Multiple sequence alignment - TraesCS2B01G043400

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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 TraesCS2B01G043400 chr2B 100.000 3194 0 0 2954 6147 20145742 20148935 0.000000e+00 5899.0
1 TraesCS2B01G043400 chr2B 100.000 2651 0 0 1 2651 20142789 20145439 0.000000e+00 4896.0
2 TraesCS2B01G043400 chr2B 74.067 1018 243 16 1281 2293 80256228 80255227 1.240000e-106 398.0
3 TraesCS2B01G043400 chr2A 87.895 2693 267 32 1 2651 14733952 14731277 0.000000e+00 3112.0
4 TraesCS2B01G043400 chr2A 93.916 1841 101 8 3501 5336 14730720 14728886 0.000000e+00 2769.0
5 TraesCS2B01G043400 chr2A 87.466 2226 215 34 3501 5680 14721395 14719188 0.000000e+00 2507.0
6 TraesCS2B01G043400 chr2A 91.002 1856 143 19 3499 5336 14712131 14710282 0.000000e+00 2481.0
7 TraesCS2B01G043400 chr2A 85.733 2313 252 39 77 2350 14743641 14741368 0.000000e+00 2372.0
8 TraesCS2B01G043400 chr2A 87.904 2042 172 34 3577 5578 14740757 14738751 0.000000e+00 2333.0
9 TraesCS2B01G043400 chr2A 87.807 1870 215 13 498 2361 14723882 14722020 0.000000e+00 2178.0
10 TraesCS2B01G043400 chr2A 87.579 1892 203 13 487 2372 14714856 14712991 0.000000e+00 2163.0
11 TraesCS2B01G043400 chr2A 88.476 1805 154 28 3561 5336 14703812 14702033 0.000000e+00 2132.0
12 TraesCS2B01G043400 chr2A 86.390 1881 230 13 487 2350 14706286 14704415 0.000000e+00 2032.0
13 TraesCS2B01G043400 chr2A 92.284 985 68 7 3817 4800 14683500 14682523 0.000000e+00 1391.0
14 TraesCS2B01G043400 chr2A 85.407 884 72 22 4823 5681 14682452 14681601 0.000000e+00 865.0
15 TraesCS2B01G043400 chr2A 86.860 723 93 1 950 1670 14693595 14692873 0.000000e+00 808.0
16 TraesCS2B01G043400 chr2A 88.286 461 46 6 3001 3457 14712570 14712114 4.190000e-151 545.0
17 TraesCS2B01G043400 chr2A 75.080 1248 265 31 1053 2281 52766387 52765167 1.950000e-149 540.0
18 TraesCS2B01G043400 chr2A 91.789 341 20 6 2983 3318 14731255 14730918 9.330000e-128 468.0
19 TraesCS2B01G043400 chr2A 90.244 328 32 0 488 815 14725328 14725001 4.400000e-116 429.0
20 TraesCS2B01G043400 chr2A 82.489 474 67 12 5683 6146 14694868 14694401 9.600000e-108 401.0
21 TraesCS2B01G043400 chr2A 90.476 294 25 3 487 780 14693887 14693597 9.670000e-103 385.0
22 TraesCS2B01G043400 chr2A 81.437 501 55 11 5683 6146 14707301 14706802 5.820000e-100 375.0
23 TraesCS2B01G043400 chr2A 79.920 503 60 21 5683 6146 14681549 14681049 1.280000e-86 331.0
24 TraesCS2B01G043400 chr2A 93.143 175 11 1 83 257 14724294 14724121 7.910000e-64 255.0
25 TraesCS2B01G043400 chr2A 81.690 284 31 11 5877 6144 14726117 14725839 3.730000e-52 217.0
26 TraesCS2B01G043400 chr2A 84.314 204 23 4 5400 5594 14728843 14728640 2.260000e-44 191.0
27 TraesCS2B01G043400 chr2A 86.806 144 16 3 6002 6144 14718687 14718546 2.290000e-34 158.0
28 TraesCS2B01G043400 chr2A 92.188 64 5 0 315 378 13402199 13402262 2.360000e-14 91.6
29 TraesCS2B01G043400 chr2D 88.138 2293 233 17 77 2361 12635604 12633343 0.000000e+00 2691.0
30 TraesCS2B01G043400 chr2D 88.712 1825 169 20 3501 5296 12632721 12630905 0.000000e+00 2194.0
31 TraesCS2B01G043400 chr2D 86.642 1909 232 13 488 2378 12629536 12627633 0.000000e+00 2091.0
32 TraesCS2B01G043400 chr2D 89.765 1319 121 13 3499 4814 12626918 12625611 0.000000e+00 1676.0
33 TraesCS2B01G043400 chr2D 85.407 884 72 21 4823 5681 12625534 12624683 0.000000e+00 865.0
34 TraesCS2B01G043400 chr2D 80.838 501 57 18 5683 6146 12624631 12624133 2.110000e-94 357.0
35 TraesCS2B01G043400 chr2D 87.500 224 15 3 5298 5508 12630817 12630594 4.760000e-61 246.0
36 TraesCS2B01G043400 chr2D 88.000 175 20 1 5971 6145 12630198 12630025 8.080000e-49 206.0
37 TraesCS2B01G043400 chr5B 80.700 1658 260 46 3665 5281 533035456 533033818 0.000000e+00 1234.0
38 TraesCS2B01G043400 chr5B 78.890 1279 249 16 1053 2325 533038164 533036901 0.000000e+00 846.0
39 TraesCS2B01G043400 chr5D 80.690 1652 261 45 3665 5281 438438826 438437198 0.000000e+00 1230.0
40 TraesCS2B01G043400 chr5A 81.134 1076 166 31 4163 5217 553491198 553490139 0.000000e+00 828.0
41 TraesCS2B01G043400 chr5A 79.414 1127 195 28 3659 4770 553480319 553479215 0.000000e+00 761.0
42 TraesCS2B01G043400 chr5A 77.143 385 80 5 1904 2281 554184177 554183794 3.730000e-52 217.0
43 TraesCS2B01G043400 chr5A 93.617 47 1 2 3455 3499 649373992 649374038 1.110000e-07 69.4
44 TraesCS2B01G043400 chr6B 100.000 43 0 0 33 75 706132698 706132656 5.110000e-11 80.5
45 TraesCS2B01G043400 chr6B 97.674 43 1 0 31 73 162174594 162174636 2.380000e-09 75.0
46 TraesCS2B01G043400 chr6D 97.674 43 1 0 31 73 85798352 85798394 2.380000e-09 75.0
47 TraesCS2B01G043400 chr6D 96.970 33 0 1 3455 3487 428886256 428886225 3.000000e-03 54.7
