Multiple sequence alignment - TraesCS1B01G401300

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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 TraesCS1B01G401300 chr1B 100.000 6287 0 0 1 6287 631822965 631816679 0.000000e+00 11611.0
1 TraesCS1B01G401300 chr1B 93.207 2591 111 26 2649 5200 631831602 631834166 0.000000e+00 3749.0
2 TraesCS1B01G401300 chr1B 88.667 1050 61 24 1241 2249 631829306 631830338 0.000000e+00 1227.0
3 TraesCS1B01G401300 chr1B 92.210 552 32 4 5546 6086 631834207 631834758 0.000000e+00 771.0
4 TraesCS1B01G401300 chr1B 81.622 370 52 10 5930 6287 381387276 381386911 6.160000e-75 292.0
5 TraesCS1B01G401300 chr1B 89.394 198 16 3 6094 6287 631848715 631848911 1.750000e-60 244.0
6 TraesCS1B01G401300 chr1B 82.099 162 27 2 5418 5577 468094689 468094850 3.060000e-28 137.0
7 TraesCS1B01G401300 chr1B 87.379 103 3 5 2365 2461 631830457 631830555 6.660000e-20 110.0
8 TraesCS1B01G401300 chr1B 100.000 28 0 0 5635 5662 631834209 631834182 1.100000e-02 52.8
9 TraesCS1B01G401300 chr1D 94.379 3202 127 26 2649 5813 459836036 459839221 0.000000e+00 4867.0
10 TraesCS1B01G401300 chr1D 90.652 1059 52 20 1241 2268 459831078 459832120 0.000000e+00 1363.0
11 TraesCS1B01G401300 chr1D 88.997 309 26 7 5894 6196 459839636 459839942 5.950000e-100 375.0
12 TraesCS1B01G401300 chr1D 81.918 365 51 9 5934 6287 280687049 280686689 1.710000e-75 294.0
13 TraesCS1B01G401300 chr1D 88.000 200 14 8 906 1096 459829442 459829640 1.760000e-55 228.0
14 TraesCS1B01G401300 chr1D 87.013 154 6 3 2312 2461 459835294 459835437 1.810000e-35 161.0
15 TraesCS1B01G401300 chr1D 97.826 46 1 0 5857 5902 459839410 459839455 5.220000e-11 80.5
16 TraesCS1B01G401300 chr6D 95.490 909 32 3 1 907 76066384 76067285 0.000000e+00 1443.0
17 TraesCS1B01G401300 chr6D 86.036 444 60 2 1592 2034 55882270 55882712 5.700000e-130 475.0
18 TraesCS1B01G401300 chr6D 78.169 568 93 25 3742 4300 55894495 55895040 3.630000e-87 333.0
19 TraesCS1B01G401300 chr1A 91.954 1044 54 10 3040 4064 551541359 551542391 0.000000e+00 1435.0
20 TraesCS1B01G401300 chr1A 88.772 1042 58 23 1241 2249 551540093 551541108 0.000000e+00 1221.0
21 TraesCS1B01G401300 chr1A 95.610 615 20 5 4100 4709 551542371 551542983 0.000000e+00 979.0
22 TraesCS1B01G401300 chr1A 93.285 417 24 2 5546 5958 551543105 551543521 4.170000e-171 612.0
23 TraesCS1B01G401300 chr1A 90.066 302 24 6 5988 6284 551543515 551543815 2.750000e-103 387.0
24 TraesCS1B01G401300 chr1A 82.065 368 52 9 5930 6287 352857499 352857136 1.020000e-77 302.0
25 TraesCS1B01G401300 chr1A 83.851 161 25 1 5419 5578 442539474 442539314 1.090000e-32 152.0
26 TraesCS1B01G401300 chr1A 90.789 76 3 1 5129 5200 551542989 551543064 1.440000e-16 99.0
27 TraesCS1B01G401300 chr1A 100.000 37 0 0 2312 2348 551541231 551541267 1.130000e-07 69.4
28 TraesCS1B01G401300 chrUn 95.800 881 36 1 1 880 201221476 201220596 0.000000e+00 1421.0
29 TraesCS1B01G401300 chrUn 85.714 448 62 2 1591 2037 332753534 332753088 7.380000e-129 472.0
30 TraesCS1B01G401300 chrUn 76.955 486 82 22 3824 4305 468581920 468582379 3.760000e-62 250.0
31 TraesCS1B01G401300 chr7B 95.687 881 32 6 1 880 25661465 25662340 0.000000e+00 1411.0
32 TraesCS1B01G401300 chr7B 94.621 911 41 2 1 910 470293704 470294607 0.000000e+00 1404.0
33 TraesCS1B01G401300 chr7B 93.963 911 46 3 1 910 470242718 470243620 0.000000e+00 1369.0
34 TraesCS1B01G401300 chr2B 94.812 906 39 2 1 905 677977717 677976819 0.000000e+00 1406.0
35 TraesCS1B01G401300 chr2B 94.046 907 43 5 1 905 212000011 211999114 0.000000e+00 1365.0
36 TraesCS1B01G401300 chr2B 94.224 883 47 3 1 880 762353276 762354157 0.000000e+00 1345.0
37 TraesCS1B01G401300 chr2B 83.088 136 21 2 5397 5531 41962508 41962642 8.560000e-24 122.0
38 TraesCS1B01G401300 chr6B 94.092 914 43 4 1 912 229144634 229143730 0.000000e+00 1378.0
39 TraesCS1B01G401300 chr6B 75.831 1233 231 49 3106 4300 125727645 125728848 1.180000e-156 564.0
40 TraesCS1B01G401300 chr6B 83.557 596 98 0 4421 5016 125728992 125729587 5.500000e-155 558.0
41 TraesCS1B01G401300 chr6B 86.036 444 60 2 1592 2034 125725315 125725757 5.700000e-130 475.0
42 TraesCS1B01G401300 chr7D 76.560 1186 229 33 3139 4305 24947564 24946409 6.970000e-169 604.0
43 TraesCS1B01G401300 chr7D 82.775 627 107 1 4411 5036 24946336 24945710 5.500000e-155 558.0
44 TraesCS1B01G401300 chr7D 86.099 446 58 4 1591 2034 25270325 25270768 1.590000e-130 477.0
45 TraesCS1B01G401300 chr7D 74.511 1228 239 46 3109 4309 25190693 25191873 3.430000e-127 466.0
46 TraesCS1B01G401300 chr7A 76.036 1231 234 43 3106 4310 37720388 37721583 3.270000e-162 582.0
47 TraesCS1B01G401300 chr7A 82.464 633 107 2 4405 5036 37721645 37722274 9.210000e-153 551.0
48 TraesCS1B01G401300 chr7A 82.297 627 110 1 4411 5036 25751297 25750671 5.540000e-150 542.0
49 TraesCS1B01G401300 chr7A 74.349 1228 238 49 3109 4305 26031508 26032689 9.610000e-123 451.0
50 TraesCS1B01G401300 chr7A 84.045 445 69 2 1591 2034 26039568 26040011 1.620000e-115 427.0
51 TraesCS1B01G401300 chr4A 82.780 633 108 1 4405 5036 708613693 708614325 1.180000e-156 564.0
