Multiple sequence alignment - TraesCS5B01G476500

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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 TraesCS5B01G476500 chr5B 100.000 4292 0 0 1 4292 648995325 648999616 0.000000e+00 7926.0
1 TraesCS5B01G476500 chr5D 91.898 3715 201 51 640 4292 516636905 516640581 0.000000e+00 5101.0
2 TraesCS5B01G476500 chr5D 95.250 400 12 2 1 400 516611501 516611893 1.010000e-175 627.0
3 TraesCS5B01G476500 chr5D 84.658 365 35 4 237 599 516636035 516636380 1.140000e-90 344.0
4 TraesCS5B01G476500 chr5D 83.408 223 27 7 19 241 516613332 516613544 9.410000e-47 198.0
5 TraesCS5B01G476500 chr5D 82.716 81 14 0 1829 1909 9227677 9227597 5.950000e-09 73.1
6 TraesCS5B01G476500 chr5A 94.707 1927 75 9 2389 4292 644103658 644105580 0.000000e+00 2968.0
7 TraesCS5B01G476500 chr5A 90.581 1550 114 13 624 2154 644097336 644098872 0.000000e+00 2025.0
8 TraesCS5B01G476500 chr5A 86.129 620 57 17 1 620 644096666 644097256 3.620000e-180 641.0
9 TraesCS5B01G476500 chr5A 93.182 132 8 1 2248 2378 644103061 644103192 4.380000e-45 193.0
10 TraesCS5B01G476500 chr1B 72.874 435 84 26 1497 1910 9579398 9579819 7.540000e-23 119.0
11 TraesCS5B01G476500 chr1B 89.773 88 9 0 1103 1190 9489987 9490074 3.510000e-21 113.0
12 TraesCS5B01G476500 chr1D 89.773 88 9 0 1103 1190 7073664 7073751 3.510000e-21 113.0
13 TraesCS5B01G476500 chr1A 89.773 88 9 0 1103 1190 8665096 8665183 3.510000e-21 113.0
14 TraesCS5B01G476500 chr6B 84.615 65 7 2 1129 1190 687959396 687959460 1.290000e-05 62.1
15 TraesCS5B01G476500 chr6A 97.222 36 1 0 1131 1166 598926665 598926630 1.290000e-05 62.1
16 TraesCS5B01G476500 chr6A 96.970 33 1 0 1131 1163 598859354 598859386 6.000000e-04 56.5
17 TraesCS5B01G476500 chr6D 96.774 31 1 0 1136 1166 452485749 452485719 8.000000e-03 52.8


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 TraesCS5B01G476500 chr5B 648995325 648999616 4291 False 7926.0 7926 100.0000 1 4292 1 chr5B.!!$F1 4291
1 TraesCS5B01G476500 chr5D 516636035 516640581 4546 False 2722.5 5101 88.2780 237 4292 2 chr5D.!!$F2 4055
2 TraesCS5B01G476500 chr5D 516611501 516613544 2043 False 412.5 627 89.3290 1 400 2 chr5D.!!$F1 399
3 TraesCS5B01G476500 chr5A 644103061 644105580 2519 False 1580.5 2968 93.9445 2248 4292 2 chr5A.!!$F2 2044
4 TraesCS5B01G476500 chr5A 644096666 644098872 2206 False 1333.0 2025 88.3550 1 2154 2 chr5A.!!$F1 2153

