Multiple sequence alignment - TraesCS5D01G448600

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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 TraesCS5D01G448600 chr5D 100.000 3915 0 0 1 3915 498087300 498083386 0.000000e+00 7230.0
1 TraesCS5D01G448600 chr5D 88.973 1188 114 14 1797 2972 498172984 498171802 0.000000e+00 1452.0
2 TraesCS5D01G448600 chr5D 88.543 1187 126 7 1798 2975 498290515 498289330 0.000000e+00 1430.0
3 TraesCS5D01G448600 chr5D 82.898 842 97 26 837 1671 498173861 498173060 0.000000e+00 713.0
4 TraesCS5D01G448600 chr5D 83.416 603 75 12 1085 1667 498291199 498290602 1.600000e-148 536.0
5 TraesCS5D01G448600 chr5D 87.978 183 19 3 3205 3384 462454618 462454800 3.060000e-51 213.0
6 TraesCS5D01G448600 chr5D 87.500 112 10 3 2975 3085 498171757 498171649 4.110000e-25 126.0
7 TraesCS5D01G448600 chr5B 94.021 1455 66 12 1754 3193 617292599 617291151 0.000000e+00 2185.0
8 TraesCS5D01G448600 chr5B 88.588 1183 122 11 1797 2971 617435926 617434749 0.000000e+00 1424.0
9 TraesCS5D01G448600 chr5B 89.248 1144 115 4 1797 2934 617601299 617600158 0.000000e+00 1424.0
10 TraesCS5D01G448600 chr5B 91.023 557 25 10 88 623 617294278 617293726 0.000000e+00 728.0
11 TraesCS5D01G448600 chr5B 91.085 516 40 1 1164 1679 617293151 617292642 0.000000e+00 693.0
12 TraesCS5D01G448600 chr5B 84.241 698 83 11 985 1671 617436681 617436000 0.000000e+00 654.0
13 TraesCS5D01G448600 chr5B 88.920 352 21 9 601 948 617293698 617293361 6.050000e-113 418.0
14 TraesCS5D01G448600 chr5B 91.500 200 15 2 3386 3584 617291154 617290956 1.390000e-69 274.0
15 TraesCS5D01G448600 chr5B 88.785 107 4 3 1 103 617294402 617294300 1.480000e-24 124.0
16 TraesCS5D01G448600 chr5B 87.255 102 8 4 2976 3075 617434720 617434622 1.150000e-20 111.0
17 TraesCS5D01G448600 chr5A 94.878 1191 54 6 1747 2935 622233752 622232567 0.000000e+00 1855.0
18 TraesCS5D01G448600 chr5A 88.712 1196 112 19 1797 2972 622393600 622392408 0.000000e+00 1439.0
19 TraesCS5D01G448600 chr5A 89.497 1133 113 6 1797 2924 622460029 622458898 0.000000e+00 1428.0
20 TraesCS5D01G448600 chr5A 91.429 525 39 1 1164 1682 622234297 622233773 0.000000e+00 715.0
21 TraesCS5D01G448600 chr5A 85.208 649 76 12 1081 1722 622394258 622393623 0.000000e+00 649.0
22 TraesCS5D01G448600 chr5A 82.389 653 73 19 1085 1722 622460677 622460052 7.450000e-147 531.0
23 TraesCS5D01G448600 chr5A 85.615 431 40 12 3474 3891 622232165 622231744 2.160000e-117 433.0
24 TraesCS5D01G448600 chr5A 91.003 289 14 6 328 613 622235280 622235001 2.860000e-101 379.0
25 TraesCS5D01G448600 chr5A 88.818 313 15 8 636 948 622234806 622234514 2.220000e-97 366.0
26 TraesCS5D01G448600 chr5A 86.992 246 16 12 2956 3193 622232572 622232335 3.000000e-66 263.0
27 TraesCS5D01G448600 chr5A 84.158 202 29 3 3190 3390 491750172 491750371 3.990000e-45 193.0
28 TraesCS5D01G448600 chr5A 78.802 217 18 18 837 1051 622394447 622394257 1.910000e-23 121.0
29 TraesCS5D01G448600 chr5A 88.608 79 8 1 3007 3085 622392142 622392065 1.160000e-15 95.3
30 TraesCS5D01G448600 chr3A 81.704 1033 168 16 1864 2889 20557818 20556800 0.000000e+00 841.0
31 TraesCS5D01G448600 chr1B 81.411 581 71 19 1124 1679 569519345 569519913 1.290000e-119 440.0
32 TraesCS5D01G448600 chr1B 84.324 185 26 3 3203 3387 548294642 548294461 1.120000e-40 178.0
33 TraesCS5D01G448600 chr1B 100.000 34 0 0 985 1018 569516847 569516880 3.270000e-06 63.9
34 TraesCS5D01G448600 chr1D 85.117 383 35 9 985 1354 420843706 420844079 4.780000e-99 372.0
35 TraesCS5D01G448600 chr1D 86.188 181 21 3 3206 3386 263194892 263194716 3.990000e-45 193.0
36 TraesCS5D01G448600 chr1D 85.083 181 23 3 3205 3384 121770867 121770690 8.640000e-42 182.0
37 TraesCS5D01G448600 chr4A 88.770 187 18 3 3206 3389 319821507 319821321 3.940000e-55 226.0
38 TraesCS5D01G448600 chr6D 87.634 186 18 4 3204 3385 388209929 388209745 1.100000e-50 211.0
39 TraesCS5D01G448600 chr3B 86.243 189 22 4 3203 3387 107966102 107966290 6.630000e-48 202.0
40 TraesCS5D01G448600 chr7A 85.083 181 23 3 3203 3383 676361610 676361434 8.640000e-42 182.0
41 TraesCS5D01G448600 chr7B 92.857 98 2 2 1037 1129 73672411 73672314 1.900000e-28 137.0


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 TraesCS5D01G448600 chr5D 498083386 498087300 3914 True 7230.000000 7230 100.000000 1 3915 1 chr5D.!!$R1 3914
1 TraesCS5D01G448600 chr5D 498289330 498291199 1869 True 983.000000 1430 85.979500 1085 2975 2 chr5D.!!$R3 1890
2 TraesCS5D01G448600 chr5D 498171649 498173861 2212 True 763.666667 1452 86.457000 837 3085 3 chr5D.!!$R2 2248
3 TraesCS5D01G448600 chr5B 617600158 617601299 1141 True 1424.000000 1424 89.248000 1797 2934 1 chr5B.!!$R1 1137
4 TraesCS5D01G448600 chr5B 617290956 617294402 3446 True 737.000000 2185 90.889000 1 3584 6 chr5B.!!$R2 3583
5 TraesCS5D01G448600 chr5B 617434622 617436681 2059 True 729.666667 1424 86.694667 985 3075 3 chr5B.!!$R3 2090
6 TraesCS5D01G448600 chr5A 622458898 622460677 1779 True 979.500000 1428 85.943000 1085 2924 2 chr5A.!!$R3 1839
7 TraesCS5D01G448600 chr5A 622231744 622235280 3536 True 668.500000 1855 89.789167 328 3891 6 chr5A.!!$R1 3563
