Multiple sequence alignment - TraesCS4A01G161600

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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 TraesCS4A01G161600 chr4A 100.000 3393 0 0 1 3393 350242367 350245759 0 6266
1 TraesCS4A01G161600 chr2D 96.801 2438 77 1 1 2437 200934935 200937372 0 4069
2 TraesCS4A01G161600 chr2D 96.102 2437 95 0 1 2437 604416906 604419342 0 3975
3 TraesCS4A01G161600 chr2D 97.170 848 22 2 2547 3393 200937759 200938605 0 1432
4 TraesCS4A01G161600 chr1A 96.678 2438 75 2 1 2437 94765603 94763171 0 4048
5 TraesCS4A01G161600 chr5D 96.637 2438 80 2 1 2437 562925174 562927610 0 4047
6 TraesCS4A01G161600 chr1D 96.349 2438 88 1 1 2437 185786577 185784140 0 4008
7 TraesCS4A01G161600 chr7A 96.308 2438 89 1 1 2437 211308107 211310544 0 4002
8 TraesCS4A01G161600 chr7A 96.308 2438 89 1 1 2437 563544632 563547069 0 4002
9 TraesCS4A01G161600 chr3D 95.939 2438 93 3 1 2437 399840807 399838375 0 3949
10 TraesCS4A01G161600 chr7D 95.897 2437 99 1 1 2436 307118245 307115809 0 3945
11 TraesCS4A01G161600 chr7D 97.524 848 19 2 2547 3393 382100066 382099220 0 1448
12 TraesCS4A01G161600 chr5A 97.524 848 19 2 2547 3393 16536045 16535199 0 1448
13 TraesCS4A01G161600 chr5A 97.406 848 19 3 2547 3393 420177650 420176805 0 1441
14 TraesCS4A01G161600 chrUn 97.406 848 20 2 2547 3393 189425445 189426291 0 1443
15 TraesCS4A01G161600 chrUn 97.406 848 20 2 2547 3393 222876016 222875170 0 1443
16 TraesCS4A01G161600 chrUn 97.288 848 21 2 2547 3393 182446361 182445515 0 1437
17 TraesCS4A01G161600 chr7B 97.285 847 21 2 2547 3392 742957274 742958119 0 1435
18 TraesCS4A01G161600 chr4D 97.052 848 23 2 2547 3393 123467151 123466305 0 1426


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 TraesCS4A01G161600 chr4A 350242367 350245759 3392 False 6266.0 6266 100.0000 1 3393 1 chr4A.!!$F1 3392
1 TraesCS4A01G161600 chr2D 604416906 604419342 2436 False 3975.0 3975 96.1020 1 2437 1 chr2D.!!$F1 2436
2 TraesCS4A01G161600 chr2D 200934935 200938605 3670 False 2750.5 4069 96.9855 1 3393 2 chr2D.!!$F2 3392
3 TraesCS4A01G161600 chr1A 94763171 94765603 2432 True 4048.0 4048 96.6780 1 2437 1 chr1A.!!$R1 2436
4 TraesCS4A01G161600 chr5D 562925174 562927610 2436 False 4047.0 4047 96.6370 1 2437 1 chr5D.!!$F1 2436
5 TraesCS4A01G161600 chr1D 185784140 185786577 2437 True 4008.0 4008 96.3490 1 2437 1 chr1D.!!$R1 2436
6 TraesCS4A01G161600 chr7A 211308107 211310544 2437 False 4002.0 4002 96.3080 1 2437 1 chr7A.!!$F1 2436
7 TraesCS4A01G161600 chr7A 563544632 563547069 2437 False 4002.0 4002 96.3080 1 2437 1 chr7A.!!$F2 2436
8 TraesCS4A01G161600 chr3D 399838375 399840807 2432 True 3949.0 3949 95.9390 1 2437 1 chr3D.!!$R1 2436
