Multiple sequence alignment - TraesCS3D01G019100

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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 TraesCS3D01G019100 chr3D 100.000 3927 0 0 1 3927 6427506 6423580 0.000000e+00 7252.0
1 TraesCS3D01G019100 chr3D 88.977 1388 128 15 1551 2936 6456163 6454799 0.000000e+00 1692.0
2 TraesCS3D01G019100 chr3D 82.178 202 36 0 859 1060 21886553 21886754 1.450000e-39 174.0
3 TraesCS3D01G019100 chr3B 89.927 2184 126 31 945 3083 6966314 6968448 0.000000e+00 2728.0
4 TraesCS3D01G019100 chr3B 89.508 1382 121 14 1551 2931 6956925 6958283 0.000000e+00 1727.0
5 TraesCS3D01G019100 chr3B 89.224 863 63 11 1 857 6965465 6966303 0.000000e+00 1051.0
6 TraesCS3D01G019100 chr3B 80.000 220 39 4 859 1074 416818071 416818289 1.460000e-34 158.0
7 TraesCS3D01G019100 chr3A 94.156 1540 75 10 1545 3083 13852149 13853674 0.000000e+00 2331.0
8 TraesCS3D01G019100 chr3A 83.569 1132 137 24 1 1103 13851043 13852154 0.000000e+00 1014.0
9 TraesCS3D01G019100 chr7D 86.159 1380 158 12 1553 2932 40118701 40120047 0.000000e+00 1459.0
10 TraesCS3D01G019100 chr7D 94.370 675 33 4 3257 3927 38669721 38669048 0.000000e+00 1031.0
11 TraesCS3D01G019100 chr7D 93.323 674 42 3 3257 3927 477407029 477407702 0.000000e+00 992.0
12 TraesCS3D01G019100 chr7D 93.047 676 39 4 3257 3927 422837777 422837105 0.000000e+00 981.0
13 TraesCS3D01G019100 chr5D 94.126 698 29 1 3242 3927 437333237 437333934 0.000000e+00 1051.0
14 TraesCS3D01G019100 chr5D 95.570 632 28 0 3296 3927 367422222 367421591 0.000000e+00 1013.0
15 TraesCS3D01G019100 chr5D 93.703 667 37 4 3266 3927 454020718 454020052 0.000000e+00 994.0
16 TraesCS3D01G019100 chr5D 93.145 671 43 3 3260 3927 438061460 438062130 0.000000e+00 981.0
17 TraesCS3D01G019100 chr5D 87.586 145 13 5 863 1005 501114878 501114737 3.140000e-36 163.0
18 TraesCS3D01G019100 chr5D 78.707 263 40 10 855 1103 441791706 441791966 1.130000e-35 161.0
19 TraesCS3D01G019100 chr2D 94.058 690 29 3 3250 3927 642968605 642969294 0.000000e+00 1037.0
20 TraesCS3D01G019100 chr7B 96.190 630 24 0 3298 3927 749426777 749427406 0.000000e+00 1031.0
21 TraesCS3D01G019100 chr7B 80.465 215 39 3 855 1069 293158601 293158390 1.130000e-35 161.0
22 TraesCS3D01G019100 chr7B 80.851 188 33 3 863 1048 112334499 112334685 1.140000e-30 145.0
23 TraesCS3D01G019100 chr7B 74.603 189 36 7 927 1103 558982082 558981894 5.440000e-09 73.1
24 TraesCS3D01G019100 chr5B 91.254 686 45 8 3242 3927 81807081 81806411 0.000000e+00 920.0
25 TraesCS3D01G019100 chr2B 84.314 153 24 0 859 1011 9842985 9843137 2.440000e-32 150.0
26 TraesCS3D01G019100 chr2B 80.303 198 38 1 866 1062 147493733 147493930 8.790000e-32 148.0
27 TraesCS3D01G019100 chr7A 79.070 215 42 3 855 1069 365080333 365080122 1.140000e-30 145.0
28 TraesCS3D01G019100 chrUn 86.842 114 12 3 1295 1405 93046263 93046376 1.480000e-24 124.0


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 TraesCS3D01G019100 chr3D 6423580 6427506 3926 True 7252.0 7252 100.0000 1 3927 1 chr3D.!!$R1 3926
1 TraesCS3D01G019100 chr3D 6454799 6456163 1364 True 1692.0 1692 88.9770 1551 2936 1 chr3D.!!$R2 1385
2 TraesCS3D01G019100 chr3B 6965465 6968448 2983 False 1889.5 2728 89.5755 1 3083 2 chr3B.!!$F3 3082
3 TraesCS3D01G019100 chr3B 6956925 6958283 1358 False 1727.0 1727 89.5080 1551 2931 1 chr3B.!!$F1 1380
4 TraesCS3D01G019100 chr3A 13851043 13853674 2631 False 1672.5 2331 88.8625 1 3083 2 chr3A.!!$F1 3082
5 TraesCS3D01G019100 chr7D 40118701 40120047 1346 False 1459.0 1459 86.1590 1553 2932 1 chr7D.!!$F1 1379
6 TraesCS3D01G019100 chr7D 38669048 38669721 673 True 1031.0 1031 94.3700 3257 3927 1 chr7D.!!$R1 670
7 TraesCS3D01G019100 chr7D 477407029 477407702 673 False 992.0 992 93.3230 3257 3927 1 chr7D.!!$F2 670
8 TraesCS3D01G019100 chr7D 422837105 422837777 672 True 981.0 981 93.0470 3257 3927 1 chr7D.!!$R2 670
9 TraesCS3D01G019100 chr5D 437333237 437333934 697 False 1051.0 1051 94.1260 3242 3927 1 chr5D.!!$F1 685
10 TraesCS3D01G019100 chr5D 367421591 367422222 631 True 1013.0 1013 95.5700 3296 3927 1 chr5D.!!$R1 631
11 TraesCS3D01G019100 chr5D 454020052 454020718 666 True 994.0 994 93.7030 3266 3927 1 chr5D.!!$R2 661
12 TraesCS3D01G019100 chr5D 438061460 438062130 670 False 981.0 981 93.1450 3260 3927 1 chr5D.!!$F2 667
13 TraesCS3D01G019100 chr2D 642968605 642969294 689 False 1037.0 1037 94.0580 3250 3927 1 chr2D.!!$F1 677
14 TraesCS3D01G019100 chr7B 749426777 749427406 629 False 1031.0 1031 96.1900 3298 3927 1 chr7B.!!$F2 629