8 TraesCS5D01G448600 chr5A 622392065 622394447 2382 True 576.075000 1439 85.332500 837 3085 4 chr5A.!!$R2 2248
9 TraesCS5D01G448600 chr3A 20556800 20557818 1018 True 841.000000 841 81.704000 1864 2889 1 chr3A.!!$R1 1025
10 TraesCS5D01G448600 chr1B 569516847 569519913 3066 False 251.950000 440 90.705500 985 1679 2 chr1B.!!$F1 694

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
300 347 0.240411 CCAGTTGAGAAAGCAGCTGC 59.760 55.0 31.53 31.53 43.23 5.25 F
1684 4410 0.036388 CATCCACGTAACCAGGTGCT 60.036 55.0 0.00 0.00 38.86 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 4435 0.309922 CGCCATCATGCAGGTCATTC 59.690 55.0 0.00 0.00 31.79 2.67 R
3360 6409 0.328592 TGGCTAGGTCTCAGTCGACT 59.671 55.0 13.58 13.58 34.38 4.18 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
22 23 5.171339 AGCACCAATAACATCTCTGTTCT 57.829 39.130 0.00 0.00 44.43 3.01
61 66 4.026744 TGTCTTCATGCTTAGCCTAGTCT 58.973 43.478 0.29 0.00 0.00 3.24
72 77 6.113411 GCTTAGCCTAGTCTTATCCAAAACA 58.887 40.000 0.00 0.00 0.00 2.83
76 81 4.640201 GCCTAGTCTTATCCAAAACATGCA 59.360 41.667 0.00 0.00 0.00 3.96
79 84 5.002464 AGTCTTATCCAAAACATGCATGC 57.998 39.130 26.53 11.82 0.00 4.06
81 86 4.025360 TCTTATCCAAAACATGCATGCCT 58.975 39.130 26.53 11.34 0.00 4.75
82 87 5.067674 GTCTTATCCAAAACATGCATGCCTA 59.932 40.000 26.53 6.89 0.00 3.93
83 88 5.834742 TCTTATCCAAAACATGCATGCCTAT 59.165 36.000 26.53 13.27 0.00 2.57
84 89 4.595762 ATCCAAAACATGCATGCCTATC 57.404 40.909 26.53 0.00 0.00 2.08
85 90 3.363627 TCCAAAACATGCATGCCTATCA 58.636 40.909 26.53 4.25 0.00 2.15
86 91 3.962063 TCCAAAACATGCATGCCTATCAT 59.038 39.130 26.53 1.90 35.31 2.45
107 145 5.594317 TCATGACGAAACTCTCTCATATCCA 59.406 40.000 0.00 0.00 0.00 3.41
111 149 7.331026 TGACGAAACTCTCTCATATCCAAAAT 58.669 34.615 0.00 0.00 0.00 1.82
124 162 4.771114 ATCCAAAATATGTCTCGTGGGA 57.229 40.909 0.00 0.00 0.00 4.37
142 180 2.025887 GGGAAGCTCAGGATGGAGAAAA 60.026 50.000 0.00 0.00 37.05 2.29
155 193 8.278017 AGGATGGAGAAAATTTCGCCTCCTTA 62.278 42.308 26.83 12.90 45.44 2.69
158 196 3.671716 AGAAAATTTCGCCTCCTTACGT 58.328 40.909 0.00 0.00 34.02 3.57
210 250 1.140052 TGAGACTTGAACTTGCGGGAA 59.860 47.619 0.00 0.00 0.00 3.97
222 262 0.817634 TGCGGGAAGACAGTGTTTGG 60.818 55.000 0.00 0.00 0.00 3.28
224 264 1.226746 CGGGAAGACAGTGTTTGGTC 58.773 55.000 0.00 0.00 0.00 4.02
226 266 0.586802 GGAAGACAGTGTTTGGTCGC 59.413 55.000 0.00 0.00 39.01 5.19
230 277 3.120321 AGACAGTGTTTGGTCGCATAA 57.880 42.857 0.00 0.00 39.01 1.90
243 290 2.354821 GTCGCATAAAATGGACCCTGAC 59.645 50.000 0.00 0.00 0.00 3.51
263 310 0.250467 CCCACATCATCCGATCCCAC 60.250 60.000 0.00 0.00 0.00 4.61
268 315 0.681733 ATCATCCGATCCCACTTCCG 59.318 55.000 0.00 0.00 0.00 4.30
300 347 0.240411 CCAGTTGAGAAAGCAGCTGC 59.760 55.000 31.53 31.53 43.23 5.25
574 629 2.236766 GAATGAGGCCTGGATTCATGG 58.763 52.381 12.00 0.00 32.23 3.66
623 735 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
754 1048 3.429141 CAAGTGAGGCGGCTGCAG 61.429 66.667 19.63 10.11 45.35 4.41
768 1062 2.751837 GCAGGTTGGCTGGCTACC 60.752 66.667 23.46 23.46 0.00 3.18
769 1063 2.044946 CAGGTTGGCTGGCTACCC 60.045 66.667 26.19 12.47 32.20 3.69
770 1064 2.204151 AGGTTGGCTGGCTACCCT 60.204 61.111 26.19 14.31 32.20 4.34
771 1065 1.852626 AGGTTGGCTGGCTACCCTT 60.853 57.895 26.19 10.37 32.20 3.95
772 1066 1.076727 GGTTGGCTGGCTACCCTTT 59.923 57.895 21.08 0.00 0.00 3.11
801 1095 5.526111 TCTTTTCTTCACGGTTACTCTTTGG 59.474 40.000 0.00 0.00 0.00 3.28
803 1097 3.986277 TCTTCACGGTTACTCTTTGGAC 58.014 45.455 0.00 0.00 0.00 4.02
805 1099 3.102052 TCACGGTTACTCTTTGGACAC 57.898 47.619 0.00 0.00 0.00 3.67
811 1105 5.187186 ACGGTTACTCTTTGGACACTGATAT 59.813 40.000 0.00 0.00 0.00 1.63
812 1106 6.379133 ACGGTTACTCTTTGGACACTGATATA 59.621 38.462 0.00 0.00 0.00 0.86
813 1107 7.069578 ACGGTTACTCTTTGGACACTGATATAT 59.930 37.037 0.00 0.00 0.00 0.86
859 1156 0.586802 CTATCTCGACATCGACGGCA 59.413 55.000 0.00 0.00 44.22 5.69
884 1181 5.293324 GCCGCCAAATTTTCCCTTTAAATAG 59.707 40.000 0.00 0.00 0.00 1.73
905 1203 1.153309 CAGCCACTGCGATCCATCA 60.153 57.895 0.00 0.00 44.33 3.07
906 1204 0.534427 CAGCCACTGCGATCCATCAT 60.534 55.000 0.00 0.00 44.33 2.45
908 1206 0.533531 GCCACTGCGATCCATCATCA 60.534 55.000 0.00 0.00 0.00 3.07
910 1208 1.224075 CACTGCGATCCATCATCACC 58.776 55.000 0.00 0.00 0.00 4.02
911 1209 1.126488 ACTGCGATCCATCATCACCT 58.874 50.000 0.00 0.00 0.00 4.00
912 1210 1.069823 ACTGCGATCCATCATCACCTC 59.930 52.381 0.00 0.00 0.00 3.85
913 1211 1.069668 CTGCGATCCATCATCACCTCA 59.930 52.381 0.00 0.00 0.00 3.86
915 1213 1.875576 GCGATCCATCATCACCTCACC 60.876 57.143 0.00 0.00 0.00 4.02
916 1214 1.270518 CGATCCATCATCACCTCACCC 60.271 57.143 0.00 0.00 0.00 4.61
917 1215 1.770658 GATCCATCATCACCTCACCCA 59.229 52.381 0.00 0.00 0.00 4.51
918 1216 0.911769 TCCATCATCACCTCACCCAC 59.088 55.000 0.00 0.00 0.00 4.61
919 1217 0.620030 CCATCATCACCTCACCCACA 59.380 55.000 0.00 0.00 0.00 4.17
920 1218 1.679944 CCATCATCACCTCACCCACAC 60.680 57.143 0.00 0.00 0.00 3.82
921 1219 0.620556 ATCATCACCTCACCCACACC 59.379 55.000 0.00 0.00 0.00 4.16
922 1220 1.375908 CATCACCTCACCCACACCG 60.376 63.158 0.00 0.00 0.00 4.94
