Multiple sequence alignment - TraesCS5D01G493800

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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 TraesCS5D01G493800 chr5D 100.000 6646 0 0 1 6646 526404159 526410804 0.000000e+00 12273
1 TraesCS5D01G493800 chr5D 82.657 986 125 17 3556 4526 526566329 526567283 0.000000e+00 832
2 TraesCS5D01G493800 chr5D 90.702 570 40 5 6085 6646 526433450 526432886 0.000000e+00 747
3 TraesCS5D01G493800 chr5D 94.521 438 21 1 6159 6593 526422933 526422496 0.000000e+00 673
4 TraesCS5D01G493800 chr5D 100.000 40 0 0 5029 5068 526409145 526409184 2.570000e-09 75
5 TraesCS5D01G493800 chr5D 100.000 40 0 0 4987 5026 526409187 526409226 2.570000e-09 75
6 TraesCS5D01G493800 chr5B 90.404 5127 268 83 2 5026 661514580 661519584 0.000000e+00 6536
7 TraesCS5D01G493800 chr5B 89.825 973 63 21 5680 6632 661523521 661524477 0.000000e+00 1216
8 TraesCS5D01G493800 chr5B 96.375 662 24 0 5027 5688 661519543 661520204 0.000000e+00 1090
9 TraesCS5D01G493800 chr5B 79.260 1297 169 56 3556 4807 662029858 662031099 0.000000e+00 813
10 TraesCS5D01G493800 chr5B 92.063 567 35 2 6085 6646 661613186 661612625 0.000000e+00 789
11 TraesCS5D01G493800 chr5B 87.255 306 36 3 3271 3574 662029401 662029705 4.930000e-91 346
12 TraesCS5D01G493800 chr5B 77.006 648 106 25 3753 4396 419845539 419844931 1.380000e-86 331
13 TraesCS5D01G493800 chr5A 91.923 4705 200 65 409 5024 653468593 653473206 0.000000e+00 6418
14 TraesCS5D01G493800 chr5A 92.689 848 39 2 5027 5853 653473167 653474012 0.000000e+00 1201
15 TraesCS5D01G493800 chr5A 94.526 548 25 3 6085 6632 653474310 653474852 0.000000e+00 841
16 TraesCS5D01G493800 chr5A 79.501 1283 166 56 3559 4807 653711957 653713176 0.000000e+00 822
17 TraesCS5D01G493800 chr5A 89.938 646 47 8 5997 6632 653564508 653563871 0.000000e+00 817
18 TraesCS5D01G493800 chr5A 83.966 237 19 13 6025 6248 653679233 653679003 6.750000e-50 209
19 TraesCS5D01G493800 chr5A 93.233 133 7 1 5917 6047 653474184 653474316 1.890000e-45 195
20 TraesCS5D01G493800 chr3D 89.579 499 43 4 6145 6643 496767521 496768010 5.660000e-175 625
21 TraesCS5D01G493800 chr3A 88.577 499 48 3 6145 6643 638015558 638016047 1.230000e-166 597
22 TraesCS5D01G493800 chr3B 87.776 499 52 3 6145 6643 656065897 656066386 5.780000e-160 575


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 TraesCS5D01G493800 chr5D 526404159 526410804 6645 False 4141.000000 12273 100.000000 1 6646 3 chr5D.!!$F2 6645
1 TraesCS5D01G493800 chr5D 526566329 526567283 954 False 832.000000 832 82.657000 3556 4526 1 chr5D.!!$F1 970
2 TraesCS5D01G493800 chr5D 526432886 526433450 564 True 747.000000 747 90.702000 6085 6646 1 chr5D.!!$R2 561
3 TraesCS5D01G493800 chr5B 661514580 661524477 9897 False 2947.333333 6536 92.201333 2 6632 3 chr5B.!!$F1 6630
4 TraesCS5D01G493800 chr5B 661612625 661613186 561 True 789.000000 789 92.063000 6085 6646 1 chr5B.!!$R2 561
5 TraesCS5D01G493800 chr5B 662029401 662031099 1698 False 579.500000 813 83.257500 3271 4807 2 chr5B.!!$F2 1536
6 TraesCS5D01G493800 chr5B 419844931 419845539 608 True 331.000000 331 77.006000 3753 4396 1 chr5B.!!$R1 643
7 TraesCS5D01G493800 chr5A 653468593 653474852 6259 False 2163.750000 6418 93.092750 409 6632 4 chr5A.!!$F2 6223
8 TraesCS5D01G493800 chr5A 653711957 653713176 1219 False 822.000000 822 79.501000 3559 4807 1 chr5A.!!$F1 1248
9 TraesCS5D01G493800 chr5A 653563871 653564508 637 True 817.000000 817 89.938000 5997 6632 1 chr5A.!!$R1 635

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
323 329 0.179094 ACTCTGTTGAAACCGCACGA 60.179 50.000 0.00 0.00 0.00 4.35 F
1148 1205 0.391130 CGATTCCTGCTTGGGTTCGA 60.391 55.000 12.46 0.00 40.53 3.71 F
1362 1439 0.608035 TGTTTTGGGGCGATCCAGTC 60.608 55.000 0.00 0.00 38.17 3.51 F
2389 2500 1.003545 CTGTTTCCCGCGCATATTCAG 60.004 52.381 8.75 4.67 0.00 3.02 F
2390 2501 1.014352 GTTTCCCGCGCATATTCAGT 58.986 50.000 8.75 0.00 0.00 3.41 F
2394 2505 1.148310 CCCGCGCATATTCAGTAAGG 58.852 55.000 8.75 0.00 0.00 2.69 F
2749 2862 1.275010 TCCATTAAGCGACAGTGCTCA 59.725 47.619 0.00 0.00 46.60 4.26 F
3674 3958 3.003480 GCACCTCTGTCCTTTATGTGAC 58.997 50.000 0.00 0.00 0.00 3.67 F
4995 5391 3.986572 TCCGCTTAATTTGCATTGTTGTG 59.013 39.130 0.00 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1284 0.739813 CGGAGTCCCCACGAAATGAC 60.740 60.000 2.80 0.00 34.14 3.06 R
2904 3017 1.012841 GACTAGCCATTGCAGTCTGC 58.987 55.000 18.32 18.32 45.29 4.26 R
3017 3130 5.339990 AGTTCCGAACACTTGACATTTTTG 58.660 37.500 13.69 0.00 0.00 2.44 R
4008 4336 1.372501 AAGTGTGAGCCCCCTACATT 58.627 50.000 0.00 0.00 0.00 2.71 R
4239 4574 6.757947 CCTGGGAAGTAAAATATGCATTTGTG 59.242 38.462 3.54 0.00 34.53 3.33 R
