Multiple sequence alignment - TraesCS3A01G212000

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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 TraesCS3A01G212000 chr3A 100.000 3004 0 0 1 3004 381291745 381294748 0.000000e+00 5548.0
1 TraesCS3A01G212000 chr3D 96.790 1402 41 3 1604 3004 290015632 290017030 0.000000e+00 2337.0
2 TraesCS3A01G212000 chr3D 97.889 758 12 2 799 1553 290014711 290015467 0.000000e+00 1308.0
3 TraesCS3A01G212000 chr3D 89.655 319 25 5 219 537 290012730 290013040 1.680000e-107 399.0
4 TraesCS3A01G212000 chr3D 95.833 168 7 0 614 781 290014561 290014728 3.820000e-69 272.0
5 TraesCS3A01G212000 chr3D 85.714 224 14 5 1 216 290012485 290012698 1.400000e-53 220.0
6 TraesCS3A01G212000 chr3D 92.715 151 11 0 522 672 290013387 290013537 5.040000e-53 219.0
7 TraesCS3A01G212000 chr3D 96.154 52 0 2 1555 1606 290015501 290015550 1.920000e-12 84.2
8 TraesCS3A01G212000 chr3D 97.500 40 1 0 665 704 290014517 290014556 5.370000e-08 69.4
9 TraesCS3A01G212000 chr3B 95.745 1457 46 5 1555 3004 382318536 382319983 0.000000e+00 2333.0
10 TraesCS3A01G212000 chr3B 98.013 755 15 0 799 1553 382317748 382318502 0.000000e+00 1312.0
11 TraesCS3A01G212000 chr3B 95.385 260 12 0 522 781 382317506 382317765 5.990000e-112 414.0
12 TraesCS3A01G212000 chr3B 89.714 175 18 0 219 393 382310336 382310510 1.080000e-54 224.0
13 TraesCS3A01G212000 chr3B 86.577 149 13 6 389 537 382317032 382317173 1.110000e-34 158.0
14 TraesCS3A01G212000 chr7A 80.220 91 12 5 457 544 166485162 166485249 2.500000e-06 63.9


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 TraesCS3A01G212000 chr3A 381291745 381294748 3003 False 5548.000 5548 100.00000 1 3004 1 chr3A.!!$F1 3003
1 TraesCS3A01G212000 chr3D 290012485 290017030 4545 False 613.575 2337 94.03125 1 3004 8 chr3D.!!$F1 3003
2 TraesCS3A01G212000 chr3B 382317032 382319983 2951 False 1054.250 2333 93.93000 389 3004 4 chr3B.!!$F2 2615

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
776 2261 0.037734 ATCCCCAACGTCTTGGTTCC 59.962 55.0 5.58 0.0 45.22 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 4204 4.199432 CTGTAGGCATTCTTCAGTGAGT 57.801 45.455 0.0 0.0 36.51 3.41 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 6.560711 GTGACTCATTTGTTTAAACCAGTGT 58.439 36.000 15.59 9.16 0.00 3.55
28 29 7.033185 GTGACTCATTTGTTTAAACCAGTGTT 58.967 34.615 15.59 4.22 35.82 3.32