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
386 387 0.458669 GACCATCAGCTGCCCAAATG 59.541 55.0 9.47 7.11 0.0 2.32 F
977 1811 0.601841 AACAAACGCCGGTAGTGAGG 60.602 55.0 1.90 0.31 0.0 3.86 F
1372 2231 0.868406 CACGAGCTTCTTCAACCACC 59.132 55.0 0.00 0.00 0.0 4.61 F
2290 3188 0.249489 GTTCACTGCTGACGTCCTGT 60.249 55.0 14.12 5.83 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 2765 0.535335 CGTAGCCTTGGGAGCACTTA 59.465 55.0 0.00 0.0 0.00 2.24 R
2004 2901 1.041447 GTAGCGGAGGGTGGCTAAGA 61.041 60.0 0.00 0.0 42.85 2.10 R
2394 3756 1.327303 TTGAAAGGTTGAAGGCGCAT 58.673 45.0 10.83 0.0 0.00 4.73 R
3597 5044 0.462047 GGCGAGTGTTACCATGGAGG 60.462 60.0 21.47 0.0 45.67 4.30 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
78 79 7.452880 AGAGAATACTGCTCTGAATAGCTAG 57.547 40.000 0.00 0.00 43.19 3.42
103 104 3.602390 ATTTGTTGTGTTTCTCCGACG 57.398 42.857 0.00 0.00 0.00 5.12
151 152 3.245087 TGTGCTAATGGTTACACCCACAT 60.245 43.478 0.00 0.00 37.50 3.21
196 197 7.056635 ACATTCCTAACCATGAGGACAATAAG 58.943 38.462 1.15 0.00 42.96 1.73
257 258 1.872952 TGCTTGAACACAAGGATGTCG 59.127 47.619 11.09 0.00 40.65 4.35
373 374 5.804639 TGGGCATTGTACATATAGACCATC 58.195 41.667 7.59 0.00 0.00 3.51
379 380 5.139435 TGTACATATAGACCATCAGCTGC 57.861 43.478 9.47 0.00 0.00 5.25
386 387 0.458669 GACCATCAGCTGCCCAAATG 59.541 55.000 9.47 7.11 0.00 2.32
403 404 4.513692 CCAAATGGATAAGCCGACGAATTA 59.486 41.667 0.00 0.00 40.66 1.40
418 421 6.739550 CCGACGAATTACCAAAATTAGTTGTC 59.260 38.462 0.00 0.00 29.86 3.18
434 437 2.060326 TGTCGAGTCATTCCGTTGTC 57.940 50.000 0.00 0.00 0.00 3.18
531 534 3.634568 TGGTTTCAATAACAAGTGGCG 57.365 42.857 0.00 0.00 0.00 5.69
532 535 2.294791 TGGTTTCAATAACAAGTGGCGG 59.705 45.455 0.00 0.00 0.00 6.13
533 536 2.324860 GTTTCAATAACAAGTGGCGGC 58.675 47.619 0.00 0.00 0.00 6.53
534 537 1.904287 TTCAATAACAAGTGGCGGCT 58.096 45.000 11.43 0.00 0.00 5.52
535 538 2.772077 TCAATAACAAGTGGCGGCTA 57.228 45.000 11.43 0.00 0.00 3.93
548 551 8.537016 ACAAGTGGCGGCTATATATAGATTAAA 58.463 33.333 21.65 3.04 32.05 1.52
573 576 3.625764 GCAAATATCAAAGGAGTGGCGTA 59.374 43.478 0.00 0.00 0.00 4.42
574 577 4.275936 GCAAATATCAAAGGAGTGGCGTAT 59.724 41.667 0.00 0.00 0.00 3.06
588 591 4.023792 AGTGGCGTATTCATGCACATATTG 60.024 41.667 0.00 0.00 38.53 1.90
