Multiple sequence alignment - TraesCS3A01G308000

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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 TraesCS3A01G308000 chr3A 100.000 4449 0 0 1 4449 546567797 546572245 0.000000e+00 8216
1 TraesCS3A01G308000 chr3B 95.192 2392 88 19 342 2720 142718130 142720507 0.000000e+00 3755
2 TraesCS3A01G308000 chr3B 93.377 1389 62 17 3084 4448 142720863 142722245 0.000000e+00 2028
3 TraesCS3A01G308000 chr3B 94.242 330 18 1 2880 3209 142720690 142721018 1.850000e-138 503
4 TraesCS3A01G308000 chr3B 91.270 126 11 0 3054 3179 142720893 142721018 5.920000e-39 172
5 TraesCS3A01G308000 chr3B 91.667 96 3 2 161 252 142717874 142717968 1.300000e-25 128
6 TraesCS3A01G308000 chr3B 98.305 59 1 0 4036 4094 142721746 142721804 2.190000e-18 104
7 TraesCS3A01G308000 chr3D 93.206 1619 62 22 1191 2787 93484755 93483163 0.000000e+00 2337
8 TraesCS3A01G308000 chr3D 95.836 1369 49 5 3084 4449 93482988 93481625 0.000000e+00 2206
9 TraesCS3A01G308000 chr3D 94.626 856 42 2 337 1192 93485684 93484833 0.000000e+00 1323
10 TraesCS3A01G308000 chr3D 92.121 330 21 3 2883 3208 93483162 93482834 1.130000e-125 460
11 TraesCS3A01G308000 chr3D 92.896 183 6 4 74 252 93488658 93488479 4.410000e-65 259
12 TraesCS3A01G308000 chr3D 91.250 80 7 0 4 83 93597560 93597481 4.700000e-20 110
13 TraesCS3A01G308000 chr5B 93.694 111 7 0 2778 2888 474772897 474772787 2.750000e-37 167
14 TraesCS3A01G308000 chr5B 94.949 99 5 0 2789 2887 693583897 693583799 5.960000e-34 156
15 TraesCS3A01G308000 chr1A 96.875 96 3 0 2789 2884 351606763 351606858 1.280000e-35 161
16 TraesCS3A01G308000 chr7B 95.918 98 4 0 2789 2886 588874918 588875015 4.610000e-35 159
17 TraesCS3A01G308000 chr7B 95.876 97 4 0 2789 2885 562993067 562993163 1.660000e-34 158
18 TraesCS3A01G308000 chr7B 95.876 97 4 0 2789 2885 589348414 589348318 1.660000e-34 158
19 TraesCS3A01G308000 chr1B 95.000 100 5 0 2789 2888 594114309 594114408 1.660000e-34 158
20 TraesCS3A01G308000 chr1B 94.175 103 5 1 2783 2884 56752386 56752488 5.960000e-34 156
21 TraesCS3A01G308000 chr4B 90.351 114 8 3 2773 2885 21198637 21198748 3.590000e-31 147


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 TraesCS3A01G308000 chr3A 546567797 546572245 4448 False 8216 8216 100.000000 1 4449 1 chr3A.!!$F1 4448
1 TraesCS3A01G308000 chr3B 142717874 142722245 4371 False 1115 3755 94.008833 161 4448 6 chr3B.!!$F1 4287
2 TraesCS3A01G308000 chr3D 93481625 93488658 7033 True 1317 2337 93.737000 74 4449 5 chr3D.!!$R2 4375

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
329 3031 0.182775 ACAGGCCTCACGTCCTTTTT 59.817 50.0 0.0 0.0 0.0 1.94 F
1123 3882 0.319728 CAGATATGGGAGGTGAGCGG 59.680 60.0 0.0 0.0 0.0 5.52 F
2802 5776 0.178876 TGAACACTCCCTCCATCCCA 60.179 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1223 4061 1.468520 GGGTGACATGACATGAAACCG 59.531 52.381 22.19 0.0 38.95 4.44 R
2854 5828 0.534203 GCCCCGAAACAAGTGTCTCA 60.534 55.000 0.00 0.0 0.00 3.27 R
3896 6893 0.179156 TAGCCGACGACGATTTCACC 60.179 55.000 9.28 0.0 42.66 4.02 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
28 29 9.612620 ACTTTCTTTAGTTCATTGATTAAAGCG 57.387 29.630 17.78 13.44 34.62 4.68
29 30 8.447787 TTTCTTTAGTTCATTGATTAAAGCGC 57.552 30.769 17.78 0.00 34.62 5.92
30 31 6.247903 TCTTTAGTTCATTGATTAAAGCGCG 58.752 36.000 17.78 0.00 34.62 6.86
31 32 5.788055 TTAGTTCATTGATTAAAGCGCGA 57.212 34.783 12.10 0.00 0.00 5.87
32 33 4.882671 AGTTCATTGATTAAAGCGCGAT 57.117 36.364 12.10 0.00 0.00 4.58
33 34 4.837567 AGTTCATTGATTAAAGCGCGATC 58.162 39.130 12.10 3.62 0.00 3.69
34 35 4.572389 AGTTCATTGATTAAAGCGCGATCT 59.428 37.500 12.10 0.00 0.00 2.75
35 36 4.715520 TCATTGATTAAAGCGCGATCTC 57.284 40.909 12.10 0.00 0.00 2.75
36 37 3.494626 TCATTGATTAAAGCGCGATCTCC 59.505 43.478 12.10 0.00 0.00 3.71
37 38 2.595124 TGATTAAAGCGCGATCTCCA 57.405 45.000 12.10 0.00 0.00 3.86
38 39 2.201732 TGATTAAAGCGCGATCTCCAC 58.798 47.619 12.10 0.00 0.00 4.02
39 40 2.201732 GATTAAAGCGCGATCTCCACA 58.798 47.619 12.10 0.00 0.00 4.17
40 41 1.355971 TTAAAGCGCGATCTCCACAC 58.644 50.000 12.10 0.00 0.00 3.82
41 42 0.245266 TAAAGCGCGATCTCCACACA 59.755 50.000 12.10 0.00 0.00 3.72
42 43 0.602638 AAAGCGCGATCTCCACACAA 60.603 50.000 12.10 0.00 0.00 3.33
43 44 1.016130 AAGCGCGATCTCCACACAAG 61.016 55.000 12.10 0.00 0.00 3.16
44 45 1.738099 GCGCGATCTCCACACAAGT 60.738 57.895 12.10 0.00 0.00 3.16
45 46 1.291877 GCGCGATCTCCACACAAGTT 61.292 55.000 12.10 0.00 0.00 2.66
46 47 1.148310 CGCGATCTCCACACAAGTTT 58.852 50.000 0.00 0.00 0.00 2.66
47 48 1.531149 CGCGATCTCCACACAAGTTTT 59.469 47.619 0.00 0.00 0.00 2.43
48 49 2.734606 CGCGATCTCCACACAAGTTTTA 59.265 45.455 0.00 0.00 0.00 1.52
