Multiple sequence alignment - TraesCS6B01G354000

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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 TraesCS6B01G354000 chr6B 100.000 2880 0 0 1 2880 619727575 619730454 0.000000e+00 5319.0
1 TraesCS6B01G354000 chr6B 93.239 710 25 6 2192 2880 31585460 31584753 0.000000e+00 1024.0
2 TraesCS6B01G354000 chr6A 88.812 1305 76 39 879 2157 556887093 556888353 0.000000e+00 1537.0
3 TraesCS6B01G354000 chr6D 92.518 842 42 10 879 1717 411921751 411922574 0.000000e+00 1186.0
4 TraesCS6B01G354000 chr6D 93.510 416 14 6 1713 2123 411922601 411923008 8.830000e-170 606.0
5 TraesCS6B01G354000 chr6D 90.637 267 21 4 246 511 411920516 411920779 4.570000e-93 351.0
6 TraesCS6B01G354000 chr6D 87.600 250 23 5 3 246 411919643 411919890 1.690000e-72 283.0
7 TraesCS6B01G354000 chr6D 98.276 58 1 0 601 658 411920782 411920839 5.080000e-18 102.0
8 TraesCS6B01G354000 chr6D 98.039 51 1 0 672 722 411921578 411921628 3.950000e-14 89.8
9 TraesCS6B01G354000 chr6D 86.420 81 10 1 530 609 272859299 272859219 1.420000e-13 87.9
10 TraesCS6B01G354000 chr6D 90.323 62 6 0 536 597 60856280 60856219 6.610000e-12 82.4
11 TraesCS6B01G354000 chr6D 93.478 46 3 0 530 575 456337185 456337140 5.150000e-08 69.4
12 TraesCS6B01G354000 chr1B 95.245 694 27 4 2190 2880 674470634 674469944 0.000000e+00 1094.0
13 TraesCS6B01G354000 chr2B 95.608 683 27 2 2192 2873 477576108 477576788 0.000000e+00 1092.0
14 TraesCS6B01G354000 chr2B 91.176 68 6 0 530 597 185416690 185416757 3.060000e-15 93.5
15 TraesCS6B01G354000 chr3B 95.231 692 26 5 2192 2880 816527536 816526849 0.000000e+00 1088.0
16 TraesCS6B01G354000 chr3B 93.918 707 21 4 2193 2880 617428178 617427475 0.000000e+00 1048.0
17 TraesCS6B01G354000 chr3B 93.497 692 39 4 2190 2880 56452207 56451521 0.000000e+00 1024.0
18 TraesCS6B01G354000 chr3B 91.489 705 36 7 2192 2880 596851978 596851282 0.000000e+00 948.0
19 TraesCS6B01G354000 chr3B 91.176 68 6 0 530 597 727791265 727791332 3.060000e-15 93.5
20 TraesCS6B01G354000 chr4B 94.058 690 35 4 2192 2880 86058237 86057553 0.000000e+00 1042.0
21 TraesCS6B01G354000 chr4B 90.367 654 32 12 2192 2834 568635514 568636147 0.000000e+00 830.0
22 TraesCS6B01G354000 chr5B 93.324 689 30 11 2192 2880 417804471 417803799 0.000000e+00 1003.0
23 TraesCS6B01G354000 chr5B 88.745 693 30 14 2192 2873 637116953 637117608 0.000000e+00 804.0
24 TraesCS6B01G354000 chr5B 90.000 70 5 2 536 604 485488922 485488854 3.950000e-14 89.8
25 TraesCS6B01G354000 chr7B 93.113 697 27 14 2202 2880 400639844 400640537 0.000000e+00 1002.0
26 TraesCS6B01G354000 chr7B 93.284 268 17 1 2192 2459 119240487 119240753 7.480000e-106 394.0
27 TraesCS6B01G354000 chr2A 91.176 68 6 0 530 597 41744503 41744436 3.060000e-15 93.5
28 TraesCS6B01G354000 chrUn 87.179 78 10 0 530 607 63661354 63661431 3.950000e-14 89.8
29 TraesCS6B01G354000 chr7D 89.706 68 7 0 530 597 6484541 6484474 1.420000e-13 87.9
30 TraesCS6B01G354000 chr7D 89.706 68 7 0 530 597 251035995 251035928 1.420000e-13 87.9
31 TraesCS6B01G354000 chr7D 89.706 68 7 0 530 597 386760805 386760872 1.420000e-13 87.9
32 TraesCS6B01G354000 chr4A 88.000 75 7 2 530 603 735001630 735001557 1.420000e-13 87.9
33 TraesCS6B01G354000 chr3D 89.706 68 7 0 530 597 606951363 606951430 1.420000e-13 87.9
34 TraesCS6B01G354000 chr3D 88.235 68 8 0 530 597 27895304 27895371 6.610000e-12 82.4
35 TraesCS6B01G354000 chr3D 90.323 62 6 0 536 597 235522802 235522741 6.610000e-12 82.4
36 TraesCS6B01G354000 chr2D 89.706 68 7 0 530 597 340252797 340252864 1.420000e-13 87.9
37 TraesCS6B01G354000 chr2D 89.706 68 5 2 530 596 565942893 565942827 5.110000e-13 86.1
38 TraesCS6B01G354000 chr1A 89.706 68 7 0 530 597 312159852 312159785 1.420000e-13 87.9
39 TraesCS6B01G354000 chr4D 88.235 68 8 0 530 597 144556586 144556653 6.610000e-12 82.4
40 TraesCS6B01G354000 chr4D 88.235 68 8 0 530 597 394190896 394190963 6.610000e-12 82.4
41 TraesCS6B01G354000 chr1D 88.235 68 8 0 530 597 406733847 406733914 6.610000e-12 82.4
42 TraesCS6B01G354000 chr1D 89.062 64 7 0 534 597 73688136 73688073 2.380000e-11 80.5
43 TraesCS6B01G354000 chr1D 87.692 65 8 0 530 594 420647344 420647408 3.080000e-10 76.8


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 TraesCS6B01G354000 chr6B 619727575 619730454 2879 False 5319.0 5319 100.000 1 2880 1 chr6B.!!$F1 2879
1 TraesCS6B01G354000 chr6B 31584753 31585460 707 True 1024.0 1024 93.239 2192 2880 1 chr6B.!!$R1 688
2 TraesCS6B01G354000 chr6A 556887093 556888353 1260 False 1537.0 1537 88.812 879 2157 1 chr6A.!!$F1 1278
3 TraesCS6B01G354000 chr6D 411919643 411923008 3365 False 436.3 1186 93.430 3 2123 6 chr6D.!!$F1 2120
4 TraesCS6B01G354000 chr1B 674469944 674470634 690 True 1094.0 1094 95.245 2190 2880 1 chr1B.!!$R1 690
5 TraesCS6B01G354000 chr2B 477576108 477576788 680 False 1092.0 1092 95.608 2192 2873 1 chr2B.!!$F2 681
6 TraesCS6B01G354000 chr3B 816526849 816527536 687 True 1088.0 1088 95.231 2192 2880 1 chr3B.!!$R4 688
7 TraesCS6B01G354000 chr3B 617427475 617428178 703 True 1048.0 1048 93.918 2193 2880 1 chr3B.!!$R3 687
