Multiple sequence alignment - TraesCS1B01G348900

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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 TraesCS1B01G348900 chr1B 100.000 3109 0 0 1 3109 579003114 579000006 0.000000e+00 5742.0
1 TraesCS1B01G348900 chr1B 83.475 1295 148 41 1179 2428 577912765 577911492 0.000000e+00 1146.0
2 TraesCS1B01G348900 chr1B 87.832 452 55 0 1187 1638 579778472 579778021 5.900000e-147 531.0
3 TraesCS1B01G348900 chr1B 88.424 406 46 1 1792 2196 578044421 578044016 3.600000e-134 488.0
4 TraesCS1B01G348900 chr1B 85.651 453 52 13 2474 2921 578052664 578052220 6.070000e-127 464.0
5 TraesCS1B01G348900 chr1B 85.588 451 56 4 658 1101 579778934 579778486 6.070000e-127 464.0
6 TraesCS1B01G348900 chr1B 88.251 366 43 0 733 1098 578045436 578045071 3.680000e-119 438.0
7 TraesCS1B01G348900 chr1B 94.241 191 8 3 128 317 579772580 579772392 3.920000e-74 289.0
8 TraesCS1B01G348900 chr1B 91.346 104 9 0 31 134 579772729 579772626 3.230000e-30 143.0
9 TraesCS1B01G348900 chr1B 97.500 40 1 0 1130 1169 577912695 577912656 5.560000e-08 69.4
10 TraesCS1B01G348900 chr1B 92.105 38 3 0 1107 1144 579001868 579001831 2.000000e-03 54.7
11 TraesCS1B01G348900 chr1D 94.338 1307 52 5 1179 2465 427371948 427370644 0.000000e+00 1984.0
12 TraesCS1B01G348900 chr1D 95.105 429 20 1 681 1109 427372379 427371952 0.000000e+00 675.0
13 TraesCS1B01G348900 chr1D 82.681 664 90 17 1770 2424 427331259 427330612 1.620000e-157 566.0
14 TraesCS1B01G348900 chr1D 90.566 424 29 7 2524 2942 427370638 427370221 4.530000e-153 551.0
15 TraesCS1B01G348900 chr1D 87.265 479 61 0 1179 1657 427319137 427318659 5.860000e-152 547.0
16 TraesCS1B01G348900 chr1D 87.473 471 57 2 1180 1648 427596534 427596064 2.730000e-150 542.0
17 TraesCS1B01G348900 chr1D 84.130 460 62 5 658 1107 427596999 427596541 4.760000e-118 435.0
18 TraesCS1B01G348900 chr1D 87.705 366 45 0 733 1098 427332244 427331879 7.970000e-116 427.0
19 TraesCS1B01G348900 chr1D 87.671 365 42 1 1760 2124 427595894 427595533 3.710000e-114 422.0
20 TraesCS1B01G348900 chr1D 81.930 487 31 23 128 584 427590719 427590260 2.950000e-95 359.0
21 TraesCS1B01G348900 chr1D 91.597 119 6 4 2922 3038 275529317 275529201 8.920000e-36 161.0
22 TraesCS1B01G348900 chr1D 95.000 40 2 0 1130 1169 427371878 427371839 2.590000e-06 63.9
23 TraesCS1B01G348900 chr1D 100.000 29 0 0 1107 1135 427371880 427371852 2.000000e-03 54.7
24 TraesCS1B01G348900 chr1A 93.745 1311 57 5 1179 2465 522535550 522534241 0.000000e+00 1943.0
25 TraesCS1B01G348900 chr1A 95.194 978 27 4 132 1109 522536511 522535554 0.000000e+00 1528.0
26 TraesCS1B01G348900 chr1A 87.891 479 58 0 1179 1657 522510480 522510002 5.820000e-157 564.0
27 TraesCS1B01G348900 chr1A 90.141 426 29 9 2524 2942 522534235 522533816 2.730000e-150 542.0
28 TraesCS1B01G348900 chr1A 85.120 457 60 4 658 1107 522882910 522882455 7.860000e-126 460.0
29 TraesCS1B01G348900 chr1A 87.438 406 40 8 1758 2161 522515355 522514959 1.020000e-124 457.0
30 TraesCS1B01G348900 chr1A 87.123 365 45 2 738 1101 522510855 522510492 2.230000e-111 412.0
31 TraesCS1B01G348900 chr1A 95.676 185 5 3 128 311 522879423 522879241 8.430000e-76 294.0
32 TraesCS1B01G348900 chr1A 94.737 133 7 0 2 134 522536692 522536560 1.130000e-49 207.0
33 TraesCS1B01G348900 chr1A 95.918 98 4 0 2941 3038 6567089 6567186 3.210000e-35 159.0
34 TraesCS1B01G348900 chr1A 91.176 102 9 0 33 134 522879570 522879469 4.180000e-29 139.0
35 TraesCS1B01G348900 chr1A 97.500 40 1 0 1130 1169 522535480 522535441 5.560000e-08 69.4
36 TraesCS1B01G348900 chr1A 100.000 29 0 0 1107 1135 522535482 522535454 2.000000e-03 54.7
37 TraesCS1B01G348900 chr5D 83.897 1124 141 22 1179 2267 523187198 523186080 0.000000e+00 1037.0
38 TraesCS1B01G348900 chr5D 83.733 1125 141 23 1179 2267 523314387 523313269 0.000000e+00 1026.0
39 TraesCS1B01G348900 chr5D 81.290 465 74 8 655 1109 523314852 523314391 6.340000e-97 364.0
40 TraesCS1B01G348900 chr5D 95.098 102 4 1 2941 3041 507553714 507553613 3.210000e-35 159.0
41 TraesCS1B01G348900 chr5D 97.500 40 1 0 1130 1169 523187128 523187089 5.560000e-08 69.4
42 TraesCS1B01G348900 chr5D 97.500 40 1 0 1130 1169 523314317 523314278 5.560000e-08 69.4
43 TraesCS1B01G348900 chr5D 100.000 29 0 0 1107 1135 523187130 523187102 2.000000e-03 54.7
44 TraesCS1B01G348900 chr5D 100.000 29 0 0 1107 1135 523314319 523314291 2.000000e-03 54.7
45 TraesCS1B01G348900 chrUn 82.510 263 42 4 2009 2267 199132292 199132554 8.670000e-56 228.0
46 TraesCS1B01G348900 chrUn 97.500 40 1 0 1130 1169 475269734 475269773 5.560000e-08 69.4
47 TraesCS1B01G348900 chrUn 100.000 29 0 0 1107 1135 475269732 475269760 2.000000e-03 54.7
48 TraesCS1B01G348900 chr3B 94.286 105 5 1 2934 3038 12406665 12406768 3.210000e-35 159.0
49 TraesCS1B01G348900 chr3A 95.918 98 4 0 2942 3039 287684686 287684783 3.210000e-35 159.0
50 TraesCS1B01G348900 chr6B 92.727 110 6 2 2930 3038 475446861 475446753 1.150000e-34 158.0
51 TraesCS1B01G348900 chr2D 94.175 103 6 0 2938 3040 206682758 206682656 1.150000e-34 158.0
52 TraesCS1B01G348900 chr4A 91.228 114 9 1 2926 3039 710665503 710665615 1.490000e-33 154.0
53 TraesCS1B01G348900 chr6A 92.381 105 7 1 2935 3039 11165158 11165055 6.950000e-32 148.0


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 TraesCS1B01G348900 chr1B 579000006 579003114 3108 True 2898.350000 5742 96.052500 1 3109 2 chr1B.!!$R4 3108
1 TraesCS1B01G348900 chr1B 577911492 577912765 1273 True 607.700000 1146 90.487500 1130 2428 2 chr1B.!!$R2 1298
