Multiple sequence alignment - TraesCS5D01G434500

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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 TraesCS5D01G434500 chr5D 100.000 5041 0 0 1 5041 489904418 489909458 0.000000e+00 9310.0
1 TraesCS5D01G434500 chr5D 83.516 455 67 5 1483 1933 490035215 490034765 7.810000e-113 418.0
2 TraesCS5D01G434500 chr5B 92.418 3851 161 60 875 4640 604064703 604068507 0.000000e+00 5373.0
3 TraesCS5D01G434500 chr5B 86.408 412 39 11 4634 5041 604068533 604068931 7.750000e-118 435.0
4 TraesCS5D01G434500 chr5B 83.516 455 67 5 1483 1933 604164052 604163602 7.810000e-113 418.0
5 TraesCS5D01G434500 chr5B 88.936 235 13 3 566 794 604064368 604064595 1.380000e-70 278.0
6 TraesCS5D01G434500 chr5B 88.542 192 6 7 384 564 604064133 604064319 8.500000e-53 219.0
7 TraesCS5D01G434500 chr5B 84.615 221 11 15 22 225 604063732 604063946 1.110000e-46 198.0
8 TraesCS5D01G434500 chr5A 94.000 3450 107 40 968 4358 611564111 611567519 0.000000e+00 5132.0
9 TraesCS5D01G434500 chr5A 82.332 849 47 44 1 786 611563067 611563875 4.250000e-180 641.0
10 TraesCS5D01G434500 chr5A 89.320 412 37 5 4634 5041 611570573 611570981 1.250000e-140 510.0
11 TraesCS5D01G434500 chr5A 84.045 445 65 3 1483 1924 611652895 611652454 1.680000e-114 424.0
12 TraesCS5D01G434500 chr5A 90.055 181 14 3 4461 4640 611570370 611570547 1.090000e-56 231.0
13 TraesCS5D01G434500 chr5A 95.775 71 3 0 4350 4420 611570031 611570101 1.150000e-21 115.0
14 TraesCS5D01G434500 chr2B 83.369 469 70 7 1472 1936 675356153 675355689 1.300000e-115 427.0
15 TraesCS5D01G434500 chr2D 83.156 469 71 7 1472 1936 564095467 564095003 6.030000e-114 422.0
16 TraesCS5D01G434500 chr2D 77.381 168 28 7 4650 4808 186949879 186950045 1.930000e-14 91.6
17 TraesCS5D01G434500 chr2A 82.979 470 70 9 1472 1936 704776722 704776258 2.810000e-112 416.0
18 TraesCS5D01G434500 chr4A 80.222 450 73 15 1483 1924 466926103 466926544 1.750000e-84 324.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G434500 chr5D 489904418 489909458 5040 False 9310.0 9310 100.0000 1 5041 1 chr5D.!!$F1 5040
1 TraesCS5D01G434500 chr5B 604063732 604068931 5199 False 1300.6 5373 88.1838 22 5041 5 chr5B.!!$F1 5019
2 TraesCS5D01G434500 chr5A 611563067 611570981 7914 False 1325.8 5132 90.2964 1 5041 5 chr5A.!!$F1 5040

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
847 1042 0.175989 GAGGTTCACCCCGTGATCTC 59.824 60.000 0.00 3.28 42.40 2.75 F
911 1160 0.323957 GAGTAGTGGGGTGGTTGGTC 59.676 60.000 0.00 0.00 0.00 4.02 F
912 1161 1.004200 GTAGTGGGGTGGTTGGTCG 60.004 63.158 0.00 0.00 0.00 4.79 F
981 1238 1.153628 CTTGGTCCCGTCGATCCAC 60.154 63.158 0.00 0.00 0.00 4.02 F
1869 2158 2.096174 CGAGAACTTCCTCTTCGTCGAT 59.904 50.000 0.00 0.00 0.00 3.59 F
2992 3304 1.150081 CTCAGGGCATCCATGGGTC 59.850 63.158 13.02 0.00 34.83 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2630 2934 1.237533 ACTGCGCATTGTGTCAATCA 58.762 45.0 12.24 0.00 0.00 2.57 R
2634 2938 1.877637 AGTAACTGCGCATTGTGTCA 58.122 45.0 12.24 0.00 0.00 3.58 R
2668 2973 5.356751 ACGCTGTAATTAGATCAAAATGGCA 59.643 36.0 0.00 0.00 0.00 4.92 R
2966 3278 0.394762 GGATGCCCTGAGACAATGCA 60.395 55.0 0.00 0.00 36.23 3.96 R
3133 3445 0.387239 AGCGAAAAGGCATGCGAAAC 60.387 50.0 12.44 0.00 34.64 2.78 R
4645 7802 0.038343 CTTTCACGGGCCATGGTTTG 60.038 55.0 14.67 5.65 0.00 2.93 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
99 105 8.693625 GGCACGGGAAATTATATATCTACTAGT 58.306 37.037 0.00 0.00 0.00 2.57
144 150 2.685380 CCACTTCGCCCCCTCTCT 60.685 66.667 0.00 0.00 0.00 3.10
216 238 0.510359 GCTCGCTAATCATTGCCTCG 59.490 55.000 0.00 0.00 0.00 4.63
223 245 4.084849 CGCTAATCATTGCCTCGTCTTAAG 60.085 45.833 0.00 0.00 0.00 1.85
227 260 4.537135 TCATTGCCTCGTCTTAAGTCTT 57.463 40.909 1.63 0.00 0.00 3.01
229 262 6.032956 TCATTGCCTCGTCTTAAGTCTTAA 57.967 37.500 1.63 4.97 0.00 1.85
230 263 5.867716 TCATTGCCTCGTCTTAAGTCTTAAC 59.132 40.000 1.63 0.00 0.00 2.01
281 332 5.565834 GCGGGTGGATTTCTTTTTGTTCATA 60.566 40.000 0.00 0.00 0.00 2.15
