Multiple sequence alignment - TraesCS4D01G233900

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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 TraesCS4D01G233900 chr4D 100.000 3327 0 0 1 3327 394356954 394360280 0.000000e+00 6144.0
1 TraesCS4D01G233900 chr4D 90.196 51 5 0 1183 1233 498949328 498949378 2.140000e-07 67.6
2 TraesCS4D01G233900 chr4A 91.949 1416 63 22 994 2361 75461586 75462998 0.000000e+00 1936.0
3 TraesCS4D01G233900 chr4A 92.936 453 26 5 268 716 75460873 75461323 0.000000e+00 654.0
4 TraesCS4D01G233900 chr4A 81.098 492 62 13 2857 3323 75463434 75463919 6.780000e-97 364.0
5 TraesCS4D01G233900 chr4A 90.876 274 18 4 1 268 75460573 75460845 8.770000e-96 361.0
6 TraesCS4D01G233900 chr4A 82.637 311 17 16 2446 2720 75463036 75463345 1.190000e-59 241.0
7 TraesCS4D01G233900 chr4B 93.728 861 40 5 988 1836 483946687 483947545 0.000000e+00 1279.0
8 TraesCS4D01G233900 chr4B 96.008 501 11 1 1870 2361 483947715 483948215 0.000000e+00 806.0
9 TraesCS4D01G233900 chr4B 82.201 736 57 34 2421 3104 483948217 483948930 1.730000e-157 566.0
10 TraesCS4D01G233900 chr4B 95.556 225 9 1 492 716 483946178 483946401 3.160000e-95 359.0
11 TraesCS4D01G233900 chr4B 88.809 277 22 5 1 268 483945542 483945818 6.880000e-87 331.0
12 TraesCS4D01G233900 chr4B 94.064 219 12 1 268 486 483945846 483946063 6.880000e-87 331.0
13 TraesCS4D01G233900 chr2A 94.643 56 3 0 1176 1231 58824656 58824711 1.640000e-13 87.9
14 TraesCS4D01G233900 chr2D 92.982 57 4 0 1175 1231 59627163 59627219 2.130000e-12 84.2
15 TraesCS4D01G233900 chr2D 97.222 36 1 0 289 324 38529877 38529912 9.970000e-06 62.1
16 TraesCS4D01G233900 chr5D 77.027 148 30 3 3155 3299 451039906 451039760 7.650000e-12 82.4
17 TraesCS4D01G233900 chr6D 91.379 58 5 0 1175 1232 90922798 90922855 2.750000e-11 80.5
18 TraesCS4D01G233900 chr6B 91.379 58 5 0 1175 1232 173391857 173391914 2.750000e-11 80.5
19 TraesCS4D01G233900 chr6A 89.655 58 6 0 1175 1232 109135820 109135877 1.280000e-09 75.0
20 TraesCS4D01G233900 chr2B 89.474 57 6 0 1175 1231 92995602 92995658 4.600000e-09 73.1
21 TraesCS4D01G233900 chr3D 84.211 76 7 5 3227 3299 14525604 14525677 5.960000e-08 69.4


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 TraesCS4D01G233900 chr4D 394356954 394360280 3326 False 6144.0 6144 100.000000 1 3327 1 chr4D.!!$F1 3326
1 TraesCS4D01G233900 chr4A 75460573 75463919 3346 False 711.2 1936 87.899200 1 3323 5 chr4A.!!$F1 3322
2 TraesCS4D01G233900 chr4B 483945542 483948930 3388 False 612.0 1279 91.727667 1 3104 6 chr4B.!!$F1 3103

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
985 1221 0.032678 ACGGTGACAGTGCTTCAGAG 59.967 55.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2755 3275 0.09473 CGCTTAACCGAAAAGCTCCG 59.905 55.0 12.42 0.0 45.73 4.63 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
25 26 3.479006 CGAGCACGTGAAATACCAAAAG 58.521 45.455 22.23 0.00 34.56 2.27
27 28 4.553938 CGAGCACGTGAAATACCAAAAGTT 60.554 41.667 22.23 0.00 34.56 2.66
185 197 0.252789 TGGTGGACCGGGGAAGAATA 60.253 55.000 6.32 0.00 39.43 1.75
214 226 3.678072 ACTATTCGTTGGTTGTCACATCG 59.322 43.478 0.00 0.00 33.61 3.84
253 265 7.401246 GGCTAGGATCATTCCATCTTAAGATT 58.599 38.462 15.49 0.00 45.30 2.40
282 322 2.035449 CAGGATAAATCGTGACGCCCTA 59.965 50.000 0.00 0.00 43.34 3.53
284 324 3.133362 AGGATAAATCGTGACGCCCTAAA 59.867 43.478 0.00 0.00 0.00 1.85
368 408 4.067896 ACGTAATCTGATCCCATTCATGC 58.932 43.478 0.00 0.00 0.00 4.06
451 491 1.091197 CACCAGTGCTCGCATGCATA 61.091 55.000 19.57 3.82 45.23 3.14
454 494 1.091197 CAGTGCTCGCATGCATACCA 61.091 55.000 19.57 5.87 45.23 3.25
549 702 0.371989 CATCGCCGAAACGTGCAATA 59.628 50.000 0.00 0.00 0.00 1.90
579 732 2.469826 GCCGCACCTAATTAATTTGGC 58.530 47.619 23.40 14.97 36.35 4.52
701 854 2.660490 GCAGTAAAAAGCGCACAATCA 58.340 42.857 11.47 0.00 0.00 2.57
706 859 2.124011 AAAAGCGCACAATCACAGTG 57.876 45.000 11.47 0.00 39.92 3.66
711 864 0.729116 CGCACAATCACAGTGATCCC 59.271 55.000 16.69 4.87 35.76 3.85
716 869 0.179000 AATCACAGTGATCCCTCGGC 59.821 55.000 16.69 0.00 35.76 5.54
736 920 1.071041 CATATGCATGCTGACGACACG 60.071 52.381 20.33 0.00 0.00 4.49
757 941 2.355009 GCACGTTGCCAAGCCAAG 60.355 61.111 0.00 0.00 37.42 3.61
758 942 2.355009 CACGTTGCCAAGCCAAGC 60.355 61.111 0.00 0.00 0.00 4.01
759 943 3.605664 ACGTTGCCAAGCCAAGCC 61.606 61.111 0.00 0.00 0.00 4.35
760 944 4.705519 CGTTGCCAAGCCAAGCCG 62.706 66.667 0.00 0.00 0.00 5.52
766 972 3.384532 CAAGCCAAGCCGCCCATT 61.385 61.111 0.00 0.00 0.00 3.16
769 975 1.322538 AAGCCAAGCCGCCCATTTAG 61.323 55.000 0.00 0.00 0.00 1.85
772 978 1.384222 CCAAGCCGCCCATTTAGTCC 61.384 60.000 0.00 0.00 0.00 3.85
785 991 4.152402 CCATTTAGTCCACGAACAGTCAAG 59.848 45.833 0.00 0.00 0.00 3.02
