Multiple sequence alignment - TraesCS1B01G428000

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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 TraesCS1B01G428000 chr1B 100.000 2995 0 0 1 2995 653234423 653237417 0.000000e+00 5531.0
1 TraesCS1B01G428000 chr1B 85.166 391 31 15 2572 2958 652577464 652577097 2.820000e-100 375.0
2 TraesCS1B01G428000 chr1B 89.259 270 19 7 1234 1503 653321729 653321988 2.230000e-86 329.0
3 TraesCS1B01G428000 chr1B 85.337 341 21 12 1235 1573 653264215 653264528 2.880000e-85 326.0
4 TraesCS1B01G428000 chr1B 90.556 180 10 2 2816 2995 652576072 652575900 6.460000e-57 231.0
5 TraesCS1B01G428000 chr1B 79.598 348 43 17 2656 2995 652640318 652639991 1.080000e-54 224.0
6 TraesCS1B01G428000 chr1B 88.360 189 13 4 2809 2995 652634452 652634271 5.030000e-53 219.0
7 TraesCS1B01G428000 chr1B 83.500 200 22 6 2246 2445 683109278 683109466 3.070000e-40 176.0
8 TraesCS1B01G428000 chr1B 80.392 204 17 13 2246 2448 653526607 653526788 1.870000e-27 134.0
9 TraesCS1B01G428000 chr1B 89.474 57 6 0 1994 2050 653264856 653264912 4.140000e-09 73.1
10 TraesCS1B01G428000 chr1B 84.810 79 4 5 1653 1730 653322141 653322212 4.140000e-09 73.1
11 TraesCS1B01G428000 chr1D 89.736 1588 75 43 1219 2785 470522518 470524038 0.000000e+00 1949.0
12 TraesCS1B01G428000 chr1D 87.247 839 37 27 1 804 470521291 470522094 0.000000e+00 893.0
13 TraesCS1B01G428000 chr1D 96.257 187 5 2 2809 2995 470524029 470524213 3.750000e-79 305.0
14 TraesCS1B01G428000 chr1D 92.810 153 11 0 1247 1399 470539981 470540133 3.890000e-54 222.0
15 TraesCS1B01G428000 chr1D 86.047 215 19 6 2 206 460596032 460596245 1.400000e-53 220.0
16 TraesCS1B01G428000 chr1D 79.300 343 45 16 2660 2995 470199872 470199549 1.810000e-52 217.0
17 TraesCS1B01G428000 chr1D 91.045 134 11 1 1441 1573 470530623 470530756 2.370000e-41 180.0
18 TraesCS1B01G428000 chr1D 83.770 191 20 5 1358 1548 460596690 460596869 1.430000e-38 171.0
19 TraesCS1B01G428000 chr1D 79.710 207 33 6 2246 2447 470536366 470536568 1.120000e-29 141.0
20 TraesCS1B01G428000 chr1D 88.889 63 7 0 1988 2050 470531097 470531159 8.900000e-11 78.7
21 TraesCS1B01G428000 chr1A 90.698 860 37 19 1207 2062 564117225 564118045 0.000000e+00 1105.0
22 TraesCS1B01G428000 chr1A 88.285 828 39 23 1 819 564116067 564116845 0.000000e+00 939.0
23 TraesCS1B01G428000 chr1A 84.179 335 30 13 875 1197 564116841 564117164 1.350000e-78 303.0
24 TraesCS1B01G428000 chr1A 82.524 206 28 4 2246 2448 564130659 564130859 1.100000e-39 174.0
25 TraesCS1B01G428000 chr1A 87.255 102 13 0 1754 1855 564142793 564142894 1.890000e-22 117.0
26 TraesCS1B01G428000 chr6D 85.455 275 34 6 924 1194 85688099 85688371 6.320000e-72 281.0
27 TraesCS1B01G428000 chr7B 86.869 198 13 5 1197 1382 608904727 608904923 3.030000e-50 209.0
28 TraesCS1B01G428000 chr7D 83.663 202 16 6 1197 1382 561004745 561004945 1.100000e-39 174.0
29 TraesCS1B01G428000 chr7A 81.313 198 16 10 1197 1382 528294323 528294511 1.120000e-29 141.0
30 TraesCS1B01G428000 chr3B 81.283 187 23 8 1208 1382 672672413 672672599 1.120000e-29 141.0


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 TraesCS1B01G428000 chr1B 653234423 653237417 2994 False 5531.000000 5531 100.000000 1 2995 1 chr1B.!!$F1 2994
1 TraesCS1B01G428000 chr1B 652575900 652577464 1564 True 303.000000 375 87.861000 2572 2995 2 chr1B.!!$R3 423
2 TraesCS1B01G428000 chr1D 470521291 470524213 2922 False 1049.000000 1949 91.080000 1 2995 3 chr1D.!!$F2 2994
3 TraesCS1B01G428000 chr1A 564116067 564118045 1978 False 782.333333 1105 87.720667 1 2062 3 chr1A.!!$F3 2061

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
386 416 0.037697 TACACCACGGTTGCTGCTAG 60.038 55.0 0.0 0.0 0.0 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2483 0.106769 TGTGTTCAAGGCCTTGCTGA 60.107 50.0 36.24 20.41 40.24 4.26 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
159 178 5.754890 GCTTTCTGCAAAGAAAAATTCCTCA 59.245 36.000 2.23 0.00 41.60 3.86
284 306 4.162320 TCATACCCTCAGAGCTGTAAAAGG 59.838 45.833 0.00 0.00 0.00 3.11
285 307 1.003696 ACCCTCAGAGCTGTAAAAGGC 59.996 52.381 0.00 0.00 0.00 4.35
344 374 6.037949 TCATATCCCATCTTATTCCATCCCA 58.962 40.000 0.00 0.00 0.00 4.37
363 393 0.328258 AATTCCCCAGAAGTCCACCG 59.672 55.000 0.00 0.00 34.86 4.94
364 394 0.840722 ATTCCCCAGAAGTCCACCGT 60.841 55.000 0.00 0.00 34.86 4.83
365 395 1.764571 TTCCCCAGAAGTCCACCGTG 61.765 60.000 0.00 0.00 0.00 4.94
366 396 2.358737 CCCAGAAGTCCACCGTGC 60.359 66.667 0.00 0.00 0.00 5.34
367 397 2.743718 CCAGAAGTCCACCGTGCT 59.256 61.111 0.00 0.00 0.00 4.40
368 398 1.541310 CCCAGAAGTCCACCGTGCTA 61.541 60.000 0.00 0.00 0.00 3.49
369 399 0.389948 CCAGAAGTCCACCGTGCTAC 60.390 60.000 0.00 0.00 0.00 3.58
370 400 0.317160 CAGAAGTCCACCGTGCTACA 59.683 55.000 0.00 0.00 0.00 2.74
371 401 0.317479 AGAAGTCCACCGTGCTACAC 59.683 55.000 0.00 0.00 0.00 2.90
372 402 0.669625 GAAGTCCACCGTGCTACACC 60.670 60.000 0.00 0.00 0.00 4.16