49 50 3.370978 CGCGATCTCCACACAAGTTTTAT 59.629 43.478 0.00 0.00 0.00 1.40
50 51 4.651994 GCGATCTCCACACAAGTTTTATG 58.348 43.478 0.00 0.00 0.00 1.90
51 52 4.391830 GCGATCTCCACACAAGTTTTATGA 59.608 41.667 0.00 0.00 0.00 2.15
52 53 5.671329 GCGATCTCCACACAAGTTTTATGAC 60.671 44.000 0.00 0.00 0.00 3.06
53 54 5.163854 CGATCTCCACACAAGTTTTATGACC 60.164 44.000 0.00 0.00 0.00 4.02
54 55 4.062293 TCTCCACACAAGTTTTATGACCG 58.938 43.478 0.00 0.00 0.00 4.79
55 56 3.811083 TCCACACAAGTTTTATGACCGT 58.189 40.909 0.00 0.00 0.00 4.83
56 57 4.958509 TCCACACAAGTTTTATGACCGTA 58.041 39.130 0.00 0.00 0.00 4.02
57 58 4.992319 TCCACACAAGTTTTATGACCGTAG 59.008 41.667 0.00 0.00 0.00 3.51
58 59 4.992319 CCACACAAGTTTTATGACCGTAGA 59.008 41.667 0.00 0.00 0.00 2.59
59 60 5.642063 CCACACAAGTTTTATGACCGTAGAT 59.358 40.000 0.00 0.00 0.00 1.98
60 61 6.402118 CCACACAAGTTTTATGACCGTAGATG 60.402 42.308 0.00 0.00 0.00 2.90
61 62 6.367695 CACACAAGTTTTATGACCGTAGATGA 59.632 38.462 0.00 0.00 0.00 2.92
62 63 6.932400 ACACAAGTTTTATGACCGTAGATGAA 59.068 34.615 0.00 0.00 0.00 2.57
63 64 7.095355 ACACAAGTTTTATGACCGTAGATGAAC 60.095 37.037 0.00 0.00 0.00 3.18
64 65 7.117812 CACAAGTTTTATGACCGTAGATGAACT 59.882 37.037 0.00 0.00 0.00 3.01
65 66 8.308931 ACAAGTTTTATGACCGTAGATGAACTA 58.691 33.333 0.00 0.00 0.00 2.24
66 67 9.314321 CAAGTTTTATGACCGTAGATGAACTAT 57.686 33.333 0.00 0.00 33.39 2.12
68 69 9.962783 AGTTTTATGACCGTAGATGAACTATAC 57.037 33.333 0.00 0.00 33.39 1.47
69 70 9.740239 GTTTTATGACCGTAGATGAACTATACA 57.260 33.333 0.00 0.00 33.39 2.29
70 71 9.740239 TTTTATGACCGTAGATGAACTATACAC 57.260 33.333 0.00 0.00 33.39 2.90
71 72 6.954487 ATGACCGTAGATGAACTATACACA 57.046 37.500 0.00 0.00 33.39 3.72
72 73 6.373186 TGACCGTAGATGAACTATACACAG 57.627 41.667 0.00 0.00 33.39 3.66
94 95 5.691754 CAGAAAAGAAAGGGCAAATGTACAC 59.308 40.000 0.00 0.00 0.00 2.90
97 98 5.606348 AAGAAAGGGCAAATGTACACAAA 57.394 34.783 0.00 0.00 0.00 2.83
98 99 5.200368 AGAAAGGGCAAATGTACACAAAG 57.800 39.130 0.00 0.00 0.00 2.77
153 154 1.945387 AGCTGAATATCACCGTGCTG 58.055 50.000 0.00 0.00 0.00 4.41
231 240 6.835819 AAAAGATTTGGGCCTAACTAGTTC 57.164 37.500 12.39 0.00 0.00 3.01
232 241 5.514500 AAGATTTGGGCCTAACTAGTTCA 57.486 39.130 12.39 0.13 0.00 3.18
243 252 6.126681 GGCCTAACTAGTTCATTTAGGGGTAA 60.127 42.308 18.74 0.00 41.53 2.85
244 253 6.765036 GCCTAACTAGTTCATTTAGGGGTAAC 59.235 42.308 18.74 3.04 41.53 2.50
261 282 2.516460 CTGGGCCTGCATGAGAGC 60.516 66.667 4.53 0.00 0.00 4.09
319 3021 1.993653 CCTTCCATCACAGGCCTCA 59.006 57.895 0.00 0.00 0.00 3.86
329 3031 0.182775 ACAGGCCTCACGTCCTTTTT 59.817 50.000 0.00 0.00 0.00 1.94
363 3119 2.042831 GGCTGCCGATTTGAGCACT 61.043 57.895 1.35 0.00 34.68 4.40
414 3170 2.917751 TCGATGCCTCCCCCGATC 60.918 66.667 0.00 0.00 0.00 3.69
565 3321 2.597805 ACCCCCGATCCGATCTCG 60.598 66.667 6.81 0.00 39.44 4.04
566 3322 2.597805 CCCCCGATCCGATCTCGT 60.598 66.667 6.81 0.00 37.74 4.18
700 3458 1.060698 GATTCGCTTGCTTGTACGGAC 59.939 52.381 0.00 0.00 0.00 4.79
758 3516 9.661954 TTAGGATTAGATATTCTGAAGAGGTGT 57.338 33.333 0.00 0.00 0.00 4.16
776 3534 3.683340 GGTGTCGGTGGTTTTCTAGATTC 59.317 47.826 0.00 0.00 0.00 2.52
778 3536 3.006110 TGTCGGTGGTTTTCTAGATTCGT 59.994 43.478 0.00 0.00 0.00 3.85
790 3548 0.596082 AGATTCGTTGCGGTTTTGGG 59.404 50.000 0.00 0.00 0.00 4.12
803 3561 0.817013 TTTTGGGGCTGATGATTCGC 59.183 50.000 0.00 0.00 0.00 4.70
836 3595 1.546476 GTATGGTCGCAGCTAGGCTAT 59.454 52.381 0.00 0.00 36.40 2.97
837 3596 1.924731 ATGGTCGCAGCTAGGCTATA 58.075 50.000 0.00 0.00 36.40 1.31
838 3597 0.959553 TGGTCGCAGCTAGGCTATAC 59.040 55.000 0.00 0.00 36.40 1.47
839 3598 1.249407 GGTCGCAGCTAGGCTATACT 58.751 55.000 0.00 0.00 36.40 2.12
840 3599 2.224695 TGGTCGCAGCTAGGCTATACTA 60.225 50.000 0.00 0.00 36.40 1.82
882 3641 2.579207 TGTCCGTATGCTGCTCTAAC 57.421 50.000 0.00 0.00 0.00 2.34
909 3668 0.389426 GTGCTGGATTGGCTGCTTTG 60.389 55.000 0.00 0.00 0.00 2.77
920 3679 0.753111 GCTGCTTTGTATGGGGAGGG 60.753 60.000 0.00 0.00 0.00 4.30
934 3693 1.246737 GGAGGGGTTTGCTCTGCTTG 61.247 60.000 0.00 0.00 0.00 4.01
942 3701 1.979855 TTGCTCTGCTTGGCTGTTTA 58.020 45.000 0.00 0.00 0.00 2.01
947 3706 2.880890 CTCTGCTTGGCTGTTTACTTGT 59.119 45.455 0.00 0.00 0.00 3.16
969 3728 3.678056 TGATGTCAGTGGTTGTAGGTC 57.322 47.619 0.00 0.00 0.00 3.85
1123 3882 0.319728 CAGATATGGGAGGTGAGCGG 59.680 60.000 0.00 0.00 0.00 5.52
1173 3932 3.281727 TTGCCTTCTGAGTGACAAGTT 57.718 42.857 0.00 0.00 0.00 2.66
1213 4051 3.008049 AGTTCCTTCTTGTACAGCGGATT 59.992 43.478 0.00 0.00 0.00 3.01
1223 4061 5.554822 TGTACAGCGGATTTATTTTGACC 57.445 39.130 0.00 0.00 0.00 4.02
1261 4099 4.158209 TCACCCATGCAAATTATGTGTGAG 59.842 41.667 0.00 0.00 37.78 3.51
