Multiple sequence alignment - TraesCS2B01G558900

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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 TraesCS2B01G558900 chr2B 100.000 3738 0 0 1 3738 753067420 753071157 0.000000e+00 6903.0
1 TraesCS2B01G558900 chr2B 97.143 945 26 1 1 944 32146610 32147554 0.000000e+00 1594.0
2 TraesCS2B01G558900 chr2B 92.407 698 52 1 1 697 43819097 43818400 0.000000e+00 994.0
3 TraesCS2B01G558900 chr2B 99.296 142 1 0 3597 3738 187868698 187868557 1.330000e-64 257.0
4 TraesCS2B01G558900 chr2B 98.630 146 1 1 3594 3738 585865276 585865421 1.330000e-64 257.0
5 TraesCS2B01G558900 chr2B 99.296 142 1 0 3597 3738 610753464 610753605 1.330000e-64 257.0
6 TraesCS2B01G558900 chr2B 97.945 146 2 1 3594 3738 187858734 187858589 6.200000e-63 252.0
7 TraesCS2B01G558900 chr2B 91.111 45 4 0 2471 2515 753069829 753069873 1.120000e-05 62.1
8 TraesCS2B01G558900 chr2B 91.111 45 4 0 2410 2454 753069890 753069934 1.120000e-05 62.1
9 TraesCS2B01G558900 chr2D 92.923 2261 93 23 1396 3599 617333141 617335391 0.000000e+00 3227.0
10 TraesCS2B01G558900 chr2D 89.510 429 42 1 1711 2139 617134667 617134242 1.180000e-149 540.0
11 TraesCS2B01G558900 chr2D 88.917 397 25 8 1294 1689 617135035 617134657 4.370000e-129 472.0
12 TraesCS2B01G558900 chr2D 87.879 330 37 1 1711 2040 617338223 617338549 5.860000e-103 385.0
13 TraesCS2B01G558900 chr2D 77.008 361 58 18 2727 3071 617133636 617133285 2.290000e-42 183.0
14 TraesCS2B01G558900 chr2D 84.239 184 24 3 954 1132 617316556 617316739 1.380000e-39 174.0
15 TraesCS2B01G558900 chr2D 84.302 172 21 5 3072 3239 617133254 617133085 2.990000e-36 163.0
16 TraesCS2B01G558900 chr2D 83.598 189 12 7 1501 1689 617338064 617338233 3.860000e-35 159.0
17 TraesCS2B01G558900 chr2D 76.033 363 39 28 2728 3072 617340012 617340344 1.080000e-30 145.0
18 TraesCS2B01G558900 chr2D 91.111 45 4 0 2471 2515 617334157 617334201 1.120000e-05 62.1
19 TraesCS2B01G558900 chr2A 95.404 1088 32 7 1376 2454 747596541 747597619 0.000000e+00 1716.0
20 TraesCS2B01G558900 chr2A 90.137 1166 67 14 2471 3603 747597575 747598725 0.000000e+00 1472.0
21 TraesCS2B01G558900 chr2A 87.576 330 38 1 1711 2040 747601215 747601541 2.720000e-101 379.0
22 TraesCS2B01G558900 chr2A 82.428 313 26 16 1383 1689 747600936 747601225 2.880000e-61 246.0
23 TraesCS2B01G558900 chr7B 97.366 949 24 1 1 948 123741047 123741995 0.000000e+00 1613.0
24 TraesCS2B01G558900 chr7B 89.030 948 102 2 1 946 635904014 635904961 0.000000e+00 1173.0
25 TraesCS2B01G558900 chr1B 96.829 946 27 3 1 944 361010816 361009872 0.000000e+00 1578.0
26 TraesCS2B01G558900 chr1B 98.592 142 2 0 3597 3738 598626706 598626847 6.200000e-63 252.0
27 TraesCS2B01G558900 chr3B 93.008 944 61 3 1 942 104265799 104266739 0.000000e+00 1373.0
28 TraesCS2B01G558900 chr3B 97.945 146 1 2 3593 3738 805078195 805078338 6.200000e-63 252.0
29 TraesCS2B01G558900 chr4A 91.966 946 74 2 1 944 589484976 589485921 0.000000e+00 1325.0
30 TraesCS2B01G558900 chr4A 89.167 960 91 8 1 948 662058015 662057057 0.000000e+00 1184.0
31 TraesCS2B01G558900 chr4A 96.364 110 4 0 2295 2404 213025565 213025456 8.250000e-42 182.0
32 TraesCS2B01G558900 chr4A 89.552 134 11 1 2270 2403 101750486 101750356 2.310000e-37 167.0
33 TraesCS2B01G558900 chr5A 90.042 944 87 5 1 943 395283530 395284467 0.000000e+00 1216.0
34 TraesCS2B01G558900 chr5A 89.474 133 10 2 2273 2404 320214238 320214367 8.310000e-37 165.0
35 TraesCS2B01G558900 chr1A 86.809 940 121 3 8 945 556597425 556596487 0.000000e+00 1046.0
36 TraesCS2B01G558900 chr7D 87.879 759 91 1 186 943 115182079 115182837 0.000000e+00 891.0
37 TraesCS2B01G558900 chr7D 90.625 128 9 1 2277 2404 397991489 397991613 2.310000e-37 167.0
38 TraesCS2B01G558900 chr7D 74.237 295 63 9 627 914 629625388 629625100 1.100000e-20 111.0
39 TraesCS2B01G558900 chr6A 89.134 543 52 5 383 924 496125316 496124780 0.000000e+00 669.0
40 TraesCS2B01G558900 chr1D 85.597 611 83 3 8 615 337205150 337204542 1.460000e-178 636.0
41 TraesCS2B01G558900 chr1D 87.879 330 38 2 621 948 337196267 337195938 1.630000e-103 387.0
42 TraesCS2B01G558900 chr5B 98.013 151 2 1 3589 3738 338893764 338893914 1.030000e-65 261.0
43 TraesCS2B01G558900 chr5B 99.296 142 1 0 3597 3738 338903052 338903193 1.330000e-64 257.0
44 TraesCS2B01G558900 chr5B 76.062 259 53 8 691 944 120575701 120575447 3.920000e-25 126.0
45 TraesCS2B01G558900 chrUn 99.296 142 1 0 3597 3738 158254361 158254220 1.330000e-64 257.0
46 TraesCS2B01G558900 chr3A 90.226 133 9 2 2273 2404 625536743 625536872 1.790000e-38 171.0
