Multiple sequence alignment - TraesCS2B01G131400

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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 TraesCS2B01G131400 chr2B 100.000 2969 0 0 1 2969 98287964 98284996 0.000000e+00 5483.0
1 TraesCS2B01G131400 chr2B 81.057 1457 191 58 1163 2590 98264701 98263301 0.000000e+00 1083.0
2 TraesCS2B01G131400 chr2B 95.792 499 19 2 1 498 444270593 444270096 0.000000e+00 804.0
3 TraesCS2B01G131400 chr2B 73.789 805 124 60 1179 1973 97933875 97933148 1.380000e-58 237.0
4 TraesCS2B01G131400 chr2B 86.364 198 19 5 1164 1360 98257069 98256879 3.000000e-50 209.0
5 TraesCS2B01G131400 chr2B 78.994 338 33 22 612 911 98265136 98264799 2.330000e-46 196.0
6 TraesCS2B01G131400 chr2B 89.231 130 4 6 1034 1163 98286886 98286767 1.430000e-33 154.0
7 TraesCS2B01G131400 chr2B 89.231 130 4 6 1079 1198 98286931 98286802 1.430000e-33 154.0
8 TraesCS2B01G131400 chr2B 90.099 101 10 0 1876 1976 98256325 98256225 6.680000e-27 132.0
9 TraesCS2B01G131400 chr2A 87.422 2568 150 72 493 2968 63611920 63609434 0.000000e+00 2793.0
10 TraesCS2B01G131400 chr2A 81.738 1473 175 62 1164 2596 63607276 63605858 0.000000e+00 1144.0
11 TraesCS2B01G131400 chr2A 79.618 314 50 14 1664 1972 63588551 63588247 2.320000e-51 213.0
12 TraesCS2B01G131400 chr2A 76.355 406 70 17 1164 1560 63589020 63588632 8.400000e-46 195.0
13 TraesCS2B01G131400 chr2A 81.281 203 18 12 1161 1359 63138215 63138029 2.380000e-31 147.0
14 TraesCS2B01G131400 chr2A 82.192 146 24 2 1645 1789 63137796 63137652 1.120000e-24 124.0
15 TraesCS2B01G131400 chr2A 88.119 101 12 0 1873 1973 63137584 63137484 1.450000e-23 121.0
16 TraesCS2B01G131400 chr2A 89.474 57 5 1 2152 2207 628780966 628780910 1.480000e-08 71.3
17 TraesCS2B01G131400 chr2D 89.883 1878 89 38 491 2328 62565799 62563983 0.000000e+00 2322.0
18 TraesCS2B01G131400 chr2D 80.626 831 99 37 1645 2461 62559279 62558497 1.190000e-163 586.0
19 TraesCS2B01G131400 chr2D 86.520 408 33 10 1163 1560 62559817 62559422 2.110000e-116 429.0
20 TraesCS2B01G131400 chr2D 84.733 393 39 7 2585 2968 62563686 62563306 1.000000e-99 374.0
21 TraesCS2B01G131400 chr2D 90.079 252 13 6 2439 2690 62563925 62563686 1.720000e-82 316.0
22 TraesCS2B01G131400 chr2D 87.591 274 29 5 2657 2927 62558473 62558202 2.220000e-81 313.0
23 TraesCS2B01G131400 chr2D 78.242 455 48 31 628 1042 62560255 62559812 8.220000e-61 244.0
24 TraesCS2B01G131400 chr2D 76.471 425 65 24 1164 1578 62553321 62552922 6.490000e-47 198.0
25 TraesCS2B01G131400 chr2D 77.070 314 44 19 1664 1973 62289432 62289143 3.960000e-34 156.0
26 TraesCS2B01G131400 chr2D 100.000 44 0 0 1129 1172 62565250 62565207 6.820000e-12 82.4
27 TraesCS2B01G131400 chr2D 97.297 37 0 1 2759 2794 62563613 62563577 8.890000e-06 62.1
28 TraesCS2B01G131400 chr7B 96.607 501 15 2 1 500 377466149 377465650 0.000000e+00 830.0
29 TraesCS2B01G131400 chr3B 97.342 489 12 1 1 489 404594119 404593632 0.000000e+00 830.0
30 TraesCS2B01G131400 chr3B 95.792 499 19 2 1 498 509274319 509273822 0.000000e+00 804.0
31 TraesCS2B01G131400 chr5B 96.939 490 13 2 1 490 188443797 188444284 0.000000e+00 821.0
32 TraesCS2B01G131400 chr3A 96.192 499 16 3 1 498 281431171 281431667 0.000000e+00 813.0
33 TraesCS2B01G131400 chr3A 95.918 49 2 0 2150 2198 549639149 549639101 2.450000e-11 80.5
34 TraesCS2B01G131400 chr6A 95.609 501 21 1 1 500 485258244 485257744 0.000000e+00 802.0
35 TraesCS2B01G131400 chr4B 94.605 519 22 5 1 517 639092342 639091828 0.000000e+00 798.0
36 TraesCS2B01G131400 chr1B 95.248 505 22 2 1 505 172609038 172608536 0.000000e+00 798.0
37 TraesCS2B01G131400 chr5A 97.917 48 1 0 2150 2197 21446694 21446741 1.900000e-12 84.2
38 TraesCS2B01G131400 chr5A 87.879 66 4 4 2152 2215 44801101 44801164 1.140000e-09 75.0
39 TraesCS2B01G131400 chr6D 96.000 50 2 0 2143 2192 24554584 24554633 6.820000e-12 82.4
40 TraesCS2B01G131400 chr5D 97.872 47 1 0 2152 2198 361646174 361646128 6.820000e-12 82.4
41 TraesCS2B01G131400 chr5D 96.000 50 1 1 2146 2195 537737413 537737365 2.450000e-11 80.5
42 TraesCS2B01G131400 chr5D 97.826 46 1 0 2150 2195 542716709 542716754 2.450000e-11 80.5
43 TraesCS2B01G131400 chr3D 88.710 62 5 2 2152 2212 349635511 349635451 1.140000e-09 75.0


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 TraesCS2B01G131400 chr2B 98284996 98287964 2968 True 1930.333333 5483 92.820667 1 2969 3 chr2B.!!$R5 2968
1 TraesCS2B01G131400 chr2B 98263301 98265136 1835 True 639.500000 1083 80.025500 612 2590 2 chr2B.!!$R4 1978
2 TraesCS2B01G131400 chr2B 97933148 97933875 727 True 237.000000 237 73.789000 1179 1973 1 chr2B.!!$R1 794
