Multiple sequence alignment - TraesCS5A01G263400

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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 TraesCS5A01G263400 chr5A 100.000 2591 0 0 1 2591 476398506 476401096 0.000000e+00 4785.0
1 TraesCS5A01G263400 chr5D 89.619 1811 97 29 817 2588 374658488 374660246 0.000000e+00 2218.0
2 TraesCS5A01G263400 chr5D 86.754 536 63 4 1 529 374656829 374657363 7.990000e-165 590.0
3 TraesCS5A01G263400 chr5B 90.330 910 38 8 813 1688 447393874 447394767 0.000000e+00 1147.0
4 TraesCS5A01G263400 chr5B 81.687 486 43 18 1850 2322 447395631 447396083 1.900000e-96 363.0
5 TraesCS5A01G263400 chr5B 88.298 282 26 3 254 529 447392366 447392646 5.340000e-87 331.0
6 TraesCS5A01G263400 chr5B 85.771 253 35 1 1 252 447376049 447376301 1.530000e-67 267.0
7 TraesCS5A01G263400 chr5B 83.650 263 13 10 2322 2563 447400895 447401148 1.210000e-53 220.0
8 TraesCS5A01G263400 chr6D 90.123 162 8 3 626 780 311580694 311580534 1.220000e-48 204.0
9 TraesCS5A01G263400 chr4D 89.349 169 9 4 626 786 230542710 230542543 1.220000e-48 204.0
10 TraesCS5A01G263400 chr4B 90.123 162 8 3 626 780 41528256 41528096 1.220000e-48 204.0
11 TraesCS5A01G263400 chr4A 88.571 175 11 4 626 792 660522378 660522551 1.220000e-48 204.0
12 TraesCS5A01G263400 chr2D 90.446 157 12 3 626 780 372926965 372927120 1.220000e-48 204.0
13 TraesCS5A01G263400 chr6B 89.157 166 8 5 626 783 82420344 82420507 5.660000e-47 198.0
14 TraesCS5A01G263400 chr1D 89.506 162 9 3 626 780 427826922 427827082 5.660000e-47 198.0
15 TraesCS5A01G263400 chr1B 89.506 162 9 3 626 780 450130782 450130942 5.660000e-47 198.0
16 TraesCS5A01G263400 chr1B 88.024 167 12 6 621 780 201758391 201758556 9.460000e-45 191.0
17 TraesCS5A01G263400 chr3A 95.556 45 2 0 563 607 573836618 573836574 3.580000e-09 73.1
18 TraesCS5A01G263400 chr3A 95.238 42 2 0 568 609 746291298 746291339 1.660000e-07 67.6
19 TraesCS5A01G263400 chrUn 92.683 41 1 2 565 604 102508772 102508811 1.000000e-04 58.4


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 TraesCS5A01G263400 chr5A 476398506 476401096 2590 False 4785.000000 4785 100.000000 1 2591 1 chr5A.!!$F1 2590
1 TraesCS5A01G263400 chr5D 374656829 374660246 3417 False 1404.000000 2218 88.186500 1 2588 2 chr5D.!!$F1 2587
2 TraesCS5A01G263400 chr5B 447392366 447396083 3717 False 613.666667 1147 86.771667 254 2322 3 chr5B.!!$F3 2068

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
341 348 0.166814 GAGCTCACAATGCACGTTCC 59.833 55.0 9.4 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 4074 0.107268 TGATGCGAGGGATCATGTGG 59.893 55.0 0.0 0.0 0.0 4.17 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
26 27 2.025793 TGGAAATATCTTGTGGCCCGAA 60.026 45.455 0.00 0.00 0.00 4.30
31 32 0.693049 ATCTTGTGGCCCGAAACTCT 59.307 50.000 0.00 0.00 0.00 3.24
33 34 0.535102 CTTGTGGCCCGAAACTCTGT 60.535 55.000 0.00 0.00 0.00 3.41
35 36 2.281484 TGGCCCGAAACTCTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
43 44 1.680338 GAAACTCTGTGCAGGGTGTT 58.320 50.000 5.38 2.95 42.33 3.32
47 48 1.233019 CTCTGTGCAGGGTGTTGAAG 58.767 55.000 0.00 0.00 0.00 3.02
65 66 6.382859 TGTTGAAGCCCACATAGAAGTAGATA 59.617 38.462 0.00 0.00 0.00 1.98
66 67 7.093068 TGTTGAAGCCCACATAGAAGTAGATAA 60.093 37.037 0.00 0.00 0.00 1.75
76 77 3.827722 AGAAGTAGATAAGCGAGCCTCT 58.172 45.455 0.00 0.00 0.00 3.69
81 82 5.134661 AGTAGATAAGCGAGCCTCTAACTT 58.865 41.667 0.00 0.00 0.00 2.66
83 84 5.699097 AGATAAGCGAGCCTCTAACTTAG 57.301 43.478 0.00 0.00 0.00 2.18
85 86 0.747852 AGCGAGCCTCTAACTTAGCC 59.252 55.000 0.00 0.00 0.00 3.93
115 117 4.070716 CCCAGCATAAACATCTCTCCATC 58.929 47.826 0.00 0.00 0.00 3.51
117 119 5.314529 CCAGCATAAACATCTCTCCATCAT 58.685 41.667 0.00 0.00 0.00 2.45
128 130 2.502947 CTCTCCATCATCCCAAGTCACA 59.497 50.000 0.00 0.00 0.00 3.58
135 137 3.073678 TCATCCCAAGTCACATTGAACG 58.926 45.455 0.00 0.00 31.55 3.95
153 155 1.626654 CGTCAATGTGGACACCTCGC 61.627 60.000 0.00 0.00 37.66 5.03
183 185 3.876341 ACAACAACCTTCGTCACCTAAA 58.124 40.909 0.00 0.00 0.00 1.85
186 188 6.056884 ACAACAACCTTCGTCACCTAAATTA 58.943 36.000 0.00 0.00 0.00 1.40
210 212 3.932089 GGCTTCTGCACTAGAAAGAAGAG 59.068 47.826 24.84 10.76 46.46 2.85
217 219 3.056179 GCACTAGAAAGAAGAGCACTCCT 60.056 47.826 0.00 0.00 0.00 3.69
237 239 3.576550 CCTCTTCATAGGCTCTAACTCCC 59.423 52.174 0.00 0.00 0.00 4.30
238 240 3.576550 CTCTTCATAGGCTCTAACTCCCC 59.423 52.174 0.00 0.00 0.00 4.81
239 241 1.996798 TCATAGGCTCTAACTCCCCG 58.003 55.000 0.00 0.00 0.00 5.73
269 271 1.975680 ACTCGCCTTGGAGAAACCTTA 59.024 47.619 0.00 0.00 39.86 2.69
272 274 1.468914 CGCCTTGGAGAAACCTTAAGC 59.531 52.381 0.00 0.00 39.86 3.09
288 295 0.543646 AAGCAAGATGCCAAGGCCTT 60.544 50.000 13.78 13.78 46.52 4.35
304 311 1.610102 GCCTTGTGTGTCTCAGAGCAT 60.610 52.381 0.00 0.00 0.00 3.79
