Multiple sequence alignment - TraesCS5D01G072200

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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 TraesCS5D01G072200 chr5D 100.000 7011 0 0 1 7011 71901335 71894325 0.000000e+00 12947.0
1 TraesCS5D01G072200 chr5D 100.000 106 0 0 1125 1230 71900158 71900053 5.550000e-46 196.0
2 TraesCS5D01G072200 chr5D 100.000 106 0 0 1178 1283 71900211 71900106 5.550000e-46 196.0
3 TraesCS5D01G072200 chr5D 100.000 53 0 0 1125 1177 71900105 71900053 1.610000e-16 99.0
4 TraesCS5D01G072200 chr5D 100.000 53 0 0 1231 1283 71900211 71900159 1.610000e-16 99.0
5 TraesCS5D01G072200 chr5B 93.967 2221 96 14 1701 3901 82464192 82466394 0.000000e+00 3325.0
6 TraesCS5D01G072200 chr5B 93.018 1375 47 12 5103 6465 82467715 82469052 0.000000e+00 1962.0
7 TraesCS5D01G072200 chr5B 95.518 1071 33 6 1 1068 82461857 82462915 0.000000e+00 1698.0
8 TraesCS5D01G072200 chr5B 92.308 390 16 3 6623 7011 82469387 82469763 6.190000e-150 542.0
9 TraesCS5D01G072200 chr5B 86.250 320 30 9 1229 1542 82463037 82463348 1.130000e-87 335.0
10 TraesCS5D01G072200 chr5B 96.970 198 6 0 4911 5108 82466391 82466588 4.050000e-87 333.0
11 TraesCS5D01G072200 chr5B 90.541 148 7 5 6464 6606 82469151 82469296 9.280000e-44 189.0
12 TraesCS5D01G072200 chr5B 87.368 95 8 1 1607 1697 82463353 82463447 9.620000e-19 106.0
13 TraesCS5D01G072200 chr5B 90.566 53 3 2 1176 1227 82463037 82463088 1.260000e-07 69.4
14 TraesCS5D01G072200 chr5A 94.290 2119 81 25 4910 7011 64375826 64373731 0.000000e+00 3206.0
15 TraesCS5D01G072200 chr5A 93.498 1615 92 8 1851 3458 64380490 64378882 0.000000e+00 2388.0
16 TraesCS5D01G072200 chr5A 96.281 995 30 5 55 1049 64382105 64381118 0.000000e+00 1626.0
17 TraesCS5D01G072200 chr5A 94.737 1026 38 5 3896 4909 76756492 76757513 0.000000e+00 1581.0
18 TraesCS5D01G072200 chr5A 89.610 462 29 9 3454 3896 64376282 64375821 2.840000e-158 569.0
19 TraesCS5D01G072200 chr5A 90.608 181 8 2 1612 1783 64380699 64380519 1.520000e-56 231.0
20 TraesCS5D01G072200 chr5A 86.857 175 18 2 1008 1177 64381102 64380928 2.580000e-44 191.0
21 TraesCS5D01G072200 chr5A 94.624 93 2 1 1453 1542 64380801 64380709 2.640000e-29 141.0
22 TraesCS5D01G072200 chr5A 81.152 191 18 11 1250 1437 64380961 64380786 3.410000e-28 137.0
23 TraesCS5D01G072200 chr5A 94.737 57 3 0 1 57 64382242 64382186 9.690000e-14 89.8
24 TraesCS5D01G072200 chr5A 100.000 34 0 0 1197 1230 64380961 64380928 5.870000e-06 63.9
25 TraesCS5D01G072200 chr3D 97.839 1018 10 1 3904 4909 404412615 404413632 0.000000e+00 1748.0
26 TraesCS5D01G072200 chr3D 97.056 1019 17 2 3904 4909 404410930 404411948 0.000000e+00 1703.0
27 TraesCS5D01G072200 chr6B 94.261 1028 40 9 3895 4909 136563778 136562757 0.000000e+00 1554.0
28 TraesCS5D01G072200 chr6B 93.872 1028 44 9 3896 4910 457199789 457200810 0.000000e+00 1531.0
29 TraesCS5D01G072200 chr6B 93.671 1027 44 9 3896 4909 136562092 136561074 0.000000e+00 1517.0
30 TraesCS5D01G072200 chr7A 94.072 1029 41 11 3896 4911 725549198 725548177 0.000000e+00 1544.0
31 TraesCS5D01G072200 chr7A 93.695 1031 42 10 3896 4909 725550887 725549863 0.000000e+00 1522.0
32 TraesCS5D01G072200 chr7A 97.635 296 6 1 3896 4190 75367251 75366956 2.260000e-139 507.0
33 TraesCS5D01G072200 chr7A 96.091 307 10 2 3895 4200 85147578 85147883 3.780000e-137 499.0
34 TraesCS5D01G072200 chr7B 93.963 1027 42 10 3896 4909 9848474 9847455 0.000000e+00 1535.0
35 TraesCS5D01G072200 chr7B 96.949 295 9 0 3896 4190 208031604 208031898 4.880000e-136 496.0
36 TraesCS5D01G072200 chr7B 93.548 62 4 0 1079 1140 27052774 27052713 7.490000e-15 93.5
37 TraesCS5D01G072200 chr1D 81.113 683 110 14 2381 3052 407216476 407215802 4.820000e-146 529.0
38 TraesCS5D01G072200 chr1D 91.803 61 4 1 1079 1139 332955050 332955109 4.510000e-12 84.2
39 TraesCS5D01G072200 chr1A 81.719 640 108 6 2418 3054 502831612 502830979 6.230000e-145 525.0
40 TraesCS5D01G072200 chr7D 97.635 296 7 0 3896 4191 500009829 500009534 6.270000e-140 508.0
41 TraesCS5D01G072200 chr2A 97.635 296 7 0 3896 4191 694513511 694513216 6.270000e-140 508.0
42 TraesCS5D01G072200 chr2A 97.635 296 7 0 3896 4191 694515116 694514821 6.270000e-140 508.0
43 TraesCS5D01G072200 chr2A 91.045 67 5 1 1079 1145 504548086 504548021 9.690000e-14 89.8
44 TraesCS5D01G072200 chr2A 91.803 61 4 1 1079 1139 74165949 74165890 4.510000e-12 84.2
45 TraesCS5D01G072200 chr3A 95.820 311 10 3 3896 4204 205323901 205324210 3.780000e-137 499.0
46 TraesCS5D01G072200 chr1B 81.549 607 107 3 2450 3054 547586559 547585956 4.880000e-136 496.0
47 TraesCS5D01G072200 chr4A 92.308 65 5 0 1079 1143 743919048 743919112 7.490000e-15 93.5
48 TraesCS5D01G072200 chr4B 94.915 59 1 2 1091 1148 487655577 487655634 2.690000e-14 91.6
