Multiple sequence alignment - TraesCS6D01G097000

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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 TraesCS6D01G097000 chr6D 100.000 4047 0 0 1 4047 60549412 60545366 0.000000e+00 7474.0
1 TraesCS6D01G097000 chr6D 93.496 246 16 0 413 658 433583829 433583584 2.300000e-97 366.0
2 TraesCS6D01G097000 chr6A 91.548 3431 176 51 655 4045 77539343 77535987 0.000000e+00 4625.0
3 TraesCS6D01G097000 chr6A 96.413 223 8 0 1 223 77539729 77539507 6.390000e-98 368.0
4 TraesCS6D01G097000 chr6A 95.604 182 6 1 235 414 77539524 77539343 1.420000e-74 291.0
5 TraesCS6D01G097000 chr6B 94.499 2745 112 24 655 3376 134827033 134824305 0.000000e+00 4196.0
6 TraesCS6D01G097000 chr6B 86.745 513 39 18 3546 4033 134824222 134823714 9.890000e-151 544.0
7 TraesCS6D01G097000 chr6B 91.573 178 13 2 239 414 134827925 134827748 1.120000e-60 244.0
8 TraesCS6D01G097000 chr6B 94.891 137 7 0 655 791 134827734 134827598 8.810000e-52 215.0
9 TraesCS6D01G097000 chr6B 85.955 178 21 3 240 414 134827209 134827033 1.920000e-43 187.0
10 TraesCS6D01G097000 chr3D 91.254 869 58 13 1481 2339 135040702 135041562 0.000000e+00 1168.0
11 TraesCS6D01G097000 chr3D 83.974 624 79 10 846 1449 135018799 135019421 2.710000e-161 579.0
12 TraesCS6D01G097000 chr3D 93.173 249 16 1 409 657 25248972 25249219 8.270000e-97 364.0
13 TraesCS6D01G097000 chr3D 93.416 243 16 0 413 655 537749544 537749302 1.070000e-95 361.0
14 TraesCS6D01G097000 chr3D 82.353 170 27 2 247 414 135018480 135018648 1.170000e-30 145.0
15 TraesCS6D01G097000 chr3A 90.132 760 53 14 1588 2339 149982968 149983713 0.000000e+00 968.0
16 TraesCS6D01G097000 chr3A 83.681 766 104 8 846 1591 149962019 149962783 0.000000e+00 702.0
17 TraesCS6D01G097000 chr2D 94.239 243 13 1 414 655 37913227 37912985 1.780000e-98 370.0
18 TraesCS6D01G097000 chr2D 93.416 243 16 0 413 655 5312331 5312089 1.070000e-95 361.0
19 TraesCS6D01G097000 chr2D 93.416 243 16 0 413 655 331384316 331384558 1.070000e-95 361.0
20 TraesCS6D01G097000 chr2D 91.154 260 22 1 410 668 227026401 227026660 6.440000e-93 351.0
21 TraesCS6D01G097000 chr7D 93.802 242 15 0 414 655 430435987 430435746 8.270000e-97 364.0
22 TraesCS6D01G097000 chr7D 95.161 62 3 0 2538 2599 528026736 528026675 9.260000e-17 99.0
23 TraesCS6D01G097000 chr4D 93.416 243 16 0 413 655 259245997 259245755 1.070000e-95 361.0
24 TraesCS6D01G097000 chr4D 82.979 94 15 1 235 327 380282046 380281953 2.590000e-12 84.2
25 TraesCS6D01G097000 chr1D 90.244 82 8 0 240 321 365984658 365984739 1.540000e-19 108.0
26 TraesCS6D01G097000 chr7B 93.548 62 4 0 2538 2599 565054729 565054668 4.310000e-15 93.5
27 TraesCS6D01G097000 chr1A 84.783 92 10 4 239 328 108760344 108760255 5.570000e-14 89.8
28 TraesCS6D01G097000 chr7A 91.935 62 5 0 2538 2599 608204629 608204568 2.000000e-13 87.9
29 TraesCS6D01G097000 chr4B 84.884 86 12 1 1971 2056 377800200 377800116 7.210000e-13 86.1
30 TraesCS6D01G097000 chr4B 83.158 95 14 2 235 327 467460590 467460496 7.210000e-13 86.1
31 TraesCS6D01G097000 chr4A 84.270 89 13 1 1968 2056 176539244 176539331 7.210000e-13 86.1
32 TraesCS6D01G097000 chr2B 85.542 83 10 2 240 321 97435718 97435637 7.210000e-13 86.1


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 TraesCS6D01G097000 chr6D 60545366 60549412 4046 True 7474.000000 7474 100.000000 1 4047 1 chr6D.!!$R1 4046
1 TraesCS6D01G097000 chr6A 77535987 77539729 3742 True 1761.333333 4625 94.521667 1 4045 3 chr6A.!!$R1 4044
2 TraesCS6D01G097000 chr6B 134823714 134827925 4211 True 1077.200000 4196 90.732600 239 4033 5 chr6B.!!$R1 3794
3 TraesCS6D01G097000 chr3D 135040702 135041562 860 False 1168.000000 1168 91.254000 1481 2339 1 chr3D.!!$F2 858
4 TraesCS6D01G097000 chr3D 135018480 135019421 941 False 362.000000 579 83.163500 247 1449 2 chr3D.!!$F3 1202
5 TraesCS6D01G097000 chr3A 149982968 149983713 745 False 968.000000 968 90.132000 1588 2339 1 chr3A.!!$F2 751
6 TraesCS6D01G097000 chr3A 149962019 149962783 764 False 702.000000 702 83.681000 846 1591 1 chr3A.!!$F1 745


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
549 1267 0.252197 ATACCCGCACTCCTTTCCAC 59.748 55.0 0.0 0.0 0.00 4.02 F
1329 2070 0.537828 TGCTGTTTGCTGCTGATCCA 60.538 50.0 0.0 0.0 43.37 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2724 1.001641 CCTTGGGAGTTGCCTCTGG 60.002 63.158 0.0 0.0 37.86 3.86 R
3272 4062 0.322816 ACAGGGAGCAATGCGACATT 60.323 50.000 0.0 0.0 0.00 2.71 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
98 99 9.124807 GTCCCAAGTGAAAATTTATAAAGTTCG 57.875 33.333 11.01 2.23 0.00 3.95
101 102 8.837059 CCAAGTGAAAATTTATAAAGTTCGACG 58.163 33.333 11.01 0.00 0.00 5.12
198 199 7.757526 TCTAACGGTATTGATTTGGAATTGTG 58.242 34.615 0.00 0.00 0.00 3.33
208 209 8.760103 TTGATTTGGAATTGTGTATGTCAATG 57.240 30.769 0.00 0.00 35.95 2.82
226 227 8.073467 TGTCAATGATTTCTTTATAAACCCCC 57.927 34.615 0.00 0.00 0.00 5.40
227 228 7.898636 TGTCAATGATTTCTTTATAAACCCCCT 59.101 33.333 0.00 0.00 0.00 4.79
228 229 8.414003 GTCAATGATTTCTTTATAAACCCCCTC 58.586 37.037 0.00 0.00 0.00 4.30
229 230 8.119246 TCAATGATTTCTTTATAAACCCCCTCA 58.881 33.333 0.00 0.00 0.00 3.86