786 992 3.380479 TTAGTCCACGAACAGTCAAGG 57.620 47.619 0.00 0.00 0.00 3.61
787 993 1.410004 AGTCCACGAACAGTCAAGGA 58.590 50.000 0.00 0.00 0.00 3.36
788 994 1.971357 AGTCCACGAACAGTCAAGGAT 59.029 47.619 0.00 0.00 31.24 3.24
789 995 3.162666 AGTCCACGAACAGTCAAGGATA 58.837 45.455 0.00 0.00 31.24 2.59
790 996 3.056749 AGTCCACGAACAGTCAAGGATAC 60.057 47.826 0.00 0.00 31.24 2.24
834 1047 8.916654 CAAGTCCATTTAGCTAGTAATATCACG 58.083 37.037 0.00 0.00 0.00 4.35
849 1063 8.141909 AGTAATATCACGCATCACTTTAAGCTA 58.858 33.333 0.00 0.00 0.00 3.32
850 1064 7.413475 AATATCACGCATCACTTTAAGCTAG 57.587 36.000 0.00 0.00 0.00 3.42
851 1065 2.930040 TCACGCATCACTTTAAGCTAGC 59.070 45.455 6.62 6.62 0.00 3.42
852 1066 2.932614 CACGCATCACTTTAAGCTAGCT 59.067 45.455 12.68 12.68 0.00 3.32
853 1067 4.112634 CACGCATCACTTTAAGCTAGCTA 58.887 43.478 19.70 0.00 0.00 3.32
854 1068 4.747108 CACGCATCACTTTAAGCTAGCTAT 59.253 41.667 19.70 10.93 0.00 2.97
855 1069 4.985409 ACGCATCACTTTAAGCTAGCTATC 59.015 41.667 19.70 0.00 0.00 2.08
856 1070 5.221342 ACGCATCACTTTAAGCTAGCTATCT 60.221 40.000 19.70 4.98 0.00 1.98
857 1071 6.016192 ACGCATCACTTTAAGCTAGCTATCTA 60.016 38.462 19.70 3.81 0.00 1.98
880 1094 8.260818 TCTATCTATATAACCTTGCAATGAGCC 58.739 37.037 8.84 0.00 44.83 4.70
881 1095 5.237815 TCTATATAACCTTGCAATGAGCCG 58.762 41.667 8.84 0.00 44.83 5.52
883 1097 1.312371 TAACCTTGCAATGAGCCGGC 61.312 55.000 21.89 21.89 44.83 6.13
893 1107 1.804396 ATGAGCCGGCAGAGATCGAG 61.804 60.000 31.54 0.00 0.00 4.04
894 1108 3.839642 GAGCCGGCAGAGATCGAGC 62.840 68.421 31.54 0.00 0.00 5.03
896 1110 4.637489 CCGGCAGAGATCGAGCGG 62.637 72.222 0.00 7.37 0.00 5.52
897 1111 3.586961 CGGCAGAGATCGAGCGGA 61.587 66.667 0.00 0.00 0.00 5.54
898 1112 2.026879 GGCAGAGATCGAGCGGAC 59.973 66.667 0.00 0.00 0.00 4.79
899 1113 2.775856 GGCAGAGATCGAGCGGACA 61.776 63.158 0.00 0.00 0.00 4.02
900 1114 1.299014 GCAGAGATCGAGCGGACAG 60.299 63.158 0.00 0.00 0.00 3.51
901 1115 1.358402 CAGAGATCGAGCGGACAGG 59.642 63.158 0.00 0.00 0.00 4.00
902 1116 2.026879 GAGATCGAGCGGACAGGC 59.973 66.667 0.00 0.00 0.00 4.85
903 1117 2.755876 AGATCGAGCGGACAGGCA 60.756 61.111 0.00 0.00 34.64 4.75
904 1118 2.583593 GATCGAGCGGACAGGCAC 60.584 66.667 0.00 0.00 34.64 5.01
905 1119 4.498520 ATCGAGCGGACAGGCACG 62.499 66.667 0.00 0.00 46.14 5.34
911 1125 2.809601 CGGACAGGCACGCAGTAC 60.810 66.667 0.00 0.00 41.61 2.73
925 1139 3.610495 CGCAGTACGTACATTCGATACA 58.390 45.455 26.55 0.00 36.87 2.29
926 1140 4.216731 CGCAGTACGTACATTCGATACAT 58.783 43.478 26.55 0.00 36.87 2.29
927 1141 5.376537 CGCAGTACGTACATTCGATACATA 58.623 41.667 26.55 0.00 36.87 2.29
928 1142 5.503720 CGCAGTACGTACATTCGATACATAG 59.496 44.000 26.55 2.61 36.87 2.23
929 1143 6.596703 GCAGTACGTACATTCGATACATAGA 58.403 40.000 26.55 0.00 34.70 1.98
930 1144 7.242079 GCAGTACGTACATTCGATACATAGAT 58.758 38.462 26.55 0.00 34.70 1.98
931 1145 7.425882 GCAGTACGTACATTCGATACATAGATC 59.574 40.741 26.55 0.00 34.70 2.75
932 1146 7.903946 CAGTACGTACATTCGATACATAGATCC 59.096 40.741 26.55 0.00 34.70 3.36
933 1147 6.812879 ACGTACATTCGATACATAGATCCA 57.187 37.500 0.00 0.00 34.70 3.41
934 1148 6.843208 ACGTACATTCGATACATAGATCCAG 58.157 40.000 0.00 0.00 34.70 3.86
935 1149 6.430308 ACGTACATTCGATACATAGATCCAGT 59.570 38.462 0.00 0.00 34.70 4.00
936 1150 6.743172 CGTACATTCGATACATAGATCCAGTG 59.257 42.308 0.00 0.00 0.00 3.66
937 1151 5.473931 ACATTCGATACATAGATCCAGTGC 58.526 41.667 0.00 0.00 0.00 4.40
938 1152 4.521130 TTCGATACATAGATCCAGTGCC 57.479 45.455 0.00 0.00 0.00 5.01
939 1153 2.488153 TCGATACATAGATCCAGTGCCG 59.512 50.000 0.00 0.00 0.00 5.69
940 1154 2.416027 CGATACATAGATCCAGTGCCGG 60.416 54.545 0.00 0.00 0.00 6.13
941 1155 2.082140 TACATAGATCCAGTGCCGGT 57.918 50.000 1.90 0.00 0.00 5.28
942 1156 0.465705 ACATAGATCCAGTGCCGGTG 59.534 55.000 1.90 0.00 0.00 4.94
943 1157 0.752658 CATAGATCCAGTGCCGGTGA 59.247 55.000 1.90 0.00 0.00 4.02
944 1158 1.345741 CATAGATCCAGTGCCGGTGAT 59.654 52.381 1.90 0.00 0.00 3.06
945 1159 1.040646 TAGATCCAGTGCCGGTGATC 58.959 55.000 1.90 7.55 35.05 2.92
946 1160 0.689080 AGATCCAGTGCCGGTGATCT 60.689 55.000 1.90 9.69 39.21 2.75
947 1161 1.040646 GATCCAGTGCCGGTGATCTA 58.959 55.000 1.90 0.00 32.70 1.98
954 1168 1.940613 GTGCCGGTGATCTATCAAACC 59.059 52.381 1.90 0.00 38.75 3.27
961 1175 2.072142 TGATCTATCAAACCGGCACGC 61.072 52.381 0.00 0.00 42.26 5.34
981 1217 2.080286 ACATACGGTGACAGTGCTTC 57.920 50.000 0.00 0.00 0.00 3.86
982 1218 1.343142 ACATACGGTGACAGTGCTTCA 59.657 47.619 0.00 0.00 0.00 3.02
983 1219 1.995484 CATACGGTGACAGTGCTTCAG 59.005 52.381 0.00 0.00 0.00 3.02
984 1220 1.324383 TACGGTGACAGTGCTTCAGA 58.676 50.000 0.00 0.00 0.00 3.27
985 1221 0.032678 ACGGTGACAGTGCTTCAGAG 59.967 55.000 0.00 0.00 0.00 3.35