373 403 1.404479 AAGTCCACCGTGCTACACCA 61.404 55.000 0.00 0.00 0.00 4.17
374 404 1.666872 GTCCACCGTGCTACACCAC 60.667 63.158 0.00 0.00 0.00 4.16
380 410 2.943653 GTGCTACACCACGGTTGC 59.056 61.111 0.00 0.00 39.47 4.17
386 416 0.037697 TACACCACGGTTGCTGCTAG 60.038 55.000 0.00 0.00 0.00 3.42
522 554 0.662619 TGCGTTCCTGAACTTGCAAG 59.337 50.000 24.84 24.84 39.08 4.01
523 555 0.663153 GCGTTCCTGAACTTGCAAGT 59.337 50.000 26.36 26.36 42.04 3.16
548 581 2.117206 TTGCATTCCCCCGCAAGT 59.883 55.556 0.00 0.00 42.93 3.16
560 593 1.491563 CGCAAGTTTCTTCGGTCGG 59.508 57.895 0.00 0.00 0.00 4.79
561 594 1.219522 CGCAAGTTTCTTCGGTCGGT 61.220 55.000 0.00 0.00 0.00 4.69
562 595 0.511653 GCAAGTTTCTTCGGTCGGTC 59.488 55.000 0.00 0.00 0.00 4.79
563 596 0.782384 CAAGTTTCTTCGGTCGGTCG 59.218 55.000 0.00 0.00 0.00 4.79
564 597 0.386838 AAGTTTCTTCGGTCGGTCGT 59.613 50.000 0.00 0.00 0.00 4.34
571 604 4.470170 CGGTCGGTCGTCGCATCA 62.470 66.667 0.00 0.00 39.05 3.07
613 648 2.508891 GCGTCGATTGGTCTCTGCG 61.509 63.158 0.00 0.00 0.00 5.18
614 649 2.508891 CGTCGATTGGTCTCTGCGC 61.509 63.158 0.00 0.00 0.00 6.09
625 660 0.721154 TCTCTGCGCGCATTGTTTAG 59.279 50.000 36.48 21.11 0.00 1.85
626 661 0.443869 CTCTGCGCGCATTGTTTAGT 59.556 50.000 36.48 0.00 0.00 2.24
627 662 0.871722 TCTGCGCGCATTGTTTAGTT 59.128 45.000 36.48 0.00 0.00 2.24
628 663 1.136085 TCTGCGCGCATTGTTTAGTTC 60.136 47.619 36.48 0.00 0.00 3.01
629 664 0.588737 TGCGCGCATTGTTTAGTTCA 59.411 45.000 33.09 1.22 0.00 3.18
630 665 1.250476 GCGCGCATTGTTTAGTTCAG 58.750 50.000 29.10 0.00 0.00 3.02
631 666 1.399727 GCGCGCATTGTTTAGTTCAGT 60.400 47.619 29.10 0.00 0.00 3.41
633 668 2.157668 CGCGCATTGTTTAGTTCAGTCT 59.842 45.455 8.75 0.00 0.00 3.24
634 669 3.363970 CGCGCATTGTTTAGTTCAGTCTT 60.364 43.478 8.75 0.00 0.00 3.01
745 782 1.076923 GGTGGTAGCGGGAGAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
746 783 1.104577 GGTGGTAGCGGGAGAGAGAG 61.105 65.000 0.00 0.00 0.00 3.20
755 792 1.681780 CGGGAGAGAGAGCAGAGACTT 60.682 57.143 0.00 0.00 0.00 3.01
764 801 2.368221 AGAGCAGAGACTTGAAGCTTGT 59.632 45.455 2.10 0.00 35.36 3.16
779 816 4.298103 AGCTTGTCCTGTTCATTCATCT 57.702 40.909 0.00 0.00 0.00 2.90
780 817 4.660168 AGCTTGTCCTGTTCATTCATCTT 58.340 39.130 0.00 0.00 0.00 2.40
811 848 2.003672 CCATTGCTGGCGTACGTAC 58.996 57.895 17.90 15.90 35.23 3.67
820 857 2.571611 CGTACGTACGCGCGTCTT 60.572 61.111 41.35 25.82 44.55 3.01
821 858 2.817758 CGTACGTACGCGCGTCTTG 61.818 63.158 41.35 30.02 44.55 3.02
822 859 1.793613 GTACGTACGCGCGTCTTGT 60.794 57.895 41.35 33.59 44.55 3.16
823 860 1.082169 TACGTACGCGCGTCTTGTT 60.082 52.632 41.35 21.73 44.55 2.83
824 861 0.660005 TACGTACGCGCGTCTTGTTT 60.660 50.000 41.35 20.27 44.55 2.83
825 862 1.199859 CGTACGCGCGTCTTGTTTT 59.800 52.632 41.35 15.35 0.00 2.43
826 863 0.382151 CGTACGCGCGTCTTGTTTTT 60.382 50.000 41.35 14.50 0.00 1.94
847 884 6.582677 TTTTCTGTTCAAAGGTTCAGTTCA 57.417 33.333 0.00 0.00 0.00 3.18
848 885 5.818136 TTCTGTTCAAAGGTTCAGTTCAG 57.182 39.130 0.00 0.00 0.00 3.02
849 886 4.843728 TCTGTTCAAAGGTTCAGTTCAGT 58.156 39.130 0.00 0.00 0.00 3.41
850 887 5.253330 TCTGTTCAAAGGTTCAGTTCAGTT 58.747 37.500 0.00 0.00 0.00 3.16
851 888 5.123820 TCTGTTCAAAGGTTCAGTTCAGTTG 59.876 40.000 0.00 0.00 0.00 3.16
852 889 4.105486 GTTCAAAGGTTCAGTTCAGTTGC 58.895 43.478 0.00 0.00 0.00 4.17
853 890 3.620488 TCAAAGGTTCAGTTCAGTTGCT 58.380 40.909 0.00 0.00 0.00 3.91
854 891 4.016444 TCAAAGGTTCAGTTCAGTTGCTT 58.984 39.130 0.00 0.00 0.00 3.91
855 892 4.107622 CAAAGGTTCAGTTCAGTTGCTTG 58.892 43.478 0.00 0.00 0.00 4.01
856 893 3.004752 AGGTTCAGTTCAGTTGCTTGT 57.995 42.857 0.00 0.00 0.00 3.16
857 894 3.356290 AGGTTCAGTTCAGTTGCTTGTT 58.644 40.909 0.00 0.00 0.00 2.83
858 895 3.378427 AGGTTCAGTTCAGTTGCTTGTTC 59.622 43.478 0.00 0.00 0.00 3.18
859 896 3.489229 GGTTCAGTTCAGTTGCTTGTTCC 60.489 47.826 0.00 0.00 0.00 3.62
860 897 3.281727 TCAGTTCAGTTGCTTGTTCCT 57.718 42.857 0.00 0.00 0.00 3.36
861 898 3.620488 TCAGTTCAGTTGCTTGTTCCTT 58.380 40.909 0.00 0.00 0.00 3.36
862 899 3.627577 TCAGTTCAGTTGCTTGTTCCTTC 59.372 43.478 0.00 0.00 0.00 3.46
863 900 3.629398 CAGTTCAGTTGCTTGTTCCTTCT 59.371 43.478 0.00 0.00 0.00 2.85
864 901 4.096984 CAGTTCAGTTGCTTGTTCCTTCTT 59.903 41.667 0.00 0.00 0.00 2.52
865 902 4.336713 AGTTCAGTTGCTTGTTCCTTCTTC 59.663 41.667 0.00 0.00 0.00 2.87
866 903 3.214328 TCAGTTGCTTGTTCCTTCTTCC 58.786 45.455 0.00 0.00 0.00 3.46
867 904 2.951642 CAGTTGCTTGTTCCTTCTTCCA 59.048 45.455 0.00 0.00 0.00 3.53
868 905 3.571401 CAGTTGCTTGTTCCTTCTTCCAT 59.429 43.478 0.00 0.00 0.00 3.41
869 906 4.038402 CAGTTGCTTGTTCCTTCTTCCATT 59.962 41.667 0.00 0.00 0.00 3.16
870 907 4.038402 AGTTGCTTGTTCCTTCTTCCATTG 59.962 41.667 0.00 0.00 0.00 2.82
871 908 2.297033 TGCTTGTTCCTTCTTCCATTGC 59.703 45.455 0.00 0.00 0.00 3.56
872 909 2.560105 GCTTGTTCCTTCTTCCATTGCT 59.440 45.455 0.00 0.00 0.00 3.91
