Multiple sequence alignment - TraesCS5D01G363600

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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 TraesCS5D01G363600 chr5D 100.000 2724 0 0 1 2724 441339189 441336466 0.000000e+00 5031
1 TraesCS5D01G363600 chr5D 91.129 248 21 1 2076 2323 548214197 548213951 4.350000e-88 335
2 TraesCS5D01G363600 chr6B 93.487 1950 97 16 1 1936 638453083 638451150 0.000000e+00 2870
3 TraesCS5D01G363600 chr6B 93.609 266 16 1 2077 2341 38922586 38922321 1.970000e-106 396
4 TraesCS5D01G363600 chr6B 93.258 267 16 2 2076 2341 647485465 647485200 2.540000e-105 392
5 TraesCS5D01G363600 chr6B 96.250 160 5 1 2338 2497 647485095 647484937 7.480000e-66 261
6 TraesCS5D01G363600 chr6B 89.091 165 13 3 1925 2084 638450035 638449871 1.650000e-47 200
7 TraesCS5D01G363600 chr6B 96.341 82 2 1 2416 2497 38891853 38891773 1.700000e-27 134
8 TraesCS5D01G363600 chr5B 95.203 271 10 3 2072 2341 216805162 216805430 2.510000e-115 425
9 TraesCS5D01G363600 chr5B 96.250 160 5 1 2338 2497 216805535 216805693 7.480000e-66 261
10 TraesCS5D01G363600 chr3B 89.513 267 24 3 2076 2341 89172539 89172276 4.350000e-88 335
11 TraesCS5D01G363600 chr7B 88.806 268 26 3 2075 2341 479753951 479753687 2.620000e-85 326
12 TraesCS5D01G363600 chr4A 88.806 268 26 3 2075 2341 642931622 642931886 2.620000e-85 326
13 TraesCS5D01G363600 chr5A 91.324 219 19 0 2505 2723 666128148 666127930 1.590000e-77 300
14 TraesCS5D01G363600 chr2A 89.700 233 22 2 2109 2340 643020544 643020313 2.050000e-76 296
15 TraesCS5D01G363600 chr2A 94.375 160 8 1 2338 2497 643020211 643020053 7.530000e-61 244
16 TraesCS5D01G363600 chr7A 83.146 267 43 2 2076 2340 516875607 516875341 2.710000e-60 243
17 TraesCS5D01G363600 chr2D 90.303 165 13 2 2335 2497 498321526 498321363 2.120000e-51 213


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 TraesCS5D01G363600 chr5D 441336466 441339189 2723 True 5031.0 5031 100.0000 1 2724 1 chr5D.!!$R1 2723
1 TraesCS5D01G363600 chr6B 638449871 638453083 3212 True 1535.0 2870 91.2890 1 2084 2 chr6B.!!$R3 2083
2 TraesCS5D01G363600 chr6B 647484937 647485465 528 True 326.5 392 94.7540 2076 2497 2 chr6B.!!$R4 421
3 TraesCS5D01G363600 chr5B 216805162 216805693 531 False 343.0 425 95.7265 2072 2497 2 chr5B.!!$F1 425

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
145 146 0.251519 AAAGGAGAAGCTTGGCCCTG 60.252 55.0 2.1 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1799 0.108424 CGTCCTCAGAAAGCCAGGAG 60.108 60.0 0.0 0.0 36.98 3.69 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
66 67 3.889815 CAAGGTGATGGAAGGAGCAATA 58.110 45.455 0.00 0.00 0.00 1.90
90 91 9.950680 ATAGAAAACATATTGCCAAATACGAAG 57.049 29.630 0.00 0.00 31.07 3.79
102 103 3.906720 AATACGAAGCATAGGTGGTGT 57.093 42.857 0.00 0.00 35.94 4.16
120 121 3.627577 GGTGTAAGTGGCATGTATTGAGG 59.372 47.826 0.00 0.00 0.00 3.86
123 124 1.755179 AGTGGCATGTATTGAGGTGC 58.245 50.000 0.00 0.00 36.88 5.01
145 146 0.251519 AAAGGAGAAGCTTGGCCCTG 60.252 55.000 2.10 0.00 0.00 4.45
151 152 2.170607 GAGAAGCTTGGCCCTGTATACA 59.829 50.000 2.10 5.25 0.00 2.29
184 185 4.278170 GTGGATTCAAACATGAGTTCCACA 59.722 41.667 23.80 3.10 44.07 4.17
339 340 1.123077 TCTCCAGTGTGTTCTGTGCT 58.877 50.000 0.00 0.00 34.02 4.40
432 433 4.036027 CCTATGCACCTATTTGTCAAGCAG 59.964 45.833 0.00 0.00 33.69 4.24
445 446 3.807622 TGTCAAGCAGTACAACAAGCTAC 59.192 43.478 0.00 0.00 36.07 3.58
460 461 1.208052 AGCTACTCCAATCACGCACAT 59.792 47.619 0.00 0.00 0.00 3.21
510 511 3.463048 AAGATGGTGAGAAGCCCAAAT 57.537 42.857 0.00 0.00 33.66 2.32
511 512 4.591321 AAGATGGTGAGAAGCCCAAATA 57.409 40.909 0.00 0.00 33.66 1.40
513 514 4.467769 AGATGGTGAGAAGCCCAAATATG 58.532 43.478 0.00 0.00 33.66 1.78
514 515 2.378038 TGGTGAGAAGCCCAAATATGC 58.622 47.619 0.00 0.00 0.00 3.14
529 531 7.095523 GCCCAAATATGCATATTTTGATGTGTC 60.096 37.037 32.52 16.14 40.07 3.67
592 601 6.560253 AGATATACAAACCCGAAATGCATC 57.440 37.500 0.00 0.00 0.00 3.91
619 628 6.116126 ACCTGTAGCTTAGATTGTTCAATCC 58.884 40.000 18.20 6.65 0.00 3.01
682 691 7.482428 CCATTTGCTTAGCATAAAATTTGTTGC 59.518 33.333 8.05 14.63 38.76 4.17
684 693 7.488187 TTGCTTAGCATAAAATTTGTTGCAA 57.512 28.000 21.15 0.00 38.76 4.08
686 695 6.927936 TGCTTAGCATAAAATTTGTTGCAAGA 59.072 30.769 23.38 0.00 37.56 3.02
693 702 8.284693 GCATAAAATTTGTTGCAAGATTGAACT 58.715 29.630 16.61 0.00 35.22 3.01
726 735 2.810274 AGCTGCTTTCTGTGTGTGTATG 59.190 45.455 0.00 0.00 0.00 2.39
727 736 2.549754 GCTGCTTTCTGTGTGTGTATGT 59.450 45.455 0.00 0.00 0.00 2.29
741 750 5.574830 TGTGTGTATGTTTGTTTGCAGAAAC 59.425 36.000 9.83 9.83 41.72 2.78
764 773 1.669211 CGAAGACTCAACGGAGGGTTC 60.669 57.143 0.00 0.00 45.81 3.62
782 791 1.000521 CCCCTTGGAAGCTGATGCA 60.001 57.895 0.00 0.00 42.74 3.96
803 812 5.785423 TGCAGCCAAGATATATACTAAGGGT 59.215 40.000 0.00 0.00 0.00 4.34
890 899 5.263599 AGCAATATGGAATTTGAGGTCACA 58.736 37.500 0.00 0.00 0.00 3.58
944 953 1.729586 TGAGGAGGTACAAGGTTGCT 58.270 50.000 0.00 0.00 0.00 3.91
948 957 3.450904 AGGAGGTACAAGGTTGCTATCA 58.549 45.455 0.00 0.00 0.00 2.15
1067 1079 7.865706 TTTTCTTCCTATGCAGGTTTCTATC 57.134 36.000 0.00 0.00 43.18 2.08
