Multiple sequence alignment - TraesCS4B01G279500

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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 TraesCS4B01G279500 chr4B 100.000 2390 0 0 1 2390 562627791 562630180 0.000000e+00 4414.0
1 TraesCS4B01G279500 chr4B 85.116 692 52 25 568 1242 562618033 562618690 0.000000e+00 660.0
2 TraesCS4B01G279500 chr4B 95.086 407 8 4 1 398 562682253 562682656 4.340000e-177 630.0
3 TraesCS4B01G279500 chr4B 88.496 226 12 8 394 619 562683199 562683410 6.550000e-66 261.0
4 TraesCS4B01G279500 chr4B 83.936 249 31 7 994 1240 562436319 562436078 1.850000e-56 230.0
5 TraesCS4B01G279500 chr2A 96.632 950 29 1 1441 2390 333734582 333735528 0.000000e+00 1574.0
6 TraesCS4B01G279500 chr5B 94.439 953 47 5 1442 2390 37794779 37795729 0.000000e+00 1461.0
7 TraesCS4B01G279500 chr4A 93.278 967 49 6 1438 2390 208820488 208819524 0.000000e+00 1411.0
8 TraesCS4B01G279500 chr4A 83.557 821 83 31 444 1242 16981687 16980897 0.000000e+00 721.0
9 TraesCS4B01G279500 chr4A 85.294 238 25 7 994 1229 17018304 17018533 1.100000e-58 237.0
10 TraesCS4B01G279500 chr4A 90.909 165 8 4 1245 1403 623991217 623991380 5.170000e-52 215.0
11 TraesCS4B01G279500 chr4A 82.329 249 35 7 994 1240 17024271 17024512 8.660000e-50 207.0
12 TraesCS4B01G279500 chr4A 77.876 226 39 8 23 239 622122528 622122751 1.930000e-26 130.0
13 TraesCS4B01G279500 chr4D 87.182 1256 82 31 1 1242 449962154 449963344 0.000000e+00 1354.0
14 TraesCS4B01G279500 chr4D 82.137 571 51 25 375 920 449967085 449967629 2.180000e-120 442.0
15 TraesCS4B01G279500 chr4D 83.937 442 35 19 489 920 449945907 449946322 8.010000e-105 390.0
16 TraesCS4B01G279500 chr4D 93.233 266 15 1 980 1242 449946340 449946605 2.880000e-104 388.0
17 TraesCS4B01G279500 chr4D 93.103 261 15 1 985 1242 449967656 449967916 1.730000e-101 379.0
18 TraesCS4B01G279500 chr4D 90.863 197 18 0 994 1190 449739404 449739208 5.070000e-67 265.0
19 TraesCS4B01G279500 chr4D 85.294 238 25 7 994 1229 449887527 449887298 1.100000e-58 237.0
20 TraesCS4B01G279500 chr4D 87.342 79 6 4 823 898 449739550 449739473 1.180000e-13 87.9
21 TraesCS4B01G279500 chr6D 89.958 956 84 9 1442 2390 448435287 448436237 0.000000e+00 1223.0
22 TraesCS4B01G279500 chr2D 93.617 799 48 3 1594 2390 109024563 109023766 0.000000e+00 1190.0
23 TraesCS4B01G279500 chr2D 94.872 39 2 0 54 92 112697484 112697522 7.130000e-06 62.1
24 TraesCS4B01G279500 chr7A 86.630 920 113 6 1476 2390 709393954 709394868 0.000000e+00 1009.0
25 TraesCS4B01G279500 chr7A 91.282 195 16 1 1249 1442 473239312 473239118 5.070000e-67 265.0
26 TraesCS4B01G279500 chr2B 85.729 960 120 14 1441 2390 175519870 175518918 0.000000e+00 998.0
27 TraesCS4B01G279500 chr2B 95.050 202 8 2 1242 1442 118710613 118710813 1.380000e-82 316.0
28 TraesCS4B01G279500 chr3B 84.969 958 129 11 1442 2390 820765410 820766361 0.000000e+00 957.0
29 TraesCS4B01G279500 chr3B 94.872 39 2 0 51 89 15752400 15752438 7.130000e-06 62.1
30 TraesCS4B01G279500 chr3B 97.143 35 1 0 55 89 15670013 15670047 2.570000e-05 60.2
31 TraesCS4B01G279500 chr3B 94.737 38 2 0 55 92 25672261 25672224 2.570000e-05 60.2
32 TraesCS4B01G279500 chr6B 84.511 962 125 18 1442 2390 125634298 125635248 0.000000e+00 929.0
33 TraesCS4B01G279500 chr6B 93.970 199 9 3 1245 1442 705880435 705880239 4.990000e-77 298.0
34 TraesCS4B01G279500 chr1B 96.078 204 6 2 1241 1442 113990498 113990295 4.920000e-87 331.0
35 TraesCS4B01G279500 chrUn 89.697 165 10 4 1245 1403 1658721 1658884 1.120000e-48 204.0
36 TraesCS4B01G279500 chrUn 89.697 165 10 4 1245 1403 1700478 1700641 1.120000e-48 204.0
37 TraesCS4B01G279500 chrUn 89.697 165 10 4 1245 1403 189284587 189284750 1.120000e-48 204.0
38 TraesCS4B01G279500 chrUn 89.697 165 10 4 1245 1403 189288805 189288968 1.120000e-48 204.0
39 TraesCS4B01G279500 chr3A 81.188 101 12 5 55 148 18650719 18650619 9.160000e-10 75.0
40 TraesCS4B01G279500 chr3D 78.641 103 8 9 59 148 886535 886636 3.320000e-04 56.5


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 TraesCS4B01G279500 chr4B 562627791 562630180 2389 False 4414.0 4414 100.000 1 2390 1 chr4B.!!$F2 2389
1 TraesCS4B01G279500 chr4B 562618033 562618690 657 False 660.0 660 85.116 568 1242 1 chr4B.!!$F1 674
2 TraesCS4B01G279500 chr4B 562682253 562683410 1157 False 445.5 630 91.791 1 619 2 chr4B.!!$F3 618
3 TraesCS4B01G279500 chr2A 333734582 333735528 946 False 1574.0 1574 96.632 1441 2390 1 chr2A.!!$F1 949
4 TraesCS4B01G279500 chr5B 37794779 37795729 950 False 1461.0 1461 94.439 1442 2390 1 chr5B.!!$F1 948
5 TraesCS4B01G279500 chr4A 208819524 208820488 964 True 1411.0 1411 93.278 1438 2390 1 chr4A.!!$R2 952
