Multiple sequence alignment - TraesCS7A01G010000

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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 TraesCS7A01G010000 chr7A 100.000 2839 0 0 1 2839 4531402 4528564 0.000000e+00 5243.0
1 TraesCS7A01G010000 chr7A 85.051 1465 154 25 359 1820 4587009 4585607 0.000000e+00 1432.0
2 TraesCS7A01G010000 chr7A 87.748 302 25 4 1967 2265 4585522 4585230 2.710000e-90 342.0
3 TraesCS7A01G010000 chr7A 92.340 235 15 1 2607 2838 4486998 4486764 5.860000e-87 331.0
4 TraesCS7A01G010000 chr7A 78.344 157 24 10 9 158 4587494 4587341 3.010000e-15 93.5
5 TraesCS7A01G010000 chr7D 94.997 1579 67 5 359 1936 4706549 4704982 0.000000e+00 2468.0
6 TraesCS7A01G010000 chr7D 87.991 891 89 12 936 1820 4718271 4717393 0.000000e+00 1037.0
7 TraesCS7A01G010000 chr7D 83.546 863 63 18 1990 2837 4704672 4703874 0.000000e+00 734.0
8 TraesCS7A01G010000 chr7D 87.744 359 19 10 12 348 4719293 4718938 2.050000e-106 396.0
9 TraesCS7A01G010000 chr7D 80.000 540 53 18 389 906 4718852 4718346 5.820000e-92 348.0
10 TraesCS7A01G010000 chr7D 87.748 302 25 4 1967 2265 4717301 4717009 2.710000e-90 342.0
11 TraesCS7A01G010000 chr7D 88.398 181 10 5 42 213 4707001 4706823 1.030000e-49 207.0
12 TraesCS7A01G010000 chr7D 100.000 42 0 0 1 42 4707076 4707035 8.430000e-11 78.7
13 TraesCS7A01G010000 chr4A 86.259 1259 120 27 359 1599 738933183 738934406 0.000000e+00 1317.0
14 TraesCS7A01G010000 chr4A 90.317 568 49 5 1644 2206 738934400 738934966 0.000000e+00 739.0
15 TraesCS7A01G010000 chr4A 79.439 321 26 20 2405 2695 738935002 738935312 1.040000e-44 191.0
16 TraesCS7A01G010000 chr4A 84.615 182 16 7 42 213 738932763 738932942 1.350000e-38 171.0
17 TraesCS7A01G010000 chr4A 93.043 115 8 0 2725 2839 738935314 738935428 4.860000e-38 169.0
18 TraesCS7A01G010000 chr4A 94.737 57 3 0 78 134 738972195 738972139 3.900000e-14 89.8
19 TraesCS7A01G010000 chr4A 100.000 39 0 0 1 39 738932688 738932726 3.920000e-09 73.1
20 TraesCS7A01G010000 chr4A 97.619 42 1 0 1 42 738972240 738972199 3.920000e-09 73.1
21 TraesCS7A01G010000 chr6D 79.946 369 47 14 357 714 12641117 12641469 2.180000e-61 246.0
22 TraesCS7A01G010000 chr5B 87.000 200 26 0 684 883 430263892 430263693 2.850000e-55 226.0
23 TraesCS7A01G010000 chr5B 85.093 161 24 0 684 844 430165843 430165683 6.290000e-37 165.0