589 592 4.024133 GTGGCGTATTCATGCACATATTGA 60.024 41.667 0.00 0.00 38.53 2.57
599 610 6.536447 TCATGCACATATTGAGGACACATAT 58.464 36.000 0.00 0.00 0.00 1.78
607 618 8.801299 ACATATTGAGGACACATATCTACTCTG 58.199 37.037 0.00 0.00 0.00 3.35
616 627 6.882656 ACACATATCTACTCTGAGCAAACAT 58.117 36.000 4.19 0.00 0.00 2.71
719 1475 9.825109 GGAGGGCTAATAATATTGAGAAGATAC 57.175 37.037 0.00 0.00 0.00 2.24
813 1577 5.618056 ATGGTTAAGAATATCAGCATGCG 57.382 39.130 13.01 7.64 34.76 4.73
814 1578 3.250762 TGGTTAAGAATATCAGCATGCGC 59.749 43.478 13.01 0.00 34.76 6.09
842 1606 8.592809 ACTTGATTGCACTAATTAATTTCCCAA 58.407 29.630 5.91 5.99 0.00 4.12
857 1623 9.752961 TTAATTTCCCAACAAAGTTAGTTAAGC 57.247 29.630 0.00 0.00 0.00 3.09
910 1743 3.084039 TGATGGAAGCAACTTGCCTAAG 58.916 45.455 10.25 0.00 46.52 2.18
912 1745 1.202927 TGGAAGCAACTTGCCTAAGCT 60.203 47.619 10.25 0.00 46.52 3.74
959 1793 5.673568 GCATCAGCGTGCTCTTGTATTTAAA 60.674 40.000 0.00 0.00 41.82 1.52
966 1800 5.164320 CGTGCTCTTGTATTTAAACAAACGC 60.164 40.000 0.00 0.00 38.81 4.84
970 1804 4.275443 TCTTGTATTTAAACAAACGCCGGT 59.725 37.500 1.90 0.00 38.81 5.28
975 1809 2.522836 TAAACAAACGCCGGTAGTGA 57.477 45.000 1.90 0.00 0.00 3.41
976 1810 1.223187 AAACAAACGCCGGTAGTGAG 58.777 50.000 1.90 3.17 0.00 3.51
977 1811 0.601841 AACAAACGCCGGTAGTGAGG 60.602 55.000 1.90 0.31 0.00 3.86
982 1816 2.412112 GCCGGTAGTGAGGCGTAG 59.588 66.667 1.90 0.00 44.22 3.51
1007 1863 5.779529 AGCAACTTCTCAACAATGTCAAT 57.220 34.783 0.00 0.00 0.00 2.57
1008 1864 6.882610 AGCAACTTCTCAACAATGTCAATA 57.117 33.333 0.00 0.00 0.00 1.90
1011 1867 5.536554 ACTTCTCAACAATGTCAATAGCG 57.463 39.130 0.00 0.00 0.00 4.26
1053 1909 1.200716 CTCCTACTGCCGTCGTTGTTA 59.799 52.381 0.00 0.00 0.00 2.41
1067 1923 2.358737 GTTAGCAGCCACCGCAGT 60.359 61.111 0.00 0.00 37.52 4.40
1194 2050 2.643933 TCGAGATCAACTGCACAGAG 57.356 50.000 4.31 0.00 0.00 3.35
1200 2056 3.560251 AACTGCACAGAGGCCGGT 61.560 61.111 1.90 0.00 0.00 5.28
1201 2057 3.832237 AACTGCACAGAGGCCGGTG 62.832 63.158 17.56 17.56 40.68 4.94
1250 2106 1.219124 CGTCCATCCAGGTGGTCAG 59.781 63.158 0.00 0.00 40.27 3.51
1259 2115 4.459089 GGTGGTCAGCCTCTCCGC 62.459 72.222 0.00 0.00 35.27 5.54
1309 2165 2.224606 CCATTAGGTGGCAGTGCTATG 58.775 52.381 16.11 3.45 42.12 2.23
1312 2168 2.691409 TAGGTGGCAGTGCTATGAAC 57.309 50.000 16.11 6.04 0.00 3.18
1339 2198 2.086869 TCTCCGACGGTAAAGTGGTAG 58.913 52.381 14.79 0.07 0.00 3.18
