Multiple sequence alignment - TraesCS4A01G320300

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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 TraesCS4A01G320300 chr4A 100.000 2985 0 0 1 2985 608881208 608878224 0.000000e+00 5513
1 TraesCS4A01G320300 chr4A 91.676 877 54 9 622 1498 722383683 722382826 0.000000e+00 1197
2 TraesCS4A01G320300 chr4A 99.487 195 1 0 2791 2985 422549725 422549531 3.660000e-94 355
3 TraesCS4A01G320300 chr4A 98.507 201 3 0 2785 2985 425840195 425840395 3.660000e-94 355
4 TraesCS4A01G320300 chr5D 96.057 2181 76 3 621 2792 292685571 292687750 0.000000e+00 3542
5 TraesCS4A01G320300 chr5D 89.671 881 66 16 621 1498 13398991 13398133 0.000000e+00 1099
6 TraesCS4A01G320300 chr5D 89.035 228 24 1 620 846 292693961 292693734 6.300000e-72 281
7 TraesCS4A01G320300 chr6A 95.321 2180 94 3 621 2792 592856793 592858972 0.000000e+00 3454
8 TraesCS4A01G320300 chr6A 94.695 1263 59 1 1538 2792 561584948 561583686 0.000000e+00 1954
9 TraesCS4A01G320300 chr6A 94.458 1263 62 1 1538 2792 561455692 561456954 0.000000e+00 1938
10 TraesCS4A01G320300 chr6A 90.067 896 54 6 621 1498 561454825 561455703 0.000000e+00 1129
11 TraesCS4A01G320300 chr6A 98.058 206 2 2 2781 2984 470201244 470201449 1.020000e-94 357
12 TraesCS4A01G320300 chrUn 95.962 1263 42 2 1538 2792 10230335 10229074 0.000000e+00 2041
13 TraesCS4A01G320300 chrUn 92.857 882 46 5 617 1498 10231188 10230324 0.000000e+00 1264
14 TraesCS4A01G320300 chrUn 90.667 225 21 0 622 846 10202186 10202410 1.740000e-77 300
15 TraesCS4A01G320300 chr1D 95.566 1263 48 1 1538 2792 416512735 416513997 0.000000e+00 2015
16 TraesCS4A01G320300 chr1D 95.079 1016 39 4 1785 2792 491850096 491849084 0.000000e+00 1589
17 TraesCS4A01G320300 chr1D 91.220 877 57 9 622 1498 386434623 386435479 0.000000e+00 1175
18 TraesCS4A01G320300 chr1D 87.179 312 21 6 613 924 416511926 416512218 1.330000e-88 337
19 TraesCS4A01G320300 chr7A 94.775 1244 55 3 1538 2772 16154454 16153212 0.000000e+00 1929
20 TraesCS4A01G320300 chr7A 93.839 1266 63 5 1538 2792 488150391 488149130 0.000000e+00 1892
21 TraesCS4A01G320300 chr7A 95.112 941 42 2 1538 2478 488485250 488484314 0.000000e+00 1480
22 TraesCS4A01G320300 chr7A 90.265 226 22 0 621 846 16129252 16129477 2.250000e-76 296
23 TraesCS4A01G320300 chr3B 94.024 1071 51 5 1735 2792 544828657 544829727 0.000000e+00 1611
24 TraesCS4A01G320300 chr4B 93.838 1071 53 4 1735 2792 634465976 634467046 0.000000e+00 1600
25 TraesCS4A01G320300 chr4B 93.639 1069 56 7 1735 2792 634962603 634961536 0.000000e+00 1587
26 TraesCS4A01G320300 chr2D 93.044 877 44 9 622 1498 81254971 81255830 0.000000e+00 1266
27 TraesCS4A01G320300 chr2D 94.656 786 31 2 2018 2792 81285102 81285887 0.000000e+00 1208
28 TraesCS4A01G320300 chr2D 90.222 225 22 0 622 846 81291528 81291304 8.090000e-76 294
29 TraesCS4A01G320300 chr5A 91.904 877 51 9 622 1498 436265264 436266120 0.000000e+00 1208
30 TraesCS4A01G320300 chr5A 99.487 195 1 0 2791 2985 58871355 58871161 3.660000e-94 355
31 TraesCS4A01G320300 chr5A 88.462 234 26 1 621 853 436269767 436269534 6.300000e-72 281
32 TraesCS4A01G320300 chr5B 86.750 883 93 14 622 1498 186149888 186150752 0.000000e+00 961
33 TraesCS4A01G320300 chr5B 88.816 608 28 24 1 603 705847591 705848163 0.000000e+00 710
34 TraesCS4A01G320300 chr3A 98.995 199 2 0 2786 2984 647526568 647526370 1.020000e-94 357
35 TraesCS4A01G320300 chr3A 98.500 200 3 0 2786 2985 524418298 524418497 1.320000e-93 353
36 TraesCS4A01G320300 chr1A 99.487 195 1 0 2791 2985 47251792 47251598 3.660000e-94 355
37 TraesCS4A01G320300 chr1A 99.487 195 1 0 2791 2985 58691524 58691330 3.660000e-94 355
38 TraesCS4A01G320300 chr1A 99.487 195 1 0 2791 2985 337960204 337960398 3.660000e-94 355


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 TraesCS4A01G320300 chr4A 608878224 608881208 2984 True 5513.0 5513 100.0000 1 2985 1 chr4A.!!$R2 2984
1 TraesCS4A01G320300 chr4A 722382826 722383683 857 True 1197.0 1197 91.6760 622 1498 1 chr4A.!!$R3 876
2 TraesCS4A01G320300 chr5D 292685571 292687750 2179 False 3542.0 3542 96.0570 621 2792 1 chr5D.!!$F1 2171
3 TraesCS4A01G320300 chr5D 13398133 13398991 858 True 1099.0 1099 89.6710 621 1498 1 chr5D.!!$R1 877
4 TraesCS4A01G320300 chr6A 592856793 592858972 2179 False 3454.0 3454 95.3210 621 2792 1 chr6A.!!$F2 2171
5 TraesCS4A01G320300 chr6A 561583686 561584948 1262 True 1954.0 1954 94.6950 1538 2792 1 chr6A.!!$R1 1254
6 TraesCS4A01G320300 chr6A 561454825 561456954 2129 False 1533.5 1938 92.2625 621 2792 2 chr6A.!!$F3 2171