48 TraesCS2B01G043400 chr6A 97.674 43 1 0 31 73 103000995 103001037 2.380000e-09 75.0
49 TraesCS2B01G043400 chr6A 91.111 45 4 0 3455 3499 40072662 40072618 1.850000e-05 62.1
50 TraesCS2B01G043400 chr1D 94.000 50 2 1 26 74 454856614 454856565 2.380000e-09 75.0
51 TraesCS2B01G043400 chr1B 95.652 46 2 0 29 74 375805867 375805912 2.380000e-09 75.0
52 TraesCS2B01G043400 chr1B 97.674 43 0 1 32 74 18211212 18211171 8.550000e-09 73.1
53 TraesCS2B01G043400 chr4B 97.619 42 1 0 33 74 139759778 139759819 8.550000e-09 73.1
54 TraesCS2B01G043400 chr3D 92.500 40 1 1 3462 3499 599206007 599206046 8.610000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G043400 chr2B 20142789 20148935 6146 False 5397.500000 5899 100.000000 1 6147 2 chr2B.!!$F1 6146
1 TraesCS2B01G043400 chr2B 80255227 80256228 1001 True 398.000000 398 74.067000 1281 2293 1 chr2B.!!$R1 1012
2 TraesCS2B01G043400 chr2A 14738751 14743641 4890 True 2352.500000 2372 86.818500 77 5578 2 chr2A.!!$R5 5501
3 TraesCS2B01G043400 chr2A 14702033 14733952 31919 True 1375.750000 3112 88.015000 1 6146 16 chr2A.!!$R4 6145
4 TraesCS2B01G043400 chr2A 14681049 14683500 2451 True 862.333333 1391 85.870333 3817 6146 3 chr2A.!!$R2 2329
5 TraesCS2B01G043400 chr2A 52765167 52766387 1220 True 540.000000 540 75.080000 1053 2281 1 chr2A.!!$R1 1228
6 TraesCS2B01G043400 chr2A 14692873 14694868 1995 True 531.333333 808 86.608333 487 6146 3 chr2A.!!$R3 5659
7 TraesCS2B01G043400 chr2D 12624133 12635604 11471 True 1290.750000 2691 86.875250 77 6146 8 chr2D.!!$R1 6069
8 TraesCS2B01G043400 chr5B 533033818 533038164 4346 True 1040.000000 1234 79.795000 1053 5281 2 chr5B.!!$R1 4228
9 TraesCS2B01G043400 chr5D 438437198 438438826 1628 True 1230.000000 1230 80.690000 3665 5281 1 chr5D.!!$R1 1616
10 TraesCS2B01G043400 chr5A 553490139 553491198 1059 True 828.000000 828 81.134000 4163 5217 1 chr5A.!!$R2 1054
11 TraesCS2B01G043400 chr5A 553479215 553480319 1104 True 761.000000 761 79.414000 3659 4770 1 chr5A.!!$R1 1111

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
443 499 0.376852 TAATTGCCGAATCGCAGCAC 59.623 50.0 6.11 0.00 40.53 4.40 F
1684 2192 0.035056 ATGGACAGGCTACCTTGTGC 60.035 55.0 10.47 0.61 0.00 4.57 F
2157 2675 0.370273 GTACATTTGAGGAGTGCGCG 59.630 55.0 0.00 0.00 0.00 6.86 F
3374 4619 1.377536 GTGAGAGGAGGATGCAAAGC 58.622 55.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2720 0.036732 TGCCACTGCTCAGGTTAAGG 59.963 55.000 1.66 0.0 38.71 2.69 R
3292 4463 1.062198 TCAGGCTCACCCATATCCTCA 60.062 52.381 0.00 0.0 36.11 3.86 R
3452 4697 1.794512 CACATGTGTCATGTGGTCGA 58.205 50.000 25.74 0.0 44.04 4.20 R
5200 39191 0.609151 TGCATGGCCATTTGTTGAGG 59.391 50.000 17.92 2.9 0.00 3.86 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
26 27 6.015180 TCAGAATCAAAAAGCTAAACCTGCAT 60.015 34.615 0.00 0.00 0.00 3.96
72 73 8.414778 TCCAAAATAAATGTCGTGGTTTTAGTT 58.585 29.630 0.00 0.00 0.00 2.24
74 75 8.696175 CAAAATAAATGTCGTGGTTTTAGTTCC 58.304 33.333 0.00 0.00 0.00 3.62
149 150 2.289694 CCTCTCCTTTGAACGGTCATGT 60.290 50.000 2.76 0.00 32.48 3.21
213 214 1.892474 GGCCTACCACAATTGAGCAAA 59.108 47.619 13.59 0.00 35.26 3.68
245 246 1.666189 GTTGGCGCATCTCTAGGTTTC 59.334 52.381 10.83 0.00 0.00 2.78
443 499 0.376852 TAATTGCCGAATCGCAGCAC 59.623 50.000 6.11 0.00 40.53 4.40
484 552 5.358725 ACTTACCGGATGAAAAGTTTGTTGT 59.641 36.000 9.46 0.00 0.00 3.32
553 1049 0.734942 CACGCGAACACGGTAGGAAT 60.735 55.000 15.93 0.00 37.37 3.01
597 1093 4.986034 CGTACATTTGTGTTAGGTCTGACA 59.014 41.667 10.38 0.00 0.00 3.58
666 1162 7.545265 GCTGGTAAATTTTATCAGCACAAATGA 59.455 33.333 34.00 0.61 46.92 2.57
683 1179 7.620600 GCACAAATGATTAATGTTTGAGCAGTG 60.621 37.037 24.34 15.63 43.81 3.66
728 1224 1.224592 GTGGCATCCCAACTCCGAT 59.775 57.895 0.00 0.00 44.33 4.18
749 1245 5.163723 CGATGTGGACAGCTGAAATGTAAAT 60.164 40.000 23.35 3.24 0.00 1.40
757 1253 6.324819 ACAGCTGAAATGTAAATTCCGAATG 58.675 36.000 23.35 0.00 0.00 2.67
802 1298 2.170166 CCAACCTGCTAGCATTCCAAA 58.830 47.619 19.72 0.00 0.00 3.28
803 1299 2.165030 CCAACCTGCTAGCATTCCAAAG 59.835 50.000 19.72 4.24 0.00 2.77
804 1300 3.084039 CAACCTGCTAGCATTCCAAAGA 58.916 45.455 19.72 0.00 0.00 2.52
805 1301 3.659183 ACCTGCTAGCATTCCAAAGAT 57.341 42.857 19.72 0.00 0.00 2.40
815 1311 7.095774 GCTAGCATTCCAAAGATTTGCATTATG 60.096 37.037 10.63 0.00 36.86 1.90
816 1312 6.880484 AGCATTCCAAAGATTTGCATTATGA 58.120 32.000 0.00 0.00 36.86 2.15
849 1345 0.535328 TTCCACGGACGAAAATGCCA 60.535 50.000 0.00 0.00 0.00 4.92
861 1357 1.041447 AAATGCCAGGATGCTGCCTC 61.041 55.000 9.03 0.00 35.66 4.70
941 1437 8.930527 TGGGTGCAAGTATATATACACTTACTT 58.069 33.333 22.00 7.85 35.77 2.24
963 1461 2.152016 GTTACTCCCACTTTGCAGACC 58.848 52.381 0.00 0.00 0.00 3.85