30 31 7.543868 TGACTCATTTGTTTAAACCAGTGTTTG 59.456 33.333 15.59 8.93 44.27 2.93
42 43 2.095768 CCAGTGTTTGTTCATAGGCGTG 60.096 50.000 0.00 0.00 0.00 5.34
44 45 3.249799 CAGTGTTTGTTCATAGGCGTGAA 59.750 43.478 4.58 4.58 35.84 3.18
48 49 5.342259 GTGTTTGTTCATAGGCGTGAAATTC 59.658 40.000 9.40 0.00 39.61 2.17
49 50 4.695217 TTGTTCATAGGCGTGAAATTCC 57.305 40.909 9.40 0.26 39.61 3.01
101 102 3.131396 GGCAGGTACGGTATTGATCTTG 58.869 50.000 0.00 0.00 0.00 3.02
136 137 8.358148 AGCAATATTTGATGATCTTGATCAACC 58.642 33.333 15.98 11.67 39.09 3.77
142 143 4.019051 TGATGATCTTGATCAACCAGGTGT 60.019 41.667 15.98 0.00 33.83 4.16
155 156 0.521291 CAGGTGTTGGTATTGTGGCG 59.479 55.000 0.00 0.00 0.00 5.69
162 163 2.389962 TGGTATTGTGGCGTTAGACC 57.610 50.000 0.00 0.00 0.00 3.85
163 164 1.283736 GGTATTGTGGCGTTAGACCG 58.716 55.000 0.00 0.00 0.00 4.79
204 212 1.956477 CTTGTTGTGAACCCTTCCAGG 59.044 52.381 0.00 0.00 34.30 4.45
213 221 2.747855 CCTTCCAGGTGGCGCTTC 60.748 66.667 7.64 0.00 34.44 3.86
214 222 2.032528 CTTCCAGGTGGCGCTTCA 59.967 61.111 7.64 0.00 34.44 3.02
215 223 2.281484 TTCCAGGTGGCGCTTCAC 60.281 61.111 7.64 7.93 36.95 3.18
216 224 2.738213 CTTCCAGGTGGCGCTTCACT 62.738 60.000 15.02 3.09 37.75 3.41
217 225 3.052082 CCAGGTGGCGCTTCACTG 61.052 66.667 15.02 13.73 37.75 3.66
237 275 0.744414 GGCTGTTTATCTGGCTCGCA 60.744 55.000 0.00 0.00 37.52 5.10
250 288 0.109132 GCTCGCAATGAGGGTTTTGG 60.109 55.000 0.00 0.00 45.38 3.28
253 291 0.038343 CGCAATGAGGGTTTTGGTGG 60.038 55.000 0.00 0.00 0.00 4.61
269 307 2.300152 TGGTGGTGTTGTTTTTGCTTCA 59.700 40.909 0.00 0.00 0.00 3.02
279 317 2.443887 TTTTGCTTCAGATTGCCTGC 57.556 45.000 0.00 0.00 42.62 4.85
288 326 3.056313 GATTGCCTGCCGCTTGTCC 62.056 63.158 0.00 0.00 38.78 4.02
291 329 4.043200 GCCTGCCGCTTGTCCAAC 62.043 66.667 0.00 0.00 0.00 3.77
292 330 2.594303 CCTGCCGCTTGTCCAACA 60.594 61.111 0.00 0.00 0.00 3.33
294 332 1.008538 CTGCCGCTTGTCCAACAAC 60.009 57.895 0.00 0.00 33.96 3.32
315 353 2.401017 TCACTCTTCAGTTCGTGACG 57.599 50.000 0.00 0.00 33.71 4.35
354 392 4.636249 GGTGGTGGCTGATATTTCTCTAG 58.364 47.826 0.00 0.00 0.00 2.43
355 393 4.503991 GGTGGTGGCTGATATTTCTCTAGG 60.504 50.000 0.00 0.00 0.00 3.02
360 398 3.055458 GGCTGATATTTCTCTAGGGGCTC 60.055 52.174 0.00 0.00 0.00 4.70
362 400 3.829601 CTGATATTTCTCTAGGGGCTCGT 59.170 47.826 0.00 0.00 0.00 4.18
