Multiple sequence alignment - TraesCS4A01G069100

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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 TraesCS4A01G069100 chr4A 100.000 2714 0 0 1 2714 67296662 67299375 0.000000e+00 5012
1 TraesCS4A01G069100 chr4B 88.368 2347 170 47 390 2704 472671421 472673696 0.000000e+00 2726
2 TraesCS4A01G069100 chr4B 81.175 1004 108 38 658 1598 472640382 472641367 0.000000e+00 732
3 TraesCS4A01G069100 chr4D 92.035 791 19 8 792 1558 386121622 386122392 0.000000e+00 1072
4 TraesCS4A01G069100 chr4D 91.290 597 27 10 1599 2188 386122390 386122968 0.000000e+00 791
5 TraesCS4A01G069100 chr4D 81.791 335 42 13 2372 2702 386143089 386143408 2.070000e-66 263
6 TraesCS4A01G069100 chr4D 96.610 118 4 0 665 782 386121295 386121412 2.130000e-46 196
7 TraesCS4A01G069100 chr4D 80.303 198 21 16 189 379 308826407 308826593 1.700000e-27 134
8 TraesCS4A01G069100 chr2B 96.809 376 12 0 1 376 39976245 39975870 1.770000e-176 628
9 TraesCS4A01G069100 chr2B 83.938 193 14 15 189 374 695682399 695682217 4.650000e-38 169
10 TraesCS4A01G069100 chr7B 87.586 145 6 7 235 374 687409266 687409403 1.010000e-34 158
11 TraesCS4A01G069100 chr5D 82.902 193 16 14 189 374 379267044 379266862 1.010000e-34 158
12 TraesCS4A01G069100 chr5A 82.383 193 13 19 189 374 589247130 589246952 6.050000e-32 148
13 TraesCS4A01G069100 chr5A 73.558 208 50 5 2499 2705 607315921 607316124 1.040000e-09 75
14 TraesCS4A01G069100 chr7A 80.435 184 26 10 196 374 653654489 653654311 6.100000e-27 132
15 TraesCS4A01G069100 chr7A 82.166 157 19 8 221 374 653621924 653621774 2.840000e-25 126
16 TraesCS4A01G069100 chr1D 79.793 193 18 17 189 374 12398785 12398607 1.320000e-23 121
17 TraesCS4A01G069100 chr6B 75.949 237 45 8 2473 2704 591255900 591256129 7.940000e-21 111


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 TraesCS4A01G069100 chr4A 67296662 67299375 2713 False 5012.000000 5012 100.000000 1 2714 1 chr4A.!!$F1 2713
1 TraesCS4A01G069100 chr4B 472671421 472673696 2275 False 2726.000000 2726 88.368000 390 2704 1 chr4B.!!$F2 2314
2 TraesCS4A01G069100 chr4B 472640382 472641367 985 False 732.000000 732 81.175000 658 1598 1 chr4B.!!$F1 940
3 TraesCS4A01G069100 chr4D 386121295 386122968 1673 False 686.333333 1072 93.311667 665 2188 3 chr4D.!!$F3 1523

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
741 743 0.038251 TGCAGACTTGAGATTCGCGT 60.038 50.0 5.77 0.0 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 2624 0.033781 CCGAACAGTCCGGGTGTTTA 59.966 55.0 20.05 0.0 43.05 2.01 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
45 46 3.857854 CGCCAGATCTGCGTGCAC 61.858 66.667 23.01 6.82 46.59 4.57
46 47 3.503363 GCCAGATCTGCGTGCACC 61.503 66.667 17.76 4.74 0.00 5.01
47 48 3.190849 CCAGATCTGCGTGCACCG 61.191 66.667 17.76 7.80 40.40 4.94
60 61 3.322466 CACCGCCCCCTCAAGTCT 61.322 66.667 0.00 0.00 0.00 3.24
61 62 3.003763 ACCGCCCCCTCAAGTCTC 61.004 66.667 0.00 0.00 0.00 3.36
62 63 3.787001 CCGCCCCCTCAAGTCTCC 61.787 72.222 0.00 0.00 0.00 3.71
63 64 4.148825 CGCCCCCTCAAGTCTCCG 62.149 72.222 0.00 0.00 0.00 4.63
64 65 3.003763 GCCCCCTCAAGTCTCCGT 61.004 66.667 0.00 0.00 0.00 4.69
65 66 3.020237 GCCCCCTCAAGTCTCCGTC 62.020 68.421 0.00 0.00 0.00 4.79
66 67 2.711922 CCCCCTCAAGTCTCCGTCG 61.712 68.421 0.00 0.00 0.00 5.12
67 68 2.182030 CCCTCAAGTCTCCGTCGC 59.818 66.667 0.00 0.00 0.00 5.19
68 69 2.202492 CCTCAAGTCTCCGTCGCG 60.202 66.667 0.00 0.00 0.00 5.87
95 96 4.388499 GACGAAGCCGCCCCTTGA 62.388 66.667 0.00 0.00 39.95 3.02
96 97 4.699522 ACGAAGCCGCCCCTTGAC 62.700 66.667 0.00 0.00 39.95 3.18
97 98 4.394712 CGAAGCCGCCCCTTGACT 62.395 66.667 0.00 0.00 0.00 3.41
98 99 2.436824 GAAGCCGCCCCTTGACTC 60.437 66.667 0.00 0.00 0.00 3.36
99 100 2.930562 AAGCCGCCCCTTGACTCT 60.931 61.111 0.00 0.00 0.00 3.24
100 101 3.259633 AAGCCGCCCCTTGACTCTG 62.260 63.158 0.00 0.00 0.00 3.35
102 103 3.710722 CCGCCCCTTGACTCTGCT 61.711 66.667 0.00 0.00 0.00 4.24
103 104 2.359169 CCGCCCCTTGACTCTGCTA 61.359 63.158 0.00 0.00 0.00 3.49
104 105 1.142748 CGCCCCTTGACTCTGCTAG 59.857 63.158 0.00 0.00 0.00 3.42
105 106 1.153269 GCCCCTTGACTCTGCTAGC 60.153 63.158 8.10 8.10 0.00 3.42
