Multiple sequence alignment - TraesCS3D01G432600

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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 TraesCS3D01G432600 chr3D 100.000 4597 0 0 1 4597 546252415 546247819 0.000000e+00 8490
1 TraesCS3D01G432600 chr3A 88.583 3521 184 103 632 4019 682979481 682976046 0.000000e+00 4074
2 TraesCS3D01G432600 chr3A 84.654 593 48 21 1 580 682980132 682979570 6.720000e-153 551
3 TraesCS3D01G432600 chr3B 91.835 2523 124 38 1968 4421 723033644 723031135 0.000000e+00 3443
4 TraesCS3D01G432600 chr3B 87.826 1380 77 35 579 1914 723035298 723033966 0.000000e+00 1533
5 TraesCS3D01G432600 chr3B 84.922 577 48 18 13 568 723035958 723035400 8.700000e-152 547
6 TraesCS3D01G432600 chr3B 93.007 143 9 1 4456 4597 723031140 723030998 1.680000e-49 207
7 TraesCS3D01G432600 chr5A 96.575 146 5 0 2777 2922 228311467 228311612 4.600000e-60 243


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 TraesCS3D01G432600 chr3D 546247819 546252415 4596 True 8490.0 8490 100.0000 1 4597 1 chr3D.!!$R1 4596
1 TraesCS3D01G432600 chr3A 682976046 682980132 4086 True 2312.5 4074 86.6185 1 4019 2 chr3A.!!$R1 4018
2 TraesCS3D01G432600 chr3B 723030998 723035958 4960 True 1432.5 3443 89.3975 13 4597 4 chr3B.!!$R1 4584

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
730 850 0.101939 TACACACGTAACACACCGCA 59.898 50.0 0.0 0.0 0.0 5.69 F
1190 1337 0.260230 ATCCGCTCCTCCTTCTCTCA 59.740 55.0 0.0 0.0 0.0 3.27 F
2038 2528 0.103208 CCACGCTCCATGACCTCTAC 59.897 60.0 0.0 0.0 0.0 2.59 F
2522 3014 0.329931 TCAACCGCCCCAATGTGTAT 59.670 50.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1987 0.108424 GTGGCAACTTGGTGTGCAAA 60.108 50.0 0.00 0.0 37.61 3.68 R
2360 2852 0.793861 GTTTGCACGCGTCTTGGATA 59.206 50.0 9.86 0.0 0.00 2.59 R
2852 3374 0.813821 GGCTGACAAAGAAGGATGCC 59.186 55.0 0.00 0.0 0.00 4.40 R
4486 5099 0.034337 TGGGAATATAAGTCGGGCGC 59.966 55.0 0.00 0.0 0.00 6.53 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
39 40 3.214328 CCTACTCAATTGGCCCACATAC 58.786 50.000 5.42 0.00 0.00 2.39
40 41 2.897271 ACTCAATTGGCCCACATACA 57.103 45.000 5.42 0.00 0.00 2.29
41 42 2.446435 ACTCAATTGGCCCACATACAC 58.554 47.619 5.42 0.00 0.00 2.90
42 43 2.224992 ACTCAATTGGCCCACATACACA 60.225 45.455 5.42 0.00 0.00 3.72
43 44 3.025978 CTCAATTGGCCCACATACACAT 58.974 45.455 5.42 0.00 0.00 3.21
45 46 2.759535 CAATTGGCCCACATACACATGA 59.240 45.455 0.00 0.00 35.96 3.07
46 47 2.824689 TTGGCCCACATACACATGAT 57.175 45.000 0.00 0.00 35.96 2.45
47 48 3.941704 TTGGCCCACATACACATGATA 57.058 42.857 0.00 0.00 35.96 2.15
48 49 3.207265 TGGCCCACATACACATGATAC 57.793 47.619 0.00 0.00 35.96 2.24
55 56 5.233225 CCACATACACATGATACTGCCTAG 58.767 45.833 0.00 0.00 35.96 3.02
77 78 3.141398 GGAGAAATCCATGCGCAAGATA 58.859 45.455 22.18 8.17 43.02 1.98
119 120 0.810031 GAGGCAGTGTTGTCGTGTGT 60.810 55.000 0.00 0.00 32.98 3.72
141 143 4.676924 GTGGCTGAAACAGAAAGAAATTCG 59.323 41.667 2.81 0.00 43.15 3.34
187 189 6.655425 AGATCTAAACTACTTTCCAACCAAGC 59.345 38.462 0.00 0.00 0.00 4.01
191 193 1.804748 CTACTTTCCAACCAAGCCGTC 59.195 52.381 0.00 0.00 0.00 4.79
239 241 2.867975 CCAACTCCAACTTAACGTCGTT 59.132 45.455 15.97 15.97 0.00 3.85
241 243 1.862827 ACTCCAACTTAACGTCGTTGC 59.137 47.619 20.62 0.00 39.24 4.17
283 288 1.399440 CAACTTCATCTCCCGCATGTG 59.601 52.381 0.00 0.00 0.00 3.21
317 323 4.213482 ACGACACTGTTCATTAGCCTTTTC 59.787 41.667 0.00 0.00 0.00 2.29
318 324 4.452455 CGACACTGTTCATTAGCCTTTTCT 59.548 41.667 0.00 0.00 0.00 2.52
319 325 5.049405 CGACACTGTTCATTAGCCTTTTCTT 60.049 40.000 0.00 0.00 0.00 2.52
320 326 6.513393 CGACACTGTTCATTAGCCTTTTCTTT 60.513 38.462 0.00 0.00 0.00 2.52
321 327 7.112452 ACACTGTTCATTAGCCTTTTCTTTT 57.888 32.000 0.00 0.00 0.00 2.27
322 328 7.555965 ACACTGTTCATTAGCCTTTTCTTTTT 58.444 30.769 0.00 0.00 0.00 1.94
323 329 7.706607 ACACTGTTCATTAGCCTTTTCTTTTTC 59.293 33.333 0.00 0.00 0.00 2.29
324 330 7.922811 CACTGTTCATTAGCCTTTTCTTTTTCT 59.077 33.333 0.00 0.00 0.00 2.52
