Multiple sequence alignment - TraesCS5A01G012300

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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 TraesCS5A01G012300 chr5A 100.000 4337 0 0 1 4337 8061196 8065532 0.000000e+00 8010.0
1 TraesCS5A01G012300 chr5A 86.139 1818 191 28 2003 3782 8112494 8114288 0.000000e+00 1905.0
2 TraesCS5A01G012300 chr5A 85.670 1298 140 23 2514 3790 8074316 8075588 0.000000e+00 1325.0
3 TraesCS5A01G012300 chr5A 90.446 628 49 6 1891 2512 8073652 8074274 0.000000e+00 817.0
4 TraesCS5A01G012300 chr5A 80.546 293 41 9 217 504 8071044 8071325 1.220000e-50 211.0
5 TraesCS5A01G012300 chr5A 85.635 181 17 3 1801 1973 8112321 8112500 9.580000e-42 182.0
6 TraesCS5A01G012300 chr5A 85.841 113 14 2 4075 4185 27236850 27236962 7.620000e-23 119.0
7 TraesCS5A01G012300 chr5B 90.848 2546 173 30 1822 4337 42155281 42152766 0.000000e+00 3356.0
8 TraesCS5A01G012300 chr5B 87.094 2216 211 35 1636 3795 10170506 10168310 0.000000e+00 2438.0
9 TraesCS5A01G012300 chr5B 86.391 1668 121 54 1626 3206 10264522 10262874 0.000000e+00 1725.0
10 TraesCS5A01G012300 chr5B 89.437 994 80 13 3351 4337 10262398 10261423 0.000000e+00 1230.0
11 TraesCS5A01G012300 chr5B 77.494 1213 134 71 122 1248 42156851 42155692 2.230000e-167 599.0
12 TraesCS5A01G012300 chr5B 80.311 579 60 33 409 960 10265847 10265296 5.260000e-104 388.0
13 TraesCS5A01G012300 chr5B 81.760 466 40 17 1313 1775 42155705 42155282 8.930000e-92 348.0
14 TraesCS5A01G012300 chr5B 86.842 266 27 7 4073 4337 42139088 42138830 1.530000e-74 291.0
15 TraesCS5A01G012300 chr5B 87.940 199 18 6 1330 1523 10265014 10264817 3.370000e-56 230.0
16 TraesCS5A01G012300 chr5B 73.343 694 111 41 219 876 10174036 10173381 5.730000e-44 189.0
17 TraesCS5A01G012300 chr5B 98.958 96 0 1 98 192 10266317 10266222 2.070000e-38 171.0
18 TraesCS5A01G012300 chr5B 88.073 109 11 1 4198 4304 10359241 10359349 1.270000e-25 128.0
19 TraesCS5A01G012300 chr5B 76.000 200 30 12 375 572 120574770 120574953 2.150000e-13 87.9
20 TraesCS5A01G012300 chr5B 85.000 80 8 2 1 77 42157036 42156958 1.290000e-10 78.7
21 TraesCS5A01G012300 chr5B 87.037 54 7 0 576 629 394976631 394976684 1.300000e-05 62.1
22 TraesCS5A01G012300 chr5D 89.086 2758 212 49 1631 4337 10042008 10044727 0.000000e+00 3343.0
23 TraesCS5A01G012300 chr5D 87.996 1941 177 27 1891 3795 10067582 10069502 0.000000e+00 2242.0
24 TraesCS5A01G012300 chr5D 87.578 322 26 10 1313 1629 10041327 10041639 1.150000e-95 361.0
25 TraesCS5A01G012300 chr5D 76.569 717 89 41 217 895 10065222 10065897 1.950000e-83 320.0
26 TraesCS5A01G012300 chr5D 88.550 262 20 8 716 970 10040818 10041076 4.210000e-80 309.0
27 TraesCS5A01G012300 chr5D 90.104 192 18 1 3591 3781 503300305 503300496 9.310000e-62 248.0
28 TraesCS5A01G012300 chr5D 93.600 125 8 0 1056 1180 10041167 10041291 2.060000e-43 187.0
29 TraesCS5A01G012300 chr5D 76.261 337 63 14 2167 2489 10469208 10469541 3.470000e-36 163.0
30 TraesCS5A01G012300 chrUn 90.625 192 17 1 3591 3781 469402981 469402790 2.000000e-63 254.0
31 TraesCS5A01G012300 chr3B 90.104 192 18 1 3591 3781 101911782 101911591 9.310000e-62 248.0
32 TraesCS5A01G012300 chr7A 73.924 395 67 19 243 621 367305478 367305104 4.550000e-25 126.0
33 TraesCS5A01G012300 chr1B 86.957 115 11 4 4073 4185 99886178 99886290 4.550000e-25 126.0
34 TraesCS5A01G012300 chr4D 83.846 130 17 3 4057 4185 326379856 326379982 2.120000e-23 121.0
35 TraesCS5A01G012300 chr6B 85.470 117 14 3 4070 4185 630603126 630603012 7.620000e-23 119.0
36 TraesCS5A01G012300 chr1D 83.898 118 17 2 4070 4185 437855383 437855266 1.270000e-20 111.0
37 TraesCS5A01G012300 chr1D 96.721 61 2 0 1251 1311 43000762 43000702 7.670000e-18 102.0
38 TraesCS5A01G012300 chr1D 93.750 64 4 0 1248 1311 480380772 480380709 3.570000e-16 97.1
39 TraesCS5A01G012300 chr4B 96.825 63 1 1 1250 1311 5063501 5063439 2.130000e-18 104.0
40 TraesCS5A01G012300 chr4B 74.011 177 35 6 470 644 38370132 38369965 1.300000e-05 62.1
41 TraesCS5A01G012300 chr7B 96.721 61 2 0 1251 1311 43698827 43698767 7.670000e-18 102.0
42 TraesCS5A01G012300 chr7B 89.189 74 7 1 1239 1311 191901584 191901511 1.660000e-14 91.6
43 TraesCS5A01G012300 chr2D 95.385 65 2 1 1248 1311 11151767 11151831 7.670000e-18 102.0
44 TraesCS5A01G012300 chr2B 96.721 61 1 1 1251 1311 725568731 725568672 2.760000e-17 100.0
45 TraesCS5A01G012300 chr7D 95.161 62 3 0 1251 1312 632039802 632039741 9.930000e-17 99.0
46 TraesCS5A01G012300 chr3D 95.238 63 2 1 1250 1311 134093166 134093104 9.930000e-17 99.0


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 TraesCS5A01G012300 chr5A 8061196 8065532 4336 False 8010.000000 8010 100.0000 1 4337 1 chr5A.!!$F1 4336
