Multiple sequence alignment - TraesCS4D01G017900

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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 TraesCS4D01G017900 chr4D 100.000 3116 0 0 1 3116 7844453 7841338 0.000000e+00 5755
1 TraesCS4D01G017900 chr4B 88.816 1073 66 30 941 1973 14108865 14109923 0.000000e+00 1267
2 TraesCS4D01G017900 chr4B 86.558 796 54 26 2321 3088 14110320 14111090 0.000000e+00 828
3 TraesCS4D01G017900 chr4B 86.376 712 49 20 1 670 14107500 14108205 0.000000e+00 734
4 TraesCS4D01G017900 chr4B 82.353 136 17 4 2057 2190 14110170 14110300 9.130000e-21 111
5 TraesCS4D01G017900 chr4A 91.588 844 47 17 1109 1944 595549890 595550717 0.000000e+00 1144
6 TraesCS4D01G017900 chr4A 89.939 825 52 17 2312 3116 595551769 595552582 0.000000e+00 1035
7 TraesCS4D01G017900 chr4A 86.149 657 46 17 1 637 595548884 595549515 0.000000e+00 667
8 TraesCS4D01G017900 chr4A 83.575 207 14 13 2056 2258 595551465 595551655 3.190000e-40 176
9 TraesCS4D01G017900 chr4A 92.553 94 7 0 980 1073 595549794 595549887 5.420000e-28 135
10 TraesCS4D01G017900 chr7B 84.459 444 56 9 1635 2076 60577847 60577415 2.870000e-115 425
11 TraesCS4D01G017900 chr7B 84.009 444 58 9 1635 2076 549271123 549270691 6.220000e-112 414
12 TraesCS4D01G017900 chr3A 85.071 422 53 7 1635 2055 160917313 160916901 3.720000e-114 422
13 TraesCS4D01G017900 chr1A 87.222 360 29 10 1635 1986 560968776 560968426 8.100000e-106 394
14 TraesCS4D01G017900 chr6D 86.782 348 29 12 1635 1974 375307492 375307830 3.800000e-99 372
15 TraesCS4D01G017900 chr6D 84.722 360 38 9 1635 1986 455141075 455141425 8.270000e-91 344
16 TraesCS4D01G017900 chr5D 85.000 360 37 10 1635 1986 390810611 390810261 1.780000e-92 350
17 TraesCS4D01G017900 chr5B 89.109 101 10 1 1410 1509 13361449 13361349 1.170000e-24 124


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 TraesCS4D01G017900 chr4D 7841338 7844453 3115 True 5755.0 5755 100.00000 1 3116 1 chr4D.!!$R1 3115
1 TraesCS4D01G017900 chr4B 14107500 14111090 3590 False 735.0 1267 86.02575 1 3088 4 chr4B.!!$F1 3087
2 TraesCS4D01G017900 chr4A 595548884 595552582 3698 False 631.4 1144 88.76080 1 3116 5 chr4A.!!$F1 3115

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
971 1432 0.03254 GACCAAACCAAAGCTGCTGG 59.967 55.0 1.35 12.56 40.05 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 3786 0.110509 GAGTGTGCTGTGCGATGTTG 60.111 55.0 0.0 0.0 0.0 3.33 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
25 26 0.108377 TACACACTACATGCTGCCCG 60.108 55.000 0.00 0.00 0.00 6.13
39 40 0.104855 TGCCCGCTGCTCTATACTTG 59.895 55.000 0.00 0.00 42.00 3.16
59 60 5.485708 ACTTGTCTCCTAGCTAGTCCAATTT 59.514 40.000 19.31 4.42 0.00 1.82
60 61 6.013293 ACTTGTCTCCTAGCTAGTCCAATTTT 60.013 38.462 19.31 0.00 0.00 1.82
242 252 2.106683 GGGACAATGAAGACGGCGG 61.107 63.158 13.24 0.00 0.00 6.13
296 306 2.182014 GTTCGTCTTTGCACGCTTTTT 58.818 42.857 0.00 0.00 39.74 1.94
375 386 3.057245 GTGCAAGGATTTTCTGGGAGTTC 60.057 47.826 0.00 0.00 0.00 3.01
395 406 7.284919 AGTTCCCAAATTTTATTCAAGACGT 57.715 32.000 0.00 0.00 0.00 4.34
407 420 1.689582 AAGACGTGGGGGATCCTCC 60.690 63.158 25.38 25.38 36.20 4.30
435 448 4.219070 TGCTCCTTCATGTGAAATTTCTGG 59.781 41.667 18.64 9.33 33.07 3.86
436 449 4.219288 GCTCCTTCATGTGAAATTTCTGGT 59.781 41.667 18.64 2.34 33.07 4.00
437 450 5.415701 GCTCCTTCATGTGAAATTTCTGGTA 59.584 40.000 18.64 3.69 33.07 3.25
470 483 2.492090 GCGCTGACTCGGATCACT 59.508 61.111 0.00 0.00 0.00 3.41
486 505 4.809958 GGATCACTGTCTGTCTTCATCATG 59.190 45.833 0.00 0.00 0.00 3.07
489 508 4.040829 TCACTGTCTGTCTTCATCATGGTT 59.959 41.667 0.00 0.00 0.00 3.67
490 509 4.153655 CACTGTCTGTCTTCATCATGGTTG 59.846 45.833 0.00 0.00 0.00 3.77
492 511 5.012046 ACTGTCTGTCTTCATCATGGTTGTA 59.988 40.000 0.00 0.00 0.00 2.41
506 535 7.074653 TCATGGTTGTAAAAGAAGGTACTCT 57.925 36.000 0.00 0.00 38.49 3.24
537 566 1.481871 GTAGCTACACCTAGGGCACA 58.518 55.000 19.15 0.00 0.00 4.57
545 574 2.180276 CACCTAGGGCACAGTTAGAGT 58.820 52.381 14.81 0.00 0.00 3.24
551 580 2.772189 CACAGTTAGAGTGCGCGC 59.228 61.111 27.26 27.26 0.00 6.86
568 602 2.202770 CCAGCTCTCTCTGCAGCG 60.203 66.667 9.47 2.08 40.84 5.18
579 613 3.691744 CTGCAGCGGAGAGGACGAC 62.692 68.421 0.00 0.00 0.00 4.34