3 TraesCS2B01G131400 chr2A 63605858 63611920 6062 True 1968.500000 2793 84.580000 493 2968 2 chr2A.!!$R4 2475
4 TraesCS2B01G131400 chr2A 63588247 63589020 773 True 204.000000 213 77.986500 1164 1972 2 chr2A.!!$R3 808
5 TraesCS2B01G131400 chr2D 62558202 62565799 7597 True 525.388889 2322 88.330111 491 2968 9 chr2D.!!$R3 2477
6 TraesCS2B01G131400 chr6A 485257744 485258244 500 True 802.000000 802 95.609000 1 500 1 chr6A.!!$R1 499
7 TraesCS2B01G131400 chr4B 639091828 639092342 514 True 798.000000 798 94.605000 1 517 1 chr4B.!!$R1 516
8 TraesCS2B01G131400 chr1B 172608536 172609038 502 True 798.000000 798 95.248000 1 505 1 chr1B.!!$R1 504

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
701 704 0.030504 CAAATCAGCACGCACCAACA 59.969 50.0 0.0 0.0 0.0 3.33 F
1084 1162 0.036577 CAGGAGCAAGACAGTGGAGG 60.037 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 7636 0.036388 TGGCGATCAGTTCTTGGACC 60.036 55.0 0.00 0.0 0.00 4.46 R
1977 7662 0.179121 CGATCGATCCAACACCGGAA 60.179 55.0 19.51 0.0 38.95 4.30 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
150 151 8.006298 TGTTCAGAAAACATCACCTACATTTT 57.994 30.769 0.00 0.00 0.00 1.82
245 246 6.767524 TTACCTCGGGTAGTTTAAACGATA 57.232 37.500 12.54 0.00 39.52 2.92
437 438 3.060602 ACTGAGCAAGCTCGAAAAGTAC 58.939 45.455 16.45 0.00 45.48 2.73
553 556 5.220529 GCAAATCTCATAAAAGTTGCCATGC 60.221 40.000 0.00 0.00 36.27 4.06
559 562 2.083167 AAAAGTTGCCATGCCGATTG 57.917 45.000 0.00 0.00 0.00 2.67
701 704 0.030504 CAAATCAGCACGCACCAACA 59.969 50.000 0.00 0.00 0.00 3.33
807 819 4.031129 CAGCCCTGGCAGCTCTGT 62.031 66.667 19.61 0.00 44.88 3.41
808 820 3.715097 AGCCCTGGCAGCTCTGTC 61.715 66.667 9.56 0.00 44.88 3.51
809 821 3.715097 GCCCTGGCAGCTCTGTCT 61.715 66.667 9.56 0.00 41.49 3.41
832 844 1.974343 GGTAACCGGCCACATGCAA 60.974 57.895 0.00 0.00 43.89 4.08
833 845 1.506262 GTAACCGGCCACATGCAAG 59.494 57.895 0.00 0.00 43.89 4.01
856 869 2.738521 CTCCCGTTCACCAGCGTG 60.739 66.667 0.00 0.00 41.72 5.34
878 891 2.357517 CCACTCTCACGCCCACAC 60.358 66.667 0.00 0.00 0.00 3.82
928 942 2.230994 CTGCCCGCAGACTTGAGCTA 62.231 60.000 11.32 0.00 46.30 3.32
984 999 3.250744 TCAGTCAGTTTTAATCCTCGCG 58.749 45.455 0.00 0.00 0.00 5.87
1053 1131 3.827898 GAGGCGAGTCCGGTGGAG 61.828 72.222 0.00 0.00 40.77 3.86
1056 1134 4.436998 GCGAGTCCGGTGGAGGTG 62.437 72.222 0.00 0.00 36.06 4.00
1057 1135 3.760035 CGAGTCCGGTGGAGGTGG 61.760 72.222 0.00 0.00 29.39 4.61
1058 1136 2.283676 GAGTCCGGTGGAGGTGGA 60.284 66.667 0.00 0.00 29.39 4.02
1059 1137 2.283966 AGTCCGGTGGAGGTGGAG 60.284 66.667 0.00 0.00 31.04 3.86
1060 1138 3.391382 GTCCGGTGGAGGTGGAGG 61.391 72.222 0.00 0.00 31.04 4.30
1061 1139 3.596799 TCCGGTGGAGGTGGAGGA 61.597 66.667 0.00 0.00 0.00 3.71
1062 1140 3.077556 CCGGTGGAGGTGGAGGAG 61.078 72.222 0.00 0.00 0.00 3.69
1063 1141 3.077556 CGGTGGAGGTGGAGGAGG 61.078 72.222 0.00 0.00 0.00 4.30
1064 1142 2.689034 GGTGGAGGTGGAGGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
1065 1143 3.403558 GTGGAGGTGGAGGAGGGC 61.404 72.222 0.00 0.00 0.00 5.19
1066 1144 3.940480 TGGAGGTGGAGGAGGGCA 61.940 66.667 0.00 0.00 0.00 5.36
1067 1145 3.086600 GGAGGTGGAGGAGGGCAG 61.087 72.222 0.00 0.00 0.00 4.85
1068 1146 3.086600 GAGGTGGAGGAGGGCAGG 61.087 72.222 0.00 0.00 0.00 4.85
1069 1147 3.615811 AGGTGGAGGAGGGCAGGA 61.616 66.667 0.00 0.00 0.00 3.86
1070 1148 3.086600 GGTGGAGGAGGGCAGGAG 61.087 72.222 0.00 0.00 0.00 3.69
1071 1149 3.791586 GTGGAGGAGGGCAGGAGC 61.792 72.222 0.00 0.00 41.10 4.70
1072 1150 4.337304 TGGAGGAGGGCAGGAGCA 62.337 66.667 0.00 0.00 44.61 4.26
1073 1151 3.011517 GGAGGAGGGCAGGAGCAA 61.012 66.667 0.00 0.00 44.61 3.91
1074 1152 2.588989 GAGGAGGGCAGGAGCAAG 59.411 66.667 0.00 0.00 44.61 4.01
1075 1153 1.992277 GAGGAGGGCAGGAGCAAGA 60.992 63.158 0.00 0.00 44.61 3.02
1076 1154 2.250741 GAGGAGGGCAGGAGCAAGAC 62.251 65.000 0.00 0.00 44.61 3.01
1077 1155 2.596851 GGAGGGCAGGAGCAAGACA 61.597 63.158 0.00 0.00 44.61 3.41
1078 1156 1.078567 GAGGGCAGGAGCAAGACAG 60.079 63.158 0.00 0.00 44.61 3.51
1079 1157 1.835927 GAGGGCAGGAGCAAGACAGT 61.836 60.000 0.00 0.00 44.61 3.55
1080 1158 1.673665 GGGCAGGAGCAAGACAGTG 60.674 63.158 0.00 0.00 44.61 3.66
1081 1159 1.673665 GGCAGGAGCAAGACAGTGG 60.674 63.158 0.00 0.00 44.61 4.00
1082 1160 1.372683 GCAGGAGCAAGACAGTGGA 59.627 57.895 0.00 0.00 41.58 4.02
1083 1161 0.673022 GCAGGAGCAAGACAGTGGAG 60.673 60.000 0.00 0.00 41.58 3.86
1084 1162 0.036577 CAGGAGCAAGACAGTGGAGG 60.037 60.000 0.00 0.00 0.00 4.30
1085 1163 1.376553 GGAGCAAGACAGTGGAGGC 60.377 63.158 0.00 0.00 0.00 4.70
1086 1164 1.739562 GAGCAAGACAGTGGAGGCG 60.740 63.158 0.00 0.00 0.00 5.52
