Multiple sequence alignment - TraesCS1A01G221200

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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 TraesCS1A01G221200 chr1A 100.000 3464 0 0 1 3464 390096845 390100308 0.000000e+00 6397.0
1 TraesCS1A01G221200 chr1B 94.326 2538 121 11 936 3464 420364926 420367449 0.000000e+00 3868.0
2 TraesCS1A01G221200 chr1B 88.889 459 29 7 1 456 420362462 420362901 2.350000e-151 545.0
3 TraesCS1A01G221200 chr1B 89.809 157 15 1 466 621 420363087 420363243 2.110000e-47 200.0
4 TraesCS1A01G221200 chr1B 88.304 171 13 1 688 851 420364753 420364923 7.580000e-47 198.0
5 TraesCS1A01G221200 chr1D 94.620 1357 61 9 2119 3464 310250959 310252314 0.000000e+00 2091.0
6 TraesCS1A01G221200 chr1D 94.338 1148 55 3 934 2077 310249816 310250957 0.000000e+00 1751.0
7 TraesCS1A01G221200 chr1D 88.986 572 41 13 1 569 310248971 310249523 0.000000e+00 688.0
8 TraesCS1A01G221200 chr1D 93.333 105 6 1 587 690 310249510 310249614 1.660000e-33 154.0
9 TraesCS1A01G221200 chr6B 88.889 90 9 1 850 939 40887433 40887345 3.660000e-20 110.0
10 TraesCS1A01G221200 chr6B 100.000 29 0 0 2822 2850 525110994 525111022 2.000000e-03 54.7
11 TraesCS1A01G221200 chr7B 89.535 86 8 1 851 936 457143784 457143700 1.310000e-19 108.0
12 TraesCS1A01G221200 chr2B 89.535 86 8 1 851 936 488199350 488199266 1.310000e-19 108.0
13 TraesCS1A01G221200 chr2B 87.209 86 10 1 851 936 177083657 177083741 2.850000e-16 97.1
14 TraesCS1A01G221200 chr2B 86.420 81 10 1 856 936 38458668 38458747 1.710000e-13 87.9
15 TraesCS1A01G221200 chr2A 85.556 90 12 1 850 939 751613885 751613797 3.680000e-15 93.5
16 TraesCS1A01G221200 chr2A 95.455 44 2 0 2075 2118 124382088 124382045 1.720000e-08 71.3
17 TraesCS1A01G221200 chr4B 86.047 86 11 1 851 936 577918580 577918496 1.320000e-14 91.6
18 TraesCS1A01G221200 chrUn 86.420 81 10 1 856 936 341781313 341781234 1.710000e-13 87.9
19 TraesCS1A01G221200 chr4A 82.979 94 10 3 851 939 671813094 671813002 2.870000e-11 80.5
20 TraesCS1A01G221200 chr3B 92.453 53 4 0 2074 2126 676615193 676615141 3.710000e-10 76.8
21 TraesCS1A01G221200 chr3B 100.000 30 0 0 2821 2850 814509269 814509240 4.830000e-04 56.5
22 TraesCS1A01G221200 chr2D 93.182 44 3 0 2075 2118 120554704 120554661 8.020000e-07 65.8
23 TraesCS1A01G221200 chr3A 90.698 43 4 0 2075 2117 670100068 670100026 1.340000e-04 58.4
24 TraesCS1A01G221200 chr3A 97.059 34 1 0 2817 2850 724803081 724803114 1.340000e-04 58.4
25 TraesCS1A01G221200 chr5D 96.875 32 1 0 2081 2112 559672137 559672106 2.000000e-03 54.7


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 TraesCS1A01G221200 chr1A 390096845 390100308 3463 False 6397.00 6397 100.00000 1 3464 1 chr1A.!!$F1 3463
1 TraesCS1A01G221200 chr1B 420362462 420367449 4987 False 1202.75 3868 90.33200 1 3464 4 chr1B.!!$F1 3463
2 TraesCS1A01G221200 chr1D 310248971 310252314 3343 False 1171.00 2091 92.81925 1 3464 4 chr1D.!!$F1 3463

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
125 129 0.255033 GGACGGGGTCTGGCTTAATT 59.745 55.0 0.0 0.0 32.47 1.40 F