8 TraesCS6B01G354000 chr3B 56451521 56452207 686 True 1024.0 1024 93.497 2190 2880 1 chr3B.!!$R1 690
9 TraesCS6B01G354000 chr3B 596851282 596851978 696 True 948.0 948 91.489 2192 2880 1 chr3B.!!$R2 688
10 TraesCS6B01G354000 chr4B 86057553 86058237 684 True 1042.0 1042 94.058 2192 2880 1 chr4B.!!$R1 688
11 TraesCS6B01G354000 chr4B 568635514 568636147 633 False 830.0 830 90.367 2192 2834 1 chr4B.!!$F1 642
12 TraesCS6B01G354000 chr5B 417803799 417804471 672 True 1003.0 1003 93.324 2192 2880 1 chr5B.!!$R1 688
13 TraesCS6B01G354000 chr5B 637116953 637117608 655 False 804.0 804 88.745 2192 2873 1 chr5B.!!$F1 681
14 TraesCS6B01G354000 chr7B 400639844 400640537 693 False 1002.0 1002 93.113 2202 2880 1 chr7B.!!$F2 678

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
813 2189 0.10741 TGGAGCAAACGGTGTGACTT 60.107 50.0 1.57 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 3614 0.318762 CTCTTATGGCCCGCCTAGTC 59.681 60.0 7.35 0.0 36.94 2.59 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
246 253 8.006298 TGTTCAGTTTTCCAGTTAATGTTCAT 57.994 30.769 0.00 0.00 0.00 2.57
247 254 7.920151 TGTTCAGTTTTCCAGTTAATGTTCATG 59.080 33.333 0.00 0.00 0.00 3.07
249 256 8.408043 TCAGTTTTCCAGTTAATGTTCATGAT 57.592 30.769 0.00 0.00 0.00 2.45
250 257 8.859090 TCAGTTTTCCAGTTAATGTTCATGATT 58.141 29.630 0.00 0.00 0.00 2.57
251 258 9.480053 CAGTTTTCCAGTTAATGTTCATGATTT 57.520 29.630 0.00 0.00 0.00 2.17
284 916 6.209192 TGTCCACAATTTAGCAGAATGTTCAT 59.791 34.615 0.00 0.00 39.31 2.57
419 1051 3.485346 AAAGGGAGCGCCGGAAACA 62.485 57.895 5.05 0.00 33.83 2.83
448 1080 2.977178 AGCAGCTTAGAGCACGCT 59.023 55.556 10.03 10.03 45.56 5.07
450 1082 0.532573 AGCAGCTTAGAGCACGCTAA 59.467 50.000 13.10 0.00 46.09 3.09
451 1083 0.926846 GCAGCTTAGAGCACGCTAAG 59.073 55.000 14.56 14.56 45.56 2.18
511 1144 2.097038 CCAACGAGCGCTTCTCAGG 61.097 63.158 13.26 6.93 41.98 3.86
513 1146 0.109272 CAACGAGCGCTTCTCAGGTA 60.109 55.000 13.26 0.00 41.98 3.08
514 1147 0.818296 AACGAGCGCTTCTCAGGTAT 59.182 50.000 13.26 0.00 41.98 2.73
515 1148 0.818296 ACGAGCGCTTCTCAGGTATT 59.182 50.000 13.26 0.00 41.98 1.89
516 1149 1.202313 ACGAGCGCTTCTCAGGTATTC 60.202 52.381 13.26 0.00 41.98 1.75
517 1150 1.859383 GAGCGCTTCTCAGGTATTCC 58.141 55.000 13.26 0.00 41.51 3.01
518 1151 0.466124 AGCGCTTCTCAGGTATTCCC 59.534 55.000 2.64 0.00 0.00 3.97
520 1153 1.539280 GCGCTTCTCAGGTATTCCCTC 60.539 57.143 0.00 0.00 43.86 4.30
521 1154 1.069358 CGCTTCTCAGGTATTCCCTCC 59.931 57.143 0.00 0.00 43.86 4.30
522 1155 1.069358 GCTTCTCAGGTATTCCCTCCG 59.931 57.143 0.00 0.00 43.86 4.63
523 1156 2.389715 CTTCTCAGGTATTCCCTCCGT 58.610 52.381 0.00 0.00 43.86 4.69
524 1157 2.068834 TCTCAGGTATTCCCTCCGTC 57.931 55.000 0.00 0.00 43.86 4.79
525 1158 1.569548 TCTCAGGTATTCCCTCCGTCT 59.430 52.381 0.00 0.00 43.86 4.18
526 1159 1.957877 CTCAGGTATTCCCTCCGTCTC 59.042 57.143 0.00 0.00 43.86 3.36
527 1160 1.286849 TCAGGTATTCCCTCCGTCTCA 59.713 52.381 0.00 0.00 43.86 3.27
528 1161 2.108168 CAGGTATTCCCTCCGTCTCAA 58.892 52.381 0.00 0.00 43.86 3.02
529 1162 2.500098 CAGGTATTCCCTCCGTCTCAAA 59.500 50.000 0.00 0.00 43.86 2.69
530 1163 3.055385 CAGGTATTCCCTCCGTCTCAAAA 60.055 47.826 0.00 0.00 43.86 2.44
531 1164 3.780850 AGGTATTCCCTCCGTCTCAAAAT 59.219 43.478 0.00 0.00 40.71 1.82
532 1165 4.127907 GGTATTCCCTCCGTCTCAAAATC 58.872 47.826 0.00 0.00 0.00 2.17
533 1166 2.781681 TTCCCTCCGTCTCAAAATCC 57.218 50.000 0.00 0.00 0.00 3.01
534 1167 1.952621 TCCCTCCGTCTCAAAATCCT 58.047 50.000 0.00 0.00 0.00 3.24
535 1168 3.110293 TCCCTCCGTCTCAAAATCCTA 57.890 47.619 0.00 0.00 0.00 2.94
536 1169 3.446968 TCCCTCCGTCTCAAAATCCTAA 58.553 45.455 0.00 0.00 0.00 2.69
537 1170 3.841845 TCCCTCCGTCTCAAAATCCTAAA 59.158 43.478 0.00 0.00 0.00 1.85
538 1171 4.287585 TCCCTCCGTCTCAAAATCCTAAAA 59.712 41.667 0.00 0.00 0.00 1.52
539 1172 4.395231 CCCTCCGTCTCAAAATCCTAAAAC 59.605 45.833 0.00 0.00 0.00 2.43
540 1173 4.092968 CCTCCGTCTCAAAATCCTAAAACG 59.907 45.833 0.00 0.00 0.00 3.60
541 1174 4.634199 TCCGTCTCAAAATCCTAAAACGT 58.366 39.130 0.00 0.00 0.00 3.99
542 1175 4.449743 TCCGTCTCAAAATCCTAAAACGTG 59.550 41.667 0.00 0.00 0.00 4.49
543 1176 4.449743 CCGTCTCAAAATCCTAAAACGTGA 59.550 41.667 0.00 0.00 0.00 4.35
544 1177 5.371629 CGTCTCAAAATCCTAAAACGTGAC 58.628 41.667 0.00 0.00 0.00 3.67
545 1178 5.176958 CGTCTCAAAATCCTAAAACGTGACT 59.823 40.000 0.00 0.00 0.00 3.41
546 1179 6.292703 CGTCTCAAAATCCTAAAACGTGACTT 60.293 38.462 0.00 0.00 0.00 3.01
547 1180 6.851330 GTCTCAAAATCCTAAAACGTGACTTG 59.149 38.462 0.00 0.00 0.00 3.16
548 1181 6.764085 TCTCAAAATCCTAAAACGTGACTTGA 59.236 34.615 0.00 0.00 0.00 3.02
549 1182 7.444183 TCTCAAAATCCTAAAACGTGACTTGAT 59.556 33.333 0.00 0.00 0.00 2.57
550 1183 8.610248 TCAAAATCCTAAAACGTGACTTGATA 57.390 30.769 0.00 0.00 0.00 2.15
551 1184 8.500773 TCAAAATCCTAAAACGTGACTTGATAC 58.499 33.333 0.00 0.00 0.00 2.24
552 1185 7.972832 AAATCCTAAAACGTGACTTGATACA 57.027 32.000 0.00 0.00 0.00 2.29
553 1186 8.561738 AAATCCTAAAACGTGACTTGATACAT 57.438 30.769 0.00 0.00 0.00 2.29
554 1187 7.772332 ATCCTAAAACGTGACTTGATACATC 57.228 36.000 0.00 0.00 0.00 3.06
