Multiple sequence alignment - TraesCS2D01G103400

Loading Multiple Alignment...

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 TraesCS2D01G103400 chr2D 100.000 2576 0 0 1 2576 55765839 55763264 0.000000e+00 4758
1 TraesCS2D01G103400 chr2D 88.508 992 89 13 7 982 39002300 39001318 0.000000e+00 1177
2 TraesCS2D01G103400 chr2B 93.843 1949 96 15 7 1943 88436022 88434086 0.000000e+00 2913
3 TraesCS2D01G103400 chr2B 88.462 494 51 4 372 861 88437198 88436707 2.210000e-165 592
4 TraesCS2D01G103400 chr2B 88.013 317 35 3 2262 2576 88433797 88433482 3.130000e-99 372
5 TraesCS2D01G103400 chr2A 92.670 1337 34 25 781 2098 57176525 57175234 0.000000e+00 1868
6 TraesCS2D01G103400 chr2A 92.430 251 9 1 2326 2576 57174947 57174707 1.470000e-92 350
7 TraesCS2D01G103400 chr2A 82.215 298 36 9 10 298 57177738 57177449 9.210000e-60 241
8 TraesCS2D01G103400 chr2A 97.030 101 3 0 2091 2191 57175047 57174947 1.230000e-38 171
9 TraesCS2D01G103400 chr7A 83.465 508 79 5 1065 1568 430814576 430814070 3.880000e-128 468
10 TraesCS2D01G103400 chr7B 83.071 508 81 5 1065 1568 377135818 377135312 8.400000e-125 457
11 TraesCS2D01G103400 chr7D 82.908 509 80 7 1065 1568 382755291 382754785 3.910000e-123 451
12 TraesCS2D01G103400 chr4A 82.218 523 82 5 1057 1575 177617908 177617393 8.460000e-120 440
13 TraesCS2D01G103400 chr4D 81.731 520 84 5 1057 1572 302399156 302399668 8.520000e-115 424
14 TraesCS2D01G103400 chr4B 81.310 519 88 5 1057 1572 377374734 377375246 1.840000e-111 412


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 TraesCS2D01G103400 chr2D 55763264 55765839 2575 True 4758.000000 4758 100.00000 1 2576 1 chr2D.!!$R2 2575
1 TraesCS2D01G103400 chr2D 39001318 39002300 982 True 1177.000000 1177 88.50800 7 982 1 chr2D.!!$R1 975
2 TraesCS2D01G103400 chr2B 88433482 88437198 3716 True 1292.333333 2913 90.10600 7 2576 3 chr2B.!!$R1 2569
3 TraesCS2D01G103400 chr2A 57174707 57177738 3031 True 657.500000 1868 91.08625 10 2576 4 chr2A.!!$R1 2566
4 TraesCS2D01G103400 chr7A 430814070 430814576 506 True 468.000000 468 83.46500 1065 1568 1 chr7A.!!$R1 503
5 TraesCS2D01G103400 chr7B 377135312 377135818 506 True 457.000000 457 83.07100 1065 1568 1 chr7B.!!$R1 503
6 TraesCS2D01G103400 chr7D 382754785 382755291 506 True 451.000000 451 82.90800 1065 1568 1 chr7D.!!$R1 503
7 TraesCS2D01G103400 chr4A 177617393 177617908 515 True 440.000000 440 82.21800 1057 1575 1 chr4A.!!$R1 518
8 TraesCS2D01G103400 chr4D 302399156 302399668 512 False 424.000000 424 81.73100 1057 1572 1 chr4D.!!$F1 515
9 TraesCS2D01G103400 chr4B 377374734 377375246 512 False 412.000000 412 81.31000 1057 1572 1 chr4B.!!$F1 515

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
196 1370 0.767375 ATGAGGCCAGCGTCCATTAT 59.233 50.0 5.01 0.0 0.00 1.28 F