282 333 5.861787 CGGGTGGATTTCTTTTTGTTCATAC 59.138 40.000 0.00 0.00 0.00 2.39
283 334 5.861787 GGGTGGATTTCTTTTTGTTCATACG 59.138 40.000 0.00 0.00 0.00 3.06
284 335 5.344933 GGTGGATTTCTTTTTGTTCATACGC 59.655 40.000 0.00 0.00 0.00 4.42
285 336 5.918011 GTGGATTTCTTTTTGTTCATACGCA 59.082 36.000 0.00 0.00 0.00 5.24
286 337 5.918011 TGGATTTCTTTTTGTTCATACGCAC 59.082 36.000 0.00 0.00 0.00 5.34
287 338 5.918011 GGATTTCTTTTTGTTCATACGCACA 59.082 36.000 0.00 0.00 0.00 4.57
288 339 6.129194 GGATTTCTTTTTGTTCATACGCACAC 60.129 38.462 0.00 0.00 0.00 3.82
289 340 4.884458 TCTTTTTGTTCATACGCACACA 57.116 36.364 0.00 0.00 0.00 3.72
290 341 4.843147 TCTTTTTGTTCATACGCACACAG 58.157 39.130 0.00 0.00 0.00 3.66
342 399 2.030274 GCTGCCATTACTTTTTGTCCGT 60.030 45.455 0.00 0.00 0.00 4.69
408 496 0.685097 TCGTCTTCCTTGTCCCCTTG 59.315 55.000 0.00 0.00 0.00 3.61
496 595 8.854312 CACAGTTTTGTTTTGTTTTGTTTGTTT 58.146 25.926 0.00 0.00 34.62 2.83
497 596 8.854312 ACAGTTTTGTTTTGTTTTGTTTGTTTG 58.146 25.926 0.00 0.00 32.28 2.93
498 597 8.854312 CAGTTTTGTTTTGTTTTGTTTGTTTGT 58.146 25.926 0.00 0.00 0.00 2.83
499 598 8.854312 AGTTTTGTTTTGTTTTGTTTGTTTGTG 58.146 25.926 0.00 0.00 0.00 3.33
508 607 0.656785 GTTTGTTTGTGGACGCCGTA 59.343 50.000 0.00 0.00 0.00 4.02
639 824 1.070758 CTTGATGCATACGTAGCCCCT 59.929 52.381 0.00 0.00 0.00 4.79
641 826 0.951040 GATGCATACGTAGCCCCTGC 60.951 60.000 10.45 10.45 37.95 4.85
644 829 3.231736 ATACGTAGCCCCTGCCCG 61.232 66.667 0.08 0.00 38.69 6.13
683 868 2.753009 ATTCCACGCTGCAGCTCCAA 62.753 55.000 34.22 21.31 39.32 3.53
793 984 5.664815 AAGGTAATAATCCTTCCCCTTCC 57.335 43.478 0.00 0.00 40.80 3.46
794 985 3.988186 AGGTAATAATCCTTCCCCTTCCC 59.012 47.826 0.00 0.00 30.18 3.97
795 986 3.075582 GGTAATAATCCTTCCCCTTCCCC 59.924 52.174 0.00 0.00 0.00 4.81
796 987 2.940011 ATAATCCTTCCCCTTCCCCT 57.060 50.000 0.00 0.00 0.00 4.79
797 988 1.907240 TAATCCTTCCCCTTCCCCTG 58.093 55.000 0.00 0.00 0.00 4.45
800 991 1.140134 TCCTTCCCCTTCCCCTGTTG 61.140 60.000 0.00 0.00 0.00 3.33
802 993 3.204467 TTCCCCTTCCCCTGTTGCG 62.204 63.158 0.00 0.00 0.00 4.85
804 995 2.672996 CCCTTCCCCTGTTGCGTG 60.673 66.667 0.00 0.00 0.00 5.34
805 996 3.365265 CCTTCCCCTGTTGCGTGC 61.365 66.667 0.00 0.00 0.00 5.34
812 1003 4.374702 CTGTTGCGTGCGTGGCTC 62.375 66.667 0.00 0.00 0.00 4.70
825 1016 4.666253 GGCTCCCCTGCACAGCAA 62.666 66.667 4.97 0.00 38.41 3.91
826 1017 3.060615 GCTCCCCTGCACAGCAAG 61.061 66.667 0.00 0.00 38.41 4.01
830 1021 2.360852 CCCTGCACAGCAAGGGAG 60.361 66.667 16.55 0.00 44.15 4.30
831 1022 2.360852 CCTGCACAGCAAGGGAGG 60.361 66.667 0.00 0.00 38.41 4.30
832 1023 2.433446 CTGCACAGCAAGGGAGGT 59.567 61.111 0.00 0.00 38.41 3.85
833 1024 1.228367 CTGCACAGCAAGGGAGGTT 60.228 57.895 0.00 0.00 38.41 3.50
834 1025 1.228245 TGCACAGCAAGGGAGGTTC 60.228 57.895 0.00 0.00 34.76 3.62
835 1026 1.228245 GCACAGCAAGGGAGGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
836 1027 1.518903 GCACAGCAAGGGAGGTTCAC 61.519 60.000 0.00 0.00 0.00 3.18
837 1028 0.890996 CACAGCAAGGGAGGTTCACC 60.891 60.000 0.00 0.00 0.00 4.02
847 1042 0.175989 GAGGTTCACCCCGTGATCTC 59.824 60.000 0.00 3.28 42.40 2.75
848 1043 1.153628 GGTTCACCCCGTGATCTCG 60.154 63.158 10.15 10.15 42.40 4.04
855 1050 2.404186 CCCGTGATCTCGTCGACCA 61.404 63.158 10.58 0.00 0.00 4.02
887 1136 2.110006 GCTCCTTGGATCCGAGGC 59.890 66.667 35.70 24.23 45.19 4.70
896 1145 2.123854 ATCCGAGGCGCAGGAGTA 60.124 61.111 20.21 2.22 40.26 2.59
901 1150 3.077556 AGGCGCAGGAGTAGTGGG 61.078 66.667 10.83 0.00 0.00 4.61
903 1152 3.391382 GCGCAGGAGTAGTGGGGT 61.391 66.667 0.30 0.00 0.00 4.95
907 1156 1.489560 GCAGGAGTAGTGGGGTGGTT 61.490 60.000 0.00 0.00 0.00 3.67
909 1158 0.840722 AGGAGTAGTGGGGTGGTTGG 60.841 60.000 0.00 0.00 0.00 3.77
911 1160 0.323957 GAGTAGTGGGGTGGTTGGTC 59.676 60.000 0.00 0.00 0.00 4.02
912 1161 1.004200 GTAGTGGGGTGGTTGGTCG 60.004 63.158 0.00 0.00 0.00 4.79
913 1162 2.218454 TAGTGGGGTGGTTGGTCGG 61.218 63.158 0.00 0.00 0.00 4.79
