Multiple sequence alignment - TraesCS6D01G165100

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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 TraesCS6D01G165100 chr6D 100.000 3960 0 0 1 3960 144092149 144088190 0.000000e+00 7313.0
1 TraesCS6D01G165100 chr6B 95.483 1417 46 10 622 2028 256448360 256446952 0.000000e+00 2246.0
2 TraesCS6D01G165100 chr6B 91.626 1218 62 9 2079 3263 256446957 256445747 0.000000e+00 1648.0
3 TraesCS6D01G165100 chr6B 80.745 644 73 26 1 624 256449287 256448675 4.660000e-124 455.0
4 TraesCS6D01G165100 chr6B 91.150 339 17 4 3635 3960 256441536 256441198 7.810000e-122 448.0
5 TraesCS6D01G165100 chr6B 77.124 612 132 8 2331 2938 257332271 257331664 8.140000e-92 348.0
6 TraesCS6D01G165100 chr6B 74.731 835 182 23 1109 1925 256016066 256015243 2.930000e-91 346.0
7 TraesCS6D01G165100 chr6B 95.570 158 5 2 3493 3648 256443774 256443617 6.570000e-63 252.0
8 TraesCS6D01G165100 chr2B 95.188 1413 52 9 624 2028 103922958 103924362 0.000000e+00 2218.0
9 TraesCS6D01G165100 chr2B 94.763 1413 58 9 624 2028 103960282 103961686 0.000000e+00 2185.0
10 TraesCS6D01G165100 chr2B 91.588 1058 69 9 2079 3125 103961681 103962729 0.000000e+00 1443.0
11 TraesCS6D01G165100 chr2B 91.021 1058 75 9 2079 3125 103924357 103925405 0.000000e+00 1410.0
12 TraesCS6D01G165100 chr2B 100.000 28 0 0 579 606 103902254 103902281 7.000000e-03 52.8
13 TraesCS6D01G165100 chr2B 100.000 28 0 0 579 606 103957962 103957989 7.000000e-03 52.8
14 TraesCS6D01G165100 chr6A 91.934 1215 64 21 1973 3165 203522468 203523670 0.000000e+00 1670.0
15 TraesCS6D01G165100 chr6A 95.440 965 41 2 998 1962 203521354 203522315 0.000000e+00 1535.0
16 TraesCS6D01G165100 chr6A 93.032 531 31 4 3431 3957 203544981 203545509 0.000000e+00 771.0
17 TraesCS6D01G165100 chr6A 97.518 282 7 0 3164 3445 203523711 203523992 2.140000e-132 483.0
18 TraesCS6D01G165100 chr6A 75.270 833 178 26 1109 1925 204717496 204718316 4.830000e-99 372.0
19 TraesCS6D01G165100 chr6A 77.325 613 135 4 2328 2938 202979377 202979987 3.760000e-95 359.0
20 TraesCS6D01G165100 chr6A 88.806 268 21 5 748 1007 203520913 203521179 1.780000e-83 320.0
21 TraesCS6D01G165100 chr6A 93.220 177 12 0 580 756 203508374 203508550 1.090000e-65 261.0
22 TraesCS6D01G165100 chr4D 73.729 826 177 26 1118 1935 503563378 503564171 1.800000e-73 287.0


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 TraesCS6D01G165100 chr6D 144088190 144092149 3959 True 7313.000000 7313 100.000000 1 3960 1 chr6D.!!$R1 3959
1 TraesCS6D01G165100 chr6B 256441198 256449287 8089 True 1009.800000 2246 90.914800 1 3960 5 chr6B.!!$R3 3959
2 TraesCS6D01G165100 chr6B 257331664 257332271 607 True 348.000000 348 77.124000 2331 2938 1 chr6B.!!$R2 607
3 TraesCS6D01G165100 chr6B 256015243 256016066 823 True 346.000000 346 74.731000 1109 1925 1 chr6B.!!$R1 816
4 TraesCS6D01G165100 chr2B 103922958 103925405 2447 False 1814.000000 2218 93.104500 624 3125 2 chr2B.!!$F2 2501
5 TraesCS6D01G165100 chr2B 103957962 103962729 4767 False 1226.933333 2185 95.450333 579 3125 3 chr2B.!!$F3 2546
6 TraesCS6D01G165100 chr6A 203520913 203523992 3079 False 1002.000000 1670 93.424500 748 3445 4 chr6A.!!$F5 2697
7 TraesCS6D01G165100 chr6A 203544981 203545509 528 False 771.000000 771 93.032000 3431 3957 1 chr6A.!!$F3 526