106 107 1.524482 CCCCTTGACTCTGCTAGCC 59.476 63.158 13.29 0.00 0.00 3.93
107 108 1.524482 CCCTTGACTCTGCTAGCCC 59.476 63.158 13.29 0.00 0.00 5.19
108 109 1.142748 CCTTGACTCTGCTAGCCCG 59.857 63.158 13.29 3.30 0.00 6.13
109 110 1.323271 CCTTGACTCTGCTAGCCCGA 61.323 60.000 13.29 7.94 0.00 5.14
110 111 0.179124 CTTGACTCTGCTAGCCCGAC 60.179 60.000 13.29 1.60 0.00 4.79
111 112 1.934220 TTGACTCTGCTAGCCCGACG 61.934 60.000 13.29 5.81 0.00 5.12
112 113 2.045242 ACTCTGCTAGCCCGACGA 60.045 61.111 13.29 0.17 0.00 4.20
113 114 2.325666 GACTCTGCTAGCCCGACGAC 62.326 65.000 13.29 0.98 0.00 4.34
114 115 3.456431 CTCTGCTAGCCCGACGACG 62.456 68.421 13.29 0.00 39.43 5.12
144 145 4.129737 GCTGCTAGCCCGACGACA 62.130 66.667 13.29 0.00 34.48 4.35
145 146 2.202623 CTGCTAGCCCGACGACAC 60.203 66.667 13.29 0.00 0.00 3.67
146 147 3.701604 CTGCTAGCCCGACGACACC 62.702 68.421 13.29 0.00 0.00 4.16
147 148 4.849329 GCTAGCCCGACGACACCG 62.849 72.222 2.29 0.00 42.50 4.94
158 159 2.737376 GACACCGTCCCTTGTCGC 60.737 66.667 0.00 0.00 33.25 5.19
159 160 4.309950 ACACCGTCCCTTGTCGCC 62.310 66.667 0.00 0.00 0.00 5.54
163 164 4.124351 CGTCCCTTGTCGCCGCTA 62.124 66.667 0.00 0.00 0.00 4.26
164 165 2.202756 GTCCCTTGTCGCCGCTAG 60.203 66.667 0.00 0.00 0.00 3.42
165 166 4.143333 TCCCTTGTCGCCGCTAGC 62.143 66.667 4.06 4.06 38.52 3.42
178 179 4.253257 CTAGCCCGACGACGCCTC 62.253 72.222 0.64 0.00 38.29 4.70
233 234 2.896443 GCGAGAGGGAGAACCAGG 59.104 66.667 0.00 0.00 43.89 4.45
234 235 2.896443 CGAGAGGGAGAACCAGGC 59.104 66.667 0.00 0.00 43.89 4.85
235 236 2.726351 CGAGAGGGAGAACCAGGCC 61.726 68.421 0.00 0.00 43.89 5.19
236 237 2.285743 AGAGGGAGAACCAGGCCC 60.286 66.667 0.00 0.00 43.89 5.80
237 238 3.412408 GAGGGAGAACCAGGCCCC 61.412 72.222 0.00 0.00 43.08 5.80
307 308 4.825679 GAGGGAGGGGAGGGGTGG 62.826 77.778 0.00 0.00 0.00 4.61
316 317 4.677151 GAGGGGTGGGGTGGGAGT 62.677 72.222 0.00 0.00 0.00 3.85
319 320 3.182996 GGGTGGGGTGGGAGTGTT 61.183 66.667 0.00 0.00 0.00 3.32
320 321 2.115266 GGTGGGGTGGGAGTGTTG 59.885 66.667 0.00 0.00 0.00 3.33
321 322 2.115266 GTGGGGTGGGAGTGTTGG 59.885 66.667 0.00 0.00 0.00 3.77
322 323 3.182263 TGGGGTGGGAGTGTTGGG 61.182 66.667 0.00 0.00 0.00 4.12
323 324 4.678743 GGGGTGGGAGTGTTGGGC 62.679 72.222 0.00 0.00 0.00 5.36
342 343 4.468689 GCGGCGCCTAGGGTTTCT 62.469 66.667 26.68 0.00 0.00 2.52
343 344 2.202892 CGGCGCCTAGGGTTTCTC 60.203 66.667 26.68 0.00 0.00 2.87
344 345 2.189784 GGCGCCTAGGGTTTCTCC 59.810 66.667 22.15 0.00 0.00 3.71
375 376 3.827898 GGGAGCGACACGGGAGAG 61.828 72.222 0.00 0.00 0.00 3.20
376 377 3.063084 GGAGCGACACGGGAGAGT 61.063 66.667 0.00 0.00 36.01 3.24
377 378 2.486042 GAGCGACACGGGAGAGTC 59.514 66.667 0.00 0.00 45.27 3.36
378 379 2.034376 AGCGACACGGGAGAGTCT 59.966 61.111 0.00 0.00 46.31 3.24
379 380 2.179517 GCGACACGGGAGAGTCTG 59.820 66.667 0.00 0.00 46.31 3.51
380 381 2.878429 CGACACGGGAGAGTCTGG 59.122 66.667 0.00 0.00 46.31 3.86
381 382 1.972223 CGACACGGGAGAGTCTGGT 60.972 63.158 0.00 0.00 46.31 4.00
382 383 1.524863 CGACACGGGAGAGTCTGGTT 61.525 60.000 0.00 0.00 46.31 3.67
383 384 1.542492 GACACGGGAGAGTCTGGTTA 58.458 55.000 0.00 0.00 45.28 2.85
384 385 1.891150 GACACGGGAGAGTCTGGTTAA 59.109 52.381 0.00 0.00 45.28 2.01
385 386 2.496470 GACACGGGAGAGTCTGGTTAAT 59.504 50.000 0.00 0.00 45.28 1.40
386 387 2.904434 ACACGGGAGAGTCTGGTTAATT 59.096 45.455 0.00 0.00 0.00 1.40
387 388 3.056035 ACACGGGAGAGTCTGGTTAATTC 60.056 47.826 0.00 0.00 0.00 2.17
388 389 3.195825 CACGGGAGAGTCTGGTTAATTCT 59.804 47.826 0.00 0.00 0.00 2.40
389 390 3.195825 ACGGGAGAGTCTGGTTAATTCTG 59.804 47.826 0.00 0.00 0.00 3.02
390 391 3.536570 GGGAGAGTCTGGTTAATTCTGC 58.463 50.000 0.00 0.00 0.00 4.26
391 392 3.536570 GGAGAGTCTGGTTAATTCTGCC 58.463 50.000 0.00 0.00 0.00 4.85
392 393 3.198853 GGAGAGTCTGGTTAATTCTGCCT 59.801 47.826 0.00 0.00 0.00 4.75
393 394 4.323868 GGAGAGTCTGGTTAATTCTGCCTT 60.324 45.833 0.00 0.00 0.00 4.35
394 395 5.104900 GGAGAGTCTGGTTAATTCTGCCTTA 60.105 44.000 0.00 0.00 0.00 2.69
395 396 5.735766 AGAGTCTGGTTAATTCTGCCTTAC 58.264 41.667 0.00 0.00 0.00 2.34
396 397 4.504858 AGTCTGGTTAATTCTGCCTTACG 58.495 43.478 0.00 0.00 0.00 3.18