2 TraesCS1B01G348900 chr1B 579778021 579778934 913 True 497.500000 531 86.710000 658 1638 2 chr1B.!!$R6 980
3 TraesCS1B01G348900 chr1B 578044016 578045436 1420 True 463.000000 488 88.337500 733 2196 2 chr1B.!!$R3 1463
4 TraesCS1B01G348900 chr1D 427370221 427372379 2158 True 665.720000 1984 95.001800 681 2942 5 chr1D.!!$R5 2261
5 TraesCS1B01G348900 chr1D 427330612 427332244 1632 True 496.500000 566 85.193000 733 2424 2 chr1D.!!$R4 1691
6 TraesCS1B01G348900 chr1D 427595533 427596999 1466 True 466.333333 542 86.424667 658 2124 3 chr1D.!!$R6 1466
7 TraesCS1B01G348900 chr1A 522533816 522536692 2876 True 724.016667 1943 95.219500 2 2942 6 chr1A.!!$R3 2940
8 TraesCS1B01G348900 chr1A 522510002 522510855 853 True 488.000000 564 87.507000 738 1657 2 chr1A.!!$R2 919
9 TraesCS1B01G348900 chr1A 522879241 522882910 3669 True 297.666667 460 90.657333 33 1107 3 chr1A.!!$R4 1074
10 TraesCS1B01G348900 chr5D 523186080 523187198 1118 True 387.033333 1037 93.799000 1107 2267 3 chr5D.!!$R2 1160
11 TraesCS1B01G348900 chr5D 523313269 523314852 1583 True 378.525000 1026 90.630750 655 2267 4 chr5D.!!$R3 1612

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
159 211 0.396435 ATTTGCGAGGTGTGAGTCCA 59.604 50.0 0.0 0.0 0.00 4.02 F
1115 1184 0.179127 CTCGTCGGTGATGCACTCAT 60.179 55.0 0.0 0.0 35.97 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1215 0.107508 CAGGGACGTGGAATGCTCAT 60.108 55.0 0.00 0.00 0.00 2.90 R
2500 2696 0.179702 ATCGAGCACAGCATGGTGAT 59.820 50.0 30.46 12.26 43.62 3.06 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
65 66 1.178276 CCTGTCGGTCTTGTAGAGCT 58.822 55.000 4.61 0.00 40.38 4.09
103 104 5.527033 TCGAGTTGCTCTCTTGATGATATG 58.473 41.667 7.61 0.00 40.75 1.78
107 108 6.647229 AGTTGCTCTCTTGATGATATGAACA 58.353 36.000 0.00 0.00 0.00 3.18
120 121 9.810870 TGATGATATGAACATTGGGAATCAATA 57.189 29.630 0.00 0.00 43.70 1.90
128 129 8.811017 TGAACATTGGGAATCAATAAAAGCTTA 58.189 29.630 0.00 0.00 43.70 3.09
159 211 0.396435 ATTTGCGAGGTGTGAGTCCA 59.604 50.000 0.00 0.00 0.00 4.02
182 234 4.237724 TGTGATCAACAAGTTAGCTCTCG 58.762 43.478 0.00 0.00 35.24 4.04
199 251 7.578310 AGCTCTCGGTAGTACAATACAAATA 57.422 36.000 2.06 0.00 0.00 1.40
201 253 8.082852 AGCTCTCGGTAGTACAATACAAATATG 58.917 37.037 2.06 0.00 0.00 1.78
202 254 7.866393 GCTCTCGGTAGTACAATACAAATATGT 59.134 37.037 2.06 0.00 43.74 2.29
203 255 9.181805 CTCTCGGTAGTACAATACAAATATGTG 57.818 37.037 2.06 0.00 40.84 3.21
206 258 9.955208 TCGGTAGTACAATACAAATATGTGTAG 57.045 33.333 11.38 1.95 40.84 2.74
207 259 8.697067 CGGTAGTACAATACAAATATGTGTAGC 58.303 37.037 11.38 0.00 40.84 3.58
208 260 9.537192 GGTAGTACAATACAAATATGTGTAGCA 57.463 33.333 11.38 0.00 40.84 3.49
210 262 8.662781 AGTACAATACAAATATGTGTAGCAGG 57.337 34.615 11.38 3.89 40.84 4.85
211 263 8.265055 AGTACAATACAAATATGTGTAGCAGGT 58.735 33.333 11.38 8.70 40.84 4.00
212 264 7.938140 ACAATACAAATATGTGTAGCAGGTT 57.062 32.000 11.38 0.00 40.84 3.50
226 278 4.806952 AGCAGGTTAGATAGGAGAGAGT 57.193 45.455 0.00 0.00 0.00 3.24
243 295 4.019321 AGAGAGTATTTTTGCTAGCCACCA 60.019 41.667 13.29 0.00 0.00 4.17
244 296 4.860022 AGAGTATTTTTGCTAGCCACCAT 58.140 39.130 13.29 2.07 0.00 3.55
250 302 0.680921 TTGCTAGCCACCATTGCTCC 60.681 55.000 13.29 0.00 40.23 4.70
281 333 1.350193 CACTAGTAGCCACAACTGCG 58.650 55.000 0.00 0.00 0.00 5.18
326 378 4.844085 TCTAACTCATTGTTCCCCAGAGAA 59.156 41.667 0.00 0.00 39.89 2.87
399 451 8.593945 AATGTTCAACCATTCATTAGGTATGT 57.406 30.769 0.00 0.00 37.07 2.29
400 452 9.693739 AATGTTCAACCATTCATTAGGTATGTA 57.306 29.630 0.00 0.00 37.07 2.29
401 453 8.500753 TGTTCAACCATTCATTAGGTATGTAC 57.499 34.615 0.00 0.00 37.07 2.90
402 454 8.103935 TGTTCAACCATTCATTAGGTATGTACA 58.896 33.333 0.00 0.00 37.07 2.90
403 455 8.612619 GTTCAACCATTCATTAGGTATGTACAG 58.387 37.037 0.33 0.00 37.07 2.74
404 456 8.084985 TCAACCATTCATTAGGTATGTACAGA 57.915 34.615 0.33 0.00 37.07 3.41
473 525 6.961554 GTGTTTAATTATGAAGAGAAGTGCGG 59.038 38.462 0.00 0.00 0.00 5.69
518 570 5.296780 TGGAGTTGAGCTAAACTTGAAACTG 59.703 40.000 17.90 0.00 40.48 3.16
577 629 6.774656 CCTGAGTAAATAGGCTTCCATGAATT 59.225 38.462 0.00 0.00 0.00 2.17
686 739 7.953005 TTGAATAATTGATTACTCAAGGCCA 57.047 32.000 5.01 0.00 44.32 5.36
695 748 7.315066 TGATTACTCAAGGCCATATCATGTA 57.685 36.000 5.01 0.00 0.00 2.29
704 757 6.515512 AGGCCATATCATGTACCTTAAACT 57.484 37.500 5.01 0.00 32.75 2.66
833 899 2.011046 GCTGCTCCAGGCTCAAGTTAG 61.011 57.143 0.00 0.00 42.39 2.34
1081 1150 3.370209 GGAGATTGTTTACGGGCTTACCT 60.370 47.826 0.00 0.00 36.97 3.08
1109 1178 1.589196 GCCTACTCGTCGGTGATGC 60.589 63.158 0.00 0.00 0.00 3.91
1111 1180 0.525668 CCTACTCGTCGGTGATGCAC 60.526 60.000 0.00 0.00 0.00 4.57
1113 1182 0.450583 TACTCGTCGGTGATGCACTC 59.549 55.000 0.00 0.00 34.40 3.51
1115 1184 0.179127 CTCGTCGGTGATGCACTCAT 60.179 55.000 0.00 0.00 35.97 2.90
1116 1185 0.458370 TCGTCGGTGATGCACTCATG 60.458 55.000 0.00 0.00 35.97 3.07
1117 1186 1.423721 CGTCGGTGATGCACTCATGG 61.424 60.000 0.00 0.00 35.97 3.66
1118 1187 0.391661 GTCGGTGATGCACTCATGGT 60.392 55.000 0.00 0.00 35.97 3.55
1119 1188 0.324614 TCGGTGATGCACTCATGGTT 59.675 50.000 0.00 0.00 35.97 3.67
1120 1189 0.729116 CGGTGATGCACTCATGGTTC 59.271 55.000 0.00 0.00 35.97 3.62
1121 1190 1.098050 GGTGATGCACTCATGGTTCC 58.902 55.000 0.00 0.00 35.97 3.62
1122 1191 1.340405 GGTGATGCACTCATGGTTCCT 60.340 52.381 0.00 0.00 35.97 3.36
1123 1192 2.092968 GGTGATGCACTCATGGTTCCTA 60.093 50.000 0.00 0.00 35.97 2.94
1124 1193 3.201290 GTGATGCACTCATGGTTCCTAG 58.799 50.000 0.00 0.00 35.97 3.02