8 TraesCS6D01G165100 chr6A 204717496 204718316 820 False 372.000000 372 75.270000 1109 1925 1 chr6A.!!$F4 816
9 TraesCS6D01G165100 chr6A 202979377 202979987 610 False 359.000000 359 77.325000 2328 2938 1 chr6A.!!$F1 610
10 TraesCS6D01G165100 chr4D 503563378 503564171 793 False 287.000000 287 73.729000 1118 1935 1 chr4D.!!$F1 817

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
61 62 0.179073 ATGCAGATCCGAAGGGTTCG 60.179 55.0 2.03 2.03 39.56 3.95 F
907 3228 0.247145 GTGACGCGGCTTATTTGTCG 60.247 55.0 15.80 0.00 38.18 4.35 F
2024 4705 0.031314 TCTGGCGATCGAGAATCAGC 59.969 55.0 21.57 0.00 33.65 4.26 F
2026 4707 0.175531 TGGCGATCGAGAATCAGCAA 59.824 50.0 21.57 0.00 36.36 3.91 F
2749 5494 0.458260 AGTTTGTTCCGTTTGGTGCC 59.542 50.0 0.00 0.00 36.30 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 4113 0.830648 GAACCTGTCCCCGATCATGA 59.169 55.0 0.00 0.00 0.00 3.07 R
2313 5058 0.859232 CTGTATGCCAATACGCGACC 59.141 55.0 15.93 0.00 41.46 4.79 R
2929 5674 1.024579 CACATGGGCTAACACGGACC 61.025 60.0 0.00 0.00 0.00 4.46 R
2940 5685 1.089920 CTACACAAGAGCACATGGGC 58.910 55.0 13.49 13.49 0.00 5.36 R
3933 10591 2.162408 GGGCAAGGAGAAAACAATCTCG 59.838 50.0 0.00 0.00 45.54 4.04 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
40 41 2.147387 AACAACAGGACGAGCCCCT 61.147 57.895 0.00 0.00 37.37 4.79
61 62 0.179073 ATGCAGATCCGAAGGGTTCG 60.179 55.000 2.03 2.03 39.56 3.95
88 89 2.428187 CCCCAAGTACGCACCACA 59.572 61.111 0.00 0.00 0.00 4.17
157 158 2.417516 CCGGGCTACCACGATCAG 59.582 66.667 0.00 0.00 36.13 2.90
247 257 3.567797 GATCTGGTCGCAAGCGGC 61.568 66.667 14.98 13.08 44.06 6.53
266 276 3.066814 GCAAGCAAGCCCCTCCAG 61.067 66.667 0.00 0.00 0.00 3.86
331 367 3.294493 CCAACCGTGGTGCCTTGG 61.294 66.667 0.00 0.00 40.42 3.61
332 368 3.977244 CAACCGTGGTGCCTTGGC 61.977 66.667 4.43 4.43 0.00 4.52
337 373 3.384532 GTGGTGCCTTGGCCCATG 61.385 66.667 19.51 0.00 0.00 3.66
338 374 4.700448 TGGTGCCTTGGCCCATGG 62.700 66.667 11.29 11.29 0.00 3.66
339 375 4.380945 GGTGCCTTGGCCCATGGA 62.381 66.667 19.41 2.13 31.33 3.41
340 376 2.283821 GTGCCTTGGCCCATGGAA 60.284 61.111 19.41 5.98 31.33 3.53
341 377 2.037687 TGCCTTGGCCCATGGAAG 59.962 61.111 19.41 9.09 31.33 3.46
342 378 3.464494 GCCTTGGCCCATGGAAGC 61.464 66.667 19.41 9.12 31.33 3.86
343 379 2.361771 CCTTGGCCCATGGAAGCT 59.638 61.111 15.22 0.00 31.33 3.74
344 380 1.305549 CCTTGGCCCATGGAAGCTT 60.306 57.895 15.22 0.00 31.33 3.74
345 381 1.325476 CCTTGGCCCATGGAAGCTTC 61.325 60.000 18.54 18.54 31.33 3.86
379 415 3.141488 CACGAGGGGACGAGGAGG 61.141 72.222 0.00 0.00 37.03 4.30
442 478 0.382515 CGGTAGAAGAGAGCGGAAGG 59.617 60.000 0.00 0.00 34.28 3.46
453 489 2.291043 GCGGAAGGTGGGAGGAAGA 61.291 63.158 0.00 0.00 0.00 2.87
457 493 1.900545 GAAGGTGGGAGGAAGACCGG 61.901 65.000 0.00 0.00 41.83 5.28
459 495 3.319198 GTGGGAGGAAGACCGGCA 61.319 66.667 0.00 0.00 41.83 5.69
460 496 2.285368 TGGGAGGAAGACCGGCAT 60.285 61.111 0.00 0.00 41.83 4.40
474 510 2.111251 GCATCGGCTAGGGTTCCC 59.889 66.667 0.00 0.00 36.96 3.97
489 525 4.838152 CCCTCCCCGTCACATGCG 62.838 72.222 0.00 0.00 0.00 4.73
498 534 3.245346 TCACATGCGGGGGTGACA 61.245 61.111 0.00 0.00 39.00 3.58
500 536 3.249189 ACATGCGGGGGTGACACT 61.249 61.111 5.39 0.00 0.00 3.55