1069 1081 6.166984 TCTTCCTATGCAGGTTTCTATCAG 57.833 41.667 0.00 0.00 43.18 2.90
1091 1104 4.553323 GCTTGTTGCTGATCAATGTTCTT 58.447 39.130 0.00 0.00 36.99 2.52
1092 1105 4.986659 GCTTGTTGCTGATCAATGTTCTTT 59.013 37.500 0.00 0.00 36.99 2.52
1096 1109 5.984926 TGTTGCTGATCAATGTTCTTTTTCC 59.015 36.000 0.00 0.00 36.99 3.13
1101 1114 7.095270 GCTGATCAATGTTCTTTTTCCTGATT 58.905 34.615 0.00 0.00 0.00 2.57
1109 1122 6.449698 TGTTCTTTTTCCTGATTGATCAAGC 58.550 36.000 16.73 16.73 36.18 4.01
1135 1148 5.454877 GGTTCTGATACGAAACGACATACTC 59.545 44.000 0.00 0.00 0.00 2.59
1141 1154 7.891782 TGATACGAAACGACATACTCAAAATC 58.108 34.615 0.00 0.00 0.00 2.17
1187 1200 2.368221 TGGACCAAAATGGCAAAGGAAG 59.632 45.455 0.00 0.00 42.67 3.46
1193 1206 0.319405 AATGGCAAAGGAAGTGCAGC 59.681 50.000 0.00 0.00 44.07 5.25
1208 1221 0.038801 GCAGCCTTCAAACCTTGCTC 60.039 55.000 0.00 0.00 0.00 4.26
1246 1259 1.863454 CAGCCAGACGATGCTTCATAC 59.137 52.381 0.08 0.00 35.12 2.39
1276 1289 1.480789 TCCTGTACATTGCCGCTCTA 58.519 50.000 0.00 0.00 0.00 2.43
1291 1304 2.732597 CGCTCTAGAAACGGTGAAGGAG 60.733 54.545 6.89 0.00 0.00 3.69
1306 1319 3.256281 GGAGACCTCCCTTTGCAAG 57.744 57.895 4.72 0.00 43.94 4.01
1392 1405 1.212935 GCTGGAGGAGGAAAGCCATAA 59.787 52.381 0.00 0.00 36.29 1.90
1396 1409 3.137176 TGGAGGAGGAAAGCCATAATGAG 59.863 47.826 0.00 0.00 36.29 2.90
1444 1457 5.589855 AGATAATTTCATTGCCATCACGTCA 59.410 36.000 0.00 0.00 0.00 4.35
1490 1503 3.618997 GCGAGTGAAATCCAAAGGTAGGA 60.619 47.826 0.00 0.00 39.97 2.94
1583 1596 8.458573 TGATAGTGTTTACAATCAACCAAACT 57.541 30.769 0.00 0.00 33.16 2.66
1595 1608 6.773976 ATCAACCAAACTTTCTGTCAGAAA 57.226 33.333 23.38 23.38 41.51 2.52
1598 1611 5.424121 ACCAAACTTTCTGTCAGAAATCG 57.576 39.130 24.69 17.51 42.66 3.34
1599 1612 4.275936 ACCAAACTTTCTGTCAGAAATCGG 59.724 41.667 24.69 22.06 42.66 4.18
1616 1629 3.150458 TCGGAAGAGACAACACCTCTA 57.850 47.619 0.00 0.00 39.88 2.43
1635 1648 6.169094 CCTCTAGCGACCATCATAATGATTT 58.831 40.000 0.00 0.00 34.28 2.17
1636 1649 6.091849 CCTCTAGCGACCATCATAATGATTTG 59.908 42.308 0.00 0.00 34.28 2.32
1637 1650 6.758254 TCTAGCGACCATCATAATGATTTGA 58.242 36.000 0.00 0.00 34.28 2.69
1671 1684 5.882557 ACAAGAGGGTTATCAAATGTAGCAG 59.117 40.000 0.00 0.00 0.00 4.24
1728 1741 0.179067 AAACGCGGGTTCTGAACTGA 60.179 50.000 18.88 0.00 34.62 3.41
1741 1754 8.375506 GGGTTCTGAACTGAATGGTATATCATA 58.624 37.037 19.05 0.00 0.00 2.15
1780 1794 5.340667 GCTGTATTTTGTTTCAGAAAGCTCG 59.659 40.000 0.00 0.00 0.00 5.03
1781 1795 6.612247 TGTATTTTGTTTCAGAAAGCTCGA 57.388 33.333 0.00 0.00 0.00 4.04
1782 1796 7.022055 TGTATTTTGTTTCAGAAAGCTCGAA 57.978 32.000 0.00 0.00 0.00 3.71
1784 1798 7.643764 TGTATTTTGTTTCAGAAAGCTCGAAAG 59.356 33.333 0.00 0.00 30.29 2.62
1805 1819 1.743252 CCTGGCTTTCTGAGGACGC 60.743 63.158 0.00 0.00 0.00 5.19
1809 1823 0.178068 GGCTTTCTGAGGACGCCATA 59.822 55.000 2.93 0.00 37.87 2.74
1812 1826 0.901827 TTTCTGAGGACGCCATAGCA 59.098 50.000 0.00 0.00 39.83 3.49
1825 1839 0.588252 CATAGCAGCCGGTTATGTGC 59.412 55.000 1.90 5.03 36.32 4.57
1837 1851 4.037021 CGGTTATGTGCACATTAATGCTG 58.963 43.478 35.45 20.71 46.28 4.41
1887 1901 1.552578 ACACTAGGACGTGGTATGCA 58.447 50.000 0.00 0.00 39.19 3.96
1894 1908 3.501349 AGGACGTGGTATGCAGATCTAT 58.499 45.455 0.00 0.00 0.00 1.98
1937 3077 0.737804 ACAAATGTGCTTGCGTGTGA 59.262 45.000 0.00 0.00 0.00 3.58
1939 3079 0.737804 AAATGTGCTTGCGTGTGACA 59.262 45.000 0.00 0.00 0.00 3.58
1943 3083 0.722469 GTGCTTGCGTGTGACAATCG 60.722 55.000 0.00 0.00 0.00 3.34
1958 3103 5.975939 GTGACAATCGTGTACCTTAGTATCC 59.024 44.000 0.00 0.00 38.41 2.59
1965 3110 8.804912 ATCGTGTACCTTAGTATCCCTATAAG 57.195 38.462 0.00 0.00 0.00 1.73
1970 3115 9.139734 TGTACCTTAGTATCCCTATAAGTTGTG 57.860 37.037 0.00 0.00 0.00 3.33
1991 3136 2.007881 TGTTTTTAGACGAAACGCGC 57.992 45.000 5.73 0.00 46.04 6.86
2032 3177 1.579698 CGCCTAGTCTCTACGTAGCA 58.420 55.000 18.00 3.85 0.00 3.49
2054 3199 0.234106 CATTGACATGAGCGATCGCC 59.766 55.000 34.89 25.58 43.17 5.54
2056 3201 2.278857 GACATGAGCGATCGCCGT 60.279 61.111 34.89 25.72 43.17 5.68
2130 3276 7.766738 TCAAATAACGGTTACATCATCAGCTAA 59.233 33.333 2.10 0.00 0.00 3.09
2148 3294 6.151144 TCAGCTAAGAATTTAACAAGGAAGCC 59.849 38.462 0.00 0.00 0.00 4.35
2230 3377 6.002653 TGAGCTACTACATTGGACTCTCTA 57.997 41.667 0.00 0.00 0.00 2.43
2244 3391 6.061441 TGGACTCTCTAAAACAATGCTCAAA 58.939 36.000 0.00 0.00 0.00 2.69
2298 3445 1.452110 CAATCATCCAACACTGGCGA 58.548 50.000 0.00 0.00 43.17 5.54
2465 3720 6.115446 TCAACATTTAGAACTAGATGCCCAG 58.885 40.000 10.79 2.09 32.68 4.45
2493 3748 2.874701 CCGAAGGCCATCTGTTTATCTG 59.125 50.000 5.01 0.00 46.14 2.90
2495 3750 3.941483 CGAAGGCCATCTGTTTATCTGTT 59.059 43.478 5.01 0.00 0.00 3.16
2496 3751 4.201851 CGAAGGCCATCTGTTTATCTGTTG 60.202 45.833 5.01 0.00 0.00 3.33
2497 3752 3.624777 AGGCCATCTGTTTATCTGTTGG 58.375 45.455 5.01 0.00 37.68 3.77
2498 3753 3.266772 AGGCCATCTGTTTATCTGTTGGA 59.733 43.478 5.01 0.00 37.16 3.53
2499 3754 4.016444 GGCCATCTGTTTATCTGTTGGAA 58.984 43.478 0.00 0.00 37.16 3.53
2500 3755 4.142381 GGCCATCTGTTTATCTGTTGGAAC 60.142 45.833 0.00 0.00 37.16 3.62
