Multiple sequence alignment - TraesCS2D01G183700

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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 TraesCS2D01G183700 chr2D 100.000 3710 0 0 1 3710 128962984 128966693 0.000000e+00 6852.0
1 TraesCS2D01G183700 chr2D 86.280 328 38 7 3386 3710 585421273 585420950 2.120000e-92 350.0
2 TraesCS2D01G183700 chr2D 94.872 78 3 1 1145 1222 7892629 7892705 1.810000e-23 121.0
3 TraesCS2D01G183700 chr2B 91.176 2074 94 38 1 2028 182568311 182570341 0.000000e+00 2734.0
4 TraesCS2D01G183700 chr2B 89.838 1358 44 42 2077 3381 182570340 182571656 0.000000e+00 1657.0
5 TraesCS2D01G183700 chr2A 92.337 1292 52 19 761 2043 135884570 135885823 0.000000e+00 1794.0
6 TraesCS2D01G183700 chr2A 94.172 755 23 7 2080 2813 135885813 135886567 0.000000e+00 1131.0
7 TraesCS2D01G183700 chr2A 95.055 546 22 2 2839 3381 135886559 135887102 0.000000e+00 854.0
8 TraesCS2D01G183700 chr2A 93.376 468 15 7 232 697 135883802 135884255 0.000000e+00 678.0
9 TraesCS2D01G183700 chr2A 85.061 328 43 6 3386 3710 601845895 601845571 2.760000e-86 329.0
10 TraesCS2D01G183700 chr6A 87.234 329 38 4 3382 3708 131228464 131228138 4.530000e-99 372.0
11 TraesCS2D01G183700 chr6A 90.000 60 4 2 2017 2075 363788000 363788058 3.970000e-10 76.8
12 TraesCS2D01G183700 chr1D 86.280 328 39 6 3386 3710 482329594 482329918 5.900000e-93 351.0
13 TraesCS2D01G183700 chr1D 85.976 328 40 6 3386 3710 431967137 431966813 2.740000e-91 346.0
14 TraesCS2D01G183700 chr7D 85.933 327 42 4 3386 3710 234186119 234186443 2.740000e-91 346.0
15 TraesCS2D01G183700 chr7D 91.525 59 3 2 2027 2083 190127332 190127390 3.070000e-11 80.5
16 TraesCS2D01G183700 chr7D 92.857 56 3 1 2034 2089 634069498 634069552 3.070000e-11 80.5
17 TraesCS2D01G183700 chr7D 97.727 44 1 0 1166 1209 204881872 204881829 3.970000e-10 76.8
18 TraesCS2D01G183700 chr5A 85.015 327 45 4 3386 3710 35062368 35062692 2.760000e-86 329.0
19 TraesCS2D01G183700 chr3B 84.940 332 43 7 3382 3710 107984336 107984009 2.760000e-86 329.0
20 TraesCS2D01G183700 chr3B 96.154 52 2 0 2034 2085 101647741 101647792 6.600000e-13 86.1
21 TraesCS2D01G183700 chr3B 96.154 52 2 0 2034 2085 250575972 250576023 6.600000e-13 86.1
22 TraesCS2D01G183700 chr3D 84.639 332 42 9 3382 3710 482342663 482342338 4.620000e-84 322.0
23 TraesCS2D01G183700 chr3D 94.444 54 2 1 2027 2079 543871668 543871615 8.540000e-12 82.4
24 TraesCS2D01G183700 chr4D 90.377 239 22 1 1076 1313 17743909 17743671 2.780000e-81 313.0
25 TraesCS2D01G183700 chr7B 83.871 124 20 0 1116 1239 2899374 2899251 6.510000e-23 119.0
26 TraesCS2D01G183700 chr7B 94.340 53 3 0 2034 2086 637751303 637751251 8.540000e-12 82.4
27 TraesCS2D01G183700 chr6D 91.803 61 2 3 2021 2079 128467245 128467304 8.540000e-12 82.4
28 TraesCS2D01G183700 chr1B 92.857 56 3 1 2024 2078 632658804 632658749 3.070000e-11 80.5


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 TraesCS2D01G183700 chr2D 128962984 128966693 3709 False 6852.00 6852 100.000 1 3710 1 chr2D.!!$F2 3709
1 TraesCS2D01G183700 chr2B 182568311 182571656 3345 False 2195.50 2734 90.507 1 3381 2 chr2B.!!$F1 3380
2 TraesCS2D01G183700 chr2A 135883802 135887102 3300 False 1114.25 1794 93.735 232 3381 4 chr2A.!!$F1 3149

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
774 1052 0.236711 GATCTGATTGCCGCCGATTG 59.763 55.0 0.0 0.0 0.00 2.67 F
1532 1815 0.251077 CTTTCACCAGCTTCCCTGCT 60.251 55.0 0.0 0.0 45.18 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1858 0.167908 CAAGCACGGAAGCGCAATAA 59.832 50.0 11.47 0.0 42.75 1.40 R
3424 3781 0.252197 ATCCGCGGCTAGTCCTTTTT 59.748 50.0 23.51 0.0 0.00 1.94 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
47 48 4.256180 GGCGCCCCTTCGATGGAT 62.256 66.667 18.11 0.00 0.00 3.41
48 49 2.974698 GCGCCCCTTCGATGGATG 60.975 66.667 18.51 10.11 0.00 3.51
51 52 1.895707 GCCCCTTCGATGGATGCAG 60.896 63.158 18.51 1.57 0.00 4.41
52 53 1.832219 CCCCTTCGATGGATGCAGA 59.168 57.895 18.51 0.00 0.00 4.26
62 66 4.096833 TCGATGGATGCAGAAAGAAAATGG 59.903 41.667 0.00 0.00 0.00 3.16
81 85 8.661352 AAAATGGTGATTTTTGTAAGGACTTG 57.339 30.769 0.00 0.00 38.40 3.16
86 90 5.915196 GTGATTTTTGTAAGGACTTGACTGC 59.085 40.000 0.00 0.00 0.00 4.40
96 100 4.464008 AGGACTTGACTGCAATTTCTCAA 58.536 39.130 0.00 0.00 32.68 3.02
100 104 4.340381 ACTTGACTGCAATTTCTCAAGCTT 59.660 37.500 13.54 0.00 42.24 3.74
109 113 6.864685 TGCAATTTCTCAAGCTTGTAAATGAG 59.135 34.615 27.58 24.30 40.46 2.90
110 114 6.309737 GCAATTTCTCAAGCTTGTAAATGAGG 59.690 38.462 27.58 22.68 39.74 3.86
120 124 8.755018 CAAGCTTGTAAATGAGGTTTTTGTAAG 58.245 33.333 18.65 0.00 0.00 2.34
121 125 7.433680 AGCTTGTAAATGAGGTTTTTGTAAGG 58.566 34.615 0.00 0.00 0.00 2.69
126 130 2.593026 TGAGGTTTTTGTAAGGGCTGG 58.407 47.619 0.00 0.00 0.00 4.85
130 134 3.778075 AGGTTTTTGTAAGGGCTGGTTTT 59.222 39.130 0.00 0.00 0.00 2.43
131 135 4.226394 AGGTTTTTGTAAGGGCTGGTTTTT 59.774 37.500 0.00 0.00 0.00 1.94
165 169 8.672815 TGAAATCTTTGACCATTTTGGAAAAAC 58.327 29.630 0.00 0.00 40.96 2.43
168 172 6.716284 TCTTTGACCATTTTGGAAAAACCTT 58.284 32.000 0.00 0.00 40.96 3.50