1125 1194 3.106827 TGATGCACTCATGGTTCCTAGA 58.893 45.455 0.00 0.00 31.96 2.43
1126 1195 3.713248 TGATGCACTCATGGTTCCTAGAT 59.287 43.478 0.00 0.00 31.96 1.98
1127 1196 3.548745 TGCACTCATGGTTCCTAGATG 57.451 47.619 0.00 0.00 0.00 2.90
1128 1197 3.106827 TGCACTCATGGTTCCTAGATGA 58.893 45.455 0.00 0.00 0.00 2.92
1129 1198 3.133542 TGCACTCATGGTTCCTAGATGAG 59.866 47.826 13.96 13.96 45.78 2.90
1130 1199 3.726607 CACTCATGGTTCCTAGATGAGC 58.273 50.000 15.00 1.53 44.70 4.26
1131 1200 3.133542 CACTCATGGTTCCTAGATGAGCA 59.866 47.826 15.00 6.37 44.70 4.26
1132 1201 3.972638 ACTCATGGTTCCTAGATGAGCAT 59.027 43.478 15.00 8.05 44.70 3.79
1133 1202 4.411540 ACTCATGGTTCCTAGATGAGCATT 59.588 41.667 15.00 0.00 44.70 3.56
1134 1203 4.965814 TCATGGTTCCTAGATGAGCATTC 58.034 43.478 0.00 0.00 29.82 2.67
1135 1204 4.409901 TCATGGTTCCTAGATGAGCATTCA 59.590 41.667 0.00 0.00 37.81 2.57
1136 1205 5.072736 TCATGGTTCCTAGATGAGCATTCAT 59.927 40.000 0.00 0.00 46.61 2.57
1137 1206 4.711399 TGGTTCCTAGATGAGCATTCATG 58.289 43.478 0.00 0.00 44.01 3.07
1138 1207 4.070716 GGTTCCTAGATGAGCATTCATGG 58.929 47.826 0.00 0.00 44.01 3.66
1139 1208 4.445448 GGTTCCTAGATGAGCATTCATGGT 60.445 45.833 0.00 0.00 44.01 3.55
1140 1209 5.128919 GTTCCTAGATGAGCATTCATGGTT 58.871 41.667 0.00 0.00 44.01 3.67
1141 1210 4.965814 TCCTAGATGAGCATTCATGGTTC 58.034 43.478 0.00 0.00 44.01 3.62
1142 1211 4.070716 CCTAGATGAGCATTCATGGTTCC 58.929 47.826 0.00 0.00 44.01 3.62
1143 1212 3.947612 AGATGAGCATTCATGGTTCCT 57.052 42.857 0.00 0.00 44.01 3.36
1144 1213 5.012458 CCTAGATGAGCATTCATGGTTCCTA 59.988 44.000 0.00 0.00 44.01 2.94
1145 1214 4.970711 AGATGAGCATTCATGGTTCCTAG 58.029 43.478 0.00 0.00 44.01 3.02
1146 1215 4.657504 AGATGAGCATTCATGGTTCCTAGA 59.342 41.667 0.00 0.00 44.01 2.43
1147 1216 5.310068 AGATGAGCATTCATGGTTCCTAGAT 59.690 40.000 0.00 0.00 44.01 1.98
1148 1217 4.711399 TGAGCATTCATGGTTCCTAGATG 58.289 43.478 0.00 0.00 38.85 2.90
1149 1218 4.409901 TGAGCATTCATGGTTCCTAGATGA 59.590 41.667 0.00 0.00 38.85 2.92
1150 1219 4.970711 AGCATTCATGGTTCCTAGATGAG 58.029 43.478 0.00 0.00 34.35 2.90
1151 1220 3.501445 GCATTCATGGTTCCTAGATGAGC 59.499 47.826 0.00 0.00 0.00 4.26
1152 1221 4.711399 CATTCATGGTTCCTAGATGAGCA 58.289 43.478 0.00 0.00 0.00 4.26
1153 1222 5.314529 CATTCATGGTTCCTAGATGAGCAT 58.685 41.667 0.00 0.00 32.23 3.79
1154 1223 5.378230 TTCATGGTTCCTAGATGAGCATT 57.622 39.130 0.00 0.00 29.82 3.56
1155 1224 4.965814 TCATGGTTCCTAGATGAGCATTC 58.034 43.478 0.00 0.00 29.82 2.67
1156 1225 3.845781 TGGTTCCTAGATGAGCATTCC 57.154 47.619 0.00 0.00 0.00 3.01
1157 1226 3.114606 TGGTTCCTAGATGAGCATTCCA 58.885 45.455 0.00 0.00 0.00 3.53
1158 1227 3.118261 TGGTTCCTAGATGAGCATTCCAC 60.118 47.826 0.00 0.00 0.00 4.02
1159 1228 3.126831 GTTCCTAGATGAGCATTCCACG 58.873 50.000 0.00 0.00 0.00 4.94
1160 1229 2.388735 TCCTAGATGAGCATTCCACGT 58.611 47.619 0.00 0.00 0.00 4.49
1161 1230 2.362397 TCCTAGATGAGCATTCCACGTC 59.638 50.000 0.00 0.00 0.00 4.34
1162 1231 2.546795 CCTAGATGAGCATTCCACGTCC 60.547 54.545 0.00 0.00 0.00 4.79
1163 1232 0.179000 AGATGAGCATTCCACGTCCC 59.821 55.000 0.00 0.00 0.00 4.46
1164 1233 0.179000 GATGAGCATTCCACGTCCCT 59.821 55.000 0.00 0.00 0.00 4.20
1165 1234 0.107508 ATGAGCATTCCACGTCCCTG 60.108 55.000 0.00 0.00 0.00 4.45
1166 1235 1.296715 GAGCATTCCACGTCCCTGT 59.703 57.895 0.00 0.00 0.00 4.00
1167 1236 0.321653 GAGCATTCCACGTCCCTGTT 60.322 55.000 0.00 0.00 0.00 3.16
1168 1237 0.321653 AGCATTCCACGTCCCTGTTC 60.322 55.000 0.00 0.00 0.00 3.18
1169 1238 0.321653 GCATTCCACGTCCCTGTTCT 60.322 55.000 0.00 0.00 0.00 3.01
1170 1239 1.442769 CATTCCACGTCCCTGTTCTG 58.557 55.000 0.00 0.00 0.00 3.02
1171 1240 1.056660 ATTCCACGTCCCTGTTCTGT 58.943 50.000 0.00 0.00 0.00 3.41
1172 1241 0.391597 TTCCACGTCCCTGTTCTGTC 59.608 55.000 0.00 0.00 0.00 3.51
1173 1242 0.469331 TCCACGTCCCTGTTCTGTCT 60.469 55.000 0.00 0.00 0.00 3.41
1174 1243 0.393077 CCACGTCCCTGTTCTGTCTT 59.607 55.000 0.00 0.00 0.00 3.01
1175 1244 1.202651 CCACGTCCCTGTTCTGTCTTT 60.203 52.381 0.00 0.00 0.00 2.52
1176 1245 1.867233 CACGTCCCTGTTCTGTCTTTG 59.133 52.381 0.00 0.00 0.00 2.77
1177 1246 1.760613 ACGTCCCTGTTCTGTCTTTGA 59.239 47.619 0.00 0.00 0.00 2.69
1277 1346 3.135348 TGGTTCCTAGATGAGCATTCCAG 59.865 47.826 0.00 0.00 0.00 3.86
1321 1390 3.092301 AGCCTTAACTTTTGGGAGATGC 58.908 45.455 0.00 0.00 0.00 3.91
1461 1530 0.187117 TTGATGTTGGTGGAGGCCAA 59.813 50.000 5.01 0.00 45.37 4.52
1688 1768 8.347771 ACACATCATCATTTGACAATATACTGC 58.652 33.333 0.00 0.00 37.11 4.40
1803 1962 1.957765 TTTTGGCTGCTGCTGTGCAA 61.958 50.000 15.64 8.08 42.83 4.08
1847 2006 3.476552 GGGTGATGAAGACTGTGTCAAA 58.523 45.455 0.46 0.00 34.60 2.69
1871 2030 7.982761 ATTATTGAAAAATTGCAAGGAAGCA 57.017 28.000 4.94 0.00 43.99 3.91
2051 2210 1.002134 CATGGAAGCTGGGTTCGGT 60.002 57.895 6.47 0.00 0.00 4.69
2140 2299 9.810545 CCATTAAAAATTACATGGTAATCGGTT 57.189 29.630 0.00 0.00 32.82 4.44
2189 2353 1.068748 CATGTGTGCTCTCTTGTTGCC 60.069 52.381 0.00 0.00 0.00 4.52
2193 2357 1.148949 TGCTCTCTTGTTGCCTGCA 59.851 52.632 0.00 0.00 0.00 4.41
2272 2442 5.155643 CGCTGTGATCAATGAATTTGTTCA 58.844 37.500 0.00 0.00 40.21 3.18
2273 2443 5.630264 CGCTGTGATCAATGAATTTGTTCAA 59.370 36.000 0.00 0.00 42.68 2.69
2315 2507 3.246301 ACCATCTGCAGCTGGTCTATAT 58.754 45.455 31.72 12.24 40.18 0.86
2431 2627 7.972832 ATACCTTTGTGAATCGAGTGTTTAA 57.027 32.000 0.00 0.00 0.00 1.52
2434 2630 7.712797 ACCTTTGTGAATCGAGTGTTTAAATT 58.287 30.769 0.00 0.00 0.00 1.82
2435 2631 8.842280 ACCTTTGTGAATCGAGTGTTTAAATTA 58.158 29.630 0.00 0.00 0.00 1.40