363 401 3.574396 TGATATTTCTCTAGGGGCTCGTG 59.426 47.826 0.00 0.00 0.00 4.35
374 412 2.035442 GGCTCGTGGCTTCAGTTCC 61.035 63.158 3.50 0.00 41.46 3.62
375 413 2.383527 GCTCGTGGCTTCAGTTCCG 61.384 63.158 0.00 0.00 38.06 4.30
397 435 2.143122 GGAGTTCAAGCATGTTCGTCA 58.857 47.619 0.00 0.00 0.00 4.35
420 458 3.250280 GCATCTCAATGTAGTGGCTCATG 59.750 47.826 0.00 0.00 35.18 3.07
454 492 8.989653 AAGTCTTGTAAGAATCTTACTAGTGC 57.010 34.615 29.47 24.63 36.68 4.40
456 494 8.808092 AGTCTTGTAAGAATCTTACTAGTGCTT 58.192 33.333 29.47 17.74 36.68 3.91
459 497 9.209175 CTTGTAAGAATCTTACTAGTGCTTTGT 57.791 33.333 27.24 0.00 0.00 2.83
460 498 8.534333 TGTAAGAATCTTACTAGTGCTTTGTG 57.466 34.615 27.24 0.00 0.00 3.33
461 499 8.148351 TGTAAGAATCTTACTAGTGCTTTGTGT 58.852 33.333 27.24 0.00 0.00 3.72
462 500 7.426929 AAGAATCTTACTAGTGCTTTGTGTG 57.573 36.000 5.39 0.00 0.00 3.82
463 501 6.525629 AGAATCTTACTAGTGCTTTGTGTGT 58.474 36.000 5.39 0.00 0.00 3.72
479 517 5.651387 TGTGTGTTTTTCATTCTGTTCCA 57.349 34.783 0.00 0.00 0.00 3.53
489 527 8.868522 TTTTCATTCTGTTCCAGATTGTATCT 57.131 30.769 13.00 0.00 40.39 1.98
588 991 3.938963 AGAAAAGTGAAAAGACGAGCACA 59.061 39.130 0.00 0.00 33.85 4.57
591 994 2.205074 AGTGAAAAGACGAGCACACAG 58.795 47.619 0.00 0.00 33.85 3.66
601 1004 0.394565 GAGCACACAGGTCTCCAACT 59.605 55.000 0.00 0.00 41.51 3.16
640 1043 0.396435 ACTGACTGGGACAATCGCAA 59.604 50.000 0.00 0.00 37.42 4.85
648 2133 1.565156 GGACAATCGCAACACGCAGA 61.565 55.000 0.00 0.00 42.60 4.26
650 2135 1.154413 CAATCGCAACACGCAGACC 60.154 57.895 0.00 0.00 42.60 3.85
672 2157 1.003580 GGAGGCAGGAATGTCTGAACA 59.996 52.381 0.00 0.00 40.38 3.18
770 2255 2.746277 GCGCATCCCCAACGTCTT 60.746 61.111 0.30 0.00 0.00 3.01
771 2256 3.039202 GCGCATCCCCAACGTCTTG 62.039 63.158 0.30 0.00 0.00 3.02
772 2257 2.398554 CGCATCCCCAACGTCTTGG 61.399 63.158 0.00 0.00 46.15 3.61
773 2258 1.303317 GCATCCCCAACGTCTTGGT 60.303 57.895 5.58 0.00 45.22 3.67
774 2259 0.893727 GCATCCCCAACGTCTTGGTT 60.894 55.000 5.58 0.00 45.22 3.67
775 2260 1.165270 CATCCCCAACGTCTTGGTTC 58.835 55.000 5.58 0.00 45.22 3.62
776 2261 0.037734 ATCCCCAACGTCTTGGTTCC 59.962 55.000 5.58 0.00 45.22 3.62
777 2262 1.602605 CCCCAACGTCTTGGTTCCC 60.603 63.158 5.58 0.00 45.22 3.97
778 2263 1.602605 CCCAACGTCTTGGTTCCCC 60.603 63.158 5.58 0.00 45.22 4.81
779 2264 1.602605 CCAACGTCTTGGTTCCCCC 60.603 63.158 0.00 0.00 42.09 5.40