172 176 7.851387 TGACCATTTTGGAAAAACCTTTTAC 57.149 32.000 0.00 0.00 40.96 2.01
219 231 1.877443 TGCCGTTTAAGCCTTTCTGAC 59.123 47.619 0.00 0.00 0.00 3.51
227 239 2.680913 GCCTTTCTGACGCGTGCAT 61.681 57.895 20.70 0.00 0.00 3.96
229 241 1.291184 CCTTTCTGACGCGTGCATGA 61.291 55.000 20.70 6.20 0.00 3.07
238 250 4.583426 TGACGCGTGCATGAATTATTTAC 58.417 39.130 20.70 0.00 0.00 2.01
240 252 4.587306 ACGCGTGCATGAATTATTTACAG 58.413 39.130 12.93 0.00 0.00 2.74
310 324 7.514721 ACAAACAGTAGGACATAGAAAAAGGA 58.485 34.615 0.00 0.00 0.00 3.36
311 325 8.164070 ACAAACAGTAGGACATAGAAAAAGGAT 58.836 33.333 0.00 0.00 0.00 3.24
321 340 9.194271 GGACATAGAAAAAGGATCGAAGTATAC 57.806 37.037 0.00 0.00 0.00 1.47
323 342 9.968870 ACATAGAAAAAGGATCGAAGTATACTC 57.031 33.333 5.70 0.00 0.00 2.59
328 347 6.394025 AAAGGATCGAAGTATACTCTGGAC 57.606 41.667 5.70 0.00 0.00 4.02
329 348 5.313280 AGGATCGAAGTATACTCTGGACT 57.687 43.478 5.70 0.00 0.00 3.85
704 731 1.294986 TCTCCTCTCCATTCCCATCCA 59.705 52.381 0.00 0.00 0.00 3.41
707 734 1.516110 CTCTCCATTCCCATCCACCT 58.484 55.000 0.00 0.00 0.00 4.00
708 735 1.419387 CTCTCCATTCCCATCCACCTC 59.581 57.143 0.00 0.00 0.00 3.85
710 737 0.993509 TCCATTCCCATCCACCTCCC 60.994 60.000 0.00 0.00 0.00 4.30
711 738 1.538666 CATTCCCATCCACCTCCCC 59.461 63.158 0.00 0.00 0.00 4.81
743 770 4.271816 CCGCTCGAGGATCCCACG 62.272 72.222 15.58 18.86 38.87 4.94
774 1052 0.236711 GATCTGATTGCCGCCGATTG 59.763 55.000 0.00 0.00 0.00 2.67
813 1091 1.619207 CGCTCGTCGATTGTTCGTC 59.381 57.895 0.00 0.00 45.65 4.20
815 1093 1.730593 GCTCGTCGATTGTTCGTCCG 61.731 60.000 0.00 0.60 45.65 4.79
817 1095 0.795698 TCGTCGATTGTTCGTCCGTA 59.204 50.000 0.00 0.00 45.65 4.02
915 1197 2.519013 GTGTTCCTGAGAATTTGGCCT 58.481 47.619 3.32 0.00 33.67 5.19
931 1214 2.078452 CCTTCTTGGAGCTTGGGGA 58.922 57.895 0.00 0.00 38.35 4.81
932 1215 0.405585 CCTTCTTGGAGCTTGGGGAA 59.594 55.000 0.00 0.00 38.35 3.97
933 1216 1.615384 CCTTCTTGGAGCTTGGGGAAG 60.615 57.143 11.11 11.11 38.35 3.46
937 1220 1.071314 TTGGAGCTTGGGGAAGGGAA 61.071 55.000 0.00 0.00 0.00 3.97
949 1232 0.748367 GAAGGGAAGGATTGGCGTCC 60.748 60.000 0.77 0.77 38.62 4.79
984 1267 2.582728 ATTGCTTGCTCTCTCTCTCG 57.417 50.000 0.00 0.00 0.00 4.04
985 1268 1.252175 TTGCTTGCTCTCTCTCTCGT 58.748 50.000 0.00 0.00 0.00 4.18
987 1270 1.201181 TGCTTGCTCTCTCTCTCGTTC 59.799 52.381 0.00 0.00 0.00 3.95
988 1271 1.472480 GCTTGCTCTCTCTCTCGTTCT 59.528 52.381 0.00 0.00 0.00 3.01
990 1273 2.779755 TGCTCTCTCTCTCGTTCTCT 57.220 50.000 0.00 0.00 0.00 3.10
992 1275 2.290008 TGCTCTCTCTCTCGTTCTCTGT 60.290 50.000 0.00 0.00 0.00 3.41
993 1276 2.095853 GCTCTCTCTCTCGTTCTCTGTG 59.904 54.545 0.00 0.00 0.00 3.66
994 1277 2.080693 TCTCTCTCTCGTTCTCTGTGC 58.919 52.381 0.00 0.00 0.00 4.57
998 1281 2.125912 CTCGTTCTCTGTGCCGGG 60.126 66.667 2.18 0.00 0.00 5.73
1477 1760 3.367743 TCGTCGACCAGGGGAACG 61.368 66.667 10.58 3.95 0.00 3.95
1530 1813 0.538057 TGCTTTCACCAGCTTCCCTG 60.538 55.000 0.00 0.00 40.79 4.45
1532 1815 0.251077 CTTTCACCAGCTTCCCTGCT 60.251 55.000 0.00 0.00 45.18 4.24
1557 1840 6.476378 ACTCCAACTATTTGCTACAATCAGT 58.524 36.000 0.00 0.00 0.00 3.41
1575 1858 3.450457 TCAGTTTGCAATTCCCACTGTTT 59.550 39.130 21.60 0.00 36.91 2.83
1588 1871 2.241722 CACTGTTTTATTGCGCTTCCG 58.758 47.619 9.73 0.00 37.57 4.30
1810 2104 4.433283 CGATGCTTCTTTTTCGCCAAATTG 60.433 41.667 0.00 0.00 0.00 2.32
1821 2115 3.806591 CCAAATTGGCTGACAGCTG 57.193 52.632 25.92 13.48 41.99 4.24
1822 2116 0.389426 CCAAATTGGCTGACAGCTGC 60.389 55.000 25.92 11.73 41.99 5.25
1829 2123 4.790962 CTGACAGCTGCCCGCCAT 62.791 66.667 15.27 0.00 40.39 4.40
1857 2151 3.903090 TGGGGAATTCTTTTCTGCACAAT 59.097 39.130 5.23 0.00 0.00 2.71
2032 2326 8.693625 TCTAAGCTTTTATTCACTACTACTCCC 58.306 37.037 3.20 0.00 0.00 4.30
2033 2327 6.869206 AGCTTTTATTCACTACTACTCCCA 57.131 37.500 0.00 0.00 0.00 4.37
2034 2328 7.253905 AGCTTTTATTCACTACTACTCCCAA 57.746 36.000 0.00 0.00 0.00 4.12
2035 2329 7.331791 AGCTTTTATTCACTACTACTCCCAAG 58.668 38.462 0.00 0.00 0.00 3.61
2036 2330 7.038231 AGCTTTTATTCACTACTACTCCCAAGT 60.038 37.037 0.00 0.00 39.66 3.16
2037 2331 7.606839 GCTTTTATTCACTACTACTCCCAAGTT 59.393 37.037 0.00 0.00 36.92 2.66
2040 2334 8.890410 TTATTCACTACTACTCCCAAGTTAGT 57.110 34.615 0.00 0.00 36.92 2.24
2041 2335 9.979897 TTATTCACTACTACTCCCAAGTTAGTA 57.020 33.333 0.00 0.00 36.92 1.82
2042 2336 7.934855 TTCACTACTACTCCCAAGTTAGTAG 57.065 40.000 11.68 11.68 46.96 2.57
2043 2337 7.262990 TCACTACTACTCCCAAGTTAGTAGA 57.737 40.000 17.73 2.58 45.29 2.59
2044 2338 7.693132 TCACTACTACTCCCAAGTTAGTAGAA 58.307 38.462 17.73 6.46 45.29 2.10
2045 2339 8.166061 TCACTACTACTCCCAAGTTAGTAGAAA 58.834 37.037 17.73 6.20 45.29 2.52
2046 2340 8.460428 CACTACTACTCCCAAGTTAGTAGAAAG 58.540 40.741 17.73 13.47 45.29 2.62
2047 2341 8.169393 ACTACTACTCCCAAGTTAGTAGAAAGT 58.831 37.037 17.73 13.91 45.29 2.66
2048 2342 7.852550 ACTACTCCCAAGTTAGTAGAAAGTT 57.147 36.000 15.25 0.00 45.29 2.66
2049 2343 7.668492 ACTACTCCCAAGTTAGTAGAAAGTTG 58.332 38.462 15.25 1.05 45.29 3.16
2050 2344 6.742559 ACTCCCAAGTTAGTAGAAAGTTGA 57.257 37.500 5.87 0.00 40.66 3.18