1364 4202 0.250945 TCTTGCACCCAATGGCGTTA 60.251 50.000 0.00 0.00 33.59 3.18
1388 4226 4.160439 GTCATCCACATGGTTACTCTGAGA 59.840 45.833 12.44 0.00 36.34 3.27
1452 4290 5.167845 GGTCTCTCAACATTGTTCTCTCTC 58.832 45.833 0.00 0.00 0.00 3.20
1648 4487 8.202745 ACTTTGGCGATTGTTTTCAAAAATAA 57.797 26.923 0.79 0.79 43.39 1.40
1790 4629 2.810274 GCGACATGTGGATATGAAGCAT 59.190 45.455 12.54 0.00 35.65 3.79
1822 4661 5.412526 TTTGTTGTAAGTAACCGCTCTTG 57.587 39.130 0.00 0.00 0.00 3.02
1882 4721 1.064463 TCACATTGATGCCCCTCCTTC 60.064 52.381 0.00 0.00 0.00 3.46
1887 4726 0.914644 TGATGCCCCTCCTTCTCTTG 59.085 55.000 0.00 0.00 0.00 3.02
2056 4904 9.049523 TGTTGATTTATGCTTTTGTTATTTGCA 57.950 25.926 0.00 0.00 38.05 4.08
2339 5190 4.438744 CCTGCGAGTTTGTCTTTTCTGTTT 60.439 41.667 0.00 0.00 0.00 2.83
2423 5279 1.152652 ATCTCCATCTCCTCGCCGT 60.153 57.895 0.00 0.00 0.00 5.68
2480 5336 4.142578 CGCAGTAGGAGCTACAGGTATATG 60.143 50.000 0.00 0.00 39.22 1.78
2531 5387 3.304257 GCTTATTCTGTGGCATGATTCCG 60.304 47.826 0.00 0.00 0.00 4.30
2537 5393 1.959985 TGTGGCATGATTCCGTTGTTT 59.040 42.857 0.00 0.00 0.00 2.83
2545 5401 5.106475 GCATGATTCCGTTGTTTTGGTAGTA 60.106 40.000 0.00 0.00 0.00 1.82
2549 5405 5.676532 TTCCGTTGTTTTGGTAGTATGTG 57.323 39.130 0.00 0.00 0.00 3.21
2550 5406 4.066490 TCCGTTGTTTTGGTAGTATGTGG 58.934 43.478 0.00 0.00 0.00 4.17
2565 5421 6.611613 AGTATGTGGAGTCTGAATTCTGAA 57.388 37.500 15.70 1.18 0.00 3.02
2576 5432 7.551585 AGTCTGAATTCTGAACATAGTACTGG 58.448 38.462 15.70 0.00 0.00 4.00
2577 5433 7.179338 AGTCTGAATTCTGAACATAGTACTGGT 59.821 37.037 15.70 0.45 0.00 4.00
2611 5467 7.801716 TCTTGCAAAACTAAAGCTCTTAAGA 57.198 32.000 4.81 4.81 0.00 2.10
2615 5471 6.546034 TGCAAAACTAAAGCTCTTAAGACCTT 59.454 34.615 7.15 7.15 0.00 3.50
2617 5473 7.379797 GCAAAACTAAAGCTCTTAAGACCTTTG 59.620 37.037 25.95 19.72 33.45 2.77
2630 5486 9.010029 TCTTAAGACCTTTGTTGTCCAATTATC 57.990 33.333 0.00 0.00 33.09 1.75
2641 5497 8.586879 TGTTGTCCAATTATCATGGTATTTCA 57.413 30.769 0.00 0.00 39.09 2.69
2682 5538 4.947388 TCCTGTTATGCATGGGTTTAGTTC 59.053 41.667 10.16 0.00 0.00 3.01
2720 5576 4.523083 TGTGGGCATAGGTTTACTTCATC 58.477 43.478 0.00 0.00 0.00 2.92
2721 5577 4.018870 TGTGGGCATAGGTTTACTTCATCA 60.019 41.667 0.00 0.00 0.00 3.07
2723 5579 6.126623 TGTGGGCATAGGTTTACTTCATCATA 60.127 38.462 0.00 0.00 0.00 2.15
2725 5581 6.126623 TGGGCATAGGTTTACTTCATCATACA 60.127 38.462 0.00 0.00 0.00 2.29
2752 5721 4.765813 ACTAACCCGCTAATGTGGTAAT 57.234 40.909 0.00 0.00 42.08 1.89
2756 5730 5.731957 AACCCGCTAATGTGGTAATTTTT 57.268 34.783 0.00 0.00 42.08 1.94
2787 5761 5.840940 ACTCGTGTTTGCTACTAATGAAC 57.159 39.130 0.00 0.00 0.00 3.18
2788 5762 5.294356 ACTCGTGTTTGCTACTAATGAACA 58.706 37.500 0.00 0.00 0.00 3.18
2789 5763 5.176958 ACTCGTGTTTGCTACTAATGAACAC 59.823 40.000 7.41 7.41 43.90 3.32
2790 5764 5.294356 TCGTGTTTGCTACTAATGAACACT 58.706 37.500 13.61 0.00 44.69 3.55
2791 5765 5.404366 TCGTGTTTGCTACTAATGAACACTC 59.596 40.000 13.61 0.00 44.69 3.51
2792 5766 5.389516 CGTGTTTGCTACTAATGAACACTCC 60.390 44.000 13.61 0.00 44.69 3.85
2793 5767 5.001232 TGTTTGCTACTAATGAACACTCCC 58.999 41.667 0.00 0.00 0.00 4.30
2794 5768 5.221843 TGTTTGCTACTAATGAACACTCCCT 60.222 40.000 0.00 0.00 0.00 4.20
2795 5769 4.737855 TGCTACTAATGAACACTCCCTC 57.262 45.455 0.00 0.00 0.00 4.30
2796 5770 3.451178 TGCTACTAATGAACACTCCCTCC 59.549 47.826 0.00 0.00 0.00 4.30
2797 5771 3.451178 GCTACTAATGAACACTCCCTCCA 59.549 47.826 0.00 0.00 0.00 3.86
2798 5772 4.101741 GCTACTAATGAACACTCCCTCCAT 59.898 45.833 0.00 0.00 0.00 3.41
2799 5773 4.762289 ACTAATGAACACTCCCTCCATC 57.238 45.455 0.00 0.00 0.00 3.51
2800 5774 3.456277 ACTAATGAACACTCCCTCCATCC 59.544 47.826 0.00 0.00 0.00 3.51
2801 5775 1.216990 ATGAACACTCCCTCCATCCC 58.783 55.000 0.00 0.00 0.00 3.85
2802 5776 0.178876 TGAACACTCCCTCCATCCCA 60.179 55.000 0.00 0.00 0.00 4.37
2803 5777 0.991920 GAACACTCCCTCCATCCCAA 59.008 55.000 0.00 0.00 0.00 4.12
2804 5778 1.354368 GAACACTCCCTCCATCCCAAA 59.646 52.381 0.00 0.00 0.00 3.28
2805 5779 1.455822 ACACTCCCTCCATCCCAAAA 58.544 50.000 0.00 0.00 0.00 2.44
2806 5780 2.003072 ACACTCCCTCCATCCCAAAAT 58.997 47.619 0.00 0.00 0.00 1.82
2807 5781 3.197983 ACACTCCCTCCATCCCAAAATA 58.802 45.455 0.00 0.00 0.00 1.40
2808 5782 3.596046 ACACTCCCTCCATCCCAAAATAA 59.404 43.478 0.00 0.00 0.00 1.40
2809 5783 4.210331 CACTCCCTCCATCCCAAAATAAG 58.790 47.826 0.00 0.00 0.00 1.73
2810 5784 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
2811 5785 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
2812 5786 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
2813 5787 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
2814 5788 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
