Multiple sequence alignment - TraesCS5A01G098500

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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 TraesCS5A01G098500 chr5A 100.000 1770 0 0 435 2204 139790946 139789177 0.000000e+00 3269.0
1 TraesCS5A01G098500 chr5A 100.000 180 0 0 1 180 139791380 139791201 1.260000e-87 333.0
2 TraesCS5A01G098500 chr5A 88.372 258 24 4 435 686 12670610 12670353 2.750000e-79 305.0
3 TraesCS5A01G098500 chr5A 90.608 181 16 1 1 180 12671092 12670912 2.830000e-59 239.0
4 TraesCS5A01G098500 chr5A 88.462 52 3 3 663 712 541949183 541949233 2.360000e-05 60.2
5 TraesCS5A01G098500 chr5B 86.408 721 62 15 733 1418 429933047 429932328 0.000000e+00 756.0
6 TraesCS5A01G098500 chr5B 89.766 342 23 4 1418 1757 658367392 658367723 5.620000e-116 427.0
7 TraesCS5A01G098500 chr5B 86.268 284 29 6 1754 2028 658367940 658368222 1.280000e-77 300.0
8 TraesCS5A01G098500 chr5B 91.919 198 14 1 492 687 86482530 86482727 2.160000e-70 276.0
9 TraesCS5A01G098500 chr5B 93.130 131 6 3 713 841 429933349 429933220 2.890000e-44 189.0
10 TraesCS5A01G098500 chr5D 89.807 569 51 4 856 1418 364372206 364371639 0.000000e+00 723.0
11 TraesCS5A01G098500 chr5D 93.130 131 6 3 713 841 364372574 364372445 2.890000e-44 189.0
12 TraesCS5A01G098500 chr6A 94.954 218 10 1 1988 2204 612168906 612168689 7.540000e-90 340.0
13 TraesCS5A01G098500 chr6A 88.462 52 3 3 663 712 158997766 158997716 2.360000e-05 60.2
14 TraesCS5A01G098500 chr4D 89.764 254 20 4 435 686 441535972 441535723 9.820000e-84 320.0
15 TraesCS5A01G098500 chr4D 91.160 181 15 1 1 180 441536231 441536051 6.080000e-61 244.0
16 TraesCS5A01G098500 chr4D 77.003 287 36 16 1556 1820 438795646 438795368 1.060000e-28 137.0
17 TraesCS5A01G098500 chr1B 88.281 256 19 8 435 686 555875926 555876174 1.650000e-76 296.0
18 TraesCS5A01G098500 chr1B 89.571 163 14 3 1 162 555875396 555875556 1.030000e-48 204.0
19 TraesCS5A01G098500 chr1A 90.608 181 16 1 1 180 7987530 7987710 2.830000e-59 239.0
20 TraesCS5A01G098500 chr1A 86.517 178 14 4 1250 1418 239946332 239946156 1.040000e-43 187.0
21 TraesCS5A01G098500 chr1A 89.333 75 7 1 435 509 7987770 7987843 2.330000e-15 93.5
22 TraesCS5A01G098500 chr1A 88.462 52 3 3 663 712 70946740 70946690 2.360000e-05 60.2
23 TraesCS5A01G098500 chr6B 89.503 181 17 2 1 180 361274445 361274624 6.120000e-56 228.0
24 TraesCS5A01G098500 chr2A 88.950 181 18 2 1 180 425029441 425029620 2.850000e-54 222.0
25 TraesCS5A01G098500 chr2A 86.517 178 14 4 1250 1418 424595148 424594972 1.040000e-43 187.0
26 TraesCS5A01G098500 chr2A 84.270 178 18 4 1250 1418 280056764 280056588 4.870000e-37 165.0
27 TraesCS5A01G098500 chr2A 88.182 110 12 1 458 567 425030022 425030130 1.780000e-26 130.0
28 TraesCS5A01G098500 chr3A 85.955 178 15 4 1250 1418 161657377 161657201 4.830000e-42 182.0
29 TraesCS5A01G098500 chr7B 86.164 159 19 3 23 179 478012920 478013077 3.760000e-38 169.0
30 TraesCS5A01G098500 chr7B 81.633 196 23 5 435 627 366775606 366775421 1.360000e-32 150.0
31 TraesCS5A01G098500 chr7A 86.000 150 20 1 6 154 370801626 370801477 2.260000e-35 159.0
32 TraesCS5A01G098500 chr7D 87.407 135 13 3 473 604 400316499 400316632 3.790000e-33 152.0
33 TraesCS5A01G098500 chr7D 86.364 132 14 4 465 594 400316452 400316581 8.200000e-30 141.0
34 TraesCS5A01G098500 chr7D 76.307 287 38 16 1556 1820 587107042 587106764 2.300000e-25 126.0
35 TraesCS5A01G098500 chr6D 86.765 136 17 1 24 158 282803599 282803464 1.360000e-32 150.0
36 TraesCS5A01G098500 chr6D 91.489 47 2 2 644 689 282827497 282827452 1.830000e-06 63.9
37 TraesCS5A01G098500 chr3B 81.503 173 18 7 466 634 409964737 409964575 1.780000e-26 130.0
38 TraesCS5A01G098500 chr3B 95.000 40 1 1 663 701 249674421 249674460 6.570000e-06 62.1
39 TraesCS5A01G098500 chr3B 83.333 72 6 5 616 686 304802945 304803011 6.570000e-06 62.1
40 TraesCS5A01G098500 chrUn 89.333 75 7 1 435 509 268290438 268290365 2.330000e-15 93.5
41 TraesCS5A01G098500 chr4B 92.000 50 1 3 663 711 451451786 451451739 1.410000e-07 67.6
42 TraesCS5A01G098500 chr3D 95.000 40 2 0 2105 2144 589010114 589010075 1.830000e-06 63.9
43 TraesCS5A01G098500 chr2B 88.462 52 4 2 663 713 709201053 709201003 6.570000e-06 62.1


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 TraesCS5A01G098500 chr5A 139789177 139791380 2203 True 1801.0 3269 100.0000 1 2204 2 chr5A.!!$R2 2203
1 TraesCS5A01G098500 chr5A 12670353 12671092 739 True 272.0 305 89.4900 1 686 2 chr5A.!!$R1 685
