Multiple sequence alignment - TraesCS3B01G218000

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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 TraesCS3B01G218000 chr3B 100.000 4136 0 0 1 4136 260841219 260845354 0.000000e+00 7638.0
1 TraesCS3B01G218000 chr3B 79.669 1087 185 27 1043 2114 226004772 226003707 0.000000e+00 750.0
2 TraesCS3B01G218000 chr3B 76.899 948 190 21 1100 2040 207733742 207734667 1.030000e-140 510.0
3 TraesCS3B01G218000 chr3B 88.148 135 14 2 3296 3430 660334740 660334608 4.280000e-35 159.0
4 TraesCS3B01G218000 chr3B 86.000 100 9 3 3587 3686 463291793 463291699 7.310000e-18 102.0
5 TraesCS3B01G218000 chr3B 100.000 40 0 0 2244 2283 323374091 323374052 1.590000e-09 75.0
6 TraesCS3B01G218000 chr3D 95.166 1593 47 14 1173 2753 182334348 182335922 0.000000e+00 2488.0
7 TraesCS3B01G218000 chr3D 81.540 1143 167 25 1001 2127 182320161 182321275 0.000000e+00 902.0
8 TraesCS3B01G218000 chr3D 87.215 571 26 23 2761 3296 182336270 182336828 1.270000e-169 606.0
9 TraesCS3B01G218000 chr3D 76.255 1036 217 24 1099 2127 148700164 148699151 1.320000e-144 523.0
10 TraesCS3B01G218000 chr3D 78.291 866 149 28 1056 1905 155675007 155675849 4.740000e-144 521.0
11 TraesCS3B01G218000 chr3D 84.187 449 14 11 768 1176 182328575 182329006 2.330000e-102 383.0
12 TraesCS3B01G218000 chr3D 84.946 186 25 3 3296 3480 499600239 499600056 7.060000e-43 185.0
13 TraesCS3B01G218000 chr3D 90.385 52 0 2 2249 2295 182335612 182335663 3.450000e-06 63.9
14 TraesCS3B01G218000 chr4B 89.637 1515 90 32 804 2295 397010720 397009250 0.000000e+00 1866.0
15 TraesCS3B01G218000 chr4B 78.947 456 50 24 2448 2873 397009296 397008857 6.820000e-68 268.0
16 TraesCS3B01G218000 chr4B 85.294 136 20 0 3303 3438 212519060 212518925 1.550000e-29 141.0
17 TraesCS3B01G218000 chr4B 97.619 42 1 0 3250 3291 397008247 397008206 5.740000e-09 73.1
18 TraesCS3B01G218000 chr4A 89.342 1520 106 39 805 2294 154354384 154355877 0.000000e+00 1858.0
19 TraesCS3B01G218000 chr4A 92.598 635 43 3 140 770 705553526 705552892 0.000000e+00 909.0
20 TraesCS3B01G218000 chr4A 81.982 444 48 21 2448 2875 154355832 154356259 8.510000e-92 348.0
21 TraesCS3B01G218000 chr4A 97.196 107 2 1 1 107 705553929 705553824 3.280000e-41 180.0
22 TraesCS3B01G218000 chr4A 92.157 51 3 1 3247 3296 154383809 154383859 2.060000e-08 71.3
23 TraesCS3B01G218000 chr4D 89.979 1417 81 35 804 2189 319328771 319327385 0.000000e+00 1773.0
24 TraesCS3B01G218000 chr4D 82.569 218 27 6 2625 2839 319320651 319320442 9.130000e-42 182.0
25 TraesCS3B01G218000 chr4D 94.017 117 7 0 2448 2564 319322148 319322032 1.180000e-40 178.0
26 TraesCS3B01G218000 chr4D 93.750 48 2 1 3250 3296 319319737 319319690 2.060000e-08 71.3
27 TraesCS3B01G218000 chr6D 97.860 841 16 2 3297 4136 307528641 307527802 0.000000e+00 1452.0
28 TraesCS3B01G218000 chr5A 94.411 841 46 1 3297 4136 401514276 401513436 0.000000e+00 1291.0
29 TraesCS3B01G218000 chr5A 90.909 682 53 6 90 767 666322696 666323372 0.000000e+00 907.0
30 TraesCS3B01G218000 chr2B 91.180 771 55 8 1 767 161215597 161216358 0.000000e+00 1035.0
31 TraesCS3B01G218000 chr2B 92.598 689 36 9 1 682 470032703 470032023 0.000000e+00 976.0
32 TraesCS3B01G218000 chr2B 91.602 643 47 5 129 767 90436759 90437398 0.000000e+00 881.0
33 TraesCS3B01G218000 chr2B 86.364 110 14 1 3305 3414 349922497 349922389 7.260000e-23 119.0
34 TraesCS3B01G218000 chr1B 91.594 690 49 6 82 767 30537119 30537803 0.000000e+00 944.0
35 TraesCS3B01G218000 chr1B 98.095 105 2 0 1 105 322397003 322397107 2.540000e-42 183.0
36 TraesCS3B01G218000 chr1A 91.304 690 49 8 82 767 485335280 485335962 0.000000e+00 931.0
37 TraesCS3B01G218000 chr1A 84.358 179 26 2 3303 3480 410783103 410783280 1.530000e-39 174.0
38 TraesCS3B01G218000 chr1A 97.101 69 1 1 1 69 113886910 113886977 9.400000e-22 115.0
39 TraesCS3B01G218000 chr3A 87.389 785 68 21 1 767 9968068 9968839 0.000000e+00 872.0
40 TraesCS3B01G218000 chr3A 79.098 1086 190 25 1040 2114 174542448 174543507 0.000000e+00 713.0
41 TraesCS3B01G218000 chr3A 75.696 1041 220 25 1096 2127 164611033 164612049 1.340000e-134 490.0
42 TraesCS3B01G218000 chr3A 83.750 160 24 2 3322 3480 192849031 192848873 2.580000e-32 150.0
43 TraesCS3B01G218000 chr5D 86.768 786 78 16 1 767 69330075 69329297 0.000000e+00 852.0
44 TraesCS3B01G218000 chr5D 97.059 34 0 1 2965 2997 386032113 386032080 5.780000e-04 56.5
45 TraesCS3B01G218000 chr7A 93.277 119 4 1 1 119 345268335 345268449 5.500000e-39 172.0
46 TraesCS3B01G218000 chr2D 87.156 109 13 1 3306 3414 272237427 272237320 5.610000e-24 122.0
47 TraesCS3B01G218000 chr5B 93.750 80 1 2 1 80 448593420 448593495 2.610000e-22 117.0
48 TraesCS3B01G218000 chr2A 77.404 208 32 8 3486 3686 410201792 410201593 4.370000e-20 110.0
49 TraesCS3B01G218000 chr7B 100.000 30 0 0 2966 2995 476510843 476510814 5.780000e-04 56.5


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 TraesCS3B01G218000 chr3B 260841219 260845354 4135 False 7638.000000 7638 100.000000 1 4136 1 chr3B.!!$F2 4135
1 TraesCS3B01G218000 chr3B 226003707 226004772 1065 True 750.000000 750 79.669000 1043 2114 1 chr3B.!!$R1 1071
2 TraesCS3B01G218000 chr3B 207733742 207734667 925 False 510.000000 510 76.899000 1100 2040 1 chr3B.!!$F1 940
3 TraesCS3B01G218000 chr3D 182334348 182336828 2480 False 1052.633333 2488 90.922000 1173 3296 3 chr3D.!!$F4 2123
4 TraesCS3B01G218000 chr3D 182320161 182321275 1114 False 902.000000 902 81.540000 1001 2127 1 chr3D.!!$F2 1126