325 331 8.478066 ACTGTTCATTAGCCTTTTCTTTTTCTT 58.522 29.630 0.00 0.00 0.00 2.52
353 359 9.974980 TTCTTTTTACAGACAAATTTACCATCC 57.025 29.630 0.00 0.00 0.00 3.51
354 360 8.581578 TCTTTTTACAGACAAATTTACCATCCC 58.418 33.333 0.00 0.00 0.00 3.85
371 377 6.152932 CCATCCCTGGTTTTATCTTGAATG 57.847 41.667 0.00 0.00 37.79 2.67
375 381 5.951747 TCCCTGGTTTTATCTTGAATGAAGG 59.048 40.000 0.00 0.00 31.85 3.46
454 471 0.315886 ACCACAACACATCGTCGCTA 59.684 50.000 0.00 0.00 0.00 4.26
459 476 3.122780 CACAACACATCGTCGCTATCAAA 59.877 43.478 0.00 0.00 0.00 2.69
485 509 1.752198 CGGCCAATTCGATCCCCTA 59.248 57.895 2.24 0.00 0.00 3.53
494 518 0.398098 TCGATCCCCTACCTCCAACC 60.398 60.000 0.00 0.00 0.00 3.77
495 519 0.689745 CGATCCCCTACCTCCAACCA 60.690 60.000 0.00 0.00 0.00 3.67
496 520 1.132500 GATCCCCTACCTCCAACCAG 58.868 60.000 0.00 0.00 0.00 4.00
497 521 0.988678 ATCCCCTACCTCCAACCAGC 60.989 60.000 0.00 0.00 0.00 4.85
501 525 0.620556 CCTACCTCCAACCAGCACAT 59.379 55.000 0.00 0.00 0.00 3.21
508 532 2.171237 CTCCAACCAGCACATCCTATCA 59.829 50.000 0.00 0.00 0.00 2.15
521 545 6.426328 GCACATCCTATCACCATTTTCTAGAG 59.574 42.308 0.00 0.00 0.00 2.43
568 594 2.478134 CGATTCGATTCCCTTCTCATGC 59.522 50.000 0.00 0.00 0.00 4.06
570 596 3.565764 TTCGATTCCCTTCTCATGCAT 57.434 42.857 0.00 0.00 0.00 3.96
571 597 2.842457 TCGATTCCCTTCTCATGCATG 58.158 47.619 21.07 21.07 0.00 4.06
574 600 3.250280 CGATTCCCTTCTCATGCATGAAG 59.750 47.826 28.39 22.72 39.32 3.02
576 602 4.305539 TTCCCTTCTCATGCATGAAGAA 57.694 40.909 28.39 26.99 41.38 2.52
577 603 4.305539 TCCCTTCTCATGCATGAAGAAA 57.694 40.909 28.39 20.44 41.38 2.52
607 724 5.997385 CACAAGTGGTGGTTCAATTACTAC 58.003 41.667 0.00 0.00 44.04 2.73
608 725 4.753107 ACAAGTGGTGGTTCAATTACTACG 59.247 41.667 0.00 0.00 32.01 3.51
612 731 3.259876 TGGTGGTTCAATTACTACGCTCT 59.740 43.478 0.00 0.00 31.00 4.09
613 732 4.251268 GGTGGTTCAATTACTACGCTCTT 58.749 43.478 0.00 0.00 31.00 2.85
621 740 5.348724 TCAATTACTACGCTCTTTGCTCAAG 59.651 40.000 0.00 0.00 40.11 3.02
626 745 0.109873 CGCTCTTTGCTCAAGCCAAG 60.110 55.000 9.03 9.03 42.94 3.61
627 746 0.243095 GCTCTTTGCTCAAGCCAAGG 59.757 55.000 13.90 7.58 42.17 3.61
628 747 1.901591 CTCTTTGCTCAAGCCAAGGA 58.098 50.000 13.90 7.18 42.17 3.36
629 748 1.811359 CTCTTTGCTCAAGCCAAGGAG 59.189 52.381 13.90 11.65 42.17 3.69
630 749 0.886563 CTTTGCTCAAGCCAAGGAGG 59.113 55.000 7.72 0.00 39.34 4.30
651 770 1.393603 GAGAGGCAAAGGGGCAATAC 58.606 55.000 0.00 0.00 46.44 1.89
662 781 4.458164 GCAATACGCCACTGCAAC 57.542 55.556 0.00 0.00 37.32 4.17
728 848 0.771756 CGTACACACGTAACACACCG 59.228 55.000 0.00 0.00 43.31 4.94
729 849 0.503961 GTACACACGTAACACACCGC 59.496 55.000 0.00 0.00 0.00 5.68
730 850 0.101939 TACACACGTAACACACCGCA 59.898 50.000 0.00 0.00 0.00 5.69
731 851 1.149361 ACACACGTAACACACCGCAG 61.149 55.000 0.00 0.00 0.00 5.18
732 852 2.241880 ACACGTAACACACCGCAGC 61.242 57.895 0.00 0.00 0.00 5.25
733 853 2.107343 ACGTAACACACCGCAGCA 59.893 55.556 0.00 0.00 0.00 4.41
734 854 2.241880 ACGTAACACACCGCAGCAC 61.242 57.895 0.00 0.00 0.00 4.40
735 855 1.954146 CGTAACACACCGCAGCACT 60.954 57.895 0.00 0.00 0.00 4.40
759 879 3.710722 CTGCTCCGGCCCTTCACT 61.711 66.667 0.00 0.00 37.74 3.41
810 930 2.740447 CCACAAGGGTCTAAGCGTAAAC 59.260 50.000 0.00 0.00 0.00 2.01
811 931 3.556423 CCACAAGGGTCTAAGCGTAAACT 60.556 47.826 0.00 0.00 0.00 2.66
829 949 1.745087 ACTGGCATTAGAAATGGTGCG 59.255 47.619 2.11 0.00 38.43 5.34
873 993 1.228124 CAACGGCAGGGACAAGGAA 60.228 57.895 0.00 0.00 0.00 3.36
875 995 2.045926 CGGCAGGGACAAGGAAGG 60.046 66.667 0.00 0.00 0.00 3.46
892 1012 3.230976 GAAGGGAAGGAGAGAGAGATCC 58.769 54.545 0.00 0.00 35.71 3.36
893 1013 1.144913 AGGGAAGGAGAGAGAGATCCG 59.855 57.143 0.00 0.00 40.73 4.18
895 1015 2.227194 GGAAGGAGAGAGAGATCCGTC 58.773 57.143 0.00 0.00 41.64 4.79
931 1056 1.635663 CCCGCTAAACCTCGCAACAG 61.636 60.000 0.00 0.00 0.00 3.16
1186 1333 1.002274 ACCATCCGCTCCTCCTTCT 59.998 57.895 0.00 0.00 0.00 2.85