2501 3756 4.702131 GCCATCTGTTTATCTGTTGGAACT 59.298 41.667 0.00 0.00 37.16 3.01
2502 3757 5.163713 GCCATCTGTTTATCTGTTGGAACTC 60.164 44.000 0.00 0.00 37.16 3.01
2503 3758 6.176183 CCATCTGTTTATCTGTTGGAACTCT 58.824 40.000 0.00 0.00 37.16 3.24
2504 3759 6.656693 CCATCTGTTTATCTGTTGGAACTCTT 59.343 38.462 0.00 0.00 37.16 2.85
2505 3760 7.175641 CCATCTGTTTATCTGTTGGAACTCTTT 59.824 37.037 0.00 0.00 37.16 2.52
2506 3761 8.571336 CATCTGTTTATCTGTTGGAACTCTTTT 58.429 33.333 0.00 0.00 0.00 2.27
2507 3762 8.519799 TCTGTTTATCTGTTGGAACTCTTTTT 57.480 30.769 0.00 0.00 0.00 1.94
2552 3807 9.842775 AGAGTTGCTATATTCATTGATCAAAGA 57.157 29.630 13.09 11.02 0.00 2.52
2554 3809 9.842775 AGTTGCTATATTCATTGATCAAAGAGA 57.157 29.630 13.09 8.26 0.00 3.10
2576 3831 1.334160 TGGTACAAAGAGACCGCTCA 58.666 50.000 0.00 0.00 38.64 4.26
2577 3832 1.272490 TGGTACAAAGAGACCGCTCAG 59.728 52.381 0.00 0.00 38.64 3.35
2578 3833 1.272769 GGTACAAAGAGACCGCTCAGT 59.727 52.381 0.00 0.00 43.81 3.41
2579 3834 2.288886 GGTACAAAGAGACCGCTCAGTT 60.289 50.000 0.00 0.00 43.81 3.16
2580 3835 3.057033 GGTACAAAGAGACCGCTCAGTTA 60.057 47.826 0.00 0.00 43.81 2.24
2581 3836 3.746045 ACAAAGAGACCGCTCAGTTAA 57.254 42.857 0.00 0.00 43.81 2.01
2582 3837 4.273148 ACAAAGAGACCGCTCAGTTAAT 57.727 40.909 0.00 0.00 43.81 1.40
2583 3838 4.642429 ACAAAGAGACCGCTCAGTTAATT 58.358 39.130 0.00 0.00 43.81 1.40
2584 3839 5.790593 ACAAAGAGACCGCTCAGTTAATTA 58.209 37.500 0.00 0.00 43.81 1.40
2585 3840 6.228258 ACAAAGAGACCGCTCAGTTAATTAA 58.772 36.000 0.00 0.00 43.81 1.40
2586 3841 6.708949 ACAAAGAGACCGCTCAGTTAATTAAA 59.291 34.615 0.00 0.00 43.81 1.52
2587 3842 7.227910 ACAAAGAGACCGCTCAGTTAATTAAAA 59.772 33.333 0.00 0.00 43.81 1.52
2588 3843 6.969828 AGAGACCGCTCAGTTAATTAAAAG 57.030 37.500 0.00 0.00 43.81 2.27
2589 3844 6.698380 AGAGACCGCTCAGTTAATTAAAAGA 58.302 36.000 0.00 0.49 43.81 2.52
2590 3845 7.159372 AGAGACCGCTCAGTTAATTAAAAGAA 58.841 34.615 0.00 0.00 43.81 2.52
2591 3846 7.660208 AGAGACCGCTCAGTTAATTAAAAGAAA 59.340 33.333 0.00 0.00 43.81 2.52
2592 3847 8.161699 AGACCGCTCAGTTAATTAAAAGAAAA 57.838 30.769 0.00 0.00 0.00 2.29
2593 3848 8.074370 AGACCGCTCAGTTAATTAAAAGAAAAC 58.926 33.333 0.00 0.00 0.00 2.43
2594 3849 7.143340 ACCGCTCAGTTAATTAAAAGAAAACC 58.857 34.615 0.00 0.00 0.00 3.27
2595 3850 6.304683 CCGCTCAGTTAATTAAAAGAAAACCG 59.695 38.462 0.00 2.69 0.00 4.44
2596 3851 7.073265 CGCTCAGTTAATTAAAAGAAAACCGA 58.927 34.615 0.00 0.00 0.00 4.69
2597 3852 7.268447 CGCTCAGTTAATTAAAAGAAAACCGAG 59.732 37.037 0.00 0.00 31.03 4.63
2598 3853 7.060748 GCTCAGTTAATTAAAAGAAAACCGAGC 59.939 37.037 0.00 3.79 40.99 5.03
2599 3854 8.161699 TCAGTTAATTAAAAGAAAACCGAGCT 57.838 30.769 0.00 0.00 0.00 4.09
2600 3855 9.275398 TCAGTTAATTAAAAGAAAACCGAGCTA 57.725 29.630 0.00 0.00 0.00 3.32
2601 3856 9.887406 CAGTTAATTAAAAGAAAACCGAGCTAA 57.113 29.630 0.00 0.00 0.00 3.09
2605 3860 8.583810 AATTAAAAGAAAACCGAGCTAAAACC 57.416 30.769 0.00 0.00 0.00 3.27
2606 3861 4.579454 AAAGAAAACCGAGCTAAAACCC 57.421 40.909 0.00 0.00 0.00 4.11
2607 3862 3.503800 AGAAAACCGAGCTAAAACCCT 57.496 42.857 0.00 0.00 0.00 4.34
2608 3863 4.628963 AGAAAACCGAGCTAAAACCCTA 57.371 40.909 0.00 0.00 0.00 3.53
2609 3864 4.976864 AGAAAACCGAGCTAAAACCCTAA 58.023 39.130 0.00 0.00 0.00 2.69
2610 3865 5.567430 AGAAAACCGAGCTAAAACCCTAAT 58.433 37.500 0.00 0.00 0.00 1.73
2611 3866 6.714278 AGAAAACCGAGCTAAAACCCTAATA 58.286 36.000 0.00 0.00 0.00 0.98
2612 3867 7.170277 AGAAAACCGAGCTAAAACCCTAATAA 58.830 34.615 0.00 0.00 0.00 1.40
2613 3868 7.666804 AGAAAACCGAGCTAAAACCCTAATAAA 59.333 33.333 0.00 0.00 0.00 1.40
2614 3869 6.748333 AACCGAGCTAAAACCCTAATAAAC 57.252 37.500 0.00 0.00 0.00 2.01
2615 3870 4.872124 ACCGAGCTAAAACCCTAATAAACG 59.128 41.667 0.00 0.00 0.00 3.60
2616 3871 4.271776 CCGAGCTAAAACCCTAATAAACGG 59.728 45.833 0.00 0.00 0.00 4.44
2617 3872 4.271776 CGAGCTAAAACCCTAATAAACGGG 59.728 45.833 0.00 0.00 46.26 5.28
2618 3873 3.949754 AGCTAAAACCCTAATAAACGGGC 59.050 43.478 0.00 0.00 44.63 6.13
2619 3874 3.695556 GCTAAAACCCTAATAAACGGGCA 59.304 43.478 0.00 0.00 44.63 5.36
2620 3875 4.158209 GCTAAAACCCTAATAAACGGGCAA 59.842 41.667 0.00 0.00 44.63 4.52
2621 3876 5.336610 GCTAAAACCCTAATAAACGGGCAAA 60.337 40.000 0.00 0.00 44.63 3.68
2622 3877 5.548181 AAAACCCTAATAAACGGGCAAAA 57.452 34.783 0.00 0.00 44.63 2.44
2623 3878 4.524316 AACCCTAATAAACGGGCAAAAC 57.476 40.909 0.00 0.00 44.63 2.43
2624 3879 2.488937 ACCCTAATAAACGGGCAAAACG 59.511 45.455 0.00 0.00 44.63 3.60
2625 3880 2.521996 CCTAATAAACGGGCAAAACGC 58.478 47.619 0.00 0.00 41.28 4.84
2626 3881 2.162809 CCTAATAAACGGGCAAAACGCT 59.837 45.455 0.00 0.00 41.91 5.07
2627 3882 3.374678 CCTAATAAACGGGCAAAACGCTA 59.625 43.478 0.00 0.00 41.91 4.26
2628 3883 3.481112 AATAAACGGGCAAAACGCTAG 57.519 42.857 0.00 0.00 41.91 3.42
2629 3884 0.518195 TAAACGGGCAAAACGCTAGC 59.482 50.000 4.06 4.06 41.91 3.42
2630 3885 1.170290 AAACGGGCAAAACGCTAGCT 61.170 50.000 13.93 0.00 41.91 3.32
2631 3886 0.320946 AACGGGCAAAACGCTAGCTA 60.321 50.000 13.93 0.00 41.91 3.32
2632 3887 0.320946 ACGGGCAAAACGCTAGCTAA 60.321 50.000 13.93 0.00 41.91 3.09
