Multiple sequence alignment - TraesCS1A01G366200

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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 TraesCS1A01G366200 chr1A 100.000 3141 0 0 1 3141 545010598 545007458 0.000000e+00 5801
1 TraesCS1A01G366200 chr1A 85.353 1106 112 32 1101 2178 544748298 544749381 0.000000e+00 1099
2 TraesCS1A01G366200 chr1A 85.166 991 103 21 1138 2126 545025221 545024273 0.000000e+00 976
3 TraesCS1A01G366200 chr1A 83.153 926 95 31 1235 2141 544927966 544928849 0.000000e+00 789
4 TraesCS1A01G366200 chr1A 87.253 659 66 10 1472 2124 545000581 545001227 0.000000e+00 736
5 TraesCS1A01G366200 chr1B 87.945 1825 128 43 433 2215 615745874 615744100 0.000000e+00 2067
6 TraesCS1A01G366200 chr1B 86.594 1738 141 45 433 2126 616133308 616131619 0.000000e+00 1834
7 TraesCS1A01G366200 chr1B 85.377 1060 109 29 942 1984 615581586 615582616 0.000000e+00 1057
8 TraesCS1A01G366200 chr1B 85.211 852 108 13 1138 1982 615625656 615626496 0.000000e+00 859
9 TraesCS1A01G366200 chr1B 88.048 661 64 9 1472 2126 615732509 615733160 0.000000e+00 769
10 TraesCS1A01G366200 chr1B 80.650 677 71 25 2495 3137 615743865 615743215 1.320000e-128 470
11 TraesCS1A01G366200 chr1B 90.157 254 20 3 1 254 615753885 615753637 3.020000e-85 326
12 TraesCS1A01G366200 chr1D 87.372 1465 110 38 749 2196 449923923 449922517 0.000000e+00 1611
13 TraesCS1A01G366200 chr1D 83.423 1116 125 41 898 1984 449660180 449661264 0.000000e+00 981
14 TraesCS1A01G366200 chr1D 80.927 1337 172 59 887 2178 449674427 449675725 0.000000e+00 979
15 TraesCS1A01G366200 chr1D 90.781 640 32 11 1 621 449924638 449924007 0.000000e+00 830
16 TraesCS1A01G366200 chr1D 80.232 1123 136 56 1101 2178 449752638 449753719 0.000000e+00 765
17 TraesCS1A01G366200 chr1D 86.989 661 70 10 1472 2125 449847234 449847885 0.000000e+00 730
18 TraesCS1A01G366200 chr1D 85.484 496 47 15 898 1379 449846635 449847119 7.830000e-136 494
19 TraesCS1A01G366200 chr1D 78.460 766 80 41 2411 3135 449919835 449919114 3.750000e-114 422
20 TraesCS1A01G366200 chr1D 83.230 483 56 19 914 1384 449983626 449983157 1.350000e-113 420
21 TraesCS1A01G366200 chr1D 81.319 182 14 11 2000 2178 449661322 449661486 2.540000e-26 130


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 TraesCS1A01G366200 chr1A 545007458 545010598 3140 True 5801.000000 5801 100.000000 1 3141 1 chr1A.!!$R1 3140