15 TraesCS3D01G019100 chr5B 81806411 81807081 670 True 920.0 920 91.2540 3242 3927 1 chr5B.!!$R1 685

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
858 869 0.031917 TAGGGGGACAGCGGTATCAA 60.032 55.0 0.00 0.0 0.0 2.57 F
1329 1363 0.318360 GCCGGAGAAAAACCCAAACG 60.318 55.0 5.05 0.0 0.0 3.60 F
2077 2145 0.396435 TCATGCAGGTGACCGAGTTT 59.604 50.0 0.00 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2671 0.982852 TCCTTGCCGGTCCTGATCAT 60.983 55.0 1.9 0.0 0.0 2.45 R
2863 2937 0.107945 CCTCCTTGAGAAAGCGGGAG 60.108 60.0 0.0 0.0 42.1 4.30 R
3462 3564 0.250901 GCAAAAGCCTCTCCTGACCA 60.251 55.0 0.0 0.0 0.0 4.02 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
71 72 1.568612 CCATGTCCCATATGTCGCGC 61.569 60.000 0.00 0.00 0.00 6.86
73 74 3.036084 GTCCCATATGTCGCGCCG 61.036 66.667 0.00 0.00 0.00 6.46
87 88 1.953138 CGCCGTGCAAAAATTGGCA 60.953 52.632 10.58 0.00 46.02 4.92
101 102 8.828644 GCAAAAATTGGCATGTAAATCATATCA 58.171 29.630 0.00 0.00 34.67 2.15
131 135 9.157104 TCTGAAAATTGTACGTTCTTGCATATA 57.843 29.630 0.00 0.00 0.00 0.86
138 142 6.578944 TGTACGTTCTTGCATATAGTGGAAT 58.421 36.000 0.00 0.00 37.53 3.01
144 148 7.254898 CGTTCTTGCATATAGTGGAATTGTGAT 60.255 37.037 0.00 0.00 37.53 3.06
147 151 8.970020 TCTTGCATATAGTGGAATTGTGATTTT 58.030 29.630 0.00 0.00 37.53 1.82
369 376 6.182627 TCAATGGATTGAGCAATAAGTCACT 58.817 36.000 0.00 0.00 41.51 3.41
483 492 5.303747 TGTGTTCTTGACAACAAATCGTT 57.696 34.783 0.00 0.00 40.65 3.85
497 506 0.536460 ATCGTTGAAAACCGGCCACT 60.536 50.000 0.00 0.00 46.28 4.00
517 526 2.663602 CTGAGCTTTGCTACACGTACAG 59.336 50.000 0.00 0.00 39.88 2.74
518 527 2.295070 TGAGCTTTGCTACACGTACAGA 59.705 45.455 0.00 0.00 39.88 3.41
572 581 3.658757 TGGCAGCTTTTAATTGGTCAC 57.341 42.857 0.00 0.00 0.00 3.67
583 592 3.802948 AATTGGTCACTAGTAGAGGCG 57.197 47.619 3.59 0.00 0.00 5.52
613 622 0.905357 CTGTCGAATTCAGGGAGGGT 59.095 55.000 6.22 0.00 0.00 4.34
614 623 0.613260 TGTCGAATTCAGGGAGGGTG 59.387 55.000 6.22 0.00 0.00 4.61
628 637 2.100749 GGAGGGTGTGTTTGGAAGTTTG 59.899 50.000 0.00 0.00 0.00 2.93
648 657 4.493819 TGGAAGGAGCCTATAGAATCCT 57.506 45.455 16.09 16.09 44.12 3.24
670 679 7.229308 TCCTCATAAAAGCCTATACGTCTAGA 58.771 38.462 9.40 0.00 0.00 2.43
678 687 7.787725 AAGCCTATACGTCTAGAATTTTTGG 57.212 36.000 9.40 0.00 0.00 3.28
679 688 6.289064 AGCCTATACGTCTAGAATTTTTGGG 58.711 40.000 9.40 0.00 0.00 4.12
680 689 5.469084 GCCTATACGTCTAGAATTTTTGGGG 59.531 44.000 9.40 0.00 0.00 4.96
688 699 3.967332 AGAATTTTTGGGGCATGTCAG 57.033 42.857 0.00 0.00 0.00 3.51
689 700 2.027837 AGAATTTTTGGGGCATGTCAGC 60.028 45.455 0.00 0.00 0.00 4.26
793 804 2.231716 GGGAGCCCCAAATAACAAGT 57.768 50.000 5.45 0.00 44.65 3.16
813 824 7.793902 ACAAGTCATCAACTTTTACGTACATC 58.206 34.615 0.00 0.00 46.26 3.06
819 830 6.922980 TCAACTTTTACGTACATCGAAGAG 57.077 37.500 0.00 0.00 43.63 2.85
850 861 1.571773 ATTGGGTGTAGGGGGACAGC 61.572 60.000 0.00 0.00 45.15 4.40
857 868 0.757935 GTAGGGGGACAGCGGTATCA 60.758 60.000 0.00 0.00 0.00 2.15
858 869 0.031917 TAGGGGGACAGCGGTATCAA 60.032 55.000 0.00 0.00 0.00 2.57
859 870 1.146263 GGGGGACAGCGGTATCAAG 59.854 63.158 0.00 0.00 0.00 3.02
861 881 1.335132 GGGGACAGCGGTATCAAGGA 61.335 60.000 0.00 0.00 0.00 3.36
869 889 5.116882 ACAGCGGTATCAAGGATTTAAGTC 58.883 41.667 0.00 0.00 0.00 3.01
882 902 7.631717 AGGATTTAAGTCCTAGATTTGCAAC 57.368 36.000 17.39 0.00 46.70 4.17
885 905 6.817765 TTTAAGTCCTAGATTTGCAACTGG 57.182 37.500 0.00 0.00 0.00 4.00
921 941 7.969690 TTTTGGATTTATTTCAGGCTATCCA 57.030 32.000 8.48 8.48 39.65 3.41
922 942 7.587037 TTTGGATTTATTTCAGGCTATCCAG 57.413 36.000 11.57 0.00 41.63 3.86
923 943 6.266131 TGGATTTATTTCAGGCTATCCAGT 57.734 37.500 8.48 0.00 37.28 4.00
931 951 2.101415 TCAGGCTATCCAGTGATGTTCG 59.899 50.000 0.00 0.00 32.18 3.95
935 955 3.521560 GCTATCCAGTGATGTTCGTTCA 58.478 45.455 0.00 0.00 32.18 3.18
942 962 4.169508 CAGTGATGTTCGTTCAGTAGGAG 58.830 47.826 0.00 0.00 0.00 3.69
951 971 2.228343 CGTTCAGTAGGAGGAGACGTTT 59.772 50.000 0.00 0.00 0.00 3.60
953 973 2.082231 TCAGTAGGAGGAGACGTTTCG 58.918 52.381 0.00 0.00 0.00 3.46
976 996 1.659601 CGACTACGAGACGTCTGTGAT 59.340 52.381 25.58 12.96 41.54 3.06
1018 1038 2.355108 GCTATGCCAGTTCAACCTCTCA 60.355 50.000 0.00 0.00 0.00 3.27
1019 1039 2.957402 ATGCCAGTTCAACCTCTCAA 57.043 45.000 0.00 0.00 0.00 3.02
1022 1042 4.365514 TGCCAGTTCAACCTCTCAAATA 57.634 40.909 0.00 0.00 0.00 1.40
1038 1058 9.381033 CCTCTCAAATATGCTCATAGAAATAGG 57.619 37.037 0.00 0.00 0.00 2.57
1069 1089 1.783071 TGCGTCCATATGGGTGAGTA 58.217 50.000 21.78 7.50 38.11 2.59
1077 1109 5.187772 GTCCATATGGGTGAGTATATGAGCA 59.812 44.000 21.78 0.00 38.80 4.26