1087 1165 2.159819 GAGCAAGACAGTGGAGGCGA 62.160 60.000 0.00 0.00 0.00 5.54
1088 1166 1.739562 GCAAGACAGTGGAGGCGAG 60.740 63.158 0.00 0.00 0.00 5.03
1089 1167 1.668294 CAAGACAGTGGAGGCGAGT 59.332 57.895 0.00 0.00 0.00 4.18
1090 1168 0.389166 CAAGACAGTGGAGGCGAGTC 60.389 60.000 0.00 0.00 0.00 3.36
1091 1169 1.536943 AAGACAGTGGAGGCGAGTCC 61.537 60.000 0.00 0.00 37.10 3.85
1221 6804 4.994201 GTGGACGACAGCGACGCA 62.994 66.667 23.70 0.00 41.64 5.24
1306 6889 2.432628 CGGTGGAGCTCGTTGTCC 60.433 66.667 7.83 4.61 0.00 4.02
1331 6914 4.351054 CAAGCCGCCCACTTCCCT 62.351 66.667 0.00 0.00 0.00 4.20
1340 6923 2.342279 CACTTCCCTCGCCGTCAA 59.658 61.111 0.00 0.00 0.00 3.18
1400 7000 2.409975 TCATCGTTTCGTCCTTTGGTC 58.590 47.619 0.00 0.00 0.00 4.02
1402 7002 1.860676 TCGTTTCGTCCTTTGGTCTG 58.139 50.000 0.00 0.00 0.00 3.51
1404 7004 1.539496 CGTTTCGTCCTTTGGTCTGGA 60.539 52.381 0.00 0.00 0.00 3.86
1405 7005 1.871676 GTTTCGTCCTTTGGTCTGGAC 59.128 52.381 0.00 0.00 46.69 4.02
1435 7035 1.069204 AGCAAAGCTCTGTCGACTGAA 59.931 47.619 23.09 9.70 30.62 3.02
1460 7070 1.134694 GGATTCGTTTCAGGCGTGC 59.865 57.895 0.35 0.00 0.00 5.34
1488 7098 0.838987 GTGGTGGGGTTAGTGGAGGA 60.839 60.000 0.00 0.00 0.00 3.71
1560 7170 3.744941 CCGCCAACTCGGTAACATA 57.255 52.632 0.00 0.00 44.18 2.29
1561 7171 2.012937 CCGCCAACTCGGTAACATAA 57.987 50.000 0.00 0.00 44.18 1.90
1562 7172 1.662122 CCGCCAACTCGGTAACATAAC 59.338 52.381 0.00 0.00 44.18 1.89
1563 7173 2.339418 CGCCAACTCGGTAACATAACA 58.661 47.619 0.00 0.00 36.97 2.41
1564 7174 2.933906 CGCCAACTCGGTAACATAACAT 59.066 45.455 0.00 0.00 36.97 2.71
1565 7175 3.000925 CGCCAACTCGGTAACATAACATC 59.999 47.826 0.00 0.00 36.97 3.06
1566 7176 3.311596 GCCAACTCGGTAACATAACATCC 59.688 47.826 0.00 0.00 36.97 3.51
1567 7177 4.509616 CCAACTCGGTAACATAACATCCA 58.490 43.478 0.00 0.00 0.00 3.41
1568 7178 4.331717 CCAACTCGGTAACATAACATCCAC 59.668 45.833 0.00 0.00 0.00 4.02
1569 7179 5.175859 CAACTCGGTAACATAACATCCACT 58.824 41.667 0.00 0.00 0.00 4.00
1570 7180 6.334989 CAACTCGGTAACATAACATCCACTA 58.665 40.000 0.00 0.00 0.00 2.74
1571 7181 5.899299 ACTCGGTAACATAACATCCACTAC 58.101 41.667 0.00 0.00 0.00 2.73
1573 7183 4.710865 TCGGTAACATAACATCCACTACCA 59.289 41.667 0.00 0.00 0.00 3.25
1578 7197 6.374417 AACATAACATCCACTACCAACTCT 57.626 37.500 0.00 0.00 0.00 3.24
1610 7238 4.582869 GCATTGCTCCATGGACAGATATA 58.417 43.478 11.44 0.00 0.00 0.86
1618 7246 6.380846 GCTCCATGGACAGATATAGAGAAGAT 59.619 42.308 11.44 0.00 0.00 2.40
1620 7248 9.645128 CTCCATGGACAGATATAGAGAAGATAT 57.355 37.037 11.44 0.00 0.00 1.63
1628 7256 9.706529 ACAGATATAGAGAAGATATACATGCCA 57.293 33.333 0.00 0.00 0.00 4.92
1633 7261 8.780616 ATAGAGAAGATATACATGCCATAGCT 57.219 34.615 0.00 0.00 40.80 3.32
1634 7262 6.876155 AGAGAAGATATACATGCCATAGCTG 58.124 40.000 0.00 0.00 40.80 4.24
1636 7264 7.617329 AGAGAAGATATACATGCCATAGCTGTA 59.383 37.037 0.00 0.00 40.80 2.74
1637 7265 7.551585 AGAAGATATACATGCCATAGCTGTAC 58.448 38.462 0.00 0.00 40.80 2.90
1638 7266 5.895928 AGATATACATGCCATAGCTGTACG 58.104 41.667 0.00 0.00 40.80 3.67
1639 7267 5.419155 AGATATACATGCCATAGCTGTACGT 59.581 40.000 0.00 0.00 40.80 3.57
1640 7268 6.602009 AGATATACATGCCATAGCTGTACGTA 59.398 38.462 0.00 0.00 40.80 3.57
1659 7337 3.000078 CGTAACTTGTGCTGCTTATACGG 60.000 47.826 0.00 0.00 33.30 4.02
1799 7477 3.950395 CCATCAGGAGGTCCTTGATTTTC 59.050 47.826 3.63 0.00 46.09 2.29
1801 7479 4.559862 TCAGGAGGTCCTTGATTTTCTC 57.440 45.455 0.00 0.00 46.09 2.87
1824 7502 1.005037 CCTGCAGTGTACGCCTTCA 60.005 57.895 13.81 0.00 0.00 3.02
1848 7526 2.673368 GCGAGACTGAAACTAATGGTGG 59.327 50.000 0.00 0.00 0.00 4.61
1850 7528 3.617531 CGAGACTGAAACTAATGGTGGCT 60.618 47.826 0.00 0.00 0.00 4.75
1852 7530 3.073062 AGACTGAAACTAATGGTGGCTGT 59.927 43.478 0.00 0.00 0.00 4.40
1855 7533 3.674997 TGAAACTAATGGTGGCTGTCTC 58.325 45.455 0.00 0.00 0.00 3.36
1862 7541 0.681733 TGGTGGCTGTCTCTTGTCTC 59.318 55.000 0.00 0.00 0.00 3.36
1936 7617 4.363990 ACGCGGACTGCTCTGTGG 62.364 66.667 12.47 0.00 43.27 4.17
1954 7635 1.503542 GTGATTGTCAAGCAGCCCG 59.496 57.895 3.20 0.00 0.00 6.13
1955 7636 1.675310 TGATTGTCAAGCAGCCCGG 60.675 57.895 0.00 0.00 0.00 5.73
1977 7662 2.749621 GTCCAAGAACTGATCGCCATTT 59.250 45.455 0.00 0.00 0.00 2.32
1987 7672 0.525761 ATCGCCATTTTCCGGTGTTG 59.474 50.000 0.00 0.00 35.45 3.33
2052 7741 3.305403 CGTGCCTACACTATGTATCCCTG 60.305 52.174 0.00 0.00 45.10 4.45
2054 7743 2.028020 GCCTACACTATGTATCCCTGCC 60.028 54.545 0.00 0.00 31.66 4.85
2055 7744 3.511477 CCTACACTATGTATCCCTGCCT 58.489 50.000 0.00 0.00 31.66 4.75
