Multiple sequence alignment - TraesCS7B01G210700

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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 TraesCS7B01G210700 chr7B 100.000 6287 0 0 1556 7842 384771940 384765654 0.000000e+00 11611
1 TraesCS7B01G210700 chr7B 100.000 1210 0 0 1 1210 384773495 384772286 0.000000e+00 2235
2 TraesCS7B01G210700 chr7B 85.714 196 21 5 1883 2074 687059843 687060035 4.800000e-47 200
3 TraesCS7B01G210700 chr7A 95.141 5433 191 35 2460 7842 440355516 440350107 0.000000e+00 8503
4 TraesCS7B01G210700 chr7A 92.030 1217 44 15 1 1210 440357932 440356762 0.000000e+00 1661
5 TraesCS7B01G210700 chr7A 94.290 613 26 4 1565 2177 440356391 440355788 0.000000e+00 929
6 TraesCS7B01G210700 chr7A 95.259 232 9 2 2179 2410 440355750 440355521 4.470000e-97 366
7 TraesCS7B01G210700 chr7D 95.794 3804 109 26 3918 7686 389461030 389457243 0.000000e+00 6091
8 TraesCS7B01G210700 chr7D 93.132 1223 44 14 1 1210 389465532 389464337 0.000000e+00 1757
9 TraesCS7B01G210700 chr7D 96.351 877 21 5 3023 3899 389462432 389461567 0.000000e+00 1432
10 TraesCS7B01G210700 chr7D 95.043 807 31 2 2177 2983 389463228 389462431 0.000000e+00 1260
11 TraesCS7B01G210700 chr7D 95.432 613 17 3 1565 2177 389463865 389463264 0.000000e+00 966
12 TraesCS7B01G210700 chr7D 95.882 170 7 0 7673 7842 389455156 389454987 7.750000e-70 276
13 TraesCS7B01G210700 chr5A 83.186 226 25 5 1852 2074 11787109 11787324 2.230000e-45 195
14 TraesCS7B01G210700 chr5A 78.894 199 29 7 5317 5514 566330513 566330699 1.070000e-23 122
15 TraesCS7B01G210700 chr4D 82.589 224 30 7 1852 2074 44035159 44035374 1.040000e-43 189
16 TraesCS7B01G210700 chr2B 83.163 196 25 6 1883 2074 592779132 592778941 1.050000e-38 172
17 TraesCS7B01G210700 chr2B 80.882 136 26 0 5921 6056 680044372 680044507 2.990000e-19 108
18 TraesCS7B01G210700 chrUn 79.825 228 46 0 2393 2620 34252194 34252421 4.870000e-37 167
19 TraesCS7B01G210700 chrUn 79.825 228 46 0 2393 2620 309430679 309430906 4.870000e-37 167
20 TraesCS7B01G210700 chr3B 79.825 228 46 0 2393 2620 5887876 5887649 4.870000e-37 167
21 TraesCS7B01G210700 chr6B 77.561 205 32 8 5311 5514 63617342 63617533 2.310000e-20 111


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 TraesCS7B01G210700 chr7B 384765654 384773495 7841 True 6923.000000 11611 100.000000 1 7842 2 chr7B.!!$R1 7841
1 TraesCS7B01G210700 chr7A 440350107 440357932 7825 True 2864.750000 8503 94.180000 1 7842 4 chr7A.!!$R1 7841
2 TraesCS7B01G210700 chr7D 389454987 389465532 10545 True 1963.666667 6091 95.272333 1 7842 6 chr7D.!!$R1 7841

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