1177 1211 2.386661 CTTAGAAGAAAGGAGGCGCA 57.613 50.000 10.83 0.00 0.00 6.09
1178 1212 2.275318 CTTAGAAGAAAGGAGGCGCAG 58.725 52.381 10.83 0.00 0.00 5.18
1192 1226 3.521995 CGCAGCAGAGAAGGAAGAA 57.478 52.632 0.00 0.00 0.00 2.52
1193 1227 1.800805 CGCAGCAGAGAAGGAAGAAA 58.199 50.000 0.00 0.00 0.00 2.52
1194 1228 2.354259 CGCAGCAGAGAAGGAAGAAAT 58.646 47.619 0.00 0.00 0.00 2.17
1195 1229 2.095532 CGCAGCAGAGAAGGAAGAAATG 59.904 50.000 0.00 0.00 0.00 2.32
1196 1230 3.341823 GCAGCAGAGAAGGAAGAAATGA 58.658 45.455 0.00 0.00 0.00 2.57
1197 1231 3.374678 GCAGCAGAGAAGGAAGAAATGAG 59.625 47.826 0.00 0.00 0.00 2.90
1198 1232 3.940221 CAGCAGAGAAGGAAGAAATGAGG 59.060 47.826 0.00 0.00 0.00 3.86
1199 1233 2.682352 GCAGAGAAGGAAGAAATGAGGC 59.318 50.000 0.00 0.00 0.00 4.70
1228 1262 0.398318 AAGGAAGAAAGAGCCGCACT 59.602 50.000 0.00 0.00 0.00 4.40
1259 1293 1.066573 CGGAGAGGCTAGCCCATTATG 60.067 57.143 30.42 12.32 36.58 1.90
1260 1294 2.260822 GGAGAGGCTAGCCCATTATGA 58.739 52.381 30.42 0.00 36.58 2.15
1263 1297 4.512484 GAGAGGCTAGCCCATTATGAATC 58.488 47.826 30.42 17.08 36.58 2.52
1281 1315 1.202769 TCTTAGGGTTTCGGGTGGGG 61.203 60.000 0.00 0.00 0.00 4.96
1282 1316 2.206182 CTTAGGGTTTCGGGTGGGGG 62.206 65.000 0.00 0.00 0.00 5.40
1309 1343 2.203153 ACGGTGGTGGTGCACTTC 60.203 61.111 17.98 9.86 34.40 3.01
1329 1363 0.318360 GCCGGAGAAAAACCCAAACG 60.318 55.000 5.05 0.00 0.00 3.60
1456 1514 3.535962 GAGCGCTGGGAGGAGGAG 61.536 72.222 18.48 0.00 0.00 3.69
1471 1529 1.222113 GGAGGAAGAAGAAGGGCCG 59.778 63.158 0.00 0.00 0.00 6.13
1477 1535 2.436824 GAAGAAGGGCCGCTGGTC 60.437 66.667 0.00 0.00 0.00 4.02
1480 1538 4.699522 GAAGGGCCGCTGGTCGTT 62.700 66.667 0.00 6.80 38.14 3.85
1481 1539 3.305177 GAAGGGCCGCTGGTCGTTA 62.305 63.158 0.00 0.00 35.47 3.18
1482 1540 2.588856 GAAGGGCCGCTGGTCGTTAT 62.589 60.000 0.00 0.00 35.47 1.89
1493 1551 3.921021 GCTGGTCGTTATATCTTCATCCG 59.079 47.826 0.00 0.00 0.00 4.18
1505 1563 5.776173 ATCTTCATCCGACGTCTAGAATT 57.224 39.130 14.70 0.00 0.00 2.17
1515 1573 4.904724 CGACGTCTAGAATTAATCGACTGG 59.095 45.833 14.70 0.00 0.00 4.00
1526 1584 2.214376 ATCGACTGGCCCAATTTCAA 57.786 45.000 0.00 0.00 0.00 2.69
1680 1739 4.641645 CAGGCCGTTGCTGGTCCA 62.642 66.667 0.00 0.00 37.74 4.02
1681 1740 3.884774 AGGCCGTTGCTGGTCCAA 61.885 61.111 0.00 0.00 37.74 3.53
2077 2145 0.396435 TCATGCAGGTGACCGAGTTT 59.604 50.000 0.00 0.00 0.00 2.66
2107 2175 1.302271 GTTCGTCCTTGGGGTCACC 60.302 63.158 0.00 0.00 40.81 4.02
2333 2401 2.190313 TGCCGATGAGCACCATCC 59.810 61.111 11.83 2.42 46.98 3.51
2603 2671 4.312443 GGACATCAAAGACGTGGTTAAGA 58.688 43.478 0.00 0.00 0.00 2.10
2613 2681 4.113354 GACGTGGTTAAGATGATCAGGAC 58.887 47.826 0.09 0.00 0.00 3.85
2959 3033 1.328680 CTTGGATCGATCGGTGCAAAG 59.671 52.381 30.81 21.74 0.00 2.77
2960 3034 1.089481 TGGATCGATCGGTGCAAAGC 61.089 55.000 20.94 0.00 0.00 3.51
2961 3035 0.811616 GGATCGATCGGTGCAAAGCT 60.812 55.000 15.61 0.00 0.00 3.74
3049 3134 3.990318 AGCTTTAAGTTTGCACTGGAC 57.010 42.857 0.00 0.00 31.60 4.02
3118 3203 8.732746 ATTTAAAGAATGTTATAGGCGTCTGT 57.267 30.769 0.00 0.00 0.00 3.41
3119 3204 8.556213 TTTAAAGAATGTTATAGGCGTCTGTT 57.444 30.769 0.00 0.00 0.00 3.16
3120 3205 8.556213 TTAAAGAATGTTATAGGCGTCTGTTT 57.444 30.769 0.00 0.00 0.00 2.83
3121 3206 7.448748 AAAGAATGTTATAGGCGTCTGTTTT 57.551 32.000 0.00 0.00 0.00 2.43
3122 3207 6.663944 AGAATGTTATAGGCGTCTGTTTTC 57.336 37.500 0.00 0.00 0.00 2.29
3123 3208 6.170506 AGAATGTTATAGGCGTCTGTTTTCA 58.829 36.000 0.00 0.00 0.00 2.69
3125 3210 4.890088 TGTTATAGGCGTCTGTTTTCAGT 58.110 39.130 0.00 0.00 46.98 3.41
3126 3211 5.302360 TGTTATAGGCGTCTGTTTTCAGTT 58.698 37.500 0.00 0.00 46.98 3.16
3127 3212 5.761234 TGTTATAGGCGTCTGTTTTCAGTTT 59.239 36.000 0.00 0.00 46.98 2.66
3128 3213 6.261381 TGTTATAGGCGTCTGTTTTCAGTTTT 59.739 34.615 0.00 0.00 46.98 2.43
3129 3214 5.767816 ATAGGCGTCTGTTTTCAGTTTTT 57.232 34.783 0.00 0.00 46.98 1.94
3130 3215 3.769536 AGGCGTCTGTTTTCAGTTTTTG 58.230 40.909 0.00 0.00 46.98 2.44
3131 3216 3.192633 AGGCGTCTGTTTTCAGTTTTTGT 59.807 39.130 0.00 0.00 46.98 2.83
3132 3217 4.396790 AGGCGTCTGTTTTCAGTTTTTGTA 59.603 37.500 0.00 0.00 46.98 2.41
3133 3218 4.733405 GGCGTCTGTTTTCAGTTTTTGTAG 59.267 41.667 0.00 0.00 46.98 2.74
3134 3219 5.448089 GGCGTCTGTTTTCAGTTTTTGTAGA 60.448 40.000 0.00 0.00 46.98 2.59
3135 3220 6.025280 GCGTCTGTTTTCAGTTTTTGTAGAA 58.975 36.000 0.00 0.00 46.98 2.10
3136 3221 6.525280 GCGTCTGTTTTCAGTTTTTGTAGAAA 59.475 34.615 0.00 0.00 46.98 2.52
3137 3222 7.461026 GCGTCTGTTTTCAGTTTTTGTAGAAAC 60.461 37.037 0.00 0.00 46.98 2.78