1 TraesCS5A01G012300 chr5A 8112321 8114288 1967 False 1043.500000 1905 85.8870 1801 3782 2 chr5A.!!$F4 1981
2 TraesCS5A01G012300 chr5A 8071044 8075588 4544 False 784.333333 1325 85.5540 217 3790 3 chr5A.!!$F3 3573
3 TraesCS5A01G012300 chr5B 10168310 10174036 5726 True 1313.500000 2438 80.2185 219 3795 2 chr5B.!!$R2 3576
4 TraesCS5A01G012300 chr5B 42152766 42157036 4270 True 1095.425000 3356 83.7755 1 4337 4 chr5B.!!$R4 4336
5 TraesCS5A01G012300 chr5B 10261423 10266317 4894 True 748.800000 1725 88.6074 98 4337 5 chr5B.!!$R3 4239
6 TraesCS5A01G012300 chr5D 10065222 10069502 4280 False 1281.000000 2242 82.2825 217 3795 2 chr5D.!!$F4 3578
7 TraesCS5A01G012300 chr5D 10040818 10044727 3909 False 1050.000000 3343 89.7035 716 4337 4 chr5D.!!$F3 3621

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
46 47 0.106519 CCCCCACAGCCTATCCAAAG 60.107 60.0 0.0 0.0 0.00 2.77 F
1088 1917 0.041535 AATCTCCCTTGCCATTGCCA 59.958 50.0 0.0 0.0 36.33 4.92 F
1295 2150 0.034767 CCCAGCCTCTGCATCAGAAA 60.035 55.0 0.0 0.0 40.18 2.52 F
2564 6164 0.396811 GCTAAGTGGTGGTGTGTCCT 59.603 55.0 0.0 0.0 37.07 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 2131 0.034767 TTTCTGATGCAGAGGCTGGG 60.035 55.0 0.00 0.00 41.75 4.45 R
2474 6021 0.034756 TTAGCGACAGAAAGCAGGCA 59.965 50.0 0.00 0.00 35.48 4.75 R
3032 6648 0.804989 CATCGTGTTCCTCCTTTGGC 59.195 55.0 0.00 0.00 0.00 4.52 R
3805 7835 0.038526 AGTACTTCAAGACGGTGCCG 60.039 55.0 9.29 9.29 46.03 5.69 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
33 34 3.347590 CCCCTTCCCTTCCCCCAC 61.348 72.222 0.00 0.00 0.00 4.61
35 36 2.616458 CCCTTCCCTTCCCCCACAG 61.616 68.421 0.00 0.00 0.00 3.66
36 37 2.356667 CTTCCCTTCCCCCACAGC 59.643 66.667 0.00 0.00 0.00 4.40
39 40 2.286121 CCCTTCCCCCACAGCCTA 60.286 66.667 0.00 0.00 0.00 3.93
46 47 0.106519 CCCCCACAGCCTATCCAAAG 60.107 60.000 0.00 0.00 0.00 2.77
47 48 0.918983 CCCCACAGCCTATCCAAAGA 59.081 55.000 0.00 0.00 0.00 2.52
49 50 1.408822 CCCACAGCCTATCCAAAGACC 60.409 57.143 0.00 0.00 0.00 3.85
50 51 1.656652 CACAGCCTATCCAAAGACCG 58.343 55.000 0.00 0.00 0.00 4.79
55 58 2.431057 AGCCTATCCAAAGACCGTACTG 59.569 50.000 0.00 0.00 0.00 2.74
59 62 0.242825 TCCAAAGACCGTACTGCTCG 59.757 55.000 0.00 0.00 0.00 5.03
77 80 2.047560 GGTGAGGTTTCCGTCCCG 60.048 66.667 0.00 0.00 0.00 5.14
79 82 1.080025 GTGAGGTTTCCGTCCCGAG 60.080 63.158 0.00 0.00 0.00 4.63
81 84 3.984200 GAGGTTTCCGTCCCGAGCG 62.984 68.421 0.00 0.00 0.00 5.03
82 85 4.060038 GGTTTCCGTCCCGAGCGA 62.060 66.667 0.00 0.00 0.00 4.93
84 87 4.060038 TTTCCGTCCCGAGCGACC 62.060 66.667 0.00 0.00 0.00 4.79
88 91 4.065281 CGTCCCGAGCGACCCTTT 62.065 66.667 0.00 0.00 0.00 3.11
89 92 2.346365 GTCCCGAGCGACCCTTTT 59.654 61.111 0.00 0.00 0.00 2.27
90 93 1.740664 GTCCCGAGCGACCCTTTTC 60.741 63.158 0.00 0.00 0.00 2.29
92 95 1.448013 CCCGAGCGACCCTTTTCTC 60.448 63.158 0.00 0.00 0.00 2.87
95 98 1.355066 CGAGCGACCCTTTTCTCTGC 61.355 60.000 0.00 0.00 0.00 4.26
96 99 1.355066 GAGCGACCCTTTTCTCTGCG 61.355 60.000 0.00 0.00 0.00 5.18
97 100 3.028366 GCGACCCTTTTCTCTGCGC 62.028 63.158 0.00 0.00 36.12 6.09
98 101 1.374758 CGACCCTTTTCTCTGCGCT 60.375 57.895 9.73 0.00 0.00 5.92
100 103 1.003233 ACCCTTTTCTCTGCGCTCC 60.003 57.895 9.73 0.00 0.00 4.70
207 375 2.058125 TTACGGTGCTTGCTTCCCCA 62.058 55.000 0.00 0.00 0.00 4.96
210 378 2.409870 GGTGCTTGCTTCCCCATCG 61.410 63.158 0.00 0.00 0.00 3.84
238 406 1.677637 GGGACTAGGAGCCACTTCCG 61.678 65.000 0.00 0.00 42.29 4.30
241 409 1.381327 CTAGGAGCCACTTCCGGGA 60.381 63.158 0.00 0.00 42.29 5.14
242 410 1.381327 TAGGAGCCACTTCCGGGAG 60.381 63.158 8.71 8.71 42.29 4.30
293 599 2.095919 GGAAACCGATGAAAACCAGACG 60.096 50.000 0.00 0.00 0.00 4.18
299 608 3.250040 CCGATGAAAACCAGACGAAAACT 59.750 43.478 0.00 0.00 32.90 2.66
302 611 6.311935 CCGATGAAAACCAGACGAAAACTATA 59.688 38.462 0.00 0.00 32.90 1.31
310 620 6.989659 ACCAGACGAAAACTATACTTTGAGA 58.010 36.000 0.00 0.00 0.00 3.27
359 681 6.543430 AATAAGATGTTTTATTGCCCTGCA 57.457 33.333 0.00 0.00 33.24 4.41
406 729 4.393062 ACGTGATGTGAGCTATGAAAAAGG 59.607 41.667 0.00 0.00 0.00 3.11
436 759 4.081406 AGCATTGAATAGTGCCAAACAGA 58.919 39.130 0.00 0.00 42.20 3.41
438 761 5.186409 AGCATTGAATAGTGCCAAACAGAAT 59.814 36.000 0.00 0.00 42.20 2.40
439 762 5.870978 GCATTGAATAGTGCCAAACAGAATT 59.129 36.000 0.00 0.00 35.35 2.17
440 763 7.035004 GCATTGAATAGTGCCAAACAGAATTA 58.965 34.615 0.00 0.00 35.35 1.40
441 764 7.221452 GCATTGAATAGTGCCAAACAGAATTAG 59.779 37.037 0.00 0.00 35.35 1.73
442 765 6.194796 TGAATAGTGCCAAACAGAATTAGC 57.805 37.500 0.00 0.00 0.00 3.09
443 766 4.882671 ATAGTGCCAAACAGAATTAGCG 57.117 40.909 0.00 0.00 0.00 4.26