1348 2207 3.813166 CGGTAAAGTGGTAGGCAATATGG 59.187 47.826 0.00 0.00 0.00 2.74
1350 2209 5.442391 GGTAAAGTGGTAGGCAATATGGAA 58.558 41.667 0.00 0.00 0.00 3.53
1370 2229 1.412710 AGACACGAGCTTCTTCAACCA 59.587 47.619 0.00 0.00 0.00 3.67
1372 2231 0.868406 CACGAGCTTCTTCAACCACC 59.132 55.000 0.00 0.00 0.00 4.61
1388 2247 5.046591 TCAACCACCAGAAGAACATACCTAG 60.047 44.000 0.00 0.00 0.00 3.02
1390 2249 3.432326 CCACCAGAAGAACATACCTAGCC 60.432 52.174 0.00 0.00 0.00 3.93
1392 2251 3.844211 ACCAGAAGAACATACCTAGCCAA 59.156 43.478 0.00 0.00 0.00 4.52
1422 2281 1.200716 CGCATCTCCAACAAGCACAAT 59.799 47.619 0.00 0.00 0.00 2.71
1423 2282 2.419673 CGCATCTCCAACAAGCACAATA 59.580 45.455 0.00 0.00 0.00 1.90
1648 2541 1.547372 AGATGCCACAAATGCTCAACC 59.453 47.619 0.00 0.00 0.00 3.77
1767 2660 1.972660 GCCTTGACTGGGCTATCCGT 61.973 60.000 0.00 0.00 45.57 4.69
2004 2901 4.483243 CCACCACCGGCGCCTATT 62.483 66.667 26.68 4.98 0.00 1.73
2016 2913 0.759346 CGCCTATTCTTAGCCACCCT 59.241 55.000 0.00 0.00 0.00 4.34
2054 2951 1.014352 ACCGCAAGTTTGTCTCACAC 58.986 50.000 0.00 0.00 0.00 3.82
2136 3033 1.568504 TTCGGCCACTTCATCCTAGT 58.431 50.000 2.24 0.00 0.00 2.57
2160 3057 1.420514 CATGCATGTGGATCTCCTCCT 59.579 52.381 18.91 0.00 45.21 3.69
2166 3063 1.221523 TGTGGATCTCCTCCTATGCCT 59.778 52.381 0.00 0.00 45.21 4.75
2172 3069 0.769873 CTCCTCCTATGCCTGCCATT 59.230 55.000 0.00 0.00 35.34 3.16
2221 3118 1.269448 GGCATCTTGAAGAACCGCAAA 59.731 47.619 13.99 0.00 0.00 3.68
2237 3135 2.587522 GCAAACCAAGGTCTTCCTCTT 58.412 47.619 0.00 0.00 44.35 2.85
2243 3141 2.575532 CAAGGTCTTCCTCTTGCAACA 58.424 47.619 0.00 0.00 44.35 3.33
2290 3188 0.249489 GTTCACTGCTGACGTCCTGT 60.249 55.000 14.12 5.83 0.00 4.00
2296 3194 1.367840 GCTGACGTCCTGTTCTGGT 59.632 57.895 14.12 0.00 0.00 4.00
2321 3219 2.026822 ACCTGCACTCGATCCTCAATTT 60.027 45.455 0.00 0.00 0.00 1.82
2336 3243 7.257790 TCCTCAATTTGATCTTAGAACCTGA 57.742 36.000 0.00 0.00 0.00 3.86
2381 3288 9.123709 TCAGTATAAAATTCACATGTTTTTCGC 57.876 29.630 9.44 3.51 0.00 4.70
2412 3774 1.327303 AATGCGCCTTCAACCTTTCA 58.673 45.000 4.18 0.00 0.00 2.69
2417 3779 2.539688 GCGCCTTCAACCTTTCAAAAAG 59.460 45.455 0.00 0.00 0.00 2.27
2464 3828 1.825474 TGGGACAGTAAGACAGCTAGC 59.175 52.381 6.62 6.62 0.00 3.42
2529 3893 6.550843 CAGTTGACAATATGGCGTAAATTCA 58.449 36.000 0.00 0.00 0.00 2.57
