Multiple sequence alignment - TraesCS5A01G411600

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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 TraesCS5A01G411600 chr5A 100.000 3302 0 0 1 3302 600141894 600138593 0.000000e+00 6098.0
1 TraesCS5A01G411600 chr5A 95.329 578 22 4 2727 3302 546715111 546715685 0.000000e+00 913.0
2 TraesCS5A01G411600 chr5B 94.030 1876 82 13 617 2470 589457391 589455524 0.000000e+00 2817.0
3 TraesCS5A01G411600 chr5B 88.380 568 48 12 2744 3302 356198625 356199183 0.000000e+00 667.0
4 TraesCS5A01G411600 chr5B 87.395 595 47 16 2729 3302 87121096 87121683 0.000000e+00 658.0
5 TraesCS5A01G411600 chr5B 86.503 163 18 3 235 396 636231105 636230946 3.390000e-40 176.0
6 TraesCS5A01G411600 chr5B 88.618 123 9 3 110 229 589459257 589459137 9.550000e-31 145.0
7 TraesCS5A01G411600 chr5D 93.717 1719 69 18 765 2458 480979387 480977683 0.000000e+00 2540.0
8 TraesCS5A01G411600 chr5D 89.234 548 38 13 2775 3302 542645712 542646258 0.000000e+00 665.0
9 TraesCS5A01G411600 chr5D 89.728 331 30 3 405 734 480983312 480982985 1.420000e-113 420.0
10 TraesCS5A01G411600 chr5D 90.476 147 12 2 84 230 480983450 480983306 3.360000e-45 193.0
11 TraesCS5A01G411600 chr5D 93.805 113 6 1 2626 2737 480976882 480976770 5.670000e-38 169.0
12 TraesCS5A01G411600 chr5D 89.855 69 7 0 2728 2796 237468642 237468574 4.540000e-14 89.8
13 TraesCS5A01G411600 chr5D 100.000 46 0 0 2577 2622 480977003 480976958 5.870000e-13 86.1
14 TraesCS5A01G411600 chr3B 97.924 578 10 2 2727 3302 55729807 55729230 0.000000e+00 1000.0
15 TraesCS5A01G411600 chr3B 86.503 163 18 3 235 396 458109625 458109466 3.390000e-40 176.0
16 TraesCS5A01G411600 chr7A 98.230 565 10 0 2738 3302 150086583 150087147 0.000000e+00 989.0
17 TraesCS5A01G411600 chr3A 97.884 567 12 0 2736 3302 101604578 101605144 0.000000e+00 981.0
18 TraesCS5A01G411600 chr3A 82.609 92 14 2 2709 2800 360727393 360727482 2.730000e-11 80.5
19 TraesCS5A01G411600 chr1B 95.374 562 24 2 2742 3302 299982275 299981715 0.000000e+00 893.0
20 TraesCS5A01G411600 chr1B 87.248 149 17 1 235 381 435243075 435243223 5.670000e-38 169.0
21 TraesCS5A01G411600 chr2B 87.117 163 17 3 235 396 359319810 359319651 7.280000e-42 182.0
22 TraesCS5A01G411600 chr7D 88.000 150 16 2 235 384 489180921 489180774 3.390000e-40 176.0
23 TraesCS5A01G411600 chr7D 87.838 74 9 0 2727 2800 26561772 26561699 1.630000e-13 87.9
24 TraesCS5A01G411600 chr1A 86.585 164 16 3 235 396 540673201 540673042 3.390000e-40 176.0
25 TraesCS5A01G411600 chr7B 85.802 162 21 2 235 396 433770320 433770161 1.580000e-38 171.0
26 TraesCS5A01G411600 chr6D 85.890 163 20 3 235 396 24267062 24266902 1.580000e-38 171.0
27 TraesCS5A01G411600 chr4D 85.890 163 20 3 235 396 163743302 163743142 1.580000e-38 171.0
28 TraesCS5A01G411600 chr2D 97.674 86 2 0 1593 1678 623330034 623329949 7.380000e-32 148.0
29 TraesCS5A01G411600 chr2D 90.164 61 6 0 1254 1314 607600348 607600288 2.730000e-11 80.5
