Multiple sequence alignment - TraesCS2B01G097300

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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 TraesCS2B01G097300 chr2B 100.000 3993 0 0 1 3993 57651933 57655925 0.000000e+00 7374.0
1 TraesCS2B01G097300 chr2B 93.809 1163 54 10 2076 3235 57421315 57422462 0.000000e+00 1733.0
2 TraesCS2B01G097300 chr2B 94.685 715 30 5 927 1640 57420139 57420846 0.000000e+00 1103.0
3 TraesCS2B01G097300 chr2B 95.475 221 5 5 672 891 71234638 71234422 8.210000e-92 348.0
4 TraesCS2B01G097300 chr2B 85.032 314 37 8 145 453 57419575 57419883 1.080000e-80 311.0
5 TraesCS2B01G097300 chr2B 87.097 62 5 2 502 562 792760590 792760649 2.580000e-07 67.6
6 TraesCS2B01G097300 chr2D 95.642 2547 77 13 859 3401 34981772 34984288 0.000000e+00 4058.0
7 TraesCS2B01G097300 chr2D 93.814 1164 58 11 2076 3238 34894211 34895361 0.000000e+00 1738.0
8 TraesCS2B01G097300 chr2D 86.257 1237 98 39 876 2074 34892815 34894017 0.000000e+00 1277.0
9 TraesCS2B01G097300 chr2D 93.194 573 31 4 1 565 34981027 34981599 0.000000e+00 835.0
10 TraesCS2B01G097300 chr2D 87.622 307 29 8 152 454 34892297 34892598 8.210000e-92 348.0
11 TraesCS2B01G097300 chr2D 97.727 132 3 0 546 677 34981659 34981790 1.120000e-55 228.0
12 TraesCS2B01G097300 chr2D 97.826 46 1 0 3700 3745 34984780 34984825 3.310000e-11 80.5
13 TraesCS2B01G097300 chr2D 88.525 61 3 4 502 559 327964335 327964276 1.990000e-08 71.3
14 TraesCS2B01G097300 chr2A 94.315 1249 63 5 2067 3314 38305980 38307221 0.000000e+00 1906.0
15 TraesCS2B01G097300 chr2A 93.109 1161 59 9 2076 3235 38219163 38220303 0.000000e+00 1681.0
16 TraesCS2B01G097300 chr2A 90.654 856 44 16 921 1752 38218100 38218943 0.000000e+00 1105.0
17 TraesCS2B01G097300 chr2A 94.603 667 29 3 859 1518 38304838 38305504 0.000000e+00 1026.0
18 TraesCS2B01G097300 chr2A 92.094 468 33 3 1 466 487646480 487646945 0.000000e+00 656.0
19 TraesCS2B01G097300 chr2A 85.885 418 46 10 80 492 38304301 38304710 2.200000e-117 433.0
20 TraesCS2B01G097300 chr2A 86.452 310 34 7 147 453 38217494 38217798 2.300000e-87 333.0
21 TraesCS2B01G097300 chr2A 78.799 283 25 23 3744 3993 38308229 38308509 1.490000e-34 158.0
22 TraesCS2B01G097300 chr2A 94.444 90 5 0 3313 3402 38307293 38307382 5.380000e-29 139.0
23 TraesCS2B01G097300 chr2A 100.000 38 0 0 500 537 73525162 73525199 1.990000e-08 71.3
24 TraesCS2B01G097300 chr5D 90.611 916 86 0 2076 2991 483227795 483226880 0.000000e+00 1216.0
25 TraesCS2B01G097300 chr5D 89.738 916 94 0 2079 2994 483371408 483370493 0.000000e+00 1171.0
26 TraesCS2B01G097300 chr5D 89.482 618 55 7 996 1610 483372418 483371808 0.000000e+00 773.0
27 TraesCS2B01G097300 chr5D 93.517 509 30 3 996 1503 483228781 483228275 0.000000e+00 754.0
28 TraesCS2B01G097300 chr5D 93.651 126 8 0 368 493 561348280 561348155 5.270000e-44 189.0
29 TraesCS2B01G097300 chr5A 90.033 923 92 0 2072 2994 604311664 604310742 0.000000e+00 1195.0
30 TraesCS2B01G097300 chr5A 89.738 916 94 0 2076 2991 603794336 603793421 0.000000e+00 1171.0
31 TraesCS2B01G097300 chr5A 89.525 611 54 7 996 1603 604312714 604312111 0.000000e+00 765.0
32 TraesCS2B01G097300 chr5A 98.953 191 2 0 677 867 485382093 485382283 3.820000e-90 342.0
33 TraesCS2B01G097300 chr5A 88.333 60 5 2 502 561 709391511 709391454 1.990000e-08 71.3
34 TraesCS2B01G097300 chr5A 90.385 52 5 0 492 543 702008542 702008491 7.160000e-08 69.4
35 TraesCS2B01G097300 chr5B 89.399 915 95 2 2080 2994 593944249 593943337 0.000000e+00 1151.0
36 TraesCS2B01G097300 chr5B 89.192 916 99 0 2076 2991 593659306 593658391 0.000000e+00 1144.0
37 TraesCS2B01G097300 chr5B 93.169 527 35 1 996 1521 593945331 593944805 0.000000e+00 773.0
38 TraesCS2B01G097300 chr5B 95.392 217 4 6 658 870 287780982 287781196 1.370000e-89 340.0
39 TraesCS2B01G097300 chr5B 95.628 183 6 1 284 466 489395658 489395478 3.900000e-75 292.0
40 TraesCS2B01G097300 chr5B 98.039 51 1 0 341 391 50565021 50564971 5.500000e-14 89.8
41 TraesCS2B01G097300 chr4A 89.205 880 95 0 2110 2989 124404859 124403980 0.000000e+00 1099.0
42 TraesCS2B01G097300 chr4A 89.040 885 97 0 2110 2994 125029020 125029904 0.000000e+00 1098.0
43 TraesCS2B01G097300 chr4A 96.209 211 4 4 659 867 365637196 365637404 3.820000e-90 342.0
44 TraesCS2B01G097300 chr4A 91.228 57 2 2 502 558 85579461 85579408 1.540000e-09 75.0
45 TraesCS2B01G097300 chr4A 93.478 46 3 0 496 541 222525778 222525823 7.160000e-08 69.4
46 TraesCS2B01G097300 chr4A 93.478 46 3 0 496 541 591109494 591109539 7.160000e-08 69.4
47 TraesCS2B01G097300 chr4B 88.927 885 98 0 2110 2994 423776094 423775210 0.000000e+00 1092.0
48 TraesCS2B01G097300 chr4B 88.409 880 102 0 2110 2989 424061385 424062264 0.000000e+00 1061.0
49 TraesCS2B01G097300 chr4B 93.450 229 10 4 658 881 551054132 551054360 6.390000e-88 335.0
50 TraesCS2B01G097300 chr4B 94.536 183 8 1 284 466 657567663 657567843 8.450000e-72 281.0