6 TraesCS4B01G279500 chr4A 16980897 16981687 790 True 721.0 721 83.557 444 1242 1 chr4A.!!$R1 798
7 TraesCS4B01G279500 chr4D 449962154 449967916 5762 False 725.0 1354 87.474 1 1242 3 chr4D.!!$F2 1241
8 TraesCS4B01G279500 chr4D 449945907 449946605 698 False 389.0 390 88.585 489 1242 2 chr4D.!!$F1 753
9 TraesCS4B01G279500 chr6D 448435287 448436237 950 False 1223.0 1223 89.958 1442 2390 1 chr6D.!!$F1 948
10 TraesCS4B01G279500 chr2D 109023766 109024563 797 True 1190.0 1190 93.617 1594 2390 1 chr2D.!!$R1 796
11 TraesCS4B01G279500 chr7A 709393954 709394868 914 False 1009.0 1009 86.630 1476 2390 1 chr7A.!!$F1 914
12 TraesCS4B01G279500 chr2B 175518918 175519870 952 True 998.0 998 85.729 1441 2390 1 chr2B.!!$R1 949
13 TraesCS4B01G279500 chr3B 820765410 820766361 951 False 957.0 957 84.969 1442 2390 1 chr3B.!!$F3 948
14 TraesCS4B01G279500 chr6B 125634298 125635248 950 False 929.0 929 84.511 1442 2390 1 chr6B.!!$F1 948

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
262 263 0.035881 ATACATGGAGGATGCAGCCG 59.964 55.0 16.75 2.94 42.42 5.52 F
1244 6446 0.109723 TAGCCGCCCACAGAGTTTTT 59.890 50.0 0.00 0.00 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 6579 0.323087 ATGCTCCTCATTGCTGTGCA 60.323 50.000 0.0 0.0 36.47 4.57 R
2221 7452 2.604686 AGGTCGCCCTGCTTGAGA 60.605 61.111 0.0 0.0 40.58 3.27 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
171 172 7.614583 ACACACAACTAGTACACATCTATAGGT 59.385 37.037 0.00 0.00 0.00 3.08
262 263 0.035881 ATACATGGAGGATGCAGCCG 59.964 55.000 16.75 2.94 42.42 5.52
270 279 2.484417 GGAGGATGCAGCCGGATATATG 60.484 54.545 16.75 0.00 0.00 1.78
343 353 6.152831 TGACATTGAAGAGTAACTAGCTAGCA 59.847 38.462 20.91 6.10 0.00 3.49
370 380 4.621068 AATGACAGTAAATGATGCACCG 57.379 40.909 0.00 0.00 0.00 4.94
371 381 3.052455 TGACAGTAAATGATGCACCGT 57.948 42.857 0.00 0.00 0.00 4.83
372 382 4.195225 TGACAGTAAATGATGCACCGTA 57.805 40.909 0.00 0.00 0.00 4.02
398 408 4.954826 ACCTCGTCTTAGCCTACAAACTAT 59.045 41.667 0.00 0.00 0.00 2.12
399 409 6.125029 ACCTCGTCTTAGCCTACAAACTATA 58.875 40.000 0.00 0.00 0.00 1.31
400 410 6.604795 ACCTCGTCTTAGCCTACAAACTATAA 59.395 38.462 0.00 0.00 0.00 0.98
401 411 7.287235 ACCTCGTCTTAGCCTACAAACTATAAT 59.713 37.037 0.00 0.00 0.00 1.28
402 412 8.790718 CCTCGTCTTAGCCTACAAACTATAATA 58.209 37.037 0.00 0.00 0.00 0.98
451 1008 7.775053 ATACACATTACAAAACCCAGTTGAT 57.225 32.000 0.00 0.00 0.00 2.57
488 1045 2.305927 CTGAGTTCTTTTCCCCTGGCTA 59.694 50.000 0.00 0.00 0.00 3.93
505 1062 4.329392 TGGCTATCATATGAGGCAACATG 58.671 43.478 24.91 0.00 44.43 3.21
524 1081 7.283127 GCAACATGGAAAGATGAAGGTCTATTA 59.717 37.037 0.00 0.00 0.00 0.98
525 1082 9.347240 CAACATGGAAAGATGAAGGTCTATTAT 57.653 33.333 0.00 0.00 0.00 1.28
526 1083 9.927081 AACATGGAAAGATGAAGGTCTATTATT 57.073 29.630 0.00 0.00 0.00 1.40
527 1084 9.927081 ACATGGAAAGATGAAGGTCTATTATTT 57.073 29.630 0.00 0.00 0.00 1.40
595 1159 0.389948 CGGCCTGCTTCTTCGTAGTT 60.390 55.000 0.00 0.00 0.00 2.24
623 1187 6.819284 TGCTTTGACCAATCTTGAATTCTTT 58.181 32.000 7.05 0.00 0.00 2.52
624 1188 7.950512 TGCTTTGACCAATCTTGAATTCTTTA 58.049 30.769 7.05 0.00 0.00 1.85
681 5847 3.932580 CTGGGTTGAGCAGCGCGTA 62.933 63.158 8.43 0.00 0.00 4.42
776 5950 3.806949 TTTCCCATTTGTCCTACTGCT 57.193 42.857 0.00 0.00 0.00 4.24
779 5953 3.450904 TCCCATTTGTCCTACTGCTAGT 58.549 45.455 0.00 0.00 0.00 2.57
780 5954 3.197766 TCCCATTTGTCCTACTGCTAGTG 59.802 47.826 0.00 0.00 0.00 2.74
782 5956 3.369892 CCATTTGTCCTACTGCTAGTGCT 60.370 47.826 0.00 0.00 40.48 4.40
783 5957 4.141937 CCATTTGTCCTACTGCTAGTGCTA 60.142 45.833 0.00 0.00 40.48 3.49
784 5958 4.720649 TTTGTCCTACTGCTAGTGCTAG 57.279 45.455 2.04 2.04 40.48 3.42
785 5959 3.646736 TGTCCTACTGCTAGTGCTAGA 57.353 47.619 10.17 0.00 40.48 2.43
786 5960 3.280295 TGTCCTACTGCTAGTGCTAGAC 58.720 50.000 10.17 2.87 40.48 2.59
787 5961 2.619646 GTCCTACTGCTAGTGCTAGACC 59.380 54.545 10.17 0.00 40.48 3.85
788 5962 1.957877 CCTACTGCTAGTGCTAGACCC 59.042 57.143 10.17 0.00 40.48 4.46
789 5963 1.604755 CTACTGCTAGTGCTAGACCCG 59.395 57.143 10.17 0.00 40.48 5.28
790 5964 0.323542 ACTGCTAGTGCTAGACCCGT 60.324 55.000 10.17 0.00 40.48 5.28
791 5965 1.064906 ACTGCTAGTGCTAGACCCGTA 60.065 52.381 10.17 0.00 40.48 4.02
792 5966 1.604755 CTGCTAGTGCTAGACCCGTAG 59.395 57.143 10.17 0.00 40.48 3.51
793 5967 1.211212 TGCTAGTGCTAGACCCGTAGA 59.789 52.381 10.17 0.00 40.48 2.59
794 5968 2.295885 GCTAGTGCTAGACCCGTAGAA 58.704 52.381 10.17 0.00 35.21 2.10
795 5969 2.291190 GCTAGTGCTAGACCCGTAGAAG 59.709 54.545 10.17 0.00 35.21 2.85
796 5970 2.510928 AGTGCTAGACCCGTAGAAGT 57.489 50.000 0.00 0.00 0.00 3.01
859 6042 6.509523 CTATAAAAGGAATCCACCACCCTA 57.490 41.667 0.61 0.00 0.00 3.53