30 TraesCS5A01G411600 chr2D 97.619 42 1 0 1272 1313 623330380 623330339 4.570000e-09 73.1
31 TraesCS5A01G411600 chr2D 97.500 40 1 0 1535 1574 623330074 623330035 5.910000e-08 69.4


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 TraesCS5A01G411600 chr5A 600138593 600141894 3301 True 6098.00 6098 100.0000 1 3302 1 chr5A.!!$R1 3301
1 TraesCS5A01G411600 chr5A 546715111 546715685 574 False 913.00 913 95.3290 2727 3302 1 chr5A.!!$F1 575
2 TraesCS5A01G411600 chr5B 589455524 589459257 3733 True 1481.00 2817 91.3240 110 2470 2 chr5B.!!$R2 2360
3 TraesCS5A01G411600 chr5B 356198625 356199183 558 False 667.00 667 88.3800 2744 3302 1 chr5B.!!$F2 558
4 TraesCS5A01G411600 chr5B 87121096 87121683 587 False 658.00 658 87.3950 2729 3302 1 chr5B.!!$F1 573
5 TraesCS5A01G411600 chr5D 480976770 480983450 6680 True 681.62 2540 93.5452 84 2737 5 chr5D.!!$R2 2653
6 TraesCS5A01G411600 chr5D 542645712 542646258 546 False 665.00 665 89.2340 2775 3302 1 chr5D.!!$F1 527
7 TraesCS5A01G411600 chr3B 55729230 55729807 577 True 1000.00 1000 97.9240 2727 3302 1 chr3B.!!$R1 575
8 TraesCS5A01G411600 chr7A 150086583 150087147 564 False 989.00 989 98.2300 2738 3302 1 chr7A.!!$F1 564
9 TraesCS5A01G411600 chr3A 101604578 101605144 566 False 981.00 981 97.8840 2736 3302 1 chr3A.!!$F1 566
10 TraesCS5A01G411600 chr1B 299981715 299982275 560 True 893.00 893 95.3740 2742 3302 1 chr1B.!!$R1 560

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
852 5981 0.104304 CCCGGTCGATTTCTACCCTG 59.896 60.0 0.0 0.0 31.68 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2630 8342 0.030908 GACCCACGCCTAATCTCTCG 59.969 60.0 0.0 0.0 0.0 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
81 82 9.474249 GTTTCGTCTTTACTTCATTATTACAGC 57.526 33.333 0.00 0.00 0.00 4.40
82 83 8.766000 TTCGTCTTTACTTCATTATTACAGCA 57.234 30.769 0.00 0.00 0.00 4.41
118 119 4.865761 GTGATGACCGCGCCGCTA 62.866 66.667 7.78 0.00 0.00 4.26
131 132 1.873165 CCGCTACATTTGCCAACGT 59.127 52.632 0.00 0.00 0.00 3.99
135 136 1.804151 GCTACATTTGCCAACGTCTCA 59.196 47.619 0.00 0.00 0.00 3.27
180 181 1.452717 CTTGTTGTTCAACGCGTGTC 58.547 50.000 14.98 4.29 32.18 3.67
209 213 1.066430 TCCAGGCAGGTTATTCGTGAC 60.066 52.381 0.00 0.00 39.95 3.67
223 227 1.201647 TCGTGACATCGTTTCCCTCTC 59.798 52.381 0.00 0.00 0.00 3.20
227 231 4.065789 GTGACATCGTTTCCCTCTCTTTT 58.934 43.478 0.00 0.00 0.00 2.27
284 404 9.741168 CATAACTATGTCACTTTTAAGTTGACG 57.259 33.333 14.54 0.00 38.61 4.35
285 405 7.781548 AACTATGTCACTTTTAAGTTGACGT 57.218 32.000 16.58 16.58 38.61 4.34
286 406 7.404139 ACTATGTCACTTTTAAGTTGACGTC 57.596 36.000 9.11 9.11 38.61 4.34
287 407 5.668558 ATGTCACTTTTAAGTTGACGTCC 57.331 39.130 14.12 0.00 38.61 4.79
288 408 4.505808 TGTCACTTTTAAGTTGACGTCCA 58.494 39.130 14.12 0.00 38.61 4.02
289 409 5.120399 TGTCACTTTTAAGTTGACGTCCAT 58.880 37.500 14.12 0.00 38.61 3.41
290 410 5.587043 TGTCACTTTTAAGTTGACGTCCATT 59.413 36.000 14.12 7.62 38.61 3.16
291 411 6.094325 TGTCACTTTTAAGTTGACGTCCATTT 59.906 34.615 14.12 7.89 38.61 2.32