61 62 0.030908 GGAGGACGCTCCATACTTCG 59.969 60.000 4.37 0.0 42.86 3.79 F
939 968 0.464735 CAGAACACCACCCCAACGAA 60.465 55.000 0.00 0.0 0.00 3.85 F
1969 2115 1.069358 GCTGGTTCTCTAGGGATTCCG 59.931 57.143 0.00 0.0 38.33 4.30 F
2543 2726 0.666913 TAGTAGCCAGCGGTCGAATC 59.333 55.000 0.00 0.0 0.00 2.52 F
2606 2789 0.925558 TTTGATAGGGCTGGCATGGA 59.074 50.000 2.88 0.0 0.00 3.41 F
3035 3218 2.235402 TGGTCGTTTCCCTTATGGTCTC 59.765 50.000 0.00 0.0 34.77 3.36 F
4592 5308 1.615392 ACCTGCAGCATGTTTTCCTTC 59.385 47.619 8.66 0.0 39.31 3.46 F
4790 5506 0.328258 GCCTCACCCACCTTACACAT 59.672 55.000 0.00 0.0 0.00 3.21 F
5874 6594 2.906389 AGTGCAATCAGTGAGTAAGGGA 59.094 45.455 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1755 0.320247 AAGAGAGCAGCACGGAACAG 60.320 55.000 0.00 0.00 0.00 3.16 R
2416 2599 0.758734 AAAACTTTGGAAGGGCAGCC 59.241 50.000 1.26 1.26 0.00 4.85 R
2939 3122 1.067295 TCAGACCAATGGAGCAACCT 58.933 50.000 6.16 0.00 39.86 3.50 R
3376 3559 1.443802 GCCTACAGTTGCTTGAGACC 58.556 55.000 0.00 0.00 0.00 3.85 R
4215 4927 1.532437 CATGACGAGAAAACTGCAGCA 59.468 47.619 15.27 0.00 0.00 4.41 R
4790 5506 1.985159 AGGTCATTCTACCCAAGTGCA 59.015 47.619 0.00 0.00 40.71 4.57 R
6305 7025 1.698506 ACGGCCTGAATAGAGGAGAG 58.301 55.000 0.00 0.00 34.69 3.20 R
6701 7421 5.103000 CGGATCGCTTATATTTCCACTAGG 58.897 45.833 0.00 0.00 0.00 3.02 R
7393 8148 1.007734 CTGTTGCTGCAGCCAAGTG 60.008 57.895 34.64 17.27 41.18 3.16 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
61 62 0.030908 GGAGGACGCTCCATACTTCG 59.969 60.000 4.37 0.00 42.86 3.79
108 109 3.332034 GCTGCCAAAAATTGAGCTTCAT 58.668 40.909 0.00 0.00 30.36 2.57
116 117 5.885230 AAAATTGAGCTTCATCGACATCA 57.115 34.783 0.00 0.00 0.00 3.07
117 118 6.446781 AAAATTGAGCTTCATCGACATCAT 57.553 33.333 0.00 0.00 0.00 2.45
123 125 4.521146 AGCTTCATCGACATCATCCTTTT 58.479 39.130 0.00 0.00 0.00 2.27
129 131 2.094906 TCGACATCATCCTTTTCGTCGT 60.095 45.455 9.26 0.00 44.75 4.34
137 139 1.721133 CTTTTCGTCGTTGCGGTGC 60.721 57.895 0.00 0.00 0.00 5.01
156 158 0.970937 CGAGTAGGAAGCCTCCCACA 60.971 60.000 2.64 0.00 43.64 4.17
426 440 7.736447 GCTACATGCACTCCTATATTTCTTT 57.264 36.000 0.00 0.00 42.31 2.52
427 441 8.833231 GCTACATGCACTCCTATATTTCTTTA 57.167 34.615 0.00 0.00 42.31 1.85
428 442 8.713271 GCTACATGCACTCCTATATTTCTTTAC 58.287 37.037 0.00 0.00 42.31 2.01
429 443 9.764363 CTACATGCACTCCTATATTTCTTTACA 57.236 33.333 0.00 0.00 0.00 2.41
430 444 8.438676 ACATGCACTCCTATATTTCTTTACAC 57.561 34.615 0.00 0.00 0.00 2.90
431 445 8.046708 ACATGCACTCCTATATTTCTTTACACA 58.953 33.333 0.00 0.00 0.00 3.72
432 446 8.892723 CATGCACTCCTATATTTCTTTACACAA 58.107 33.333 0.00 0.00 0.00 3.33