4409 4744 6.127897 GCAGAATACTGGCTTGATAAAACAGT 60.128 38.462 0.00 0.00 43.62 3.55 R
4410 4745 6.127925 TGCAGAATACTGGCTTGATAAAACAG 60.128 38.462 0.00 0.00 43.62 3.16 R
5097 5493 1.020437 GCTGAATAGGAGCTGTTGGC 58.980 55.000 0.00 0.00 42.19 4.52 R
6023 9875 0.307760 GACGCGGGCAATCCTATTTG 59.692 55.000 12.47 0.00 0.00 2.32 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
27 28 2.025418 GGACGGTGTTTGTCGCGAT 61.025 57.895 14.06 0.00 37.22 4.58
28 29 1.129809 GACGGTGTTTGTCGCGATG 59.870 57.895 14.06 0.00 0.00 3.84
29 30 2.202171 CGGTGTTTGTCGCGATGC 60.202 61.111 14.06 0.00 0.00 3.91
67 68 2.163815 ACATGTCGGTACTTTCTCTCGG 59.836 50.000 0.00 0.00 0.00 4.63
76 77 3.453059 ACTTTCTCTCGGAGGTTAGGA 57.547 47.619 4.96 0.00 0.00 2.94
78 79 3.955551 ACTTTCTCTCGGAGGTTAGGATC 59.044 47.826 4.96 0.00 0.00 3.36
84 85 1.048724 CGGAGGTTAGGATCTGGGCA 61.049 60.000 0.00 0.00 0.00 5.36
93 94 0.467804 GGATCTGGGCAGGAGAGAAC 59.532 60.000 0.00 0.00 0.00 3.01
100 102 0.322816 GGCAGGAGAGAACCAATGCA 60.323 55.000 0.00 0.00 34.27 3.96
107 109 2.413453 GAGAGAACCAATGCACGAGAAC 59.587 50.000 0.00 0.00 0.00 3.01
108 110 2.037772 AGAGAACCAATGCACGAGAACT 59.962 45.455 0.00 0.00 0.00 3.01
110 112 2.143122 GAACCAATGCACGAGAACTGA 58.857 47.619 0.00 0.00 0.00 3.41
111 113 2.254546 ACCAATGCACGAGAACTGAA 57.745 45.000 0.00 0.00 0.00 3.02
114 116 2.222886 CCAATGCACGAGAACTGAATCG 60.223 50.000 0.00 0.00 44.36 3.34
156 158 1.796459 ACGCTAATGTTTGTCGTGACC 59.204 47.619 0.00 0.00 31.74 4.02
190 194 0.529337 ACAGCAAGATCCGCATCGAG 60.529 55.000 7.42 0.00 33.75 4.04
237 243 1.300620 CGACACAGCGGGAGAAACA 60.301 57.895 0.00 0.00 0.00 2.83
243 249 1.754803 ACAGCGGGAGAAACATATCGA 59.245 47.619 0.00 0.00 0.00 3.59
259 265 2.181021 GATGTCCGTCGCGACCTT 59.819 61.111 31.84 16.59 31.35 3.50
272 278 3.876589 GACCTTGTCGAAGCCCGCA 62.877 63.158 0.00 0.00 38.37 5.69
273 279 2.436646 CCTTGTCGAAGCCCGCAT 60.437 61.111 0.00 0.00 38.37 4.73
298 304 0.729140 GAGAAACGCGCCCACATTTG 60.729 55.000 5.73 0.00 0.00 2.32
311 317 1.526887 CACATTTGTCGCGACTCTGTT 59.473 47.619 36.27 17.48 0.00 3.16
323 329 0.179094 ACTCTGTTGAAACCGCACGA 60.179 50.000 0.00 0.00 0.00 4.35
336 342 1.153289 GCACGAGCATCCATCCACT 60.153 57.895 0.00 0.00 41.58 4.00
353 359 6.096705 CCATCCACTCACCAAATATAGCAAAA 59.903 38.462 0.00 0.00 0.00 2.44
359 365 7.552687 CACTCACCAAATATAGCAAAACCTCTA 59.447 37.037 0.00 0.00 0.00 2.43
362 368 8.271458 TCACCAAATATAGCAAAACCTCTATCA 58.729 33.333 0.00 0.00 0.00 2.15
371 377 4.141869 GCAAAACCTCTATCAATGCCCATT 60.142 41.667 0.00 0.00 0.00 3.16
377 383 4.039973 CCTCTATCAATGCCCATTTGCAAT 59.960 41.667 0.00 0.00 45.84 3.56
380 386 6.050432 TCTATCAATGCCCATTTGCAATTTC 58.950 36.000 0.00 0.00 45.84 2.17
393 399 7.042791 CCATTTGCAATTTCTTTCAACGTTAGT 60.043 33.333 0.00 0.00 0.00 2.24
394 400 8.963130 CATTTGCAATTTCTTTCAACGTTAGTA 58.037 29.630 0.00 0.00 0.00 1.82
397 403 6.261381 TGCAATTTCTTTCAACGTTAGTAGGT 59.739 34.615 0.00 0.00 0.00 3.08
398 404 6.577427 GCAATTTCTTTCAACGTTAGTAGGTG 59.423 38.462 0.00 0.00 0.00 4.00
399 405 6.796705 ATTTCTTTCAACGTTAGTAGGTGG 57.203 37.500 0.00 0.00 0.00 4.61
402 408 2.736144 TCAACGTTAGTAGGTGGCAG 57.264 50.000 0.00 0.00 0.00 4.85
404 410 0.682852 AACGTTAGTAGGTGGCAGCA 59.317 50.000 20.04 1.95 0.00 4.41
405 411 0.682852 ACGTTAGTAGGTGGCAGCAA 59.317 50.000 20.04 0.86 0.00 3.91
406 412 1.076332 CGTTAGTAGGTGGCAGCAAC 58.924 55.000 20.04 12.84 0.00 4.17
407 413 1.076332 GTTAGTAGGTGGCAGCAACG 58.924 55.000 20.04 0.00 0.00 4.10
858 891 2.764547 GAGGAACCCTAGCCCGCT 60.765 66.667 0.00 0.00 31.76 5.52
959 1010 2.663075 GGGTTGGTCCGGTAGGGTC 61.663 68.421 0.00 0.00 38.33 4.46
967 1018 2.813908 CGGTAGGGTCGTTGCTGC 60.814 66.667 0.00 0.00 0.00 5.25
970 1021 1.004918 GTAGGGTCGTTGCTGCTGT 60.005 57.895 0.00 0.00 0.00 4.40
972 1023 0.602638 TAGGGTCGTTGCTGCTGTTG 60.603 55.000 0.00 0.00 0.00 3.33
1083 1140 3.093172 CTTCTCCTCCCCTGGCCC 61.093 72.222 0.00 0.00 0.00 5.80
1093 1150 2.418083 CCCTGGCCCGCTGATTTTC 61.418 63.158 0.00 0.00 0.00 2.29
1100 1157 1.644786 CCCGCTGATTTTCCGGTGAC 61.645 60.000 0.00 0.00 40.38 3.67
1101 1158 1.644786 CCGCTGATTTTCCGGTGACC 61.645 60.000 0.00 0.00 37.36 4.02
1142 1199 3.204827 CGGCCGATTCCTGCTTGG 61.205 66.667 24.07 0.00 37.10 3.61
1144 1201 2.044946 GCCGATTCCTGCTTGGGT 60.045 61.111 0.00 0.00 36.20 4.51
1145 1202 1.678970 GCCGATTCCTGCTTGGGTT 60.679 57.895 0.00 0.00 36.20 4.11
1147 1204 1.369091 CCGATTCCTGCTTGGGTTCG 61.369 60.000 11.52 11.52 39.01 3.95
1148 1205 0.391130 CGATTCCTGCTTGGGTTCGA 60.391 55.000 12.46 0.00 40.53 3.71
1149 1206 1.743772 CGATTCCTGCTTGGGTTCGAT 60.744 52.381 12.46 0.00 40.53 3.59
1151 1208 0.690192 TTCCTGCTTGGGTTCGATGA 59.310 50.000 0.00 0.00 36.20 2.92
1152 1209 0.911769 TCCTGCTTGGGTTCGATGAT 59.088 50.000 0.00 0.00 36.20 2.45