293 1470 6.970043 TCACTTTTAAGTTGACGTCCATTTTG 59.030 34.615 14.12 0.50 37.08 2.44
295 1472 7.274686 CACTTTTAAGTTGACGTCCATTTTGTT 59.725 33.333 14.12 0.00 37.08 2.83
298 1475 4.712122 AGTTGACGTCCATTTTGTTTGT 57.288 36.364 14.12 0.00 0.00 2.83
300 1477 3.428746 TGACGTCCATTTTGTTTGTGG 57.571 42.857 14.12 0.00 0.00 4.17
304 1481 4.200874 ACGTCCATTTTGTTTGTGGTCTA 58.799 39.130 0.00 0.00 34.61 2.59
307 1484 6.183360 ACGTCCATTTTGTTTGTGGTCTATTT 60.183 34.615 0.00 0.00 34.61 1.40
370 1547 6.808321 ATATTTGTAGGAGCTTAGGTGTGA 57.192 37.500 0.00 0.00 0.00 3.58
371 1548 3.955650 TTGTAGGAGCTTAGGTGTGAC 57.044 47.619 0.00 0.00 0.00 3.67
372 1549 2.884320 TGTAGGAGCTTAGGTGTGACA 58.116 47.619 0.00 0.00 0.00 3.58
373 1550 3.441101 TGTAGGAGCTTAGGTGTGACAT 58.559 45.455 0.00 0.00 0.00 3.06
375 1552 4.401519 TGTAGGAGCTTAGGTGTGACATAC 59.598 45.833 0.00 0.00 0.00 2.39
376 1553 3.714144 AGGAGCTTAGGTGTGACATACT 58.286 45.455 2.14 0.00 0.00 2.12
382 1693 7.389607 GGAGCTTAGGTGTGACATACTTAAAAA 59.610 37.037 8.01 0.00 0.00 1.94
432 1983 1.083015 CGCCTTTTTGTCGTCGTGG 60.083 57.895 0.00 0.00 0.00 4.94
452 2003 2.418884 GGGATCCTCGGACTCACTTTTC 60.419 54.545 12.58 0.00 0.00 2.29
513 2064 0.109272 TCGTAGAGCAACTGGAAGCG 60.109 55.000 0.00 0.00 37.60 4.68
519 2070 2.131183 GAGCAACTGGAAGCGCTATAG 58.869 52.381 12.05 12.22 44.96 1.31
521 2072 1.861575 GCAACTGGAAGCGCTATAGTC 59.138 52.381 12.05 3.81 37.60 2.59
522 2073 2.738643 GCAACTGGAAGCGCTATAGTCA 60.739 50.000 12.05 4.09 37.60 3.41
523 2074 3.722147 CAACTGGAAGCGCTATAGTCAT 58.278 45.455 12.05 0.00 37.60 3.06
524 2075 3.651803 ACTGGAAGCGCTATAGTCATC 57.348 47.619 12.05 1.52 37.60 2.92
539 2090 7.232941 GCTATAGTCATCAAGGAAGGGTAACTA 59.767 40.741 0.84 0.00 0.00 2.24
556 2107 2.409975 ACTAACACGACAACCGATTGG 58.590 47.619 0.00 0.00 40.42 3.16
557 2108 1.127951 CTAACACGACAACCGATTGGC 59.872 52.381 0.00 0.00 40.88 4.52
563 2114 2.174060 GACAACCGATTGGCGATTTC 57.826 50.000 0.00 0.00 44.57 2.17
564 2115 1.737793 GACAACCGATTGGCGATTTCT 59.262 47.619 0.00 0.00 44.57 2.52
566 2117 1.468520 CAACCGATTGGCGATTTCTGT 59.531 47.619 0.00 0.00 44.57 3.41
568 2119 0.378257 CCGATTGGCGATTTCTGTGG 59.622 55.000 0.00 0.00 44.57 4.17
571 2122 2.223112 CGATTGGCGATTTCTGTGGAAG 60.223 50.000 0.00 0.00 44.57 3.46
573 2124 0.960364 TGGCGATTTCTGTGGAAGCC 60.960 55.000 0.00 0.00 39.37 4.35
579 2130 0.320374 TTTCTGTGGAAGCCGATCGT 59.680 50.000 15.09 0.00 32.61 3.73
581 2132 0.320374 TCTGTGGAAGCCGATCGTTT 59.680 50.000 15.09 8.09 0.00 3.60
597 2149 3.527533 TCGTTTGAATCGGGAGGTTATG 58.472 45.455 0.00 0.00 29.80 1.90
604 2156 5.940617 TGAATCGGGAGGTTATGAATCAAT 58.059 37.500 0.00 0.00 29.80 2.57
612 2164 7.308229 CGGGAGGTTATGAATCAATCAGATTTC 60.308 40.741 0.00 0.00 46.76 2.17
669 2221 1.465777 CCGATTTTAAAACGGCCGTCT 59.534 47.619 34.29 23.93 40.19 4.18
852 5981 0.104304 CCCGGTCGATTTCTACCCTG 59.896 60.000 0.00 0.00 31.68 4.45
904 6038 1.169661 AATTTCCACGAAGCCGCACA 61.170 50.000 0.00 0.00 39.95 4.57