916 1165 4.717313 GGGGTGGTTGGTCGGCTC 62.717 72.222 0.00 0.00 0.00 4.70
917 1166 4.717313 GGGTGGTTGGTCGGCTCC 62.717 72.222 0.00 0.00 0.00 4.70
918 1167 3.637273 GGTGGTTGGTCGGCTCCT 61.637 66.667 0.00 0.00 0.00 3.69
919 1168 2.358737 GTGGTTGGTCGGCTCCTG 60.359 66.667 0.00 0.00 0.00 3.86
922 1171 2.047179 GTTGGTCGGCTCCTGTCC 60.047 66.667 0.00 0.00 0.00 4.02
929 1186 3.775654 GGCTCCTGTCCTGTCCCG 61.776 72.222 0.00 0.00 0.00 5.14
971 1228 2.513897 CGATTCCGCCTTGGTCCC 60.514 66.667 0.00 0.00 39.52 4.46
973 1230 3.325201 GATTCCGCCTTGGTCCCGT 62.325 63.158 0.00 0.00 39.52 5.28
974 1231 3.325201 ATTCCGCCTTGGTCCCGTC 62.325 63.158 0.00 0.00 39.52 4.79
977 1234 4.143333 CGCCTTGGTCCCGTCGAT 62.143 66.667 0.00 0.00 0.00 3.59
978 1235 2.202892 GCCTTGGTCCCGTCGATC 60.203 66.667 0.00 0.00 0.00 3.69
980 1237 2.355986 CCTTGGTCCCGTCGATCCA 61.356 63.158 0.00 0.00 0.00 3.41
981 1238 1.153628 CTTGGTCCCGTCGATCCAC 60.154 63.158 0.00 0.00 0.00 4.02
1167 1450 2.889617 CTGGCCGTCCACATCGTA 59.110 61.111 0.00 0.00 37.47 3.43
1869 2158 2.096174 CGAGAACTTCCTCTTCGTCGAT 59.904 50.000 0.00 0.00 0.00 3.59
1951 2240 3.214328 GGTGAGTTGTTGGTCAATCTGT 58.786 45.455 0.00 0.00 38.38 3.41
1952 2241 3.003689 GGTGAGTTGTTGGTCAATCTGTG 59.996 47.826 0.00 0.00 38.38 3.66
1953 2242 3.627577 GTGAGTTGTTGGTCAATCTGTGT 59.372 43.478 0.00 0.00 38.38 3.72
2006 2298 5.669477 AGCTAGAGTTCATCTCCATTGTTC 58.331 41.667 0.00 0.00 43.71 3.18
2033 2325 3.942130 AAAGGAAACACTTGCCTATGC 57.058 42.857 0.00 0.00 38.26 3.14
2052 2345 8.012241 GCCTATGCTCGTATTTATTTTTCAGAG 58.988 37.037 0.00 0.00 33.53 3.35
2066 2359 9.925268 TTATTTTTCAGAGAAGTAAACACGAAC 57.075 29.630 0.00 0.00 0.00 3.95
2068 2361 6.971527 TTTCAGAGAAGTAAACACGAACAA 57.028 33.333 0.00 0.00 0.00 2.83
2069 2362 7.548196 TTTCAGAGAAGTAAACACGAACAAT 57.452 32.000 0.00 0.00 0.00 2.71
2071 2364 8.651391 TTCAGAGAAGTAAACACGAACAATAA 57.349 30.769 0.00 0.00 0.00 1.40
2072 2365 8.294341 TCAGAGAAGTAAACACGAACAATAAG 57.706 34.615 0.00 0.00 0.00 1.73
2074 2367 9.188588 CAGAGAAGTAAACACGAACAATAAGTA 57.811 33.333 0.00 0.00 0.00 2.24
2075 2368 9.189723 AGAGAAGTAAACACGAACAATAAGTAC 57.810 33.333 0.00 0.00 0.00 2.73
2076 2369 8.302965 AGAAGTAAACACGAACAATAAGTACC 57.697 34.615 0.00 0.00 0.00 3.34
2078 2371 8.611654 AAGTAAACACGAACAATAAGTACCAT 57.388 30.769 0.00 0.00 0.00 3.55
2108 2402 2.621998 GGCATTGCACTGCATCTAGATT 59.378 45.455 27.58 0.00 44.12 2.40
2122 2416 8.922931 TGCATCTAGATTGGCAAGAAAATATA 57.077 30.769 13.75 0.00 32.54 0.86
2207 2501 2.280389 CGGGCTCACATCCCATCG 60.280 66.667 0.00 0.00 44.11 3.84
2287 2581 2.136728 TGCAATGCATTGTGCTTTCAC 58.863 42.857 33.67 18.53 45.31 3.18
2299 2593 3.540314 TGCTTTCACCAGCATGTTTTT 57.460 38.095 0.00 0.00 45.14 1.94
2330 2624 7.993101 TCTTTCTGAGAAATTATGCCATTCAG 58.007 34.615 8.23 0.00 33.63 3.02
2337 2631 4.682778 AATTATGCCATTCAGCTGCAAT 57.317 36.364 9.47 7.19 38.69 3.56
2347 2641 5.163591 CCATTCAGCTGCAATCATAAACAGA 60.164 40.000 9.47 0.00 31.67 3.41
2361 2655 3.665745 AAACAGATTGGTTGCACATCC 57.334 42.857 0.00 0.00 0.00 3.51
2369 2663 4.987408 TTGGTTGCACATCCTTATCATG 57.013 40.909 0.00 0.00 0.00 3.07
2375 2669 2.287427 GCACATCCTTATCATGCTGCAC 60.287 50.000 3.57 0.00 32.80 4.57
2382 2676 3.311871 CCTTATCATGCTGCACTCTGAAC 59.688 47.826 3.57 0.00 0.00 3.18
2570 2873 5.352293 TGTGATCATCTACATTCTGTTGTGC 59.648 40.000 0.00 0.00 0.00 4.57
2614 2917 6.514870 GCAGGTATGAATTGTGTTCACTTTCA 60.515 38.462 17.09 17.09 33.49 2.69
2622 2926 8.735315 TGAATTGTGTTCACTTTCAAGTTCTTA 58.265 29.630 14.43 0.00 37.08 2.10
2648 2952 2.334971 TTGATTGACACAATGCGCAG 57.665 45.000 18.32 5.51 0.00 5.18
2691 2996 5.820131 TGCCATTTTGATCTAATTACAGCG 58.180 37.500 0.00 0.00 0.00 5.18
2992 3304 1.150081 CTCAGGGCATCCATGGGTC 59.850 63.158 13.02 0.00 34.83 4.46
3104 3416 1.902508 TGGCTCTCAGGGTAAGAAGTG 59.097 52.381 0.00 0.00 0.00 3.16
3133 3445 2.995258 CCCGGCTTGAAATGATTGTTTG 59.005 45.455 0.00 0.00 0.00 2.93
3147 3459 2.593346 TGTTTGTTTCGCATGCCTTT 57.407 40.000 13.15 0.00 0.00 3.11