1154 1211 1.679944 CCTGCTTGGGTTCGATGATGT 60.680 52.381 0.00 0.00 0.00 3.06
1156 1213 1.003003 TGCTTGGGTTCGATGATGTGA 59.997 47.619 0.00 0.00 0.00 3.58
1159 1216 0.739462 TGGGTTCGATGATGTGACGC 60.739 55.000 0.00 0.00 0.00 5.19
1165 1227 2.813179 GATGATGTGACGCGGTGGC 61.813 63.158 12.47 0.00 0.00 5.01
1168 1230 3.649277 GATGTGACGCGGTGGCTCT 62.649 63.158 12.47 0.00 36.88 4.09
1169 1231 3.939837 ATGTGACGCGGTGGCTCTG 62.940 63.158 12.47 0.00 36.88 3.35
1185 1247 2.507484 CTCTGAGATGCCAACACCAAA 58.493 47.619 0.00 0.00 0.00 3.28
1186 1248 3.087031 CTCTGAGATGCCAACACCAAAT 58.913 45.455 0.00 0.00 0.00 2.32
1188 1250 2.165030 CTGAGATGCCAACACCAAATCC 59.835 50.000 0.00 0.00 0.00 3.01
1189 1251 2.170166 GAGATGCCAACACCAAATCCA 58.830 47.619 0.00 0.00 0.00 3.41
1191 1253 3.175594 AGATGCCAACACCAAATCCATT 58.824 40.909 0.00 0.00 0.00 3.16
1194 1256 1.901833 GCCAACACCAAATCCATTCCT 59.098 47.619 0.00 0.00 0.00 3.36
1195 1257 3.096092 GCCAACACCAAATCCATTCCTA 58.904 45.455 0.00 0.00 0.00 2.94
1196 1258 3.131046 GCCAACACCAAATCCATTCCTAG 59.869 47.826 0.00 0.00 0.00 3.02
1198 1260 4.772100 CCAACACCAAATCCATTCCTAGTT 59.228 41.667 0.00 0.00 0.00 2.24
1199 1261 5.245977 CCAACACCAAATCCATTCCTAGTTT 59.754 40.000 0.00 0.00 0.00 2.66
1200 1262 6.239572 CCAACACCAAATCCATTCCTAGTTTT 60.240 38.462 0.00 0.00 0.00 2.43
1222 1284 4.418013 TTCATTCGTATGCACTGTTTGG 57.582 40.909 0.00 0.00 0.00 3.28
1224 1286 3.435327 TCATTCGTATGCACTGTTTGGTC 59.565 43.478 0.00 0.00 0.00 4.02
1226 1288 3.052455 TCGTATGCACTGTTTGGTCAT 57.948 42.857 0.00 0.00 0.00 3.06
1229 1291 4.083537 TCGTATGCACTGTTTGGTCATTTC 60.084 41.667 0.00 0.00 0.00 2.17
1230 1292 2.772568 TGCACTGTTTGGTCATTTCG 57.227 45.000 0.00 0.00 0.00 3.46
1231 1293 2.020720 TGCACTGTTTGGTCATTTCGT 58.979 42.857 0.00 0.00 0.00 3.85
1232 1294 2.223456 TGCACTGTTTGGTCATTTCGTG 60.223 45.455 0.00 0.00 0.00 4.35
1233 1295 2.858260 GCACTGTTTGGTCATTTCGTGG 60.858 50.000 0.00 0.00 0.00 4.94
1237 1299 1.268625 GTTTGGTCATTTCGTGGGGAC 59.731 52.381 0.00 0.00 0.00 4.46
1251 1328 1.993391 GGGACTCCGGTGGGAATCA 60.993 63.158 8.63 0.00 40.38 2.57
1268 1345 5.127845 GGGAATCAGAGATATCAGCGGATTA 59.872 44.000 17.37 0.00 34.89 1.75
1289 1366 3.691049 TTATTGTGCGCAATTAGCCTC 57.309 42.857 28.90 0.00 42.19 4.70
1293 1370 0.734889 GTGCGCAATTAGCCTCATGT 59.265 50.000 14.00 0.00 41.38 3.21
1294 1371 1.016627 TGCGCAATTAGCCTCATGTC 58.983 50.000 8.16 0.00 41.38 3.06
1344 1421 1.303236 TGATTCGGTTGGTGGCCTG 60.303 57.895 3.32 0.00 0.00 4.85
1362 1439 0.608035 TGTTTTGGGGCGATCCAGTC 60.608 55.000 0.00 0.00 38.17 3.51
1415 1498 1.537202 AGCCTCAAAGTGTTCAATCGC 59.463 47.619 0.00 0.00 0.00 4.58
1538 1621 2.025321 AGGCTTTATTAGGTGGTGGGTG 60.025 50.000 0.00 0.00 0.00 4.61
1545 1628 1.198759 TAGGTGGTGGGTGCCTTCTC 61.199 60.000 0.00 0.00 34.07 2.87
1624 1711 6.754702 AGTACCATGTGTAGTACTGTAGTG 57.245 41.667 5.39 0.00 45.69 2.74
1634 1721 4.543590 AGTACTGTAGTGCATGCTCTTT 57.456 40.909 25.78 11.59 32.87 2.52
1653 1740 8.212995 TGCTCTTTCATCATGAATTGGATAGTA 58.787 33.333 0.00 0.00 36.11 1.82
1672 1759 9.012161 GGATAGTACTTATCGTTATCAGAAGGT 57.988 37.037 0.00 0.00 39.29 3.50
1721 1813 2.205074 CTCTCAGTGTGGTGTGTGTTC 58.795 52.381 0.00 0.00 0.00 3.18
1772 1866 3.797256 GCATCGTATGTGTTGGTACTCTC 59.203 47.826 0.00 0.00 0.00 3.20
1773 1867 4.676986 GCATCGTATGTGTTGGTACTCTCA 60.677 45.833 0.00 0.00 0.00 3.27
1775 1869 4.329392 TCGTATGTGTTGGTACTCTCAGA 58.671 43.478 0.00 0.00 0.00 3.27
1805 1899 6.803320 CACTTAGCACGATGAATTCAAAACAT 59.197 34.615 13.09 0.00 0.00 2.71
1818 1912 8.423349 TGAATTCAAAACATCCTTGATTCAGTT 58.577 29.630 5.45 0.00 32.98 3.16
1819 1913 8.597662 AATTCAAAACATCCTTGATTCAGTTG 57.402 30.769 0.00 0.00 32.98 3.16
1820 1914 5.531634 TCAAAACATCCTTGATTCAGTTGC 58.468 37.500 0.00 0.00 0.00 4.17
1821 1915 5.302568 TCAAAACATCCTTGATTCAGTTGCT 59.697 36.000 0.00 0.00 0.00 3.91
1822 1916 4.778534 AACATCCTTGATTCAGTTGCTG 57.221 40.909 0.00 0.00 0.00 4.41
1823 1917 4.025040 ACATCCTTGATTCAGTTGCTGA 57.975 40.909 0.00 0.00 38.87 4.26
1848 1948 4.151157 GCTGACCAAGAAACATTTGATTGC 59.849 41.667 0.00 0.00 0.00 3.56
1856 1956 2.945447 ACATTTGATTGCGGTGGATG 57.055 45.000 0.00 0.00 0.00 3.51
1874 1974 7.765819 CGGTGGATGATTTTAGCATCATATCTA 59.234 37.037 7.17 0.00 42.85 1.98
1884 1984 9.639601 TTTTAGCATCATATCTATTGGTACTCG 57.360 33.333 0.00 0.00 0.00 4.18
1920 2020 4.161001 AGCTTGATGAATTCAAATCACCCC 59.839 41.667 13.09 3.97 43.64 4.95
2389 2500 1.003545 CTGTTTCCCGCGCATATTCAG 60.004 52.381 8.75 4.67 0.00 3.02
2390 2501 1.014352 GTTTCCCGCGCATATTCAGT 58.986 50.000 8.75 0.00 0.00 3.41
2391 2502 2.206750 GTTTCCCGCGCATATTCAGTA 58.793 47.619 8.75 0.00 0.00 2.74
2392 2503 2.605837 TTCCCGCGCATATTCAGTAA 57.394 45.000 8.75 0.00 0.00 2.24
