Multiple sequence alignment - TraesCS1A01G412100

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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 TraesCS1A01G412100 chr1A 100.000 5930 0 0 1 5930 572570729 572576658 0.000000e+00 10951.0
1 TraesCS1A01G412100 chr1B 88.076 2541 171 55 2598 5085 663045536 663047997 0.000000e+00 2892.0
2 TraesCS1A01G412100 chr1B 88.339 1415 72 31 816 2203 663043796 663045144 0.000000e+00 1613.0
3 TraesCS1A01G412100 chr1B 93.544 821 33 5 5129 5930 663079095 663079914 0.000000e+00 1205.0
4 TraesCS1A01G412100 chr1B 82.973 370 33 14 2209 2567 663045182 663045532 2.080000e-79 307.0
5 TraesCS1A01G412100 chr1B 89.730 185 8 4 1 177 663043183 663043364 5.980000e-55 226.0
6 TraesCS1A01G412100 chr1B 82.400 125 9 8 505 618 663043367 663043489 4.890000e-16 97.1
7 TraesCS1A01G412100 chr1D 89.051 2256 141 52 1 2203 476701285 476703487 0.000000e+00 2700.0
8 TraesCS1A01G412100 chr1D 91.984 1472 99 11 3631 5085 476704921 476706390 0.000000e+00 2047.0
9 TraesCS1A01G412100 chr1D 86.653 1431 97 46 2209 3592 476703539 476704922 0.000000e+00 1498.0
10 TraesCS1A01G412100 chr1D 93.260 816 37 2 5133 5930 476706588 476707403 0.000000e+00 1186.0
11 TraesCS1A01G412100 chr1D 83.497 509 48 22 4179 4652 32440748 32441255 5.450000e-120 442.0
12 TraesCS1A01G412100 chr5B 83.333 642 85 12 5300 5927 38782483 38781850 1.850000e-159 573.0
13 TraesCS1A01G412100 chr5B 83.890 509 44 18 4180 4652 641906294 641905788 9.060000e-123 451.0
14 TraesCS1A01G412100 chr7B 84.921 504 48 11 989 1474 236328560 236328067 8.940000e-133 484.0
15 TraesCS1A01G412100 chr7B 87.850 214 22 4 4249 4459 666404533 666404321 1.280000e-61 248.0
16 TraesCS1A01G412100 chr7B 85.246 122 14 2 1259 1379 713752062 713751944 8.070000e-24 122.0
17 TraesCS1A01G412100 chr2B 84.314 510 42 18 4179 4652 133645532 133646039 1.160000e-126 464.0
18 TraesCS1A01G412100 chr2B 83.170 511 46 19 4179 4652 129743388 129743895 1.180000e-116 431.0
19 TraesCS1A01G412100 chr2B 85.417 288 27 9 5264 5536 39408402 39408689 9.730000e-73 285.0
20 TraesCS1A01G412100 chr2B 88.950 181 17 1 5753 5930 232892469 232892289 2.780000e-53 220.0
21 TraesCS1A01G412100 chr2B 82.787 122 17 2 1259 1379 573128465 573128347 8.130000e-19 106.0
22 TraesCS1A01G412100 chr3B 83.725 510 45 17 4179 4652 739401686 739402193 1.170000e-121 448.0
23 TraesCS1A01G412100 chr3B 79.907 428 72 11 3124 3544 422917385 422916965 9.660000e-78 302.0
24 TraesCS1A01G412100 chr3B 88.500 200 18 3 5734 5930 574013701 574013898 2.760000e-58 237.0
25 TraesCS1A01G412100 chr3B 83.607 122 16 2 1259 1379 32567936 32568054 1.750000e-20 111.0
26 TraesCS1A01G412100 chr6A 90.311 289 21 6 4174 4456 428362467 428362180 7.260000e-99 372.0
27 TraesCS1A01G412100 chr6A 89.655 145 13 2 4509 4652 428362097 428361954 3.650000e-42 183.0
28 TraesCS1A01G412100 chr6A 84.426 122 15 2 1259 1379 435591784 435591666 3.750000e-22 117.0
29 TraesCS1A01G412100 chr2A 90.311 289 21 6 4174 4456 732555312 732555025 7.260000e-99 372.0
30 TraesCS1A01G412100 chr2A 88.500 200 17 4 5734 5930 735688225 735688421 2.760000e-58 237.0
31 TraesCS1A01G412100 chr2A 88.966 145 14 2 4509 4652 732554942 732554799 1.700000e-40 178.0
32 TraesCS1A01G412100 chr3A 80.178 449 66 15 3105 3542 439915383 439915819 1.240000e-81 315.0
33 TraesCS1A01G412100 chr6B 89.944 179 15 1 5753 5928 644806623 644806445 1.660000e-55 228.0
34 TraesCS1A01G412100 chr4A 88.950 181 17 1 5753 5930 602949338 602949158 2.780000e-53 220.0
35 TraesCS1A01G412100 chr7A 88.398 181 18 1 5753 5930 12074893 12075073 1.290000e-51 215.0
36 TraesCS1A01G412100 chr4B 79.118 340 36 16 4346 4652 565627563 565627226 1.010000e-47 202.0
37 TraesCS1A01G412100 chr3D 82.941 170 21 5 1074 1240 570492265 570492101 4.790000e-31 147.0
38 TraesCS1A01G412100 chr7D 88.034 117 11 1 1259 1375 474193474 474193361 1.040000e-27 135.0
39 TraesCS1A01G412100 chr5A 92.473 93 6 1 989 1081 586022609 586022700 1.340000e-26 132.0
40 TraesCS1A01G412100 chr4D 85.833 120 13 2 1260 1379 465184588 465184703 2.240000e-24 124.0


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 TraesCS1A01G412100 chr1A 572570729 572576658 5929 False 10951.00 10951 100.0000 1 5930 1 chr1A.!!$F1 5929
1 TraesCS1A01G412100 chr1B 663079095 663079914 819 False 1205.00 1205 93.5440 5129 5930 1 chr1B.!!$F1 801
2 TraesCS1A01G412100 chr1B 663043183 663047997 4814 False 1027.02 2892 86.3036 1 5085 5 chr1B.!!$F2 5084
3 TraesCS1A01G412100 chr1D 476701285 476707403 6118 False 1857.75 2700 90.2370 1 5930 4 chr1D.!!$F2 5929
4 TraesCS1A01G412100 chr1D 32440748 32441255 507 False 442.00 442 83.4970 4179 4652 1 chr1D.!!$F1 473
5 TraesCS1A01G412100 chr5B 38781850 38782483 633 True 573.00 573 83.3330 5300 5927 1 chr5B.!!$R1 627
6 TraesCS1A01G412100 chr5B 641905788 641906294 506 True 451.00 451 83.8900 4180 4652 1 chr5B.!!$R2 472
7 TraesCS1A01G412100 chr2B 133645532 133646039 507 False 464.00 464 84.3140 4179 4652 1 chr2B.!!$F3 473
8 TraesCS1A01G412100 chr2B 129743388 129743895 507 False 431.00 431 83.1700 4179 4652 1 chr2B.!!$F2 473