433 447 8.492673 TGCACTCCTATATTTCTTTACACAAG 57.507 34.615 0.00 0.00 0.00 3.16
460 474 8.189119 AGTATTTTGCATTTTTGGAGGAGTTA 57.811 30.769 0.00 0.00 0.00 2.24
461 475 8.646900 AGTATTTTGCATTTTTGGAGGAGTTAA 58.353 29.630 0.00 0.00 0.00 2.01
516 531 6.073276 GCAGATTGACATGTACACTGTACAAA 60.073 38.462 22.79 14.21 0.00 2.83
691 710 4.651503 CAGTGTAGGTGGTGATAGATTCCT 59.348 45.833 0.00 0.00 0.00 3.36
719 738 8.698854 ACAACAAACAATGCGAGTAATAAATTG 58.301 29.630 0.00 0.00 34.99 2.32
789 808 1.286553 AGTCACCTCCTGGACCTAGAG 59.713 57.143 0.00 4.77 34.58 2.43
939 968 0.464735 CAGAACACCACCCCAACGAA 60.465 55.000 0.00 0.00 0.00 3.85
1711 1857 5.296813 AGATCTTGCGCTTTTAATTTCGT 57.703 34.783 9.73 0.00 0.00 3.85
1768 1914 5.348164 CGAATTGACTTTTGGACCTGTTTT 58.652 37.500 0.00 0.00 0.00 2.43
1769 1915 5.810074 CGAATTGACTTTTGGACCTGTTTTT 59.190 36.000 0.00 0.00 0.00 1.94
1958 2104 1.672356 ATGCCGTGTGCTGGTTCTC 60.672 57.895 0.00 0.00 42.00 2.87
1969 2115 1.069358 GCTGGTTCTCTAGGGATTCCG 59.931 57.143 0.00 0.00 38.33 4.30
2127 2273 3.445008 TCTCTGTGCCCTTCATCTTAGT 58.555 45.455 0.00 0.00 0.00 2.24
2277 2459 2.173569 ACTCCACCTGAAAAAGCTGTCT 59.826 45.455 0.00 0.00 0.00 3.41
2278 2460 3.217626 CTCCACCTGAAAAAGCTGTCTT 58.782 45.455 0.00 0.00 0.00 3.01
2311 2494 1.895131 ACAATGGGATTCACTTGGTGC 59.105 47.619 0.00 0.00 32.98 5.01
2410 2593 2.353610 GGGGCTGTTTGGATGGCAG 61.354 63.158 0.00 0.00 0.00 4.85
2411 2594 1.607467 GGGCTGTTTGGATGGCAGT 60.607 57.895 0.00 0.00 33.18 4.40
2431 2614 2.282462 ACGGCTGCCCTTCCAAAG 60.282 61.111 14.12 0.00 0.00 2.77
2453 2636 0.963355 TTGGCCGTTGACCAATAGGC 60.963 55.000 17.76 17.76 42.23 3.93
2454 2637 3.509659 GCCGTTGACCAATAGGCC 58.490 61.111 16.17 0.00 39.44 5.19
2455 2638 2.469516 GCCGTTGACCAATAGGCCG 61.470 63.158 16.17 2.96 39.44 6.13
2456 2639 1.817941 CCGTTGACCAATAGGCCGG 60.818 63.158 0.00 0.00 39.06 6.13
2457 2640 2.469516 CGTTGACCAATAGGCCGGC 61.470 63.158 21.18 21.18 39.06 6.13
2458 2641 2.124901 TTGACCAATAGGCCGGCG 60.125 61.111 22.54 7.92 39.06 6.46
2537 2720 1.409427 GATTCTGTAGTAGCCAGCGGT 59.591 52.381 0.00 0.00 0.00 5.68
2543 2726 0.666913 TAGTAGCCAGCGGTCGAATC 59.333 55.000 0.00 0.00 0.00 2.52
2563 2746 2.599875 TGGCGGCAAATTCCTGCA 60.600 55.556 10.22 0.00 44.52 4.41
2591 2774 1.107114 TTGGCAAGCCTTCGTTTTGA 58.893 45.000 12.96 0.00 36.94 2.69
2606 2789 0.925558 TTTGATAGGGCTGGCATGGA 59.074 50.000 2.88 0.00 0.00 3.41
2847 3030 5.214417 CGATCACATTTCAAGCAAGTCAAA 58.786 37.500 0.00 0.00 0.00 2.69
2921 3104 7.578203 TCTGTGAGGTTCATCTCTCTCTTATA 58.422 38.462 0.00 0.00 34.98 0.98
2986 3169 5.521735 CGAGTATGCTTCAGCTTAATCAACT 59.478 40.000 17.29 5.33 42.23 3.16
