Multiple sequence alignment - TraesCS5A01G239500

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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 TraesCS5A01G239500 chr5A 100.000 6401 0 0 1 6401 455534442 455528042 0.000000e+00 11821.0
1 TraesCS5A01G239500 chr5A 93.651 126 7 1 3961 4085 694973816 694973941 3.050000e-43 187.0
2 TraesCS5A01G239500 chr5B 94.210 2729 102 18 1272 3959 418922846 418920133 0.000000e+00 4113.0
3 TraesCS5A01G239500 chr5B 90.611 2375 128 38 4059 6387 418920137 418917812 0.000000e+00 3062.0
4 TraesCS5A01G239500 chr5B 90.683 805 24 22 377 1153 418923664 418922883 0.000000e+00 1024.0
5 TraesCS5A01G239500 chr5B 89.418 189 18 2 191 378 418924375 418924188 2.980000e-58 237.0
6 TraesCS5A01G239500 chr5B 95.575 113 5 0 3961 4073 278886984 278886872 1.420000e-41 182.0
7 TraesCS5A01G239500 chr5D 94.858 2042 69 9 1943 3959 354533733 354531703 0.000000e+00 3157.0
8 TraesCS5A01G239500 chr5D 93.684 1900 61 30 4059 5913 354531707 354529822 0.000000e+00 2789.0
9 TraesCS5A01G239500 chr5D 89.426 1986 84 50 2 1893 354535698 354533745 0.000000e+00 2388.0
10 TraesCS5A01G239500 chr5D 85.979 485 42 9 5904 6364 354525310 354524828 4.460000e-136 496.0
11 TraesCS5A01G239500 chr5D 80.311 193 34 4 187 378 101749976 101750165 6.690000e-30 143.0
12 TraesCS5A01G239500 chr5D 78.392 199 37 6 179 373 1889369 1889565 2.420000e-24 124.0
13 TraesCS5A01G239500 chr3D 93.673 2023 97 11 1964 3962 605094751 605096766 0.000000e+00 2998.0
14 TraesCS5A01G239500 chr3D 90.929 904 48 11 4059 4952 605096759 605097638 0.000000e+00 1184.0
15 TraesCS5A01G239500 chr3D 88.530 837 43 26 1147 1955 605084733 605085544 0.000000e+00 965.0
16 TraesCS5A01G239500 chr3D 86.337 849 43 35 250 1054 605083893 605084712 0.000000e+00 857.0
17 TraesCS5A01G239500 chr3A 91.042 1987 127 18 1577 3537 736678563 736680524 0.000000e+00 2636.0
18 TraesCS5A01G239500 chr3A 90.430 1442 110 13 2539 3962 736890073 736891504 0.000000e+00 1873.0
19 TraesCS5A01G239500 chr3A 92.181 908 62 6 1577 2476 736874616 736875522 0.000000e+00 1275.0
20 TraesCS5A01G239500 chr3A 91.748 921 66 4 1577 2489 736889152 736890070 0.000000e+00 1271.0
21 TraesCS5A01G239500 chr3A 91.372 904 66 5 4059 4952 736680908 736681809 0.000000e+00 1227.0
22 TraesCS5A01G239500 chr3A 91.511 801 56 5 4162 4952 736891565 736892363 0.000000e+00 1092.0
23 TraesCS5A01G239500 chr3A 91.837 637 44 6 2539 3172 736875535 736876166 0.000000e+00 881.0
24 TraesCS5A01G239500 chr3A 86.043 695 55 19 502 1179 736879407 736880076 0.000000e+00 708.0
25 TraesCS5A01G239500 chr3A 92.784 388 27 1 3575 3962 736680529 736680915 1.560000e-155 560.0
26 TraesCS5A01G239500 chr3A 82.912 673 54 26 502 1157 736864889 736865517 3.370000e-152 549.0
27 TraesCS5A01G239500 chr3A 94.512 328 14 3 2059 2386 303564954 303564631 2.660000e-138 503.0
28 TraesCS5A01G239500 chr3A 85.952 420 31 15 388 789 736766364 736766773 2.130000e-114 424.0
29 TraesCS5A01G239500 chr3A 88.103 311 29 4 1274 1579 736880117 736880424 4.720000e-96 363.0
30 TraesCS5A01G239500 chr3A 87.460 311 31 4 1274 1579 736865580 736865887 1.020000e-92 351.0
31 TraesCS5A01G239500 chr3A 87.248 149 14 5 3926 4073 692889778 692889922 1.430000e-36 165.0
32 TraesCS5A01G239500 chr6D 96.341 328 10 2 2059 2386 110866623 110866298 7.300000e-149 538.0
33 TraesCS5A01G239500 chr6D 90.580 138 9 3 3958 4092 455884013 455884149 5.100000e-41 180.0
34 TraesCS5A01G239500 chr2D 85.938 320 22 16 2059 2378 110058837 110058541 2.880000e-83 320.0
35 TraesCS5A01G239500 chr7A 95.763 118 4 1 3951 4068 82179641 82179757 8.470000e-44 189.0
36 TraesCS5A01G239500 chr2B 96.396 111 4 0 3958 4068 651077302 651077412 3.940000e-42 183.0
37 TraesCS5A01G239500 chr4A 92.308 130 6 4 3948 4073 59261914 59262043 1.420000e-41 182.0
38 TraesCS5A01G239500 chr4A 90.511 137 11 2 3938 4073 557549920 557549785 5.100000e-41 180.0
39 TraesCS5A01G239500 chr2A 92.742 124 6 2 3944 4065 468295424 468295302 6.600000e-40 176.0
40 TraesCS5A01G239500 chr2A 80.645 124 18 6 179 300 586915711 586915592 2.460000e-14 91.6
41 TraesCS5A01G239500 chr3B 82.011 189 31 3 191 378 30279801 30279615 2.390000e-34 158.0
42 TraesCS5A01G239500 chr1B 77.387 199 38 7 179 373 512697563 512697758 1.890000e-20 111.0
43 TraesCS5A01G239500 chr6A 87.654 81 9 1 6235 6314 556550000 556549920 6.830000e-15 93.5


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 TraesCS5A01G239500 chr5A 455528042 455534442 6400 True 11821.000000 11821 100.000000 1 6401 1 chr5A.!!$R1 6400
1 TraesCS5A01G239500 chr5B 418917812 418924375 6563 True 2109.000000 4113 91.230500 191 6387 4 chr5B.!!$R2 6196
2 TraesCS5A01G239500 chr5D 354529822 354535698 5876 True 2778.000000 3157 92.656000 2 5913 3 chr5D.!!$R2 5911