2633 3888 0.800012 CGGGCAAAACGCTAGCTAAA 59.200 50.000 13.93 0.00 41.91 1.85
2634 3889 1.465187 CGGGCAAAACGCTAGCTAAAC 60.465 52.381 13.93 0.00 41.91 2.01
2635 3890 1.810755 GGGCAAAACGCTAGCTAAACT 59.189 47.619 13.93 0.00 41.91 2.66
2636 3891 3.004862 GGGCAAAACGCTAGCTAAACTA 58.995 45.455 13.93 0.00 41.91 2.24
2647 3902 5.584253 CTAGCTAAACTAGGTCAAGAGCA 57.416 43.478 0.00 0.00 44.14 4.26
2648 3903 4.195225 AGCTAAACTAGGTCAAGAGCAC 57.805 45.455 1.84 0.00 0.00 4.40
2649 3904 3.055747 AGCTAAACTAGGTCAAGAGCACC 60.056 47.826 1.84 0.00 0.00 5.01
2650 3905 3.306780 GCTAAACTAGGTCAAGAGCACCA 60.307 47.826 1.84 0.00 36.23 4.17
2651 3906 2.841442 AACTAGGTCAAGAGCACCAC 57.159 50.000 1.84 0.00 36.23 4.16
2652 3907 1.717032 ACTAGGTCAAGAGCACCACA 58.283 50.000 1.84 0.00 36.23 4.17
2653 3908 2.047061 ACTAGGTCAAGAGCACCACAA 58.953 47.619 1.84 0.00 36.23 3.33
2654 3909 2.438021 ACTAGGTCAAGAGCACCACAAA 59.562 45.455 1.84 0.00 36.23 2.83
2655 3910 2.664402 AGGTCAAGAGCACCACAAAT 57.336 45.000 1.84 0.00 36.23 2.32
2656 3911 2.508526 AGGTCAAGAGCACCACAAATC 58.491 47.619 1.84 0.00 36.23 2.17
2657 3912 1.197721 GGTCAAGAGCACCACAAATCG 59.802 52.381 0.00 0.00 33.63 3.34
2658 3913 0.874390 TCAAGAGCACCACAAATCGC 59.126 50.000 0.00 0.00 0.00 4.58
2659 3914 0.592637 CAAGAGCACCACAAATCGCA 59.407 50.000 0.00 0.00 0.00 5.10
2660 3915 1.001487 CAAGAGCACCACAAATCGCAA 60.001 47.619 0.00 0.00 0.00 4.85
2661 3916 0.593128 AGAGCACCACAAATCGCAAC 59.407 50.000 0.00 0.00 0.00 4.17
2662 3917 0.387239 GAGCACCACAAATCGCAACC 60.387 55.000 0.00 0.00 0.00 3.77
2663 3918 1.106351 AGCACCACAAATCGCAACCA 61.106 50.000 0.00 0.00 0.00 3.67
2664 3919 0.939106 GCACCACAAATCGCAACCAC 60.939 55.000 0.00 0.00 0.00 4.16
2665 3920 0.318614 CACCACAAATCGCAACCACC 60.319 55.000 0.00 0.00 0.00 4.61
2666 3921 1.081509 CCACAAATCGCAACCACCG 60.082 57.895 0.00 0.00 0.00 4.94
2667 3922 1.081509 CACAAATCGCAACCACCGG 60.082 57.895 0.00 0.00 0.00 5.28
2668 3923 2.126502 CAAATCGCAACCACCGGC 60.127 61.111 0.00 0.00 0.00 6.13
2669 3924 3.370231 AAATCGCAACCACCGGCC 61.370 61.111 0.00 0.00 0.00 6.13
2670 3925 4.652131 AATCGCAACCACCGGCCA 62.652 61.111 0.00 0.00 0.00 5.36
2674 3929 4.947147 GCAACCACCGGCCAGTGA 62.947 66.667 21.10 0.00 40.34 3.41
2675 3930 2.978010 CAACCACCGGCCAGTGAC 60.978 66.667 21.10 0.00 40.34 3.67
2676 3931 3.484806 AACCACCGGCCAGTGACA 61.485 61.111 21.10 0.00 40.34 3.58
2677 3932 3.050354 AACCACCGGCCAGTGACAA 62.050 57.895 21.10 0.00 40.34 3.18
2678 3933 2.669569 CCACCGGCCAGTGACAAG 60.670 66.667 21.10 0.00 40.34 3.16
2679 3934 3.357079 CACCGGCCAGTGACAAGC 61.357 66.667 14.31 0.00 40.34 4.01
2680 3935 3.560251 ACCGGCCAGTGACAAGCT 61.560 61.111 0.00 0.00 0.00 3.74
2681 3936 2.214216 ACCGGCCAGTGACAAGCTA 61.214 57.895 0.00 0.00 0.00 3.32
2682 3937 1.741770 CCGGCCAGTGACAAGCTAC 60.742 63.158 2.24 0.00 0.00 3.58
2683 3938 1.005037 CGGCCAGTGACAAGCTACA 60.005 57.895 2.24 0.00 0.00 2.74
2684 3939 0.602638 CGGCCAGTGACAAGCTACAA 60.603 55.000 2.24 0.00 0.00 2.41
2685 3940 1.160137 GGCCAGTGACAAGCTACAAG 58.840 55.000 0.00 0.00 0.00 3.16
2686 3941 0.519077 GCCAGTGACAAGCTACAAGC 59.481 55.000 0.00 0.00 42.84 4.01
2687 3942 1.882912 CCAGTGACAAGCTACAAGCA 58.117 50.000 1.22 0.00 45.56 3.91
2688 3943 2.221169 CCAGTGACAAGCTACAAGCAA 58.779 47.619 1.22 0.00 45.56 3.91
2689 3944 2.031682 CCAGTGACAAGCTACAAGCAAC 60.032 50.000 1.22 0.00 45.56 4.17
2690 3945 2.874701 CAGTGACAAGCTACAAGCAACT 59.125 45.455 1.22 0.00 45.56 3.16
2691 3946 3.059325 CAGTGACAAGCTACAAGCAACTC 60.059 47.826 1.22 0.00 45.56 3.01
2692 3947 3.134458 GTGACAAGCTACAAGCAACTCT 58.866 45.455 1.22 0.00 45.56 3.24
2693 3948 3.185391 GTGACAAGCTACAAGCAACTCTC 59.815 47.826 1.22 0.00 45.56 3.20
2694 3949 2.739379 GACAAGCTACAAGCAACTCTCC 59.261 50.000 1.22 0.00 45.56 3.71
2695 3950 2.079925 CAAGCTACAAGCAACTCTCCC 58.920 52.381 1.22 0.00 45.56 4.30
2696 3951 0.247736 AGCTACAAGCAACTCTCCCG 59.752 55.000 1.22 0.00 45.56 5.14
2697 3952 0.246635 GCTACAAGCAACTCTCCCGA 59.753 55.000 0.00 0.00 41.89 5.14
2698 3953 1.997669 CTACAAGCAACTCTCCCGAC 58.002 55.000 0.00 0.00 0.00 4.79
2699 3954 1.272490 CTACAAGCAACTCTCCCGACA 59.728 52.381 0.00 0.00 0.00 4.35
2700 3955 0.468226 ACAAGCAACTCTCCCGACAA 59.532 50.000 0.00 0.00 0.00 3.18
2701 3956 0.868406 CAAGCAACTCTCCCGACAAC 59.132 55.000 0.00 0.00 0.00 3.32
2702 3957 0.250338 AAGCAACTCTCCCGACAACC 60.250 55.000 0.00 0.00 0.00 3.77
2703 3958 1.070786 GCAACTCTCCCGACAACCA 59.929 57.895 0.00 0.00 0.00 3.67
2704 3959 1.228657 GCAACTCTCCCGACAACCAC 61.229 60.000 0.00 0.00 0.00 4.16
2705 3960 0.105964 CAACTCTCCCGACAACCACA 59.894 55.000 0.00 0.00 0.00 4.17
2706 3961 0.106149 AACTCTCCCGACAACCACAC 59.894 55.000 0.00 0.00 0.00 3.82
2707 3962 1.372997 CTCTCCCGACAACCACACG 60.373 63.158 0.00 0.00 0.00 4.49
2708 3963 1.802337 CTCTCCCGACAACCACACGA 61.802 60.000 0.00 0.00 0.00 4.35
2709 3964 1.068417 CTCCCGACAACCACACGAA 59.932 57.895 0.00 0.00 0.00 3.85
2710 3965 1.219522 CTCCCGACAACCACACGAAC 61.220 60.000 0.00 0.00 0.00 3.95
2711 3966 2.248835 CCCGACAACCACACGAACC 61.249 63.158 0.00 0.00 0.00 3.62
2712 3967 2.248835 CCGACAACCACACGAACCC 61.249 63.158 0.00 0.00 0.00 4.11