3245 3563 5.449297 TGGTGGATGTTATCATGGAAGAA 57.551 39.130 0.00 0.00 34.06 2.52
3254 3572 7.214467 TGTTATCATGGAAGAAACCAAGAAC 57.786 36.000 0.00 0.00 43.47 3.01
3269 3588 3.052036 CAAGAACGCAAAACCATCCAAG 58.948 45.455 0.00 0.00 0.00 3.61
3271 3590 2.693074 AGAACGCAAAACCATCCAAGTT 59.307 40.909 0.00 0.00 0.00 2.66
3289 3610 2.691526 AGTTGACTTGTCCTGACGTGTA 59.308 45.455 0.00 0.00 0.00 2.90
3291 3612 3.297830 TGACTTGTCCTGACGTGTATG 57.702 47.619 0.00 0.00 0.00 2.39
3293 3614 3.822167 TGACTTGTCCTGACGTGTATGTA 59.178 43.478 0.00 0.00 0.00 2.29
3294 3615 4.278919 TGACTTGTCCTGACGTGTATGTAA 59.721 41.667 0.00 0.00 0.00 2.41
3374 3701 3.381590 TGTTCAAGATGATCGACTCGGAT 59.618 43.478 0.00 0.00 0.00 4.18
3446 3773 2.671682 GCCAACCTCCAGGAGTCC 59.328 66.667 15.86 0.00 38.94 3.85
3467 3794 0.103026 AGATCTACGCGCTCATGCAA 59.897 50.000 5.73 0.00 39.64 4.08
3632 3975 1.771073 CGACGCTGCACCTGAACAAA 61.771 55.000 0.00 0.00 0.00 2.83
3820 4163 1.078823 TCACAGCTTCCCTCCCTTCTA 59.921 52.381 0.00 0.00 0.00 2.10
3821 4164 1.208293 CACAGCTTCCCTCCCTTCTAC 59.792 57.143 0.00 0.00 0.00 2.59
3822 4165 1.079658 ACAGCTTCCCTCCCTTCTACT 59.920 52.381 0.00 0.00 0.00 2.57
3823 4166 2.315155 ACAGCTTCCCTCCCTTCTACTA 59.685 50.000 0.00 0.00 0.00 1.82
3824 4167 2.962421 CAGCTTCCCTCCCTTCTACTAG 59.038 54.545 0.00 0.00 0.00 2.57
3856 4199 3.708220 CTTCGGGGCGCTCTGACTC 62.708 68.421 20.95 0.00 0.00 3.36
3874 4219 4.051237 GACTCAACTGAAACCAAAATGCC 58.949 43.478 0.00 0.00 0.00 4.40
3882 4227 3.763360 TGAAACCAAAATGCCGATGATCT 59.237 39.130 0.00 0.00 0.00 2.75
3883 4228 4.142403 TGAAACCAAAATGCCGATGATCTC 60.142 41.667 0.00 0.00 0.00 2.75
4127 4476 2.028112 TGTTGTAGAGACATGGTGAGGC 60.028 50.000 0.00 0.00 34.86 4.70
4147 4497 3.312697 GGCGATTGAGTTTTCATAGGGTC 59.687 47.826 0.00 0.00 32.27 4.46
4202 4556 2.732658 GGACTCGGGACAACGTGT 59.267 61.111 0.00 0.00 34.94 4.49
4241 4607 1.250840 GCAGGCCCGGTGATTTTCTT 61.251 55.000 0.00 0.00 0.00 2.52
4329 4698 7.148018 CCTCCTTGTATACAGTACGGTTAGAAA 60.148 40.741 3.39 0.00 0.00 2.52
4421 7310 0.538287 AGAGCCCCAAACTCAAGTGC 60.538 55.000 0.00 0.00 36.58 4.40
4427 7316 2.161609 CCCCAAACTCAAGTGCGAATAC 59.838 50.000 0.00 0.00 0.00 1.89
4452 7575 3.760580 AGGGGATTTTCTCTAGCATCG 57.239 47.619 0.00 0.00 0.00 3.84
4481 7604 4.779733 TCGGTGGCTCTCCTCCCC 62.780 72.222 0.00 0.00 41.84 4.81
4485 7608 3.673597 TGGCTCTCCTCCCCGTCT 61.674 66.667 0.00 0.00 0.00 4.18
4509 7633 2.202810 GCCACGAGTAGAGCAGCC 60.203 66.667 0.00 0.00 0.00 4.85
4602 7726 4.530388 CCAACATCGATTCCAATGATTCG 58.470 43.478 0.00 0.00 42.70 3.34
4618 7743 1.529226 TTCGTTGCATTTCGGACCAT 58.471 45.000 0.00 0.00 0.00 3.55
4623 7748 0.897401 TGCATTTCGGACCATGCCAA 60.897 50.000 15.39 0.01 44.49 4.52
4624 7749 0.461135 GCATTTCGGACCATGCCAAT 59.539 50.000 9.31 0.00 40.04 3.16
4643 7800 4.418392 CAATGTGCCACTAGAAGAAATGC 58.582 43.478 0.00 0.00 0.00 3.56
4645 7802 3.338249 TGTGCCACTAGAAGAAATGCTC 58.662 45.455 0.00 0.00 0.00 4.26
4651 7808 4.761739 CCACTAGAAGAAATGCTCAAACCA 59.238 41.667 0.00 0.00 0.00 3.67
4658 7815 1.606885 AATGCTCAAACCATGGCCCG 61.607 55.000 13.04 0.00 0.00 6.13
4661 7818 1.303236 CTCAAACCATGGCCCGTGA 60.303 57.895 13.04 9.23 0.00 4.35
4666 7823 0.039618 AACCATGGCCCGTGAAAGAT 59.960 50.000 13.04 0.00 0.00 2.40
4676 7833 2.095853 CCCGTGAAAGATGAATTCCACG 59.904 50.000 19.40 19.40 34.32 4.94
4683 7840 7.015877 GTGAAAGATGAATTCCACGTACTTTC 58.984 38.462 18.10 18.10 40.89 2.62
4714 7871 3.009026 TCACATGCGTACAATCATGCTT 58.991 40.909 15.48 0.00 42.72 3.91
4766 7923 5.245075 GTGGATCATATATCCTAGCCCTAGC 59.755 48.000 5.67 0.00 38.95 3.42
4782 7939 2.896044 CCTAGCTAGCTCATGGACATCA 59.104 50.000 23.26 0.00 0.00 3.07
4784 7941 4.020396 CCTAGCTAGCTCATGGACATCATT 60.020 45.833 23.26 0.00 32.92 2.57
4802 7959 4.832248 TCATTTAGTGGCGAGAAGTCATT 58.168 39.130 0.00 0.00 36.54 2.57
4813 7970 2.227388 GAGAAGTCATTGTTGGCCACAG 59.773 50.000 3.88 0.00 36.48 3.66
4821 7978 0.178992 TGTTGGCCACAGGAAAGGAG 60.179 55.000 3.88 0.00 0.00 3.69