586 620 1.666011 GGAGAGGACGACTGTTGCA 59.334 57.895 0.00 0.00 0.00 4.08
608 642 1.072806 ACAGAGCAGATGCCAGTTTGA 59.927 47.619 0.14 0.00 43.38 2.69
621 655 2.422479 CCAGTTTGAGCCTGACATCATG 59.578 50.000 0.00 0.00 31.38 3.07
637 671 1.358787 TCATGGACTGAATTTGCCCCT 59.641 47.619 0.00 0.00 0.00 4.79
639 673 0.776810 TGGACTGAATTTGCCCCTCA 59.223 50.000 0.00 0.00 0.00 3.86
640 674 1.146774 TGGACTGAATTTGCCCCTCAA 59.853 47.619 0.00 0.00 0.00 3.02
643 677 3.554960 GGACTGAATTTGCCCCTCAAAAC 60.555 47.826 0.00 0.00 46.60 2.43
644 678 2.035832 ACTGAATTTGCCCCTCAAAACG 59.964 45.455 0.00 0.00 46.60 3.60
701 808 1.351017 TCTGCTAACCACTTTGAGGGG 59.649 52.381 0.00 0.00 46.86 4.79
707 814 3.346426 CCACTTTGAGGGGTCCTTG 57.654 57.895 0.00 0.00 32.85 3.61
729 837 0.606604 AAGTGGACGTGGAATAGCGT 59.393 50.000 0.00 0.00 44.50 5.07
730 838 0.606604 AGTGGACGTGGAATAGCGTT 59.393 50.000 0.00 0.00 41.70 4.84
731 839 0.997196 GTGGACGTGGAATAGCGTTC 59.003 55.000 0.00 0.00 41.70 3.95
732 840 0.604073 TGGACGTGGAATAGCGTTCA 59.396 50.000 0.00 0.00 43.36 3.18
733 841 1.001068 TGGACGTGGAATAGCGTTCAA 59.999 47.619 0.00 0.00 42.73 2.69
734 842 1.392510 GGACGTGGAATAGCGTTCAAC 59.607 52.381 0.00 5.12 41.70 3.18
736 844 2.066262 ACGTGGAATAGCGTTCAACAG 58.934 47.619 11.39 7.51 38.21 3.16
737 845 2.066262 CGTGGAATAGCGTTCAACAGT 58.934 47.619 11.39 0.00 0.00 3.55
747 864 0.385390 GTTCAACAGTGGGCTTGTGG 59.615 55.000 0.00 0.00 0.00 4.17
780 930 8.076781 TGAGAAACGAGCTCATAGTATATTGTC 58.923 37.037 15.40 4.37 37.46 3.18
781 931 7.941919 AGAAACGAGCTCATAGTATATTGTCA 58.058 34.615 15.40 0.00 0.00 3.58
782 932 8.580720 AGAAACGAGCTCATAGTATATTGTCAT 58.419 33.333 15.40 0.00 0.00 3.06
783 933 8.749841 AAACGAGCTCATAGTATATTGTCATC 57.250 34.615 15.40 0.00 0.00 2.92
784 934 6.857956 ACGAGCTCATAGTATATTGTCATCC 58.142 40.000 15.40 0.00 0.00 3.51
785 935 6.434340 ACGAGCTCATAGTATATTGTCATCCA 59.566 38.462 15.40 0.00 0.00 3.41
786 936 7.039714 ACGAGCTCATAGTATATTGTCATCCAA 60.040 37.037 15.40 0.00 37.49 3.53
790 942 7.388776 GCTCATAGTATATTGTCATCCAAAGCA 59.611 37.037 0.00 0.00 36.44 3.91
791 943 9.445878 CTCATAGTATATTGTCATCCAAAGCAT 57.554 33.333 0.00 0.00 36.44 3.79
795 947 6.713903 AGTATATTGTCATCCAAAGCATCCTG 59.286 38.462 0.00 0.00 36.44 3.86
796 948 3.438216 TTGTCATCCAAAGCATCCTGA 57.562 42.857 0.00 0.00 0.00 3.86
806 958 4.380233 CCAAAGCATCCTGACAACAATCTC 60.380 45.833 0.00 0.00 0.00 2.75
807 959 2.625737 AGCATCCTGACAACAATCTCG 58.374 47.619 0.00 0.00 0.00 4.04
812 964 3.210227 TCCTGACAACAATCTCGCAAAA 58.790 40.909 0.00 0.00 0.00 2.44
816 968 4.350346 TGACAACAATCTCGCAAAACTTG 58.650 39.130 0.00 0.00 0.00 3.16
819 971 3.253371 ACAATCTCGCAAAACTTGTCG 57.747 42.857 0.00 0.00 0.00 4.35
820 972 2.032030 ACAATCTCGCAAAACTTGTCGG 60.032 45.455 0.00 0.00 33.29 4.79
827 979 3.046390 CGCAAAACTTGTCGGCATAAAA 58.954 40.909 0.00 0.00 0.00 1.52
830 982 5.216648 GCAAAACTTGTCGGCATAAAAGTA 58.783 37.500 0.00 0.00 32.69 2.24
832 984 7.024768 GCAAAACTTGTCGGCATAAAAGTATA 58.975 34.615 0.00 0.00 32.69 1.47
833 985 7.700656 GCAAAACTTGTCGGCATAAAAGTATAT 59.299 33.333 0.00 0.00 32.69 0.86
863 1294 7.506114 TGAGGAGAAAAGTTAGACTTGCTAAA 58.494 34.615 0.00 0.00 40.60 1.85
930 1391 7.636259 TTTTGAAGCAAATCATAAACTTCGG 57.364 32.000 0.00 0.00 39.64 4.30
931 1392 4.732784 TGAAGCAAATCATAAACTTCGGC 58.267 39.130 0.00 0.00 39.64 5.54
932 1393 4.217334 TGAAGCAAATCATAAACTTCGGCA 59.783 37.500 0.00 0.00 39.64 5.69
933 1394 4.096732 AGCAAATCATAAACTTCGGCAC 57.903 40.909 0.00 0.00 0.00 5.01
934 1395 3.758554 AGCAAATCATAAACTTCGGCACT 59.241 39.130 0.00 0.00 0.00 4.40
935 1396 4.941263 AGCAAATCATAAACTTCGGCACTA 59.059 37.500 0.00 0.00 0.00 2.74
936 1397 5.065218 AGCAAATCATAAACTTCGGCACTAG 59.935 40.000 0.00 0.00 0.00 2.57
937 1398 5.266242 CAAATCATAAACTTCGGCACTAGC 58.734 41.667 0.00 0.00 41.10 3.42
963 1424 0.741915 GCGTTGGAGACCAAACCAAA 59.258 50.000 4.75 0.00 45.73 3.28
964 1425 1.269051 GCGTTGGAGACCAAACCAAAG 60.269 52.381 4.75 0.00 45.73 2.77
965 1426 1.269051 CGTTGGAGACCAAACCAAAGC 60.269 52.381 4.75 0.00 45.73 3.51
966 1427 2.031870 GTTGGAGACCAAACCAAAGCT 58.968 47.619 4.75 0.00 45.73 3.74
967 1428 1.691196 TGGAGACCAAACCAAAGCTG 58.309 50.000 0.00 0.00 32.93 4.24
969 1430 1.322442 GAGACCAAACCAAAGCTGCT 58.678 50.000 0.00 0.00 0.00 4.24