1188 1335 0.758685 CCATCCGCTCCTCCTTCTCT 60.759 60.000 0.00 0.00 0.00 3.10
1189 1336 0.673437 CATCCGCTCCTCCTTCTCTC 59.327 60.000 0.00 0.00 0.00 3.20
1190 1337 0.260230 ATCCGCTCCTCCTTCTCTCA 59.740 55.000 0.00 0.00 0.00 3.27
1223 1392 2.786539 TTCGTGATTCCGCTGCTGCT 62.787 55.000 14.03 0.00 36.97 4.24
1338 1514 2.730183 TTGTCTTGTTCACGCTTTCG 57.270 45.000 0.00 0.00 42.43 3.46
1361 1537 3.439540 CGAATTGCGGTGGGTGGG 61.440 66.667 0.00 0.00 36.03 4.61
1362 1538 2.282887 GAATTGCGGTGGGTGGGT 60.283 61.111 0.00 0.00 0.00 4.51
1363 1539 2.600173 AATTGCGGTGGGTGGGTG 60.600 61.111 0.00 0.00 0.00 4.61
1364 1540 4.676951 ATTGCGGTGGGTGGGTGG 62.677 66.667 0.00 0.00 0.00 4.61
1534 1743 3.192922 GATCGGGTGGTTTCGCGG 61.193 66.667 6.13 0.00 42.48 6.46
1679 1892 1.148759 GCCGTCGCTTCTGGATTCTC 61.149 60.000 0.00 0.00 0.00 2.87
1728 1941 2.891191 TAGCCTCCCGTTTTTCCATT 57.109 45.000 0.00 0.00 0.00 3.16
1778 1991 3.552604 TCCTGCGTTCACTAATTTTGC 57.447 42.857 0.00 0.00 0.00 3.68
1795 2008 2.721231 CACACCAAGTTGCCACCG 59.279 61.111 0.00 0.00 0.00 4.94
1800 2013 4.368808 CAAGTTGCCACCGCGTCG 62.369 66.667 4.92 0.00 38.08 5.12
1804 2017 4.281947 TTGCCACCGCGTCGTGTA 62.282 61.111 13.31 1.27 38.08 2.90
1819 2032 5.913514 GCGTCGTGTACATGTATAGAAGAAT 59.086 40.000 14.63 0.00 0.00 2.40
1865 2085 7.771826 TGCTCATGATCATGAATAGAAAGTTCA 59.228 33.333 32.38 14.38 46.10 3.18
1935 2412 9.452287 TTGTATATATGTATGTGATGCAGCAAT 57.548 29.630 6.05 5.54 0.00 3.56
1941 2418 5.968254 TGTATGTGATGCAGCAATCATTTT 58.032 33.333 6.05 0.00 38.76 1.82
1942 2419 7.098074 TGTATGTGATGCAGCAATCATTTTA 57.902 32.000 6.05 0.00 38.76 1.52
2038 2528 0.103208 CCACGCTCCATGACCTCTAC 59.897 60.000 0.00 0.00 0.00 2.59
2204 2694 1.097232 TATGGCTTGCTCATGTGTGC 58.903 50.000 0.00 0.40 35.32 4.57
2360 2852 3.775316 ACTGGGAACTCGTCATAAAGGAT 59.225 43.478 0.00 0.00 0.00 3.24
2396 2888 3.445096 GCAAACTGTTTGAGCCCATCTAT 59.555 43.478 31.35 0.00 43.26 1.98
2411 2903 2.632987 TCTATGACGAGACCGATGGA 57.367 50.000 0.00 0.00 39.50 3.41
2474 2966 0.476771 ATGACACCCAAGGAACCGTT 59.523 50.000 0.00 0.00 0.00 4.44
2522 3014 0.329931 TCAACCGCCCCAATGTGTAT 59.670 50.000 0.00 0.00 0.00 2.29
2597 3089 1.466856 ATGGCATCAGCGTCAATGTT 58.533 45.000 0.00 0.00 43.41 2.71
2618 3110 2.739885 CTGTAAGTGCTGAGCTCTGT 57.260 50.000 20.24 4.80 32.56 3.41
2623 3115 2.453983 AGTGCTGAGCTCTGTCTTTC 57.546 50.000 20.24 5.52 30.96 2.62
2625 3117 1.001860 GTGCTGAGCTCTGTCTTTCCT 59.998 52.381 20.24 0.00 0.00 3.36
2626 3118 1.696336 TGCTGAGCTCTGTCTTTCCTT 59.304 47.619 20.24 0.00 0.00 3.36
2627 3119 2.899900 TGCTGAGCTCTGTCTTTCCTTA 59.100 45.455 20.24 0.00 0.00 2.69
2628 3120 3.258228 GCTGAGCTCTGTCTTTCCTTAC 58.742 50.000 20.24 0.00 0.00 2.34
2652 3147 8.331931 ACCATTATCTTGTATCTCCTTGGTTA 57.668 34.615 0.00 0.00 29.81 2.85
2653 3148 8.949421 ACCATTATCTTGTATCTCCTTGGTTAT 58.051 33.333 0.00 0.00 29.81 1.89
2659 3154 6.767902 TCTTGTATCTCCTTGGTTATCAATGC 59.232 38.462 0.00 0.00 34.45 3.56
2663 3158 5.378230 TCTCCTTGGTTATCAATGCATCT 57.622 39.130 0.00 0.00 34.45 2.90
2665 3160 5.591472 TCTCCTTGGTTATCAATGCATCTTG 59.409 40.000 0.00 0.00 34.45 3.02
2715 3237 7.826744 TGCTGTGGTTGTTATATACTTTGATGA 59.173 33.333 0.00 0.00 0.00 2.92
2748 3270 7.433708 TTGATCACAAGTTTATTGATGTCGT 57.566 32.000 0.00 0.00 29.93 4.34
2834 3356 1.069636 GCTTCTGGTTTGAGCGACTTG 60.070 52.381 0.00 0.00 0.00 3.16
2849 3371 1.374758 CTTGTCCCGAGTGACCAGC 60.375 63.158 0.00 0.00 34.25 4.85
2852 3374 3.680786 TCCCGAGTGACCAGCGTG 61.681 66.667 0.00 0.00 0.00 5.34
2999 3521 9.944376 AGTAGCAGAACTTTCTAAATTATCACA 57.056 29.630 0.00 0.00 35.34 3.58
3255 3779 3.694566 AGCAAGTTCCTTTCGTCTTGTTT 59.305 39.130 0.00 0.00 39.28 2.83
3283 3807 5.300752 GGATCATAATCACCGACTTGTCAT 58.699 41.667 0.00 0.00 33.21 3.06
3284 3808 5.760253 GGATCATAATCACCGACTTGTCATT 59.240 40.000 0.00 0.00 33.21 2.57
3330 3854 1.083806 CGCATCCTAACTTGCTCGCA 61.084 55.000 0.00 0.00 36.71 5.10
3509 4033 4.463879 CAGCTGGAGCACGAGGGG 62.464 72.222 5.57 0.00 45.16 4.79