51 TraesCS2B01G097300 chr4B 98.851 87 0 1 341 426 555697926 555698012 1.920000e-33 154.0
52 TraesCS2B01G097300 chr4B 97.778 45 0 1 383 426 578297850 578297806 4.280000e-10 76.8
53 TraesCS2B01G097300 chr4D 88.977 880 97 0 2110 2989 341924039 341924918 0.000000e+00 1088.0
54 TraesCS2B01G097300 chr4D 88.814 885 99 0 2110 2994 341695995 341695111 0.000000e+00 1086.0
55 TraesCS2B01G097300 chr6D 94.243 469 20 6 1 466 67714879 67714415 0.000000e+00 710.0
56 TraesCS2B01G097300 chr6D 92.094 468 23 8 1 466 452249893 452250348 0.000000e+00 647.0
57 TraesCS2B01G097300 chr6D 87.805 369 37 1 2132 2492 440204421 440204789 3.690000e-115 425.0
58 TraesCS2B01G097300 chr6D 89.655 58 5 1 502 559 424819724 424819668 5.540000e-09 73.1
59 TraesCS2B01G097300 chr6D 95.238 42 2 0 502 543 132761390 132761349 2.580000e-07 67.6
60 TraesCS2B01G097300 chr3A 93.191 470 28 3 1 468 42410258 42409791 0.000000e+00 688.0
61 TraesCS2B01G097300 chr3A 99.476 191 1 0 677 867 83748684 83748874 8.210000e-92 348.0
62 TraesCS2B01G097300 chr3A 97.500 40 1 0 502 541 718808339 718808300 7.160000e-08 69.4
63 TraesCS2B01G097300 chr7A 98.964 193 1 1 669 860 184334091 184333899 1.060000e-90 344.0
64 TraesCS2B01G097300 chr6B 96.226 212 4 3 670 879 338654713 338654922 1.060000e-90 344.0
65 TraesCS2B01G097300 chr6B 92.647 68 5 0 284 351 362490524 362490591 9.130000e-17 99.0
66 TraesCS2B01G097300 chr6B 94.000 50 2 1 502 551 195466205 195466157 1.540000e-09 75.0
67 TraesCS2B01G097300 chr3B 98.469 196 0 3 678 871 359224608 359224414 3.820000e-90 342.0
68 TraesCS2B01G097300 chr3B 96.175 183 5 1 284 466 7637177 7636997 8.390000e-77 298.0
69 TraesCS2B01G097300 chr3B 95.082 183 7 1 284 466 506259313 506259493 1.820000e-73 287.0
70 TraesCS2B01G097300 chr1A 95.082 183 7 1 284 466 169669053 169669233 1.820000e-73 287.0
71 TraesCS2B01G097300 chr1A 95.082 183 7 1 284 466 200865547 200865727 1.820000e-73 287.0
72 TraesCS2B01G097300 chr1A 91.057 123 11 0 368 490 346785708 346785830 2.470000e-37 167.0
73 TraesCS2B01G097300 chr7D 94.444 126 7 0 368 493 556662945 556662820 1.130000e-45 195.0
74 TraesCS2B01G097300 chr7D 100.000 38 0 0 500 537 184267360 184267397 1.990000e-08 71.3
75 TraesCS2B01G097300 chr1D 92.593 54 3 1 502 555 452590841 452590789 4.280000e-10 76.8
76 TraesCS2B01G097300 chrUn 93.617 47 3 0 495 541 37224132 37224086 1.990000e-08 71.3
77 TraesCS2B01G097300 chrUn 100.000 28 0 0 366 393 67153915 67153942 7.000000e-03 52.8
78 TraesCS2B01G097300 chr3D 87.097 62 6 2 502 562 47189788 47189848 7.160000e-08 69.4


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 TraesCS2B01G097300 chr2B 57651933 57655925 3992 False 7374.000000 7374 100.000000 1 3993 1 chr2B.!!$F1 3992
1 TraesCS2B01G097300 chr2B 57419575 57422462 2887 False 1049.000000 1733 91.175333 145 3235 3 chr2B.!!$F3 3090
2 TraesCS2B01G097300 chr2D 34981027 34984825 3798 False 1300.375000 4058 96.097250 1 3745 4 chr2D.!!$F2 3744
3 TraesCS2B01G097300 chr2D 34892297 34895361 3064 False 1121.000000 1738 89.231000 152 3238 3 chr2D.!!$F1 3086
4 TraesCS2B01G097300 chr2A 38217494 38220303 2809 False 1039.666667 1681 90.071667 147 3235 3 chr2A.!!$F3 3088
5 TraesCS2B01G097300 chr2A 38304301 38308509 4208 False 732.400000 1906 89.609200 80 3993 5 chr2A.!!$F4 3913
6 TraesCS2B01G097300 chr5D 483226880 483228781 1901 True 985.000000 1216 92.064000 996 2991 2 chr5D.!!$R2 1995
7 TraesCS2B01G097300 chr5D 483370493 483372418 1925 True 972.000000 1171 89.610000 996 2994 2 chr5D.!!$R3 1998
8 TraesCS2B01G097300 chr5A 603793421 603794336 915 True 1171.000000 1171 89.738000 2076 2991 1 chr5A.!!$R1 915
9 TraesCS2B01G097300 chr5A 604310742 604312714 1972 True 980.000000 1195 89.779000 996 2994 2 chr5A.!!$R4 1998
10 TraesCS2B01G097300 chr5B 593658391 593659306 915 True 1144.000000 1144 89.192000 2076 2991 1 chr5B.!!$R3 915
11 TraesCS2B01G097300 chr5B 593943337 593945331 1994 True 962.000000 1151 91.284000 996 2994 2 chr5B.!!$R4 1998
12 TraesCS2B01G097300 chr4A 124403980 124404859 879 True 1099.000000 1099 89.205000 2110 2989 1 chr4A.!!$R2 879
13 TraesCS2B01G097300 chr4A 125029020 125029904 884 False 1098.000000 1098 89.040000 2110 2994 1 chr4A.!!$F1 884
14 TraesCS2B01G097300 chr4B 423775210 423776094 884 True 1092.000000 1092 88.927000 2110 2994 1 chr4B.!!$R1 884
15 TraesCS2B01G097300 chr4B 424061385 424062264 879 False 1061.000000 1061 88.409000 2110 2989 1 chr4B.!!$F1 879
16 TraesCS2B01G097300 chr4D 341924039 341924918 879 False 1088.000000 1088 88.977000 2110 2989 1 chr4D.!!$F1 879
17 TraesCS2B01G097300 chr4D 341695111 341695995 884 True 1086.000000 1086 88.814000 2110 2994 1 chr4D.!!$R1 884

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
829 934 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.0 44.78 4.85 F
842 947 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.0 0.0 0.0 38.40 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2719 3516 1.272781 GGATCTCAGCGAACTTGACG 58.727 55.0 0.0 0.0 0.0 4.35 R
