Multiple sequence alignment - TraesCS1D01G312100

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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 TraesCS1D01G312100 chr1D 100.000 6061 0 0 1 6061 407870491 407876551 0.000000e+00 11193.0
1 TraesCS1D01G312100 chr1B 91.939 2444 142 40 3653 6061 548536333 548538756 0.000000e+00 3371.0
2 TraesCS1D01G312100 chr1B 96.258 775 29 0 2889 3663 548535539 548536313 0.000000e+00 1271.0
3 TraesCS1D01G312100 chr1B 88.985 926 53 16 2011 2900 548534544 548535456 0.000000e+00 1099.0
4 TraesCS1D01G312100 chr1B 84.551 1081 90 23 285 1323 548531486 548532531 0.000000e+00 1000.0
5 TraesCS1D01G312100 chr1B 94.336 459 26 0 1496 1954 548532846 548533304 0.000000e+00 704.0
6 TraesCS1D01G312100 chr1B 90.254 236 22 1 1 236 548517475 548517709 2.120000e-79 307.0
7 TraesCS1D01G312100 chr1B 79.535 215 41 3 3752 3965 343121465 343121253 3.780000e-32 150.0
8 TraesCS1D01G312100 chr1B 94.915 59 1 2 1947 2005 548533328 548533384 2.330000e-14 91.6
9 TraesCS1D01G312100 chr1A 94.281 1731 75 14 1954 3662 503369707 503371435 0.000000e+00 2627.0
10 TraesCS1D01G312100 chr1A 94.909 1041 37 7 3661 4698 503371464 503372491 0.000000e+00 1615.0
11 TraesCS1D01G312100 chr1A 88.113 1304 111 26 683 1954 503368387 503369678 0.000000e+00 1509.0
12 TraesCS1D01G312100 chr1A 90.147 680 52 8 1 668 503367727 503368403 0.000000e+00 870.0
13 TraesCS1D01G312100 chr1A 90.087 575 39 9 5490 6061 503373110 503373669 0.000000e+00 730.0
14 TraesCS1D01G312100 chr1A 92.814 501 27 9 4749 5243 503372514 503373011 0.000000e+00 717.0
15 TraesCS1D01G312100 chr1A 100.000 41 0 0 5314 5354 503373052 503373092 6.510000e-10 76.8
16 TraesCS1D01G312100 chr4B 80.000 215 40 3 3752 3965 445971362 445971574 8.130000e-34 156.0
17 TraesCS1D01G312100 chr4B 91.111 90 7 1 2846 2935 91298396 91298308 2.970000e-23 121.0
18 TraesCS1D01G312100 chr4B 88.776 98 7 2 2839 2933 379084983 379084887 3.840000e-22 117.0
19 TraesCS1D01G312100 chr4A 79.535 215 42 2 3752 3965 698596939 698596726 1.050000e-32 152.0
20 TraesCS1D01G312100 chr7B 79.439 214 43 1 3752 3965 136967726 136967514 3.780000e-32 150.0
21 TraesCS1D01G312100 chr6A 79.535 215 40 4 3752 3965 169859908 169860119 3.780000e-32 150.0
22 TraesCS1D01G312100 chr6A 89.583 96 8 2 2836 2930 147460898 147460804 2.970000e-23 121.0
23 TraesCS1D01G312100 chr3B 79.535 215 41 3 3752 3965 239581198 239581410 3.780000e-32 150.0
24 TraesCS1D01G312100 chr3B 89.583 96 5 4 2836 2930 492208428 492208337 3.840000e-22 117.0
25 TraesCS1D01G312100 chr5B 78.761 226 44 4 3742 3965 113728829 113728606 1.360000e-31 148.0
26 TraesCS1D01G312100 chr6B 91.111 90 6 2 2846 2934 520230433 520230345 2.970000e-23 121.0
27 TraesCS1D01G312100 chr3D 89.583 96 7 2 2847 2941 537914051 537914144 1.070000e-22 119.0
28 TraesCS1D01G312100 chr4D 89.474 95 7 3 2839 2933 303843557 303843466 3.840000e-22 117.0


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 TraesCS1D01G312100 chr1D 407870491 407876551 6060 False 11193.000000 11193 100.000000 1 6061 1 chr1D.!!$F1 6060
1 TraesCS1D01G312100 chr1B 548531486 548538756 7270 False 1256.100000 3371 91.830667 285 6061 6 chr1B.!!$F2 5776
2 TraesCS1D01G312100 chr1A 503367727 503373669 5942 False 1163.542857 2627 92.907286 1 6061 7 chr1A.!!$F1 6060

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
899 962 0.033894 GTCGTCTCCCTCCTCTCCTT 60.034 60.000 0.0 0.0 0.00 3.36 F
902 965 0.336737 GTCTCCCTCCTCTCCTTGGA 59.663 60.000 0.0 0.0 0.00 3.53 F
1388 1486 0.602638 GTGGGACATCGCAGTGTTGA 60.603 55.000 0.0 0.0 44.52 3.18 F
1429 1527 1.396996 CGGATTTACAGTTGCCTTCCG 59.603 52.381 0.0 0.0 38.71 4.30 F
3213 4810 1.066071 GTACTGGTTCTGAGGGAAGGC 60.066 57.143 0.0 0.0 34.23 4.35 F
3296 4893 0.617413 CTGTCAGGATGGACCAAGCT 59.383 55.000 0.0 0.0 42.04 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 3501 1.070601 TGCAGCTTAACAGTGAGCAGA 59.929 47.619 10.83 0.0 38.82 4.26 R
2371 3858 1.910580 TTTAGCTTGCGAGGAGGGGG 61.911 60.000 2.37 0.0 0.00 5.40 R
3213 4810 1.066858 AGCCACTTGATGACGTACAGG 60.067 52.381 0.00 0.0 0.00 4.00 R
3296 4893 5.222254 ACTGCCTTTACTCCCTTTATTTGGA 60.222 40.000 0.00 0.0 0.00 3.53 R
5017 6653 0.109226 GTCCTGGAGAACCGAGTTCG 60.109 60.000 0.00 0.0 45.96 3.95 R
5250 6904 1.975660 TCCCAACGAAGGTTCCAAAG 58.024 50.000 0.00 0.0 32.98 2.77 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
