Multiple sequence alignment - TraesCS2A01G437500

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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 TraesCS2A01G437500 chr2A 100.000 4455 0 0 1 4455 689202548 689198094 0.000000e+00 8227.0
1 TraesCS2A01G437500 chr2A 92.199 141 9 2 2248 2387 86445880 86446019 9.770000e-47 198.0
2 TraesCS2A01G437500 chr2A 91.176 136 10 1 2248 2383 107386527 107386660 2.740000e-42 183.0
3 TraesCS2A01G437500 chr2B 89.961 2032 129 23 268 2231 652411633 652413657 0.000000e+00 2553.0
4 TraesCS2A01G437500 chr2B 94.090 1049 33 8 2790 3822 652413916 652414951 0.000000e+00 1567.0
5 TraesCS2A01G437500 chr2B 93.676 253 11 3 2378 2628 652413662 652413911 1.510000e-99 374.0
6 TraesCS2A01G437500 chr2B 79.726 365 41 16 3871 4210 652414958 652415314 2.680000e-57 233.0
7 TraesCS2A01G437500 chr2B 92.025 163 11 1 2645 2805 608226738 608226900 1.250000e-55 228.0
8 TraesCS2A01G437500 chr2B 92.199 141 9 2 2248 2387 139077903 139078042 9.770000e-47 198.0
9 TraesCS2A01G437500 chr2B 90.066 151 14 1 4298 4447 652417391 652417541 1.260000e-45 195.0
10 TraesCS2A01G437500 chr2B 91.453 117 10 0 43 159 652411250 652411366 1.280000e-35 161.0
11 TraesCS2A01G437500 chr2B 90.526 95 9 0 4208 4302 652415371 652415465 4.680000e-25 126.0
12 TraesCS2A01G437500 chr2D 89.668 1655 108 25 43 1661 545852649 545854276 0.000000e+00 2050.0
13 TraesCS2A01G437500 chr2D 95.885 972 23 2 2789 3745 545855338 545856307 0.000000e+00 1557.0
14 TraesCS2A01G437500 chr2D 87.477 535 40 9 1659 2169 545854369 545854900 3.840000e-165 592.0
15 TraesCS2A01G437500 chr2D 97.222 252 6 1 2378 2628 545855079 545855330 4.120000e-115 425.0
16 TraesCS2A01G437500 chr2D 84.872 390 25 9 1256 1644 451009166 451008810 3.280000e-96 363.0
17 TraesCS2A01G437500 chr2D 91.713 181 13 2 4275 4455 545856952 545857130 2.660000e-62 250.0
18 TraesCS2A01G437500 chr2D 91.489 141 11 1 2248 2387 86085985 86086125 4.550000e-45 193.0
19 TraesCS2A01G437500 chr2D 90.141 142 11 3 2248 2387 556055790 556055650 9.840000e-42 182.0
20 TraesCS2A01G437500 chr2D 88.158 152 5 2 3793 3931 545856307 545856458 7.660000e-38 169.0
21 TraesCS2A01G437500 chr2D 80.000 145 9 8 3929 4057 545856617 545856757 6.140000e-14 89.8
22 TraesCS2A01G437500 chr7B 84.940 498 54 7 1147 1644 60368814 60368338 6.700000e-133 484.0
23 TraesCS2A01G437500 chr7B 83.203 512 51 14 1147 1644 486730815 486731305 1.900000e-118 436.0
24 TraesCS2A01G437500 chr7B 93.960 149 7 1 2645 2791 490208003 490208151 1.610000e-54 224.0
25 TraesCS2A01G437500 chr4B 84.538 498 56 7 1147 1644 59871465 59871941 1.450000e-129 473.0
26 TraesCS2A01G437500 chr6D 84.314 459 51 7 1190 1648 14447767 14448204 3.180000e-116 429.0
27 TraesCS2A01G437500 chr6D 95.597 159 7 0 588 746 2957882 2958040 5.720000e-64 255.0
28 TraesCS2A01G437500 chr6D 94.000 150 7 1 2645 2792 428908486 428908337 4.480000e-55 226.0
29 TraesCS2A01G437500 chr3A 84.987 393 38 9 2896 3273 108028107 108028493 3.250000e-101 379.0
30 TraesCS2A01G437500 chr3A 86.385 213 24 4 588 795 707465558 707465770 1.250000e-55 228.0
31 TraesCS2A01G437500 chr3A 91.124 169 7 5 2645 2805 585500336 585500168 5.800000e-54 222.0
32 TraesCS2A01G437500 chr3A 83.871 93 13 2 3852 3943 218471118 218471209 2.210000e-13 87.9
33 TraesCS2A01G437500 chr1A 84.987 393 38 7 2896 3273 537063778 537063392 3.250000e-101 379.0
34 TraesCS2A01G437500 chr1A 90.977 133 12 0 2248 2380 516570488 516570620 3.540000e-41 180.0
35 TraesCS2A01G437500 chr5B 86.025 322 24 8 1147 1468 42945218 42945518 4.300000e-85 326.0
36 TraesCS2A01G437500 chr7A 96.753 154 5 0 589 742 23331772 23331925 1.590000e-64 257.0
37 TraesCS2A01G437500 chr7A 93.893 131 8 0 2253 2383 130229568 130229698 9.770000e-47 198.0
38 TraesCS2A01G437500 chr7A 88.158 76 9 0 3865 3940 23306564 23306489 1.710000e-14 91.6
39 TraesCS2A01G437500 chr7A 83.516 91 13 2 3853 3942 112480879 112480790 2.860000e-12 84.2
40 TraesCS2A01G437500 chr7D 88.479 217 17 5 589 801 22782056 22782268 5.720000e-64 255.0
41 TraesCS2A01G437500 chr7D 94.558 147 7 1 2645 2791 586500041 586500186 4.480000e-55 226.0
42 TraesCS2A01G437500 chr7D 91.045 134 12 0 2248 2381 457148817 457148950 9.840000e-42 182.0
43 TraesCS2A01G437500 chrUn 92.045 176 12 2 43 216 299704160 299703985 3.440000e-61 246.0
44 TraesCS2A01G437500 chrUn 90.977 133 12 0 2248 2380 95996442 95996574 3.540000e-41 180.0
45 TraesCS2A01G437500 chrUn 92.727 110 8 0 43 152 352728750 352728641 4.610000e-35 159.0
46 TraesCS2A01G437500 chrUn 92.727 110 8 0 43 152 407129623 407129732 4.610000e-35 159.0
47 TraesCS2A01G437500 chr4A 94.904 157 8 0 589 745 707037085 707036929 3.440000e-61 246.0
48 TraesCS2A01G437500 chr4A 94.156 154 6 2 2645 2796 137966992 137967144 9.640000e-57 231.0
49 TraesCS2A01G437500 chr4A 94.156 154 6 2 2645 2796 137972817 137972665 9.640000e-57 231.0
50 TraesCS2A01G437500 chr4A 74.648 284 39 19 3853 4112 210983445 210983171 1.320000e-15 95.3
51 TraesCS2A01G437500 chr4A 84.946 93 12 2 3851 3942 684393100 684393191 4.740000e-15 93.5
52 TraesCS2A01G437500 chr3D 92.045 176 12 2 43 216 29476367 29476542 3.440000e-61 246.0
53 TraesCS2A01G437500 chr3D 92.045 176 12 2 43 216 29510479 29510654 3.440000e-61 246.0
54 TraesCS2A01G437500 chr3D 92.045 176 12 2 43 216 29549901 29550076 3.440000e-61 246.0