4833 7990 4.202514 ACAGGAAAGGAGGAAGAAGAAAGG 60.203 45.833 0.00 0.00 0.00 3.11
4835 7992 3.498661 GGAAAGGAGGAAGAAGAAAGGCA 60.499 47.826 0.00 0.00 0.00 4.75
4898 8055 5.045213 GGGTTGAATTGGTTTGGGGAATAAT 60.045 40.000 0.00 0.00 0.00 1.28
4907 8064 5.034200 GGTTTGGGGAATAATTTTAGGGGT 58.966 41.667 0.00 0.00 0.00 4.95
4908 8065 5.129815 GGTTTGGGGAATAATTTTAGGGGTC 59.870 44.000 0.00 0.00 0.00 4.46
4928 8086 8.049721 AGGGGTCTTCTAGATGAATAAAAGTTG 58.950 37.037 9.74 0.00 33.71 3.16
4938 8096 8.753497 AGATGAATAAAAGTTGAATCCCCTAC 57.247 34.615 0.00 0.00 0.00 3.18
4941 8099 8.713708 TGAATAAAAGTTGAATCCCCTACAAA 57.286 30.769 0.00 0.00 0.00 2.83
4942 8100 9.320295 TGAATAAAAGTTGAATCCCCTACAAAT 57.680 29.630 0.00 0.00 0.00 2.32
4955 8113 9.715119 AATCCCCTACAAATTAGCTTTTTAGAT 57.285 29.630 0.00 0.00 31.48 1.98
4964 8122 9.136323 CAAATTAGCTTTTTAGATGATAGGGGT 57.864 33.333 0.00 0.00 0.00 4.95
4968 8126 6.289064 AGCTTTTTAGATGATAGGGGTTACG 58.711 40.000 0.00 0.00 0.00 3.18
4970 8128 6.764560 GCTTTTTAGATGATAGGGGTTACGAA 59.235 38.462 0.00 0.00 0.00 3.85
4977 8135 8.437274 AGATGATAGGGGTTACGAAATAGAAT 57.563 34.615 0.00 0.00 0.00 2.40
5037 8197 7.069344 GCCCATTCCCCAAAAGCTATATATAT 58.931 38.462 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 101 6.481976 AGAGGAAGATCGATCGCATATACTAG 59.518 42.308 19.33 0.00 0.00 2.57
96 102 6.350103 AGAGGAAGATCGATCGCATATACTA 58.650 40.000 19.33 0.00 0.00 1.82
97 103 5.189928 AGAGGAAGATCGATCGCATATACT 58.810 41.667 19.33 10.50 0.00 2.12
98 104 5.493133 AGAGGAAGATCGATCGCATATAC 57.507 43.478 19.33 9.24 0.00 1.47
99 105 4.271291 CGAGAGGAAGATCGATCGCATATA 59.729 45.833 19.33 0.00 41.40 0.86
100 106 3.064682 CGAGAGGAAGATCGATCGCATAT 59.935 47.826 19.33 10.79 41.40 1.78
101 107 2.416893 CGAGAGGAAGATCGATCGCATA 59.583 50.000 19.33 0.00 41.40 3.14
102 108 1.198867 CGAGAGGAAGATCGATCGCAT 59.801 52.381 19.33 13.24 41.40 4.73
108 114 0.955178 GGATGCGAGAGGAAGATCGA 59.045 55.000 0.00 0.00 41.40 3.59
144 150 2.997315 CACAGCACGGGGGAGAGA 60.997 66.667 0.00 0.00 0.00 3.10
216 238 6.035217 CCGCCTCTTAGTTAAGACTTAAGAC 58.965 44.000 10.09 2.62 37.40 3.01
223 245 2.667473 TGCCGCCTCTTAGTTAAGAC 57.333 50.000 0.00 0.00 37.40 3.01
227 260 0.978151 TGGTTGCCGCCTCTTAGTTA 59.022 50.000 0.00 0.00 0.00 2.24
229 262 1.003718 GTGGTTGCCGCCTCTTAGT 60.004 57.895 0.00 0.00 0.00 2.24
230 263 3.890674 GTGGTTGCCGCCTCTTAG 58.109 61.111 0.00 0.00 0.00 2.18
258 309 4.314740 TGAACAAAAAGAAATCCACCCG 57.685 40.909 0.00 0.00 0.00 5.28
261 312 5.918011 TGCGTATGAACAAAAAGAAATCCAC 59.082 36.000 0.00 0.00 0.00 4.02
281 332 2.927580 CGGGAGGTACTGTGTGCGT 61.928 63.158 0.00 0.00 41.55 5.24
282 333 2.126071 CGGGAGGTACTGTGTGCG 60.126 66.667 0.00 0.00 41.55 5.34
283 334 1.080025 GACGGGAGGTACTGTGTGC 60.080 63.158 0.00 0.00 41.55 4.57
284 335 0.038526 GTGACGGGAGGTACTGTGTG 60.039 60.000 0.00 0.00 41.55 3.82
285 336 1.521450 CGTGACGGGAGGTACTGTGT 61.521 60.000 0.00 0.00 41.55 3.72
286 337 1.211969 CGTGACGGGAGGTACTGTG 59.788 63.158 0.00 0.00 41.55 3.66
287 338 0.036732 TACGTGACGGGAGGTACTGT 59.963 55.000 10.66 0.00 41.55 3.55
288 339 0.449388 GTACGTGACGGGAGGTACTG 59.551 60.000 10.66 0.00 41.55 2.74
289 340 1.947678 CAGTACGTGACGGGAGGTACT 60.948 57.143 10.66 12.89 44.48 2.73
290 341 0.449388 CAGTACGTGACGGGAGGTAC 59.551 60.000 10.66 2.05 37.43 3.34
342 399 6.297080 TCTAAGACGAAGGAGAAGACTAGA 57.703 41.667 0.00 0.00 0.00 2.43
388 476 1.279271 CAAGGGGACAAGGAAGACGAT 59.721 52.381 0.00 0.00 0.00 3.73
408 496 7.205992 TGATGATATACTGTTGTGAAGAGAGC 58.794 38.462 0.00 0.00 0.00 4.09
496 595 1.301087 CAAAGGTACGGCGTCCACA 60.301 57.895 19.21 0.00 0.00 4.17
497 596 2.674084 GCAAAGGTACGGCGTCCAC 61.674 63.158 19.21 10.65 0.00 4.02
498 597 2.357760 GCAAAGGTACGGCGTCCA 60.358 61.111 19.21 0.00 0.00 4.02
499 598 1.670083 AAGCAAAGGTACGGCGTCC 60.670 57.895 19.21 17.90 0.00 4.79
641 826 1.459455 ATGATCTGACGCCTCTCGGG 61.459 60.000 0.00 0.00 43.86 5.14
644 829 0.599728 GCCATGATCTGACGCCTCTC 60.600 60.000 0.00 0.00 0.00 3.20