2630 3994 1.077501 GTATCCTTGCTGGCAGCCA 60.078 57.895 34.58 24.31 41.51 4.75
2794 4228 7.807680 ACATCGATTTTCTCTTTTGTTAGACC 58.192 34.615 0.00 0.00 0.00 3.85
2901 4337 4.442706 TCGATCTCTTGCCAAAGGAATAC 58.557 43.478 0.00 0.00 33.90 1.89
3097 4534 4.624015 ACGTAAAGCAGTTGTTAGCACTA 58.376 39.130 0.00 0.00 0.00 2.74
3101 4538 4.884668 AAGCAGTTGTTAGCACTACCTA 57.115 40.909 0.00 0.00 29.60 3.08
3145 4592 4.001652 TGTGGCCAAAATTAACATGCATG 58.998 39.130 25.09 25.09 0.00 4.06
3181 4628 6.461640 TCTCTATGCATGATCATTGTAGGTG 58.538 40.000 10.16 0.00 0.00 4.00
3188 4635 6.153170 TGCATGATCATTGTAGGTGTCATTTT 59.847 34.615 5.16 0.00 0.00 1.82
3205 4652 5.532779 GTCATTTTGGGCTCCTCCTTATTAG 59.467 44.000 0.00 0.00 34.39 1.73
3245 4692 1.279271 GCTACTGAGGCTCCAAAGGAA 59.721 52.381 12.86 0.00 0.00 3.36
3289 4736 3.903530 AGAATGGAGGTTTGGTCCTTT 57.096 42.857 0.00 0.00 38.02 3.11
3398 4845 5.622233 GCTTTGGCAAAGTATACAAAGGGAG 60.622 44.000 33.45 10.91 45.95 4.30
3628 5075 4.810191 AACACTCGCCTCTCTAATTTCT 57.190 40.909 0.00 0.00 0.00 2.52
3741 5188 2.304470 TGTCAAGCCAGCCAACATACTA 59.696 45.455 0.00 0.00 0.00 1.82
3777 5224 5.151297 ACATGCCAAAAATCTCGGATTTT 57.849 34.783 14.87 14.87 33.12 1.82
3867 5314 0.107081 ACCCGATGTTCCGTGAAACA 59.893 50.000 0.00 0.00 42.92 2.83
3967 5414 5.349817 GTGTATGATGGAAATCATAGGCTCG 59.650 44.000 8.34 0.00 42.30 5.03
4083 5530 0.322277 AGATTGGCAGACTGGCTGTG 60.322 55.000 27.23 0.00 46.62 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 6.555315 GGAGAAACACAACAAATATGCCTAG 58.445 40.000 0.00 0.00 0.00 3.02
76 77 5.123186 CGGAGAAACACAACAAATATGCCTA 59.877 40.000 0.00 0.00 0.00 3.93
77 78 4.082787 CGGAGAAACACAACAAATATGCCT 60.083 41.667 0.00 0.00 0.00 4.75
78 79 4.083003 TCGGAGAAACACAACAAATATGCC 60.083 41.667 0.00 0.00 0.00 4.40
196 197 1.036707 CTACTACCTCTGGCTCTGGC 58.963 60.000 0.00 0.00 37.82 4.85
257 258 0.868406 CAAAAGGCTCTCGTGGTGAC 59.132 55.000 0.00 0.00 0.00 3.67
373 374 1.068127 GCTTATCCATTTGGGCAGCTG 59.932 52.381 10.11 10.11 36.21 4.24
379 380 0.944386 CGTCGGCTTATCCATTTGGG 59.056 55.000 0.00 0.00 35.41 4.12
386 387 3.102052 TGGTAATTCGTCGGCTTATCC 57.898 47.619 0.00 0.00 0.00 2.59
403 404 6.072673 GGAATGACTCGACAACTAATTTTGGT 60.073 38.462 0.00 0.00 0.00 3.67
418 421 1.068474 GGTGACAACGGAATGACTCG 58.932 55.000 0.00 0.00 0.00 4.18
521 524 5.995565 TCTATATATAGCCGCCACTTGTT 57.004 39.130 14.03 0.00 0.00 2.83