52 TraesCS1B01G401300 chr4A 86.343 432 59 0 1603 2034 708610440 708610871 7.380000e-129 472.0
53 TraesCS1B01G401300 chr3A 85.294 204 28 2 5418 5620 377235517 377235719 6.390000e-50 209.0
54 TraesCS1B01G401300 chr3A 83.028 218 35 2 5410 5626 156118358 156118142 4.970000e-46 196.0
55 TraesCS1B01G401300 chr3A 100.000 30 0 0 878 907 111071823 111071852 8.800000e-04 56.5
56 TraesCS1B01G401300 chr5B 85.714 161 22 1 5419 5578 325963962 325963802 1.080000e-37 169.0
57 TraesCS1B01G401300 chr5B 84.568 162 22 3 5418 5578 705607861 705607702 2.350000e-34 158.0
58 TraesCS1B01G401300 chr3B 84.211 171 25 2 5410 5578 178481536 178481706 1.400000e-36 165.0


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 TraesCS1B01G401300 chr1B 631816679 631822965 6286 True 11611.000000 11611 100.000000 1 6287 1 chr1B.!!$R2 6286
1 TraesCS1B01G401300 chr1B 631829306 631834758 5452 False 1464.250000 3749 90.365750 1241 6086 4 chr1B.!!$F3 4845
2 TraesCS1B01G401300 chr1D 459829442 459839942 10500 False 1179.083333 4867 91.144500 906 6196 6 chr1D.!!$F1 5290
3 TraesCS1B01G401300 chr6D 76066384 76067285 901 False 1443.000000 1443 95.490000 1 907 1 chr6D.!!$F3 906
4 TraesCS1B01G401300 chr6D 55894495 55895040 545 False 333.000000 333 78.169000 3742 4300 1 chr6D.!!$F2 558
5 TraesCS1B01G401300 chr1A 551540093 551543815 3722 False 686.057143 1435 92.925143 1241 6284 7 chr1A.!!$F1 5043
6 TraesCS1B01G401300 chrUn 201220596 201221476 880 True 1421.000000 1421 95.800000 1 880 1 chrUn.!!$R1 879
7 TraesCS1B01G401300 chr7B 25661465 25662340 875 False 1411.000000 1411 95.687000 1 880 1 chr7B.!!$F1 879
8 TraesCS1B01G401300 chr7B 470293704 470294607 903 False 1404.000000 1404 94.621000 1 910 1 chr7B.!!$F3 909
9 TraesCS1B01G401300 chr7B 470242718 470243620 902 False 1369.000000 1369 93.963000 1 910 1 chr7B.!!$F2 909
10 TraesCS1B01G401300 chr2B 677976819 677977717 898 True 1406.000000 1406 94.812000 1 905 1 chr2B.!!$R2 904
11 TraesCS1B01G401300 chr2B 211999114 212000011 897 True 1365.000000 1365 94.046000 1 905 1 chr2B.!!$R1 904
12 TraesCS1B01G401300 chr2B 762353276 762354157 881 False 1345.000000 1345 94.224000 1 880 1 chr2B.!!$F2 879
13 TraesCS1B01G401300 chr6B 229143730 229144634 904 True 1378.000000 1378 94.092000 1 912 1 chr6B.!!$R1 911
14 TraesCS1B01G401300 chr6B 125725315 125729587 4272 False 532.333333 564 81.808000 1592 5016 3 chr6B.!!$F1 3424
15 TraesCS1B01G401300 chr7D 24945710 24947564 1854 True 581.000000 604 79.667500 3139 5036 2 chr7D.!!$R1 1897
16 TraesCS1B01G401300 chr7D 25190693 25191873 1180 False 466.000000 466 74.511000 3109 4309 1 chr7D.!!$F1 1200
17 TraesCS1B01G401300 chr7A 37720388 37722274 1886 False 566.500000 582 79.250000 3106 5036 2 chr7A.!!$F3 1930
18 TraesCS1B01G401300 chr7A 25750671 25751297 626 True 542.000000 542 82.297000 4411 5036 1 chr7A.!!$R1 625
19 TraesCS1B01G401300 chr7A 26031508 26032689 1181 False 451.000000 451 74.349000 3109 4305 1 chr7A.!!$F1 1196
20 TraesCS1B01G401300 chr4A 708610440 708614325 3885 False 518.000000 564 84.561500 1603 5036 2 chr4A.!!$F1 3433

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
935 942 0.037697 AGTTGTGAAGCGGACGCATA 60.038 50.0 19.48 1.51 44.88 3.14 F
1105 1129 0.036164 TGGACCGGTGTGATCCTTTG 59.964 55.0 14.63 0.00 0.00 2.77 F
1531 2892 0.108615 CTGGAAGACGCCGACTGATT 60.109 55.0 0.00 0.00 34.07 2.57 F
2028 3404 0.536687 TTCTCGTCGTCCTCACCAGT 60.537 55.0 0.00 0.00 0.00 4.00 F
2385 7039 0.933097 CAGTGTCGTAGCATCATGCC 59.067 55.0 5.84 0.00 46.52 4.40 F
3502 10135 0.981183 ATGGCCTCTTTACGGTGACA 59.019 50.0 3.32 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 3498 0.462047 CGAACCCCAGCACCTACATC 60.462 60.000 0.0 0.0 0.00 3.06 R
2411 7065 1.144057 CCATGACCCGCTACCACTC 59.856 63.158 0.0 0.0 0.00 3.51 R
3423 10048 0.670546 CCAATAGGCGATGGGCGTAG 60.671 60.000 0.0 0.0 44.41 3.51 R
3487 10120 1.616865 TGACCTGTCACCGTAAAGAGG 59.383 52.381 0.0 0.0 34.14 3.69 R
4019 10684 1.668751 TGTGCGTTCAAGTTTGGAGTC 59.331 47.619 0.0 0.0 0.00 3.36 R
5436 12201 1.133792 CCAATTCAATACGGAGCCCCT 60.134 52.381 0.0 0.0 0.00 4.79 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
710 716 2.682155 TGCATGCGTACATTCCACTA 57.318 45.000 14.09 0.00 32.87 2.74
723 729 8.500773 CGTACATTCCACTACAAAAAGTATTGT 58.499 33.333 0.00 0.00 45.14 2.71
730 736 7.016268 TCCACTACAAAAAGTATTGTCTCTCCT 59.984 37.037 0.00 0.00 42.33 3.69
753 759 2.959707 GACATGGACCCTACTAGTCTGG 59.040 54.545 0.00 3.60 34.56 3.86
833 840 3.455910 TGAGCCCTACTTATGCACAGATT 59.544 43.478 1.67 0.00 0.00 2.40
850 857 6.057533 CACAGATTATAAAGCATGTGGAGGA 58.942 40.000 11.77 0.00 35.54 3.71
862 869 2.377810 TGGAGGATGGATGCGGCTT 61.378 57.895 0.00 0.00 0.00 4.35
880 887 3.925090 CGGTACATCCCGCCTCCC 61.925 72.222 0.00 0.00 41.78 4.30
881 888 3.925090 GGTACATCCCGCCTCCCG 61.925 72.222 0.00 0.00 0.00 5.14
882 889 4.603946 GTACATCCCGCCTCCCGC 62.604 72.222 0.00 0.00 35.03 6.13
935 942 0.037697 AGTTGTGAAGCGGACGCATA 60.038 50.000 19.48 1.51 44.88 3.14
939 946 0.855349 GTGAAGCGGACGCATATCAG 59.145 55.000 19.48 0.00 44.88 2.90
940 947 0.459899 TGAAGCGGACGCATATCAGT 59.540 50.000 19.48 0.00 44.88 3.41
941 948 1.679153 TGAAGCGGACGCATATCAGTA 59.321 47.619 19.48 0.00 44.88 2.74
