Multiple sequence alignment - TraesCS5D01G477500

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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 TraesCS5D01G477500 chr5D 100.000 3781 0 0 1 3781 516784828 516788608 0.000000e+00 6983
1 TraesCS5D01G477500 chr5B 90.419 1816 95 38 685 2459 649021842 649023619 0.000000e+00 2316
2 TraesCS5D01G477500 chr5B 91.238 719 36 9 2549 3254 649023644 649024348 0.000000e+00 953
3 TraesCS5D01G477500 chr5B 90.833 480 13 12 3314 3781 649024347 649024807 6.940000e-172 614
4 TraesCS5D01G477500 chr5A 87.520 1875 103 53 580 2417 644120206 644121986 0.000000e+00 2045
5 TraesCS5D01G477500 chr5A 85.268 1249 88 38 2549 3757 644122062 644123254 0.000000e+00 1199
6 TraesCS5D01G477500 chr5A 90.698 516 33 6 2 511 644119702 644120208 0.000000e+00 673
7 TraesCS5D01G477500 chr7D 86.634 202 26 1 2578 2779 552285458 552285258 4.920000e-54 222
8 TraesCS5D01G477500 chr7B 87.179 195 25 0 2585 2779 597311080 597310886 4.920000e-54 222
9 TraesCS5D01G477500 chr7A 85.644 202 28 1 2578 2779 637948774 637948574 1.060000e-50 211


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 TraesCS5D01G477500 chr5D 516784828 516788608 3780 False 6983.000000 6983 100.000000 1 3781 1 chr5D.!!$F1 3780
1 TraesCS5D01G477500 chr5B 649021842 649024807 2965 False 1294.333333 2316 90.830000 685 3781 3 chr5B.!!$F1 3096
2 TraesCS5D01G477500 chr5A 644119702 644123254 3552 False 1305.666667 2045 87.828667 2 3757 3 chr5A.!!$F1 3755

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
233 238 0.109086 CGTGTCTGTCTTGATCCGCT 60.109 55.0 0.0 0.0 0.0 5.52 F
911 929 0.249238 AGCAAGATCATCGACCGAGC 60.249 55.0 0.0 0.0 0.0 5.03 F
2417 2498 0.318441 TTTGTCCGAGAGAGCCACTG 59.682 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
2001 2070 0.036732 GCTGAGTCCACCAACCATCA 59.963 55.0 0.00 0.00 0.00 3.07 R
2463 2544 0.255890 GCAGCATGGAGGAAAGGGTA 59.744 55.0 0.00 0.00 35.86 3.69 R
3704 3842 0.108138 CCAGACAAGGCCCGTCTTAG 60.108 60.0 20.19 12.35 41.80 2.18 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
24 25 2.039879 AGACATTGGTTAAGCCTCCGTT 59.960 45.455 1.51 0.00 38.35 4.44
30 31 2.158726 TGGTTAAGCCTCCGTTTGACTT 60.159 45.455 1.51 0.00 38.35 3.01
53 54 0.809385 CGAGACTATGGTGTCACCGT 59.191 55.000 20.50 20.50 42.58 4.83
55 56 2.223203 CGAGACTATGGTGTCACCGTAC 60.223 54.545 18.41 10.91 42.58 3.67
61 62 2.051076 GTGTCACCGTACGCGTGA 60.051 61.111 25.68 25.68 36.15 4.35
63 64 1.005294 GTGTCACCGTACGCGTGAAT 61.005 55.000 28.87 1.03 36.15 2.57
64 65 0.520847 TGTCACCGTACGCGTGAATA 59.479 50.000 28.87 21.47 36.15 1.75
65 66 1.068679 TGTCACCGTACGCGTGAATAA 60.069 47.619 28.87 19.45 36.15 1.40
66 67 1.984990 GTCACCGTACGCGTGAATAAA 59.015 47.619 28.87 13.16 36.15 1.40
67 68 2.027214 GTCACCGTACGCGTGAATAAAG 59.973 50.000 28.87 3.10 36.15 1.85
68 69 1.987770 CACCGTACGCGTGAATAAAGT 59.012 47.619 24.59 6.54 36.15 2.66
72 73 3.423571 CGTACGCGTGAATAAAGTCTCT 58.576 45.455 24.59 0.00 0.00 3.10
73 74 3.477802 CGTACGCGTGAATAAAGTCTCTC 59.522 47.826 24.59 0.00 0.00 3.20
74 75 2.877335 ACGCGTGAATAAAGTCTCTCC 58.123 47.619 12.93 0.00 0.00 3.71
75 76 2.230508 ACGCGTGAATAAAGTCTCTCCA 59.769 45.455 12.93 0.00 0.00 3.86
76 77 2.599082 CGCGTGAATAAAGTCTCTCCAC 59.401 50.000 0.00 0.00 0.00 4.02
77 78 2.930682 GCGTGAATAAAGTCTCTCCACC 59.069 50.000 0.00 0.00 0.00 4.61
78 79 3.368531 GCGTGAATAAAGTCTCTCCACCT 60.369 47.826 0.00 0.00 0.00 4.00
79 80 4.425520 CGTGAATAAAGTCTCTCCACCTC 58.574 47.826 0.00 0.00 0.00 3.85
80 81 4.082190 CGTGAATAAAGTCTCTCCACCTCA 60.082 45.833 0.00 0.00 0.00 3.86
101 102 0.174845 CCTCGTTCCGGTGATGCTTA 59.825 55.000 0.00 0.00 0.00 3.09
109 110 3.909430 TCCGGTGATGCTTATTCGTATC 58.091 45.455 0.00 0.00 0.00 2.24
112 113 2.412089 GGTGATGCTTATTCGTATCGCC 59.588 50.000 5.88 5.88 45.04 5.54
119 120 1.991121 TATTCGTATCGCCAGGAGGT 58.009 50.000 0.00 0.00 37.19 3.85
148 149 5.350504 AAGATGGTGTGTCCTAAGATCTG 57.649 43.478 0.00 0.00 37.07 2.90
149 150 3.708631 AGATGGTGTGTCCTAAGATCTGG 59.291 47.826 0.00 0.00 37.07 3.86
156 157 5.046950 GTGTGTCCTAAGATCTGGTTCTTCT 60.047 44.000 0.00 0.00 37.20 2.85
190 191 1.305201 TTTGCAGGTTTGTCTCGGTC 58.695 50.000 0.00 0.00 0.00 4.79
197 198 1.443194 TTTGTCTCGGTCGCGCTAC 60.443 57.895 5.56 4.17 0.00 3.58
233 238 0.109086 CGTGTCTGTCTTGATCCGCT 60.109 55.000 0.00 0.00 0.00 5.52
270 275 1.347320 GCGAAGGTTAACCAGACTCG 58.653 55.000 26.26 24.46 38.89 4.18
305 310 2.096218 GCGTGTGAGATTTGTGTTCTCC 60.096 50.000 0.00 0.00 39.10 3.71
317 322 3.068691 TTCTCCGGCTCCGTCTGG 61.069 66.667 7.59 0.00 37.81 3.86
359 364 3.681313 GCCCTCTCAACCATCTTCTTCTC 60.681 52.174 0.00 0.00 0.00 2.87
380 385 3.376859 TCCATAGCGGCAATTTGTTACAG 59.623 43.478 1.45 0.00 33.14 2.74