307 314 2.445565 TGTGTGTCTCAGAGCATGAC 57.554 50.000 0.00 0.00 33.22 3.06
340 347 0.179240 CGAGCTCACAATGCACGTTC 60.179 55.000 15.40 0.00 39.08 3.95
341 348 0.166814 GAGCTCACAATGCACGTTCC 59.833 55.000 9.40 0.00 0.00 3.62
357 364 2.692557 CGTTCCAGAGAGATGACTCCAT 59.307 50.000 0.00 0.00 43.53 3.41
371 378 2.749621 GACTCCATCCGATGCAAGTTTT 59.250 45.455 13.08 0.00 0.00 2.43
372 379 3.157087 ACTCCATCCGATGCAAGTTTTT 58.843 40.909 2.53 0.00 0.00 1.94
401 408 0.460284 GTCACGGTGCTATGTCCTGG 60.460 60.000 2.51 0.00 0.00 4.45
415 422 1.139498 TCCTGGATGCCCACTTGGAA 61.139 55.000 0.00 0.00 37.58 3.53
480 487 9.939424 AGTATAGAAATACTCTACTTGGTCCTT 57.061 33.333 0.00 0.00 44.05 3.36
481 488 9.968870 GTATAGAAATACTCTACTTGGTCCTTG 57.031 37.037 0.00 0.00 39.52 3.61
529 536 1.013596 CAAGTTCCTCAACACGCACA 58.986 50.000 0.00 0.00 34.60 4.57
530 537 1.003545 CAAGTTCCTCAACACGCACAG 60.004 52.381 0.00 0.00 34.60 3.66
531 538 0.464036 AGTTCCTCAACACGCACAGA 59.536 50.000 0.00 0.00 34.60 3.41
532 539 1.134521 AGTTCCTCAACACGCACAGAA 60.135 47.619 0.00 0.00 34.60 3.02
533 540 1.873591 GTTCCTCAACACGCACAGAAT 59.126 47.619 0.00 0.00 32.14 2.40
534 541 2.254546 TCCTCAACACGCACAGAATT 57.745 45.000 0.00 0.00 0.00 2.17
535 542 2.571212 TCCTCAACACGCACAGAATTT 58.429 42.857 0.00 0.00 0.00 1.82
536 543 2.948979 TCCTCAACACGCACAGAATTTT 59.051 40.909 0.00 0.00 0.00 1.82
537 544 3.380004 TCCTCAACACGCACAGAATTTTT 59.620 39.130 0.00 0.00 0.00 1.94
568 575 8.761689 AGAAAAAGATTACCATGGTATTTGCAT 58.238 29.630 25.12 14.96 0.00 3.96
570 577 7.902920 AAAGATTACCATGGTATTTGCATCT 57.097 32.000 25.12 23.49 29.53 2.90
571 578 6.889301 AGATTACCATGGTATTTGCATCTG 57.111 37.500 25.36 0.00 28.15 2.90
572 579 5.771666 AGATTACCATGGTATTTGCATCTGG 59.228 40.000 25.36 0.00 28.15 3.86
574 581 3.290710 ACCATGGTATTTGCATCTGGAC 58.709 45.455 18.10 0.00 0.00 4.02
575 582 2.291465 CCATGGTATTTGCATCTGGACG 59.709 50.000 2.57 0.00 0.00 4.79
584 591 1.568025 CATCTGGACGATGCATGCG 59.432 57.895 14.09 10.48 42.75 4.73
585 592 1.596203 ATCTGGACGATGCATGCGG 60.596 57.895 14.09 7.44 0.00 5.69
586 593 2.315781 ATCTGGACGATGCATGCGGT 62.316 55.000 14.09 10.91 0.00 5.68
588 627 0.809636 CTGGACGATGCATGCGGTTA 60.810 55.000 14.09 0.00 0.00 2.85
590 629 0.944386 GGACGATGCATGCGGTTATT 59.056 50.000 14.09 0.00 0.00 1.40
593 632 3.002862 GGACGATGCATGCGGTTATTTTA 59.997 43.478 14.09 0.00 0.00 1.52
596 635 6.307031 ACGATGCATGCGGTTATTTTATTA 57.693 33.333 14.09 0.00 0.00 0.98
597 636 6.730175 ACGATGCATGCGGTTATTTTATTAA 58.270 32.000 14.09 0.00 0.00 1.40
598 637 7.367285 ACGATGCATGCGGTTATTTTATTAAT 58.633 30.769 14.09 0.00 0.00 1.40
634 673 3.536956 TGTAAAATAGCACTCCCTCCG 57.463 47.619 0.00 0.00 0.00 4.63
635 674 3.101437 TGTAAAATAGCACTCCCTCCGA 58.899 45.455 0.00 0.00 0.00 4.55
637 676 3.933861 AAAATAGCACTCCCTCCGATT 57.066 42.857 0.00 0.00 0.00 3.34
638 677 3.477210 AAATAGCACTCCCTCCGATTC 57.523 47.619 0.00 0.00 0.00 2.52
639 678 1.343069 ATAGCACTCCCTCCGATTCC 58.657 55.000 0.00 0.00 0.00 3.01
641 680 0.261991 AGCACTCCCTCCGATTCCTA 59.738 55.000 0.00 0.00 0.00 2.94
643 682 1.485066 GCACTCCCTCCGATTCCTAAA 59.515 52.381 0.00 0.00 0.00 1.85
644 683 2.104963 GCACTCCCTCCGATTCCTAAAT 59.895 50.000 0.00 0.00 0.00 1.40
646 685 4.020128 GCACTCCCTCCGATTCCTAAATAT 60.020 45.833 0.00 0.00 0.00 1.28
647 686 5.187186 GCACTCCCTCCGATTCCTAAATATA 59.813 44.000 0.00 0.00 0.00 0.86
649 688 7.324178 CACTCCCTCCGATTCCTAAATATAAG 58.676 42.308 0.00 0.00 0.00 1.73
654 693 8.784043 CCCTCCGATTCCTAAATATAAGTTTTG 58.216 37.037 0.00 0.00 0.00 2.44
655 694 9.338622 CCTCCGATTCCTAAATATAAGTTTTGT 57.661 33.333 0.00 0.00 0.00 2.83
682 1057 9.701098 AAAGATTTCACTACAAACTACATACGA 57.299 29.630 0.00 0.00 0.00 3.43
684 1067 9.355215 AGATTTCACTACAAACTACATACGAAG 57.645 33.333 0.00 0.00 0.00 3.79
685 1068 6.939551 TTCACTACAAACTACATACGAAGC 57.060 37.500 0.00 0.00 0.00 3.86
690 1073 8.065407 CACTACAAACTACATACGAAGCAAAAA 58.935 33.333 0.00 0.00 0.00 1.94
694 1077 7.012044 ACAAACTACATACGAAGCAAAAAGAGT 59.988 33.333 0.00 0.00 0.00 3.24
698 1081 9.216117 ACTACATACGAAGCAAAAAGAGTAAAT 57.784 29.630 0.00 0.00 0.00 1.40
700 1083 8.324163 ACATACGAAGCAAAAAGAGTAAATCT 57.676 30.769 0.00 0.00 41.27 2.40
701 1084 9.431887 ACATACGAAGCAAAAAGAGTAAATCTA 57.568 29.630 0.00 0.00 37.23 1.98
703 1086 7.724305 ACGAAGCAAAAAGAGTAAATCTACA 57.276 32.000 0.00 0.00 37.23 2.74
704 1087 7.573627 ACGAAGCAAAAAGAGTAAATCTACAC 58.426 34.615 0.00 0.00 37.23 2.90
705 1088 7.441458 ACGAAGCAAAAAGAGTAAATCTACACT 59.559 33.333 0.00 0.00 37.23 3.55
706 1089 7.952637 CGAAGCAAAAAGAGTAAATCTACACTC 59.047 37.037 0.00 0.00 41.25 3.51
734 1117 9.797642 AAAATGCATCTAGATATATGTGGTTCA 57.202 29.630 4.54 0.00 0.00 3.18
735 1118 9.970553 AAATGCATCTAGATATATGTGGTTCAT 57.029 29.630 4.54 0.00 40.25 2.57