3138 3223 7.535940 CGTCTGTTTTCAGTTTTTGTAGAAACA 59.464 33.333 3.68 0.00 46.98 2.83
3139 3224 8.635983 GTCTGTTTTCAGTTTTTGTAGAAACAC 58.364 33.333 3.68 0.00 46.98 3.32
3140 3225 8.353684 TCTGTTTTCAGTTTTTGTAGAAACACA 58.646 29.630 4.66 0.00 46.98 3.72
3141 3226 9.139174 CTGTTTTCAGTTTTTGTAGAAACACAT 57.861 29.630 4.66 0.00 40.98 3.21
3142 3227 9.134734 TGTTTTCAGTTTTTGTAGAAACACATC 57.865 29.630 4.66 0.00 40.98 3.06
3143 3228 9.353999 GTTTTCAGTTTTTGTAGAAACACATCT 57.646 29.630 4.66 0.00 40.98 2.90
3146 3231 9.997482 TTCAGTTTTTGTAGAAACACATCTAAC 57.003 29.630 4.66 0.00 40.98 2.34
3147 3232 9.391006 TCAGTTTTTGTAGAAACACATCTAACT 57.609 29.630 4.66 0.00 40.98 2.24
3187 3272 7.464830 AACAGTTATAGATACACAACGATGC 57.535 36.000 0.00 0.00 0.00 3.91
3188 3273 6.569780 ACAGTTATAGATACACAACGATGCA 58.430 36.000 0.00 0.00 0.00 3.96
3189 3274 7.039270 ACAGTTATAGATACACAACGATGCAA 58.961 34.615 0.00 0.00 0.00 4.08
3190 3275 7.710907 ACAGTTATAGATACACAACGATGCAAT 59.289 33.333 0.00 0.00 0.00 3.56
3191 3276 9.191995 CAGTTATAGATACACAACGATGCAATA 57.808 33.333 0.00 0.00 0.00 1.90
3192 3277 9.411801 AGTTATAGATACACAACGATGCAATAG 57.588 33.333 0.00 0.00 0.00 1.73
3193 3278 9.406828 GTTATAGATACACAACGATGCAATAGA 57.593 33.333 0.00 0.00 0.00 1.98
3194 3279 9.626045 TTATAGATACACAACGATGCAATAGAG 57.374 33.333 0.00 0.00 0.00 2.43
3195 3280 5.292765 AGATACACAACGATGCAATAGAGG 58.707 41.667 0.00 0.00 0.00 3.69
3196 3281 2.009774 ACACAACGATGCAATAGAGGC 58.990 47.619 0.00 0.00 0.00 4.70
3197 3282 2.009051 CACAACGATGCAATAGAGGCA 58.991 47.619 0.00 0.00 46.66 4.75
3205 3290 3.632643 TGCAATAGAGGCATGACTCAA 57.367 42.857 30.08 5.72 39.97 3.02
3206 3291 3.273434 TGCAATAGAGGCATGACTCAAC 58.727 45.455 30.08 14.19 39.97 3.18
3207 3292 3.273434 GCAATAGAGGCATGACTCAACA 58.727 45.455 30.08 15.04 39.97 3.33
3208 3293 3.691118 GCAATAGAGGCATGACTCAACAA 59.309 43.478 30.08 12.83 39.97 2.83
3209 3294 4.156556 GCAATAGAGGCATGACTCAACAAA 59.843 41.667 30.08 10.33 39.97 2.83
3210 3295 5.634896 CAATAGAGGCATGACTCAACAAAC 58.365 41.667 30.08 1.77 39.97 2.93
3211 3296 3.213206 AGAGGCATGACTCAACAAACA 57.787 42.857 30.08 0.00 39.97 2.83
3212 3297 3.554934 AGAGGCATGACTCAACAAACAA 58.445 40.909 30.08 0.00 39.97 2.83
3213 3298 3.316308 AGAGGCATGACTCAACAAACAAC 59.684 43.478 30.08 0.00 39.97 3.32
3214 3299 2.362077 AGGCATGACTCAACAAACAACC 59.638 45.455 0.00 0.00 0.00 3.77
3215 3300 2.362077 GGCATGACTCAACAAACAACCT 59.638 45.455 0.00 0.00 0.00 3.50
3216 3301 3.568007 GGCATGACTCAACAAACAACCTA 59.432 43.478 0.00 0.00 0.00 3.08
3217 3302 4.320494 GGCATGACTCAACAAACAACCTAG 60.320 45.833 0.00 0.00 0.00 3.02
3218 3303 4.515191 GCATGACTCAACAAACAACCTAGA 59.485 41.667 0.00 0.00 0.00 2.43
3219 3304 5.008613 GCATGACTCAACAAACAACCTAGAA 59.991 40.000 0.00 0.00 0.00 2.10
3220 3305 6.662616 CATGACTCAACAAACAACCTAGAAG 58.337 40.000 0.00 0.00 0.00 2.85
3221 3306 5.984725 TGACTCAACAAACAACCTAGAAGA 58.015 37.500 0.00 0.00 0.00 2.87
3222 3307 5.815740 TGACTCAACAAACAACCTAGAAGAC 59.184 40.000 0.00 0.00 0.00 3.01
3223 3308 5.741011 ACTCAACAAACAACCTAGAAGACA 58.259 37.500 0.00 0.00 0.00 3.41
3224 3309 5.585047 ACTCAACAAACAACCTAGAAGACAC 59.415 40.000 0.00 0.00 0.00 3.67
3225 3310 5.492895 TCAACAAACAACCTAGAAGACACA 58.507 37.500 0.00 0.00 0.00 3.72
3226 3311 5.941058 TCAACAAACAACCTAGAAGACACAA 59.059 36.000 0.00 0.00 0.00 3.33
3227 3312 5.813080 ACAAACAACCTAGAAGACACAAC 57.187 39.130 0.00 0.00 0.00 3.32
3228 3313 4.331717 ACAAACAACCTAGAAGACACAACG 59.668 41.667 0.00 0.00 0.00 4.10
3229 3314 2.480845 ACAACCTAGAAGACACAACGC 58.519 47.619 0.00 0.00 0.00 4.84
3230 3315 1.798813 CAACCTAGAAGACACAACGCC 59.201 52.381 0.00 0.00 0.00 5.68
3231 3316 0.320697 ACCTAGAAGACACAACGCCC 59.679 55.000 0.00 0.00 0.00 6.13
3232 3317 0.736325 CCTAGAAGACACAACGCCCG 60.736 60.000 0.00 0.00 0.00 6.13
3233 3318 1.352156 CTAGAAGACACAACGCCCGC 61.352 60.000 0.00 0.00 0.00 6.13
3234 3319 2.089887 TAGAAGACACAACGCCCGCA 62.090 55.000 0.00 0.00 0.00 5.69
3235 3320 2.954753 GAAGACACAACGCCCGCAG 61.955 63.158 0.00 0.00 0.00 5.18
3236 3321 3.454587 AAGACACAACGCCCGCAGA 62.455 57.895 0.00 0.00 0.00 4.26
3237 3322 2.933878 AAGACACAACGCCCGCAGAA 62.934 55.000 0.00 0.00 0.00 3.02
3238 3323 2.954753 GACACAACGCCCGCAGAAG 61.955 63.158 0.00 0.00 0.00 2.85
3239 3324 4.389576 CACAACGCCCGCAGAAGC 62.390 66.667 0.00 0.00 37.42 3.86
3240 3325 4.626081 ACAACGCCCGCAGAAGCT 62.626 61.111 0.00 0.00 39.10 3.74
3255 3340 4.836825 CAGAAGCTGGAAAAGTAGGATCA 58.163 43.478 0.00 0.00 0.00 2.92
3285 3372 2.798689 CGATCAGGAGGCGACGAA 59.201 61.111 0.00 0.00 0.00 3.85
