Multiple sequence alignment - TraesCS5D01G525800

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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 TraesCS5D01G525800 chr5D 100.000 4426 0 0 1 4426 543834206 543838631 0.000000e+00 8174.0
1 TraesCS5D01G525800 chr5D 77.895 1615 254 59 1359 2913 543707121 543705550 0.000000e+00 909.0
2 TraesCS5D01G525800 chr5D 80.801 724 116 18 1 718 232423903 232424609 3.010000e-151 545.0
3 TraesCS5D01G525800 chr5D 76.584 931 202 13 1525 2447 480031144 480032066 8.550000e-137 497.0
4 TraesCS5D01G525800 chr5D 83.117 77 11 2 3189 3264 543667994 543668069 7.940000e-08 69.4
5 TraesCS5D01G525800 chr4A 93.155 2133 116 18 1359 3462 625252790 625250659 0.000000e+00 3103.0
6 TraesCS5D01G525800 chr4A 79.620 1580 263 46 1360 2906 625394764 625396317 0.000000e+00 1079.0
7 TraesCS5D01G525800 chr4A 94.272 646 23 7 31 669 625255312 625254674 0.000000e+00 976.0
8 TraesCS5D01G525800 chr4A 94.253 348 15 1 723 1070 625253572 625253230 1.090000e-145 527.0
9 TraesCS5D01G525800 chr4A 84.942 518 33 19 3716 4195 625250339 625249829 2.390000e-132 483.0
10 TraesCS5D01G525800 chr4A 76.221 921 184 29 1535 2439 623337827 623338728 5.220000e-124 455.0
11 TraesCS5D01G525800 chr4A 90.997 311 21 3 1066 1370 625253126 625252817 3.190000e-111 412.0
12 TraesCS5D01G525800 chr4A 93.694 222 14 0 3464 3685 625250552 625250331 2.550000e-87 333.0
13 TraesCS5D01G525800 chr4A 93.464 153 8 1 4199 4349 625249776 625249624 4.450000e-55 226.0
14 TraesCS5D01G525800 chr4A 84.524 168 24 1 2639 2804 625538839 625539006 9.850000e-37 165.0
15 TraesCS5D01G525800 chr5B 90.932 2018 117 26 921 2913 685653795 685651819 0.000000e+00 2652.0
16 TraesCS5D01G525800 chr5B 92.337 783 44 10 2914 3680 685651791 685651009 0.000000e+00 1099.0
17 TraesCS5D01G525800 chr5B 79.082 1568 274 43 1384 2913 685604917 685603366 0.000000e+00 1029.0
18 TraesCS5D01G525800 chr5B 86.826 668 32 23 3812 4426 685990771 685991435 0.000000e+00 695.0
19 TraesCS5D01G525800 chr5B 93.820 356 21 1 3223 3577 685989965 685990320 6.520000e-148 534.0
20 TraesCS5D01G525800 chr5B 76.262 931 205 15 1525 2447 587786811 587787733 8.610000e-132 481.0
21 TraesCS5D01G525800 chr5B 76.564 943 180 31 1535 2457 689210177 689209256 3.100000e-131 479.0
22 TraesCS5D01G525800 chr5B 76.961 803 177 8 1525 2323 587762615 587763413 6.750000e-123 451.0
23 TraesCS5D01G525800 chr5B 94.961 258 12 1 3559 3815 685990412 685990669 1.920000e-108 403.0
24 TraesCS5D01G525800 chr5B 94.760 229 9 2 4199 4425 685650421 685650194 1.960000e-93 353.0