47 TraesCS2B01G558900 chr3D 90.152 132 9 2 2273 2404 363866170 363866043 6.420000e-38 169.0
48 TraesCS2B01G558900 chr3D 90.625 128 9 1 2277 2404 87925999 87926123 2.310000e-37 167.0
49 TraesCS2B01G558900 chr7A 73.934 211 37 13 745 944 732451915 732451712 6.700000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G558900 chr2B 753067420 753071157 3737 False 2342.40 6903 94.07400 1 3738 3 chr2B.!!$F4 3737
1 TraesCS2B01G558900 chr2B 32146610 32147554 944 False 1594.00 1594 97.14300 1 944 1 chr2B.!!$F1 943
2 TraesCS2B01G558900 chr2B 43818400 43819097 697 True 994.00 994 92.40700 1 697 1 chr2B.!!$R1 696
3 TraesCS2B01G558900 chr2D 617333141 617340344 7203 False 795.62 3227 86.30880 1396 3599 5 chr2D.!!$F2 2203
4 TraesCS2B01G558900 chr2D 617133085 617135035 1950 True 339.50 540 84.93425 1294 3239 4 chr2D.!!$R1 1945
5 TraesCS2B01G558900 chr2A 747596541 747601541 5000 False 953.25 1716 88.88625 1376 3603 4 chr2A.!!$F1 2227
6 TraesCS2B01G558900 chr7B 123741047 123741995 948 False 1613.00 1613 97.36600 1 948 1 chr7B.!!$F1 947
7 TraesCS2B01G558900 chr7B 635904014 635904961 947 False 1173.00 1173 89.03000 1 946 1 chr7B.!!$F2 945
8 TraesCS2B01G558900 chr1B 361009872 361010816 944 True 1578.00 1578 96.82900 1 944 1 chr1B.!!$R1 943
9 TraesCS2B01G558900 chr3B 104265799 104266739 940 False 1373.00 1373 93.00800 1 942 1 chr3B.!!$F1 941
10 TraesCS2B01G558900 chr4A 589484976 589485921 945 False 1325.00 1325 91.96600 1 944 1 chr4A.!!$F1 943
11 TraesCS2B01G558900 chr4A 662057057 662058015 958 True 1184.00 1184 89.16700 1 948 1 chr4A.!!$R3 947
12 TraesCS2B01G558900 chr5A 395283530 395284467 937 False 1216.00 1216 90.04200 1 943 1 chr5A.!!$F2 942
13 TraesCS2B01G558900 chr1A 556596487 556597425 938 True 1046.00 1046 86.80900 8 945 1 chr1A.!!$R1 937
14 TraesCS2B01G558900 chr7D 115182079 115182837 758 False 891.00 891 87.87900 186 943 1 chr7D.!!$F1 757
15 TraesCS2B01G558900 chr6A 496124780 496125316 536 True 669.00 669 89.13400 383 924 1 chr6A.!!$R1 541
16 TraesCS2B01G558900 chr1D 337204542 337205150 608 True 636.00 636 85.59700 8 615 1 chr1D.!!$R2 607

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
66 67 0.395586 TGCTTGCCCCATATGTCACC 60.396 55.0 1.24 0.00 0.00 4.02 F
1168 1184 0.247185 AAAATGTTCGGGGCATGCAG 59.753 50.0 21.36 10.35 0.00 4.41 F
1270 1286 0.037046 CAAAATTGAGGGCCCTGTGC 60.037 55.0 34.59 16.71 40.16 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1267 0.037046 GCACAGGGCCCTCAATTTTG 60.037 55.0 25.77 13.03 36.11 2.44 R
2064 2085 1.965083 CGCGGAGGACATCGTTATAG 58.035 55.0 0.00 0.00 0.00 1.31 R
3268 3634 0.607217 CACATGTGGCAGCTTCTCCA 60.607 55.0 18.51 0.00 0.00 3.86 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
46 47 1.376683 GGCACGTTGGCATACAGGA 60.377 57.895 0.00 0.00 43.14 3.86
66 67 0.395586 TGCTTGCCCCATATGTCACC 60.396 55.000 1.24 0.00 0.00 4.02
137 138 1.194781 AGATGTGGACTCGGCTTGGT 61.195 55.000 0.00 0.00 0.00 3.67
174 176 5.643664 TCAATGAAGCGAAAAGGATTGATG 58.356 37.500 0.00 0.00 0.00 3.07
553 559 3.502211 GCACCCAATGTATCTTTATCCCG 59.498 47.826 0.00 0.00 0.00 5.14
896 911 4.695455 CAGACCTTGTGGACGATGTAATTT 59.305 41.667 0.00 0.00 37.04 1.82
899 915 6.045072 ACCTTGTGGACGATGTAATTTCTA 57.955 37.500 0.00 0.00 37.04 2.10
1079 1095 9.926158 ATGTTCATTGCATACTAAAATTGTTCA 57.074 25.926 0.00 0.00 0.00 3.18
1080 1096 9.926158 TGTTCATTGCATACTAAAATTGTTCAT 57.074 25.926 0.00 0.00 0.00 2.57
1140 1156 9.545105 AAAGTTCAAAGCATAAATTGTTCATCA 57.455 25.926 0.00 0.00 0.00 3.07
1141 1157 9.715121 AAGTTCAAAGCATAAATTGTTCATCAT 57.285 25.926 0.00 0.00 0.00 2.45
1162 1178 9.139174 CATCATATATTTTAAAATGTTCGGGGC 57.861 33.333 21.19 0.00 0.00 5.80
1163 1179 8.239038 TCATATATTTTAAAATGTTCGGGGCA 57.761 30.769 21.19 0.80 0.00 5.36
1164 1180 8.865090 TCATATATTTTAAAATGTTCGGGGCAT 58.135 29.630 21.19 7.71 0.00 4.40
1165 1181 8.924691 CATATATTTTAAAATGTTCGGGGCATG 58.075 33.333 21.19 10.53 0.00 4.06
1166 1182 2.663826 TTAAAATGTTCGGGGCATGC 57.336 45.000 9.90 9.90 0.00 4.06
1167 1183 1.550327 TAAAATGTTCGGGGCATGCA 58.450 45.000 21.36 0.00 0.00 3.96
1168 1184 0.247185 AAAATGTTCGGGGCATGCAG 59.753 50.000 21.36 10.35 0.00 4.41
1169 1185 2.229690 AAATGTTCGGGGCATGCAGC 62.230 55.000 21.36 2.19 44.65 5.25
1180 1196 2.660189 GCATGCAGCACCATACTTTT 57.340 45.000 14.21 0.00 44.79 2.27
1181 1197 2.963432 GCATGCAGCACCATACTTTTT 58.037 42.857 14.21 0.00 44.79 1.94
1208 1224 5.794687 TTGAGAAAAGCACCATACATACG 57.205 39.130 0.00 0.00 0.00 3.06
1209 1225 4.827692 TGAGAAAAGCACCATACATACGT 58.172 39.130 0.00 0.00 0.00 3.57