444 767 2.504367 AGTGCCAAACAGAATTAGCGT 58.496 42.857 0.00 0.00 0.00 5.07
457 780 6.649141 ACAGAATTAGCGTTGTCACTATTCAA 59.351 34.615 0.00 0.00 0.00 2.69
458 781 7.334421 ACAGAATTAGCGTTGTCACTATTCAAT 59.666 33.333 0.00 0.00 0.00 2.57
459 782 8.177663 CAGAATTAGCGTTGTCACTATTCAATT 58.822 33.333 0.00 0.00 0.00 2.32
460 783 8.391106 AGAATTAGCGTTGTCACTATTCAATTC 58.609 33.333 0.00 0.00 0.00 2.17
461 784 7.609760 ATTAGCGTTGTCACTATTCAATTCA 57.390 32.000 0.00 0.00 0.00 2.57
462 785 5.940192 AGCGTTGTCACTATTCAATTCAA 57.060 34.783 0.00 0.00 0.00 2.69
491 817 1.880340 GTCTTCTCCATGGCTCGCG 60.880 63.158 6.96 0.00 0.00 5.87
507 833 2.195096 TCGCGTCCCGTAATATGTTTG 58.805 47.619 5.77 0.00 38.35 2.93
510 836 3.181518 CGCGTCCCGTAATATGTTTGTTT 60.182 43.478 0.00 0.00 0.00 2.83
514 840 5.505446 CGTCCCGTAATATGTTTGTTTTTCG 59.495 40.000 0.00 0.00 0.00 3.46
515 841 6.601264 GTCCCGTAATATGTTTGTTTTTCGA 58.399 36.000 0.00 0.00 0.00 3.71
516 842 7.245604 GTCCCGTAATATGTTTGTTTTTCGAT 58.754 34.615 0.00 0.00 0.00 3.59
517 843 7.217447 GTCCCGTAATATGTTTGTTTTTCGATG 59.783 37.037 0.00 0.00 0.00 3.84
518 844 6.470877 CCCGTAATATGTTTGTTTTTCGATGG 59.529 38.462 0.00 0.00 0.00 3.51
521 847 7.960738 CGTAATATGTTTGTTTTTCGATGGAGT 59.039 33.333 0.00 0.00 0.00 3.85
531 1129 5.611796 TTTTCGATGGAGTTTCACATGAG 57.388 39.130 0.00 0.00 0.00 2.90
540 1138 5.869344 TGGAGTTTCACATGAGAATAGAACG 59.131 40.000 6.40 0.00 0.00 3.95
543 1141 5.573282 AGTTTCACATGAGAATAGAACGTCG 59.427 40.000 6.40 0.00 0.00 5.12
604 1211 8.626526 TCTGGAACTTTTAAGTATGGTTTTCAC 58.373 33.333 0.00 0.00 38.57 3.18
629 1238 9.150348 ACGAAGTTTTCTTTGAATGTTGATTTT 57.850 25.926 0.00 0.00 37.78 1.82
631 1240 9.920826 GAAGTTTTCTTTGAATGTTGATTTTCC 57.079 29.630 0.00 0.00 40.61 3.13
651 1260 9.712305 ATTTTCCTATGATATTGTCTACTTCCG 57.288 33.333 0.00 0.00 0.00 4.30
652 1261 7.834881 TTCCTATGATATTGTCTACTTCCGT 57.165 36.000 0.00 0.00 0.00 4.69
654 1263 6.208797 TCCTATGATATTGTCTACTTCCGTGG 59.791 42.308 0.00 0.00 0.00 4.94
658 1267 0.753867 TTGTCTACTTCCGTGGCACA 59.246 50.000 19.09 0.00 0.00 4.57
659 1268 0.753867 TGTCTACTTCCGTGGCACAA 59.246 50.000 19.09 4.25 44.16 3.33
661 1270 2.563620 TGTCTACTTCCGTGGCACAATA 59.436 45.455 19.09 0.00 44.16 1.90
743 1377 7.934855 TTTCGTACTCTCCTATGAGTAACTT 57.065 36.000 6.03 0.00 46.91 2.66
747 1381 3.707102 ACTCTCCTATGAGTAACTTGGCC 59.293 47.826 0.00 0.00 44.53 5.36
762 1400 4.198087 GCCTCTGCCCCTTTTTGT 57.802 55.556 0.00 0.00 0.00 2.83
769 1407 3.044894 TCTGCCCCTTTTTGTGGAAAAT 58.955 40.909 0.00 0.00 36.68 1.82
820 1462 0.248866 CTTTTTGGTGTGGCGTGGTC 60.249 55.000 0.00 0.00 0.00 4.02
821 1463 0.681564 TTTTTGGTGTGGCGTGGTCT 60.682 50.000 0.00 0.00 0.00 3.85
822 1464 1.380403 TTTTGGTGTGGCGTGGTCTG 61.380 55.000 0.00 0.00 0.00 3.51
823 1465 2.544590 TTTGGTGTGGCGTGGTCTGT 62.545 55.000 0.00 0.00 0.00 3.41
824 1466 2.665185 GGTGTGGCGTGGTCTGTC 60.665 66.667 0.00 0.00 0.00 3.51
833 1475 1.293963 CGTGGTCTGTCTGGCACATG 61.294 60.000 0.00 0.00 38.20 3.21
936 1623 2.233271 CACCAGTGCCAAAATCTGTCT 58.767 47.619 0.00 0.00 0.00 3.41
937 1624 2.030540 CACCAGTGCCAAAATCTGTCTG 60.031 50.000 0.00 0.00 0.00 3.51
944 1631 2.362077 GCCAAAATCTGTCTGTGTGGTT 59.638 45.455 0.00 0.00 0.00 3.67
978 1690 4.463515 CATCACATGCATGCAGTAGTAC 57.536 45.455 26.69 0.00 0.00 2.73
1012 1724 1.197721 GCAAATCTGTCACGGACAAGG 59.802 52.381 7.90 0.00 42.26 3.61
1013 1725 1.197721 CAAATCTGTCACGGACAAGGC 59.802 52.381 7.90 0.00 42.26 4.35
1028 1745 2.686835 GGCAGGCCCTCTCACTCT 60.687 66.667 0.00 0.00 0.00 3.24
1042 1759 5.602145 CCTCTCACTCTTCTCCTATCCATTT 59.398 44.000 0.00 0.00 0.00 2.32
1052 1769 4.104897 TCTCCTATCCATTTCTCCTCTCGA 59.895 45.833 0.00 0.00 0.00 4.04
1088 1917 0.041535 AATCTCCCTTGCCATTGCCA 59.958 50.000 0.00 0.00 36.33 4.92
1120 1949 0.340208 TCCTCTTCCCTTCTCTCCCC 59.660 60.000 0.00 0.00 0.00 4.81
1121 1950 1.045911 CCTCTTCCCTTCTCTCCCCG 61.046 65.000 0.00 0.00 0.00 5.73
1122 1951 1.681486 CTCTTCCCTTCTCTCCCCGC 61.681 65.000 0.00 0.00 0.00 6.13
1123 1952 3.075005 TTCCCTTCTCTCCCCGCG 61.075 66.667 0.00 0.00 0.00 6.46
1220 2075 0.251386 TGCTTGATTTGGGCCGGTTA 60.251 50.000 1.90 0.00 0.00 2.85
1224 2079 1.377594 GATTTGGGCCGGTTACCGT 60.378 57.895 22.78 1.30 46.80 4.83
1225 2080 1.371337 GATTTGGGCCGGTTACCGTC 61.371 60.000 22.78 10.10 46.80 4.79
1226 2081 3.880162 TTTGGGCCGGTTACCGTCG 62.880 63.158 22.78 9.34 46.80 5.12
1232 2087 1.297893 CCGGTTACCGTCGATCGAC 60.298 63.158 33.22 33.22 46.80 4.20
1242 2097 1.264557 CGTCGATCGACTTGGAGCTAT 59.735 52.381 37.12 0.00 42.54 2.97
1243 2098 2.479275 CGTCGATCGACTTGGAGCTATA 59.521 50.000 37.12 3.48 42.54 1.31