977 1475 3.357203 TGCAGACCAGTTTTGTACCAAA 58.643 40.909 0.00 0.00 0.00 3.28
979 1477 4.142271 TGCAGACCAGTTTTGTACCAAAAG 60.142 41.667 2.56 0.00 0.00 2.27
999 1497 0.958091 TTTTGTGGCCTGGTTGATCG 59.042 50.000 3.32 0.00 0.00 3.69
1112 1610 2.427753 GCTCTCCCCCGGCAATAG 59.572 66.667 0.00 0.00 0.00 1.73
1170 1668 1.835494 TCTCTCCTACCAACTCCACG 58.165 55.000 0.00 0.00 0.00 4.94
1182 1680 2.289592 ACTCCACGAGTACTCCAACT 57.710 50.000 17.23 0.00 41.51 3.16
1263 1761 1.298667 CCGAGAAACCCCGGTCATT 59.701 57.895 0.00 0.00 40.78 2.57
1298 1799 1.478631 TCACCGATGCTCTCACTCAT 58.521 50.000 0.00 0.00 0.00 2.90
1317 1818 4.326826 TCATCAACACCTCCAATCTTGTC 58.673 43.478 0.00 0.00 0.00 3.18
1367 1868 2.356382 TCATTTGGACGACAACCAACAC 59.644 45.455 0.00 0.00 45.38 3.32
1391 1892 0.106619 ACTACCCCAGGCTCGTCTAG 60.107 60.000 0.00 0.00 0.00 2.43
1426 1930 1.464734 TTTGAACAACGGCAACCTCA 58.535 45.000 0.00 0.00 0.00 3.86
1435 1939 1.526917 GGCAACCTCATCATCCGGG 60.527 63.158 0.00 0.00 0.00 5.73
1437 1941 1.224315 CAACCTCATCATCCGGGCA 59.776 57.895 0.00 0.00 0.00 5.36
1547 2055 1.375908 GTGACCATGAGCGCCTTGA 60.376 57.895 2.29 0.00 0.00 3.02
1602 2110 1.529418 CGCTTCTCTTACGGAGTCGAC 60.529 57.143 7.70 7.70 43.93 4.20
1639 2147 0.321996 GATATTCCTCTGGGACGGGC 59.678 60.000 0.00 0.00 42.05 6.13
1684 2192 0.035056 ATGGACAGGCTACCTTGTGC 60.035 55.000 10.47 0.61 0.00 4.57
1734 2242 1.632409 ACCAGCACAGAGGTCATCATT 59.368 47.619 0.00 0.00 30.79 2.57
1825 2343 6.801718 ACATTAGGTATGTGCTAACCTACA 57.198 37.500 0.76 0.00 45.76 2.74
1881 2399 2.106683 GTCGGCGTGGGAAATCCTG 61.107 63.158 6.85 0.00 36.20 3.86
1893 2411 1.636003 GAAATCCTGGGGAACTGGTCT 59.364 52.381 0.00 0.00 39.12 3.85
2014 2532 1.341156 GGCTAGCATGGAGGAGTGGT 61.341 60.000 18.24 0.00 0.00 4.16
2061 2579 4.016706 CGGAAGGAGCCGTTGGGT 62.017 66.667 0.00 0.00 46.07 4.51
2157 2675 0.370273 GTACATTTGAGGAGTGCGCG 59.630 55.000 0.00 0.00 0.00 6.86
2163 2684 4.742201 GAGGAGTGCGCGGCAGAA 62.742 66.667 8.83 0.00 40.08 3.02
2199 2720 3.367051 CTGTGTGGCATACGCGCAC 62.367 63.158 5.73 6.42 44.48 5.34
2200 2721 4.160635 GTGTGGCATACGCGCACC 62.161 66.667 5.73 2.67 39.81 5.01
2201 2722 4.386951 TGTGGCATACGCGCACCT 62.387 61.111 5.73 0.00 38.07 4.00
2241 2762 3.454375 GTCTGAAGGAAACGTGACAAGA 58.546 45.455 0.00 0.00 0.00 3.02
2326 2847 1.874231 CGCTCTATCTCCGAGTTGCTA 59.126 52.381 0.00 0.00 0.00 3.49
2352 2874 5.880332 CCTATATGTGGCATATGGTACCAAC 59.120 44.000 20.76 11.98 34.63 3.77
2365 2887 5.237236 TGGTACCAACTCTTTCCCTTTAG 57.763 43.478 13.60 0.00 0.00 1.85
2404 2926 8.947115 ACACTGCCTCTATAAAGAAATAAACAC 58.053 33.333 0.00 0.00 0.00 3.32
2478 3007 7.898918 AGGGAGTCTCTTCTTTTACTAGTTTC 58.101 38.462 0.00 0.00 0.00 2.78
2517 3046 6.016192 TCCGTTGTTTGCCATTTCTATGTTAA 60.016 34.615 0.00 0.00 0.00 2.01
2542 3071 5.226396 TGTATGCATTGCAACAGGTAAAAC 58.774 37.500 16.46 4.00 43.62 2.43
2551 3080 5.117584 TGCAACAGGTAAAACGACTAAGAA 58.882 37.500 0.00 0.00 0.00 2.52
2559 3088 8.767085 CAGGTAAAACGACTAAGAACAATACAA 58.233 33.333 0.00 0.00 0.00 2.41
2583 3112 2.110578 GGATTGGGCTGCCAGTTTTAT 58.889 47.619 22.05 3.70 0.00 1.40
2595 3127 5.129634 TGCCAGTTTTATCAAGTGTTCTGA 58.870 37.500 0.00 0.00 0.00 3.27
2611 3143 6.780031 AGTGTTCTGATACTCCTATGCATAGT 59.220 38.462 27.75 17.41 0.00 2.12
3039 3587 5.008217 TGAAATCCTTGGACACGTAAAACTG 59.992 40.000 0.00 0.00 0.00 3.16
3041 3589 1.877443 CCTTGGACACGTAAAACTGGG 59.123 52.381 0.00 0.00 0.00 4.45
3056 3604 4.914177 AACTGGGGCAAATCATGAAATT 57.086 36.364 0.00 0.00 0.00 1.82
3057 3605 4.476628 ACTGGGGCAAATCATGAAATTC 57.523 40.909 0.00 0.00 0.00 2.17
3099 4168 6.888430 AGCAAATAACAGTTAGACGAGTTTG 58.112 36.000 9.20 9.20 0.00 2.93
3141 4216 5.730550 TCACAATGGACAATGTACTACTCC 58.269 41.667 0.00 0.00 0.00 3.85
3149 4224 5.301298 GGACAATGTACTACTCCCTACGATT 59.699 44.000 0.00 0.00 0.00 3.34
3161 4236 5.585047 ACTCCCTACGATTCAAAATAAGTGC 59.415 40.000 0.00 0.00 0.00 4.40
3218 4385 3.558931 ATATTGGAGTCGACATGCCAA 57.441 42.857 28.00 28.00 43.79 4.52
3219 4386 2.425143 ATTGGAGTCGACATGCCAAT 57.575 45.000 29.24 29.24 44.10 3.16
3263 4434 4.355543 TTCATAAAACAAGAGCGATGCC 57.644 40.909 0.00 0.00 0.00 4.40
3278 4449 1.867233 GATGCCGTGTTACCATGCTAG 59.133 52.381 0.00 0.00 0.00 3.42
3292 4463 3.181461 CCATGCTAGGAATTCGAGGTCTT 60.181 47.826 0.00 0.00 0.00 3.01
3374 4619 1.377536 GTGAGAGGAGGATGCAAAGC 58.622 55.000 0.00 0.00 0.00 3.51
3404 4649 7.647715 AGAAACATTATTTTCCAACACGTGAAG 59.352 33.333 25.01 13.62 36.31 3.02
3408 4653 7.221838 ACATTATTTTCCAACACGTGAAGTTTG 59.778 33.333 25.01 15.70 0.00 2.93
3420 4665 8.149973 ACACGTGAAGTTTGTCTTATATGTTT 57.850 30.769 25.01 0.00 36.40 2.83
3440 4685 1.742761 ATTCCTCGCCACATTGTCAG 58.257 50.000 0.00 0.00 0.00 3.51
3449 4694 3.378112 CGCCACATTGTCAGGTTTATCAT 59.622 43.478 0.00 0.00 0.00 2.45