3581 4105 2.032681 GGCAACGCCCTCAAGACT 59.967 61.111 0.00 0.00 44.06 3.24
3655 4179 1.330521 CTGGCCATCAAACGATTACCG 59.669 52.381 5.51 0.00 45.44 4.02
3730 4254 2.012673 CAGTTATCTGGGTGAGCTTGC 58.987 52.381 0.00 0.00 37.97 4.01
3731 4255 1.912043 AGTTATCTGGGTGAGCTTGCT 59.088 47.619 0.00 0.00 0.00 3.91
3732 4256 2.307098 AGTTATCTGGGTGAGCTTGCTT 59.693 45.455 0.00 0.00 0.00 3.91
3733 4257 2.680339 GTTATCTGGGTGAGCTTGCTTC 59.320 50.000 0.00 0.00 0.00 3.86
3776 4300 2.744202 CTGTCATTGTGTAACTGAGGCC 59.256 50.000 0.00 0.00 38.04 5.19
3801 4325 2.095768 TGCTTGCAACTGCTATTCGTTC 60.096 45.455 11.46 0.00 42.66 3.95
3850 4374 5.067674 TGAGCCATATTTGTGTATCTTTGGC 59.932 40.000 2.47 2.47 46.78 4.52
3896 4460 5.106475 TGTTATCCGTATGTTGGCAACTTTC 60.106 40.000 28.71 19.38 37.61 2.62
3905 4469 2.472695 TGGCAACTTTCGCTCAGTAT 57.527 45.000 0.00 0.00 37.61 2.12
3913 4477 7.413657 GGCAACTTTCGCTCAGTATATGTTTTA 60.414 37.037 0.00 0.00 0.00 1.52
3947 4511 7.396907 TCAGACCCATGTTATGTTTTCATTGAT 59.603 33.333 0.00 0.00 41.25 2.57
4020 4597 5.450818 TCTTTATGCCATTTGTAGGACCT 57.549 39.130 0.00 0.00 0.00 3.85
4029 4606 7.851228 TGCCATTTGTAGGACCTATATATCTG 58.149 38.462 4.06 0.00 0.00 2.90
4034 4611 7.704578 TTGTAGGACCTATATATCTGTGCTC 57.295 40.000 4.06 5.70 31.57 4.26
4037 4614 6.849085 AGGACCTATATATCTGTGCTCAAG 57.151 41.667 0.00 0.00 0.00 3.02
4042 4619 8.200024 ACCTATATATCTGTGCTCAAGATTGT 57.800 34.615 0.00 0.00 0.00 2.71
4082 4660 8.013947 CACTTCAGCAAAGATCATATATTTCGG 58.986 37.037 5.93 0.00 38.44 4.30
4101 4679 3.954904 TCGGGTGAAATTTTGGAACTTCA 59.045 39.130 0.00 0.00 0.00 3.02
4110 4688 0.841289 TTGGAACTTCAAGGACGGGT 59.159 50.000 0.00 0.00 0.00 5.28
4111 4689 0.841289 TGGAACTTCAAGGACGGGTT 59.159 50.000 0.00 0.00 0.00 4.11
4112 4690 2.048601 TGGAACTTCAAGGACGGGTTA 58.951 47.619 0.00 0.00 0.00 2.85
4113 4691 2.224354 TGGAACTTCAAGGACGGGTTAC 60.224 50.000 0.00 0.00 0.00 2.50
4146 4741 4.655963 ACTGCTATCAACATTGGTCTGTT 58.344 39.130 0.00 0.00 39.91 3.16
4218 4813 6.488769 TCTTAAACACAAGACACCTTAGGA 57.511 37.500 4.77 0.00 29.55 2.94
4235 4830 7.013846 CACCTTAGGAACACTTTATTTGGACAA 59.986 37.037 4.77 0.00 0.00 3.18
4239 4834 4.929211 GGAACACTTTATTTGGACAATGGC 59.071 41.667 0.00 0.00 0.00 4.40
4242 4837 4.082787 ACACTTTATTTGGACAATGGCGAG 60.083 41.667 0.00 0.00 0.00 5.03
4262 4875 2.420022 AGTGTCGCAACAATAATGAGCC 59.580 45.455 0.00 0.00 37.08 4.70
4270 4883 4.202050 GCAACAATAATGAGCCAACCTAGG 60.202 45.833 7.41 7.41 0.00 3.02
4271 4884 4.862641 ACAATAATGAGCCAACCTAGGT 57.137 40.909 9.21 9.21 0.00 3.08
4272 4885 5.968676 ACAATAATGAGCCAACCTAGGTA 57.031 39.130 16.67 0.00 0.00 3.08
4273 4886 5.681639 ACAATAATGAGCCAACCTAGGTAC 58.318 41.667 16.67 8.15 0.00 3.34
4274 4887 5.428783 ACAATAATGAGCCAACCTAGGTACT 59.571 40.000 16.67 13.24 46.37 2.73
4275 4888 5.810080 ATAATGAGCCAACCTAGGTACTC 57.190 43.478 23.34 23.34 41.75 2.59
4276 4889 2.921834 TGAGCCAACCTAGGTACTCT 57.078 50.000 27.14 19.32 41.75 3.24
4277 4890 4.537945 ATGAGCCAACCTAGGTACTCTA 57.462 45.455 27.14 18.86 41.75 2.43
4280 4893 5.278061 TGAGCCAACCTAGGTACTCTATTT 58.722 41.667 27.14 6.82 41.75 1.40
4281 4894 5.128827 TGAGCCAACCTAGGTACTCTATTTG 59.871 44.000 27.14 16.19 41.75 2.32
4282 4895 4.127907 GCCAACCTAGGTACTCTATTTGC 58.872 47.826 16.67 1.00 41.75 3.68
4283 4896 4.369182 CCAACCTAGGTACTCTATTTGCG 58.631 47.826 16.67 0.00 41.75 4.85
4284 4897 4.369182 CAACCTAGGTACTCTATTTGCGG 58.631 47.826 16.67 0.00 41.75 5.69
4285 4898 3.639952 ACCTAGGTACTCTATTTGCGGT 58.360 45.455 14.41 0.00 41.75 5.68
4286 4899 4.796606 ACCTAGGTACTCTATTTGCGGTA 58.203 43.478 14.41 0.00 41.75 4.02
4287 4900 4.582240 ACCTAGGTACTCTATTTGCGGTAC 59.418 45.833 14.41 0.00 41.75 3.34
4288 4901 4.826183 CCTAGGTACTCTATTTGCGGTACT 59.174 45.833 0.00 0.00 41.75 2.73
4289 4902 5.301298 CCTAGGTACTCTATTTGCGGTACTT 59.699 44.000 0.00 0.00 41.75 2.24
4290 4903 5.259832 AGGTACTCTATTTGCGGTACTTC 57.740 43.478 0.00 0.00 36.01 3.01
4291 4904 4.708421 AGGTACTCTATTTGCGGTACTTCA 59.292 41.667 0.00 0.00 36.01 3.02