873 910 3.613432 GCTTGTTCCTTCTTCCATTGCTG 60.613 47.826 0.00 0.00 0.00 4.41
874 911 2.517959 TGTTCCTTCTTCCATTGCTGG 58.482 47.619 0.00 0.00 44.64 4.85
875 912 1.203287 GTTCCTTCTTCCATTGCTGGC 59.797 52.381 0.00 0.00 42.80 4.85
876 913 0.405198 TCCTTCTTCCATTGCTGGCA 59.595 50.000 0.00 0.00 42.80 4.92
877 914 1.006281 TCCTTCTTCCATTGCTGGCAT 59.994 47.619 0.00 0.00 42.80 4.40
878 915 1.407979 CCTTCTTCCATTGCTGGCATC 59.592 52.381 0.00 0.00 42.80 3.91
883 920 0.881600 TCCATTGCTGGCATCGATCG 60.882 55.000 9.36 9.36 42.80 3.69
889 926 1.202568 TGCTGGCATCGATCGATCTTT 60.203 47.619 27.20 5.27 31.62 2.52
890 927 1.869767 GCTGGCATCGATCGATCTTTT 59.130 47.619 27.20 4.84 31.62 2.27
956 1013 4.040461 TCTTTTCGATCTTCTTGGAGGTGT 59.960 41.667 0.00 0.00 0.00 4.16
960 1017 3.071023 TCGATCTTCTTGGAGGTGTTTGT 59.929 43.478 0.00 0.00 0.00 2.83
964 1021 4.855340 TCTTCTTGGAGGTGTTTGTTCTT 58.145 39.130 0.00 0.00 0.00 2.52
965 1022 4.640201 TCTTCTTGGAGGTGTTTGTTCTTG 59.360 41.667 0.00 0.00 0.00 3.02
966 1023 2.687935 TCTTGGAGGTGTTTGTTCTTGC 59.312 45.455 0.00 0.00 0.00 4.01
968 1025 0.310854 GGAGGTGTTTGTTCTTGCCG 59.689 55.000 0.00 0.00 0.00 5.69
969 1026 1.305201 GAGGTGTTTGTTCTTGCCGA 58.695 50.000 0.00 0.00 0.00 5.54
971 1028 0.310854 GGTGTTTGTTCTTGCCGAGG 59.689 55.000 0.00 0.00 0.00 4.63
973 1030 1.002792 GTGTTTGTTCTTGCCGAGGTC 60.003 52.381 0.00 0.00 0.00 3.85
974 1031 0.591659 GTTTGTTCTTGCCGAGGTCC 59.408 55.000 0.00 0.00 0.00 4.46
976 1033 1.750341 TTGTTCTTGCCGAGGTCCGA 61.750 55.000 0.00 0.00 41.76 4.55
978 1035 1.906824 TTCTTGCCGAGGTCCGAGT 60.907 57.895 0.00 0.00 41.76 4.18
979 1036 2.125912 CTTGCCGAGGTCCGAGTG 60.126 66.667 0.00 0.00 41.76 3.51
980 1037 2.599281 TTGCCGAGGTCCGAGTGA 60.599 61.111 0.00 0.00 41.76 3.41
981 1038 2.549611 CTTGCCGAGGTCCGAGTGAG 62.550 65.000 0.00 0.00 41.76 3.51
982 1039 2.750637 GCCGAGGTCCGAGTGAGA 60.751 66.667 0.00 0.00 41.76 3.27
983 1040 3.053849 GCCGAGGTCCGAGTGAGAC 62.054 68.421 0.00 0.00 41.76 3.36
987 1044 1.535833 GAGGTCCGAGTGAGACTGAA 58.464 55.000 0.00 0.00 34.56 3.02
988 1045 2.096248 GAGGTCCGAGTGAGACTGAAT 58.904 52.381 0.00 0.00 34.56 2.57
989 1046 2.096248 AGGTCCGAGTGAGACTGAATC 58.904 52.381 0.00 0.00 34.56 2.52
991 1048 2.159310 GGTCCGAGTGAGACTGAATCAG 60.159 54.545 8.98 8.98 37.52 2.90
992 1049 1.474478 TCCGAGTGAGACTGAATCAGC 59.526 52.381 10.62 3.43 34.37 4.26
1018 1079 5.634896 CATCAATGCTACTGTTTGGAAGAC 58.365 41.667 0.00 0.00 0.00 3.01
1095 1156 4.352386 GGCGCTTCAGATAGCCTC 57.648 61.111 7.64 0.00 45.67 4.70
1121 1182 4.327680 GGTCTGAACCAAAGCTACAAGAT 58.672 43.478 0.00 0.00 45.68 2.40
1143 1204 2.817258 CGTTCAGCCATTGGAGGTAAAA 59.183 45.455 6.95 0.00 0.00 1.52
1144 1205 3.443681 CGTTCAGCCATTGGAGGTAAAAT 59.556 43.478 6.95 0.00 0.00 1.82
1145 1206 4.675146 CGTTCAGCCATTGGAGGTAAAATG 60.675 45.833 6.95 0.00 34.26 2.32
1147 1208 4.870636 TCAGCCATTGGAGGTAAAATGAT 58.129 39.130 6.95 0.00 36.13 2.45
1148 1209 5.271598 TCAGCCATTGGAGGTAAAATGATT 58.728 37.500 6.95 0.00 36.13 2.57
1151 1212 5.105228 AGCCATTGGAGGTAAAATGATTGTG 60.105 40.000 6.95 0.00 36.13 3.33
1152 1213 5.105392 GCCATTGGAGGTAAAATGATTGTGA 60.105 40.000 6.95 0.00 36.13 3.58
1153 1214 6.574073 GCCATTGGAGGTAAAATGATTGTGAA 60.574 38.462 6.95 0.00 36.13 3.18
1154 1215 7.037438 CCATTGGAGGTAAAATGATTGTGAAG 58.963 38.462 0.00 0.00 36.13 3.02
1155 1216 7.309990 CCATTGGAGGTAAAATGATTGTGAAGT 60.310 37.037 0.00 0.00 36.13 3.01
1156 1217 7.595819 TTGGAGGTAAAATGATTGTGAAGTT 57.404 32.000 0.00 0.00 0.00 2.66
1157 1218 7.214467 TGGAGGTAAAATGATTGTGAAGTTC 57.786 36.000 0.00 0.00 0.00 3.01
1159 1220 7.174946 TGGAGGTAAAATGATTGTGAAGTTCTC 59.825 37.037 4.17 0.83 0.00 2.87
1160 1221 7.362142 GGAGGTAAAATGATTGTGAAGTTCTCC 60.362 40.741 4.17 0.00 0.00 3.71
1163 1224 8.360390 GGTAAAATGATTGTGAAGTTCTCCTTT 58.640 33.333 4.17 0.00 32.03 3.11
1174 1235 2.640332 AGTTCTCCTTTTCTCCCCTGTC 59.360 50.000 0.00 0.00 0.00 3.51
1176 1237 2.260822 TCTCCTTTTCTCCCCTGTCAG 58.739 52.381 0.00 0.00 0.00 3.51
1190 1251 4.223923 CCCCTGTCAGTAAGTTTCAGAGAT 59.776 45.833 0.00 0.00 0.00 2.75
1214 1297 2.105006 TCTGCAAGAATCTGGCTGAC 57.895 50.000 14.16 0.00 42.31 3.51
1216 1299 1.738350 CTGCAAGAATCTGGCTGACTG 59.262 52.381 11.36 0.00 32.17 3.51
1217 1300 0.450983 GCAAGAATCTGGCTGACTGC 59.549 55.000 1.60 0.00 41.94 4.40
1242 1354 4.319177 ACTTACACTTGGATGAACTGCTC 58.681 43.478 0.00 0.00 0.00 4.26
1298 1410 2.037136 CAAGCTCCACGCCTTCCTG 61.037 63.158 0.00 0.00 40.39 3.86
1497 1609 1.757682 GTTCAACAACACCCACCAGA 58.242 50.000 0.00 0.00 32.14 3.86
1567 1679 4.087892 CCTCAGGCCCGACAGGTG 62.088 72.222 0.00 0.00 38.26 4.00
1568 1680 4.087892 CTCAGGCCCGACAGGTGG 62.088 72.222 0.00 0.00 38.26 4.61
1569 1681 4.954118 TCAGGCCCGACAGGTGGT 62.954 66.667 0.00 0.00 38.26 4.16
1570 1682 3.953775 CAGGCCCGACAGGTGGTT 61.954 66.667 0.00 0.00 38.26 3.67
1573 1685 2.436115 GCCCGACAGGTGGTTAGC 60.436 66.667 0.00 0.00 38.26 3.09
1576 1688 0.673644 CCCGACAGGTGGTTAGCTTG 60.674 60.000 0.00 0.00 35.12 4.01