873 6056 1.683917 CACCCTATCTCTCCTCCAACG 59.316 57.143 0.00 0.00 0.00 4.10
885 6069 0.249868 CTCCAACGACCACTCAAGCA 60.250 55.000 0.00 0.00 0.00 3.91
895 6079 1.068055 CCACTCAAGCAAGGCATTCAC 60.068 52.381 0.00 0.00 0.00 3.18
920 6112 0.464373 CAGCCCCGTATCAGCAACAT 60.464 55.000 0.00 0.00 0.00 2.71
921 6113 0.255890 AGCCCCGTATCAGCAACATT 59.744 50.000 0.00 0.00 0.00 2.71
922 6114 0.663153 GCCCCGTATCAGCAACATTC 59.337 55.000 0.00 0.00 0.00 2.67
929 6121 3.542875 CGTATCAGCAACATTCGCTCAAG 60.543 47.826 0.00 0.00 37.72 3.02
932 6124 0.953727 AGCAACATTCGCTCAAGCAA 59.046 45.000 2.50 0.00 42.21 3.91
935 6127 2.523015 CAACATTCGCTCAAGCAATCC 58.477 47.619 2.50 0.00 42.21 3.01
936 6128 0.729116 ACATTCGCTCAAGCAATCCG 59.271 50.000 2.50 0.00 42.21 4.18
937 6129 0.590732 CATTCGCTCAAGCAATCCGC 60.591 55.000 2.50 0.00 42.21 5.54
941 6133 3.204827 CTCAAGCAATCCGCCCGG 61.205 66.667 0.00 0.00 44.04 5.73
960 6152 1.207339 CCGTACGCGTGTGTACTCA 59.793 57.895 24.59 0.00 42.00 3.41
965 6157 0.949397 ACGCGTGTGTACTCAGAGAA 59.051 50.000 12.93 0.00 0.00 2.87
972 6164 4.214545 CGTGTGTACTCAGAGAAAGAGAGT 59.785 45.833 3.79 0.00 44.25 3.24
981 6173 7.001674 ACTCAGAGAAAGAGAGTTCAACTAGA 58.998 38.462 3.79 0.00 39.45 2.43
1011 6210 4.451150 GCGACGATGGTGAGGGCA 62.451 66.667 0.00 0.00 0.00 5.36
1046 6245 3.054503 GCTGGTCCAGTGCTGCAG 61.055 66.667 20.24 10.11 33.43 4.41
1173 6372 1.002990 GGTAGGAACACCCAACCCG 60.003 63.158 0.00 0.00 37.41 5.28
1175 6374 0.975887 GTAGGAACACCCAACCCGTA 59.024 55.000 0.00 0.00 37.41 4.02
1242 6444 1.296715 CTAGCCGCCCACAGAGTTT 59.703 57.895 0.00 0.00 0.00 2.66
1243 6445 0.321653 CTAGCCGCCCACAGAGTTTT 60.322 55.000 0.00 0.00 0.00 2.43
1244 6446 0.109723 TAGCCGCCCACAGAGTTTTT 59.890 50.000 0.00 0.00 0.00 1.94
1267 6469 6.687081 TTTCTTTTATAACCGCCATACTGG 57.313 37.500 0.00 0.00 41.55 4.00
1289 6491 7.712205 ACTGGCAATTTTATTCAATAATCAGGC 59.288 33.333 0.00 0.00 0.00 4.85
1290 6492 6.700960 TGGCAATTTTATTCAATAATCAGGCG 59.299 34.615 0.00 0.00 0.00 5.52
1291 6493 6.146021 GGCAATTTTATTCAATAATCAGGCGG 59.854 38.462 0.00 0.00 0.00 6.13
1292 6494 6.701400 GCAATTTTATTCAATAATCAGGCGGT 59.299 34.615 0.00 0.00 0.00 5.68
1293 6495 7.224557 GCAATTTTATTCAATAATCAGGCGGTT 59.775 33.333 0.00 0.00 0.00 4.44
1294 6496 9.097257 CAATTTTATTCAATAATCAGGCGGTTT 57.903 29.630 0.00 0.00 0.00 3.27
1296 6498 9.744468 ATTTTATTCAATAATCAGGCGGTTTAC 57.256 29.630 0.00 0.00 0.00 2.01
1297 6499 7.867305 TTATTCAATAATCAGGCGGTTTACA 57.133 32.000 0.00 0.00 0.00 2.41
1298 6500 6.959639 ATTCAATAATCAGGCGGTTTACAT 57.040 33.333 0.00 0.00 0.00 2.29
1299 6501 6.371809 TTCAATAATCAGGCGGTTTACATC 57.628 37.500 0.00 0.00 0.00 3.06
1300 6502 5.680619 TCAATAATCAGGCGGTTTACATCT 58.319 37.500 0.00 0.00 0.00 2.90
1301 6503 5.527214 TCAATAATCAGGCGGTTTACATCTG 59.473 40.000 0.00 0.00 0.00 2.90
1302 6504 3.627395 AATCAGGCGGTTTACATCTGA 57.373 42.857 0.00 0.00 38.59 3.27
1303 6505 3.845781 ATCAGGCGGTTTACATCTGAT 57.154 42.857 0.00 0.00 39.50 2.90
1304 6506 3.627395 TCAGGCGGTTTACATCTGATT 57.373 42.857 0.00 0.00 30.58 2.57
1305 6507 3.270027 TCAGGCGGTTTACATCTGATTG 58.730 45.455 0.00 0.00 30.58 2.67
1306 6508 2.017049 AGGCGGTTTACATCTGATTGC 58.983 47.619 0.00 0.00 0.00 3.56
1307 6509 1.742831 GGCGGTTTACATCTGATTGCA 59.257 47.619 0.00 0.00 0.00 4.08
1308 6510 2.358898 GGCGGTTTACATCTGATTGCAT 59.641 45.455 0.00 0.00 0.00 3.96
1309 6511 3.365832 GCGGTTTACATCTGATTGCATG 58.634 45.455 0.00 0.00 0.00 4.06
1310 6512 3.793129 GCGGTTTACATCTGATTGCATGG 60.793 47.826 0.00 0.00 0.00 3.66
1311 6513 3.378112 CGGTTTACATCTGATTGCATGGT 59.622 43.478 0.00 0.00 0.00 3.55
1312 6514 4.142403 CGGTTTACATCTGATTGCATGGTT 60.142 41.667 0.00 0.00 0.00 3.67
1313 6515 5.104374 GGTTTACATCTGATTGCATGGTTG 58.896 41.667 0.00 0.00 0.00 3.77
1327 6529 3.655486 CATGGTTGCAATCAAGAAAGCA 58.345 40.909 17.88 0.07 38.77 3.91
1328 6530 3.374220 TGGTTGCAATCAAGAAAGCAG 57.626 42.857 10.70 0.00 38.35 4.24
1329 6531 2.036217 TGGTTGCAATCAAGAAAGCAGG 59.964 45.455 10.70 0.00 38.35 4.85
1330 6532 2.297033 GGTTGCAATCAAGAAAGCAGGA 59.703 45.455 4.39 0.00 38.35 3.86
1331 6533 3.056322 GGTTGCAATCAAGAAAGCAGGAT 60.056 43.478 4.39 0.00 38.35 3.24
1332 6534 4.562143 GGTTGCAATCAAGAAAGCAGGATT 60.562 41.667 4.39 0.00 38.35 3.01
1333 6535 5.336690 GGTTGCAATCAAGAAAGCAGGATTA 60.337 40.000 4.39 0.00 38.35 1.75
1334 6536 5.314923 TGCAATCAAGAAAGCAGGATTAC 57.685 39.130 0.00 0.00 32.48 1.89
1335 6537 4.766373 TGCAATCAAGAAAGCAGGATTACA 59.234 37.500 0.00 0.00 32.48 2.41
1336 6538 5.419788 TGCAATCAAGAAAGCAGGATTACAT 59.580 36.000 0.00 0.00 32.48 2.29
1337 6539 5.975939 GCAATCAAGAAAGCAGGATTACATC 59.024 40.000 0.00 0.00 0.00 3.06