4292 4905 4.802563 GGTACTCTATTTGCGGTACTTCAC 59.197 45.833 0.00 0.00 36.01 3.18
4293 4906 3.508762 ACTCTATTTGCGGTACTTCACG 58.491 45.455 0.00 0.00 0.00 4.35
4299 4912 4.807039 CGGTACTTCACGCCCCCG 62.807 72.222 0.00 0.00 41.14 5.73
4330 4943 8.919145 ACCCATTAACTCATGAACAAAAACTTA 58.081 29.630 0.00 0.00 0.00 2.24
4344 4957 8.831715 AACAAAAACTTATAAAGCATTCCCTG 57.168 30.769 0.00 0.00 0.00 4.45
4366 4979 4.061596 GCAGACAGGAATATAAGTCAGGC 58.938 47.826 0.00 0.00 33.56 4.85
4406 5019 4.214545 TCCATTTAACGAGCGAAACATGTT 59.785 37.500 4.92 4.92 0.00 2.71
4417 5030 6.147864 AGCGAAACATGTTTAATATGCCAT 57.852 33.333 23.33 6.01 32.11 4.40
4418 5031 7.270757 AGCGAAACATGTTTAATATGCCATA 57.729 32.000 23.33 0.00 32.11 2.74
4419 5032 7.138736 AGCGAAACATGTTTAATATGCCATAC 58.861 34.615 23.33 6.05 32.11 2.39
4420 5033 6.915300 GCGAAACATGTTTAATATGCCATACA 59.085 34.615 23.33 0.00 32.11 2.29
4421 5034 7.113404 GCGAAACATGTTTAATATGCCATACAG 59.887 37.037 23.33 5.19 32.11 2.74
4422 5035 8.128582 CGAAACATGTTTAATATGCCATACAGT 58.871 33.333 23.33 0.00 32.11 3.55
4423 5036 9.450807 GAAACATGTTTAATATGCCATACAGTC 57.549 33.333 23.33 1.75 32.11 3.51
4424 5037 7.189693 ACATGTTTAATATGCCATACAGTCG 57.810 36.000 1.60 0.00 0.00 4.18
4425 5038 6.989759 ACATGTTTAATATGCCATACAGTCGA 59.010 34.615 1.60 0.00 0.00 4.20
4426 5039 7.497579 ACATGTTTAATATGCCATACAGTCGAA 59.502 33.333 1.60 0.00 0.00 3.71
4427 5040 7.477144 TGTTTAATATGCCATACAGTCGAAG 57.523 36.000 0.00 0.00 0.00 3.79
4428 5041 7.269316 TGTTTAATATGCCATACAGTCGAAGA 58.731 34.615 0.00 0.00 0.00 2.87
4471 5084 6.385843 GCATACAACACACAATAACCAATCA 58.614 36.000 0.00 0.00 0.00 2.57
4475 5088 9.995003 ATACAACACACAATAACCAATCAAAAT 57.005 25.926 0.00 0.00 0.00 1.82
4479 5092 9.612066 AACACACAATAACCAATCAAAATTCTT 57.388 25.926 0.00 0.00 0.00 2.52
4486 5099 3.447229 ACCAATCAAAATTCTTAGGCCCG 59.553 43.478 0.00 0.00 0.00 6.13
4539 5152 2.553172 AGTACTATCGAACTCCATCGCC 59.447 50.000 0.00 0.00 42.44 5.54
4576 5190 7.421530 ACAATATACACACGAAATATCCAGC 57.578 36.000 0.00 0.00 0.00 4.85
4593 5207 4.134563 TCCAGCAAGACTTTTTGGTAGAC 58.865 43.478 12.32 0.00 36.71 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.584551 ATTGAGTAGGTCCACCTCTTTTT 57.415 39.130 0.09 0.00 44.77 1.94
39 40 3.234353 TCTCCCTAGGCAGTATCATGTG 58.766 50.000 2.05 0.00 0.00 3.21
40 41 3.619900 TCTCCCTAGGCAGTATCATGT 57.380 47.619 2.05 0.00 0.00 3.21
41 42 4.963318 TTTCTCCCTAGGCAGTATCATG 57.037 45.455 2.05 0.00 0.00 3.07
42 43 4.534103 GGATTTCTCCCTAGGCAGTATCAT 59.466 45.833 15.12 0.00 35.28 2.45
43 44 3.904339 GGATTTCTCCCTAGGCAGTATCA 59.096 47.826 15.12 0.00 35.28 2.15
45 46 3.941629 TGGATTTCTCCCTAGGCAGTAT 58.058 45.455 2.05 0.00 41.29 2.12
46 47 3.414759 TGGATTTCTCCCTAGGCAGTA 57.585 47.619 2.05 0.00 41.29 2.74
47 48 2.270434 TGGATTTCTCCCTAGGCAGT 57.730 50.000 2.05 0.00 41.29 4.40
48 49 2.813354 GCATGGATTTCTCCCTAGGCAG 60.813 54.545 2.05 0.00 41.29 4.85
55 56 0.383231 CTTGCGCATGGATTTCTCCC 59.617 55.000 12.75 0.00 41.29 4.30
77 78 3.440872 TGTTGTGTTTTCGGTAGCAAAGT 59.559 39.130 0.00 0.00 0.00 2.66
119 120 4.792704 GCGAATTTCTTTCTGTTTCAGCCA 60.793 41.667 0.00 0.00 31.73 4.75
141 143 8.411683 AGATCTTCAAGAAATATCCAATGTTGC 58.588 33.333 0.00 0.00 0.00 4.17
187 189 2.898920 TAGGTAGCACGGAGGGACGG 62.899 65.000 0.00 0.00 38.39 4.79
191 193 1.633774 ATGATAGGTAGCACGGAGGG 58.366 55.000 0.00 0.00 0.00 4.30
239 241 0.843309 TGTCCACTTTCTCCTTGGCA 59.157 50.000 0.00 0.00 0.00 4.92
241 243 4.584325 TGAATTTGTCCACTTTCTCCTTGG 59.416 41.667 0.00 0.00 0.00 3.61
268 273 1.452110 CAAACACATGCGGGAGATGA 58.548 50.000 0.00 0.00 0.00 2.92
283 288 1.885850 AGTGTCGTGTCCCGCAAAC 60.886 57.895 0.00 0.00 36.19 2.93
353 359 6.434028 TGACCTTCATTCAAGATAAAACCAGG 59.566 38.462 0.00 0.00 33.29 4.45
354 360 7.452880 TGACCTTCATTCAAGATAAAACCAG 57.547 36.000 0.00 0.00 33.29 4.00
375 381 9.921637 TTGGGTGAATCATAGTTTATTTTTGAC 57.078 29.630 0.00 0.00 0.00 3.18
385 391 2.311542 TGGCCTTGGGTGAATCATAGTT 59.688 45.455 3.32 0.00 0.00 2.24
