Multiple sequence alignment - TraesCS6A01G018000

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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 TraesCS6A01G018000 chr6A 100.000 3521 0 0 1 3521 8793808 8790288 0.000000e+00 6503.0
1 TraesCS6A01G018000 chr6A 90.909 2442 171 32 1103 3521 8869041 8866628 0.000000e+00 3232.0
2 TraesCS6A01G018000 chr6A 86.090 1560 200 11 949 2507 8755162 8753619 0.000000e+00 1663.0
3 TraesCS6A01G018000 chr6A 80.263 684 132 3 10 692 219629378 219630059 2.420000e-141 512.0
4 TraesCS6A01G018000 chr6A 87.500 176 18 4 976 1150 8968492 8968320 2.140000e-47 200.0
5 TraesCS6A01G018000 chr6D 91.128 2536 167 21 203 2691 8387483 8384959 0.000000e+00 3384.0
6 TraesCS6A01G018000 chr6D 88.284 1801 141 33 949 2688 8349076 8347285 0.000000e+00 2093.0
7 TraesCS6A01G018000 chr6D 85.650 1561 205 12 949 2507 8316745 8315202 0.000000e+00 1624.0
8 TraesCS6A01G018000 chr6D 83.936 498 75 4 1105 1598 420569130 420568634 4.110000e-129 472.0
9 TraesCS6A01G018000 chr6D 82.073 357 55 8 3163 3515 321985923 321986274 2.660000e-76 296.0
10 TraesCS6A01G018000 chr6B 89.225 1652 119 18 864 2512 16240706 16242301 0.000000e+00 2010.0
11 TraesCS6A01G018000 chr6B 86.341 1003 136 1 1506 2507 16246893 16247895 0.000000e+00 1092.0
12 TraesCS6A01G018000 chr6B 90.490 694 60 6 22 714 16239942 16240630 0.000000e+00 911.0
13 TraesCS6A01G018000 chr6B 84.568 486 70 4 1105 1586 633730705 633731189 8.840000e-131 477.0
14 TraesCS6A01G018000 chr4D 88.750 1440 135 15 1075 2499 477911940 477913367 0.000000e+00 1736.0
15 TraesCS6A01G018000 chr4D 80.548 694 128 7 10 701 319281187 319281875 8.660000e-146 527.0
16 TraesCS6A01G018000 chr4B 87.898 1446 151 10 1075 2505 604139303 604140739 0.000000e+00 1679.0
17 TraesCS6A01G018000 chr1B 87.986 849 73 14 1 832 630681461 630682297 0.000000e+00 976.0
18 TraesCS6A01G018000 chr1B 84.034 357 51 4 3161 3513 268101775 268101421 4.350000e-89 339.0
19 TraesCS6A01G018000 chr1B 97.260 73 2 0 894 966 630682307 630682379 1.330000e-24 124.0
20 TraesCS6A01G018000 chr5A 87.032 802 97 5 1707 2506 680709641 680710437 0.000000e+00 898.0
21 TraesCS6A01G018000 chr5A 87.639 631 75 1 1075 1705 680708645 680709272 0.000000e+00 730.0
22 TraesCS6A01G018000 chr4A 86.194 775 86 8 1383 2145 684610552 684611317 0.000000e+00 819.0
23 TraesCS6A01G018000 chr4A 80.435 138 17 8 2993 3125 727717108 727717240 2.890000e-16 97.1