2713 3968 1.521906 CGACAACCACACGAACCCA 60.522 57.895 0.00 0.00 0.00 4.51
2714 3969 1.090625 CGACAACCACACGAACCCAA 61.091 55.000 0.00 0.00 0.00 4.12
2715 3970 0.661020 GACAACCACACGAACCCAAG 59.339 55.000 0.00 0.00 0.00 3.61
2716 3971 1.358759 CAACCACACGAACCCAAGC 59.641 57.895 0.00 0.00 0.00 4.01
2717 3972 1.101049 CAACCACACGAACCCAAGCT 61.101 55.000 0.00 0.00 0.00 3.74
2718 3973 0.818040 AACCACACGAACCCAAGCTC 60.818 55.000 0.00 0.00 0.00 4.09
2719 3974 1.966451 CCACACGAACCCAAGCTCC 60.966 63.158 0.00 0.00 0.00 4.70
2720 3975 1.227823 CACACGAACCCAAGCTCCA 60.228 57.895 0.00 0.00 0.00 3.86
2721 3976 1.227853 ACACGAACCCAAGCTCCAC 60.228 57.895 0.00 0.00 0.00 4.02
2722 3977 1.966451 CACGAACCCAAGCTCCACC 60.966 63.158 0.00 0.00 0.00 4.61
2723 3978 2.742372 CGAACCCAAGCTCCACCG 60.742 66.667 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.457466 TGCACTGATCTGCACATAATGAT 58.543 39.130 5.58 0.00 42.36 2.45
29 30 2.026915 ACCTTGCACTGATCTGCACATA 60.027 45.455 9.01 0.00 46.90 2.29
30 31 1.271762 ACCTTGCACTGATCTGCACAT 60.272 47.619 9.01 0.00 46.90 3.21
50 51 5.569355 TGTTTTCTATTGCTCCTTCCATCA 58.431 37.500 0.00 0.00 0.00 3.07
66 67 6.751888 GCTTCGTATTTGGCAATATGTTTTCT 59.248 34.615 0.00 0.00 34.56 2.52
87 88 3.270877 CCACTTACACCACCTATGCTTC 58.729 50.000 0.00 0.00 0.00 3.86
90 91 1.339631 TGCCACTTACACCACCTATGC 60.340 52.381 0.00 0.00 0.00 3.14
102 103 3.278574 GCACCTCAATACATGCCACTTA 58.721 45.455 0.00 0.00 31.71 2.24
120 121 0.386478 CAAGCTTCTCCTTTGCGCAC 60.386 55.000 11.12 0.00 0.00 5.34
123 124 1.211190 GCCAAGCTTCTCCTTTGCG 59.789 57.895 0.00 0.00 0.00 4.85
145 146 6.341316 TGAATCCACTCTTCTTGCTGTATAC 58.659 40.000 0.00 0.00 0.00 1.47
151 152 4.464008 TGTTTGAATCCACTCTTCTTGCT 58.536 39.130 0.00 0.00 0.00 3.91
206 207 5.242393 CACTTTCCCTCAAATTCTGTGACAT 59.758 40.000 0.00 0.00 0.00 3.06
213 214 2.110721 AGCCCACTTTCCCTCAAATTCT 59.889 45.455 0.00 0.00 0.00 2.40
339 340 2.611971 GCGTTGAGTACTTGTCATCCCA 60.612 50.000 0.00 0.00 0.00 4.37
379 380 3.859961 CGAGGTATGTACTGTTTCAGCAG 59.140 47.826 0.00 0.00 41.92 4.24
432 433 4.091509 CGTGATTGGAGTAGCTTGTTGTAC 59.908 45.833 0.00 0.00 0.00 2.90
445 446 0.460109 TCCGATGTGCGTGATTGGAG 60.460 55.000 0.00 0.00 38.67 3.86
460 461 3.473647 CTGCCTGCCCTCATCCGA 61.474 66.667 0.00 0.00 0.00 4.55
483 484 3.128242 GGCTTCTCACCATCTTTGTCATG 59.872 47.826 0.00 0.00 0.00 3.07
564 573 7.717436 TGCATTTCGGGTTTGTATATCTTATGA 59.283 33.333 0.00 0.00 0.00 2.15
582 591 3.127548 AGCTACAGGTTTGATGCATTTCG 59.872 43.478 0.00 0.00 0.00 3.46
592 601 6.801539 TGAACAATCTAAGCTACAGGTTTG 57.198 37.500 0.00 0.00 37.00 2.93
665 674 9.486497 TTCAATCTTGCAACAAATTTTATGCTA 57.514 25.926 19.98 14.17 39.49 3.49
672 681 8.947055 ACTAAGTTCAATCTTGCAACAAATTT 57.053 26.923 0.00 0.00 0.00 1.82
684 693 9.050601 GCAGCTTGATTATACTAAGTTCAATCT 57.949 33.333 0.00 0.00 0.00 2.40
686 695 8.970859 AGCAGCTTGATTATACTAAGTTCAAT 57.029 30.769 0.00 0.00 0.00 2.57
693 702 7.824289 ACACAGAAAGCAGCTTGATTATACTAA 59.176 33.333 8.88 0.00 0.00 2.24
706 715 2.549754 ACATACACACACAGAAAGCAGC 59.450 45.455 0.00 0.00 0.00 5.25
709 718 4.920376 ACAAACATACACACACAGAAAGC 58.080 39.130 0.00 0.00 0.00 3.51
726 735 2.776330 TCGACGTTTCTGCAAACAAAC 58.224 42.857 2.41 4.27 41.94 2.93
727 736 3.125487 TCTTCGACGTTTCTGCAAACAAA 59.875 39.130 2.41 0.00 41.94 2.83
764 773 1.000521 TGCATCAGCTTCCAAGGGG 60.001 57.895 0.00 0.00 42.74 4.79
782 791 6.787957 ACACACCCTTAGTATATATCTTGGCT 59.212 38.462 0.00 0.00 0.00 4.75
803 812 7.231317 AGCTCCTCTTCAAATTTAATGAACACA 59.769 33.333 0.00 0.00 33.47 3.72
890 899 3.069946 TAATCCGGTCGGGCACGT 61.070 61.111 8.89 0.00 41.85 4.49
944 953 5.955961 TGAAATCACCACCATCTCTGATA 57.044 39.130 0.00 0.00 0.00 2.15
948 957 5.664908 AGTCTATGAAATCACCACCATCTCT 59.335 40.000 0.00 0.00 0.00 3.10
1055 1067 3.671702 GCAACAAGCTGATAGAAACCTGC 60.672 47.826 0.00 0.00 41.15 4.85
1056 1068 4.088823 GCAACAAGCTGATAGAAACCTG 57.911 45.455 0.00 0.00 41.15 4.00
1069 1081 4.170292 AGAACATTGATCAGCAACAAGC 57.830 40.909 0.00 0.00 39.78 4.01
1096 1109 4.259356 TCAGAACCTGCTTGATCAATCAG 58.741 43.478 25.61 25.61 38.19 2.90
1101 1114 3.447229 TCGTATCAGAACCTGCTTGATCA 59.553 43.478 0.00 0.00 0.00 2.92
1109 1122 3.571571 TGTCGTTTCGTATCAGAACCTG 58.428 45.455 0.00 0.00 0.00 4.00
1135 1148 4.630069 ACGATGTTCTTACTCGGGATTTTG 59.370 41.667 0.00 0.00 36.74 2.44
1141 1154 2.933495 TCACGATGTTCTTACTCGGG 57.067 50.000 0.00 0.00 37.16 5.14
1187 1200 0.598419 GCAAGGTTTGAAGGCTGCAC 60.598 55.000 0.00 0.00 0.00 4.57
1193 1206 0.600057 GGCAGAGCAAGGTTTGAAGG 59.400 55.000 0.00 0.00 0.00 3.46
1224 1237 0.321346 TGAAGCATCGTCTGGCTGAA 59.679 50.000 0.00 0.00 40.93 3.02
1246 1259 4.792704 GCAATGTACAGGATATTTTGCCGG 60.793 45.833 14.35 0.00 33.64 6.13
1276 1289 1.619332 GAGGTCTCCTTCACCGTTTCT 59.381 52.381 0.00 0.00 39.13 2.52
1302 1315 0.389426 CTTGTCAAGCATGCCCTTGC 60.389 55.000 15.66 10.00 41.47 4.01
1303 1316 1.068055 GTCTTGTCAAGCATGCCCTTG 60.068 52.381 15.66 13.66 42.73 3.61
1304 1317 1.251251 GTCTTGTCAAGCATGCCCTT 58.749 50.000 15.66 0.00 0.00 3.95
1305 1318 0.111061 TGTCTTGTCAAGCATGCCCT 59.889 50.000 15.66 0.00 0.00 5.19
