCTACTGAAGTTAAGATCT 58.585 41.667 0.00 0.00 0.00 2.75
1279 2050 3.429141 GACGAGGAGCACGACGGA 61.429 66.667 0.00 0.00 34.70 4.69
1365 2136 0.694444 GGGAGCTGGAGGGGTTCATA 60.694 60.000 0.00 0.00 0.00 2.15
1488 2259 3.104512 AGGATTGAATGTCTCCGGTACA 58.895 45.455 13.46 13.46 34.13 2.90
1491 2262 2.100916 CGTAGGATTGAATGTCTCCGGT 59.899 50.000 0.00 0.00 34.13 5.28
1921 2692 4.684134 GGCCTTGGCCCTCAGCAA 62.684 66.667 19.46 0.00 46.50 3.91
2076 2849 7.362056 CCATGTTTCCCAGAATACTACAAACAG 60.362 40.741 0.00 0.00 34.58 3.16
2101 2922 0.827368 TTGTTTGCCTTCACCAACCC 59.173 50.000 0.00 0.00 0.00 4.11
2188 3098 3.800531 ACAATACCGTTATTCCTTCCCG 58.199 45.455 0.00 0.00 0.00 5.14
2232 3142 1.227999 AACGTTCGCATGTCACCCTG 61.228 55.000 0.00 0.00 0.00 4.45
2280 3191 1.066929 CAAAAAGGGGAGGATTTGCCG 60.067 52.381 0.00 0.00 43.43 5.69
2366 3278 4.024977 GCGACAATTTTGACTGGCAATTTT 60.025 37.500 0.00 0.00 36.15 1.82
2385 3297 3.758931 GGGGGTGGCAATTGCGAC 61.759 66.667 30.69 30.69 46.89 5.19
2403 3315 4.803426 GCGACCGTCAGCTGGGAG 62.803 72.222 15.13 9.00 0.00 4.30
2416 3328 3.538634 AGTACCCTCTTATTTGGCGAC 57.461 47.619 0.00 0.00 0.00 5.19
2448 3360 9.695526 GCAACAAGGCATATGAAATATTATCAA 57.304 29.630 6.97 0.00 37.44 2.57
2513 3429 5.103982 AGGACCAACATACATGAATGGATCA 60.104 40.000 18.88 0.00 43.67 2.92
2514 3430 5.380043 AGGACCAACATACATGAATGGATC 58.620 41.667 18.88 13.79 39.17 3.36
2575 3491 2.089201 CAACTGCATCCTCATCTGCAA 58.911 47.619 0.00 0.00 46.87 4.08
2585 3501 3.676646 GCAAAGTCAAATCAACTGCATCC 59.323 43.478 0.00 0.00 0.00 3.51
2636 3552 3.762823 CCCTACTCGGTTATCCCATCTAC 59.237 52.174 0.00 0.00 0.00 2.59
2651 3567 8.411683 TCGATTTGAACTAGTTAATCCCTACTC 58.588 37.037 18.89 2.32 0.00 2.59
2730 3646 2.098443 GCAAACGAACTGGAACTGGAAA 59.902 45.455 0.00 0.00 0.00 3.13
2919 3835 3.632145 AGCCCTGTTCAAAGTGTAAACAG 59.368 43.478 7.35 7.35 45.99 3.16
3143 4059 2.674380 GCAGTGGCTGAGTTGGGG 60.674 66.667 0.00 0.00 36.96 4.96
3198 4114 3.937814 ACTAGACATCGGTTTGCATCAA 58.062 40.909 0.00 0.00 0.00 2.57
3287 4203 4.265073 GTCTTCAATAACCACCTCAGCAT 58.735 43.478 0.00 0.00 0.00 3.79
3452 4886 7.680730 ACAATGATAAGGAGTACCCATATCAC 58.319 38.462 20.81 4.90 42.64 3.06
3583 5020 5.453339 GCAGCCCATATTGTTAGACTAGACA 60.453 44.000 0.00 0.00 0.00 3.41
3682 5131 8.352201 TCATCATTCAAGTAACCTGTGAAAAAG 58.648 33.333 0.00 0.00 35.07 2.27
3741 5193 1.348036 AGTAAGCAAGGTCACCAGTCC 59.652 52.381 0.00 0.00 0.00 3.85