24 TraesCS6A01G018000 chr7B 80.406 689 129 6 10 695 113567824 113567139 1.450000e-143 520.0
25 TraesCS6A01G018000 chr7B 76.582 158 23 12 2971 3121 737179436 737179586 1.360000e-09 75.0
26 TraesCS6A01G018000 chr7B 75.484 155 31 7 2971 3122 737480276 737480426 6.310000e-08 69.4
27 TraesCS6A01G018000 chr3A 80.261 689 130 6 10 695 738105406 738106091 6.740000e-142 514.0
28 TraesCS6A01G018000 chr3A 85.083 362 48 4 3165 3521 716944599 716944239 7.180000e-97 364.0
29 TraesCS6A01G018000 chr3A 80.833 360 62 5 3163 3518 745372895 745373251 3.460000e-70 276.0
30 TraesCS6A01G018000 chr2A 79.797 688 134 5 10 695 349738552 349739236 2.440000e-136 496.0
31 TraesCS6A01G018000 chr7A 79.710 690 132 8 10 695 712840047 712839362 3.160000e-135 492.0
32 TraesCS6A01G018000 chr2D 83.784 370 51 6 3160 3521 558377161 558377529 3.370000e-90 342.0
33 TraesCS6A01G018000 chr2B 81.843 369 60 3 3160 3521 679303890 679303522 1.590000e-78 303.0
34 TraesCS6A01G018000 chr3B 81.686 344 50 8 3180 3519 728587091 728586757 1.250000e-69 274.0
35 TraesCS6A01G018000 chr3B 81.197 117 17 5 3007 3122 761042956 761043068 4.840000e-14 89.8
36 TraesCS6A01G018000 chr3D 81.765 340 48 9 3163 3498 549075177 549074848 4.480000e-69 272.0
37 TraesCS6A01G018000 chrUn 80.180 111 17 5 3013 3122 47461986 47462092 1.050000e-10 78.7


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 TraesCS6A01G018000 chr6A 8790288 8793808 3520 True 6503.0 6503 100.0000 1 3521 1 chr6A.!!$R2 3520
1 TraesCS6A01G018000 chr6A 8866628 8869041 2413 True 3232.0 3232 90.9090 1103 3521 1 chr6A.!!$R3 2418
2 TraesCS6A01G018000 chr6A 8753619 8755162 1543 True 1663.0 1663 86.0900 949 2507 1 chr6A.!!$R1 1558
3 TraesCS6A01G018000 chr6A 219629378 219630059 681 False 512.0 512 80.2630 10 692 1 chr6A.!!$F1 682
4 TraesCS6A01G018000 chr6D 8384959 8387483 2524 True 3384.0 3384 91.1280 203 2691 1 chr6D.!!$R3 2488
5 TraesCS6A01G018000 chr6D 8347285 8349076 1791 True 2093.0 2093 88.2840 949 2688 1 chr6D.!!$R2 1739
6 TraesCS6A01G018000 chr6D 8315202 8316745 1543 True 1624.0 1624 85.6500 949 2507 1 chr6D.!!$R1 1558
7 TraesCS6A01G018000 chr6B 16239942 16242301 2359 False 1460.5 2010 89.8575 22 2512 2 chr6B.!!$F3 2490
8 TraesCS6A01G018000 chr6B 16246893 16247895 1002 False 1092.0 1092 86.3410 1506 2507 1 chr6B.!!$F1 1001
9 TraesCS6A01G018000 chr4D 477911940 477913367 1427 False 1736.0 1736 88.7500 1075 2499 1 chr4D.!!$F2 1424