942 949 2.296190 TGAAGCGGACGCATATCAGTAT 59.704 45.455 19.48 0.00 44.88 2.12
943 950 3.504520 TGAAGCGGACGCATATCAGTATA 59.495 43.478 19.48 0.00 44.88 1.47
944 951 4.157840 TGAAGCGGACGCATATCAGTATAT 59.842 41.667 19.48 0.00 44.88 0.86
945 952 4.294416 AGCGGACGCATATCAGTATATC 57.706 45.455 19.48 0.00 44.88 1.63
946 953 3.694566 AGCGGACGCATATCAGTATATCA 59.305 43.478 19.48 0.00 44.88 2.15
983 1006 2.093106 CACGGCCTCAACTAGACTACT 58.907 52.381 0.00 0.00 0.00 2.57
987 1010 2.691011 GGCCTCAACTAGACTACTCCTG 59.309 54.545 0.00 0.00 0.00 3.86
1034 1058 2.468532 AAAAACACTCAAAGCGACCG 57.531 45.000 0.00 0.00 0.00 4.79
1096 1120 2.751436 GCATGCATGGACCGGTGT 60.751 61.111 27.34 0.00 0.00 4.16
1097 1121 3.055080 GCATGCATGGACCGGTGTG 62.055 63.158 27.34 9.55 0.00 3.82
1098 1122 1.377072 CATGCATGGACCGGTGTGA 60.377 57.895 14.63 0.00 0.00 3.58
1102 1126 1.907739 CATGGACCGGTGTGATCCT 59.092 57.895 14.63 0.00 0.00 3.24
1104 1128 0.991920 ATGGACCGGTGTGATCCTTT 59.008 50.000 14.63 0.00 0.00 3.11
1105 1129 0.036164 TGGACCGGTGTGATCCTTTG 59.964 55.000 14.63 0.00 0.00 2.77
1106 1130 0.676782 GGACCGGTGTGATCCTTTGG 60.677 60.000 14.63 0.00 0.00 3.28
1109 1133 1.700739 ACCGGTGTGATCCTTTGGTAA 59.299 47.619 6.12 0.00 0.00 2.85
1110 1134 2.106857 ACCGGTGTGATCCTTTGGTAAA 59.893 45.455 6.12 0.00 0.00 2.01
1111 1135 3.245122 ACCGGTGTGATCCTTTGGTAAAT 60.245 43.478 6.12 0.00 0.00 1.40
1112 1136 3.377172 CCGGTGTGATCCTTTGGTAAATC 59.623 47.826 0.00 0.00 0.00 2.17
1113 1137 4.261801 CGGTGTGATCCTTTGGTAAATCT 58.738 43.478 0.00 0.00 0.00 2.40
1115 1139 6.055588 CGGTGTGATCCTTTGGTAAATCTAT 58.944 40.000 0.00 0.00 0.00 1.98
1117 1141 7.878127 CGGTGTGATCCTTTGGTAAATCTATAT 59.122 37.037 0.00 0.00 0.00 0.86
1118 1142 9.574516 GGTGTGATCCTTTGGTAAATCTATATT 57.425 33.333 0.00 0.00 0.00 1.28
1143 1167 6.573664 TGTTAATCTGGTTATATGCATGCC 57.426 37.500 16.68 6.95 0.00 4.40
1144 1168 5.181056 TGTTAATCTGGTTATATGCATGCCG 59.819 40.000 16.68 3.81 0.00 5.69
1145 1169 2.928801 TCTGGTTATATGCATGCCGT 57.071 45.000 16.68 6.58 0.00 5.68
1146 1170 4.551702 ATCTGGTTATATGCATGCCGTA 57.448 40.909 16.68 8.83 0.00 4.02
1148 1172 4.062293 TCTGGTTATATGCATGCCGTAAC 58.938 43.478 16.68 18.92 0.00 2.50
1149 1173 4.065088 CTGGTTATATGCATGCCGTAACT 58.935 43.478 24.01 7.38 0.00 2.24
1151 1175 5.234752 TGGTTATATGCATGCCGTAACTAG 58.765 41.667 24.01 0.00 0.00 2.57
1152 1176 5.221561 TGGTTATATGCATGCCGTAACTAGT 60.222 40.000 24.01 0.00 0.00 2.57
1153 1177 5.120208 GGTTATATGCATGCCGTAACTAGTG 59.880 44.000 24.01 0.00 0.00 2.74
1155 1179 2.753055 TGCATGCCGTAACTAGTGAA 57.247 45.000 16.68 0.00 0.00 3.18
1157 1181 3.605634 TGCATGCCGTAACTAGTGAAAT 58.394 40.909 16.68 0.00 0.00 2.17
1158 1182 3.373748 TGCATGCCGTAACTAGTGAAATG 59.626 43.478 16.68 0.00 0.00 2.32
1161 1185 2.303600 TGCCGTAACTAGTGAAATGGGT 59.696 45.455 0.00 0.00 0.00 4.51
1162 1186 2.676342 GCCGTAACTAGTGAAATGGGTG 59.324 50.000 0.00 0.00 0.00 4.61
1163 1187 3.618019 GCCGTAACTAGTGAAATGGGTGA 60.618 47.826 0.00 0.00 0.00 4.02
1164 1188 4.571919 CCGTAACTAGTGAAATGGGTGAA 58.428 43.478 0.00 0.00 0.00 3.18
1165 1189 4.998672 CCGTAACTAGTGAAATGGGTGAAA 59.001 41.667 0.00 0.00 0.00 2.69
1169 2143 7.762615 CGTAACTAGTGAAATGGGTGAAATCTA 59.237 37.037 0.00 0.00 0.00 1.98
1170 2144 9.444600 GTAACTAGTGAAATGGGTGAAATCTAA 57.555 33.333 0.00 0.00 0.00 2.10
1171 2145 7.923414 ACTAGTGAAATGGGTGAAATCTAAC 57.077 36.000 0.00 0.00 0.00 2.34
1176 2150 6.378280 GTGAAATGGGTGAAATCTAACCAGAT 59.622 38.462 0.00 0.00 43.67 2.90
1180 2154 5.437060 TGGGTGAAATCTAACCAGATAAGC 58.563 41.667 0.00 0.00 40.81 3.09
1183 2157 6.547510 GGGTGAAATCTAACCAGATAAGCAAT 59.452 38.462 0.00 0.00 40.81 3.56
1184 2158 7.420800 GGTGAAATCTAACCAGATAAGCAATG 58.579 38.462 0.00 0.00 40.81 2.82
1186 2160 7.912250 GTGAAATCTAACCAGATAAGCAATGTG 59.088 37.037 0.00 0.00 40.81 3.21
1187 2161 7.828717 TGAAATCTAACCAGATAAGCAATGTGA 59.171 33.333 0.00 0.00 40.81 3.58
1188 2162 8.757982 AAATCTAACCAGATAAGCAATGTGAT 57.242 30.769 0.00 0.00 40.81 3.06
1194 2168 5.954150 ACCAGATAAGCAATGTGATCCTTTT 59.046 36.000 0.00 0.00 30.31 2.27
1212 2186 2.884663 TTTTACTTATGTGGCGCGTG 57.115 45.000 8.43 0.00 0.00 5.34
1213 2187 1.798283 TTTACTTATGTGGCGCGTGT 58.202 45.000 8.43 0.00 0.00 4.49
1214 2188 1.072391 TTACTTATGTGGCGCGTGTG 58.928 50.000 8.43 0.00 0.00 3.82
1215 2189 0.244178 TACTTATGTGGCGCGTGTGA 59.756 50.000 8.43 0.00 0.00 3.58
1226 2497 1.927174 GCGCGTGTGATCTTGATAAGT 59.073 47.619 8.43 0.00 0.00 2.24
1242 2559 2.592102 AAGTGTGCCATGTGATCCTT 57.408 45.000 0.00 0.00 0.00 3.36
1357 2674 5.259632 ACAAGCTTCCAGAGAGCATAATTT 58.740 37.500 0.00 0.00 42.56 1.82
1373 2690 5.048083 GCATAATTTCAAGTCCCAACACTCA 60.048 40.000 0.00 0.00 0.00 3.41
1444 2791 2.660258 AAGACCACCACGACCAGCAC 62.660 60.000 0.00 0.00 0.00 4.40
1478 2825 1.214589 GCTCCACTTCGTAAGCCGA 59.785 57.895 0.00 0.00 45.66 5.54
1507 2867 2.414691 GCTCAATCTTTTTCTGGGCGTC 60.415 50.000 0.00 0.00 0.00 5.19
1508 2868 2.813754 CTCAATCTTTTTCTGGGCGTCA 59.186 45.455 0.00 0.00 0.00 4.35
1509 2869 3.218453 TCAATCTTTTTCTGGGCGTCAA 58.782 40.909 0.00 0.00 0.00 3.18
1510 2870 3.004315 TCAATCTTTTTCTGGGCGTCAAC 59.996 43.478 0.00 0.00 0.00 3.18
