Multiple sequence alignment - TraesCS5A01G097800

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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 TraesCS5A01G097800 chr5A 100.000 5010 0 0 2190 7199 139082656 139077647 0.000000e+00 9252.0
1 TraesCS5A01G097800 chr5A 100.000 2027 0 0 1 2027 139084845 139082819 0.000000e+00 3744.0
2 TraesCS5A01G097800 chr5A 95.020 763 28 2 1 753 139204255 139203493 0.000000e+00 1190.0
3 TraesCS5A01G097800 chr5D 95.289 1316 39 8 568 1864 124858402 124857091 0.000000e+00 2065.0
4 TraesCS5A01G097800 chr5D 91.858 1437 60 20 5172 6558 124848420 124846991 0.000000e+00 1953.0
5 TraesCS5A01G097800 chr5D 94.288 1103 38 7 3310 4405 124855621 124854537 0.000000e+00 1664.0
6 TraesCS5A01G097800 chr5D 87.549 1028 41 40 2190 3166 124856684 124855693 0.000000e+00 1109.0
7 TraesCS5A01G097800 chr5D 91.351 659 37 13 4457 5103 124853789 124853139 0.000000e+00 883.0
8 TraesCS5A01G097800 chr5D 98.438 64 1 0 5121 5184 124852286 124852223 5.900000e-21 113.0
9 TraesCS5A01G097800 chr5D 97.500 40 1 0 1943 1982 124856868 124856829 1.300000e-07 69.4
10 TraesCS5A01G097800 chr5D 95.122 41 2 0 1941 1981 547973142 547973182 1.680000e-06 65.8
11 TraesCS5A01G097800 chr5B 92.367 1415 51 19 4963 6327 137667066 137665659 0.000000e+00 1962.0
12 TraesCS5A01G097800 chr5B 93.998 1283 31 20 616 1867 137672526 137671259 0.000000e+00 1901.0
13 TraesCS5A01G097800 chr5B 94.807 674 23 5 3734 4405 137668969 137668306 0.000000e+00 1040.0
14 TraesCS5A01G097800 chr5B 86.154 975 45 39 2190 3113 137670448 137669513 0.000000e+00 970.0
15 TraesCS5A01G097800 chr5B 92.063 378 10 3 3369 3738 137669492 137669127 1.380000e-141 514.0
16 TraesCS5A01G097800 chr5B 84.725 491 51 17 4457 4931 137667539 137667057 3.040000e-128 470.0
17 TraesCS5A01G097800 chr5B 93.227 251 8 3 6312 6558 137665641 137665396 1.910000e-95 361.0
18 TraesCS5A01G097800 chr5B 85.547 256 19 9 231 471 137672809 137672557 1.200000e-62 252.0
19 TraesCS5A01G097800 chr5B 77.876 113 19 6 4597 4705 393567536 393567646 1.680000e-06 65.8
20 TraesCS5A01G097800 chr2A 98.754 642 7 1 6558 7199 720554016 720554656 0.000000e+00 1140.0
21 TraesCS5A01G097800 chr2A 98.598 642 8 1 6558 7199 7387212 7387852 0.000000e+00 1134.0
22 TraesCS5A01G097800 chr2A 79.464 112 18 3 1292 1402 418794956 418795063 2.790000e-09 75.0
23 TraesCS5A01G097800 chr2A 96.970 33 0 1 3261 3292 757112105 757112137 4.000000e-03 54.7
24 TraesCS5A01G097800 chr7A 86.100 259 26 6 6584 6832 347260303 347260045 3.310000e-68 270.0
25 TraesCS5A01G097800 chr7A 82.677 127 19 2 1348 1471 617385923 617385797 7.640000e-20 110.0
26 TraesCS5A01G097800 chr7A 82.407 108 19 0 468 575 633283443 633283550 2.140000e-15 95.3
27 TraesCS5A01G097800 chr1D 84.387 269 20 6 6767 7019 155959749 155960011 2.010000e-60 244.0
28 TraesCS5A01G097800 chr6A 83.764 271 21 9 6767 7019 87232209 87231944 1.210000e-57 235.0
29 TraesCS5A01G097800 chr6A 80.142 141 28 0 1347 1487 107686182 107686042 9.880000e-19 106.0
30 TraesCS5A01G097800 chr6A 77.876 113 17 7 4597 4705 574656070 574656178 6.030000e-06 63.9
31 TraesCS5A01G097800 chr3D 82.963 270 23 6 6767 7019 31574466 31574729 9.400000e-54 222.0
32 TraesCS5A01G097800 chr3D 88.083 193 16 5 6830 7021 31575924 31576110 9.400000e-54 222.0
33 TraesCS5A01G097800 chr3D 86.387 191 19 6 6830 7019 31575242 31575426 1.220000e-47 202.0
34 TraesCS5A01G097800 chr6B 82.156 269 25 7 6767 7019 123825877 123825616 7.320000e-50 209.0
35 TraesCS5A01G097800 chr6B 85.714 98 14 0 467 564 36138895 36138992 3.550000e-18 104.0
36 TraesCS5A01G097800 chr6B 76.596 188 44 0 1300 1487 171709518 171709331 3.550000e-18 104.0
37 TraesCS5A01G097800 chr7B 86.224 196 20 5 6830 7024 323223463 323223274 9.470000e-49 206.0
38 TraesCS5A01G097800 chr7B 83.333 126 17 3 6581 6706 726373188 726373309 5.900000e-21 113.0
39 TraesCS5A01G097800 chr7B 83.333 126 17 3 6581 6706 726381893 726382014 5.900000e-21 113.0
40 TraesCS5A01G097800 chr7B 83.898 118 16 2 1348 1462 578438875 578438992 7.640000e-20 110.0
41 TraesCS5A01G097800 chr7B 82.927 123 16 3 1350 1468 504456392 504456513 9.880000e-19 106.0
42 TraesCS5A01G097800 chr2D 84.921 126 15 3 6581 6706 68592215 68592336 2.730000e-24 124.0
43 TraesCS5A01G097800 chr2D 83.333 126 17 3 6581 6706 68660188 68660309 5.900000e-21 113.0
44 TraesCS5A01G097800 chr2D 90.476 84 8 0 482 565 33850346 33850263 2.120000e-20 111.0
45 TraesCS5A01G097800 chr2D 81.132 106 15 3 1298 1402 316328476 316328375 5.990000e-11 80.5
46 TraesCS5A01G097800 chr2D 92.683 41 3 0 1941 1981 607674023 607674063 7.800000e-05 60.2
47 TraesCS5A01G097800 chr7D 84.127 126 16 3 6581 6706 635016347 635016468 1.270000e-22 119.0
48 TraesCS5A01G097800 chr7D 82.927 123 16 3 1350 1468 478576075 478576196 9.880000e-19 106.0
49 TraesCS5A01G097800 chr7D 100.000 32 0 0 4668 4699 501086856 501086887 7.800000e-05 60.2
50 TraesCS5A01G097800 chr7D 90.698 43 4 0 1186 1228 152087158 152087200 2.810000e-04 58.4
51 TraesCS5A01G097800 chr4D 87.000 100 13 0 465 564 234381194 234381293 5.900000e-21 113.0
52 TraesCS5A01G097800 chr4D 82.540 126 18 3 6581 6706 120835436 120835557 2.750000e-19 108.0
53 TraesCS5A01G097800 chr4B 86.598 97 13 0 468 564 154020997 154020901 2.750000e-19 108.0
54 TraesCS5A01G097800 chr2B 89.286 84 9 0 482 565 410266443 410266526 9.880000e-19 106.0
55 TraesCS5A01G097800 chr2B 81.132 106 15 3 1298 1402 384400544 384400443 5.990000e-11 80.5
56 TraesCS5A01G097800 chr6D 88.506 87 9 1 482 568 471932256 471932341 3.550000e-18 104.0