7 TraesCS4A01G320300 chrUn 10229074 10231188 2114 True 1652.5 2041 94.4095 617 2792 2 chrUn.!!$R1 2175
8 TraesCS4A01G320300 chr1D 491849084 491850096 1012 True 1589.0 1589 95.0790 1785 2792 1 chr1D.!!$R1 1007
9 TraesCS4A01G320300 chr1D 416511926 416513997 2071 False 1176.0 2015 91.3725 613 2792 2 chr1D.!!$F2 2179
10 TraesCS4A01G320300 chr1D 386434623 386435479 856 False 1175.0 1175 91.2200 622 1498 1 chr1D.!!$F1 876
11 TraesCS4A01G320300 chr7A 16153212 16154454 1242 True 1929.0 1929 94.7750 1538 2772 1 chr7A.!!$R1 1234
12 TraesCS4A01G320300 chr7A 488149130 488150391 1261 True 1892.0 1892 93.8390 1538 2792 1 chr7A.!!$R2 1254
13 TraesCS4A01G320300 chr7A 488484314 488485250 936 True 1480.0 1480 95.1120 1538 2478 1 chr7A.!!$R3 940
14 TraesCS4A01G320300 chr3B 544828657 544829727 1070 False 1611.0 1611 94.0240 1735 2792 1 chr3B.!!$F1 1057
15 TraesCS4A01G320300 chr4B 634465976 634467046 1070 False 1600.0 1600 93.8380 1735 2792 1 chr4B.!!$F1 1057
16 TraesCS4A01G320300 chr4B 634961536 634962603 1067 True 1587.0 1587 93.6390 1735 2792 1 chr4B.!!$R1 1057
17 TraesCS4A01G320300 chr2D 81254971 81255830 859 False 1266.0 1266 93.0440 622 1498 1 chr2D.!!$F1 876
18 TraesCS4A01G320300 chr2D 81285102 81285887 785 False 1208.0 1208 94.6560 2018 2792 1 chr2D.!!$F2 774
19 TraesCS4A01G320300 chr5A 436265264 436266120 856 False 1208.0 1208 91.9040 622 1498 1 chr5A.!!$F1 876
20 TraesCS4A01G320300 chr5B 186149888 186150752 864 False 961.0 961 86.7500 622 1498 1 chr5B.!!$F1 876
21 TraesCS4A01G320300 chr5B 705847591 705848163 572 False 710.0 710 88.8160 1 603 1 chr5B.!!$F2 602

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
603 613 0.031994 ACGTTCAAATGCCAACCAGC 59.968 50.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2430 0.895559 CTGCCTTCAAGTTCCCCACC 60.896 60.0 0.0 0.0 0.0 4.61 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
84 85 4.508128 GGCGCTCCATCGGTTCGA 62.508 66.667 7.64 0.00 41.13 3.71
112 113 3.454082 CTCTTCTCTTGGATAAGGCCTGT 59.546 47.826 5.69 0.00 34.59 4.00
113 114 3.198635 TCTTCTCTTGGATAAGGCCTGTG 59.801 47.826 5.69 0.00 34.59 3.66
120 121 1.153289 ATAAGGCCTGTGCGAGCTG 60.153 57.895 5.69 0.00 38.85 4.24
160 161 3.673338 CACGTACTGTGTGTGTTGGATAG 59.327 47.826 8.95 0.00 43.88 2.08
193 199 5.542779 CTCCTGTGTATGTCCCTTTATAGC 58.457 45.833 0.00 0.00 0.00 2.97
194 200 5.216622 TCCTGTGTATGTCCCTTTATAGCT 58.783 41.667 0.00 0.00 0.00 3.32
195 201 6.378745 TCCTGTGTATGTCCCTTTATAGCTA 58.621 40.000 0.00 0.00 0.00 3.32
197 203 6.267928 CCTGTGTATGTCCCTTTATAGCTAGT 59.732 42.308 0.00 0.00 0.00 2.57
198 204 7.050970 TGTGTATGTCCCTTTATAGCTAGTG 57.949 40.000 0.00 0.00 0.00 2.74
199 205 6.610020 TGTGTATGTCCCTTTATAGCTAGTGT 59.390 38.462 0.00 0.00 0.00 3.55
200 206 7.146648 GTGTATGTCCCTTTATAGCTAGTGTC 58.853 42.308 0.00 0.00 0.00 3.67
201 207 7.014422 GTGTATGTCCCTTTATAGCTAGTGTCT 59.986 40.741 0.00 0.00 0.00 3.41
202 208 8.222637 TGTATGTCCCTTTATAGCTAGTGTCTA 58.777 37.037 0.00 0.00 0.00 2.59
203 209 6.956202 TGTCCCTTTATAGCTAGTGTCTAC 57.044 41.667 0.00 0.00 0.00 2.59
204 210 6.429151 TGTCCCTTTATAGCTAGTGTCTACA 58.571 40.000 0.00 0.00 0.00 2.74
205 211 6.893554 TGTCCCTTTATAGCTAGTGTCTACAA 59.106 38.462 0.00 0.00 0.00 2.41
206 212 7.147949 TGTCCCTTTATAGCTAGTGTCTACAAC 60.148 40.741 0.00 0.00 0.00 3.32
207 213 6.323225 TCCCTTTATAGCTAGTGTCTACAACC 59.677 42.308 0.00 0.00 0.00 3.77
208 214 6.207213 CCTTTATAGCTAGTGTCTACAACCG 58.793 44.000 0.00 0.00 0.00 4.44
209 215 6.039047 CCTTTATAGCTAGTGTCTACAACCGA 59.961 42.308 0.00 0.00 0.00 4.69
210 216 4.897025 ATAGCTAGTGTCTACAACCGAC 57.103 45.455 0.00 0.00 0.00 4.79
211 217 2.792878 AGCTAGTGTCTACAACCGACT 58.207 47.619 0.00 0.00 32.70 4.18
212 218 3.155501 AGCTAGTGTCTACAACCGACTT 58.844 45.455 0.00 0.00 32.70 3.01
213 219 3.057456 AGCTAGTGTCTACAACCGACTTG 60.057 47.826 0.00 0.00 35.77 3.16
214 220 2.814280 AGTGTCTACAACCGACTTGG 57.186 50.000 0.00 0.00 46.41 3.61
215 221 2.313317 AGTGTCTACAACCGACTTGGA 58.687 47.619 0.00 0.00 42.00 3.53
216 222 2.296471 AGTGTCTACAACCGACTTGGAG 59.704 50.000 0.00 0.00 41.83 3.86
217 223 2.295349 GTGTCTACAACCGACTTGGAGA 59.705 50.000 4.13 4.13 46.27 3.71
219 225 3.150458 TCTACAACCGACTTGGAGAGA 57.850 47.619 4.13 0.00 43.95 3.10
220 226 3.082548 TCTACAACCGACTTGGAGAGAG 58.917 50.000 4.13 0.00 43.95 3.20
221 227 0.318762 ACAACCGACTTGGAGAGAGC 59.681 55.000 0.00 0.00 42.00 4.09
222 228 0.605589 CAACCGACTTGGAGAGAGCT 59.394 55.000 0.00 0.00 42.00 4.09
223 229 0.605589 AACCGACTTGGAGAGAGCTG 59.394 55.000 0.00 0.00 42.00 4.24
224 230 1.153667 CCGACTTGGAGAGAGCTGC 60.154 63.158 0.00 0.00 42.00 5.25