402 410 0.872388 ACAACGACGAAGAAATGGCC 59.128 50.000 0.00 0.00 0.00 5.36
454 471 0.541764 TTGGCCGCTTTCCCTTTGAT 60.542 50.000 0.00 0.00 0.00 2.57
459 476 2.046285 CGAATTGGCCGCTTTCCCT 61.046 57.895 0.00 0.00 0.00 4.20
485 509 1.136329 AGGATGTGCTGGTTGGAGGT 61.136 55.000 0.00 0.00 0.00 3.85
494 518 4.885907 AGAAAATGGTGATAGGATGTGCTG 59.114 41.667 0.00 0.00 0.00 4.41
495 519 5.121380 AGAAAATGGTGATAGGATGTGCT 57.879 39.130 0.00 0.00 0.00 4.40
496 520 6.291377 TCTAGAAAATGGTGATAGGATGTGC 58.709 40.000 0.00 0.00 0.00 4.57
497 521 6.426328 GCTCTAGAAAATGGTGATAGGATGTG 59.574 42.308 0.00 0.00 0.00 3.21
501 525 4.893524 TCGCTCTAGAAAATGGTGATAGGA 59.106 41.667 0.00 0.00 0.00 2.94
508 532 2.633488 GCCTTCGCTCTAGAAAATGGT 58.367 47.619 0.00 0.00 0.00 3.55
568 594 6.154445 CCACTTGTGAGGATTTTTCTTCATG 58.846 40.000 1.89 0.00 0.00 3.07
570 596 5.200483 ACCACTTGTGAGGATTTTTCTTCA 58.800 37.500 1.89 0.00 0.00 3.02
571 597 5.774498 ACCACTTGTGAGGATTTTTCTTC 57.226 39.130 1.89 0.00 0.00 2.87
612 731 0.540365 CCCTCCTTGGCTTGAGCAAA 60.540 55.000 5.24 0.00 44.36 3.68
613 732 1.075482 CCCTCCTTGGCTTGAGCAA 59.925 57.895 5.24 0.00 44.36 3.91
621 740 3.803162 GCCTCTCCCCTCCTTGGC 61.803 72.222 0.00 0.00 0.00 4.52
626 745 2.684499 CCCTTTGCCTCTCCCCTCC 61.684 68.421 0.00 0.00 0.00 4.30
627 746 2.684499 CCCCTTTGCCTCTCCCCTC 61.684 68.421 0.00 0.00 0.00 4.30
628 747 2.615288 CCCCTTTGCCTCTCCCCT 60.615 66.667 0.00 0.00 0.00 4.79
629 748 4.448976 GCCCCTTTGCCTCTCCCC 62.449 72.222 0.00 0.00 0.00 4.81
630 749 2.520657 ATTGCCCCTTTGCCTCTCCC 62.521 60.000 0.00 0.00 0.00 4.30
651 770 3.372676 GAGATGCGTTGCAGTGGCG 62.373 63.158 0.00 0.00 43.65 5.69
718 838 1.569493 CAGTGCTGCGGTGTGTTAC 59.431 57.895 0.00 0.00 0.00 2.50
719 839 4.041617 CAGTGCTGCGGTGTGTTA 57.958 55.556 0.00 0.00 0.00 2.41
750 870 0.464554 GTCATGGGCTAGTGAAGGGC 60.465 60.000 0.00 0.00 0.00 5.19
759 879 0.767998 TTGTGGTGTGTCATGGGCTA 59.232 50.000 0.00 0.00 0.00 3.93
803 923 4.142469 ACCATTTCTAATGCCAGTTTACGC 60.142 41.667 0.00 0.00 0.00 4.42
810 930 1.745087 ACGCACCATTTCTAATGCCAG 59.255 47.619 0.00 0.00 34.49 4.85
811 931 1.742831 GACGCACCATTTCTAATGCCA 59.257 47.619 0.00 0.00 34.49 4.92
829 949 7.042658 GGTCCTTGTCATCGTCAATAAATAGAC 60.043 40.741 0.00 0.00 0.00 2.59
873 993 1.144913 CGGATCTCTCTCTCCTTCCCT 59.855 57.143 0.00 0.00 0.00 4.20
875 995 2.227194 GACGGATCTCTCTCTCCTTCC 58.773 57.143 0.00 0.00 0.00 3.46
893 1013 3.406361 CTGCCTCACACGCACGAC 61.406 66.667 0.00 0.00 31.61 4.34
979 1109 2.185608 GGCTCTGCTTCCGACTCC 59.814 66.667 0.00 0.00 0.00 3.85
1147 1292 5.825151 TGGTGTGTGTAATTTCTCACATGAA 59.175 36.000 18.72 8.47 44.48 2.57
1186 1333 5.185056 TCACGAATCTAATCAACCAGTGAGA 59.815 40.000 0.00 0.00 40.43 3.27
1188 1335 5.400066 TCACGAATCTAATCAACCAGTGA 57.600 39.130 0.00 0.00 41.67 3.41
1189 1336 6.238211 GGAATCACGAATCTAATCAACCAGTG 60.238 42.308 0.00 0.00 0.00 3.66
1190 1337 5.817816 GGAATCACGAATCTAATCAACCAGT 59.182 40.000 0.00 0.00 0.00 4.00
1338 1514 1.154225 CCACCGCAATTCGAACTGC 60.154 57.895 20.99 20.99 41.67 4.40
1679 1892 3.825014 CCCTATCAATCAATCAAGCAGGG 59.175 47.826 0.00 0.00 34.63 4.45
1728 1941 4.873827 GCCATACGAGATTACCAGAAACAA 59.126 41.667 0.00 0.00 0.00 2.83
1766 1979 5.347342 CAACTTGGTGTGCAAAATTAGTGA 58.653 37.500 0.00 0.00 0.00 3.41
1774 1987 0.108424 GTGGCAACTTGGTGTGCAAA 60.108 50.000 0.00 0.00 37.61 3.68
1778 1991 2.721231 CGGTGGCAACTTGGTGTG 59.279 61.111 0.00 0.00 37.61 3.82
1795 2008 4.840911 TCTTCTATACATGTACACGACGC 58.159 43.478 7.96 0.00 0.00 5.19
1800 2013 7.435488 AGCGAACATTCTTCTATACATGTACAC 59.565 37.037 7.96 0.00 0.00 2.90
1804 2017 7.979537 TGTTAGCGAACATTCTTCTATACATGT 59.020 33.333 8.43 2.69 40.72 3.21
1908 2130 8.255394 TGCTGCATCACATACATATATACAAC 57.745 34.615 0.00 0.00 0.00 3.32
1935 2412 9.123709 GCAAGAATTAACGTCACATTAAAATGA 57.876 29.630 9.60 0.00 39.67 2.57
1941 2418 5.250200 AGGGCAAGAATTAACGTCACATTA 58.750 37.500 0.00 0.00 0.00 1.90