3 TraesCS5A01G239500 chr3D 605094751 605097638 2887 False 2091.000000 2998 92.301000 1964 4952 2 chr3D.!!$F2 2988
4 TraesCS5A01G239500 chr3D 605083893 605085544 1651 False 911.000000 965 87.433500 250 1955 2 chr3D.!!$F1 1705
5 TraesCS5A01G239500 chr3A 736678563 736681809 3246 False 1474.333333 2636 91.732667 1577 4952 3 chr3A.!!$F3 3375
6 TraesCS5A01G239500 chr3A 736889152 736892363 3211 False 1412.000000 1873 91.229667 1577 4952 3 chr3A.!!$F6 3375
7 TraesCS5A01G239500 chr3A 736874616 736880424 5808 False 806.750000 1275 89.541000 502 3172 4 chr3A.!!$F5 2670
8 TraesCS5A01G239500 chr3A 736864889 736865887 998 False 450.000000 549 85.186000 502 1579 2 chr3A.!!$F4 1077

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
948 1547 0.371645 CGTTGGATTGAGCGCTCTTC 59.628 55.000 35.27 28.97 0.00 2.87 F
1241 1870 0.395311 CATGCCCATGCCTGTCTCTT 60.395 55.000 0.00 0.00 36.33 2.85 F
1376 2017 0.812014 TTTCTCTGTCGCGTTTGGCA 60.812 50.000 5.77 0.00 43.84 4.92 F
1377 2018 1.221466 TTCTCTGTCGCGTTTGGCAG 61.221 55.000 5.77 8.36 43.84 4.85 F
3258 3936 1.066215 TCGCTCACTGCACCACATATT 60.066 47.619 0.00 0.00 43.06 1.28 F
3974 4689 0.252103 AGGTGCTCCCTCCGTTCTAA 60.252 55.000 0.00 0.00 40.71 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 3243 1.299541 CCAACTCAAGAGCACAACGT 58.700 50.000 0.00 0.0 0.00 3.99 R
2720 3377 2.346766 AACAGTGATGTCAGGTGCAA 57.653 45.000 0.00 0.0 0.00 4.08 R
3178 3843 2.497368 TCACCAACATCCATATCCCCA 58.503 47.619 0.00 0.0 0.00 4.96 R
3353 4055 4.232188 AGAAGCAGATCACACCATGAAT 57.768 40.909 0.00 0.0 41.93 2.57 R
4545 6910 2.291741 GGAAACAGCAGACAAGTTGAGG 59.708 50.000 10.54 0.0 0.00 3.86 R
5913 8323 0.035152 ACCACATCGCACCACATCAT 60.035 50.000 0.00 0.0 0.00 2.45 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
59 60 1.375523 GTTGAACCCGTCGGCTGAT 60.376 57.895 5.50 0.00 0.00 2.90
135 136 7.875554 ACACGGGTTTTATTGCAGAATTATTTT 59.124 29.630 0.00 0.00 0.00 1.82
288 291 8.698210 AGACCATTGCAACATCATATATGTTTT 58.302 29.630 12.42 2.20 39.94 2.43
374 378 0.915872 TGTCATGCAGGGGAGGTGAT 60.916 55.000 0.00 0.00 0.00 3.06
518 1052 0.761323 TCACCTGACCCCGTCAAAGA 60.761 55.000 0.00 0.00 42.26 2.52
521 1055 1.003718 CTGACCCCGTCAAAGACCC 60.004 63.158 0.00 0.00 42.26 4.46
522 1056 2.047560 GACCCCGTCAAAGACCCG 60.048 66.667 0.00 0.00 32.09 5.28
523 1057 4.324991 ACCCCGTCAAAGACCCGC 62.325 66.667 0.00 0.00 0.00 6.13
524 1058 4.323477 CCCCGTCAAAGACCCGCA 62.323 66.667 0.00 0.00 0.00 5.69
526 1060 3.047877 CCGTCAAAGACCCGCACC 61.048 66.667 0.00 0.00 0.00 5.01
527 1061 2.280524 CGTCAAAGACCCGCACCA 60.281 61.111 0.00 0.00 0.00 4.17
528 1062 2.604174 CGTCAAAGACCCGCACCAC 61.604 63.158 0.00 0.00 0.00 4.16
529 1063 2.112297 TCAAAGACCCGCACCACC 59.888 61.111 0.00 0.00 0.00 4.61
634 1179 4.758251 CCACGCACGCATCCTCCA 62.758 66.667 0.00 0.00 0.00 3.86
669 1225 0.670854 GGAACAAGAGAGGGACGCAC 60.671 60.000 0.00 0.00 0.00 5.34
778 1353 1.508088 CAAAGCATTCGTGCCCCTC 59.492 57.895 0.00 0.00 34.90 4.30
779 1354 0.962356 CAAAGCATTCGTGCCCCTCT 60.962 55.000 0.00 0.00 34.90 3.69
792 1367 1.694525 CCCTCTTCCCTCCCTTCCC 60.695 68.421 0.00 0.00 0.00 3.97
877 1464 0.801836 GGCATTCCGCGTGGATTTTG 60.802 55.000 20.33 17.13 45.91 2.44
948 1547 0.371645 CGTTGGATTGAGCGCTCTTC 59.628 55.000 35.27 28.97 0.00 2.87
963 1575 1.383803 CTTCCTGGGAGGAGGAGGG 60.384 68.421 0.00 0.00 46.73 4.30
964 1576 2.184631 TTCCTGGGAGGAGGAGGGT 61.185 63.158 0.00 0.00 46.73 4.34
967 1587 1.566298 CCTGGGAGGAGGAGGGTTTG 61.566 65.000 0.00 0.00 37.67 2.93
1204 1824 3.202001 CGGTACTGCATTGCCCCG 61.202 66.667 6.12 8.73 0.00 5.73
1206 1826 3.876198 GTACTGCATTGCCCCGCG 61.876 66.667 6.12 0.00 0.00 6.46
1241 1870 0.395311 CATGCCCATGCCTGTCTCTT 60.395 55.000 0.00 0.00 36.33 2.85
1246 1875 1.134461 CCCATGCCTGTCTCTTGAGAG 60.134 57.143 0.00 1.51 43.36 3.20
1247 1876 1.554160 CCATGCCTGTCTCTTGAGAGT 59.446 52.381 7.82 0.00 42.60 3.24
1248 1877 2.418471 CCATGCCTGTCTCTTGAGAGTC 60.418 54.545 7.82 3.45 42.60 3.36
1249 1878 0.884514 TGCCTGTCTCTTGAGAGTCG 59.115 55.000 7.82 0.66 42.60 4.18
1250 1879 1.169577 GCCTGTCTCTTGAGAGTCGA 58.830 55.000 7.82 0.00 42.60 4.20
1252 1881 2.705730 CCTGTCTCTTGAGAGTCGAGA 58.294 52.381 7.82 0.00 42.60 4.04
1255 1884 3.078097 TGTCTCTTGAGAGTCGAGAAGG 58.922 50.000 7.82 0.00 42.60 3.46
1256 1885 3.078837 GTCTCTTGAGAGTCGAGAAGGT 58.921 50.000 7.82 0.00 42.60 3.50
1294 1931 1.125633 GGTTCTAGAATACCCGCCCA 58.874 55.000 8.75 0.00 0.00 5.36
1376 2017 0.812014 TTTCTCTGTCGCGTTTGGCA 60.812 50.000 5.77 0.00 43.84 4.92
1377 2018 1.221466 TTCTCTGTCGCGTTTGGCAG 61.221 55.000 5.77 8.36 43.84 4.85
1378 2019 3.300667 CTCTGTCGCGTTTGGCAGC 62.301 63.158 5.77 0.00 43.84 5.25