1522 2883 1.853319 CGTCAACACTGGAAGACGC 59.147 57.895 0.00 0.00 45.68 5.19
1523 2884 1.557443 CGTCAACACTGGAAGACGCC 61.557 60.000 0.00 0.00 45.68 5.68
1525 2886 1.300620 CAACACTGGAAGACGCCGA 60.301 57.895 0.00 0.00 37.43 5.54
1529 2890 1.901948 ACTGGAAGACGCCGACTGA 60.902 57.895 0.00 0.00 37.43 3.41
1530 2891 1.251527 ACTGGAAGACGCCGACTGAT 61.252 55.000 0.00 0.00 37.43 2.90
1531 2892 0.108615 CTGGAAGACGCCGACTGATT 60.109 55.000 0.00 0.00 34.07 2.57
1532 2893 1.134367 CTGGAAGACGCCGACTGATTA 59.866 52.381 0.00 0.00 34.07 1.75
1542 2903 2.724839 GCCGACTGATTAACGTTGCTTG 60.725 50.000 11.99 0.00 0.00 4.01
1548 2909 5.057149 ACTGATTAACGTTGCTTGACTTCT 58.943 37.500 11.99 0.00 0.00 2.85
1549 2910 5.050091 ACTGATTAACGTTGCTTGACTTCTG 60.050 40.000 11.99 3.27 0.00 3.02
1567 2928 3.807538 GTGCAGTGCAGCCATCGG 61.808 66.667 20.42 0.00 40.08 4.18
1915 3291 2.001357 CACGTGCTCATCACCATCG 58.999 57.895 0.82 0.00 42.69 3.84
2028 3404 0.536687 TTCTCGTCGTCCTCACCAGT 60.537 55.000 0.00 0.00 0.00 4.00
2116 3498 1.227380 GTACTCTGCTCGGCCATGG 60.227 63.158 7.63 7.63 0.00 3.66
2136 3518 2.436115 GTAGGTGCTGGGGTTCGC 60.436 66.667 0.00 0.00 0.00 4.70
2255 3638 8.494433 TCTGAATCTGCCATAAATTAGTTACCT 58.506 33.333 0.00 0.00 0.00 3.08
2284 3667 5.403897 AAATACAACGTCACTTCACACAG 57.596 39.130 0.00 0.00 0.00 3.66
2285 3668 2.665649 ACAACGTCACTTCACACAGA 57.334 45.000 0.00 0.00 0.00 3.41
2286 3669 3.179443 ACAACGTCACTTCACACAGAT 57.821 42.857 0.00 0.00 0.00 2.90
2287 3670 3.531538 ACAACGTCACTTCACACAGATT 58.468 40.909 0.00 0.00 0.00 2.40
2290 3673 5.758296 ACAACGTCACTTCACACAGATTATT 59.242 36.000 0.00 0.00 0.00 1.40
2292 3838 7.116376 ACAACGTCACTTCACACAGATTATTAG 59.884 37.037 0.00 0.00 0.00 1.73
2359 7013 6.814506 TTCTTATACGTACCTAGATCAGCC 57.185 41.667 0.00 0.00 0.00 4.85
2360 7014 5.872963 TCTTATACGTACCTAGATCAGCCA 58.127 41.667 0.00 0.00 0.00 4.75
2361 7015 5.704515 TCTTATACGTACCTAGATCAGCCAC 59.295 44.000 0.00 0.00 0.00 5.01
2362 7016 2.438800 ACGTACCTAGATCAGCCACT 57.561 50.000 0.00 0.00 0.00 4.00
2363 7017 2.025155 ACGTACCTAGATCAGCCACTG 58.975 52.381 0.00 0.00 0.00 3.66
2385 7039 0.933097 CAGTGTCGTAGCATCATGCC 59.067 55.000 5.84 0.00 46.52 4.40
2411 7065 7.909267 TGACGAATTGTTCTAGCTAATGATTG 58.091 34.615 0.00 0.00 0.00 2.67
2412 7066 7.763985 TGACGAATTGTTCTAGCTAATGATTGA 59.236 33.333 0.00 0.00 0.00 2.57
2413 7067 8.136057 ACGAATTGTTCTAGCTAATGATTGAG 57.864 34.615 0.00 0.00 0.00 3.02
2414 7068 7.766278 ACGAATTGTTCTAGCTAATGATTGAGT 59.234 33.333 0.00 0.00 0.00 3.41
2415 7069 8.060679 CGAATTGTTCTAGCTAATGATTGAGTG 58.939 37.037 0.00 0.00 0.00 3.51
2418 7072 7.418337 TGTTCTAGCTAATGATTGAGTGGTA 57.582 36.000 0.00 0.00 0.00 3.25
2420 7074 6.090483 TCTAGCTAATGATTGAGTGGTAGC 57.910 41.667 0.00 0.00 35.32 3.58
2421 7075 3.722147 AGCTAATGATTGAGTGGTAGCG 58.278 45.455 0.00 0.00 39.12 4.26
2461 7121 4.393062 CAGCCTTGAATGTTAGGTAGTGTG 59.607 45.833 0.00 0.00 33.91 3.82
2463 7123 5.001232 GCCTTGAATGTTAGGTAGTGTGAA 58.999 41.667 0.00 0.00 33.91 3.18
2464 7124 5.648092 GCCTTGAATGTTAGGTAGTGTGAAT 59.352 40.000 0.00 0.00 33.91 2.57
2465 7125 6.821665 GCCTTGAATGTTAGGTAGTGTGAATA 59.178 38.462 0.00 0.00 33.91 1.75
2466 7126 7.011482 GCCTTGAATGTTAGGTAGTGTGAATAG 59.989 40.741 0.00 0.00 33.91 1.73
2467 7127 8.041323 CCTTGAATGTTAGGTAGTGTGAATAGT 58.959 37.037 0.00 0.00 0.00 2.12
2503 7518 6.536582 ACATTCGATTCTATCACTTTCCTGTG 59.463 38.462 0.00 0.00 39.15 3.66
2504 7519 4.433615 TCGATTCTATCACTTTCCTGTGC 58.566 43.478 0.00 0.00 37.81 4.57
2505 7520 4.081697 TCGATTCTATCACTTTCCTGTGCA 60.082 41.667 0.00 0.00 37.81 4.57
2506 7521 4.631377 CGATTCTATCACTTTCCTGTGCAA 59.369 41.667 0.00 0.00 37.81 4.08
2507 7522 5.295292 CGATTCTATCACTTTCCTGTGCAAT 59.705 40.000 0.00 0.00 37.81 3.56
2531 7546 7.425577 TCACTTAGACACTGACATGAAATTG 57.574 36.000 0.00 0.00 0.00 2.32
2600 8032 2.853731 AACTTCTGGATCGAGCTACG 57.146 50.000 0.00 0.00 44.09 3.51
2624 8056 6.468956 CGAAAATGGACAGAAATCAATTACCG 59.531 38.462 0.00 0.00 0.00 4.02
2646 8078 8.575649 ACCGATTCAAGAATAAAACCATTACT 57.424 30.769 0.00 0.00 0.00 2.24
2720 8858 6.462073 TTCTGTGAAGCTAACGACAATAAC 57.538 37.500 0.00 0.00 0.00 1.89
2806 9191 9.613428 CCAAAGATTCAATCACCTACTGTATTA 57.387 33.333 0.00 0.00 0.00 0.98
2862 9252 3.138283 TCCTGAACTGAGGTCCACAATTT 59.862 43.478 0.00 0.00 34.36 1.82
2891 9281 5.639757 TGCATGGATAAATTTGTGACTTCG 58.360 37.500 0.00 0.00 0.00 3.79
2914 9304 1.303309 ATTAGCAAGCACGCTCATCC 58.697 50.000 2.81 0.00 42.62 3.51
2992 9506 4.935702 TCAGCACTTTGTCAGGAAATTTG 58.064 39.130 0.00 0.00 0.00 2.32
3015 9529 7.820044 TGTAACAGTTTGTTGAAATGAAACC 57.180 32.000 4.78 0.00 41.30 3.27
3021 9535 6.632834 CAGTTTGTTGAAATGAAACCTCTACG 59.367 38.462 0.00 0.00 35.41 3.51
3034 9548 8.976986 TGAAACCTCTACGAACTAATAAGAAC 57.023 34.615 0.00 0.00 0.00 3.01
3045 9559 9.250624 ACGAACTAATAAGAACATAGAATGAGC 57.749 33.333 0.00 0.00 0.00 4.26
3087 9601 8.322906 TGAACAAGTAACTTACAGATTCATGG 57.677 34.615 1.79 0.00 0.00 3.66
3182 9807 1.462616 TTCTTCATGGTGGCATTCGG 58.537 50.000 0.00 0.00 0.00 4.30
3207 9832 5.629079 GCAGTTTTGCCTACTACATCTTT 57.371 39.130 0.00 0.00 44.74 2.52