986 1222 0.315251 CGGTGACAGTGCTTCAGAGA 59.685 55.000 0.00 0.00 0.00 3.10
987 1223 1.789506 GGTGACAGTGCTTCAGAGAC 58.210 55.000 0.00 0.00 0.00 3.36
988 1224 1.069204 GGTGACAGTGCTTCAGAGACA 59.931 52.381 0.00 0.00 0.00 3.41
992 1228 4.803088 GTGACAGTGCTTCAGAGACATATC 59.197 45.833 0.00 0.00 0.00 1.63
1017 1263 2.765699 AGAAATGGAGCCTCTCAGAGAC 59.234 50.000 2.09 0.00 31.08 3.36
1030 1276 2.512515 GAGACCATGGTGCGAGCC 60.513 66.667 25.52 6.49 0.00 4.70
1066 1312 3.876236 TGGTGCTGCTGTGGCTGA 61.876 61.111 0.00 0.00 39.31 4.26
1284 1537 6.219473 TGCTTTCTTAGACTCTCAAGTGAAG 58.781 40.000 0.00 0.00 35.28 3.02
1291 1544 7.606839 TCTTAGACTCTCAAGTGAAGATCGTTA 59.393 37.037 0.00 0.00 35.28 3.18
1299 1552 7.441157 TCTCAAGTGAAGATCGTTAATTGTTGT 59.559 33.333 11.90 0.00 0.00 3.32
1338 1595 1.590147 GTGTGACGGGTCGATCCTT 59.410 57.895 14.05 2.30 36.25 3.36
1521 1778 2.029649 CGTACGTTCCTTCCTTCCTTCA 60.030 50.000 7.22 0.00 0.00 3.02
1528 1785 1.557371 CCTTCCTTCCTTCACTCCCTC 59.443 57.143 0.00 0.00 0.00 4.30
1538 1795 0.902531 TCACTCCCTCCGAATTCACC 59.097 55.000 6.22 0.00 0.00 4.02
1689 1966 1.346068 GGAGGGCCTGACTATGATGTC 59.654 57.143 12.95 0.00 37.47 3.06
1806 2083 3.582780 GTTCAAGGACGTCGGTCTTAAT 58.417 45.455 9.92 0.00 42.97 1.40
1865 2263 6.822170 TGTACTAGACTCACCACTACTGTATG 59.178 42.308 0.00 0.00 0.00 2.39
2242 2667 1.153745 CTTCCTCTGCGACTTCGGG 60.154 63.158 0.02 0.00 40.23 5.14
2319 2744 2.877582 CAAGAAATGCAGCGCCGC 60.878 61.111 9.12 9.12 0.00 6.53
2349 2778 1.817099 GCGCCACTGCATCTAGCTT 60.817 57.895 0.00 0.00 45.94 3.74
2355 2784 2.514592 TGCATCTAGCTTGCCGGC 60.515 61.111 22.73 22.73 45.94 6.13
2361 2790 1.447838 CTAGCTTGCCGGCGAAGAA 60.448 57.895 30.45 17.23 37.29 2.52
2362 2791 1.424493 CTAGCTTGCCGGCGAAGAAG 61.424 60.000 30.45 24.72 37.29 2.85
2363 2792 1.884075 TAGCTTGCCGGCGAAGAAGA 61.884 55.000 30.45 17.32 37.29 2.87
2364 2793 3.028366 GCTTGCCGGCGAAGAAGAC 62.028 63.158 30.45 17.69 0.00 3.01
2365 2794 1.667830 CTTGCCGGCGAAGAAGACA 60.668 57.895 25.31 3.14 0.00 3.41
2366 2795 1.630244 CTTGCCGGCGAAGAAGACAG 61.630 60.000 25.31 6.81 0.00 3.51
2367 2796 2.094757 TTGCCGGCGAAGAAGACAGA 62.095 55.000 23.90 0.00 0.00 3.41
2368 2797 1.153549 GCCGGCGAAGAAGACAGAT 60.154 57.895 12.58 0.00 0.00 2.90
2369 2798 1.424493 GCCGGCGAAGAAGACAGATG 61.424 60.000 12.58 0.00 0.00 2.90
2370 2799 1.424493 CCGGCGAAGAAGACAGATGC 61.424 60.000 9.30 0.00 0.00 3.91
2371 2800 0.459237 CGGCGAAGAAGACAGATGCT 60.459 55.000 0.00 0.00 0.00 3.79
2372 2801 1.005340 GGCGAAGAAGACAGATGCTG 58.995 55.000 0.00 0.00 37.52 4.41
2373 2802 0.373024 GCGAAGAAGACAGATGCTGC 59.627 55.000 0.00 0.00 34.37 5.25
2374 2803 1.718396 CGAAGAAGACAGATGCTGCA 58.282 50.000 4.13 4.13 34.37 4.41
2375 2804 2.277969 CGAAGAAGACAGATGCTGCAT 58.722 47.619 16.20 16.20 34.37 3.96
2376 2805 2.030579 CGAAGAAGACAGATGCTGCATG 59.969 50.000 21.53 10.94 34.37 4.06
2377 2806 1.380524 AGAAGACAGATGCTGCATGC 58.619 50.000 21.53 11.82 43.25 4.06
2386 2815 2.360852 GCTGCATGCACCTGACCT 60.361 61.111 18.46 0.00 42.31 3.85
2387 2816 1.975407 GCTGCATGCACCTGACCTT 60.975 57.895 18.46 0.00 42.31 3.50
2388 2817 1.880894 CTGCATGCACCTGACCTTG 59.119 57.895 18.46 0.00 0.00 3.61
2389 2818 1.592400 CTGCATGCACCTGACCTTGG 61.592 60.000 18.46 0.00 0.00 3.61
2390 2819 1.604593 GCATGCACCTGACCTTGGT 60.605 57.895 14.21 0.00 38.53 3.67
2394 2823 4.828409 CACCTGACCTTGGTGCAT 57.172 55.556 0.00 0.00 46.73 3.96
2395 2824 2.260247 CACCTGACCTTGGTGCATG 58.740 57.895 0.00 0.00 46.73 4.06
2396 2825 1.604593 ACCTGACCTTGGTGCATGC 60.605 57.895 11.82 11.82 36.30 4.06
2397 2826 2.345760 CCTGACCTTGGTGCATGCC 61.346 63.158 16.68 6.42 0.00 4.40
2398 2827 2.283101 TGACCTTGGTGCATGCCC 60.283 61.111 16.68 16.23 0.00 5.36
2399 2828 2.283101 GACCTTGGTGCATGCCCA 60.283 61.111 20.10 20.10 0.00 5.36
2400 2829 1.683365 GACCTTGGTGCATGCCCAT 60.683 57.895 23.25 12.41 0.00 4.00
2401 2830 1.669999 GACCTTGGTGCATGCCCATC 61.670 60.000 23.25 16.17 0.00 3.51
2402 2831 1.380785 CCTTGGTGCATGCCCATCT 60.381 57.895 23.25 0.00 0.00 2.90
2403 2832 1.389609 CCTTGGTGCATGCCCATCTC 61.390 60.000 23.25 5.64 0.00 2.75
2404 2833 1.721664 CTTGGTGCATGCCCATCTCG 61.722 60.000 23.25 11.85 0.00 4.04
2405 2834 3.589881 GGTGCATGCCCATCTCGC 61.590 66.667 16.68 0.00 0.00 5.03
2406 2835 3.945434 GTGCATGCCCATCTCGCG 61.945 66.667 16.68 0.00 0.00 5.87
2407 2836 4.471908 TGCATGCCCATCTCGCGT 62.472 61.111 16.68 0.00 0.00 6.01
2408 2837 3.204827 GCATGCCCATCTCGCGTT 61.205 61.111 6.36 0.00 0.00 4.84
2409 2838 2.711311 CATGCCCATCTCGCGTTG 59.289 61.111 5.77 2.54 0.00 4.10
2410 2839 2.108514 CATGCCCATCTCGCGTTGT 61.109 57.895 5.77 0.00 0.00 3.32
2411 2840 1.815421 ATGCCCATCTCGCGTTGTC 60.815 57.895 5.77 0.00 0.00 3.18