1338 6540 6.405065 GCAATCAAGAAAGCAGGATTACATCA 60.405 38.462 0.00 0.00 0.00 3.07
1339 6541 7.683704 GCAATCAAGAAAGCAGGATTACATCAT 60.684 37.037 0.00 0.00 0.00 2.45
1340 6542 8.843262 CAATCAAGAAAGCAGGATTACATCATA 58.157 33.333 0.00 0.00 0.00 2.15
1341 6543 7.792374 TCAAGAAAGCAGGATTACATCATAC 57.208 36.000 0.00 0.00 0.00 2.39
1342 6544 6.479990 TCAAGAAAGCAGGATTACATCATACG 59.520 38.462 0.00 0.00 0.00 3.06
1343 6545 5.918608 AGAAAGCAGGATTACATCATACGT 58.081 37.500 0.00 0.00 0.00 3.57
1344 6546 7.050970 AGAAAGCAGGATTACATCATACGTA 57.949 36.000 0.00 0.00 0.00 3.57
1345 6547 7.497595 AGAAAGCAGGATTACATCATACGTAA 58.502 34.615 0.00 0.00 33.59 3.18
1346 6548 7.438459 AGAAAGCAGGATTACATCATACGTAAC 59.562 37.037 0.00 0.00 31.94 2.50
1347 6549 6.156748 AGCAGGATTACATCATACGTAACA 57.843 37.500 0.00 0.00 31.94 2.41
1348 6550 6.578944 AGCAGGATTACATCATACGTAACAA 58.421 36.000 0.00 0.00 31.94 2.83
1349 6551 6.479001 AGCAGGATTACATCATACGTAACAAC 59.521 38.462 0.00 0.00 31.94 3.32
1350 6552 6.256975 GCAGGATTACATCATACGTAACAACA 59.743 38.462 0.00 0.00 31.94 3.33
1351 6553 7.618442 CAGGATTACATCATACGTAACAACAC 58.382 38.462 0.00 0.00 31.94 3.32
1352 6554 7.491372 CAGGATTACATCATACGTAACAACACT 59.509 37.037 0.00 0.00 31.94 3.55
1353 6555 7.705325 AGGATTACATCATACGTAACAACACTC 59.295 37.037 0.00 0.00 31.94 3.51
1354 6556 6.858104 TTACATCATACGTAACAACACTCG 57.142 37.500 0.00 0.00 0.00 4.18
1355 6557 5.050644 ACATCATACGTAACAACACTCGA 57.949 39.130 0.00 0.00 0.00 4.04
1356 6558 5.463286 ACATCATACGTAACAACACTCGAA 58.537 37.500 0.00 0.00 0.00 3.71
1357 6559 5.571741 ACATCATACGTAACAACACTCGAAG 59.428 40.000 0.00 0.00 0.00 3.79
1358 6560 3.916172 TCATACGTAACAACACTCGAAGC 59.084 43.478 0.00 0.00 0.00 3.86
1359 6561 2.212869 ACGTAACAACACTCGAAGCA 57.787 45.000 0.00 0.00 0.00 3.91
1360 6562 2.124903 ACGTAACAACACTCGAAGCAG 58.875 47.619 0.00 0.00 0.00 4.24
1361 6563 2.124903 CGTAACAACACTCGAAGCAGT 58.875 47.619 0.00 0.00 0.00 4.40
1362 6564 3.243168 ACGTAACAACACTCGAAGCAGTA 60.243 43.478 0.00 0.00 0.00 2.74
1363 6565 3.732219 CGTAACAACACTCGAAGCAGTAA 59.268 43.478 0.00 0.00 0.00 2.24
1364 6566 4.374707 CGTAACAACACTCGAAGCAGTAAC 60.375 45.833 0.00 0.00 0.00 2.50
1365 6567 3.454371 ACAACACTCGAAGCAGTAACT 57.546 42.857 0.00 0.00 0.00 2.24
1366 6568 4.579454 ACAACACTCGAAGCAGTAACTA 57.421 40.909 0.00 0.00 0.00 2.24
1367 6569 4.940463 ACAACACTCGAAGCAGTAACTAA 58.060 39.130 0.00 0.00 0.00 2.24
1368 6570 5.353938 ACAACACTCGAAGCAGTAACTAAA 58.646 37.500 0.00 0.00 0.00 1.85
1369 6571 5.233689 ACAACACTCGAAGCAGTAACTAAAC 59.766 40.000 0.00 0.00 0.00 2.01
1370 6572 4.304939 ACACTCGAAGCAGTAACTAAACC 58.695 43.478 0.00 0.00 0.00 3.27
1371 6573 3.678548 CACTCGAAGCAGTAACTAAACCC 59.321 47.826 0.00 0.00 0.00 4.11
1372 6574 3.577415 ACTCGAAGCAGTAACTAAACCCT 59.423 43.478 0.00 0.00 0.00 4.34
1373 6575 4.174762 CTCGAAGCAGTAACTAAACCCTC 58.825 47.826 0.00 0.00 0.00 4.30
1374 6576 3.056322 TCGAAGCAGTAACTAAACCCTCC 60.056 47.826 0.00 0.00 0.00 4.30
1375 6577 3.056035 CGAAGCAGTAACTAAACCCTCCT 60.056 47.826 0.00 0.00 0.00 3.69
1376 6578 4.562963 CGAAGCAGTAACTAAACCCTCCTT 60.563 45.833 0.00 0.00 0.00 3.36
1377 6579 4.995624 AGCAGTAACTAAACCCTCCTTT 57.004 40.909 0.00 0.00 0.00 3.11
1378 6580 4.652822 AGCAGTAACTAAACCCTCCTTTG 58.347 43.478 0.00 0.00 0.00 2.77
1379 6581 3.190744 GCAGTAACTAAACCCTCCTTTGC 59.809 47.826 0.00 0.00 0.00 3.68
1380 6582 4.394729 CAGTAACTAAACCCTCCTTTGCA 58.605 43.478 0.00 0.00 0.00 4.08
1381 6583 4.215613 CAGTAACTAAACCCTCCTTTGCAC 59.784 45.833 0.00 0.00 0.00 4.57
1382 6584 3.306472 AACTAAACCCTCCTTTGCACA 57.694 42.857 0.00 0.00 0.00 4.57
1383 6585 2.863809 ACTAAACCCTCCTTTGCACAG 58.136 47.619 0.00 0.00 0.00 3.66
1384 6586 1.541588 CTAAACCCTCCTTTGCACAGC 59.458 52.381 0.00 0.00 0.00 4.40
1385 6587 0.396974 AAACCCTCCTTTGCACAGCA 60.397 50.000 0.00 0.00 36.47 4.41
1392 6594 1.202915 TCCTTTGCACAGCAATGAGGA 60.203 47.619 16.96 16.96 46.68 3.71
1393 6595 3.137579 TCCTTTGCACAGCAATGAGGAG 61.138 50.000 16.96 7.08 45.12 3.69
1394 6596 2.260247 TTGCACAGCAATGAGGAGC 58.740 52.632 0.00 0.00 43.99 4.70
1395 6597 0.537828 TTGCACAGCAATGAGGAGCA 60.538 50.000 0.00 0.00 43.99 4.26
1396 6598 0.323087 TGCACAGCAATGAGGAGCAT 60.323 50.000 0.00 0.00 39.43 3.79
1397 6599 0.381089 GCACAGCAATGAGGAGCATC 59.619 55.000 0.00 0.00 35.78 3.91
1398 6600 1.746470 CACAGCAATGAGGAGCATCA 58.254 50.000 0.00 0.00 35.78 3.07
1399 6601 2.298610 CACAGCAATGAGGAGCATCAT 58.701 47.619 0.00 0.00 41.72 2.45
1404 6606 2.750141 AATGAGGAGCATCATTGGCT 57.250 45.000 9.29 0.00 45.82 4.75
1405 6607 2.750141 ATGAGGAGCATCATTGGCTT 57.250 45.000 0.00 0.00 42.78 4.35