555 1188 6.931838 TCCTAAAACGTGACTTGATACATCT 58.068 36.000 0.00 0.00 0.00 2.90
556 1189 6.811665 TCCTAAAACGTGACTTGATACATCTG 59.188 38.462 0.00 0.00 0.00 2.90
557 1190 6.590292 CCTAAAACGTGACTTGATACATCTGT 59.410 38.462 0.00 0.00 0.00 3.41
558 1191 7.758076 CCTAAAACGTGACTTGATACATCTGTA 59.242 37.037 0.00 0.00 34.67 2.74
559 1192 9.302345 CTAAAACGTGACTTGATACATCTGTAT 57.698 33.333 2.53 2.53 43.38 2.29
560 1193 8.547967 AAAACGTGACTTGATACATCTGTATT 57.452 30.769 4.44 0.00 40.99 1.89
561 1194 8.547967 AAACGTGACTTGATACATCTGTATTT 57.452 30.769 4.44 0.00 40.99 1.40
562 1195 9.647797 AAACGTGACTTGATACATCTGTATTTA 57.352 29.630 4.44 0.00 40.99 1.40
563 1196 8.858003 ACGTGACTTGATACATCTGTATTTAG 57.142 34.615 4.44 7.42 40.99 1.85
564 1197 7.921214 ACGTGACTTGATACATCTGTATTTAGG 59.079 37.037 4.44 1.66 40.99 2.69
565 1198 7.921214 CGTGACTTGATACATCTGTATTTAGGT 59.079 37.037 4.44 4.33 40.99 3.08
576 1209 9.780186 ACATCTGTATTTAGGTAAATCTAAGGC 57.220 33.333 0.00 0.00 37.16 4.35
577 1210 9.778741 CATCTGTATTTAGGTAAATCTAAGGCA 57.221 33.333 0.00 0.00 37.16 4.75
588 1221 9.710900 AGGTAAATCTAAGGCAAAATTTTTGAG 57.289 29.630 22.78 12.38 0.00 3.02
589 1222 9.705290 GGTAAATCTAAGGCAAAATTTTTGAGA 57.295 29.630 22.78 16.45 0.00 3.27
591 1224 7.873739 AATCTAAGGCAAAATTTTTGAGACG 57.126 32.000 22.78 8.52 0.00 4.18
592 1225 5.768317 TCTAAGGCAAAATTTTTGAGACGG 58.232 37.500 22.78 10.66 0.00 4.79
593 1226 4.664150 AAGGCAAAATTTTTGAGACGGA 57.336 36.364 22.78 0.00 0.00 4.69
594 1227 4.243007 AGGCAAAATTTTTGAGACGGAG 57.757 40.909 22.78 0.00 0.00 4.63
595 1228 3.005791 AGGCAAAATTTTTGAGACGGAGG 59.994 43.478 22.78 0.00 0.00 4.30
596 1229 3.317150 GCAAAATTTTTGAGACGGAGGG 58.683 45.455 22.78 0.00 0.00 4.30
597 1230 3.317150 CAAAATTTTTGAGACGGAGGGC 58.683 45.455 15.30 0.00 0.00 5.19
598 1231 1.165270 AATTTTTGAGACGGAGGGCG 58.835 50.000 0.00 0.00 0.00 6.13
599 1232 1.305930 ATTTTTGAGACGGAGGGCGC 61.306 55.000 0.00 0.00 0.00 6.53
619 1252 0.613260 AGTTGCTCCCGTATTGCTCA 59.387 50.000 0.00 0.00 0.00 4.26
666 1299 1.523938 GGGCTCCCGTATTGCTCAC 60.524 63.158 0.00 0.00 0.00 3.51
668 1301 1.522569 GCTCCCGTATTGCTCACCT 59.477 57.895 0.00 0.00 0.00 4.00
669 1302 0.530870 GCTCCCGTATTGCTCACCTC 60.531 60.000 0.00 0.00 0.00 3.85
670 1303 1.115467 CTCCCGTATTGCTCACCTCT 58.885 55.000 0.00 0.00 0.00 3.69
727 2085 8.859236 AGGACCATTAGTACTTAAAAACCTTC 57.141 34.615 0.00 0.00 35.39 3.46
728 2086 8.442374 AGGACCATTAGTACTTAAAAACCTTCA 58.558 33.333 0.00 0.00 35.39 3.02
729 2087 8.727910 GGACCATTAGTACTTAAAAACCTTCAG 58.272 37.037 0.00 0.00 0.00 3.02
731 2089 7.094933 ACCATTAGTACTTAAAAACCTTCAGCG 60.095 37.037 0.00 0.00 0.00 5.18
732 2090 7.118680 CCATTAGTACTTAAAAACCTTCAGCGA 59.881 37.037 0.00 0.00 0.00 4.93
733 2091 8.500773 CATTAGTACTTAAAAACCTTCAGCGAA 58.499 33.333 0.00 0.00 0.00 4.70
734 2092 6.541111 AGTACTTAAAAACCTTCAGCGAAG 57.459 37.500 10.22 10.22 39.17 3.79
735 2093 6.285990 AGTACTTAAAAACCTTCAGCGAAGA 58.714 36.000 16.51 0.00 41.71 2.87
736 2094 5.419760 ACTTAAAAACCTTCAGCGAAGAC 57.580 39.130 16.51 0.00 41.71 3.01
737 2095 5.123936 ACTTAAAAACCTTCAGCGAAGACT 58.876 37.500 16.51 4.03 41.71 3.24
738 2096 5.236695 ACTTAAAAACCTTCAGCGAAGACTC 59.763 40.000 16.51 0.00 41.71 3.36
739 2097 2.910688 AAACCTTCAGCGAAGACTCA 57.089 45.000 16.51 0.00 41.71 3.41
740 2098 3.409026 AAACCTTCAGCGAAGACTCAT 57.591 42.857 16.51 0.53 41.71 2.90
741 2099 2.663826 ACCTTCAGCGAAGACTCATC 57.336 50.000 16.51 0.00 41.71 2.92
742 2100 2.175202 ACCTTCAGCGAAGACTCATCT 58.825 47.619 16.51 0.00 41.71 2.90
743 2101 3.357203 ACCTTCAGCGAAGACTCATCTA 58.643 45.455 16.51 0.00 41.71 1.98
744 2102 3.957497 ACCTTCAGCGAAGACTCATCTAT 59.043 43.478 16.51 0.00 41.71 1.98
745 2103 4.404073 ACCTTCAGCGAAGACTCATCTATT 59.596 41.667 16.51 0.00 41.71 1.73
747 2105 6.096987 ACCTTCAGCGAAGACTCATCTATTTA 59.903 38.462 16.51 0.00 41.71 1.40
748 2106 6.419413 CCTTCAGCGAAGACTCATCTATTTAC 59.581 42.308 16.51 0.00 41.71 2.01
749 2107 5.833082 TCAGCGAAGACTCATCTATTTACC 58.167 41.667 0.00 0.00 33.57 2.85
750 2108 4.677378 CAGCGAAGACTCATCTATTTACCG 59.323 45.833 0.00 0.00 33.57 4.02
751 2109 3.425858 GCGAAGACTCATCTATTTACCGC 59.574 47.826 0.00 0.00 33.57 5.68
753 2111 4.441415 CGAAGACTCATCTATTTACCGCAC 59.559 45.833 0.00 0.00 33.57 5.34
755 2113 4.683832 AGACTCATCTATTTACCGCACAC 58.316 43.478 0.00 0.00 31.46 3.82
756 2114 3.444916 ACTCATCTATTTACCGCACACG 58.555 45.455 0.00 0.00 39.67 4.49
767 2125 2.384309 CGCACACGGACGGCAAATA 61.384 57.895 0.00 0.00 34.97 1.40
768 2126 1.423845 GCACACGGACGGCAAATAG 59.576 57.895 0.00 0.00 0.00 1.73
769 2127 1.977594 GCACACGGACGGCAAATAGG 61.978 60.000 0.00 0.00 0.00 2.57
770 2128 0.390603 CACACGGACGGCAAATAGGA 60.391 55.000 0.00 0.00 0.00 2.94
773 2131 1.597663 CACGGACGGCAAATAGGATTC 59.402 52.381 0.00 0.00 0.00 2.52
774 2132 0.859232 CGGACGGCAAATAGGATTCG 59.141 55.000 0.00 0.00 0.00 3.34
775 2133 1.805120 CGGACGGCAAATAGGATTCGT 60.805 52.381 0.00 0.00 0.00 3.85
792 2168 1.968540 GTCCTTGTGTCCAGCTGCC 60.969 63.158 8.66 0.90 0.00 4.85
794 2170 1.303888 CCTTGTGTCCAGCTGCCAT 60.304 57.895 8.66 0.00 0.00 4.40
795 2171 1.592400 CCTTGTGTCCAGCTGCCATG 61.592 60.000 8.66 4.32 0.00 3.66