908 6042 4.059459 CACGAAGCCGCACACGTC 62.059 66.667 6.55 0.00 39.95 4.34
912 6046 2.789203 GAAGCCGCACACGTCGATC 61.789 63.158 0.00 0.00 37.70 3.69
928 6062 1.001487 CGATCTCGATCTGCTCTGCTT 60.001 52.381 5.47 0.00 43.02 3.91
959 6093 3.121030 CGGAGCGGCAGACAAAGG 61.121 66.667 1.45 0.00 0.00 3.11
960 6094 2.032681 GGAGCGGCAGACAAAGGT 59.967 61.111 1.45 0.00 0.00 3.50
1252 6389 3.833645 CGCGAAGGATGTCCGGGA 61.834 66.667 0.00 0.00 42.08 5.14
1356 6493 4.394712 GAGGGGGTCACCGTGCTG 62.395 72.222 0.00 0.00 41.60 4.41
1761 6898 1.760875 GATGGTACTCTGCCCCGGA 60.761 63.158 0.73 0.00 0.00 5.14
1837 6974 2.341257 GTGATCATGACAACAGCGTCT 58.659 47.619 0.00 0.00 36.82 4.18
2151 7291 1.599576 GGTGGCTCAGGAGGAAGAC 59.400 63.158 0.00 0.00 0.00 3.01
2324 7464 1.021968 GACTTTGGTTGGTTGCTCGT 58.978 50.000 0.00 0.00 0.00 4.18
2325 7465 0.738389 ACTTTGGTTGGTTGCTCGTG 59.262 50.000 0.00 0.00 0.00 4.35
2329 7469 2.904866 GTTGGTTGCTCGTGGGCA 60.905 61.111 0.00 0.00 40.74 5.36
2330 7470 2.904866 TTGGTTGCTCGTGGGCAC 60.905 61.111 0.00 0.00 42.27 5.01
2332 7472 2.046009 TTGGTTGCTCGTGGGCACTA 62.046 55.000 0.00 0.00 42.27 2.74
2333 7473 1.741770 GGTTGCTCGTGGGCACTAG 60.742 63.158 0.00 0.00 42.27 2.57
2338 7489 1.682684 CTCGTGGGCACTAGGAGGT 60.683 63.158 0.00 0.00 45.78 3.85
2350 7501 4.316645 CACTAGGAGGTATCGATCGAGAA 58.683 47.826 23.84 11.30 0.00 2.87
2358 7509 6.583050 GGAGGTATCGATCGAGAAAATAAGTG 59.417 42.308 23.84 0.00 0.00 3.16
2362 7513 3.863424 TCGATCGAGAAAATAAGTGGTGC 59.137 43.478 15.15 0.00 0.00 5.01
2365 7516 3.250744 TCGAGAAAATAAGTGGTGCGAG 58.749 45.455 0.00 0.00 0.00 5.03
2404 7555 8.873215 TCTAAGAACTTGACACTTTCAGTTAG 57.127 34.615 0.00 0.00 34.94 2.34
2406 7557 9.745880 CTAAGAACTTGACACTTTCAGTTAGTA 57.254 33.333 0.00 0.00 34.94 1.82
2407 7558 8.421673 AAGAACTTGACACTTTCAGTTAGTAC 57.578 34.615 0.00 0.00 34.94 2.73
2408 7559 7.783042 AGAACTTGACACTTTCAGTTAGTACT 58.217 34.615 0.00 0.00 34.94 2.73
2424 7575 9.784680 CAGTTAGTACTGTGTATTACTACTTGG 57.215 37.037 5.39 0.00 45.46 3.61
2430 7581 7.735326 ACTGTGTATTACTACTTGGATTCCT 57.265 36.000 3.95 0.00 0.00 3.36
2453 7604 1.102154 TGTGTGTTGAACTGCCAAGG 58.898 50.000 0.00 0.00 0.00 3.61
2458 7609 0.881796 GTTGAACTGCCAAGGCCTAC 59.118 55.000 5.16 0.00 41.09 3.18
2459 7610 0.251165 TTGAACTGCCAAGGCCTACC 60.251 55.000 5.16 0.00 41.09 3.18
2484 7954 7.827236 CCATTACATTTAGAAACAGAGGGTGTA 59.173 37.037 0.00 0.00 39.03 2.90
2485 7955 8.665685 CATTACATTTAGAAACAGAGGGTGTAC 58.334 37.037 0.00 0.00 39.03 2.90
2486 7956 6.435292 ACATTTAGAAACAGAGGGTGTACT 57.565 37.500 0.00 0.00 39.03 2.73
2487 7957 7.549147 ACATTTAGAAACAGAGGGTGTACTA 57.451 36.000 0.00 0.00 39.03 1.82
2488 7958 7.612677 ACATTTAGAAACAGAGGGTGTACTAG 58.387 38.462 0.00 0.00 39.03 2.57
2489 7959 6.600882 TTTAGAAACAGAGGGTGTACTAGG 57.399 41.667 0.00 0.00 39.03 3.02
2491 7961 1.183549 AACAGAGGGTGTACTAGGCG 58.816 55.000 0.00 0.00 39.03 5.52
2528 7998 2.095919 CCGATTTCCGACAGGTTGTTTC 60.096 50.000 0.00 0.00 41.76 2.78