9 TraesCS4A01G161600 chr7D 307115809 307118245 2436 True 3945.0 3945 95.8970 1 2436 1 chr7D.!!$R1 2435
10 TraesCS4A01G161600 chr7D 382099220 382100066 846 True 1448.0 1448 97.5240 2547 3393 1 chr7D.!!$R2 846
11 TraesCS4A01G161600 chr5A 16535199 16536045 846 True 1448.0 1448 97.5240 2547 3393 1 chr5A.!!$R1 846
12 TraesCS4A01G161600 chr5A 420176805 420177650 845 True 1441.0 1441 97.4060 2547 3393 1 chr5A.!!$R2 846
13 TraesCS4A01G161600 chrUn 189425445 189426291 846 False 1443.0 1443 97.4060 2547 3393 1 chrUn.!!$F1 846
14 TraesCS4A01G161600 chrUn 222875170 222876016 846 True 1443.0 1443 97.4060 2547 3393 1 chrUn.!!$R2 846
15 TraesCS4A01G161600 chrUn 182445515 182446361 846 True 1437.0 1437 97.2880 2547 3393 1 chrUn.!!$R1 846
16 TraesCS4A01G161600 chr7B 742957274 742958119 845 False 1435.0 1435 97.2850 2547 3392 1 chr7B.!!$F1 845
17 TraesCS4A01G161600 chr4D 123466305 123467151 846 True 1426.0 1426 97.0520 2547 3393 1 chr4D.!!$R1 846

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
575 576 0.262285 GGTGACTAGCCCTACCCTCT 59.738 60.0 0.0 0.0 0.0 3.69 F
1021 1022 0.034896 GTCTGGAAGCACGGGAGAAA 59.965 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2187 0.250727 TCCTTCCTCGGCCTTGTTTG 60.251 55.0 0.0 0.0 0.0 2.93 R
2936 3216 1.927487 TAGTGTAGAGTTCCCCGCAA 58.073 50.0 0.0 0.0 0.0 4.85 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
195 196 8.915057 ATCATTCTCCTAGTATTGGAAACATG 57.085 34.615 0.00 0.00 42.32 3.21
253 254 6.016610 GTGTACCTTCCTATTTGCTTTGTCAA 60.017 38.462 0.00 0.00 0.00 3.18
264 265 6.875948 TTTGCTTTGTCAACTCATTAGCTA 57.124 33.333 6.31 0.00 0.00 3.32
267 268 6.697395 TGCTTTGTCAACTCATTAGCTACTA 58.303 36.000 0.00 0.00 0.00 1.82
426 427 9.563748 AGTAAATAGTGTTTTTGTTAGCCACTA 57.436 29.630 0.00 0.00 41.37 2.74
437 438 4.146564 TGTTAGCCACTACACTCACACTA 58.853 43.478 0.00 0.00 0.00 2.74
575 576 0.262285 GGTGACTAGCCCTACCCTCT 59.738 60.000 0.00 0.00 0.00 3.69
621 622 3.515602 ACCTCTGCCTGTGAAAAGAAT 57.484 42.857 0.00 0.00 0.00 2.40
801 802 0.533491 AGCTGGTAACCAATACGCGA 59.467 50.000 15.93 0.00 35.19 5.87
818 819 3.323979 ACGCGACCCCTATTGATTCTTAT 59.676 43.478 15.93 0.00 0.00 1.73
852 853 7.106239 TGTGAAAAGAAGTGTTCTCTTTCTCT 58.894 34.615 16.46 0.00 39.61 3.10
1021 1022 0.034896 GTCTGGAAGCACGGGAGAAA 59.965 55.000 0.00 0.00 0.00 2.52
1030 1031 1.609320 GCACGGGAGAAAGCTCTTCTT 60.609 52.381 11.00 0.00 41.06 2.52
1113 1114 3.322254 TCATTGCGGGTTGGTTATTTGTT 59.678 39.130 0.00 0.00 0.00 2.83
1151 1152 9.846248 CACTTGGAAAAATAGGAGATTTAGTTG 57.154 33.333 0.00 0.00 0.00 3.16
1160 1161 3.821033 AGGAGATTTAGTTGCACGCTTTT 59.179 39.130 0.00 0.00 0.00 2.27
1169 1170 3.818773 AGTTGCACGCTTTTATTGGTAGT 59.181 39.130 0.00 0.00 0.00 2.73