1379 2020 3.648982 CTGTCGCGTTTGGCAGCA 61.649 61.111 5.77 0.00 43.84 4.41
1438 2079 2.506438 GTCGTCTGCACGTAGGCC 60.506 66.667 0.00 0.00 46.76 5.19
1462 2107 4.757149 GCTAGTTCATGACCAAGAGTGTTT 59.243 41.667 0.00 0.00 0.00 2.83
1484 2129 4.439057 TGGATCCTGCTACGTATGAAAAC 58.561 43.478 14.23 0.00 0.00 2.43
1652 2298 6.017605 GTGTTTCTGTTGATTGATCACTGACT 60.018 38.462 0.00 0.00 36.36 3.41
1653 2299 6.203530 TGTTTCTGTTGATTGATCACTGACTC 59.796 38.462 0.00 0.00 36.36 3.36
1728 2382 2.977405 ACGCAAAGAACAATCTGCTC 57.023 45.000 0.00 0.00 35.59 4.26
1875 2529 4.398358 GGCCTATCCTTGTTTACCTTGTTC 59.602 45.833 0.00 0.00 0.00 3.18
1897 2551 7.123547 TGTTCATGTAAAGTTTCCAGTTCCTTT 59.876 33.333 0.00 0.00 0.00 3.11
1946 2600 4.102649 TCATATGACTGTTCGTTAGTGCG 58.897 43.478 0.00 0.00 0.00 5.34
2062 2716 3.806949 TGTATTCCAAGCAGGGACTTT 57.193 42.857 0.00 0.00 34.60 2.66
2095 2749 5.644636 TTTGTTGTCAAGGACGAAGTAAAGT 59.355 36.000 0.00 0.00 36.22 2.66
2274 2929 5.248870 TCTTCTGAAACAGTCTTTTTGCC 57.751 39.130 0.00 0.00 32.61 4.52
2491 3146 2.805671 TGTGCAGTTTATGACCTGTTCG 59.194 45.455 0.00 0.00 0.00 3.95
2665 3322 8.105829 ACCAATCTGATAGTTCTCATTTTCTGT 58.894 33.333 0.00 0.00 0.00 3.41
2807 3464 4.216257 GGACTAAATTTCTTGTGCTGCTGA 59.784 41.667 0.00 0.00 0.00 4.26
2871 3528 7.577616 GCCCTGCAGATTTTATTTAACAACTCT 60.578 37.037 17.39 0.00 0.00 3.24
2897 3554 6.262273 TGTTGTTGTTCCCTCTCTGTATTTTC 59.738 38.462 0.00 0.00 0.00 2.29
2904 3561 2.280628 CTCTCTGTATTTTCCGTGGGC 58.719 52.381 0.00 0.00 0.00 5.36
2940 3598 5.512473 TGAATACTTTGGTTGCGTGTAAAC 58.488 37.500 0.00 0.00 0.00 2.01
2949 3607 1.246649 TGCGTGTAAACCTCTACCGA 58.753 50.000 0.00 0.00 0.00 4.69
2963 3621 5.109903 CCTCTACCGAGTTTGTATTCCAAG 58.890 45.833 0.00 0.00 35.43 3.61
3100 3759 8.801913 GTTTTGCTTGCTATAATCATTTCTGTC 58.198 33.333 0.00 0.00 0.00 3.51
3178 3843 6.543831 GTGGTTTGTGCCTATCTAGATCAATT 59.456 38.462 8.95 0.00 0.00 2.32
3239 3904 1.940613 ACGTGAAGCAAGTGAAGGTTC 59.059 47.619 0.00 0.00 42.24 3.62
3258 3936 1.066215 TCGCTCACTGCACCACATATT 60.066 47.619 0.00 0.00 43.06 1.28
3291 3993 7.936496 ATTTTCAGATGTTTTTGTTTGGGTT 57.064 28.000 0.00 0.00 0.00 4.11
3296 3998 5.983118 CAGATGTTTTTGTTTGGGTTCCTAC 59.017 40.000 0.00 0.00 0.00 3.18
3311 4013 8.561536 TGGGTTCCTACTTATCATCAGATTTA 57.438 34.615 0.00 0.00 35.67 1.40
3420 4135 4.997395 AGTTCGCTGTGACACTATTTTGAT 59.003 37.500 7.20 0.00 0.00 2.57
3537 4252 5.053145 GCTCTTGAATGTTCTCGTGGATAT 58.947 41.667 0.00 0.00 0.00 1.63
3744 4459 3.306472 AACTAGCTCCTAGTCCTCCAG 57.694 52.381 5.46 0.00 45.28 3.86
3797 4512 6.668541 AATATGTTCCGTGTTGATCTGAAG 57.331 37.500 0.00 0.00 0.00 3.02
3918 4633 3.444742 TGCCATGCTTTCAAGAAGGTATG 59.555 43.478 13.43 13.43 39.15 2.39
3932 4647 7.942341 TCAAGAAGGTATGTTCTGTTAACCAAT 59.058 33.333 2.48 0.00 36.86 3.16
3964 4679 1.981256 TTTTCACTTGAGGTGCTCCC 58.019 50.000 0.00 0.00 44.98 4.30
3972 4687 2.120718 AGGTGCTCCCTCCGTTCT 59.879 61.111 0.00 0.00 40.71 3.01
3973 4688 1.386945 AGGTGCTCCCTCCGTTCTA 59.613 57.895 0.00 0.00 40.71 2.10
3974 4689 0.252103 AGGTGCTCCCTCCGTTCTAA 60.252 55.000 0.00 0.00 40.71 2.10
3975 4690 0.611714 GGTGCTCCCTCCGTTCTAAA 59.388 55.000 0.00 0.00 0.00 1.85
3976 4691 1.209747 GGTGCTCCCTCCGTTCTAAAT 59.790 52.381 0.00 0.00 0.00 1.40
3977 4692 2.355818 GGTGCTCCCTCCGTTCTAAATT 60.356 50.000 0.00 0.00 0.00 1.82
3978 4693 3.118519 GGTGCTCCCTCCGTTCTAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
3979 4694 3.869832 GTGCTCCCTCCGTTCTAAATTAC 59.130 47.826 0.00 0.00 0.00 1.89
3980 4695 3.773119 TGCTCCCTCCGTTCTAAATTACT 59.227 43.478 0.00 0.00 0.00 2.24
3981 4696 4.224370 TGCTCCCTCCGTTCTAAATTACTT 59.776 41.667 0.00 0.00 0.00 2.24
3982 4697 4.571176 GCTCCCTCCGTTCTAAATTACTTG 59.429 45.833 0.00 0.00 0.00 3.16
3984 4699 5.727434 TCCCTCCGTTCTAAATTACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
3986 4701 4.032558 CCTCCGTTCTAAATTACTTGTCGC 59.967 45.833 0.00 0.00 0.00 5.19
3988 4703 4.624024 TCCGTTCTAAATTACTTGTCGCAG 59.376 41.667 0.00 0.00 0.00 5.18
3994 4709 6.869695 TCTAAATTACTTGTCGCAGGTATGA 58.130 36.000 3.46 0.00 0.00 2.15
4001 4716 5.050490 ACTTGTCGCAGGTATGAATGTATC 58.950 41.667 0.00 0.00 0.00 2.24
4004 4719 6.013842 TGTCGCAGGTATGAATGTATCTAG 57.986 41.667 0.00 0.00 0.00 2.43
4007 4722 6.749578 GTCGCAGGTATGAATGTATCTAGATG 59.250 42.308 15.79 0.00 0.00 2.90
4037 4752 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
4038 4753 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
4039 4754 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
4040 4755 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
4041 4756 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
4042 4757 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
4043 4758 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