49 TraesCS5D01G072200 chr4B 94.828 58 3 0 1089 1146 670967744 670967801 2.690000e-14 91.6
50 TraesCS5D01G072200 chr2B 96.000 50 2 0 1090 1139 45786909 45786860 1.620000e-11 82.4


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 TraesCS5D01G072200 chr5D 71894325 71901335 7010 True 2707.400000 12947 100.0000 1 7011 5 chr5D.!!$R1 7010
1 TraesCS5D01G072200 chr5B 82461857 82469763 7906 False 951.044444 3325 91.8340 1 7011 9 chr5B.!!$F1 7010
2 TraesCS5D01G072200 chr5A 76756492 76757513 1021 False 1581.000000 1581 94.7370 3896 4909 1 chr5A.!!$F1 1013
3 TraesCS5D01G072200 chr5A 64373731 64382242 8511 True 864.270000 3206 92.1657 1 7011 10 chr5A.!!$R1 7010
4 TraesCS5D01G072200 chr3D 404410930 404413632 2702 False 1725.500000 1748 97.4475 3904 4909 2 chr3D.!!$F1 1005
5 TraesCS5D01G072200 chr6B 136561074 136563778 2704 True 1535.500000 1554 93.9660 3895 4909 2 chr6B.!!$R1 1014
6 TraesCS5D01G072200 chr6B 457199789 457200810 1021 False 1531.000000 1531 93.8720 3896 4910 1 chr6B.!!$F1 1014
7 TraesCS5D01G072200 chr7A 725548177 725550887 2710 True 1533.000000 1544 93.8835 3896 4911 2 chr7A.!!$R2 1015
8 TraesCS5D01G072200 chr7B 9847455 9848474 1019 True 1535.000000 1535 93.9630 3896 4909 1 chr7B.!!$R1 1013
9 TraesCS5D01G072200 chr1D 407215802 407216476 674 True 529.000000 529 81.1130 2381 3052 1 chr1D.!!$R1 671
10 TraesCS5D01G072200 chr1A 502830979 502831612 633 True 525.000000 525 81.7190 2418 3054 1 chr1A.!!$R1 636
11 TraesCS5D01G072200 chr2A 694513216 694515116 1900 True 508.000000 508 97.6350 3896 4191 2 chr2A.!!$R3 295
12 TraesCS5D01G072200 chr1B 547585956 547586559 603 True 496.000000 496 81.5490 2450 3054 1 chr1B.!!$R1 604

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
982 1074 1.448985 TGTTCTTATCAACTGCGCCC 58.551 50.000 4.18 0.0 0.00 6.13 F
1876 2796 0.325203 GGCTCCTCTCCCACTCTTCT 60.325 60.000 0.00 0.0 0.00 2.85 F
2277 3201 0.037512 CTGTGAGCTCAGTGGTCTGG 60.038 60.000 18.89 0.0 43.13 3.86 F
2495 3422 1.063764 CCTTGCTCTAGGACGTACGTC 59.936 57.143 34.70 34.7 43.87 4.34 F
2522 3449 1.879380 GCATATGCCGATGCCTTAACA 59.121 47.619 17.26 0.0 45.41 2.41 F
4618 13383 1.683917 TCCAACCGAAAATTGGTGGTG 59.316 47.619 3.81 0.0 45.83 4.17 F
4619 13384 1.270041 CCAACCGAAAATTGGTGGTGG 60.270 52.381 0.00 0.0 41.55 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2989 0.682209 AGGCAGCAGCATACCCAAAG 60.682 55.000 2.65 0.0 44.61 2.77 R
3269 4204 2.369394 GGACAGCAAGGACCAAATAGG 58.631 52.381 0.00 0.0 45.67 2.57 R
4052 7611 1.513586 CGCGTGAGTACCTTCGTCC 60.514 63.158 0.00 0.0 0.00 4.79 R
4617 13382 7.065803 GCAGATATAAAACAAGTTCAGCTACCA 59.934 37.037 0.00 0.0 0.00 3.25 R
4620 13385 7.222805 CGAGCAGATATAAAACAAGTTCAGCTA 59.777 37.037 0.00 0.0 0.00 3.32 R
5858 15764 0.108804 GTCGCGTGGAGATTCTGGAA 60.109 55.000 5.77 0.0 0.00 3.53 R
6370 16283 0.179045 ACAAGTGCTCGCTTCAACCT 60.179 50.000 0.00 0.0 0.00 3.50 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
274 359 5.643379 TTAGTTGGATTCACTTGCATTCC 57.357 39.130 0.00 0.00 0.00 3.01
279 364 2.033801 GGATTCACTTGCATTCCCATCG 59.966 50.000 0.00 0.00 0.00 3.84
368 453 3.474798 TCTGTCAAGTCCTATCCCACT 57.525 47.619 0.00 0.00 0.00 4.00
469 554 4.804261 GCAGCTCCTACCTCTTCAAAGAAA 60.804 45.833 0.00 0.00 34.03 2.52
475 560 3.864789 ACCTCTTCAAAGAAAGGAGCA 57.135 42.857 11.99 0.00 34.03 4.26
620 705 6.146760 AGAAGTACCCTTGATCATATGAGGT 58.853 40.000 15.60 15.60 0.00 3.85
653 738 7.503566 GGTCCTTTCCTTATTGATGATCATTCA 59.496 37.037 10.14 6.69 36.00 2.57
654 739 8.906867 GTCCTTTCCTTATTGATGATCATTCAA 58.093 33.333 10.14 14.73 34.96 2.69
655 740 9.650714 TCCTTTCCTTATTGATGATCATTCAAT 57.349 29.630 24.18 24.18 37.73 2.57
732 823 7.201902 GGTTATTTGGTGGAATTAGATGCATCA 60.202 37.037 27.81 9.38 29.13 3.07
733 824 6.989155 ATTTGGTGGAATTAGATGCATCAT 57.011 33.333 27.81 15.23 31.49 2.45
956 1048 8.303876 GGAGTACAACATTTGGATAAATTGTGT 58.696 33.333 0.00 0.00 34.34 3.72
981 1073 3.764885 AATGTTCTTATCAACTGCGCC 57.235 42.857 4.18 0.00 0.00 6.53
982 1074 1.448985 TGTTCTTATCAACTGCGCCC 58.551 50.000 4.18 0.00 0.00 6.13
990 1082 2.121291 TCAACTGCGCCCATCATTTA 57.879 45.000 4.18 0.00 0.00 1.40
1011 1103 9.345517 CATTTATGTTTCACTATGAACAAGTGG 57.654 33.333 3.60 0.00 43.69 4.00
1012 1104 4.829064 TGTTTCACTATGAACAAGTGGC 57.171 40.909 3.60 0.00 43.69 5.01
1013 1105 4.460263 TGTTTCACTATGAACAAGTGGCT 58.540 39.130 3.60 0.00 43.69 4.75
1062 1216 1.904144 CACCGACGTACCATACACAG 58.096 55.000 0.00 0.00 0.00 3.66
1066 1221 1.468565 CGACGTACCATACACAGGTGG 60.469 57.143 4.24 0.00 40.26 4.61
1087 1242 2.289506 GCCGTTCCATTATACTCCCTCC 60.290 54.545 0.00 0.00 0.00 4.30
1088 1243 2.969950 CCGTTCCATTATACTCCCTCCA 59.030 50.000 0.00 0.00 0.00 3.86