397 398 3.621715 GTCTGGTTAATTCTGCCTTACGG 59.378 47.826 0.00 0.00 0.00 4.02
398 399 3.262405 TCTGGTTAATTCTGCCTTACGGT 59.738 43.478 0.00 0.00 0.00 4.83
403 404 5.631929 GGTTAATTCTGCCTTACGGTTTTTG 59.368 40.000 0.00 0.00 0.00 2.44
412 413 4.266739 GCCTTACGGTTTTTGTCAAACTTG 59.733 41.667 0.00 0.00 0.00 3.16
424 425 9.462174 TTTTTGTCAAACTTGATGTATGATGAC 57.538 29.630 0.00 0.00 39.73 3.06
425 426 7.742556 TTGTCAAACTTGATGTATGATGACA 57.257 32.000 0.00 0.00 42.77 3.58
426 427 7.926674 TGTCAAACTTGATGTATGATGACAT 57.073 32.000 0.00 0.00 40.48 3.06
427 428 9.447157 TTGTCAAACTTGATGTATGATGACATA 57.553 29.630 6.15 0.00 43.58 2.29
428 429 8.882736 TGTCAAACTTGATGTATGATGACATAC 58.117 33.333 11.80 11.80 43.49 2.39
430 431 9.317936 TCAAACTTGATGTATGATGACATACTC 57.682 33.333 17.26 13.28 43.56 2.59
444 445 5.529289 TGACATACTCCTCAGATAAGGGTT 58.471 41.667 0.00 0.00 37.02 4.11
445 446 6.679542 TGACATACTCCTCAGATAAGGGTTA 58.320 40.000 0.00 0.00 37.02 2.85
446 447 6.550108 TGACATACTCCTCAGATAAGGGTTAC 59.450 42.308 0.00 0.00 37.02 2.50
449 450 2.628657 CTCCTCAGATAAGGGTTACGGG 59.371 54.545 0.00 0.00 37.02 5.28
452 453 3.181468 CCTCAGATAAGGGTTACGGGAAC 60.181 52.174 0.00 0.00 37.31 3.62
473 474 1.193874 GAACGGGTAAAACTGACAGCG 59.806 52.381 1.25 0.00 0.00 5.18
475 476 0.788391 CGGGTAAAACTGACAGCGAC 59.212 55.000 1.25 0.00 0.00 5.19
500 501 3.360867 TGCTTTTCTCAAGTTCCCAACA 58.639 40.909 0.00 0.00 0.00 3.33
503 504 4.746611 GCTTTTCTCAAGTTCCCAACATTG 59.253 41.667 0.00 0.00 0.00 2.82
593 594 0.108329 CAGATGTCGGCCCTTACGTT 60.108 55.000 0.00 0.00 0.00 3.99
596 597 0.179129 ATGTCGGCCCTTACGTTACG 60.179 55.000 2.19 2.19 0.00 3.18
607 609 3.853671 CCTTACGTTACGTGACATGTACC 59.146 47.826 21.22 0.00 41.39 3.34
637 639 2.351726 GCAGCCGGAACTATTTGTGTAG 59.648 50.000 5.05 0.00 0.00 2.74
638 640 3.596214 CAGCCGGAACTATTTGTGTAGT 58.404 45.455 5.05 0.00 36.50 2.73
639 641 4.751060 CAGCCGGAACTATTTGTGTAGTA 58.249 43.478 5.05 0.00 33.92 1.82
640 642 4.565564 CAGCCGGAACTATTTGTGTAGTAC 59.434 45.833 5.05 0.00 33.92 2.73
641 643 3.549070 GCCGGAACTATTTGTGTAGTACG 59.451 47.826 5.05 0.00 33.92 3.67
648 650 7.433425 GGAACTATTTGTGTAGTACGTATGTCC 59.567 40.741 0.00 0.00 33.92 4.02
649 651 6.799512 ACTATTTGTGTAGTACGTATGTCCC 58.200 40.000 0.00 0.00 33.29 4.46
656 658 3.083122 AGTACGTATGTCCCTGTCACT 57.917 47.619 0.00 0.00 0.00 3.41
706 708 1.332904 CCGTGAACGACTGCTTCAAAC 60.333 52.381 4.03 0.00 43.02 2.93
741 743 0.038251 TGCAGACTTGAGATTCGCGT 60.038 50.000 5.77 0.00 0.00 6.01
751 753 2.933906 TGAGATTCGCGTTAACCCAATC 59.066 45.455 5.77 6.15 0.00 2.67
808 1010 1.153289 AGAGGCACATGACCGCATC 60.153 57.895 13.64 12.49 39.16 3.91
818 1020 2.828549 ACCGCATCCCGCCAAATC 60.829 61.111 0.00 0.00 37.30 2.17
819 1021 3.595758 CCGCATCCCGCCAAATCC 61.596 66.667 0.00 0.00 37.30 3.01
820 1022 3.952675 CGCATCCCGCCAAATCCG 61.953 66.667 0.00 0.00 37.30 4.18
821 1023 2.515991 GCATCCCGCCAAATCCGA 60.516 61.111 0.00 0.00 32.94 4.55
822 1024 2.118404 GCATCCCGCCAAATCCGAA 61.118 57.895 0.00 0.00 32.94 4.30
823 1025 1.662438 GCATCCCGCCAAATCCGAAA 61.662 55.000 0.00 0.00 32.94 3.46
824 1026 1.032014 CATCCCGCCAAATCCGAAAT 58.968 50.000 0.00 0.00 0.00 2.17
825 1027 2.226330 CATCCCGCCAAATCCGAAATA 58.774 47.619 0.00 0.00 0.00 1.40
826 1028 2.421751 TCCCGCCAAATCCGAAATAA 57.578 45.000 0.00 0.00 0.00 1.40
827 1029 2.294074 TCCCGCCAAATCCGAAATAAG 58.706 47.619 0.00 0.00 0.00 1.73
951 1173 4.163552 GTTAACGAATAGCCAAAGCCAAC 58.836 43.478 0.00 0.00 41.25 3.77
978 1200 1.098050 AAATGCCTCGTCTGATTGGC 58.902 50.000 10.27 10.27 45.10 4.52
996 1218 2.586357 GATTGCCTCCTCGTCCGC 60.586 66.667 0.00 0.00 0.00 5.54
997 1219 4.162690 ATTGCCTCCTCGTCCGCC 62.163 66.667 0.00 0.00 0.00 6.13
1381 1666 2.565394 CGCCGACGACTTCATACGC 61.565 63.158 0.00 0.00 43.93 4.42
1710 1996 1.093159 CGGGTCACTACGCTTCTAGT 58.907 55.000 0.00 0.00 36.45 2.57
1711 1997 2.283298 CGGGTCACTACGCTTCTAGTA 58.717 52.381 0.00 0.00 36.45 1.82
1712 1998 2.287373 CGGGTCACTACGCTTCTAGTAG 59.713 54.545 2.25 2.25 45.11 2.57
1780 2074 3.198068 CACTTCGCTGTGGCTTGTATAT 58.802 45.455 0.60 0.00 34.56 0.86
1781 2075 3.001634 CACTTCGCTGTGGCTTGTATATG 59.998 47.826 0.60 0.00 34.56 1.78