5 TraesCS3B01G218000 chr3D 148699151 148700164 1013 True 523.000000 523 76.255000 1099 2127 1 chr3D.!!$R1 1028
6 TraesCS3B01G218000 chr3D 155675007 155675849 842 False 521.000000 521 78.291000 1056 1905 1 chr3D.!!$F1 849
7 TraesCS3B01G218000 chr4B 397008206 397010720 2514 True 735.700000 1866 88.734333 804 3291 3 chr4B.!!$R2 2487
8 TraesCS3B01G218000 chr4A 154354384 154356259 1875 False 1103.000000 1858 85.662000 805 2875 2 chr4A.!!$F2 2070
9 TraesCS3B01G218000 chr4A 705552892 705553929 1037 True 544.500000 909 94.897000 1 770 2 chr4A.!!$R1 769
10 TraesCS3B01G218000 chr4D 319327385 319328771 1386 True 1773.000000 1773 89.979000 804 2189 1 chr4D.!!$R1 1385
11 TraesCS3B01G218000 chr6D 307527802 307528641 839 True 1452.000000 1452 97.860000 3297 4136 1 chr6D.!!$R1 839
12 TraesCS3B01G218000 chr5A 401513436 401514276 840 True 1291.000000 1291 94.411000 3297 4136 1 chr5A.!!$R1 839
13 TraesCS3B01G218000 chr5A 666322696 666323372 676 False 907.000000 907 90.909000 90 767 1 chr5A.!!$F1 677
14 TraesCS3B01G218000 chr2B 161215597 161216358 761 False 1035.000000 1035 91.180000 1 767 1 chr2B.!!$F2 766
15 TraesCS3B01G218000 chr2B 470032023 470032703 680 True 976.000000 976 92.598000 1 682 1 chr2B.!!$R2 681
16 TraesCS3B01G218000 chr2B 90436759 90437398 639 False 881.000000 881 91.602000 129 767 1 chr2B.!!$F1 638
17 TraesCS3B01G218000 chr1B 30537119 30537803 684 False 944.000000 944 91.594000 82 767 1 chr1B.!!$F1 685
18 TraesCS3B01G218000 chr1A 485335280 485335962 682 False 931.000000 931 91.304000 82 767 1 chr1A.!!$F3 685
19 TraesCS3B01G218000 chr3A 9968068 9968839 771 False 872.000000 872 87.389000 1 767 1 chr3A.!!$F1 766
20 TraesCS3B01G218000 chr3A 174542448 174543507 1059 False 713.000000 713 79.098000 1040 2114 1 chr3A.!!$F3 1074
21 TraesCS3B01G218000 chr3A 164611033 164612049 1016 False 490.000000 490 75.696000 1096 2127 1 chr3A.!!$F2 1031
22 TraesCS3B01G218000 chr5D 69329297 69330075 778 True 852.000000 852 86.768000 1 767 1 chr5D.!!$R1 766

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
920 1219 0.179020 CTTCTTCTGCACCACCACCA 60.179 55.0 0.00 0.0 0.0 4.17 F
981 1299 0.456995 CCAGTCTCCTTCGCTTCGTC 60.457 60.0 0.00 0.0 0.0 4.20 F
2064 2427 0.958382 TGTATGGTCTTGTTGCGCCC 60.958 55.0 4.18 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2496 0.736325 GGCAGCAGAGCAAAGCATTG 60.736 55.0 0.0 0.0 39.65 2.82 R
2470 2835 1.262417 TGGTCGTGTAGAGGCATGAA 58.738 50.0 0.0 0.0 36.32 2.57 R
3178 4177 0.251165 GGCAAACTGACTTAGCCCCA 60.251 55.0 0.0 0.0 39.42 4.96 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
55 72 1.140772 AAAGACCCCCTCAAGGACCC 61.141 60.000 0.00 0.00 38.24 4.46
56 73 3.015753 GACCCCCTCAAGGACCCC 61.016 72.222 0.00 0.00 38.24 4.95
57 74 4.695791 ACCCCCTCAAGGACCCCC 62.696 72.222 0.00 0.00 38.24 5.40
125 145 0.826062 CATTGCCCTTGATTGACCCC 59.174 55.000 0.00 0.00 0.00 4.95
126 146 0.325577 ATTGCCCTTGATTGACCCCC 60.326 55.000 0.00 0.00 0.00 5.40
152 437 4.186159 CAATTCCCCAAATCAGCATCAAC 58.814 43.478 0.00 0.00 0.00 3.18
247 533 4.558496 GCAGATCGACCCAATTTTCACAAA 60.558 41.667 0.00 0.00 0.00 2.83
252 538 6.392625 TCGACCCAATTTTCACAAAACATA 57.607 33.333 0.00 0.00 32.37 2.29
278 564 2.241176 TGATCGGCCTCAAAAACCCTAT 59.759 45.455 0.00 0.00 0.00 2.57
324 614 1.536662 AGAGGAACAGGGGAAGCGT 60.537 57.895 0.00 0.00 0.00 5.07
468 758 2.744760 CAGAGATGAGGAGGAACAGGA 58.255 52.381 0.00 0.00 0.00 3.86
515 810 2.781431 GAAGGGGTTTGCATCGGGGT 62.781 60.000 0.00 0.00 0.00 4.95
517 812 2.034999 GGGTTTGCATCGGGGTCA 59.965 61.111 0.00 0.00 0.00 4.02
565 861 1.879380 TGGACTTGTCTGCGAAATTGG 59.121 47.619 0.61 0.00 0.00 3.16
572 868 2.881513 TGTCTGCGAAATTGGTAAAGCA 59.118 40.909 0.00 0.00 0.00 3.91
593 892 5.068591 AGCACGAGGGTTTCTTTGTAAAAAT 59.931 36.000 0.00 0.00 0.00 1.82
621 920 1.455217 GCCCGACAGAGCCTACCTA 60.455 63.158 0.00 0.00 0.00 3.08
686 985 0.984230 TAGCAGACAAGTTGGAGGGG 59.016 55.000 7.96 0.00 0.00 4.79
704 1003 1.763545 GGGCAGTTTTGTGGGGTTTTA 59.236 47.619 0.00 0.00 0.00 1.52
707 1006 4.040584 GGGCAGTTTTGTGGGGTTTTATAA 59.959 41.667 0.00 0.00 0.00 0.98
774 1073 9.667107 CCAATAGTGGTATTAACTCAAAGAAGA 57.333 33.333 0.00 0.00 40.42 2.87
791 1090 5.956068 AGAAGAAATCTTGTGGAAAGCTC 57.044 39.130 0.00 0.00 33.39 4.09
792 1091 5.380043 AGAAGAAATCTTGTGGAAAGCTCA 58.620 37.500 0.00 0.00 33.39 4.26
793 1092 5.472820 AGAAGAAATCTTGTGGAAAGCTCAG 59.527 40.000 0.00 0.00 33.39 3.35
794 1093 4.978099 AGAAATCTTGTGGAAAGCTCAGA 58.022 39.130 0.00 0.00 0.00 3.27
795 1094 5.380043 AGAAATCTTGTGGAAAGCTCAGAA 58.620 37.500 0.00 0.00 0.00 3.02
796 1095 5.829924 AGAAATCTTGTGGAAAGCTCAGAAA 59.170 36.000 0.00 0.00 0.00 2.52
797 1096 5.702349 AATCTTGTGGAAAGCTCAGAAAG 57.298 39.130 0.00 0.00 0.00 2.62
811 1110 4.201763 GCTCAGAAAGCGACAAGAAATAGG 60.202 45.833 0.00 0.00 42.21 2.57
812 1111 5.147330 TCAGAAAGCGACAAGAAATAGGA 57.853 39.130 0.00 0.00 0.00 2.94
813 1112 5.734720 TCAGAAAGCGACAAGAAATAGGAT 58.265 37.500 0.00 0.00 0.00 3.24
818 1117 5.344743 AGCGACAAGAAATAGGATGAGAA 57.655 39.130 0.00 0.00 0.00 2.87
840 1139 4.063689 AGAGACGAGACGTTCAAACTAGA 58.936 43.478 0.00 0.00 41.37 2.43
862 1161 2.360475 GCTGCCACTCCCCTGTTC 60.360 66.667 0.00 0.00 0.00 3.18
916 1215 2.328099 CGCCTTCTTCTGCACCACC 61.328 63.158 0.00 0.00 0.00 4.61
917 1216 1.228245 GCCTTCTTCTGCACCACCA 60.228 57.895 0.00 0.00 0.00 4.17
918 1217 1.518903 GCCTTCTTCTGCACCACCAC 61.519 60.000 0.00 0.00 0.00 4.16
919 1218 0.890996 CCTTCTTCTGCACCACCACC 60.891 60.000 0.00 0.00 0.00 4.61
920 1219 0.179020 CTTCTTCTGCACCACCACCA 60.179 55.000 0.00 0.00 0.00 4.17