1125 1280 4.477302 AAAACCACGACAAGTATTTCGG 57.523 40.909 0.00 0.00 39.63 4.30
1148 1303 7.143514 GGAACGGAGGAAGTACTATATAGTG 57.856 44.000 23.09 7.44 37.10 2.74
1149 1304 6.714356 GGAACGGAGGAAGTACTATATAGTGT 59.286 42.308 23.09 9.28 37.10 3.55
1150 1305 7.880195 GGAACGGAGGAAGTACTATATAGTGTA 59.120 40.741 23.09 3.58 37.10 2.90
1151 1306 8.845413 AACGGAGGAAGTACTATATAGTGTAG 57.155 38.462 23.09 8.19 37.10 2.74
1152 1307 7.393216 ACGGAGGAAGTACTATATAGTGTAGG 58.607 42.308 23.09 7.09 37.10 3.18
1153 1308 7.017056 ACGGAGGAAGTACTATATAGTGTAGGT 59.983 40.741 23.09 6.00 37.10 3.08
1154 1309 7.882271 CGGAGGAAGTACTATATAGTGTAGGTT 59.118 40.741 23.09 10.16 37.10 3.50
1171 1326 9.975218 AGTGTAGGTTAAATTAGGAACATTCAT 57.025 29.630 0.00 0.00 0.00 2.57
1181 1336 9.710900 AAATTAGGAACATTCATTTCTTGGAAC 57.289 29.630 0.00 0.00 0.00 3.62
1182 1337 5.376854 AGGAACATTCATTTCTTGGAACG 57.623 39.130 0.00 0.00 0.00 3.95
1183 1338 4.218417 AGGAACATTCATTTCTTGGAACGG 59.782 41.667 0.00 0.00 0.00 4.44
1184 1339 4.217550 GGAACATTCATTTCTTGGAACGGA 59.782 41.667 0.00 0.00 0.00 4.69
1185 1340 5.376854 AACATTCATTTCTTGGAACGGAG 57.623 39.130 0.00 0.00 0.00 4.63
1186 1341 3.758554 ACATTCATTTCTTGGAACGGAGG 59.241 43.478 0.00 0.00 0.00 4.30
1187 1342 3.780804 TTCATTTCTTGGAACGGAGGA 57.219 42.857 0.00 0.00 0.00 3.71
1188 1343 3.780804 TCATTTCTTGGAACGGAGGAA 57.219 42.857 0.00 0.00 0.00 3.36
1189 1344 3.674997 TCATTTCTTGGAACGGAGGAAG 58.325 45.455 0.00 0.00 0.00 3.46
1190 1345 3.072476 TCATTTCTTGGAACGGAGGAAGT 59.928 43.478 0.00 0.00 0.00 3.01
1191 1346 4.285003 TCATTTCTTGGAACGGAGGAAGTA 59.715 41.667 0.00 0.00 0.00 2.24
1192 1347 3.672767 TTCTTGGAACGGAGGAAGTAC 57.327 47.619 0.00 0.00 0.00 2.73
1193 1348 2.885616 TCTTGGAACGGAGGAAGTACT 58.114 47.619 0.00 0.00 0.00 2.73
1194 1349 4.038271 TCTTGGAACGGAGGAAGTACTA 57.962 45.455 0.00 0.00 0.00 1.82
1195 1350 4.607239 TCTTGGAACGGAGGAAGTACTAT 58.393 43.478 0.00 0.00 0.00 2.12
1196 1351 5.759059 TCTTGGAACGGAGGAAGTACTATA 58.241 41.667 0.00 0.00 0.00 1.31
1197 1352 6.371278 TCTTGGAACGGAGGAAGTACTATAT 58.629 40.000 0.00 0.00 0.00 0.86
1198 1353 7.520798 TCTTGGAACGGAGGAAGTACTATATA 58.479 38.462 0.00 0.00 0.00 0.86
1199 1354 7.664731 TCTTGGAACGGAGGAAGTACTATATAG 59.335 40.741 8.27 8.27 0.00 1.31
1200 1355 6.845908 TGGAACGGAGGAAGTACTATATAGT 58.154 40.000 19.07 19.07 40.24 2.12
1201 1356 6.713903 TGGAACGGAGGAAGTACTATATAGTG 59.286 42.308 23.09 7.44 37.10 2.74
1202 1357 6.714356 GGAACGGAGGAAGTACTATATAGTGT 59.286 42.308 23.09 9.28 37.10 3.55
1203 1358 7.880195 GGAACGGAGGAAGTACTATATAGTGTA 59.120 40.741 23.09 3.58 37.10 2.90
1204 1359 8.845413 AACGGAGGAAGTACTATATAGTGTAG 57.155 38.462 23.09 8.19 37.10 2.74
1205 1360 7.393216 ACGGAGGAAGTACTATATAGTGTAGG 58.607 42.308 23.09 7.09 37.10 3.18
1206 1361 7.017056 ACGGAGGAAGTACTATATAGTGTAGGT 59.983 40.741 23.09 6.00 37.10 3.08
1207 1362 7.882271 CGGAGGAAGTACTATATAGTGTAGGTT 59.118 40.741 23.09 10.16 37.10 3.50
1224 1379 9.975218 AGTGTAGGTTAAATTAGGAACATTCAT 57.025 29.630 0.00 0.00 0.00 2.57
1234 1389 9.710900 AAATTAGGAACATTCATTTCTTGGAAC 57.289 29.630 0.00 0.00 0.00 3.62
1235 1390 5.376854 AGGAACATTCATTTCTTGGAACG 57.623 39.130 0.00 0.00 0.00 3.95
1236 1391 4.218417 AGGAACATTCATTTCTTGGAACGG 59.782 41.667 0.00 0.00 0.00 4.44
1237 1392 4.217550 GGAACATTCATTTCTTGGAACGGA 59.782 41.667 0.00 0.00 0.00 4.69
1238 1393 5.376854 AACATTCATTTCTTGGAACGGAG 57.623 39.130 0.00 0.00 0.00 4.63
1239 1394 3.758554 ACATTCATTTCTTGGAACGGAGG 59.241 43.478 0.00 0.00 0.00 4.30
1240 1395 3.780804 TTCATTTCTTGGAACGGAGGA 57.219 42.857 0.00 0.00 0.00 3.71
1241 1396 3.780804 TCATTTCTTGGAACGGAGGAA 57.219 42.857 0.00 0.00 0.00 3.36
1242 1397 3.674997 TCATTTCTTGGAACGGAGGAAG 58.325 45.455 0.00 0.00 0.00 3.46
1243 1398 3.072476 TCATTTCTTGGAACGGAGGAAGT 59.928 43.478 0.00 0.00 0.00 3.01
1244 1399 4.285003 TCATTTCTTGGAACGGAGGAAGTA 59.715 41.667 0.00 0.00 0.00 2.24
1245 1400 3.672767 TTCTTGGAACGGAGGAAGTAC 57.327 47.619 0.00 0.00 0.00 2.73
1296 1451 8.517878 ACATTCATTTCTTTCTCAATGTTCGAT 58.482 29.630 0.00 0.00 31.88 3.59
1297 1452 8.795341 CATTCATTTCTTTCTCAATGTTCGATG 58.205 33.333 0.00 0.00 32.96 3.84
1334 1489 4.383444 CCTTGTGTGCTCCTATGAATCTCA 60.383 45.833 0.00 0.00 0.00 3.27
1337 1492 5.748402 TGTGTGCTCCTATGAATCTCATTT 58.252 37.500 0.00 0.00 38.26 2.32
1338 1493 6.182627 TGTGTGCTCCTATGAATCTCATTTT 58.817 36.000 0.00 0.00 38.26 1.82
1339 1494 6.660521 TGTGTGCTCCTATGAATCTCATTTTT 59.339 34.615 0.00 0.00 38.26 1.94
1356 1511 9.388506 TCTCATTTTTAGATCAGATGGTTCTTC 57.611 33.333 0.00 0.00 0.00 2.87
1365 1520 1.344438 AGATGGTTCTTCGCAGTGACA 59.656 47.619 0.00 0.00 0.00 3.58
1387 1542 6.942976 ACATAGAAATAGTCGTCTGGGAAAA 58.057 36.000 0.00 0.00 0.00 2.29