2057 7746 5.084519 CCTACACTATGTATCCCTGCCTAA 58.915 45.833 0.00 0.00 31.66 2.69
2066 7755 9.388506 CTATGTATCCCTGCCTAATTATTTCTG 57.611 37.037 0.00 0.00 0.00 3.02
2073 7762 5.221126 CCTGCCTAATTATTTCTGCTCCAAC 60.221 44.000 0.00 0.00 0.00 3.77
2074 7763 4.644685 TGCCTAATTATTTCTGCTCCAACC 59.355 41.667 0.00 0.00 0.00 3.77
2075 7764 4.261197 GCCTAATTATTTCTGCTCCAACCG 60.261 45.833 0.00 0.00 0.00 4.44
2081 7770 2.851263 TTCTGCTCCAACCGTTGTAT 57.149 45.000 10.34 0.00 0.00 2.29
2087 7777 2.930682 GCTCCAACCGTTGTATTCTCTC 59.069 50.000 10.34 0.00 0.00 3.20
2089 7779 4.177026 CTCCAACCGTTGTATTCTCTCTG 58.823 47.826 10.34 0.00 0.00 3.35
2103 7793 8.749354 TGTATTCTCTCTGTTATTTACTCTGCA 58.251 33.333 0.00 0.00 0.00 4.41
2104 7794 9.757227 GTATTCTCTCTGTTATTTACTCTGCAT 57.243 33.333 0.00 0.00 0.00 3.96
2123 7813 4.038042 TGCATAATACTAGCAGTCGAGCTT 59.962 41.667 4.33 0.00 43.70 3.74
2137 7828 6.430451 CAGTCGAGCTTTGTAAACTTTGATT 58.570 36.000 0.00 0.00 0.00 2.57
2200 7891 8.247666 AGTTTACAGAGGGAGTACAATATACC 57.752 38.462 0.00 0.00 0.00 2.73
2201 7892 7.289549 AGTTTACAGAGGGAGTACAATATACCC 59.710 40.741 0.00 0.00 40.71 3.69
2208 7899 5.013183 AGGGAGTACAATATACCCAATCAGC 59.987 44.000 0.00 0.00 42.62 4.26
2211 7902 6.247229 AGTACAATATACCCAATCAGCACA 57.753 37.500 0.00 0.00 0.00 4.57
2212 7903 6.658849 AGTACAATATACCCAATCAGCACAA 58.341 36.000 0.00 0.00 0.00 3.33
2223 7914 5.688621 CCCAATCAGCACAATAAATTCATCG 59.311 40.000 0.00 0.00 0.00 3.84
2232 7923 9.289303 AGCACAATAAATTCATCGTTGAAATAC 57.711 29.630 12.62 0.00 44.70 1.89
2263 7959 9.378551 TCACATTAAATAGACTTGCTTTCGTAT 57.621 29.630 0.00 0.00 0.00 3.06
2268 7964 7.447243 AAATAGACTTGCTTTCGTATACGTC 57.553 36.000 23.67 11.86 40.80 4.34
2280 7976 7.585286 TTTCGTATACGTCTGTATTGCTTTT 57.415 32.000 23.67 0.00 41.50 2.27
2324 8020 9.917129 TTTATATTGTTTGACTTACGACAGAGA 57.083 29.630 0.00 0.00 0.00 3.10
2352 8053 8.687824 ATATGCAAAGTAAATGAAACGGAAAG 57.312 30.769 0.00 0.00 0.00 2.62
2354 8055 6.565234 TGCAAAGTAAATGAAACGGAAAGAA 58.435 32.000 0.00 0.00 0.00 2.52
2356 8057 7.168972 TGCAAAGTAAATGAAACGGAAAGAATG 59.831 33.333 0.00 0.00 0.00 2.67
2369 8070 2.645838 AAGAATGCTATCGGTGCCAT 57.354 45.000 0.00 0.00 0.00 4.40
2377 8078 3.244526 TGCTATCGGTGCCATACATGATT 60.245 43.478 0.00 0.00 31.15 2.57
2381 8082 3.884895 TCGGTGCCATACATGATTCTTT 58.115 40.909 0.00 0.00 0.00 2.52
2384 8085 3.068590 GGTGCCATACATGATTCTTTGGG 59.931 47.826 0.00 0.00 0.00 4.12
2393 8094 4.463891 ACATGATTCTTTGGGTGTTCATCC 59.536 41.667 0.00 0.00 0.00 3.51
2424 8126 4.403432 TCATCATCAATTTGCCCTTCTTCC 59.597 41.667 0.00 0.00 0.00 3.46
2432 8134 1.734655 TGCCCTTCTTCCAGAGACTT 58.265 50.000 0.00 0.00 33.02 3.01
2437 8139 3.055747 CCCTTCTTCCAGAGACTTACCAC 60.056 52.174 0.00 0.00 33.02 4.16
2445 8147 4.220821 TCCAGAGACTTACCACTCAATGAC 59.779 45.833 0.00 0.00 35.83 3.06
2462 8164 0.955919 GACCCCTCTCCTTTGTTGCG 60.956 60.000 0.00 0.00 0.00 4.85
2471 8173 5.507315 CCTCTCCTTTGTTGCGTTTTTATGT 60.507 40.000 0.00 0.00 0.00 2.29
2475 8177 7.806014 TCTCCTTTGTTGCGTTTTTATGTAATC 59.194 33.333 0.00 0.00 0.00 1.75
2476 8178 6.579292 TCCTTTGTTGCGTTTTTATGTAATCG 59.421 34.615 0.00 0.00 0.00 3.34
2480 8182 7.681125 TGTTGCGTTTTTATGTAATCGTTTT 57.319 28.000 0.00 0.00 0.00 2.43
2501 8203 6.959639 TTTGTTTCTAGTGGATCTGCTTTT 57.040 33.333 0.00 0.00 0.00 2.27
2505 8207 3.002791 TCTAGTGGATCTGCTTTTTGCG 58.997 45.455 0.00 0.00 46.63 4.85
2508 8210 1.537202 GTGGATCTGCTTTTTGCGTCT 59.463 47.619 0.00 0.00 46.63 4.18
2511 8213 3.188460 TGGATCTGCTTTTTGCGTCTAAC 59.812 43.478 0.00 0.00 46.63 2.34
2513 8215 2.206750 TCTGCTTTTTGCGTCTAACGT 58.793 42.857 1.14 0.00 44.73 3.99
2526 8228 2.662156 GTCTAACGTGTTGTCAGCTAGC 59.338 50.000 6.62 6.62 0.00 3.42
2530 8232 1.784062 GTGTTGTCAGCTAGCGCAG 59.216 57.895 11.47 6.31 39.10 5.18
2563 8265 5.979517 GGGCACTACATTGAATAATTGCTTC 59.020 40.000 0.00 0.00 30.65 3.86
2566 8268 6.412072 GCACTACATTGAATAATTGCTTCGAC 59.588 38.462 0.00 0.00 0.00 4.20
2567 8269 7.463544 CACTACATTGAATAATTGCTTCGACA 58.536 34.615 0.00 0.00 0.00 4.35
2590 8292 7.281098 ACATCTGTTCGTTATCTCTCCTACTA 58.719 38.462 0.00 0.00 0.00 1.82
2630 8332 7.949903 ATAACACGTAAAGTTATGTCACACA 57.050 32.000 8.50 0.00 39.85 3.72
2631 8333 6.854496 AACACGTAAAGTTATGTCACACAT 57.146 33.333 0.00 0.00 42.35 3.21
2632 8334 6.854496 ACACGTAAAGTTATGTCACACATT 57.146 33.333 0.00 0.00 39.88 2.71
2633 8335 6.884187 ACACGTAAAGTTATGTCACACATTC 58.116 36.000 0.00 0.00 39.88 2.67
2634 8336 6.704493 ACACGTAAAGTTATGTCACACATTCT 59.296 34.615 0.00 0.00 39.88 2.40
2635 8337 7.009440 CACGTAAAGTTATGTCACACATTCTG 58.991 38.462 0.00 0.00 39.88 3.02
2636 8338 6.704493 ACGTAAAGTTATGTCACACATTCTGT 59.296 34.615 0.00 0.00 39.88 3.41