3450 4695 4.142403 CGCCACATTGTCAGGTTTATCATT 60.142 41.667 0.00 0.00 0.00 2.57
3451 4696 5.622007 CGCCACATTGTCAGGTTTATCATTT 60.622 40.000 0.00 0.00 0.00 2.32
3452 4697 6.165577 GCCACATTGTCAGGTTTATCATTTT 58.834 36.000 0.00 0.00 0.00 1.82
3453 4698 6.311200 GCCACATTGTCAGGTTTATCATTTTC 59.689 38.462 0.00 0.00 0.00 2.29
3454 4699 6.527722 CCACATTGTCAGGTTTATCATTTTCG 59.472 38.462 0.00 0.00 0.00 3.46
3455 4700 7.304735 CACATTGTCAGGTTTATCATTTTCGA 58.695 34.615 0.00 0.00 0.00 3.71
3456 4701 7.271223 CACATTGTCAGGTTTATCATTTTCGAC 59.729 37.037 0.00 0.00 0.00 4.20
3457 4702 5.873179 TGTCAGGTTTATCATTTTCGACC 57.127 39.130 0.00 0.00 0.00 4.79
3458 4703 5.309638 TGTCAGGTTTATCATTTTCGACCA 58.690 37.500 0.00 0.00 0.00 4.02
3459 4704 5.180492 TGTCAGGTTTATCATTTTCGACCAC 59.820 40.000 0.00 0.00 0.00 4.16
3460 4705 5.180492 GTCAGGTTTATCATTTTCGACCACA 59.820 40.000 0.00 0.00 0.00 4.17
3461 4706 5.943416 TCAGGTTTATCATTTTCGACCACAT 59.057 36.000 0.00 0.00 0.00 3.21
3462 4707 6.029607 CAGGTTTATCATTTTCGACCACATG 58.970 40.000 0.00 0.00 0.00 3.21
3463 4708 5.943416 AGGTTTATCATTTTCGACCACATGA 59.057 36.000 0.00 0.00 0.00 3.07
3464 4709 6.027749 GGTTTATCATTTTCGACCACATGAC 58.972 40.000 0.00 0.00 0.00 3.06
3465 4710 6.348950 GGTTTATCATTTTCGACCACATGACA 60.349 38.462 0.00 0.00 0.00 3.58
3466 4711 4.685169 ATCATTTTCGACCACATGACAC 57.315 40.909 0.00 0.00 0.00 3.67
3467 4712 3.471680 TCATTTTCGACCACATGACACA 58.528 40.909 0.00 0.00 0.00 3.72
3468 4713 4.071423 TCATTTTCGACCACATGACACAT 58.929 39.130 0.00 0.00 0.00 3.21
3469 4714 3.894782 TTTTCGACCACATGACACATG 57.105 42.857 0.00 9.72 0.00 3.21
3470 4715 2.542020 TTCGACCACATGACACATGT 57.458 45.000 10.94 10.94 0.00 3.21
3471 4716 1.794512 TCGACCACATGACACATGTG 58.205 50.000 27.39 27.39 46.49 3.21
3477 4722 3.476295 CACATGACACATGTGGTAAGC 57.524 47.619 28.64 13.03 44.04 3.09
3478 4723 2.813172 CACATGACACATGTGGTAAGCA 59.187 45.455 28.64 17.63 44.04 3.91
3479 4724 3.252944 CACATGACACATGTGGTAAGCAA 59.747 43.478 28.64 7.21 44.04 3.91
3480 4725 3.253188 ACATGACACATGTGGTAAGCAAC 59.747 43.478 28.64 10.20 34.19 4.17
3492 4737 4.922471 GGTAAGCAACCCAAACAACTAA 57.078 40.909 0.00 0.00 43.16 2.24
3493 4738 5.265350 GGTAAGCAACCCAAACAACTAAA 57.735 39.130 0.00 0.00 43.16 1.85
3494 4739 5.662456 GGTAAGCAACCCAAACAACTAAAA 58.338 37.500 0.00 0.00 43.16 1.52
3495 4740 6.107343 GGTAAGCAACCCAAACAACTAAAAA 58.893 36.000 0.00 0.00 43.16 1.94
3541 4786 3.192466 ACCGACGTGCCTTATGAATTAC 58.808 45.455 0.00 0.00 0.00 1.89
3554 4799 7.414762 GCCTTATGAATTACGTTTCTTTGGCTA 60.415 37.037 16.41 0.00 33.52 3.93
3610 4856 2.673258 ACGGTTCCAAGGGTCAAAAAT 58.327 42.857 0.00 0.00 0.00 1.82
3696 4944 4.761739 TGTGGAAGCAGGTAAGATCAAAAG 59.238 41.667 0.00 0.00 0.00 2.27
4047 37946 5.069119 ACAAGGAACAAAGGAATTCAGGAAC 59.931 40.000 7.93 0.00 0.00 3.62
4057 37956 8.726988 CAAAGGAATTCAGGAACGAAGTAATTA 58.273 33.333 7.93 0.00 45.00 1.40
4185 38084 5.298527 GGATGCTACCCTTTTTGGTACATAC 59.701 44.000 0.00 0.00 39.30 2.39
4194 38093 6.828785 CCCTTTTTGGTACATACTCTAGCAAT 59.171 38.462 0.00 0.00 39.30 3.56
4259 38166 8.718102 TGCTTACATTCCTTCTATTTACAGAC 57.282 34.615 0.00 0.00 0.00 3.51
4316 38223 8.215050 ACACGGTTCAATATAATCAAAGGGATA 58.785 33.333 0.00 0.00 34.28 2.59
4460 38367 3.134458 GAGGATCTTTGGCGATAACCAG 58.866 50.000 0.00 0.00 41.82 4.00
4509 38416 4.105217 TCGGGACCTAGTGAGTATCCATTA 59.895 45.833 0.00 0.00 30.65 1.90
4510 38417 4.459685 CGGGACCTAGTGAGTATCCATTAG 59.540 50.000 0.00 0.00 30.65 1.73
4657 38569 2.004583 TGTATACAGCTTCGGTGTGC 57.995 50.000 0.08 1.00 44.23 4.57
4695 38607 7.072177 TGTAACTGGCATTAGAAGAAATTCG 57.928 36.000 0.00 0.00 0.00 3.34
4699 38611 6.789262 ACTGGCATTAGAAGAAATTCGAATG 58.211 36.000 12.25 15.27 42.82 2.67
4738 38650 6.068461 TCCCTAGCCTCATAGTCTATGTAG 57.932 45.833 17.55 12.06 37.45 2.74
4745 38659 5.183522 GCCTCATAGTCTATGTAGGTACACC 59.816 48.000 24.41 13.24 39.30 4.16
4882 38870 3.766691 GGGCGGGCAGACGAGTTA 61.767 66.667 3.27 0.00 35.47 2.24
4892 38880 2.030185 GCAGACGAGTTACCAGACTCAA 60.030 50.000 5.94 0.00 44.98 3.02
4999 38987 6.054941 CAGGCCACTTATGTCATATGTTGTA 58.945 40.000 5.01 0.00 0.00 2.41
5020 39008 1.938585 TCGTCCTGGAGAATGGAAGT 58.061 50.000 0.00 0.00 34.32 3.01
5086 39074 6.035843 GCGAAGAATTGAAATGGAGCAAATA 58.964 36.000 0.00 0.00 0.00 1.40
5151 39139 5.462398 CCGAAATAGAGGGACGTTGAAATAG 59.538 44.000 0.00 0.00 0.00 1.73
5200 39191 2.745281 ACATTGCCAAAAGAATGCATGC 59.255 40.909 11.82 11.82 33.59 4.06
5228 39222 1.849977 ATGGCCATGCATTGTGTGTA 58.150 45.000 20.04 0.00 0.00 2.90
5254 39248 9.730705 AGTTCAGAAGTCATTATCTTTGAATGA 57.269 29.630 0.00 0.00 40.23 2.57
5292 39288 3.954904 TGGCCTTGATAGTAGTCTCAGTC 59.045 47.826 3.32 0.00 0.00 3.51