1388 1543 7.042335 ACATAGAAATAGTCGTCTGGGAAAAG 58.958 38.462 0.00 0.00 0.00 2.27
1440 1599 7.240674 TCAACGAGATGAAAAACGGAATATTG 58.759 34.615 0.00 0.00 0.00 1.90
1542 1705 8.070034 TCTTTGATCATGTATGCAAAATTCCT 57.930 30.769 0.00 0.00 30.78 3.36
1544 1707 9.158233 CTTTGATCATGTATGCAAAATTCCTTT 57.842 29.630 0.00 0.00 30.78 3.11
1545 1708 8.706492 TTGATCATGTATGCAAAATTCCTTTC 57.294 30.769 0.00 0.00 0.00 2.62
1546 1709 7.267128 TGATCATGTATGCAAAATTCCTTTCC 58.733 34.615 0.00 0.00 0.00 3.13
1547 1710 5.976458 TCATGTATGCAAAATTCCTTTCCC 58.024 37.500 0.00 0.00 0.00 3.97
1548 1711 5.721000 TCATGTATGCAAAATTCCTTTCCCT 59.279 36.000 0.00 0.00 0.00 4.20
1549 1712 6.894654 TCATGTATGCAAAATTCCTTTCCCTA 59.105 34.615 0.00 0.00 0.00 3.53
1550 1713 7.398618 TCATGTATGCAAAATTCCTTTCCCTAA 59.601 33.333 0.00 0.00 0.00 2.69
1551 1714 7.546250 TGTATGCAAAATTCCTTTCCCTAAA 57.454 32.000 0.00 0.00 0.00 1.85
1552 1715 7.967908 TGTATGCAAAATTCCTTTCCCTAAAA 58.032 30.769 0.00 0.00 0.00 1.52
1553 1716 8.432805 TGTATGCAAAATTCCTTTCCCTAAAAA 58.567 29.630 0.00 0.00 0.00 1.94
1576 1739 7.999450 AAAAATGTATGCAAAATTCCACCAT 57.001 28.000 0.00 0.00 0.00 3.55
1578 1741 8.491331 AAAATGTATGCAAAATTCCACCATAC 57.509 30.769 0.00 0.00 38.94 2.39
1579 1742 7.422465 AATGTATGCAAAATTCCACCATACT 57.578 32.000 14.29 4.17 39.13 2.12
1580 1743 6.449635 TGTATGCAAAATTCCACCATACTC 57.550 37.500 14.29 0.00 39.13 2.59
1581 1744 5.948758 TGTATGCAAAATTCCACCATACTCA 59.051 36.000 14.29 0.00 39.13 3.41
1582 1745 6.606796 TGTATGCAAAATTCCACCATACTCAT 59.393 34.615 14.29 0.00 39.13 2.90
1583 1746 7.777440 TGTATGCAAAATTCCACCATACTCATA 59.223 33.333 14.29 0.00 39.13 2.15
1584 1747 6.449635 TGCAAAATTCCACCATACTCATAC 57.550 37.500 0.00 0.00 0.00 2.39
1585 1748 6.186957 TGCAAAATTCCACCATACTCATACT 58.813 36.000 0.00 0.00 0.00 2.12
1586 1749 7.342581 TGCAAAATTCCACCATACTCATACTA 58.657 34.615 0.00 0.00 0.00 1.82
1587 1750 7.998383 TGCAAAATTCCACCATACTCATACTAT 59.002 33.333 0.00 0.00 0.00 2.12
1588 1751 8.850156 GCAAAATTCCACCATACTCATACTATT 58.150 33.333 0.00 0.00 0.00 1.73
1614 1777 7.789273 TTTTTGTGAGAAACCGTACTTCATA 57.211 32.000 0.00 0.00 0.00 2.15
1805 2716 3.851128 GAGGGCCAGCGGGTACTC 61.851 72.222 6.18 8.83 36.17 2.59
1870 2790 2.683933 TTCCGGCTCCTCTCCCAC 60.684 66.667 0.00 0.00 0.00 4.61
1876 2796 0.325203 GGCTCCTCTCCCACTCTTCT 60.325 60.000 0.00 0.00 0.00 2.85
1879 2799 0.336737 TCCTCTCCCACTCTTCTCCC 59.663 60.000 0.00 0.00 0.00 4.30
1959 2879 0.457851 CTTGGATCTCCGACGCTTCT 59.542 55.000 0.00 0.00 39.43 2.85
2069 2989 1.315257 AATCTGCAACCCGTCCATGC 61.315 55.000 0.00 0.00 40.45 4.06
2093 3013 1.748122 GTATGCTGCTGCCTGCTGT 60.748 57.895 13.47 7.15 43.37 4.40
2172 3092 2.296920 AAGCTCCCACGCTTCCATA 58.703 52.632 0.00 0.00 46.68 2.74
2207 3131 2.224744 TGATGTAGCCTCAGCCACAAAA 60.225 45.455 0.00 0.00 43.94 2.44
2230 3154 0.179026 AGCAGGATATGTGCAGCAGG 60.179 55.000 0.00 0.00 43.82 4.85
2277 3201 0.037512 CTGTGAGCTCAGTGGTCTGG 60.038 60.000 18.89 0.00 43.13 3.86
2303 3227 6.482641 TGTAATTAACTGTACCTCGTTTGCAA 59.517 34.615 0.00 0.00 0.00 4.08
2306 3231 4.483476 AACTGTACCTCGTTTGCAATTC 57.517 40.909 0.00 0.00 0.00 2.17
2327 3252 8.829612 CAATTCTTTAGGAAAATTGTTTGCACT 58.170 29.630 0.00 0.00 37.52 4.40
2355 3281 5.110814 ACATGCCATACTTTTAGGTGCTA 57.889 39.130 0.00 0.00 0.00 3.49
2356 3282 4.881850 ACATGCCATACTTTTAGGTGCTAC 59.118 41.667 0.00 0.00 0.00 3.58
2357 3283 3.527533 TGCCATACTTTTAGGTGCTACG 58.472 45.455 0.00 0.00 0.00 3.51
2358 3284 3.055675 TGCCATACTTTTAGGTGCTACGT 60.056 43.478 0.00 0.00 0.00 3.57
2375 3301 7.043656 GGTGCTACGTATATTTTGAATTTTGGC 60.044 37.037 0.00 0.00 0.00 4.52
2409 3335 8.564574 TGTTCCAAGTTGTTTCATACAGTATTC 58.435 33.333 1.45 0.00 38.19 1.75
2431 3358 6.971726 TCTGTTGACAAGTTCTAACTCCTA 57.028 37.500 0.00 0.00 38.57 2.94
2471 3398 4.497300 GCAACCAGCAATATGTCAATTGT 58.503 39.130 5.13 0.00 44.79 2.71
2495 3422 1.063764 CCTTGCTCTAGGACGTACGTC 59.936 57.143 34.70 34.70 43.87 4.34
2522 3449 1.879380 GCATATGCCGATGCCTTAACA 59.121 47.619 17.26 0.00 45.41 2.41
2559 3486 5.344743 ACATCATGACTTGACCGAAGTAT 57.655 39.130 0.00 0.00 45.48 2.12
2568 3495 4.954202 ACTTGACCGAAGTATCTGATACCA 59.046 41.667 21.08 10.20 43.54 3.25
2663 3590 2.032376 GGTTCCCACCGCCGTTTA 59.968 61.111 0.00 0.00 31.60 2.01
2703 3630 7.994425 TTTGGTAACTTCAAAGATGCTATGA 57.006 32.000 0.00 0.00 37.61 2.15
3124 4059 4.319190 CGAAGCATAGGTCAAACGAAAACA 60.319 41.667 0.00 0.00 0.00 2.83
3142 4077 9.503427 ACGAAAACAAAATGAAACAAAAACAAA 57.497 22.222 0.00 0.00 0.00 2.83
3269 4204 3.181491 TGCTAACAAACAGCCAACTTGAC 60.181 43.478 0.00 0.00 38.29 3.18
3318 4253 3.058914 GCGCATGCTTCTTATACGGAAAT 60.059 43.478 17.13 0.00 38.39 2.17
3427 4362 8.504005 GTTCTGGTGGTTATATGCATATTACAC 58.496 37.037 27.89 26.23 0.00 2.90
