Multiple sequence alignment - TraesCS2A01G551600

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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 TraesCS2A01G551600 chr2A 100.000 2993 0 0 1 2993 758313474 758310482 0.000000e+00 5528.0
1 TraesCS2A01G551600 chr2B 92.319 1419 50 22 915 2310 770186709 770185327 0.000000e+00 1962.0
2 TraesCS2A01G551600 chr2B 88.372 344 40 0 1 344 770231718 770231375 5.970000e-112 414.0
3 TraesCS2A01G551600 chr2B 87.791 344 42 0 1 344 770198683 770198340 1.290000e-108 403.0
4 TraesCS2A01G551600 chr2B 81.548 504 43 26 2501 2992 770185213 770184748 1.310000e-98 370.0
5 TraesCS2A01G551600 chr2B 82.558 430 59 12 1 427 770232149 770231733 6.100000e-97 364.0
6 TraesCS2A01G551600 chr2B 82.326 430 60 12 1 427 770199114 770198698 2.840000e-95 359.0
7 TraesCS2A01G551600 chr2B 84.615 351 52 2 1 351 770263315 770262967 6.140000e-92 348.0
8 TraesCS2A01G551600 chr2B 81.265 427 66 8 1 427 770221987 770221575 1.720000e-87 333.0
9 TraesCS2A01G551600 chr2B 80.841 428 64 13 1 427 770254203 770253793 1.340000e-83 320.0
10 TraesCS2A01G551600 chr2B 81.928 332 18 14 471 795 770187529 770187233 2.980000e-60 243.0
11 TraesCS2A01G551600 chr2D 92.460 1313 59 20 1011 2310 627855715 627854430 0.000000e+00 1840.0
12 TraesCS2A01G551600 chr2D 85.455 495 25 15 2515 2993 627854303 627853840 3.490000e-129 472.0
13 TraesCS2A01G551600 chr2D 93.103 319 19 1 1473 1791 431383135 431383450 5.840000e-127 464.0
14 TraesCS2A01G551600 chr2D 84.848 495 23 22 470 952 627856513 627856059 4.550000e-123 451.0
15 TraesCS2A01G551600 chr2D 84.946 372 51 5 70 440 627856873 627856506 3.640000e-99 372.0
16 TraesCS2A01G551600 chr2D 82.517 429 55 13 1 427 627857340 627856930 2.840000e-95 359.0
17 TraesCS2A01G551600 chr1D 88.209 441 47 3 1175 1615 2161607 2161172 3.420000e-144 521.0
18 TraesCS2A01G551600 chr6D 87.696 447 51 2 1169 1615 101240020 101239578 4.420000e-143 518.0
19 TraesCS2A01G551600 chr6D 87.248 447 53 2 1169 1615 408918090 408917648 9.570000e-140 507.0
20 TraesCS2A01G551600 chr5D 87.643 437 46 5 1181 1615 306575421 306574991 4.450000e-138 501.0
21 TraesCS2A01G551600 chr7D 87.500 432 46 5 1186 1615 634078362 634078787 2.680000e-135 492.0
22 TraesCS2A01G551600 chr3D 86.111 432 52 5 1186 1615 395069196 395068771 2.720000e-125 459.0
23 TraesCS2A01G551600 chr3D 95.763 118 5 0 1167 1284 141355765 141355882 1.100000e-44 191.0
24 TraesCS2A01G551600 chr3D 91.667 48 4 0 1955 2002 141355725 141355772 1.930000e-07 67.6
25 TraesCS2A01G551600 chr3D 97.297 37 1 0 1966 2002 560963297 560963261 2.490000e-06 63.9
26 TraesCS2A01G551600 chr4D 97.297 37 1 0 1966 2002 418853415 418853451 2.490000e-06 63.9


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 TraesCS2A01G551600 chr2A 758310482 758313474 2992 True 5528.000000 5528 100.0000 1 2993 1 chr2A.!!$R1 2992
1 TraesCS2A01G551600 chr2B 770184748 770187529 2781 True 858.333333 1962 85.2650 471 2992 3 chr2B.!!$R4 2521
2 TraesCS2A01G551600 chr2B 770231375 770232149 774 True 389.000000 414 85.4650 1 427 2 chr2B.!!$R6 426
3 TraesCS2A01G551600 chr2B 770198340 770199114 774 True 381.000000 403 85.0585 1 427 2 chr2B.!!$R5 426
4 TraesCS2A01G551600 chr2D 627853840 627857340 3500 True 698.800000 1840 86.0452 1 2993 5 chr2D.!!$R1 2992

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
303 738 0.036952 TCGAAGGAAGAGCAGCAAGG 60.037 55.0 0.00 0.0 0.0 3.61 F
428 863 0.175989 GGGACGAGCTCTAGGGTTTG 59.824 60.0 12.85 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 2607 0.108233 CAGAGCAGAAGAGGGAGTGC 60.108 60.0 0.0 0.0 36.1 4.40 R
2344 3523 0.035317 AAGCTCATCACCTCACGCAA 59.965 50.0 0.0 0.0 0.0 4.85 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
20 21 2.604046 ACACGCAATTAGAGGCTAGG 57.396 50.000 0.00 0.00 0.00 3.02
38 39 1.599576 GAAGAGCCCACTCCCTCAC 59.400 63.158 0.00 0.00 44.65 3.51
39 40 0.907230 GAAGAGCCCACTCCCTCACT 60.907 60.000 0.00 0.00 44.65 3.41
40 41 1.197430 AAGAGCCCACTCCCTCACTG 61.197 60.000 0.00 0.00 44.65 3.66
41 42 2.608988 AGCCCACTCCCTCACTGG 60.609 66.667 0.00 0.00 0.00 4.00
45 46 2.219875 CCACTCCCTCACTGGCACT 61.220 63.158 0.00 0.00 0.00 4.40
49 50 1.152247 TCCCTCACTGGCACTCACT 60.152 57.895 0.00 0.00 0.00 3.41
50 51 1.004080 CCCTCACTGGCACTCACTG 60.004 63.158 0.00 0.00 0.00 3.66