25 TraesCS5D01G525800 chr5B 80.682 352 21 10 3888 4193 685650826 685650476 3.440000e-56 230.0
26 TraesCS5D01G525800 chr5B 74.899 494 99 19 1980 2457 689148704 689148220 7.510000e-48 202.0
27 TraesCS5D01G525800 chr5B 77.493 351 63 16 2105 2447 687168792 687168450 3.490000e-46 196.0
28 TraesCS5D01G525800 chr5B 84.524 168 26 0 2635 2802 685438992 685439159 2.740000e-37 167.0
29 TraesCS5D01G525800 chr5B 83.626 171 28 0 2635 2805 685197830 685197660 1.270000e-35 161.0
30 TraesCS5D01G525800 chr1D 83.967 736 92 13 2994 3722 15061766 15061050 0.000000e+00 682.0
31 TraesCS5D01G525800 chr1D 80.689 668 110 17 62 721 290353368 290354024 6.610000e-138 501.0
32 TraesCS5D01G525800 chr1D 90.878 296 25 2 2204 2497 15604973 15605268 3.210000e-106 396.0
33 TraesCS5D01G525800 chr5A 76.948 924 199 13 1531 2447 598520692 598521608 8.490000e-142 514.0
34 TraesCS5D01G525800 chr5A 80.531 678 110 13 15 679 291533432 291534100 6.610000e-138 501.0
35 TraesCS5D01G525800 chr6A 78.926 726 125 23 4 720 102044978 102044272 6.700000e-128 468.0
36 TraesCS5D01G525800 chr2B 82.661 496 74 12 63 552 69076935 69076446 3.160000e-116 429.0
37 TraesCS5D01G525800 chr2B 81.382 521 85 10 62 575 453333672 453334187 8.860000e-112 414.0
38 TraesCS5D01G525800 chr2D 81.004 558 85 15 62 608 630345649 630345102 1.470000e-114 424.0
39 TraesCS5D01G525800 chr2A 79.928 558 91 19 60 608 632536716 632537261 1.490000e-104 390.0
40 TraesCS5D01G525800 chr2A 76.016 763 111 40 7 718 160015650 160014909 3.300000e-86 329.0
41 TraesCS5D01G525800 chr1A 83.140 172 27 2 2635 2805 569457991 569457821 5.930000e-34 156.0


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 TraesCS5D01G525800 chr5D 543834206 543838631 4425 False 8174.000000 8174 100.00000 1 4426 1 chr5D.!!$F4 4425
1 TraesCS5D01G525800 chr5D 543705550 543707121 1571 True 909.000000 909 77.89500 1359 2913 1 chr5D.!!$R1 1554
2 TraesCS5D01G525800 chr5D 232423903 232424609 706 False 545.000000 545 80.80100 1 718 1 chr5D.!!$F1 717
3 TraesCS5D01G525800 chr5D 480031144 480032066 922 False 497.000000 497 76.58400 1525 2447 1 chr5D.!!$F2 922
4 TraesCS5D01G525800 chr4A 625394764 625396317 1553 False 1079.000000 1079 79.62000 1360 2906 1 chr4A.!!$F2 1546
5 TraesCS5D01G525800 chr4A 625249624 625255312 5688 True 865.714286 3103 92.11100 31 4349 7 chr4A.!!$R1 4318
6 TraesCS5D01G525800 chr4A 623337827 623338728 901 False 455.000000 455 76.22100 1535 2439 1 chr4A.!!$F1 904
7 TraesCS5D01G525800 chr5B 685650194 685653795 3601 True 1083.500000 2652 89.67775 921 4425 4 chr5B.!!$R6 3504