504 540 2.063015 ATGCGGGGGTGACACTGAAA 62.063 55.000 5.39 0.00 45.83 2.69
522 558 0.830444 AAGTGTGAGTGGGGAGCGTA 60.830 55.000 0.00 0.00 0.00 4.42
539 575 2.651455 CGTACTCTCCCATGTACTCCA 58.349 52.381 0.00 0.00 37.47 3.86
542 578 3.697190 ACTCTCCCATGTACTCCATCT 57.303 47.619 0.00 0.00 0.00 2.90
543 579 3.303938 ACTCTCCCATGTACTCCATCTG 58.696 50.000 0.00 0.00 0.00 2.90
544 580 3.303938 CTCTCCCATGTACTCCATCTGT 58.696 50.000 0.00 0.00 0.00 3.41
549 585 2.158900 CCATGTACTCCATCTGTCCCAC 60.159 54.545 0.00 0.00 0.00 4.61
550 586 2.319025 TGTACTCCATCTGTCCCACA 57.681 50.000 0.00 0.00 0.00 4.17
551 587 2.615391 TGTACTCCATCTGTCCCACAA 58.385 47.619 0.00 0.00 0.00 3.33
553 589 2.795231 ACTCCATCTGTCCCACAATG 57.205 50.000 0.00 0.00 0.00 2.82
555 591 3.181329 ACTCCATCTGTCCCACAATGTA 58.819 45.455 0.00 0.00 0.00 2.29
556 592 3.198635 ACTCCATCTGTCCCACAATGTAG 59.801 47.826 0.00 0.00 0.00 2.74
557 593 2.505407 TCCATCTGTCCCACAATGTAGG 59.495 50.000 0.00 0.00 0.00 3.18
563 599 2.774687 GTCCCACAATGTAGGACGTTT 58.225 47.619 14.70 0.00 40.65 3.60
564 600 3.143728 GTCCCACAATGTAGGACGTTTT 58.856 45.455 14.70 0.00 40.65 2.43
565 601 3.566742 GTCCCACAATGTAGGACGTTTTT 59.433 43.478 14.70 0.00 40.65 1.94
566 602 3.816523 TCCCACAATGTAGGACGTTTTTC 59.183 43.478 0.00 0.00 0.00 2.29
567 603 3.364565 CCCACAATGTAGGACGTTTTTCG 60.365 47.826 0.00 0.00 46.00 3.46
568 604 3.495377 CCACAATGTAGGACGTTTTTCGA 59.505 43.478 0.00 0.00 42.86 3.71
569 605 4.153475 CCACAATGTAGGACGTTTTTCGAT 59.847 41.667 0.00 0.00 42.86 3.59
571 607 6.238508 CACAATGTAGGACGTTTTTCGATAC 58.761 40.000 0.00 0.00 42.86 2.24
575 611 1.545582 AGGACGTTTTTCGATACGGGA 59.454 47.619 16.23 0.00 41.81 5.14
576 612 1.655597 GGACGTTTTTCGATACGGGAC 59.344 52.381 16.23 9.13 41.81 4.46
606 650 1.627834 AGTTTGAGAGCTGGGAAGAGG 59.372 52.381 0.00 0.00 0.00 3.69
620 674 1.815003 GAAGAGGAGCAAACATGGGTG 59.185 52.381 0.00 0.00 0.00 4.61
695 3014 3.419915 CGTGCATACAGTTTGCTGATTC 58.580 45.455 15.91 2.87 45.28 2.52
759 3078 6.148976 ACCGTCTTACTTGAATTAGAAAAGGC 59.851 38.462 0.00 0.00 0.00 4.35
760 3079 6.371825 CCGTCTTACTTGAATTAGAAAAGGCT 59.628 38.462 0.00 0.00 0.00 4.58
830 3149 1.213537 CCAATGACGCCAAGCCAAG 59.786 57.895 0.00 0.00 0.00 3.61
907 3228 0.247145 GTGACGCGGCTTATTTGTCG 60.247 55.000 15.80 0.00 38.18 4.35
924 3245 4.908877 GCGTACTCCCTCGAGCGC 62.909 72.222 15.19 15.19 40.03 5.92
931 3252 4.519437 CCCTCGAGCGCTGCATGA 62.519 66.667 18.48 6.34 0.00 3.07
932 3253 2.510012 CCTCGAGCGCTGCATGAA 60.510 61.111 18.48 0.00 0.00 2.57
956 3285 5.540337 ACTCTTCACAAGAACTGACCATCTA 59.460 40.000 0.00 0.00 37.02 1.98
959 3288 3.055819 TCACAAGAACTGACCATCTAGGC 60.056 47.826 0.00 0.00 43.14 3.93
1053 3574 1.040339 ACCTCCTCTGCATCGTCCTC 61.040 60.000 0.00 0.00 0.00 3.71
1885 4421 0.876342 GATACAGAAGGAAGGCGGCG 60.876 60.000 0.51 0.51 0.00 6.46
1952 4488 8.434392 CCTTGTAAGGCCCATTTTACTACTATA 58.566 37.037 12.38 0.00 39.76 1.31
2021 4702 2.815478 AGTTTCTGGCGATCGAGAATC 58.185 47.619 21.57 17.30 0.00 2.52
2022 4703 2.166459 AGTTTCTGGCGATCGAGAATCA 59.834 45.455 21.57 3.16 33.65 2.57
2023 4704 2.498807 TTCTGGCGATCGAGAATCAG 57.501 50.000 21.57 16.00 33.65 2.90
2024 4705 0.031314 TCTGGCGATCGAGAATCAGC 59.969 55.000 21.57 0.00 33.65 4.26
2025 4706 0.249197 CTGGCGATCGAGAATCAGCA 60.249 55.000 21.57 0.00 36.36 4.41