52 53 1.475169 CCTCACTGGCACTCACTGGA 61.475 60.000 0.00 0.00 0.00 3.86
60 494 0.961019 GCACTCACTGGAAAATGGCA 59.039 50.000 0.00 0.00 0.00 4.92
106 540 6.398234 AATGACGACAAGAGTATGCTAGAT 57.602 37.500 0.00 0.00 0.00 1.98
115 549 5.022227 AGAGTATGCTAGATGGGGATCTT 57.978 43.478 0.00 0.00 32.36 2.40
186 621 1.595466 AGTCTCGACGACACTCTTGT 58.405 50.000 14.62 0.00 45.32 3.16
211 646 2.433604 TCCCACATGCTCTCTTCTCATC 59.566 50.000 0.00 0.00 0.00 2.92
296 731 1.082690 CCAGCTTTCGAAGGAAGAGC 58.917 55.000 12.00 10.97 36.96 4.09
303 738 0.036952 TCGAAGGAAGAGCAGCAAGG 60.037 55.000 0.00 0.00 0.00 3.61
306 741 2.753446 GGAAGAGCAGCAAGGGGC 60.753 66.667 0.00 0.00 45.30 5.80
323 758 2.365293 GGGGCAATTGTATCCCATGTTC 59.635 50.000 21.02 3.91 41.85 3.18
329 764 3.536956 TTGTATCCCATGTTCCGAGAC 57.463 47.619 0.00 0.00 0.00 3.36
332 767 1.285280 ATCCCATGTTCCGAGACCAA 58.715 50.000 0.00 0.00 0.00 3.67
372 807 3.477504 CAATGGTTGCGACAAGGTG 57.522 52.632 6.39 0.00 0.00 4.00
374 809 1.178534 AATGGTTGCGACAAGGTGGG 61.179 55.000 6.39 0.00 0.00 4.61
375 810 2.203294 GGTTGCGACAAGGTGGGT 60.203 61.111 6.39 0.00 0.00 4.51
376 811 2.258726 GGTTGCGACAAGGTGGGTC 61.259 63.158 6.39 0.00 0.00 4.46
383 818 1.303317 ACAAGGTGGGTCGATTGCC 60.303 57.895 0.00 0.00 0.00 4.52
385 820 3.622060 AAGGTGGGTCGATTGCCGG 62.622 63.158 0.00 0.00 39.14 6.13
386 821 4.090588 GGTGGGTCGATTGCCGGA 62.091 66.667 5.05 0.00 39.14 5.14
427 862 0.976590 GGGGACGAGCTCTAGGGTTT 60.977 60.000 12.85 0.00 0.00 3.27
428 863 0.175989 GGGACGAGCTCTAGGGTTTG 59.824 60.000 12.85 0.00 0.00 2.93
429 864 0.460459 GGACGAGCTCTAGGGTTTGC 60.460 60.000 12.85 0.00 0.00 3.68
431 866 0.685097 ACGAGCTCTAGGGTTTGCAA 59.315 50.000 12.85 0.00 0.00 4.08
432 867 1.279271 ACGAGCTCTAGGGTTTGCAAT 59.721 47.619 12.85 0.00 0.00 3.56
433 868 2.500098 ACGAGCTCTAGGGTTTGCAATA 59.500 45.455 12.85 0.00 0.00 1.90
434 869 3.126831 CGAGCTCTAGGGTTTGCAATAG 58.873 50.000 12.85 0.00 0.00 1.73
435 870 3.471680 GAGCTCTAGGGTTTGCAATAGG 58.528 50.000 6.43 0.00 0.00 2.57
436 871 2.173569 AGCTCTAGGGTTTGCAATAGGG 59.826 50.000 0.00 0.00 0.00 3.53
437 872 2.092375 GCTCTAGGGTTTGCAATAGGGT 60.092 50.000 0.00 0.00 0.00 4.34
438 873 3.624959 GCTCTAGGGTTTGCAATAGGGTT 60.625 47.826 0.00 0.00 0.00 4.11
439 874 3.947834 CTCTAGGGTTTGCAATAGGGTTG 59.052 47.826 0.00 0.00 0.00 3.77
440 875 1.266178 AGGGTTTGCAATAGGGTTGC 58.734 50.000 0.00 5.85 45.11 4.17
441 876 0.249120 GGGTTTGCAATAGGGTTGCC 59.751 55.000 0.00 0.00 44.32 4.52
442 877 0.972883 GGTTTGCAATAGGGTTGCCA 59.027 50.000 0.00 0.00 44.32 4.92
443 878 1.337728 GGTTTGCAATAGGGTTGCCAC 60.338 52.381 0.00 6.90 44.32 5.01
444 879 1.342819 GTTTGCAATAGGGTTGCCACA 59.657 47.619 0.00 0.00 44.32 4.17
445 880 0.965439 TTGCAATAGGGTTGCCACAC 59.035 50.000 9.94 0.00 44.32 3.82
446 881 0.897863 TGCAATAGGGTTGCCACACC 60.898 55.000 9.94 0.00 44.32 4.16
447 882 0.611896 GCAATAGGGTTGCCACACCT 60.612 55.000 1.46 3.92 39.38 4.00
448 883 1.923356 CAATAGGGTTGCCACACCTT 58.077 50.000 3.79 0.00 36.97 3.50
449 884 2.247358 CAATAGGGTTGCCACACCTTT 58.753 47.619 3.79 0.00 36.97 3.11
450 885 2.632512 CAATAGGGTTGCCACACCTTTT 59.367 45.455 3.79 0.95 36.97 2.27
451 886 2.463047 TAGGGTTGCCACACCTTTTT 57.537 45.000 3.79 0.00 36.97 1.94
452 887 0.829990 AGGGTTGCCACACCTTTTTG 59.170 50.000 0.00 0.00 36.97 2.44
453 888 0.827368 GGGTTGCCACACCTTTTTGA 59.173 50.000 0.00 0.00 36.97 2.69
454 889 1.208293 GGGTTGCCACACCTTTTTGAA 59.792 47.619 0.00 0.00 36.97 2.69
455 890 2.355209 GGGTTGCCACACCTTTTTGAAA 60.355 45.455 0.00 0.00 36.97 2.69
456 891 3.540617 GGTTGCCACACCTTTTTGAAAT 58.459 40.909 0.00 0.00 33.50 2.17
457 892 4.443598 GGGTTGCCACACCTTTTTGAAATA 60.444 41.667 0.00 0.00 36.97 1.40
458 893 4.749598 GGTTGCCACACCTTTTTGAAATAG 59.250 41.667 0.00 0.00 33.50 1.73
459 894 4.599047 TGCCACACCTTTTTGAAATAGG 57.401 40.909 12.05 12.05 35.14 2.57
460 895 3.323403 TGCCACACCTTTTTGAAATAGGG 59.677 43.478 16.86 9.41 33.22 3.53
461 896 3.323691 GCCACACCTTTTTGAAATAGGGT 59.676 43.478 16.86 9.93 33.22 4.34
462 897 4.202315 GCCACACCTTTTTGAAATAGGGTT 60.202 41.667 16.86 2.60 33.22 4.11
463 898 5.686387 GCCACACCTTTTTGAAATAGGGTTT 60.686 40.000 16.86 0.43 33.22 3.27
464 899 5.989168 CCACACCTTTTTGAAATAGGGTTTC 59.011 40.000 16.86 0.00 33.22 2.78
465 900 5.989168 CACACCTTTTTGAAATAGGGTTTCC 59.011 40.000 16.86 0.00 33.22 3.13