1406 6608 2.048444 TGAGGAGCATCATTGGCTTC 57.952 50.000 0.00 0.00 42.78 3.86
1408 6610 2.345124 AGGAGCATCATTGGCTTCTC 57.655 50.000 0.00 0.00 43.84 2.87
1409 6611 1.845143 AGGAGCATCATTGGCTTCTCT 59.155 47.619 0.00 0.00 43.84 3.10
1410 6612 2.158784 AGGAGCATCATTGGCTTCTCTC 60.159 50.000 0.00 0.00 43.84 3.20
1411 6613 2.220313 GAGCATCATTGGCTTCTCTCC 58.780 52.381 0.00 0.00 42.78 3.71
1412 6614 0.942962 GCATCATTGGCTTCTCTCCG 59.057 55.000 0.00 0.00 0.00 4.63
1413 6615 1.473965 GCATCATTGGCTTCTCTCCGA 60.474 52.381 0.00 0.00 0.00 4.55
1414 6616 2.481854 CATCATTGGCTTCTCTCCGAG 58.518 52.381 0.00 0.00 0.00 4.63
1415 6617 0.176680 TCATTGGCTTCTCTCCGAGC 59.823 55.000 0.00 0.00 0.00 5.03
1416 6618 1.142748 ATTGGCTTCTCTCCGAGCG 59.857 57.895 0.00 0.00 0.00 5.03
1417 6619 1.608717 ATTGGCTTCTCTCCGAGCGT 61.609 55.000 0.00 0.00 0.00 5.07
1418 6620 0.963856 TTGGCTTCTCTCCGAGCGTA 60.964 55.000 0.00 0.00 0.00 4.42
1419 6621 1.357334 GGCTTCTCTCCGAGCGTAG 59.643 63.158 0.00 0.00 0.00 3.51
1420 6622 1.378124 GGCTTCTCTCCGAGCGTAGT 61.378 60.000 0.00 0.00 0.00 2.73
1421 6623 0.248296 GCTTCTCTCCGAGCGTAGTG 60.248 60.000 0.00 0.00 0.00 2.74
1422 6624 0.378962 CTTCTCTCCGAGCGTAGTGG 59.621 60.000 0.00 0.00 0.00 4.00
1423 6625 0.035725 TTCTCTCCGAGCGTAGTGGA 60.036 55.000 0.00 0.00 0.00 4.02
1424 6626 0.180642 TCTCTCCGAGCGTAGTGGAT 59.819 55.000 0.00 0.00 0.00 3.41
1425 6627 0.309302 CTCTCCGAGCGTAGTGGATG 59.691 60.000 0.00 0.00 0.00 3.51
1426 6628 1.299468 CTCCGAGCGTAGTGGATGC 60.299 63.158 0.00 0.00 40.75 3.91
1433 6635 1.854227 GCGTAGTGGATGCTAAGACC 58.146 55.000 0.00 0.00 37.09 3.85
1434 6636 1.538419 GCGTAGTGGATGCTAAGACCC 60.538 57.143 0.00 0.00 37.09 4.46
1435 6637 2.032620 CGTAGTGGATGCTAAGACCCT 58.967 52.381 0.00 0.00 0.00 4.34
1436 6638 2.223829 CGTAGTGGATGCTAAGACCCTG 60.224 54.545 0.00 0.00 0.00 4.45
1618 6833 9.681692 CATTGATTCAGTGAATACAGAAACAAA 57.318 29.630 18.28 3.12 43.17 2.83
1679 6906 1.899437 GACTCATTCCTCCACCGCCA 61.899 60.000 0.00 0.00 0.00 5.69
1680 6907 1.153289 CTCATTCCTCCACCGCCAG 60.153 63.158 0.00 0.00 0.00 4.85
1726 6953 1.018148 GCGATCTCTCGTCCTCTTCA 58.982 55.000 0.00 0.00 46.71 3.02
1727 6954 1.268335 GCGATCTCTCGTCCTCTTCAC 60.268 57.143 0.00 0.00 46.71 3.18
1737 6964 4.379243 CTCTTCACCGGCGCCTGT 62.379 66.667 26.68 22.69 0.00 4.00
1848 7076 0.106918 TTTGCCCCTCTGTTCAACGT 60.107 50.000 0.00 0.00 0.00 3.99
1867 7095 2.436824 GGCGTTCTTCCTGCTCCC 60.437 66.667 0.00 0.00 0.00 4.30
1934 7162 4.397417 CCAATCACATCAAGTTTCTCCTCC 59.603 45.833 0.00 0.00 0.00 4.30
2029 7260 4.875713 ATTGACCATCCGCCGCCC 62.876 66.667 0.00 0.00 0.00 6.13
2083 7314 2.234661 TGCTCATGTCGTTCTCTGGATT 59.765 45.455 0.00 0.00 0.00 3.01
2221 7452 1.665679 CTCAATCGCAAGTACCGCAAT 59.334 47.619 5.79 0.00 39.48 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
262 263 7.438459 CGCCAATACTAAGCTAACCATATATCC 59.562 40.741 0.00 0.00 0.00 2.59
270 279 2.801111 GAGCGCCAATACTAAGCTAACC 59.199 50.000 2.29 0.00 38.39 2.85
343 353 8.408601 GGTGCATCATTTACTGTCATTTAAGAT 58.591 33.333 0.00 0.00 0.00 2.40
370 380 4.446371 TGTAGGCTAAGACGAGGTACTAC 58.554 47.826 0.00 0.00 41.55 2.73
371 381 4.760530 TGTAGGCTAAGACGAGGTACTA 57.239 45.455 0.00 0.00 41.55 1.82
451 1008 2.039480 ACTCAGAGACAGTACGGTGGTA 59.961 50.000 2.49 0.00 0.00 3.25
488 1045 5.698104 TCTTTCCATGTTGCCTCATATGAT 58.302 37.500 5.72 0.00 0.00 2.45
533 1090 8.517878 GCTGTCGGGTACTAACTCATAATTATA 58.482 37.037 0.00 0.00 0.00 0.98
534 1091 7.376615 GCTGTCGGGTACTAACTCATAATTAT 58.623 38.462 0.00 0.00 0.00 1.28
535 1092 6.239120 GGCTGTCGGGTACTAACTCATAATTA 60.239 42.308 0.00 0.00 0.00 1.40
548 1105 2.189521 CCCATGGCTGTCGGGTAC 59.810 66.667 6.09 0.00 35.03 3.34
549 1106 3.087253 CCCCATGGCTGTCGGGTA 61.087 66.667 6.09 0.00 38.40 3.69
551 1108 4.802051 CACCCCATGGCTGTCGGG 62.802 72.222 6.09 3.24 41.71 5.14
552 1109 3.567579 AACACCCCATGGCTGTCGG 62.568 63.158 6.09 4.08 33.59 4.79
553 1110 2.034066 AACACCCCATGGCTGTCG 59.966 61.111 6.09 3.79 33.59 4.35
554 1111 0.962356 CTGAACACCCCATGGCTGTC 60.962 60.000 6.09 5.06 33.59 3.51
623 1187 4.081642 GGCTGACCAGAGTACTGTTGATTA 60.082 45.833 0.00 0.00 42.05 1.75
624 1188 3.307059 GGCTGACCAGAGTACTGTTGATT 60.307 47.826 0.00 0.00 42.05 2.57
657 5823 0.253044 GCTGCTCAACCCAGTCCATA 59.747 55.000 0.00 0.00 32.93 2.74
664 5830 2.997952 TTTACGCGCTGCTCAACCCA 62.998 55.000 5.73 0.00 0.00 4.51
681 5847 0.739813 GCAGCGTGTAGGTCGGATTT 60.740 55.000 0.00 0.00 0.00 2.17
711 5885 2.409715 GGTTGTACTTTTACGCTCGTCC 59.590 50.000 0.00 0.00 0.00 4.79
776 5950 3.641434 ACTTCTACGGGTCTAGCACTA 57.359 47.619 0.00 0.00 0.00 2.74
779 5953 4.226427 TCTAACTTCTACGGGTCTAGCA 57.774 45.455 0.00 0.00 0.00 3.49