243 249 0.609406 CACTGTGAGAGAGGGACGGA 60.609 60.000 0.32 0.00 0.00 4.69
254 260 2.032681 GGACGGACAAGCAAGCCT 59.967 61.111 0.00 0.00 0.00 4.58
298 304 2.564771 TGGATTCATTGGAGATCACGC 58.435 47.619 0.00 0.00 0.00 5.34
309 315 0.313987 AGATCACGCGCGGAATATGA 59.686 50.000 35.22 26.97 0.00 2.15
322 328 4.129380 CGGAATATGATTCTGCTCCAACA 58.871 43.478 0.00 0.00 0.00 3.33
327 333 1.338105 TGATTCTGCTCCAACAGGACG 60.338 52.381 0.00 0.00 38.26 4.79
390 396 2.632028 ACGGATCCAATCTCTCATCCAG 59.368 50.000 13.41 0.00 35.42 3.86
439 446 5.400066 TTCACCTCAAATCGACAGATACA 57.600 39.130 0.00 0.00 35.74 2.29
440 447 5.598416 TCACCTCAAATCGACAGATACAT 57.402 39.130 0.00 0.00 35.74 2.29
441 448 5.592054 TCACCTCAAATCGACAGATACATC 58.408 41.667 0.00 0.00 35.74 3.06
453 460 2.418628 CAGATACATCGGCCGTTGTTTT 59.581 45.455 38.33 27.98 31.46 2.43
457 464 0.309302 CATCGGCCGTTGTTTTGACA 59.691 50.000 27.15 0.67 0.00 3.58
458 465 0.309612 ATCGGCCGTTGTTTTGACAC 59.690 50.000 27.15 0.00 0.00 3.67
461 468 0.526739 GGCCGTTGTTTTGACACCAC 60.527 55.000 0.00 0.00 0.00 4.16
462 469 0.171455 GCCGTTGTTTTGACACCACA 59.829 50.000 0.00 0.00 0.00 4.17
464 471 1.468395 CCGTTGTTTTGACACCACACC 60.468 52.381 0.00 0.00 0.00 4.16
465 472 1.200252 CGTTGTTTTGACACCACACCA 59.800 47.619 0.00 0.00 0.00 4.17
467 474 3.443976 GTTGTTTTGACACCACACCATC 58.556 45.455 0.00 0.00 0.00 3.51
468 475 1.673400 TGTTTTGACACCACACCATCG 59.327 47.619 0.00 0.00 0.00 3.84
469 476 1.001815 GTTTTGACACCACACCATCGG 60.002 52.381 0.00 0.00 0.00 4.18
470 477 1.169661 TTTGACACCACACCATCGGC 61.170 55.000 0.00 0.00 0.00 5.54
493 502 2.361119 CCATCAAATCCTCCACTGCATG 59.639 50.000 0.00 0.00 0.00 4.06
505 514 2.613595 CCACTGCATGCTTTATTCGCTA 59.386 45.455 20.33 0.00 0.00 4.26
555 565 3.992427 CGTGCATGTGATATGTGCTATCT 59.008 43.478 0.00 0.00 39.52 1.98
582 592 0.976641 TCAGCCTCAAATCGACCACT 59.023 50.000 0.00 0.00 0.00 4.00
583 593 1.066858 TCAGCCTCAAATCGACCACTC 60.067 52.381 0.00 0.00 0.00 3.51
584 594 0.976641 AGCCTCAAATCGACCACTCA 59.023 50.000 0.00 0.00 0.00 3.41
585 595 1.079503 GCCTCAAATCGACCACTCAC 58.920 55.000 0.00 0.00 0.00 3.51
586 596 1.350193 CCTCAAATCGACCACTCACG 58.650 55.000 0.00 0.00 0.00 4.35
603 613 0.031994 ACGTTCAAATGCCAACCAGC 59.968 50.000 0.00 0.00 0.00 4.85
604 614 0.667184 CGTTCAAATGCCAACCAGCC 60.667 55.000 0.00 0.00 0.00 4.85
605 615 0.392336 GTTCAAATGCCAACCAGCCA 59.608 50.000 0.00 0.00 0.00 4.75
606 616 1.126488 TTCAAATGCCAACCAGCCAA 58.874 45.000 0.00 0.00 0.00 4.52
607 617 0.392336 TCAAATGCCAACCAGCCAAC 59.608 50.000 0.00 0.00 0.00 3.77
608 618 0.603439 CAAATGCCAACCAGCCAACC 60.603 55.000 0.00 0.00 0.00 3.77
609 619 1.053264 AAATGCCAACCAGCCAACCA 61.053 50.000 0.00 0.00 0.00 3.67
610 620 1.474332 AATGCCAACCAGCCAACCAG 61.474 55.000 0.00 0.00 0.00 4.00
611 621 3.305516 GCCAACCAGCCAACCAGG 61.306 66.667 0.00 0.00 41.84 4.45
697 708 5.508200 TCTACGTTTTTGTGCCAGAAAAT 57.492 34.783 0.17 0.00 0.00 1.82
698 709 5.277825 TCTACGTTTTTGTGCCAGAAAATG 58.722 37.500 0.17 2.87 37.62 2.32
745 757 4.334481 CAGAAAACACCTAACCGTCTGTTT 59.666 41.667 0.00 0.00 38.24 2.83
773 785 7.334671 GGCAGTTTAACCTCTATTATGATAGGC 59.665 40.741 4.79 0.00 36.65 3.93
824 836 3.782244 GCAAGCTCACGCCGTCTG 61.782 66.667 0.00 0.00 36.60 3.51
883 912 0.250814 TCCGCCGTGTGGGTAAAAAT 60.251 50.000 4.03 0.00 38.44 1.82
1202 1236 1.299165 GCTACGATGCACGATCCGT 60.299 57.895 14.18 9.62 45.77 4.69
1223 1257 1.246649 TTTCAATGGCACTGACGCAT 58.753 45.000 0.00 0.00 0.00 4.73
1290 1324 2.973694 GCATTTGAAGGGATGCACAT 57.026 45.000 0.00 0.00 46.03 3.21
1336 1370 6.989169 GTGCTAAGAAGGTATGATTCACATCT 59.011 38.462 0.00 0.00 40.07 2.90
1425 1461 7.041372 GGTCTTTGTTTAGCTTGTTCTGACATA 60.041 37.037 0.00 0.00 35.29 2.29
1502 1606 9.862585 CCTTTGTTTATCAAGTTGTTAATTTGC 57.137 29.630 2.11 0.00 37.35 3.68
1503 1607 9.862585 CTTTGTTTATCAAGTTGTTAATTTGCC 57.137 29.630 2.11 0.00 37.35 4.52
1504 1608 9.606631 TTTGTTTATCAAGTTGTTAATTTGCCT 57.393 25.926 2.11 0.00 37.35 4.75
1505 1609 9.606631 TTGTTTATCAAGTTGTTAATTTGCCTT 57.393 25.926 2.11 0.00 0.00 4.35
1506 1610 9.255304 TGTTTATCAAGTTGTTAATTTGCCTTC 57.745 29.630 2.11 0.00 0.00 3.46
1507 1611 9.255304 GTTTATCAAGTTGTTAATTTGCCTTCA 57.745 29.630 2.11 0.00 0.00 3.02
1508 1612 9.823647 TTTATCAAGTTGTTAATTTGCCTTCAA 57.176 25.926 2.11 0.00 0.00 2.69
1509 1613 7.951530 ATCAAGTTGTTAATTTGCCTTCAAG 57.048 32.000 2.11 0.00 33.12 3.02
1510 1614 6.872920 TCAAGTTGTTAATTTGCCTTCAAGT 58.127 32.000 2.11 0.00 33.12 3.16
1511 1615 7.327214 TCAAGTTGTTAATTTGCCTTCAAGTT 58.673 30.769 2.11 0.00 36.35 2.66