3035 3218 2.235402 TGGTCGTTTCCCTTATGGTCTC 59.765 50.000 0.00 0.00 34.77 3.36
3189 3372 4.225042 TGGCAATAGTGTGGTAAGATGTCT 59.775 41.667 0.00 0.00 0.00 3.41
3229 3412 7.983484 CCTTTTCCCTCCAATCATATTCTTTTG 59.017 37.037 0.00 0.00 0.00 2.44
3243 3426 7.545265 TCATATTCTTTTGAATTTGCTTTCGGG 59.455 33.333 0.00 0.00 46.12 5.14
3284 3467 7.327518 ACGTTTAATAGCACACAAATTAAAGGC 59.672 33.333 14.50 0.00 40.80 4.35
3332 3515 6.758806 TTACACCTTTCTAAGTTCCTTCCT 57.241 37.500 0.00 0.00 0.00 3.36
3376 3559 6.088085 GGCACTTCATCGAATAGTTTGTTTTG 59.912 38.462 0.00 0.00 0.00 2.44
3411 3594 3.435327 TGTAGGCGTAACAGAAAAGCATG 59.565 43.478 0.00 0.00 0.00 4.06
3739 3928 6.234177 CCATCTCAATAAATACCCCTGACTC 58.766 44.000 0.00 0.00 0.00 3.36
3828 4017 5.588648 ACAGTTTAATTATATGGCGCAGTGT 59.411 36.000 10.83 0.00 0.00 3.55
3908 4097 8.942338 TTGACTTTGTGTATGGTCATATCTAC 57.058 34.615 0.00 0.00 38.29 2.59
3911 4100 7.500992 ACTTTGTGTATGGTCATATCTACCTG 58.499 38.462 5.56 0.00 37.91 4.00
3915 4104 6.782494 TGTGTATGGTCATATCTACCTGATGT 59.218 38.462 5.56 0.00 37.91 3.06
4215 4927 5.564550 AGAGCTGATTTTGGTTCATGTACT 58.435 37.500 0.00 0.00 0.00 2.73
4469 5185 6.227298 TCTAGAGGAAATAAAGGAGCAGTG 57.773 41.667 0.00 0.00 0.00 3.66
4586 5302 2.276732 ACACTACCTGCAGCATGTTT 57.723 45.000 8.66 0.00 39.31 2.83
4592 5308 1.615392 ACCTGCAGCATGTTTTCCTTC 59.385 47.619 8.66 0.00 39.31 3.46
4681 5397 3.564235 TTTGATGCTGTGATGCACTTC 57.436 42.857 0.00 0.00 46.33 3.01
4740 5456 2.104963 CCCTTAGGTAAGCCATCACCTC 59.895 54.545 0.00 0.00 44.17 3.85
4766 5482 4.081365 TGACAGTTTGACACACTTCACCTA 60.081 41.667 0.00 0.00 0.00 3.08
4790 5506 0.328258 GCCTCACCCACCTTACACAT 59.672 55.000 0.00 0.00 0.00 3.21
4915 5631 3.744940 ATGTCAACCCCTCAATCATGT 57.255 42.857 0.00 0.00 0.00 3.21
5283 6002 6.420604 GCAAAATTCAGTGCTGCTACTTAAAA 59.579 34.615 0.00 0.00 37.78 1.52
5338 6057 5.838529 TCATGTATGTACCTGTATTCACGG 58.161 41.667 0.00 0.00 0.00 4.94
5342 6062 6.699366 TGTATGTACCTGTATTCACGGAAAA 58.301 36.000 0.00 0.00 32.22 2.29
5439 6159 3.192633 CACAGTTGCCAATTAACCCCTAC 59.807 47.826 0.00 0.00 0.00 3.18
5728 6448 8.743714 AGTCATTTCAGGATTGAAGGTATTTTC 58.256 33.333 0.00 0.00 43.76 2.29
5729 6449 8.743714 GTCATTTCAGGATTGAAGGTATTTTCT 58.256 33.333 0.00 0.00 43.76 2.52
5874 6594 2.906389 AGTGCAATCAGTGAGTAAGGGA 59.094 45.455 0.00 0.00 0.00 4.20
6134 6854 6.309494 CACACAAGGACAAAGCATATCATTTG 59.691 38.462 7.36 7.36 41.22 2.32
6141 6861 9.017509 AGGACAAAGCATATCATTTGTATATGG 57.982 33.333 12.55 0.00 46.67 2.74
6305 7025 3.499338 TGTCAAATCATGCCCATATCCC 58.501 45.455 0.00 0.00 0.00 3.85
6786 7506 7.342194 CAAATTGCTTGATTGAAAGAACTGTG 58.658 34.615 0.00 0.00 37.17 3.66