1244 2099 3.059120 CGTCGATCGACTTGGAGCTATAA 60.059 47.826 37.12 3.03 42.54 0.98
1246 2101 3.059120 TCGATCGACTTGGAGCTATAACG 60.059 47.826 15.15 0.00 0.00 3.18
1248 2103 3.416119 TCGACTTGGAGCTATAACGTG 57.584 47.619 0.00 0.00 0.00 4.49
1249 2104 2.751259 TCGACTTGGAGCTATAACGTGT 59.249 45.455 0.00 0.00 0.00 4.49
1250 2105 3.192001 TCGACTTGGAGCTATAACGTGTT 59.808 43.478 0.00 0.00 0.00 3.32
1253 2108 5.107220 CGACTTGGAGCTATAACGTGTTTTT 60.107 40.000 0.00 0.00 0.00 1.94
1288 2143 1.340991 GGTTTTATCCCAGCCTCTGCA 60.341 52.381 0.00 0.00 41.13 4.41
1289 2144 2.659428 GTTTTATCCCAGCCTCTGCAT 58.341 47.619 0.00 0.00 41.13 3.96
1291 2146 1.510492 TTATCCCAGCCTCTGCATCA 58.490 50.000 0.00 0.00 41.13 3.07
1292 2147 1.054231 TATCCCAGCCTCTGCATCAG 58.946 55.000 0.00 0.00 41.13 2.90
1293 2148 0.693430 ATCCCAGCCTCTGCATCAGA 60.693 55.000 0.00 0.00 41.13 3.27
1295 2150 0.034767 CCCAGCCTCTGCATCAGAAA 60.035 55.000 0.00 0.00 40.18 2.52
1296 2151 1.380524 CCAGCCTCTGCATCAGAAAG 58.619 55.000 0.00 0.00 40.18 2.62
1297 2152 1.065636 CCAGCCTCTGCATCAGAAAGA 60.066 52.381 0.00 0.00 40.18 2.52
1298 2153 2.421670 CCAGCCTCTGCATCAGAAAGAT 60.422 50.000 0.00 0.00 40.18 2.40
1307 2162 3.532892 CATCAGAAAGATGCATACGGC 57.467 47.619 0.00 0.00 46.90 5.68
1308 2163 2.988010 TCAGAAAGATGCATACGGCT 57.012 45.000 0.00 0.00 45.15 5.52
1309 2164 2.826428 TCAGAAAGATGCATACGGCTC 58.174 47.619 0.00 0.00 45.15 4.70
1310 2165 2.168313 TCAGAAAGATGCATACGGCTCA 59.832 45.455 0.00 0.00 45.15 4.26
1311 2166 2.938451 CAGAAAGATGCATACGGCTCAA 59.062 45.455 0.00 0.00 45.15 3.02
1416 4196 1.732259 CGGGAGATTGGTTTCAGTTCG 59.268 52.381 0.00 0.00 0.00 3.95
1417 4197 2.084546 GGGAGATTGGTTTCAGTTCGG 58.915 52.381 0.00 0.00 0.00 4.30
1429 4209 1.093496 CAGTTCGGTTTATCCCCGCC 61.093 60.000 0.00 0.00 45.09 6.13
1486 4268 9.237187 TGATTATTTGCTGATTTAAGTGTGGTA 57.763 29.630 0.00 0.00 0.00 3.25
1491 4273 8.810652 TTTGCTGATTTAAGTGTGGTATTTTC 57.189 30.769 0.00 0.00 0.00 2.29
1492 4274 6.607689 TGCTGATTTAAGTGTGGTATTTTCG 58.392 36.000 0.00 0.00 0.00 3.46
1551 4342 2.268076 CCGGTCAACAAAGGGGCTG 61.268 63.158 0.00 0.00 0.00 4.85
1574 4365 3.705579 CACAGCCCCCATTTTCATTATGA 59.294 43.478 0.00 0.00 0.00 2.15
1632 5088 6.169094 CCATTGAGATCATACATCCCTGTAC 58.831 44.000 0.00 0.00 40.57 2.90
1656 5112 1.008538 GGCAACAAAGACACCGCTG 60.009 57.895 0.00 0.00 0.00 5.18
1661 5117 1.156736 ACAAAGACACCGCTGCATAC 58.843 50.000 0.00 0.00 0.00 2.39
1667 5123 1.014044 ACACCGCTGCATACAACTCG 61.014 55.000 0.00 0.00 0.00 4.18
1668 5125 2.100631 ACCGCTGCATACAACTCGC 61.101 57.895 0.00 0.00 0.00 5.03
1674 5131 3.109230 CTGCATACAACTCGCAGTTTC 57.891 47.619 0.00 0.00 46.36 2.78
1687 5144 1.074775 AGTTTCCGCCATGCTTGGA 59.925 52.632 22.21 0.00 46.92 3.53
1840 5312 0.975887 AACAATGTGGGTGGCAATCC 59.024 50.000 0.00 0.00 0.00 3.01
1866 5338 4.279326 GAGGTAGCCCATCCTCGT 57.721 61.111 0.00 0.00 40.36 4.18
1950 5458 3.194861 TGCGACAATGCACTATCTAACC 58.805 45.455 0.00 0.00 40.62 2.85
1979 5487 5.356190 TGTTCCGATTAGTAGTGAGATCGTT 59.644 40.000 0.00 0.00 39.63 3.85
1980 5488 6.127814 TGTTCCGATTAGTAGTGAGATCGTTT 60.128 38.462 0.00 0.00 39.63 3.60
2146 5688 7.068226 GCTATCTCTTTCTCACTCTAACCTTCT 59.932 40.741 0.00 0.00 0.00 2.85
2160 5703 6.248433 TCTAACCTTCTGCCAAGATTTCAAT 58.752 36.000 0.00 0.00 30.72 2.57
2472 6019 6.687081 TTTGGTTATTCACAACCCGATATC 57.313 37.500 2.73 0.00 46.29 1.63
2474 6021 4.410883 TGGTTATTCACAACCCGATATCCT 59.589 41.667 0.00 0.00 46.29 3.24
2507 6085 7.482654 TCTGTCGCTAATCAAGGAAAATATG 57.517 36.000 0.00 0.00 0.00 1.78
2564 6164 0.396811 GCTAAGTGGTGGTGTGTCCT 59.603 55.000 0.00 0.00 37.07 3.85
2698 6302 1.408969 TATGGTCTCTACGCCATGCA 58.591 50.000 6.35 0.00 44.43 3.96
2793 6397 3.118542 CTCTGCAAAGAAAACTGTTGGC 58.881 45.455 0.00 0.00 0.00 4.52
2952 6568 4.952335 CCTCCTTTTGTGCCATCTAAAGAT 59.048 41.667 0.00 0.00 34.10 2.40
2979 6595 2.583441 CGGTTCTGCTCCTCCACCA 61.583 63.158 0.00 0.00 0.00 4.17
3013 6629 1.879575 AGGTTAGCTCTGCCACCATA 58.120 50.000 0.00 0.00 35.54 2.74
3032 6648 1.915141 AGCATGGTTGTCTTTCCCTG 58.085 50.000 0.00 0.00 0.00 4.45
3161 6777 9.741647 AAGTCATGAGAAAGAATTCAAAAGTTC 57.258 29.630 8.44 3.44 38.06 3.01
3293 7302 2.917971 GTCACTCATGTGCGTCTCTTAC 59.082 50.000 0.00 0.00 43.49 2.34
3315 7337 2.867109 CCATTGGGTCTGTTCTCACT 57.133 50.000 0.00 0.00 0.00 3.41
3400 7423 6.672266 ATATCTATTGAACCGAGTGTCCAT 57.328 37.500 0.00 0.00 0.00 3.41
3404 7427 6.280643 TCTATTGAACCGAGTGTCCATATTG 58.719 40.000 0.00 0.00 0.00 1.90
3431 7454 0.678395 TTTACACCGTTGCGTCCCTA 59.322 50.000 0.00 0.00 0.00 3.53
3546 7571 5.063438 CCCTCTGAAACAACATATGTGTACG 59.937 44.000 9.63 1.36 42.99 3.67