970 1431 1.000938 GAGACCAAACCAAAGCTGCTG 60.001 52.381 1.35 0.00 0.00 4.41
971 1432 0.032540 GACCAAACCAAAGCTGCTGG 59.967 55.000 1.35 12.56 40.05 4.85
1112 1582 1.607756 AGCTCCAACTCCTGCTCGA 60.608 57.895 0.00 0.00 0.00 4.04
1361 1834 2.055042 CAGGGACTCTCACCTCCGG 61.055 68.421 0.00 0.00 34.60 5.14
1379 1852 2.799176 GCCTCTCGCCCATGATTTT 58.201 52.632 0.00 0.00 0.00 1.82
1383 1856 1.945394 CTCTCGCCCATGATTTTCCTG 59.055 52.381 0.00 0.00 0.00 3.86
1385 1858 1.672881 CTCGCCCATGATTTTCCTGTC 59.327 52.381 0.00 0.00 0.00 3.51
1391 1864 2.659428 CATGATTTTCCTGTCCCCCTC 58.341 52.381 0.00 0.00 0.00 4.30
1394 1867 0.704664 ATTTTCCTGTCCCCCTCACC 59.295 55.000 0.00 0.00 0.00 4.02
1401 1880 1.003718 GTCCCCCTCACCGTTTCTG 60.004 63.158 0.00 0.00 0.00 3.02
1589 2076 3.110178 CCCACCGCTTCGTTCGTC 61.110 66.667 0.00 0.00 0.00 4.20
1763 2250 2.297315 GCAGATGATCGTCCAGGTGATA 59.703 50.000 11.42 0.00 0.00 2.15
1901 2388 5.104444 TGGTCTGTGTTAAGGTTTAGGTTGA 60.104 40.000 0.00 0.00 0.00 3.18
1944 2439 1.340889 CCCACCTTTGATGGTTGTGTG 59.659 52.381 0.00 0.00 38.45 3.82
1945 2440 2.031120 CCACCTTTGATGGTTGTGTGT 58.969 47.619 0.00 0.00 38.45 3.72
1946 2441 2.034558 CCACCTTTGATGGTTGTGTGTC 59.965 50.000 0.00 0.00 38.45 3.67
1962 2470 6.266168 TGTGTGTCATGTTAAATGGAATCC 57.734 37.500 0.00 0.00 0.00 3.01
1974 2482 5.630415 AAATGGAATCCCGTGATCTCTTA 57.370 39.130 0.00 0.00 34.29 2.10
1977 2485 3.772572 TGGAATCCCGTGATCTCTTACAA 59.227 43.478 0.00 0.00 34.29 2.41
1980 2488 3.710326 TCCCGTGATCTCTTACAATCG 57.290 47.619 0.00 0.00 0.00 3.34
1985 2493 4.914504 CCGTGATCTCTTACAATCGAGATG 59.085 45.833 6.52 0.00 44.63 2.90
1988 2496 6.075152 CGTGATCTCTTACAATCGAGATGTTG 60.075 42.308 11.37 3.63 44.63 3.33
1989 2497 6.975197 GTGATCTCTTACAATCGAGATGTTGA 59.025 38.462 11.37 9.51 44.63 3.18
1990 2498 7.489435 GTGATCTCTTACAATCGAGATGTTGAA 59.511 37.037 11.37 1.64 44.63 2.69
1991 2499 8.200120 TGATCTCTTACAATCGAGATGTTGAAT 58.800 33.333 11.37 7.54 44.63 2.57
1993 2501 7.323420 TCTCTTACAATCGAGATGTTGAATGT 58.677 34.615 11.37 6.11 34.91 2.71
1994 2502 7.819415 TCTCTTACAATCGAGATGTTGAATGTT 59.181 33.333 11.37 0.00 33.06 2.71
1995 2503 7.742151 TCTTACAATCGAGATGTTGAATGTTG 58.258 34.615 11.37 0.00 33.06 3.33
1996 2504 4.726416 ACAATCGAGATGTTGAATGTTGC 58.274 39.130 3.59 0.00 26.94 4.17
2005 2526 4.868314 TGTTGAATGTTGCATCCATGAA 57.132 36.364 0.00 0.00 0.00 2.57
2013 2534 1.063649 GCATCCATGAACGCTGCAG 59.936 57.895 10.11 10.11 33.13 4.41
2024 2545 1.442769 ACGCTGCAGGTGTTAAGATG 58.557 50.000 17.12 0.00 34.69 2.90
2034 2555 4.452455 CAGGTGTTAAGATGGTTCTGTGAC 59.548 45.833 0.00 0.00 30.72 3.67
2035 2556 3.751698 GGTGTTAAGATGGTTCTGTGACC 59.248 47.826 0.00 0.00 40.23 4.02
2036 2557 4.505039 GGTGTTAAGATGGTTCTGTGACCT 60.505 45.833 0.00 0.00 40.47 3.85
2038 2559 6.228258 GTGTTAAGATGGTTCTGTGACCTTA 58.772 40.000 0.00 0.00 40.47 2.69
2039 2560 6.369065 GTGTTAAGATGGTTCTGTGACCTTAG 59.631 42.308 0.00 0.00 40.47 2.18
2042 2563 5.568620 AGATGGTTCTGTGACCTTAGTTT 57.431 39.130 0.00 0.00 40.47 2.66
2043 2564 6.681729 AGATGGTTCTGTGACCTTAGTTTA 57.318 37.500 0.00 0.00 40.47 2.01
2045 2566 7.331791 AGATGGTTCTGTGACCTTAGTTTATC 58.668 38.462 0.00 0.00 40.47 1.75
2046 2567 5.801380 TGGTTCTGTGACCTTAGTTTATCC 58.199 41.667 0.00 0.00 40.47 2.59
2047 2568 5.546499 TGGTTCTGTGACCTTAGTTTATCCT 59.454 40.000 0.00 0.00 40.47 3.24
2049 2570 5.086104 TCTGTGACCTTAGTTTATCCTGC 57.914 43.478 0.00 0.00 0.00 4.85
2050 2571 4.530553 TCTGTGACCTTAGTTTATCCTGCA 59.469 41.667 0.00 0.00 0.00 4.41
2051 2572 4.575885 TGTGACCTTAGTTTATCCTGCAC 58.424 43.478 0.00 0.00 0.00 4.57
2052 2573 4.286032 TGTGACCTTAGTTTATCCTGCACT 59.714 41.667 0.00 0.00 0.00 4.40
2053 2574 4.631813 GTGACCTTAGTTTATCCTGCACTG 59.368 45.833 0.00 0.00 0.00 3.66
2054 2575 4.192317 GACCTTAGTTTATCCTGCACTGG 58.808 47.826 0.00 0.00 0.00 4.00
2055 2576 3.054361 ACCTTAGTTTATCCTGCACTGGG 60.054 47.826 0.00 0.00 0.00 4.45
2066 3207 1.008538 GCACTGGGCACGTTTTCTG 60.009 57.895 0.00 0.00 43.97 3.02
2090 3232 5.300969 TCTTGCATTTTGAGAATCCTTCG 57.699 39.130 0.00 0.00 34.02 3.79
2098 3240 7.490402 GCATTTTGAGAATCCTTCGAATCAAAT 59.510 33.333 18.09 9.41 36.76 2.32
2104 3246 7.495934 TGAGAATCCTTCGAATCAAATAAGACC 59.504 37.037 0.00 0.00 34.02 3.85