21 22 4.708726 CCCCATTCTTTGTAGCTTCAAG 57.291 45.455 5.88 0.00 0.00 3.02
24 25 5.355350 CCCCATTCTTTGTAGCTTCAAGTAG 59.645 44.000 5.88 2.56 0.00 2.57
26 27 5.940470 CCATTCTTTGTAGCTTCAAGTAGGT 59.060 40.000 5.88 0.00 0.00 3.08
34 35 2.564947 AGCTTCAAGTAGGTGGAGTGAG 59.435 50.000 0.00 0.00 0.00 3.51
36 37 3.244249 GCTTCAAGTAGGTGGAGTGAGTT 60.244 47.826 0.00 0.00 0.00 3.01
46 47 1.189403 GGAGTGAGTTATCGCGAACG 58.811 55.000 15.24 0.00 41.02 3.95
59 60 0.735287 GCGAACGAGAGGTGGGTTAC 60.735 60.000 0.00 0.00 0.00 2.50
127 128 1.553248 CCTCCACCCGATGAAGTAACA 59.447 52.381 0.00 0.00 0.00 2.41
152 153 2.358737 CCTCTCCCCGCACACAAC 60.359 66.667 0.00 0.00 0.00 3.32
173 174 5.201713 ACAGGAACATGTACGAGGATATG 57.798 43.478 0.00 0.00 0.00 1.78
195 196 0.178831 ATCCCCTTGACCAAGACCCT 60.179 55.000 11.06 0.00 40.79 4.34
209 210 1.539869 ACCCTGGCATGAGACCACT 60.540 57.895 0.00 0.00 32.49 4.00
223 224 1.816835 GACCACTGTCTCCGTGTATGA 59.183 52.381 0.00 0.00 38.53 2.15
245 246 6.898041 TGATGTGTACACTTTGAACTTATGC 58.102 36.000 25.60 5.47 0.00 3.14
257 258 3.679502 TGAACTTATGCGTCACACATCTG 59.320 43.478 0.00 0.00 0.00 2.90
275 276 3.349927 TCTGATGCATTTGGAGGTCAAG 58.650 45.455 0.00 0.00 36.62 3.02
276 277 3.087031 CTGATGCATTTGGAGGTCAAGT 58.913 45.455 0.00 0.00 36.62 3.16
360 372 5.332055 CGTAGTCGTGACTTGTAAGTTTTGG 60.332 44.000 7.97 0.00 42.54 3.28
383 395 1.891919 GTCAAACGTGAGGGCTGCA 60.892 57.895 0.50 0.00 33.27 4.41
398 410 2.653766 GCAAAACACGCACCACCG 60.654 61.111 0.00 0.00 0.00 4.94
448 460 2.159558 TCTCGTAAGTGAGCACGATGTC 60.160 50.000 0.00 0.00 45.28 3.06
467 479 4.285020 TGTCATCTGAGATAAGCCTCACT 58.715 43.478 0.00 0.00 38.18 3.41
468 480 5.449553 TGTCATCTGAGATAAGCCTCACTA 58.550 41.667 0.00 0.00 38.18 2.74
490 502 9.149225 CACTAATAGGAATGCACTCTGATTATC 57.851 37.037 0.00 0.00 0.00 1.75
507 519 8.891720 TCTGATTATCTGATATGATCTCTCGTG 58.108 37.037 9.56 0.00 0.00 4.35
576 588 2.161855 CAATGTTGCAGAGGCTAACCA 58.838 47.619 0.00 0.00 41.91 3.67
632 645 1.674962 GGCCAGATGTTGATCTCAAGC 59.325 52.381 0.00 0.00 36.75 4.01
663 677 9.449719 TTTAGAGTGATCTCAAGTTTATTTCCC 57.550 33.333 0.00 0.00 42.66 3.97
664 678 6.109359 AGAGTGATCTCAAGTTTATTTCCCG 58.891 40.000 0.00 0.00 42.66 5.14
665 679 5.186198 AGTGATCTCAAGTTTATTTCCCGG 58.814 41.667 0.00 0.00 0.00 5.73
666 680 5.045869 AGTGATCTCAAGTTTATTTCCCGGA 60.046 40.000 0.73 0.00 0.00 5.14
667 681 5.823045 GTGATCTCAAGTTTATTTCCCGGAT 59.177 40.000 0.73 0.00 0.00 4.18
668 682 6.318900 GTGATCTCAAGTTTATTTCCCGGATT 59.681 38.462 0.73 0.00 0.00 3.01
669 683 6.889722 TGATCTCAAGTTTATTTCCCGGATTT 59.110 34.615 0.73 0.00 0.00 2.17
670 684 7.396055 TGATCTCAAGTTTATTTCCCGGATTTT 59.604 33.333 0.73 0.00 0.00 1.82
671 685 6.919721 TCTCAAGTTTATTTCCCGGATTTTG 58.080 36.000 0.73 0.00 0.00 2.44
672 686 6.492087 TCTCAAGTTTATTTCCCGGATTTTGT 59.508 34.615 0.73 0.00 0.00 2.83
673 687 7.014808 TCTCAAGTTTATTTCCCGGATTTTGTT 59.985 33.333 0.73 0.00 0.00 2.83
674 688 7.501844 TCAAGTTTATTTCCCGGATTTTGTTT 58.498 30.769 0.73 0.00 0.00 2.83
675 689 7.988028 TCAAGTTTATTTCCCGGATTTTGTTTT 59.012 29.630 0.73 0.00 0.00 2.43
676 690 7.722795 AGTTTATTTCCCGGATTTTGTTTTG 57.277 32.000 0.73 0.00 0.00 2.44
677 691 7.501844 AGTTTATTTCCCGGATTTTGTTTTGA 58.498 30.769 0.73 0.00 0.00 2.69
678 692 7.655732 AGTTTATTTCCCGGATTTTGTTTTGAG 59.344 33.333 0.73 0.00 0.00 3.02
679 693 4.329462 TTTCCCGGATTTTGTTTTGAGG 57.671 40.909 0.73 0.00 0.00 3.86
680 694 2.243810 TCCCGGATTTTGTTTTGAGGG 58.756 47.619 0.73 0.00 38.95 4.30
681 695 1.275010 CCCGGATTTTGTTTTGAGGGG 59.725 52.381 0.73 0.00 34.19 4.79
682 696 2.243810 CCGGATTTTGTTTTGAGGGGA 58.756 47.619 0.00 0.00 0.00 4.81
683 697 2.630580 CCGGATTTTGTTTTGAGGGGAA 59.369 45.455 0.00 0.00 0.00 3.97
684 698 3.306019 CCGGATTTTGTTTTGAGGGGAAG 60.306 47.826 0.00 0.00 0.00 3.46
685 699 3.320826 CGGATTTTGTTTTGAGGGGAAGT 59.679 43.478 0.00 0.00 0.00 3.01
739 788 1.961277 GGAACGTGTCCAGCCAGTG 60.961 63.158 10.67 0.00 46.97 3.66
760 809 2.045926 CAGGCCAAACTCTCCGGG 60.046 66.667 5.01 0.00 0.00 5.73
765 814 1.179174 GCCAAACTCTCCGGGCTTTT 61.179 55.000 0.00 0.00 43.09 2.27
766 815 0.881796 CCAAACTCTCCGGGCTTTTC 59.118 55.000 0.00 0.00 0.00 2.29
767 816 1.545651 CCAAACTCTCCGGGCTTTTCT 60.546 52.381 0.00 0.00 0.00 2.52
768 817 1.537202 CAAACTCTCCGGGCTTTTCTG 59.463 52.381 0.00 0.00 0.00 3.02
769 818 0.606673 AACTCTCCGGGCTTTTCTGC 60.607 55.000 0.00 0.00 0.00 4.26
770 819 2.047274 TCTCCGGGCTTTTCTGCG 60.047 61.111 0.00 0.00 0.00 5.18