459 2294 1.346062 ACAGTCAGTGAGGCAGACAT 58.654 50.0 0.00 0.0 36.25 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 3400 0.242825 TTGAACTCGCCGAAGTCGAT 59.757 50.0 1.43 0.0 37.2 3.59 R
2308 4537 0.036388 CGGAGGGCAGAAGCTACAAA 60.036 55.0 0.00 0.0 41.7 2.83 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
166 1340 8.575736 TTTATATACCTTTTGGAGATGGAGGA 57.424 34.615 0.00 0.00 44.07 3.71
189 1363 4.101448 GGGACATGAGGCCAGCGT 62.101 66.667 5.01 0.00 0.00 5.07
196 1370 0.767375 ATGAGGCCAGCGTCCATTAT 59.233 50.000 5.01 0.00 0.00 1.28
203 1384 2.884639 GCCAGCGTCCATTATACCATTT 59.115 45.455 0.00 0.00 0.00 2.32
241 1422 2.748058 GAACAAAGCAGAGGGGGCGA 62.748 60.000 0.00 0.00 36.08 5.54
242 1423 2.142292 AACAAAGCAGAGGGGGCGAT 62.142 55.000 0.00 0.00 36.08 4.58
299 1480 2.100749 GCCCATTCCCATCCTTAAAACG 59.899 50.000 0.00 0.00 0.00 3.60
390 2189 4.217550 GGATCTAGCTGACACATAGACCTC 59.782 50.000 0.00 0.00 0.00 3.85
392 2191 5.632034 TCTAGCTGACACATAGACCTCTA 57.368 43.478 0.00 0.00 0.00 2.43
425 2251 9.884465 GAAAGAGGGAATATTTGATATGAAACG 57.116 33.333 0.00 0.00 0.00 3.60
459 2294 1.346062 ACAGTCAGTGAGGCAGACAT 58.654 50.000 0.00 0.00 36.25 3.06
460 2295 1.696336 ACAGTCAGTGAGGCAGACATT 59.304 47.619 0.00 0.00 36.25 2.71
500 2335 6.773638 ACCAGAACATCACTCTCTTAACATT 58.226 36.000 0.00 0.00 0.00 2.71
505 2340 5.794894 ACATCACTCTCTTAACATTCCGTT 58.205 37.500 0.00 0.00 41.91 4.44
546 2383 9.627395 TCTAAAACTTCAAAACATCGTTTTCAA 57.373 25.926 1.96 0.00 38.36 2.69
595 2440 6.421377 TGTTGGTTTCGACATGATATTCTG 57.579 37.500 0.00 0.00 32.62 3.02
626 2471 3.329743 CAAGGTATGAATGCGAGCTTG 57.670 47.619 0.00 0.00 40.92 4.01
745 2593 2.547826 GGGCAACATACCTAACTCGAC 58.452 52.381 0.00 0.00 39.74 4.20
847 2706 2.169832 ATGGTAGGCGATGGATTTCG 57.830 50.000 0.00 0.00 41.99 3.46
998 2861 1.466950 CGTCCGAAAATAAGCAAGGCA 59.533 47.619 0.00 0.00 0.00 4.75
1586 3458 4.362932 TCAACGTCTGATCTGATCTCAC 57.637 45.455 17.82 12.66 0.00 3.51
1587 3459 3.104470 CAACGTCTGATCTGATCTCACG 58.896 50.000 26.32 26.32 39.40 4.35
1588 3460 1.064803 ACGTCTGATCTGATCTCACGC 59.935 52.381 27.16 11.99 38.05 5.34
1589 3461 1.752753 GTCTGATCTGATCTCACGCG 58.247 55.000 17.82 3.53 0.00 6.01
1590 3462 0.029967 TCTGATCTGATCTCACGCGC 59.970 55.000 17.82 0.00 0.00 6.86
1591 3463 1.267449 CTGATCTGATCTCACGCGCG 61.267 60.000 30.96 30.96 0.00 6.86
1592 3464 2.643644 GATCTGATCTCACGCGCGC 61.644 63.158 32.58 23.91 0.00 6.86
1615 3487 0.316278 CGTCTTCGCACGATCGATCT 60.316 55.000 24.34 7.60 42.69 2.75
1621 3509 1.065928 GCACGATCGATCTTCGGGT 59.934 57.895 24.34 10.13 41.96 5.28
1635 3523 6.959311 CGATCTTCGGGTTTTTACAATTACAG 59.041 38.462 0.00 0.00 36.00 2.74
1711 3601 6.431234 TGAAGAACAGCCCTTTCTTATCTTTC 59.569 38.462 5.11 0.00 42.21 2.62
1859 3750 0.664761 CAGGGCCGTTGAGCATTATG 59.335 55.000 0.00 0.00 0.00 1.90
1899 3790 3.759086 TGTGGTGCTGTAAACTTTTGTCA 59.241 39.130 0.00 0.00 0.00 3.58