55 TraesCS2A01G437500 chr3D 91.477 176 13 2 43 216 29547191 29547366 1.600000e-59 241.0
56 TraesCS2A01G437500 chr3D 94.667 150 6 1 2645 2792 540564894 540564745 9.640000e-57 231.0
57 TraesCS2A01G437500 chr3D 91.515 165 8 5 2647 2805 444679385 444679221 5.800000e-54 222.0
58 TraesCS2A01G437500 chr6A 92.899 169 10 1 588 756 1985592 1985426 1.240000e-60 244.0
59 TraesCS2A01G437500 chr6A 85.859 99 12 2 3846 3943 535538213 535538116 2.190000e-18 104.0
60 TraesCS2A01G437500 chr6B 94.304 158 9 0 588 745 6168471 6168628 4.450000e-60 243.0
61 TraesCS2A01G437500 chr5A 87.209 172 16 5 2790 2961 345360313 345360148 1.640000e-44 191.0
62 TraesCS2A01G437500 chr5A 84.158 101 9 6 3853 3950 44323482 44323386 1.710000e-14 91.6
63 TraesCS2A01G437500 chr1D 89.286 56 5 1 3853 3907 415320212 415320267 8.000000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G437500 chr2A 689198094 689202548 4454 True 8227.000000 8227 100.000000 1 4455 1 chr2A.!!$R1 4454
1 TraesCS2A01G437500 chr2B 652411250 652417541 6291 False 744.142857 2553 89.928286 43 4447 7 chr2B.!!$F3 4404
2 TraesCS2A01G437500 chr2D 545852649 545857130 4481 False 733.257143 2050 90.017571 43 4455 7 chr2D.!!$F2 4412
3 TraesCS2A01G437500 chr3D 29547191 29550076 2885 False 243.500000 246 91.761000 43 216 2 chr3D.!!$F3 173

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
446 1722 0.596082 CGCACCCAAACCCAAAGTAG 59.404 55.0 0.0 0.0 0.00 2.57 F
1229 2547 0.594602 TTCCACGTGATTCGAGTCGT 59.405 50.0 19.3 0.0 42.86 4.34 F
1384 2703 0.031314 GATTCGATCCTGCTCGCTCA 59.969 55.0 0.0 0.0 38.52 4.26 F
2748 4433 0.101759 TTGCTCCGTATGTAGTCCGC 59.898 55.0 0.0 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 2703 0.179140 CGCCCAAATTGCAATAGCGT 60.179 50.0 25.5 6.7 46.23 5.07 R
2773 4458 0.106318 GGTACTCCCTCCGCTCCTAA 60.106 60.0 0.0 0.0 0.00 2.69 R
2776 4461 0.178970 TATGGTACTCCCTCCGCTCC 60.179 60.0 0.0 0.0 0.00 4.70 R
4156 6264 0.689745 ATAGCCTGCCCGGTAACTGA 60.690 55.0 0.0 0.0 34.25 3.41 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
23 24 4.457466 ACACCATCAACGAAGGTAAAAGT 58.543 39.130 0.00 0.00 31.49 2.66
24 25 4.274950 ACACCATCAACGAAGGTAAAAGTG 59.725 41.667 0.00 0.00 31.49 3.16
25 26 3.252458 ACCATCAACGAAGGTAAAAGTGC 59.748 43.478 0.00 0.00 31.49 4.40
26 27 3.252215 CCATCAACGAAGGTAAAAGTGCA 59.748 43.478 0.00 0.00 0.00 4.57
27 28 4.466828 CATCAACGAAGGTAAAAGTGCAG 58.533 43.478 0.00 0.00 0.00 4.41
28 29 3.537580 TCAACGAAGGTAAAAGTGCAGT 58.462 40.909 0.00 0.00 0.00 4.40
29 30 4.695396 TCAACGAAGGTAAAAGTGCAGTA 58.305 39.130 0.00 0.00 0.00 2.74
30 31 4.748102 TCAACGAAGGTAAAAGTGCAGTAG 59.252 41.667 0.00 0.00 0.00 2.57
31 32 3.064931 ACGAAGGTAAAAGTGCAGTAGC 58.935 45.455 0.00 0.00 42.57 3.58
47 48 4.157656 GCAGTAGCATACCCATGAACAAAA 59.842 41.667 0.00 0.00 44.47 2.44
71 72 9.651913 AAAAACAATGTCCATGAACCAATATAC 57.348 29.630 0.00 0.00 0.00 1.47
219 228 5.970140 TCACACATTTTGCACTTGAAATG 57.030 34.783 16.43 16.43 44.68 2.32
227 236 5.793026 TTTGCACTTGAAATGTTTTGACC 57.207 34.783 0.00 0.00 0.00 4.02
303 501 6.946229 ACTGAAATACGACTGTACATCAAC 57.054 37.500 0.00 0.00 31.74 3.18
326 524 4.079253 TGGAAACTGAAACCTAAGATGGC 58.921 43.478 0.00 0.00 0.00 4.40
328 526 4.082733 GGAAACTGAAACCTAAGATGGCAC 60.083 45.833 0.00 0.00 0.00 5.01
332 530 4.018960 ACTGAAACCTAAGATGGCACTCAT 60.019 41.667 0.00 0.00 39.13 2.90
368 716 8.531622 CACAATGTGTGCTTAAATATGGAAAA 57.468 30.769 5.00 0.00 41.89 2.29
446 1722 0.596082 CGCACCCAAACCCAAAGTAG 59.404 55.000 0.00 0.00 0.00 2.57
481 1757 4.008330 ACGTTGTAGATCCTCTTCTTCGA 58.992 43.478 0.00 0.00 0.00 3.71
540 1816 2.325583 ATTAGCCTCATTCCGCGAAA 57.674 45.000 8.23 0.00 0.00 3.46
547 1823 1.209127 CATTCCGCGAAACACCCAC 59.791 57.895 8.23 0.00 0.00 4.61
551 1827 2.356075 CGCGAAACACCCACGGTA 60.356 61.111 0.00 0.00 32.11 4.02
576 1852 3.195661 ACGGATAGAAATCGAGCCAAAC 58.804 45.455 0.00 0.00 32.44 2.93
637 1913 3.573598 GATGTAGCAGTCGATCATCTGG 58.426 50.000 13.56 0.26 34.12 3.86
1047 2361 3.118038 CCTTATTAGTGCTAACAGGCCCA 60.118 47.826 0.00 0.00 0.00 5.36
1120 2434 3.603770 GCACAAGACAACGATACAATTGC 59.396 43.478 5.05 0.00 0.00 3.56
1141 2455 2.407361 CGCGGCCGTAATAAATAGTCTG 59.593 50.000 28.70 0.00 0.00 3.51
1229 2547 0.594602 TTCCACGTGATTCGAGTCGT 59.405 50.000 19.30 0.00 42.86 4.34
1240 2558 4.211986 GAGTCGTCTCGCCTCTCT 57.788 61.111 0.00 0.00 0.00 3.10
1384 2703 0.031314 GATTCGATCCTGCTCGCTCA 59.969 55.000 0.00 0.00 38.52 4.26
1531 2850 2.819608 TGGATTTGCAGTTTGAGGTAGC 59.180 45.455 0.00 0.00 0.00 3.58
1561 2884 1.997311 TGTGGGCATCTAGCTGGCT 60.997 57.895 18.26 0.00 44.79 4.75
1605 2928 4.503991 CCTGGGTAGATCCAACTATTCTGC 60.504 50.000 0.00 0.00 36.21 4.26
1633 2956 4.963953 GCTGTTGCTATGTACGCTAAATTG 59.036 41.667 0.00 0.00 36.03 2.32
1637 2960 5.018539 TGCTATGTACGCTAAATTGACCT 57.981 39.130 0.00 0.00 0.00 3.85
1644 2967 6.636705 TGTACGCTAAATTGACCTGATTAGT 58.363 36.000 0.00 0.00 0.00 2.24
1648 2971 6.430000 ACGCTAAATTGACCTGATTAGTTTGT 59.570 34.615 0.00 0.00 0.00 2.83
1651 2974 7.062255 GCTAAATTGACCTGATTAGTTTGTTGC 59.938 37.037 0.00 0.00 0.00 4.17
1663 3081 3.477530 AGTTTGTTGCTCCAAGGTAGTC 58.522 45.455 0.00 0.00 0.00 2.59
1664 3082 3.118038 AGTTTGTTGCTCCAAGGTAGTCA 60.118 43.478 0.00 0.00 0.00 3.41
1667 3085 0.324943 TTGCTCCAAGGTAGTCAGGC 59.675 55.000 0.00 0.00 0.00 4.85
