Multiple sequence alignment - TraesCS7A01G159400

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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 TraesCS7A01G159400 chr7A 100.000 2620 0 0 395 3014 115818820 115816201 0.000000e+00 4839
1 TraesCS7A01G159400 chr7A 100.000 114 0 0 1 114 115819214 115819101 8.470000e-51 211
2 TraesCS7A01G159400 chr7A 77.714 175 35 4 403 574 544067448 544067621 1.480000e-18 104
3 TraesCS7A01G159400 chr7B 92.277 2292 101 29 742 3014 69581925 69584159 0.000000e+00 3182
4 TraesCS7A01G159400 chr7D 95.802 1453 47 9 819 2267 110566120 110567562 0.000000e+00 2333
5 TraesCS7A01G159400 chr7D 94.152 342 17 2 2674 3014 110567627 110567966 4.450000e-143 518
6 TraesCS7A01G159400 chr5B 82.143 168 29 1 407 574 539077079 539076913 3.130000e-30 143
7 TraesCS7A01G159400 chr5B 79.348 184 35 3 433 615 24371687 24371868 3.150000e-25 126
8 TraesCS7A01G159400 chr5B 78.142 183 39 1 433 615 24355780 24355961 6.830000e-22 115
9 TraesCS7A01G159400 chr3D 77.570 214 48 0 404 617 495809399 495809612 2.440000e-26 130
10 TraesCS7A01G159400 chr2B 77.419 217 42 6 405 619 105762896 105762685 4.080000e-24 122
11 TraesCS7A01G159400 chr2A 80.625 160 26 2 434 592 90032741 90032586 5.280000e-23 119
12 TraesCS7A01G159400 chr2A 76.882 186 42 1 428 613 733876093 733876277 1.480000e-18 104
13 TraesCS7A01G159400 chr1D 82.787 122 21 0 449 570 431601371 431601492 3.180000e-20 110


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 TraesCS7A01G159400 chr7A 115816201 115819214 3013 True 2525.0 4839 100.000 1 3014 2 chr7A.!!$R1 3013
1 TraesCS7A01G159400 chr7B 69581925 69584159 2234 False 3182.0 3182 92.277 742 3014 1 chr7B.!!$F1 2272
2 TraesCS7A01G159400 chr7D 110566120 110567966 1846 False 1425.5 2333 94.977 819 3014 2 chr7D.!!$F1 2195

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
102 103 0.038343 CGCATTTTCCCCCAACACTG 60.038 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2109 1.067706 TCTGAACCAAAATGCCATGCG 60.068 47.619 0.0 0.0 0.0 4.73 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
22 23 3.993736 TCAAATCACACACATACGTCTGG 59.006 43.478 5.87 0.00 0.00 3.86
23 24 3.953712 AATCACACACATACGTCTGGA 57.046 42.857 5.87 0.00 0.00 3.86
24 25 2.717580 TCACACACATACGTCTGGAC 57.282 50.000 5.87 0.00 0.00 4.02
25 26 1.271379 TCACACACATACGTCTGGACC 59.729 52.381 5.87 0.00 0.00 4.46
26 27 0.242825 ACACACATACGTCTGGACCG 59.757 55.000 5.87 0.00 0.00 4.79
27 28 0.242825 CACACATACGTCTGGACCGT 59.757 55.000 5.87 0.00 42.06 4.83
28 29 0.242825 ACACATACGTCTGGACCGTG 59.757 55.000 5.87 0.00 39.22 4.94
29 30 0.242825 CACATACGTCTGGACCGTGT 59.757 55.000 5.87 2.97 39.22 4.49
30 31 3.030209 CATACGTCTGGACCGTGTG 57.970 57.895 0.00 0.00 40.19 3.82
31 32 0.457853 CATACGTCTGGACCGTGTGG 60.458 60.000 0.00 0.00 41.74 4.17
41 42 3.148084 CCGTGTGGTTCAGTCCCT 58.852 61.111 0.00 0.00 0.00 4.20
42 43 1.301716 CCGTGTGGTTCAGTCCCTG 60.302 63.158 0.00 0.00 0.00 4.45
43 44 1.301716 CGTGTGGTTCAGTCCCTGG 60.302 63.158 0.00 0.00 31.51 4.45
44 45 1.754380 CGTGTGGTTCAGTCCCTGGA 61.754 60.000 0.00 0.00 31.51 3.86
45 46 0.472471 GTGTGGTTCAGTCCCTGGAA 59.528 55.000 0.00 0.00 31.51 3.53
46 47 0.764890 TGTGGTTCAGTCCCTGGAAG 59.235 55.000 0.00 0.00 31.51 3.46
47 48 0.606673 GTGGTTCAGTCCCTGGAAGC 60.607 60.000 0.00 0.00 31.51 3.86
48 49 1.002011 GGTTCAGTCCCTGGAAGCC 60.002 63.158 0.00 0.00 31.51 4.35
49 50 1.761174 GTTCAGTCCCTGGAAGCCA 59.239 57.895 0.00 0.00 31.51 4.75
50 51 0.329596 GTTCAGTCCCTGGAAGCCAT 59.670 55.000 0.00 0.00 30.82 4.40
51 52 0.620556 TTCAGTCCCTGGAAGCCATC 59.379 55.000 0.00 0.00 30.82 3.51
62 63 1.243902 GAAGCCATCCAAAACGGTCA 58.756 50.000 0.00 0.00 35.57 4.02
63 64 1.818674 GAAGCCATCCAAAACGGTCAT 59.181 47.619 0.00 0.00 35.57 3.06
64 65 1.176527 AGCCATCCAAAACGGTCATG 58.823 50.000 0.00 0.00 35.57 3.07
65 66 0.887933 GCCATCCAAAACGGTCATGT 59.112 50.000 0.00 0.00 35.57 3.21
66 67 2.088423 GCCATCCAAAACGGTCATGTA 58.912 47.619 0.00 0.00 35.57 2.29
67 68 2.687935 GCCATCCAAAACGGTCATGTAT 59.312 45.455 0.00 0.00 35.57 2.29
68 69 3.243068 GCCATCCAAAACGGTCATGTATC 60.243 47.826 0.00 0.00 35.57 2.24
69 70 3.002246 CCATCCAAAACGGTCATGTATCG 59.998 47.826 0.00 0.00 37.86 2.92
70 71 2.623535 TCCAAAACGGTCATGTATCGG 58.376 47.619 0.00 0.00 35.41 4.18
71 72 2.027929 TCCAAAACGGTCATGTATCGGT 60.028 45.455 0.00 0.00 35.41 4.69
72 73 2.350498 CCAAAACGGTCATGTATCGGTC 59.650 50.000 0.00 0.00 35.41 4.79
73 74 2.304751 AAACGGTCATGTATCGGTCC 57.695 50.000 0.00 0.00 35.41 4.46
74 75 0.101759 AACGGTCATGTATCGGTCCG 59.898 55.000 4.39 4.39 42.94 4.79
75 76 1.660575 CGGTCATGTATCGGTCCGC 60.661 63.158 6.34 0.00 0.00 5.54
76 77 1.740285 GGTCATGTATCGGTCCGCT 59.260 57.895 6.34 0.00 0.00 5.52