3548 7573 6.401047 CCTCTGAAACAACATATGTGTACGTG 60.401 42.308 9.63 6.03 42.99 4.49
3550 7575 5.057819 TGAAACAACATATGTGTACGTGGT 58.942 37.500 9.63 0.00 42.99 4.16
3553 7578 4.497300 ACAACATATGTGTACGTGGTACC 58.503 43.478 9.63 4.43 41.93 3.34
3574 7599 0.179023 TTGTTTGGTGTACCCCCGTC 60.179 55.000 0.00 0.00 34.29 4.79
3580 7605 2.285069 TGTACCCCCGTCCAGCAT 60.285 61.111 0.00 0.00 0.00 3.79
3606 7631 1.542472 TGGCAGATTGACATGCACTTG 59.458 47.619 0.00 0.00 44.37 3.16
3797 7827 3.196207 TTGCTCTCCCAGTGTGCCC 62.196 63.158 0.00 0.00 0.00 5.36
3800 7830 1.298014 CTCTCCCAGTGTGCCCTTC 59.702 63.158 0.00 0.00 0.00 3.46
3805 7835 1.302832 CCAGTGTGCCCTTCCTGAC 60.303 63.158 0.00 0.00 0.00 3.51
3864 7902 6.147821 CACAGTTTTATTCCTTCGTGATGACT 59.852 38.462 0.00 0.00 0.00 3.41
3865 7903 6.369065 ACAGTTTTATTCCTTCGTGATGACTC 59.631 38.462 0.00 0.00 0.00 3.36
3866 7904 5.577164 AGTTTTATTCCTTCGTGATGACTCG 59.423 40.000 0.00 0.00 34.87 4.18
3867 7905 4.713824 TTATTCCTTCGTGATGACTCGT 57.286 40.909 0.00 0.00 35.08 4.18
3868 7906 3.594603 ATTCCTTCGTGATGACTCGTT 57.405 42.857 0.00 0.00 35.08 3.85
3869 7907 4.713824 ATTCCTTCGTGATGACTCGTTA 57.286 40.909 0.00 0.00 35.08 3.18
3870 7908 4.508461 TTCCTTCGTGATGACTCGTTAA 57.492 40.909 0.00 0.00 35.08 2.01
3871 7909 3.829948 TCCTTCGTGATGACTCGTTAAC 58.170 45.455 0.00 0.00 35.08 2.01
3872 7910 3.253921 TCCTTCGTGATGACTCGTTAACA 59.746 43.478 6.39 0.00 35.08 2.41
3911 7949 3.222603 CTTCAAGTGGTGCCTTAGGTTT 58.777 45.455 0.00 0.00 0.00 3.27
3929 7970 8.718102 TTAGGTTTCTATGTGTAGATTGCTTC 57.282 34.615 0.00 0.00 36.84 3.86
3998 8039 3.950397 TGTATGGGTTGAACTGGATGTC 58.050 45.455 0.00 0.00 0.00 3.06
4216 8266 6.549433 AATAAAAATCTGTGCATGGATGGT 57.451 33.333 0.00 0.00 0.00 3.55
4219 8269 6.549433 AAAAATCTGTGCATGGATGGTAAT 57.451 33.333 0.00 0.00 0.00 1.89
4233 8283 5.989168 TGGATGGTAATAACGAGTGCATTAG 59.011 40.000 0.00 0.00 0.00 1.73
4326 8376 5.065474 GCAAAAACTACATATCACGCCCTAA 59.935 40.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.431057 AGTACGGTCTTTGGATAGGCTG 59.569 50.000 0.00 0.00 32.33 4.85
35 36 2.822764 CAGTACGGTCTTTGGATAGGC 58.177 52.381 0.00 0.00 0.00 3.93
36 37 2.431057 AGCAGTACGGTCTTTGGATAGG 59.569 50.000 0.00 0.00 0.00 2.57
39 40 1.135083 CGAGCAGTACGGTCTTTGGAT 60.135 52.381 12.62 0.00 40.13 3.41
49 50 1.874345 AACCTCACCCGAGCAGTACG 61.874 60.000 0.00 0.00 38.00 3.67
50 51 0.320697 AAACCTCACCCGAGCAGTAC 59.679 55.000 0.00 0.00 38.00 2.73
55 58 2.434359 CGGAAACCTCACCCGAGC 60.434 66.667 0.00 0.00 45.58 5.03
59 62 2.350134 GGGACGGAAACCTCACCC 59.650 66.667 0.00 0.00 0.00 4.61
77 80 1.355066 CGCAGAGAAAAGGGTCGCTC 61.355 60.000 0.00 0.00 0.00 5.03
79 82 3.028366 GCGCAGAGAAAAGGGTCGC 62.028 63.158 0.30 0.00 0.00 5.19
81 84 1.021920 GGAGCGCAGAGAAAAGGGTC 61.022 60.000 11.47 0.00 0.00 4.46
82 85 1.003233 GGAGCGCAGAGAAAAGGGT 60.003 57.895 11.47 0.00 0.00 4.34
84 87 1.746991 GGGGAGCGCAGAGAAAAGG 60.747 63.158 11.47 0.00 0.00 3.11
85 88 0.322008 AAGGGGAGCGCAGAGAAAAG 60.322 55.000 11.47 0.00 0.00 2.27
86 89 0.110486 AAAGGGGAGCGCAGAGAAAA 59.890 50.000 11.47 0.00 0.00 2.29
87 90 0.321653 GAAAGGGGAGCGCAGAGAAA 60.322 55.000 11.47 0.00 0.00 2.52
88 91 1.194781 AGAAAGGGGAGCGCAGAGAA 61.195 55.000 11.47 0.00 0.00 2.87
89 92 1.608717 GAGAAAGGGGAGCGCAGAGA 61.609 60.000 11.47 0.00 0.00 3.10
90 93 1.153469 GAGAAAGGGGAGCGCAGAG 60.153 63.158 11.47 0.00 0.00 3.35
92 95 1.449246 CAGAGAAAGGGGAGCGCAG 60.449 63.158 11.47 0.00 0.00 5.18
95 98 0.103937 CTAGCAGAGAAAGGGGAGCG 59.896 60.000 0.00 0.00 0.00 5.03
96 99 1.412343 CTCTAGCAGAGAAAGGGGAGC 59.588 57.143 7.22 0.00 45.07 4.70
97 100 1.412343 GCTCTAGCAGAGAAAGGGGAG 59.588 57.143 14.86 0.00 45.07 4.30
98 101 1.007721 AGCTCTAGCAGAGAAAGGGGA 59.992 52.381 14.86 0.00 45.07 4.81
100 103 3.295973 ACTAGCTCTAGCAGAGAAAGGG 58.704 50.000 14.86 4.83 45.07 3.95
210 378 1.337387 GCTCCTAGTCCCGTCACATAC 59.663 57.143 0.00 0.00 0.00 2.39
238 406 3.491766 TGTATGATATCCTCCCCTCCC 57.508 52.381 0.00 0.00 0.00 4.30
241 409 5.435041 TGGTTTTTGTATGATATCCTCCCCT 59.565 40.000 0.00 0.00 0.00 4.79
242 410 5.701224 TGGTTTTTGTATGATATCCTCCCC 58.299 41.667 0.00 0.00 0.00 4.81
355 677 6.073873 TGTGTTTGAGTTTGAAAGTTTTGCAG 60.074 34.615 0.00 0.00 0.00 4.41
359 681 8.643752 CGTAATGTGTTTGAGTTTGAAAGTTTT 58.356 29.630 0.00 0.00 0.00 2.43
363 685 7.136954 CACGTAATGTGTTTGAGTTTGAAAG 57.863 36.000 0.00 0.00 43.88 2.62
406 729 5.811613 TGGCACTATTCAATGCTAATTTTGC 59.188 36.000 0.00 0.00 41.74 3.68
436 759 8.039603 TGAATTGAATAGTGACAACGCTAATT 57.960 30.769 0.00 0.00 41.48 1.40
438 761 7.428282 TTGAATTGAATAGTGACAACGCTAA 57.572 32.000 0.00 0.00 41.48 3.09
439 762 7.463544 CATTGAATTGAATAGTGACAACGCTA 58.536 34.615 0.00 0.00 42.19 4.26
