Multiple sequence alignment - TraesCS3D01G415400

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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 TraesCS3D01G415400 chr3D 100.000 2668 0 0 1 2668 527134869 527137536 0.000000e+00 4927.0
1 TraesCS3D01G415400 chr3D 84.977 639 52 29 921 1558 527126602 527127197 2.270000e-170 608.0
2 TraesCS3D01G415400 chr3D 81.679 131 23 1 3 133 582815554 582815683 1.010000e-19 108.0
3 TraesCS3D01G415400 chr3B 91.847 1521 62 19 225 1739 696789237 696787773 0.000000e+00 2065.0
4 TraesCS3D01G415400 chr3B 84.873 866 73 31 921 1756 696777964 696778801 0.000000e+00 821.0
5 TraesCS3D01G415400 chr3B 90.531 433 32 2 2155 2587 696855267 696855690 4.990000e-157 564.0
6 TraesCS3D01G415400 chr3B 87.432 366 19 10 1776 2140 696854084 696854423 1.920000e-106 396.0
7 TraesCS3D01G415400 chr3B 95.575 226 10 0 1 226 696789531 696789306 1.950000e-96 363.0
8 TraesCS3D01G415400 chr3B 93.023 86 6 0 2583 2668 696857406 696857491 2.790000e-25 126.0
9 TraesCS3D01G415400 chr3B 83.871 124 19 1 6 129 179660544 179660422 1.680000e-22 117.0
10 TraesCS3D01G415400 chr3B 83.636 110 17 1 14 123 2140978 2140870 4.700000e-18 102.0
11 TraesCS3D01G415400 chr3B 81.148 122 22 1 15 136 778471485 778471365 2.190000e-16 97.1
12 TraesCS3D01G415400 chr3A 93.280 1116 55 12 320 1425 661786548 661787653 0.000000e+00 1628.0
13 TraesCS3D01G415400 chr3A 87.340 782 66 15 921 1680 661655101 661655871 0.000000e+00 865.0
14 TraesCS3D01G415400 chr3A 86.795 621 50 20 1504 2114 661787666 661788264 0.000000e+00 664.0
15 TraesCS3D01G415400 chr3A 85.217 115 16 1 6 120 739714084 739713971 1.680000e-22 117.0
16 TraesCS3D01G415400 chr3A 100.000 30 0 0 223 252 474958180 474958151 3.710000e-04 56.5
17 TraesCS3D01G415400 chr5D 82.394 142 23 2 1 141 447136651 447136791 3.610000e-24 122.0
18 TraesCS3D01G415400 chr5D 94.286 70 4 0 141 210 537690216 537690147 1.010000e-19 108.0
19 TraesCS3D01G415400 chr6D 84.127 126 18 2 5 129 312186212 312186088 1.300000e-23 121.0
20 TraesCS3D01G415400 chr4B 93.671 79 4 1 250 327 642539836 642539758 1.680000e-22 117.0
21 TraesCS3D01G415400 chr4B 89.744 78 7 1 250 326 63991279 63991202 6.080000e-17 99.0
22 TraesCS3D01G415400 chr7A 92.208 77 5 1 252 327 30034798 30034722 1.010000e-19 108.0
23 TraesCS3D01G415400 chr5B 87.912 91 9 2 240 328 331245235 331245325 3.630000e-19 106.0
24 TraesCS3D01G415400 chr2B 85.000 100 15 0 34 133 614381570 614381669 4.700000e-18 102.0
25 TraesCS3D01G415400 chr1A 90.789 76 6 1 254 328 15317494 15317419 1.690000e-17 100.0
26 TraesCS3D01G415400 chr1A 89.024 82 8 1 252 332 462395804 462395723 1.690000e-17 100.0