77 78 0.104304 GGTCATGTATCGGTCCGCTT 59.896 55.000 6.34 0.00 0.00 4.68
78 79 1.488527 GTCATGTATCGGTCCGCTTC 58.511 55.000 6.34 0.00 0.00 3.86
79 80 0.387929 TCATGTATCGGTCCGCTTCC 59.612 55.000 6.34 0.00 0.00 3.46
90 91 2.867472 CGCTTCCGGACGCATTTT 59.133 55.556 29.76 0.00 0.00 1.82
91 92 1.226018 CGCTTCCGGACGCATTTTC 60.226 57.895 29.76 2.52 0.00 2.29
92 93 1.136774 GCTTCCGGACGCATTTTCC 59.863 57.895 26.63 0.00 0.00 3.13
93 94 1.800681 CTTCCGGACGCATTTTCCC 59.199 57.895 1.83 0.00 0.00 3.97
94 95 1.654023 CTTCCGGACGCATTTTCCCC 61.654 60.000 1.83 0.00 0.00 4.81
95 96 3.138128 CCGGACGCATTTTCCCCC 61.138 66.667 0.00 0.00 0.00 5.40
96 97 2.360600 CGGACGCATTTTCCCCCA 60.361 61.111 0.00 0.00 0.00 4.96
97 98 1.974343 CGGACGCATTTTCCCCCAA 60.974 57.895 0.00 0.00 0.00 4.12
98 99 1.589630 GGACGCATTTTCCCCCAAC 59.410 57.895 0.00 0.00 0.00 3.77
99 100 1.182385 GGACGCATTTTCCCCCAACA 61.182 55.000 0.00 0.00 0.00 3.33
100 101 0.038618 GACGCATTTTCCCCCAACAC 60.039 55.000 0.00 0.00 0.00 3.32
101 102 0.469144 ACGCATTTTCCCCCAACACT 60.469 50.000 0.00 0.00 0.00 3.55
102 103 0.038343 CGCATTTTCCCCCAACACTG 60.038 55.000 0.00 0.00 0.00 3.66
103 104 1.337118 GCATTTTCCCCCAACACTGA 58.663 50.000 0.00 0.00 0.00 3.41
104 105 1.000843 GCATTTTCCCCCAACACTGAC 59.999 52.381 0.00 0.00 0.00 3.51
105 106 1.618343 CATTTTCCCCCAACACTGACC 59.382 52.381 0.00 0.00 0.00 4.02
106 107 0.105913 TTTTCCCCCAACACTGACCC 60.106 55.000 0.00 0.00 0.00 4.46
107 108 2.014033 TTTCCCCCAACACTGACCCC 62.014 60.000 0.00 0.00 0.00 4.95
108 109 3.182263 CCCCCAACACTGACCCCA 61.182 66.667 0.00 0.00 0.00 4.96
109 110 2.773527 CCCCCAACACTGACCCCAA 61.774 63.158 0.00 0.00 0.00 4.12
110 111 1.231641 CCCCAACACTGACCCCAAA 59.768 57.895 0.00 0.00 0.00 3.28
111 112 0.397816 CCCCAACACTGACCCCAAAA 60.398 55.000 0.00 0.00 0.00 2.44
112 113 1.715785 CCCAACACTGACCCCAAAAT 58.284 50.000 0.00 0.00 0.00 1.82
113 114 1.618343 CCCAACACTGACCCCAAAATC 59.382 52.381 0.00 0.00 0.00 2.17
411 412 3.259751 GACCGTTATCACGCCCGC 61.260 66.667 0.00 0.00 45.72 6.13
412 413 3.711541 GACCGTTATCACGCCCGCT 62.712 63.158 0.00 0.00 45.72 5.52
413 414 2.960129 CCGTTATCACGCCCGCTC 60.960 66.667 0.00 0.00 45.72 5.03
414 415 2.960129 CGTTATCACGCCCGCTCC 60.960 66.667 0.00 0.00 40.18 4.70
415 416 2.499685 GTTATCACGCCCGCTCCT 59.500 61.111 0.00 0.00 0.00 3.69
416 417 1.883084 GTTATCACGCCCGCTCCTG 60.883 63.158 0.00 0.00 0.00 3.86
417 418 2.055633 TTATCACGCCCGCTCCTGA 61.056 57.895 0.00 0.00 0.00 3.86
418 419 2.292794 TTATCACGCCCGCTCCTGAC 62.293 60.000 0.00 0.00 0.00 3.51
420 421 3.449227 CACGCCCGCTCCTGACTA 61.449 66.667 0.00 0.00 0.00 2.59
421 422 2.442272 ACGCCCGCTCCTGACTAT 60.442 61.111 0.00 0.00 0.00 2.12
422 423 2.336809 CGCCCGCTCCTGACTATC 59.663 66.667 0.00 0.00 0.00 2.08
423 424 2.737830 GCCCGCTCCTGACTATCC 59.262 66.667 0.00 0.00 0.00 2.59
424 425 2.873525 GCCCGCTCCTGACTATCCC 61.874 68.421 0.00 0.00 0.00 3.85
425 426 2.565645 CCCGCTCCTGACTATCCCG 61.566 68.421 0.00 0.00 0.00 5.14
426 427 1.528542 CCGCTCCTGACTATCCCGA 60.529 63.158 0.00 0.00 0.00 5.14
427 428 1.655329 CGCTCCTGACTATCCCGAC 59.345 63.158 0.00 0.00 0.00 4.79
428 429 1.797211 CGCTCCTGACTATCCCGACC 61.797 65.000 0.00 0.00 0.00 4.79
429 430 1.465200 GCTCCTGACTATCCCGACCC 61.465 65.000 0.00 0.00 0.00 4.46
430 431 0.106167 CTCCTGACTATCCCGACCCA 60.106 60.000 0.00 0.00 0.00 4.51
431 432 0.337082 TCCTGACTATCCCGACCCAA 59.663 55.000 0.00 0.00 0.00 4.12
432 433 1.200519 CCTGACTATCCCGACCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
433 434 1.557832 CCTGACTATCCCGACCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
434 435 2.026636 CCTGACTATCCCGACCCAAAAA 60.027 50.000 0.00 0.00 0.00 1.94
454 455 1.562783 AAACCCTCCTCCTTCTCTCG 58.437 55.000 0.00 0.00 0.00 4.04
455 456 0.973496 AACCCTCCTCCTTCTCTCGC 60.973 60.000 0.00 0.00 0.00 5.03
456 457 2.485795 CCCTCCTCCTTCTCTCGCG 61.486 68.421 0.00 0.00 0.00 5.87
457 458 1.751162 CCTCCTCCTTCTCTCGCGT 60.751 63.158 5.77 0.00 0.00 6.01
458 459 1.431440 CTCCTCCTTCTCTCGCGTG 59.569 63.158 5.77 3.13 0.00 5.34
459 460 2.202676 CCTCCTTCTCTCGCGTGC 60.203 66.667 5.77 0.00 0.00 5.34
460 461 2.568612 CTCCTTCTCTCGCGTGCA 59.431 61.111 5.77 0.00 0.00 4.57
461 462 1.140589 CTCCTTCTCTCGCGTGCAT 59.859 57.895 5.77 0.00 0.00 3.96
462 463 0.459237 CTCCTTCTCTCGCGTGCATT 60.459 55.000 5.77 0.00 0.00 3.56
463 464 0.458543 TCCTTCTCTCGCGTGCATTC 60.459 55.000 5.77 0.00 0.00 2.67
464 465 1.424493 CCTTCTCTCGCGTGCATTCC 61.424 60.000 5.77 0.00 0.00 3.01
465 466 1.424493 CTTCTCTCGCGTGCATTCCC 61.424 60.000 5.77 0.00 0.00 3.97
466 467 3.257561 CTCTCGCGTGCATTCCCG 61.258 66.667 5.77 0.00 0.00 5.14
473 474 3.443045 GTGCATTCCCGCCCAGTG 61.443 66.667 0.00 0.00 0.00 3.66