387 391 0.324943 ACAGGGTTCCACTTCGATGG 59.675 55.0 0.0 0.0 41.57 3.51 F
1510 3164 0.388649 CCACCACTTCGTCTTCTCCG 60.389 60.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 3304 0.252881 TCACCTGAAGCTGGAGGGAT 60.253 55.0 14.37 0.0 33.16 3.85 R
2376 4039 0.174845 CAAGGCCATCGACCGTCTTA 59.825 55.0 5.01 0.0 0.00 2.10 R
3303 4975 0.750249 TTGACAACTGCGAGGAGTCA 59.250 50.0 0.00 0.0 37.43 3.41 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
124 128 0.620700 AGGACGGGGTCTGGCTTAAT 60.621 55.000 0.00 0.00 32.47 1.40
125 129 0.255033 GGACGGGGTCTGGCTTAATT 59.745 55.000 0.00 0.00 32.47 1.40
185 189 2.112998 CAGCCCCATGTTGGAATGATT 58.887 47.619 2.80 0.00 40.96 2.57
237 241 0.883833 GACCTTGATGTGGCAACTGG 59.116 55.000 0.00 0.00 37.61 4.00
238 242 1.181098 ACCTTGATGTGGCAACTGGC 61.181 55.000 0.00 0.00 43.74 4.85
249 253 1.501169 GCAACTGGCAACCATGTTTC 58.499 50.000 0.00 0.00 43.97 2.78
250 254 1.873486 GCAACTGGCAACCATGTTTCC 60.873 52.381 0.00 0.00 43.97 3.13
251 255 1.688197 CAACTGGCAACCATGTTTCCT 59.312 47.619 0.00 0.00 30.82 3.36
252 256 2.086610 ACTGGCAACCATGTTTCCTT 57.913 45.000 0.00 0.00 30.82 3.36
253 257 2.397597 ACTGGCAACCATGTTTCCTTT 58.602 42.857 0.00 0.00 30.82 3.11
254 258 2.102925 ACTGGCAACCATGTTTCCTTTG 59.897 45.455 0.00 0.00 30.82 2.77
255 259 2.102925 CTGGCAACCATGTTTCCTTTGT 59.897 45.455 0.00 0.00 30.82 2.83
256 260 2.503356 TGGCAACCATGTTTCCTTTGTT 59.497 40.909 0.00 0.00 0.00 2.83
257 261 2.871633 GGCAACCATGTTTCCTTTGTTG 59.128 45.455 0.00 0.00 36.92 3.33
271 275 3.243068 CCTTTGTTGTGTGTCTGCCTTAC 60.243 47.826 0.00 0.00 0.00 2.34
307 311 0.814410 TTTTCGCGGCTGTTACACCA 60.814 50.000 6.13 0.00 0.00 4.17
313 317 2.561569 GCGGCTGTTACACCATATCTT 58.438 47.619 0.00 0.00 0.00 2.40
321 325 6.480320 GCTGTTACACCATATCTTTAGACAGG 59.520 42.308 0.00 0.00 33.34 4.00
324 328 5.028549 ACACCATATCTTTAGACAGGCAG 57.971 43.478 0.00 0.00 0.00 4.85
357 361 5.587289 TCATGCTTACACTTTGTTGGTTTC 58.413 37.500 0.00 0.00 0.00 2.78
387 391 0.324943 ACAGGGTTCCACTTCGATGG 59.675 55.000 0.00 0.00 41.57 3.51
388 392 1.026718 CAGGGTTCCACTTCGATGGC 61.027 60.000 0.00 0.00 39.85 4.40
399 403 2.030805 ACTTCGATGGCTCAAACTTTGC 60.031 45.455 3.12 0.00 0.00 3.68
407 411 1.067516 GCTCAAACTTTGCTGCCAAGA 59.932 47.619 18.99 0.00 31.52 3.02
447 451 7.849515 CGTACAATGAAATCAGTGAATCATGAG 59.150 37.037 19.70 17.49 43.86 2.90
458 462 1.674962 GAATCATGAGGGTGCAAGCTC 59.325 52.381 0.09 0.00 0.00 4.09
459 463 0.622136 ATCATGAGGGTGCAAGCTCA 59.378 50.000 0.09 0.00 0.00 4.26
462 466 0.403271 ATGAGGGTGCAAGCTCACTT 59.597 50.000 5.61 0.00 37.16 3.16
464 468 1.322442 GAGGGTGCAAGCTCACTTTT 58.678 50.000 5.61 0.00 37.16 2.27
505 686 7.152645 TGCCAGAATCGTATAGGAAATAAGTC 58.847 38.462 0.00 0.00 0.00 3.01
529 710 1.601903 CGTGAAGCAACAAACTGCCTA 59.398 47.619 0.00 0.00 43.73 3.93
574 755 4.642429 ACTACCTGCTCATCGTTTTTCTT 58.358 39.130 0.00 0.00 0.00 2.52
623 805 3.264193 ACAGCACTAGATCAACCATTCCA 59.736 43.478 0.00 0.00 0.00 3.53
636 2234 4.207891 ACCATTCCATCGGCAGTATATC 57.792 45.455 0.00 0.00 0.00 1.63