2815 5789 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
2816 5790 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
2817 5791 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
2818 5792 5.945784 TCCATCCCAAAATAAGTGTCTCAAG 59.054 40.000 0.00 0.00 0.00 3.02
2819 5793 5.393461 CCATCCCAAAATAAGTGTCTCAAGC 60.393 44.000 0.00 0.00 0.00 4.01
2820 5794 4.985538 TCCCAAAATAAGTGTCTCAAGCT 58.014 39.130 0.00 0.00 0.00 3.74
2821 5795 5.385198 TCCCAAAATAAGTGTCTCAAGCTT 58.615 37.500 0.00 0.00 0.00 3.74
2822 5796 6.539173 TCCCAAAATAAGTGTCTCAAGCTTA 58.461 36.000 0.00 0.00 0.00 3.09
2823 5797 6.655003 TCCCAAAATAAGTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
2824 5798 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
2825 5799 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
2826 5800 8.443937 CCAAAATAAGTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
2827 5801 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
2828 5802 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
2829 5803 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
2830 5804 5.793030 AGTGTCTCAAGCTTAGTACAACT 57.207 39.130 0.00 0.00 0.00 3.16
2831 5805 6.163135 AGTGTCTCAAGCTTAGTACAACTT 57.837 37.500 0.00 0.00 0.00 2.66
2832 5806 6.583562 AGTGTCTCAAGCTTAGTACAACTTT 58.416 36.000 0.00 0.00 0.00 2.66
2833 5807 6.480320 AGTGTCTCAAGCTTAGTACAACTTTG 59.520 38.462 0.00 0.00 0.00 2.77
2834 5808 6.258068 GTGTCTCAAGCTTAGTACAACTTTGT 59.742 38.462 0.00 0.00 44.86 2.83
2835 5809 7.437267 GTGTCTCAAGCTTAGTACAACTTTGTA 59.563 37.037 0.00 0.00 42.35 2.41
2860 5834 8.461249 ACTAGAGTTAGTACAAAGTTGAGACA 57.539 34.615 0.00 0.00 38.35 3.41
2861 5835 8.351461 ACTAGAGTTAGTACAAAGTTGAGACAC 58.649 37.037 0.00 0.00 38.35 3.67
2862 5836 7.349412 AGAGTTAGTACAAAGTTGAGACACT 57.651 36.000 0.00 0.00 0.00 3.55
2863 5837 7.783042 AGAGTTAGTACAAAGTTGAGACACTT 58.217 34.615 0.00 0.00 38.74 3.16
2864 5838 7.707035 AGAGTTAGTACAAAGTTGAGACACTTG 59.293 37.037 0.00 0.00 37.07 3.16
2865 5839 7.328737 AGTTAGTACAAAGTTGAGACACTTGT 58.671 34.615 0.00 0.00 37.07 3.16
2866 5840 7.822822 AGTTAGTACAAAGTTGAGACACTTGTT 59.177 33.333 0.00 0.00 37.07 2.83
2867 5841 8.448615 GTTAGTACAAAGTTGAGACACTTGTTT 58.551 33.333 0.00 0.00 37.07 2.83
2868 5842 7.073342 AGTACAAAGTTGAGACACTTGTTTC 57.927 36.000 0.00 0.00 37.07 2.78
2869 5843 4.969816 ACAAAGTTGAGACACTTGTTTCG 58.030 39.130 0.00 0.00 37.07 3.46
2870 5844 4.142687 ACAAAGTTGAGACACTTGTTTCGG 60.143 41.667 0.00 0.00 37.07 4.30
2871 5845 2.561569 AGTTGAGACACTTGTTTCGGG 58.438 47.619 0.00 0.00 32.42 5.14
2872 5846 1.602377 GTTGAGACACTTGTTTCGGGG 59.398 52.381 0.00 0.00 32.42 5.73
2873 5847 0.534203 TGAGACACTTGTTTCGGGGC 60.534 55.000 0.00 0.00 32.42 5.80
2874 5848 1.566018 GAGACACTTGTTTCGGGGCG 61.566 60.000 0.00 0.00 0.00 6.13
2875 5849 2.593436 ACACTTGTTTCGGGGCGG 60.593 61.111 0.00 0.00 0.00 6.13
2876 5850 2.281208 CACTTGTTTCGGGGCGGA 60.281 61.111 0.00 0.00 0.00 5.54
2877 5851 2.032071 ACTTGTTTCGGGGCGGAG 59.968 61.111 0.00 0.00 0.00 4.63
2878 5852 2.746277 CTTGTTTCGGGGCGGAGG 60.746 66.667 0.00 0.00 0.00 4.30
2879 5853 4.338710 TTGTTTCGGGGCGGAGGG 62.339 66.667 0.00 0.00 0.00 4.30
2881 5855 4.468689 GTTTCGGGGCGGAGGGAG 62.469 72.222 0.00 0.00 0.00 4.30
2891 5865 0.685097 GCGGAGGGAGTATATGCCAA 59.315 55.000 0.00 0.00 43.31 4.52
2945 5922 5.115021 GCTTTTAAACATACTCGTGTTGTGC 59.885 40.000 0.00 0.00 41.22 4.57
2948 5925 4.893424 AAACATACTCGTGTTGTGCTTT 57.107 36.364 0.00 0.00 41.22 3.51
2954 5931 6.426937 ACATACTCGTGTTGTGCTTTAATTCT 59.573 34.615 0.00 0.00 0.00 2.40
3084 6061 2.435586 CAGTCGCAGCCCAAGGAG 60.436 66.667 0.00 0.00 0.00 3.69
3085 6062 3.710722 AGTCGCAGCCCAAGGAGG 61.711 66.667 0.00 0.00 37.03 4.30
3086 6063 3.706373 GTCGCAGCCCAAGGAGGA 61.706 66.667 0.00 0.00 41.22 3.71
3087 6064 3.393970 TCGCAGCCCAAGGAGGAG 61.394 66.667 0.00 0.00 41.22 3.69
3089 6066 4.811364 GCAGCCCAAGGAGGAGCC 62.811 72.222 0.00 0.00 41.22 4.70
3090 6067 4.120755 CAGCCCAAGGAGGAGCCC 62.121 72.222 0.00 0.00 41.22 5.19
3095 6072 4.101448 CAAGGAGGAGCCCCCGTG 62.101 72.222 0.00 0.00 40.87 4.94
3096 6073 4.332543 AAGGAGGAGCCCCCGTGA 62.333 66.667 0.00 0.00 40.87 4.35
3099 6076 3.775654 GAGGAGCCCCCGTGACAG 61.776 72.222 0.00 0.00 40.87 3.51
3100 6077 4.640690 AGGAGCCCCCGTGACAGT 62.641 66.667 0.00 0.00 40.87 3.55
3101 6078 4.083862 GGAGCCCCCGTGACAGTC 62.084 72.222 0.00 0.00 0.00 3.51
3102 6079 4.436998 GAGCCCCCGTGACAGTCG 62.437 72.222 0.00 0.00 0.00 4.18
3105 6082 4.742201 CCCCCGTGACAGTCGCAG 62.742 72.222 14.49 2.55 0.00 5.18
3109 6086 4.662961 CGTGACAGTCGCAGCCCA 62.663 66.667 14.49 0.00 0.00 5.36
3110 6087 2.280797 GTGACAGTCGCAGCCCAA 60.281 61.111 9.36 0.00 0.00 4.12
3111 6088 2.031012 TGACAGTCGCAGCCCAAG 59.969 61.111 0.00 0.00 0.00 3.61