8 TraesCS5D01G525800 chr5B 685603366 685604917 1551 True 1029.000000 1029 79.08200 1384 2913 1 chr5B.!!$R2 1529
9 TraesCS5D01G525800 chr5B 685989965 685991435 1470 False 544.000000 695 91.86900 3223 4426 3 chr5B.!!$F4 1203
10 TraesCS5D01G525800 chr5B 587786811 587787733 922 False 481.000000 481 76.26200 1525 2447 1 chr5B.!!$F2 922
11 TraesCS5D01G525800 chr5B 689209256 689210177 921 True 479.000000 479 76.56400 1535 2457 1 chr5B.!!$R5 922
12 TraesCS5D01G525800 chr5B 587762615 587763413 798 False 451.000000 451 76.96100 1525 2323 1 chr5B.!!$F1 798
13 TraesCS5D01G525800 chr1D 15061050 15061766 716 True 682.000000 682 83.96700 2994 3722 1 chr1D.!!$R1 728
14 TraesCS5D01G525800 chr1D 290353368 290354024 656 False 501.000000 501 80.68900 62 721 1 chr1D.!!$F2 659
15 TraesCS5D01G525800 chr5A 598520692 598521608 916 False 514.000000 514 76.94800 1531 2447 1 chr5A.!!$F2 916
16 TraesCS5D01G525800 chr5A 291533432 291534100 668 False 501.000000 501 80.53100 15 679 1 chr5A.!!$F1 664
17 TraesCS5D01G525800 chr6A 102044272 102044978 706 True 468.000000 468 78.92600 4 720 1 chr6A.!!$R1 716
18 TraesCS5D01G525800 chr2B 453333672 453334187 515 False 414.000000 414 81.38200 62 575 1 chr2B.!!$F1 513
19 TraesCS5D01G525800 chr2D 630345102 630345649 547 True 424.000000 424 81.00400 62 608 1 chr2D.!!$R1 546
20 TraesCS5D01G525800 chr2A 632536716 632537261 545 False 390.000000 390 79.92800 60 608 1 chr2A.!!$F1 548
21 TraesCS5D01G525800 chr2A 160014909 160015650 741 True 329.000000 329 76.01600 7 718 1 chr2A.!!$R1 711

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
801 2160 1.497309 AAATCTGGGACTTGGCCGGA 61.497 55.000 5.05 0.0 0.00 5.14 F
1401 2911 0.320374 TGTGCTAGTTTGGGTCTCGG 59.680 55.000 0.00 0.0 0.00 4.63 F
1542 3073 1.019673 ATTTCTGTATGCAGCAGCCG 58.980 50.000 14.18 0.0 42.29 5.52 F
2034 3565 1.885388 TGTGTTCGGTTGCCTCACG 60.885 57.895 0.00 0.0 32.55 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 3764 1.558756 CTCCAGTTCTGGAAGGCAGAT 59.441 52.381 20.06 0.00 37.55 2.90 R
2945 4567 1.384525 TTTTGGTGTGTGTTCGAGGG 58.615 50.000 0.00 0.00 0.00 4.30 R
3200 4832 2.240493 ACGCAAACTGCTGTTCTAGT 57.760 45.000 9.60 7.06 42.25 2.57 R
3671 5529 2.723322 CAATCTTGGAGGCCATCTCA 57.277 50.000 5.01 0.00 44.19 3.27 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
111 219 6.668323 TCAAATCCGATGAACTTTCTTGAAC 58.332 36.000 0.00 0.00 0.00 3.18
166 320 8.560355 ACTTTTTCCAAATTTAGTGCACTTTT 57.440 26.923 27.06 16.69 0.00 2.27
167 321 9.008965 ACTTTTTCCAAATTTAGTGCACTTTTT 57.991 25.926 27.06 18.55 0.00 1.94