2026 4707 0.175531 TGGCGATCGAGAATCAGCAA 59.824 50.000 21.57 0.00 36.36 3.91
2027 4708 1.290203 GGCGATCGAGAATCAGCAAA 58.710 50.000 21.57 0.00 36.36 3.68
2028 4709 1.665679 GGCGATCGAGAATCAGCAAAA 59.334 47.619 21.57 0.00 36.36 2.44
2029 4710 2.286067 GGCGATCGAGAATCAGCAAAAG 60.286 50.000 21.57 0.00 36.36 2.27
2030 4711 2.349886 GCGATCGAGAATCAGCAAAAGT 59.650 45.455 21.57 0.00 35.41 2.66
2031 4712 3.783548 GCGATCGAGAATCAGCAAAAGTG 60.784 47.826 21.57 0.00 35.41 3.16
2032 4713 3.614176 CGATCGAGAATCAGCAAAAGTGA 59.386 43.478 10.26 0.00 33.65 3.41
2033 4714 4.259730 CGATCGAGAATCAGCAAAAGTGAG 60.260 45.833 10.26 0.00 33.65 3.51
2034 4715 4.257267 TCGAGAATCAGCAAAAGTGAGA 57.743 40.909 0.00 0.00 33.17 3.27
2035 4716 3.990469 TCGAGAATCAGCAAAAGTGAGAC 59.010 43.478 0.00 0.00 33.17 3.36
2036 4717 3.993081 CGAGAATCAGCAAAAGTGAGACT 59.007 43.478 0.00 0.00 33.17 3.24
2037 4718 5.048013 TCGAGAATCAGCAAAAGTGAGACTA 60.048 40.000 0.00 0.00 33.17 2.59
2038 4719 5.809562 CGAGAATCAGCAAAAGTGAGACTAT 59.190 40.000 0.00 0.00 33.17 2.12
2039 4720 6.312426 CGAGAATCAGCAAAAGTGAGACTATT 59.688 38.462 0.00 0.00 33.17 1.73
2040 4721 7.148507 CGAGAATCAGCAAAAGTGAGACTATTT 60.149 37.037 0.00 0.00 33.17 1.40
2041 4722 8.038492 AGAATCAGCAAAAGTGAGACTATTTC 57.962 34.615 0.00 0.00 0.00 2.17
2042 4723 6.749923 ATCAGCAAAAGTGAGACTATTTCC 57.250 37.500 0.00 0.00 0.00 3.13
2043 4724 5.869579 TCAGCAAAAGTGAGACTATTTCCT 58.130 37.500 0.00 0.00 0.00 3.36
2044 4725 5.702670 TCAGCAAAAGTGAGACTATTTCCTG 59.297 40.000 0.00 0.00 0.00 3.86
2045 4726 5.006386 AGCAAAAGTGAGACTATTTCCTGG 58.994 41.667 0.00 0.00 0.00 4.45
2046 4727 4.156739 GCAAAAGTGAGACTATTTCCTGGG 59.843 45.833 0.00 0.00 0.00 4.45
2047 4728 5.560724 CAAAAGTGAGACTATTTCCTGGGA 58.439 41.667 0.00 0.00 0.00 4.37
2048 4729 5.843019 AAAGTGAGACTATTTCCTGGGAA 57.157 39.130 0.00 0.00 0.00 3.97
2049 4730 4.828072 AGTGAGACTATTTCCTGGGAAC 57.172 45.455 1.04 0.00 33.41 3.62
2069 4750 7.562454 GGAACCATAATTAAAATCTCGGTCA 57.438 36.000 0.00 0.00 0.00 4.02
2070 4751 8.166422 GGAACCATAATTAAAATCTCGGTCAT 57.834 34.615 0.00 0.00 0.00 3.06
2071 4752 9.280174 GGAACCATAATTAAAATCTCGGTCATA 57.720 33.333 0.00 0.00 0.00 2.15
2100 4838 4.942852 AGCAAACGATCCAAATCAACAAA 58.057 34.783 0.00 0.00 31.76 2.83
2174 4913 5.008217 TCAGTTAGGTTGCACACATACAAAC 59.992 40.000 0.00 0.00 33.57 2.93
2211 4952 1.155889 TAAGAGTGTGCAATGTGGCG 58.844 50.000 0.00 0.00 36.28 5.69
2233 4977 5.331902 CGCAATTTTCAAGAATGTACCGAT 58.668 37.500 0.00 0.00 0.00 4.18
2265 5009 8.774586 GCAAAAGTGAGACTACTATTTCTGAAA 58.225 33.333 5.15 5.15 0.00 2.69
2313 5058 5.920193 TTTTCCCAAAAGCTGATGGATAG 57.080 39.130 17.46 3.67 39.12 2.08
2316 5061 3.117888 TCCCAAAAGCTGATGGATAGGTC 60.118 47.826 17.46 0.00 39.12 3.85
2318 5063 2.246719 AAAGCTGATGGATAGGTCGC 57.753 50.000 0.00 0.00 0.00 5.19
2365 5110 2.895680 GGGAGCGAGACATCAGCA 59.104 61.111 0.00 0.00 0.00 4.41
2416 5161 5.396884 GCTAATGAGGAACCCACTAGTGATT 60.397 44.000 24.68 17.03 0.00 2.57
2623 5368 3.343421 GGCACCACCGTGTTCGTC 61.343 66.667 0.00 0.00 42.39 4.20
2749 5494 0.458260 AGTTTGTTCCGTTTGGTGCC 59.542 50.000 0.00 0.00 36.30 5.01
2809 5554 3.136763 CAATATGGAGATTGTGCTCGCT 58.863 45.455 0.00 0.00 35.74 4.93
2926 5671 3.056035 AGAACGATCTTTACCTGTGTCCC 60.056 47.826 0.00 0.00 29.15 4.46