5296 39292 6.407525 GGCCTTGATAGTAGTCTCAGTCAAAT 60.408 42.308 0.00 0.00 0.00 2.32
5359 39355 5.120674 TGCAGATAACACAAAGTCGATGAAG 59.879 40.000 0.00 0.00 0.00 3.02
5362 39358 7.222805 GCAGATAACACAAAGTCGATGAAGATA 59.777 37.037 0.00 0.00 0.00 1.98
5396 39392 2.039879 ACACAAGTGATTAGGTGGGGTC 59.960 50.000 7.28 0.00 35.62 4.46
5445 39454 4.002906 TGCTAAAGAAATGACAGGACGT 57.997 40.909 0.00 0.00 0.00 4.34
5463 39472 4.084328 GGACGTTCAGACAAAATCACAGAG 60.084 45.833 0.00 0.00 0.00 3.35
5464 39473 3.248602 ACGTTCAGACAAAATCACAGAGC 59.751 43.478 0.00 0.00 0.00 4.09
5472 39481 0.239347 AAATCACAGAGCAAGCACGC 59.761 50.000 0.00 0.00 0.00 5.34
5504 39513 3.757493 TGAAGTGTGCATGCATTCATACA 59.243 39.130 25.64 13.14 0.00 2.29
5549 39566 5.343307 AAATAGCCATGTGGTGGATTTTC 57.657 39.130 0.35 0.00 46.77 2.29
5564 39581 5.649395 GTGGATTTTCAGTCCAATCATCAGA 59.351 40.000 0.00 0.00 46.67 3.27
5572 39589 4.094590 CAGTCCAATCATCAGAAGCAACTC 59.905 45.833 0.00 0.00 0.00 3.01
5573 39590 4.005650 GTCCAATCATCAGAAGCAACTCA 58.994 43.478 0.00 0.00 0.00 3.41
5588 39605 3.119708 GCAACTCAGCAAGGTGATTTAGG 60.120 47.826 8.24 0.00 46.43 2.69
5602 39619 3.582647 TGATTTAGGCAGGTTCAGACTCA 59.417 43.478 0.00 0.00 0.00 3.41
5638 39656 4.936891 AGAAAACACAGCAAATGGTTCTC 58.063 39.130 0.00 0.00 0.00 2.87
5639 39657 4.402155 AGAAAACACAGCAAATGGTTCTCA 59.598 37.500 0.00 0.00 0.00 3.27
5640 39658 3.996150 AACACAGCAAATGGTTCTCAG 57.004 42.857 0.00 0.00 0.00 3.35
5641 39659 2.936202 ACACAGCAAATGGTTCTCAGT 58.064 42.857 0.00 0.00 0.00 3.41
5642 39660 4.085357 ACACAGCAAATGGTTCTCAGTA 57.915 40.909 0.00 0.00 0.00 2.74
5643 39661 4.655963 ACACAGCAAATGGTTCTCAGTAT 58.344 39.130 0.00 0.00 0.00 2.12
5644 39662 5.804639 ACACAGCAAATGGTTCTCAGTATA 58.195 37.500 0.00 0.00 0.00 1.47
5645 39663 6.237901 ACACAGCAAATGGTTCTCAGTATAA 58.762 36.000 0.00 0.00 0.00 0.98
5696 39764 2.685897 TCTTGGCGTTTATATGGTTGGC 59.314 45.455 0.00 0.00 0.00 4.52
5697 39765 2.130272 TGGCGTTTATATGGTTGGCA 57.870 45.000 0.00 0.00 0.00 4.92
5707 39775 2.668632 GGTTGGCACCGAGATCCA 59.331 61.111 0.00 0.00 31.60 3.41
5717 39785 4.202223 GGCACCGAGATCCAAGAAATAGTA 60.202 45.833 0.00 0.00 0.00 1.82
5753 39821 5.671493 ACAAGTTATGGAGTTATCTTCGGG 58.329 41.667 0.00 0.00 0.00 5.14
5758 39826 3.110293 TGGAGTTATCTTCGGGAAGGA 57.890 47.619 8.46 0.00 38.88 3.36
5761 39829 3.705072 GGAGTTATCTTCGGGAAGGAGAA 59.295 47.826 8.46 0.00 38.88 2.87
5763 39831 5.163290 GGAGTTATCTTCGGGAAGGAGAAAT 60.163 44.000 8.46 0.83 38.88 2.17
5771 39839 2.095461 GGGAAGGAGAAATGAGTTGCC 58.905 52.381 0.00 0.00 0.00 4.52
5776 39844 3.152341 AGGAGAAATGAGTTGCCAGTTG 58.848 45.455 0.00 0.00 0.00 3.16
5778 39846 3.304928 GGAGAAATGAGTTGCCAGTTGTG 60.305 47.826 0.00 0.00 0.00 3.33
5779 39847 3.290710 AGAAATGAGTTGCCAGTTGTGT 58.709 40.909 0.00 0.00 0.00 3.72
5780 39848 3.067180 AGAAATGAGTTGCCAGTTGTGTG 59.933 43.478 0.00 0.00 0.00 3.82
5784 39852 2.358582 TGAGTTGCCAGTTGTGTGAATG 59.641 45.455 0.00 0.00 0.00 2.67
5788 39856 0.523072 GCCAGTTGTGTGAATGCGAT 59.477 50.000 0.00 0.00 0.00 4.58
5789 39857 1.068333 GCCAGTTGTGTGAATGCGATT 60.068 47.619 0.00 0.00 0.00 3.34
5790 39858 2.161410 GCCAGTTGTGTGAATGCGATTA 59.839 45.455 0.00 0.00 0.00 1.75
5835 39903 6.855836 TGAAATGTTTCATAGCTAAAGCTGG 58.144 36.000 14.71 6.90 45.56 4.85
5838 39906 7.486232 GAAATGTTTCATAGCTAAAGCTGGTTC 59.514 37.037 14.71 2.72 43.08 3.62
5856 39924 8.962679 AGCTGGTTCGGAATATTTTAAAATGTA 58.037 29.630 21.19 4.92 0.00 2.29
5915 39992 2.429610 AGAAATGGCCAAGATCATGCAC 59.570 45.455 10.96 0.00 0.00 4.57
5936 40013 2.166870 CGGTGTACCCTTGTGCATACTA 59.833 50.000 0.00 0.00 39.36 1.82
5940 40017 6.350906 GGTGTACCCTTGTGCATACTAATAA 58.649 40.000 0.00 0.00 39.36 1.40
5952 40029 7.065683 TGTGCATACTAATAACTCAACACATGG 59.934 37.037 0.00 0.00 30.03 3.66
5955 40032 8.673711 GCATACTAATAACTCAACACATGGAAA 58.326 33.333 0.00 0.00 0.00 3.13
5971 40078 4.213564 TGGAAACAAAAATGCAACCTGT 57.786 36.364 0.00 0.00 37.44 4.00
5977 40084 1.616159 AAAATGCAACCTGTAGGCGT 58.384 45.000 0.00 0.00 39.32 5.68
6020 40127 0.843309 TGGAAACAGGCAAGGAGACA 59.157 50.000 0.00 0.00 35.01 3.41
6029 40136 0.321122 GCAAGGAGACACAGGTGGAG 60.321 60.000 4.24 0.00 34.19 3.86
6032 40139 0.764369 AGGAGACACAGGTGGAGCAA 60.764 55.000 4.24 0.00 34.19 3.91
6047 40154 0.823356 AGCAAGCACCAATGAACGGT 60.823 50.000 0.00 0.00 37.16 4.83
6048 40155 0.878416 GCAAGCACCAATGAACGGTA 59.122 50.000 0.00 0.00 34.02 4.02
6054 40161 2.033550 GCACCAATGAACGGTACAACAA 59.966 45.455 0.00 0.00 34.02 2.83
6085 40192 3.370231 GCCCACCGCAACCGAAAT 61.370 61.111 0.00 0.00 37.47 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.985059 GGGAGTACTAACTAATGCAGGTTTAG 59.015 42.308 0.00 6.03 35.56 1.85