2446 2642 6.299966 CGAGTGTTTAAATTACTTTGTGCTCG 59.700 38.462 8.80 0.00 34.73 5.03
2458 2654 0.039798 TGTGCTCGTGAGGTCGTTAC 60.040 55.000 0.00 0.00 0.00 2.50
2460 2656 0.039798 TGCTCGTGAGGTCGTTACAC 60.040 55.000 0.00 0.00 0.00 2.90
2465 2661 1.137513 GTGAGGTCGTTACACACTGC 58.862 55.000 0.00 0.00 34.13 4.40
2467 2663 1.411246 TGAGGTCGTTACACACTGCTT 59.589 47.619 0.00 0.00 0.00 3.91
2468 2664 1.792949 GAGGTCGTTACACACTGCTTG 59.207 52.381 0.00 0.00 0.00 4.01
2470 2666 0.934496 GTCGTTACACACTGCTTGCA 59.066 50.000 0.00 0.00 0.00 4.08
2471 2667 1.070577 GTCGTTACACACTGCTTGCAG 60.071 52.381 19.62 19.62 0.00 4.41
2472 2668 0.235665 CGTTACACACTGCTTGCAGG 59.764 55.000 23.98 15.80 0.00 4.85
2473 2669 1.308998 GTTACACACTGCTTGCAGGT 58.691 50.000 23.98 16.35 0.00 4.00
2474 2670 1.002468 GTTACACACTGCTTGCAGGTG 60.002 52.381 26.78 26.78 37.05 4.00
2475 2671 0.180171 TACACACTGCTTGCAGGTGT 59.820 50.000 31.48 31.48 43.74 4.16
2476 2672 1.097547 ACACACTGCTTGCAGGTGTC 61.098 55.000 27.64 0.00 41.45 3.67
2477 2673 1.096967 CACACTGCTTGCAGGTGTCA 61.097 55.000 23.98 0.00 41.45 3.58
2478 2674 0.816825 ACACTGCTTGCAGGTGTCAG 60.817 55.000 23.98 10.44 39.59 3.51
2479 2675 0.533531 CACTGCTTGCAGGTGTCAGA 60.534 55.000 23.98 0.00 0.00 3.27
2480 2676 0.250209 ACTGCTTGCAGGTGTCAGAG 60.250 55.000 23.98 0.00 0.00 3.35
2481 2677 1.575576 CTGCTTGCAGGTGTCAGAGC 61.576 60.000 14.25 0.00 0.00 4.09
2482 2678 2.675056 GCTTGCAGGTGTCAGAGCG 61.675 63.158 0.00 0.00 0.00 5.03
2484 2680 1.563435 CTTGCAGGTGTCAGAGCGTG 61.563 60.000 0.00 0.00 0.00 5.34
2485 2681 2.740055 GCAGGTGTCAGAGCGTGG 60.740 66.667 0.00 0.00 0.00 4.94
2486 2682 2.737180 CAGGTGTCAGAGCGTGGT 59.263 61.111 0.00 0.00 0.00 4.16
2487 2683 1.665916 CAGGTGTCAGAGCGTGGTG 60.666 63.158 0.00 0.00 0.00 4.17
2488 2684 3.044305 GGTGTCAGAGCGTGGTGC 61.044 66.667 0.00 0.00 46.98 5.01
2500 2696 3.303881 GCGTGGTGCTCTATATGATCA 57.696 47.619 0.00 0.00 41.73 2.92
2501 2697 3.854666 GCGTGGTGCTCTATATGATCAT 58.145 45.455 13.81 13.81 41.73 2.45
2502 2698 3.862267 GCGTGGTGCTCTATATGATCATC 59.138 47.826 12.53 0.00 41.73 2.92
2504 2700 4.861462 CGTGGTGCTCTATATGATCATCAC 59.139 45.833 12.53 12.40 44.80 3.06
2507 2703 5.486419 TGGTGCTCTATATGATCATCACCAT 59.514 40.000 28.02 14.53 45.18 3.55
2508 2704 5.816258 GGTGCTCTATATGATCATCACCATG 59.184 44.000 25.83 11.47 41.56 3.66
2509 2705 5.293814 GTGCTCTATATGATCATCACCATGC 59.706 44.000 12.53 11.24 0.00 4.06
2511 2707 5.524281 GCTCTATATGATCATCACCATGCTG 59.476 44.000 12.53 0.00 0.00 4.41
2512 2708 6.616237 TCTATATGATCATCACCATGCTGT 57.384 37.500 12.53 0.00 0.00 4.40
2513 2709 6.403878 TCTATATGATCATCACCATGCTGTG 58.596 40.000 12.53 0.00 37.59 3.66
2516 2712 1.602851 GATCATCACCATGCTGTGCTC 59.397 52.381 0.00 0.00 36.17 4.26
2517 2713 0.741927 TCATCACCATGCTGTGCTCG 60.742 55.000 0.00 0.00 36.17 5.03
2518 2714 0.741927 CATCACCATGCTGTGCTCGA 60.742 55.000 0.00 0.00 36.17 4.04
2520 2716 0.460811 TCACCATGCTGTGCTCGATC 60.461 55.000 0.00 0.00 36.17 3.69
2522 2718 2.624811 CATGCTGTGCTCGATCGC 59.375 61.111 11.09 0.00 0.00 4.58
2546 2742 6.293081 GCTCGATGTGATACTGTAATGCAATT 60.293 38.462 0.00 0.00 41.28 2.32
2547 2743 7.552458 TCGATGTGATACTGTAATGCAATTT 57.448 32.000 0.00 0.00 37.87 1.82
2602 3107 7.654568 TCCTTGCTTGCATATAATCATTTCAG 58.345 34.615 0.00 0.00 0.00 3.02
2641 3146 7.760340 AGTGTCGTATTTTCCTCTGTCTATTTC 59.240 37.037 0.00 0.00 0.00 2.17
2650 3155 3.865745 CCTCTGTCTATTTCGCGTCATTT 59.134 43.478 5.77 0.00 0.00 2.32
2667 3172 5.339611 CGTCATTTACTTGCAACTTTACAGC 59.660 40.000 0.00 0.00 0.00 4.40
2698 3208 4.706476 TCCAAAAGTTATGCTTGGATCCAG 59.294 41.667 15.53 10.43 42.86 3.86
2734 3244 1.283487 CGCATGCTGCTGTGTTCAA 59.717 52.632 17.13 0.00 42.25 2.69
2778 3288 9.071276 AGTGTGATACAATTCTGAATTTCAGTT 57.929 29.630 22.44 10.50 44.58 3.16
2779 3289 9.334693 GTGTGATACAATTCTGAATTTCAGTTC 57.665 33.333 22.44 11.43 44.58 3.01
2821 3331 1.734655 TTTCAGGTCCTCTCTGCCTT 58.265 50.000 0.00 0.00 32.63 4.35
2829 3339 2.101750 GTCCTCTCTGCCTTAGGTAAGC 59.898 54.545 0.00 0.00 32.02 3.09
2848 3409 3.497332 AGCCCCTCTTTTGGAAGTTTAC 58.503 45.455 0.00 0.00 34.41 2.01
2875 3436 3.151554 AGACTGTTCATGCAGCAATTGA 58.848 40.909 10.34 0.00 39.96 2.57
2884 3445 1.399440 TGCAGCAATTGAGAAGCGATC 59.601 47.619 10.34 0.00 0.00 3.69
2906 4283 2.093890 TGGCATCCACATTGTGACATC 58.906 47.619 18.33 4.75 35.23 3.06
2914 4291 3.365666 CCACATTGTGACATCACTTGAGC 60.366 47.826 18.33 0.00 46.55 4.26
2952 4329 5.579753 TTCTGTCTATATACTCCCTCCGT 57.420 43.478 0.00 0.00 0.00 4.69
2953 4330 5.163281 TCTGTCTATATACTCCCTCCGTC 57.837 47.826 0.00 0.00 0.00 4.79
2954 4331 4.019501 TCTGTCTATATACTCCCTCCGTCC 60.020 50.000 0.00 0.00 0.00 4.79
2955 4332 3.009916 TGTCTATATACTCCCTCCGTCCC 59.990 52.174 0.00 0.00 0.00 4.46
2956 4333 3.009916 GTCTATATACTCCCTCCGTCCCA 59.990 52.174 0.00 0.00 0.00 4.37
2958 4335 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2959 4336 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2963 4340 2.238898 ACTCCCTCCGTCCCAAAATTAG 59.761 50.000 0.00 0.00 0.00 1.73
2964 4341 2.238898 CTCCCTCCGTCCCAAAATTAGT 59.761 50.000 0.00 0.00 0.00 2.24
2965 4342 2.026636 TCCCTCCGTCCCAAAATTAGTG 60.027 50.000 0.00 0.00 0.00 2.74
2966 4343 2.026636 CCCTCCGTCCCAAAATTAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
2967 4344 3.007635 CCTCCGTCCCAAAATTAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
2968 4345 3.307480 CCTCCGTCCCAAAATTAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
2969 4346 3.933332 CTCCGTCCCAAAATTAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
