Multiple sequence alignment - TraesCS2D01G520100

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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 TraesCS2D01G520100 chr2D 100.000 4260 0 0 1 4260 609486472 609490731 0.000000e+00 7867
1 TraesCS2D01G520100 chr2D 88.474 911 41 17 3212 4073 612043025 612042130 0.000000e+00 1042
2 TraesCS2D01G520100 chr2D 84.116 894 52 29 3216 4024 134404585 134403697 0.000000e+00 782
3 TraesCS2D01G520100 chr2B 92.989 2011 97 22 1238 3213 743744582 743746583 0.000000e+00 2892
4 TraesCS2D01G520100 chr2B 85.784 619 49 14 568 1183 743743610 743744192 1.680000e-173 619
5 TraesCS2D01G520100 chr2B 89.038 447 25 15 1355 1785 171019299 171019737 2.260000e-147 532
6 TraesCS2D01G520100 chr2A 92.649 1986 88 18 1266 3213 742153724 742155689 0.000000e+00 2806
7 TraesCS2D01G520100 chr2A 89.870 1234 60 24 1 1194 742152127 742153335 0.000000e+00 1526
8 TraesCS2D01G520100 chr7D 91.478 927 27 7 3217 4101 240776198 240775282 0.000000e+00 1227
9 TraesCS2D01G520100 chr7D 89.124 947 32 20 3215 4101 578728670 578729605 0.000000e+00 1112
10 TraesCS2D01G520100 chr3D 90.890 933 36 11 3210 4105 93826184 93827104 0.000000e+00 1206
11 TraesCS2D01G520100 chr3D 90.381 946 23 11 3216 4101 550640569 550641506 0.000000e+00 1181
12 TraesCS2D01G520100 chr3D 88.141 936 29 19 3216 4109 600831818 600832713 0.000000e+00 1038
13 TraesCS2D01G520100 chr3D 96.070 229 7 2 3874 4101 261739909 261739682 5.200000e-99 372
14 TraesCS2D01G520100 chr3D 94.000 250 8 7 3860 4104 550640813 550640566 5.200000e-99 372
15 TraesCS2D01G520100 chr5D 91.046 927 32 11 3217 4100 97345077 97344159 0.000000e+00 1205
16 TraesCS2D01G520100 chr5D 95.056 445 10 2 3654 4098 386728549 386728981 0.000000e+00 689
17 TraesCS2D01G520100 chr5D 92.647 408 19 6 3216 3621 371069654 371069256 1.030000e-160 577
18 TraesCS2D01G520100 chr5D 96.087 230 7 2 3874 4101 386727962 386727733 1.450000e-99 374
19 TraesCS2D01G520100 chr5D 90.037 271 19 7 3218 3485 539648673 539648408 1.130000e-90 344
20 TraesCS2D01G520100 chr5D 86.306 314 36 4 3215 3523 297506725 297506414 6.830000e-88 335
21 TraesCS2D01G520100 chr4D 95.887 462 9 4 3640 4101 30519449 30519900 0.000000e+00 739
22 TraesCS2D01G520100 chr4D 92.400 250 15 4 3218 3466 471894782 471894536 1.880000e-93 353
23 TraesCS2D01G520100 chr6D 95.455 462 9 4 3640 4101 409842419 409842868 0.000000e+00 726
24 TraesCS2D01G520100 chr6D 94.167 240 10 4 3874 4110 409841750 409841512 3.130000e-96 363
25 TraesCS2D01G520100 chr6D 94.787 211 9 2 3412 3621 409841743 409841952 1.140000e-85 327
26 TraesCS2D01G520100 chr3A 88.768 552 41 14 1240 1785 734395908 734396444 0.000000e+00 656
27 TraesCS2D01G520100 chr3A 88.043 552 44 12 1240 1785 403130488 403129953 6.010000e-178 634
28 TraesCS2D01G520100 chr3B 88.214 560 42 12 1240 1785 356352383 356352932 0.000000e+00 647
29 TraesCS2D01G520100 chrUn 87.857 560 47 15 1240 1785 11895190 11895742 4.650000e-179 638
30 TraesCS2D01G520100 chrUn 87.857 560 47 15 1240 1785 11987541 11986989 4.650000e-179 638
31 TraesCS2D01G520100 chr5B 88.964 444 31 10 1355 1785 590591649 590591211 2.260000e-147 532
32 TraesCS2D01G520100 chr1B 88.514 444 33 10 1355 1785 82452691 82452253 4.880000e-144 521
33 TraesCS2D01G520100 chr6B 88.315 445 32 10 1355 1785 715365049 715364611 2.270000e-142 516
34 TraesCS2D01G520100 chr4A 88.063 444 34 11 1355 1785 698953518 698953955 3.800000e-140 508
35 TraesCS2D01G520100 chr4A 85.549 173 15 6 1044 1216 725487689 725487851 5.660000e-39 172
36 TraesCS2D01G520100 chr4A 93.590 78 5 0 1295 1372 725488248 725488325 2.690000e-22 117
37 TraesCS2D01G520100 chr7A 89.701 301 19 6 3217 3507 705249604 705249306 1.450000e-99 374
38 TraesCS2D01G520100 chr4B 92.771 249 10 6 3853 4100 450929478 450929237 1.880000e-93 353
39 TraesCS2D01G520100 chr1D 86.984 315 36 5 3210 3523 73149461 73149771 2.440000e-92 350
40 TraesCS2D01G520100 chr6A 95.312 64 3 0 1722 1785 158668815 158668878 7.540000e-18 102


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 TraesCS2D01G520100 chr2D 609486472 609490731 4259 False 7867.0 7867 100.0000 1 4260 1 chr2D.!!$F1 4259
1 TraesCS2D01G520100 chr2D 612042130 612043025 895 True 1042.0 1042 88.4740 3212 4073 1 chr2D.!!$R2 861
2 TraesCS2D01G520100 chr2D 134403697 134404585 888 True 782.0 782 84.1160 3216 4024 1 chr2D.!!$R1 808
3 TraesCS2D01G520100 chr2B 743743610 743746583 2973 False 1755.5 2892 89.3865 568 3213 2 chr2B.!!$F2 2645
4 TraesCS2D01G520100 chr2A 742152127 742155689 3562 False 2166.0 2806 91.2595 1 3213 2 chr2A.!!$F1 3212
5 TraesCS2D01G520100 chr7D 240775282 240776198 916 True 1227.0 1227 91.4780 3217 4101 1 chr7D.!!$R1 884
6 TraesCS2D01G520100 chr7D 578728670 578729605 935 False 1112.0 1112 89.1240 3215 4101 1 chr7D.!!$F1 886
7 TraesCS2D01G520100 chr3D 93826184 93827104 920 False 1206.0 1206 90.8900 3210 4105 1 chr3D.!!$F1 895
8 TraesCS2D01G520100 chr3D 550640569 550641506 937 False 1181.0 1181 90.3810 3216 4101 1 chr3D.!!$F2 885
9 TraesCS2D01G520100 chr3D 600831818 600832713 895 False 1038.0 1038 88.1410 3216 4109 1 chr3D.!!$F3 893
10 TraesCS2D01G520100 chr5D 97344159 97345077 918 True 1205.0 1205 91.0460 3217 4100 1 chr5D.!!$R1 883
11 TraesCS2D01G520100 chr6D 409841743 409842868 1125 False 526.5 726 95.1210 3412 4101 2 chr6D.!!$F1 689
12 TraesCS2D01G520100 chr3A 734395908 734396444 536 False 656.0 656 88.7680 1240 1785 1 chr3A.!!$F1 545