190 344 8.709386 TTTTCAAATTCGATGAACTTTTTCCA 57.291 26.923 0.00 0.00 36.57 3.53
191 345 8.885494 TTTCAAATTCGATGAACTTTTTCCAT 57.115 26.923 0.00 0.00 36.57 3.41
192 346 9.973450 TTTCAAATTCGATGAACTTTTTCCATA 57.027 25.926 0.00 0.00 36.57 2.74
200 354 8.673711 TCGATGAACTTTTTCCATATTTAGTGG 58.326 33.333 0.00 0.00 38.11 4.00
201 355 8.673711 CGATGAACTTTTTCCATATTTAGTGGA 58.326 33.333 0.00 0.00 43.77 4.02
202 356 9.788960 GATGAACTTTTTCCATATTTAGTGGAC 57.211 33.333 0.00 0.00 45.05 4.02
203 357 8.934023 TGAACTTTTTCCATATTTAGTGGACT 57.066 30.769 0.00 0.00 45.05 3.85
204 358 9.010029 TGAACTTTTTCCATATTTAGTGGACTC 57.990 33.333 0.00 0.00 45.05 3.36
205 359 7.611213 ACTTTTTCCATATTTAGTGGACTCG 57.389 36.000 0.00 0.00 45.05 4.18
223 377 6.695278 TGGACTCGTTTTCAAATTCAATGAAC 59.305 34.615 0.00 0.00 36.57 3.18
298 540 3.037549 TGCACCTTTTTCCCTTTCATGT 58.962 40.909 0.00 0.00 0.00 3.21
721 2080 3.597728 CCGAGTAGGCGCTCCCTC 61.598 72.222 7.64 8.94 44.96 4.30
728 2087 2.589610 TAGGCGCTCCCTCCATCTGT 62.590 60.000 7.64 0.00 44.96 3.41
801 2160 1.497309 AAATCTGGGACTTGGCCGGA 61.497 55.000 5.05 0.00 0.00 5.14
1025 2384 2.746277 CCCCGTGGCGAAGAAAGG 60.746 66.667 0.00 0.00 0.00 3.11
1142 2609 7.533900 CCGATTTGTAATCAAAACAGTGTAGTG 59.466 37.037 0.00 0.00 44.97 2.74
1164 2631 3.317430 GGTTCTTCATTGATGATCAGGGC 59.683 47.826 0.09 0.00 36.56 5.19
1173 2640 4.508551 TGATGATCAGGGCAATTACAGT 57.491 40.909 0.09 0.00 0.00 3.55
1216 2688 1.346068 ACAGAACAGACTCCTGAAGGC 59.654 52.381 0.00 0.00 43.02 4.35
1225 2697 1.242076 CTCCTGAAGGCTTTGGTGTG 58.758 55.000 16.29 7.65 34.44 3.82
1278 2750 1.826024 CATTCTCCTCGACCCCCAG 59.174 63.158 0.00 0.00 0.00 4.45
1284 2756 2.279073 CTCGACCCCCAGCTAGGA 59.721 66.667 0.00 0.00 41.22 2.94
1309 2782 1.218047 CAAGTAGTAGGCGCCTGCA 59.782 57.895 40.12 25.63 45.35 4.41
1314 2787 4.840005 GTAGGCGCCTGCAGGTCC 62.840 72.222 38.98 30.22 45.35 4.46
1348 2821 1.339151 GGGATTGACACTGACTGGGAC 60.339 57.143 0.00 0.00 0.00 4.46
1401 2911 0.320374 TGTGCTAGTTTGGGTCTCGG 59.680 55.000 0.00 0.00 0.00 4.63
1415 2927 3.899980 GGGTCTCGGGTAGGTACATATTT 59.100 47.826 0.00 0.00 0.00 1.40
1418 2930 5.163374 GGTCTCGGGTAGGTACATATTTGTT 60.163 44.000 0.00 0.00 37.28 2.83
1428 2940 7.448748 AGGTACATATTTGTTGTTCTTGTCC 57.551 36.000 0.00 0.00 37.28 4.02
1514 3045 8.289440 TGTTAACTGATAGTGACAAAGTAACG 57.711 34.615 7.22 0.00 0.00 3.18
1542 3073 1.019673 ATTTCTGTATGCAGCAGCCG 58.980 50.000 14.18 0.00 42.29 5.52
1788 3319 2.584492 AAGCAGCCAAGTGTTTGTTC 57.416 45.000 0.00 0.00 32.21 3.18