230 231 8.757877 CAATGATTTCTTTATAAACCCCCTCAA 58.242 33.333 0.00 0.00 0.00 3.02
231 232 8.909423 ATGATTTCTTTATAAACCCCCTCAAA 57.091 30.769 0.00 0.00 0.00 2.69
232 233 8.728596 TGATTTCTTTATAAACCCCCTCAAAA 57.271 30.769 0.00 0.00 0.00 2.44
233 234 9.160412 TGATTTCTTTATAAACCCCCTCAAAAA 57.840 29.630 0.00 0.00 0.00 1.94
328 1044 3.447944 AGAAACGGAGGGAGTGTCTATTC 59.552 47.826 0.00 0.00 34.62 1.75
374 1092 8.791327 ATTTCATGGTTTGTGAAAAGAAGTTT 57.209 26.923 5.52 0.00 45.50 2.66
375 1093 8.614469 TTTCATGGTTTGTGAAAAGAAGTTTT 57.386 26.923 0.00 0.00 41.23 2.43
408 1126 4.550831 CGTAGCAATCATAGGAAGCAAACG 60.551 45.833 13.91 13.91 35.60 3.60
414 1132 6.369005 CAATCATAGGAAGCAAACGATCATC 58.631 40.000 0.00 0.00 0.00 2.92
415 1133 5.282055 TCATAGGAAGCAAACGATCATCT 57.718 39.130 0.00 0.00 0.00 2.90
416 1134 5.292765 TCATAGGAAGCAAACGATCATCTC 58.707 41.667 0.00 0.00 0.00 2.75
417 1135 3.902881 AGGAAGCAAACGATCATCTCT 57.097 42.857 0.00 0.00 0.00 3.10
418 1136 6.265422 TCATAGGAAGCAAACGATCATCTCTA 59.735 38.462 0.00 0.00 0.00 2.43
419 1137 4.688021 AGGAAGCAAACGATCATCTCTAC 58.312 43.478 0.00 0.00 0.00 2.59
420 1138 4.404073 AGGAAGCAAACGATCATCTCTACT 59.596 41.667 0.00 0.00 0.00 2.57
421 1139 4.742659 GGAAGCAAACGATCATCTCTACTC 59.257 45.833 0.00 0.00 0.00 2.59
422 1140 5.451242 GGAAGCAAACGATCATCTCTACTCT 60.451 44.000 0.00 0.00 0.00 3.24
423 1141 5.590530 AGCAAACGATCATCTCTACTCTT 57.409 39.130 0.00 0.00 0.00 2.85
424 1142 6.701145 AGCAAACGATCATCTCTACTCTTA 57.299 37.500 0.00 0.00 0.00 2.10
425 1143 7.283625 AGCAAACGATCATCTCTACTCTTAT 57.716 36.000 0.00 0.00 0.00 1.73
426 1144 8.397575 AGCAAACGATCATCTCTACTCTTATA 57.602 34.615 0.00 0.00 0.00 0.98
427 1145 8.851145 AGCAAACGATCATCTCTACTCTTATAA 58.149 33.333 0.00 0.00 0.00 0.98
428 1146 9.464714 GCAAACGATCATCTCTACTCTTATAAA 57.535 33.333 0.00 0.00 0.00 1.40
449 1167 5.410355 AAAAATGGAGTTGGTGATGATGG 57.590 39.130 0.00 0.00 0.00 3.51
450 1168 3.744940 AATGGAGTTGGTGATGATGGT 57.255 42.857 0.00 0.00 0.00 3.55
451 1169 2.495155 TGGAGTTGGTGATGATGGTG 57.505 50.000 0.00 0.00 0.00 4.17
452 1170 1.704628 TGGAGTTGGTGATGATGGTGT 59.295 47.619 0.00 0.00 0.00 4.16
453 1171 2.086869 GGAGTTGGTGATGATGGTGTG 58.913 52.381 0.00 0.00 0.00 3.82
454 1172 1.470098 GAGTTGGTGATGATGGTGTGC 59.530 52.381 0.00 0.00 0.00 4.57
455 1173 0.527565 GTTGGTGATGATGGTGTGCC 59.472 55.000 0.00 0.00 0.00 5.01
456 1174 0.405198 TTGGTGATGATGGTGTGCCT 59.595 50.000 0.00 0.00 35.27 4.75
457 1175 0.322726 TGGTGATGATGGTGTGCCTG 60.323 55.000 0.00 0.00 35.27 4.85
458 1176 1.660560 GGTGATGATGGTGTGCCTGC 61.661 60.000 0.00 0.00 35.27 4.85
459 1177 1.378911 TGATGATGGTGTGCCTGCC 60.379 57.895 0.00 0.00 35.27 4.85
460 1178 1.378911 GATGATGGTGTGCCTGCCA 60.379 57.895 0.00 0.00 39.33 4.92
463 1181 2.043652 ATGGTGTGCCTGCCATCC 60.044 61.111 0.00 0.00 41.24 3.51
464 1182 3.667217 ATGGTGTGCCTGCCATCCC 62.667 63.158 0.00 0.00 41.24 3.85
471 1189 2.440796 CCTGCCATCCCGCAACAT 60.441 61.111 0.00 0.00 38.56 2.71
472 1190 1.152984 CCTGCCATCCCGCAACATA 60.153 57.895 0.00 0.00 38.56 2.29
473 1191 1.168407 CCTGCCATCCCGCAACATAG 61.168 60.000 0.00 0.00 38.56 2.23
474 1192 1.152984 TGCCATCCCGCAACATAGG 60.153 57.895 0.00 0.00 35.32 2.57
475 1193 2.555547 GCCATCCCGCAACATAGGC 61.556 63.158 0.00 0.00 0.00 3.93
476 1194 1.898574 CCATCCCGCAACATAGGCC 60.899 63.158 0.00 0.00 0.00 5.19
477 1195 2.111043 ATCCCGCAACATAGGCCG 59.889 61.111 0.00 0.00 0.00 6.13
478 1196 2.742116 ATCCCGCAACATAGGCCGT 61.742 57.895 0.00 0.00 0.00 5.68
479 1197 2.660258 ATCCCGCAACATAGGCCGTC 62.660 60.000 0.00 0.00 0.00 4.79
480 1198 2.895372 CCGCAACATAGGCCGTCC 60.895 66.667 0.00 0.00 0.00 4.79
481 1199 3.261951 CGCAACATAGGCCGTCCG 61.262 66.667 0.00 0.00 37.47 4.79
482 1200 2.185867 GCAACATAGGCCGTCCGA 59.814 61.111 0.00 0.00 37.47 4.55
483 1201 1.227556 GCAACATAGGCCGTCCGAT 60.228 57.895 0.00 0.00 37.47 4.18
484 1202 1.222115 GCAACATAGGCCGTCCGATC 61.222 60.000 0.00 0.00 37.47 3.69
485 1203 0.389391 CAACATAGGCCGTCCGATCT 59.611 55.000 0.00 0.00 37.47 2.75
486 1204 1.611977 CAACATAGGCCGTCCGATCTA 59.388 52.381 0.00 0.00 37.47 1.98
487 1205 2.217510 ACATAGGCCGTCCGATCTAT 57.782 50.000 0.00 0.00 37.47 1.98
488 1206 3.361281 ACATAGGCCGTCCGATCTATA 57.639 47.619 0.00 0.00 37.47 1.31
489 1207 3.899726 ACATAGGCCGTCCGATCTATAT 58.100 45.455 0.00 0.00 37.47 0.86
490 1208 3.884091 ACATAGGCCGTCCGATCTATATC 59.116 47.826 0.00 0.00 37.47 1.63
491 1209 2.810870 AGGCCGTCCGATCTATATCT 57.189 50.000 0.00 0.00 37.47 1.98
492 1210 2.370349 AGGCCGTCCGATCTATATCTG 58.630 52.381 0.00 0.00 37.47 2.90
493 1211 2.026169 AGGCCGTCCGATCTATATCTGA 60.026 50.000 0.00 0.00 37.47 3.27
494 1212 2.952978 GGCCGTCCGATCTATATCTGAT 59.047 50.000 0.00 0.00 29.47 2.90
495 1213 3.243234 GGCCGTCCGATCTATATCTGATG 60.243 52.174 0.00 0.00 34.08 3.07
496 1214 4.560136 CCGTCCGATCTATATCTGATGG 57.440 50.000 0.00 6.44 42.54 3.51
500 1218 7.127917 CGTCCGATCTATATCTGATGGATAG 57.872 44.000 0.00 1.10 39.89 2.08
501 1219 6.148645 CGTCCGATCTATATCTGATGGATAGG 59.851 46.154 15.64 15.64 39.89 2.57
502 1220 7.227873 GTCCGATCTATATCTGATGGATAGGA 58.772 42.308 18.10 18.10 39.89 2.94
503 1221 7.721842 GTCCGATCTATATCTGATGGATAGGAA 59.278 40.741 20.88 11.19 38.93 3.36