771 820 3.127533 CTCCGGGCTTTTCTGCGG 61.128 66.667 0.00 0.00 0.00 5.69
772 821 3.901797 CTCCGGGCTTTTCTGCGGT 62.902 63.158 0.00 0.00 0.00 5.68
773 822 3.737172 CCGGGCTTTTCTGCGGTG 61.737 66.667 0.00 0.00 0.00 4.94
816 876 1.208535 TCCGTCAATCGCTTTACCCAT 59.791 47.619 0.00 0.00 38.35 4.00
888 951 4.838486 CGCTGCCTCGTCGTCTCC 62.838 72.222 0.00 0.00 0.00 3.71
892 955 3.519930 GCCTCGTCGTCTCCCTCC 61.520 72.222 0.00 0.00 0.00 4.30
893 956 2.272797 CCTCGTCGTCTCCCTCCT 59.727 66.667 0.00 0.00 0.00 3.69
894 957 1.820481 CCTCGTCGTCTCCCTCCTC 60.820 68.421 0.00 0.00 0.00 3.71
895 958 1.222387 CTCGTCGTCTCCCTCCTCT 59.778 63.158 0.00 0.00 0.00 3.69
896 959 0.812412 CTCGTCGTCTCCCTCCTCTC 60.812 65.000 0.00 0.00 0.00 3.20
899 962 0.033894 GTCGTCTCCCTCCTCTCCTT 60.034 60.000 0.00 0.00 0.00 3.36
901 964 1.040339 CGTCTCCCTCCTCTCCTTGG 61.040 65.000 0.00 0.00 0.00 3.61
902 965 0.336737 GTCTCCCTCCTCTCCTTGGA 59.663 60.000 0.00 0.00 0.00 3.53
1149 1242 1.063567 CCCTCCCTGCTAGAGTACTGT 60.064 57.143 0.00 0.00 0.00 3.55
1197 1291 3.428282 GTTTCCACGGCCGCGATT 61.428 61.111 28.58 1.31 0.00 3.34
1278 1376 4.323477 CGGGCGTCAGGGGTTTGA 62.323 66.667 0.00 0.00 0.00 2.69
1314 1412 0.821711 TACTGGGTGTTTGGTGCTGC 60.822 55.000 0.00 0.00 0.00 5.25
1315 1413 1.829533 CTGGGTGTTTGGTGCTGCT 60.830 57.895 0.00 0.00 0.00 4.24
1316 1414 2.079020 CTGGGTGTTTGGTGCTGCTG 62.079 60.000 0.00 0.00 0.00 4.41
1317 1415 2.028043 GGTGTTTGGTGCTGCTGC 59.972 61.111 8.89 8.89 40.20 5.25
1332 1430 2.951315 CTGCTGTGCGCACTGTGAG 61.951 63.158 37.00 29.85 45.47 3.51
1337 1435 3.601685 TGCGCACTGTGAGACCGA 61.602 61.111 15.86 0.00 0.00 4.69
1344 1442 1.444553 CTGTGAGACCGAGTTCGCC 60.445 63.158 0.00 0.00 38.18 5.54
1388 1486 0.602638 GTGGGACATCGCAGTGTTGA 60.603 55.000 0.00 0.00 44.52 3.18
1408 1506 6.016360 TGTTGAAGTTTGATTCCATGGTAGTG 60.016 38.462 12.58 0.00 0.00 2.74
1410 1508 3.009723 AGTTTGATTCCATGGTAGTGCG 58.990 45.455 12.58 0.00 0.00 5.34
1429 1527 1.396996 CGGATTTACAGTTGCCTTCCG 59.603 52.381 0.00 0.00 38.71 4.30
1437 1535 2.749621 ACAGTTGCCTTCCGATTTCATC 59.250 45.455 0.00 0.00 0.00 2.92
1463 1561 2.930682 GGTTCGAACCTTGCATAGTCTC 59.069 50.000 34.98 8.19 45.75 3.36
1468 1566 2.656560 ACCTTGCATAGTCTCGTGTC 57.343 50.000 0.00 0.00 0.00 3.67
1522 1796 4.279169 TGCTTAGCTAAATCCCATTGATGC 59.721 41.667 7.74 3.54 32.68 3.91
1542 1816 3.751175 TGCGAATCTTAAACCAGTTGAGG 59.249 43.478 0.00 0.00 0.00 3.86
1549 1823 2.185004 AAACCAGTTGAGGGTGATCG 57.815 50.000 0.00 0.00 39.01 3.69
1561 1835 1.412710 GGGTGATCGGCTCATCTGTAA 59.587 52.381 0.00 0.00 35.17 2.41
1727 2001 6.893583 ACATCATGAGGTAAGCAGAGTAATT 58.106 36.000 12.06 0.00 0.00 1.40
1750 2024 7.667043 TTAAGCCATGTTAGTGTTTACTGAG 57.333 36.000 0.00 0.00 37.78 3.35
1842 2116 7.471721 TCATATGGAAATTCAAAGTGTTAGCG 58.528 34.615 2.13 0.00 0.00 4.26
2136 3615 5.733676 TCTGACTGAAGTATATTTGCTGCA 58.266 37.500 0.00 0.00 0.00 4.41
2178 3657 6.272318 TCTTTGTGAGCTGTGTTAATTTTGG 58.728 36.000 0.00 0.00 0.00 3.28
2204 3685 3.819245 TGGTACAGGCAAAAGCTGT 57.181 47.368 0.00 0.00 35.35 4.40
2368 3855 2.827921 GGTGAGAATGCCAAAACATCCT 59.172 45.455 0.00 0.00 0.00 3.24
2369 3856 3.119352 GGTGAGAATGCCAAAACATCCTC 60.119 47.826 0.00 0.00 32.44 3.71
2370 3857 3.091545 TGAGAATGCCAAAACATCCTCC 58.908 45.455 0.00 0.00 30.87 4.30
2371 3858 2.428530 GAGAATGCCAAAACATCCTCCC 59.571 50.000 0.00 0.00 25.82 4.30
2400 3888 5.535030 TCCTCGCAAGCTAAAGATCATAGTA 59.465 40.000 0.00 0.00 37.18 1.82
2531 4026 6.705863 AGGAATTGCTCACATCTAATTTCC 57.294 37.500 0.00 0.00 0.00 3.13
2540 4035 6.588719 TCACATCTAATTTCCTGTTTTGGG 57.411 37.500 0.00 0.00 0.00 4.12
2541 4036 6.074648 TCACATCTAATTTCCTGTTTTGGGT 58.925 36.000 0.00 0.00 0.00 4.51
2543 4038 7.070571 TCACATCTAATTTCCTGTTTTGGGTTT 59.929 33.333 0.00 0.00 0.00 3.27
2576 4071 5.039333 GTCTGTTATGCTTGCCATTGATTC 58.961 41.667 0.00 0.00 35.34 2.52
2580 4075 6.973843 TGTTATGCTTGCCATTGATTCTATC 58.026 36.000 0.00 0.00 35.34 2.08
2589 4084 4.889409 GCCATTGATTCTATCCTCACCAAA 59.111 41.667 0.00 0.00 0.00 3.28
2735 4238 2.680841 GCACCGCAACCTTTATCATACA 59.319 45.455 0.00 0.00 0.00 2.29
2822 4325 6.228977 TCCTCCTGGCTATACCTAATAACT 57.771 41.667 0.00 0.00 40.22 2.24
2878 4382 7.013369 GTCCCAAAATAAGTGTCTCAACTTTCT 59.987 37.037 0.00 0.00 40.77 2.52
2882 4386 9.869844 CAAAATAAGTGTCTCAACTTTCTACTG 57.130 33.333 0.00 0.00 40.77 2.74
2892 4489 9.962783 GTCTCAACTTTCTACTGACTTTAGTAA 57.037 33.333 0.00 0.00 33.09 2.24