2548 8019 1.269051 CGTTCCTGGTTTGGAAAGTGC 60.269 52.381 0.00 0.00 46.34 4.40
2564 8035 6.759827 TGGAAAGTGCGTAGGATTACTTATTC 59.240 38.462 0.00 0.00 33.37 1.75
2565 8036 6.202379 GGAAAGTGCGTAGGATTACTTATTCC 59.798 42.308 0.00 0.00 33.37 3.01
2566 8037 5.211174 AGTGCGTAGGATTACTTATTCCC 57.789 43.478 0.00 0.00 32.05 3.97
2569 8040 5.995897 GTGCGTAGGATTACTTATTCCCAAT 59.004 40.000 0.00 0.00 32.05 3.16
2570 8041 6.147328 GTGCGTAGGATTACTTATTCCCAATC 59.853 42.308 0.00 0.00 32.05 2.67
2571 8042 5.347907 GCGTAGGATTACTTATTCCCAATCG 59.652 44.000 0.00 0.00 32.05 3.34
2572 8043 5.347907 CGTAGGATTACTTATTCCCAATCGC 59.652 44.000 0.00 0.00 32.05 4.58
2573 8044 5.568620 AGGATTACTTATTCCCAATCGCT 57.431 39.130 0.00 0.00 32.05 4.93
2574 8045 5.308825 AGGATTACTTATTCCCAATCGCTG 58.691 41.667 0.00 0.00 32.05 5.18
2622 8334 7.158697 AGATTTGCAATAAGTGGGGTTTAAAC 58.841 34.615 9.98 9.98 0.00 2.01
2623 8335 5.871396 TTGCAATAAGTGGGGTTTAAACA 57.129 34.783 19.57 0.00 0.00 2.83
2624 8336 5.461032 TGCAATAAGTGGGGTTTAAACAG 57.539 39.130 19.57 0.00 0.00 3.16
2625 8337 4.282195 TGCAATAAGTGGGGTTTAAACAGG 59.718 41.667 19.57 0.00 0.00 4.00
2626 8338 4.322424 GCAATAAGTGGGGTTTAAACAGGG 60.322 45.833 19.57 0.00 0.00 4.45
2629 8341 1.156566 TGGGGTTTAAACAGGGGGC 59.843 57.895 19.57 1.42 0.00 5.80
2630 8342 1.611261 GGGGTTTAAACAGGGGGCC 60.611 63.158 19.57 10.06 0.00 5.80
2669 8454 4.751539 GCATGTCATGTCGTGCAC 57.248 55.556 25.79 6.82 46.02 4.57
2673 8458 1.724082 CATGTCATGTCGTGCACGTTA 59.276 47.619 35.74 25.95 40.80 3.18
2693 8478 2.260869 CCTTGGCCTCGTGTTGTGG 61.261 63.158 3.32 0.00 0.00 4.17
2706 8491 4.678499 TGTGGCTGACGCGCATGA 62.678 61.111 5.73 0.00 36.88 3.07
2752 8539 1.176527 ATTGAACCAGGACAATGCCG 58.823 50.000 13.13 0.00 35.75 5.69
3062 8863 2.039818 TGAACGTGCACCCTAACAAA 57.960 45.000 12.15 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 9.474249 GCTGTAATAATGAAGTAAAGACGAAAC 57.526 33.333 0.00 0.00 0.00 2.78
56 57 9.210329 TGCTGTAATAATGAAGTAAAGACGAAA 57.790 29.630 0.00 0.00 0.00 3.46
57 58 8.766000 TGCTGTAATAATGAAGTAAAGACGAA 57.234 30.769 0.00 0.00 0.00 3.85
58 59 8.033038 ACTGCTGTAATAATGAAGTAAAGACGA 58.967 33.333 0.00 0.00 0.00 4.20
59 60 8.186178 ACTGCTGTAATAATGAAGTAAAGACG 57.814 34.615 0.00 0.00 0.00 4.18
60 61 8.321716 CGACTGCTGTAATAATGAAGTAAAGAC 58.678 37.037 0.00 0.00 0.00 3.01
61 62 8.033038 ACGACTGCTGTAATAATGAAGTAAAGA 58.967 33.333 0.00 0.00 0.00 2.52
62 63 8.186178 ACGACTGCTGTAATAATGAAGTAAAG 57.814 34.615 0.00 0.00 0.00 1.85
63 64 7.815549 TGACGACTGCTGTAATAATGAAGTAAA 59.184 33.333 0.00 0.00 0.00 2.01
64 65 7.274904 GTGACGACTGCTGTAATAATGAAGTAA 59.725 37.037 0.00 0.00 0.00 2.24
65 66 6.750501 GTGACGACTGCTGTAATAATGAAGTA 59.249 38.462 0.00 0.00 0.00 2.24
66 67 5.577164 GTGACGACTGCTGTAATAATGAAGT 59.423 40.000 0.00 0.00 0.00 3.01
67 68 5.275927 CGTGACGACTGCTGTAATAATGAAG 60.276 44.000 0.00 0.00 0.00 3.02
68 69 4.561213 CGTGACGACTGCTGTAATAATGAA 59.439 41.667 0.00 0.00 0.00 2.57