391 396 0.584396 TTGTTACAGAAACTGCGGCG 59.416 50.000 0.51 0.51 38.99 6.46
446 452 3.800506 TCGGCGCTACTTTTATAAGCTTC 59.199 43.478 7.64 0.00 34.60 3.86
450 456 6.552629 GGCGCTACTTTTATAAGCTTCTTTT 58.447 36.000 7.64 0.00 34.60 2.27
487 493 1.416401 GCTCCGATGAAATAGGGACCA 59.584 52.381 0.00 0.00 39.86 4.02
492 499 3.118038 CCGATGAAATAGGGACCAAAGGA 60.118 47.826 0.00 0.00 35.19 3.36
495 502 2.580783 TGAAATAGGGACCAAAGGAGGG 59.419 50.000 0.00 0.00 0.00 4.30
500 507 0.845102 GGGACCAAAGGAGGGAAGGA 60.845 60.000 0.00 0.00 0.00 3.36
533 540 4.602259 CGCCGCCGATGTATGGGT 62.602 66.667 0.00 0.00 36.29 4.51
534 541 2.972505 GCCGCCGATGTATGGGTG 60.973 66.667 0.09 0.09 36.13 4.61
536 543 2.280797 CGCCGATGTATGGGTGGG 60.281 66.667 0.00 0.00 33.22 4.61
537 544 2.113139 GCCGATGTATGGGTGGGG 59.887 66.667 0.00 0.00 0.00 4.96
538 545 2.836154 CCGATGTATGGGTGGGGG 59.164 66.667 0.00 0.00 0.00 5.40
553 560 1.003233 GGGGGAGAACACTGAGTGC 60.003 63.158 13.37 0.00 36.98 4.40
554 561 1.003233 GGGGAGAACACTGAGTGCC 60.003 63.158 13.37 5.44 36.98 5.01
555 562 1.003233 GGGAGAACACTGAGTGCCC 60.003 63.158 13.37 11.28 36.98 5.36
556 563 1.484444 GGGAGAACACTGAGTGCCCT 61.484 60.000 13.37 9.74 36.98 5.19
557 564 1.267121 GGAGAACACTGAGTGCCCTA 58.733 55.000 13.37 0.00 36.98 3.53
558 565 1.623811 GGAGAACACTGAGTGCCCTAA 59.376 52.381 13.37 0.00 36.98 2.69
559 566 2.038557 GGAGAACACTGAGTGCCCTAAA 59.961 50.000 13.37 0.00 36.98 1.85
560 567 3.330267 GAGAACACTGAGTGCCCTAAAG 58.670 50.000 13.37 0.00 36.98 1.85
561 568 2.972713 AGAACACTGAGTGCCCTAAAGA 59.027 45.455 13.37 0.00 36.98 2.52
562 569 3.391296 AGAACACTGAGTGCCCTAAAGAA 59.609 43.478 13.37 0.00 36.98 2.52
563 570 3.857157 ACACTGAGTGCCCTAAAGAAA 57.143 42.857 13.37 0.00 36.98 2.52
564 571 4.373156 ACACTGAGTGCCCTAAAGAAAT 57.627 40.909 13.37 0.00 36.98 2.17
565 572 4.729868 ACACTGAGTGCCCTAAAGAAATT 58.270 39.130 13.37 0.00 36.98 1.82
566 573 4.520492 ACACTGAGTGCCCTAAAGAAATTG 59.480 41.667 13.37 0.00 36.98 2.32
567 574 4.082125 ACTGAGTGCCCTAAAGAAATTGG 58.918 43.478 0.00 0.00 0.00 3.16
568 575 4.202567 ACTGAGTGCCCTAAAGAAATTGGA 60.203 41.667 0.00 0.00 0.00 3.53
569 576 4.934356 TGAGTGCCCTAAAGAAATTGGAT 58.066 39.130 0.00 0.00 0.00 3.41
570 577 4.706476 TGAGTGCCCTAAAGAAATTGGATG 59.294 41.667 0.00 0.00 0.00 3.51
571 578 4.677182 AGTGCCCTAAAGAAATTGGATGT 58.323 39.130 0.00 0.00 0.00 3.06
572 579 5.826643 AGTGCCCTAAAGAAATTGGATGTA 58.173 37.500 0.00 0.00 0.00 2.29
573 580 6.435164 AGTGCCCTAAAGAAATTGGATGTAT 58.565 36.000 0.00 0.00 0.00 2.29
574 581 6.897413 AGTGCCCTAAAGAAATTGGATGTATT 59.103 34.615 0.00 0.00 0.00 1.89
575 582 7.400052 AGTGCCCTAAAGAAATTGGATGTATTT 59.600 33.333 0.00 0.00 0.00 1.40
576 583 8.040727 GTGCCCTAAAGAAATTGGATGTATTTT 58.959 33.333 0.00 0.00 0.00 1.82
577 584 8.601546 TGCCCTAAAGAAATTGGATGTATTTTT 58.398 29.630 0.00 0.00 0.00 1.94
615 622 8.132362 GTGTCTTTGTACACCATAATGTCAAAA 58.868 33.333 0.00 0.00 43.23 2.44
652 659 2.168496 TCGGACTGAGGGAGTACTTTG 58.832 52.381 0.00 0.00 32.49 2.77
657 671 5.008811 CGGACTGAGGGAGTACTTTGTATAG 59.991 48.000 0.00 0.00 32.49 1.31
673 687 8.837389 ACTTTGTATAGTGTCTTTGGACTTTTC 58.163 33.333 0.00 0.00 42.54 2.29
854 868 5.707298 CAGATTGATATAACCACACCCCATC 59.293 44.000 0.00 0.00 0.00 3.51
855 869 5.372363 AGATTGATATAACCACACCCCATCA 59.628 40.000 0.00 0.00 0.00 3.07
856 870 4.431416 TGATATAACCACACCCCATCAC 57.569 45.455 0.00 0.00 0.00 3.06
857 871 3.137544 TGATATAACCACACCCCATCACC 59.862 47.826 0.00 0.00 0.00 4.02
905 923 2.884827 CTGACACAGCAAGATCATCGA 58.115 47.619 0.00 0.00 0.00 3.59
906 924 2.602211 CTGACACAGCAAGATCATCGAC 59.398 50.000 0.00 0.00 0.00 4.20
907 925 1.929836 GACACAGCAAGATCATCGACC 59.070 52.381 0.00 0.00 0.00 4.79
908 926 0.926155 CACAGCAAGATCATCGACCG 59.074 55.000 0.00 0.00 0.00 4.79
909 927 0.817654 ACAGCAAGATCATCGACCGA 59.182 50.000 0.00 0.00 0.00 4.69
910 928 1.202348 ACAGCAAGATCATCGACCGAG 60.202 52.381 0.00 0.00 0.00 4.63
911 929 0.249238 AGCAAGATCATCGACCGAGC 60.249 55.000 0.00 0.00 0.00 5.03
912 930 0.528466 GCAAGATCATCGACCGAGCA 60.528 55.000 4.91 0.00 0.00 4.26
913 931 1.485397 CAAGATCATCGACCGAGCAG 58.515 55.000 4.91 0.00 0.00 4.24
914 932 1.107114 AAGATCATCGACCGAGCAGT 58.893 50.000 4.91 0.00 0.00 4.40
920 945 0.678366 ATCGACCGAGCAGTGAGTCT 60.678 55.000 0.00 0.00 0.00 3.24
1738 1784 9.823647 TCAAGAAGATTGAGGTAATGATTACTC 57.176 33.333 14.34 10.38 36.39 2.59
1739 1785 9.829507 CAAGAAGATTGAGGTAATGATTACTCT 57.170 33.333 14.34 9.92 36.39 3.24
1770 1816 3.297134 TTCTTCACCTCCTTTTGCACT 57.703 42.857 0.00 0.00 0.00 4.40
1785 1831 6.927381 CCTTTTGCACTTCTTTTCTGATGATT 59.073 34.615 0.00 0.00 0.00 2.57
1825 1877 6.573664 TCTGCTTGCTTTGAGCTTAATTTA 57.426 33.333 1.29 0.00 42.97 1.40
1852 1913 3.159472 AGCATCATCTTTCCTTGCAACA 58.841 40.909 0.00 0.00 35.79 3.33