1 TraesCS1A01G366200 chr1A 544748298 544749381 1083 False 1099.000000 1099 85.353000 1101 2178 1 chr1A.!!$F1 1077
2 TraesCS1A01G366200 chr1A 545024273 545025221 948 True 976.000000 976 85.166000 1138 2126 1 chr1A.!!$R2 988
3 TraesCS1A01G366200 chr1A 544927966 544928849 883 False 789.000000 789 83.153000 1235 2141 1 chr1A.!!$F2 906
4 TraesCS1A01G366200 chr1A 545000581 545001227 646 False 736.000000 736 87.253000 1472 2124 1 chr1A.!!$F3 652
5 TraesCS1A01G366200 chr1B 616131619 616133308 1689 True 1834.000000 1834 86.594000 433 2126 1 chr1B.!!$R2 1693
6 TraesCS1A01G366200 chr1B 615743215 615745874 2659 True 1268.500000 2067 84.297500 433 3137 2 chr1B.!!$R3 2704
7 TraesCS1A01G366200 chr1B 615581586 615582616 1030 False 1057.000000 1057 85.377000 942 1984 1 chr1B.!!$F1 1042
8 TraesCS1A01G366200 chr1B 615625656 615626496 840 False 859.000000 859 85.211000 1138 1982 1 chr1B.!!$F2 844
9 TraesCS1A01G366200 chr1B 615732509 615733160 651 False 769.000000 769 88.048000 1472 2126 1 chr1B.!!$F3 654
10 TraesCS1A01G366200 chr1D 449674427 449675725 1298 False 979.000000 979 80.927000 887 2178 1 chr1D.!!$F1 1291
11 TraesCS1A01G366200 chr1D 449919114 449924638 5524 True 954.333333 1611 85.537667 1 3135 3 chr1D.!!$R2 3134
12 TraesCS1A01G366200 chr1D 449752638 449753719 1081 False 765.000000 765 80.232000 1101 2178 1 chr1D.!!$F2 1077
13 TraesCS1A01G366200 chr1D 449846635 449847885 1250 False 612.000000 730 86.236500 898 2125 2 chr1D.!!$F4 1227
14 TraesCS1A01G366200 chr1D 449660180 449661486 1306 False 555.500000 981 82.371000 898 2178 2 chr1D.!!$F3 1280

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
763 795 0.517316 GAGGCGGCACACTACTTTTG 59.483 55.0 13.08 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2442 4932 0.03601 ATCGTTGCTTGGACTCCTGG 60.036 55.0 0.0 0.0 0.0 4.45 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
27 28 9.614792 ACTTCTATCTTACAGTGTGTTCTTTTT 57.385 29.630 5.88 0.00 0.00 1.94
76 79 7.602753 ACAACTCTAAATTGAAATTGGTAGGC 58.397 34.615 0.00 0.00 0.00 3.93
84 87 2.433646 AAATTGGTAGGCGCACCCCA 62.434 55.000 10.83 8.56 37.84 4.96
176 179 2.624838 AGAACAAAATGACCAGTGCCTG 59.375 45.455 0.00 0.00 0.00 4.85
228 231 1.502163 GAACGACTGTGCAGCAAGCT 61.502 55.000 0.00 0.00 45.94 3.74
275 282 2.668550 GCCGCTGTCCTTCGGTTT 60.669 61.111 2.58 0.00 46.79 3.27