466 901 5.663556 ACACCTTTTTGAAATAGGGTTTCCA 59.336 36.000 16.86 0.00 33.22 3.53
467 902 6.328934 ACACCTTTTTGAAATAGGGTTTCCAT 59.671 34.615 16.86 0.00 33.22 3.41
468 903 6.650390 CACCTTTTTGAAATAGGGTTTCCATG 59.350 38.462 16.86 2.88 33.22 3.66
533 969 0.405973 AGGAAGCAAAAGAGACCCCC 59.594 55.000 0.00 0.00 0.00 5.40
534 970 0.960861 GGAAGCAAAAGAGACCCCCG 60.961 60.000 0.00 0.00 0.00 5.73
553 990 4.082949 CCCCGAGTACTTCCATTTTTGTTC 60.083 45.833 0.00 0.00 0.00 3.18
567 1004 1.234821 TTGTTCCTTGACGTCCATGC 58.765 50.000 14.12 0.00 0.00 4.06
598 1040 3.909995 TCTCCCCTGAGATGACAAAAGAA 59.090 43.478 0.00 0.00 42.73 2.52
608 1051 7.491682 TGAGATGACAAAAGAAAAGAAAAGGG 58.508 34.615 0.00 0.00 0.00 3.95
638 1081 0.664466 GCGTGAAGGAGCAAAAAGGC 60.664 55.000 0.00 0.00 0.00 4.35
640 1083 0.668535 GTGAAGGAGCAAAAAGGCGT 59.331 50.000 0.00 0.00 39.27 5.68
641 1084 0.951558 TGAAGGAGCAAAAAGGCGTC 59.048 50.000 0.00 0.00 39.27 5.19
642 1085 0.241213 GAAGGAGCAAAAAGGCGTCC 59.759 55.000 0.00 0.00 39.27 4.79
644 1087 1.172812 AGGAGCAAAAAGGCGTCCAC 61.173 55.000 0.00 0.00 39.27 4.02
645 1088 1.285950 GAGCAAAAAGGCGTCCACC 59.714 57.895 0.00 0.00 39.27 4.61
646 1089 2.142357 GAGCAAAAAGGCGTCCACCC 62.142 60.000 0.00 0.00 39.27 4.61
647 1090 2.642700 CAAAAAGGCGTCCACCCG 59.357 61.111 0.00 0.00 0.00 5.28
660 1103 4.572571 ACCCGCCCGCAGAAACAA 62.573 61.111 0.00 0.00 0.00 2.83
661 1104 3.291383 CCCGCCCGCAGAAACAAA 61.291 61.111 0.00 0.00 0.00 2.83
662 1105 2.255252 CCGCCCGCAGAAACAAAG 59.745 61.111 0.00 0.00 0.00 2.77
663 1106 2.258013 CCGCCCGCAGAAACAAAGA 61.258 57.895 0.00 0.00 0.00 2.52
664 1107 1.207593 CGCCCGCAGAAACAAAGAG 59.792 57.895 0.00 0.00 0.00 2.85
677 1124 3.493767 ACAAAGAGAGAGGTGTTTCCC 57.506 47.619 0.00 0.00 36.75 3.97
735 1182 1.691127 CGTCCCGATCATCATCTTCG 58.309 55.000 0.00 0.00 0.00 3.79
736 1183 1.001268 CGTCCCGATCATCATCTTCGT 60.001 52.381 0.00 0.00 0.00 3.85
737 1184 2.667137 GTCCCGATCATCATCTTCGTC 58.333 52.381 0.00 0.00 0.00 4.20
738 1185 2.294791 GTCCCGATCATCATCTTCGTCT 59.705 50.000 0.00 0.00 0.00 4.18
739 1186 2.959030 TCCCGATCATCATCTTCGTCTT 59.041 45.455 0.00 0.00 0.00 3.01
740 1187 3.004839 TCCCGATCATCATCTTCGTCTTC 59.995 47.826 0.00 0.00 0.00 2.87
741 1188 3.312828 CCGATCATCATCTTCGTCTTCC 58.687 50.000 0.00 0.00 0.00 3.46
742 1189 3.312828 CGATCATCATCTTCGTCTTCCC 58.687 50.000 0.00 0.00 0.00 3.97
743 1190 2.871182 TCATCATCTTCGTCTTCCCG 57.129 50.000 0.00 0.00 0.00 5.14
744 1191 1.409064 TCATCATCTTCGTCTTCCCGG 59.591 52.381 0.00 0.00 0.00 5.73
745 1192 1.409064 CATCATCTTCGTCTTCCCGGA 59.591 52.381 0.73 0.00 0.00 5.14
746 1193 1.103803 TCATCTTCGTCTTCCCGGAG 58.896 55.000 0.73 0.00 34.66 4.63
766 1213 4.903010 AGACGCGTTGTTGCCGGT 62.903 61.111 15.53 0.00 0.00 5.28
796 1243 4.530857 CCGCCATCTCCGGTCCAC 62.531 72.222 0.00 0.00 40.84 4.02
797 1244 4.873129 CGCCATCTCCGGTCCACG 62.873 72.222 0.00 0.00 43.80 4.94
798 1245 3.771160 GCCATCTCCGGTCCACGT 61.771 66.667 0.00 0.00 42.24 4.49
799 1246 2.494918 CCATCTCCGGTCCACGTC 59.505 66.667 0.00 0.00 42.24 4.34
847 1294 3.267597 CTTGCCTTGCCCCGTTTCG 62.268 63.158 0.00 0.00 0.00 3.46
858 1305 2.549282 CGTTTCGCACCTCAACCG 59.451 61.111 0.00 0.00 0.00 4.44
860 1307 2.281208 TTTCGCACCTCAACCGGG 60.281 61.111 6.32 0.00 0.00 5.73
910 1364 2.043450 CCGCCTCCAGACCTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
952 1803 3.137459 CGACGCCAGCTCTCCTCT 61.137 66.667 0.00 0.00 0.00 3.69
953 1804 2.804856 GACGCCAGCTCTCCTCTC 59.195 66.667 0.00 0.00 0.00 3.20
955 1806 2.441901 CGCCAGCTCTCCTCTCCT 60.442 66.667 0.00 0.00 0.00 3.69
956 1807 2.489275 CGCCAGCTCTCCTCTCCTC 61.489 68.421 0.00 0.00 0.00 3.71
957 1808 1.076044 GCCAGCTCTCCTCTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
958 1809 1.109323 GCCAGCTCTCCTCTCCTCTC 61.109 65.000 0.00 0.00 0.00 3.20
959 1810 0.468029 CCAGCTCTCCTCTCCTCTCC 60.468 65.000 0.00 0.00 0.00 3.71
960 1811 0.552848 CAGCTCTCCTCTCCTCTCCT 59.447 60.000 0.00 0.00 0.00 3.69
965 1816 0.468029 CTCCTCTCCTCTCCTCAGCC 60.468 65.000 0.00 0.00 0.00 4.85
989 1840 4.514585 GCACACCACCACCACCCA 62.515 66.667 0.00 0.00 0.00 4.51
990 1841 2.203337 CACACCACCACCACCCAG 60.203 66.667 0.00 0.00 0.00 4.45
991 1842 4.204028 ACACCACCACCACCCAGC 62.204 66.667 0.00 0.00 0.00 4.85
992 1843 4.974721 CACCACCACCACCCAGCC 62.975 72.222 0.00 0.00 0.00 4.85
1387 2534 1.078356 CTCCACCTCGTCTCCTCGA 60.078 63.158 0.00 0.00 38.19 4.04