797 2173 2.066700 TTGTGTCCAGCTGCCATGGA 62.067 55.000 18.40 6.53 44.63 3.41
800 2176 3.332385 TCCAGCTGCCATGGAGCA 61.332 61.111 27.31 15.24 41.96 4.26
802 2178 1.980232 CCAGCTGCCATGGAGCAAA 60.980 57.895 27.31 5.46 43.52 3.68
803 2179 1.214589 CAGCTGCCATGGAGCAAAC 59.785 57.895 27.31 11.70 43.52 2.93
804 2180 2.180017 GCTGCCATGGAGCAAACG 59.820 61.111 18.40 0.00 43.52 3.60
805 2181 2.879907 CTGCCATGGAGCAAACGG 59.120 61.111 18.40 0.00 43.52 4.44
806 2182 1.973281 CTGCCATGGAGCAAACGGT 60.973 57.895 18.40 0.00 43.52 4.83
807 2183 2.203972 CTGCCATGGAGCAAACGGTG 62.204 60.000 18.40 0.00 43.52 4.94
809 2185 1.580942 CCATGGAGCAAACGGTGTG 59.419 57.895 5.56 0.00 0.00 3.82
810 2186 0.888736 CCATGGAGCAAACGGTGTGA 60.889 55.000 5.56 0.00 0.00 3.58
812 2188 0.108585 ATGGAGCAAACGGTGTGACT 59.891 50.000 1.57 0.00 0.00 3.41
813 2189 0.107410 TGGAGCAAACGGTGTGACTT 60.107 50.000 1.57 0.00 0.00 3.01
814 2190 0.307760 GGAGCAAACGGTGTGACTTG 59.692 55.000 1.57 0.00 0.00 3.16
815 2191 0.317020 GAGCAAACGGTGTGACTTGC 60.317 55.000 1.57 4.42 43.56 4.01
816 2192 1.299089 GCAAACGGTGTGACTTGCC 60.299 57.895 1.57 0.00 38.56 4.52
817 2193 1.724582 GCAAACGGTGTGACTTGCCT 61.725 55.000 1.57 0.00 38.56 4.75
818 2194 1.588674 CAAACGGTGTGACTTGCCTA 58.411 50.000 0.00 0.00 0.00 3.93
819 2195 1.944024 CAAACGGTGTGACTTGCCTAA 59.056 47.619 0.00 0.00 0.00 2.69
820 2196 1.878953 AACGGTGTGACTTGCCTAAG 58.121 50.000 0.00 0.00 39.86 2.18
821 2197 1.045407 ACGGTGTGACTTGCCTAAGA 58.955 50.000 0.00 0.00 37.36 2.10
822 2198 1.414919 ACGGTGTGACTTGCCTAAGAA 59.585 47.619 0.00 0.00 37.36 2.52
823 2199 2.158871 ACGGTGTGACTTGCCTAAGAAA 60.159 45.455 0.00 0.00 37.36 2.52
824 2200 2.875933 CGGTGTGACTTGCCTAAGAAAA 59.124 45.455 0.00 0.00 37.36 2.29
825 2201 3.314080 CGGTGTGACTTGCCTAAGAAAAA 59.686 43.478 0.00 0.00 37.36 1.94
847 2223 2.725815 GCAAACGGTGCGACTTGC 60.726 61.111 0.00 0.00 45.10 4.01
848 2224 2.051345 CAAACGGTGCGACTTGCC 60.051 61.111 0.00 0.00 45.60 4.52
849 2225 2.203153 AAACGGTGCGACTTGCCT 60.203 55.556 0.00 0.00 45.60 4.75
857 2233 2.292292 GGTGCGACTTGCCTAAGAAAAA 59.708 45.455 0.00 0.00 45.60 1.94
875 2251 2.844122 AAAAGAGCAAACGGTGTGAC 57.156 45.000 1.57 0.00 0.00 3.67
876 2252 2.038387 AAAGAGCAAACGGTGTGACT 57.962 45.000 1.57 0.00 0.00 3.41
877 2253 2.038387 AAGAGCAAACGGTGTGACTT 57.962 45.000 1.57 4.16 0.00 3.01
973 2351 0.474660 GCACCATCCCTATCCCCTCT 60.475 60.000 0.00 0.00 0.00 3.69
974 2352 1.650528 CACCATCCCTATCCCCTCTC 58.349 60.000 0.00 0.00 0.00 3.20
983 2361 0.423956 TATCCCCTCTCCAAACCCCA 59.576 55.000 0.00 0.00 0.00 4.96
985 2363 1.852626 CCCCTCTCCAAACCCCACT 60.853 63.158 0.00 0.00 0.00 4.00
987 2365 0.482887 CCCTCTCCAAACCCCACTTT 59.517 55.000 0.00 0.00 0.00 2.66
988 2366 1.620822 CCTCTCCAAACCCCACTTTG 58.379 55.000 0.00 0.00 0.00 2.77
1009 2390 0.251832 ATCCATCCCTATCGCCGTCT 60.252 55.000 0.00 0.00 0.00 4.18
1010 2391 0.894184 TCCATCCCTATCGCCGTCTC 60.894 60.000 0.00 0.00 0.00 3.36
1011 2392 0.896019 CCATCCCTATCGCCGTCTCT 60.896 60.000 0.00 0.00 0.00 3.10
1050 2432 4.089757 CTTCCTCCCCTCCCCCGA 62.090 72.222 0.00 0.00 0.00 5.14
1051 2433 4.089757 TTCCTCCCCTCCCCCGAG 62.090 72.222 0.00 0.00 35.72 4.63
1072 2454 4.012895 CCTCACGCACGCACAACC 62.013 66.667 0.00 0.00 0.00 3.77
1360 2745 3.081409 CCCCGTCTTCCCCGTCAT 61.081 66.667 0.00 0.00 0.00 3.06
1383 2768 1.532604 CGACTACTGGGTGCTCCACA 61.533 60.000 7.20 1.73 41.46 4.17
1397 2782 1.099295 TCCACATCGACGACGCCTAT 61.099 55.000 0.00 0.00 39.58 2.57
1402 2787 1.529865 CATCGACGACGCCTATCAGTA 59.470 52.381 0.00 0.00 39.58 2.74
1458 2843 5.909477 TCTGGGTACGTAATTCGATTGAAT 58.091 37.500 2.01 2.01 46.75 2.57
1467 2852 1.164411 TTCGATTGAATTGCGGTGCT 58.836 45.000 0.00 0.00 0.00 4.40
1470 2855 0.527565 GATTGAATTGCGGTGCTGGT 59.472 50.000 0.00 0.00 0.00 4.00
1473 2858 2.203480 AATTGCGGTGCTGGTGGT 60.203 55.556 0.00 0.00 0.00 4.16
1486 2871 2.364324 GCTGGTGGTGGTAGATCGATAA 59.636 50.000 0.00 0.00 0.00 1.75
1504 2889 5.304357 TCGATAACCAATCTAATCTCTGCCA 59.696 40.000 0.00 0.00 31.87 4.92
1505 2890 6.014242 TCGATAACCAATCTAATCTCTGCCAT 60.014 38.462 0.00 0.00 31.87 4.40
1507 2892 5.378230 AACCAATCTAATCTCTGCCATGA 57.622 39.130 0.00 0.00 0.00 3.07
1564 2949 4.147449 CGCAGATGGACGAGGGCA 62.147 66.667 0.00 0.00 0.00 5.36
1570 2955 0.464036 GATGGACGAGGGCATGTACA 59.536 55.000 0.00 0.00 32.49 2.90
1617 3002 0.390124 AAGGGTACGACGTGAGCAAA 59.610 50.000 11.56 0.00 0.00 3.68
1807 3227 0.459585 GTTCGTCGCTGCAGGGAATA 60.460 55.000 32.30 20.97 38.76 1.75
1843 3267 4.782195 GCTTGTTTGTGTCGAACTGTAGTG 60.782 45.833 0.00 0.00 0.00 2.74
1844 3268 4.112716 TGTTTGTGTCGAACTGTAGTGA 57.887 40.909 0.00 0.00 0.00 3.41
1943 3375 2.140065 TGCTCGGATTCAGAATAGCG 57.860 50.000 10.52 0.00 32.67 4.26
1944 3376 0.787183 GCTCGGATTCAGAATAGCGC 59.213 55.000 0.00 0.00 0.00 5.92
1945 3377 1.869754 GCTCGGATTCAGAATAGCGCA 60.870 52.381 11.47 0.00 0.00 6.09
1946 3378 2.681706 CTCGGATTCAGAATAGCGCAT 58.318 47.619 11.47 0.00 0.00 4.73
2048 3487 1.462238 ACAGGGCTGGAAGGTCTGT 60.462 57.895 0.00 0.00 34.30 3.41
2051 3490 2.224159 GGGCTGGAAGGTCTGTGGA 61.224 63.158 0.00 0.00 0.00 4.02