24 TraesCS7A01G010000 chr3B 86.500 200 27 0 684 883 202592363 202592562 1.320000e-53 220.0
25 TraesCS7A01G010000 chrUn 85.093 161 24 0 684 844 342509007 342509167 6.290000e-37 165.0
26 TraesCS7A01G010000 chrUn 85.093 161 24 0 684 844 382684603 382684443 6.290000e-37 165.0
27 TraesCS7A01G010000 chrUn 85.093 161 24 0 684 844 399641170 399641010 6.290000e-37 165.0


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 TraesCS7A01G010000 chr7A 4528564 4531402 2838 True 5243.000 5243 100.000000 1 2839 1 chr7A.!!$R2 2838
1 TraesCS7A01G010000 chr7A 4585230 4587494 2264 True 622.500 1432 83.714333 9 2265 3 chr7A.!!$R3 2256
2 TraesCS7A01G010000 chr7D 4703874 4707076 3202 True 871.925 2468 91.735250 1 2837 4 chr7D.!!$R1 2836
3 TraesCS7A01G010000 chr7D 4717009 4719293 2284 True 530.750 1037 85.870750 12 2265 4 chr7D.!!$R2 2253
4 TraesCS7A01G010000 chr4A 738932688 738935428 2740 False 443.350 1317 88.945500 1 2839 6 chr4A.!!$F1 2838

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
147 183 0.03779 GCTCCTGCGTTCAAGAGACT 60.038 55.0 0.0 0.0 33.58 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 2236 0.67895 TCACAGCGAACTCATGGACA 59.321 50.0 0.0 0.0 0.0 4.02 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
147 183 0.037790 GCTCCTGCGTTCAAGAGACT 60.038 55.000 0.00 0.00 33.58 3.24
171 207 3.440872 CCAAGCTCTCTAGTAACACGTCT 59.559 47.826 0.00 0.00 0.00 4.18
172 208 4.634883 CCAAGCTCTCTAGTAACACGTCTA 59.365 45.833 0.00 0.00 0.00 2.59
209 264 2.742053 TGCATCGTGAAAGGTTAGCTTC 59.258 45.455 0.00 0.00 0.00 3.86
222 326 3.118445 GGTTAGCTTCCTCTGCTCTGATT 60.118 47.826 0.00 0.00 41.46 2.57
315 443 2.158652 GGTAGAGGGTAAAGATTGGCCC 60.159 54.545 0.00 0.00 41.36 5.80
369 597 0.676782 TTCCGCCCTTAGCTTTCTGC 60.677 55.000 0.00 0.00 40.39 4.26
378 606 4.381292 CCCTTAGCTTTCTGCCATTTCTTG 60.381 45.833 0.00 0.00 44.23 3.02
379 607 4.219288 CCTTAGCTTTCTGCCATTTCTTGT 59.781 41.667 0.00 0.00 44.23 3.16
380 608 5.279156 CCTTAGCTTTCTGCCATTTCTTGTT 60.279 40.000 0.00 0.00 44.23 2.83
397 627 9.994432 ATTTCTTGTTATTTCAGCTAGATTTCG 57.006 29.630 0.00 0.00 0.00 3.46
399 629 5.734855 TGTTATTTCAGCTAGATTTCGGC 57.265 39.130 0.00 0.00 0.00 5.54
414 644 0.812549 TCGGCTGTATACTTGTGCGA 59.187 50.000 4.17 3.75 0.00 5.10