3112 6089 2.743928 GACAGTCGCAGCCCAAGG 60.744 66.667 0.00 0.00 0.00 3.61
3113 6090 3.240134 GACAGTCGCAGCCCAAGGA 62.240 63.158 0.00 0.00 0.00 3.36
3484 6461 0.179029 CTTCCGGTGTTCACCCAGTT 60.179 55.000 15.20 0.00 0.00 3.16
3531 6511 7.471260 CGAGAGATGGATCAAATTCTTCCTACT 60.471 40.741 0.00 0.00 0.00 2.57
3533 6513 6.060788 AGATGGATCAAATTCTTCCTACTGC 58.939 40.000 0.00 0.00 0.00 4.40
3536 6516 6.349300 TGGATCAAATTCTTCCTACTGCTAC 58.651 40.000 0.00 0.00 0.00 3.58
3546 6526 3.952931 TCCTACTGCTACGAAACTCTCT 58.047 45.455 0.00 0.00 0.00 3.10
3590 6571 6.811253 TGCCTGTACGAGTTTGATTTTATT 57.189 33.333 0.00 0.00 0.00 1.40
3731 6728 1.396648 TGCTACATGGTCGAAAATGCG 59.603 47.619 8.18 2.57 0.00 4.73
3757 6754 8.784043 GTGTAGTATTTGTCCTTTGAAAGATGT 58.216 33.333 6.49 0.00 0.00 3.06
3893 6890 0.326904 AGGTCCCTCTCATGGATGCA 60.327 55.000 0.00 0.00 33.65 3.96
3896 6893 0.683412 TCCCTCTCATGGATGCATCG 59.317 55.000 20.15 7.15 0.00 3.84
3908 6905 0.930310 ATGCATCGGTGAAATCGTCG 59.070 50.000 0.00 0.00 0.00 5.12
3944 6944 4.555709 TCCACGCTGCCGGTTTGT 62.556 61.111 1.90 0.00 39.22 2.83
3983 6983 0.607217 CCATGTTGAGGCTGCTCACA 60.607 55.000 0.00 0.00 32.47 3.58
3991 6991 1.227205 GGCTGCTCACATCGGAGAG 60.227 63.158 0.00 0.00 43.63 3.20
3993 6993 1.440893 CTGCTCACATCGGAGAGGG 59.559 63.158 0.00 0.00 45.68 4.30
4013 7013 1.141881 CAGGCCGTCGCTATCAACT 59.858 57.895 0.00 0.00 34.44 3.16
4033 7033 2.202676 GCTTCTCTGACGGCGAGG 60.203 66.667 16.62 2.73 0.00 4.63
4034 7034 2.995872 GCTTCTCTGACGGCGAGGT 61.996 63.158 16.62 0.00 0.00 3.85
4094 7094 2.283529 GGAGAAGTCCAGGCCGTCA 61.284 63.158 0.00 0.00 43.31 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.612620 CGCTTTAATCAATGAACTAAAGAAAGT 57.387 29.630 22.07 0.00 34.63 2.66
3 4 8.578769 GCGCTTTAATCAATGAACTAAAGAAAG 58.421 33.333 22.07 15.82 34.63 2.62
4 5 7.270365 CGCGCTTTAATCAATGAACTAAAGAAA 59.730 33.333 22.07 3.40 34.63 2.52
5 6 6.740905 CGCGCTTTAATCAATGAACTAAAGAA 59.259 34.615 22.07 0.00 34.63 2.52
6 7 6.091577 TCGCGCTTTAATCAATGAACTAAAGA 59.908 34.615 22.07 7.54 34.63 2.52
7 8 6.247903 TCGCGCTTTAATCAATGAACTAAAG 58.752 36.000 17.15 17.15 35.42 1.85
8 9 6.171932 TCGCGCTTTAATCAATGAACTAAA 57.828 33.333 5.56 0.00 0.00 1.85
9 10 5.788055 TCGCGCTTTAATCAATGAACTAA 57.212 34.783 5.56 0.00 0.00 2.24
10 11 5.753438 AGATCGCGCTTTAATCAATGAACTA 59.247 36.000 5.56 0.00 0.00 2.24
11 12 4.572389 AGATCGCGCTTTAATCAATGAACT 59.428 37.500 5.56 0.00 0.00 3.01
12 13 4.837567 AGATCGCGCTTTAATCAATGAAC 58.162 39.130 5.56 0.00 0.00 3.18
13 14 4.024893 GGAGATCGCGCTTTAATCAATGAA 60.025 41.667 5.56 0.00 0.00 2.57
14 15 3.494626 GGAGATCGCGCTTTAATCAATGA 59.505 43.478 5.56 0.00 0.00 2.57
15 16 3.248363 TGGAGATCGCGCTTTAATCAATG 59.752 43.478 5.56 0.00 0.00 2.82
16 17 3.248602 GTGGAGATCGCGCTTTAATCAAT 59.751 43.478 5.56 0.00 0.00 2.57
17 18 2.607635 GTGGAGATCGCGCTTTAATCAA 59.392 45.455 5.56 0.00 0.00 2.57
18 19 2.201732 GTGGAGATCGCGCTTTAATCA 58.798 47.619 5.56 0.00 0.00 2.57
19 20 2.033662 GTGTGGAGATCGCGCTTTAATC 60.034 50.000 5.56 0.00 33.88 1.75
20 21 1.933853 GTGTGGAGATCGCGCTTTAAT 59.066 47.619 5.56 0.00 33.88 1.40
21 22 1.337354 TGTGTGGAGATCGCGCTTTAA 60.337 47.619 5.56 0.00 37.29 1.52
22 23 0.245266 TGTGTGGAGATCGCGCTTTA 59.755 50.000 5.56 0.00 37.29 1.85
23 24 0.602638 TTGTGTGGAGATCGCGCTTT 60.603 50.000 5.56 0.00 37.29 3.51
24 25 1.005037 TTGTGTGGAGATCGCGCTT 60.005 52.632 5.56 0.00 37.29 4.68
25 26 1.446792 CTTGTGTGGAGATCGCGCT 60.447 57.895 5.56 0.00 37.29 5.92
26 27 1.291877 AACTTGTGTGGAGATCGCGC 61.292 55.000 0.00 0.00 36.94 6.86
27 28 1.148310 AAACTTGTGTGGAGATCGCG 58.852 50.000 0.00 0.00 0.00 5.87
28 29 4.391830 TCATAAAACTTGTGTGGAGATCGC 59.608 41.667 0.00 0.00 0.00 4.58
29 30 5.163854 GGTCATAAAACTTGTGTGGAGATCG 60.164 44.000 0.00 0.00 0.00 3.69
30 31 5.163854 CGGTCATAAAACTTGTGTGGAGATC 60.164 44.000 0.00 0.00 0.00 2.75
31 32 4.695455 CGGTCATAAAACTTGTGTGGAGAT 59.305 41.667 0.00 0.00 0.00 2.75
32 33 4.062293 CGGTCATAAAACTTGTGTGGAGA 58.938 43.478 0.00 0.00 0.00 3.71
33 34 3.813166 ACGGTCATAAAACTTGTGTGGAG 59.187 43.478 0.00 0.00 0.00 3.86
34 35 3.811083 ACGGTCATAAAACTTGTGTGGA 58.189 40.909 0.00 0.00 0.00 4.02
35 36 4.992319 TCTACGGTCATAAAACTTGTGTGG 59.008 41.667 0.00 0.00 0.00 4.17
36 37 6.367695 TCATCTACGGTCATAAAACTTGTGTG 59.632 38.462 0.00 0.00 0.00 3.82
37 38 6.460781 TCATCTACGGTCATAAAACTTGTGT 58.539 36.000 0.00 0.00 0.00 3.72
38 39 6.961359 TCATCTACGGTCATAAAACTTGTG 57.039 37.500 0.00 0.00 0.00 3.33
39 40 7.159372 AGTTCATCTACGGTCATAAAACTTGT 58.841 34.615 0.00 0.00 0.00 3.16
40 41 7.596749 AGTTCATCTACGGTCATAAAACTTG 57.403 36.000 0.00 0.00 0.00 3.16
42 43 9.962783 GTATAGTTCATCTACGGTCATAAAACT 57.037 33.333 0.00 0.00 0.00 2.66