921 1220 0.465460 TTCTTCTGCACCACCACCAC 60.465 55.000 0.00 0.00 0.00 4.16
922 1221 1.898574 CTTCTGCACCACCACCACC 60.899 63.158 0.00 0.00 0.00 4.61
923 1222 2.623094 CTTCTGCACCACCACCACCA 62.623 60.000 0.00 0.00 0.00 4.17
924 1223 2.902423 TTCTGCACCACCACCACCAC 62.902 60.000 0.00 0.00 0.00 4.16
925 1224 4.514585 TGCACCACCACCACCACC 62.515 66.667 0.00 0.00 0.00 4.61
926 1225 4.514585 GCACCACCACCACCACCA 62.515 66.667 0.00 0.00 0.00 4.17
927 1226 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
928 1227 4.183858 ACCACCACCACCACCACG 62.184 66.667 0.00 0.00 0.00 4.94
929 1228 4.947147 CCACCACCACCACCACGG 62.947 72.222 0.00 0.00 42.50 4.94
949 1259 3.264052 CCCATCCCACCCACACCA 61.264 66.667 0.00 0.00 0.00 4.17
950 1260 2.035626 CCATCCCACCCACACCAC 59.964 66.667 0.00 0.00 0.00 4.16
965 1283 1.675641 CCACCTCCGCTTTTCCCAG 60.676 63.158 0.00 0.00 0.00 4.45
974 1292 1.443802 GCTTTTCCCAGTCTCCTTCG 58.556 55.000 0.00 0.00 0.00 3.79
975 1293 1.443802 CTTTTCCCAGTCTCCTTCGC 58.556 55.000 0.00 0.00 0.00 4.70
977 1295 1.056660 TTTCCCAGTCTCCTTCGCTT 58.943 50.000 0.00 0.00 0.00 4.68
978 1296 0.608640 TTCCCAGTCTCCTTCGCTTC 59.391 55.000 0.00 0.00 0.00 3.86
979 1297 1.153745 CCCAGTCTCCTTCGCTTCG 60.154 63.158 0.00 0.00 0.00 3.79
981 1299 0.456995 CCAGTCTCCTTCGCTTCGTC 60.457 60.000 0.00 0.00 0.00 4.20
1814 2177 4.457496 CGGCGCTCACACTCCCAT 62.457 66.667 7.64 0.00 0.00 4.00
1944 2307 1.144936 GGAGAAGATCCCCACGCTG 59.855 63.158 0.00 0.00 43.01 5.18
2021 2384 1.983196 TTTGGTGTTGACGTGCGTGG 61.983 55.000 0.67 0.00 0.00 4.94
2064 2427 0.958382 TGTATGGTCTTGTTGCGCCC 60.958 55.000 4.18 0.00 0.00 6.13
2133 2496 4.219999 GCGCTCTCCTCCTCAGGC 62.220 72.222 0.00 0.00 40.12 4.85
2276 2641 9.628746 TCTGATTGATATTGTGTTTGTTTCATG 57.371 29.630 0.00 0.00 0.00 3.07
2277 2642 9.414295 CTGATTGATATTGTGTTTGTTTCATGT 57.586 29.630 0.00 0.00 0.00 3.21
2278 2643 9.409312 TGATTGATATTGTGTTTGTTTCATGTC 57.591 29.630 0.00 0.00 0.00 3.06
2279 2644 9.630098 GATTGATATTGTGTTTGTTTCATGTCT 57.370 29.630 0.00 0.00 0.00 3.41
2280 2645 9.630098 ATTGATATTGTGTTTGTTTCATGTCTC 57.370 29.630 0.00 0.00 0.00 3.36
2281 2646 8.394971 TGATATTGTGTTTGTTTCATGTCTCT 57.605 30.769 0.00 0.00 0.00 3.10
2282 2647 9.500785 TGATATTGTGTTTGTTTCATGTCTCTA 57.499 29.630 0.00 0.00 0.00 2.43
2283 2648 9.760660 GATATTGTGTTTGTTTCATGTCTCTAC 57.239 33.333 0.00 0.00 0.00 2.59
2284 2649 6.993786 TTGTGTTTGTTTCATGTCTCTACA 57.006 33.333 0.00 0.00 40.69 2.74
2285 2650 6.358118 TGTGTTTGTTTCATGTCTCTACAC 57.642 37.500 0.00 0.00 38.78 2.90
2286 2651 5.006261 TGTGTTTGTTTCATGTCTCTACACG 59.994 40.000 0.00 0.00 38.78 4.49
2287 2652 5.233476 GTGTTTGTTTCATGTCTCTACACGA 59.767 40.000 0.00 0.00 38.78 4.35
2288 2653 5.233476 TGTTTGTTTCATGTCTCTACACGAC 59.767 40.000 0.00 0.00 38.78 4.34
2289 2654 3.909430 TGTTTCATGTCTCTACACGACC 58.091 45.455 0.00 0.00 38.78 4.79
2290 2655 3.319689 TGTTTCATGTCTCTACACGACCA 59.680 43.478 0.00 0.00 38.78 4.02
2291 2656 4.021456 TGTTTCATGTCTCTACACGACCAT 60.021 41.667 0.00 0.00 38.78 3.55
2292 2657 4.801330 TTCATGTCTCTACACGACCATT 57.199 40.909 0.00 0.00 38.78 3.16
2293 2658 4.801330 TCATGTCTCTACACGACCATTT 57.199 40.909 0.00 0.00 38.78 2.32
2294 2659 4.744570 TCATGTCTCTACACGACCATTTC 58.255 43.478 0.00 0.00 38.78 2.17
2306 2671 4.102404 CGACCATTTCGTGAATCATACG 57.898 45.455 0.00 0.00 43.24 3.06
2307 2672 3.550275 CGACCATTTCGTGAATCATACGT 59.450 43.478 0.00 0.00 43.24 3.57
2308 2673 4.736307 CGACCATTTCGTGAATCATACGTA 59.264 41.667 0.00 0.00 43.24 3.57
2309 2674 5.331309 CGACCATTTCGTGAATCATACGTAC 60.331 44.000 0.00 0.00 43.24 3.67
2310 2675 5.657474 ACCATTTCGTGAATCATACGTACT 58.343 37.500 0.00 0.00 41.91 2.73
2311 2676 5.518847 ACCATTTCGTGAATCATACGTACTG 59.481 40.000 0.00 0.00 41.91 2.74
2312 2677 5.423717 CATTTCGTGAATCATACGTACTGC 58.576 41.667 0.00 0.00 41.91 4.40
2313 2678 3.074504 TCGTGAATCATACGTACTGCC 57.925 47.619 0.00 0.00 41.91 4.85
2314 2679 2.124903 CGTGAATCATACGTACTGCCC 58.875 52.381 0.00 0.00 36.83 5.36
2315 2680 2.480587 CGTGAATCATACGTACTGCCCA 60.481 50.000 0.00 0.00 36.83 5.36
2316 2681 3.728845 GTGAATCATACGTACTGCCCAT 58.271 45.455 0.00 0.00 0.00 4.00
2317 2682 4.557895 CGTGAATCATACGTACTGCCCATA 60.558 45.833 0.00 0.00 36.83 2.74
2318 2683 5.479306 GTGAATCATACGTACTGCCCATAT 58.521 41.667 0.00 0.00 0.00 1.78
2319 2684 6.624204 CGTGAATCATACGTACTGCCCATATA 60.624 42.308 0.00 0.00 36.83 0.86
2320 2685 6.530534 GTGAATCATACGTACTGCCCATATAC 59.469 42.308 0.00 0.00 0.00 1.47
2321 2686 6.209788 TGAATCATACGTACTGCCCATATACA 59.790 38.462 0.00 0.00 0.00 2.29
2322 2687 6.791867 ATCATACGTACTGCCCATATACAT 57.208 37.500 0.00 0.00 0.00 2.29
2323 2688 5.961272 TCATACGTACTGCCCATATACATG 58.039 41.667 0.00 0.00 0.00 3.21
2345 2710 5.732633 TGGCATTTCCACCATCTTTATTTG 58.267 37.500 0.00 0.00 40.72 2.32
2346 2711 4.571984 GGCATTTCCACCATCTTTATTTGC 59.428 41.667 0.00 0.00 34.01 3.68
2347 2712 4.571984 GCATTTCCACCATCTTTATTTGCC 59.428 41.667 0.00 0.00 0.00 4.52
2348 2713 5.627503 GCATTTCCACCATCTTTATTTGCCT 60.628 40.000 0.00 0.00 0.00 4.75
2349 2714 5.659440 TTTCCACCATCTTTATTTGCCTC 57.341 39.130 0.00 0.00 0.00 4.70
2350 2715 3.631250 TCCACCATCTTTATTTGCCTCC 58.369 45.455 0.00 0.00 0.00 4.30
2351 2716 3.011144 TCCACCATCTTTATTTGCCTCCA 59.989 43.478 0.00 0.00 0.00 3.86
2352 2717 3.962718 CCACCATCTTTATTTGCCTCCAT 59.037 43.478 0.00 0.00 0.00 3.41
2353 2718 4.202182 CCACCATCTTTATTTGCCTCCATG 60.202 45.833 0.00 0.00 0.00 3.66
2354 2719 3.385755 ACCATCTTTATTTGCCTCCATGC 59.614 43.478 0.00 0.00 0.00 4.06