13 TraesCS2D01G520100 chr3A 403129953 403130488 535 True 634.0 634 88.0430 1240 1785 1 chr3A.!!$R1 545
14 TraesCS2D01G520100 chr3B 356352383 356352932 549 False 647.0 647 88.2140 1240 1785 1 chr3B.!!$F1 545
15 TraesCS2D01G520100 chrUn 11895190 11895742 552 False 638.0 638 87.8570 1240 1785 1 chrUn.!!$F1 545
16 TraesCS2D01G520100 chrUn 11986989 11987541 552 True 638.0 638 87.8570 1240 1785 1 chrUn.!!$R1 545

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
400 413 0.034670 GGGAGCCTGAAATCAGTGCT 60.035 55.0 19.56 19.56 46.01 4.40 F
1211 1257 0.105964 CCACCTCAACGAACTGGTCA 59.894 55.0 0.00 0.00 0.00 4.02 F
1222 1268 0.747255 AACTGGTCAGATCCGATCCG 59.253 55.0 4.67 0.00 0.00 4.18 F
2398 2828 0.036483 TTCATGGCAACTCGCTAGCA 60.036 50.0 16.45 0.92 41.91 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 2818 0.037232 GGGTTTGAGTGCTAGCGAGT 60.037 55.000 10.77 2.15 0.00 4.18 R
2397 2827 0.320771 CCTCGACCTGGGTTTGAGTG 60.321 60.000 16.29 8.45 32.58 3.51 R
2407 2837 1.006102 GACACACACCCTCGACCTG 60.006 63.158 0.00 0.00 0.00 4.00 R
4119 5095 0.378257 CGCCACTGCACATAACATCC 59.622 55.000 0.00 0.00 37.32 3.51 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
37 38 5.522097 CCAAGTTTTCGGCAATAAACTGTTT 59.478 36.000 10.98 10.98 42.17 2.83
58 71 5.524971 TTCAGAAGAAGAGAACCGTGTTA 57.475 39.130 0.00 0.00 0.00 2.41
110 123 1.063031 GGTGTACTTAACGGTCGTGC 58.937 55.000 0.00 0.00 0.00 5.34
156 169 4.681483 CGCATCGAGTAGCTTTGATGATAA 59.319 41.667 16.72 0.00 40.45 1.75
192 205 4.584638 ACTACCAATAAAGATGGGCACA 57.415 40.909 0.00 0.00 42.48 4.57
197 210 3.374745 CAATAAAGATGGGCACAATCGC 58.625 45.455 0.00 0.00 0.00 4.58
245 258 4.844085 TCTAACAACTGAGAAATGAGGGGA 59.156 41.667 0.00 0.00 0.00 4.81
252 265 4.829492 ACTGAGAAATGAGGGGAAAAACAG 59.171 41.667 0.00 0.00 0.00 3.16
275 288 2.202987 GCTAGCATGCTCGGCTGT 60.203 61.111 26.57 0.00 42.62 4.40
280 293 2.758089 GCATGCTCGGCTGTTCCTG 61.758 63.158 11.37 0.00 0.00 3.86
283 296 2.435059 GCTCGGCTGTTCCTGGAC 60.435 66.667 0.00 0.00 0.00 4.02
293 306 3.562557 GCTGTTCCTGGACGAAACTAAAA 59.437 43.478 0.00 0.00 0.00 1.52
295 308 4.515361 TGTTCCTGGACGAAACTAAAACA 58.485 39.130 0.00 0.00 0.00 2.83
343 356 5.960202 AGAATGAATCCTAAACTGCCCAATT 59.040 36.000 0.00 0.00 0.00 2.32
344 357 5.603170 ATGAATCCTAAACTGCCCAATTG 57.397 39.130 0.00 0.00 0.00 2.32
355 368 0.525455 GCCCAATTGAATCGGTTCGC 60.525 55.000 7.12 0.00 37.15 4.70
376 389 0.163146 GCGTCGGAGCAGTTTGTAAC 59.837 55.000 0.00 0.00 37.05 2.50
379 392 2.480845 GTCGGAGCAGTTTGTAACAGT 58.519 47.619 0.00 0.00 0.00 3.55
382 395 1.798813 GGAGCAGTTTGTAACAGTCGG 59.201 52.381 0.00 0.00 0.00 4.79
387 400 1.154197 GTTTGTAACAGTCGGGAGCC 58.846 55.000 0.00 0.00 0.00 4.70
400 413 0.034670 GGGAGCCTGAAATCAGTGCT 60.035 55.000 19.56 19.56 46.01 4.40
402 415 1.005340 GAGCCTGAAATCAGTGCTCG 58.995 55.000 24.69 8.09 46.57 5.03
403 416 0.392193 AGCCTGAAATCAGTGCTCGG 60.392 55.000 15.98 1.49 42.60 4.63
408 421 1.347707 TGAAATCAGTGCTCGGGTTCT 59.652 47.619 0.00 0.00 0.00 3.01
413 426 1.228894 AGTGCTCGGGTTCTCTGGA 60.229 57.895 0.00 0.00 0.00 3.86
427 440 3.372123 TGGAACAGACGCGGATCA 58.628 55.556 12.47 0.00 0.00 2.92
429 442 0.389817 TGGAACAGACGCGGATCAAG 60.390 55.000 12.47 0.00 0.00 3.02
468 481 3.411517 CCACCGAGCATCCCCCTT 61.412 66.667 0.00 0.00 0.00 3.95
469 482 2.124570 CACCGAGCATCCCCCTTG 60.125 66.667 0.00 0.00 0.00 3.61
470 483 2.610859 ACCGAGCATCCCCCTTGT 60.611 61.111 0.00 0.00 0.00 3.16
471 484 2.124570 CCGAGCATCCCCCTTGTG 60.125 66.667 0.00 0.00 0.00 3.33
472 485 2.825836 CGAGCATCCCCCTTGTGC 60.826 66.667 0.00 0.00 39.10 4.57
473 486 2.356278 GAGCATCCCCCTTGTGCA 59.644 61.111 0.00 0.00 41.19 4.57
474 487 1.304381 GAGCATCCCCCTTGTGCAA 60.304 57.895 0.00 0.00 41.19 4.08
475 488 0.685458 GAGCATCCCCCTTGTGCAAT 60.685 55.000 0.00 0.00 41.19 3.56
476 489 0.685458 AGCATCCCCCTTGTGCAATC 60.685 55.000 0.00 0.00 41.19 2.67
478 491 0.819582 CATCCCCCTTGTGCAATCAC 59.180 55.000 0.00 0.00 43.40 3.06
489 502 3.733443 GTGCAATCACAAGGGAAAACT 57.267 42.857 0.00 0.00 42.66 2.66
539 552 1.846648 GCATACGCTTCCATCGACG 59.153 57.895 0.00 0.00 34.30 5.12
554 567 6.263344 TCCATCGACGAGTAGAAAAATACAG 58.737 40.000 3.01 0.00 0.00 2.74
556 569 6.918569 CCATCGACGAGTAGAAAAATACAGAT 59.081 38.462 3.01 0.00 0.00 2.90
673 686 0.745845 ATGCGTACGTACCGAGACCT 60.746 55.000 19.67 0.00 0.00 3.85
674 687 1.349973 GCGTACGTACCGAGACCTC 59.650 63.158 19.67 0.00 0.00 3.85
845 875 0.241213 GAAGCGGCTGAAAACTTCCC 59.759 55.000 1.81 0.00 33.90 3.97
862 898 1.304547 CCCTGTGTCCGTCTCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
863 899 1.599606 CCCTGTGTCCGTCTCTCCTG 61.600 65.000 0.00 0.00 0.00 3.86
866 902 1.179174 TGTGTCCGTCTCTCCTGTGG 61.179 60.000 0.00 0.00 0.00 4.17
922 958 3.746949 CTCCCGGCCTGTCAGATGC 62.747 68.421 0.00 0.00 0.00 3.91
932 968 2.769621 TCAGATGCTCGGGCCCAT 60.770 61.111 24.92 7.45 37.74 4.00
942 978 2.659063 CGGGCCCATCTGTCAGTCA 61.659 63.158 24.92 0.00 0.00 3.41
1194 1240 2.355837 GAACTGCGAGACGTGCCA 60.356 61.111 0.00 0.00 0.00 4.92
1195 1241 2.658707 GAACTGCGAGACGTGCCAC 61.659 63.158 0.00 0.00 0.00 5.01
1196 1242 4.664677 ACTGCGAGACGTGCCACC 62.665 66.667 0.00 0.00 0.00 4.61
1197 1243 4.363990 CTGCGAGACGTGCCACCT 62.364 66.667 0.00 0.00 0.00 4.00
1198 1244 4.357947 TGCGAGACGTGCCACCTC 62.358 66.667 0.00 0.00 0.00 3.85