2125 3268 5.540911 ACCCACAACATTCTTAAAATGCAG 58.459 37.500 0.00 6.04 0.00 4.41
2139 3282 9.995003 TCTTAAAATGCAGGAATACAAAAATGT 57.005 25.926 0.00 0.00 0.00 2.71
2147 3290 6.476706 GCAGGAATACAAAAATGTTATCTGGC 59.523 38.462 0.00 0.00 0.00 4.85
2149 3292 7.703621 CAGGAATACAAAAATGTTATCTGGCTG 59.296 37.037 0.00 0.00 0.00 4.85
2151 3294 4.870123 ACAAAAATGTTATCTGGCTGCA 57.130 36.364 0.50 0.00 0.00 4.41
2152 3295 5.212532 ACAAAAATGTTATCTGGCTGCAA 57.787 34.783 0.50 0.00 0.00 4.08
2212 3355 5.334879 GGTTTGTTTGACTGCATCGTAGAAT 60.335 40.000 0.00 0.00 43.58 2.40
2213 3356 6.128391 GGTTTGTTTGACTGCATCGTAGAATA 60.128 38.462 0.00 0.00 43.58 1.75
2214 3357 6.647212 TTGTTTGACTGCATCGTAGAATAG 57.353 37.500 0.00 0.00 43.58 1.73
2215 3358 5.109210 TGTTTGACTGCATCGTAGAATAGG 58.891 41.667 0.00 0.00 43.58 2.57
2219 3362 6.161855 TGACTGCATCGTAGAATAGGAAAT 57.838 37.500 0.00 0.00 43.58 2.17
2239 3382 9.367160 AGGAAATAAAGGATTCTTCTTTTCACA 57.633 29.630 17.04 0.00 36.51 3.58
2240 3383 9.981114 GGAAATAAAGGATTCTTCTTTTCACAA 57.019 29.630 17.04 0.00 36.51 3.33
2242 3385 9.987272 AAATAAAGGATTCTTCTTTTCACAAGG 57.013 29.630 0.00 0.00 36.12 3.61
2243 3386 8.712228 ATAAAGGATTCTTCTTTTCACAAGGT 57.288 30.769 0.00 0.00 36.12 3.50
2244 3387 9.807921 ATAAAGGATTCTTCTTTTCACAAGGTA 57.192 29.630 0.00 0.00 36.12 3.08
2258 3401 5.547465 TCACAAGGTAGTATGGTGTTGAAG 58.453 41.667 0.00 0.00 0.00 3.02
2259 3402 5.071250 TCACAAGGTAGTATGGTGTTGAAGT 59.929 40.000 0.00 0.00 0.00 3.01
2260 3403 6.268158 TCACAAGGTAGTATGGTGTTGAAGTA 59.732 38.462 0.00 0.00 0.00 2.24
2261 3404 7.038587 TCACAAGGTAGTATGGTGTTGAAGTAT 60.039 37.037 0.00 0.00 0.00 2.12
2262 3405 8.255206 CACAAGGTAGTATGGTGTTGAAGTATA 58.745 37.037 0.00 0.00 0.00 1.47
2265 3408 8.008513 AGGTAGTATGGTGTTGAAGTATACAG 57.991 38.462 5.50 0.00 0.00 2.74
2266 3409 7.837689 AGGTAGTATGGTGTTGAAGTATACAGA 59.162 37.037 5.50 0.00 0.00 3.41
2267 3410 7.919621 GGTAGTATGGTGTTGAAGTATACAGAC 59.080 40.741 5.50 0.00 0.00 3.51
2268 3411 7.476540 AGTATGGTGTTGAAGTATACAGACA 57.523 36.000 5.50 1.53 0.00 3.41
2269 3412 7.548097 AGTATGGTGTTGAAGTATACAGACAG 58.452 38.462 5.50 0.00 0.00 3.51
2270 3413 4.566004 TGGTGTTGAAGTATACAGACAGC 58.434 43.478 5.50 12.69 36.40 4.40
2271 3414 3.933332 GGTGTTGAAGTATACAGACAGCC 59.067 47.826 5.50 5.22 31.44 4.85
2272 3415 4.562757 GGTGTTGAAGTATACAGACAGCCA 60.563 45.833 5.50 1.31 31.44 4.75
2273 3416 4.627467 GTGTTGAAGTATACAGACAGCCAG 59.373 45.833 5.50 0.00 0.00 4.85
2274 3417 4.184629 GTTGAAGTATACAGACAGCCAGG 58.815 47.826 5.50 0.00 0.00 4.45
2284 3427 1.630369 AGACAGCCAGGCAGTGAAATA 59.370 47.619 15.44 0.00 0.00 1.40
2292 3435 1.654023 GGCAGTGAAATACGTGGGCC 61.654 60.000 0.00 0.00 32.83 5.80
2299 3442 0.623723 AAATACGTGGGCCACTGGAT 59.376 50.000 32.28 24.02 31.34 3.41
2300 3443 0.623723 AATACGTGGGCCACTGGATT 59.376 50.000 32.28 27.59 31.34 3.01
2301 3444 0.107214 ATACGTGGGCCACTGGATTG 60.107 55.000 32.28 18.82 31.34 2.67
2302 3445 1.485294 TACGTGGGCCACTGGATTGT 61.485 55.000 32.28 23.18 31.34 2.71
2303 3446 1.298340 CGTGGGCCACTGGATTGTA 59.702 57.895 32.28 0.00 31.34 2.41
2306 3449 1.750778 GTGGGCCACTGGATTGTATTG 59.249 52.381 29.22 0.00 0.00 1.90
2307 3450 1.357420 TGGGCCACTGGATTGTATTGT 59.643 47.619 0.00 0.00 0.00 2.71
2308 3451 2.578480 TGGGCCACTGGATTGTATTGTA 59.422 45.455 0.00 0.00 0.00 2.41
2309 3452 2.949644 GGGCCACTGGATTGTATTGTAC 59.050 50.000 4.39 0.00 0.00 2.90
2340 3553 1.021390 GTGGATGGCTCACTGAACGG 61.021 60.000 0.00 0.00 32.78 4.44
2344 3557 1.194781 ATGGCTCACTGAACGGTCCT 61.195 55.000 0.00 0.00 0.00 3.85
2552 3782 2.486636 TACGCTGACTTGACCAGGCG 62.487 60.000 0.00 0.00 37.27 5.52
2556 3786 1.845809 CTGACTTGACCAGGCGCAAC 61.846 60.000 10.83 0.00 29.50 4.17
2557 3787 1.891919 GACTTGACCAGGCGCAACA 60.892 57.895 10.83 0.00 0.00 3.33
2558 3788 1.444119 GACTTGACCAGGCGCAACAA 61.444 55.000 10.83 6.75 0.00 2.83
2559 3789 1.008538 CTTGACCAGGCGCAACAAC 60.009 57.895 10.83 0.00 0.00 3.32
2561 3791 1.106351 TTGACCAGGCGCAACAACAT 61.106 50.000 10.83 0.00 0.00 2.71
2562 3792 1.210155 GACCAGGCGCAACAACATC 59.790 57.895 10.83 0.00 0.00 3.06
2563 3793 2.176546 CCAGGCGCAACAACATCG 59.823 61.111 10.83 0.00 0.00 3.84
2576 3815 0.250038 AACATCGCACAGCACACTCT 60.250 50.000 0.00 0.00 0.00 3.24