1306 1319 0.242017 GTGTCTTGTCAAGCATGCCC 59.758 55.000 15.66 0.30 0.00 5.36
1307 1320 1.242076 AGTGTCTTGTCAAGCATGCC 58.758 50.000 15.66 0.00 0.00 4.40
1308 1321 4.488126 TTTAGTGTCTTGTCAAGCATGC 57.512 40.909 10.51 10.51 0.00 4.06
1392 1405 2.990479 GTCCTTCACCCGGCTCAT 59.010 61.111 0.00 0.00 0.00 2.90
1412 1425 5.127356 TGGCAATGAAATTATCTGCATCACA 59.873 36.000 0.00 0.00 32.46 3.58
1444 1457 1.651240 GCGGATGCAACTGCTCACAT 61.651 55.000 19.65 0.00 42.66 3.21
1583 1596 5.221441 TGTCTCTTCCGATTTCTGACAGAAA 60.221 40.000 28.10 28.10 46.89 2.52
1595 1608 2.530701 AGAGGTGTTGTCTCTTCCGAT 58.469 47.619 0.00 0.00 38.32 4.18
1598 1611 2.416162 CGCTAGAGGTGTTGTCTCTTCC 60.416 54.545 0.00 0.00 41.37 3.46
1599 1612 2.488545 TCGCTAGAGGTGTTGTCTCTTC 59.511 50.000 0.00 0.00 41.37 2.87
1616 1629 7.281774 GGATATCAAATCATTATGATGGTCGCT 59.718 37.037 8.60 0.00 37.15 4.93
1635 1648 7.888514 ATAACCCTCTTGTATTGGGATATCA 57.111 36.000 4.83 0.00 43.47 2.15
1636 1649 7.918076 TGATAACCCTCTTGTATTGGGATATC 58.082 38.462 15.94 15.94 46.82 1.63
1637 1650 7.888514 TGATAACCCTCTTGTATTGGGATAT 57.111 36.000 4.11 2.19 43.47 1.63
1671 1684 7.235812 ACCTATTATGACCTTCTCCCTTACATC 59.764 40.741 0.00 0.00 0.00 3.06
1741 1754 7.067008 ACAAAATACAGCTTTCTAATACGCCAT 59.933 33.333 0.00 0.00 0.00 4.40
1784 1798 0.392327 GTCCTCAGAAAGCCAGGAGC 60.392 60.000 0.00 0.00 36.98 4.70
1785 1799 0.108424 CGTCCTCAGAAAGCCAGGAG 60.108 60.000 0.00 0.00 36.98 3.69
1786 1800 1.975327 CGTCCTCAGAAAGCCAGGA 59.025 57.895 0.00 0.00 33.68 3.86
1787 1801 1.743252 GCGTCCTCAGAAAGCCAGG 60.743 63.158 0.00 0.00 0.00 4.45
1788 1802 1.743252 GGCGTCCTCAGAAAGCCAG 60.743 63.158 0.00 0.00 43.73 4.85
1789 1803 2.347490 GGCGTCCTCAGAAAGCCA 59.653 61.111 0.00 0.00 43.73 4.75
1790 1804 0.178068 TATGGCGTCCTCAGAAAGCC 59.822 55.000 0.00 0.00 44.24 4.35
1791 1805 1.576356 CTATGGCGTCCTCAGAAAGC 58.424 55.000 0.00 0.00 0.00 3.51
1805 1819 1.229428 CACATAACCGGCTGCTATGG 58.771 55.000 0.00 7.75 0.00 2.74
1809 1823 2.040544 GTGCACATAACCGGCTGCT 61.041 57.895 13.17 0.00 0.00 4.24
1812 1826 2.411628 TAATGTGCACATAACCGGCT 57.588 45.000 31.55 16.92 35.10 5.52
1825 1839 8.446273 GCCTGAATATAGTACAGCATTAATGTG 58.554 37.037 16.61 14.65 32.02 3.21
1837 1851 6.163135 AGACAAGGTGCCTGAATATAGTAC 57.837 41.667 0.00 0.00 0.00 2.73
1916 1930 1.255859 CACACGCAAGCACATTTGTTG 59.744 47.619 0.00 0.00 45.62 3.33
1937 3077 5.206587 AGGGATACTAAGGTACACGATTGT 58.793 41.667 0.00 0.00 40.02 2.71
1939 3079 9.240734 CTTATAGGGATACTAAGGTACACGATT 57.759 37.037 0.00 0.00 34.79 3.34
1943 3083 9.140874 ACAACTTATAGGGATACTAAGGTACAC 57.859 37.037 0.00 0.00 34.79 2.90
1958 3103 9.146984 TCGTCTAAAAACATCACAACTTATAGG 57.853 33.333 0.00 0.00 0.00 2.57
1965 3110 5.108891 GCGTTTCGTCTAAAAACATCACAAC 60.109 40.000 0.00 0.00 36.60 3.32
1970 3115 2.582519 GCGCGTTTCGTCTAAAAACATC 59.417 45.455 8.43 0.00 41.07 3.06
1990 3135 2.447244 ATCTAAGTAGGCATGCTCGC 57.553 50.000 18.92 7.69 0.00 5.03
1991 3136 3.321497 GGAATCTAAGTAGGCATGCTCG 58.679 50.000 18.92 0.00 0.00 5.03
2032 3177 1.590932 GATCGCTCATGTCAATGCCT 58.409 50.000 0.00 0.00 33.47 4.75
2054 3199 1.299541 AGAGTTCCAACACTTGCACG 58.700 50.000 0.00 0.00 0.00 5.34
2056 3201 6.463995 AAAAATAGAGTTCCAACACTTGCA 57.536 33.333 0.00 0.00 32.16 4.08
2130 3276 4.998051 TCCTGGCTTCCTTGTTAAATTCT 58.002 39.130 0.00 0.00 0.00 2.40
2162 3308 0.841289 AACGACCCTTCTGTTTGGGA 59.159 50.000 4.93 0.00 46.15 4.37
2219 3365 5.620206 TGAGCATTGTTTTAGAGAGTCCAA 58.380 37.500 0.00 0.00 0.00 3.53
2230 3377 7.226523 GGAAAGGTTACATTTGAGCATTGTTTT 59.773 33.333 0.00 0.00 0.00 2.43
2244 3391 6.723298 TGTGTGATTTTGGAAAGGTTACAT 57.277 33.333 0.00 0.00 0.00 2.29
2298 3445 1.893808 GGCCATTCGATGACGGCAT 60.894 57.895 1.48 1.48 40.21 4.40
2385 3640 6.939132 CTTGTGGAGCAATTATCAGAGATT 57.061 37.500 0.00 0.00 36.36 2.40
2465 3720 1.069935 GATGGCCTTCGGTCCTAGC 59.930 63.158 3.32 0.00 0.00 3.42
2526 3781 9.842775 TCTTTGATCAATGAATATAGCAACTCT 57.157 29.630 18.79 0.00 0.00 3.24
2528 3783 9.842775 TCTCTTTGATCAATGAATATAGCAACT 57.157 29.630 20.72 0.00 0.00 3.16
2537 3792 9.246670 TGTACCATTTCTCTTTGATCAATGAAT 57.753 29.630 20.72 11.58 29.01 2.57
2538 3793 8.634335 TGTACCATTTCTCTTTGATCAATGAA 57.366 30.769 20.72 16.20 29.01 2.57
2539 3794 8.634335 TTGTACCATTTCTCTTTGATCAATGA 57.366 30.769 19.59 19.59 29.01 2.57
2540 3795 9.350357 CTTTGTACCATTTCTCTTTGATCAATG 57.650 33.333 9.40 11.92 0.00 2.82
2541 3796 9.300681 TCTTTGTACCATTTCTCTTTGATCAAT 57.699 29.630 9.40 0.00 0.00 2.57
2542 3797 8.690203 TCTTTGTACCATTTCTCTTTGATCAA 57.310 30.769 3.38 3.38 0.00 2.57
2543 3798 8.156820 TCTCTTTGTACCATTTCTCTTTGATCA 58.843 33.333 0.00 0.00 0.00 2.92
2544 3799 8.447053 GTCTCTTTGTACCATTTCTCTTTGATC 58.553 37.037 0.00 0.00 0.00 2.92
2545 3800 7.391833 GGTCTCTTTGTACCATTTCTCTTTGAT 59.608 37.037 0.00 0.00 35.73 2.57
2546 3801 6.710744 GGTCTCTTTGTACCATTTCTCTTTGA 59.289 38.462 0.00 0.00 35.73 2.69
2547 3802 6.347725 CGGTCTCTTTGTACCATTTCTCTTTG 60.348 42.308 0.00 0.00 35.35 2.77
2548 3803 5.701290 CGGTCTCTTTGTACCATTTCTCTTT 59.299 40.000 0.00 0.00 35.35 2.52
2549 3804 5.238583 CGGTCTCTTTGTACCATTTCTCTT 58.761 41.667 0.00 0.00 35.35 2.85