1949 3840 0.027979 TATACGCACGTACACTCGCC 59.972 55.000 4.84 0.00 33.01 5.54
1989 3883 2.832733 ACACCCTACTAAGAGCACCTTC 59.167 50.000 0.00 0.00 36.34 3.46
1991 3885 3.260884 CACCCTACTAAGAGCACCTTCAA 59.739 47.826 0.00 0.00 36.34 2.69
1992 3886 3.908103 ACCCTACTAAGAGCACCTTCAAA 59.092 43.478 0.00 0.00 36.34 2.69
2029 3924 8.225603 ACACACATCTTAAGATTGACAAAGTT 57.774 30.769 23.11 6.69 31.21 2.66
2080 3979 5.607477 ACGTCTCCTCTAAACAAACATTGA 58.393 37.500 0.00 0.00 0.00 2.57
2184 4277 2.627945 CTAACCATTTGGCTACGCTCA 58.372 47.619 0.00 0.00 39.32 4.26
2191 4420 3.827898 GGCTACGCTCAGGTCGCT 61.828 66.667 0.00 0.00 0.00 4.93
2192 4421 2.278271 GCTACGCTCAGGTCGCTC 60.278 66.667 0.00 0.00 0.00 5.03
2193 4422 2.766400 GCTACGCTCAGGTCGCTCT 61.766 63.158 0.00 0.00 0.00 4.09
2194 4423 1.803943 CTACGCTCAGGTCGCTCTT 59.196 57.895 0.00 0.00 0.00 2.85
2195 4424 0.524392 CTACGCTCAGGTCGCTCTTG 60.524 60.000 0.00 0.00 0.00 3.02
2196 4425 1.934220 TACGCTCAGGTCGCTCTTGG 61.934 60.000 0.00 0.00 0.00 3.61
2197 4426 2.973899 GCTCAGGTCGCTCTTGGA 59.026 61.111 0.00 0.00 0.00 3.53
2198 4427 1.446966 GCTCAGGTCGCTCTTGGAC 60.447 63.158 0.00 0.00 0.00 4.02
2199 4428 1.967535 CTCAGGTCGCTCTTGGACA 59.032 57.895 0.00 0.00 36.12 4.02
2200 4429 0.534412 CTCAGGTCGCTCTTGGACAT 59.466 55.000 0.00 0.00 36.12 3.06
2201 4430 0.976641 TCAGGTCGCTCTTGGACATT 59.023 50.000 0.00 0.00 36.12 2.71
2202 4431 1.347707 TCAGGTCGCTCTTGGACATTT 59.652 47.619 0.00 0.00 36.12 2.32
2203 4432 2.565391 TCAGGTCGCTCTTGGACATTTA 59.435 45.455 0.00 0.00 36.12 1.40
2204 4433 3.197766 TCAGGTCGCTCTTGGACATTTAT 59.802 43.478 0.00 0.00 36.12 1.40
2205 4434 3.557595 CAGGTCGCTCTTGGACATTTATC 59.442 47.826 0.00 0.00 36.12 1.75
2206 4435 3.197766 AGGTCGCTCTTGGACATTTATCA 59.802 43.478 0.00 0.00 36.12 2.15
2207 4436 3.557595 GGTCGCTCTTGGACATTTATCAG 59.442 47.826 0.00 0.00 36.12 2.90
2208 4437 3.557595 GTCGCTCTTGGACATTTATCAGG 59.442 47.826 0.00 0.00 34.56 3.86
2209 4438 3.197766 TCGCTCTTGGACATTTATCAGGT 59.802 43.478 0.00 0.00 0.00 4.00
2210 4439 3.557595 CGCTCTTGGACATTTATCAGGTC 59.442 47.826 0.00 0.00 0.00 3.85
2220 4449 6.875972 ACATTTATCAGGTCCAGTAGAAGT 57.124 37.500 0.00 0.00 0.00 3.01
2221 4450 7.259088 ACATTTATCAGGTCCAGTAGAAGTT 57.741 36.000 0.00 0.00 0.00 2.66
2222 4451 7.331791 ACATTTATCAGGTCCAGTAGAAGTTC 58.668 38.462 0.00 0.00 0.00 3.01
2223 4452 6.928348 TTTATCAGGTCCAGTAGAAGTTCA 57.072 37.500 5.50 0.00 0.00 3.18
2224 4453 6.928348 TTATCAGGTCCAGTAGAAGTTCAA 57.072 37.500 5.50 0.00 0.00 2.69
2225 4454 5.825593 ATCAGGTCCAGTAGAAGTTCAAA 57.174 39.130 5.50 0.00 0.00 2.69
2226 4455 5.623956 TCAGGTCCAGTAGAAGTTCAAAA 57.376 39.130 5.50 0.00 0.00 2.44
2227 4456 5.996644 TCAGGTCCAGTAGAAGTTCAAAAA 58.003 37.500 5.50 0.00 0.00 1.94
2251 4480 6.757897 AAATGATGAGAAAATAAGACCGCA 57.242 33.333 0.00 0.00 0.00 5.69
2252 4481 5.741388 ATGATGAGAAAATAAGACCGCAC 57.259 39.130 0.00 0.00 0.00 5.34