3038 3835 1.901654 TATACCGCCACCACCACCAC 61.902 60.0 0.0 0.0 0.0 4.16 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
35 36 2.753931 CTTTGCGCCCTGCTTGGTTC 62.754 60.000 4.18 0.00 46.63 3.62
68 69 3.206964 TGTCGCATGAACTGGTTGTTTA 58.793 40.909 0.00 0.00 39.30 2.01
70 71 3.496884 GTCGCATGAACTGGTTGTTTAGA 59.503 43.478 0.00 0.00 39.30 2.10
95 96 3.068165 TCTGTATGTATGTCTCTTGGGCG 59.932 47.826 0.00 0.00 0.00 6.13
206 209 2.490509 TGTCAGCAAATTGGAGATGCAG 59.509 45.455 2.16 0.00 42.45 4.41
228 232 1.134401 AGTGCCCATCGTCTAATGGTG 60.134 52.381 2.49 0.00 44.05 4.17
250 254 2.348998 CTGAAGGCCTCCTTGCGT 59.651 61.111 5.23 0.00 44.82 5.24
281 285 6.323996 TCTCATGTAGGTTCGATTCCTATTGT 59.676 38.462 16.36 6.63 39.36 2.71
282 286 6.513180 TCATGTAGGTTCGATTCCTATTGTC 58.487 40.000 16.36 7.48 39.36 3.18
302 306 2.948720 GCTTCTGCAGACGACCCCT 61.949 63.158 23.29 0.00 39.41 4.79
421 426 5.330233 TGACAAGGTATTCTGGTCTGTAGA 58.670 41.667 2.72 0.00 44.85 2.59
423 428 6.127338 TGACAAGGTATTCTGGTCTGTAGATG 60.127 42.308 2.72 0.00 44.85 2.90
424 429 4.946478 AGGTATTCTGGTCTGTAGATGC 57.054 45.455 0.00 0.00 0.00 3.91
445 452 9.638176 AGATGCATCTTATTCCTGTTAAGAATT 57.362 29.630 23.75 0.00 38.72 2.17
457 464 8.106247 TCCTGTTAAGAATTGTTTGGATGTAC 57.894 34.615 0.00 0.00 0.00 2.90
500 507 6.202954 AGTCAGATTTAGTTTTGGTTCTGTCG 59.797 38.462 0.00 0.00 33.88 4.35
509 516 1.745232 TGGTTCTGTCGCAACTTGTT 58.255 45.000 0.00 0.00 0.00 2.83
534 547 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
538 551 6.560711 ACTAAAGGCTTTGTTGTTGTTGTAG 58.439 36.000 22.32 9.26 0.00 2.74
652 757 9.546909 GTTGCCTGATAATTTGTATAATCATCG 57.453 33.333 0.00 0.00 0.00 3.84
701 806 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
702 807 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
703 808 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
704 809 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
705 810 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
711 816 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
712 817 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
713 818 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
714 819 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
717 822 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
729 834 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
730 835 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
731 836 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
732 837 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
733 838 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
734 839 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
735 840 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
736 841 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
737 842 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
738 843 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
739 844 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
740 845 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
741 846 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
742 847 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
743 848 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
744 849 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
745 850 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
746 851 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
747 852 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
757 862 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
758 863 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
759 864 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
760 865 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
761 866 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
762 867 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
763 868 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
764 869 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
765 870 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
766 871 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
767 872 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
768 873 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
769 874 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
770 875 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
771 876 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
772 877 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
773 878 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
774 879 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
775 880 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
776 881 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
777 882 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