440 763 5.940192 TTGAATTGAATAGTGACAACGCT 57.060 34.783 0.00 0.00 40.21 5.07
441 764 5.003778 GCATTGAATTGAATAGTGACAACGC 59.996 40.000 0.00 0.00 0.00 4.84
442 765 6.249893 CAGCATTGAATTGAATAGTGACAACG 59.750 38.462 0.00 0.00 0.00 4.10
443 766 7.307694 TCAGCATTGAATTGAATAGTGACAAC 58.692 34.615 0.00 0.00 0.00 3.32
444 767 7.451501 TCAGCATTGAATTGAATAGTGACAA 57.548 32.000 0.00 0.00 0.00 3.18
458 781 5.535783 TGGAGAAGACAAATTCAGCATTGAA 59.464 36.000 0.00 0.00 46.67 2.69
459 782 5.072055 TGGAGAAGACAAATTCAGCATTGA 58.928 37.500 0.00 0.00 0.00 2.57
460 783 5.381174 TGGAGAAGACAAATTCAGCATTG 57.619 39.130 0.00 0.00 0.00 2.82
461 784 5.105473 CCATGGAGAAGACAAATTCAGCATT 60.105 40.000 5.56 0.00 0.00 3.56
462 785 4.401519 CCATGGAGAAGACAAATTCAGCAT 59.598 41.667 5.56 0.00 0.00 3.79
478 804 4.899239 GGGACGCGAGCCATGGAG 62.899 72.222 18.40 6.95 0.00 3.86
491 817 6.601264 TCGAAAAACAAACATATTACGGGAC 58.399 36.000 0.00 0.00 0.00 4.46
507 833 5.757886 TCATGTGAAACTCCATCGAAAAAC 58.242 37.500 0.00 0.00 38.04 2.43
510 836 4.893608 TCTCATGTGAAACTCCATCGAAA 58.106 39.130 0.00 0.00 38.04 3.46
514 840 7.254252 CGTTCTATTCTCATGTGAAACTCCATC 60.254 40.741 13.74 2.65 38.04 3.51
515 841 6.536582 CGTTCTATTCTCATGTGAAACTCCAT 59.463 38.462 13.74 0.06 38.04 3.41
516 842 5.869344 CGTTCTATTCTCATGTGAAACTCCA 59.131 40.000 13.74 0.00 38.04 3.86
517 843 5.869888 ACGTTCTATTCTCATGTGAAACTCC 59.130 40.000 13.74 2.07 38.04 3.85
518 844 6.237332 CGACGTTCTATTCTCATGTGAAACTC 60.237 42.308 13.74 6.79 38.04 3.01
521 847 5.466819 ACGACGTTCTATTCTCATGTGAAA 58.533 37.500 13.74 3.92 0.00 2.69
531 1129 7.044183 GGATGTTAAGAAGACGACGTTCTATTC 60.044 40.741 0.13 5.13 32.93 1.75
540 1138 7.787725 AAATATGGGATGTTAAGAAGACGAC 57.212 36.000 0.00 0.00 0.00 4.34
571 1177 9.292195 CCATACTTAAAAGTTCCAGAAAACCTA 57.708 33.333 0.00 0.00 40.37 3.08
573 1179 7.948357 ACCATACTTAAAAGTTCCAGAAAACC 58.052 34.615 0.00 0.00 40.37 3.27
574 1180 9.811995 AAACCATACTTAAAAGTTCCAGAAAAC 57.188 29.630 0.00 0.00 40.37 2.43
577 1183 9.191479 TGAAAACCATACTTAAAAGTTCCAGAA 57.809 29.630 0.00 0.00 40.37 3.02
578 1184 8.626526 GTGAAAACCATACTTAAAAGTTCCAGA 58.373 33.333 0.00 0.00 40.37 3.86
579 1185 7.589954 CGTGAAAACCATACTTAAAAGTTCCAG 59.410 37.037 0.00 0.00 40.37 3.86
580 1186 7.282675 TCGTGAAAACCATACTTAAAAGTTCCA 59.717 33.333 0.00 0.00 40.37 3.53
581 1187 7.641760 TCGTGAAAACCATACTTAAAAGTTCC 58.358 34.615 0.00 0.00 40.37 3.62
582 1188 9.166126 CTTCGTGAAAACCATACTTAAAAGTTC 57.834 33.333 0.00 0.00 40.37 3.01
589 1195 8.441312 AGAAAACTTCGTGAAAACCATACTTA 57.559 30.769 0.00 0.00 34.02 2.24
592 1198 7.698970 TCAAAGAAAACTTCGTGAAAACCATAC 59.301 33.333 0.00 0.00 34.02 2.39
594 1200 6.626302 TCAAAGAAAACTTCGTGAAAACCAT 58.374 32.000 0.00 0.00 34.02 3.55
602 1209 7.684062 ATCAACATTCAAAGAAAACTTCGTG 57.316 32.000 0.00 0.00 34.02 4.35
604 1211 9.623687 GAAAATCAACATTCAAAGAAAACTTCG 57.376 29.630 0.00 0.00 34.02 3.79
651 1260 1.200020 GCCACAGTTCTATTGTGCCAC 59.800 52.381 0.03 0.00 43.50 5.01
652 1261 1.073763 AGCCACAGTTCTATTGTGCCA 59.926 47.619 0.03 0.00 43.50 4.92
654 1263 2.554032 ACAAGCCACAGTTCTATTGTGC 59.446 45.455 0.03 0.00 43.50 4.57
658 1267 4.036734 CACAACACAAGCCACAGTTCTATT 59.963 41.667 0.00 0.00 0.00 1.73
659 1268 3.565482 CACAACACAAGCCACAGTTCTAT 59.435 43.478 0.00 0.00 0.00 1.98
661 1270 1.745087 CACAACACAAGCCACAGTTCT 59.255 47.619 0.00 0.00 0.00 3.01
702 1332 5.883503 ACGAAAAATAGAAATTACGGGCA 57.116 34.783 0.00 0.00 0.00 5.36
704 1334 8.416485 AGAGTACGAAAAATAGAAATTACGGG 57.584 34.615 0.00 0.00 0.00 5.28
747 1381 1.703411 TTCCACAAAAAGGGGCAGAG 58.297 50.000 0.00 0.00 42.23 3.35
760 1398 6.485313 ACACGAGATTCACTTTATTTTCCACA 59.515 34.615 0.00 0.00 0.00 4.17
762 1400 7.504924 AACACGAGATTCACTTTATTTTCCA 57.495 32.000 0.00 0.00 0.00 3.53
769 1407 4.624015 ACCGAAACACGAGATTCACTTTA 58.376 39.130 3.98 0.00 45.77 1.85
814 1456 1.004560 ATGTGCCAGACAGACCACG 60.005 57.895 0.00 0.00 38.23 4.94
820 1462 2.747822 GCGCTCATGTGCCAGACAG 61.748 63.158 13.81 0.43 43.34 3.51
821 1463 2.743538 GCGCTCATGTGCCAGACA 60.744 61.111 13.81 0.00 43.34 3.41
936 1623 2.617788 GCAGGATCCATACAACCACACA 60.618 50.000 15.82 0.00 0.00 3.72
937 1624 2.017049 GCAGGATCCATACAACCACAC 58.983 52.381 15.82 0.00 0.00 3.82
944 1631 3.746940 CATGTGATGCAGGATCCATACA 58.253 45.455 15.82 9.21 0.00 2.29
973 1685 6.558771 TTTGCGTGAAGTAGTACTGTACTA 57.441 37.500 20.74 20.74 40.14 1.82
974 1686 5.443185 TTTGCGTGAAGTAGTACTGTACT 57.557 39.130 22.72 22.72 42.68 2.73
975 1687 6.033619 CAGATTTGCGTGAAGTAGTACTGTAC 59.966 42.308 9.93 9.93 0.00 2.90
976 1688 6.090783 CAGATTTGCGTGAAGTAGTACTGTA 58.909 40.000 5.39 0.00 0.00 2.74
