Multiple sequence alignment - TraesCS1A01G088100

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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 TraesCS1A01G088100 chr1A 100.000 7052 0 0 810 7861 76492268 76485217 0.000000e+00 13023.0
1 TraesCS1A01G088100 chr1A 100.000 200 0 0 1 200 76493077 76492878 3.460000e-98 370.0
2 TraesCS1A01G088100 chr1A 78.469 418 66 18 7205 7611 399478881 399479285 1.310000e-62 252.0
3 TraesCS1A01G088100 chr1A 97.872 47 0 1 1126 1171 76491605 76491559 6.540000e-11 80.5
4 TraesCS1A01G088100 chr1A 97.872 47 0 1 1473 1519 76491952 76491907 6.540000e-11 80.5
5 TraesCS1A01G088100 chr1D 95.907 2883 89 16 1184 4055 75659964 75657100 0.000000e+00 4643.0
6 TraesCS1A01G088100 chr1D 96.188 1889 56 9 5401 7288 75657095 75655222 0.000000e+00 3075.0
7 TraesCS1A01G088100 chr1D 90.847 437 36 4 7416 7849 75655232 75654797 4.090000e-162 582.0
8 TraesCS1A01G088100 chr1D 95.431 197 3 1 931 1127 75660180 75659990 7.660000e-80 309.0
9 TraesCS1A01G088100 chr1D 93.564 202 8 3 1 200 75660486 75660288 5.960000e-76 296.0
10 TraesCS1A01G088100 chr1D 77.228 404 48 26 7206 7582 25973741 25973355 6.220000e-46 196.0
11 TraesCS1A01G088100 chr1D 97.872 47 0 1 1126 1171 75659682 75659636 6.540000e-11 80.5
12 TraesCS1A01G088100 chr1B 95.691 2901 88 23 1167 4055 119103642 119100767 0.000000e+00 4630.0
13 TraesCS1A01G088100 chr1B 95.919 1887 52 9 5407 7286 119100753 119098885 0.000000e+00 3035.0
14 TraesCS1A01G088100 chr1B 88.539 445 39 6 7416 7853 119098893 119098454 5.400000e-146 529.0
15 TraesCS1A01G088100 chr1B 92.790 319 16 2 810 1127 119103958 119103646 9.300000e-124 455.0
16 TraesCS1A01G088100 chr1B 93.171 205 5 4 1 200 119104194 119103994 7.720000e-75 292.0
17 TraesCS1A01G088100 chr1B 95.000 40 1 1 7206 7245 473280982 473281020 2.370000e-05 62.1
18 TraesCS1A01G088100 chr7A 94.885 1349 57 8 4057 5401 522500784 522499444 0.000000e+00 2098.0
19 TraesCS1A01G088100 chr7A 93.648 1354 68 9 4051 5401 423560509 423561847 0.000000e+00 2008.0
20 TraesCS1A01G088100 chr7A 92.746 1351 78 11 4052 5401 232317113 232318444 0.000000e+00 1934.0
21 TraesCS1A01G088100 chr7A 79.250 400 65 15 7208 7600 652340604 652340992 6.050000e-66 263.0
22 TraesCS1A01G088100 chr7A 93.491 169 11 0 4057 4225 391909615 391909447 1.310000e-62 252.0
23 TraesCS1A01G088100 chr7A 77.804 419 65 21 7207 7611 470595172 470595576 4.740000e-57 233.0
24 TraesCS1A01G088100 chr7A 81.022 274 38 8 7234 7506 722870793 722871053 1.030000e-48 206.0
25 TraesCS1A01G088100 chr3A 94.510 1348 66 6 4057 5401 405987379 405986037 0.000000e+00 2073.0
26 TraesCS1A01G088100 chr4A 93.741 1358 70 7 4058 5401 658762415 658761059 0.000000e+00 2023.0
27 TraesCS1A01G088100 chr4A 93.373 1358 75 7 4058 5401 658779908 658778552 0.000000e+00 1995.0
28 TraesCS1A01G088100 chr6B 93.608 1361 69 9 4055 5401 439389904 439388548 0.000000e+00 2015.0
29 TraesCS1A01G088100 chr6B 93.539 1362 73 7 4054 5401 118960108 118961468 0.000000e+00 2013.0
30 TraesCS1A01G088100 chr2D 86.330 1346 182 2 4057 5401 239723726 239725070 0.000000e+00 1465.0
31 TraesCS1A01G088100 chr5A 89.759 332 26 2 4057 4381 193148488 193148158 1.220000e-112 418.0
32 TraesCS1A01G088100 chr5A 78.425 292 55 6 7322 7611 661988699 661988414 4.840000e-42 183.0
33 TraesCS1A01G088100 chr5D 83.000 400 52 11 7205 7601 538668688 538669074 1.620000e-91 348.0
34 TraesCS1A01G088100 chr2B 81.553 412 61 11 7205 7611 780869644 780870045 7.610000e-85 326.0
35 TraesCS1A01G088100 chr3B 79.012 405 60 15 7206 7601 105471386 105471774 3.640000e-63 254.0
36 TraesCS1A01G088100 chrUn 97.315 149 3 1 4058 4206 208767107 208767254 1.310000e-62 252.0
37 TraesCS1A01G088100 chr7B 82.707 266 36 10 7326 7589 103998474 103998731 2.210000e-55 228.0
38 TraesCS1A01G088100 chr5B 76.528 409 66 21 7207 7601 10405878 10405486 6.220000e-46 196.0
39 TraesCS1A01G088100 chr5B 79.878 164 24 7 7433 7593 338490460 338490617 2.320000e-20 111.0


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 TraesCS1A01G088100 chr1A 76485217 76493077 7860 True 3388.500000 13023 98.936000 1 7861 4 chr1A.!!$R1 7860
1 TraesCS1A01G088100 chr1D 75654797 75660486 5689 True 1497.583333 4643 94.968167 1 7849 6 chr1D.!!$R2 7848
2 TraesCS1A01G088100 chr1B 119098454 119104194 5740 True 1788.200000 4630 93.222000 1 7853 5 chr1B.!!$R1 7852
3 TraesCS1A01G088100 chr7A 522499444 522500784 1340 True 2098.000000 2098 94.885000 4057 5401 1 chr7A.!!$R2 1344
4 TraesCS1A01G088100 chr7A 423560509 423561847 1338 False 2008.000000 2008 93.648000 4051 5401 1 chr7A.!!$F2 1350
5 TraesCS1A01G088100 chr7A 232317113 232318444 1331 False 1934.000000 1934 92.746000 4052 5401 1 chr7A.!!$F1 1349
6 TraesCS1A01G088100 chr3A 405986037 405987379 1342 True 2073.000000 2073 94.510000 4057 5401 1 chr3A.!!$R1 1344
7 TraesCS1A01G088100 chr4A 658761059 658762415 1356 True 2023.000000 2023 93.741000 4058 5401 1 chr4A.!!$R1 1343
8 TraesCS1A01G088100 chr4A 658778552 658779908 1356 True 1995.000000 1995 93.373000 4058 5401 1 chr4A.!!$R2 1343