2393 2504 2.148916 TCCCGCGCATATTCAGTAAG 57.851 50.000 8.75 0.00 0.00 2.34
2394 2505 1.148310 CCCGCGCATATTCAGTAAGG 58.852 55.000 8.75 0.00 0.00 2.69
2395 2506 1.540363 CCCGCGCATATTCAGTAAGGT 60.540 52.381 8.75 0.00 0.00 3.50
2396 2507 2.210116 CCGCGCATATTCAGTAAGGTT 58.790 47.619 8.75 0.00 0.00 3.50
2397 2508 2.612212 CCGCGCATATTCAGTAAGGTTT 59.388 45.455 8.75 0.00 0.00 3.27
2398 2509 3.064820 CCGCGCATATTCAGTAAGGTTTT 59.935 43.478 8.75 0.00 0.00 2.43
2418 2529 7.033185 GGTTTTCCAGTCATTAATTGCGTATT 58.967 34.615 0.00 0.00 40.31 1.89
2513 2626 6.671614 TTTTTGTGATTGACGTGTACTTCT 57.328 33.333 0.00 0.00 0.00 2.85
2520 2633 3.818961 TGACGTGTACTTCTAGTTCCG 57.181 47.619 0.00 0.00 0.00 4.30
2736 2849 9.565090 CTCTCTGATTTTCACCATATCCATTAA 57.435 33.333 0.00 0.00 0.00 1.40
2749 2862 1.275010 TCCATTAAGCGACAGTGCTCA 59.725 47.619 0.00 0.00 46.60 4.26
2904 3017 4.744136 TTATCACTAGCATCGTCTACCG 57.256 45.455 0.00 0.00 38.13 4.02
3017 3130 8.303876 TCCTAATTACTGTGCAAAATTTCCTTC 58.696 33.333 0.00 0.00 0.00 3.46
3072 3185 3.072915 TGATGTTCATTCTGTGGACCTGT 59.927 43.478 0.00 0.00 35.26 4.00
3674 3958 3.003480 GCACCTCTGTCCTTTATGTGAC 58.997 50.000 0.00 0.00 0.00 3.67
4409 4744 6.322712 ACAGGTAACCTTTGACTTGCAATTTA 59.677 34.615 0.00 0.00 34.33 1.40
4410 4745 6.640907 CAGGTAACCTTTGACTTGCAATTTAC 59.359 38.462 0.00 0.00 34.33 2.01
4576 4939 4.695455 GTGTAAGCTGTTTCCTCTTATGCA 59.305 41.667 0.00 0.00 0.00 3.96
4689 5055 7.877097 GTCAGGCTCTGATTGAATATCTAACAT 59.123 37.037 7.95 0.00 42.73 2.71
4754 5122 9.059260 GGTGTACCTTTTCTTTTGTGAACTATA 57.941 33.333 0.00 0.00 0.00 1.31
4804 5174 6.438186 AGGGAAATGTTTGATGGTGATTTT 57.562 33.333 0.00 0.00 0.00 1.82
4984 5380 9.921637 TCTAACATTTTGAATTCCGCTTAATTT 57.078 25.926 2.27 0.00 0.00 1.82
4985 5381 9.956797 CTAACATTTTGAATTCCGCTTAATTTG 57.043 29.630 2.27 0.00 0.00 2.32
4986 5382 6.830736 ACATTTTGAATTCCGCTTAATTTGC 58.169 32.000 2.27 0.00 0.00 3.68
4987 5383 6.426328 ACATTTTGAATTCCGCTTAATTTGCA 59.574 30.769 2.27 0.00 0.00 4.08
4988 5384 7.119553 ACATTTTGAATTCCGCTTAATTTGCAT 59.880 29.630 2.27 0.00 0.00 3.96
4989 5385 7.432350 TTTTGAATTCCGCTTAATTTGCATT 57.568 28.000 2.27 0.00 0.00 3.56
4990 5386 6.406093 TTGAATTCCGCTTAATTTGCATTG 57.594 33.333 2.27 0.00 0.00 2.82
4991 5387 5.477510 TGAATTCCGCTTAATTTGCATTGT 58.522 33.333 2.27 0.00 0.00 2.71
4992 5388 5.931146 TGAATTCCGCTTAATTTGCATTGTT 59.069 32.000 2.27 0.00 0.00 2.83
4993 5389 5.783100 ATTCCGCTTAATTTGCATTGTTG 57.217 34.783 0.00 0.00 0.00 3.33
4994 5390 4.250116 TCCGCTTAATTTGCATTGTTGT 57.750 36.364 0.00 0.00 0.00 3.32
4995 5391 3.986572 TCCGCTTAATTTGCATTGTTGTG 59.013 39.130 0.00 0.00 0.00 3.33
4996 5392 3.986572 CCGCTTAATTTGCATTGTTGTGA 59.013 39.130 0.00 0.00 0.00 3.58
4997 5393 4.090354 CCGCTTAATTTGCATTGTTGTGAG 59.910 41.667 0.00 0.00 0.00 3.51
4998 5394 4.916831 CGCTTAATTTGCATTGTTGTGAGA 59.083 37.500 0.00 0.00 0.00 3.27
4999 5395 5.401972 CGCTTAATTTGCATTGTTGTGAGAA 59.598 36.000 0.00 0.00 0.00 2.87
5000 5396 6.089820 CGCTTAATTTGCATTGTTGTGAGAAT 59.910 34.615 0.00 0.00 0.00 2.40
5001 5397 7.273164 CGCTTAATTTGCATTGTTGTGAGAATA 59.727 33.333 0.00 0.00 0.00 1.75
5002 5398 9.090692 GCTTAATTTGCATTGTTGTGAGAATAT 57.909 29.630 0.00 0.00 0.00 1.28
5014 5410 9.638239 TTGTTGTGAGAATATTAAAATTCTGCC 57.362 29.630 3.93 0.00 44.38 4.85
5015 5411 9.023962 TGTTGTGAGAATATTAAAATTCTGCCT 57.976 29.630 3.93 0.00 44.38 4.75
5016 5412 9.860898 GTTGTGAGAATATTAAAATTCTGCCTT 57.139 29.630 3.93 0.00 44.38 4.35
5018 5414 9.466497 TGTGAGAATATTAAAATTCTGCCTTCT 57.534 29.630 3.93 0.00 44.38 2.85
5022 5418 9.072375 AGAATATTAAAATTCTGCCTTCTAGGC 57.928 33.333 10.75 10.75 44.66 3.93
5080 5476 8.128322 CCTTCTAGGCACAGAACATACTATAT 57.872 38.462 0.00 0.00 31.34 0.86
5159 5555 4.379652 ACAAATCAACATTTTCAGGCCAC 58.620 39.130 5.01 0.00 28.97 5.01
5366 5762 0.400213 TGAACGGAGCCCAGACAATT 59.600 50.000 0.00 0.00 0.00 2.32
5372 5768 1.941999 GAGCCCAGACAATTGCTGCC 61.942 60.000 18.69 13.43 33.41 4.85
5375 5771 1.318158 CCCAGACAATTGCTGCCCTC 61.318 60.000 18.69 4.37 32.06 4.30
5396 5792 1.269831 GCTGTCGAGTGTCTGTCCTTT 60.270 52.381 0.00 0.00 0.00 3.11
5504 5921 1.488705 ATCCAACCAGAAGACCGGCA 61.489 55.000 0.00 0.00 0.00 5.69
5807 9551 3.059884 GCATTGAAGTCTGAGTTCGTCA 58.940 45.455 17.77 7.23 30.24 4.35
5815 9559 1.827344 TCTGAGTTCGTCATGCATCCT 59.173 47.619 0.00 0.00 33.51 3.24
5816 9560 2.159184 TCTGAGTTCGTCATGCATCCTC 60.159 50.000 0.00 0.00 33.51 3.71
5817 9561 1.827344 TGAGTTCGTCATGCATCCTCT 59.173 47.619 0.00 0.00 0.00 3.69
5846 9590 2.738846 CTGTGTGTGCATAGTCTTCACC 59.261 50.000 0.00 0.00 0.00 4.02
5901 9695 8.497910 AGTATATCAGTGGTATGATTCTGGTT 57.502 34.615 6.14 0.00 40.40 3.67