778 883 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
779 884 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
780 885 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
781 886 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
782 887 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
783 888 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
795 900 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
796 901 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
797 902 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
798 903 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
799 904 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
800 905 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
801 906 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
802 907 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
803 908 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
804 909 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
805 910 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
806 911 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
807 912 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
808 913 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
809 914 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
810 915 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
811 916 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
812 917 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
813 918 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
814 919 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
815 920 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
816 921 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
828 933 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
829 934 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
830 935 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
831 936 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
832 937 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
833 938 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
834 939 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
835 940 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
836 941 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
837 942 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
838 943 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
839 944 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
840 945 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
841 946 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
842 947 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
843 948 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
847 952 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
848 953 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
849 954 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
850 955 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
851 956 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
852 957 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
853 958 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
854 959 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
1570 1723 9.495754 GCTCAGAATTACTTATTCAATGTCAAC 57.504 33.333 0.00 0.00 44.25 3.18
1610 1763 7.865707 AGAACATTCTGTAAACTGATTGACAC 58.134 34.615 14.74 8.15 35.89 3.67
1624 1777 2.507407 TGACACCCTTTTGCTATCCC 57.493 50.000 0.00 0.00 0.00 3.85
1646 1817 5.245977 CCCCTTGATGTTAAGGTTGTCAATT 59.754 40.000 0.00 0.00 44.65 2.32
1652 1823 9.474920 TTGATGTTAAGGTTGTCAATTTTCATC 57.525 29.630 14.61 14.61 0.00 2.92
1697 1868 2.093783 GGTTTGACGTCTTTGCTATCCG 59.906 50.000 17.92 0.00 0.00 4.18
1897 2306 7.595819 TTAAATGTCCAGGTTCAGTTGATTT 57.404 32.000 9.23 0.00 0.00 2.17
2719 3516 3.118454 CACACGTCCCACATCGCC 61.118 66.667 0.00 0.00 0.00 5.54
3024 3821 2.050168 GTGGCGTCGTTCGTGGTA 60.050 61.111 0.00 0.00 42.13 3.25
3068 3871 1.218854 GCGGTATACGGTGGTGGTT 59.781 57.895 11.59 0.00 44.51 3.67
3084 3887 3.181497 GGTGGTTATAGTCGTGTTAGCGA 60.181 47.826 0.00 0.00 38.68 4.93
3107 3910 4.893424 TTTGCGAACTTGTTAAGCTTCT 57.107 36.364 0.00 0.00 0.00 2.85
3159 3966 8.705594 ACTGCTTATTACTGTGGTCATAGTATT 58.294 33.333 8.09 7.60 35.45 1.89
3194 4001 6.316640 TGTTGGTGAAACTTCGTCAGATAAAA 59.683 34.615 0.00 0.00 39.70 1.52
3228 4035 9.936759 TTTATATATGCGTGATATTTGGAGTCA 57.063 29.630 0.00 0.00 0.00 3.41
3249 4056 1.742761 TTTATGTCTGCTGCTGCCTC 58.257 50.000 13.47 4.21 38.71 4.70
3251 4058 1.780503 TATGTCTGCTGCTGCCTCTA 58.219 50.000 13.47 0.00 38.71 2.43
3256 4063 0.036577 CTGCTGCTGCCTCTACAAGT 60.037 55.000 13.47 0.00 38.71 3.16
3285 4092 6.841443 TGATAATGGTGTTTGTTTTGCAAG 57.159 33.333 0.00 0.00 38.47 4.01
3393 4274 3.256558 CAGCTGCTTTATTTTTCCAGGC 58.743 45.455 0.00 0.00 0.00 4.85
3402 4283 1.999648 TTTTTCCAGGCTGCATCTGT 58.000 45.000 9.56 0.00 0.00 3.41