925 1223 3.941188 ACCTCACCCACACCGCAG 61.941 66.667 0.00 0.00 0.00 5.18
949 1247 1.837051 ACCACAACCGAGAGAGCCA 60.837 57.895 0.00 0.00 0.00 4.75
953 1251 1.739562 CAACCGAGAGAGCCAGTGC 60.740 63.158 0.00 0.00 37.95 4.40
963 1261 3.034030 GCCAGTGCTTGTTTCGCT 58.966 55.556 0.00 0.00 33.53 4.93
964 1262 1.081840 GCCAGTGCTTGTTTCGCTC 60.082 57.895 0.00 0.00 33.53 5.03
965 1263 1.510480 GCCAGTGCTTGTTTCGCTCT 61.510 55.000 0.00 0.00 33.53 4.09
967 1265 1.069636 CCAGTGCTTGTTTCGCTCTTC 60.070 52.381 0.00 0.00 0.00 2.87
968 1266 1.599071 CAGTGCTTGTTTCGCTCTTCA 59.401 47.619 0.00 0.00 0.00 3.02
969 1267 2.032054 CAGTGCTTGTTTCGCTCTTCAA 59.968 45.455 0.00 0.00 0.00 2.69
970 1268 2.682856 AGTGCTTGTTTCGCTCTTCAAA 59.317 40.909 0.00 0.00 0.00 2.69
971 1269 3.128589 AGTGCTTGTTTCGCTCTTCAAAA 59.871 39.130 0.00 0.00 0.00 2.44
972 1270 3.240631 GTGCTTGTTTCGCTCTTCAAAAC 59.759 43.478 0.00 0.00 34.30 2.43
973 1271 3.128589 TGCTTGTTTCGCTCTTCAAAACT 59.871 39.130 0.00 0.00 34.69 2.66
974 1272 3.726235 GCTTGTTTCGCTCTTCAAAACTC 59.274 43.478 0.00 0.00 34.69 3.01
975 1273 4.730613 GCTTGTTTCGCTCTTCAAAACTCA 60.731 41.667 0.00 0.00 34.69 3.41
976 1274 4.273005 TGTTTCGCTCTTCAAAACTCAC 57.727 40.909 0.00 0.00 34.69 3.51
977 1275 3.938963 TGTTTCGCTCTTCAAAACTCACT 59.061 39.130 0.00 0.00 34.69 3.41
978 1276 4.201812 TGTTTCGCTCTTCAAAACTCACTG 60.202 41.667 0.00 0.00 34.69 3.66
979 1277 1.867233 TCGCTCTTCAAAACTCACTGC 59.133 47.619 0.00 0.00 0.00 4.40
980 1278 1.869767 CGCTCTTCAAAACTCACTGCT 59.130 47.619 0.00 0.00 0.00 4.24
981 1279 2.349249 CGCTCTTCAAAACTCACTGCTG 60.349 50.000 0.00 0.00 0.00 4.41
982 1280 2.874701 GCTCTTCAAAACTCACTGCTGA 59.125 45.455 0.00 0.00 0.00 4.26
1027 1459 4.891992 AGCACTCAGGTATGTACAAGTT 57.108 40.909 0.00 0.00 0.00 2.66
1073 2151 1.293924 CATGCAGCTAGGTGTGTAGC 58.706 55.000 22.21 8.86 45.06 3.58
1074 2152 0.904649 ATGCAGCTAGGTGTGTAGCA 59.095 50.000 22.21 14.20 46.81 3.49
1103 3066 1.202510 CCATGAGTCCAGCTAGCTCAC 60.203 57.143 16.15 14.53 41.33 3.51
1210 3909 0.390340 ACTATGCTGTCCGTGCACAG 60.390 55.000 18.64 5.51 45.82 3.66
1281 3989 2.718073 GGCCGGTACATCCTCGTGT 61.718 63.158 1.90 0.00 36.13 4.49
1450 4170 1.144969 GACGACAATGGCAACGAGAA 58.855 50.000 12.01 0.00 42.51 2.87
1679 4405 0.378257 GCATGCATCCACGTAACCAG 59.622 55.000 14.21 0.00 0.00 4.00
1684 4410 0.036388 CATCCACGTAACCAGGTGCT 60.036 55.000 0.00 0.00 38.86 4.40
1685 4411 1.206132 CATCCACGTAACCAGGTGCTA 59.794 52.381 0.00 0.00 38.86 3.49
1686 4412 0.604578 TCCACGTAACCAGGTGCTAC 59.395 55.000 0.00 0.00 38.86 3.58
1721 4448 4.424061 TTTTTCGAGAATGACCTGCATG 57.576 40.909 0.00 0.00 37.28 4.06
1722 4449 3.333029 TTTCGAGAATGACCTGCATGA 57.667 42.857 0.00 0.00 37.28 3.07
1723 4450 3.548745 TTCGAGAATGACCTGCATGAT 57.451 42.857 0.00 0.00 37.28 2.45
1724 4451 2.830104 TCGAGAATGACCTGCATGATG 58.170 47.619 0.00 0.00 37.28 3.07
1725 4452 1.871676 CGAGAATGACCTGCATGATGG 59.128 52.381 0.00 0.00 37.28 3.51
1726 4453 1.607628 GAGAATGACCTGCATGATGGC 59.392 52.381 0.00 0.00 37.28 4.40
1727 4454 0.309922 GAATGACCTGCATGATGGCG 59.690 55.000 0.00 0.00 37.28 5.69
1728 4455 1.731433 AATGACCTGCATGATGGCGC 61.731 55.000 0.00 0.00 37.28 6.53
1729 4456 3.945434 GACCTGCATGATGGCGCG 61.945 66.667 0.00 0.00 36.28 6.86
1768 4541 0.666913 GGCTCTGCATGCATACTTGG 59.333 55.000 22.97 8.55 0.00 3.61
2059 4851 0.536687 TCCTCGACTTCTGTGACCGT 60.537 55.000 0.00 0.00 0.00 4.83
2827 5619 2.681848 CAGATACGTCGTGGAGGTTACT 59.318 50.000 8.47 0.00 32.77 2.24
2831 5623 0.453390 CGTCGTGGAGGTTACTACCC 59.547 60.000 0.00 0.00 46.28 3.69
2921 5720 3.733960 CCGACGCCTGACTGACGA 61.734 66.667 0.00 0.00 0.00 4.20
3070 6109 6.218108 AGTGTAAGGTATTGTACTGCCTAC 57.782 41.667 0.00 0.00 30.21 3.18
3098 6137 4.743057 TGTCGATGGAGATGATTGAAGT 57.257 40.909 0.00 0.00 0.00 3.01
3215 6264 9.938280 ATAAGTATAACACAACAGTCTTGCTAA 57.062 29.630 0.00 0.00 0.00 3.09
3216 6265 7.891183 AGTATAACACAACAGTCTTGCTAAG 57.109 36.000 0.00 0.00 0.00 2.18
3217 6266 7.442656 AGTATAACACAACAGTCTTGCTAAGT 58.557 34.615 0.00 0.00 0.00 2.24
3218 6267 6.787085 ATAACACAACAGTCTTGCTAAGTC 57.213 37.500 0.00 0.00 0.00 3.01
3219 6268 4.408182 ACACAACAGTCTTGCTAAGTCT 57.592 40.909 0.00 0.00 0.00 3.24
3220 6269 4.372656 ACACAACAGTCTTGCTAAGTCTC 58.627 43.478 0.00 0.00 0.00 3.36
3221 6270 4.141937 ACACAACAGTCTTGCTAAGTCTCA 60.142 41.667 0.00 0.00 0.00 3.27
3222 6271 4.447054 CACAACAGTCTTGCTAAGTCTCAG 59.553 45.833 0.00 0.00 0.00 3.35
3223 6272 4.100189 ACAACAGTCTTGCTAAGTCTCAGT 59.900 41.667 0.00 0.00 0.00 3.41
3224 6273 4.513198 ACAGTCTTGCTAAGTCTCAGTC 57.487 45.455 0.00 0.00 0.00 3.51
3225 6274 3.057876 ACAGTCTTGCTAAGTCTCAGTCG 60.058 47.826 0.00 0.00 0.00 4.18
3226 6275 3.189495 CAGTCTTGCTAAGTCTCAGTCGA 59.811 47.826 0.00 0.00 0.00 4.20
3227 6276 3.189702 AGTCTTGCTAAGTCTCAGTCGAC 59.810 47.826 7.70 7.70 0.00 4.20
3228 6277 3.189702 GTCTTGCTAAGTCTCAGTCGACT 59.810 47.826 13.58 13.58 45.73 4.18
3229 6278 3.189495 TCTTGCTAAGTCTCAGTCGACTG 59.811 47.826 34.76 34.76 43.14 3.51
3254 6303 4.724303 ACTTCGTTAAGTCTCTGTCGATG 58.276 43.478 0.00 0.00 42.42 3.84
3255 6304 3.132629 TCGTTAAGTCTCTGTCGATGC 57.867 47.619 0.00 0.00 0.00 3.91