3462 3564 1.747325 TTTCTCCGGGTTCCGTTCGT 61.747 55.000 0.00 0.00 46.80 3.85
3470 3572 1.364901 GTTCCGTTCGTGGTCAGGA 59.635 57.895 0.00 0.00 0.00 3.86
3556 3658 3.190738 TTTGGTGGCTGGAGGTCCG 62.191 63.158 0.00 0.00 39.43 4.79
3600 3702 1.135094 AGATGGGCGATGGATTCAGT 58.865 50.000 0.00 0.00 0.00 3.41
3634 3736 5.162980 ACCCTTCTTCTTCCTTGTTGGTATT 60.163 40.000 0.00 0.00 37.07 1.89
3872 3974 4.697352 GTCAAGAAAAGAGGAAGCAGCATA 59.303 41.667 0.00 0.00 0.00 3.14
3892 3994 2.249692 CGGCAATTGTACCGTGGTT 58.750 52.632 14.30 0.00 44.46 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 1.510776 ACATGCCAATTTTTGCACGG 58.489 45.000 0.00 0.00 40.88 4.94
73 74 6.238610 TGATTTACATGCCAATTTTTGCAC 57.761 33.333 0.00 0.00 40.88 4.57
101 102 6.636850 GCAAGAACGTACAATTTTCAGACAAT 59.363 34.615 0.00 0.00 0.00 2.71
314 321 5.393678 GCAAAATTCTTGGGCCGACTAATAA 60.394 40.000 0.00 0.00 0.00 1.40
363 370 1.689273 GGGTGTGACTCTTCAGTGACT 59.311 52.381 0.00 0.00 37.62 3.41
369 376 0.679505 CTTCCGGGTGTGACTCTTCA 59.320 55.000 0.00 0.00 0.00 3.02
483 492 1.896660 GCTCAGTGGCCGGTTTTCA 60.897 57.895 1.90 0.00 0.00 2.69
486 495 1.152756 AAAGCTCAGTGGCCGGTTT 60.153 52.632 1.90 0.00 0.00 3.27
497 506 2.295070 TCTGTACGTGTAGCAAAGCTCA 59.705 45.455 0.00 0.00 40.44 4.26
517 526 1.486726 CCCCTCATCCCTGTAACACTC 59.513 57.143 0.00 0.00 0.00 3.51
518 527 1.080498 TCCCCTCATCCCTGTAACACT 59.920 52.381 0.00 0.00 0.00 3.55
596 605 0.613777 ACACCCTCCCTGAATTCGAC 59.386 55.000 0.04 0.00 0.00 4.20
598 607 0.324943 ACACACCCTCCCTGAATTCG 59.675 55.000 0.04 0.00 0.00 3.34
613 622 3.699038 CTCCTTCCAAACTTCCAAACACA 59.301 43.478 0.00 0.00 0.00 3.72
614 623 3.490933 GCTCCTTCCAAACTTCCAAACAC 60.491 47.826 0.00 0.00 0.00 3.32
628 637 4.421131 TGAGGATTCTATAGGCTCCTTCC 58.579 47.826 19.15 11.57 38.24 3.46
670 679 1.980036 AGCTGACATGCCCCAAAAATT 59.020 42.857 0.00 0.00 0.00 1.82
678 687 2.555757 GGATTATTGAGCTGACATGCCC 59.444 50.000 0.00 0.00 0.00 5.36
679 688 3.484407 AGGATTATTGAGCTGACATGCC 58.516 45.455 0.00 0.00 0.00 4.40
680 689 5.407995 GTCTAGGATTATTGAGCTGACATGC 59.592 44.000 0.00 0.00 0.00 4.06
688 699 7.727181 TCTTTGTAGGTCTAGGATTATTGAGC 58.273 38.462 0.00 0.00 0.00 4.26
741 752 5.686397 CGACGTGGAGGAAAGAATTATAGTC 59.314 44.000 0.00 0.00 0.00 2.59
761 772 1.883084 GCTCCCCTTACATGCGACG 60.883 63.158 0.00 0.00 0.00 5.12
793 804 7.085746 TCTTCGATGTACGTAAAAGTTGATGA 58.914 34.615 0.00 0.00 43.13 2.92
813 824 3.558505 CAATTTGTTGGCACTCTCTTCG 58.441 45.455 0.00 0.00 0.00 3.79
819 830 1.412343 ACACCCAATTTGTTGGCACTC 59.588 47.619 1.67 0.00 40.74 3.51
859 870 7.415653 CCAGTTGCAAATCTAGGACTTAAATCC 60.416 40.741 0.00 0.00 39.28 3.01
861 881 6.948309 ACCAGTTGCAAATCTAGGACTTAAAT 59.052 34.615 0.00 0.00 0.00 1.40
879 899 2.138596 AAAAATGCGAGCACCAGTTG 57.861 45.000 0.00 0.00 0.00 3.16
899 919 6.547141 CACTGGATAGCCTGAAATAAATCCAA 59.453 38.462 11.23 0.00 41.61 3.53
915 935 4.748892 ACTGAACGAACATCACTGGATAG 58.251 43.478 0.00 0.00 30.87 2.08
916 936 4.801330 ACTGAACGAACATCACTGGATA 57.199 40.909 0.00 0.00 30.87 2.59
917 937 3.685139 ACTGAACGAACATCACTGGAT 57.315 42.857 0.00 0.00 0.00 3.41
918 938 3.056821 CCTACTGAACGAACATCACTGGA 60.057 47.826 0.00 0.00 0.00 3.86
919 939 3.056821 TCCTACTGAACGAACATCACTGG 60.057 47.826 0.00 0.00 0.00 4.00
920 940 4.169508 CTCCTACTGAACGAACATCACTG 58.830 47.826 0.00 0.00 0.00 3.66
921 941 3.193691 CCTCCTACTGAACGAACATCACT 59.806 47.826 0.00 0.00 0.00 3.41
922 942 3.192844 TCCTCCTACTGAACGAACATCAC 59.807 47.826 0.00 0.00 0.00 3.06
923 943 3.427573 TCCTCCTACTGAACGAACATCA 58.572 45.455 0.00 0.00 0.00 3.07
931 951 3.670091 CGAAACGTCTCCTCCTACTGAAC 60.670 52.174 0.00 0.00 0.00 3.18
935 955 1.271817 ACCGAAACGTCTCCTCCTACT 60.272 52.381 0.00 0.00 0.00 2.57
942 962 0.798776 TAGTCGACCGAAACGTCTCC 59.201 55.000 13.01 0.00 32.52 3.71
951 971 1.073216 GACGTCTCGTAGTCGACCGA 61.073 60.000 13.01 14.03 41.37 4.69
953 973 0.369589 CAGACGTCTCGTAGTCGACC 59.630 60.000 16.96 0.00 41.37 4.79
1019 1039 9.445878 CACACATCCTATTTCTATGAGCATATT 57.554 33.333 0.00 0.00 0.00 1.28
1022 1042 6.709397 CACACACATCCTATTTCTATGAGCAT 59.291 38.462 0.00 0.00 0.00 3.79
1038 1058 1.135315 GGACGCATGCACACACATC 59.865 57.895 19.57 2.88 0.00 3.06
1039 1059 0.961857 ATGGACGCATGCACACACAT 60.962 50.000 19.57 11.04 0.00 3.21
1044 1064 0.818852 CCCATATGGACGCATGCACA 60.819 55.000 24.00 13.61 37.39 4.57
1069 1089 4.034858 CAGCACAATCGAAGTTGCTCATAT 59.965 41.667 13.40 0.00 32.32 1.78
1077 1109 5.493133 TTTAACACAGCACAATCGAAGTT 57.507 34.783 0.00 0.00 0.00 2.66