1512 1616 7.277539 TCAAGTTGTTAATTTGCCTTCAAGTTG 59.722 33.333 13.55 13.55 42.48 3.16
1513 1617 6.639563 AGTTGTTAATTTGCCTTCAAGTTGT 58.360 32.000 2.11 0.00 34.56 3.32
1514 1618 7.102993 AGTTGTTAATTTGCCTTCAAGTTGTT 58.897 30.769 2.11 0.00 34.56 2.83
1515 1619 7.606073 AGTTGTTAATTTGCCTTCAAGTTGTTT 59.394 29.630 2.11 0.00 34.56 2.83
1516 1620 8.874816 GTTGTTAATTTGCCTTCAAGTTGTTTA 58.125 29.630 2.11 0.00 34.56 2.01
1517 1621 8.413899 TGTTAATTTGCCTTCAAGTTGTTTAC 57.586 30.769 2.11 0.00 34.56 2.01
1518 1622 8.254508 TGTTAATTTGCCTTCAAGTTGTTTACT 58.745 29.630 2.11 0.00 39.32 2.24
1650 1754 7.066284 AGTCATTGTTTATTATGGTCAGTGCTC 59.934 37.037 0.00 0.00 0.00 4.26
1677 1781 0.965439 TGTTTACCAGTGGGCATTGC 59.035 50.000 15.21 0.00 37.90 3.56
1949 2059 5.425217 TCAGCTAGGACCAATGACAATCTAA 59.575 40.000 0.00 0.00 0.00 2.10
1982 2092 3.890756 TGCAATTCACAACCTGACAGAAT 59.109 39.130 3.32 0.00 0.00 2.40
2041 2151 4.430137 TGCTGATGTGAATGCTCTTTTC 57.570 40.909 0.00 0.00 0.00 2.29
2068 2178 2.976490 GCAGCAGAGGGGTGTGGAT 61.976 63.158 0.00 0.00 46.68 3.41
2195 2305 6.104146 AGAAGAAGAAACTACAGGAGAACC 57.896 41.667 0.00 0.00 0.00 3.62
2320 2430 4.063689 AGATTGTTGAGCTTGAGACTGTG 58.936 43.478 0.00 0.00 0.00 3.66
2353 2463 1.871080 AGGCAGAGTTGTCAAAGACG 58.129 50.000 0.00 0.00 34.95 4.18
2406 2519 6.696411 ACTATGAAACTCTGAAGAACCTGAG 58.304 40.000 0.00 0.00 37.89 3.35
2478 2591 1.206849 GAAGGAGAGGCTGACAGAAGG 59.793 57.143 6.65 0.00 0.00 3.46
2480 2593 1.220477 GAGAGGCTGACAGAAGGGC 59.780 63.158 6.65 0.00 0.00 5.19
2657 2779 6.976934 ATGAATTTGTGACCCAAGTACTTT 57.023 33.333 5.07 0.00 33.75 2.66
2813 2936 6.749036 ACTGTTGGAAATATACCCTAGAGG 57.251 41.667 0.00 0.00 43.78 3.69
2814 2937 5.071923 ACTGTTGGAAATATACCCTAGAGGC 59.928 44.000 0.00 0.00 40.58 4.70
2815 2938 4.972568 TGTTGGAAATATACCCTAGAGGCA 59.027 41.667 0.00 0.00 40.58 4.75
2816 2939 5.430417 TGTTGGAAATATACCCTAGAGGCAA 59.570 40.000 0.00 0.00 40.58 4.52
2817 2940 6.102615 TGTTGGAAATATACCCTAGAGGCAAT 59.897 38.462 0.00 0.00 40.58 3.56
2818 2941 7.293771 TGTTGGAAATATACCCTAGAGGCAATA 59.706 37.037 0.00 0.00 40.58 1.90
2819 2942 7.881912 TGGAAATATACCCTAGAGGCAATAA 57.118 36.000 0.00 0.00 40.58 1.40
2820 2943 8.463055 TGGAAATATACCCTAGAGGCAATAAT 57.537 34.615 0.00 0.00 40.58 1.28
2821 2944 9.569074 TGGAAATATACCCTAGAGGCAATAATA 57.431 33.333 0.00 0.00 40.58 0.98
2887 3010 8.902540 TCGTTTATTATCCATGCTAGAATTGT 57.097 30.769 0.00 0.00 0.00 2.71
2888 3011 9.990360 TCGTTTATTATCCATGCTAGAATTGTA 57.010 29.630 0.00 0.00 0.00 2.41
2897 3020 8.206126 TCCATGCTAGAATTGTATTGATAGGA 57.794 34.615 0.00 0.00 0.00 2.94
2898 3021 8.659527 TCCATGCTAGAATTGTATTGATAGGAA 58.340 33.333 0.00 0.00 0.00 3.36
2899 3022 9.288576 CCATGCTAGAATTGTATTGATAGGAAA 57.711 33.333 0.00 0.00 0.00 3.13
2902 3025 9.547753 TGCTAGAATTGTATTGATAGGAAACTC 57.452 33.333 0.00 0.00 43.67 3.01
2903 3026 9.547753 GCTAGAATTGTATTGATAGGAAACTCA 57.452 33.333 0.00 0.00 43.67 3.41
2911 3034 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
2912 3035 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
2913 3036 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
2914 3037 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
2915 3038 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
2916 3039 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
2917 3040 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
2918 3041 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
2919 3042 6.384015 AGGAAACTCAGATACATGTGTGGATA 59.616 38.462 9.11 0.00 32.90 2.59
2920 3043 6.480320 GGAAACTCAGATACATGTGTGGATAC 59.520 42.308 9.11 0.00 0.00 2.24
2936 3059 5.692115 TGGATACATAGACAACACCATGT 57.308 39.130 0.00 0.00 46.17 3.21
2937 3060 5.670485 TGGATACATAGACAACACCATGTC 58.330 41.667 0.00 0.00 45.97 3.06
2938 3061 5.396324 TGGATACATAGACAACACCATGTCC 60.396 44.000 3.95 0.00 46.44 4.02
2939 3062 8.319752 TGGATACATAGACAACACCATGTCCC 62.320 46.154 3.95 0.00 46.44 4.46
2945 3068 4.546829 GACAACACCATGTCCCTAGTAA 57.453 45.455 0.00 0.00 43.11 2.24
2946 3069 4.504858 GACAACACCATGTCCCTAGTAAG 58.495 47.826 0.00 0.00 43.11 2.34
2947 3070 3.270877 CAACACCATGTCCCTAGTAAGC 58.729 50.000 0.00 0.00 0.00 3.09
2948 3071 1.838077 ACACCATGTCCCTAGTAAGCC 59.162 52.381 0.00 0.00 0.00 4.35
2949 3072 2.119495 CACCATGTCCCTAGTAAGCCT 58.881 52.381 0.00 0.00 0.00 4.58
2950 3073 2.103263 CACCATGTCCCTAGTAAGCCTC 59.897 54.545 0.00 0.00 0.00 4.70
2951 3074 2.022918 ACCATGTCCCTAGTAAGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
2952 3075 3.206866 ACCATGTCCCTAGTAAGCCTCTA 59.793 47.826 0.00 0.00 0.00 2.43