4047 4762 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
4048 4763 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
4050 4765 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
4051 4766 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
4052 4767 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
4054 4769 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
4055 4770 2.734606 CTGCGACGAGTAATTTGGAACA 59.265 45.455 0.00 0.00 0.00 3.18
4056 4771 2.734606 TGCGACGAGTAATTTGGAACAG 59.265 45.455 0.00 0.00 42.39 3.16
4057 4772 2.991190 GCGACGAGTAATTTGGAACAGA 59.009 45.455 0.00 0.00 42.39 3.41
4059 4774 3.612860 CGACGAGTAATTTGGAACAGAGG 59.387 47.826 0.00 0.00 42.39 3.69
4060 4775 3.933332 GACGAGTAATTTGGAACAGAGGG 59.067 47.826 0.00 0.00 42.39 4.30
4061 4776 3.581332 ACGAGTAATTTGGAACAGAGGGA 59.419 43.478 0.00 0.00 42.39 4.20
4063 4778 4.322801 CGAGTAATTTGGAACAGAGGGAGT 60.323 45.833 0.00 0.00 42.39 3.85
4064 4779 5.105473 CGAGTAATTTGGAACAGAGGGAGTA 60.105 44.000 0.00 0.00 42.39 2.59
4079 4794 3.590182 AGGGAGTACTAGATAGGAGCTCC 59.410 52.174 26.22 26.22 38.10 4.70
4390 6595 6.720288 TGTAGCTTCTCCAGTTACCTATATCC 59.280 42.308 0.00 0.00 38.20 2.59
4439 6804 4.124970 CAAGCTGATATTGCTGTCTGCTA 58.875 43.478 7.09 0.00 43.62 3.49
4450 6815 5.932619 TGCTGTCTGCTAATAGTAGGAAA 57.067 39.130 5.57 0.00 43.37 3.13
4526 6891 2.694628 TGCAGCCCATTTATGTTCCATC 59.305 45.455 0.00 0.00 0.00 3.51
4545 6910 8.958043 GTTCCATCGCATAGTTTCATTTTAATC 58.042 33.333 0.00 0.00 0.00 1.75
4551 6916 8.181573 TCGCATAGTTTCATTTTAATCCTCAAC 58.818 33.333 0.00 0.00 0.00 3.18
4582 6947 3.895041 TGTTTCCTTTTCCAATCTCCACC 59.105 43.478 0.00 0.00 0.00 4.61
4638 7003 6.166984 ACATATTGATGTCCTCGATCAAGT 57.833 37.500 4.84 0.00 43.01 3.16
4686 7052 5.215252 AGTGGCATAGCGTAGTATCAATT 57.785 39.130 0.00 0.00 0.00 2.32
4691 7057 6.208797 TGGCATAGCGTAGTATCAATTACTCT 59.791 38.462 0.00 0.00 40.41 3.24
4723 7089 3.248602 AGCAGTGAAGCTAAAAGTGTTCG 59.751 43.478 0.00 0.00 44.50 3.95
4983 7362 4.663636 ATACGTCTTGCTTGTAACAAGC 57.336 40.909 17.75 17.75 43.40 4.01
5095 7474 2.202987 CCCTCCAGCTGTGCGATC 60.203 66.667 13.81 0.00 0.00 3.69
5146 7525 3.502211 GGATTTCCATACATGCTAACCCG 59.498 47.826 0.00 0.00 35.64 5.28
5155 7534 1.586154 ATGCTAACCCGCTGCAACAC 61.586 55.000 0.00 0.00 40.24 3.32
5314 7693 5.163713 GCAGTGCCTTTTCTCGAAGAAATAT 60.164 40.000 2.85 0.00 43.06 1.28
5376 7783 6.648879 TGTAACCTGCTAATTTGCTCTTTT 57.351 33.333 12.99 4.22 0.00 2.27
5426 7833 1.975363 GCAGATGCCTTCAGTCACGC 61.975 60.000 0.00 0.00 34.31 5.34
5429 7836 2.835701 GATGCCTTCAGTCACGCGGA 62.836 60.000 12.47 1.33 0.00 5.54
5470 7877 7.890127 TGAAACCATTCTTTGATAGACATTCCT 59.110 33.333 0.00 0.00 36.48 3.36
5492 7899 5.746721 CCTTTTGTTTTCTTTACCAGGAACG 59.253 40.000 0.00 0.00 0.00 3.95
5511 7918 4.067972 ACGTTAGTCAGTTGACCACATT 57.932 40.909 8.57 0.00 45.85 2.71
5576 7985 8.164070 AGTATTCTTGACAAGTTAGGTTGGAAT 58.836 33.333 14.75 6.86 0.00 3.01
5592 8001 5.335127 GTTGGAATTTCATTGATCAGTCGG 58.665 41.667 0.00 0.00 0.00 4.79
5596 8005 3.694043 TTTCATTGATCAGTCGGACCA 57.306 42.857 4.14 0.00 0.00 4.02
5603 8012 0.253044 ATCAGTCGGACCAACATGGG 59.747 55.000 4.14 0.00 43.37 4.00
5666 8075 6.534634 AGAATTTTAGCTTGACTGTACAGGT 58.465 36.000 26.12 12.20 0.00 4.00
5732 8141 4.993905 ACGGTGGTTGAGAAAAAGAAAAG 58.006 39.130 0.00 0.00 0.00 2.27
5744 8153 8.100164 TGAGAAAAAGAAAAGGTTTGGTGATTT 58.900 29.630 0.00 0.00 0.00 2.17
5861 8271 9.725019 ATGTGAAGTAGTTTTAACATCTGATGA 57.275 29.630 23.59 0.00 0.00 2.92
5862 8272 9.208022 TGTGAAGTAGTTTTAACATCTGATGAG 57.792 33.333 23.59 0.00 0.00 2.90
5863 8273 9.209175 GTGAAGTAGTTTTAACATCTGATGAGT 57.791 33.333 23.59 13.01 0.00 3.41
5864 8274 9.208022 TGAAGTAGTTTTAACATCTGATGAGTG 57.792 33.333 23.59 0.00 0.00 3.51
5865 8275 9.424319 GAAGTAGTTTTAACATCTGATGAGTGA 57.576 33.333 23.59 5.69 0.00 3.41
5866 8276 9.950496 AAGTAGTTTTAACATCTGATGAGTGAT 57.050 29.630 23.59 7.14 0.00 3.06
5867 8277 9.376075 AGTAGTTTTAACATCTGATGAGTGATG 57.624 33.333 23.59 0.00 43.90 3.07
5868 8278 9.371136 GTAGTTTTAACATCTGATGAGTGATGA 57.629 33.333 23.59 1.55 41.69 2.92
5900 8310 2.114670 ACATGCGAGGAAATGGCCG 61.115 57.895 0.00 0.00 0.00 6.13
5910 8320 3.636764 GAGGAAATGGCCGATGGTTTTAT 59.363 43.478 0.00 0.00 0.00 1.40
5912 8322 4.583073 AGGAAATGGCCGATGGTTTTATAC 59.417 41.667 0.00 0.00 0.00 1.47
5913 8323 4.339814 GGAAATGGCCGATGGTTTTATACA 59.660 41.667 0.00 0.00 0.00 2.29
5950 8360 0.601558 GTCTTGTGACTGGCGGTAGA 59.398 55.000 0.00 0.00 39.94 2.59
5965 8375 1.153086 TAGACGCGGGTAGGGAGAC 60.153 63.158 12.47 0.00 36.53 3.36
5966 8376 2.930385 TAGACGCGGGTAGGGAGACG 62.930 65.000 12.47 0.00 36.53 4.18