1942 2419 4.079253 AGGGCAAGAATTAACGTCACATT 58.921 39.130 0.00 0.00 0.00 2.71
2038 2528 1.374758 GGACTGACCCTGTTGCTCG 60.375 63.158 0.00 0.00 0.00 5.03
2204 2694 1.068748 GCAGGAACATTGCAGACACAG 60.069 52.381 0.00 0.00 41.17 3.66
2360 2852 0.793861 GTTTGCACGCGTCTTGGATA 59.206 50.000 9.86 0.00 0.00 2.59
2396 2888 1.378646 AGCTCCATCGGTCTCGTCA 60.379 57.895 0.00 0.00 37.69 4.35
2411 2903 3.067106 CACTGAAACGTAACCATCAGCT 58.933 45.455 12.33 0.00 42.34 4.24
2448 2940 1.047002 CCTTGGGTGTCATTTGCCAA 58.953 50.000 0.00 0.00 0.00 4.52
2474 2966 1.202592 TGTAACCACTTCGCAGCTTCA 60.203 47.619 0.00 0.00 0.00 3.02
2522 3014 3.308401 TGCAGTAGCTGGGATCTTGATA 58.692 45.455 0.00 0.00 42.74 2.15
2597 3089 3.157881 ACAGAGCTCAGCACTTACAGTA 58.842 45.455 17.77 0.00 0.00 2.74
2623 3115 7.880195 CCAAGGAGATACAAGATAATGGTAAGG 59.120 40.741 0.00 0.00 0.00 2.69
2625 3117 8.331931 ACCAAGGAGATACAAGATAATGGTAA 57.668 34.615 0.00 0.00 35.79 2.85
2626 3118 7.931015 ACCAAGGAGATACAAGATAATGGTA 57.069 36.000 0.00 0.00 35.79 3.25
2627 3119 6.831664 ACCAAGGAGATACAAGATAATGGT 57.168 37.500 0.00 0.00 32.86 3.55
2628 3120 9.442047 GATAACCAAGGAGATACAAGATAATGG 57.558 37.037 0.00 0.00 0.00 3.16
2676 3171 2.086869 CCACAGCAAATAGTCCAGTGG 58.913 52.381 1.40 1.40 39.04 4.00
2678 3173 3.149196 CAACCACAGCAAATAGTCCAGT 58.851 45.455 0.00 0.00 0.00 4.00
2680 3175 3.222173 ACAACCACAGCAAATAGTCCA 57.778 42.857 0.00 0.00 0.00 4.02
2681 3176 5.897377 ATAACAACCACAGCAAATAGTCC 57.103 39.130 0.00 0.00 0.00 3.85
2682 3177 9.326413 AGTATATAACAACCACAGCAAATAGTC 57.674 33.333 0.00 0.00 0.00 2.59
2683 3178 9.681062 AAGTATATAACAACCACAGCAAATAGT 57.319 29.630 0.00 0.00 0.00 2.12
2748 3270 3.002791 CAACGGAGAAGATAAGCTGCAA 58.997 45.455 1.02 0.00 0.00 4.08
2834 3356 3.681835 ACGCTGGTCACTCGGGAC 61.682 66.667 0.00 0.00 37.06 4.46
2849 3371 1.466167 CTGACAAAGAAGGATGCCACG 59.534 52.381 0.00 0.00 0.00 4.94
2852 3374 0.813821 GGCTGACAAAGAAGGATGCC 59.186 55.000 0.00 0.00 0.00 4.40
2998 3520 6.475402 GGTGGTTGTTAGTCAAAACTTGATTG 59.525 38.462 0.00 0.00 42.47 2.67
2999 3521 6.406512 GGGTGGTTGTTAGTCAAAACTTGATT 60.407 38.462 0.00 0.00 42.47 2.57
3255 3779 2.312390 TCGGTGATTATGATCCCGACA 58.688 47.619 19.25 5.73 43.68 4.35
3330 3854 1.963515 GACCTGAATGTGCAAAGGGTT 59.036 47.619 0.00 0.00 33.87 4.11
3509 4033 1.201429 TCCCCTTGAAGGAGCTCACC 61.201 60.000 13.97 0.00 37.67 4.02
3581 4105 4.715523 GCCTACAGGTTGGCGGCA 62.716 66.667 7.97 7.97 41.22 5.69
3655 4179 4.852609 CAGCAAGCTGGCATTTTTATTC 57.147 40.909 17.28 0.00 40.17 1.75
3729 4253 2.285488 GCACGCCTAGAATACAAGAAGC 59.715 50.000 0.00 0.00 0.00 3.86
3730 4254 2.866762 GGCACGCCTAGAATACAAGAAG 59.133 50.000 0.00 0.00 0.00 2.85
3731 4255 2.500098 AGGCACGCCTAGAATACAAGAA 59.500 45.455 9.35 0.00 46.14 2.52
3732 4256 2.108168 AGGCACGCCTAGAATACAAGA 58.892 47.619 9.35 0.00 46.14 3.02
3733 4257 2.205074 CAGGCACGCCTAGAATACAAG 58.795 52.381 10.95 0.00 46.28 3.16
3801 4325 6.921857 ACTTGCTCAAAAACAATTGATCAGAG 59.078 34.615 13.59 12.62 36.94 3.35
3850 4374 6.449698 ACAACAGTAAGGAGAAATGCATTTG 58.550 36.000 28.67 14.05 0.00 2.32
3934 4498 7.053316 TCAAAGTGTCCATCAATGAAAACAT 57.947 32.000 0.00 0.00 0.00 2.71
3947 4511 8.918202 ATTGTTTAGTTAGATCAAAGTGTCCA 57.082 30.769 0.00 0.00 0.00 4.02
4020 4597 8.427902 AGGACAATCTTGAGCACAGATATATA 57.572 34.615 0.00 0.00 0.00 0.86
4027 4604 6.037610 GGTATAAAGGACAATCTTGAGCACAG 59.962 42.308 0.00 0.00 0.00 3.66
4029 4606 5.006746 CGGTATAAAGGACAATCTTGAGCAC 59.993 44.000 0.00 0.00 0.00 4.40
4034 4611 5.006746 GTGAGCGGTATAAAGGACAATCTTG 59.993 44.000 0.00 0.00 0.00 3.02
4037 4614 4.694339 AGTGAGCGGTATAAAGGACAATC 58.306 43.478 0.00 0.00 0.00 2.67
4042 4619 3.430374 GCTGAAGTGAGCGGTATAAAGGA 60.430 47.826 0.00 0.00 0.00 3.36
4080 4658 4.314740 TGAAGTTCCAAAATTTCACCCG 57.685 40.909 0.00 0.00 36.52 5.28
4082 4660 5.753438 GTCCTTGAAGTTCCAAAATTTCACC 59.247 40.000 0.00 0.00 39.82 4.02
4093 4671 2.420642 GTAACCCGTCCTTGAAGTTCC 58.579 52.381 0.00 0.00 0.00 3.62