476 477 4.738998 CATTCCCGCCCAGTGCCA 62.739 66.667 0.00 0.00 36.24 4.92
477 478 4.431131 ATTCCCGCCCAGTGCCAG 62.431 66.667 0.00 0.00 36.24 4.85
487 488 4.666253 AGTGCCAGTTGCCCGCAT 62.666 61.111 0.00 0.00 40.16 4.73
488 489 3.683937 GTGCCAGTTGCCCGCATT 61.684 61.111 0.00 0.00 40.16 3.56
489 490 3.372730 TGCCAGTTGCCCGCATTC 61.373 61.111 0.00 0.00 40.16 2.67
490 491 3.372730 GCCAGTTGCCCGCATTCA 61.373 61.111 0.00 0.00 0.00 2.57
491 492 2.713967 GCCAGTTGCCCGCATTCAT 61.714 57.895 0.00 0.00 0.00 2.57
492 493 1.140161 CCAGTTGCCCGCATTCATG 59.860 57.895 0.00 0.00 0.00 3.07
523 524 3.204827 GCCGCTCCGCATTGACAT 61.205 61.111 0.00 0.00 0.00 3.06
524 525 3.017323 CCGCTCCGCATTGACATC 58.983 61.111 0.00 0.00 0.00 3.06
525 526 2.622629 CGCTCCGCATTGACATCG 59.377 61.111 0.00 0.00 0.00 3.84
526 527 2.874694 CGCTCCGCATTGACATCGG 61.875 63.158 5.30 5.30 44.16 4.18
527 528 3.017323 CTCCGCATTGACATCGGC 58.983 61.111 6.47 0.00 42.65 5.54
530 531 3.863543 CGCATTGACATCGGCGCA 61.864 61.111 10.83 0.00 43.14 6.09
531 532 2.023741 GCATTGACATCGGCGCAG 59.976 61.111 10.83 5.07 0.00 5.18
532 533 2.463620 GCATTGACATCGGCGCAGA 61.464 57.895 13.82 13.82 0.00 4.26
533 534 1.640069 CATTGACATCGGCGCAGAG 59.360 57.895 16.84 10.47 0.00 3.35
545 546 4.427661 GCAGAGCAGACGCGACCT 62.428 66.667 15.93 6.53 45.49 3.85
546 547 2.202544 CAGAGCAGACGCGACCTC 60.203 66.667 15.93 10.04 45.49 3.85
547 548 2.360600 AGAGCAGACGCGACCTCT 60.361 61.111 15.93 12.40 45.49 3.69
548 549 2.101380 GAGCAGACGCGACCTCTC 59.899 66.667 15.93 12.42 45.49 3.20
549 550 2.673341 AGCAGACGCGACCTCTCA 60.673 61.111 15.93 0.00 45.49 3.27
550 551 2.505118 GCAGACGCGACCTCTCAC 60.505 66.667 15.93 0.00 0.00 3.51
551 552 2.983930 GCAGACGCGACCTCTCACT 61.984 63.158 15.93 0.00 0.00 3.41
552 553 1.581954 CAGACGCGACCTCTCACTT 59.418 57.895 15.93 0.00 0.00 3.16
553 554 0.730834 CAGACGCGACCTCTCACTTG 60.731 60.000 15.93 0.00 0.00 3.16
554 555 2.049063 ACGCGACCTCTCACTTGC 60.049 61.111 15.93 0.00 0.00 4.01
555 556 2.049156 CGCGACCTCTCACTTGCA 60.049 61.111 0.00 0.00 0.00 4.08
556 557 2.375766 CGCGACCTCTCACTTGCAC 61.376 63.158 0.00 0.00 0.00 4.57
557 558 2.029844 GCGACCTCTCACTTGCACC 61.030 63.158 0.00 0.00 0.00 5.01
558 559 1.367471 CGACCTCTCACTTGCACCA 59.633 57.895 0.00 0.00 0.00 4.17
559 560 0.668706 CGACCTCTCACTTGCACCAG 60.669 60.000 0.00 0.00 0.00 4.00
560 561 0.952984 GACCTCTCACTTGCACCAGC 60.953 60.000 0.00 0.00 42.57 4.85
570 571 3.730761 GCACCAGCACTGAAGCGG 61.731 66.667 0.00 0.00 41.58 5.52
571 572 3.730761 CACCAGCACTGAAGCGGC 61.731 66.667 0.00 0.00 40.15 6.53
618 619 4.974989 GTCCCCGTTGTCCGCGTT 62.975 66.667 4.92 0.00 34.38 4.84
619 620 3.301554 TCCCCGTTGTCCGCGTTA 61.302 61.111 4.92 0.00 34.38 3.18
620 621 2.125431 CCCCGTTGTCCGCGTTAT 60.125 61.111 4.92 0.00 34.38 1.89
621 622 1.742510 CCCCGTTGTCCGCGTTATT 60.743 57.895 4.92 0.00 34.38 1.40
622 623 1.300266 CCCCGTTGTCCGCGTTATTT 61.300 55.000 4.92 0.00 34.38 1.40
623 624 0.518195 CCCGTTGTCCGCGTTATTTT 59.482 50.000 4.92 0.00 34.38 1.82
624 625 1.464521 CCCGTTGTCCGCGTTATTTTC 60.465 52.381 4.92 0.00 34.38 2.29
625 626 1.505898 CGTTGTCCGCGTTATTTTCG 58.494 50.000 4.92 0.00 0.00 3.46
766 767 2.256117 ATATGCAACCTCTTACCGGC 57.744 50.000 0.00 0.00 0.00 6.13
812 823 2.039624 AGCGAGGGTGGAGGACAT 59.960 61.111 0.00 0.00 0.00 3.06
813 824 2.187946 GCGAGGGTGGAGGACATG 59.812 66.667 0.00 0.00 0.00 3.21
822 833 3.561313 GGGTGGAGGACATGCTTTAAGAA 60.561 47.826 0.00 0.00 0.00 2.52
825 836 5.010617 GGTGGAGGACATGCTTTAAGAAAAA 59.989 40.000 0.00 0.00 0.00 1.94
832 843 7.874528 AGGACATGCTTTAAGAAAAAGAAATGG 59.125 33.333 0.00 0.00 32.14 3.16
845 856 4.337264 AAGAAATGGTTAAGGCCCAGAT 57.663 40.909 0.00 0.00 34.92 2.90
947 962 2.755952 ACTTTTCCCCTGTTTGCTCT 57.244 45.000 0.00 0.00 0.00 4.09
948 963 3.876309 ACTTTTCCCCTGTTTGCTCTA 57.124 42.857 0.00 0.00 0.00 2.43
950 965 4.336280 ACTTTTCCCCTGTTTGCTCTATC 58.664 43.478 0.00 0.00 0.00 2.08
951 966 4.202567 ACTTTTCCCCTGTTTGCTCTATCA 60.203 41.667 0.00 0.00 0.00 2.15
952 967 3.350219 TTCCCCTGTTTGCTCTATCAC 57.650 47.619 0.00 0.00 0.00 3.06
953 968 1.559682 TCCCCTGTTTGCTCTATCACC 59.440 52.381 0.00 0.00 0.00 4.02
955 970 2.636830 CCCTGTTTGCTCTATCACCTG 58.363 52.381 0.00 0.00 0.00 4.00
1002 1018 1.478105 CCAGATCCACATCCACCCATG 60.478 57.143 0.00 0.00 0.00 3.66
1016 1032 4.169271 CATGGCCATGGCGATCTT 57.831 55.556 34.31 9.44 43.06 2.40
1779 1795 2.415625 CGTCTTCTTCTACCAGGGTTCG 60.416 54.545 0.00 0.00 0.00 3.95
1812 1828 3.365265 GCAGAGGGGTTTGCCGTG 61.365 66.667 0.00 0.00 34.28 4.94
1852 1868 0.761187 GGGGCTGATGATAGCTGTGA 59.239 55.000 0.00 0.00 43.22 3.58
1974 1990 3.107601 CCTGGATAACTGGAAGACTGGA 58.892 50.000 0.00 0.00 40.42 3.86
1977 1993 5.545723 CCTGGATAACTGGAAGACTGGATAT 59.454 44.000 0.00 0.00 40.42 1.63