668 2266 4.635223 TGGACAGCTCTGTATATTGCATC 58.365 43.478 2.07 0.00 45.05 3.91
677 2275 8.519526 AGCTCTGTATATTGCATCTTAGACTAC 58.480 37.037 0.00 0.00 0.00 2.73
728 2374 3.186409 TGAGCTTTCGTGTTGCATAAGTC 59.814 43.478 0.00 0.00 0.00 3.01
736 2382 6.880822 TCGTGTTGCATAAGTCTGTTATAC 57.119 37.500 0.00 0.00 0.00 1.47
744 2390 7.390823 TGCATAAGTCTGTTATACCAAGTTGA 58.609 34.615 3.87 0.00 0.00 3.18
799 2452 0.395312 GGAGGGGAACGTTGACTTCA 59.605 55.000 5.00 0.00 0.00 3.02
800 2453 1.003233 GGAGGGGAACGTTGACTTCAT 59.997 52.381 5.00 0.00 0.00 2.57
806 2459 3.502211 GGGAACGTTGACTTCATTGATGT 59.498 43.478 5.00 4.97 0.00 3.06
819 2472 6.435277 ACTTCATTGATGTAGAATGGCTTGTT 59.565 34.615 3.52 0.00 32.57 2.83
828 2481 2.557924 AGAATGGCTTGTTTGAATCGCA 59.442 40.909 0.00 0.00 0.00 5.10
829 2482 2.352503 ATGGCTTGTTTGAATCGCAC 57.647 45.000 0.00 0.00 0.00 5.34
851 2504 4.262617 CTCGCCTGCCTAGATACATACTA 58.737 47.826 0.00 0.00 0.00 1.82
852 2505 4.008330 TCGCCTGCCTAGATACATACTAC 58.992 47.826 0.00 0.00 0.00 2.73
853 2506 4.011023 CGCCTGCCTAGATACATACTACT 58.989 47.826 0.00 0.00 0.00 2.57
854 2507 4.095185 CGCCTGCCTAGATACATACTACTC 59.905 50.000 0.00 0.00 0.00 2.59
855 2508 4.399934 GCCTGCCTAGATACATACTACTCC 59.600 50.000 0.00 0.00 0.00 3.85
856 2509 4.951094 CCTGCCTAGATACATACTACTCCC 59.049 50.000 0.00 0.00 0.00 4.30
857 2510 5.281297 CCTGCCTAGATACATACTACTCCCT 60.281 48.000 0.00 0.00 0.00 4.20
858 2511 6.215515 TGCCTAGATACATACTACTCCCTT 57.784 41.667 0.00 0.00 0.00 3.95
859 2512 6.621394 TGCCTAGATACATACTACTCCCTTT 58.379 40.000 0.00 0.00 0.00 3.11
860 2513 6.493802 TGCCTAGATACATACTACTCCCTTTG 59.506 42.308 0.00 0.00 0.00 2.77
861 2514 6.494146 GCCTAGATACATACTACTCCCTTTGT 59.506 42.308 0.00 0.00 0.00 2.83
862 2515 7.309316 GCCTAGATACATACTACTCCCTTTGTC 60.309 44.444 0.00 0.00 0.00 3.18
863 2516 7.945664 CCTAGATACATACTACTCCCTTTGTCT 59.054 40.741 0.00 0.00 0.00 3.41
864 2517 7.826918 AGATACATACTACTCCCTTTGTCTC 57.173 40.000 0.00 0.00 0.00 3.36
865 2518 4.985538 ACATACTACTCCCTTTGTCTCG 57.014 45.455 0.00 0.00 0.00 4.04
866 2519 4.342359 ACATACTACTCCCTTTGTCTCGT 58.658 43.478 0.00 0.00 0.00 4.18
867 2520 5.503927 ACATACTACTCCCTTTGTCTCGTA 58.496 41.667 0.00 0.00 0.00 3.43
868 2521 5.948162 ACATACTACTCCCTTTGTCTCGTAA 59.052 40.000 0.00 0.00 0.00 3.18
869 2522 6.606395 ACATACTACTCCCTTTGTCTCGTAAT 59.394 38.462 0.00 0.00 0.00 1.89
870 2523 5.326200 ACTACTCCCTTTGTCTCGTAATG 57.674 43.478 0.00 0.00 0.00 1.90
871 2524 4.771054 ACTACTCCCTTTGTCTCGTAATGT 59.229 41.667 0.00 0.00 0.00 2.71
872 2525 5.948162 ACTACTCCCTTTGTCTCGTAATGTA 59.052 40.000 0.00 0.00 0.00 2.29
873 2526 5.733620 ACTCCCTTTGTCTCGTAATGTAA 57.266 39.130 0.00 0.00 0.00 2.41
874 2527 5.721232 ACTCCCTTTGTCTCGTAATGTAAG 58.279 41.667 0.00 0.00 0.00 2.34
875 2528 5.479375 ACTCCCTTTGTCTCGTAATGTAAGA 59.521 40.000 0.00 0.00 0.00 2.10
876 2529 5.717119 TCCCTTTGTCTCGTAATGTAAGAC 58.283 41.667 0.00 0.00 39.87 3.01
877 2530 4.561606 CCCTTTGTCTCGTAATGTAAGACG 59.438 45.833 0.00 0.00 41.84 4.18
878 2531 5.159209 CCTTTGTCTCGTAATGTAAGACGT 58.841 41.667 0.00 0.00 41.84 4.34