2100 3539 1.202132 CGGACTGTGGTGTGTTTGTTG 60.202 52.381 0.00 0.00 0.00 3.33
2101 3540 1.816224 GGACTGTGGTGTGTTTGTTGT 59.184 47.619 0.00 0.00 0.00 3.32
2102 3541 2.159435 GGACTGTGGTGTGTTTGTTGTC 60.159 50.000 0.00 0.00 0.00 3.18
2125 3564 4.566545 TGGTTGTTGCACTTTGATGTAG 57.433 40.909 0.00 0.00 0.00 2.74
2126 3565 3.951037 TGGTTGTTGCACTTTGATGTAGT 59.049 39.130 0.00 0.00 0.00 2.73
2127 3566 5.126779 TGGTTGTTGCACTTTGATGTAGTA 58.873 37.500 0.00 0.00 0.00 1.82
2134 3573 4.098807 TGCACTTTGATGTAGTATAGCCGA 59.901 41.667 0.00 0.00 0.00 5.54
2141 3580 0.602060 GTAGTATAGCCGACAGCCCC 59.398 60.000 0.00 0.00 45.47 5.80
2142 3581 0.892358 TAGTATAGCCGACAGCCCCG 60.892 60.000 0.00 0.00 45.47 5.73
2143 3582 2.196502 TATAGCCGACAGCCCCGA 59.803 61.111 0.00 0.00 45.47 5.14
2151 3590 1.810030 GACAGCCCCGATGAACGTC 60.810 63.158 0.00 0.00 40.78 4.34
2157 3596 2.165301 CCCGATGAACGTCCGCTTC 61.165 63.158 0.00 0.00 40.78 3.86
2158 3597 1.153823 CCGATGAACGTCCGCTTCT 60.154 57.895 0.00 0.00 40.78 2.85
2159 3598 0.736325 CCGATGAACGTCCGCTTCTT 60.736 55.000 0.00 0.00 40.78 2.52
2160 3599 1.068474 CGATGAACGTCCGCTTCTTT 58.932 50.000 0.00 0.00 37.22 2.52
2161 3600 1.459592 CGATGAACGTCCGCTTCTTTT 59.540 47.619 0.00 0.00 37.22 2.27
2162 3601 2.096417 CGATGAACGTCCGCTTCTTTTT 60.096 45.455 0.00 0.00 37.22 1.94
2163 3602 3.479949 GATGAACGTCCGCTTCTTTTTC 58.520 45.455 0.00 0.00 0.00 2.29
2164 3603 1.259507 TGAACGTCCGCTTCTTTTTCG 59.740 47.619 0.00 0.00 0.00 3.46
2165 3604 0.041576 AACGTCCGCTTCTTTTTCGC 60.042 50.000 0.00 0.00 0.00 4.70
2166 3605 1.155424 ACGTCCGCTTCTTTTTCGCA 61.155 50.000 0.00 0.00 0.00 5.10
2167 3606 0.165944 CGTCCGCTTCTTTTTCGCAT 59.834 50.000 0.00 0.00 0.00 4.73
2168 3607 1.392168 CGTCCGCTTCTTTTTCGCATA 59.608 47.619 0.00 0.00 0.00 3.14
2169 3608 2.534939 CGTCCGCTTCTTTTTCGCATAG 60.535 50.000 0.00 0.00 0.00 2.23
2170 3609 2.671396 GTCCGCTTCTTTTTCGCATAGA 59.329 45.455 0.00 0.00 0.00 1.98
2171 3610 2.930040 TCCGCTTCTTTTTCGCATAGAG 59.070 45.455 0.00 0.00 0.00 2.43
2172 3611 2.673368 CCGCTTCTTTTTCGCATAGAGT 59.327 45.455 0.00 0.00 0.00 3.24
2173 3612 3.863424 CCGCTTCTTTTTCGCATAGAGTA 59.137 43.478 0.00 0.00 0.00 2.59
2174 3613 4.259850 CCGCTTCTTTTTCGCATAGAGTAC 60.260 45.833 0.00 0.00 0.00 2.73
2175 3614 4.546456 CGCTTCTTTTTCGCATAGAGTACG 60.546 45.833 0.00 0.00 0.00 3.67
2176 3615 4.561606 GCTTCTTTTTCGCATAGAGTACGA 59.438 41.667 0.00 0.00 0.00 3.43
2177 3616 5.498859 GCTTCTTTTTCGCATAGAGTACGAC 60.499 44.000 0.00 0.00 35.20 4.34
2178 3617 5.306532 TCTTTTTCGCATAGAGTACGACT 57.693 39.130 0.00 1.75 35.20 4.18
2179 3618 6.426980 TCTTTTTCGCATAGAGTACGACTA 57.573 37.500 0.00 5.57 35.20 2.59
2180 3619 6.484540 TCTTTTTCGCATAGAGTACGACTAG 58.515 40.000 0.00 0.00 35.20 2.57
2181 3620 4.808077 TTTCGCATAGAGTACGACTAGG 57.192 45.455 9.30 9.30 35.20 3.02
2182 3621 2.141517 TCGCATAGAGTACGACTAGGC 58.858 52.381 20.90 20.90 41.94 3.93
2183 3622 2.598000 GCATAGAGTACGACTAGGCG 57.402 55.000 18.57 18.57 37.75 5.52
2184 3623 1.197264 GCATAGAGTACGACTAGGCGG 59.803 57.143 24.42 4.23 37.75 6.13
2185 3624 1.805345 CATAGAGTACGACTAGGCGGG 59.195 57.143 24.42 0.00 35.12 6.13
2186 3625 0.533755 TAGAGTACGACTAGGCGGGC 60.534 60.000 24.42 14.38 35.12 6.13
2187 3626 2.832201 AGTACGACTAGGCGGGCC 60.832 66.667 24.42 9.37 35.12 5.80
2188 3627 3.142838 GTACGACTAGGCGGGCCA 61.143 66.667 24.42 0.83 38.92 5.36
2210 3649 3.382803 GAGCATCTCCAGCAGCCGT 62.383 63.158 0.00 0.00 0.00 5.68
2246 3685 3.427309 AAAAACTTGTTTGCCGCGT 57.573 42.105 4.92 0.00 0.00 6.01
2316 3757 1.821241 CTATAATGCAGCACGCGCGT 61.821 55.000 32.73 32.73 46.97 6.01
2699 4196 2.749621 GGAGGCACATCGAAAGACATTT 59.250 45.455 0.00 0.00 46.97 2.32
2709 4206 2.819608 CGAAAGACATTTCACCCATGGT 59.180 45.455 11.73 0.00 44.27 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 96 9.558648 CAAATTCGTGAACATTCTCATAAATCA 57.441 29.630 0.00 0.00 0.00 2.57
104 109 8.918961 ACATTCTTTTTACAAATTCGTGAACA 57.081 26.923 0.00 0.00 0.00 3.18
361 993 2.430546 TTTTCCGCACGCATTTCATT 57.569 40.000 0.00 0.00 0.00 2.57
414 1046 1.798223 TGCTGCTACGTGTCATGTTTC 59.202 47.619 2.34 0.00 0.00 2.78
419 1051 4.192000 GCTGCTGCTACGTGTCAT 57.808 55.556 8.53 0.00 36.03 3.06
448 1080 4.451150 CTGAGGGCGCGCCACTTA 62.451 66.667 46.88 34.06 37.98 2.24
460 1092 2.034687 CACTTGGGTGGGCTGAGG 59.965 66.667 0.00 0.00 39.59 3.86
511 1144 4.127907 GGATTTTGAGACGGAGGGAATAC 58.872 47.826 0.00 0.00 0.00 1.89
513 1146 2.846827 AGGATTTTGAGACGGAGGGAAT 59.153 45.455 0.00 0.00 0.00 3.01
514 1147 2.266279 AGGATTTTGAGACGGAGGGAA 58.734 47.619 0.00 0.00 0.00 3.97
515 1148 1.952621 AGGATTTTGAGACGGAGGGA 58.047 50.000 0.00 0.00 0.00 4.20
516 1149 3.906720 TTAGGATTTTGAGACGGAGGG 57.093 47.619 0.00 0.00 0.00 4.30
517 1150 4.092968 CGTTTTAGGATTTTGAGACGGAGG 59.907 45.833 0.00 0.00 0.00 4.30
518 1151 4.689345 ACGTTTTAGGATTTTGAGACGGAG 59.311 41.667 0.00 0.00 33.95 4.63
519 1152 4.449743 CACGTTTTAGGATTTTGAGACGGA 59.550 41.667 0.00 0.00 33.95 4.69
520 1153 4.449743 TCACGTTTTAGGATTTTGAGACGG 59.550 41.667 0.00 0.00 33.95 4.79
521 1154 5.176958 AGTCACGTTTTAGGATTTTGAGACG 59.823 40.000 0.00 0.00 35.59 4.18