3211 9836 6.206634 CAGTTTTGCCTACTACATCTTTCCAA 59.793 38.462 0.00 0.00 0.00 3.53
3423 10048 2.139118 GCGGGCTTCTTCATCTACATC 58.861 52.381 0.00 0.00 0.00 3.06
3498 10131 1.568504 TCAGATGGCCTCTTTACGGT 58.431 50.000 3.32 0.00 29.16 4.83
3502 10135 0.981183 ATGGCCTCTTTACGGTGACA 59.019 50.000 3.32 0.00 0.00 3.58
3643 10276 4.043200 GCTTGCCTGACCGCAACC 62.043 66.667 0.00 0.00 43.65 3.77
3764 10428 3.384467 ACTTGTGTCCAGTGAAATTTGGG 59.616 43.478 0.00 0.00 35.13 4.12
4320 11007 4.142643 GGTCAGCTACTACACTAGTCACAC 60.143 50.000 0.00 0.00 40.14 3.82
4345 11032 2.600470 ACGACCGTTACTTGTCCAAA 57.400 45.000 0.00 0.00 0.00 3.28
4346 11033 2.476821 ACGACCGTTACTTGTCCAAAG 58.523 47.619 0.00 0.00 0.00 2.77
4347 11034 2.159057 ACGACCGTTACTTGTCCAAAGT 60.159 45.455 0.00 0.00 0.00 2.66
4558 11311 4.814771 CCTGTCCTTACGACCATTTATTCC 59.185 45.833 0.00 0.00 41.18 3.01
4608 11361 1.941812 CCCACGCAGAATATTCGGC 59.058 57.895 25.19 25.19 43.50 5.54
4743 11496 1.689243 ATATGCCTGTGCTGCTCGGA 61.689 55.000 11.85 0.00 38.71 4.55
4866 11619 5.734720 TGGTGGAAGAGACACAATTATCTC 58.265 41.667 5.72 5.72 41.50 2.75
5220 11984 1.260544 ATTGCTTTCAGGTGCCCTTC 58.739 50.000 0.00 0.00 0.00 3.46
5244 12008 2.035832 GCTGCTTTGGCTTTAAAGGTCA 59.964 45.455 16.78 2.91 37.96 4.02
5285 12049 8.954950 ACATAGGAATAGAGAACATCAGTTTG 57.045 34.615 0.00 0.00 38.30 2.93
5312 12076 1.150986 TGGGGAAATGGTTTGGATGGT 59.849 47.619 0.00 0.00 0.00 3.55
5356 12120 8.397172 AGGTATAACTATAGAAGAATACCCGGT 58.603 37.037 20.97 0.00 42.53 5.28
5363 12127 9.240734 ACTATAGAAGAATACCCGGTACATAAG 57.759 37.037 6.78 0.00 0.00 1.73
5386 12150 4.559862 AAGAATCTTCTCGTCCATGGTT 57.440 40.909 12.58 0.00 36.28 3.67
5388 12152 3.515502 AGAATCTTCTCGTCCATGGTTGA 59.484 43.478 12.58 9.93 29.94 3.18
5436 12201 5.812127 CGATCTGTTTGGATGTCTGTATTGA 59.188 40.000 0.00 0.00 0.00 2.57
5460 12225 2.099098 GGCTCCGTATTGAATTGGTTGG 59.901 50.000 0.00 0.00 0.00 3.77
5485 12250 2.053627 CCAAATCAGCAACGAAACTGC 58.946 47.619 0.00 0.00 40.24 4.40
5534 12299 2.450476 AGATGTTCACTGAATTGGCCC 58.550 47.619 0.00 0.00 0.00 5.80
5537 12302 1.894466 TGTTCACTGAATTGGCCCATG 59.106 47.619 0.00 0.00 0.00 3.66
5540 12305 1.076841 TCACTGAATTGGCCCATGGAA 59.923 47.619 15.22 0.00 0.00 3.53
5591 12356 4.037446 TGTTTGGATGGCAAACTCTGTAAC 59.963 41.667 1.28 0.00 41.58 2.50
5595 12360 2.340210 TGGCAAACTCTGTAACTGCA 57.660 45.000 0.00 0.00 34.66 4.41
5603 12368 6.669977 GCAAACTCTGTAACTGCATAGTAACG 60.670 42.308 0.00 0.00 35.69 3.18
5633 12398 5.412640 TGAAGATAATGCCTTGCACATTTG 58.587 37.500 6.37 0.00 43.04 2.32
5674 12439 4.134563 ACCCAAATTCGGATAATTCGAGG 58.865 43.478 0.00 0.00 37.93 4.63
5778 12548 4.749245 AATCAACTGTTCTACGGCAAAG 57.251 40.909 0.00 0.00 0.00 2.77
5854 12786 5.004448 TGCATTCGGTAAACACATTCCTTA 58.996 37.500 0.00 0.00 0.00 2.69
5908 13029 6.072618 ACTGACGATAGGAGGTAACGATAATG 60.073 42.308 0.00 0.00 42.33 1.90
5909 13030 5.766670 TGACGATAGGAGGTAACGATAATGT 59.233 40.000 0.00 0.00 42.33 2.71
5958 13079 6.526674 GTCTCGCCTTTTATAACAAAACCATG 59.473 38.462 0.00 0.00 0.00 3.66
5966 13087 0.463620 AACAAAACCATGCGCCTTGT 59.536 45.000 4.18 2.10 0.00 3.16
6023 13144 5.112686 TGAAATTGGTTTACCTGTTGCAAC 58.887 37.500 22.83 22.83 36.82 4.17
6052 13176 2.236395 CGGGGTAAACTGGAGAGTTCAT 59.764 50.000 0.00 0.00 41.87 2.57
6088 13212 5.362556 AATTTCTTCAACGTCATGTCTGG 57.637 39.130 0.00 0.00 0.00 3.86
6091 13215 2.560981 TCTTCAACGTCATGTCTGGCTA 59.439 45.455 0.00 0.00 0.00 3.93
6092 13216 3.006430 TCTTCAACGTCATGTCTGGCTAA 59.994 43.478 0.00 0.00 0.00 3.09
6093 13217 2.959516 TCAACGTCATGTCTGGCTAAG 58.040 47.619 0.00 0.00 0.00 2.18
6124 13249 4.627467 GTGTAAGCTATGAGTGACCAACTG 59.373 45.833 0.00 0.00 40.07 3.16
6208 13334 6.990349 CAGAAAATTATACATAGGTCCCACGT 59.010 38.462 0.00 0.00 0.00 4.49
6219 13345 2.140717 GGTCCCACGTTCACAAGTAAG 58.859 52.381 0.00 0.00 0.00 2.34
6244 13370 1.225855 TAACTGAAGCAACGGCACTG 58.774 50.000 0.00 0.00 44.61 3.66
6248 13374 1.601903 CTGAAGCAACGGCACTGTAAA 59.398 47.619 0.00 0.00 44.61 2.01
6284 13410 4.437239 ACTTACTCTGCAGAAATCCATCG 58.563 43.478 18.85 5.82 0.00 3.84
6285 13411 4.160439 ACTTACTCTGCAGAAATCCATCGA 59.840 41.667 18.85 0.00 0.00 3.59
6286 13412 3.834489 ACTCTGCAGAAATCCATCGAT 57.166 42.857 18.85 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 159 7.956420 ACGACTTTTTCATTGTGTGATACTA 57.044 32.000 0.00 0.00 36.54 1.82
370 372 8.043113 TGTGAGTTTCATATTCTAGCTTGTGAT 58.957 33.333 0.00 0.00 0.00 3.06
710 716 7.054124 TGTCAAGGAGAGACAATACTTTTTGT 58.946 34.615 0.00 0.00 42.57 2.83
723 729 1.079490 AGGGTCCATGTCAAGGAGAGA 59.921 52.381 0.00 0.00 35.42 3.10
730 736 4.023980 CAGACTAGTAGGGTCCATGTCAA 58.976 47.826 0.00 0.00 34.56 3.18
772 778 8.598916 TCATGTATTAAGACAGGTGACCTTTTA 58.401 33.333 13.87 0.00 32.97 1.52
833 840 5.563592 CATCCATCCTCCACATGCTTTATA 58.436 41.667 0.00 0.00 0.00 0.98
850 857 1.227556 GTACCGAAGCCGCATCCAT 60.228 57.895 0.00 0.00 0.00 3.41
883 890 3.551551 CGCAAACTCCTTTTTACCGAAG 58.448 45.455 0.00 0.00 0.00 3.79
884 891 2.291190 CCGCAAACTCCTTTTTACCGAA 59.709 45.455 0.00 0.00 0.00 4.30
885 892 1.874872 CCGCAAACTCCTTTTTACCGA 59.125 47.619 0.00 0.00 0.00 4.69