9 TraesCS1A01G088100 chr6B 439388548 439389904 1356 True 2015.000000 2015 93.608000 4055 5401 1 chr6B.!!$R1 1346
10 TraesCS1A01G088100 chr6B 118960108 118961468 1360 False 2013.000000 2013 93.539000 4054 5401 1 chr6B.!!$F1 1347
11 TraesCS1A01G088100 chr2D 239723726 239725070 1344 False 1465.000000 1465 86.330000 4057 5401 1 chr2D.!!$F1 1344

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
890 900 1.073722 CCCTCAGCTGGAGCAACAA 59.926 57.895 15.13 0.00 45.16 2.83 F
1129 1139 0.254178 AGCGATTCCCACAGCATTCT 59.746 50.000 0.00 0.00 0.00 2.40 F
1130 1140 1.098050 GCGATTCCCACAGCATTCTT 58.902 50.000 0.00 0.00 0.00 2.52 F
1357 1379 1.676014 GCATATCGGCCTGGTATGGAC 60.676 57.143 21.53 8.77 0.00 4.02 F
1460 1482 1.757699 GGATGGAGTGGAGTGAGTACC 59.242 57.143 0.00 0.00 0.00 3.34 F
3332 3363 2.057922 ACACATCCAACCAGAGAACCT 58.942 47.619 0.00 0.00 0.00 3.50 F
4381 4430 0.179140 CAGTGTTGGCGTGTTTTGCT 60.179 50.000 0.00 0.00 0.00 3.91 F
4687 4736 0.257039 GCAAGTCATGGATCCCTGGT 59.743 55.000 16.09 2.57 0.00 4.00 F
5345 5395 0.532862 CGGACTTCACCAGTGCAAGT 60.533 55.000 12.41 12.41 44.09 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2016 3.438297 AGTAAATGGACAGTCGGATCG 57.562 47.619 0.00 0.0 0.00 3.69 R
3056 3087 0.402504 ATCCGGTTACCAGGTGCAAA 59.597 50.000 0.76 0.0 0.00 3.68 R
3332 3363 6.884295 AGCTGGTTTAACAAGATGCAAGTATA 59.116 34.615 3.27 0.0 0.00 1.47 R
3347 3378 2.500229 CTTCGGGACAAGCTGGTTTAA 58.500 47.619 0.00 0.0 0.00 1.52 R
3788 3820 2.622942 GTGTTTCCATGCCAAAGAGTGA 59.377 45.455 0.00 0.0 0.00 3.41 R
5345 5395 0.109532 TGATGAACAAACCTGGGCGA 59.890 50.000 0.00 0.0 0.00 5.54 R
5708 5762 0.389296 CCATGCCACAACATGCACTG 60.389 55.000 0.00 0.0 44.98 3.66 R
6680 6736 0.615544 TACCAGAGGGGGTGTTACCG 60.616 60.000 0.00 0.0 42.39 4.02 R
7630 7691 2.762887 CTCAGATAGAGGGAGCACAACA 59.237 50.000 0.00 0.0 40.84 3.33 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
61 62 4.804420 TCCCGGCCATCCTCTGCT 62.804 66.667 2.24 0.00 0.00 4.24
62 63 4.559063 CCCGGCCATCCTCTGCTG 62.559 72.222 2.24 0.00 0.00 4.41
115 121 6.805760 GGTTTGATCATCTTTCTGAGCTTTTC 59.194 38.462 0.00 0.00 32.81 2.29
123 131 3.976793 TTCTGAGCTTTTCTTGTGCTG 57.023 42.857 0.00 0.00 37.16 4.41
833 843 2.781595 TTTTGCCTCGGAGTCGCTCC 62.782 60.000 13.87 13.87 46.44 4.70
889 899 2.149383 ACCCTCAGCTGGAGCAACA 61.149 57.895 15.13 0.00 45.16 3.33
890 900 1.073722 CCCTCAGCTGGAGCAACAA 59.926 57.895 15.13 0.00 45.16 2.83
918 928 5.123820 CCGAAATCCTCTGTTCAGCAATAAA 59.876 40.000 0.00 0.00 0.00 1.40
919 929 6.349280 CCGAAATCCTCTGTTCAGCAATAAAA 60.349 38.462 0.00 0.00 0.00 1.52
920 930 7.083858 CGAAATCCTCTGTTCAGCAATAAAAA 58.916 34.615 0.00 0.00 0.00 1.94
970 980 1.354368 TCTCCCACTTCATTCCCCAAC 59.646 52.381 0.00 0.00 0.00 3.77
971 981 1.355720 CTCCCACTTCATTCCCCAACT 59.644 52.381 0.00 0.00 0.00 3.16
972 982 1.786441 TCCCACTTCATTCCCCAACTT 59.214 47.619 0.00 0.00 0.00 2.66
973 983 2.178984 TCCCACTTCATTCCCCAACTTT 59.821 45.455 0.00 0.00 0.00 2.66
974 984 2.299867 CCCACTTCATTCCCCAACTTTG 59.700 50.000 0.00 0.00 0.00 2.77
975 985 2.289010 CCACTTCATTCCCCAACTTTGC 60.289 50.000 0.00 0.00 0.00 3.68
1117 1127 0.391661 TGAGGCAAGGACAGCGATTC 60.392 55.000 0.00 0.00 0.00 2.52
1119 1129 2.115291 GGCAAGGACAGCGATTCCC 61.115 63.158 0.00 0.00 33.01 3.97
1127 1137 0.322816 ACAGCGATTCCCACAGCATT 60.323 50.000 0.00 0.00 0.00 3.56
1128 1138 0.379669 CAGCGATTCCCACAGCATTC 59.620 55.000 0.00 0.00 0.00 2.67
1129 1139 0.254178 AGCGATTCCCACAGCATTCT 59.746 50.000 0.00 0.00 0.00 2.40
1130 1140 1.098050 GCGATTCCCACAGCATTCTT 58.902 50.000 0.00 0.00 0.00 2.52
1131 1141 2.092968 AGCGATTCCCACAGCATTCTTA 60.093 45.455 0.00 0.00 0.00 2.10
1132 1142 2.289002 GCGATTCCCACAGCATTCTTAG 59.711 50.000 0.00 0.00 0.00 2.18
1133 1143 3.535561 CGATTCCCACAGCATTCTTAGT 58.464 45.455 0.00 0.00 0.00 2.24
1134 1144 3.941483 CGATTCCCACAGCATTCTTAGTT 59.059 43.478 0.00 0.00 0.00 2.24
1135 1145 4.396166 CGATTCCCACAGCATTCTTAGTTT 59.604 41.667 0.00 0.00 0.00 2.66
1136 1146 5.644644 GATTCCCACAGCATTCTTAGTTTG 58.355 41.667 0.00 0.00 0.00 2.93
1137 1147 3.420893 TCCCACAGCATTCTTAGTTTGG 58.579 45.455 0.00 0.00 0.00 3.28
1138 1148 3.073798 TCCCACAGCATTCTTAGTTTGGA 59.926 43.478 0.00 0.00 0.00 3.53
1139 1149 3.191371 CCCACAGCATTCTTAGTTTGGAC 59.809 47.826 0.00 0.00 0.00 4.02
1140 1150 3.191371 CCACAGCATTCTTAGTTTGGACC 59.809 47.826 0.00 0.00 0.00 4.46
1141 1151 4.074970 CACAGCATTCTTAGTTTGGACCT 58.925 43.478 0.00 0.00 0.00 3.85
1142 1152 5.245531 CACAGCATTCTTAGTTTGGACCTA 58.754 41.667 0.00 0.00 0.00 3.08
1143 1153 5.352569 CACAGCATTCTTAGTTTGGACCTAG 59.647 44.000 0.00 0.00 0.00 3.02
1144 1154 4.878397 CAGCATTCTTAGTTTGGACCTAGG 59.122 45.833 7.41 7.41 0.00 3.02
1145 1155 4.783227 AGCATTCTTAGTTTGGACCTAGGA 59.217 41.667 17.98 0.00 0.00 2.94
1146 1156 5.250774 AGCATTCTTAGTTTGGACCTAGGAA 59.749 40.000 17.98 0.00 0.00 3.36
1147 1157 6.069381 AGCATTCTTAGTTTGGACCTAGGAAT 60.069 38.462 17.98 0.00 32.19 3.01
1148 1158 6.603599 GCATTCTTAGTTTGGACCTAGGAATT 59.396 38.462 17.98 0.00 30.45 2.17