1998 2014 1.410083 GGCATTCATACCTTCTGGCCA 60.410 52.381 4.71 4.71 39.88 5.36
2033 2049 0.949105 ATGTTGTCTCAACCGGCGAC 60.949 55.000 9.30 3.94 0.00 5.19
2071 2087 6.260936 CCTTTGGTTGCAGAGGTATGTAATAG 59.739 42.308 0.00 0.00 0.00 1.73
2090 2106 8.204836 TGTAATAGTATCTCTTCTTTTCCCTGC 58.795 37.037 0.00 0.00 0.00 4.85
2093 2109 2.191128 TCTCTTCTTTTCCCTGCTGC 57.809 50.000 0.00 0.00 0.00 5.25
2094 2110 0.801251 CTCTTCTTTTCCCTGCTGCG 59.199 55.000 0.00 0.00 0.00 5.18
2112 2128 1.352114 CGCATGGCATTTTGGTTCAG 58.648 50.000 0.00 0.00 0.00 3.02
2115 2131 2.933906 GCATGGCATTTTGGTTCAGATG 59.066 45.455 0.00 0.00 0.00 2.90
2143 2159 9.602568 TTTCAATTTGAATATTGGACATGATGG 57.397 29.630 12.39 0.00 36.11 3.51
2146 2162 7.679732 ATTTGAATATTGGACATGATGGGTT 57.320 32.000 0.00 0.00 0.00 4.11
2147 2163 7.493499 TTTGAATATTGGACATGATGGGTTT 57.507 32.000 0.00 0.00 0.00 3.27
2198 2214 8.768957 TCTTGTTAGATGAGTCAGAGAATTTG 57.231 34.615 0.00 0.00 0.00 2.32
2199 2215 8.370940 TCTTGTTAGATGAGTCAGAGAATTTGT 58.629 33.333 0.00 0.00 0.00 2.83
2216 2232 7.216494 AGAATTTGTCATTTCGGAAATGGTTT 58.784 30.769 32.05 21.33 46.40 3.27
2251 2267 4.506288 CGAAATGCACACCGACTCATAATA 59.494 41.667 0.00 0.00 0.00 0.98
2259 2275 6.237942 GCACACCGACTCATAATATCATATGC 60.238 42.308 0.00 0.00 34.05 3.14
2268 2284 8.699130 ACTCATAATATCATATGCGATTCTCCA 58.301 33.333 0.00 0.00 34.05 3.86
2279 2295 8.773645 CATATGCGATTCTCCAACTGTAATAAA 58.226 33.333 0.00 0.00 0.00 1.40
2283 2299 7.064609 TGCGATTCTCCAACTGTAATAAAGAAG 59.935 37.037 0.00 0.00 0.00 2.85
2345 2362 4.082463 TCAAAATTACTTTGGGACGCATCC 60.082 41.667 0.00 0.00 44.00 3.51
2361 2378 3.425659 GCATCCCTCAACTTCTTTCCTT 58.574 45.455 0.00 0.00 0.00 3.36
2381 2399 7.353414 TCCTTGATTCTGAAGACTAGTATGG 57.647 40.000 0.00 0.00 0.00 2.74
2449 2467 2.343758 GCTCCCTCAGCGTCACAA 59.656 61.111 0.00 0.00 38.76 3.33
2450 2468 1.078848 GCTCCCTCAGCGTCACAAT 60.079 57.895 0.00 0.00 38.76 2.71
2451 2469 1.364626 GCTCCCTCAGCGTCACAATG 61.365 60.000 0.00 0.00 38.76 2.82
2452 2470 0.036952 CTCCCTCAGCGTCACAATGT 60.037 55.000 0.00 0.00 0.00 2.71
2453 2471 1.204704 CTCCCTCAGCGTCACAATGTA 59.795 52.381 0.00 0.00 0.00 2.29
2454 2472 1.831106 TCCCTCAGCGTCACAATGTAT 59.169 47.619 0.00 0.00 0.00 2.29
2455 2473 1.935873 CCCTCAGCGTCACAATGTATG 59.064 52.381 0.00 0.00 0.00 2.39
2456 2474 2.621338 CCTCAGCGTCACAATGTATGT 58.379 47.619 0.00 0.00 45.34 2.29
2457 2475 3.002791 CCTCAGCGTCACAATGTATGTT 58.997 45.455 0.00 0.00 41.46 2.71
2458 2476 3.181517 CCTCAGCGTCACAATGTATGTTG 60.182 47.826 0.00 0.00 41.46 3.33
2459 2477 3.398406 TCAGCGTCACAATGTATGTTGT 58.602 40.909 0.00 0.00 41.46 3.32
2460 2478 3.812609 TCAGCGTCACAATGTATGTTGTT 59.187 39.130 0.00 0.00 41.46 2.83
2461 2479 4.274705 TCAGCGTCACAATGTATGTTGTTT 59.725 37.500 0.00 0.00 41.46 2.83
2462 2480 4.379498 CAGCGTCACAATGTATGTTGTTTG 59.621 41.667 0.00 0.00 41.46 2.93
2463 2481 4.274705 AGCGTCACAATGTATGTTGTTTGA 59.725 37.500 0.00 0.00 41.46 2.69
2464 2482 4.612614 GCGTCACAATGTATGTTGTTTGAG 59.387 41.667 0.00 0.00 41.46 3.02
2465 2483 5.559991 GCGTCACAATGTATGTTGTTTGAGA 60.560 40.000 0.00 0.00 41.46 3.27
2466 2484 6.602179 CGTCACAATGTATGTTGTTTGAGAT 58.398 36.000 0.00 0.00 41.46 2.75
2467 2485 6.738200 CGTCACAATGTATGTTGTTTGAGATC 59.262 38.462 0.00 0.00 41.46 2.75
2468 2486 7.023575 GTCACAATGTATGTTGTTTGAGATCC 58.976 38.462 0.00 0.00 41.46 3.36
2469 2487 6.714356 TCACAATGTATGTTGTTTGAGATCCA 59.286 34.615 0.00 0.00 41.46 3.41
2472 2490 7.177216 ACAATGTATGTTGTTTGAGATCCACAT 59.823 33.333 0.00 0.00 40.06 3.21
2491 2509 8.877864 TCCACATCAGTTAATCATTTTAAGGT 57.122 30.769 0.00 0.00 0.00 3.50
2522 2540 9.046846 CCATGGATATAGGAAAACCTATCTACA 57.953 37.037 5.56 9.72 35.07 2.74
2559 2577 9.770097 TGGAATCATAATTCTAGATTCACTGTC 57.230 33.333 20.08 9.60 45.82 3.51
2620 2638 8.259411 TCAAGAAGCATATTTTAATTGGCATGT 58.741 29.630 0.00 0.00 0.00 3.21
2622 2640 9.754382 AAGAAGCATATTTTAATTGGCATGTAG 57.246 29.630 0.00 0.00 0.00 2.74
2631 2649 9.855021 ATTTTAATTGGCATGTAGTAAAGTGAC 57.145 29.630 0.00 0.00 0.00 3.67
2633 2651 5.880054 ATTGGCATGTAGTAAAGTGACAC 57.120 39.130 0.00 0.00 0.00 3.67
2635 2653 2.671396 GGCATGTAGTAAAGTGACACGG 59.329 50.000 0.00 0.00 0.00 4.94
2636 2654 3.581755 GCATGTAGTAAAGTGACACGGA 58.418 45.455 0.00 0.00 0.00 4.69
2637 2655 3.991773 GCATGTAGTAAAGTGACACGGAA 59.008 43.478 0.00 0.00 0.00 4.30
2638 2656 4.630069 GCATGTAGTAAAGTGACACGGAAT 59.370 41.667 0.00 0.00 0.00 3.01
2639 2657 5.808540 GCATGTAGTAAAGTGACACGGAATA 59.191 40.000 0.00 0.00 0.00 1.75
2640 2658 6.311935 GCATGTAGTAAAGTGACACGGAATAA 59.688 38.462 0.00 0.00 0.00 1.40
2641 2659 7.148540 GCATGTAGTAAAGTGACACGGAATAAA 60.149 37.037 0.00 0.00 0.00 1.40