1210 1226 5.968254 TGAGAAAAGCACCATACATACGTA 58.032 37.500 0.00 0.00 0.00 3.57
1211 1227 5.808540 TGAGAAAAGCACCATACATACGTAC 59.191 40.000 0.00 0.00 0.00 3.67
1212 1228 5.114081 AGAAAAGCACCATACATACGTACC 58.886 41.667 0.00 0.00 0.00 3.34
1213 1229 4.475051 AAAGCACCATACATACGTACCA 57.525 40.909 0.00 0.00 0.00 3.25
1214 1230 4.682778 AAGCACCATACATACGTACCAT 57.317 40.909 0.00 0.00 0.00 3.55
1215 1231 4.682778 AGCACCATACATACGTACCATT 57.317 40.909 0.00 0.00 0.00 3.16
1216 1232 4.377021 AGCACCATACATACGTACCATTG 58.623 43.478 0.00 0.00 0.00 2.82
1217 1233 4.100344 AGCACCATACATACGTACCATTGA 59.900 41.667 0.00 0.00 0.00 2.57
1218 1234 4.812091 GCACCATACATACGTACCATTGAA 59.188 41.667 0.00 0.00 0.00 2.69
1219 1235 5.050363 GCACCATACATACGTACCATTGAAG 60.050 44.000 0.00 0.00 0.00 3.02
1220 1236 6.277605 CACCATACATACGTACCATTGAAGA 58.722 40.000 0.00 0.00 0.00 2.87
1221 1237 6.759356 CACCATACATACGTACCATTGAAGAA 59.241 38.462 0.00 0.00 0.00 2.52
1222 1238 7.279090 CACCATACATACGTACCATTGAAGAAA 59.721 37.037 0.00 0.00 0.00 2.52
1223 1239 7.825270 ACCATACATACGTACCATTGAAGAAAA 59.175 33.333 0.00 0.00 0.00 2.29
1224 1240 8.670135 CCATACATACGTACCATTGAAGAAAAA 58.330 33.333 0.00 0.00 0.00 1.94
1242 1258 2.994186 AAATGCTGCAATGGGAATCC 57.006 45.000 6.36 0.00 0.00 3.01
1243 1259 0.748450 AATGCTGCAATGGGAATCCG 59.252 50.000 6.36 0.00 35.24 4.18
1244 1260 1.111116 ATGCTGCAATGGGAATCCGG 61.111 55.000 6.36 0.00 35.24 5.14
1245 1261 2.492773 GCTGCAATGGGAATCCGGG 61.493 63.158 0.00 0.00 35.24 5.73
1246 1262 2.441901 TGCAATGGGAATCCGGGC 60.442 61.111 0.00 0.00 35.24 6.13
1247 1263 3.226537 GCAATGGGAATCCGGGCC 61.227 66.667 0.00 0.00 35.24 5.80
1248 1264 2.521708 CAATGGGAATCCGGGCCC 60.522 66.667 13.57 13.57 44.93 5.80
1249 1265 3.832846 AATGGGAATCCGGGCCCC 61.833 66.667 18.66 18.67 44.03 5.80
1264 1280 3.726004 CCCCCAAAATTGAGGGCC 58.274 61.111 9.48 0.00 39.50 5.80
1265 1281 1.995066 CCCCCAAAATTGAGGGCCC 60.995 63.158 16.46 16.46 39.50 5.80
1266 1282 1.080907 CCCCAAAATTGAGGGCCCT 59.919 57.895 29.18 29.18 44.06 5.19
1267 1283 1.266867 CCCCAAAATTGAGGGCCCTG 61.267 60.000 34.59 14.32 44.06 4.45
1268 1284 0.545071 CCCAAAATTGAGGGCCCTGT 60.545 55.000 34.59 12.74 38.44 4.00
1269 1285 0.609662 CCAAAATTGAGGGCCCTGTG 59.390 55.000 34.59 16.36 0.00 3.66
1270 1286 0.037046 CAAAATTGAGGGCCCTGTGC 60.037 55.000 34.59 16.71 40.16 4.57
1271 1287 1.535204 AAAATTGAGGGCCCTGTGCG 61.535 55.000 34.59 0.00 42.61 5.34
1272 1288 3.944250 AATTGAGGGCCCTGTGCGG 62.944 63.158 34.59 0.00 42.61 5.69
1279 1295 4.980805 GCCCTGTGCGGTCGAACA 62.981 66.667 0.00 4.00 31.89 3.18
1282 1298 3.414700 CTGTGCGGTCGAACAGGC 61.415 66.667 20.49 0.00 45.64 4.85
1283 1299 4.980805 TGTGCGGTCGAACAGGCC 62.981 66.667 0.00 0.00 42.52 5.19
1288 1304 3.499737 GGTCGAACAGGCCGCATG 61.500 66.667 2.89 2.89 33.32 4.06
1289 1305 4.166011 GTCGAACAGGCCGCATGC 62.166 66.667 7.91 7.91 40.16 4.06
1333 1349 2.736347 TCGTTTGTTTTGGGGAAAGGA 58.264 42.857 0.00 0.00 0.00 3.36
1346 1362 3.487563 GGAAAGGATTTGCGTAACAGG 57.512 47.619 0.00 0.00 39.27 4.00
1482 1499 5.750352 ATTTCACGGGAGTAAGGAAGTAA 57.250 39.130 0.00 0.00 44.67 2.24
1483 1500 5.549742 TTTCACGGGAGTAAGGAAGTAAA 57.450 39.130 0.00 0.00 44.67 2.01
1485 1502 5.750352 TCACGGGAGTAAGGAAGTAAAAT 57.250 39.130 0.00 0.00 44.67 1.82
1486 1503 6.855763 TCACGGGAGTAAGGAAGTAAAATA 57.144 37.500 0.00 0.00 44.67 1.40
1487 1504 6.870769 TCACGGGAGTAAGGAAGTAAAATAG 58.129 40.000 0.00 0.00 44.67 1.73
1488 1505 5.522824 CACGGGAGTAAGGAAGTAAAATAGC 59.477 44.000 0.00 0.00 44.67 2.97
1489 1506 5.188359 ACGGGAGTAAGGAAGTAAAATAGCA 59.812 40.000 0.00 0.00 44.60 3.49
1490 1507 6.110707 CGGGAGTAAGGAAGTAAAATAGCAA 58.889 40.000 0.00 0.00 0.00 3.91
1491 1508 6.766467 CGGGAGTAAGGAAGTAAAATAGCAAT 59.234 38.462 0.00 0.00 0.00 3.56
1492 1509 7.929785 CGGGAGTAAGGAAGTAAAATAGCAATA 59.070 37.037 0.00 0.00 0.00 1.90
1494 1511 9.833917 GGAGTAAGGAAGTAAAATAGCAATACT 57.166 33.333 0.00 0.00 0.00 2.12
1513 1534 0.249676 TGTTAAACCTATGGCGGCGA 59.750 50.000 12.98 0.00 0.00 5.54
1560 1581 1.675310 CGGCCATGAAGAGTGCCAA 60.675 57.895 2.24 0.00 44.22 4.52
1843 1864 1.604378 GTGGATGGTCCTGTCCCTG 59.396 63.158 10.32 0.00 37.46 4.45
1872 1893 1.464997 GAGTCCTTGAAGCGCGAAAAT 59.535 47.619 12.10 0.00 0.00 1.82
1922 1943 0.773644 ATGGACAGCTGGAAGGTTGT 59.226 50.000 19.93 0.00 46.63 3.32
2079 2100 2.607282 CCGTGCCTATAACGATGTCCTC 60.607 54.545 0.00 0.00 43.68 3.71
2110 2131 3.568538 GCAATGAAATATGTCGCCCATC 58.431 45.455 0.00 0.00 34.86 3.51