1149 1159 7.773690 GCATTCTTAGTTTGGACCTAGGAATTA 59.226 37.037 17.98 0.00 30.45 1.40
1150 1160 9.331282 CATTCTTAGTTTGGACCTAGGAATTAG 57.669 37.037 17.98 0.00 30.45 1.73
1151 1161 8.674925 TTCTTAGTTTGGACCTAGGAATTAGA 57.325 34.615 17.98 0.00 0.00 2.10
1152 1162 8.855804 TCTTAGTTTGGACCTAGGAATTAGAT 57.144 34.615 17.98 0.00 0.00 1.98
1153 1163 8.925338 TCTTAGTTTGGACCTAGGAATTAGATC 58.075 37.037 17.98 0.00 0.00 2.75
1154 1164 8.618240 TTAGTTTGGACCTAGGAATTAGATCA 57.382 34.615 17.98 0.00 0.00 2.92
1155 1165 7.510675 AGTTTGGACCTAGGAATTAGATCAA 57.489 36.000 17.98 5.00 0.00 2.57
1156 1166 7.569240 AGTTTGGACCTAGGAATTAGATCAAG 58.431 38.462 17.98 0.00 0.00 3.02
1157 1167 7.182930 AGTTTGGACCTAGGAATTAGATCAAGT 59.817 37.037 17.98 0.00 0.00 3.16
1158 1168 6.732896 TGGACCTAGGAATTAGATCAAGTC 57.267 41.667 17.98 0.00 0.00 3.01
1159 1169 6.444704 TGGACCTAGGAATTAGATCAAGTCT 58.555 40.000 17.98 0.00 41.11 3.24
1160 1170 7.592736 TGGACCTAGGAATTAGATCAAGTCTA 58.407 38.462 17.98 0.00 38.42 2.59
1161 1171 8.235230 TGGACCTAGGAATTAGATCAAGTCTAT 58.765 37.037 17.98 0.00 39.14 1.98
1162 1172 9.095700 GGACCTAGGAATTAGATCAAGTCTATT 57.904 37.037 17.98 0.00 39.14 1.73
1163 1173 9.921637 GACCTAGGAATTAGATCAAGTCTATTG 57.078 37.037 17.98 0.00 39.14 1.90
1164 1174 9.440761 ACCTAGGAATTAGATCAAGTCTATTGT 57.559 33.333 17.98 0.00 39.14 2.71
1165 1175 9.703892 CCTAGGAATTAGATCAAGTCTATTGTG 57.296 37.037 1.05 0.00 39.14 3.33
1228 1246 2.224257 TGGGGTTGAATTTCTTGCTTGC 60.224 45.455 0.00 0.00 0.00 4.01
1229 1247 2.037641 GGGGTTGAATTTCTTGCTTGCT 59.962 45.455 0.00 0.00 0.00 3.91
1230 1248 3.494924 GGGGTTGAATTTCTTGCTTGCTT 60.495 43.478 0.00 0.00 0.00 3.91
1231 1249 3.495753 GGGTTGAATTTCTTGCTTGCTTG 59.504 43.478 0.00 0.00 0.00 4.01
1292 1314 2.515523 GCATGCGCCCTGATCTGT 60.516 61.111 4.18 0.00 0.00 3.41
1313 1335 3.302365 TGAATGTGGCTAAAGCTTTGC 57.698 42.857 22.02 20.34 41.70 3.68
1354 1376 2.408271 ATGCATATCGGCCTGGTATG 57.592 50.000 18.08 18.08 0.00 2.39
1357 1379 1.676014 GCATATCGGCCTGGTATGGAC 60.676 57.143 21.53 8.77 0.00 4.02
1370 1392 4.439057 TGGTATGGACGCTTTTCTCATAC 58.561 43.478 0.00 0.00 39.33 2.39
1374 1396 3.745799 TGGACGCTTTTCTCATACCAAA 58.254 40.909 0.00 0.00 0.00 3.28
1375 1397 3.500680 TGGACGCTTTTCTCATACCAAAC 59.499 43.478 0.00 0.00 0.00 2.93
1378 1400 5.410439 GGACGCTTTTCTCATACCAAACTTA 59.590 40.000 0.00 0.00 0.00 2.24
1379 1401 6.402226 GGACGCTTTTCTCATACCAAACTTAG 60.402 42.308 0.00 0.00 0.00 2.18
1380 1402 5.106673 ACGCTTTTCTCATACCAAACTTAGC 60.107 40.000 0.00 0.00 0.00 3.09
1381 1403 5.324697 GCTTTTCTCATACCAAACTTAGCG 58.675 41.667 0.00 0.00 0.00 4.26
1382 1404 5.106673 GCTTTTCTCATACCAAACTTAGCGT 60.107 40.000 0.00 0.00 0.00 5.07
1383 1405 6.476243 TTTTCTCATACCAAACTTAGCGTC 57.524 37.500 0.00 0.00 0.00 5.19
1385 1407 5.401531 TCTCATACCAAACTTAGCGTCTT 57.598 39.130 0.00 0.00 0.00 3.01
1386 1408 5.408356 TCTCATACCAAACTTAGCGTCTTC 58.592 41.667 0.00 0.00 0.00 2.87
1460 1482 1.757699 GGATGGAGTGGAGTGAGTACC 59.242 57.143 0.00 0.00 0.00 3.34
1619 1644 4.889409 AGTTGTGCATACTTTGGGATATGG 59.111 41.667 0.00 0.00 30.75 2.74
1635 1660 5.449553 GGATATGGAAAGGACACCTTGAAT 58.550 41.667 3.73 2.02 43.92 2.57
1731 1756 4.660789 ATTAGGTTTGAGGATTGCATGC 57.339 40.909 11.82 11.82 0.00 4.06
2045 2070 2.233922 AGGTTTACGATGCTGCTGTAGT 59.766 45.455 0.00 0.00 0.00 2.73
2053 2084 3.243401 CGATGCTGCTGTAGTACCATGTA 60.243 47.826 0.00 0.00 0.00 2.29
2268 2299 4.218265 TCGATTTGACTTGCACATTTTCG 58.782 39.130 0.00 0.00 0.00 3.46
2325 2356 7.693952 TGGTTGCTATTTCGTTCTTCATTATC 58.306 34.615 0.00 0.00 0.00 1.75
2686 2717 8.722480 ATATGTTGACATATTCATATCACCCG 57.278 34.615 10.14 0.00 44.66 5.28
2942 2973 7.646446 TTTGATTTCTTGCACATGAATTGAG 57.354 32.000 0.00 0.00 0.00 3.02
3056 3087 3.256704 TCCTCCTGATTAGGTTGTTGGT 58.743 45.455 3.04 0.00 44.88 3.67
3332 3363 2.057922 ACACATCCAACCAGAGAACCT 58.942 47.619 0.00 0.00 0.00 3.50
3347 3378 6.344500 CAGAGAACCTATACTTGCATCTTGT 58.656 40.000 0.00 0.00 0.00 3.16
3828 3860 4.405548 ACACGAGGTTAGAGTTAGGACTT 58.594 43.478 0.00 0.00 35.88 3.01
3835 3867 4.963628 GGTTAGAGTTAGGACTTGGGAGAT 59.036 45.833 0.00 0.00 35.88 2.75
3844 3876 7.625682 AGTTAGGACTTGGGAGATCTATTCTTT 59.374 37.037 0.00 0.00 30.03 2.52
3845 3877 6.899892 AGGACTTGGGAGATCTATTCTTTT 57.100 37.500 0.00 0.00 33.74 2.27
3846 3878 7.277405 AGGACTTGGGAGATCTATTCTTTTT 57.723 36.000 0.00 0.00 33.74 1.94
3894 3926 6.855763 TTACCCTACAGGAGAACGAAAATA 57.144 37.500 0.00 0.00 39.89 1.40
3955 3990 9.029243 CACTCTTGTTGTTTGCACATTAAATTA 57.971 29.630 0.00 0.00 31.06 1.40
4014 4049 3.640967 GTGATTCCTCCTGCTCTCTACAT 59.359 47.826 0.00 0.00 0.00 2.29
4233 4282 2.033141 GCTCTTGCCCACTGCTCA 59.967 61.111 0.00 0.00 42.00 4.26
4260 4309 3.186119 CTCTTTGATCTTCGAGACCAGC 58.814 50.000 0.00 0.00 0.00 4.85
4320 4369 0.393402 TGCGCTGCTTCCAGATCATT 60.393 50.000 9.73 0.00 41.77 2.57
4322 4371 0.580578 CGCTGCTTCCAGATCATTCG 59.419 55.000 0.00 0.00 41.77 3.34
4361 4410 2.820261 GGCTAGGCCCTTACGGAC 59.180 66.667 4.61 0.00 44.06 4.79