2 TraesCS5A01G098500 chr5B 429932328 429933349 1021 True 472.5 756 89.7690 713 1418 2 chr5B.!!$R1 705
3 TraesCS5A01G098500 chr5B 658367392 658368222 830 False 363.5 427 88.0170 1418 2028 2 chr5B.!!$F2 610
4 TraesCS5A01G098500 chr5D 364371639 364372574 935 True 456.0 723 91.4685 713 1418 2 chr5D.!!$R1 705
5 TraesCS5A01G098500 chr4D 441535723 441536231 508 True 282.0 320 90.4620 1 686 2 chr4D.!!$R2 685
6 TraesCS5A01G098500 chr1B 555875396 555876174 778 False 250.0 296 88.9260 1 686 2 chr1B.!!$F1 685

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
725 1159 0.784778 GAGCGTGACACAACTACAGC 59.215 55.0 6.37 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2932 0.039618 GGAGCCTCCCATGGTTTTCA 59.96 55.0 11.73 0.0 0.0 2.69 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
21 22 3.807538 GCCTGCAGTGATGGCGTG 61.808 66.667 13.81 0.00 37.11 5.34
109 110 2.440817 GCCAGGCGTAGTATGGGGT 61.441 63.158 0.00 0.00 36.10 4.95
580 1010 4.052518 GTGGGGCTGGCCATCACT 62.053 66.667 22.68 0.00 38.14 3.41
621 1051 3.009115 GCAGGAGTGGGTGGGCTA 61.009 66.667 0.00 0.00 0.00 3.93
656 1090 2.474112 TCCTTCACGCCCTTTATAGGT 58.526 47.619 0.00 0.00 40.19 3.08
674 1108 3.924922 AGGTCGAGGGGTAACAGAATAT 58.075 45.455 0.00 0.00 39.74 1.28
692 1126 8.522178 CAGAATATTATTCTGTTACCCTCGAC 57.478 38.462 27.48 0.00 40.63 4.20
693 1127 7.599245 CAGAATATTATTCTGTTACCCTCGACC 59.401 40.741 27.48 0.00 40.63 4.79
694 1128 4.684484 ATTATTCTGTTACCCTCGACCC 57.316 45.455 0.00 0.00 0.00 4.46
695 1129 2.249309 ATTCTGTTACCCTCGACCCT 57.751 50.000 0.00 0.00 0.00 4.34
696 1130 2.905415 TTCTGTTACCCTCGACCCTA 57.095 50.000 0.00 0.00 0.00 3.53
697 1131 3.393426 TTCTGTTACCCTCGACCCTAT 57.607 47.619 0.00 0.00 0.00 2.57
698 1132 4.524802 TTCTGTTACCCTCGACCCTATA 57.475 45.455 0.00 0.00 0.00 1.31
699 1133 4.736611 TCTGTTACCCTCGACCCTATAT 57.263 45.455 0.00 0.00 0.00 0.86
700 1134 5.848286 TCTGTTACCCTCGACCCTATATA 57.152 43.478 0.00 0.00 0.00 0.86
701 1135 5.813383 TCTGTTACCCTCGACCCTATATAG 58.187 45.833 2.46 2.46 0.00 1.31
702 1136 5.549228 TCTGTTACCCTCGACCCTATATAGA 59.451 44.000 11.53 0.00 0.00 1.98
703 1137 5.564550 TGTTACCCTCGACCCTATATAGAC 58.435 45.833 11.53 2.09 0.00 2.59
704 1138 5.073554 TGTTACCCTCGACCCTATATAGACA 59.926 44.000 11.53 0.42 0.00 3.41
705 1139 4.031636 ACCCTCGACCCTATATAGACAC 57.968 50.000 11.53 1.44 0.00 3.67
706 1140 3.008330 CCCTCGACCCTATATAGACACG 58.992 54.545 11.53 12.20 0.00 4.49
707 1141 3.307269 CCCTCGACCCTATATAGACACGA 60.307 52.174 11.53 15.17 0.00 4.35
708 1142 3.933955 CCTCGACCCTATATAGACACGAG 59.066 52.174 26.31 26.31 43.23 4.18
709 1143 3.332919 TCGACCCTATATAGACACGAGC 58.667 50.000 11.53 0.00 0.00 5.03
710 1144 2.093941 CGACCCTATATAGACACGAGCG 59.906 54.545 11.53 1.94 0.00 5.03
711 1145 3.072944 GACCCTATATAGACACGAGCGT 58.927 50.000 11.53 0.00 0.00 5.07
725 1159 0.784778 GAGCGTGACACAACTACAGC 59.215 55.000 6.37 0.00 0.00 4.40
727 1161 1.202533 AGCGTGACACAACTACAGCTT 60.203 47.619 6.37 0.00 0.00 3.74
729 1163 2.743938 CGTGACACAACTACAGCTTCT 58.256 47.619 6.37 0.00 0.00 2.85
730 1164 2.726760 CGTGACACAACTACAGCTTCTC 59.273 50.000 6.37 0.00 0.00 2.87
731 1165 2.726760 GTGACACAACTACAGCTTCTCG 59.273 50.000 0.00 0.00 0.00 4.04
737 1171 3.258372 ACAACTACAGCTTCTCGATCCAA 59.742 43.478 0.00 0.00 0.00 3.53
754 1188 2.448582 AACCCACCAGCTCGAACCA 61.449 57.895 0.00 0.00 0.00 3.67
755 1189 1.779061 AACCCACCAGCTCGAACCAT 61.779 55.000 0.00 0.00 0.00 3.55
829 1264 1.427753 CCCCCAAACCACCTACTTTCT 59.572 52.381 0.00 0.00 0.00 2.52
841 1276 3.892588 ACCTACTTTCTCGATCCCATCTC 59.107 47.826 0.00 0.00 0.00 2.75
842 1277 3.057876 CCTACTTTCTCGATCCCATCTCG 60.058 52.174 0.00 0.00 37.47 4.04
843 1278 2.379972 ACTTTCTCGATCCCATCTCGT 58.620 47.619 0.00 0.00 37.40 4.18
844 1279 2.761208 ACTTTCTCGATCCCATCTCGTT 59.239 45.455 0.00 0.00 37.40 3.85
845 1280 2.871182 TTCTCGATCCCATCTCGTTG 57.129 50.000 0.00 0.00 37.40 4.10
846 1281 1.763968 TCTCGATCCCATCTCGTTGT 58.236 50.000 0.00 0.00 37.40 3.32
1048 1793 1.421410 CCTCCGCGTGAAGATTTCCG 61.421 60.000 4.92 0.00 0.00 4.30
1049 1794 1.421410 CTCCGCGTGAAGATTTCCGG 61.421 60.000 4.92 0.00 34.60 5.14
1050 1795 2.399611 CGCGTGAAGATTTCCGGC 59.600 61.111 0.00 0.00 0.00 6.13
1052 1797 2.098233 GCGTGAAGATTTCCGGCGA 61.098 57.895 9.30 0.00 0.00 5.54
1053 1798 1.429148 GCGTGAAGATTTCCGGCGAT 61.429 55.000 9.30 0.00 0.00 4.58
1066 1811 2.279517 GCGATGAGATCCGGCGTT 60.280 61.111 6.01 0.00 0.00 4.84
1096 1842 2.201771 GGGTAGGAGGCGGAGGAT 59.798 66.667 0.00 0.00 0.00 3.24