423 653 5.743467 TGTATACTTGTGCGACTGTTTTTG 58.257 37.500 4.17 0.00 0.00 2.44
553 793 5.590259 GCCTTGGCTACTTTTCTGAATATCA 59.410 40.000 4.11 0.00 0.00 2.15
783 1047 4.691860 ACTCTGTTGTTATGCTTCATGC 57.308 40.909 0.00 0.00 43.25 4.06
866 1130 7.709269 TTAGTACAAAAGCAGAGTGTAGTTG 57.291 36.000 0.00 0.00 34.19 3.16
906 1170 2.513753 CTAGGGTCACAAATGTTGGCA 58.486 47.619 0.00 0.00 34.12 4.92
922 1199 1.023513 GGCACAAGCTCTGCTACTGG 61.024 60.000 14.28 0.00 38.25 4.00
929 1206 1.202463 AGCTCTGCTACTGGTTATGCG 60.202 52.381 0.00 0.00 36.99 4.73
932 1209 2.860735 CTCTGCTACTGGTTATGCGAAC 59.139 50.000 0.00 0.00 0.00 3.95
934 1211 3.697542 TCTGCTACTGGTTATGCGAACTA 59.302 43.478 0.00 0.00 0.00 2.24
938 1215 4.262079 GCTACTGGTTATGCGAACTATCCT 60.262 45.833 0.00 0.00 0.00 3.24
1008 1317 9.116080 TGAACTTCCAGGTTATATATGGATGAT 57.884 33.333 17.44 9.84 42.53 2.45
1185 1494 9.713684 ATTAATATGGTCATGGAAGAAAAGGAA 57.286 29.630 0.00 0.00 0.00 3.36
1311 1624 1.740380 GCGCAGTAATCAAGGAGCAGA 60.740 52.381 0.30 0.00 0.00 4.26
1314 1627 3.739209 CGCAGTAATCAAGGAGCAGATGA 60.739 47.826 0.00 0.00 0.00 2.92
1321 1634 5.640189 ATCAAGGAGCAGATGACAAAAAG 57.360 39.130 0.00 0.00 0.00 2.27
1388 1701 2.967362 CATGAACATGTGGCAGCAAAT 58.033 42.857 0.00 0.00 34.23 2.32
1800 2117 3.443681 ACATCGCCAAAAGAAACATAGGG 59.556 43.478 0.00 0.00 0.00 3.53
1900 2218 9.469807 CTGAATTTGTACTGATCATCTACCTAC 57.530 37.037 0.00 0.00 0.00 3.18
1904 2222 8.768501 TTTGTACTGATCATCTACCTACAGAT 57.231 34.615 0.00 0.00 35.60 2.90
1906 2224 9.862149 TTGTACTGATCATCTACCTACAGATTA 57.138 33.333 0.00 0.00 32.83 1.75
1950 2268 5.707764 AGTTCGCTGTGAGCATATAGATAGA 59.292 40.000 7.78 0.00 42.58 1.98
1954 2272 5.742926 CGCTGTGAGCATATAGATAGATGTG 59.257 44.000 0.00 0.00 42.58 3.21
1992 2574 3.134458 GACATACAGGTATGGCTTCAGC 58.866 50.000 20.19 0.00 45.75 4.26
2092 2695 6.374417 AATTAAGTTAGTCCTTGCTCCTGA 57.626 37.500 0.00 0.00 0.00 3.86
2095 2698 4.213564 AGTTAGTCCTTGCTCCTGATTG 57.786 45.455 0.00 0.00 0.00 2.67
2096 2699 3.054802 AGTTAGTCCTTGCTCCTGATTGG 60.055 47.826 0.00 0.00 37.10 3.16
2097 2700 1.661463 AGTCCTTGCTCCTGATTGGA 58.339 50.000 0.00 0.00 43.86 3.53
2105 2708 2.914908 TCCTGATTGGAGCATCGGA 58.085 52.632 0.00 0.00 40.56 4.55
2106 2709 0.465705 TCCTGATTGGAGCATCGGAC 59.534 55.000 0.00 0.00 40.56 4.79