3403 4284 1.999648 TTTTCCAGGCTGCATCTGTT 58.000 45.000 9.56 0.00 0.00 3.16
3406 4293 1.999648 TCCAGGCTGCATCTGTTTTT 58.000 45.000 9.56 0.00 0.00 1.94
3418 4305 2.294074 TCTGTTTTTCAACCCGGACTG 58.706 47.619 0.73 0.00 31.02 3.51
3420 4307 0.741915 GTTTTTCAACCCGGACTGCA 59.258 50.000 0.73 0.00 0.00 4.41
3425 4369 2.107950 TCAACCCGGACTGCAAATAG 57.892 50.000 0.73 0.00 0.00 1.73
3426 4370 1.094785 CAACCCGGACTGCAAATAGG 58.905 55.000 0.73 0.00 0.00 2.57
3428 4372 1.152963 CCCGGACTGCAAATAGGGG 60.153 63.158 0.73 2.72 35.36 4.79
3430 4374 1.224592 CGGACTGCAAATAGGGGCT 59.775 57.895 0.00 0.00 0.00 5.19
3448 4392 5.365314 AGGGGCTTTTCATACTTTGTTCAAA 59.635 36.000 0.00 0.00 0.00 2.69
3457 4401 7.416154 TCATACTTTGTTCAAAAGTACTCCG 57.584 36.000 11.70 3.67 43.14 4.63
3459 4403 8.143193 TCATACTTTGTTCAAAAGTACTCCGTA 58.857 33.333 11.70 1.69 43.14 4.02
3461 4405 7.417496 ACTTTGTTCAAAAGTACTCCGTATC 57.583 36.000 0.00 0.00 38.58 2.24
3463 4407 7.170998 ACTTTGTTCAAAAGTACTCCGTATCTG 59.829 37.037 0.00 0.00 38.58 2.90
3464 4408 6.092955 TGTTCAAAAGTACTCCGTATCTGT 57.907 37.500 0.00 0.00 0.00 3.41
3468 4412 8.340443 GTTCAAAAGTACTCCGTATCTGTTTTT 58.660 33.333 0.00 0.00 0.00 1.94
3470 4414 6.701432 AAAGTACTCCGTATCTGTTTTTCG 57.299 37.500 0.00 0.00 0.00 3.46
3471 4415 5.633830 AGTACTCCGTATCTGTTTTTCGA 57.366 39.130 0.00 0.00 0.00 3.71
3472 4416 5.638783 AGTACTCCGTATCTGTTTTTCGAG 58.361 41.667 0.00 0.00 0.00 4.04
3473 4417 4.516365 ACTCCGTATCTGTTTTTCGAGT 57.484 40.909 0.00 0.00 0.00 4.18
3475 4419 5.295152 ACTCCGTATCTGTTTTTCGAGTTT 58.705 37.500 0.00 0.00 0.00 2.66
3476 4420 5.756833 ACTCCGTATCTGTTTTTCGAGTTTT 59.243 36.000 0.00 0.00 0.00 2.43
3477 4421 6.925165 ACTCCGTATCTGTTTTTCGAGTTTTA 59.075 34.615 0.00 0.00 0.00 1.52
3478 4422 7.095899 ACTCCGTATCTGTTTTTCGAGTTTTAC 60.096 37.037 0.00 0.00 0.00 2.01
3481 4425 7.007697 CGTATCTGTTTTTCGAGTTTTACCTG 58.992 38.462 0.00 0.00 0.00 4.00
3482 4426 7.095940 CGTATCTGTTTTTCGAGTTTTACCTGA 60.096 37.037 0.00 0.00 0.00 3.86
3484 4428 7.011828 TCTGTTTTTCGAGTTTTACCTGAAG 57.988 36.000 0.00 0.00 0.00 3.02
3485 4429 6.037830 TCTGTTTTTCGAGTTTTACCTGAAGG 59.962 38.462 0.00 0.00 42.17 3.46
3486 4430 5.881443 TGTTTTTCGAGTTTTACCTGAAGGA 59.119 36.000 2.62 0.00 38.94 3.36
3490 4434 8.680039 TTTTCGAGTTTTACCTGAAGGAATAA 57.320 30.769 2.62 0.00 38.94 1.40
3491 4435 7.900782 TTCGAGTTTTACCTGAAGGAATAAG 57.099 36.000 2.62 0.00 38.94 1.73
3494 4438 7.386848 TCGAGTTTTACCTGAAGGAATAAGTTG 59.613 37.037 2.62 1.69 38.94 3.16
3496 4440 6.208797 AGTTTTACCTGAAGGAATAAGTTGCC 59.791 38.462 2.62 0.00 38.94 4.52
3502 4446 3.193267 TGAAGGAATAAGTTGCCATGTGC 59.807 43.478 0.00 0.00 41.77 4.57
3503 4447 3.091633 AGGAATAAGTTGCCATGTGCT 57.908 42.857 7.54 0.00 42.00 4.40
3507 4451 4.082026 GGAATAAGTTGCCATGTGCTCTTT 60.082 41.667 15.51 7.83 42.00 2.52
3508 4452 2.806608 AAGTTGCCATGTGCTCTTTG 57.193 45.000 7.54 0.00 42.00 2.77
3509 4453 1.696063 AGTTGCCATGTGCTCTTTGT 58.304 45.000 7.54 0.00 42.00 2.83
3510 4454 1.610522 AGTTGCCATGTGCTCTTTGTC 59.389 47.619 7.54 0.00 42.00 3.18
3511 4455 0.961019 TTGCCATGTGCTCTTTGTCC 59.039 50.000 7.54 0.00 42.00 4.02
3514 4458 0.798776 CCATGTGCTCTTTGTCCGTC 59.201 55.000 0.00 0.00 0.00 4.79
3515 4459 1.511850 CATGTGCTCTTTGTCCGTCA 58.488 50.000 0.00 0.00 0.00 4.35
3516 4460 1.872952 CATGTGCTCTTTGTCCGTCAA 59.127 47.619 0.00 0.00 0.00 3.18
3565 4867 2.122783 TCCACCGGGATGATTTGAAC 57.877 50.000 6.32 0.00 38.64 3.18
3584 4886 2.510238 CGGCCTCTTCTTCCTGCG 60.510 66.667 0.00 0.00 0.00 5.18
3586 4888 2.821810 GCCTCTTCTTCCTGCGGC 60.822 66.667 0.00 0.00 0.00 6.53
3588 4890 1.449246 CCTCTTCTTCCTGCGGCAG 60.449 63.158 22.84 22.84 0.00 4.85
3589 4891 2.046892 TCTTCTTCCTGCGGCAGC 60.047 61.111 24.27 0.31 45.41 5.25
3605 4930 4.357947 GCGGCCTCACACGTCTCA 62.358 66.667 0.00 0.00 0.00 3.27
3629 4954 3.181967 CCGCCTTCGTCGAAGCTG 61.182 66.667 26.21 19.67 38.24 4.24
3633 4958 1.077089 GCCTTCGTCGAAGCTGTACC 61.077 60.000 26.21 8.35 38.24 3.34
3665 5006 2.286872 CAATGGCTTAGAGCTGACCAG 58.713 52.381 0.00 0.00 41.99 4.00
3731 5115 0.813184 CTGCTGTTGCTATTGGGGTG 59.187 55.000 0.00 0.00 40.48 4.61
3756 5197 5.748592 AGCACGAGACTTCAAAAATTACAC 58.251 37.500 0.00 0.00 0.00 2.90
3893 5360 9.814899 AGATGAAGTAACATCAGACTTTAGATG 57.185 33.333 0.00 0.00 46.11 2.90
3918 5417 9.056005 TGTACAGATGGAGTATTTTGCATTATC 57.944 33.333 0.00 0.00 0.00 1.75
3928 5427 2.882927 TTGCATTATCGTAGTCGGCT 57.117 45.000 0.00 0.00 37.69 5.52
3936 5435 1.655484 TCGTAGTCGGCTATGAACGA 58.345 50.000 16.43 12.43 39.51 3.85
3941 5440 3.627732 AGTCGGCTATGAACGATGTAG 57.372 47.619 0.00 0.00 41.53 2.74
3942 5441 2.052157 GTCGGCTATGAACGATGTAGC 58.948 52.381 0.00 0.00 41.53 3.58
3983 5482 3.007074 TGATCCTACACGCAGTTTGGTAA 59.993 43.478 0.00 0.00 41.61 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.873165 GCAAAGGCGAACCGAATCA 59.127 52.632 0.00 0.00 42.76 2.57