1199 1245 4.357947 GCGAGACGTGCCACCTCA 62.358 66.667 0.00 0.00 0.00 3.86
1200 1246 2.338620 CGAGACGTGCCACCTCAA 59.661 61.111 0.00 0.00 0.00 3.02
1201 1247 2.022129 CGAGACGTGCCACCTCAAC 61.022 63.158 0.00 0.00 0.00 3.18
1202 1248 2.022129 GAGACGTGCCACCTCAACG 61.022 63.158 0.00 0.00 0.00 4.10
1203 1249 2.028484 GACGTGCCACCTCAACGA 59.972 61.111 0.00 0.00 0.00 3.85
1204 1250 1.593209 GACGTGCCACCTCAACGAA 60.593 57.895 0.00 0.00 0.00 3.85
1205 1251 1.828331 GACGTGCCACCTCAACGAAC 61.828 60.000 0.00 0.00 0.00 3.95
1206 1252 1.594293 CGTGCCACCTCAACGAACT 60.594 57.895 0.00 0.00 0.00 3.01
1207 1253 1.831389 CGTGCCACCTCAACGAACTG 61.831 60.000 0.00 0.00 0.00 3.16
1208 1254 1.227823 TGCCACCTCAACGAACTGG 60.228 57.895 0.00 0.00 0.00 4.00
1209 1255 1.227853 GCCACCTCAACGAACTGGT 60.228 57.895 0.00 0.00 0.00 4.00
1210 1256 1.228657 GCCACCTCAACGAACTGGTC 61.229 60.000 0.00 0.00 0.00 4.02
1211 1257 0.105964 CCACCTCAACGAACTGGTCA 59.894 55.000 0.00 0.00 0.00 4.02
1212 1258 1.502231 CACCTCAACGAACTGGTCAG 58.498 55.000 0.00 0.00 0.00 3.51
1213 1259 1.068588 CACCTCAACGAACTGGTCAGA 59.931 52.381 4.84 0.00 0.00 3.27
1214 1260 1.971357 ACCTCAACGAACTGGTCAGAT 59.029 47.619 4.84 0.00 0.00 2.90
1215 1261 2.028930 ACCTCAACGAACTGGTCAGATC 60.029 50.000 4.84 1.67 0.00 2.75
1216 1262 2.611518 CTCAACGAACTGGTCAGATCC 58.388 52.381 4.84 0.00 0.00 3.36
1217 1263 1.067846 TCAACGAACTGGTCAGATCCG 60.068 52.381 4.84 7.27 0.00 4.18
1218 1264 1.067846 CAACGAACTGGTCAGATCCGA 60.068 52.381 4.84 0.00 0.00 4.55
1219 1265 1.475403 ACGAACTGGTCAGATCCGAT 58.525 50.000 4.84 0.00 0.00 4.18
1220 1266 1.405821 ACGAACTGGTCAGATCCGATC 59.594 52.381 4.84 0.00 0.00 3.69
1221 1267 1.269309 CGAACTGGTCAGATCCGATCC 60.269 57.143 4.67 0.00 0.00 3.36
1222 1268 0.747255 AACTGGTCAGATCCGATCCG 59.253 55.000 4.67 0.00 0.00 4.18
1233 1279 2.913060 CGATCCGGACCCCCTCTC 60.913 72.222 6.12 0.00 0.00 3.20
1234 1280 2.524640 GATCCGGACCCCCTCTCC 60.525 72.222 6.12 0.00 0.00 3.71
1235 1281 4.173701 ATCCGGACCCCCTCTCCC 62.174 72.222 6.12 0.00 0.00 4.30
1237 1283 4.416601 CCGGACCCCCTCTCCCTT 62.417 72.222 0.00 0.00 0.00 3.95
1337 1719 2.068519 TGTGCTGCGATGTAAGTTCTG 58.931 47.619 0.00 0.00 0.00 3.02
1473 1868 8.954950 AAATCCACTCTTTGATACTGATGTAG 57.045 34.615 0.00 0.00 31.51 2.74
1475 1870 8.768501 ATCCACTCTTTGATACTGATGTAGTA 57.231 34.615 0.00 0.00 45.50 1.82
1476 1871 7.997482 TCCACTCTTTGATACTGATGTAGTAC 58.003 38.462 0.00 0.00 44.30 2.73
1477 1872 7.834681 TCCACTCTTTGATACTGATGTAGTACT 59.165 37.037 0.00 0.00 44.30 2.73
1478 1873 7.918033 CCACTCTTTGATACTGATGTAGTACTG 59.082 40.741 5.39 0.00 44.30 2.74
1490 1885 7.927629 ACTGATGTAGTACTGAGTAGTAGTAGC 59.072 40.741 5.39 4.23 42.87 3.58
1495 1890 8.099537 TGTAGTACTGAGTAGTAGTAGCAGTTT 58.900 37.037 14.78 8.97 42.87 2.66
1496 1891 9.593134 GTAGTACTGAGTAGTAGTAGCAGTTTA 57.407 37.037 14.78 8.30 42.87 2.01
1564 1959 0.947244 AGTTGCAACTGCTGTACTGC 59.053 50.000 30.66 17.07 42.66 4.40
1574 1969 1.005037 CTGTACTGCTGTGCCGGAA 60.005 57.895 5.05 0.00 0.00 4.30
1634 2029 4.081077 GCACTTGTGCAAAAAGAAAAACG 58.919 39.130 19.36 0.00 33.78 3.60
1649 2048 4.211794 AGAAAAACGGAAGCAATTGCATTG 59.788 37.500 30.89 19.19 45.16 2.82
1726 2125 7.797038 TCTTTTTAGTGTGGTTCTCTTTACC 57.203 36.000 0.00 0.00 36.17 2.85
1873 2276 6.639563 TGTGAGTATTACTGAATAGCTGCAA 58.360 36.000 1.02 0.00 0.00 4.08
1906 2310 2.159393 CCTCCATGTATTTGGTGTTGCG 60.159 50.000 0.00 0.00 38.01 4.85
1946 2350 3.501062 CCAAGATATATGCTGGTGTGCTG 59.499 47.826 0.00 0.00 0.00 4.41
1947 2351 4.383173 CAAGATATATGCTGGTGTGCTGA 58.617 43.478 0.00 0.00 0.00 4.26
1948 2352 4.904895 AGATATATGCTGGTGTGCTGAT 57.095 40.909 0.00 0.00 0.00 2.90
1950 2354 4.531339 AGATATATGCTGGTGTGCTGATCT 59.469 41.667 0.00 0.00 0.00 2.75
1951 2355 3.572632 ATATGCTGGTGTGCTGATCTT 57.427 42.857 0.00 0.00 0.00 2.40
1953 2357 1.241165 TGCTGGTGTGCTGATCTTTG 58.759 50.000 0.00 0.00 0.00 2.77
1966 2375 2.306805 TGATCTTTGTGACCTGCTCCAT 59.693 45.455 0.00 0.00 0.00 3.41
1969 2378 2.082231 CTTTGTGACCTGCTCCATCTG 58.918 52.381 0.00 0.00 0.00 2.90
1973 2382 2.106338 TGTGACCTGCTCCATCTGAAAA 59.894 45.455 0.00 0.00 0.00 2.29
2041 2451 5.063880 GGACTTGCAGAACTAGAAAAGGAA 58.936 41.667 0.00 0.00 0.00 3.36
2110 2520 1.247567 ATCGGAAAAGCCAGGTTGTG 58.752 50.000 0.00 0.00 35.94 3.33
2132 2542 4.273235 TGCGATAAGGCTGAACAACATATG 59.727 41.667 0.00 0.00 0.00 1.78
2178 2608 7.942990 AGGATTTTCGTTTTAACACATGGTAA 58.057 30.769 0.00 0.00 0.00 2.85
2184 2614 6.717413 TCGTTTTAACACATGGTAACTGAAC 58.283 36.000 0.00 0.00 37.61 3.18
2372 2802 9.528489 AAAGGTAGTTCCATTTTTATAAGCAGA 57.472 29.630 0.00 0.00 39.02 4.26
2376 2806 9.162764 GTAGTTCCATTTTTATAAGCAGAGTCA 57.837 33.333 0.00 0.00 0.00 3.41
2377 2807 8.814038 AGTTCCATTTTTATAAGCAGAGTCAT 57.186 30.769 0.00 0.00 0.00 3.06
2387 2817 2.799017 AGCAGAGTCATTTTCATGGCA 58.201 42.857 0.00 0.00 37.49 4.92
2388 2818 3.159472 AGCAGAGTCATTTTCATGGCAA 58.841 40.909 0.00 0.00 37.49 4.52
2397 2827 1.086696 TTTCATGGCAACTCGCTAGC 58.913 50.000 4.06 4.06 41.91 3.42
2398 2828 0.036483 TTCATGGCAACTCGCTAGCA 60.036 50.000 16.45 0.92 41.91 3.49
2407 2837 0.037232 ACTCGCTAGCACTCAAACCC 60.037 55.000 16.45 0.00 0.00 4.11
2476 2906 8.770828 TCGTAGGAATAGTTTTGCTAATTATGC 58.229 33.333 0.00 0.00 32.72 3.14
2484 2914 7.651027 AGTTTTGCTAATTATGCCATCTTCT 57.349 32.000 4.99 0.00 0.00 2.85
2485 2915 8.071177 AGTTTTGCTAATTATGCCATCTTCTT 57.929 30.769 4.99 0.00 0.00 2.52