27 TraesCS3D01G415400 chr1A 88.750 80 8 1 248 326 68377847 68377926 2.190000e-16 97.1
28 TraesCS3D01G415400 chr2A 89.610 77 8 0 247 323 207332046 207331970 6.080000e-17 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G415400 chr3D 527134869 527137536 2667 False 4927 4927 100.000000 1 2668 1 chr3D.!!$F2 2667
1 TraesCS3D01G415400 chr3D 527126602 527127197 595 False 608 608 84.977000 921 1558 1 chr3D.!!$F1 637
2 TraesCS3D01G415400 chr3B 696787773 696789531 1758 True 1214 2065 93.711000 1 1739 2 chr3B.!!$R4 1738
3 TraesCS3D01G415400 chr3B 696777964 696778801 837 False 821 821 84.873000 921 1756 1 chr3B.!!$F1 835
4 TraesCS3D01G415400 chr3B 696854084 696857491 3407 False 362 564 90.328667 1776 2668 3 chr3B.!!$F2 892
5 TraesCS3D01G415400 chr3A 661786548 661788264 1716 False 1146 1628 90.037500 320 2114 2 chr3A.!!$F2 1794
6 TraesCS3D01G415400 chr3A 661655101 661655871 770 False 865 865 87.340000 921 1680 1 chr3A.!!$F1 759

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
98 99 0.036294 GAGTTGGTTCCTCGGGAAGG 60.036 60.0 5.71 0.0 42.88 3.46 F
591 664 0.313043 ACCACGTCAGACAACCTACG 59.687 55.0 0.41 0.0 40.99 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1672 1.226267 CAACACAAAGCACGCACGT 60.226 52.632 0.00 0.00 0.00 4.49 R
2435 3405 0.031857 ATGCTCTTGAGCTCGATCGG 59.968 55.000 21.17 7.26 35.49 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.614057 CAGAGCAGGGCTTAAATAACCG 59.386 50.000 0.00 0.00 39.88 4.44
46 47 1.224592 CTTAGGCCATGCGAAGGGT 59.775 57.895 5.01 0.00 0.00 4.34
98 99 0.036294 GAGTTGGTTCCTCGGGAAGG 60.036 60.000 5.71 0.00 42.88 3.46
135 136 2.743928 CGGCTCCTGAGTGGTTGC 60.744 66.667 0.00 0.00 37.07 4.17
223 224 9.367444 GTGCAACCATATATGATACTTACCTAC 57.633 37.037 14.54 0.00 0.00 3.18
253 324 4.974645 ACTTGTCTTGGGATGTGTTAGA 57.025 40.909 0.00 0.00 0.00 2.10
267 338 6.546403 GGATGTGTTAGACTAGTCATAGTGGA 59.454 42.308 24.44 3.55 42.46 4.02
269 340 5.357314 TGTGTTAGACTAGTCATAGTGGAGC 59.643 44.000 24.44 6.30 42.46 4.70
274 345 5.378332 AGACTAGTCATAGTGGAGCGTAAT 58.622 41.667 24.44 0.00 42.46 1.89
315 386 8.352942 TGCATATGACACTAGTCTATGTTACTG 58.647 37.037 6.97 0.00 45.20 2.74
317 388 9.885934 CATATGACACTAGTCTATGTTACTGTC 57.114 37.037 0.00 0.00 45.20 3.51
367 438 9.890629 AGATAATTGCTATCTTGTTACACAGAA 57.109 29.630 0.00 0.00 43.68 3.02
372 443 8.445275 TTGCTATCTTGTTACACAGAAGAAAA 57.555 30.769 0.00 0.00 0.00 2.29
375 446 9.334693 GCTATCTTGTTACACAGAAGAAAATTG 57.665 33.333 0.00 0.00 0.00 2.32
517 590 2.042464 TCTATGGCATGACCTCACCTC 58.958 52.381 10.98 0.00 40.22 3.85