10 TraesCS6A01G018000 chr4D 319281187 319281875 688 False 527.0 527 80.5480 10 701 1 chr4D.!!$F1 691
11 TraesCS6A01G018000 chr4B 604139303 604140739 1436 False 1679.0 1679 87.8980 1075 2505 1 chr4B.!!$F1 1430
12 TraesCS6A01G018000 chr1B 630681461 630682379 918 False 550.0 976 92.6230 1 966 2 chr1B.!!$F1 965
13 TraesCS6A01G018000 chr5A 680708645 680710437 1792 False 814.0 898 87.3355 1075 2506 2 chr5A.!!$F1 1431
14 TraesCS6A01G018000 chr4A 684610552 684611317 765 False 819.0 819 86.1940 1383 2145 1 chr4A.!!$F1 762
15 TraesCS6A01G018000 chr7B 113567139 113567824 685 True 520.0 520 80.4060 10 695 1 chr7B.!!$R1 685
16 TraesCS6A01G018000 chr3A 738105406 738106091 685 False 514.0 514 80.2610 10 695 1 chr3A.!!$F1 685
17 TraesCS6A01G018000 chr2A 349738552 349739236 684 False 496.0 496 79.7970 10 695 1 chr2A.!!$F1 685
18 TraesCS6A01G018000 chr7A 712839362 712840047 685 True 492.0 492 79.7100 10 695 1 chr7A.!!$R1 685

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
640 644 0.249447 CAGCTGAGGTTCACACGTCA 60.249 55.0 8.42 0.0 43.87 4.35 F
645 649 0.309922 GAGGTTCACACGTCAGTCGA 59.690 55.0 0.00 0.0 42.86 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2523 0.17576 GGAGCTGCTCGTTGGTCATA 59.824 55.0 22.25 0.0 32.93 2.15 R
2566 3134 0.40404 ATTCTCAAAACCGGCCTCCA 59.596 50.0 0.00 0.0 0.00 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.992519 GCCCTCAGATCAGCACCCAT 61.993 60.000 0.00 0.00 0.00 4.00
145 149 3.741476 GGCTGCTGCTTGAACCCG 61.741 66.667 15.64 0.00 39.59 5.28
150 154 2.383527 GCTGCTTGAACCCGACGAG 61.384 63.158 0.00 0.00 0.00 4.18
151 155 1.738099 CTGCTTGAACCCGACGAGG 60.738 63.158 0.00 0.00 40.63 4.63
252 256 1.001974 CCCCTGACGAGAACAACATGA 59.998 52.381 0.00 0.00 0.00 3.07
284 288 1.207329 GAACCAATCCTAGTGACCGCT 59.793 52.381 0.00 0.00 0.00 5.52
291 295 1.004394 TCCTAGTGACCGCTCTCAGAA 59.996 52.381 0.00 0.00 0.00 3.02
325 329 5.308237 GGAACATAATCTCCCACTGGATAGT 59.692 44.000 0.00 0.00 40.80 2.12
358 362 0.535335 TCCAACACACTCCGGATAGC 59.465 55.000 3.57 0.00 0.00 2.97
372 376 2.547826 GGATAGCGTCCACCTGTTTAC 58.452 52.381 6.34 0.00 46.96 2.01
393 397 0.912486 GGTCCATGTGAACCTAGCCT 59.088 55.000 0.00 0.00 0.00 4.58
445 449 3.065233 TCCGCTATGCAATCATTGAACAC 59.935 43.478 0.00 0.00 34.22 3.32
446 450 3.181498 CCGCTATGCAATCATTGAACACA 60.181 43.478 0.00 0.00 34.22 3.72
531 535 4.111016 CAGCGACTACGACCGGCA 62.111 66.667 0.00 0.00 42.66 5.69