3539 7078 7.307278 GCATGTGTTTATTGCAGAACATTCAAA 60.307 33.333 13.23 2.24 37.98 2.69
3713 7272 2.185310 AAACTGGCTAGTGGCGGAGG 62.185 60.000 2.40 0.00 46.76 4.30
3773 7332 7.422399 ACTGCACGTGACAATAAATTTACTTT 58.578 30.769 22.23 0.00 0.00 2.66
3866 7425 7.340122 TCATTGTACATTTGAGTGTTTTGGA 57.660 32.000 0.00 0.00 33.62 3.53
3891 7450 9.436957 GATTTCATCTCTGTAGGTTGAGTTTAA 57.563 33.333 0.00 0.00 0.00 1.52
4052 7611 2.413765 CCAGCACGAGAAAAGCAATCTG 60.414 50.000 0.00 0.00 0.00 2.90
4617 13382 1.960689 CTCCAACCGAAAATTGGTGGT 59.039 47.619 3.81 0.00 45.83 4.16
4618 13383 1.683917 TCCAACCGAAAATTGGTGGTG 59.316 47.619 3.81 0.00 45.83 4.17
4619 13384 1.270041 CCAACCGAAAATTGGTGGTGG 60.270 52.381 0.00 0.00 41.55 4.61
4620 13385 1.410882 CAACCGAAAATTGGTGGTGGT 59.589 47.619 0.00 0.00 40.35 4.16
4879 13644 5.175859 CAACAATAGGGTCGACAACTACAT 58.824 41.667 18.91 8.91 0.00 2.29
5010 13775 4.725490 ACAAGGGTAACTGCAGTTATGTT 58.275 39.130 35.13 25.72 41.85 2.71
5176 15074 4.253685 TGCTCCAGGAAATAACGAGAAAG 58.746 43.478 0.00 0.00 0.00 2.62
5299 15197 2.750166 TGAAAGTTTTGCCTCGTTGTCA 59.250 40.909 0.00 0.00 0.00 3.58
5359 15257 5.304686 TGGATATCCATAACAGTTGGACC 57.695 43.478 20.98 0.00 45.71 4.46
5540 15442 7.543520 CCTAGCAGGCTATTTCTTTTTGAAAAG 59.456 37.037 9.40 9.40 46.32 2.27
5752 15658 6.348540 CCCTAGCTGATTGCCGTATTTATTTC 60.349 42.308 0.00 0.00 44.23 2.17
5835 15741 3.495453 CGTTACAGGAGAAAGGAAACCCA 60.495 47.826 0.00 0.00 0.00 4.51
5849 15755 2.587060 AACCCATCCTGATCCCTGTA 57.413 50.000 0.00 0.00 0.00 2.74
5858 15764 0.327480 TGATCCCTGTATGTGGGCCT 60.327 55.000 4.53 0.00 44.23 5.19
5875 15781 0.807667 CCTTCCAGAATCTCCACGCG 60.808 60.000 3.53 3.53 0.00 6.01
5881 15787 4.814294 AATCTCCACGCGACGCCC 62.814 66.667 15.93 0.00 0.00 6.13
5950 15856 3.555168 CGGGATTTGTATCTAGCCTCACC 60.555 52.174 0.00 0.00 0.00 4.02
6005 15911 4.611367 AGTCTTAGCAGCTTCCCTAACTA 58.389 43.478 0.00 0.00 0.00 2.24
6124 16031 3.662195 CGTACTTTTACGCGTCATTTGCA 60.662 43.478 18.63 0.00 44.38 4.08
6289 16196 1.217882 GTGACCTTGTCCTGTTGTCG 58.782 55.000 0.00 0.00 0.00 4.35
6465 16378 7.071321 ACCTGATCACCTCCCTTATTTTACTAG 59.929 40.741 0.00 0.00 0.00 2.57
6544 16557 6.015856 TGACTTTCCAAGCAATTTTCCGATAA 60.016 34.615 0.00 0.00 0.00 1.75
6547 16560 7.877612 ACTTTCCAAGCAATTTTCCGATAAAAT 59.122 29.630 3.46 3.46 0.00 1.82
6549 16562 8.614469 TTCCAAGCAATTTTCCGATAAAATTT 57.386 26.923 14.64 0.00 37.64 1.82
6553 16566 9.875675 CAAGCAATTTTCCGATAAAATTTTTGA 57.124 25.926 20.79 0.00 37.64 2.69
6607 16625 2.167662 CCGGGCACTTTTCACCTAATT 58.832 47.619 0.00 0.00 0.00 1.40
6611 16629 3.193479 GGGCACTTTTCACCTAATTCCAG 59.807 47.826 0.00 0.00 0.00 3.86
6671 16762 6.478344 TGTTTCTTTTGTGCAATCAATGGTAC 59.522 34.615 0.00 0.00 0.00 3.34
6873 16965 3.299977 TGGTGGGTCTCGGTCACG 61.300 66.667 0.00 0.00 42.74 4.35
6940 17038 1.740380 GCTGCTTCGCCTAGTGAATGA 60.740 52.381 0.00 0.00 31.50 2.57
6941 17039 2.831333 CTGCTTCGCCTAGTGAATGAT 58.169 47.619 0.00 0.00 31.50 2.45
6967 17065 4.152402 CGCTGTTATTCTACATACATGGCC 59.848 45.833 0.00 0.00 0.00 5.36
6968 17066 5.063204 GCTGTTATTCTACATACATGGCCA 58.937 41.667 8.56 8.56 0.00 5.36
6969 17067 5.049405 GCTGTTATTCTACATACATGGCCAC 60.049 44.000 8.16 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 6.851222 AAGAACAACAATCTAGTCTGTGTG 57.149 37.500 1.09 4.79 0.00 3.82
148 233 6.472016 TGCAATCTGGATGACAACTAAACTA 58.528 36.000 0.00 0.00 0.00 2.24
274 359 1.399572 CGACGCTGAGAATACGATGG 58.600 55.000 0.00 0.00 0.00 3.51
279 364 1.201343 GAAGGCGACGCTGAGAATAC 58.799 55.000 20.77 0.00 0.00 1.89
368 453 3.819368 TGATTTCAGACTCAAGCCACAA 58.181 40.909 0.00 0.00 0.00 3.33
469 554 4.978099 TCTCAAATTCTGTCTTTGCTCCT 58.022 39.130 0.00 0.00 34.36 3.69
475 560 7.254932 CCGAGTTTCTTCTCAAATTCTGTCTTT 60.255 37.037 0.00 0.00 34.46 2.52
620 705 4.352595 TCAATAAGGAAAGGACCCTGTCAA 59.647 41.667 8.41 0.00 33.68 3.18
657 742 9.136323 ACAAATTGGAGTAATGTTCTTCTCTTT 57.864 29.630 0.00 0.00 0.00 2.52
658 743 8.571336 CACAAATTGGAGTAATGTTCTTCTCTT 58.429 33.333 0.00 0.00 0.00 2.85
860 952 7.878477 TGTGAAAAACAACTATAGTACCTCG 57.122 36.000 5.65 0.00 35.24 4.63
956 1048 4.155826 CGCAGTTGATAAGAACATTTCCCA 59.844 41.667 0.00 0.00 0.00 4.37
990 1082 5.072741 AGCCACTTGTTCATAGTGAAACAT 58.927 37.500 4.66 0.00 44.52 2.71
1011 1103 4.662145 ACTTATGAATAGTGCGCAAAAGC 58.338 39.130 14.00 0.00 37.71 3.51
1012 1104 6.546395 AGAACTTATGAATAGTGCGCAAAAG 58.454 36.000 14.00 8.38 0.00 2.27
1013 1105 6.148645 TGAGAACTTATGAATAGTGCGCAAAA 59.851 34.615 14.00 2.74 29.40 2.44
1066 1221 2.289506 GGAGGGAGTATAATGGAACGGC 60.290 54.545 0.00 0.00 0.00 5.68
1125 1280 7.742556 ACACTATATAGTACTTCCTCCGTTC 57.257 40.000 15.03 0.00 34.13 3.95