560 633 2.668144 TTGGTTCTTTCCGGGACAAT 57.332 45.000 0.00 0.00 0.00 2.71
561 634 3.791953 TTGGTTCTTTCCGGGACAATA 57.208 42.857 0.00 0.00 0.00 1.90
562 635 3.791953 TGGTTCTTTCCGGGACAATAA 57.208 42.857 0.00 0.00 0.00 1.40
588 661 1.046472 TCCACCACGTCAGACAACCT 61.046 55.000 0.41 0.00 0.00 3.50
589 662 0.677288 CCACCACGTCAGACAACCTA 59.323 55.000 0.41 0.00 0.00 3.08
590 663 1.604693 CCACCACGTCAGACAACCTAC 60.605 57.143 0.41 0.00 0.00 3.18
591 664 0.313043 ACCACGTCAGACAACCTACG 59.687 55.000 0.41 0.00 40.99 3.51
778 856 3.723260 CCGCCTCTTTCTCCTCTAATTC 58.277 50.000 0.00 0.00 0.00 2.17
826 906 1.144708 TCATGCCAGTCCCTTGTTCAA 59.855 47.619 0.00 0.00 0.00 2.69
1009 1095 1.593196 CAAACGTGACACACCCAGAT 58.407 50.000 6.37 0.00 0.00 2.90
1019 1105 3.347216 ACACACCCAGATAATCAACTGC 58.653 45.455 0.00 0.00 33.40 4.40
1422 1517 1.676529 TCCTGCTAGTCACGCACTATC 59.323 52.381 0.00 0.00 36.96 2.08
1434 1529 1.269257 CGCACTATCCAGCTCGATTCA 60.269 52.381 0.00 0.00 0.00 2.57
1497 1592 6.546311 CGAGTAAATCGTAACGTCGTATTTC 58.454 40.000 0.00 0.00 46.62 2.17
1561 1672 1.574925 GCTCGCTGATCCGATCGTA 59.425 57.895 15.09 0.00 36.54 3.43
1594 1708 0.323633 TGTTGGCCATGCATGCTACT 60.324 50.000 21.69 0.25 0.00 2.57
1595 1709 0.383231 GTTGGCCATGCATGCTACTC 59.617 55.000 21.69 7.33 0.00 2.59
1844 1980 6.349363 GGGAGAGTCTTCGCAAAATGTATTTT 60.349 38.462 0.00 0.00 40.37 1.82
1845 1981 7.084486 GGAGAGTCTTCGCAAAATGTATTTTT 58.916 34.615 0.00 0.00 37.86 1.94
1900 2038 1.850345 AGGAACACCCCTTCTCAACAA 59.150 47.619 0.00 0.00 30.99 2.83
1930 2069 1.333702 CGAAACCACCACAATGTGACG 60.334 52.381 15.91 5.01 38.55 4.35
2000 2140 4.892934 ACCAAAGGCAGTTAATCTTTGACA 59.107 37.500 14.28 0.00 45.89 3.58
2041 2181 1.135960 TGACCCAGGTTGTGATGTGA 58.864 50.000 0.00 0.00 0.00 3.58
2110 2250 6.862608 TCGTTAACTGACAAAGCGTTAAGATA 59.137 34.615 3.71 0.00 34.78 1.98
2111 2251 6.946584 CGTTAACTGACAAAGCGTTAAGATAC 59.053 38.462 3.71 0.00 34.78 2.24
2113 2253 4.890088 ACTGACAAAGCGTTAAGATACCA 58.110 39.130 0.00 0.00 0.00 3.25
2114 2254 4.929808 ACTGACAAAGCGTTAAGATACCAG 59.070 41.667 0.00 0.00 0.00 4.00
2120 2261 1.540580 GCGTTAAGATACCAGAGGGCC 60.541 57.143 0.00 0.00 37.90 5.80
2140 2281 0.902531 CACCCGTCAGTATGTTCCCT 59.097 55.000 0.00 0.00 37.40 4.20
2141 2282 2.104967 CACCCGTCAGTATGTTCCCTA 58.895 52.381 0.00 0.00 37.40 3.53
2142 2283 2.105766 ACCCGTCAGTATGTTCCCTAC 58.894 52.381 0.00 0.00 37.40 3.18
2143 2284 2.292061 ACCCGTCAGTATGTTCCCTACT 60.292 50.000 0.00 0.00 37.40 2.57
2144 2285 3.053395 ACCCGTCAGTATGTTCCCTACTA 60.053 47.826 0.00 0.00 37.40 1.82
2145 2286 4.150359 CCCGTCAGTATGTTCCCTACTAT 58.850 47.826 0.00 0.00 37.40 2.12