886 893 1.068816 CCCGCAAACTCCTTTTTACCG 60.069 52.381 0.00 0.00 0.00 4.02
924 931 3.694566 TGATATACTGATATGCGTCCGCT 59.305 43.478 13.31 1.40 42.51 5.52
935 942 8.082852 GTCATGGAGTAAACGTGATATACTGAT 58.917 37.037 7.93 0.16 36.38 2.90
939 946 5.116680 GCGTCATGGAGTAAACGTGATATAC 59.883 44.000 0.00 0.00 36.38 1.47
940 947 5.217393 GCGTCATGGAGTAAACGTGATATA 58.783 41.667 0.00 0.00 36.38 0.86
941 948 4.049186 GCGTCATGGAGTAAACGTGATAT 58.951 43.478 0.00 0.00 36.38 1.63
942 949 3.119424 TGCGTCATGGAGTAAACGTGATA 60.119 43.478 0.00 0.00 36.38 2.15
943 950 2.268298 GCGTCATGGAGTAAACGTGAT 58.732 47.619 0.00 0.00 36.38 3.06
944 951 1.000052 TGCGTCATGGAGTAAACGTGA 60.000 47.619 0.00 0.00 37.45 4.35
945 952 1.126113 GTGCGTCATGGAGTAAACGTG 59.874 52.381 0.00 0.00 37.45 4.49
946 953 1.425412 GTGCGTCATGGAGTAAACGT 58.575 50.000 4.57 0.00 37.45 3.99
983 1006 1.444119 GCTTGCGGTGTTGAACAGGA 61.444 55.000 0.00 0.00 0.00 3.86
987 1010 1.082756 CGAGCTTGCGGTGTTGAAC 60.083 57.895 0.00 0.00 0.00 3.18
1048 1072 0.093026 GAGACGCGCACACACATTAC 59.907 55.000 5.73 0.00 0.00 1.89
1073 1097 1.525941 CGGTCCATGCATGCATATGA 58.474 50.000 31.73 26.03 36.36 2.15
1117 1141 7.925483 GGCATGCATATAACCAGATTAACAAAA 59.075 33.333 21.36 0.00 0.00 2.44
1118 1142 7.432869 GGCATGCATATAACCAGATTAACAAA 58.567 34.615 21.36 0.00 0.00 2.83
1119 1143 6.293900 CGGCATGCATATAACCAGATTAACAA 60.294 38.462 21.36 0.00 0.00 2.83
1120 1144 5.181056 CGGCATGCATATAACCAGATTAACA 59.819 40.000 21.36 0.00 0.00 2.41
1121 1145 5.181245 ACGGCATGCATATAACCAGATTAAC 59.819 40.000 21.36 0.00 0.00 2.01
1122 1146 5.312895 ACGGCATGCATATAACCAGATTAA 58.687 37.500 21.36 0.00 0.00 1.40
1124 1148 3.754965 ACGGCATGCATATAACCAGATT 58.245 40.909 21.36 0.00 0.00 2.40
1125 1149 3.423539 ACGGCATGCATATAACCAGAT 57.576 42.857 21.36 0.00 0.00 2.90
1126 1150 2.928801 ACGGCATGCATATAACCAGA 57.071 45.000 21.36 0.00 0.00 3.86
1127 1151 4.065088 AGTTACGGCATGCATATAACCAG 58.935 43.478 21.36 1.31 0.00 4.00
1128 1152 4.079980 AGTTACGGCATGCATATAACCA 57.920 40.909 21.36 0.00 0.00 3.67
1129 1153 5.120208 CACTAGTTACGGCATGCATATAACC 59.880 44.000 21.36 8.97 0.00 2.85
1130 1154 5.924254 TCACTAGTTACGGCATGCATATAAC 59.076 40.000 21.36 21.38 0.00 1.89
1131 1155 6.091718 TCACTAGTTACGGCATGCATATAA 57.908 37.500 21.36 11.38 0.00 0.98
1132 1156 5.715434 TCACTAGTTACGGCATGCATATA 57.285 39.130 21.36 5.33 0.00 0.86
1133 1157 4.600692 TCACTAGTTACGGCATGCATAT 57.399 40.909 21.36 6.41 0.00 1.78
1135 1159 2.979814 TCACTAGTTACGGCATGCAT 57.020 45.000 21.36 9.61 0.00 3.96
1136 1160 2.753055 TTCACTAGTTACGGCATGCA 57.247 45.000 21.36 0.00 0.00 3.96
1137 1161 3.242739 CCATTTCACTAGTTACGGCATGC 60.243 47.826 9.90 9.90 0.00 4.06
1138 1162 3.312421 CCCATTTCACTAGTTACGGCATG 59.688 47.826 0.00 0.00 0.00 4.06
1139 1163 3.054655 ACCCATTTCACTAGTTACGGCAT 60.055 43.478 0.00 0.00 0.00 4.40
1140 1164 2.303600 ACCCATTTCACTAGTTACGGCA 59.696 45.455 0.00 0.00 0.00 5.69
1141 1165 2.676342 CACCCATTTCACTAGTTACGGC 59.324 50.000 0.00 0.00 0.00 5.68
1143 1167 6.594159 AGATTTCACCCATTTCACTAGTTACG 59.406 38.462 0.00 0.00 0.00 3.18
1144 1168 7.923414 AGATTTCACCCATTTCACTAGTTAC 57.077 36.000 0.00 0.00 0.00 2.50
1145 1169 9.444600 GTTAGATTTCACCCATTTCACTAGTTA 57.555 33.333 0.00 0.00 0.00 2.24
1146 1170 7.393515 GGTTAGATTTCACCCATTTCACTAGTT 59.606 37.037 0.00 0.00 0.00 2.24
1148 1172 6.884295 TGGTTAGATTTCACCCATTTCACTAG 59.116 38.462 0.00 0.00 31.24 2.57
1149 1173 6.785076 TGGTTAGATTTCACCCATTTCACTA 58.215 36.000 0.00 0.00 31.24 2.74
1151 1175 5.710099 TCTGGTTAGATTTCACCCATTTCAC 59.290 40.000 0.00 0.00 31.24 3.18
1152 1176 5.886609 TCTGGTTAGATTTCACCCATTTCA 58.113 37.500 0.00 0.00 31.24 2.69
1153 1177 8.519799 TTATCTGGTTAGATTTCACCCATTTC 57.480 34.615 0.00 0.00 40.79 2.17
1155 1179 6.547510 GCTTATCTGGTTAGATTTCACCCATT 59.452 38.462 0.00 0.00 40.79 3.16
1157 1181 5.045213 TGCTTATCTGGTTAGATTTCACCCA 60.045 40.000 0.00 0.00 40.79 4.51
1158 1182 5.437060 TGCTTATCTGGTTAGATTTCACCC 58.563 41.667 0.00 0.00 40.79 4.61
1161 1185 7.828717 TCACATTGCTTATCTGGTTAGATTTCA 59.171 33.333 0.00 0.00 40.79 2.69
1162 1186 8.213518 TCACATTGCTTATCTGGTTAGATTTC 57.786 34.615 0.00 0.00 40.79 2.17
1163 1187 8.757982 ATCACATTGCTTATCTGGTTAGATTT 57.242 30.769 0.00 0.00 40.79 2.17
1164 1188 7.446625 GGATCACATTGCTTATCTGGTTAGATT 59.553 37.037 0.00 0.00 40.79 2.40
1165 1189 6.939163 GGATCACATTGCTTATCTGGTTAGAT 59.061 38.462 0.00 0.00 45.45 1.98
1169 2143 5.121380 AGGATCACATTGCTTATCTGGTT 57.879 39.130 0.00 0.00 0.00 3.67
1170 2144 4.785346 AGGATCACATTGCTTATCTGGT 57.215 40.909 0.00 0.00 0.00 4.00
1171 2145 6.461110 AAAAGGATCACATTGCTTATCTGG 57.539 37.500 0.00 0.00 0.00 3.86
1194 2168 1.461512 CACACGCGCCACATAAGTAAA 59.538 47.619 5.73 0.00 0.00 2.01
1197 2171 0.391130 ATCACACGCGCCACATAAGT 60.391 50.000 5.73 0.00 0.00 2.24
1199 2173 0.108377 AGATCACACGCGCCACATAA 60.108 50.000 5.73 0.00 0.00 1.90
1201 2175 1.375908 AAGATCACACGCGCCACAT 60.376 52.632 5.73 0.00 0.00 3.21
1203 2177 1.361668 ATCAAGATCACACGCGCCAC 61.362 55.000 5.73 0.00 0.00 5.01
1204 2178 0.174617 TATCAAGATCACACGCGCCA 59.825 50.000 5.73 0.00 0.00 5.69
1205 2179 1.258982 CTTATCAAGATCACACGCGCC 59.741 52.381 5.73 0.00 0.00 6.53