57 TraesCS5A01G097800 chr6D 79.433 141 29 0 1347 1487 89308683 89308543 4.600000e-17 100.0
58 TraesCS5A01G097800 chrUn 84.694 98 15 0 468 565 81701235 81701332 1.650000e-16 99.0
59 TraesCS5A01G097800 chr3B 92.500 40 1 2 1941 1980 507500766 507500729 1.000000e-03 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G097800 chr5A 139077647 139084845 7198 True 6498.000000 9252 100.000000 1 7199 2 chr5A.!!$R2 7198
1 TraesCS5A01G097800 chr5A 139203493 139204255 762 True 1190.000000 1190 95.020000 1 753 1 chr5A.!!$R1 752
2 TraesCS5A01G097800 chr5D 124846991 124858402 11411 True 1122.342857 2065 93.753286 568 6558 7 chr5D.!!$R1 5990
3 TraesCS5A01G097800 chr5B 137665396 137672809 7413 True 933.750000 1962 90.361000 231 6558 8 chr5B.!!$R1 6327
4 TraesCS5A01G097800 chr2A 720554016 720554656 640 False 1140.000000 1140 98.754000 6558 7199 1 chr2A.!!$F3 641
5 TraesCS5A01G097800 chr2A 7387212 7387852 640 False 1134.000000 1134 98.598000 6558 7199 1 chr2A.!!$F1 641
6 TraesCS5A01G097800 chr3D 31574466 31576110 1644 False 215.333333 222 85.811000 6767 7021 3 chr3D.!!$F1 254

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
137 139 0.035056 ATGGGCAAGAAGAAGGACGG 60.035 55.000 0.00 0.00 0.00 4.79 F
898 925 0.179097 TAAGCGCACACAGACACACA 60.179 50.000 11.47 0.00 0.00 3.72 F
927 954 1.003580 CCACACACCCATAAGCTGAGT 59.996 52.381 0.00 0.00 0.00 3.41 F
2665 3298 0.034476 ATGAGCGATGATGCACCGAT 59.966 50.000 0.00 0.00 37.31 4.18 F
2668 3301 0.034476 AGCGATGATGCACCGATCAT 59.966 50.000 0.12 0.12 44.24 2.45 F
2673 3306 0.461693 TGATGCACCGATCATTCGCA 60.462 50.000 0.00 0.00 44.12 5.10 F
3196 3866 0.512952 GCGATAAATAGGGCGTGCAG 59.487 55.000 0.00 0.00 0.00 4.41 F
4443 5952 0.321671 TCCGAAGCAGTCTCCCAAAG 59.678 55.000 0.00 0.00 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 1346 0.239082 ACGTACACGAATCAGCACGA 59.761 50.000 9.04 0.00 43.02 4.35 R
2561 3187 0.251209 ACTGTGGCCACTCTCTCGTA 60.251 55.000 34.75 12.61 0.00 3.43 R
2683 3316 1.073964 CGATCCATCGGTGCATCATC 58.926 55.000 0.00 0.00 45.93 2.92 R
3606 4286 0.250727 TTACAACTCAGTGCTGGCCC 60.251 55.000 0.00 0.00 0.00 5.80 R
4425 5934 0.321671 TCTTTGGGAGACTGCTTCGG 59.678 55.000 0.00 0.00 0.00 4.30 R
4426 5935 2.393271 ATCTTTGGGAGACTGCTTCG 57.607 50.000 0.00 0.00 37.17 3.79 R
5104 6708 1.002251 TCAAATCAAAACGTCGGCCAC 60.002 47.619 2.24 0.00 0.00 5.01 R
6353 12719 0.474184 ACCCAAGAATCCATAGCCGG 59.526 55.000 0.00 0.00 0.00 6.13 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
94 95 7.616528 TCTATCAATGGAATGATACACTCCA 57.383 36.000 4.49 4.49 43.26 3.86
95 96 7.445121 TCTATCAATGGAATGATACACTCCAC 58.555 38.462 4.11 0.00 41.95 4.02
96 97 4.441792 TCAATGGAATGATACACTCCACG 58.558 43.478 4.11 0.17 41.95 4.94
97 98 2.309528 TGGAATGATACACTCCACGC 57.690 50.000 0.00 0.00 34.26 5.34
98 99 1.552792 TGGAATGATACACTCCACGCA 59.447 47.619 0.00 0.00 34.26 5.24
104 106 3.638484 TGATACACTCCACGCATATTCG 58.362 45.455 0.00 0.00 0.00 3.34
137 139 0.035056 ATGGGCAAGAAGAAGGACGG 60.035 55.000 0.00 0.00 0.00 4.79
139 141 2.391389 GGCAAGAAGAAGGACGGCG 61.391 63.158 4.80 4.80 0.00 6.46
190 192 4.007940 CGTTGTGACCAACCGCCG 62.008 66.667 0.38 0.00 46.71 6.46
211 213 2.103143 CTGCCGCACTAGGAGACG 59.897 66.667 0.00 0.00 0.00 4.18
451 468 3.055819 AGGCTAGCCATATTACGTCCATG 60.056 47.826 34.70 0.00 38.92 3.66
453 470 2.859165 AGCCATATTACGTCCATGGG 57.141 50.000 13.02 0.00 39.74 4.00
480 497 9.797556 GATTGTTTTGTAGTACTTCCTTTGTTT 57.202 29.630 0.00 0.00 0.00 2.83
791 818 1.437986 GACAATCGGACGGCTAGCT 59.562 57.895 15.72 0.00 0.00 3.32
890 917 2.432444 AGCCTTTAATAAGCGCACACA 58.568 42.857 11.47 0.00 32.97 3.72
897 924 1.148310 ATAAGCGCACACAGACACAC 58.852 50.000 11.47 0.00 0.00 3.82
898 925 0.179097 TAAGCGCACACAGACACACA 60.179 50.000 11.47 0.00 0.00 3.72
900 927 2.460275 GCGCACACAGACACACACA 61.460 57.895 0.30 0.00 0.00 3.72
901 928 1.637934 CGCACACAGACACACACAG 59.362 57.895 0.00 0.00 0.00 3.66
902 929 1.353103 GCACACAGACACACACAGC 59.647 57.895 0.00 0.00 0.00 4.40
903 930 2.016961 CACACAGACACACACAGCC 58.983 57.895 0.00 0.00 0.00 4.85
927 954 1.003580 CCACACACCCATAAGCTGAGT 59.996 52.381 0.00 0.00 0.00 3.41
988 1042 4.603216 CGTCATCCTACGTACGCC 57.397 61.111 16.72 0.00 38.07 5.68
989 1043 1.368493 CGTCATCCTACGTACGCCG 60.368 63.158 16.72 6.28 44.03 6.46
991 1045 2.354305 CATCCTACGTACGCCGGC 60.354 66.667 19.07 19.07 42.24 6.13
992 1046 2.517875 ATCCTACGTACGCCGGCT 60.518 61.111 26.68 14.27 42.24 5.52
1279 1346 2.736995 CGCATGGTTGACGGACGT 60.737 61.111 0.00 0.00 0.00 4.34
1330 1397 3.197614 TCGGTGCTGATCGACTCC 58.802 61.111 0.00 0.00 26.62 3.85
1332 1399 1.037579 TCGGTGCTGATCGACTCCAT 61.038 55.000 0.00 0.00 26.62 3.41
1548 1624 8.533965 CAATTAAAGTACAATGTATGCATGCAC 58.466 33.333 25.37 12.32 35.15 4.57
1608 1684 2.351548 CGTGCGCTGCATGCATAC 60.352 61.111 22.97 15.54 45.34 2.39
1797 1873 4.198530 TCGGGTACGTACATATCAAGTCA 58.801 43.478 26.02 0.00 41.85 3.41
1843 1920 5.506832 CGCGGAACATCATTAAGTTTAACAC 59.493 40.000 0.00 0.00 0.00 3.32
1847 1924 6.741358 GGAACATCATTAAGTTTAACACGAGC 59.259 38.462 0.00 0.00 0.00 5.03
1898 2205 3.009916 GGTCCCATCGATACTACTCCCTA 59.990 52.174 0.00 0.00 0.00 3.53
1899 2206 4.325187 GGTCCCATCGATACTACTCCCTAT 60.325 50.000 0.00 0.00 0.00 2.57
1905 2212 3.008330 CGATACTACTCCCTATGTCCCG 58.992 54.545 0.00 0.00 0.00 5.14
1982 2389 6.076981 TGTGAAGAAATTCTTTTGAGGAGC 57.923 37.500 9.84 0.00 36.73 4.70
1983 2390 5.010012 TGTGAAGAAATTCTTTTGAGGAGCC 59.990 40.000 9.84 0.00 36.73 4.70