2107 2710 0.467384 CCTGATTGGAGCATCGGACT 59.533 55.000 0.00 0.00 38.35 3.85
2108 2711 1.688735 CCTGATTGGAGCATCGGACTA 59.311 52.381 0.00 0.00 38.35 2.59
2109 2712 2.288702 CCTGATTGGAGCATCGGACTAG 60.289 54.545 0.00 0.00 38.35 2.57
2110 2713 2.363680 CTGATTGGAGCATCGGACTAGT 59.636 50.000 0.00 0.00 34.37 2.57
2111 2714 2.766263 TGATTGGAGCATCGGACTAGTT 59.234 45.455 0.00 0.00 34.37 2.24
2112 2715 3.197766 TGATTGGAGCATCGGACTAGTTT 59.802 43.478 0.00 0.00 34.37 2.66
2210 2813 8.840833 TTGTTATTCTCTTTGTACATACTGCA 57.159 30.769 0.00 0.00 0.00 4.41
2211 2814 9.448438 TTGTTATTCTCTTTGTACATACTGCAT 57.552 29.630 0.00 0.00 0.00 3.96
2215 2818 8.879342 ATTCTCTTTGTACATACTGCATAGTC 57.121 34.615 0.00 0.00 38.36 2.59
2221 2824 6.378710 TGTACATACTGCATAGTCTCTGTC 57.621 41.667 0.00 0.00 38.36 3.51
2224 2827 7.939588 TGTACATACTGCATAGTCTCTGTCTAT 59.060 37.037 0.00 0.00 38.36 1.98
2228 2831 8.787852 CATACTGCATAGTCTCTGTCTATACAA 58.212 37.037 0.00 0.00 38.36 2.41
2246 2849 8.687242 TCTATACAACCTGTATATATGCTCAGC 58.313 37.037 6.91 0.00 42.80 4.26
2252 2855 8.355169 CAACCTGTATATATGCTCAGCAAAAAT 58.645 33.333 1.73 0.00 43.62 1.82
2265 2868 8.313292 TGCTCAGCAAAAATAGGTCAATATTTT 58.687 29.630 0.00 0.00 43.72 1.82
2276 2879 9.719355 AATAGGTCAATATTTTTGTTTTCCCAC 57.281 29.630 0.00 0.00 0.00 4.61
2293 2896 7.852971 TTTCCCACAGTAAAAATATAGACCG 57.147 36.000 0.00 0.00 0.00 4.79
2343 2946 0.180406 AGCAACAACACGAGAACCCT 59.820 50.000 0.00 0.00 0.00 4.34
2350 2953 3.057734 CAACACGAGAACCCTGTTAGAC 58.942 50.000 0.00 0.00 0.00 2.59
2360 2963 4.373156 ACCCTGTTAGACTTGAATTGCT 57.627 40.909 0.00 0.00 0.00 3.91
2367 2970 5.997129 TGTTAGACTTGAATTGCTCATGTGA 59.003 36.000 0.00 0.00 41.29 3.58
2381 2984 7.920160 TGCTCATGTGAAATTTGTAGATACA 57.080 32.000 0.00 0.00 0.00 2.29
2389 2992 9.689976 TGTGAAATTTGTAGATACATTTTGGTG 57.310 29.630 0.00 0.00 35.89 4.17
2391 2994 9.689976 TGAAATTTGTAGATACATTTTGGTGTG 57.310 29.630 0.00 0.00 35.89 3.82
2403 3014 6.118170 ACATTTTGGTGTGATCCTATCTGAG 58.882 40.000 0.00 0.00 0.00 3.35
2420 3031 9.406113 CCTATCTGAGAAAGGATCAAAAGAATT 57.594 33.333 0.00 0.00 31.64 2.17
2428 3039 9.171877 AGAAAGGATCAAAAGAATTAGTAGCAG 57.828 33.333 0.00 0.00 0.00 4.24
2430 3041 9.520515 AAAGGATCAAAAGAATTAGTAGCAGAA 57.479 29.630 0.00 0.00 0.00 3.02
2433 3044 9.601217 GGATCAAAAGAATTAGTAGCAGAAGTA 57.399 33.333 0.00 0.00 0.00 2.24