5961 9813 3.262151 TGGGATTTGTCACCAATAGTCGA 59.738 43.478 0.00 0.00 0.00 4.20
5974 9826 1.089920 TAGTCGAAGTAGACCACCGC 58.910 55.000 0.00 0.00 41.83 5.68
6008 9860 0.590195 CACTGTGCTGCCTGAGTTTC 59.410 55.000 0.00 0.00 0.00 2.78
6023 9875 5.464030 TGAGTTTCCAGGTCTAACAGTAC 57.536 43.478 0.00 0.00 0.00 2.73
6040 9897 1.263217 GTACAAATAGGATTGCCCGCG 59.737 52.381 0.00 0.00 40.87 6.46
6044 9901 0.532862 AATAGGATTGCCCGCGTCAG 60.533 55.000 4.92 0.00 40.87 3.51
6050 9907 4.961511 TGCCCGCGTCAGTGTCAC 62.962 66.667 4.92 0.00 0.00 3.67
6054 9911 1.583495 CCCGCGTCAGTGTCACTAGA 61.583 60.000 4.85 3.25 0.00 2.43
6072 9929 9.381033 GTCACTAGACAAATCTCTGTAGTACTA 57.619 37.037 0.00 0.00 44.34 1.82
6075 9932 9.908747 ACTAGACAAATCTCTGTAGTACTATGT 57.091 33.333 5.75 3.60 36.29 2.29
6078 9935 9.862371 AGACAAATCTCTGTAGTACTATGTTTG 57.138 33.333 5.75 12.32 0.00 2.93
6079 9936 9.088512 GACAAATCTCTGTAGTACTATGTTTGG 57.911 37.037 5.75 0.45 0.00 3.28
6080 9937 7.549488 ACAAATCTCTGTAGTACTATGTTTGGC 59.451 37.037 5.75 0.00 0.00 4.52
6081 9938 7.425224 AATCTCTGTAGTACTATGTTTGGCT 57.575 36.000 5.75 0.00 0.00 4.75
6082 9939 6.452494 TCTCTGTAGTACTATGTTTGGCTC 57.548 41.667 5.75 0.00 0.00 4.70
6100 9957 9.216117 GTTTGGCTCATTCTAGTAGAAAAACTA 57.784 33.333 16.37 2.78 37.82 2.24
6104 9964 8.338986 GGCTCATTCTAGTAGAAAAACTATTGC 58.661 37.037 16.37 11.30 37.82 3.56
6141 10003 1.343075 ACACAGATATCCGGACCCTGT 60.343 52.381 22.28 22.28 38.48 4.00
6253 10124 1.078848 CGCCTTGGACTCCTTCCTG 60.079 63.158 0.00 0.00 46.10 3.86
6300 10171 2.029623 GTACATCCTCTTGGCCTCGTA 58.970 52.381 3.32 0.00 0.00 3.43
6412 10283 2.203788 TCCTCCACGGTCAGGCTT 60.204 61.111 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.107557 AAACACCGTCCCGACAAAGT 60.108 50.000 0.00 0.00 0.00 2.66
12 13 2.202171 GCATCGCGACAAACACCG 60.202 61.111 12.93 0.00 0.00 4.94
14 15 1.793613 GCAGCATCGCGACAAACAC 60.794 57.895 12.93 0.00 0.00 3.32
62 63 1.133450 CCCAGATCCTAACCTCCGAGA 60.133 57.143 0.00 0.00 0.00 4.04
67 68 0.761802 CCTGCCCAGATCCTAACCTC 59.238 60.000 0.00 0.00 0.00 3.85
76 77 0.252881 TGGTTCTCTCCTGCCCAGAT 60.253 55.000 0.00 0.00 0.00 2.90
78 79 0.622665 ATTGGTTCTCTCCTGCCCAG 59.377 55.000 0.00 0.00 0.00 4.45
84 85 0.976641 TCGTGCATTGGTTCTCTCCT 59.023 50.000 0.00 0.00 0.00 3.69
93 94 2.222886 CGATTCAGTTCTCGTGCATTGG 60.223 50.000 0.00 0.00 0.00 3.16
100 102 0.818296 CCCTCCGATTCAGTTCTCGT 59.182 55.000 0.00 0.00 33.11 4.18
107 109 1.826024 CCACCTCCCTCCGATTCAG 59.174 63.158 0.00 0.00 0.00 3.02
108 110 2.367202 GCCACCTCCCTCCGATTCA 61.367 63.158 0.00 0.00 0.00 2.57
110 112 3.470888 CGCCACCTCCCTCCGATT 61.471 66.667 0.00 0.00 0.00 3.34
111 113 4.458829 TCGCCACCTCCCTCCGAT 62.459 66.667 0.00 0.00 0.00 4.18
114 116 1.838073 TTTTCTCGCCACCTCCCTCC 61.838 60.000 0.00 0.00 0.00 4.30
141 143 1.512156 GCGGGGTCACGACAAACATT 61.512 55.000 0.00 0.00 35.47 2.71
144 146 2.280592 AGCGGGGTCACGACAAAC 60.281 61.111 0.00 0.00 35.47 2.93
149 151 3.998672 GTTCCAGCGGGGTCACGA 61.999 66.667 2.05 0.00 38.11 4.35
152 154 2.525629 TCTGTTCCAGCGGGGTCA 60.526 61.111 2.05 2.00 38.11 4.02
156 158 1.669115 CTGTGTCTGTTCCAGCGGG 60.669 63.158 0.00 0.00 0.00 6.13
174 176 0.811616 AACCTCGATGCGGATCTTGC 60.812 55.000 15.31 3.88 0.00 4.01
176 178 1.656652 CAAACCTCGATGCGGATCTT 58.343 50.000 15.31 0.00 0.00 2.40
190 194 3.236618 GACACAGTCGCGGCAAACC 62.237 63.158 15.58 0.00 0.00 3.27
226 230 2.731976 GACATCGATATGTTTCTCCCGC 59.268 50.000 0.00 0.00 46.49 6.13
227 231 3.318017 GGACATCGATATGTTTCTCCCG 58.682 50.000 0.00 0.00 46.49 5.14
229 233 3.978687 ACGGACATCGATATGTTTCTCC 58.021 45.455 0.00 0.00 46.49 3.71
237 243 0.110328 GTCGCGACGGACATCGATAT 60.110 55.000 25.19 0.00 45.13 1.63
243 249 2.126071 CAAGGTCGCGACGGACAT 60.126 61.111 30.99 13.30 38.70 3.06
259 265 1.807981 CGTTATGCGGGCTTCGACA 60.808 57.895 4.34 2.84 42.43 4.35
272 278 1.812507 GGCGCGTTTCTCCCGTTAT 60.813 57.895 8.43 0.00 0.00 1.89
273 279 2.432972 GGCGCGTTTCTCCCGTTA 60.433 61.111 8.43 0.00 0.00 3.18
298 304 0.507358 GGTTTCAACAGAGTCGCGAC 59.493 55.000 31.30 31.30 0.00 5.19
311 317 2.032634 GGATGCTCGTGCGGTTTCA 61.033 57.895 4.84 0.00 43.34 2.69
323 329 0.994247 TTGGTGAGTGGATGGATGCT 59.006 50.000 0.00 0.00 0.00 3.79
336 342 8.271458 TGATAGAGGTTTTGCTATATTTGGTGA 58.729 33.333 0.00 0.00 0.00 4.02
353 359 2.961062 GCAAATGGGCATTGATAGAGGT 59.039 45.455 1.71 0.00 0.00 3.85
359 365 4.850680 AGAAATTGCAAATGGGCATTGAT 58.149 34.783 1.71 0.00 44.48 2.57
362 368 5.071370 TGAAAGAAATTGCAAATGGGCATT 58.929 33.333 1.71 0.00 44.48 3.56
371 377 7.136119 CCTACTAACGTTGAAAGAAATTGCAA 58.864 34.615 11.99 0.00 0.00 4.08
377 383 4.512571 GCCACCTACTAACGTTGAAAGAAA 59.487 41.667 11.99 0.00 0.00 2.52
380 386 3.395639 TGCCACCTACTAACGTTGAAAG 58.604 45.455 11.99 2.66 0.00 2.62