1853 1914 3.575256 AGCATCATCTTTCCTTGCAACAA 59.425 39.130 0.00 0.00 35.79 2.83
1854 1915 4.039488 AGCATCATCTTTCCTTGCAACAAA 59.961 37.500 0.00 0.00 35.79 2.83
1855 1916 4.387862 GCATCATCTTTCCTTGCAACAAAG 59.612 41.667 15.67 15.67 33.58 2.77
1856 1917 5.775686 CATCATCTTTCCTTGCAACAAAGA 58.224 37.500 22.40 22.40 39.77 2.52
1857 1918 5.850557 TCATCTTTCCTTGCAACAAAGAA 57.149 34.783 23.34 11.91 39.11 2.52
1864 1925 7.659390 TCTTTCCTTGCAACAAAGAAAGAAAAA 59.341 29.630 22.52 8.24 34.04 1.94
1888 1952 2.889512 TCTCCAAGCTTGACAGTCCTA 58.110 47.619 28.05 4.47 0.00 2.94
1900 1964 6.036953 GCTTGACAGTCCTATCAATTCAAGAG 59.963 42.308 11.60 0.00 40.51 2.85
1935 1999 7.910162 AGTAAAGCATGACAAATTAATACAGCG 59.090 33.333 0.00 0.00 0.00 5.18
1959 2023 7.621219 GCGACTAAACTGCCCAAAAATATTTTG 60.621 37.037 14.04 8.27 0.00 2.44
1962 2026 8.428852 ACTAAACTGCCCAAAAATATTTTGTCT 58.571 29.630 14.04 0.00 0.00 3.41
1969 2033 6.566376 GCCCAAAAATATTTTGTCTTGCACAG 60.566 38.462 14.04 0.71 35.97 3.66
1978 2043 4.990543 TTGTCTTGCACAGATTAGAACG 57.009 40.909 0.00 0.00 35.97 3.95
1984 2049 1.659098 GCACAGATTAGAACGGTTCCG 59.341 52.381 16.84 9.81 0.00 4.30
1986 2051 3.782046 CACAGATTAGAACGGTTCCGAT 58.218 45.455 18.28 11.09 0.00 4.18
1991 2056 4.885907 AGATTAGAACGGTTCCGATACTGA 59.114 41.667 18.28 10.13 0.00 3.41
1992 2057 5.359009 AGATTAGAACGGTTCCGATACTGAA 59.641 40.000 18.28 4.76 0.00 3.02
1997 2066 5.535406 AGAACGGTTCCGATACTGAATAGAT 59.465 40.000 18.28 0.00 0.00 1.98
1998 2067 6.713903 AGAACGGTTCCGATACTGAATAGATA 59.286 38.462 18.28 0.00 0.00 1.98
2000 2069 6.675987 ACGGTTCCGATACTGAATAGATAAC 58.324 40.000 18.28 0.00 0.00 1.89
2001 2070 6.489361 ACGGTTCCGATACTGAATAGATAACT 59.511 38.462 18.28 0.00 0.00 2.24
2010 2079 9.429359 GATACTGAATAGATAACTGATGGTTGG 57.571 37.037 0.00 0.00 38.75 3.77
2013 2082 6.356556 TGAATAGATAACTGATGGTTGGTGG 58.643 40.000 0.00 0.00 38.75 4.61
2015 2084 4.222124 AGATAACTGATGGTTGGTGGAC 57.778 45.455 0.00 0.00 38.75 4.02
2036 2105 7.012704 GTGGACTCAGCACATATAATTTGTGAT 59.987 37.037 11.98 3.58 45.83 3.06
2140 2211 8.064336 TCCTTTTGAGTAGAATAGTACTCCAC 57.936 38.462 0.00 0.00 45.81 4.02
2160 2231 8.993424 ACTCCACTATTGGTTATCTATTCTTGT 58.007 33.333 0.00 0.00 44.35 3.16
2251 2324 2.493675 GTCTCAATTGCCCCTTTCCTTC 59.506 50.000 0.00 0.00 0.00 3.46
2350 2425 7.805163 TGTTTACCTGTGAGATTATCATGGAT 58.195 34.615 9.32 0.00 40.92 3.41
2378 2453 2.222213 CACGTTGGTTTCACAGCGATAA 59.778 45.455 9.28 0.00 46.02 1.75
2382 2457 2.695359 TGGTTTCACAGCGATAAGACC 58.305 47.619 0.00 0.00 0.00 3.85
2384 2459 2.673368 GGTTTCACAGCGATAAGACCAG 59.327 50.000 0.00 0.00 0.00 4.00
2406 2487 0.391597 GAGTGGTGGTCTTTGTCCGA 59.608 55.000 0.00 0.00 0.00 4.55
2411 2492 1.067495 GGTGGTCTTTGTCCGAGAGAG 60.067 57.143 0.00 0.00 0.00 3.20
2417 2498 0.318441 TTTGTCCGAGAGAGCCACTG 59.682 55.000 0.00 0.00 0.00 3.66
2441 2522 5.350091 GGCTATCAGTTCAGTTTCAGAGTTC 59.650 44.000 0.00 0.00 0.00 3.01
2459 2540 5.760743 AGAGTTCTCCTTTAGCTTTTCACAC 59.239 40.000 0.00 0.00 0.00 3.82
2460 2541 5.437060 AGTTCTCCTTTAGCTTTTCACACA 58.563 37.500 0.00 0.00 0.00 3.72
2461 2542 5.297029 AGTTCTCCTTTAGCTTTTCACACAC 59.703 40.000 0.00 0.00 0.00 3.82
2462 2543 4.776349 TCTCCTTTAGCTTTTCACACACA 58.224 39.130 0.00 0.00 0.00 3.72
2463 2544 5.376625 TCTCCTTTAGCTTTTCACACACAT 58.623 37.500 0.00 0.00 0.00 3.21
2464 2545 6.530120 TCTCCTTTAGCTTTTCACACACATA 58.470 36.000 0.00 0.00 0.00 2.29
2465 2546 6.426937 TCTCCTTTAGCTTTTCACACACATAC 59.573 38.462 0.00 0.00 0.00 2.39
2466 2547 5.472137 TCCTTTAGCTTTTCACACACATACC 59.528 40.000 0.00 0.00 0.00 2.73
2467 2548 5.335661 CCTTTAGCTTTTCACACACATACCC 60.336 44.000 0.00 0.00 0.00 3.69
2468 2549 3.508845 AGCTTTTCACACACATACCCT 57.491 42.857 0.00 0.00 0.00 4.34
2469 2550 3.832527 AGCTTTTCACACACATACCCTT 58.167 40.909 0.00 0.00 0.00 3.95
2470 2551 4.215109 AGCTTTTCACACACATACCCTTT 58.785 39.130 0.00 0.00 0.00 3.11
2471 2552 4.278419 AGCTTTTCACACACATACCCTTTC 59.722 41.667 0.00 0.00 0.00 2.62
2472 2553 4.558697 GCTTTTCACACACATACCCTTTCC 60.559 45.833 0.00 0.00 0.00 3.13
2473 2554 4.447138 TTTCACACACATACCCTTTCCT 57.553 40.909 0.00 0.00 0.00 3.36
2474 2555 3.695830 TCACACACATACCCTTTCCTC 57.304 47.619 0.00 0.00 0.00 3.71
2475 2556 2.304761 TCACACACATACCCTTTCCTCC 59.695 50.000 0.00 0.00 0.00 4.30
2476 2557 2.039746 CACACACATACCCTTTCCTCCA 59.960 50.000 0.00 0.00 0.00 3.86
2477 2558 2.919602 ACACACATACCCTTTCCTCCAT 59.080 45.455 0.00 0.00 0.00 3.41
2478 2559 3.282021 CACACATACCCTTTCCTCCATG 58.718 50.000 0.00 0.00 0.00 3.66
2479 2560 2.301346 CACATACCCTTTCCTCCATGC 58.699 52.381 0.00 0.00 0.00 4.06
2480 2561 2.092212 CACATACCCTTTCCTCCATGCT 60.092 50.000 0.00 0.00 0.00 3.79
2481 2562 2.092212 ACATACCCTTTCCTCCATGCTG 60.092 50.000 0.00 0.00 0.00 4.41