3061 4658 8.218338 AGCTTCCATCTATAGTGAACATTTTG 57.782 34.615 0.00 0.00 0.00 2.44
3092 4689 1.939255 GTGAAGATTCCTGCTAGCAGC 59.061 52.381 34.82 22.55 42.35 5.25
3114 4711 4.553547 GCATTATGTTGTAGTAGCAGCTGC 60.554 45.833 31.53 31.53 42.49 5.25
3213 4810 1.066071 GTACTGGTTCTGAGGGAAGGC 60.066 57.143 0.00 0.00 34.23 4.35
3267 4864 2.466846 CAACCAAAGAAGCAAGTGCAG 58.533 47.619 6.00 0.00 45.16 4.41
3296 4893 0.617413 CTGTCAGGATGGACCAAGCT 59.383 55.000 0.00 0.00 42.04 3.74
3685 5312 5.259632 AGAATTGCTATTCTTGCAGTCCTT 58.740 37.500 16.34 0.00 46.53 3.36
3686 5313 5.713861 AGAATTGCTATTCTTGCAGTCCTTT 59.286 36.000 16.34 0.00 46.53 3.11
3861 5488 9.454859 AAAATGAACTAGATTAGACAAAGGGAG 57.545 33.333 0.00 0.00 0.00 4.30
3911 5538 7.232737 ACCAACCAAACCAAAACCAAATTTTTA 59.767 29.630 0.00 0.00 38.50 1.52
4207 5834 7.872993 TCTGTACCATAAACTCTTCTGTTCTTG 59.127 37.037 0.00 0.00 0.00 3.02
4302 5929 4.496341 CGTTGTCTTGTCTGTGCAATTCTT 60.496 41.667 0.00 0.00 0.00 2.52
4333 5962 3.737850 TGTTGTTTCCATGCATTTTCCC 58.262 40.909 0.00 0.00 0.00 3.97
4336 5966 2.302445 TGTTTCCATGCATTTTCCCCTG 59.698 45.455 0.00 0.00 0.00 4.45
4340 5970 1.066716 CCATGCATTTTCCCCTGTGTG 60.067 52.381 0.00 0.00 0.00 3.82
4346 5976 3.552068 GCATTTTCCCCTGTGTGTGTAAC 60.552 47.826 0.00 0.00 37.35 2.50
4391 6021 9.569167 TCTTTACGTAAGATCTGTATTCAGTTG 57.431 33.333 8.23 0.00 38.98 3.16
4410 6040 5.743872 CAGTTGGACTTAAGTTTTTCTGTGC 59.256 40.000 10.02 0.00 0.00 4.57
4548 6178 5.602628 GGTTAGGCTAACCTCTCTACATTG 58.397 45.833 37.59 0.00 46.34 2.82
4750 6386 4.207165 AGGCTTTCTGCAAAGTGAAGTTA 58.793 39.130 0.36 0.00 45.15 2.24
5003 6639 7.890515 TGAAATGATGTAGATAGAGATCGCTT 58.109 34.615 3.68 0.00 37.15 4.68
5004 6640 8.026026 TGAAATGATGTAGATAGAGATCGCTTC 58.974 37.037 3.68 2.69 37.15 3.86
5014 6650 0.739561 AGATCGCTTCCTACCGTGAC 59.260 55.000 0.00 0.00 0.00 3.67
5016 6652 2.001361 ATCGCTTCCTACCGTGACCG 62.001 60.000 0.00 0.00 0.00 4.79
5017 6653 2.508663 GCTTCCTACCGTGACCGC 60.509 66.667 0.00 0.00 0.00 5.68
5036 6672 0.109226 CGAACTCGGTTCTCCAGGAC 60.109 60.000 12.80 0.00 40.05 3.85
5061 6698 3.513912 TGCATAAAGAGGTCTTTCTCCGA 59.486 43.478 8.25 0.00 44.34 4.55
5065 6702 1.783071 AGAGGTCTTTCTCCGATCCC 58.217 55.000 0.00 0.00 34.46 3.85
5072 6709 0.822164 TTTCTCCGATCCCGTCCTTC 59.178 55.000 0.00 0.00 0.00 3.46
5073 6710 0.323999 TTCTCCGATCCCGTCCTTCA 60.324 55.000 0.00 0.00 0.00 3.02
5074 6711 0.106167 TCTCCGATCCCGTCCTTCAT 60.106 55.000 0.00 0.00 0.00 2.57
5075 6712 0.753262 CTCCGATCCCGTCCTTCATT 59.247 55.000 0.00 0.00 0.00 2.57
5078 6715 1.670811 CCGATCCCGTCCTTCATTTTG 59.329 52.381 0.00 0.00 0.00 2.44
5111 6750 2.216940 CGACTTTTGAACTAACGCGACA 59.783 45.455 15.93 0.00 0.00 4.35
5175 6815 6.070710 AGTCTTAACTACTGACAATTCCCTCC 60.071 42.308 0.00 0.00 32.59 4.30
5246 6900 9.097257 ACAACCAAGAACTATTTCATGTTTTTG 57.903 29.630 0.00 0.00 37.74 2.44
5250 6904 9.191995 CCAAGAACTATTTCATGTTTTTGGTAC 57.808 33.333 15.48 0.00 45.43 3.34
5255 6909 9.541143 AACTATTTCATGTTTTTGGTACTTTGG 57.459 29.630 0.00 0.00 0.00 3.28
5276 6930 3.118371 GGAACCTTCGTTGGGATACATCT 60.118 47.826 2.03 0.00 31.44 2.90
5304 6958 1.098712 GTGCACGTTTCAACCCCTGA 61.099 55.000 0.00 0.00 0.00 3.86
5305 6959 0.179004 TGCACGTTTCAACCCCTGAT 60.179 50.000 0.00 0.00 32.78 2.90
5306 6960 1.072489 TGCACGTTTCAACCCCTGATA 59.928 47.619 0.00 0.00 32.78 2.15
5307 6961 1.737793 GCACGTTTCAACCCCTGATAG 59.262 52.381 0.00 0.00 32.78 2.08
5308 6962 1.737793 CACGTTTCAACCCCTGATAGC 59.262 52.381 0.00 0.00 32.78 2.97
5309 6963 1.339727 ACGTTTCAACCCCTGATAGCC 60.340 52.381 0.00 0.00 32.78 3.93
5310 6964 1.763968 GTTTCAACCCCTGATAGCCC 58.236 55.000 0.00 0.00 32.78 5.19
5311 6965 1.285078 GTTTCAACCCCTGATAGCCCT 59.715 52.381 0.00 0.00 32.78 5.19
5354 7031 0.682209 GGCCAGTGTTGATCCATGCT 60.682 55.000 0.00 0.00 0.00 3.79
5355 7032 0.454600 GCCAGTGTTGATCCATGCTG 59.545 55.000 0.00 0.00 0.00 4.41
5356 7033 0.454600 CCAGTGTTGATCCATGCTGC 59.545 55.000 0.00 0.00 0.00 5.25
5357 7034 1.460504 CAGTGTTGATCCATGCTGCT 58.539 50.000 0.00 0.00 0.00 4.24
5358 7035 1.132453 CAGTGTTGATCCATGCTGCTG 59.868 52.381 0.00 0.00 0.00 4.41
5359 7036 0.179145 GTGTTGATCCATGCTGCTGC 60.179 55.000 8.89 8.89 40.20 5.25
5361 7038 0.100682 GTTGATCCATGCTGCTGCTG 59.899 55.000 17.00 11.64 40.48 4.41
5362 7039 1.035385 TTGATCCATGCTGCTGCTGG 61.035 55.000 20.44 20.44 40.48 4.85
5370 7047 4.415332 CTGCTGCTGGGCGCTTTG 62.415 66.667 7.64 0.00 40.11 2.77