504 1222 7.941790 TCCGATCTATATCTGATGGATAGGAAG 59.058 40.741 18.92 8.36 39.89 3.46
505 1223 7.176515 CCGATCTATATCTGATGGATAGGAAGG 59.823 44.444 16.23 9.96 39.89 3.46
506 1224 7.941790 CGATCTATATCTGATGGATAGGAAGGA 59.058 40.741 0.00 0.00 39.89 3.36
507 1225 9.653516 GATCTATATCTGATGGATAGGAAGGAA 57.346 37.037 0.00 0.00 39.89 3.36
509 1227 9.261035 TCTATATCTGATGGATAGGAAGGAAAC 57.739 37.037 0.00 0.00 39.89 2.78
510 1228 9.265862 CTATATCTGATGGATAGGAAGGAAACT 57.734 37.037 0.00 0.00 40.65 2.66
512 1230 9.796242 ATATCTGATGGATAGGAAGGAAACTAT 57.204 33.333 0.00 0.00 39.04 2.12
513 1231 7.308450 TCTGATGGATAGGAAGGAAACTATG 57.692 40.000 0.00 0.00 42.68 2.23
514 1232 7.075797 TCTGATGGATAGGAAGGAAACTATGA 58.924 38.462 0.00 0.00 42.68 2.15
515 1233 7.015682 TCTGATGGATAGGAAGGAAACTATGAC 59.984 40.741 0.00 0.00 42.68 3.06
516 1234 6.615316 TGATGGATAGGAAGGAAACTATGACA 59.385 38.462 0.00 0.00 42.68 3.58
517 1235 6.884472 TGGATAGGAAGGAAACTATGACAA 57.116 37.500 0.00 0.00 42.68 3.18
518 1236 7.451731 TGGATAGGAAGGAAACTATGACAAT 57.548 36.000 0.00 0.00 42.68 2.71
519 1237 7.872138 TGGATAGGAAGGAAACTATGACAATT 58.128 34.615 0.00 0.00 42.68 2.32
520 1238 8.336235 TGGATAGGAAGGAAACTATGACAATTT 58.664 33.333 0.00 0.00 42.68 1.82
521 1239 9.190317 GGATAGGAAGGAAACTATGACAATTTT 57.810 33.333 0.00 0.00 42.68 1.82
523 1241 6.691508 AGGAAGGAAACTATGACAATTTTGC 58.308 36.000 0.00 0.00 42.68 3.68
524 1242 6.267471 AGGAAGGAAACTATGACAATTTTGCA 59.733 34.615 0.00 0.00 42.68 4.08
525 1243 6.928492 GGAAGGAAACTATGACAATTTTGCAA 59.072 34.615 0.00 0.00 42.68 4.08
526 1244 7.440856 GGAAGGAAACTATGACAATTTTGCAAA 59.559 33.333 8.05 8.05 42.68 3.68
527 1245 8.729805 AAGGAAACTATGACAATTTTGCAAAA 57.270 26.923 25.76 25.76 42.68 2.44
528 1246 8.729805 AGGAAACTATGACAATTTTGCAAAAA 57.270 26.923 27.10 11.87 40.61 1.94
529 1247 8.829612 AGGAAACTATGACAATTTTGCAAAAAG 58.170 29.630 27.10 22.99 40.61 2.27
530 1248 8.825745 GGAAACTATGACAATTTTGCAAAAAGA 58.174 29.630 27.10 6.60 0.00 2.52
534 1252 9.423061 ACTATGACAATTTTGCAAAAAGATACC 57.577 29.630 27.10 14.67 0.00 2.73
535 1253 7.671495 ATGACAATTTTGCAAAAAGATACCC 57.329 32.000 27.10 13.32 0.00 3.69
536 1254 5.694006 TGACAATTTTGCAAAAAGATACCCG 59.306 36.000 27.10 12.09 0.00 5.28
537 1255 4.450757 ACAATTTTGCAAAAAGATACCCGC 59.549 37.500 27.10 0.00 0.00 6.13
538 1256 3.735237 TTTTGCAAAAAGATACCCGCA 57.265 38.095 21.94 0.00 0.00 5.69
539 1257 2.715737 TTGCAAAAAGATACCCGCAC 57.284 45.000 0.00 0.00 0.00 5.34
540 1258 1.904287 TGCAAAAAGATACCCGCACT 58.096 45.000 0.00 0.00 0.00 4.40
541 1259 1.810151 TGCAAAAAGATACCCGCACTC 59.190 47.619 0.00 0.00 0.00 3.51
542 1260 1.132453 GCAAAAAGATACCCGCACTCC 59.868 52.381 0.00 0.00 0.00 3.85
543 1261 2.711542 CAAAAAGATACCCGCACTCCT 58.288 47.619 0.00 0.00 0.00 3.69
544 1262 3.081804 CAAAAAGATACCCGCACTCCTT 58.918 45.455 0.00 0.00 0.00 3.36
545 1263 3.434940 AAAAGATACCCGCACTCCTTT 57.565 42.857 0.00 0.00 0.00 3.11
546 1264 2.693267 AAGATACCCGCACTCCTTTC 57.307 50.000 0.00 0.00 0.00 2.62
547 1265 0.831307 AGATACCCGCACTCCTTTCC 59.169 55.000 0.00 0.00 0.00 3.13
548 1266 0.539986 GATACCCGCACTCCTTTCCA 59.460 55.000 0.00 0.00 0.00 3.53
549 1267 0.252197 ATACCCGCACTCCTTTCCAC 59.748 55.000 0.00 0.00 0.00 4.02
550 1268 1.122632 TACCCGCACTCCTTTCCACA 61.123 55.000 0.00 0.00 0.00 4.17
551 1269 1.002134 CCCGCACTCCTTTCCACAT 60.002 57.895 0.00 0.00 0.00 3.21
552 1270 0.609131 CCCGCACTCCTTTCCACATT 60.609 55.000 0.00 0.00 0.00 2.71
553 1271 1.247567 CCGCACTCCTTTCCACATTT 58.752 50.000 0.00 0.00 0.00 2.32
554 1272 1.068333 CCGCACTCCTTTCCACATTTG 60.068 52.381 0.00 0.00 0.00 2.32
555 1273 1.666888 CGCACTCCTTTCCACATTTGC 60.667 52.381 0.00 0.00 0.00 3.68
556 1274 1.340889 GCACTCCTTTCCACATTTGCA 59.659 47.619 0.00 0.00 0.00 4.08
557 1275 2.608752 GCACTCCTTTCCACATTTGCAG 60.609 50.000 0.00 0.00 0.00 4.41
558 1276 2.886523 CACTCCTTTCCACATTTGCAGA 59.113 45.455 0.00 0.00 0.00 4.26
559 1277 3.508793 CACTCCTTTCCACATTTGCAGAT 59.491 43.478 0.00 0.00 0.00 2.90
560 1278 4.701651 CACTCCTTTCCACATTTGCAGATA 59.298 41.667 0.00 0.00 0.00 1.98
561 1279 5.183713 CACTCCTTTCCACATTTGCAGATAA 59.816 40.000 0.00 0.00 0.00 1.75
562 1280 5.416952 ACTCCTTTCCACATTTGCAGATAAG 59.583 40.000 0.00 0.00 0.00 1.73
563 1281 4.706476 TCCTTTCCACATTTGCAGATAAGG 59.294 41.667 8.70 8.70 0.00 2.69
564 1282 4.427312 CTTTCCACATTTGCAGATAAGGC 58.573 43.478 0.00 0.00 0.00 4.35
565 1283 2.378038 TCCACATTTGCAGATAAGGCC 58.622 47.619 0.00 0.00 0.00 5.19
566 1284 2.025037 TCCACATTTGCAGATAAGGCCT 60.025 45.455 0.00 0.00 0.00 5.19
567 1285 2.762327 CCACATTTGCAGATAAGGCCTT 59.238 45.455 24.18 24.18 0.00 4.35
568 1286 3.181483 CCACATTTGCAGATAAGGCCTTC 60.181 47.826 24.49 9.18 0.00 3.46
569 1287 3.026694 ACATTTGCAGATAAGGCCTTCC 58.973 45.455 24.49 15.44 0.00 3.46
570 1288 2.143876 TTTGCAGATAAGGCCTTCCC 57.856 50.000 24.49 15.04 0.00 3.97
579 1297 3.987594 AGGCCTTCCCTTGTTCATC 57.012 52.632 0.00 0.00 43.06 2.92
580 1298 1.376649 AGGCCTTCCCTTGTTCATCT 58.623 50.000 0.00 0.00 43.06 2.90
581 1299 1.713078 AGGCCTTCCCTTGTTCATCTT 59.287 47.619 0.00 0.00 43.06 2.40
582 1300 2.110721 AGGCCTTCCCTTGTTCATCTTT 59.889 45.455 0.00 0.00 43.06 2.52