712 903 0.106335 AGCAGGATCGATGAGCCAAG 59.894 55.000 0.54 0.00 41.08 3.61
778 969 1.083912 ACAGGGGAAGGGGAAGGATTA 59.916 52.381 0.00 0.00 0.00 1.75
788 979 3.365265 GCACGCAACAGGGGAAGG 61.365 66.667 0.00 0.00 0.00 3.46
789 980 3.726517 CGCACGCAACAGGGGAAG 61.727 66.667 0.00 0.00 0.00 3.46
795 986 4.374702 GAGCCACGCACGCAACAG 62.375 66.667 0.00 0.00 0.00 3.16
816 1007 1.228245 GAACCTCCCTTGCTGTGCA 60.228 57.895 0.00 0.00 36.47 4.57
817 1008 1.228245 TGAACCTCCCTTGCTGTGC 60.228 57.895 0.00 0.00 0.00 4.57
821 1012 2.539081 GGGGTGAACCTCCCTTGCT 61.539 63.158 0.00 0.00 44.07 3.91
822 1013 2.035783 GGGGTGAACCTCCCTTGC 59.964 66.667 0.00 0.00 44.07 4.01
824 1015 2.122099 ACGGGGTGAACCTCCCTT 60.122 61.111 0.00 0.00 44.07 3.95
825 1016 2.765705 ATCACGGGGTGAACCTCCCT 62.766 60.000 2.20 0.00 45.96 4.20
826 1017 2.253403 GATCACGGGGTGAACCTCCC 62.253 65.000 2.20 0.00 45.96 4.30
829 1020 1.605058 CGAGATCACGGGGTGAACCT 61.605 60.000 4.47 3.53 45.96 3.50
830 1021 1.153628 CGAGATCACGGGGTGAACC 60.154 63.158 4.47 0.00 45.96 3.62
831 1022 0.458025 GACGAGATCACGGGGTGAAC 60.458 60.000 16.88 0.20 45.96 3.18
832 1023 1.888018 GACGAGATCACGGGGTGAA 59.112 57.895 16.88 0.00 45.96 3.18
833 1024 2.404186 CGACGAGATCACGGGGTGA 61.404 63.158 16.88 0.38 46.90 4.02
834 1025 2.102357 CGACGAGATCACGGGGTG 59.898 66.667 16.88 0.00 37.61 4.61
835 1026 2.045634 TCGACGAGATCACGGGGT 60.046 61.111 16.88 0.00 37.61 4.95
836 1027 2.408022 GTCGACGAGATCACGGGG 59.592 66.667 16.88 7.96 37.61 5.73
837 1028 2.404186 TGGTCGACGAGATCACGGG 61.404 63.158 16.88 8.30 34.48 5.28
867 1062 4.207281 TCGGATCCAAGGAGCGCG 62.207 66.667 13.41 0.00 0.00 6.86
869 1064 2.419198 CCTCGGATCCAAGGAGCG 59.581 66.667 14.19 1.60 34.35 5.03
872 1067 3.849951 GCGCCTCGGATCCAAGGA 61.850 66.667 23.83 5.23 34.35 3.36
883 1132 2.496817 CCACTACTCCTGCGCCTC 59.503 66.667 4.18 0.00 0.00 4.70
887 1136 2.579201 CACCCCACTACTCCTGCG 59.421 66.667 0.00 0.00 0.00 5.18
896 1145 3.566210 CCGACCAACCACCCCACT 61.566 66.667 0.00 0.00 0.00 4.00
901 1150 3.637273 AGGAGCCGACCAACCACC 61.637 66.667 0.00 0.00 0.00 4.61
903 1152 2.847234 ACAGGAGCCGACCAACCA 60.847 61.111 0.00 0.00 0.00 3.67
907 1156 2.997315 CAGGACAGGAGCCGACCA 60.997 66.667 0.00 0.00 0.00 4.02
909 1158 2.574399 GACAGGACAGGAGCCGAC 59.426 66.667 0.00 0.00 0.00 4.79
911 1160 3.775654 GGGACAGGACAGGAGCCG 61.776 72.222 0.00 0.00 0.00 5.52
912 1161 3.775654 CGGGACAGGACAGGAGCC 61.776 72.222 0.00 0.00 0.00 4.70
913 1162 3.775654 CCGGGACAGGACAGGAGC 61.776 72.222 0.00 0.00 0.00 4.70
914 1163 3.775654 GCCGGGACAGGACAGGAG 61.776 72.222 2.18 0.00 0.00 3.69
929 1186 3.310860 CTATATGGGTCGCCGGGCC 62.311 68.421 14.55 0.00 0.00 5.80
935 1192 1.641577 GCCGAATCTATATGGGTCGC 58.358 55.000 7.32 1.83 0.00 5.19
938 1195 3.118738 GGAATCGCCGAATCTATATGGGT 60.119 47.826 1.76 0.00 0.00 4.51
939 1196 3.458189 GGAATCGCCGAATCTATATGGG 58.542 50.000 1.76 0.00 0.00 4.00
962 1219 2.355986 TGGATCGACGGGACCAAGG 61.356 63.158 0.00 0.00 0.00 3.61
966 1223 3.846430 GGGTGGATCGACGGGACC 61.846 72.222 1.47 0.00 0.00 4.46
970 1227 2.027605 CGATGGGTGGATCGACGG 59.972 66.667 1.47 0.00 46.72 4.79
971 1228 2.027605 CCGATGGGTGGATCGACG 59.972 66.667 4.53 0.00 46.72 5.12
973 1230 2.762043 TGCCGATGGGTGGATCGA 60.762 61.111 4.53 0.00 46.72 3.59
974 1231 2.280389 CTGCCGATGGGTGGATCG 60.280 66.667 0.00 0.00 44.00 3.69
975 1232 2.592861 GCTGCCGATGGGTGGATC 60.593 66.667 0.00 0.00 34.97 3.36
976 1233 4.552365 CGCTGCCGATGGGTGGAT 62.552 66.667 0.00 0.00 36.29 3.41
1157 1440 0.739462 CGCCTTGCTTACGATGTGGA 60.739 55.000 0.00 0.00 0.00 4.02
1531 1820 4.452733 GGCGTACTCCTTGCCGCT 62.453 66.667 0.00 0.00 45.11 5.52
2006 2298 4.098501 AGGCAAGTGTTTCCTTTTCTGAAG 59.901 41.667 0.00 0.00 0.00 3.02
2052 2345 8.075593 TGGTACTTATTGTTCGTGTTTACTTC 57.924 34.615 0.00 0.00 0.00 3.01
2062 2355 7.910162 CCTTGAATGAATGGTACTTATTGTTCG 59.090 37.037 0.00 0.00 0.00 3.95
2066 2359 7.099266 TGCCTTGAATGAATGGTACTTATTG 57.901 36.000 0.00 0.00 0.00 1.90
2068 2361 7.685155 GCAATGCCTTGAATGAATGGTACTTAT 60.685 37.037 5.85 0.00 34.04 1.73