2970 4347 3.325425 TCCGTCCCAAAATTAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
2971 4348 4.069304 CCGTCCCAAAATTAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2972 4349 4.083484 CCGTCCCAAAATTAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2974 4351 5.238650 CGTCCCAAAATTAGTGACTCAACTT 59.761 40.000 0.00 0.00 0.00 2.66
2975 4352 6.238648 CGTCCCAAAATTAGTGACTCAACTTT 60.239 38.462 0.00 0.00 0.00 2.66
2976 4353 6.918022 GTCCCAAAATTAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 0.00 2.77
2977 4354 6.605594 TCCCAAAATTAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 0.00 2.83
2978 4355 7.776030 TCCCAAAATTAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 0.00 2.41
2979 4356 7.860872 CCCAAAATTAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 0.00 2.90
2988 4365 9.310716 AGTGACTCAACTTTGTACTAAGTTTAC 57.689 33.333 26.14 19.62 43.85 2.01
3013 4390 9.310716 ACTACAAAGTTAGTACAAACTTGAGTC 57.689 33.333 2.97 0.00 46.40 3.36
3015 4392 7.971455 ACAAAGTTAGTACAAACTTGAGTCAC 58.029 34.615 2.97 0.00 46.40 3.67
3016 4393 7.822822 ACAAAGTTAGTACAAACTTGAGTCACT 59.177 33.333 2.97 0.00 46.40 3.41
3018 4395 9.880157 AAAGTTAGTACAAACTTGAGTCACTTA 57.120 29.630 2.97 0.00 46.40 2.24
3024 4401 8.621286 AGTACAAACTTGAGTCACTTATTTTGG 58.379 33.333 9.57 0.00 29.00 3.28
3026 4403 6.605594 ACAAACTTGAGTCACTTATTTTGGGA 59.394 34.615 9.57 0.00 0.00 4.37
3027 4404 7.287696 ACAAACTTGAGTCACTTATTTTGGGAT 59.712 33.333 9.57 0.00 0.00 3.85
3032 4672 4.860022 AGTCACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
3041 4681 3.951563 TTGGGATGGAGGGAGTATTTG 57.048 47.619 0.00 0.00 0.00 2.32
3042 4682 2.135189 TGGGATGGAGGGAGTATTTGG 58.865 52.381 0.00 0.00 0.00 3.28
3043 4683 1.202940 GGGATGGAGGGAGTATTTGGC 60.203 57.143 0.00 0.00 0.00 4.52
3044 4684 1.494721 GGATGGAGGGAGTATTTGGCA 59.505 52.381 0.00 0.00 0.00 4.92
3045 4685 2.487986 GGATGGAGGGAGTATTTGGCAG 60.488 54.545 0.00 0.00 0.00 4.85
3046 4686 1.668826 TGGAGGGAGTATTTGGCAGT 58.331 50.000 0.00 0.00 0.00 4.40
3048 4688 1.408822 GGAGGGAGTATTTGGCAGTGG 60.409 57.143 0.00 0.00 0.00 4.00
3053 4693 0.405585 AGTATTTGGCAGTGGCACCT 59.594 50.000 20.46 11.89 43.71 4.00
3054 4694 0.527565 GTATTTGGCAGTGGCACCTG 59.472 55.000 20.46 12.83 43.71 4.00
3055 4695 0.112218 TATTTGGCAGTGGCACCTGT 59.888 50.000 20.46 8.09 43.71 4.00
3056 4696 1.181098 ATTTGGCAGTGGCACCTGTC 61.181 55.000 20.46 13.69 43.71 3.51
3057 4697 2.564561 TTTGGCAGTGGCACCTGTCA 62.565 55.000 20.46 16.12 44.87 3.58
3058 4698 2.203337 GGCAGTGGCACCTGTCAA 60.203 61.111 15.27 0.00 43.71 3.18
3059 4699 2.555547 GGCAGTGGCACCTGTCAAC 61.556 63.158 15.27 0.00 43.71 3.18
3061 4701 1.152984 CAGTGGCACCTGTCAACCA 60.153 57.895 15.27 0.00 0.00 3.67
3063 4703 1.148273 GTGGCACCTGTCAACCAGA 59.852 57.895 6.29 0.00 44.49 3.86
3064 4704 1.148273 TGGCACCTGTCAACCAGAC 59.852 57.895 0.00 0.00 44.49 3.51
3073 4713 2.859165 GTCAACCAGACCAATGGAGA 57.141 50.000 6.16 0.00 43.57 3.71
3074 4714 3.356529 GTCAACCAGACCAATGGAGAT 57.643 47.619 6.16 0.00 43.57 2.75
3075 4715 4.487714 GTCAACCAGACCAATGGAGATA 57.512 45.455 6.16 0.00 43.57 1.98
3076 4716 4.843728 GTCAACCAGACCAATGGAGATAA 58.156 43.478 6.16 0.00 43.57 1.75
3079 4719 5.250543 TCAACCAGACCAATGGAGATAAAGA 59.749 40.000 6.16 0.00 43.57 2.52
3080 4720 5.365021 ACCAGACCAATGGAGATAAAGAG 57.635 43.478 6.16 0.00 43.57 2.85
3081 4721 5.032846 ACCAGACCAATGGAGATAAAGAGA 58.967 41.667 6.16 0.00 43.57 3.10
3082 4722 5.488919 ACCAGACCAATGGAGATAAAGAGAA 59.511 40.000 6.16 0.00 43.57 2.87
3083 4723 6.054295 CCAGACCAATGGAGATAAAGAGAAG 58.946 44.000 6.16 0.00 43.57 2.85
3084 4724 6.352565 CCAGACCAATGGAGATAAAGAGAAGT 60.353 42.308 6.16 0.00 43.57 3.01
3085 4725 7.147655 CCAGACCAATGGAGATAAAGAGAAGTA 60.148 40.741 6.16 0.00 43.57 2.24
3086 4726 8.428063 CAGACCAATGGAGATAAAGAGAAGTAT 58.572 37.037 6.16 0.00 0.00 2.12
3100 4740 6.780198 AGAGAAGTATATATTTGGCCCCAA 57.220 37.500 0.00 0.00 0.00 4.12
3101 4741 6.543735 AGAGAAGTATATATTTGGCCCCAAC 58.456 40.000 0.00 0.00 35.46 3.77
3102 4742 6.102615 AGAGAAGTATATATTTGGCCCCAACA 59.897 38.462 0.00 0.00 35.46 3.33
3103 4743 6.068670 AGAAGTATATATTTGGCCCCAACAC 58.931 40.000 0.00 0.00 35.46 3.32
3105 4745 6.025793 AGTATATATTTGGCCCCAACACTT 57.974 37.500 0.00 0.00 35.46 3.16
3106 4746 5.833131 AGTATATATTTGGCCCCAACACTTG 59.167 40.000 0.00 0.00 35.46 3.16
3107 4747 0.972883 TATTTGGCCCCAACACTTGC 59.027 50.000 0.00 0.00 35.46 4.01
3108 4748 1.767654 ATTTGGCCCCAACACTTGCC 61.768 55.000 0.00 0.00 44.27 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.154197 GACCGACAGGCCAGTTTTAC 58.846 55.000 5.01 0.00 42.76 2.01
44 45 0.173708 CTCTACAAGACCGACAGGCC 59.826 60.000 0.00 0.00 42.76 5.19
103 104 9.822185 ATAAGCTTTTATTGATTCCCAATGTTC 57.178 29.630 3.20 0.00 44.67 3.18
120 121 7.542130 CGCAAATAACTCCAAAGATAAGCTTTT 59.458 33.333 3.20 0.00 44.24 2.27
128 129 4.396166 CACCTCGCAAATAACTCCAAAGAT 59.604 41.667 0.00 0.00 0.00 2.40
159 211 4.867047 CGAGAGCTAACTTGTTGATCACAT 59.133 41.667 0.00 0.00 34.43 3.21
182 234 9.537192 TGCTACACATATTTGTATTGTACTACC 57.463 33.333 2.27 0.00 33.76 3.18
199 251 5.706447 TCTCCTATCTAACCTGCTACACAT 58.294 41.667 0.00 0.00 0.00 3.21
201 253 5.378332 TCTCTCCTATCTAACCTGCTACAC 58.622 45.833 0.00 0.00 0.00 2.90
202 254 5.132985 ACTCTCTCCTATCTAACCTGCTACA 59.867 44.000 0.00 0.00 0.00 2.74
203 255 5.627135 ACTCTCTCCTATCTAACCTGCTAC 58.373 45.833 0.00 0.00 0.00 3.58
206 258 7.533289 AAATACTCTCTCCTATCTAACCTGC 57.467 40.000 0.00 0.00 0.00 4.85
207 259 9.757227 CAAAAATACTCTCTCCTATCTAACCTG 57.243 37.037 0.00 0.00 0.00 4.00