780 2265 1.149627 CAACGTCTTGGTTCCCCCA 59.850 57.895 0.00 0.00 43.27 4.96
781 2266 1.149854 AACGTCTTGGTTCCCCCAC 59.850 57.895 0.00 0.00 45.19 4.61
782 2267 2.033602 CGTCTTGGTTCCCCCACC 59.966 66.667 0.00 0.00 45.19 4.61
783 2268 2.439245 GTCTTGGTTCCCCCACCC 59.561 66.667 0.00 0.00 45.19 4.61
784 2269 3.253838 TCTTGGTTCCCCCACCCG 61.254 66.667 0.00 0.00 45.19 5.28
785 2270 3.253838 CTTGGTTCCCCCACCCGA 61.254 66.667 0.00 0.00 45.19 5.14
786 2271 2.533232 TTGGTTCCCCCACCCGAT 60.533 61.111 0.00 0.00 45.19 4.18
787 2272 2.552231 CTTGGTTCCCCCACCCGATC 62.552 65.000 0.00 0.00 45.19 3.69
788 2273 3.012722 GGTTCCCCCACCCGATCA 61.013 66.667 0.00 0.00 0.00 2.92
789 2274 2.608550 GGTTCCCCCACCCGATCAA 61.609 63.158 0.00 0.00 0.00 2.57
790 2275 1.381076 GTTCCCCCACCCGATCAAA 59.619 57.895 0.00 0.00 0.00 2.69
791 2276 0.251430 GTTCCCCCACCCGATCAAAA 60.251 55.000 0.00 0.00 0.00 2.44
792 2277 0.483328 TTCCCCCACCCGATCAAAAA 59.517 50.000 0.00 0.00 0.00 1.94
793 2278 0.039035 TCCCCCACCCGATCAAAAAG 59.961 55.000 0.00 0.00 0.00 2.27
794 2279 0.039035 CCCCCACCCGATCAAAAAGA 59.961 55.000 0.00 0.00 0.00 2.52
795 2280 1.549037 CCCCCACCCGATCAAAAAGAA 60.549 52.381 0.00 0.00 0.00 2.52
796 2281 2.243810 CCCCACCCGATCAAAAAGAAA 58.756 47.619 0.00 0.00 0.00 2.52
797 2282 2.630580 CCCCACCCGATCAAAAAGAAAA 59.369 45.455 0.00 0.00 0.00 2.29
867 2352 4.326826 CACCACACACTCTTATCCACAAT 58.673 43.478 0.00 0.00 0.00 2.71
944 2429 0.256464 TCTTCCCCTCCGTCTCTCTC 59.744 60.000 0.00 0.00 0.00 3.20
957 2442 1.077828 TCTCTCTCTTCCTTCCTGCCA 59.922 52.381 0.00 0.00 0.00 4.92
1052 2537 2.264794 GAAGGTGGGACGCATCGT 59.735 61.111 0.00 0.00 45.10 3.73
1098 2583 1.154093 GTCGTTCGCCGTGATCAGA 60.154 57.895 0.00 0.00 37.94 3.27
1362 2850 9.490379 GAACTACAGGAATACTTCAAGAAGAAA 57.510 33.333 16.16 4.75 40.79 2.52
1594 3114 2.647299 TGGTCCACAATAATCAGGGTGT 59.353 45.455 0.00 0.00 0.00 4.16
1595 3115 3.847184 TGGTCCACAATAATCAGGGTGTA 59.153 43.478 0.00 0.00 0.00 2.90
1640 3244 5.009610 CACAGCATACCCTTAACAAACAACT 59.990 40.000 0.00 0.00 0.00 3.16
1677 3281 7.480760 AGTTTTTGGGCATGTTAATGAGTAT 57.519 32.000 0.00 0.00 35.67 2.12
1744 3348 4.733077 TTTCCCCTCATGTACTTCCAAA 57.267 40.909 0.00 0.00 0.00 3.28
1752 3356 7.777910 CCCCTCATGTACTTCCAAATTATACAA 59.222 37.037 0.00 0.00 30.06 2.41
1807 3411 4.880886 TGTTGAAATGCAGGATGATACG 57.119 40.909 0.00 0.00 39.69 3.06