2642 2660 8.714179 CATGTAGTAAAGTGACACGGAATAAAA 58.286 33.333 0.00 0.00 0.00 1.52
2643 2661 8.836268 TGTAGTAAAGTGACACGGAATAAAAT 57.164 30.769 0.00 0.00 0.00 1.82
2672 2690 3.171528 GGTAGAGTGGTAGGTTGTCCTT 58.828 50.000 0.00 0.00 42.12 3.36
2673 2691 3.581770 GGTAGAGTGGTAGGTTGTCCTTT 59.418 47.826 0.00 0.00 42.12 3.11
2674 2692 3.771577 AGAGTGGTAGGTTGTCCTTTG 57.228 47.619 0.00 0.00 42.12 2.77
2675 2693 3.046374 AGAGTGGTAGGTTGTCCTTTGT 58.954 45.455 0.00 0.00 42.12 2.83
2676 2694 3.071167 AGAGTGGTAGGTTGTCCTTTGTC 59.929 47.826 0.00 0.00 42.12 3.18
2772 2791 8.607459 CACTTTATGATAGACACTTCAATGACC 58.393 37.037 0.00 0.00 0.00 4.02
2985 3004 1.568597 CCATGTGTCCTCCCCCATTTA 59.431 52.381 0.00 0.00 0.00 1.40
2988 3007 3.380471 TGTGTCCTCCCCCATTTATTG 57.620 47.619 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.993736 CCAGACGTATGTGTGTGATTTGA 59.006 43.478 9.66 0.00 37.67 2.69
1 2 3.993736 TCCAGACGTATGTGTGTGATTTG 59.006 43.478 9.66 0.00 37.67 2.32
5 6 1.271379 GGTCCAGACGTATGTGTGTGA 59.729 52.381 9.66 5.60 37.67 3.58
6 7 1.710013 GGTCCAGACGTATGTGTGTG 58.290 55.000 9.66 3.51 37.67 3.82
7 8 0.242825 CGGTCCAGACGTATGTGTGT 59.757 55.000 9.66 0.00 37.67 3.72
8 9 0.242825 ACGGTCCAGACGTATGTGTG 59.757 55.000 9.66 5.25 43.60 3.82
9 10 0.242825 CACGGTCCAGACGTATGTGT 59.757 55.000 9.66 0.00 43.58 3.72
10 11 0.242825 ACACGGTCCAGACGTATGTG 59.757 55.000 9.66 2.84 43.58 3.21
11 12 0.242825 CACACGGTCCAGACGTATGT 59.757 55.000 9.66 0.00 43.58 2.29
12 13 0.457853 CCACACGGTCCAGACGTATG 60.458 60.000 2.43 2.43 43.58 2.39
13 14 0.896940 ACCACACGGTCCAGACGTAT 60.897 55.000 0.00 0.00 44.71 3.06
14 15 1.529010 ACCACACGGTCCAGACGTA 60.529 57.895 0.00 0.00 44.71 3.57
15 16 2.836360 ACCACACGGTCCAGACGT 60.836 61.111 0.00 0.00 44.71 4.34
22 23 1.755393 AGGGACTGAACCACACGGTC 61.755 60.000 0.00 0.00 41.78 4.79
23 24 1.764854 AGGGACTGAACCACACGGT 60.765 57.895 0.00 0.00 44.36 4.83
24 25 3.148084 AGGGACTGAACCACACGG 58.852 61.111 0.00 0.00 37.18 4.94
35 36 3.746957 GGATGGCTTCCAGGGACT 58.253 61.111 14.15 0.00 44.74 3.85
42 43 0.526211 GACCGTTTTGGATGGCTTCC 59.474 55.000 12.30 12.30 45.69 3.46
43 44 1.243902 TGACCGTTTTGGATGGCTTC 58.756 50.000 0.00 0.00 42.00 3.86
44 45 1.545582 CATGACCGTTTTGGATGGCTT 59.454 47.619 0.00 0.00 42.00 4.35
45 46 1.176527 CATGACCGTTTTGGATGGCT 58.823 50.000 0.00 0.00 42.00 4.75
46 47 0.887933 ACATGACCGTTTTGGATGGC 59.112 50.000 0.00 0.00 42.00 4.40
47 48 3.002246 CGATACATGACCGTTTTGGATGG 59.998 47.826 0.00 0.00 42.00 3.51
48 49 3.002246 CCGATACATGACCGTTTTGGATG 59.998 47.826 0.00 0.00 42.00 3.51
49 50 3.202906 CCGATACATGACCGTTTTGGAT 58.797 45.455 0.00 0.00 42.00 3.41
50 51 2.027929 ACCGATACATGACCGTTTTGGA 60.028 45.455 0.00 0.00 42.00 3.53
51 52 2.350498 GACCGATACATGACCGTTTTGG 59.650 50.000 0.00 0.00 46.41 3.28
52 53 2.350498 GGACCGATACATGACCGTTTTG 59.650 50.000 0.00 0.00 0.00 2.44
53 54 2.624636 GGACCGATACATGACCGTTTT 58.375 47.619 0.00 0.00 0.00 2.43
54 55 1.470285 CGGACCGATACATGACCGTTT 60.470 52.381 8.64 0.00 36.38 3.60
55 56 0.101759 CGGACCGATACATGACCGTT 59.898 55.000 8.64 0.00 36.38 4.44
56 57 1.731700 CGGACCGATACATGACCGT 59.268 57.895 8.64 0.00 36.38 4.83
57 58 1.660575 GCGGACCGATACATGACCG 60.661 63.158 20.50 0.00 42.63 4.79
58 59 0.104304 AAGCGGACCGATACATGACC 59.896 55.000 20.50 0.00 0.00 4.02
59 60 1.488527 GAAGCGGACCGATACATGAC 58.511 55.000 20.50 0.00 0.00 3.06
60 61 0.387929 GGAAGCGGACCGATACATGA 59.612 55.000 20.50 0.00 0.00 3.07
61 62 2.900528 GGAAGCGGACCGATACATG 58.099 57.895 20.50 0.00 0.00 3.21
71 72 3.599285 AAATGCGTCCGGAAGCGGA 62.599 57.895 32.29 22.46 38.66 5.54
72 73 2.577763 GAAAATGCGTCCGGAAGCGG 62.578 60.000 32.29 12.53 38.66 5.52
73 74 1.226018 GAAAATGCGTCCGGAAGCG 60.226 57.895 32.29 21.98 38.66 4.68
74 75 1.136774 GGAAAATGCGTCCGGAAGC 59.863 57.895 32.12 32.12 36.35 3.86
75 76 1.654023 GGGGAAAATGCGTCCGGAAG 61.654 60.000 13.59 13.59 35.86 3.46
76 77 1.676303 GGGGAAAATGCGTCCGGAA 60.676 57.895 5.23 0.00 35.86 4.30
77 78 2.045731 GGGGAAAATGCGTCCGGA 60.046 61.111 0.00 0.00 35.86 5.14
78 79 3.138128 GGGGGAAAATGCGTCCGG 61.138 66.667 0.00 0.00 35.86 5.14
79 80 1.974343 TTGGGGGAAAATGCGTCCG 60.974 57.895 0.00 0.00 35.86 4.79
80 81 1.182385 TGTTGGGGGAAAATGCGTCC 61.182 55.000 0.00 0.00 0.00 4.79
81 82 0.038618 GTGTTGGGGGAAAATGCGTC 60.039 55.000 0.00 0.00 0.00 5.19
82 83 0.469144 AGTGTTGGGGGAAAATGCGT 60.469 50.000 0.00 0.00 0.00 5.24
83 84 0.038343 CAGTGTTGGGGGAAAATGCG 60.038 55.000 0.00 0.00 0.00 4.73
84 85 1.000843 GTCAGTGTTGGGGGAAAATGC 59.999 52.381 0.00 0.00 0.00 3.56
85 86 1.618343 GGTCAGTGTTGGGGGAAAATG 59.382 52.381 0.00 0.00 0.00 2.32
86 87 1.482365 GGGTCAGTGTTGGGGGAAAAT 60.482 52.381 0.00 0.00 0.00 1.82
87 88 0.105913 GGGTCAGTGTTGGGGGAAAA 60.106 55.000 0.00 0.00 0.00 2.29