780 5954 4.202000 GGTTCTAACTTCTACGGGTCTAGC 60.202 50.000 0.00 0.00 0.00 3.42
782 5956 4.018050 AGGGTTCTAACTTCTACGGGTCTA 60.018 45.833 0.00 0.00 0.00 2.59
783 5957 3.095332 GGGTTCTAACTTCTACGGGTCT 58.905 50.000 0.00 0.00 0.00 3.85
784 5958 3.095332 AGGGTTCTAACTTCTACGGGTC 58.905 50.000 0.00 0.00 0.00 4.46
785 5959 3.181393 AGGGTTCTAACTTCTACGGGT 57.819 47.619 0.00 0.00 0.00 5.28
786 5960 5.597594 AGATTAGGGTTCTAACTTCTACGGG 59.402 44.000 0.00 0.00 38.19 5.28
787 5961 6.712179 AGATTAGGGTTCTAACTTCTACGG 57.288 41.667 0.00 0.00 38.19 4.02
788 5962 8.248945 TGAAAGATTAGGGTTCTAACTTCTACG 58.751 37.037 0.00 0.00 38.19 3.51
789 5963 9.939802 TTGAAAGATTAGGGTTCTAACTTCTAC 57.060 33.333 0.00 0.00 38.19 2.59
790 5964 9.939802 GTTGAAAGATTAGGGTTCTAACTTCTA 57.060 33.333 0.00 0.00 38.19 2.10
791 5965 7.883833 GGTTGAAAGATTAGGGTTCTAACTTCT 59.116 37.037 0.00 0.00 38.19 2.85
792 5966 7.664318 TGGTTGAAAGATTAGGGTTCTAACTTC 59.336 37.037 0.00 0.00 38.19 3.01
793 5967 7.523415 TGGTTGAAAGATTAGGGTTCTAACTT 58.477 34.615 0.00 0.00 38.19 2.66
794 5968 7.086685 TGGTTGAAAGATTAGGGTTCTAACT 57.913 36.000 0.00 0.00 38.19 2.24
795 5969 6.374613 CCTGGTTGAAAGATTAGGGTTCTAAC 59.625 42.308 0.00 0.00 38.19 2.34
796 5970 6.481643 CCTGGTTGAAAGATTAGGGTTCTAA 58.518 40.000 0.00 0.00 39.51 2.10
855 6038 1.957877 GTCGTTGGAGGAGAGATAGGG 59.042 57.143 0.00 0.00 0.00 3.53
859 6042 1.187087 GTGGTCGTTGGAGGAGAGAT 58.813 55.000 0.00 0.00 0.00 2.75
873 6056 1.200948 GAATGCCTTGCTTGAGTGGTC 59.799 52.381 0.00 0.00 0.00 4.02
885 6069 1.188863 GCTGGATTGGTGAATGCCTT 58.811 50.000 0.00 0.00 0.00 4.35
895 6079 0.250467 CTGATACGGGGCTGGATTGG 60.250 60.000 0.00 0.00 0.00 3.16
920 6112 2.398554 GGCGGATTGCTTGAGCGAA 61.399 57.895 0.00 0.00 45.83 4.70
921 6113 2.819595 GGCGGATTGCTTGAGCGA 60.820 61.111 0.00 0.00 45.83 4.93
922 6114 3.880846 GGGCGGATTGCTTGAGCG 61.881 66.667 0.00 0.00 45.83 5.03
941 6133 2.126734 AGTACACACGCGTACGGC 60.127 61.111 13.44 8.47 45.25 5.68
942 6134 0.791983 CTGAGTACACACGCGTACGG 60.792 60.000 13.44 6.96 45.25 4.02
943 6135 0.164432 TCTGAGTACACACGCGTACG 59.836 55.000 13.44 11.84 45.25 3.67
944 6136 1.462283 TCTCTGAGTACACACGCGTAC 59.538 52.381 13.44 6.60 41.75 3.67
945 6137 1.799544 TCTCTGAGTACACACGCGTA 58.200 50.000 13.44 0.00 0.00 4.42
946 6138 0.949397 TTCTCTGAGTACACACGCGT 59.051 50.000 5.58 5.58 0.00 6.01
947 6139 1.979469 CTTTCTCTGAGTACACACGCG 59.021 52.381 3.53 3.53 0.00 6.01
948 6140 3.058155 TCTCTTTCTCTGAGTACACACGC 60.058 47.826 4.32 0.00 33.59 5.34
972 6164 7.592533 GTCGCCATATACGTATTTCTAGTTGAA 59.407 37.037 14.33 0.00 0.00 2.69
981 6173 4.171005 CCATCGTCGCCATATACGTATTT 58.829 43.478 14.33 2.61 39.99 1.40
1113 6312 1.526686 CTGCATGATAAGCGCCCCA 60.527 57.895 2.29 0.00 33.85 4.96
1148 6347 4.105553 GTGTTCCTACCCCGGGGC 62.106 72.222 40.67 22.53 39.32 5.80
1157 6356 0.975887 GTACGGGTTGGGTGTTCCTA 59.024 55.000 0.00 0.00 36.20 2.94
1173 6372 1.219935 GATGGGGTCGTGGGTGTAC 59.780 63.158 0.00 0.00 0.00 2.90
1175 6374 2.150719 TTGATGGGGTCGTGGGTGT 61.151 57.895 0.00 0.00 0.00 4.16
1263 6465 7.712205 GCCTGATTATTGAATAAAATTGCCAGT 59.288 33.333 1.27 0.00 0.00 4.00
1264 6466 7.095940 CGCCTGATTATTGAATAAAATTGCCAG 60.096 37.037 1.27 3.73 0.00 4.85
1265 6467 6.700960 CGCCTGATTATTGAATAAAATTGCCA 59.299 34.615 1.27 0.00 0.00 4.92
1266 6468 6.146021 CCGCCTGATTATTGAATAAAATTGCC 59.854 38.462 1.27 0.00 0.00 4.52
1267 6469 6.701400 ACCGCCTGATTATTGAATAAAATTGC 59.299 34.615 1.27 2.99 0.00 3.56
1268 6470 8.647143 AACCGCCTGATTATTGAATAAAATTG 57.353 30.769 1.27 0.00 0.00 2.32
1270 6472 9.744468 GTAAACCGCCTGATTATTGAATAAAAT 57.256 29.630 1.27 0.00 0.00 1.82
1271 6473 8.740906 TGTAAACCGCCTGATTATTGAATAAAA 58.259 29.630 1.27 0.00 0.00 1.52
1272 6474 8.282455 TGTAAACCGCCTGATTATTGAATAAA 57.718 30.769 1.27 0.00 0.00 1.40
1273 6475 7.867305 TGTAAACCGCCTGATTATTGAATAA 57.133 32.000 0.00 0.00 0.00 1.40
1274 6476 7.936847 AGATGTAAACCGCCTGATTATTGAATA 59.063 33.333 0.00 0.00 0.00 1.75
1275 6477 6.772716 AGATGTAAACCGCCTGATTATTGAAT 59.227 34.615 0.00 0.00 0.00 2.57
1276 6478 6.038161 CAGATGTAAACCGCCTGATTATTGAA 59.962 38.462 0.00 0.00 0.00 2.69
1277 6479 5.527214 CAGATGTAAACCGCCTGATTATTGA 59.473 40.000 0.00 0.00 0.00 2.57
1278 6480 5.527214 TCAGATGTAAACCGCCTGATTATTG 59.473 40.000 0.00 0.00 0.00 1.90
1279 6481 5.680619 TCAGATGTAAACCGCCTGATTATT 58.319 37.500 0.00 0.00 0.00 1.40
1280 6482 5.290493 TCAGATGTAAACCGCCTGATTAT 57.710 39.130 0.00 0.00 0.00 1.28
1281 6483 4.746535 TCAGATGTAAACCGCCTGATTA 57.253 40.909 0.00 0.00 0.00 1.75
1282 6484 3.627395 TCAGATGTAAACCGCCTGATT 57.373 42.857 0.00 0.00 0.00 2.57
1283 6485 3.845781 ATCAGATGTAAACCGCCTGAT 57.154 42.857 0.00 0.00 39.10 2.90