43 44 9.740239 TGTATAGTTCATCTACGGTCATAAAAC 57.260 33.333 0.00 0.00 0.00 2.43
44 45 9.740239 GTGTATAGTTCATCTACGGTCATAAAA 57.260 33.333 0.00 0.00 0.00 1.52
45 46 8.905850 TGTGTATAGTTCATCTACGGTCATAAA 58.094 33.333 0.00 0.00 0.00 1.40
46 47 8.454570 TGTGTATAGTTCATCTACGGTCATAA 57.545 34.615 0.00 0.00 0.00 1.90
47 48 7.935210 TCTGTGTATAGTTCATCTACGGTCATA 59.065 37.037 0.00 0.00 0.00 2.15
48 49 6.771267 TCTGTGTATAGTTCATCTACGGTCAT 59.229 38.462 0.00 0.00 0.00 3.06
49 50 6.117488 TCTGTGTATAGTTCATCTACGGTCA 58.883 40.000 0.00 0.00 0.00 4.02
50 51 6.615264 TCTGTGTATAGTTCATCTACGGTC 57.385 41.667 0.00 0.00 0.00 4.79
51 52 7.400599 TTTCTGTGTATAGTTCATCTACGGT 57.599 36.000 0.00 0.00 0.00 4.83
52 53 8.188799 TCTTTTCTGTGTATAGTTCATCTACGG 58.811 37.037 0.00 0.00 0.00 4.02
53 54 9.569167 TTCTTTTCTGTGTATAGTTCATCTACG 57.431 33.333 0.00 0.00 0.00 3.51
56 57 9.442047 CCTTTCTTTTCTGTGTATAGTTCATCT 57.558 33.333 0.00 0.00 0.00 2.90
57 58 8.669243 CCCTTTCTTTTCTGTGTATAGTTCATC 58.331 37.037 0.00 0.00 0.00 2.92
58 59 7.121315 GCCCTTTCTTTTCTGTGTATAGTTCAT 59.879 37.037 0.00 0.00 0.00 2.57
59 60 6.430000 GCCCTTTCTTTTCTGTGTATAGTTCA 59.570 38.462 0.00 0.00 0.00 3.18
60 61 6.430000 TGCCCTTTCTTTTCTGTGTATAGTTC 59.570 38.462 0.00 0.00 0.00 3.01
61 62 6.303839 TGCCCTTTCTTTTCTGTGTATAGTT 58.696 36.000 0.00 0.00 0.00 2.24
62 63 5.876357 TGCCCTTTCTTTTCTGTGTATAGT 58.124 37.500 0.00 0.00 0.00 2.12
63 64 6.817765 TTGCCCTTTCTTTTCTGTGTATAG 57.182 37.500 0.00 0.00 0.00 1.31
64 65 7.232534 ACATTTGCCCTTTCTTTTCTGTGTATA 59.767 33.333 0.00 0.00 0.00 1.47
65 66 6.041979 ACATTTGCCCTTTCTTTTCTGTGTAT 59.958 34.615 0.00 0.00 0.00 2.29
66 67 5.362430 ACATTTGCCCTTTCTTTTCTGTGTA 59.638 36.000 0.00 0.00 0.00 2.90
67 68 4.162131 ACATTTGCCCTTTCTTTTCTGTGT 59.838 37.500 0.00 0.00 0.00 3.72
68 69 4.696455 ACATTTGCCCTTTCTTTTCTGTG 58.304 39.130 0.00 0.00 0.00 3.66
69 70 5.362430 TGTACATTTGCCCTTTCTTTTCTGT 59.638 36.000 0.00 0.00 0.00 3.41
70 71 5.691754 GTGTACATTTGCCCTTTCTTTTCTG 59.308 40.000 0.00 0.00 0.00 3.02
71 72 5.362430 TGTGTACATTTGCCCTTTCTTTTCT 59.638 36.000 0.00 0.00 0.00 2.52
72 73 5.596845 TGTGTACATTTGCCCTTTCTTTTC 58.403 37.500 0.00 0.00 0.00 2.29
98 99 9.305925 CCATGGTCTTGCTTCTTATTTTTATTC 57.694 33.333 2.57 0.00 0.00 1.75
153 154 6.854496 TTGTCACTTTGTTGTGATACTACC 57.146 37.500 0.64 0.00 46.77 3.18
159 160 4.411327 CGTGTTTGTCACTTTGTTGTGAT 58.589 39.130 0.64 0.00 46.77 3.06
231 240 1.569072 AGGCCCAGTTACCCCTAAATG 59.431 52.381 0.00 0.00 0.00 2.32
232 241 1.569072 CAGGCCCAGTTACCCCTAAAT 59.431 52.381 0.00 0.00 0.00 1.40
243 252 2.996395 CTCTCATGCAGGCCCAGT 59.004 61.111 0.00 0.00 0.00 4.00
244 253 2.516460 GCTCTCATGCAGGCCCAG 60.516 66.667 0.00 0.00 0.00 4.45
263 284 2.112998 TCATGTTTAGACCCCCGGTAG 58.887 52.381 0.00 0.00 35.25 3.18
329 3031 2.223947 GCAGCCGGAAAGAAAAGGAAAA 60.224 45.455 5.05 0.00 0.00 2.29
332 3034 0.893727 GGCAGCCGGAAAGAAAAGGA 60.894 55.000 5.05 0.00 0.00 3.36
334 3070 1.210155 CGGCAGCCGGAAAGAAAAG 59.790 57.895 27.32 0.00 44.15 2.27
414 3170 1.826054 TTTGGACGGCAGGTGTTGG 60.826 57.895 0.00 0.00 0.00 3.77
565 3321 3.607370 GAAGGACAGACGGGGGCAC 62.607 68.421 0.00 0.00 0.00 5.01
566 3322 3.319198 GAAGGACAGACGGGGGCA 61.319 66.667 0.00 0.00 0.00 5.36
700 3458 3.664495 GCCATGGATGCGGATCTG 58.336 61.111 18.40 7.96 0.00 2.90
758 3516 3.947910 ACGAATCTAGAAAACCACCGA 57.052 42.857 0.00 0.00 0.00 4.69
776 3534 3.601685 AGCCCCAAAACCGCAACG 61.602 61.111 0.00 0.00 0.00 4.10
778 3536 1.532794 ATCAGCCCCAAAACCGCAA 60.533 52.632 0.00 0.00 0.00 4.85
790 3548 1.450531 CCCCTTGCGAATCATCAGCC 61.451 60.000 0.00 0.00 0.00 4.85
836 3595 5.234116 TCGTGACGCAATCTATTACGTAGTA 59.766 40.000 0.00 0.00 45.11 1.82
838 3597 4.521010 TCGTGACGCAATCTATTACGTAG 58.479 43.478 0.00 0.00 39.62 3.51
839 3598 4.270808 TCTCGTGACGCAATCTATTACGTA 59.729 41.667 0.00 0.00 39.62 3.57
840 3599 3.064408 TCTCGTGACGCAATCTATTACGT 59.936 43.478 0.00 0.74 41.95 3.57
882 3641 2.232941 AGCCAATCCAGCACAAATTCAG 59.767 45.455 0.00 0.00 0.00 3.02
909 3668 0.106669 GAGCAAACCCCTCCCCATAC 60.107 60.000 0.00 0.00 0.00 2.39
920 3679 1.288127 CAGCCAAGCAGAGCAAACC 59.712 57.895 0.00 0.00 0.00 3.27
934 3693 5.643777 ACTGACATCATACAAGTAAACAGCC 59.356 40.000 0.00 0.00 0.00 4.85
942 3701 4.973168 ACAACCACTGACATCATACAAGT 58.027 39.130 0.00 0.00 0.00 3.16
947 3706 4.142249 CGACCTACAACCACTGACATCATA 60.142 45.833 0.00 0.00 0.00 2.15
969 3728 2.124011 ACAAGCAGCAAAATGTCACG 57.876 45.000 0.00 0.00 0.00 4.35
1213 4051 6.015856 ACATGACATGAAACCGGTCAAAATAA 60.016 34.615 22.19 0.00 43.93 1.40
1223 4061 1.468520 GGGTGACATGACATGAAACCG 59.531 52.381 22.19 0.00 38.95 4.44
1261 4099 8.443937 CACAGACCTATTTGACTAAAAGCTAAC 58.556 37.037 0.00 0.00 0.00 2.34