2929 5674 2.618053 GATCTTTACCTGTGTCCCGTG 58.382 52.381 0.00 0.00 0.00 4.94
2940 5685 1.080298 GTCCCGTGGTCCGTGTTAG 60.080 63.158 0.00 0.00 33.66 2.34
2961 5706 1.089920 CCATGTGCTCTTGTGTAGCC 58.910 55.000 0.00 0.00 39.30 3.93
3170 5975 8.834465 CCATGTTTGTAAAAATGTCCAAATCAA 58.166 29.630 6.73 0.00 32.79 2.57
3390 7163 8.877864 TTTCCTTGGTGTATCACAAATTATCT 57.122 30.769 2.41 0.00 35.86 1.98
3572 8121 9.652114 AAAGGCATTTCTTTTATCAGATCCTAT 57.348 29.630 0.00 0.00 33.62 2.57
3717 10361 0.941542 CCTGTCGGCGAAACTTTTCA 59.058 50.000 12.92 2.01 37.01 2.69
3745 10389 7.072328 TCCTCTATTGTATGGATGATTCAACCA 59.928 37.037 16.92 16.92 40.43 3.67
3777 10421 9.832445 GTCTCTTATATGAATAGGGTGTTTCAA 57.168 33.333 0.00 0.00 35.63 2.69
3794 10438 6.206634 GTGTTTCAAGGTTAACATGAGATGGA 59.793 38.462 8.10 0.00 36.72 3.41
3816 10460 7.825709 TGGATTATAATGGAGTTGAGGGAAAT 58.174 34.615 1.78 0.00 0.00 2.17
3840 10484 6.624423 TCATTCCAGCTAAAGAATCAAAAGC 58.376 36.000 3.48 0.00 30.29 3.51
3843 10487 6.743575 TCCAGCTAAAGAATCAAAAGCTAC 57.256 37.500 3.55 0.00 41.44 3.58
3847 10494 7.362401 CCAGCTAAAGAATCAAAAGCTACATGT 60.362 37.037 2.69 2.69 41.44 3.21
3901 10549 3.194861 TGGCGAAACATAGTAGATGTGC 58.805 45.455 0.00 0.00 31.80 4.57
3933 10591 4.522405 TGCTATCTGCTCCTAGAATCAGAC 59.478 45.833 9.05 1.07 43.37 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.911769 AACCCTTCGGATCTGCATCA 59.088 50.000 0.00 0.00 0.00 3.07
74 75 0.802494 GGGAATGTGGTGCGTACTTG 59.198 55.000 3.01 0.00 0.00 3.16
78 79 2.266372 CCGGGAATGTGGTGCGTA 59.734 61.111 0.00 0.00 0.00 4.42
88 89 1.987807 CTGCTGGATGTCCCGGGAAT 61.988 60.000 28.84 20.68 41.44 3.01
146 147 3.071837 TGGCGGCTGATCGTGGTA 61.072 61.111 11.43 0.00 0.00 3.25
283 293 2.047274 CGTCAGGTGGCATCCGTT 60.047 61.111 0.00 0.00 0.00 4.44
285 295 2.509336 GACGTCAGGTGGCATCCG 60.509 66.667 11.55 0.00 0.00 4.18
321 357 4.700448 CCATGGGCCAAGGCACCA 62.700 66.667 15.90 19.14 45.41 4.17
322 358 3.903281 TTCCATGGGCCAAGGCACC 62.903 63.158 22.89 10.91 45.41 5.01
323 359 2.283821 TTCCATGGGCCAAGGCAC 60.284 61.111 22.89 10.36 46.35 5.01
324 360 2.037687 CTTCCATGGGCCAAGGCA 59.962 61.111 22.89 11.71 44.11 4.75
325 361 3.464494 GCTTCCATGGGCCAAGGC 61.464 66.667 22.89 9.06 41.06 4.35
326 362 1.305549 AAGCTTCCATGGGCCAAGG 60.306 57.895 21.77 21.77 0.00 3.61
327 363 1.325476 GGAAGCTTCCATGGGCCAAG 61.325 60.000 35.71 5.87 46.76 3.61
328 364 1.305213 GGAAGCTTCCATGGGCCAA 60.305 57.895 35.71 0.00 46.76 4.52
329 365 2.360191 GGAAGCTTCCATGGGCCA 59.640 61.111 35.71 9.61 46.76 5.36
357 393 3.282745 CTCGTCCCCTCGTGTGTGG 62.283 68.421 0.00 0.00 0.00 4.17
358 394 2.258591 CTCGTCCCCTCGTGTGTG 59.741 66.667 0.00 0.00 0.00 3.82
359 395 2.989824 CCTCGTCCCCTCGTGTGT 60.990 66.667 0.00 0.00 0.00 3.72
360 396 2.675423 TCCTCGTCCCCTCGTGTG 60.675 66.667 0.00 0.00 0.00 3.82
361 397 2.361357 CTCCTCGTCCCCTCGTGT 60.361 66.667 0.00 0.00 0.00 4.49
362 398 3.141488 CCTCCTCGTCCCCTCGTG 61.141 72.222 0.00 0.00 0.00 4.35
417 453 3.471244 CTCTCTTCTACCGCCGCCG 62.471 68.421 0.00 0.00 0.00 6.46
426 462 1.475403 CCACCTTCCGCTCTCTTCTA 58.525 55.000 0.00 0.00 0.00 2.10
427 463 1.261238 CCCACCTTCCGCTCTCTTCT 61.261 60.000 0.00 0.00 0.00 2.85
432 468 2.685380 CCTCCCACCTTCCGCTCT 60.685 66.667 0.00 0.00 0.00 4.09
442 478 2.595009 GATGCCGGTCTTCCTCCCAC 62.595 65.000 1.90 0.00 0.00 4.61