1577 1689 0.320374 CCGACAGGTGGTTAGCTTGA 59.680 55.000 0.00 0.00 30.85 3.02
1578 1690 1.429463 CGACAGGTGGTTAGCTTGAC 58.571 55.000 0.00 0.00 30.85 3.18
1588 1700 2.603560 GGTTAGCTTGACTGACGCATAC 59.396 50.000 0.00 0.00 35.75 2.39
1595 1707 2.526077 TGACTGACGCATACATTCGAC 58.474 47.619 0.00 0.00 0.00 4.20
1598 1710 2.267426 CTGACGCATACATTCGACCAA 58.733 47.619 0.00 0.00 0.00 3.67
1599 1711 2.670905 CTGACGCATACATTCGACCAAA 59.329 45.455 0.00 0.00 0.00 3.28
1600 1712 2.670905 TGACGCATACATTCGACCAAAG 59.329 45.455 0.00 0.00 0.00 2.77
1602 1714 3.071479 ACGCATACATTCGACCAAAGTT 58.929 40.909 0.00 0.00 0.00 2.66
1603 1715 3.124636 ACGCATACATTCGACCAAAGTTC 59.875 43.478 0.00 0.00 0.00 3.01
1604 1716 3.124466 CGCATACATTCGACCAAAGTTCA 59.876 43.478 0.00 0.00 0.00 3.18
1606 1718 4.154195 GCATACATTCGACCAAAGTTCAGT 59.846 41.667 0.00 0.00 0.00 3.41
1607 1719 5.671329 GCATACATTCGACCAAAGTTCAGTC 60.671 44.000 0.00 0.00 0.00 3.51
1608 1720 3.139077 ACATTCGACCAAAGTTCAGTCC 58.861 45.455 0.00 0.00 0.00 3.85
1610 1722 2.526304 TCGACCAAAGTTCAGTCCTG 57.474 50.000 0.00 0.00 0.00 3.86
1611 1723 2.036387 TCGACCAAAGTTCAGTCCTGA 58.964 47.619 0.00 0.00 37.91 3.86
1612 1724 2.035961 TCGACCAAAGTTCAGTCCTGAG 59.964 50.000 0.00 0.00 41.13 3.35
1613 1725 2.224066 CGACCAAAGTTCAGTCCTGAGT 60.224 50.000 0.00 0.00 41.13 3.41
1614 1726 3.394719 GACCAAAGTTCAGTCCTGAGTC 58.605 50.000 0.00 0.00 41.13 3.36
1615 1727 2.104963 ACCAAAGTTCAGTCCTGAGTCC 59.895 50.000 0.00 0.00 41.13 3.85
1616 1728 2.370189 CCAAAGTTCAGTCCTGAGTCCT 59.630 50.000 0.00 0.00 41.13 3.85
1617 1729 3.397482 CAAAGTTCAGTCCTGAGTCCTG 58.603 50.000 0.00 0.00 41.13 3.86
1618 1730 2.685106 AGTTCAGTCCTGAGTCCTGA 57.315 50.000 0.00 0.00 41.13 3.86
1619 1731 2.243810 AGTTCAGTCCTGAGTCCTGAC 58.756 52.381 0.00 1.83 41.13 3.51
1620 1732 2.158385 AGTTCAGTCCTGAGTCCTGACT 60.158 50.000 0.00 0.00 45.84 3.41
1633 1745 3.316308 AGTCCTGACTGAAATTTGTGTGC 59.684 43.478 0.00 0.00 40.75 4.57
1635 1747 3.565482 TCCTGACTGAAATTTGTGTGCTC 59.435 43.478 0.00 0.00 0.00 4.26
1638 1750 2.887152 GACTGAAATTTGTGTGCTCCCT 59.113 45.455 0.00 0.00 0.00 4.20
1648 1760 0.325933 TGTGCTCCCTGACTGAATGG 59.674 55.000 0.00 0.00 0.00 3.16
1665 1777 4.761739 TGAATGGAGGTTTGTGATGTCTTC 59.238 41.667 0.00 0.00 0.00 2.87
1945 2061 3.500222 GGAGACGTCCGAGGAGTC 58.500 66.667 13.01 0.61 31.37 3.36
1946 2062 1.078285 GGAGACGTCCGAGGAGTCT 60.078 63.158 13.01 17.80 46.61 3.24
2027 2145 2.048603 GGAGCTCGCTTGGGCAAAT 61.049 57.895 7.83 0.00 38.60 2.32
2036 2154 0.393820 CTTGGGCAAATGCAACACCT 59.606 50.000 7.80 0.00 44.36 4.00
2064 2183 1.955778 CAGTTCATGTGTGCTTGGGAA 59.044 47.619 0.00 0.00 0.00 3.97
2067 2186 1.548081 TCATGTGTGCTTGGGAATGG 58.452 50.000 0.00 0.00 0.00 3.16
2068 2187 0.533491 CATGTGTGCTTGGGAATGGG 59.467 55.000 0.00 0.00 0.00 4.00
2069 2188 0.409092 ATGTGTGCTTGGGAATGGGA 59.591 50.000 0.00 0.00 0.00 4.37
2070 2189 0.409092 TGTGTGCTTGGGAATGGGAT 59.591 50.000 0.00 0.00 0.00 3.85
2071 2190 1.203162 TGTGTGCTTGGGAATGGGATT 60.203 47.619 0.00 0.00 0.00 3.01
2072 2191 1.205417 GTGTGCTTGGGAATGGGATTG 59.795 52.381 0.00 0.00 0.00 2.67
2073 2192 1.203162 TGTGCTTGGGAATGGGATTGT 60.203 47.619 0.00 0.00 0.00 2.71
2086 2205 4.015872 TGGGATTGTGTCTTGGTAACTC 57.984 45.455 0.00 0.00 37.61 3.01
2093 2212 2.991866 GTGTCTTGGTAACTCGTTAGCC 59.008 50.000 14.29 8.34 41.42 3.93
2132 2252 6.935741 ACAGCTTACAGTGAGAGTAGATAG 57.064 41.667 0.00 0.00 0.00 2.08
2135 2255 7.612244 ACAGCTTACAGTGAGAGTAGATAGAAA 59.388 37.037 0.00 0.00 0.00 2.52
2141 2261 7.379750 ACAGTGAGAGTAGATAGAAAACAACC 58.620 38.462 0.00 0.00 0.00 3.77
2149 2269 4.576879 AGATAGAAAACAACCCTCGGTTC 58.423 43.478 0.00 0.00 43.05 3.62
2184 2304 1.338973 CCGGGGATTGCTTGATCAATG 59.661 52.381 8.96 4.68 36.85 2.82
2203 2327 6.830736 TCAATGAACATGAGATTTACACACG 58.169 36.000 0.00 0.00 0.00 4.49
2213 2337 6.880484 TGAGATTTACACACGGTACCAATAT 58.120 36.000 13.54 0.00 0.00 1.28
2235 2359 4.013267 AGTGAGACATTCCAGGAACAAG 57.987 45.455 3.18 0.03 0.00 3.16
2250 2374 5.636965 CAGGAACAAGAGTCACAGTATCAAG 59.363 44.000 0.00 0.00 0.00 3.02
2312 2436 4.394712 CGCCGACTTCCCCTGCTT 62.395 66.667 0.00 0.00 0.00 3.91
2315 2439 2.269241 CGACTTCCCCTGCTTCCC 59.731 66.667 0.00 0.00 0.00 3.97
2316 2440 2.677848 GACTTCCCCTGCTTCCCC 59.322 66.667 0.00 0.00 0.00 4.81
2317 2441 1.925972 GACTTCCCCTGCTTCCCCT 60.926 63.158 0.00 0.00 0.00 4.79
2318 2442 1.466186 ACTTCCCCTGCTTCCCCTT 60.466 57.895 0.00 0.00 0.00 3.95
2319 2443 1.304617 CTTCCCCTGCTTCCCCTTC 59.695 63.158 0.00 0.00 0.00 3.46
2320 2444 2.216782 CTTCCCCTGCTTCCCCTTCC 62.217 65.000 0.00 0.00 0.00 3.46
2321 2445 2.941025 CCCCTGCTTCCCCTTCCA 60.941 66.667 0.00 0.00 0.00 3.53
2322 2446 2.356667 CCCTGCTTCCCCTTCCAC 59.643 66.667 0.00 0.00 0.00 4.02
2323 2447 2.356667 CCTGCTTCCCCTTCCACC 59.643 66.667 0.00 0.00 0.00 4.61
2324 2448 2.234296 CCTGCTTCCCCTTCCACCT 61.234 63.158 0.00 0.00 0.00 4.00