2550 3805 4.822026 CGGTCTCTTTGTACCATTTCTCT 58.178 43.478 0.00 0.00 35.35 3.10
2551 3806 3.371285 GCGGTCTCTTTGTACCATTTCTC 59.629 47.826 0.00 0.00 35.35 2.87
2552 3807 3.008049 AGCGGTCTCTTTGTACCATTTCT 59.992 43.478 0.00 0.00 35.35 2.52
2553 3808 3.335579 AGCGGTCTCTTTGTACCATTTC 58.664 45.455 0.00 0.00 35.35 2.17
2554 3809 3.244422 TGAGCGGTCTCTTTGTACCATTT 60.244 43.478 16.64 0.00 40.03 2.32
2555 3810 2.301870 TGAGCGGTCTCTTTGTACCATT 59.698 45.455 16.64 0.00 40.03 3.16
2556 3811 1.899814 TGAGCGGTCTCTTTGTACCAT 59.100 47.619 16.64 0.00 40.03 3.55
2557 3812 1.272490 CTGAGCGGTCTCTTTGTACCA 59.728 52.381 16.64 0.00 40.03 3.25
2558 3813 1.272769 ACTGAGCGGTCTCTTTGTACC 59.727 52.381 16.64 0.00 40.03 3.34
2559 3814 2.726832 ACTGAGCGGTCTCTTTGTAC 57.273 50.000 16.64 0.00 40.03 2.90
2560 3815 4.859304 TTAACTGAGCGGTCTCTTTGTA 57.141 40.909 16.64 0.00 40.03 2.41
2561 3816 3.746045 TTAACTGAGCGGTCTCTTTGT 57.254 42.857 16.64 4.34 40.03 2.83
2562 3817 6.721571 TTAATTAACTGAGCGGTCTCTTTG 57.278 37.500 16.64 3.74 40.03 2.77
2563 3818 7.660208 TCTTTTAATTAACTGAGCGGTCTCTTT 59.340 33.333 16.64 8.44 40.03 2.52
2564 3819 7.159372 TCTTTTAATTAACTGAGCGGTCTCTT 58.841 34.615 16.64 9.10 40.03 2.85
2565 3820 6.698380 TCTTTTAATTAACTGAGCGGTCTCT 58.302 36.000 16.64 2.68 40.03 3.10
2566 3821 6.963049 TCTTTTAATTAACTGAGCGGTCTC 57.037 37.500 16.64 0.00 39.78 3.36
2567 3822 7.739498 TTTCTTTTAATTAACTGAGCGGTCT 57.261 32.000 16.64 0.00 0.00 3.85
2568 3823 7.325338 GGTTTTCTTTTAATTAACTGAGCGGTC 59.675 37.037 7.89 7.89 0.00 4.79
2569 3824 7.143340 GGTTTTCTTTTAATTAACTGAGCGGT 58.857 34.615 0.00 0.00 0.00 5.68
2570 3825 6.304683 CGGTTTTCTTTTAATTAACTGAGCGG 59.695 38.462 0.00 0.00 0.00 5.52
2571 3826 7.073265 TCGGTTTTCTTTTAATTAACTGAGCG 58.927 34.615 0.00 3.60 32.15 5.03
2572 3827 8.436156 CTCGGTTTTCTTTTAATTAACTGAGC 57.564 34.615 9.70 0.00 42.13 4.26
2574 3829 8.161699 AGCTCGGTTTTCTTTTAATTAACTGA 57.838 30.769 0.00 0.00 34.12 3.41
2575 3830 9.887406 TTAGCTCGGTTTTCTTTTAATTAACTG 57.113 29.630 0.00 0.00 0.00 3.16
2579 3834 9.681692 GGTTTTAGCTCGGTTTTCTTTTAATTA 57.318 29.630 0.00 0.00 0.00 1.40
2580 3835 7.654520 GGGTTTTAGCTCGGTTTTCTTTTAATT 59.345 33.333 0.00 0.00 0.00 1.40
2581 3836 7.014905 AGGGTTTTAGCTCGGTTTTCTTTTAAT 59.985 33.333 0.00 0.00 0.00 1.40
2582 3837 6.321945 AGGGTTTTAGCTCGGTTTTCTTTTAA 59.678 34.615 0.00 0.00 0.00 1.52
2583 3838 5.829391 AGGGTTTTAGCTCGGTTTTCTTTTA 59.171 36.000 0.00 0.00 0.00 1.52
2584 3839 4.647853 AGGGTTTTAGCTCGGTTTTCTTTT 59.352 37.500 0.00 0.00 0.00 2.27
2585 3840 4.212716 AGGGTTTTAGCTCGGTTTTCTTT 58.787 39.130 0.00 0.00 0.00 2.52
2586 3841 3.828921 AGGGTTTTAGCTCGGTTTTCTT 58.171 40.909 0.00 0.00 0.00 2.52
2587 3842 3.503800 AGGGTTTTAGCTCGGTTTTCT 57.496 42.857 0.00 0.00 0.00 2.52
2588 3843 5.892160 ATTAGGGTTTTAGCTCGGTTTTC 57.108 39.130 0.00 0.00 0.00 2.29
2589 3844 7.573656 CGTTTATTAGGGTTTTAGCTCGGTTTT 60.574 37.037 0.00 0.00 0.00 2.43
2590 3845 6.128200 CGTTTATTAGGGTTTTAGCTCGGTTT 60.128 38.462 0.00 0.00 0.00 3.27
2591 3846 5.352293 CGTTTATTAGGGTTTTAGCTCGGTT 59.648 40.000 0.00 0.00 0.00 4.44
2592 3847 4.872124 CGTTTATTAGGGTTTTAGCTCGGT 59.128 41.667 0.00 0.00 0.00 4.69
2593 3848 4.271776 CCGTTTATTAGGGTTTTAGCTCGG 59.728 45.833 0.00 0.00 0.00 4.63
2594 3849 4.271776 CCCGTTTATTAGGGTTTTAGCTCG 59.728 45.833 0.00 0.00 42.67 5.03
2595 3850 5.746307 CCCGTTTATTAGGGTTTTAGCTC 57.254 43.478 0.00 0.00 42.67 4.09
2605 3860 2.521996 GCGTTTTGCCCGTTTATTAGG 58.478 47.619 0.00 0.00 37.76 2.69
2617 3872 3.683340 ACCTAGTTTAGCTAGCGTTTTGC 59.317 43.478 9.55 0.00 44.47 3.68
2618 3873 4.927425 TGACCTAGTTTAGCTAGCGTTTTG 59.073 41.667 9.55 0.00 44.47 2.44
2619 3874 5.143376 TGACCTAGTTTAGCTAGCGTTTT 57.857 39.130 9.55 0.00 44.47 2.43
2620 3875 4.796038 TGACCTAGTTTAGCTAGCGTTT 57.204 40.909 9.55 0.00 44.47 3.60
2621 3876 4.461781 TCTTGACCTAGTTTAGCTAGCGTT 59.538 41.667 9.55 0.00 44.47 4.84
2622 3877 4.015084 TCTTGACCTAGTTTAGCTAGCGT 58.985 43.478 9.55 0.00 44.47 5.07
2623 3878 4.602995 CTCTTGACCTAGTTTAGCTAGCG 58.397 47.826 9.55 0.00 44.47 4.26
2624 3879 4.142138 TGCTCTTGACCTAGTTTAGCTAGC 60.142 45.833 6.62 6.62 44.47 3.42
2625 3880 5.344884 GTGCTCTTGACCTAGTTTAGCTAG 58.655 45.833 0.00 0.00 45.21 3.42
2626 3881 4.159879 GGTGCTCTTGACCTAGTTTAGCTA 59.840 45.833 0.00 0.00 0.00 3.32
2627 3882 3.055747 GGTGCTCTTGACCTAGTTTAGCT 60.056 47.826 0.00 0.00 0.00 3.32
2628 3883 3.263261 GGTGCTCTTGACCTAGTTTAGC 58.737 50.000 0.00 0.00 0.00 3.09
2629 3884 4.246458 GTGGTGCTCTTGACCTAGTTTAG 58.754 47.826 0.00 0.00 34.26 1.85
2630 3885 3.644265 TGTGGTGCTCTTGACCTAGTTTA 59.356 43.478 0.00 0.00 34.26 2.01
2631 3886 2.438021 TGTGGTGCTCTTGACCTAGTTT 59.562 45.455 0.00 0.00 34.26 2.66
2632 3887 2.047061 TGTGGTGCTCTTGACCTAGTT 58.953 47.619 0.00 0.00 34.26 2.24
2633 3888 1.717032 TGTGGTGCTCTTGACCTAGT 58.283 50.000 0.00 0.00 34.26 2.57
2634 3889 2.839486 TTGTGGTGCTCTTGACCTAG 57.161 50.000 0.00 0.00 34.26 3.02
2635 3890 3.674997 GATTTGTGGTGCTCTTGACCTA 58.325 45.455 0.00 0.00 34.26 3.08
2636 3891 2.508526 GATTTGTGGTGCTCTTGACCT 58.491 47.619 0.00 0.00 34.26 3.85
2637 3892 1.197721 CGATTTGTGGTGCTCTTGACC 59.802 52.381 0.00 0.00 0.00 4.02