35 36 1.148157 ATGCGACAGGCTCGAAATCG 61.148 55.000 0.00 0.00 46.14 3.34
68 69 6.493115 CCCAAGAGACATACATACAGAGATCT 59.507 42.308 0.00 0.00 0.00 2.75
70 71 5.011533 GCCCAAGAGACATACATACAGAGAT 59.988 44.000 0.00 0.00 0.00 2.75
95 96 5.118817 CAGTAAGGACTCGCAAACTAGTTTC 59.881 44.000 18.00 11.71 31.73 2.78
206 209 2.213499 CCATTAGACGATGGGCACTTC 58.787 52.381 0.00 0.00 42.36 3.01
228 232 1.948144 GCAAGGAGGCCTTCAGTCTTC 60.948 57.143 15.31 0.00 42.67 2.87
250 254 1.207089 CGAACCTACATGAGAAGGCCA 59.793 52.381 5.01 0.00 36.24 5.36
302 306 3.192001 GTCAGAGCAAATTGGAGATGCAA 59.808 43.478 0.00 0.00 42.45 4.08
421 426 9.193806 ACAATTCTTAACAGGAATAAGATGCAT 57.806 29.630 0.00 0.00 38.72 3.96
423 428 9.860898 AAACAATTCTTAACAGGAATAAGATGC 57.139 29.630 0.00 0.00 38.72 3.91
445 452 9.747898 AGGTAAAATTAGATGTACATCCAAACA 57.252 29.630 28.26 11.32 38.58 2.83
500 507 3.798889 GCCTTTAGTCCCAAACAAGTTGC 60.799 47.826 1.81 0.00 35.74 4.17
509 516 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
534 547 8.935844 CATGCAAAACTAAATCTGACTACTACA 58.064 33.333 0.00 0.00 0.00 2.74
538 551 6.030228 GGCATGCAAAACTAAATCTGACTAC 58.970 40.000 21.36 0.00 0.00 2.73
678 783 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
679 784 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
680 785 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
681 786 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
682 787 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
683 788 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
684 789 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
685 790 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
686 791 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
687 792 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
712 817 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
713 818 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
714 819 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
715 820 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
716 821 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
717 822 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
718 823 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
719 824 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
720 825 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
721 826 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
722 827 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
723 828 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
724 829 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
725 830 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
726 831 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
727 832 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
728 833 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
729 834 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
730 835 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
731 836 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
736 841 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
737 842 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
738 843 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
739 844 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
740 845 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
741 846 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
742 847 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
743 848 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
744 849 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
745 850 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
746 851 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
747 852 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
748 853 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
749 854 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
750 855 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
751 856 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
752 857 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
753 858 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
754 859 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
755 860 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
756 861 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
757 862 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
758 863 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
759 864 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
760 865 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
761 866 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
762 867 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
763 868 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
764 869 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
765 870 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