2051 2345 6.760291 ACTCCCAAGTTAGTAGAAAGTTGAG 58.240 40.000 5.87 0.00 40.66 3.02
2052 2346 6.326843 ACTCCCAAGTTAGTAGAAAGTTGAGT 59.673 38.462 5.87 0.00 40.66 3.41
2053 2347 6.756221 TCCCAAGTTAGTAGAAAGTTGAGTC 58.244 40.000 5.87 0.00 40.66 3.36
2054 2348 6.325545 TCCCAAGTTAGTAGAAAGTTGAGTCA 59.674 38.462 5.87 0.00 40.66 3.41
2055 2349 7.016268 TCCCAAGTTAGTAGAAAGTTGAGTCAT 59.984 37.037 0.00 0.00 40.66 3.06
2056 2350 7.332182 CCCAAGTTAGTAGAAAGTTGAGTCATC 59.668 40.741 0.00 0.00 40.66 2.92
2057 2351 8.091449 CCAAGTTAGTAGAAAGTTGAGTCATCT 58.909 37.037 0.00 0.00 40.66 2.90
2064 2358 9.442047 AGTAGAAAGTTGAGTCATCTATTTTGG 57.558 33.333 4.14 0.00 0.00 3.28
2065 2359 9.436957 GTAGAAAGTTGAGTCATCTATTTTGGA 57.563 33.333 4.14 0.00 0.00 3.53
2066 2360 8.924511 AGAAAGTTGAGTCATCTATTTTGGAA 57.075 30.769 4.14 0.00 0.00 3.53
2067 2361 8.787852 AGAAAGTTGAGTCATCTATTTTGGAAC 58.212 33.333 4.14 0.00 0.00 3.62
2068 2362 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2069 2363 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2070 2364 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2071 2365 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2072 2366 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2073 2367 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2074 2368 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2075 2369 4.412199 TCATCTATTTTGGAACGGAGGGAT 59.588 41.667 0.00 0.00 0.00 3.85
2076 2370 4.855298 TCTATTTTGGAACGGAGGGATT 57.145 40.909 0.00 0.00 0.00 3.01
2077 2371 5.961398 TCTATTTTGGAACGGAGGGATTA 57.039 39.130 0.00 0.00 0.00 1.75
2078 2372 6.316280 TCTATTTTGGAACGGAGGGATTAA 57.684 37.500 0.00 0.00 0.00 1.40
2091 2385 5.620879 CGGAGGGATTAATAGTTACGTAGCC 60.621 48.000 5.74 0.00 0.00 3.93
2111 2405 5.158141 AGCCTCAGGGTATGATTATTCAGA 58.842 41.667 0.00 0.00 37.28 3.27
2135 2429 3.601443 ATCATTATCCGAGCAGCTACC 57.399 47.619 0.00 0.00 0.00 3.18
2139 2433 3.838244 TTATCCGAGCAGCTACCAAAT 57.162 42.857 0.00 0.00 0.00 2.32
2145 2446 5.962433 TCCGAGCAGCTACCAAATATATAC 58.038 41.667 0.00 0.00 0.00 1.47
2219 2520 5.351458 GGAAAAGAACACATTGGGATATGC 58.649 41.667 0.00 0.00 0.00 3.14
2508 2833 1.227674 GGACATGCCGATGGTCTCC 60.228 63.158 0.00 0.00 33.39 3.71
2723 3051 3.191669 TCTTGTAATGCCGGAATGTACG 58.808 45.455 5.05 0.00 0.00 3.67
2841 3169 2.686835 GGAGAGGAGTGCAGGGCT 60.687 66.667 0.00 0.00 0.00 5.19
2967 3295 1.727880 TCGCGGTAACTGTAAATGTGC 59.272 47.619 6.13 0.00 0.00 4.57
2977 3305 5.705609 ACTGTAAATGTGCAAGGTTTAGG 57.294 39.130 0.00 0.00 0.00 2.69
2978 3306 5.381757 ACTGTAAATGTGCAAGGTTTAGGA 58.618 37.500 0.00 0.00 0.00 2.94
3046 3374 0.762418 TCAACTCCAACACCATCCGT 59.238 50.000 0.00 0.00 0.00 4.69
3083 3411 2.158842 AGCTATTGCGCTTTGGAGATCT 60.159 45.455 9.73 0.00 45.42 2.75
3097 3425 0.036010 AGATCTCGGCCAAGTTGGTG 60.036 55.000 22.85 15.56 40.46 4.17
3182 3533 8.251026 TGTACAGTACTGTAGAAATCTCCAATG 58.749 37.037 31.32 0.84 45.61 2.82
3256 3607 3.178046 GTTCCTCTCTTTCCCCTCTTCT 58.822 50.000 0.00 0.00 0.00 2.85
3308 3665 3.535561 ACCGATGAGAATTGTGGTGATC 58.464 45.455 0.00 0.00 0.00 2.92
3317 3674 5.380043 AGAATTGTGGTGATCCATATGTCC 58.620 41.667 1.24 0.00 46.20 4.02
3356 3713 1.111116 ATTGCATGGCTTGGATCCGG 61.111 55.000 7.39 0.00 0.00 5.14
3409 3766 1.419381 TTTTCAAAAGGACCCCCTGC 58.581 50.000 0.00 0.00 43.48 4.85
3410 3767 0.471022 TTTCAAAAGGACCCCCTGCC 60.471 55.000 0.00 0.00 43.48 4.85
3411 3768 2.676471 CAAAAGGACCCCCTGCCG 60.676 66.667 0.00 0.00 43.48 5.69
3412 3769 2.856988 AAAAGGACCCCCTGCCGA 60.857 61.111 0.00 0.00 43.48 5.54
3413 3770 2.466186 AAAAGGACCCCCTGCCGAA 61.466 57.895 0.00 0.00 43.48 4.30
3414 3771 2.708593 AAAAGGACCCCCTGCCGAAC 62.709 60.000 0.00 0.00 43.48 3.95
3419 3776 3.861797 CCCCCTGCCGAACGCTAT 61.862 66.667 0.00 0.00 38.78 2.97
3420 3777 2.189521 CCCCTGCCGAACGCTATT 59.810 61.111 0.00 0.00 38.78 1.73
3421 3778 2.180204 CCCCTGCCGAACGCTATTG 61.180 63.158 0.00 0.00 38.78 1.90
3422 3779 1.153449 CCCTGCCGAACGCTATTGA 60.153 57.895 0.00 0.00 38.78 2.57
3423 3780 1.429148 CCCTGCCGAACGCTATTGAC 61.429 60.000 0.00 0.00 38.78 3.18
3424 3781 0.739462 CCTGCCGAACGCTATTGACA 60.739 55.000 0.00 0.00 38.78 3.58
3425 3782 1.075542 CTGCCGAACGCTATTGACAA 58.924 50.000 0.00 0.00 38.78 3.18
3426 3783 1.463056 CTGCCGAACGCTATTGACAAA 59.537 47.619 0.00 0.00 38.78 2.83
3427 3784 1.874231 TGCCGAACGCTATTGACAAAA 59.126 42.857 0.00 0.00 38.78 2.44
3428 3785 2.290916 TGCCGAACGCTATTGACAAAAA 59.709 40.909 0.00 0.00 38.78 1.94
3429 3786 2.908626 GCCGAACGCTATTGACAAAAAG 59.091 45.455 0.00 0.00 0.00 2.27
3430 3787 3.488489 CCGAACGCTATTGACAAAAAGG 58.512 45.455 0.00 0.00 0.00 3.11
3431 3788 3.187637 CCGAACGCTATTGACAAAAAGGA 59.812 43.478 0.00 0.00 0.00 3.36
3432 3789 4.148891 CGAACGCTATTGACAAAAAGGAC 58.851 43.478 0.00 0.00 0.00 3.85
3433 3790 4.084013 CGAACGCTATTGACAAAAAGGACT 60.084 41.667 0.00 0.00 0.00 3.85
3434 3791 5.119588 CGAACGCTATTGACAAAAAGGACTA 59.880 40.000 0.00 0.00 0.00 2.59
3435 3792 6.481954 AACGCTATTGACAAAAAGGACTAG 57.518 37.500 0.00 0.00 0.00 2.57
3436 3793 4.392138 ACGCTATTGACAAAAAGGACTAGC 59.608 41.667 0.00 0.00 0.00 3.42