393 399 2.668212 GTGCGTTGCTGCCACCTA 60.668 61.111 0.00 0.00 0.00 3.08
397 403 3.597675 TATCCGTGCGTTGCTGCCA 62.598 57.895 0.00 0.00 0.00 4.92
398 404 1.714899 ATTATCCGTGCGTTGCTGCC 61.715 55.000 0.00 0.00 0.00 4.85
399 405 0.589729 CATTATCCGTGCGTTGCTGC 60.590 55.000 0.00 0.00 0.00 5.25
402 408 1.534028 CAACATTATCCGTGCGTTGC 58.466 50.000 0.00 0.00 31.53 4.17
404 410 1.466950 CACCAACATTATCCGTGCGTT 59.533 47.619 0.00 0.00 0.00 4.84
405 411 1.083489 CACCAACATTATCCGTGCGT 58.917 50.000 0.00 0.00 0.00 5.24
406 412 1.364721 TCACCAACATTATCCGTGCG 58.635 50.000 0.00 0.00 0.00 5.34
407 413 2.942376 TGATCACCAACATTATCCGTGC 59.058 45.455 0.00 0.00 0.00 5.34
492 512 1.353358 CTTTCCTTACCGTTTCCCCCT 59.647 52.381 0.00 0.00 0.00 4.79
605 627 3.494336 GTAGGCAGCACAGCAGCG 61.494 66.667 0.00 0.00 41.94 5.18
869 902 4.564110 GGAATTCGGGGGAGCGGG 62.564 72.222 0.00 0.00 0.00 6.13
870 903 4.564110 GGGAATTCGGGGGAGCGG 62.564 72.222 0.00 0.00 0.00 5.52
871 904 3.792736 TGGGAATTCGGGGGAGCG 61.793 66.667 0.00 0.00 0.00 5.03
872 905 2.124278 GTGGGAATTCGGGGGAGC 60.124 66.667 0.00 0.00 0.00 4.70
873 906 2.595655 GGTGGGAATTCGGGGGAG 59.404 66.667 0.00 0.00 0.00 4.30
874 907 3.018805 GGGTGGGAATTCGGGGGA 61.019 66.667 0.00 0.00 0.00 4.81
875 908 4.137615 GGGGTGGGAATTCGGGGG 62.138 72.222 0.00 0.00 0.00 5.40
876 909 4.137615 GGGGGTGGGAATTCGGGG 62.138 72.222 0.00 0.00 0.00 5.73
934 967 4.452733 CGGACCAACCCTCGGCTC 62.453 72.222 0.00 0.00 34.64 4.70
938 971 2.718073 CCTACCGGACCAACCCTCG 61.718 68.421 9.46 0.00 34.64 4.63
939 972 2.364780 CCCTACCGGACCAACCCTC 61.365 68.421 9.46 0.00 34.64 4.30
940 973 2.285144 CCCTACCGGACCAACCCT 60.285 66.667 9.46 0.00 34.64 4.34
941 974 2.608678 ACCCTACCGGACCAACCC 60.609 66.667 9.46 0.00 34.64 4.11
942 975 2.984623 GACCCTACCGGACCAACC 59.015 66.667 9.46 0.00 34.64 3.77
943 976 1.820010 AACGACCCTACCGGACCAAC 61.820 60.000 9.46 0.00 34.64 3.77
959 1010 4.347453 GCCCCAACAGCAGCAACG 62.347 66.667 0.00 0.00 0.00 4.10
967 1018 2.198426 ACCAACCAGCCCCAACAG 59.802 61.111 0.00 0.00 0.00 3.16
1083 1140 1.644786 GGGTCACCGGAAAATCAGCG 61.645 60.000 9.46 0.00 0.00 5.18
1084 1141 1.313091 GGGGTCACCGGAAAATCAGC 61.313 60.000 9.46 0.00 37.78 4.26
1085 1142 0.037590 TGGGGTCACCGGAAAATCAG 59.962 55.000 9.46 0.00 44.64 2.90
1088 1145 0.324275 CCATGGGGTCACCGGAAAAT 60.324 55.000 9.46 0.00 44.64 1.82
1093 1150 2.192979 CATCCATGGGGTCACCGG 59.807 66.667 13.02 0.00 44.64 5.28
1117 1174 3.199891 GAATCGGCCGAAACCCCG 61.200 66.667 34.66 0.00 45.64 5.73
1119 1176 2.112815 CAGGAATCGGCCGAAACCC 61.113 63.158 34.47 30.71 0.00 4.11
1142 1199 1.631072 CGCGTCACATCATCGAACC 59.369 57.895 0.00 0.00 0.00 3.62
1144 1201 1.075979 CACCGCGTCACATCATCGAA 61.076 55.000 4.92 0.00 0.00 3.71
1145 1202 1.516169 CACCGCGTCACATCATCGA 60.516 57.895 4.92 0.00 0.00 3.59
1147 1204 2.813179 GCCACCGCGTCACATCATC 61.813 63.158 4.92 0.00 0.00 2.92
1148 1205 2.819595 GCCACCGCGTCACATCAT 60.820 61.111 4.92 0.00 0.00 2.45
1149 1206 3.932580 GAGCCACCGCGTCACATCA 62.933 63.158 4.92 0.00 41.18 3.07
1151 1208 3.695606 AGAGCCACCGCGTCACAT 61.696 61.111 4.92 0.00 41.18 3.21
1152 1209 4.662961 CAGAGCCACCGCGTCACA 62.663 66.667 4.92 0.00 41.18 3.58
1154 1211 4.056125 CTCAGAGCCACCGCGTCA 62.056 66.667 4.92 0.00 41.18 4.35
1156 1213 3.071206 ATCTCAGAGCCACCGCGT 61.071 61.111 4.92 0.00 41.18 6.01
1165 1227 2.189594 TTGGTGTTGGCATCTCAGAG 57.810 50.000 0.00 0.00 0.00 3.35
1168 1230 2.170166 GGATTTGGTGTTGGCATCTCA 58.830 47.619 0.00 0.00 0.00 3.27
1169 1231 2.170166 TGGATTTGGTGTTGGCATCTC 58.830 47.619 0.00 0.00 0.00 2.75
1176 1238 5.982890 AACTAGGAATGGATTTGGTGTTG 57.017 39.130 0.00 0.00 0.00 3.33
1198 1260 5.689514 CCAAACAGTGCATACGAATGAAAAA 59.310 36.000 0.00 0.00 34.84 1.94
1199 1261 5.218885 CCAAACAGTGCATACGAATGAAAA 58.781 37.500 0.00 0.00 34.84 2.29
1200 1262 4.277174 ACCAAACAGTGCATACGAATGAAA 59.723 37.500 0.00 0.00 34.84 2.69
1202 1264 3.407698 ACCAAACAGTGCATACGAATGA 58.592 40.909 0.00 0.00 34.84 2.57
1203 1265 3.188254 TGACCAAACAGTGCATACGAATG 59.812 43.478 0.00 0.00 36.09 2.67
1204 1266 3.407698 TGACCAAACAGTGCATACGAAT 58.592 40.909 0.00 0.00 0.00 3.34
1205 1267 2.839975 TGACCAAACAGTGCATACGAA 58.160 42.857 0.00 0.00 0.00 3.85
1206 1268 2.535012 TGACCAAACAGTGCATACGA 57.465 45.000 0.00 0.00 0.00 3.43
1207 1269 3.829886 AATGACCAAACAGTGCATACG 57.170 42.857 0.00 0.00 0.00 3.06
1208 1270 4.158384 CGAAATGACCAAACAGTGCATAC 58.842 43.478 0.00 0.00 0.00 2.39
1211 1273 2.020720 ACGAAATGACCAAACAGTGCA 58.979 42.857 0.00 0.00 0.00 4.57
1212 1274 2.384382 CACGAAATGACCAAACAGTGC 58.616 47.619 0.00 0.00 0.00 4.40
1213 1275 2.287547 CCCACGAAATGACCAAACAGTG 60.288 50.000 0.00 0.00 0.00 3.66
1214 1276 1.953686 CCCACGAAATGACCAAACAGT 59.046 47.619 0.00 0.00 0.00 3.55