3777 5229 2.833631 ACGGCCCACTATGTATAAGC 57.166 50.000 0.00 0.00 0.00 3.09
3847 5299 1.363246 TGTGGTGTATTGTAGGGCCA 58.637 50.000 6.18 0.00 0.00 5.36
3851 5303 4.943705 AGAGCAAATGTGGTGTATTGTAGG 59.056 41.667 0.00 0.00 35.00 3.18
3855 5307 5.125100 ACAAGAGCAAATGTGGTGTATTG 57.875 39.130 0.00 0.00 35.00 1.90
3864 5316 4.158394 ACTGTGACAAACAAGAGCAAATGT 59.842 37.500 0.00 0.00 38.67 2.71
3865 5317 4.675510 ACTGTGACAAACAAGAGCAAATG 58.324 39.130 0.00 0.00 38.67 2.32
3866 5318 4.989279 ACTGTGACAAACAAGAGCAAAT 57.011 36.364 0.00 0.00 38.67 2.32
3867 5319 4.022416 ACAACTGTGACAAACAAGAGCAAA 60.022 37.500 0.00 0.00 38.67 3.68
3883 5335 4.159506 ACCAATAACTTGTTGCACAACTGT 59.840 37.500 14.16 10.09 41.67 3.55
3884 5336 4.681744 ACCAATAACTTGTTGCACAACTG 58.318 39.130 14.16 9.54 41.67 3.16
3886 5338 8.696175 GTTATAACCAATAACTTGTTGCACAAC 58.304 33.333 4.11 6.57 44.46 3.32
4010 5467 6.257411 CGAGTATTCTCTAACTAACGGTCTCA 59.743 42.308 0.00 0.00 38.45 3.27
4013 5470 6.356757 ACGAGTATTCTCTAACTAACGGTC 57.643 41.667 0.00 0.00 38.45 4.79
4015 5472 9.804547 GTAATACGAGTATTCTCTAACTAACGG 57.195 37.037 11.29 0.00 38.45 4.44
4017 5474 9.312146 GCGTAATACGAGTATTCTCTAACTAAC 57.688 37.037 17.71 1.91 46.05 2.34
4018 5475 9.265901 AGCGTAATACGAGTATTCTCTAACTAA 57.734 33.333 17.71 0.00 46.05 2.24
4020 5477 7.307870 CCAGCGTAATACGAGTATTCTCTAACT 60.308 40.741 17.71 0.00 46.05 2.24
4021 5478 6.796072 CCAGCGTAATACGAGTATTCTCTAAC 59.204 42.308 17.71 4.32 46.05 2.34
4022 5479 6.484643 ACCAGCGTAATACGAGTATTCTCTAA 59.515 38.462 17.71 0.00 46.05 2.10
4023 5480 5.994054 ACCAGCGTAATACGAGTATTCTCTA 59.006 40.000 17.71 0.00 46.05 2.43
4024 5481 4.820716 ACCAGCGTAATACGAGTATTCTCT 59.179 41.667 17.71 0.00 46.05 3.10
4025 5482 5.105834 ACCAGCGTAATACGAGTATTCTC 57.894 43.478 17.71 6.44 46.05 2.87
4027 5484 5.276270 TCAACCAGCGTAATACGAGTATTC 58.724 41.667 17.71 0.00 46.05 1.75
4028 5485 5.252969 TCAACCAGCGTAATACGAGTATT 57.747 39.130 17.71 12.41 46.05 1.89
4029 5486 4.906065 TCAACCAGCGTAATACGAGTAT 57.094 40.909 17.71 0.00 46.05 2.12
4030 5487 4.156556 AGTTCAACCAGCGTAATACGAGTA 59.843 41.667 17.71 0.00 46.05 2.59
4031 5488 3.057033 AGTTCAACCAGCGTAATACGAGT 60.057 43.478 17.71 7.33 46.05 4.18
4032 5489 3.508762 AGTTCAACCAGCGTAATACGAG 58.491 45.455 17.71 7.79 46.05 4.18
4033 5490 3.581024 AGTTCAACCAGCGTAATACGA 57.419 42.857 17.71 0.00 46.05 3.43
4034 5491 5.747197 AGATAAGTTCAACCAGCGTAATACG 59.253 40.000 8.64 8.64 45.88 3.06