879 2532 5.632347 CCTTTGTCTCGTAATGTAAGACGTT 59.368 40.000 0.00 0.00 41.84 3.99
880 2533 6.145048 CCTTTGTCTCGTAATGTAAGACGTTT 59.855 38.462 0.00 0.00 41.84 3.60
881 2534 7.306983 CCTTTGTCTCGTAATGTAAGACGTTTT 60.307 37.037 0.00 0.00 41.84 2.43
882 2535 7.467557 TTGTCTCGTAATGTAAGACGTTTTT 57.532 32.000 0.00 0.00 41.84 1.94
931 2584 5.769484 GTCTTACATTATGAGACGGAGGA 57.231 43.478 0.00 0.00 34.53 3.71
932 2585 6.145338 GTCTTACATTATGAGACGGAGGAA 57.855 41.667 0.00 0.00 34.53 3.36
985 2638 4.551702 TTGATCACCAGCAAAGCTAGTA 57.448 40.909 0.00 0.00 36.40 1.82
1005 2658 0.684479 GGACCAAAGGAAGGATGGCC 60.684 60.000 0.00 0.00 37.77 5.36
1014 2667 4.153957 AGGATGGCCGAGTCCTTT 57.846 55.556 16.16 0.00 42.09 3.11
1017 2670 0.462759 GGATGGCCGAGTCCTTTGAG 60.463 60.000 12.94 0.00 0.00 3.02
1023 2676 2.545731 GCCGAGTCCTTTGAGAAGATC 58.454 52.381 0.00 0.00 34.71 2.75
1053 2706 0.904865 TCACCGGCCATGAAGAGAGT 60.905 55.000 0.00 0.00 0.00 3.24
1125 2778 0.749649 ACATCAGGCAGGAGATCGAC 59.250 55.000 0.00 0.00 0.00 4.20
1170 2823 3.695606 GGTCCTGCTCTGCCGACA 61.696 66.667 8.43 0.00 31.33 4.35
1184 2837 1.939974 CCGACAATCGACATGTCCAT 58.060 50.000 20.03 10.35 43.74 3.41
1236 2889 2.417516 GCTAAGCTCGGATCCGCA 59.582 61.111 29.62 16.64 39.59 5.69
1274 2927 1.334869 CTTCCAGGTCTGCAACAACAC 59.665 52.381 0.00 0.00 0.00 3.32
1293 2946 2.032054 CACCATTCCATTCCACGATTCG 59.968 50.000 4.14 4.14 0.00 3.34
1510 3164 0.388649 CCACCACTTCGTCTTCTCCG 60.389 60.000 0.00 0.00 0.00 4.63
1555 3209 4.329545 TGCTGTTCCTCGCCACCC 62.330 66.667 0.00 0.00 0.00 4.61
1650 3304 4.765339 TCTCTGTTTCGTCAACTAGATCCA 59.235 41.667 0.00 0.00 36.21 3.41
1693 3351 5.011329 ACATGAACCTGAATGTTTCAAGCAT 59.989 36.000 0.00 0.00 39.58 3.79
1694 3352 5.534207 TGAACCTGAATGTTTCAAGCATT 57.466 34.783 0.00 0.00 39.58 3.56
1802 3461 1.171308 CTGTTCAGGTTCATGGCCAG 58.829 55.000 13.05 3.43 0.00 4.85
1848 3507 4.929807 CTTGGCACCTTCAAGGGT 57.070 55.556 8.75 0.00 40.58 4.34
1998 3657 1.698532 CAGATCAGGAAGGATGGGGAG 59.301 57.143 0.00 0.00 0.00 4.30
2078 3737 1.900486 GGTGTGTTCCTAGCCAGTACT 59.100 52.381 0.00 0.00 0.00 2.73
2083 3742 2.584031 TGTTCCTAGCCAGTACTCCCTA 59.416 50.000 0.00 0.00 0.00 3.53
2090 3749 1.843368 CCAGTACTCCCTACGTTCCA 58.157 55.000 0.00 0.00 0.00 3.53
2109 3768 6.747280 CGTTCCATAATTCTTGTCATGGTTTC 59.253 38.462 3.23 0.00 39.21 2.78
2223 3886 7.595819 AAAACACTGAGAAATTACCATTGGA 57.404 32.000 10.37 0.00 0.00 3.53
2310 3973 2.997899 GGAGAGGATCACCATTGCG 58.002 57.895 0.00 0.00 45.93 4.85
2343 4006 1.675641 GCACCTTCCCTGCACGATT 60.676 57.895 0.00 0.00 34.56 3.34
2364 4027 2.750350 CCGTTTCAGGAGCTGGGT 59.250 61.111 0.00 0.00 31.51 4.51
2376 4039 2.184322 CTGGGTGACGCACGCTAT 59.816 61.111 21.04 0.00 45.53 2.97
2452 4115 3.957919 GGAGGTACCTGGAGAGCC 58.042 66.667 22.10 9.45 35.41 4.70
2491 4154 0.610174 TGATGGTCACTGGTCAGAGC 59.390 55.000 4.84 0.00 0.00 4.09
2597 4264 8.043113 TGTTATGTGCAGTCTTCTCATAGAATT 58.957 33.333 0.00 0.00 33.13 2.17
2814 4485 3.515502 CCTTCTGTTGTGATCTACTCCCA 59.484 47.826 0.00 0.00 0.00 4.37