9 TraesCS1A01G412100 chr3B 739401686 739402193 507 False 448.00 448 83.7250 4179 4652 1 chr3B.!!$F3 473
10 TraesCS1A01G412100 chr6A 428361954 428362467 513 True 277.50 372 89.9830 4174 4652 2 chr6A.!!$R2 478
11 TraesCS1A01G412100 chr2A 732554799 732555312 513 True 275.00 372 89.6385 4174 4652 2 chr2A.!!$R1 478

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
132 135 0.386985 GGATATCGTCGTCTTCCGGC 60.387 60.0 0.00 0.0 37.97 6.13 F
547 560 0.949397 CCGAGACCGATGAACCGATA 59.051 55.0 0.00 0.0 38.22 2.92 F
2255 2517 0.383491 CCAAATCATCATCGTCGCGC 60.383 55.0 0.00 0.0 0.00 6.86 F
2748 3035 0.111446 TTGCAGTGGATCCGGGAAAA 59.889 50.0 7.39 0.0 0.00 2.29 F
3620 3948 0.172803 CAATCTGCCTTCTGCTTGCC 59.827 55.0 0.00 0.0 42.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1736 1.094073 CGGCAATCCTCTGCTCCTTG 61.094 60.0 0.00 0.00 42.25 3.61 R
2347 2613 0.179100 CAACCACTCTCATCGGCGAT 60.179 55.0 18.14 18.14 0.00 4.58 R
3104 3429 0.401738 CCCCCACACATCAGACAGTT 59.598 55.0 0.00 0.00 0.00 3.16 R
4500 4847 0.178767 TGACTGTCACTTGCTGCACT 59.821 50.0 6.36 0.00 0.00 4.40 R
5100 5476 0.103937 TACACATGATCGCGCATCCA 59.896 50.0 8.75 0.93 0.00 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
68 69 9.897744 GATTCAAGAGTTTAATGTGATGTGAAA 57.102 29.630 0.00 0.00 0.00 2.69
83 84 2.118683 GTGAAACACACGCACGTAGTA 58.881 47.619 0.00 0.00 38.20 1.82
84 85 2.152489 GTGAAACACACGCACGTAGTAG 59.848 50.000 0.00 0.00 38.20 2.57
85 86 1.123756 GAAACACACGCACGTAGTAGC 59.876 52.381 0.00 0.00 41.61 3.58
91 92 2.582498 GCACGTAGTAGCGGCAGG 60.582 66.667 1.45 0.00 41.61 4.85
117 120 8.023021 AGTAAATAACATGCAGACTCTGGATA 57.977 34.615 12.32 0.00 40.43 2.59
125 128 2.350007 GCAGACTCTGGATATCGTCGTC 60.350 54.545 8.17 1.44 31.21 4.20
127 130 3.562141 CAGACTCTGGATATCGTCGTCTT 59.438 47.826 10.83 0.00 0.00 3.01
128 131 3.810941 AGACTCTGGATATCGTCGTCTTC 59.189 47.826 8.76 0.00 0.00 2.87
129 132 2.879646 ACTCTGGATATCGTCGTCTTCC 59.120 50.000 0.00 0.00 0.00 3.46
130 133 1.871676 TCTGGATATCGTCGTCTTCCG 59.128 52.381 0.00 0.00 38.13 4.30
132 135 0.386985 GGATATCGTCGTCTTCCGGC 60.387 60.000 0.00 0.00 37.97 6.13
178 189 2.969443 CGAAGCAAAACGGACATCTT 57.031 45.000 0.00 0.00 0.00 2.40
179 190 2.839474 CGAAGCAAAACGGACATCTTC 58.161 47.619 0.00 0.00 0.00 2.87
180 191 2.223144 CGAAGCAAAACGGACATCTTCA 59.777 45.455 0.00 0.00 32.53 3.02
181 192 3.303725 CGAAGCAAAACGGACATCTTCAA 60.304 43.478 0.00 0.00 32.53 2.69
182 193 3.904136 AGCAAAACGGACATCTTCAAG 57.096 42.857 0.00 0.00 0.00 3.02
183 194 3.476552 AGCAAAACGGACATCTTCAAGA 58.523 40.909 0.00 0.00 0.00 3.02
184 195 3.499918 AGCAAAACGGACATCTTCAAGAG 59.500 43.478 0.00 0.00 0.00 2.85
196 207 6.686630 ACATCTTCAAGAGTCAAGACTACTG 58.313 40.000 2.15 4.00 42.66 2.74
217 228 9.213799 CTACTGCTCTCTCATTTTCTTTTTAGT 57.786 33.333 0.00 0.00 0.00 2.24
219 230 7.174080 ACTGCTCTCTCATTTTCTTTTTAGTCC 59.826 37.037 0.00 0.00 0.00 3.85
224 235 7.822334 TCTCTCATTTTCTTTTTAGTCCGCATA 59.178 33.333 0.00 0.00 0.00 3.14
379 392 3.054878 GTGTTGTAGTTGAGTACCACGG 58.945 50.000 0.00 0.00 0.00 4.94
402 415 1.613061 GGGTCCGGGTCAAATCCAT 59.387 57.895 0.00 0.00 0.00 3.41
409 422 3.257127 TCCGGGTCAAATCCATTTCAAAC 59.743 43.478 0.00 0.00 0.00 2.93
429 442 2.234168 ACCCGAGACCTTTTCTTCTAGC 59.766 50.000 0.00 0.00 33.22 3.42
430 443 2.418884 CCCGAGACCTTTTCTTCTAGCC 60.419 54.545 0.00 0.00 33.22 3.93
432 445 2.272678 GAGACCTTTTCTTCTAGCCGC 58.727 52.381 0.00 0.00 33.22 6.53
451 464 2.414824 CGCAGTAGAGTTGAGTCACTCC 60.415 54.545 1.24 0.00 43.89 3.85
510 523 5.182001 CACTTGGCAGTAAAGCAGATAAACT 59.818 40.000 0.00 0.00 35.83 2.66
547 560 0.949397 CCGAGACCGATGAACCGATA 59.051 55.000 0.00 0.00 38.22 2.92
556 569 8.928270 AGACCGATGAACCGATAATAATAATC 57.072 34.615 0.00 0.00 0.00 1.75
557 570 8.750298 AGACCGATGAACCGATAATAATAATCT 58.250 33.333 0.00 0.00 0.00 2.40
560 573 9.464714 CCGATGAACCGATAATAATAATCTAGG 57.535 37.037 0.00 0.00 0.00 3.02
618 763 4.051237 GCAAAGCGAAAAAGGTCAAGATT 58.949 39.130 0.00 0.00 0.00 2.40
621 766 3.642705 AGCGAAAAAGGTCAAGATTTGC 58.357 40.909 0.00 0.00 0.00 3.68
627 772 6.524586 CGAAAAAGGTCAAGATTTGCATAGAC 59.475 38.462 0.00 0.00 0.00 2.59
629 774 5.886960 AAGGTCAAGATTTGCATAGACAC 57.113 39.130 0.00 0.00 0.00 3.67
632 777 5.413833 AGGTCAAGATTTGCATAGACACTTG 59.586 40.000 0.00 0.00 35.90 3.16
656 801 1.644786 TTCAGATCGTGCGAGCGAGA 61.645 55.000 4.20 4.39 44.43 4.04
657 802 1.653835 CAGATCGTGCGAGCGAGAG 60.654 63.158 4.20 0.00 44.43 3.20
731 902 2.608090 GCTCCAGTATTTTACCGCTCAC 59.392 50.000 0.00 0.00 0.00 3.51
744 915 3.625897 CTCACACCGGCCACCTCA 61.626 66.667 0.00 0.00 0.00 3.86
748 925 4.394712 CACCGGCCACCTCACTCC 62.395 72.222 0.00 0.00 0.00 3.85
754 931 3.077556 CCACCTCACTCCCTCCCG 61.078 72.222 0.00 0.00 0.00 5.14
777 954 1.371183 CTCAGACCAACCGAGCCAA 59.629 57.895 0.00 0.00 0.00 4.52
852 1031 2.123208 TCGACACCCCACACCTCA 60.123 61.111 0.00 0.00 0.00 3.86
853 1032 2.030562 CGACACCCCACACCTCAC 59.969 66.667 0.00 0.00 0.00 3.51