738 1121 9.259832 TGCATCTAGATATATGTGGTTCATAGT 57.740 33.333 4.54 0.00 41.55 2.12
739 1122 9.526713 GCATCTAGATATATGTGGTTCATAGTG 57.473 37.037 4.54 0.00 41.55 2.74
751 1134 6.611236 TGTGGTTCATAGTGATATCTCTCCAA 59.389 38.462 10.49 0.83 0.00 3.53
753 1136 7.655328 GTGGTTCATAGTGATATCTCTCCAAAG 59.345 40.741 10.49 0.00 0.00 2.77
754 1137 7.565029 TGGTTCATAGTGATATCTCTCCAAAGA 59.435 37.037 10.49 1.72 0.00 2.52
755 1138 7.870445 GGTTCATAGTGATATCTCTCCAAAGAC 59.130 40.741 10.49 4.62 0.00 3.01
756 1139 8.637986 GTTCATAGTGATATCTCTCCAAAGACT 58.362 37.037 10.49 1.70 0.00 3.24
757 1140 8.774546 TCATAGTGATATCTCTCCAAAGACTT 57.225 34.615 10.49 0.00 0.00 3.01
758 1141 9.868160 TCATAGTGATATCTCTCCAAAGACTTA 57.132 33.333 10.49 0.00 0.00 2.24
770 1153 9.250624 CTCTCCAAAGACTTATATTTAGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
771 1154 8.202137 TCTCCAAAGACTTATATTTAGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
772 1155 8.081517 TCCAAAGACTTATATTTAGGAACGGA 57.918 34.615 0.00 0.00 0.00 4.69
773 1156 8.202137 TCCAAAGACTTATATTTAGGAACGGAG 58.798 37.037 0.00 0.00 0.00 4.63
774 1157 7.441458 CCAAAGACTTATATTTAGGAACGGAGG 59.559 40.741 0.00 0.00 0.00 4.30
775 1158 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
776 1159 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
777 1160 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
779 1162 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
780 1163 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
782 1165 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
783 1166 1.777941 AGGAACGGAGGGAGTACATC 58.222 55.000 0.00 0.00 0.00 3.06
784 1167 1.288335 AGGAACGGAGGGAGTACATCT 59.712 52.381 0.00 0.00 0.00 2.90
786 1169 3.053095 AGGAACGGAGGGAGTACATCTTA 60.053 47.826 0.00 0.00 0.00 2.10
788 1171 4.202131 GGAACGGAGGGAGTACATCTTAAG 60.202 50.000 0.00 0.00 0.00 1.85
790 1173 2.036089 CGGAGGGAGTACATCTTAAGCC 59.964 54.545 0.00 0.00 0.00 4.35
792 1175 3.181464 GGAGGGAGTACATCTTAAGCCAC 60.181 52.174 0.00 0.00 0.00 5.01
795 1178 2.202566 GAGTACATCTTAAGCCACGCC 58.797 52.381 0.00 0.00 0.00 5.68
796 1179 1.831736 AGTACATCTTAAGCCACGCCT 59.168 47.619 0.00 0.00 0.00 5.52
797 1180 2.236395 AGTACATCTTAAGCCACGCCTT 59.764 45.455 0.00 0.00 0.00 4.35
798 1181 3.449737 AGTACATCTTAAGCCACGCCTTA 59.550 43.478 0.00 0.00 0.00 2.69
799 1182 2.906354 ACATCTTAAGCCACGCCTTAG 58.094 47.619 0.00 0.00 0.00 2.18
800 1183 1.599542 CATCTTAAGCCACGCCTTAGC 59.400 52.381 0.00 0.00 0.00 3.09
801 1184 0.611200 TCTTAAGCCACGCCTTAGCA 59.389 50.000 0.00 0.00 39.83 3.49
803 1186 1.130561 CTTAAGCCACGCCTTAGCAAC 59.869 52.381 0.00 0.00 39.83 4.17
805 1188 0.955919 AAGCCACGCCTTAGCAACTC 60.956 55.000 0.00 0.00 39.83 3.01
807 1190 1.296715 CCACGCCTTAGCAACTCCT 59.703 57.895 0.00 0.00 39.83 3.69
808 1191 0.535335 CCACGCCTTAGCAACTCCTA 59.465 55.000 0.00 0.00 39.83 2.94
810 1193 2.420129 CCACGCCTTAGCAACTCCTATT 60.420 50.000 0.00 0.00 39.83 1.73
811 1194 2.866762 CACGCCTTAGCAACTCCTATTC 59.133 50.000 0.00 0.00 39.83 1.75
812 1195 2.500098 ACGCCTTAGCAACTCCTATTCA 59.500 45.455 0.00 0.00 39.83 2.57
813 1196 2.866762 CGCCTTAGCAACTCCTATTCAC 59.133 50.000 0.00 0.00 39.83 3.18
814 1197 3.430929 CGCCTTAGCAACTCCTATTCACT 60.431 47.826 0.00 0.00 39.83 3.41
815 1198 4.123506 GCCTTAGCAACTCCTATTCACTC 58.876 47.826 0.00 0.00 39.53 3.51
931 1993 0.829602 TCCATCTCCATCGCTCTCCC 60.830 60.000 0.00 0.00 0.00 4.30
1586 2660 2.506438 GGCCGACGGAGAAGAACG 60.506 66.667 20.50 0.00 0.00 3.95
1591 2665 0.801251 CGACGGAGAAGAACGGTAGT 59.199 55.000 0.00 0.00 0.00 2.73
1593 2667 0.886563 ACGGAGAAGAACGGTAGTGG 59.113 55.000 0.00 0.00 0.00 4.00
1594 2668 0.886563 CGGAGAAGAACGGTAGTGGT 59.113 55.000 0.00 0.00 0.00 4.16
1596 2670 2.489329 CGGAGAAGAACGGTAGTGGTAA 59.511 50.000 0.00 0.00 0.00 2.85
1641 2736 3.941483 ACTGATGTGTAAATACTGGCTGC 59.059 43.478 0.00 0.00 0.00 5.25
1642 2737 3.278574 TGATGTGTAAATACTGGCTGCC 58.721 45.455 12.87 12.87 0.00 4.85
1666 2761 5.803967 CAGGCAATAAGAAGTGAAATTCTGC 59.196 40.000 0.00 0.00 39.47 4.26
1677 2772 4.445385 AGTGAAATTCTGCAAATTCGCAAC 59.555 37.500 13.18 0.00 42.45 4.17
1678 2773 3.424861 TGAAATTCTGCAAATTCGCAACG 59.575 39.130 0.00 0.00 42.45 4.10
1688 2783 2.830772 ATTCGCAACGTCCATTGATG 57.169 45.000 0.00 0.00 0.00 3.07
1697 2792 4.100707 ACGTCCATTGATGAAATTGCTG 57.899 40.909 0.00 0.00 0.00 4.41
1701 2796 3.448301 TCCATTGATGAAATTGCTGGACC 59.552 43.478 0.00 0.00 0.00 4.46
1787 3612 1.377725 AGCAGCAGGGGTCAAATCG 60.378 57.895 0.00 0.00 0.00 3.34
1807 3632 1.865340 GTCGTCACAGGTGTTCTTTCC 59.135 52.381 0.00 0.00 0.00 3.13
1832 3658 5.241662 AGAGGATAAAACTTCAGTGCTCAC 58.758 41.667 0.00 0.00 30.77 3.51
1833 3659 4.973168 AGGATAAAACTTCAGTGCTCACA 58.027 39.130 2.63 0.00 0.00 3.58