1782 2076 2.979814 TCGCTGTGGCTTGTATATGT 57.020 45.000 0.00 0.00 36.09 2.29
1783 2077 4.142026 ACTTCGCTGTGGCTTGTATATGTA 60.142 41.667 0.00 0.00 36.09 2.29
1784 2078 4.600692 TCGCTGTGGCTTGTATATGTAT 57.399 40.909 0.00 0.00 36.09 2.29
1785 2079 5.715434 TCGCTGTGGCTTGTATATGTATA 57.285 39.130 0.00 0.00 36.09 1.47
1823 2117 1.636340 GATGTATGGCGTCGTGTGC 59.364 57.895 0.00 0.00 0.00 4.57
1848 2142 5.397326 ACGTCCGTCTATTTTGAAGTCTAC 58.603 41.667 0.00 0.00 0.00 2.59
1849 2143 5.182760 ACGTCCGTCTATTTTGAAGTCTACT 59.817 40.000 0.00 0.00 0.00 2.57
1850 2144 5.512082 CGTCCGTCTATTTTGAAGTCTACTG 59.488 44.000 0.00 0.00 0.00 2.74
1851 2145 6.388278 GTCCGTCTATTTTGAAGTCTACTGT 58.612 40.000 0.00 0.00 0.00 3.55
1852 2146 7.533426 GTCCGTCTATTTTGAAGTCTACTGTA 58.467 38.462 0.00 0.00 0.00 2.74
1853 2147 8.189460 GTCCGTCTATTTTGAAGTCTACTGTAT 58.811 37.037 0.00 0.00 0.00 2.29
1854 2148 8.746530 TCCGTCTATTTTGAAGTCTACTGTATT 58.253 33.333 0.00 0.00 0.00 1.89
1872 2166 3.698029 ATTATGCATGTTCGGCTTGAC 57.302 42.857 10.16 0.00 0.00 3.18
1904 2198 7.827819 TCTGACAGTAGGATTTGTTAAATCG 57.172 36.000 1.59 0.00 46.45 3.34
1954 2248 1.528824 CCGGATGGTGATCTTGGCT 59.471 57.895 0.00 0.00 0.00 4.75
2155 2450 4.343526 TGCTTTGCTCTAATTTGGTTTCCA 59.656 37.500 0.00 0.00 0.00 3.53
2193 2488 6.065374 CAGGAGGACAGAATCTTAGCTACTA 58.935 44.000 0.00 0.00 0.00 1.82
2211 2506 2.165641 ACTATCGCTGTCCGTCATGAAA 59.834 45.455 0.00 0.00 38.35 2.69
2214 2509 2.422597 TCGCTGTCCGTCATGAAAATT 58.577 42.857 0.00 0.00 38.35 1.82
2219 2514 4.083003 GCTGTCCGTCATGAAAATTTACCA 60.083 41.667 0.00 0.00 0.00 3.25
2223 2526 6.711194 TGTCCGTCATGAAAATTTACCACTAA 59.289 34.615 0.00 0.00 0.00 2.24
2228 2531 8.372521 CGTCATGAAAATTTACCACTAAAATGC 58.627 33.333 0.00 0.00 0.00 3.56
2230 2533 9.638239 TCATGAAAATTTACCACTAAAATGCTC 57.362 29.630 0.00 0.00 0.00 4.26
2231 2534 9.643693 CATGAAAATTTACCACTAAAATGCTCT 57.356 29.630 0.00 0.00 0.00 4.09
2261 2564 3.094062 GCATCTACAGCCGGGCAGA 62.094 63.158 23.09 15.75 0.00 4.26
2266 2569 0.107456 CTACAGCCGGGCAGATCAAT 59.893 55.000 23.09 0.00 0.00 2.57
2267 2570 0.106708 TACAGCCGGGCAGATCAATC 59.893 55.000 23.09 0.00 0.00 2.67
2274 2577 1.453745 GGCAGATCAATCCGGCCAA 60.454 57.895 2.24 0.00 43.40 4.52
2290 2593 0.870307 CCAAACGCTCGGATAGACGG 60.870 60.000 0.00 0.00 0.00 4.79
2294 2597 0.534427 ACGCTCGGATAGACGGATCA 60.534 55.000 0.00 0.00 0.00 2.92
2295 2598 0.805614 CGCTCGGATAGACGGATCAT 59.194 55.000 0.00 0.00 0.00 2.45
2297 2600 2.729467 CGCTCGGATAGACGGATCATTC 60.729 54.545 0.00 0.00 0.00 2.67
2298 2601 2.229062 GCTCGGATAGACGGATCATTCA 59.771 50.000 0.00 0.00 0.00 2.57
2299 2602 3.305403 GCTCGGATAGACGGATCATTCAA 60.305 47.826 0.00 0.00 0.00 2.69
2300 2603 4.796290 GCTCGGATAGACGGATCATTCAAA 60.796 45.833 0.00 0.00 0.00 2.69
2301 2604 5.270893 TCGGATAGACGGATCATTCAAAA 57.729 39.130 0.00 0.00 0.00 2.44
2302 2605 5.666462 TCGGATAGACGGATCATTCAAAAA 58.334 37.500 0.00 0.00 0.00 1.94
2337 2640 1.271707 CCCATAAACACCCGGACTGTT 60.272 52.381 0.73 7.41 33.09 3.16
2343 2646 3.319198 ACCCGGACTGTTCGGCAT 61.319 61.111 22.16 9.30 45.60 4.40
2347 2650 2.990479 GGACTGTTCGGCATCCCT 59.010 61.111 0.00 0.00 0.00 4.20
2348 2651 1.153349 GGACTGTTCGGCATCCCTC 60.153 63.158 0.00 0.00 0.00 4.30
2366 2669 4.913355 TCCCTCATATCAAGCCCAAATCTA 59.087 41.667 0.00 0.00 0.00 1.98
2368 2671 5.251764 CCTCATATCAAGCCCAAATCTAGG 58.748 45.833 0.00 0.00 0.00 3.02
2386 2689 3.916392 GACGGATATGAGGCGGCCG 62.916 68.421 24.05 24.05 46.83 6.13
2413 2716 2.509336 GGTGAGTCCGCCACATCG 60.509 66.667 0.00 0.00 42.48 3.84
2414 2717 2.571757 GTGAGTCCGCCACATCGA 59.428 61.111 0.00 0.00 34.81 3.59
2416 2719 1.080093 TGAGTCCGCCACATCGAAC 60.080 57.895 0.00 0.00 0.00 3.95
2417 2720 2.126071 AGTCCGCCACATCGAACG 60.126 61.111 0.00 0.00 0.00 3.95
2425 2728 0.738975 CCACATCGAACGAGCCTAGA 59.261 55.000 2.94 0.00 0.00 2.43
2463 2766 5.116084 CCCCCACAAATATCTTCTTCTCA 57.884 43.478 0.00 0.00 0.00 3.27
2477 2780 7.913674 TCTTCTTCTCAAGAATCTTAAAGCC 57.086 36.000 0.00 0.00 45.75 4.35
2496 2799 1.413077 CCCTAGACCGAAGTCCAATCC 59.587 57.143 0.00 0.00 44.72 3.01
2497 2800 2.108168 CCTAGACCGAAGTCCAATCCA 58.892 52.381 0.00 0.00 44.72 3.41