1097 1843 1.909287 GGGTAGGAGGCGGAGGATC 60.909 68.421 0.00 0.00 0.00 3.36
1108 1854 3.298958 GAGGATCCAGCGGTGACA 58.701 61.111 17.83 1.97 0.00 3.58
1133 1879 1.055040 GCTAGGGATGCAGAGGACAT 58.945 55.000 0.00 0.00 0.00 3.06
1147 1893 2.874694 GACATGCATGACGCGCGAT 61.875 57.895 39.36 21.24 46.97 4.58
1178 1924 2.751036 CATGGGTGGTGATGCGCA 60.751 61.111 14.96 14.96 0.00 6.09
1183 1929 2.334946 GGTGGTGATGCGCATGTGT 61.335 57.895 30.76 3.52 0.00 3.72
1197 1943 0.627451 ATGTGTGCCACTCCATCCAT 59.373 50.000 0.00 0.00 35.11 3.41
1245 1991 1.141881 ATGCCGTCGACTCATCCAC 59.858 57.895 14.70 0.00 0.00 4.02
1246 1992 2.202756 GCCGTCGACTCATCCACC 60.203 66.667 14.70 0.00 0.00 4.61
1255 2001 2.531428 TCATCCACCCACTGCCCA 60.531 61.111 0.00 0.00 0.00 5.36
1258 2004 1.229820 ATCCACCCACTGCCCACTA 60.230 57.895 0.00 0.00 0.00 2.74
1318 2064 0.671796 TCGTCGGCAGTTCTTCTTCA 59.328 50.000 0.00 0.00 0.00 3.02
1321 2067 1.048601 TCGGCAGTTCTTCTTCACCT 58.951 50.000 0.00 0.00 0.00 4.00
1327 2073 3.244249 GCAGTTCTTCTTCACCTACACCT 60.244 47.826 0.00 0.00 0.00 4.00
1359 2109 1.144503 GGCATCTCATCCCCACATCTT 59.855 52.381 0.00 0.00 0.00 2.40
1375 2126 6.205464 CCCACATCTTCGTATAATTGATGCTT 59.795 38.462 0.00 0.00 38.33 3.91
1396 2147 5.616424 GCTTGCTTGACAGTTCATAGACAAG 60.616 44.000 0.00 0.00 39.41 3.16
1422 2173 0.900647 AGCGGTGGTCTCTAGCAGTT 60.901 55.000 0.00 0.00 32.75 3.16
1424 2175 0.737715 CGGTGGTCTCTAGCAGTTGC 60.738 60.000 0.00 0.00 42.49 4.17
1447 2198 4.380867 CGGATCCAGAAATTCAACTTTGGG 60.381 45.833 13.41 0.00 0.00 4.12
1448 2199 4.498241 GATCCAGAAATTCAACTTTGGGC 58.502 43.478 0.00 0.00 0.00 5.36
1449 2200 3.303938 TCCAGAAATTCAACTTTGGGCA 58.696 40.909 0.00 0.00 0.00 5.36
1453 2204 5.299148 CAGAAATTCAACTTTGGGCATTCA 58.701 37.500 0.00 0.00 0.00 2.57
1459 2210 7.585579 ATTCAACTTTGGGCATTCAAATTTT 57.414 28.000 0.00 0.00 36.24 1.82
1557 2308 9.959775 CTAGAAGATTAACGAAATTGTTCACTC 57.040 33.333 0.00 0.00 32.89 3.51
1585 2336 9.696917 ACTCCATAAAGTTTTCAAATCAATGTC 57.303 29.630 0.00 0.00 0.00 3.06
1593 2344 5.982890 TTTCAAATCAATGTCCTTCCTCC 57.017 39.130 0.00 0.00 0.00 4.30
1607 2358 6.004574 GTCCTTCCTCCTAAGTTTTGAATGT 58.995 40.000 0.00 0.00 0.00 2.71
1608 2359 6.490381 GTCCTTCCTCCTAAGTTTTGAATGTT 59.510 38.462 0.00 0.00 0.00 2.71
1609 2360 7.664318 GTCCTTCCTCCTAAGTTTTGAATGTTA 59.336 37.037 0.00 0.00 0.00 2.41
1610 2361 8.390921 TCCTTCCTCCTAAGTTTTGAATGTTAT 58.609 33.333 0.00 0.00 0.00 1.89
1611 2362 9.681062 CCTTCCTCCTAAGTTTTGAATGTTATA 57.319 33.333 0.00 0.00 0.00 0.98
1635 2386 7.054491 ACTGCCTACAATTCAAAGACAATTT 57.946 32.000 0.00 0.00 0.00 1.82
1735 2488 6.359617 CCGAAAATAAGCAACACACTTAGTTG 59.640 38.462 0.00 0.00 46.86 3.16
1774 2747 6.762187 ACATTCAGTGAACATTGCAATTTCAA 59.238 30.769 25.21 16.57 31.21 2.69
1775 2748 7.280428 ACATTCAGTGAACATTGCAATTTCAAA 59.720 29.630 25.21 19.76 31.21 2.69
1797 2770 6.641161 AAATTGGAAAGGGATTTGCCTTAT 57.359 33.333 3.61 0.00 36.66 1.73
1801 2774 3.452264 GGAAAGGGATTTGCCTTATGCTT 59.548 43.478 3.61 0.00 42.00 3.91
1818 2791 7.201679 CCTTATGCTTAGAGATTGAGGTTGTTG 60.202 40.741 0.00 0.00 0.00 3.33
1822 2795 5.734720 CTTAGAGATTGAGGTTGTTGGCTA 58.265 41.667 0.00 0.00 0.00 3.93
1837 2810 1.134128 TGGCTACACTGGTATGGCATG 60.134 52.381 10.98 0.00 32.48 4.06
1844 2817 0.465705 CTGGTATGGCATGGACGACT 59.534 55.000 10.98 0.00 0.00 4.18
1850 2823 3.503363 GCATGGACGACTGCAGCC 61.503 66.667 15.27 7.45 38.28 4.85
1896 2878 2.514592 CGGTGCATCGCAATCCCT 60.515 61.111 6.36 0.00 41.47 4.20
1897 2879 1.227527 CGGTGCATCGCAATCCCTA 60.228 57.895 6.36 0.00 41.47 3.53
1902 2884 1.133823 TGCATCGCAATCCCTATTGGT 60.134 47.619 0.00 0.00 42.39 3.67
1908 2890 1.686115 GCAATCCCTATTGGTGGCAGT 60.686 52.381 0.00 0.00 42.39 4.40
1934 2916 3.289834 CACCGTGCAGCTTGCCTT 61.290 61.111 5.82 0.00 44.23 4.35
1944 2926 1.600916 GCTTGCCTTTGTCCTCCGT 60.601 57.895 0.00 0.00 0.00 4.69
1947 2929 1.002087 CTTGCCTTTGTCCTCCGTAGT 59.998 52.381 0.00 0.00 0.00 2.73
1950 2932 0.974383 CCTTTGTCCTCCGTAGTGGT 59.026 55.000 0.00 0.00 39.52 4.16
1964 2946 2.292828 AGTGGTGAAAACCATGGGAG 57.707 50.000 18.09 0.00 42.41 4.30
1966 2948 0.541764 TGGTGAAAACCATGGGAGGC 60.542 55.000 18.09 3.28 34.33 4.70
1977 2959 3.090532 GGGAGGCTCCATCCCGTT 61.091 66.667 33.27 0.00 46.85 4.44
1983 2965 4.143333 CTCCATCCCGTTCGGCGT 62.143 66.667 6.85 0.00 39.32 5.68
1997 2979 4.980805 GCGTCGGTGGCTTGGTCA 62.981 66.667 0.00 0.00 0.00 4.02
2013 2995 1.687146 TCAAGCTCTCCCTCGCCAT 60.687 57.895 0.00 0.00 0.00 4.40
