Multiple sequence alignment - TraesCS7D01G189100

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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 TraesCS7D01G189100 chr7D 100.000 3709 0 0 1 3709 141635332 141631624 0.000000e+00 6850.0
1 TraesCS7D01G189100 chr7D 90.291 103 10 0 3263 3365 613794521 613794623 6.460000e-28 135.0
2 TraesCS7D01G189100 chr7D 97.872 47 1 0 1143 1189 141634147 141634101 8.540000e-12 82.4
3 TraesCS7D01G189100 chr7D 97.872 47 1 0 1186 1232 141634190 141634144 8.540000e-12 82.4
4 TraesCS7D01G189100 chr7B 93.432 2101 93 24 1188 3266 106774558 106776635 0.000000e+00 3073.0
5 TraesCS7D01G189100 chr7B 92.069 807 45 6 387 1189 106773812 106774603 0.000000e+00 1118.0
6 TraesCS7D01G189100 chr7B 91.632 239 16 3 1 239 106773580 106773814 9.930000e-86 327.0
7 TraesCS7D01G189100 chr7B 82.292 96 7 3 3262 3347 244757627 244757532 1.430000e-09 75.0
8 TraesCS7D01G189100 chr7A 95.032 1711 69 10 1186 2886 144128194 144129898 0.000000e+00 2675.0
9 TraesCS7D01G189100 chr7A 96.134 1190 33 8 1 1186 144127057 144128237 0.000000e+00 1930.0
10 TraesCS7D01G189100 chr7A 87.749 351 28 7 3369 3709 144130362 144130707 2.680000e-106 396.0
11 TraesCS7D01G189100 chr7A 83.171 410 20 28 2888 3267 144129974 144130364 2.760000e-86 329.0
12 TraesCS7D01G189100 chr6D 90.123 162 15 1 237 397 392273073 392273234 3.750000e-50 209.0
13 TraesCS7D01G189100 chr6D 92.754 138 10 0 237 374 221843147 221843010 2.260000e-47 200.0
14 TraesCS7D01G189100 chr6D 93.056 72 3 2 3304 3374 452132541 452132471 1.820000e-18 104.0
15 TraesCS7D01G189100 chr6D 90.909 77 6 1 3304 3379 305136478 305136402 6.550000e-18 102.0
16 TraesCS7D01G189100 chr2B 86.000 200 23 4 3482 3677 540439003 540438805 3.750000e-50 209.0
17 TraesCS7D01G189100 chr2B 91.156 147 13 0 236 382 190023045 190022899 2.260000e-47 200.0
18 TraesCS7D01G189100 chr2B 93.333 75 4 1 3299 3372 95798112 95798038 3.920000e-20 110.0
19 TraesCS7D01G189100 chr2B 83.962 106 15 1 3265 3368 442576370 442576265 2.360000e-17 100.0
20 TraesCS7D01G189100 chr2B 81.513 119 11 5 3265 3372 107096073 107096191 1.840000e-13 87.9
21 TraesCS7D01G189100 chr2B 79.167 120 14 5 3263 3371 314788226 314788107 5.140000e-09 73.1
22 TraesCS7D01G189100 chr6A 90.446 157 14 1 242 397 538097683 538097839 4.860000e-49 206.0
23 TraesCS7D01G189100 chr6A 92.754 138 10 0 237 374 263887018 263886881 2.260000e-47 200.0
24 TraesCS7D01G189100 chr3B 91.549 142 10 2 256 396 521797904 521797764 1.050000e-45 195.0
25 TraesCS7D01G189100 chr3B 88.889 81 7 2 3301 3381 166564294 166564372 8.480000e-17 99.0
26 TraesCS7D01G189100 chr3B 80.702 114 12 3 3265 3368 519770554 519770441 3.070000e-11 80.5
27 TraesCS7D01G189100 chr2D 89.933 149 13 2 237 384 467062614 467062467 1.360000e-44 191.0
28 TraesCS7D01G189100 chr2D 93.056 72 4 1 3301 3371 489410117 489410188 1.820000e-18 104.0
29 TraesCS7D01G189100 chr3D 88.387 155 17 1 237 390 85449521 85449367 6.330000e-43 185.0
30 TraesCS7D01G189100 chr3D 90.667 75 6 1 3304 3378 445862466 445862393 8.480000e-17 99.0
31 TraesCS7D01G189100 chr5A 77.727 220 32 14 3467 3674 676971220 676971006 6.510000e-23 119.0
32 TraesCS7D01G189100 chr5A 88.889 45 3 2 3639 3682 586165401 586165358 2.000000e-03 54.7
33 TraesCS7D01G189100 chr4A 94.444 72 3 1 3301 3371 691397680 691397609 3.920000e-20 110.0
34 TraesCS7D01G189100 chr5B 83.333 120 9 6 3263 3371 295212848 295212729 2.360000e-17 100.0
35 TraesCS7D01G189100 chr5B 82.540 126 11 4 3258 3372 653800155 653800280 2.360000e-17 100.0
36 TraesCS7D01G189100 chr5B 88.710 62 4 3 3617 3678 470277477 470277535 5.140000e-09 73.1
37 TraesCS7D01G189100 chr4B 82.051 117 11 3 3262 3368 21371964 21371848 1.420000e-14 91.6
38 TraesCS7D01G189100 chr5D 88.889 63 5 2 3617 3678 390344877 390344938 3.970000e-10 76.8
39 TraesCS7D01G189100 chr3A 82.278 79 8 3 3604 3678 599572645 599572569 3.090000e-06 63.9
40 TraesCS7D01G189100 chrUn 97.222 36 1 0 3639 3674 8798137 8798102 1.110000e-05 62.1


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 TraesCS7D01G189100 chr7D 141631624 141635332 3708 True 2338.266667 6850 98.581333 1 3709 3 chr7D.!!$R1 3708