522 1155 6.541111 AGTCACGTTTTAGGATTTTGAGAC 57.459 37.500 0.00 0.00 0.00 3.36
523 1156 6.764085 TCAAGTCACGTTTTAGGATTTTGAGA 59.236 34.615 0.00 0.00 0.00 3.27
524 1157 6.954944 TCAAGTCACGTTTTAGGATTTTGAG 58.045 36.000 0.00 0.00 0.00 3.02
525 1158 6.928979 TCAAGTCACGTTTTAGGATTTTGA 57.071 33.333 0.00 0.00 0.00 2.69
526 1159 8.286800 TGTATCAAGTCACGTTTTAGGATTTTG 58.713 33.333 0.00 0.00 0.00 2.44
527 1160 8.385898 TGTATCAAGTCACGTTTTAGGATTTT 57.614 30.769 0.00 0.00 0.00 1.82
528 1161 7.972832 TGTATCAAGTCACGTTTTAGGATTT 57.027 32.000 0.00 0.00 0.00 2.17
529 1162 8.041323 AGATGTATCAAGTCACGTTTTAGGATT 58.959 33.333 0.00 0.00 0.00 3.01
530 1163 7.492669 CAGATGTATCAAGTCACGTTTTAGGAT 59.507 37.037 0.00 0.00 0.00 3.24
531 1164 6.811665 CAGATGTATCAAGTCACGTTTTAGGA 59.188 38.462 0.00 0.00 0.00 2.94
532 1165 6.590292 ACAGATGTATCAAGTCACGTTTTAGG 59.410 38.462 0.00 0.00 0.00 2.69
533 1166 7.582435 ACAGATGTATCAAGTCACGTTTTAG 57.418 36.000 0.00 0.00 0.00 1.85
534 1167 9.647797 AATACAGATGTATCAAGTCACGTTTTA 57.352 29.630 5.97 0.00 40.10 1.52
535 1168 8.547967 AATACAGATGTATCAAGTCACGTTTT 57.452 30.769 5.97 0.00 40.10 2.43
536 1169 8.547967 AAATACAGATGTATCAAGTCACGTTT 57.452 30.769 5.97 0.00 40.10 3.60
537 1170 9.302345 CTAAATACAGATGTATCAAGTCACGTT 57.698 33.333 5.97 0.00 40.10 3.99
538 1171 7.921214 CCTAAATACAGATGTATCAAGTCACGT 59.079 37.037 5.97 0.00 40.10 4.49
539 1172 7.921214 ACCTAAATACAGATGTATCAAGTCACG 59.079 37.037 5.97 0.00 40.10 4.35
550 1183 9.780186 GCCTTAGATTTACCTAAATACAGATGT 57.220 33.333 0.00 0.00 36.13 3.06
551 1184 9.778741 TGCCTTAGATTTACCTAAATACAGATG 57.221 33.333 0.00 0.00 36.13 2.90
562 1195 9.710900 CTCAAAAATTTTGCCTTAGATTTACCT 57.289 29.630 13.19 0.00 0.00 3.08
563 1196 9.705290 TCTCAAAAATTTTGCCTTAGATTTACC 57.295 29.630 13.19 0.00 0.00 2.85
565 1198 9.405587 CGTCTCAAAAATTTTGCCTTAGATTTA 57.594 29.630 13.19 0.00 0.00 1.40
566 1199 7.384932 CCGTCTCAAAAATTTTGCCTTAGATTT 59.615 33.333 13.19 0.00 0.00 2.17
567 1200 6.868339 CCGTCTCAAAAATTTTGCCTTAGATT 59.132 34.615 13.19 0.00 0.00 2.40
568 1201 6.208599 TCCGTCTCAAAAATTTTGCCTTAGAT 59.791 34.615 13.19 0.00 0.00 1.98
569 1202 5.533154 TCCGTCTCAAAAATTTTGCCTTAGA 59.467 36.000 13.19 8.24 0.00 2.10
570 1203 5.768317 TCCGTCTCAAAAATTTTGCCTTAG 58.232 37.500 13.19 6.14 0.00 2.18
571 1204 5.278758 CCTCCGTCTCAAAAATTTTGCCTTA 60.279 40.000 13.19 0.00 0.00 2.69
572 1205 4.501400 CCTCCGTCTCAAAAATTTTGCCTT 60.501 41.667 13.19 0.00 0.00 4.35
573 1206 3.005791 CCTCCGTCTCAAAAATTTTGCCT 59.994 43.478 13.19 0.00 0.00 4.75
574 1207 3.317150 CCTCCGTCTCAAAAATTTTGCC 58.683 45.455 13.19 3.66 0.00 4.52
575 1208 3.317150 CCCTCCGTCTCAAAAATTTTGC 58.683 45.455 13.19 0.00 0.00 3.68
576 1209 3.317150 GCCCTCCGTCTCAAAAATTTTG 58.683 45.455 11.92 11.92 0.00 2.44
577 1210 2.030274 CGCCCTCCGTCTCAAAAATTTT 60.030 45.455 0.00 0.00 0.00 1.82
578 1211 1.539827 CGCCCTCCGTCTCAAAAATTT 59.460 47.619 0.00 0.00 0.00 1.82
579 1212 1.165270 CGCCCTCCGTCTCAAAAATT 58.835 50.000 0.00 0.00 0.00 1.82
580 1213 1.305930 GCGCCCTCCGTCTCAAAAAT 61.306 55.000 0.00 0.00 39.71 1.82
581 1214 1.964373 GCGCCCTCCGTCTCAAAAA 60.964 57.895 0.00 0.00 39.71 1.94
582 1215 2.358247 GCGCCCTCCGTCTCAAAA 60.358 61.111 0.00 0.00 39.71 2.44
583 1216 3.589654 CTGCGCCCTCCGTCTCAAA 62.590 63.158 4.18 0.00 39.71 2.69
584 1217 4.069232 CTGCGCCCTCCGTCTCAA 62.069 66.667 4.18 0.00 39.71 3.02
586 1219 4.070552 AACTGCGCCCTCCGTCTC 62.071 66.667 4.18 0.00 39.71 3.36
587 1220 4.379243 CAACTGCGCCCTCCGTCT 62.379 66.667 4.18 0.00 39.71 4.18
598 1231 1.026718 AGCAATACGGGAGCAACTGC 61.027 55.000 0.00 0.00 42.49 4.40
599 1232 1.009829 GAGCAATACGGGAGCAACTG 58.990 55.000 0.00 0.00 0.00 3.16
619 1252 4.263462 TGTTGATGCATTAGGACAAGAGGT 60.263 41.667 0.00 0.00 0.00 3.85
658 1291 0.323178 CAGGGCAAGAGGTGAGCAAT 60.323 55.000 0.00 0.00 0.00 3.56
659 1292 1.073722 CAGGGCAAGAGGTGAGCAA 59.926 57.895 0.00 0.00 0.00 3.91
660 1293 1.708993 AACAGGGCAAGAGGTGAGCA 61.709 55.000 0.00 0.00 0.00 4.26
661 1294 0.538287 AAACAGGGCAAGAGGTGAGC 60.538 55.000 0.00 0.00 0.00 4.26
662 1295 1.882623 GAAAACAGGGCAAGAGGTGAG 59.117 52.381 0.00 0.00 0.00 3.51
663 1296 1.478654 GGAAAACAGGGCAAGAGGTGA 60.479 52.381 0.00 0.00 0.00 4.02
664 1297 0.961753 GGAAAACAGGGCAAGAGGTG 59.038 55.000 0.00 0.00 0.00 4.00
666 1299 1.251251 CTGGAAAACAGGGCAAGAGG 58.749 55.000 0.00 0.00 43.70 3.69
714 2072 5.123936 AGTCTTCGCTGAAGGTTTTTAAGT 58.876 37.500 15.15 0.00 39.82 2.24
722 2080 2.175202 AGATGAGTCTTCGCTGAAGGT 58.825 47.619 15.15 6.26 39.82 3.50
723 2081 2.957491 AGATGAGTCTTCGCTGAAGG 57.043 50.000 15.15 1.82 39.82 3.46
724 2082 6.419413 GGTAAATAGATGAGTCTTCGCTGAAG 59.581 42.308 10.75 10.75 40.65 3.02
725 2083 6.273825 GGTAAATAGATGAGTCTTCGCTGAA 58.726 40.000 0.69 0.00 35.87 3.02
726 2084 5.505819 CGGTAAATAGATGAGTCTTCGCTGA 60.506 44.000 0.69 0.00 35.87 4.26
727 2085 4.677378 CGGTAAATAGATGAGTCTTCGCTG 59.323 45.833 0.69 0.00 35.87 5.18
728 2086 4.793353 GCGGTAAATAGATGAGTCTTCGCT 60.793 45.833 0.00 0.00 35.87 4.93
729 2087 3.425858 GCGGTAAATAGATGAGTCTTCGC 59.574 47.826 0.69 0.00 35.87 4.70