2953 3076 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
2954 3077 4.475345 CATGTCCCTAGTAAGCCTCTAGT 58.525 47.826 0.00 0.00 34.72 2.57
2955 3078 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
2956 3079 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
2957 3080 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
2958 3081 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
2959 3082 4.230041 TCCCTAGTAAGCCTCTAGTTGACT 59.770 45.833 0.00 0.00 34.72 3.41
2960 3083 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
2961 3084 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
2962 3085 5.239963 CCTAGTAAGCCTCTAGTTGACTAGC 59.760 48.000 12.30 3.61 44.24 3.42
2963 3086 4.862371 AGTAAGCCTCTAGTTGACTAGCT 58.138 43.478 12.30 5.64 44.24 3.32
2964 3087 4.885325 AGTAAGCCTCTAGTTGACTAGCTC 59.115 45.833 12.30 5.16 44.24 4.09
2965 3088 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
2966 3089 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
2967 3090 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
2968 3091 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
2969 3092 3.690139 CCTCTAGTTGACTAGCTCGTTGA 59.310 47.826 12.30 0.00 44.24 3.18
2970 3093 4.336993 CCTCTAGTTGACTAGCTCGTTGAT 59.663 45.833 12.30 0.00 44.24 2.57
2971 3094 5.487153 TCTAGTTGACTAGCTCGTTGATC 57.513 43.478 12.30 0.00 44.24 2.92
2972 3095 4.941873 TCTAGTTGACTAGCTCGTTGATCA 59.058 41.667 12.30 0.00 44.24 2.92
2973 3096 4.521130 AGTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
2974 3097 5.078411 AGTTGACTAGCTCGTTGATCAAT 57.922 39.130 12.12 0.00 0.00 2.57
2975 3098 6.208988 AGTTGACTAGCTCGTTGATCAATA 57.791 37.500 12.12 2.38 0.00 1.90
2976 3099 6.269315 AGTTGACTAGCTCGTTGATCAATAG 58.731 40.000 12.12 13.07 0.00 1.73
2977 3100 6.095580 AGTTGACTAGCTCGTTGATCAATAGA 59.904 38.462 19.51 16.55 0.00 1.98
2978 3101 6.641169 TGACTAGCTCGTTGATCAATAGAT 57.359 37.500 19.51 16.66 37.13 1.98
2979 3102 6.442112 TGACTAGCTCGTTGATCAATAGATG 58.558 40.000 19.51 12.48 33.72 2.90
2980 3103 5.777802 ACTAGCTCGTTGATCAATAGATGG 58.222 41.667 19.51 17.62 33.72 3.51
2981 3104 4.679373 AGCTCGTTGATCAATAGATGGT 57.321 40.909 19.51 14.02 33.72 3.55
2982 3105 5.028549 AGCTCGTTGATCAATAGATGGTT 57.971 39.130 19.51 6.05 33.72 3.67
2983 3106 6.161855 AGCTCGTTGATCAATAGATGGTTA 57.838 37.500 19.51 0.00 33.72 2.85
2984 3107 6.763355 AGCTCGTTGATCAATAGATGGTTAT 58.237 36.000 19.51 2.79 33.72 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 5.397334 GCCTTATCCAAGAGAAGAGACCAAT 60.397 44.000 0.67 0.00 33.30 3.16
141 142 5.539048 AGTTCTATCCAACACACACAGTAC 58.461 41.667 0.00 0.00 0.00 2.73
142 143 5.801531 AGTTCTATCCAACACACACAGTA 57.198 39.130 0.00 0.00 0.00 2.74
143 144 4.689612 AGTTCTATCCAACACACACAGT 57.310 40.909 0.00 0.00 0.00 3.55
144 145 4.214119 CCAAGTTCTATCCAACACACACAG 59.786 45.833 0.00 0.00 0.00 3.66
160 161 3.265791 CATACACAGGAGCTCCAAGTTC 58.734 50.000 33.90 6.40 38.89 3.01
193 199 3.504906 TCCAAGTCGGTTGTAGACACTAG 59.495 47.826 0.00 0.00 40.84 2.57
194 200 3.489355 TCCAAGTCGGTTGTAGACACTA 58.511 45.455 0.00 0.00 40.84 2.74
195 201 2.296471 CTCCAAGTCGGTTGTAGACACT 59.704 50.000 0.00 0.00 40.84 3.55
197 203 2.557056 CTCTCCAAGTCGGTTGTAGACA 59.443 50.000 0.00 0.00 40.84 3.41
198 204 2.818432 TCTCTCCAAGTCGGTTGTAGAC 59.182 50.000 0.00 0.00 38.81 2.59
199 205 3.082548 CTCTCTCCAAGTCGGTTGTAGA 58.917 50.000 0.00 0.00 33.87 2.59
200 206 2.416162 GCTCTCTCCAAGTCGGTTGTAG 60.416 54.545 0.00 0.00 33.87 2.74
201 207 1.544691 GCTCTCTCCAAGTCGGTTGTA 59.455 52.381 0.00 0.00 33.87 2.41
202 208 0.318762 GCTCTCTCCAAGTCGGTTGT 59.681 55.000 0.00 0.00 33.87 3.32
203 209 0.605589 AGCTCTCTCCAAGTCGGTTG 59.394 55.000 0.00 0.00 35.57 3.77
204 210 0.605589 CAGCTCTCTCCAAGTCGGTT 59.394 55.000 0.00 0.00 35.57 4.44
205 211 1.882989 GCAGCTCTCTCCAAGTCGGT 61.883 60.000 0.00 0.00 35.57 4.69
206 212 1.153667 GCAGCTCTCTCCAAGTCGG 60.154 63.158 0.00 0.00 0.00 4.79
207 213 0.735632 GTGCAGCTCTCTCCAAGTCG 60.736 60.000 0.00 0.00 0.00 4.18
208 214 0.607620 AGTGCAGCTCTCTCCAAGTC 59.392 55.000 0.00 0.00 0.00 3.01
209 215 0.321021 CAGTGCAGCTCTCTCCAAGT 59.679 55.000 0.00 0.00 0.00 3.16
210 216 0.321021 ACAGTGCAGCTCTCTCCAAG 59.679 55.000 0.00 0.00 0.00 3.61
211 217 0.034476 CACAGTGCAGCTCTCTCCAA 59.966 55.000 0.00 0.00 0.00 3.53
212 218 0.829182 TCACAGTGCAGCTCTCTCCA 60.829 55.000 0.00 0.00 0.00 3.86
213 219 0.108709 CTCACAGTGCAGCTCTCTCC 60.109 60.000 0.00 0.00 0.00 3.71
214 220 0.887247 TCTCACAGTGCAGCTCTCTC 59.113 55.000 0.00 0.00 0.00 3.20
215 221 0.889994 CTCTCACAGTGCAGCTCTCT 59.110 55.000 0.00 0.00 0.00 3.10