4094 4672 2.064014 CGTAACCCGTCCTTGAAGTTC 58.936 52.381 0.00 0.00 0.00 3.01
4110 4688 0.682852 AGCAGTAGTTGTGGGCGTAA 59.317 50.000 0.00 0.00 0.00 3.18
4111 4689 1.548081 TAGCAGTAGTTGTGGGCGTA 58.452 50.000 0.00 0.00 0.00 4.42
4112 4690 0.902531 ATAGCAGTAGTTGTGGGCGT 59.097 50.000 0.00 0.00 0.00 5.68
4113 4691 1.134818 TGATAGCAGTAGTTGTGGGCG 60.135 52.381 0.00 0.00 0.00 6.13
4115 4693 3.937814 TGTTGATAGCAGTAGTTGTGGG 58.062 45.455 0.00 0.00 0.00 4.61
4116 4694 5.163723 CCAATGTTGATAGCAGTAGTTGTGG 60.164 44.000 0.00 0.00 0.00 4.17
4146 4741 4.380531 CAAACTGCAGTTAGAGGACTTCA 58.619 43.478 31.31 0.00 37.25 3.02
4186 4781 9.357652 GGTGTCTTGTGTTTAAGAATATACGTA 57.642 33.333 0.00 0.00 38.33 3.57
4188 4783 8.475331 AGGTGTCTTGTGTTTAAGAATATACG 57.525 34.615 0.00 0.00 38.33 3.06
4206 4801 6.715264 CCAAATAAAGTGTTCCTAAGGTGTCT 59.285 38.462 0.00 0.00 0.00 3.41
4218 4813 4.279671 TCGCCATTGTCCAAATAAAGTGTT 59.720 37.500 0.00 0.00 0.00 3.32
4239 4834 3.782250 GCTCATTATTGTTGCGACACTCG 60.782 47.826 6.19 0.00 43.89 4.18
4242 4837 2.161410 TGGCTCATTATTGTTGCGACAC 59.839 45.455 6.19 0.00 34.98 3.67
4262 4875 4.142004 ACCGCAAATAGAGTACCTAGGTTG 60.142 45.833 22.11 10.70 33.10 3.77
4270 4883 4.498323 CGTGAAGTACCGCAAATAGAGTAC 59.502 45.833 0.00 0.00 36.23 2.73
4271 4884 4.665212 CGTGAAGTACCGCAAATAGAGTA 58.335 43.478 0.00 0.00 0.00 2.59
4272 4885 3.508762 CGTGAAGTACCGCAAATAGAGT 58.491 45.455 0.00 0.00 0.00 3.24
4282 4895 4.807039 CGGGGGCGTGAAGTACCG 62.807 72.222 0.00 0.00 35.01 4.02
4283 4896 4.462280 CCGGGGGCGTGAAGTACC 62.462 72.222 0.00 0.00 0.00 3.34
4284 4897 3.366739 CTCCGGGGGCGTGAAGTAC 62.367 68.421 0.00 0.00 0.00 2.73
4285 4898 3.072468 CTCCGGGGGCGTGAAGTA 61.072 66.667 0.00 0.00 0.00 2.24
4294 4907 1.694882 TTAATGGGTCCTCCGGGGG 60.695 63.158 16.89 16.89 38.76 5.40
4295 4908 0.986550 AGTTAATGGGTCCTCCGGGG 60.987 60.000 0.00 0.00 38.76 5.73
4296 4909 0.468648 GAGTTAATGGGTCCTCCGGG 59.531 60.000 0.00 0.00 38.76 5.73
4297 4910 1.200519 TGAGTTAATGGGTCCTCCGG 58.799 55.000 0.00 0.00 38.76 5.14
4298 4911 2.434336 TCATGAGTTAATGGGTCCTCCG 59.566 50.000 0.00 0.00 38.76 4.63
4299 4912 4.200092 GTTCATGAGTTAATGGGTCCTCC 58.800 47.826 0.00 0.00 0.00 4.30
4344 4957 4.061596 GCCTGACTTATATTCCTGTCTGC 58.938 47.826 0.00 0.00 0.00 4.26
4366 4979 5.880054 AATGGACGACCTAAAATCAAGTG 57.120 39.130 5.33 0.00 37.04 3.16
4406 5019 6.811954 TGTCTTCGACTGTATGGCATATTAA 58.188 36.000 10.92 0.00 33.15 1.40
4441 5054 6.480320 GGTTATTGTGTGTTGTATGCCAAAAA 59.520 34.615 0.00 0.00 34.07 1.94
4442 5055 5.986135 GGTTATTGTGTGTTGTATGCCAAAA 59.014 36.000 0.00 0.00 34.07 2.44
4443 5056 5.069119 TGGTTATTGTGTGTTGTATGCCAAA 59.931 36.000 0.00 0.00 34.07 3.28
4444 5057 4.584743 TGGTTATTGTGTGTTGTATGCCAA 59.415 37.500 0.00 0.00 0.00 4.52
4445 5058 4.145052 TGGTTATTGTGTGTTGTATGCCA 58.855 39.130 0.00 0.00 0.00 4.92
4446 5059 4.775058 TGGTTATTGTGTGTTGTATGCC 57.225 40.909 0.00 0.00 0.00 4.40
4447 5060 6.385843 TGATTGGTTATTGTGTGTTGTATGC 58.614 36.000 0.00 0.00 0.00 3.14
4448 5061 8.809159 TTTGATTGGTTATTGTGTGTTGTATG 57.191 30.769 0.00 0.00 0.00 2.39
4449 5062 9.995003 ATTTTGATTGGTTATTGTGTGTTGTAT 57.005 25.926 0.00 0.00 0.00 2.29
4450 5063 9.823647 AATTTTGATTGGTTATTGTGTGTTGTA 57.176 25.926 0.00 0.00 0.00 2.41
4451 5064 8.729805 AATTTTGATTGGTTATTGTGTGTTGT 57.270 26.923 0.00 0.00 0.00 3.32
4452 5065 9.044150 AGAATTTTGATTGGTTATTGTGTGTTG 57.956 29.630 0.00 0.00 0.00 3.33
4453 5066 9.612066 AAGAATTTTGATTGGTTATTGTGTGTT 57.388 25.926 0.00 0.00 0.00 3.32
4456 5069 9.927668 CCTAAGAATTTTGATTGGTTATTGTGT 57.072 29.630 0.00 0.00 0.00 3.72
4461 5074 6.183360 CGGGCCTAAGAATTTTGATTGGTTAT 60.183 38.462 0.84 0.00 0.00 1.89
4471 5084 1.807226 GCGCGGGCCTAAGAATTTT 59.193 52.632 14.45 0.00 0.00 1.82
4486 5099 0.034337 TGGGAATATAAGTCGGGCGC 59.966 55.000 0.00 0.00 0.00 6.53
4519 5132 2.292569 TGGCGATGGAGTTCGATAGTAC 59.707 50.000 0.00 0.00 41.62 2.73
4539 5152 6.527722 GTGTGTATATTGTTGAATGGCAGTTG 59.472 38.462 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.