2508 2811 5.501156 GAAGTCCAATCCATTAGTCCACTT 58.499 41.667 0.00 0.00 0.00 3.16
2514 2817 5.338708 CCAATCCATTAGTCCACTTCACTCT 60.339 44.000 0.00 0.00 0.00 3.24
2521 2824 4.112634 AGTCCACTTCACTCTCTTCTCT 57.887 45.455 0.00 0.00 0.00 3.10
2526 2829 2.817258 ACTTCACTCTCTTCTCTGTCCG 59.183 50.000 0.00 0.00 0.00 4.79
2540 2843 1.153997 GTCCGCTCCACTTCGAGTC 60.154 63.158 0.00 0.00 32.11 3.36
2545 2848 1.950973 GCTCCACTTCGAGTCCCCTC 61.951 65.000 0.00 0.00 32.11 4.30
2552 2855 1.041447 TTCGAGTCCCCTCCGATTCC 61.041 60.000 0.00 0.00 33.93 3.01
2554 2857 1.455217 GAGTCCCCTCCGATTCCGA 60.455 63.158 0.00 0.00 38.22 4.55
2564 2867 3.862124 GATTCCGATCGATGGCCG 58.138 61.111 18.66 0.00 40.25 6.13
2569 2872 2.894879 CGATCGATGGCCGGCAAA 60.895 61.111 30.85 17.01 39.14 3.68
2571 2874 2.516930 ATCGATGGCCGGCAAAGG 60.517 61.111 30.85 13.81 39.14 3.11
2579 2882 2.867472 CCGGCAAAGGTAGCAACG 59.133 61.111 0.00 0.00 0.00 4.10
2583 2886 1.495951 GCAAAGGTAGCAACGTCGG 59.504 57.895 0.00 0.00 0.00 4.79
2600 2903 3.054503 GCACCAGTGGCAGCTCAG 61.055 66.667 17.50 0.00 0.00 3.35
2610 2913 4.463879 CAGCTCAGGTGGCTCCGG 62.464 72.222 0.00 0.00 41.99 5.14
2688 2991 0.039256 TGCATTGCTTTGAGGCGTTC 60.039 50.000 10.49 0.00 34.52 3.95
2704 3007 2.738521 TCGCTGCTCGAACAAGGC 60.739 61.111 0.00 0.00 45.36 4.35
2705 3008 3.043713 CGCTGCTCGAACAAGGCA 61.044 61.111 0.00 0.00 41.67 4.75
2707 3010 2.866028 CTGCTCGAACAAGGCAGC 59.134 61.111 10.23 0.00 45.04 5.25
2708 3011 3.020026 CTGCTCGAACAAGGCAGCG 62.020 63.158 10.23 0.00 45.04 5.18
2709 3012 3.793144 GCTCGAACAAGGCAGCGG 61.793 66.667 0.00 0.00 0.00 5.52
2710 3013 3.793144 CTCGAACAAGGCAGCGGC 61.793 66.667 0.00 0.00 40.13 6.53
2711 3014 4.617520 TCGAACAAGGCAGCGGCA 62.618 61.111 11.88 0.00 43.71 5.69
2712 3015 4.093952 CGAACAAGGCAGCGGCAG 62.094 66.667 11.88 2.26 43.71 4.85
2713 3016 4.410743 GAACAAGGCAGCGGCAGC 62.411 66.667 11.88 9.05 43.71 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.503363 GGTGCACGCAGATCTGGC 61.503 66.667 23.89 18.32 0.00 4.85
30 31 3.190849 CGGTGCACGCAGATCTGG 61.191 66.667 23.89 15.76 34.82 3.86
43 44 3.316573 GAGACTTGAGGGGGCGGTG 62.317 68.421 0.00 0.00 0.00 4.94
44 45 3.003763 GAGACTTGAGGGGGCGGT 61.004 66.667 0.00 0.00 0.00 5.68
45 46 3.787001 GGAGACTTGAGGGGGCGG 61.787 72.222 0.00 0.00 0.00 6.13
46 47 4.148825 CGGAGACTTGAGGGGGCG 62.149 72.222 0.00 0.00 0.00 6.13
47 48 3.003763 ACGGAGACTTGAGGGGGC 61.004 66.667 0.00 0.00 0.00 5.80
48 49 2.711922 CGACGGAGACTTGAGGGGG 61.712 68.421 0.00 0.00 0.00 5.40
49 50 2.885861 CGACGGAGACTTGAGGGG 59.114 66.667 0.00 0.00 0.00 4.79
50 51 2.182030 GCGACGGAGACTTGAGGG 59.818 66.667 0.00 0.00 0.00 4.30
51 52 2.202492 CGCGACGGAGACTTGAGG 60.202 66.667 0.00 0.00 0.00 3.86
78 79 4.388499 TCAAGGGGCGGCTTCGTC 62.388 66.667 9.56 0.00 37.85 4.20
79 80 4.699522 GTCAAGGGGCGGCTTCGT 62.700 66.667 9.56 0.00 36.07 3.85
80 81 4.394712 AGTCAAGGGGCGGCTTCG 62.395 66.667 9.56 0.00 0.00 3.79
81 82 2.436824 GAGTCAAGGGGCGGCTTC 60.437 66.667 9.56 1.42 0.00 3.86
82 83 2.930562 AGAGTCAAGGGGCGGCTT 60.931 61.111 9.56 0.00 0.00 4.35
83 84 3.710722 CAGAGTCAAGGGGCGGCT 61.711 66.667 9.56 0.00 0.00 5.52
85 86 2.303549 CTAGCAGAGTCAAGGGGCGG 62.304 65.000 0.00 0.00 0.00 6.13
86 87 1.142748 CTAGCAGAGTCAAGGGGCG 59.857 63.158 0.00 0.00 0.00 6.13
87 88 1.153269 GCTAGCAGAGTCAAGGGGC 60.153 63.158 10.63 0.00 0.00 5.80
88 89 1.524482 GGCTAGCAGAGTCAAGGGG 59.476 63.158 18.24 0.00 0.00 4.79
89 90 1.524482 GGGCTAGCAGAGTCAAGGG 59.476 63.158 18.24 0.00 0.00 3.95
90 91 1.142748 CGGGCTAGCAGAGTCAAGG 59.857 63.158 18.24 0.00 0.00 3.61
91 92 0.179124 GTCGGGCTAGCAGAGTCAAG 60.179 60.000 18.24 0.00 0.00 3.02
92 93 1.890894 GTCGGGCTAGCAGAGTCAA 59.109 57.895 18.24 0.00 0.00 3.18
93 94 2.407428 CGTCGGGCTAGCAGAGTCA 61.407 63.158 18.24 0.00 0.00 3.41
94 95 2.113433 TCGTCGGGCTAGCAGAGTC 61.113 63.158 18.24 3.97 0.00 3.36
95 96 2.045242 TCGTCGGGCTAGCAGAGT 60.045 61.111 18.24 0.00 0.00 3.24
96 97 2.409651 GTCGTCGGGCTAGCAGAG 59.590 66.667 18.24 7.02 0.00 3.35
97 98 3.506096 CGTCGTCGGGCTAGCAGA 61.506 66.667 18.24 12.51 0.00 4.26
127 128 4.129737 TGTCGTCGGGCTAGCAGC 62.130 66.667 18.24 0.00 41.46 5.25
128 129 2.202623 GTGTCGTCGGGCTAGCAG 60.203 66.667 18.24 10.13 0.00 4.24