1885 3416 4.663120 ACATTGGCCCACTATTAGGTGATA 59.337 41.667 0.00 0.00 39.34 2.15
1980 3511 2.102438 GCACATGCTACAGCTCGCA 61.102 57.895 2.44 4.54 42.66 5.10
2034 3565 1.885388 TGTGTTCGGTTGCCTCACG 60.885 57.895 0.00 0.00 32.55 4.35
2230 3764 7.041635 TGTTGCTTTGAGAGAATTGATTTGA 57.958 32.000 0.00 0.00 0.00 2.69
2522 4094 7.069331 AGAGCTATCTAGTTATACCATGGATGC 59.931 40.741 21.47 3.63 32.54 3.91
2623 4198 2.378038 TGCTCCTGAACTGCTTTGTTT 58.622 42.857 0.00 0.00 0.00 2.83
2624 4199 2.099592 TGCTCCTGAACTGCTTTGTTTG 59.900 45.455 0.00 0.00 0.00 2.93
2680 4255 3.858503 GCAACCTGAAATGAAGCAACTCC 60.859 47.826 0.00 0.00 0.00 3.85
2742 4317 7.271223 CGTGGTATCTTTGTTGAATTTGACATC 59.729 37.037 0.00 0.00 0.00 3.06
2743 4318 7.542130 GTGGTATCTTTGTTGAATTTGACATCC 59.458 37.037 0.00 0.00 0.00 3.51
2750 4325 7.959658 TTGTTGAATTTGACATCCTATGGAT 57.040 32.000 0.00 0.00 44.21 3.41
2823 4403 5.294552 GGTAATGCTGTTTGAGTCTACCATC 59.705 44.000 0.00 0.00 0.00 3.51
2839 4428 6.263617 GTCTACCATCCCAGTTTTGTTGTTAA 59.736 38.462 0.00 0.00 0.00 2.01
2876 4467 7.833285 ATGTTTGTAAGCTTTTCTCCCTTAA 57.167 32.000 3.20 0.00 0.00 1.85
2877 4468 7.034685 TGTTTGTAAGCTTTTCTCCCTTAAC 57.965 36.000 3.20 0.00 0.00 2.01
2945 4567 5.262588 TCTTGTTGCCTTCCTTTTTCTTC 57.737 39.130 0.00 0.00 0.00 2.87
2956 4578 3.118186 TCCTTTTTCTTCCCTCGAACACA 60.118 43.478 0.00 0.00 0.00 3.72
2959 4581 2.234300 TTCTTCCCTCGAACACACAC 57.766 50.000 0.00 0.00 0.00 3.82
2970 4594 3.122297 CGAACACACACCAAAATGCATT 58.878 40.909 5.99 5.99 0.00 3.56
2973 4597 5.233050 CGAACACACACCAAAATGCATTTTA 59.767 36.000 31.33 0.00 37.86 1.52
3176 4808 4.102524 TCCAAGAACTGGCTACTGAAAGAA 59.897 41.667 0.00 0.00 45.98 2.52
3200 4832 2.489971 CAGTTTGTCGGCTTTAGGTCA 58.510 47.619 0.00 0.00 0.00 4.02
3406 5038 0.033208 GATGGCAAATCCTCACCCCA 60.033 55.000 0.00 0.00 35.26 4.96
3457 5092 3.393687 TGGGGATCAGCCTTATGTAACT 58.606 45.455 0.00 0.00 36.66 2.24
3517 5258 6.238484 GGAGCTGTTATGTACCAGCAAATAAG 60.238 42.308 19.68 0.00 42.60 1.73
3524 5268 8.565416 GTTATGTACCAGCAAATAAGGTATTCC 58.435 37.037 0.00 0.00 39.83 3.01
3560 5308 4.892655 TGAGAATTGCAAATAAGCGTACG 58.107 39.130 11.84 11.84 37.31 3.67
3627 5485 9.944663 GTTTGTTTGTTCAGATGATGTAAACTA 57.055 29.630 13.44 7.37 33.55 2.24
3630 5488 8.729756 TGTTTGTTCAGATGATGTAAACTATGG 58.270 33.333 13.44 0.00 33.55 2.74
3671 5529 5.777802 CTGAGTATGCGAATGGACTTAGAT 58.222 41.667 0.00 0.00 29.44 1.98
4039 6111 4.068599 GGCTGGAGATAATAAACTGGAGC 58.931 47.826 0.00 0.00 0.00 4.70
4137 6221 8.565896 TCTGTCAGCACATTATCAACTAAAAT 57.434 30.769 0.00 0.00 0.00 1.82