562 566 4.504826 GCGTTCTACCTTATCTTTCAGCTC 59.495 45.833 0.00 0.00 0.00 4.09
579 583 4.697756 CGGCCAAGAAGTCCGCCA 62.698 66.667 2.24 0.00 41.71 5.69
592 596 3.055719 CGCCAACCGCCAGTGAAT 61.056 61.111 0.00 0.00 0.00 2.57
640 644 0.249447 CAGCTGAGGTTCACACGTCA 60.249 55.000 8.42 0.00 43.87 4.35
645 649 0.309922 GAGGTTCACACGTCAGTCGA 59.690 55.000 0.00 0.00 42.86 4.20
671 675 9.927081 ATAATGGACATACTGAGGAAAAATTCT 57.073 29.630 0.00 0.00 0.00 2.40
695 699 1.420430 GGTCCATATCCTCCACCGAA 58.580 55.000 0.00 0.00 0.00 4.30
709 713 4.597004 TCCACCGAAATAGAGTAGTGTCT 58.403 43.478 0.00 0.00 0.00 3.41
804 827 5.587388 CATGTCCATGTGGAGCTTAATTT 57.413 39.130 1.07 0.00 46.49 1.82
923 946 2.031157 CCACGACACCAATTCAAAGACC 60.031 50.000 0.00 0.00 0.00 3.85
925 948 4.062293 CACGACACCAATTCAAAGACCTA 58.938 43.478 0.00 0.00 0.00 3.08
940 963 4.473477 AGACCTAGTCAGTATGTTTGCC 57.527 45.455 0.00 0.00 37.40 4.52
941 964 3.197983 AGACCTAGTCAGTATGTTTGCCC 59.802 47.826 0.00 0.00 37.40 5.36
942 965 2.910319 ACCTAGTCAGTATGTTTGCCCA 59.090 45.455 0.00 0.00 37.40 5.36
943 966 3.523564 ACCTAGTCAGTATGTTTGCCCAT 59.476 43.478 0.00 0.00 37.40 4.00
944 967 4.130118 CCTAGTCAGTATGTTTGCCCATC 58.870 47.826 0.00 0.00 37.40 3.51
945 968 2.632377 AGTCAGTATGTTTGCCCATCG 58.368 47.619 0.00 0.00 37.40 3.84
946 969 1.064060 GTCAGTATGTTTGCCCATCGC 59.936 52.381 0.00 0.00 37.40 4.58
947 970 0.381801 CAGTATGTTTGCCCATCGCC 59.618 55.000 0.00 0.00 36.24 5.54
973 1023 9.905713 CTGCCACCTATAAATAATGTATGGTAT 57.094 33.333 0.00 0.00 0.00 2.73
1028 1085 2.094417 CGCATAGCATCATCATCAGCAG 59.906 50.000 0.00 0.00 0.00 4.24
1302 1385 2.745884 CGCTTCGCCACCATTCCA 60.746 61.111 0.00 0.00 0.00 3.53
1425 1517 1.001641 GCTCAATGACCCAGCCACT 60.002 57.895 0.00 0.00 0.00 4.00
1563 1661 4.446413 GGTGTCCGCCACTACCGG 62.446 72.222 0.00 0.00 46.88 5.28
1600 1699 0.389817 CCTCGCACCGATCAAAGACA 60.390 55.000 0.00 0.00 34.61 3.41
2004 2541 1.661112 GTTATGACCAACGAGCAGCTC 59.339 52.381 12.94 12.94 0.00 4.09
2046 2583 2.660189 CCAAGAGCGGCAATCATTTT 57.340 45.000 1.45 0.00 0.00 1.82
2301 2839 2.031919 TGCCGGTACCAGTGCAAG 59.968 61.111 13.54 0.00 0.00 4.01
2436 2974 1.376037 GTGGAGGGAGAAAGCGGTG 60.376 63.158 0.00 0.00 0.00 4.94
2566 3134 4.903045 TCTGAATCCCTTCTTTTACGGT 57.097 40.909 0.00 0.00 32.29 4.83
2697 3269 0.251916 TGCAATTAGTAGTGCCCGCT 59.748 50.000 5.68 0.00 44.40 5.52
2710 3282 1.291132 GCCCGCTCACTTCATTACTC 58.709 55.000 0.00 0.00 0.00 2.59