3437 3794 4.201822 CGCTATTGACAAAAAGGACTAGCC 60.202 45.833 8.42 0.00 0.00 3.93
3438 3795 4.201822 GCTATTGACAAAAAGGACTAGCCG 60.202 45.833 0.00 0.00 43.43 5.52
3439 3796 1.519408 TGACAAAAAGGACTAGCCGC 58.481 50.000 0.00 0.00 43.43 6.53
3440 3797 0.442699 GACAAAAAGGACTAGCCGCG 59.557 55.000 0.00 0.00 43.43 6.46
3441 3798 0.953960 ACAAAAAGGACTAGCCGCGG 60.954 55.000 24.05 24.05 43.43 6.46
3442 3799 0.672401 CAAAAAGGACTAGCCGCGGA 60.672 55.000 33.48 8.14 43.43 5.54
3443 3800 0.252197 AAAAAGGACTAGCCGCGGAT 59.748 50.000 33.48 28.73 43.43 4.18
3444 3801 1.117150 AAAAGGACTAGCCGCGGATA 58.883 50.000 33.48 28.18 43.43 2.59
3445 3802 1.117150 AAAGGACTAGCCGCGGATAA 58.883 50.000 33.48 12.22 43.43 1.75
3446 3803 1.117150 AAGGACTAGCCGCGGATAAA 58.883 50.000 33.48 7.74 43.43 1.40
3447 3804 1.117150 AGGACTAGCCGCGGATAAAA 58.883 50.000 33.48 6.79 43.43 1.52
3448 3805 1.692519 AGGACTAGCCGCGGATAAAAT 59.307 47.619 33.48 15.72 43.43 1.82
3449 3806 2.104281 AGGACTAGCCGCGGATAAAATT 59.896 45.455 33.48 11.51 43.43 1.82
3450 3807 2.223377 GGACTAGCCGCGGATAAAATTG 59.777 50.000 33.48 17.52 0.00 2.32
3451 3808 2.870411 GACTAGCCGCGGATAAAATTGT 59.130 45.455 33.48 21.03 0.00 2.71
3452 3809 2.870411 ACTAGCCGCGGATAAAATTGTC 59.130 45.455 33.48 6.65 0.00 3.18
3453 3810 1.745232 AGCCGCGGATAAAATTGTCA 58.255 45.000 33.48 0.00 0.00 3.58
3454 3811 2.088423 AGCCGCGGATAAAATTGTCAA 58.912 42.857 33.48 0.00 0.00 3.18
3455 3812 2.490115 AGCCGCGGATAAAATTGTCAAA 59.510 40.909 33.48 0.00 0.00 2.69
3456 3813 3.057174 AGCCGCGGATAAAATTGTCAAAA 60.057 39.130 33.48 0.00 0.00 2.44
3457 3814 3.675698 GCCGCGGATAAAATTGTCAAAAA 59.324 39.130 33.48 0.00 0.00 1.94
3458 3815 4.201580 GCCGCGGATAAAATTGTCAAAAAG 60.202 41.667 33.48 0.00 0.00 2.27
3459 3816 4.326009 CCGCGGATAAAATTGTCAAAAAGG 59.674 41.667 24.07 0.00 0.00 3.11
3460 3817 5.157781 CGCGGATAAAATTGTCAAAAAGGA 58.842 37.500 0.00 0.00 0.00 3.36
3461 3818 5.060446 CGCGGATAAAATTGTCAAAAAGGAC 59.940 40.000 0.00 0.00 38.29 3.85
3462 3819 5.347635 GCGGATAAAATTGTCAAAAAGGACC 59.652 40.000 0.00 0.00 36.97 4.46
3463 3820 5.867174 CGGATAAAATTGTCAAAAAGGACCC 59.133 40.000 0.00 0.00 36.97 4.46
3464 3821 6.170506 GGATAAAATTGTCAAAAAGGACCCC 58.829 40.000 0.00 0.00 36.97 4.95
3465 3822 4.431416 AAAATTGTCAAAAAGGACCCCC 57.569 40.909 0.00 0.00 36.97 5.40
3467 3824 2.375014 TTGTCAAAAAGGACCCCCTC 57.625 50.000 0.00 0.00 43.48 4.30
3468 3825 1.227249 TGTCAAAAAGGACCCCCTCA 58.773 50.000 0.00 0.00 43.48 3.86
3469 3826 1.133606 TGTCAAAAAGGACCCCCTCAC 60.134 52.381 0.00 0.00 43.48 3.51
3470 3827 1.145119 GTCAAAAAGGACCCCCTCACT 59.855 52.381 0.00 0.00 43.48 3.41
3471 3828 2.374170 GTCAAAAAGGACCCCCTCACTA 59.626 50.000 0.00 0.00 43.48 2.74
3472 3829 2.642807 TCAAAAAGGACCCCCTCACTAG 59.357 50.000 0.00 0.00 43.48 2.57
3473 3830 2.375509 CAAAAAGGACCCCCTCACTAGT 59.624 50.000 0.00 0.00 43.48 2.57
3474 3831 1.657804 AAAGGACCCCCTCACTAGTG 58.342 55.000 17.17 17.17 43.48 2.74
3475 3832 0.252742 AAGGACCCCCTCACTAGTGG 60.253 60.000 22.48 12.85 43.48 4.00
3476 3833 2.368011 GGACCCCCTCACTAGTGGC 61.368 68.421 22.48 0.00 0.00 5.01
3477 3834 2.683933 ACCCCCTCACTAGTGGCG 60.684 66.667 22.48 13.49 0.00 5.69
3478 3835 4.162690 CCCCCTCACTAGTGGCGC 62.163 72.222 22.48 0.00 0.00 6.53
3479 3836 4.162690 CCCCTCACTAGTGGCGCC 62.163 72.222 22.73 22.73 0.00 6.53
3480 3837 3.390521 CCCTCACTAGTGGCGCCA 61.391 66.667 29.03 29.03 0.00 5.69
3481 3838 2.185350 CCTCACTAGTGGCGCCAG 59.815 66.667 33.73 21.79 0.00 4.85
3482 3839 2.185350 CTCACTAGTGGCGCCAGG 59.815 66.667 33.73 24.47 0.00 4.45
3483 3840 4.082523 TCACTAGTGGCGCCAGGC 62.083 66.667 33.73 20.32 44.11 4.85
3568 3925 4.244463 GCGGCCGGCAAGGGTATA 62.244 66.667 30.85 0.00 42.87 1.47
3569 3926 2.506962 CGGCCGGCAAGGGTATAA 59.493 61.111 30.85 0.00 41.48 0.98
3570 3927 1.890510 CGGCCGGCAAGGGTATAAC 60.891 63.158 30.85 5.23 41.48 1.89
3571 3928 1.890510 GGCCGGCAAGGGTATAACG 60.891 63.158 30.85 0.00 41.48 3.18
3572 3929 1.890510 GCCGGCAAGGGTATAACGG 60.891 63.158 24.80 0.00 43.81 4.44
3573 3930 1.227734 CCGGCAAGGGTATAACGGG 60.228 63.158 0.00 0.00 37.80 5.28
3574 3931 1.523524 CGGCAAGGGTATAACGGGT 59.476 57.895 0.00 0.00 0.00 5.28
3575 3932 0.107557 CGGCAAGGGTATAACGGGTT 60.108 55.000 0.00 0.00 0.00 4.11
3576 3933 1.679640 CGGCAAGGGTATAACGGGTTT 60.680 52.381 0.00 0.00 0.00 3.27
3577 3934 2.449464 GGCAAGGGTATAACGGGTTTT 58.551 47.619 0.00 0.00 0.00 2.43
3578 3935 2.424601 GGCAAGGGTATAACGGGTTTTC 59.575 50.000 0.00 0.00 0.00 2.29
3579 3936 2.424601 GCAAGGGTATAACGGGTTTTCC 59.575 50.000 0.00 0.00 39.75 3.13
3590 3947 3.892200 GGTTTTCCCACAGTGCATG 57.108 52.632 0.00 0.00 0.00 4.06
3591 3948 0.318120 GGTTTTCCCACAGTGCATGG 59.682 55.000 0.00 0.00 36.94 3.66
3592 3949 1.039856 GTTTTCCCACAGTGCATGGT 58.960 50.000 4.19 0.00 35.23 3.55
3593 3950 1.412343 GTTTTCCCACAGTGCATGGTT 59.588 47.619 4.19 0.00 35.23 3.67
3594 3951 1.039068 TTTCCCACAGTGCATGGTTG 58.961 50.000 4.19 0.00 35.23 3.77
3595 3952 0.827089 TTCCCACAGTGCATGGTTGG 60.827 55.000 4.19 4.58 35.23 3.77
3596 3953 2.277591 CCCACAGTGCATGGTTGGG 61.278 63.158 10.28 10.28 38.49 4.12