2412 2841 2.434185 GCCCATCTCGCGTTGTCA 60.434 61.111 5.77 0.00 0.00 3.58
2413 2842 2.032634 GCCCATCTCGCGTTGTCAA 61.033 57.895 5.77 0.00 0.00 3.18
2414 2843 1.787847 CCCATCTCGCGTTGTCAAC 59.212 57.895 5.77 5.58 0.00 3.18
2415 2844 0.948623 CCCATCTCGCGTTGTCAACA 60.949 55.000 15.79 0.00 0.00 3.33
2416 2845 0.439985 CCATCTCGCGTTGTCAACAG 59.560 55.000 15.79 8.85 0.00 3.16
2417 2846 1.139989 CATCTCGCGTTGTCAACAGT 58.860 50.000 15.79 0.00 0.00 3.55
2418 2847 1.125021 CATCTCGCGTTGTCAACAGTC 59.875 52.381 15.79 3.50 0.00 3.51
2419 2848 0.101579 TCTCGCGTTGTCAACAGTCA 59.898 50.000 15.79 0.00 0.00 3.41
2433 2862 2.732366 ACAGTCATCATATCGTGCGTC 58.268 47.619 0.00 0.00 0.00 5.19
2439 2885 2.422276 TCATATCGTGCGTCTGGATG 57.578 50.000 0.00 0.00 0.00 3.51
2440 2886 0.786581 CATATCGTGCGTCTGGATGC 59.213 55.000 7.75 7.75 43.39 3.91
2441 2887 0.664466 ATATCGTGCGTCTGGATGCG 60.664 55.000 9.76 0.00 45.93 4.73
2442 2888 2.000215 TATCGTGCGTCTGGATGCGT 62.000 55.000 9.76 0.00 45.93 5.24
2443 2889 2.000215 ATCGTGCGTCTGGATGCGTA 62.000 55.000 9.76 0.00 45.93 4.42
2444 2890 2.505498 CGTGCGTCTGGATGCGTAC 61.505 63.158 9.76 3.48 45.93 3.67
2568 3061 1.829096 TCGGTTGACGGGTGAGTGA 60.829 57.895 0.00 0.00 44.45 3.41
2569 3062 1.372997 CGGTTGACGGGTGAGTGAG 60.373 63.158 0.00 0.00 39.42 3.51
2570 3063 1.746517 GGTTGACGGGTGAGTGAGT 59.253 57.895 0.00 0.00 0.00 3.41
2571 3064 0.600255 GGTTGACGGGTGAGTGAGTG 60.600 60.000 0.00 0.00 0.00 3.51
2572 3065 0.600255 GTTGACGGGTGAGTGAGTGG 60.600 60.000 0.00 0.00 0.00 4.00
2573 3066 1.046472 TTGACGGGTGAGTGAGTGGT 61.046 55.000 0.00 0.00 0.00 4.16
2574 3067 0.178984 TGACGGGTGAGTGAGTGGTA 60.179 55.000 0.00 0.00 0.00 3.25
2575 3068 0.243095 GACGGGTGAGTGAGTGGTAC 59.757 60.000 0.00 0.00 0.00 3.34
2576 3069 0.178970 ACGGGTGAGTGAGTGGTACT 60.179 55.000 0.00 0.00 0.00 2.73
2577 3070 0.243907 CGGGTGAGTGAGTGGTACTG 59.756 60.000 0.00 0.00 0.00 2.74
2578 3071 1.339097 GGGTGAGTGAGTGGTACTGT 58.661 55.000 0.00 0.00 0.00 3.55
2579 3072 1.000955 GGGTGAGTGAGTGGTACTGTG 59.999 57.143 0.00 0.00 0.00 3.66
2585 3081 2.891580 AGTGAGTGGTACTGTGGTAGTG 59.108 50.000 0.00 0.00 40.65 2.74
2613 3109 0.179111 GGCTGTGTGATAGTAGCGCA 60.179 55.000 11.47 0.00 37.05 6.09
2632 3128 5.521010 AGCGCACAAAATGAATAATGGAATG 59.479 36.000 11.47 0.00 0.00 2.67
2635 3131 6.310956 CGCACAAAATGAATAATGGAATGTGT 59.689 34.615 0.00 0.00 38.26 3.72
2636 3132 7.487509 CGCACAAAATGAATAATGGAATGTGTA 59.512 33.333 0.00 0.00 38.26 2.90
2637 3133 8.810427 GCACAAAATGAATAATGGAATGTGTAG 58.190 33.333 0.00 0.00 38.26 2.74
2638 3134 8.810427 CACAAAATGAATAATGGAATGTGTAGC 58.190 33.333 0.00 0.00 32.99 3.58
2752 3272 1.218316 GGTCCTGCGTCCCTGTAAG 59.782 63.158 0.00 0.00 0.00 2.34
2764 3284 3.249687 CTGTAAGGCCGGAGCTTTT 57.750 52.632 5.05 0.00 39.36 2.27
2778 3298 0.109919 GCTTTTCGGTTAAGCGTGGG 60.110 55.000 24.71 14.73 38.68 4.61
2779 3299 1.515081 CTTTTCGGTTAAGCGTGGGA 58.485 50.000 24.71 4.54 0.00 4.37
2788 3308 0.251634 TAAGCGTGGGACATGATGCA 59.748 50.000 0.00 0.00 46.36 3.96
2793 3313 1.089920 GTGGGACATGATGCAGTGAC 58.910 55.000 0.00 0.00 44.52 3.67
2830 3350 1.922135 GCCAATCGCATCAACGTGGT 61.922 55.000 0.00 0.00 37.47 4.16
2835 3355 4.222886 CAATCGCATCAACGTGGTTAAAA 58.777 39.130 0.00 0.00 0.00 1.52
2837 3357 5.804692 ATCGCATCAACGTGGTTAAAATA 57.195 34.783 0.00 0.00 0.00 1.40
2845 3365 5.640357 TCAACGTGGTTAAAATAGTAGGCAG 59.360 40.000 0.00 0.00 0.00 4.85
2851 3371 4.213482 GGTTAAAATAGTAGGCAGGCATCG 59.787 45.833 0.00 0.00 0.00 3.84
2918 3438 1.388065 TTGGGGAGCAAAACACCGTG 61.388 55.000 0.00 0.00 32.79 4.94
2919 3439 2.561037 GGGGAGCAAAACACCGTGG 61.561 63.158 3.03 0.00 0.00 4.94
2921 3441 2.335011 GAGCAAAACACCGTGGGC 59.665 61.111 3.03 1.38 0.00 5.36
3005 3525 0.179067 TCAGGTTGTCCGGTGTTCAC 60.179 55.000 0.00 0.00 39.05 3.18
3008 3528 0.463116 GGTTGTCCGGTGTTCACTGT 60.463 55.000 0.00 0.00 0.00 3.55
3046 3566 7.118101 ACGTGCCAGTCGTCTAAATTATTTTTA 59.882 33.333 0.00 0.00 36.85 1.52
3053 3573 9.117183 AGTCGTCTAAATTATTTTTATGGGGTC 57.883 33.333 0.00 0.00 0.00 4.46
3080 3600 1.456196 TTTTTCAACCGCCCGATGCA 61.456 50.000 0.00 0.00 41.33 3.96
3085 3605 0.453793 CAACCGCCCGATGCAAAATA 59.546 50.000 0.00 0.00 41.33 1.40
3087 3607 0.454196 ACCGCCCGATGCAAAATAAC 59.546 50.000 0.00 0.00 41.33 1.89
3088 3608 0.453793 CCGCCCGATGCAAAATAACA 59.546 50.000 0.00 0.00 41.33 2.41
3089 3609 1.135257 CCGCCCGATGCAAAATAACAA 60.135 47.619 0.00 0.00 41.33 2.83
3090 3610 1.917303 CGCCCGATGCAAAATAACAAC 59.083 47.619 0.00 0.00 41.33 3.32
3091 3611 2.415357 CGCCCGATGCAAAATAACAACT 60.415 45.455 0.00 0.00 41.33 3.16
3093 3613 3.119495 GCCCGATGCAAAATAACAACTCT 60.119 43.478 0.00 0.00 40.77 3.24
3116 3657 1.219393 CCTTCTCCCTTCTCCACGC 59.781 63.158 0.00 0.00 0.00 5.34