1984 2391 5.242615 GTGAAGAAATTCTTTTGAGGAGCCT 59.757 40.000 9.84 0.00 36.73 4.58
1989 2396 2.867109 TCTTTTGAGGAGCCTTGAGG 57.133 50.000 0.00 0.00 38.53 3.86
1990 2397 2.057922 TCTTTTGAGGAGCCTTGAGGT 58.942 47.619 0.00 0.00 37.57 3.85
2012 2434 9.325198 GAGGTTATATTTTGCCCCTTAAAATTG 57.675 33.333 0.00 0.00 38.36 2.32
2013 2435 8.271458 AGGTTATATTTTGCCCCTTAAAATTGG 58.729 33.333 0.00 0.00 38.36 3.16
2016 2438 4.779993 TTTTGCCCCTTAAAATTGGTGT 57.220 36.364 0.00 0.00 0.00 4.16
2017 2439 4.779993 TTTGCCCCTTAAAATTGGTGTT 57.220 36.364 0.00 0.00 0.00 3.32
2018 2440 4.779993 TTGCCCCTTAAAATTGGTGTTT 57.220 36.364 0.00 0.00 0.00 2.83
2019 2441 4.344359 TGCCCCTTAAAATTGGTGTTTC 57.656 40.909 0.00 0.00 0.00 2.78
2021 2443 4.349342 TGCCCCTTAAAATTGGTGTTTCAT 59.651 37.500 0.00 0.00 0.00 2.57
2022 2444 4.935205 GCCCCTTAAAATTGGTGTTTCATC 59.065 41.667 0.00 0.00 0.00 2.92
2023 2445 5.279960 GCCCCTTAAAATTGGTGTTTCATCT 60.280 40.000 0.00 0.00 0.00 2.90
2025 2447 7.364673 GCCCCTTAAAATTGGTGTTTCATCTAT 60.365 37.037 0.00 0.00 0.00 1.98
2026 2448 8.539544 CCCCTTAAAATTGGTGTTTCATCTATT 58.460 33.333 0.00 0.00 0.00 1.73
2345 2946 9.503399 AGACGAAAGAAACATAGTATTTTCCTT 57.497 29.630 0.00 7.32 32.98 3.36
2480 3086 2.297315 TGTCACATCTGAGGACACTGTC 59.703 50.000 0.00 0.00 36.69 3.51
2658 3291 1.197036 GGACATGCATGAGCGATGATG 59.803 52.381 32.75 4.22 46.23 3.07
2659 3292 0.591659 ACATGCATGAGCGATGATGC 59.408 50.000 32.75 18.39 46.23 3.91
2661 3294 4.916412 GCATGAGCGATGATGCAC 57.084 55.556 20.19 0.00 43.75 4.57
2662 3295 1.281960 GCATGAGCGATGATGCACC 59.718 57.895 20.19 0.00 43.75 5.01
2663 3296 1.568025 CATGAGCGATGATGCACCG 59.432 57.895 0.00 0.00 37.31 4.94
2664 3297 0.877213 CATGAGCGATGATGCACCGA 60.877 55.000 0.00 0.00 37.31 4.69
2665 3298 0.034476 ATGAGCGATGATGCACCGAT 59.966 50.000 0.00 0.00 37.31 4.18
2666 3299 0.598419 TGAGCGATGATGCACCGATC 60.598 55.000 9.81 9.81 38.92 3.69
2667 3300 0.598419 GAGCGATGATGCACCGATCA 60.598 55.000 11.27 2.11 38.42 2.92
2668 3301 0.034476 AGCGATGATGCACCGATCAT 59.966 50.000 0.12 0.12 44.24 2.45
2669 3302 0.870393 GCGATGATGCACCGATCATT 59.130 50.000 2.21 0.00 42.10 2.57
2670 3303 1.136141 GCGATGATGCACCGATCATTC 60.136 52.381 2.21 0.00 42.10 2.67
2671 3304 1.125566 CGATGATGCACCGATCATTCG 59.874 52.381 2.21 4.41 42.10 3.34
2672 3305 0.870393 ATGATGCACCGATCATTCGC 59.130 50.000 0.00 0.00 44.12 4.70
2673 3306 0.461693 TGATGCACCGATCATTCGCA 60.462 50.000 0.00 0.00 44.12 5.10
2674 3307 0.657312 GATGCACCGATCATTCGCAA 59.343 50.000 0.00 0.00 44.12 4.85
2675 3308 1.063912 GATGCACCGATCATTCGCAAA 59.936 47.619 0.00 0.00 44.12 3.68
2676 3309 0.877743 TGCACCGATCATTCGCAAAA 59.122 45.000 0.00 0.00 44.12 2.44
2677 3310 1.268079 TGCACCGATCATTCGCAAAAA 59.732 42.857 0.00 0.00 44.12 1.94
2981 3638 2.232208 GGTAGCCAAAAGAAATGCAGCT 59.768 45.455 0.00 0.00 0.00 4.24
3080 3750 2.024176 GCCATCGCCTGACTTTAGAA 57.976 50.000 0.00 0.00 0.00 2.10
3109 3779 5.695851 AAAGTAGGACAAAGCAAGTCATG 57.304 39.130 5.72 0.00 37.74 3.07
3121 3791 1.518056 AAGTCATGCAACCACGGCAG 61.518 55.000 0.00 0.00 45.68 4.85
3123 3793 0.953471 GTCATGCAACCACGGCAGTA 60.953 55.000 0.00 0.00 45.68 2.74
3147 3817 1.748493 TGGTGCAGAAGTTCCAACAAC 59.252 47.619 0.00 0.00 0.00 3.32
3159 3829 5.356426 AGTTCCAACAACATAGCCAAAAAC 58.644 37.500 0.00 0.00 0.00 2.43
3160 3830 5.105146 AGTTCCAACAACATAGCCAAAAACA 60.105 36.000 0.00 0.00 0.00 2.83
3161 3831 4.942852 TCCAACAACATAGCCAAAAACAG 58.057 39.130 0.00 0.00 0.00 3.16
3162 3832 4.404073 TCCAACAACATAGCCAAAAACAGT 59.596 37.500 0.00 0.00 0.00 3.55
3163 3833 5.594725 TCCAACAACATAGCCAAAAACAGTA 59.405 36.000 0.00 0.00 0.00 2.74
3164 3834 5.689961 CCAACAACATAGCCAAAAACAGTAC 59.310 40.000 0.00 0.00 0.00 2.73
3165 3835 6.269315 CAACAACATAGCCAAAAACAGTACA 58.731 36.000 0.00 0.00 0.00 2.90
3166 3836 6.458232 ACAACATAGCCAAAAACAGTACAA 57.542 33.333 0.00 0.00 0.00 2.41
3167 3837 6.868622 ACAACATAGCCAAAAACAGTACAAA 58.131 32.000 0.00 0.00 0.00 2.83
3168 3838 6.978080 ACAACATAGCCAAAAACAGTACAAAG 59.022 34.615 0.00 0.00 0.00 2.77
3169 3839 5.528870 ACATAGCCAAAAACAGTACAAAGC 58.471 37.500 0.00 0.00 0.00 3.51
3170 3840 5.301805 ACATAGCCAAAAACAGTACAAAGCT 59.698 36.000 0.00 0.00 0.00 3.74
3171 3841 6.488683 ACATAGCCAAAAACAGTACAAAGCTA 59.511 34.615 0.00 0.00 35.04 3.32
3172 3842 5.845391 AGCCAAAAACAGTACAAAGCTAA 57.155 34.783 0.00 0.00 0.00 3.09
3173 3843 5.588240 AGCCAAAAACAGTACAAAGCTAAC 58.412 37.500 0.00 0.00 0.00 2.34
3174 3844 5.126384 AGCCAAAAACAGTACAAAGCTAACA 59.874 36.000 0.00 0.00 0.00 2.41
3175 3845 5.983118 GCCAAAAACAGTACAAAGCTAACAT 59.017 36.000 0.00 0.00 0.00 2.71
3176 3846 6.074356 GCCAAAAACAGTACAAAGCTAACATG 60.074 38.462 0.00 0.00 0.00 3.21
3177 3847 6.420604 CCAAAAACAGTACAAAGCTAACATGG 59.579 38.462 0.00 0.00 0.00 3.66
3178 3848 4.766404 AACAGTACAAAGCTAACATGGC 57.234 40.909 0.00 0.00 0.00 4.40
3179 3849 2.742053 ACAGTACAAAGCTAACATGGCG 59.258 45.455 0.00 0.00 34.52 5.69
3180 3850 3.000041 CAGTACAAAGCTAACATGGCGA 59.000 45.455 0.00 0.00 34.52 5.54
3181 3851 3.623060 CAGTACAAAGCTAACATGGCGAT 59.377 43.478 0.00 0.00 34.52 4.58
3182 3852 4.808895 CAGTACAAAGCTAACATGGCGATA 59.191 41.667 0.00 0.00 34.52 2.92
3183 3853 5.293324 CAGTACAAAGCTAACATGGCGATAA 59.707 40.000 0.00 0.00 34.52 1.75
3184 3854 5.878116 AGTACAAAGCTAACATGGCGATAAA 59.122 36.000 0.00 0.00 34.52 1.40
3185 3855 5.835113 ACAAAGCTAACATGGCGATAAAT 57.165 34.783 0.00 0.00 34.52 1.40
3186 3856 6.935741 ACAAAGCTAACATGGCGATAAATA 57.064 33.333 0.00 0.00 34.52 1.40
3187 3857 6.959361 ACAAAGCTAACATGGCGATAAATAG 58.041 36.000 0.00 0.00 34.52 1.73