1351 1352 2.537529 CGCTGATACGCTGTTTGGATTG 60.538 50.000 0.00 0.00 0.00 2.67
1384 1385 4.924305 ATCGGTTGTAGTATTTCCGCTA 57.076 40.909 0.00 0.00 40.81 4.26
1392 1393 8.923683 GGTTGTAGTATTTCCGCTATTTCTATC 58.076 37.037 0.00 0.00 0.00 2.08
1403 1404 6.490381 TCCGCTATTTCTATCAGCTAAGAGAA 59.510 38.462 0.00 0.00 33.03 2.87
1427 1428 3.308595 TGTCGCATAATCGGTTGTTCATC 59.691 43.478 0.00 0.00 0.00 2.92
1460 1461 2.270352 TGGACCAAAGTCGCAAATCT 57.730 45.000 0.00 0.00 44.54 2.40
1500 1501 3.411446 TGAGTTCATTCAAAGTCGGCAT 58.589 40.909 0.00 0.00 32.30 4.40
1544 1545 7.148255 GCTGTTTAGTCAACAATCATGACCATA 60.148 37.037 0.00 0.00 45.11 2.74
1590 1592 2.717515 ACCCCGGATCTACTAGTCATCT 59.282 50.000 0.73 0.00 0.00 2.90
1598 1600 6.293735 CGGATCTACTAGTCATCTCCTTTGAC 60.294 46.154 0.00 0.00 43.05 3.18
1657 1660 5.415701 TGATTCAGAAAGGAAAGGTATGTGC 59.584 40.000 0.00 0.00 0.00 4.57
1659 1662 3.007506 TCAGAAAGGAAAGGTATGTGCGA 59.992 43.478 0.00 0.00 0.00 5.10
1679 1682 6.752351 GTGCGAAGACATTGAGTTAGAGATTA 59.248 38.462 0.00 0.00 0.00 1.75
1680 1683 7.436673 GTGCGAAGACATTGAGTTAGAGATTAT 59.563 37.037 0.00 0.00 0.00 1.28
1945 1948 7.781056 ACCTTGCTTTTCTGTAAAATTCTCAA 58.219 30.769 0.00 0.00 34.18 3.02
1974 1977 8.879759 GCTATAGCTGTGTAAAAACAATACTCA 58.120 33.333 17.75 0.00 38.21 3.41
2092 2095 5.237561 TGACTATTGCTTGAAACAAGCGTTA 59.762 36.000 24.44 18.42 45.80 3.18
2096 2099 4.624336 TGCTTGAAACAAGCGTTAAAGA 57.376 36.364 24.44 8.55 45.80 2.52
2129 2132 2.159626 GCGAACGGTTAAGCTAATGCAA 60.160 45.455 11.91 0.00 42.74 4.08
2172 2175 3.632145 GTGTCCAAAAATCGGATATGCCT 59.368 43.478 0.00 0.00 34.32 4.75
2184 2187 7.907214 ATCGGATATGCCTAGTGAAAATTAC 57.093 36.000 0.00 0.00 0.00 1.89
2229 2232 1.531423 ACTGCCACAATGCTCTTGAG 58.469 50.000 6.59 0.00 0.00 3.02
2339 2342 5.823045 AGCCGACAAGGGATTTTCTTAATAG 59.177 40.000 0.00 0.00 41.48 1.73
2422 2425 3.321968 TCCATGACCATAGATCGAACCTG 59.678 47.826 0.00 0.00 0.00 4.00
2443 2446 5.560722 TGTCCCATTTTGACAGAGAGTAA 57.439 39.130 0.00 0.00 37.80 2.24
2444 2447 5.935945 TGTCCCATTTTGACAGAGAGTAAA 58.064 37.500 0.00 0.00 37.80 2.01
2445 2448 5.763204 TGTCCCATTTTGACAGAGAGTAAAC 59.237 40.000 0.00 0.00 37.80 2.01
2446 2449 5.763204 GTCCCATTTTGACAGAGAGTAAACA 59.237 40.000 0.00 0.00 32.91 2.83
2447 2450 6.431234 GTCCCATTTTGACAGAGAGTAAACAT 59.569 38.462 0.00 0.00 32.91 2.71
2448 2451 7.606456 GTCCCATTTTGACAGAGAGTAAACATA 59.394 37.037 0.00 0.00 32.91 2.29
2449 2452 8.328758 TCCCATTTTGACAGAGAGTAAACATAT 58.671 33.333 0.00 0.00 0.00 1.78
2450 2453 8.616076 CCCATTTTGACAGAGAGTAAACATATC 58.384 37.037 0.00 0.00 0.00 1.63
2451 2454 8.331022 CCATTTTGACAGAGAGTAAACATATCG 58.669 37.037 0.00 0.00 0.00 2.92