2355 2720 3.243975 CCATCTTTATTTGCCTCCATGCC 60.244 47.826 0.00 0.00 0.00 4.40
2356 2721 3.386932 TCTTTATTTGCCTCCATGCCT 57.613 42.857 0.00 0.00 0.00 4.75
2357 2722 3.711863 TCTTTATTTGCCTCCATGCCTT 58.288 40.909 0.00 0.00 0.00 4.35
2358 2723 4.865905 TCTTTATTTGCCTCCATGCCTTA 58.134 39.130 0.00 0.00 0.00 2.69
2359 2724 4.644685 TCTTTATTTGCCTCCATGCCTTAC 59.355 41.667 0.00 0.00 0.00 2.34
2360 2725 2.834638 ATTTGCCTCCATGCCTTACT 57.165 45.000 0.00 0.00 0.00 2.24
2361 2726 1.838112 TTTGCCTCCATGCCTTACTG 58.162 50.000 0.00 0.00 0.00 2.74
2362 2727 0.991146 TTGCCTCCATGCCTTACTGA 59.009 50.000 0.00 0.00 0.00 3.41
2363 2728 1.216064 TGCCTCCATGCCTTACTGAT 58.784 50.000 0.00 0.00 0.00 2.90
2364 2729 1.141657 TGCCTCCATGCCTTACTGATC 59.858 52.381 0.00 0.00 0.00 2.92
2365 2730 1.419387 GCCTCCATGCCTTACTGATCT 59.581 52.381 0.00 0.00 0.00 2.75
2366 2731 2.809665 GCCTCCATGCCTTACTGATCTG 60.810 54.545 0.00 0.00 0.00 2.90
2367 2732 2.702478 CCTCCATGCCTTACTGATCTGA 59.298 50.000 6.60 0.00 0.00 3.27
2368 2733 3.327172 CCTCCATGCCTTACTGATCTGAT 59.673 47.826 6.60 0.00 0.00 2.90
2369 2734 4.529769 CCTCCATGCCTTACTGATCTGATA 59.470 45.833 6.60 0.00 0.00 2.15
2370 2735 5.189342 CCTCCATGCCTTACTGATCTGATAT 59.811 44.000 6.60 0.00 0.00 1.63
2371 2736 6.296317 CCTCCATGCCTTACTGATCTGATATT 60.296 42.308 6.60 0.00 0.00 1.28
2372 2737 7.093156 CCTCCATGCCTTACTGATCTGATATTA 60.093 40.741 6.60 0.00 0.00 0.98
2373 2738 8.384693 TCCATGCCTTACTGATCTGATATTAT 57.615 34.615 6.60 0.00 0.00 1.28
2374 2739 8.829746 TCCATGCCTTACTGATCTGATATTATT 58.170 33.333 6.60 0.00 0.00 1.40
2375 2740 9.458727 CCATGCCTTACTGATCTGATATTATTT 57.541 33.333 6.60 0.00 0.00 1.40
2378 2743 9.851686 TGCCTTACTGATCTGATATTATTTGTT 57.148 29.630 6.60 0.00 0.00 2.83
2394 2759 8.915871 ATTATTTGTTAGTGTGAATGTGATGC 57.084 30.769 0.00 0.00 0.00 3.91
2395 2760 5.764487 TTTGTTAGTGTGAATGTGATGCA 57.236 34.783 0.00 0.00 0.00 3.96
2396 2761 5.963176 TTGTTAGTGTGAATGTGATGCAT 57.037 34.783 0.00 0.00 40.03 3.96
2398 2763 6.330004 TGTTAGTGTGAATGTGATGCATTT 57.670 33.333 0.00 0.00 46.90 2.32
2399 2764 7.446001 TGTTAGTGTGAATGTGATGCATTTA 57.554 32.000 0.00 0.00 46.90 1.40
2400 2765 7.304735 TGTTAGTGTGAATGTGATGCATTTAC 58.695 34.615 0.00 4.29 46.90 2.01
2401 2766 5.314923 AGTGTGAATGTGATGCATTTACC 57.685 39.130 0.00 0.00 46.96 2.85
2402 2767 4.766373 AGTGTGAATGTGATGCATTTACCA 59.234 37.500 0.00 0.00 46.96 3.25
2403 2768 5.097529 GTGTGAATGTGATGCATTTACCAG 58.902 41.667 0.00 0.00 46.96 4.00
2404 2769 4.107622 GTGAATGTGATGCATTTACCAGC 58.892 43.478 0.00 0.00 46.90 4.85
2405 2770 4.018490 TGAATGTGATGCATTTACCAGCT 58.982 39.130 0.00 0.00 46.90 4.24
2406 2771 4.463539 TGAATGTGATGCATTTACCAGCTT 59.536 37.500 0.00 0.00 46.90 3.74
2407 2772 5.651576 TGAATGTGATGCATTTACCAGCTTA 59.348 36.000 0.00 0.00 46.90 3.09
2408 2773 6.321945 TGAATGTGATGCATTTACCAGCTTAT 59.678 34.615 0.00 0.00 46.90 1.73
2409 2774 5.756195 TGTGATGCATTTACCAGCTTATC 57.244 39.130 0.00 0.00 0.00 1.75
2410 2775 5.439721 TGTGATGCATTTACCAGCTTATCT 58.560 37.500 0.00 0.00 0.00 1.98
2411 2776 5.887598 TGTGATGCATTTACCAGCTTATCTT 59.112 36.000 0.00 0.00 0.00 2.40
2412 2777 6.183360 TGTGATGCATTTACCAGCTTATCTTG 60.183 38.462 0.00 0.00 0.00 3.02
2413 2778 4.637483 TGCATTTACCAGCTTATCTTGC 57.363 40.909 0.00 0.00 0.00 4.01
2414 2779 4.272489 TGCATTTACCAGCTTATCTTGCT 58.728 39.130 0.00 0.00 42.06 3.91
2415 2780 5.436175 TGCATTTACCAGCTTATCTTGCTA 58.564 37.500 0.00 0.00 38.92 3.49
2416 2781 5.885352 TGCATTTACCAGCTTATCTTGCTAA 59.115 36.000 0.00 0.00 38.92 3.09
2417 2782 6.038603 TGCATTTACCAGCTTATCTTGCTAAG 59.961 38.462 0.00 0.00 38.92 2.18
2418 2783 6.260936 GCATTTACCAGCTTATCTTGCTAAGA 59.739 38.462 1.85 1.85 42.69 2.10
2419 2784 7.519649 GCATTTACCAGCTTATCTTGCTAAGAG 60.520 40.741 5.15 0.00 41.61 2.85
2420 2785 3.802866 ACCAGCTTATCTTGCTAAGAGC 58.197 45.455 5.15 0.00 41.61 4.09
2434 2799 5.898630 GCTAAGAGCATTGCTAACTCTAC 57.101 43.478 11.96 0.00 41.89 2.59
2435 2800 5.596845 GCTAAGAGCATTGCTAACTCTACT 58.403 41.667 11.96 0.00 41.89 2.57
2436 2801 5.461737 GCTAAGAGCATTGCTAACTCTACTG 59.538 44.000 11.96 0.72 41.89 2.74
2437 2802 3.791245 AGAGCATTGCTAACTCTACTGC 58.209 45.455 11.96 0.00 39.88 4.40
2438 2803 3.196469 AGAGCATTGCTAACTCTACTGCA 59.804 43.478 11.96 0.00 39.88 4.41
2439 2804 4.125703 GAGCATTGCTAACTCTACTGCAT 58.874 43.478 11.96 0.00 39.88 3.96
2440 2805 4.125703 AGCATTGCTAACTCTACTGCATC 58.874 43.478 10.00 0.00 36.99 3.91
2441 2806 4.125703 GCATTGCTAACTCTACTGCATCT 58.874 43.478 0.16 0.00 35.27 2.90
2442 2807 4.025061 GCATTGCTAACTCTACTGCATCTG 60.025 45.833 0.16 0.00 35.27 2.90
2443 2808 3.808466 TGCTAACTCTACTGCATCTGG 57.192 47.619 0.00 0.00 0.00 3.86
2444 2809 3.365472 TGCTAACTCTACTGCATCTGGA 58.635 45.455 0.00 0.00 0.00 3.86
2445 2810 3.963374 TGCTAACTCTACTGCATCTGGAT 59.037 43.478 0.00 0.00 0.00 3.41
2446 2811 5.140454 TGCTAACTCTACTGCATCTGGATA 58.860 41.667 0.00 0.00 0.00 2.59
2447 2812 5.777223 TGCTAACTCTACTGCATCTGGATAT 59.223 40.000 0.00 0.00 0.00 1.63
2448 2813 6.268617 TGCTAACTCTACTGCATCTGGATATT 59.731 38.462 0.00 0.00 0.00 1.28
2449 2814 7.158021 GCTAACTCTACTGCATCTGGATATTT 58.842 38.462 0.00 0.00 0.00 1.40
2450 2815 7.330700 GCTAACTCTACTGCATCTGGATATTTC 59.669 40.741 0.00 0.00 0.00 2.17
2451 2816 6.992664 ACTCTACTGCATCTGGATATTTCT 57.007 37.500 0.00 0.00 0.00 2.52
2452 2817 6.757237 ACTCTACTGCATCTGGATATTTCTG 58.243 40.000 0.00 0.00 0.00 3.02
2453 2818 6.552725 ACTCTACTGCATCTGGATATTTCTGA 59.447 38.462 0.00 0.00 0.00 3.27
2454 2819 7.235193 ACTCTACTGCATCTGGATATTTCTGAT 59.765 37.037 0.00 0.00 0.00 2.90