216 222 0.887247 TCTCTCACAGTGCAGCTCTC 59.113 55.000 0.00 0.00 0.00 3.20
217 223 0.889994 CTCTCTCACAGTGCAGCTCT 59.110 55.000 0.00 0.00 0.00 4.09
218 224 0.108709 CCTCTCTCACAGTGCAGCTC 60.109 60.000 0.00 0.00 0.00 4.09
219 225 1.543065 CCCTCTCTCACAGTGCAGCT 61.543 60.000 0.00 0.00 0.00 4.24
220 226 1.079266 CCCTCTCTCACAGTGCAGC 60.079 63.158 0.00 0.00 0.00 5.25
221 227 0.246086 GTCCCTCTCTCACAGTGCAG 59.754 60.000 0.00 0.00 0.00 4.41
222 228 1.527433 CGTCCCTCTCTCACAGTGCA 61.527 60.000 0.00 0.00 0.00 4.57
223 229 1.214062 CGTCCCTCTCTCACAGTGC 59.786 63.158 0.00 0.00 0.00 4.40
224 230 0.609406 TCCGTCCCTCTCTCACAGTG 60.609 60.000 0.00 0.00 0.00 3.66
254 260 2.346803 CAACTGCCGAAAAGCTAGCTA 58.653 47.619 19.70 0.00 0.00 3.32
264 270 2.091541 GAATCCAATCCAACTGCCGAA 58.908 47.619 0.00 0.00 0.00 4.30
265 271 1.004161 TGAATCCAATCCAACTGCCGA 59.996 47.619 0.00 0.00 0.00 5.54
298 304 1.728971 GGAGCAGAATCATATTCCGCG 59.271 52.381 0.00 0.00 0.00 6.46
309 315 0.976641 TCGTCCTGTTGGAGCAGAAT 59.023 50.000 0.00 0.00 44.16 2.40
322 328 0.179100 CATCGCATCCAGTTCGTCCT 60.179 55.000 0.00 0.00 0.00 3.85
327 333 0.820891 ATGGGCATCGCATCCAGTTC 60.821 55.000 0.00 0.00 31.37 3.01
351 357 0.109597 GTGGTGCATGCTACAACTGC 60.110 55.000 20.33 2.38 36.45 4.40
352 358 0.166597 CGTGGTGCATGCTACAACTG 59.833 55.000 20.33 10.94 0.00 3.16
356 362 0.461870 GATCCGTGGTGCATGCTACA 60.462 55.000 20.33 14.69 0.00 2.74
390 396 1.827789 TTTGTGGGCAGCACTGGAC 60.828 57.895 0.00 0.00 0.00 4.02
439 446 0.309612 GTGTCAAAACAACGGCCGAT 59.690 50.000 35.90 19.90 37.08 4.18
440 447 1.716826 GGTGTCAAAACAACGGCCGA 61.717 55.000 35.90 2.60 37.08 5.54
441 448 1.298788 GGTGTCAAAACAACGGCCG 60.299 57.895 26.86 26.86 37.08 6.13
453 460 2.031919 GCCGATGGTGTGGTGTCA 59.968 61.111 0.00 0.00 0.00 3.58
461 468 1.727511 ATTTGATGGCGCCGATGGTG 61.728 55.000 23.90 0.00 36.10 4.17
462 469 1.447317 GATTTGATGGCGCCGATGGT 61.447 55.000 23.90 5.78 0.00 3.55
464 471 1.168407 AGGATTTGATGGCGCCGATG 61.168 55.000 23.90 0.00 0.00 3.84
465 472 0.886490 GAGGATTTGATGGCGCCGAT 60.886 55.000 23.90 16.46 0.00 4.18
467 474 2.546494 GGAGGATTTGATGGCGCCG 61.546 63.158 23.90 0.00 0.00 6.46
468 475 1.453745 TGGAGGATTTGATGGCGCC 60.454 57.895 22.73 22.73 0.00 6.53
469 476 0.749454 AGTGGAGGATTTGATGGCGC 60.749 55.000 0.00 0.00 0.00 6.53
470 477 1.019673 CAGTGGAGGATTTGATGGCG 58.980 55.000 0.00 0.00 0.00 5.69
493 502 2.097466 TGCCAAAGCTAGCGAATAAAGC 59.903 45.455 9.55 7.98 40.80 3.51
505 514 0.183492 TGAGGTTGAGTGCCAAAGCT 59.817 50.000 0.00 0.00 40.80 3.74
555 565 2.030893 CGATTTGAGGCTGAGTGCAAAA 60.031 45.455 0.00 0.00 45.15 2.44
566 576 1.079503 GTGAGTGGTCGATTTGAGGC 58.920 55.000 0.00 0.00 0.00 4.70
582 592 1.336440 CTGGTTGGCATTTGAACGTGA 59.664 47.619 0.00 0.00 0.00 4.35
583 593 1.769733 CTGGTTGGCATTTGAACGTG 58.230 50.000 0.00 0.00 0.00 4.49
584 594 0.031994 GCTGGTTGGCATTTGAACGT 59.968 50.000 0.00 0.00 0.00 3.99
585 595 0.667184 GGCTGGTTGGCATTTGAACG 60.667 55.000 0.00 0.00 41.37 3.95
586 596 0.392336 TGGCTGGTTGGCATTTGAAC 59.608 50.000 0.00 0.00 46.76 3.18
603 613 1.153289 CCTCTCGATGCCTGGTTGG 60.153 63.158 0.00 0.00 39.35 3.77
604 614 0.179089 CTCCTCTCGATGCCTGGTTG 60.179 60.000 0.00 0.00 0.00 3.77
605 615 0.616111 ACTCCTCTCGATGCCTGGTT 60.616 55.000 0.00 0.00 0.00 3.67
606 616 1.000993 ACTCCTCTCGATGCCTGGT 59.999 57.895 0.00 0.00 0.00 4.00
607 617 1.039785 TCACTCCTCTCGATGCCTGG 61.040 60.000 0.00 0.00 0.00 4.45
608 618 0.820226 TTCACTCCTCTCGATGCCTG 59.180 55.000 0.00 0.00 0.00 4.85
609 619 1.786937 ATTCACTCCTCTCGATGCCT 58.213 50.000 0.00 0.00 0.00 4.75
610 620 2.208431 CAATTCACTCCTCTCGATGCC 58.792 52.381 0.00 0.00 0.00 4.40
611 621 1.596727 GCAATTCACTCCTCTCGATGC 59.403 52.381 0.00 0.00 0.00 3.91
612 622 2.897436 TGCAATTCACTCCTCTCGATG 58.103 47.619 0.00 0.00 0.00 3.84
613 623 3.616956 TTGCAATTCACTCCTCTCGAT 57.383 42.857 0.00 0.00 0.00 3.59
614 624 3.401033 TTTGCAATTCACTCCTCTCGA 57.599 42.857 0.00 0.00 0.00 4.04
615 625 4.488126 TTTTTGCAATTCACTCCTCTCG 57.512 40.909 0.00 0.00 0.00 4.04
638 649 1.281867 CCCTAGGCTTCAATGTGGTGA 59.718 52.381 2.05 0.00 0.00 4.02
697 708 2.984562 TGATTAGGCGTGAAATCAGCA 58.015 42.857 1.40 0.00 37.23 4.41
698 709 4.558538 AATGATTAGGCGTGAAATCAGC 57.441 40.909 9.68 0.00 43.34 4.26
745 757 6.569127 TCATAATAGAGGTTAAACTGCCCA 57.431 37.500 0.00 0.00 0.00 5.36
773 785 1.472480 CATAGACAAAACAAGGCCCCG 59.528 52.381 0.00 0.00 0.00 5.73
824 836 1.301401 TTGCCACTGTAGCACCGTC 60.301 57.895 0.00 0.00 40.69 4.79
979 1013 3.011517 ACCGGGGAGCAGCAGAAT 61.012 61.111 6.32 0.00 0.00 2.40