1206 2180 1.927174 ACTTATCAAGATCACACGCGC 59.073 47.619 5.73 0.00 0.00 6.86
1207 2181 2.923655 ACACTTATCAAGATCACACGCG 59.076 45.455 3.53 3.53 0.00 6.01
1208 2182 3.484229 GCACACTTATCAAGATCACACGC 60.484 47.826 0.00 0.00 0.00 5.34
1209 2183 3.062639 GGCACACTTATCAAGATCACACG 59.937 47.826 0.00 0.00 0.00 4.49
1210 2184 4.002982 TGGCACACTTATCAAGATCACAC 58.997 43.478 0.00 0.00 0.00 3.82
1211 2185 4.284829 TGGCACACTTATCAAGATCACA 57.715 40.909 0.00 0.00 0.00 3.58
1226 2497 1.891889 CCCAAAGGATCACATGGCACA 60.892 52.381 0.00 0.00 38.17 4.57
1242 2559 3.864983 AAGCTCCCCGAGTCCCCAA 62.865 63.158 0.00 0.00 31.39 4.12
1357 2674 3.392947 TGGTTATGAGTGTTGGGACTTGA 59.607 43.478 0.00 0.00 0.00 3.02
1373 2690 1.439543 GAGGAGGAGGCCATGGTTAT 58.560 55.000 14.67 0.00 0.00 1.89
1481 2828 3.181493 CCCAGAAAAAGATTGAGCCGATG 60.181 47.826 0.00 0.00 0.00 3.84
1491 2851 2.293399 GTGTTGACGCCCAGAAAAAGAT 59.707 45.455 0.00 0.00 0.00 2.40
1494 2854 1.403679 CAGTGTTGACGCCCAGAAAAA 59.596 47.619 0.00 0.00 0.00 1.94
1507 2867 1.300620 TCGGCGTCTTCCAGTGTTG 60.301 57.895 6.85 0.00 0.00 3.33
1508 2868 1.300697 GTCGGCGTCTTCCAGTGTT 60.301 57.895 6.85 0.00 0.00 3.32
1509 2869 2.201022 AGTCGGCGTCTTCCAGTGT 61.201 57.895 6.85 0.00 0.00 3.55
1510 2870 1.734477 CAGTCGGCGTCTTCCAGTG 60.734 63.158 6.85 0.00 0.00 3.66
1522 2883 2.734606 TCAAGCAACGTTAATCAGTCGG 59.265 45.455 0.00 0.00 0.00 4.79
1523 2884 3.428870 AGTCAAGCAACGTTAATCAGTCG 59.571 43.478 0.00 0.00 0.00 4.18
1525 2886 5.050091 CAGAAGTCAAGCAACGTTAATCAGT 60.050 40.000 0.00 0.00 0.00 3.41
1529 2890 4.024048 CACCAGAAGTCAAGCAACGTTAAT 60.024 41.667 0.00 0.00 0.00 1.40
1530 2891 3.311322 CACCAGAAGTCAAGCAACGTTAA 59.689 43.478 0.00 0.00 0.00 2.01
1531 2892 2.869801 CACCAGAAGTCAAGCAACGTTA 59.130 45.455 0.00 0.00 0.00 3.18
1532 2893 1.670811 CACCAGAAGTCAAGCAACGTT 59.329 47.619 0.00 0.00 0.00 3.99
1542 2903 1.849976 GCTGCACTGCACCAGAAGTC 61.850 60.000 0.00 0.00 28.17 3.01
1548 2909 2.674033 GATGGCTGCACTGCACCA 60.674 61.111 20.65 20.65 41.25 4.17
1549 2910 3.807538 CGATGGCTGCACTGCACC 61.808 66.667 0.00 7.56 33.79 5.01
1578 2939 2.630592 CTTCCTCCGGCGAACTAGGC 62.631 65.000 9.30 0.00 0.00 3.93
1579 2940 1.437986 CTTCCTCCGGCGAACTAGG 59.562 63.158 9.30 9.84 0.00 3.02
1580 2941 1.035932 TCCTTCCTCCGGCGAACTAG 61.036 60.000 9.30 0.00 0.00 2.57
1581 2942 1.000521 TCCTTCCTCCGGCGAACTA 60.001 57.895 9.30 0.00 0.00 2.24
2028 3404 4.705507 AGCTATGAAGTACGAAGAACCTGA 59.294 41.667 0.00 0.00 0.00 3.86
2036 3412 7.867909 CCTTGAATATCAGCTATGAAGTACGAA 59.132 37.037 0.00 0.00 39.39 3.85
2038 3414 7.115520 CACCTTGAATATCAGCTATGAAGTACG 59.884 40.741 0.00 0.00 39.39 3.67
2116 3498 0.462047 CGAACCCCAGCACCTACATC 60.462 60.000 0.00 0.00 0.00 3.06
2136 3518 2.978010 GGAATATGCCCGCCCACG 60.978 66.667 0.00 0.00 39.67 4.94
2263 3646 4.689071 TCTGTGTGAAGTGACGTTGTATT 58.311 39.130 0.00 0.00 0.00 1.89
2268 3651 7.152645 ACTAATAATCTGTGTGAAGTGACGTT 58.847 34.615 0.00 0.00 0.00 3.99
2269 3652 6.688578 ACTAATAATCTGTGTGAAGTGACGT 58.311 36.000 0.00 0.00 0.00 4.34
2300 3846 7.816945 GCAAACTGCAATAAAACTGTGATAT 57.183 32.000 0.00 0.00 44.26 1.63
2360 7014 2.817844 TGATGCTACGACACTGTACAGT 59.182 45.455 22.95 22.95 43.61 3.55
2361 7015 3.487563 TGATGCTACGACACTGTACAG 57.512 47.619 21.44 21.44 0.00 2.74
2362 7016 3.769536 CATGATGCTACGACACTGTACA 58.230 45.455 0.00 0.00 0.00 2.90
2363 7017 2.535984 GCATGATGCTACGACACTGTAC 59.464 50.000 10.72 0.00 40.96 2.90
2385 7039 7.706281 ATCATTAGCTAGAACAATTCGTCAG 57.294 36.000 0.00 0.00 34.02 3.51
2411 7065 1.144057 CCATGACCCGCTACCACTC 59.856 63.158 0.00 0.00 0.00 3.51
2412 7066 1.305802 TCCATGACCCGCTACCACT 60.306 57.895 0.00 0.00 0.00 4.00
2413 7067 1.144057 CTCCATGACCCGCTACCAC 59.856 63.158 0.00 0.00 0.00 4.16
2414 7068 1.305802 ACTCCATGACCCGCTACCA 60.306 57.895 0.00 0.00 0.00 3.25
2415 7069 1.442148 GACTCCATGACCCGCTACC 59.558 63.158 0.00 0.00 0.00 3.18
2418 7072 2.680352 ACGACTCCATGACCCGCT 60.680 61.111 0.00 0.00 0.00 5.52
2420 7074 2.102357 CGACGACTCCATGACCCG 59.898 66.667 0.00 0.00 0.00 5.28
2421 7075 2.202756 GCGACGACTCCATGACCC 60.203 66.667 0.00 0.00 0.00 4.46
2471 7131 9.436957 AAAGTGATAGAATCGAATGTTTACAGT 57.563 29.630 0.00 0.00 0.00 3.55
2472 7132 9.907576 GAAAGTGATAGAATCGAATGTTTACAG 57.092 33.333 0.00 0.00 0.00 2.74
2476 7486 7.607991 ACAGGAAAGTGATAGAATCGAATGTTT 59.392 33.333 0.00 0.00 0.00 2.83
2503 7518 4.931601 TCATGTCAGTGTCTAAGTGATTGC 59.068 41.667 0.00 0.00 40.39 3.56
2504 7519 7.425577 TTTCATGTCAGTGTCTAAGTGATTG 57.574 36.000 0.00 0.00 40.39 2.67
2505 7520 8.509690 CAATTTCATGTCAGTGTCTAAGTGATT 58.490 33.333 0.00 0.00 40.39 2.57
2506 7521 7.879677 TCAATTTCATGTCAGTGTCTAAGTGAT 59.120 33.333 0.00 0.00 40.39 3.06
2507 7522 7.171508 GTCAATTTCATGTCAGTGTCTAAGTGA 59.828 37.037 0.00 0.00 35.79 3.41
2531 7546 4.211374 ACATCTACTTTTTGTGACAGCGTC 59.789 41.667 2.32 2.32 0.00 5.19
2566 7998 9.120538 GATCCAGAAGTTTTGTAAGGCAATATA 57.879 33.333 0.00 0.00 36.89 0.86
2600 8032 7.535139 TCGGTAATTGATTTCTGTCCATTTTC 58.465 34.615 0.00 0.00 0.00 2.29
2644 8076 9.574458 GTTCTTTAAAGCTTTCTTTCTTTCAGT 57.426 29.630 16.57 0.00 41.34 3.41