3188 3858 6.017109 ACAAAGCTAACATGGCGATAAATAGG 60.017 38.462 0.00 0.00 34.52 2.57
3189 3859 4.579869 AGCTAACATGGCGATAAATAGGG 58.420 43.478 0.00 0.00 34.52 3.53
3190 3860 3.127030 GCTAACATGGCGATAAATAGGGC 59.873 47.826 0.00 0.00 0.00 5.19
3191 3861 1.808411 ACATGGCGATAAATAGGGCG 58.192 50.000 0.00 0.00 0.00 6.13
3192 3862 1.071699 ACATGGCGATAAATAGGGCGT 59.928 47.619 0.00 0.00 0.00 5.68
3193 3863 1.464608 CATGGCGATAAATAGGGCGTG 59.535 52.381 0.00 0.00 36.99 5.34
3194 3864 0.882927 TGGCGATAAATAGGGCGTGC 60.883 55.000 0.00 0.00 0.00 5.34
3195 3865 0.882927 GGCGATAAATAGGGCGTGCA 60.883 55.000 0.00 0.00 0.00 4.57
3196 3866 0.512952 GCGATAAATAGGGCGTGCAG 59.487 55.000 0.00 0.00 0.00 4.41
3197 3867 1.148310 CGATAAATAGGGCGTGCAGG 58.852 55.000 1.01 1.01 0.00 4.85
3198 3868 1.540363 CGATAAATAGGGCGTGCAGGT 60.540 52.381 8.40 0.00 0.00 4.00
3199 3869 2.143925 GATAAATAGGGCGTGCAGGTC 58.856 52.381 8.40 5.17 0.00 3.85
3200 3870 0.906066 TAAATAGGGCGTGCAGGTCA 59.094 50.000 13.68 0.00 0.00 4.02
3201 3871 0.676782 AAATAGGGCGTGCAGGTCAC 60.677 55.000 13.68 4.22 42.23 3.67
3202 3872 1.836999 AATAGGGCGTGCAGGTCACA 61.837 55.000 13.68 0.00 45.92 3.58
3228 3898 5.578157 ACCAACAAACTAACTAGGGACAT 57.422 39.130 0.00 0.00 0.00 3.06
3280 3950 1.202557 AGTTGCCGAACCTCGTTAACA 60.203 47.619 6.39 0.00 38.40 2.41
3281 3951 1.598601 GTTGCCGAACCTCGTTAACAA 59.401 47.619 6.39 0.00 38.40 2.83
3282 3952 1.950828 TGCCGAACCTCGTTAACAAA 58.049 45.000 6.39 0.00 38.40 2.83
3283 3953 2.496111 TGCCGAACCTCGTTAACAAAT 58.504 42.857 6.39 0.00 38.40 2.32
3284 3954 2.481185 TGCCGAACCTCGTTAACAAATC 59.519 45.455 6.39 0.00 38.40 2.17
3285 3955 2.740447 GCCGAACCTCGTTAACAAATCT 59.260 45.455 6.39 0.00 38.40 2.40
3286 3956 3.187842 GCCGAACCTCGTTAACAAATCTT 59.812 43.478 6.39 0.00 38.40 2.40
3287 3957 4.389687 GCCGAACCTCGTTAACAAATCTTA 59.610 41.667 6.39 0.00 38.40 2.10
3288 3958 5.445540 GCCGAACCTCGTTAACAAATCTTAG 60.446 44.000 6.39 0.00 38.40 2.18
3289 3959 5.636543 CCGAACCTCGTTAACAAATCTTAGT 59.363 40.000 6.39 0.00 38.40 2.24
3290 3960 6.400727 CCGAACCTCGTTAACAAATCTTAGTG 60.401 42.308 6.39 0.00 38.40 2.74
3291 3961 6.145048 CGAACCTCGTTAACAAATCTTAGTGT 59.855 38.462 6.39 0.00 34.72 3.55
3292 3962 7.306983 CGAACCTCGTTAACAAATCTTAGTGTT 60.307 37.037 6.39 0.00 37.15 3.32
3293 3963 7.186021 ACCTCGTTAACAAATCTTAGTGTTG 57.814 36.000 6.39 0.00 38.40 3.33
3294 3964 6.987992 ACCTCGTTAACAAATCTTAGTGTTGA 59.012 34.615 6.39 0.00 38.40 3.18
3295 3965 7.660208 ACCTCGTTAACAAATCTTAGTGTTGAT 59.340 33.333 6.39 0.00 38.40 2.57
3296 3966 8.504005 CCTCGTTAACAAATCTTAGTGTTGATT 58.496 33.333 6.39 0.00 38.40 2.57
3297 3967 9.530129 CTCGTTAACAAATCTTAGTGTTGATTC 57.470 33.333 6.39 0.00 38.40 2.52
3298 3968 9.268268 TCGTTAACAAATCTTAGTGTTGATTCT 57.732 29.630 6.39 0.00 38.40 2.40
3299 3969 9.530129 CGTTAACAAATCTTAGTGTTGATTCTC 57.470 33.333 6.39 0.00 38.40 2.87
3330 4000 7.760131 AAAAACAAATCTCAGTGTTGTCATG 57.240 32.000 0.00 0.00 37.99 3.07
3331 4001 4.494350 ACAAATCTCAGTGTTGTCATGC 57.506 40.909 0.00 0.00 29.57 4.06
3337 4007 3.055602 TCTCAGTGTTGTCATGCTGCTAT 60.056 43.478 0.00 0.00 0.00 2.97
3350 4020 4.100707 TGCTGCTATGATTGCTTGTTTC 57.899 40.909 0.00 0.00 0.00 2.78
3353 4023 5.065602 TGCTGCTATGATTGCTTGTTTCTAG 59.934 40.000 0.00 0.00 0.00 2.43
3361 4031 2.972625 TGCTTGTTTCTAGGTGGATCG 58.027 47.619 0.00 0.00 0.00 3.69
3365 4035 4.680708 GCTTGTTTCTAGGTGGATCGATCA 60.681 45.833 25.93 10.23 0.00 2.92
3412 4082 8.156165 TCAATGCACTTCCAAAAATCCTAAAAT 58.844 29.630 0.00 0.00 0.00 1.82
3540 4218 2.787723 GCAATAACGCTCATGGTTGTCG 60.788 50.000 0.00 0.00 0.00 4.35
3606 4286 4.937201 AGTTTTGCCCTTTCCACTAAAG 57.063 40.909 0.00 0.00 43.66 1.85
3815 4657 2.625737 ACAGCTACATGTGATGCACTC 58.374 47.619 9.11 0.00 35.11 3.51
3824 4666 1.260206 GTGATGCACTCGACAGTACG 58.740 55.000 0.00 0.00 0.00 3.67
4026 4868 4.926238 CCAACAAGAGTACACTGCTTCTAG 59.074 45.833 0.00 0.00 0.00 2.43
4057 4899 2.685850 ACGTAGTAGTCCCAATTGCC 57.314 50.000 0.00 0.00 41.94 4.52
4260 5102 1.557832 CTGGGAAAGATCAACCGGGTA 59.442 52.381 6.32 0.00 0.00 3.69
4298 5141 3.064207 TGGAGTTGTTTCACGTAGCATC 58.936 45.455 0.00 0.00 0.00 3.91
4299 5142 3.064207 GGAGTTGTTTCACGTAGCATCA 58.936 45.455 0.00 0.00 0.00 3.07
4300 5143 3.496884 GGAGTTGTTTCACGTAGCATCAA 59.503 43.478 0.00 0.00 0.00 2.57
4301 5144 4.154195 GGAGTTGTTTCACGTAGCATCAAT 59.846 41.667 0.00 0.00 0.00 2.57
4308 5151 2.816672 TCACGTAGCATCAATTTGCCAA 59.183 40.909 0.00 0.00 43.83 4.52
4385 5232 4.385754 GCCAAAATATTCTCTCACCTCCCT 60.386 45.833 0.00 0.00 0.00 4.20
4405 5252 7.497249 CCTCCCTTGAACAAGACTTATATTCAG 59.503 40.741 14.99 4.83 40.79 3.02
4407 5254 8.041323 TCCCTTGAACAAGACTTATATTCAGTC 58.959 37.037 14.99 6.63 40.79 3.51
4408 5255 7.010552 CCCTTGAACAAGACTTATATTCAGTCG 59.989 40.741 14.99 0.93 44.73 4.18
4411 5920 8.827177 TGAACAAGACTTATATTCAGTCGTTT 57.173 30.769 8.41 4.65 44.73 3.60
4428 5937 7.118535 TCAGTCGTTTAAATGAATGAAATCCGA 59.881 33.333 28.88 11.82 43.49 4.55
4429 5938 7.748683 CAGTCGTTTAAATGAATGAAATCCGAA 59.251 33.333 26.12 0.00 41.20 4.30
4430 5939 7.962918 AGTCGTTTAAATGAATGAAATCCGAAG 59.037 33.333 11.66 0.00 0.00 3.79
4431 5940 6.745450 TCGTTTAAATGAATGAAATCCGAAGC 59.255 34.615 7.67 0.00 0.00 3.86
4432 5941 6.526325 CGTTTAAATGAATGAAATCCGAAGCA 59.474 34.615 0.79 0.00 0.00 3.91
4433 5942 7.253420 CGTTTAAATGAATGAAATCCGAAGCAG 60.253 37.037 0.79 0.00 0.00 4.24
4434 5943 5.649782 AAATGAATGAAATCCGAAGCAGT 57.350 34.783 0.00 0.00 0.00 4.40
4435 5944 4.889832 ATGAATGAAATCCGAAGCAGTC 57.110 40.909 0.00 0.00 0.00 3.51