1476 2623 3.397906 GGCACTCCCTCTTCTGCT 58.602 61.111 0.00 0.00 0.00 4.24
1482 2629 1.229304 TCCCTCTTCTGCTCTGCCA 60.229 57.895 0.00 0.00 0.00 4.92
1747 2894 2.109126 GGCACCAGCAACGAGATCC 61.109 63.158 0.00 0.00 44.61 3.36
2072 3231 3.318557 TGTGTCGTGTCCAAGTGTATACA 59.681 43.478 0.08 0.08 0.00 2.29
2073 3232 3.918591 GTGTCGTGTCCAAGTGTATACAG 59.081 47.826 5.62 0.00 0.00 2.74
2133 3301 2.108168 ACATACAGCCATACAGTCGGT 58.892 47.619 0.00 0.00 0.00 4.69
2226 3403 4.013728 TGGAAATGTGGAATCCGGTTAAG 58.986 43.478 0.00 0.00 35.96 1.85
2234 3411 5.187687 GTGGAATCCGGTTAAGGTAAATGA 58.812 41.667 0.00 0.00 0.00 2.57
2259 3436 2.699251 AAACCGTCGGAAAATTGCTC 57.301 45.000 20.51 0.00 0.00 4.26
2294 3473 4.462132 TCTCCTGTCTCTCTCTGTGATTTG 59.538 45.833 0.00 0.00 0.00 2.32
2296 3475 5.325239 TCCTGTCTCTCTCTGTGATTTGTA 58.675 41.667 0.00 0.00 0.00 2.41
2307 3486 4.023279 TCTGTGATTTGTAATGCTTGCGTT 60.023 37.500 5.38 5.38 0.00 4.84
2310 3489 7.065204 TCTGTGATTTGTAATGCTTGCGTTATA 59.935 33.333 10.01 5.44 0.00 0.98
2311 3490 7.186128 TGTGATTTGTAATGCTTGCGTTATAG 58.814 34.615 10.01 0.00 0.00 1.31
2312 3491 7.148323 TGTGATTTGTAATGCTTGCGTTATAGT 60.148 33.333 10.01 2.13 0.00 2.12
2313 3492 7.696453 GTGATTTGTAATGCTTGCGTTATAGTT 59.304 33.333 10.01 0.85 0.00 2.24
2314 3493 8.240682 TGATTTGTAATGCTTGCGTTATAGTTT 58.759 29.630 10.01 0.00 0.00 2.66
2315 3494 8.980143 ATTTGTAATGCTTGCGTTATAGTTTT 57.020 26.923 10.01 0.00 0.00 2.43
2316 3495 8.804688 TTTGTAATGCTTGCGTTATAGTTTTT 57.195 26.923 10.01 0.00 0.00 1.94
2346 3525 7.718272 TTTTGAGAAAAGGAAATGATGCTTG 57.282 32.000 0.00 0.00 38.99 4.01
2347 3526 4.813027 TGAGAAAAGGAAATGATGCTTGC 58.187 39.130 0.00 0.00 38.99 4.01
2348 3527 3.841643 AGAAAAGGAAATGATGCTTGCG 58.158 40.909 0.00 0.00 38.99 4.85
2349 3528 3.256631 AGAAAAGGAAATGATGCTTGCGT 59.743 39.130 0.00 0.00 38.99 5.24
2350 3529 2.642139 AAGGAAATGATGCTTGCGTG 57.358 45.000 0.00 0.00 38.42 5.34
2351 3530 1.825090 AGGAAATGATGCTTGCGTGA 58.175 45.000 0.00 0.00 0.00 4.35
2352 3531 1.741706 AGGAAATGATGCTTGCGTGAG 59.258 47.619 0.00 0.00 0.00 3.51
2391 3570 4.323417 TGACATATTTGCTGGTCGACTTT 58.677 39.130 16.46 0.00 33.04 2.66
2392 3571 4.391830 TGACATATTTGCTGGTCGACTTTC 59.608 41.667 16.46 5.10 33.04 2.62
2393 3572 4.579869 ACATATTTGCTGGTCGACTTTCT 58.420 39.130 16.46 0.00 0.00 2.52
2394 3573 5.730550 ACATATTTGCTGGTCGACTTTCTA 58.269 37.500 16.46 0.00 0.00 2.10
2395 3574 6.349300 ACATATTTGCTGGTCGACTTTCTAT 58.651 36.000 16.46 5.35 0.00 1.98
2397 3576 3.953712 TTGCTGGTCGACTTTCTATCA 57.046 42.857 16.46 1.75 0.00 2.15
2400 3579 3.258372 TGCTGGTCGACTTTCTATCAGTT 59.742 43.478 16.46 0.00 0.00 3.16
2401 3580 3.614616 GCTGGTCGACTTTCTATCAGTTG 59.385 47.826 16.46 0.00 0.00 3.16
2406 3585 5.105752 GTCGACTTTCTATCAGTTGATGCT 58.894 41.667 8.70 0.00 37.09 3.79
2410 3589 6.312426 CGACTTTCTATCAGTTGATGCTTCTT 59.688 38.462 4.90 0.00 36.05 2.52
2415 3594 7.549615 TCTATCAGTTGATGCTTCTTTGATG 57.450 36.000 16.67 10.78 36.05 3.07
2417 3596 5.618056 TCAGTTGATGCTTCTTTGATGAC 57.382 39.130 0.88 0.00 0.00 3.06
2421 3600 5.708697 AGTTGATGCTTCTTTGATGACATGA 59.291 36.000 0.00 0.00 0.00 3.07
2438 3617 2.106477 TGAAATGCATCGGTAGCACA 57.894 45.000 0.00 0.00 45.95 4.57
2440 3619 2.613595 TGAAATGCATCGGTAGCACATC 59.386 45.455 0.00 0.00 45.95 3.06
2441 3620 1.597742 AATGCATCGGTAGCACATCC 58.402 50.000 0.00 0.00 45.95 3.51
2442 3621 0.761187 ATGCATCGGTAGCACATCCT 59.239 50.000 0.00 0.00 45.95 3.24
2445 3624 1.473257 GCATCGGTAGCACATCCTTGA 60.473 52.381 0.00 0.00 0.00 3.02
2448 3627 0.249120 CGGTAGCACATCCTTGACCA 59.751 55.000 0.00 0.00 0.00 4.02
2449 3628 1.134401 CGGTAGCACATCCTTGACCAT 60.134 52.381 0.00 0.00 0.00 3.55
2453 3632 1.996786 GCACATCCTTGACCATGCCG 61.997 60.000 0.00 0.00 0.00 5.69
2454 3633 0.677731 CACATCCTTGACCATGCCGT 60.678 55.000 0.00 0.00 0.00 5.68
2455 3634 0.038166 ACATCCTTGACCATGCCGTT 59.962 50.000 0.00 0.00 0.00 4.44
2456 3635 0.734889 CATCCTTGACCATGCCGTTC 59.265 55.000 0.00 0.00 0.00 3.95
2457 3636 0.620556 ATCCTTGACCATGCCGTTCT 59.379 50.000 0.00 0.00 0.00 3.01
2472 3651 2.273179 TTCTAGAGCACGCACGGGT 61.273 57.895 0.00 0.00 0.00 5.28
2473 3652 2.486636 TTCTAGAGCACGCACGGGTG 62.487 60.000 9.69 9.69 40.89 4.61
2530 3709 0.811616 GGCCATGCCGTTCTAGACTG 60.812 60.000 0.00 0.00 39.62 3.51