3123 3664 1.738099 CCTTCTCCACGCTGAACCG 60.738 63.158 0.00 0.00 0.00 4.44
3152 3693 2.675075 CCGGCCGAACCCATTTGT 60.675 61.111 30.73 0.00 33.26 2.83
3164 3705 1.523154 CCATTTGTGACCACCACCCG 61.523 60.000 0.00 0.00 45.09 5.28
3215 3756 3.003173 CCGCCCTCTCTGGAACCA 61.003 66.667 0.00 0.00 38.35 3.67
3218 3759 2.982130 CCCTCTCTGGAACCACCG 59.018 66.667 0.00 0.00 42.61 4.94
3221 3762 2.525629 TCTCTGGAACCACCGCCA 60.526 61.111 0.00 0.00 42.61 5.69
3222 3763 1.903877 CTCTCTGGAACCACCGCCAT 61.904 60.000 0.00 0.00 42.61 4.40
3223 3764 1.450312 CTCTGGAACCACCGCCATC 60.450 63.158 0.00 0.00 42.61 3.51
3225 3766 3.253061 TGGAACCACCGCCATCCA 61.253 61.111 0.00 0.00 42.61 3.41
3226 3767 2.438434 GGAACCACCGCCATCCAG 60.438 66.667 0.00 0.00 32.08 3.86
3227 3768 2.351276 GAACCACCGCCATCCAGT 59.649 61.111 0.00 0.00 0.00 4.00
3228 3769 1.745489 GAACCACCGCCATCCAGTC 60.745 63.158 0.00 0.00 0.00 3.51
3229 3770 2.185310 GAACCACCGCCATCCAGTCT 62.185 60.000 0.00 0.00 0.00 3.24
3231 3772 1.746615 CCACCGCCATCCAGTCTTG 60.747 63.158 0.00 0.00 0.00 3.02
3232 3773 2.045926 ACCGCCATCCAGTCTTGC 60.046 61.111 0.00 0.00 0.00 4.01
3233 3774 3.197790 CCGCCATCCAGTCTTGCG 61.198 66.667 0.00 0.00 44.47 4.85
3234 3775 3.869272 CGCCATCCAGTCTTGCGC 61.869 66.667 0.00 0.00 38.69 6.09
3259 3804 1.461075 CAGCCATCCCTCTAGCCCT 60.461 63.158 0.00 0.00 0.00 5.19
3262 3807 1.074167 CCATCCCTCTAGCCCTGGT 60.074 63.158 0.00 0.00 0.00 4.00
3267 3812 2.759973 CTCTAGCCCTGGTGCCGA 60.760 66.667 3.90 1.58 0.00 5.54
3269 3814 4.514577 CTAGCCCTGGTGCCGACG 62.515 72.222 3.90 0.00 0.00 5.12
3280 3825 1.439679 GTGCCGACGGAGATTTTCTT 58.560 50.000 20.50 0.00 0.00 2.52
3281 3826 1.393883 GTGCCGACGGAGATTTTCTTC 59.606 52.381 20.50 0.00 0.00 2.87
3300 3845 4.683334 GCGAAGTTGCACCACCGC 62.683 66.667 4.77 4.77 35.91 5.68
3325 3870 4.653888 CCACCCCCACCACCGTTC 62.654 72.222 0.00 0.00 0.00 3.95
3326 3871 3.566210 CACCCCCACCACCGTTCT 61.566 66.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 197 0.324943 ACCAACGAATAGTGCCTGCT 59.675 50.000 0.00 0.00 0.00 4.24
214 226 0.318275 CTAGCCGTCGGATCTTCAGC 60.318 60.000 17.49 0.00 0.00 4.26
253 265 5.691754 CGTCACGATTTATCCTGATCATCAA 59.308 40.000 0.00 0.00 0.00 2.57
257 269 3.381045 GCGTCACGATTTATCCTGATCA 58.619 45.455 0.00 0.00 0.00 2.92
260 272 1.202486 GGGCGTCACGATTTATCCTGA 60.202 52.381 0.00 0.00 0.00 3.86
282 322 6.210185 AGTCTGAAGCAATATGAAGCCTTTTT 59.790 34.615 0.00 0.00 0.00 1.94
284 324 5.259632 AGTCTGAAGCAATATGAAGCCTTT 58.740 37.500 0.00 0.00 0.00 3.11
368 408 1.755783 GGGGCCTCAGCAAGATTGG 60.756 63.158 0.84 0.00 42.56 3.16
454 494 1.253593 TGGAGCGTGACAGAGATGCT 61.254 55.000 0.00 0.00 38.42 3.79
487 527 1.764723 TGCATGCATCTAGCTAGGTGT 59.235 47.619 29.98 12.83 45.94 4.16
549 702 1.183030 TAGGTGCGGCCGCTGTATAT 61.183 55.000 45.79 28.21 43.70 0.86
615 768 3.504134 TGCCGCTGCTAATTTTCTGTTTA 59.496 39.130 0.70 0.00 38.71 2.01
616 769 2.295909 TGCCGCTGCTAATTTTCTGTTT 59.704 40.909 0.70 0.00 38.71 2.83
701 854 1.345741 CATATGCCGAGGGATCACTGT 59.654 52.381 0.00 0.00 0.00 3.55
706 859 1.376543 CATGCATATGCCGAGGGATC 58.623 55.000 24.54 0.00 41.18 3.36
716 869 1.071041 CGTGTCGTCAGCATGCATATG 60.071 52.381 21.98 12.54 37.36 1.78
751 935 1.754234 CTAAATGGGCGGCTTGGCT 60.754 57.895 9.56 0.00 44.11 4.75
752 936 2.004808 GACTAAATGGGCGGCTTGGC 62.005 60.000 9.56 0.00 43.88 4.52
753 937 1.384222 GGACTAAATGGGCGGCTTGG 61.384 60.000 9.56 0.00 0.00 3.61
754 938 0.679640 TGGACTAAATGGGCGGCTTG 60.680 55.000 9.56 0.00 0.00 4.01
755 939 0.679960 GTGGACTAAATGGGCGGCTT 60.680 55.000 9.56 0.00 0.00 4.35
756 940 1.077716 GTGGACTAAATGGGCGGCT 60.078 57.895 9.56 0.00 0.00 5.52
757 941 2.469516 CGTGGACTAAATGGGCGGC 61.470 63.158 0.00 0.00 0.00 6.53
758 942 0.391927 TTCGTGGACTAAATGGGCGG 60.392 55.000 0.00 0.00 0.00 6.13
759 943 0.725117 GTTCGTGGACTAAATGGGCG 59.275 55.000 0.00 0.00 0.00 6.13
760 944 1.737793 CTGTTCGTGGACTAAATGGGC 59.262 52.381 0.00 0.00 0.00 5.36
761 945 3.000727 GACTGTTCGTGGACTAAATGGG 58.999 50.000 0.00 0.00 0.00 4.00
762 946 3.659786 TGACTGTTCGTGGACTAAATGG 58.340 45.455 0.00 0.00 0.00 3.16
766 972 2.960384 TCCTTGACTGTTCGTGGACTAA 59.040 45.455 0.00 0.00 0.00 2.24
769 975 2.457366 ATCCTTGACTGTTCGTGGAC 57.543 50.000 0.00 0.00 31.20 4.02
772 978 4.174411 TCAGTATCCTTGACTGTTCGTG 57.826 45.455 2.95 0.00 43.95 4.35
809 1015 7.599245 GCGTGATATTACTAGCTAAATGGACTT 59.401 37.037 0.00 0.00 0.00 3.01
816 1022 7.658261 AGTGATGCGTGATATTACTAGCTAAA 58.342 34.615 0.00 0.00 0.00 1.85
817 1023 7.215719 AGTGATGCGTGATATTACTAGCTAA 57.784 36.000 0.00 0.00 0.00 3.09
822 1035 8.141909 AGCTTAAAGTGATGCGTGATATTACTA 58.858 33.333 0.00 0.00 0.00 1.82
823 1036 6.986817 AGCTTAAAGTGATGCGTGATATTACT 59.013 34.615 0.00 0.00 0.00 2.24