208 260 8.425703 GCAAAAATACTCTCTCCTATCTAACCT 58.574 37.037 0.00 0.00 0.00 3.50
209 261 8.425703 AGCAAAAATACTCTCTCCTATCTAACC 58.574 37.037 0.00 0.00 0.00 2.85
212 264 8.798402 GCTAGCAAAAATACTCTCTCCTATCTA 58.202 37.037 10.63 0.00 0.00 1.98
226 278 3.768757 AGCAATGGTGGCTAGCAAAAATA 59.231 39.130 18.24 0.00 40.47 1.40
243 295 0.179000 GGGACAGATCACGGAGCAAT 59.821 55.000 0.00 0.00 0.00 3.56
244 296 1.191489 TGGGACAGATCACGGAGCAA 61.191 55.000 0.00 0.00 0.00 3.91
250 302 2.033550 GCTACTAGTGGGACAGATCACG 59.966 54.545 5.39 0.00 41.80 4.35
431 483 7.556733 TTAAACACAGTCCGACACTTTAATT 57.443 32.000 0.40 0.00 30.26 1.40
435 487 7.442969 TCATAATTAAACACAGTCCGACACTTT 59.557 33.333 0.40 0.00 30.26 2.66
473 525 3.944422 TTTCAGACGTTTCACTTGAGC 57.056 42.857 0.00 0.00 0.00 4.26
518 570 7.840797 CGTTCAAATCAAATGTTCACAAAAGAC 59.159 33.333 0.00 0.00 0.00 3.01
581 633 9.884636 AATTGCAGACAGTACAAATACACTATA 57.115 29.630 0.00 0.00 33.30 1.31
582 634 8.668353 CAATTGCAGACAGTACAAATACACTAT 58.332 33.333 0.00 0.00 33.30 2.12
695 748 8.741603 ATACACAAGTACAACAAGTTTAAGGT 57.258 30.769 0.00 0.00 31.96 3.50
704 757 9.531942 CCGGTTATATATACACAAGTACAACAA 57.468 33.333 0.00 0.00 31.96 2.83
939 1005 3.941483 CGATCTTTGTGGCCAACTCTTAT 59.059 43.478 7.24 0.00 0.00 1.73
941 1007 2.154462 CGATCTTTGTGGCCAACTCTT 58.846 47.619 7.24 0.00 0.00 2.85
1081 1150 1.287815 CGAGTAGGCGTGTGGTTGA 59.712 57.895 0.00 0.00 0.00 3.18
1109 1178 3.133542 TGCTCATCTAGGAACCATGAGTG 59.866 47.826 15.85 0.00 43.74 3.51
1111 1180 4.620589 ATGCTCATCTAGGAACCATGAG 57.379 45.455 12.04 12.04 44.39 2.90
1113 1182 4.711399 TGAATGCTCATCTAGGAACCATG 58.289 43.478 0.00 0.00 0.00 3.66
1115 1184 4.445305 CCATGAATGCTCATCTAGGAACCA 60.445 45.833 0.00 0.00 40.49 3.67
1116 1185 4.070716 CCATGAATGCTCATCTAGGAACC 58.929 47.826 0.00 0.00 40.49 3.62
1117 1186 4.712476 ACCATGAATGCTCATCTAGGAAC 58.288 43.478 0.00 0.00 40.49 3.62
1118 1187 5.371526 GAACCATGAATGCTCATCTAGGAA 58.628 41.667 0.00 0.00 40.49 3.36
1119 1188 4.202398 GGAACCATGAATGCTCATCTAGGA 60.202 45.833 0.00 0.00 40.49 2.94
1120 1189 4.070716 GGAACCATGAATGCTCATCTAGG 58.929 47.826 0.00 0.00 40.49 3.02
1121 1190 4.970711 AGGAACCATGAATGCTCATCTAG 58.029 43.478 0.00 0.00 40.49 2.43
1122 1191 5.840693 TCTAGGAACCATGAATGCTCATCTA 59.159 40.000 0.00 0.00 40.49 1.98
1123 1192 3.947612 AGGAACCATGAATGCTCATCT 57.052 42.857 0.00 0.00 40.49 2.90
1124 1193 4.965814 TCTAGGAACCATGAATGCTCATC 58.034 43.478 0.00 0.00 40.49 2.92
1125 1194 5.072736 TCATCTAGGAACCATGAATGCTCAT 59.927 40.000 0.00 0.00 43.40 2.90
1126 1195 4.409901 TCATCTAGGAACCATGAATGCTCA 59.590 41.667 0.00 0.00 35.56 4.26
1127 1196 4.965814 TCATCTAGGAACCATGAATGCTC 58.034 43.478 0.00 0.00 0.00 4.26
1128 1197 4.746089 GCTCATCTAGGAACCATGAATGCT 60.746 45.833 0.00 0.00 0.00 3.79
1129 1198 3.501445 GCTCATCTAGGAACCATGAATGC 59.499 47.826 0.00 0.00 0.00 3.56
1130 1199 4.711399 TGCTCATCTAGGAACCATGAATG 58.289 43.478 0.00 0.00 0.00 2.67
1131 1200 5.579753 ATGCTCATCTAGGAACCATGAAT 57.420 39.130 0.00 0.00 0.00 2.57
1132 1201 5.371526 GAATGCTCATCTAGGAACCATGAA 58.628 41.667 0.00 0.00 0.00 2.57
1133 1202 4.202398 GGAATGCTCATCTAGGAACCATGA 60.202 45.833 0.00 0.00 0.00 3.07
1134 1203 4.070716 GGAATGCTCATCTAGGAACCATG 58.929 47.826 0.00 0.00 0.00 3.66
1135 1204 3.718434 TGGAATGCTCATCTAGGAACCAT 59.282 43.478 0.00 0.00 33.55 3.55
1136 1205 3.114606 TGGAATGCTCATCTAGGAACCA 58.885 45.455 0.00 0.00 35.12 3.67
1137 1206 3.471680 GTGGAATGCTCATCTAGGAACC 58.528 50.000 0.00 0.00 0.00 3.62
1138 1207 3.126831 CGTGGAATGCTCATCTAGGAAC 58.873 50.000 0.00 0.00 0.00 3.62
1139 1208 2.766263 ACGTGGAATGCTCATCTAGGAA 59.234 45.455 0.00 0.00 0.00 3.36
1140 1209 2.362397 GACGTGGAATGCTCATCTAGGA 59.638 50.000 0.00 0.00 0.00 2.94
1141 1210 2.546795 GGACGTGGAATGCTCATCTAGG 60.547 54.545 0.00 0.00 0.00 3.02
1142 1211 2.546795 GGGACGTGGAATGCTCATCTAG 60.547 54.545 0.00 0.00 0.00 2.43
1143 1212 1.412710 GGGACGTGGAATGCTCATCTA 59.587 52.381 0.00 0.00 0.00 1.98
1144 1213 0.179000 GGGACGTGGAATGCTCATCT 59.821 55.000 0.00 0.00 0.00 2.90
1145 1214 0.179000 AGGGACGTGGAATGCTCATC 59.821 55.000 0.00 0.00 0.00 2.92
1146 1215 0.107508 CAGGGACGTGGAATGCTCAT 60.108 55.000 0.00 0.00 0.00 2.90
1147 1216 1.296392 CAGGGACGTGGAATGCTCA 59.704 57.895 0.00 0.00 0.00 4.26
1148 1217 0.321653 AACAGGGACGTGGAATGCTC 60.322 55.000 0.00 0.00 0.00 4.26
1149 1218 0.321653 GAACAGGGACGTGGAATGCT 60.322 55.000 0.00 0.00 0.00 3.79
1150 1219 0.321653 AGAACAGGGACGTGGAATGC 60.322 55.000 0.00 0.00 0.00 3.56
1151 1220 1.270839 ACAGAACAGGGACGTGGAATG 60.271 52.381 0.00 0.00 0.00 2.67
1152 1221 1.002087 GACAGAACAGGGACGTGGAAT 59.998 52.381 0.00 0.00 0.00 3.01
1153 1222 0.391597 GACAGAACAGGGACGTGGAA 59.608 55.000 0.00 0.00 0.00 3.53
1154 1223 0.469331 AGACAGAACAGGGACGTGGA 60.469 55.000 0.00 0.00 0.00 4.02
1155 1224 0.393077 AAGACAGAACAGGGACGTGG 59.607 55.000 0.00 0.00 0.00 4.94
1156 1225 1.867233 CAAAGACAGAACAGGGACGTG 59.133 52.381 0.00 0.00 0.00 4.49
1157 1226 1.760613 TCAAAGACAGAACAGGGACGT 59.239 47.619 0.00 0.00 0.00 4.34
1158 1227 2.526304 TCAAAGACAGAACAGGGACG 57.474 50.000 0.00 0.00 0.00 4.79
1159 1228 6.877611 TTTAATCAAAGACAGAACAGGGAC 57.122 37.500 0.00 0.00 0.00 4.46
1160 1229 7.230747 TGATTTAATCAAAGACAGAACAGGGA 58.769 34.615 5.03 0.00 36.11 4.20
1161 1230 7.452880 TGATTTAATCAAAGACAGAACAGGG 57.547 36.000 5.03 0.00 36.11 4.45
1277 1346 1.613925 GAGCCTTTTTGAACAGGGACC 59.386 52.381 0.00 0.00 0.00 4.46
1688 1768 8.827677 GCTAAATACACACTTTAGGAGTTATGG 58.172 37.037 5.31 0.00 36.10 2.74