5969 8379 2.439883 GCGGGTAGGGAGACGTCT 60.440 66.667 20.18 20.18 0.00 4.18
5970 8380 1.153086 GCGGGTAGGGAGACGTCTA 60.153 63.158 20.09 0.00 0.00 2.59
5971 8381 1.165284 GCGGGTAGGGAGACGTCTAG 61.165 65.000 20.09 4.00 0.00 2.43
5973 8383 0.550432 GGGTAGGGAGACGTCTAGGT 59.450 60.000 20.09 8.15 0.00 3.08
5974 8384 1.677942 GGTAGGGAGACGTCTAGGTG 58.322 60.000 20.09 0.00 0.00 4.00
5976 8386 0.106819 TAGGGAGACGTCTAGGTGGC 60.107 60.000 20.09 4.44 0.00 5.01
6030 8461 3.726291 CCCAAAAATAGGGCATAACCG 57.274 47.619 0.00 0.00 39.96 4.44
6043 8474 4.202111 GGGCATAACCGCTTTTTACATCAT 60.202 41.667 0.00 0.00 40.62 2.45
6056 8487 6.855763 TTTTACATCATGAGGGAGCAAAAT 57.144 33.333 12.66 0.00 0.00 1.82
6058 8489 2.947652 ACATCATGAGGGAGCAAAATCG 59.052 45.455 12.66 0.00 0.00 3.34
6093 8526 5.662657 AGGTGCCCTATATGCAAAAGAAAAT 59.337 36.000 0.00 0.00 41.06 1.82
6098 8531 7.559533 TGCCCTATATGCAAAAGAAAATACTCA 59.440 33.333 0.00 0.00 35.40 3.41
6130 8565 3.243704 GCAGTTGCAAAATACTTGGGTGA 60.244 43.478 0.00 0.00 41.59 4.02
6136 8571 5.133941 TGCAAAATACTTGGGTGACTGTAA 58.866 37.500 0.00 0.00 0.00 2.41
6137 8572 5.009210 TGCAAAATACTTGGGTGACTGTAAC 59.991 40.000 0.00 0.00 0.00 2.50
6138 8573 5.009210 GCAAAATACTTGGGTGACTGTAACA 59.991 40.000 0.00 0.00 0.00 2.41
6147 8584 5.991861 TGGGTGACTGTAACAAACTTTAGA 58.008 37.500 0.00 0.00 0.00 2.10
6151 8588 6.204882 GGTGACTGTAACAAACTTTAGAGCAT 59.795 38.462 0.00 0.00 0.00 3.79
6171 8608 3.433306 TCTGGGACCACATAAAACCAG 57.567 47.619 0.00 0.00 45.18 4.00
6210 8647 1.135603 CATCACAATGTTGCTCCACCG 60.136 52.381 0.00 0.00 0.00 4.94
6242 8679 8.923270 CCTAATTTTAGGGCATCAATTTTAGGA 58.077 33.333 8.28 0.00 45.29 2.94
6244 8681 7.732222 ATTTTAGGGCATCAATTTTAGGACA 57.268 32.000 0.00 0.00 0.00 4.02
6245 8682 7.546250 TTTTAGGGCATCAATTTTAGGACAA 57.454 32.000 0.00 0.00 0.00 3.18
6248 8685 4.463891 AGGGCATCAATTTTAGGACAACTG 59.536 41.667 0.00 0.00 0.00 3.16
6250 8687 5.279456 GGGCATCAATTTTAGGACAACTGTT 60.279 40.000 0.00 0.00 0.00 3.16
6251 8688 6.223120 GGCATCAATTTTAGGACAACTGTTT 58.777 36.000 0.00 0.00 0.00 2.83
6301 8738 1.888512 GCTCCAAGCCAACTTTGATGA 59.111 47.619 0.00 0.00 34.48 2.92
6344 8788 2.215196 GTAAGGAAGCGTTGGTTGTCA 58.785 47.619 0.00 0.00 0.00 3.58
6347 8791 0.586802 GGAAGCGTTGGTTGTCACTC 59.413 55.000 0.00 0.00 0.00 3.51
6352 8796 1.847818 CGTTGGTTGTCACTCGAGAA 58.152 50.000 21.68 3.52 0.00 2.87
6362 8806 1.971357 TCACTCGAGAAAAGAAGGGCT 59.029 47.619 21.68 0.00 0.00 5.19
6363 8807 2.072298 CACTCGAGAAAAGAAGGGCTG 58.928 52.381 21.68 0.00 0.00 4.85
6387 8831 0.985490 GGAATCAGGTGAGGAGGGCT 60.985 60.000 0.00 0.00 0.00 5.19
6389 8833 0.252881 AATCAGGTGAGGAGGGCTGA 60.253 55.000 0.00 0.00 0.00 4.26
6390 8834 0.690411 ATCAGGTGAGGAGGGCTGAG 60.690 60.000 0.00 0.00 0.00 3.35
6391 8835 1.305633 CAGGTGAGGAGGGCTGAGA 60.306 63.158 0.00 0.00 0.00 3.27
6392 8836 0.690411 CAGGTGAGGAGGGCTGAGAT 60.690 60.000 0.00 0.00 0.00 2.75
6393 8837 0.690411 AGGTGAGGAGGGCTGAGATG 60.690 60.000 0.00 0.00 0.00 2.90
6394 8838 0.689080 GGTGAGGAGGGCTGAGATGA 60.689 60.000 0.00 0.00 0.00 2.92
6396 8840 0.337773 TGAGGAGGGCTGAGATGACT 59.662 55.000 0.00 0.00 0.00 3.41
6397 8841 0.752054 GAGGAGGGCTGAGATGACTG 59.248 60.000 0.00 0.00 0.00 3.51
6398 8842 0.042431 AGGAGGGCTGAGATGACTGT 59.958 55.000 0.00 0.00 0.00 3.55
6400 8844 0.461693 GAGGGCTGAGATGACTGTGC 60.462 60.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.515020 TTTACTTTTGACAAATCATCAACACTC 57.485 29.630 0.50 0.00 35.82 3.51
32 33 0.395312 ACGGGTTCAACGGTTCAGAT 59.605 50.000 0.00 0.00 35.23 2.90
33 34 0.249573 GACGGGTTCAACGGTTCAGA 60.250 55.000 0.00 0.00 35.23 3.27
46 47 2.240162 GAAAGGATCAGCCGACGGGT 62.240 60.000 13.98 13.98 43.43 5.28
59 60 1.745087 GATGCGGCAGATTTGAAAGGA 59.255 47.619 9.25 0.00 0.00 3.36
108 109 3.907894 TTCTGCAATAAAACCCGTGTC 57.092 42.857 0.00 0.00 0.00 3.67
135 136 2.615869 GCAAGAAAACCTGTGTTGCAA 58.384 42.857 0.00 0.00 42.48 4.08
173 174 5.931146 TGTCAAAAGAATGCAACAAACAGTT 59.069 32.000 0.00 0.00 42.42 3.16
175 176 6.091169 AGTTGTCAAAAGAATGCAACAAACAG 59.909 34.615 0.00 0.00 38.56 3.16
176 177 5.931146 AGTTGTCAAAAGAATGCAACAAACA 59.069 32.000 0.00 0.00 38.56 2.83
195 198 2.092968 TCTGCAACAAGACCTCAGTTGT 60.093 45.455 13.22 0.00 43.31 3.32
288 291 5.414789 TTGTAACAGGTGCTATGCTTCTA 57.585 39.130 0.00 0.00 0.00 2.10
367 371 2.555199 CAGAAACGGATCCATCACCTC 58.445 52.381 13.41 0.00 0.00 3.85
374 378 1.065491 CCATCACCAGAAACGGATCCA 60.065 52.381 13.41 0.00 0.00 3.41
522 1056 4.832608 GATCGGACGGGGTGGTGC 62.833 72.222 0.00 0.00 0.00 5.01
523 1057 4.508128 CGATCGGACGGGGTGGTG 62.508 72.222 7.38 0.00 0.00 4.17
524 1058 4.746309 TCGATCGGACGGGGTGGT 62.746 66.667 16.41 0.00 0.00 4.16
669 1225 2.737252 GTTCCGTTAGTTTCTGCTCTGG 59.263 50.000 0.00 0.00 0.00 3.86