2815 4486 4.020218 CCTTCTGTTGTGATCTACTCCCAA 60.020 45.833 0.00 0.00 0.00 4.12
2818 4489 2.000447 GTTGTGATCTACTCCCAACGC 59.000 52.381 0.00 0.00 0.00 4.84
2827 4498 2.360600 TCCCAACGCCCGGAAATG 60.361 61.111 0.73 0.00 0.00 2.32
2855 4527 5.588648 GTCGGAGAAATGGATGTATTTCCAA 59.411 40.000 7.41 0.00 44.27 3.53
2892 4564 6.918022 GTGTAGGTTGTGATTTTCTTTTGGAG 59.082 38.462 0.00 0.00 0.00 3.86
3012 4684 5.939764 AGTGCTGTAAGATGGATCAAGTA 57.060 39.130 0.00 0.00 34.07 2.24
3018 4690 6.371548 GCTGTAAGATGGATCAAGTACAACAA 59.628 38.462 0.00 0.00 34.07 2.83
3097 4769 0.395862 TCGGTCTCTTGGGAGCTAGG 60.396 60.000 0.00 0.00 39.31 3.02
3255 4927 3.468770 ACATTGATCATCAGCTCTCTGC 58.531 45.455 0.00 0.00 40.13 4.26
3303 4975 5.394663 CGAAGAACACCTATCCTCAAGATGT 60.395 44.000 0.00 0.00 36.33 3.06
3392 5064 6.154706 TCGAAAGTAAAAAGGCCTCTATCTCT 59.845 38.462 5.23 0.00 0.00 3.10
3395 5067 4.471386 AGTAAAAAGGCCTCTATCTCTGCA 59.529 41.667 5.23 0.00 0.00 4.41
3397 5069 4.307032 AAAAGGCCTCTATCTCTGCAAA 57.693 40.909 5.23 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 96 0.977395 CCGTCCTTCTTCTCCTTGGT 59.023 55.000 0.00 0.00 0.00 3.67
124 128 7.556733 AAAGTACAACCGTTGATGAGTAAAA 57.443 32.000 18.19 0.00 0.00 1.52
125 129 7.171337 GGTAAAGTACAACCGTTGATGAGTAAA 59.829 37.037 18.19 0.00 0.00 2.01
185 189 1.754226 GGAACCAAAAAGCACCAGTCA 59.246 47.619 0.00 0.00 0.00 3.41
237 241 3.309410 CACAACAAAGGAAACATGGTTGC 59.691 43.478 6.94 6.94 0.00 4.17
238 242 4.329528 CACACAACAAAGGAAACATGGTTG 59.670 41.667 0.00 3.10 0.00 3.77
239 243 4.020662 ACACACAACAAAGGAAACATGGTT 60.021 37.500 0.00 0.00 0.00 3.67
240 244 3.513515 ACACACAACAAAGGAAACATGGT 59.486 39.130 0.00 0.00 0.00 3.55
241 245 4.111916 GACACACAACAAAGGAAACATGG 58.888 43.478 0.00 0.00 0.00 3.66
242 246 4.799949 CAGACACACAACAAAGGAAACATG 59.200 41.667 0.00 0.00 0.00 3.21
243 247 4.677779 GCAGACACACAACAAAGGAAACAT 60.678 41.667 0.00 0.00 0.00 2.71
245 249 3.179048 GCAGACACACAACAAAGGAAAC 58.821 45.455 0.00 0.00 0.00 2.78
247 251 1.748493 GGCAGACACACAACAAAGGAA 59.252 47.619 0.00 0.00 0.00 3.36
249 253 1.392589 AGGCAGACACACAACAAAGG 58.607 50.000 0.00 0.00 0.00 3.11
250 254 3.546020 CGTAAGGCAGACACACAACAAAG 60.546 47.826 0.00 0.00 0.00 2.77
251 255 2.353269 CGTAAGGCAGACACACAACAAA 59.647 45.455 0.00 0.00 0.00 2.83
252 256 1.937223 CGTAAGGCAGACACACAACAA 59.063 47.619 0.00 0.00 0.00 2.83
253 257 1.134640 ACGTAAGGCAGACACACAACA 60.135 47.619 0.00 0.00 46.39 3.33
254 258 1.260561 CACGTAAGGCAGACACACAAC 59.739 52.381 0.00 0.00 46.39 3.32
255 259 1.134640 ACACGTAAGGCAGACACACAA 60.135 47.619 0.00 0.00 46.39 3.33
256 260 0.462375 ACACGTAAGGCAGACACACA 59.538 50.000 0.00 0.00 46.39 3.72
257 261 0.859232 CACACGTAAGGCAGACACAC 59.141 55.000 0.00 0.00 46.39 3.82
291 295 0.462375 ATATGGTGTAACAGCCGCGA 59.538 50.000 8.23 0.00 39.98 5.87
292 296 0.859232 GATATGGTGTAACAGCCGCG 59.141 55.000 0.00 0.00 39.98 6.46
324 328 4.620982 AGTGTAAGCATGAAAAAGGCAAC 58.379 39.130 0.00 0.00 38.31 4.17
329 333 6.534793 ACCAACAAAGTGTAAGCATGAAAAAG 59.465 34.615 0.00 0.00 0.00 2.27