2582 3767 4.160635 CCGGCGCCAACGATTGAC 62.161 66.667 28.98 0.00 43.93 3.18
2583 3768 4.160635 CGGCGCCAACGATTGACC 62.161 66.667 28.98 0.00 43.93 4.02
2584 3769 4.160635 GGCGCCAACGATTGACCG 62.161 66.667 24.80 0.00 43.93 4.79
2585 3770 4.160635 GCGCCAACGATTGACCGG 62.161 66.667 0.00 0.00 43.93 5.28
2586 3771 4.160635 CGCCAACGATTGACCGGC 62.161 66.667 0.00 0.00 43.93 6.13
2587 3772 4.160635 GCCAACGATTGACCGGCG 62.161 66.667 0.00 0.00 32.14 6.46
2588 3773 3.496131 CCAACGATTGACCGGCGG 61.496 66.667 27.06 27.06 0.00 6.13
2589 3774 3.496131 CAACGATTGACCGGCGGG 61.496 66.667 31.78 13.71 40.11 6.13
2976 4193 1.602851 TCGATAGACGGAAGCAGCTAC 59.397 52.381 0.00 0.00 42.67 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.907230 AGTGAGGGAGTGGGCTCTTC 60.907 60.000 0.00 0.00 41.38 2.87
38 39 1.542915 CCATTTTCCAGTGAGTGCCAG 59.457 52.381 0.00 0.00 0.00 4.85
39 40 1.619654 CCATTTTCCAGTGAGTGCCA 58.380 50.000 0.00 0.00 0.00 4.92
40 41 0.244721 GCCATTTTCCAGTGAGTGCC 59.755 55.000 0.00 0.00 0.00 5.01
41 42 0.961019 TGCCATTTTCCAGTGAGTGC 59.039 50.000 0.00 0.00 0.00 4.40
52 53 9.260002 CGCTTTCCTTTAAATATATGCCATTTT 57.740 29.630 0.00 0.00 0.00 1.82
60 494 9.260002 CATTTTGGCGCTTTCCTTTAAATATAT 57.740 29.630 7.64 0.00 0.00 0.86
106 540 0.679505 CGATAGGCGAAAGATCCCCA 59.320 55.000 0.00 0.00 44.57 4.96
186 621 2.111384 GAAGAGAGCATGTGGGAGGTA 58.889 52.381 0.00 0.00 0.00 3.08
211 646 0.248134 CTAGCCGTTCTCGTCCTTCG 60.248 60.000 0.00 0.00 41.41 3.79
296 731 1.410153 GGATACAATTGCCCCTTGCTG 59.590 52.381 5.05 0.00 42.00 4.41
303 738 2.365293 GGAACATGGGATACAATTGCCC 59.635 50.000 11.60 11.60 42.38 5.36
306 741 4.273480 GTCTCGGAACATGGGATACAATTG 59.727 45.833 3.24 3.24 39.74 2.32
310 745 1.760613 GGTCTCGGAACATGGGATACA 59.239 52.381 0.00 0.00 39.74 2.29
311 746 1.760613 TGGTCTCGGAACATGGGATAC 59.239 52.381 0.00 0.00 0.00 2.24
314 749 0.323629 GTTGGTCTCGGAACATGGGA 59.676 55.000 0.00 0.00 0.00 4.37
323 758 0.319211 TTGCACGTAGTTGGTCTCGG 60.319 55.000 0.00 0.00 41.61 4.63
368 803 4.096003 CCGGCAATCGACCCACCT 62.096 66.667 0.00 0.00 42.43 4.00
370 805 2.511600 CTCCGGCAATCGACCCAC 60.512 66.667 0.00 0.00 42.43 4.61
371 806 3.781307 CCTCCGGCAATCGACCCA 61.781 66.667 0.00 0.00 42.43 4.51
372 807 4.547367 CCCTCCGGCAATCGACCC 62.547 72.222 0.00 0.00 42.43 4.46
374 809 4.547367 CCCCCTCCGGCAATCGAC 62.547 72.222 0.00 0.00 42.43 4.20
392 827 3.787001 CCCTCCCTCCGACTTGGC 61.787 72.222 0.00 0.00 37.80 4.52
393 828 3.083997 CCCCTCCCTCCGACTTGG 61.084 72.222 0.00 0.00 40.09 3.61
394 829 3.083997 CCCCCTCCCTCCGACTTG 61.084 72.222 0.00 0.00 0.00 3.16
427 862 0.897863 GGTGTGGCAACCCTATTGCA 60.898 55.000 13.20 0.00 46.58 4.08
428 863 0.611896 AGGTGTGGCAACCCTATTGC 60.612 55.000 13.08 3.00 41.54 3.56
429 864 1.923356 AAGGTGTGGCAACCCTATTG 58.077 50.000 13.08 0.00 41.54 1.90
431 866 2.632512 CAAAAAGGTGTGGCAACCCTAT 59.367 45.455 13.08 1.99 41.54 2.57
432 867 2.035632 CAAAAAGGTGTGGCAACCCTA 58.964 47.619 13.08 0.00 41.54 3.53
433 868 0.829990 CAAAAAGGTGTGGCAACCCT 59.170 50.000 13.08 7.63 41.54 4.34
434 869 0.827368 TCAAAAAGGTGTGGCAACCC 59.173 50.000 13.08 5.57 41.54 4.11
435 870 2.682155 TTCAAAAAGGTGTGGCAACC 57.318 45.000 9.86 9.86 40.85 3.77
436 871 4.749598 CCTATTTCAAAAAGGTGTGGCAAC 59.250 41.667 0.00 0.00 0.00 4.17
437 872 4.202305 CCCTATTTCAAAAAGGTGTGGCAA 60.202 41.667 0.00 0.00 0.00 4.52
438 873 3.323403 CCCTATTTCAAAAAGGTGTGGCA 59.677 43.478 0.00 0.00 0.00 4.92
439 874 3.323691 ACCCTATTTCAAAAAGGTGTGGC 59.676 43.478 0.00 0.00 0.00 5.01
440 875 5.545063 AACCCTATTTCAAAAAGGTGTGG 57.455 39.130 0.00 0.00 0.00 4.17
441 876 5.989168 GGAAACCCTATTTCAAAAAGGTGTG 59.011 40.000 2.14 0.00 0.00 3.82
442 877 5.663556 TGGAAACCCTATTTCAAAAAGGTGT 59.336 36.000 2.14 0.00 0.00 4.16
443 878 6.168270 TGGAAACCCTATTTCAAAAAGGTG 57.832 37.500 2.14 0.00 0.00 4.00
444 879 6.328934 ACATGGAAACCCTATTTCAAAAAGGT 59.671 34.615 0.00 0.00 0.00 3.50
445 880 6.768483 ACATGGAAACCCTATTTCAAAAAGG 58.232 36.000 0.00 0.00 0.00 3.11
446 881 8.034804 CCTACATGGAAACCCTATTTCAAAAAG 58.965 37.037 0.00 0.00 38.35 2.27
447 882 7.038658 CCCTACATGGAAACCCTATTTCAAAAA 60.039 37.037 0.00 0.00 38.35 1.94
448 883 6.439058 CCCTACATGGAAACCCTATTTCAAAA 59.561 38.462 0.00 0.00 38.35 2.44
449 884 5.955355 CCCTACATGGAAACCCTATTTCAAA 59.045 40.000 0.00 0.00 38.35 2.69
450 885 5.015817 ACCCTACATGGAAACCCTATTTCAA 59.984 40.000 0.00 0.00 38.35 2.69