339 346 0.817229 TCTGCATTTGGACGCACACA 60.817 50.000 0.00 0.00 33.75 3.72
377 396 1.347062 GTTTGGCCCCCTGATTGAAA 58.653 50.000 0.00 0.00 0.00 2.69
405 424 2.517875 GCAGGGCCGCTGATTCAT 60.518 61.111 21.37 0.00 0.00 2.57
406 425 1.227943 GCAGGGCCGCTGATTCATA 60.228 57.895 21.37 0.00 0.00 2.15
410 429 1.595382 GGCCGCTGATTCATACGCT 60.595 57.895 0.00 0.00 0.00 5.07
411 430 1.160329 GGCCGCTGATTCATACGCTT 61.160 55.000 0.00 0.00 0.00 4.68
428 447 2.032894 CGCTTGACGTGATTTGTGACTT 60.033 45.455 0.00 0.00 36.87 3.01
436 455 4.034048 ACGTGATTTGTGACTTGACTTGAC 59.966 41.667 0.00 0.00 0.00 3.18
454 473 2.302733 TGACCAATTAGTGAGCTGAGCA 59.697 45.455 7.39 0.00 0.00 4.26
457 476 3.076621 CCAATTAGTGAGCTGAGCAACA 58.923 45.455 7.39 3.48 0.00 3.33
469 488 6.651714 GAGCTGAGCAACAGATGATTAAGCA 61.652 44.000 7.39 0.00 45.71 3.91
524 543 1.062525 GGTGCCATGACGCGATTTC 59.937 57.895 15.93 0.00 0.00 2.17
525 544 1.369091 GGTGCCATGACGCGATTTCT 61.369 55.000 15.93 0.00 0.00 2.52
612 631 1.153353 TTAGCAGTGCCGTGTTAAGC 58.847 50.000 12.58 0.00 0.00 3.09
638 657 1.226974 GATTAGCAGCGCGTGGAGA 60.227 57.895 8.43 0.00 0.00 3.71
649 668 1.144057 CGTGGAGACTATGGGTGCC 59.856 63.158 0.00 0.00 0.00 5.01
678 697 1.298859 CCTTCTTTTCTCGTGCGGGG 61.299 60.000 0.00 0.00 0.00 5.73
715 734 0.530650 CAACACCGTCTCAGCACAGT 60.531 55.000 0.00 0.00 0.00 3.55
716 735 0.530650 AACACCGTCTCAGCACAGTG 60.531 55.000 0.00 0.00 0.00 3.66
717 736 1.665916 CACCGTCTCAGCACAGTGG 60.666 63.158 1.84 0.00 0.00 4.00
743 762 2.093921 GGTCTAGTCTTGGACTCTTGGC 60.094 54.545 3.32 0.00 42.40 4.52
763 795 0.517316 GAGGCGGCACACTACTTTTG 59.483 55.000 13.08 0.00 0.00 2.44
843 875 2.433145 TGCGCTCCTTGCTTCGAG 60.433 61.111 9.73 0.00 40.11 4.04
877 914 0.902516 GCCTCACCTCACCTCACTCT 60.903 60.000 0.00 0.00 0.00 3.24
891 928 1.203112 TCACTCTCTCACCAAGCTCCT 60.203 52.381 0.00 0.00 0.00 3.69
893 930 0.823460 CTCTCTCACCAAGCTCCTCC 59.177 60.000 0.00 0.00 0.00 4.30
894 931 0.616111 TCTCTCACCAAGCTCCTCCC 60.616 60.000 0.00 0.00 0.00 4.30
895 932 1.613630 TCTCACCAAGCTCCTCCCC 60.614 63.158 0.00 0.00 0.00 4.81
896 933 2.610859 TCACCAAGCTCCTCCCCC 60.611 66.667 0.00 0.00 0.00 5.40
999 1036 1.301244 CAGCCATCGATCGGAAGGG 60.301 63.158 16.41 9.28 34.02 3.95
1089 1157 1.542492 CAACAGCTGCCAGGAAGATT 58.458 50.000 15.27 0.00 0.00 2.40