479 515 4.386951 TCACCCCCGCATGTGACG 62.387 66.667 8.11 0.00 36.62 4.35
483 519 3.249189 AGTGTCACCCCCGCATGT 61.249 61.111 0.00 0.00 0.00 3.21
489 525 3.021451 CACTTTCAGTGTCACCCCC 57.979 57.895 0.00 0.00 41.19 5.40
498 534 1.417890 CTCCCCACTCACACTTTCAGT 59.582 52.381 0.00 0.00 0.00 3.41
500 536 0.108585 GCTCCCCACTCACACTTTCA 59.891 55.000 0.00 0.00 0.00 2.69
504 540 1.228769 TACGCTCCCCACTCACACT 60.229 57.895 0.00 0.00 0.00 3.55
506 542 1.228769 AGTACGCTCCCCACTCACA 60.229 57.895 0.00 0.00 0.00 3.58
510 546 4.340620 GAGAGTACGCTCCCCACT 57.659 61.111 15.08 0.00 42.59 4.00
522 558 3.303938 CAGATGGAGTACATGGGAGAGT 58.696 50.000 0.00 0.00 40.72 3.24
544 580 3.495434 AAAACGTCCTACATTGTGGGA 57.505 42.857 17.14 17.14 40.84 4.37
549 585 5.478001 CGTATCGAAAAACGTCCTACATTG 58.522 41.667 9.40 0.00 43.13 2.82
550 586 4.563976 CCGTATCGAAAAACGTCCTACATT 59.436 41.667 14.56 0.00 43.13 2.71
551 587 4.107622 CCGTATCGAAAAACGTCCTACAT 58.892 43.478 14.56 0.00 43.13 2.29
553 589 2.854185 CCCGTATCGAAAAACGTCCTAC 59.146 50.000 14.56 0.00 43.13 3.18
555 591 1.545582 TCCCGTATCGAAAAACGTCCT 59.454 47.619 14.56 0.00 43.13 3.85
556 592 1.655597 GTCCCGTATCGAAAAACGTCC 59.344 52.381 14.56 2.21 43.13 4.79
557 593 2.599659 AGTCCCGTATCGAAAAACGTC 58.400 47.619 14.56 7.16 43.13 4.34
559 595 3.762779 AGTAGTCCCGTATCGAAAAACG 58.237 45.455 10.35 10.35 44.09 3.60
560 596 5.741040 CAGTAGTAGTCCCGTATCGAAAAAC 59.259 44.000 0.00 0.00 0.00 2.43
561 597 5.647658 TCAGTAGTAGTCCCGTATCGAAAAA 59.352 40.000 0.00 0.00 0.00 1.94
563 599 4.769688 TCAGTAGTAGTCCCGTATCGAAA 58.230 43.478 0.00 0.00 0.00 3.46
564 600 4.406648 TCAGTAGTAGTCCCGTATCGAA 57.593 45.455 0.00 0.00 0.00 3.71
565 601 4.141846 ACTTCAGTAGTAGTCCCGTATCGA 60.142 45.833 0.00 0.00 34.56 3.59
566 602 4.125703 ACTTCAGTAGTAGTCCCGTATCG 58.874 47.826 0.00 0.00 34.56 2.92
567 603 6.094603 TCAAACTTCAGTAGTAGTCCCGTATC 59.905 42.308 0.00 0.00 35.54 2.24
568 604 5.948162 TCAAACTTCAGTAGTAGTCCCGTAT 59.052 40.000 0.00 0.00 35.54 3.06
569 605 5.316167 TCAAACTTCAGTAGTAGTCCCGTA 58.684 41.667 0.00 0.00 35.54 4.02
571 607 4.458295 TCTCAAACTTCAGTAGTAGTCCCG 59.542 45.833 0.00 0.00 35.54 5.14
575 611 5.047660 CCAGCTCTCAAACTTCAGTAGTAGT 60.048 44.000 0.00 0.00 35.54 2.73
576 612 5.406649 CCAGCTCTCAAACTTCAGTAGTAG 58.593 45.833 0.00 0.00 35.54 2.57
641 2960 7.782049 TGATATATGAACTCCGAAAAGACTGT 58.218 34.615 0.00 0.00 0.00 3.55
695 3014 2.251040 CCGTCAGTGAGTAATCGTGTG 58.749 52.381 0.00 0.00 0.00 3.82
759 3078 5.185454 TGCCTGTTGTGATAATGGAAGTAG 58.815 41.667 0.00 0.00 0.00 2.57
760 3079 5.172687 TGCCTGTTGTGATAATGGAAGTA 57.827 39.130 0.00 0.00 0.00 2.24
830 3149 5.118642 AGAGTCGACTTTAGTGTTGGTAC 57.881 43.478 21.08 1.52 0.00 3.34
907 3228 4.908877 GCGCTCGAGGGAGTACGC 62.909 72.222 31.36 22.83 41.92 4.42
909 3230 2.409651 CAGCGCTCGAGGGAGTAC 59.590 66.667 31.36 14.37 42.53 2.73
924 3245 4.514441 AGTTCTTGTGAAGAGTTCATGCAG 59.486 41.667 0.00 0.00 42.47 4.41
931 3252 4.487714 TGGTCAGTTCTTGTGAAGAGTT 57.512 40.909 0.00 0.00 39.03 3.01
932 3253 4.346418 AGATGGTCAGTTCTTGTGAAGAGT 59.654 41.667 0.00 0.00 39.03 3.24
956 3285 4.451241 CACATATGCTCAGCGCCT 57.549 55.556 2.29 0.00 38.05 5.52
1053 3574 1.515020 CGGAGGGAGAAGCAGAGTG 59.485 63.158 0.00 0.00 0.00 3.51