451 886 4.542525 ACCCTACATGGAAACCCTATTTCA 59.457 41.667 0.00 0.00 38.35 2.69
452 887 5.125367 ACCCTACATGGAAACCCTATTTC 57.875 43.478 0.00 0.00 38.35 2.17
453 888 5.269189 CAACCCTACATGGAAACCCTATTT 58.731 41.667 0.00 0.00 38.35 1.40
454 889 4.325816 CCAACCCTACATGGAAACCCTATT 60.326 45.833 0.00 0.00 39.12 1.73
455 890 3.204382 CCAACCCTACATGGAAACCCTAT 59.796 47.826 0.00 0.00 39.12 2.57
456 891 2.578940 CCAACCCTACATGGAAACCCTA 59.421 50.000 0.00 0.00 39.12 3.53
457 892 1.357761 CCAACCCTACATGGAAACCCT 59.642 52.381 0.00 0.00 39.12 4.34
458 893 1.076513 ACCAACCCTACATGGAAACCC 59.923 52.381 0.00 0.00 39.12 4.11
459 894 2.597578 ACCAACCCTACATGGAAACC 57.402 50.000 0.00 0.00 39.12 3.27
460 895 4.023726 TGTACCAACCCTACATGGAAAC 57.976 45.455 0.00 0.00 39.12 2.78
461 896 4.594970 CATGTACCAACCCTACATGGAAA 58.405 43.478 9.70 0.00 44.08 3.13
462 897 4.229304 CATGTACCAACCCTACATGGAA 57.771 45.455 9.70 0.00 44.08 3.53
463 898 3.924114 CATGTACCAACCCTACATGGA 57.076 47.619 9.70 0.00 44.08 3.41
465 900 3.644966 ACCATGTACCAACCCTACATG 57.355 47.619 10.37 10.37 46.01 3.21
466 901 3.135895 GCTACCATGTACCAACCCTACAT 59.864 47.826 0.00 0.00 35.58 2.29
467 902 2.502538 GCTACCATGTACCAACCCTACA 59.497 50.000 0.00 0.00 0.00 2.74
468 903 2.502538 TGCTACCATGTACCAACCCTAC 59.497 50.000 0.00 0.00 0.00 3.18
533 969 5.941948 AGGAACAAAAATGGAAGTACTCG 57.058 39.130 0.00 0.00 0.00 4.18
534 970 7.139392 GTCAAGGAACAAAAATGGAAGTACTC 58.861 38.462 0.00 0.00 0.00 2.59
553 990 0.677731 ATGTGGCATGGACGTCAAGG 60.678 55.000 18.91 9.45 0.00 3.61
567 1004 2.191400 TCTCAGGGGAGAGAAATGTGG 58.809 52.381 0.00 0.00 45.12 4.17
598 1040 5.127194 ACGCTTCTCTTTTTCCCTTTTCTTT 59.873 36.000 0.00 0.00 0.00 2.52
608 1051 3.364465 GCTCCTTCACGCTTCTCTTTTTC 60.364 47.826 0.00 0.00 0.00 2.29
644 1087 3.267597 CTTTGTTTCTGCGGGCGGG 62.268 63.158 0.00 0.00 0.00 6.13
645 1088 2.187599 CTCTTTGTTTCTGCGGGCGG 62.188 60.000 0.00 0.00 0.00 6.13
646 1089 1.207593 CTCTTTGTTTCTGCGGGCG 59.792 57.895 0.00 0.00 0.00 6.13
647 1090 0.519077 CTCTCTTTGTTTCTGCGGGC 59.481 55.000 0.00 0.00 0.00 6.13
648 1091 2.072298 CTCTCTCTTTGTTTCTGCGGG 58.928 52.381 0.00 0.00 0.00 6.13
649 1092 2.072298 CCTCTCTCTTTGTTTCTGCGG 58.928 52.381 0.00 0.00 0.00 5.69
650 1093 2.478134 CACCTCTCTCTTTGTTTCTGCG 59.522 50.000 0.00 0.00 0.00 5.18
651 1094 3.471680 ACACCTCTCTCTTTGTTTCTGC 58.528 45.455 0.00 0.00 0.00 4.26
655 1098 4.079730 AGGGAAACACCTCTCTCTTTGTTT 60.080 41.667 0.00 0.00 43.22 2.83
656 1099 3.459969 AGGGAAACACCTCTCTCTTTGTT 59.540 43.478 0.00 0.00 35.43 2.83
657 1100 3.049344 AGGGAAACACCTCTCTCTTTGT 58.951 45.455 0.00 0.00 35.43 2.83
658 1101 3.778954 AGGGAAACACCTCTCTCTTTG 57.221 47.619 0.00 0.00 35.43 2.77
659 1102 4.262506 CGTAAGGGAAACACCTCTCTCTTT 60.263 45.833 0.00 0.00 40.87 2.52
660 1103 3.258622 CGTAAGGGAAACACCTCTCTCTT 59.741 47.826 0.00 0.00 40.87 2.85
661 1104 2.826725 CGTAAGGGAAACACCTCTCTCT 59.173 50.000 0.00 0.00 40.87 3.10
662 1105 2.674462 GCGTAAGGGAAACACCTCTCTC 60.674 54.545 0.00 0.00 40.87 3.20
663 1106 1.275573 GCGTAAGGGAAACACCTCTCT 59.724 52.381 0.00 0.00 40.87 3.10
664 1107 1.723220 GCGTAAGGGAAACACCTCTC 58.277 55.000 0.00 0.00 40.87 3.20
722 1169 3.312828 CGGGAAGACGAAGATGATGATC 58.687 50.000 0.00 0.00 35.47 2.92
741 1188 4.796231 CAACGCGTCTCCCTCCGG 62.796 72.222 14.44 0.00 0.00 5.14
742 1189 3.569049 AACAACGCGTCTCCCTCCG 62.569 63.158 14.44 0.00 0.00 4.63
743 1190 2.027625 CAACAACGCGTCTCCCTCC 61.028 63.158 14.44 0.00 0.00 4.30
744 1191 2.668280 GCAACAACGCGTCTCCCTC 61.668 63.158 14.44 0.00 0.00 4.30
745 1192 2.665185 GCAACAACGCGTCTCCCT 60.665 61.111 14.44 0.00 0.00 4.20
746 1193 3.723348 GGCAACAACGCGTCTCCC 61.723 66.667 14.44 5.36 0.00 4.30
766 1213 2.909965 GGCGGGTGGCTTTTGTCA 60.910 61.111 0.00 0.00 42.94 3.58
898 1345 0.253610 GACGAGGAGAGAGGTCTGGA 59.746 60.000 0.00 0.00 30.97 3.86
901 1348 1.450669 GCGACGAGGAGAGAGGTCT 60.451 63.158 0.00 0.00 34.86 3.85
902 1349 1.745864 TGCGACGAGGAGAGAGGTC 60.746 63.158 0.00 0.00 0.00 3.85
903 1350 2.041686 GTGCGACGAGGAGAGAGGT 61.042 63.158 0.00 0.00 0.00 3.85
941 1792 0.552848 AGGAGAGGAGAGGAGAGCTG 59.447 60.000 0.00 0.00 0.00 4.24
952 1803 2.364842 GCTGGGCTGAGGAGAGGA 60.365 66.667 0.00 0.00 0.00 3.71
953 1804 3.478274 GGCTGGGCTGAGGAGAGG 61.478 72.222 0.00 0.00 0.00 3.69