2017 3621 3.699413 TGGATTGATGGCTCATGTTTGA 58.301 40.909 0.00 0.00 0.00 2.69
2125 3735 5.417266 TCCTTGAGTTTCATTTGTGTTGTCA 59.583 36.000 0.00 0.00 0.00 3.58
2164 3774 8.855110 TGAATGTAAAATTCACTTTCCAGCTTA 58.145 29.630 12.44 0.00 33.55 3.09
2269 3879 5.960202 AGAATAATTGCAGGGTTTCAATCCT 59.040 36.000 0.00 0.00 41.23 3.24
2287 3897 4.584638 TCCTAAATTAGCTTTCTGGCCA 57.415 40.909 4.71 4.71 0.00 5.36
2594 4204 6.184789 TCGTGGAGTATGCTATACATGGATA 58.815 40.000 0.00 0.00 40.06 2.59
2616 4226 3.580458 ACTCACTGAAGAATGCCTACAGT 59.420 43.478 0.00 0.00 41.52 3.55
2625 4235 4.764172 AGAATGCCTACAGTTAAGCAGAG 58.236 43.478 0.00 0.00 38.89 3.35
2660 4270 2.890808 TTCTAAGCCGCATAGGAGTG 57.109 50.000 2.93 0.00 45.00 3.51
2665 4275 0.833287 AGCCGCATAGGAGTGTTCAT 59.167 50.000 0.00 0.00 45.00 2.57
2678 4288 5.045578 AGGAGTGTTCATATAGCACCAAACT 60.046 40.000 0.00 0.00 39.98 2.66
2782 4393 1.381165 GGCGGCCATAAATTCACGGT 61.381 55.000 15.62 0.00 0.00 4.83
2787 4398 3.304391 CGGCCATAAATTCACGGTAATGG 60.304 47.826 2.24 0.00 37.52 3.16
2819 4430 9.855021 ATTACATGTACCTTTGAATAGCAAAAC 57.145 29.630 4.68 0.00 45.26 2.43
2843 4454 7.837863 ACTGACCTCAAATTCGAGATAAGTTA 58.162 34.615 0.00 0.00 34.79 2.24
2916 4528 5.560724 ACAATAGCTTGTCACTGTTACCAT 58.439 37.500 0.00 0.00 41.86 3.55
2918 4530 5.683876 ATAGCTTGTCACTGTTACCATCT 57.316 39.130 0.00 0.00 0.00 2.90
2922 4534 5.877012 AGCTTGTCACTGTTACCATCTTATG 59.123 40.000 0.00 0.00 0.00 1.90
2956 4568 5.514136 CCAGTAATCCCCACAAGAACACTTA 60.514 44.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.544217 ACAAACACTGGTTTAAACAAATGAGTC 59.456 33.333 19.57 0.83 45.18 3.36
22 23 2.805671 TCACGCCTATGAACAAACACTG 59.194 45.455 0.00 0.00 0.00 3.66
27 28 4.764823 AGGAATTTCACGCCTATGAACAAA 59.235 37.500 0.00 0.00 38.31 2.83
28 29 4.155826 CAGGAATTTCACGCCTATGAACAA 59.844 41.667 0.00 0.00 38.31 2.83
30 31 3.487544 GCAGGAATTTCACGCCTATGAAC 60.488 47.826 0.00 0.00 38.31 3.18
42 43 3.625313 GTGGAGCTAGAAGCAGGAATTTC 59.375 47.826 1.22 0.00 45.56 2.17
44 45 2.843113 AGTGGAGCTAGAAGCAGGAATT 59.157 45.455 1.22 0.00 45.56 2.17
48 49 2.289945 ACAAAGTGGAGCTAGAAGCAGG 60.290 50.000 1.22 0.00 45.56 4.85
49 50 2.999355 GACAAAGTGGAGCTAGAAGCAG 59.001 50.000 1.22 0.00 45.56 4.24
92 93 3.617284 TGCTGCATCAGACAAGATCAAT 58.383 40.909 0.00 0.00 32.44 2.57
101 102 6.068473 TCATCAAATATTGCTGCATCAGAC 57.932 37.500 1.84 0.00 32.44 3.51