2069 2362 6.405731 GCAATGCCTTGAATGAATGGTACTTA 60.406 38.462 5.85 0.00 34.04 2.24
2071 2364 4.142093 GCAATGCCTTGAATGAATGGTACT 60.142 41.667 5.85 0.00 34.04 2.73
2072 2365 4.114794 GCAATGCCTTGAATGAATGGTAC 58.885 43.478 5.85 0.00 34.04 3.34
2074 2367 2.568062 TGCAATGCCTTGAATGAATGGT 59.432 40.909 1.53 0.00 34.04 3.55
2075 2368 2.933906 GTGCAATGCCTTGAATGAATGG 59.066 45.455 1.53 0.00 34.04 3.16
2076 2369 3.616821 CAGTGCAATGCCTTGAATGAATG 59.383 43.478 0.00 0.00 34.04 2.67
2078 2371 2.610976 GCAGTGCAATGCCTTGAATGAA 60.611 45.455 27.88 0.00 40.43 2.57
2108 2402 8.868103 TGCCAAATCATATATATTTTCTTGCCA 58.132 29.630 0.00 0.00 0.00 4.92
2122 2416 6.482898 TGGTAGCAAAATGCCAAATCATAT 57.517 33.333 0.00 0.00 46.52 1.78
2132 2426 3.056607 ACAGAACCATGGTAGCAAAATGC 60.057 43.478 20.12 0.00 45.46 3.56
2207 2501 4.511527 ACATGGTCACATCAATCAGTCTC 58.488 43.478 0.00 0.00 34.35 3.36
2298 2592 9.696917 GGCATAATTTCTCAGAAAGAAGAAAAA 57.303 29.630 5.94 0.00 44.69 1.94
2299 2593 8.859090 TGGCATAATTTCTCAGAAAGAAGAAAA 58.141 29.630 5.94 0.00 44.69 2.29
2300 2594 8.408043 TGGCATAATTTCTCAGAAAGAAGAAA 57.592 30.769 5.94 0.53 44.69 2.52
2306 2600 6.696148 GCTGAATGGCATAATTTCTCAGAAAG 59.304 38.462 22.43 3.85 0.00 2.62
2330 2624 5.002464 ACCAATCTGTTTATGATTGCAGC 57.998 39.130 10.02 0.00 45.44 5.25
2337 2631 5.105797 GGATGTGCAACCAATCTGTTTATGA 60.106 40.000 0.00 0.00 34.36 2.15
2347 2641 4.202182 GCATGATAAGGATGTGCAACCAAT 60.202 41.667 0.00 2.32 35.93 3.16
2361 2655 3.311871 GGTTCAGAGTGCAGCATGATAAG 59.688 47.826 0.00 0.00 39.69 1.73
2369 2663 2.284190 GGATAAGGTTCAGAGTGCAGC 58.716 52.381 0.00 0.00 0.00 5.25
2375 2669 7.278135 TCAAATCTGATGGATAAGGTTCAGAG 58.722 38.462 7.45 0.00 45.50 3.35
2382 2676 7.937942 AGAATGTCTCAAATCTGATGGATAAGG 59.062 37.037 0.00 0.00 33.71 2.69
2534 2837 4.760047 ATCACACCGGCGCTCCAC 62.760 66.667 7.64 0.00 0.00 4.02
2622 2926 4.977963 CGCATTGTGTCAATCAAAGAAGTT 59.022 37.500 0.00 0.00 0.00 2.66
2630 2934 1.237533 ACTGCGCATTGTGTCAATCA 58.762 45.000 12.24 0.00 0.00 2.57
2631 2935 2.336554 AACTGCGCATTGTGTCAATC 57.663 45.000 12.24 0.00 0.00 2.67
2632 2936 2.813754 AGTAACTGCGCATTGTGTCAAT 59.186 40.909 12.24 0.00 0.00 2.57
2633 2937 2.217750 AGTAACTGCGCATTGTGTCAA 58.782 42.857 12.24 0.00 0.00 3.18
2634 2938 1.877637 AGTAACTGCGCATTGTGTCA 58.122 45.000 12.24 0.00 0.00 3.58
2667 2972 6.127758 ACGCTGTAATTAGATCAAAATGGCAA 60.128 34.615 0.00 0.00 0.00 4.52
2668 2973 5.356751 ACGCTGTAATTAGATCAAAATGGCA 59.643 36.000 0.00 0.00 0.00 4.92
2669 2974 5.821204 ACGCTGTAATTAGATCAAAATGGC 58.179 37.500 0.00 0.00 0.00 4.40
2670 2975 7.754924 ACAAACGCTGTAATTAGATCAAAATGG 59.245 33.333 0.00 0.00 36.10 3.16
2691 2996 7.576236 TCTCTGATCGATGAAAAGAAACAAAC 58.424 34.615 0.54 0.00 0.00 2.93
2928 3233 9.607988 TCTTCAGTAACACAATTCACTAAAGAA 57.392 29.630 0.00 0.00 25.27 2.52
2966 3278 0.394762 GGATGCCCTGAGACAATGCA 60.395 55.000 0.00 0.00 36.23 3.96
3104 3416 1.314730 TTTCAAGCCGGGAAGTGAAC 58.685 50.000 2.18 0.00 30.00 3.18
3133 3445 0.387239 AGCGAAAAGGCATGCGAAAC 60.387 50.000 12.44 0.00 34.64 2.78
3147 3459 3.125829 GCAAGATGACAATTCAGAGCGAA 59.874 43.478 0.00 0.00 38.22 4.70
3245 3563 2.223947 GGATGGTTTTGCGTTCTTGGTT 60.224 45.455 0.00 0.00 0.00 3.67
3254 3572 2.034558 AGTCAACTTGGATGGTTTTGCG 59.965 45.455 0.00 0.00 0.00 4.85
3269 3588 1.935933 ACACGTCAGGACAAGTCAAC 58.064 50.000 2.29 0.00 0.00 3.18
3271 3590 2.626266 ACATACACGTCAGGACAAGTCA 59.374 45.455 2.29 0.00 0.00 3.41
3289 3610 3.347216 GCAATCACCTGGACAGTTACAT 58.653 45.455 0.00 0.00 0.00 2.29
3291 3612 1.732259 CGCAATCACCTGGACAGTTAC 59.268 52.381 0.00 0.00 0.00 2.50
3293 3614 0.606401 CCGCAATCACCTGGACAGTT 60.606 55.000 0.00 0.00 0.00 3.16
3294 3615 1.003355 CCGCAATCACCTGGACAGT 60.003 57.895 0.00 0.00 0.00 3.55
3374 3701 1.153647 CGTGATCTGCCCGCTGTTA 60.154 57.895 0.00 0.00 0.00 2.41
3446 3773 1.333584 GCATGAGCGCGTAGATCTCG 61.334 60.000 8.43 4.27 35.99 4.04
3467 3794 2.902705 TGAGTGACAAACTTACGGCT 57.097 45.000 0.00 0.00 40.07 5.52