3256 6305 2.747989 TCGTTAAGTCTCTGTCGATGCT 59.252 45.455 0.00 0.00 0.00 3.79
3257 6306 3.937079 TCGTTAAGTCTCTGTCGATGCTA 59.063 43.478 0.00 0.00 0.00 3.49
3258 6307 4.575236 TCGTTAAGTCTCTGTCGATGCTAT 59.425 41.667 0.00 0.00 0.00 2.97
3259 6308 5.756833 TCGTTAAGTCTCTGTCGATGCTATA 59.243 40.000 0.00 0.00 0.00 1.31
3260 6309 6.427242 TCGTTAAGTCTCTGTCGATGCTATAT 59.573 38.462 0.00 0.00 0.00 0.86
3261 6310 6.739100 CGTTAAGTCTCTGTCGATGCTATATC 59.261 42.308 0.00 0.00 0.00 1.63
3262 6311 5.637006 AAGTCTCTGTCGATGCTATATCC 57.363 43.478 0.00 0.00 0.00 2.59
3263 6312 4.657013 AGTCTCTGTCGATGCTATATCCA 58.343 43.478 0.00 0.00 0.00 3.41
3264 6313 5.260424 AGTCTCTGTCGATGCTATATCCAT 58.740 41.667 0.00 0.00 0.00 3.41
3265 6314 6.418946 AGTCTCTGTCGATGCTATATCCATA 58.581 40.000 0.00 0.00 0.00 2.74
3266 6315 6.887002 AGTCTCTGTCGATGCTATATCCATAA 59.113 38.462 0.00 0.00 0.00 1.90
3267 6316 7.394641 AGTCTCTGTCGATGCTATATCCATAAA 59.605 37.037 0.00 0.00 0.00 1.40
3268 6317 8.029522 GTCTCTGTCGATGCTATATCCATAAAA 58.970 37.037 0.00 0.00 0.00 1.52
3269 6318 8.753133 TCTCTGTCGATGCTATATCCATAAAAT 58.247 33.333 0.00 0.00 0.00 1.82
3270 6319 8.932945 TCTGTCGATGCTATATCCATAAAATC 57.067 34.615 0.00 0.00 0.00 2.17
3271 6320 8.753133 TCTGTCGATGCTATATCCATAAAATCT 58.247 33.333 0.00 0.00 0.00 2.40
3272 6321 9.376075 CTGTCGATGCTATATCCATAAAATCTT 57.624 33.333 0.00 0.00 0.00 2.40
3286 6335 9.184523 TCCATAAAATCTTACATTGAAATCCGT 57.815 29.630 0.00 0.00 0.00 4.69
3287 6336 9.236691 CCATAAAATCTTACATTGAAATCCGTG 57.763 33.333 0.00 0.00 0.00 4.94
3288 6337 8.745837 CATAAAATCTTACATTGAAATCCGTGC 58.254 33.333 0.00 0.00 0.00 5.34
3289 6338 5.895636 AATCTTACATTGAAATCCGTGCA 57.104 34.783 0.00 0.00 0.00 4.57
3290 6339 5.895636 ATCTTACATTGAAATCCGTGCAA 57.104 34.783 0.00 0.00 0.00 4.08
3291 6340 5.697473 TCTTACATTGAAATCCGTGCAAA 57.303 34.783 0.00 0.00 0.00 3.68
3292 6341 6.078202 TCTTACATTGAAATCCGTGCAAAA 57.922 33.333 0.00 0.00 0.00 2.44
3293 6342 6.507900 TCTTACATTGAAATCCGTGCAAAAA 58.492 32.000 0.00 0.00 0.00 1.94
3340 6389 9.841880 TCGCTCTTATATATTATGTCACTTGAC 57.158 33.333 2.19 2.19 44.97 3.18
3341 6390 9.847706 CGCTCTTATATATTATGTCACTTGACT 57.152 33.333 10.63 0.00 44.99 3.41
3347 6396 6.814954 ATATTATGTCACTTGACTGGGACT 57.185 37.500 10.63 0.00 44.99 3.85
3348 6397 4.974645 TTATGTCACTTGACTGGGACTT 57.025 40.909 10.63 0.00 44.99 3.01
3349 6398 3.864789 ATGTCACTTGACTGGGACTTT 57.135 42.857 10.63 0.00 44.99 2.66
3350 6399 2.917933 TGTCACTTGACTGGGACTTTG 58.082 47.619 10.63 0.00 44.99 2.77
3351 6400 2.238646 TGTCACTTGACTGGGACTTTGT 59.761 45.455 10.63 0.00 44.99 2.83
3352 6401 3.279434 GTCACTTGACTGGGACTTTGTT 58.721 45.455 1.92 0.00 41.65 2.83
3353 6402 4.080807 TGTCACTTGACTGGGACTTTGTTA 60.081 41.667 10.63 0.00 44.99 2.41
3354 6403 4.879545 GTCACTTGACTGGGACTTTGTTAA 59.120 41.667 1.92 0.00 41.65 2.01
3355 6404 5.355910 GTCACTTGACTGGGACTTTGTTAAA 59.644 40.000 1.92 0.00 41.65 1.52
3356 6405 6.039382 GTCACTTGACTGGGACTTTGTTAAAT 59.961 38.462 1.92 0.00 41.65 1.40
3357 6406 6.262273 TCACTTGACTGGGACTTTGTTAAATC 59.738 38.462 0.00 0.00 0.00 2.17
3358 6407 6.263168 CACTTGACTGGGACTTTGTTAAATCT 59.737 38.462 0.00 0.00 0.00 2.40
3359 6408 6.486993 ACTTGACTGGGACTTTGTTAAATCTC 59.513 38.462 0.00 0.00 0.00 2.75
3360 6409 5.935945 TGACTGGGACTTTGTTAAATCTCA 58.064 37.500 0.00 0.00 0.00 3.27
3361 6410 5.997746 TGACTGGGACTTTGTTAAATCTCAG 59.002 40.000 0.00 0.00 0.00 3.35
3362 6411 5.941788 ACTGGGACTTTGTTAAATCTCAGT 58.058 37.500 0.00 0.00 0.00 3.41
3363 6412 5.998363 ACTGGGACTTTGTTAAATCTCAGTC 59.002 40.000 0.00 0.00 0.00 3.51
3364 6413 4.994852 TGGGACTTTGTTAAATCTCAGTCG 59.005 41.667 0.00 0.00 0.00 4.18
3365 6414 5.221561 TGGGACTTTGTTAAATCTCAGTCGA 60.222 40.000 0.00 0.00 0.00 4.20
3366 6415 5.120363 GGGACTTTGTTAAATCTCAGTCGAC 59.880 44.000 7.70 7.70 0.00 4.20
3367 6416 5.927115 GGACTTTGTTAAATCTCAGTCGACT 59.073 40.000 13.58 13.58 0.00 4.18
3368 6417 6.128795 GGACTTTGTTAAATCTCAGTCGACTG 60.129 42.308 34.76 34.76 45.08 3.51
3378 6427 0.736053 CAGTCGACTGAGACCTAGCC 59.264 60.000 36.73 0.00 46.59 3.93
3379 6428 0.328592 AGTCGACTGAGACCTAGCCA 59.671 55.000 19.30 0.00 41.83 4.75
3380 6429 1.064314 AGTCGACTGAGACCTAGCCAT 60.064 52.381 19.30 0.00 41.83 4.40
3381 6430 2.172930 AGTCGACTGAGACCTAGCCATA 59.827 50.000 19.30 0.00 41.83 2.74
3382 6431 2.291190 GTCGACTGAGACCTAGCCATAC 59.709 54.545 8.70 0.00 35.22 2.39
3383 6432 1.609555 CGACTGAGACCTAGCCATACC 59.390 57.143 0.00 0.00 0.00 2.73
3384 6433 1.964933 GACTGAGACCTAGCCATACCC 59.035 57.143 0.00 0.00 0.00 3.69
3436 6485 4.640771 AAGAAGCTCAACTGATACCCAA 57.359 40.909 0.00 0.00 0.00 4.12
3526 6660 3.527507 TGTGTAGGCCCCATGTTTAAA 57.472 42.857 0.00 0.00 0.00 1.52
3540 6674 5.505780 CATGTTTAAATGACTAGGGGGACA 58.494 41.667 0.00 0.00 0.00 4.02
3556 6690 1.270839 GGACAGCTTGGCTTGAGTACA 60.271 52.381 0.00 0.00 36.40 2.90
3561 6696 3.077359 AGCTTGGCTTGAGTACATTGAC 58.923 45.455 0.00 0.00 33.89 3.18
3591 6732 4.796231 CGAGGGCGAGACCAACCG 62.796 72.222 0.00 0.00 42.05 4.44
3618 6759 0.679002 ATGCATATGGGGCTCATCGC 60.679 55.000 1.35 9.09 37.30 4.58
3637 6778 4.357699 GAGGATCGCATGCCTCTG 57.642 61.111 13.15 0.00 45.72 3.35