129 130 3.755628 GGTGTCGTCGGGCTAGCA 61.756 66.667 18.24 0.00 0.00 3.49
130 131 4.849329 CGGTGTCGTCGGGCTAGC 62.849 72.222 6.04 6.04 0.00 3.42
141 142 2.737376 GCGACAAGGGACGGTGTC 60.737 66.667 0.00 0.00 42.25 3.67
142 143 4.309950 GGCGACAAGGGACGGTGT 62.310 66.667 0.00 0.00 34.31 4.16
146 147 4.124351 TAGCGGCGACAAGGGACG 62.124 66.667 12.98 0.00 35.31 4.79
147 148 2.202756 CTAGCGGCGACAAGGGAC 60.203 66.667 12.98 0.00 0.00 4.46
148 149 4.143333 GCTAGCGGCGACAAGGGA 62.143 66.667 12.98 0.00 0.00 4.20
161 162 4.253257 GAGGCGTCGTCGGGCTAG 62.253 72.222 3.90 0.00 40.78 3.42
213 214 1.999071 CTGGTTCTCCCTCTCGCGAG 61.999 65.000 30.03 30.03 37.01 5.03
214 215 2.035155 TGGTTCTCCCTCTCGCGA 59.965 61.111 9.26 9.26 0.00 5.87
215 216 2.492090 CTGGTTCTCCCTCTCGCG 59.508 66.667 0.00 0.00 0.00 5.87
216 217 2.896443 CCTGGTTCTCCCTCTCGC 59.104 66.667 0.00 0.00 0.00 5.03
217 218 2.726351 GGCCTGGTTCTCCCTCTCG 61.726 68.421 0.00 0.00 0.00 4.04
218 219 2.371259 GGGCCTGGTTCTCCCTCTC 61.371 68.421 0.84 0.00 37.08 3.20
219 220 2.285743 GGGCCTGGTTCTCCCTCT 60.286 66.667 0.84 0.00 37.08 3.69
220 221 3.412408 GGGGCCTGGTTCTCCCTC 61.412 72.222 0.84 0.00 39.95 4.30
290 291 4.825679 CCACCCCTCCCCTCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
299 300 4.677151 ACTCCCACCCCACCCCTC 62.677 72.222 0.00 0.00 0.00 4.30
302 303 3.182996 AACACTCCCACCCCACCC 61.183 66.667 0.00 0.00 0.00 4.61
303 304 2.115266 CAACACTCCCACCCCACC 59.885 66.667 0.00 0.00 0.00 4.61
304 305 2.115266 CCAACACTCCCACCCCAC 59.885 66.667 0.00 0.00 0.00 4.61
305 306 3.182263 CCCAACACTCCCACCCCA 61.182 66.667 0.00 0.00 0.00 4.96
306 307 4.678743 GCCCAACACTCCCACCCC 62.679 72.222 0.00 0.00 0.00 4.95
325 326 4.468689 AGAAACCCTAGGCGCCGC 62.469 66.667 23.20 0.00 0.00 6.53
326 327 2.202892 GAGAAACCCTAGGCGCCG 60.203 66.667 23.20 9.47 0.00 6.46
327 328 2.189784 GGAGAAACCCTAGGCGCC 59.810 66.667 21.89 21.89 0.00 6.53
358 359 3.827898 CTCTCCCGTGTCGCTCCC 61.828 72.222 0.00 0.00 0.00 4.30
359 360 3.053849 GACTCTCCCGTGTCGCTCC 62.054 68.421 0.00 0.00 0.00 4.70
360 361 2.041686 AGACTCTCCCGTGTCGCTC 61.042 63.158 0.00 0.00 38.38 5.03
361 362 2.034376 AGACTCTCCCGTGTCGCT 59.966 61.111 0.00 0.00 38.38 4.93
362 363 2.179517 CAGACTCTCCCGTGTCGC 59.820 66.667 0.00 0.00 38.38 5.19
363 364 1.524863 AACCAGACTCTCCCGTGTCG 61.525 60.000 0.00 0.00 38.38 4.35
364 365 1.542492 TAACCAGACTCTCCCGTGTC 58.458 55.000 0.00 0.00 34.66 3.67
365 366 2.005370 TTAACCAGACTCTCCCGTGT 57.995 50.000 0.00 0.00 0.00 4.49
366 367 3.195825 AGAATTAACCAGACTCTCCCGTG 59.804 47.826 0.00 0.00 0.00 4.94
367 368 3.195825 CAGAATTAACCAGACTCTCCCGT 59.804 47.826 0.00 0.00 0.00 5.28
368 369 3.786635 CAGAATTAACCAGACTCTCCCG 58.213 50.000 0.00 0.00 0.00 5.14
369 370 3.536570 GCAGAATTAACCAGACTCTCCC 58.463 50.000 0.00 0.00 0.00 4.30
370 371 3.198853 AGGCAGAATTAACCAGACTCTCC 59.801 47.826 0.00 0.00 0.00 3.71
371 372 4.479786 AGGCAGAATTAACCAGACTCTC 57.520 45.455 0.00 0.00 0.00 3.20
372 373 4.917906 AAGGCAGAATTAACCAGACTCT 57.082 40.909 0.00 0.00 0.00 3.24
373 374 4.567159 CGTAAGGCAGAATTAACCAGACTC 59.433 45.833 0.00 0.00 0.00 3.36
374 375 4.504858 CGTAAGGCAGAATTAACCAGACT 58.495 43.478 0.00 0.00 0.00 3.24
375 376 4.859629 CGTAAGGCAGAATTAACCAGAC 57.140 45.455 0.00 0.00 0.00 3.51
391 392 6.750039 ACATCAAGTTTGACAAAAACCGTAAG 59.250 34.615 1.27 0.00 40.49 2.34
392 393 6.622549 ACATCAAGTTTGACAAAAACCGTAA 58.377 32.000 1.27 0.00 40.49 3.18
393 394 6.197364 ACATCAAGTTTGACAAAAACCGTA 57.803 33.333 1.27 0.00 40.49 4.02
394 395 5.066968 ACATCAAGTTTGACAAAAACCGT 57.933 34.783 1.27 0.00 40.49 4.83
395 396 6.915300 TCATACATCAAGTTTGACAAAAACCG 59.085 34.615 1.27 0.00 40.49 4.44
396 397 8.702438 CATCATACATCAAGTTTGACAAAAACC 58.298 33.333 1.27 0.00 40.27 3.27
397 398 9.462174 TCATCATACATCAAGTTTGACAAAAAC 57.538 29.630 1.27 0.00 40.27 2.43
398 399 9.462174 GTCATCATACATCAAGTTTGACAAAAA 57.538 29.630 1.27 0.00 40.27 1.94
424 425 5.047943 CCGTAACCCTTATCTGAGGAGTATG 60.048 48.000 0.00 0.00 39.25 2.39
425 426 5.078256 CCGTAACCCTTATCTGAGGAGTAT 58.922 45.833 0.00 0.00 39.25 2.12
426 427 4.467769 CCGTAACCCTTATCTGAGGAGTA 58.532 47.826 0.00 0.00 39.25 2.59