2482 2563 0.255890 TACCCTTTCCTCCATGCTGC 59.744 55.000 0.00 0.00 0.00 5.25
2509 2590 5.237815 TCATGCTTAGTTACTGTCTGGTTG 58.762 41.667 0.00 0.00 0.00 3.77
2514 2595 3.470645 AGTTACTGTCTGGTTGGTGTC 57.529 47.619 0.00 0.00 0.00 3.67
2516 2597 3.454812 AGTTACTGTCTGGTTGGTGTCTT 59.545 43.478 0.00 0.00 0.00 3.01
2517 2598 4.080526 AGTTACTGTCTGGTTGGTGTCTTT 60.081 41.667 0.00 0.00 0.00 2.52
2522 2603 5.042463 TGTCTGGTTGGTGTCTTTTATCA 57.958 39.130 0.00 0.00 0.00 2.15
2523 2604 5.441500 TGTCTGGTTGGTGTCTTTTATCAA 58.558 37.500 0.00 0.00 0.00 2.57
2524 2605 5.530915 TGTCTGGTTGGTGTCTTTTATCAAG 59.469 40.000 0.00 0.00 0.00 3.02
2526 2607 6.262273 GTCTGGTTGGTGTCTTTTATCAAGAA 59.738 38.462 0.00 0.00 0.00 2.52
2528 2609 5.009610 TGGTTGGTGTCTTTTATCAAGAAGC 59.990 40.000 0.00 0.00 0.00 3.86
2529 2610 5.009610 GGTTGGTGTCTTTTATCAAGAAGCA 59.990 40.000 0.00 0.00 0.00 3.91
2532 2613 5.239306 TGGTGTCTTTTATCAAGAAGCACAG 59.761 40.000 7.33 0.00 34.54 3.66
2533 2614 5.239525 GGTGTCTTTTATCAAGAAGCACAGT 59.760 40.000 7.33 0.00 34.54 3.55
2534 2615 6.426937 GGTGTCTTTTATCAAGAAGCACAGTA 59.573 38.462 7.33 0.00 34.54 2.74
2536 2617 6.989759 TGTCTTTTATCAAGAAGCACAGTACA 59.010 34.615 0.00 0.00 0.00 2.90
2538 2619 7.385205 GTCTTTTATCAAGAAGCACAGTACAGA 59.615 37.037 0.00 0.00 0.00 3.41
2540 2621 4.881019 ATCAAGAAGCACAGTACAGACT 57.119 40.909 0.00 0.00 35.80 3.24
2542 2623 3.891977 TCAAGAAGCACAGTACAGACTCT 59.108 43.478 0.00 0.00 31.73 3.24
2543 2624 3.932545 AGAAGCACAGTACAGACTCTG 57.067 47.619 4.36 4.36 37.52 3.35
2545 2626 4.399219 AGAAGCACAGTACAGACTCTGTA 58.601 43.478 13.96 13.96 43.46 2.74
2546 2627 5.013547 AGAAGCACAGTACAGACTCTGTAT 58.986 41.667 19.64 8.26 46.56 2.29
2547 2628 4.974368 AGCACAGTACAGACTCTGTATC 57.026 45.455 19.64 13.73 46.56 2.24
2809 2890 4.475135 GCCGGCCTCCCTCAACTC 62.475 72.222 18.11 0.00 0.00 3.01
2810 2891 2.685380 CCGGCCTCCCTCAACTCT 60.685 66.667 0.00 0.00 0.00 3.24
2811 2892 2.581354 CGGCCTCCCTCAACTCTG 59.419 66.667 0.00 0.00 0.00 3.35
2819 2904 2.170187 CTCCCTCAACTCTGGAATCCTG 59.830 54.545 0.00 0.00 0.00 3.86
2821 2906 2.093235 CCCTCAACTCTGGAATCCTGTC 60.093 54.545 0.00 0.00 0.00 3.51
2832 2917 2.029020 GGAATCCTGTCTGTTTTTGCCC 60.029 50.000 0.00 0.00 0.00 5.36
2956 3049 0.319297 GTTGTATACTAGCCGCCGGG 60.319 60.000 4.77 0.00 0.00 5.73
3022 3116 0.453793 TGCACGAAAAACTGGTGTGG 59.546 50.000 0.00 0.00 34.25 4.17
3083 3177 6.111768 ACATTCAGAGCAATTGTTCGTATC 57.888 37.500 15.51 1.75 0.00 2.24
3218 3329 1.553704 GGTGGAGACGATTGTTACCCT 59.446 52.381 0.00 0.00 0.00 4.34
3235 3352 0.962356 CCTTGCACACCCAGGATCAC 60.962 60.000 0.00 0.00 0.00 3.06
3244 3361 1.559682 ACCCAGGATCACGCAATAAGT 59.440 47.619 0.00 0.00 0.00 2.24
3252 3369 4.638865 GGATCACGCAATAAGTTAACCCTT 59.361 41.667 0.88 0.00 0.00 3.95
3253 3370 5.448632 GGATCACGCAATAAGTTAACCCTTG 60.449 44.000 0.88 5.16 0.00 3.61
3254 3371 4.391155 TCACGCAATAAGTTAACCCTTGT 58.609 39.130 0.88 0.00 0.00 3.16
3255 3372 4.214545 TCACGCAATAAGTTAACCCTTGTG 59.785 41.667 17.51 17.51 34.41 3.33
3256 3373 4.023536 CACGCAATAAGTTAACCCTTGTGT 60.024 41.667 18.40 18.40 40.17 3.72
3257 3374 4.023536 ACGCAATAAGTTAACCCTTGTGTG 60.024 41.667 21.22 14.18 38.65 3.82
3262 3379 2.021457 AGTTAACCCTTGTGTGTGTGC 58.979 47.619 0.88 0.00 0.00 4.57
3265 3382 1.653094 AACCCTTGTGTGTGTGCGTG 61.653 55.000 0.00 0.00 0.00 5.34
3267 3384 2.351097 CTTGTGTGTGTGCGTGCG 60.351 61.111 0.00 0.00 0.00 5.34
3268 3385 3.094661 CTTGTGTGTGTGCGTGCGT 62.095 57.895 0.00 0.00 0.00 5.24
3269 3386 2.576287 CTTGTGTGTGTGCGTGCGTT 62.576 55.000 0.00 0.00 0.00 4.84
3270 3387 2.099446 GTGTGTGTGCGTGCGTTT 59.901 55.556 0.00 0.00 0.00 3.60
3271 3388 1.932564 GTGTGTGTGCGTGCGTTTC 60.933 57.895 0.00 0.00 0.00 2.78
3272 3389 2.717190 GTGTGTGCGTGCGTTTCG 60.717 61.111 0.00 0.00 0.00 3.46
3274 3391 2.423039 GTGTGCGTGCGTTTCGAC 60.423 61.111 0.00 0.00 0.00 4.20
3275 3392 3.978764 TGTGCGTGCGTTTCGACG 61.979 61.111 0.00 0.00 35.11 5.12
3276 3393 3.684315 GTGCGTGCGTTTCGACGA 61.684 61.111 2.79 0.00 34.41 4.20
3277 3394 2.955391 TGCGTGCGTTTCGACGAA 60.955 55.556 6.10 6.10 34.41 3.85
3362 3492 1.854126 CTTGGTTTTGCAGCGACTTTG 59.146 47.619 0.00 0.00 0.00 2.77
3380 3513 5.423886 ACTTTGCTATTAGTCTTCCAGCTC 58.576 41.667 0.00 0.00 33.38 4.09
3389 3522 0.115152 TCTTCCAGCTCCAGAGTCCA 59.885 55.000 0.00 0.00 0.00 4.02
3390 3523 0.248843 CTTCCAGCTCCAGAGTCCAC 59.751 60.000 0.00 0.00 0.00 4.02
3508 3641 2.017559 GATAACTCGAGCCGGGCACT 62.018 60.000 23.09 0.00 0.00 4.40
3509 3642 2.298158 ATAACTCGAGCCGGGCACTG 62.298 60.000 23.09 12.62 0.00 3.66
3584 3717 0.109319 GTCACCGCATTCGCCATTTT 60.109 50.000 0.00 0.00 33.11 1.82
3602 3740 4.561735 TTTTCATTTCCCTCGTGACAAC 57.438 40.909 0.00 0.00 0.00 3.32