2018 3000 1.953017 CTCTCCCTCGCCATACTCG 59.047 63.158 0.00 0.00 0.00 4.18
2021 3003 3.536917 CCCTCGCCATACTCGCCA 61.537 66.667 0.00 0.00 0.00 5.69
2042 3024 3.598715 GCACACAGCAAGCCAGCA 61.599 61.111 0.55 0.00 44.79 4.41
2043 3025 3.121934 CACACAGCAAGCCAGCAA 58.878 55.556 0.55 0.00 36.85 3.91
2044 3026 1.299620 CACACAGCAAGCCAGCAAC 60.300 57.895 0.55 0.00 36.85 4.17
2045 3027 2.050714 CACAGCAAGCCAGCAACG 60.051 61.111 0.55 0.00 36.85 4.10
2046 3028 2.516930 ACAGCAAGCCAGCAACGT 60.517 55.556 0.55 0.00 36.85 3.99
2047 3029 2.050714 CAGCAAGCCAGCAACGTG 60.051 61.111 0.00 0.00 36.85 4.49
2048 3030 2.516930 AGCAAGCCAGCAACGTGT 60.517 55.556 0.00 0.00 36.85 4.49
2049 3031 2.050985 GCAAGCCAGCAACGTGTC 60.051 61.111 0.00 0.00 0.00 3.67
2050 3032 2.249309 CAAGCCAGCAACGTGTCG 59.751 61.111 0.00 0.00 0.00 4.35
2051 3033 3.649986 AAGCCAGCAACGTGTCGC 61.650 61.111 0.00 0.00 0.00 5.19
2054 3036 4.012895 CCAGCAACGTGTCGCCAC 62.013 66.667 0.00 0.00 38.27 5.01
2055 3037 4.012895 CAGCAACGTGTCGCCACC 62.013 66.667 0.00 0.00 38.41 4.61
2056 3038 4.235762 AGCAACGTGTCGCCACCT 62.236 61.111 0.00 0.00 38.41 4.00
2057 3039 2.356553 GCAACGTGTCGCCACCTA 60.357 61.111 0.00 0.00 38.41 3.08
2058 3040 2.380410 GCAACGTGTCGCCACCTAG 61.380 63.158 0.00 0.00 38.41 3.02
2059 3041 1.006571 CAACGTGTCGCCACCTAGT 60.007 57.895 0.00 0.00 38.41 2.57
2060 3042 1.007336 CAACGTGTCGCCACCTAGTC 61.007 60.000 0.00 0.00 38.41 2.59
2061 3043 2.151049 AACGTGTCGCCACCTAGTCC 62.151 60.000 0.00 0.00 38.41 3.85
2062 3044 2.632544 CGTGTCGCCACCTAGTCCA 61.633 63.158 0.00 0.00 38.41 4.02
2063 3045 1.898154 GTGTCGCCACCTAGTCCAT 59.102 57.895 0.00 0.00 35.44 3.41
2064 3046 0.460284 GTGTCGCCACCTAGTCCATG 60.460 60.000 0.00 0.00 35.44 3.66
2065 3047 1.144057 GTCGCCACCTAGTCCATGG 59.856 63.158 4.97 4.97 36.51 3.66
2066 3048 2.063979 TCGCCACCTAGTCCATGGG 61.064 63.158 13.02 0.00 33.81 4.00
2067 3049 2.193248 GCCACCTAGTCCATGGGC 59.807 66.667 8.79 8.79 33.81 5.36
2068 3050 2.679342 GCCACCTAGTCCATGGGCA 61.679 63.158 20.74 3.57 41.02 5.36
2069 3051 1.528824 CCACCTAGTCCATGGGCAG 59.471 63.158 20.74 13.48 31.04 4.85
2070 3052 0.982852 CCACCTAGTCCATGGGCAGA 60.983 60.000 20.74 4.80 31.04 4.26
2071 3053 1.135094 CACCTAGTCCATGGGCAGAT 58.865 55.000 20.74 0.00 31.04 2.90
2072 3054 1.135094 ACCTAGTCCATGGGCAGATG 58.865 55.000 20.74 6.37 31.04 2.90
2073 3055 1.344393 ACCTAGTCCATGGGCAGATGA 60.344 52.381 20.74 0.00 31.04 2.92
2074 3056 1.770658 CCTAGTCCATGGGCAGATGAA 59.229 52.381 20.74 0.00 0.00 2.57
2075 3057 2.173356 CCTAGTCCATGGGCAGATGAAA 59.827 50.000 20.74 0.00 0.00 2.69
2076 3058 3.181436 CCTAGTCCATGGGCAGATGAAAT 60.181 47.826 20.74 0.00 0.00 2.17
2077 3059 3.393426 AGTCCATGGGCAGATGAAATT 57.607 42.857 20.74 0.00 0.00 1.82
2078 3060 3.028850 AGTCCATGGGCAGATGAAATTG 58.971 45.455 20.74 0.00 0.00 2.32
2079 3061 3.025978 GTCCATGGGCAGATGAAATTGA 58.974 45.455 12.68 0.00 0.00 2.57
2080 3062 3.640029 GTCCATGGGCAGATGAAATTGAT 59.360 43.478 12.68 0.00 0.00 2.57
2081 3063 3.639561 TCCATGGGCAGATGAAATTGATG 59.360 43.478 13.02 0.00 0.00 3.07
2082 3064 3.244078 CCATGGGCAGATGAAATTGATGG 60.244 47.826 2.85 0.00 0.00 3.51
2083 3065 1.758280 TGGGCAGATGAAATTGATGGC 59.242 47.619 0.00 0.00 35.85 4.40
2084 3066 2.037144 GGGCAGATGAAATTGATGGCT 58.963 47.619 0.00 0.00 36.73 4.75
2085 3067 2.223971 GGGCAGATGAAATTGATGGCTG 60.224 50.000 0.00 0.00 36.73 4.85
2086 3068 2.223971 GGCAGATGAAATTGATGGCTGG 60.224 50.000 0.00 0.00 33.97 4.85
2087 3069 2.802057 GCAGATGAAATTGATGGCTGGC 60.802 50.000 0.00 0.00 0.00 4.85
2088 3070 2.693591 CAGATGAAATTGATGGCTGGCT 59.306 45.455 2.00 0.00 0.00 4.75
2089 3071 2.693591 AGATGAAATTGATGGCTGGCTG 59.306 45.455 2.00 0.00 0.00 4.85
2090 3072 0.533491 TGAAATTGATGGCTGGCTGC 59.467 50.000 7.96 7.96 41.94 5.25
2091 3073 0.533491 GAAATTGATGGCTGGCTGCA 59.467 50.000 18.32 4.95 45.15 4.41
2092 3074 1.138266 GAAATTGATGGCTGGCTGCAT 59.862 47.619 18.32 9.46 45.15 3.96
2093 3075 0.464036 AATTGATGGCTGGCTGCATG 59.536 50.000 18.32 0.00 45.15 4.06
2094 3076 2.028125 ATTGATGGCTGGCTGCATGC 62.028 55.000 18.32 11.82 45.15 4.06
2095 3077 4.266070 GATGGCTGGCTGCATGCG 62.266 66.667 18.32 9.16 45.15 4.73
2099 3081 3.740397 GCTGGCTGCATGCGTGAA 61.740 61.111 14.09 0.00 44.05 3.18
2100 3082 2.483745 CTGGCTGCATGCGTGAAG 59.516 61.111 14.09 10.35 44.05 3.02
2101 3083 2.032376 TGGCTGCATGCGTGAAGA 59.968 55.556 18.78 0.00 44.05 2.87
2102 3084 2.249557 CTGGCTGCATGCGTGAAGAC 62.250 60.000 18.78 16.23 39.80 3.01