2943 3376 7.869937 TCACTGAACTGAAGATCTTTGTTAGAG 59.130 37.037 20.39 19.67 36.02 2.43
3071 3504 0.675837 GCTGCTGACTCATGGAAGCA 60.676 55.000 10.61 10.61 43.10 3.91
3295 3735 7.610305 TGATCTATTTTTCGGCTTCTTTTACCT 59.390 33.333 0.00 0.00 0.00 3.08
3302 3742 3.089284 CGGCTTCTTTTACCTCCCAAAT 58.911 45.455 0.00 0.00 0.00 2.32
3374 3815 2.613977 GCTGATGTGGCACTAGTCAACT 60.614 50.000 19.83 0.00 0.00 3.16
3503 3977 2.516888 CCACCTCCCTCACCACGTT 61.517 63.158 0.00 0.00 0.00 3.99
3648 4563 3.834799 CCGAGTACCCACCGCCTC 61.835 72.222 0.00 0.00 0.00 4.70
3649 4564 3.834799 CGAGTACCCACCGCCTCC 61.835 72.222 0.00 0.00 0.00 4.30
3650 4565 2.682494 GAGTACCCACCGCCTCCA 60.682 66.667 0.00 0.00 0.00 3.86
3651 4566 3.001406 AGTACCCACCGCCTCCAC 61.001 66.667 0.00 0.00 0.00 4.02
3652 4567 4.091939 GTACCCACCGCCTCCACC 62.092 72.222 0.00 0.00 0.00 4.61
3881 4841 1.770294 GGGTGTACCTGGAGAGAGAG 58.230 60.000 0.00 0.00 35.85 3.20
3882 4842 1.285373 GGGTGTACCTGGAGAGAGAGA 59.715 57.143 0.00 0.00 35.85 3.10
3883 4843 2.650322 GGTGTACCTGGAGAGAGAGAG 58.350 57.143 0.00 0.00 0.00 3.20
3884 4844 2.240160 GGTGTACCTGGAGAGAGAGAGA 59.760 54.545 0.00 0.00 0.00 3.10
3900 4872 5.103473 AGAGAGAGAGAGAGAGAGAGAGGTA 60.103 48.000 0.00 0.00 0.00 3.08
3991 4963 0.112412 GAGAAAAACCAGCCAGGGGA 59.888 55.000 0.00 0.00 43.89 4.81
4124 5100 9.685276 TCTGAAAAATATGTGTATTCAGGATGT 57.315 29.630 12.34 0.00 44.38 3.06
4131 5107 6.624352 ATGTGTATTCAGGATGTTATGTGC 57.376 37.500 0.00 0.00 37.40 4.57
4132 5108 5.495640 TGTGTATTCAGGATGTTATGTGCA 58.504 37.500 0.00 0.00 37.40 4.57
4133 5109 5.585844 TGTGTATTCAGGATGTTATGTGCAG 59.414 40.000 0.00 0.00 37.40 4.41
4134 5110 5.586243 GTGTATTCAGGATGTTATGTGCAGT 59.414 40.000 0.00 0.00 37.40 4.40
4135 5111 5.585844 TGTATTCAGGATGTTATGTGCAGTG 59.414 40.000 0.00 0.00 37.40 3.66
4136 5112 2.989909 TCAGGATGTTATGTGCAGTGG 58.010 47.619 0.00 0.00 37.40 4.00
4137 5113 1.402968 CAGGATGTTATGTGCAGTGGC 59.597 52.381 0.00 0.00 41.68 5.01
4138 5114 0.378257 GGATGTTATGTGCAGTGGCG 59.622 55.000 0.00 0.00 45.35 5.69
4139 5115 1.086696 GATGTTATGTGCAGTGGCGT 58.913 50.000 0.00 0.00 45.35 5.68
4140 5116 1.468520 GATGTTATGTGCAGTGGCGTT 59.531 47.619 0.00 0.00 45.35 4.84
4141 5117 1.313772 TGTTATGTGCAGTGGCGTTT 58.686 45.000 0.00 0.00 45.35 3.60
4142 5118 2.495084 TGTTATGTGCAGTGGCGTTTA 58.505 42.857 0.00 0.00 45.35 2.01
4143 5119 3.078097 TGTTATGTGCAGTGGCGTTTAT 58.922 40.909 0.00 0.00 45.35 1.40
4144 5120 3.504134 TGTTATGTGCAGTGGCGTTTATT 59.496 39.130 0.00 0.00 45.35 1.40
4145 5121 2.919666 ATGTGCAGTGGCGTTTATTC 57.080 45.000 0.00 0.00 45.35 1.75
4146 5122 1.598882 TGTGCAGTGGCGTTTATTCA 58.401 45.000 0.00 0.00 45.35 2.57
4147 5123 1.950216 TGTGCAGTGGCGTTTATTCAA 59.050 42.857 0.00 0.00 45.35 2.69
4148 5124 2.556189 TGTGCAGTGGCGTTTATTCAAT 59.444 40.909 0.00 0.00 45.35 2.57
4149 5125 2.916716 GTGCAGTGGCGTTTATTCAATG 59.083 45.455 0.00 0.00 45.35 2.82
4150 5126 2.556189 TGCAGTGGCGTTTATTCAATGT 59.444 40.909 0.00 0.00 45.35 2.71
4151 5127 2.916716 GCAGTGGCGTTTATTCAATGTG 59.083 45.455 0.00 0.00 0.00 3.21
4152 5128 2.916716 CAGTGGCGTTTATTCAATGTGC 59.083 45.455 0.00 0.00 0.00 4.57
4153 5129 2.819608 AGTGGCGTTTATTCAATGTGCT 59.180 40.909 0.00 0.00 0.00 4.40
4154 5130 2.916716 GTGGCGTTTATTCAATGTGCTG 59.083 45.455 0.00 0.00 0.00 4.41
4155 5131 2.816672 TGGCGTTTATTCAATGTGCTGA 59.183 40.909 0.00 0.00 0.00 4.26
4156 5132 3.443329 TGGCGTTTATTCAATGTGCTGAT 59.557 39.130 0.00 0.00 0.00 2.90
4157 5133 4.637977 TGGCGTTTATTCAATGTGCTGATA 59.362 37.500 0.00 0.00 0.00 2.15
4158 5134 4.970003 GGCGTTTATTCAATGTGCTGATAC 59.030 41.667 0.00 0.00 0.00 2.24
4159 5135 5.448496 GGCGTTTATTCAATGTGCTGATACA 60.448 40.000 0.00 0.00 34.63 2.29
4160 5136 6.027131 GCGTTTATTCAATGTGCTGATACAA 58.973 36.000 0.00 0.00 33.69 2.41
4161 5137 6.195244 GCGTTTATTCAATGTGCTGATACAAG 59.805 38.462 0.00 0.00 33.69 3.16
4162 5138 6.688385 CGTTTATTCAATGTGCTGATACAAGG 59.312 38.462 0.00 0.00 33.69 3.61
4163 5139 7.413988 CGTTTATTCAATGTGCTGATACAAGGA 60.414 37.037 0.00 0.00 33.69 3.36
4164 5140 7.936496 TTATTCAATGTGCTGATACAAGGAA 57.064 32.000 0.00 0.00 33.90 3.36
4165 5141 5.885230 TTCAATGTGCTGATACAAGGAAG 57.115 39.130 0.00 0.00 33.69 3.46
4166 5142 5.164620 TCAATGTGCTGATACAAGGAAGA 57.835 39.130 0.00 0.00 33.69 2.87
4167 5143 5.748402 TCAATGTGCTGATACAAGGAAGAT 58.252 37.500 0.00 0.00 33.69 2.40
4168 5144 6.888105 TCAATGTGCTGATACAAGGAAGATA 58.112 36.000 0.00 0.00 33.69 1.98
4169 5145 7.337938 TCAATGTGCTGATACAAGGAAGATAA 58.662 34.615 0.00 0.00 33.69 1.75
4170 5146 7.280876 TCAATGTGCTGATACAAGGAAGATAAC 59.719 37.037 0.00 0.00 33.69 1.89
4171 5147 6.299805 TGTGCTGATACAAGGAAGATAACT 57.700 37.500 0.00 0.00 0.00 2.24
4172 5148 6.108687 TGTGCTGATACAAGGAAGATAACTG 58.891 40.000 0.00 0.00 0.00 3.16
4173 5149 5.525378 GTGCTGATACAAGGAAGATAACTGG 59.475 44.000 0.00 0.00 0.00 4.00
4174 5150 5.425217 TGCTGATACAAGGAAGATAACTGGA 59.575 40.000 0.00 0.00 0.00 3.86
4175 5151 5.988561 GCTGATACAAGGAAGATAACTGGAG 59.011 44.000 0.00 0.00 0.00 3.86
4176 5152 6.407525 GCTGATACAAGGAAGATAACTGGAGT 60.408 42.308 0.00 0.00 0.00 3.85
4177 5153 6.878317 TGATACAAGGAAGATAACTGGAGTG 58.122 40.000 0.00 0.00 0.00 3.51
4178 5154 4.559862 ACAAGGAAGATAACTGGAGTGG 57.440 45.455 0.00 0.00 0.00 4.00
4179 5155 3.264450 ACAAGGAAGATAACTGGAGTGGG 59.736 47.826 0.00 0.00 0.00 4.61
4180 5156 3.491766 AGGAAGATAACTGGAGTGGGA 57.508 47.619 0.00 0.00 0.00 4.37