1803 1962 5.245977 CCCAATCATGAAAAACCCACTAAGT 59.754 40.000 0.00 0.00 0.00 2.24
1847 2006 7.982761 TGCTTCCTTGCAATTTTTCAATAAT 57.017 28.000 0.00 0.00 40.29 1.28
1871 2030 1.138568 CAGCATCTCTGGGAGGGATT 58.861 55.000 0.00 0.00 39.15 3.01
2051 2210 7.436933 CCAGCACTGATATAATCTTGTAGTCA 58.563 38.462 0.00 0.00 0.00 3.41
2140 2299 5.416013 TCATGCCCGTTTATGAACATACAAA 59.584 36.000 0.95 0.00 35.44 2.83
2202 2368 5.927281 AGGTAGTAGACTTTTCGCCATAA 57.073 39.130 0.00 0.00 0.00 1.90
2367 2563 3.077359 AGAGTAAGCACTGAAACATGGC 58.923 45.455 0.00 0.00 34.21 4.40
2398 2594 1.164411 CACAAAGGTATTGGCGCTGA 58.836 50.000 7.64 0.00 0.00 4.26
2404 2600 4.695455 ACACTCGATTCACAAAGGTATTGG 59.305 41.667 0.00 0.00 0.00 3.16
2407 2603 7.972832 TTAAACACTCGATTCACAAAGGTAT 57.027 32.000 0.00 0.00 0.00 2.73
2431 2627 3.740115 ACCTCACGAGCACAAAGTAATT 58.260 40.909 0.00 0.00 0.00 1.40
2434 2630 1.335597 CGACCTCACGAGCACAAAGTA 60.336 52.381 0.00 0.00 35.09 2.24
2435 2631 0.597637 CGACCTCACGAGCACAAAGT 60.598 55.000 0.00 0.00 35.09 2.66
2446 2642 1.137513 GCAGTGTGTAACGACCTCAC 58.862 55.000 0.00 0.00 42.39 3.51
2458 2654 1.096967 TGACACCTGCAAGCAGTGTG 61.097 55.000 27.07 27.07 43.83 3.82
2460 2656 0.533531 TCTGACACCTGCAAGCAGTG 60.534 55.000 19.60 18.19 42.15 3.66
2465 2661 1.301244 ACGCTCTGACACCTGCAAG 60.301 57.895 0.00 0.00 0.00 4.01
2467 2663 2.029518 CACGCTCTGACACCTGCA 59.970 61.111 0.00 0.00 0.00 4.41
2468 2664 2.740055 CCACGCTCTGACACCTGC 60.740 66.667 0.00 0.00 0.00 4.85
2470 2666 2.737180 CACCACGCTCTGACACCT 59.263 61.111 0.00 0.00 0.00 4.00
2471 2667 3.044305 GCACCACGCTCTGACACC 61.044 66.667 0.00 0.00 37.77 4.16
2480 2676 3.303881 TGATCATATAGAGCACCACGC 57.696 47.619 0.00 0.00 37.82 5.34
2481 2677 4.861462 GTGATGATCATATAGAGCACCACG 59.139 45.833 8.54 0.00 46.33 4.94
2484 2680 5.411831 TGGTGATGATCATATAGAGCACC 57.588 43.478 24.79 24.79 46.85 5.01
2485 2681 5.293814 GCATGGTGATGATCATATAGAGCAC 59.706 44.000 8.54 10.90 46.85 4.40
2486 2682 9.156190 ACAGCATGGTGATGATCATATAGAGCA 62.156 40.741 30.46 9.16 44.67 4.26
2487 2683 5.524281 CAGCATGGTGATGATCATATAGAGC 59.476 44.000 20.20 9.01 35.45 4.09
2488 2684 6.535508 CACAGCATGGTGATGATCATATAGAG 59.464 42.308 30.46 0.00 43.62 2.43
2491 2687 4.939439 GCACAGCATGGTGATGATCATATA 59.061 41.667 30.46 0.00 43.62 0.86
2493 2689 3.143728 GCACAGCATGGTGATGATCATA 58.856 45.455 30.46 0.00 43.62 2.15
2496 2692 1.602851 GAGCACAGCATGGTGATGATC 59.397 52.381 30.46 24.81 43.62 2.92
2497 2693 1.676746 GAGCACAGCATGGTGATGAT 58.323 50.000 30.46 21.65 43.62 2.45
2498 2694 0.741927 CGAGCACAGCATGGTGATGA 60.742 55.000 30.46 0.00 43.62 2.92
2499 2695 0.741927 TCGAGCACAGCATGGTGATG 60.742 55.000 30.46 22.91 43.62 3.07
2500 2696 0.179702 ATCGAGCACAGCATGGTGAT 59.820 50.000 30.46 12.26 43.62 3.06
2501 2697 0.460811 GATCGAGCACAGCATGGTGA 60.461 55.000 30.46 8.05 43.62 4.02
2502 2698 1.759293 CGATCGAGCACAGCATGGTG 61.759 60.000 22.91 22.91 43.62 4.17
2504 2700 2.879070 GCGATCGAGCACAGCATGG 61.879 63.158 21.57 0.00 43.62 3.66
2507 2703 2.202663 GAGCGATCGAGCACAGCA 60.203 61.111 21.57 0.00 40.15 4.41
2508 2704 2.997621 ATCGAGCGATCGAGCACAGC 62.998 60.000 30.27 0.00 45.70 4.40
2509 2705 1.009108 ATCGAGCGATCGAGCACAG 60.009 57.895 30.27 3.25 45.70 3.66
2511 2707 1.298713 ACATCGAGCGATCGAGCAC 60.299 57.895 30.27 0.00 45.70 4.40
2512 2708 1.298638 CACATCGAGCGATCGAGCA 60.299 57.895 30.27 8.81 45.70 4.26
2513 2709 0.386605 ATCACATCGAGCGATCGAGC 60.387 55.000 30.27 8.50 45.70 5.03
2516 2712 2.237526 CAGTATCACATCGAGCGATCG 58.762 52.381 18.51 18.51 31.62 3.69
2517 2713 3.275400 ACAGTATCACATCGAGCGATC 57.725 47.619 1.86 0.00 31.62 3.69
2518 2714 4.830826 TTACAGTATCACATCGAGCGAT 57.169 40.909 0.00 0.00 34.81 4.58
2520 2716 3.120286 GCATTACAGTATCACATCGAGCG 59.880 47.826 0.00 0.00 0.00 5.03
2522 2718 6.775939 ATTGCATTACAGTATCACATCGAG 57.224 37.500 0.00 0.00 0.00 4.04
2602 3107 6.657836 AATACGACACTGCTAAAATACACC 57.342 37.500 0.00 0.00 0.00 4.16
2641 3146 2.594529 AGTTGCAAGTAAATGACGCG 57.405 45.000 4.57 3.53 0.00 6.01
2677 3182 5.649782 ACTGGATCCAAGCATAACTTTTG 57.350 39.130 17.00 1.42 36.04 2.44
2678 3183 6.670695 AAACTGGATCCAAGCATAACTTTT 57.329 33.333 17.00 2.67 36.04 2.27
2679 3184 6.948309 ACTAAACTGGATCCAAGCATAACTTT 59.052 34.615 17.00 7.83 36.04 2.66
2680 3185 6.485171 ACTAAACTGGATCCAAGCATAACTT 58.515 36.000 17.00 3.20 40.05 2.66
2682 3187 7.769044 TCTTACTAAACTGGATCCAAGCATAAC 59.231 37.037 17.00 0.00 0.00 1.89
2683 3188 7.769044 GTCTTACTAAACTGGATCCAAGCATAA 59.231 37.037 17.00 8.86 0.00 1.90
2698 3208 3.927552 GCGGATGCAGTCTTACTAAAC 57.072 47.619 0.00 0.00 42.15 2.01
2734 3244 4.022589 CACACTGAATCACCAAGAGCAATT 60.023 41.667 0.00 0.00 0.00 2.32
2778 3288 1.338674 GGGTCCATTCGTCACATGTGA 60.339 52.381 24.56 24.56 37.24 3.58
2779 3289 1.086696 GGGTCCATTCGTCACATGTG 58.913 55.000 20.18 20.18 0.00 3.21
2821 3331 2.923908 TCCAAAAGAGGGGCTTACCTA 58.076 47.619 0.00 0.00 42.10 3.08
2829 3339 3.572682 GGTGTAAACTTCCAAAAGAGGGG 59.427 47.826 0.00 0.00 36.30 4.79
2848 3409 2.417933 GCTGCATGAACAGTCTTAGGTG 59.582 50.000 0.00 0.00 39.96 4.00
2875 3436 0.471191 TGGATGCCATGATCGCTTCT 59.529 50.000 0.00 0.00 32.53 2.85
2884 3445 1.819903 TGTCACAATGTGGATGCCATG 59.180 47.619 13.95 0.00 35.28 3.66
2929 4306 6.142259 ACGGAGGGAGTATATAGACAGAAT 57.858 41.667 0.00 0.00 0.00 2.40
2930 4307 5.514484 GGACGGAGGGAGTATATAGACAGAA 60.514 48.000 0.00 0.00 0.00 3.02
2932 4309 4.263435 GGACGGAGGGAGTATATAGACAG 58.737 52.174 0.00 0.00 0.00 3.51
2936 4313 3.733883 TGGGACGGAGGGAGTATATAG 57.266 52.381 0.00 0.00 0.00 1.31