1 TraesCS7D01G189100 chr7B 106773580 106776635 3055 False 1506.000000 3073 92.377667 1 3266 3 chr7B.!!$F1 3265
2 TraesCS7D01G189100 chr7A 144127057 144130707 3650 False 1332.500000 2675 90.521500 1 3709 4 chr7A.!!$F1 3708

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
927 935 0.453390 GTGCTCTGCTAATGCCAACC 59.547 55.0 0.0 0.0 38.71 3.77 F
1980 1988 0.034896 AACCACAAACGATCCGAGCT 59.965 50.0 0.0 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2279 0.610687 CCTGGGACTTCAGTGACTCC 59.389 60.0 7.32 7.32 33.14 3.85 R
3284 3420 0.255890 CATCCATTCCCCCGACAAGT 59.744 55.0 0.00 0.00 0.00 3.16 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
149 151 9.912634 ATTTACTGTTCTGGTTTATTCACATTG 57.087 29.630 0.00 0.00 0.00 2.82
247 249 8.527135 TGAATAATTTGTATATACCCCCTCCA 57.473 34.615 10.38 0.00 0.00 3.86
296 298 9.658799 ACCATTTTCTGAATCGGATGTATATAG 57.341 33.333 0.00 0.00 0.00 1.31
301 303 9.860898 TTTCTGAATCGGATGTATATAGACATG 57.139 33.333 17.40 4.78 40.18 3.21
670 676 1.689273 AGAAGACGGAGCAACTTCACT 59.311 47.619 0.00 0.00 41.37 3.41
681 687 1.338020 CAACTTCACTTGTTCCCTGCC 59.662 52.381 0.00 0.00 0.00 4.85
808 815 7.959733 TGAGAAATCGAACATACATTGTACAC 58.040 34.615 0.00 0.00 37.68 2.90
827 834 3.338275 ATCCGCTTTGCCGCCCTTA 62.338 57.895 0.00 0.00 0.00 2.69
836 843 2.038837 GCCGCCCTTACAACTCCAC 61.039 63.158 0.00 0.00 0.00 4.02
927 935 0.453390 GTGCTCTGCTAATGCCAACC 59.547 55.000 0.00 0.00 38.71 3.77
977 985 3.521947 AGGTAATGAACACGGTCTAGC 57.478 47.619 0.00 0.00 0.00 3.42
1170 1178 1.337384 TGTGCCGCCTCATATGTCCT 61.337 55.000 1.90 0.00 0.00 3.85
1171 1179 0.601311 GTGCCGCCTCATATGTCCTC 60.601 60.000 1.90 0.00 0.00 3.71
1172 1180 0.760567 TGCCGCCTCATATGTCCTCT 60.761 55.000 1.90 0.00 0.00 3.69
1173 1181 0.394565 GCCGCCTCATATGTCCTCTT 59.605 55.000 1.90 0.00 0.00 2.85
1174 1182 1.875576 GCCGCCTCATATGTCCTCTTG 60.876 57.143 1.90 0.00 0.00 3.02
1175 1183 1.688735 CCGCCTCATATGTCCTCTTGA 59.311 52.381 1.90 0.00 0.00 3.02
1176 1184 2.103094 CCGCCTCATATGTCCTCTTGAA 59.897 50.000 1.90 0.00 0.00 2.69
1177 1185 3.126831 CGCCTCATATGTCCTCTTGAAC 58.873 50.000 1.90 0.00 0.00 3.18
1178 1186 3.471680 GCCTCATATGTCCTCTTGAACC 58.528 50.000 1.90 0.00 0.00 3.62
1179 1187 3.135530 GCCTCATATGTCCTCTTGAACCT 59.864 47.826 1.90 0.00 0.00 3.50
1180 1188 4.384647 GCCTCATATGTCCTCTTGAACCTT 60.385 45.833 1.90 0.00 0.00 3.50
1181 1189 5.121811 CCTCATATGTCCTCTTGAACCTTG 58.878 45.833 1.90 0.00 0.00 3.61
1182 1190 4.517285 TCATATGTCCTCTTGAACCTTGC 58.483 43.478 1.90 0.00 0.00 4.01
1183 1191 4.225942 TCATATGTCCTCTTGAACCTTGCT 59.774 41.667 1.90 0.00 0.00 3.91
1184 1192 5.425217 TCATATGTCCTCTTGAACCTTGCTA 59.575 40.000 1.90 0.00 0.00 3.49
1185 1193 4.640771 ATGTCCTCTTGAACCTTGCTAA 57.359 40.909 0.00 0.00 0.00 3.09
1186 1194 3.740115 TGTCCTCTTGAACCTTGCTAAC 58.260 45.455 0.00 0.00 0.00 2.34
1187 1195 3.391296 TGTCCTCTTGAACCTTGCTAACT 59.609 43.478 0.00 0.00 0.00 2.24
1188 1196 4.141482 TGTCCTCTTGAACCTTGCTAACTT 60.141 41.667 0.00 0.00 0.00 2.66
1189 1197 5.071250 TGTCCTCTTGAACCTTGCTAACTTA 59.929 40.000 0.00 0.00 0.00 2.24
1190 1198 5.408909 GTCCTCTTGAACCTTGCTAACTTAC 59.591 44.000 0.00 0.00 0.00 2.34
1191 1199 5.307196 TCCTCTTGAACCTTGCTAACTTACT 59.693 40.000 0.00 0.00 0.00 2.24
1192 1200 5.639931 CCTCTTGAACCTTGCTAACTTACTC 59.360 44.000 0.00 0.00 0.00 2.59
1193 1201 5.548406 TCTTGAACCTTGCTAACTTACTCC 58.452 41.667 0.00 0.00 0.00 3.85
1194 1202 5.307196 TCTTGAACCTTGCTAACTTACTCCT 59.693 40.000 0.00 0.00 0.00 3.69
1195 1203 4.894784 TGAACCTTGCTAACTTACTCCTG 58.105 43.478 0.00 0.00 0.00 3.86
1199 1207 2.762535 TGCTAACTTACTCCTGTGCC 57.237 50.000 0.00 0.00 0.00 5.01
1245 1253 7.094762 ACCTTGCTAACTTGCAGTATTAACTTC 60.095 37.037 0.00 0.00 44.27 3.01
1450 1458 3.561725 GCCGGAAAGGAAGAATCATAGTG 59.438 47.826 5.05 0.00 45.00 2.74
1453 1461 3.561725 GGAAAGGAAGAATCATAGTGGCG 59.438 47.826 0.00 0.00 0.00 5.69
1504 1512 7.742556 TGTGGCAATCGATTTCATGATATTA 57.257 32.000 8.21 0.00 0.00 0.98
1559 1567 1.081892 CGACTTCCATGTTGCTGGAG 58.918 55.000 0.00 0.00 45.80 3.86
1615 1623 1.300080 CAGCCTGTTGGTTTTGCCG 60.300 57.895 0.00 0.00 41.21 5.69
1675 1683 0.036010 CTGTTGGAGGAATCGTGGCT 60.036 55.000 0.00 0.00 0.00 4.75