2455 2458 7.024340 TGACAGAGAGTAAACATATCGTACC 57.976 40.000 0.00 0.00 0.00 3.34
2456 2459 6.827251 TGACAGAGAGTAAACATATCGTACCT 59.173 38.462 0.00 0.00 0.00 3.08
2457 2460 7.989170 TGACAGAGAGTAAACATATCGTACCTA 59.011 37.037 0.00 0.00 0.00 3.08
2458 2461 8.743085 ACAGAGAGTAAACATATCGTACCTAA 57.257 34.615 0.00 0.00 0.00 2.69
2459 2462 9.352191 ACAGAGAGTAAACATATCGTACCTAAT 57.648 33.333 0.00 0.00 0.00 1.73
2460 2463 9.613957 CAGAGAGTAAACATATCGTACCTAATG 57.386 37.037 0.00 0.00 0.00 1.90
2461 2464 9.570468 AGAGAGTAAACATATCGTACCTAATGA 57.430 33.333 3.69 0.00 0.00 2.57
2462 2465 9.609950 GAGAGTAAACATATCGTACCTAATGAC 57.390 37.037 3.69 0.00 0.00 3.06
2463 2466 9.128404 AGAGTAAACATATCGTACCTAATGACA 57.872 33.333 3.69 0.00 0.00 3.58
2464 2467 9.740239 GAGTAAACATATCGTACCTAATGACAA 57.260 33.333 3.69 0.00 0.00 3.18
2465 2468 9.525409 AGTAAACATATCGTACCTAATGACAAC 57.475 33.333 3.69 0.18 0.00 3.32
2466 2469 9.525409 GTAAACATATCGTACCTAATGACAACT 57.475 33.333 3.69 0.00 0.00 3.16
2468 2471 8.644318 AACATATCGTACCTAATGACAACTTC 57.356 34.615 3.69 0.00 0.00 3.01
2469 2472 6.916387 ACATATCGTACCTAATGACAACTTCG 59.084 38.462 3.69 0.00 0.00 3.79
2471 2474 5.878332 TCGTACCTAATGACAACTTCGTA 57.122 39.130 0.00 0.00 0.00 3.43
2472 2475 6.252967 TCGTACCTAATGACAACTTCGTAA 57.747 37.500 0.00 0.00 0.00 3.18
2473 2476 6.317088 TCGTACCTAATGACAACTTCGTAAG 58.683 40.000 0.00 0.00 0.00 2.34
2498 2501 9.771534 AGAATTTTACTTCTATCATACTCCTGC 57.228 33.333 0.00 0.00 33.73 4.85
2500 2503 5.707242 TTACTTCTATCATACTCCTGCCG 57.293 43.478 0.00 0.00 0.00 5.69
2501 2504 3.567397 ACTTCTATCATACTCCTGCCGT 58.433 45.455 0.00 0.00 0.00 5.68
2502 2505 4.726583 ACTTCTATCATACTCCTGCCGTA 58.273 43.478 0.00 0.00 0.00 4.02
2504 2507 5.597182 ACTTCTATCATACTCCTGCCGTAAA 59.403 40.000 0.00 0.00 0.00 2.01
2506 2509 6.085555 TCTATCATACTCCTGCCGTAAAAG 57.914 41.667 0.00 0.00 0.00 2.27
2508 2511 5.552870 ATCATACTCCTGCCGTAAAAGAT 57.447 39.130 0.00 0.00 0.00 2.40
2510 2513 6.085555 TCATACTCCTGCCGTAAAAGATAG 57.914 41.667 0.00 0.00 0.00 2.08
2512 2515 4.820894 ACTCCTGCCGTAAAAGATAGTT 57.179 40.909 0.00 0.00 0.00 2.24
2513 2516 4.504858 ACTCCTGCCGTAAAAGATAGTTG 58.495 43.478 0.00 0.00 0.00 3.16
2515 2518 2.354821 CCTGCCGTAAAAGATAGTTGCC 59.645 50.000 0.00 0.00 0.00 4.52
2517 2520 3.616219 TGCCGTAAAAGATAGTTGCCAT 58.384 40.909 0.00 0.00 0.00 4.40
2518 2521 3.625764 TGCCGTAAAAGATAGTTGCCATC 59.374 43.478 0.00 0.00 0.00 3.51
2519 2522 3.877508 GCCGTAAAAGATAGTTGCCATCT 59.122 43.478 0.00 0.00 34.15 2.90
2520 2523 4.024809 GCCGTAAAAGATAGTTGCCATCTC 60.025 45.833 0.00 0.00 31.45 2.75
2521 2524 4.209288 CCGTAAAAGATAGTTGCCATCTCG 59.791 45.833 0.00 0.00 31.45 4.04