88 89 1.539665 GGGTCAGTGTTGGGGGAAA 59.460 57.895 0.00 0.00 0.00 3.13
89 90 2.466186 GGGGTCAGTGTTGGGGGAA 61.466 63.158 0.00 0.00 0.00 3.97
90 91 2.856988 GGGGTCAGTGTTGGGGGA 60.857 66.667 0.00 0.00 0.00 4.81
91 92 2.305314 TTTGGGGTCAGTGTTGGGGG 62.305 60.000 0.00 0.00 0.00 5.40
92 93 0.397816 TTTTGGGGTCAGTGTTGGGG 60.398 55.000 0.00 0.00 0.00 4.96
93 94 1.618343 GATTTTGGGGTCAGTGTTGGG 59.382 52.381 0.00 0.00 0.00 4.12
394 395 3.259751 GCGGGCGTGATAACGGTC 61.260 66.667 4.40 0.00 0.00 4.79
395 396 3.711541 GAGCGGGCGTGATAACGGT 62.712 63.158 4.40 0.00 39.96 4.83
396 397 2.960129 GAGCGGGCGTGATAACGG 60.960 66.667 4.40 0.00 0.00 4.44
397 398 2.960129 GGAGCGGGCGTGATAACG 60.960 66.667 0.00 0.00 0.00 3.18
398 399 1.883084 CAGGAGCGGGCGTGATAAC 60.883 63.158 0.00 0.00 0.00 1.89
399 400 2.055633 TCAGGAGCGGGCGTGATAA 61.056 57.895 0.00 0.00 0.00 1.75
400 401 2.441348 TCAGGAGCGGGCGTGATA 60.441 61.111 0.00 0.00 0.00 2.15
401 402 4.148825 GTCAGGAGCGGGCGTGAT 62.149 66.667 0.00 0.00 35.44 3.06
402 403 3.931190 TAGTCAGGAGCGGGCGTGA 62.931 63.158 0.00 0.00 0.00 4.35
403 404 2.685387 GATAGTCAGGAGCGGGCGTG 62.685 65.000 0.00 0.00 0.00 5.34
404 405 2.442272 ATAGTCAGGAGCGGGCGT 60.442 61.111 0.00 0.00 0.00 5.68
405 406 2.336809 GATAGTCAGGAGCGGGCG 59.663 66.667 0.00 0.00 0.00 6.13
406 407 2.737830 GGATAGTCAGGAGCGGGC 59.262 66.667 0.00 0.00 0.00 6.13
407 408 2.565645 CGGGATAGTCAGGAGCGGG 61.566 68.421 0.00 0.00 0.00 6.13
408 409 1.528542 TCGGGATAGTCAGGAGCGG 60.529 63.158 0.00 0.00 0.00 5.52
409 410 1.655329 GTCGGGATAGTCAGGAGCG 59.345 63.158 0.00 0.00 0.00 5.03
410 411 1.465200 GGGTCGGGATAGTCAGGAGC 61.465 65.000 0.00 0.00 0.00 4.70
411 412 0.106167 TGGGTCGGGATAGTCAGGAG 60.106 60.000 0.00 0.00 0.00 3.69
412 413 0.337082 TTGGGTCGGGATAGTCAGGA 59.663 55.000 0.00 0.00 0.00 3.86
413 414 1.200519 TTTGGGTCGGGATAGTCAGG 58.799 55.000 0.00 0.00 0.00 3.86
414 415 3.343941 TTTTTGGGTCGGGATAGTCAG 57.656 47.619 0.00 0.00 0.00 3.51
433 434 2.303311 CGAGAGAAGGAGGAGGGTTTTT 59.697 50.000 0.00 0.00 0.00 1.94
434 435 1.903183 CGAGAGAAGGAGGAGGGTTTT 59.097 52.381 0.00 0.00 0.00 2.43
435 436 1.562783 CGAGAGAAGGAGGAGGGTTT 58.437 55.000 0.00 0.00 0.00 3.27
436 437 0.973496 GCGAGAGAAGGAGGAGGGTT 60.973 60.000 0.00 0.00 0.00 4.11
437 438 1.380650 GCGAGAGAAGGAGGAGGGT 60.381 63.158 0.00 0.00 0.00 4.34
438 439 2.485795 CGCGAGAGAAGGAGGAGGG 61.486 68.421 0.00 0.00 0.00 4.30
439 440 1.751162 ACGCGAGAGAAGGAGGAGG 60.751 63.158 15.93 0.00 0.00 4.30
440 441 1.431440 CACGCGAGAGAAGGAGGAG 59.569 63.158 15.93 0.00 0.00 3.69
441 442 2.701780 GCACGCGAGAGAAGGAGGA 61.702 63.158 15.93 0.00 0.00 3.71
442 443 2.202676 GCACGCGAGAGAAGGAGG 60.203 66.667 15.93 0.00 0.00 4.30
443 444 0.459237 AATGCACGCGAGAGAAGGAG 60.459 55.000 15.93 0.00 0.00 3.69
444 445 0.458543 GAATGCACGCGAGAGAAGGA 60.459 55.000 15.93 0.00 0.00 3.36
445 446 1.424493 GGAATGCACGCGAGAGAAGG 61.424 60.000 15.93 0.00 0.00 3.46
446 447 1.424493 GGGAATGCACGCGAGAGAAG 61.424 60.000 15.93 0.00 0.00 2.85
447 448 1.447838 GGGAATGCACGCGAGAGAA 60.448 57.895 15.93 0.00 0.00 2.87
448 449 2.184322 GGGAATGCACGCGAGAGA 59.816 61.111 15.93 0.00 0.00 3.10
449 450 3.257561 CGGGAATGCACGCGAGAG 61.258 66.667 15.93 2.87 46.30 3.20
456 457 3.443045 CACTGGGCGGGAATGCAC 61.443 66.667 0.00 0.00 39.27 4.57
459 460 4.738998 TGGCACTGGGCGGGAATG 62.739 66.667 0.00 0.00 46.16 2.67
460 461 4.431131 CTGGCACTGGGCGGGAAT 62.431 66.667 0.00 0.00 46.16 3.01
470 471 4.666253 ATGCGGGCAACTGGCACT 62.666 61.111 5.56 0.00 46.58 4.40
471 472 3.631487 GAATGCGGGCAACTGGCAC 62.631 63.158 5.56 0.00 45.84 5.01
473 474 2.713967 ATGAATGCGGGCAACTGGC 61.714 57.895 0.00 0.00 45.89 4.85
474 475 1.140161 CATGAATGCGGGCAACTGG 59.860 57.895 0.00 0.00 45.89 4.00
475 476 1.517694 GCATGAATGCGGGCAACTG 60.518 57.895 0.00 0.00 44.67 3.16
476 477 2.887360 GCATGAATGCGGGCAACT 59.113 55.556 0.00 0.00 44.67 3.16
483 484 4.112687 GCTCTATAGCGGCATGAATGCG 62.113 54.545 9.07 6.07 46.23 4.73
484 485 1.396301 GCTCTATAGCGGCATGAATGC 59.604 52.381 6.73 6.73 45.32 3.56
512 513 4.596180 GCGCCGATGTCAATGCGG 62.596 66.667 13.57 10.68 46.59 5.69
514 515 2.023741 CTGCGCCGATGTCAATGC 59.976 61.111 4.18 0.00 0.00 3.56
515 516 1.640069 CTCTGCGCCGATGTCAATG 59.360 57.895 4.18 0.00 0.00 2.82
516 517 2.176273 GCTCTGCGCCGATGTCAAT 61.176 57.895 4.18 0.00 0.00 2.57
517 518 2.815211 GCTCTGCGCCGATGTCAA 60.815 61.111 4.18 0.00 0.00 3.18
518 519 3.995219 CTGCTCTGCGCCGATGTCA 62.995 63.158 4.18 1.72 38.05 3.58
519 520 3.260483 CTGCTCTGCGCCGATGTC 61.260 66.667 4.18 0.00 38.05 3.06
520 521 3.763356 TCTGCTCTGCGCCGATGT 61.763 61.111 4.18 0.00 38.05 3.06
521 522 3.260483 GTCTGCTCTGCGCCGATG 61.260 66.667 4.18 0.00 38.05 3.84