1215 1277 1.269448 CCCCACGAAATGACCAAACAG 59.731 52.381 0.00 0.00 0.00 3.16
1218 1280 1.144093 AGTCCCCACGAAATGACCAAA 59.856 47.619 0.00 0.00 0.00 3.28
1222 1284 0.739813 CGGAGTCCCCACGAAATGAC 60.740 60.000 2.80 0.00 34.14 3.06
1224 1286 1.449601 CCGGAGTCCCCACGAAATG 60.450 63.158 2.80 0.00 34.14 2.32
1226 1288 2.524887 ACCGGAGTCCCCACGAAA 60.525 61.111 9.46 0.00 34.14 3.46
1231 1293 3.572715 ATTCCCACCGGAGTCCCCA 62.573 63.158 9.46 0.00 40.10 4.96
1232 1294 2.691252 ATTCCCACCGGAGTCCCC 60.691 66.667 9.46 0.00 40.10 4.81
1233 1295 1.972660 CTGATTCCCACCGGAGTCCC 61.973 65.000 9.46 0.00 42.82 4.46
1237 1299 1.418334 ATCTCTGATTCCCACCGGAG 58.582 55.000 9.46 0.00 40.10 4.63
1246 1323 9.979578 ATAATAATCCGCTGATATCTCTGATTC 57.020 33.333 3.98 0.00 0.00 2.52
1251 1328 7.493971 GCACAATAATAATCCGCTGATATCTCT 59.506 37.037 3.98 0.00 0.00 3.10
1268 1345 3.631686 TGAGGCTAATTGCGCACAATAAT 59.368 39.130 11.12 0.00 45.90 1.28
1294 1371 0.788391 AGTTAAGCCTTTCGCGAACG 59.212 50.000 23.33 20.16 44.76 3.95
1344 1421 1.644786 CGACTGGATCGCCCCAAAAC 61.645 60.000 0.00 0.00 45.52 2.43
1362 1439 2.159338 AGCTATGCAACCAAATCAAGCG 60.159 45.455 0.00 0.00 34.01 4.68
1514 1597 4.141251 ACCCACCACCTAATAAAGCCTATG 60.141 45.833 0.00 0.00 0.00 2.23
1538 1621 3.686726 CCAATGACTGTACAAGAGAAGGC 59.313 47.826 0.00 0.00 0.00 4.35
1545 1628 6.549061 CATCAATGTCCAATGACTGTACAAG 58.451 40.000 0.00 0.00 42.28 3.16
1624 1711 4.745125 CCAATTCATGATGAAAGAGCATGC 59.255 41.667 12.36 10.51 40.12 4.06
1634 1721 9.860898 CGATAAGTACTATCCAATTCATGATGA 57.139 33.333 0.00 0.00 33.96 2.92
1653 1740 7.938715 ACGATTACCTTCTGATAACGATAAGT 58.061 34.615 0.00 0.00 0.00 2.24
1669 1756 2.963782 GTCCTGTCCCATACGATTACCT 59.036 50.000 0.00 0.00 0.00 3.08
1672 1759 3.964688 ACATGTCCTGTCCCATACGATTA 59.035 43.478 0.00 0.00 29.94 1.75
1676 1763 2.223971 GGTACATGTCCTGTCCCATACG 60.224 54.545 0.00 0.00 39.39 3.06
1721 1813 1.077068 ACACCACACCCCAACACAG 60.077 57.895 0.00 0.00 0.00 3.66
1772 1866 4.682787 TCATCGTGCTAAGTGGTTATCTG 58.317 43.478 0.00 0.00 0.00 2.90
1773 1867 5.339008 TTCATCGTGCTAAGTGGTTATCT 57.661 39.130 0.00 0.00 0.00 1.98
1775 1869 6.112734 TGAATTCATCGTGCTAAGTGGTTAT 58.887 36.000 3.38 0.00 0.00 1.89
1805 1899 2.751259 GCATCAGCAACTGAATCAAGGA 59.249 45.455 0.74 0.00 44.04 3.36
1818 1912 1.881973 GTTTCTTGGTCAGCATCAGCA 59.118 47.619 0.00 0.00 45.49 4.41
1819 1913 1.881973 TGTTTCTTGGTCAGCATCAGC 59.118 47.619 0.00 0.00 42.56 4.26
1820 1914 4.778534 AATGTTTCTTGGTCAGCATCAG 57.221 40.909 0.00 0.00 0.00 2.90
1821 1915 4.583907 TCAAATGTTTCTTGGTCAGCATCA 59.416 37.500 0.00 0.00 0.00 3.07
1822 1916 5.125100 TCAAATGTTTCTTGGTCAGCATC 57.875 39.130 0.00 0.00 0.00 3.91
1823 1917 5.733620 ATCAAATGTTTCTTGGTCAGCAT 57.266 34.783 0.00 0.00 0.00 3.79
1848 1948 6.596888 AGATATGATGCTAAAATCATCCACCG 59.403 38.462 3.06 0.00 42.38 4.94
1874 1974 0.973632 TGTCAGTGCCGAGTACCAAT 59.026 50.000 0.00 0.00 0.00 3.16
1884 1984 2.169832 TCAAGCTAAGTGTCAGTGCC 57.830 50.000 0.00 0.00 0.00 5.01
1920 2020 5.659463 TCAAATTTCTTGGTCAACAACAGG 58.341 37.500 0.00 0.00 34.76 4.00
2020 2122 5.230306 GCACTGTAGTATTAGTCTTGCTTCG 59.770 44.000 0.00 0.00 0.00 3.79
2120 2222 8.091449 TGTGACACACTTTTTAAGGAAAAACAT 58.909 29.630 3.56 0.00 38.60 2.71
2389 2500 6.526674 CGCAATTAATGACTGGAAAACCTTAC 59.473 38.462 0.00 0.00 0.00 2.34
2390 2501 6.207810 ACGCAATTAATGACTGGAAAACCTTA 59.792 34.615 0.00 0.00 0.00 2.69
2391 2502 5.010617 ACGCAATTAATGACTGGAAAACCTT 59.989 36.000 0.00 0.00 0.00 3.50
2392 2503 4.522789 ACGCAATTAATGACTGGAAAACCT 59.477 37.500 0.00 0.00 0.00 3.50
2393 2504 4.805219 ACGCAATTAATGACTGGAAAACC 58.195 39.130 0.00 0.00 0.00 3.27
2394 2505 8.460831 AAATACGCAATTAATGACTGGAAAAC 57.539 30.769 0.00 0.00 0.00 2.43
2395 2506 9.134734 GAAAATACGCAATTAATGACTGGAAAA 57.865 29.630 0.00 0.00 0.00 2.29
2396 2507 7.757624 GGAAAATACGCAATTAATGACTGGAAA 59.242 33.333 0.00 0.00 0.00 3.13
2397 2508 7.094162 TGGAAAATACGCAATTAATGACTGGAA 60.094 33.333 0.00 0.00 0.00 3.53
2398 2509 6.375736 TGGAAAATACGCAATTAATGACTGGA 59.624 34.615 0.00 0.00 0.00 3.86
2418 2529 6.968263 TCCAATTGTTTGTAGACATGGAAA 57.032 33.333 4.43 0.00 36.35 3.13
2491 2603 6.982141 ACTAGAAGTACACGTCAATCACAAAA 59.018 34.615 0.00 0.00 0.00 2.44
2513 2626 6.092955 AGACACAGTTGAATAACGGAACTA 57.907 37.500 0.00 0.00 41.71 2.24
2811 2924 3.045142 CAAGCAACAGGGCACAGG 58.955 61.111 0.00 0.00 35.83 4.00
2904 3017 1.012841 GACTAGCCATTGCAGTCTGC 58.987 55.000 18.32 18.32 45.29 4.26
2961 3074 5.875224 TGTAACAAGGAATCATCACTTGGA 58.125 37.500 8.30 0.00 44.35 3.53
3017 3130 5.339990 AGTTCCGAACACTTGACATTTTTG 58.660 37.500 13.69 0.00 0.00 2.44
3072 3185 9.719355 TGAATTAGTTTTTGCACTAGTCTATCA 57.281 29.630 0.00 0.00 30.77 2.15