1092 1160 1.307097 CAGCTGCCAGGAAGATTAGC 58.693 55.000 0.00 0.00 0.00 3.09
1093 1161 0.182299 AGCTGCCAGGAAGATTAGCC 59.818 55.000 0.00 0.00 31.82 3.93
1132 1212 4.101448 GTCTGGGGGCGTGCAGAT 62.101 66.667 0.00 0.00 0.00 2.90
1349 1429 0.972983 AGGAGGAGGACCACATCGTG 60.973 60.000 0.00 0.00 38.94 4.35
1367 1447 2.134287 GGCGCTCCACCAGATCCTA 61.134 63.158 7.64 0.00 0.00 2.94
1420 1521 8.259411 TGCATCCAGTTCTTATTAATTTTGCAT 58.741 29.630 0.00 0.00 0.00 3.96
1421 1539 8.758715 GCATCCAGTTCTTATTAATTTTGCATC 58.241 33.333 0.00 0.00 0.00 3.91
1430 1556 0.887933 AATTTTGCATCGCGGAGGTT 59.112 45.000 6.13 0.00 0.00 3.50
1435 1561 1.353103 GCATCGCGGAGGTTGATTG 59.647 57.895 6.13 0.00 0.00 2.67
1466 1592 3.769300 AGAAAGATTTGGGGCAACATACC 59.231 43.478 0.00 0.00 39.74 2.73
1581 1735 0.376502 GCATCAAGAAGAAGCTCCGC 59.623 55.000 0.00 0.00 37.93 5.54
1582 1736 1.730501 CATCAAGAAGAAGCTCCGCA 58.269 50.000 0.00 0.00 0.00 5.69
1833 1998 2.250939 CCAGTTCGGCGACTGCAAA 61.251 57.895 24.40 3.60 44.45 3.68
1951 2122 1.003718 AGCAACTGGAACTACGGCC 60.004 57.895 0.00 0.00 0.00 6.13
2044 2257 3.777925 CGCCGGAGCACAAGTTCG 61.778 66.667 5.05 0.00 39.83 3.95
2163 2384 1.747444 TTCCCTGCTTTTCTCCCTCT 58.253 50.000 0.00 0.00 0.00 3.69
2217 2440 6.152661 CAGGTAATTTCTAGCACCAATTCCAA 59.847 38.462 0.00 0.00 33.27 3.53
2261 2528 3.561143 ACTACAAAACAAGGATGGTGCA 58.439 40.909 0.00 0.00 0.00 4.57
2282 2549 0.037419 GTTGCGGCACCATCCATTTT 60.037 50.000 0.05 0.00 0.00 1.82
2286 2553 0.175531 CGGCACCATCCATTTTTCCC 59.824 55.000 0.00 0.00 0.00 3.97
2291 2558 2.899256 CACCATCCATTTTTCCCACTGT 59.101 45.455 0.00 0.00 0.00 3.55
2299 2566 6.895782 TCCATTTTTCCCACTGTACTATAGG 58.104 40.000 4.43 0.00 0.00 2.57
2416 4906 6.767524 TGGCAATGAATAAATTAGGACGTT 57.232 33.333 0.00 0.00 0.00 3.99
2432 4922 1.067212 ACGTTGATAGGTGGAGATCGC 59.933 52.381 0.00 0.00 0.00 4.58
2449 4939 3.710722 CCAGCTTCGGCCAGGAGT 61.711 66.667 2.24 0.00 43.01 3.85
2454 4948 1.078848 CTTCGGCCAGGAGTCCAAG 60.079 63.158 12.86 2.72 0.00 3.61
2480 4974 0.109532 TTGGTTCGTCCCAGCATGAA 59.890 50.000 0.00 0.00 39.69 2.57
2484 4978 0.249120 TTCGTCCCAGCATGAACGAT 59.751 50.000 0.00 0.00 42.94 3.73
2485 4979 0.179111 TCGTCCCAGCATGAACGATC 60.179 55.000 0.00 0.00 39.69 3.69
2486 4980 1.482621 CGTCCCAGCATGAACGATCG 61.483 60.000 14.88 14.88 39.69 3.69
2487 4981 0.179111 GTCCCAGCATGAACGATCGA 60.179 55.000 24.34 0.00 39.69 3.59