2146 2287 4.022242 CCCGTCAGTATGTTCCCTACTATG 60.022 50.000 0.00 0.00 37.40 2.23
2148 2289 4.547532 GTCAGTATGTTCCCTACTATGCG 58.452 47.826 0.00 0.00 37.40 4.73
2151 2292 1.128200 ATGTTCCCTACTATGCGCCA 58.872 50.000 4.18 0.00 0.00 5.69
2152 2293 1.128200 TGTTCCCTACTATGCGCCAT 58.872 50.000 4.18 0.63 0.00 4.40
2153 2294 1.488812 TGTTCCCTACTATGCGCCATT 59.511 47.619 4.18 0.00 0.00 3.16
2160 3130 1.732941 ACTATGCGCCATTTCGAACA 58.267 45.000 4.18 0.00 0.00 3.18
2177 3147 0.179076 ACATCTCGAATCATGCGCCA 60.179 50.000 4.18 0.00 0.00 5.69
2183 3153 0.027194 CGAATCATGCGCCACTTCTG 59.973 55.000 4.18 0.00 0.00 3.02
2198 3168 6.199154 CGCCACTTCTGTTATCTACTATGTTG 59.801 42.308 0.00 0.00 0.00 3.33
2199 3169 7.042335 GCCACTTCTGTTATCTACTATGTTGT 58.958 38.462 0.00 0.00 0.00 3.32
2224 3194 4.104086 TCTGCCCCAAGAAGAGATTTAGA 58.896 43.478 0.00 0.00 0.00 2.10
2231 3201 6.039159 CCCCAAGAAGAGATTTAGATTTGAGC 59.961 42.308 0.00 0.00 0.00 4.26
2233 3203 7.989741 CCCAAGAAGAGATTTAGATTTGAGCTA 59.010 37.037 0.00 0.00 0.00 3.32
2251 3221 5.105310 TGAGCTATTCTAGACCAAGTTGGAC 60.105 44.000 28.80 21.91 40.96 4.02
2255 3225 0.249398 CTAGACCAAGTTGGACGGGG 59.751 60.000 28.80 13.05 40.96 5.73
2276 3246 1.003464 TCCTGGATGTGGTGTGTGATG 59.997 52.381 0.00 0.00 0.00 3.07
2333 3303 1.596477 CGCCTAGATGCCTTGCTCC 60.596 63.158 0.00 0.00 0.00 4.70
2342 3312 1.896660 GCCTTGCTCCGGAACACAA 60.897 57.895 7.15 10.30 0.00 3.33
2360 3330 6.207691 ACACAACTCATGTTTTACAAGCTT 57.792 33.333 0.00 0.00 41.46 3.74
2361 3331 6.035843 ACACAACTCATGTTTTACAAGCTTG 58.964 36.000 24.84 24.84 41.46 4.01
2362 3332 5.459762 CACAACTCATGTTTTACAAGCTTGG 59.540 40.000 29.18 12.28 41.46 3.61
2363 3333 5.127031 ACAACTCATGTTTTACAAGCTTGGT 59.873 36.000 29.18 17.13 40.06 3.67
2364 3334 5.186996 ACTCATGTTTTACAAGCTTGGTG 57.813 39.130 29.18 15.14 0.00 4.17
2365 3335 4.644685 ACTCATGTTTTACAAGCTTGGTGT 59.355 37.500 29.18 12.95 0.00 4.16
2366 3336 4.930963 TCATGTTTTACAAGCTTGGTGTG 58.069 39.130 29.18 16.66 0.00 3.82
2367 3337 4.642437 TCATGTTTTACAAGCTTGGTGTGA 59.358 37.500 29.18 18.36 0.00 3.58
2371 3341 2.949177 TACAAGCTTGGTGTGATGGT 57.051 45.000 29.18 8.41 0.00 3.55
2399 3369 2.302733 GGAAGGTGGGCAACATCAAAAT 59.697 45.455 0.00 0.00 39.74 1.82
2405 3375 4.485163 GTGGGCAACATCAAAATACAGAC 58.515 43.478 0.00 0.00 39.74 3.51
2409 3379 3.416277 CAACATCAAAATACAGACGGCG 58.584 45.455 4.80 4.80 0.00 6.46
2412 3382 3.191669 CATCAAAATACAGACGGCGGTA 58.808 45.455 13.24 3.03 0.00 4.02
2430 3400 4.918583 GCGGTAGCTAACTATGTCATTCTC 59.081 45.833 7.30 0.00 41.01 2.87
2431 3401 5.462405 CGGTAGCTAACTATGTCATTCTCC 58.538 45.833 7.30 0.00 0.00 3.71