854 1033 2.430367 GACACCCCACACCTCACC 59.570 66.667 0.00 0.00 0.00 4.02
857 1036 2.923035 ACCCCACACCTCACCTCG 60.923 66.667 0.00 0.00 0.00 4.63
888 1067 2.949106 CTGCCAACCAGAAGCACG 59.051 61.111 0.00 0.00 44.64 5.34
939 1127 4.212913 GCGCGAGGAGGAGCATGA 62.213 66.667 12.10 0.00 32.60 3.07
963 1151 2.969238 CGCAATCCTAGCTGCCCG 60.969 66.667 0.00 0.00 35.01 6.13
965 1153 1.889573 GCAATCCTAGCTGCCCGTC 60.890 63.158 0.00 0.00 32.18 4.79
970 1158 2.409651 CTAGCTGCCCGTCTCGTC 59.590 66.667 0.00 0.00 0.00 4.20
987 1175 2.434359 CTTCTTCCACGGCCGGAC 60.434 66.667 31.76 0.00 33.75 4.79
988 1176 3.952628 CTTCTTCCACGGCCGGACC 62.953 68.421 31.76 4.99 33.75 4.46
1069 1257 3.003173 CGCCCAAGACCTCCTCCA 61.003 66.667 0.00 0.00 0.00 3.86
1073 1261 1.679898 CCAAGACCTCCTCCACCAC 59.320 63.158 0.00 0.00 0.00 4.16
1077 1265 2.529389 ACCTCCTCCACCACCACC 60.529 66.667 0.00 0.00 0.00 4.61
1078 1266 2.203998 CCTCCTCCACCACCACCT 60.204 66.667 0.00 0.00 0.00 4.00
1079 1267 2.294078 CCTCCTCCACCACCACCTC 61.294 68.421 0.00 0.00 0.00 3.85
1080 1268 2.203938 TCCTCCACCACCACCTCC 60.204 66.667 0.00 0.00 0.00 4.30
1081 1269 2.203998 CCTCCACCACCACCTCCT 60.204 66.667 0.00 0.00 0.00 3.69
1082 1270 2.294078 CCTCCACCACCACCTCCTC 61.294 68.421 0.00 0.00 0.00 3.71
1083 1271 2.603473 TCCACCACCACCTCCTCG 60.603 66.667 0.00 0.00 0.00 4.63
1084 1272 4.394712 CCACCACCACCTCCTCGC 62.395 72.222 0.00 0.00 0.00 5.03
1085 1273 4.742201 CACCACCACCTCCTCGCG 62.742 72.222 0.00 0.00 0.00 5.87
1088 1276 4.680237 CACCACCTCCTCGCGCAA 62.680 66.667 8.75 0.00 0.00 4.85
1089 1277 4.379243 ACCACCTCCTCGCGCAAG 62.379 66.667 8.75 0.00 43.44 4.01
1090 1278 4.379243 CCACCTCCTCGCGCAAGT 62.379 66.667 8.75 0.00 41.68 3.16
1127 1315 4.980805 GTCGCAGAACACCGCCCA 62.981 66.667 0.00 0.00 39.69 5.36
1548 1739 3.378552 GCTAGTGTCGCGAGCAAG 58.621 61.111 10.24 6.17 43.90 4.01
1756 1956 1.340114 CCAAGCCCAAGTCCTACTTCC 60.340 57.143 0.00 0.00 36.03 3.46
1764 1964 2.042230 TCCTACTTCCCCGGCTCC 60.042 66.667 0.00 0.00 0.00 4.70
1881 2081 2.690881 AAGCTGCCCCCGATACCA 60.691 61.111 0.00 0.00 0.00 3.25
1915 2118 4.402528 CCCCACCGTCAATGCCGA 62.403 66.667 0.00 0.00 0.00 5.54
2198 2410 2.355986 ACCTCATCGCGGTAAGCCA 61.356 57.895 6.13 0.00 44.76 4.75
2205 2417 3.053896 GCGGTAAGCCAAGCCGTT 61.054 61.111 4.16 0.00 46.41 4.44
2206 2418 2.622962 GCGGTAAGCCAAGCCGTTT 61.623 57.895 4.16 0.00 46.41 3.60
2233 2491 5.652994 TCCCTCCCGTTTAATTTCATTTG 57.347 39.130 0.00 0.00 0.00 2.32
2234 2492 5.081032 TCCCTCCCGTTTAATTTCATTTGT 58.919 37.500 0.00 0.00 0.00 2.83
2236 2494 5.867174 CCCTCCCGTTTAATTTCATTTGTTC 59.133 40.000 0.00 0.00 0.00 3.18
2255 2517 0.383491 CCAAATCATCATCGTCGCGC 60.383 55.000 0.00 0.00 0.00 6.86
2280 2542 7.113544 GCTAGACAAAATCTGAAACCGAAAAAG 59.886 37.037 0.00 0.00 38.49 2.27
2293 2556 3.181494 ACCGAAAAAGGGTTTCACGAAAG 60.181 43.478 0.00 0.00 32.70 2.62
2347 2613 5.720520 TGGATGGGTGAATCAAATCAATCAA 59.279 36.000 0.00 0.00 0.00 2.57
2372 2638 1.135859 CGATGAGAGTGGTTGCTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
2373 2639 2.157738 GATGAGAGTGGTTGCTTTGCT 58.842 47.619 0.00 0.00 0.00 3.91
2374 2640 2.057137 TGAGAGTGGTTGCTTTGCTT 57.943 45.000 0.00 0.00 0.00 3.91
2375 2641 2.378038 TGAGAGTGGTTGCTTTGCTTT 58.622 42.857 0.00 0.00 0.00 3.51
2376 2642 2.099592 TGAGAGTGGTTGCTTTGCTTTG 59.900 45.455 0.00 0.00 0.00 2.77
2436 2702 1.027792 TTATCGTCTTTTGGGGCGCC 61.028 55.000 21.18 21.18 0.00 6.53
2476 2757 4.818546 AGGCACATACAGATGCAGATAAAC 59.181 41.667 0.00 0.00 43.93 2.01
2479 2760 3.490896 ACATACAGATGCAGATAAACGCG 59.509 43.478 3.53 3.53 36.43 6.01
2491 2772 0.305313 TAAACGCGGCTGAACAACAC 59.695 50.000 12.47 0.00 0.00 3.32
2517 2798 9.219603 CACAGATAAATACAGAGGTGAAAAGAA 57.780 33.333 0.00 0.00 0.00 2.52
2526 2807 6.799512 ACAGAGGTGAAAAGAAAGAAACATG 58.200 36.000 0.00 0.00 0.00 3.21
2535 2816 5.372343 AAGAAAGAAACATGGGCCTTTTT 57.628 34.783 4.53 0.73 0.00 1.94
2539 2820 2.634453 AGAAACATGGGCCTTTTTCCAG 59.366 45.455 16.53 0.00 36.38 3.86
2582 2863 1.815421 CCCGCGTTCCATGGAGAAG 60.815 63.158 15.53 11.29 0.00 2.85
2589 2870 0.846427 TTCCATGGAGAAGCCCACCT 60.846 55.000 15.53 0.00 39.34 4.00
2591 2872 1.225704 CATGGAGAAGCCCACCTCC 59.774 63.158 0.00 0.00 46.99 4.30
2592 2873 1.083706 ATGGAGAAGCCCACCTCCT 59.916 57.895 9.49 0.00 46.94 3.69
2593 2874 0.985490 ATGGAGAAGCCCACCTCCTC 60.985 60.000 9.49 0.00 46.94 3.71
2594 2875 1.613630 GGAGAAGCCCACCTCCTCA 60.614 63.158 0.00 0.00 44.23 3.86
2595 2876 1.599576 GAGAAGCCCACCTCCTCAC 59.400 63.158 0.00 0.00 0.00 3.51
2596 2877 1.152030 AGAAGCCCACCTCCTCACA 60.152 57.895 0.00 0.00 0.00 3.58
2597 2878 1.003233 GAAGCCCACCTCCTCACAC 60.003 63.158 0.00 0.00 0.00 3.82
2598 2879 1.768684 GAAGCCCACCTCCTCACACA 61.769 60.000 0.00 0.00 0.00 3.72
2599 2880 2.032681 GCCCACCTCCTCACACAC 59.967 66.667 0.00 0.00 0.00 3.82
2639 2920 6.790232 TTCTTTCTCTTGGATTTTTGTGGT 57.210 33.333 0.00 0.00 0.00 4.16
2650 2931 5.045578 TGGATTTTTGTGGTTTTTGGAGGAA 60.046 36.000 0.00 0.00 0.00 3.36
2725 3012 4.348863 AAAAACAATGGCAGCATTGGTA 57.651 36.364 16.80 0.00 41.18 3.25