731 2089 5.232414 GTGTGCGGTAAATAGATGAGTCTTC 59.768 44.000 0.00 0.00 35.87 2.87
732 2090 5.109903 GTGTGCGGTAAATAGATGAGTCTT 58.890 41.667 0.00 0.00 35.87 3.01
733 2091 4.683832 GTGTGCGGTAAATAGATGAGTCT 58.316 43.478 0.00 0.00 38.52 3.24
734 2092 3.486108 CGTGTGCGGTAAATAGATGAGTC 59.514 47.826 0.00 0.00 0.00 3.36
735 2093 3.444916 CGTGTGCGGTAAATAGATGAGT 58.555 45.455 0.00 0.00 0.00 3.41
749 2107 2.291508 CTATTTGCCGTCCGTGTGCG 62.292 60.000 0.00 0.00 37.95 5.34
750 2108 1.423845 CTATTTGCCGTCCGTGTGC 59.576 57.895 0.00 0.00 0.00 4.57
751 2109 0.390603 TCCTATTTGCCGTCCGTGTG 60.391 55.000 0.00 0.00 0.00 3.82
753 2111 1.597663 GAATCCTATTTGCCGTCCGTG 59.402 52.381 0.00 0.00 0.00 4.94
755 2113 0.859232 CGAATCCTATTTGCCGTCCG 59.141 55.000 0.00 0.00 0.00 4.79
756 2114 1.865340 GACGAATCCTATTTGCCGTCC 59.135 52.381 0.00 0.00 40.03 4.79
758 2116 1.949465 GGACGAATCCTATTTGCCGT 58.051 50.000 0.00 0.00 42.45 5.68
768 2126 1.726853 CTGGACACAAGGACGAATCC 58.273 55.000 0.00 0.00 46.69 3.01
769 2127 1.079503 GCTGGACACAAGGACGAATC 58.920 55.000 0.00 0.00 0.00 2.52
770 2128 0.687354 AGCTGGACACAAGGACGAAT 59.313 50.000 0.00 0.00 0.00 3.34
773 2131 2.320587 GCAGCTGGACACAAGGACG 61.321 63.158 17.12 0.00 0.00 4.79
774 2132 1.968540 GGCAGCTGGACACAAGGAC 60.969 63.158 17.12 0.00 0.00 3.85
775 2133 1.782201 ATGGCAGCTGGACACAAGGA 61.782 55.000 17.12 0.00 37.33 3.36
792 2168 0.238289 GTCACACCGTTTGCTCCATG 59.762 55.000 0.00 0.00 0.00 3.66
794 2170 0.107410 AAGTCACACCGTTTGCTCCA 60.107 50.000 0.00 0.00 0.00 3.86
795 2171 0.307760 CAAGTCACACCGTTTGCTCC 59.692 55.000 0.00 0.00 0.00 4.70
797 2173 1.724582 GGCAAGTCACACCGTTTGCT 61.725 55.000 7.82 0.00 43.96 3.91
798 2174 1.299089 GGCAAGTCACACCGTTTGC 60.299 57.895 0.00 0.00 43.81 3.68
799 2175 1.588674 TAGGCAAGTCACACCGTTTG 58.411 50.000 0.00 0.00 0.00 2.93
800 2176 2.158871 TCTTAGGCAAGTCACACCGTTT 60.159 45.455 0.00 0.00 33.20 3.60
802 2178 1.045407 TCTTAGGCAAGTCACACCGT 58.955 50.000 0.00 0.00 33.20 4.83
803 2179 2.163818 TTCTTAGGCAAGTCACACCG 57.836 50.000 0.00 0.00 33.20 4.94
804 2180 4.911514 TTTTTCTTAGGCAAGTCACACC 57.088 40.909 0.00 0.00 33.20 4.16
831 2207 1.225376 TAGGCAAGTCGCACCGTTTG 61.225 55.000 0.00 0.00 45.17 2.93
832 2208 0.533308 TTAGGCAAGTCGCACCGTTT 60.533 50.000 0.00 0.00 45.17 3.60
833 2209 0.949105 CTTAGGCAAGTCGCACCGTT 60.949 55.000 0.00 0.00 45.17 4.44
834 2210 1.374252 CTTAGGCAAGTCGCACCGT 60.374 57.895 0.00 0.00 45.17 4.83
835 2211 0.669318 TTCTTAGGCAAGTCGCACCG 60.669 55.000 0.00 0.00 45.17 4.94
836 2212 1.519408 TTTCTTAGGCAAGTCGCACC 58.481 50.000 0.00 0.00 45.17 5.01
837 2213 3.619233 TTTTTCTTAGGCAAGTCGCAC 57.381 42.857 0.00 0.00 45.17 5.34
857 2233 2.038387 AGTCACACCGTTTGCTCTTT 57.962 45.000 0.00 0.00 0.00 2.52
862 2238 2.182014 GTTTGAAGTCACACCGTTTGC 58.818 47.619 0.00 0.00 0.00 3.68
863 2239 2.436670 CGTTTGAAGTCACACCGTTTG 58.563 47.619 0.00 0.00 0.00 2.93
864 2240 1.399089 CCGTTTGAAGTCACACCGTTT 59.601 47.619 0.00 0.00 0.00 3.60
865 2241 1.011333 CCGTTTGAAGTCACACCGTT 58.989 50.000 0.00 0.00 0.00 4.44
866 2242 1.433837 GCCGTTTGAAGTCACACCGT 61.434 55.000 0.00 0.00 0.00 4.83
867 2243 1.278637 GCCGTTTGAAGTCACACCG 59.721 57.895 0.00 0.00 0.00 4.94
868 2244 1.155424 TCGCCGTTTGAAGTCACACC 61.155 55.000 0.00 0.00 0.00 4.16
869 2245 0.042448 GTCGCCGTTTGAAGTCACAC 60.042 55.000 0.00 0.00 0.00 3.82
870 2246 0.179094 AGTCGCCGTTTGAAGTCACA 60.179 50.000 0.00 0.00 0.00 3.58
871 2247 0.935196 AAGTCGCCGTTTGAAGTCAC 59.065 50.000 0.00 0.00 0.00 3.67
872 2248 1.658994 AAAGTCGCCGTTTGAAGTCA 58.341 45.000 0.00 0.00 0.00 3.41
873 2249 3.865224 TTAAAGTCGCCGTTTGAAGTC 57.135 42.857 0.00 0.00 0.00 3.01
874 2250 4.062991 AGATTAAAGTCGCCGTTTGAAGT 58.937 39.130 0.00 0.00 0.00 3.01
875 2251 4.663636 AGATTAAAGTCGCCGTTTGAAG 57.336 40.909 0.00 0.00 0.00 3.02
876 2252 4.319911 CCAAGATTAAAGTCGCCGTTTGAA 60.320 41.667 0.00 0.00 0.00 2.69
877 2253 3.187637 CCAAGATTAAAGTCGCCGTTTGA 59.812 43.478 0.00 0.00 0.00 2.69
973 2351 1.337118 GATGCAAAGTGGGGTTTGGA 58.663 50.000 0.00 0.00 41.33 3.53
974 2352 0.321346 GGATGCAAAGTGGGGTTTGG 59.679 55.000 0.00 0.00 37.80 3.28
983 2361 2.811873 GCGATAGGGATGGATGCAAAGT 60.812 50.000 0.00 0.00 0.00 2.66
985 2363 1.545428 GGCGATAGGGATGGATGCAAA 60.545 52.381 0.00 0.00 0.00 3.68
987 2365 1.679311 GGCGATAGGGATGGATGCA 59.321 57.895 0.00 0.00 0.00 3.96
988 2366 1.448540 CGGCGATAGGGATGGATGC 60.449 63.158 0.00 0.00 0.00 3.91
1009 2390 3.691342 CGGCGTGGGTTGAGGAGA 61.691 66.667 0.00 0.00 0.00 3.71
1054 2436 4.012895 GTTGTGCGTGCGTGAGGG 62.013 66.667 0.00 0.00 0.00 4.30
1055 2437 4.012895 GGTTGTGCGTGCGTGAGG 62.013 66.667 0.00 0.00 0.00 3.86
1056 2438 1.014044 ATAGGTTGTGCGTGCGTGAG 61.014 55.000 0.00 0.00 0.00 3.51
1057 2439 1.005512 ATAGGTTGTGCGTGCGTGA 60.006 52.632 0.00 0.00 0.00 4.35
1058 2440 1.132436 CATAGGTTGTGCGTGCGTG 59.868 57.895 0.00 0.00 0.00 5.34
1059 2441 2.032634 CCATAGGTTGTGCGTGCGT 61.033 57.895 0.00 0.00 0.00 5.24
1060 2442 2.784596 CCATAGGTTGTGCGTGCG 59.215 61.111 0.00 0.00 0.00 5.34
1061 2443 2.485122 GCCATAGGTTGTGCGTGC 59.515 61.111 0.00 0.00 0.00 5.34
1067 2449 1.453745 CATGGCCGCCATAGGTTGT 60.454 57.895 24.66 0.00 43.15 3.32