3754 3892 1.878522 GGCGTGGCTGTAGACATCG 60.879 63.158 0.00 0.00 34.33 3.84
3756 3894 1.878522 CGTGGCTGTAGACATCGGC 60.879 63.158 0.00 0.00 34.33 5.54
3757 3895 1.218047 GTGGCTGTAGACATCGGCA 59.782 57.895 0.00 0.00 38.75 5.69
3764 3902 0.319900 GTAGACATCGGCATCGGCAT 60.320 55.000 0.00 0.00 43.71 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.280628 GGAGGCTTAACCAATGTCTCG 58.719 52.381 0.00 0.00 43.14 4.04
2 3 2.280628 CGGAGGCTTAACCAATGTCTC 58.719 52.381 0.00 0.00 43.14 3.36
5 6 2.556622 CAAACGGAGGCTTAACCAATGT 59.443 45.455 0.00 0.00 43.14 2.71
6 7 2.817258 TCAAACGGAGGCTTAACCAATG 59.183 45.455 0.00 0.00 43.14 2.82
7 8 2.817844 GTCAAACGGAGGCTTAACCAAT 59.182 45.455 0.00 0.00 43.14 3.16
9 10 1.418637 AGTCAAACGGAGGCTTAACCA 59.581 47.619 0.00 0.00 43.14 3.67
10 11 2.180432 AGTCAAACGGAGGCTTAACC 57.820 50.000 0.00 0.00 39.61 2.85
15 16 1.172812 GCCAAAGTCAAACGGAGGCT 61.173 55.000 0.00 0.00 37.67 4.58
24 25 2.301870 ACCATAGTCTCGCCAAAGTCAA 59.698 45.455 0.00 0.00 0.00 3.18
30 31 1.067142 GTGACACCATAGTCTCGCCAA 60.067 52.381 0.00 0.00 39.27 4.52
53 54 3.441222 TGGAGAGACTTTATTCACGCGTA 59.559 43.478 13.44 0.00 0.00 4.42
55 56 2.599082 GTGGAGAGACTTTATTCACGCG 59.401 50.000 3.53 3.53 0.00 6.01
61 62 3.519913 GGGTGAGGTGGAGAGACTTTATT 59.480 47.826 0.00 0.00 0.00 1.40
63 64 2.111972 AGGGTGAGGTGGAGAGACTTTA 59.888 50.000 0.00 0.00 0.00 1.85
64 65 1.132689 AGGGTGAGGTGGAGAGACTTT 60.133 52.381 0.00 0.00 0.00 2.66
65 66 0.489567 AGGGTGAGGTGGAGAGACTT 59.510 55.000 0.00 0.00 0.00 3.01
66 67 0.040499 GAGGGTGAGGTGGAGAGACT 59.960 60.000 0.00 0.00 0.00 3.24
67 68 1.316706 CGAGGGTGAGGTGGAGAGAC 61.317 65.000 0.00 0.00 0.00 3.36
68 69 1.000771 CGAGGGTGAGGTGGAGAGA 60.001 63.158 0.00 0.00 0.00 3.10
72 73 1.911766 GGAACGAGGGTGAGGTGGA 60.912 63.158 0.00 0.00 0.00 4.02
73 74 2.663196 GGAACGAGGGTGAGGTGG 59.337 66.667 0.00 0.00 0.00 4.61
101 102 0.389391 CACCTCCTGGCGATACGAAT 59.611 55.000 0.00 0.00 36.63 3.34
109 110 3.177194 TTCCACACACCTCCTGGCG 62.177 63.158 0.00 0.00 36.63 5.69
112 113 1.339438 CCATCTTCCACACACCTCCTG 60.339 57.143 0.00 0.00 0.00 3.86
119 120 1.202758 GGACACACCATCTTCCACACA 60.203 52.381 0.00 0.00 38.79 3.72
148 149 2.640316 AACACCAGACCAGAAGAACC 57.360 50.000 0.00 0.00 0.00 3.62
149 150 3.809905 AGAAACACCAGACCAGAAGAAC 58.190 45.455 0.00 0.00 0.00 3.01
156 157 2.426738 CTGCAAAAGAAACACCAGACCA 59.573 45.455 0.00 0.00 0.00 4.02
203 204 2.164624 AGACAGACACGTTATCTGCTCC 59.835 50.000 21.28 13.19 46.33 4.70
209 210 3.791887 CGGATCAAGACAGACACGTTATC 59.208 47.826 0.00 0.00 0.00 1.75
233 238 0.960364 GCCGATCAAAACTGGAGCCA 60.960 55.000 0.00 0.00 0.00 4.75
285 290 2.155732 CGGAGAACACAAATCTCACACG 59.844 50.000 5.96 0.00 44.13 4.49
317 322 0.034863 TTGTAGACCCCAATTCCGGC 60.035 55.000 0.00 0.00 0.00 6.13
359 364 3.376859 TCTGTAACAAATTGCCGCTATGG 59.623 43.478 0.00 0.00 42.50 2.74
391 396 1.136057 GTTGATTTGAAGACGTCGGCC 60.136 52.381 10.46 0.00 0.00 6.13
446 452 6.183360 GGAGCAAACTTGTTTAAACCCAAAAG 60.183 38.462 15.59 13.68 0.00 2.27
450 456 3.181485 CGGAGCAAACTTGTTTAAACCCA 60.181 43.478 15.59 1.80 0.00 4.51
487 493 1.548809 GCAAAGCTCCTTCCCTCCTTT 60.549 52.381 0.00 0.00 0.00 3.11
516 523 4.602259 ACCCATACATCGGCGGCG 62.602 66.667 27.15 27.15 0.00 6.46
517 524 2.972505 CACCCATACATCGGCGGC 60.973 66.667 7.21 0.00 0.00 6.53
518 525 2.280797 CCACCCATACATCGGCGG 60.281 66.667 7.21 0.00 0.00 6.13
519 526 2.280797 CCCACCCATACATCGGCG 60.281 66.667 0.00 0.00 0.00 6.46
520 527 2.113139 CCCCACCCATACATCGGC 59.887 66.667 0.00 0.00 0.00 5.54
521 528 2.836154 CCCCCACCCATACATCGG 59.164 66.667 0.00 0.00 0.00 4.18
535 542 1.003233 GCACTCAGTGTTCTCCCCC 60.003 63.158 6.68 0.00 35.75 5.40
536 543 1.003233 GGCACTCAGTGTTCTCCCC 60.003 63.158 6.68 0.00 35.75 4.81
537 544 1.003233 GGGCACTCAGTGTTCTCCC 60.003 63.158 6.68 4.47 35.75 4.30
538 545 1.267121 TAGGGCACTCAGTGTTCTCC 58.733 55.000 6.68 3.78 35.75 3.71
539 546 3.006967 TCTTTAGGGCACTCAGTGTTCTC 59.993 47.826 6.68 0.00 35.75 2.87
540 547 2.972713 TCTTTAGGGCACTCAGTGTTCT 59.027 45.455 6.68 6.95 35.75 3.01
541 548 3.402628 TCTTTAGGGCACTCAGTGTTC 57.597 47.619 6.68 0.00 35.75 3.18
542 549 3.857157 TTCTTTAGGGCACTCAGTGTT 57.143 42.857 6.68 0.00 35.75 3.32
543 550 3.857157 TTTCTTTAGGGCACTCAGTGT 57.143 42.857 6.68 0.00 35.75 3.55
544 551 4.082571 CCAATTTCTTTAGGGCACTCAGTG 60.083 45.833 0.00 0.00 36.51 3.66
545 552 4.082125 CCAATTTCTTTAGGGCACTCAGT 58.918 43.478 0.00 0.00 0.00 3.41
546 553 4.335416 TCCAATTTCTTTAGGGCACTCAG 58.665 43.478 0.00 0.00 0.00 3.35
547 554 4.380843 TCCAATTTCTTTAGGGCACTCA 57.619 40.909 0.00 0.00 0.00 3.41
548 555 4.706962 ACATCCAATTTCTTTAGGGCACTC 59.293 41.667 0.00 0.00 0.00 3.51
549 556 4.677182 ACATCCAATTTCTTTAGGGCACT 58.323 39.130 0.00 0.00 0.00 4.40