972 1823 4.514585 TGGGTGGTGGTGGTGTGC 62.515 66.667 0.00 0.00 0.00 4.57
988 1839 1.136147 GAAACATCTGCGCTGGCTG 59.864 57.895 14.70 13.94 40.82 4.85
989 1840 1.002868 AGAAACATCTGCGCTGGCT 60.003 52.632 14.70 0.00 40.82 4.75
990 1841 1.300971 TGAGAAACATCTGCGCTGGC 61.301 55.000 14.70 0.00 40.52 4.85
991 1842 0.445436 GTGAGAAACATCTGCGCTGG 59.555 55.000 14.70 4.50 0.00 4.85
992 1843 0.445436 GGTGAGAAACATCTGCGCTG 59.555 55.000 9.73 8.88 0.00 5.18
1460 2607 0.108233 CAGAGCAGAAGAGGGAGTGC 60.108 60.000 0.00 0.00 36.10 4.40
1462 2609 1.264045 GGCAGAGCAGAAGAGGGAGT 61.264 60.000 0.00 0.00 0.00 3.85
1465 2612 1.221293 CTGGCAGAGCAGAAGAGGG 59.779 63.158 9.42 0.00 0.00 4.30
1475 2622 4.093291 AAGGGAGCGCTGGCAGAG 62.093 66.667 18.48 17.43 43.41 3.35
1476 2623 4.087892 GAAGGGAGCGCTGGCAGA 62.088 66.667 18.48 0.00 43.41 4.26
1482 2629 3.483869 GGGATGGAAGGGAGCGCT 61.484 66.667 11.27 11.27 0.00 5.92
1554 2701 4.047059 TTCACGGCGAGGACGACC 62.047 66.667 16.62 0.00 45.81 4.79
1569 2716 3.644399 GAGGGAGGACACGGCGTTC 62.644 68.421 11.19 11.66 0.00 3.95
1623 2770 1.301401 GTCACGGTTGGTGCTGCTA 60.301 57.895 0.00 0.00 46.56 3.49
1730 2877 1.375908 TGGATCTCGTTGCTGGTGC 60.376 57.895 0.00 0.00 40.20 5.01
2015 3174 9.927668 ACTTACTGCTACTAGTACTAGTATAGC 57.072 37.037 32.71 32.71 44.76 2.97
2050 3209 3.318557 TGTATACACTTGGACACGACACA 59.681 43.478 0.08 0.00 0.00 3.72
2072 3231 2.942376 CTGACTCTGTCTGTATCGCTCT 59.058 50.000 0.00 0.00 33.15 4.09
2073 3232 2.032799 CCTGACTCTGTCTGTATCGCTC 59.967 54.545 0.00 0.00 33.15 5.03
2133 3301 2.243957 GCACACACGCAGCAGTACA 61.244 57.895 0.00 0.00 0.00 2.90
2226 3403 4.913345 CCGACGGTTTTCTTTTCATTTACC 59.087 41.667 5.48 0.00 0.00 2.85
2234 3411 4.269123 GCAATTTTCCGACGGTTTTCTTTT 59.731 37.500 14.79 0.00 0.00 2.27
2275 3452 6.035866 GCATTACAAATCACAGAGAGAGACAG 59.964 42.308 0.00 0.00 0.00 3.51
2321 3500 7.254863 GCAAGCATCATTTCCTTTTCTCAAAAA 60.255 33.333 0.00 0.00 33.42 1.94
2322 3501 6.203338 GCAAGCATCATTTCCTTTTCTCAAAA 59.797 34.615 0.00 0.00 0.00 2.44
2323 3502 5.697633 GCAAGCATCATTTCCTTTTCTCAAA 59.302 36.000 0.00 0.00 0.00 2.69
2324 3503 5.232463 GCAAGCATCATTTCCTTTTCTCAA 58.768 37.500 0.00 0.00 0.00 3.02
2325 3504 4.616604 CGCAAGCATCATTTCCTTTTCTCA 60.617 41.667 0.00 0.00 0.00 3.27
2326 3505 3.855950 CGCAAGCATCATTTCCTTTTCTC 59.144 43.478 0.00 0.00 0.00 2.87
2327 3506 3.256631 ACGCAAGCATCATTTCCTTTTCT 59.743 39.130 0.00 0.00 45.62 2.52
2328 3507 3.365820 CACGCAAGCATCATTTCCTTTTC 59.634 43.478 0.00 0.00 45.62 2.29
2329 3508 3.005684 TCACGCAAGCATCATTTCCTTTT 59.994 39.130 0.00 0.00 45.62 2.27
2330 3509 2.557924 TCACGCAAGCATCATTTCCTTT 59.442 40.909 0.00 0.00 45.62 3.11
2331 3510 2.161855 TCACGCAAGCATCATTTCCTT 58.838 42.857 0.00 0.00 45.62 3.36
2332 3511 1.741706 CTCACGCAAGCATCATTTCCT 59.258 47.619 0.00 0.00 45.62 3.36
2333 3512 1.202222 CCTCACGCAAGCATCATTTCC 60.202 52.381 0.00 0.00 45.62 3.13
2334 3513 1.470098 ACCTCACGCAAGCATCATTTC 59.530 47.619 0.00 0.00 45.62 2.17
2335 3514 1.200716 CACCTCACGCAAGCATCATTT 59.799 47.619 0.00 0.00 45.62 2.32
2336 3515 0.806868 CACCTCACGCAAGCATCATT 59.193 50.000 0.00 0.00 45.62 2.57
2337 3516 0.036105 TCACCTCACGCAAGCATCAT 60.036 50.000 0.00 0.00 45.62 2.45
2338 3517 0.036105 ATCACCTCACGCAAGCATCA 60.036 50.000 0.00 0.00 45.62 3.07
2339 3518 0.376152 CATCACCTCACGCAAGCATC 59.624 55.000 0.00 0.00 45.62 3.91
2340 3519 0.036105 TCATCACCTCACGCAAGCAT 60.036 50.000 0.00 0.00 45.62 3.79
2341 3520 0.671472 CTCATCACCTCACGCAAGCA 60.671 55.000 0.00 0.00 45.62 3.91
2342 3521 1.975363 GCTCATCACCTCACGCAAGC 61.975 60.000 0.00 0.00 45.62 4.01
2344 3523 0.035317 AAGCTCATCACCTCACGCAA 59.965 50.000 0.00 0.00 0.00 4.85
2345 3524 0.671472 CAAGCTCATCACCTCACGCA 60.671 55.000 0.00 0.00 0.00 5.24
2346 3525 0.671781 ACAAGCTCATCACCTCACGC 60.672 55.000 0.00 0.00 0.00 5.34
2347 3526 1.073964 CACAAGCTCATCACCTCACG 58.926 55.000 0.00 0.00 0.00 4.35
2348 3527 0.801251 GCACAAGCTCATCACCTCAC 59.199 55.000 0.00 0.00 37.91 3.51
2349 3528 3.238232 GCACAAGCTCATCACCTCA 57.762 52.632 0.00 0.00 37.91 3.86
2375 3554 4.832248 TGATAGAAAGTCGACCAGCAAAT 58.168 39.130 13.01 0.00 0.00 2.32
2379 3558 3.512033 ACTGATAGAAAGTCGACCAGC 57.488 47.619 13.01 1.14 0.00 4.85
2391 3570 7.279536 GTCATCAAAGAAGCATCAACTGATAGA 59.720 37.037 0.00 0.00 32.63 1.98
2392 3571 7.065443 TGTCATCAAAGAAGCATCAACTGATAG 59.935 37.037 0.00 0.00 32.63 2.08