1284 6486 3.270027 CAATCAGATGTAAACCGCCTGA 58.730 45.455 0.00 0.00 38.12 3.86
1285 6487 2.223340 GCAATCAGATGTAAACCGCCTG 60.223 50.000 0.00 0.00 0.00 4.85
1286 6488 2.017049 GCAATCAGATGTAAACCGCCT 58.983 47.619 0.00 0.00 0.00 5.52
1287 6489 1.742831 TGCAATCAGATGTAAACCGCC 59.257 47.619 0.00 0.00 0.00 6.13
1288 6490 3.365832 CATGCAATCAGATGTAAACCGC 58.634 45.455 0.00 0.00 0.00 5.68
1289 6491 3.378112 ACCATGCAATCAGATGTAAACCG 59.622 43.478 0.00 0.00 0.00 4.44
1290 6492 4.989279 ACCATGCAATCAGATGTAAACC 57.011 40.909 0.00 0.00 0.00 3.27
1306 6508 3.655486 TGCTTTCTTGATTGCAACCATG 58.345 40.909 0.00 0.00 32.12 3.66
1307 6509 3.306502 CCTGCTTTCTTGATTGCAACCAT 60.307 43.478 0.00 0.00 34.90 3.55
1308 6510 2.036217 CCTGCTTTCTTGATTGCAACCA 59.964 45.455 0.00 0.00 34.90 3.67
1309 6511 2.297033 TCCTGCTTTCTTGATTGCAACC 59.703 45.455 0.00 0.00 34.90 3.77
1310 6512 3.648339 TCCTGCTTTCTTGATTGCAAC 57.352 42.857 0.00 0.00 34.90 4.17
1311 6513 4.877378 AATCCTGCTTTCTTGATTGCAA 57.123 36.364 0.00 0.00 34.90 4.08
1312 6514 4.766373 TGTAATCCTGCTTTCTTGATTGCA 59.234 37.500 0.00 0.00 37.44 4.08
1313 6515 5.314923 TGTAATCCTGCTTTCTTGATTGC 57.685 39.130 0.00 0.00 32.57 3.56
1314 6516 7.092137 TGATGTAATCCTGCTTTCTTGATTG 57.908 36.000 0.00 0.00 44.73 2.67
1315 6517 7.893124 ATGATGTAATCCTGCTTTCTTGATT 57.107 32.000 0.00 0.00 44.73 2.57
1316 6518 7.172190 CGTATGATGTAATCCTGCTTTCTTGAT 59.828 37.037 0.00 0.00 44.73 2.57
1317 6519 6.479990 CGTATGATGTAATCCTGCTTTCTTGA 59.520 38.462 0.00 0.00 44.73 3.02
1318 6520 6.258727 ACGTATGATGTAATCCTGCTTTCTTG 59.741 38.462 0.00 0.00 44.73 3.02
1319 6521 6.349300 ACGTATGATGTAATCCTGCTTTCTT 58.651 36.000 0.00 0.00 44.73 2.52
1320 6522 5.918608 ACGTATGATGTAATCCTGCTTTCT 58.081 37.500 0.00 0.00 44.73 2.52
1321 6523 7.223971 TGTTACGTATGATGTAATCCTGCTTTC 59.776 37.037 0.00 0.00 44.73 2.62
1322 6524 7.045416 TGTTACGTATGATGTAATCCTGCTTT 58.955 34.615 0.00 0.00 44.73 3.51
1323 6525 6.578944 TGTTACGTATGATGTAATCCTGCTT 58.421 36.000 0.00 0.00 44.73 3.91
1324 6526 6.156748 TGTTACGTATGATGTAATCCTGCT 57.843 37.500 0.00 0.00 44.73 4.24
1325 6527 6.256975 TGTTGTTACGTATGATGTAATCCTGC 59.743 38.462 0.00 0.00 44.73 4.85
1326 6528 7.491372 AGTGTTGTTACGTATGATGTAATCCTG 59.509 37.037 0.00 0.00 44.73 3.86
1327 6529 7.553334 AGTGTTGTTACGTATGATGTAATCCT 58.447 34.615 0.00 0.00 44.73 3.24
1328 6530 7.305820 CGAGTGTTGTTACGTATGATGTAATCC 60.306 40.741 0.00 0.00 44.73 3.01
1329 6531 7.430211 TCGAGTGTTGTTACGTATGATGTAATC 59.570 37.037 0.00 0.00 45.83 1.75
1330 6532 7.252708 TCGAGTGTTGTTACGTATGATGTAAT 58.747 34.615 0.00 0.00 32.79 1.89
1331 6533 6.610456 TCGAGTGTTGTTACGTATGATGTAA 58.390 36.000 0.00 0.00 0.00 2.41
1332 6534 6.180771 TCGAGTGTTGTTACGTATGATGTA 57.819 37.500 0.00 0.00 0.00 2.29
1333 6535 5.050644 TCGAGTGTTGTTACGTATGATGT 57.949 39.130 0.00 0.00 0.00 3.06
1334 6536 5.498700 GCTTCGAGTGTTGTTACGTATGATG 60.499 44.000 0.00 0.00 0.00 3.07
1335 6537 4.561606 GCTTCGAGTGTTGTTACGTATGAT 59.438 41.667 0.00 0.00 0.00 2.45
1336 6538 3.916172 GCTTCGAGTGTTGTTACGTATGA 59.084 43.478 0.00 0.00 0.00 2.15
1337 6539 3.671459 TGCTTCGAGTGTTGTTACGTATG 59.329 43.478 0.00 0.00 0.00 2.39
1338 6540 3.904571 TGCTTCGAGTGTTGTTACGTAT 58.095 40.909 0.00 0.00 0.00 3.06
1339 6541 3.243168 ACTGCTTCGAGTGTTGTTACGTA 60.243 43.478 0.00 0.00 0.00 3.57
1340 6542 2.124903 CTGCTTCGAGTGTTGTTACGT 58.875 47.619 0.00 0.00 0.00 3.57
1341 6543 2.124903 ACTGCTTCGAGTGTTGTTACG 58.875 47.619 0.00 0.00 0.00 3.18
1342 6544 4.743644 AGTTACTGCTTCGAGTGTTGTTAC 59.256 41.667 0.00 0.00 0.00 2.50
1343 6545 4.940463 AGTTACTGCTTCGAGTGTTGTTA 58.060 39.130 0.00 0.00 0.00 2.41
1344 6546 3.793559 AGTTACTGCTTCGAGTGTTGTT 58.206 40.909 0.00 0.00 0.00 2.83
1345 6547 3.454371 AGTTACTGCTTCGAGTGTTGT 57.546 42.857 0.00 0.00 0.00 3.32
1346 6548 5.333111 GGTTTAGTTACTGCTTCGAGTGTTG 60.333 44.000 0.00 0.00 0.00 3.33
1347 6549 4.748600 GGTTTAGTTACTGCTTCGAGTGTT 59.251 41.667 0.00 0.00 0.00 3.32
1348 6550 4.304939 GGTTTAGTTACTGCTTCGAGTGT 58.695 43.478 0.00 0.00 0.00 3.55
1349 6551 3.678548 GGGTTTAGTTACTGCTTCGAGTG 59.321 47.826 0.00 0.00 0.00 3.51
1350 6552 3.577415 AGGGTTTAGTTACTGCTTCGAGT 59.423 43.478 0.00 0.00 0.00 4.18
1351 6553 4.174762 GAGGGTTTAGTTACTGCTTCGAG 58.825 47.826 0.00 0.00 0.00 4.04
1352 6554 3.056322 GGAGGGTTTAGTTACTGCTTCGA 60.056 47.826 0.00 0.00 0.00 3.71
1353 6555 3.056035 AGGAGGGTTTAGTTACTGCTTCG 60.056 47.826 0.00 0.00 0.00 3.79
1354 6556 4.554960 AGGAGGGTTTAGTTACTGCTTC 57.445 45.455 0.00 0.00 0.00 3.86
1355 6557 4.995624 AAGGAGGGTTTAGTTACTGCTT 57.004 40.909 0.00 0.00 36.90 3.91
1356 6558 4.652822 CAAAGGAGGGTTTAGTTACTGCT 58.347 43.478 0.00 0.00 32.80 4.24