4181 5157 3.379452 AGGAAGATAACTGGAGTGGGAG 58.621 50.000 0.00 0.00 0.00 4.30
4182 5158 2.436173 GGAAGATAACTGGAGTGGGAGG 59.564 54.545 0.00 0.00 0.00 4.30
4183 5159 2.950990 AGATAACTGGAGTGGGAGGT 57.049 50.000 0.00 0.00 0.00 3.85
4184 5160 3.207044 AGATAACTGGAGTGGGAGGTT 57.793 47.619 0.00 0.00 0.00 3.50
4185 5161 2.840651 AGATAACTGGAGTGGGAGGTTG 59.159 50.000 0.00 0.00 0.00 3.77
4186 5162 2.112279 TAACTGGAGTGGGAGGTTGT 57.888 50.000 0.00 0.00 0.00 3.32
4187 5163 1.222567 AACTGGAGTGGGAGGTTGTT 58.777 50.000 0.00 0.00 0.00 2.83
4188 5164 1.222567 ACTGGAGTGGGAGGTTGTTT 58.777 50.000 0.00 0.00 0.00 2.83
4189 5165 1.569072 ACTGGAGTGGGAGGTTGTTTT 59.431 47.619 0.00 0.00 0.00 2.43
4190 5166 1.956477 CTGGAGTGGGAGGTTGTTTTG 59.044 52.381 0.00 0.00 0.00 2.44
4191 5167 1.566703 TGGAGTGGGAGGTTGTTTTGA 59.433 47.619 0.00 0.00 0.00 2.69
4192 5168 1.954382 GGAGTGGGAGGTTGTTTTGAC 59.046 52.381 0.00 0.00 0.00 3.18
4193 5169 2.422945 GGAGTGGGAGGTTGTTTTGACT 60.423 50.000 0.00 0.00 0.00 3.41
4194 5170 2.618709 GAGTGGGAGGTTGTTTTGACTG 59.381 50.000 0.00 0.00 0.00 3.51
4195 5171 2.241176 AGTGGGAGGTTGTTTTGACTGA 59.759 45.455 0.00 0.00 0.00 3.41
4196 5172 3.117512 AGTGGGAGGTTGTTTTGACTGAT 60.118 43.478 0.00 0.00 0.00 2.90
4197 5173 3.253432 GTGGGAGGTTGTTTTGACTGATC 59.747 47.826 0.00 0.00 0.00 2.92
4198 5174 3.117701 TGGGAGGTTGTTTTGACTGATCA 60.118 43.478 0.00 0.00 0.00 2.92
4199 5175 3.888930 GGGAGGTTGTTTTGACTGATCAA 59.111 43.478 0.00 0.00 43.28 2.57
4214 5190 9.734620 TTGACTGATCAAATTGTCACTTTTTAG 57.265 29.630 13.41 0.00 41.99 1.85
4215 5191 9.119418 TGACTGATCAAATTGTCACTTTTTAGA 57.881 29.630 10.55 0.00 34.94 2.10
4216 5192 9.604626 GACTGATCAAATTGTCACTTTTTAGAG 57.395 33.333 7.71 0.00 0.00 2.43
4217 5193 9.125026 ACTGATCAAATTGTCACTTTTTAGAGT 57.875 29.630 0.00 0.00 0.00 3.24
4218 5194 9.390795 CTGATCAAATTGTCACTTTTTAGAGTG 57.609 33.333 0.00 0.00 46.58 3.51
4219 5195 8.352201 TGATCAAATTGTCACTTTTTAGAGTGG 58.648 33.333 0.00 0.00 45.54 4.00
4220 5196 7.873719 TCAAATTGTCACTTTTTAGAGTGGA 57.126 32.000 5.31 0.00 45.54 4.02
4221 5197 8.463930 TCAAATTGTCACTTTTTAGAGTGGAT 57.536 30.769 5.31 0.00 45.54 3.41
4222 5198 9.567776 TCAAATTGTCACTTTTTAGAGTGGATA 57.432 29.630 5.31 0.00 45.54 2.59
4227 5203 8.740123 TGTCACTTTTTAGAGTGGATAAAACA 57.260 30.769 5.31 0.00 45.54 2.83
4228 5204 8.617809 TGTCACTTTTTAGAGTGGATAAAACAC 58.382 33.333 5.31 0.00 45.54 3.32
4229 5205 8.617809 GTCACTTTTTAGAGTGGATAAAACACA 58.382 33.333 5.31 0.00 45.54 3.72
4230 5206 9.349713 TCACTTTTTAGAGTGGATAAAACACAT 57.650 29.630 5.31 0.00 45.54 3.21
4231 5207 9.965824 CACTTTTTAGAGTGGATAAAACACATT 57.034 29.630 0.00 0.00 42.58 2.71
4235 5211 8.810652 TTTAGAGTGGATAAAACACATTTTGC 57.189 30.769 0.00 0.00 41.21 3.68
4236 5212 6.403866 AGAGTGGATAAAACACATTTTGCA 57.596 33.333 0.00 0.00 41.21 4.08
4237 5213 6.996509 AGAGTGGATAAAACACATTTTGCAT 58.003 32.000 0.00 0.00 41.21 3.96
4238 5214 7.444299 AGAGTGGATAAAACACATTTTGCATT 58.556 30.769 0.00 0.00 41.21 3.56
4239 5215 7.933033 AGAGTGGATAAAACACATTTTGCATTT 59.067 29.630 0.00 0.00 41.21 2.32
4240 5216 7.863666 AGTGGATAAAACACATTTTGCATTTG 58.136 30.769 0.00 0.00 41.21 2.32
4241 5217 7.041235 AGTGGATAAAACACATTTTGCATTTGG 60.041 33.333 0.00 0.00 41.21 3.28
4242 5218 6.994496 TGGATAAAACACATTTTGCATTTGGA 59.006 30.769 0.00 0.00 38.50 3.53
4243 5219 7.500227 TGGATAAAACACATTTTGCATTTGGAA 59.500 29.630 0.00 0.00 38.50 3.53
4244 5220 8.513774 GGATAAAACACATTTTGCATTTGGAAT 58.486 29.630 0.00 0.00 38.50 3.01
4245 5221 9.896263 GATAAAACACATTTTGCATTTGGAATT 57.104 25.926 0.00 0.00 38.50 2.17
4247 5223 8.999220 AAAACACATTTTGCATTTGGAATTTT 57.001 23.077 0.00 0.00 36.64 1.82
4248 5224 8.999220 AAACACATTTTGCATTTGGAATTTTT 57.001 23.077 0.00 0.00 0.00 1.94
4249 5225 7.988904 ACACATTTTGCATTTGGAATTTTTG 57.011 28.000 0.00 0.00 0.00 2.44
4250 5226 6.476053 ACACATTTTGCATTTGGAATTTTTGC 59.524 30.769 0.00 0.00 0.00 3.68
4251 5227 6.697892 CACATTTTGCATTTGGAATTTTTGCT 59.302 30.769 0.00 0.00 34.47 3.91
4252 5228 7.222999 CACATTTTGCATTTGGAATTTTTGCTT 59.777 29.630 0.00 0.00 34.47 3.91
4253 5229 7.764901 ACATTTTGCATTTGGAATTTTTGCTTT 59.235 25.926 0.00 0.00 34.47 3.51
4254 5230 7.521509 TTTTGCATTTGGAATTTTTGCTTTG 57.478 28.000 0.00 0.00 34.47 2.77
4255 5231 6.446781 TTGCATTTGGAATTTTTGCTTTGA 57.553 29.167 0.00 0.00 34.47 2.69
4256 5232 6.062434 TGCATTTGGAATTTTTGCTTTGAG 57.938 33.333 0.00 0.00 34.47 3.02
4257 5233 5.821470 TGCATTTGGAATTTTTGCTTTGAGA 59.179 32.000 0.00 0.00 34.47 3.27
4258 5234 6.487331 TGCATTTGGAATTTTTGCTTTGAGAT 59.513 30.769 0.00 0.00 34.47 2.75
4259 5235 6.799925 GCATTTGGAATTTTTGCTTTGAGATG 59.200 34.615 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.068591 AGTTTATTGCCGAAAACTTGGAGTT 59.931 36.000 2.55 0.00 41.89 3.01
23 24 6.970484 TCTTCTTCTGAAACAGTTTATTGCC 58.030 36.000 0.00 0.00 32.61 4.52
37 38 5.524971 TTAACACGGTTCTCTTCTTCTGA 57.475 39.130 0.00 0.00 0.00 3.27
58 71 6.680148 ACCTGCCATTACCTTTACATTTTT 57.320 33.333 0.00 0.00 0.00 1.94
110 123 0.320247 GCCGGCATCTCCACTCTATG 60.320 60.000 24.80 0.00 34.01 2.23
136 149 7.881643 GATGTTATCATCAAAGCTACTCGAT 57.118 36.000 8.61 0.00 46.78 3.59
192 205 7.649306 GCCTCAATTATTTTAACATCAGCGATT 59.351 33.333 0.00 0.00 0.00 3.34
197 210 9.294030 GAGTTGCCTCAATTATTTTAACATCAG 57.706 33.333 0.00 0.00 37.67 2.90
245 258 3.688673 GCATGCTAGCTCTCTCTGTTTTT 59.311 43.478 17.23 0.00 0.00 1.94
275 288 4.131596 CCTGTTTTAGTTTCGTCCAGGAA 58.868 43.478 0.00 0.00 40.29 3.36