17 18 5.487845 AGGGAGTACTAACTAATGCAGGTTT 59.512 40.000 0.00 0.00 35.56 3.27
20 21 4.039366 GGAGGGAGTACTAACTAATGCAGG 59.961 50.000 0.00 0.00 35.56 4.85
26 27 4.166725 TGGATCGGAGGGAGTACTAACTAA 59.833 45.833 0.00 0.00 35.56 2.24
72 73 5.430417 TGTGGCAAAATAATACTCCCTAGGA 59.570 40.000 11.48 0.00 0.00 2.94
74 75 7.823745 AATGTGGCAAAATAATACTCCCTAG 57.176 36.000 0.00 0.00 0.00 3.02
213 214 2.036256 GCCAACACAGGGGATGCT 59.964 61.111 0.00 0.00 0.00 3.79
245 246 7.873505 AGAAAGTTACTGAACTAGTTGCCTTAG 59.126 37.037 14.14 5.95 45.50 2.18
553 1049 1.414919 ACCAACGAACAAGCTAGGTGA 59.585 47.619 0.00 0.00 0.00 4.02
597 1093 7.336931 CCCTGTAGTAATTCTAGTTGTTGCATT 59.663 37.037 0.00 0.00 0.00 3.56
666 1162 7.332926 CAGACTAGTCACTGCTCAAACATTAAT 59.667 37.037 24.44 0.00 0.00 1.40
728 1224 5.048083 GGAATTTACATTTCAGCTGTCCACA 60.048 40.000 14.67 0.00 0.00 4.17
749 1245 4.221924 TGAGAGTGTATTGGACATTCGGAA 59.778 41.667 0.00 0.00 46.62 4.30
757 1253 2.159028 GGGAGCTGAGAGTGTATTGGAC 60.159 54.545 0.00 0.00 0.00 4.02
802 1298 9.624373 AAGTAGATGACTTCATAATGCAAATCT 57.376 29.630 0.00 0.00 45.81 2.40
825 1321 2.607631 TTTTCGTCCGTGGAAGAAGT 57.392 45.000 15.18 0.00 41.85 3.01
849 1345 1.224039 GAAGCAGAGGCAGCATCCT 59.776 57.895 2.72 0.00 44.61 3.24
861 1357 2.740981 AGCTTTGACGAAGATGAAGCAG 59.259 45.455 6.62 0.00 43.78 4.24
909 1405 3.685139 ATATACTTGCACCCATCGAGG 57.315 47.619 0.00 0.00 37.03 4.63
913 1409 9.367444 GTAAGTGTATATATACTTGCACCCATC 57.633 37.037 26.42 9.36 38.91 3.51
941 1437 3.007614 GGTCTGCAAAGTGGGAGTAACTA 59.992 47.826 0.00 0.00 0.00 2.24
977 1475 1.859302 TCAACCAGGCCACAAAACTT 58.141 45.000 5.01 0.00 0.00 2.66
979 1477 1.335872 CGATCAACCAGGCCACAAAAC 60.336 52.381 5.01 0.00 0.00 2.43
999 1497 0.182061 TGAGAGCCAGCCAATCCATC 59.818 55.000 0.00 0.00 0.00 3.51
1036 1534 0.606673 GGCAGGAACAGAAGGACCAC 60.607 60.000 0.00 0.00 0.00 4.16
1155 1653 2.040813 AGTACTCGTGGAGTTGGTAGGA 59.959 50.000 3.32 0.00 40.28 2.94
1170 1668 6.587206 AGGTACAACTTAGTTGGAGTACTC 57.413 41.667 26.09 14.87 46.50 2.59
1182 1680 5.444744 ACCATATGCCAAGGTACAACTTA 57.555 39.130 0.00 0.00 32.92 2.24
1263 1761 2.231478 CGGTGAAGAGGAAGAGCTGTTA 59.769 50.000 0.00 0.00 0.00 2.41
1298 1799 2.711009 AGGACAAGATTGGAGGTGTTGA 59.289 45.455 0.00 0.00 0.00 3.18
1317 1818 2.809665 GCTGCCATCACCATTAGAGAGG 60.810 54.545 0.00 0.00 0.00 3.69
1426 1930 1.624336 CCATTTGATGCCCGGATGAT 58.376 50.000 0.73 0.00 0.00 2.45
1435 1939 2.004017 CAACATGGTGCCATTTGATGC 58.996 47.619 0.00 0.00 33.90 3.91
1437 1941 2.027929 CCACAACATGGTGCCATTTGAT 60.028 45.455 11.63 10.80 44.46 2.57
1602 2110 3.246112 TGGAGGAACGTGGTGGGG 61.246 66.667 0.00 0.00 0.00 4.96
1674 2182 3.041874 CTCGCTCAGCACAAGGTAG 57.958 57.895 0.00 0.00 0.00 3.18
1697 2205 1.562575 GGTGTTCGCCTGTTGGTACG 61.563 60.000 0.00 0.00 35.27 3.67
1734 2242 2.672651 TCGACGACGGCCCAGTAA 60.673 61.111 7.55 0.00 40.21 2.24
1805 2319 4.098349 CGGTGTAGGTTAGCACATACCTAA 59.902 45.833 0.00 0.00 45.85 2.69
1818 2332 1.598701 GGTACTCGCCGGTGTAGGTT 61.599 60.000 16.01 0.00 0.00 3.50
1825 2343 1.219935 GGATTTGGTACTCGCCGGT 59.780 57.895 1.90 0.00 0.00 5.28
1893 2411 2.978156 AGAGGTTGCATTTGAGGGAA 57.022 45.000 0.00 0.00 0.00 3.97
2014 2532 0.325296 ATAGAGAACCTGCCACCGGA 60.325 55.000 9.46 0.00 0.00 5.14
2061 2579 4.178169 AAACCGTCACCGCACCCA 62.178 61.111 0.00 0.00 0.00 4.51
2106 2624 1.535226 CCGACGAGTGTGAACTTGTCA 60.535 52.381 20.68 0.00 46.44 3.58
2131 2649 4.573900 CACTCCTCAAATGTACTCTTGCT 58.426 43.478 0.00 0.00 0.00 3.91
2199 2720 0.036732 TGCCACTGCTCAGGTTAAGG 59.963 55.000 1.66 0.00 38.71 2.69
2200 2721 1.446907 CTGCCACTGCTCAGGTTAAG 58.553 55.000 1.66 0.00 38.71 1.85
2201 2722 0.036732 CCTGCCACTGCTCAGGTTAA 59.963 55.000 1.66 0.00 43.66 2.01
2241 2762 1.536174 CCCACCCCAAACCAAGCAT 60.536 57.895 0.00 0.00 0.00 3.79
2379 2901 8.946085 TGTGTTTATTTCTTTATAGAGGCAGTG 58.054 33.333 0.00 0.00 0.00 3.66
2452 2981 7.470935 AACTAGTAAAAGAAGAGACTCCCTC 57.529 40.000 0.00 0.00 42.28 4.30
2542 3071 8.331022 CAATCCTCATTGTATTGTTCTTAGTCG 58.669 37.037 0.00 0.00 35.53 4.18
2551 3080 3.956199 CAGCCCAATCCTCATTGTATTGT 59.044 43.478 0.00 0.00 38.22 2.71
2559 3088 1.229359 CTGGCAGCCCAATCCTCAT 59.771 57.895 9.64 0.00 41.58 2.90
2583 3112 5.422012 TGCATAGGAGTATCAGAACACTTGA 59.578 40.000 0.00 0.00 36.25 3.02
2595 3127 4.840680 TGCCAAGACTATGCATAGGAGTAT 59.159 41.667 31.87 14.88 34.69 2.12
2611 3143 6.325286 ACCTTTAAACTTTAACCATGCCAAGA 59.675 34.615 0.00 0.00 0.00 3.02
2978 3510 8.405531 TGGTAGTAAATAATGAATTGCAAGCTC 58.594 33.333 4.94 4.80 0.00 4.09
3039 3587 3.451902 TCCAGAATTTCATGATTTGCCCC 59.548 43.478 0.00 0.00 0.00 5.80
3041 3589 4.107622 CGTCCAGAATTTCATGATTTGCC 58.892 43.478 0.00 0.00 0.00 4.52
3056 3604 3.194755 TGCTCTAGTTTTATGCGTCCAGA 59.805 43.478 0.00 0.00 0.00 3.86