2720 3292 4.162320 TCACTTCATTACTCCCCAGATGTC 59.838 45.833 0.00 0.00 0.00 3.06
2731 3303 2.366916 CCCCAGATGTCGATTCTAAGCT 59.633 50.000 0.00 0.00 0.00 3.74
2733 3305 3.388308 CCAGATGTCGATTCTAAGCTGG 58.612 50.000 0.00 0.00 36.14 4.85
2737 3309 3.795623 TGTCGATTCTAAGCTGGTACC 57.204 47.619 4.43 4.43 0.00 3.34
2738 3310 3.362706 TGTCGATTCTAAGCTGGTACCT 58.637 45.455 14.36 0.00 0.00 3.08
2739 3311 3.380637 TGTCGATTCTAAGCTGGTACCTC 59.619 47.826 14.36 5.02 0.00 3.85
2740 3312 2.617308 TCGATTCTAAGCTGGTACCTCG 59.383 50.000 14.36 10.56 0.00 4.63
2741 3313 2.745102 GATTCTAAGCTGGTACCTCGC 58.255 52.381 14.36 15.37 0.00 5.03
2742 3314 1.552578 TTCTAAGCTGGTACCTCGCA 58.447 50.000 22.85 7.70 0.00 5.10
2745 3317 1.204941 CTAAGCTGGTACCTCGCACTT 59.795 52.381 22.85 15.92 0.00 3.16
2775 3347 4.328667 GACGAAACGATTTGAATAACCCG 58.671 43.478 0.00 0.00 0.00 5.28
3089 3666 3.076621 GTTCCCTAACCCAGTAAAACCG 58.923 50.000 0.00 0.00 0.00 4.44
3091 3668 1.340308 CCCTAACCCAGTAAAACCGGG 60.340 57.143 6.32 0.00 46.22 5.73
3121 3698 3.335579 CTCTAGAAGGTTCCCAAAACCG 58.664 50.000 0.00 0.00 44.82 4.44
3136 3713 0.841289 AACCGGAACTTCCAAGGTCA 59.159 50.000 9.46 0.00 44.60 4.02
3146 3723 0.317160 TCCAAGGTCACGTACTGCAG 59.683 55.000 13.48 13.48 0.00 4.41
3148 3725 0.317160 CAAGGTCACGTACTGCAGGA 59.683 55.000 19.93 6.60 0.00 3.86
3156 3733 0.529337 CGTACTGCAGGAGATGGCTG 60.529 60.000 19.93 0.00 35.41 4.85
3157 3734 0.179062 GTACTGCAGGAGATGGCTGG 60.179 60.000 19.93 0.00 33.82 4.85
3158 3735 1.976132 TACTGCAGGAGATGGCTGGC 61.976 60.000 19.93 0.00 33.82 4.85
3159 3736 3.332385 TGCAGGAGATGGCTGGCA 61.332 61.111 6.31 6.31 0.00 4.92
3261 3917 0.926293 TGGATCTTTCATCCACCCCC 59.074 55.000 0.00 0.00 42.81 5.40
3280 3936 2.093128 CCCCACGCACCTTACTTCTAAT 60.093 50.000 0.00 0.00 0.00 1.73
3331 3987 1.487142 AGTCTCTCTAGGAGCACGCTA 59.513 52.381 0.00 0.00 41.60 4.26
3362 4018 0.874390 GCAGGAAATCACACGCAAGA 59.126 50.000 0.00 0.00 43.62 3.02
3411 4067 2.846039 TAGACCGAAAGAGCGACATC 57.154 50.000 0.00 0.00 0.00 3.06
3433 4089 9.499479 ACATCCATTCTTCATTGTCTATATCAC 57.501 33.333 0.00 0.00 0.00 3.06
3436 4092 8.370940 TCCATTCTTCATTGTCTATATCACCTC 58.629 37.037 0.00 0.00 0.00 3.85
3492 4151 5.006746 CCGACTATAGTTGCCAAATTGAGAC 59.993 44.000 13.95 0.00 0.00 3.36
3498 4157 3.706086 AGTTGCCAAATTGAGACCAAACT 59.294 39.130 0.00 0.00 35.67 2.66