1592 4113 0.830648 GAACCTGTCCCCGATCATGA 59.169 55.000 0.00 0.00 0.00 3.07
1966 4647 8.114331 TCTCAATCAATGTTGCAAATTACTCT 57.886 30.769 0.00 0.00 0.00 3.24
1967 4648 8.922058 ATCTCAATCAATGTTGCAAATTACTC 57.078 30.769 0.00 0.00 0.00 2.59
1968 4649 9.715121 AAATCTCAATCAATGTTGCAAATTACT 57.285 25.926 0.00 0.00 0.00 2.24
1984 4665 6.585322 CCAGAAACTTGCTGAAAATCTCAATC 59.415 38.462 0.00 0.00 35.39 2.67
2021 4702 5.106396 CCAGGAAATAGTCTCACTTTTGCTG 60.106 44.000 16.64 16.64 40.18 4.41
2022 4703 5.006386 CCAGGAAATAGTCTCACTTTTGCT 58.994 41.667 0.00 0.00 32.17 3.91
2023 4704 4.156739 CCCAGGAAATAGTCTCACTTTTGC 59.843 45.833 0.00 0.00 0.00 3.68
2024 4705 5.560724 TCCCAGGAAATAGTCTCACTTTTG 58.439 41.667 0.00 0.00 0.00 2.44
2025 4706 5.843019 TCCCAGGAAATAGTCTCACTTTT 57.157 39.130 0.00 0.00 0.00 2.27
2026 4707 5.515008 GGTTCCCAGGAAATAGTCTCACTTT 60.515 44.000 0.00 0.00 35.75 2.66
2027 4708 4.019231 GGTTCCCAGGAAATAGTCTCACTT 60.019 45.833 0.00 0.00 35.75 3.16
2028 4709 3.519913 GGTTCCCAGGAAATAGTCTCACT 59.480 47.826 0.00 0.00 35.75 3.41
2029 4710 3.263425 TGGTTCCCAGGAAATAGTCTCAC 59.737 47.826 0.00 0.00 35.75 3.51
2030 4711 3.526899 TGGTTCCCAGGAAATAGTCTCA 58.473 45.455 0.00 0.00 35.75 3.27
2031 4712 4.779993 ATGGTTCCCAGGAAATAGTCTC 57.220 45.455 0.00 0.00 36.75 3.36
2032 4713 6.848562 ATTATGGTTCCCAGGAAATAGTCT 57.151 37.500 0.00 0.00 36.75 3.24
2033 4714 8.990163 TTAATTATGGTTCCCAGGAAATAGTC 57.010 34.615 0.00 0.00 36.75 2.59
2034 4715 9.777008 TTTTAATTATGGTTCCCAGGAAATAGT 57.223 29.630 0.00 0.00 36.75 2.12
2037 4718 9.506042 AGATTTTAATTATGGTTCCCAGGAAAT 57.494 29.630 0.00 0.00 36.75 2.17
2038 4719 8.909423 AGATTTTAATTATGGTTCCCAGGAAA 57.091 30.769 0.00 0.00 36.75 3.13
2039 4720 7.284489 CGAGATTTTAATTATGGTTCCCAGGAA 59.716 37.037 0.00 0.00 36.75 3.36
2040 4721 6.770785 CGAGATTTTAATTATGGTTCCCAGGA 59.229 38.462 0.00 0.00 36.75 3.86
2041 4722 6.016276 CCGAGATTTTAATTATGGTTCCCAGG 60.016 42.308 0.00 0.00 36.75 4.45
2042 4723 6.546034 ACCGAGATTTTAATTATGGTTCCCAG 59.454 38.462 0.00 0.00 36.75 4.45
2043 4724 6.428295 ACCGAGATTTTAATTATGGTTCCCA 58.572 36.000 0.00 0.00 38.19 4.37
2044 4725 6.544564 TGACCGAGATTTTAATTATGGTTCCC 59.455 38.462 0.00 0.00 0.00 3.97
2045 4726 7.562454 TGACCGAGATTTTAATTATGGTTCC 57.438 36.000 0.00 0.00 0.00 3.62
2057 4738 9.921637 TTTGCTTTAAAATATGACCGAGATTTT 57.078 25.926 0.00 0.00 38.65 1.82
2058 4739 9.353999 GTTTGCTTTAAAATATGACCGAGATTT 57.646 29.630 0.00 0.00 0.00 2.17
2059 4740 7.696453 CGTTTGCTTTAAAATATGACCGAGATT 59.304 33.333 0.00 0.00 0.00 2.40
2060 4741 7.065324 TCGTTTGCTTTAAAATATGACCGAGAT 59.935 33.333 0.00 0.00 0.00 2.75
2061 4742 6.369340 TCGTTTGCTTTAAAATATGACCGAGA 59.631 34.615 0.00 0.00 0.00 4.04
2062 4743 6.539324 TCGTTTGCTTTAAAATATGACCGAG 58.461 36.000 0.00 0.00 0.00 4.63
2063 4744 6.483385 TCGTTTGCTTTAAAATATGACCGA 57.517 33.333 0.00 0.00 0.00 4.69
2064 4745 6.413818 GGATCGTTTGCTTTAAAATATGACCG 59.586 38.462 0.00 0.00 0.00 4.79
2065 4746 7.254852 TGGATCGTTTGCTTTAAAATATGACC 58.745 34.615 0.00 0.00 0.00 4.02
2066 4747 8.682128 TTGGATCGTTTGCTTTAAAATATGAC 57.318 30.769 0.00 0.00 0.00 3.06
2067 4748 9.868277 ATTTGGATCGTTTGCTTTAAAATATGA 57.132 25.926 0.00 0.00 0.00 2.15
2069 4750 9.868277 TGATTTGGATCGTTTGCTTTAAAATAT 57.132 25.926 0.00 0.00 34.91 1.28
2070 4751 9.698309 TTGATTTGGATCGTTTGCTTTAAAATA 57.302 25.926 0.00 0.00 34.91 1.40