2726 3013 4.348863 AAAACAATGGCAGCATTGGTAA 57.651 36.364 16.80 0.00 41.18 2.85
2727 3014 3.598019 AACAATGGCAGCATTGGTAAG 57.402 42.857 16.80 0.00 44.44 2.34
2728 3015 1.826720 ACAATGGCAGCATTGGTAAGG 59.173 47.619 16.80 0.00 44.44 2.69
2729 3016 1.826720 CAATGGCAGCATTGGTAAGGT 59.173 47.619 7.57 0.00 38.52 3.50
2742 3029 1.369625 GTAAGGTTGCAGTGGATCCG 58.630 55.000 7.39 0.00 0.00 4.18
2745 3032 2.668632 GTTGCAGTGGATCCGGGA 59.331 61.111 7.39 0.00 0.00 5.14
2746 3033 1.002624 GTTGCAGTGGATCCGGGAA 60.003 57.895 7.39 3.99 0.00 3.97
2748 3035 0.111446 TTGCAGTGGATCCGGGAAAA 59.889 50.000 7.39 0.00 0.00 2.29
2750 3037 0.322546 GCAGTGGATCCGGGAAAAGT 60.323 55.000 7.39 0.00 0.00 2.66
2751 3038 1.886655 GCAGTGGATCCGGGAAAAGTT 60.887 52.381 7.39 0.00 0.00 2.66
2752 3039 1.812571 CAGTGGATCCGGGAAAAGTTG 59.187 52.381 7.39 0.00 0.00 3.16
2753 3040 0.526211 GTGGATCCGGGAAAAGTTGC 59.474 55.000 7.39 0.00 0.00 4.17
2754 3041 0.404040 TGGATCCGGGAAAAGTTGCT 59.596 50.000 7.39 0.00 0.00 3.91
2840 3156 6.854496 TTCAAATATCATTACCGGTAGTGC 57.146 37.500 27.42 0.00 0.00 4.40
2843 3159 4.967084 ATATCATTACCGGTAGTGCCAA 57.033 40.909 27.42 16.95 36.97 4.52
2844 3160 2.389962 TCATTACCGGTAGTGCCAAC 57.610 50.000 27.42 0.00 36.97 3.77
2845 3161 1.903860 TCATTACCGGTAGTGCCAACT 59.096 47.619 27.42 0.00 40.67 3.16
2848 3164 1.189524 TACCGGTAGTGCCAACTGCT 61.190 55.000 11.16 0.00 38.90 4.24
2849 3165 2.034879 CCGGTAGTGCCAACTGCTG 61.035 63.158 0.00 0.00 43.09 4.41
2953 3278 2.009888 CTTCGCGCCATTTCCTCTC 58.990 57.895 0.00 0.00 0.00 3.20
2986 3311 4.214332 GCGAGGAGAGTTTGAAACTTTGAT 59.786 41.667 12.37 0.00 43.03 2.57
3014 3339 1.181098 AAACCATGTGCCACTGCTCC 61.181 55.000 0.00 0.00 38.71 4.70
3104 3429 9.485206 GGAGTAATAATTAATTAAGCCTGACGA 57.515 33.333 11.80 0.00 31.82 4.20
3120 3447 2.061773 GACGAACTGTCTGATGTGTGG 58.938 52.381 0.00 0.00 44.58 4.17
3262 3589 2.202544 GTCGAGCTCTCACGCCTG 60.203 66.667 12.85 0.00 0.00 4.85
3288 3615 2.434185 TAACCAAGCTCGCCTGCG 60.434 61.111 4.92 4.92 41.35 5.18
3314 3641 1.537348 CGTCGTCCCAAGTTCAGTGAA 60.537 52.381 0.08 0.08 0.00 3.18
3321 3648 4.214332 GTCCCAAGTTCAGTGAATCTTGTC 59.786 45.833 27.62 19.93 33.38 3.18
3460 3787 2.281830 CCTCAAGAAGGTCGAGGCT 58.718 57.895 0.00 0.00 39.95 4.58
3487 3814 2.695314 GGCATTCTGTGACGATCCC 58.305 57.895 0.00 0.00 0.00 3.85
3566 3894 5.524284 CCGTTCTCTTCCTGTACTATCATG 58.476 45.833 0.00 0.00 0.00 3.07
3590 3918 6.051717 GCATCTTCTTCTACCTATGAGCAAA 58.948 40.000 0.00 0.00 0.00 3.68
3593 3921 7.423844 TCTTCTTCTACCTATGAGCAAATGA 57.576 36.000 0.00 0.00 0.00 2.57
3602 3930 2.275134 TGAGCAAATGACCAGCTTCA 57.725 45.000 0.00 0.00 39.02 3.02
3603 3931 2.585330 TGAGCAAATGACCAGCTTCAA 58.415 42.857 0.00 0.00 39.02 2.69
3604 3932 3.159472 TGAGCAAATGACCAGCTTCAAT 58.841 40.909 0.00 0.00 39.02 2.57
3605 3933 3.192001 TGAGCAAATGACCAGCTTCAATC 59.808 43.478 0.00 0.00 39.02 2.67
3606 3934 3.428532 AGCAAATGACCAGCTTCAATCT 58.571 40.909 0.00 0.00 34.37 2.40
3607 3935 3.192844 AGCAAATGACCAGCTTCAATCTG 59.807 43.478 0.00 0.00 34.37 2.90
3608 3936 3.508762 CAAATGACCAGCTTCAATCTGC 58.491 45.455 0.00 0.00 0.00 4.26
3609 3937 1.760192 ATGACCAGCTTCAATCTGCC 58.240 50.000 0.00 0.00 0.00 4.85
3610 3938 0.694771 TGACCAGCTTCAATCTGCCT 59.305 50.000 0.00 0.00 0.00 4.75
3620 3948 0.172803 CAATCTGCCTTCTGCTTGCC 59.827 55.000 0.00 0.00 42.00 4.52
3624 3952 3.066814 GCCTTCTGCTTGCCCCTG 61.067 66.667 0.00 0.00 36.87 4.45
3625 3953 2.437897 CCTTCTGCTTGCCCCTGT 59.562 61.111 0.00 0.00 0.00 4.00
3626 3954 1.975407 CCTTCTGCTTGCCCCTGTG 60.975 63.158 0.00 0.00 0.00 3.66
3627 3955 2.598394 TTCTGCTTGCCCCTGTGC 60.598 61.111 0.00 0.00 0.00 4.57
3628 3956 3.137385 TTCTGCTTGCCCCTGTGCT 62.137 57.895 0.00 0.00 0.00 4.40
3629 3957 3.060615 CTGCTTGCCCCTGTGCTC 61.061 66.667 0.00 0.00 0.00 4.26
3636 3964 1.890979 GCCCCTGTGCTCATCATCG 60.891 63.158 0.00 0.00 0.00 3.84
3795 4123 7.646548 TTCAGTTATCTAGTAGCACATGACT 57.353 36.000 0.00 0.00 0.00 3.41
3819 4147 8.725148 ACTTACAGACAAACAGATCAATCATTC 58.275 33.333 0.00 0.00 0.00 2.67
3853 4181 4.986054 TTTCTTGTTAGAACCTAGCCCA 57.014 40.909 0.00 0.00 40.04 5.36
3877 4205 7.815068 CCAAGTATAGAATGATGCACTAGGTAC 59.185 40.741 0.00 0.00 0.00 3.34
3878 4206 8.360390 CAAGTATAGAATGATGCACTAGGTACA 58.640 37.037 0.00 0.00 0.00 2.90
3883 4211 2.985896 TGATGCACTAGGTACAAAGGC 58.014 47.619 0.00 0.00 0.00 4.35
3984 4312 3.639538 CATTGAGAATGCTATGGCTTGC 58.360 45.455 1.68 0.00 39.59 4.01
4015 4343 8.469125 GTGTTCGAATGTAGTGAATTTGTTTTC 58.531 33.333 0.00 0.00 0.00 2.29
4093 4422 3.187022 CGCAAATCTGAACACACTGATCA 59.813 43.478 0.00 0.00 0.00 2.92
4107 4436 6.051074 CACACTGATCATATTGGTGCTAGAA 58.949 40.000 10.93 0.00 0.00 2.10
4260 4591 8.930846 ATAGAATATTTTGAGTTGATCCTGGG 57.069 34.615 0.00 0.00 0.00 4.45
4285 4617 4.513442 TGTGCAAGTGTACCCAATATCTC 58.487 43.478 0.00 0.00 0.00 2.75
4297 4629 7.552687 TGTACCCAATATCTCTTCATTTGTCAC 59.447 37.037 0.00 0.00 0.00 3.67
4298 4630 6.725364 ACCCAATATCTCTTCATTTGTCACT 58.275 36.000 0.00 0.00 0.00 3.41
4446 4781 5.236263 GCAACTTTGGGTAGGAAAATGTTTG 59.764 40.000 0.00 0.00 0.00 2.93