2253 4482 3.616821 TGATGAGAAAATAAGACCGCACG 59.383 43.478 0.00 0.00 0.00 5.34
2254 4483 3.306917 TGAGAAAATAAGACCGCACGA 57.693 42.857 0.00 0.00 0.00 4.35
2255 4484 2.991190 TGAGAAAATAAGACCGCACGAC 59.009 45.455 0.00 0.00 0.00 4.34
2256 4485 3.251571 GAGAAAATAAGACCGCACGACT 58.748 45.455 0.00 0.00 0.00 4.18
2257 4486 2.993899 AGAAAATAAGACCGCACGACTG 59.006 45.455 0.00 0.00 0.00 3.51
2258 4487 2.736144 AAATAAGACCGCACGACTGA 57.264 45.000 0.00 0.00 0.00 3.41
2259 4488 2.279582 AATAAGACCGCACGACTGAG 57.720 50.000 0.00 0.00 0.00 3.35
2260 4489 1.174783 ATAAGACCGCACGACTGAGT 58.825 50.000 0.00 0.00 0.00 3.41
2261 4490 0.240145 TAAGACCGCACGACTGAGTG 59.760 55.000 0.00 4.25 44.47 3.51
2262 4491 1.452953 AAGACCGCACGACTGAGTGA 61.453 55.000 10.98 0.00 44.43 3.41
2263 4492 1.213013 GACCGCACGACTGAGTGAT 59.787 57.895 10.98 0.00 44.43 3.06
2264 4493 1.073216 GACCGCACGACTGAGTGATG 61.073 60.000 10.98 0.00 44.43 3.07
2265 4494 1.212751 CCGCACGACTGAGTGATGA 59.787 57.895 10.98 0.00 44.43 2.92
2266 4495 1.073216 CCGCACGACTGAGTGATGAC 61.073 60.000 10.98 0.00 44.43 3.06
2267 4496 1.073216 CGCACGACTGAGTGATGACC 61.073 60.000 10.98 0.00 44.43 4.02
2268 4497 0.244994 GCACGACTGAGTGATGACCT 59.755 55.000 10.98 0.00 44.43 3.85
2269 4498 1.988063 CACGACTGAGTGATGACCTG 58.012 55.000 0.00 0.00 44.43 4.00
2270 4499 1.541588 CACGACTGAGTGATGACCTGA 59.458 52.381 0.00 0.00 44.43 3.86
2271 4500 2.165234 CACGACTGAGTGATGACCTGAT 59.835 50.000 0.00 0.00 44.43 2.90
2272 4501 3.378427 CACGACTGAGTGATGACCTGATA 59.622 47.826 0.00 0.00 44.43 2.15
2273 4502 3.378742 ACGACTGAGTGATGACCTGATAC 59.621 47.826 0.00 0.00 0.00 2.24
2274 4503 3.378427 CGACTGAGTGATGACCTGATACA 59.622 47.826 0.00 0.00 0.00 2.29
2275 4504 4.497173 CGACTGAGTGATGACCTGATACAG 60.497 50.000 0.00 0.00 0.00 2.74
2306 4535 8.145316 TCGAGGAAATAATAAATTACAACCCG 57.855 34.615 0.00 0.00 0.00 5.28
2307 4536 7.227116 TCGAGGAAATAATAAATTACAACCCGG 59.773 37.037 0.00 0.00 0.00 5.73
2308 4537 7.012610 CGAGGAAATAATAAATTACAACCCGGT 59.987 37.037 0.00 0.00 0.00 5.28
2309 4538 8.598202 AGGAAATAATAAATTACAACCCGGTT 57.402 30.769 0.00 0.00 0.00 4.44
2310 4539 9.038072 AGGAAATAATAAATTACAACCCGGTTT 57.962 29.630 0.00 0.00 0.00 3.27
2311 4540 9.089601 GGAAATAATAAATTACAACCCGGTTTG 57.910 33.333 10.60 10.60 0.00 2.93
2312 4541 9.642327 GAAATAATAAATTACAACCCGGTTTGT 57.358 29.630 21.74 21.74 42.46 2.83
2315 4544 4.508461 AAATTACAACCCGGTTTGTAGC 57.492 40.909 21.81 0.00 41.75 3.58
2316 4545 2.934886 TTACAACCCGGTTTGTAGCT 57.065 45.000 21.81 1.47 41.75 3.32
2317 4546 2.934886 TACAACCCGGTTTGTAGCTT 57.065 45.000 19.53 0.00 40.29 3.74
2318 4547 1.601166 ACAACCCGGTTTGTAGCTTC 58.399 50.000 16.64 0.00 37.96 3.86
2319 4548 1.142262 ACAACCCGGTTTGTAGCTTCT 59.858 47.619 16.64 0.00 37.96 2.85
2320 4549 1.535462 CAACCCGGTTTGTAGCTTCTG 59.465 52.381 3.08 0.00 0.00 3.02