357 361 1.750778 GGAACCCTGTGCCATATGTTG 59.249 52.381 1.24 0.00 29.85 3.33
376 380 1.813513 AGTTTGAGCCATCGAAGTGG 58.186 50.000 0.37 0.37 42.35 4.00
387 391 1.067516 TCTTGGCAGCAAAGTTTGAGC 59.932 47.619 19.82 19.54 34.02 4.26
388 392 3.441496 TTCTTGGCAGCAAAGTTTGAG 57.559 42.857 19.82 11.36 0.00 3.02
399 403 1.588674 TGGTGTACGTTTCTTGGCAG 58.411 50.000 0.00 0.00 0.00 4.85
447 451 3.005791 ACAATAAAAGTGAGCTTGCACCC 59.994 43.478 2.09 0.00 39.59 4.61
458 462 7.655328 TGGCAATAAAGGTCAACAATAAAAGTG 59.345 33.333 0.00 0.00 0.00 3.16
459 463 7.731054 TGGCAATAAAGGTCAACAATAAAAGT 58.269 30.769 0.00 0.00 0.00 2.66
462 466 7.531857 TCTGGCAATAAAGGTCAACAATAAA 57.468 32.000 0.00 0.00 0.00 1.40
464 468 7.415095 CGATTCTGGCAATAAAGGTCAACAATA 60.415 37.037 0.00 0.00 0.00 1.90
501 682 4.096382 AGTTTGTTGCTTCACGATTGACTT 59.904 37.500 0.00 0.00 0.00 3.01
505 686 2.468777 GCAGTTTGTTGCTTCACGATTG 59.531 45.455 0.00 0.00 40.89 2.67
574 755 1.216678 TGAGCAGGTCCCCTTGAAAAA 59.783 47.619 0.00 0.00 0.00 1.94
579 760 1.153289 CGATGAGCAGGTCCCCTTG 60.153 63.158 0.00 0.00 0.00 3.61
580 761 1.201429 AACGATGAGCAGGTCCCCTT 61.201 55.000 0.00 0.00 0.00 3.95
585 766 1.354040 CTGTCAACGATGAGCAGGTC 58.646 55.000 13.59 0.00 35.88 3.85
623 805 6.350528 CCATGTCTACAAGATATACTGCCGAT 60.351 42.308 0.00 0.00 0.00 4.18
636 2234 3.056250 ACAGAGCTGTCCATGTCTACAAG 60.056 47.826 0.00 0.00 40.24 3.16
668 2266 9.360093 CAGAAAGTGTCCAAATAGTAGTCTAAG 57.640 37.037 0.00 0.00 0.00 2.18
677 2275 8.842358 TTAGGTAACAGAAAGTGTCCAAATAG 57.158 34.615 0.00 0.00 39.03 1.73
728 2374 7.667043 TTGTTAGCTCAACTTGGTATAACAG 57.333 36.000 0.00 0.00 38.05 3.16
771 2424 0.457035 CGTTCCCCTCCAATTGCATG 59.543 55.000 0.00 0.00 0.00 4.06
799 2452 6.839124 TCAAACAAGCCATTCTACATCAAT 57.161 33.333 0.00 0.00 0.00 2.57
800 2453 6.647334 TTCAAACAAGCCATTCTACATCAA 57.353 33.333 0.00 0.00 0.00 2.57
806 2459 3.755905 TGCGATTCAAACAAGCCATTCTA 59.244 39.130 0.00 0.00 0.00 2.10
819 2472 2.390599 GCAGGCGAGTGCGATTCAA 61.391 57.895 0.00 0.00 44.10 2.69
828 2481 2.002505 ATGTATCTAGGCAGGCGAGT 57.997 50.000 3.96 0.00 0.00 4.18
829 2482 3.085533 AGTATGTATCTAGGCAGGCGAG 58.914 50.000 0.00 0.00 0.00 5.03
851 2504 5.479375 TCTTACATTACGAGACAAAGGGAGT 59.521 40.000 0.00 0.00 0.00 3.85
852 2505 5.805994 GTCTTACATTACGAGACAAAGGGAG 59.194 44.000 0.00 0.00 39.59 4.30
853 2506 5.620654 CGTCTTACATTACGAGACAAAGGGA 60.621 44.000 0.00 0.00 41.55 4.20
854 2507 4.561606 CGTCTTACATTACGAGACAAAGGG 59.438 45.833 0.00 0.00 41.55 3.95
855 2508 5.159209 ACGTCTTACATTACGAGACAAAGG 58.841 41.667 1.45 0.00 41.55 3.11
856 2509 6.686130 AACGTCTTACATTACGAGACAAAG 57.314 37.500 1.45 0.00 41.55 2.77
857 2510 7.467557 AAAACGTCTTACATTACGAGACAAA 57.532 32.000 1.45 0.00 41.55 2.83
858 2511 7.467557 AAAAACGTCTTACATTACGAGACAA 57.532 32.000 1.45 0.00 41.55 3.18
909 2562 5.769484 TCCTCCGTCTCATAATGTAAGAC 57.231 43.478 0.00 0.00 36.82 3.01
910 2563 5.892119 ACTTCCTCCGTCTCATAATGTAAGA 59.108 40.000 0.00 0.00 0.00 2.10
911 2564 6.150396 ACTTCCTCCGTCTCATAATGTAAG 57.850 41.667 0.00 0.00 0.00 2.34