2435 3405 4.038162 AGCTAACTATGTCATTCTCCGTCC 59.962 45.833 0.00 0.00 0.00 4.79
2443 3413 0.039978 CATTCTCCGTCCCGATCGAG 60.040 60.000 18.66 2.49 0.00 4.04
2444 3414 1.797211 ATTCTCCGTCCCGATCGAGC 61.797 60.000 18.66 5.08 0.00 5.03
2502 3472 5.084519 TGGCTAAGGAGAACTCTGAAGTTA 58.915 41.667 1.86 0.00 45.80 2.24
2553 3523 5.828328 ACGTACCATTGAGAGACATAGATCA 59.172 40.000 0.00 0.00 0.00 2.92
2554 3524 6.491745 ACGTACCATTGAGAGACATAGATCAT 59.508 38.462 0.00 0.00 0.00 2.45
2568 3538 7.455953 AGACATAGATCATGATTAAGGTGGCTA 59.544 37.037 10.14 4.44 38.10 3.93
2572 3542 6.302269 AGATCATGATTAAGGTGGCTAAAGG 58.698 40.000 10.14 0.00 0.00 3.11
2610 5300 1.208614 GCTCTTTCAGCTTGTGGCG 59.791 57.895 0.00 0.00 45.83 5.69
2620 5310 1.165270 GCTTGTGGCGAATGGTAAGT 58.835 50.000 0.00 0.00 0.00 2.24
2621 5311 1.135689 GCTTGTGGCGAATGGTAAGTG 60.136 52.381 0.00 0.00 0.00 3.16
2649 5339 6.770746 AAGAATTTGATCCCTCACATCAAG 57.229 37.500 0.00 0.00 40.51 3.02
2653 5343 3.740631 TGATCCCTCACATCAAGATCG 57.259 47.619 0.00 0.00 36.88 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.766143 CTTCGCATGGCCTAAGTCGC 61.766 60.000 3.32 0.00 0.00 5.19
74 75 2.046217 GAGGAACCAACTCCGGCC 60.046 66.667 0.00 0.00 40.75 6.13
197 198 9.367444 GTAGGTAAGTATCATATATGGTTGCAC 57.633 37.037 12.78 1.30 0.00 4.57
223 224 7.174946 ACACATCCCAAGACAAGTTTACTTATG 59.825 37.037 0.00 0.00 34.28 1.90
226 227 5.445964 ACACATCCCAAGACAAGTTTACTT 58.554 37.500 0.00 0.00 36.45 2.24
253 324 6.466885 AAATTACGCTCCACTATGACTAGT 57.533 37.500 0.00 0.00 38.79 2.57
269 340 6.641176 TGCATGACACTAGTGTAAATTACG 57.359 37.500 27.98 13.53 45.05 3.18
309 380 9.817809 TCTCATTATCCACATAAAGACAGTAAC 57.182 33.333 0.00 0.00 0.00 2.50
315 386 7.939039 TCCCAATCTCATTATCCACATAAAGAC 59.061 37.037 0.00 0.00 0.00 3.01
317 388 8.159447 TCTCCCAATCTCATTATCCACATAAAG 58.841 37.037 0.00 0.00 0.00 1.85
517 590 2.366590 TGACGATGGGAGAGATTCATGG 59.633 50.000 0.00 0.00 0.00 3.66
560 633 2.036733 CTGACGTGGTGGAGGTCTTTTA 59.963 50.000 0.00 0.00 39.73 1.52
561 634 0.834612 TGACGTGGTGGAGGTCTTTT 59.165 50.000 0.00 0.00 39.73 2.27
562 635 0.393077 CTGACGTGGTGGAGGTCTTT 59.607 55.000 0.00 0.00 39.73 2.52
588 661 6.985117 ACAATGTTTCTACAAGAGGTACGTA 58.015 36.000 0.00 0.00 37.91 3.57
589 662 5.850614 ACAATGTTTCTACAAGAGGTACGT 58.149 37.500 0.00 0.00 37.91 3.57
590 663 6.422701 TGAACAATGTTTCTACAAGAGGTACG 59.577 38.462 0.00 0.00 37.91 3.67
591 664 7.724305 TGAACAATGTTTCTACAAGAGGTAC 57.276 36.000 0.00 0.00 37.91 3.34
778 856 2.288213 TGACTGTGAAAGCGGTGTAGAG 60.288 50.000 0.00 0.00 0.00 2.43
826 906 7.824289 AGTACTAACAGTGTGCATATGATTGTT 59.176 33.333 6.97 7.81 0.00 2.83