1747 3174 3.644265 TCTGTGGTAGTTTTGTAGCTCCA 59.356 43.478 0.00 0.00 0.00 3.86
1748 3175 3.997021 CTGTGGTAGTTTTGTAGCTCCAG 59.003 47.826 0.00 0.00 0.00 3.86
1749 3176 2.742589 GTGGTAGTTTTGTAGCTCCAGC 59.257 50.000 0.00 0.00 42.49 4.85
1807 3243 4.094887 TGTGCGATTTTTCTTCCAGCTATC 59.905 41.667 0.00 0.00 0.00 2.08
1809 3245 4.572389 TGCGATTTTTCTTCCAGCTATCTC 59.428 41.667 0.00 0.00 0.00 2.75
1814 3250 4.744795 TTTCTTCCAGCTATCTCTGTCC 57.255 45.455 0.00 0.00 32.32 4.02
1827 3263 2.069273 CTCTGTCCGTAAAACTGCAGG 58.931 52.381 19.93 0.00 0.00 4.85
1829 3265 1.531149 CTGTCCGTAAAACTGCAGGTG 59.469 52.381 19.93 0.00 0.00 4.00
1836 3282 3.059188 CGTAAAACTGCAGGTGGTTACAG 60.059 47.826 20.81 12.52 32.89 2.74
1848 3294 2.614057 GTGGTTACAGCATGGATAGTGC 59.386 50.000 0.00 0.00 43.62 4.40
1859 3305 4.764172 CATGGATAGTGCTATAGGCTTCC 58.236 47.826 1.04 0.00 42.39 3.46
1897 3345 6.513806 TTTGGGATGTTATGTGACATTCTG 57.486 37.500 2.29 0.00 40.21 3.02
1903 3351 7.370383 GGATGTTATGTGACATTCTGTGTTTT 58.630 34.615 2.29 0.00 42.36 2.43
1906 3354 7.870826 TGTTATGTGACATTCTGTGTTTTAGG 58.129 34.615 2.29 0.00 42.36 2.69
1907 3355 7.717436 TGTTATGTGACATTCTGTGTTTTAGGA 59.283 33.333 2.29 0.00 42.36 2.94
1935 3383 9.062524 TCCTAACCATGTAACAATATTGCATAC 57.937 33.333 15.48 17.26 0.00 2.39
2201 3755 8.169977 ACTTATATTTTGATGCATTCACCGAT 57.830 30.769 0.00 0.00 32.84 4.18
2223 3777 7.645340 CCGATTTTTGTAGGATTTGTCATGATC 59.355 37.037 0.00 0.00 0.00 2.92
2252 3806 6.024552 TCATTTTCTAATGAACACAAGGCC 57.975 37.500 0.00 0.00 45.38 5.19
2253 3807 5.774690 TCATTTTCTAATGAACACAAGGCCT 59.225 36.000 0.00 0.00 45.38 5.19
2254 3808 6.267471 TCATTTTCTAATGAACACAAGGCCTT 59.733 34.615 13.78 13.78 45.38 4.35
2255 3809 6.478512 TTTTCTAATGAACACAAGGCCTTT 57.521 33.333 17.61 0.00 31.02 3.11
2256 3810 6.478512 TTTCTAATGAACACAAGGCCTTTT 57.521 33.333 17.61 6.85 31.02 2.27
2257 3811 7.589958 TTTCTAATGAACACAAGGCCTTTTA 57.410 32.000 17.61 9.26 31.02 1.52
2258 3812 6.817765 TCTAATGAACACAAGGCCTTTTAG 57.182 37.500 17.61 18.33 0.00 1.85
2259 3813 3.942130 ATGAACACAAGGCCTTTTAGC 57.058 42.857 17.61 5.21 0.00 3.09
2260 3814 2.944129 TGAACACAAGGCCTTTTAGCT 58.056 42.857 17.61 0.00 0.00 3.32
2261 3815 3.295973 TGAACACAAGGCCTTTTAGCTT 58.704 40.909 17.61 2.69 0.00 3.74
2262 3816 3.704061 TGAACACAAGGCCTTTTAGCTTT 59.296 39.130 17.61 3.18 31.30 3.51
2263 3817 4.161377 TGAACACAAGGCCTTTTAGCTTTT 59.839 37.500 17.61 2.03 28.15 2.27
2264 3818 4.753516 ACACAAGGCCTTTTAGCTTTTT 57.246 36.364 17.61 0.00 28.15 1.94
2265 3819 4.693283 ACACAAGGCCTTTTAGCTTTTTC 58.307 39.130 17.61 0.00 28.15 2.29
2266 3820 4.058124 CACAAGGCCTTTTAGCTTTTTCC 58.942 43.478 17.61 0.00 28.15 3.13
2267 3821 3.967326 ACAAGGCCTTTTAGCTTTTTCCT 59.033 39.130 17.61 0.00 28.15 3.36
2268 3822 4.202253 ACAAGGCCTTTTAGCTTTTTCCTG 60.202 41.667 17.61 2.02 28.15 3.86
2269 3823 3.844640 AGGCCTTTTAGCTTTTTCCTGA 58.155 40.909 0.00 0.00 0.00 3.86
2270 3824 4.420206 AGGCCTTTTAGCTTTTTCCTGAT 58.580 39.130 0.00 0.00 0.00 2.90
2271 3825 4.840680 AGGCCTTTTAGCTTTTTCCTGATT 59.159 37.500 0.00 0.00 0.00 2.57
2272 3826 5.047021 AGGCCTTTTAGCTTTTTCCTGATTC 60.047 40.000 0.00 0.00 0.00 2.52
2273 3827 4.859245 GCCTTTTAGCTTTTTCCTGATTCG 59.141 41.667 0.00 0.00 0.00 3.34
2274 3828 5.564848 GCCTTTTAGCTTTTTCCTGATTCGT 60.565 40.000 0.00 0.00 0.00 3.85
2275 3829 6.349033 GCCTTTTAGCTTTTTCCTGATTCGTA 60.349 38.462 0.00 0.00 0.00 3.43
2276 3830 7.628580 GCCTTTTAGCTTTTTCCTGATTCGTAT 60.629 37.037 0.00 0.00 0.00 3.06
2277 3831 7.698130 CCTTTTAGCTTTTTCCTGATTCGTATG 59.302 37.037 0.00 0.00 0.00 2.39
2278 3832 7.681939 TTTAGCTTTTTCCTGATTCGTATGT 57.318 32.000 0.00 0.00 0.00 2.29
2279 3833 8.780846 TTTAGCTTTTTCCTGATTCGTATGTA 57.219 30.769 0.00 0.00 0.00 2.29
2280 3834 8.958119 TTAGCTTTTTCCTGATTCGTATGTAT 57.042 30.769 0.00 0.00 0.00 2.29
2281 3835 7.484035 AGCTTTTTCCTGATTCGTATGTATC 57.516 36.000 0.00 0.00 0.00 2.24
2282 3836 7.275920 AGCTTTTTCCTGATTCGTATGTATCT 58.724 34.615 3.57 0.00 0.00 1.98
2283 3837 8.421784 AGCTTTTTCCTGATTCGTATGTATCTA 58.578 33.333 3.57 0.00 0.00 1.98
2284 3838 8.704234 GCTTTTTCCTGATTCGTATGTATCTAG 58.296 37.037 3.57 0.00 0.00 2.43
2285 3839 9.967346 CTTTTTCCTGATTCGTATGTATCTAGA 57.033 33.333 0.00 0.00 0.00 2.43
2286 3840 9.745880 TTTTTCCTGATTCGTATGTATCTAGAC 57.254 33.333 0.00 0.00 0.00 2.59
2287 3841 8.459911 TTTCCTGATTCGTATGTATCTAGACA 57.540 34.615 0.00 0.00 0.00 3.41
2288 3842 7.436430 TCCTGATTCGTATGTATCTAGACAC 57.564 40.000 0.00 0.00 30.52 3.67
2289 3843 6.996282 TCCTGATTCGTATGTATCTAGACACA 59.004 38.462 6.26 6.26 30.52 3.72
2290 3844 7.665974 TCCTGATTCGTATGTATCTAGACACAT 59.334 37.037 19.95 19.95 38.81 3.21
2291 3845 8.300286 CCTGATTCGTATGTATCTAGACACATT 58.700 37.037 21.14 3.51 36.74 2.71
2292 3846 9.684448 CTGATTCGTATGTATCTAGACACATTT 57.316 33.333 21.14 2.21 36.74 2.32
2309 3863 9.944376 AGACACATTTTAGTATGTATGTTCACT 57.056 29.630 0.00 0.00 36.64 3.41
2311 3865 9.719355 ACACATTTTAGTATGTATGTTCACTCA 57.281 29.630 0.00 0.00 36.64 3.41
2354 3908 8.593945 TCAATATTTTGAAATGGCTAAGAGGT 57.406 30.769 0.00 0.00 38.90 3.85
2356 3910 9.657419 CAATATTTTGAAATGGCTAAGAGGTTT 57.343 29.630 0.00 0.00 34.60 3.27
2365 3919 9.803315 GAAATGGCTAAGAGGTTTTATTTTAGG 57.197 33.333 0.00 0.00 0.00 2.69
2366 3920 7.898014 ATGGCTAAGAGGTTTTATTTTAGGG 57.102 36.000 0.00 0.00 0.00 3.53