2325 2449 1.301293 CTGCTTCCCCTTCCACCTC 59.699 63.158 0.00 0.00 0.00 3.85
2359 2483 2.485426 TCGAGTCGGTGTAGACGAAATT 59.515 45.455 13.54 0.00 45.26 1.82
2360 2484 2.844804 CGAGTCGGTGTAGACGAAATTC 59.155 50.000 4.10 0.00 45.26 2.17
2369 2493 1.168714 AGACGAAATTCAGCAAGGCC 58.831 50.000 0.00 0.00 0.00 5.19
2385 2509 1.154225 GCCTTGAACACATTCGGCG 60.154 57.895 0.00 0.00 37.69 6.46
2410 2534 5.363101 CATGTCTTGTATCTGTATGGCACT 58.637 41.667 0.00 0.00 0.00 4.40
2485 2609 2.309613 TGGCAACTTGAGCATGAAACT 58.690 42.857 0.00 0.00 37.61 2.66
2496 2620 3.067106 AGCATGAAACTACCTGACGTTG 58.933 45.455 0.00 0.00 0.00 4.10
2500 2624 4.659111 TGAAACTACCTGACGTTGAAGA 57.341 40.909 0.00 0.00 0.00 2.87
2501 2625 5.013568 TGAAACTACCTGACGTTGAAGAA 57.986 39.130 0.00 0.00 0.00 2.52
2502 2626 5.607477 TGAAACTACCTGACGTTGAAGAAT 58.393 37.500 0.00 0.00 0.00 2.40
2503 2627 5.465390 TGAAACTACCTGACGTTGAAGAATG 59.535 40.000 0.00 0.00 0.00 2.67
2504 2628 4.866508 ACTACCTGACGTTGAAGAATGA 57.133 40.909 0.00 0.00 0.00 2.57
2505 2629 5.209818 ACTACCTGACGTTGAAGAATGAA 57.790 39.130 0.00 0.00 0.00 2.57
2506 2630 5.230942 ACTACCTGACGTTGAAGAATGAAG 58.769 41.667 0.00 0.00 0.00 3.02
2507 2631 4.336889 ACCTGACGTTGAAGAATGAAGA 57.663 40.909 0.00 0.00 0.00 2.87
2508 2632 4.899502 ACCTGACGTTGAAGAATGAAGAT 58.100 39.130 0.00 0.00 0.00 2.40
2509 2633 4.692625 ACCTGACGTTGAAGAATGAAGATG 59.307 41.667 0.00 0.00 0.00 2.90
2510 2634 4.931601 CCTGACGTTGAAGAATGAAGATGA 59.068 41.667 0.00 0.00 0.00 2.92
2513 2637 4.318332 ACGTTGAAGAATGAAGATGAGCA 58.682 39.130 0.00 0.00 0.00 4.26
2517 2641 6.091305 CGTTGAAGAATGAAGATGAGCAACTA 59.909 38.462 0.00 0.00 33.07 2.24
2519 2643 7.369803 TGAAGAATGAAGATGAGCAACTAAC 57.630 36.000 0.00 0.00 0.00 2.34
2534 2658 4.184629 CAACTAACTTGCTAGCTACAGGG 58.815 47.826 17.23 5.13 0.00 4.45
2542 2666 3.371034 TGCTAGCTACAGGGTGACAATA 58.629 45.455 17.23 0.00 0.00 1.90
2543 2667 3.772572 TGCTAGCTACAGGGTGACAATAA 59.227 43.478 17.23 0.00 0.00 1.40
2562 2686 6.486993 ACAATAAAGACCAAGAAAGAGACCAC 59.513 38.462 0.00 0.00 0.00 4.16
2570 2694 1.004044 AGAAAGAGACCACCATGCCAG 59.996 52.381 0.00 0.00 0.00 4.85
2588 2723 2.610433 CAGAGATAAGCAGCAACACGA 58.390 47.619 0.00 0.00 0.00 4.35
2597 2732 5.376854 AAGCAGCAACACGATTTTAAGAT 57.623 34.783 0.00 0.00 0.00 2.40
2598 2733 4.974591 AGCAGCAACACGATTTTAAGATC 58.025 39.130 0.00 0.00 0.00 2.75
2599 2734 4.455533 AGCAGCAACACGATTTTAAGATCA 59.544 37.500 6.78 0.00 0.00 2.92
2600 2735 4.554973 GCAGCAACACGATTTTAAGATCAC 59.445 41.667 6.78 0.00 0.00 3.06
2629 2768 1.271054 CCACAGTAGCAGCAAACCTCT 60.271 52.381 0.00 0.00 0.00 3.69
2764 2903 3.830192 GCATTCCCGGCTTGCAGG 61.830 66.667 14.38 4.81 36.40 4.85
2847 4148 3.679389 CCATAGCATGGTCAGATAACCC 58.321 50.000 0.00 0.00 45.54 4.11
2848 4149 3.329386 CATAGCATGGTCAGATAACCCG 58.671 50.000 0.00 0.00 38.65 5.28
2879 4180 0.882927 TTGCATAGCGATAACGGGCC 60.883 55.000 0.00 0.00 40.15 5.80
2964 4265 1.508088 GCACCGCTTCCAGGAAATG 59.492 57.895 2.72 1.08 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.103042 AAGATCAGCGCAACTCGGC 61.103 57.895 11.47 0.00 38.94 5.54
344 374 0.328258 CGGTGGACTTCTGGGGAATT 59.672 55.000 0.00 0.00 0.00 2.17
363 393 1.597027 AGCAACCGTGGTGTAGCAC 60.597 57.895 12.10 4.22 33.11 4.40
364 394 1.596752 CAGCAACCGTGGTGTAGCA 60.597 57.895 12.10 0.00 46.13 3.49
365 395 3.253955 CAGCAACCGTGGTGTAGC 58.746 61.111 0.00 0.00 46.13 3.58
370 400 2.347490 CCTAGCAGCAACCGTGGT 59.653 61.111 0.00 0.00 35.28 4.16
371 401 3.127533 GCCTAGCAGCAACCGTGG 61.128 66.667 0.00 0.00 0.00 4.94
372 402 3.490759 CGCCTAGCAGCAACCGTG 61.491 66.667 0.00 0.00 0.00 4.94
373 403 4.760047 CCGCCTAGCAGCAACCGT 62.760 66.667 0.00 0.00 0.00 4.83
376 406 3.055719 TTGCCGCCTAGCAGCAAC 61.056 61.111 6.13 0.00 45.24 4.17
378 408 2.282110 TTTTGCCGCCTAGCAGCA 60.282 55.556 0.00 0.00 45.13 4.41
379 409 2.486966 CTTTTGCCGCCTAGCAGC 59.513 61.111 0.00 0.00 45.13 5.25
380 410 2.486966 GCTTTTGCCGCCTAGCAG 59.513 61.111 4.21 0.00 45.13 4.24
522 554 2.027385 GGGGGAATGCAAGAATCTGAC 58.973 52.381 0.00 0.00 0.00 3.51
523 555 1.408683 CGGGGGAATGCAAGAATCTGA 60.409 52.381 0.00 0.00 0.00 3.27
548 581 1.081906 CGACGACCGACCGAAGAAA 60.082 57.895 3.56 0.00 41.76 2.52
599 634 3.918220 GCGCGCAGAGACCAATCG 61.918 66.667 29.10 0.00 0.00 3.34
613 648 3.813529 AGACTGAACTAAACAATGCGC 57.186 42.857 0.00 0.00 0.00 6.09
614 649 4.024048 ACCAAGACTGAACTAAACAATGCG 60.024 41.667 0.00 0.00 0.00 4.73
625 660 7.089770 AGAGAAAAAGAAACCAAGACTGAAC 57.910 36.000 0.00 0.00 0.00 3.18
626 661 7.176690 ACAAGAGAAAAAGAAACCAAGACTGAA 59.823 33.333 0.00 0.00 0.00 3.02
627 662 6.659242 ACAAGAGAAAAAGAAACCAAGACTGA 59.341 34.615 0.00 0.00 0.00 3.41
628 663 6.856895 ACAAGAGAAAAAGAAACCAAGACTG 58.143 36.000 0.00 0.00 0.00 3.51
629 664 7.176690 TGAACAAGAGAAAAAGAAACCAAGACT 59.823 33.333 0.00 0.00 0.00 3.24
630 665 7.312899 TGAACAAGAGAAAAAGAAACCAAGAC 58.687 34.615 0.00 0.00 0.00 3.01