2455 2820 7.971201 TCTACTGCATCTGGATATTTCTGATT 58.029 34.615 0.00 0.00 0.00 2.57
2456 2821 6.879276 ACTGCATCTGGATATTTCTGATTG 57.121 37.500 0.00 0.00 0.00 2.67
2457 2822 6.598503 ACTGCATCTGGATATTTCTGATTGA 58.401 36.000 0.00 0.00 0.00 2.57
2458 2823 6.485984 ACTGCATCTGGATATTTCTGATTGAC 59.514 38.462 0.00 0.00 0.00 3.18
2459 2824 6.358991 TGCATCTGGATATTTCTGATTGACA 58.641 36.000 0.00 0.00 0.00 3.58
2460 2825 7.002276 TGCATCTGGATATTTCTGATTGACAT 58.998 34.615 0.00 0.00 0.00 3.06
2461 2826 7.504574 TGCATCTGGATATTTCTGATTGACATT 59.495 33.333 0.00 0.00 0.00 2.71
2462 2827 7.808381 GCATCTGGATATTTCTGATTGACATTG 59.192 37.037 0.00 0.00 0.00 2.82
2463 2828 7.268199 TCTGGATATTTCTGATTGACATTGC 57.732 36.000 0.00 0.00 0.00 3.56
2464 2829 6.017687 TCTGGATATTTCTGATTGACATTGCG 60.018 38.462 0.00 0.00 0.00 4.85
2465 2830 5.589855 TGGATATTTCTGATTGACATTGCGT 59.410 36.000 0.00 0.00 0.00 5.24
2466 2831 6.095300 TGGATATTTCTGATTGACATTGCGTT 59.905 34.615 0.00 0.00 0.00 4.84
2467 2832 6.974622 GGATATTTCTGATTGACATTGCGTTT 59.025 34.615 0.00 0.00 0.00 3.60
2468 2833 7.043854 GGATATTTCTGATTGACATTGCGTTTG 60.044 37.037 0.00 0.00 0.00 2.93
2469 2834 4.566545 TTCTGATTGACATTGCGTTTGT 57.433 36.364 0.00 0.00 0.00 2.83
2470 2835 4.566545 TCTGATTGACATTGCGTTTGTT 57.433 36.364 0.00 0.00 0.00 2.83
2471 2836 4.930963 TCTGATTGACATTGCGTTTGTTT 58.069 34.783 0.00 0.00 0.00 2.83
2472 2837 4.975502 TCTGATTGACATTGCGTTTGTTTC 59.024 37.500 0.00 0.00 0.00 2.78
2473 2838 4.676546 TGATTGACATTGCGTTTGTTTCA 58.323 34.783 0.00 0.00 0.00 2.69
2507 3062 5.168569 CGACCATTTCTAACTCTACTGCAA 58.831 41.667 0.00 0.00 0.00 4.08
2561 3116 9.814899 CTCTAGTTGTTCAGTATTCATCTGATT 57.185 33.333 0.00 0.00 40.83 2.57
2568 3125 9.371136 TGTTCAGTATTCATCTGATTTACTCAC 57.629 33.333 0.00 0.00 40.83 3.51
2624 3214 5.104527 TGCTAATTAAGGCCATAGAGTGTGT 60.105 40.000 5.01 0.00 0.00 3.72
2645 3235 6.816640 TGTGTAGTGTGCACTAATATTCTTCC 59.183 38.462 19.41 0.09 44.62 3.46
2788 3724 3.262420 CCGGGTCTCTTACTGTGAATTG 58.738 50.000 0.00 0.00 0.00 2.32
2841 3777 9.293404 ACTGTGCTCTATAACCGATAGTATTAA 57.707 33.333 0.00 0.00 38.99 1.40
2903 3898 7.741785 TCTACTTGTTTGGTTTATCCTTGAGA 58.258 34.615 0.00 0.00 37.07 3.27
2974 3973 9.458727 TGCTACTGTATATTATGTACTACTCCC 57.541 37.037 1.15 0.00 0.00 4.30
2975 3974 9.683870 GCTACTGTATATTATGTACTACTCCCT 57.316 37.037 1.15 0.00 0.00 4.20
2979 3978 9.742144 CTGTATATTATGTACTACTCCCTCTGT 57.258 37.037 1.15 0.00 0.00 3.41
2983 3982 7.973048 ATTATGTACTACTCCCTCTGTTCAA 57.027 36.000 0.00 0.00 0.00 2.69
2985 3984 6.875972 ATGTACTACTCCCTCTGTTCAATT 57.124 37.500 0.00 0.00 0.00 2.32
2987 3986 7.074653 TGTACTACTCCCTCTGTTCAATTTT 57.925 36.000 0.00 0.00 0.00 1.82
2989 3988 8.822805 TGTACTACTCCCTCTGTTCAATTTTAT 58.177 33.333 0.00 0.00 0.00 1.40
2994 3993 8.794335 ACTCCCTCTGTTCAATTTTATAAGAC 57.206 34.615 0.00 0.00 0.00 3.01
2995 3994 7.549488 ACTCCCTCTGTTCAATTTTATAAGACG 59.451 37.037 0.00 0.00 0.00 4.18
2996 3995 7.391620 TCCCTCTGTTCAATTTTATAAGACGT 58.608 34.615 0.00 0.00 0.00 4.34
2997 3996 8.533657 TCCCTCTGTTCAATTTTATAAGACGTA 58.466 33.333 0.00 0.00 0.00 3.57
2998 3997 9.158233 CCCTCTGTTCAATTTTATAAGACGTAA 57.842 33.333 0.00 0.00 0.00 3.18
3137 4136 4.523173 CAGGATAGCATGCAAAGGATGAAT 59.477 41.667 21.98 0.00 0.00 2.57
3293 4508 1.302511 CCGGAAGTGTGACTTGGGG 60.303 63.158 0.00 0.00 38.80 4.96
3294 4509 1.450211 CGGAAGTGTGACTTGGGGT 59.550 57.895 0.00 0.00 38.80 4.95
3295 4510 0.884704 CGGAAGTGTGACTTGGGGTG 60.885 60.000 0.00 0.00 38.80 4.61
3335 4550 6.429521 AGCCACTACTTACTTTGGACTTTA 57.570 37.500 0.00 0.00 0.00 1.85
3374 4589 8.621487 CGCTTATATTGTAATTGATCTTTTGCG 58.379 33.333 0.00 0.00 0.00 4.85
3730 4947 4.135153 CCAGCGTCCTCTCCACCG 62.135 72.222 0.00 0.00 0.00 4.94
3746 4963 4.200283 CGTGGCCGAGCTCCTCTC 62.200 72.222 8.47 0.00 38.47 3.20
3821 5038 3.282157 CAGCTGTTGCACACGCCT 61.282 61.111 5.25 0.00 42.74 5.52
3822 5039 2.516930 AGCTGTTGCACACGCCTT 60.517 55.556 0.00 0.00 42.74 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 96 5.593095 GGATTTGATCTAGGGTTTTGGGTAC 59.407 44.000 0.00 0.00 0.00 3.34
126 146 1.499368 CTGATTTGGGGAATTGGGGG 58.501 55.000 0.00 0.00 0.00 5.40
152 437 3.012518 CCATGAGCTTGTCTAGGGTTTG 58.987 50.000 0.00 0.00 0.00 2.93
247 533 3.329300 GGCCGATCATGCCTATGTT 57.671 52.632 14.48 0.00 45.70 2.71
324 614 0.392461 GGTAAGCACCTGCCGATTCA 60.392 55.000 0.00 0.00 42.11 2.57
382 672 2.360350 CACAAGGCGCCATGGAGT 60.360 61.111 32.78 18.26 0.00 3.85
435 725 0.188342 ATCTCTGCCCTCTCCTCCTC 59.812 60.000 0.00 0.00 0.00 3.71
468 758 1.477685 TTCCCTTCTTTCGCCCGTCT 61.478 55.000 0.00 0.00 0.00 4.18
517 812 3.863400 CGATAGAAAACCACCTGGTCGTT 60.863 47.826 3.85 3.85 44.59 3.85
565 861 3.314357 ACAAAGAAACCCTCGTGCTTTAC 59.686 43.478 0.00 0.00 30.52 2.01
572 868 5.286438 GCATTTTTACAAAGAAACCCTCGT 58.714 37.500 0.00 0.00 0.00 4.18
686 985 7.737972 AAATTATAAAACCCCACAAAACTGC 57.262 32.000 0.00 0.00 0.00 4.40
767 1066 6.322201 TGAGCTTTCCACAAGATTTCTTCTTT 59.678 34.615 0.00 0.00 42.15 2.52
770 1069 5.471456 TCTGAGCTTTCCACAAGATTTCTTC 59.529 40.000 0.00 0.00 33.11 2.87
771 1070 5.380043 TCTGAGCTTTCCACAAGATTTCTT 58.620 37.500 0.00 0.00 36.45 2.52
772 1071 4.978099 TCTGAGCTTTCCACAAGATTTCT 58.022 39.130 0.00 0.00 0.00 2.52
773 1072 5.695851 TTCTGAGCTTTCCACAAGATTTC 57.304 39.130 0.00 0.00 0.00 2.17
774 1073 6.081872 CTTTCTGAGCTTTCCACAAGATTT 57.918 37.500 0.00 0.00 0.00 2.17
775 1074 5.702349 CTTTCTGAGCTTTCCACAAGATT 57.298 39.130 0.00 0.00 0.00 2.40