2103 3085 2.327343 GGCTGCATGCGTGAAGACA 61.327 57.895 18.78 0.77 39.09 3.41
2104 3086 1.134075 GCTGCATGCGTGAAGACAG 59.866 57.895 18.78 11.98 32.12 3.51
2105 3087 1.134075 CTGCATGCGTGAAGACAGC 59.866 57.895 8.38 0.00 32.12 4.40
2106 3088 1.296755 CTGCATGCGTGAAGACAGCT 61.297 55.000 8.38 0.00 32.12 4.24
2107 3089 1.293963 TGCATGCGTGAAGACAGCTC 61.294 55.000 14.09 0.00 0.00 4.09
2108 3090 1.293963 GCATGCGTGAAGACAGCTCA 61.294 55.000 10.93 0.00 0.00 4.26
2109 3091 0.441533 CATGCGTGAAGACAGCTCAC 59.558 55.000 0.00 0.00 0.00 3.51
2110 3092 0.319728 ATGCGTGAAGACAGCTCACT 59.680 50.000 2.09 0.00 32.68 3.41
2121 3103 1.875009 CAGCTCACTGTTGCTTCTGA 58.125 50.000 2.76 0.00 39.22 3.27
2122 3104 2.216046 CAGCTCACTGTTGCTTCTGAA 58.784 47.619 2.76 0.00 39.22 3.02
2123 3105 2.615447 CAGCTCACTGTTGCTTCTGAAA 59.385 45.455 2.76 0.00 39.22 2.69
2124 3106 3.252701 CAGCTCACTGTTGCTTCTGAAAT 59.747 43.478 2.76 0.00 39.22 2.17
2125 3107 3.252701 AGCTCACTGTTGCTTCTGAAATG 59.747 43.478 0.00 0.00 35.86 2.32
2126 3108 3.611057 GCTCACTGTTGCTTCTGAAATGG 60.611 47.826 0.00 0.00 0.00 3.16
2127 3109 2.886523 TCACTGTTGCTTCTGAAATGGG 59.113 45.455 0.00 0.00 0.00 4.00
2128 3110 1.615392 ACTGTTGCTTCTGAAATGGGC 59.385 47.619 0.00 0.00 0.00 5.36
2129 3111 1.891150 CTGTTGCTTCTGAAATGGGCT 59.109 47.619 0.00 0.00 0.00 5.19
2130 3112 3.084039 CTGTTGCTTCTGAAATGGGCTA 58.916 45.455 0.00 0.00 0.00 3.93
2131 3113 2.819608 TGTTGCTTCTGAAATGGGCTAC 59.180 45.455 6.88 6.88 0.00 3.58
2132 3114 3.084786 GTTGCTTCTGAAATGGGCTACT 58.915 45.455 6.67 0.00 0.00 2.57
2133 3115 4.261801 GTTGCTTCTGAAATGGGCTACTA 58.738 43.478 6.67 0.00 0.00 1.82
2134 3116 4.568072 TGCTTCTGAAATGGGCTACTAA 57.432 40.909 0.00 0.00 0.00 2.24
2135 3117 5.116084 TGCTTCTGAAATGGGCTACTAAT 57.884 39.130 0.00 0.00 0.00 1.73
2136 3118 4.883585 TGCTTCTGAAATGGGCTACTAATG 59.116 41.667 0.00 0.00 0.00 1.90
2137 3119 4.276926 GCTTCTGAAATGGGCTACTAATGG 59.723 45.833 0.00 0.00 0.00 3.16
2138 3120 4.437682 TCTGAAATGGGCTACTAATGGG 57.562 45.455 0.00 0.00 0.00 4.00
2139 3121 2.887152 CTGAAATGGGCTACTAATGGGC 59.113 50.000 0.00 0.00 0.00 5.36
2148 3130 5.437191 GGCTACTAATGGGCCTATACATT 57.563 43.478 0.24 6.10 42.31 2.71
2149 3131 5.186198 GGCTACTAATGGGCCTATACATTG 58.814 45.833 13.42 7.43 42.31 2.82
2150 3132 5.280521 GGCTACTAATGGGCCTATACATTGT 60.281 44.000 13.42 11.53 42.31 2.71
2151 3133 6.070424 GGCTACTAATGGGCCTATACATTGTA 60.070 42.308 13.42 11.91 42.31 2.41
2152 3134 7.042335 GCTACTAATGGGCCTATACATTGTAG 58.958 42.308 21.33 21.33 39.04 2.74
2153 3135 7.093465 GCTACTAATGGGCCTATACATTGTAGA 60.093 40.741 25.09 0.00 38.77 2.59
2154 3136 7.814693 ACTAATGGGCCTATACATTGTAGAT 57.185 36.000 13.42 0.00 37.80 1.98
2155 3137 8.219660 ACTAATGGGCCTATACATTGTAGATT 57.780 34.615 13.42 0.00 37.80 2.40
2156 3138 9.333961 ACTAATGGGCCTATACATTGTAGATTA 57.666 33.333 13.42 0.00 37.80 1.75
2159 3141 9.466497 AATGGGCCTATACATTGTAGATTATTG 57.534 33.333 0.24 0.00 36.07 1.90
2160 3142 7.984475 TGGGCCTATACATTGTAGATTATTGT 58.016 34.615 4.53 0.00 0.00 2.71
2161 3143 8.100791 TGGGCCTATACATTGTAGATTATTGTC 58.899 37.037 4.53 0.00 0.00 3.18
2162 3144 8.322091 GGGCCTATACATTGTAGATTATTGTCT 58.678 37.037 0.84 0.00 0.00 3.41
2163 3145 9.372369 GGCCTATACATTGTAGATTATTGTCTC 57.628 37.037 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 2.129146 CGACGCCCACCCCATACTA 61.129 63.158 0.00 0.00 0.00 1.82
109 110 3.072468 CCTCCTAACCGACGCCCA 61.072 66.667 0.00 0.00 0.00 5.36
441 842 1.427072 CCCCACCTTCTTCCCAGTGT 61.427 60.000 0.00 0.00 0.00 3.55
443 844 1.072930 ACCCCACCTTCTTCCCAGT 60.073 57.895 0.00 0.00 0.00 4.00
469 870 2.348998 CACCTTCTTCCTGGCGCT 59.651 61.111 7.64 0.00 0.00 5.92
542 970 1.751143 TTCTCCCCTGTCTGGACCCT 61.751 60.000 0.00 0.00 38.35 4.34
580 1010 2.764128 GTCTCCGGCTGGATCCCA 60.764 66.667 16.52 0.00 45.33 4.37
606 1036 0.044855 AATCTAGCCCACCCACTCCT 59.955 55.000 0.00 0.00 0.00 3.69
648 1082 4.870636 TCTGTTACCCCTCGACCTATAAA 58.129 43.478 0.00 0.00 0.00 1.40
656 1090 7.667557 CAGAATAATATTCTGTTACCCCTCGA 58.332 38.462 26.63 0.00 40.63 4.04
674 1108 3.716431 AGGGTCGAGGGTAACAGAATAA 58.284 45.455 0.00 0.00 39.74 1.40
686 1120 3.933955 CTCGTGTCTATATAGGGTCGAGG 59.066 52.174 25.36 15.91 39.46 4.63
687 1121 3.371591 GCTCGTGTCTATATAGGGTCGAG 59.628 52.174 26.91 26.91 43.78 4.04
688 1122 3.332919 GCTCGTGTCTATATAGGGTCGA 58.667 50.000 9.89 14.11 0.00 4.20
689 1123 2.093941 CGCTCGTGTCTATATAGGGTCG 59.906 54.545 9.89 11.13 0.00 4.79