1175 1209 3.341823 TCATTTCTTCCTTCTCTGCTGC 58.658 45.455 0.00 0.00 0.00 5.25
1176 1210 3.940221 CCTCATTTCTTCCTTCTCTGCTG 59.060 47.826 0.00 0.00 0.00 4.41
1177 1211 3.621958 GCCTCATTTCTTCCTTCTCTGCT 60.622 47.826 0.00 0.00 0.00 4.24
1178 1212 2.682352 GCCTCATTTCTTCCTTCTCTGC 59.318 50.000 0.00 0.00 0.00 4.26
1179 1213 2.935201 CGCCTCATTTCTTCCTTCTCTG 59.065 50.000 0.00 0.00 0.00 3.35
1180 1214 2.679349 GCGCCTCATTTCTTCCTTCTCT 60.679 50.000 0.00 0.00 0.00 3.10
1181 1215 1.668237 GCGCCTCATTTCTTCCTTCTC 59.332 52.381 0.00 0.00 0.00 2.87
1182 1216 1.280421 AGCGCCTCATTTCTTCCTTCT 59.720 47.619 2.29 0.00 0.00 2.85
1183 1217 1.399791 CAGCGCCTCATTTCTTCCTTC 59.600 52.381 2.29 0.00 0.00 3.46
1184 1218 1.457346 CAGCGCCTCATTTCTTCCTT 58.543 50.000 2.29 0.00 0.00 3.36
1185 1219 0.393537 CCAGCGCCTCATTTCTTCCT 60.394 55.000 2.29 0.00 0.00 3.36
1186 1220 0.392998 TCCAGCGCCTCATTTCTTCC 60.393 55.000 2.29 0.00 0.00 3.46
1187 1221 1.012841 CTCCAGCGCCTCATTTCTTC 58.987 55.000 2.29 0.00 0.00 2.87
1188 1222 0.615331 TCTCCAGCGCCTCATTTCTT 59.385 50.000 2.29 0.00 0.00 2.52
1189 1223 0.177604 CTCTCCAGCGCCTCATTTCT 59.822 55.000 2.29 0.00 0.00 2.52
1190 1224 0.176680 TCTCTCCAGCGCCTCATTTC 59.823 55.000 2.29 0.00 0.00 2.17
1191 1225 0.615331 TTCTCTCCAGCGCCTCATTT 59.385 50.000 2.29 0.00 0.00 2.32
1192 1226 0.177604 CTTCTCTCCAGCGCCTCATT 59.822 55.000 2.29 0.00 0.00 2.57
1193 1227 1.684386 CCTTCTCTCCAGCGCCTCAT 61.684 60.000 2.29 0.00 0.00 2.90
1194 1228 2.354401 CCTTCTCTCCAGCGCCTCA 61.354 63.158 2.29 0.00 0.00 3.86
1195 1229 1.608717 TTCCTTCTCTCCAGCGCCTC 61.609 60.000 2.29 0.00 0.00 4.70
1196 1230 1.610673 TTCCTTCTCTCCAGCGCCT 60.611 57.895 2.29 0.00 0.00 5.52
1197 1231 1.153469 CTTCCTTCTCTCCAGCGCC 60.153 63.158 2.29 0.00 0.00 6.53
1198 1232 0.247736 TTCTTCCTTCTCTCCAGCGC 59.752 55.000 0.00 0.00 0.00 5.92
1199 1233 2.232452 TCTTTCTTCCTTCTCTCCAGCG 59.768 50.000 0.00 0.00 0.00 5.18
1250 1284 5.048713 CGAAACCCTAAGATTCATAATGGGC 60.049 44.000 0.00 0.00 36.78 5.36
1253 1287 6.017109 CACCCGAAACCCTAAGATTCATAATG 60.017 42.308 0.00 0.00 0.00 1.90
1259 1293 2.640184 CCACCCGAAACCCTAAGATTC 58.360 52.381 0.00 0.00 0.00 2.52
1260 1294 1.283905 CCCACCCGAAACCCTAAGATT 59.716 52.381 0.00 0.00 0.00 2.40
1263 1297 1.301954 CCCCACCCGAAACCCTAAG 59.698 63.158 0.00 0.00 0.00 2.18
1285 1319 4.388499 ACCACCACCGTCCATCGC 62.388 66.667 0.00 0.00 38.35 4.58
1286 1320 2.434185 CACCACCACCGTCCATCG 60.434 66.667 0.00 0.00 39.52 3.84
1287 1321 2.746277 GCACCACCACCGTCCATC 60.746 66.667 0.00 0.00 0.00 3.51
1288 1322 3.565214 TGCACCACCACCGTCCAT 61.565 61.111 0.00 0.00 0.00 3.41
1289 1323 4.555709 GTGCACCACCACCGTCCA 62.556 66.667 5.22 0.00 0.00 4.02
1290 1324 3.767630 AAGTGCACCACCACCGTCC 62.768 63.158 14.63 0.00 36.38 4.79
1291 1325 2.203153 AAGTGCACCACCACCGTC 60.203 61.111 14.63 0.00 36.38 4.79
1292 1326 2.203153 GAAGTGCACCACCACCGT 60.203 61.111 14.63 0.00 36.38 4.83
1293 1327 3.345808 CGAAGTGCACCACCACCG 61.346 66.667 14.63 4.56 36.38 4.94
1309 1343 0.318360 GTTTGGGTTTTTCTCCGGCG 60.318 55.000 0.00 0.00 0.00 6.46
1436 1494 4.154347 CTCCTCCCAGCGCTCCAC 62.154 72.222 7.13 0.00 0.00 4.02
1439 1497 3.535962 CTCCTCCTCCCAGCGCTC 61.536 72.222 7.13 0.00 0.00 5.03
1443 1501 0.618968 TTCTTCCTCCTCCTCCCAGC 60.619 60.000 0.00 0.00 0.00 4.85
1456 1514 1.746991 CAGCGGCCCTTCTTCTTCC 60.747 63.158 0.00 0.00 0.00 3.46
1471 1529 3.921021 CGGATGAAGATATAACGACCAGC 59.079 47.826 0.00 0.00 0.00 4.85
1477 1535 5.032100 AGACGTCGGATGAAGATATAACG 57.968 43.478 10.46 0.00 35.20 3.18
1480 1538 8.563123 AATTCTAGACGTCGGATGAAGATATA 57.437 34.615 10.46 0.00 0.00 0.86
1481 1539 7.455641 AATTCTAGACGTCGGATGAAGATAT 57.544 36.000 10.46 0.00 0.00 1.63
1482 1540 6.879276 AATTCTAGACGTCGGATGAAGATA 57.121 37.500 10.46 0.00 0.00 1.98
1493 1551 4.676018 GCCAGTCGATTAATTCTAGACGTC 59.324 45.833 7.70 7.70 36.97 4.34
1505 1563 3.358111 TGAAATTGGGCCAGTCGATTA 57.642 42.857 6.23 0.00 0.00 1.75
1526 1584 5.685520 TTTTTGGGTTAGGCTCTGTTTTT 57.314 34.783 0.00 0.00 0.00 1.94
1880 1945 2.099831 GAGATCGCCGTCGTCGTT 59.900 61.111 0.71 0.00 36.96 3.85
2107 2175 3.103911 GCGACGACGTGGTTCCAG 61.104 66.667 4.58 0.00 41.98 3.86
2333 2401 2.787249 CTCGGCTTTGATGCGGTG 59.213 61.111 0.00 0.00 35.27 4.94
2603 2671 0.982852 TCCTTGCCGGTCCTGATCAT 60.983 55.000 1.90 0.00 0.00 2.45
2613 2681 2.280186 GTATCCGCTCCTTGCCGG 60.280 66.667 0.00 0.00 38.78 6.13
2625 2693 2.108362 CGAAGGTGGCCGGTATCC 59.892 66.667 1.90 2.83 0.00 2.59
2782 2856 2.904905 GGCCCCACGTAGCACATA 59.095 61.111 0.00 0.00 0.00 2.29
2863 2937 0.107945 CCTCCTTGAGAAAGCGGGAG 60.108 60.000 0.00 0.00 42.10 4.30