778 1353 1.694525 GGGAGGGAAGGGAGGGAAG 60.695 68.421 0.00 0.00 0.00 3.46
779 1354 2.191846 AGGGAGGGAAGGGAGGGAA 61.192 63.158 0.00 0.00 0.00 3.97
792 1367 3.299190 GGCGATCGAGGGAGGGAG 61.299 72.222 21.57 0.00 0.00 4.30
877 1464 1.892441 AAGAGGGAGGGAGGGAGGAC 61.892 65.000 0.00 0.00 0.00 3.85
948 1547 1.229984 AAACCCTCCTCCTCCCAGG 60.230 63.158 0.00 0.00 36.46 4.45
1270 1899 3.893813 GGCGGGTATTCTAGAACCTTCTA 59.106 47.826 7.48 0.00 38.70 2.10
1294 1931 1.742761 CCTCCATGTCGCACAATTCT 58.257 50.000 0.00 0.00 0.00 2.40
1378 2019 0.606604 AAAAAGGCATGGCAGCTCTG 59.393 50.000 22.64 0.00 34.17 3.35
1379 2020 0.606604 CAAAAAGGCATGGCAGCTCT 59.393 50.000 22.64 0.00 34.17 4.09
1438 2079 2.926200 CACTCTTGGTCATGAACTAGCG 59.074 50.000 16.30 13.15 0.00 4.26
1462 2107 4.161565 AGTTTTCATACGTAGCAGGATCCA 59.838 41.667 15.82 0.00 0.00 3.41
1466 2111 6.276832 AGTAAGTTTTCATACGTAGCAGGA 57.723 37.500 0.08 0.00 0.00 3.86
1504 2149 8.980481 ATCAAAGGTAATATTTCCTAGTGGTG 57.020 34.615 13.47 7.78 33.27 4.17
1507 2152 9.627123 TTGGATCAAAGGTAATATTTCCTAGTG 57.373 33.333 13.47 13.85 33.27 2.74
1569 2215 4.669206 AATAAATCAAATGATGGCGCCA 57.331 36.364 34.80 34.80 34.49 5.69
1619 2265 0.380378 CAACAGAAACACACCACCCG 59.620 55.000 0.00 0.00 0.00 5.28
1652 2298 5.793817 ACAGCTATAAACATGACACAGTGA 58.206 37.500 7.81 0.00 0.00 3.41
1653 2299 6.486253 AACAGCTATAAACATGACACAGTG 57.514 37.500 0.00 0.00 0.00 3.66
1728 2382 1.135972 GTAGCACGCAGGACATTGTTG 60.136 52.381 0.00 0.00 0.00 3.33
1875 2529 7.447238 TCCTAAAGGAACTGGAAACTTTACATG 59.553 37.037 0.00 0.00 42.18 3.21
1897 2551 7.670605 AACTACAGTGTATGCCTATTTCCTA 57.329 36.000 2.82 0.00 0.00 2.94
1946 2600 5.743872 GCCTAAATAAACAGTAACAGCATGC 59.256 40.000 10.51 10.51 42.53 4.06
2062 2716 3.256879 TCCTTGACAACAAACAAACTGCA 59.743 39.130 0.00 0.00 35.49 4.41
2241 2896 7.602265 AGACTGTTTCAGAAGATAAAAGAGAGC 59.398 37.037 3.70 0.00 35.18 4.09
2274 2929 2.614057 ACCAGAACTTTCAGCTGAAACG 59.386 45.455 32.86 28.08 38.94 3.60
2491 3146 2.291365 ACACGTTCCACCCTGTAAAAC 58.709 47.619 0.00 0.00 0.00 2.43
2586 3243 1.299541 CCAACTCAAGAGCACAACGT 58.700 50.000 0.00 0.00 0.00 3.99
2665 3322 6.212791 AGAAACAGATGGTTAGCAGGTTACTA 59.787 38.462 0.00 0.00 39.29 1.82
2716 3373 2.998670 CAGTGATGTCAGGTGCAAGTAG 59.001 50.000 0.00 0.00 0.00 2.57
2720 3377 2.346766 AACAGTGATGTCAGGTGCAA 57.653 45.000 0.00 0.00 0.00 4.08
2780 3437 5.567423 GCAGCACAAGAAATTTAGTCCCATT 60.567 40.000 0.00 0.00 0.00 3.16
2783 3440 3.507622 AGCAGCACAAGAAATTTAGTCCC 59.492 43.478 0.00 0.00 0.00 4.46
2871 3528 3.644966 ACAGAGAGGGAACAACAACAA 57.355 42.857 0.00 0.00 0.00 2.83
2897 3554 3.569277 TCAATATTCATCAATGCCCACGG 59.431 43.478 0.00 0.00 0.00 4.94
2940 3598 5.080969 TTGGAATACAAACTCGGTAGAGG 57.919 43.478 0.44 0.00 40.50 3.69
3178 3843 2.497368 TCACCAACATCCATATCCCCA 58.503 47.619 0.00 0.00 0.00 4.96
3266 3967 9.103861 GAACCCAAACAAAAACATCTGAAAATA 57.896 29.630 0.00 0.00 0.00 1.40
3267 3968 7.066887 GGAACCCAAACAAAAACATCTGAAAAT 59.933 33.333 0.00 0.00 0.00 1.82
3274 3976 6.156748 AGTAGGAACCCAAACAAAAACATC 57.843 37.500 0.00 0.00 0.00 3.06
3353 4055 4.232188 AGAAGCAGATCACACCATGAAT 57.768 40.909 0.00 0.00 41.93 2.57
3537 4252 1.937191 TGGCAGCTATATCGGATGGA 58.063 50.000 0.00 0.00 0.00 3.41
3716 4431 4.383226 GGACTAGGAGCTAGTTTTTCTGGG 60.383 50.000 0.00 0.00 45.90 4.45
3744 4459 0.249868 GTTTTCCCCTGCCACTTTGC 60.250 55.000 0.00 0.00 0.00 3.68
3797 4512 3.750639 TTTCGGCGGAACATGTTATTC 57.249 42.857 11.95 0.00 0.00 1.75
3918 4633 7.054751 AGGCCTAGAATATTGGTTAACAGAAC 58.945 38.462 1.29 0.00 0.00 3.01
3962 4677 4.565564 CGACAAGTAATTTAGAACGGAGGG 59.434 45.833 0.00 0.00 0.00 4.30
3963 4678 4.032558 GCGACAAGTAATTTAGAACGGAGG 59.967 45.833 0.00 0.00 0.00 4.30
3964 4679 4.624024 TGCGACAAGTAATTTAGAACGGAG 59.376 41.667 0.00 0.00 0.00 4.63
3965 4680 4.558178 TGCGACAAGTAATTTAGAACGGA 58.442 39.130 0.00 0.00 0.00 4.69
3966 4681 4.201685 CCTGCGACAAGTAATTTAGAACGG 60.202 45.833 0.00 0.00 0.00 4.44
3967 4682 4.387862 ACCTGCGACAAGTAATTTAGAACG 59.612 41.667 0.00 0.00 0.00 3.95
3968 4683 5.857822 ACCTGCGACAAGTAATTTAGAAC 57.142 39.130 0.00 0.00 0.00 3.01
3969 4684 7.324935 TCATACCTGCGACAAGTAATTTAGAA 58.675 34.615 0.00 0.00 0.00 2.10
3970 4685 6.869695 TCATACCTGCGACAAGTAATTTAGA 58.130 36.000 0.00 0.00 0.00 2.10
3971 4686 7.534085 TTCATACCTGCGACAAGTAATTTAG 57.466 36.000 0.00 0.00 0.00 1.85
3972 4687 7.551262 ACATTCATACCTGCGACAAGTAATTTA 59.449 33.333 0.00 0.00 0.00 1.40
3973 4688 6.374333 ACATTCATACCTGCGACAAGTAATTT 59.626 34.615 0.00 0.00 0.00 1.82
3974 4689 5.880332 ACATTCATACCTGCGACAAGTAATT 59.120 36.000 0.00 0.00 0.00 1.40
3975 4690 5.428253 ACATTCATACCTGCGACAAGTAAT 58.572 37.500 0.00 0.00 0.00 1.89