1846 3672 1.673665 CTCACAAGGGAGCAGTGGC 60.674 63.158 0.00 0.00 41.61 5.01
1857 3683 2.639286 CAGTGGCCGTGAGTTTGC 59.361 61.111 0.00 0.00 0.00 3.68
1879 3705 3.447586 CGATGACTGGGAGGAGAAACTAA 59.552 47.826 0.00 0.00 0.00 2.24
1936 3762 4.715523 TGGTAAGTGGCCGGCTGC 62.716 66.667 28.56 19.12 40.16 5.25
1989 3815 4.297891 CACACCACACACGCGCTG 62.298 66.667 5.73 6.58 0.00 5.18
2015 3841 2.954020 GATTCAGGATCGCCGCGTCA 62.954 60.000 13.39 0.00 39.96 4.35
2016 3842 3.982372 TTCAGGATCGCCGCGTCAC 62.982 63.158 13.39 4.04 39.96 3.67
2054 3886 0.734253 CTGTCCGAAAGACCTGAGCG 60.734 60.000 0.00 0.00 45.68 5.03
2055 3887 1.176619 TGTCCGAAAGACCTGAGCGA 61.177 55.000 0.00 0.00 45.68 4.93
2056 3888 0.456995 GTCCGAAAGACCTGAGCGAG 60.457 60.000 0.00 0.00 39.84 5.03
2057 3889 0.608308 TCCGAAAGACCTGAGCGAGA 60.608 55.000 0.00 0.00 0.00 4.04
2058 3890 0.179150 CCGAAAGACCTGAGCGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
2086 3922 1.079543 TCCGAAAGAGAGCAGCAGC 60.080 57.895 0.00 0.00 42.56 5.25
2118 3954 2.277084 CGCTGTTGGATTACTACCACC 58.723 52.381 0.00 0.00 37.13 4.61
2125 3961 5.104693 TGTTGGATTACTACCACCGAATGAT 60.105 40.000 0.00 0.00 37.13 2.45
2126 3962 4.956085 TGGATTACTACCACCGAATGATG 58.044 43.478 0.00 0.00 32.03 3.07
2127 3963 4.651962 TGGATTACTACCACCGAATGATGA 59.348 41.667 0.00 0.00 32.03 2.92
2142 3978 0.249489 GATGAATGTAGGCGAGCCGT 60.249 55.000 8.63 0.12 41.95 5.68
2156 3992 2.031314 CGAGCCGTAAGACGATTCTACA 59.969 50.000 0.00 0.00 46.05 2.74
2157 3993 3.361414 GAGCCGTAAGACGATTCTACAC 58.639 50.000 0.00 0.00 46.05 2.90
2158 3994 3.015327 AGCCGTAAGACGATTCTACACT 58.985 45.455 0.00 0.00 46.05 3.55
2193 4039 0.482446 TTCTGCCTTTGGGGACACAT 59.518 50.000 0.00 0.00 42.67 3.21
2194 4040 1.367346 TCTGCCTTTGGGGACACATA 58.633 50.000 0.00 0.00 42.67 2.29
2195 4041 1.004277 TCTGCCTTTGGGGACACATAC 59.996 52.381 0.00 0.00 42.67 2.39
2196 4042 0.774276 TGCCTTTGGGGACACATACA 59.226 50.000 0.00 0.00 42.67 2.29
2197 4043 1.357420 TGCCTTTGGGGACACATACAT 59.643 47.619 0.00 0.00 42.67 2.29
2198 4044 2.578480 TGCCTTTGGGGACACATACATA 59.422 45.455 0.00 0.00 42.67 2.29
2199 4045 3.204158 TGCCTTTGGGGACACATACATAT 59.796 43.478 0.00 0.00 42.67 1.78
2200 4046 3.569701 GCCTTTGGGGACACATACATATG 59.430 47.826 0.00 0.00 42.67 1.78
2233 4079 4.753662 CCAGCCAGCCAGCCACAT 62.754 66.667 0.00 0.00 0.00 3.21
2234 4080 3.449227 CAGCCAGCCAGCCACATG 61.449 66.667 0.00 0.00 0.00 3.21
2235 4081 3.654143 AGCCAGCCAGCCACATGA 61.654 61.111 0.00 0.00 0.00 3.07
2236 4082 2.441532 GCCAGCCAGCCACATGAT 60.442 61.111 0.00 0.00 0.00 2.45
2237 4083 2.487532 GCCAGCCAGCCACATGATC 61.488 63.158 0.00 0.00 0.00 2.92
2267 4114 2.376808 AGATATCGCTAGTGGCATGC 57.623 50.000 9.90 9.90 41.91 4.06
2271 4118 4.228097 CGCTAGTGGCATGCACGC 62.228 66.667 21.36 15.13 41.91 5.34
2313 4160 3.486108 CGCACGACTAACAATCCAGATAC 59.514 47.826 0.00 0.00 0.00 2.24
2322 4169 7.044181 ACTAACAATCCAGATACACACATCAG 58.956 38.462 0.00 0.00 0.00 2.90
2326 4173 2.118679 CCAGATACACACATCAGGGGA 58.881 52.381 0.00 0.00 30.08 4.81
2359 4206 2.187946 CCGGTCCTCATGCACTCC 59.812 66.667 0.00 0.00 0.00 3.85
2388 4235 5.219226 AGCTAGGATATTATTCGTCGACG 57.781 43.478 31.30 31.30 41.45 5.12
2432 4279 4.351938 TCCTTGACGTGTCGGCCG 62.352 66.667 22.12 22.12 31.60 6.13
2433 4280 4.657824 CCTTGACGTGTCGGCCGT 62.658 66.667 27.15 4.54 42.06 5.68
2449 4296 3.764049 GTTCGAGCCGCACACGTC 61.764 66.667 0.00 0.00 37.70 4.34
2461 4308 1.006102 ACACGTCTCGGCTTCCTTG 60.006 57.895 0.00 0.00 0.00 3.61
2464 4311 0.243095 ACGTCTCGGCTTCCTTGTAC 59.757 55.000 0.00 0.00 0.00 2.90
2485 4332 2.042831 ATGCGCCAGCCTCTCAAAC 61.043 57.895 4.18 0.00 44.33 2.93
2488 4335 1.448540 CGCCAGCCTCTCAAACGAT 60.449 57.895 0.00 0.00 0.00 3.73
2495 4342 3.935203 CAGCCTCTCAAACGATATGTTGT 59.065 43.478 0.00 0.00 40.84 3.32
2496 4343 5.109210 CAGCCTCTCAAACGATATGTTGTA 58.891 41.667 0.00 0.00 40.84 2.41
2507 4354 3.427528 CGATATGTTGTATACGTGGCACC 59.572 47.826 12.86 0.00 0.00 5.01
2522 4369 1.524621 CACCCGGCACCTCATCATC 60.525 63.158 0.00 0.00 0.00 2.92
2524 4371 1.348008 ACCCGGCACCTCATCATCAT 61.348 55.000 0.00 0.00 0.00 2.45
2525 4372 0.179009 CCCGGCACCTCATCATCATT 60.179 55.000 0.00 0.00 0.00 2.57
2526 4373 1.072173 CCCGGCACCTCATCATCATTA 59.928 52.381 0.00 0.00 0.00 1.90
2527 4374 2.487086 CCCGGCACCTCATCATCATTAA 60.487 50.000 0.00 0.00 0.00 1.40
2529 4376 3.003689 CCGGCACCTCATCATCATTAAAC 59.996 47.826 0.00 0.00 0.00 2.01
2530 4377 3.879295 CGGCACCTCATCATCATTAAACT 59.121 43.478 0.00 0.00 0.00 2.66
2531 4378 5.056480 CGGCACCTCATCATCATTAAACTA 58.944 41.667 0.00 0.00 0.00 2.24
2532 4379 5.527214 CGGCACCTCATCATCATTAAACTAA 59.473 40.000 0.00 0.00 0.00 2.24
2550 4397 7.829378 AAACTAAACTAAGCTAGAATCACGG 57.171 36.000 0.00 0.00 0.00 4.94
2551 4398 5.349809 ACTAAACTAAGCTAGAATCACGGC 58.650 41.667 0.00 0.00 0.00 5.68