824 1037 7.178712 AGCTTAAAGTGATGCGTGATATTAC 57.821 36.000 0.00 0.00 0.00 1.89
827 1040 5.406780 GCTAGCTTAAAGTGATGCGTGATAT 59.593 40.000 7.70 0.00 0.00 1.63
834 1047 8.250332 AGATAGATAGCTAGCTTAAAGTGATGC 58.750 37.037 24.88 3.51 40.26 3.91
853 1067 9.829507 GCTCATTGCAAGGTTATATAGATAGAT 57.170 33.333 11.36 0.00 42.31 1.98
854 1068 8.260818 GGCTCATTGCAAGGTTATATAGATAGA 58.739 37.037 11.36 0.00 45.15 1.98
855 1069 7.223582 CGGCTCATTGCAAGGTTATATAGATAG 59.776 40.741 11.36 0.00 45.15 2.08
856 1070 7.041721 CGGCTCATTGCAAGGTTATATAGATA 58.958 38.462 11.36 0.00 45.15 1.98
857 1071 5.877012 CGGCTCATTGCAAGGTTATATAGAT 59.123 40.000 11.36 0.00 45.15 1.98
874 1088 1.804396 CTCGATCTCTGCCGGCTCAT 61.804 60.000 29.70 13.71 0.00 2.90
876 1090 2.334653 CTCGATCTCTGCCGGCTC 59.665 66.667 29.70 15.54 0.00 4.70
880 1094 3.586961 TCCGCTCGATCTCTGCCG 61.587 66.667 0.00 0.00 0.00 5.69
881 1095 2.026879 GTCCGCTCGATCTCTGCC 59.973 66.667 0.00 0.00 0.00 4.85
883 1097 1.358402 CCTGTCCGCTCGATCTCTG 59.642 63.158 0.00 0.00 0.00 3.35
894 1108 2.809601 GTACTGCGTGCCTGTCCG 60.810 66.667 0.00 0.00 0.00 4.79
895 1109 2.809601 CGTACTGCGTGCCTGTCC 60.810 66.667 0.00 0.00 35.54 4.02
905 1119 6.596703 TCTATGTATCGAATGTACGTACTGC 58.403 40.000 25.12 13.56 34.70 4.40
906 1120 7.903946 GGATCTATGTATCGAATGTACGTACTG 59.096 40.741 25.12 12.98 34.70 2.74
907 1121 7.605309 TGGATCTATGTATCGAATGTACGTACT 59.395 37.037 25.12 7.23 34.70 2.73
908 1122 7.745972 TGGATCTATGTATCGAATGTACGTAC 58.254 38.462 18.90 18.90 34.70 3.67
909 1123 7.605309 ACTGGATCTATGTATCGAATGTACGTA 59.395 37.037 0.00 0.00 34.70 3.57
910 1124 6.430308 ACTGGATCTATGTATCGAATGTACGT 59.570 38.462 0.00 0.00 34.70 3.57
911 1125 6.743172 CACTGGATCTATGTATCGAATGTACG 59.257 42.308 0.00 0.00 0.00 3.67
912 1126 6.528423 GCACTGGATCTATGTATCGAATGTAC 59.472 42.308 0.00 0.00 0.00 2.90
913 1127 6.350194 GGCACTGGATCTATGTATCGAATGTA 60.350 42.308 0.00 0.00 0.00 2.29
914 1128 5.473931 GCACTGGATCTATGTATCGAATGT 58.526 41.667 0.00 0.00 0.00 2.71
915 1129 4.867047 GGCACTGGATCTATGTATCGAATG 59.133 45.833 0.00 0.00 0.00 2.67
916 1130 4.380973 CGGCACTGGATCTATGTATCGAAT 60.381 45.833 0.00 0.00 0.00 3.34
917 1131 3.057526 CGGCACTGGATCTATGTATCGAA 60.058 47.826 0.00 0.00 0.00 3.71
918 1132 2.488153 CGGCACTGGATCTATGTATCGA 59.512 50.000 0.00 0.00 0.00 3.59
919 1133 2.416027 CCGGCACTGGATCTATGTATCG 60.416 54.545 0.00 0.00 0.00 2.92
920 1134 2.563179 ACCGGCACTGGATCTATGTATC 59.437 50.000 0.00 0.00 0.00 2.24
921 1135 2.300152 CACCGGCACTGGATCTATGTAT 59.700 50.000 0.00 0.00 0.00 2.29
922 1136 1.686587 CACCGGCACTGGATCTATGTA 59.313 52.381 0.00 0.00 0.00 2.29
923 1137 0.465705 CACCGGCACTGGATCTATGT 59.534 55.000 0.00 0.00 0.00 2.29
924 1138 0.752658 TCACCGGCACTGGATCTATG 59.247 55.000 0.00 0.00 0.00 2.23
925 1139 1.620819 GATCACCGGCACTGGATCTAT 59.379 52.381 0.00 0.00 34.68 1.98
926 1140 1.040646 GATCACCGGCACTGGATCTA 58.959 55.000 0.00 0.00 34.68 1.98
927 1141 0.689080 AGATCACCGGCACTGGATCT 60.689 55.000 0.00 9.26 41.11 2.75
928 1142 1.040646 TAGATCACCGGCACTGGATC 58.959 55.000 0.00 6.95 37.11 3.36
929 1143 1.620819 GATAGATCACCGGCACTGGAT 59.379 52.381 0.00 0.00 0.00 3.41
930 1144 1.040646 GATAGATCACCGGCACTGGA 58.959 55.000 0.00 0.00 0.00 3.86
931 1145 0.752658 TGATAGATCACCGGCACTGG 59.247 55.000 0.00 0.00 0.00 4.00
932 1146 2.602257 TTGATAGATCACCGGCACTG 57.398 50.000 0.00 0.00 36.36 3.66
933 1147 2.420129 GGTTTGATAGATCACCGGCACT 60.420 50.000 0.00 0.00 36.36 4.40
934 1148 1.940613 GGTTTGATAGATCACCGGCAC 59.059 52.381 0.00 0.00 36.36 5.01
935 1149 1.472552 CGGTTTGATAGATCACCGGCA 60.473 52.381 0.00 0.00 40.61 5.69
936 1150 1.217882 CGGTTTGATAGATCACCGGC 58.782 55.000 0.00 0.00 40.61 6.13
938 1152 1.217882 GCCGGTTTGATAGATCACCG 58.782 55.000 11.92 11.92 42.62 4.94
939 1153 1.940613 GTGCCGGTTTGATAGATCACC 59.059 52.381 1.90 0.00 36.36 4.02
940 1154 1.593006 CGTGCCGGTTTGATAGATCAC 59.407 52.381 1.90 0.00 36.36 3.06
941 1155 1.934589 CGTGCCGGTTTGATAGATCA 58.065 50.000 1.90 0.00 34.44 2.92
942 1156 0.582005 GCGTGCCGGTTTGATAGATC 59.418 55.000 1.90 0.00 0.00 2.75
943 1157 0.107897 TGCGTGCCGGTTTGATAGAT 60.108 50.000 1.90 0.00 0.00 1.98
944 1158 1.017177 GTGCGTGCCGGTTTGATAGA 61.017 55.000 1.90 0.00 0.00 1.98
945 1159 1.295357 TGTGCGTGCCGGTTTGATAG 61.295 55.000 1.90 0.00 0.00 2.08
946 1160 0.675208 ATGTGCGTGCCGGTTTGATA 60.675 50.000 1.90 0.00 0.00 2.15
947 1161 0.675208 TATGTGCGTGCCGGTTTGAT 60.675 50.000 1.90 0.00 0.00 2.57
954 1168 3.848830 CACCGTATGTGCGTGCCG 61.849 66.667 0.00 0.00 38.34 5.69
961 1175 1.726791 GAAGCACTGTCACCGTATGTG 59.273 52.381 0.00 0.00 46.88 3.21
964 1178 1.893137 TCTGAAGCACTGTCACCGTAT 59.107 47.619 0.00 0.00 0.00 3.06
972 1208 5.128335 TGATGATATGTCTCTGAAGCACTGT 59.872 40.000 0.00 0.00 0.00 3.55