69 70 4.102649 CGTGACGACTGCTGTAATAATGA 58.897 43.478 0.00 0.00 0.00 2.57
70 71 3.857665 ACGTGACGACTGCTGTAATAATG 59.142 43.478 13.70 0.00 0.00 1.90
71 72 4.103357 GACGTGACGACTGCTGTAATAAT 58.897 43.478 13.70 0.00 0.00 1.28
72 73 3.495193 GACGTGACGACTGCTGTAATAA 58.505 45.455 13.70 0.00 0.00 1.40
73 74 2.475022 CGACGTGACGACTGCTGTAATA 60.475 50.000 13.70 0.00 35.09 0.98
74 75 1.728179 CGACGTGACGACTGCTGTAAT 60.728 52.381 13.70 0.00 35.09 1.89
75 76 0.385098 CGACGTGACGACTGCTGTAA 60.385 55.000 13.70 0.00 35.09 2.41
76 77 1.205820 CGACGTGACGACTGCTGTA 59.794 57.895 13.70 0.00 35.09 2.74
77 78 2.051256 CGACGTGACGACTGCTGT 60.051 61.111 13.70 0.00 35.09 4.40
78 79 2.801162 CCGACGTGACGACTGCTG 60.801 66.667 13.70 0.00 35.09 4.41
79 80 2.967473 CTCCGACGTGACGACTGCT 61.967 63.158 13.70 0.00 35.09 4.24
80 81 2.502080 CTCCGACGTGACGACTGC 60.502 66.667 13.70 0.00 35.09 4.40
81 82 2.502080 GCTCCGACGTGACGACTG 60.502 66.667 13.70 1.50 35.09 3.51
82 83 4.086178 CGCTCCGACGTGACGACT 62.086 66.667 13.70 0.00 35.09 4.18
102 103 4.865761 GTAGCGGCGCGGTCATCA 62.866 66.667 27.59 3.84 38.83 3.07
105 106 3.943479 AAATGTAGCGGCGCGGTCA 62.943 57.895 27.59 24.66 38.83 4.02
118 119 3.552684 CCAAATGAGACGTTGGCAAATGT 60.553 43.478 0.00 3.40 38.04 2.71
131 132 2.673893 CGATGTCGACCACCAAATGAGA 60.674 50.000 14.12 0.00 43.02 3.27
135 136 1.722011 GACGATGTCGACCACCAAAT 58.278 50.000 14.12 0.00 43.02 2.32
180 181 1.859302 ACCTGCCTGGACTAGAAGAG 58.141 55.000 0.00 0.00 39.71 2.85
234 238 7.518188 TGTCACATCTAGATATGTCCTAGACA 58.482 38.462 10.72 10.80 46.90 3.41
239 243 8.948401 AGTTATGTCACATCTAGATATGTCCT 57.052 34.615 10.72 1.66 38.01 3.85
272 392 7.599245 ACAAACAAAATGGACGTCAACTTAAAA 59.401 29.630 18.91 0.00 0.00 1.52
274 394 6.528423 CACAAACAAAATGGACGTCAACTTAA 59.472 34.615 18.91 0.00 0.00 1.85
277 397 4.420168 CACAAACAAAATGGACGTCAACT 58.580 39.130 18.91 0.00 0.00 3.16
278 398 3.549873 CCACAAACAAAATGGACGTCAAC 59.450 43.478 18.91 0.81 35.33 3.18
280 400 2.755655 ACCACAAACAAAATGGACGTCA 59.244 40.909 18.91 3.91 36.94 4.35
281 401 3.066203 AGACCACAAACAAAATGGACGTC 59.934 43.478 7.13 7.13 36.94 4.34
282 402 3.020984 AGACCACAAACAAAATGGACGT 58.979 40.909 0.00 0.00 36.94 4.34
283 403 3.708563 AGACCACAAACAAAATGGACG 57.291 42.857 0.00 0.00 36.94 4.79
284 404 8.432110 AAAAATAGACCACAAACAAAATGGAC 57.568 30.769 0.00 0.00 36.94 4.02
344 1521 9.596308 TCACACCTAAGCTCCTACAAATATATA 57.404 33.333 0.00 0.00 0.00 0.86
345 1522 8.368668 GTCACACCTAAGCTCCTACAAATATAT 58.631 37.037 0.00 0.00 0.00 0.86
346 1523 7.343574 TGTCACACCTAAGCTCCTACAAATATA 59.656 37.037 0.00 0.00 0.00 0.86
347 1524 6.156256 TGTCACACCTAAGCTCCTACAAATAT 59.844 38.462 0.00 0.00 0.00 1.28
349 1526 4.286032 TGTCACACCTAAGCTCCTACAAAT 59.714 41.667 0.00 0.00 0.00 2.32
351 1528 3.236047 TGTCACACCTAAGCTCCTACAA 58.764 45.455 0.00 0.00 0.00 2.41
352 1529 2.884320 TGTCACACCTAAGCTCCTACA 58.116 47.619 0.00 0.00 0.00 2.74
356 1533 4.473477 AAGTATGTCACACCTAAGCTCC 57.527 45.455 0.00 0.00 0.00 4.70