3976 4691 4.827692 ACATTCATACCTGCGACAAGTAA 58.172 39.130 0.00 0.00 0.00 2.24
3977 4692 4.465632 ACATTCATACCTGCGACAAGTA 57.534 40.909 0.00 0.00 0.00 2.24
3978 4693 3.334583 ACATTCATACCTGCGACAAGT 57.665 42.857 0.00 0.00 0.00 3.16
3979 4694 5.292765 AGATACATTCATACCTGCGACAAG 58.707 41.667 0.00 0.00 0.00 3.16
3980 4695 5.276461 AGATACATTCATACCTGCGACAA 57.724 39.130 0.00 0.00 0.00 3.18
3981 4696 4.937201 AGATACATTCATACCTGCGACA 57.063 40.909 0.00 0.00 0.00 4.35
3982 4697 6.255596 TCTAGATACATTCATACCTGCGAC 57.744 41.667 0.00 0.00 0.00 5.19
3984 4699 6.625362 ACATCTAGATACATTCATACCTGCG 58.375 40.000 4.54 0.00 0.00 5.18
4011 4726 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
4013 4728 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
4015 4730 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
4019 4734 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
4020 4735 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
4021 4736 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
4023 4738 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
4024 4739 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
4025 4740 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
4026 4741 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
4027 4742 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
4028 4743 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
4029 4744 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
4030 4745 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
4031 4746 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
4032 4747 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
4034 4749 2.734606 TGTTCCAAATTACTCGTCGCAG 59.265 45.455 0.00 0.00 0.00 5.18
4035 4750 2.734606 CTGTTCCAAATTACTCGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
4037 4752 3.612860 CCTCTGTTCCAAATTACTCGTCG 59.387 47.826 0.00 0.00 0.00 5.12
4038 4753 3.933332 CCCTCTGTTCCAAATTACTCGTC 59.067 47.826 0.00 0.00 0.00 4.20
4039 4754 3.581332 TCCCTCTGTTCCAAATTACTCGT 59.419 43.478 0.00 0.00 0.00 4.18
4040 4755 4.184629 CTCCCTCTGTTCCAAATTACTCG 58.815 47.826 0.00 0.00 0.00 4.18
4041 4756 5.167303 ACTCCCTCTGTTCCAAATTACTC 57.833 43.478 0.00 0.00 0.00 2.59
4042 4757 5.785940 AGTACTCCCTCTGTTCCAAATTACT 59.214 40.000 0.00 0.00 0.00 2.24
4043 4758 6.051179 AGTACTCCCTCTGTTCCAAATTAC 57.949 41.667 0.00 0.00 0.00 1.89
4047 4762 5.006896 TCTAGTACTCCCTCTGTTCCAAA 57.993 43.478 0.00 0.00 0.00 3.28
4048 4763 4.669866 TCTAGTACTCCCTCTGTTCCAA 57.330 45.455 0.00 0.00 0.00 3.53
4050 4765 5.073417 TCCTATCTAGTACTCCCTCTGTTCC 59.927 48.000 0.00 0.00 0.00 3.62
4051 4766 6.190346 TCCTATCTAGTACTCCCTCTGTTC 57.810 45.833 0.00 0.00 0.00 3.18
4052 4767 5.457052 GCTCCTATCTAGTACTCCCTCTGTT 60.457 48.000 0.00 0.00 0.00 3.16
4054 4769 4.288626 AGCTCCTATCTAGTACTCCCTCTG 59.711 50.000 0.00 0.00 0.00 3.35
4055 4770 4.509321 AGCTCCTATCTAGTACTCCCTCT 58.491 47.826 0.00 0.00 0.00 3.69
4056 4771 4.324022 GGAGCTCCTATCTAGTACTCCCTC 60.324 54.167 26.25 0.00 36.95 4.30
4057 4772 3.590182 GGAGCTCCTATCTAGTACTCCCT 59.410 52.174 26.25 0.00 36.95 4.20
4059 4774 4.644163 TGGAGCTCCTATCTAGTACTCC 57.356 50.000 32.28 2.97 42.08 3.85
4060 4775 7.169591 TGTTATGGAGCTCCTATCTAGTACTC 58.830 42.308 32.28 11.01 36.82 2.59
4061 4776 7.092748 TGTTATGGAGCTCCTATCTAGTACT 57.907 40.000 32.28 0.00 36.82 2.73
4063 4778 7.092748 ACTGTTATGGAGCTCCTATCTAGTA 57.907 40.000 32.28 11.02 36.82 1.82
4064 4779 5.959512 ACTGTTATGGAGCTCCTATCTAGT 58.040 41.667 32.28 24.96 36.82 2.57
4079 4794 8.833231 TGTCCTTTTCTCTTAGAACTGTTATG 57.167 34.615 0.00 0.00 33.26 1.90
4118 6323 6.713903 CACAATGGACAATCCTAATGCTCTAT 59.286 38.462 0.00 0.00 37.46 1.98
4121 6326 4.641989 ACACAATGGACAATCCTAATGCTC 59.358 41.667 0.00 0.00 37.46 4.26
4267 6472 2.584492 ATTGATGCTTTTAAGGCCGC 57.416 45.000 0.00 0.00 0.00 6.53
4268 6473 5.048782 TGCTATATTGATGCTTTTAAGGCCG 60.049 40.000 0.00 0.00 0.00 6.13
4343 6548 9.832445 CTACAAATCCAAGACTAATAAGCCTAA 57.168 33.333 0.00 0.00 0.00 2.69
4390 6595 6.487668 TGCCCATATGAGACAATCAAATACAG 59.512 38.462 3.65 0.00 42.53 2.74
4450 6815 5.831525 TCATCTGCTGCTTCCAATAATTCAT 59.168 36.000 0.00 0.00 0.00 2.57
4526 6891 8.184192 AGTTGAGGATTAAAATGAAACTATGCG 58.816 33.333 0.00 0.00 0.00 4.73
4545 6910 2.291741 GGAAACAGCAGACAAGTTGAGG 59.708 50.000 10.54 0.00 0.00 3.86
4551 6916 3.381272 TGGAAAAGGAAACAGCAGACAAG 59.619 43.478 0.00 0.00 0.00 3.16
4582 6947 4.401925 AGAAAAGAAGAGGGTCCAATGTG 58.598 43.478 0.00 0.00 0.00 3.21
4638 7003 4.717877 ACACATCAACCATGTCTTTCTGA 58.282 39.130 0.00 0.00 44.60 3.27
4744 7110 9.007494 AGTAACCATCCCATCTAATATATGCAT 57.993 33.333 3.79 3.79 0.00 3.96
5426 7833 1.153086 AGCAATTAGGCCTGCTCCG 60.153 57.895 17.99 0.57 45.79 4.63