3057 3605 3.521560 TGCTCTAGTTTTATGCGTCCAG 58.478 45.455 0.00 0.00 0.00 3.86
3099 4168 8.819974 CATTGTGATAAAATCATTTGGTAAGCC 58.180 33.333 0.00 0.00 42.04 4.35
3141 4216 4.331717 ACGGCACTTATTTTGAATCGTAGG 59.668 41.667 0.00 0.00 0.00 3.18
3149 4224 9.968870 AAAATAAAACTACGGCACTTATTTTGA 57.031 25.926 9.04 0.00 39.18 2.69
3161 4236 4.002316 TCCGGTCCAAAATAAAACTACGG 58.998 43.478 0.00 0.00 38.97 4.02
3195 4362 4.377021 TGGCATGTCGACTCCAATATTAC 58.623 43.478 17.92 0.00 0.00 1.89
3209 4376 4.556942 TCGATGATTTCATTGGCATGTC 57.443 40.909 7.74 0.00 38.11 3.06
3218 4385 5.319453 ACCAGGCAATATCGATGATTTCAT 58.681 37.500 8.54 0.00 39.70 2.57
3219 4386 4.717877 ACCAGGCAATATCGATGATTTCA 58.282 39.130 8.54 0.00 0.00 2.69
3278 4449 3.828875 ATCCTCAAGACCTCGAATTCC 57.171 47.619 0.00 0.00 0.00 3.01
3292 4463 1.062198 TCAGGCTCACCCATATCCTCA 60.062 52.381 0.00 0.00 36.11 3.86
3336 4581 2.565645 CGCTACCTCCTCATCCCCG 61.566 68.421 0.00 0.00 0.00 5.73
3374 4619 7.223777 ACGTGTTGGAAAATAATGTTTCTTTGG 59.776 33.333 0.00 0.00 37.60 3.28
3404 4649 8.068380 GGCGAGGAATAAACATATAAGACAAAC 58.932 37.037 0.00 0.00 0.00 2.93
3408 4653 6.704493 TGTGGCGAGGAATAAACATATAAGAC 59.296 38.462 0.00 0.00 0.00 3.01
3420 4665 2.419990 CCTGACAATGTGGCGAGGAATA 60.420 50.000 0.00 0.00 28.88 1.75
3440 4685 6.027749 GTCATGTGGTCGAAAATGATAAACC 58.972 40.000 0.00 0.00 32.07 3.27
3449 4694 3.003171 CACATGTGTCATGTGGTCGAAAA 59.997 43.478 25.74 0.00 44.04 2.29
3450 4695 2.547634 CACATGTGTCATGTGGTCGAAA 59.452 45.455 25.74 0.00 44.04 3.46
3451 4696 2.142319 CACATGTGTCATGTGGTCGAA 58.858 47.619 25.74 0.00 44.04 3.71
3452 4697 1.794512 CACATGTGTCATGTGGTCGA 58.205 50.000 25.74 0.00 44.04 4.20
3457 4702 2.813172 TGCTTACCACATGTGTCATGTG 59.187 45.455 26.20 26.20 46.49 3.21
3458 4703 3.138884 TGCTTACCACATGTGTCATGT 57.861 42.857 23.79 16.29 0.00 3.21
3459 4704 3.366273 GGTTGCTTACCACATGTGTCATG 60.366 47.826 23.79 11.29 46.92 3.07
3460 4705 2.819608 GGTTGCTTACCACATGTGTCAT 59.180 45.455 23.79 11.74 46.92 3.06
3461 4706 2.226330 GGTTGCTTACCACATGTGTCA 58.774 47.619 23.79 8.71 46.92 3.58
3462 4707 2.989422 GGTTGCTTACCACATGTGTC 57.011 50.000 23.79 8.37 46.92 3.67
3471 4716 4.922471 TTAGTTGTTTGGGTTGCTTACC 57.078 40.909 0.43 0.43 46.99 2.85
3494 4739 5.684184 GCTGTCGAAAACGATAAACCTTTTT 59.316 36.000 0.00 0.00 0.00 1.94
3495 4740 5.209977 GCTGTCGAAAACGATAAACCTTTT 58.790 37.500 0.00 0.00 0.00 2.27
3496 4741 4.609783 CGCTGTCGAAAACGATAAACCTTT 60.610 41.667 0.00 0.00 38.10 3.11
3497 4742 3.120786 CGCTGTCGAAAACGATAAACCTT 60.121 43.478 0.00 0.00 38.10 3.50
3498 4743 2.410730 CGCTGTCGAAAACGATAAACCT 59.589 45.455 0.00 0.00 38.10 3.50
3499 4744 2.409378 TCGCTGTCGAAAACGATAAACC 59.591 45.455 0.00 0.00 42.44 3.27
3500 4745 3.693300 TCGCTGTCGAAAACGATAAAC 57.307 42.857 0.00 0.00 42.44 2.01
3517 4762 2.202703 ATAAGGCACGTCGGTCGC 60.203 61.111 0.00 0.00 44.19 5.19
3525 4770 5.464965 AGAAACGTAATTCATAAGGCACG 57.535 39.130 3.01 0.00 35.62 5.34
3532 4777 8.500753 ACATAGCCAAAGAAACGTAATTCATA 57.499 30.769 3.01 0.00 0.00 2.15
3541 4786 6.236017 TGAACTTACATAGCCAAAGAAACG 57.764 37.500 0.00 0.00 0.00 3.60
3554 4799 5.514500 ACACACCCCTTATGAACTTACAT 57.486 39.130 0.00 0.00 0.00 2.29
3588 4834 2.146920 TTTGACCCTTGGAACCGTTT 57.853 45.000 0.00 0.00 0.00 3.60
3696 4944 2.863401 ACTTTTGCGTTTTCTCCACC 57.137 45.000 0.00 0.00 0.00 4.61
3964 37863 2.699321 GACCACCTAACATCCCCTAGAC 59.301 54.545 0.00 0.00 0.00 2.59
4063 37962 6.183360 ACCAAGTTCCTATGTTGCAATTTTGA 60.183 34.615 0.59 0.00 0.00 2.69
4065 37964 6.173427 ACCAAGTTCCTATGTTGCAATTTT 57.827 33.333 0.59 0.00 0.00 1.82
4259 38166 9.746711 CAATCTAGTAACAATTTTCTTGAGTCG 57.253 33.333 0.00 0.00 0.00 4.18
4316 38223 3.201045 GGAGATAAAGAAGTCCCCTTGCT 59.799 47.826 0.00 0.00 0.00 3.91
4460 38367 3.480185 CGCGTTGAGTATTTGCATTTTGC 60.480 43.478 0.00 0.00 45.29 3.68
4540 38452 9.730420 TTGCAAGAGTTACTAAATTGAAAGTTC 57.270 29.630 0.00 0.00 0.00 3.01
4657 38569 7.108841 TGCCAGTTACAACCTCTAATAGTAG 57.891 40.000 0.00 0.00 0.00 2.57
4738 38650 1.201880 GTGAGAAGTCCTCGGTGTACC 59.798 57.143 0.00 0.00 44.92 3.34
4745 38659 3.717707 TGAAACTTGTGAGAAGTCCTCG 58.282 45.455 0.00 0.00 44.92 4.63
4821 38805 6.547141 TGACTGAAACAACCAAGAAGATCATT 59.453 34.615 0.00 0.00 0.00 2.57
4882 38870 4.444022 GCATCCATGATAGTTGAGTCTGGT 60.444 45.833 0.00 0.00 0.00 4.00
4892 38880 5.108187 AGTGAACAAGCATCCATGATAGT 57.892 39.130 0.00 0.00 0.00 2.12
4999 38987 2.840651 ACTTCCATTCTCCAGGACGAAT 59.159 45.455 7.85 7.85 32.62 3.34
5020 39008 1.914764 GGGGTCCGGAAGTGTGGTA 60.915 63.158 5.23 0.00 0.00 3.25
5200 39191 0.609151 TGCATGGCCATTTGTTGAGG 59.391 50.000 17.92 2.90 0.00 3.86
5228 39222 9.730705 TCATTCAAAGATAATGACTTCTGAACT 57.269 29.630 0.00 0.00 38.19 3.01