2269 2295 1.396653 CCATTCCTTGATGAGCACCC 58.603 55.000 0.00 0.00 0.00 4.61
2285 2311 4.047883 AGCACCCTGAATAATACTCCCTT 58.952 43.478 0.00 0.00 0.00 3.95
2476 2506 1.968050 AATCTACAACGGGCGGAGGG 61.968 60.000 0.00 0.00 0.00 4.30
2480 2510 2.497792 TACAACGGGCGGAGGGAGTA 62.498 60.000 0.00 0.00 0.00 2.59
2508 2542 6.875972 ACTAGTTCATCCAGTTATGTCCTT 57.124 37.500 0.00 0.00 0.00 3.36
2520 2554 6.347402 CCAGTTATGTCCTTTTCGTAAGTGTG 60.347 42.308 0.00 0.00 36.64 3.82
2580 2626 9.538508 TCATATATCAGTGTCATTCTTGAACTG 57.461 33.333 0.00 0.00 39.60 3.16
2784 3031 2.223805 GCCTCTTATTTGGGCCAATTCG 60.224 50.000 21.65 11.26 39.96 3.34
2792 3039 1.374560 TGGGCCAATTCGATTACACG 58.625 50.000 2.13 0.00 0.00 4.49
2907 3154 2.748461 TTGCACTTACAAAGACACGC 57.252 45.000 0.00 0.00 0.00 5.34
3041 3325 2.439409 TGCATTCAGTGATCACCAAGG 58.561 47.619 22.21 16.90 0.00 3.61
3205 3547 2.288763 GGAATTTGCAACGTCCAACCAT 60.289 45.455 18.64 0.00 0.00 3.55
3253 3619 0.474854 TAGGTTCCTTGCCCTCACCA 60.475 55.000 0.00 0.00 32.08 4.17
3268 3634 2.147387 ACCAACTCTCCCCGCTGTT 61.147 57.895 0.00 0.00 0.00 3.16
3292 3663 1.518056 AAGCTGCCACATGTGAACCG 61.518 55.000 27.46 15.16 0.00 4.44
3303 3674 3.552384 TGAACCGAAGCACCCCGT 61.552 61.111 0.00 0.00 0.00 5.28
3364 3735 0.738412 GCCACATCCAAAGCATGTGC 60.738 55.000 8.26 0.00 46.71 4.57
3367 3738 0.608856 ACATCCAAAGCATGTGCCGA 60.609 50.000 0.57 0.00 43.38 5.54
3368 3739 0.179156 CATCCAAAGCATGTGCCGAC 60.179 55.000 0.57 0.00 43.38 4.79
3371 3742 1.210931 CAAAGCATGTGCCGACCAG 59.789 57.895 0.57 0.00 43.38 4.00
3393 3764 4.899239 CCGTCTCCCGAGCCATGC 62.899 72.222 0.00 0.00 39.56 4.06
3463 3834 2.287194 CCTTCCCACCTCCCCCAT 60.287 66.667 0.00 0.00 0.00 4.00
3472 3843 1.383664 CCTCCCCCATGAGCTCTCA 60.384 63.158 16.19 1.67 44.59 3.27
3481 3852 2.609984 CCATGAGCTCTCACCGATCATC 60.610 54.545 16.19 0.00 43.11 2.92
3493 3864 2.819667 GATCATCGCGGTGATCTGG 58.180 57.895 41.29 10.37 46.97 3.86
3495 3866 1.752358 ATCATCGCGGTGATCTGGCT 61.752 55.000 28.62 7.10 33.69 4.75
3539 3910 4.394920 GGACAAAGGAGCGAATGTATTTCA 59.605 41.667 0.00 0.00 33.66 2.69
3581 3953 8.087136 TGCAAAATTGTACTTGAAGATTGCATA 58.913 29.630 0.00 0.00 43.77 3.14
3600 3972 9.872721 ATTGCATAAATGAATTAACATGTGTGA 57.127 25.926 0.00 0.00 31.30 3.58
3601 3973 8.686397 TGCATAAATGAATTAACATGTGTGAC 57.314 30.769 0.00 0.00 31.30 3.67
3602 3974 8.302438 TGCATAAATGAATTAACATGTGTGACA 58.698 29.630 0.00 0.00 31.30 3.58
3603 3975 8.586273 GCATAAATGAATTAACATGTGTGACAC 58.414 33.333 9.14 9.14 31.30 3.67
3604 3976 9.844790 CATAAATGAATTAACATGTGTGACACT 57.155 29.630 17.47 0.00 35.11 3.55
3606 3978 5.940192 TGAATTAACATGTGTGACACTCC 57.060 39.130 17.47 0.00 35.11 3.85
3607 3979 5.372373 TGAATTAACATGTGTGACACTCCA 58.628 37.500 17.47 4.15 35.11 3.86
3609 3981 6.319911 TGAATTAACATGTGTGACACTCCAAA 59.680 34.615 17.47 5.55 35.11 3.28
3610 3982 6.707440 ATTAACATGTGTGACACTCCAAAA 57.293 33.333 17.47 6.56 35.11 2.44
3614 3986 5.976458 ACATGTGTGACACTCCAAAATTTT 58.024 33.333 17.47 0.00 35.11 1.82
3616 3988 6.313411 ACATGTGTGACACTCCAAAATTTTTG 59.687 34.615 17.47 13.76 35.11 2.44
3617 3989 5.174395 TGTGTGACACTCCAAAATTTTTGG 58.826 37.500 27.83 27.83 35.11 3.28
3619 3991 5.063312 GTGTGACACTCCAAAATTTTTGGTG 59.937 40.000 30.54 29.54 40.40 4.17
3620 3992 4.570369 GTGACACTCCAAAATTTTTGGTGG 59.430 41.667 31.26 26.64 40.40 4.61
3621 3993 4.223923 TGACACTCCAAAATTTTTGGTGGT 59.776 37.500 31.26 26.78 40.40 4.16
3622 3994 5.172687 ACACTCCAAAATTTTTGGTGGTT 57.827 34.783 31.26 21.13 40.40 3.67
3623 3995 5.565509 ACACTCCAAAATTTTTGGTGGTTT 58.434 33.333 31.26 23.10 40.40 3.27
3625 3997 5.414144 CACTCCAAAATTTTTGGTGGTTTGT 59.586 36.000 31.26 21.13 40.40 2.83
3626 3998 6.007076 ACTCCAAAATTTTTGGTGGTTTGTT 58.993 32.000 31.26 16.43 40.40 2.83
3628 4000 7.014711 ACTCCAAAATTTTTGGTGGTTTGTTTT 59.985 29.630 31.26 15.41 40.40 2.43
3629 4001 7.726216 TCCAAAATTTTTGGTGGTTTGTTTTT 58.274 26.923 30.54 0.00 40.40 1.94
3630 4002 7.867909 TCCAAAATTTTTGGTGGTTTGTTTTTC 59.132 29.630 30.54 0.00 40.40 2.29
3633 4005 9.599866 AAAATTTTTGGTGGTTTGTTTTTCAAA 57.400 22.222 0.00 0.00 42.79 2.69
3636 4008 7.568199 TTTTGGTGGTTTGTTTTTCAAAAGA 57.432 28.000 0.00 0.00 45.84 2.52
3637 4009 6.793492 TTGGTGGTTTGTTTTTCAAAAGAG 57.207 33.333 0.00 0.00 45.84 2.85
3638 4010 4.693095 TGGTGGTTTGTTTTTCAAAAGAGC 59.307 37.500 0.00 0.00 45.84 4.09
3639 4011 4.094294 GGTGGTTTGTTTTTCAAAAGAGCC 59.906 41.667 0.00 0.00 45.84 4.70
3640 4012 4.935205 GTGGTTTGTTTTTCAAAAGAGCCT 59.065 37.500 0.00 0.00 45.84 4.58
3641 4013 5.411361 GTGGTTTGTTTTTCAAAAGAGCCTT 59.589 36.000 0.00 0.00 45.84 4.35