2637 8339 7.225931 ACGTAAAGTTATGTCACACATTCTGTT 59.774 33.333 0.00 0.00 39.88 3.16
2638 8340 8.705134 CGTAAAGTTATGTCACACATTCTGTTA 58.295 33.333 0.00 0.00 39.88 2.41
2705 8408 9.767228 TTAGTGTTTACTTGCATAAGTCAACTA 57.233 29.630 13.86 7.40 45.06 2.24
2707 8410 9.938280 AGTGTTTACTTGCATAAGTCAACTATA 57.062 29.630 13.86 0.00 45.06 1.31
2757 8460 9.191995 CTAAAAATCTTGTTAAATGACCGCTTT 57.808 29.630 0.00 0.00 0.00 3.51
2760 8463 8.687824 AAATCTTGTTAAATGACCGCTTTATG 57.312 30.769 0.00 0.00 0.00 1.90
2764 8467 8.138712 TCTTGTTAAATGACCGCTTTATGTTTT 58.861 29.630 0.00 0.00 0.00 2.43
2795 8498 9.730420 AGTGTTTACTTGCATAAAACAACTAAG 57.270 29.630 17.96 0.00 42.79 2.18
2815 8518 9.832445 AACTAAGAAAAGATTGTTGTAGACTCA 57.168 29.630 0.00 0.00 0.00 3.41
2829 8532 6.012658 TGTAGACTCAACAAAAATGGCATC 57.987 37.500 0.00 0.00 0.00 3.91
2852 8555 6.875076 TCCACTTAGCCTGAAAATCTACTAC 58.125 40.000 0.00 0.00 0.00 2.73
2857 8560 7.397761 ACTTAGCCTGAAAATCTACTACACTCT 59.602 37.037 0.00 0.00 0.00 3.24
2858 8561 8.818622 TTAGCCTGAAAATCTACTACACTCTA 57.181 34.615 0.00 0.00 0.00 2.43
2922 8626 3.508793 ACATTCCAACAATGCAAGAGAGG 59.491 43.478 0.00 0.00 0.00 3.69
2925 8629 1.272092 CCAACAATGCAAGAGAGGGGA 60.272 52.381 0.00 0.00 0.00 4.81
2926 8630 1.815003 CAACAATGCAAGAGAGGGGAC 59.185 52.381 0.00 0.00 0.00 4.46
2941 8645 2.265589 GGGACCATAAACCCCGTATG 57.734 55.000 0.00 0.00 40.19 2.39
2942 8646 1.770061 GGGACCATAAACCCCGTATGA 59.230 52.381 0.00 0.00 40.19 2.15
2943 8647 2.173143 GGGACCATAAACCCCGTATGAA 59.827 50.000 0.00 0.00 40.19 2.57
2944 8648 3.371810 GGGACCATAAACCCCGTATGAAA 60.372 47.826 0.00 0.00 40.19 2.69
2945 8649 4.271661 GGACCATAAACCCCGTATGAAAA 58.728 43.478 0.00 0.00 31.71 2.29
2946 8650 4.891168 GGACCATAAACCCCGTATGAAAAT 59.109 41.667 0.00 0.00 31.71 1.82
2947 8651 5.221165 GGACCATAAACCCCGTATGAAAATG 60.221 44.000 0.00 0.00 31.71 2.32
2948 8652 5.265989 ACCATAAACCCCGTATGAAAATGT 58.734 37.500 0.00 0.00 31.71 2.71
2949 8653 5.717654 ACCATAAACCCCGTATGAAAATGTT 59.282 36.000 0.00 0.00 31.71 2.71
2950 8654 6.039616 CCATAAACCCCGTATGAAAATGTTG 58.960 40.000 0.00 0.00 31.71 3.33
2951 8655 6.350612 CCATAAACCCCGTATGAAAATGTTGT 60.351 38.462 0.00 0.00 31.71 3.32
2952 8656 5.538849 AAACCCCGTATGAAAATGTTGTT 57.461 34.783 0.00 0.00 0.00 2.83
2953 8657 4.513198 ACCCCGTATGAAAATGTTGTTG 57.487 40.909 0.00 0.00 0.00 3.33
2954 8658 4.145807 ACCCCGTATGAAAATGTTGTTGA 58.854 39.130 0.00 0.00 0.00 3.18
2955 8659 4.770010 ACCCCGTATGAAAATGTTGTTGAT 59.230 37.500 0.00 0.00 0.00 2.57
2956 8660 5.245075 ACCCCGTATGAAAATGTTGTTGATT 59.755 36.000 0.00 0.00 0.00 2.57
2957 8661 5.804979 CCCCGTATGAAAATGTTGTTGATTC 59.195 40.000 0.00 0.00 0.00 2.52
2958 8662 6.385843 CCCGTATGAAAATGTTGTTGATTCA 58.614 36.000 0.00 0.00 34.80 2.57
2959 8663 6.865726 CCCGTATGAAAATGTTGTTGATTCAA 59.134 34.615 0.00 0.00 34.09 2.69
2960 8664 7.062138 CCCGTATGAAAATGTTGTTGATTCAAG 59.938 37.037 0.00 0.00 34.09 3.02
2961 8665 7.807433 CCGTATGAAAATGTTGTTGATTCAAGA 59.193 33.333 0.00 0.00 34.09 3.02
2962 8666 9.179552 CGTATGAAAATGTTGTTGATTCAAGAA 57.820 29.630 4.96 4.96 34.09 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 9.958180 TTCTGAACATCCTGATAACTTATTTGA 57.042 29.630 0.00 0.00 0.00 2.69
217 218 7.544217 TCGTTTAAACTACCCGAGGTAATTAAC 59.456 37.037 16.01 0.00 37.76 2.01
245 246 5.534207 TCATTTGCATTCAGGACAAAAGT 57.466 34.783 0.00 0.00 36.90 2.66
365 366 1.807742 CGAATGCCCTTTGACCGTTTA 59.192 47.619 0.00 0.00 0.00 2.01
553 556 1.135315 CAGCAAACGCTCCAATCGG 59.865 57.895 0.00 0.00 37.77 4.18
559 562 1.333619 TGTTTTCTCAGCAAACGCTCC 59.666 47.619 0.00 0.00 37.77 4.70
701 704 2.293399 GCATGGTGGTCGTTTCTTTTCT 59.707 45.455 0.00 0.00 0.00 2.52
871 884 4.314440 TCAGTCGGCAGTGTGGGC 62.314 66.667 0.00 0.00 0.00 5.36
878 891 1.071605 GCTTACTTGTCAGTCGGCAG 58.928 55.000 0.00 0.00 34.06 4.85
928 942 4.432712 GTTTGAAGTGGTTTGCAGATGTT 58.567 39.130 0.00 0.00 0.00 2.71
984 999 5.609088 GCCATCATATAACAATCGAACGTC 58.391 41.667 0.00 0.00 0.00 4.34
1028 1043 4.373116 GACTCGCCTCCACCGCAA 62.373 66.667 0.00 0.00 0.00 4.85
1053 1131 3.086600 CTCCTGCCCTCCTCCACC 61.087 72.222 0.00 0.00 0.00 4.61
1054 1132 3.791586 GCTCCTGCCCTCCTCCAC 61.792 72.222 0.00 0.00 0.00 4.02
1055 1133 3.870607 TTGCTCCTGCCCTCCTCCA 62.871 63.158 0.00 0.00 38.71 3.86
1056 1134 3.011517 TTGCTCCTGCCCTCCTCC 61.012 66.667 0.00 0.00 38.71 4.30
1057 1135 1.992277 TCTTGCTCCTGCCCTCCTC 60.992 63.158 0.00 0.00 38.71 3.71
1058 1136 2.123632 TCTTGCTCCTGCCCTCCT 59.876 61.111 0.00 0.00 38.71 3.69
1059 1137 2.270527 GTCTTGCTCCTGCCCTCC 59.729 66.667 0.00 0.00 38.71 4.30