3648 6789 2.277969 CATGCCTCTGAAGCTGTACAG 58.722 52.381 18.93 18.93 35.72 2.74
3661 6808 0.690762 TGTACAGGAAGGGGCTTGAC 59.309 55.000 0.00 0.00 0.00 3.18
3694 6841 2.663196 GGACCGTCCAAGAGTGGG 59.337 66.667 13.05 0.00 46.01 4.61
3699 6846 1.987855 CGTCCAAGAGTGGGGCCTA 60.988 63.158 0.84 0.00 46.01 3.93
3700 6847 1.908483 GTCCAAGAGTGGGGCCTAG 59.092 63.158 0.84 0.00 46.01 3.02
3701 6848 1.306997 TCCAAGAGTGGGGCCTAGG 60.307 63.158 3.67 3.67 46.01 3.02
3702 6849 2.592308 CAAGAGTGGGGCCTAGGC 59.408 66.667 26.55 26.55 41.06 3.93
3706 6853 1.995626 GAGTGGGGCCTAGGCTGAA 60.996 63.158 32.18 15.44 41.60 3.02
3707 6854 1.977293 GAGTGGGGCCTAGGCTGAAG 61.977 65.000 32.18 0.00 41.60 3.02
3708 6855 2.124996 TGGGGCCTAGGCTGAAGT 59.875 61.111 32.18 0.00 41.60 3.01
3709 6856 2.300967 TGGGGCCTAGGCTGAAGTG 61.301 63.158 32.18 0.00 41.60 3.16
3710 6857 1.995626 GGGGCCTAGGCTGAAGTGA 60.996 63.158 32.18 0.00 41.60 3.41
3711 6858 1.348775 GGGGCCTAGGCTGAAGTGAT 61.349 60.000 32.18 0.00 41.60 3.06
3712 6859 0.107643 GGGCCTAGGCTGAAGTGATC 59.892 60.000 32.18 12.68 41.60 2.92
3713 6860 0.833287 GGCCTAGGCTGAAGTGATCA 59.167 55.000 32.18 0.00 41.60 2.92
3725 6872 4.568956 TGAAGTGATCAAGCTTTCATCGA 58.431 39.130 4.22 0.00 34.30 3.59
3733 6880 7.965107 GTGATCAAGCTTTCATCGAAATAGTTT 59.035 33.333 4.22 0.00 30.85 2.66
3741 6888 9.675553 GCTTTCATCGAAATAGTTTAAATTTGC 57.324 29.630 0.00 0.00 30.85 3.68
3746 6893 8.586273 CATCGAAATAGTTTAAATTTGCACTGG 58.414 33.333 12.23 1.08 0.00 4.00
3759 6906 0.527565 GCACTGGGCAATGTACTTGG 59.472 55.000 0.00 0.00 43.97 3.61
3760 6907 1.886222 GCACTGGGCAATGTACTTGGA 60.886 52.381 0.00 0.00 43.97 3.53
3761 6908 2.513753 CACTGGGCAATGTACTTGGAA 58.486 47.619 0.00 0.00 35.25 3.53
3762 6909 3.091545 CACTGGGCAATGTACTTGGAAT 58.908 45.455 0.00 0.00 35.25 3.01
3763 6910 3.511146 CACTGGGCAATGTACTTGGAATT 59.489 43.478 0.00 0.00 35.25 2.17
3764 6911 4.021192 CACTGGGCAATGTACTTGGAATTT 60.021 41.667 0.00 0.00 35.25 1.82
3765 6912 5.184864 CACTGGGCAATGTACTTGGAATTTA 59.815 40.000 0.00 0.00 35.25 1.40
3766 6913 5.418840 ACTGGGCAATGTACTTGGAATTTAG 59.581 40.000 0.00 0.00 35.25 1.85
3777 6924 9.555727 TGTACTTGGAATTTAGTTATGCTATCC 57.444 33.333 0.00 0.00 30.58 2.59
3821 6968 3.417069 ACATGGTGATTGAAAGGACGA 57.583 42.857 0.00 0.00 0.00 4.20
3825 6972 2.158885 TGGTGATTGAAAGGACGACACA 60.159 45.455 0.00 0.00 0.00 3.72
3838 6985 3.118738 GGACGACACATCCAGGAATAAGT 60.119 47.826 0.00 0.00 36.15 2.24
3891 7038 7.172532 TGGTAACAGTATTGTGCTTTGTAAGAG 59.827 37.037 0.00 0.00 46.17 2.85
3892 7039 7.386848 GGTAACAGTATTGTGCTTTGTAAGAGA 59.613 37.037 0.00 0.00 37.67 3.10
3893 7040 7.801716 AACAGTATTGTGCTTTGTAAGAGAA 57.198 32.000 0.00 0.00 37.67 2.87
3894 7041 7.426929 ACAGTATTGTGCTTTGTAAGAGAAG 57.573 36.000 0.00 0.00 35.83 2.85
3895 7042 6.992715 ACAGTATTGTGCTTTGTAAGAGAAGT 59.007 34.615 0.00 0.00 35.83 3.01
3896 7043 7.041780 ACAGTATTGTGCTTTGTAAGAGAAGTG 60.042 37.037 0.00 0.00 35.83 3.16
3897 7044 4.552166 TTGTGCTTTGTAAGAGAAGTGC 57.448 40.909 0.00 0.00 0.00 4.40
3898 7045 3.540617 TGTGCTTTGTAAGAGAAGTGCA 58.459 40.909 0.00 0.00 0.00 4.57
3899 7046 3.944650 TGTGCTTTGTAAGAGAAGTGCAA 59.055 39.130 0.00 0.00 0.00 4.08
3900 7047 4.035558 TGTGCTTTGTAAGAGAAGTGCAAG 59.964 41.667 0.00 0.00 0.00 4.01
3901 7048 3.565482 TGCTTTGTAAGAGAAGTGCAAGG 59.435 43.478 0.00 0.00 0.00 3.61
3902 7049 3.565902 GCTTTGTAAGAGAAGTGCAAGGT 59.434 43.478 0.00 0.00 0.00 3.50
3903 7050 4.755123 GCTTTGTAAGAGAAGTGCAAGGTA 59.245 41.667 0.00 0.00 0.00 3.08
3904 7051 5.412904 GCTTTGTAAGAGAAGTGCAAGGTAT 59.587 40.000 0.00 0.00 0.00 2.73
3905 7052 6.072452 GCTTTGTAAGAGAAGTGCAAGGTATT 60.072 38.462 0.00 0.00 0.00 1.89
3906 7053 6.801539 TTGTAAGAGAAGTGCAAGGTATTG 57.198 37.500 0.00 0.00 39.57 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.076100 GACATCGCCAATTGTGTGAGA 58.924 47.619 4.43 0.00 0.00 3.27
61 66 5.597594 TGATAGGCATGCATGTTTTGGATAA 59.402 36.000 26.79 4.24 34.15 1.75
76 81 4.343526 AGAGAGTTTCGTCATGATAGGCAT 59.656 41.667 0.00 0.00 37.85 4.40
79 84 5.506686 TGAGAGAGTTTCGTCATGATAGG 57.493 43.478 0.00 0.00 0.00 2.57
81 86 7.448469 TGGATATGAGAGAGTTTCGTCATGATA 59.552 37.037 0.00 0.00 32.01 2.15
82 87 6.266330 TGGATATGAGAGAGTTTCGTCATGAT 59.734 38.462 0.00 0.00 32.01 2.45
83 88 5.594317 TGGATATGAGAGAGTTTCGTCATGA 59.406 40.000 0.00 0.00 32.01 3.07
84 89 5.836347 TGGATATGAGAGAGTTTCGTCATG 58.164 41.667 0.00 0.00 32.01 3.07
85 90 6.471233 TTGGATATGAGAGAGTTTCGTCAT 57.529 37.500 0.00 0.00 34.11 3.06
86 91 5.914898 TTGGATATGAGAGAGTTTCGTCA 57.085 39.130 0.00 0.00 0.00 4.35
107 145 4.192317 GAGCTTCCCACGAGACATATTTT 58.808 43.478 0.00 0.00 0.00 1.82
111 149 1.751351 CTGAGCTTCCCACGAGACATA 59.249 52.381 0.00 0.00 0.00 2.29
124 162 4.397417 CGAAATTTTCTCCATCCTGAGCTT 59.603 41.667 7.50 0.00 32.22 3.74
142 180 2.467566 AACACGTAAGGAGGCGAAAT 57.532 45.000 0.00 0.00 46.39 2.17
178 218 7.269477 AGTTCAAGTCTCATTCCTCAAAAAG 57.731 36.000 0.00 0.00 0.00 2.27
210 250 2.831685 TATGCGACCAAACACTGTCT 57.168 45.000 0.00 0.00 0.00 3.41
222 262 2.354821 GTCAGGGTCCATTTTATGCGAC 59.645 50.000 0.00 0.00 32.91 5.19
224 264 1.676006 GGTCAGGGTCCATTTTATGCG 59.324 52.381 0.00 0.00 0.00 4.73