3642 4014 5.411053 TGGTTTGTTTTTCAAAAGAGCCTTG 59.589 36.000 0.00 0.00 45.84 3.61
3643 4015 5.323900 GTTTGTTTTTCAAAAGAGCCTTGC 58.676 37.500 0.00 0.00 45.84 4.01
3644 4016 4.470334 TGTTTTTCAAAAGAGCCTTGCT 57.530 36.364 0.00 0.00 43.88 3.91
3645 4017 4.831107 TGTTTTTCAAAAGAGCCTTGCTT 58.169 34.783 0.00 0.00 39.88 3.91
3646 4018 4.630940 TGTTTTTCAAAAGAGCCTTGCTTG 59.369 37.500 0.00 0.00 39.88 4.01
3648 4020 2.071778 TCAAAAGAGCCTTGCTTGGT 57.928 45.000 0.00 0.00 39.88 3.67
3649 4021 2.387757 TCAAAAGAGCCTTGCTTGGTT 58.612 42.857 0.00 0.00 39.88 3.67
3650 4022 2.765699 TCAAAAGAGCCTTGCTTGGTTT 59.234 40.909 0.00 0.00 39.88 3.27
3651 4023 3.957497 TCAAAAGAGCCTTGCTTGGTTTA 59.043 39.130 0.00 0.00 39.88 2.01
3652 4024 4.404073 TCAAAAGAGCCTTGCTTGGTTTAA 59.596 37.500 0.00 0.00 39.88 1.52
3654 4026 5.351948 AAAGAGCCTTGCTTGGTTTAAAA 57.648 34.783 0.00 0.00 39.88 1.52
3656 4028 4.215109 AGAGCCTTGCTTGGTTTAAAAGA 58.785 39.130 0.00 0.00 39.88 2.52
3658 4030 4.948847 AGCCTTGCTTGGTTTAAAAGAAG 58.051 39.130 0.00 0.00 33.89 2.85
3659 4031 4.058124 GCCTTGCTTGGTTTAAAAGAAGG 58.942 43.478 8.72 0.00 36.30 3.46
3661 4033 5.289595 CCTTGCTTGGTTTAAAAGAAGGTC 58.710 41.667 8.72 0.00 32.77 3.85
3662 4034 5.163457 CCTTGCTTGGTTTAAAAGAAGGTCA 60.163 40.000 8.72 0.00 32.77 4.02
3663 4035 6.462909 CCTTGCTTGGTTTAAAAGAAGGTCAT 60.463 38.462 8.72 0.00 32.77 3.06
3664 4036 6.478512 TGCTTGGTTTAAAAGAAGGTCATT 57.521 33.333 8.72 0.00 0.00 2.57
3665 4037 6.883744 TGCTTGGTTTAAAAGAAGGTCATTT 58.116 32.000 8.72 0.00 0.00 2.32
3666 4038 8.012957 TGCTTGGTTTAAAAGAAGGTCATTTA 57.987 30.769 8.72 0.00 0.00 1.40
3668 4040 9.320352 GCTTGGTTTAAAAGAAGGTCATTTAAA 57.680 29.630 6.92 6.92 37.25 1.52
3673 4045 9.826574 GTTTAAAAGAAGGTCATTTAAACCCTT 57.173 29.630 20.42 12.93 45.26 3.95
3679 4051 7.770366 GAAGGTCATTTAAACCCTTCCTAAA 57.230 36.000 21.61 0.00 44.67 1.85
3680 4052 8.185506 GAAGGTCATTTAAACCCTTCCTAAAA 57.814 34.615 21.61 0.00 44.67 1.52
3682 4054 7.959175 AGGTCATTTAAACCCTTCCTAAAAAC 58.041 34.615 0.00 0.00 37.52 2.43
3683 4055 7.015877 AGGTCATTTAAACCCTTCCTAAAAACC 59.984 37.037 0.00 0.00 37.52 3.27
3685 4057 8.372459 GTCATTTAAACCCTTCCTAAAAACCAT 58.628 33.333 0.00 0.00 0.00 3.55
3686 4058 8.590204 TCATTTAAACCCTTCCTAAAAACCATC 58.410 33.333 0.00 0.00 0.00 3.51
3688 4060 8.555896 TTTAAACCCTTCCTAAAAACCATCTT 57.444 30.769 0.00 0.00 0.00 2.40
3689 4061 6.665992 AAACCCTTCCTAAAAACCATCTTC 57.334 37.500 0.00 0.00 0.00 2.87
3691 4063 6.713731 ACCCTTCCTAAAAACCATCTTCTA 57.286 37.500 0.00 0.00 0.00 2.10
3692 4064 7.098845 ACCCTTCCTAAAAACCATCTTCTAA 57.901 36.000 0.00 0.00 0.00 2.10
3693 4065 7.175797 ACCCTTCCTAAAAACCATCTTCTAAG 58.824 38.462 0.00 0.00 0.00 2.18
3698 4070 7.882179 TCCTAAAAACCATCTTCTAAGTTTGC 58.118 34.615 0.00 0.00 32.97 3.68
3699 4071 7.039993 TCCTAAAAACCATCTTCTAAGTTTGCC 60.040 37.037 0.00 0.00 32.97 4.52
3700 4072 5.468540 AAAACCATCTTCTAAGTTTGCCC 57.531 39.130 0.00 0.00 32.97 5.36
3702 4074 3.956744 ACCATCTTCTAAGTTTGCCCTC 58.043 45.455 0.00 0.00 0.00 4.30
3703 4075 3.589288 ACCATCTTCTAAGTTTGCCCTCT 59.411 43.478 0.00 0.00 0.00 3.69
3704 4076 4.195416 CCATCTTCTAAGTTTGCCCTCTC 58.805 47.826 0.00 0.00 0.00 3.20
3706 4078 4.974645 TCTTCTAAGTTTGCCCTCTCAA 57.025 40.909 0.00 0.00 0.00 3.02
3707 4079 5.304686 TCTTCTAAGTTTGCCCTCTCAAA 57.695 39.130 0.00 0.00 33.94 2.69
3710 4820 6.777580 TCTTCTAAGTTTGCCCTCTCAAAAAT 59.222 34.615 0.00 0.00 37.65 1.82
3713 4823 3.849527 AGTTTGCCCTCTCAAAAATCCT 58.150 40.909 0.00 0.00 37.65 3.24
3715 4825 4.655649 AGTTTGCCCTCTCAAAAATCCTTT 59.344 37.500 0.00 0.00 37.65 3.11
3719 4829 4.901250 TGCCCTCTCAAAAATCCTTTTCTT 59.099 37.500 0.00 0.00 32.24 2.52
3722 4832 5.539955 CCCTCTCAAAAATCCTTTTCTTGGA 59.460 40.000 0.00 0.00 38.06 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.696063 GTGACATATGGGGCAAGCAT 58.304 50.000 7.80 0.00 0.00 3.79
66 67 1.769098 CTCACATCTTCGGCCGCATG 61.769 60.000 23.51 22.94 0.00 4.06
137 138 6.155049 TCGCTTCATTGATGATATCCAGGATA 59.845 38.462 11.86 11.86 36.56 2.59
174 176 4.087182 TCTAGTATGATTGACCCCGATCC 58.913 47.826 0.00 0.00 33.15 3.36
553 559 0.537143 TGACCACACTTGATGCCACC 60.537 55.000 0.00 0.00 0.00 4.61
655 661 3.369147 CGCAGGAGTCAATCACTGTTAAG 59.631 47.826 0.00 0.00 34.41 1.85
1053 1069 9.926158 TGAACAATTTTAGTATGCAATGAACAT 57.074 25.926 0.00 0.00 0.00 2.71
1054 1070 9.926158 ATGAACAATTTTAGTATGCAATGAACA 57.074 25.926 0.00 0.00 0.00 3.18
1114 1130 9.545105 TGATGAACAATTTATGCTTTGAACTTT 57.455 25.926 0.00 0.00 0.00 2.66
1115 1131 9.715121 ATGATGAACAATTTATGCTTTGAACTT 57.285 25.926 0.00 0.00 0.00 2.66