2522 2525 4.804139 CGTAAAAGATAGTTGCCATCTCGT 59.196 41.667 0.00 0.00 31.45 4.18
2523 2526 5.276395 CGTAAAAGATAGTTGCCATCTCGTG 60.276 44.000 0.00 0.00 31.45 4.35
2533 2536 2.751166 CCATCTCGTGGGTATCCATC 57.249 55.000 0.00 0.00 46.09 3.51
2534 2537 1.276421 CCATCTCGTGGGTATCCATCC 59.724 57.143 0.00 0.00 46.09 3.51
2535 2538 2.251818 CATCTCGTGGGTATCCATCCT 58.748 52.381 0.00 0.00 46.09 3.24
2537 2540 3.827817 TCTCGTGGGTATCCATCCTAT 57.172 47.619 0.00 0.00 46.09 2.57
2538 2541 3.698289 TCTCGTGGGTATCCATCCTATC 58.302 50.000 0.00 0.00 46.09 2.08
2539 2542 3.333980 TCTCGTGGGTATCCATCCTATCT 59.666 47.826 0.00 0.00 46.09 1.98
2540 2543 4.538891 TCTCGTGGGTATCCATCCTATCTA 59.461 45.833 0.00 0.00 46.09 1.98
2541 2544 5.193930 TCTCGTGGGTATCCATCCTATCTAT 59.806 44.000 0.00 0.00 46.09 1.98
2542 2545 5.838955 TCGTGGGTATCCATCCTATCTATT 58.161 41.667 0.00 0.00 46.09 1.73
2543 2546 5.892119 TCGTGGGTATCCATCCTATCTATTC 59.108 44.000 0.00 0.00 46.09 1.75
2545 2548 6.154534 CGTGGGTATCCATCCTATCTATTCAA 59.845 42.308 0.00 0.00 46.09 2.69
2572 2852 3.695060 CCAGGAACGTCATCTACTACTGT 59.305 47.826 0.00 0.00 0.00 3.55
2704 2984 6.452494 TGCTAGATTTCTAGTCGTTAGCTT 57.548 37.500 14.43 0.00 45.85 3.74
2715 2995 8.053026 TCTAGTCGTTAGCTTTTAGTGAAGAT 57.947 34.615 0.00 0.00 0.00 2.40
2737 3017 0.109153 ATTGCTATCATCTGCGGGCA 59.891 50.000 0.00 0.00 0.00 5.36
2796 3076 7.360575 ACCAAATTCACTATTGACTTACGAC 57.639 36.000 0.00 0.00 0.00 4.34
2913 3193 6.645306 AGTTCTTTATAGCTCTTTCACCTCC 58.355 40.000 0.00 0.00 0.00 4.30
2936 3216 8.635765 TCCTTTAGACTCTTTGCAATGTTTAT 57.364 30.769 11.67 1.42 0.00 1.40
2964 3244 5.221009 GGGGAACTCTACACTATTGTACTCG 60.221 48.000 0.00 0.00 37.15 4.18
3139 3420 1.003580 TCTTCACCCAATGGAGCAGAC 59.996 52.381 0.00 0.00 33.25 3.51
3141 3422 0.770499 TCACCCAATGGAGCAGACAA 59.230 50.000 0.00 0.00 34.81 3.18
3325 3606 7.413446 AGGATCAAAGAAAAGGGAATATCACA 58.587 34.615 0.00 0.00 0.00 3.58
3341 3622 6.699575 ATATCACAAAGGTAAGCACATTCC 57.300 37.500 0.00 0.00 0.00 3.01
3353 3634 8.815912 AGGTAAGCACATTCCATTTTTCTTAAT 58.184 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
426 427 4.330944 TCCGAACAAATAGTGTGAGTGT 57.669 40.909 0.00 0.00 40.60 3.55
437 438 5.001874 GGAGGACTTACTTTCCGAACAAAT 58.998 41.667 0.00 0.00 38.29 2.32
575 576 6.500751 ACCAACCTATCTTTCTAAGGAAGACA 59.499 38.462 0.00 0.00 32.51 3.41
621 622 5.780793 AGCCTTTCTTAAAGTGGTCTCTCTA 59.219 40.000 0.00 0.00 36.77 2.43
743 744 2.494059 CCTTTGTCTCGCTTTCCTTCA 58.506 47.619 0.00 0.00 0.00 3.02
801 802 9.411848 AGGATTTCTATAAGAATCAATAGGGGT 57.588 33.333 8.96 0.00 33.67 4.95
818 819 7.993183 AGAACACTTCTTTTCACAGGATTTCTA 59.007 33.333 0.00 0.00 36.36 2.10
852 853 2.287970 TGCGAGACTGTTCTTTTCGCTA 60.288 45.455 16.52 2.82 41.12 4.26