2367 3921 7.034967 TGGCTAAGAGGTTTTATTTTAGGGA 57.965 36.000 0.00 0.00 0.00 4.20
2369 3923 7.395206 TGGCTAAGAGGTTTTATTTTAGGGAAC 59.605 37.037 0.00 0.00 0.00 3.62
2370 3924 7.414873 GGCTAAGAGGTTTTATTTTAGGGAACG 60.415 40.741 0.00 0.00 0.00 3.95
2371 3925 6.829229 AAGAGGTTTTATTTTAGGGAACGG 57.171 37.500 0.00 0.00 0.00 4.44
2372 3926 6.130692 AGAGGTTTTATTTTAGGGAACGGA 57.869 37.500 0.00 0.00 0.00 4.69
2373 3927 6.178324 AGAGGTTTTATTTTAGGGAACGGAG 58.822 40.000 0.00 0.00 0.00 4.63
2374 3928 6.013119 AGAGGTTTTATTTTAGGGAACGGAGA 60.013 38.462 0.00 0.00 0.00 3.71
2375 3929 6.178324 AGGTTTTATTTTAGGGAACGGAGAG 58.822 40.000 0.00 0.00 0.00 3.20
2376 3930 6.013119 AGGTTTTATTTTAGGGAACGGAGAGA 60.013 38.462 0.00 0.00 0.00 3.10
2469 4152 7.713942 TGAGTTATGAGATCATCATCTGGTTTG 59.286 37.037 9.91 0.00 46.01 2.93
2496 4179 4.771684 GCATGGTTGCTAGCGTTG 57.228 55.556 10.77 4.20 45.77 4.10
2518 4202 4.212425 TGTGTAACTCTTTGCGTGGTAATG 59.788 41.667 0.00 0.00 38.04 1.90
2628 4313 7.081976 GCAAAATCTGTTACGGTTATCAAAGT 58.918 34.615 0.00 0.00 0.00 2.66
2629 4314 7.270579 GCAAAATCTGTTACGGTTATCAAAGTC 59.729 37.037 0.00 0.00 0.00 3.01
2633 4318 7.416154 TCTGTTACGGTTATCAAAGTCTTTG 57.584 36.000 17.73 17.73 41.96 2.77
2634 4319 6.425721 TCTGTTACGGTTATCAAAGTCTTTGG 59.574 38.462 22.23 9.73 40.98 3.28
2635 4320 5.470777 TGTTACGGTTATCAAAGTCTTTGGG 59.529 40.000 22.23 9.55 40.98 4.12
2636 4321 4.094830 ACGGTTATCAAAGTCTTTGGGT 57.905 40.909 22.23 14.76 40.98 4.51
2637 4322 4.466827 ACGGTTATCAAAGTCTTTGGGTT 58.533 39.130 22.23 11.83 40.98 4.11
2638 4323 4.517832 ACGGTTATCAAAGTCTTTGGGTTC 59.482 41.667 22.23 12.09 40.98 3.62
2639 4324 4.082949 CGGTTATCAAAGTCTTTGGGTTCC 60.083 45.833 22.23 17.68 40.98 3.62
2640 4325 4.082949 GGTTATCAAAGTCTTTGGGTTCCG 60.083 45.833 22.23 0.00 40.98 4.30
2641 4326 1.975660 TCAAAGTCTTTGGGTTCCGG 58.024 50.000 22.23 0.00 40.98 5.14
2643 4328 0.178973 AAAGTCTTTGGGTTCCGGGG 60.179 55.000 0.00 0.00 0.00 5.73
2644 4329 2.675423 GTCTTTGGGTTCCGGGGC 60.675 66.667 0.00 0.00 0.00 5.80
2645 4330 3.974293 TCTTTGGGTTCCGGGGCC 61.974 66.667 0.00 3.82 0.00 5.80
2646 4331 3.979497 CTTTGGGTTCCGGGGCCT 61.979 66.667 0.84 0.00 0.00 5.19
2647 4332 2.532199 TTTGGGTTCCGGGGCCTA 60.532 61.111 0.84 0.00 0.00 3.93
2648 4333 2.144859 CTTTGGGTTCCGGGGCCTAA 62.145 60.000 0.84 5.72 0.00 2.69
2649 4334 1.727215 TTTGGGTTCCGGGGCCTAAA 61.727 55.000 17.78 17.78 33.74 1.85
2650 4335 1.511316 TTGGGTTCCGGGGCCTAAAT 61.511 55.000 0.84 0.00 0.00 1.40
2651 4336 0.623911 TGGGTTCCGGGGCCTAAATA 60.624 55.000 0.84 0.00 0.00 1.40
2652 4337 0.775542 GGGTTCCGGGGCCTAAATAT 59.224 55.000 0.84 0.00 0.00 1.28
2653 4338 1.987368 GGGTTCCGGGGCCTAAATATA 59.013 52.381 0.84 0.00 0.00 0.86
2654 4339 2.376181 GGGTTCCGGGGCCTAAATATAA 59.624 50.000 0.84 0.00 0.00 0.98
2655 4340 3.560668 GGGTTCCGGGGCCTAAATATAAG 60.561 52.174 0.84 0.00 0.00 1.73
2656 4341 3.073503 GGTTCCGGGGCCTAAATATAAGT 59.926 47.826 0.84 0.00 0.00 2.24
2657 4342 4.321718 GTTCCGGGGCCTAAATATAAGTC 58.678 47.826 0.84 0.00 0.00 3.01
2658 4343 3.865571 TCCGGGGCCTAAATATAAGTCT 58.134 45.455 0.84 0.00 0.00 3.24
2659 4344 4.237018 TCCGGGGCCTAAATATAAGTCTT 58.763 43.478 0.84 0.00 0.00 3.01
2660 4345 4.661709 TCCGGGGCCTAAATATAAGTCTTT 59.338 41.667 0.84 0.00 0.00 2.52
2661 4346 5.133153 TCCGGGGCCTAAATATAAGTCTTTT 59.867 40.000 0.84 0.00 0.00 2.27
2662 4347 5.831525 CCGGGGCCTAAATATAAGTCTTTTT 59.168 40.000 0.84 0.00 0.00 1.94
2663 4348 6.999871 CCGGGGCCTAAATATAAGTCTTTTTA 59.000 38.462 0.84 0.00 0.00 1.52
2666 4351 9.286170 GGGGCCTAAATATAAGTCTTTTTAGAG 57.714 37.037 0.84 7.53 34.90 2.43
2733 4418 5.220710 AGTGTAGACTCACTCATTTTGCT 57.779 39.130 0.00 0.00 44.07 3.91
2734 4419 5.233988 AGTGTAGACTCACTCATTTTGCTC 58.766 41.667 0.00 0.00 44.07 4.26
2735 4420 4.390297 GTGTAGACTCACTCATTTTGCTCC 59.610 45.833 0.00 0.00 35.68 4.70
2736 4421 2.693069 AGACTCACTCATTTTGCTCCG 58.307 47.619 0.00 0.00 0.00 4.63
2737 4422 2.037772 AGACTCACTCATTTTGCTCCGT 59.962 45.455 0.00 0.00 0.00 4.69
2738 4423 3.258372 AGACTCACTCATTTTGCTCCGTA 59.742 43.478 0.00 0.00 0.00 4.02
2740 4425 3.935203 ACTCACTCATTTTGCTCCGTATG 59.065 43.478 0.00 0.00 0.00 2.39
2742 4427 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2743 4428 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2744 4429 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2745 4430 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2747 4432 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
2748 4433 0.101759 TTGCTCCGTATGTAGTCCGC 59.898 55.000 0.00 0.00 0.00 5.54
2749 4434 1.033202 TGCTCCGTATGTAGTCCGCA 61.033 55.000 0.00 0.00 0.00 5.69
2750 4435 0.314302 GCTCCGTATGTAGTCCGCAT 59.686 55.000 0.00 0.00 0.00 4.73
2751 4436 1.269621 GCTCCGTATGTAGTCCGCATT 60.270 52.381 0.00 0.00 0.00 3.56
2752 4437 2.394708 CTCCGTATGTAGTCCGCATTG 58.605 52.381 0.00 0.00 0.00 2.82
2753 4438 1.067974 TCCGTATGTAGTCCGCATTGG 59.932 52.381 0.00 0.00 40.09 3.16
2766 4451 5.818136 TCCGCATTGGAATCTCTAAAAAG 57.182 39.130 0.00 0.00 46.38 2.27
2767 4452 5.496556 TCCGCATTGGAATCTCTAAAAAGA 58.503 37.500 0.00 0.00 46.38 2.52
2768 4453 5.354234 TCCGCATTGGAATCTCTAAAAAGAC 59.646 40.000 0.00 0.00 46.38 3.01
2769 4454 5.123820 CCGCATTGGAATCTCTAAAAAGACA 59.876 40.000 0.00 0.00 42.00 3.41
2770 4455 6.183360 CCGCATTGGAATCTCTAAAAAGACAT 60.183 38.462 0.00 0.00 42.00 3.06