3503 4162 5.304101 TGCCAAATTGAGACCAAACTGTAAT 59.696 36.000 0.00 0.00 35.67 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.474570 GCTGATCTGAGGGCCCGT 61.475 66.667 18.44 4.45 0.00 5.28
134 138 2.342279 CCTCGTCGGGTTCAAGCA 59.658 61.111 0.00 0.00 0.00 3.91
145 149 2.396590 TGAAATGGTAAGGCCTCGTC 57.603 50.000 5.23 0.00 38.35 4.20
150 154 3.056107 GGGTTCTTTGAAATGGTAAGGCC 60.056 47.826 0.00 0.00 37.90 5.19
151 155 3.056107 GGGGTTCTTTGAAATGGTAAGGC 60.056 47.826 0.00 0.00 0.00 4.35
252 256 3.545703 GGATTGGTTCCGATCATGTTCT 58.454 45.455 17.68 0.00 33.93 3.01
284 288 1.423584 TCCCACTGTGCTTTCTGAGA 58.576 50.000 1.29 0.00 0.00 3.27
291 295 4.265073 GAGATTATGTTCCCACTGTGCTT 58.735 43.478 1.29 0.00 0.00 3.91
336 340 1.275666 ATCCGGAGTGTGTTGGATCA 58.724 50.000 11.34 0.00 36.50 2.92
343 347 1.664321 GGACGCTATCCGGAGTGTGT 61.664 60.000 20.83 20.83 40.24 3.72
358 362 1.607251 GGACCAGTAAACAGGTGGACG 60.607 57.143 1.46 0.00 35.77 4.79
372 376 1.407437 GGCTAGGTTCACATGGACCAG 60.407 57.143 12.02 7.98 0.00 4.00
393 397 1.306148 CGTGAGATAGCCCGTGTAGA 58.694 55.000 0.00 0.00 0.00 2.59
531 535 4.585162 AGATAAGGTAGAACGCTGCACTAT 59.415 41.667 0.00 0.00 0.00 2.12
579 583 1.449601 CGGCTATTCACTGGCGGTT 60.450 57.895 0.00 0.00 46.17 4.44
586 590 0.687354 CTATGGCCCGGCTATTCACT 59.313 55.000 14.21 0.00 31.02 3.41
591 595 1.003580 CATTGTCTATGGCCCGGCTAT 59.996 52.381 13.46 13.46 33.54 2.97
592 596 0.396435 CATTGTCTATGGCCCGGCTA 59.604 55.000 9.86 2.83 0.00 3.93
640 644 5.386060 TCCTCAGTATGTCCATTATCGACT 58.614 41.667 0.00 0.00 37.40 4.18
645 649 9.927081 AGAATTTTTCCTCAGTATGTCCATTAT 57.073 29.630 0.00 0.00 37.40 1.28
671 675 0.857675 TGGAGGATATGGACCGAGGA 59.142 55.000 0.00 0.00 0.00 3.71
737 760 1.293924 CTCGCTCCAAATGCTAGGTG 58.706 55.000 0.00 0.00 0.00 4.00
804 827 3.323691 TCGAGGATGGAAACTTTCAGTGA 59.676 43.478 3.93 0.00 0.00 3.41
923 946 3.804325 CGATGGGCAAACATACTGACTAG 59.196 47.826 0.00 0.00 0.00 2.57
925 948 2.632377 CGATGGGCAAACATACTGACT 58.368 47.619 0.00 0.00 0.00 3.41
940 963 0.396435 TTATAGGTGGCAGGCGATGG 59.604 55.000 0.00 0.00 0.00 3.51
941 964 2.254546 TTTATAGGTGGCAGGCGATG 57.745 50.000 0.00 0.00 0.00 3.84
942 965 4.634012 TTATTTATAGGTGGCAGGCGAT 57.366 40.909 0.00 0.00 0.00 4.58
943 966 4.202419 ACATTATTTATAGGTGGCAGGCGA 60.202 41.667 0.00 0.00 0.00 5.54
944 967 4.072131 ACATTATTTATAGGTGGCAGGCG 58.928 43.478 0.00 0.00 0.00 5.52
945 968 6.095440 CCATACATTATTTATAGGTGGCAGGC 59.905 42.308 0.00 0.00 0.00 4.85