136 137 0.521291 CGCCACAATACCAACACCTG 59.479 55.000 0.00 0.00 0.00 4.00
142 143 2.702261 GGTCTAACGCCACAATACCAA 58.298 47.619 0.00 0.00 0.00 3.67
155 156 2.415512 GCAATGTCCAGAACGGTCTAAC 59.584 50.000 0.64 5.35 35.57 2.34
162 163 1.621107 GCAATGCAATGTCCAGAACG 58.379 50.000 0.00 0.00 0.00 3.95
163 164 1.621107 CGCAATGCAATGTCCAGAAC 58.379 50.000 5.91 0.00 0.00 3.01
213 221 1.098050 GCCAGATAAACAGCCCAGTG 58.902 55.000 0.00 0.00 0.00 3.66
214 222 0.995024 AGCCAGATAAACAGCCCAGT 59.005 50.000 0.00 0.00 0.00 4.00
215 223 1.673168 GAGCCAGATAAACAGCCCAG 58.327 55.000 0.00 0.00 0.00 4.45
216 224 0.107703 CGAGCCAGATAAACAGCCCA 60.108 55.000 0.00 0.00 0.00 5.36
217 225 1.440145 GCGAGCCAGATAAACAGCCC 61.440 60.000 0.00 0.00 0.00 5.19
237 275 2.433970 CAACACCACCAAAACCCTCATT 59.566 45.455 0.00 0.00 0.00 2.57
250 288 3.843999 TCTGAAGCAAAAACAACACCAC 58.156 40.909 0.00 0.00 0.00 4.16
253 291 4.260334 GGCAATCTGAAGCAAAAACAACAC 60.260 41.667 7.59 0.00 0.00 3.32
279 317 1.021202 TGAAGTTGTTGGACAAGCGG 58.979 50.000 0.00 0.00 39.00 5.52
288 326 4.330074 ACGAACTGAAGAGTGAAGTTGTTG 59.670 41.667 0.00 0.00 34.37 3.33
291 329 4.026475 GTCACGAACTGAAGAGTGAAGTTG 60.026 45.833 0.00 0.00 43.96 3.16
292 330 4.113354 GTCACGAACTGAAGAGTGAAGTT 58.887 43.478 0.00 0.00 43.96 2.66
294 332 2.721603 CGTCACGAACTGAAGAGTGAAG 59.278 50.000 0.00 0.00 43.96 3.02
315 353 1.993370 CACCGAACCGACAGAAGAATC 59.007 52.381 0.00 0.00 0.00 2.52
354 392 3.553095 AACTGAAGCCACGAGCCCC 62.553 63.158 0.00 0.00 45.47 5.80
355 393 2.032681 AACTGAAGCCACGAGCCC 59.967 61.111 0.00 0.00 45.47 5.19
360 398 2.317609 CCACGGAACTGAAGCCACG 61.318 63.158 0.00 0.00 0.00 4.94
362 400 1.371183 CTCCACGGAACTGAAGCCA 59.629 57.895 0.00 0.00 0.00 4.75
363 401 0.250338 AACTCCACGGAACTGAAGCC 60.250 55.000 0.00 0.00 0.00 4.35
374 412 1.136252 CGAACATGCTTGAACTCCACG 60.136 52.381 6.60 0.00 0.00 4.94
375 413 1.873591 ACGAACATGCTTGAACTCCAC 59.126 47.619 6.60 0.00 0.00 4.02
397 435 2.502947 TGAGCCACTACATTGAGATGCT 59.497 45.455 0.00 0.00 36.72 3.79
420 458 8.989653 AGATTCTTACAAGACTTAGCTAACAC 57.010 34.615 0.86 0.00 34.13 3.32
448 486 6.974622 AGAATGAAAAACACACAAAGCACTAG 59.025 34.615 0.00 0.00 0.00 2.57
450 488 5.577945 CAGAATGAAAAACACACAAAGCACT 59.422 36.000 0.00 0.00 39.69 4.40
451 489 5.348451 ACAGAATGAAAAACACACAAAGCAC 59.652 36.000 0.00 0.00 39.69 4.40
453 491 6.407475 AACAGAATGAAAAACACACAAAGC 57.593 33.333 0.00 0.00 39.69 3.51