789 1088 5.171476 TCCTATTTCTTGTCGCTTTCTGAG 58.829 41.667 0.00 0.00 0.00 3.35
790 1089 5.147330 TCCTATTTCTTGTCGCTTTCTGA 57.853 39.130 0.00 0.00 0.00 3.27
791 1090 5.582269 TCATCCTATTTCTTGTCGCTTTCTG 59.418 40.000 0.00 0.00 0.00 3.02
792 1091 5.734720 TCATCCTATTTCTTGTCGCTTTCT 58.265 37.500 0.00 0.00 0.00 2.52
793 1092 5.812642 TCTCATCCTATTTCTTGTCGCTTTC 59.187 40.000 0.00 0.00 0.00 2.62
794 1093 5.734720 TCTCATCCTATTTCTTGTCGCTTT 58.265 37.500 0.00 0.00 0.00 3.51
795 1094 5.344743 TCTCATCCTATTTCTTGTCGCTT 57.655 39.130 0.00 0.00 0.00 4.68
796 1095 5.127845 TCTTCTCATCCTATTTCTTGTCGCT 59.872 40.000 0.00 0.00 0.00 4.93
797 1096 5.352284 TCTTCTCATCCTATTTCTTGTCGC 58.648 41.667 0.00 0.00 0.00 5.19
798 1097 6.695278 GTCTCTTCTCATCCTATTTCTTGTCG 59.305 42.308 0.00 0.00 0.00 4.35
799 1098 6.695278 CGTCTCTTCTCATCCTATTTCTTGTC 59.305 42.308 0.00 0.00 0.00 3.18
800 1099 6.378564 TCGTCTCTTCTCATCCTATTTCTTGT 59.621 38.462 0.00 0.00 0.00 3.16
801 1100 6.800543 TCGTCTCTTCTCATCCTATTTCTTG 58.199 40.000 0.00 0.00 0.00 3.02
802 1101 6.831353 TCTCGTCTCTTCTCATCCTATTTCTT 59.169 38.462 0.00 0.00 0.00 2.52
803 1102 6.262273 GTCTCGTCTCTTCTCATCCTATTTCT 59.738 42.308 0.00 0.00 0.00 2.52
806 1105 4.513692 CGTCTCGTCTCTTCTCATCCTATT 59.486 45.833 0.00 0.00 0.00 1.73
811 1110 3.125487 TGAACGTCTCGTCTCTTCTCATC 59.875 47.826 0.00 0.00 39.99 2.92
812 1111 3.075148 TGAACGTCTCGTCTCTTCTCAT 58.925 45.455 0.00 0.00 39.99 2.90
813 1112 2.490991 TGAACGTCTCGTCTCTTCTCA 58.509 47.619 0.00 0.00 39.99 3.27
818 1117 4.063689 TCTAGTTTGAACGTCTCGTCTCT 58.936 43.478 0.00 0.00 39.99 3.10
840 1139 2.118294 GGGGAGTGGCAGCCTTTT 59.882 61.111 14.15 0.00 0.00 2.27
881 1180 2.051518 CGCAGAGGGAGAGCTGACT 61.052 63.158 0.00 0.00 34.06 3.41
882 1181 2.493973 CGCAGAGGGAGAGCTGAC 59.506 66.667 0.00 0.00 34.06 3.51
884 1183 4.527583 GGCGCAGAGGGAGAGCTG 62.528 72.222 10.83 0.00 35.28 4.24
885 1184 4.775977 AGGCGCAGAGGGAGAGCT 62.776 66.667 10.83 0.00 0.00 4.09
886 1185 3.731653 GAAGGCGCAGAGGGAGAGC 62.732 68.421 10.83 0.00 0.00 4.09
887 1186 1.612395 AAGAAGGCGCAGAGGGAGAG 61.612 60.000 10.83 0.00 0.00 3.20
888 1187 1.608717 GAAGAAGGCGCAGAGGGAGA 61.609 60.000 10.83 0.00 0.00 3.71
889 1188 1.153469 GAAGAAGGCGCAGAGGGAG 60.153 63.158 10.83 0.00 0.00 4.30
890 1189 1.610673 AGAAGAAGGCGCAGAGGGA 60.611 57.895 10.83 0.00 0.00 4.20
891 1190 1.449246 CAGAAGAAGGCGCAGAGGG 60.449 63.158 10.83 0.00 0.00 4.30
892 1191 2.105466 GCAGAAGAAGGCGCAGAGG 61.105 63.158 10.83 0.00 0.00 3.69
919 1218 4.659172 ATGGGTGCCGTGGTGGTG 62.659 66.667 0.00 0.00 41.21 4.17
920 1219 4.344865 GATGGGTGCCGTGGTGGT 62.345 66.667 0.00 0.00 41.21 4.16
928 1227 4.759205 GTGGGTGGGATGGGTGCC 62.759 72.222 0.00 0.00 36.16 5.01
929 1228 3.978193 TGTGGGTGGGATGGGTGC 61.978 66.667 0.00 0.00 0.00 5.01
949 1259 1.128188 AGACTGGGAAAAGCGGAGGT 61.128 55.000 0.00 0.00 44.60 3.85
950 1260 0.391793 GAGACTGGGAAAAGCGGAGG 60.392 60.000 0.00 0.00 0.00 4.30
957 1274 1.056660 AGCGAAGGAGACTGGGAAAA 58.943 50.000 0.00 0.00 42.68 2.29
965 1283 1.514443 CGGACGAAGCGAAGGAGAC 60.514 63.158 0.00 0.00 0.00 3.36
974 1292 4.135493 GCTCGCAACGGACGAAGC 62.135 66.667 0.00 0.90 39.39 3.86
975 1293 3.479269 GGCTCGCAACGGACGAAG 61.479 66.667 0.00 0.00 39.39 3.79
979 1297 3.665675 ATCTGGGCTCGCAACGGAC 62.666 63.158 0.00 0.00 0.00 4.79
981 1299 2.892425 GATCTGGGCTCGCAACGG 60.892 66.667 0.00 0.00 0.00 4.44
1343 1667 4.719369 GCTGGAACGACGAGCCGT 62.719 66.667 0.00 0.00 43.00 5.68
1558 1894 1.305297 AGACCACGCAGATGGGAGA 60.305 57.895 3.67 0.00 44.81 3.71
1944 2307 2.361104 TTGGGGTGAATGAGCGCC 60.361 61.111 2.29 0.00 37.72 6.53
2021 2384 1.961277 CACTCCACCACCTTGCGAC 60.961 63.158 0.00 0.00 0.00 5.19
2133 2496 0.736325 GGCAGCAGAGCAAAGCATTG 60.736 55.000 0.00 0.00 39.65 2.82
2275 2640 3.211803 CGAAATGGTCGTGTAGAGACA 57.788 47.619 0.00 0.00 45.09 3.41
2286 2651 5.747197 AGTACGTATGATTCACGAAATGGTC 59.253 40.000 0.00 0.00 41.91 4.02
2287 2652 5.518847 CAGTACGTATGATTCACGAAATGGT 59.481 40.000 0.00 0.00 41.91 3.55
2288 2653 5.556382 GCAGTACGTATGATTCACGAAATGG 60.556 44.000 0.00 0.00 41.91 3.16
2289 2654 5.423717 GCAGTACGTATGATTCACGAAATG 58.576 41.667 0.00 0.00 41.91 2.32
2290 2655 4.506654 GGCAGTACGTATGATTCACGAAAT 59.493 41.667 0.00 0.00 41.91 2.17
2291 2656 3.861113 GGCAGTACGTATGATTCACGAAA 59.139 43.478 0.00 0.00 41.91 3.46
2292 2657 3.441163 GGCAGTACGTATGATTCACGAA 58.559 45.455 0.00 0.00 41.91 3.85
2293 2658 2.223641 GGGCAGTACGTATGATTCACGA 60.224 50.000 0.00 0.00 41.91 4.35
2294 2659 2.124903 GGGCAGTACGTATGATTCACG 58.875 52.381 0.00 0.00 44.80 4.35
2295 2660 3.173668 TGGGCAGTACGTATGATTCAC 57.826 47.619 0.00 0.00 0.00 3.18
2296 2661 5.738619 ATATGGGCAGTACGTATGATTCA 57.261 39.130 0.00 0.00 0.00 2.57
2297 2662 6.627243 TGTATATGGGCAGTACGTATGATTC 58.373 40.000 0.00 0.00 0.00 2.52
2298 2663 6.599356 TGTATATGGGCAGTACGTATGATT 57.401 37.500 0.00 0.00 0.00 2.57
2299 2664 6.573434 CATGTATATGGGCAGTACGTATGAT 58.427 40.000 0.00 0.00 0.00 2.45
2300 2665 5.961272 CATGTATATGGGCAGTACGTATGA 58.039 41.667 0.00 0.00 0.00 2.15
2322 2687 5.732633 CAAATAAAGATGGTGGAAATGCCA 58.267 37.500 0.00 0.00 46.96 4.92
2323 2688 4.571984 GCAAATAAAGATGGTGGAAATGCC 59.428 41.667 0.00 0.00 37.10 4.40
2324 2689 4.571984 GGCAAATAAAGATGGTGGAAATGC 59.428 41.667 0.00 0.00 0.00 3.56
2325 2690 5.981174 AGGCAAATAAAGATGGTGGAAATG 58.019 37.500 0.00 0.00 0.00 2.32
2326 2691 5.129320 GGAGGCAAATAAAGATGGTGGAAAT 59.871 40.000 0.00 0.00 0.00 2.17
2327 2692 4.466015 GGAGGCAAATAAAGATGGTGGAAA 59.534 41.667 0.00 0.00 0.00 3.13
2328 2693 4.023291 GGAGGCAAATAAAGATGGTGGAA 58.977 43.478 0.00 0.00 0.00 3.53