6824 7544 4.283978 TGCCATTCAAATCTGATGGTTGTT 59.716 37.500 3.81 0.00 34.89 2.83
6848 7568 0.678048 GAAGCCGGCTGTGAAATCCT 60.678 55.000 33.60 11.20 0.00 3.24
6897 7617 1.615392 GCCCACTTCTCATGCTGTTTT 59.385 47.619 0.00 0.00 0.00 2.43
6905 7625 4.389890 TCTCATGCTGTTTTTGCACTTT 57.610 36.364 0.00 0.00 43.59 2.66
6991 7711 2.142356 ATCCGGGCACATGAATTTCA 57.858 45.000 0.00 0.75 0.00 2.69
7135 7862 3.861834 CGAGGTTTTCGTCAAAAGTCTG 58.138 45.455 0.00 0.00 44.27 3.51
7138 7865 3.442273 AGGTTTTCGTCAAAAGTCTGCAA 59.558 39.130 0.00 0.00 31.92 4.08
7181 7909 5.043248 AGAACAAAAAGAAGAAATGCCACG 58.957 37.500 0.00 0.00 0.00 4.94
7182 7910 3.716601 ACAAAAAGAAGAAATGCCACGG 58.283 40.909 0.00 0.00 0.00 4.94
7188 7916 3.690460 AGAAGAAATGCCACGGAAATCT 58.310 40.909 0.00 0.00 0.00 2.40
7202 7930 3.495100 CGGAAATCTGCAGGCCTAATAGT 60.495 47.826 15.13 0.00 0.00 2.12
7208 7936 4.740902 TCTGCAGGCCTAATAGTATCAGA 58.259 43.478 15.13 5.57 0.00 3.27
7216 7944 6.726299 AGGCCTAATAGTATCAGAACTGCATA 59.274 38.462 1.29 0.00 0.00 3.14
7273 8001 6.233434 TGATCTCTGACTAAACACATGCTTT 58.767 36.000 0.00 0.00 0.00 3.51
7274 8002 6.712095 TGATCTCTGACTAAACACATGCTTTT 59.288 34.615 0.00 0.00 0.00 2.27
7339 8067 2.287849 GCAGTGCTCTTTTGAGGGTTTC 60.288 50.000 8.18 0.00 46.30 2.78
7358 8106 1.409064 TCTCTCTGTGTGTGTGTGGTC 59.591 52.381 0.00 0.00 0.00 4.02
7359 8107 1.410517 CTCTCTGTGTGTGTGTGGTCT 59.589 52.381 0.00 0.00 0.00 3.85
7393 8148 8.443953 AGAAAAATATAGATGACTGAACAGCC 57.556 34.615 1.46 0.00 0.00 4.85
7589 8356 1.189524 TGCTAGTTGGCCTACGGTGT 61.190 55.000 11.80 0.00 0.00 4.16
7629 8396 5.119588 CACATGTTTTCATTTCTGATGTGCC 59.880 40.000 0.00 0.00 38.64 5.01
7630 8397 5.011329 ACATGTTTTCATTTCTGATGTGCCT 59.989 36.000 0.00 0.00 38.64 4.75
7631 8398 5.534207 TGTTTTCATTTCTGATGTGCCTT 57.466 34.783 0.00 0.00 0.00 4.35
7634 8404 6.479660 TGTTTTCATTTCTGATGTGCCTTTTC 59.520 34.615 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.188469 GCGATGGAGGCGGGTTTA 59.812 61.111 0.00 0.00 0.00 2.01
61 62 1.806542 TCGATTCCAAGCAAGTTGAGC 59.193 47.619 7.16 0.00 38.60 4.26
116 117 0.601841 ACCGCAACGACGAAAAGGAT 60.602 50.000 0.00 0.00 34.06 3.24
117 118 1.227321 ACCGCAACGACGAAAAGGA 60.227 52.632 0.00 0.00 34.06 3.36
129 131 1.080093 CTTCCTACTCGCACCGCAA 60.080 57.895 0.00 0.00 0.00 4.85
137 139 4.356979 TGGGAGGCTTCCTACTCG 57.643 61.111 14.33 0.00 43.49 4.18
156 158 1.161113 AGGCAGGTTGAGGTAGGGT 59.839 57.895 0.00 0.00 0.00 4.34
408 422 7.552687 CCTTGTGTAAAGAAATATAGGAGTGCA 59.447 37.037 0.00 0.00 0.00 4.57
409 423 7.769044 TCCTTGTGTAAAGAAATATAGGAGTGC 59.231 37.037 0.00 0.00 0.00 4.40
410 424 9.319143 CTCCTTGTGTAAAGAAATATAGGAGTG 57.681 37.037 0.00 0.00 40.71 3.51