4156 6245 4.436113 AATTGGCAAGAAAACCACCATT 57.564 36.364 5.96 0.00 35.10 3.16
4176 6265 8.301720 CACCATTATCCAATACATTCATTCAGG 58.698 37.037 0.00 0.00 0.00 3.86
4195 6284 5.512298 TCAGGTCAACAATGAATGATCCAT 58.488 37.500 0.00 0.00 37.30 3.41
4230 6368 5.164119 GTAGAATACACGACAAGTTTGTCCG 60.164 44.000 16.88 14.23 46.60 4.79
4243 6381 2.389962 TTGTCCGCAATAGTACCCAC 57.610 50.000 0.00 0.00 0.00 4.61
4356 6496 3.355378 ACAAATGCAATCCCGATCTTCA 58.645 40.909 0.00 0.00 0.00 3.02
4403 6543 5.306532 CAGCATGCCCATACAGATTAATC 57.693 43.478 15.66 7.41 0.00 1.75
4407 6547 5.063944 GCATGCCCATACAGATTAATCGTAG 59.936 44.000 6.36 12.32 0.00 3.51
4413 6553 6.645415 CCCATACAGATTAATCGTAGTTGGAC 59.355 42.308 23.77 0.90 0.00 4.02
4419 6559 7.606456 ACAGATTAATCGTAGTTGGACACAAAT 59.394 33.333 9.78 0.00 38.54 2.32
4425 6565 8.964420 AATCGTAGTTGGACACAAATAAATTG 57.036 30.769 0.00 0.00 38.67 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.915437 TTGGAAAAAGCCTCATCGAAC 57.085 42.857 0.00 0.00 0.00 3.95
12 13 6.908870 AAGTTCACTGAATTTGGAAAAAGC 57.091 33.333 0.00 0.00 0.00 3.51
75 183 6.902341 TCATCGGATTTGAAAAAGACTTCAG 58.098 36.000 0.00 0.00 36.69 3.02
80 188 7.862873 AGAAAGTTCATCGGATTTGAAAAAGAC 59.137 33.333 0.00 0.00 35.03 3.01
166 320 8.885494 ATGGAAAAAGTTCATCGAATTTGAAA 57.115 26.923 0.00 0.00 35.03 2.69
174 328 8.673711 CCACTAAATATGGAAAAAGTTCATCGA 58.326 33.333 0.00 0.00 39.87 3.59
175 329 8.673711 TCCACTAAATATGGAAAAAGTTCATCG 58.326 33.333 0.00 0.00 43.43 3.84
187 341 6.703319 TGAAAACGAGTCCACTAAATATGGA 58.297 36.000 0.00 0.00 44.20 3.41
188 342 6.978343 TGAAAACGAGTCCACTAAATATGG 57.022 37.500 0.00 0.00 38.71 2.74
189 343 9.840427 AATTTGAAAACGAGTCCACTAAATATG 57.160 29.630 0.00 0.00 0.00 1.78
191 345 9.058174 TGAATTTGAAAACGAGTCCACTAAATA 57.942 29.630 0.00 0.00 0.00 1.40
192 346 7.936584 TGAATTTGAAAACGAGTCCACTAAAT 58.063 30.769 0.00 0.00 0.00 1.40
193 347 7.323049 TGAATTTGAAAACGAGTCCACTAAA 57.677 32.000 0.00 0.00 0.00 1.85
194 348 6.928979 TGAATTTGAAAACGAGTCCACTAA 57.071 33.333 0.00 0.00 0.00 2.24
195 349 6.928979 TTGAATTTGAAAACGAGTCCACTA 57.071 33.333 0.00 0.00 0.00 2.74
196 350 5.828299 TTGAATTTGAAAACGAGTCCACT 57.172 34.783 0.00 0.00 0.00 4.00
197 351 6.205784 TCATTGAATTTGAAAACGAGTCCAC 58.794 36.000 0.00 0.00 0.00 4.02
198 352 6.384258 TCATTGAATTTGAAAACGAGTCCA 57.616 33.333 0.00 0.00 0.00 4.02
199 353 6.918022 AGTTCATTGAATTTGAAAACGAGTCC 59.082 34.615 1.78 0.00 35.03 3.85
200 354 7.914537 AGTTCATTGAATTTGAAAACGAGTC 57.085 32.000 1.78 0.00 35.03 3.36