280 293 7.080099 GGTTTTATCCTGTTTTAGTTTCGTCC 58.920 38.462 0.00 0.00 0.00 4.79
283 296 7.753580 GGATGGTTTTATCCTGTTTTAGTTTCG 59.246 37.037 0.00 0.00 42.73 3.46
314 327 4.191544 CAGTTTAGGATTCATTCTCGGCA 58.808 43.478 0.00 0.00 0.00 5.69
362 375 1.798813 CCGACTGTTACAAACTGCTCC 59.201 52.381 0.00 0.00 34.11 4.70
371 384 0.541063 TCAGGCTCCCGACTGTTACA 60.541 55.000 0.00 0.00 46.80 2.41
408 421 1.248101 TGATCCGCGTCTGTTCCAGA 61.248 55.000 4.92 0.00 38.25 3.86
413 426 0.391661 ATGCTTGATCCGCGTCTGTT 60.392 50.000 4.92 0.00 0.00 3.16
427 440 1.002888 CTCCCTGTGTCAGTGATGCTT 59.997 52.381 0.00 0.00 0.00 3.91
429 442 0.392193 CCTCCCTGTGTCAGTGATGC 60.392 60.000 0.00 0.00 0.00 3.91
469 482 3.733443 AGTTTTCCCTTGTGATTGCAC 57.267 42.857 0.00 0.00 45.35 4.57
470 483 5.136828 TCTTAGTTTTCCCTTGTGATTGCA 58.863 37.500 0.00 0.00 0.00 4.08
471 484 5.705609 TCTTAGTTTTCCCTTGTGATTGC 57.294 39.130 0.00 0.00 0.00 3.56
472 485 8.025445 CAGATTCTTAGTTTTCCCTTGTGATTG 58.975 37.037 0.00 0.00 0.00 2.67
473 486 7.177392 CCAGATTCTTAGTTTTCCCTTGTGATT 59.823 37.037 0.00 0.00 0.00 2.57
474 487 6.660949 CCAGATTCTTAGTTTTCCCTTGTGAT 59.339 38.462 0.00 0.00 0.00 3.06
475 488 6.003950 CCAGATTCTTAGTTTTCCCTTGTGA 58.996 40.000 0.00 0.00 0.00 3.58
476 489 5.335976 GCCAGATTCTTAGTTTTCCCTTGTG 60.336 44.000 0.00 0.00 0.00 3.33
478 491 4.158579 GGCCAGATTCTTAGTTTTCCCTTG 59.841 45.833 0.00 0.00 0.00 3.61
480 493 3.622455 CGGCCAGATTCTTAGTTTTCCCT 60.622 47.826 2.24 0.00 0.00 4.20
481 494 2.683362 CGGCCAGATTCTTAGTTTTCCC 59.317 50.000 2.24 0.00 0.00 3.97
482 495 2.097629 GCGGCCAGATTCTTAGTTTTCC 59.902 50.000 2.24 0.00 0.00 3.13
483 496 2.747446 TGCGGCCAGATTCTTAGTTTTC 59.253 45.455 2.24 0.00 0.00 2.29
484 497 2.749621 CTGCGGCCAGATTCTTAGTTTT 59.250 45.455 2.24 0.00 41.77 2.43
485 498 2.359900 CTGCGGCCAGATTCTTAGTTT 58.640 47.619 2.24 0.00 41.77 2.66
486 499 2.014068 GCTGCGGCCAGATTCTTAGTT 61.014 52.381 6.12 0.00 41.77 2.24
487 500 0.462759 GCTGCGGCCAGATTCTTAGT 60.463 55.000 6.12 0.00 41.77 2.24
488 501 0.462581 TGCTGCGGCCAGATTCTTAG 60.463 55.000 16.57 0.00 41.77 2.18
489 502 0.181114 ATGCTGCGGCCAGATTCTTA 59.819 50.000 16.57 0.00 41.77 2.10
539 552 6.706716 GCCTGGGTATCTGTATTTTTCTACTC 59.293 42.308 0.00 0.00 0.00 2.59
554 567 1.071471 CCGGATGTGCCTGGGTATC 59.929 63.158 0.00 0.00 0.00 2.24
556 569 3.792736 GCCGGATGTGCCTGGGTA 61.793 66.667 5.05 0.00 32.90 3.69
759 788 4.719369 AACGACAGCCGACGCCTC 62.719 66.667 0.00 0.00 41.76 4.70
845 875 0.896019 ACAGGAGAGACGGACACAGG 60.896 60.000 0.00 0.00 0.00 4.00
866 902 3.986006 TGCTCGGGGTGACGTCAC 61.986 66.667 35.26 35.26 45.72 3.67
890 926 2.272471 GGAGCTTACAGGTGGGGC 59.728 66.667 0.00 0.00 0.00 5.80
891 927 2.998949 GGGAGCTTACAGGTGGGG 59.001 66.667 0.00 0.00 0.00 4.96
922 958 2.303549 GACTGACAGATGGGCCCGAG 62.304 65.000 19.37 9.27 0.00 4.63
932 968 3.680786 CGGGCCGTGACTGACAGA 61.681 66.667 19.97 0.00 0.00 3.41
1194 1240 1.410004 TCTGACCAGTTCGTTGAGGT 58.590 50.000 0.00 0.00 37.00 3.85
1195 1241 2.611518 GATCTGACCAGTTCGTTGAGG 58.388 52.381 0.00 0.00 0.00 3.86
1196 1242 2.611518 GGATCTGACCAGTTCGTTGAG 58.388 52.381 0.00 0.00 0.00 3.02
1197 1243 1.067846 CGGATCTGACCAGTTCGTTGA 60.068 52.381 0.00 0.00 0.00 3.18
1198 1244 1.067846 TCGGATCTGACCAGTTCGTTG 60.068 52.381 0.00 0.00 0.00 4.10
1199 1245 1.254026 TCGGATCTGACCAGTTCGTT 58.746 50.000 0.00 0.00 0.00 3.85
1200 1246 1.405821 GATCGGATCTGACCAGTTCGT 59.594 52.381 6.33 0.00 0.00 3.85
1201 1247 1.269309 GGATCGGATCTGACCAGTTCG 60.269 57.143 16.96 0.00 0.00 3.95
1202 1248 1.269309 CGGATCGGATCTGACCAGTTC 60.269 57.143 19.89 0.00 37.90 3.01
1203 1249 0.747255 CGGATCGGATCTGACCAGTT 59.253 55.000 19.89 0.00 37.90 3.16
1204 1250 2.420138 CGGATCGGATCTGACCAGT 58.580 57.895 19.89 0.00 37.90 4.00
1216 1262 2.913060 GAGAGGGGGTCCGGATCG 60.913 72.222 7.81 0.00 38.33 3.69
1217 1263 2.524640 GGAGAGGGGGTCCGGATC 60.525 72.222 7.81 6.88 38.33 3.36
1218 1264 4.173701 GGGAGAGGGGGTCCGGAT 62.174 72.222 7.81 0.00 38.33 4.18
1220 1266 4.416601 AAGGGAGAGGGGGTCCGG 62.417 72.222 0.00 0.00 38.33 5.14
1221 1267 2.764547 GAAGGGAGAGGGGGTCCG 60.765 72.222 0.00 0.00 38.33 4.79
1222 1268 2.367107 GGAAGGGAGAGGGGGTCC 60.367 72.222 0.00 0.00 0.00 4.46
1223 1269 2.367107 GGGAAGGGAGAGGGGGTC 60.367 72.222 0.00 0.00 0.00 4.46
1224 1270 4.040198 GGGGAAGGGAGAGGGGGT 62.040 72.222 0.00 0.00 0.00 4.95
1225 1271 4.845307 GGGGGAAGGGAGAGGGGG 62.845 77.778 0.00 0.00 0.00 5.40
1243 1625 2.417933 CAGGAACGCAAGGAGAAATCAG 59.582 50.000 0.00 0.00 46.39 2.90
1337 1719 1.408405 GGGAATCGAAGGGGAAAGACC 60.408 57.143 0.00 0.00 38.08 3.85
1434 1829 5.047235 AGAGTGGATTTCGGCTACCATATAC 60.047 44.000 0.00 0.00 34.87 1.47
1495 1890 8.917088 GGGGCCACGATATACTAGTAAATTATA 58.083 37.037 6.70 0.00 0.00 0.98
1496 1891 7.417116 CGGGGCCACGATATACTAGTAAATTAT 60.417 40.741 27.22 0.38 35.47 1.28
1564 1959 2.566952 GGAATCAATTTCCGGCACAG 57.433 50.000 0.00 0.00 44.46 3.66
1574 1969 3.012518 CAAGGAGCTCACGGAATCAATT 58.987 45.455 17.19 0.00 0.00 2.32
1584 1979 3.304928 CCAACATGAAACAAGGAGCTCAC 60.305 47.826 17.19 5.01 0.00 3.51
1649 2048 5.626211 GTTTGAAGACTAAATGCAGAGAGC 58.374 41.667 0.00 0.00 45.96 4.09
1659 2058 4.411256 ACTGGTCCGTTTGAAGACTAAA 57.589 40.909 0.00 0.00 33.39 1.85
1726 2125 9.423061 TCATACATGATAATCATTAGGAACACG 57.577 33.333 0.00 0.00 34.28 4.49
1873 2276 8.820831 CCAAATACATGGAGGAGATAGAGTTAT 58.179 37.037 0.00 0.00 43.54 1.89