2321 4550 0.605589 ACCCGGTTTGTAGCTTCTGC 60.606 55.000 0.00 0.00 40.05 4.26
2322 4551 1.305930 CCCGGTTTGTAGCTTCTGCC 61.306 60.000 0.00 0.00 40.80 4.85
2323 4552 1.305930 CCGGTTTGTAGCTTCTGCCC 61.306 60.000 0.00 0.00 40.80 5.36
2324 4553 0.321653 CGGTTTGTAGCTTCTGCCCT 60.322 55.000 0.00 0.00 40.80 5.19
2325 4554 1.454201 GGTTTGTAGCTTCTGCCCTC 58.546 55.000 0.00 0.00 40.80 4.30
2347 4576 6.255596 TCCGACGATAGAAGATATTTCAGG 57.744 41.667 0.00 0.00 41.38 3.86
2367 4596 7.865706 TCAGGAAATTAGCAAAATAGGACTC 57.134 36.000 0.00 0.00 0.00 3.36
2369 4598 6.538742 CAGGAAATTAGCAAAATAGGACTCGA 59.461 38.462 0.00 0.00 0.00 4.04
2398 4627 1.589196 GCCCGATCACTAGCACGAC 60.589 63.158 0.00 0.00 0.00 4.34
2403 4632 1.799181 CGATCACTAGCACGACCCAAG 60.799 57.143 0.00 0.00 0.00 3.61
2515 4744 1.186267 ACGCCCCGAAGAAGAAGTCT 61.186 55.000 0.00 0.00 38.69 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.542497 TGTATCCATTTAGTGTTGTAGTTGAC 57.458 34.615 0.00 0.00 0.00 3.18
97 1271 7.707774 ATGTAATGTTTGCCAAAGTTTGTAC 57.292 32.000 14.36 8.00 0.00 2.90
156 1330 3.850752 TGTCCCTATTCTCCTCCATCTC 58.149 50.000 0.00 0.00 0.00 2.75
166 1340 2.053244 CTGGCCTCATGTCCCTATTCT 58.947 52.381 3.32 0.00 0.00 2.40
189 1363 3.137544 AGTCGGCCAAATGGTATAATGGA 59.862 43.478 2.24 0.00 37.57 3.41
196 1370 2.799126 ATGAAGTCGGCCAAATGGTA 57.201 45.000 2.24 0.00 37.57 3.25
203 1384 1.754380 CGGGGATATGAAGTCGGCCA 61.754 60.000 2.24 0.00 0.00 5.36
241 1422 2.035632 GGACCTGCTACTGCTACTCAT 58.964 52.381 0.00 0.00 40.48 2.90
242 1423 1.475403 GGACCTGCTACTGCTACTCA 58.525 55.000 0.00 0.00 40.48 3.41
276 1457 0.184933 TTAAGGATGGGAATGGGCCG 59.815 55.000 0.00 0.00 0.00 6.13
299 1480 0.793861 TGTCAACCTAACGAATGCGC 59.206 50.000 0.00 0.00 42.48 6.09
367 2166 4.148838 AGGTCTATGTGTCAGCTAGATCC 58.851 47.826 0.00 0.00 0.00 3.36
413 2239 7.096551 TCATGTGTCTTCTCGTTTCATATCAA 58.903 34.615 0.00 0.00 0.00 2.57
421 2247 4.876107 ACTGTTTCATGTGTCTTCTCGTTT 59.124 37.500 0.00 0.00 0.00 3.60
425 2251 5.050499 CACTGACTGTTTCATGTGTCTTCTC 60.050 44.000 0.00 0.00 32.76 2.87
459 2294 4.531854 TCTGGTTCACTGATTGTTTCCAA 58.468 39.130 0.00 0.00 34.45 3.53
460 2295 4.163441 TCTGGTTCACTGATTGTTTCCA 57.837 40.909 0.00 0.00 0.00 3.53
468 2303 4.630644 AGTGATGTTCTGGTTCACTGAT 57.369 40.909 4.15 0.00 46.19 2.90
476 2311 5.808366 TGTTAAGAGAGTGATGTTCTGGT 57.192 39.130 0.00 0.00 0.00 4.00
595 2440 1.078426 ATACCTTGTGTCTGCCGGC 60.078 57.895 22.73 22.73 0.00 6.13
606 2451 2.540361 GCAAGCTCGCATTCATACCTTG 60.540 50.000 0.00 0.00 33.32 3.61
626 2471 0.669625 GTGAACCTCTGGTACCGTGC 60.670 60.000 7.57 0.00 33.12 5.34
632 2480 3.385433 TCTTCGTTTGTGAACCTCTGGTA 59.615 43.478 0.00 0.00 33.12 3.25
713 2561 0.474854 TGTTGCCCCTAACCTGAGGA 60.475 55.000 4.99 0.00 39.15 3.71
745 2593 1.951130 CACGCTGGGAATCGATCGG 60.951 63.158 16.41 0.00 0.00 4.18
847 2706 0.523519 CCTTCCTTTTTCTCTGCCGC 59.476 55.000 0.00 0.00 0.00 6.53