631 666 7.461182 TGAACAAGAGAAAAAGAAACCAAGA 57.539 32.000 0.00 0.00 0.00 3.02
633 668 8.934825 CATTTGAACAAGAGAAAAAGAAACCAA 58.065 29.630 0.00 0.00 0.00 3.67
634 669 7.064490 GCATTTGAACAAGAGAAAAAGAAACCA 59.936 33.333 0.00 0.00 0.00 3.67
745 782 2.549778 GGACAAGCTTCAAGTCTCTGCT 60.550 50.000 13.34 0.00 35.30 4.24
746 783 1.803555 GGACAAGCTTCAAGTCTCTGC 59.196 52.381 13.34 0.00 32.98 4.26
755 792 3.819368 TGAATGAACAGGACAAGCTTCA 58.181 40.909 0.00 0.00 0.00 3.02
764 801 5.486775 AGGAGAAGAAGATGAATGAACAGGA 59.513 40.000 0.00 0.00 0.00 3.86
779 816 2.040813 AGCAATGGCAGAAGGAGAAGAA 59.959 45.455 0.00 0.00 44.61 2.52
780 817 1.632409 AGCAATGGCAGAAGGAGAAGA 59.368 47.619 0.00 0.00 44.61 2.87
823 860 6.987386 TGAACTGAACCTTTGAACAGAAAAA 58.013 32.000 0.00 0.00 34.88 1.94
824 861 6.208599 ACTGAACTGAACCTTTGAACAGAAAA 59.791 34.615 0.00 0.00 34.88 2.29
825 862 5.710099 ACTGAACTGAACCTTTGAACAGAAA 59.290 36.000 0.00 0.00 34.88 2.52
826 863 5.253330 ACTGAACTGAACCTTTGAACAGAA 58.747 37.500 0.00 0.00 34.88 3.02
827 864 4.843728 ACTGAACTGAACCTTTGAACAGA 58.156 39.130 0.00 0.00 34.88 3.41
828 865 5.335127 CAACTGAACTGAACCTTTGAACAG 58.665 41.667 0.00 0.00 36.58 3.16
829 866 4.380444 GCAACTGAACTGAACCTTTGAACA 60.380 41.667 0.00 0.00 0.00 3.18
830 867 4.105486 GCAACTGAACTGAACCTTTGAAC 58.895 43.478 0.00 0.00 0.00 3.18
831 868 4.016444 AGCAACTGAACTGAACCTTTGAA 58.984 39.130 0.00 0.00 0.00 2.69
832 869 3.620488 AGCAACTGAACTGAACCTTTGA 58.380 40.909 0.00 0.00 0.00 2.69
833 870 4.107622 CAAGCAACTGAACTGAACCTTTG 58.892 43.478 0.00 0.00 0.00 2.77
834 871 3.763897 ACAAGCAACTGAACTGAACCTTT 59.236 39.130 0.00 0.00 0.00 3.11
835 872 3.356290 ACAAGCAACTGAACTGAACCTT 58.644 40.909 0.00 0.00 0.00 3.50
836 873 3.004752 ACAAGCAACTGAACTGAACCT 57.995 42.857 0.00 0.00 0.00 3.50
837 874 3.489229 GGAACAAGCAACTGAACTGAACC 60.489 47.826 0.00 0.00 0.00 3.62
838 875 3.378427 AGGAACAAGCAACTGAACTGAAC 59.622 43.478 0.00 0.00 0.00 3.18
839 876 3.620488 AGGAACAAGCAACTGAACTGAA 58.380 40.909 0.00 0.00 0.00 3.02
840 877 3.281727 AGGAACAAGCAACTGAACTGA 57.718 42.857 0.00 0.00 0.00 3.41
841 878 3.629398 AGAAGGAACAAGCAACTGAACTG 59.371 43.478 0.00 0.00 0.00 3.16
842 879 3.891049 AGAAGGAACAAGCAACTGAACT 58.109 40.909 0.00 0.00 0.00 3.01
843 880 4.498177 GGAAGAAGGAACAAGCAACTGAAC 60.498 45.833 0.00 0.00 0.00 3.18
844 881 3.632145 GGAAGAAGGAACAAGCAACTGAA 59.368 43.478 0.00 0.00 0.00 3.02
845 882 3.214328 GGAAGAAGGAACAAGCAACTGA 58.786 45.455 0.00 0.00 0.00 3.41
846 883 2.951642 TGGAAGAAGGAACAAGCAACTG 59.048 45.455 0.00 0.00 0.00 3.16
847 884 3.297134 TGGAAGAAGGAACAAGCAACT 57.703 42.857 0.00 0.00 0.00 3.16
848 885 4.301628 CAATGGAAGAAGGAACAAGCAAC 58.698 43.478 0.00 0.00 0.00 4.17
849 886 3.243839 GCAATGGAAGAAGGAACAAGCAA 60.244 43.478 0.00 0.00 0.00 3.91
850 887 2.297033 GCAATGGAAGAAGGAACAAGCA 59.703 45.455 0.00 0.00 0.00 3.91
851 888 2.560105 AGCAATGGAAGAAGGAACAAGC 59.440 45.455 0.00 0.00 0.00 4.01
852 889 3.057033 CCAGCAATGGAAGAAGGAACAAG 60.057 47.826 0.00 0.00 0.00 3.16
853 890 2.892852 CCAGCAATGGAAGAAGGAACAA 59.107 45.455 0.00 0.00 0.00 2.83
854 891 2.517959 CCAGCAATGGAAGAAGGAACA 58.482 47.619 0.00 0.00 0.00 3.18
855 892 1.203287 GCCAGCAATGGAAGAAGGAAC 59.797 52.381 0.00 0.00 0.00 3.62
856 893 1.203038 TGCCAGCAATGGAAGAAGGAA 60.203 47.619 0.00 0.00 0.00 3.36
857 894 0.405198 TGCCAGCAATGGAAGAAGGA 59.595 50.000 0.00 0.00 0.00 3.36
858 895 1.407979 GATGCCAGCAATGGAAGAAGG 59.592 52.381 0.00 0.00 0.00 3.46
859 896 1.065102 CGATGCCAGCAATGGAAGAAG 59.935 52.381 0.00 0.00 0.00 2.85
860 897 1.097232 CGATGCCAGCAATGGAAGAA 58.903 50.000 0.00 0.00 0.00 2.52
861 898 0.252761 TCGATGCCAGCAATGGAAGA 59.747 50.000 0.00 0.00 0.00 2.87
862 899 1.266175 GATCGATGCCAGCAATGGAAG 59.734 52.381 0.54 0.00 0.00 3.46
863 900 1.311859 GATCGATGCCAGCAATGGAA 58.688 50.000 0.54 0.00 0.00 3.53
864 901 0.881600 CGATCGATGCCAGCAATGGA 60.882 55.000 10.26 0.00 0.00 3.41
865 902 0.881600 TCGATCGATGCCAGCAATGG 60.882 55.000 15.15 0.00 0.00 3.16
866 903 1.128136 GATCGATCGATGCCAGCAATG 59.872 52.381 33.86 0.00 34.60 2.82
867 904 1.001746 AGATCGATCGATGCCAGCAAT 59.998 47.619 33.86 8.66 34.60 3.56
868 905 0.390492 AGATCGATCGATGCCAGCAA 59.610 50.000 33.86 2.17 34.60 3.91
869 906 0.390492 AAGATCGATCGATGCCAGCA 59.610 50.000 33.86 2.99 34.60 4.41
870 907 1.506493 AAAGATCGATCGATGCCAGC 58.494 50.000 33.86 18.97 34.60 4.85
889 926 3.801594 GCAGCAAAAGATGAAACCGAAAA 59.198 39.130 0.00 0.00 0.00 2.29
890 927 3.068024 AGCAGCAAAAGATGAAACCGAAA 59.932 39.130 0.00 0.00 0.00 3.46
899 936 2.818432 ACCTCTTGAGCAGCAAAAGATG 59.182 45.455 9.55 9.50 35.74 2.90
956 1013 0.882927 CGGACCTCGGCAAGAACAAA 60.883 55.000 0.00 0.00 34.75 2.83
960 1017 1.906824 ACTCGGACCTCGGCAAGAA 60.907 57.895 0.00 0.00 39.77 2.52
964 1021 3.062466 CTCACTCGGACCTCGGCA 61.062 66.667 0.00 0.00 39.77 5.69
965 1022 2.750637 TCTCACTCGGACCTCGGC 60.751 66.667 0.00 0.00 39.77 5.54