201 355 8.702163 AAAGTTCATTGAATTTGAAAACGAGT 57.298 26.923 7.78 0.00 35.03 4.18
202 356 9.971744 AAAAAGTTCATTGAATTTGAAAACGAG 57.028 25.926 7.78 0.00 35.03 4.18
231 385 4.973663 ACAATGAAAAACGACCACGAATTC 59.026 37.500 0.00 0.00 42.66 2.17
235 389 3.127203 ACAACAATGAAAAACGACCACGA 59.873 39.130 0.00 0.00 42.66 4.35
282 524 8.716646 AACAAAAGTACATGAAAGGGAAAAAG 57.283 30.769 0.00 0.00 0.00 2.27
366 608 4.933505 TGGAAAGTTGATGAACATGCAA 57.066 36.364 0.00 0.00 34.17 4.08
721 2080 3.129502 CCAGCACCGCACAGATGG 61.130 66.667 0.00 0.00 0.00 3.51
757 2116 2.582978 GTTCTGGTCCCCCGCTAC 59.417 66.667 0.00 0.00 0.00 3.58
793 2152 0.965439 CTGGACAAATTTCCGGCCAA 59.035 50.000 2.24 0.00 38.69 4.52
795 2154 1.405463 GATCTGGACAAATTTCCGGCC 59.595 52.381 0.00 0.00 41.37 6.13
801 2160 7.693969 AGAAAATCTCGATCTGGACAAATTT 57.306 32.000 0.00 0.00 0.00 1.82
877 2236 1.375523 CTACCACACAACCCTCGGC 60.376 63.158 0.00 0.00 0.00 5.54
878 2237 1.295423 CCTACCACACAACCCTCGG 59.705 63.158 0.00 0.00 0.00 4.63
917 2276 3.702048 TAGGCGGCTCACACCACC 61.702 66.667 17.67 0.00 31.53 4.61
918 2277 2.434359 GTAGGCGGCTCACACCAC 60.434 66.667 17.67 2.48 0.00 4.16
1017 2376 2.833631 TTCTCACCGTCCCTTTCTTC 57.166 50.000 0.00 0.00 0.00 2.87
1025 2384 1.144057 ATGGCGATTCTCACCGTCC 59.856 57.895 0.00 0.00 0.00 4.79
1142 2609 3.317430 GCCCTGATCATCAATGAAGAACC 59.683 47.826 0.00 0.00 40.69 3.62
1164 2631 5.066505 GGTTGATCCCTGCTTACTGTAATTG 59.933 44.000 0.00 0.00 0.00 2.32
1216 2688 3.242936 CCGAAACAAGTACCACACCAAAG 60.243 47.826 0.00 0.00 0.00 2.77
1225 2697 2.683859 GCCGGCCGAAACAAGTACC 61.684 63.158 30.73 0.00 0.00 3.34
1258 2730 2.367202 GGGGGTCGAGGAGAATGCA 61.367 63.158 0.00 0.00 0.00 3.96
1278 2750 1.409427 ACTACTTGATGCCGTCCTAGC 59.591 52.381 0.00 0.00 0.00 3.42
1284 2756 0.102481 CGCCTACTACTTGATGCCGT 59.898 55.000 0.00 0.00 0.00 5.68
1309 2782 0.909623 CCTTCCAATACACCGGACCT 59.090 55.000 9.46 0.00 0.00 3.85
1314 2787 2.092646 TCAATCCCCTTCCAATACACCG 60.093 50.000 0.00 0.00 0.00 4.94
1348 2821 3.690460 AGCACCCCAAAAATCTCACTAG 58.310 45.455 0.00 0.00 0.00 2.57
1401 2911 8.331730 ACAAGAACAACAAATATGTACCTACC 57.668 34.615 0.00 0.00 39.40 3.18
1415 2927 3.750371 CCATACAGGGACAAGAACAACA 58.250 45.455 0.00 0.00 0.00 3.33
1418 2930 1.985159 AGCCATACAGGGACAAGAACA 59.015 47.619 0.00 0.00 38.09 3.18
1428 2940 3.451178 ACAGTAGTACCAAGCCATACAGG 59.549 47.826 0.00 0.00 41.84 4.00
1542 3073 2.367241 GCTCAACCTATCTTCCTCCTCC 59.633 54.545 0.00 0.00 0.00 4.30
1788 3319 4.093556 GTGGATTTTCTCTGAGGTTTAGCG 59.906 45.833 4.59 0.00 0.00 4.26
1885 3416 3.489355 TCAGCAAACCACTGTCAATCAT 58.511 40.909 0.00 0.00 36.50 2.45