1060 1138 1.078567 CTGTCTTGCTCCTGCCCTC 60.079 63.158 0.00 0.00 38.71 4.30
1061 1139 1.845205 ACTGTCTTGCTCCTGCCCT 60.845 57.895 0.00 0.00 38.71 5.19
1062 1140 1.673665 CACTGTCTTGCTCCTGCCC 60.674 63.158 0.00 0.00 38.71 5.36
1063 1141 1.673665 CCACTGTCTTGCTCCTGCC 60.674 63.158 0.00 0.00 38.71 4.85
1064 1142 0.673022 CTCCACTGTCTTGCTCCTGC 60.673 60.000 0.00 0.00 40.20 4.85
1065 1143 0.036577 CCTCCACTGTCTTGCTCCTG 60.037 60.000 0.00 0.00 0.00 3.86
1066 1144 1.835927 GCCTCCACTGTCTTGCTCCT 61.836 60.000 0.00 0.00 0.00 3.69
1067 1145 1.376553 GCCTCCACTGTCTTGCTCC 60.377 63.158 0.00 0.00 0.00 4.70
1068 1146 1.739562 CGCCTCCACTGTCTTGCTC 60.740 63.158 0.00 0.00 0.00 4.26
1069 1147 2.164865 CTCGCCTCCACTGTCTTGCT 62.165 60.000 0.00 0.00 0.00 3.91
1070 1148 1.739562 CTCGCCTCCACTGTCTTGC 60.740 63.158 0.00 0.00 0.00 4.01
1071 1149 0.389166 GACTCGCCTCCACTGTCTTG 60.389 60.000 0.00 0.00 0.00 3.02
1072 1150 1.536943 GGACTCGCCTCCACTGTCTT 61.537 60.000 0.00 0.00 0.00 3.01
1073 1151 1.979693 GGACTCGCCTCCACTGTCT 60.980 63.158 0.00 0.00 0.00 3.41
1074 1152 2.574399 GGACTCGCCTCCACTGTC 59.426 66.667 0.00 0.00 0.00 3.51
1075 1153 3.374402 CGGACTCGCCTCCACTGT 61.374 66.667 0.00 0.00 0.00 3.55
1076 1154 4.135153 CCGGACTCGCCTCCACTG 62.135 72.222 0.00 0.00 34.56 3.66
1077 1155 4.680537 ACCGGACTCGCCTCCACT 62.681 66.667 9.46 0.00 34.56 4.00
1078 1156 4.436998 CACCGGACTCGCCTCCAC 62.437 72.222 9.46 0.00 34.56 4.02
1081 1159 3.827898 CTCCACCGGACTCGCCTC 61.828 72.222 9.46 0.00 34.56 4.70
1084 1162 3.827898 CTCCTCCACCGGACTCGC 61.828 72.222 9.46 0.00 34.56 5.03
1085 1163 3.141488 CCTCCTCCACCGGACTCG 61.141 72.222 9.46 0.00 0.00 4.18
1086 1164 2.760385 CCCTCCTCCACCGGACTC 60.760 72.222 9.46 0.00 0.00 3.36
1087 1165 4.400251 CCCCTCCTCCACCGGACT 62.400 72.222 9.46 0.00 0.00 3.85
1088 1166 4.393778 TCCCCTCCTCCACCGGAC 62.394 72.222 9.46 0.00 0.00 4.79
1089 1167 4.075793 CTCCCCTCCTCCACCGGA 62.076 72.222 9.46 0.00 0.00 5.14
1091 1169 4.075793 TCCTCCCCTCCTCCACCG 62.076 72.222 0.00 0.00 0.00 4.94
1287 6870 3.575351 GACAACGAGCTCCACCGCT 62.575 63.158 8.47 0.00 44.33 5.52
1302 6885 4.329545 GGCTTGGCGTGGAGGACA 62.330 66.667 0.00 0.00 0.00 4.02
1324 6907 1.827399 ATGTTGACGGCGAGGGAAGT 61.827 55.000 16.62 0.00 0.00 3.01
1362 6945 1.632409 TGAAGCATTGAAGAGGAGGCT 59.368 47.619 0.00 0.00 0.00 4.58
1406 7006 3.640407 AGCTTTGCTCCAGCCGGA 61.640 61.111 5.05 0.00 41.18 5.14
1418 7018 3.993081 CAGAATTCAGTCGACAGAGCTTT 59.007 43.478 19.50 10.01 0.00 3.51
1419 7019 3.583806 CAGAATTCAGTCGACAGAGCTT 58.416 45.455 19.50 12.26 0.00 3.74
1422 7022 2.417924 CCCCAGAATTCAGTCGACAGAG 60.418 54.545 19.50 7.34 0.00 3.35
1427 7027 2.159099 CGAATCCCCAGAATTCAGTCGA 60.159 50.000 8.44 0.00 0.00 4.20
1428 7028 2.205074 CGAATCCCCAGAATTCAGTCG 58.795 52.381 8.44 3.28 0.00 4.18
1435 7035 2.945890 GCCTGAAACGAATCCCCAGAAT 60.946 50.000 0.00 0.00 0.00 2.40
1475 7085 0.042881 AGGTCCTCCTCCACTAACCC 59.957 60.000 0.00 0.00 40.58 4.11
1488 7098 2.348998 CCTTCTTGCGCAGGTCCT 59.651 61.111 19.74 0.00 0.00 3.85
1560 7170 2.233922 CGGAGAGTTGGTAGTGGATGTT 59.766 50.000 0.00 0.00 0.00 2.71
1561 7171 1.825474 CGGAGAGTTGGTAGTGGATGT 59.175 52.381 0.00 0.00 0.00 3.06
1562 7172 1.471676 GCGGAGAGTTGGTAGTGGATG 60.472 57.143 0.00 0.00 0.00 3.51
1563 7173 0.824759 GCGGAGAGTTGGTAGTGGAT 59.175 55.000 0.00 0.00 0.00 3.41
1564 7174 0.251653 AGCGGAGAGTTGGTAGTGGA 60.252 55.000 0.00 0.00 0.00 4.02
1565 7175 1.405821 CTAGCGGAGAGTTGGTAGTGG 59.594 57.143 0.00 0.00 32.85 4.00
1566 7176 1.202313 GCTAGCGGAGAGTTGGTAGTG 60.202 57.143 0.00 0.00 38.21 2.74
1567 7177 1.104630 GCTAGCGGAGAGTTGGTAGT 58.895 55.000 0.00 0.00 38.21 2.73
1568 7178 0.386113 GGCTAGCGGAGAGTTGGTAG 59.614 60.000 9.00 0.00 38.78 3.18
1569 7179 1.381928 CGGCTAGCGGAGAGTTGGTA 61.382 60.000 16.80 0.00 0.00 3.25
1570 7180 2.711922 CGGCTAGCGGAGAGTTGGT 61.712 63.158 16.80 0.00 0.00 3.67
1571 7181 2.105128 CGGCTAGCGGAGAGTTGG 59.895 66.667 16.80 0.00 0.00 3.77
1610 7238 6.440010 ACAGCTATGGCATGTATATCTTCTCT 59.560 38.462 10.98 0.00 41.70 3.10
1618 7246 6.208007 AGTTACGTACAGCTATGGCATGTATA 59.792 38.462 10.98 0.00 41.70 1.47
1620 7248 4.340097 AGTTACGTACAGCTATGGCATGTA 59.660 41.667 10.98 2.05 41.70 2.29
1621 7249 3.132289 AGTTACGTACAGCTATGGCATGT 59.868 43.478 10.98 3.17 41.70 3.21
1622 7250 3.717707 AGTTACGTACAGCTATGGCATG 58.282 45.455 10.98 0.00 41.70 4.06
1623 7251 4.119862 CAAGTTACGTACAGCTATGGCAT 58.880 43.478 4.88 4.88 41.70 4.40
1624 7252 3.056393 ACAAGTTACGTACAGCTATGGCA 60.056 43.478 3.10 0.00 41.70 4.92
1625 7253 3.306166 CACAAGTTACGTACAGCTATGGC 59.694 47.826 0.00 0.00 39.06 4.40