1136 1152 9.139174 GCCCCGAACATTTTAAAATATATGATG 57.861 33.333 12.98 3.80 0.00 3.07
1137 1153 8.865090 TGCCCCGAACATTTTAAAATATATGAT 58.135 29.630 12.98 0.00 0.00 2.45
1138 1154 8.239038 TGCCCCGAACATTTTAAAATATATGA 57.761 30.769 12.98 0.00 0.00 2.15
1139 1155 8.924691 CATGCCCCGAACATTTTAAAATATATG 58.075 33.333 12.98 5.52 0.00 1.78
1140 1156 7.602265 GCATGCCCCGAACATTTTAAAATATAT 59.398 33.333 12.98 3.00 0.00 0.86
1141 1157 6.926272 GCATGCCCCGAACATTTTAAAATATA 59.074 34.615 12.98 0.00 0.00 0.86
1142 1158 5.757808 GCATGCCCCGAACATTTTAAAATAT 59.242 36.000 12.98 0.00 0.00 1.28
1143 1159 5.112686 GCATGCCCCGAACATTTTAAAATA 58.887 37.500 12.98 0.00 0.00 1.40
1144 1160 3.938334 GCATGCCCCGAACATTTTAAAAT 59.062 39.130 6.36 7.64 0.00 1.82
1145 1161 3.244215 TGCATGCCCCGAACATTTTAAAA 60.244 39.130 16.68 2.51 0.00 1.52
1146 1162 2.300152 TGCATGCCCCGAACATTTTAAA 59.700 40.909 16.68 0.00 0.00 1.52
1147 1163 1.895798 TGCATGCCCCGAACATTTTAA 59.104 42.857 16.68 0.00 0.00 1.52
1148 1164 1.476085 CTGCATGCCCCGAACATTTTA 59.524 47.619 16.68 0.00 0.00 1.52
1149 1165 0.247185 CTGCATGCCCCGAACATTTT 59.753 50.000 16.68 0.00 0.00 1.82
1150 1166 1.892338 CTGCATGCCCCGAACATTT 59.108 52.632 16.68 0.00 0.00 2.32
1151 1167 2.713967 GCTGCATGCCCCGAACATT 61.714 57.895 16.68 0.00 35.15 2.71
1152 1168 3.142838 GCTGCATGCCCCGAACAT 61.143 61.111 16.68 0.00 35.15 2.71
1153 1169 4.657408 TGCTGCATGCCCCGAACA 62.657 61.111 16.68 1.19 42.00 3.18
1154 1170 4.120331 GTGCTGCATGCCCCGAAC 62.120 66.667 16.68 4.63 42.00 3.95
1158 1174 2.123769 TATGGTGCTGCATGCCCC 60.124 61.111 16.68 10.36 42.00 5.80
1159 1175 1.039233 AAGTATGGTGCTGCATGCCC 61.039 55.000 16.68 9.62 42.00 5.36
1160 1176 0.819582 AAAGTATGGTGCTGCATGCC 59.180 50.000 16.68 3.66 42.00 4.40
1161 1177 2.660189 AAAAGTATGGTGCTGCATGC 57.340 45.000 11.82 11.82 43.25 4.06
1183 1199 7.081349 CGTATGTATGGTGCTTTTCTCAAAAA 58.919 34.615 0.00 0.00 33.42 1.94
1184 1200 6.205853 ACGTATGTATGGTGCTTTTCTCAAAA 59.794 34.615 0.00 0.00 0.00 2.44
1185 1201 5.703592 ACGTATGTATGGTGCTTTTCTCAAA 59.296 36.000 0.00 0.00 0.00 2.69
1186 1202 5.242434 ACGTATGTATGGTGCTTTTCTCAA 58.758 37.500 0.00 0.00 0.00 3.02
1187 1203 4.827692 ACGTATGTATGGTGCTTTTCTCA 58.172 39.130 0.00 0.00 0.00 3.27
1188 1204 5.233689 GGTACGTATGTATGGTGCTTTTCTC 59.766 44.000 0.00 0.00 32.11 2.87
1189 1205 5.114081 GGTACGTATGTATGGTGCTTTTCT 58.886 41.667 0.00 0.00 32.11 2.52
1190 1206 4.871557 TGGTACGTATGTATGGTGCTTTTC 59.128 41.667 0.00 0.00 32.11 2.29
1191 1207 4.834534 TGGTACGTATGTATGGTGCTTTT 58.165 39.130 0.00 0.00 32.11 2.27
1192 1208 4.475051 TGGTACGTATGTATGGTGCTTT 57.525 40.909 0.00 0.00 32.11 3.51
1193 1209 4.682778 ATGGTACGTATGTATGGTGCTT 57.317 40.909 0.00 0.00 32.11 3.91
1194 1210 4.100344 TCAATGGTACGTATGTATGGTGCT 59.900 41.667 0.00 0.00 32.11 4.40
1195 1211 4.373527 TCAATGGTACGTATGTATGGTGC 58.626 43.478 0.00 0.00 32.11 5.01
1196 1212 6.277605 TCTTCAATGGTACGTATGTATGGTG 58.722 40.000 0.00 0.00 32.11 4.17
1197 1213 6.474140 TCTTCAATGGTACGTATGTATGGT 57.526 37.500 0.00 0.00 32.11 3.55
1198 1214 7.780008 TTTCTTCAATGGTACGTATGTATGG 57.220 36.000 0.00 0.00 32.11 2.74
1221 1237 3.613030 GGATTCCCATTGCAGCATTTTT 58.387 40.909 0.00 0.00 0.00 1.94
1222 1238 2.419021 CGGATTCCCATTGCAGCATTTT 60.419 45.455 0.00 0.00 0.00 1.82
1223 1239 1.137479 CGGATTCCCATTGCAGCATTT 59.863 47.619 0.00 0.00 0.00 2.32
1224 1240 0.748450 CGGATTCCCATTGCAGCATT 59.252 50.000 0.00 0.00 0.00 3.56
1225 1241 1.111116 CCGGATTCCCATTGCAGCAT 61.111 55.000 0.00 0.00 0.00 3.79
1226 1242 1.753848 CCGGATTCCCATTGCAGCA 60.754 57.895 0.00 0.00 0.00 4.41
1227 1243 2.492773 CCCGGATTCCCATTGCAGC 61.493 63.158 0.73 0.00 0.00 5.25
1228 1244 2.492773 GCCCGGATTCCCATTGCAG 61.493 63.158 0.73 0.00 0.00 4.41
1229 1245 2.441901 GCCCGGATTCCCATTGCA 60.442 61.111 0.73 0.00 0.00 4.08
1230 1246 3.226537 GGCCCGGATTCCCATTGC 61.227 66.667 0.73 0.00 0.00 3.56
1231 1247 2.521708 GGGCCCGGATTCCCATTG 60.522 66.667 5.69 0.00 42.18 2.82
1232 1248 3.832846 GGGGCCCGGATTCCCATT 61.833 66.667 17.79 0.00 44.43 3.16
1249 1265 0.545071 ACAGGGCCCTCAATTTTGGG 60.545 55.000 25.77 10.27 46.00 4.12
1250 1266 0.609662 CACAGGGCCCTCAATTTTGG 59.390 55.000 25.77 11.13 0.00 3.28
1251 1267 0.037046 GCACAGGGCCCTCAATTTTG 60.037 55.000 25.77 13.03 36.11 2.44
1252 1268 1.535204 CGCACAGGGCCCTCAATTTT 61.535 55.000 25.77 0.00 40.31 1.82
1253 1269 1.978617 CGCACAGGGCCCTCAATTT 60.979 57.895 25.77 0.00 40.31 1.82
1254 1270 2.361610 CGCACAGGGCCCTCAATT 60.362 61.111 25.77 3.07 40.31 2.32