2455 3066 9.838339 AAGTAGAATTGATAGGTTTCAGGTATG 57.162 33.333 0.00 0.00 0.00 2.39
2456 3067 9.213777 AGTAGAATTGATAGGTTTCAGGTATGA 57.786 33.333 0.00 0.00 0.00 2.15
2465 3076 3.069729 GGTTTCAGGTATGACGCCTATCT 59.930 47.826 0.00 0.00 34.35 1.98
2513 3128 2.298163 AGAAACCTTTGGATGCAAGCAG 59.702 45.455 0.00 0.00 0.00 4.24
2517 3132 2.552585 CTTTGGATGCAAGCAGGCGG 62.553 60.000 0.00 0.00 36.28 6.13
2519 3134 2.124736 GGATGCAAGCAGGCGGTA 60.125 61.111 0.00 0.00 36.28 4.02
2521 3136 1.745115 GATGCAAGCAGGCGGTACA 60.745 57.895 0.00 0.00 36.28 2.90
2530 3145 0.899720 CAGGCGGTACAGGTTTAGGA 59.100 55.000 0.00 0.00 0.00 2.94
2569 3185 5.011635 TCTGGTGAAGTTACATAGCTGAACA 59.988 40.000 0.00 0.00 0.00 3.18
2570 3186 5.237815 TGGTGAAGTTACATAGCTGAACAG 58.762 41.667 0.00 0.00 0.00 3.16
2604 3246 0.112606 ACCTCGACCTGACCTCTTGA 59.887 55.000 0.00 0.00 0.00 3.02
2715 3360 6.828785 TCCATTATCTAAAGAAGAGGGCAAAC 59.171 38.462 0.00 0.00 37.74 2.93
2743 3388 3.179443 TGTGAATCGAGTTCCTATGCC 57.821 47.619 0.00 0.00 35.91 4.40
2832 3477 0.392998 GCGAGGAAGGAAGCCATCAA 60.393 55.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 183 3.825014 ACGTGTTACTAGAGAGCTTGGAA 59.175 43.478 0.00 0.00 0.00 3.53
171 207 3.394674 TGCACAAATTGACGAGACCTA 57.605 42.857 0.00 0.00 0.00 3.08
172 208 2.254546 TGCACAAATTGACGAGACCT 57.745 45.000 0.00 0.00 0.00 3.85
209 264 0.035725 TGGTGCAATCAGAGCAGAGG 60.036 55.000 0.00 0.00 43.63 3.69
222 326 2.611800 AGAGGCTGGGATGGTGCA 60.612 61.111 0.00 0.00 0.00 4.57
277 382 4.794334 TCTACCTCTAGGAACAGCTAAGG 58.206 47.826 2.23 0.00 38.94 2.69
278 383 4.825085 CCTCTACCTCTAGGAACAGCTAAG 59.175 50.000 2.23 0.00 38.94 2.18
355 583 3.359950 AGAAATGGCAGAAAGCTAAGGG 58.640 45.455 0.00 0.00 44.79 3.95
362 590 7.148689 GCTGAAATAACAAGAAATGGCAGAAAG 60.149 37.037 0.00 0.00 0.00 2.62
378 606 5.993106 AGCCGAAATCTAGCTGAAATAAC 57.007 39.130 0.00 0.00 34.99 1.89
397 627 1.927174 CAGTCGCACAAGTATACAGCC 59.073 52.381 5.50 0.00 0.00 4.85
399 629 5.591643 AAAACAGTCGCACAAGTATACAG 57.408 39.130 5.50 0.00 0.00 2.74
403 633 4.893424 ACAAAAACAGTCGCACAAGTAT 57.107 36.364 0.00 0.00 0.00 2.12
406 636 3.497118 TGAACAAAAACAGTCGCACAAG 58.503 40.909 0.00 0.00 0.00 3.16
414 644 5.976458 ACAATCCACATGAACAAAAACAGT 58.024 33.333 0.00 0.00 0.00 3.55
