Multiple sequence alignment - TraesCS3A01G438900

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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 TraesCS3A01G438900 chr3A 100.000 3248 0 0 1 3248 681746810 681750057 0.000000e+00 5999
1 TraesCS3A01G438900 chr3D 86.306 3403 203 98 3 3248 545338514 545341810 0.000000e+00 3459
2 TraesCS3A01G438900 chr3B 86.785 2868 193 81 477 3248 721493134 721495911 0.000000e+00 3025
3 TraesCS3A01G438900 chr3B 86.580 462 35 13 3 459 721492644 721493083 4.870000e-133 484


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 TraesCS3A01G438900 chr3A 681746810 681750057 3247 False 5999.0 5999 100.0000 1 3248 1 chr3A.!!$F1 3247
1 TraesCS3A01G438900 chr3D 545338514 545341810 3296 False 3459.0 3459 86.3060 3 3248 1 chr3D.!!$F1 3245
2 TraesCS3A01G438900 chr3B 721492644 721495911 3267 False 1754.5 3025 86.6825 3 3248 2 chr3B.!!$F1 3245

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
651 740 0.51382 GGAATTTCGTTTCGACGGCA 59.486 50.0 0.0 0.0 34.89 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2354 2520 0.25064 CTGCTTTCTCTGCACCACCT 60.251 55.0 0.0 0.0 36.37 4.0 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
48 49 3.134127 GCACCCATGGACGAAGGC 61.134 66.667 15.22 3.40 0.00 4.35
52 56 2.046023 CCATGGACGAAGGCAGCA 60.046 61.111 5.56 0.00 0.00 4.41
53 57 2.110967 CCATGGACGAAGGCAGCAG 61.111 63.158 5.56 0.00 0.00 4.24
290 327 1.896220 TGCATTTGACTCCGAAAGCT 58.104 45.000 0.00 0.00 32.97 3.74
296 333 0.601046 TGACTCCGAAAGCTGCTGTG 60.601 55.000 1.35 0.00 0.00 3.66
346 383 2.741985 CGGCGCACTCATCACCAA 60.742 61.111 10.83 0.00 0.00 3.67
347 384 2.324330 CGGCGCACTCATCACCAAA 61.324 57.895 10.83 0.00 0.00 3.28
348 385 1.210155 GGCGCACTCATCACCAAAC 59.790 57.895 10.83 0.00 0.00 2.93
349 386 1.154413 GCGCACTCATCACCAAACG 60.154 57.895 0.30 0.00 0.00 3.60
350 387 1.841663 GCGCACTCATCACCAAACGT 61.842 55.000 0.30 0.00 0.00 3.99
355 392 3.849645 GCACTCATCACCAAACGTTTCAG 60.850 47.826 11.37 8.29 0.00 3.02
362 399 1.574428 CAAACGTTTCAGCCCGGAG 59.426 57.895 11.37 0.00 0.00 4.63
376 413 2.266055 GGAGGGTGAACTGGCGAG 59.734 66.667 0.00 0.00 0.00 5.03
388 425 2.906354 ACTGGCGAGGTAATTAAGCTG 58.094 47.619 0.00 0.00 35.60 4.24
392 429 2.872858 GGCGAGGTAATTAAGCTGGAAG 59.127 50.000 0.00 0.00 35.60 3.46
394 431 2.872858 CGAGGTAATTAAGCTGGAAGGC 59.127 50.000 0.00 0.00 35.60 4.35
400 437 1.538047 TTAAGCTGGAAGGCTGCTTG 58.462 50.000 17.25 1.13 45.21 4.01
402 439 1.177256 AAGCTGGAAGGCTGCTTGTG 61.177 55.000 8.80 0.00 44.16 3.33
429 466 1.369091 CCATCCGTCTCTTTTGGGCG 61.369 60.000 0.00 0.00 0.00 6.13