3597 3954 1.228521 CCACAGTGCATGGTTGGGA 60.229 57.895 0.00 0.00 32.08 4.37
3598 3955 1.526575 CCACAGTGCATGGTTGGGAC 61.527 60.000 0.00 0.00 32.08 4.46
3599 3956 1.600636 ACAGTGCATGGTTGGGACG 60.601 57.895 0.00 0.00 0.00 4.79
3600 3957 2.034066 AGTGCATGGTTGGGACGG 59.966 61.111 0.00 0.00 0.00 4.79
3601 3958 2.033448 GTGCATGGTTGGGACGGA 59.967 61.111 0.00 0.00 0.00 4.69
3602 3959 1.602323 GTGCATGGTTGGGACGGAA 60.602 57.895 0.00 0.00 0.00 4.30
3603 3960 1.602323 TGCATGGTTGGGACGGAAC 60.602 57.895 0.00 0.00 0.00 3.62
3616 3973 4.452733 GGAACGGGCGAGGACAGG 62.453 72.222 0.00 0.00 0.00 4.00
3617 3974 3.692406 GAACGGGCGAGGACAGGT 61.692 66.667 0.00 0.00 0.00 4.00
3618 3975 3.934391 GAACGGGCGAGGACAGGTG 62.934 68.421 0.00 0.00 0.00 4.00
3661 4018 3.660111 GCCACTGTTGCCGGTGTC 61.660 66.667 1.90 0.00 44.96 3.67
3662 4019 3.345808 CCACTGTTGCCGGTGTCG 61.346 66.667 1.90 0.00 44.96 4.35
3663 4020 4.012895 CACTGTTGCCGGTGTCGC 62.013 66.667 1.90 0.00 42.07 5.19
3664 4021 4.235762 ACTGTTGCCGGTGTCGCT 62.236 61.111 1.90 0.00 34.56 4.93
3665 4022 3.414700 CTGTTGCCGGTGTCGCTC 61.415 66.667 1.90 0.00 34.56 5.03
3676 4033 4.266070 GTCGCTCGCAGGCCGATA 62.266 66.667 0.00 0.00 46.31 2.92
3677 4034 3.966104 TCGCTCGCAGGCCGATAG 61.966 66.667 0.00 0.00 46.31 2.08
3689 4046 2.659897 CGATAGGCCGTGCTGCTC 60.660 66.667 0.00 0.00 0.00 4.26
3690 4047 2.659897 GATAGGCCGTGCTGCTCG 60.660 66.667 16.35 16.35 0.00 5.03
3691 4048 4.899239 ATAGGCCGTGCTGCTCGC 62.899 66.667 17.69 12.83 39.77 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.895707 CTGCATCCATCGAAGGGGC 60.896 63.158 14.61 14.61 0.00 5.80
35 36 1.945394 CTTTCTGCATCCATCGAAGGG 59.055 52.381 6.88 3.30 0.00 3.95
36 37 2.910199 TCTTTCTGCATCCATCGAAGG 58.090 47.619 0.00 0.00 0.00 3.46
41 42 5.105635 TCACCATTTTCTTTCTGCATCCATC 60.106 40.000 0.00 0.00 0.00 3.51
43 44 4.151121 TCACCATTTTCTTTCTGCATCCA 58.849 39.130 0.00 0.00 0.00 3.41
44 45 4.789012 TCACCATTTTCTTTCTGCATCC 57.211 40.909 0.00 0.00 0.00 3.51
46 47 7.499895 ACAAAAATCACCATTTTCTTTCTGCAT 59.500 29.630 0.00 0.00 40.68 3.96
47 48 6.822676 ACAAAAATCACCATTTTCTTTCTGCA 59.177 30.769 0.00 0.00 40.68 4.41
48 49 7.250445 ACAAAAATCACCATTTTCTTTCTGC 57.750 32.000 0.00 0.00 40.68 4.26
51 52 9.541143 TCCTTACAAAAATCACCATTTTCTTTC 57.459 29.630 0.00 0.00 40.68 2.62
52 53 9.325198 GTCCTTACAAAAATCACCATTTTCTTT 57.675 29.630 0.00 0.00 40.68 2.52
62 66 5.915196 GCAGTCAAGTCCTTACAAAAATCAC 59.085 40.000 0.00 0.00 0.00 3.06
81 85 4.234530 ACAAGCTTGAGAAATTGCAGTC 57.765 40.909 32.50 0.00 0.00 3.51
86 90 7.373493 ACCTCATTTACAAGCTTGAGAAATTG 58.627 34.615 32.50 23.57 38.25 2.32
96 100 7.433680 CCTTACAAAAACCTCATTTACAAGCT 58.566 34.615 0.00 0.00 0.00 3.74
100 104 5.836358 AGCCCTTACAAAAACCTCATTTACA 59.164 36.000 0.00 0.00 0.00 2.41
109 113 3.830744 AAACCAGCCCTTACAAAAACC 57.169 42.857 0.00 0.00 0.00 3.27
136 140 9.487790 TTTCCAAAATGGTCAAAGATTTCATAC 57.512 29.630 0.00 0.00 39.03 2.39
141 145 7.833682 AGGTTTTTCCAAAATGGTCAAAGATTT 59.166 29.630 0.00 0.00 39.03 2.17
142 146 7.345691 AGGTTTTTCCAAAATGGTCAAAGATT 58.654 30.769 0.00 0.00 39.03 2.40
193 199 2.483014 AGGCTTAAACGGCATGTACA 57.517 45.000 0.00 0.00 0.00 2.90
219 231 3.418619 GCTGTAAATAATTCATGCACGCG 59.581 43.478 3.53 3.53 0.00 6.01
227 239 6.849085 ATGTTGGTGGCTGTAAATAATTCA 57.151 33.333 0.00 0.00 0.00 2.57
229 241 8.038351 GGTAAATGTTGGTGGCTGTAAATAATT 58.962 33.333 0.00 0.00 0.00 1.40
238 250 0.525761 CCGGTAAATGTTGGTGGCTG 59.474 55.000 0.00 0.00 0.00 4.85
240 252 0.808755 CTCCGGTAAATGTTGGTGGC 59.191 55.000 0.00 0.00 0.00 5.01
272 286 9.601217 GTCCTACTGTTTGTATGATTGTAATCT 57.399 33.333 6.21 0.00 36.39 2.40
273 287 9.378551 TGTCCTACTGTTTGTATGATTGTAATC 57.621 33.333 0.00 0.00 35.97 1.75
274 288 9.905713 ATGTCCTACTGTTTGTATGATTGTAAT 57.094 29.630 0.00 0.00 30.59 1.89
310 324 4.822896 GTCCAGTCCAGAGTATACTTCGAT 59.177 45.833 6.88 0.00 0.00 3.59
311 325 4.197750 GTCCAGTCCAGAGTATACTTCGA 58.802 47.826 6.88 0.35 0.00 3.71
321 340 2.262915 GCGGTGTCCAGTCCAGAG 59.737 66.667 0.00 0.00 0.00 3.35
323 342 2.357517 GTGCGGTGTCCAGTCCAG 60.358 66.667 0.00 0.00 0.00 3.86
347 366 3.691342 CCGGTTCTCAGGGCACGA 61.691 66.667 0.00 0.00 0.00 4.35
654 681 4.093291 AGAAGGAGGCCTGCGCTG 62.093 66.667 19.62 8.47 33.44 5.18
655 682 3.780173 GAGAAGGAGGCCTGCGCT 61.780 66.667 19.62 19.60 33.44 5.92
656 683 3.322318 AAGAGAAGGAGGCCTGCGC 62.322 63.158 19.62 14.99 33.44 6.09
710 737 4.179599 GGGAGAGGGGAGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
711 738 4.548513 CGGGAGAGGGGAGAGGGG 62.549 77.778 0.00 0.00 0.00 4.79
717 744 4.507916 CTCGAGCGGGAGAGGGGA 62.508 72.222 0.00 0.00 36.08 4.81
722 749 2.203365 GGATCCTCGAGCGGGAGA 60.203 66.667 6.99 0.00 36.08 3.71
726 753 4.271816 CGTGGGATCCTCGAGCGG 62.272 72.222 19.59 0.00 42.19 5.52
743 770 4.933064 CAGATCCCTCCGACGCGC 62.933 72.222 5.73 0.00 0.00 6.86
747 774 0.250081 GGCAATCAGATCCCTCCGAC 60.250 60.000 0.00 0.00 0.00 4.79
748 775 1.748329 CGGCAATCAGATCCCTCCGA 61.748 60.000 6.71 0.00 37.79 4.55
751 778 1.599240 GGCGGCAATCAGATCCCTC 60.599 63.158 3.07 0.00 0.00 4.30