1357 6559 3.190744 GCAAAGGAGGGTTTAGTTACTGC 59.809 47.826 0.00 0.00 0.00 4.40
1358 6560 4.215613 GTGCAAAGGAGGGTTTAGTTACTG 59.784 45.833 0.00 0.00 0.00 2.74
1359 6561 4.141344 TGTGCAAAGGAGGGTTTAGTTACT 60.141 41.667 0.00 0.00 0.00 2.24
1360 6562 4.139038 TGTGCAAAGGAGGGTTTAGTTAC 58.861 43.478 0.00 0.00 0.00 2.50
1361 6563 4.394729 CTGTGCAAAGGAGGGTTTAGTTA 58.605 43.478 0.00 0.00 0.00 2.24
1362 6564 3.222603 CTGTGCAAAGGAGGGTTTAGTT 58.777 45.455 0.00 0.00 0.00 2.24
1363 6565 2.863809 CTGTGCAAAGGAGGGTTTAGT 58.136 47.619 0.00 0.00 0.00 2.24
1364 6566 1.541588 GCTGTGCAAAGGAGGGTTTAG 59.458 52.381 5.91 0.00 0.00 1.85
1365 6567 1.133637 TGCTGTGCAAAGGAGGGTTTA 60.134 47.619 5.91 0.00 34.76 2.01
1366 6568 0.396974 TGCTGTGCAAAGGAGGGTTT 60.397 50.000 5.91 0.00 34.76 3.27
1367 6569 0.396974 TTGCTGTGCAAAGGAGGGTT 60.397 50.000 5.91 0.00 45.96 4.11
1368 6570 1.229927 TTGCTGTGCAAAGGAGGGT 59.770 52.632 5.91 0.00 45.96 4.34
1369 6571 4.179361 TTGCTGTGCAAAGGAGGG 57.821 55.556 5.91 0.00 45.96 4.30
1377 6579 0.323087 ATGCTCCTCATTGCTGTGCA 60.323 50.000 0.00 0.00 36.47 4.57
1378 6580 0.381089 GATGCTCCTCATTGCTGTGC 59.619 55.000 0.00 0.00 35.05 4.57
1379 6581 1.746470 TGATGCTCCTCATTGCTGTG 58.254 50.000 0.00 0.00 35.05 3.66
1380 6582 2.730934 ATGATGCTCCTCATTGCTGT 57.269 45.000 0.00 0.00 35.05 4.40
1385 6587 2.750141 AGCCAATGATGCTCCTCATT 57.250 45.000 4.54 4.54 44.66 2.57
1386 6588 2.175069 AGAAGCCAATGATGCTCCTCAT 59.825 45.455 0.00 0.00 38.34 2.90
1387 6589 1.562942 AGAAGCCAATGATGCTCCTCA 59.437 47.619 0.00 0.00 38.34 3.86
1388 6590 2.158784 AGAGAAGCCAATGATGCTCCTC 60.159 50.000 0.00 0.00 38.34 3.71
1389 6591 1.845143 AGAGAAGCCAATGATGCTCCT 59.155 47.619 0.00 0.00 38.34 3.69
1390 6592 2.220313 GAGAGAAGCCAATGATGCTCC 58.780 52.381 0.00 0.00 38.34 4.70
1391 6593 2.220313 GGAGAGAAGCCAATGATGCTC 58.780 52.381 0.00 0.00 38.34 4.26
1392 6594 1.474677 CGGAGAGAAGCCAATGATGCT 60.475 52.381 0.00 0.00 41.89 3.79
1393 6595 0.942962 CGGAGAGAAGCCAATGATGC 59.057 55.000 0.00 0.00 0.00 3.91
1394 6596 2.609427 TCGGAGAGAAGCCAATGATG 57.391 50.000 0.00 0.00 0.00 3.07
1407 6609 1.725557 GCATCCACTACGCTCGGAGA 61.726 60.000 9.69 0.00 30.84 3.71
1408 6610 1.299468 GCATCCACTACGCTCGGAG 60.299 63.158 0.00 0.00 30.84 4.63
1409 6611 0.464916 TAGCATCCACTACGCTCGGA 60.465 55.000 0.00 0.00 37.20 4.55
1410 6612 0.384309 TTAGCATCCACTACGCTCGG 59.616 55.000 0.00 0.00 37.20 4.63
1411 6613 1.333931 TCTTAGCATCCACTACGCTCG 59.666 52.381 0.00 0.00 37.20 5.03
1412 6614 2.544069 GGTCTTAGCATCCACTACGCTC 60.544 54.545 0.00 0.00 37.20 5.03
1413 6615 1.409427 GGTCTTAGCATCCACTACGCT 59.591 52.381 0.00 0.00 39.80 5.07
1414 6616 1.538419 GGGTCTTAGCATCCACTACGC 60.538 57.143 0.00 0.00 0.00 4.42
1415 6617 2.032620 AGGGTCTTAGCATCCACTACG 58.967 52.381 0.00 0.00 0.00 3.51
1416 6618 3.031736 TCAGGGTCTTAGCATCCACTAC 58.968 50.000 0.00 0.00 0.00 2.73
1417 6619 3.398318 TCAGGGTCTTAGCATCCACTA 57.602 47.619 0.00 0.00 0.00 2.74
1418 6620 2.254152 TCAGGGTCTTAGCATCCACT 57.746 50.000 0.00 0.00 0.00 4.00
1419 6621 3.274288 CTTTCAGGGTCTTAGCATCCAC 58.726 50.000 0.00 0.00 0.00 4.02
1420 6622 2.912956 ACTTTCAGGGTCTTAGCATCCA 59.087 45.455 0.00 0.00 0.00 3.41
1421 6623 3.274288 CACTTTCAGGGTCTTAGCATCC 58.726 50.000 0.00 0.00 0.00 3.51
1422 6624 3.944087 ACACTTTCAGGGTCTTAGCATC 58.056 45.455 0.00 0.00 0.00 3.91
1423 6625 4.373156 AACACTTTCAGGGTCTTAGCAT 57.627 40.909 0.00 0.00 24.25 3.79
1424 6626 3.857157 AACACTTTCAGGGTCTTAGCA 57.143 42.857 0.00 0.00 24.25 3.49
1425 6627 5.333875 CGTTTAACACTTTCAGGGTCTTAGC 60.334 44.000 0.00 0.00 24.25 3.09
1426 6628 5.178809 CCGTTTAACACTTTCAGGGTCTTAG 59.821 44.000 0.00 0.00 24.25 2.18
1427 6629 5.058490 CCGTTTAACACTTTCAGGGTCTTA 58.942 41.667 0.00 0.00 24.25 2.10
1428 6630 3.881089 CCGTTTAACACTTTCAGGGTCTT 59.119 43.478 0.00 0.00 24.25 3.01
1429 6631 3.118149 ACCGTTTAACACTTTCAGGGTCT 60.118 43.478 0.00 0.00 24.25 3.85
1430 6632 3.208594 ACCGTTTAACACTTTCAGGGTC 58.791 45.455 0.00 0.00 24.25 4.46
1431 6633 3.208594 GACCGTTTAACACTTTCAGGGT 58.791 45.455 0.00 0.00 29.33 4.34
1432 6634 3.002965 GTGACCGTTTAACACTTTCAGGG 59.997 47.826 0.00 0.00 0.00 4.45
1433 6635 3.875134 AGTGACCGTTTAACACTTTCAGG 59.125 43.478 0.00 0.00 41.21 3.86
1618 6833 6.038997 GTAACTGATACCAAGTTGGAGAGT 57.961 41.667 28.80 18.47 40.96 3.24
1774 7001 4.097361 GAGGGGGAGGTGCCGAAC 62.097 72.222 0.00 0.00 37.63 3.95
1848 7076 2.261671 GAGCAGGAAGAACGCCGA 59.738 61.111 0.00 0.00 0.00 5.54
1934 7162 2.233605 TAGTTGTGATCGGCGGGGTG 62.234 60.000 7.21 0.00 0.00 4.61
2221 7452 2.604686 AGGTCGCCCTGCTTGAGA 60.605 61.111 0.00 0.00 40.58 3.27


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

AutoCloner maintained by Alex Coulton.