1946 2350 2.479566 TGGAGCAGGTCACAAAGATC 57.520 50.000 1.20 0.00 0.00 2.75
1947 2351 2.575279 AGATGGAGCAGGTCACAAAGAT 59.425 45.455 1.20 0.00 0.00 2.40
1948 2352 1.980765 AGATGGAGCAGGTCACAAAGA 59.019 47.619 1.20 0.00 0.00 2.52
1950 2354 1.699083 TCAGATGGAGCAGGTCACAAA 59.301 47.619 1.20 0.00 0.00 2.83
1951 2355 1.351076 TCAGATGGAGCAGGTCACAA 58.649 50.000 1.20 0.00 0.00 3.33
1953 2357 2.479566 TTTCAGATGGAGCAGGTCAC 57.520 50.000 1.20 0.00 0.00 3.67
2110 2520 4.776743 CATATGTTGTTCAGCCTTATCGC 58.223 43.478 0.00 0.00 0.00 4.58
2154 2584 7.863877 AGTTACCATGTGTTAAAACGAAAATCC 59.136 33.333 0.00 0.00 0.00 3.01
2155 2585 8.687301 CAGTTACCATGTGTTAAAACGAAAATC 58.313 33.333 0.00 0.00 0.00 2.17
2178 2608 3.329300 GGCACACCTGATGTTCAGT 57.671 52.632 4.00 0.00 42.80 3.41
2336 2766 8.879427 AAATGGAACTACCTTTAGTATTTGCT 57.121 30.769 0.00 0.00 37.59 3.91
2366 2796 3.159472 TGCCATGAAAATGACTCTGCTT 58.841 40.909 0.00 0.00 0.00 3.91
2367 2797 2.799017 TGCCATGAAAATGACTCTGCT 58.201 42.857 0.00 0.00 0.00 4.24
2368 2798 3.057033 AGTTGCCATGAAAATGACTCTGC 60.057 43.478 0.00 0.00 0.00 4.26
2372 2802 2.095059 GCGAGTTGCCATGAAAATGACT 60.095 45.455 0.00 0.00 37.76 3.41
2387 2817 1.608283 GGGTTTGAGTGCTAGCGAGTT 60.608 52.381 10.77 0.00 0.00 3.01
2388 2818 0.037232 GGGTTTGAGTGCTAGCGAGT 60.037 55.000 10.77 2.15 0.00 4.18
2397 2827 0.320771 CCTCGACCTGGGTTTGAGTG 60.321 60.000 16.29 8.45 32.58 3.51
2398 2828 1.481056 CCCTCGACCTGGGTTTGAGT 61.481 60.000 16.29 0.00 39.82 3.41
2407 2837 1.006102 GACACACACCCTCGACCTG 60.006 63.158 0.00 0.00 0.00 4.00
2741 3174 2.706890 GGTATCAAAGAAGGTTGCCGA 58.293 47.619 0.00 0.00 0.00 5.54
2943 3376 4.377431 CCAACATCTTCGTTTAGTGCAGTC 60.377 45.833 0.00 0.00 0.00 3.51
3194 3628 5.550290 TCTACTTTTCACATCTGCATGACA 58.450 37.500 0.00 0.00 33.72 3.58
3195 3629 6.486253 TTCTACTTTTCACATCTGCATGAC 57.514 37.500 0.00 0.00 33.72 3.06
3196 3630 7.509141 TTTTCTACTTTTCACATCTGCATGA 57.491 32.000 0.00 0.00 33.72 3.07
3295 3735 2.158355 TCCGGTTTGGGTTTATTTGGGA 60.158 45.455 0.00 0.00 38.76 4.37
3302 3742 3.094572 TGTTTTGTCCGGTTTGGGTTTA 58.905 40.909 0.00 0.00 38.76 2.01
3329 3770 1.524008 GGTGGAGAAAAACCAGCCGG 61.524 60.000 0.00 0.00 46.25 6.13
3330 3771 1.956802 GGTGGAGAAAAACCAGCCG 59.043 57.895 0.00 0.00 46.25 5.52
3548 4033 2.363147 GGACGAGGCTCCTCTGGT 60.363 66.667 9.32 0.00 40.69 4.00
3881 4841 5.598830 TCTCTTACCTCTCTCTCTCTCTCTC 59.401 48.000 0.00 0.00 0.00 3.20
3882 4842 5.529289 TCTCTTACCTCTCTCTCTCTCTCT 58.471 45.833 0.00 0.00 0.00 3.10
3883 4843 5.871396 TCTCTTACCTCTCTCTCTCTCTC 57.129 47.826 0.00 0.00 0.00 3.20
3884 4844 6.415573 GTTTCTCTTACCTCTCTCTCTCTCT 58.584 44.000 0.00 0.00 0.00 3.10
3900 4872 2.224646 GCCCTCTTGTCAGGTTTCTCTT 60.225 50.000 0.00 0.00 0.00 2.85
3991 4963 1.783071 ACCCAAACCGGACAAAACAT 58.217 45.000 9.46 0.00 36.56 2.71
4109 5085 5.495640 TGCACATAACATCCTGAATACACA 58.504 37.500 0.00 0.00 0.00 3.72
4110 5086 5.586243 ACTGCACATAACATCCTGAATACAC 59.414 40.000 0.00 0.00 0.00 2.90
4111 5087 5.585844 CACTGCACATAACATCCTGAATACA 59.414 40.000 0.00 0.00 0.00 2.29
4112 5088 5.008019 CCACTGCACATAACATCCTGAATAC 59.992 44.000 0.00 0.00 0.00 1.89
4113 5089 5.125356 CCACTGCACATAACATCCTGAATA 58.875 41.667 0.00 0.00 0.00 1.75
4114 5090 3.949754 CCACTGCACATAACATCCTGAAT 59.050 43.478 0.00 0.00 0.00 2.57
4115 5091 3.346315 CCACTGCACATAACATCCTGAA 58.654 45.455 0.00 0.00 0.00 3.02
4116 5092 2.940971 GCCACTGCACATAACATCCTGA 60.941 50.000 0.00 0.00 37.47 3.86
4117 5093 1.402968 GCCACTGCACATAACATCCTG 59.597 52.381 0.00 0.00 37.47 3.86
4118 5094 1.755179 GCCACTGCACATAACATCCT 58.245 50.000 0.00 0.00 37.47 3.24
4119 5095 0.378257 CGCCACTGCACATAACATCC 59.622 55.000 0.00 0.00 37.32 3.51
4120 5096 1.086696 ACGCCACTGCACATAACATC 58.913 50.000 0.00 0.00 37.32 3.06
4121 5097 1.533625 AACGCCACTGCACATAACAT 58.466 45.000 0.00 0.00 37.32 2.71
4122 5098 1.313772 AAACGCCACTGCACATAACA 58.686 45.000 0.00 0.00 37.32 2.41
4123 5099 3.757745 ATAAACGCCACTGCACATAAC 57.242 42.857 0.00 0.00 37.32 1.89
4124 5100 3.753797 TGAATAAACGCCACTGCACATAA 59.246 39.130 0.00 0.00 37.32 1.90
4125 5101 3.339141 TGAATAAACGCCACTGCACATA 58.661 40.909 0.00 0.00 37.32 2.29
4126 5102 2.158559 TGAATAAACGCCACTGCACAT 58.841 42.857 0.00 0.00 37.32 3.21
4127 5103 1.598882 TGAATAAACGCCACTGCACA 58.401 45.000 0.00 0.00 37.32 4.57
4128 5104 2.697431 TTGAATAAACGCCACTGCAC 57.303 45.000 0.00 0.00 37.32 4.57
4129 5105 2.556189 ACATTGAATAAACGCCACTGCA 59.444 40.909 0.00 0.00 37.32 4.41
4130 5106 2.916716 CACATTGAATAAACGCCACTGC 59.083 45.455 0.00 0.00 0.00 4.40
4131 5107 2.916716 GCACATTGAATAAACGCCACTG 59.083 45.455 0.00 0.00 0.00 3.66
4132 5108 2.819608 AGCACATTGAATAAACGCCACT 59.180 40.909 0.00 0.00 0.00 4.00
4133 5109 2.916716 CAGCACATTGAATAAACGCCAC 59.083 45.455 0.00 0.00 0.00 5.01
4134 5110 2.816672 TCAGCACATTGAATAAACGCCA 59.183 40.909 0.00 0.00 0.00 5.69
4135 5111 3.485947 TCAGCACATTGAATAAACGCC 57.514 42.857 0.00 0.00 0.00 5.68
4136 5112 5.568482 TGTATCAGCACATTGAATAAACGC 58.432 37.500 0.00 0.00 0.00 4.84
4137 5113 6.688385 CCTTGTATCAGCACATTGAATAAACG 59.312 38.462 0.00 0.00 0.00 3.60
4138 5114 7.761409 TCCTTGTATCAGCACATTGAATAAAC 58.239 34.615 0.00 0.00 0.00 2.01
4139 5115 7.936496 TCCTTGTATCAGCACATTGAATAAA 57.064 32.000 0.00 0.00 0.00 1.40
4140 5116 7.828717 TCTTCCTTGTATCAGCACATTGAATAA 59.171 33.333 0.00 0.00 0.00 1.40