1678 1686 0.984230 TTGGAGGAATCGTGGCTTCT 59.016 50.000 0.00 0.00 0.00 2.85
1682 1690 0.108615 AGGAATCGTGGCTTCTGTCG 60.109 55.000 0.00 0.00 0.00 4.35
1744 1752 1.070289 GTTGGTTTCCACGAGAGAGGT 59.930 52.381 0.00 0.00 42.91 3.85
1904 1912 4.517453 CCCTTTCACCGATCTTTTGTGTTA 59.483 41.667 0.00 0.00 0.00 2.41
1951 1959 4.414999 CTGTGTAGCACGTCAGTACTTA 57.585 45.455 0.00 0.00 37.14 2.24
1976 1984 1.231221 TGGAAACCACAAACGATCCG 58.769 50.000 0.00 0.00 0.00 4.18
1980 1988 0.034896 AACCACAAACGATCCGAGCT 59.965 50.000 0.00 0.00 0.00 4.09
2018 2026 5.719173 TGGTTAAATCTTGCTTTACATGCC 58.281 37.500 0.00 0.00 0.00 4.40
2021 2029 1.392589 ATCTTGCTTTACATGCCCCG 58.607 50.000 0.00 0.00 0.00 5.73
2125 2136 6.464322 GGAATCCTGTCAAAACTTTCCCATTT 60.464 38.462 0.00 0.00 0.00 2.32
2135 2146 8.210265 TCAAAACTTTCCCATTTCATAAAGCTT 58.790 29.630 0.00 0.00 33.25 3.74
2145 2156 7.412853 CCATTTCATAAAGCTTGCAGTACTAG 58.587 38.462 0.00 0.00 0.00 2.57
2178 2189 1.909986 GTGCTTAACCCCTCTTCTCCT 59.090 52.381 0.00 0.00 0.00 3.69
2184 2195 2.861147 ACCCCTCTTCTCCTTTTTCG 57.139 50.000 0.00 0.00 0.00 3.46
2198 2210 5.067273 TCCTTTTTCGAATTTCAGGTGCTA 58.933 37.500 0.00 0.00 0.00 3.49
2369 2381 1.890041 CCCGTTCACCAAGTTCGCA 60.890 57.895 0.00 0.00 0.00 5.10
2642 2654 2.819154 TGCGTGGGCATCATCGTG 60.819 61.111 0.00 0.00 46.21 4.35
2705 2717 3.708121 TGAAGCAGATCATCCAGAGCTTA 59.292 43.478 0.00 0.00 40.91 3.09
2713 2725 6.711194 CAGATCATCCAGAGCTTATGAAATGT 59.289 38.462 0.00 0.00 40.91 2.71
2718 2730 7.876582 TCATCCAGAGCTTATGAAATGTATGAG 59.123 37.037 1.64 0.00 0.00 2.90
2719 2731 7.129457 TCCAGAGCTTATGAAATGTATGAGT 57.871 36.000 1.64 0.00 0.00 3.41
2737 2758 5.614324 TGAGTAGGGATGAACAACCATAG 57.386 43.478 3.73 0.00 0.00 2.23
2804 2825 5.577100 TGTAGTCTGTACCTATGTTCTGGT 58.423 41.667 0.00 0.00 40.12 4.00
2807 2828 6.527057 AGTCTGTACCTATGTTCTGGTAAC 57.473 41.667 0.00 0.00 40.09 2.50
2986 3084 6.749118 GTGGTTGTTTCTTGCTAATGATGATC 59.251 38.462 0.00 0.00 0.00 2.92
3041 3142 4.873817 CAAAATCTGCTGTTCCAACATCA 58.126 39.130 0.00 0.00 38.41 3.07
3050 3151 5.638657 TGCTGTTCCAACATCATTTTTATGC 59.361 36.000 0.00 0.00 38.41 3.14
3084 3185 1.734465 CTGTGAATTCTTCGCACCTCC 59.266 52.381 7.05 0.00 44.54 4.30
3106 3207 4.353437 ACCCAGACCGCGACGAAC 62.353 66.667 8.23 0.00 0.00 3.95
3141 3250 2.616960 GCATTCAGGTATGTCGACACA 58.383 47.619 22.71 6.35 36.78 3.72
3142 3251 2.604914 GCATTCAGGTATGTCGACACAG 59.395 50.000 22.71 9.16 35.41 3.66
3144 3253 2.209690 TCAGGTATGTCGACACAGGA 57.790 50.000 22.71 11.42 35.41 3.86
3145 3254 1.816835 TCAGGTATGTCGACACAGGAC 59.183 52.381 22.71 15.71 35.41 3.85
3147 3256 1.544691 AGGTATGTCGACACAGGACAC 59.455 52.381 22.71 11.38 46.22 3.67
3148 3257 1.271379 GGTATGTCGACACAGGACACA 59.729 52.381 22.71 0.00 46.22 3.72
3149 3258 2.094182 GGTATGTCGACACAGGACACAT 60.094 50.000 22.71 3.87 46.22 3.21
3156 3272 2.413837 GACACAGGACACATACACACC 58.586 52.381 0.00 0.00 0.00 4.16
3157 3273 2.037251 GACACAGGACACATACACACCT 59.963 50.000 0.00 0.00 0.00 4.00
3175 3291 2.893489 ACCTTGAAGTTGAAATGAGCCC 59.107 45.455 0.00 0.00 0.00 5.19
3176 3292 2.892852 CCTTGAAGTTGAAATGAGCCCA 59.107 45.455 0.00 0.00 0.00 5.36
3180 3296 1.188863 AGTTGAAATGAGCCCATGCC 58.811 50.000 0.00 0.00 38.69 4.40
3230 3365 6.431852 TCTGCCCATATGTTGATGTATTGATG 59.568 38.462 1.24 0.00 0.00 3.07
3267 3403 9.396022 CAATACATGAATACCCAAAGAAGTACT 57.604 33.333 0.00 0.00 0.00 2.73
3268 3404 9.614792 AATACATGAATACCCAAAGAAGTACTC 57.385 33.333 0.00 0.00 0.00 2.59
3269 3405 6.415573 ACATGAATACCCAAAGAAGTACTCC 58.584 40.000 0.00 0.00 0.00 3.85
3270 3406 5.431179 TGAATACCCAAAGAAGTACTCCC 57.569 43.478 0.00 0.00 0.00 4.30
3271 3407 5.098663 TGAATACCCAAAGAAGTACTCCCT 58.901 41.667 0.00 0.00 0.00 4.20
3272 3408 5.550403 TGAATACCCAAAGAAGTACTCCCTT 59.450 40.000 0.00 0.00 0.00 3.95
3273 3409 3.790089 ACCCAAAGAAGTACTCCCTTG 57.210 47.619 10.19 7.30 0.00 3.61
3274 3410 2.375509 ACCCAAAGAAGTACTCCCTTGG 59.624 50.000 17.14 17.14 37.31 3.61
3275 3411 2.375509 CCCAAAGAAGTACTCCCTTGGT 59.624 50.000 20.20 3.89 36.45 3.67
3276 3412 3.559384 CCCAAAGAAGTACTCCCTTGGTC 60.559 52.174 20.20 5.14 36.45 4.02