2646 8078 9.573133 CTGTTCTTTAAAGCTTTCTTTCTTTCA 57.427 29.630 16.57 6.38 41.34 2.69
2679 8816 7.685481 TCACAGAATCTTGGAAGTGGTAATAA 58.315 34.615 0.00 0.00 0.00 1.40
2720 8858 3.386402 TCCTGTTTTTGCCCCTTGTAAAG 59.614 43.478 0.00 0.00 45.69 1.85
2806 9191 5.796424 AAGAGACTGCATTTTGGTCAAAT 57.204 34.783 5.90 0.00 35.24 2.32
2853 9243 5.735285 TCCATGCATTTACAAATTGTGGA 57.265 34.783 9.15 1.27 32.60 4.02
2862 9252 8.530311 AGTCACAAATTTATCCATGCATTTACA 58.470 29.630 0.00 0.00 0.00 2.41
2957 9347 2.863809 AGTGCTGAATTTTTCCGAGGT 58.136 42.857 0.00 0.00 0.00 3.85
2992 9506 7.973944 AGAGGTTTCATTTCAACAAACTGTTAC 59.026 33.333 0.00 0.00 38.77 2.50
3034 9548 6.279123 ACACATCAGTAGTGCTCATTCTATG 58.721 40.000 0.00 0.00 40.59 2.23
3045 9559 8.087982 ACTTGTTCATAAACACATCAGTAGTG 57.912 34.615 0.00 0.00 44.90 2.74
3087 9601 7.549842 GCCCTGATCAGCATATATATCATGATC 59.450 40.741 24.43 24.43 42.05 2.92
3097 9611 3.647590 TGAAGTGCCCTGATCAGCATATA 59.352 43.478 17.76 0.00 41.86 0.86
3182 9807 2.500229 TGTAGTAGGCAAAACTGCACC 58.500 47.619 0.00 0.00 35.10 5.01
3207 9832 3.869912 GCATCTCAAACAGGTAGCTTGGA 60.870 47.826 0.00 0.00 0.00 3.53
3211 9836 2.568956 TGAGCATCTCAAACAGGTAGCT 59.431 45.455 0.00 0.00 37.57 3.32
3423 10048 0.670546 CCAATAGGCGATGGGCGTAG 60.671 60.000 0.00 0.00 44.41 3.51
3461 10094 3.397618 TCTGAAAAGATGGGGAAGTTCCA 59.602 43.478 23.33 4.93 38.64 3.53
3487 10120 1.616865 TGACCTGTCACCGTAAAGAGG 59.383 52.381 0.00 0.00 34.14 3.69
3498 10131 4.588951 AGATGTTGTACTTCTGACCTGTCA 59.411 41.667 0.00 0.00 32.24 3.58
3502 10135 6.249951 ACTAGAGATGTTGTACTTCTGACCT 58.750 40.000 0.00 0.00 33.42 3.85
3643 10276 4.523943 TGGAAAAGGAGAACATGGACAATG 59.476 41.667 0.00 0.00 42.48 2.82
4019 10684 1.668751 TGTGCGTTCAAGTTTGGAGTC 59.331 47.619 0.00 0.00 0.00 3.36
4320 11007 1.854126 ACAAGTAACGGTCGTTGTTCG 59.146 47.619 17.57 7.32 38.92 3.95
4369 11057 5.175859 AGGGACACGTACAATTGATACAAG 58.824 41.667 13.59 8.38 0.00 3.16
4558 11311 2.740447 CCCATATGACTGATGCATCGTG 59.260 50.000 22.77 19.08 0.00 4.35
4608 11361 3.372206 CAGCAGAGTAAGTTCCCAAATCG 59.628 47.826 0.00 0.00 0.00 3.34
4743 11496 3.327172 CAGGAGGCATATGACTGATTCCT 59.673 47.826 18.06 13.66 30.09 3.36
5160 11924 7.387948 TCTTTCTAAATGCAGACCTTTAGTGAC 59.612 37.037 14.24 0.00 36.67 3.67
5220 11984 2.997986 CCTTTAAAGCCAAAGCAGCATG 59.002 45.455 9.86 0.00 43.56 4.06
5285 12049 1.951209 AACCATTTCCCCACCAATCC 58.049 50.000 0.00 0.00 0.00 3.01
5356 12120 8.515695 TGGACGAGAAGATTCTTACTTATGTA 57.484 34.615 0.00 0.00 37.73 2.29
5363 12127 5.012328 ACCATGGACGAGAAGATTCTTAC 57.988 43.478 21.47 0.00 37.73 2.34
5388 12152 9.280174 TCGTTAAGACAATTCAGTTTTTATCCT 57.720 29.630 0.00 0.00 0.00 3.24
5436 12201 1.133792 CCAATTCAATACGGAGCCCCT 60.134 52.381 0.00 0.00 0.00 4.79
5460 12225 5.569059 CAGTTTCGTTGCTGATTTGGTATTC 59.431 40.000 0.00 0.00 34.87 1.75
5485 12250 5.804944 TTAATTGGTATTCATGCCCATGG 57.195 39.130 4.14 4.14 39.24 3.66
5534 12299 7.646314 CATTAAAGCCTCACTAAGATTCCATG 58.354 38.462 0.00 0.00 0.00 3.66
5537 12302 6.066054 GCATTAAAGCCTCACTAAGATTCC 57.934 41.667 0.00 0.00 0.00 3.01
5591 12356 6.495706 TCTTCATACTGACGTTACTATGCAG 58.504 40.000 0.00 0.00 0.00 4.41
5595 12360 9.627395 GCATTATCTTCATACTGACGTTACTAT 57.373 33.333 0.00 0.00 0.00 2.12
5603 12368 5.528690 TGCAAGGCATTATCTTCATACTGAC 59.471 40.000 0.00 0.00 31.71 3.51
5633 12398 2.747989 GGTACCTGGCTTTTAGCAAGTC 59.252 50.000 4.06 0.00 40.73 3.01
5674 12439 3.096489 TGTGCAAGGCAATGTTTTCTC 57.904 42.857 0.00 0.00 41.47 2.87
5815 12585 4.683832 GAATGCACTCTACGTACCTCATT 58.316 43.478 0.00 0.00 0.00 2.57
5825 12595 3.991773 TGTGTTTACCGAATGCACTCTAC 59.008 43.478 0.00 0.00 0.00 2.59
5828 12598 4.403453 GAATGTGTTTACCGAATGCACTC 58.597 43.478 0.00 0.00 0.00 3.51
5854 12786 4.080129 ACATTCTGCTATCACCCTGAACAT 60.080 41.667 0.00 0.00 0.00 2.71
5958 13079 6.119144 TCTCATATTTTTCTTACAAGGCGC 57.881 37.500 0.00 0.00 0.00 6.53
6023 13144 4.345837 TCTCCAGTTTACCCCGTTATATGG 59.654 45.833 0.00 0.00 0.00 2.74
6088 13212 8.480643 TCATAGCTTACACTTTCTTTCTTAGC 57.519 34.615 0.00 0.00 0.00 3.09
6091 13215 8.150945 TCACTCATAGCTTACACTTTCTTTCTT 58.849 33.333 0.00 0.00 0.00 2.52
6092 13216 7.600752 GTCACTCATAGCTTACACTTTCTTTCT 59.399 37.037 0.00 0.00 0.00 2.52
6093 13217 7.148557 GGTCACTCATAGCTTACACTTTCTTTC 60.149 40.741 0.00 0.00 0.00 2.62
6124 13249 8.910944 TCCCTTAAATACACTCTCTGTACATAC 58.089 37.037 0.00 0.00 38.22 2.39
6138 13263 9.010029 GTTGAGTTCTGATTTCCCTTAAATACA 57.990 33.333 0.00 0.00 37.93 2.29
6196 13321 1.975680 ACTTGTGAACGTGGGACCTAT 59.024 47.619 0.00 0.00 0.00 2.57
6197 13322 1.416243 ACTTGTGAACGTGGGACCTA 58.584 50.000 0.00 0.00 0.00 3.08
6198 13323 1.416243 TACTTGTGAACGTGGGACCT 58.584 50.000 0.00 0.00 0.00 3.85
6199 13324 2.140717 CTTACTTGTGAACGTGGGACC 58.859 52.381 0.00 0.00 0.00 4.46
6219 13345 5.028375 GTGCCGTTGCTTCAGTTAATATTC 58.972 41.667 0.00 0.00 38.71 1.75
6244 13370 6.338937 AGTAAGTAGCTATGCCACAGTTTAC 58.661 40.000 0.00 0.00 0.00 2.01
6248 13374 4.098654 CAGAGTAAGTAGCTATGCCACAGT 59.901 45.833 0.00 0.00 0.00 3.55
6258 13384 4.467795 TGGATTTCTGCAGAGTAAGTAGCT 59.532 41.667 17.43 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.