690 1124 3.072944 ACGCTCGTGTCTATATAGGGTC 58.927 50.000 9.89 2.51 0.00 4.46
691 1125 2.812591 CACGCTCGTGTCTATATAGGGT 59.187 50.000 13.66 0.00 40.91 4.34
692 1126 3.072211 TCACGCTCGTGTCTATATAGGG 58.928 50.000 19.95 0.00 45.55 3.53
693 1127 3.497262 TGTCACGCTCGTGTCTATATAGG 59.503 47.826 19.95 0.00 45.55 2.57
694 1128 4.025145 TGTGTCACGCTCGTGTCTATATAG 60.025 45.833 19.95 3.10 45.55 1.31
695 1129 3.872771 TGTGTCACGCTCGTGTCTATATA 59.127 43.478 19.95 0.00 45.55 0.86
696 1130 2.681344 TGTGTCACGCTCGTGTCTATAT 59.319 45.455 19.95 0.00 45.55 0.86
697 1131 2.078392 TGTGTCACGCTCGTGTCTATA 58.922 47.619 19.95 5.73 45.55 1.31
698 1132 0.879090 TGTGTCACGCTCGTGTCTAT 59.121 50.000 19.95 0.00 45.55 1.98
699 1133 0.664224 TTGTGTCACGCTCGTGTCTA 59.336 50.000 19.95 7.45 45.55 2.59
700 1134 0.870307 GTTGTGTCACGCTCGTGTCT 60.870 55.000 19.95 0.00 45.55 3.41
701 1135 0.870307 AGTTGTGTCACGCTCGTGTC 60.870 55.000 19.95 15.63 45.55 3.67
702 1136 0.382873 TAGTTGTGTCACGCTCGTGT 59.617 50.000 19.95 3.91 45.55 4.49
703 1137 0.776451 GTAGTTGTGTCACGCTCGTG 59.224 55.000 15.49 15.49 46.64 4.35
704 1138 0.382873 TGTAGTTGTGTCACGCTCGT 59.617 50.000 0.00 0.00 0.00 4.18
705 1139 1.053048 CTGTAGTTGTGTCACGCTCG 58.947 55.000 0.00 0.00 0.00 5.03
706 1140 0.784778 GCTGTAGTTGTGTCACGCTC 59.215 55.000 0.00 0.00 0.00 5.03
707 1141 0.389391 AGCTGTAGTTGTGTCACGCT 59.611 50.000 0.00 2.03 0.00 5.07
708 1142 1.192534 GAAGCTGTAGTTGTGTCACGC 59.807 52.381 0.00 0.00 0.00 5.34
709 1143 2.726760 GAGAAGCTGTAGTTGTGTCACG 59.273 50.000 0.00 0.00 0.00 4.35
710 1144 2.726760 CGAGAAGCTGTAGTTGTGTCAC 59.273 50.000 0.00 0.00 0.00 3.67
711 1145 2.621526 TCGAGAAGCTGTAGTTGTGTCA 59.378 45.455 0.00 0.00 0.00 3.58
718 1152 2.166664 GGTTGGATCGAGAAGCTGTAGT 59.833 50.000 0.00 0.00 0.00 2.73
725 1159 0.613260 TGGTGGGTTGGATCGAGAAG 59.387 55.000 0.00 0.00 0.00 2.85
727 1161 1.899437 GCTGGTGGGTTGGATCGAGA 61.899 60.000 0.00 0.00 0.00 4.04
729 1163 1.899437 GAGCTGGTGGGTTGGATCGA 61.899 60.000 0.00 0.00 0.00 3.59
730 1164 1.450312 GAGCTGGTGGGTTGGATCG 60.450 63.158 0.00 0.00 0.00 3.69
731 1165 1.450312 CGAGCTGGTGGGTTGGATC 60.450 63.158 0.00 0.00 0.00 3.36
737 1171 2.185310 GATGGTTCGAGCTGGTGGGT 62.185 60.000 0.00 0.00 0.00 4.51
754 1188 8.417273 TTTTTCTTTTCCTTTTCTATCGGGAT 57.583 30.769 0.00 0.00 0.00 3.85
755 1189 7.826918 TTTTTCTTTTCCTTTTCTATCGGGA 57.173 32.000 0.00 0.00 0.00 5.14
829 1264 0.380733 CGACAACGAGATGGGATCGA 59.619 55.000 1.94 0.00 42.76 3.59
951 1696 3.474570 GCGAGGGATGGTGGCTCT 61.475 66.667 0.00 0.00 0.00 4.09
1026 1771 0.320374 AAATCTTCACGCGGAGGTCA 59.680 50.000 12.47 0.00 0.00 4.02
1048 1793 3.792053 AACGCCGGATCTCATCGCC 62.792 63.158 5.05 0.00 0.00 5.54
1049 1794 1.883084 AAACGCCGGATCTCATCGC 60.883 57.895 5.05 0.00 0.00 4.58
1050 1795 1.927210 CAAACGCCGGATCTCATCG 59.073 57.895 5.05 0.00 0.00 3.84
1052 1797 0.392998 AAGCAAACGCCGGATCTCAT 60.393 50.000 5.05 0.00 0.00 2.90
1053 1798 1.003839 AAGCAAACGCCGGATCTCA 60.004 52.632 5.05 0.00 0.00 3.27
1062 1807 1.441016 CCGCAGAAGAAGCAAACGC 60.441 57.895 0.00 0.00 0.00 4.84
1066 1811 0.036388 CCTACCCGCAGAAGAAGCAA 60.036 55.000 0.00 0.00 0.00 3.91
1096 1842 3.936203 GTGGGTGTCACCGCTGGA 61.936 66.667 15.93 0.00 39.83 3.86
1137 1883 2.509111 ATCTTGCATCGCGCGTCA 60.509 55.556 30.98 21.99 46.97 4.35
1147 1893 0.323633 CCCATGACCACCATCTTGCA 60.324 55.000 0.00 0.00 31.94 4.08
1228 1974 2.571757 GTGGATGAGTCGACGGCA 59.428 61.111 10.46 13.03 0.00 5.69
1233 1979 1.888436 GCAGTGGGTGGATGAGTCGA 61.888 60.000 0.00 0.00 0.00 4.20
1245 1991 1.201429 AGGAAGTAGTGGGCAGTGGG 61.201 60.000 0.00 0.00 0.00 4.61
1246 1992 0.250513 GAGGAAGTAGTGGGCAGTGG 59.749 60.000 0.00 0.00 0.00 4.00
1255 2001 0.912486 GCCACATGGGAGGAAGTAGT 59.088 55.000 0.00 0.00 40.01 2.73
1258 2004 1.142688 AAGGCCACATGGGAGGAAGT 61.143 55.000 5.01 0.00 40.01 3.01
1327 2073 1.069978 TGAGATGCCGAAACACAGACA 59.930 47.619 0.00 0.00 0.00 3.41
1340 2090 2.502295 GAAGATGTGGGGATGAGATGC 58.498 52.381 0.00 0.00 0.00 3.91
1359 2109 5.584251 TGTCAAGCAAGCATCAATTATACGA 59.416 36.000 0.00 0.00 0.00 3.43
1375 2126 5.213891 TCTTGTCTATGAACTGTCAAGCA 57.786 39.130 0.00 0.00 37.30 3.91
1396 2147 2.100605 AGAGACCACCGCTCAAATTC 57.899 50.000 0.00 0.00 34.85 2.17
1422 2173 3.071874 AGTTGAATTTCTGGATCCGCA 57.928 42.857 7.39 0.00 0.00 5.69
1424 2175 4.380867 CCCAAAGTTGAATTTCTGGATCCG 60.381 45.833 7.39 2.06 0.00 4.18
1459 2210 5.309543 TGGATTCTCTGTTAGGGTGAGAAAA 59.690 40.000 8.42 0.00 45.87 2.29