2938 4315 3.339713 TTTGGGACGGAGGGAGTATAT 57.660 47.619 0.00 0.00 0.00 0.86
2943 4320 2.238898 ACTAATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2944 4321 2.026636 CACTAATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2945 4322 2.026636 TCACTAATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2946 4323 3.007635 GTCACTAATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2947 4324 3.933332 GAGTCACTAATTTTGGGACGGAG 59.067 47.826 7.44 0.00 33.84 4.63
2948 4325 3.325425 TGAGTCACTAATTTTGGGACGGA 59.675 43.478 7.44 0.00 33.84 4.69
2949 4326 3.670625 TGAGTCACTAATTTTGGGACGG 58.329 45.455 7.44 0.00 33.84 4.79
2950 4327 4.755123 AGTTGAGTCACTAATTTTGGGACG 59.245 41.667 7.44 0.00 33.84 4.79
2952 4329 6.605594 ACAAAGTTGAGTCACTAATTTTGGGA 59.394 34.615 12.94 0.00 37.63 4.37
2953 4330 6.805713 ACAAAGTTGAGTCACTAATTTTGGG 58.194 36.000 12.94 0.00 37.63 4.12
2954 4331 8.621286 AGTACAAAGTTGAGTCACTAATTTTGG 58.379 33.333 12.94 0.00 37.63 3.28
2963 4340 9.310716 AGTAAACTTAGTACAAAGTTGAGTCAC 57.689 33.333 2.97 0.00 46.40 3.67
2987 4364 9.310716 GACTCAAGTTTGTACTAACTTTGTAGT 57.689 33.333 26.14 25.61 43.85 2.73
2988 4365 9.309516 TGACTCAAGTTTGTACTAACTTTGTAG 57.690 33.333 26.14 23.51 43.85 2.74
2990 4367 7.822822 AGTGACTCAAGTTTGTACTAACTTTGT 59.177 33.333 26.14 25.01 43.85 2.83
2991 4368 8.197988 AGTGACTCAAGTTTGTACTAACTTTG 57.802 34.615 26.14 22.84 43.85 2.77
2992 4369 8.788325 AAGTGACTCAAGTTTGTACTAACTTT 57.212 30.769 26.14 15.97 43.85 2.66
2998 4375 8.621286 CCAAAATAAGTGACTCAAGTTTGTACT 58.379 33.333 15.07 0.00 35.68 2.73
2999 4376 7.860872 CCCAAAATAAGTGACTCAAGTTTGTAC 59.139 37.037 15.07 0.00 0.00 2.90
3001 4378 6.605594 TCCCAAAATAAGTGACTCAAGTTTGT 59.394 34.615 15.07 0.00 0.00 2.83
3004 4381 6.209391 CCATCCCAAAATAAGTGACTCAAGTT 59.791 38.462 0.00 0.00 0.00 2.66
3005 4382 5.711976 CCATCCCAAAATAAGTGACTCAAGT 59.288 40.000 0.00 0.00 0.00 3.16
3006 4383 5.945784 TCCATCCCAAAATAAGTGACTCAAG 59.054 40.000 0.00 0.00 0.00 3.02
3007 4384 5.886609 TCCATCCCAAAATAAGTGACTCAA 58.113 37.500 0.00 0.00 0.00 3.02
3008 4385 5.500234 CTCCATCCCAAAATAAGTGACTCA 58.500 41.667 0.00 0.00 0.00 3.41
3009 4386 4.884164 CCTCCATCCCAAAATAAGTGACTC 59.116 45.833 0.00 0.00 0.00 3.36
3011 4388 3.954258 CCCTCCATCCCAAAATAAGTGAC 59.046 47.826 0.00 0.00 0.00 3.67
3013 4390 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
3015 4392 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
3016 4393 6.606241 AATACTCCCTCCATCCCAAAATAA 57.394 37.500 0.00 0.00 0.00 1.40
3018 4395 5.211201 CAAATACTCCCTCCATCCCAAAAT 58.789 41.667 0.00 0.00 0.00 1.82
3019 4396 4.571792 CCAAATACTCCCTCCATCCCAAAA 60.572 45.833 0.00 0.00 0.00 2.44
3022 4399 2.135189 CCAAATACTCCCTCCATCCCA 58.865 52.381 0.00 0.00 0.00 4.37
3023 4400 1.202940 GCCAAATACTCCCTCCATCCC 60.203 57.143 0.00 0.00 0.00 3.85
3024 4401 1.494721 TGCCAAATACTCCCTCCATCC 59.505 52.381 0.00 0.00 0.00 3.51
3026 4403 2.092212 CACTGCCAAATACTCCCTCCAT 60.092 50.000 0.00 0.00 0.00 3.41
3027 4404 1.281867 CACTGCCAAATACTCCCTCCA 59.718 52.381 0.00 0.00 0.00 3.86
3032 4672 0.811281 GTGCCACTGCCAAATACTCC 59.189 55.000 0.00 0.00 36.33 3.85
3041 4681 2.203337 TTGACAGGTGCCACTGCC 60.203 61.111 4.80 0.00 42.21 4.85
3042 4682 2.555547 GGTTGACAGGTGCCACTGC 61.556 63.158 4.80 0.00 42.21 4.40
3043 4683 1.152984 TGGTTGACAGGTGCCACTG 60.153 57.895 0.00 3.45 44.03 3.66
3044 4684 1.149174 CTGGTTGACAGGTGCCACT 59.851 57.895 0.00 0.00 43.70 4.00
3045 4685 3.749981 CTGGTTGACAGGTGCCAC 58.250 61.111 0.00 0.00 43.70 5.01
3054 4694 2.859165 TCTCCATTGGTCTGGTTGAC 57.141 50.000 1.86 0.00 44.63 3.18
3055 4695 5.250543 TCTTTATCTCCATTGGTCTGGTTGA 59.749 40.000 1.86 0.00 37.57 3.18
3056 4696 5.500234 TCTTTATCTCCATTGGTCTGGTTG 58.500 41.667 1.86 0.00 37.57 3.77
3057 4697 5.488919 TCTCTTTATCTCCATTGGTCTGGTT 59.511 40.000 1.86 0.00 37.57 3.67
3058 4698 5.032846 TCTCTTTATCTCCATTGGTCTGGT 58.967 41.667 1.86 0.00 37.57 4.00
3059 4699 5.620738 TCTCTTTATCTCCATTGGTCTGG 57.379 43.478 1.86 0.00 37.66 3.86
3061 4701 6.882768 ACTTCTCTTTATCTCCATTGGTCT 57.117 37.500 1.86 0.00 0.00 3.85
3072 4712 9.397280 GGGGCCAAATATATACTTCTCTTTATC 57.603 37.037 4.39 0.00 0.00 1.75
3073 4713 8.900802 TGGGGCCAAATATATACTTCTCTTTAT 58.099 33.333 4.39 0.00 0.00 1.40
3074 4714 8.282801 TGGGGCCAAATATATACTTCTCTTTA 57.717 34.615 4.39 0.00 0.00 1.85
3075 4715 7.161715 TGGGGCCAAATATATACTTCTCTTT 57.838 36.000 4.39 0.00 0.00 2.52
3076 4716 6.780198 TGGGGCCAAATATATACTTCTCTT 57.220 37.500 4.39 0.00 0.00 2.85
3079 4719 6.068670 GTGTTGGGGCCAAATATATACTTCT 58.931 40.000 4.39 0.00 37.70 2.85
3080 4720 6.068670 AGTGTTGGGGCCAAATATATACTTC 58.931 40.000 4.39 0.00 37.70 3.01
3081 4721 6.025793 AGTGTTGGGGCCAAATATATACTT 57.974 37.500 4.39 0.00 37.70 2.24
3082 4722 5.663158 AGTGTTGGGGCCAAATATATACT 57.337 39.130 4.39 0.00 37.70 2.12
3083 4723 5.508994 GCAAGTGTTGGGGCCAAATATATAC 60.509 44.000 4.39 0.00 37.70 1.47
3084 4724 4.586841 GCAAGTGTTGGGGCCAAATATATA 59.413 41.667 4.39 0.00 37.70 0.86
3085 4725 3.387699 GCAAGTGTTGGGGCCAAATATAT 59.612 43.478 4.39 0.00 37.70 0.86
3086 4726 2.763448 GCAAGTGTTGGGGCCAAATATA 59.237 45.455 4.39 0.00 37.70 0.86
3088 4728 0.972883 GCAAGTGTTGGGGCCAAATA 59.027 50.000 4.39 0.00 37.70 1.40
3089 4729 1.754107 GCAAGTGTTGGGGCCAAAT 59.246 52.632 4.39 0.00 37.70 2.32
3090 4730 2.439104 GGCAAGTGTTGGGGCCAAA 61.439 57.895 4.39 0.00 45.70 3.28
3091 4731 2.841988 GGCAAGTGTTGGGGCCAA 60.842 61.111 4.39 0.00 45.70 4.52


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

AutoCloner maintained by Alex Coulton.