998 2861 3.211963 GATGCTCGCCGGCCATTT 61.212 61.111 23.46 1.34 0.00 2.32
1528 3400 0.242825 TTGAACTCGCCGAAGTCGAT 59.757 50.000 1.43 0.00 37.20 3.59
1594 3466 0.654160 ATCGATCGTGCGAAGACGTA 59.346 50.000 15.94 0.00 44.22 3.57
1595 3467 0.589229 GATCGATCGTGCGAAGACGT 60.589 55.000 15.94 0.00 44.22 4.34
1596 3468 0.316278 AGATCGATCGTGCGAAGACG 60.316 55.000 19.33 5.75 44.22 4.18
1597 3469 1.776333 GAAGATCGATCGTGCGAAGAC 59.224 52.381 18.77 0.00 44.22 3.01
1598 3470 1.594760 CGAAGATCGATCGTGCGAAGA 60.595 52.381 18.77 2.21 43.74 2.87
1599 3471 0.767108 CGAAGATCGATCGTGCGAAG 59.233 55.000 18.77 4.43 43.74 3.79
1600 3472 0.591488 CCGAAGATCGATCGTGCGAA 60.591 55.000 27.14 0.00 43.74 4.70
1601 3473 1.010013 CCGAAGATCGATCGTGCGA 60.010 57.895 27.14 5.01 43.74 5.10
1615 3487 6.939132 TGTCTGTAATTGTAAAAACCCGAA 57.061 33.333 0.00 0.00 0.00 4.30
1621 3509 6.644592 GCATGGCTTGTCTGTAATTGTAAAAA 59.355 34.615 2.12 0.00 0.00 1.94
1635 3523 0.594028 CGATGCATGCATGGCTTGTC 60.594 55.000 36.73 20.18 36.70 3.18
1736 3626 2.089980 AGAGGTTGCATTGCATCTGAC 58.910 47.619 12.95 7.40 38.76 3.51
1859 3750 5.914635 CACCACATGATTAGACACACAAAAC 59.085 40.000 0.00 0.00 0.00 2.43
1949 3840 2.419673 TGTGTGTACGTACGTCCATAGG 59.580 50.000 26.53 0.00 0.00 2.57
1989 3883 0.956410 TGTGTCGGCCCGGTAATTTG 60.956 55.000 1.90 0.00 0.00 2.32
1991 3885 1.376295 GTGTGTCGGCCCGGTAATT 60.376 57.895 1.90 0.00 0.00 1.40
1992 3886 1.906105 ATGTGTGTCGGCCCGGTAAT 61.906 55.000 1.90 0.00 0.00 1.89
2029 3924 0.824109 ACTAAGAGGCGCATGTGCTA 59.176 50.000 28.86 13.57 39.32 3.49
2107 4200 0.385029 TTGGCACTTGTGCACACATC 59.615 50.000 21.56 8.95 41.52 3.06
2184 4277 3.197766 TGATAAATGTCCAAGAGCGACCT 59.802 43.478 0.00 0.00 0.00 3.85
2196 4425 6.879400 ACTTCTACTGGACCTGATAAATGTC 58.121 40.000 5.22 0.00 0.00 3.06
2197 4426 6.875972 ACTTCTACTGGACCTGATAAATGT 57.124 37.500 5.22 0.00 0.00 2.71
2198 4427 7.331026 TGAACTTCTACTGGACCTGATAAATG 58.669 38.462 5.22 0.00 0.00 2.32
2199 4428 7.496346 TGAACTTCTACTGGACCTGATAAAT 57.504 36.000 5.22 0.00 0.00 1.40
2200 4429 6.928348 TGAACTTCTACTGGACCTGATAAA 57.072 37.500 5.22 0.00 0.00 1.40
2201 4430 6.928348 TTGAACTTCTACTGGACCTGATAA 57.072 37.500 5.22 0.00 0.00 1.75
2202 4431 6.928348 TTTGAACTTCTACTGGACCTGATA 57.072 37.500 5.22 0.00 0.00 2.15
2203 4432 5.825593 TTTGAACTTCTACTGGACCTGAT 57.174 39.130 5.22 0.00 0.00 2.90
2204 4433 5.623956 TTTTGAACTTCTACTGGACCTGA 57.376 39.130 5.22 0.00 0.00 3.86
2226 4455 7.542130 GTGCGGTCTTATTTTCTCATCATTTTT 59.458 33.333 0.00 0.00 0.00 1.94
2227 4456 7.029563 GTGCGGTCTTATTTTCTCATCATTTT 58.970 34.615 0.00 0.00 0.00 1.82
2228 4457 6.555315 GTGCGGTCTTATTTTCTCATCATTT 58.445 36.000 0.00 0.00 0.00 2.32
2229 4458 5.220662 CGTGCGGTCTTATTTTCTCATCATT 60.221 40.000 0.00 0.00 0.00 2.57
2230 4459 4.271049 CGTGCGGTCTTATTTTCTCATCAT 59.729 41.667 0.00 0.00 0.00 2.45