550 557 6.715347 ATACATCCAATTTCTTTAGGGCAC 57.285 37.500 0.00 0.00 0.00 5.01
551 558 7.732222 AAATACATCCAATTTCTTTAGGGCA 57.268 32.000 0.00 0.00 0.00 5.36
575 582 4.081198 ACAAAGACACCCTTGCATGAAAAA 60.081 37.500 0.00 0.00 34.79 1.94
576 583 3.450457 ACAAAGACACCCTTGCATGAAAA 59.550 39.130 0.00 0.00 34.79 2.29
577 584 3.030291 ACAAAGACACCCTTGCATGAAA 58.970 40.909 0.00 0.00 34.79 2.69
578 585 2.665165 ACAAAGACACCCTTGCATGAA 58.335 42.857 0.00 0.00 34.79 2.57
579 586 2.363306 ACAAAGACACCCTTGCATGA 57.637 45.000 0.00 0.00 34.79 3.07
580 587 2.884012 TGTACAAAGACACCCTTGCATG 59.116 45.455 0.00 0.00 34.79 4.06
581 588 2.884639 GTGTACAAAGACACCCTTGCAT 59.115 45.455 0.00 0.00 43.30 3.96
582 589 2.294074 GTGTACAAAGACACCCTTGCA 58.706 47.619 0.00 0.00 43.30 4.08
615 622 8.786826 TCAGTCCGATAATGTAAGACATTTTT 57.213 30.769 9.92 0.00 45.80 1.94
619 626 5.011125 CCCTCAGTCCGATAATGTAAGACAT 59.989 44.000 0.00 0.00 41.31 3.06
620 627 4.341235 CCCTCAGTCCGATAATGTAAGACA 59.659 45.833 0.00 0.00 0.00 3.41
686 700 6.394025 TGTTCGTTTAAGCCTTGGTTTTAT 57.606 33.333 0.00 0.00 0.00 1.40
687 701 5.831702 TGTTCGTTTAAGCCTTGGTTTTA 57.168 34.783 0.00 0.00 0.00 1.52
689 703 4.929819 ATGTTCGTTTAAGCCTTGGTTT 57.070 36.364 0.00 0.00 0.00 3.27
690 704 4.555906 CGAATGTTCGTTTAAGCCTTGGTT 60.556 41.667 6.97 0.00 45.09 3.67
691 705 3.058501 CGAATGTTCGTTTAAGCCTTGGT 60.059 43.478 6.97 0.00 45.09 3.67
692 706 3.488489 CGAATGTTCGTTTAAGCCTTGG 58.512 45.455 6.97 0.00 45.09 3.61
806 820 4.530857 CGTCCATCTGTCCCGGGC 62.531 72.222 18.49 12.24 0.00 6.13
854 868 2.518349 GGTGTGTGTGGGTGGGTG 60.518 66.667 0.00 0.00 0.00 4.61
855 869 3.018193 TGGTGTGTGTGGGTGGGT 61.018 61.111 0.00 0.00 0.00 4.51
856 870 2.518349 GTGGTGTGTGTGGGTGGG 60.518 66.667 0.00 0.00 0.00 4.61
857 871 2.518349 GGTGGTGTGTGTGGGTGG 60.518 66.667 0.00 0.00 0.00 4.61
901 919 0.678366 AGACTCACTGCTCGGTCGAT 60.678 55.000 0.00 0.00 34.34 3.59
902 920 1.302591 AGACTCACTGCTCGGTCGA 60.303 57.895 0.00 0.00 34.34 4.20
903 921 1.154131 CAGACTCACTGCTCGGTCG 60.154 63.158 0.00 0.00 39.86 4.79
904 922 4.878774 CAGACTCACTGCTCGGTC 57.121 61.111 0.00 0.00 39.86 4.79
912 930 0.972883 GCCCTCTTGACAGACTCACT 59.027 55.000 0.00 0.00 0.00 3.41
913 931 0.389166 CGCCCTCTTGACAGACTCAC 60.389 60.000 0.00 0.00 0.00 3.51
914 932 0.539669 TCGCCCTCTTGACAGACTCA 60.540 55.000 0.00 0.00 0.00 3.41
920 945 4.069232 CGCCTCGCCCTCTTGACA 62.069 66.667 0.00 0.00 0.00 3.58
1060 1091 4.452733 GCCCTCCTCGTCGTTGGG 62.453 72.222 9.17 9.17 40.74 4.12
1754 1800 3.297134 AAGAAGTGCAAAAGGAGGTGA 57.703 42.857 0.00 0.00 0.00 4.02
1785 1831 7.340232 AGCAAGCAGAATTCCAGTGATATTTTA 59.660 33.333 0.65 0.00 0.00 1.52
1791 1843 3.083122 AGCAAGCAGAATTCCAGTGAT 57.917 42.857 0.65 0.00 0.00 3.06
1792 1844 2.574006 AGCAAGCAGAATTCCAGTGA 57.426 45.000 0.65 0.00 0.00 3.41
1794 1846 3.225104 TCAAAGCAAGCAGAATTCCAGT 58.775 40.909 0.65 0.00 0.00 4.00
1795 1847 3.834610 CTCAAAGCAAGCAGAATTCCAG 58.165 45.455 0.65 0.00 0.00 3.86
1802 1854 5.458041 AAATTAAGCTCAAAGCAAGCAGA 57.542 34.783 1.29 0.00 45.56 4.26
1805 1857 7.031975 AGATGTAAATTAAGCTCAAAGCAAGC 58.968 34.615 1.29 0.00 45.56 4.01
1825 1877 4.820716 GCAAGGAAAGATGATGCTAGATGT 59.179 41.667 0.00 0.00 34.29 3.06
1864 1925 3.823304 GGACTGTCAAGCTTGGAGATTTT 59.177 43.478 25.73 6.76 0.00 1.82
1867 1928 2.264455 AGGACTGTCAAGCTTGGAGAT 58.736 47.619 25.73 9.98 0.00 2.75
1879 1940 7.106439 TCTCTCTTGAATTGATAGGACTGTC 57.894 40.000 0.00 0.00 0.00 3.51
1888 1952 9.799106 TTTACTCCTTTTCTCTCTTGAATTGAT 57.201 29.630 0.00 0.00 0.00 2.57
1900 1964 6.560253 TTGTCATGCTTTACTCCTTTTCTC 57.440 37.500 0.00 0.00 0.00 2.87
1913 1977 6.094048 AGTCGCTGTATTAATTTGTCATGCTT 59.906 34.615 0.00 0.00 0.00 3.91
1935 1999 8.601845 ACAAAATATTTTTGGGCAGTTTAGTC 57.398 30.769 10.77 0.00 33.92 2.59
1959 2023 3.326747 ACCGTTCTAATCTGTGCAAGAC 58.673 45.455 0.00 0.00 37.88 3.01
1962 2026 3.071479 GGAACCGTTCTAATCTGTGCAA 58.929 45.455 11.03 0.00 0.00 4.08
1969 2033 5.179045 TCAGTATCGGAACCGTTCTAATC 57.821 43.478 12.93 0.00 40.74 1.75
1975 2040 5.786264 ATCTATTCAGTATCGGAACCGTT 57.214 39.130 12.93 7.53 40.74 4.44
1978 2043 7.883217 TCAGTTATCTATTCAGTATCGGAACC 58.117 38.462 0.00 0.00 0.00 3.62
1984 2049 9.429359 CCAACCATCAGTTATCTATTCAGTATC 57.571 37.037 0.00 0.00 36.18 2.24
1986 2051 8.204160 CACCAACCATCAGTTATCTATTCAGTA 58.796 37.037 0.00 0.00 36.18 2.74
1991 2056 6.158695 AGTCCACCAACCATCAGTTATCTATT 59.841 38.462 0.00 0.00 36.18 1.73
1992 2057 5.667626 AGTCCACCAACCATCAGTTATCTAT 59.332 40.000 0.00 0.00 36.18 1.98
1997 2066 2.976185 TGAGTCCACCAACCATCAGTTA 59.024 45.455 0.00 0.00 36.18 2.24
1998 2067 1.774254 TGAGTCCACCAACCATCAGTT 59.226 47.619 0.00 0.00 40.16 3.16
2000 2069 1.947678 GCTGAGTCCACCAACCATCAG 60.948 57.143 0.00 0.00 37.74 2.90