766 871 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
767 872 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
768 873 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
769 874 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
770 875 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
771 876 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
772 877 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
773 878 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
787 892 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
788 893 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
789 894 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
790 895 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
791 896 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
792 897 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
793 898 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
794 899 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
795 900 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
796 901 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
811 916 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
812 917 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
813 918 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
814 919 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
815 920 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
816 921 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
817 922 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
818 923 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
819 924 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
820 925 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
821 926 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
822 927 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
823 928 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
824 929 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
825 930 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
830 935 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
831 936 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
832 937 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
833 938 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
834 939 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
835 940 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
836 941 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
843 948 3.421728 ATAAGGGGAGCCTTGGCGC 62.422 63.158 6.84 6.84 0.00 6.53
844 949 1.526917 CATAAGGGGAGCCTTGGCG 60.527 63.158 5.95 0.00 0.00 5.69
845 950 0.480252 ATCATAAGGGGAGCCTTGGC 59.520 55.000 2.97 2.97 0.00 4.52
846 951 3.319031 AAATCATAAGGGGAGCCTTGG 57.681 47.619 0.00 0.00 0.00 3.61
847 952 6.983906 AATTAAATCATAAGGGGAGCCTTG 57.016 37.500 0.00 0.00 0.00 3.61
848 953 7.402941 ACAAAATTAAATCATAAGGGGAGCCTT 59.597 33.333 0.00 0.00 0.00 4.35
849 954 6.902974 ACAAAATTAAATCATAAGGGGAGCCT 59.097 34.615 0.00 0.00 0.00 4.58
850 955 7.124573 ACAAAATTAAATCATAAGGGGAGCC 57.875 36.000 0.00 0.00 0.00 4.70
925 1036 8.589335 AACGCGTTCAGATAATTCAATACTAT 57.411 30.769 20.79 0.00 0.00 2.12
946 1097 1.541379 AATTAGGGGTGGTGAAACGC 58.459 50.000 0.00 0.00 38.12 4.84
1570 1723 7.889745 CAGAATGTTCTCTGTACTAATGAACG 58.110 38.462 12.87 0.00 39.61 3.95
1610 1763 2.826674 TCAAGGGGATAGCAAAAGGG 57.173 50.000 0.00 0.00 0.00 3.95
1697 1868 3.754188 ATTCTGAGTTTCGCATCAAGC 57.246 42.857 0.00 0.00 40.87 4.01
1897 2306 7.817478 ACGACAATATCAACATGAACAGAAGTA 59.183 33.333 0.00 0.00 0.00 2.24
2719 3516 1.272781 GGATCTCAGCGAACTTGACG 58.727 55.000 0.00 0.00 0.00 4.35
3038 3835 1.901654 TATACCGCCACCACCACCAC 61.902 60.000 0.00 0.00 0.00 4.16
3068 3871 4.205588 CGCAAATTCGCTAACACGACTATA 59.794 41.667 0.00 0.00 42.78 1.31
3084 3887 5.687285 CAGAAGCTTAACAAGTTCGCAAATT 59.313 36.000 0.00 0.00 0.00 1.82
3107 3910 3.462982 ACACTGCTCGACACAAATAACA 58.537 40.909 0.00 0.00 0.00 2.41
3159 3966 1.822506 TTCACCAACACAACCGAACA 58.177 45.000 0.00 0.00 0.00 3.18
3228 4035 2.686915 GAGGCAGCAGCAGACATAAAAT 59.313 45.455 2.65 0.00 44.61 1.82
3272 4079 5.559427 AAAATCCACCTTGCAAAACAAAC 57.441 34.783 0.00 0.00 37.96 2.93
3300 4107 4.041740 TCAGCATAAGTAGTTAGCACCG 57.958 45.455 11.73 0.00 0.00 4.94
3302 4109 6.969828 AGTTTCAGCATAAGTAGTTAGCAC 57.030 37.500 11.73 4.46 0.00 4.40
3314 4194 4.002982 CAGCACAGGTAAGTTTCAGCATA 58.997 43.478 0.00 0.00 0.00 3.14
3393 4274 2.607771 CCGGGTTGAAAAACAGATGCAG 60.608 50.000 0.00 0.00 32.77 4.41
3402 4283 1.475403 TTGCAGTCCGGGTTGAAAAA 58.525 45.000 0.00 0.00 0.00 1.94
3403 4284 1.475403 TTTGCAGTCCGGGTTGAAAA 58.525 45.000 0.00 4.82 0.00 2.29
3406 4293 1.339631 CCTATTTGCAGTCCGGGTTGA 60.340 52.381 0.00 0.00 0.00 3.18
3418 4305 5.598416 AAGTATGAAAAGCCCCTATTTGC 57.402 39.130 0.00 0.00 0.00 3.68