4381 4430 0.179140 CAGTGTTGGCGTGTTTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
4461 4510 2.632996 CCGTAGCCAGGATAGGATTTCA 59.367 50.000 5.98 0.00 0.00 2.69
4541 4590 1.126948 TGGTCACAGAGTGGGCATCA 61.127 55.000 0.00 0.00 33.87 3.07
4573 4622 1.935327 GAGACCGCGTCTAGCCAAGT 61.935 60.000 4.92 0.00 43.53 3.16
4662 4711 5.773680 CCAATTCTTCCATATGAGCTTCCAT 59.226 40.000 3.65 0.00 0.00 3.41
4687 4736 0.257039 GCAAGTCATGGATCCCTGGT 59.743 55.000 16.09 2.57 0.00 4.00
4764 4813 1.007721 ACTAGCTGATCAGGGGTGTCT 59.992 52.381 23.89 13.22 0.00 3.41
4885 4934 1.604023 AGTCCTTCAGCGACGGTCT 60.604 57.895 6.57 0.00 35.33 3.85
4932 4981 1.303317 CTTGTAAAGTGCCGGGGCT 60.303 57.895 11.55 0.00 39.70 5.19
5115 5164 1.738099 CCATAGCCATCGTAGCCGC 60.738 63.158 0.00 0.00 0.00 6.53
5162 5211 3.003763 GACTCCCAGGCCTCCGTT 61.004 66.667 0.00 0.00 0.00 4.44
5243 5292 2.598394 GCCAGCCCACAAGAAGCA 60.598 61.111 0.00 0.00 0.00 3.91
5246 5295 1.900016 CAGCCCACAAGAAGCAGCA 60.900 57.895 0.00 0.00 0.00 4.41
5318 5368 3.279504 TTGATGCACGGGGATGGCA 62.280 57.895 0.00 0.00 42.43 4.92
5345 5395 0.532862 CGGACTTCACCAGTGCAAGT 60.533 55.000 12.41 12.41 44.09 3.16
5573 5627 3.194116 CAGATGGCCTGCACTAAAATGTT 59.806 43.478 3.32 0.00 35.89 2.71
5574 5628 4.398988 CAGATGGCCTGCACTAAAATGTTA 59.601 41.667 3.32 0.00 35.89 2.41
5575 5629 4.399303 AGATGGCCTGCACTAAAATGTTAC 59.601 41.667 3.32 0.00 0.00 2.50
5708 5762 3.357897 GCAGCAGCTTCGATCATTTTAC 58.642 45.455 0.00 0.00 37.91 2.01
5769 5823 3.897505 ACTTCCTGAAATGTTTCCCCTTG 59.102 43.478 3.26 0.00 36.36 3.61
5784 5840 5.920193 TCCCCTTGCTAATGAATTTTCTG 57.080 39.130 0.00 0.00 0.00 3.02
5819 5875 5.017294 AGACAGGCTCTAGTTATTCTTGC 57.983 43.478 0.00 0.00 0.00 4.01
5884 5940 5.363580 ACAGTTTTCATTTGACCAACATCCT 59.636 36.000 5.18 0.00 0.00 3.24
5896 5952 7.437713 TGACCAACATCCTCTTATAGAATGT 57.562 36.000 0.00 0.00 29.50 2.71
5905 5961 9.561270 CATCCTCTTATAGAATGTGTGTATACG 57.439 37.037 0.00 0.00 0.00 3.06
6325 6381 2.674380 GAGTGGCCAAGCACAGGG 60.674 66.667 7.24 0.00 0.00 4.45
6416 6472 8.410141 TCATCGAAACCTAACAAAAGTCAAAAT 58.590 29.630 0.00 0.00 0.00 1.82
6433 6489 5.344933 GTCAAAATAACAACCCTTCGATTGC 59.655 40.000 0.00 0.00 0.00 3.56
6667 6723 2.711542 ACCTGTAGAAAATGAAGCCGG 58.288 47.619 0.00 0.00 0.00 6.13
6901 6961 1.746787 GCATGTCACAGCATTGATGGA 59.253 47.619 6.88 0.00 0.00 3.41
6927 6987 6.562608 TGCTTCCCCCTATTAAGTTCTGATAT 59.437 38.462 0.00 0.00 0.00 1.63
6974 7034 8.723311 TGTTGCAGGTGTACTATTACAAATTAC 58.277 33.333 0.00 0.00 40.00 1.89
6978 7038 7.767198 GCAGGTGTACTATTACAAATTACTCCA 59.233 37.037 0.00 0.00 40.00 3.86
6979 7039 9.095065 CAGGTGTACTATTACAAATTACTCCAC 57.905 37.037 0.00 0.00 40.00 4.02
6980 7040 8.818860 AGGTGTACTATTACAAATTACTCCACA 58.181 33.333 0.00 0.00 40.00 4.17
6982 7042 8.876790 GTGTACTATTACAAATTACTCCACACC 58.123 37.037 0.00 0.00 40.00 4.16
6983 7043 8.042515 TGTACTATTACAAATTACTCCACACCC 58.957 37.037 0.00 0.00 35.14 4.61
6984 7044 7.266905 ACTATTACAAATTACTCCACACCCT 57.733 36.000 0.00 0.00 0.00 4.34
6985 7045 8.383374 ACTATTACAAATTACTCCACACCCTA 57.617 34.615 0.00 0.00 0.00 3.53
6986 7046 8.999895 ACTATTACAAATTACTCCACACCCTAT 58.000 33.333 0.00 0.00 0.00 2.57
6987 7047 9.847224 CTATTACAAATTACTCCACACCCTATT 57.153 33.333 0.00 0.00 0.00 1.73
6993 7053 8.674607 CAAATTACTCCACACCCTATTAAGTTC 58.325 37.037 0.00 0.00 0.00 3.01
7097 7157 4.447054 GGCGTATTTGTCATGATCAGAGAG 59.553 45.833 0.00 0.00 0.00 3.20
7115 7175 4.002316 GAGAGATTCAGCTGAACTGCTTT 58.998 43.478 30.66 21.22 46.76 3.51
7133 7193 4.346129 GCTTTTGCTTTCATGGTATCGAG 58.654 43.478 0.00 0.00 43.35 4.04
7140 7200 4.752101 GCTTTCATGGTATCGAGTATTGCT 59.248 41.667 0.00 0.00 0.00 3.91
7154 7214 4.683832 AGTATTGCTTCTGCTAGGTTACG 58.316 43.478 0.00 0.00 40.48 3.18
7177 7237 3.240302 AGCTAGTTATCCATACGGCCTT 58.760 45.455 0.00 0.00 0.00 4.35
7203 7263 1.153901 CTGCAAATGCTGGCTTCGG 60.154 57.895 6.97 0.00 42.66 4.30
7251 7311 4.026052 CTCCATGGAGGCCTTAATTTTGT 58.974 43.478 31.14 0.00 38.51 2.83
7320 7380 5.755409 AAATATGCATATACCCGGAGACA 57.245 39.130 19.39 0.00 0.00 3.41
7321 7381 5.957771 AATATGCATATACCCGGAGACAT 57.042 39.130 19.39 0.00 0.00 3.06
7322 7382 7.432148 AAATATGCATATACCCGGAGACATA 57.568 36.000 19.39 1.37 0.00 2.29
7323 7383 7.432148 AATATGCATATACCCGGAGACATAA 57.568 36.000 19.39 0.00 0.00 1.90
7324 7384 5.957771 ATGCATATACCCGGAGACATAAT 57.042 39.130 0.73 0.00 0.00 1.28
7325 7385 5.084818 TGCATATACCCGGAGACATAATG 57.915 43.478 0.73 0.00 0.00 1.90
7326 7386 4.530553 TGCATATACCCGGAGACATAATGT 59.469 41.667 0.73 0.00 0.00 2.71
7327 7387 5.717654 TGCATATACCCGGAGACATAATGTA 59.282 40.000 0.73 0.00 0.00 2.29
7328 7388 6.040878 GCATATACCCGGAGACATAATGTAC 58.959 44.000 0.73 0.00 0.00 2.90
7329 7389 6.350696 GCATATACCCGGAGACATAATGTACA 60.351 42.308 0.73 0.00 0.00 2.90
7330 7390 7.632898 GCATATACCCGGAGACATAATGTACAT 60.633 40.741 0.73 1.41 0.00 2.29
7331 7391 8.909923 CATATACCCGGAGACATAATGTACATA 58.090 37.037 9.21 0.00 0.00 2.29
7332 7392 7.973048 ATACCCGGAGACATAATGTACATAT 57.027 36.000 9.21 2.47 0.00 1.78