2552 4399 3.887621 AACTAAGCTAGAATCACGGCA 57.112 42.857 0.00 0.00 0.00 5.69
2588 4435 0.804933 GAGCCAATCGACCACGTACC 60.805 60.000 0.00 0.00 40.69 3.34
2589 4436 1.812507 GCCAATCGACCACGTACCC 60.813 63.158 0.00 0.00 40.69 3.69
2590 4437 1.517694 CCAATCGACCACGTACCCG 60.518 63.158 0.00 0.00 40.69 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.562008 TCGGGCCACAAGATATTTCCA 59.438 47.619 4.39 0.00 0.00 3.53
9 10 3.054361 AGAGTTTCGGGCCACAAGATATT 60.054 43.478 4.39 0.00 0.00 1.28
12 13 0.693049 AGAGTTTCGGGCCACAAGAT 59.307 50.000 4.39 0.00 0.00 2.40
16 17 1.227823 CACAGAGTTTCGGGCCACA 60.228 57.895 4.39 0.00 0.00 4.17
19 20 2.281484 TGCACAGAGTTTCGGGCC 60.281 61.111 0.00 0.00 0.00 5.80
21 22 1.672356 CCCTGCACAGAGTTTCGGG 60.672 63.158 0.00 0.00 0.00 5.14
26 27 0.546122 TCAACACCCTGCACAGAGTT 59.454 50.000 0.00 0.00 0.00 3.01
31 32 1.827789 GGCTTCAACACCCTGCACA 60.828 57.895 0.00 0.00 0.00 4.57
33 34 2.203480 GGGCTTCAACACCCTGCA 60.203 61.111 0.00 0.00 43.36 4.41
43 44 6.463049 GCTTATCTACTTCTATGTGGGCTTCA 60.463 42.308 0.00 0.00 0.00 3.02
47 48 4.022242 TCGCTTATCTACTTCTATGTGGGC 60.022 45.833 0.00 0.00 0.00 5.36
51 52 5.074115 AGGCTCGCTTATCTACTTCTATGT 58.926 41.667 0.00 0.00 0.00 2.29
65 66 1.137282 GGCTAAGTTAGAGGCTCGCTT 59.863 52.381 14.27 19.78 36.58 4.68
66 67 0.747852 GGCTAAGTTAGAGGCTCGCT 59.252 55.000 14.27 6.18 36.58 4.93
76 77 2.832129 CTGGGTGAGAGTGGCTAAGTTA 59.168 50.000 0.00 0.00 0.00 2.24
81 82 0.618680 ATGCTGGGTGAGAGTGGCTA 60.619 55.000 0.00 0.00 0.00 3.93
83 84 0.253044 TTATGCTGGGTGAGAGTGGC 59.747 55.000 0.00 0.00 0.00 5.01
85 86 3.057969 TGTTTATGCTGGGTGAGAGTG 57.942 47.619 0.00 0.00 0.00 3.51
115 117 2.813754 ACGTTCAATGTGACTTGGGATG 59.186 45.455 0.00 0.00 0.00 3.51
117 119 2.158885 TGACGTTCAATGTGACTTGGGA 60.159 45.455 0.00 0.00 0.00 4.37
135 137 1.298859 GGCGAGGTGTCCACATTGAC 61.299 60.000 3.61 0.00 35.77 3.18
153 155 0.829990 AAGGTTGTTGTTGCCAAGGG 59.170 50.000 0.00 0.00 0.00 3.95
163 165 5.432885 AATTTAGGTGACGAAGGTTGTTG 57.567 39.130 0.00 0.00 0.00 3.33
165 167 5.243207 CCTAATTTAGGTGACGAAGGTTGT 58.757 41.667 13.48 0.00 41.18 3.32
167 169 4.840271 CCCTAATTTAGGTGACGAAGGTT 58.160 43.478 18.92 0.00 44.73 3.50
183 185 4.471386 TCTTTCTAGTGCAGAAGCCCTAAT 59.529 41.667 0.00 0.00 44.10 1.73
186 188 2.260822 TCTTTCTAGTGCAGAAGCCCT 58.739 47.619 0.00 0.00 44.10 5.19
195 197 3.056179 AGGAGTGCTCTTCTTTCTAGTGC 60.056 47.826 0.00 0.00 33.84 4.40
210 212 2.038659 AGAGCCTATGAAGAGGAGTGC 58.961 52.381 0.00 0.00 39.15 4.40
217 219 3.577919 GGGGAGTTAGAGCCTATGAAGA 58.422 50.000 0.00 0.00 0.00 2.87
269 271 0.543646 AAGGCCTTGGCATCTTGCTT 60.544 50.000 19.73 3.62 44.28 3.91
272 274 0.245539 CACAAGGCCTTGGCATCTTG 59.754 55.000 41.04 27.95 44.45 3.02
288 295 1.336240 CGTCATGCTCTGAGACACACA 60.336 52.381 9.28 0.00 33.51 3.72
322 329 0.166814 GGAACGTGCATTGTGAGCTC 59.833 55.000 6.82 6.82 0.00 4.09
340 347 1.612950 CGGATGGAGTCATCTCTCTGG 59.387 57.143 6.37 0.00 46.70 3.86
341 348 2.580962 TCGGATGGAGTCATCTCTCTG 58.419 52.381 6.37 0.00 46.70 3.35
371 378 0.817634 CACCGTGACAAGGCCAAGAA 60.818 55.000 5.01 0.00 0.00 2.52
372 379 1.227823 CACCGTGACAAGGCCAAGA 60.228 57.895 5.01 0.00 0.00 3.02
401 408 1.017387 GTCGATTCCAAGTGGGCATC 58.983 55.000 0.00 0.00 36.21 3.91
415 422 4.277476 AGTCTGAGAAGGATCTTGTCGAT 58.723 43.478 0.00 0.00 35.54 3.59
541 548 8.592809 TGCAAATACCATGGTAATCTTTTTCTT 58.407 29.630 27.93 11.74 33.99 2.52
542 549 8.133024 TGCAAATACCATGGTAATCTTTTTCT 57.867 30.769 27.93 5.87 33.99 2.52
543 550 8.947055 ATGCAAATACCATGGTAATCTTTTTC 57.053 30.769 27.93 17.40 33.99 2.29
544 551 8.761689 AGATGCAAATACCATGGTAATCTTTTT 58.238 29.630 27.93 19.33 33.99 1.94
545 552 8.199449 CAGATGCAAATACCATGGTAATCTTTT 58.801 33.333 27.93 19.68 33.99 2.27
546 553 7.201938 CCAGATGCAAATACCATGGTAATCTTT 60.202 37.037 27.93 20.02 33.99 2.52
547 554 6.266103 CCAGATGCAAATACCATGGTAATCTT 59.734 38.462 27.93 17.77 33.99 2.40
548 555 5.771666 CCAGATGCAAATACCATGGTAATCT 59.228 40.000 27.93 24.65 33.99 2.40
549 556 5.769662 TCCAGATGCAAATACCATGGTAATC 59.230 40.000 27.93 23.02 33.99 1.75
550 557 5.536161 GTCCAGATGCAAATACCATGGTAAT 59.464 40.000 27.93 17.81 33.99 1.89
551 558 4.887071 GTCCAGATGCAAATACCATGGTAA 59.113 41.667 27.93 12.08 33.99 2.85
552 559 4.460263 GTCCAGATGCAAATACCATGGTA 58.540 43.478 26.54 26.54 34.87 3.25
553 560 3.290710 GTCCAGATGCAAATACCATGGT 58.709 45.455 23.55 23.55 0.00 3.55
555 562 3.205338 TCGTCCAGATGCAAATACCATG 58.795 45.455 0.00 0.00 0.00 3.66
557 564 3.558931 ATCGTCCAGATGCAAATACCA 57.441 42.857 0.00 0.00 38.36 3.25
568 575 2.202919 CCGCATGCATCGTCCAGA 60.203 61.111 19.57 0.00 0.00 3.86
570 577 0.179059 ATAACCGCATGCATCGTCCA 60.179 50.000 19.57 2.81 0.00 4.02
571 578 0.944386 AATAACCGCATGCATCGTCC 59.056 50.000 19.57 0.00 0.00 4.79