1364 4202 4.096681 TCAGAGTAACCATGTGGATGACT 58.903 43.478 5.96 5.62 38.94 3.41
1407 4245 2.105477 ACAGGGTGCTGGCTTAGATATG 59.895 50.000 0.00 0.00 0.00 1.78
1648 4487 7.222872 TGTGATTTCCATTAAAACAGGCAATT 58.777 30.769 0.00 0.00 31.29 2.32
1790 4629 6.975772 GGTTACTTACAACAAATGCAAACTCA 59.024 34.615 0.00 0.00 0.00 3.41
1822 4661 7.648112 GGATTAAGAAGTCAAAACAAGGTGAAC 59.352 37.037 0.00 0.00 0.00 3.18
1882 4721 9.553064 ACTCCTGCAATAAGATTTATACAAGAG 57.447 33.333 0.00 0.00 0.00 2.85
2363 5217 4.432712 GCCTGTTTTCATCAACACAACTT 58.567 39.130 0.00 0.00 33.04 2.66
2423 5279 0.616395 TCCTATCACGCACCCTTCCA 60.616 55.000 0.00 0.00 0.00 3.53
2480 5336 3.243035 GGTGCCCAAATTTTCAAAGCAAC 60.243 43.478 0.00 0.00 0.00 4.17
2484 5340 2.832563 ACGGTGCCCAAATTTTCAAAG 58.167 42.857 0.00 0.00 0.00 2.77
2531 5387 5.995897 AGACTCCACATACTACCAAAACAAC 59.004 40.000 0.00 0.00 0.00 3.32
2537 5393 6.440647 AGAATTCAGACTCCACATACTACCAA 59.559 38.462 8.44 0.00 0.00 3.67
2545 5401 5.233083 TGTTCAGAATTCAGACTCCACAT 57.767 39.130 8.44 0.00 0.00 3.21
2549 5405 7.704472 CAGTACTATGTTCAGAATTCAGACTCC 59.296 40.741 8.44 0.00 0.00 3.85
2550 5406 7.704472 CCAGTACTATGTTCAGAATTCAGACTC 59.296 40.741 8.44 2.22 0.00 3.36
2602 5458 4.134563 TGGACAACAAAGGTCTTAAGAGC 58.865 43.478 24.02 24.02 42.47 4.09
2611 5467 5.779771 ACCATGATAATTGGACAACAAAGGT 59.220 36.000 0.00 0.00 43.46 3.50
2615 5471 9.029368 TGAAATACCATGATAATTGGACAACAA 57.971 29.630 0.00 0.00 44.54 2.83
2682 5538 2.219458 CCACAGAATAGCAGCAGATGG 58.781 52.381 0.00 0.00 0.00 3.51
2720 5576 8.617809 ACATTAGCGGGTTAGTAAAAATGTATG 58.382 33.333 0.00 0.00 35.25 2.39
2721 5577 8.617809 CACATTAGCGGGTTAGTAAAAATGTAT 58.382 33.333 0.00 0.00 35.25 2.29
2723 5579 6.127842 CCACATTAGCGGGTTAGTAAAAATGT 60.128 38.462 0.00 0.00 36.91 2.71
2725 5581 5.947566 ACCACATTAGCGGGTTAGTAAAAAT 59.052 36.000 0.00 0.00 0.00 1.82
2777 5751 4.654262 GGATGGAGGGAGTGTTCATTAGTA 59.346 45.833 0.00 0.00 0.00 1.82
2787 5761 2.834638 ATTTTGGGATGGAGGGAGTG 57.165 50.000 0.00 0.00 0.00 3.51
2788 5762 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
2789 5763 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
2790 5764 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
2791 5765 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
2792 5766 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
2793 5767 5.500234 TGAGACACTTATTTTGGGATGGAG 58.500 41.667 0.00 0.00 0.00 3.86
2794 5768 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
2795 5769 5.393461 GCTTGAGACACTTATTTTGGGATGG 60.393 44.000 0.00 0.00 0.00 3.51
2796 5770 5.416952 AGCTTGAGACACTTATTTTGGGATG 59.583 40.000 0.00 0.00 0.00 3.51
2797 5771 5.574188 AGCTTGAGACACTTATTTTGGGAT 58.426 37.500 0.00 0.00 0.00 3.85
2798 5772 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
2799 5773 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
2800 5774 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
2801 5775 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
2802 5776 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
2803 5777 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
2804 5778 8.368668 AGTTGTACTAAGCTTGAGACACTTATT 58.631 33.333 9.86 0.00 0.00 1.40
2805 5779 7.897864 AGTTGTACTAAGCTTGAGACACTTAT 58.102 34.615 9.86 0.00 0.00 1.73
2806 5780 7.286215 AGTTGTACTAAGCTTGAGACACTTA 57.714 36.000 9.86 0.00 0.00 2.24
2807 5781 6.163135 AGTTGTACTAAGCTTGAGACACTT 57.837 37.500 9.86 0.00 0.00 3.16
2808 5782 5.793030 AGTTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 7.29 0.00 3.55
2809 5783 6.258068 ACAAAGTTGTACTAAGCTTGAGACAC 59.742 38.462 9.86 7.18 40.16 3.67
2810 5784 6.346096 ACAAAGTTGTACTAAGCTTGAGACA 58.654 36.000 9.86 7.12 40.16 3.41
2811 5785 6.846325 ACAAAGTTGTACTAAGCTTGAGAC 57.154 37.500 9.86 4.39 40.16 3.36
2834 5808 9.565090 TGTCTCAACTTTGTACTAACTCTAGTA 57.435 33.333 0.00 0.00 39.23 1.82
2835 5809 8.351461 GTGTCTCAACTTTGTACTAACTCTAGT 58.649 37.037 0.00 0.00 41.43 2.57
2836 5810 8.569641 AGTGTCTCAACTTTGTACTAACTCTAG 58.430 37.037 0.00 0.00 0.00 2.43
2837 5811 8.461249 AGTGTCTCAACTTTGTACTAACTCTA 57.539 34.615 0.00 0.00 0.00 2.43
2838 5812 7.349412 AGTGTCTCAACTTTGTACTAACTCT 57.651 36.000 0.00 0.00 0.00 3.24
2839 5813 7.491696 ACAAGTGTCTCAACTTTGTACTAACTC 59.508 37.037 0.00 0.00 38.34 3.01
2840 5814 7.328737 ACAAGTGTCTCAACTTTGTACTAACT 58.671 34.615 0.00 0.00 38.34 2.24
2841 5815 7.535489 ACAAGTGTCTCAACTTTGTACTAAC 57.465 36.000 0.00 0.00 38.34 2.34
2842 5816 8.556213 AAACAAGTGTCTCAACTTTGTACTAA 57.444 30.769 0.00 0.00 38.34 2.24
2843 5817 7.009815 CGAAACAAGTGTCTCAACTTTGTACTA 59.990 37.037 0.00 0.00 38.34 1.82
2844 5818 6.183360 CGAAACAAGTGTCTCAACTTTGTACT 60.183 38.462 0.00 0.00 38.34 2.73