4461 4796 7.380333 GGAAAATGTTTGTTTTTCTAGGTACCG 59.620 37.037 6.18 0.00 40.98 4.02
4478 4824 3.848272 ACCGCACAAATTAACTGGATG 57.152 42.857 0.00 0.00 0.00 3.51
4532 4897 4.051922 GTGACAGTCACCACTAGTTTCTG 58.948 47.826 21.52 0.68 41.37 3.02
4563 4928 1.336755 GGCATTCGGTTGACAAGTTGT 59.663 47.619 8.61 8.61 0.00 3.32
4694 5059 2.060383 CATGCTCCAGGGAGTCCGA 61.060 63.158 16.31 0.00 43.70 4.55
4743 5109 1.563410 CCCAGCTCCTCCATTTTCTCT 59.437 52.381 0.00 0.00 0.00 3.10
4764 5131 5.529289 TCTTACACTCACTCTATCCCCATT 58.471 41.667 0.00 0.00 0.00 3.16
4765 5132 5.964477 TCTTACACTCACTCTATCCCCATTT 59.036 40.000 0.00 0.00 0.00 2.32
4782 5155 4.711355 CCCATTTTTGGACATGGTACTCAT 59.289 41.667 0.00 0.00 38.72 2.90
4866 5239 1.374758 CAAGGAGAAGGCGAACGCT 60.375 57.895 18.14 0.00 41.60 5.07
4955 5329 7.738524 AGACCTGAGAGTACCTACCATATACTA 59.261 40.741 0.00 0.00 29.25 1.82
5047 5423 8.846943 TGAATACTTATTTGCTCTCACTGAAA 57.153 30.769 0.00 0.00 0.00 2.69
5060 5436 4.835056 TCTCACTGAAATCTTCCAGAGTCA 59.165 41.667 0.00 0.00 34.65 3.41
5085 5461 6.542370 AGTGTGTTTGCTATAACTTGTGAACT 59.458 34.615 0.00 0.00 0.00 3.01
5086 5462 7.713507 AGTGTGTTTGCTATAACTTGTGAACTA 59.286 33.333 0.00 0.00 0.00 2.24
5087 5463 8.339714 GTGTGTTTGCTATAACTTGTGAACTAA 58.660 33.333 0.00 0.00 0.00 2.24
5088 5464 9.062524 TGTGTTTGCTATAACTTGTGAACTAAT 57.937 29.630 0.00 0.00 0.00 1.73
5091 5467 9.983804 GTTTGCTATAACTTGTGAACTAATACC 57.016 33.333 0.00 0.00 0.00 2.73
5092 5468 8.726870 TTGCTATAACTTGTGAACTAATACCC 57.273 34.615 0.00 0.00 0.00 3.69
5093 5469 6.982141 TGCTATAACTTGTGAACTAATACCCG 59.018 38.462 0.00 0.00 0.00 5.28
5094 5470 7.147863 TGCTATAACTTGTGAACTAATACCCGA 60.148 37.037 0.00 0.00 0.00 5.14
5095 5471 7.381678 GCTATAACTTGTGAACTAATACCCGAG 59.618 40.741 0.00 0.00 0.00 4.63
5096 5472 5.733620 AACTTGTGAACTAATACCCGAGA 57.266 39.130 0.00 0.00 0.00 4.04
5097 5473 5.733620 ACTTGTGAACTAATACCCGAGAA 57.266 39.130 0.00 0.00 0.00 2.87
5098 5474 5.476614 ACTTGTGAACTAATACCCGAGAAC 58.523 41.667 0.00 0.00 0.00 3.01
5099 5475 5.011329 ACTTGTGAACTAATACCCGAGAACA 59.989 40.000 0.00 0.00 0.00 3.18
5100 5476 5.670792 TGTGAACTAATACCCGAGAACAT 57.329 39.130 0.00 0.00 0.00 2.71
5102 5478 4.809426 GTGAACTAATACCCGAGAACATGG 59.191 45.833 0.00 0.00 0.00 3.66
5104 5480 5.365605 TGAACTAATACCCGAGAACATGGAT 59.634 40.000 0.00 0.00 0.00 3.41
5106 5482 2.550830 ATACCCGAGAACATGGATGC 57.449 50.000 0.00 0.00 0.00 3.91
5111 5487 1.217585 CGAGAACATGGATGCGCGAT 61.218 55.000 12.10 0.00 0.00 4.58
5113 5489 0.179076 AGAACATGGATGCGCGATCA 60.179 50.000 12.10 0.00 31.91 2.92
5114 5490 0.870393 GAACATGGATGCGCGATCAT 59.130 50.000 12.10 4.12 31.91 2.45
5116 5492 0.533531 ACATGGATGCGCGATCATGT 60.534 50.000 25.81 25.81 32.47 3.21
5117 5493 0.110373 CATGGATGCGCGATCATGTG 60.110 55.000 12.10 12.62 31.91 3.21
5130 5506 5.574443 CGCGATCATGTGTAGATGATATGTT 59.426 40.000 0.00 0.00 42.10 2.71
5200 5736 8.902540 TGACAAGCTAGAAAGAAACATAGAAA 57.097 30.769 0.00 0.00 0.00 2.52
5215 5751 5.719173 ACATAGAAAGAGAACTGAGCACTC 58.281 41.667 0.00 0.00 0.00 3.51
5237 5773 1.933500 GCACATTGTTCAGCAAGGCAG 60.934 52.381 0.00 0.00 42.07 4.85
5271 5807 2.404995 GCTGGCCACTAGCTGCTTG 61.405 63.158 7.79 8.80 43.05 4.01
5472 6024 0.031585 CGTCGTCCTTGAACCACTGA 59.968 55.000 0.00 0.00 0.00 3.41
5776 6336 1.437772 CTCCGCTGTCGTCTCCGTAT 61.438 60.000 0.00 0.00 35.01 3.06
5783 6343 0.669077 GTCGTCTCCGTATGCTCCAT 59.331 55.000 0.00 0.00 35.01 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.365741 TCTTGAATCTTCAGAAATCTTTGCAC 58.634 34.615 0.00 0.00 38.61 4.57
68 69 1.441515 CGCTACTACGTGCGTGTGT 60.442 57.895 9.58 8.59 46.09 3.72
83 84 3.206150 CATGTTATTTACTCCTGCCGCT 58.794 45.455 0.00 0.00 0.00 5.52
84 85 2.287009 GCATGTTATTTACTCCTGCCGC 60.287 50.000 0.00 0.00 0.00 6.53
85 86 2.942376 TGCATGTTATTTACTCCTGCCG 59.058 45.455 0.00 0.00 31.02 5.69
91 92 6.341316 TCCAGAGTCTGCATGTTATTTACTC 58.659 40.000 15.10 0.00 33.67 2.59
125 128 0.870393 CATTGATGATCCGCCGGAAG 59.130 55.000 11.19 0.00 34.34 3.46
127 130 0.467804 TTCATTGATGATCCGCCGGA 59.532 50.000 8.97 8.97 36.56 5.14
128 131 0.870393 CTTCATTGATGATCCGCCGG 59.130 55.000 0.00 0.00 36.56 6.13
129 132 0.236711 GCTTCATTGATGATCCGCCG 59.763 55.000 3.86 0.00 36.56 6.46
130 133 1.266175 CTGCTTCATTGATGATCCGCC 59.734 52.381 3.86 0.00 36.56 6.13
132 135 1.944709 TGCTGCTTCATTGATGATCCG 59.055 47.619 0.00 0.00 36.56 4.18
177 188 4.830046 AGAGCAGTAGTCTTGACTCTTGAA 59.170 41.667 6.55 0.00 30.52 2.69
178 189 4.402829 AGAGCAGTAGTCTTGACTCTTGA 58.597 43.478 6.55 0.00 30.52 3.02
179 190 4.458989 AGAGAGCAGTAGTCTTGACTCTTG 59.541 45.833 6.55 8.02 34.75 3.02
180 191 4.662278 AGAGAGCAGTAGTCTTGACTCTT 58.338 43.478 6.55 0.00 34.75 2.85
181 192 4.261801 GAGAGAGCAGTAGTCTTGACTCT 58.738 47.826 6.55 0.00 37.21 3.24
182 193 4.006989 TGAGAGAGCAGTAGTCTTGACTC 58.993 47.826 6.55 0.00 0.00 3.36
183 194 4.027674 TGAGAGAGCAGTAGTCTTGACT 57.972 45.455 8.41 8.41 0.00 3.41
184 195 4.981806 ATGAGAGAGCAGTAGTCTTGAC 57.018 45.455 0.00 0.00 0.00 3.18