980 1216 7.607615 TCCATTTCTGATGATATGTCTCTGA 57.392 36.000 0.00 0.00 32.25 3.27
981 1217 6.369340 GCTCCATTTCTGATGATATGTCTCTG 59.631 42.308 0.00 0.00 32.25 3.35
982 1218 6.465948 GCTCCATTTCTGATGATATGTCTCT 58.534 40.000 0.00 0.00 32.25 3.10
983 1219 5.642919 GGCTCCATTTCTGATGATATGTCTC 59.357 44.000 0.00 0.00 32.25 3.36
984 1220 5.310068 AGGCTCCATTTCTGATGATATGTCT 59.690 40.000 0.00 0.00 32.25 3.41
985 1221 5.558818 AGGCTCCATTTCTGATGATATGTC 58.441 41.667 0.00 0.00 32.25 3.06
986 1222 5.310068 AGAGGCTCCATTTCTGATGATATGT 59.690 40.000 11.71 0.00 32.25 2.29
987 1223 5.806818 AGAGGCTCCATTTCTGATGATATG 58.193 41.667 11.71 0.00 33.39 1.78
988 1224 5.546887 TGAGAGGCTCCATTTCTGATGATAT 59.453 40.000 11.71 0.00 0.00 1.63
992 1228 3.134262 TCTGAGAGGCTCCATTTCTGATG 59.866 47.826 11.71 0.00 0.00 3.07
1048 1294 3.667282 CAGCCACAGCAGCACCAC 61.667 66.667 0.00 0.00 43.56 4.16
1284 1537 6.771076 TGCATGTAGACAACAATTAACGATC 58.229 36.000 0.00 0.00 42.70 3.69
1291 1544 4.787260 TGCATGCATGTAGACAACAATT 57.213 36.364 26.79 0.00 42.70 2.32
1482 1739 2.288666 ACGAGGAGTACGCCGTATTTA 58.711 47.619 10.22 0.00 33.01 1.40
1521 1778 0.613777 GTGGTGAATTCGGAGGGAGT 59.386 55.000 0.04 0.00 0.00 3.85
1528 1785 0.036164 TGGAGTGGTGGTGAATTCGG 59.964 55.000 0.04 0.00 0.00 4.30
1538 1795 3.270877 GGTTAGCTATGTTGGAGTGGTG 58.729 50.000 0.00 0.00 0.00 4.17
1806 2083 5.184287 TGATAAGATGACCACGTCTGTTGTA 59.816 40.000 0.00 0.00 40.96 2.41
1851 2249 3.611113 GCGTACAACATACAGTAGTGGTG 59.389 47.826 1.92 3.30 38.95 4.17
1853 2251 3.840468 TGCGTACAACATACAGTAGTGG 58.160 45.455 1.92 0.00 0.00 4.00
2083 2508 2.029964 TGGTTGTCGAAGGCGTCC 59.970 61.111 0.00 0.00 38.98 4.79
2242 2667 1.524621 CATCCTGACCATGGCGTCC 60.525 63.158 13.04 0.00 31.35 4.79
2333 2758 1.722636 GGCAAGCTAGATGCAGTGGC 61.723 60.000 18.89 5.85 45.60 5.01
2349 2778 1.888436 ATCTGTCTTCTTCGCCGGCA 61.888 55.000 28.98 11.20 0.00 5.69
2355 2784 1.718396 TGCAGCATCTGTCTTCTTCG 58.282 50.000 0.00 0.00 33.43 3.79
2369 2798 1.975407 AAGGTCAGGTGCATGCAGC 60.975 57.895 36.42 36.42 43.95 5.25
2370 2799 1.592400 CCAAGGTCAGGTGCATGCAG 61.592 60.000 23.41 10.15 0.00 4.41
2371 2800 1.604308 CCAAGGTCAGGTGCATGCA 60.604 57.895 18.46 18.46 0.00 3.96
2372 2801 1.604593 ACCAAGGTCAGGTGCATGC 60.605 57.895 11.82 11.82 38.13 4.06
2373 2802 4.828409 ACCAAGGTCAGGTGCATG 57.172 55.556 0.00 0.00 38.13 4.06
2378 2807 1.604593 GCATGCACCAAGGTCAGGT 60.605 57.895 14.21 0.00 40.85 4.00
2379 2808 2.345760 GGCATGCACCAAGGTCAGG 61.346 63.158 21.36 0.00 0.00 3.86
2380 2809 2.345760 GGGCATGCACCAAGGTCAG 61.346 63.158 21.36 0.00 0.00 3.51
2381 2810 2.283101 GGGCATGCACCAAGGTCA 60.283 61.111 21.36 0.00 0.00 4.02
2382 2811 1.669999 GATGGGCATGCACCAAGGTC 61.670 60.000 25.44 17.25 42.17 3.85
2383 2812 1.683365 GATGGGCATGCACCAAGGT 60.683 57.895 25.44 13.61 42.17 3.50
2384 2813 1.380785 AGATGGGCATGCACCAAGG 60.381 57.895 25.44 0.00 42.17 3.61
2385 2814 1.721664 CGAGATGGGCATGCACCAAG 61.722 60.000 25.44 15.80 42.17 3.61
2386 2815 1.750018 CGAGATGGGCATGCACCAA 60.750 57.895 25.44 7.19 42.17 3.67
2387 2816 2.124612 CGAGATGGGCATGCACCA 60.125 61.111 24.35 24.35 43.22 4.17
2388 2817 3.589881 GCGAGATGGGCATGCACC 61.590 66.667 19.33 17.30 0.00 5.01
2389 2818 3.945434 CGCGAGATGGGCATGCAC 61.945 66.667 21.36 18.25 0.00 4.57
2390 2819 3.974835 AACGCGAGATGGGCATGCA 62.975 57.895 21.36 0.00 0.00 3.96
2391 2820 3.204827 AACGCGAGATGGGCATGC 61.205 61.111 15.93 9.90 0.00 4.06
2392 2821 2.040213 GACAACGCGAGATGGGCATG 62.040 60.000 15.93 0.00 38.32 4.06
2393 2822 1.815421 GACAACGCGAGATGGGCAT 60.815 57.895 15.93 0.00 38.32 4.40
2394 2823 2.434185 GACAACGCGAGATGGGCA 60.434 61.111 15.93 0.00 38.32 5.36
2395 2824 2.032634 TTGACAACGCGAGATGGGC 61.033 57.895 15.93 6.33 38.32 5.36
2396 2825 0.948623 TGTTGACAACGCGAGATGGG 60.949 55.000 15.93 0.00 38.32 4.00
2397 2826 0.439985 CTGTTGACAACGCGAGATGG 59.560 55.000 15.93 0.00 38.32 3.51
2398 2827 1.125021 GACTGTTGACAACGCGAGATG 59.875 52.381 15.93 11.60 40.07 2.90
2399 2828 1.269569 TGACTGTTGACAACGCGAGAT 60.270 47.619 15.93 0.00 0.00 2.75
2400 2829 0.101579 TGACTGTTGACAACGCGAGA 59.898 50.000 15.93 0.00 0.00 4.04
2401 2830 1.125021 GATGACTGTTGACAACGCGAG 59.875 52.381 15.93 7.57 0.00 5.03
2402 2831 1.136690 GATGACTGTTGACAACGCGA 58.863 50.000 15.93 0.00 0.00 5.87
2403 2832 0.858583 TGATGACTGTTGACAACGCG 59.141 50.000 13.46 3.53 0.00 6.01
2404 2833 4.548916 CGATATGATGACTGTTGACAACGC 60.549 45.833 13.46 6.31 0.00 4.84
2405 2834 4.562789 ACGATATGATGACTGTTGACAACG 59.437 41.667 13.46 10.47 0.00 4.10
2406 2835 5.725042 GCACGATATGATGACTGTTGACAAC 60.725 44.000 11.54 11.54 0.00 3.32
2407 2836 4.329801 GCACGATATGATGACTGTTGACAA 59.670 41.667 0.00 0.00 0.00 3.18