774 1052 2.749441 GGGAAGCAGAGCCAGCAC 60.749 66.667 0.00 0.00 0.00 4.40
813 1091 1.421410 GAACATCACAGCGCCTACGG 61.421 60.000 2.29 0.00 40.57 4.02
815 1093 1.661112 GAAGAACATCACAGCGCCTAC 59.339 52.381 2.29 0.00 0.00 3.18
817 1095 0.674895 GGAAGAACATCACAGCGCCT 60.675 55.000 2.29 0.00 0.00 5.52
915 1197 0.405585 CCTTCCCCAAGCTCCAAGAA 59.594 55.000 0.00 0.00 0.00 2.52
931 1214 1.303282 GGACGCCAATCCTTCCCTT 59.697 57.895 0.00 0.00 35.68 3.95
932 1215 2.998949 GGACGCCAATCCTTCCCT 59.001 61.111 0.00 0.00 35.68 4.20
933 1216 2.513897 CGGACGCCAATCCTTCCC 60.514 66.667 0.00 0.00 36.52 3.97
937 1220 2.125106 GAAGCGGACGCCAATCCT 60.125 61.111 13.63 0.00 43.17 3.24
984 1267 2.045926 ATGCCCGGCACAGAGAAC 60.046 61.111 16.16 0.00 43.04 3.01
985 1268 2.046023 CATGCCCGGCACAGAGAA 60.046 61.111 16.16 0.00 43.04 2.87
998 1281 3.665675 AAGTCCCTCGACGCCATGC 62.666 63.158 0.00 0.00 44.28 4.06
1479 1762 1.078214 CTCCGGCATGCTTGAGGAA 60.078 57.895 18.92 6.00 32.96 3.36
1530 1813 6.538742 TGATTGTAGCAAATAGTTGGAGTAGC 59.461 38.462 4.91 0.00 35.10 3.58
1532 1815 7.620880 ACTGATTGTAGCAAATAGTTGGAGTA 58.379 34.615 4.91 0.00 35.10 2.59
1557 1840 5.238214 GCAATAAAACAGTGGGAATTGCAAA 59.762 36.000 20.53 0.00 45.25 3.68
1575 1858 0.167908 CAAGCACGGAAGCGCAATAA 59.832 50.000 11.47 0.00 42.75 1.40
1709 2001 1.872952 CATGGCAAAGAACACTCGACA 59.127 47.619 0.00 0.00 0.00 4.35
1819 2113 2.788640 CCATTTCCATGGCGGGCAG 61.789 63.158 6.96 2.38 43.95 4.85
1820 2114 2.759149 CCATTTCCATGGCGGGCA 60.759 61.111 6.96 6.74 43.95 5.36
1827 2121 6.110707 CAGAAAAGAATTCCCCATTTCCATG 58.889 40.000 0.65 1.48 31.91 3.66
1828 2122 5.338626 GCAGAAAAGAATTCCCCATTTCCAT 60.339 40.000 0.65 0.00 31.91 3.41
1829 2123 4.020307 GCAGAAAAGAATTCCCCATTTCCA 60.020 41.667 0.65 0.00 31.91 3.53
1830 2124 4.020307 TGCAGAAAAGAATTCCCCATTTCC 60.020 41.667 0.65 0.00 31.91 3.13
1857 2151 4.812626 TGCGTACGTAGAAGTATCATCAGA 59.187 41.667 17.90 0.00 0.00 3.27
2018 2312 7.693132 TCTACTAACTTGGGAGTAGTAGTGAA 58.307 38.462 13.84 0.00 43.73 3.18
2028 2322 6.760291 ACTCAACTTTCTACTAACTTGGGAG 58.240 40.000 0.00 0.00 0.00 4.30
2031 2325 8.091449 AGATGACTCAACTTTCTACTAACTTGG 58.909 37.037 0.00 0.00 0.00 3.61
2038 2332 9.442047 CCAAAATAGATGACTCAACTTTCTACT 57.558 33.333 0.00 0.00 0.00 2.57
2039 2333 9.436957 TCCAAAATAGATGACTCAACTTTCTAC 57.563 33.333 0.00 0.00 0.00 2.59
2041 2335 8.787852 GTTCCAAAATAGATGACTCAACTTTCT 58.212 33.333 0.00 0.00 0.00 2.52
2042 2336 7.746475 CGTTCCAAAATAGATGACTCAACTTTC 59.254 37.037 0.00 0.00 0.00 2.62
2043 2337 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2044 2338 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2045 2339 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2046 2340 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2047 2341 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2048 2342 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2049 2343 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2050 2344 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2051 2345 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2052 2346 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2053 2347 4.150897 TCCCTCCGTTCCAAAATAGATG 57.849 45.455 0.00 0.00 0.00 2.90
2054 2348 5.388599 AATCCCTCCGTTCCAAAATAGAT 57.611 39.130 0.00 0.00 0.00 1.98
2055 2349 4.855298 AATCCCTCCGTTCCAAAATAGA 57.145 40.909 0.00 0.00 0.00 1.98
2056 2350 7.937394 ACTATTAATCCCTCCGTTCCAAAATAG 59.063 37.037 0.00 0.00 32.24 1.73
2057 2351 7.808218 ACTATTAATCCCTCCGTTCCAAAATA 58.192 34.615 0.00 0.00 0.00 1.40
2058 2352 6.669631 ACTATTAATCCCTCCGTTCCAAAAT 58.330 36.000 0.00 0.00 0.00 1.82
2059 2353 6.069705 ACTATTAATCCCTCCGTTCCAAAA 57.930 37.500 0.00 0.00 0.00 2.44
2060 2354 5.703730 ACTATTAATCCCTCCGTTCCAAA 57.296 39.130 0.00 0.00 0.00 3.28
2061 2355 5.703730 AACTATTAATCCCTCCGTTCCAA 57.296 39.130 0.00 0.00 0.00 3.53
2062 2356 5.221303 CGTAACTATTAATCCCTCCGTTCCA 60.221 44.000 0.00 0.00 0.00 3.53
2063 2357 5.221322 ACGTAACTATTAATCCCTCCGTTCC 60.221 44.000 0.00 0.00 0.00 3.62
2064 2358 5.836347 ACGTAACTATTAATCCCTCCGTTC 58.164 41.667 0.00 0.00 0.00 3.95
2065 2359 5.859205 ACGTAACTATTAATCCCTCCGTT 57.141 39.130 0.00 0.00 0.00 4.44
2066 2360 5.048434 GCTACGTAACTATTAATCCCTCCGT 60.048 44.000 0.00 0.00 0.00 4.69
2067 2361 5.397326 GCTACGTAACTATTAATCCCTCCG 58.603 45.833 0.00 0.00 0.00 4.63
2068 2362 5.479724 AGGCTACGTAACTATTAATCCCTCC 59.520 44.000 0.00 0.00 0.00 4.30
2069 2363 6.208204 TGAGGCTACGTAACTATTAATCCCTC 59.792 42.308 0.00 0.00 35.67 4.30
2070 2364 6.073314 TGAGGCTACGTAACTATTAATCCCT 58.927 40.000 0.00 0.00 0.00 4.20
2071 2365 6.336842 TGAGGCTACGTAACTATTAATCCC 57.663 41.667 0.00 0.00 0.00 3.85
2072 2366 6.388278 CCTGAGGCTACGTAACTATTAATCC 58.612 44.000 0.00 0.00 0.00 3.01
2073 2367 6.015603 ACCCTGAGGCTACGTAACTATTAATC 60.016 42.308 0.00 0.00 36.11 1.75
2074 2368 5.837438 ACCCTGAGGCTACGTAACTATTAAT 59.163 40.000 0.00 0.00 36.11 1.40
2075 2369 5.203528 ACCCTGAGGCTACGTAACTATTAA 58.796 41.667 0.00 0.00 36.11 1.40
2076 2370 4.796606 ACCCTGAGGCTACGTAACTATTA 58.203 43.478 0.00 0.00 36.11 0.98