196 207 6.538444 CGGACTAAAAAGAAAATGAGAGAGC 58.462 40.000 0.00 0.00 0.00 4.09
311 324 8.470805 AGAGTACATTTCATAACGAATCTGACT 58.529 33.333 0.00 0.00 32.32 3.41
355 368 4.913924 CGTGGTACTCAACTACAACACTAC 59.086 45.833 0.00 0.00 39.44 2.73
358 371 3.054878 CCGTGGTACTCAACTACAACAC 58.945 50.000 0.00 0.00 39.44 3.32
360 373 2.064014 GCCGTGGTACTCAACTACAAC 58.936 52.381 0.00 0.00 39.44 3.32
363 376 2.064014 GTTGCCGTGGTACTCAACTAC 58.936 52.381 0.00 0.00 36.72 2.73
365 378 0.599204 CGTTGCCGTGGTACTCAACT 60.599 55.000 0.00 0.00 37.31 3.16
368 381 2.340809 CCGTTGCCGTGGTACTCA 59.659 61.111 0.00 0.00 0.00 3.41
372 385 4.006357 GGACCCGTTGCCGTGGTA 62.006 66.667 0.00 0.00 37.63 3.25
379 392 4.629523 TTGACCCGGACCCGTTGC 62.630 66.667 0.73 0.00 37.81 4.17
390 403 3.616317 CGGGTTTGAAATGGATTTGACCC 60.616 47.826 13.27 13.27 38.87 4.46
402 415 3.893521 AGAAAAGGTCTCGGGTTTGAAA 58.106 40.909 0.00 0.00 0.00 2.69
409 422 2.418884 GGCTAGAAGAAAAGGTCTCGGG 60.419 54.545 0.00 0.00 34.56 5.14
429 442 1.542030 AGTGACTCAACTCTACTGCGG 59.458 52.381 0.00 0.00 0.00 5.69
430 443 2.414824 GGAGTGACTCAACTCTACTGCG 60.415 54.545 15.33 0.00 44.98 5.18
432 445 2.414824 GCGGAGTGACTCAACTCTACTG 60.415 54.545 15.33 0.00 44.98 2.74
451 464 2.375766 GCTTCTGGTGAGTGTCGCG 61.376 63.158 0.00 0.00 0.00 5.87
490 503 5.165961 AGAGTTTATCTGCTTTACTGCCA 57.834 39.130 0.00 0.00 36.69 4.92
510 523 2.626266 TCGGCAGACAGAAAAGTGTAGA 59.374 45.455 0.00 0.00 0.00 2.59
556 569 4.892934 ACAGCTCTTTGGATCTACTCCTAG 59.107 45.833 0.00 0.00 45.21 3.02
557 570 4.873010 ACAGCTCTTTGGATCTACTCCTA 58.127 43.478 0.00 0.00 45.21 2.94
560 573 5.078411 TCAACAGCTCTTTGGATCTACTC 57.922 43.478 5.02 0.00 0.00 2.59
562 575 4.081420 TCCTCAACAGCTCTTTGGATCTAC 60.081 45.833 5.02 0.00 0.00 2.59
564 577 2.909006 TCCTCAACAGCTCTTTGGATCT 59.091 45.455 5.02 0.00 0.00 2.75
565 578 3.340814 TCCTCAACAGCTCTTTGGATC 57.659 47.619 5.02 0.00 0.00 3.36
567 580 3.214328 GTTTCCTCAACAGCTCTTTGGA 58.786 45.455 5.02 0.00 35.18 3.53
568 581 2.031682 CGTTTCCTCAACAGCTCTTTGG 60.032 50.000 5.02 0.00 34.68 3.28
618 763 5.046376 TCTGAATCTCCAAGTGTCTATGCAA 60.046 40.000 0.00 0.00 0.00 4.08
621 766 5.919707 CGATCTGAATCTCCAAGTGTCTATG 59.080 44.000 0.00 0.00 0.00 2.23
627 772 2.606725 GCACGATCTGAATCTCCAAGTG 59.393 50.000 0.00 0.00 0.00 3.16
629 774 1.857217 CGCACGATCTGAATCTCCAAG 59.143 52.381 0.00 0.00 0.00 3.61
632 777 1.764851 CTCGCACGATCTGAATCTCC 58.235 55.000 0.00 0.00 0.00 3.71
656 801 2.980233 GCACCTGCTTTGGTCGCT 60.980 61.111 0.00 0.00 38.45 4.93
657 802 2.533391 GATGCACCTGCTTTGGTCGC 62.533 60.000 0.00 0.00 42.66 5.19
661 806 0.109597 GTTCGATGCACCTGCTTTGG 60.110 55.000 0.00 0.00 42.66 3.28
731 902 4.394712 GGAGTGAGGTGGCCGGTG 62.395 72.222 1.90 0.00 0.00 4.94
739 910 1.609794 GTTCGGGAGGGAGTGAGGT 60.610 63.158 0.00 0.00 0.00 3.85
740 911 2.711922 CGTTCGGGAGGGAGTGAGG 61.712 68.421 0.00 0.00 0.00 3.86
742 913 3.379445 GCGTTCGGGAGGGAGTGA 61.379 66.667 0.00 0.00 0.00 3.41
743 914 3.358076 GAGCGTTCGGGAGGGAGTG 62.358 68.421 0.00 0.00 0.00 3.51
744 915 3.069318 GAGCGTTCGGGAGGGAGT 61.069 66.667 0.00 0.00 0.00 3.85
748 925 2.182030 GTCTGAGCGTTCGGGAGG 59.818 66.667 8.34 0.00 0.00 4.30
754 931 1.006571 TCGGTTGGTCTGAGCGTTC 60.007 57.895 2.07 0.00 38.93 3.95
777 954 2.344203 CGAGGAACGGTCTCTGGCT 61.344 63.158 0.00 0.00 38.46 4.75
888 1067 4.980805 TTCACTCCGTGGCCGTGC 62.981 66.667 0.00 0.00 33.87 5.34
939 1127 2.186903 CTAGGATTGCGCCACGGT 59.813 61.111 4.18 0.00 0.00 4.83
963 1151 0.733223 GCCGTGGAAGAAGACGAGAC 60.733 60.000 0.00 0.00 37.81 3.36
965 1153 1.446272 GGCCGTGGAAGAAGACGAG 60.446 63.158 0.00 0.00 37.81 4.18
970 1158 2.434359 GTCCGGCCGTGGAAGAAG 60.434 66.667 26.12 5.84 40.44 2.85
1073 1261 4.379243 ACTTGCGCGAGGAGGTGG 62.379 66.667 27.88 2.80 40.95 4.61
1304 1495 2.507992 CGAGCTCGGCAACCTCTG 60.508 66.667 28.40 0.00 35.37 3.35
1305 1496 4.443266 GCGAGCTCGGCAACCTCT 62.443 66.667 35.10 0.00 40.23 3.69
1533 1724 1.506718 CTCCTTGCTCGCGACACTA 59.493 57.895 3.71 0.00 0.00 2.74
1535 1726 3.482783 GCTCCTTGCTCGCGACAC 61.483 66.667 3.71 0.00 38.95 3.67
1540 1731 2.308968 ATCCTCTGCTCCTTGCTCGC 62.309 60.000 0.00 0.00 43.37 5.03
1542 1733 1.666054 CAATCCTCTGCTCCTTGCTC 58.334 55.000 0.00 0.00 43.37 4.26
1545 1736 1.094073 CGGCAATCCTCTGCTCCTTG 61.094 60.000 0.00 0.00 42.25 3.61
1548 1739 1.227497 CTCGGCAATCCTCTGCTCC 60.227 63.158 0.00 0.00 42.25 4.70
1673 1870 3.491652 GAACGGGCTTGCTCGCTC 61.492 66.667 15.21 8.71 0.00 5.03
1733 1933 3.622060 TAGGACTTGGGCTTGGCGC 62.622 63.158 0.00 0.00 41.94 6.53
1863 2063 2.111251 GGTATCGGGGGCAGCTTC 59.889 66.667 0.00 0.00 0.00 3.86
2198 2410 2.453521 GGGAGGGAAATTAAACGGCTT 58.546 47.619 0.00 0.00 0.00 4.35
2203 2415 8.089597 TGAAATTAAACGGGAGGGAAATTAAAC 58.910 33.333 0.00 0.00 0.00 2.01
2204 2416 8.191534 TGAAATTAAACGGGAGGGAAATTAAA 57.808 30.769 0.00 0.00 0.00 1.52
2205 2417 7.778185 TGAAATTAAACGGGAGGGAAATTAA 57.222 32.000 0.00 0.00 0.00 1.40
2206 2418 7.964666 ATGAAATTAAACGGGAGGGAAATTA 57.035 32.000 0.00 0.00 0.00 1.40
2233 2491 2.597505 CGCGACGATGATGATTTGGAAC 60.598 50.000 0.00 0.00 0.00 3.62