1017 1051 2.828520 GACTGAATCCTCACTGGTCTCA 59.171 50.000 0.00 0.00 37.07 3.27
1202 1236 2.431454 TGCGTCAGTGCCATTGAAATA 58.569 42.857 0.00 0.00 0.00 1.40
1223 1257 5.050431 CGTGTTCACACAAGACATTCACATA 60.050 40.000 10.61 0.00 46.75 2.29
1290 1324 1.065410 TCCAAGAAACCTCCTGCCCA 61.065 55.000 0.00 0.00 0.00 5.36
1336 1370 5.652994 AGCAAACAACTTCCTTTACACAA 57.347 34.783 0.00 0.00 0.00 3.33
1425 1461 5.938125 GTGTACAATCCACTAATGACAAGGT 59.062 40.000 0.00 0.00 0.00 3.50
1498 1602 5.406649 CACAGTAAACAACTTGAAGGCAAA 58.593 37.500 0.00 0.00 35.76 3.68
1499 1603 4.142271 CCACAGTAAACAACTTGAAGGCAA 60.142 41.667 0.00 0.00 35.76 4.52
1500 1604 3.380004 CCACAGTAAACAACTTGAAGGCA 59.620 43.478 0.00 0.00 35.76 4.75
1501 1605 3.380320 ACCACAGTAAACAACTTGAAGGC 59.620 43.478 0.00 0.00 35.76 4.35
1502 1606 4.638421 TGACCACAGTAAACAACTTGAAGG 59.362 41.667 0.00 0.00 35.76 3.46
1503 1607 5.810525 CTGACCACAGTAAACAACTTGAAG 58.189 41.667 0.00 0.00 35.76 3.02
1504 1608 5.811399 CTGACCACAGTAAACAACTTGAA 57.189 39.130 0.00 0.00 35.76 2.69
1517 1621 1.670406 GGCAGAGCACTGACCACAG 60.670 63.158 15.88 0.00 45.71 3.66
1518 1622 2.427320 GGCAGAGCACTGACCACA 59.573 61.111 15.88 0.00 45.71 4.17
1531 1635 4.293415 CAAGCTTAACAACTTGAAGGCAG 58.707 43.478 0.00 0.00 44.89 4.85
1650 1754 3.305335 GCCCACTGGTAAACAAGTCATTG 60.305 47.826 0.00 0.00 42.46 2.82
1677 1781 8.786826 TCCTTACCATACAACAGACAAATTAG 57.213 34.615 0.00 0.00 0.00 1.73
1949 2059 5.351458 GTTGTGAATTGCAAAGGAACTCTT 58.649 37.500 1.71 0.00 38.49 2.85
1982 2092 9.756571 ATAGTTCTCCTGTAGTTTCTTCTTCTA 57.243 33.333 0.00 0.00 0.00 2.10
2041 2151 2.895865 CTCTGCTGCTGGGCATCG 60.896 66.667 6.69 0.00 41.63 3.84
2068 2178 6.723298 TTCTGCTCCTTTTGATTGGTTAAA 57.277 33.333 0.00 0.00 0.00 1.52
2195 2305 5.122711 TCACATCAGCATACAAACTGTCATG 59.877 40.000 0.00 0.00 35.37 3.07
2245 2355 3.673543 TTGTTTAACTCCACACCCCTT 57.326 42.857 0.00 0.00 0.00 3.95
2320 2430 0.895559 CTGCCTTCAAGTTCCCCACC 60.896 60.000 0.00 0.00 0.00 4.61
2353 2463 3.181466 GCATCTTCTTCTTCTCCTCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
2406 2519 1.814394 TCACATTGGCTTGAGCACATC 59.186 47.619 5.24 0.00 44.36 3.06
2478 2591 2.017049 AGAAATGTGATACAAGCCGCC 58.983 47.619 0.00 0.00 0.00 6.13
2480 2593 3.242543 GCTCAGAAATGTGATACAAGCCG 60.243 47.826 0.00 0.00 0.00 5.52
2550 2672 3.643792 GCACCCTACTCATCTAAGATGGT 59.356 47.826 0.00 0.00 0.00 3.55
2657 2779 8.267183 ACACCATAGATCACAAATTCATCACTA 58.733 33.333 0.00 0.00 0.00 2.74
2792 2915 4.972568 TGCCTCTAGGGTATATTTCCAACA 59.027 41.667 0.00 0.00 37.43 3.33
2793 2916 5.562298 TGCCTCTAGGGTATATTTCCAAC 57.438 43.478 0.00 0.00 37.43 3.77
2794 2917 6.780198 ATTGCCTCTAGGGTATATTTCCAA 57.220 37.500 0.00 0.00 37.43 3.53
2795 2918 7.881912 TTATTGCCTCTAGGGTATATTTCCA 57.118 36.000 0.00 0.00 37.43 3.53
2861 2984 9.507329 ACAATTCTAGCATGGATAATAAACGAT 57.493 29.630 0.00 0.00 0.00 3.73
2862 2985 8.902540 ACAATTCTAGCATGGATAATAAACGA 57.097 30.769 0.00 0.00 0.00 3.85
2871 2994 8.829746 TCCTATCAATACAATTCTAGCATGGAT 58.170 33.333 0.00 0.00 0.00 3.41
2872 2995 8.206126 TCCTATCAATACAATTCTAGCATGGA 57.794 34.615 0.00 0.00 0.00 3.41
2873 2996 8.853077 TTCCTATCAATACAATTCTAGCATGG 57.147 34.615 0.00 0.00 0.00 3.66
2876 2999 9.547753 GAGTTTCCTATCAATACAATTCTAGCA 57.452 33.333 0.00 0.00 0.00 3.49
2877 3000 9.547753 TGAGTTTCCTATCAATACAATTCTAGC 57.452 33.333 0.00 0.00 0.00 3.42
2885 3008 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
2886 3009 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
2887 3010 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
2888 3011 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
2889 3012 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
2890 3013 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
2891 3014 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
2892 3015 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
2893 3016 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
2894 3017 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
2895 3018 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
2896 3019 7.041721 TGTATCCACACATGTATCTGAGTTTC 58.958 38.462 0.00 0.00 0.00 2.78
2897 3020 6.946340 TGTATCCACACATGTATCTGAGTTT 58.054 36.000 0.00 0.00 0.00 2.66
2898 3021 6.544928 TGTATCCACACATGTATCTGAGTT 57.455 37.500 0.00 0.00 0.00 3.01
2899 3022 6.737720 ATGTATCCACACATGTATCTGAGT 57.262 37.500 0.00 0.00 37.74 3.41
2900 3023 8.026026 GTCTATGTATCCACACATGTATCTGAG 58.974 40.741 0.00 0.00 39.46 3.35
2901 3024 7.505585 TGTCTATGTATCCACACATGTATCTGA 59.494 37.037 0.00 0.00 39.46 3.27