3277 3413 3.559384 CCAAAGAAGTACTCCCTTGGTCC 60.559 52.174 16.34 0.00 34.72 4.46
3278 3414 2.715763 AGAAGTACTCCCTTGGTCCA 57.284 50.000 0.00 0.00 0.00 4.02
3279 3415 2.541466 AGAAGTACTCCCTTGGTCCAG 58.459 52.381 0.00 0.00 0.00 3.86
3280 3416 2.111972 AGAAGTACTCCCTTGGTCCAGA 59.888 50.000 0.00 0.00 0.00 3.86
3281 3417 2.715763 AGTACTCCCTTGGTCCAGAA 57.284 50.000 0.00 0.00 0.00 3.02
3282 3418 2.986050 AGTACTCCCTTGGTCCAGAAA 58.014 47.619 0.00 0.00 0.00 2.52
3283 3419 3.532102 AGTACTCCCTTGGTCCAGAAAT 58.468 45.455 0.00 0.00 0.00 2.17
3284 3420 4.695606 AGTACTCCCTTGGTCCAGAAATA 58.304 43.478 0.00 0.00 0.00 1.40
3285 3421 4.470304 AGTACTCCCTTGGTCCAGAAATAC 59.530 45.833 0.00 0.00 0.00 1.89
3286 3422 3.532102 ACTCCCTTGGTCCAGAAATACT 58.468 45.455 0.00 0.00 0.00 2.12
3287 3423 3.916989 ACTCCCTTGGTCCAGAAATACTT 59.083 43.478 0.00 0.00 0.00 2.24
3288 3424 4.263506 ACTCCCTTGGTCCAGAAATACTTG 60.264 45.833 0.00 0.00 0.00 3.16
3289 3425 3.655777 TCCCTTGGTCCAGAAATACTTGT 59.344 43.478 0.00 0.00 0.00 3.16
3290 3426 4.010349 CCCTTGGTCCAGAAATACTTGTC 58.990 47.826 0.00 0.00 0.00 3.18
3291 3427 3.684788 CCTTGGTCCAGAAATACTTGTCG 59.315 47.826 0.00 0.00 0.00 4.35
3292 3428 3.328382 TGGTCCAGAAATACTTGTCGG 57.672 47.619 0.00 0.00 0.00 4.79
3293 3429 2.027561 TGGTCCAGAAATACTTGTCGGG 60.028 50.000 0.00 0.00 0.00 5.14
3294 3430 2.629051 GTCCAGAAATACTTGTCGGGG 58.371 52.381 0.00 0.00 30.83 5.73
3295 3431 1.557832 TCCAGAAATACTTGTCGGGGG 59.442 52.381 0.00 0.00 30.83 5.40
3296 3432 1.557832 CCAGAAATACTTGTCGGGGGA 59.442 52.381 0.00 0.00 0.00 4.81
3297 3433 2.026636 CCAGAAATACTTGTCGGGGGAA 60.027 50.000 0.00 0.00 0.00 3.97
3298 3434 3.371595 CCAGAAATACTTGTCGGGGGAAT 60.372 47.826 0.00 0.00 0.00 3.01
3299 3435 3.627577 CAGAAATACTTGTCGGGGGAATG 59.372 47.826 0.00 0.00 0.00 2.67
3300 3436 2.729028 AATACTTGTCGGGGGAATGG 57.271 50.000 0.00 0.00 0.00 3.16
3301 3437 1.887797 ATACTTGTCGGGGGAATGGA 58.112 50.000 0.00 0.00 0.00 3.41
3302 3438 1.887797 TACTTGTCGGGGGAATGGAT 58.112 50.000 0.00 0.00 0.00 3.41
3303 3439 0.255890 ACTTGTCGGGGGAATGGATG 59.744 55.000 0.00 0.00 0.00 3.51
3304 3440 0.255890 CTTGTCGGGGGAATGGATGT 59.744 55.000 0.00 0.00 0.00 3.06
3305 3441 1.488812 CTTGTCGGGGGAATGGATGTA 59.511 52.381 0.00 0.00 0.00 2.29
3306 3442 1.814429 TGTCGGGGGAATGGATGTAT 58.186 50.000 0.00 0.00 0.00 2.29
3307 3443 2.131854 TGTCGGGGGAATGGATGTATT 58.868 47.619 0.00 0.00 0.00 1.89
3308 3444 2.512056 TGTCGGGGGAATGGATGTATTT 59.488 45.455 0.00 0.00 0.00 1.40
3309 3445 3.053245 TGTCGGGGGAATGGATGTATTTT 60.053 43.478 0.00 0.00 0.00 1.82
3310 3446 4.166337 TGTCGGGGGAATGGATGTATTTTA 59.834 41.667 0.00 0.00 0.00 1.52
3311 3447 5.134661 GTCGGGGGAATGGATGTATTTTAA 58.865 41.667 0.00 0.00 0.00 1.52
3312 3448 5.773176 GTCGGGGGAATGGATGTATTTTAAT 59.227 40.000 0.00 0.00 0.00 1.40
3313 3449 6.266786 GTCGGGGGAATGGATGTATTTTAATT 59.733 38.462 0.00 0.00 0.00 1.40
3314 3450 6.492087 TCGGGGGAATGGATGTATTTTAATTC 59.508 38.462 0.00 0.00 0.00 2.17
3315 3451 6.493458 CGGGGGAATGGATGTATTTTAATTCT 59.507 38.462 0.00 0.00 0.00 2.40
3316 3452 7.668052 CGGGGGAATGGATGTATTTTAATTCTA 59.332 37.037 0.00 0.00 0.00 2.10
3317 3453 9.025041 GGGGGAATGGATGTATTTTAATTCTAG 57.975 37.037 0.00 0.00 0.00 2.43
3318 3454 9.807921 GGGGAATGGATGTATTTTAATTCTAGA 57.192 33.333 0.00 0.00 0.00 2.43
3344 3480 7.042797 ACATCCATTTTTATCCATTTCTCCG 57.957 36.000 0.00 0.00 0.00 4.63
3345 3481 6.833416 ACATCCATTTTTATCCATTTCTCCGA 59.167 34.615 0.00 0.00 0.00 4.55
3346 3482 6.693315 TCCATTTTTATCCATTTCTCCGAC 57.307 37.500 0.00 0.00 0.00 4.79
3347 3483 6.184068 TCCATTTTTATCCATTTCTCCGACA 58.816 36.000 0.00 0.00 0.00 4.35
3348 3484 6.661377 TCCATTTTTATCCATTTCTCCGACAA 59.339 34.615 0.00 0.00 0.00 3.18
3349 3485 7.177568 TCCATTTTTATCCATTTCTCCGACAAA 59.822 33.333 0.00 0.00 0.00 2.83
3350 3486 7.981225 CCATTTTTATCCATTTCTCCGACAAAT 59.019 33.333 0.00 0.00 0.00 2.32
3356 3492 9.627123 TTATCCATTTCTCCGACAAATATTTCT 57.373 29.630 0.00 0.00 0.00 2.52
3357 3493 7.320443 TCCATTTCTCCGACAAATATTTCTG 57.680 36.000 0.00 0.00 0.00 3.02
3358 3494 6.318648 TCCATTTCTCCGACAAATATTTCTGG 59.681 38.462 0.00 0.92 0.00 3.86
3359 3495 6.318648 CCATTTCTCCGACAAATATTTCTGGA 59.681 38.462 0.00 5.24 0.00 3.86