572 579 2.755836 AAATAACCGCATGCATCGTC 57.244 45.000 19.57 0.27 0.00 4.20
574 581 7.795431 ATTAATAAAATAACCGCATGCATCG 57.205 32.000 19.57 6.69 0.00 3.84
611 650 4.881850 CGGAGGGAGTGCTATTTTACAAAT 59.118 41.667 0.00 0.00 0.00 2.32
615 654 3.814005 TCGGAGGGAGTGCTATTTTAC 57.186 47.619 0.00 0.00 0.00 2.01
616 655 4.202326 GGAATCGGAGGGAGTGCTATTTTA 60.202 45.833 0.00 0.00 0.00 1.52
620 659 1.133009 AGGAATCGGAGGGAGTGCTAT 60.133 52.381 0.00 0.00 39.75 2.97
622 661 0.261991 TAGGAATCGGAGGGAGTGCT 59.738 55.000 0.00 0.00 43.95 4.40
623 662 1.120530 TTAGGAATCGGAGGGAGTGC 58.879 55.000 0.00 0.00 0.00 4.40
624 663 5.746990 ATATTTAGGAATCGGAGGGAGTG 57.253 43.478 0.00 0.00 0.00 3.51
625 664 7.017531 ACTTATATTTAGGAATCGGAGGGAGT 58.982 38.462 0.00 0.00 0.00 3.85
626 665 7.483580 ACTTATATTTAGGAATCGGAGGGAG 57.516 40.000 0.00 0.00 0.00 4.30
627 666 7.867160 AACTTATATTTAGGAATCGGAGGGA 57.133 36.000 0.00 0.00 0.00 4.20
628 667 8.784043 CAAAACTTATATTTAGGAATCGGAGGG 58.216 37.037 0.00 0.00 0.00 4.30
629 668 9.338622 ACAAAACTTATATTTAGGAATCGGAGG 57.661 33.333 0.00 0.00 0.00 4.30
658 697 9.355215 CTTCGTATGTAGTTTGTAGTGAAATCT 57.645 33.333 0.00 0.00 0.00 2.40
659 698 8.108782 GCTTCGTATGTAGTTTGTAGTGAAATC 58.891 37.037 0.00 0.00 0.00 2.17
661 700 6.924612 TGCTTCGTATGTAGTTTGTAGTGAAA 59.075 34.615 0.00 0.00 0.00 2.69
663 702 6.016213 TGCTTCGTATGTAGTTTGTAGTGA 57.984 37.500 0.00 0.00 0.00 3.41
664 703 6.699895 TTGCTTCGTATGTAGTTTGTAGTG 57.300 37.500 0.00 0.00 0.00 2.74
665 704 7.718272 TTTTGCTTCGTATGTAGTTTGTAGT 57.282 32.000 0.00 0.00 0.00 2.73
666 705 8.492748 TCTTTTTGCTTCGTATGTAGTTTGTAG 58.507 33.333 0.00 0.00 0.00 2.74
668 707 7.012044 ACTCTTTTTGCTTCGTATGTAGTTTGT 59.988 33.333 0.00 0.00 0.00 2.83
669 708 7.352739 ACTCTTTTTGCTTCGTATGTAGTTTG 58.647 34.615 0.00 0.00 0.00 2.93
673 1048 9.690434 GATTTACTCTTTTTGCTTCGTATGTAG 57.310 33.333 0.00 0.00 0.00 2.74
679 1054 7.441458 AGTGTAGATTTACTCTTTTTGCTTCGT 59.559 33.333 0.00 0.00 35.28 3.85
712 1095 9.259832 ACTATGAACCACATATATCTAGATGCA 57.740 33.333 15.79 3.10 40.18 3.96
713 1096 9.526713 CACTATGAACCACATATATCTAGATGC 57.473 37.037 15.79 0.00 40.18 3.91
723 1106 8.976353 GGAGAGATATCACTATGAACCACATAT 58.024 37.037 5.32 0.00 40.18 1.78
724 1107 7.950124 TGGAGAGATATCACTATGAACCACATA 59.050 37.037 5.32 0.00 40.07 2.29
725 1108 6.784473 TGGAGAGATATCACTATGAACCACAT 59.216 38.462 5.32 0.00 42.39 3.21
726 1109 6.136155 TGGAGAGATATCACTATGAACCACA 58.864 40.000 5.32 0.00 0.00 4.17
728 1111 7.565029 TCTTTGGAGAGATATCACTATGAACCA 59.435 37.037 5.32 4.63 0.00 3.67
729 1112 7.870445 GTCTTTGGAGAGATATCACTATGAACC 59.130 40.741 5.32 2.03 31.07 3.62
732 1115 8.774546 AAGTCTTTGGAGAGATATCACTATGA 57.225 34.615 5.32 0.00 31.07 2.15
744 1127 9.250624 CGTTCCTAAATATAAGTCTTTGGAGAG 57.749 37.037 0.00 0.00 31.07 3.20
746 1129 8.202137 TCCGTTCCTAAATATAAGTCTTTGGAG 58.798 37.037 0.00 0.00 0.00 3.86
747 1130 8.081517 TCCGTTCCTAAATATAAGTCTTTGGA 57.918 34.615 0.00 0.00 0.00 3.53
748 1131 7.441458 CCTCCGTTCCTAAATATAAGTCTTTGG 59.559 40.741 0.00 0.00 0.00 3.28
751 1134 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
753 1136 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
754 1137 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
755 1138 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
756 1139 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
757 1140 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
758 1141 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
759 1142 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
763 1146 2.512896 AGATGTACTCCCTCCGTTCCTA 59.487 50.000 0.00 0.00 0.00 2.94
764 1147 1.288335 AGATGTACTCCCTCCGTTCCT 59.712 52.381 0.00 0.00 0.00 3.36
765 1148 1.777941 AGATGTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
766 1149 4.737055 GCTTAAGATGTACTCCCTCCGTTC 60.737 50.000 6.67 0.00 0.00 3.95
767 1150 3.132467 GCTTAAGATGTACTCCCTCCGTT 59.868 47.826 6.67 0.00 0.00 4.44
768 1151 2.694109 GCTTAAGATGTACTCCCTCCGT 59.306 50.000 6.67 0.00 0.00 4.69
769 1152 2.036089 GGCTTAAGATGTACTCCCTCCG 59.964 54.545 6.67 0.00 0.00 4.63
770 1153 3.039011 TGGCTTAAGATGTACTCCCTCC 58.961 50.000 6.67 0.00 0.00 4.30
771 1154 3.491104 CGTGGCTTAAGATGTACTCCCTC 60.491 52.174 6.67 0.00 0.00 4.30
772 1155 2.431057 CGTGGCTTAAGATGTACTCCCT 59.569 50.000 6.67 0.00 0.00 4.20
773 1156 2.822764 CGTGGCTTAAGATGTACTCCC 58.177 52.381 6.67 0.00 0.00 4.30
774 1157 2.202566 GCGTGGCTTAAGATGTACTCC 58.797 52.381 6.67 0.00 0.00 3.85
775 1158 2.159085 AGGCGTGGCTTAAGATGTACTC 60.159 50.000 6.67 0.00 0.00 2.59
776 1159 1.831736 AGGCGTGGCTTAAGATGTACT 59.168 47.619 6.67 0.00 0.00 2.73
777 1160 2.311124 AGGCGTGGCTTAAGATGTAC 57.689 50.000 6.67 0.00 0.00 2.90
779 1162 2.906354 CTAAGGCGTGGCTTAAGATGT 58.094 47.619 15.53 0.00 0.00 3.06