4436 5945 3.942829 TGAATGAAATCCGAAGCAGTCT 58.057 40.909 0.00 0.00 0.00 3.24
4437 5946 3.935203 TGAATGAAATCCGAAGCAGTCTC 59.065 43.478 0.00 0.00 0.00 3.36
4438 5947 2.386661 TGAAATCCGAAGCAGTCTCC 57.613 50.000 0.00 0.00 0.00 3.71
4439 5948 1.066143 TGAAATCCGAAGCAGTCTCCC 60.066 52.381 0.00 0.00 0.00 4.30
4442 5951 0.984230 ATCCGAAGCAGTCTCCCAAA 59.016 50.000 0.00 0.00 0.00 3.28
4443 5952 0.321671 TCCGAAGCAGTCTCCCAAAG 59.678 55.000 0.00 0.00 0.00 2.77
4445 5954 1.065854 CCGAAGCAGTCTCCCAAAGAT 60.066 52.381 0.00 0.00 36.11 2.40
4446 5955 2.168521 CCGAAGCAGTCTCCCAAAGATA 59.831 50.000 0.00 0.00 36.11 1.98
4447 5956 3.369471 CCGAAGCAGTCTCCCAAAGATAA 60.369 47.826 0.00 0.00 36.11 1.75
4448 5957 3.868077 CGAAGCAGTCTCCCAAAGATAAG 59.132 47.826 0.00 0.00 36.11 1.73
4449 5958 4.621747 CGAAGCAGTCTCCCAAAGATAAGT 60.622 45.833 0.00 0.00 36.11 2.24
4450 5959 4.917906 AGCAGTCTCCCAAAGATAAGTT 57.082 40.909 0.00 0.00 36.11 2.66
4451 5960 4.583871 AGCAGTCTCCCAAAGATAAGTTG 58.416 43.478 0.00 0.00 36.11 3.16
4452 5961 3.127721 GCAGTCTCCCAAAGATAAGTTGC 59.872 47.826 0.00 0.00 36.11 4.17
4453 5962 4.326826 CAGTCTCCCAAAGATAAGTTGCA 58.673 43.478 0.00 0.00 36.11 4.08
4454 5963 4.154918 CAGTCTCCCAAAGATAAGTTGCAC 59.845 45.833 0.00 0.00 36.11 4.57
4455 5964 3.440522 GTCTCCCAAAGATAAGTTGCACC 59.559 47.826 0.00 0.00 36.11 5.01
4459 6029 4.898861 TCCCAAAGATAAGTTGCACCTTTT 59.101 37.500 0.40 0.00 0.00 2.27
4474 6044 7.903995 TGCACCTTTTAAATGAATGAAATCC 57.096 32.000 2.77 0.00 0.00 3.01
4506 6076 5.685841 TCAGTCGTTTCAAAAATCGATTCC 58.314 37.500 11.83 0.00 38.47 3.01
4644 6243 5.418310 TTTCACTCGGTTCAGAAAACATC 57.582 39.130 0.00 0.00 0.00 3.06
4655 6254 7.080724 GGTTCAGAAAACATCTTTCACTCATC 58.919 38.462 0.52 0.00 35.73 2.92
4657 6256 7.430992 TCAGAAAACATCTTTCACTCATCTG 57.569 36.000 0.00 0.00 35.73 2.90
4666 6265 9.512588 ACATCTTTCACTCATCTGAAAAACTAT 57.487 29.630 0.00 0.00 39.19 2.12
4751 6350 9.472361 CACTCATTTGAGAAAAACAGATTTCAT 57.528 29.630 14.29 0.00 44.74 2.57
4821 6420 6.072838 ACACTGAAATAAGCAGATTCACACAG 60.073 38.462 0.00 0.00 36.86 3.66
5005 6609 9.868160 ATAATAACCAAGGAGGAATAAAAGAGG 57.132 33.333 0.00 0.00 41.22 3.69
5103 6707 2.042464 AGAGATGAGGTGTGTGTGTGT 58.958 47.619 0.00 0.00 0.00 3.72
5104 6708 2.138320 GAGATGAGGTGTGTGTGTGTG 58.862 52.381 0.00 0.00 0.00 3.82
5105 6709 1.486310 AGATGAGGTGTGTGTGTGTGT 59.514 47.619 0.00 0.00 0.00 3.72
5106 6710 1.599071 GATGAGGTGTGTGTGTGTGTG 59.401 52.381 0.00 0.00 0.00 3.82
5107 6711 0.392327 TGAGGTGTGTGTGTGTGTGG 60.392 55.000 0.00 0.00 0.00 4.17
5109 6713 2.770589 GGTGTGTGTGTGTGTGGCC 61.771 63.158 0.00 0.00 0.00 5.36
5110 6714 2.821810 TGTGTGTGTGTGTGGCCG 60.822 61.111 0.00 0.00 0.00 6.13
5112 6716 2.512745 TGTGTGTGTGTGGCCGAC 60.513 61.111 0.00 0.00 0.00 4.79
5113 6717 3.636043 GTGTGTGTGTGGCCGACG 61.636 66.667 0.00 0.00 0.00 5.12
5114 6718 4.150203 TGTGTGTGTGGCCGACGT 62.150 61.111 0.00 0.00 0.00 4.34
5115 6719 2.893404 GTGTGTGTGGCCGACGTT 60.893 61.111 0.00 0.00 0.00 3.99
5116 6720 2.125065 TGTGTGTGGCCGACGTTT 60.125 55.556 0.00 0.00 0.00 3.60
5117 6721 1.745864 TGTGTGTGGCCGACGTTTT 60.746 52.632 0.00 0.00 0.00 2.43
5207 11467 8.685427 CATGAATATCAAAGTGAATGGTTGGTA 58.315 33.333 0.00 0.00 0.00 3.25
5222 11483 8.429237 AATGGTTGGTAGATTTTTCACCATTA 57.571 30.769 11.13 0.00 41.77 1.90
5253 11515 3.294102 CCGTTAAAAACCTCTTTGCGTC 58.706 45.455 0.00 0.00 0.00 5.19
5298 11560 2.670905 TCGATGAACCAATTGTACTGCG 59.329 45.455 4.43 1.54 0.00 5.18
5304 11566 1.953686 ACCAATTGTACTGCGCACTTT 59.046 42.857 5.66 0.00 0.00 2.66
5339 11608 9.531412 CACGAATAAGACTATATAGAACACTCG 57.469 37.037 16.79 16.33 0.00 4.18
5345 11614 2.135664 ATATAGAACACTCGCCGCAC 57.864 50.000 0.00 0.00 0.00 5.34
5423 11694 6.037610 ACTCAAAAGTGTTCTTCAGCAGTAAG 59.962 38.462 0.00 0.00 33.32 2.34
5506 11792 6.039616 GTGTTTCACTTGCATCCAAAGTTTA 58.960 36.000 0.00 0.00 0.00 2.01
5539 11825 4.999311 TGACATTCATGAAAGTCCAGACAG 59.001 41.667 30.61 8.53 38.00 3.51
5850 12164 1.053835 TCTTCAGCTCCACCACCACA 61.054 55.000 0.00 0.00 0.00 4.17
5958 12272 4.910585 GCCGTGCCTATGGACCCG 62.911 72.222 0.00 0.00 34.72 5.28
6301 12634 1.073763 CCTTGGTGTTGACATGAGGGA 59.926 52.381 0.00 0.00 0.00 4.20
6353 12719 1.077089 GAACACGAAGACTAGGCCGC 61.077 60.000 0.00 0.00 0.00 6.53
6354 12720 2.202756 CACGAAGACTAGGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
6355 12721 3.823330 ACGAAGACTAGGCCGCCG 61.823 66.667 3.05 0.00 0.00 6.46
6366 12732 3.050275 GCCGCCGGCTATGGATTC 61.050 66.667 26.68 1.91 46.69 2.52
6413 12779 4.418013 TGTGGTTTCGAGTTGCATAATG 57.582 40.909 0.00 0.00 0.00 1.90
6453 12819 4.708909 AGAGAAATGAGATTTTCCTTGGGC 59.291 41.667 0.00 0.00 36.47 5.36
7080 14841 0.465097 CTGGACATGCATGGTCTCCC 60.465 60.000 29.41 20.28 35.61 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.770010 TGAGAGAAAACAAGGTTTTGTGGT 59.230 37.500 11.41 0.00 46.54 4.16
118 120 0.035056 CCGTCCTTCTTCTTGCCCAT 60.035 55.000 0.00 0.00 0.00 4.00
139 141 2.048503 CACCACGACCGGGTCTTC 60.049 66.667 23.86 0.00 36.19 2.87
190 192 4.082523 TCCTAGTGCGGCAGTGGC 62.083 66.667 20.19 6.62 40.13 5.01
195 197 2.360726 TCGTCTCCTAGTGCGGCA 60.361 61.111 0.00 0.00 0.00 5.69
211 213 0.462759 CAAAGCTCCCCACGGATCTC 60.463 60.000 0.00 0.00 33.32 2.75
227 229 0.393132 TGGTGCGAACCTGACACAAA 60.393 50.000 15.35 0.00 36.00 2.83
248 250 6.183361 TGGACGATATTTAGGCAGTTGGATAA 60.183 38.462 0.00 0.00 0.00 1.75
451 468 5.567430 AGGAAGTACTACAAAACAATCCCC 58.433 41.667 0.00 0.00 0.00 4.81