2001 2070 0.036732 GCTGAGTCCACCAACCATCA 59.963 55.000 0.00 0.00 0.00 3.07
2010 2079 6.316140 TCACAAATTATATGTGCTGAGTCCAC 59.684 38.462 4.21 0.00 46.05 4.02
2013 2082 8.066595 GTGATCACAAATTATATGTGCTGAGTC 58.933 37.037 21.07 0.00 46.05 3.36
2015 2084 8.068380 CAGTGATCACAAATTATATGTGCTGAG 58.932 37.037 27.02 0.00 46.05 3.35
2025 2094 8.133627 GCTTGCTAATCAGTGATCACAAATTAT 58.866 33.333 27.02 10.01 0.00 1.28
2026 2095 7.337689 AGCTTGCTAATCAGTGATCACAAATTA 59.662 33.333 27.02 23.83 0.00 1.40
2027 2096 6.152323 AGCTTGCTAATCAGTGATCACAAATT 59.848 34.615 27.02 23.98 0.00 1.82
2036 2105 3.423539 AACCAGCTTGCTAATCAGTGA 57.576 42.857 0.00 0.00 0.00 3.41
2074 2145 3.797312 AGGCCTAGAAACTTCCTCTCTT 58.203 45.455 1.29 0.00 0.00 2.85
2076 2147 3.069016 GCTAGGCCTAGAAACTTCCTCTC 59.931 52.174 38.74 15.57 35.21 3.20
2078 2149 2.766828 TGCTAGGCCTAGAAACTTCCTC 59.233 50.000 38.74 19.92 35.21 3.71
2204 2275 5.568825 GCCACTCAGATGTAACACCTCTAAA 60.569 44.000 0.00 0.00 0.00 1.85
2221 2292 1.527034 GCAATTGAGACAGCCACTCA 58.473 50.000 10.34 0.00 41.70 3.41
2251 2324 2.260154 TTCACATGCACGCACCCAG 61.260 57.895 0.00 0.00 0.00 4.45
2350 2425 2.994401 TGTGAAACCAACGTGCTAACGA 60.994 45.455 5.12 0.00 45.30 3.85
2363 2438 2.673368 CTGGTCTTATCGCTGTGAAACC 59.327 50.000 0.00 2.19 34.36 3.27
2364 2439 3.326747 ACTGGTCTTATCGCTGTGAAAC 58.673 45.455 0.00 0.00 37.35 2.78
2366 2441 4.014406 TCTACTGGTCTTATCGCTGTGAA 58.986 43.478 0.00 0.00 0.00 3.18
2382 2457 3.555168 GGACAAAGACCACCACTCTACTG 60.555 52.174 0.00 0.00 0.00 2.74
2384 2459 2.609737 CGGACAAAGACCACCACTCTAC 60.610 54.545 0.00 0.00 0.00 2.59
2417 2498 4.826556 ACTCTGAAACTGAACTGATAGCC 58.173 43.478 0.00 0.00 0.00 3.93
2420 2501 6.495181 AGGAGAACTCTGAAACTGAACTGATA 59.505 38.462 1.86 0.00 0.00 2.15
2423 2504 4.954875 AGGAGAACTCTGAAACTGAACTG 58.045 43.478 1.86 0.00 0.00 3.16
2424 2505 5.622346 AAGGAGAACTCTGAAACTGAACT 57.378 39.130 1.86 0.00 0.00 3.01
2425 2506 6.073494 GCTAAAGGAGAACTCTGAAACTGAAC 60.073 42.308 1.86 0.00 0.00 3.18
2427 2508 5.305644 AGCTAAAGGAGAACTCTGAAACTGA 59.694 40.000 1.86 0.00 0.00 3.41
2428 2509 5.546526 AGCTAAAGGAGAACTCTGAAACTG 58.453 41.667 1.86 0.00 0.00 3.16
2429 2510 5.816955 AGCTAAAGGAGAACTCTGAAACT 57.183 39.130 1.86 0.00 0.00 2.66
2430 2511 6.869315 AAAGCTAAAGGAGAACTCTGAAAC 57.131 37.500 1.86 0.00 0.00 2.78
2431 2512 7.012421 GTGAAAAGCTAAAGGAGAACTCTGAAA 59.988 37.037 1.86 0.00 0.00 2.69
2441 2522 5.695851 ATGTGTGTGAAAAGCTAAAGGAG 57.304 39.130 0.00 0.00 0.00 3.69
2459 2540 2.092212 AGCATGGAGGAAAGGGTATGTG 60.092 50.000 0.00 0.00 0.00 3.21
2460 2541 2.092212 CAGCATGGAGGAAAGGGTATGT 60.092 50.000 0.00 0.00 0.00 2.29
2461 2542 2.579873 CAGCATGGAGGAAAGGGTATG 58.420 52.381 0.00 0.00 0.00 2.39
2462 2543 1.133668 GCAGCATGGAGGAAAGGGTAT 60.134 52.381 0.00 0.00 35.86 2.73
2463 2544 0.255890 GCAGCATGGAGGAAAGGGTA 59.744 55.000 0.00 0.00 35.86 3.69
2464 2545 1.000396 GCAGCATGGAGGAAAGGGT 60.000 57.895 0.00 0.00 35.86 4.34
2465 2546 0.612732 TTGCAGCATGGAGGAAAGGG 60.613 55.000 0.00 0.00 38.09 3.95
2466 2547 1.259609 TTTGCAGCATGGAGGAAAGG 58.740 50.000 0.00 0.00 38.09 3.11
2467 2548 2.494471 TGATTTGCAGCATGGAGGAAAG 59.506 45.455 0.00 0.00 38.09 2.62
2468 2549 2.527497 TGATTTGCAGCATGGAGGAAA 58.473 42.857 0.00 0.00 38.09 3.13
2469 2550 2.219080 TGATTTGCAGCATGGAGGAA 57.781 45.000 0.00 0.00 38.09 3.36
2470 2551 2.028876 CATGATTTGCAGCATGGAGGA 58.971 47.619 14.79 0.00 38.09 3.71
2471 2552 2.509052 CATGATTTGCAGCATGGAGG 57.491 50.000 14.79 0.00 38.09 4.30
2482 2563 6.372659 ACCAGACAGTAACTAAGCATGATTTG 59.627 38.462 0.00 1.85 0.00 2.32
2494 2575 3.039011 AGACACCAACCAGACAGTAACT 58.961 45.455 0.00 0.00 0.00 2.24
2495 2576 3.470645 AGACACCAACCAGACAGTAAC 57.529 47.619 0.00 0.00 0.00 2.50
2498 2579 3.366052 AAAAGACACCAACCAGACAGT 57.634 42.857 0.00 0.00 0.00 3.55
2504 2585 5.009610 GCTTCTTGATAAAAGACACCAACCA 59.990 40.000 0.00 0.00 0.00 3.67
2505 2586 5.009610 TGCTTCTTGATAAAAGACACCAACC 59.990 40.000 0.00 0.00 0.00 3.77
2509 2590 5.239525 ACTGTGCTTCTTGATAAAAGACACC 59.760 40.000 6.45 0.00 32.98 4.16
2514 2595 7.386299 AGTCTGTACTGTGCTTCTTGATAAAAG 59.614 37.037 0.00 0.00 33.57 2.27
2516 2597 6.759272 AGTCTGTACTGTGCTTCTTGATAAA 58.241 36.000 0.00 0.00 33.57 1.40
2517 2598 6.209589 AGAGTCTGTACTGTGCTTCTTGATAA 59.790 38.462 0.00 0.00 35.56 1.75
2522 2603 4.250116 CAGAGTCTGTACTGTGCTTCTT 57.750 45.455 12.28 0.00 39.81 2.52
2523 2604 3.932545 CAGAGTCTGTACTGTGCTTCT 57.067 47.619 12.28 0.00 39.81 2.85
2536 2617 8.268605 TCACAGTTAGACATAGATACAGAGTCT 58.731 37.037 0.00 0.00 41.88 3.24
2538 2619 8.845227 CATCACAGTTAGACATAGATACAGAGT 58.155 37.037 0.00 0.00 0.00 3.24
2540 2621 7.998964 TCCATCACAGTTAGACATAGATACAGA 59.001 37.037 0.00 0.00 0.00 3.41