2077 2371 3.639952 ACCCTGAGGCTACGTAACTATT 58.360 45.455 0.00 0.00 36.11 1.73
2078 2372 3.309600 ACCCTGAGGCTACGTAACTAT 57.690 47.619 0.00 0.00 36.11 2.12
2091 2385 9.868277 GATTAGTCTGAATAATCATACCCTGAG 57.132 37.037 24.87 0.00 38.79 3.35
2111 2405 4.881019 AGCTGCTCGGATAATGATTAGT 57.119 40.909 0.00 0.00 0.00 2.24
2145 2446 8.076178 AGTTTTTCAGGTAGACAATTCAAATCG 58.924 33.333 0.00 0.00 0.00 3.34
2661 2986 3.356639 GACGATGTGCCTGAGCGGA 62.357 63.158 0.00 0.00 44.31 5.54
2841 3169 4.141574 ACTTACAGTAAACACCTCAGGCAA 60.142 41.667 0.00 0.00 0.00 4.52
2951 3279 5.447624 AACCTTGCACATTTACAGTTACC 57.552 39.130 0.00 0.00 0.00 2.85
2967 3295 4.785511 TCGACTTCTCTCCTAAACCTTG 57.214 45.455 0.00 0.00 0.00 3.61
2977 3305 3.686726 ACATGGCAAAATCGACTTCTCTC 59.313 43.478 0.00 0.00 0.00 3.20
2978 3306 3.679389 ACATGGCAAAATCGACTTCTCT 58.321 40.909 0.00 0.00 0.00 3.10
3046 3374 6.494842 GCAATAGCTTCCGAATATGTGAAAA 58.505 36.000 0.00 0.00 37.91 2.29
3083 3411 0.470766 AGTTACACCAACTTGGCCGA 59.529 50.000 7.81 0.00 45.54 5.54
3097 3425 4.625028 ACTCTTCGTTACCAACCAGTTAC 58.375 43.478 0.00 0.00 0.00 2.50
3308 3665 3.641906 AGTAGGAAGGAACGGACATATGG 59.358 47.826 7.80 0.00 0.00 2.74
3317 3674 3.396260 TGGTTCAAGTAGGAAGGAACG 57.604 47.619 0.00 0.00 40.30 3.95
3389 3746 1.765904 GCAGGGGGTCCTTTTGAAAAA 59.234 47.619 0.00 0.00 42.67 1.94
3390 3747 1.419381 GCAGGGGGTCCTTTTGAAAA 58.581 50.000 0.00 0.00 42.67 2.29
3391 3748 0.471022 GGCAGGGGGTCCTTTTGAAA 60.471 55.000 0.00 0.00 42.67 2.69
3392 3749 1.155155 GGCAGGGGGTCCTTTTGAA 59.845 57.895 0.00 0.00 42.67 2.69
3393 3750 2.851045 GGCAGGGGGTCCTTTTGA 59.149 61.111 0.00 0.00 42.67 2.69
3394 3751 2.676471 CGGCAGGGGGTCCTTTTG 60.676 66.667 0.00 0.00 42.67 2.44
3395 3752 2.466186 TTCGGCAGGGGGTCCTTTT 61.466 57.895 0.00 0.00 42.67 2.27
3396 3753 2.856988 TTCGGCAGGGGGTCCTTT 60.857 61.111 0.00 0.00 42.67 3.11
3397 3754 3.647771 GTTCGGCAGGGGGTCCTT 61.648 66.667 0.00 0.00 42.67 3.36
3408 3765 2.604969 TTTTGTCAATAGCGTTCGGC 57.395 45.000 0.00 0.00 44.05 5.54
3409 3766 3.187637 TCCTTTTTGTCAATAGCGTTCGG 59.812 43.478 0.00 0.00 0.00 4.30
3410 3767 4.084013 AGTCCTTTTTGTCAATAGCGTTCG 60.084 41.667 0.00 0.00 0.00 3.95
3411 3768 5.358298 AGTCCTTTTTGTCAATAGCGTTC 57.642 39.130 0.00 0.00 0.00 3.95
3412 3769 5.106673 GCTAGTCCTTTTTGTCAATAGCGTT 60.107 40.000 0.00 0.00 0.00 4.84
3413 3770 4.392138 GCTAGTCCTTTTTGTCAATAGCGT 59.608 41.667 0.00 0.00 0.00 5.07
3414 3771 4.201822 GGCTAGTCCTTTTTGTCAATAGCG 60.202 45.833 6.18 0.00 36.19 4.26
3415 3772 4.201822 CGGCTAGTCCTTTTTGTCAATAGC 60.202 45.833 4.27 4.27 34.93 2.97
3416 3773 4.201822 GCGGCTAGTCCTTTTTGTCAATAG 60.202 45.833 0.00 0.00 0.00 1.73
3417 3774 3.687698 GCGGCTAGTCCTTTTTGTCAATA 59.312 43.478 0.00 0.00 0.00 1.90
3418 3775 2.488153 GCGGCTAGTCCTTTTTGTCAAT 59.512 45.455 0.00 0.00 0.00 2.57
3419 3776 1.877443 GCGGCTAGTCCTTTTTGTCAA 59.123 47.619 0.00 0.00 0.00 3.18
3420 3777 1.519408 GCGGCTAGTCCTTTTTGTCA 58.481 50.000 0.00 0.00 0.00 3.58
3421 3778 0.442699 CGCGGCTAGTCCTTTTTGTC 59.557 55.000 0.00 0.00 0.00 3.18
3422 3779 0.953960 CCGCGGCTAGTCCTTTTTGT 60.954 55.000 14.67 0.00 0.00 2.83
3423 3780 0.672401 TCCGCGGCTAGTCCTTTTTG 60.672 55.000 23.51 0.00 0.00 2.44
3424 3781 0.252197 ATCCGCGGCTAGTCCTTTTT 59.748 50.000 23.51 0.00 0.00 1.94
3425 3782 1.117150 TATCCGCGGCTAGTCCTTTT 58.883 50.000 23.51 0.00 0.00 2.27
3426 3783 1.117150 TTATCCGCGGCTAGTCCTTT 58.883 50.000 23.51 0.00 0.00 3.11
3427 3784 1.117150 TTTATCCGCGGCTAGTCCTT 58.883 50.000 23.51 0.00 0.00 3.36
3428 3785 1.117150 TTTTATCCGCGGCTAGTCCT 58.883 50.000 23.51 0.83 0.00 3.85
3429 3786 2.165319 ATTTTATCCGCGGCTAGTCC 57.835 50.000 23.51 0.00 0.00 3.85
3430 3787 2.870411 ACAATTTTATCCGCGGCTAGTC 59.130 45.455 23.51 0.00 0.00 2.59
3431 3788 2.870411 GACAATTTTATCCGCGGCTAGT 59.130 45.455 23.51 9.05 0.00 2.57
3432 3789 2.869801 TGACAATTTTATCCGCGGCTAG 59.130 45.455 23.51 5.39 0.00 3.42
3433 3790 2.907634 TGACAATTTTATCCGCGGCTA 58.092 42.857 23.51 13.71 0.00 3.93
3434 3791 1.745232 TGACAATTTTATCCGCGGCT 58.255 45.000 23.51 15.09 0.00 5.52
3435 3792 2.553079 TTGACAATTTTATCCGCGGC 57.447 45.000 23.51 2.12 0.00 6.53
3436 3793 4.326009 CCTTTTTGACAATTTTATCCGCGG 59.674 41.667 22.12 22.12 0.00 6.46
3437 3794 5.060446 GTCCTTTTTGACAATTTTATCCGCG 59.940 40.000 0.00 0.00 35.29 6.46
3438 3795 5.347635 GGTCCTTTTTGACAATTTTATCCGC 59.652 40.000 0.00 0.00 36.97 5.54
3439 3796 5.867174 GGGTCCTTTTTGACAATTTTATCCG 59.133 40.000 0.00 0.00 36.97 4.18
3440 3797 6.170506 GGGGTCCTTTTTGACAATTTTATCC 58.829 40.000 0.00 0.00 36.97 2.59
3441 3798 6.013725 AGGGGGTCCTTTTTGACAATTTTATC 60.014 38.462 0.00 0.00 41.56 1.75
3442 3799 5.849475 AGGGGGTCCTTTTTGACAATTTTAT 59.151 36.000 0.00 0.00 41.56 1.40
3443 3800 5.220521 AGGGGGTCCTTTTTGACAATTTTA 58.779 37.500 0.00 0.00 41.56 1.52
3444 3801 4.044308 AGGGGGTCCTTTTTGACAATTTT 58.956 39.130 0.00 0.00 41.56 1.82
3445 3802 3.646162 GAGGGGGTCCTTTTTGACAATTT 59.354 43.478 0.00 0.00 45.05 1.82
3446 3803 3.239449 GAGGGGGTCCTTTTTGACAATT 58.761 45.455 0.00 0.00 45.05 2.32
3447 3804 2.178984 TGAGGGGGTCCTTTTTGACAAT 59.821 45.455 0.00 0.00 45.05 2.71