966 1023 1.377463 AGTCTCACTCGGACCTCGG 60.377 63.158 0.00 0.00 39.77 4.63
968 1025 1.535833 TTCAGTCTCACTCGGACCTC 58.464 55.000 0.00 0.00 34.56 3.85
969 1026 2.096248 GATTCAGTCTCACTCGGACCT 58.904 52.381 0.00 0.00 34.56 3.85
971 1028 2.733858 GCTGATTCAGTCTCACTCGGAC 60.734 54.545 14.90 0.00 33.43 4.79
973 1030 1.203287 TGCTGATTCAGTCTCACTCGG 59.797 52.381 14.90 0.00 33.43 4.63
974 1031 2.528125 CTGCTGATTCAGTCTCACTCG 58.472 52.381 14.90 0.00 33.43 4.18
976 1033 1.622312 TGCTGCTGATTCAGTCTCACT 59.378 47.619 14.90 0.00 36.49 3.41
978 1035 2.235402 TGATGCTGCTGATTCAGTCTCA 59.765 45.455 14.90 10.07 36.49 3.27
979 1036 2.902523 TGATGCTGCTGATTCAGTCTC 58.097 47.619 14.90 5.19 36.49 3.36
980 1037 3.345508 TTGATGCTGCTGATTCAGTCT 57.654 42.857 14.90 0.00 36.49 3.24
981 1038 3.953766 CATTGATGCTGCTGATTCAGTC 58.046 45.455 14.90 8.08 36.49 3.51
1044 1105 4.859304 TGCAAGCAAGAGAATCACAAAT 57.141 36.364 0.00 0.00 37.82 2.32
1095 1156 0.035458 AGCTTTGGTTCAGACCCTCG 59.965 55.000 0.00 0.00 45.92 4.63
1121 1182 1.271856 TACCTCCAATGGCTGAACGA 58.728 50.000 0.00 0.00 0.00 3.85
1143 1204 6.432472 GGAGAAAAGGAGAACTTCACAATCAT 59.568 38.462 0.00 0.00 38.85 2.45
1144 1205 5.765182 GGAGAAAAGGAGAACTTCACAATCA 59.235 40.000 0.00 0.00 38.85 2.57
1145 1206 5.182190 GGGAGAAAAGGAGAACTTCACAATC 59.818 44.000 0.00 0.00 38.85 2.67
1147 1208 4.461198 GGGAGAAAAGGAGAACTTCACAA 58.539 43.478 0.00 0.00 38.85 3.33
1148 1209 3.181443 GGGGAGAAAAGGAGAACTTCACA 60.181 47.826 0.00 0.00 38.85 3.58
1151 1212 3.073209 ACAGGGGAGAAAAGGAGAACTTC 59.927 47.826 0.00 0.00 38.85 3.01
1152 1213 3.056832 ACAGGGGAGAAAAGGAGAACTT 58.943 45.455 0.00 0.00 42.52 2.66
1153 1214 2.640332 GACAGGGGAGAAAAGGAGAACT 59.360 50.000 0.00 0.00 0.00 3.01
1154 1215 2.372172 TGACAGGGGAGAAAAGGAGAAC 59.628 50.000 0.00 0.00 0.00 3.01
1155 1216 2.639839 CTGACAGGGGAGAAAAGGAGAA 59.360 50.000 0.00 0.00 0.00 2.87
1156 1217 2.260822 CTGACAGGGGAGAAAAGGAGA 58.739 52.381 0.00 0.00 0.00 3.71
1157 1218 1.981495 ACTGACAGGGGAGAAAAGGAG 59.019 52.381 7.51 0.00 0.00 3.69
1159 1220 3.328050 ACTTACTGACAGGGGAGAAAAGG 59.672 47.826 7.51 0.00 0.00 3.11
1160 1221 4.625607 ACTTACTGACAGGGGAGAAAAG 57.374 45.455 7.51 1.91 0.00 2.27
1163 1224 3.971305 TGAAACTTACTGACAGGGGAGAA 59.029 43.478 7.51 0.00 0.00 2.87
1174 1235 7.172190 TGCAGAAAGAATCTCTGAAACTTACTG 59.828 37.037 3.99 0.00 42.51 2.74
1176 1237 7.426929 TGCAGAAAGAATCTCTGAAACTTAC 57.573 36.000 3.99 0.00 42.51 2.34
1209 1292 3.548818 CCAAGTGTAAGTTTGCAGTCAGC 60.549 47.826 0.00 0.00 45.96 4.26
1210 1293 3.876914 TCCAAGTGTAAGTTTGCAGTCAG 59.123 43.478 0.00 0.00 0.00 3.51
1213 1296 4.460263 TCATCCAAGTGTAAGTTTGCAGT 58.540 39.130 0.00 0.00 0.00 4.40
1214 1297 5.009010 AGTTCATCCAAGTGTAAGTTTGCAG 59.991 40.000 0.00 0.00 0.00 4.41
1216 1299 5.215160 CAGTTCATCCAAGTGTAAGTTTGC 58.785 41.667 0.00 0.00 31.46 3.68
1217 1300 5.009010 AGCAGTTCATCCAAGTGTAAGTTTG 59.991 40.000 0.00 0.00 37.70 2.93
1298 1410 4.477975 CCGACGGACGACCAGAGC 62.478 72.222 8.64 0.00 45.77 4.09
1567 1679 1.726853 ATGCGTCAGTCAAGCTAACC 58.273 50.000 0.00 0.00 0.00 2.85
1568 1680 3.250744 TGTATGCGTCAGTCAAGCTAAC 58.749 45.455 0.00 0.00 0.00 2.34
1569 1681 3.586100 TGTATGCGTCAGTCAAGCTAA 57.414 42.857 0.00 0.00 0.00 3.09
1570 1682 3.801114 ATGTATGCGTCAGTCAAGCTA 57.199 42.857 0.00 0.00 0.00 3.32
1573 1685 3.000674 GTCGAATGTATGCGTCAGTCAAG 60.001 47.826 0.00 0.00 31.51 3.02
1576 1688 1.852895 GGTCGAATGTATGCGTCAGTC 59.147 52.381 0.00 0.00 0.00 3.51
1577 1689 1.203758 TGGTCGAATGTATGCGTCAGT 59.796 47.619 0.00 0.00 0.00 3.41
1578 1690 1.921243 TGGTCGAATGTATGCGTCAG 58.079 50.000 0.00 0.00 0.00 3.51
1588 1700 3.187227 CAGGACTGAACTTTGGTCGAATG 59.813 47.826 0.00 0.00 0.00 2.67
1595 1707 2.370189 AGGACTCAGGACTGAACTTTGG 59.630 50.000 3.35 0.00 39.39 3.28
1598 1710 2.630580 GTCAGGACTCAGGACTGAACTT 59.369 50.000 3.35 0.00 42.30 2.66
1599 1711 2.158385 AGTCAGGACTCAGGACTGAACT 60.158 50.000 3.35 0.40 42.30 3.01
1600 1712 2.243810 AGTCAGGACTCAGGACTGAAC 58.756 52.381 3.35 0.00 42.30 3.18
1604 1716 2.685106 TTCAGTCAGGACTCAGGACT 57.315 50.000 0.00 0.00 42.32 3.85
1606 1718 4.103153 ACAAATTTCAGTCAGGACTCAGGA 59.897 41.667 0.00 0.00 40.20 3.86
1607 1719 4.214971 CACAAATTTCAGTCAGGACTCAGG 59.785 45.833 0.00 0.00 40.20 3.86
1608 1720 4.818546 ACACAAATTTCAGTCAGGACTCAG 59.181 41.667 0.00 0.00 40.20 3.35
1610 1722 4.555511 GCACACAAATTTCAGTCAGGACTC 60.556 45.833 0.00 0.00 40.20 3.36
1611 1723 3.316308 GCACACAAATTTCAGTCAGGACT 59.684 43.478 0.00 0.00 43.61 3.85
1612 1724 3.316308 AGCACACAAATTTCAGTCAGGAC 59.684 43.478 0.00 0.00 0.00 3.85
1613 1725 3.554934 AGCACACAAATTTCAGTCAGGA 58.445 40.909 0.00 0.00 0.00 3.86
1614 1726 3.304928 GGAGCACACAAATTTCAGTCAGG 60.305 47.826 0.00 0.00 0.00 3.86
1615 1727 3.304928 GGGAGCACACAAATTTCAGTCAG 60.305 47.826 0.00 0.00 0.00 3.51
1616 1728 2.622942 GGGAGCACACAAATTTCAGTCA 59.377 45.455 0.00 0.00 0.00 3.41
1617 1729 2.887152 AGGGAGCACACAAATTTCAGTC 59.113 45.455 0.00 0.00 0.00 3.51