977 1689 4.923871 CAGATTTGCGTGAAGTAGTACTGT 59.076 41.667 5.39 0.00 0.00 3.55
978 1690 4.923871 ACAGATTTGCGTGAAGTAGTACTG 59.076 41.667 5.39 0.00 0.00 2.74
991 1703 0.865111 TTGTCCGTGACAGATTTGCG 59.135 50.000 6.79 0.00 43.69 4.85
993 1705 1.197721 GCCTTGTCCGTGACAGATTTG 59.802 52.381 6.79 0.00 43.69 2.32
1012 1724 1.220477 GAAGAGTGAGAGGGCCTGC 59.780 63.158 12.95 2.77 0.00 4.85
1013 1725 0.823460 GAGAAGAGTGAGAGGGCCTG 59.177 60.000 12.95 0.00 0.00 4.85
1028 1745 4.830046 CGAGAGGAGAAATGGATAGGAGAA 59.170 45.833 0.00 0.00 0.00 2.87
1042 1759 0.179004 GGAGGCAGATCGAGAGGAGA 60.179 60.000 0.00 0.00 0.00 3.71
1052 1769 3.645687 GAGATTAGTTGGAGGAGGCAGAT 59.354 47.826 0.00 0.00 0.00 2.90
1088 1917 0.106149 AAGAGGAACCAACGAAGCGT 59.894 50.000 0.00 0.00 43.97 5.07
1129 1958 0.456312 CCGAGAGTTACCGTGAGCAC 60.456 60.000 0.00 0.00 0.00 4.40
1130 1959 1.880894 CCGAGAGTTACCGTGAGCA 59.119 57.895 0.00 0.00 0.00 4.26
1131 1960 1.516603 GCCGAGAGTTACCGTGAGC 60.517 63.158 0.00 0.00 0.00 4.26
1132 1961 1.139095 GGCCGAGAGTTACCGTGAG 59.861 63.158 0.00 0.00 0.00 3.51
1133 1962 2.693762 CGGCCGAGAGTTACCGTGA 61.694 63.158 24.07 0.00 40.77 4.35
1134 1963 2.202570 CGGCCGAGAGTTACCGTG 60.203 66.667 24.07 0.00 40.77 4.94
1223 2078 4.220572 GTTATAGCTCCAAGTCGATCGAC 58.779 47.826 35.26 35.26 44.86 4.20
1224 2079 3.059120 CGTTATAGCTCCAAGTCGATCGA 60.059 47.826 15.15 15.15 0.00 3.59
1225 2080 3.227147 CGTTATAGCTCCAAGTCGATCG 58.773 50.000 9.36 9.36 0.00 3.69
1226 2081 3.975670 CACGTTATAGCTCCAAGTCGATC 59.024 47.826 0.00 0.00 0.00 3.69
1267 2122 4.608930 TGCAGAGGCTGGGATAAAACCC 62.609 54.545 0.00 0.00 43.38 4.11
1268 2123 1.340991 TGCAGAGGCTGGGATAAAACC 60.341 52.381 0.00 0.00 41.91 3.27
1269 2124 2.128771 TGCAGAGGCTGGGATAAAAC 57.871 50.000 0.00 0.00 41.91 2.43
1270 2125 2.241941 TGATGCAGAGGCTGGGATAAAA 59.758 45.455 0.00 0.00 41.91 1.52
1272 2127 1.419012 CTGATGCAGAGGCTGGGATAA 59.581 52.381 0.00 0.00 41.91 1.75
1273 2128 1.054231 CTGATGCAGAGGCTGGGATA 58.946 55.000 0.00 0.00 41.91 2.59
1275 2130 0.911045 TTCTGATGCAGAGGCTGGGA 60.911 55.000 0.00 0.00 41.75 4.37
1276 2131 0.034767 TTTCTGATGCAGAGGCTGGG 60.035 55.000 0.00 0.00 41.75 4.45
1277 2132 1.065636 TCTTTCTGATGCAGAGGCTGG 60.066 52.381 0.00 0.00 41.75 4.85
1278 2133 2.398252 TCTTTCTGATGCAGAGGCTG 57.602 50.000 0.00 0.00 41.75 4.85
1279 2134 2.920524 CATCTTTCTGATGCAGAGGCT 58.079 47.619 0.00 0.00 44.96 4.58
1288 2143 3.181462 TGAGCCGTATGCATCTTTCTGAT 60.181 43.478 0.19 0.00 44.83 2.90
1289 2144 2.168313 TGAGCCGTATGCATCTTTCTGA 59.832 45.455 0.19 0.00 44.83 3.27
1291 2146 2.988010 TGAGCCGTATGCATCTTTCT 57.012 45.000 0.19 0.00 44.83 2.52
1292 2147 3.304257 CCATTGAGCCGTATGCATCTTTC 60.304 47.826 0.19 0.00 44.83 2.62
1293 2148 2.620115 CCATTGAGCCGTATGCATCTTT 59.380 45.455 0.19 0.00 44.83 2.52
1295 2150 1.417517 TCCATTGAGCCGTATGCATCT 59.582 47.619 0.19 0.00 44.83 2.90
1296 2151 1.802960 CTCCATTGAGCCGTATGCATC 59.197 52.381 0.19 0.00 44.83 3.91
1297 2152 1.888215 CTCCATTGAGCCGTATGCAT 58.112 50.000 3.79 3.79 44.83 3.96
1298 2153 3.384816 CTCCATTGAGCCGTATGCA 57.615 52.632 0.00 0.00 44.83 3.96
1307 2162 6.073327 TCTACACGTTATAGCTCCATTGAG 57.927 41.667 0.00 0.00 41.84 3.02
1308 2163 6.650427 ATCTACACGTTATAGCTCCATTGA 57.350 37.500 0.00 0.00 0.00 2.57
1309 2164 6.366332 GGAATCTACACGTTATAGCTCCATTG 59.634 42.308 14.04 0.00 0.00 2.82
1310 2165 6.267928 AGGAATCTACACGTTATAGCTCCATT 59.732 38.462 17.84 7.26 29.87 3.16
1311 2166 5.775701 AGGAATCTACACGTTATAGCTCCAT 59.224 40.000 17.84 0.00 29.87 3.41
1326 2266 2.890945 GAGGAGGAGCAGAGGAATCTAC 59.109 54.545 0.00 0.00 0.00 2.59
1327 2267 2.788807 AGAGGAGGAGCAGAGGAATCTA 59.211 50.000 0.00 0.00 0.00 1.98
1416 4196 0.323087 ACACAAGGCGGGGATAAACC 60.323 55.000 0.00 0.00 38.08 3.27
1417 4197 1.541379 AACACAAGGCGGGGATAAAC 58.459 50.000 0.00 0.00 0.00 2.01
1429 4209 0.110823 GCACCGCGAACTAACACAAG 60.111 55.000 8.23 0.00 0.00 3.16
1486 4268 0.952010 CGGGTCGTGGTTCCGAAAAT 60.952 55.000 0.00 0.00 45.96 1.82
1491 4273 4.675029 AAGCGGGTCGTGGTTCCG 62.675 66.667 0.00 0.00 45.84 4.30
1492 4274 3.047877 CAAGCGGGTCGTGGTTCC 61.048 66.667 0.00 0.00 0.00 3.62
1532 4323 2.114411 GCCCCTTTGTTGACCGGA 59.886 61.111 9.46 0.00 0.00 5.14
1533 4324 2.115266 AGCCCCTTTGTTGACCGG 59.885 61.111 0.00 0.00 0.00 5.28
1534 4325 2.919494 GCAGCCCCTTTGTTGACCG 61.919 63.158 0.00 0.00 0.00 4.79
1535 4326 1.832167 TGCAGCCCCTTTGTTGACC 60.832 57.895 0.00 0.00 0.00 4.02
1536 4327 1.363807 GTGCAGCCCCTTTGTTGAC 59.636 57.895 0.00 0.00 0.00 3.18
1537 4328 1.076412 TGTGCAGCCCCTTTGTTGA 60.076 52.632 0.00 0.00 0.00 3.18
1551 4342 0.614812 AATGAAAATGGGGGCTGTGC 59.385 50.000 0.00 0.00 0.00 4.57