3360 3496 6.737254 TTTCTCCGACAAATATTTCTGGAC 57.263 37.500 0.00 0.00 0.00 4.02
3361 3497 4.430007 TCTCCGACAAATATTTCTGGACG 58.570 43.478 0.00 0.35 0.00 4.79
3362 3498 3.527533 TCCGACAAATATTTCTGGACGG 58.472 45.455 16.31 16.31 37.69 4.79
3363 3499 3.196039 TCCGACAAATATTTCTGGACGGA 59.804 43.478 19.16 19.16 40.51 4.69
3364 3500 3.555956 CCGACAAATATTTCTGGACGGAG 59.444 47.826 17.03 0.14 38.18 4.63
3385 3521 8.242053 ACGGAGTGATATACAATATTAACGAGG 58.758 37.037 0.00 0.00 42.51 4.63
3395 3531 7.596749 ACAATATTAACGAGGAACAGAGTTG 57.403 36.000 0.00 0.00 0.00 3.16
3416 3559 2.291741 GCAATCTGCAGGCATAAGGTAC 59.708 50.000 15.13 0.00 44.26 3.34
3425 3568 0.804544 GCATAAGGTACGCGACAGCA 60.805 55.000 15.93 0.00 45.49 4.41
3470 3613 4.020128 AGGAGGGTCTTGAGATGTTTGTAC 60.020 45.833 0.00 0.00 0.00 2.90
3477 3620 6.128526 GGTCTTGAGATGTTTGTACTGTTAGC 60.129 42.308 0.00 0.00 0.00 3.09
3480 3623 6.096673 TGAGATGTTTGTACTGTTAGCAGA 57.903 37.500 14.09 0.00 45.28 4.26
3489 3632 2.084546 ACTGTTAGCAGATTTTCGCCC 58.915 47.619 14.09 0.00 45.28 6.13
3522 3665 0.390340 TCGAGCTTGAGCATCCACAC 60.390 55.000 0.00 0.00 45.16 3.82
3525 3668 1.672356 GCTTGAGCATCCACACCGT 60.672 57.895 0.00 0.00 41.59 4.83
3542 3685 1.812571 CCGTGTTTCCTGCTAATGCTT 59.187 47.619 0.00 0.00 40.48 3.91
3548 3691 4.216257 TGTTTCCTGCTAATGCTTCAACTC 59.784 41.667 0.00 0.00 40.48 3.01
3553 3696 2.002586 GCTAATGCTTCAACTCGCTCA 58.997 47.619 0.00 0.00 36.03 4.26
3556 3699 2.687700 ATGCTTCAACTCGCTCATCT 57.312 45.000 0.00 0.00 0.00 2.90
3566 3709 1.884926 CGCTCATCTCTTTCCCGCC 60.885 63.158 0.00 0.00 0.00 6.13
3586 3729 4.452825 GCCCCCTTATCTCTGTTAGTTTC 58.547 47.826 0.00 0.00 0.00 2.78
3591 3734 7.168905 CCCCTTATCTCTGTTAGTTTCAGTTT 58.831 38.462 0.00 0.00 34.86 2.66
3615 3758 5.105716 TCCTTGCTGTGTCTGAACTACTATC 60.106 44.000 0.00 0.00 0.00 2.08
3652 3798 5.067283 CCGTTAAGTGATTAATGGAAAGGGG 59.933 44.000 11.83 0.00 43.13 4.79
3668 3814 2.836154 GGTGTGAGCCCAGTTGGA 59.164 61.111 0.00 0.00 37.39 3.53
3669 3815 1.600916 GGTGTGAGCCCAGTTGGAC 60.601 63.158 0.00 0.00 37.39 4.02
3674 3820 1.067060 GTGAGCCCAGTTGGACAAAAC 59.933 52.381 0.00 0.00 37.39 2.43
3677 3823 1.756538 AGCCCAGTTGGACAAAACAAG 59.243 47.619 0.00 0.00 37.39 3.16
3680 3826 1.202521 CCAGTTGGACAAAACAAGGGC 60.203 52.381 0.00 0.00 37.39 5.19
3684 3830 2.338620 GACAAAACAAGGGCCCGC 59.661 61.111 18.44 0.00 0.00 6.13
3704 3850 3.617368 GGAGCTCCGTTCTAGCCA 58.383 61.111 19.06 0.00 41.02 4.75
3705 3851 1.142097 GGAGCTCCGTTCTAGCCAC 59.858 63.158 19.06 0.00 41.02 5.01
3706 3852 1.226717 GAGCTCCGTTCTAGCCACG 60.227 63.158 0.87 7.19 41.02 4.94
3708 3854 1.080025 GCTCCGTTCTAGCCACGTT 60.080 57.895 11.83 0.00 35.81 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 151 6.060136 AGAGGGAAACTGTAACCTAACAAAC 58.940 40.000 0.00 0.00 32.42 2.93
296 298 9.382244 GAGTGAATAAACACACTAAAACATGTC 57.618 33.333 0.00 0.00 42.45 3.06
298 300 9.897744 ATGAGTGAATAAACACACTAAAACATG 57.102 29.630 0.00 0.00 42.45 3.21
518 522 6.778834 AGGTAGGCTAGTACTTTCTTCTTC 57.221 41.667 0.00 0.00 0.00 2.87
827 834 2.717639 AAAGCACTGAGTGGAGTTGT 57.282 45.000 15.24 0.00 33.64 3.32
836 843 5.978934 AAAAATGCAAGAAAAGCACTGAG 57.021 34.783 0.00 0.00 45.95 3.35
927 935 0.037303 AGACAAGGGTGGTGCATGAG 59.963 55.000 0.00 0.00 0.00 2.90
977 985 3.498397 CACAAACTAGTAGTGCTGTTGGG 59.502 47.826 13.47 7.65 0.00 4.12
1102 1110 0.250234 CTCCAATCTCACGCTTGGGA 59.750 55.000 0.00 0.00 41.85 4.37
1104 1112 2.099141 TTCTCCAATCTCACGCTTGG 57.901 50.000 0.00 0.00 42.72 3.61
1110 1118 8.789825 ATATAGCATGATTTCTCCAATCTCAC 57.210 34.615 0.00 0.00 41.91 3.51
1170 1178 5.307196 AGGAGTAAGTTAGCAAGGTTCAAGA 59.693 40.000 0.00 0.00 0.00 3.02
1171 1179 5.409826 CAGGAGTAAGTTAGCAAGGTTCAAG 59.590 44.000 0.00 0.00 0.00 3.02
1172 1180 5.163237 ACAGGAGTAAGTTAGCAAGGTTCAA 60.163 40.000 0.00 0.00 0.00 2.69
1173 1181 4.347000 ACAGGAGTAAGTTAGCAAGGTTCA 59.653 41.667 0.00 0.00 0.00 3.18
1174 1182 4.691216 CACAGGAGTAAGTTAGCAAGGTTC 59.309 45.833 0.00 0.00 0.00 3.62
1175 1183 4.642429 CACAGGAGTAAGTTAGCAAGGTT 58.358 43.478 0.00 0.00 0.00 3.50
1176 1184 3.557264 GCACAGGAGTAAGTTAGCAAGGT 60.557 47.826 0.00 0.00 0.00 3.50