548 551 4.440525 CGCCACTCCTTTGATATTTGCATT 60.441 41.667 0.00 0.00 0.00 3.56
559 562 2.223340 GCATGAATACGCCACTCCTTTG 60.223 50.000 0.00 0.00 0.00 2.77
568 571 4.378770 CCTCAATATGTGCATGAATACGCC 60.379 45.833 0.00 0.00 0.00 5.68
573 576 5.195185 TGTGTCCTCAATATGTGCATGAAT 58.805 37.500 0.00 0.00 0.00 2.57
574 577 4.587891 TGTGTCCTCAATATGTGCATGAA 58.412 39.130 0.00 0.00 0.00 2.57
588 591 4.824537 TGCTCAGAGTAGATATGTGTCCTC 59.175 45.833 0.00 0.00 0.00 3.71
589 592 4.797743 TGCTCAGAGTAGATATGTGTCCT 58.202 43.478 0.00 0.00 0.00 3.85
599 610 6.291377 ACTTTTGATGTTTGCTCAGAGTAGA 58.709 36.000 0.00 0.00 0.00 2.59
607 618 4.722194 TGCGATACTTTTGATGTTTGCTC 58.278 39.130 0.00 0.00 0.00 4.26
616 627 5.062934 CGACCTTACATTGCGATACTTTTGA 59.937 40.000 0.00 0.00 0.00 2.69
719 1475 2.361610 GCACCACCCCATGACAGG 60.362 66.667 0.00 0.00 0.00 4.00
777 1541 6.061022 TCTTAACCATTCCACAGCTATTGA 57.939 37.500 0.00 0.00 0.00 2.57
814 1578 8.872845 GGGAAATTAATTAGTGCAATCAAGTTG 58.127 33.333 0.01 0.00 40.90 3.16
842 1606 5.063880 CCTCACCAGCTTAACTAACTTTGT 58.936 41.667 0.00 0.00 0.00 2.83
857 1623 4.087892 CCAGGCCGACCTCACCAG 62.088 72.222 0.00 0.00 46.34 4.00
943 1777 5.116528 GGCGTTTGTTTAAATACAAGAGCAC 59.883 40.000 16.49 4.46 40.62 4.40
959 1793 1.005394 CCTCACTACCGGCGTTTGT 60.005 57.895 6.01 0.00 0.00 2.83
966 1800 1.940883 TTGCTACGCCTCACTACCGG 61.941 60.000 0.00 0.00 0.00 5.28
970 1804 0.606096 TTGCTTGCTACGCCTCACTA 59.394 50.000 0.00 0.00 0.00 2.74
975 1809 0.035458 AGAAGTTGCTTGCTACGCCT 59.965 50.000 2.03 1.40 0.00 5.52
976 1810 0.444260 GAGAAGTTGCTTGCTACGCC 59.556 55.000 2.03 0.00 0.00 5.68
977 1811 1.148310 TGAGAAGTTGCTTGCTACGC 58.852 50.000 2.03 0.00 0.00 4.42
979 1813 4.552166 TTGTTGAGAAGTTGCTTGCTAC 57.448 40.909 0.00 0.00 0.00 3.58
980 1814 4.580167 ACATTGTTGAGAAGTTGCTTGCTA 59.420 37.500 0.00 0.00 0.00 3.49
982 1816 3.709987 ACATTGTTGAGAAGTTGCTTGC 58.290 40.909 0.00 0.00 0.00 4.01
983 1817 4.923893 TGACATTGTTGAGAAGTTGCTTG 58.076 39.130 0.00 0.00 0.00 4.01
984 1818 5.581126 TTGACATTGTTGAGAAGTTGCTT 57.419 34.783 0.00 0.00 0.00 3.91
985 1819 5.779529 ATTGACATTGTTGAGAAGTTGCT 57.220 34.783 0.00 0.00 0.00 3.91
986 1820 5.570589 GCTATTGACATTGTTGAGAAGTTGC 59.429 40.000 0.00 0.00 0.00 4.17
987 1821 5.791974 CGCTATTGACATTGTTGAGAAGTTG 59.208 40.000 0.00 0.00 0.00 3.16