4043 5500 3.820467 TGCCAACAGATAAGTTCAACCAG 59.180 43.478 0.00 0.00 0.00 4.00
4061 5518 2.905415 AAGGATTCAGTTCCATGCCA 57.095 45.000 0.00 0.00 38.32 4.92
4076 5533 4.573201 TCGAGAAAAGCGAAAGAAAAAGGA 59.427 37.500 0.00 0.00 34.45 3.36
4114 5571 3.130164 TCTCTCCAGCTTCTTCATCTTCG 59.870 47.826 0.00 0.00 0.00 3.79
4201 5658 0.671251 TTTTTACCTGCTTGGCCACG 59.329 50.000 3.88 4.24 40.22 4.94
4235 5692 3.588906 TGCTGTGCTGTGCTGTGC 61.589 61.111 0.00 0.00 0.00 4.57
4236 5693 1.792118 ATGTGCTGTGCTGTGCTGTG 61.792 55.000 0.00 0.00 0.00 3.66
4237 5694 1.512996 GATGTGCTGTGCTGTGCTGT 61.513 55.000 0.00 0.00 0.00 4.40
4238 5695 1.209383 GATGTGCTGTGCTGTGCTG 59.791 57.895 0.00 0.00 0.00 4.41
4239 5696 1.228033 TGATGTGCTGTGCTGTGCT 60.228 52.632 0.00 0.00 0.00 4.40
4283 5740 2.561733 TACTGCTATGACACGTCAGC 57.438 50.000 6.01 5.37 43.61 4.26
4297 5757 4.875544 TTAAAAGGATGCGTCATACTGC 57.124 40.909 8.47 0.00 34.89 4.40
4573 6048 1.379527 GGTCATGGGTTCGATTGGTC 58.620 55.000 0.00 0.00 0.00 4.02
4591 6066 0.379669 GCGCATCACTCTTGAATGGG 59.620 55.000 0.30 0.00 34.61 4.00
4647 6122 2.743928 CAGCCAGACAAGGTCGCC 60.744 66.667 0.00 0.00 37.67 5.54
4663 6138 2.594131 TCCTTGAACGTCTCTCTTCCA 58.406 47.619 0.00 0.00 0.00 3.53
4769 6244 5.779922 ACTGTCTACAGAATCGCAAGTAAA 58.220 37.500 16.74 0.00 46.59 2.01
4771 6246 6.505044 TTACTGTCTACAGAATCGCAAGTA 57.495 37.500 16.74 0.00 46.59 2.24
4804 6279 1.675483 TCGCAGCTTCAGCAAAGAAAA 59.325 42.857 0.75 0.00 45.16 2.29
4808 6284 1.983605 CAATTCGCAGCTTCAGCAAAG 59.016 47.619 0.75 0.00 45.16 2.77
4870 6348 0.937304 CCACGAATATCACCTTGCGG 59.063 55.000 0.00 0.00 0.00 5.69
4981 6459 2.054799 AGTCTTGAGCTGGGTTTGGTA 58.945 47.619 0.00 0.00 0.00 3.25
4993 6471 3.058432 TCGACTCCGTTTACAGTCTTGAG 60.058 47.826 0.00 0.00 37.49 3.02
5040 6518 1.466950 TGCGGCAGCTAAAACATGTAC 59.533 47.619 10.92 0.00 45.42 2.90
5057 6535 3.063670 TCACACACAAAAAGACATGCG 57.936 42.857 0.00 0.00 0.00 4.73
5059 6537 7.115236 CCAACATATCACACACAAAAAGACATG 59.885 37.037 0.00 0.00 0.00 3.21
5112 6591 4.989168 GGTATGGTACTGCTAGTATGCAAC 59.011 45.833 0.00 0.00 42.83 4.17
5158 6637 5.357257 AGACATGTATTCCATTGACGTACC 58.643 41.667 0.00 0.00 0.00 3.34
5161 6640 5.111989 CAGAGACATGTATTCCATTGACGT 58.888 41.667 0.00 0.00 0.00 4.34
5179 6658 5.746284 ACAGACTATAGTAGCACACAGAGA 58.254 41.667 5.09 0.00 0.00 3.10
5180 6659 6.987404 TCTACAGACTATAGTAGCACACAGAG 59.013 42.308 5.09 0.00 38.05 3.35