1072 2454 1.149174 ACCTTCATGGCCGCCATAG 59.851 57.895 24.66 18.37 43.15 2.23
1103 2488 1.226974 CATGTACCGCTCCAGGTCG 60.227 63.158 0.00 0.00 44.68 4.79
1296 2681 4.443266 GAGCTTGGCCTCGTCGCT 62.443 66.667 3.32 4.30 0.00 4.93
1360 2745 3.755628 GCACCCAGTAGTCGCCGA 61.756 66.667 0.00 0.00 0.00 5.54
1383 2768 1.530293 GTACTGATAGGCGTCGTCGAT 59.470 52.381 6.17 0.00 39.71 3.59
1467 2852 2.696707 GGTTATCGATCTACCACCACCA 59.303 50.000 19.50 0.00 32.12 4.17
1470 2855 4.899457 AGATTGGTTATCGATCTACCACCA 59.101 41.667 24.34 16.48 43.14 4.17
1473 2858 8.651589 AGATTAGATTGGTTATCGATCTACCA 57.348 34.615 21.97 21.97 44.47 3.25
1486 2871 5.163120 ACATCATGGCAGAGATTAGATTGGT 60.163 40.000 2.79 0.00 0.00 3.67
1504 2889 1.837439 ACACCGATACACCCACATCAT 59.163 47.619 0.00 0.00 0.00 2.45
1505 2890 1.066502 CACACCGATACACCCACATCA 60.067 52.381 0.00 0.00 0.00 3.07
1507 2892 0.981183 ACACACCGATACACCCACAT 59.019 50.000 0.00 0.00 0.00 3.21
1517 2902 3.849911 CACAAGATCTACACACACCGAT 58.150 45.455 0.00 0.00 0.00 4.18
1564 2949 1.556911 CTCCACCAGCTCCTTGTACAT 59.443 52.381 0.00 0.00 0.00 2.29
1570 2955 1.614824 CCCTCTCCACCAGCTCCTT 60.615 63.158 0.00 0.00 0.00 3.36
1762 3179 5.482908 ACTAGATTGAACTGTACAAGGCAG 58.517 41.667 0.00 0.00 39.67 4.85
1807 3227 7.096106 CGACACAAACAAGCAAAACATATTCAT 60.096 33.333 0.00 0.00 0.00 2.57
1944 3376 2.202570 GCCGAGCAAGCAAGCATG 60.203 61.111 3.19 0.00 36.85 4.06
1945 3377 1.930908 GAAGCCGAGCAAGCAAGCAT 61.931 55.000 3.19 0.00 36.85 3.79
1946 3378 2.595463 AAGCCGAGCAAGCAAGCA 60.595 55.556 3.19 0.00 36.85 3.91
1949 3381 1.968017 CCTGAAGCCGAGCAAGCAA 60.968 57.895 0.00 0.00 0.00 3.91
2048 3487 2.702592 AAACAAACTCTGGACGTCCA 57.297 45.000 34.13 34.13 45.30 4.02
2051 3490 4.196193 TCATGAAAACAAACTCTGGACGT 58.804 39.130 0.00 0.00 0.00 4.34
2061 3500 2.351253 CCGCGACCATCATGAAAACAAA 60.351 45.455 8.23 0.00 0.00 2.83
2100 3539 3.502191 TCAAAGTGCAACAACCAAGAC 57.498 42.857 0.00 0.00 41.43 3.01
2101 3540 3.446873 ACATCAAAGTGCAACAACCAAGA 59.553 39.130 0.00 0.00 41.43 3.02
2102 3541 3.784338 ACATCAAAGTGCAACAACCAAG 58.216 40.909 0.00 0.00 41.43 3.61
2125 3564 1.533469 ATCGGGGCTGTCGGCTATAC 61.533 60.000 3.10 0.00 41.46 1.47
2126 3565 1.228769 ATCGGGGCTGTCGGCTATA 60.229 57.895 3.10 0.00 41.46 1.31
2127 3566 2.524394 ATCGGGGCTGTCGGCTAT 60.524 61.111 3.10 0.00 41.46 2.97
2134 3573 2.264794 GACGTTCATCGGGGCTGT 59.735 61.111 0.00 0.00 44.69 4.40
2141 3580 1.068474 AAAGAAGCGGACGTTCATCG 58.932 50.000 0.00 0.00 46.00 3.84
2142 3581 3.479949 GAAAAAGAAGCGGACGTTCATC 58.520 45.455 0.00 0.00 0.00 2.92
2143 3582 2.096417 CGAAAAAGAAGCGGACGTTCAT 60.096 45.455 0.00 0.00 0.00 2.57
2151 3590 2.673368 ACTCTATGCGAAAAAGAAGCGG 59.327 45.455 0.00 0.00 0.00 5.52
2162 3601 2.141517 GCCTAGTCGTACTCTATGCGA 58.858 52.381 0.00 0.00 43.71 5.10
2163 3602 1.136308 CGCCTAGTCGTACTCTATGCG 60.136 57.143 20.10 20.10 42.34 4.73
2164 3603 1.197264 CCGCCTAGTCGTACTCTATGC 59.803 57.143 0.00 10.04 0.00 3.14
2165 3604 1.805345 CCCGCCTAGTCGTACTCTATG 59.195 57.143 0.00 0.00 0.00 2.23
2166 3605 1.881498 GCCCGCCTAGTCGTACTCTAT 60.881 57.143 0.00 0.00 0.00 1.98
2167 3606 0.533755 GCCCGCCTAGTCGTACTCTA 60.534 60.000 0.00 0.00 0.00 2.43
2168 3607 1.823041 GCCCGCCTAGTCGTACTCT 60.823 63.158 0.00 0.00 0.00 3.24
2169 3608 2.720605 GCCCGCCTAGTCGTACTC 59.279 66.667 0.00 0.00 0.00 2.59
2170 3609 2.832201 GGCCCGCCTAGTCGTACT 60.832 66.667 0.00 0.00 0.00 2.73
2171 3610 1.174712 TATGGCCCGCCTAGTCGTAC 61.175 60.000 7.35 0.00 36.94 3.67
2172 3611 0.467844 TTATGGCCCGCCTAGTCGTA 60.468 55.000 7.35 0.00 36.94 3.43
2173 3612 1.745320 CTTATGGCCCGCCTAGTCGT 61.745 60.000 7.35 0.00 36.94 4.34
2174 3613 1.006102 CTTATGGCCCGCCTAGTCG 60.006 63.158 7.35 0.00 36.94 4.18
2175 3614 0.318762 CTCTTATGGCCCGCCTAGTC 59.681 60.000 7.35 0.00 36.94 2.59
2176 3615 1.759459 GCTCTTATGGCCCGCCTAGT 61.759 60.000 7.35 0.00 36.94 2.57
2177 3616 1.004440 GCTCTTATGGCCCGCCTAG 60.004 63.158 7.35 2.38 36.94 3.02
2178 3617 1.127567 ATGCTCTTATGGCCCGCCTA 61.128 55.000 7.35 0.00 36.94 3.93
2179 3618 2.403132 GATGCTCTTATGGCCCGCCT 62.403 60.000 7.35 0.00 36.94 5.52
2180 3619 1.968540 GATGCTCTTATGGCCCGCC 60.969 63.158 0.00 0.00 0.00 6.13
2181 3620 0.952984 GAGATGCTCTTATGGCCCGC 60.953 60.000 0.00 0.00 0.00 6.13
2182 3621 0.321122 GGAGATGCTCTTATGGCCCG 60.321 60.000 0.00 0.00 0.00 6.13
2183 3622 0.767375 TGGAGATGCTCTTATGGCCC 59.233 55.000 0.00 0.00 0.00 5.80
2184 3623 1.881498 GCTGGAGATGCTCTTATGGCC 60.881 57.143 0.00 0.00 0.00 5.36
2185 3624 1.202734 TGCTGGAGATGCTCTTATGGC 60.203 52.381 0.00 0.00 0.00 4.40
2186 3625 2.768698 CTGCTGGAGATGCTCTTATGG 58.231 52.381 0.00 0.00 0.00 2.74
2187 3626 2.144730 GCTGCTGGAGATGCTCTTATG 58.855 52.381 0.00 0.00 0.00 1.90
2188 3627 1.072015 GGCTGCTGGAGATGCTCTTAT 59.928 52.381 0.00 0.00 0.00 1.73
2246 3685 1.956043 CTAAACCAGCCAAAGCGCA 59.044 52.632 11.47 0.00 46.67 6.09
2532 4029 2.404923 AGATGAGGACGAAGACGAGA 57.595 50.000 0.00 0.00 42.66 4.04
2699 4196 2.121832 ACCTCCGACCATGGGTGA 59.878 61.111 18.09 8.28 35.25 4.02


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

AutoCloner maintained by Alex Coulton.