453 470 7.937649 ACAAAGGAAGTACTACAAAACAATCC 58.062 34.615 0.00 0.00 0.00 3.01
532 549 7.555554 CCTCCATCTCAAAATAAGTGTCTCAAT 59.444 37.037 0.00 0.00 0.00 2.57
550 567 4.355588 AGCTAGTACATACTCCCTCCATCT 59.644 45.833 0.00 0.00 37.73 2.90
612 638 2.683362 CGCCAGTACAGAGACACTATCA 59.317 50.000 0.00 0.00 0.00 2.15
791 818 2.621338 CCAAGTAGAAATCGCAGCTCA 58.379 47.619 0.00 0.00 0.00 4.26
890 917 1.526917 GGCAAGGCTGTGTGTGTCT 60.527 57.895 0.00 0.00 0.00 3.41
897 924 2.723746 GTGTGTGGCAAGGCTGTG 59.276 61.111 0.00 0.00 0.00 3.66
898 925 2.519302 GGTGTGTGGCAAGGCTGT 60.519 61.111 0.00 0.00 0.00 4.40
900 927 1.788518 TATGGGTGTGTGGCAAGGCT 61.789 55.000 0.00 0.00 0.00 4.58
901 928 0.897863 TTATGGGTGTGTGGCAAGGC 60.898 55.000 0.00 0.00 0.00 4.35
902 929 1.176527 CTTATGGGTGTGTGGCAAGG 58.823 55.000 0.00 0.00 0.00 3.61
903 930 0.527565 GCTTATGGGTGTGTGGCAAG 59.472 55.000 0.00 0.00 0.00 4.01
927 954 2.421388 CGGCAGGTGAGAATAATGGGAA 60.421 50.000 0.00 0.00 0.00 3.97
988 1042 2.663188 GGCCATCGAGCTAAGCCG 60.663 66.667 0.00 0.00 33.18 5.52
989 1043 1.596477 CTGGCCATCGAGCTAAGCC 60.596 63.158 5.51 6.93 44.13 4.35
991 1045 0.249657 GGTCTGGCCATCGAGCTAAG 60.250 60.000 5.51 0.00 37.17 2.18
992 1046 0.975556 TGGTCTGGCCATCGAGCTAA 60.976 55.000 20.89 3.55 43.61 3.09
1024 1079 1.891919 GCACGACCAACAGGAGCAA 60.892 57.895 0.00 0.00 0.00 3.91
1260 1327 4.147322 GTCCGTCAACCATGCGCG 62.147 66.667 0.00 0.00 0.00 6.86
1261 1328 4.147322 CGTCCGTCAACCATGCGC 62.147 66.667 0.00 0.00 0.00 6.09
1262 1329 2.726691 GACGTCCGTCAACCATGCG 61.727 63.158 14.48 0.00 44.02 4.73
1263 1330 2.726691 CGACGTCCGTCAACCATGC 61.727 63.158 18.69 0.00 44.77 4.06
1264 1331 3.459027 CGACGTCCGTCAACCATG 58.541 61.111 18.69 0.00 44.77 3.66
1279 1346 0.239082 ACGTACACGAATCAGCACGA 59.761 50.000 9.04 0.00 43.02 4.35
1316 1383 1.156645 GCCATGGAGTCGATCAGCAC 61.157 60.000 18.40 0.00 0.00 4.40
1387 1454 2.879462 GCGGTGTCGATGACGTCC 60.879 66.667 14.12 0.00 40.69 4.79
1548 1624 4.093703 TCCATTTTGTTAATCAGCCGTACG 59.906 41.667 8.69 8.69 0.00 3.67
1608 1684 3.103911 GGTCACGACCGAACTGCG 61.104 66.667 0.00 0.00 42.29 5.18
1797 1873 5.793457 GCGCAAAGATAAACTTAACGATGTT 59.207 36.000 0.30 0.00 38.46 2.71
1880 2163 4.641094 GGACATAGGGAGTAGTATCGATGG 59.359 50.000 8.54 0.00 0.00 3.51
1898 2205 6.542370 CCTAAAATATGTGTCTTTCGGGACAT 59.458 38.462 9.24 0.00 46.04 3.06
1899 2206 5.878116 CCTAAAATATGTGTCTTTCGGGACA 59.122 40.000 3.45 3.45 42.96 4.02
1905 2212 6.456988 CCGTCAGCCTAAAATATGTGTCTTTC 60.457 42.308 0.00 0.00 0.00 2.62
1940 2328 2.162681 CAAACTAGTCAAAGCTGGGGG 58.837 52.381 0.00 0.00 0.00 5.40
1982 2389 4.546674 AGGGGCAAAATATAACCTCAAGG 58.453 43.478 0.00 0.00 42.17 3.61
1983 2390 7.654022 TTAAGGGGCAAAATATAACCTCAAG 57.346 36.000 0.00 0.00 0.00 3.02
1984 2391 8.437274 TTTTAAGGGGCAAAATATAACCTCAA 57.563 30.769 0.00 0.00 0.00 3.02
1989 2396 8.888716 CACCAATTTTAAGGGGCAAAATATAAC 58.111 33.333 0.00 0.00 35.15 1.89
1990 2397 8.606830 ACACCAATTTTAAGGGGCAAAATATAA 58.393 29.630 0.00 0.00 35.15 0.98
2404 3010 7.484007 TCGAATACTATGTTTCTTTCGTCTCAC 59.516 37.037 0.00 0.00 37.71 3.51
2501 3127 2.032681 GCGGTGTGGCCTTCTCTT 59.967 61.111 3.32 0.00 34.25 2.85
2561 3187 0.251209 ACTGTGGCCACTCTCTCGTA 60.251 55.000 34.75 12.61 0.00 3.43
2635 3268 2.037511 TCATCGCTCATGCATGTCCATA 59.962 45.455 25.43 9.79 39.64 2.74
2678 3311 3.355378 TCCATCGGTGCATCATCTTTTT 58.645 40.909 0.00 0.00 0.00 1.94
2679 3312 3.003394 TCCATCGGTGCATCATCTTTT 57.997 42.857 0.00 0.00 0.00 2.27
2680 3313 2.715749 TCCATCGGTGCATCATCTTT 57.284 45.000 0.00 0.00 0.00 2.52
2681 3314 2.775890 GATCCATCGGTGCATCATCTT 58.224 47.619 0.00 0.00 0.00 2.40
2682 3315 1.337541 CGATCCATCGGTGCATCATCT 60.338 52.381 0.00 0.00 45.93 2.90
2683 3316 1.073964 CGATCCATCGGTGCATCATC 58.926 55.000 0.00 0.00 45.93 2.92
2684 3317 3.222053 CGATCCATCGGTGCATCAT 57.778 52.632 0.00 0.00 45.93 2.45
2685 3318 4.756630 CGATCCATCGGTGCATCA 57.243 55.556 0.00 0.00 45.93 3.07
2723 3356 1.157870 CGCCAACAAACAGACGGACT 61.158 55.000 0.00 0.00 0.00 3.85
2910 3543 2.512286 CCGGCTCGTCACATGCAT 60.512 61.111 0.00 0.00 0.00 3.96
2913 3546 2.613739 ATCGACCGGCTCGTCACATG 62.614 60.000 20.62 0.00 43.45 3.21
2914 3547 2.415608 ATCGACCGGCTCGTCACAT 61.416 57.895 20.62 8.65 43.45 3.21
2915 3548 3.060000 ATCGACCGGCTCGTCACA 61.060 61.111 20.62 7.03 43.45 3.58
2916 3549 2.579787 CATCGACCGGCTCGTCAC 60.580 66.667 20.62 0.00 43.45 3.67
2917 3550 4.492160 GCATCGACCGGCTCGTCA 62.492 66.667 20.62 7.90 43.45 4.35
2918 3551 3.774959 ATGCATCGACCGGCTCGTC 62.775 63.158 20.62 13.69 43.45 4.20
2919 3552 3.838271 ATGCATCGACCGGCTCGT 61.838 61.111 20.62 9.69 43.45 4.18
2981 3638 1.344438 CCGTATGGCAGCTATCCTTGA 59.656 52.381 0.00 0.00 0.00 3.02
3080 3750 8.063200 ACTTGCTTTGTCCTACTTTAGTTTTT 57.937 30.769 0.00 0.00 0.00 1.94
3087 3757 5.695851 CATGACTTGCTTTGTCCTACTTT 57.304 39.130 0.00 0.00 33.83 2.66
3109 3779 1.740296 ATCGTACTGCCGTGGTTGC 60.740 57.895 0.00 0.00 0.00 4.17
3121 3791 2.000447 GGAACTTCTGCACCATCGTAC 59.000 52.381 0.00 0.00 0.00 3.67
3123 3793 0.396435 TGGAACTTCTGCACCATCGT 59.604 50.000 0.00 0.00 0.00 3.73
3147 3817 5.772521 AGCTTTGTACTGTTTTTGGCTATG 58.227 37.500 0.00 0.00 0.00 2.23
3159 3829 3.000041 TCGCCATGTTAGCTTTGTACTG 59.000 45.455 0.00 0.00 0.00 2.74
3160 3830 3.328382 TCGCCATGTTAGCTTTGTACT 57.672 42.857 0.00 0.00 0.00 2.73
3161 3831 5.728351 TTATCGCCATGTTAGCTTTGTAC 57.272 39.130 0.00 0.00 0.00 2.90
3162 3832 6.935741 ATTTATCGCCATGTTAGCTTTGTA 57.064 33.333 0.00 0.00 0.00 2.41