1980 3511 7.599998 GCATTGAAGAAACCATACATGTCTTTT 59.400 33.333 0.00 0.00 0.00 2.27
2034 3565 1.824230 ACACCATGCAGAGAGAGTCTC 59.176 52.381 12.54 12.54 43.70 3.36
2230 3764 1.558756 CTCCAGTTCTGGAAGGCAGAT 59.441 52.381 20.06 0.00 37.55 2.90
2522 4094 5.030295 GTGTTCTCCATCATGCAAAATACG 58.970 41.667 0.00 0.00 0.00 3.06
2607 4182 6.980397 AGAAAATACAAACAAAGCAGTTCAGG 59.020 34.615 0.00 0.00 0.00 3.86
2680 4255 2.082366 GCTTGTTGAATGCGGTGCG 61.082 57.895 0.00 0.00 0.00 5.34
2742 4317 4.103153 TCAAGGAAGGCTGTTATCCATAGG 59.897 45.833 5.78 0.00 35.62 2.57
2743 4318 5.296151 TCAAGGAAGGCTGTTATCCATAG 57.704 43.478 5.78 0.00 35.62 2.23
2812 4391 4.287766 ACAAAACTGGGATGGTAGACTC 57.712 45.455 0.00 0.00 0.00 3.36
2823 4403 5.725362 TGAAAGGTTAACAACAAAACTGGG 58.275 37.500 8.10 0.00 0.00 4.45
2839 4428 9.830975 AAGCTTACAAACATTAAAATGAAAGGT 57.169 25.926 9.60 7.27 39.67 3.50
2876 4467 7.390718 GGAAGGTAGAAATGTGTTCATAAGTGT 59.609 37.037 0.00 0.00 33.49 3.55
2877 4468 7.390440 TGGAAGGTAGAAATGTGTTCATAAGTG 59.610 37.037 0.00 0.00 33.49 3.16
2945 4567 1.384525 TTTTGGTGTGTGTTCGAGGG 58.615 50.000 0.00 0.00 0.00 4.30
2973 4597 9.592196 ACATTTCCCTTATTATGTATGAGCAAT 57.408 29.630 0.00 0.00 29.93 3.56
3176 4808 2.550208 CCTAAAGCCGACAAACTGGAGT 60.550 50.000 0.00 0.00 0.00 3.85
3200 4832 2.240493 ACGCAAACTGCTGTTCTAGT 57.760 45.000 9.60 7.06 42.25 2.57
3406 5038 5.195940 ACGATCATTCATGGAAAATCACCT 58.804 37.500 0.00 0.00 0.00 4.00
3443 5075 8.723942 AACATAGAGAAAGTTACATAAGGCTG 57.276 34.615 0.00 0.00 0.00 4.85
3457 5092 7.497579 TGCAACTGTTTGACTAACATAGAGAAA 59.502 33.333 2.91 0.00 45.31 2.52
3560 5308 4.513318 GCAGGGCAAATATAGAAGAGTCAC 59.487 45.833 0.00 0.00 0.00 3.67
3627 5485 4.021229 AGCATGATCAAACATCACACCAT 58.979 39.130 0.00 0.00 0.00 3.55
3630 5488 4.690184 TCAGCATGATCAAACATCACAC 57.310 40.909 0.00 0.00 42.56 3.82
3671 5529 2.723322 CAATCTTGGAGGCCATCTCA 57.277 50.000 5.01 0.00 44.19 3.27
4039 6111 3.945921 TCGTAGGAATGTACTGTCCTCTG 59.054 47.826 17.94 12.94 43.44 3.35
4137 6221 4.020662 GGATAATGGTGGTTTTCTTGCCAA 60.021 41.667 0.00 0.00 36.41 4.52
4156 6245 8.052141 TGTTGACCTGAATGAATGTATTGGATA 58.948 33.333 0.00 0.00 0.00 2.59
4176 6265 4.646040 TCCCATGGATCATTCATTGTTGAC 59.354 41.667 15.22 0.00 0.00 3.18
4195 6284 3.949754 CGTGTATTCTACTGTACCTCCCA 59.050 47.826 0.00 0.00 0.00 4.37
4230 6368 5.352016 TCAAATGTAACGTGGGTACTATTGC 59.648 40.000 0.00 0.00 0.00 3.56
4356 6496 6.177310 TGTTACTACTGGTTGTATTGTGGT 57.823 37.500 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.