2638 3893 1.400242 GCGATTTGTGGTGCTCTTGAC 60.400 52.381 0.00 0.00 0.00 3.18
2639 3894 0.874390 GCGATTTGTGGTGCTCTTGA 59.126 50.000 0.00 0.00 0.00 3.02
2640 3895 0.592637 TGCGATTTGTGGTGCTCTTG 59.407 50.000 0.00 0.00 0.00 3.02
2641 3896 1.001378 GTTGCGATTTGTGGTGCTCTT 60.001 47.619 0.00 0.00 0.00 2.85
2642 3897 0.593128 GTTGCGATTTGTGGTGCTCT 59.407 50.000 0.00 0.00 0.00 4.09
2643 3898 0.387239 GGTTGCGATTTGTGGTGCTC 60.387 55.000 0.00 0.00 0.00 4.26
2644 3899 1.106351 TGGTTGCGATTTGTGGTGCT 61.106 50.000 0.00 0.00 0.00 4.40
2645 3900 0.939106 GTGGTTGCGATTTGTGGTGC 60.939 55.000 0.00 0.00 0.00 5.01
2646 3901 0.318614 GGTGGTTGCGATTTGTGGTG 60.319 55.000 0.00 0.00 0.00 4.17
2647 3902 1.791103 CGGTGGTTGCGATTTGTGGT 61.791 55.000 0.00 0.00 0.00 4.16
2648 3903 1.081509 CGGTGGTTGCGATTTGTGG 60.082 57.895 0.00 0.00 0.00 4.17
2649 3904 1.081509 CCGGTGGTTGCGATTTGTG 60.082 57.895 0.00 0.00 0.00 3.33
2650 3905 2.914908 GCCGGTGGTTGCGATTTGT 61.915 57.895 1.90 0.00 0.00 2.83
2651 3906 2.126502 GCCGGTGGTTGCGATTTG 60.127 61.111 1.90 0.00 0.00 2.32
2652 3907 3.370231 GGCCGGTGGTTGCGATTT 61.370 61.111 1.90 0.00 0.00 2.17
2653 3908 4.652131 TGGCCGGTGGTTGCGATT 62.652 61.111 1.90 0.00 0.00 3.34
2657 3912 4.947147 TCACTGGCCGGTGGTTGC 62.947 66.667 38.20 0.00 37.75 4.17
2658 3913 2.978010 GTCACTGGCCGGTGGTTG 60.978 66.667 38.20 18.25 37.75 3.77
2659 3914 2.958578 CTTGTCACTGGCCGGTGGTT 62.959 60.000 38.20 5.64 37.75 3.67
2660 3915 3.476031 CTTGTCACTGGCCGGTGGT 62.476 63.158 38.20 14.09 37.75 4.16
2661 3916 2.669569 CTTGTCACTGGCCGGTGG 60.670 66.667 38.20 22.05 37.75 4.61
2662 3917 2.449031 TAGCTTGTCACTGGCCGGTG 62.449 60.000 35.06 35.06 38.44 4.94
2663 3918 2.214216 TAGCTTGTCACTGGCCGGT 61.214 57.895 12.85 12.85 0.00 5.28
2664 3919 1.741770 GTAGCTTGTCACTGGCCGG 60.742 63.158 11.02 11.02 0.00 6.13
2665 3920 0.602638 TTGTAGCTTGTCACTGGCCG 60.603 55.000 0.00 0.00 0.00 6.13
2666 3921 1.160137 CTTGTAGCTTGTCACTGGCC 58.840 55.000 0.00 0.00 0.00 5.36
2667 3922 0.519077 GCTTGTAGCTTGTCACTGGC 59.481 55.000 0.00 0.00 38.45 4.85
2668 3923 1.882912 TGCTTGTAGCTTGTCACTGG 58.117 50.000 0.00 0.00 42.97 4.00
2669 3924 2.874701 AGTTGCTTGTAGCTTGTCACTG 59.125 45.455 0.00 0.00 42.97 3.66
2670 3925 3.134458 GAGTTGCTTGTAGCTTGTCACT 58.866 45.455 0.00 0.00 42.97 3.41
2671 3926 3.134458 AGAGTTGCTTGTAGCTTGTCAC 58.866 45.455 0.00 0.00 42.97 3.67
2672 3927 3.393800 GAGAGTTGCTTGTAGCTTGTCA 58.606 45.455 0.00 0.00 42.97 3.58
2673 3928 2.739379 GGAGAGTTGCTTGTAGCTTGTC 59.261 50.000 0.00 0.00 42.97 3.18
2674 3929 2.551071 GGGAGAGTTGCTTGTAGCTTGT 60.551 50.000 0.00 0.00 42.97 3.16
2675 3930 2.079925 GGGAGAGTTGCTTGTAGCTTG 58.920 52.381 0.00 0.00 42.97 4.01
2676 3931 1.338200 CGGGAGAGTTGCTTGTAGCTT 60.338 52.381 0.00 0.00 42.97 3.74
2677 3932 0.247736 CGGGAGAGTTGCTTGTAGCT 59.752 55.000 0.00 0.00 42.97 3.32
2678 3933 0.246635 TCGGGAGAGTTGCTTGTAGC 59.753 55.000 0.00 0.00 42.82 3.58
2679 3934 1.272490 TGTCGGGAGAGTTGCTTGTAG 59.728 52.381 0.00 0.00 41.26 2.74
2680 3935 1.334160 TGTCGGGAGAGTTGCTTGTA 58.666 50.000 0.00 0.00 41.26 2.41
2681 3936 0.468226 TTGTCGGGAGAGTTGCTTGT 59.532 50.000 0.00 0.00 41.26 3.16
2682 3937 0.868406 GTTGTCGGGAGAGTTGCTTG 59.132 55.000 0.00 0.00 41.26 4.01
2683 3938 0.250338 GGTTGTCGGGAGAGTTGCTT 60.250 55.000 0.00 0.00 41.26 3.91
2684 3939 1.371558 GGTTGTCGGGAGAGTTGCT 59.628 57.895 0.00 0.00 41.26 3.91
2685 3940 1.070786 TGGTTGTCGGGAGAGTTGC 59.929 57.895 0.00 0.00 41.26 4.17
2686 3941 0.105964 TGTGGTTGTCGGGAGAGTTG 59.894 55.000 0.00 0.00 41.26 3.16
2687 3942 0.106149 GTGTGGTTGTCGGGAGAGTT 59.894 55.000 0.00 0.00 41.26 3.01
2688 3943 1.746517 GTGTGGTTGTCGGGAGAGT 59.253 57.895 0.00 0.00 41.26 3.24
2689 3944 1.372997 CGTGTGGTTGTCGGGAGAG 60.373 63.158 0.00 0.00 41.26 3.20
2690 3945 1.393487 TTCGTGTGGTTGTCGGGAGA 61.393 55.000 0.00 0.00 0.00 3.71
2691 3946 1.068417 TTCGTGTGGTTGTCGGGAG 59.932 57.895 0.00 0.00 0.00 4.30
2692 3947 1.227321 GTTCGTGTGGTTGTCGGGA 60.227 57.895 0.00 0.00 0.00 5.14
2693 3948 2.248835 GGTTCGTGTGGTTGTCGGG 61.249 63.158 0.00 0.00 0.00 5.14
2694 3949 2.248835 GGGTTCGTGTGGTTGTCGG 61.249 63.158 0.00 0.00 0.00 4.79
2695 3950 1.090625 TTGGGTTCGTGTGGTTGTCG 61.091 55.000 0.00 0.00 0.00 4.35
2696 3951 0.661020 CTTGGGTTCGTGTGGTTGTC 59.339 55.000 0.00 0.00 0.00 3.18
2697 3952 1.381165 GCTTGGGTTCGTGTGGTTGT 61.381 55.000 0.00 0.00 0.00 3.32
2698 3953 1.101049 AGCTTGGGTTCGTGTGGTTG 61.101 55.000 0.00 0.00 0.00 3.77
2699 3954 0.818040 GAGCTTGGGTTCGTGTGGTT 60.818 55.000 0.00 0.00 0.00 3.67
2700 3955 1.227853 GAGCTTGGGTTCGTGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
2701 3956 1.966451 GGAGCTTGGGTTCGTGTGG 60.966 63.158 0.00 0.00 0.00 4.17
2702 3957 1.227823 TGGAGCTTGGGTTCGTGTG 60.228 57.895 0.00 0.00 0.00 3.82
2703 3958 1.227853 GTGGAGCTTGGGTTCGTGT 60.228 57.895 0.00 0.00 0.00 4.49
2704 3959 1.966451 GGTGGAGCTTGGGTTCGTG 60.966 63.158 0.00 0.00 0.00 4.35
2705 3960 2.430367 GGTGGAGCTTGGGTTCGT 59.570 61.111 0.00 0.00 0.00 3.85
2706 3961 2.742372 CGGTGGAGCTTGGGTTCG 60.742 66.667 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.