583 1301 3.333680 AGGCCTTCCCTTGTTCATCTTTA 59.666 43.478 0.00 0.00 43.06 1.85
584 1302 4.017130 AGGCCTTCCCTTGTTCATCTTTAT 60.017 41.667 0.00 0.00 43.06 1.40
585 1303 4.339530 GGCCTTCCCTTGTTCATCTTTATC 59.660 45.833 0.00 0.00 0.00 1.75
586 1304 5.196695 GCCTTCCCTTGTTCATCTTTATCT 58.803 41.667 0.00 0.00 0.00 1.98
587 1305 5.298026 GCCTTCCCTTGTTCATCTTTATCTC 59.702 44.000 0.00 0.00 0.00 2.75
588 1306 5.825151 CCTTCCCTTGTTCATCTTTATCTCC 59.175 44.000 0.00 0.00 0.00 3.71
589 1307 5.373812 TCCCTTGTTCATCTTTATCTCCC 57.626 43.478 0.00 0.00 0.00 4.30
590 1308 4.788075 TCCCTTGTTCATCTTTATCTCCCA 59.212 41.667 0.00 0.00 0.00 4.37
591 1309 5.252863 TCCCTTGTTCATCTTTATCTCCCAA 59.747 40.000 0.00 0.00 0.00 4.12
592 1310 5.951747 CCCTTGTTCATCTTTATCTCCCAAA 59.048 40.000 0.00 0.00 0.00 3.28
593 1311 6.437162 CCCTTGTTCATCTTTATCTCCCAAAA 59.563 38.462 0.00 0.00 0.00 2.44
594 1312 7.363268 CCCTTGTTCATCTTTATCTCCCAAAAG 60.363 40.741 0.00 0.00 34.65 2.27
595 1313 7.394359 CCTTGTTCATCTTTATCTCCCAAAAGA 59.606 37.037 0.46 0.46 43.72 2.52
597 1315 9.973661 TTGTTCATCTTTATCTCCCAAAAGATA 57.026 29.630 9.32 0.00 45.92 1.98
598 1316 9.973661 TGTTCATCTTTATCTCCCAAAAGATAA 57.026 29.630 9.32 2.94 45.92 1.75
628 1346 8.790718 ACTCATATAAATGCATCTTGATGTTCC 58.209 33.333 0.00 0.00 32.76 3.62
629 1347 7.809665 TCATATAAATGCATCTTGATGTTCCG 58.190 34.615 0.00 0.00 32.76 4.30
630 1348 7.445096 TCATATAAATGCATCTTGATGTTCCGT 59.555 33.333 0.00 0.00 32.76 4.69
631 1349 3.770263 AATGCATCTTGATGTTCCGTG 57.230 42.857 0.00 0.00 0.00 4.94
632 1350 0.804364 TGCATCTTGATGTTCCGTGC 59.196 50.000 11.61 0.00 0.00 5.34
633 1351 0.804364 GCATCTTGATGTTCCGTGCA 59.196 50.000 11.61 0.00 0.00 4.57
634 1352 1.199789 GCATCTTGATGTTCCGTGCAA 59.800 47.619 11.61 0.00 0.00 4.08
635 1353 2.159338 GCATCTTGATGTTCCGTGCAAT 60.159 45.455 11.61 0.00 0.00 3.56
636 1354 3.431856 CATCTTGATGTTCCGTGCAATG 58.568 45.455 0.00 0.00 0.00 2.82
637 1355 1.199789 TCTTGATGTTCCGTGCAATGC 59.800 47.619 0.00 0.00 0.00 3.56
638 1356 0.957362 TTGATGTTCCGTGCAATGCA 59.043 45.000 2.72 2.72 35.60 3.96
653 1371 3.414272 GCACGGGCATCTTGCTAG 58.586 61.111 3.77 0.00 44.28 3.42
654 1372 1.450312 GCACGGGCATCTTGCTAGT 60.450 57.895 3.77 0.00 44.28 2.57
679 1397 6.107901 ACCTCTGAAATATGAGTGGCTATC 57.892 41.667 0.00 0.00 0.00 2.08
773 1491 7.986704 AGGTCAATCTGGATCATTCTATTGAT 58.013 34.615 0.00 0.00 39.04 2.57
848 1569 4.223032 TCCACTGGACAAGATTAGACTTCC 59.777 45.833 0.00 0.00 0.00 3.46
852 1573 3.190874 GGACAAGATTAGACTTCCTGCG 58.809 50.000 0.00 0.00 0.00 5.18
908 1630 6.403866 TTGAAATACATTGTTTGACAGGCT 57.596 33.333 0.00 0.00 0.00 4.58
1329 2070 0.537828 TGCTGTTTGCTGCTGATCCA 60.538 50.000 0.00 0.00 43.37 3.41
1539 2280 5.359009 TCGGTTAGATGTGAGTACCTTTAGG 59.641 44.000 0.00 0.00 42.17 2.69
1761 2505 2.033602 GTGGGGGTTCTCCGGTTG 59.966 66.667 0.00 0.00 36.01 3.77
1765 2509 1.674651 GGGGTTCTCCGGTTGAAGC 60.675 63.158 23.55 23.55 40.10 3.86
1775 2519 1.841663 CGGTTGAAGCCCAGTTGACG 61.842 60.000 0.00 0.00 0.00 4.35
1783 2527 0.602638 GCCCAGTTGACGTCATCACA 60.603 55.000 24.47 6.48 36.92 3.58
1896 2645 1.138464 GACCGGAAAGTAGGGTGATCC 59.862 57.143 9.46 0.00 33.28 3.36
1942 2693 8.812147 AATTTTTCTTGAAAATAGAACCGTCC 57.188 30.769 9.02 0.00 44.98 4.79
1943 2694 5.952526 TTTCTTGAAAATAGAACCGTCCC 57.047 39.130 0.00 0.00 31.68 4.46
1973 2724 9.722056 GATGTTTTGTTCCATGTACATATCTTC 57.278 33.333 8.32 0.00 0.00 2.87
2120 2871 8.934507 TCATCACATTACGATGTTTATACACA 57.065 30.769 0.00 0.00 43.92 3.72
2210 2962 5.701224 ACAACTAAGGTGAAGGGAAAATCA 58.299 37.500 0.00 0.00 0.00 2.57
2291 3043 9.841295 TCATTCATAATCTTGTCATTCTCATGA 57.159 29.630 0.00 0.00 37.05 3.07
2389 3141 6.876257 AGAGACCATGTTCAGAAGATAACAAC 59.124 38.462 0.00 0.00 38.95 3.32
2422 3174 4.679662 CATCTGGAATTGATTCTGGCAAC 58.320 43.478 3.94 0.00 37.00 4.17
2489 3241 1.648116 ATGAGGGGCATGCAAAAACT 58.352 45.000 21.36 9.21 35.42 2.66
2501 3253 5.557514 GCATGCAAAAACTGTGTCATCAAAG 60.558 40.000 14.21 0.00 35.19 2.77
2545 3297 2.962421 AGGAGTTTTCAAATGGCGGAAA 59.038 40.909 0.00 0.00 0.00 3.13
2618 3373 7.179338 AGAGGTAACAGTGTGATAAGAAGATGT 59.821 37.037 0.00 0.00 41.41 3.06
2823 3587 2.353610 GGCCATCAGGTGCAAAGGG 61.354 63.158 0.00 0.00 37.19 3.95
2898 3662 4.985538 ACAACAGAAGGCCAGAAAATCTA 58.014 39.130 5.01 0.00 0.00 1.98
2903 3667 2.403252 AGGCCAGAAAATCTACGGTG 57.597 50.000 5.01 0.00 0.00 4.94
2949 3713 1.598130 AACACCACTTCAGCTCCGC 60.598 57.895 0.00 0.00 0.00 5.54
3055 3821 6.169800 TGAAAGTGAACCATGATGAACGATA 58.830 36.000 0.00 0.00 0.00 2.92
3154 3944 3.931907 CCTTATGACAAGGTCCATCCA 57.068 47.619 0.00 0.00 39.02 3.41
3155 3945 4.443978 CCTTATGACAAGGTCCATCCAT 57.556 45.455 0.00 0.00 39.02 3.41
3156 3946 4.796606 CCTTATGACAAGGTCCATCCATT 58.203 43.478 0.00 0.00 39.02 3.16
3157 3947 5.940617 CCTTATGACAAGGTCCATCCATTA 58.059 41.667 0.00 0.00 39.02 1.90
3158 3948 6.364701 CCTTATGACAAGGTCCATCCATTAA 58.635 40.000 0.00 0.00 39.02 1.40
3159 3949 7.006509 CCTTATGACAAGGTCCATCCATTAAT 58.993 38.462 0.00 0.00 39.02 1.40
3160 3950 7.040201 CCTTATGACAAGGTCCATCCATTAATG 60.040 40.741 8.58 8.58 39.02 1.90
3161 3951 3.953612 TGACAAGGTCCATCCATTAATGC 59.046 43.478 10.11 0.00 39.02 3.56
3162 3952 4.210331 GACAAGGTCCATCCATTAATGCT 58.790 43.478 10.11 0.00 39.02 3.79