780 1163 1.599542 GCTAAGGCGTGGCTTAAGATG 59.400 52.381 15.53 6.58 0.00 2.90
782 1165 0.611200 TGCTAAGGCGTGGCTTAAGA 59.389 50.000 15.53 4.09 42.25 2.10
783 1166 1.130561 GTTGCTAAGGCGTGGCTTAAG 59.869 52.381 15.53 11.11 42.25 1.85
784 1167 1.161843 GTTGCTAAGGCGTGGCTTAA 58.838 50.000 15.53 2.15 42.25 1.85
786 1169 0.955919 GAGTTGCTAAGGCGTGGCTT 60.956 55.000 13.45 13.45 42.25 4.35
788 1171 2.399356 GGAGTTGCTAAGGCGTGGC 61.399 63.158 1.10 1.10 42.25 5.01
790 1173 2.604046 ATAGGAGTTGCTAAGGCGTG 57.396 50.000 0.00 0.00 42.25 5.34
792 1175 2.866762 GTGAATAGGAGTTGCTAAGGCG 59.133 50.000 0.00 0.00 42.25 5.52
795 1178 5.452636 GGAGGAGTGAATAGGAGTTGCTAAG 60.453 48.000 0.00 0.00 0.00 2.18
796 1179 4.406003 GGAGGAGTGAATAGGAGTTGCTAA 59.594 45.833 0.00 0.00 0.00 3.09
797 1180 3.961408 GGAGGAGTGAATAGGAGTTGCTA 59.039 47.826 0.00 0.00 0.00 3.49
798 1181 2.769095 GGAGGAGTGAATAGGAGTTGCT 59.231 50.000 0.00 0.00 0.00 3.91
799 1182 2.158885 GGGAGGAGTGAATAGGAGTTGC 60.159 54.545 0.00 0.00 0.00 4.17
800 1183 2.101582 CGGGAGGAGTGAATAGGAGTTG 59.898 54.545 0.00 0.00 0.00 3.16
801 1184 2.389715 CGGGAGGAGTGAATAGGAGTT 58.610 52.381 0.00 0.00 0.00 3.01
803 1186 0.676736 GCGGGAGGAGTGAATAGGAG 59.323 60.000 0.00 0.00 0.00 3.69
805 1188 0.390860 CTGCGGGAGGAGTGAATAGG 59.609 60.000 0.00 0.00 44.01 2.57
807 1190 5.484607 ATTCATCTGCGGGAGGAGTGAATA 61.485 45.833 17.10 1.53 46.16 1.75
814 1197 1.748329 CGGATTCATCTGCGGGAGGA 61.748 60.000 0.00 0.00 32.56 3.71
815 1198 1.301244 CGGATTCATCTGCGGGAGG 60.301 63.158 0.00 0.00 0.00 4.30
931 1993 4.222847 GGCCGGCGAGGTAGAAGG 62.223 72.222 22.54 0.00 43.70 3.46
991 2053 1.604438 CGAGACCACCATTGTCGTTGA 60.604 52.381 0.00 0.00 37.80 3.18
992 2054 0.790207 CGAGACCACCATTGTCGTTG 59.210 55.000 0.00 0.00 37.80 4.10
993 2055 0.391597 ACGAGACCACCATTGTCGTT 59.608 50.000 0.00 0.00 40.84 3.85
994 2056 1.068055 GTACGAGACCACCATTGTCGT 60.068 52.381 1.01 1.01 45.32 4.34
995 2057 1.068125 TGTACGAGACCACCATTGTCG 60.068 52.381 0.00 0.00 37.80 4.35
996 2058 2.334838 GTGTACGAGACCACCATTGTC 58.665 52.381 0.00 0.00 0.00 3.18
997 2059 1.336517 CGTGTACGAGACCACCATTGT 60.337 52.381 0.00 0.00 43.02 2.71
1511 2585 2.180862 TCGCAGATCCTCTCGACGG 61.181 63.158 0.00 0.00 0.00 4.79
1586 2660 2.093447 AGCATGCTCTGTTACCACTACC 60.093 50.000 16.30 0.00 0.00 3.18
1591 2665 0.740868 GCGAGCATGCTCTGTTACCA 60.741 55.000 37.44 0.00 40.69 3.25
1593 2667 3.056628 AGCGAGCATGCTCTGTTAC 57.943 52.632 37.44 23.59 42.95 2.50
1641 2736 6.327934 CAGAATTTCACTTCTTATTGCCTGG 58.672 40.000 0.00 0.00 33.18 4.45
1642 2737 5.803967 GCAGAATTTCACTTCTTATTGCCTG 59.196 40.000 0.00 0.00 33.18 4.85
1666 2761 2.927429 TCAATGGACGTTGCGAATTTG 58.073 42.857 0.00 0.00 0.00 2.32
1677 2772 3.129113 TCCAGCAATTTCATCAATGGACG 59.871 43.478 0.00 0.00 30.63 4.79
1678 2773 4.427312 GTCCAGCAATTTCATCAATGGAC 58.573 43.478 5.77 5.77 45.86 4.02
1688 2783 2.821969 ACATGACAGGTCCAGCAATTTC 59.178 45.455 0.00 0.00 0.00 2.17
1697 2792 1.168714 GCCAAGAACATGACAGGTCC 58.831 55.000 0.00 0.00 0.00 4.46
1701 2796 1.531423 AGCTGCCAAGAACATGACAG 58.469 50.000 0.00 0.00 0.00 3.51
1787 3612 1.865340 GGAAAGAACACCTGTGACGAC 59.135 52.381 3.94 0.00 0.00 4.34
1807 3632 4.499183 AGCACTGAAGTTTTATCCTCTCG 58.501 43.478 0.00 0.00 0.00 4.04
1814 3639 4.520492 CCCTTGTGAGCACTGAAGTTTTAT 59.480 41.667 1.99 0.00 0.00 1.40
1820 3646 1.805869 CTCCCTTGTGAGCACTGAAG 58.194 55.000 1.99 0.00 0.00 3.02
1832 3658 4.335647 ACGGCCACTGCTCCCTTG 62.336 66.667 2.24 0.00 37.74 3.61
1833 3659 4.335647 CACGGCCACTGCTCCCTT 62.336 66.667 2.24 0.00 37.74 3.95
1846 3672 0.439985 CAGTCATCGCAAACTCACGG 59.560 55.000 0.00 0.00 0.00 4.94
1857 3683 1.827969 AGTTTCTCCTCCCAGTCATCG 59.172 52.381 0.00 0.00 0.00 3.84
1879 3705 1.809684 GGCGCACTAGAAGAAACCTT 58.190 50.000 10.83 0.00 0.00 3.50
1921 3747 4.752879 TCGCAGCCGGCCACTTAC 62.753 66.667 26.15 5.28 40.31 2.34
1989 3815 1.270571 GGCGATCCTGAATCTTCTCCC 60.271 57.143 0.00 0.00 31.68 4.30
2015 3841 1.200948 GGTTTACTGGAGTAGACGCGT 59.799 52.381 13.85 13.85 36.73 6.01
2016 3842 1.471684 AGGTTTACTGGAGTAGACGCG 59.528 52.381 3.53 3.53 36.73 6.01
2017 3843 2.877335 CAGGTTTACTGGAGTAGACGC 58.123 52.381 2.40 0.00 43.70 5.19
2054 3886 1.330655 TTCGGACAGGATGCCCTCTC 61.331 60.000 0.00 0.00 42.02 3.20
2055 3887 0.909610 TTTCGGACAGGATGCCCTCT 60.910 55.000 0.00 0.00 42.02 3.69
2056 3888 0.462759 CTTTCGGACAGGATGCCCTC 60.463 60.000 0.00 0.00 42.02 4.30
2057 3889 0.909610 TCTTTCGGACAGGATGCCCT 60.910 55.000 0.00 0.00 45.74 5.19
2058 3890 0.462759 CTCTTTCGGACAGGATGCCC 60.463 60.000 0.00 0.00 42.53 5.36
2118 3954 2.156504 GCTCGCCTACATTCATCATTCG 59.843 50.000 0.00 0.00 0.00 3.34
2125 3961 0.818938 TTACGGCTCGCCTACATTCA 59.181 50.000 6.35 0.00 0.00 2.57
2126 3962 1.066605 TCTTACGGCTCGCCTACATTC 59.933 52.381 6.35 0.00 0.00 2.67