3448 3805 1.571457 TGAGGGGGTCCTTTTTGACAA 59.429 47.619 0.00 0.00 45.05 3.18
3449 3806 1.133606 GTGAGGGGGTCCTTTTTGACA 60.134 52.381 0.00 0.00 45.05 3.58
3450 3807 1.145119 AGTGAGGGGGTCCTTTTTGAC 59.855 52.381 0.00 0.00 45.05 3.18
3451 3808 1.529744 AGTGAGGGGGTCCTTTTTGA 58.470 50.000 0.00 0.00 45.05 2.69
3452 3809 2.375509 ACTAGTGAGGGGGTCCTTTTTG 59.624 50.000 0.00 0.00 45.05 2.44
3453 3810 2.375509 CACTAGTGAGGGGGTCCTTTTT 59.624 50.000 18.45 0.00 45.05 1.94
3454 3811 1.985895 CACTAGTGAGGGGGTCCTTTT 59.014 52.381 18.45 0.00 45.05 2.27
3455 3812 1.657804 CACTAGTGAGGGGGTCCTTT 58.342 55.000 18.45 0.00 45.05 3.11
3456 3813 0.252742 CCACTAGTGAGGGGGTCCTT 60.253 60.000 24.68 0.00 43.43 3.36
3457 3814 1.392534 CCACTAGTGAGGGGGTCCT 59.607 63.158 24.68 0.00 43.43 3.85
3458 3815 4.051932 CCACTAGTGAGGGGGTCC 57.948 66.667 24.68 0.00 43.43 4.46
3463 3820 3.376935 CTGGCGCCACTAGTGAGGG 62.377 68.421 29.03 20.69 0.00 4.30
3464 3821 2.185350 CTGGCGCCACTAGTGAGG 59.815 66.667 29.03 9.73 0.00 3.86
3465 3822 2.185350 CCTGGCGCCACTAGTGAG 59.815 66.667 29.03 14.38 0.00 3.51
3466 3823 4.082523 GCCTGGCGCCACTAGTGA 62.083 66.667 29.03 1.63 0.00 3.41
3551 3908 3.760700 TTATACCCTTGCCGGCCGC 62.761 63.158 26.77 16.45 38.31 6.53
3552 3909 1.890510 GTTATACCCTTGCCGGCCG 60.891 63.158 26.77 21.04 0.00 6.13
3553 3910 1.890510 CGTTATACCCTTGCCGGCC 60.891 63.158 26.77 6.44 0.00 6.13
3554 3911 1.890510 CCGTTATACCCTTGCCGGC 60.891 63.158 22.73 22.73 0.00 6.13
3555 3912 1.227734 CCCGTTATACCCTTGCCGG 60.228 63.158 0.00 0.00 35.32 6.13
3556 3913 0.107557 AACCCGTTATACCCTTGCCG 60.108 55.000 0.00 0.00 0.00 5.69
3557 3914 2.133281 AAACCCGTTATACCCTTGCC 57.867 50.000 0.00 0.00 0.00 4.52
3558 3915 2.424601 GGAAAACCCGTTATACCCTTGC 59.575 50.000 0.00 0.00 0.00 4.01
3559 3916 3.018856 GGGAAAACCCGTTATACCCTTG 58.981 50.000 0.00 0.00 35.07 3.61
3560 3917 2.648808 TGGGAAAACCCGTTATACCCTT 59.351 45.455 0.00 0.00 39.07 3.95
3561 3918 2.025981 GTGGGAAAACCCGTTATACCCT 60.026 50.000 0.00 0.00 39.07 4.34
3562 3919 2.290832 TGTGGGAAAACCCGTTATACCC 60.291 50.000 0.00 0.00 39.07 3.69
3563 3920 3.011818 CTGTGGGAAAACCCGTTATACC 58.988 50.000 0.00 0.00 39.07 2.73
3564 3921 3.437741 CACTGTGGGAAAACCCGTTATAC 59.562 47.826 0.00 0.00 39.07 1.47
3565 3922 3.677190 CACTGTGGGAAAACCCGTTATA 58.323 45.455 0.00 0.00 39.07 0.98
3566 3923 2.510613 CACTGTGGGAAAACCCGTTAT 58.489 47.619 0.00 0.00 39.07 1.89
3567 3924 1.970092 CACTGTGGGAAAACCCGTTA 58.030 50.000 0.00 0.00 39.07 3.18
3568 3925 1.388837 GCACTGTGGGAAAACCCGTT 61.389 55.000 10.21 0.00 39.07 4.44
3569 3926 1.826487 GCACTGTGGGAAAACCCGT 60.826 57.895 10.21 0.00 39.07 5.28
3570 3927 1.178534 ATGCACTGTGGGAAAACCCG 61.179 55.000 10.21 0.00 39.07 5.28
3571 3928 0.318120 CATGCACTGTGGGAAAACCC 59.682 55.000 10.21 0.00 39.07 4.11
3572 3929 0.318120 CCATGCACTGTGGGAAAACC 59.682 55.000 10.21 0.00 40.81 3.27
3573 3930 1.039856 ACCATGCACTGTGGGAAAAC 58.960 50.000 10.21 0.00 41.14 2.43
3574 3931 1.411977 CAACCATGCACTGTGGGAAAA 59.588 47.619 10.21 0.00 41.14 2.29
3575 3932 1.039068 CAACCATGCACTGTGGGAAA 58.961 50.000 10.21 0.00 41.14 3.13
3576 3933 0.827089 CCAACCATGCACTGTGGGAA 60.827 55.000 10.21 0.00 41.14 3.97
3577 3934 1.228521 CCAACCATGCACTGTGGGA 60.229 57.895 10.21 0.00 41.14 4.37
3578 3935 2.277591 CCCAACCATGCACTGTGGG 61.278 63.158 10.21 10.40 41.14 4.61
3579 3936 1.228521 TCCCAACCATGCACTGTGG 60.229 57.895 10.21 3.18 42.55 4.17
3580 3937 1.855213 CGTCCCAACCATGCACTGTG 61.855 60.000 2.76 2.76 0.00 3.66
3581 3938 1.600636 CGTCCCAACCATGCACTGT 60.601 57.895 0.00 0.00 0.00 3.55
3582 3939 2.334946 CCGTCCCAACCATGCACTG 61.335 63.158 0.00 0.00 0.00 3.66
3583 3940 2.034066 CCGTCCCAACCATGCACT 59.966 61.111 0.00 0.00 0.00 4.40
3584 3941 1.602323 TTCCGTCCCAACCATGCAC 60.602 57.895 0.00 0.00 0.00 4.57
3585 3942 1.602323 GTTCCGTCCCAACCATGCA 60.602 57.895 0.00 0.00 0.00 3.96
3586 3943 2.686816 CGTTCCGTCCCAACCATGC 61.687 63.158 0.00 0.00 0.00 4.06
3587 3944 2.038269 CCGTTCCGTCCCAACCATG 61.038 63.158 0.00 0.00 0.00 3.66
3588 3945 2.349755 CCGTTCCGTCCCAACCAT 59.650 61.111 0.00 0.00 0.00 3.55
3589 3946 3.943691 CCCGTTCCGTCCCAACCA 61.944 66.667 0.00 0.00 0.00 3.67
3596 3953 4.790861 GTCCTCGCCCGTTCCGTC 62.791 72.222 0.00 0.00 0.00 4.79
3598 3955 4.796231 CTGTCCTCGCCCGTTCCG 62.796 72.222 0.00 0.00 0.00 4.30
3599 3956 4.452733 CCTGTCCTCGCCCGTTCC 62.453 72.222 0.00 0.00 0.00 3.62
3600 3957 3.692406 ACCTGTCCTCGCCCGTTC 61.692 66.667 0.00 0.00 0.00 3.95
3601 3958 4.003788 CACCTGTCCTCGCCCGTT 62.004 66.667 0.00 0.00 0.00 4.44
3647 4004 4.235762 AGCGACACCGGCAACAGT 62.236 61.111 0.00 0.00 36.06 3.55
3648 4005 3.414700 GAGCGACACCGGCAACAG 61.415 66.667 0.00 0.00 36.06 3.16
3659 4016 4.266070 TATCGGCCTGCGAGCGAC 62.266 66.667 0.00 0.00 0.00 5.19
3660 4017 3.966104 CTATCGGCCTGCGAGCGA 61.966 66.667 0.00 0.00 0.00 4.93
3671 4028 4.227134 AGCAGCACGGCCTATCGG 62.227 66.667 0.00 0.00 0.00 4.18
3672 4029 2.659897 GAGCAGCACGGCCTATCG 60.660 66.667 0.00 0.00 0.00 2.92
3673 4030 2.659897 CGAGCAGCACGGCCTATC 60.660 66.667 4.04 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.