1574 4365 4.759693 TGCTTGTATCGTGACTCCATTTTT 59.240 37.500 0.00 0.00 0.00 1.94
1632 5088 2.192861 TGTCTTTGTTGCCGGCCTG 61.193 57.895 26.77 7.53 0.00 4.85
1656 5112 1.201921 CGGAAACTGCGAGTTGTATGC 60.202 52.381 2.88 0.00 38.66 3.14
1661 5117 1.577328 ATGGCGGAAACTGCGAGTTG 61.577 55.000 2.88 0.00 38.66 3.16
1667 5123 1.444895 CAAGCATGGCGGAAACTGC 60.445 57.895 0.00 0.00 34.85 4.40
1668 5125 1.213537 CCAAGCATGGCGGAAACTG 59.786 57.895 0.00 0.00 40.58 3.16
1687 5144 1.303282 GTCAAGAATTCCCGCCCCT 59.697 57.895 0.65 0.00 0.00 4.79
1692 5149 0.673644 AGCGGTGTCAAGAATTCCCG 60.674 55.000 12.52 12.52 38.45 5.14
1828 5300 1.380246 GCATGAGGATTGCCACCCA 60.380 57.895 0.00 0.00 36.29 4.51
1840 5312 0.543277 TGGGCTACCTCTTGCATGAG 59.457 55.000 20.00 20.00 37.76 2.90
1866 5338 6.418819 GCGACGTTAGCTTGAATAAGGTTATA 59.581 38.462 9.31 0.00 41.61 0.98
1950 5458 5.299531 TCTCACTACTAATCGGAACAGATGG 59.700 44.000 0.00 0.00 0.00 3.51
1979 5487 3.010138 CACCAGACCTTTCTTCCCCATAA 59.990 47.826 0.00 0.00 0.00 1.90
1980 5488 2.576191 CACCAGACCTTTCTTCCCCATA 59.424 50.000 0.00 0.00 0.00 2.74
2160 5703 3.945346 TGCTTGGCCGAAGTTTCTTATA 58.055 40.909 14.04 0.00 33.73 0.98
2219 5766 0.099259 ATGAATGAATGCACACCGCG 59.901 50.000 0.00 0.00 46.97 6.46
2220 5767 1.552226 CATGAATGAATGCACACCGC 58.448 50.000 0.00 0.00 42.89 5.68
2472 6019 2.684843 GCGACAGAAAGCAGGCAGG 61.685 63.158 0.00 0.00 0.00 4.85
2474 6021 0.034756 TTAGCGACAGAAAGCAGGCA 59.965 50.000 0.00 0.00 35.48 4.75
2537 6130 1.596752 CACCACTTAGCGCACCACA 60.597 57.895 11.47 0.00 0.00 4.17
2698 6302 3.195825 GCGAGGACCCTGCAAGTATATAT 59.804 47.826 0.00 0.00 0.00 0.86
2793 6397 2.158900 ACCTCCGACAATCCTAGCATTG 60.159 50.000 4.77 4.77 39.35 2.82
2831 6435 1.511147 CAAGAAACAAAAACGTCGCGG 59.489 47.619 6.13 0.00 0.00 6.46
2979 6595 6.013293 AGAGCTAACCTTAGACTTGATTTGGT 60.013 38.462 0.00 0.00 32.47 3.67
3013 6629 1.915141 CAGGGAAAGACAACCATGCT 58.085 50.000 0.00 0.00 31.55 3.79
3032 6648 0.804989 CATCGTGTTCCTCCTTTGGC 59.195 55.000 0.00 0.00 0.00 4.52
3161 6777 6.019881 CACATATGTTTCAAGCAATGCAGATG 60.020 38.462 8.35 3.59 33.46 2.90
3305 7327 2.233431 CCTTCTCCTCCAGTGAGAACAG 59.767 54.545 0.00 0.00 42.38 3.16
3315 7337 0.771127 CAAACCACCCTTCTCCTCCA 59.229 55.000 0.00 0.00 0.00 3.86
3373 7396 5.529791 ACACTCGGTTCAATAGATATTCCG 58.470 41.667 5.33 5.33 38.16 4.30
3400 7423 2.281517 CGGTGTAAATGGTCCGCAATA 58.718 47.619 0.00 0.00 36.68 1.90
3404 7427 0.167251 CAACGGTGTAAATGGTCCGC 59.833 55.000 0.00 0.00 45.76 5.54
3463 7487 8.028938 GCTTGAAAAAGCTCATTGAAACCTATA 58.971 33.333 3.24 0.00 42.32 1.31
3546 7571 1.381522 ACACCAAACAACGGTACCAC 58.618 50.000 13.54 0.00 34.02 4.16
3548 7573 1.872952 GGTACACCAAACAACGGTACC 59.127 52.381 0.16 0.16 44.87 3.34
3550 7575 1.202746 GGGGTACACCAAACAACGGTA 60.203 52.381 10.04 0.00 42.91 4.02
3553 7578 1.508808 CGGGGGTACACCAAACAACG 61.509 60.000 17.96 5.04 42.91 4.10
3574 7599 3.887110 TCAATCTGCCAATCTTATGCTGG 59.113 43.478 0.00 0.00 0.00 4.85
3580 7605 4.096833 GTGCATGTCAATCTGCCAATCTTA 59.903 41.667 0.00 0.00 37.59 2.10
3805 7835 0.038526 AGTACTTCAAGACGGTGCCG 60.039 55.000 9.29 9.29 46.03 5.69
3836 7866 5.120399 TCACGAAGGAATAAAACTGTGTGT 58.880 37.500 0.00 0.00 0.00 3.72
3864 7902 3.334691 CAGAGCCCTCAATTGTTAACGA 58.665 45.455 5.13 0.00 0.00 3.85
3865 7903 2.420022 CCAGAGCCCTCAATTGTTAACG 59.580 50.000 5.13 0.00 0.00 3.18
3866 7904 3.440522 GTCCAGAGCCCTCAATTGTTAAC 59.559 47.826 5.13 0.00 0.00 2.01
3867 7905 3.073798 TGTCCAGAGCCCTCAATTGTTAA 59.926 43.478 5.13 0.00 0.00 2.01
3868 7906 2.642311 TGTCCAGAGCCCTCAATTGTTA 59.358 45.455 5.13 0.00 0.00 2.41
3869 7907 1.425066 TGTCCAGAGCCCTCAATTGTT 59.575 47.619 5.13 0.00 0.00 2.83
3870 7908 1.067295 TGTCCAGAGCCCTCAATTGT 58.933 50.000 5.13 0.00 0.00 2.71
3871 7909 1.004044 AGTGTCCAGAGCCCTCAATTG 59.996 52.381 0.00 0.00 0.00 2.32
3872 7910 1.366319 AGTGTCCAGAGCCCTCAATT 58.634 50.000 0.00 0.00 0.00 2.32
3911 7949 5.450550 CCACTCGAAGCAATCTACACATAGA 60.451 44.000 0.00 0.00 41.76 1.98
3929 7970 3.893200 TCTACATAACCCCATACCACTCG 59.107 47.826 0.00 0.00 0.00 4.18
3958 7999 4.893424 ACAACTTGACACCACAATACAC 57.107 40.909 0.00 0.00 0.00 2.90
3998 8039 4.833126 CTTTATCGATAAAGCACCAACCG 58.167 43.478 33.52 15.92 41.69 4.44
4196 8246 5.999205 TTACCATCCATGCACAGATTTTT 57.001 34.783 0.00 0.00 0.00 1.94
4213 8263 5.018539 AGCTAATGCACTCGTTATTACCA 57.981 39.130 0.00 0.00 42.74 3.25
4216 8266 6.151663 TGGTAGCTAATGCACTCGTTATTA 57.848 37.500 0.00 0.00 42.74 0.98
4219 8269 4.459390 TTGGTAGCTAATGCACTCGTTA 57.541 40.909 0.00 0.00 42.74 3.18
4233 8283 4.211164 GGAGTTTTTGCACAAATTGGTAGC 59.789 41.667 0.64 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.