2393 3572 6.880529 TGTCATCAAAGAAGCATCAACTGATA 59.119 34.615 0.00 0.00 32.63 2.15
2394 3573 5.708697 TGTCATCAAAGAAGCATCAACTGAT 59.291 36.000 0.00 0.00 34.56 2.90
2395 3574 5.065235 TGTCATCAAAGAAGCATCAACTGA 58.935 37.500 0.00 0.00 0.00 3.41
2397 3576 5.708697 TCATGTCATCAAAGAAGCATCAACT 59.291 36.000 0.00 0.00 0.00 3.16
2400 3579 6.578163 TTTCATGTCATCAAAGAAGCATCA 57.422 33.333 0.00 0.00 0.00 3.07
2401 3580 6.019801 GCATTTCATGTCATCAAAGAAGCATC 60.020 38.462 0.00 0.00 0.00 3.91
2406 3585 6.031471 CGATGCATTTCATGTCATCAAAGAA 58.969 36.000 0.00 0.00 40.53 2.52
2410 3589 3.695556 ACCGATGCATTTCATGTCATCAA 59.304 39.130 0.00 0.00 40.53 2.57
2415 3594 2.613595 TGCTACCGATGCATTTCATGTC 59.386 45.455 0.00 0.00 35.05 3.06
2417 3596 2.355444 TGTGCTACCGATGCATTTCATG 59.645 45.455 0.00 0.00 42.69 3.07
2421 3600 1.949525 GGATGTGCTACCGATGCATTT 59.050 47.619 0.00 0.00 42.69 2.32
2426 3605 2.205074 GTCAAGGATGTGCTACCGATG 58.795 52.381 0.00 0.00 0.00 3.84
2429 3608 0.249120 TGGTCAAGGATGTGCTACCG 59.751 55.000 0.00 0.00 0.00 4.02
2431 3610 1.672881 GCATGGTCAAGGATGTGCTAC 59.327 52.381 0.00 0.00 0.00 3.58
2432 3611 1.408683 GGCATGGTCAAGGATGTGCTA 60.409 52.381 0.00 0.00 33.38 3.49
2433 3612 0.682209 GGCATGGTCAAGGATGTGCT 60.682 55.000 0.00 0.00 33.38 4.40
2434 3613 1.811860 GGCATGGTCAAGGATGTGC 59.188 57.895 0.00 0.00 0.00 4.57
2435 3614 0.677731 ACGGCATGGTCAAGGATGTG 60.678 55.000 0.00 0.00 0.00 3.21
2438 3617 0.620556 AGAACGGCATGGTCAAGGAT 59.379 50.000 0.00 0.00 0.00 3.24
2440 3619 1.207089 TCTAGAACGGCATGGTCAAGG 59.793 52.381 0.00 0.00 0.00 3.61
2441 3620 2.544685 CTCTAGAACGGCATGGTCAAG 58.455 52.381 0.00 0.00 0.00 3.02
2442 3621 1.405526 GCTCTAGAACGGCATGGTCAA 60.406 52.381 0.00 0.00 0.00 3.18
2445 3624 0.108138 GTGCTCTAGAACGGCATGGT 60.108 55.000 8.25 0.00 38.27 3.55
2448 3627 1.519455 GCGTGCTCTAGAACGGCAT 60.519 57.895 16.52 0.00 46.80 4.40
2449 3628 2.126071 GCGTGCTCTAGAACGGCA 60.126 61.111 16.52 9.63 46.80 5.69
2453 3632 1.805945 CCCGTGCGTGCTCTAGAAC 60.806 63.158 0.00 0.00 0.00 3.01
2454 3633 2.273179 ACCCGTGCGTGCTCTAGAA 61.273 57.895 0.00 0.00 0.00 2.10
2455 3634 2.675423 ACCCGTGCGTGCTCTAGA 60.675 61.111 0.00 0.00 0.00 2.43
2456 3635 2.507102 CACCCGTGCGTGCTCTAG 60.507 66.667 0.00 0.00 0.00 2.43
2457 3636 4.063967 CCACCCGTGCGTGCTCTA 62.064 66.667 0.00 0.00 32.10 2.43
2493 3672 4.493747 AAGCGCCGCGTAGGACTC 62.494 66.667 15.34 0.00 45.00 3.36
2494 3673 4.796231 CAAGCGCCGCGTAGGACT 62.796 66.667 15.34 0.00 45.00 3.85
2571 3756 3.496131 CCGCCGGTCAATCGTTGG 61.496 66.667 1.90 0.00 0.00 3.77
2572 3757 3.496131 CCCGCCGGTCAATCGTTG 61.496 66.667 1.90 0.00 0.00 4.10
2573 3758 2.530958 AATCCCGCCGGTCAATCGTT 62.531 55.000 1.90 0.00 0.00 3.85
2574 3759 3.026431 AATCCCGCCGGTCAATCGT 62.026 57.895 1.90 0.00 0.00 3.73
2575 3760 2.203015 AATCCCGCCGGTCAATCG 60.203 61.111 1.90 0.00 0.00 3.34
2576 3761 1.153249 TCAATCCCGCCGGTCAATC 60.153 57.895 1.90 0.00 0.00 2.67
2577 3762 1.451387 GTCAATCCCGCCGGTCAAT 60.451 57.895 1.90 0.00 0.00 2.57
2578 3763 2.046700 GTCAATCCCGCCGGTCAA 60.047 61.111 1.90 0.00 0.00 3.18
2579 3764 4.090588 GGTCAATCCCGCCGGTCA 62.091 66.667 1.90 0.00 0.00 4.02
2587 3772 1.808390 CGTTCCGTCGGTCAATCCC 60.808 63.158 11.88 0.00 0.00 3.85
2588 3773 2.450345 GCGTTCCGTCGGTCAATCC 61.450 63.158 11.88 0.00 0.00 3.01
2589 3774 1.445582 AGCGTTCCGTCGGTCAATC 60.446 57.895 11.88 0.00 36.89 2.67
2622 3807 4.947147 TTCAACGGCCGGCAAGCT 62.947 61.111 31.76 10.28 0.00 3.74
2668 3885 2.438254 TGACATCGTGCCATGGCC 60.438 61.111 33.44 22.58 41.09 5.36
2669 3886 2.793946 GTGACATCGTGCCATGGC 59.206 61.111 30.54 30.54 42.35 4.40
2670 3887 0.811219 ATCGTGACATCGTGCCATGG 60.811 55.000 7.63 7.63 0.00 3.66
2671 3888 0.302589 CATCGTGACATCGTGCCATG 59.697 55.000 0.00 0.00 0.00 3.66
2672 3889 0.175531 TCATCGTGACATCGTGCCAT 59.824 50.000 0.00 0.00 0.00 4.40
2673 3890 0.735978 GTCATCGTGACATCGTGCCA 60.736 55.000 11.62 0.00 46.22 4.92
2674 3891 1.999051 GTCATCGTGACATCGTGCC 59.001 57.895 11.62 0.00 46.22 5.01
2682 3899 0.872021 GCCATCTCCGTCATCGTGAC 60.872 60.000 7.74 7.74 43.65 3.67
2790 4007 2.202932 AGGACGACATGGCATCGC 60.203 61.111 10.21 3.91 43.46 4.58
2961 4178 2.711922 CCGGTAGCTGCTTCCGTCT 61.712 63.158 34.88 3.91 41.66 4.18


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

AutoCloner maintained by Alex Coulton.