2231 4460 3.616821 CGTGCGGTCTTATTTTCTCATCA 59.383 43.478 0.00 0.00 0.00 3.07
2232 4461 3.863424 TCGTGCGGTCTTATTTTCTCATC 59.137 43.478 0.00 0.00 0.00 2.92
2233 4462 3.617263 GTCGTGCGGTCTTATTTTCTCAT 59.383 43.478 0.00 0.00 0.00 2.90
2234 4463 2.991190 GTCGTGCGGTCTTATTTTCTCA 59.009 45.455 0.00 0.00 0.00 3.27
2235 4464 3.060895 CAGTCGTGCGGTCTTATTTTCTC 59.939 47.826 0.00 0.00 0.00 2.87
2236 4465 2.993899 CAGTCGTGCGGTCTTATTTTCT 59.006 45.455 0.00 0.00 0.00 2.52
2237 4466 2.991190 TCAGTCGTGCGGTCTTATTTTC 59.009 45.455 0.00 0.00 0.00 2.29
2238 4467 2.993899 CTCAGTCGTGCGGTCTTATTTT 59.006 45.455 0.00 0.00 0.00 1.82
2239 4468 2.029290 ACTCAGTCGTGCGGTCTTATTT 60.029 45.455 0.00 0.00 0.00 1.40
2240 4469 1.544691 ACTCAGTCGTGCGGTCTTATT 59.455 47.619 0.00 0.00 0.00 1.40
2241 4470 1.135373 CACTCAGTCGTGCGGTCTTAT 60.135 52.381 0.00 0.00 0.00 1.73
2242 4471 0.240145 CACTCAGTCGTGCGGTCTTA 59.760 55.000 0.00 0.00 0.00 2.10
2243 4472 1.007271 CACTCAGTCGTGCGGTCTT 60.007 57.895 0.00 0.00 0.00 3.01
2244 4473 1.244697 ATCACTCAGTCGTGCGGTCT 61.245 55.000 0.00 0.00 34.92 3.85
2245 4474 1.073216 CATCACTCAGTCGTGCGGTC 61.073 60.000 0.00 0.00 34.92 4.79
2246 4475 1.080501 CATCACTCAGTCGTGCGGT 60.081 57.895 0.00 0.00 34.92 5.68
2247 4476 1.073216 GTCATCACTCAGTCGTGCGG 61.073 60.000 0.00 0.00 34.92 5.69
2248 4477 1.073216 GGTCATCACTCAGTCGTGCG 61.073 60.000 0.00 0.00 34.92 5.34
2249 4478 0.244994 AGGTCATCACTCAGTCGTGC 59.755 55.000 0.00 0.00 34.92 5.34
2250 4479 1.541588 TCAGGTCATCACTCAGTCGTG 59.458 52.381 0.00 0.00 36.25 4.35
2251 4480 1.911057 TCAGGTCATCACTCAGTCGT 58.089 50.000 0.00 0.00 0.00 4.34
2252 4481 3.378427 TGTATCAGGTCATCACTCAGTCG 59.622 47.826 0.00 0.00 0.00 4.18
2253 4482 4.202101 CCTGTATCAGGTCATCACTCAGTC 60.202 50.000 7.55 0.00 45.82 3.51
2254 4483 3.703556 CCTGTATCAGGTCATCACTCAGT 59.296 47.826 7.55 0.00 45.82 3.41
2255 4484 4.319139 CCTGTATCAGGTCATCACTCAG 57.681 50.000 7.55 0.00 45.82 3.35
2280 4509 8.614346 CGGGTTGTAATTTATTATTTCCTCGAA 58.386 33.333 0.00 0.00 0.00 3.71
2281 4510 7.227116 CCGGGTTGTAATTTATTATTTCCTCGA 59.773 37.037 0.00 0.00 0.00 4.04
2282 4511 7.012610 ACCGGGTTGTAATTTATTATTTCCTCG 59.987 37.037 6.32 0.00 0.00 4.63
2283 4512 8.229253 ACCGGGTTGTAATTTATTATTTCCTC 57.771 34.615 6.32 0.00 0.00 3.71
2284 4513 8.598202 AACCGGGTTGTAATTTATTATTTCCT 57.402 30.769 12.53 0.00 0.00 3.36
2285 4514 9.089601 CAAACCGGGTTGTAATTTATTATTTCC 57.910 33.333 24.60 0.00 0.00 3.13
2286 4515 9.642327 ACAAACCGGGTTGTAATTTATTATTTC 57.358 29.630 35.99 0.00 39.94 2.17
2289 4518 8.407832 GCTACAAACCGGGTTGTAATTTATTAT 58.592 33.333 37.28 16.54 42.03 1.28
2290 4519 7.611079 AGCTACAAACCGGGTTGTAATTTATTA 59.389 33.333 37.28 20.48 42.03 0.98
2291 4520 6.434965 AGCTACAAACCGGGTTGTAATTTATT 59.565 34.615 37.28 20.17 42.03 1.40
2292 4521 5.947566 AGCTACAAACCGGGTTGTAATTTAT 59.052 36.000 37.28 22.02 42.03 1.40