946 969 7.175104 ACCATACATTATTTATAGGTGGCAGG 58.825 38.462 0.00 0.00 0.00 4.85
947 970 9.905713 ATACCATACATTATTTATAGGTGGCAG 57.094 33.333 0.00 0.00 0.00 4.85
973 1023 2.106511 GGCTCTGCCCATCTTACCATTA 59.893 50.000 0.00 0.00 44.06 1.90
974 1024 1.133668 GGCTCTGCCCATCTTACCATT 60.134 52.381 0.00 0.00 44.06 3.16
975 1025 0.475906 GGCTCTGCCCATCTTACCAT 59.524 55.000 0.00 0.00 44.06 3.55
976 1026 1.915228 GGCTCTGCCCATCTTACCA 59.085 57.895 0.00 0.00 44.06 3.25
977 1027 4.887615 GGCTCTGCCCATCTTACC 57.112 61.111 0.00 0.00 44.06 2.85
1028 1085 1.646189 GCCAGTAGCTAGTGTCTTGC 58.354 55.000 23.78 16.92 38.99 4.01
1321 1404 1.733041 CCTGCGTGACATCGTCGTT 60.733 57.895 0.00 0.00 34.95 3.85
1563 1661 2.182030 CCACGGTCGAAGAGGAGC 59.818 66.667 0.00 0.00 36.95 4.70
1600 1699 3.418995 ACTCATTTGTCAGCTGCTTGAT 58.581 40.909 9.47 0.00 0.00 2.57
1923 2460 3.247056 TTTGCCGTCGAGCCATGGA 62.247 57.895 18.40 0.00 0.00 3.41
1941 2478 0.613292 ACATGACTGAGCCGACCTCT 60.613 55.000 0.00 0.00 41.35 3.69
1986 2523 0.175760 GGAGCTGCTCGTTGGTCATA 59.824 55.000 22.25 0.00 32.93 2.15
2004 2541 4.760047 CCCCACGCGAACTCCAGG 62.760 72.222 15.93 1.76 0.00 4.45
2040 2577 4.443457 GGACGGATGATCCAGAGAAAATGA 60.443 45.833 12.67 0.00 35.91 2.57
2046 2583 3.133437 GGGACGGATGATCCAGAGA 57.867 57.895 12.67 0.00 38.06 3.10
2301 2839 1.526917 CATGCCGACTCCCCATTCC 60.527 63.158 0.00 0.00 0.00 3.01
2367 2905 1.383664 CTCCCCCTCCATGAGCTCA 60.384 63.158 20.79 20.79 0.00 4.26
2499 3037 3.150335 CCAGAGCGGCTAGGAGCA 61.150 66.667 14.04 0.00 44.75 4.26
2545 3109 4.564821 CCACCGTAAAAGAAGGGATTCAGA 60.565 45.833 0.00 0.00 0.00 3.27
2547 3111 3.328343 TCCACCGTAAAAGAAGGGATTCA 59.672 43.478 0.00 0.00 0.00 2.57
2548 3112 3.939592 CTCCACCGTAAAAGAAGGGATTC 59.060 47.826 0.00 0.00 0.00 2.52
2555 3122 3.637184 GGCCTCCACCGTAAAAGAA 57.363 52.632 0.00 0.00 0.00 2.52
2566 3134 0.404040 ATTCTCAAAACCGGCCTCCA 59.596 50.000 0.00 0.00 0.00 3.86
2640 3208 9.757859 CAATTACATTTATTTTGGCACATTGTC 57.242 29.630 0.00 0.00 39.30 3.18
2645 3213 7.490725 CGGATCAATTACATTTATTTTGGCACA 59.509 33.333 0.00 0.00 0.00 4.57
2646 3214 7.491048 ACGGATCAATTACATTTATTTTGGCAC 59.509 33.333 0.00 0.00 0.00 5.01
2668 3240 4.214545 CACTACTAATTGCAAAACCACGGA 59.785 41.667 1.71 0.00 0.00 4.69
2697 3269 4.104086 ACATCTGGGGAGTAATGAAGTGA 58.896 43.478 0.00 0.00 0.00 3.41
2710 3282 2.366916 AGCTTAGAATCGACATCTGGGG 59.633 50.000 11.75 4.43 0.00 4.96