5373 7050 3.677648 CTGCTGGGCGCTTTGCTT 61.678 61.111 7.64 0.00 45.43 3.91
5374 7051 3.621892 CTGCTGGGCGCTTTGCTTC 62.622 63.158 7.64 0.00 45.43 3.86
5392 7069 5.988287 TGCTTCCCAAAAGTTTCTTCAAAT 58.012 33.333 0.00 0.00 0.00 2.32
5394 7071 7.560368 TGCTTCCCAAAAGTTTCTTCAAATTA 58.440 30.769 0.00 0.00 0.00 1.40
5408 7085 4.448537 TCAAATTAAATCGGCTGGTTGG 57.551 40.909 0.00 0.00 0.00 3.77
5429 7106 3.184683 GCTGACGCTTCTCTGCCG 61.185 66.667 0.00 0.00 0.00 5.69
5434 7111 0.798771 GACGCTTCTCTGCCGTACTG 60.799 60.000 0.00 0.00 0.00 2.74
5455 7134 3.850122 GGTTCTTCCCTATGCAAACAC 57.150 47.619 0.00 0.00 0.00 3.32
5456 7135 2.492088 GGTTCTTCCCTATGCAAACACC 59.508 50.000 0.00 0.00 0.00 4.16
5475 7154 1.273688 CAAGTCGTTCGTGTGTGTGA 58.726 50.000 0.00 0.00 0.00 3.58
5477 7156 1.556564 AGTCGTTCGTGTGTGTGAAG 58.443 50.000 0.00 0.00 0.00 3.02
5485 7164 3.381045 TCGTGTGTGTGAAGATGAAGTC 58.619 45.455 0.00 0.00 0.00 3.01
5486 7165 2.153817 CGTGTGTGTGAAGATGAAGTCG 59.846 50.000 0.00 0.00 0.00 4.18
5487 7166 2.096713 GTGTGTGTGAAGATGAAGTCGC 60.097 50.000 0.00 0.00 0.00 5.19
5505 7188 4.935205 AGTCGCTTTACATGTGAGCAAATA 59.065 37.500 25.87 12.10 36.22 1.40
5567 7251 4.284234 CCTGGTTTGGAATGTGGAGATTTT 59.716 41.667 0.00 0.00 0.00 1.82
5609 7293 6.296026 AGTTGATTGTTCTGCCAAGTTAGTA 58.704 36.000 0.00 0.00 0.00 1.82
5649 7333 2.288763 GGTGCCCAATGAAATTTCACGT 60.289 45.455 22.71 11.29 40.49 4.49
5677 7361 4.207891 ACCTCATTGTGGTGAGATGTAC 57.792 45.455 9.54 0.00 46.77 2.90
5678 7362 3.190079 CCTCATTGTGGTGAGATGTACG 58.810 50.000 5.53 0.00 46.77 3.67
5680 7364 4.142249 CCTCATTGTGGTGAGATGTACGTA 60.142 45.833 5.53 0.00 46.77 3.57
5681 7365 4.993905 TCATTGTGGTGAGATGTACGTAG 58.006 43.478 0.00 0.00 0.00 3.51
5683 7367 5.184287 TCATTGTGGTGAGATGTACGTAGAA 59.816 40.000 0.00 0.00 0.00 2.10
5684 7368 5.654603 TTGTGGTGAGATGTACGTAGAAT 57.345 39.130 0.00 0.00 0.00 2.40
5685 7369 4.993905 TGTGGTGAGATGTACGTAGAATG 58.006 43.478 0.00 0.00 0.00 2.67
5699 7383 5.032863 ACGTAGAATGAGAAAATACCGTCG 58.967 41.667 0.00 0.00 0.00 5.12
5766 7450 2.224281 TGCCAACTGCCTAGATAATCCG 60.224 50.000 0.00 0.00 40.16 4.18
5867 7551 5.691508 ATAAACATGTAGCGTACACGAAC 57.308 39.130 5.84 3.55 42.23 3.95
5875 7559 3.476295 AGCGTACACGAACGAAATCTA 57.524 42.857 5.84 0.00 45.68 1.98
5879 7563 4.258782 GCGTACACGAACGAAATCTAAGTC 60.259 45.833 5.84 0.00 45.68 3.01
5891 7575 7.136119 ACGAAATCTAAGTCGCAATTGAAAAA 58.864 30.769 10.34 0.00 40.95 1.94
5892 7576 7.112984 ACGAAATCTAAGTCGCAATTGAAAAAC 59.887 33.333 10.34 0.86 40.95 2.43
5951 7635 0.462759 CGAGATGAAAGGGAGTGGCC 60.463 60.000 0.00 0.00 0.00 5.36
5972 7656 1.142465 AGCCAATGATCAGCCTACAGG 59.858 52.381 0.09 0.00 38.53 4.00
6057 7744 2.348059 CAGCTCAATTCAGACTTCGCTC 59.652 50.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.894784 TCCACCTACTTGAAGCTACAAAG 58.105 43.478 0.00 0.00 0.00 2.77
21 22 2.541178 CGCGATAACTCACTCCACCTAC 60.541 54.545 0.00 0.00 0.00 3.18
24 25 0.454600 TCGCGATAACTCACTCCACC 59.545 55.000 3.71 0.00 0.00 4.61
26 27 1.466866 CGTTCGCGATAACTCACTCCA 60.467 52.381 10.88 0.00 44.71 3.86
92 93 1.648467 GGAGGTTGCAGGACGATTGC 61.648 60.000 0.00 0.00 41.86 3.56
127 128 0.907704 TGCGGGGAGAGGTTATGTGT 60.908 55.000 0.00 0.00 0.00 3.72
152 153 4.560128 CCATATCCTCGTACATGTTCCTG 58.440 47.826 2.30 0.00 0.00 3.86
173 174 0.256177 GTCTTGGTCAAGGGGATCCC 59.744 60.000 23.95 23.95 45.90 3.85
209 210 3.759618 TGTACACATCATACACGGAGACA 59.240 43.478 0.00 0.00 0.00 3.41
223 224 5.468746 ACGCATAAGTTCAAAGTGTACACAT 59.531 36.000 27.06 13.66 0.00 3.21
245 246 3.422655 CAAATGCATCAGATGTGTGACG 58.577 45.455 12.18 0.00 0.00 4.35
257 258 3.507233 TGAACTTGACCTCCAAATGCATC 59.493 43.478 0.00 0.00 33.76 3.91
275 276 4.186926 GGGTTCCGGAGTAATTAGTGAAC 58.813 47.826 3.34 11.11 0.00 3.18
276 277 3.198417 GGGGTTCCGGAGTAATTAGTGAA 59.802 47.826 3.34 0.00 0.00 3.18
334 337 4.531332 AACTTACAAGTCACGACTACGTC 58.469 43.478 0.00 0.00 44.22 4.34
335 338 4.558538 AACTTACAAGTCACGACTACGT 57.441 40.909 0.00 4.04 45.79 3.57
355 367 4.036971 CCCTCACGTTTGACATAACCAAAA 59.963 41.667 0.00 0.00 35.57 2.44
360 372 2.159627 CAGCCCTCACGTTTGACATAAC 59.840 50.000 0.00 0.00 0.00 1.89
383 395 2.124653 TCCGGTGGTGCGTGTTTT 60.125 55.556 0.00 0.00 0.00 2.43
398 410 5.124617 CCATTTCCTAAAACAGAAGAGCTCC 59.875 44.000 10.93 0.00 0.00 4.70
436 448 2.094675 TCTCAGATGACATCGTGCTCA 58.905 47.619 9.77 0.00 0.00 4.26