423 653 3.069443 ACCCAACAACAATCCACATGAAC 59.931 43.478 0.00 0.00 0.00 3.18
783 1047 3.629398 GTCAAAGATGGTAGCAGAATGGG 59.371 47.826 0.00 0.00 35.86 4.00
866 1130 3.658709 AGCTCAGTAGTTGAAACAGAGC 58.341 45.455 11.31 11.31 45.32 4.09
906 1170 3.866651 CATAACCAGTAGCAGAGCTTGT 58.133 45.455 0.00 0.00 40.44 3.16
922 1199 5.961395 TTCGAAAGGATAGTTCGCATAAC 57.039 39.130 0.00 0.00 45.79 1.89
929 1206 8.664211 AATAGGTCATTTCGAAAGGATAGTTC 57.336 34.615 25.90 13.69 30.90 3.01
934 1211 8.875168 AGATAGAATAGGTCATTTCGAAAGGAT 58.125 33.333 25.90 14.85 30.90 3.24
938 1215 9.667107 ACAAAGATAGAATAGGTCATTTCGAAA 57.333 29.630 13.91 13.91 0.00 3.46
1008 1317 7.035004 GCTTAAGAACCAATGCATCAACAATA 58.965 34.615 6.67 0.00 0.00 1.90
1185 1494 7.944729 ACCTTGATAGTCATGCTGTAAATTT 57.055 32.000 0.00 0.00 0.00 1.82
1311 1624 2.893489 GTTGCTCCTCCCTTTTTGTCAT 59.107 45.455 0.00 0.00 0.00 3.06
1314 1627 2.695147 CAAGTTGCTCCTCCCTTTTTGT 59.305 45.455 0.00 0.00 0.00 2.83
1321 1634 1.882623 CAGTTTCAAGTTGCTCCTCCC 59.117 52.381 0.00 0.00 0.00 4.30
1388 1701 5.690865 TGTTTTTCTTCCTCAAGCTCCTTA 58.309 37.500 0.00 0.00 0.00 2.69
1486 1799 7.390162 CACTCTCTTGAAGCTTCTTCCTTAAAT 59.610 37.037 26.09 3.11 0.00 1.40
1800 2117 0.752743 TGGGTTGCATGCTGATAGGC 60.753 55.000 20.33 1.10 0.00 3.93
1906 2224 7.371159 CGAACTCATGGACATATAGTGTATGT 58.629 38.462 11.90 11.90 42.36 2.29
1918 2236 0.678950 TCACAGCGAACTCATGGACA 59.321 50.000 0.00 0.00 0.00 4.02
1919 2237 1.354040 CTCACAGCGAACTCATGGAC 58.646 55.000 0.00 0.00 0.00 4.02
1950 2268 6.649155 TGTCTGTACAATGTATAAGCCACAT 58.351 36.000 0.00 0.00 38.25 3.21
1954 2272 7.385205 CCTGTATGTCTGTACAATGTATAAGCC 59.615 40.741 0.00 0.00 39.58 4.35
1964 2546 4.714802 AGCCATACCTGTATGTCTGTACAA 59.285 41.667 14.42 0.00 40.90 2.41
1992 2574 8.425577 AGATGGTTGTACTAAATTCAGAATCG 57.574 34.615 0.00 0.00 0.00 3.34
2002 2584 4.794278 TCAGCGAGATGGTTGTACTAAA 57.206 40.909 0.00 0.00 0.00 1.85
2092 2695 3.914426 AAACTAGTCCGATGCTCCAAT 57.086 42.857 0.00 0.00 0.00 3.16
2095 2698 3.982058 CGATAAAACTAGTCCGATGCTCC 59.018 47.826 0.00 0.00 0.00 4.70
2096 2699 3.425858 GCGATAAAACTAGTCCGATGCTC 59.574 47.826 0.00 0.00 0.00 4.26
2097 2700 3.381949 GCGATAAAACTAGTCCGATGCT 58.618 45.455 0.00 0.00 0.00 3.79
2098 2701 2.475487 GGCGATAAAACTAGTCCGATGC 59.525 50.000 0.00 0.00 0.00 3.91