357 1534 7.900782 TTTTAAGTATGTCACACCTAAGCTC 57.099 36.000 0.00 0.00 0.00 4.09
422 1973 2.404186 CGAGGATCCCACGACGACA 61.404 63.158 19.84 0.00 39.84 4.35
432 1983 2.418884 GGAAAAGTGAGTCCGAGGATCC 60.419 54.545 2.48 2.48 0.00 3.36
511 2062 3.321497 CCTTCCTTGATGACTATAGCGC 58.679 50.000 0.00 0.00 0.00 5.92
513 2064 4.965200 ACCCTTCCTTGATGACTATAGC 57.035 45.455 0.00 0.00 0.00 2.97
519 2070 5.642491 GTGTTAGTTACCCTTCCTTGATGAC 59.358 44.000 0.00 0.00 0.00 3.06
521 2072 4.630069 CGTGTTAGTTACCCTTCCTTGATG 59.370 45.833 0.00 0.00 0.00 3.07
522 2073 4.529377 TCGTGTTAGTTACCCTTCCTTGAT 59.471 41.667 0.00 0.00 0.00 2.57
523 2074 3.896888 TCGTGTTAGTTACCCTTCCTTGA 59.103 43.478 0.00 0.00 0.00 3.02
524 2075 3.992427 GTCGTGTTAGTTACCCTTCCTTG 59.008 47.826 0.00 0.00 0.00 3.61
539 2090 1.837538 CGCCAATCGGTTGTCGTGTT 61.838 55.000 3.24 0.00 40.32 3.32
556 2107 1.019278 TCGGCTTCCACAGAAATCGC 61.019 55.000 0.00 0.00 31.52 4.58
557 2108 1.594862 GATCGGCTTCCACAGAAATCG 59.405 52.381 0.00 0.00 0.00 3.34
563 2114 0.443869 CAAACGATCGGCTTCCACAG 59.556 55.000 20.98 0.00 0.00 3.66
564 2115 0.034198 TCAAACGATCGGCTTCCACA 59.966 50.000 20.98 0.00 0.00 4.17
566 2117 2.006888 GATTCAAACGATCGGCTTCCA 58.993 47.619 20.98 0.00 0.00 3.53
568 2119 2.353257 CGATTCAAACGATCGGCTTC 57.647 50.000 20.98 6.40 41.89 3.86
573 2124 1.209128 CCTCCCGATTCAAACGATCG 58.791 55.000 14.88 14.88 44.40 3.69
579 2130 5.750524 TGATTCATAACCTCCCGATTCAAA 58.249 37.500 0.00 0.00 0.00 2.69
581 2132 5.366482 TTGATTCATAACCTCCCGATTCA 57.634 39.130 0.00 0.00 0.00 2.57
597 2149 6.035650 TCCGTTGTACGAAATCTGATTGATTC 59.964 38.462 3.22 0.00 46.05 2.52
604 2156 6.139048 TGATATCCGTTGTACGAAATCTGA 57.861 37.500 0.00 0.00 46.05 3.27
612 2164 2.124903 GGTGCTGATATCCGTTGTACG 58.875 52.381 0.00 0.00 42.11 3.67
662 2214 2.046217 GGGAGGAACAAGACGGCC 60.046 66.667 0.00 0.00 0.00 6.13
663 2215 2.046217 GGGGAGGAACAAGACGGC 60.046 66.667 0.00 0.00 0.00 5.68
783 5902 2.745884 CGAGGGGTCAATGCGCAA 60.746 61.111 17.11 0.00 0.00 4.85
908 6042 0.592637 AGCAGAGCAGATCGAGATCG 59.407 55.000 7.37 0.00 42.48 3.69
910 6044 1.755959 ACAAGCAGAGCAGATCGAGAT 59.244 47.619 0.00 0.00 0.00 2.75
912 6046 2.857152 GTTACAAGCAGAGCAGATCGAG 59.143 50.000 0.00 0.00 0.00 4.04
947 6081 2.740714 GCGCTACCTTTGTCTGCCG 61.741 63.158 0.00 0.00 0.00 5.69
948 6082 2.740714 CGCGCTACCTTTGTCTGCC 61.741 63.158 5.56 0.00 0.00 4.85
1240 6377 0.397254 ACGAAGATCCCGGACATCCT 60.397 55.000 0.73 0.00 0.00 3.24
1252 6389 2.998949 GGCCTTGGGGACGAAGAT 59.001 61.111 0.00 0.00 33.58 2.40
1761 6898 3.320879 CTCCCACATGCCGCTGTCT 62.321 63.158 0.00 0.00 0.00 3.41
2142 7279 1.107945 CCTCTTCCTCGTCTTCCTCC 58.892 60.000 0.00 0.00 0.00 4.30
2151 7291 2.167487 CTCCTCCTTTTCCTCTTCCTCG 59.833 54.545 0.00 0.00 0.00 4.63
2324 7464 0.554305 TCGATACCTCCTAGTGCCCA 59.446 55.000 0.00 0.00 0.00 5.36
2325 7465 1.819903 GATCGATACCTCCTAGTGCCC 59.180 57.143 0.00 0.00 0.00 5.36
2329 7469 4.620589 TTCTCGATCGATACCTCCTAGT 57.379 45.455 19.78 0.00 0.00 2.57