912 2565 6.604396 TGTACTTCCTCCGTCTCATAATGTAA 59.396 38.462 0.00 0.00 0.00 2.41
913 2566 6.124340 TGTACTTCCTCCGTCTCATAATGTA 58.876 40.000 0.00 0.00 0.00 2.29
914 2567 4.954202 TGTACTTCCTCCGTCTCATAATGT 59.046 41.667 0.00 0.00 0.00 2.71
915 2568 5.515797 TGTACTTCCTCCGTCTCATAATG 57.484 43.478 0.00 0.00 0.00 1.90
916 2569 6.071984 AGATGTACTTCCTCCGTCTCATAAT 58.928 40.000 5.19 0.00 0.00 1.28
917 2570 5.446860 AGATGTACTTCCTCCGTCTCATAA 58.553 41.667 5.19 0.00 0.00 1.90
918 2571 5.050126 AGATGTACTTCCTCCGTCTCATA 57.950 43.478 5.19 0.00 0.00 2.15
919 2572 3.886505 GAGATGTACTTCCTCCGTCTCAT 59.113 47.826 5.19 0.00 39.79 2.90
920 2573 3.280295 GAGATGTACTTCCTCCGTCTCA 58.720 50.000 5.19 0.00 39.79 3.27
921 2574 3.280295 TGAGATGTACTTCCTCCGTCTC 58.720 50.000 5.19 0.00 40.22 3.36
922 2575 3.283751 CTGAGATGTACTTCCTCCGTCT 58.716 50.000 5.19 0.00 0.00 4.18
923 2576 2.223618 GCTGAGATGTACTTCCTCCGTC 60.224 54.545 5.19 0.00 0.00 4.79
924 2577 1.751924 GCTGAGATGTACTTCCTCCGT 59.248 52.381 5.19 0.00 0.00 4.69
925 2578 2.028130 AGCTGAGATGTACTTCCTCCG 58.972 52.381 5.19 2.05 0.00 4.63
926 2579 4.830046 TGATAGCTGAGATGTACTTCCTCC 59.170 45.833 0.00 0.00 0.00 4.30
927 2580 5.767665 TCTGATAGCTGAGATGTACTTCCTC 59.232 44.000 0.00 4.39 0.00 3.71
928 2581 5.534654 GTCTGATAGCTGAGATGTACTTCCT 59.465 44.000 0.00 0.00 0.00 3.36
929 2582 5.561919 CGTCTGATAGCTGAGATGTACTTCC 60.562 48.000 0.00 0.00 0.00 3.46
930 2583 5.448438 CGTCTGATAGCTGAGATGTACTTC 58.552 45.833 0.00 0.50 0.00 3.01
931 2584 4.261405 GCGTCTGATAGCTGAGATGTACTT 60.261 45.833 0.00 0.00 0.00 2.24
932 2585 3.252215 GCGTCTGATAGCTGAGATGTACT 59.748 47.826 0.00 0.00 0.00 2.73
985 2638 0.332972 GCCATCCTTCCTTTGGTCCT 59.667 55.000 0.00 0.00 32.90 3.85
1005 2658 4.180057 CCTTGATCTTCTCAAAGGACTCG 58.820 47.826 1.83 0.00 43.20 4.18
1014 2667 3.903714 TGAACTCCACCTTGATCTTCTCA 59.096 43.478 0.00 0.00 0.00 3.27
1038 2691 1.364626 GCACACTCTCTTCATGGCCG 61.365 60.000 0.00 0.00 0.00 6.13
1152 2805 3.695606 GTCGGCAGAGCAGGACCA 61.696 66.667 0.00 0.00 30.86 4.02
1157 2810 1.153765 TCGATTGTCGGCAGAGCAG 60.154 57.895 0.00 0.00 40.88 4.24
1170 2823 1.019673 GCAGCATGGACATGTCGATT 58.980 50.000 19.47 5.02 40.80 3.34
1236 2889 3.628646 GAACCCCCAGTGCTCGCAT 62.629 63.158 0.00 0.00 0.00 4.73
1251 2904 1.967319 TGTTGCAGACCTGGAAGAAC 58.033 50.000 0.00 0.00 41.50 3.01
1274 2927 2.288666 ACGAATCGTGGAATGGAATGG 58.711 47.619 7.77 0.00 39.18 3.16
1293 2946 0.731417 GCTGCCTGATGACATGACAC 59.269 55.000 0.00 0.00 0.00 3.67
1422 3075 1.078143 CAGGGGAAGGCCGAAGAAG 60.078 63.158 0.00 0.00 33.83 2.85
1564 3218 4.500116 GTCCAGGCTCCGCTCGTC 62.500 72.222 0.00 0.00 0.00 4.20
1566 3220 3.708220 GAAGTCCAGGCTCCGCTCG 62.708 68.421 0.00 0.00 0.00 5.03
1650 3304 0.252881 TCACCTGAAGCTGGAGGGAT 60.253 55.000 14.37 0.00 33.16 3.85
1802 3461 1.842381 CTGGTCAACTCCCAGGTCCC 61.842 65.000 0.00 0.00 44.77 4.46
1848 3507 4.007644 CTCACGCACTGGGGCAGA 62.008 66.667 0.00 0.00 35.18 4.26
1947 3606 3.744719 TCGTTCGCGTGGAGGAGG 61.745 66.667 5.77 0.00 42.11 4.30
1959 3618 2.665185 AGCCCTTGCACGTCGTTC 60.665 61.111 0.00 0.00 41.13 3.95