2985 3059 7.111466 AGTAGAGTACTAGGACCAAACAGTAG 58.889 42.308 0.00 0.00 37.23 2.57
3021 3105 7.224557 CCAGTGCAAACTTAAAGCTATTTTTGT 59.775 33.333 0.00 0.00 0.00 2.83
3022 3106 7.437862 TCCAGTGCAAACTTAAAGCTATTTTTG 59.562 33.333 0.00 0.00 0.00 2.44
3027 3112 5.070001 TGTCCAGTGCAAACTTAAAGCTAT 58.930 37.500 0.00 0.00 0.00 2.97
3049 3134 9.608617 GTGATACAATCAAATATTCTCTGCATG 57.391 33.333 0.00 0.00 41.69 4.06
3092 3177 9.826574 ACAGACGCCTATAACATTCTTTAAATA 57.173 29.630 0.00 0.00 0.00 1.40
3093 3178 8.732746 ACAGACGCCTATAACATTCTTTAAAT 57.267 30.769 0.00 0.00 0.00 1.40
3094 3179 8.556213 AACAGACGCCTATAACATTCTTTAAA 57.444 30.769 0.00 0.00 0.00 1.52
3095 3180 8.556213 AAACAGACGCCTATAACATTCTTTAA 57.444 30.769 0.00 0.00 0.00 1.52
3096 3181 8.556213 AAAACAGACGCCTATAACATTCTTTA 57.444 30.769 0.00 0.00 0.00 1.85
3097 3182 7.174253 TGAAAACAGACGCCTATAACATTCTTT 59.826 33.333 0.00 0.00 0.00 2.52
3098 3183 6.653320 TGAAAACAGACGCCTATAACATTCTT 59.347 34.615 0.00 0.00 0.00 2.52
3099 3184 6.170506 TGAAAACAGACGCCTATAACATTCT 58.829 36.000 0.00 0.00 0.00 2.40
3100 3185 6.092259 ACTGAAAACAGACGCCTATAACATTC 59.908 38.462 0.00 0.00 0.00 2.67
3101 3186 5.938125 ACTGAAAACAGACGCCTATAACATT 59.062 36.000 0.00 0.00 0.00 2.71
3102 3187 5.488341 ACTGAAAACAGACGCCTATAACAT 58.512 37.500 0.00 0.00 0.00 2.71
3103 3188 4.890088 ACTGAAAACAGACGCCTATAACA 58.110 39.130 0.00 0.00 0.00 2.41
3104 3189 5.857822 AACTGAAAACAGACGCCTATAAC 57.142 39.130 0.00 0.00 0.00 1.89
3105 3190 6.870971 AAAACTGAAAACAGACGCCTATAA 57.129 33.333 0.00 0.00 0.00 0.98
3106 3191 6.261381 ACAAAAACTGAAAACAGACGCCTATA 59.739 34.615 0.00 0.00 0.00 1.31
3107 3192 5.067283 ACAAAAACTGAAAACAGACGCCTAT 59.933 36.000 0.00 0.00 0.00 2.57
3108 3193 4.396790 ACAAAAACTGAAAACAGACGCCTA 59.603 37.500 0.00 0.00 0.00 3.93
3109 3194 3.192633 ACAAAAACTGAAAACAGACGCCT 59.807 39.130 0.00 0.00 0.00 5.52
3110 3195 3.507786 ACAAAAACTGAAAACAGACGCC 58.492 40.909 0.00 0.00 0.00 5.68
3111 3196 5.565695 TCTACAAAAACTGAAAACAGACGC 58.434 37.500 0.00 0.00 0.00 5.19
3112 3197 7.535940 TGTTTCTACAAAAACTGAAAACAGACG 59.464 33.333 0.00 0.00 39.39 4.18
3113 3198 8.635983 GTGTTTCTACAAAAACTGAAAACAGAC 58.364 33.333 0.00 0.00 39.39 3.51
3114 3199 8.353684 TGTGTTTCTACAAAAACTGAAAACAGA 58.646 29.630 0.00 0.00 39.39 3.41
3115 3200 8.514136 TGTGTTTCTACAAAAACTGAAAACAG 57.486 30.769 0.00 0.00 39.39 3.16
3116 3201 9.134734 GATGTGTTTCTACAAAAACTGAAAACA 57.865 29.630 0.00 0.00 39.39 2.83
3117 3202 9.353999 AGATGTGTTTCTACAAAAACTGAAAAC 57.646 29.630 1.73 0.00 39.39 2.43
3120 3205 9.997482 GTTAGATGTGTTTCTACAAAAACTGAA 57.003 29.630 1.73 0.00 39.39 3.02
3121 3206 9.391006 AGTTAGATGTGTTTCTACAAAAACTGA 57.609 29.630 1.73 0.00 39.39 3.41
3161 3246 9.193133 GCATCGTTGTGTATCTATAACTGTTAT 57.807 33.333 16.51 16.51 0.00 1.89
3162 3247 8.192110 TGCATCGTTGTGTATCTATAACTGTTA 58.808 33.333 2.26 2.26 0.00 2.41
3163 3248 7.039270 TGCATCGTTGTGTATCTATAACTGTT 58.961 34.615 0.00 0.00 0.00 3.16
3164 3249 6.569780 TGCATCGTTGTGTATCTATAACTGT 58.430 36.000 0.00 0.00 0.00 3.55
3165 3250 7.463469 TTGCATCGTTGTGTATCTATAACTG 57.537 36.000 0.00 0.00 0.00 3.16
3166 3251 9.411801 CTATTGCATCGTTGTGTATCTATAACT 57.588 33.333 0.00 0.00 0.00 2.24
3167 3252 9.406828 TCTATTGCATCGTTGTGTATCTATAAC 57.593 33.333 0.00 0.00 0.00 1.89
3168 3253 9.626045 CTCTATTGCATCGTTGTGTATCTATAA 57.374 33.333 0.00 0.00 0.00 0.98
3169 3254 8.244113 CCTCTATTGCATCGTTGTGTATCTATA 58.756 37.037 0.00 0.00 0.00 1.31
3170 3255 7.093354 CCTCTATTGCATCGTTGTGTATCTAT 58.907 38.462 0.00 0.00 0.00 1.98
3171 3256 6.447162 CCTCTATTGCATCGTTGTGTATCTA 58.553 40.000 0.00 0.00 0.00 1.98
3172 3257 5.292765 CCTCTATTGCATCGTTGTGTATCT 58.707 41.667 0.00 0.00 0.00 1.98
3173 3258 4.084328 GCCTCTATTGCATCGTTGTGTATC 60.084 45.833 0.00 0.00 0.00 2.24
3174 3259 3.809832 GCCTCTATTGCATCGTTGTGTAT 59.190 43.478 0.00 0.00 0.00 2.29
3175 3260 3.194861 GCCTCTATTGCATCGTTGTGTA 58.805 45.455 0.00 0.00 0.00 2.90
3176 3261 2.009774 GCCTCTATTGCATCGTTGTGT 58.990 47.619 0.00 0.00 0.00 3.72
3177 3262 2.009051 TGCCTCTATTGCATCGTTGTG 58.991 47.619 0.00 0.00 32.85 3.33
3178 3263 2.401583 TGCCTCTATTGCATCGTTGT 57.598 45.000 0.00 0.00 32.85 3.32
3179 3264 2.874086 TCATGCCTCTATTGCATCGTTG 59.126 45.455 0.00 0.00 46.04 4.10
3180 3265 2.874701 GTCATGCCTCTATTGCATCGTT 59.125 45.455 0.00 0.00 46.04 3.85
3181 3266 2.103771 AGTCATGCCTCTATTGCATCGT 59.896 45.455 0.00 0.00 46.04 3.73
3182 3267 2.735663 GAGTCATGCCTCTATTGCATCG 59.264 50.000 0.00 0.00 46.04 3.84
3183 3268 3.736720 TGAGTCATGCCTCTATTGCATC 58.263 45.455 5.22 0.00 46.04 3.91