2330 7470 5.943706 TTTTCTCGATCGATACCTCCTAG 57.056 43.478 19.78 3.46 0.00 3.02
2332 7472 6.490721 ACTTATTTTCTCGATCGATACCTCCT 59.509 38.462 19.78 3.38 0.00 3.69
2333 7473 6.583050 CACTTATTTTCTCGATCGATACCTCC 59.417 42.308 19.78 0.00 0.00 4.30
2336 7487 6.144080 CACCACTTATTTTCTCGATCGATACC 59.856 42.308 19.78 0.00 0.00 2.73
2338 7489 5.690409 GCACCACTTATTTTCTCGATCGATA 59.310 40.000 19.78 8.96 0.00 2.92
2350 7501 2.185004 AGCACTCGCACCACTTATTT 57.815 45.000 0.00 0.00 42.27 1.40
2358 7509 4.811557 AGAAGAATTAATAGCACTCGCACC 59.188 41.667 0.00 0.00 42.27 5.01
2362 7513 9.522804 AGTTCTTAGAAGAATTAATAGCACTCG 57.477 33.333 7.91 0.00 45.83 4.18
2404 7555 8.693625 AGGAATCCAAGTAGTAATACACAGTAC 58.306 37.037 0.61 0.00 0.00 2.73
2406 7557 7.735326 AGGAATCCAAGTAGTAATACACAGT 57.265 36.000 0.61 0.00 0.00 3.55
2413 7564 9.396022 CACACATTTAGGAATCCAAGTAGTAAT 57.604 33.333 0.61 0.00 0.00 1.89
2414 7565 8.380099 ACACACATTTAGGAATCCAAGTAGTAA 58.620 33.333 0.61 0.00 0.00 2.24
2421 7572 6.549364 AGTTCAACACACATTTAGGAATCCAA 59.451 34.615 0.61 0.00 0.00 3.53
2424 7575 5.858581 GCAGTTCAACACACATTTAGGAATC 59.141 40.000 0.00 0.00 0.00 2.52
2430 7581 4.202101 CCTTGGCAGTTCAACACACATTTA 60.202 41.667 0.00 0.00 0.00 1.40
2453 7604 7.012421 CCTCTGTTTCTAAATGTAATGGTAGGC 59.988 40.741 0.00 0.00 0.00 3.93
2458 7609 6.659242 ACACCCTCTGTTTCTAAATGTAATGG 59.341 38.462 0.00 0.00 0.00 3.16
2459 7610 7.687941 ACACCCTCTGTTTCTAAATGTAATG 57.312 36.000 0.00 0.00 0.00 1.90
2499 7969 3.199891 CGGAAATCGGCCGTTCCC 61.200 66.667 31.06 22.78 43.66 3.97
2516 7986 1.602377 CCAGGAACGAAACAACCTGTC 59.398 52.381 0.00 0.00 45.65 3.51
2528 7998 1.269051 GCACTTTCCAAACCAGGAACG 60.269 52.381 0.00 0.00 46.85 3.95
2548 8019 5.347907 GCGATTGGGAATAAGTAATCCTACG 59.652 44.000 0.00 0.00 35.95 3.51
2564 8035 1.672881 GATTTCAGGACAGCGATTGGG 59.327 52.381 0.00 0.00 0.00 4.12
2565 8036 2.353889 CTGATTTCAGGACAGCGATTGG 59.646 50.000 0.00 0.00 40.20 3.16
2566 8037 3.670311 CTGATTTCAGGACAGCGATTG 57.330 47.619 0.00 0.00 40.20 2.67
2622 8334 1.476007 CCTAATCTCTCGGCCCCCTG 61.476 65.000 0.00 0.00 0.00 4.45
2623 8335 1.152226 CCTAATCTCTCGGCCCCCT 60.152 63.158 0.00 0.00 0.00 4.79
2624 8336 2.884980 GCCTAATCTCTCGGCCCCC 61.885 68.421 0.00 0.00 37.86 5.40
2625 8337 2.744377 GCCTAATCTCTCGGCCCC 59.256 66.667 0.00 0.00 37.86 5.80
2626 8338 2.340443 CGCCTAATCTCTCGGCCC 59.660 66.667 0.00 0.00 40.70 5.80
2629 8341 1.364171 CCCACGCCTAATCTCTCGG 59.636 63.158 0.00 0.00 0.00 4.63
2630 8342 0.030908 GACCCACGCCTAATCTCTCG 59.969 60.000 0.00 0.00 0.00 4.04
2669 8454 1.740296 CACGAGGCCAAGGGTAACG 60.740 63.158 5.01 0.00 37.60 3.18
2673 8458 2.113139 CAACACGAGGCCAAGGGT 59.887 61.111 5.01 1.52 0.00 4.34
2693 8478 4.531708 TTTTTCATGCGCGTCAGC 57.468 50.000 8.43 0.00 40.74 4.26
2740 8527 3.803082 CGCACCGGCATTGTCCTG 61.803 66.667 0.00 0.00 41.24 3.86
2987 8788 7.120285 CACCACAAAGCTATATTATCATCCAGG 59.880 40.741 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.