522 523 4.862092 CGTCTGCTCTGCGCCGAT 62.862 66.667 4.18 0.00 38.05 4.18
528 529 4.427661 AGGTCGCGTCTGCTCTGC 62.428 66.667 5.77 0.00 39.65 4.26
529 530 2.202544 GAGGTCGCGTCTGCTCTG 60.203 66.667 5.77 0.00 39.65 3.35
530 531 2.360600 AGAGGTCGCGTCTGCTCT 60.361 61.111 5.77 6.15 39.65 4.09
531 532 2.101380 GAGAGGTCGCGTCTGCTC 59.899 66.667 5.77 8.04 39.65 4.26
532 533 2.673341 TGAGAGGTCGCGTCTGCT 60.673 61.111 5.77 1.84 39.65 4.24
533 534 2.479412 AAGTGAGAGGTCGCGTCTGC 62.479 60.000 5.77 0.00 38.32 4.26
534 535 0.730834 CAAGTGAGAGGTCGCGTCTG 60.731 60.000 5.77 0.00 38.32 3.51
535 536 1.581954 CAAGTGAGAGGTCGCGTCT 59.418 57.895 5.77 0.52 38.32 4.18
536 537 2.089349 GCAAGTGAGAGGTCGCGTC 61.089 63.158 5.77 0.00 38.32 5.19
537 538 2.049063 GCAAGTGAGAGGTCGCGT 60.049 61.111 5.77 0.00 38.32 6.01
538 539 2.049156 TGCAAGTGAGAGGTCGCG 60.049 61.111 0.00 0.00 38.32 5.87
539 540 2.029844 GGTGCAAGTGAGAGGTCGC 61.030 63.158 0.00 0.00 0.00 5.19
540 541 0.668706 CTGGTGCAAGTGAGAGGTCG 60.669 60.000 0.00 0.00 0.00 4.79
541 542 0.952984 GCTGGTGCAAGTGAGAGGTC 60.953 60.000 0.00 0.00 39.41 3.85
542 543 1.072159 GCTGGTGCAAGTGAGAGGT 59.928 57.895 0.00 0.00 39.41 3.85
543 544 3.978272 GCTGGTGCAAGTGAGAGG 58.022 61.111 0.00 0.00 39.41 3.69
553 554 3.730761 CCGCTTCAGTGCTGGTGC 61.731 66.667 0.00 3.83 40.20 5.01
554 555 3.730761 GCCGCTTCAGTGCTGGTG 61.731 66.667 0.00 0.00 0.00 4.17
605 606 1.784115 CGAAAATAACGCGGACAACGG 60.784 52.381 12.47 0.00 44.51 4.44
606 607 2.356311 GCGAAAATAACGCGGACAACG 61.356 52.381 12.47 8.46 46.05 4.10
607 608 1.244352 GCGAAAATAACGCGGACAAC 58.756 50.000 12.47 0.00 46.05 3.32
608 609 3.661229 GCGAAAATAACGCGGACAA 57.339 47.368 12.47 0.00 46.05 3.18
739 740 9.661563 CCGGTAAGAGGTTGCATATATATTTTA 57.338 33.333 0.00 0.00 0.00 1.52
740 741 7.120726 GCCGGTAAGAGGTTGCATATATATTTT 59.879 37.037 1.90 0.00 0.00 1.82
794 795 2.060980 ATGTCCTCCACCCTCGCTC 61.061 63.158 0.00 0.00 0.00 5.03
798 799 0.329596 AAAGCATGTCCTCCACCCTC 59.670 55.000 0.00 0.00 0.00 4.30
799 800 1.668826 TAAAGCATGTCCTCCACCCT 58.331 50.000 0.00 0.00 0.00 4.34
802 803 5.705609 TTTTCTTAAAGCATGTCCTCCAC 57.294 39.130 0.00 0.00 0.00 4.02
812 823 9.541143 CCTTAACCATTTCTTTTTCTTAAAGCA 57.459 29.630 0.00 0.00 0.00 3.91
813 824 8.495949 GCCTTAACCATTTCTTTTTCTTAAAGC 58.504 33.333 0.00 0.00 0.00 3.51
822 833 4.488770 TCTGGGCCTTAACCATTTCTTTT 58.511 39.130 4.53 0.00 37.38 2.27
825 836 4.337264 AATCTGGGCCTTAACCATTTCT 57.663 40.909 4.53 0.00 37.38 2.52
832 843 2.672961 GCCAAAATCTGGGCCTTAAC 57.327 50.000 4.53 0.00 46.54 2.01
845 856 0.396060 GAGGTTGCAATGGGCCAAAA 59.604 50.000 11.89 0.00 43.89 2.44
947 962 2.346803 GCGAAAACTGAGCAGGTGATA 58.653 47.619 2.20 0.00 0.00 2.15
948 963 1.160137 GCGAAAACTGAGCAGGTGAT 58.840 50.000 2.20 0.00 0.00 3.06
950 965 1.576421 GGCGAAAACTGAGCAGGTG 59.424 57.895 2.20 0.00 0.00 4.00
951 966 1.961277 CGGCGAAAACTGAGCAGGT 60.961 57.895 0.00 0.00 0.00 4.00
952 967 1.901650 GACGGCGAAAACTGAGCAGG 61.902 60.000 16.62 0.00 0.00 4.85
953 968 1.493311 GACGGCGAAAACTGAGCAG 59.507 57.895 16.62 0.00 0.00 4.24
955 970 2.470286 CGACGGCGAAAACTGAGC 59.530 61.111 16.62 0.00 40.82 4.26
1002 1018 2.595754 GGGAAGATCGCCATGGCC 60.596 66.667 30.79 17.04 37.98 5.36
1434 1450 4.823276 GACTGGTCCATCTGCTCG 57.177 61.111 0.00 0.00 0.00 5.03
1852 1868 2.224606 CTTCACCAGCAAGTGTGTCAT 58.775 47.619 6.09 0.00 38.91 3.06
1912 1928 2.044053 CCACCCAACCGCCATGAT 60.044 61.111 0.00 0.00 0.00 2.45
1920 1936 4.218686 ACTGCCCACCACCCAACC 62.219 66.667 0.00 0.00 0.00 3.77
1921 1937 2.597510 GACTGCCCACCACCCAAC 60.598 66.667 0.00 0.00 0.00 3.77
1923 1939 3.569210 CTGACTGCCCACCACCCA 61.569 66.667 0.00 0.00 0.00 4.51
1974 1990 4.338879 GCCAGAAGGTATGAATGCCATAT 58.661 43.478 0.06 0.00 39.69 1.78
1977 1993 1.410083 GGCCAGAAGGTATGAATGCCA 60.410 52.381 0.00 0.00 37.58 4.92
1998 2014 5.013183 AGACAACATTTACCTCCAGCTACTT 59.987 40.000 0.00 0.00 0.00 2.24
2033 2049 2.162681 ACCAAAGGAAAGAAGCATCGG 58.837 47.619 0.00 0.00 0.00 4.18
2071 2087 3.625313 GCAGCAGGGAAAAGAAGAGATAC 59.375 47.826 0.00 0.00 0.00 2.24
2093 2109 1.067706 TCTGAACCAAAATGCCATGCG 60.068 47.619 0.00 0.00 0.00 4.73
2094 2110 2.747396 TCTGAACCAAAATGCCATGC 57.253 45.000 0.00 0.00 0.00 4.06
2154 2170 7.008021 ACAAGATTGGGTGAATTGCTAAAAT 57.992 32.000 0.00 0.00 0.00 1.82
2169 2185 6.871844 TCTCTGACTCATCTAACAAGATTGG 58.128 40.000 0.00 0.00 0.00 3.16
2176 2192 7.670364 TGACAAATTCTCTGACTCATCTAACA 58.330 34.615 0.00 0.00 0.00 2.41
2216 2232 5.391523 GGTGTGCATTTCGTTTCAGCTATAA 60.392 40.000 0.00 0.00 0.00 0.98
2251 2267 4.965814 ACAGTTGGAGAATCGCATATGAT 58.034 39.130 6.97 0.00 34.37 2.45
2259 2275 8.703604 TCTTCTTTATTACAGTTGGAGAATCG 57.296 34.615 0.00 0.00 34.37 3.34