427 428 3.297736 CCGTAACCCTTATCTGAGGAGT 58.702 50.000 0.00 0.00 39.25 3.85
428 429 2.628657 CCCGTAACCCTTATCTGAGGAG 59.371 54.545 0.00 0.00 39.25 3.69
430 431 2.674420 TCCCGTAACCCTTATCTGAGG 58.326 52.381 0.00 0.00 36.52 3.86
444 445 0.962489 TTTACCCGTTCGTTCCCGTA 59.038 50.000 0.00 0.00 35.01 4.02
445 446 0.105778 TTTTACCCGTTCGTTCCCGT 59.894 50.000 0.00 0.00 35.01 5.28
446 447 0.512518 GTTTTACCCGTTCGTTCCCG 59.487 55.000 0.00 0.00 0.00 5.14
449 450 2.865551 TGTCAGTTTTACCCGTTCGTTC 59.134 45.455 0.00 0.00 0.00 3.95
452 453 1.193874 GCTGTCAGTTTTACCCGTTCG 59.806 52.381 0.93 0.00 0.00 3.95
457 458 2.165319 AGTCGCTGTCAGTTTTACCC 57.835 50.000 0.93 0.00 0.00 3.69
458 459 4.435651 GCATAAGTCGCTGTCAGTTTTACC 60.436 45.833 0.93 0.00 0.00 2.85
473 474 5.473504 TGGGAACTTGAGAAAAGCATAAGTC 59.526 40.000 0.00 0.00 31.71 3.01
475 476 5.964958 TGGGAACTTGAGAAAAGCATAAG 57.035 39.130 0.00 0.00 0.00 1.73
561 562 4.552355 CCGACATCTGTACACACTTTGTA 58.448 43.478 0.00 0.00 39.91 2.41
563 564 2.157668 GCCGACATCTGTACACACTTTG 59.842 50.000 0.00 0.00 0.00 2.77
564 565 2.413837 GCCGACATCTGTACACACTTT 58.586 47.619 0.00 0.00 0.00 2.66
565 566 1.337823 GGCCGACATCTGTACACACTT 60.338 52.381 0.00 0.00 0.00 3.16
566 567 0.246635 GGCCGACATCTGTACACACT 59.753 55.000 0.00 0.00 0.00 3.55
567 568 0.739813 GGGCCGACATCTGTACACAC 60.740 60.000 0.00 0.00 0.00 3.82
568 569 0.902984 AGGGCCGACATCTGTACACA 60.903 55.000 0.00 0.00 0.00 3.72
593 594 1.403647 GCTGCAGGTACATGTCACGTA 60.404 52.381 17.12 0.00 0.00 3.57
596 597 0.321564 TGGCTGCAGGTACATGTCAC 60.322 55.000 17.12 0.00 0.00 3.67
624 626 7.123247 AGGGACATACGTACTACACAAATAGTT 59.877 37.037 0.00 0.00 36.74 2.24
637 639 4.577693 TCATAGTGACAGGGACATACGTAC 59.422 45.833 0.00 0.00 0.00 3.67
638 640 4.784177 TCATAGTGACAGGGACATACGTA 58.216 43.478 0.00 0.00 0.00 3.57
639 641 3.628008 TCATAGTGACAGGGACATACGT 58.372 45.455 0.00 0.00 0.00 3.57
640 642 4.649088 TTCATAGTGACAGGGACATACG 57.351 45.455 0.00 0.00 0.00 3.06
641 643 6.161855 TGATTCATAGTGACAGGGACATAC 57.838 41.667 0.00 0.00 0.00 2.39
648 650 3.813724 CAGGCATGATTCATAGTGACAGG 59.186 47.826 0.00 0.00 0.00 4.00
649 651 3.250280 GCAGGCATGATTCATAGTGACAG 59.750 47.826 0.62 0.00 0.00 3.51
656 658 6.772360 TTTAGTTTGCAGGCATGATTCATA 57.228 33.333 0.62 0.00 0.00 2.15
706 708 0.927537 TGCAACTGTGACGAGTTTCG 59.072 50.000 0.00 0.00 46.93 3.46
741 743 3.142951 CAACACCTCGTGATTGGGTTAA 58.857 45.455 0.00 0.00 36.96 2.01
751 753 2.627791 TTGCCATCAACACCTCGTG 58.372 52.632 0.00 0.00 39.75 4.35
808 1010 1.269051 GCTTATTTCGGATTTGGCGGG 60.269 52.381 0.00 0.00 0.00 6.13
818 1020 0.464452 ACTCGAGGGGCTTATTTCGG 59.536 55.000 18.41 0.00 34.08 4.30
819 1021 1.933853 CAACTCGAGGGGCTTATTTCG 59.066 52.381 18.41 0.00 34.56 3.46
820 1022 1.671328 GCAACTCGAGGGGCTTATTTC 59.329 52.381 18.41 0.00 0.00 2.17
821 1023 1.751437 GCAACTCGAGGGGCTTATTT 58.249 50.000 18.41 0.00 0.00 1.40
822 1024 0.462047 CGCAACTCGAGGGGCTTATT 60.462 55.000 22.67 3.13 41.67 1.40
823 1025 1.144057 CGCAACTCGAGGGGCTTAT 59.856 57.895 22.67 0.00 41.67 1.73
824 1026 2.577059 CGCAACTCGAGGGGCTTA 59.423 61.111 22.67 0.00 41.67 3.09
846 1049 4.764771 TGCTCCCATTGGCTGGCC 62.765 66.667 4.43 4.43 44.46 5.36
978 1200 2.278857 CGGACGAGGAGGCAATCG 60.279 66.667 0.00 4.75 44.36 3.34
996 1218 0.598065 AGGCTGCTTTTTAACGCTGG 59.402 50.000 0.00 0.00 0.00 4.85
997 1219 1.725931 CGAGGCTGCTTTTTAACGCTG 60.726 52.381 0.00 0.00 0.00 5.18
998 1220 0.517316 CGAGGCTGCTTTTTAACGCT 59.483 50.000 0.00 0.00 0.00 5.07
1198 1462 2.270527 GAGCAGGAGAAGGTGGCC 59.729 66.667 0.00 0.00 0.00 5.36
1739 2033 5.839621 AGTGTGAGACTAATTGTACGTTGT 58.160 37.500 0.00 0.00 30.86 3.32
1804 2098 1.762222 GCACACGACGCCATACATCC 61.762 60.000 0.00 0.00 0.00 3.51
1848 2142 4.273235 TCAAGCCGAACATGCATAATACAG 59.727 41.667 0.00 0.00 0.00 2.74
1849 2143 4.035091 GTCAAGCCGAACATGCATAATACA 59.965 41.667 0.00 0.00 0.00 2.29
1850 2144 4.527564 GTCAAGCCGAACATGCATAATAC 58.472 43.478 0.00 0.00 0.00 1.89
1851 2145 3.247411 CGTCAAGCCGAACATGCATAATA 59.753 43.478 0.00 0.00 0.00 0.98
1852 2146 2.032054 CGTCAAGCCGAACATGCATAAT 59.968 45.455 0.00 0.00 0.00 1.28
1853 2147 1.396648 CGTCAAGCCGAACATGCATAA 59.603 47.619 0.00 0.00 0.00 1.90