2542 2623 8.712228 ATCCATCACAGTTAGACATAGATACA 57.288 34.615 0.00 0.00 0.00 2.29
2543 2624 8.247562 GGATCCATCACAGTTAGACATAGATAC 58.752 40.741 6.95 0.00 0.00 2.24
2544 2625 7.397476 GGGATCCATCACAGTTAGACATAGATA 59.603 40.741 15.23 0.00 0.00 1.98
2545 2626 6.212388 GGGATCCATCACAGTTAGACATAGAT 59.788 42.308 15.23 0.00 0.00 1.98
2546 2627 5.540337 GGGATCCATCACAGTTAGACATAGA 59.460 44.000 15.23 0.00 0.00 1.98
2547 2628 5.305386 TGGGATCCATCACAGTTAGACATAG 59.695 44.000 15.23 0.00 34.77 2.23
2792 2873 4.475135 GAGTTGAGGGAGGCCGGC 62.475 72.222 21.18 21.18 0.00 6.13
2793 2874 2.685380 AGAGTTGAGGGAGGCCGG 60.685 66.667 0.00 0.00 0.00 6.13
2794 2875 2.581354 CAGAGTTGAGGGAGGCCG 59.419 66.667 0.00 0.00 0.00 6.13
2795 2876 1.201429 TTCCAGAGTTGAGGGAGGCC 61.201 60.000 0.00 0.00 31.19 5.19
2797 2878 1.488393 GGATTCCAGAGTTGAGGGAGG 59.512 57.143 0.00 0.00 31.19 4.30
2798 2879 2.170187 CAGGATTCCAGAGTTGAGGGAG 59.830 54.545 5.29 0.00 31.19 4.30
2799 2880 2.191400 CAGGATTCCAGAGTTGAGGGA 58.809 52.381 5.29 0.00 0.00 4.20
2800 2881 1.912043 ACAGGATTCCAGAGTTGAGGG 59.088 52.381 5.29 0.00 0.00 4.30
2809 2890 3.305608 GGCAAAAACAGACAGGATTCCAG 60.306 47.826 5.29 0.00 0.00 3.86
2810 2891 2.627699 GGCAAAAACAGACAGGATTCCA 59.372 45.455 5.29 0.00 0.00 3.53
2811 2892 2.029020 GGGCAAAAACAGACAGGATTCC 60.029 50.000 0.00 0.00 0.00 3.01
2819 2904 1.047801 ACCCATGGGCAAAAACAGAC 58.952 50.000 31.73 0.00 39.32 3.51
2821 2906 2.247358 ACTACCCATGGGCAAAAACAG 58.753 47.619 31.73 17.13 39.32 3.16
2832 2917 4.334481 CGCCCTTACTTTTTACTACCCATG 59.666 45.833 0.00 0.00 0.00 3.66
2956 3049 1.091771 CGTGTGATCAGTGATGGCCC 61.092 60.000 11.20 0.00 0.00 5.80
2960 3053 1.362768 CCACCGTGTGATCAGTGATG 58.637 55.000 11.20 0.00 35.23 3.07
3022 3116 5.004726 GCAAACACGCTATTCATTCCATTTC 59.995 40.000 0.00 0.00 0.00 2.17
3151 3254 2.756760 TCGTGATAGGCGTTAAAGGACT 59.243 45.455 0.00 0.00 0.00 3.85
3218 3329 1.302431 CGTGATCCTGGGTGTGCAA 60.302 57.895 0.00 0.00 0.00 4.08
3235 3352 4.023536 ACACACAAGGGTTAACTTATTGCG 60.024 41.667 5.42 5.28 0.00 4.85
3244 3361 1.018148 CGCACACACACAAGGGTTAA 58.982 50.000 0.00 0.00 0.00 2.01
3252 3369 2.570402 GAAACGCACGCACACACACA 62.570 55.000 0.00 0.00 0.00 3.72
3253 3370 1.932564 GAAACGCACGCACACACAC 60.933 57.895 0.00 0.00 0.00 3.82
3254 3371 2.401592 GAAACGCACGCACACACA 59.598 55.556 0.00 0.00 0.00 3.72
3255 3372 2.717190 CGAAACGCACGCACACAC 60.717 61.111 0.00 0.00 0.00 3.82
3256 3373 2.886124 TCGAAACGCACGCACACA 60.886 55.556 0.00 0.00 0.00 3.72
3257 3374 2.423039 GTCGAAACGCACGCACAC 60.423 61.111 0.00 0.00 0.00 3.82
3267 3384 1.788886 ACTAAGCCGTTTCGTCGAAAC 59.211 47.619 31.64 31.64 45.65 2.78
3268 3385 2.138596 ACTAAGCCGTTTCGTCGAAA 57.861 45.000 16.22 16.22 0.00 3.46
3269 3386 2.138596 AACTAAGCCGTTTCGTCGAA 57.861 45.000 2.90 2.90 0.00 3.71
3270 3387 2.138596 AAACTAAGCCGTTTCGTCGA 57.861 45.000 0.00 0.00 31.87 4.20
3271 3388 2.936050 AAAACTAAGCCGTTTCGTCG 57.064 45.000 0.00 0.00 36.16 5.12
3272 3389 4.199840 TGAAAAACTAAGCCGTTTCGTC 57.800 40.909 0.00 0.00 36.16 4.20
3274 3391 3.416352 CGTTGAAAAACTAAGCCGTTTCG 59.584 43.478 0.00 0.00 36.16 3.46
3275 3392 4.203563 CACGTTGAAAAACTAAGCCGTTTC 59.796 41.667 0.00 0.00 36.16 2.78
3276 3393 4.099824 CACGTTGAAAAACTAAGCCGTTT 58.900 39.130 0.00 0.00 38.66 3.60
3277 3394 3.687200 CACGTTGAAAAACTAAGCCGTT 58.313 40.909 0.00 0.00 0.00 4.44
3283 3400 2.223618 GGGCAGCACGTTGAAAAACTAA 60.224 45.455 0.00 0.00 0.00 2.24
3345 3473 0.249031 AGCAAAGTCGCTGCAAAACC 60.249 50.000 0.00 0.00 41.85 3.27
3349 3477 3.334691 ACTAATAGCAAAGTCGCTGCAA 58.665 40.909 0.00 0.00 43.68 4.08
3362 3492 3.639094 TCTGGAGCTGGAAGACTAATAGC 59.361 47.826 0.00 0.00 34.07 2.97
3389 3522 0.755327 AGAAAACGCAAGCCAAGGGT 60.755 50.000 0.00 0.00 45.62 4.34
3390 3523 0.389025 AAGAAAACGCAAGCCAAGGG 59.611 50.000 0.00 0.00 45.62 3.95
3508 3641 3.783478 CTCGACGGGCACACACACA 62.783 63.158 0.00 0.00 0.00 3.72
3509 3642 2.410638 TACTCGACGGGCACACACAC 62.411 60.000 0.00 0.00 0.00 3.82
3510 3643 2.194889 TACTCGACGGGCACACACA 61.195 57.895 0.00 0.00 0.00 3.72
3511 3644 1.731969 GTACTCGACGGGCACACAC 60.732 63.158 0.00 0.00 0.00 3.82
3602 3740 0.946221 GATGATTCCACTAGCCGGCG 60.946 60.000 23.20 10.77 0.00 6.46
3633 3771 7.201652 CGCCATTCAGACGATAGATAGATAGAA 60.202 40.741 0.00 0.00 41.38 2.10
3649 3787 1.019278 GGTCGCTTTCGCCATTCAGA 61.019 55.000 0.00 0.00 33.90 3.27
3701 3839 1.002087 AGACAAGGCCCGTCTTAGTTG 59.998 52.381 17.68 7.48 40.89 3.16
3703 3841 0.608640 CAGACAAGGCCCGTCTTAGT 59.391 55.000 20.19 0.29 41.80 2.24
3704 3842 0.108138 CCAGACAAGGCCCGTCTTAG 60.108 60.000 20.19 12.35 41.80 2.18
3705 3843 1.980052 CCAGACAAGGCCCGTCTTA 59.020 57.895 20.19 0.00 41.80 2.10


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

AutoCloner maintained by Alex Coulton.