3163 3953 3.956199 ACAAGGTCCATCCATTAATGCTG 59.044 43.478 10.11 9.17 39.02 4.41
3164 3954 4.209538 CAAGGTCCATCCATTAATGCTGA 58.790 43.478 10.11 3.51 39.02 4.26
3165 3955 4.524802 AGGTCCATCCATTAATGCTGAA 57.475 40.909 10.11 0.00 39.02 3.02
3166 3956 4.870636 AGGTCCATCCATTAATGCTGAAA 58.129 39.130 10.11 0.04 39.02 2.69
3167 3957 5.461327 AGGTCCATCCATTAATGCTGAAAT 58.539 37.500 10.11 0.00 39.02 2.17
3168 3958 6.613699 AGGTCCATCCATTAATGCTGAAATA 58.386 36.000 10.11 0.00 39.02 1.40
3169 3959 6.718454 AGGTCCATCCATTAATGCTGAAATAG 59.282 38.462 10.11 0.00 39.02 1.73
3170 3960 6.071728 GGTCCATCCATTAATGCTGAAATAGG 60.072 42.308 10.11 5.18 35.97 2.57
3171 3961 6.491403 GTCCATCCATTAATGCTGAAATAGGT 59.509 38.462 10.11 0.00 0.00 3.08
3420 4210 1.663739 GCACTGGACACTACGGACA 59.336 57.895 0.00 0.00 0.00 4.02
3446 4236 1.376683 GGCATGCCTGGACGTTACA 60.377 57.895 29.98 0.00 0.00 2.41
3468 4258 0.736325 CGTCCTGAGCACCCTAAACG 60.736 60.000 0.00 0.00 0.00 3.60
3472 4262 0.321653 CTGAGCACCCTAAACGCCTT 60.322 55.000 0.00 0.00 0.00 4.35
3473 4263 0.321298 TGAGCACCCTAAACGCCTTC 60.321 55.000 0.00 0.00 0.00 3.46
3474 4264 1.359459 GAGCACCCTAAACGCCTTCG 61.359 60.000 0.00 0.00 42.43 3.79
3519 4309 0.543749 CAAAGGTAGCCAGGAGGGAG 59.456 60.000 0.00 0.00 40.01 4.30
3521 4311 0.417841 AAGGTAGCCAGGAGGGAGAA 59.582 55.000 0.00 0.00 40.01 2.87
3522 4312 0.417841 AGGTAGCCAGGAGGGAGAAA 59.582 55.000 0.00 0.00 40.01 2.52
3541 4331 5.094387 AGAAAAGGAATCAGGTGGTCTCTA 58.906 41.667 0.00 0.00 0.00 2.43
3575 4367 5.452636 CCATCTAAGCCTCTAAGGAGTTGAC 60.453 48.000 0.00 0.00 37.67 3.18
3619 4412 9.874205 GAATTTGATGGAATGGAATAAGTTGAA 57.126 29.630 0.00 0.00 0.00 2.69
3620 4413 9.657419 AATTTGATGGAATGGAATAAGTTGAAC 57.343 29.630 0.00 0.00 0.00 3.18
3621 4414 6.773976 TGATGGAATGGAATAAGTTGAACC 57.226 37.500 0.00 0.00 0.00 3.62
3672 4467 3.708403 AATGATGAGACCTGCACTTGA 57.292 42.857 0.00 0.00 0.00 3.02
3801 4609 9.742144 TTTACCTGTATTGCCTATCTACAAAAA 57.258 29.630 0.00 0.00 0.00 1.94
3826 4634 1.333619 TGTGCGGCTTTCTGAAAAGAC 59.666 47.619 4.18 0.00 45.59 3.01
3843 4651 4.691860 AAGACTTTCAAGAATGGATGCG 57.308 40.909 0.00 0.00 0.00 4.73
3933 4748 4.624024 CCTGATTGCAAATGTTGTCACATC 59.376 41.667 1.71 0.00 43.34 3.06
3939 4754 4.084066 TGCAAATGTTGTCACATCGTAGAC 60.084 41.667 0.00 0.00 43.34 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.493022 ACCCAGTGCCAAACTTGACTA 59.507 47.619 0.00 0.00 36.83 2.59
161 162 6.097696 TCAATACCGTTAGATTCATCACTGGA 59.902 38.462 0.00 0.00 0.00 3.86
307 1023 3.447944 AGAATAGACACTCCCTCCGTTTC 59.552 47.826 0.00 0.00 0.00 2.78
374 1092 4.729227 TGATTGCTACGGTCATGTCTAA 57.271 40.909 0.00 0.00 0.00 2.10
375 1093 4.937201 ATGATTGCTACGGTCATGTCTA 57.063 40.909 0.00 0.00 31.75 2.59
427 1145 4.840115 ACCATCATCACCAACTCCATTTTT 59.160 37.500 0.00 0.00 0.00 1.94
428 1146 4.221262 CACCATCATCACCAACTCCATTTT 59.779 41.667 0.00 0.00 0.00 1.82
429 1147 3.765511 CACCATCATCACCAACTCCATTT 59.234 43.478 0.00 0.00 0.00 2.32
430 1148 3.245371 ACACCATCATCACCAACTCCATT 60.245 43.478 0.00 0.00 0.00 3.16
431 1149 2.309755 ACACCATCATCACCAACTCCAT 59.690 45.455 0.00 0.00 0.00 3.41
432 1150 1.704628 ACACCATCATCACCAACTCCA 59.295 47.619 0.00 0.00 0.00 3.86
433 1151 2.086869 CACACCATCATCACCAACTCC 58.913 52.381 0.00 0.00 0.00 3.85
434 1152 1.470098 GCACACCATCATCACCAACTC 59.530 52.381 0.00 0.00 0.00 3.01
435 1153 1.538047 GCACACCATCATCACCAACT 58.462 50.000 0.00 0.00 0.00 3.16
436 1154 0.527565 GGCACACCATCATCACCAAC 59.472 55.000 0.00 0.00 35.26 3.77
437 1155 0.405198 AGGCACACCATCATCACCAA 59.595 50.000 0.00 0.00 39.06 3.67
438 1156 0.322726 CAGGCACACCATCATCACCA 60.323 55.000 0.00 0.00 39.06 4.17
439 1157 1.660560 GCAGGCACACCATCATCACC 61.661 60.000 0.00 0.00 39.06 4.02
440 1158 1.660560 GGCAGGCACACCATCATCAC 61.661 60.000 0.00 0.00 39.06 3.06
441 1159 1.378911 GGCAGGCACACCATCATCA 60.379 57.895 0.00 0.00 39.06 3.07
442 1160 0.754217 ATGGCAGGCACACCATCATC 60.754 55.000 0.00 0.00 42.69 2.92
443 1161 1.308666 ATGGCAGGCACACCATCAT 59.691 52.632 0.00 0.00 42.69 2.45
444 1162 2.765279 ATGGCAGGCACACCATCA 59.235 55.556 0.00 0.00 42.69 3.07
447 1165 4.365111 GGGATGGCAGGCACACCA 62.365 66.667 19.13 0.00 41.01 4.17
454 1172 1.152984 TATGTTGCGGGATGGCAGG 60.153 57.895 0.00 0.00 44.94 4.85
455 1173 1.168407 CCTATGTTGCGGGATGGCAG 61.168 60.000 0.00 0.00 44.94 4.85
456 1174 1.152984 CCTATGTTGCGGGATGGCA 60.153 57.895 0.00 0.00 42.12 4.92
457 1175 2.555547 GCCTATGTTGCGGGATGGC 61.556 63.158 0.00 0.00 0.00 4.40
458 1176 1.898574 GGCCTATGTTGCGGGATGG 60.899 63.158 0.00 0.00 0.00 3.51
459 1177 2.253758 CGGCCTATGTTGCGGGATG 61.254 63.158 0.00 0.00 0.00 3.51
460 1178 2.111043 CGGCCTATGTTGCGGGAT 59.889 61.111 0.00 0.00 0.00 3.85
461 1179 3.379865 GACGGCCTATGTTGCGGGA 62.380 63.158 0.00 0.00 33.78 5.14
462 1180 2.895372 GACGGCCTATGTTGCGGG 60.895 66.667 0.00 0.00 33.78 6.13
463 1181 2.895372 GGACGGCCTATGTTGCGG 60.895 66.667 0.00 0.00 35.42 5.69
464 1182 2.971428 ATCGGACGGCCTATGTTGCG 62.971 60.000 5.33 0.00 0.00 4.85
465 1183 1.222115 GATCGGACGGCCTATGTTGC 61.222 60.000 5.33 0.00 0.00 4.17
466 1184 0.389391 AGATCGGACGGCCTATGTTG 59.611 55.000 5.33 0.00 0.00 3.33