938 939 8.429237 GAATTGATTCCTTCTCTAGATAGGGA 57.571 38.462 16.87 11.76 0.00 4.20
1048 1049 8.862325 ATGCTATGAATAACCCAATATCGAAA 57.138 30.769 0.00 0.00 0.00 3.46
1079 1080 2.358898 CCCGCAATGAATAAGGAAGGTG 59.641 50.000 0.00 0.00 0.00 4.00
1113 1114 1.002624 CCAAGTGAAAGCCGGGCTA 60.003 57.895 24.16 3.39 38.25 3.93
1151 1152 5.220605 CCTTCTACTACCAATAAAAGCGTGC 60.221 44.000 0.00 0.00 0.00 5.34
1160 1161 3.584294 GCCCTCCCTTCTACTACCAATA 58.416 50.000 0.00 0.00 0.00 1.90
1169 1170 2.682494 AACGCGCCCTCCCTTCTA 60.682 61.111 5.73 0.00 0.00 2.10
1191 1192 8.869109 TGTTGAATATCCAAGAAAAATGAAGGT 58.131 29.630 0.00 0.00 0.00 3.50
1351 1352 2.210116 ACAACCGATATTGCGACATCC 58.790 47.619 0.00 0.00 32.47 3.51
1384 1385 7.170658 GCGACATTTCTCTTAGCTGATAGAAAT 59.829 37.037 19.83 19.83 45.13 2.17
1392 1393 5.973651 TTATGCGACATTTCTCTTAGCTG 57.026 39.130 0.00 0.00 0.00 4.24
1403 1404 3.687212 TGAACAACCGATTATGCGACATT 59.313 39.130 0.00 0.00 0.00 2.71
1427 1428 8.285394 CGACTTTGGTCCATGAATTATAAGATG 58.715 37.037 0.00 0.00 39.15 2.90
1486 1487 0.331278 TCCCCATGCCGACTTTGAAT 59.669 50.000 0.00 0.00 0.00 2.57
1500 1501 0.625849 GCCCTTTCTCTGATTCCCCA 59.374 55.000 0.00 0.00 0.00 4.96
1590 1592 1.216678 TGCTTTTCCCAGGTCAAAGGA 59.783 47.619 8.92 4.34 0.00 3.36
1598 1600 2.497273 CAGGGTAAATGCTTTTCCCAGG 59.503 50.000 22.78 15.49 35.92 4.45
1679 1682 3.928754 TCTCTAGTGTGCCCCTTCATAT 58.071 45.455 0.00 0.00 0.00 1.78
1680 1683 3.398318 TCTCTAGTGTGCCCCTTCATA 57.602 47.619 0.00 0.00 0.00 2.15
1870 1873 7.334421 CGACATTCCTTCTTCTTTCCAAGATTA 59.666 37.037 0.00 0.00 37.38 1.75
1873 1876 4.997395 CGACATTCCTTCTTCTTTCCAAGA 59.003 41.667 0.00 0.00 35.26 3.02
2008 2011 6.668541 AATCAGTGACTAATATGCACACAC 57.331 37.500 0.00 0.00 35.08 3.82
2092 2095 4.537015 CGTTCGCTTCTTTCCATTTCTTT 58.463 39.130 0.00 0.00 0.00 2.52
2096 2099 2.227194 ACCGTTCGCTTCTTTCCATTT 58.773 42.857 0.00 0.00 0.00 2.32
2129 2132 1.999648 TGCTGCATCCCTTTTCTTGT 58.000 45.000 0.00 0.00 0.00 3.16
2172 2175 5.531659 TCGGCCTTGTTTGTAATTTTCACTA 59.468 36.000 0.00 0.00 0.00 2.74
2184 2187 0.250727 TCCTTCCTCGGCCTTGTTTG 60.251 55.000 0.00 0.00 0.00 2.93
2229 2232 4.060038 TCGGTATTCATGCTTCCTTCTC 57.940 45.455 0.00 0.00 0.00 2.87
2371 2374 8.766151 GCCTCCTAAAAAGATCTACTAAATTCG 58.234 37.037 0.00 0.00 0.00 3.34
2422 2425 5.763204 TGTTTACTCTCTGTCAAAATGGGAC 59.237 40.000 0.00 0.00 35.83 4.46
2437 2440 9.128404 TGTCATTAGGTACGATATGTTTACTCT 57.872 33.333 0.00 0.00 0.00 3.24
2438 2441 9.740239 TTGTCATTAGGTACGATATGTTTACTC 57.260 33.333 0.00 0.00 0.00 2.59
2439 2442 9.525409 GTTGTCATTAGGTACGATATGTTTACT 57.475 33.333 0.00 0.00 0.00 2.24