226 266 2.024464 TGGGGTCAGGGTCCATTTTATG 60.024 50.000 0.00 0.00 0.00 1.90
230 277 1.071314 TGTGGGGTCAGGGTCCATTT 61.071 55.000 0.00 0.00 32.71 2.32
243 290 1.376466 GGGATCGGATGATGTGGGG 59.624 63.158 0.00 0.00 34.09 4.96
268 315 2.206750 TCAACTGGTTGTCGTGCTAAC 58.793 47.619 12.34 0.00 41.16 2.34
375 426 2.287608 CCACGGAAGAGGCAAGTTTTTC 60.288 50.000 0.00 0.00 34.36 2.29
574 629 6.294787 CCAGTATCCAGTGGTCACATATCTAC 60.295 46.154 9.54 0.00 40.03 2.59
623 735 4.696455 CGTTGTAATTAACCCGGGATAGT 58.304 43.478 32.02 14.81 0.00 2.12
754 1048 0.965866 GAAAGGGTAGCCAGCCAACC 60.966 60.000 14.62 3.69 45.35 3.77
765 1059 5.529800 CGTGAAGAAAAGAAAGGAAAGGGTA 59.470 40.000 0.00 0.00 0.00 3.69
768 1062 4.338400 ACCGTGAAGAAAAGAAAGGAAAGG 59.662 41.667 0.00 0.00 0.00 3.11
769 1063 5.500645 ACCGTGAAGAAAAGAAAGGAAAG 57.499 39.130 0.00 0.00 0.00 2.62
770 1064 5.907866 AACCGTGAAGAAAAGAAAGGAAA 57.092 34.783 0.00 0.00 0.00 3.13
771 1065 6.117488 AGTAACCGTGAAGAAAAGAAAGGAA 58.883 36.000 0.00 0.00 0.00 3.36
772 1066 5.677567 AGTAACCGTGAAGAAAAGAAAGGA 58.322 37.500 0.00 0.00 0.00 3.36
826 1123 9.991388 GATGTCGAGATAGATATGGTTTACTAC 57.009 37.037 0.00 0.00 0.00 2.73
859 1156 1.055849 AAAGGGAAAATTTGGCGGCT 58.944 45.000 11.43 0.00 0.00 5.52
905 1203 3.068881 CGGTGTGGGTGAGGTGAT 58.931 61.111 0.00 0.00 0.00 3.06
906 1204 3.936203 GCGGTGTGGGTGAGGTGA 61.936 66.667 0.00 0.00 0.00 4.02
908 1206 3.941188 CTGCGGTGTGGGTGAGGT 61.941 66.667 0.00 0.00 0.00 3.85
910 1208 2.666190 CACTGCGGTGTGGGTGAG 60.666 66.667 17.96 0.00 38.54 3.51
911 1209 4.927782 GCACTGCGGTGTGGGTGA 62.928 66.667 26.00 0.00 44.65 4.02
915 1213 3.952675 GTGTGCACTGCGGTGTGG 61.953 66.667 26.00 2.06 44.65 4.17
916 1214 3.952675 GGTGTGCACTGCGGTGTG 61.953 66.667 26.00 13.05 44.65 3.82
917 1215 4.481617 TGGTGTGCACTGCGGTGT 62.482 61.111 26.00 0.00 44.65 4.16
918 1216 3.952675 GTGGTGTGCACTGCGGTG 61.953 66.667 21.79 21.79 45.53 4.94
919 1217 3.986072 TTGTGGTGTGCACTGCGGT 62.986 57.895 19.41 0.00 0.00 5.68
920 1218 3.208383 TTGTGGTGTGCACTGCGG 61.208 61.111 19.41 0.00 0.00 5.69
921 1219 2.024588 GTTGTGGTGTGCACTGCG 59.975 61.111 19.41 0.00 0.00 5.18
922 1220 2.412937 GGTTGTGGTGTGCACTGC 59.587 61.111 19.41 10.77 0.00 4.40
925 1223 1.498865 CTCTCGGTTGTGGTGTGCAC 61.499 60.000 10.75 10.75 0.00 4.57
930 1228 1.374758 GGCTCTCTCGGTTGTGGTG 60.375 63.158 0.00 0.00 0.00 4.17
949 1247 1.953559 TGAAGAGCGAAACAAGCACT 58.046 45.000 0.00 0.00 37.13 4.40
956 1254 4.274865 CAGTGAGTTTTGAAGAGCGAAAC 58.725 43.478 0.00 0.00 46.75 2.78
957 1255 3.242739 GCAGTGAGTTTTGAAGAGCGAAA 60.243 43.478 0.00 0.00 0.00 3.46
958 1256 2.287915 GCAGTGAGTTTTGAAGAGCGAA 59.712 45.455 0.00 0.00 0.00 4.70
959 1257 1.867233 GCAGTGAGTTTTGAAGAGCGA 59.133 47.619 0.00 0.00 0.00 4.93
960 1258 1.869767 AGCAGTGAGTTTTGAAGAGCG 59.130 47.619 0.00 0.00 0.00 5.03
973 1271 1.534959 AGTGGGAGCTCAGCAGTGA 60.535 57.895 17.19 0.00 0.00 3.41
974 1272 1.079266 GAGTGGGAGCTCAGCAGTG 60.079 63.158 17.19 0.00 35.67 3.66
975 1273 2.644212 CGAGTGGGAGCTCAGCAGT 61.644 63.158 17.19 0.00 35.33 4.40
976 1274 2.183811 CGAGTGGGAGCTCAGCAG 59.816 66.667 17.19 0.00 35.33 4.24
977 1275 4.074526 GCGAGTGGGAGCTCAGCA 62.075 66.667 17.19 0.00 36.14 4.41
979 1277 3.753434 ACGCGAGTGGGAGCTCAG 61.753 66.667 15.93 0.30 46.97 3.35
1027 1459 4.829518 CGATCGACCGTGCGCTGA 62.830 66.667 10.26 0.00 0.00 4.26
1073 2151 1.276138 TGGACTCATGGTGTGCTACTG 59.724 52.381 11.08 0.00 0.00 2.74
1074 2152 1.552337 CTGGACTCATGGTGTGCTACT 59.448 52.381 11.08 0.00 0.00 2.57
1193 3892 0.670239 CACTGTGCACGGACAGCATA 60.670 55.000 31.98 0.00 46.28 3.14
1210 3909 2.060980 ATGGCCGTCTCCTCCTCAC 61.061 63.158 0.00 0.00 0.00 3.51
1364 4072 3.016971 CCCAGGCTGATCCACCCA 61.017 66.667 17.94 0.00 37.29 4.51
1580 4306 3.261897 AGACACGAAGATCCATGACCTTT 59.738 43.478 0.00 0.00 0.00 3.11
1705 4432 1.871676 CCATCATGCAGGTCATTCTCG 59.128 52.381 0.00 0.00 31.79 4.04
1706 4433 1.607628 GCCATCATGCAGGTCATTCTC 59.392 52.381 0.00 0.00 31.79 2.87
1707 4434 1.688772 GCCATCATGCAGGTCATTCT 58.311 50.000 0.00 0.00 31.79 2.40
1708 4435 0.309922 CGCCATCATGCAGGTCATTC 59.690 55.000 0.00 0.00 31.79 2.67
1709 4436 1.731433 GCGCCATCATGCAGGTCATT 61.731 55.000 0.00 0.00 31.79 2.57
1710 4437 2.191513 GCGCCATCATGCAGGTCAT 61.192 57.895 0.00 0.00 35.31 3.06
1711 4438 2.825387 GCGCCATCATGCAGGTCA 60.825 61.111 0.00 0.00 0.00 4.02
1712 4439 3.945434 CGCGCCATCATGCAGGTC 61.945 66.667 0.00 0.00 0.00 3.85
1727 4454 2.817834 TTACGTGGATGCAGGCGC 60.818 61.111 6.84 0.00 39.24 6.53
1728 4455 2.461110 GGTTACGTGGATGCAGGCG 61.461 63.158 6.84 1.02 0.00 5.52
1729 4456 0.748005 ATGGTTACGTGGATGCAGGC 60.748 55.000 6.84 0.00 0.00 4.85
1730 4457 1.016627 CATGGTTACGTGGATGCAGG 58.983 55.000 5.28 5.28 0.00 4.85
1783 4556 1.652563 CGCCTGTGCATGGATCATG 59.347 57.895 12.16 3.72 43.91 3.07
1784 4557 2.191513 GCGCCTGTGCATGGATCAT 61.192 57.895 12.16 0.00 37.32 2.45
1785 4558 2.825387 GCGCCTGTGCATGGATCA 60.825 61.111 12.16 0.00 37.32 2.92
1786 4559 3.945434 CGCGCCTGTGCATGGATC 61.945 66.667 12.16 2.74 37.32 3.36
2368 5160 2.049802 TTGTCCGGAGTCGCGTTC 60.050 61.111 3.06 5.34 34.56 3.95