1145 1300 9.975218 ATGAATGTTCCTAATTTAACCTACACT 57.025 29.630 0.00 0.00 0.00 3.55
1155 1310 9.710900 GTTCCAAGAAATGAATGTTCCTAATTT 57.289 29.630 0.00 0.00 0.00 1.82
1156 1311 8.028938 CGTTCCAAGAAATGAATGTTCCTAATT 58.971 33.333 0.00 0.00 0.00 1.40
1157 1312 7.362920 CCGTTCCAAGAAATGAATGTTCCTAAT 60.363 37.037 0.00 0.00 0.00 1.73
1158 1313 6.072175 CCGTTCCAAGAAATGAATGTTCCTAA 60.072 38.462 0.00 0.00 0.00 2.69
1159 1314 5.414454 CCGTTCCAAGAAATGAATGTTCCTA 59.586 40.000 0.00 0.00 0.00 2.94
1160 1315 4.218417 CCGTTCCAAGAAATGAATGTTCCT 59.782 41.667 0.00 0.00 0.00 3.36
1161 1316 4.217550 TCCGTTCCAAGAAATGAATGTTCC 59.782 41.667 0.00 0.00 0.00 3.62
1162 1317 5.371115 TCCGTTCCAAGAAATGAATGTTC 57.629 39.130 0.00 0.00 0.00 3.18
1163 1318 4.218417 CCTCCGTTCCAAGAAATGAATGTT 59.782 41.667 0.00 0.00 0.00 2.71
1164 1319 3.758554 CCTCCGTTCCAAGAAATGAATGT 59.241 43.478 0.00 0.00 0.00 2.71
1165 1320 4.009675 TCCTCCGTTCCAAGAAATGAATG 58.990 43.478 0.00 0.00 0.00 2.67
1166 1321 4.301072 TCCTCCGTTCCAAGAAATGAAT 57.699 40.909 0.00 0.00 0.00 2.57
1167 1322 3.780804 TCCTCCGTTCCAAGAAATGAA 57.219 42.857 0.00 0.00 0.00 2.57
1168 1323 3.072476 ACTTCCTCCGTTCCAAGAAATGA 59.928 43.478 0.00 0.00 0.00 2.57
1169 1324 3.412386 ACTTCCTCCGTTCCAAGAAATG 58.588 45.455 0.00 0.00 0.00 2.32
1170 1325 3.790089 ACTTCCTCCGTTCCAAGAAAT 57.210 42.857 0.00 0.00 0.00 2.17
1171 1326 3.644738 AGTACTTCCTCCGTTCCAAGAAA 59.355 43.478 0.00 0.00 0.00 2.52
1172 1327 3.236896 AGTACTTCCTCCGTTCCAAGAA 58.763 45.455 0.00 0.00 0.00 2.52
1173 1328 2.885616 AGTACTTCCTCCGTTCCAAGA 58.114 47.619 0.00 0.00 0.00 3.02
1174 1329 6.651975 ATATAGTACTTCCTCCGTTCCAAG 57.348 41.667 0.00 0.00 0.00 3.61
1175 1330 7.230108 CACTATATAGTACTTCCTCCGTTCCAA 59.770 40.741 15.03 0.00 34.13 3.53
1176 1331 6.713903 CACTATATAGTACTTCCTCCGTTCCA 59.286 42.308 15.03 0.00 34.13 3.53
1177 1332 6.714356 ACACTATATAGTACTTCCTCCGTTCC 59.286 42.308 15.03 0.00 34.13 3.62
1178 1333 7.742556 ACACTATATAGTACTTCCTCCGTTC 57.257 40.000 15.03 0.00 34.13 3.95
1179 1334 7.882271 CCTACACTATATAGTACTTCCTCCGTT 59.118 40.741 15.03 0.00 34.13 4.44
1180 1335 7.017056 ACCTACACTATATAGTACTTCCTCCGT 59.983 40.741 15.03 8.21 34.13 4.69
1181 1336 7.393216 ACCTACACTATATAGTACTTCCTCCG 58.607 42.308 15.03 2.73 34.13 4.63
1198 1353 9.975218 ATGAATGTTCCTAATTTAACCTACACT 57.025 29.630 0.00 0.00 0.00 3.55
1208 1363 9.710900 GTTCCAAGAAATGAATGTTCCTAATTT 57.289 29.630 0.00 0.00 0.00 1.82
1209 1364 8.028938 CGTTCCAAGAAATGAATGTTCCTAATT 58.971 33.333 0.00 0.00 0.00 1.40
1210 1365 7.362920 CCGTTCCAAGAAATGAATGTTCCTAAT 60.363 37.037 0.00 0.00 0.00 1.73
1211 1366 6.072175 CCGTTCCAAGAAATGAATGTTCCTAA 60.072 38.462 0.00 0.00 0.00 2.69
1212 1367 5.414454 CCGTTCCAAGAAATGAATGTTCCTA 59.586 40.000 0.00 0.00 0.00 2.94
1213 1368 4.218417 CCGTTCCAAGAAATGAATGTTCCT 59.782 41.667 0.00 0.00 0.00 3.36
1214 1369 4.217550 TCCGTTCCAAGAAATGAATGTTCC 59.782 41.667 0.00 0.00 0.00 3.62
1215 1370 5.371115 TCCGTTCCAAGAAATGAATGTTC 57.629 39.130 0.00 0.00 0.00 3.18
1216 1371 4.218417 CCTCCGTTCCAAGAAATGAATGTT 59.782 41.667 0.00 0.00 0.00 2.71
1217 1372 3.758554 CCTCCGTTCCAAGAAATGAATGT 59.241 43.478 0.00 0.00 0.00 2.71
1218 1373 4.009675 TCCTCCGTTCCAAGAAATGAATG 58.990 43.478 0.00 0.00 0.00 2.67
1219 1374 4.301072 TCCTCCGTTCCAAGAAATGAAT 57.699 40.909 0.00 0.00 0.00 2.57
1220 1375 3.780804 TCCTCCGTTCCAAGAAATGAA 57.219 42.857 0.00 0.00 0.00 2.57
1221 1376 3.072476 ACTTCCTCCGTTCCAAGAAATGA 59.928 43.478 0.00 0.00 0.00 2.57
1222 1377 3.412386 ACTTCCTCCGTTCCAAGAAATG 58.588 45.455 0.00 0.00 0.00 2.32
1223 1378 3.790089 ACTTCCTCCGTTCCAAGAAAT 57.210 42.857 0.00 0.00 0.00 2.17
1224 1379 3.644738 AGTACTTCCTCCGTTCCAAGAAA 59.355 43.478 0.00 0.00 0.00 2.52
1225 1380 3.236896 AGTACTTCCTCCGTTCCAAGAA 58.763 45.455 0.00 0.00 0.00 2.52
1226 1381 2.885616 AGTACTTCCTCCGTTCCAAGA 58.114 47.619 0.00 0.00 0.00 3.02
1227 1382 6.651975 ATATAGTACTTCCTCCGTTCCAAG 57.348 41.667 0.00 0.00 0.00 3.61
1228 1383 7.230108 CACTATATAGTACTTCCTCCGTTCCAA 59.770 40.741 15.03 0.00 34.13 3.53
1229 1384 6.713903 CACTATATAGTACTTCCTCCGTTCCA 59.286 42.308 15.03 0.00 34.13 3.53
1230 1385 6.714356 ACACTATATAGTACTTCCTCCGTTCC 59.286 42.308 15.03 0.00 34.13 3.62
1231 1386 7.742556 ACACTATATAGTACTTCCTCCGTTC 57.257 40.000 15.03 0.00 34.13 3.95
1232 1387 7.882271 CCTACACTATATAGTACTTCCTCCGTT 59.118 40.741 15.03 0.00 34.13 4.44
1233 1388 7.017056 ACCTACACTATATAGTACTTCCTCCGT 59.983 40.741 15.03 8.21 34.13 4.69
1234 1389 7.393216 ACCTACACTATATAGTACTTCCTCCG 58.607 42.308 15.03 2.73 34.13 4.63
1289 1444 7.782897 AGGGATATAAAGATCTCATCGAACA 57.217 36.000 0.00 0.00 0.00 3.18
1296 1451 6.100279 AGCACACAAGGGATATAAAGATCTCA 59.900 38.462 0.00 0.00 0.00 3.27