4141 5117 7.337938 TCTTCCTTGTATCAGCACATTGAATA 58.662 34.615 0.00 0.00 0.00 1.75
4142 5118 6.182627 TCTTCCTTGTATCAGCACATTGAAT 58.817 36.000 0.00 0.00 0.00 2.57
4143 5119 5.559770 TCTTCCTTGTATCAGCACATTGAA 58.440 37.500 0.00 0.00 0.00 2.69
4144 5120 5.164620 TCTTCCTTGTATCAGCACATTGA 57.835 39.130 0.00 0.00 0.00 2.57
4145 5121 7.281774 AGTTATCTTCCTTGTATCAGCACATTG 59.718 37.037 0.00 0.00 0.00 2.82
4146 5122 7.281774 CAGTTATCTTCCTTGTATCAGCACATT 59.718 37.037 0.00 0.00 0.00 2.71
4147 5123 6.765036 CAGTTATCTTCCTTGTATCAGCACAT 59.235 38.462 0.00 0.00 0.00 3.21
4148 5124 6.108687 CAGTTATCTTCCTTGTATCAGCACA 58.891 40.000 0.00 0.00 0.00 4.57
4149 5125 5.525378 CCAGTTATCTTCCTTGTATCAGCAC 59.475 44.000 0.00 0.00 0.00 4.40
4150 5126 5.425217 TCCAGTTATCTTCCTTGTATCAGCA 59.575 40.000 0.00 0.00 0.00 4.41
4151 5127 5.918608 TCCAGTTATCTTCCTTGTATCAGC 58.081 41.667 0.00 0.00 0.00 4.26
4152 5128 6.983307 CACTCCAGTTATCTTCCTTGTATCAG 59.017 42.308 0.00 0.00 0.00 2.90
4153 5129 6.127054 CCACTCCAGTTATCTTCCTTGTATCA 60.127 42.308 0.00 0.00 0.00 2.15
4154 5130 6.284459 CCACTCCAGTTATCTTCCTTGTATC 58.716 44.000 0.00 0.00 0.00 2.24
4155 5131 5.131142 CCCACTCCAGTTATCTTCCTTGTAT 59.869 44.000 0.00 0.00 0.00 2.29
4156 5132 4.469945 CCCACTCCAGTTATCTTCCTTGTA 59.530 45.833 0.00 0.00 0.00 2.41
4157 5133 3.264450 CCCACTCCAGTTATCTTCCTTGT 59.736 47.826 0.00 0.00 0.00 3.16
4158 5134 3.519510 TCCCACTCCAGTTATCTTCCTTG 59.480 47.826 0.00 0.00 0.00 3.61
4159 5135 3.777522 CTCCCACTCCAGTTATCTTCCTT 59.222 47.826 0.00 0.00 0.00 3.36
4160 5136 3.379452 CTCCCACTCCAGTTATCTTCCT 58.621 50.000 0.00 0.00 0.00 3.36
4161 5137 2.436173 CCTCCCACTCCAGTTATCTTCC 59.564 54.545 0.00 0.00 0.00 3.46
4162 5138 3.108376 ACCTCCCACTCCAGTTATCTTC 58.892 50.000 0.00 0.00 0.00 2.87
4163 5139 3.207044 ACCTCCCACTCCAGTTATCTT 57.793 47.619 0.00 0.00 0.00 2.40
4164 5140 2.840651 CAACCTCCCACTCCAGTTATCT 59.159 50.000 0.00 0.00 0.00 1.98
4165 5141 2.572104 ACAACCTCCCACTCCAGTTATC 59.428 50.000 0.00 0.00 0.00 1.75
4166 5142 2.632537 ACAACCTCCCACTCCAGTTAT 58.367 47.619 0.00 0.00 0.00 1.89
4167 5143 2.112279 ACAACCTCCCACTCCAGTTA 57.888 50.000 0.00 0.00 0.00 2.24
4168 5144 1.222567 AACAACCTCCCACTCCAGTT 58.777 50.000 0.00 0.00 0.00 3.16
4169 5145 1.222567 AAACAACCTCCCACTCCAGT 58.777 50.000 0.00 0.00 0.00 4.00
4170 5146 1.956477 CAAAACAACCTCCCACTCCAG 59.044 52.381 0.00 0.00 0.00 3.86
4171 5147 1.566703 TCAAAACAACCTCCCACTCCA 59.433 47.619 0.00 0.00 0.00 3.86
4172 5148 1.954382 GTCAAAACAACCTCCCACTCC 59.046 52.381 0.00 0.00 0.00 3.85
4173 5149 2.618709 CAGTCAAAACAACCTCCCACTC 59.381 50.000 0.00 0.00 0.00 3.51
4174 5150 2.241176 TCAGTCAAAACAACCTCCCACT 59.759 45.455 0.00 0.00 0.00 4.00
4175 5151 2.650322 TCAGTCAAAACAACCTCCCAC 58.350 47.619 0.00 0.00 0.00 4.61
4176 5152 3.117701 TGATCAGTCAAAACAACCTCCCA 60.118 43.478 0.00 0.00 0.00 4.37
4177 5153 3.486383 TGATCAGTCAAAACAACCTCCC 58.514 45.455 0.00 0.00 0.00 4.30
4188 5164 9.734620 CTAAAAAGTGACAATTTGATCAGTCAA 57.265 29.630 14.93 0.00 42.03 3.18
4189 5165 9.119418 TCTAAAAAGTGACAATTTGATCAGTCA 57.881 29.630 10.55 10.55 38.56 3.41
4190 5166 9.604626 CTCTAAAAAGTGACAATTTGATCAGTC 57.395 33.333 0.99 6.00 0.00 3.51
4191 5167 9.125026 ACTCTAAAAAGTGACAATTTGATCAGT 57.875 29.630 0.99 3.87 0.00 3.41
4205 5181 9.965824 AATGTGTTTTATCCACTCTAAAAAGTG 57.034 29.630 0.00 0.00 45.10 3.16
4209 5185 9.255304 GCAAAATGTGTTTTATCCACTCTAAAA 57.745 29.630 0.00 0.00 35.83 1.52
4210 5186 8.417106 TGCAAAATGTGTTTTATCCACTCTAAA 58.583 29.630 0.00 0.00 35.83 1.85
4211 5187 7.946207 TGCAAAATGTGTTTTATCCACTCTAA 58.054 30.769 0.00 0.00 35.83 2.10
4212 5188 7.517614 TGCAAAATGTGTTTTATCCACTCTA 57.482 32.000 0.00 0.00 35.83 2.43
4213 5189 6.403866 TGCAAAATGTGTTTTATCCACTCT 57.596 33.333 0.00 0.00 35.83 3.24
4214 5190 7.656707 AATGCAAAATGTGTTTTATCCACTC 57.343 32.000 0.00 0.00 35.83 3.51
4215 5191 7.041235 CCAAATGCAAAATGTGTTTTATCCACT 60.041 33.333 0.00 0.00 35.83 4.00
4216 5192 7.041508 TCCAAATGCAAAATGTGTTTTATCCAC 60.042 33.333 0.00 0.00 35.83 4.02
4217 5193 6.994496 TCCAAATGCAAAATGTGTTTTATCCA 59.006 30.769 0.00 0.00 35.83 3.41
4218 5194 7.432350 TCCAAATGCAAAATGTGTTTTATCC 57.568 32.000 0.00 0.00 35.83 2.59
4219 5195 9.896263 AATTCCAAATGCAAAATGTGTTTTATC 57.104 25.926 0.00 0.00 35.83 1.75
4222 5198 8.999220 AAAATTCCAAATGCAAAATGTGTTTT 57.001 23.077 0.00 0.00 38.03 2.43
4223 5199 8.870879 CAAAAATTCCAAATGCAAAATGTGTTT 58.129 25.926 0.00 0.00 0.00 2.83
4224 5200 7.010275 GCAAAAATTCCAAATGCAAAATGTGTT 59.990 29.630 0.00 0.00 37.00 3.32
4225 5201 6.476053 GCAAAAATTCCAAATGCAAAATGTGT 59.524 30.769 0.00 0.00 37.00 3.72
4226 5202 6.697892 AGCAAAAATTCCAAATGCAAAATGTG 59.302 30.769 0.00 0.00 39.42 3.21
4227 5203 6.807789 AGCAAAAATTCCAAATGCAAAATGT 58.192 28.000 0.00 0.00 39.42 2.71
4228 5204 7.701809 AAGCAAAAATTCCAAATGCAAAATG 57.298 28.000 0.00 0.00 39.42 2.32
4229 5205 7.980099 TCAAAGCAAAAATTCCAAATGCAAAAT 59.020 25.926 0.00 0.00 39.42 1.82
4230 5206 7.318141 TCAAAGCAAAAATTCCAAATGCAAAA 58.682 26.923 0.00 0.00 39.42 2.44
4231 5207 6.860080 TCAAAGCAAAAATTCCAAATGCAAA 58.140 28.000 0.00 0.00 39.42 3.68
4232 5208 6.318144 TCTCAAAGCAAAAATTCCAAATGCAA 59.682 30.769 0.00 0.00 39.42 4.08
4233 5209 5.821470 TCTCAAAGCAAAAATTCCAAATGCA 59.179 32.000 0.00 0.00 39.42 3.96
4234 5210 6.303021 TCTCAAAGCAAAAATTCCAAATGC 57.697 33.333 0.00 0.00 37.28 3.56


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

AutoCloner maintained by Alex Coulton.