1854 2148 1.006086 CGTCAAGCCGAACATGCATA 58.994 50.000 0.00 0.00 0.00 3.14
1872 2166 2.092323 TCCTACTGTCAGATCACCACG 58.908 52.381 6.91 0.00 0.00 4.94
1904 2198 2.102252 CTCCAGGAGTCCAGCTCATTAC 59.898 54.545 12.86 0.00 45.88 1.89
1954 2248 1.454276 CGCACGCGAGAAGAAAAGTAA 59.546 47.619 15.93 0.00 42.83 2.24
2032 2326 2.028930 TCTCTCGAAGAAAACAGGGAGC 60.029 50.000 0.00 0.00 34.09 4.70
2155 2450 1.949847 CTCCTGGAGTGGCGAACGAT 61.950 60.000 15.76 0.00 0.00 3.73
2193 2488 2.093306 TTTTCATGACGGACAGCGAT 57.907 45.000 0.00 0.00 0.00 4.58
2211 2506 6.434028 TCTGCAGAGCATTTTAGTGGTAAATT 59.566 34.615 13.74 0.00 38.13 1.82
2214 2509 4.905429 TCTGCAGAGCATTTTAGTGGTAA 58.095 39.130 13.74 0.00 38.13 2.85
2219 2514 6.042638 TCTAGTTCTGCAGAGCATTTTAGT 57.957 37.500 29.15 13.10 38.13 2.24
2228 2531 4.337836 TGTAGATGCTCTAGTTCTGCAGAG 59.662 45.833 17.43 5.37 40.18 3.35
2230 2533 4.609947 CTGTAGATGCTCTAGTTCTGCAG 58.390 47.826 7.63 7.63 41.55 4.41
2231 2534 3.181482 GCTGTAGATGCTCTAGTTCTGCA 60.181 47.826 0.00 0.00 41.13 4.41
2254 2557 2.974698 GCCGGATTGATCTGCCCG 60.975 66.667 5.05 11.49 41.47 6.13
2255 2558 2.595754 GGCCGGATTGATCTGCCC 60.596 66.667 5.05 0.07 38.14 5.36
2261 2564 1.376609 GAGCGTTTGGCCGGATTGAT 61.377 55.000 5.05 0.00 45.17 2.57
2274 2577 0.592148 GATCCGTCTATCCGAGCGTT 59.408 55.000 0.00 0.00 0.00 4.84
2321 2624 0.033781 CCGAACAGTCCGGGTGTTTA 59.966 55.000 20.05 0.00 43.05 2.01
2326 2629 3.310860 GATGCCGAACAGTCCGGGT 62.311 63.158 0.00 0.00 46.55 5.28
2337 2640 1.002430 GCTTGATATGAGGGATGCCGA 59.998 52.381 0.00 0.00 0.00 5.54
2343 2646 3.723681 AGATTTGGGCTTGATATGAGGGA 59.276 43.478 0.00 0.00 0.00 4.20
2347 2650 5.511373 CGTCCTAGATTTGGGCTTGATATGA 60.511 44.000 0.00 0.00 0.00 2.15
2348 2651 4.692625 CGTCCTAGATTTGGGCTTGATATG 59.307 45.833 0.00 0.00 0.00 1.78
2366 2669 2.574955 GCCGCCTCATATCCGTCCT 61.575 63.158 0.00 0.00 0.00 3.85
2368 2671 2.048127 GGCCGCCTCATATCCGTC 60.048 66.667 0.71 0.00 0.00 4.79
2386 2689 4.500116 GACTCACCCGAGCGCTCC 62.500 72.222 30.66 13.79 43.66 4.70
2405 2708 0.872021 CTAGGCTCGTTCGATGTGGC 60.872 60.000 0.00 5.90 0.00 5.01
2458 2761 7.331791 GTCTAGGGCTTTAAGATTCTTGAGAA 58.668 38.462 9.22 0.00 38.56 2.87
2461 2764 5.395324 CGGTCTAGGGCTTTAAGATTCTTGA 60.395 44.000 9.22 0.00 0.00 3.02
2462 2765 4.811557 CGGTCTAGGGCTTTAAGATTCTTG 59.188 45.833 9.22 0.00 0.00 3.02
2463 2766 4.715297 TCGGTCTAGGGCTTTAAGATTCTT 59.285 41.667 4.03 4.03 0.00 2.52
2473 2776 0.252103 TGGACTTCGGTCTAGGGCTT 60.252 55.000 0.00 0.00 43.94 4.35
2476 2779 1.413077 GGATTGGACTTCGGTCTAGGG 59.587 57.143 0.00 0.00 43.94 3.53
2477 2780 2.108168 TGGATTGGACTTCGGTCTAGG 58.892 52.381 0.00 0.00 43.94 3.02
2496 2799 6.152661 AGAGAAGAGAGTGAAGTGGACTAATG 59.847 42.308 0.00 0.00 0.00 1.90
2497 2800 6.152661 CAGAGAAGAGAGTGAAGTGGACTAAT 59.847 42.308 0.00 0.00 0.00 1.73
2508 2811 1.169577 GCGGACAGAGAAGAGAGTGA 58.830 55.000 0.00 0.00 0.00 3.41
2514 2817 0.251386 AGTGGAGCGGACAGAGAAGA 60.251 55.000 0.00 0.00 0.00 2.87
2521 2824 1.863662 GACTCGAAGTGGAGCGGACA 61.864 60.000 0.00 0.00 37.57 4.02
2526 2829 1.985116 AGGGGACTCGAAGTGGAGC 60.985 63.158 0.00 0.00 37.57 4.70
2552 2855 2.885676 CTTTGCCGGCCATCGATCG 61.886 63.158 26.77 9.36 42.43 3.69
2554 2857 1.978455 TACCTTTGCCGGCCATCGAT 61.978 55.000 26.77 7.76 42.43 3.59
2564 2867 1.495951 CGACGTTGCTACCTTTGCC 59.504 57.895 0.00 0.00 0.00 4.52
2567 2870 1.070105 TGCCGACGTTGCTACCTTT 59.930 52.632 11.58 0.00 0.00 3.11
2569 2872 2.048503 GTGCCGACGTTGCTACCT 60.049 61.111 11.58 0.00 0.00 3.08
2571 2874 2.356553 TGGTGCCGACGTTGCTAC 60.357 61.111 11.58 5.97 0.00 3.58
2583 2886 3.054503 CTGAGCTGCCACTGGTGC 61.055 66.667 0.00 6.99 0.00 5.01
2610 2913 1.598130 AACAGGCTCAACCAGTCGC 60.598 57.895 0.00 0.00 37.12 5.19
2618 2921 1.855213 GCATCGCACAACAGGCTCAA 61.855 55.000 0.00 0.00 0.00 3.02
2619 2922 2.327343 GCATCGCACAACAGGCTCA 61.327 57.895 0.00 0.00 0.00 4.26
2669 2972 0.039256 GAACGCCTCAAAGCAATGCA 60.039 50.000 8.35 0.00 0.00 3.96
2688 2991 3.020026 CTGCCTTGTTCGAGCAGCG 62.020 63.158 10.23 2.50 46.60 5.18


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

AutoCloner maintained by Alex Coulton.