2902 3025 7.661040 TGTCTATGTATCCACACATGTATCTG 58.339 38.462 0.00 0.00 39.46 2.90
2903 3026 7.839680 TGTCTATGTATCCACACATGTATCT 57.160 36.000 0.00 0.00 39.46 1.98
2904 3027 7.926018 TGTTGTCTATGTATCCACACATGTATC 59.074 37.037 0.00 0.00 39.46 2.24
2905 3028 7.710907 GTGTTGTCTATGTATCCACACATGTAT 59.289 37.037 0.00 0.00 39.46 2.29
2906 3029 7.039270 GTGTTGTCTATGTATCCACACATGTA 58.961 38.462 0.00 0.00 39.46 2.29
2907 3030 5.874810 GTGTTGTCTATGTATCCACACATGT 59.125 40.000 0.00 0.00 39.46 3.21
2908 3031 5.294306 GGTGTTGTCTATGTATCCACACATG 59.706 44.000 0.00 0.00 39.46 3.21
2909 3032 5.045942 TGGTGTTGTCTATGTATCCACACAT 60.046 40.000 0.00 0.00 41.88 3.21
2910 3033 4.284746 TGGTGTTGTCTATGTATCCACACA 59.715 41.667 0.00 0.00 37.54 3.72
2911 3034 4.827692 TGGTGTTGTCTATGTATCCACAC 58.172 43.478 0.00 0.00 37.54 3.82
2912 3035 5.045942 ACATGGTGTTGTCTATGTATCCACA 60.046 40.000 0.00 0.00 39.52 4.17
2913 3036 5.428253 ACATGGTGTTGTCTATGTATCCAC 58.572 41.667 0.00 0.00 32.41 4.02
2914 3037 5.396324 GGACATGGTGTTGTCTATGTATCCA 60.396 44.000 0.00 0.00 44.39 3.41
2915 3038 5.057149 GGACATGGTGTTGTCTATGTATCC 58.943 45.833 0.00 0.00 44.39 2.59
2916 3039 5.057149 GGGACATGGTGTTGTCTATGTATC 58.943 45.833 0.00 0.00 44.39 2.24
2917 3040 4.721776 AGGGACATGGTGTTGTCTATGTAT 59.278 41.667 0.00 0.00 44.39 2.29
2918 3041 4.101114 AGGGACATGGTGTTGTCTATGTA 58.899 43.478 0.00 0.00 44.39 2.29
2919 3042 2.912956 AGGGACATGGTGTTGTCTATGT 59.087 45.455 0.00 0.00 44.39 2.29
2920 3043 3.634397 AGGGACATGGTGTTGTCTATG 57.366 47.619 0.00 0.00 44.39 2.23
2921 3044 4.362677 ACTAGGGACATGGTGTTGTCTAT 58.637 43.478 0.00 0.00 44.39 1.98
2922 3045 3.786553 ACTAGGGACATGGTGTTGTCTA 58.213 45.455 0.00 0.00 44.39 2.59
2923 3046 2.621070 ACTAGGGACATGGTGTTGTCT 58.379 47.619 0.00 0.00 44.39 3.41
2924 3047 4.504858 CTTACTAGGGACATGGTGTTGTC 58.495 47.826 0.00 0.00 44.27 3.18
2925 3048 3.307480 GCTTACTAGGGACATGGTGTTGT 60.307 47.826 0.00 0.00 0.00 3.32
2926 3049 3.270877 GCTTACTAGGGACATGGTGTTG 58.729 50.000 0.00 0.00 0.00 3.33
2927 3050 2.238898 GGCTTACTAGGGACATGGTGTT 59.761 50.000 0.00 0.00 0.00 3.32
2928 3051 1.838077 GGCTTACTAGGGACATGGTGT 59.162 52.381 0.00 0.00 0.00 4.16
2929 3052 2.103263 GAGGCTTACTAGGGACATGGTG 59.897 54.545 0.00 0.00 0.00 4.17
2930 3053 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
2931 3054 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
2932 3055 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
2933 3056 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
2934 3057 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
2935 3058 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
2936 3059 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
2937 3060 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
2938 3061 5.239963 GCTAGTCAACTAGAGGCTTACTAGG 59.760 48.000 19.03 0.00 46.80 3.02
2939 3062 6.059484 AGCTAGTCAACTAGAGGCTTACTAG 58.941 44.000 19.03 8.32 46.80 2.57
2940 3063 6.003859 AGCTAGTCAACTAGAGGCTTACTA 57.996 41.667 19.03 0.00 46.80 1.82
2941 3064 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
2942 3065 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
2943 3066 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
2944 3067 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
2945 3068 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
2946 3069 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
2947 3070 3.690139 TCAACGAGCTAGTCAACTAGAGG 59.310 47.826 19.03 10.05 46.80 3.69
2948 3071 4.948608 TCAACGAGCTAGTCAACTAGAG 57.051 45.455 19.03 11.89 46.80 2.43
2949 3072 4.941873 TGATCAACGAGCTAGTCAACTAGA 59.058 41.667 19.03 0.00 46.80 2.43
2950 3073 5.236655 TGATCAACGAGCTAGTCAACTAG 57.763 43.478 11.99 11.99 46.63 2.57
2951 3074 5.638596 TTGATCAACGAGCTAGTCAACTA 57.361 39.130 3.38 0.00 0.00 2.24
2952 3075 4.521130 TTGATCAACGAGCTAGTCAACT 57.479 40.909 3.38 0.00 0.00 3.16
2953 3076 6.266323 TCTATTGATCAACGAGCTAGTCAAC 58.734 40.000 11.07 0.00 0.00 3.18
2954 3077 6.451064 TCTATTGATCAACGAGCTAGTCAA 57.549 37.500 11.07 0.55 0.00 3.18
2955 3078 6.442112 CATCTATTGATCAACGAGCTAGTCA 58.558 40.000 11.07 0.00 0.00 3.41
2956 3079 5.861251 CCATCTATTGATCAACGAGCTAGTC 59.139 44.000 11.07 0.00 0.00 2.59
2957 3080 5.303078 ACCATCTATTGATCAACGAGCTAGT 59.697 40.000 11.07 6.23 0.00 2.57
2958 3081 5.777802 ACCATCTATTGATCAACGAGCTAG 58.222 41.667 11.07 8.38 0.00 3.42
2959 3082 5.791336 ACCATCTATTGATCAACGAGCTA 57.209 39.130 11.07 0.00 0.00 3.32
2960 3083 4.679373 ACCATCTATTGATCAACGAGCT 57.321 40.909 11.07 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.