2321 2338 5.565834 GGATGCGTCCCAAAGTAATTTTGAA 60.566 40.000 14.58 0.00 44.74 2.69
2322 2339 4.082463 GGATGCGTCCCAAAGTAATTTTGA 60.082 41.667 14.58 0.00 44.74 2.69
2345 2362 6.000219 TCAGAATCAAGGAAAGAAGTTGAGG 59.000 40.000 0.00 0.00 33.83 3.86
2349 2366 7.286313 AGTCTTCAGAATCAAGGAAAGAAGTT 58.714 34.615 0.00 0.00 34.28 2.66
2361 2378 5.893824 TCTGCCATACTAGTCTTCAGAATCA 59.106 40.000 0.00 0.00 0.00 2.57
2381 2399 6.713792 AAGAAACGAAAGAAGTCTATCTGC 57.286 37.500 0.00 0.00 0.00 4.26
2447 2465 6.912082 TGTGGATCTCAAACAACATACATTG 58.088 36.000 0.00 0.00 35.59 2.82
2448 2466 7.394077 TGATGTGGATCTCAAACAACATACATT 59.606 33.333 0.00 0.00 0.00 2.71
2449 2467 6.885918 TGATGTGGATCTCAAACAACATACAT 59.114 34.615 0.00 0.00 0.00 2.29
2450 2468 6.237154 TGATGTGGATCTCAAACAACATACA 58.763 36.000 0.00 0.00 0.00 2.29
2451 2469 6.372659 ACTGATGTGGATCTCAAACAACATAC 59.627 38.462 0.00 0.00 0.00 2.39
2452 2470 6.475504 ACTGATGTGGATCTCAAACAACATA 58.524 36.000 0.00 0.00 0.00 2.29
2453 2471 5.319453 ACTGATGTGGATCTCAAACAACAT 58.681 37.500 0.00 0.00 0.00 2.71
2454 2472 4.717877 ACTGATGTGGATCTCAAACAACA 58.282 39.130 0.00 0.00 0.00 3.33
2455 2473 5.695851 AACTGATGTGGATCTCAAACAAC 57.304 39.130 0.00 0.00 0.00 3.32
2456 2474 7.665145 TGATTAACTGATGTGGATCTCAAACAA 59.335 33.333 0.00 0.00 0.00 2.83
2457 2475 7.167535 TGATTAACTGATGTGGATCTCAAACA 58.832 34.615 0.00 0.00 0.00 2.83
2458 2476 7.615582 TGATTAACTGATGTGGATCTCAAAC 57.384 36.000 0.00 0.00 0.00 2.93
2459 2477 8.812513 AATGATTAACTGATGTGGATCTCAAA 57.187 30.769 0.00 0.00 0.00 2.69
2460 2478 8.812513 AAATGATTAACTGATGTGGATCTCAA 57.187 30.769 0.00 0.00 0.00 3.02
2461 2479 8.812513 AAAATGATTAACTGATGTGGATCTCA 57.187 30.769 0.00 0.00 0.00 3.27
2464 2482 9.956720 CCTTAAAATGATTAACTGATGTGGATC 57.043 33.333 0.00 0.00 0.00 3.36
2465 2483 9.479549 ACCTTAAAATGATTAACTGATGTGGAT 57.520 29.630 0.00 0.00 0.00 3.41
2466 2484 8.877864 ACCTTAAAATGATTAACTGATGTGGA 57.122 30.769 0.00 0.00 0.00 4.02
2472 2490 8.607713 TGGTCCTACCTTAAAATGATTAACTGA 58.392 33.333 0.00 0.00 39.58 3.41
2491 2509 6.697641 GGTTTTCCTATATCCATGGTCCTA 57.302 41.667 12.58 2.82 36.94 2.94
2609 2627 6.091577 CGTGTCACTTTACTACATGCCAATTA 59.908 38.462 0.65 0.00 0.00 1.40
2620 2638 8.095792 TCCATTTTATTCCGTGTCACTTTACTA 58.904 33.333 0.65 0.00 0.00 1.82
2622 2640 7.094933 ACTCCATTTTATTCCGTGTCACTTTAC 60.095 37.037 0.65 0.00 0.00 2.01
2624 2642 5.768164 ACTCCATTTTATTCCGTGTCACTTT 59.232 36.000 0.65 0.00 0.00 2.66
2625 2643 5.313712 ACTCCATTTTATTCCGTGTCACTT 58.686 37.500 0.65 0.00 0.00 3.16
2626 2644 4.906618 ACTCCATTTTATTCCGTGTCACT 58.093 39.130 0.65 0.00 0.00 3.41
2627 2645 6.238374 CCATACTCCATTTTATTCCGTGTCAC 60.238 42.308 0.00 0.00 0.00 3.67
2628 2646 5.820423 CCATACTCCATTTTATTCCGTGTCA 59.180 40.000 0.00 0.00 0.00 3.58
2629 2647 5.820947 ACCATACTCCATTTTATTCCGTGTC 59.179 40.000 0.00 0.00 0.00 3.67
2630 2648 5.751586 ACCATACTCCATTTTATTCCGTGT 58.248 37.500 0.00 0.00 0.00 4.49
2631 2649 7.214381 TCTACCATACTCCATTTTATTCCGTG 58.786 38.462 0.00 0.00 0.00 4.94
2633 2651 7.385205 CACTCTACCATACTCCATTTTATTCCG 59.615 40.741 0.00 0.00 0.00 4.30
2635 2653 8.211629 ACCACTCTACCATACTCCATTTTATTC 58.788 37.037 0.00 0.00 0.00 1.75
2636 2654 8.102484 ACCACTCTACCATACTCCATTTTATT 57.898 34.615 0.00 0.00 0.00 1.40
2637 2655 7.691993 ACCACTCTACCATACTCCATTTTAT 57.308 36.000 0.00 0.00 0.00 1.40
2638 2656 7.289317 CCTACCACTCTACCATACTCCATTTTA 59.711 40.741 0.00 0.00 0.00 1.52
2639 2657 6.099845 CCTACCACTCTACCATACTCCATTTT 59.900 42.308 0.00 0.00 0.00 1.82
2640 2658 5.602978 CCTACCACTCTACCATACTCCATTT 59.397 44.000 0.00 0.00 0.00 2.32
2641 2659 5.148502 CCTACCACTCTACCATACTCCATT 58.851 45.833 0.00 0.00 0.00 3.16
2642 2660 4.170251 ACCTACCACTCTACCATACTCCAT 59.830 45.833 0.00 0.00 0.00 3.41
2643 2661 3.530564 ACCTACCACTCTACCATACTCCA 59.469 47.826 0.00 0.00 0.00 3.86
2671 2689 5.593909 AGTCATCACATTCCACAAAGACAAA 59.406 36.000 0.00 0.00 0.00 2.83
2672 2690 5.132502 AGTCATCACATTCCACAAAGACAA 58.867 37.500 0.00 0.00 0.00 3.18
2673 2691 4.717877 AGTCATCACATTCCACAAAGACA 58.282 39.130 0.00 0.00 0.00 3.41
2674 2692 5.695851 AAGTCATCACATTCCACAAAGAC 57.304 39.130 0.00 0.00 0.00 3.01
2675 2693 5.827267 TCAAAGTCATCACATTCCACAAAGA 59.173 36.000 0.00 0.00 0.00 2.52
2676 2694 6.075762 TCAAAGTCATCACATTCCACAAAG 57.924 37.500 0.00 0.00 0.00 2.77
2840 2859 7.665559 TCTTGTTGCCTCACTGTTTTAAGATAT 59.334 33.333 0.00 0.00 0.00 1.63
2849 2868 3.290710 ACAATCTTGTTGCCTCACTGTT 58.709 40.909 0.00 0.00 38.47 3.16
2850 2869 2.936202 ACAATCTTGTTGCCTCACTGT 58.064 42.857 0.00 0.00 38.47 3.55
2897 2916 2.271800 CGTGAATCTAGGTGAAGGCAC 58.728 52.381 0.00 0.00 44.39 5.01


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

AutoCloner maintained by Alex Coulton.