1463 2214 4.223923 AGTTGGATTCTCTGTTAGGGTGAG 59.776 45.833 0.00 0.00 0.00 3.51
1480 2231 0.179004 ATTGCGTGAACCCAGTTGGA 60.179 50.000 0.00 0.00 37.39 3.53
1495 2246 7.579589 TGCTATTGTGAACAATTTGTATTGC 57.420 32.000 13.53 5.74 43.48 3.56
1532 2283 9.706691 AGAGTGAACAATTTCGTTAATCTTCTA 57.293 29.630 0.00 0.00 34.04 2.10
1533 2284 8.608844 AGAGTGAACAATTTCGTTAATCTTCT 57.391 30.769 0.00 0.00 34.04 2.85
1534 2285 9.742552 GTAGAGTGAACAATTTCGTTAATCTTC 57.257 33.333 0.00 0.00 34.04 2.87
1543 2294 7.827819 TTATGGAGTAGAGTGAACAATTTCG 57.172 36.000 0.00 0.00 34.04 3.46
1585 2336 6.901081 AACATTCAAAACTTAGGAGGAAGG 57.099 37.500 0.00 0.00 0.00 3.46
1607 2358 8.856153 TTGTCTTTGAATTGTAGGCAGTATAA 57.144 30.769 0.00 0.00 0.00 0.98
1608 2359 9.461312 AATTGTCTTTGAATTGTAGGCAGTATA 57.539 29.630 0.00 0.00 0.00 1.47
1609 2360 7.944729 ATTGTCTTTGAATTGTAGGCAGTAT 57.055 32.000 0.00 0.00 0.00 2.12
1610 2361 7.759489 AATTGTCTTTGAATTGTAGGCAGTA 57.241 32.000 0.00 0.00 0.00 2.74
1611 2362 6.655078 AATTGTCTTTGAATTGTAGGCAGT 57.345 33.333 0.00 0.00 0.00 4.40
1612 2363 9.643693 AATAAATTGTCTTTGAATTGTAGGCAG 57.356 29.630 0.00 0.00 0.00 4.85
1649 2400 8.000709 TGAGGATCTGGTTGATTTAATTAGCAT 58.999 33.333 0.00 0.00 35.14 3.79
1655 2406 6.962182 TGAGTGAGGATCTGGTTGATTTAAT 58.038 36.000 0.00 0.00 35.14 1.40
1687 2438 9.649316 TCGGATAGAGAGATATAGATCTACAGA 57.351 37.037 4.10 0.00 42.80 3.41
1735 2488 3.236816 CTGAATGTGTTGTGAATTCCGC 58.763 45.455 2.27 0.00 30.75 5.54
1736 2489 4.024133 TCACTGAATGTGTTGTGAATTCCG 60.024 41.667 2.27 0.00 46.27 4.30
1740 2493 5.833406 TGTTCACTGAATGTGTTGTGAAT 57.167 34.783 9.98 0.00 46.49 2.57
1774 2747 4.999469 AAGGCAAATCCCTTTCCAATTT 57.001 36.364 0.00 0.00 42.48 1.82
1775 2748 5.629834 GCATAAGGCAAATCCCTTTCCAATT 60.630 40.000 0.00 0.00 42.48 2.32
1791 2764 4.967036 ACCTCAATCTCTAAGCATAAGGC 58.033 43.478 0.00 0.00 45.30 4.35
1797 2770 4.326826 CCAACAACCTCAATCTCTAAGCA 58.673 43.478 0.00 0.00 0.00 3.91
1801 2774 4.530553 TGTAGCCAACAACCTCAATCTCTA 59.469 41.667 0.00 0.00 34.29 2.43
1818 2791 1.597742 CATGCCATACCAGTGTAGCC 58.402 55.000 0.00 0.00 0.00 3.93
1822 2795 0.107703 CGTCCATGCCATACCAGTGT 60.108 55.000 0.00 0.00 0.00 3.55
1856 2829 2.357881 GGGGACAACCGGACGAAC 60.358 66.667 9.46 0.00 41.60 3.95
1857 2830 2.843411 TGGGGACAACCGGACGAA 60.843 61.111 9.46 0.00 41.60 3.85
1896 2878 2.045438 CGCCCACTGCCACCAATA 60.045 61.111 0.00 0.00 36.24 1.90
1934 2916 1.707106 TTCACCACTACGGAGGACAA 58.293 50.000 0.00 0.00 38.63 3.18
1950 2932 0.039618 GGAGCCTCCCATGGTTTTCA 59.960 55.000 11.73 0.00 0.00 2.69
1997 2979 0.397816 AGTATGGCGAGGGAGAGCTT 60.398 55.000 0.00 0.00 0.00 3.74
2021 3003 2.993264 GGCTTGCTGTGTGCCCAT 60.993 61.111 0.00 0.00 40.71 4.00
2028 3010 2.050714 CGTTGCTGGCTTGCTGTG 60.051 61.111 4.89 0.00 0.00 3.66
2029 3011 2.516930 ACGTTGCTGGCTTGCTGT 60.517 55.556 4.89 0.00 0.00 4.40
2030 3012 2.050714 CACGTTGCTGGCTTGCTG 60.051 61.111 0.00 0.00 0.00 4.41
2031 3013 2.516930 ACACGTTGCTGGCTTGCT 60.517 55.556 0.00 0.00 0.00 3.91
2032 3014 2.050985 GACACGTTGCTGGCTTGC 60.051 61.111 0.00 0.00 0.00 4.01
2033 3015 2.249309 CGACACGTTGCTGGCTTG 59.751 61.111 0.00 0.00 0.00 4.01
2034 3016 3.649986 GCGACACGTTGCTGGCTT 61.650 61.111 1.99 0.00 37.03 4.35
2046 3028 1.613317 CCATGGACTAGGTGGCGACA 61.613 60.000 5.56 0.00 38.70 4.35
2047 3029 1.144057 CCATGGACTAGGTGGCGAC 59.856 63.158 5.56 0.00 0.00 5.19
2048 3030 2.063979 CCCATGGACTAGGTGGCGA 61.064 63.158 15.22 0.00 0.00 5.54
2049 3031 2.505982 CCCATGGACTAGGTGGCG 59.494 66.667 15.22 0.00 0.00 5.69
2050 3032 2.193248 GCCCATGGACTAGGTGGC 59.807 66.667 15.22 0.69 0.00 5.01
2051 3033 0.982852 TCTGCCCATGGACTAGGTGG 60.983 60.000 15.22 0.00 0.00 4.61
2052 3034 1.135094 ATCTGCCCATGGACTAGGTG 58.865 55.000 15.22 0.00 0.00 4.00
2053 3035 1.135094 CATCTGCCCATGGACTAGGT 58.865 55.000 15.22 1.18 0.00 3.08
2054 3036 1.427809 TCATCTGCCCATGGACTAGG 58.572 55.000 15.22 0.00 0.00 3.02
2055 3037 3.565764 TTTCATCTGCCCATGGACTAG 57.434 47.619 15.22 8.40 0.00 2.57
2056 3038 4.079844 TCAATTTCATCTGCCCATGGACTA 60.080 41.667 15.22 0.00 0.00 2.59
2057 3039 3.028850 CAATTTCATCTGCCCATGGACT 58.971 45.455 15.22 0.00 0.00 3.85
2058 3040 3.025978 TCAATTTCATCTGCCCATGGAC 58.974 45.455 15.22 0.55 0.00 4.02
2059 3041 3.385314 TCAATTTCATCTGCCCATGGA 57.615 42.857 15.22 0.00 0.00 3.41
2060 3042 3.244078 CCATCAATTTCATCTGCCCATGG 60.244 47.826 4.14 4.14 0.00 3.66
2061 3043 3.802329 GCCATCAATTTCATCTGCCCATG 60.802 47.826 0.00 0.00 0.00 3.66