2772 4457 7.852945 CGCATTGGAATCTCTAAAAAGACATAC 59.147 37.037 0.00 0.00 0.00 2.39
2773 4458 8.897752 GCATTGGAATCTCTAAAAAGACATACT 58.102 33.333 0.00 0.00 0.00 2.12
2780 4465 9.825109 AATCTCTAAAAAGACATACTTAGGAGC 57.175 33.333 0.00 0.00 37.93 4.70
2781 4466 7.481642 TCTCTAAAAAGACATACTTAGGAGCG 58.518 38.462 0.00 0.00 37.93 5.03
2803 4679 5.046520 GCGGAGGGAGTACCATAGAAATATT 60.047 44.000 0.00 0.00 43.89 1.28
2996 4872 2.026822 TGATTTCCAGAGGAAGCTCACC 60.027 50.000 8.28 2.14 43.06 4.02
3037 4913 4.275689 TCTGCACATTCAATCTGTTCGTTT 59.724 37.500 0.00 0.00 0.00 3.60
3038 4914 5.468409 TCTGCACATTCAATCTGTTCGTTTA 59.532 36.000 0.00 0.00 0.00 2.01
3409 5300 6.065374 TGCTAAACCTTTGGTGATTAGTTCA 58.935 36.000 8.89 0.41 35.34 3.18
3429 5320 6.526674 AGTTCATAAATTTTGTCGATTTCCGC 59.473 34.615 0.00 0.00 38.37 5.54
3613 5505 4.229096 TCGAAAGCTTTTGAATGCATGAC 58.771 39.130 24.06 1.77 0.00 3.06
3632 5524 5.204409 TGACTTTTAGACGCTGGAAAGTA 57.796 39.130 15.70 8.07 41.08 2.24
3746 5638 6.823286 TCTTAGGATATGTTTGGATGGTGA 57.177 37.500 0.00 0.00 0.00 4.02
3972 6048 2.736144 ATGCAAACATGCTTGTCCTG 57.264 45.000 10.38 7.85 34.06 3.86
4110 6218 8.876275 ACCATTGACATATATTGCAAACATTC 57.124 30.769 1.71 0.00 0.00 2.67
4111 6219 7.927629 ACCATTGACATATATTGCAAACATTCC 59.072 33.333 1.71 0.00 0.00 3.01
4112 6220 7.385752 CCATTGACATATATTGCAAACATTCCC 59.614 37.037 1.71 0.00 0.00 3.97
4113 6221 7.658525 TTGACATATATTGCAAACATTCCCT 57.341 32.000 1.71 0.00 0.00 4.20
4114 6222 7.658525 TGACATATATTGCAAACATTCCCTT 57.341 32.000 1.71 0.00 0.00 3.95
4136 6244 2.902705 TACACCTTCTGAACAAGCGT 57.097 45.000 0.00 0.00 0.00 5.07
4155 6263 3.610677 GCGTGTTGGGTTTTATGTTATGC 59.389 43.478 0.00 0.00 0.00 3.14
4156 6264 4.617298 GCGTGTTGGGTTTTATGTTATGCT 60.617 41.667 0.00 0.00 0.00 3.79
4166 6274 6.457799 GGTTTTATGTTATGCTCAGTTACCGG 60.458 42.308 0.00 0.00 0.00 5.28
4201 6309 1.476891 GTGTAAGGATCGCCTCACTCA 59.523 52.381 0.00 0.00 46.28 3.41
4205 6313 1.047596 AGGATCGCCTCACTCATGCT 61.048 55.000 0.00 0.00 42.19 3.79
4229 6397 6.173339 TGCCTTTAGGATCAACAGTAAAGAG 58.827 40.000 0.00 0.00 35.40 2.85
4232 6400 7.554476 GCCTTTAGGATCAACAGTAAAGAGAAT 59.446 37.037 0.00 0.00 35.40 2.40
4239 6407 8.557864 GGATCAACAGTAAAGAGAATCATGATG 58.442 37.037 9.46 0.00 37.82 3.07
4241 6409 7.108194 TCAACAGTAAAGAGAATCATGATGCT 58.892 34.615 16.63 16.63 37.82 3.79
4346 8445 7.510549 TTCAAAGGGTGAAAGATACTTCAAG 57.489 36.000 0.00 0.00 43.43 3.02
4387 8486 2.303022 TCTTGGTCTAGCAGGAAGTTGG 59.697 50.000 0.00 0.00 0.00 3.77
4389 8488 1.623811 TGGTCTAGCAGGAAGTTGGTC 59.376 52.381 0.00 0.00 0.00 4.02
4400 8499 0.321653 AAGTTGGTCGCCTCATGTCC 60.322 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.467399 CACTTTTACCTTCGTTGATGGTGTA 59.533 40.000 13.02 1.10 39.80 2.90
1 2 4.274950 CACTTTTACCTTCGTTGATGGTGT 59.725 41.667 13.02 1.94 39.80 4.16
2 3 4.783242 CACTTTTACCTTCGTTGATGGTG 58.217 43.478 13.02 1.42 39.80 4.17
3 4 3.252458 GCACTTTTACCTTCGTTGATGGT 59.748 43.478 9.06 9.06 41.81 3.55
4 5 3.252215 TGCACTTTTACCTTCGTTGATGG 59.748 43.478 0.00 0.00 33.73 3.51
5 6 4.024048 ACTGCACTTTTACCTTCGTTGATG 60.024 41.667 0.00 0.00 0.00 3.07
6 7 4.134563 ACTGCACTTTTACCTTCGTTGAT 58.865 39.130 0.00 0.00 0.00 2.57
7 8 3.537580 ACTGCACTTTTACCTTCGTTGA 58.462 40.909 0.00 0.00 0.00 3.18
8 9 3.963383 ACTGCACTTTTACCTTCGTTG 57.037 42.857 0.00 0.00 0.00 4.10
9 10 3.497262 GCTACTGCACTTTTACCTTCGTT 59.503 43.478 0.00 0.00 39.41 3.85
10 11 3.064931 GCTACTGCACTTTTACCTTCGT 58.935 45.455 0.00 0.00 39.41 3.85
11 12 3.064207 TGCTACTGCACTTTTACCTTCG 58.936 45.455 0.00 0.00 45.31 3.79
24 25 2.917933 TGTTCATGGGTATGCTACTGC 58.082 47.619 0.00 0.00 40.20 4.40
25 26 5.895636 TTTTGTTCATGGGTATGCTACTG 57.104 39.130 0.00 0.00 34.21 2.74
47 48 7.147742 GGGTATATTGGTTCATGGACATTGTTT 60.148 37.037 6.44 0.00 0.00 2.83
71 72 2.025981 TCTGTGATCCTTTGGTGATGGG 60.026 50.000 0.00 0.00 0.00 4.00
219 228 0.948678 TGCTAACTGCGGGTCAAAAC 59.051 50.000 0.00 0.00 46.63 2.43
225 234 0.893727 CCCTTTTGCTAACTGCGGGT 60.894 55.000 0.00 0.00 46.63 5.28
227 236 0.240945 CACCCTTTTGCTAACTGCGG 59.759 55.000 0.00 0.00 46.63 5.69
283 292 6.097356 TCCAGTTGATGTACAGTCGTATTTC 58.903 40.000 0.33 0.00 0.00 2.17
284 293 6.032956 TCCAGTTGATGTACAGTCGTATTT 57.967 37.500 0.33 0.00 0.00 1.40
285 294 5.654603 TCCAGTTGATGTACAGTCGTATT 57.345 39.130 0.33 0.00 0.00 1.89
286 295 5.654603 TTCCAGTTGATGTACAGTCGTAT 57.345 39.130 0.33 0.00 0.00 3.06
288 297 4.056050 GTTTCCAGTTGATGTACAGTCGT 58.944 43.478 0.33 0.00 0.00 4.34
289 298 4.150627 CAGTTTCCAGTTGATGTACAGTCG 59.849 45.833 0.33 0.00 0.00 4.18
303 501 4.156739 GCCATCTTAGGTTTCAGTTTCCAG 59.843 45.833 0.00 0.00 0.00 3.86
326 524 8.843262 ACACATTGTGATAATTGGATATGAGTG 58.157 33.333 23.12 0.00 36.96 3.51
446 1722 2.661866 AACGTGTCCTGTGAGCGC 60.662 61.111 0.00 0.00 0.00 5.92
481 1757 1.749638 CGGTGTAGCGAGGAGGAGT 60.750 63.158 0.00 0.00 0.00 3.85
547 1823 2.095364 CGATTTCTATCCGTCCCTACCG 60.095 54.545 0.00 0.00 0.00 4.02
551 1827 1.614413 GCTCGATTTCTATCCGTCCCT 59.386 52.381 0.00 0.00 0.00 4.20
555 1831 3.195661 GTTTGGCTCGATTTCTATCCGT 58.804 45.455 0.00 0.00 0.00 4.69
927 2206 1.153127 CCTCCGCTCGTCTCCTACT 60.153 63.158 0.00 0.00 0.00 2.57
929 2208 1.146485 CTCCTCCGCTCGTCTCCTA 59.854 63.158 0.00 0.00 0.00 2.94