419 433 8.637986 TGCAAAATACTCCTTGTGTAAAGAAAT 58.362 29.630 0.00 0.00 0.00 2.17
420 434 8.001881 TGCAAAATACTCCTTGTGTAAAGAAA 57.998 30.769 0.00 0.00 0.00 2.52
421 435 7.575414 TGCAAAATACTCCTTGTGTAAAGAA 57.425 32.000 0.00 0.00 0.00 2.52
422 436 7.759489 ATGCAAAATACTCCTTGTGTAAAGA 57.241 32.000 0.00 0.00 0.00 2.52
423 437 8.816640 AAATGCAAAATACTCCTTGTGTAAAG 57.183 30.769 0.00 0.00 0.00 1.85
424 438 9.606631 AAAAATGCAAAATACTCCTTGTGTAAA 57.393 25.926 0.00 0.00 0.00 2.01
425 439 9.039870 CAAAAATGCAAAATACTCCTTGTGTAA 57.960 29.630 0.00 0.00 0.00 2.41
426 440 7.655328 CCAAAAATGCAAAATACTCCTTGTGTA 59.345 33.333 0.00 0.00 0.00 2.90
427 441 6.482973 CCAAAAATGCAAAATACTCCTTGTGT 59.517 34.615 0.00 0.00 0.00 3.72
428 442 6.705381 TCCAAAAATGCAAAATACTCCTTGTG 59.295 34.615 0.00 0.00 0.00 3.33
429 443 6.825610 TCCAAAAATGCAAAATACTCCTTGT 58.174 32.000 0.00 0.00 0.00 3.16
430 444 6.369615 CCTCCAAAAATGCAAAATACTCCTTG 59.630 38.462 0.00 0.00 0.00 3.61
431 445 6.269769 TCCTCCAAAAATGCAAAATACTCCTT 59.730 34.615 0.00 0.00 0.00 3.36
432 446 5.779771 TCCTCCAAAAATGCAAAATACTCCT 59.220 36.000 0.00 0.00 0.00 3.69
433 447 6.036577 TCCTCCAAAAATGCAAAATACTCC 57.963 37.500 0.00 0.00 0.00 3.85
516 531 3.243670 CGAGACACTGCCTGACATGATAT 60.244 47.826 0.00 0.00 0.00 1.63
644 661 3.035942 CTGCAAACTTTTCTACGTGCAC 58.964 45.455 6.82 6.82 37.09 4.57
651 670 3.694072 ACACTGCACTGCAAACTTTTCTA 59.306 39.130 4.99 0.00 38.41 2.10
661 680 1.071299 CCACCTACACTGCACTGCA 59.929 57.895 3.11 3.11 36.92 4.41
691 710 9.900710 ATTTATTACTCGCATTGTTTGTTGTTA 57.099 25.926 0.00 0.00 0.00 2.41
719 738 4.453819 CCAGGACTGAATCTCAAGTTTCAC 59.546 45.833 0.00 0.00 32.30 3.18
789 808 4.735338 CGTTTCTTGCTTTTCTTTCTCACC 59.265 41.667 0.00 0.00 0.00 4.02
939 968 4.400251 CACGGGAGAGGAGGGGGT 62.400 72.222 0.00 0.00 0.00 4.95
1602 1748 2.809601 GCACGGAACAGCGACGAT 60.810 61.111 0.00 0.00 0.00 3.73
1609 1755 0.320247 AAGAGAGCAGCACGGAACAG 60.320 55.000 0.00 0.00 0.00 3.16
1711 1857 6.935741 TCTCGAATTCAGAAAAGGACAAAA 57.064 33.333 6.22 0.00 0.00 2.44
1768 1914 5.928264 CCAATTGGCCAAAACAAAAACAAAA 59.072 32.000 24.71 0.00 0.00 2.44
1769 1915 5.011023 ACCAATTGGCCAAAACAAAAACAAA 59.989 32.000 24.71 0.00 39.32 2.83
1770 1916 4.524328 ACCAATTGGCCAAAACAAAAACAA 59.476 33.333 24.71 0.00 39.32 2.83
1958 2104 0.890996 GCCAATGGCGGAATCCCTAG 60.891 60.000 9.14 0.00 39.62 3.02
2152 2298 4.722526 AGCCATGGCAATTAGGTGTATA 57.277 40.909 37.18 0.00 44.88 1.47
2153 2299 3.600448 AGCCATGGCAATTAGGTGTAT 57.400 42.857 37.18 10.31 44.88 2.29
2311 2494 3.240069 GAAAGCTAAGCATGCACTTGTG 58.760 45.455 21.98 5.45 0.00 3.33
2352 2535 6.710295 TGAAACAGCACAGTATCACTAACAAT 59.290 34.615 0.00 0.00 0.00 2.71