467 1185 1.991121 TAGATCGGACGGCCTATGTT 58.009 50.000 5.33 0.00 0.00 2.71
468 1186 2.217510 ATAGATCGGACGGCCTATGT 57.782 50.000 5.33 0.00 0.00 2.29
469 1187 4.023622 CAGATATAGATCGGACGGCCTATG 60.024 50.000 5.33 0.00 37.15 2.23
470 1188 4.138290 CAGATATAGATCGGACGGCCTAT 58.862 47.826 5.33 0.00 37.15 2.57
471 1189 3.199289 TCAGATATAGATCGGACGGCCTA 59.801 47.826 5.33 0.00 37.15 3.93
472 1190 2.026169 TCAGATATAGATCGGACGGCCT 60.026 50.000 5.33 0.00 37.15 5.19
473 1191 2.366533 TCAGATATAGATCGGACGGCC 58.633 52.381 0.00 0.00 37.15 6.13
474 1192 3.243234 CCATCAGATATAGATCGGACGGC 60.243 52.174 2.19 0.00 38.82 5.68
475 1193 4.200092 TCCATCAGATATAGATCGGACGG 58.800 47.826 6.30 6.30 39.94 4.79
476 1194 6.148645 CCTATCCATCAGATATAGATCGGACG 59.851 46.154 2.19 0.00 38.82 4.79
477 1195 7.227873 TCCTATCCATCAGATATAGATCGGAC 58.772 42.308 2.19 0.00 38.82 4.79
478 1196 7.394144 TCCTATCCATCAGATATAGATCGGA 57.606 40.000 2.64 2.64 40.05 4.55
479 1197 7.176515 CCTTCCTATCCATCAGATATAGATCGG 59.823 44.444 2.72 0.00 36.84 4.18
480 1198 7.941790 TCCTTCCTATCCATCAGATATAGATCG 59.058 40.741 2.72 0.00 36.84 3.69
481 1199 9.653516 TTCCTTCCTATCCATCAGATATAGATC 57.346 37.037 2.72 0.00 36.84 2.75
483 1201 9.261035 GTTTCCTTCCTATCCATCAGATATAGA 57.739 37.037 2.72 0.00 36.84 1.98
484 1202 9.265862 AGTTTCCTTCCTATCCATCAGATATAG 57.734 37.037 0.00 0.00 36.84 1.31
486 1204 9.796242 ATAGTTTCCTTCCTATCCATCAGATAT 57.204 33.333 0.00 0.00 36.84 1.63
487 1205 9.040259 CATAGTTTCCTTCCTATCCATCAGATA 57.960 37.037 0.00 0.00 36.33 1.98
488 1206 7.736691 TCATAGTTTCCTTCCTATCCATCAGAT 59.263 37.037 0.00 0.00 39.15 2.90
489 1207 7.015682 GTCATAGTTTCCTTCCTATCCATCAGA 59.984 40.741 0.00 0.00 0.00 3.27
490 1208 7.158021 GTCATAGTTTCCTTCCTATCCATCAG 58.842 42.308 0.00 0.00 0.00 2.90
491 1209 6.615316 TGTCATAGTTTCCTTCCTATCCATCA 59.385 38.462 0.00 0.00 0.00 3.07
492 1210 7.067496 TGTCATAGTTTCCTTCCTATCCATC 57.933 40.000 0.00 0.00 0.00 3.51
493 1211 7.451731 TTGTCATAGTTTCCTTCCTATCCAT 57.548 36.000 0.00 0.00 0.00 3.41
494 1212 6.884472 TTGTCATAGTTTCCTTCCTATCCA 57.116 37.500 0.00 0.00 0.00 3.41
495 1213 8.753497 AAATTGTCATAGTTTCCTTCCTATCC 57.247 34.615 0.00 0.00 0.00 2.59
497 1215 8.470002 GCAAAATTGTCATAGTTTCCTTCCTAT 58.530 33.333 0.00 0.00 0.00 2.57
498 1216 7.450014 TGCAAAATTGTCATAGTTTCCTTCCTA 59.550 33.333 0.00 0.00 0.00 2.94
499 1217 6.267471 TGCAAAATTGTCATAGTTTCCTTCCT 59.733 34.615 0.00 0.00 0.00 3.36
500 1218 6.454795 TGCAAAATTGTCATAGTTTCCTTCC 58.545 36.000 0.00 0.00 0.00 3.46
501 1219 7.945033 TTGCAAAATTGTCATAGTTTCCTTC 57.055 32.000 0.00 0.00 0.00 3.46
502 1220 8.729805 TTTTGCAAAATTGTCATAGTTTCCTT 57.270 26.923 20.46 0.00 0.00 3.36
503 1221 8.729805 TTTTTGCAAAATTGTCATAGTTTCCT 57.270 26.923 24.39 0.00 0.00 3.36
504 1222 8.825745 TCTTTTTGCAAAATTGTCATAGTTTCC 58.174 29.630 24.39 0.00 0.00 3.13
508 1226 9.423061 GGTATCTTTTTGCAAAATTGTCATAGT 57.577 29.630 24.39 10.32 0.00 2.12
509 1227 8.872845 GGGTATCTTTTTGCAAAATTGTCATAG 58.127 33.333 24.39 16.41 0.00 2.23
510 1228 7.543868 CGGGTATCTTTTTGCAAAATTGTCATA 59.456 33.333 24.39 12.99 0.00 2.15
511 1229 6.368516 CGGGTATCTTTTTGCAAAATTGTCAT 59.631 34.615 24.39 13.84 0.00 3.06
512 1230 5.694006 CGGGTATCTTTTTGCAAAATTGTCA 59.306 36.000 24.39 9.07 0.00 3.58
513 1231 5.389411 GCGGGTATCTTTTTGCAAAATTGTC 60.389 40.000 24.39 13.66 0.00 3.18
514 1232 4.450757 GCGGGTATCTTTTTGCAAAATTGT 59.549 37.500 24.39 14.99 0.00 2.71
515 1233 4.450419 TGCGGGTATCTTTTTGCAAAATTG 59.550 37.500 24.39 19.07 0.00 2.32
516 1234 4.450757 GTGCGGGTATCTTTTTGCAAAATT 59.549 37.500 24.39 14.72 33.67 1.82
517 1235 3.993736 GTGCGGGTATCTTTTTGCAAAAT 59.006 39.130 24.39 12.94 33.67 1.82
518 1236 3.068873 AGTGCGGGTATCTTTTTGCAAAA 59.931 39.130 20.46 20.46 33.67 2.44
519 1237 2.625790 AGTGCGGGTATCTTTTTGCAAA 59.374 40.909 8.05 8.05 33.67 3.68
520 1238 2.227865 GAGTGCGGGTATCTTTTTGCAA 59.772 45.455 0.00 0.00 33.67 4.08
521 1239 1.810151 GAGTGCGGGTATCTTTTTGCA 59.190 47.619 0.00 0.00 0.00 4.08
522 1240 1.132453 GGAGTGCGGGTATCTTTTTGC 59.868 52.381 0.00 0.00 0.00 3.68
523 1241 2.711542 AGGAGTGCGGGTATCTTTTTG 58.288 47.619 0.00 0.00 0.00 2.44
524 1242 3.434940 AAGGAGTGCGGGTATCTTTTT 57.565 42.857 0.00 0.00 0.00 1.94
525 1243 3.344515 GAAAGGAGTGCGGGTATCTTTT 58.655 45.455 0.00 0.00 0.00 2.27
526 1244 2.355818 GGAAAGGAGTGCGGGTATCTTT 60.356 50.000 0.00 0.00 0.00 2.52
527 1245 1.209747 GGAAAGGAGTGCGGGTATCTT 59.790 52.381 0.00 0.00 0.00 2.40
528 1246 0.831307 GGAAAGGAGTGCGGGTATCT 59.169 55.000 0.00 0.00 0.00 1.98
529 1247 0.539986 TGGAAAGGAGTGCGGGTATC 59.460 55.000 0.00 0.00 0.00 2.24
530 1248 0.252197 GTGGAAAGGAGTGCGGGTAT 59.748 55.000 0.00 0.00 0.00 2.73
531 1249 1.122632 TGTGGAAAGGAGTGCGGGTA 61.123 55.000 0.00 0.00 0.00 3.69
532 1250 1.779061 ATGTGGAAAGGAGTGCGGGT 61.779 55.000 0.00 0.00 0.00 5.28
533 1251 0.609131 AATGTGGAAAGGAGTGCGGG 60.609 55.000 0.00 0.00 0.00 6.13
534 1252 1.068333 CAAATGTGGAAAGGAGTGCGG 60.068 52.381 0.00 0.00 0.00 5.69
535 1253 1.666888 GCAAATGTGGAAAGGAGTGCG 60.667 52.381 0.00 0.00 0.00 5.34
536 1254 1.340889 TGCAAATGTGGAAAGGAGTGC 59.659 47.619 0.00 0.00 0.00 4.40
537 1255 2.886523 TCTGCAAATGTGGAAAGGAGTG 59.113 45.455 0.00 0.00 0.00 3.51