1998 3657 3.712881 GCGTGCACGGAGAACCAC 61.713 66.667 37.47 16.66 40.23 4.16
2078 3737 5.188163 TGACAAGAATTATGGAACGTAGGGA 59.812 40.000 0.00 0.00 0.00 4.20
2083 3742 5.253330 ACCATGACAAGAATTATGGAACGT 58.747 37.500 9.22 0.00 42.05 3.99
2090 3749 8.408043 TGAACTGAAACCATGACAAGAATTAT 57.592 30.769 0.00 0.00 0.00 1.28
2109 3768 7.840342 ACAGAGCAGATACTAATTTGAACTG 57.160 36.000 0.00 0.00 33.03 3.16
2215 3878 4.939255 AGGATCTGTTTGAATCCAATGGT 58.061 39.130 0.00 0.00 35.71 3.55
2223 3886 3.438087 CGTTGCTGAGGATCTGTTTGAAT 59.562 43.478 0.00 0.00 36.33 2.57
2343 4006 3.249189 AGCTCCTGAAACGGGCCA 61.249 61.111 4.39 0.00 0.00 5.36
2364 4027 0.248336 CCGTCTTATAGCGTGCGTCA 60.248 55.000 0.00 0.00 0.00 4.35
2376 4039 0.174845 CAAGGCCATCGACCGTCTTA 59.825 55.000 5.01 0.00 0.00 2.10
2409 4072 2.434359 AGCTTGGCGGCGAAGTAC 60.434 61.111 22.81 9.78 37.29 2.73
2421 4084 1.378250 CCTCCTGCCTTCCAGCTTG 60.378 63.158 0.00 0.00 40.36 4.01
2452 4115 7.660617 ACCATCATCATTTGACTATAGCTTCAG 59.339 37.037 0.00 0.00 37.11 3.02
2464 4127 4.263418 TGACCAGTGACCATCATCATTTGA 60.263 41.667 0.00 0.00 39.12 2.69
2467 4130 3.520721 TCTGACCAGTGACCATCATCATT 59.479 43.478 0.00 0.00 0.00 2.57
2491 4154 7.539712 AGTGAATTAATCATAACACTCACCG 57.460 36.000 8.37 0.00 40.97 4.94
2531 4194 9.006839 CAACACATATGATACATAGGAAGCAAT 57.993 33.333 10.38 0.00 0.00 3.56
2532 4195 7.041167 GCAACACATATGATACATAGGAAGCAA 60.041 37.037 10.38 0.00 0.00 3.91
2534 4197 6.652481 AGCAACACATATGATACATAGGAAGC 59.348 38.462 10.38 7.70 0.00 3.86
2535 4198 8.613060 AAGCAACACATATGATACATAGGAAG 57.387 34.615 10.38 5.27 0.00 3.46
2617 4284 5.009854 ACCACAAAACATTCTGTTCTTGG 57.990 39.130 13.91 12.36 40.14 3.61
2663 4330 6.775629 ACACCCAGTACATTAAGTTCACAAAT 59.224 34.615 0.00 0.00 0.00 2.32
2681 4348 3.009723 CACAGGCAGTATTTACACCCAG 58.990 50.000 0.00 0.00 0.00 4.45
2683 4350 2.026636 TCCACAGGCAGTATTTACACCC 60.027 50.000 0.00 0.00 0.00 4.61
2814 4485 1.862602 GACAAGCATTTCCGGGCGTT 61.863 55.000 0.00 0.00 34.54 4.84
2815 4486 2.282180 ACAAGCATTTCCGGGCGT 60.282 55.556 0.00 0.00 34.54 5.68
2818 4489 1.369091 CTCCGACAAGCATTTCCGGG 61.369 60.000 0.00 0.00 40.48 5.73
2827 4498 2.359900 ACATCCATTTCTCCGACAAGC 58.640 47.619 0.00 0.00 0.00 4.01
2855 4527 1.125633 ACCTACACACTCCCAACGTT 58.874 50.000 0.00 0.00 0.00 3.99
2867 4539 6.801575 TCCAAAAGAAAATCACAACCTACAC 58.198 36.000 0.00 0.00 0.00 2.90
2892 4564 8.465999 CCTATCATACTGTGGATCTCTATTGTC 58.534 40.741 0.00 0.00 0.00 3.18
3012 4684 7.566760 TGTCTATGATTGAGTTTGTTGTTGT 57.433 32.000 0.00 0.00 0.00 3.32
3018 4690 7.607607 TGTATTGCTGTCTATGATTGAGTTTGT 59.392 33.333 0.00 0.00 0.00 2.83
3097 4769 2.900122 TGAGCTTTTATTCAGCGTGC 57.100 45.000 0.00 0.00 42.55 5.34
3255 4927 6.348950 CGATAGCTACAGGGAATAGACAGAAG 60.349 46.154 0.00 0.00 0.00 2.85
3303 4975 0.750249 TTGACAACTGCGAGGAGTCA 59.250 50.000 0.00 0.00 37.43 3.41
3395 5067 5.338300 GGTTAGTGATGATGGGGCAAAATTT 60.338 40.000 0.00 0.00 0.00 1.82
3397 5069 3.706086 GGTTAGTGATGATGGGGCAAAAT 59.294 43.478 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.