1255 1271 4.431131 CCGCACAGGGCCCTCAAT 62.431 66.667 25.77 7.80 40.31 2.57
1263 1279 2.738521 CTGTTCGACCGCACAGGG 60.739 66.667 12.98 0.00 46.96 4.45
1265 1281 3.414700 GCCTGTTCGACCGCACAG 61.415 66.667 13.67 13.67 38.71 3.66
1266 1282 4.980805 GGCCTGTTCGACCGCACA 62.981 66.667 0.00 0.00 0.00 4.57
1271 1287 3.499737 CATGCGGCCTGTTCGACC 61.500 66.667 0.00 0.00 0.00 4.79
1272 1288 4.166011 GCATGCGGCCTGTTCGAC 62.166 66.667 0.00 0.00 36.11 4.20
1299 1315 2.530958 AAACGATGGTACCAGGCCCG 62.531 60.000 21.41 20.62 0.00 6.13
1333 1349 2.615493 CCTCCACTCCTGTTACGCAAAT 60.615 50.000 0.00 0.00 0.00 2.32
1368 1384 2.813061 CAAGTTTGCTTGGTTGGACAG 58.187 47.619 0.00 0.00 46.17 3.51
1482 1499 8.630037 GCCATAGGTTTAACAGTATTGCTATTT 58.370 33.333 0.00 0.00 0.00 1.40
1483 1500 7.041372 CGCCATAGGTTTAACAGTATTGCTATT 60.041 37.037 0.00 0.00 0.00 1.73
1485 1502 5.756347 CGCCATAGGTTTAACAGTATTGCTA 59.244 40.000 0.00 0.00 0.00 3.49
1486 1503 4.574828 CGCCATAGGTTTAACAGTATTGCT 59.425 41.667 0.00 0.00 0.00 3.91
1487 1504 4.261031 CCGCCATAGGTTTAACAGTATTGC 60.261 45.833 0.00 0.95 0.00 3.56
1488 1505 4.261031 GCCGCCATAGGTTTAACAGTATTG 60.261 45.833 0.00 0.00 0.00 1.90
1489 1506 3.881089 GCCGCCATAGGTTTAACAGTATT 59.119 43.478 0.00 0.00 0.00 1.89
1490 1507 3.473625 GCCGCCATAGGTTTAACAGTAT 58.526 45.455 0.00 0.00 0.00 2.12
1491 1508 2.739287 CGCCGCCATAGGTTTAACAGTA 60.739 50.000 0.00 0.00 0.00 2.74
1492 1509 1.746470 GCCGCCATAGGTTTAACAGT 58.254 50.000 0.00 0.00 0.00 3.55
1494 1511 0.249676 TCGCCGCCATAGGTTTAACA 59.750 50.000 0.00 0.00 0.00 2.41
1495 1512 1.371595 TTCGCCGCCATAGGTTTAAC 58.628 50.000 0.00 0.00 0.00 2.01
1513 1534 1.888436 TTGCTCGCCGACTCCTCATT 61.888 55.000 0.00 0.00 0.00 2.57
1553 1574 5.105554 TCAACACTACAATTTTGTTGGCACT 60.106 36.000 12.42 0.00 46.66 4.40
1560 1581 6.095440 AGCACTTCTCAACACTACAATTTTGT 59.905 34.615 1.08 1.08 44.86 2.83
1610 1631 1.303317 TCCTCGGCCTTCCTTTTGC 60.303 57.895 0.00 0.00 0.00 3.68
1843 1864 3.440228 GCTTCAAGGACTCGTAGTGATC 58.560 50.000 0.00 0.00 0.00 2.92
1872 1893 4.039092 GAGGGCAGCAAGCTGGGA 62.039 66.667 22.20 0.00 43.77 4.37
1922 1943 2.479837 CGCGGCAACCATTATAGAGAA 58.520 47.619 0.00 0.00 0.00 2.87
2064 2085 1.965083 CGCGGAGGACATCGTTATAG 58.035 55.000 0.00 0.00 0.00 1.31
2079 2100 2.561549 ATTTCATTGCCTTGGCGCGG 62.562 55.000 8.83 0.00 0.00 6.46
2155 2176 5.824624 TGCCATCCAACTCAATCTATTCTTC 59.175 40.000 0.00 0.00 0.00 2.87
2269 2295 8.929487 AGGAGAAACTAAGGGAGTATTATTCAG 58.071 37.037 0.00 0.00 37.44 3.02
2480 2510 9.080097 GGACATAACTGGATGAACTAGTATACT 57.920 37.037 10.87 10.87 39.36 2.12
2580 2626 3.127548 AGTTAGCACAGCATACACATTGC 59.872 43.478 0.00 0.00 40.45 3.56
2784 3031 8.635877 ACTTTCTATCTGAACATCGTGTAATC 57.364 34.615 0.00 0.00 33.88 1.75
2792 3039 8.470805 TGAGGTTCTACTTTCTATCTGAACATC 58.529 37.037 10.15 10.15 42.05 3.06
2907 3154 8.480643 ACTAATAATCTGAGACTTGGTTTTCG 57.519 34.615 0.00 0.00 0.00 3.46
3041 3325 6.683974 TGATTGTTTCCTAGAATGCTAAGC 57.316 37.500 0.00 0.00 0.00 3.09
3253 3619 1.841556 TCCAACAGCGGGGAGAGTT 60.842 57.895 0.00 0.00 0.00 3.01
3268 3634 0.607217 CACATGTGGCAGCTTCTCCA 60.607 55.000 18.51 0.00 0.00 3.86
3303 3674 3.551496 CTCCCTTGAGCACCGGCAA 62.551 63.158 0.00 0.00 44.61 4.52
3428 3799 0.962356 GGTGTGTGGGATGCAAGGAG 60.962 60.000 0.00 0.00 0.00 3.69
3441 3812 2.154074 GGGAGGTGGGAAGGTGTGT 61.154 63.158 0.00 0.00 0.00 3.72
3463 3834 0.665298 CGATGATCGGTGAGAGCTCA 59.335 55.000 17.77 0.00 36.00 4.26
3481 3852 2.913054 ATCACAGCCAGATCACCGCG 62.913 60.000 0.00 0.00 0.00 6.46
3488 3859 8.701908 ATAATTTATGTTCATCACAGCCAGAT 57.298 30.769 0.00 0.00 39.40 2.90
3490 3861 9.027129 CAAATAATTTATGTTCATCACAGCCAG 57.973 33.333 0.00 0.00 39.40 4.85
3493 3864 9.023967 GTCCAAATAATTTATGTTCATCACAGC 57.976 33.333 0.00 0.00 39.40 4.40
3556 3928 6.768029 TGCAATCTTCAAGTACAATTTTGC 57.232 33.333 0.00 0.00 37.90 3.68
3581 3953 7.014134 TGGAGTGTCACACATGTTAATTCATTT 59.986 33.333 11.40 0.00 36.74 2.32
3592 3964 6.238157 CCAAAAATTTTGGAGTGTCACACATG 60.238 38.462 28.34 0.00 42.06 3.21
3596 3968 5.174395 CACCAAAAATTTTGGAGTGTCACA 58.826 37.500 35.81 0.00 42.06 3.58
3597 3969 4.570369 CCACCAAAAATTTTGGAGTGTCAC 59.430 41.667 35.81 0.00 42.06 3.67
3598 3970 4.223923 ACCACCAAAAATTTTGGAGTGTCA 59.776 37.500 35.81 0.00 42.06 3.58
3599 3971 4.765273 ACCACCAAAAATTTTGGAGTGTC 58.235 39.130 35.81 0.00 42.06 3.67
3600 3972 4.835284 ACCACCAAAAATTTTGGAGTGT 57.165 36.364 35.81 25.95 42.06 3.55
3601 3973 5.414144 ACAAACCACCAAAAATTTTGGAGTG 59.586 36.000 35.81 25.68 42.06 3.51