2488 4982 0.103026 TCCCAGCATGAACGATCGAG 59.897 55.000 24.34 6.99 39.69 4.04
2489 4983 1.493950 CCCAGCATGAACGATCGAGC 61.494 60.000 24.34 16.16 39.69 5.03
2490 4984 0.807275 CCAGCATGAACGATCGAGCA 60.807 55.000 24.34 18.64 39.69 4.26
2491 4985 1.001624 CAGCATGAACGATCGAGCAA 58.998 50.000 24.34 4.52 39.69 3.91
2546 5049 3.827524 AAAAACGCGCGATGCAAG 58.172 50.000 39.36 5.57 46.97 4.01
2547 5050 1.729131 AAAAACGCGCGATGCAAGG 60.729 52.632 39.36 4.66 46.97 3.61
2569 5280 2.749800 GCTGGCCGAGAAAAATAGGGAT 60.750 50.000 0.00 0.00 0.00 3.85
2686 5411 6.625532 AAAAATTGCCAGGGTCTGATATTT 57.374 33.333 0.00 0.00 32.44 1.40
2687 5412 6.625532 AAAATTGCCAGGGTCTGATATTTT 57.374 33.333 0.00 0.00 32.44 1.82
2722 5448 2.009051 TCATTTCTGTACAGCATGGCG 58.991 47.619 23.97 10.86 43.62 5.69
2739 5465 7.964011 CAGCATGGCGAATTTTGAAATTATTTT 59.036 29.630 1.93 0.00 38.64 1.82
2778 5504 9.758651 AGTAGATTTACCAAAACAATGTTTTCC 57.241 29.630 19.89 5.32 0.00 3.13
2779 5505 9.535878 GTAGATTTACCAAAACAATGTTTTCCA 57.464 29.630 19.89 6.66 0.00 3.53
2787 5513 9.571816 ACCAAAACAATGTTTTCCATAAATGAT 57.428 25.926 19.89 0.00 31.97 2.45
2832 5558 9.698309 TTTGCCATAATATTCAAAGAAAAACGA 57.302 25.926 0.00 0.00 0.00 3.85
2888 5623 5.220643 CCTCAAACAACCAACAAGAAAATGC 60.221 40.000 0.00 0.00 0.00 3.56
2893 5628 3.405823 ACCAACAAGAAAATGCCATGG 57.594 42.857 7.63 7.63 0.00 3.66
2929 5664 7.440523 AAAAACACCTACAACAAATTGCAAA 57.559 28.000 1.71 0.00 39.66 3.68
2935 5670 4.445385 CCTACAACAAATTGCAAAGCTCAC 59.555 41.667 1.71 0.00 39.66 3.51
2977 5714 7.226720 AGGTGGCGAAATATGACATAGTAAAAG 59.773 37.037 0.98 0.00 0.00 2.27
3023 5766 4.021192 CCATTGCCAAAGTCACCTACAAAT 60.021 41.667 0.00 0.00 0.00 2.32
3025 5768 5.957842 TTGCCAAAGTCACCTACAAATAG 57.042 39.130 0.00 0.00 0.00 1.73
3079 5835 2.747396 AAACGCATGACATTGCCATT 57.253 40.000 0.00 0.00 39.52 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.228906 TGTCACTATTTGTACCCGATTGAAAAA 59.771 33.333 0.00 0.00 0.00 1.94
28 29 6.711194 TGTCACTATTTGTACCCGATTGAAAA 59.289 34.615 0.00 0.00 0.00 2.29
29 30 6.231951 TGTCACTATTTGTACCCGATTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
30 31 5.795972 TGTCACTATTTGTACCCGATTGAA 58.204 37.500 0.00 0.00 0.00 2.69
46 47 9.349713 ACCAATTTCAATTTAGAGTTGTCACTA 57.650 29.630 0.00 0.00 31.22 2.74
68 69 3.561120 CTTGGGGTGCGCCTACCAA 62.561 63.158 21.39 21.39 42.69 3.67