538 1256 3.228188 TCTGCAAATGTGGAAAGGAGT 57.772 42.857 0.00 0.00 0.00 3.85
539 1257 5.163581 CCTTATCTGCAAATGTGGAAAGGAG 60.164 44.000 1.03 0.00 34.23 3.69
540 1258 4.706476 CCTTATCTGCAAATGTGGAAAGGA 59.294 41.667 1.03 0.00 34.23 3.36
541 1259 4.678840 GCCTTATCTGCAAATGTGGAAAGG 60.679 45.833 2.69 2.69 35.22 3.11
542 1260 4.427312 GCCTTATCTGCAAATGTGGAAAG 58.573 43.478 0.00 0.00 0.00 2.62
543 1261 3.195396 GGCCTTATCTGCAAATGTGGAAA 59.805 43.478 0.00 0.00 0.00 3.13
544 1262 2.760092 GGCCTTATCTGCAAATGTGGAA 59.240 45.455 0.00 0.00 0.00 3.53
545 1263 2.025037 AGGCCTTATCTGCAAATGTGGA 60.025 45.455 0.00 0.00 0.00 4.02
546 1264 2.381911 AGGCCTTATCTGCAAATGTGG 58.618 47.619 0.00 0.00 0.00 4.17
547 1265 3.181483 GGAAGGCCTTATCTGCAAATGTG 60.181 47.826 20.54 0.00 0.00 3.21
548 1266 3.026694 GGAAGGCCTTATCTGCAAATGT 58.973 45.455 20.54 0.00 0.00 2.71
549 1267 2.363359 GGGAAGGCCTTATCTGCAAATG 59.637 50.000 20.54 0.00 0.00 2.32
550 1268 2.245806 AGGGAAGGCCTTATCTGCAAAT 59.754 45.455 20.54 0.00 0.00 2.32
551 1269 1.640670 AGGGAAGGCCTTATCTGCAAA 59.359 47.619 20.54 0.00 0.00 3.68
552 1270 1.298953 AGGGAAGGCCTTATCTGCAA 58.701 50.000 20.54 0.00 0.00 4.08
553 1271 1.064463 CAAGGGAAGGCCTTATCTGCA 60.064 52.381 20.54 0.00 0.00 4.41
554 1272 1.064389 ACAAGGGAAGGCCTTATCTGC 60.064 52.381 20.54 5.12 0.00 4.26
555 1273 3.282885 GAACAAGGGAAGGCCTTATCTG 58.717 50.000 20.54 15.47 0.00 2.90
556 1274 2.919602 TGAACAAGGGAAGGCCTTATCT 59.080 45.455 20.54 15.86 0.00 1.98
557 1275 3.366052 TGAACAAGGGAAGGCCTTATC 57.634 47.619 20.54 13.81 0.00 1.75
558 1276 3.529319 AGATGAACAAGGGAAGGCCTTAT 59.471 43.478 20.54 4.41 0.00 1.73
559 1277 2.919602 AGATGAACAAGGGAAGGCCTTA 59.080 45.455 20.54 0.00 0.00 2.69
560 1278 1.713078 AGATGAACAAGGGAAGGCCTT 59.287 47.619 20.65 20.65 0.00 4.35
561 1279 1.376649 AGATGAACAAGGGAAGGCCT 58.623 50.000 0.00 0.00 0.00 5.19
562 1280 2.222227 AAGATGAACAAGGGAAGGCC 57.778 50.000 0.00 0.00 0.00 5.19
563 1281 5.196695 AGATAAAGATGAACAAGGGAAGGC 58.803 41.667 0.00 0.00 0.00 4.35
564 1282 5.825151 GGAGATAAAGATGAACAAGGGAAGG 59.175 44.000 0.00 0.00 0.00 3.46
565 1283 5.825151 GGGAGATAAAGATGAACAAGGGAAG 59.175 44.000 0.00 0.00 0.00 3.46
566 1284 5.252863 TGGGAGATAAAGATGAACAAGGGAA 59.747 40.000 0.00 0.00 0.00 3.97
567 1285 4.788075 TGGGAGATAAAGATGAACAAGGGA 59.212 41.667 0.00 0.00 0.00 4.20
568 1286 5.116084 TGGGAGATAAAGATGAACAAGGG 57.884 43.478 0.00 0.00 0.00 3.95
569 1287 7.394359 TCTTTTGGGAGATAAAGATGAACAAGG 59.606 37.037 0.00 0.00 35.93 3.61
570 1288 8.340618 TCTTTTGGGAGATAAAGATGAACAAG 57.659 34.615 0.00 0.00 35.93 3.16
571 1289 8.884124 ATCTTTTGGGAGATAAAGATGAACAA 57.116 30.769 8.75 0.00 44.92 2.83
572 1290 9.973661 TTATCTTTTGGGAGATAAAGATGAACA 57.026 29.630 16.29 0.00 45.69 3.18
602 1320 8.790718 GGAACATCAAGATGCATTTATATGAGT 58.209 33.333 14.86 5.91 42.39 3.41
603 1321 7.961283 CGGAACATCAAGATGCATTTATATGAG 59.039 37.037 14.86 7.08 42.39 2.90
604 1322 7.445096 ACGGAACATCAAGATGCATTTATATGA 59.555 33.333 14.86 9.71 42.39 2.15
605 1323 7.536281 CACGGAACATCAAGATGCATTTATATG 59.464 37.037 9.85 5.48 42.39 1.78
606 1324 7.587629 CACGGAACATCAAGATGCATTTATAT 58.412 34.615 9.85 0.00 42.39 0.86
607 1325 6.513230 GCACGGAACATCAAGATGCATTTATA 60.513 38.462 9.85 0.00 42.39 0.98
608 1326 5.734220 GCACGGAACATCAAGATGCATTTAT 60.734 40.000 9.85 0.00 42.39 1.40
609 1327 4.438608 GCACGGAACATCAAGATGCATTTA 60.439 41.667 9.85 0.00 42.39 1.40
610 1328 3.674138 GCACGGAACATCAAGATGCATTT 60.674 43.478 9.85 0.00 42.39 2.32
611 1329 2.159338 GCACGGAACATCAAGATGCATT 60.159 45.455 9.85 0.00 42.39 3.56
612 1330 1.402968 GCACGGAACATCAAGATGCAT 59.597 47.619 9.85 0.00 42.39 3.96
613 1331 0.804364 GCACGGAACATCAAGATGCA 59.196 50.000 9.85 0.00 42.39 3.96
614 1332 0.804364 TGCACGGAACATCAAGATGC 59.196 50.000 9.85 0.00 42.39 3.91
615 1333 3.431856 CATTGCACGGAACATCAAGATG 58.568 45.455 8.45 8.45 44.15 2.90
616 1334 2.159338 GCATTGCACGGAACATCAAGAT 60.159 45.455 3.15 0.00 0.00 2.40
617 1335 1.199789 GCATTGCACGGAACATCAAGA 59.800 47.619 3.15 0.00 0.00 3.02
618 1336 1.068402 TGCATTGCACGGAACATCAAG 60.068 47.619 7.38 0.00 31.71 3.02
619 1337 0.957362 TGCATTGCACGGAACATCAA 59.043 45.000 7.38 0.00 31.71 2.57
620 1338 2.638744 TGCATTGCACGGAACATCA 58.361 47.368 7.38 0.00 31.71 3.07
636 1354 1.026718 AACTAGCAAGATGCCCGTGC 61.027 55.000 6.11 6.11 46.52 5.34
637 1355 1.933853 GTAACTAGCAAGATGCCCGTG 59.066 52.381 0.00 0.00 46.52 4.94
638 1356 1.134491 GGTAACTAGCAAGATGCCCGT 60.134 52.381 0.00 0.00 46.52 5.28
639 1357 1.583054 GGTAACTAGCAAGATGCCCG 58.417 55.000 0.00 0.00 46.52 6.13
653 1371 5.675538 AGCCACTCATATTTCAGAGGTAAC 58.324 41.667 0.00 0.00 36.20 2.50
654 1372 5.957771 AGCCACTCATATTTCAGAGGTAA 57.042 39.130 0.00 0.00 36.20 2.85
679 1397 4.572389 CCAGATGATTTAGACCCTTCAACG 59.428 45.833 0.00 0.00 0.00 4.10
773 1491 9.710818 ATTATTTGACTTGGGAGTACTAGTCTA 57.289 33.333 19.42 12.25 38.23 2.59
827 1548 5.174395 CAGGAAGTCTAATCTTGTCCAGTG 58.826 45.833 0.00 0.00 0.00 3.66
848 1569 4.566545 TTGTTCATAAATATGGGCGCAG 57.433 40.909 10.83 0.00 34.50 5.18
908 1630 7.309133 CCAGTCAAGCACAATATAAGTTCCAAA 60.309 37.037 0.00 0.00 0.00 3.28
1329 2070 1.228245 ACCATGAACGCCAGTGCTT 60.228 52.632 0.00 0.00 34.43 3.91