1297 1452 6.529220 AGCACACAAGGGATATAAAGATCTC 58.471 40.000 0.00 0.00 0.00 2.75
1334 1489 6.599244 TGCGAAGAACCATCTGATCTAAAAAT 59.401 34.615 0.00 0.00 35.59 1.82
1337 1492 5.084818 TGCGAAGAACCATCTGATCTAAA 57.915 39.130 0.00 0.00 35.59 1.85
1338 1493 4.160439 ACTGCGAAGAACCATCTGATCTAA 59.840 41.667 0.00 0.00 35.59 2.10
1339 1494 3.701542 ACTGCGAAGAACCATCTGATCTA 59.298 43.478 0.00 0.00 35.59 1.98
1346 1501 1.795768 TGTCACTGCGAAGAACCATC 58.204 50.000 0.00 0.00 0.00 3.51
1356 1511 4.352039 ACGACTATTTCTATGTCACTGCG 58.648 43.478 0.00 0.00 0.00 5.18
1365 1520 7.419711 TCTTTTCCCAGACGACTATTTCTAT 57.580 36.000 0.00 0.00 0.00 1.98
1387 1542 8.419076 AAACACGCTTGAAAACAAAAATATCT 57.581 26.923 0.00 0.00 0.00 1.98
1388 1543 9.562752 GTAAACACGCTTGAAAACAAAAATATC 57.437 29.630 0.00 0.00 0.00 1.63
1462 1622 2.744202 CAGTTTGGTCTTCTCCATTCCG 59.256 50.000 0.00 0.00 37.33 4.30
1552 1715 7.999450 ATGGTGGAATTTTGCATACATTTTT 57.001 28.000 0.00 0.00 29.62 1.94
1553 1716 8.320617 AGTATGGTGGAATTTTGCATACATTTT 58.679 29.630 0.00 0.02 33.55 1.82
1554 1717 7.850193 AGTATGGTGGAATTTTGCATACATTT 58.150 30.769 0.00 0.26 33.55 2.32
1555 1718 7.123997 TGAGTATGGTGGAATTTTGCATACATT 59.876 33.333 0.00 0.00 33.55 2.71
1556 1719 6.606796 TGAGTATGGTGGAATTTTGCATACAT 59.393 34.615 0.00 8.92 34.91 2.29
1557 1720 5.948758 TGAGTATGGTGGAATTTTGCATACA 59.051 36.000 0.00 0.00 0.00 2.29
1558 1721 6.449635 TGAGTATGGTGGAATTTTGCATAC 57.550 37.500 0.00 0.00 0.00 2.39
1559 1722 7.998383 AGTATGAGTATGGTGGAATTTTGCATA 59.002 33.333 0.00 0.00 0.00 3.14
1560 1723 6.835488 AGTATGAGTATGGTGGAATTTTGCAT 59.165 34.615 0.00 0.00 0.00 3.96
1561 1724 6.186957 AGTATGAGTATGGTGGAATTTTGCA 58.813 36.000 0.00 0.00 0.00 4.08
1562 1725 6.699575 AGTATGAGTATGGTGGAATTTTGC 57.300 37.500 0.00 0.00 0.00 3.68
1590 1753 6.687081 ATGAAGTACGGTTTCTCACAAAAA 57.313 33.333 0.00 0.00 0.00 1.94
1591 1754 6.987992 AGTATGAAGTACGGTTTCTCACAAAA 59.012 34.615 0.00 0.00 38.38 2.44
1592 1755 6.518493 AGTATGAAGTACGGTTTCTCACAAA 58.482 36.000 0.00 0.00 38.38 2.83
1593 1756 6.092955 AGTATGAAGTACGGTTTCTCACAA 57.907 37.500 0.00 0.00 38.38 3.33
1594 1757 5.242171 TGAGTATGAAGTACGGTTTCTCACA 59.758 40.000 0.00 0.00 38.38 3.58
1595 1758 5.706916 TGAGTATGAAGTACGGTTTCTCAC 58.293 41.667 0.00 0.00 38.38 3.51
1596 1759 5.970317 TGAGTATGAAGTACGGTTTCTCA 57.030 39.130 0.00 0.00 38.38 3.27
1597 1760 7.140048 CCTATGAGTATGAAGTACGGTTTCTC 58.860 42.308 0.00 0.00 38.38 2.87
1598 1761 6.040616 CCCTATGAGTATGAAGTACGGTTTCT 59.959 42.308 0.00 0.00 38.38 2.52
1599 1762 6.040166 TCCCTATGAGTATGAAGTACGGTTTC 59.960 42.308 0.00 0.00 38.38 2.78
1600 1763 5.895534 TCCCTATGAGTATGAAGTACGGTTT 59.104 40.000 0.00 0.00 38.38 3.27
1601 1764 5.301298 GTCCCTATGAGTATGAAGTACGGTT 59.699 44.000 0.00 0.00 38.38 4.44
1602 1765 4.826183 GTCCCTATGAGTATGAAGTACGGT 59.174 45.833 0.00 0.00 38.38 4.83
1603 1766 5.071370 AGTCCCTATGAGTATGAAGTACGG 58.929 45.833 0.00 0.00 38.38 4.02
1604 1767 6.935771 ACTAGTCCCTATGAGTATGAAGTACG 59.064 42.308 0.00 0.00 38.38 3.67
1605 1768 8.694581 AACTAGTCCCTATGAGTATGAAGTAC 57.305 38.462 0.00 0.00 0.00 2.73
1609 1772 7.618117 TCACAAACTAGTCCCTATGAGTATGAA 59.382 37.037 0.00 0.00 0.00 2.57
1614 1777 6.681729 TTTCACAAACTAGTCCCTATGAGT 57.318 37.500 0.00 0.00 0.00 3.41
1657 1824 4.907809 CATGAAGATGCAGGGATCTATGT 58.092 43.478 3.64 0.00 32.11 2.29
1799 2710 3.525545 GAGGACCGCCGGAGTACC 61.526 72.222 11.71 7.81 39.96 3.34
1800 2711 3.885521 CGAGGACCGCCGGAGTAC 61.886 72.222 11.71 1.32 39.96 2.73
1801 2712 4.100084 TCGAGGACCGCCGGAGTA 62.100 66.667 11.71 0.00 39.96 2.59
1870 2790 1.698532 CATGGAGATGGGGGAGAAGAG 59.301 57.143 0.00 0.00 0.00 2.85
1959 2879 1.806247 CGCACCTGCTTATCCGATGAA 60.806 52.381 0.00 0.00 39.32 2.57
1986 2906 0.740737 CCAGGCGAATCCATTCCAAC 59.259 55.000 0.00 0.00 37.29 3.77
2017 2937 4.763874 TCGCACAAAAATGTTAGTACACG 58.236 39.130 0.00 0.00 37.03 4.49
2069 2989 0.682209 AGGCAGCAGCATACCCAAAG 60.682 55.000 2.65 0.00 44.61 2.77
2093 3013 1.760086 CACAAGCCCCAACCAACCA 60.760 57.895 0.00 0.00 0.00 3.67
2149 3069 4.314440 AGCGTGGGAGCTTTGCGA 62.314 61.111 0.00 0.00 46.80 5.10
2172 3092 2.592102 ACATCACCAATGGCAAGACT 57.408 45.000 0.00 0.00 39.90 3.24
2207 3131 1.474677 GCTGCACATATCCTGCTGAGT 60.475 52.381 11.15 0.00 36.06 3.41
2230 3154 7.642978 CAGCAAACTTAATCTAACATGAGATGC 59.357 37.037 0.00 0.00 36.28 3.91
2277 3201 6.073657 TGCAAACGAGGTACAGTTAATTACAC 60.074 38.462 0.00 0.00 0.00 2.90
2303 3227 8.962884 AAGTGCAAACAATTTTCCTAAAGAAT 57.037 26.923 0.00 0.00 33.44 2.40
2306 3231 8.764287 CCTAAAGTGCAAACAATTTTCCTAAAG 58.236 33.333 0.00 0.00 41.00 1.85
2327 3252 6.601613 CACCTAAAAGTATGGCATGTCCTAAA 59.398 38.462 10.98 0.00 35.26 1.85
2355 3281 5.287513 GCACGCCAAAATTCAAAATATACGT 59.712 36.000 0.00 0.00 0.00 3.57