5201 6680 8.254508 ACAGTCTTTCCTGACAAATCTATCTAC 58.745 37.037 0.00 0.00 39.27 2.59
5212 6691 4.136796 CCAATCAACAGTCTTTCCTGACA 58.863 43.478 0.00 0.00 39.27 3.58
5253 6732 2.948979 TCATGACAAACGCTTTCACCTT 59.051 40.909 0.00 0.00 0.00 3.50
5256 6735 3.952535 AGTTCATGACAAACGCTTTCAC 58.047 40.909 0.00 0.00 0.00 3.18
5264 6743 7.274250 GCCTGATCAATAAAGTTCATGACAAAC 59.726 37.037 0.00 0.00 0.00 2.93
5281 6760 0.321346 TCGCTGTTGAGCCTGATCAA 59.679 50.000 0.00 0.00 42.91 2.57
5289 6768 0.111089 CAAGTTCGTCGCTGTTGAGC 60.111 55.000 0.00 0.00 42.37 4.26
5290 6769 0.508641 CCAAGTTCGTCGCTGTTGAG 59.491 55.000 0.00 0.00 0.00 3.02
5294 6773 1.300697 GACCCAAGTTCGTCGCTGT 60.301 57.895 0.00 0.00 0.00 4.40
5387 6893 2.831526 GGAATAAACACCCTTGCACCAT 59.168 45.455 0.00 0.00 0.00 3.55
5391 6897 4.112634 AGAAGGAATAAACACCCTTGCA 57.887 40.909 0.00 0.00 40.14 4.08
5399 6905 6.183360 ACAACGCTTTCAAGAAGGAATAAACA 60.183 34.615 0.00 0.00 0.00 2.83
5411 6917 2.525891 CGTTCACAACAACGCTTTCAAG 59.474 45.455 0.00 0.00 42.45 3.02
5420 6926 1.563111 TCGACCTCGTTCACAACAAC 58.437 50.000 0.00 0.00 40.80 3.32
5427 6933 4.713824 ATGACTAAATCGACCTCGTTCA 57.286 40.909 0.00 0.00 40.80 3.18
5431 6937 4.036498 ACACCTATGACTAAATCGACCTCG 59.964 45.833 0.00 0.00 41.45 4.63
5501 7008 4.410099 ACCACACATCCATCACAAGAATT 58.590 39.130 0.00 0.00 0.00 2.17
5537 7044 3.181497 CCATTTTAGCAGATCCACGTTGG 60.181 47.826 0.00 0.00 39.43 3.77
5547 7054 4.245660 CACTCGAGTTCCATTTTAGCAGA 58.754 43.478 17.26 0.00 0.00 4.26
5786 7321 7.649306 AGATGCACAAAGTGAAATTTACTGTTC 59.351 33.333 0.58 0.00 35.23 3.18
5826 7361 7.839907 TCTTTAAATGAGTAATTGCTTGCCAT 58.160 30.769 0.00 0.00 0.00 4.40
5879 7414 8.443160 TCTTGTTAGCTTCATAAGAAACATTCG 58.557 33.333 0.00 0.00 36.47 3.34
5916 7451 1.203100 AGTGCCCAAAGAAATGGCTCT 60.203 47.619 0.00 0.00 45.56 4.09
5919 7454 0.671472 GCAGTGCCCAAAGAAATGGC 60.671 55.000 2.85 0.00 45.56 4.40
5925 7460 2.093890 CACATATGCAGTGCCCAAAGA 58.906 47.619 13.72 0.00 0.00 2.52
5937 7472 1.185315 ACCCTTTGCCACACATATGC 58.815 50.000 1.58 0.00 0.00 3.14
5941 7476 2.178580 CCATAACCCTTTGCCACACAT 58.821 47.619 0.00 0.00 0.00 3.21
5945 7480 0.902516 TGCCCATAACCCTTTGCCAC 60.903 55.000 0.00 0.00 0.00 5.01
5951 7486 1.681780 CGTGATGTGCCCATAACCCTT 60.682 52.381 0.00 0.00 29.55 3.95


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

AutoCloner maintained by Alex Coulton.