476 528 1.817209 GCTCCGATTCCTTCTCCGT 59.183 57.895 0.00 0.00 0.00 4.69
477 529 1.030457 GCTCCGATTCCTTCTCCGTA 58.970 55.000 0.00 0.00 0.00 4.02
479 531 2.299521 CTCCGATTCCTTCTCCGTAGT 58.700 52.381 0.00 0.00 0.00 2.73
480 532 3.474600 CTCCGATTCCTTCTCCGTAGTA 58.525 50.000 0.00 0.00 0.00 1.82
483 535 4.706476 TCCGATTCCTTCTCCGTAGTAAAA 59.294 41.667 0.00 0.00 0.00 1.52
484 536 5.185635 TCCGATTCCTTCTCCGTAGTAAAAA 59.814 40.000 0.00 0.00 0.00 1.94
508 579 5.547181 AGTAAGCTCTTAAATTGAACGCC 57.453 39.130 0.00 0.00 0.00 5.68
530 601 1.205460 AATCCAAGGTAGGTGGCCGT 61.205 55.000 0.00 0.00 35.99 5.68
531 602 1.623542 ATCCAAGGTAGGTGGCCGTC 61.624 60.000 0.00 0.00 35.99 4.79
543 623 3.192922 GCCGTCGATTCCCCGTTG 61.193 66.667 0.00 0.00 0.00 4.10
599 683 1.298014 CTCCCTCCTCCAGCACAAC 59.702 63.158 0.00 0.00 0.00 3.32
607 691 3.565307 TCCTCCAGCACAACAGAAAAAT 58.435 40.909 0.00 0.00 0.00 1.82
608 692 3.318839 TCCTCCAGCACAACAGAAAAATG 59.681 43.478 0.00 0.00 0.00 2.32
609 693 3.553508 CCTCCAGCACAACAGAAAAATGG 60.554 47.826 0.00 0.00 0.00 3.16
613 697 4.874966 CCAGCACAACAGAAAAATGGAAAA 59.125 37.500 0.00 0.00 0.00 2.29
628 712 2.578021 TGGAAAAGAAGGGAGGAGATGG 59.422 50.000 0.00 0.00 0.00 3.51
650 739 0.794473 AGGAATTTCGTTTCGACGGC 59.206 50.000 0.00 0.00 34.89 5.68
651 740 0.513820 GGAATTTCGTTTCGACGGCA 59.486 50.000 0.00 0.00 34.89 5.69
653 742 0.515564 AATTTCGTTTCGACGGCAGG 59.484 50.000 0.00 0.00 34.89 4.85
654 743 1.296056 ATTTCGTTTCGACGGCAGGG 61.296 55.000 0.00 0.00 34.89 4.45
667 756 1.596477 GCAGGGCGGCATAGAGAAG 60.596 63.158 12.47 0.00 0.00 2.85
713 802 2.145905 GGCGCGCACGAAAAAGATG 61.146 57.895 34.42 0.00 43.93 2.90
715 804 2.145905 CGCGCACGAAAAAGATGGC 61.146 57.895 8.75 0.00 43.93 4.40
772 876 1.612395 GGAGACAGGTGCAGAGGGAG 61.612 65.000 0.00 0.00 0.00 4.30
773 877 1.611851 AGACAGGTGCAGAGGGAGG 60.612 63.158 0.00 0.00 0.00 4.30
774 878 2.608988 ACAGGTGCAGAGGGAGGG 60.609 66.667 0.00 0.00 0.00 4.30
775 879 2.284921 CAGGTGCAGAGGGAGGGA 60.285 66.667 0.00 0.00 0.00 4.20
776 880 2.040278 AGGTGCAGAGGGAGGGAG 59.960 66.667 0.00 0.00 0.00 4.30
777 881 3.086600 GGTGCAGAGGGAGGGAGG 61.087 72.222 0.00 0.00 0.00 4.30
778 882 3.086600 GTGCAGAGGGAGGGAGGG 61.087 72.222 0.00 0.00 0.00 4.30
779 883 3.615811 TGCAGAGGGAGGGAGGGT 61.616 66.667 0.00 0.00 0.00 4.34
896 1006 1.325476 GCTTGATGGAAAGGGCAGGG 61.325 60.000 0.00 0.00 0.00 4.45
897 1007 1.305213 TTGATGGAAAGGGCAGGGC 60.305 57.895 0.00 0.00 0.00 5.19
898 1008 2.091640 TTGATGGAAAGGGCAGGGCA 62.092 55.000 0.00 0.00 0.00 5.36
899 1009 1.305213 GATGGAAAGGGCAGGGCAA 60.305 57.895 0.00 0.00 0.00 4.52
900 1010 1.305549 ATGGAAAGGGCAGGGCAAG 60.306 57.895 0.00 0.00 0.00 4.01