2234 2492 1.592543 CGCGACGATGATGATTTGGAA 59.407 47.619 0.00 0.00 0.00 3.53
2236 2494 0.383491 GCGCGACGATGATGATTTGG 60.383 55.000 12.10 0.00 0.00 3.28
2255 2517 7.591426 CCTTTTTCGGTTTCAGATTTTGTCTAG 59.409 37.037 0.00 0.00 34.69 2.43
2280 2542 1.572941 GTCGGCTTTCGTGAAACCC 59.427 57.895 0.00 0.00 40.32 4.11
2347 2613 0.179100 CAACCACTCTCATCGGCGAT 60.179 55.000 18.14 18.14 0.00 4.58
2372 2638 2.026014 ACCGCGTGCAAAGCAAAG 59.974 55.556 14.60 6.04 43.29 2.77
2373 2639 2.278466 CACCGCGTGCAAAGCAAA 60.278 55.556 14.60 0.00 43.29 3.68
2436 2702 3.408755 TGTGAGCGTGCACAGTTG 58.591 55.556 18.64 0.81 43.35 3.16
2476 2757 2.052237 GTGTGTTGTTCAGCCGCG 60.052 61.111 0.00 0.00 0.00 6.46
2479 2760 4.829064 TTTATCTGTGTGTTGTTCAGCC 57.171 40.909 0.00 0.00 0.00 4.85
2491 2772 8.777865 TCTTTTCACCTCTGTATTTATCTGTG 57.222 34.615 0.00 0.00 0.00 3.66
2517 2798 3.044894 TGGAAAAAGGCCCATGTTTCTT 58.955 40.909 0.00 0.00 31.94 2.52
2535 2816 0.608308 TCGAGAAAGACGAGCCTGGA 60.608 55.000 0.00 0.00 34.85 3.86
2544 2825 1.073768 GTGGCGAGCTCGAGAAAGAC 61.074 60.000 38.74 18.82 43.02 3.01
2569 2850 0.681243 GGTGGGCTTCTCCATGGAAC 60.681 60.000 17.00 8.91 39.26 3.62
2582 2863 2.032681 GTGTGTGAGGAGGTGGGC 59.967 66.667 0.00 0.00 0.00 5.36
2639 2920 4.855340 ACTGAGTTGAGTTCCTCCAAAAA 58.145 39.130 0.00 0.00 0.00 1.94
2650 2931 7.726033 ATTGTCCTATCTTACTGAGTTGAGT 57.274 36.000 0.00 0.00 0.00 3.41
2660 2941 4.814771 CCCAACCGAATTGTCCTATCTTAC 59.185 45.833 0.00 0.00 36.47 2.34
2725 3012 1.002134 CCGGATCCACTGCAACCTT 60.002 57.895 13.41 0.00 0.00 3.50
2726 3013 2.671070 CCGGATCCACTGCAACCT 59.329 61.111 13.41 0.00 0.00 3.50
2727 3014 2.438434 CCCGGATCCACTGCAACC 60.438 66.667 13.41 0.00 0.00 3.77
2728 3015 0.608035 TTTCCCGGATCCACTGCAAC 60.608 55.000 13.41 0.00 0.00 4.17
2729 3016 0.111446 TTTTCCCGGATCCACTGCAA 59.889 50.000 13.41 0.00 0.00 4.08
2742 3029 3.003793 GTCTGACAAGAGCAACTTTTCCC 59.996 47.826 2.24 0.00 35.25 3.97
2745 3032 3.629398 CCAGTCTGACAAGAGCAACTTTT 59.371 43.478 10.88 0.00 36.61 2.27
2746 3033 3.209410 CCAGTCTGACAAGAGCAACTTT 58.791 45.455 10.88 0.00 36.61 2.66
2748 3035 1.542108 GCCAGTCTGACAAGAGCAACT 60.542 52.381 10.88 0.00 31.37 3.16
2750 3037 0.761187 AGCCAGTCTGACAAGAGCAA 59.239 50.000 10.88 0.00 31.37 3.91
2751 3038 0.319728 GAGCCAGTCTGACAAGAGCA 59.680 55.000 10.88 0.00 31.37 4.26
2752 3039 0.735632 CGAGCCAGTCTGACAAGAGC 60.736 60.000 10.88 6.89 31.37 4.09
2753 3040 0.600557 ACGAGCCAGTCTGACAAGAG 59.399 55.000 10.88 0.00 31.37 2.85
2754 3041 1.813178 CTACGAGCCAGTCTGACAAGA 59.187 52.381 10.88 0.00 0.00 3.02
2781 3084 3.655810 CTCTGGTCAGCGTGCTCCC 62.656 68.421 0.00 0.00 0.00 4.30
2823 3139 3.707611 AGTTGGCACTACCGGTAATGATA 59.292 43.478 26.38 11.05 43.94 2.15
2826 3142 2.006888 CAGTTGGCACTACCGGTAATG 58.993 52.381 18.57 18.57 43.94 1.90
2921 3245 1.082104 CGAAGCAACGGTCAAAGCC 60.082 57.895 0.00 0.00 0.00 4.35
2986 3311 4.125703 GTGGCACATGGTTTGATTTCAAA 58.874 39.130 13.86 1.66 44.52 2.69
3014 3339 6.521151 AAGCATGATCAAGAACTTTTAGGG 57.479 37.500 0.00 0.00 0.00 3.53
3054 3379 5.068591 CCATCAATCCAAGCATGATCAAGAA 59.931 40.000 0.00 0.00 31.65 2.52
3104 3429 0.401738 CCCCCACACATCAGACAGTT 59.598 55.000 0.00 0.00 0.00 3.16
3120 3447 1.077429 GACCTGATCTGCAACCCCC 60.077 63.158 0.00 0.00 0.00 5.40
3288 3615 4.452733 CTTGGGACGACGGAGGGC 62.453 72.222 0.00 0.00 0.00 5.19
3314 3641 2.237392 GTCACCTAGCCCTTGACAAGAT 59.763 50.000 16.99 4.94 39.60 2.40
3321 3648 1.745141 GCATCAGTCACCTAGCCCTTG 60.745 57.143 0.00 0.00 0.00 3.61
3502 3829 3.248495 TGCATCTTCTTGAGAGCAGAG 57.752 47.619 0.00 0.00 37.93 3.35
3566 3894 5.207110 TGCTCATAGGTAGAAGAAGATGC 57.793 43.478 0.00 0.00 0.00 3.91
3590 3918 1.284198 AGGCAGATTGAAGCTGGTCAT 59.716 47.619 12.75 0.00 34.00 3.06
3593 3921 1.353694 AGAAGGCAGATTGAAGCTGGT 59.646 47.619 12.75 0.00 34.00 4.00
3607 3935 3.066814 CAGGGGCAAGCAGAAGGC 61.067 66.667 0.00 0.00 45.30 4.35
3608 3936 1.975407 CACAGGGGCAAGCAGAAGG 60.975 63.158 0.00 0.00 0.00 3.46
3609 3937 2.633509 GCACAGGGGCAAGCAGAAG 61.634 63.158 0.00 0.00 0.00 2.85
3610 3938 2.598394 GCACAGGGGCAAGCAGAA 60.598 61.111 0.00 0.00 0.00 3.02
3620 3948 1.293924 GAACGATGATGAGCACAGGG 58.706 55.000 0.00 0.00 0.00 4.45
3624 3952 2.283298 ACCATGAACGATGATGAGCAC 58.717 47.619 0.00 0.00 33.31 4.40
3625 3953 2.679336 CAACCATGAACGATGATGAGCA 59.321 45.455 0.00 0.00 33.31 4.26
3626 3954 2.679837 ACAACCATGAACGATGATGAGC 59.320 45.455 0.00 0.00 33.31 4.26
3627 3955 4.437794 CCAACAACCATGAACGATGATGAG 60.438 45.833 0.00 0.00 33.31 2.90
3628 3956 3.439825 CCAACAACCATGAACGATGATGA 59.560 43.478 0.00 0.00 33.31 2.92
3629 3957 3.761657 CCAACAACCATGAACGATGATG 58.238 45.455 0.00 0.00 33.31 3.07
3636 3964 1.039856 ACCTGCCAACAACCATGAAC 58.960 50.000 0.00 0.00 0.00 3.18
3708 4036 1.618487 GGATCTGGTACCCTCGGTAG 58.382 60.000 10.07 0.00 39.02 3.18
3795 4123 7.602265 TCGAATGATTGATCTGTTTGTCTGTAA 59.398 33.333 0.00 0.00 0.00 2.41
3853 4181 8.478775 TGTACCTAGTGCATCATTCTATACTT 57.521 34.615 0.00 0.00 0.00 2.24