7333 7393 6.037786 ACCCGGAGACATAATGTACATATG 57.962 41.667 9.21 14.35 0.00 1.78
7334 7394 5.542635 ACCCGGAGACATAATGTACATATGT 59.457 40.000 21.05 21.05 37.16 2.29
7335 7395 5.869344 CCCGGAGACATAATGTACATATGTG 59.131 44.000 23.76 18.07 34.89 3.21
7336 7396 6.455647 CCGGAGACATAATGTACATATGTGT 58.544 40.000 23.76 21.32 42.39 3.72
7337 7397 7.309560 CCCGGAGACATAATGTACATATGTGTA 60.310 40.741 23.76 7.43 39.77 2.90
7338 7398 8.085909 CCGGAGACATAATGTACATATGTGTAA 58.914 37.037 23.76 4.13 42.18 2.41
7339 7399 9.471084 CGGAGACATAATGTACATATGTGTAAA 57.529 33.333 23.76 0.00 42.18 2.01
7385 7445 8.634475 AAAATGAGAGCTACAAAAAGAAACAC 57.366 30.769 0.00 0.00 0.00 3.32
7386 7446 6.942532 ATGAGAGCTACAAAAAGAAACACA 57.057 33.333 0.00 0.00 0.00 3.72
7387 7447 6.751514 TGAGAGCTACAAAAAGAAACACAA 57.248 33.333 0.00 0.00 0.00 3.33
7388 7448 7.151999 TGAGAGCTACAAAAAGAAACACAAA 57.848 32.000 0.00 0.00 0.00 2.83
7389 7449 7.771183 TGAGAGCTACAAAAAGAAACACAAAT 58.229 30.769 0.00 0.00 0.00 2.32
7390 7450 8.898761 TGAGAGCTACAAAAAGAAACACAAATA 58.101 29.630 0.00 0.00 0.00 1.40
7391 7451 9.899226 GAGAGCTACAAAAAGAAACACAAATAT 57.101 29.630 0.00 0.00 0.00 1.28
7392 7452 9.683069 AGAGCTACAAAAAGAAACACAAATATG 57.317 29.630 0.00 0.00 0.00 1.78
7393 7453 9.463443 GAGCTACAAAAAGAAACACAAATATGT 57.537 29.630 0.00 0.00 41.61 2.29
7407 7467 6.343716 ACAAATATGTGGCTTTTCATCACA 57.656 33.333 0.00 0.00 44.12 3.58
7413 7473 5.981088 TGTGGCTTTTCATCACATGTATT 57.019 34.783 0.00 0.00 36.61 1.89
7414 7474 5.712004 TGTGGCTTTTCATCACATGTATTG 58.288 37.500 0.00 0.00 36.61 1.90
7415 7475 5.243507 TGTGGCTTTTCATCACATGTATTGT 59.756 36.000 0.00 0.00 39.91 2.71
7416 7476 6.158598 GTGGCTTTTCATCACATGTATTGTT 58.841 36.000 0.00 0.00 36.00 2.83
7417 7477 6.308766 GTGGCTTTTCATCACATGTATTGTTC 59.691 38.462 0.00 0.00 36.00 3.18
7418 7478 6.015603 TGGCTTTTCATCACATGTATTGTTCA 60.016 34.615 0.00 0.00 36.00 3.18
7419 7479 7.037438 GGCTTTTCATCACATGTATTGTTCAT 58.963 34.615 0.00 0.00 36.00 2.57
7420 7480 7.546667 GGCTTTTCATCACATGTATTGTTCATT 59.453 33.333 0.00 0.00 36.00 2.57
7421 7481 8.589629 GCTTTTCATCACATGTATTGTTCATTC 58.410 33.333 0.00 0.00 36.00 2.67
7422 7482 9.850628 CTTTTCATCACATGTATTGTTCATTCT 57.149 29.630 0.00 0.00 36.00 2.40
7423 7483 9.844790 TTTTCATCACATGTATTGTTCATTCTC 57.155 29.630 0.00 0.00 36.00 2.87
7463 7523 1.689959 GCAACTCGCAATTCAAGGTG 58.310 50.000 0.00 0.00 41.79 4.00
7611 7672 3.763057 GGTATCCAAAACACCCAACTCT 58.237 45.455 0.00 0.00 0.00 3.24
7616 7677 2.168313 CCAAAACACCCAACTCTGCTTT 59.832 45.455 0.00 0.00 0.00 3.51
7619 7680 4.649088 AAACACCCAACTCTGCTTTAAC 57.351 40.909 0.00 0.00 0.00 2.01
7623 7684 1.545841 CCAACTCTGCTTTAACCCCC 58.454 55.000 0.00 0.00 0.00 5.40
7652 7719 2.763448 GTTGTGCTCCCTCTATCTGAGT 59.237 50.000 0.00 0.00 41.11 3.41
7669 7736 3.938963 CTGAGTTTATAACGTGGGCACAT 59.061 43.478 0.00 0.00 36.23 3.21
7677 7744 1.614996 ACGTGGGCACATGATTTTCA 58.385 45.000 16.89 0.00 37.07 2.69
7791 7858 9.031537 TGTCATCAGTGTATAGAAACTAAGGAA 57.968 33.333 0.00 0.00 0.00 3.36
7803 7870 6.129874 AGAAACTAAGGAAGGATTAATGGGC 58.870 40.000 0.00 0.00 0.00 5.36
7805 7872 6.841781 AACTAAGGAAGGATTAATGGGCTA 57.158 37.500 0.00 0.00 0.00 3.93
7808 7875 5.734031 AAGGAAGGATTAATGGGCTACTT 57.266 39.130 0.00 0.00 0.00 2.24
7850 7917 9.118236 GACTTGTTAATCTCATGTTTGTTAAGC 57.882 33.333 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 121 6.218746 AGAAAATTAAGGAAAGCAGCACAAG 58.781 36.000 0.00 0.00 0.00 3.16
123 131 5.171476 GCCAGGAAGAAAATTAAGGAAAGC 58.829 41.667 0.00 0.00 0.00 3.51
809 819 1.281899 GACTCCGAGGCAAAAGATCG 58.718 55.000 0.00 0.00 36.24 3.69
810 820 1.281899 CGACTCCGAGGCAAAAGATC 58.718 55.000 1.23 0.00 38.22 2.75
811 821 0.741221 GCGACTCCGAGGCAAAAGAT 60.741 55.000 1.23 0.00 38.22 2.40
812 822 1.374252 GCGACTCCGAGGCAAAAGA 60.374 57.895 1.23 0.00 38.22 2.52
813 823 1.355066 GAGCGACTCCGAGGCAAAAG 61.355 60.000 1.23 0.00 38.22 2.27
889 899 4.822026 CTGAACAGAGGATTTCGGTAGTT 58.178 43.478 0.00 0.00 32.79 2.24
890 900 3.368531 GCTGAACAGAGGATTTCGGTAGT 60.369 47.826 5.97 0.00 32.79 2.73
921 931 3.434882 CCCTTGCCCAAAACTGGATTTTT 60.435 43.478 0.00 0.00 38.50 1.94
922 932 2.106338 CCCTTGCCCAAAACTGGATTTT 59.894 45.455 0.00 0.00 41.38 1.82
923 933 1.699083 CCCTTGCCCAAAACTGGATTT 59.301 47.619 0.00 0.00 0.00 2.17
924 934 1.132881 TCCCTTGCCCAAAACTGGATT 60.133 47.619 0.00 0.00 0.00 3.01
925 935 0.486879 TCCCTTGCCCAAAACTGGAT 59.513 50.000 0.00 0.00 0.00 3.41
1117 1127 3.191371 GTCCAAACTAAGAATGCTGTGGG 59.809 47.826 0.00 0.00 0.00 4.61
1119 1129 4.074970 AGGTCCAAACTAAGAATGCTGTG 58.925 43.478 0.00 0.00 0.00 3.66
1127 1137 8.855804 ATCTAATTCCTAGGTCCAAACTAAGA 57.144 34.615 9.08 0.74 0.00 2.10
1128 1138 8.705594 TGATCTAATTCCTAGGTCCAAACTAAG 58.294 37.037 9.08 0.00 36.99 2.18
1129 1139 8.618240 TGATCTAATTCCTAGGTCCAAACTAA 57.382 34.615 9.08 0.00 36.99 2.24
1130 1140 8.618240 TTGATCTAATTCCTAGGTCCAAACTA 57.382 34.615 9.08 0.00 36.99 2.24
1131 1141 7.182930 ACTTGATCTAATTCCTAGGTCCAAACT 59.817 37.037 9.08 0.00 36.99 2.66