3145 3258 7.201478 GCAGATTCTACTGACTGAAACATACAC 60.201 40.741 0.00 0.00 39.94 2.90
3632 3916 3.004315 GCGAACCATTGGACTTTTGAAGA 59.996 43.478 10.37 0.00 0.00 2.87
3674 3958 8.489990 AATATCCTCTAATGAATTCAGATGCG 57.510 34.615 14.54 2.50 0.00 4.73
4008 4336 1.372501 AAGTGTGAGCCCCCTACATT 58.627 50.000 0.00 0.00 0.00 2.71
4187 4518 9.890629 GGTTAGCTATGGTATATTGATGATTCA 57.109 33.333 0.00 0.00 0.00 2.57
4190 4521 9.499369 AGAGGTTAGCTATGGTATATTGATGAT 57.501 33.333 0.00 0.00 0.00 2.45
4191 4522 8.901472 AGAGGTTAGCTATGGTATATTGATGA 57.099 34.615 0.00 0.00 0.00 2.92
4194 4525 9.990868 TCATAGAGGTTAGCTATGGTATATTGA 57.009 33.333 0.00 0.00 43.33 2.57
4239 4574 6.757947 CCTGGGAAGTAAAATATGCATTTGTG 59.242 38.462 3.54 0.00 34.53 3.33
4409 4744 6.127897 GCAGAATACTGGCTTGATAAAACAGT 60.128 38.462 0.00 0.00 43.62 3.55
4410 4745 6.127925 TGCAGAATACTGGCTTGATAAAACAG 60.128 38.462 0.00 0.00 43.62 3.16
4689 5055 6.576641 ATGCATTTCAAGTATTGGCATTTGGA 60.577 34.615 0.00 0.00 44.12 3.53
4754 5122 9.515226 ACATAGTTTGTATTCACACCTTTGTAT 57.485 29.630 0.00 0.00 36.57 2.29
4988 5384 9.638239 GGCAGAATTTTAATATTCTCACAACAA 57.362 29.630 15.68 0.00 41.68 2.83
4989 5385 9.023962 AGGCAGAATTTTAATATTCTCACAACA 57.976 29.630 15.68 0.00 41.68 3.33
4990 5386 9.860898 AAGGCAGAATTTTAATATTCTCACAAC 57.139 29.630 15.68 7.09 41.68 3.32
4992 5388 9.466497 AGAAGGCAGAATTTTAATATTCTCACA 57.534 29.630 15.68 0.00 41.68 3.58
5013 5409 4.943705 ACAACAATGTATGTGCCTAGAAGG 59.056 41.667 0.00 0.00 42.99 3.46
5014 5410 5.643348 TCACAACAATGTATGTGCCTAGAAG 59.357 40.000 17.59 0.77 45.08 2.85
5015 5411 5.555966 TCACAACAATGTATGTGCCTAGAA 58.444 37.500 17.59 3.95 45.08 2.10
5016 5412 5.046663 TCTCACAACAATGTATGTGCCTAGA 60.047 40.000 17.59 14.05 45.08 2.43
5017 5413 5.178061 TCTCACAACAATGTATGTGCCTAG 58.822 41.667 17.59 12.66 45.08 3.02
5018 5414 5.159273 TCTCACAACAATGTATGTGCCTA 57.841 39.130 17.59 7.83 45.08 3.93
5019 5415 4.019792 TCTCACAACAATGTATGTGCCT 57.980 40.909 17.59 0.00 45.08 4.75
5020 5416 4.764679 TTCTCACAACAATGTATGTGCC 57.235 40.909 17.59 0.00 45.08 5.01
5097 5493 1.020437 GCTGAATAGGAGCTGTTGGC 58.980 55.000 0.00 0.00 42.19 4.52
5134 5530 6.146021 GTGGCCTGAAAATGTTGATTTGTTAG 59.854 38.462 3.32 0.00 31.83 2.34
5159 5555 1.739562 GTCGCTCTTGGCAGTGAGG 60.740 63.158 17.24 10.02 41.91 3.86
5375 5771 1.442857 GGACAGACACTCGACAGCG 60.443 63.158 0.00 0.00 39.35 5.18
5387 5783 5.337894 CCTCATCTTAGCTTCAAAGGACAGA 60.338 44.000 0.00 0.00 0.00 3.41
5396 5792 1.137086 GACGGCCTCATCTTAGCTTCA 59.863 52.381 0.00 0.00 0.00 3.02
5429 5825 6.031964 TGTATCCCTTCCAGAATAGAGACT 57.968 41.667 6.29 0.00 0.00 3.24
5504 5921 1.264045 GGTCTTGAGGCCTCTCTGCT 61.264 60.000 32.28 0.00 40.58 4.24
5807 9551 1.047596 AGGCACGAGAGAGGATGCAT 61.048 55.000 0.00 0.00 39.92 3.96
5815 9559 1.363807 CACACACAGGCACGAGAGA 59.636 57.895 0.00 0.00 0.00 3.10
5816 9560 2.313172 GCACACACAGGCACGAGAG 61.313 63.158 0.00 0.00 0.00 3.20
5817 9561 2.280119 GCACACACAGGCACGAGA 60.280 61.111 0.00 0.00 0.00 4.04
5846 9590 7.602753 TGAGTATATGGTATGAACTTGATCCG 58.397 38.462 0.00 0.00 0.00 4.18
5901 9695 4.662961 CGGCACTCACTGACGCCA 62.663 66.667 13.03 0.00 46.85 5.69
5974 9826 3.554524 CACAGTGCTCACAATTAAACCG 58.445 45.455 2.63 0.00 0.00 4.44
6004 9856 7.333672 CCTATTTGTACTGTTAGACCTGGAAAC 59.666 40.741 0.00 2.59 0.00 2.78
6008 9860 6.540438 TCCTATTTGTACTGTTAGACCTGG 57.460 41.667 0.00 0.00 0.00 4.45
6023 9875 0.307760 GACGCGGGCAATCCTATTTG 59.692 55.000 12.47 0.00 0.00 2.32
6054 9911 7.549488 GCCAAACATAGTACTACAGAGATTTGT 59.451 37.037 4.31 0.14 35.09 2.83
6067 9924 8.630917 TCTACTAGAATGAGCCAAACATAGTAC 58.369 37.037 0.00 0.00 0.00 2.73
6069 9926 7.661536 TCTACTAGAATGAGCCAAACATAGT 57.338 36.000 0.00 0.00 0.00 2.12
6070 9927 8.948631 TTTCTACTAGAATGAGCCAAACATAG 57.051 34.615 0.00 0.00 33.67 2.23
6072 9929 8.515414 GTTTTTCTACTAGAATGAGCCAAACAT 58.485 33.333 12.59 0.00 33.67 2.71
6075 9932 9.959721 ATAGTTTTTCTACTAGAATGAGCCAAA 57.040 29.630 0.00 0.00 33.67 3.28
6078 9935 8.338986 GCAATAGTTTTTCTACTAGAATGAGCC 58.661 37.037 0.00 0.00 33.67 4.70
6079 9936 8.883731 TGCAATAGTTTTTCTACTAGAATGAGC 58.116 33.333 0.00 0.00 33.67 4.26
6081 9938 9.719355 TGTGCAATAGTTTTTCTACTAGAATGA 57.281 29.630 0.00 0.00 33.67 2.57
6100 9957 2.229792 ACCTCGTGAAACATGTGCAAT 58.770 42.857 0.00 0.00 35.74 3.56
6104 9964 3.127589 TGTGTACCTCGTGAAACATGTG 58.872 45.455 0.00 0.00 35.74 3.21
6141 10003 1.025113 CGTGCTCCGGTAGAGTCAGA 61.025 60.000 0.00 0.00 45.21 3.27
6253 10124 2.270527 GTGAGGAGCAAGAGGGGC 59.729 66.667 0.00 0.00 0.00 5.80
6300 10171 1.031112 AGGAGGGGAGAGGGAAAGAT 58.969 55.000 0.00 0.00 0.00 2.40
6619 10493 4.452733 CGGGTGGCCTCGTTCTCC 62.453 72.222 3.32 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.