2442 2445 9.095065 GAAGTTGTCATTAGGTACGATATGTTT 57.905 33.333 0.00 0.00 0.00 2.83
2443 2446 7.434307 CGAAGTTGTCATTAGGTACGATATGTT 59.566 37.037 0.00 0.00 0.00 2.71
2444 2447 6.916387 CGAAGTTGTCATTAGGTACGATATGT 59.084 38.462 0.00 0.00 0.00 2.29
2445 2448 6.916387 ACGAAGTTGTCATTAGGTACGATATG 59.084 38.462 0.00 0.00 37.78 1.78
2446 2449 7.035840 ACGAAGTTGTCATTAGGTACGATAT 57.964 36.000 0.00 0.00 37.78 1.63
2447 2450 6.441093 ACGAAGTTGTCATTAGGTACGATA 57.559 37.500 0.00 0.00 37.78 2.92
2448 2451 5.320549 ACGAAGTTGTCATTAGGTACGAT 57.679 39.130 0.00 0.00 37.78 3.73
2449 2452 4.771590 ACGAAGTTGTCATTAGGTACGA 57.228 40.909 0.00 0.00 37.78 3.43
2450 2453 6.317088 TCTTACGAAGTTGTCATTAGGTACG 58.683 40.000 0.00 0.00 37.78 3.67
2451 2454 8.699283 ATTCTTACGAAGTTGTCATTAGGTAC 57.301 34.615 0.00 0.00 37.78 3.34
2453 2456 8.617290 AAATTCTTACGAAGTTGTCATTAGGT 57.383 30.769 0.00 0.00 37.78 3.08
2459 2462 9.321562 AGAAGTAAAATTCTTACGAAGTTGTCA 57.678 29.630 0.00 0.00 37.49 3.58
2472 2475 9.771534 GCAGGAGTATGATAGAAGTAAAATTCT 57.228 33.333 0.00 0.00 42.20 2.40
2473 2476 8.994170 GGCAGGAGTATGATAGAAGTAAAATTC 58.006 37.037 0.00 0.00 0.00 2.17
2475 2478 7.155328 CGGCAGGAGTATGATAGAAGTAAAAT 58.845 38.462 0.00 0.00 0.00 1.82
2476 2479 6.097839 ACGGCAGGAGTATGATAGAAGTAAAA 59.902 38.462 0.00 0.00 0.00 1.52
2477 2480 5.597182 ACGGCAGGAGTATGATAGAAGTAAA 59.403 40.000 0.00 0.00 0.00 2.01
2478 2481 5.138276 ACGGCAGGAGTATGATAGAAGTAA 58.862 41.667 0.00 0.00 0.00 2.24
2479 2482 4.726583 ACGGCAGGAGTATGATAGAAGTA 58.273 43.478 0.00 0.00 0.00 2.24
2482 2485 6.322969 TCTTTTACGGCAGGAGTATGATAGAA 59.677 38.462 0.00 0.00 0.00 2.10
2483 2486 5.831525 TCTTTTACGGCAGGAGTATGATAGA 59.168 40.000 0.00 0.00 0.00 1.98
2484 2487 6.085555 TCTTTTACGGCAGGAGTATGATAG 57.914 41.667 0.00 0.00 0.00 2.08
2488 2491 5.844004 ACTATCTTTTACGGCAGGAGTATG 58.156 41.667 0.00 0.00 0.00 2.39
2490 2493 5.657474 CAACTATCTTTTACGGCAGGAGTA 58.343 41.667 0.00 0.00 0.00 2.59
2492 2495 3.309954 GCAACTATCTTTTACGGCAGGAG 59.690 47.826 0.00 0.00 0.00 3.69
2495 2498 3.006940 TGGCAACTATCTTTTACGGCAG 58.993 45.455 0.00 0.00 37.61 4.85
2496 2499 3.060736 TGGCAACTATCTTTTACGGCA 57.939 42.857 0.00 0.00 37.61 5.69
2497 2500 3.877508 AGATGGCAACTATCTTTTACGGC 59.122 43.478 0.00 0.00 32.73 5.68
2498 2501 4.209288 CGAGATGGCAACTATCTTTTACGG 59.791 45.833 0.00 0.00 35.49 4.02
2500 2503 5.006746 CCACGAGATGGCAACTATCTTTTAC 59.993 44.000 0.00 0.00 43.24 2.01
2501 2504 5.116180 CCACGAGATGGCAACTATCTTTTA 58.884 41.667 0.00 0.00 43.24 1.52
2502 2505 3.941483 CCACGAGATGGCAACTATCTTTT 59.059 43.478 0.00 0.00 43.24 2.27
2504 2507 3.185246 CCACGAGATGGCAACTATCTT 57.815 47.619 0.00 0.00 43.24 2.40
2515 2518 2.251818 AGGATGGATACCCACGAGATG 58.748 52.381 0.00 0.00 46.98 2.90