2356 3282 5.514914 AGCACGCCAAAATTCAAAATATACG 59.485 36.000 0.00 0.00 0.00 3.06
2357 3283 6.885735 AGCACGCCAAAATTCAAAATATAC 57.114 33.333 0.00 0.00 0.00 1.47
2358 3284 7.897575 AAAGCACGCCAAAATTCAAAATATA 57.102 28.000 0.00 0.00 0.00 0.86
2409 3335 8.091449 AGAATAGGAGTTAGAACTTGTCAACAG 58.909 37.037 0.00 0.00 39.88 3.16
2431 3358 1.242076 GCTGTGTGCCTGTTCAGAAT 58.758 50.000 1.00 0.00 35.15 2.40
2471 3398 1.776662 ACGTCCTAGAGCAAGGCATA 58.223 50.000 0.00 0.00 36.51 3.14
2519 3446 1.141657 TGTTGAGAGAGCTGGCTTGTT 59.858 47.619 0.00 0.00 0.00 2.83
2522 3449 1.627329 TGATGTTGAGAGAGCTGGCTT 59.373 47.619 0.00 0.00 0.00 4.35
2559 3486 6.413783 TTTACACAAGTCAGTGGTATCAGA 57.586 37.500 0.00 0.00 43.72 3.27
2568 3495 3.877508 GCAAGTCCTTTACACAAGTCAGT 59.122 43.478 0.00 0.00 0.00 3.41
2689 3616 8.843262 CAAGGAATTGTATCATAGCATCTTTGA 58.157 33.333 0.00 0.00 0.00 2.69
2703 3630 6.152323 GCATCATAGCCATCAAGGAATTGTAT 59.848 38.462 0.00 0.00 41.22 2.29
2984 3919 5.590259 GGTTATAGTCCATTGATGTGCTTGT 59.410 40.000 0.00 0.00 0.00 3.16
3124 4059 9.937175 TCGTTTCTTTTGTTTTTGTTTCATTTT 57.063 22.222 0.00 0.00 0.00 1.82
3142 4077 8.434733 AGTTAGTTTAGCTTCTTTCGTTTCTT 57.565 30.769 0.00 0.00 0.00 2.52
3269 4204 2.369394 GGACAGCAAGGACCAAATAGG 58.631 52.381 0.00 0.00 45.67 2.57
3397 4332 3.009584 TGCATATAACCACCAGAACACCA 59.990 43.478 0.00 0.00 0.00 4.17
3398 4333 3.616219 TGCATATAACCACCAGAACACC 58.384 45.455 0.00 0.00 0.00 4.16
3427 4362 3.565482 CGTTGTTCAATATCCATCAGGGG 59.435 47.826 0.00 0.00 37.22 4.79
3713 7272 6.509418 TTAAATTTGCCAGATGTAGTCCAC 57.491 37.500 0.00 0.00 0.00 4.02
3773 7332 5.127194 CCTGTCCTTGTTGACTGTATAGCTA 59.873 44.000 0.00 0.00 36.21 3.32
3866 7425 9.965902 ATTAAACTCAACCTACAGAGATGAAAT 57.034 29.630 0.00 0.00 35.83 2.17
3891 7450 6.319152 CCTCGAGGTTCGGTCTATATCAATAT 59.681 42.308 24.04 0.00 40.88 1.28
3893 7452 4.459685 CCTCGAGGTTCGGTCTATATCAAT 59.540 45.833 24.04 0.00 40.88 2.57
4052 7611 1.513586 CGCGTGAGTACCTTCGTCC 60.514 63.158 0.00 0.00 0.00 4.79
4617 13382 7.065803 GCAGATATAAAACAAGTTCAGCTACCA 59.934 37.037 0.00 0.00 0.00 3.25
4618 13383 7.281100 AGCAGATATAAAACAAGTTCAGCTACC 59.719 37.037 0.00 0.00 0.00 3.18
4619 13384 8.202745 AGCAGATATAAAACAAGTTCAGCTAC 57.797 34.615 0.00 0.00 0.00 3.58
4620 13385 7.222805 CGAGCAGATATAAAACAAGTTCAGCTA 59.777 37.037 0.00 0.00 0.00 3.32
4879 13644 6.388689 AGGTCCATGACTATACCAAATACCAA 59.611 38.462 0.00 0.00 34.29 3.67
4917 13682 5.391629 GGTGTGTACAATTTAGGTAAGCAGC 60.392 44.000 0.00 0.00 0.00 5.25
5010 13775 9.764363 CCATTTCACTAGCTACACTTTATGATA 57.236 33.333 0.00 0.00 0.00 2.15
5114 15012 5.670485 ACGCATTGTAGGACATTTCAGATA 58.330 37.500 0.00 0.00 0.00 1.98
5176 15074 3.989817 CCACAAATGTAGCTTTCTTTGCC 59.010 43.478 12.03 0.00 33.03 4.52
5299 15197 9.737844 AAATGAAGGGCAAACATAAATAAACAT 57.262 25.926 0.00 0.00 0.00 2.71
5395 15293 5.184892 AGAAGTTGACCATGATAAAGCCT 57.815 39.130 0.00 0.00 0.00 4.58
5396 15294 4.034510 CGAGAAGTTGACCATGATAAAGCC 59.965 45.833 0.00 0.00 0.00 4.35
5509 15411 4.414337 AGAAATAGCCTGCTAGGAGTTG 57.586 45.455 10.65 0.00 37.67 3.16
5540 15442 2.950309 TGAATAGTCTGCTAGGACCGAC 59.050 50.000 0.00 0.00 36.95 4.79
5752 15658 2.119655 GCTGGCATCAAGAGGCTGG 61.120 63.158 6.67 1.63 38.32 4.85
5849 15755 1.213926 GAGATTCTGGAAGGCCCACAT 59.786 52.381 0.00 0.00 40.82 3.21
5858 15764 0.108804 GTCGCGTGGAGATTCTGGAA 60.109 55.000 5.77 0.00 0.00 3.53
5875 15781 3.119096 GCTTTCTCCACGGGCGTC 61.119 66.667 0.00 0.00 0.00 5.19
5881 15787 2.753966 CCATGCGGCTTTCTCCACG 61.754 63.158 0.00 0.00 0.00 4.94
5950 15856 3.255149 AGCAAACCAGAGCTGAAATGAAG 59.745 43.478 0.00 0.00 40.13 3.02
6005 15911 4.689345 GCGTTTCCAGTACTTGTATCAAGT 59.311 41.667 17.18 17.18 0.00 3.16
6172 16079 3.631227 GGCTTCAGAATTTCAGATCTGGG 59.369 47.826 22.42 0.00 42.62 4.45
6370 16283 0.179045 ACAAGTGCTCGCTTCAACCT 60.179 50.000 0.00 0.00 0.00 3.50
6561 16579 5.705441 AGGCGAAATGTGAGAGTTTCAAATA 59.295 36.000 0.00 0.00 37.61 1.40
6574 16592 3.808036 CCCGGTAGGCGAAATGTG 58.192 61.111 0.00 0.00 35.76 3.21
6638 16729 8.034215 TGATTGCACAAAAGAAACAATATAGGG 58.966 33.333 0.00 0.00 31.40 3.53
6671 16762 5.305386 TGTCAGTTCATCCTACATGATAGGG 59.695 44.000 16.55 6.60 35.45 3.53
6873 16965 0.527817 CCGACGTGGAGATTACTGCC 60.528 60.000 0.00 0.00 42.00 4.85
6940 17038 6.646653 CCATGTATGTAGAATAACAGCGACAT 59.353 38.462 0.00 0.00 34.22 3.06
6941 17039 5.983118 CCATGTATGTAGAATAACAGCGACA 59.017 40.000 0.00 0.00 31.70 4.35
6967 17065 1.071471 GTCCCTATCCATGGCCGTG 59.929 63.158 18.73 18.73 0.00 4.94
6968 17066 2.147387 GGTCCCTATCCATGGCCGT 61.147 63.158 6.96 0.00 0.00 5.68
6969 17067 1.831652 GAGGTCCCTATCCATGGCCG 61.832 65.000 6.96 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.