1030 2344 3.352648 GAATTGGGCCTGTTAGCACTAA 58.647 45.455 4.53 0.00 36.97 2.24
1031 2345 2.679639 CGAATTGGGCCTGTTAGCACTA 60.680 50.000 4.53 0.00 36.97 2.74
1032 2346 1.839424 GAATTGGGCCTGTTAGCACT 58.161 50.000 4.53 0.00 36.97 4.40
1120 2434 2.407361 CAGACTATTTATTACGGCCGCG 59.593 50.000 28.58 1.99 0.00 6.46
1229 2547 1.450491 CTGACGGAGAGAGGCGAGA 60.450 63.158 0.00 0.00 0.00 4.04
1282 2601 3.215975 ACGGGAAAAGAAATCAACGGAA 58.784 40.909 0.00 0.00 0.00 4.30
1351 2670 1.726845 CGAATCGACGAAACGACCCG 61.727 60.000 17.64 1.63 44.84 5.28
1384 2703 0.179140 CGCCCAAATTGCAATAGCGT 60.179 50.000 25.50 6.70 46.23 5.07
1531 2850 2.104253 GCCCACACATTACGGACCG 61.104 63.158 13.61 13.61 0.00 4.79
1561 2884 3.399330 GCAGGTCTACACAAGCTTACAA 58.601 45.455 0.00 0.00 0.00 2.41
1578 2901 0.181350 GTTGGATCTACCCAGGCAGG 59.819 60.000 0.00 0.00 37.53 4.85
1605 2928 1.660607 CGTACATAGCAACAGCCACTG 59.339 52.381 0.00 0.00 37.52 3.66
1633 2956 4.072131 TGGAGCAACAAACTAATCAGGTC 58.928 43.478 0.00 0.00 0.00 3.85
1637 2960 4.469657 ACCTTGGAGCAACAAACTAATCA 58.530 39.130 0.00 0.00 0.00 2.57
1644 2967 3.476552 CTGACTACCTTGGAGCAACAAA 58.523 45.455 0.00 0.00 0.00 2.83
1648 2971 0.324943 GCCTGACTACCTTGGAGCAA 59.675 55.000 0.00 0.00 0.00 3.91
1651 2974 0.618968 AGGGCCTGACTACCTTGGAG 60.619 60.000 4.50 0.00 0.00 3.86
1721 3145 3.188667 GCTACAAAACTACCACAGAAGGC 59.811 47.826 0.00 0.00 0.00 4.35
1722 3146 4.642429 AGCTACAAAACTACCACAGAAGG 58.358 43.478 0.00 0.00 0.00 3.46
1747 3174 9.851686 TCAGAATACCAAATATCAACATTAGCT 57.148 29.630 0.00 0.00 0.00 3.32
1781 3214 3.989817 GCTGGAAGAAAAATCGCACAAAT 59.010 39.130 0.00 0.00 34.07 2.32
1788 3224 5.814705 ACAGAGATAGCTGGAAGAAAAATCG 59.185 40.000 0.00 0.00 40.20 3.34
1795 3231 2.302260 CGGACAGAGATAGCTGGAAGA 58.698 52.381 0.00 0.00 40.20 2.87
1796 3232 2.028130 ACGGACAGAGATAGCTGGAAG 58.972 52.381 0.00 0.00 40.20 3.46
1807 3243 2.069273 CCTGCAGTTTTACGGACAGAG 58.931 52.381 13.81 0.00 0.00 3.35
1809 3245 1.531149 CACCTGCAGTTTTACGGACAG 59.469 52.381 13.81 0.00 0.00 3.51
1814 3250 2.873472 TGTAACCACCTGCAGTTTTACG 59.127 45.455 13.81 0.00 31.16 3.18
1827 3263 2.614057 GCACTATCCATGCTGTAACCAC 59.386 50.000 0.00 0.00 40.08 4.16
1848 3294 6.126739 ACTCCTAACAAAAGGGAAGCCTATAG 60.127 42.308 0.00 0.00 37.24 1.31
1859 3305 5.304357 ACATCCCAAAACTCCTAACAAAAGG 59.696 40.000 0.00 0.00 38.06 3.11
1897 3345 5.557866 ACATGGTTAGGAGTCCTAAAACAC 58.442 41.667 29.33 19.02 46.12 3.32
1903 3351 8.792830 ATATTGTTACATGGTTAGGAGTCCTA 57.207 34.615 15.33 15.33 34.61 2.94
1906 3354 7.282224 TGCAATATTGTTACATGGTTAGGAGTC 59.718 37.037 16.61 0.00 0.00 3.36
1907 3355 7.116075 TGCAATATTGTTACATGGTTAGGAGT 58.884 34.615 16.61 0.00 0.00 3.85
1935 3383 6.313411 ACAATAATCAACGAAATGCAAATGGG 59.687 34.615 0.00 0.00 0.00 4.00
1970 3418 3.776158 GTCCATGTTTGGGCTGCA 58.224 55.556 0.50 0.00 44.72 4.41
2238 3792 3.897505 AGCTAAAAGGCCTTGTGTTCATT 59.102 39.130 21.33 10.25 0.00 2.57
2241 3795 4.322080 AAAGCTAAAAGGCCTTGTGTTC 57.678 40.909 21.33 7.14 0.00 3.18
2242 3796 4.753516 AAAAGCTAAAAGGCCTTGTGTT 57.246 36.364 21.33 12.64 0.00 3.32
2243 3797 4.442893 GGAAAAAGCTAAAAGGCCTTGTGT 60.443 41.667 21.33 10.34 0.00 3.72
2244 3798 4.058124 GGAAAAAGCTAAAAGGCCTTGTG 58.942 43.478 21.33 13.21 0.00 3.33
2245 3799 3.967326 AGGAAAAAGCTAAAAGGCCTTGT 59.033 39.130 21.33 17.54 0.00 3.16
2246 3800 4.039124 TCAGGAAAAAGCTAAAAGGCCTTG 59.961 41.667 21.33 7.98 0.00 3.61
2247 3801 4.223144 TCAGGAAAAAGCTAAAAGGCCTT 58.777 39.130 13.78 13.78 0.00 4.35
2248 3802 3.844640 TCAGGAAAAAGCTAAAAGGCCT 58.155 40.909 0.00 0.00 0.00 5.19
2249 3803 4.808414 ATCAGGAAAAAGCTAAAAGGCC 57.192 40.909 0.00 0.00 0.00 5.19
2250 3804 4.859245 CGAATCAGGAAAAAGCTAAAAGGC 59.141 41.667 0.00 0.00 0.00 4.35
2251 3805 6.013842 ACGAATCAGGAAAAAGCTAAAAGG 57.986 37.500 0.00 0.00 0.00 3.11
2252 3806 8.237267 ACATACGAATCAGGAAAAAGCTAAAAG 58.763 33.333 0.00 0.00 0.00 2.27
2253 3807 8.106247 ACATACGAATCAGGAAAAAGCTAAAA 57.894 30.769 0.00 0.00 0.00 1.52
2254 3808 7.681939 ACATACGAATCAGGAAAAAGCTAAA 57.318 32.000 0.00 0.00 0.00 1.85
2255 3809 8.958119 ATACATACGAATCAGGAAAAAGCTAA 57.042 30.769 0.00 0.00 0.00 3.09
2256 3810 8.421784 AGATACATACGAATCAGGAAAAAGCTA 58.578 33.333 0.00 0.00 0.00 3.32
2257 3811 7.275920 AGATACATACGAATCAGGAAAAAGCT 58.724 34.615 0.00 0.00 0.00 3.74
2258 3812 7.484035 AGATACATACGAATCAGGAAAAAGC 57.516 36.000 0.00 0.00 0.00 3.51
2259 3813 9.967346 TCTAGATACATACGAATCAGGAAAAAG 57.033 33.333 0.00 0.00 0.00 2.27
2260 3814 9.745880 GTCTAGATACATACGAATCAGGAAAAA 57.254 33.333 0.00 0.00 0.00 1.94
2261 3815 8.909923 TGTCTAGATACATACGAATCAGGAAAA 58.090 33.333 0.00 0.00 0.00 2.29
2262 3816 8.350722 GTGTCTAGATACATACGAATCAGGAAA 58.649 37.037 14.20 0.00 0.00 3.13
2263 3817 7.501225 TGTGTCTAGATACATACGAATCAGGAA 59.499 37.037 17.43 0.00 0.00 3.36
2264 3818 6.996282 TGTGTCTAGATACATACGAATCAGGA 59.004 38.462 17.43 0.00 0.00 3.86
2265 3819 7.203255 TGTGTCTAGATACATACGAATCAGG 57.797 40.000 17.43 0.00 0.00 3.86
2266 3820 9.684448 AAATGTGTCTAGATACATACGAATCAG 57.316 33.333 28.78 0.00 41.35 2.90
2283 3837 9.944376 AGTGAACATACATACTAAAATGTGTCT 57.056 29.630 0.00 0.00 40.29 3.41
2285 3839 9.719355 TGAGTGAACATACATACTAAAATGTGT 57.281 29.630 0.00 0.00 40.29 3.72
2339 3893 9.803315 CCTAAAATAAAACCTCTTAGCCATTTC 57.197 33.333 0.00 0.00 0.00 2.17