3163 3833 5.835113 ATTTATCGCCATGTTAGCTTTGT 57.165 34.783 0.00 0.00 0.00 2.83
3164 3834 6.373779 CCTATTTATCGCCATGTTAGCTTTG 58.626 40.000 0.00 0.00 0.00 2.77
3165 3835 5.473504 CCCTATTTATCGCCATGTTAGCTTT 59.526 40.000 0.00 0.00 0.00 3.51
3166 3836 5.003804 CCCTATTTATCGCCATGTTAGCTT 58.996 41.667 0.00 0.00 0.00 3.74
3167 3837 4.579869 CCCTATTTATCGCCATGTTAGCT 58.420 43.478 0.00 0.00 0.00 3.32
3168 3838 3.127030 GCCCTATTTATCGCCATGTTAGC 59.873 47.826 0.00 0.00 0.00 3.09
3169 3839 3.370978 CGCCCTATTTATCGCCATGTTAG 59.629 47.826 0.00 0.00 0.00 2.34
3170 3840 3.244284 ACGCCCTATTTATCGCCATGTTA 60.244 43.478 0.00 0.00 0.00 2.41
3171 3841 2.151202 CGCCCTATTTATCGCCATGTT 58.849 47.619 0.00 0.00 0.00 2.71
3172 3842 1.071699 ACGCCCTATTTATCGCCATGT 59.928 47.619 0.00 0.00 0.00 3.21
3173 3843 1.464608 CACGCCCTATTTATCGCCATG 59.535 52.381 0.00 0.00 0.00 3.66
3174 3844 1.808411 CACGCCCTATTTATCGCCAT 58.192 50.000 0.00 0.00 0.00 4.40
3175 3845 0.882927 GCACGCCCTATTTATCGCCA 60.883 55.000 0.00 0.00 0.00 5.69
3176 3846 0.882927 TGCACGCCCTATTTATCGCC 60.883 55.000 0.00 0.00 0.00 5.54
3177 3847 0.512952 CTGCACGCCCTATTTATCGC 59.487 55.000 0.00 0.00 0.00 4.58
3178 3848 1.148310 CCTGCACGCCCTATTTATCG 58.852 55.000 0.00 0.00 0.00 2.92
3179 3849 2.143925 GACCTGCACGCCCTATTTATC 58.856 52.381 0.00 0.00 0.00 1.75
3180 3850 1.488812 TGACCTGCACGCCCTATTTAT 59.511 47.619 0.00 0.00 0.00 1.40
3181 3851 0.906066 TGACCTGCACGCCCTATTTA 59.094 50.000 0.00 0.00 0.00 1.40
3182 3852 0.676782 GTGACCTGCACGCCCTATTT 60.677 55.000 0.00 0.00 37.83 1.40
3183 3853 1.078426 GTGACCTGCACGCCCTATT 60.078 57.895 0.00 0.00 37.83 1.73
3184 3854 2.584608 GTGACCTGCACGCCCTAT 59.415 61.111 0.00 0.00 37.83 2.57
3192 3862 1.210722 TGTTGGTACTTGTGACCTGCA 59.789 47.619 0.00 0.00 37.88 4.41
3193 3863 1.961793 TGTTGGTACTTGTGACCTGC 58.038 50.000 0.00 0.00 37.88 4.85
3194 3864 3.945285 AGTTTGTTGGTACTTGTGACCTG 59.055 43.478 0.00 0.00 37.88 4.00
3195 3865 4.230745 AGTTTGTTGGTACTTGTGACCT 57.769 40.909 0.00 0.00 37.88 3.85
3196 3866 5.587443 AGTTAGTTTGTTGGTACTTGTGACC 59.413 40.000 0.00 0.00 37.49 4.02
3197 3867 6.673154 AGTTAGTTTGTTGGTACTTGTGAC 57.327 37.500 0.00 0.00 0.00 3.67
3198 3868 6.987992 CCTAGTTAGTTTGTTGGTACTTGTGA 59.012 38.462 0.00 0.00 0.00 3.58
3199 3869 6.204108 CCCTAGTTAGTTTGTTGGTACTTGTG 59.796 42.308 0.00 0.00 0.00 3.33
3200 3870 6.100134 TCCCTAGTTAGTTTGTTGGTACTTGT 59.900 38.462 0.00 0.00 0.00 3.16
3201 3871 6.426025 GTCCCTAGTTAGTTTGTTGGTACTTG 59.574 42.308 0.00 0.00 0.00 3.16
3202 3872 6.100134 TGTCCCTAGTTAGTTTGTTGGTACTT 59.900 38.462 0.00 0.00 0.00 2.24
3261 3931 1.219646 TGTTAACGAGGTTCGGCAAC 58.780 50.000 0.26 6.89 45.59 4.17
3306 3976 6.256321 GCATGACAACACTGAGATTTGTTTTT 59.744 34.615 0.00 0.00 33.59 1.94
3307 3977 5.750067 GCATGACAACACTGAGATTTGTTTT 59.250 36.000 0.00 0.00 33.59 2.43
3308 3978 5.068198 AGCATGACAACACTGAGATTTGTTT 59.932 36.000 0.00 0.00 33.59 2.83
3309 3979 4.581824 AGCATGACAACACTGAGATTTGTT 59.418 37.500 0.00 0.00 36.35 2.83
3310 3980 4.023450 CAGCATGACAACACTGAGATTTGT 60.023 41.667 0.00 3.69 39.69 2.83
3311 3981 4.473199 CAGCATGACAACACTGAGATTTG 58.527 43.478 0.00 0.00 39.69 2.32
3312 3982 3.057736 GCAGCATGACAACACTGAGATTT 60.058 43.478 0.00 0.00 39.69 2.17
3317 3987 2.837532 TAGCAGCATGACAACACTGA 57.162 45.000 0.00 0.00 39.69 3.41
3319 3989 3.339253 TCATAGCAGCATGACAACACT 57.661 42.857 0.00 0.00 39.69 3.55
3321 3991 3.181494 GCAATCATAGCAGCATGACAACA 60.181 43.478 0.00 0.00 39.69 3.33
3330 4000 4.367386 AGAAACAAGCAATCATAGCAGC 57.633 40.909 0.00 0.00 0.00 5.25
3331 4001 5.587844 ACCTAGAAACAAGCAATCATAGCAG 59.412 40.000 0.00 0.00 0.00 4.24
3337 4007 4.365514 TCCACCTAGAAACAAGCAATCA 57.634 40.909 0.00 0.00 0.00 2.57
3350 4020 2.225963 GGTACGTGATCGATCCACCTAG 59.774 54.545 22.31 9.53 40.62 3.02
3353 4023 1.001597 GAGGTACGTGATCGATCCACC 60.002 57.143 22.31 20.84 40.62 4.61
3361 4031 5.770417 AGAATTAATCCGAGGTACGTGATC 58.230 41.667 0.00 0.00 40.78 2.92
3365 4035 6.889301 TGATAGAATTAATCCGAGGTACGT 57.111 37.500 0.00 0.00 40.78 3.57
3503 4181 1.942677 TTGCCATGCAAGCATATTGC 58.057 45.000 14.74 11.00 43.99 3.56
3526 4204 0.871722 TTTTCCGACAACCATGAGCG 59.128 50.000 0.00 0.00 0.00 5.03
3540 4218 2.606108 GCCATGACAAACGGATTTTCC 58.394 47.619 0.00 0.00 0.00 3.13
3606 4286 0.250727 TTACAACTCAGTGCTGGCCC 60.251 55.000 0.00 0.00 0.00 5.80
3647 4327 3.044059 GATTGAGCAGGGCACACGC 62.044 63.158 0.00 0.00 37.44 5.34
3648 4328 1.642037 CTGATTGAGCAGGGCACACG 61.642 60.000 0.00 0.00 32.26 4.49
3649 4329 2.177950 CTGATTGAGCAGGGCACAC 58.822 57.895 0.00 0.00 32.26 3.82
3650 4330 4.728409 CTGATTGAGCAGGGCACA 57.272 55.556 0.00 0.00 32.26 4.57
3730 4410 4.142093 GCCTCCTTTGGTTGATAGTACGTA 60.142 45.833 0.00 0.00 0.00 3.57
3815 4657 2.790468 GCACTAACTAGGCGTACTGTCG 60.790 54.545 0.00 0.00 0.00 4.35
3824 4666 2.044123 AAGGCATGCACTAACTAGGC 57.956 50.000 21.36 0.00 0.00 3.93
4026 4868 4.270102 GACTACTACGTCGCTACATCAAC 58.730 47.826 0.00 0.00 0.00 3.18
4056 4898 1.342174 AGCTCACTTTGTGGCATTTGG 59.658 47.619 0.00 0.00 34.10 3.28
4057 4899 2.223876 ACAGCTCACTTTGTGGCATTTG 60.224 45.455 0.00 5.99 34.10 2.32
4260 5102 2.905736 CTCCACCAATCCCCAAAACAAT 59.094 45.455 0.00 0.00 0.00 2.71
4298 5141 6.072563 CCCTCCTAACAAAAATTGGCAAATTG 60.073 38.462 3.01 12.49 36.11 2.32
4299 5142 6.003326 CCCTCCTAACAAAAATTGGCAAATT 58.997 36.000 3.01 0.00 37.61 1.82
4300 5143 5.309282 TCCCTCCTAACAAAAATTGGCAAAT 59.691 36.000 3.01 0.00 34.12 2.32
4301 5144 4.656112 TCCCTCCTAACAAAAATTGGCAAA 59.344 37.500 3.01 0.00 34.12 3.68