2062 3044 2.367567 GCCATCAATTTCATCTGCCCAT 59.632 45.455 0.00 0.00 0.00 4.00
2063 3045 1.758280 GCCATCAATTTCATCTGCCCA 59.242 47.619 0.00 0.00 0.00 5.36
2064 3046 2.037144 AGCCATCAATTTCATCTGCCC 58.963 47.619 0.00 0.00 0.00 5.36
2065 3047 2.223971 CCAGCCATCAATTTCATCTGCC 60.224 50.000 0.00 0.00 0.00 4.85
2066 3048 2.802057 GCCAGCCATCAATTTCATCTGC 60.802 50.000 0.00 0.00 0.00 4.26
2067 3049 2.693591 AGCCAGCCATCAATTTCATCTG 59.306 45.455 0.00 0.00 0.00 2.90
2068 3050 2.693591 CAGCCAGCCATCAATTTCATCT 59.306 45.455 0.00 0.00 0.00 2.90
2069 3051 2.802057 GCAGCCAGCCATCAATTTCATC 60.802 50.000 0.00 0.00 37.23 2.92
2070 3052 1.138266 GCAGCCAGCCATCAATTTCAT 59.862 47.619 0.00 0.00 37.23 2.57
2071 3053 0.533491 GCAGCCAGCCATCAATTTCA 59.467 50.000 0.00 0.00 37.23 2.69
2072 3054 0.533491 TGCAGCCAGCCATCAATTTC 59.467 50.000 0.00 0.00 44.83 2.17
2073 3055 1.134521 CATGCAGCCAGCCATCAATTT 60.135 47.619 0.00 0.00 44.83 1.82
2074 3056 0.464036 CATGCAGCCAGCCATCAATT 59.536 50.000 0.00 0.00 44.83 2.32
2075 3057 2.028125 GCATGCAGCCAGCCATCAAT 62.028 55.000 14.21 0.00 44.83 2.57
2076 3058 2.717044 GCATGCAGCCAGCCATCAA 61.717 57.895 14.21 0.00 44.83 2.57
2077 3059 3.144871 GCATGCAGCCAGCCATCA 61.145 61.111 14.21 0.00 44.83 3.07
2078 3060 4.266070 CGCATGCAGCCAGCCATC 62.266 66.667 19.57 0.00 44.83 3.51
2082 3064 3.678717 CTTCACGCATGCAGCCAGC 62.679 63.158 19.57 0.00 45.96 4.85
2083 3065 2.036571 TCTTCACGCATGCAGCCAG 61.037 57.895 19.57 8.01 41.38 4.85
2084 3066 2.032376 TCTTCACGCATGCAGCCA 59.968 55.556 19.57 0.00 41.38 4.75
2085 3067 2.249557 CTGTCTTCACGCATGCAGCC 62.250 60.000 19.57 0.00 41.38 4.85
2086 3068 1.134075 CTGTCTTCACGCATGCAGC 59.866 57.895 19.57 4.62 40.87 5.25
2087 3069 1.134075 GCTGTCTTCACGCATGCAG 59.866 57.895 19.57 12.98 0.00 4.41
2088 3070 1.293963 GAGCTGTCTTCACGCATGCA 61.294 55.000 19.57 0.00 0.00 3.96
2089 3071 1.293963 TGAGCTGTCTTCACGCATGC 61.294 55.000 7.91 7.91 0.00 4.06
2090 3072 0.441533 GTGAGCTGTCTTCACGCATG 59.558 55.000 0.00 0.00 0.00 4.06
2091 3073 0.319728 AGTGAGCTGTCTTCACGCAT 59.680 50.000 0.00 0.00 39.18 4.73
2092 3074 0.598419 CAGTGAGCTGTCTTCACGCA 60.598 55.000 0.00 0.00 39.18 5.24
2093 3075 2.148687 CAGTGAGCTGTCTTCACGC 58.851 57.895 0.00 0.00 39.18 5.34
2103 3085 2.627515 TTCAGAAGCAACAGTGAGCT 57.372 45.000 8.65 8.65 44.31 4.09
2104 3086 3.562505 CATTTCAGAAGCAACAGTGAGC 58.437 45.455 0.00 0.00 0.00 4.26
2105 3087 3.057736 CCCATTTCAGAAGCAACAGTGAG 60.058 47.826 0.00 0.00 0.00 3.51
2106 3088 2.886523 CCCATTTCAGAAGCAACAGTGA 59.113 45.455 0.00 0.00 0.00 3.41
2107 3089 2.608752 GCCCATTTCAGAAGCAACAGTG 60.609 50.000 0.00 0.00 0.00 3.66
2108 3090 1.615392 GCCCATTTCAGAAGCAACAGT 59.385 47.619 0.00 0.00 0.00 3.55
2109 3091 1.891150 AGCCCATTTCAGAAGCAACAG 59.109 47.619 0.00 0.00 0.00 3.16
2110 3092 1.999648 AGCCCATTTCAGAAGCAACA 58.000 45.000 0.00 0.00 0.00 3.33
2111 3093 3.084786 AGTAGCCCATTTCAGAAGCAAC 58.915 45.455 0.00 0.00 0.00 4.17
2112 3094 3.439857 AGTAGCCCATTTCAGAAGCAA 57.560 42.857 0.00 0.00 0.00 3.91
2113 3095 4.568072 TTAGTAGCCCATTTCAGAAGCA 57.432 40.909 0.00 0.00 0.00 3.91
2114 3096 4.276926 CCATTAGTAGCCCATTTCAGAAGC 59.723 45.833 0.00 0.00 0.00 3.86
2115 3097 4.823989 CCCATTAGTAGCCCATTTCAGAAG 59.176 45.833 0.00 0.00 0.00 2.85
2116 3098 4.792068 CCCATTAGTAGCCCATTTCAGAA 58.208 43.478 0.00 0.00 0.00 3.02
2117 3099 3.435026 GCCCATTAGTAGCCCATTTCAGA 60.435 47.826 0.00 0.00 0.00 3.27
2118 3100 2.887152 GCCCATTAGTAGCCCATTTCAG 59.113 50.000 0.00 0.00 0.00 3.02
2119 3101 2.424234 GGCCCATTAGTAGCCCATTTCA 60.424 50.000 0.00 0.00 41.00 2.69
2120 3102 2.239400 GGCCCATTAGTAGCCCATTTC 58.761 52.381 0.00 0.00 41.00 2.17
2121 3103 2.381752 GGCCCATTAGTAGCCCATTT 57.618 50.000 0.00 0.00 41.00 2.32
2127 3109 5.805728 ACAATGTATAGGCCCATTAGTAGC 58.194 41.667 0.00 0.00 30.41 3.58
2128 3110 8.362464 TCTACAATGTATAGGCCCATTAGTAG 57.638 38.462 20.57 20.57 36.04 2.57
2129 3111 8.911018 ATCTACAATGTATAGGCCCATTAGTA 57.089 34.615 0.00 6.80 30.41 1.82
2130 3112 7.814693 ATCTACAATGTATAGGCCCATTAGT 57.185 36.000 0.00 6.04 30.41 2.24
2133 3115 9.466497 CAATAATCTACAATGTATAGGCCCATT 57.534 33.333 0.00 0.00 0.00 3.16
2134 3116 8.614814 ACAATAATCTACAATGTATAGGCCCAT 58.385 33.333 0.00 0.00 0.00 4.00
2135 3117 7.984475 ACAATAATCTACAATGTATAGGCCCA 58.016 34.615 0.00 0.00 0.00 5.36
2136 3118 8.322091 AGACAATAATCTACAATGTATAGGCCC 58.678 37.037 0.00 0.00 0.00 5.80
2137 3119 9.372369 GAGACAATAATCTACAATGTATAGGCC 57.628 37.037 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.