2720 3292 2.859032 GCGAGGTACCAGCTTAGAATCG 60.859 54.545 20.83 15.22 0.00 3.34
2731 3303 1.301401 GTGCAAGTGCGAGGTACCA 60.301 57.895 15.94 0.00 45.83 3.25
2733 3305 0.443869 CATGTGCAAGTGCGAGGTAC 59.556 55.000 0.00 0.00 45.83 3.34
2737 3309 1.499056 GTCCATGTGCAAGTGCGAG 59.501 57.895 0.00 0.00 45.83 5.03
2738 3310 2.316867 CGTCCATGTGCAAGTGCGA 61.317 57.895 0.00 0.00 45.83 5.10
2739 3311 1.840630 TTCGTCCATGTGCAAGTGCG 61.841 55.000 0.00 0.00 45.83 5.34
2740 3312 0.310543 TTTCGTCCATGTGCAAGTGC 59.689 50.000 0.00 0.00 42.50 4.40
2741 3313 1.660052 CGTTTCGTCCATGTGCAAGTG 60.660 52.381 0.00 0.00 0.00 3.16
2742 3314 0.586319 CGTTTCGTCCATGTGCAAGT 59.414 50.000 0.00 0.00 0.00 3.16
2745 3317 1.518325 AATCGTTTCGTCCATGTGCA 58.482 45.000 0.00 0.00 0.00 4.57
3041 3617 8.533569 TTTTAGAAGATTCCTGGACTGTTTTT 57.466 30.769 0.00 0.00 0.00 1.94
3046 3622 7.148171 GGAACATTTTAGAAGATTCCTGGACTG 60.148 40.741 0.00 0.00 33.22 3.51
3049 3625 6.011628 AGGGAACATTTTAGAAGATTCCTGGA 60.012 38.462 0.00 0.00 34.98 3.86
3050 3626 6.190587 AGGGAACATTTTAGAAGATTCCTGG 58.809 40.000 9.60 0.00 34.98 4.45
3051 3627 8.678199 GTTAGGGAACATTTTAGAAGATTCCTG 58.322 37.037 9.60 0.00 34.98 3.86
3064 3641 5.541101 GGTTTTACTGGGTTAGGGAACATTT 59.459 40.000 0.00 0.00 37.29 2.32
3121 3698 2.036862 AGTACGTGACCTTGGAAGTTCC 59.963 50.000 15.50 15.50 36.96 3.62
3136 3713 0.972983 AGCCATCTCCTGCAGTACGT 60.973 55.000 13.81 0.00 0.00 3.57
3146 3723 3.339253 AAAAATTTGCCAGCCATCTCC 57.661 42.857 0.00 0.00 0.00 3.71
3176 3754 8.201554 TGATCACATTGCAATAAAGAGTAGTC 57.798 34.615 12.53 7.46 0.00 2.59
3222 3878 9.480861 AGATCCATCCGTAGAGATCATTAATAA 57.519 33.333 0.00 0.00 38.06 1.40
3230 3886 5.713792 TGAAAGATCCATCCGTAGAGATC 57.286 43.478 0.00 0.00 36.25 2.75
3261 3917 5.416947 ACTAATTAGAAGTAAGGTGCGTGG 58.583 41.667 19.38 0.00 0.00 4.94
3265 3921 6.374613 AGCCAAACTAATTAGAAGTAAGGTGC 59.625 38.462 19.38 8.36 0.00 5.01
3280 3936 4.348486 TGCCCATGATTTAGCCAAACTAA 58.652 39.130 0.00 0.00 39.14 2.24
3411 4067 7.330454 CGAGGTGATATAGACAATGAAGAATGG 59.670 40.741 0.00 0.00 0.00 3.16
3474 4133 5.539955 AGTTTGGTCTCAATTTGGCAACTAT 59.460 36.000 0.00 0.00 32.28 2.12
3492 4151 1.067635 GGCACAGGCATTACAGTTTGG 60.068 52.381 0.00 0.00 43.71 3.28
3498 4157 1.078497 CCGAGGCACAGGCATTACA 60.078 57.895 0.00 0.00 43.71 2.41


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

AutoCloner maintained by Alex Coulton.