2845 5819 5.957796 CGAAACAAGTGTCTCAACTTTGTAC 59.042 40.000 0.00 0.00 38.34 2.90
2846 5820 5.064198 CCGAAACAAGTGTCTCAACTTTGTA 59.936 40.000 0.00 0.00 38.34 2.41
2847 5821 4.142687 CCGAAACAAGTGTCTCAACTTTGT 60.143 41.667 0.00 0.00 38.34 2.83
2848 5822 4.342772 CCGAAACAAGTGTCTCAACTTTG 58.657 43.478 0.00 0.00 38.34 2.77
2849 5823 3.377172 CCCGAAACAAGTGTCTCAACTTT 59.623 43.478 0.00 0.00 38.34 2.66
2850 5824 2.943033 CCCGAAACAAGTGTCTCAACTT 59.057 45.455 0.00 0.00 41.08 2.66
2851 5825 2.561569 CCCGAAACAAGTGTCTCAACT 58.438 47.619 0.00 0.00 0.00 3.16
2852 5826 1.602377 CCCCGAAACAAGTGTCTCAAC 59.398 52.381 0.00 0.00 0.00 3.18
2853 5827 1.961793 CCCCGAAACAAGTGTCTCAA 58.038 50.000 0.00 0.00 0.00 3.02
2854 5828 0.534203 GCCCCGAAACAAGTGTCTCA 60.534 55.000 0.00 0.00 0.00 3.27
2855 5829 1.566018 CGCCCCGAAACAAGTGTCTC 61.566 60.000 0.00 0.00 0.00 3.36
2856 5830 1.597027 CGCCCCGAAACAAGTGTCT 60.597 57.895 0.00 0.00 0.00 3.41
2857 5831 2.613506 CCGCCCCGAAACAAGTGTC 61.614 63.158 0.00 0.00 0.00 3.67
2858 5832 2.593436 CCGCCCCGAAACAAGTGT 60.593 61.111 0.00 0.00 0.00 3.55
2859 5833 2.281208 TCCGCCCCGAAACAAGTG 60.281 61.111 0.00 0.00 0.00 3.16
2860 5834 2.032071 CTCCGCCCCGAAACAAGT 59.968 61.111 0.00 0.00 0.00 3.16
2861 5835 2.746277 CCTCCGCCCCGAAACAAG 60.746 66.667 0.00 0.00 0.00 3.16
2862 5836 4.338710 CCCTCCGCCCCGAAACAA 62.339 66.667 0.00 0.00 0.00 2.83
2864 5838 4.468689 CTCCCTCCGCCCCGAAAC 62.469 72.222 0.00 0.00 0.00 2.78
2865 5839 2.884179 ATACTCCCTCCGCCCCGAAA 62.884 60.000 0.00 0.00 0.00 3.46
2866 5840 2.010412 TATACTCCCTCCGCCCCGAA 62.010 60.000 0.00 0.00 0.00 4.30
2867 5841 1.797018 ATATACTCCCTCCGCCCCGA 61.797 60.000 0.00 0.00 0.00 5.14
2868 5842 1.305046 ATATACTCCCTCCGCCCCG 60.305 63.158 0.00 0.00 0.00 5.73
2869 5843 1.900545 GCATATACTCCCTCCGCCCC 61.901 65.000 0.00 0.00 0.00 5.80
2870 5844 1.597461 GCATATACTCCCTCCGCCC 59.403 63.158 0.00 0.00 0.00 6.13
2871 5845 1.192146 TGGCATATACTCCCTCCGCC 61.192 60.000 0.00 0.00 38.56 6.13
2872 5846 0.685097 TTGGCATATACTCCCTCCGC 59.315 55.000 0.00 0.00 0.00 5.54
2873 5847 2.303022 ACATTGGCATATACTCCCTCCG 59.697 50.000 0.00 0.00 0.00 4.63
2874 5848 5.499004 TTACATTGGCATATACTCCCTCC 57.501 43.478 0.00 0.00 0.00 4.30
2875 5849 7.817418 TTTTTACATTGGCATATACTCCCTC 57.183 36.000 0.00 0.00 0.00 4.30
3084 6061 4.083862 GACTGTCACGGGGGCTCC 62.084 72.222 0.00 0.00 0.00 4.70
3085 6062 4.436998 CGACTGTCACGGGGGCTC 62.437 72.222 8.73 0.00 0.00 4.70
3088 6065 4.742201 CTGCGACTGTCACGGGGG 62.742 72.222 8.73 0.00 0.00 5.40
3092 6069 4.662961 TGGGCTGCGACTGTCACG 62.663 66.667 8.73 0.00 0.00 4.35
3093 6070 2.280797 TTGGGCTGCGACTGTCAC 60.281 61.111 8.73 0.00 0.00 3.67
3094 6071 2.031012 CTTGGGCTGCGACTGTCA 59.969 61.111 8.73 0.00 0.00 3.58
3095 6072 2.743928 CCTTGGGCTGCGACTGTC 60.744 66.667 0.00 0.00 0.00 3.51
3096 6073 3.241530 TCCTTGGGCTGCGACTGT 61.242 61.111 0.00 0.00 0.00 3.55
3097 6074 2.435586 CTCCTTGGGCTGCGACTG 60.436 66.667 0.00 0.00 0.00 3.51
3098 6075 3.710722 CCTCCTTGGGCTGCGACT 61.711 66.667 0.00 0.00 0.00 4.18
3099 6076 3.672295 CTCCTCCTTGGGCTGCGAC 62.672 68.421 0.00 0.00 36.20 5.19
3100 6077 3.393970 CTCCTCCTTGGGCTGCGA 61.394 66.667 0.00 0.00 36.20 5.10
3102 6079 4.811364 GGCTCCTCCTTGGGCTGC 62.811 72.222 0.00 0.00 36.20 5.25
3103 6080 4.120755 GGGCTCCTCCTTGGGCTG 62.121 72.222 0.00 0.00 36.20 4.85
3108 6085 4.101448 CACGGGGGCTCCTCCTTG 62.101 72.222 0.52 0.00 34.39 3.61
3109 6086 4.332543 TCACGGGGGCTCCTCCTT 62.333 66.667 0.52 0.00 34.39 3.36
3112 6089 3.775654 CTGTCACGGGGGCTCCTC 61.776 72.222 0.52 0.00 0.00 3.71
3113 6090 4.640690 ACTGTCACGGGGGCTCCT 62.641 66.667 0.52 0.00 0.00 3.69
3484 6461 0.764890 CCCTCACCAGGTGAACTTCA 59.235 55.000 23.11 0.00 42.26 3.02
3531 6511 5.779922 ACATGTTTAGAGAGTTTCGTAGCA 58.220 37.500 0.00 0.00 0.00 3.49
3533 6513 7.869016 TCAACATGTTTAGAGAGTTTCGTAG 57.131 36.000 8.77 0.00 0.00 3.51
3536 6516 6.943981 TGTTCAACATGTTTAGAGAGTTTCG 58.056 36.000 8.77 0.00 0.00 3.46
3546 6526 6.039616 GGCAAGTCTTTGTTCAACATGTTTA 58.960 36.000 8.77 0.00 36.65 2.01
3590 6571 9.128404 AGTATCAATACCGAAATAGAGTACACA 57.872 33.333 0.00 0.00 33.79 3.72
3731 6728 8.784043 ACATCTTTCAAAGGACAAATACTACAC 58.216 33.333 0.00 0.00 0.00 2.90
3893 6890 0.524816 CCGACGACGATTTCACCGAT 60.525 55.000 9.28 0.00 42.66 4.18
3896 6893 0.179156 TAGCCGACGACGATTTCACC 60.179 55.000 9.28 0.00 42.66 4.02
3993 6993 3.733344 TTGATAGCGACGGCCTGGC 62.733 63.158 11.05 11.05 41.24 4.85
4006 7006 2.732282 CGTCAGAGAAGCGCAGTTGATA 60.732 50.000 11.47 0.00 0.00 2.15
4241 7241 1.686052 GAGCTGGAGAAGATCGTGGAT 59.314 52.381 0.00 0.00 30.22 3.41


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

AutoCloner maintained by Alex Coulton.