2071 4752 8.495148 GTTGATTTGGATCGTTTGCTTTAAAAT 58.505 29.630 0.00 0.00 34.91 1.82
2072 4753 7.492669 TGTTGATTTGGATCGTTTGCTTTAAAA 59.507 29.630 0.00 0.00 34.91 1.52
2073 4754 6.980978 TGTTGATTTGGATCGTTTGCTTTAAA 59.019 30.769 0.00 0.00 34.91 1.52
2074 4755 6.507900 TGTTGATTTGGATCGTTTGCTTTAA 58.492 32.000 0.00 0.00 34.91 1.52
2075 4756 6.078202 TGTTGATTTGGATCGTTTGCTTTA 57.922 33.333 0.00 0.00 34.91 1.85
2076 4757 4.942852 TGTTGATTTGGATCGTTTGCTTT 58.057 34.783 0.00 0.00 34.91 3.51
2077 4758 4.582701 TGTTGATTTGGATCGTTTGCTT 57.417 36.364 0.00 0.00 34.91 3.91
2157 4896 5.524284 TGTAATGTTTGTATGTGTGCAACC 58.476 37.500 0.00 0.00 34.36 3.77
2197 4938 0.945265 AATTGCGCCACATTGCACAC 60.945 50.000 4.18 0.00 41.57 3.82
2211 4952 6.321717 TCATCGGTACATTCTTGAAAATTGC 58.678 36.000 0.00 0.00 0.00 3.56
2233 4977 9.944376 AAATAGTAGTCTCACTTTTGCTAATCA 57.056 29.630 0.00 0.00 0.00 2.57
2295 5040 3.217626 GACCTATCCATCAGCTTTTGGG 58.782 50.000 10.99 0.00 33.62 4.12
2313 5058 0.859232 CTGTATGCCAATACGCGACC 59.141 55.000 15.93 0.00 41.46 4.79
2316 5061 0.859232 GTCCTGTATGCCAATACGCG 59.141 55.000 3.53 3.53 41.46 6.01
2318 5063 2.365617 AGAGGTCCTGTATGCCAATACG 59.634 50.000 0.00 0.00 41.46 3.06
2365 5110 2.917713 TGGCCCATTGGAGTGTATTT 57.082 45.000 3.62 0.00 0.00 1.40
2416 5161 0.880278 GCTCGACTTGTGCCTTGTGA 60.880 55.000 0.00 0.00 0.00 3.58
2480 5225 1.133809 AGGTACTTCAGGCCAGCCAA 61.134 55.000 12.03 0.00 33.92 4.52
2809 5554 1.137282 TCGAAGTGGTACAACAGTGCA 59.863 47.619 2.54 0.00 44.16 4.57
2926 5671 2.515996 ATGGGCTAACACGGACCACG 62.516 60.000 0.00 0.00 45.57 4.94
2929 5674 1.024579 CACATGGGCTAACACGGACC 61.025 60.000 0.00 0.00 0.00 4.46
2940 5685 1.089920 CTACACAAGAGCACATGGGC 58.910 55.000 13.49 13.49 0.00 5.36
2961 5706 2.548057 ACATGGTGTGACAAGTAAAGCG 59.452 45.455 0.00 0.00 0.00 4.68
3170 5975 4.463891 CCATACAGAAAGCACCCAGAAAAT 59.536 41.667 0.00 0.00 0.00 1.82
3390 7163 5.636123 TGGCCTGAAAGAATAACCTTGTAA 58.364 37.500 3.32 0.00 34.07 2.41
3438 7211 9.167311 CTGCTAGTAAAAAGAGAACCAATATGT 57.833 33.333 0.00 0.00 0.00 2.29
3572 8121 8.946085 CATAGCATTTGAGTAGTTACCTTTGAA 58.054 33.333 0.00 0.00 0.00 2.69
3717 10361 9.512588 GTTGAATCATCCATACAATAGAGGAAT 57.487 33.333 0.00 0.00 33.17 3.01
3761 10405 6.366340 TGTTAACCTTGAAACACCCTATTCA 58.634 36.000 2.48 0.00 33.93 2.57
3766 10410 4.798882 TCATGTTAACCTTGAAACACCCT 58.201 39.130 2.48 0.00 38.35 4.34
3777 10421 9.745018 CCATTATAATCCATCTCATGTTAACCT 57.255 33.333 2.48 0.00 0.00 3.50
3782 10426 9.293404 CAACTCCATTATAATCCATCTCATGTT 57.707 33.333 0.00 0.00 0.00 2.71
3794 10438 9.887862 AATGATTTCCCTCAACTCCATTATAAT 57.112 29.630 0.00 0.00 0.00 1.28
3816 10460 6.435277 AGCTTTTGATTCTTTAGCTGGAATGA 59.565 34.615 13.48 5.44 40.45 2.57
3836 10480 7.829211 AGTATGACAACCATAACATGTAGCTTT 59.171 33.333 0.00 0.00 39.29 3.51
3840 10484 7.465916 GCACAGTATGACAACCATAACATGTAG 60.466 40.741 0.00 0.00 39.29 2.74
3843 10487 5.355071 AGCACAGTATGACAACCATAACATG 59.645 40.000 0.00 0.00 39.29 3.21
3847 10494 3.689161 GCAGCACAGTATGACAACCATAA 59.311 43.478 0.00 0.00 39.29 1.90
3933 10591 2.162408 GGGCAAGGAGAAAACAATCTCG 59.838 50.000 0.00 0.00 45.54 4.04


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

AutoCloner maintained by Alex Coulton.