2293 4522 5.315348 AGCTACAAACCGGGTTGTAATTTA 58.685 37.500 37.28 22.50 42.03 1.40
2294 4523 4.146564 AGCTACAAACCGGGTTGTAATTT 58.853 39.130 37.28 25.19 42.03 1.82
2295 4524 3.758425 AGCTACAAACCGGGTTGTAATT 58.242 40.909 37.28 27.31 42.03 1.40
2296 4525 3.428413 AGCTACAAACCGGGTTGTAAT 57.572 42.857 37.28 28.06 42.03 1.89
2297 4526 2.934886 AGCTACAAACCGGGTTGTAA 57.065 45.000 37.28 24.24 42.03 2.41
2298 4527 2.369532 AGAAGCTACAAACCGGGTTGTA 59.630 45.455 36.24 36.24 41.84 2.41
2299 4528 1.142262 AGAAGCTACAAACCGGGTTGT 59.858 47.619 37.91 37.91 43.95 3.32
2300 4529 1.535462 CAGAAGCTACAAACCGGGTTG 59.465 52.381 30.58 30.58 34.52 3.77
2301 4530 1.892209 CAGAAGCTACAAACCGGGTT 58.108 50.000 6.59 6.59 0.00 4.11
2302 4531 0.605589 GCAGAAGCTACAAACCGGGT 60.606 55.000 6.32 0.00 37.91 5.28
2303 4532 1.305930 GGCAGAAGCTACAAACCGGG 61.306 60.000 6.32 0.00 41.70 5.73
2304 4533 1.305930 GGGCAGAAGCTACAAACCGG 61.306 60.000 0.00 0.00 41.70 5.28
2305 4534 0.321653 AGGGCAGAAGCTACAAACCG 60.322 55.000 0.00 0.00 41.70 4.44
2306 4535 1.454201 GAGGGCAGAAGCTACAAACC 58.546 55.000 0.00 0.00 41.70 3.27
2307 4536 1.454201 GGAGGGCAGAAGCTACAAAC 58.546 55.000 0.00 0.00 41.70 2.93
2308 4537 0.036388 CGGAGGGCAGAAGCTACAAA 60.036 55.000 0.00 0.00 41.70 2.83
2309 4538 0.902984 TCGGAGGGCAGAAGCTACAA 60.903 55.000 0.00 0.00 41.70 2.41
2310 4539 1.304962 TCGGAGGGCAGAAGCTACA 60.305 57.895 0.00 0.00 41.70 2.74
2311 4540 1.142097 GTCGGAGGGCAGAAGCTAC 59.858 63.158 0.00 0.00 41.70 3.58
2312 4541 2.415608 CGTCGGAGGGCAGAAGCTA 61.416 63.158 0.00 0.00 41.70 3.32
2313 4542 3.764466 CGTCGGAGGGCAGAAGCT 61.764 66.667 0.00 0.00 41.70 3.74
2314 4543 1.735376 TATCGTCGGAGGGCAGAAGC 61.735 60.000 0.00 0.00 41.10 3.86
2315 4544 0.312416 CTATCGTCGGAGGGCAGAAG 59.688 60.000 0.00 0.00 0.00 2.85
2316 4545 0.106868 TCTATCGTCGGAGGGCAGAA 60.107 55.000 0.00 0.00 0.00 3.02
2317 4546 0.106868 TTCTATCGTCGGAGGGCAGA 60.107 55.000 0.00 0.00 0.00 4.26
2318 4547 0.312416 CTTCTATCGTCGGAGGGCAG 59.688 60.000 0.00 0.00 0.00 4.85
2319 4548 0.106868 TCTTCTATCGTCGGAGGGCA 60.107 55.000 0.00 0.00 0.00 5.36
2320 4549 1.249407 ATCTTCTATCGTCGGAGGGC 58.751 55.000 0.00 0.00 0.00 5.19
2321 4550 5.183331 TGAAATATCTTCTATCGTCGGAGGG 59.817 44.000 0.00 0.00 0.00 4.30
2322 4551 6.255596 TGAAATATCTTCTATCGTCGGAGG 57.744 41.667 0.00 0.00 0.00 4.30
2323 4552 6.149640 TCCTGAAATATCTTCTATCGTCGGAG 59.850 42.308 0.00 0.00 0.00 4.63
2324 4553 6.002082 TCCTGAAATATCTTCTATCGTCGGA 58.998 40.000 0.00 0.00 0.00 4.55
2325 4554 6.255596 TCCTGAAATATCTTCTATCGTCGG 57.744 41.667 0.00 0.00 0.00 4.79
2347 4576 8.831550 AGAATCGAGTCCTATTTTGCTAATTTC 58.168 33.333 9.63 0.00 0.00 2.17
2367 4596 3.921021 GTGATCGGGCTATGTAAGAATCG 59.079 47.826 0.00 0.00 0.00 3.34
2369 4598 5.336849 GCTAGTGATCGGGCTATGTAAGAAT 60.337 44.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.