2343 3897 7.034967 TCCCTAAAATAAAACCTCTTAGCCA 57.965 36.000 0.00 0.00 0.00 4.75
2346 3900 7.825761 TCCGTTCCCTAAAATAAAACCTCTTAG 59.174 37.037 0.00 0.00 0.00 2.18
2348 3902 6.545567 TCCGTTCCCTAAAATAAAACCTCTT 58.454 36.000 0.00 0.00 0.00 2.85
2350 3904 6.175471 TCTCCGTTCCCTAAAATAAAACCTC 58.825 40.000 0.00 0.00 0.00 3.85
2351 3905 6.013119 TCTCTCCGTTCCCTAAAATAAAACCT 60.013 38.462 0.00 0.00 0.00 3.50
2352 3906 6.175471 TCTCTCCGTTCCCTAAAATAAAACC 58.825 40.000 0.00 0.00 0.00 3.27
2353 3907 6.877855 ACTCTCTCCGTTCCCTAAAATAAAAC 59.122 38.462 0.00 0.00 0.00 2.43
2354 3908 7.012661 ACTCTCTCCGTTCCCTAAAATAAAA 57.987 36.000 0.00 0.00 0.00 1.52
2356 3910 7.909485 ATACTCTCTCCGTTCCCTAAAATAA 57.091 36.000 0.00 0.00 0.00 1.40
2357 3911 7.909485 AATACTCTCTCCGTTCCCTAAAATA 57.091 36.000 0.00 0.00 0.00 1.40
2358 3912 6.809976 AATACTCTCTCCGTTCCCTAAAAT 57.190 37.500 0.00 0.00 0.00 1.82
2360 3914 5.626116 GCAAATACTCTCTCCGTTCCCTAAA 60.626 44.000 0.00 0.00 0.00 1.85
2361 3915 4.142004 GCAAATACTCTCTCCGTTCCCTAA 60.142 45.833 0.00 0.00 0.00 2.69
2362 3916 3.383825 GCAAATACTCTCTCCGTTCCCTA 59.616 47.826 0.00 0.00 0.00 3.53
2364 3918 2.168728 AGCAAATACTCTCTCCGTTCCC 59.831 50.000 0.00 0.00 0.00 3.97
2365 3919 3.528597 AGCAAATACTCTCTCCGTTCC 57.471 47.619 0.00 0.00 0.00 3.62
2366 3920 5.593010 ACATAGCAAATACTCTCTCCGTTC 58.407 41.667 0.00 0.00 0.00 3.95
2367 3921 5.361285 AGACATAGCAAATACTCTCTCCGTT 59.639 40.000 0.00 0.00 0.00 4.44
2369 3923 5.446143 AGACATAGCAAATACTCTCTCCG 57.554 43.478 0.00 0.00 0.00 4.63
2370 3924 6.578023 ACAAGACATAGCAAATACTCTCTCC 58.422 40.000 0.00 0.00 0.00 3.71
2371 3925 7.434897 CAGACAAGACATAGCAAATACTCTCTC 59.565 40.741 0.00 0.00 0.00 3.20
2372 3926 7.264221 CAGACAAGACATAGCAAATACTCTCT 58.736 38.462 0.00 0.00 0.00 3.10
2373 3927 6.019156 GCAGACAAGACATAGCAAATACTCTC 60.019 42.308 0.00 0.00 0.00 3.20
2374 3928 5.814705 GCAGACAAGACATAGCAAATACTCT 59.185 40.000 0.00 0.00 0.00 3.24
2375 3929 5.814705 AGCAGACAAGACATAGCAAATACTC 59.185 40.000 0.00 0.00 0.00 2.59
2376 3930 5.738909 AGCAGACAAGACATAGCAAATACT 58.261 37.500 0.00 0.00 0.00 2.12
2496 4179 4.212636 ACATTACCACGCAAAGAGTTACAC 59.787 41.667 0.00 0.00 0.00 2.90
2518 4202 5.938125 TGGCCTATCAAGTAAGAAAGACAAC 59.062 40.000 3.32 0.00 0.00 3.32
2628 4313 3.974293 GGCCCCGGAACCCAAAGA 61.974 66.667 0.73 0.00 0.00 2.52
2629 4314 2.144859 TTAGGCCCCGGAACCCAAAG 62.145 60.000 0.73 0.00 0.00 2.77
2633 4318 0.775542 ATATTTAGGCCCCGGAACCC 59.224 55.000 0.73 0.00 0.00 4.11
2634 4319 3.073503 ACTTATATTTAGGCCCCGGAACC 59.926 47.826 0.73 3.16 0.00 3.62
2635 4320 4.041321 AGACTTATATTTAGGCCCCGGAAC 59.959 45.833 0.73 0.00 0.00 3.62
2636 4321 4.237018 AGACTTATATTTAGGCCCCGGAA 58.763 43.478 0.73 0.00 0.00 4.30
2637 4322 3.865571 AGACTTATATTTAGGCCCCGGA 58.134 45.455 0.73 0.00 0.00 5.14
2638 4323 4.635699 AAGACTTATATTTAGGCCCCGG 57.364 45.455 0.00 0.00 0.00 5.73
2639 4324 6.954487 AAAAAGACTTATATTTAGGCCCCG 57.046 37.500 0.00 0.00 0.00 5.73
2640 4325 9.286170 CTCTAAAAAGACTTATATTTAGGCCCC 57.714 37.037 13.94 0.00 36.48 5.80
2663 4348 8.361139 CCGTATGTAGTCCTTATTGAAATCTCT 58.639 37.037 0.00 0.00 0.00 3.10
2712 4397 4.390297 GGAGCAAAATGAGTGAGTCTACAC 59.610 45.833 0.00 0.00 40.60 2.90
2713 4398 4.569943 GGAGCAAAATGAGTGAGTCTACA 58.430 43.478 0.00 0.00 0.00 2.74
2714 4399 3.614616 CGGAGCAAAATGAGTGAGTCTAC 59.385 47.826 0.00 0.00 0.00 2.59
2715 4400 3.258372 ACGGAGCAAAATGAGTGAGTCTA 59.742 43.478 0.00 0.00 0.00 2.59
2717 4402 2.417719 ACGGAGCAAAATGAGTGAGTC 58.582 47.619 0.00 0.00 0.00 3.36
2718 4403 2.550830 ACGGAGCAAAATGAGTGAGT 57.449 45.000 0.00 0.00 0.00 3.41
2721 4406 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2722 4407 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2723 4408 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
2724 4409 4.439057 GGACTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
2726 4411 3.454375 CGGACTACATACGGAGCAAAAT 58.546 45.455 0.00 0.00 0.00 1.82
2727 4412 2.883574 CGGACTACATACGGAGCAAAA 58.116 47.619 0.00 0.00 0.00 2.44
2728 4413 1.470285 GCGGACTACATACGGAGCAAA 60.470 52.381 0.00 0.00 0.00 3.68
2730 4415 1.033202 TGCGGACTACATACGGAGCA 61.033 55.000 0.00 0.00 0.00 4.26
2733 4418 1.067974 CCAATGCGGACTACATACGGA 59.932 52.381 0.00 0.00 36.56 4.69
2734 4419 1.067974 TCCAATGCGGACTACATACGG 59.932 52.381 0.00 0.00 39.64 4.02
2735 4420 2.502213 TCCAATGCGGACTACATACG 57.498 50.000 0.00 0.00 39.64 3.06
2736 4421 4.632153 AGATTCCAATGCGGACTACATAC 58.368 43.478 0.00 0.00 46.36 2.39
2737 4422 4.588951 AGAGATTCCAATGCGGACTACATA 59.411 41.667 0.00 0.00 46.36 2.29
2738 4423 3.389329 AGAGATTCCAATGCGGACTACAT 59.611 43.478 0.00 0.00 46.36 2.29
2740 4425 3.460857 AGAGATTCCAATGCGGACTAC 57.539 47.619 0.00 0.00 46.36 2.73
2742 4427 4.487714 TTTAGAGATTCCAATGCGGACT 57.512 40.909 0.00 0.00 46.36 3.85
2743 4428 5.354234 TCTTTTTAGAGATTCCAATGCGGAC 59.646 40.000 0.00 0.00 46.36 4.79
2744 4429 5.354234 GTCTTTTTAGAGATTCCAATGCGGA 59.646 40.000 0.00 0.00 44.40 5.54
2745 4430 5.123820 TGTCTTTTTAGAGATTCCAATGCGG 59.876 40.000 0.00 0.00 0.00 5.69
2747 4432 8.897752 AGTATGTCTTTTTAGAGATTCCAATGC 58.102 33.333 0.00 0.00 0.00 3.56
2754 4439 9.825109 GCTCCTAAGTATGTCTTTTTAGAGATT 57.175 33.333 0.00 0.00 37.56 2.40
2756 4441 7.416438 CCGCTCCTAAGTATGTCTTTTTAGAGA 60.416 40.741 0.00 0.00 37.56 3.10