4308 5151 5.788014 AGACTCTCTCCCTCCTAACAAAAAT 59.212 40.000 0.00 0.00 0.00 1.82
4363 5209 5.379706 AGGGAGGTGAGAGAATATTTTGG 57.620 43.478 0.00 0.00 0.00 3.28
4385 5232 8.827177 AACGACTGAATATAAGTCTTGTTCAA 57.173 30.769 13.70 0.00 41.60 2.69
4405 5252 7.253321 GCTTCGGATTTCATTCATTTAAACGAC 60.253 37.037 0.00 0.00 0.00 4.34
4407 5254 6.526325 TGCTTCGGATTTCATTCATTTAAACG 59.474 34.615 0.00 0.00 0.00 3.60
4408 5255 7.542130 ACTGCTTCGGATTTCATTCATTTAAAC 59.458 33.333 0.00 0.00 0.00 2.01
4411 5920 6.599244 AGACTGCTTCGGATTTCATTCATTTA 59.401 34.615 0.00 0.00 0.00 1.40
4418 5927 2.420687 GGGAGACTGCTTCGGATTTCAT 60.421 50.000 0.00 0.00 0.00 2.57
4425 5934 0.321671 TCTTTGGGAGACTGCTTCGG 59.678 55.000 0.00 0.00 0.00 4.30
4426 5935 2.393271 ATCTTTGGGAGACTGCTTCG 57.607 50.000 0.00 0.00 37.17 3.79
4428 5937 4.917906 ACTTATCTTTGGGAGACTGCTT 57.082 40.909 0.00 0.00 37.17 3.91
4429 5938 4.583871 CAACTTATCTTTGGGAGACTGCT 58.416 43.478 0.00 0.00 37.17 4.24
4430 5939 3.127721 GCAACTTATCTTTGGGAGACTGC 59.872 47.826 0.00 0.00 37.17 4.40
4431 5940 4.154918 GTGCAACTTATCTTTGGGAGACTG 59.845 45.833 0.00 0.00 37.17 3.51
4432 5941 4.327680 GTGCAACTTATCTTTGGGAGACT 58.672 43.478 0.00 0.00 37.17 3.24
4433 5942 3.440522 GGTGCAACTTATCTTTGGGAGAC 59.559 47.826 0.00 0.00 35.09 3.36
4434 5943 3.330701 AGGTGCAACTTATCTTTGGGAGA 59.669 43.478 0.00 0.00 36.28 3.71
4435 5944 3.690460 AGGTGCAACTTATCTTTGGGAG 58.310 45.455 0.00 0.00 36.74 4.30
4436 5945 3.806949 AGGTGCAACTTATCTTTGGGA 57.193 42.857 0.00 0.00 36.74 4.37
4437 5946 4.871933 AAAGGTGCAACTTATCTTTGGG 57.128 40.909 19.31 0.00 36.74 4.12
4438 5947 8.711457 CATTTAAAAGGTGCAACTTATCTTTGG 58.289 33.333 19.31 1.46 36.74 3.28
4439 5948 9.474920 TCATTTAAAAGGTGCAACTTATCTTTG 57.525 29.630 19.31 13.08 36.74 2.77
4442 5951 9.643693 CATTCATTTAAAAGGTGCAACTTATCT 57.356 29.630 19.31 8.14 36.74 1.98
4443 5952 9.638239 TCATTCATTTAAAAGGTGCAACTTATC 57.362 29.630 19.31 0.00 36.74 1.75
4445 5954 9.823647 TTTCATTCATTTAAAAGGTGCAACTTA 57.176 25.926 19.31 1.50 36.74 2.24
4446 5955 8.729805 TTTCATTCATTTAAAAGGTGCAACTT 57.270 26.923 12.33 12.33 36.74 2.66
4447 5956 8.907222 ATTTCATTCATTTAAAAGGTGCAACT 57.093 26.923 0.00 0.00 36.74 3.16
4448 5957 8.229811 GGATTTCATTCATTTAAAAGGTGCAAC 58.770 33.333 0.00 0.00 0.00 4.17
4449 5958 7.117523 CGGATTTCATTCATTTAAAAGGTGCAA 59.882 33.333 0.00 0.00 0.00 4.08
4450 5959 6.589523 CGGATTTCATTCATTTAAAAGGTGCA 59.410 34.615 0.00 0.00 0.00 4.57
4451 5960 6.589907 ACGGATTTCATTCATTTAAAAGGTGC 59.410 34.615 0.00 0.00 0.00 5.01
4452 5961 8.532977 AACGGATTTCATTCATTTAAAAGGTG 57.467 30.769 0.00 0.00 0.00 4.00
4453 5962 9.554395 AAAACGGATTTCATTCATTTAAAAGGT 57.446 25.926 0.00 0.00 0.00 3.50
4486 6056 3.844099 CCGGAATCGATTTTTGAAACGAC 59.156 43.478 12.81 0.00 39.00 4.34
4556 6150 5.338381 GGATTCAGTCATTGAGTGGGTTCTA 60.338 44.000 18.99 0.00 37.07 2.10
4557 6151 4.566488 GGATTCAGTCATTGAGTGGGTTCT 60.566 45.833 18.99 2.80 37.07 3.01
4558 6152 3.691609 GGATTCAGTCATTGAGTGGGTTC 59.308 47.826 18.99 13.34 37.07 3.62
4560 6154 2.644299 TGGATTCAGTCATTGAGTGGGT 59.356 45.455 18.99 9.66 37.07 4.51
4563 6157 7.621428 AATAAGTGGATTCAGTCATTGAGTG 57.379 36.000 14.24 14.24 37.07 3.51
4564 6158 7.884877 TGAAATAAGTGGATTCAGTCATTGAGT 59.115 33.333 0.00 0.00 37.07 3.41
4623 6221 4.703897 AGATGTTTTCTGAACCGAGTGAA 58.296 39.130 0.00 0.00 31.79 3.18
4636 6235 9.520204 TTTTTCAGATGAGTGAAAGATGTTTTC 57.480 29.630 0.00 0.00 45.00 2.29
4711 6310 5.239306 TCAAATGAGTGAAATGTGTGGACTC 59.761 40.000 0.00 0.00 34.79 3.36
4767 6366 8.279800 CGTGCCGATAATTGTGAGAATTAATTA 58.720 33.333 0.00 0.00 32.66 1.40
4801 6400 6.486253 TCACTGTGTGAATCTGCTTATTTC 57.514 37.500 7.79 0.00 39.78 2.17
4890 6493 7.472334 AGCATCAAAACCTATTCAACAAGAT 57.528 32.000 0.00 0.00 0.00 2.40
4901 6504 7.575414 TTTGAACTTGTAGCATCAAAACCTA 57.425 32.000 0.00 0.00 38.45 3.08
4985 6589 4.263949 CCACCTCTTTTATTCCTCCTTGGT 60.264 45.833 0.00 0.00 37.07 3.67
5005 6609 3.531538 TCTCTCTCACACAACAAACCAC 58.468 45.455 0.00 0.00 0.00 4.16
5103 6707 1.025812 AAATCAAAACGTCGGCCACA 58.974 45.000 2.24 0.00 0.00 4.17
5104 6708 1.002251 TCAAATCAAAACGTCGGCCAC 60.002 47.619 2.24 0.00 0.00 5.01
5105 6709 1.309950 TCAAATCAAAACGTCGGCCA 58.690 45.000 2.24 0.00 0.00 5.36
5106 6710 2.629639 ATCAAATCAAAACGTCGGCC 57.370 45.000 0.00 0.00 0.00 6.13
5107 6711 7.129622 TGATTATATCAAATCAAAACGTCGGC 58.870 34.615 0.00 0.00 41.67 5.54
5207 11467 4.638865 GGGCTACGTAATGGTGAAAAATCT 59.361 41.667 0.00 0.00 0.00 2.40
5222 11483 0.602372 TTTTTAACGGCGGGCTACGT 60.602 50.000 13.24 0.00 46.52 3.57
5253 11515 2.161012 TGTCGTAGTTTGACTCTAGCCG 59.839 50.000 0.00 0.00 37.26 5.52
5402 11673 6.514048 GCATCTTACTGCTGAAGAACACTTTT 60.514 38.462 0.00 0.00 39.12 2.27
5482 11768 4.045636 ACTTTGGATGCAAGTGAAACAC 57.954 40.909 0.00 0.00 41.43 3.32
5506 11792 9.582431 GACTTTCATGAATGTCATTTCATCATT 57.418 29.630 33.28 9.67 42.90 2.57
5634 11921 6.647334 TGATTGTTTCAGCTATGTGGAAAA 57.353 33.333 0.00 0.00 32.85 2.29
5643 11930 7.264221 ACAAACATTGTTGATTGTTTCAGCTA 58.736 30.769 2.13 0.00 43.80 3.32
6301 12634 3.821033 GGCCTGATTATTCATTACGGCTT 59.179 43.478 12.62 0.00 38.74 4.35
6353 12719 0.474184 ACCCAAGAATCCATAGCCGG 59.526 55.000 0.00 0.00 0.00 6.13
6354 12720 1.949525 CAACCCAAGAATCCATAGCCG 59.050 52.381 0.00 0.00 0.00 5.52
6355 12721 1.683385 GCAACCCAAGAATCCATAGCC 59.317 52.381 0.00 0.00 0.00 3.93
6413 12779 2.548057 TCTCTTTTCAACGCATCCACAC 59.452 45.455 0.00 0.00 0.00 3.82
6907 14667 4.538746 AAGTGGAGTAGTGGAGTAAAGC 57.461 45.455 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.