988 1822 5.106555 CCGCTATTGACATTGTTGAGAAGTT 60.107 40.000 0.00 0.00 0.00 2.66
992 1848 2.677836 GCCGCTATTGACATTGTTGAGA 59.322 45.455 0.00 0.00 0.00 3.27
993 1849 2.419673 TGCCGCTATTGACATTGTTGAG 59.580 45.455 0.00 0.00 0.00 3.02
1166 2022 1.902508 AGTTGATCTCGAAGCCCTTGA 59.097 47.619 0.00 0.00 0.00 3.02
1222 2078 1.449601 GGATGGACGTGTTGGCGAT 60.450 57.895 0.00 0.00 35.59 4.58
1250 2106 4.593864 GTGGATCGGCGGAGAGGC 62.594 72.222 7.21 0.00 42.76 4.70
1259 2115 2.494918 GTGACTCGGGTGGATCGG 59.505 66.667 0.00 0.00 0.00 4.18
1339 2198 1.599542 GCTCGTGTCTTCCATATTGCC 59.400 52.381 0.00 0.00 0.00 4.52
1348 2207 2.476997 GGTTGAAGAAGCTCGTGTCTTC 59.523 50.000 15.91 15.91 46.60 2.87
1350 2209 1.412710 TGGTTGAAGAAGCTCGTGTCT 59.587 47.619 0.00 0.00 0.00 3.41
1370 2229 3.450904 TGGCTAGGTATGTTCTTCTGGT 58.549 45.455 0.00 0.00 0.00 4.00
1372 2231 4.446371 CCTTGGCTAGGTATGTTCTTCTG 58.554 47.826 6.84 0.00 39.39 3.02
1388 2247 0.804989 GATGCGGTATATGCCTTGGC 59.195 55.000 8.32 4.43 0.00 4.52
1390 2249 2.289631 TGGAGATGCGGTATATGCCTTG 60.290 50.000 8.32 0.00 0.00 3.61
1392 2251 1.644509 TGGAGATGCGGTATATGCCT 58.355 50.000 8.32 0.00 0.00 4.75
1396 2255 3.181455 TGCTTGTTGGAGATGCGGTATAT 60.181 43.478 0.00 0.00 0.00 0.86
1422 2281 0.752009 AGCCGAGGACGAAGAGCATA 60.752 55.000 0.00 0.00 42.66 3.14
1423 2282 2.055042 AGCCGAGGACGAAGAGCAT 61.055 57.895 0.00 0.00 42.66 3.79
1614 2507 4.019411 TGTGGCATCTCTTTCCTGATGTTA 60.019 41.667 0.00 0.00 41.33 2.41
1648 2541 2.167219 CGTAGTCGCATGGGCTGTG 61.167 63.158 4.59 0.16 38.10 3.66
1767 2660 3.430862 GCGCAGGACGGCATTTCA 61.431 61.111 0.30 0.00 43.93 2.69
1872 2765 0.535335 CGTAGCCTTGGGAGCACTTA 59.465 55.000 0.00 0.00 0.00 2.24
1902 2795 1.683790 CGCTTTCGCCGACAAGGTAG 61.684 60.000 9.80 0.00 43.70 3.18
2004 2901 1.041447 GTAGCGGAGGGTGGCTAAGA 61.041 60.000 0.00 0.00 42.85 2.10
2016 2913 2.058125 TTTGCACTTGGGGTAGCGGA 62.058 55.000 0.00 0.00 0.00 5.54
2043 2940 1.134220 GGTGGTGGAGTGTGAGACAAA 60.134 52.381 0.00 0.00 0.00 2.83
2054 2951 4.096003 AATCCGGCGGTGGTGGAG 62.096 66.667 27.32 0.00 34.75 3.86
2160 3057 1.776667 AGAAGGCTAATGGCAGGCATA 59.223 47.619 10.42 0.00 43.32 3.14
2237 3135 2.618241 GTGTCTGGTTGAAGATGTTGCA 59.382 45.455 0.00 0.00 0.00 4.08
2243 3141 2.887152 GCAAAGGTGTCTGGTTGAAGAT 59.113 45.455 0.00 0.00 0.00 2.40
2321 3219 4.890158 TTGCACTCAGGTTCTAAGATCA 57.110 40.909 0.00 0.00 0.00 2.92