5470 7877 6.270156 ACGTTCCTGGTAAAGAAAACAAAA 57.730 33.333 0.00 0.00 0.00 2.44
5576 7985 3.694043 TGGTCCGACTGATCAATGAAA 57.306 42.857 0.00 0.00 28.74 2.69
5592 8001 0.541764 TGCCCTTTCCCATGTTGGTC 60.542 55.000 0.00 0.00 35.17 4.02
5596 8005 1.229177 GGGTGCCCTTTCCCATGTT 60.229 57.895 0.00 0.00 42.95 2.71
5627 8036 8.947115 AGCTAAAATTCTAACGACTATGCTTTT 58.053 29.630 0.00 0.00 0.00 2.27
5744 8153 7.329226 GCACAGATAAGCTTAAAGCATTCAAAA 59.671 33.333 10.85 0.00 45.56 2.44
5855 8265 3.379688 TCTCTTCCGTCATCACTCATCAG 59.620 47.826 0.00 0.00 0.00 2.90
5861 8271 1.137872 GGCATCTCTTCCGTCATCACT 59.862 52.381 0.00 0.00 0.00 3.41
5862 8272 1.134699 TGGCATCTCTTCCGTCATCAC 60.135 52.381 0.00 0.00 0.00 3.06
5863 8273 1.134699 GTGGCATCTCTTCCGTCATCA 60.135 52.381 0.00 0.00 0.00 3.07
5864 8274 1.134699 TGTGGCATCTCTTCCGTCATC 60.135 52.381 0.00 0.00 0.00 2.92
5865 8275 0.904649 TGTGGCATCTCTTCCGTCAT 59.095 50.000 0.00 0.00 0.00 3.06
5866 8276 0.904649 ATGTGGCATCTCTTCCGTCA 59.095 50.000 0.00 0.00 0.00 4.35
5867 8277 1.293924 CATGTGGCATCTCTTCCGTC 58.706 55.000 0.00 0.00 0.00 4.79
5868 8278 0.745845 GCATGTGGCATCTCTTCCGT 60.746 55.000 0.00 0.00 43.97 4.69
5900 8310 6.208644 GCACCACATCATGTATAAAACCATC 58.791 40.000 0.00 0.00 0.00 3.51
5910 8320 2.278854 CACATCGCACCACATCATGTA 58.721 47.619 0.00 0.00 0.00 2.29
5912 8322 0.379316 CCACATCGCACCACATCATG 59.621 55.000 0.00 0.00 0.00 3.07
5913 8323 0.035152 ACCACATCGCACCACATCAT 60.035 50.000 0.00 0.00 0.00 2.45
5950 8360 4.729918 ACGTCTCCCTACCCGCGT 62.730 66.667 4.92 0.00 0.00 6.01
5965 8375 0.244450 TGTTAACCGCCACCTAGACG 59.756 55.000 2.48 0.00 0.00 4.18
5966 8376 1.405121 CCTGTTAACCGCCACCTAGAC 60.405 57.143 2.48 0.00 0.00 2.59
5969 8379 0.322322 CACCTGTTAACCGCCACCTA 59.678 55.000 2.48 0.00 0.00 3.08
5970 8380 1.072505 CACCTGTTAACCGCCACCT 59.927 57.895 2.48 0.00 0.00 4.00
5971 8381 0.035176 TACACCTGTTAACCGCCACC 59.965 55.000 2.48 0.00 0.00 4.61
5973 8383 1.693062 TCTTACACCTGTTAACCGCCA 59.307 47.619 2.48 0.00 0.00 5.69
5974 8384 2.344025 CTCTTACACCTGTTAACCGCC 58.656 52.381 2.48 0.00 0.00 6.13
5976 8386 3.034721 TGCTCTTACACCTGTTAACCG 57.965 47.619 2.48 0.00 0.00 4.44
5977 8387 4.833390 AGATGCTCTTACACCTGTTAACC 58.167 43.478 2.48 0.00 0.00 2.85
6027 8458 3.016736 CCCTCATGATGTAAAAAGCGGT 58.983 45.455 0.00 0.00 0.00 5.68
6028 8459 3.278574 TCCCTCATGATGTAAAAAGCGG 58.721 45.455 0.00 0.00 0.00 5.52
6030 8461 3.696051 TGCTCCCTCATGATGTAAAAAGC 59.304 43.478 0.00 0.00 0.00 3.51
6043 8474 1.308069 GCAGCGATTTTGCTCCCTCA 61.308 55.000 0.00 0.00 45.23 3.86
6056 8487 0.744414 GGCACCTATTGAAGCAGCGA 60.744 55.000 0.00 0.00 0.00 4.93
6093 8526 5.862924 GCAACTGCACTATTCTTTGAGTA 57.137 39.130 0.00 0.00 41.59 2.59
6118 8551 6.362248 AGTTTGTTACAGTCACCCAAGTATT 58.638 36.000 0.00 0.00 0.00 1.89
6130 8565 6.428159 CCAGATGCTCTAAAGTTTGTTACAGT 59.572 38.462 0.00 0.00 0.00 3.55
6136 8571 4.327680 GTCCCAGATGCTCTAAAGTTTGT 58.672 43.478 0.00 0.00 0.00 2.83
6137 8572 3.691609 GGTCCCAGATGCTCTAAAGTTTG 59.308 47.826 0.00 0.00 0.00 2.93
6138 8573 3.330701 TGGTCCCAGATGCTCTAAAGTTT 59.669 43.478 0.00 0.00 0.00 2.66
6147 8584 3.356290 GTTTTATGTGGTCCCAGATGCT 58.644 45.455 6.24 0.00 32.10 3.79
6151 8588 2.983192 TCTGGTTTTATGTGGTCCCAGA 59.017 45.455 0.00 0.00 44.55 3.86
6161 8598 6.262601 ACACGTGTTTTCTTCTGGTTTTATG 58.737 36.000 17.22 0.00 0.00 1.90
6163 8600 5.883503 ACACGTGTTTTCTTCTGGTTTTA 57.116 34.783 17.22 0.00 0.00 1.52
6196 8633 3.166434 TCCCGGTGGAGCAACATT 58.834 55.556 0.00 0.00 35.03 2.71
6234 8671 7.581213 TCATCACAAACAGTTGTCCTAAAAT 57.419 32.000 0.00 0.00 45.00 1.82
6239 8676 4.269183 TGTTCATCACAAACAGTTGTCCT 58.731 39.130 0.00 0.00 45.00 3.85
6241 8678 7.393327 CAAAATGTTCATCACAAACAGTTGTC 58.607 34.615 2.92 0.00 45.00 3.18
6244 8681 6.313411 CACCAAAATGTTCATCACAAACAGTT 59.687 34.615 0.00 0.00 44.14 3.16
6245 8682 5.811613 CACCAAAATGTTCATCACAAACAGT 59.188 36.000 0.00 0.00 39.78 3.55
6248 8685 6.476896 CAACACCAAAATGTTCATCACAAAC 58.523 36.000 0.00 0.00 40.89 2.93
6250 8687 4.569966 GCAACACCAAAATGTTCATCACAA 59.430 37.500 0.00 0.00 40.89 3.33
6251 8688 4.118410 GCAACACCAAAATGTTCATCACA 58.882 39.130 0.00 0.00 40.89 3.58
6301 8738 4.530161 CAGCATCTCTAGCCCTATTTAGGT 59.470 45.833 3.05 0.00 42.03 3.08
6319 8762 1.271379 ACCAACGCTTCCTTACAGCAT 60.271 47.619 0.00 0.00 37.07 3.79
6344 8788 1.002544 CCAGCCCTTCTTTTCTCGAGT 59.997 52.381 13.13 0.00 0.00 4.18
6347 8791 1.002544 ACTCCAGCCCTTCTTTTCTCG 59.997 52.381 0.00 0.00 0.00 4.04
6352 8796 1.149101 TTCCACTCCAGCCCTTCTTT 58.851 50.000 0.00 0.00 0.00 2.52
6362 8806 1.203300 TCCTCACCTGATTCCACTCCA 60.203 52.381 0.00 0.00 0.00 3.86
6363 8807 1.484240 CTCCTCACCTGATTCCACTCC 59.516 57.143 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.