76 79 4.619227 ACGGTGTCTTGGGGTGCG 62.619 66.667 0.00 0.00 0.00 5.34
100 103 3.680786 GTTTGCTTCGTGGGGGCC 61.681 66.667 0.00 0.00 0.00 5.80
176 179 2.166664 AGAACGATCAGTGAACCTAGCC 59.833 50.000 0.00 0.00 0.00 3.93
177 180 3.440228 GAGAACGATCAGTGAACCTAGC 58.560 50.000 0.00 0.00 0.00 3.42
178 181 3.181485 GGGAGAACGATCAGTGAACCTAG 60.181 52.174 0.00 0.00 0.00 3.02
179 182 2.758979 GGGAGAACGATCAGTGAACCTA 59.241 50.000 0.00 0.00 0.00 3.08
275 282 3.250762 GTGCAGTGCAAACTAATCACTCA 59.749 43.478 21.67 0.00 41.47 3.41
306 313 0.108945 TGCAGACAGACATGAGCTCG 60.109 55.000 9.64 0.00 0.00 5.03
317 324 2.246841 TGCGTCCAAATGCAGACAG 58.753 52.632 4.88 0.00 42.47 3.51
359 366 1.132881 ACTTTCAATCAGGGGGCCAAA 60.133 47.619 4.39 0.00 0.00 3.28
410 429 4.188462 AGTCAAGTCACAAATCACGTCAA 58.812 39.130 0.00 0.00 0.00 3.18
411 430 3.792401 AGTCAAGTCACAAATCACGTCA 58.208 40.909 0.00 0.00 0.00 4.35
428 447 4.040339 TCAGCTCACTAATTGGTCAAGTCA 59.960 41.667 0.00 0.00 0.00 3.41
436 455 3.076621 TGTTGCTCAGCTCACTAATTGG 58.923 45.455 0.00 0.00 0.00 3.16
638 657 1.449601 CGCTTTCGGCACCCATAGT 60.450 57.895 0.00 0.00 41.91 2.12
649 668 2.143925 AGAAAAGAAGGTCCGCTTTCG 58.856 47.619 11.61 0.00 36.05 3.46
659 678 1.298859 CCCCGCACGAGAAAAGAAGG 61.299 60.000 0.00 0.00 0.00 3.46
678 697 2.700773 GGTTGGCGACATGGGCTTC 61.701 63.158 7.28 2.82 42.32 3.86
715 734 3.053842 AGTCCAAGACTAGACCGATACCA 60.054 47.826 0.00 0.00 41.51 3.25
716 735 3.553904 AGTCCAAGACTAGACCGATACC 58.446 50.000 0.00 0.00 41.51 2.73
717 736 4.453751 AGAGTCCAAGACTAGACCGATAC 58.546 47.826 0.00 0.00 43.53 2.24
743 762 0.949105 AAAAGTAGTGTGCCGCCTCG 60.949 55.000 0.00 0.00 0.00 4.63
750 769 1.263217 CGTGGGACAAAAGTAGTGTGC 59.737 52.381 0.00 0.00 44.16 4.57
751 770 1.871039 CCGTGGGACAAAAGTAGTGTG 59.129 52.381 0.00 0.00 44.16 3.82
753 772 0.872388 GCCGTGGGACAAAAGTAGTG 59.128 55.000 0.00 0.00 44.16 2.74
754 773 0.601841 CGCCGTGGGACAAAAGTAGT 60.602 55.000 0.00 0.00 44.16 2.73
755 774 0.601841 ACGCCGTGGGACAAAAGTAG 60.602 55.000 0.00 0.00 44.16 2.57
756 775 0.881159 CACGCCGTGGGACAAAAGTA 60.881 55.000 9.90 0.00 44.16 2.24
757 776 2.184167 CACGCCGTGGGACAAAAGT 61.184 57.895 9.90 0.00 44.16 2.66
843 875 3.198489 GGCAGCGCTCAAGTAGGC 61.198 66.667 7.13 5.91 0.00 3.93
877 914 1.613630 GGGGAGGAGCTTGGTGAGA 60.614 63.158 0.00 0.00 0.00 3.27