2524 5316 1.296715 GTCCAGCTCCGTGAACCAT 59.703 57.895 0.00 0.00 0.00 3.55
2831 5623 2.202932 CATCTGCTTCCCCGTCGG 60.203 66.667 3.60 3.60 0.00 4.79
3070 6109 4.516365 TCATCTCCATCGACATGAGATG 57.484 45.455 28.14 28.14 40.97 2.90
3189 6238 9.938280 TTAGCAAGACTGTTGTGTTATACTTAT 57.062 29.630 0.00 0.00 0.00 1.73
3190 6239 9.419297 CTTAGCAAGACTGTTGTGTTATACTTA 57.581 33.333 0.00 0.00 0.00 2.24
3191 6240 7.931948 ACTTAGCAAGACTGTTGTGTTATACTT 59.068 33.333 3.37 0.00 0.00 2.24
3192 6241 7.442656 ACTTAGCAAGACTGTTGTGTTATACT 58.557 34.615 3.37 0.00 0.00 2.12
3193 6242 7.599245 AGACTTAGCAAGACTGTTGTGTTATAC 59.401 37.037 3.37 0.00 32.40 1.47
3194 6243 7.667557 AGACTTAGCAAGACTGTTGTGTTATA 58.332 34.615 3.37 0.00 32.40 0.98
3195 6244 6.525629 AGACTTAGCAAGACTGTTGTGTTAT 58.474 36.000 3.37 0.00 32.40 1.89
3196 6245 5.914033 AGACTTAGCAAGACTGTTGTGTTA 58.086 37.500 3.37 0.00 32.40 2.41
3197 6246 4.770795 AGACTTAGCAAGACTGTTGTGTT 58.229 39.130 3.37 0.00 32.40 3.32
3198 6247 4.141937 TGAGACTTAGCAAGACTGTTGTGT 60.142 41.667 5.85 0.00 33.75 3.72
3199 6248 4.371786 TGAGACTTAGCAAGACTGTTGTG 58.628 43.478 5.85 0.00 33.75 3.33
3200 6249 4.100189 ACTGAGACTTAGCAAGACTGTTGT 59.900 41.667 5.85 0.00 33.75 3.32
3201 6250 4.626042 ACTGAGACTTAGCAAGACTGTTG 58.374 43.478 5.85 0.00 33.75 3.33
3202 6251 4.557695 CGACTGAGACTTAGCAAGACTGTT 60.558 45.833 5.85 0.00 33.75 3.16
3203 6252 3.057876 CGACTGAGACTTAGCAAGACTGT 60.058 47.826 5.85 0.00 33.75 3.55
3204 6253 3.189495 TCGACTGAGACTTAGCAAGACTG 59.811 47.826 5.85 0.00 33.75 3.51
3205 6254 3.189702 GTCGACTGAGACTTAGCAAGACT 59.810 47.826 8.70 2.60 38.09 3.24
3206 6255 3.494232 GTCGACTGAGACTTAGCAAGAC 58.506 50.000 8.70 0.00 38.09 3.01
3207 6256 3.833545 GTCGACTGAGACTTAGCAAGA 57.166 47.619 8.70 0.00 38.09 3.02
3219 6268 1.880271 ACGAAGTCTCAGTCGACTGA 58.120 50.000 38.24 38.24 44.92 3.41
3220 6269 2.690173 AACGAAGTCTCAGTCGACTG 57.310 50.000 34.76 34.76 45.00 3.51
3221 6270 3.814283 ACTTAACGAAGTCTCAGTCGACT 59.186 43.478 13.58 13.58 45.00 4.18
3222 6271 4.144534 ACTTAACGAAGTCTCAGTCGAC 57.855 45.455 7.70 7.70 45.00 4.20
3233 6282 3.544285 GCATCGACAGAGACTTAACGAAG 59.456 47.826 0.00 0.00 38.76 3.79
3234 6283 3.190744 AGCATCGACAGAGACTTAACGAA 59.809 43.478 0.00 0.00 33.77 3.85
3235 6284 2.747989 AGCATCGACAGAGACTTAACGA 59.252 45.455 0.00 0.00 0.00 3.85
3236 6285 3.138205 AGCATCGACAGAGACTTAACG 57.862 47.619 0.00 0.00 0.00 3.18
3237 6286 7.024768 GGATATAGCATCGACAGAGACTTAAC 58.975 42.308 0.00 0.00 0.00 2.01
3238 6287 6.715264 TGGATATAGCATCGACAGAGACTTAA 59.285 38.462 0.00 0.00 0.00 1.85
3239 6288 6.238648 TGGATATAGCATCGACAGAGACTTA 58.761 40.000 0.00 0.00 0.00 2.24
3240 6289 5.073428 TGGATATAGCATCGACAGAGACTT 58.927 41.667 0.00 0.00 0.00 3.01
3241 6290 4.657013 TGGATATAGCATCGACAGAGACT 58.343 43.478 0.00 0.00 0.00 3.24
3242 6291 5.574891 ATGGATATAGCATCGACAGAGAC 57.425 43.478 0.00 0.00 0.00 3.36
3243 6292 7.703058 TTTATGGATATAGCATCGACAGAGA 57.297 36.000 0.00 0.00 0.00 3.10
3244 6293 8.939201 ATTTTATGGATATAGCATCGACAGAG 57.061 34.615 0.00 0.00 0.00 3.35
3245 6294 8.753133 AGATTTTATGGATATAGCATCGACAGA 58.247 33.333 0.00 0.00 0.00 3.41
3246 6295 8.939201 AGATTTTATGGATATAGCATCGACAG 57.061 34.615 0.00 0.00 0.00 3.51
3260 6309 9.184523 ACGGATTTCAATGTAAGATTTTATGGA 57.815 29.630 0.00 0.00 0.00 3.41
3261 6310 9.236691 CACGGATTTCAATGTAAGATTTTATGG 57.763 33.333 0.00 0.00 0.00 2.74
3262 6311 8.745837 GCACGGATTTCAATGTAAGATTTTATG 58.254 33.333 0.00 0.00 0.00 1.90
3263 6312 8.465999 TGCACGGATTTCAATGTAAGATTTTAT 58.534 29.630 0.00 0.00 0.00 1.40
3264 6313 7.821652 TGCACGGATTTCAATGTAAGATTTTA 58.178 30.769 0.00 0.00 0.00 1.52
3265 6314 6.686630 TGCACGGATTTCAATGTAAGATTTT 58.313 32.000 0.00 0.00 0.00 1.82
3266 6315 6.266168 TGCACGGATTTCAATGTAAGATTT 57.734 33.333 0.00 0.00 0.00 2.17
3267 6316 5.895636 TGCACGGATTTCAATGTAAGATT 57.104 34.783 0.00 0.00 0.00 2.40
3268 6317 5.895636 TTGCACGGATTTCAATGTAAGAT 57.104 34.783 0.00 0.00 0.00 2.40
3269 6318 5.697473 TTTGCACGGATTTCAATGTAAGA 57.303 34.783 0.00 0.00 0.00 2.10
3270 6319 6.761731 TTTTTGCACGGATTTCAATGTAAG 57.238 33.333 0.00 0.00 0.00 2.34
3314 6363 9.841880 GTCAAGTGACATAATATATAAGAGCGA 57.158 33.333 6.57 0.00 44.18 4.93
3331 6380 2.919228 ACAAAGTCCCAGTCAAGTGAC 58.081 47.619 3.12 3.12 45.08 3.67
3332 6381 3.644966 AACAAAGTCCCAGTCAAGTGA 57.355 42.857 0.00 0.00 0.00 3.41
3333 6382 5.828299 TTTAACAAAGTCCCAGTCAAGTG 57.172 39.130 0.00 0.00 0.00 3.16
3334 6383 6.365520 AGATTTAACAAAGTCCCAGTCAAGT 58.634 36.000 0.00 0.00 0.00 3.16
3335 6384 6.486657 TGAGATTTAACAAAGTCCCAGTCAAG 59.513 38.462 0.00 0.00 0.00 3.02
3336 6385 6.361433 TGAGATTTAACAAAGTCCCAGTCAA 58.639 36.000 0.00 0.00 0.00 3.18
3337 6386 5.935945 TGAGATTTAACAAAGTCCCAGTCA 58.064 37.500 0.00 0.00 0.00 3.41
3338 6387 5.998363 ACTGAGATTTAACAAAGTCCCAGTC 59.002 40.000 0.00 0.00 0.00 3.51
3339 6388 5.941788 ACTGAGATTTAACAAAGTCCCAGT 58.058 37.500 0.00 0.00 0.00 4.00
3340 6389 5.120830 CGACTGAGATTTAACAAAGTCCCAG 59.879 44.000 0.00 0.00 32.29 4.45
3341 6390 4.994852 CGACTGAGATTTAACAAAGTCCCA 59.005 41.667 0.00 0.00 32.29 4.37
3342 6391 5.120363 GTCGACTGAGATTTAACAAAGTCCC 59.880 44.000 8.70 0.00 32.29 4.46