3877 4205 7.514784 TGATTGATCTATATTGGTGCCTTTG 57.485 36.000 0.00 0.00 0.00 2.77
3878 4206 8.716674 AATGATTGATCTATATTGGTGCCTTT 57.283 30.769 0.00 0.00 0.00 3.11
3909 4237 5.431765 ACCATGTGCCATATAGCTAATAGC 58.568 41.667 3.66 3.66 42.84 2.97
3910 4238 6.882656 AGACCATGTGCCATATAGCTAATAG 58.117 40.000 0.00 0.00 0.00 1.73
3946 4274 3.803082 GCGCCGAAATCAGCAGCA 61.803 61.111 0.00 0.00 0.00 4.41
4045 4374 7.444487 GTCTTTGTTTCAGAAGGTGGTACTATT 59.556 37.037 0.00 0.00 0.00 1.73
4054 4383 2.639065 TGCGTCTTTGTTTCAGAAGGT 58.361 42.857 0.00 0.00 0.00 3.50
4066 4395 3.627577 AGTGTGTTCAGATTTGCGTCTTT 59.372 39.130 0.00 0.00 0.00 2.52
4134 4463 9.705290 GTTTGCCTTTTTGATTAATTTCCTCTA 57.295 29.630 0.00 0.00 0.00 2.43
4147 4476 3.614092 TGCCATTTGTTTGCCTTTTTGA 58.386 36.364 0.00 0.00 0.00 2.69
4260 4591 6.055588 AGATATTGGGTACACTTGCACATAC 58.944 40.000 0.00 0.00 0.00 2.39
4285 4617 2.921069 GCAGCAGCAGTGACAAATGAAG 60.921 50.000 0.00 0.00 41.58 3.02
4297 4629 1.035923 TAGCCTAGTAGCAGCAGCAG 58.964 55.000 3.17 0.00 45.49 4.24
4298 4630 1.485124 TTAGCCTAGTAGCAGCAGCA 58.515 50.000 3.17 0.00 45.49 4.41
4392 4725 4.212214 GGATCATTGCCTAGTTTAAGAGCG 59.788 45.833 0.00 0.00 0.00 5.03
4446 4781 4.816786 TTTGTGCGGTACCTAGAAAAAC 57.183 40.909 10.90 0.00 0.00 2.43
4459 4794 4.433186 TTCATCCAGTTAATTTGTGCGG 57.567 40.909 0.00 0.00 0.00 5.69
4461 4796 5.928264 AGCTTTTCATCCAGTTAATTTGTGC 59.072 36.000 0.00 0.00 0.00 4.57
4500 4847 0.178767 TGACTGTCACTTGCTGCACT 59.821 50.000 6.36 0.00 0.00 4.40
4502 4849 0.815213 GGTGACTGTCACTTGCTGCA 60.815 55.000 32.66 0.00 46.19 4.41
4532 4897 3.025287 ACCGAATGCCATTTTGTTCAC 57.975 42.857 0.00 0.00 0.00 3.18
4563 4928 2.289819 TGATCTGCAGCATCAAGACACA 60.290 45.455 19.88 0.00 0.00 3.72
4694 5059 1.899814 TGGTGTACTCTGAAGGCGAAT 59.100 47.619 0.00 0.00 0.00 3.34
4743 5109 6.636454 AAAATGGGGATAGAGTGAGTGTAA 57.364 37.500 0.00 0.00 0.00 2.41
4764 5131 6.009589 ACATGAATGAGTACCATGTCCAAAA 58.990 36.000 0.00 0.00 45.25 2.44
4765 5132 5.569355 ACATGAATGAGTACCATGTCCAAA 58.431 37.500 0.00 0.00 45.25 3.28
4836 5209 3.521126 CCTTCTCCTTGATCTCCTGGAAA 59.479 47.826 0.00 0.00 0.00 3.13
4955 5329 4.703897 TGAACTTTCCTCTGACAACGAAT 58.296 39.130 0.00 0.00 0.00 3.34
5026 5402 9.155975 GAAGATTTCAGTGAGAGCAAATAAGTA 57.844 33.333 1.45 0.00 0.00 2.24
5031 5407 5.319453 TGGAAGATTTCAGTGAGAGCAAAT 58.681 37.500 1.45 0.00 0.00 2.32
5034 5410 3.580022 TCTGGAAGATTTCAGTGAGAGCA 59.420 43.478 1.45 0.00 38.67 4.26
5036 5412 5.047448 TGACTCTGGAAGATTTCAGTGAGAG 60.047 44.000 9.37 0.00 45.62 3.20
5047 5423 4.384056 CAAACACACTGACTCTGGAAGAT 58.616 43.478 0.00 0.00 45.62 2.40
5060 5436 6.542370 AGTTCACAAGTTATAGCAAACACACT 59.458 34.615 0.00 0.00 0.00 3.55
5085 5461 3.554129 CGCATCCATGTTCTCGGGTATTA 60.554 47.826 0.00 0.00 0.00 0.98
5086 5462 2.806745 CGCATCCATGTTCTCGGGTATT 60.807 50.000 0.00 0.00 0.00 1.89
5087 5463 1.270305 CGCATCCATGTTCTCGGGTAT 60.270 52.381 0.00 0.00 0.00 2.73
5088 5464 0.104120 CGCATCCATGTTCTCGGGTA 59.896 55.000 0.00 0.00 0.00 3.69
5089 5465 1.153369 CGCATCCATGTTCTCGGGT 60.153 57.895 0.00 0.00 0.00 5.28
5091 5467 2.874694 CGCGCATCCATGTTCTCGG 61.875 63.158 8.75 0.00 0.00 4.63
5092 5468 1.217585 ATCGCGCATCCATGTTCTCG 61.218 55.000 8.75 0.00 0.00 4.04
5093 5469 0.510359 GATCGCGCATCCATGTTCTC 59.490 55.000 8.75 0.00 0.00 2.87
5094 5470 0.179076 TGATCGCGCATCCATGTTCT 60.179 50.000 8.75 0.00 0.00 3.01
5095 5471 0.870393 ATGATCGCGCATCCATGTTC 59.130 50.000 8.75 0.00 0.00 3.18
5096 5472 0.589708 CATGATCGCGCATCCATGTT 59.410 50.000 18.80 0.00 0.00 2.71
5097 5473 0.533531 ACATGATCGCGCATCCATGT 60.534 50.000 23.87 23.87 32.65 3.21
5098 5474 0.110373 CACATGATCGCGCATCCATG 60.110 55.000 22.88 22.88 0.00 3.66
5099 5475 0.533531 ACACATGATCGCGCATCCAT 60.534 50.000 8.75 3.70 0.00 3.41
5100 5476 0.103937 TACACATGATCGCGCATCCA 59.896 50.000 8.75 0.93 0.00 3.41
5102 5478 1.770957 TCTACACATGATCGCGCATC 58.229 50.000 8.75 10.45 0.00 3.91
5104 5480 1.066908 TCATCTACACATGATCGCGCA 59.933 47.619 8.75 0.00 0.00 6.09
5106 5482 5.098211 ACATATCATCTACACATGATCGCG 58.902 41.667 0.00 0.00 41.70 5.87
5111 5487 8.810041 AGATAGCAACATATCATCTACACATGA 58.190 33.333 0.00 0.00 37.20 3.07
5113 5489 8.810041 TCAGATAGCAACATATCATCTACACAT 58.190 33.333 0.00 0.00 35.07 3.21
5114 5490 8.181904 TCAGATAGCAACATATCATCTACACA 57.818 34.615 0.00 0.00 35.07 3.72
5130 5506 6.569780 TCTTAGCGTGTAAATTCAGATAGCA 58.430 36.000 0.00 0.00 0.00 3.49
5181 5717 9.430623 AGTTCTCTTTCTATGTTTCTTTCTAGC 57.569 33.333 0.00 0.00 0.00 3.42
5197 5733 2.736192 GCAGAGTGCTCAGTTCTCTTTC 59.264 50.000 1.82 0.00 40.96 2.62
5200 5736 1.000731 GTGCAGAGTGCTCAGTTCTCT 59.999 52.381 0.00 0.00 45.31 3.10
5215 5751 1.933500 GCCTTGCTGAACAATGTGCAG 60.934 52.381 16.89 16.89 41.88 4.41
5262 5798 1.671054 GACCAACGCCAAGCAGCTA 60.671 57.895 0.00 0.00 0.00 3.32
5271 5807 2.677003 CGTGGACATGACCAACGCC 61.677 63.158 18.63 5.55 41.87 5.68
5472 6024 3.017581 AGGGCGGCCAAGATCCTT 61.018 61.111 31.59 3.02 0.00 3.36


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

AutoCloner maintained by Alex Coulton.