3185 3270 3.273434 GTTGAGTCATGCCTCTATTGCA 58.727 45.455 5.22 0.00 43.97 4.08
3186 3271 3.273434 TGTTGAGTCATGCCTCTATTGC 58.727 45.455 5.22 0.00 32.50 3.56
3187 3272 5.181811 TGTTTGTTGAGTCATGCCTCTATTG 59.818 40.000 5.22 0.00 32.50 1.90
3188 3273 5.316167 TGTTTGTTGAGTCATGCCTCTATT 58.684 37.500 5.22 0.00 32.50 1.73
3189 3274 4.910195 TGTTTGTTGAGTCATGCCTCTAT 58.090 39.130 5.22 0.00 32.50 1.98
3190 3275 4.350368 TGTTTGTTGAGTCATGCCTCTA 57.650 40.909 5.22 0.00 32.50 2.43
3191 3276 3.213206 TGTTTGTTGAGTCATGCCTCT 57.787 42.857 5.22 0.00 32.50 3.69
3192 3277 3.550842 GGTTGTTTGTTGAGTCATGCCTC 60.551 47.826 0.00 0.00 0.00 4.70
3193 3278 2.362077 GGTTGTTTGTTGAGTCATGCCT 59.638 45.455 0.00 0.00 0.00 4.75
3194 3279 2.362077 AGGTTGTTTGTTGAGTCATGCC 59.638 45.455 0.00 0.00 0.00 4.40
3195 3280 3.715628 AGGTTGTTTGTTGAGTCATGC 57.284 42.857 0.00 0.00 0.00 4.06
3196 3281 6.483307 TCTTCTAGGTTGTTTGTTGAGTCATG 59.517 38.462 0.00 0.00 0.00 3.07
3197 3282 6.483640 GTCTTCTAGGTTGTTTGTTGAGTCAT 59.516 38.462 0.00 0.00 0.00 3.06
3198 3283 5.815740 GTCTTCTAGGTTGTTTGTTGAGTCA 59.184 40.000 0.00 0.00 0.00 3.41
3199 3284 5.815740 TGTCTTCTAGGTTGTTTGTTGAGTC 59.184 40.000 0.00 0.00 0.00 3.36
3200 3285 5.585047 GTGTCTTCTAGGTTGTTTGTTGAGT 59.415 40.000 0.00 0.00 0.00 3.41
3201 3286 5.584649 TGTGTCTTCTAGGTTGTTTGTTGAG 59.415 40.000 0.00 0.00 0.00 3.02
3202 3287 5.492895 TGTGTCTTCTAGGTTGTTTGTTGA 58.507 37.500 0.00 0.00 0.00 3.18
3203 3288 5.811399 TGTGTCTTCTAGGTTGTTTGTTG 57.189 39.130 0.00 0.00 0.00 3.33
3204 3289 5.163794 CGTTGTGTCTTCTAGGTTGTTTGTT 60.164 40.000 0.00 0.00 0.00 2.83
3205 3290 4.331717 CGTTGTGTCTTCTAGGTTGTTTGT 59.668 41.667 0.00 0.00 0.00 2.83
3206 3291 4.785341 GCGTTGTGTCTTCTAGGTTGTTTG 60.785 45.833 0.00 0.00 0.00 2.93
3207 3292 3.311596 GCGTTGTGTCTTCTAGGTTGTTT 59.688 43.478 0.00 0.00 0.00 2.83
3208 3293 2.870411 GCGTTGTGTCTTCTAGGTTGTT 59.130 45.455 0.00 0.00 0.00 2.83
3209 3294 2.480845 GCGTTGTGTCTTCTAGGTTGT 58.519 47.619 0.00 0.00 0.00 3.32
3210 3295 1.798813 GGCGTTGTGTCTTCTAGGTTG 59.201 52.381 0.00 0.00 0.00 3.77
3211 3296 1.270678 GGGCGTTGTGTCTTCTAGGTT 60.271 52.381 0.00 0.00 0.00 3.50
3212 3297 0.320697 GGGCGTTGTGTCTTCTAGGT 59.679 55.000 0.00 0.00 0.00 3.08
3213 3298 0.736325 CGGGCGTTGTGTCTTCTAGG 60.736 60.000 0.00 0.00 0.00 3.02
3214 3299 1.352156 GCGGGCGTTGTGTCTTCTAG 61.352 60.000 0.00 0.00 0.00 2.43
3215 3300 1.373748 GCGGGCGTTGTGTCTTCTA 60.374 57.895 0.00 0.00 0.00 2.10
3216 3301 2.665185 GCGGGCGTTGTGTCTTCT 60.665 61.111 0.00 0.00 0.00 2.85
3217 3302 2.954753 CTGCGGGCGTTGTGTCTTC 61.955 63.158 0.00 0.00 0.00 2.87
3218 3303 2.933878 TTCTGCGGGCGTTGTGTCTT 62.934 55.000 0.00 0.00 0.00 3.01
3219 3304 3.454587 TTCTGCGGGCGTTGTGTCT 62.455 57.895 0.00 0.00 0.00 3.41
3220 3305 2.954753 CTTCTGCGGGCGTTGTGTC 61.955 63.158 0.00 0.00 0.00 3.67
3221 3306 2.972505 CTTCTGCGGGCGTTGTGT 60.973 61.111 0.00 0.00 0.00 3.72
3222 3307 4.389576 GCTTCTGCGGGCGTTGTG 62.390 66.667 0.00 0.00 0.00 3.33
3223 3308 4.626081 AGCTTCTGCGGGCGTTGT 62.626 61.111 0.00 0.00 45.42 3.32
3224 3309 4.093952 CAGCTTCTGCGGGCGTTG 62.094 66.667 0.00 0.00 45.42 4.10
3230 3315 1.734465 CTACTTTTCCAGCTTCTGCGG 59.266 52.381 0.00 0.00 45.42 5.69
3231 3316 1.734465 CCTACTTTTCCAGCTTCTGCG 59.266 52.381 0.00 0.00 45.42 5.18
3232 3317 3.059352 TCCTACTTTTCCAGCTTCTGC 57.941 47.619 0.00 0.00 40.05 4.26
3233 3318 4.836825 TGATCCTACTTTTCCAGCTTCTG 58.163 43.478 0.00 0.00 0.00 3.02
3234 3319 4.780021 TCTGATCCTACTTTTCCAGCTTCT 59.220 41.667 0.00 0.00 0.00 2.85
3235 3320 5.091261 TCTGATCCTACTTTTCCAGCTTC 57.909 43.478 0.00 0.00 0.00 3.86
3236 3321 5.679601 GATCTGATCCTACTTTTCCAGCTT 58.320 41.667 6.37 0.00 0.00 3.74
3237 3322 4.202202 CGATCTGATCCTACTTTTCCAGCT 60.202 45.833 11.84 0.00 0.00 4.24
3238 3323 4.054671 CGATCTGATCCTACTTTTCCAGC 58.945 47.826 11.84 0.00 0.00 4.85
3239 3324 4.054671 GCGATCTGATCCTACTTTTCCAG 58.945 47.826 11.84 0.00 0.00 3.86
3240 3325 3.450817 TGCGATCTGATCCTACTTTTCCA 59.549 43.478 11.84 0.00 0.00 3.53
3462 3564 0.250901 GCAAAAGCCTCTCCTGACCA 60.251 55.000 0.00 0.00 0.00 4.02
3470 3572 0.398318 AGACGAAGGCAAAAGCCTCT 59.602 50.000 9.77 0.00 39.63 3.69
3634 3736 3.415212 AGAAGAACAGCAGCAGCAAATA 58.585 40.909 3.17 0.00 45.49 1.40
3717 3819 1.064906 TCATCCGACCGGTCTAGAACT 60.065 52.381 30.92 11.67 36.47 3.01
3720 3822 0.545171 AGTCATCCGACCGGTCTAGA 59.455 55.000 30.92 26.07 43.73 2.43
3723 3825 2.113433 CGAGTCATCCGACCGGTCT 61.113 63.158 30.92 11.62 43.73 3.85
3892 3994 2.362736 GCAAGCAGGTCATCATCTTCA 58.637 47.619 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.