2329 2694 3.011144 TGGAGGCAAATAAAGATGGTGGA 59.989 43.478 0.00 0.00 0.00 4.02
2330 2695 3.364549 TGGAGGCAAATAAAGATGGTGG 58.635 45.455 0.00 0.00 0.00 4.61
2331 2696 4.738541 GCATGGAGGCAAATAAAGATGGTG 60.739 45.833 0.00 0.00 0.00 4.17
2332 2697 3.385755 GCATGGAGGCAAATAAAGATGGT 59.614 43.478 0.00 0.00 0.00 3.55
2333 2698 3.243975 GGCATGGAGGCAAATAAAGATGG 60.244 47.826 0.00 0.00 43.51 3.51
2334 2699 3.986277 GGCATGGAGGCAAATAAAGATG 58.014 45.455 0.00 0.00 43.51 2.90
2345 2710 1.419387 AGATCAGTAAGGCATGGAGGC 59.581 52.381 0.00 0.00 44.61 4.70
2346 2711 2.702478 TCAGATCAGTAAGGCATGGAGG 59.298 50.000 0.00 0.00 0.00 4.30
2347 2712 4.620589 ATCAGATCAGTAAGGCATGGAG 57.379 45.455 0.00 0.00 0.00 3.86
2348 2713 6.692849 AATATCAGATCAGTAAGGCATGGA 57.307 37.500 0.00 0.00 0.00 3.41
2349 2714 9.458727 AAATAATATCAGATCAGTAAGGCATGG 57.541 33.333 0.00 0.00 0.00 3.66
2352 2717 9.851686 AACAAATAATATCAGATCAGTAAGGCA 57.148 29.630 0.00 0.00 0.00 4.75
2369 2734 8.522003 TGCATCACATTCACACTAACAAATAAT 58.478 29.630 0.00 0.00 0.00 1.28
2370 2735 7.880105 TGCATCACATTCACACTAACAAATAA 58.120 30.769 0.00 0.00 0.00 1.40
2371 2736 7.446001 TGCATCACATTCACACTAACAAATA 57.554 32.000 0.00 0.00 0.00 1.40
2372 2737 6.330004 TGCATCACATTCACACTAACAAAT 57.670 33.333 0.00 0.00 0.00 2.32
2373 2738 5.764487 TGCATCACATTCACACTAACAAA 57.236 34.783 0.00 0.00 0.00 2.83
2374 2739 5.963176 ATGCATCACATTCACACTAACAA 57.037 34.783 0.00 0.00 34.40 2.83
2375 2740 5.963176 AATGCATCACATTCACACTAACA 57.037 34.783 0.00 0.00 46.28 2.41
2386 2751 6.066690 AGATAAGCTGGTAAATGCATCACAT 58.933 36.000 0.00 0.00 42.30 3.21
2387 2752 5.439721 AGATAAGCTGGTAAATGCATCACA 58.560 37.500 0.00 0.00 0.00 3.58
2388 2753 6.204359 CAAGATAAGCTGGTAAATGCATCAC 58.796 40.000 0.00 0.72 0.00 3.06
2389 2754 5.221106 GCAAGATAAGCTGGTAAATGCATCA 60.221 40.000 0.00 0.00 0.00 3.07
2390 2755 5.009410 AGCAAGATAAGCTGGTAAATGCATC 59.991 40.000 0.00 0.00 41.61 3.91
2391 2756 4.891756 AGCAAGATAAGCTGGTAAATGCAT 59.108 37.500 11.58 0.00 41.61 3.96
2392 2757 4.272489 AGCAAGATAAGCTGGTAAATGCA 58.728 39.130 11.58 0.00 41.61 3.96
2393 2758 4.907879 AGCAAGATAAGCTGGTAAATGC 57.092 40.909 0.00 0.00 41.61 3.56
2394 2759 7.519649 GCTCTTAGCAAGATAAGCTGGTAAATG 60.520 40.741 0.41 0.00 43.33 2.32
2395 2760 6.484977 GCTCTTAGCAAGATAAGCTGGTAAAT 59.515 38.462 0.41 0.00 43.33 1.40
2396 2761 5.817816 GCTCTTAGCAAGATAAGCTGGTAAA 59.182 40.000 0.41 0.00 43.33 2.01
2397 2762 5.360591 GCTCTTAGCAAGATAAGCTGGTAA 58.639 41.667 0.41 0.00 43.33 2.85
2398 2763 4.950050 GCTCTTAGCAAGATAAGCTGGTA 58.050 43.478 0.41 0.00 43.33 3.25
2399 2764 3.802866 GCTCTTAGCAAGATAAGCTGGT 58.197 45.455 0.41 0.00 43.33 4.00
2412 2777 5.461737 CAGTAGAGTTAGCAATGCTCTTAGC 59.538 44.000 12.53 0.00 40.44 3.09
2413 2778 5.461737 GCAGTAGAGTTAGCAATGCTCTTAG 59.538 44.000 12.53 0.00 40.44 2.18
2414 2779 5.105351 TGCAGTAGAGTTAGCAATGCTCTTA 60.105 40.000 12.53 0.00 40.44 2.10
2415 2780 4.187694 GCAGTAGAGTTAGCAATGCTCTT 58.812 43.478 12.53 0.00 40.44 2.85
2416 2781 3.196469 TGCAGTAGAGTTAGCAATGCTCT 59.804 43.478 12.53 2.99 40.44 4.09
2417 2782 3.525537 TGCAGTAGAGTTAGCAATGCTC 58.474 45.455 12.53 0.00 40.44 4.26
2418 2783 3.616956 TGCAGTAGAGTTAGCAATGCT 57.383 42.857 13.92 13.92 43.41 3.79
2419 2784 4.025061 CAGATGCAGTAGAGTTAGCAATGC 60.025 45.833 0.00 0.00 40.76 3.56
2420 2785 4.510711 CCAGATGCAGTAGAGTTAGCAATG 59.489 45.833 0.00 0.00 40.76 2.82
2421 2786 4.406972 TCCAGATGCAGTAGAGTTAGCAAT 59.593 41.667 0.00 0.00 40.76 3.56
2422 2787 3.769300 TCCAGATGCAGTAGAGTTAGCAA 59.231 43.478 0.00 0.00 40.76 3.91
2423 2788 3.365472 TCCAGATGCAGTAGAGTTAGCA 58.635 45.455 0.00 0.00 41.73 3.49
2424 2789 4.599047 ATCCAGATGCAGTAGAGTTAGC 57.401 45.455 0.00 0.00 0.00 3.09
2425 2790 8.584157 AGAAATATCCAGATGCAGTAGAGTTAG 58.416 37.037 0.00 0.00 0.00 2.34
2426 2791 8.363390 CAGAAATATCCAGATGCAGTAGAGTTA 58.637 37.037 0.00 0.00 0.00 2.24
2427 2792 7.070447 TCAGAAATATCCAGATGCAGTAGAGTT 59.930 37.037 0.00 0.00 0.00 3.01
2428 2793 6.552725 TCAGAAATATCCAGATGCAGTAGAGT 59.447 38.462 0.00 0.00 0.00 3.24
2429 2794 6.990798 TCAGAAATATCCAGATGCAGTAGAG 58.009 40.000 0.00 0.00 0.00 2.43
2430 2795 6.983906 TCAGAAATATCCAGATGCAGTAGA 57.016 37.500 0.00 0.00 0.00 2.59
2431 2796 7.876582 TCAATCAGAAATATCCAGATGCAGTAG 59.123 37.037 0.00 0.00 0.00 2.57
2432 2797 7.658982 GTCAATCAGAAATATCCAGATGCAGTA 59.341 37.037 0.00 0.00 0.00 2.74
2433 2798 6.485984 GTCAATCAGAAATATCCAGATGCAGT 59.514 38.462 0.00 0.00 0.00 4.40
2434 2799 6.485648 TGTCAATCAGAAATATCCAGATGCAG 59.514 38.462 0.00 0.00 0.00 4.41
2435 2800 6.358991 TGTCAATCAGAAATATCCAGATGCA 58.641 36.000 0.00 0.00 0.00 3.96
2436 2801 6.872628 TGTCAATCAGAAATATCCAGATGC 57.127 37.500 0.00 0.00 0.00 3.91
2437 2802 7.808381 GCAATGTCAATCAGAAATATCCAGATG 59.192 37.037 0.00 0.00 0.00 2.90
2438 2803 7.308408 CGCAATGTCAATCAGAAATATCCAGAT 60.308 37.037 0.00 0.00 0.00 2.90
2439 2804 6.017687 CGCAATGTCAATCAGAAATATCCAGA 60.018 38.462 0.00 0.00 0.00 3.86
2440 2805 6.140786 CGCAATGTCAATCAGAAATATCCAG 58.859 40.000 0.00 0.00 0.00 3.86
2441 2806 5.589855 ACGCAATGTCAATCAGAAATATCCA 59.410 36.000 0.00 0.00 0.00 3.41
2442 2807 6.064846 ACGCAATGTCAATCAGAAATATCC 57.935 37.500 0.00 0.00 0.00 2.59
2443 2808 7.485913 ACAAACGCAATGTCAATCAGAAATATC 59.514 33.333 0.00 0.00 0.00 1.63
2444 2809 7.315142 ACAAACGCAATGTCAATCAGAAATAT 58.685 30.769 0.00 0.00 0.00 1.28
2445 2810 6.676950 ACAAACGCAATGTCAATCAGAAATA 58.323 32.000 0.00 0.00 0.00 1.40
2446 2811 5.531634 ACAAACGCAATGTCAATCAGAAAT 58.468 33.333 0.00 0.00 0.00 2.17