454 492 6.589523 TGGAACAGAATGAAAAACACACAAAG 59.410 34.615 0.00 0.00 39.69 2.77
456 494 6.030548 TGGAACAGAATGAAAAACACACAA 57.969 33.333 0.00 0.00 39.69 3.33
479 517 5.071115 GCAAAGAGTCCCCTAGATACAATCT 59.929 44.000 0.00 0.00 43.33 2.40
489 527 3.181434 ACAACATTGCAAAGAGTCCCCTA 60.181 43.478 8.96 0.00 0.00 3.53
552 955 4.566759 TCACTTTTCTGAACGTGAGACTTG 59.433 41.667 14.28 0.00 38.61 3.16
588 991 2.119495 ACTTGTCAGTTGGAGACCTGT 58.881 47.619 0.00 0.00 35.15 4.00
591 994 3.069729 AGTGTACTTGTCAGTTGGAGACC 59.930 47.826 0.00 0.00 35.15 3.85
601 1004 2.097110 AGTCCCCAGTGTACTTGTCA 57.903 50.000 0.00 0.00 0.00 3.58
640 1043 4.008933 GCCTCCTGGTCTGCGTGT 62.009 66.667 0.00 0.00 35.27 4.49
648 2133 0.548682 AGACATTCCTGCCTCCTGGT 60.549 55.000 0.00 0.00 35.27 4.00
650 2135 0.907486 TCAGACATTCCTGCCTCCTG 59.093 55.000 0.00 0.00 34.28 3.86
772 2257 0.251430 TTTTGATCGGGTGGGGGAAC 60.251 55.000 0.00 0.00 0.00 3.62
773 2258 0.483328 TTTTTGATCGGGTGGGGGAA 59.517 50.000 0.00 0.00 0.00 3.97
774 2259 0.039035 CTTTTTGATCGGGTGGGGGA 59.961 55.000 0.00 0.00 0.00 4.81
775 2260 0.039035 TCTTTTTGATCGGGTGGGGG 59.961 55.000 0.00 0.00 0.00 5.40
776 2261 1.917872 TTCTTTTTGATCGGGTGGGG 58.082 50.000 0.00 0.00 0.00 4.96
777 2262 4.329462 TTTTTCTTTTTGATCGGGTGGG 57.671 40.909 0.00 0.00 0.00 4.61
795 2280 0.826256 GGGGGAGCCAAGACGTTTTT 60.826 55.000 0.00 0.00 0.00 1.94
796 2281 1.228459 GGGGGAGCCAAGACGTTTT 60.228 57.895 0.00 0.00 0.00 2.43
797 2282 2.411765 CTGGGGGAGCCAAGACGTTT 62.412 60.000 0.00 0.00 0.00 3.60
944 2429 1.283029 TCTTGGATGGCAGGAAGGAAG 59.717 52.381 0.00 0.00 0.00 3.46
957 2442 3.686726 GCGTTCTTGATTGTCTCTTGGAT 59.313 43.478 0.00 0.00 0.00 3.41
1098 2583 3.721706 CCCTCGGCCTTGGAGCTT 61.722 66.667 11.89 0.00 0.00 3.74
1362 2850 0.402121 GGTTGGTCTCCTCCAGCTTT 59.598 55.000 0.00 0.00 38.47 3.51
1475 2963 7.286316 CCCTGATTGCTAGTTAGAAAATCCAAT 59.714 37.037 0.00 0.00 31.92 3.16
1553 3041 7.039434 TGGACCATCAATTTGCAATTTAGTACA 60.039 33.333 0.00 3.66 0.00 2.90
1594 3114 8.554835 TGTGTGCTATTTGTTACAAGCTTATA 57.445 30.769 0.00 0.00 35.95 0.98
1595 3115 7.447374 TGTGTGCTATTTGTTACAAGCTTAT 57.553 32.000 0.00 0.00 35.95 1.73
1625 3229 6.391227 ACAAGATCAGTTGTTTGTTAAGGG 57.609 37.500 0.00 0.00 37.36 3.95
1640 3244 7.531857 TGCCCAAAAACTAATTACAAGATCA 57.468 32.000 0.00 0.00 0.00 2.92