956 1066 2.589442 TGTTTCACGACACCGGCC 60.589 61.111 0.00 0.00 40.78 6.13
1040 1163 1.173043 CGAGCTCAACCACTCTCTCT 58.827 55.000 15.40 0.00 0.00 3.10
1041 1164 1.132262 CGAGCTCAACCACTCTCTCTC 59.868 57.143 15.40 0.00 0.00 3.20
1042 1165 2.446435 GAGCTCAACCACTCTCTCTCT 58.554 52.381 9.40 0.00 0.00 3.10
1043 1166 2.423538 GAGCTCAACCACTCTCTCTCTC 59.576 54.545 9.40 0.00 0.00 3.20
1044 1167 2.041620 AGCTCAACCACTCTCTCTCTCT 59.958 50.000 0.00 0.00 0.00 3.10
1045 1168 2.423538 GCTCAACCACTCTCTCTCTCTC 59.576 54.545 0.00 0.00 0.00 3.20
1046 1169 3.873801 GCTCAACCACTCTCTCTCTCTCT 60.874 52.174 0.00 0.00 0.00 3.10
1047 1170 3.941483 CTCAACCACTCTCTCTCTCTCTC 59.059 52.174 0.00 0.00 0.00 3.20
1053 1176 5.104900 ACCACTCTCTCTCTCTCTCTTCTAC 60.105 48.000 0.00 0.00 0.00 2.59
1059 1182 5.277250 TCTCTCTCTCTCTTCTACCTCTGA 58.723 45.833 0.00 0.00 0.00 3.27
1093 1216 4.357947 GGGCGAGCGAGTGTGTGA 62.358 66.667 0.00 0.00 0.00 3.58
1094 1217 2.807045 GGCGAGCGAGTGTGTGAG 60.807 66.667 0.00 0.00 0.00 3.51
1095 1218 2.049985 GCGAGCGAGTGTGTGAGT 60.050 61.111 0.00 0.00 0.00 3.41
1118 1241 0.801251 GTCTGACTTGCATGTGAGCC 59.199 55.000 13.32 0.00 0.00 4.70
1146 1277 4.101448 GAGCACACGGCCCATCCT 62.101 66.667 0.00 0.00 46.50 3.24
1201 1332 2.316108 CTTGCTTAGTTGGGTTGGGTT 58.684 47.619 0.00 0.00 0.00 4.11
1202 1333 1.698506 TGCTTAGTTGGGTTGGGTTG 58.301 50.000 0.00 0.00 0.00 3.77
1203 1334 0.966179 GCTTAGTTGGGTTGGGTTGG 59.034 55.000 0.00 0.00 0.00 3.77
1204 1335 1.627864 CTTAGTTGGGTTGGGTTGGG 58.372 55.000 0.00 0.00 0.00 4.12
1205 1336 0.935194 TTAGTTGGGTTGGGTTGGGT 59.065 50.000 0.00 0.00 0.00 4.51
1206 1337 0.935194 TAGTTGGGTTGGGTTGGGTT 59.065 50.000 0.00 0.00 0.00 4.11
1207 1338 0.689412 AGTTGGGTTGGGTTGGGTTG 60.689 55.000 0.00 0.00 0.00 3.77
1208 1339 0.978667 GTTGGGTTGGGTTGGGTTGT 60.979 55.000 0.00 0.00 0.00 3.32
1209 1340 0.978146 TTGGGTTGGGTTGGGTTGTG 60.978 55.000 0.00 0.00 0.00 3.33
1222 1357 1.139226 GGTTGTGCTTTGTGTGTGCG 61.139 55.000 0.00 0.00 0.00 5.34
1466 1601 1.985447 TACGCTCCACTTACTCGCCG 61.985 60.000 0.00 0.00 0.00 6.46
1489 1624 2.743928 CTGACCAACGGAGCTGCC 60.744 66.667 0.00 0.00 0.00 4.85
1713 1856 4.069232 CTCGTCTTCTGCCGCCCA 62.069 66.667 0.00 0.00 0.00 5.36
1755 1898 2.167219 CATGCACGAGTACCGCCTG 61.167 63.158 0.00 0.00 43.32 4.85
1962 2111 2.143419 GGGCATGGAGGAGGACGAT 61.143 63.158 0.00 0.00 0.00 3.73
1977 2126 0.753479 ACGATGATGAGACCGCCTCT 60.753 55.000 0.00 0.00 42.44 3.69
1980 2129 2.605823 CGATGATGAGACCGCCTCTAAC 60.606 54.545 4.98 0.00 42.44 2.34
1981 2130 1.112113 TGATGAGACCGCCTCTAACC 58.888 55.000 4.98 0.00 42.44 2.85
1982 2131 1.342076 TGATGAGACCGCCTCTAACCT 60.342 52.381 4.98 0.00 42.44 3.50