1539 2280 3.356529 AGTGAAGGATCAACCATGGAC 57.643 47.619 21.47 1.23 42.04 4.02
1659 2400 6.724351 TGCCATATATGTCCTAAGCAATGAT 58.276 36.000 11.73 0.00 0.00 2.45
1761 2505 1.079503 GATGACGTCAACTGGGCTTC 58.920 55.000 24.13 9.09 0.00 3.86
1765 2509 2.099141 ATGTGATGACGTCAACTGGG 57.901 50.000 24.13 0.00 38.90 4.45
1775 2519 4.272991 GCTCCAGATGAAGAATGTGATGAC 59.727 45.833 0.00 0.00 31.04 3.06
1783 2527 4.597004 ACATGTTGCTCCAGATGAAGAAT 58.403 39.130 0.00 0.00 0.00 2.40
1896 2645 9.567776 AAAATTACCCCAAAAATTTAACAGAGG 57.432 29.630 0.00 0.00 34.93 3.69
1973 2724 1.001641 CCTTGGGAGTTGCCTCTGG 60.002 63.158 0.00 0.00 37.86 3.86
2120 2871 8.947055 AGTTCTGCATTTTGAAATAACAAGTT 57.053 26.923 0.00 0.00 0.00 2.66
2291 3043 8.998377 ACAAAATTACAACTCAAAGCAACTTTT 58.002 25.926 0.00 0.00 30.60 2.27
2292 3044 8.546597 ACAAAATTACAACTCAAAGCAACTTT 57.453 26.923 0.00 0.00 33.58 2.66
2351 3103 8.253810 TGAACATGGTCTCTTCACTAGATTTAG 58.746 37.037 12.94 0.00 30.92 1.85
2389 3141 2.925578 TTCCAGATGCTGATTTTGCG 57.074 45.000 0.00 0.00 32.44 4.85
2422 3174 4.541705 TCTGGAGAGGGAGATACTTCTTG 58.458 47.826 0.00 0.00 30.30 3.02
2484 3236 6.266168 TGTGAACTTTGATGACACAGTTTT 57.734 33.333 0.00 0.00 43.94 2.43
2489 3241 4.376146 TCGATGTGAACTTTGATGACACA 58.624 39.130 0.00 0.00 43.70 3.72
2501 3253 7.065803 TCCTAAGAAATGGAAATCGATGTGAAC 59.934 37.037 0.00 0.00 0.00 3.18
2545 3297 2.158900 CCTCCATTTGCATCCGTAGAGT 60.159 50.000 0.00 0.00 0.00 3.24
2618 3373 6.486657 CCAAGAACTGTTTCTGAACCTATCAA 59.513 38.462 0.00 0.00 41.56 2.57
2794 3558 2.503356 ACCTGATGGCCAAAACAACAAA 59.497 40.909 10.96 0.00 36.63 2.83
2898 3662 2.030562 CTCTGGTTTCGGCACCGT 59.969 61.111 9.23 0.00 40.09 4.83
2903 3667 1.535896 GTTTTCTCCTCTGGTTTCGGC 59.464 52.381 0.00 0.00 0.00 5.54
3055 3821 2.497273 GAGGGTTAAAGCATGCACCATT 59.503 45.455 21.98 10.31 0.00 3.16
3148 3938 6.906157 ACCTATTTCAGCATTAATGGATGG 57.094 37.500 17.02 8.86 0.00 3.51
3149 3939 8.174733 AGAACCTATTTCAGCATTAATGGATG 57.825 34.615 17.02 7.11 36.57 3.51
3150 3940 9.512588 CTAGAACCTATTTCAGCATTAATGGAT 57.487 33.333 17.02 0.00 36.57 3.41
3151 3941 7.445402 GCTAGAACCTATTTCAGCATTAATGGA 59.555 37.037 17.02 4.09 37.85 3.41
3152 3942 7.446625 AGCTAGAACCTATTTCAGCATTAATGG 59.553 37.037 17.02 1.65 39.19 3.16
3153 3943 8.388484 AGCTAGAACCTATTTCAGCATTAATG 57.612 34.615 11.27 11.27 39.19 1.90
3155 3945 9.547753 CTTAGCTAGAACCTATTTCAGCATTAA 57.452 33.333 0.00 0.00 39.19 1.40
3156 3946 7.657761 GCTTAGCTAGAACCTATTTCAGCATTA 59.342 37.037 0.00 0.00 39.19 1.90
3157 3947 6.484977 GCTTAGCTAGAACCTATTTCAGCATT 59.515 38.462 0.00 0.00 39.19 3.56
3158 3948 5.994668 GCTTAGCTAGAACCTATTTCAGCAT 59.005 40.000 0.00 0.00 39.19 3.79
3159 3949 5.360591 GCTTAGCTAGAACCTATTTCAGCA 58.639 41.667 0.00 0.00 39.19 4.41
3160 3950 4.752604 GGCTTAGCTAGAACCTATTTCAGC 59.247 45.833 3.59 0.00 38.04 4.26
3161 3951 5.918608 TGGCTTAGCTAGAACCTATTTCAG 58.081 41.667 3.59 0.00 36.57 3.02
3162 3952 5.950544 TGGCTTAGCTAGAACCTATTTCA 57.049 39.130 3.59 0.00 36.57 2.69
3163 3953 6.768381 ACAATGGCTTAGCTAGAACCTATTTC 59.232 38.462 3.59 0.00 33.95 2.17
3164 3954 6.663734 ACAATGGCTTAGCTAGAACCTATTT 58.336 36.000 3.59 0.00 0.00 1.40
3165 3955 6.253946 ACAATGGCTTAGCTAGAACCTATT 57.746 37.500 3.59 5.86 0.00 1.73
3166 3956 5.896073 ACAATGGCTTAGCTAGAACCTAT 57.104 39.130 3.59 1.32 0.00 2.57
3167 3957 6.996180 ATACAATGGCTTAGCTAGAACCTA 57.004 37.500 3.59 0.00 0.00 3.08
3168 3958 5.896073 ATACAATGGCTTAGCTAGAACCT 57.104 39.130 3.59 0.00 0.00 3.50
3169 3959 9.892130 ATTATATACAATGGCTTAGCTAGAACC 57.108 33.333 3.59 0.00 0.00 3.62
3272 4062 0.322816 ACAGGGAGCAATGCGACATT 60.323 50.000 0.00 0.00 0.00 2.71
3306 4096 9.638176 ATTCAGTTTATCTTGGATGCTTAAGAT 57.362 29.630 6.67 5.36 43.80 2.40
3412 4202 2.417516 CCGCCAGGATGTCCGTAG 59.582 66.667 0.00 0.00 42.08 3.51
3446 4236 0.251653 TTAGGGTGCTCAGGACGTCT 60.252 55.000 16.46 0.00 0.00 4.18
3468 4258 1.425428 CAATCCAAGCGACGAAGGC 59.575 57.895 0.00 0.00 0.00 4.35
3501 4291 0.417841 TCTCCCTCCTGGCTACCTTT 59.582 55.000 0.00 0.00 0.00 3.11
3519 4309 4.293662 AGAGACCACCTGATTCCTTTTC 57.706 45.455 0.00 0.00 0.00 2.29
3521 4311 5.094387 TCTTAGAGACCACCTGATTCCTTT 58.906 41.667 0.00 0.00 0.00 3.11
3522 4312 4.689062 TCTTAGAGACCACCTGATTCCTT 58.311 43.478 0.00 0.00 0.00 3.36
3541 4331 9.084533 CTTAGAGGCTTAGATGGTATACTTCTT 57.915 37.037 12.17 0.00 35.44 2.52
3575 4367 2.627863 TCAAACCCATCGAAATTGCG 57.372 45.000 0.00 0.00 0.00 4.85
3619 4412 5.943416 TGTAAGATCAATCAAAACATCGGGT 59.057 36.000 0.00 0.00 0.00 5.28
3620 4413 6.435430 TGTAAGATCAATCAAAACATCGGG 57.565 37.500 0.00 0.00 0.00 5.14
3621 4414 7.475015 ACATGTAAGATCAATCAAAACATCGG 58.525 34.615 0.00 0.00 0.00 4.18
3801 4609 0.035152 TCAGAAAGCCGCACATCCAT 60.035 50.000 0.00 0.00 0.00 3.41
3826 4634 3.119743 TCAAGCGCATCCATTCTTGAAAG 60.120 43.478 11.47 0.00 41.08 2.62
3843 4651 5.123027 CCTCACATTTAGAGGTCTTTCAAGC 59.877 44.000 0.00 0.00 46.07 4.01
3933 4748 6.378710 TGGATTCTACAGAAGATGTCTACG 57.621 41.667 0.00 0.00 42.70 3.51
3939 4754 5.557576 TCCCATGGATTCTACAGAAGATG 57.442 43.478 15.22 1.01 37.48 2.90



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

AutoCloner maintained by Alex Coulton.