448 460 7.395772 TCCTATTAGTGAGGCTTATCTCAGATG 59.604 40.741 0.00 0.00 43.54 2.90
467 479 9.093458 TCAGATAATCAGAGTGCATTCCTATTA 57.907 33.333 5.47 10.22 0.00 0.98
468 480 7.971201 TCAGATAATCAGAGTGCATTCCTATT 58.029 34.615 5.47 8.43 0.00 1.73
490 502 6.251655 TCATCACACGAGAGATCATATCAG 57.748 41.667 0.00 0.00 0.00 2.90
507 519 6.509418 TGCCAATAGGTTAAAGTTCATCAC 57.491 37.500 0.00 0.00 37.19 3.06
576 588 0.106918 TGTTTCCAAGGTCGTTGCCT 60.107 50.000 0.00 0.00 41.41 4.75
582 594 2.357637 TGAAGCTTTGTTTCCAAGGTCG 59.642 45.455 0.00 0.00 30.74 4.79
655 669 6.459923 CCTCAAAACAAAATCCGGGAAATAA 58.540 36.000 0.00 0.00 0.00 1.40
656 670 5.046950 CCCTCAAAACAAAATCCGGGAAATA 60.047 40.000 0.00 0.00 32.10 1.40
657 671 4.262851 CCCTCAAAACAAAATCCGGGAAAT 60.263 41.667 0.00 0.00 32.10 2.17
658 672 3.070302 CCCTCAAAACAAAATCCGGGAAA 59.930 43.478 0.00 0.00 32.10 3.13
659 673 2.630580 CCCTCAAAACAAAATCCGGGAA 59.369 45.455 0.00 0.00 32.10 3.97
660 674 2.243810 CCCTCAAAACAAAATCCGGGA 58.756 47.619 0.00 0.00 32.10 5.14
661 675 1.275010 CCCCTCAAAACAAAATCCGGG 59.725 52.381 0.00 0.00 0.00 5.73
662 676 2.243810 TCCCCTCAAAACAAAATCCGG 58.756 47.619 0.00 0.00 0.00 5.14
663 677 3.320826 ACTTCCCCTCAAAACAAAATCCG 59.679 43.478 0.00 0.00 0.00 4.18
664 678 4.955811 ACTTCCCCTCAAAACAAAATCC 57.044 40.909 0.00 0.00 0.00 3.01
665 679 8.902540 AATAAACTTCCCCTCAAAACAAAATC 57.097 30.769 0.00 0.00 0.00 2.17
666 680 9.337396 GAAATAAACTTCCCCTCAAAACAAAAT 57.663 29.630 0.00 0.00 0.00 1.82
667 681 7.771361 GGAAATAAACTTCCCCTCAAAACAAAA 59.229 33.333 0.00 0.00 39.26 2.44
668 682 7.276658 GGAAATAAACTTCCCCTCAAAACAAA 58.723 34.615 0.00 0.00 39.26 2.83
669 683 6.822442 GGAAATAAACTTCCCCTCAAAACAA 58.178 36.000 0.00 0.00 39.26 2.83
670 684 6.413783 GGAAATAAACTTCCCCTCAAAACA 57.586 37.500 0.00 0.00 39.26 2.83
680 694 2.361119 GCCATCCGGGAAATAAACTTCC 59.639 50.000 0.00 0.00 43.69 3.46
681 695 2.032924 CGCCATCCGGGAAATAAACTTC 59.967 50.000 0.00 0.00 40.01 3.01
682 696 2.021457 CGCCATCCGGGAAATAAACTT 58.979 47.619 0.00 0.00 40.01 2.66
683 697 1.675552 CGCCATCCGGGAAATAAACT 58.324 50.000 0.00 0.00 40.01 2.66
684 698 0.030235 GCGCCATCCGGGAAATAAAC 59.970 55.000 0.00 0.00 40.01 2.01
685 699 1.104577 GGCGCCATCCGGGAAATAAA 61.105 55.000 24.80 0.00 40.01 1.40
741 790 3.121030 CGGAGAGTTTGGCCTGCG 61.121 66.667 3.32 0.00 37.84 5.18
749 798 1.897560 CAGAAAAGCCCGGAGAGTTT 58.102 50.000 0.73 0.00 0.00 2.66
760 809 2.427410 CGCACACCGCAGAAAAGC 60.427 61.111 0.00 0.00 42.60 3.51
802 851 2.415357 CGCACAAATGGGTAAAGCGATT 60.415 45.455 0.00 0.00 45.78 3.34
803 852 1.132262 CGCACAAATGGGTAAAGCGAT 59.868 47.619 0.00 0.00 45.78 4.58
816 876 1.646540 CGAACTTGAGCCGCACAAA 59.353 52.632 4.75 0.00 0.00 2.83
871 934 4.838486 GGAGACGACGAGGCAGCG 62.838 72.222 0.00 0.00 37.29 5.18
888 951 1.040339 CGAGGTCCAAGGAGAGGAGG 61.040 65.000 0.00 0.00 35.42 4.30
892 955 1.803943 CGTCGAGGTCCAAGGAGAG 59.196 63.158 0.00 0.00 0.00 3.20
893 956 2.341101 GCGTCGAGGTCCAAGGAGA 61.341 63.158 7.01 0.00 0.00 3.71
894 957 2.182030 GCGTCGAGGTCCAAGGAG 59.818 66.667 7.01 0.00 0.00 3.69
895 958 3.379445 GGCGTCGAGGTCCAAGGA 61.379 66.667 7.01 0.00 0.00 3.36
896 959 4.796231 CGGCGTCGAGGTCCAAGG 62.796 72.222 1.44 0.00 39.00 3.61
944 1013 1.435515 CCTCGCCTCTCTTCCTTCG 59.564 63.158 0.00 0.00 0.00 3.79
1278 1376 4.134563 CCAGTAATTTTAGGCCTACGCAT 58.865 43.478 13.46 1.53 36.38 4.73
1317 1415 2.313172 GGTCTCACAGTGCGCACAG 61.313 63.158 39.21 33.95 0.00 3.66
1332 1430 2.022129 CACAGTGGCGAACTCGGTC 61.022 63.158 0.69 0.00 36.83 4.79
1337 1435 2.546494 GCAAGCACAGTGGCGAACT 61.546 57.895 1.84 0.00 40.93 3.01
1344 1442 2.443146 CTCGAGAGCAAGCACAGTG 58.557 57.895 6.58 0.00 0.00 3.66
1363 1461 2.187946 GCGATGTCCCACCCTCTG 59.812 66.667 0.00 0.00 0.00 3.35
1388 1486 3.440173 CGCACTACCATGGAATCAAACTT 59.560 43.478 21.47 0.00 0.00 2.66
1429 1527 2.596904 TCGAACCCCGAGATGAAATC 57.403 50.000 0.00 0.00 43.23 2.17
1455 1553 4.541779 GGCTAGATTGACACGAGACTATG 58.458 47.826 0.00 0.00 0.00 2.23
1463 1561 0.541863 AAGGGGGCTAGATTGACACG 59.458 55.000 0.00 0.00 0.00 4.49
1468 1566 2.957402 TGCATAAGGGGGCTAGATTG 57.043 50.000 0.00 0.00 0.00 2.67
1522 1796 4.154195 CACCCTCAACTGGTTTAAGATTCG 59.846 45.833 0.00 0.00 32.46 3.34
1542 1816 2.362397 TCTTACAGATGAGCCGATCACC 59.638 50.000 0.00 0.00 41.91 4.02
1549 1823 5.994054 TGCTTGATTATCTTACAGATGAGCC 59.006 40.000 0.00 0.00 35.37 4.70
1580 1854 7.683578 AGATAATGCAACTGGCTATTAGATGA 58.316 34.615 0.00 0.00 45.15 2.92