2517 2520 3.333980 AGATAGGATGGATACCCACGAGA 59.666 47.826 0.00 0.00 46.98 4.04
2518 2521 3.702792 AGATAGGATGGATACCCACGAG 58.297 50.000 0.00 0.00 46.98 4.18
2519 2522 3.827817 AGATAGGATGGATACCCACGA 57.172 47.619 0.00 0.00 46.98 4.35
2520 2523 5.656859 TGAATAGATAGGATGGATACCCACG 59.343 44.000 0.00 0.00 46.98 4.94
2521 2524 7.496346 TTGAATAGATAGGATGGATACCCAC 57.504 40.000 0.00 0.00 46.98 4.61
2523 2526 8.152023 ACTTTGAATAGATAGGATGGATACCC 57.848 38.462 0.00 0.00 0.00 3.69
2526 2529 9.837681 TGGTACTTTGAATAGATAGGATGGATA 57.162 33.333 0.00 0.00 0.00 2.59
2528 2531 7.235606 CCTGGTACTTTGAATAGATAGGATGGA 59.764 40.741 0.00 0.00 0.00 3.41
2529 2532 7.235606 TCCTGGTACTTTGAATAGATAGGATGG 59.764 40.741 0.00 0.00 0.00 3.51
2531 2534 8.652290 GTTCCTGGTACTTTGAATAGATAGGAT 58.348 37.037 0.00 0.00 31.37 3.24
2533 2536 6.924060 CGTTCCTGGTACTTTGAATAGATAGG 59.076 42.308 1.90 0.00 0.00 2.57
2534 2537 7.490000 ACGTTCCTGGTACTTTGAATAGATAG 58.510 38.462 1.90 0.00 0.00 2.08
2535 2538 7.123098 TGACGTTCCTGGTACTTTGAATAGATA 59.877 37.037 1.90 0.00 0.00 1.98
2537 2540 5.244402 TGACGTTCCTGGTACTTTGAATAGA 59.756 40.000 1.90 0.00 0.00 1.98
2538 2541 5.475719 TGACGTTCCTGGTACTTTGAATAG 58.524 41.667 1.90 0.00 0.00 1.73
2539 2542 5.471556 TGACGTTCCTGGTACTTTGAATA 57.528 39.130 1.90 0.00 0.00 1.75
2540 2543 4.345859 TGACGTTCCTGGTACTTTGAAT 57.654 40.909 1.90 0.00 0.00 2.57
2541 2544 3.823281 TGACGTTCCTGGTACTTTGAA 57.177 42.857 1.90 0.00 0.00 2.69
2542 2545 3.576982 AGATGACGTTCCTGGTACTTTGA 59.423 43.478 1.90 0.00 0.00 2.69
2543 2546 3.926616 AGATGACGTTCCTGGTACTTTG 58.073 45.455 1.90 0.00 0.00 2.77
2545 2548 4.342359 AGTAGATGACGTTCCTGGTACTT 58.658 43.478 1.90 0.00 0.00 2.24
2572 2852 3.315949 CGTCCCCCGGGAGTTTCA 61.316 66.667 26.32 0.00 46.16 2.69
2715 2995 2.497138 CCCGCAGATGATAGCAATTCA 58.503 47.619 0.00 0.00 0.00 2.57
2737 3017 5.183904 GCGGATAAATTCAATAATGAGGGCT 59.816 40.000 0.00 0.00 36.78 5.19
2796 3076 8.121086 CGATATAGGAATGAAGCATGCATAAAG 58.879 37.037 21.98 0.89 27.94 1.85
2843 3123 5.777732 ACTAAGAGGAAGATGTCTCACAACT 59.222 40.000 0.00 0.00 32.27 3.16
2936 3216 1.927487 TAGTGTAGAGTTCCCCGCAA 58.073 50.000 0.00 0.00 0.00 4.85
2964 3244 7.095439 CGATACTTTCTTGAAGGAATAGCATCC 60.095 40.741 0.00 0.00 39.79 3.51
3121 3402 0.770499 TGTCTGCTCCATTGGGTGAA 59.230 50.000 2.09 0.00 34.93 3.18
3141 3422 9.298250 GGAGTTATTTCTTTCTTAAAGGAAGGT 57.702 33.333 0.00 0.00 39.27 3.50
3325 3606 7.066307 AGAAAAATGGAATGTGCTTACCTTT 57.934 32.000 0.00 0.00 0.00 3.11
3353 3634 7.048629 TGATAACTCCATTTGCTTTGTCAAA 57.951 32.000 0.00 0.00 39.87 2.69


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

AutoCloner maintained by Alex Coulton.