893 930 2.197324 CGAGAGGGAGAGAGGGGG 59.803 72.222 0.00 0.00 0.00 5.40
894 931 2.520741 GCGAGAGGGAGAGAGGGG 60.521 72.222 0.00 0.00 0.00 4.79
895 932 2.520741 GGCGAGAGGGAGAGAGGG 60.521 72.222 0.00 0.00 0.00 4.30
896 933 2.520741 GGGCGAGAGGGAGAGAGG 60.521 72.222 0.00 0.00 0.00 3.69
1081 1149 1.327690 TGACGCCGGCTAATCTTCCT 61.328 55.000 26.68 0.00 0.00 3.36
1089 1157 3.078196 TCCCATTGACGCCGGCTA 61.078 61.111 26.68 7.95 0.00 3.93
1349 1429 2.093537 CTAGGATCTGGTGGAGCGCC 62.094 65.000 2.29 0.00 34.12 6.53
1367 1447 2.743718 CGGACAGACCTGTTGCCT 59.256 61.111 3.98 0.00 45.05 4.75
1399 1490 6.075415 CGCGATGCAAAATTAATAAGAACTGG 60.075 38.462 0.00 0.00 0.00 4.00
1420 1521 1.218047 CTCCAATCAACCTCCGCGA 59.782 57.895 8.23 0.00 0.00 5.87
1421 1539 2.464459 GCTCCAATCAACCTCCGCG 61.464 63.158 0.00 0.00 0.00 6.46
1430 1556 4.767578 ATCTTTCTGCTAGCTCCAATCA 57.232 40.909 17.23 0.00 0.00 2.57
1435 1561 2.948315 CCCAAATCTTTCTGCTAGCTCC 59.052 50.000 17.23 0.00 0.00 4.70
1466 1592 3.721791 CGCACACACACATCAGTAATTCG 60.722 47.826 0.00 0.00 0.00 3.34
1581 1735 2.409870 GGGGTCGATGCCTTGCTTG 61.410 63.158 0.00 0.00 0.00 4.01
1582 1736 2.044946 GGGGTCGATGCCTTGCTT 60.045 61.111 0.00 0.00 0.00 3.91
1627 1789 4.856801 GGTGGCCGCCGTGATCAT 62.857 66.667 22.03 0.00 0.00 2.45
1670 1835 1.302993 GCAAGGGGCTTACGGTCAA 60.303 57.895 0.00 0.00 40.25 3.18
1671 1836 2.349755 GCAAGGGGCTTACGGTCA 59.650 61.111 0.00 0.00 40.25 4.02
1722 1887 2.267961 GGGTCAAACTCCGGCGAT 59.732 61.111 9.30 0.00 0.00 4.58
1843 2008 3.041940 GAACCCTGTGTCGCCGTG 61.042 66.667 0.00 0.00 0.00 4.94
2030 2243 4.430423 GCGCGAACTTGTGCTCCG 62.430 66.667 12.10 0.00 42.01 4.63
2233 2456 8.883731 CACCATCCTTGTTTTGTAGTATCTTAG 58.116 37.037 0.00 0.00 0.00 2.18
2234 2457 7.335924 GCACCATCCTTGTTTTGTAGTATCTTA 59.664 37.037 0.00 0.00 0.00 2.10
2235 2458 6.151144 GCACCATCCTTGTTTTGTAGTATCTT 59.849 38.462 0.00 0.00 0.00 2.40
2236 2459 5.648092 GCACCATCCTTGTTTTGTAGTATCT 59.352 40.000 0.00 0.00 0.00 1.98
2237 2460 5.414454 TGCACCATCCTTGTTTTGTAGTATC 59.586 40.000 0.00 0.00 0.00 2.24
2239 2462 4.517453 GTGCACCATCCTTGTTTTGTAGTA 59.483 41.667 5.22 0.00 0.00 1.82
2240 2463 3.317993 GTGCACCATCCTTGTTTTGTAGT 59.682 43.478 5.22 0.00 0.00 2.73
2241 2464 3.609175 CGTGCACCATCCTTGTTTTGTAG 60.609 47.826 12.15 0.00 0.00 2.74
2246 2513 1.066908 CAACGTGCACCATCCTTGTTT 59.933 47.619 12.15 0.00 0.00 2.83