3602 3974 5.565509 ACAAACCACCAAAAATTTTGGAGT 58.434 33.333 35.81 28.49 42.06 3.85
3603 3975 6.507958 AACAAACCACCAAAAATTTTGGAG 57.492 33.333 35.81 28.98 42.06 3.86
3604 3976 6.901081 AAACAAACCACCAAAAATTTTGGA 57.099 29.167 35.81 0.00 42.06 3.53
3605 3977 7.653311 TGAAAAACAAACCACCAAAAATTTTGG 59.347 29.630 29.81 29.81 44.91 3.28
3606 3978 8.579682 TGAAAAACAAACCACCAAAAATTTTG 57.420 26.923 11.24 11.24 34.10 2.44
3607 3979 9.599866 TTTGAAAAACAAACCACCAAAAATTTT 57.400 22.222 0.00 0.00 42.57 1.82
3609 3981 9.254133 CTTTTGAAAAACAAACCACCAAAAATT 57.746 25.926 0.00 0.00 46.32 1.82
3610 3982 8.633561 TCTTTTGAAAAACAAACCACCAAAAAT 58.366 25.926 0.00 0.00 46.32 1.82
3614 3986 5.180304 GCTCTTTTGAAAAACAAACCACCAA 59.820 36.000 0.00 0.00 46.32 3.67
3616 3988 4.094294 GGCTCTTTTGAAAAACAAACCACC 59.906 41.667 0.00 0.00 46.32 4.61
3617 3989 4.935205 AGGCTCTTTTGAAAAACAAACCAC 59.065 37.500 0.00 0.00 46.32 4.16
3619 3991 5.673568 GCAAGGCTCTTTTGAAAAACAAACC 60.674 40.000 0.00 0.00 46.32 3.27
3620 3992 5.122239 AGCAAGGCTCTTTTGAAAAACAAAC 59.878 36.000 0.00 0.00 40.48 2.93
3621 3993 5.244755 AGCAAGGCTCTTTTGAAAAACAAA 58.755 33.333 0.00 0.00 39.61 2.83
3622 3994 4.831107 AGCAAGGCTCTTTTGAAAAACAA 58.169 34.783 0.00 0.00 30.62 2.83
3623 3995 4.470334 AGCAAGGCTCTTTTGAAAAACA 57.530 36.364 0.00 0.00 30.62 2.83
3625 3997 4.190772 CCAAGCAAGGCTCTTTTGAAAAA 58.809 39.130 6.44 0.00 38.25 1.94
3626 3998 3.197549 ACCAAGCAAGGCTCTTTTGAAAA 59.802 39.130 6.44 0.00 38.25 2.29
3628 4000 2.387757 ACCAAGCAAGGCTCTTTTGAA 58.612 42.857 6.44 0.00 38.25 2.69
3629 4001 2.071778 ACCAAGCAAGGCTCTTTTGA 57.928 45.000 6.44 0.00 38.25 2.69
3630 4002 2.896745 AACCAAGCAAGGCTCTTTTG 57.103 45.000 0.00 0.00 38.25 2.44
3633 4005 4.649218 TCTTTTAAACCAAGCAAGGCTCTT 59.351 37.500 0.00 0.00 38.25 2.85
3636 4008 4.202253 CCTTCTTTTAAACCAAGCAAGGCT 60.202 41.667 0.00 0.00 42.56 4.58
3637 4009 4.058124 CCTTCTTTTAAACCAAGCAAGGC 58.942 43.478 0.00 0.00 29.55 4.35
3638 4010 5.163457 TGACCTTCTTTTAAACCAAGCAAGG 60.163 40.000 11.27 11.27 36.10 3.61
3639 4011 5.901552 TGACCTTCTTTTAAACCAAGCAAG 58.098 37.500 0.00 0.00 0.00 4.01
3640 4012 5.923733 TGACCTTCTTTTAAACCAAGCAA 57.076 34.783 0.00 0.00 0.00 3.91
3641 4013 6.478512 AATGACCTTCTTTTAAACCAAGCA 57.521 33.333 0.00 0.00 0.00 3.91
3642 4014 8.880878 TTAAATGACCTTCTTTTAAACCAAGC 57.119 30.769 5.12 0.00 34.88 4.01
3656 4028 8.426489 GTTTTTAGGAAGGGTTTAAATGACCTT 58.574 33.333 16.80 16.80 45.50 3.50
3658 4030 7.156673 GGTTTTTAGGAAGGGTTTAAATGACC 58.843 38.462 0.00 0.00 36.41 4.02
3659 4031 7.728148 TGGTTTTTAGGAAGGGTTTAAATGAC 58.272 34.615 0.00 0.00 0.00 3.06
3661 4033 8.593679 AGATGGTTTTTAGGAAGGGTTTAAATG 58.406 33.333 0.00 0.00 0.00 2.32
3662 4034 8.736097 AGATGGTTTTTAGGAAGGGTTTAAAT 57.264 30.769 0.00 0.00 0.00 1.40
3663 4035 8.555896 AAGATGGTTTTTAGGAAGGGTTTAAA 57.444 30.769 0.00 0.00 0.00 1.52
3664 4036 8.008332 AGAAGATGGTTTTTAGGAAGGGTTTAA 58.992 33.333 0.00 0.00 0.00 1.52
3665 4037 7.532199 AGAAGATGGTTTTTAGGAAGGGTTTA 58.468 34.615 0.00 0.00 0.00 2.01
3666 4038 6.382087 AGAAGATGGTTTTTAGGAAGGGTTT 58.618 36.000 0.00 0.00 0.00 3.27
3668 4040 5.600669 AGAAGATGGTTTTTAGGAAGGGT 57.399 39.130 0.00 0.00 0.00 4.34
3671 4043 9.899226 CAAACTTAGAAGATGGTTTTTAGGAAG 57.101 33.333 0.00 0.00 30.78 3.46
3672 4044 8.357402 GCAAACTTAGAAGATGGTTTTTAGGAA 58.643 33.333 0.00 0.00 30.78 3.36
3673 4045 7.039993 GGCAAACTTAGAAGATGGTTTTTAGGA 60.040 37.037 0.00 0.00 30.78 2.94
3675 4047 7.039714 AGGGCAAACTTAGAAGATGGTTTTTAG 60.040 37.037 0.00 0.00 30.78 1.85
3676 4048 6.780522 AGGGCAAACTTAGAAGATGGTTTTTA 59.219 34.615 0.00 0.00 30.78 1.52
3679 4051 4.740902 AGGGCAAACTTAGAAGATGGTTT 58.259 39.130 0.00 0.00 32.99 3.27
3680 4052 4.043435 AGAGGGCAAACTTAGAAGATGGTT 59.957 41.667 0.00 0.00 0.00 3.67
3682 4054 4.195416 GAGAGGGCAAACTTAGAAGATGG 58.805 47.826 0.00 0.00 0.00 3.51
3683 4055 4.836825 TGAGAGGGCAAACTTAGAAGATG 58.163 43.478 0.00 0.00 0.00 2.90
3685 4057 4.974645 TTGAGAGGGCAAACTTAGAAGA 57.025 40.909 0.00 0.00 0.00 2.87
3686 4058 6.391227 TTTTTGAGAGGGCAAACTTAGAAG 57.609 37.500 0.00 0.00 37.48 2.85
3688 4060 5.476945 GGATTTTTGAGAGGGCAAACTTAGA 59.523 40.000 0.00 0.00 37.48 2.10
3689 4061 5.478332 AGGATTTTTGAGAGGGCAAACTTAG 59.522 40.000 0.00 0.00 37.48 2.18
3691 4063 4.226384 AGGATTTTTGAGAGGGCAAACTT 58.774 39.130 0.00 0.00 37.48 2.66
3692 4064 3.849527 AGGATTTTTGAGAGGGCAAACT 58.150 40.909 0.00 0.00 37.48 2.66
3693 4065 4.607293 AAGGATTTTTGAGAGGGCAAAC 57.393 40.909 0.00 0.00 37.48 2.93


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

AutoCloner maintained by Alex Coulton.