1132 1142 7.339482 ACTTGATCTAATTCCTAGGTCCAAAC 58.661 38.462 9.08 0.00 36.99 2.93
1133 1143 7.403231 AGACTTGATCTAATTCCTAGGTCCAAA 59.597 37.037 9.08 0.00 36.99 3.28
1134 1144 6.903534 AGACTTGATCTAATTCCTAGGTCCAA 59.096 38.462 9.08 0.00 36.99 3.53
1135 1145 6.444704 AGACTTGATCTAATTCCTAGGTCCA 58.555 40.000 9.08 0.00 36.99 4.02
1136 1146 6.987403 AGACTTGATCTAATTCCTAGGTCC 57.013 41.667 9.08 0.00 36.99 4.46
1137 1147 9.921637 CAATAGACTTGATCTAATTCCTAGGTC 57.078 37.037 9.08 0.00 43.33 3.85
1138 1148 9.440761 ACAATAGACTTGATCTAATTCCTAGGT 57.559 33.333 9.08 0.00 43.33 3.08
1139 1149 9.703892 CACAATAGACTTGATCTAATTCCTAGG 57.296 37.037 0.82 0.82 43.33 3.02
1140 1150 9.703892 CCACAATAGACTTGATCTAATTCCTAG 57.296 37.037 0.00 0.00 43.33 3.02
1141 1151 9.213777 ACCACAATAGACTTGATCTAATTCCTA 57.786 33.333 0.00 0.00 43.33 2.94
1142 1152 8.095452 ACCACAATAGACTTGATCTAATTCCT 57.905 34.615 0.00 0.00 43.33 3.36
1143 1153 8.207545 AGACCACAATAGACTTGATCTAATTCC 58.792 37.037 0.00 0.00 43.33 3.01
1144 1154 9.606631 AAGACCACAATAGACTTGATCTAATTC 57.393 33.333 0.00 0.00 43.33 2.17
1145 1155 9.388506 CAAGACCACAATAGACTTGATCTAATT 57.611 33.333 0.00 0.00 43.33 1.40
1146 1156 8.543774 ACAAGACCACAATAGACTTGATCTAAT 58.456 33.333 0.00 0.00 43.33 1.73
1147 1157 7.907389 ACAAGACCACAATAGACTTGATCTAA 58.093 34.615 0.00 0.00 43.33 2.10
1148 1158 7.482169 ACAAGACCACAATAGACTTGATCTA 57.518 36.000 0.00 0.00 44.25 1.98
1149 1159 6.365970 ACAAGACCACAATAGACTTGATCT 57.634 37.500 0.00 0.00 39.84 2.75
1150 1160 8.547967 TTTACAAGACCACAATAGACTTGATC 57.452 34.615 0.00 0.00 39.84 2.92
1151 1161 7.119846 GCTTTACAAGACCACAATAGACTTGAT 59.880 37.037 0.00 0.00 39.84 2.57
1152 1162 6.426937 GCTTTACAAGACCACAATAGACTTGA 59.573 38.462 0.00 0.00 39.84 3.02
1153 1163 6.428159 AGCTTTACAAGACCACAATAGACTTG 59.572 38.462 0.00 0.00 42.11 3.16
1154 1164 6.428159 CAGCTTTACAAGACCACAATAGACTT 59.572 38.462 0.00 0.00 0.00 3.01
1155 1165 5.934625 CAGCTTTACAAGACCACAATAGACT 59.065 40.000 0.00 0.00 0.00 3.24
1156 1166 5.122396 CCAGCTTTACAAGACCACAATAGAC 59.878 44.000 0.00 0.00 0.00 2.59
1157 1167 5.245531 CCAGCTTTACAAGACCACAATAGA 58.754 41.667 0.00 0.00 0.00 1.98
1158 1168 4.396166 CCCAGCTTTACAAGACCACAATAG 59.604 45.833 0.00 0.00 0.00 1.73
1159 1169 4.042311 TCCCAGCTTTACAAGACCACAATA 59.958 41.667 0.00 0.00 0.00 1.90
1160 1170 3.157087 CCCAGCTTTACAAGACCACAAT 58.843 45.455 0.00 0.00 0.00 2.71
1161 1171 2.173782 TCCCAGCTTTACAAGACCACAA 59.826 45.455 0.00 0.00 0.00 3.33
1162 1172 1.771854 TCCCAGCTTTACAAGACCACA 59.228 47.619 0.00 0.00 0.00 4.17
1163 1173 2.561478 TCCCAGCTTTACAAGACCAC 57.439 50.000 0.00 0.00 0.00 4.16
1164 1174 3.073798 TGATTCCCAGCTTTACAAGACCA 59.926 43.478 0.00 0.00 0.00 4.02
1165 1175 3.686016 TGATTCCCAGCTTTACAAGACC 58.314 45.455 0.00 0.00 0.00 3.85
1228 1246 2.507484 TCCTTGTCAATCCACTGCAAG 58.493 47.619 0.00 0.00 42.29 4.01
1229 1247 2.655090 TCCTTGTCAATCCACTGCAA 57.345 45.000 0.00 0.00 0.00 4.08
1230 1248 2.507484 CTTCCTTGTCAATCCACTGCA 58.493 47.619 0.00 0.00 0.00 4.41
1231 1249 1.815003 CCTTCCTTGTCAATCCACTGC 59.185 52.381 0.00 0.00 0.00 4.40
1292 1314 3.321682 AGCAAAGCTTTAGCCACATTCAA 59.678 39.130 21.98 0.00 43.38 2.69
1313 1335 2.361757 TCACATTTGCACCCAACTCAAG 59.638 45.455 0.00 0.00 0.00 3.02
1318 1340 1.799994 GCATTCACATTTGCACCCAAC 59.200 47.619 0.00 0.00 38.72 3.77
1354 1376 3.751698 AGTTTGGTATGAGAAAAGCGTCC 59.248 43.478 0.00 0.00 0.00 4.79
1357 1379 5.324697 GCTAAGTTTGGTATGAGAAAAGCG 58.675 41.667 0.00 0.00 0.00 4.68
1380 1402 6.074782 GGAGATAATCAACTAAAGCGAAGACG 60.075 42.308 0.00 0.00 42.93 4.18
1381 1403 6.757010 TGGAGATAATCAACTAAAGCGAAGAC 59.243 38.462 0.00 0.00 0.00 3.01
1382 1404 6.873997 TGGAGATAATCAACTAAAGCGAAGA 58.126 36.000 0.00 0.00 0.00 2.87
1383 1405 7.721286 ATGGAGATAATCAACTAAAGCGAAG 57.279 36.000 0.00 0.00 0.00 3.79
1385 1407 9.778741 AATAATGGAGATAATCAACTAAAGCGA 57.221 29.630 0.00 0.00 0.00 4.93
1421 1443 6.161348 TCCATCCAGAAAAATCCCCTGTTATA 59.839 38.462 0.00 0.00 0.00 0.98
1619 1644 7.941919 AGTTAGAAAATTCAAGGTGTCCTTTC 58.058 34.615 0.00 0.00 41.69 2.62
1731 1756 4.873817 TGAGTTGATTCTGTTTTGCATGG 58.126 39.130 0.00 0.00 0.00 3.66
1907 1932 5.086621 AGAAAAGGGAGGCATTACAACAAT 58.913 37.500 0.00 0.00 0.00 2.71
1991 2016 3.438297 AGTAAATGGACAGTCGGATCG 57.562 47.619 0.00 0.00 0.00 3.69
2045 2070 6.788598 ATGGCAAACAATTGATACATGGTA 57.211 33.333 13.59 0.00 38.94 3.25
2053 2084 8.414778 ACAAAATTCAAATGGCAAACAATTGAT 58.585 25.926 13.59 0.00 45.61 2.57
2216 2247 7.448748 AATAAAGCAAAATAGGACGTGAAGT 57.551 32.000 0.00 0.00 0.00 3.01
2268 2299 9.900264 CAACTTAAAGAACAAATAGCAACAAAC 57.100 29.630 0.00 0.00 0.00 2.93
2325 2356 3.618690 AAGAGAAATCCGTCCCTGAAG 57.381 47.619 0.00 0.00 0.00 3.02
2686 2717 6.503524 TCCATAAAAGAGTTGTTCACTTTGC 58.496 36.000 0.00 0.00 37.13 3.68
3056 3087 0.402504 ATCCGGTTACCAGGTGCAAA 59.597 50.000 0.76 0.00 0.00 3.68
3332 3363 6.884295 AGCTGGTTTAACAAGATGCAAGTATA 59.116 34.615 3.27 0.00 0.00 1.47
3347 3378 2.500229 CTTCGGGACAAGCTGGTTTAA 58.500 47.619 0.00 0.00 0.00 1.52