1618 1730 2.624838 CAGGGAGCACACAAATTTCAGT 59.375 45.455 0.00 0.00 0.00 3.41
1619 1731 2.886523 TCAGGGAGCACACAAATTTCAG 59.113 45.455 0.00 0.00 0.00 3.02
1620 1732 2.622942 GTCAGGGAGCACACAAATTTCA 59.377 45.455 0.00 0.00 0.00 2.69
1633 1745 1.577736 ACCTCCATTCAGTCAGGGAG 58.422 55.000 0.00 0.00 45.20 4.30
1635 1747 2.224867 ACAAACCTCCATTCAGTCAGGG 60.225 50.000 0.00 0.00 0.00 4.45
1638 1750 3.855255 TCACAAACCTCCATTCAGTCA 57.145 42.857 0.00 0.00 0.00 3.41
1648 1760 6.377327 TGAAAAGAAGACATCACAAACCTC 57.623 37.500 0.00 0.00 0.00 3.85
1665 1777 1.866853 GCCTTCACGCCCCTGAAAAG 61.867 60.000 0.00 0.00 29.66 2.27
1937 2053 1.427592 GGTACGACGGAGACTCCTCG 61.428 65.000 27.53 27.53 40.49 4.63
2027 2145 4.039852 TGAACTGTACAGATAGGTGTTGCA 59.960 41.667 29.30 6.16 31.46 4.08
2036 2154 5.405935 AGCACACATGAACTGTACAGATA 57.594 39.130 29.30 14.32 35.91 1.98
2064 2183 4.589908 GAGTTACCAAGACACAATCCCAT 58.410 43.478 0.00 0.00 0.00 4.00
2067 2186 3.660865 ACGAGTTACCAAGACACAATCC 58.339 45.455 0.00 0.00 0.00 3.01
2068 2187 5.163982 GCTAACGAGTTACCAAGACACAATC 60.164 44.000 0.00 0.00 0.00 2.67
2069 2188 4.689345 GCTAACGAGTTACCAAGACACAAT 59.311 41.667 0.00 0.00 0.00 2.71
2070 2189 4.053295 GCTAACGAGTTACCAAGACACAA 58.947 43.478 0.00 0.00 0.00 3.33
2071 2190 3.553508 GGCTAACGAGTTACCAAGACACA 60.554 47.826 0.00 0.00 0.00 3.72
2072 2191 2.991866 GGCTAACGAGTTACCAAGACAC 59.008 50.000 0.00 0.00 0.00 3.67
2073 2192 3.308438 GGCTAACGAGTTACCAAGACA 57.692 47.619 0.00 0.00 0.00 3.41
2093 2212 2.522372 CTGTTCAATCTGCAGCTTCG 57.478 50.000 9.47 1.26 0.00 3.79
2116 2235 7.379750 GGTTGTTTTCTATCTACTCTCACTGT 58.620 38.462 0.00 0.00 0.00 3.55
2132 2252 1.001706 GCAGAACCGAGGGTTGTTTTC 60.002 52.381 4.49 0.00 46.95 2.29
2135 2255 0.110486 ATGCAGAACCGAGGGTTGTT 59.890 50.000 4.49 0.00 46.95 2.83
2141 2261 0.811281 GGGAAAATGCAGAACCGAGG 59.189 55.000 0.00 0.00 0.00 4.63
2148 2268 1.678635 CGGCCAGGGAAAATGCAGA 60.679 57.895 2.24 0.00 0.00 4.26
2149 2269 2.713967 CCGGCCAGGGAAAATGCAG 61.714 63.158 2.24 0.00 35.97 4.41
2175 2295 9.012161 TGTGTAAATCTCATGTTCATTGATCAA 57.988 29.630 11.26 11.26 0.00 2.57
2184 2304 5.063060 GGTACCGTGTGTAAATCTCATGTTC 59.937 44.000 0.00 0.00 0.00 3.18
2203 2327 7.062749 TGGAATGTCTCACTATATTGGTACC 57.937 40.000 4.43 4.43 0.00 3.34
2213 2337 4.838423 TCTTGTTCCTGGAATGTCTCACTA 59.162 41.667 13.07 0.00 0.00 2.74
2235 2359 4.557695 CGGATAGGCTTGATACTGTGACTC 60.558 50.000 0.00 0.00 0.00 3.36
2311 2435 0.919289 GATGGGAGGTGGAAGGGGAA 60.919 60.000 0.00 0.00 0.00 3.97
2312 2436 1.307866 GATGGGAGGTGGAAGGGGA 60.308 63.158 0.00 0.00 0.00 4.81
2315 2439 0.257039 CCAAGATGGGAGGTGGAAGG 59.743 60.000 0.00 0.00 32.67 3.46
2316 2440 3.890527 CCAAGATGGGAGGTGGAAG 57.109 57.895 0.00 0.00 32.67 3.46
2359 2483 0.106769 TGTGTTCAAGGCCTTGCTGA 60.107 50.000 36.24 20.41 40.24 4.26
2360 2484 0.963962 ATGTGTTCAAGGCCTTGCTG 59.036 50.000 36.24 18.29 40.24 4.41
2369 2493 1.154225 GGCGCCGAATGTGTTCAAG 60.154 57.895 12.58 0.00 33.86 3.02
2410 2534 0.255890 GAGGGGATTGCTACAGCCAA 59.744 55.000 0.00 0.00 41.18 4.52
2485 2609 5.462530 TCTTCATTCTTCAACGTCAGGTA 57.537 39.130 0.00 0.00 0.00 3.08
2496 2620 7.608308 AGTTAGTTGCTCATCTTCATTCTTC 57.392 36.000 0.00 0.00 0.00 2.87
2513 2637 3.838903 ACCCTGTAGCTAGCAAGTTAGTT 59.161 43.478 18.83 0.00 0.00 2.24
2517 2641 2.028020 GTCACCCTGTAGCTAGCAAGTT 60.028 50.000 18.83 0.00 0.00 2.66
2519 2643 1.550524 TGTCACCCTGTAGCTAGCAAG 59.449 52.381 18.83 11.06 0.00 4.01
2534 2658 7.308049 GGTCTCTTTCTTGGTCTTTATTGTCAC 60.308 40.741 0.00 0.00 0.00 3.67
2542 2666 3.202151 TGGTGGTCTCTTTCTTGGTCTTT 59.798 43.478 0.00 0.00 0.00 2.52
2543 2667 2.777692 TGGTGGTCTCTTTCTTGGTCTT 59.222 45.455 0.00 0.00 0.00 3.01
2562 2686 1.236628 GCTGCTTATCTCTGGCATGG 58.763 55.000 0.00 0.00 35.37 3.66
2570 2694 4.606457 AAATCGTGTTGCTGCTTATCTC 57.394 40.909 0.00 0.00 0.00 2.75
2588 2723 8.812513 TGTGGATGAATGAGTGATCTTAAAAT 57.187 30.769 0.00 0.00 0.00 1.82
2597 2732 3.515104 TGCTACTGTGGATGAATGAGTGA 59.485 43.478 0.00 0.00 0.00 3.41
2598 2733 3.865446 TGCTACTGTGGATGAATGAGTG 58.135 45.455 0.00 0.00 0.00 3.51
2599 2734 3.681034 GCTGCTACTGTGGATGAATGAGT 60.681 47.826 0.00 0.00 0.00 3.41
2600 2735 2.871022 GCTGCTACTGTGGATGAATGAG 59.129 50.000 0.00 0.00 0.00 2.90
2629 2768 3.942829 AGCTAGCTGTTATCTGCACAAA 58.057 40.909 18.57 0.00 40.25 2.83
2746 2885 2.753043 CTGCAAGCCGGGAATGCT 60.753 61.111 20.46 0.00 41.89 3.79
2764 2903 4.929808 AGATGTTGTCGTTCTGTGGTTATC 59.070 41.667 0.00 0.00 0.00 1.75
2813 2952 4.345288 CATGCTATGGATGTTGTTGTTCG 58.655 43.478 0.00 0.00 0.00 3.95
2848 4149 1.445716 CTATGCAAGCTGCTCCCTGC 61.446 60.000 15.90 15.90 45.31 4.85
2879 4180 5.007385 AGAGGTTGTTATACTGTTAGCCG 57.993 43.478 0.00 0.00 0.00 5.52
2964 4265 0.320946 TCGGTTCCGGTGATCCAAAC 60.321 55.000 11.37 0.00 31.66 2.93


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

AutoCloner maintained by Alex Coulton.