1581 1855 7.918536 AGATAATGCAACTGGCTATTAGATG 57.081 36.000 0.00 0.00 45.15 2.90
1727 2001 6.765403 ACTCAGTAAACACTAACATGGCTTA 58.235 36.000 0.00 0.00 0.00 3.09
1750 2024 7.544622 TCTGTCATACATACAGTTGTCCTTAC 58.455 38.462 0.00 0.00 43.88 2.34
1842 2116 2.615869 CAGTAAAGCTGGAGACTGAGC 58.384 52.381 10.52 0.00 41.51 4.26
2044 3501 1.070601 TGCAGCTTAACAGTGAGCAGA 59.929 47.619 10.83 0.00 38.82 4.26
2109 3588 7.637229 CAGCAAATATACTTCAGTCAGATTGG 58.363 38.462 0.00 0.00 0.00 3.16
2111 3590 6.825213 TGCAGCAAATATACTTCAGTCAGATT 59.175 34.615 0.00 0.00 0.00 2.40
2136 3615 3.508845 AGAATGTACACAGGCACCTTT 57.491 42.857 0.00 0.00 0.00 3.11
2143 3622 4.067896 AGCTCACAAAGAATGTACACAGG 58.932 43.478 0.00 0.00 41.46 4.00
2178 3657 4.351192 CTTTTGCCTGTACCATAAATCGC 58.649 43.478 0.00 0.00 0.00 4.58
2371 3858 1.910580 TTTAGCTTGCGAGGAGGGGG 61.911 60.000 2.37 0.00 0.00 5.40
2400 3888 4.373156 AGGCTGACCAAGTTCAGTTTAT 57.627 40.909 2.30 0.00 44.34 1.40
2531 4026 2.107366 ACCAGTGGAAACCCAAAACAG 58.893 47.619 18.40 0.00 35.07 3.16
2540 4035 4.556699 GCATAACAGACAACCAGTGGAAAC 60.557 45.833 18.40 4.29 0.00 2.78
2541 4036 3.568007 GCATAACAGACAACCAGTGGAAA 59.432 43.478 18.40 0.00 0.00 3.13
2543 4038 2.371841 AGCATAACAGACAACCAGTGGA 59.628 45.455 18.40 0.00 0.00 4.02
2576 4071 7.816995 GCTATCTGACTATTTTGGTGAGGATAG 59.183 40.741 0.00 0.00 0.00 2.08
2580 4075 5.674525 TGCTATCTGACTATTTTGGTGAGG 58.325 41.667 0.00 0.00 0.00 3.86
2589 4084 8.011844 TCTGTACAACATGCTATCTGACTATT 57.988 34.615 0.00 0.00 0.00 1.73
2717 4220 3.376859 TGCTTGTATGATAAAGGTTGCGG 59.623 43.478 0.00 0.00 0.00 5.69
2718 4221 4.614555 TGCTTGTATGATAAAGGTTGCG 57.385 40.909 0.00 0.00 0.00 4.85
2844 4347 2.645797 ACTTATTTTGGGACGGAGGGAA 59.354 45.455 0.00 0.00 0.00 3.97
2948 4545 5.805486 TCATGCAGCTTTACTAGTTCTAACG 59.195 40.000 0.00 0.00 0.00 3.18
3061 4658 6.150140 AGCAGGAATCTTCACAGAAAATACAC 59.850 38.462 0.00 0.00 30.76 2.90
3092 4689 4.571984 TGCAGCTGCTACTACAACATAATG 59.428 41.667 36.61 0.00 42.66 1.90
3213 4810 1.066858 AGCCACTTGATGACGTACAGG 60.067 52.381 0.00 0.00 0.00 4.00
3296 4893 5.222254 ACTGCCTTTACTCCCTTTATTTGGA 60.222 40.000 0.00 0.00 0.00 3.53
3861 5488 4.317488 ACCATTGTTTTGGCATGTCAATC 58.683 39.130 14.57 10.76 40.68 2.67
4207 5834 2.107204 AGTGCTACCCATCCATCCATTC 59.893 50.000 0.00 0.00 0.00 2.67
4250 5877 9.506018 AAAAACTATGGAAGCATAAAAGCATTT 57.494 25.926 0.00 0.00 42.41 2.32
4333 5962 5.108517 AGCAATTTTTGTTACACACACAGG 58.891 37.500 0.00 0.00 33.98 4.00
4336 5966 6.885735 AGAAGCAATTTTTGTTACACACAC 57.114 33.333 0.00 0.00 33.98 3.82
4340 5970 7.532682 TCCAAAGAAGCAATTTTTGTTACAC 57.467 32.000 0.00 0.00 31.55 2.90
4346 5976 8.216453 CGTAAAGATCCAAAGAAGCAATTTTTG 58.784 33.333 0.00 0.00 0.00 2.44
4391 6021 4.578928 TCAGGCACAGAAAAACTTAAGTCC 59.421 41.667 8.95 2.35 0.00 3.85
4410 6040 8.447924 AACATGTTTCAGATGAGAATATCAGG 57.552 34.615 4.92 0.00 42.53 3.86
4548 6178 4.215965 CACAACAATACGTGCAAGGTAAC 58.784 43.478 4.26 0.00 40.93 2.50
4712 6342 5.767168 AGAAAGCCTATAAGCCAATAAGCTG 59.233 40.000 0.00 0.00 44.11 4.24
4713 6343 7.687874 GCAGAAAGCCTATAAGCCAATAAGCT 61.688 42.308 0.00 0.00 40.75 3.74
4884 6520 1.429148 GAATCCGTGTCCATGCCGAC 61.429 60.000 0.00 0.00 0.00 4.79
4940 6576 2.030371 TCAACAGCAAAATCTGTGCCA 58.970 42.857 0.00 0.00 45.77 4.92
5003 6639 2.672651 TTCGCGGTCACGGTAGGA 60.673 61.111 6.13 0.00 41.36 2.94
5004 6640 2.505557 GTTCGCGGTCACGGTAGG 60.506 66.667 6.13 0.00 41.36 3.18
5016 6652 1.446272 CCTGGAGAACCGAGTTCGC 60.446 63.158 10.49 10.49 45.96 4.70
5017 6653 0.109226 GTCCTGGAGAACCGAGTTCG 60.109 60.000 0.00 0.00 45.96 3.95
5036 6672 5.163814 CGGAGAAAGACCTCTTTATGCAAAG 60.164 44.000 12.55 0.00 45.37 2.77
5061 6698 3.190535 CGTTTCAAAATGAAGGACGGGAT 59.809 43.478 8.64 0.00 37.11 3.85
5065 6702 2.719046 GTGCGTTTCAAAATGAAGGACG 59.281 45.455 11.11 11.11 41.13 4.79
5111 6750 5.505181 AATGAGTAACCATCACAGGTCTT 57.495 39.130 0.00 0.00 42.25 3.01
5237 6891 5.912892 AGGTTCCAAAGTACCAAAAACATG 58.087 37.500 0.00 0.00 35.94 3.21
5246 6900 2.551032 CCAACGAAGGTTCCAAAGTACC 59.449 50.000 0.00 0.00 32.98 3.34
5248 6902 2.438763 TCCCAACGAAGGTTCCAAAGTA 59.561 45.455 0.00 0.00 32.98 2.24
5250 6904 1.975660 TCCCAACGAAGGTTCCAAAG 58.024 50.000 0.00 0.00 32.98 2.77
5255 6909 4.138487 AGATGTATCCCAACGAAGGTTC 57.862 45.455 0.00 0.00 32.98 3.62
5304 6958 0.105593 CATCACACGAGCAGGGCTAT 59.894 55.000 0.00 0.00 39.88 2.97