1177 1185 3.003480 GCACAGGAGTAAGTTAGCAAGG 58.997 50.000 0.00 0.00 0.00 3.61
1178 1186 3.003480 GGCACAGGAGTAAGTTAGCAAG 58.997 50.000 0.00 0.00 0.00 4.01
1179 1187 2.611971 CGGCACAGGAGTAAGTTAGCAA 60.612 50.000 0.00 0.00 0.00 3.91
1180 1188 1.067142 CGGCACAGGAGTAAGTTAGCA 60.067 52.381 0.00 0.00 0.00 3.49
1181 1189 1.641577 CGGCACAGGAGTAAGTTAGC 58.358 55.000 0.00 0.00 0.00 3.09
1182 1190 1.641577 GCGGCACAGGAGTAAGTTAG 58.358 55.000 0.00 0.00 0.00 2.34
1183 1191 0.248289 GGCGGCACAGGAGTAAGTTA 59.752 55.000 3.07 0.00 0.00 2.24
1184 1192 1.003718 GGCGGCACAGGAGTAAGTT 60.004 57.895 3.07 0.00 0.00 2.66
1185 1193 1.889530 GAGGCGGCACAGGAGTAAGT 61.890 60.000 13.08 0.00 0.00 2.24
1186 1194 1.153549 GAGGCGGCACAGGAGTAAG 60.154 63.158 13.08 0.00 0.00 2.34
1187 1195 1.264749 ATGAGGCGGCACAGGAGTAA 61.265 55.000 15.18 0.00 0.00 2.24
1188 1196 0.396556 TATGAGGCGGCACAGGAGTA 60.397 55.000 15.18 0.00 0.00 2.59
1189 1197 1.050988 ATATGAGGCGGCACAGGAGT 61.051 55.000 15.18 0.32 0.00 3.85
1190 1198 0.602106 CATATGAGGCGGCACAGGAG 60.602 60.000 15.18 3.10 0.00 3.69
1191 1199 1.337384 ACATATGAGGCGGCACAGGA 61.337 55.000 15.18 5.79 0.00 3.86
1192 1200 0.882042 GACATATGAGGCGGCACAGG 60.882 60.000 15.18 9.22 0.00 4.00
1193 1201 0.882042 GGACATATGAGGCGGCACAG 60.882 60.000 15.18 4.02 0.00 3.66
1194 1202 1.146041 GGACATATGAGGCGGCACA 59.854 57.895 12.13 12.13 0.00 4.57
1195 1203 0.601311 GAGGACATATGAGGCGGCAC 60.601 60.000 13.08 5.35 0.00 5.01
1199 1207 4.058817 GGTTAAAGAGGACATATGAGGCG 58.941 47.826 10.38 0.00 0.00 5.52
1245 1253 2.230130 TCCAACCCCTGCAAAATAGG 57.770 50.000 0.00 0.00 35.01 2.57
1450 1458 3.589988 CTCCAGGTACATGAATATCGCC 58.410 50.000 9.54 0.00 0.00 5.54
1453 1461 5.220710 ACAGCTCCAGGTACATGAATATC 57.779 43.478 9.54 0.00 0.00 1.63
1504 1512 9.981460 AATAATTTCTCCAAGTTATCACCTTCT 57.019 29.630 0.00 0.00 0.00 2.85
1559 1567 1.538047 TGCTTGCCTCCAATCTTGAC 58.462 50.000 0.00 0.00 0.00 3.18
1615 1623 0.389948 AGCTCCGAAACCATGTCGTC 60.390 55.000 3.85 0.00 36.77 4.20
1675 1683 0.456142 CCGCGATGAGAACGACAGAA 60.456 55.000 8.23 0.00 0.00 3.02
1678 1686 2.506217 GCCGCGATGAGAACGACA 60.506 61.111 8.23 0.00 0.00 4.35
1682 1690 1.523095 GATAACAGCCGCGATGAGAAC 59.477 52.381 8.23 0.00 0.00 3.01
1744 1752 2.203337 GCCCAGTGGACAAGCACA 60.203 61.111 11.95 0.00 0.00 4.57
1904 1912 9.533253 GCAGTTATATTTGCTTATTGGTCAAAT 57.467 29.630 0.00 0.00 41.56 2.32
1936 1944 4.451096 CCAACAAATAAGTACTGACGTGCT 59.549 41.667 0.00 0.00 37.73 4.40
1943 1951 7.033530 TGTGGTTTCCAACAAATAAGTACTG 57.966 36.000 0.00 0.00 34.18 2.74
1951 1959 4.457834 TCGTTTGTGGTTTCCAACAAAT 57.542 36.364 14.36 0.00 37.12 2.32
1969 1977 4.162690 GGGGCAAGCTCGGATCGT 62.163 66.667 0.00 0.00 0.00 3.73
1976 1984 2.887152 CCATAATAGTTGGGGCAAGCTC 59.113 50.000 0.00 0.00 0.00 4.09
1980 1988 7.129425 AGATTTAACCATAATAGTTGGGGCAA 58.871 34.615 0.00 0.00 38.64 4.52
2018 2026 7.352739 GTTATACTATTTTGCATTGACTCGGG 58.647 38.462 0.00 0.00 0.00 5.14
2125 2136 4.714802 TCCCTAGTACTGCAAGCTTTATGA 59.285 41.667 5.39 0.00 37.60 2.15
2135 2146 2.453521 ACGTGATTCCCTAGTACTGCA 58.546 47.619 5.39 0.00 0.00 4.41
2145 2156 3.561503 GTTAAGCACAAACGTGATTCCC 58.438 45.455 0.00 0.00 41.85 3.97
2178 2189 5.048991 GGAGTAGCACCTGAAATTCGAAAAA 60.049 40.000 0.00 0.00 0.00 1.94
2184 2195 4.187694 CAGAGGAGTAGCACCTGAAATTC 58.812 47.826 0.00 0.00 37.93 2.17
2198 2210 2.158928 GCAGATGATGAAGCAGAGGAGT 60.159 50.000 0.00 0.00 0.00 3.85
2267 2279 0.610687 CCTGGGACTTCAGTGACTCC 59.389 60.000 7.32 7.32 33.14 3.85
2642 2654 3.007323 ACAAGCCCTACCCCGACC 61.007 66.667 0.00 0.00 0.00 4.79
2705 2717 7.805163 TGTTCATCCCTACTCATACATTTCAT 58.195 34.615 0.00 0.00 0.00 2.57
2713 2725 6.270000 CCTATGGTTGTTCATCCCTACTCATA 59.730 42.308 0.00 0.00 0.00 2.15
2718 2730 3.118038 TGCCTATGGTTGTTCATCCCTAC 60.118 47.826 0.00 0.00 0.00 3.18
2719 2731 3.119319 TGCCTATGGTTGTTCATCCCTA 58.881 45.455 0.00 0.00 0.00 3.53
2886 2910 3.845781 ACAGGCAGTTTCTTCTGAAGA 57.154 42.857 15.82 15.82 37.61 2.87
2986 3084 2.110901 AGGCTGAAACTCTGCTGATG 57.889 50.000 5.65 0.00 40.57 3.07
3084 3185 4.680237 TCGCGGTCTGGGTGCTTG 62.680 66.667 6.13 0.00 0.00 4.01