2593 3832 1.664649 CTGTCTCGGCAAACTGCGA 60.665 57.895 0.00 0.00 46.21 5.10
2605 3844 3.860378 GCAAACTGCGATTTCCATTGGAA 60.860 43.478 14.24 14.24 34.94 3.53
2827 4082 4.038162 ACGGTTAGATAGAATGCTGGAGTC 59.962 45.833 0.00 0.00 0.00 3.36
2868 4123 2.082231 CACTTGCAGGTCTCTCCATTG 58.918 52.381 0.00 0.00 39.02 2.82
2919 4174 5.369993 AGAGGGAAAATCTGTCTATAACCCC 59.630 44.000 0.00 0.00 35.87 4.95
2920 4175 5.043762 AGGGAAAATCTGTCTATAACCCCA 58.956 41.667 0.00 0.00 35.87 4.96
2922 4177 5.131067 GGAAAATCTGTCTATAACCCCACC 58.869 45.833 0.00 0.00 0.00 4.61
2923 4178 4.417426 AAATCTGTCTATAACCCCACCG 57.583 45.455 0.00 0.00 0.00 4.94
2935 4190 1.622312 ACCCCACCGAGAAGTACTTTC 59.378 52.381 10.02 8.38 35.97 2.62
2936 4191 1.621814 CCCCACCGAGAAGTACTTTCA 59.378 52.381 10.02 0.00 38.31 2.69
3027 4283 3.233578 GTTGAATGTACCACAATGTGCG 58.766 45.455 8.05 4.15 31.34 5.34
3088 4346 7.600065 TGGAAATATAGCATAAGACGTCCTAC 58.400 38.462 13.01 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.448686 GGCAGCATGTAGTGTGTACTAG 58.551 50.000 0.00 0.00 39.96 2.57
25 26 4.320935 GCTAGGAGACAAGTATAGAGCAGC 60.321 50.000 0.00 0.00 0.00 5.25
39 40 5.065346 GCAAAAATTGGACTAGCTAGGAGAC 59.935 44.000 24.35 11.59 0.00 3.36
59 60 4.902443 TGACAAACAGATAAACGGCAAA 57.098 36.364 0.00 0.00 0.00 3.68
242 252 4.425577 AACCGAGATCAAATTCAGTTGC 57.574 40.909 0.00 0.00 0.00 4.17
296 306 3.691342 CCGCACGGAACCCTCTGA 61.691 66.667 2.01 0.00 37.50 3.27
343 353 5.362430 AGAAAATCCTTGCACAAAACTACCA 59.638 36.000 0.00 0.00 0.00 3.25
344 354 5.691754 CAGAAAATCCTTGCACAAAACTACC 59.308 40.000 0.00 0.00 0.00 3.18
345 355 5.691754 CCAGAAAATCCTTGCACAAAACTAC 59.308 40.000 0.00 0.00 0.00 2.73
375 386 5.167845 CCCACGTCTTGAATAAAATTTGGG 58.832 41.667 0.00 0.00 34.31 4.12
407 420 0.907486 TCACATGAAGGAGCAGGAGG 59.093 55.000 0.00 0.00 0.00 4.30
408 421 2.775911 TTCACATGAAGGAGCAGGAG 57.224 50.000 0.00 0.00 0.00 3.69
409 422 3.726557 ATTTCACATGAAGGAGCAGGA 57.273 42.857 0.00 0.00 35.21 3.86
435 448 5.087397 CAGCGCCTCGATTTATAGTACTAC 58.913 45.833 2.29 0.00 0.00 2.73
436 449 4.999311 TCAGCGCCTCGATTTATAGTACTA 59.001 41.667 2.29 4.77 0.00 1.82
437 450 3.819337 TCAGCGCCTCGATTTATAGTACT 59.181 43.478 2.29 0.00 0.00 2.73
470 483 4.356405 ACAACCATGATGAAGACAGACA 57.644 40.909 0.00 0.00 0.00 3.41
486 505 7.563888 AAACAGAGTACCTTCTTTTACAACC 57.436 36.000 0.00 0.00 0.00 3.77
489 508 8.795842 TGAAAAACAGAGTACCTTCTTTTACA 57.204 30.769 0.00 0.00 0.00 2.41
492 511 8.197439 CCAATGAAAAACAGAGTACCTTCTTTT 58.803 33.333 0.00 0.00 0.00 2.27
506 535 5.381757 AGGTGTAGCTACCAATGAAAAACA 58.618 37.500 21.01 0.00 43.37 2.83
537 566 2.125912 CTGGCGCGCACTCTAACT 60.126 61.111 34.42 0.00 0.00 2.24
549 578 2.202770 CTGCAGAGAGAGCTGGCG 60.203 66.667 8.42 0.00 36.41 5.69
550 579 2.512057 GCTGCAGAGAGAGCTGGC 60.512 66.667 20.43 0.00 36.41 4.85
551 580 2.202770 CGCTGCAGAGAGAGCTGG 60.203 66.667 20.43 0.00 36.41 4.85
568 602 0.033504 TTGCAACAGTCGTCCTCTCC 59.966 55.000 0.00 0.00 0.00 3.71
586 620 2.283145 AACTGGCATCTGCTCTGTTT 57.717 45.000 1.70 0.00 41.70 2.83
593 627 0.964358 AGGCTCAAACTGGCATCTGC 60.964 55.000 0.00 0.00 41.14 4.26
597 631 0.111061 TGTCAGGCTCAAACTGGCAT 59.889 50.000 0.00 0.00 44.82 4.40
608 642 1.576577 TCAGTCCATGATGTCAGGCT 58.423 50.000 0.00 0.00 31.12 4.58
621 655 1.923356 TTGAGGGGCAAATTCAGTCC 58.077 50.000 0.00 0.00 32.46 3.85
637 671 7.973388 AGATCACAAAATTCAACTTCGTTTTGA 59.027 29.630 14.18 2.27 41.61 2.69
639 673 8.702163 AAGATCACAAAATTCAACTTCGTTTT 57.298 26.923 0.00 0.00 0.00 2.43
640 674 9.796120 TTAAGATCACAAAATTCAACTTCGTTT 57.204 25.926 0.00 0.00 0.00 3.60
641 675 9.796120 TTTAAGATCACAAAATTCAACTTCGTT 57.204 25.926 0.00 0.00 0.00 3.85
692 799 0.178964 TTGGCAAGGACCCCTCAAAG 60.179 55.000 0.00 0.00 30.89 2.77
701 808 1.227853 ACGTCCACTTGGCAAGGAC 60.228 57.895 29.26 25.44 46.48 3.85
707 814 1.369625 CTATTCCACGTCCACTTGGC 58.630 55.000 0.00 0.00 35.46 4.52
729 837 0.033601 ACCACAAGCCCACTGTTGAA 60.034 50.000 0.00 0.00 0.00 2.69
730 838 0.840617 TACCACAAGCCCACTGTTGA 59.159 50.000 0.00 0.00 0.00 3.18
731 839 1.238439 CTACCACAAGCCCACTGTTG 58.762 55.000 0.00 0.00 0.00 3.33
732 840 0.843984 ACTACCACAAGCCCACTGTT 59.156 50.000 0.00 0.00 0.00 3.16
733 841 0.108585 CACTACCACAAGCCCACTGT 59.891 55.000 0.00 0.00 0.00 3.55