2447 2812 4.930963 ACAAACGCAATGTCAATCAGAAA 58.069 34.783 0.00 0.00 0.00 2.52
2448 2813 4.566545 ACAAACGCAATGTCAATCAGAA 57.433 36.364 0.00 0.00 0.00 3.02
2449 2814 4.566545 AACAAACGCAATGTCAATCAGA 57.433 36.364 0.00 0.00 0.00 3.27
2450 2815 4.739228 TGAAACAAACGCAATGTCAATCAG 59.261 37.500 0.00 0.00 0.00 2.90
2451 2816 4.676546 TGAAACAAACGCAATGTCAATCA 58.323 34.783 0.00 0.00 0.00 2.57
2452 2817 5.601582 CATGAAACAAACGCAATGTCAATC 58.398 37.500 0.00 0.00 0.00 2.67
2453 2818 4.084433 GCATGAAACAAACGCAATGTCAAT 60.084 37.500 0.00 0.00 0.00 2.57
2454 2819 3.244814 GCATGAAACAAACGCAATGTCAA 59.755 39.130 0.00 0.00 0.00 3.18
2455 2820 2.793790 GCATGAAACAAACGCAATGTCA 59.206 40.909 0.00 0.00 0.00 3.58
2456 2821 2.155539 GGCATGAAACAAACGCAATGTC 59.844 45.455 0.00 0.00 0.00 3.06
2457 2822 2.134346 GGCATGAAACAAACGCAATGT 58.866 42.857 0.00 0.00 0.00 2.71
2458 2823 2.406130 AGGCATGAAACAAACGCAATG 58.594 42.857 0.00 0.00 0.00 2.82
2459 2824 2.297033 AGAGGCATGAAACAAACGCAAT 59.703 40.909 0.00 0.00 0.00 3.56
2460 2825 1.680735 AGAGGCATGAAACAAACGCAA 59.319 42.857 0.00 0.00 0.00 4.85
2461 2826 1.317613 AGAGGCATGAAACAAACGCA 58.682 45.000 0.00 0.00 0.00 5.24
2462 2827 2.225491 TGTAGAGGCATGAAACAAACGC 59.775 45.455 0.00 0.00 0.00 4.84
2463 2828 3.664276 CGTGTAGAGGCATGAAACAAACG 60.664 47.826 0.00 0.00 0.00 3.60
2464 2829 3.496884 TCGTGTAGAGGCATGAAACAAAC 59.503 43.478 0.00 0.00 32.11 2.93
2465 2830 3.496884 GTCGTGTAGAGGCATGAAACAAA 59.503 43.478 0.00 0.00 36.32 2.83
2466 2831 3.064207 GTCGTGTAGAGGCATGAAACAA 58.936 45.455 0.00 0.00 36.32 2.83
2467 2832 2.611971 GGTCGTGTAGAGGCATGAAACA 60.612 50.000 0.00 0.00 36.32 2.83
2468 2833 2.000447 GGTCGTGTAGAGGCATGAAAC 59.000 52.381 0.00 0.00 36.32 2.78
2469 2834 1.621317 TGGTCGTGTAGAGGCATGAAA 59.379 47.619 0.00 0.00 36.32 2.69
2470 2835 1.262417 TGGTCGTGTAGAGGCATGAA 58.738 50.000 0.00 0.00 36.32 2.57
2471 2836 1.485124 ATGGTCGTGTAGAGGCATGA 58.515 50.000 0.00 0.00 32.55 3.07
2472 2837 2.315925 AATGGTCGTGTAGAGGCATG 57.684 50.000 0.00 0.00 0.00 4.06
2473 2838 2.501723 AGAAATGGTCGTGTAGAGGCAT 59.498 45.455 0.00 0.00 0.00 4.40
2561 3116 3.695556 CCATGCATCAACCATGTGAGTAA 59.304 43.478 0.00 0.00 38.67 2.24
2564 3119 2.098607 GTCCATGCATCAACCATGTGAG 59.901 50.000 0.00 0.00 38.67 3.51
2568 3125 3.548770 AGTAGTCCATGCATCAACCATG 58.451 45.455 0.00 0.00 39.74 3.66
2624 3214 6.408092 CCCAGGAAGAATATTAGTGCACACTA 60.408 42.308 21.04 6.41 42.54 2.74
2771 3646 6.128172 CCCATTCACAATTCACAGTAAGAGAC 60.128 42.308 0.00 0.00 0.00 3.36
2772 3647 5.939883 CCCATTCACAATTCACAGTAAGAGA 59.060 40.000 0.00 0.00 0.00 3.10
2788 3724 6.521151 AAAATCTGATTCTCACCCATTCAC 57.479 37.500 2.92 0.00 0.00 3.18
2841 3777 5.372547 TTCTCGACTGCAAGCGTATATAT 57.627 39.130 7.61 0.00 37.60 0.86
2879 3874 7.979444 TCTCAAGGATAAACCAAACAAGTAG 57.021 36.000 0.00 0.00 42.04 2.57
2882 3877 7.116805 GCAAATCTCAAGGATAAACCAAACAAG 59.883 37.037 0.00 0.00 42.04 3.16
2903 3898 4.559862 AGACTTGGTACTGCTAGCAAAT 57.440 40.909 19.86 12.43 39.34 2.32
2958 3957 9.656323 ATTGAACAGAGGGAGTAGTACATAATA 57.344 33.333 2.52 0.00 0.00 0.98
2969 3968 7.549488 CGTCTTATAAAATTGAACAGAGGGAGT 59.451 37.037 0.00 0.00 0.00 3.85
2970 3969 7.549488 ACGTCTTATAAAATTGAACAGAGGGAG 59.451 37.037 0.00 0.00 0.00 4.30
2971 3970 7.391620 ACGTCTTATAAAATTGAACAGAGGGA 58.608 34.615 0.00 0.00 0.00 4.20
2972 3971 7.611213 ACGTCTTATAAAATTGAACAGAGGG 57.389 36.000 0.00 0.00 0.00 4.30
2985 3984 9.976511 AGCAGCAGTATTATTACGTCTTATAAA 57.023 29.630 0.00 0.00 33.32 1.40
2987 3986 9.406828 CAAGCAGCAGTATTATTACGTCTTATA 57.593 33.333 0.00 0.00 33.32 0.98
2989 3988 7.262772 ACAAGCAGCAGTATTATTACGTCTTA 58.737 34.615 0.00 0.00 33.32 2.10
2990 3989 6.106673 ACAAGCAGCAGTATTATTACGTCTT 58.893 36.000 0.00 0.00 33.32 3.01
2993 3992 5.661458 AGACAAGCAGCAGTATTATTACGT 58.339 37.500 0.00 0.00 33.32 3.57
2994 3993 6.589830 AAGACAAGCAGCAGTATTATTACG 57.410 37.500 0.00 0.00 33.32 3.18
2995 3994 7.974675 TCAAAGACAAGCAGCAGTATTATTAC 58.025 34.615 0.00 0.00 0.00 1.89
2996 3995 8.560355 TTCAAAGACAAGCAGCAGTATTATTA 57.440 30.769 0.00 0.00 0.00 0.98
2997 3996 7.362401 CCTTCAAAGACAAGCAGCAGTATTATT 60.362 37.037 0.00 0.00 0.00 1.40
2998 3997 6.094603 CCTTCAAAGACAAGCAGCAGTATTAT 59.905 38.462 0.00 0.00 0.00 1.28
3066 4065 2.016704 CGATCGCTGGTATGGACGC 61.017 63.158 0.26 0.00 0.00 5.19
3080 4079 1.625818 AGTGATAATCCCCTGCCGATC 59.374 52.381 0.00 0.00 0.00 3.69
3137 4136 2.642311 TGCTTCATGTTCCTACCTCCAA 59.358 45.455 0.00 0.00 0.00 3.53
3175 4174 3.555966 GCAAACTGACTTAGCCCCATAT 58.444 45.455 0.00 0.00 0.00 1.78
3178 4177 0.251165 GGCAAACTGACTTAGCCCCA 60.251 55.000 0.00 0.00 39.42 4.96
3254 4469 1.067295 ACAAGTGCTCCATCCAAGGA 58.933 50.000 0.00 0.00 36.00 3.36
3293 4508 3.186909 GCTTAAAATCAAATCGCCCCAC 58.813 45.455 0.00 0.00 0.00 4.61
3294 4509 2.167487 GGCTTAAAATCAAATCGCCCCA 59.833 45.455 0.00 0.00 0.00 4.96
3295 4510 2.167487 TGGCTTAAAATCAAATCGCCCC 59.833 45.455 0.00 0.00 35.28 5.80
3335 4550 7.049799 ACAATATAAGCGGTGGCAAATTATT 57.950 32.000 0.00 0.00 43.41 1.40
3374 4589 9.468532 AAAGATCAAAGTGCAAACTAAAGAATC 57.531 29.630 0.00 0.00 0.00 2.52
3730 4947 3.844090 GGAGAGGAGCTCGGCCAC 61.844 72.222 7.83 0.00 44.91 5.01
3821 5038 2.586245 CTGGAGCTCCCATCGCAA 59.414 61.111 29.95 8.46 45.57 4.85
3822 5039 4.166888 GCTGGAGCTCCCATCGCA 62.167 66.667 29.95 9.24 45.57 5.10
4078 5295 4.602259 CGCCCACTCACGGTGTGT 62.602 66.667 9.85 9.85 43.94 3.72


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

AutoCloner maintained by Alex Coulton.