2416 2599 0.758734 AAAACTTTGGAAGGGCAGCC 59.241 50.000 1.26 1.26 0.00 4.85
2438 2621 1.817941 CCGGCCTATTGGTCAACGG 60.818 63.158 0.00 2.91 37.98 4.44
2453 2636 4.160635 GATCCAAACGCACGCCGG 62.161 66.667 0.00 0.00 42.52 6.13
2454 2637 2.749865 ATGATCCAAACGCACGCCG 61.750 57.895 0.00 0.00 44.21 6.46
2455 2638 1.226379 CATGATCCAAACGCACGCC 60.226 57.895 0.00 0.00 0.00 5.68
2456 2639 1.226379 CCATGATCCAAACGCACGC 60.226 57.895 0.00 0.00 0.00 5.34
2457 2640 1.226379 GCCATGATCCAAACGCACG 60.226 57.895 0.00 0.00 0.00 5.34
2458 2641 1.139520 GGCCATGATCCAAACGCAC 59.860 57.895 0.00 0.00 0.00 5.34
2510 2693 5.221342 GCTGGCTACTACAGAATCACATAGT 60.221 44.000 0.00 0.00 38.20 2.12
2537 2720 2.550699 ATTTGCCGCCAGGGATTCGA 62.551 55.000 0.00 0.00 37.83 3.71
2543 2726 2.362889 AGGAATTTGCCGCCAGGG 60.363 61.111 0.00 0.00 38.20 4.45
2591 2774 1.533711 GTGTCCATGCCAGCCCTAT 59.466 57.895 0.00 0.00 0.00 2.57
2606 2789 1.760480 GGGGCTGTTTGGTTGGTGT 60.760 57.895 0.00 0.00 0.00 4.16
2677 2860 7.934120 ACATCTTTAATGTCTATGTAAGGAGCC 59.066 37.037 0.00 0.00 0.00 4.70
2889 3072 8.547173 AGAGAGATGAACCTCACAGAAAATAAT 58.453 33.333 0.00 0.00 35.68 1.28
2921 3104 5.581085 GCAACCTAGTCGATTAGAACAATGT 59.419 40.000 15.91 2.03 0.00 2.71
2939 3122 1.067295 TCAGACCAATGGAGCAACCT 58.933 50.000 6.16 0.00 39.86 3.50
3035 3218 6.884295 TCCATCCCTATCAACAACAAAAGTAG 59.116 38.462 0.00 0.00 0.00 2.57
3189 3372 6.492772 GGAGGGAAAAGGATAAGAGATACGTA 59.507 42.308 0.00 0.00 0.00 3.57
3229 3412 4.440839 AACTGATCCCGAAAGCAAATTC 57.559 40.909 0.00 0.00 0.00 2.17
3256 3439 8.508800 TTTAATTTGTGTGCTATTAAACGTGG 57.491 30.769 0.00 0.00 32.01 4.94
3376 3559 1.443802 GCCTACAGTTGCTTGAGACC 58.556 55.000 0.00 0.00 0.00 3.85
3411 3594 7.624360 TGTATTCAATAACCCAAGTGATGAC 57.376 36.000 0.00 0.00 0.00 3.06
3515 3704 2.751259 TCACTTTCATCATCTGCTTGCC 59.249 45.455 0.00 0.00 0.00 4.52
3739 3928 9.034544 CCAAATAGTTTTTCTTCAACAGGAAAG 57.965 33.333 0.00 0.00 31.02 2.62
3946 4653 4.411869 TGATATCATACCCAAGCTTCACCA 59.588 41.667 0.00 0.00 0.00 4.17
4215 4927 1.532437 CATGACGAGAAAACTGCAGCA 59.468 47.619 15.27 0.00 0.00 4.41
4469 5185 5.562890 CGGAAACAATTCTTGGAGAACCTTC 60.563 44.000 0.00 0.00 37.00 3.46
4586 5302 8.918202 ACAAGAACAATATAACTGTGAAGGAA 57.082 30.769 0.00 0.00 0.00 3.36
4740 5456 5.030295 GTGAAGTGTGTCAAACTGTCAATG 58.970 41.667 0.00 0.00 0.00 2.82
4766 5482 2.916934 TGTAAGGTGGGTGAGGCTTAAT 59.083 45.455 0.00 0.00 0.00 1.40
4790 5506 1.985159 AGGTCATTCTACCCAAGTGCA 59.015 47.619 0.00 0.00 40.71 4.57
4947 5663 7.251994 AGTCGAGACTGTCAAATCTATAACAC 58.748 38.462 10.88 0.00 40.75 3.32
5154 5870 5.127031 AGCCATGTTAAAAATAATCGCCTGT 59.873 36.000 0.00 0.00 0.00 4.00