2336 3243 3.682696 TGATGATGAGAAGCTTTGCACT 58.317 40.909 0.00 0.00 0.00 4.40
2394 3756 1.327303 TTGAAAGGTTGAAGGCGCAT 58.673 45.000 10.83 0.00 0.00 4.73
2464 3828 9.734620 TTTTAGATATTCTTTTGATCCATTGCG 57.265 29.630 0.00 0.00 0.00 4.85
2529 3893 4.367386 GTGTACACCACTAGTTATCGCT 57.633 45.455 15.42 0.00 41.11 4.93
2623 3987 1.789078 CGCACATATTCCTGGCTGCC 61.789 60.000 12.87 12.87 0.00 4.85
2630 3994 2.967362 TCGTTGTTCGCACATATTCCT 58.033 42.857 0.00 0.00 39.67 3.36
2635 3999 2.442212 TCCTTCGTTGTTCGCACATA 57.558 45.000 0.00 0.00 39.67 2.29
2774 4138 7.230712 TCCCTTGGTCTAACAAAAGAGAAAATC 59.769 37.037 0.00 0.00 0.00 2.17
2787 4219 5.294552 CGAATGAAATCTCCCTTGGTCTAAC 59.705 44.000 0.00 0.00 0.00 2.34
2789 4221 4.469945 ACGAATGAAATCTCCCTTGGTCTA 59.530 41.667 0.00 0.00 0.00 2.59
2790 4222 3.264450 ACGAATGAAATCTCCCTTGGTCT 59.736 43.478 0.00 0.00 0.00 3.85
2794 4228 2.098117 GCCACGAATGAAATCTCCCTTG 59.902 50.000 0.00 0.00 0.00 3.61
2832 4266 6.043938 AGTCCCTTATTCCAGTTAGACACAAA 59.956 38.462 0.00 0.00 0.00 2.83
2839 4273 9.681062 TGAAAATAAGTCCCTTATTCCAGTTAG 57.319 33.333 9.09 0.00 43.27 2.34
2949 4386 6.252036 GCATTCGCAATGAAACTATTGAAG 57.748 37.500 11.52 0.00 41.46 3.02
2975 4412 6.313658 TGGTATATATGTGAATTGCGCATCTC 59.686 38.462 12.75 11.84 44.07 2.75
2982 4419 9.184062 CAAATGTGTGGTATATATGTGAATTGC 57.816 33.333 0.00 0.00 0.00 3.56
3097 4534 6.900194 ACATAGCAATACAAAGTGGATAGGT 58.100 36.000 0.00 0.00 0.00 3.08
3101 4538 7.315142 CACAAACATAGCAATACAAAGTGGAT 58.685 34.615 0.00 0.00 0.00 3.41
3181 4628 2.222227 AAGGAGGAGCCCAAAATGAC 57.778 50.000 0.00 0.00 37.37 3.06
3188 4635 3.460825 ACAACTAATAAGGAGGAGCCCA 58.539 45.455 0.00 0.00 37.37 5.36
3205 4652 2.409879 GCGTCGAAAGTAGAGCAACAAC 60.410 50.000 0.00 0.00 0.00 3.32
3597 5044 0.462047 GGCGAGTGTTACCATGGAGG 60.462 60.000 21.47 0.00 45.67 4.30
3628 5075 1.834188 TCCAGTCGCATGTCTAGTGA 58.166 50.000 0.00 0.00 0.00 3.41
3741 5188 9.729281 ATTTTTGGCATGTTCTTTTCATCTAAT 57.271 25.926 0.00 0.00 0.00 1.73
3777 5224 4.610605 TGTAAGAAACTTCGATGTCCCA 57.389 40.909 4.21 0.00 0.00 4.37
3867 5314 6.174720 TCACTCTTCTGTGTTAATTGTCCT 57.825 37.500 0.00 0.00 38.90 3.85
3967 5414 9.979270 CTGATAAACATCACAGAAATCAACTAC 57.021 33.333 0.00 0.00 32.90 2.73


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

AutoCloner maintained by Alex Coulton.