734 842 0.396435 TCACTACCACAAGCCCACTG 59.604 55.000 0.00 0.00 0.00 3.66
736 844 1.003118 TCATCACTACCACAAGCCCAC 59.997 52.381 0.00 0.00 0.00 4.61
737 845 1.278985 CTCATCACTACCACAAGCCCA 59.721 52.381 0.00 0.00 0.00 5.36
747 864 4.098055 TGAGCTCGTTTCTCATCACTAC 57.902 45.455 9.64 0.00 35.81 2.73
771 921 6.712095 TCAGGATGCTTTGGATGACAATATAC 59.288 38.462 0.00 0.00 35.64 1.47
777 927 2.040145 TGTCAGGATGCTTTGGATGACA 59.960 45.455 1.92 1.92 43.33 3.58
778 928 2.715046 TGTCAGGATGCTTTGGATGAC 58.285 47.619 0.00 0.00 38.00 3.06
780 930 2.821378 TGTTGTCAGGATGCTTTGGATG 59.179 45.455 0.00 0.00 34.76 3.51
781 931 3.159213 TGTTGTCAGGATGCTTTGGAT 57.841 42.857 0.00 0.00 34.76 3.41
782 932 2.655090 TGTTGTCAGGATGCTTTGGA 57.345 45.000 0.00 0.00 34.76 3.53
783 933 3.508793 AGATTGTTGTCAGGATGCTTTGG 59.491 43.478 0.00 0.00 34.76 3.28
784 934 4.670992 CGAGATTGTTGTCAGGATGCTTTG 60.671 45.833 0.00 0.00 34.76 2.77
785 935 3.438087 CGAGATTGTTGTCAGGATGCTTT 59.562 43.478 0.00 0.00 34.76 3.51
786 936 3.005554 CGAGATTGTTGTCAGGATGCTT 58.994 45.455 0.00 0.00 34.76 3.91
790 942 2.768253 TGCGAGATTGTTGTCAGGAT 57.232 45.000 0.00 0.00 0.00 3.24
791 943 2.542020 TTGCGAGATTGTTGTCAGGA 57.458 45.000 0.00 0.00 0.00 3.86
795 947 4.351192 ACAAGTTTTGCGAGATTGTTGTC 58.649 39.130 0.00 0.00 30.18 3.18
796 948 4.351192 GACAAGTTTTGCGAGATTGTTGT 58.649 39.130 0.00 0.00 34.41 3.32
806 958 2.323939 TTATGCCGACAAGTTTTGCG 57.676 45.000 0.00 0.00 0.00 4.85
807 959 4.048504 ACTTTTATGCCGACAAGTTTTGC 58.951 39.130 0.00 0.00 0.00 3.68
812 964 9.609346 AACTTATATACTTTTATGCCGACAAGT 57.391 29.630 0.00 0.00 33.95 3.16
816 968 8.709646 CCTCAACTTATATACTTTTATGCCGAC 58.290 37.037 0.00 0.00 0.00 4.79
819 971 9.998106 TCTCCTCAACTTATATACTTTTATGCC 57.002 33.333 0.00 0.00 0.00 4.40
832 984 9.495572 CAAGTCTAACTTTTCTCCTCAACTTAT 57.504 33.333 0.00 0.00 36.03 1.73
833 985 7.441458 GCAAGTCTAACTTTTCTCCTCAACTTA 59.559 37.037 0.00 0.00 36.03 2.24
836 988 5.760743 AGCAAGTCTAACTTTTCTCCTCAAC 59.239 40.000 0.00 0.00 36.03 3.18
905 1366 7.307101 GCCGAAGTTTATGATTTGCTTCAAAAA 60.307 33.333 0.00 0.00 36.90 1.94
906 1367 6.145371 GCCGAAGTTTATGATTTGCTTCAAAA 59.855 34.615 0.00 0.00 36.90 2.44
907 1368 5.633182 GCCGAAGTTTATGATTTGCTTCAAA 59.367 36.000 0.00 0.00 37.75 2.69
908 1369 5.160641 GCCGAAGTTTATGATTTGCTTCAA 58.839 37.500 0.00 0.00 36.34 2.69
963 1424 1.481772 TGCAAAGAAAAACCAGCAGCT 59.518 42.857 0.00 0.00 0.00 4.24
964 1425 1.594397 GTGCAAAGAAAAACCAGCAGC 59.406 47.619 0.00 0.00 32.03 5.25
965 1426 1.854126 CGTGCAAAGAAAAACCAGCAG 59.146 47.619 0.00 0.00 32.03 4.24
966 1427 1.474478 TCGTGCAAAGAAAAACCAGCA 59.526 42.857 0.00 0.00 0.00 4.41
967 1428 2.202295 TCGTGCAAAGAAAAACCAGC 57.798 45.000 0.00 0.00 0.00 4.85
969 1430 2.287308 CCGATCGTGCAAAGAAAAACCA 60.287 45.455 15.09 0.00 0.00 3.67
970 1431 2.287368 ACCGATCGTGCAAAGAAAAACC 60.287 45.455 15.09 0.00 0.00 3.27
971 1432 2.719046 CACCGATCGTGCAAAGAAAAAC 59.281 45.455 15.09 0.00 35.18 2.43
976 1437 1.270094 ACTTCACCGATCGTGCAAAGA 60.270 47.619 15.09 0.00 42.69 2.52
995 1456 3.780902 CCAAATTCTCCCGCCATAAAAC 58.219 45.455 0.00 0.00 0.00 2.43
1089 1553 1.078567 CAGGAGTTGGAGCTGGAGC 60.079 63.158 0.00 0.00 42.49 4.70
1095 1565 1.446966 GTCGAGCAGGAGTTGGAGC 60.447 63.158 0.00 0.00 0.00 4.70
1112 1582 3.496160 GCGAGAGATAGAAGGAGAGGAGT 60.496 52.174 0.00 0.00 0.00 3.85
1379 1852 2.976284 AAACGGTGAGGGGGACAGGA 62.976 60.000 0.00 0.00 0.00 3.86
1383 1856 1.003718 CAGAAACGGTGAGGGGGAC 60.004 63.158 0.00 0.00 0.00 4.46
1385 1858 1.302511 CACAGAAACGGTGAGGGGG 60.303 63.158 0.00 0.00 38.54 5.40
1391 1864 1.068474 GATCGGACACAGAAACGGTG 58.932 55.000 0.00 0.00 41.95 4.94
1394 1867 2.254459 CTGAGATCGGACACAGAAACG 58.746 52.381 0.00 0.00 31.94 3.60
1401 1880 2.951745 CGCGCTGAGATCGGACAC 60.952 66.667 5.56 0.00 0.00 3.67
1533 2012 2.252260 CGCAGCCAAGAAACGTGG 59.748 61.111 0.00 0.00 39.33 4.94
1589 2076 2.477845 CTCGGCGCTGCAAAGAAG 59.522 61.111 12.58 0.00 0.00 2.85
1676 2163 4.681978 AAGAGCACGACGCCCACC 62.682 66.667 0.00 0.00 44.04 4.61
1901 2388 1.596496 CTTCCCTAGGGTTCCACCAT 58.404 55.000 27.58 0.00 41.02 3.55
1944 2439 4.638421 TCACGGGATTCCATTTAACATGAC 59.362 41.667 4.80 0.00 0.00 3.06
1945 2440 4.849518 TCACGGGATTCCATTTAACATGA 58.150 39.130 4.80 0.00 0.00 3.07