3420 4307 7.234577 TGAACAAAGTATGAAAAGCCCCTATTT 59.765 33.333 0.00 0.00 0.00 1.40
3425 4369 4.864704 TGAACAAAGTATGAAAAGCCCC 57.135 40.909 0.00 0.00 0.00 5.80
3426 4370 6.761242 ACTTTTGAACAAAGTATGAAAAGCCC 59.239 34.615 0.00 0.00 38.58 5.19
3428 4372 9.516314 AGTACTTTTGAACAAAGTATGAAAAGC 57.484 29.630 9.74 0.00 42.54 3.51
3456 4400 7.007697 CAGGTAAAACTCGAAAAACAGATACG 58.992 38.462 0.00 0.00 0.00 3.06
3457 4401 8.080083 TCAGGTAAAACTCGAAAAACAGATAC 57.920 34.615 0.00 0.00 0.00 2.24
3459 4403 7.255139 CCTTCAGGTAAAACTCGAAAAACAGAT 60.255 37.037 0.00 0.00 0.00 2.90
3461 4405 6.037830 TCCTTCAGGTAAAACTCGAAAAACAG 59.962 38.462 0.00 0.00 36.34 3.16
3463 4407 6.367686 TCCTTCAGGTAAAACTCGAAAAAC 57.632 37.500 0.00 0.00 36.34 2.43
3464 4408 7.576861 ATTCCTTCAGGTAAAACTCGAAAAA 57.423 32.000 0.00 0.00 36.34 1.94
3468 4412 7.001099 ACTTATTCCTTCAGGTAAAACTCGA 57.999 36.000 0.00 0.00 36.34 4.04
3470 4414 7.306213 GCAACTTATTCCTTCAGGTAAAACTC 58.694 38.462 0.00 0.00 36.34 3.01
3471 4415 6.208797 GGCAACTTATTCCTTCAGGTAAAACT 59.791 38.462 0.00 0.00 36.34 2.66
3472 4416 6.015772 TGGCAACTTATTCCTTCAGGTAAAAC 60.016 38.462 0.00 0.00 34.92 2.43
3473 4417 6.071984 TGGCAACTTATTCCTTCAGGTAAAA 58.928 36.000 0.00 0.00 34.92 1.52
3475 4419 5.249780 TGGCAACTTATTCCTTCAGGTAA 57.750 39.130 0.00 0.00 34.92 2.85
3476 4420 4.919774 TGGCAACTTATTCCTTCAGGTA 57.080 40.909 0.00 0.00 34.92 3.08
3477 4421 3.806949 TGGCAACTTATTCCTTCAGGT 57.193 42.857 0.00 0.00 34.92 4.00
3478 4422 4.019174 ACATGGCAACTTATTCCTTCAGG 58.981 43.478 0.00 0.00 37.61 3.86
3481 4425 3.774066 GCACATGGCAACTTATTCCTTC 58.226 45.455 0.00 0.00 43.97 3.46
3482 4426 3.874392 GCACATGGCAACTTATTCCTT 57.126 42.857 0.00 0.00 43.97 3.36
3494 4438 1.237285 ACGGACAAAGAGCACATGGC 61.237 55.000 0.00 0.00 45.30 4.40
3496 4440 1.511850 TGACGGACAAAGAGCACATG 58.488 50.000 0.00 0.00 0.00 3.21
3507 4451 4.941263 CCTTGGATAAATCTTTGACGGACA 59.059 41.667 0.00 0.00 0.00 4.02
3508 4452 4.335594 CCCTTGGATAAATCTTTGACGGAC 59.664 45.833 0.00 0.00 0.00 4.79
3509 4453 4.523083 CCCTTGGATAAATCTTTGACGGA 58.477 43.478 0.00 0.00 0.00 4.69
3510 4454 3.632145 CCCCTTGGATAAATCTTTGACGG 59.368 47.826 0.00 0.00 0.00 4.79
3511 4455 4.523083 TCCCCTTGGATAAATCTTTGACG 58.477 43.478 0.00 0.00 35.03 4.35
3525 4469 3.370840 TGATCTCAACAATCCCCTTGG 57.629 47.619 0.00 0.00 39.30 3.61
3533 4835 2.421952 CCCGGTGGATGATCTCAACAAT 60.422 50.000 0.00 0.00 28.16 2.71
3555 4857 2.496899 AGAGGCCGTGTTCAAATCAT 57.503 45.000 0.00 0.00 0.00 2.45
3556 4858 2.151202 GAAGAGGCCGTGTTCAAATCA 58.849 47.619 0.00 0.00 0.00 2.57
3558 4860 2.568623 AGAAGAGGCCGTGTTCAAAT 57.431 45.000 14.76 0.00 30.53 2.32
3559 4861 2.218603 GAAGAAGAGGCCGTGTTCAAA 58.781 47.619 14.76 0.00 30.53 2.69
3560 4862 1.542547 GGAAGAAGAGGCCGTGTTCAA 60.543 52.381 14.76 0.00 30.53 2.69
3565 4867 1.743252 GCAGGAAGAAGAGGCCGTG 60.743 63.158 0.00 0.00 0.00 4.94
3586 4888 4.363990 AGACGTGTGAGGCCGCTG 62.364 66.667 8.34 0.00 0.00 5.18
3588 4890 4.357947 TGAGACGTGTGAGGCCGC 62.358 66.667 0.00 0.00 0.00 6.53
3589 4891 2.430921 GTGAGACGTGTGAGGCCG 60.431 66.667 0.00 0.00 0.00 6.13
3647 4972 0.835941 CCTGGTCAGCTCTAAGCCAT 59.164 55.000 0.00 0.00 43.77 4.40
3650 4975 0.176910 GTCCCTGGTCAGCTCTAAGC 59.823 60.000 0.00 0.00 42.84 3.09
3653 4978 0.704664 TCTGTCCCTGGTCAGCTCTA 59.295 55.000 5.67 0.00 32.73 2.43
3687 5028 2.982744 GAAAAGCACTCCCAGCGGC 61.983 63.158 0.00 0.00 37.01 6.53
3689 5030 0.239347 CAAGAAAAGCACTCCCAGCG 59.761 55.000 0.00 0.00 37.01 5.18
3690 5031 1.322442 ACAAGAAAAGCACTCCCAGC 58.678 50.000 0.00 0.00 0.00 4.85
3698 5082 1.477700 ACAGCAGCAACAAGAAAAGCA 59.522 42.857 0.00 0.00 0.00 3.91
3731 5115 4.489679 AATTTTTGAAGTCTCGTGCTCC 57.510 40.909 0.00 0.00 0.00 4.70
3860 5327 9.030452 AGTCTGATGTTACTTCATCTTAAGTCT 57.970 33.333 1.63 0.00 43.03 3.24
3861 5328 9.646427 AAGTCTGATGTTACTTCATCTTAAGTC 57.354 33.333 1.63 0.00 43.03 3.01
3867 5334 9.814899 CATCTAAAGTCTGATGTTACTTCATCT 57.185 33.333 1.43 1.95 43.03 2.90
3881 5348 7.106439 ACTCCATCTGTACATCTAAAGTCTG 57.894 40.000 0.00 0.00 0.00 3.51
3889 5356 6.653020 TGCAAAATACTCCATCTGTACATCT 58.347 36.000 0.00 0.00 0.00 2.90
3890 5357 6.925610 TGCAAAATACTCCATCTGTACATC 57.074 37.500 0.00 0.00 0.00 3.06
3892 5359 8.978874 ATAATGCAAAATACTCCATCTGTACA 57.021 30.769 0.00 0.00 0.00 2.90
3893 5360 8.223769 CGATAATGCAAAATACTCCATCTGTAC 58.776 37.037 0.00 0.00 0.00 2.90
3900 5399 6.419710 CGACTACGATAATGCAAAATACTCCA 59.580 38.462 0.00 0.00 42.66 3.86
3918 5417 2.286831 ACATCGTTCATAGCCGACTACG 60.287 50.000 0.00 0.00 35.69 3.51
3936 5435 3.399046 TGGAGGCAACGGCTACAT 58.601 55.556 0.00 0.00 44.28 2.29
3941 5440 2.676471 ACCAATGGAGGCAACGGC 60.676 61.111 6.16 0.00 46.39 5.68
3942 5441 0.609131 AAGACCAATGGAGGCAACGG 60.609 55.000 6.16 0.00 46.39 4.44
3943 5442 0.523072 CAAGACCAATGGAGGCAACG 59.477 55.000 6.16 0.00 46.39 4.10


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

AutoCloner maintained by Alex Coulton.