3343 6392 5.927115 AGTCGACTGAGATTTAACAAAGTCC 59.073 40.000 19.30 0.00 32.29 3.85
3344 6393 6.812312 CAGTCGACTGAGATTTAACAAAGTC 58.188 40.000 36.73 0.00 46.59 3.01
3345 6394 6.771188 CAGTCGACTGAGATTTAACAAAGT 57.229 37.500 36.73 0.00 46.59 2.66
3359 6408 0.736053 GGCTAGGTCTCAGTCGACTG 59.264 60.000 34.76 34.76 45.08 3.51
3360 6409 0.328592 TGGCTAGGTCTCAGTCGACT 59.671 55.000 13.58 13.58 34.38 4.18
3361 6410 1.394618 ATGGCTAGGTCTCAGTCGAC 58.605 55.000 7.70 7.70 0.00 4.20
3362 6411 2.573369 GTATGGCTAGGTCTCAGTCGA 58.427 52.381 0.00 0.00 0.00 4.20
3363 6412 1.609555 GGTATGGCTAGGTCTCAGTCG 59.390 57.143 0.00 0.00 0.00 4.18
3364 6413 1.964933 GGGTATGGCTAGGTCTCAGTC 59.035 57.143 0.00 0.00 0.00 3.51
3365 6414 1.291033 TGGGTATGGCTAGGTCTCAGT 59.709 52.381 0.00 0.00 0.00 3.41
3366 6415 2.088104 TGGGTATGGCTAGGTCTCAG 57.912 55.000 0.00 0.00 0.00 3.35
3367 6416 2.795291 ATGGGTATGGCTAGGTCTCA 57.205 50.000 0.00 0.00 0.00 3.27
3368 6417 3.901844 TGTTATGGGTATGGCTAGGTCTC 59.098 47.826 0.00 0.00 0.00 3.36
3369 6418 3.646637 GTGTTATGGGTATGGCTAGGTCT 59.353 47.826 0.00 0.00 0.00 3.85
3370 6419 3.389983 TGTGTTATGGGTATGGCTAGGTC 59.610 47.826 0.00 0.00 0.00 3.85
3371 6420 3.389866 TGTGTTATGGGTATGGCTAGGT 58.610 45.455 0.00 0.00 0.00 3.08
3372 6421 4.431416 TTGTGTTATGGGTATGGCTAGG 57.569 45.455 0.00 0.00 0.00 3.02
3373 6422 5.067283 GGTTTTGTGTTATGGGTATGGCTAG 59.933 44.000 0.00 0.00 0.00 3.42
3374 6423 4.951094 GGTTTTGTGTTATGGGTATGGCTA 59.049 41.667 0.00 0.00 0.00 3.93
3375 6424 3.767131 GGTTTTGTGTTATGGGTATGGCT 59.233 43.478 0.00 0.00 0.00 4.75
3376 6425 3.511934 TGGTTTTGTGTTATGGGTATGGC 59.488 43.478 0.00 0.00 0.00 4.40
3377 6426 4.524714 TGTGGTTTTGTGTTATGGGTATGG 59.475 41.667 0.00 0.00 0.00 2.74
3378 6427 5.713792 TGTGGTTTTGTGTTATGGGTATG 57.286 39.130 0.00 0.00 0.00 2.39
3379 6428 6.926630 AATGTGGTTTTGTGTTATGGGTAT 57.073 33.333 0.00 0.00 0.00 2.73
3380 6429 6.551601 AGAAATGTGGTTTTGTGTTATGGGTA 59.448 34.615 0.00 0.00 0.00 3.69
3381 6430 5.365314 AGAAATGTGGTTTTGTGTTATGGGT 59.635 36.000 0.00 0.00 0.00 4.51
3382 6431 5.852827 AGAAATGTGGTTTTGTGTTATGGG 58.147 37.500 0.00 0.00 0.00 4.00
3383 6432 8.879342 TTTAGAAATGTGGTTTTGTGTTATGG 57.121 30.769 0.00 0.00 0.00 2.74
3384 6433 9.528018 ACTTTAGAAATGTGGTTTTGTGTTATG 57.472 29.630 0.00 0.00 0.00 1.90
3420 6469 4.327680 AGAGTTTTGGGTATCAGTTGAGC 58.672 43.478 0.00 0.00 0.00 4.26
3421 6470 6.070767 TCCTAGAGTTTTGGGTATCAGTTGAG 60.071 42.308 0.00 0.00 0.00 3.02
3436 6485 4.217983 CGTCACTACTTGGTCCTAGAGTTT 59.782 45.833 7.38 0.00 0.00 2.66
3511 6645 3.473113 AGTCATTTAAACATGGGGCCT 57.527 42.857 0.84 0.00 0.00 5.19
3526 6660 1.207791 CAAGCTGTCCCCCTAGTCAT 58.792 55.000 0.00 0.00 0.00 3.06
3540 6674 3.077359 GTCAATGTACTCAAGCCAAGCT 58.923 45.455 0.00 0.00 42.56 3.74
3591 6732 2.034879 CCCATATGCATCCGTCGGC 61.035 63.158 0.19 0.00 0.00 5.54
3618 6759 2.356793 GAGGCATGCGATCCTCGG 60.357 66.667 12.44 0.00 40.84 4.63
3633 6774 2.093764 CCCTTCCTGTACAGCTTCAGAG 60.094 54.545 17.86 7.65 34.02 3.35
3637 6778 0.393132 GCCCCTTCCTGTACAGCTTC 60.393 60.000 17.86 0.00 0.00 3.86
3648 6789 2.434359 CGTCGTCAAGCCCCTTCC 60.434 66.667 0.00 0.00 0.00 3.46
3661 6808 3.862402 CCGTCCTCGTCCTCGTCG 61.862 72.222 0.00 0.00 38.33 5.12
3694 6841 0.833287 TGATCACTTCAGCCTAGGCC 59.167 55.000 30.42 12.55 43.17 5.19
3699 6846 2.875094 AAGCTTGATCACTTCAGCCT 57.125 45.000 12.46 0.00 35.27 4.58
3700 6847 2.816087 TGAAAGCTTGATCACTTCAGCC 59.184 45.455 12.46 0.48 35.27 4.85
3701 6848 4.660105 GATGAAAGCTTGATCACTTCAGC 58.340 43.478 8.76 8.76 35.27 4.26
3702 6849 4.628766 TCGATGAAAGCTTGATCACTTCAG 59.371 41.667 15.54 0.00 35.27 3.02
3706 6853 6.820656 ACTATTTCGATGAAAGCTTGATCACT 59.179 34.615 15.54 0.00 34.92 3.41
3707 6854 7.009568 ACTATTTCGATGAAAGCTTGATCAC 57.990 36.000 15.54 5.56 34.92 3.06
3708 6855 7.615582 AACTATTTCGATGAAAGCTTGATCA 57.384 32.000 15.54 10.50 34.92 2.92
3709 6856 9.988350 TTAAACTATTTCGATGAAAGCTTGATC 57.012 29.630 0.00 4.14 34.92 2.92
3741 6888 2.198827 TCCAAGTACATTGCCCAGTG 57.801 50.000 0.00 0.00 37.60 3.66
3743 6890 4.806640 AAATTCCAAGTACATTGCCCAG 57.193 40.909 0.00 0.00 37.60 4.45
3746 6893 7.435192 GCATAACTAAATTCCAAGTACATTGCC 59.565 37.037 0.00 0.00 37.60 4.52
3810 6957 2.549992 CCTGGATGTGTCGTCCTTTCAA 60.550 50.000 9.05 0.00 40.04 2.69
3821 6968 9.920946 ATTATACAAACTTATTCCTGGATGTGT 57.079 29.630 0.00 0.00 0.00 3.72
3851 6998 5.984725 ACTGTTACCATGGATCGAATGTAA 58.015 37.500 21.47 0.39 0.00 2.41
3852 6999 5.607939 ACTGTTACCATGGATCGAATGTA 57.392 39.130 21.47 0.00 0.00 2.29
3853 7000 4.487714 ACTGTTACCATGGATCGAATGT 57.512 40.909 21.47 5.31 0.00 2.71
3854 7001 6.483307 ACAATACTGTTACCATGGATCGAATG 59.517 38.462 21.47 8.43 28.57 2.67
3855 7002 6.483307 CACAATACTGTTACCATGGATCGAAT 59.517 38.462 21.47 1.98 31.64 3.34
3862 7009 5.048083 ACAAAGCACAATACTGTTACCATGG 60.048 40.000 11.19 11.19 31.64 3.66
3863 7010 6.012658 ACAAAGCACAATACTGTTACCATG 57.987 37.500 0.00 0.00 31.64 3.66
3865 7012 6.993308 TCTTACAAAGCACAATACTGTTACCA 59.007 34.615 0.00 0.00 31.64 3.25
3880 7027 3.565902 ACCTTGCACTTCTCTTACAAAGC 59.434 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.