2099 2702 2.724690 CGGCGATAAAACTAGTCCGATG 59.275 50.000 10.52 0.00 37.79 3.84
2100 2703 2.861360 GCGGCGATAAAACTAGTCCGAT 60.861 50.000 18.11 2.62 37.79 4.18
2101 2704 1.534595 GCGGCGATAAAACTAGTCCGA 60.535 52.381 18.11 0.00 37.79 4.55
2102 2705 0.850856 GCGGCGATAAAACTAGTCCG 59.149 55.000 12.98 11.45 38.51 4.79
2103 2706 2.220479 AGCGGCGATAAAACTAGTCC 57.780 50.000 12.98 0.00 0.00 3.85
2104 2707 4.331962 CAAAAGCGGCGATAAAACTAGTC 58.668 43.478 12.98 0.00 0.00 2.59
2105 2708 3.126343 CCAAAAGCGGCGATAAAACTAGT 59.874 43.478 12.98 0.00 0.00 2.57
2106 2709 3.680789 CCAAAAGCGGCGATAAAACTAG 58.319 45.455 12.98 0.00 0.00 2.57
2107 2710 2.159490 GCCAAAAGCGGCGATAAAACTA 60.159 45.455 12.98 0.00 43.52 2.24
2108 2711 1.402325 GCCAAAAGCGGCGATAAAACT 60.402 47.619 12.98 0.00 43.52 2.66
2109 2712 0.989164 GCCAAAAGCGGCGATAAAAC 59.011 50.000 12.98 0.00 43.52 2.43
2110 2713 3.410098 GCCAAAAGCGGCGATAAAA 57.590 47.368 12.98 0.00 43.52 1.52
2195 2798 7.261325 ACAGAGACTATGCAGTATGTACAAAG 58.739 38.462 0.00 0.00 39.31 2.77
2201 2804 7.939588 TGTATAGACAGAGACTATGCAGTATGT 59.060 37.037 0.00 0.00 37.77 2.29
2206 2809 6.264292 AGGTTGTATAGACAGAGACTATGCAG 59.736 42.308 0.00 0.00 41.29 4.41
2207 2810 6.039829 CAGGTTGTATAGACAGAGACTATGCA 59.960 42.308 0.00 0.00 39.68 3.96
2208 2811 6.039941 ACAGGTTGTATAGACAGAGACTATGC 59.960 42.308 0.00 0.00 36.76 3.14
2209 2812 7.575414 ACAGGTTGTATAGACAGAGACTATG 57.425 40.000 0.00 0.00 36.76 2.23
2221 2824 8.470002 TGCTGAGCATATATACAGGTTGTATAG 58.530 37.037 1.40 3.55 40.01 1.31
2224 2827 6.664428 TGCTGAGCATATATACAGGTTGTA 57.336 37.500 1.40 0.00 33.29 2.41
2228 2831 9.224267 CTATTTTTGCTGAGCATATATACAGGT 57.776 33.333 8.44 0.00 38.76 4.00
2252 2855 8.251383 TGTGGGAAAACAAAAATATTGACCTA 57.749 30.769 0.00 0.00 0.00 3.08
2266 2869 9.016438 GGTCTATATTTTTACTGTGGGAAAACA 57.984 33.333 0.00 0.00 0.00 2.83
2267 2870 8.179615 CGGTCTATATTTTTACTGTGGGAAAAC 58.820 37.037 0.00 0.00 0.00 2.43
2268 2871 7.884354 ACGGTCTATATTTTTACTGTGGGAAAA 59.116 33.333 0.00 0.00 30.43 2.29
2269 2872 7.396418 ACGGTCTATATTTTTACTGTGGGAAA 58.604 34.615 0.00 0.00 30.43 3.13
2270 2873 6.949715 ACGGTCTATATTTTTACTGTGGGAA 58.050 36.000 0.00 0.00 30.43 3.97
2271 2874 6.549433 ACGGTCTATATTTTTACTGTGGGA 57.451 37.500 0.00 0.00 30.43 4.37
2272 2875 7.719483 TCTACGGTCTATATTTTTACTGTGGG 58.281 38.462 0.00 0.00 33.62 4.61