876 959 6.577103 TGCTATCAATGGAGAGACAAGTAAG 58.423 40.000 0.00 0.00 34.21 2.34
882 965 5.601729 AGAAGATGCTATCAATGGAGAGACA 59.398 40.000 0.00 0.00 34.21 3.41
983 1066 0.753479 TGTGTCACGTTTGGGCCATT 60.753 50.000 7.26 0.00 0.00 3.16
986 1070 2.719354 GTGTGTCACGTTTGGGCC 59.281 61.111 0.00 0.00 0.00 5.80
1053 1140 1.364171 GGATCGATCGACTGGTGGG 59.636 63.158 22.06 0.00 0.00 4.61
1422 1517 3.257561 CGGCGTGAATCGAGCTGG 61.258 66.667 0.00 0.00 42.86 4.85
1497 1592 3.420544 CGAACGAGTGAAAGTTGACATCG 60.421 47.826 0.00 0.00 35.00 3.84
1561 1672 1.226267 CAACACAAAGCACGCACGT 60.226 52.632 0.00 0.00 0.00 4.49
1594 1708 3.958798 CGGAAGAGGATACAAAGGTAGGA 59.041 47.826 0.00 0.00 41.41 2.94
1595 1709 3.492829 GCGGAAGAGGATACAAAGGTAGG 60.493 52.174 0.00 0.00 41.41 3.18
1651 1765 9.087424 GGAAATAAGTTTTATTTCTGCCACATC 57.913 33.333 23.13 9.14 41.32 3.06
1817 1953 2.169832 TTTTGCGAAGACTCTCCCAG 57.830 50.000 0.00 0.00 0.00 4.45
1818 1954 2.224523 ACATTTTGCGAAGACTCTCCCA 60.225 45.455 0.00 0.00 0.00 4.37
1900 2038 2.556622 GTGGTGGTTTCGTGGATTTCAT 59.443 45.455 0.00 0.00 0.00 2.57
2005 2145 2.897326 GGTCAAGGGGCATTTAGTGTTT 59.103 45.455 0.00 0.00 0.00 2.83
2059 2199 3.126831 CACCCAATATCGTCTGCTCTTC 58.873 50.000 0.00 0.00 0.00 2.87
2120 2261 0.107848 GGGAACATACTGACGGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
2140 2281 2.894902 TGTTCGAAATGGCGCATAGTA 58.105 42.857 10.83 0.00 0.00 1.82
2141 2282 1.732941 TGTTCGAAATGGCGCATAGT 58.267 45.000 10.83 0.00 0.00 2.12
2142 2283 2.545526 AGATGTTCGAAATGGCGCATAG 59.454 45.455 10.83 0.00 0.00 2.23
2143 2284 2.543848 GAGATGTTCGAAATGGCGCATA 59.456 45.455 10.83 0.00 0.00 3.14
2144 2285 1.331756 GAGATGTTCGAAATGGCGCAT 59.668 47.619 10.83 0.00 0.00 4.73
2145 2286 0.726827 GAGATGTTCGAAATGGCGCA 59.273 50.000 10.83 0.00 0.00 6.09
2146 2287 3.516263 GAGATGTTCGAAATGGCGC 57.484 52.632 0.00 0.00 0.00 6.53
2160 3130 0.105593 AGTGGCGCATGATTCGAGAT 59.894 50.000 10.83 0.00 0.00 2.75
2166 3136 1.538047 AACAGAAGTGGCGCATGATT 58.462 45.000 10.83 0.00 0.00 2.57
2177 3147 9.640963 GAACACAACATAGTAGATAACAGAAGT 57.359 33.333 0.00 0.00 0.00 3.01
2183 3153 6.258068 GGGCAGAACACAACATAGTAGATAAC 59.742 42.308 0.00 0.00 0.00 1.89
2198 3168 1.072331 TCTCTTCTTGGGGCAGAACAC 59.928 52.381 0.00 0.00 0.00 3.32
2199 3169 1.434188 TCTCTTCTTGGGGCAGAACA 58.566 50.000 0.00 0.00 0.00 3.18
2224 3194 6.825721 CCAACTTGGTCTAGAATAGCTCAAAT 59.174 38.462 0.00 0.00 38.99 2.32
2231 3201 4.441634 CCCGTCCAACTTGGTCTAGAATAG 60.442 50.000 7.72 0.00 39.03 1.73
2233 3203 2.236395 CCCGTCCAACTTGGTCTAGAAT 59.764 50.000 7.72 0.00 39.03 2.40