2757 4442 6.697892 CCGCTCCTAAGTATGTCTTTTTAGAG 59.302 42.308 0.00 0.00 37.56 2.43
2759 4444 6.570692 TCCGCTCCTAAGTATGTCTTTTTAG 58.429 40.000 0.00 0.00 37.56 1.85
2760 4445 6.406624 CCTCCGCTCCTAAGTATGTCTTTTTA 60.407 42.308 0.00 0.00 37.56 1.52
2761 4446 5.416271 TCCGCTCCTAAGTATGTCTTTTT 57.584 39.130 0.00 0.00 37.56 1.94
2762 4447 4.141914 CCTCCGCTCCTAAGTATGTCTTTT 60.142 45.833 0.00 0.00 37.56 2.27
2765 4450 2.588620 CCTCCGCTCCTAAGTATGTCT 58.411 52.381 0.00 0.00 0.00 3.41
2766 4451 1.614413 CCCTCCGCTCCTAAGTATGTC 59.386 57.143 0.00 0.00 0.00 3.06
2767 4452 1.217183 TCCCTCCGCTCCTAAGTATGT 59.783 52.381 0.00 0.00 0.00 2.29
2768 4453 1.889829 CTCCCTCCGCTCCTAAGTATG 59.110 57.143 0.00 0.00 0.00 2.39
2769 4454 1.499870 ACTCCCTCCGCTCCTAAGTAT 59.500 52.381 0.00 0.00 0.00 2.12
2770 4455 0.924823 ACTCCCTCCGCTCCTAAGTA 59.075 55.000 0.00 0.00 0.00 2.24
2772 4457 1.320507 GTACTCCCTCCGCTCCTAAG 58.679 60.000 0.00 0.00 0.00 2.18
2773 4458 0.106318 GGTACTCCCTCCGCTCCTAA 60.106 60.000 0.00 0.00 0.00 2.69
2774 4459 1.284111 TGGTACTCCCTCCGCTCCTA 61.284 60.000 0.00 0.00 0.00 2.94
2776 4461 0.178970 TATGGTACTCCCTCCGCTCC 60.179 60.000 0.00 0.00 0.00 4.70
2780 4465 6.607004 AATATTTCTATGGTACTCCCTCCG 57.393 41.667 0.00 0.00 0.00 4.63
2781 4466 7.974504 TCAAATATTTCTATGGTACTCCCTCC 58.025 38.462 0.00 0.00 0.00 4.30
2865 4741 7.980662 AGACATCAGATTTCAGTTCATAGACAG 59.019 37.037 0.00 0.00 0.00 3.51
2873 4749 6.162079 TGACAGAGACATCAGATTTCAGTTC 58.838 40.000 0.00 0.00 0.00 3.01
3429 5320 3.229697 ACAAGGGAGAGACAAAAAGGG 57.770 47.619 0.00 0.00 0.00 3.95
3566 5458 5.335897 GCATCTGAAGCACTCCATTTTTACA 60.336 40.000 0.00 0.00 0.00 2.41
3613 5505 6.148811 TCCAAATACTTTCCAGCGTCTAAAAG 59.851 38.462 9.94 9.94 35.38 2.27
3782 5674 5.559148 ACAATCCAAACAAAGGCCAATAA 57.441 34.783 5.01 0.00 0.00 1.40
3856 5749 6.561070 AGTGTGGGGTGGCTATTTAGATATTA 59.439 38.462 0.00 0.00 0.00 0.98
4084 6192 9.964303 GAATGTTTGCAATATATGTCAATGGTA 57.036 29.630 0.00 0.00 0.00 3.25
4085 6193 7.927629 GGAATGTTTGCAATATATGTCAATGGT 59.072 33.333 0.00 0.00 0.00 3.55
4086 6194 7.385752 GGGAATGTTTGCAATATATGTCAATGG 59.614 37.037 0.00 0.00 0.00 3.16
4087 6195 8.145767 AGGGAATGTTTGCAATATATGTCAATG 58.854 33.333 0.00 0.00 0.00 2.82
4088 6196 8.253867 AGGGAATGTTTGCAATATATGTCAAT 57.746 30.769 0.00 0.00 0.00 2.57
4089 6197 7.658525 AGGGAATGTTTGCAATATATGTCAA 57.341 32.000 0.00 0.00 0.00 3.18
4090 6198 7.658525 AAGGGAATGTTTGCAATATATGTCA 57.341 32.000 0.00 0.00 0.00 3.58
4096 6204 8.421002 GGTGTATTAAGGGAATGTTTGCAATAT 58.579 33.333 0.00 0.00 0.00 1.28
4097 6205 7.617723 AGGTGTATTAAGGGAATGTTTGCAATA 59.382 33.333 0.00 0.00 0.00 1.90
4098 6206 6.440328 AGGTGTATTAAGGGAATGTTTGCAAT 59.560 34.615 0.00 0.00 0.00 3.56
4099 6207 5.777732 AGGTGTATTAAGGGAATGTTTGCAA 59.222 36.000 0.00 0.00 0.00 4.08
4100 6208 5.329399 AGGTGTATTAAGGGAATGTTTGCA 58.671 37.500 0.00 0.00 0.00 4.08
4101 6209 5.914898 AGGTGTATTAAGGGAATGTTTGC 57.085 39.130 0.00 0.00 0.00 3.68
4102 6210 7.393234 TCAGAAGGTGTATTAAGGGAATGTTTG 59.607 37.037 0.00 0.00 0.00 2.93
4103 6211 7.466804 TCAGAAGGTGTATTAAGGGAATGTTT 58.533 34.615 0.00 0.00 0.00 2.83
4104 6212 7.027874 TCAGAAGGTGTATTAAGGGAATGTT 57.972 36.000 0.00 0.00 0.00 2.71
4105 6213 6.636454 TCAGAAGGTGTATTAAGGGAATGT 57.364 37.500 0.00 0.00 0.00 2.71
4106 6214 6.884295 TGTTCAGAAGGTGTATTAAGGGAATG 59.116 38.462 0.00 0.00 0.00 2.67
4107 6215 7.027874 TGTTCAGAAGGTGTATTAAGGGAAT 57.972 36.000 0.00 0.00 0.00 3.01
4108 6216 6.442541 TGTTCAGAAGGTGTATTAAGGGAA 57.557 37.500 0.00 0.00 0.00 3.97
4109 6217 6.442541 TTGTTCAGAAGGTGTATTAAGGGA 57.557 37.500 0.00 0.00 0.00 4.20
4110 6218 5.123979 GCTTGTTCAGAAGGTGTATTAAGGG 59.876 44.000 0.00 0.00 0.00 3.95
4111 6219 5.163854 CGCTTGTTCAGAAGGTGTATTAAGG 60.164 44.000 0.00 0.00 0.00 2.69
4112 6220 5.408604 ACGCTTGTTCAGAAGGTGTATTAAG 59.591 40.000 0.00 0.00 0.00 1.85
4113 6221 5.178623 CACGCTTGTTCAGAAGGTGTATTAA 59.821 40.000 0.00 0.00 0.00 1.40
4114 6222 4.688879 CACGCTTGTTCAGAAGGTGTATTA 59.311 41.667 0.00 0.00 0.00 0.98
4136 6244 5.772672 ACTGAGCATAACATAAAACCCAACA 59.227 36.000 0.00 0.00 0.00 3.33
4155 6263 1.327690 TAGCCTGCCCGGTAACTGAG 61.328 60.000 0.00 0.00 34.25 3.35
4156 6264 0.689745 ATAGCCTGCCCGGTAACTGA 60.690 55.000 0.00 0.00 34.25 3.41
4166 6274 3.877508 CCTTACACTAAACATAGCCTGCC 59.122 47.826 0.00 0.00 0.00 4.85
4201 6309 3.285484 CTGTTGATCCTAAAGGCAGCAT 58.715 45.455 0.00 0.00 34.44 3.79
4205 6313 6.013725 TCTCTTTACTGTTGATCCTAAAGGCA 60.014 38.462 0.00 0.00 34.44 4.75
4229 6397 9.745880 AACATAAAATGAGAAGCATCATGATTC 57.254 29.630 7.60 7.60 42.60 2.52
4232 6400 8.058667 ACAACATAAAATGAGAAGCATCATGA 57.941 30.769 0.00 0.00 39.84 3.07
4239 6407 5.125417 TGGGCTACAACATAAAATGAGAAGC 59.875 40.000 0.00 0.00 0.00 3.86
4241 6409 7.309744 CCTTTGGGCTACAACATAAAATGAGAA 60.310 37.037 0.00 0.00 39.19 2.87
4309 8408 1.203174 CCTTTGAAATGGGGTGAGGGT 60.203 52.381 0.00 0.00 0.00 4.34
4336 8435 9.463443 GAAAAGAGCTCTCTATCTTGAAGTATC 57.537 37.037 18.55 0.00 39.39 2.24
4346 8445 6.980397 CCAAGAGAAGAAAAGAGCTCTCTATC 59.020 42.308 18.55 15.06 39.39 2.08
4387 8486 3.740128 ATGGCGGACATGAGGCGAC 62.740 63.158 0.00 0.00 38.70 5.19
4389 8488 2.514592 AATGGCGGACATGAGGCG 60.515 61.111 0.00 0.00 40.44 5.52
4400 8499 1.148157 CTGCTCGTAGGTCAATGGCG 61.148 60.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.