1946 2441 5.532406 AGATCACGGGATTCCATTTAACATG 59.468 40.000 0.00 0.00 32.67 3.21
1962 2470 4.553756 TCTCGATTGTAAGAGATCACGG 57.446 45.455 0.00 0.00 38.46 4.94
1974 2482 4.216042 TGCAACATTCAACATCTCGATTGT 59.784 37.500 0.00 0.00 0.00 2.71
1977 2485 4.036027 GGATGCAACATTCAACATCTCGAT 59.964 41.667 0.00 0.00 39.10 3.59
1980 2488 4.707030 TGGATGCAACATTCAACATCTC 57.293 40.909 0.00 0.00 39.10 2.75
1985 2493 3.609373 CGTTCATGGATGCAACATTCAAC 59.391 43.478 4.66 9.30 0.00 3.18
1988 2496 2.159338 AGCGTTCATGGATGCAACATTC 60.159 45.455 20.42 0.00 0.00 2.67
1989 2497 1.820519 AGCGTTCATGGATGCAACATT 59.179 42.857 20.42 0.00 0.00 2.71
1990 2498 1.133598 CAGCGTTCATGGATGCAACAT 59.866 47.619 20.42 0.00 0.00 2.71
1991 2499 0.522626 CAGCGTTCATGGATGCAACA 59.477 50.000 20.42 0.00 0.00 3.33
1993 2501 1.507630 GCAGCGTTCATGGATGCAA 59.492 52.632 20.42 0.00 45.55 4.08
1994 2502 3.189921 GCAGCGTTCATGGATGCA 58.810 55.556 20.42 0.00 45.55 3.96
1995 2503 1.063649 CTGCAGCGTTCATGGATGC 59.936 57.895 10.47 10.47 46.37 3.91
1996 2504 1.028330 ACCTGCAGCGTTCATGGATG 61.028 55.000 8.66 0.00 0.00 3.51
2005 2526 1.442769 CATCTTAACACCTGCAGCGT 58.557 50.000 8.66 4.50 0.00 5.07
2013 2534 3.751698 GGTCACAGAACCATCTTAACACC 59.248 47.826 0.00 0.00 39.27 4.16
2024 2545 5.875359 CAGGATAAACTAAGGTCACAGAACC 59.125 44.000 0.00 0.00 39.80 3.62
2034 2555 3.545703 CCCAGTGCAGGATAAACTAAGG 58.454 50.000 0.00 0.00 0.00 2.69
2035 2556 2.945668 GCCCAGTGCAGGATAAACTAAG 59.054 50.000 0.00 0.00 40.77 2.18
2036 2557 2.999331 GCCCAGTGCAGGATAAACTAA 58.001 47.619 0.00 0.00 40.77 2.24
2038 2559 3.577389 GCCCAGTGCAGGATAAACT 57.423 52.632 0.00 0.00 40.77 2.66
2049 2570 0.738389 AACAGAAAACGTGCCCAGTG 59.262 50.000 0.00 0.00 0.00 3.66
2050 2571 1.021968 GAACAGAAAACGTGCCCAGT 58.978 50.000 0.00 0.00 0.00 4.00
2051 2572 1.308998 AGAACAGAAAACGTGCCCAG 58.691 50.000 0.00 0.00 0.00 4.45
2052 2573 1.403679 CAAGAACAGAAAACGTGCCCA 59.596 47.619 0.00 0.00 0.00 5.36
2053 2574 1.864029 GCAAGAACAGAAAACGTGCCC 60.864 52.381 0.00 0.00 34.20 5.36
2054 2575 1.202245 TGCAAGAACAGAAAACGTGCC 60.202 47.619 0.00 0.00 37.99 5.01
2055 2576 2.187351 TGCAAGAACAGAAAACGTGC 57.813 45.000 0.00 0.00 38.88 5.34
2059 3200 7.524294 TTCTCAAAATGCAAGAACAGAAAAC 57.476 32.000 0.00 0.00 0.00 2.43
2066 3207 5.570589 CGAAGGATTCTCAAAATGCAAGAAC 59.429 40.000 0.00 0.00 44.75 3.01
2090 3232 7.830739 AGAATGTTGTGGGTCTTATTTGATTC 58.169 34.615 0.00 0.00 0.00 2.52
2098 3240 7.014711 TGCATTTTAAGAATGTTGTGGGTCTTA 59.985 33.333 10.20 0.00 32.69 2.10
2104 3246 5.782047 TCCTGCATTTTAAGAATGTTGTGG 58.218 37.500 0.00 8.21 0.00 4.17
2125 3268 6.476706 GCAGCCAGATAACATTTTTGTATTCC 59.523 38.462 0.00 0.00 0.00 3.01
2147 3290 1.887242 GCATGGCATGGCATTGCAG 60.887 57.895 32.08 23.55 44.59 4.41
2156 3299 0.762418 ATTCCAATGGGCATGGCATG 59.238 50.000 22.99 22.99 37.88 4.06
2160 3303 4.217510 TCTTAGAATTCCAATGGGCATGG 58.782 43.478 0.65 0.00 39.41 3.66
2213 3356 9.367160 TGTGAAAAGAAGAATCCTTTATTTCCT 57.633 29.630 0.00 0.00 36.95 3.36
2214 3357 9.981114 TTGTGAAAAGAAGAATCCTTTATTTCC 57.019 29.630 0.00 0.00 36.95 3.13
2219 3362 9.284968 CTACCTTGTGAAAAGAAGAATCCTTTA 57.715 33.333 0.00 0.00 33.85 1.85
2231 3374 6.485313 TCAACACCATACTACCTTGTGAAAAG 59.515 38.462 0.00 0.00 0.00 2.27
2233 3376 5.931294 TCAACACCATACTACCTTGTGAAA 58.069 37.500 0.00 0.00 0.00 2.69
2234 3377 5.554437 TCAACACCATACTACCTTGTGAA 57.446 39.130 0.00 0.00 0.00 3.18
2235 3378 5.071250 ACTTCAACACCATACTACCTTGTGA 59.929 40.000 0.00 0.00 0.00 3.58
2236 3379 5.305585 ACTTCAACACCATACTACCTTGTG 58.694 41.667 0.00 0.00 0.00 3.33
2237 3380 5.562298 ACTTCAACACCATACTACCTTGT 57.438 39.130 0.00 0.00 0.00 3.16
2238 3381 8.255206 TGTATACTTCAACACCATACTACCTTG 58.745 37.037 4.17 0.00 0.00 3.61
2239 3382 8.370266 TGTATACTTCAACACCATACTACCTT 57.630 34.615 4.17 0.00 0.00 3.50
2240 3383 7.837689 TCTGTATACTTCAACACCATACTACCT 59.162 37.037 4.17 0.00 0.00 3.08
2241 3384 7.919621 GTCTGTATACTTCAACACCATACTACC 59.080 40.741 4.17 0.00 0.00 3.18
2242 3385 8.464404 TGTCTGTATACTTCAACACCATACTAC 58.536 37.037 4.17 0.00 0.00 2.73
2243 3386 8.584063 TGTCTGTATACTTCAACACCATACTA 57.416 34.615 4.17 0.00 0.00 1.82
2244 3387 7.476540 TGTCTGTATACTTCAACACCATACT 57.523 36.000 4.17 0.00 0.00 2.12