2127 3963 1.108776 TCTTACGGCTCGCCTACATT 58.891 50.000 6.35 0.00 0.00 2.71
2156 3992 9.740710 AAGGCAGAAATATCTTGTAAAGTAAGT 57.259 29.630 0.00 0.00 46.34 2.24
2193 4039 4.262292 GCTGGGACCGAACATACATATGTA 60.262 45.833 17.65 17.65 45.55 2.29
2195 4041 3.067106 GCTGGGACCGAACATACATATG 58.933 50.000 0.00 0.00 39.55 1.78
2196 4042 2.038557 GGCTGGGACCGAACATACATAT 59.961 50.000 0.00 0.00 0.00 1.78
2197 4043 1.414919 GGCTGGGACCGAACATACATA 59.585 52.381 0.00 0.00 0.00 2.29
2198 4044 0.180406 GGCTGGGACCGAACATACAT 59.820 55.000 0.00 0.00 0.00 2.29
2199 4045 1.195442 TGGCTGGGACCGAACATACA 61.195 55.000 0.00 0.00 0.00 2.29
2200 4046 0.462047 CTGGCTGGGACCGAACATAC 60.462 60.000 0.00 0.00 0.00 2.39
2227 4073 1.228063 ATGCGAGGGATCATGTGGC 60.228 57.895 0.00 0.00 0.00 5.01
2228 4074 0.107268 TGATGCGAGGGATCATGTGG 59.893 55.000 0.00 0.00 0.00 4.17
2229 4075 1.871676 CTTGATGCGAGGGATCATGTG 59.128 52.381 0.62 0.00 29.96 3.21
2230 4076 1.764723 TCTTGATGCGAGGGATCATGT 59.235 47.619 10.99 0.00 29.96 3.21
2231 4077 2.538512 TCTTGATGCGAGGGATCATG 57.461 50.000 0.62 4.06 29.96 3.07
2232 4078 4.441217 CGATATCTTGATGCGAGGGATCAT 60.441 45.833 0.34 0.00 29.96 2.45
2233 4079 3.119352 CGATATCTTGATGCGAGGGATCA 60.119 47.826 0.34 0.00 0.00 2.92
2234 4080 3.443037 CGATATCTTGATGCGAGGGATC 58.557 50.000 0.34 0.00 0.00 3.36
2235 4081 2.417924 GCGATATCTTGATGCGAGGGAT 60.418 50.000 0.34 0.00 0.00 3.85
2236 4082 1.067565 GCGATATCTTGATGCGAGGGA 60.068 52.381 0.34 0.00 0.00 4.20
2237 4083 1.067283 AGCGATATCTTGATGCGAGGG 60.067 52.381 0.34 0.00 0.00 4.30
2271 4118 4.244463 ACGTCACCAACACCGGGG 62.244 66.667 0.00 0.00 0.00 5.73
2273 4120 2.202960 ACACGTCACCAACACCGG 60.203 61.111 0.00 0.00 0.00 5.28
2298 4145 6.481313 CCTGATGTGTGTATCTGGATTGTTAG 59.519 42.308 5.96 0.00 44.46 2.34
2313 4160 2.268920 CCGGTCCCCTGATGTGTG 59.731 66.667 0.00 0.00 0.00 3.82
2359 4206 7.219154 CGACGAATAATATCCTAGCTTAGCTTG 59.781 40.741 13.44 10.73 40.44 4.01
2432 4279 3.764049 GACGTGTGCGGCTCGAAC 61.764 66.667 16.17 0.00 44.12 3.95
2442 4289 1.006102 AAGGAAGCCGAGACGTGTG 60.006 57.895 0.00 0.00 0.00 3.82
2443 4290 1.006102 CAAGGAAGCCGAGACGTGT 60.006 57.895 0.00 0.00 0.00 4.49
2444 4291 0.242825 TACAAGGAAGCCGAGACGTG 59.757 55.000 0.00 0.00 0.00 4.49
2449 4296 2.002586 CATGTGTACAAGGAAGCCGAG 58.997 52.381 0.00 0.00 0.00 4.63
2452 4299 0.447801 CGCATGTGTACAAGGAAGCC 59.552 55.000 0.00 0.00 0.00 4.35
2461 4308 2.436646 AGGCTGGCGCATGTGTAC 60.437 61.111 10.83 2.20 38.10 2.90
2464 4311 3.200593 GAGAGGCTGGCGCATGTG 61.201 66.667 10.83 0.66 38.10 3.21
2485 4332 3.427528 GGTGCCACGTATACAACATATCG 59.572 47.826 3.32 0.00 0.00 2.92
2488 4335 2.481622 CGGGTGCCACGTATACAACATA 60.482 50.000 3.32 0.00 0.00 2.29
2495 4342 3.075641 TGCCGGGTGCCACGTATA 61.076 61.111 2.18 0.00 40.16 1.47
2496 4343 4.770874 GTGCCGGGTGCCACGTAT 62.771 66.667 2.18 0.00 40.16 3.06
2507 4354 2.549064 TAATGATGATGAGGTGCCGG 57.451 50.000 0.00 0.00 0.00 6.13
2524 4371 9.362539 CCGTGATTCTAGCTTAGTTTAGTTTAA 57.637 33.333 0.00 0.00 0.00 1.52
2525 4372 7.490402 GCCGTGATTCTAGCTTAGTTTAGTTTA 59.510 37.037 0.00 0.00 0.00 2.01
2526 4373 6.313164 GCCGTGATTCTAGCTTAGTTTAGTTT 59.687 38.462 0.00 0.00 0.00 2.66
2527 4374 5.811100 GCCGTGATTCTAGCTTAGTTTAGTT 59.189 40.000 0.00 0.00 0.00 2.24
2529 4376 5.348986 TGCCGTGATTCTAGCTTAGTTTAG 58.651 41.667 0.00 0.00 0.00 1.85
2530 4377 5.333299 TGCCGTGATTCTAGCTTAGTTTA 57.667 39.130 0.00 0.00 0.00 2.01
2531 4378 4.202245 TGCCGTGATTCTAGCTTAGTTT 57.798 40.909 0.00 0.00 0.00 2.66
2532 4379 3.887621 TGCCGTGATTCTAGCTTAGTT 57.112 42.857 0.00 0.00 0.00 2.24
2537 4384 1.339055 TGCTTTGCCGTGATTCTAGCT 60.339 47.619 0.00 0.00 0.00 3.32
2538 4385 1.086696 TGCTTTGCCGTGATTCTAGC 58.913 50.000 0.00 0.00 0.00 3.42
2539 4386 2.744202 ACTTGCTTTGCCGTGATTCTAG 59.256 45.455 0.00 0.00 0.00 2.43
2541 4388 1.267806 CACTTGCTTTGCCGTGATTCT 59.732 47.619 3.98 0.00 33.11 2.40
2542 4389 1.266718 TCACTTGCTTTGCCGTGATTC 59.733 47.619 7.39 0.00 34.70 2.52
2543 4390 1.001378 GTCACTTGCTTTGCCGTGATT 60.001 47.619 12.38 0.00 39.07 2.57
2544 4391 0.593128 GTCACTTGCTTTGCCGTGAT 59.407 50.000 12.38 0.00 39.07 3.06
2545 4392 1.771073 CGTCACTTGCTTTGCCGTGA 61.771 55.000 7.39 7.39 36.29 4.35
2546 4393 1.369209 CGTCACTTGCTTTGCCGTG 60.369 57.895 0.00 0.00 32.79 4.94
2547 4394 3.022287 CGTCACTTGCTTTGCCGT 58.978 55.556 0.00 0.00 0.00 5.68
2548 4395 2.427410 GCGTCACTTGCTTTGCCG 60.427 61.111 0.00 0.00 0.00 5.69
2549 4396 1.065600 TTGCGTCACTTGCTTTGCC 59.934 52.632 0.00 0.00 0.00 4.52
2550 4397 1.531522 CGTTGCGTCACTTGCTTTGC 61.532 55.000 0.00 0.00 0.00 3.68
2551 4398 0.027455 TCGTTGCGTCACTTGCTTTG 59.973 50.000 0.00 0.00 0.00 2.77
2552 4399 0.304705 CTCGTTGCGTCACTTGCTTT 59.695 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.