3106 3207 2.358582 TGAATGCGCACCAATATCCTTG 59.641 45.455 14.90 0.00 0.00 3.61
3141 3250 3.391296 ACTTCAAGGTGTGTATGTGTCCT 59.609 43.478 0.00 0.00 0.00 3.85
3142 3251 3.740115 ACTTCAAGGTGTGTATGTGTCC 58.260 45.455 0.00 0.00 0.00 4.02
3144 3253 4.776349 TCAACTTCAAGGTGTGTATGTGT 58.224 39.130 1.39 0.00 33.77 3.72
3145 3254 5.749596 TTCAACTTCAAGGTGTGTATGTG 57.250 39.130 1.39 0.00 33.77 3.21
3146 3255 6.545666 TCATTTCAACTTCAAGGTGTGTATGT 59.454 34.615 1.39 0.00 33.77 2.29
3147 3256 6.969366 TCATTTCAACTTCAAGGTGTGTATG 58.031 36.000 1.39 5.28 33.77 2.39
3148 3257 6.294176 GCTCATTTCAACTTCAAGGTGTGTAT 60.294 38.462 1.39 0.00 33.77 2.29
3149 3258 5.008613 GCTCATTTCAACTTCAAGGTGTGTA 59.991 40.000 1.39 0.00 33.77 2.90
3156 3272 4.491676 CATGGGCTCATTTCAACTTCAAG 58.508 43.478 0.00 0.00 0.00 3.02
3157 3273 3.306225 GCATGGGCTCATTTCAACTTCAA 60.306 43.478 0.00 0.00 36.96 2.69
3180 3296 2.178912 TAACTTCAGGAAAGCCACGG 57.821 50.000 0.00 0.00 38.67 4.94
3230 3365 6.649557 GGTATTCATGTATTGGTAGGCAGTAC 59.350 42.308 0.00 0.00 0.00 2.73
3267 3403 3.655777 ACAAGTATTTCTGGACCAAGGGA 59.344 43.478 0.00 0.00 0.00 4.20
3268 3404 4.010349 GACAAGTATTTCTGGACCAAGGG 58.990 47.826 0.00 0.00 0.00 3.95
3269 3405 3.684788 CGACAAGTATTTCTGGACCAAGG 59.315 47.826 0.00 0.00 0.00 3.61
3270 3406 3.684788 CCGACAAGTATTTCTGGACCAAG 59.315 47.826 0.00 0.00 0.00 3.61
3271 3407 3.558321 CCCGACAAGTATTTCTGGACCAA 60.558 47.826 0.00 0.00 0.00 3.67
3272 3408 2.027561 CCCGACAAGTATTTCTGGACCA 60.028 50.000 0.00 0.00 0.00 4.02
3273 3409 2.629051 CCCGACAAGTATTTCTGGACC 58.371 52.381 0.00 0.00 0.00 4.46
3274 3410 2.629051 CCCCGACAAGTATTTCTGGAC 58.371 52.381 0.00 0.00 0.00 4.02
3275 3411 1.557832 CCCCCGACAAGTATTTCTGGA 59.442 52.381 0.00 0.00 0.00 3.86
3276 3412 1.557832 TCCCCCGACAAGTATTTCTGG 59.442 52.381 0.00 0.00 0.00 3.86
3277 3413 3.343941 TTCCCCCGACAAGTATTTCTG 57.656 47.619 0.00 0.00 0.00 3.02
3278 3414 3.371595 CCATTCCCCCGACAAGTATTTCT 60.372 47.826 0.00 0.00 0.00 2.52
3279 3415 2.949644 CCATTCCCCCGACAAGTATTTC 59.050 50.000 0.00 0.00 0.00 2.17
3280 3416 2.578940 TCCATTCCCCCGACAAGTATTT 59.421 45.455 0.00 0.00 0.00 1.40
3281 3417 2.201830 TCCATTCCCCCGACAAGTATT 58.798 47.619 0.00 0.00 0.00 1.89
3282 3418 1.887797 TCCATTCCCCCGACAAGTAT 58.112 50.000 0.00 0.00 0.00 2.12
3283 3419 1.488812 CATCCATTCCCCCGACAAGTA 59.511 52.381 0.00 0.00 0.00 2.24
3284 3420 0.255890 CATCCATTCCCCCGACAAGT 59.744 55.000 0.00 0.00 0.00 3.16
3285 3421 0.255890 ACATCCATTCCCCCGACAAG 59.744 55.000 0.00 0.00 0.00 3.16
3286 3422 1.585895 TACATCCATTCCCCCGACAA 58.414 50.000 0.00 0.00 0.00 3.18
3287 3423 1.814429 ATACATCCATTCCCCCGACA 58.186 50.000 0.00 0.00 0.00 4.35
3288 3424 2.951229 AATACATCCATTCCCCCGAC 57.049 50.000 0.00 0.00 0.00 4.79
3289 3425 3.963476 AAAATACATCCATTCCCCCGA 57.037 42.857 0.00 0.00 0.00 5.14
3290 3426 6.493458 AGAATTAAAATACATCCATTCCCCCG 59.507 38.462 0.00 0.00 0.00 5.73
3291 3427 7.855784 AGAATTAAAATACATCCATTCCCCC 57.144 36.000 0.00 0.00 0.00 5.40
3292 3428 9.807921 TCTAGAATTAAAATACATCCATTCCCC 57.192 33.333 0.00 0.00 0.00 4.81
3318 3454 8.796475 CGGAGAAATGGATAAAAATGGATGTAT 58.204 33.333 0.00 0.00 0.00 2.29
3319 3455 7.996066 TCGGAGAAATGGATAAAAATGGATGTA 59.004 33.333 0.00 0.00 0.00 2.29
3320 3456 6.833416 TCGGAGAAATGGATAAAAATGGATGT 59.167 34.615 0.00 0.00 0.00 3.06
3321 3457 7.141363 GTCGGAGAAATGGATAAAAATGGATG 58.859 38.462 0.00 0.00 39.69 3.51
3322 3458 6.833416 TGTCGGAGAAATGGATAAAAATGGAT 59.167 34.615 0.00 0.00 39.69 3.41
3323 3459 6.184068 TGTCGGAGAAATGGATAAAAATGGA 58.816 36.000 0.00 0.00 39.69 3.41
3324 3460 6.449635 TGTCGGAGAAATGGATAAAAATGG 57.550 37.500 0.00 0.00 39.69 3.16
3325 3461 8.931385 ATTTGTCGGAGAAATGGATAAAAATG 57.069 30.769 11.81 0.00 39.69 2.32
3330 3466 9.627123 AGAAATATTTGTCGGAGAAATGGATAA 57.373 29.630 19.84 3.51 39.69 1.75
3331 3467 9.056005 CAGAAATATTTGTCGGAGAAATGGATA 57.944 33.333 19.84 3.83 39.69 2.59
3332 3468 7.013655 CCAGAAATATTTGTCGGAGAAATGGAT 59.986 37.037 19.84 6.69 39.69 3.41
3333 3469 6.318648 CCAGAAATATTTGTCGGAGAAATGGA 59.681 38.462 19.84 4.79 39.69 3.41
3334 3470 6.318648 TCCAGAAATATTTGTCGGAGAAATGG 59.681 38.462 19.84 13.93 39.69 3.16