2258 3401 1.482593 ACTGCCTGGCTGTCTGTATAC 59.517 52.381 23.51 0.00 35.96 1.47
2259 3402 1.482182 CACTGCCTGGCTGTCTGTATA 59.518 52.381 25.88 0.00 38.59 1.47
2260 3403 0.251354 CACTGCCTGGCTGTCTGTAT 59.749 55.000 25.88 3.39 38.59 2.29
2261 3404 0.831711 TCACTGCCTGGCTGTCTGTA 60.832 55.000 25.88 10.91 38.59 2.74
2262 3405 1.699054 TTCACTGCCTGGCTGTCTGT 61.699 55.000 25.88 11.20 38.59 3.41
2265 3408 1.740025 GTATTTCACTGCCTGGCTGTC 59.260 52.381 25.88 11.79 38.59 3.51
2266 3409 1.826385 GTATTTCACTGCCTGGCTGT 58.174 50.000 23.51 23.51 41.16 4.40
2267 3410 0.729116 CGTATTTCACTGCCTGGCTG 59.271 55.000 22.17 22.17 0.00 4.85
2268 3411 0.324943 ACGTATTTCACTGCCTGGCT 59.675 50.000 21.03 0.00 0.00 4.75
2269 3412 0.447801 CACGTATTTCACTGCCTGGC 59.552 55.000 12.87 12.87 0.00 4.85
2270 3413 1.086696 CCACGTATTTCACTGCCTGG 58.913 55.000 0.00 0.00 0.00 4.45
2271 3414 1.086696 CCCACGTATTTCACTGCCTG 58.913 55.000 0.00 0.00 0.00 4.85
2272 3415 0.676782 GCCCACGTATTTCACTGCCT 60.677 55.000 0.00 0.00 0.00 4.75
2273 3416 1.654023 GGCCCACGTATTTCACTGCC 61.654 60.000 0.00 0.00 0.00 4.85
2274 3417 0.958382 TGGCCCACGTATTTCACTGC 60.958 55.000 0.00 0.00 0.00 4.40
2284 3427 1.485294 TACAATCCAGTGGCCCACGT 61.485 55.000 8.52 1.46 39.64 4.49
2292 3435 6.370593 GTGTTGTGTACAATACAATCCAGTG 58.629 40.000 16.49 0.00 44.19 3.66
2299 3442 6.366604 CCACTATCGTGTTGTGTACAATACAA 59.633 38.462 19.76 6.59 44.75 2.41
2300 3443 5.865013 CCACTATCGTGTTGTGTACAATACA 59.135 40.000 19.76 1.83 44.75 2.29
2301 3444 6.094719 TCCACTATCGTGTTGTGTACAATAC 58.905 40.000 12.77 12.77 42.26 1.89
2302 3445 6.270156 TCCACTATCGTGTTGTGTACAATA 57.730 37.500 0.00 0.00 38.80 1.90
2303 3446 5.142061 TCCACTATCGTGTTGTGTACAAT 57.858 39.130 0.00 0.00 38.80 2.71
2306 3449 3.863424 CCATCCACTATCGTGTTGTGTAC 59.137 47.826 0.00 0.00 39.55 2.90
2307 3450 3.677700 GCCATCCACTATCGTGTTGTGTA 60.678 47.826 0.00 0.00 39.55 2.90
2308 3451 2.935238 GCCATCCACTATCGTGTTGTGT 60.935 50.000 0.00 0.00 39.55 3.72
2309 3452 1.665679 GCCATCCACTATCGTGTTGTG 59.334 52.381 0.00 0.00 39.55 3.33
2324 3537 0.741221 GGACCGTTCAGTGAGCCATC 60.741 60.000 0.93 0.00 0.00 3.51
2340 3553 1.160137 GCTGTGATGGTTGACAGGAC 58.840 55.000 0.00 0.00 40.06 3.85
2344 3557 1.308047 GTGTGCTGTGATGGTTGACA 58.692 50.000 0.00 0.00 0.00 3.58
2386 3599 6.539649 TTTGTTCGTTTCTGGAGTAAGATG 57.460 37.500 0.00 0.00 0.00 2.90
2552 3782 1.008652 TGCTGTGCGATGTTGTTGC 60.009 52.632 0.00 0.00 37.76 4.17
2556 3786 0.110509 GAGTGTGCTGTGCGATGTTG 60.111 55.000 0.00 0.00 0.00 3.33
2557 3787 0.250038 AGAGTGTGCTGTGCGATGTT 60.250 50.000 0.00 0.00 0.00 2.71
2558 3788 0.947660 CAGAGTGTGCTGTGCGATGT 60.948 55.000 0.00 0.00 0.00 3.06
2559 3789 0.947660 ACAGAGTGTGCTGTGCGATG 60.948 55.000 0.00 0.00 46.72 3.84
2561 3791 2.814604 ACAGAGTGTGCTGTGCGA 59.185 55.556 0.00 0.00 46.72 5.10
2576 3815 0.602638 AATCGCAGTTTGCCGAGACA 60.603 50.000 0.00 0.00 41.12 3.41
2605 3844 4.952335 GGAATCCATGAATCTCCTGTTGTT 59.048 41.667 0.00 0.00 0.00 2.83
2707 3958 1.669440 GTGTTCTCCCCGTGCTGTA 59.331 57.895 0.00 0.00 0.00 2.74
2730 3981 1.210478 GCAAGATAGTCTGAAGCCCCA 59.790 52.381 0.00 0.00 0.00 4.96
2827 4082 7.133891 AGTGAAATGGAATGAACTTTAGTCG 57.866 36.000 0.00 0.00 0.00 4.18
2868 4123 9.095065 CAATGAGGTACTGTACTATTTGTTACC 57.905 37.037 16.79 0.00 41.55 2.85
2901 4156 4.472108 TCGGTGGGGTTATAGACAGATTTT 59.528 41.667 0.00 0.00 0.00 1.82
2919 4174 4.238761 TCAGTGAAAGTACTTCTCGGTG 57.761 45.455 8.95 9.69 34.86 4.94
2920 4175 5.393243 GCTATCAGTGAAAGTACTTCTCGGT 60.393 44.000 8.95 0.00 34.86 4.69
2922 4177 5.641709 TGCTATCAGTGAAAGTACTTCTCG 58.358 41.667 8.95 0.00 34.86 4.04
2923 4178 7.412455 GCTTTGCTATCAGTGAAAGTACTTCTC 60.412 40.741 8.95 9.31 34.86 2.87
2935 4190 3.402058 GCTCTTGCTTTGCTATCAGTG 57.598 47.619 0.00 0.00 36.03 3.66
2964 4219 6.107901 TGCCTTTTATTTTGCAATACCTGT 57.892 33.333 0.00 0.00 0.00 4.00
2968 4223 6.250089 GTGCATGCCTTTTATTTTGCAATAC 58.750 36.000 16.68 0.00 41.26 1.89
2984 4240 1.767759 ATACTGAAAGGGTGCATGCC 58.232 50.000 16.68 6.42 39.30 4.40
3027 4283 6.601741 TTGTCCATCTTTTGAAACAATTGC 57.398 33.333 5.05 0.00 30.13 3.56
3088 4346 7.383029 TCAGTTGTAGGACAAAGTTTACATACG 59.617 37.037 10.12 0.00 40.15 3.06


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

AutoCloner maintained by Alex Coulton.