2261 2528 3.918253 ATGGATGGTGCCGCAACGT 62.918 57.895 1.77 1.77 0.00 3.99
2272 2539 4.344104 AGTACAGTGGGAAAAATGGATGG 58.656 43.478 0.00 0.00 0.00 3.51
2282 2549 7.504926 ACAAATTCCTATAGTACAGTGGGAA 57.495 36.000 14.63 14.63 37.28 3.97
2319 2586 5.195001 TGGTTAGTCTTGCAATTTCAACC 57.805 39.130 18.89 18.89 35.76 3.77
2357 2687 7.713507 TCCAAATATTACCAAATACTCACTCCG 59.286 37.037 0.00 0.00 30.42 4.63
2389 2719 8.257306 ACGTCCTAATTTATTCATTGCCAATTT 58.743 29.630 0.00 0.00 0.00 1.82
2416 4906 1.332195 CTGGCGATCTCCACCTATCA 58.668 55.000 0.00 0.00 31.74 2.15
2432 4922 3.672295 GACTCCTGGCCGAAGCTGG 62.672 68.421 0.00 0.00 39.73 4.85
2438 4928 3.706373 GCTTGGACTCCTGGCCGA 61.706 66.667 0.00 0.00 0.00 5.54
2442 4932 0.036010 ATCGTTGCTTGGACTCCTGG 60.036 55.000 0.00 0.00 0.00 4.45
2443 4933 1.466167 CAATCGTTGCTTGGACTCCTG 59.534 52.381 0.00 0.00 0.00 3.86
2449 4939 0.871722 CGAACCAATCGTTGCTTGGA 59.128 50.000 8.55 0.00 44.95 3.53
2473 4967 1.394917 GTTTGCTCGATCGTTCATGCT 59.605 47.619 15.94 0.00 0.00 3.79
2506 5000 2.203070 GGATGGTACCCGCTGCAG 60.203 66.667 10.11 10.11 0.00 4.41
2546 5049 1.025041 CTATTTTTCTCGGCCAGCCC 58.975 55.000 2.24 0.00 0.00 5.19
2547 5050 1.025041 CCTATTTTTCTCGGCCAGCC 58.975 55.000 2.24 0.00 0.00 4.85
2555 5058 2.544267 CCACGCGATCCCTATTTTTCTC 59.456 50.000 15.93 0.00 0.00 2.87
2686 5411 6.827762 ACAGAAATGATTTTCCTTGGCAAAAA 59.172 30.769 0.00 0.00 41.86 1.94
2687 5412 6.355747 ACAGAAATGATTTTCCTTGGCAAAA 58.644 32.000 0.00 0.00 41.86 2.44
2806 5532 9.698309 TCGTTTTTCTTTGAATATTATGGCAAA 57.302 25.926 0.00 0.00 0.00 3.68
2807 5533 9.868277 ATCGTTTTTCTTTGAATATTATGGCAA 57.132 25.926 0.00 0.00 0.00 4.52
2808 5534 9.299963 CATCGTTTTTCTTTGAATATTATGGCA 57.700 29.630 0.00 0.00 0.00 4.92
2809 5535 9.515020 TCATCGTTTTTCTTTGAATATTATGGC 57.485 29.630 0.00 0.00 0.00 4.40
2846 5581 9.566432 TGTTTGAGGTTTATTATGGCAATTTTT 57.434 25.926 0.00 0.00 0.00 1.94
2850 5585 7.102993 GGTTGTTTGAGGTTTATTATGGCAAT 58.897 34.615 0.00 0.00 0.00 3.56
2853 5588 6.031751 TGGTTGTTTGAGGTTTATTATGGC 57.968 37.500 0.00 0.00 0.00 4.40
3064 5820 3.119388 AGTGTACAATGGCAATGTCATGC 60.119 43.478 12.21 2.41 45.67 4.06
3065 5821 4.707030 AGTGTACAATGGCAATGTCATG 57.293 40.909 12.21 0.00 32.27 3.07
3070 5826 7.887996 ATGTTTTAAGTGTACAATGGCAATG 57.112 32.000 0.00 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.