2238 3208 1.765597 GACCCCGTCCAACTTGGTCT 61.766 60.000 7.72 0.00 41.77 3.85
2251 3221 3.009115 ACCACATCCAGGACCCCG 61.009 66.667 0.00 0.00 0.00 5.73
2255 3225 0.396435 TCACACACCACATCCAGGAC 59.604 55.000 0.00 0.00 0.00 3.85
2276 3246 0.883833 CCTTCATCACACACCCAAGC 59.116 55.000 0.00 0.00 0.00 4.01
2333 3303 5.163302 TGTAAAACATGAGTTGTGTTCCG 57.837 39.130 0.00 0.00 38.76 4.30
2342 3312 4.644685 ACACCAAGCTTGTAAAACATGAGT 59.355 37.500 24.35 8.58 0.00 3.41
2360 3330 1.492599 TCCTTTGACACCATCACACCA 59.507 47.619 0.00 0.00 36.92 4.17
2361 3331 2.270352 TCCTTTGACACCATCACACC 57.730 50.000 0.00 0.00 36.92 4.16
2362 3332 2.554032 CCTTCCTTTGACACCATCACAC 59.446 50.000 0.00 0.00 36.92 3.82
2363 3333 2.174639 ACCTTCCTTTGACACCATCACA 59.825 45.455 0.00 0.00 36.92 3.58
2364 3334 2.554032 CACCTTCCTTTGACACCATCAC 59.446 50.000 0.00 0.00 36.92 3.06
2365 3335 2.488891 CCACCTTCCTTTGACACCATCA 60.489 50.000 0.00 0.00 34.65 3.07
2366 3336 2.162681 CCACCTTCCTTTGACACCATC 58.837 52.381 0.00 0.00 0.00 3.51
2367 3337 1.203050 CCCACCTTCCTTTGACACCAT 60.203 52.381 0.00 0.00 0.00 3.55
2371 3341 0.260230 TTGCCCACCTTCCTTTGACA 59.740 50.000 0.00 0.00 0.00 3.58
2399 3369 0.734889 GTTAGCTACCGCCGTCTGTA 59.265 55.000 0.00 0.00 36.60 2.74
2405 3375 1.335810 TGACATAGTTAGCTACCGCCG 59.664 52.381 0.00 0.00 36.60 6.46
2409 3379 5.009811 ACGGAGAATGACATAGTTAGCTACC 59.990 44.000 0.00 0.00 0.00 3.18
2412 3382 4.038162 GGACGGAGAATGACATAGTTAGCT 59.962 45.833 0.00 0.00 0.00 3.32
2435 3405 0.031857 ATGCTCTTGAGCTCGATCGG 59.968 55.000 21.17 7.26 35.49 4.18
2443 3413 4.050553 GTGATGAGTCTATGCTCTTGAGC 58.949 47.826 15.01 15.01 36.51 4.26
2444 3414 5.283294 CAGTGATGAGTCTATGCTCTTGAG 58.717 45.833 0.00 0.00 36.51 3.02
2454 3424 1.064685 TCCTCGGCAGTGATGAGTCTA 60.065 52.381 10.15 0.00 0.00 2.59
2461 3431 0.392193 CAAAGCTCCTCGGCAGTGAT 60.392 55.000 0.00 0.00 34.17 3.06
2482 3452 5.394773 GGGCTAACTTCAGAGTTCTCCTTAG 60.395 48.000 0.00 0.00 44.75 2.18
2553 3523 4.141158 CCCTCCTTTAGCCACCTTAATCAT 60.141 45.833 0.00 0.00 0.00 2.45
2554 3524 3.202151 CCCTCCTTTAGCCACCTTAATCA 59.798 47.826 0.00 0.00 0.00 2.57
2568 3538 2.239907 GGTGTTAGCATCTCCCTCCTTT 59.760 50.000 0.00 0.00 0.00 3.11
2572 3542 2.911484 CTTGGTGTTAGCATCTCCCTC 58.089 52.381 0.00 0.00 0.00 4.30
2610 5300 6.922957 TCAAATTCTTTGTGCACTTACCATTC 59.077 34.615 19.41 0.00 41.36 2.67
2620 5310 4.022068 GTGAGGGATCAAATTCTTTGTGCA 60.022 41.667 0.00 0.00 41.36 4.57
2621 5311 4.022068 TGTGAGGGATCAAATTCTTTGTGC 60.022 41.667 0.00 0.00 41.36 4.57
2634 5324 2.630098 TCCGATCTTGATGTGAGGGATC 59.370 50.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.