3335 3471 7.189512 GTCCAGAAATATTTGTCGGAGAAATG 58.810 38.462 19.84 6.54 39.69 2.32
3336 3472 6.037172 CGTCCAGAAATATTTGTCGGAGAAAT 59.963 38.462 16.10 16.10 39.69 2.17
3337 3473 5.350365 CGTCCAGAAATATTTGTCGGAGAAA 59.650 40.000 5.17 2.59 39.69 2.52
3338 3474 4.868171 CGTCCAGAAATATTTGTCGGAGAA 59.132 41.667 5.17 0.00 39.69 2.87
3339 3475 4.430007 CGTCCAGAAATATTTGTCGGAGA 58.570 43.478 5.17 0.00 0.00 3.71
3340 3476 3.555956 CCGTCCAGAAATATTTGTCGGAG 59.444 47.826 15.02 9.96 38.03 4.63
3341 3477 3.196039 TCCGTCCAGAAATATTTGTCGGA 59.804 43.478 17.46 17.46 41.50 4.55
3342 3478 3.527533 TCCGTCCAGAAATATTTGTCGG 58.472 45.455 14.32 14.32 37.29 4.79
3343 3479 4.032900 CACTCCGTCCAGAAATATTTGTCG 59.967 45.833 5.17 1.89 0.00 4.35
3344 3480 5.175859 TCACTCCGTCCAGAAATATTTGTC 58.824 41.667 5.17 0.00 0.00 3.18
3345 3481 5.160607 TCACTCCGTCCAGAAATATTTGT 57.839 39.130 5.17 0.00 0.00 2.83
3346 3482 7.969536 ATATCACTCCGTCCAGAAATATTTG 57.030 36.000 5.17 0.00 0.00 2.32
3347 3483 8.647796 TGTATATCACTCCGTCCAGAAATATTT 58.352 33.333 0.00 0.00 0.00 1.40
3348 3484 8.190326 TGTATATCACTCCGTCCAGAAATATT 57.810 34.615 0.00 0.00 0.00 1.28
3349 3485 7.776618 TGTATATCACTCCGTCCAGAAATAT 57.223 36.000 0.00 0.00 0.00 1.28
3350 3486 7.591421 TTGTATATCACTCCGTCCAGAAATA 57.409 36.000 0.00 0.00 0.00 1.40
3351 3487 6.479972 TTGTATATCACTCCGTCCAGAAAT 57.520 37.500 0.00 0.00 0.00 2.17
3352 3488 5.925506 TTGTATATCACTCCGTCCAGAAA 57.074 39.130 0.00 0.00 0.00 2.52
3353 3489 7.776618 ATATTGTATATCACTCCGTCCAGAA 57.223 36.000 0.00 0.00 0.00 3.02
3354 3490 7.776618 AATATTGTATATCACTCCGTCCAGA 57.223 36.000 0.00 0.00 0.00 3.86
3355 3491 9.355215 GTTAATATTGTATATCACTCCGTCCAG 57.645 37.037 0.00 0.00 0.00 3.86
3356 3492 8.024865 CGTTAATATTGTATATCACTCCGTCCA 58.975 37.037 0.00 0.00 0.00 4.02
3357 3493 8.239314 TCGTTAATATTGTATATCACTCCGTCC 58.761 37.037 0.00 0.00 0.00 4.79
3358 3494 9.275231 CTCGTTAATATTGTATATCACTCCGTC 57.725 37.037 0.00 0.00 0.00 4.79
3359 3495 8.242053 CCTCGTTAATATTGTATATCACTCCGT 58.758 37.037 0.00 0.00 0.00 4.69
3360 3496 8.456471 TCCTCGTTAATATTGTATATCACTCCG 58.544 37.037 0.00 0.00 0.00 4.63
3369 3505 9.314321 CAACTCTGTTCCTCGTTAATATTGTAT 57.686 33.333 0.00 0.00 0.00 2.29
3370 3506 7.277098 GCAACTCTGTTCCTCGTTAATATTGTA 59.723 37.037 0.00 0.00 0.00 2.41
3395 3531 1.396653 ACCTTATGCCTGCAGATTGC 58.603 50.000 17.39 11.14 45.29 3.56
3416 3559 3.260483 GCTCCTGATGCTGTCGCG 61.260 66.667 0.00 0.00 39.65 5.87
3425 3568 0.674895 GGTTGCAAGACGCTCCTGAT 60.675 55.000 0.00 0.00 43.06 2.90
3470 3613 1.401905 GGGGCGAAAATCTGCTAACAG 59.598 52.381 0.00 0.00 45.95 3.16
3477 3620 1.674322 ACCACGGGGCGAAAATCTG 60.674 57.895 1.73 0.00 37.90 2.90
3480 3623 2.493273 ATCCACCACGGGGCGAAAAT 62.493 55.000 1.73 0.00 37.90 1.82
3522 3665 1.453155 AGCATTAGCAGGAAACACGG 58.547 50.000 0.00 0.00 45.49 4.94
3525 3668 4.144297 AGTTGAAGCATTAGCAGGAAACA 58.856 39.130 0.00 0.00 45.49 2.83
3542 3685 2.093973 GGGAAAGAGATGAGCGAGTTGA 60.094 50.000 0.00 0.00 0.00 3.18
3548 3691 1.884926 GGCGGGAAAGAGATGAGCG 60.885 63.158 0.00 0.00 0.00 5.03
3553 3696 0.327191 TAAGGGGGCGGGAAAGAGAT 60.327 55.000 0.00 0.00 0.00 2.75
3556 3699 0.327191 AGATAAGGGGGCGGGAAAGA 60.327 55.000 0.00 0.00 0.00 2.52
3566 3709 6.301169 ACTGAAACTAACAGAGATAAGGGG 57.699 41.667 0.00 0.00 38.55 4.79
3586 3729 2.564771 TCAGACACAGCAAGGAAACTG 58.435 47.619 0.00 0.00 42.68 3.16
3591 3734 2.965831 AGTAGTTCAGACACAGCAAGGA 59.034 45.455 0.00 0.00 0.00 3.36
3627 3773 5.883673 CCCTTTCCATTAATCACTTAACGGA 59.116 40.000 0.00 0.00 37.40 4.69
3630 3776 6.436218 ACACCCCTTTCCATTAATCACTTAAC 59.564 38.462 0.00 0.00 29.85 2.01
3652 3798 0.465460 TTGTCCAACTGGGCTCACAC 60.465 55.000 1.39 0.00 41.34 3.82
3662 3808 1.119684 GGCCCTTGTTTTGTCCAACT 58.880 50.000 0.00 0.00 0.00 3.16
3664 3810 1.395826 CGGGCCCTTGTTTTGTCCAA 61.396 55.000 22.43 0.00 0.00 3.53
3667 3813 2.338620 GCGGGCCCTTGTTTTGTC 59.661 61.111 22.43 0.00 0.00 3.18
3668 3814 3.601685 CGCGGGCCCTTGTTTTGT 61.602 61.111 22.43 0.00 0.00 2.83
3688 3834 1.226717 CGTGGCTAGAACGGAGCTC 60.227 63.158 4.71 4.71 39.98 4.09


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

AutoCloner maintained by Alex Coulton.