5342 6062 8.398878 TGTTCCGACAAGGTAAATAGATTTTT 57.601 30.769 0.00 0.00 41.99 1.94
5734 6454 5.435686 ACCTGCTCCAGTCAATATACAAA 57.564 39.130 0.00 0.00 0.00 2.83
5874 6594 5.988310 TTGTCAAAATCCATCAGCTTCAT 57.012 34.783 0.00 0.00 0.00 2.57
6092 6812 6.449635 TTGTGTGAGCAAAGAATTAACTGT 57.550 33.333 0.00 0.00 0.00 3.55
6134 6854 9.066892 TGTTCTTCTATGCCAATTTCCATATAC 57.933 33.333 0.00 0.00 0.00 1.47
6141 6861 5.653507 TGCATGTTCTTCTATGCCAATTTC 58.346 37.500 6.73 0.00 46.91 2.17
6305 7025 1.698506 ACGGCCTGAATAGAGGAGAG 58.301 55.000 0.00 0.00 34.69 3.20
6701 7421 5.103000 CGGATCGCTTATATTTCCACTAGG 58.897 45.833 0.00 0.00 0.00 3.02
6824 7544 2.047655 CACAGCCGGCTTCCGTTA 60.048 61.111 30.60 0.00 46.80 3.18
6848 7568 1.326328 TGCATAGCCAAACACAGCAA 58.674 45.000 0.00 0.00 0.00 3.91
6991 7711 9.545105 ACATGAATTCAACACATTTTTACATGT 57.455 25.926 13.09 2.69 37.93 3.21
7004 7724 5.850557 AGTTGGAACACATGAATTCAACA 57.149 34.783 13.09 0.91 39.29 3.33
7007 7727 4.099113 TGCAAGTTGGAACACATGAATTCA 59.901 37.500 11.26 11.26 39.29 2.57
7008 7728 4.619973 TGCAAGTTGGAACACATGAATTC 58.380 39.130 4.75 0.00 39.29 2.17
7054 7774 3.434319 GGCTGGTCACCATGCACG 61.434 66.667 17.00 0.00 32.24 5.34
7131 7858 2.798976 TGGTCAGCATTTTTGCAGAC 57.201 45.000 13.18 13.18 46.25 3.51
7167 7895 3.441572 CAGATTTCCGTGGCATTTCTTCT 59.558 43.478 0.00 0.00 0.00 2.85
7181 7909 4.092116 ACTATTAGGCCTGCAGATTTCC 57.908 45.455 17.99 10.53 0.00 3.13
7182 7910 6.467677 TGATACTATTAGGCCTGCAGATTTC 58.532 40.000 17.99 5.80 0.00 2.17
7188 7916 4.901849 AGTTCTGATACTATTAGGCCTGCA 59.098 41.667 17.99 1.23 0.00 4.41
7202 7930 8.534954 ACTTACCTAACTATGCAGTTCTGATA 57.465 34.615 3.84 0.00 44.04 2.15
7208 7936 4.941873 GGCAACTTACCTAACTATGCAGTT 59.058 41.667 0.00 0.00 46.77 3.16
7216 7944 2.224450 ACTTGCGGCAACTTACCTAACT 60.224 45.455 12.11 0.00 0.00 2.24
7273 8001 5.070446 CCTCACTACTGATTGCCCTACATAA 59.930 44.000 0.00 0.00 0.00 1.90
7274 8002 4.588951 CCTCACTACTGATTGCCCTACATA 59.411 45.833 0.00 0.00 0.00 2.29
7339 8067 1.410517 AGACCACACACACACAGAGAG 59.589 52.381 0.00 0.00 0.00 3.20
7393 8148 1.007734 CTGTTGCTGCAGCCAAGTG 60.008 57.895 34.64 17.27 41.18 3.16
7562 8321 4.156008 CGTAGGCCAACTAGCATTCTTTTT 59.844 41.667 5.01 0.00 30.77 1.94
7563 8322 3.689649 CGTAGGCCAACTAGCATTCTTTT 59.310 43.478 5.01 0.00 30.77 2.27
7564 8323 3.270877 CGTAGGCCAACTAGCATTCTTT 58.729 45.455 5.01 0.00 30.77 2.52
7565 8324 2.420129 CCGTAGGCCAACTAGCATTCTT 60.420 50.000 5.01 0.00 46.14 2.52
7589 8356 5.745312 ACATGTGTTTCTGGATAGAGACA 57.255 39.130 0.00 0.00 43.42 3.41


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

AutoCloner maintained by Alex Coulton.