3788 3820 2.622942 GTGTTTCCATGCCAAAGAGTGA 59.377 45.455 0.00 0.00 0.00 3.41
3852 3884 5.278808 GGGTAAAACCAAACTCATGAGTTCC 60.279 44.000 34.98 27.62 43.31 3.62
3894 3926 5.284861 TGACTATGTGTGTGGTTGTAGTT 57.715 39.130 0.00 0.00 0.00 2.24
3955 3990 9.601217 AAATAACGAACTAGCTTTATGTGAGAT 57.399 29.630 0.00 0.00 0.00 2.75
4014 4049 0.108851 ATACATGTGTGCACGAGCGA 60.109 50.000 13.13 0.00 46.23 4.93
4062 4098 1.272212 GCCCTTTGCATTTTCTCGGAA 59.728 47.619 0.00 0.00 40.77 4.30
4064 4100 0.890683 AGCCCTTTGCATTTTCTCGG 59.109 50.000 0.00 0.00 44.83 4.63
4233 4282 3.766591 TCTCGAAGATCAAAGAGGAAGCT 59.233 43.478 10.17 0.00 33.89 3.74
4320 4369 0.176910 TTGCTCTGTTGACACCACGA 59.823 50.000 0.00 0.00 0.00 4.35
4322 4371 1.267806 CCATTGCTCTGTTGACACCAC 59.732 52.381 0.00 0.00 0.00 4.16
4359 4408 0.454196 AAAACACGCCAACACTGGTC 59.546 50.000 0.00 0.00 45.53 4.02
4361 4410 1.145162 GCAAAACACGCCAACACTGG 61.145 55.000 0.00 0.00 46.65 4.00
4541 4590 2.673523 GTCTCCAGCACCAGCCAT 59.326 61.111 0.00 0.00 43.56 4.40
4573 4622 4.612412 GTGTTGGACGGCCGACCA 62.612 66.667 39.37 39.37 46.45 4.02
4662 4711 2.092753 GGGATCCATGACTTGCTTCTCA 60.093 50.000 15.23 0.00 0.00 3.27
4687 4736 2.042464 CTCCTGCTATCTTGCCACCTA 58.958 52.381 0.00 0.00 0.00 3.08
4709 4758 2.424246 GCCTCCGGTATATACTCTGCTC 59.576 54.545 12.54 0.00 0.00 4.26
4885 4934 4.049640 GCACCGGCGCAAAATCCA 62.050 61.111 10.19 0.00 0.00 3.41
5115 5164 3.260483 CGCGCTAGCCTTGCTCTG 61.260 66.667 9.66 0.00 40.44 3.35
5162 5211 1.525077 GTTTGCCGCCCCATATCGA 60.525 57.895 0.00 0.00 0.00 3.59
5243 5292 4.083110 CGTCAAATTGGAAGATTGAGTGCT 60.083 41.667 0.00 0.00 34.02 4.40
5246 5295 5.335191 GCTTCGTCAAATTGGAAGATTGAGT 60.335 40.000 13.61 0.00 39.56 3.41
5318 5368 1.367840 GGTGAAGTCCGTGCTGAGT 59.632 57.895 0.00 0.00 0.00 3.41
5345 5395 0.109532 TGATGAACAAACCTGGGCGA 59.890 50.000 0.00 0.00 0.00 5.54
5530 5584 6.463360 TCTGACAGAAAACATGCTATGTACA 58.537 36.000 1.64 0.00 44.07 2.90
5573 5627 9.073475 AGTCCAAGTTTTATTTGCAACATAGTA 57.927 29.630 0.00 0.00 0.00 1.82
5574 5628 7.951591 AGTCCAAGTTTTATTTGCAACATAGT 58.048 30.769 0.00 0.00 0.00 2.12
5575 5629 8.816640 AAGTCCAAGTTTTATTTGCAACATAG 57.183 30.769 0.00 0.00 0.00 2.23
5708 5762 0.389296 CCATGCCACAACATGCACTG 60.389 55.000 0.00 0.00 44.98 3.66
5769 5823 8.891720 AGATCTTGAGACAGAAAATTCATTAGC 58.108 33.333 0.00 0.00 0.00 3.09
5819 5875 9.442047 AATCTTCCAAACTAGTTCAGAACATAG 57.558 33.333 15.85 14.63 0.00 2.23
5896 5952 6.053650 ACTGAGCTATGTACTCGTATACACA 58.946 40.000 3.32 0.00 37.88 3.72
5904 5960 4.895224 TGGTTACTGAGCTATGTACTCG 57.105 45.455 0.00 0.00 36.94 4.18
5905 5961 9.765795 AATTATTGGTTACTGAGCTATGTACTC 57.234 33.333 0.00 0.00 34.62 2.59
5913 5969 7.720957 TGCATCATAATTATTGGTTACTGAGCT 59.279 33.333 0.00 0.00 0.00 4.09
6061 6117 1.202348 GAACCATGCTGGCAACCTAAC 59.798 52.381 0.00 0.00 42.67 2.34
6137 6193 1.148759 GAGTCGATTCCGCTGAAGGC 61.149 60.000 0.00 0.00 33.05 4.35
6416 6472 2.459060 TCGCAATCGAAGGGTTGTTA 57.541 45.000 0.00 0.00 42.44 2.41
6433 6489 2.271800 GAAGTGCCTCAGGTGTAATCG 58.728 52.381 0.00 0.00 0.00 3.34
6680 6736 0.615544 TACCAGAGGGGGTGTTACCG 60.616 60.000 0.00 0.00 42.39 4.02
6901 6961 4.726825 TCAGAACTTAATAGGGGGAAGCAT 59.273 41.667 0.00 0.00 0.00 3.79
6927 6987 8.397906 GCAACAGCAATATAACATTACTTCTCA 58.602 33.333 0.00 0.00 0.00 3.27
6974 7034 6.986817 CACATAGAACTTAATAGGGTGTGGAG 59.013 42.308 0.00 0.00 32.91 3.86
6978 7038 8.554490 AGATCACATAGAACTTAATAGGGTGT 57.446 34.615 0.00 0.00 0.00 4.16
6979 7039 9.265901 CAAGATCACATAGAACTTAATAGGGTG 57.734 37.037 0.00 0.00 37.26 4.61
6980 7040 9.213777 TCAAGATCACATAGAACTTAATAGGGT 57.786 33.333 0.00 0.00 37.26 4.34
6986 7046 9.587772 GTAGCTTCAAGATCACATAGAACTTAA 57.412 33.333 0.00 0.00 37.26 1.85
6987 7047 8.749354 TGTAGCTTCAAGATCACATAGAACTTA 58.251 33.333 0.00 0.00 37.26 2.24
6988 7048 7.615403 TGTAGCTTCAAGATCACATAGAACTT 58.385 34.615 0.00 0.00 39.65 2.66
6989 7049 7.175347 TGTAGCTTCAAGATCACATAGAACT 57.825 36.000 0.00 0.00 0.00 3.01
6993 7053 6.815641 AGTGTTGTAGCTTCAAGATCACATAG 59.184 38.462 20.04 0.00 29.95 2.23
7054 7114 3.408634 CCCACACTCTTCGGTACAAAAT 58.591 45.455 0.00 0.00 0.00 1.82
7115 7175 5.007626 GCAATACTCGATACCATGAAAGCAA 59.992 40.000 0.00 0.00 0.00 3.91
7133 7193 4.679662 TCGTAACCTAGCAGAAGCAATAC 58.320 43.478 0.00 0.00 45.49 1.89
7140 7200 4.015084 ACTAGCTTCGTAACCTAGCAGAA 58.985 43.478 0.00 0.00 37.37 3.02
7154 7214 3.258622 AGGCCGTATGGATAACTAGCTTC 59.741 47.826 4.73 0.00 37.49 3.86
7203 7263 2.879826 CCTCCATTTGGCATTTTCGTC 58.120 47.619 0.00 0.00 34.44 4.20
7296 7356 6.539173 TGTCTCCGGGTATATGCATATTTTT 58.461 36.000 23.71 3.63 0.00 1.94
7297 7357 6.121776 TGTCTCCGGGTATATGCATATTTT 57.878 37.500 23.71 4.01 0.00 1.82
7298 7358 5.755409 TGTCTCCGGGTATATGCATATTT 57.245 39.130 23.71 4.77 0.00 1.40
7299 7359 5.957771 ATGTCTCCGGGTATATGCATATT 57.042 39.130 23.71 8.88 0.00 1.28
7300 7360 7.071196 ACATTATGTCTCCGGGTATATGCATAT 59.929 37.037 22.31 22.31 0.00 1.78