1627 7255 4.031765 CAGCACAAGTTACGTACAGCTATG 59.968 45.833 0.00 0.00 0.00 2.23
1628 7256 4.174009 CAGCACAAGTTACGTACAGCTAT 58.826 43.478 0.00 0.00 0.00 2.97
1629 7257 3.571571 CAGCACAAGTTACGTACAGCTA 58.428 45.455 0.00 0.00 0.00 3.32
1630 7258 2.404215 CAGCACAAGTTACGTACAGCT 58.596 47.619 0.00 0.00 0.00 4.24
1631 7259 1.136336 GCAGCACAAGTTACGTACAGC 60.136 52.381 0.00 0.00 0.00 4.40
1632 7260 2.404215 AGCAGCACAAGTTACGTACAG 58.596 47.619 0.00 0.00 0.00 2.74
1633 7261 2.519377 AGCAGCACAAGTTACGTACA 57.481 45.000 0.00 0.00 0.00 2.90
1634 7262 5.275602 CGTATAAGCAGCACAAGTTACGTAC 60.276 44.000 0.00 0.00 0.00 3.67
1636 7264 3.611113 CGTATAAGCAGCACAAGTTACGT 59.389 43.478 0.00 0.00 0.00 3.57
1637 7265 3.000078 CCGTATAAGCAGCACAAGTTACG 60.000 47.826 0.00 0.00 0.00 3.18
1638 7266 4.178540 TCCGTATAAGCAGCACAAGTTAC 58.821 43.478 0.00 0.00 0.00 2.50
1639 7267 4.459390 TCCGTATAAGCAGCACAAGTTA 57.541 40.909 0.00 0.00 0.00 2.24
1640 7268 3.328382 TCCGTATAAGCAGCACAAGTT 57.672 42.857 0.00 0.00 0.00 2.66
1783 7461 5.172687 AGAAGAGAAAATCAAGGACCTCC 57.827 43.478 0.00 0.00 0.00 4.30
1799 7477 1.734047 GCGTACACTGCAGGAGAAGAG 60.734 57.143 19.93 4.19 0.00 2.85
1801 7479 0.737715 GGCGTACACTGCAGGAGAAG 60.738 60.000 19.93 7.51 0.00 2.85
1824 7502 2.607187 CATTAGTTTCAGTCTCGCGGT 58.393 47.619 6.13 0.00 0.00 5.68
1848 7526 2.298729 AGGAGTTGAGACAAGAGACAGC 59.701 50.000 0.00 0.00 0.00 4.40
1850 7528 3.838565 AGAGGAGTTGAGACAAGAGACA 58.161 45.455 0.00 0.00 0.00 3.41
1852 7530 5.144100 AGAAAGAGGAGTTGAGACAAGAGA 58.856 41.667 0.00 0.00 0.00 3.10
1855 7533 4.213059 GCAAGAAAGAGGAGTTGAGACAAG 59.787 45.833 0.00 0.00 0.00 3.16
1862 7541 2.157738 CCCTGCAAGAAAGAGGAGTTG 58.842 52.381 0.00 0.00 34.07 3.16
1924 7605 2.072298 GACAATCACCACAGAGCAGTC 58.928 52.381 0.00 0.00 0.00 3.51
1936 7617 1.503542 CGGGCTGCTTGACAATCAC 59.496 57.895 0.00 0.00 0.00 3.06
1954 7635 0.744771 GGCGATCAGTTCTTGGACCC 60.745 60.000 0.00 0.00 0.00 4.46
1955 7636 0.036388 TGGCGATCAGTTCTTGGACC 60.036 55.000 0.00 0.00 0.00 4.46
1977 7662 0.179121 CGATCGATCCAACACCGGAA 60.179 55.000 19.51 0.00 38.95 4.30
1987 7672 0.876342 GAACTGGGCACGATCGATCC 60.876 60.000 24.34 20.30 0.00 3.36
2052 7741 4.261197 CGGTTGGAGCAGAAATAATTAGGC 60.261 45.833 0.00 0.00 0.00 3.93
2054 7743 6.128007 ACAACGGTTGGAGCAGAAATAATTAG 60.128 38.462 23.51 0.00 34.12 1.73
2055 7744 5.708230 ACAACGGTTGGAGCAGAAATAATTA 59.292 36.000 23.51 0.00 34.12 1.40
2057 7746 4.079253 ACAACGGTTGGAGCAGAAATAAT 58.921 39.130 23.51 0.00 34.12 1.28
2066 7755 2.930682 GAGAGAATACAACGGTTGGAGC 59.069 50.000 23.51 12.27 34.12 4.70
2073 7762 8.928270 AGTAAATAACAGAGAGAATACAACGG 57.072 34.615 0.00 0.00 0.00 4.44
2074 7763 9.790389 AGAGTAAATAACAGAGAGAATACAACG 57.210 33.333 0.00 0.00 0.00 4.10
2103 7793 6.150396 ACAAAGCTCGACTGCTAGTATTAT 57.850 37.500 0.00 0.00 43.24 1.28
2104 7794 5.578005 ACAAAGCTCGACTGCTAGTATTA 57.422 39.130 0.00 0.00 43.24 0.98
2105 7795 4.457834 ACAAAGCTCGACTGCTAGTATT 57.542 40.909 0.00 0.00 43.24 1.89
2109 7799 4.238514 AGTTTACAAAGCTCGACTGCTAG 58.761 43.478 0.00 0.00 43.24 3.42
2174 7865 9.359653 GGTATATTGTACTCCCTCTGTAAACTA 57.640 37.037 0.00 0.00 0.00 2.24
2175 7866 7.289549 GGGTATATTGTACTCCCTCTGTAAACT 59.710 40.741 0.00 0.00 35.63 2.66
2176 7867 7.070322 TGGGTATATTGTACTCCCTCTGTAAAC 59.930 40.741 0.00 0.00 38.95 2.01
2177 7868 7.134162 TGGGTATATTGTACTCCCTCTGTAAA 58.866 38.462 0.00 0.00 38.95 2.01
2178 7869 6.685541 TGGGTATATTGTACTCCCTCTGTAA 58.314 40.000 0.00 0.00 38.95 2.41
2179 7870 6.283948 TGGGTATATTGTACTCCCTCTGTA 57.716 41.667 0.00 0.00 38.95 2.74
2180 7871 5.152306 TGGGTATATTGTACTCCCTCTGT 57.848 43.478 0.00 0.00 38.95 3.41
2183 7874 6.681729 TGATTGGGTATATTGTACTCCCTC 57.318 41.667 0.00 0.00 38.95 4.30
2185 7876 5.221843 TGCTGATTGGGTATATTGTACTCCC 60.222 44.000 0.00 0.00 38.68 4.30
2186 7877 5.701290 GTGCTGATTGGGTATATTGTACTCC 59.299 44.000 0.00 0.00 0.00 3.85
2187 7878 6.288294 TGTGCTGATTGGGTATATTGTACTC 58.712 40.000 0.00 0.00 0.00 2.59
2194 7885 9.365906 TGAATTTATTGTGCTGATTGGGTATAT 57.634 29.630 0.00 0.00 0.00 0.86
2195 7886 8.759481 TGAATTTATTGTGCTGATTGGGTATA 57.241 30.769 0.00 0.00 0.00 1.47
2200 7891 6.267817 ACGATGAATTTATTGTGCTGATTGG 58.732 36.000 2.39 0.00 0.00 3.16
2201 7892 7.485595 TCAACGATGAATTTATTGTGCTGATTG 59.514 33.333 3.97 0.00 30.99 2.67
2245 7941 6.691818 CAGACGTATACGAAAGCAAGTCTATT 59.308 38.462 30.77 3.58 43.02 1.73
2249 7945 4.164294 ACAGACGTATACGAAAGCAAGTC 58.836 43.478 30.77 15.04 43.02 3.01
2250 7946 4.170292 ACAGACGTATACGAAAGCAAGT 57.830 40.909 30.77 15.08 43.02 3.16
2255 7951 6.807708 AAGCAATACAGACGTATACGAAAG 57.192 37.500 30.77 19.86 43.02 2.62