3632 3975 4.316823 TGGTCCTCCCGCTCCACT 62.317 66.667 0.00 0.00 35.15 4.00
3820 4163 5.184287 CCCGAAGAGAAGAGAAGAAACTAGT 59.816 44.000 0.00 0.00 0.00 2.57
3821 4164 5.393678 CCCCGAAGAGAAGAGAAGAAACTAG 60.394 48.000 0.00 0.00 0.00 2.57
3822 4165 4.463186 CCCCGAAGAGAAGAGAAGAAACTA 59.537 45.833 0.00 0.00 0.00 2.24
3823 4166 3.259625 CCCCGAAGAGAAGAGAAGAAACT 59.740 47.826 0.00 0.00 0.00 2.66
3824 4167 3.591023 CCCCGAAGAGAAGAGAAGAAAC 58.409 50.000 0.00 0.00 0.00 2.78
3856 4199 3.090952 TCGGCATTTTGGTTTCAGTTG 57.909 42.857 0.00 0.00 0.00 3.16
3882 4227 1.942677 AACAACCAACACACGATCGA 58.057 45.000 24.34 0.00 0.00 3.59
3883 4228 2.748461 AAACAACCAACACACGATCG 57.252 45.000 14.88 14.88 0.00 3.69
3884 4229 3.112580 CCAAAACAACCAACACACGATC 58.887 45.455 0.00 0.00 0.00 3.69
3885 4230 2.737039 GCCAAAACAACCAACACACGAT 60.737 45.455 0.00 0.00 0.00 3.73
4127 4476 4.430007 TCGACCCTATGAAAACTCAATCG 58.570 43.478 0.00 0.00 0.00 3.34
4147 4497 3.123620 GGAGCTGCTGCCACTTCG 61.124 66.667 7.01 0.00 40.80 3.79
4202 4556 1.186200 CTGCCTGCCTCTACTACACA 58.814 55.000 0.00 0.00 0.00 3.72
4241 4607 2.176045 TGAACCAATCCAGTAGCGAGA 58.824 47.619 0.00 0.00 0.00 4.04
4291 4659 2.598565 ACAAGGAGGGGAAAAGCTTTC 58.401 47.619 13.10 6.15 0.00 2.62
4294 4662 3.850173 TGTATACAAGGAGGGGAAAAGCT 59.150 43.478 2.20 0.00 0.00 3.74
4329 4698 2.665165 TCCAACTTGTGCAGGTTTCAT 58.335 42.857 0.00 0.00 0.00 2.57
4421 7310 6.047231 AGAGAAAATCCCCTAAACGTATTCG 58.953 40.000 0.00 0.00 43.34 3.34
4427 7316 4.766375 TGCTAGAGAAAATCCCCTAAACG 58.234 43.478 0.00 0.00 0.00 3.60
4481 7604 1.734477 CTCGTGGCCAGTGAAGACG 60.734 63.158 5.11 4.05 0.00 4.18
4485 7608 0.888619 CTCTACTCGTGGCCAGTGAA 59.111 55.000 5.11 0.00 0.00 3.18
4509 7633 1.374758 GAGTCCGTCTGCTTGGGTG 60.375 63.158 0.00 0.00 0.00 4.61
4564 7688 0.825425 TTGGCGGCCATGTTTCTCAA 60.825 50.000 24.49 0.52 31.53 3.02
4602 7726 3.034569 GCATGGTCCGAAATGCAAC 57.965 52.632 7.60 0.00 46.75 4.17
4623 7748 3.944015 GAGCATTTCTTCTAGTGGCACAT 59.056 43.478 21.41 7.59 44.52 3.21
4624 7749 3.244526 TGAGCATTTCTTCTAGTGGCACA 60.245 43.478 21.41 5.00 0.00 4.57
4643 7800 0.893270 TTCACGGGCCATGGTTTGAG 60.893 55.000 14.67 3.56 0.00 3.02
4645 7802 0.038343 CTTTCACGGGCCATGGTTTG 60.038 55.000 14.67 5.65 0.00 2.93
4651 7808 2.442236 ATTCATCTTTCACGGGCCAT 57.558 45.000 4.39 0.00 0.00 4.40
4658 7815 6.481954 AAGTACGTGGAATTCATCTTTCAC 57.518 37.500 7.93 4.16 0.00 3.18
4661 7818 8.311836 TCTAGAAAGTACGTGGAATTCATCTTT 58.688 33.333 7.93 7.82 0.00 2.52
4666 7823 6.349944 GGAGTCTAGAAAGTACGTGGAATTCA 60.350 42.308 7.93 0.00 0.00 2.57
4676 7833 5.808030 GCATGTGAAGGAGTCTAGAAAGTAC 59.192 44.000 0.00 0.00 0.00 2.73
4683 7840 2.949451 ACGCATGTGAAGGAGTCTAG 57.051 50.000 14.43 0.00 0.00 2.43
4743 7900 5.398236 GCTAGGGCTAGGATATATGATCCA 58.602 45.833 10.27 0.00 36.75 3.41
4766 7923 5.699915 CCACTAAATGATGTCCATGAGCTAG 59.300 44.000 0.00 0.00 35.24 3.42
4782 7939 4.579869 ACAATGACTTCTCGCCACTAAAT 58.420 39.130 0.00 0.00 0.00 1.40
4784 7941 3.678056 ACAATGACTTCTCGCCACTAA 57.322 42.857 0.00 0.00 0.00 2.24
4802 7959 0.178992 CTCCTTTCCTGTGGCCAACA 60.179 55.000 7.24 7.50 37.22 3.33
4813 7970 3.085533 GCCTTTCTTCTTCCTCCTTTCC 58.914 50.000 0.00 0.00 0.00 3.13
4821 7978 4.393834 ACTTCTTCTGCCTTTCTTCTTCC 58.606 43.478 0.00 0.00 0.00 3.46
4833 7990 7.816995 TCTTCATCTTCTTCTTACTTCTTCTGC 59.183 37.037 0.00 0.00 0.00 4.26
4835 7992 9.308000 TCTCTTCATCTTCTTCTTACTTCTTCT 57.692 33.333 0.00 0.00 0.00 2.85
4920 8078 8.745590 GCTAATTTGTAGGGGATTCAACTTTTA 58.254 33.333 0.00 0.00 0.00 1.52
4928 8086 9.185680 TCTAAAAAGCTAATTTGTAGGGGATTC 57.814 33.333 7.48 0.00 38.69 2.52
4938 8096 9.136323 ACCCCTATCATCTAAAAAGCTAATTTG 57.864 33.333 7.48 0.00 0.00 2.32
4941 8099 9.794719 GTAACCCCTATCATCTAAAAAGCTAAT 57.205 33.333 0.00 0.00 0.00 1.73
4942 8100 7.929785 CGTAACCCCTATCATCTAAAAAGCTAA 59.070 37.037 0.00 0.00 0.00 3.09
5009 8169 1.078656 AGCTTTTGGGGAATGGGCTAA 59.921 47.619 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.