7301 7361 6.382859 ACATTATGTCTCCGGGTATATGCATA 59.617 38.462 9.27 9.27 0.00 3.14
7302 7362 5.189736 ACATTATGTCTCCGGGTATATGCAT 59.810 40.000 3.79 3.79 0.00 3.96
7303 7363 4.530553 ACATTATGTCTCCGGGTATATGCA 59.469 41.667 0.00 0.00 0.00 3.96
7304 7364 5.086104 ACATTATGTCTCCGGGTATATGC 57.914 43.478 0.00 0.00 0.00 3.14
7305 7365 7.165460 TGTACATTATGTCTCCGGGTATATG 57.835 40.000 0.00 0.00 0.00 1.78
7306 7366 7.973048 ATGTACATTATGTCTCCGGGTATAT 57.027 36.000 1.41 0.00 0.00 0.86
7307 7367 8.909923 CATATGTACATTATGTCTCCGGGTATA 58.090 37.037 14.77 0.00 0.00 1.47
7308 7368 7.399191 ACATATGTACATTATGTCTCCGGGTAT 59.601 37.037 14.77 0.00 29.28 2.73
7309 7369 6.722590 ACATATGTACATTATGTCTCCGGGTA 59.277 38.462 14.77 0.00 29.28 3.69
7310 7370 5.542635 ACATATGTACATTATGTCTCCGGGT 59.457 40.000 14.77 0.00 29.28 5.28
7311 7371 5.869344 CACATATGTACATTATGTCTCCGGG 59.131 44.000 14.77 5.56 32.67 5.73
7312 7372 6.455647 ACACATATGTACATTATGTCTCCGG 58.544 40.000 14.77 10.83 37.26 5.14
7313 7373 9.471084 TTTACACATATGTACATTATGTCTCCG 57.529 33.333 14.77 11.11 41.12 4.63
7359 7419 9.730420 GTGTTTCTTTTTGTAGCTCTCATTTTA 57.270 29.630 0.00 0.00 0.00 1.52
7360 7420 8.250332 TGTGTTTCTTTTTGTAGCTCTCATTTT 58.750 29.630 0.00 0.00 0.00 1.82
7361 7421 7.771183 TGTGTTTCTTTTTGTAGCTCTCATTT 58.229 30.769 0.00 0.00 0.00 2.32
7362 7422 7.333528 TGTGTTTCTTTTTGTAGCTCTCATT 57.666 32.000 0.00 0.00 0.00 2.57
7363 7423 6.942532 TGTGTTTCTTTTTGTAGCTCTCAT 57.057 33.333 0.00 0.00 0.00 2.90
7364 7424 6.751514 TTGTGTTTCTTTTTGTAGCTCTCA 57.248 33.333 0.00 0.00 0.00 3.27
7365 7425 9.899226 ATATTTGTGTTTCTTTTTGTAGCTCTC 57.101 29.630 0.00 0.00 0.00 3.20
7366 7426 9.683069 CATATTTGTGTTTCTTTTTGTAGCTCT 57.317 29.630 0.00 0.00 0.00 4.09
7367 7427 9.463443 ACATATTTGTGTTTCTTTTTGTAGCTC 57.537 29.630 0.00 0.00 33.85 4.09
7368 7428 9.248291 CACATATTTGTGTTTCTTTTTGTAGCT 57.752 29.630 8.02 0.00 46.68 3.32
7384 7444 6.343716 TGTGATGAAAAGCCACATATTTGT 57.656 33.333 0.00 0.00 36.07 2.83
7385 7445 6.814644 ACATGTGATGAAAAGCCACATATTTG 59.185 34.615 0.00 0.00 46.23 2.32
7386 7446 6.938507 ACATGTGATGAAAAGCCACATATTT 58.061 32.000 0.00 0.00 46.23 1.40
7387 7447 6.534475 ACATGTGATGAAAAGCCACATATT 57.466 33.333 0.00 0.00 46.23 1.28
7388 7448 7.828508 ATACATGTGATGAAAAGCCACATAT 57.171 32.000 9.11 0.00 46.23 1.78
7389 7449 7.122501 ACAATACATGTGATGAAAAGCCACATA 59.877 33.333 9.11 0.00 46.23 2.29
7391 7451 5.243507 ACAATACATGTGATGAAAAGCCACA 59.756 36.000 9.11 0.00 41.93 4.17
7392 7452 5.713025 ACAATACATGTGATGAAAAGCCAC 58.287 37.500 9.11 0.00 41.93 5.01
7393 7453 5.981088 ACAATACATGTGATGAAAAGCCA 57.019 34.783 9.11 0.00 41.93 4.75
7394 7454 6.389091 TGAACAATACATGTGATGAAAAGCC 58.611 36.000 9.11 0.00 42.99 4.35
7395 7455 8.470040 AATGAACAATACATGTGATGAAAAGC 57.530 30.769 9.11 0.00 42.99 3.51
7396 7456 9.850628 AGAATGAACAATACATGTGATGAAAAG 57.149 29.630 9.11 0.00 42.99 2.27
7397 7457 9.844790 GAGAATGAACAATACATGTGATGAAAA 57.155 29.630 9.11 0.00 42.99 2.29
7398 7458 9.234827 AGAGAATGAACAATACATGTGATGAAA 57.765 29.630 9.11 0.00 42.99 2.69
7399 7459 8.797350 AGAGAATGAACAATACATGTGATGAA 57.203 30.769 9.11 0.20 42.99 2.57
7400 7460 9.889128 TTAGAGAATGAACAATACATGTGATGA 57.111 29.630 9.11 0.00 42.99 2.92
7402 7462 9.896645 ACTTAGAGAATGAACAATACATGTGAT 57.103 29.630 9.11 0.00 42.99 3.06
7403 7463 9.371136 GACTTAGAGAATGAACAATACATGTGA 57.629 33.333 9.11 0.00 42.99 3.58
7404 7464 8.607459 GGACTTAGAGAATGAACAATACATGTG 58.393 37.037 9.11 0.00 42.99 3.21
7405 7465 8.321353 TGGACTTAGAGAATGAACAATACATGT 58.679 33.333 2.69 2.69 46.82 3.21
7406 7466 8.722480 TGGACTTAGAGAATGAACAATACATG 57.278 34.615 0.00 0.00 0.00 3.21
7407 7467 9.334947 CATGGACTTAGAGAATGAACAATACAT 57.665 33.333 0.00 0.00 0.00 2.29
7408 7468 8.321353 ACATGGACTTAGAGAATGAACAATACA 58.679 33.333 0.00 0.00 0.00 2.29
7409 7469 8.723942 ACATGGACTTAGAGAATGAACAATAC 57.276 34.615 0.00 0.00 0.00 1.89
7410 7470 9.739276 AAACATGGACTTAGAGAATGAACAATA 57.261 29.630 0.00 0.00 0.00 1.90
7411 7471 8.641498 AAACATGGACTTAGAGAATGAACAAT 57.359 30.769 0.00 0.00 0.00 2.71
7412 7472 8.463930 AAAACATGGACTTAGAGAATGAACAA 57.536 30.769 0.00 0.00 0.00 2.83
7413 7473 8.463930 AAAAACATGGACTTAGAGAATGAACA 57.536 30.769 0.00 0.00 0.00 3.18
7630 7691 2.762887 CTCAGATAGAGGGAGCACAACA 59.237 50.000 0.00 0.00 40.84 3.33
7652 7719 5.906113 AAATCATGTGCCCACGTTATAAA 57.094 34.783 0.00 0.00 0.00 1.40
7769 7836 8.840200 TCCTTCCTTAGTTTCTATACACTGAT 57.160 34.615 0.00 0.00 0.00 2.90
7783 7850 5.911766 AGTAGCCCATTAATCCTTCCTTAGT 59.088 40.000 0.00 0.00 0.00 2.24
7787 7854 4.726825 TCAAGTAGCCCATTAATCCTTCCT 59.273 41.667 0.00 0.00 0.00 3.36
7791 7858 6.824958 TTAGTCAAGTAGCCCATTAATCCT 57.175 37.500 0.00 0.00 0.00 3.24
7799 7866 6.001449 AGCATTAATTAGTCAAGTAGCCCA 57.999 37.500 0.00 0.00 0.00 5.36
7801 7868 7.281100 AGTCAAGCATTAATTAGTCAAGTAGCC 59.719 37.037 0.00 0.00 0.00 3.93
7803 7870 9.979270 CAAGTCAAGCATTAATTAGTCAAGTAG 57.021 33.333 0.00 0.00 0.00 2.57
7805 7872 8.396272 ACAAGTCAAGCATTAATTAGTCAAGT 57.604 30.769 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.