5254 39248 3.763057 AGGCCAAAACGGAATAGAAACT 58.237 40.909 5.01 0.00 36.56 2.66
5336 39332 5.348724 TCTTCATCGACTTTGTGTTATCTGC 59.651 40.000 0.00 0.00 0.00 4.26
5359 39355 7.592938 TCACTTGTGTCCAATGTGAAATTATC 58.407 34.615 0.46 0.00 36.59 1.75
5362 39358 5.850557 TCACTTGTGTCCAATGTGAAATT 57.149 34.783 0.46 0.00 36.59 1.82
5407 39416 3.025287 AGCAAATAAGCACAAAACCCG 57.975 42.857 0.00 0.00 36.85 5.28
5445 39454 4.261322 GCTTGCTCTGTGATTTTGTCTGAA 60.261 41.667 0.00 0.00 0.00 3.02
5463 39472 2.675056 CCTCAGTCAGCGTGCTTGC 61.675 63.158 0.00 0.00 0.00 4.01
5464 39473 1.301244 ACCTCAGTCAGCGTGCTTG 60.301 57.895 0.00 0.00 0.00 4.01
5472 39481 1.202568 TGCACACTTCACCTCAGTCAG 60.203 52.381 0.00 0.00 0.00 3.51
5549 39566 4.008330 AGTTGCTTCTGATGATTGGACTG 58.992 43.478 0.00 0.00 0.00 3.51
5564 39581 2.283145 ATCACCTTGCTGAGTTGCTT 57.717 45.000 0.00 0.00 0.00 3.91
5572 39589 1.747355 CCTGCCTAAATCACCTTGCTG 59.253 52.381 0.00 0.00 0.00 4.41
5573 39590 1.355720 ACCTGCCTAAATCACCTTGCT 59.644 47.619 0.00 0.00 0.00 3.91
5588 39605 5.048504 TGAAATCATTTGAGTCTGAACCTGC 60.049 40.000 0.00 0.00 0.00 4.85
5602 39619 7.765360 TGCTGTGTTTTCTTTCTGAAATCATTT 59.235 29.630 2.88 0.00 42.64 2.32
5624 39642 6.769822 AGGATTATACTGAGAACCATTTGCTG 59.230 38.462 0.00 0.00 0.00 4.41
5654 39672 1.165907 TTGGCTCAACGTGCTTCCTG 61.166 55.000 0.00 0.00 0.00 3.86
5696 39764 7.437748 AGAATACTATTTCTTGGATCTCGGTG 58.562 38.462 0.00 0.00 31.94 4.94
5697 39765 7.604657 AGAATACTATTTCTTGGATCTCGGT 57.395 36.000 0.00 0.00 31.94 4.69
5707 39775 9.715121 TTGTCGTTGGTTAGAATACTATTTCTT 57.285 29.630 0.00 0.00 37.20 2.52
5717 39785 6.469410 TCCATAACTTGTCGTTGGTTAGAAT 58.531 36.000 0.00 0.00 37.05 2.40
5728 39796 5.459107 CCGAAGATAACTCCATAACTTGTCG 59.541 44.000 0.00 0.00 0.00 4.35
5753 39821 3.416156 ACTGGCAACTCATTTCTCCTTC 58.584 45.455 0.00 0.00 37.61 3.46
5758 39826 3.067180 CACACAACTGGCAACTCATTTCT 59.933 43.478 0.00 0.00 37.61 2.52
5761 39829 2.653726 TCACACAACTGGCAACTCATT 58.346 42.857 0.00 0.00 37.61 2.57
5763 39831 2.121291 TTCACACAACTGGCAACTCA 57.879 45.000 0.00 0.00 37.61 3.41
5771 39839 4.152223 TGTCTAATCGCATTCACACAACTG 59.848 41.667 0.00 0.00 0.00 3.16
5776 39844 5.868257 TCAATTGTCTAATCGCATTCACAC 58.132 37.500 5.13 0.00 0.00 3.82
5778 39846 6.718388 TGATCAATTGTCTAATCGCATTCAC 58.282 36.000 5.13 0.00 0.00 3.18
5779 39847 6.923928 TGATCAATTGTCTAATCGCATTCA 57.076 33.333 5.13 0.00 0.00 2.57
5780 39848 7.804712 AGATGATCAATTGTCTAATCGCATTC 58.195 34.615 5.13 0.00 0.00 2.67
5784 39852 7.418840 AAGAGATGATCAATTGTCTAATCGC 57.581 36.000 5.13 6.98 0.00 4.58
5788 39856 9.948964 TTCAGAAAGAGATGATCAATTGTCTAA 57.051 29.630 5.13 0.00 0.00 2.10
5789 39857 9.948964 TTTCAGAAAGAGATGATCAATTGTCTA 57.051 29.630 5.13 0.00 0.00 2.59
5790 39858 8.859236 TTTCAGAAAGAGATGATCAATTGTCT 57.141 30.769 5.13 0.00 0.00 3.41
5868 39936 7.447238 TCGGAAGAAAGAAAAATGAAGTACCAT 59.553 33.333 0.00 0.00 37.03 3.55
5870 39938 7.172703 TCTCGGAAGAAAGAAAAATGAAGTACC 59.827 37.037 0.00 0.00 41.32 3.34
5871 39939 8.084590 TCTCGGAAGAAAGAAAAATGAAGTAC 57.915 34.615 0.00 0.00 41.32 2.73
5872 39940 8.671384 TTCTCGGAAGAAAGAAAAATGAAGTA 57.329 30.769 0.00 0.00 38.58 2.24
5873 39941 7.568199 TTCTCGGAAGAAAGAAAAATGAAGT 57.432 32.000 0.00 0.00 38.58 3.01
5891 39968 2.042686 TGATCTTGGCCATTTCTCGG 57.957 50.000 6.09 0.00 0.00 4.63
5915 39992 1.066430 AGTATGCACAAGGGTACACCG 60.066 52.381 0.00 0.00 46.96 4.94
5936 40013 9.612066 ATTTTTGTTTCCATGTGTTGAGTTATT 57.388 25.926 0.00 0.00 0.00 1.40
5940 40017 5.294060 GCATTTTTGTTTCCATGTGTTGAGT 59.706 36.000 0.00 0.00 0.00 3.41
5952 40029 4.211164 GCCTACAGGTTGCATTTTTGTTTC 59.789 41.667 0.00 0.00 37.57 2.78
5955 40032 2.288152 CGCCTACAGGTTGCATTTTTGT 60.288 45.455 0.00 0.00 37.57 2.83
5963 40040 1.805945 CTCGACGCCTACAGGTTGC 60.806 63.158 0.00 0.00 37.57 4.17
5971 40078 0.382158 CAGCATCTTCTCGACGCCTA 59.618 55.000 0.00 0.00 29.26 3.93
5977 40084 2.558359 TCTTGACACAGCATCTTCTCGA 59.442 45.455 0.00 0.00 0.00 4.04
5989 40096 4.009675 GCCTGTTTCCATATCTTGACACA 58.990 43.478 0.00 0.00 0.00 3.72
5990 40097 4.009675 TGCCTGTTTCCATATCTTGACAC 58.990 43.478 0.00 0.00 0.00 3.67
6029 40136 0.878416 TACCGTTCATTGGTGCTTGC 59.122 50.000 0.00 0.00 40.73 4.01
6032 40139 1.877443 GTTGTACCGTTCATTGGTGCT 59.123 47.619 2.10 0.00 41.98 4.40
6047 40154 3.306088 GCTCCTGTGTAGCTCTTGTTGTA 60.306 47.826 0.00 0.00 37.01 2.41
6048 40155 2.548920 GCTCCTGTGTAGCTCTTGTTGT 60.549 50.000 0.00 0.00 37.01 3.32
6054 40161 1.079256 TGGGCTCCTGTGTAGCTCT 59.921 57.895 0.00 0.00 41.27 4.09
6077 40184 3.492337 TGTTCCAGCCTTTATTTCGGTT 58.508 40.909 0.00 0.00 0.00 4.44
6085 40192 9.747898 TTATCTTAAATTCTGTTCCAGCCTTTA 57.252 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.