2305 8001 9.516314 CATATTATCTCTGTCGTAAGTCAAACA 57.484 33.333 0.00 0.00 34.37 2.83
2306 8002 8.480853 GCATATTATCTCTGTCGTAAGTCAAAC 58.519 37.037 0.00 0.00 34.37 2.93
2329 8025 6.744112 TCTTTCCGTTTCATTTACTTTGCAT 58.256 32.000 0.00 0.00 0.00 3.96
2346 8042 1.261619 GCACCGATAGCATTCTTTCCG 59.738 52.381 0.00 0.00 0.00 4.30
2347 8043 1.604278 GGCACCGATAGCATTCTTTCC 59.396 52.381 0.00 0.00 0.00 3.13
2352 8053 2.766313 TGTATGGCACCGATAGCATTC 58.234 47.619 0.00 0.00 0.00 2.67
2354 8055 2.302733 TCATGTATGGCACCGATAGCAT 59.697 45.455 0.00 0.00 0.00 3.79
2356 8057 2.455674 TCATGTATGGCACCGATAGC 57.544 50.000 0.00 0.00 0.00 2.97
2369 8070 5.652014 GGATGAACACCCAAAGAATCATGTA 59.348 40.000 0.00 0.00 0.00 2.29
2377 8078 2.978978 TCAGAGGATGAACACCCAAAGA 59.021 45.455 0.00 0.00 34.02 2.52
2381 8082 4.297768 TGATATCAGAGGATGAACACCCA 58.702 43.478 0.00 0.00 42.53 4.51
2384 8085 7.384477 TGATGATGATATCAGAGGATGAACAC 58.616 38.462 11.78 0.00 43.53 3.32
2393 8094 6.659668 AGGGCAAATTGATGATGATATCAGAG 59.340 38.462 11.78 0.00 43.53 3.35
2424 8126 4.499183 GGTCATTGAGTGGTAAGTCTCTG 58.501 47.826 0.00 0.00 0.00 3.35
2432 8134 2.467880 GAGAGGGGTCATTGAGTGGTA 58.532 52.381 0.00 0.00 0.00 3.25
2437 8139 2.307098 ACAAAGGAGAGGGGTCATTGAG 59.693 50.000 0.00 0.00 0.00 3.02
2445 8147 0.537371 AACGCAACAAAGGAGAGGGG 60.537 55.000 0.00 0.00 0.00 4.79
2471 8173 7.148474 GCAGATCCACTAGAAACAAAACGATTA 60.148 37.037 0.00 0.00 0.00 1.75
2475 8177 4.452455 AGCAGATCCACTAGAAACAAAACG 59.548 41.667 0.00 0.00 0.00 3.60
2476 8178 5.948992 AGCAGATCCACTAGAAACAAAAC 57.051 39.130 0.00 0.00 0.00 2.43
2480 8182 5.278463 GCAAAAAGCAGATCCACTAGAAACA 60.278 40.000 0.00 0.00 44.79 2.83
2505 8207 2.662156 GCTAGCTGACAACACGTTAGAC 59.338 50.000 7.70 0.00 33.01 2.59
2508 8210 1.693467 CGCTAGCTGACAACACGTTA 58.307 50.000 13.93 0.00 0.00 3.18
2511 8213 1.949015 CTGCGCTAGCTGACAACACG 61.949 60.000 13.93 0.00 43.85 4.49
2513 8215 0.667487 GACTGCGCTAGCTGACAACA 60.667 55.000 13.93 0.60 43.85 3.33
2530 8232 2.506438 GTAGTGCCCACGAGCGAC 60.506 66.667 0.00 0.00 36.20 5.19
2563 8265 4.035792 AGGAGAGATAACGAACAGATGTCG 59.964 45.833 0.00 0.00 0.00 4.35
2566 8268 6.627395 AGTAGGAGAGATAACGAACAGATG 57.373 41.667 0.00 0.00 0.00 2.90
2567 8269 8.927675 AATAGTAGGAGAGATAACGAACAGAT 57.072 34.615 0.00 0.00 0.00 2.90
2604 8306 8.828644 TGTGTGACATAACTTTACGTGTTATTT 58.171 29.630 0.00 0.00 38.20 1.40
2605 8307 8.367943 TGTGTGACATAACTTTACGTGTTATT 57.632 30.769 0.00 0.00 38.20 1.40
2606 8308 7.949903 TGTGTGACATAACTTTACGTGTTAT 57.050 32.000 0.00 0.69 40.11 1.89
2607 8309 7.949903 ATGTGTGACATAACTTTACGTGTTA 57.050 32.000 0.00 0.00 36.99 2.41
2608 8310 6.854496 ATGTGTGACATAACTTTACGTGTT 57.146 33.333 0.00 0.00 36.99 3.32
2609 8311 6.704493 AGAATGTGTGACATAACTTTACGTGT 59.296 34.615 0.00 0.00 37.97 4.49
2610 8312 7.009440 CAGAATGTGTGACATAACTTTACGTG 58.991 38.462 0.00 0.00 37.97 4.49
2611 8313 7.117241 CAGAATGTGTGACATAACTTTACGT 57.883 36.000 0.00 0.00 37.97 3.57
2739 8442 7.867445 AAACATAAAGCGGTCATTTAACAAG 57.133 32.000 0.00 0.00 0.00 3.16
2749 8452 8.959734 AACACTAATAAAAACATAAAGCGGTC 57.040 30.769 0.00 0.00 0.00 4.79
2814 8517 4.389687 GCTAAGTGGATGCCATTTTTGTTG 59.610 41.667 0.00 0.00 35.19 3.33
2815 8518 4.563374 GGCTAAGTGGATGCCATTTTTGTT 60.563 41.667 0.00 0.00 45.46 2.83
2824 8527 2.128771 TTTCAGGCTAAGTGGATGCC 57.871 50.000 0.00 0.00 46.42 4.40
2829 8532 6.535508 GTGTAGTAGATTTTCAGGCTAAGTGG 59.464 42.308 0.00 0.00 0.00 4.00
2867 8571 6.532657 CCGTTTTTGAACCGATACTACTGTAT 59.467 38.462 0.00 0.00 41.65 2.29
2880 8584 5.427036 TGTGTCTATTCCGTTTTTGAACC 57.573 39.130 0.00 0.00 0.00 3.62
2922 8626 1.770061 TCATACGGGGTTTATGGTCCC 59.230 52.381 0.00 0.00 42.73 4.46
2925 8629 5.265989 ACATTTTCATACGGGGTTTATGGT 58.734 37.500 0.00 0.00 0.00 3.55
2926 8630 5.845391 ACATTTTCATACGGGGTTTATGG 57.155 39.130 0.00 0.00 0.00 2.74
2928 8632 6.844097 ACAACATTTTCATACGGGGTTTAT 57.156 33.333 0.00 0.00 0.00 1.40
2929 8633 6.264744 TCAACAACATTTTCATACGGGGTTTA 59.735 34.615 0.00 0.00 0.00 2.01
2930 8634 5.069251 TCAACAACATTTTCATACGGGGTTT 59.931 36.000 0.00 0.00 0.00 3.27
2931 8635 4.585162 TCAACAACATTTTCATACGGGGTT 59.415 37.500 0.00 0.00 0.00 4.11
2932 8636 4.145807 TCAACAACATTTTCATACGGGGT 58.854 39.130 0.00 0.00 0.00 4.95
2933 8637 4.775058 TCAACAACATTTTCATACGGGG 57.225 40.909 0.00 0.00 0.00 5.73
2934 8638 6.385843 TGAATCAACAACATTTTCATACGGG 58.614 36.000 0.00 0.00 0.00 5.28
2935 8639 7.807433 TCTTGAATCAACAACATTTTCATACGG 59.193 33.333 0.00 0.00 0.00 4.02
2936 8640 8.726650 TCTTGAATCAACAACATTTTCATACG 57.273 30.769 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.