2300 2903 7.328493 GCTTCAACCACCTACAAATATGTTTTC 59.672 37.037 0.00 0.00 41.05 2.29
2305 2908 5.895636 TGCTTCAACCACCTACAAATATG 57.104 39.130 0.00 0.00 0.00 1.78
2308 2911 3.957497 TGTTGCTTCAACCACCTACAAAT 59.043 39.130 7.17 0.00 42.96 2.32
2309 2912 3.357203 TGTTGCTTCAACCACCTACAAA 58.643 40.909 7.17 0.00 42.96 2.83
2310 2913 3.006112 TGTTGCTTCAACCACCTACAA 57.994 42.857 7.17 0.00 42.96 2.41
2320 2923 2.096819 GGTTCTCGTGTTGTTGCTTCAA 59.903 45.455 0.00 0.00 0.00 2.69
2343 2946 5.997129 TCACATGAGCAATTCAAGTCTAACA 59.003 36.000 0.00 0.00 39.77 2.41
2350 2953 7.416154 ACAAATTTCACATGAGCAATTCAAG 57.584 32.000 0.00 0.00 39.77 3.02
2381 2984 6.566079 TCTCAGATAGGATCACACCAAAAT 57.434 37.500 0.00 0.00 0.00 1.82
2403 3014 9.167311 TCTGCTACTAATTCTTTTGATCCTTTC 57.833 33.333 0.00 0.00 0.00 2.62
2420 3031 8.998277 ACCTATCAATTCTACTTCTGCTACTA 57.002 34.615 0.00 0.00 0.00 1.82
2430 3041 9.213777 TCATACCTGAAACCTATCAATTCTACT 57.786 33.333 0.00 0.00 0.00 2.57
2433 3044 6.986817 CGTCATACCTGAAACCTATCAATTCT 59.013 38.462 0.00 0.00 31.85 2.40
2454 3065 5.339008 AAGTCACATTAAGATAGGCGTCA 57.661 39.130 0.00 0.00 0.00 4.35
2455 3066 6.366332 CCATAAGTCACATTAAGATAGGCGTC 59.634 42.308 0.00 0.00 0.00 5.19
2456 3067 6.183360 ACCATAAGTCACATTAAGATAGGCGT 60.183 38.462 0.00 0.00 0.00 5.68
2513 3128 2.558378 GATTCCTAAACCTGTACCGCC 58.442 52.381 0.00 0.00 0.00 6.13
2517 3132 7.618137 TGAAACTAGGATTCCTAAACCTGTAC 58.382 38.462 13.41 6.57 35.49 2.90
2519 3134 6.272558 ACTGAAACTAGGATTCCTAAACCTGT 59.727 38.462 13.41 5.02 35.49 4.00
2521 3136 6.954352 ACTGAAACTAGGATTCCTAAACCT 57.046 37.500 13.41 0.00 35.49 3.50
2530 3145 5.825593 TCACCAGAACTGAAACTAGGATT 57.174 39.130 3.19 0.00 0.00 3.01
2570 3186 3.613299 GTCGAGGTTTAGAAGCTAACTGC 59.387 47.826 0.00 0.00 39.77 4.40
2571 3187 4.082136 AGGTCGAGGTTTAGAAGCTAACTG 60.082 45.833 0.00 0.00 39.77 3.16
2572 3188 4.082136 CAGGTCGAGGTTTAGAAGCTAACT 60.082 45.833 0.00 0.00 39.77 2.24
2573 3189 4.082354 TCAGGTCGAGGTTTAGAAGCTAAC 60.082 45.833 0.00 0.00 39.77 2.34
2574 3190 4.082354 GTCAGGTCGAGGTTTAGAAGCTAA 60.082 45.833 0.00 0.00 39.77 3.09
2604 3246 2.558359 GGCATACACAGAGCAAAAGGTT 59.442 45.455 0.00 0.00 0.00 3.50
2715 3360 1.813513 ACTCGATTCACAAGGCCAAG 58.186 50.000 5.01 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.