1657 3261 7.395772 TCTTGAATACTCATTAACATGCCCAAA 59.604 33.333 0.00 0.00 0.00 3.28
1677 3281 6.479006 ACTTCACCATGATCTCATTCTTGAA 58.521 36.000 0.00 0.23 33.61 2.69
1744 3348 9.988815 CTAGCACCTTCTATCTGTTTGTATAAT 57.011 33.333 0.00 0.00 0.00 1.28
1752 3356 8.634444 CATAGTTACTAGCACCTTCTATCTGTT 58.366 37.037 0.00 0.00 0.00 3.16
1756 3360 8.167605 TGTCATAGTTACTAGCACCTTCTATC 57.832 38.462 0.00 0.00 0.00 2.08
1760 3364 5.520649 GCTTGTCATAGTTACTAGCACCTTC 59.479 44.000 0.00 0.00 42.72 3.46
2017 3621 5.010314 TCAGACTTATACAGAACAACACCGT 59.990 40.000 0.00 0.00 0.00 4.83
2120 3730 7.041635 ACATTCATCAAAACTGACATGACAA 57.958 32.000 0.00 0.00 0.00 3.18
2150 3760 4.947388 ACAAACAAGTAAGCTGGAAAGTGA 59.053 37.500 0.00 0.00 0.00 3.41
2153 3763 9.394477 GTATTAACAAACAAGTAAGCTGGAAAG 57.606 33.333 0.00 0.00 0.00 2.62
2219 3829 7.850193 AGATAACCCTTTACCATGTACGTTAA 58.150 34.615 0.00 0.00 0.00 2.01
2269 3879 6.266558 TGTTCTTTGGCCAGAAAGCTAATTTA 59.733 34.615 5.11 0.00 34.50 1.40
2287 3897 5.873164 ACTCAAACTACGTGACTTGTTCTTT 59.127 36.000 0.00 0.00 0.00 2.52
2380 3990 5.710613 TTGATCGCAAAAACAAGAAAACC 57.289 34.783 0.00 0.00 0.00 3.27
2381 3991 6.988329 TCTTTGATCGCAAAAACAAGAAAAC 58.012 32.000 0.00 0.00 42.96 2.43
2418 4028 8.731605 CGTGGTGTAGACATGATATTATACTCT 58.268 37.037 0.00 0.00 0.00 3.24
2436 4046 6.954487 ATATCTTCAGTACATCGTGGTGTA 57.046 37.500 0.00 0.00 33.62 2.90
2443 4053 8.317891 AGTCTCACTATATCTTCAGTACATCG 57.682 38.462 0.00 0.00 0.00 3.84
2478 4088 4.831107 AGTTCACTTTTTGCACAAACCAT 58.169 34.783 0.00 0.00 0.00 3.55
2594 4204 4.199432 CTGTAGGCATTCTTCAGTGAGT 57.801 45.455 0.00 0.00 36.51 3.41
2625 4235 5.278218 GGCTTAGAATTAGCAATCTGGAAGC 60.278 44.000 1.35 0.00 40.42 3.86
2660 4270 4.963276 TGCAGTTTGGTGCTATATGAAC 57.037 40.909 0.00 0.00 44.32 3.18
2665 4275 4.588899 AGTTGATGCAGTTTGGTGCTATA 58.411 39.130 0.00 0.00 44.32 1.31
2678 4288 7.105588 ACATGAATACTGACTTAGTTGATGCA 58.894 34.615 0.00 0.00 40.89 3.96
2782 4393 9.173021 CAAAGGTACATGTAATCTGTTCCATTA 57.827 33.333 7.25 0.00 36.74 1.90
2819 4430 8.703604 TTAACTTATCTCGAATTTGAGGTCAG 57.296 34.615 20.44 16.82 36.61 3.51
2916 4528 7.272978 GGATTACTGGTAGCTTGTTCATAAGA 58.727 38.462 0.00 0.00 0.00 2.10
2918 4530 6.354130 GGGATTACTGGTAGCTTGTTCATAA 58.646 40.000 0.00 0.00 0.00 1.90
2922 4534 3.054655 TGGGGATTACTGGTAGCTTGTTC 60.055 47.826 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.