5305 6959 1.257750 ACATCACACGAGCAGGGCTA 61.258 55.000 0.00 0.00 39.88 3.93
5306 6960 2.116983 AACATCACACGAGCAGGGCT 62.117 55.000 0.00 0.00 43.88 5.19
5307 6961 1.672356 AACATCACACGAGCAGGGC 60.672 57.895 0.00 0.00 0.00 5.19
5308 6962 0.320683 TCAACATCACACGAGCAGGG 60.321 55.000 0.00 0.00 0.00 4.45
5309 6963 1.395954 CATCAACATCACACGAGCAGG 59.604 52.381 0.00 0.00 0.00 4.85
5310 6964 1.201998 GCATCAACATCACACGAGCAG 60.202 52.381 0.00 0.00 0.00 4.24
5311 6965 0.798159 GCATCAACATCACACGAGCA 59.202 50.000 0.00 0.00 0.00 4.26
5359 7036 3.752339 GGGAAGCAAAGCGCCCAG 61.752 66.667 2.29 0.00 43.78 4.45
5361 7038 2.376228 TTTTGGGAAGCAAAGCGCCC 62.376 55.000 2.29 13.66 44.30 6.13
5362 7039 0.945743 CTTTTGGGAAGCAAAGCGCC 60.946 55.000 2.29 0.00 44.04 6.53
5365 7042 3.797039 AGAAACTTTTGGGAAGCAAAGC 58.203 40.909 0.00 0.00 33.92 3.51
5366 7043 5.418676 TGAAGAAACTTTTGGGAAGCAAAG 58.581 37.500 0.00 0.00 36.28 2.77
5367 7044 5.413309 TGAAGAAACTTTTGGGAAGCAAA 57.587 34.783 0.00 0.00 0.00 3.68
5368 7045 5.413309 TTGAAGAAACTTTTGGGAAGCAA 57.587 34.783 0.00 0.00 0.00 3.91
5369 7046 5.413309 TTTGAAGAAACTTTTGGGAAGCA 57.587 34.783 0.00 0.00 0.00 3.91
5370 7047 6.925610 AATTTGAAGAAACTTTTGGGAAGC 57.074 33.333 0.00 0.00 0.00 3.86
5373 7050 9.255304 CGATTTAATTTGAAGAAACTTTTGGGA 57.745 29.630 0.00 0.00 0.00 4.37
5374 7051 8.495148 CCGATTTAATTTGAAGAAACTTTTGGG 58.505 33.333 0.00 0.00 0.00 4.12
5392 7069 0.885196 GCACCAACCAGCCGATTTAA 59.115 50.000 0.00 0.00 0.00 1.52
5394 7071 2.625823 CGCACCAACCAGCCGATTT 61.626 57.895 0.00 0.00 0.00 2.17
5419 7096 0.608640 AACCCAGTACGGCAGAGAAG 59.391 55.000 0.00 0.00 0.00 2.85
5446 7125 1.002900 CGAACGACTTGGTGTTTGCAT 60.003 47.619 0.00 0.00 0.00 3.96
5453 7132 0.300491 CACACACGAACGACTTGGTG 59.700 55.000 0.14 0.00 40.84 4.17
5455 7134 0.300491 CACACACACGAACGACTTGG 59.700 55.000 0.14 0.00 0.00 3.61
5456 7135 1.273688 TCACACACACGAACGACTTG 58.726 50.000 0.14 0.00 0.00 3.16
5475 7154 5.237815 TCACATGTAAAGCGACTTCATCTT 58.762 37.500 0.00 0.00 0.00 2.40
5477 7156 4.493220 GCTCACATGTAAAGCGACTTCATC 60.493 45.833 14.53 0.00 0.00 2.92
5485 7164 7.253750 GGAAATTATTTGCTCACATGTAAAGCG 60.254 37.037 21.09 1.52 38.90 4.68
5486 7165 7.761249 AGGAAATTATTTGCTCACATGTAAAGC 59.239 33.333 20.23 20.23 36.54 3.51
5487 7166 9.643693 AAGGAAATTATTTGCTCACATGTAAAG 57.356 29.630 11.89 0.00 40.66 1.85
5505 7188 2.867624 TCTGCTGAGCACAAGGAAATT 58.132 42.857 1.40 0.00 33.79 1.82
5547 7230 6.339587 TGTAAAATCTCCACATTCCAAACC 57.660 37.500 0.00 0.00 0.00 3.27
5584 7268 4.574599 AACTTGGCAGAACAATCAACTC 57.425 40.909 0.00 0.00 0.00 3.01
5609 7293 2.173519 CCTTTGGAATGCCACTGTGAT 58.826 47.619 9.86 0.00 45.94 3.06
5649 7333 0.478072 ACCACAATGAGGTGAAGGCA 59.522 50.000 0.52 0.00 41.32 4.75
5677 7361 4.085721 GCGACGGTATTTTCTCATTCTACG 60.086 45.833 0.00 0.00 0.00 3.51
5678 7362 4.208666 GGCGACGGTATTTTCTCATTCTAC 59.791 45.833 0.00 0.00 0.00 2.59
5680 7364 3.195661 GGCGACGGTATTTTCTCATTCT 58.804 45.455 0.00 0.00 0.00 2.40
5681 7365 2.933906 TGGCGACGGTATTTTCTCATTC 59.066 45.455 0.00 0.00 0.00 2.67
5683 7367 2.684001 TGGCGACGGTATTTTCTCAT 57.316 45.000 0.00 0.00 0.00 2.90
5684 7368 2.093921 TGATGGCGACGGTATTTTCTCA 60.094 45.455 0.00 0.00 0.00 3.27
5685 7369 2.540101 CTGATGGCGACGGTATTTTCTC 59.460 50.000 0.00 0.00 0.00 2.87
5699 7383 2.887568 CACGTCTCCGCTGATGGC 60.888 66.667 0.00 0.00 37.70 4.40
5730 7414 0.669318 TGGCAATCCTGACGTTCGTC 60.669 55.000 16.85 16.85 30.46 4.20
5732 7416 0.165944 GTTGGCAATCCTGACGTTCG 59.834 55.000 1.92 0.00 30.46 3.95
5733 7417 1.197721 CAGTTGGCAATCCTGACGTTC 59.802 52.381 11.31 0.00 30.46 3.95
5839 7523 7.328005 TCGTGTACGCTACATGTTTATAAACAA 59.672 33.333 29.44 15.76 44.39 2.83
5846 7530 3.603343 CGTTCGTGTACGCTACATGTTTA 59.397 43.478 2.30 0.00 44.16 2.01
5847 7531 2.406024 CGTTCGTGTACGCTACATGTTT 59.594 45.455 2.30 0.00 44.16 2.83
5848 7532 1.980844 CGTTCGTGTACGCTACATGTT 59.019 47.619 2.30 0.00 44.16 2.71
5849 7533 1.197492 TCGTTCGTGTACGCTACATGT 59.803 47.619 2.69 2.69 44.16 3.21
5867 7551 7.429284 GTTTTTCAATTGCGACTTAGATTTCG 58.571 34.615 0.00 0.00 38.31 3.46
5875 7559 4.527564 CTCTCGTTTTTCAATTGCGACTT 58.472 39.130 0.00 0.00 0.00 3.01
5879 7563 3.058914 AGTCCTCTCGTTTTTCAATTGCG 60.059 43.478 0.00 0.00 0.00 4.85
5951 7635 2.219458 CTGTAGGCTGATCATTGGCTG 58.781 52.381 18.05 1.73 39.45 4.85
5972 7656 0.394352 ATCATTGACAGCCCCGGAAC 60.394 55.000 0.73 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.