2408 2837 3.865164 GCACGATATGATGACTGTTGACA 59.135 43.478 0.00 0.00 0.00 3.58
2409 2838 3.060940 CGCACGATATGATGACTGTTGAC 60.061 47.826 0.00 0.00 0.00 3.18
2410 2839 3.115554 CGCACGATATGATGACTGTTGA 58.884 45.455 0.00 0.00 0.00 3.18
2411 2840 2.860136 ACGCACGATATGATGACTGTTG 59.140 45.455 0.00 0.00 0.00 3.33
2412 2841 3.116300 GACGCACGATATGATGACTGTT 58.884 45.455 0.00 0.00 0.00 3.16
2413 2842 2.359214 AGACGCACGATATGATGACTGT 59.641 45.455 0.00 0.00 0.00 3.55
2414 2843 2.723143 CAGACGCACGATATGATGACTG 59.277 50.000 0.00 0.00 0.00 3.51
2415 2844 2.287849 CCAGACGCACGATATGATGACT 60.288 50.000 0.00 0.00 0.00 3.41
2416 2845 2.054363 CCAGACGCACGATATGATGAC 58.946 52.381 0.00 0.00 0.00 3.06
2417 2846 1.953686 TCCAGACGCACGATATGATGA 59.046 47.619 0.00 0.00 0.00 2.92
2418 2847 2.422276 TCCAGACGCACGATATGATG 57.578 50.000 0.00 0.00 0.00 3.07
2419 2848 2.928301 GCATCCAGACGCACGATATGAT 60.928 50.000 0.00 0.00 0.00 2.45
2468 2914 1.869132 GAAACGGTACACAGGACAACC 59.131 52.381 0.00 0.00 0.00 3.77
2568 3061 0.974383 GGCACTACCACAGTACCACT 59.026 55.000 0.00 0.00 40.13 4.00
2569 3062 0.974383 AGGCACTACCACAGTACCAC 59.026 55.000 0.00 0.00 42.57 4.16
2570 3063 2.608593 TAGGCACTACCACAGTACCA 57.391 50.000 0.00 0.00 42.57 3.25
2613 3109 8.752187 AGCTACACATTCCATTATTCATTTTGT 58.248 29.630 0.00 0.00 0.00 2.83
2638 3134 0.460811 TGCAGACTTCATGCGGCTAG 60.461 55.000 0.00 0.00 46.87 3.42
2738 3257 2.125106 GGCCTTACAGGGACGCAG 60.125 66.667 0.00 0.00 35.37 5.18
2755 3275 0.094730 CGCTTAACCGAAAAGCTCCG 59.905 55.000 12.42 0.00 45.73 4.63
2756 3276 1.136057 CACGCTTAACCGAAAAGCTCC 60.136 52.381 12.42 0.00 45.73 4.70
2759 3279 0.109919 CCCACGCTTAACCGAAAAGC 60.110 55.000 0.00 6.35 44.72 3.51
2764 3284 0.390603 CATGTCCCACGCTTAACCGA 60.391 55.000 0.00 0.00 0.00 4.69
2771 3291 1.450848 CTGCATCATGTCCCACGCT 60.451 57.895 0.00 0.00 0.00 5.07
2778 3298 1.857217 CGCTAGTCACTGCATCATGTC 59.143 52.381 0.00 0.00 0.00 3.06
2779 3299 1.472201 CCGCTAGTCACTGCATCATGT 60.472 52.381 0.00 0.00 0.00 3.21
2788 3308 1.077930 TCGCTACCCGCTAGTCACT 60.078 57.895 0.00 0.00 36.73 3.41
2793 3313 2.026301 GCTGTCGCTACCCGCTAG 59.974 66.667 0.00 0.00 36.73 3.42
2814 3334 4.491234 TTTTAACCACGTTGATGCGATT 57.509 36.364 0.00 0.00 35.59 3.34
2830 3350 5.054477 GTCGATGCCTGCCTACTATTTTAA 58.946 41.667 0.00 0.00 0.00 1.52
2835 3355 0.969894 GGTCGATGCCTGCCTACTAT 59.030 55.000 0.00 0.00 0.00 2.12
2837 3357 2.786495 CGGTCGATGCCTGCCTACT 61.786 63.158 0.00 0.00 0.00 2.57
2845 3365 3.640000 CGCCAATCGGTCGATGCC 61.640 66.667 6.63 0.00 34.85 4.40
2918 3438 2.591715 ATGATAACCGCTGCGCCC 60.592 61.111 18.00 3.64 0.00 6.13
2919 3439 1.160329 AAGATGATAACCGCTGCGCC 61.160 55.000 18.00 3.29 0.00 6.53
2921 3441 1.595489 GCAAAGATGATAACCGCTGCG 60.595 52.381 16.34 16.34 0.00 5.18
2937 3457 2.546373 GCCTGTCAAATTCAGCAGCAAA 60.546 45.455 0.00 0.00 0.00 3.68
2971 3491 4.896482 ACAACCTGAACTCTGAAGTACTCT 59.104 41.667 0.00 0.00 33.48 3.24
3019 3539 1.710013 ATTTAGACGACTGGCACGTG 58.290 50.000 12.28 12.28 43.97 4.49
3080 3600 6.207614 GGAGAAGGAAGCAGAGTTGTTATTTT 59.792 38.462 0.00 0.00 0.00 1.82
3085 3605 2.224646 GGGAGAAGGAAGCAGAGTTGTT 60.225 50.000 0.00 0.00 0.00 2.83
3087 3607 1.627834 AGGGAGAAGGAAGCAGAGTTG 59.372 52.381 0.00 0.00 0.00 3.16
3088 3608 2.037385 AGGGAGAAGGAAGCAGAGTT 57.963 50.000 0.00 0.00 0.00 3.01
3089 3609 1.905894 GAAGGGAGAAGGAAGCAGAGT 59.094 52.381 0.00 0.00 0.00 3.24
3090 3610 2.168313 GAGAAGGGAGAAGGAAGCAGAG 59.832 54.545 0.00 0.00 0.00 3.35
3091 3611 2.183679 GAGAAGGGAGAAGGAAGCAGA 58.816 52.381 0.00 0.00 0.00 4.26
3093 3613 1.280457 GGAGAAGGGAGAAGGAAGCA 58.720 55.000 0.00 0.00 0.00 3.91
3141 3682 1.339929 GTGGTGGTCACAAATGGGTTC 59.660 52.381 3.40 0.00 45.39 3.62
3196 3737 2.683933 GTTCCAGAGAGGGCGGGA 60.684 66.667 0.00 0.00 38.24 5.14
3197 3738 3.787001 GGTTCCAGAGAGGGCGGG 61.787 72.222 0.00 0.00 38.24 6.13
3201 3742 2.982130 CGGTGGTTCCAGAGAGGG 59.018 66.667 0.00 0.00 38.24 4.30
3215 3756 2.045926 GCAAGACTGGATGGCGGT 60.046 61.111 0.00 0.00 0.00 5.68
3242 3787 1.461075 CAGGGCTAGAGGGATGGCT 60.461 63.158 0.00 0.00 0.00 4.75
3259 3804 0.672401 GAAAATCTCCGTCGGCACCA 60.672 55.000 6.34 0.00 0.00 4.17
3262 3807 1.722011 GAAGAAAATCTCCGTCGGCA 58.278 50.000 6.34 0.00 0.00 5.69
3267 3812 0.245539 TCGCCGAAGAAAATCTCCGT 59.754 50.000 0.00 0.00 0.00 4.69
3269 3814 2.347731 ACTTCGCCGAAGAAAATCTCC 58.652 47.619 31.61 0.00 41.71 3.71
3270 3815 3.737305 CAACTTCGCCGAAGAAAATCTC 58.263 45.455 31.61 0.00 41.71 2.75
3280 3825 2.970324 GTGGTGCAACTTCGCCGA 60.970 61.111 2.04 0.00 39.42 5.54
3281 3826 4.025401 GGTGGTGCAACTTCGCCG 62.025 66.667 2.04 0.00 39.42 6.46
3309 3854 3.566210 AGAACGGTGGTGGGGGTG 61.566 66.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.