1984 2133 0.970937 TGAGACCGCCTCTAACCTGG 60.971 60.000 0.00 0.00 42.44 4.45
2055 2204 5.826643 TGTAATTTTCTAATGAGTGCCCCT 58.173 37.500 0.00 0.00 0.00 4.79
2065 2214 2.432444 TGAGTGCCCCTTTAATTCGTG 58.568 47.619 0.00 0.00 0.00 4.35
2070 2219 2.241176 TGCCCCTTTAATTCGTGGATCT 59.759 45.455 0.00 0.00 0.00 2.75
2083 2232 3.123804 CGTGGATCTGCTAATGTGGTAC 58.876 50.000 0.00 0.00 0.00 3.34
2084 2233 3.181475 CGTGGATCTGCTAATGTGGTACT 60.181 47.826 0.00 0.00 0.00 2.73
2086 2235 5.533482 GTGGATCTGCTAATGTGGTACTAG 58.467 45.833 0.00 0.00 0.00 2.57
2088 2237 5.302059 TGGATCTGCTAATGTGGTACTAGTC 59.698 44.000 0.00 0.00 0.00 2.59
2089 2238 5.279056 GGATCTGCTAATGTGGTACTAGTCC 60.279 48.000 0.00 1.20 0.00 3.85
2090 2239 3.630769 TCTGCTAATGTGGTACTAGTCCG 59.369 47.826 0.00 0.00 0.00 4.79
2091 2240 3.359033 TGCTAATGTGGTACTAGTCCGT 58.641 45.455 0.00 0.00 0.00 4.69
2092 2241 4.525996 TGCTAATGTGGTACTAGTCCGTA 58.474 43.478 0.00 0.00 0.00 4.02
2093 2242 4.577693 TGCTAATGTGGTACTAGTCCGTAG 59.422 45.833 0.00 3.52 34.52 3.51
2094 2243 4.578105 GCTAATGTGGTACTAGTCCGTAGT 59.422 45.833 0.00 0.00 44.69 2.73
2095 2244 5.760253 GCTAATGTGGTACTAGTCCGTAGTA 59.240 44.000 0.00 0.00 42.40 1.82
2096 2245 6.073331 GCTAATGTGGTACTAGTCCGTAGTAG 60.073 46.154 0.00 7.87 43.61 2.57
2100 2249 3.876242 GTACTAGTCCGTAGTAGCAGC 57.124 52.381 0.00 0.00 43.61 5.25
2116 2265 3.726607 AGCAGCAGTAGTAATCATCAGC 58.273 45.455 0.00 0.00 0.00 4.26
2141 2290 5.048013 CCCAACTTATCAGGAGAAACAAACC 60.048 44.000 0.00 0.00 0.00 3.27
2213 2362 1.610363 TTGACGAGTGAGCTGAGACT 58.390 50.000 0.00 0.00 0.00 3.24
2250 2401 6.638468 GTGAATCAAAGAGTTCATGTTCCAAC 59.362 38.462 0.00 0.00 36.79 3.77
2258 2409 7.272037 AGAGTTCATGTTCCAACGTTAAATT 57.728 32.000 0.00 0.00 0.00 1.82
2300 2463 7.059945 GTGAATTTCAGCTTCTTGTACAAATCG 59.940 37.037 10.03 0.00 0.00 3.34
2350 2513 5.673337 CTGCAAACAGCTACAGTAGAAAA 57.327 39.130 12.15 0.00 45.94 2.29
2351 2514 5.418310 TGCAAACAGCTACAGTAGAAAAC 57.582 39.130 12.15 0.00 45.94 2.43
2354 2520 5.236478 GCAAACAGCTACAGTAGAAAACAGA 59.764 40.000 12.15 0.00 41.15 3.41
2357 2523 4.589374 ACAGCTACAGTAGAAAACAGAGGT 59.411 41.667 12.15 0.00 0.00 3.85
2360 2526 4.262506 GCTACAGTAGAAAACAGAGGTGGT 60.263 45.833 12.15 0.00 0.00 4.16
2547 2718 3.004944 GGATACTCGAATCCACTCAGACC 59.995 52.174 10.68 0.00 44.26 3.85
2662 2834 2.772287 CAAGAGGAATAGGAATCCCGC 58.228 52.381 0.00 0.00 37.71 6.13
2664 2836 0.037232 GAGGAATAGGAATCCCGCCG 60.037 60.000 0.00 0.00 37.71 6.46
2666 2838 1.752833 GAATAGGAATCCCGCCGGT 59.247 57.895 1.90 0.00 37.58 5.28
2698 2883 1.347378 ACAATTTTGCTTCCGGCCATT 59.653 42.857 2.24 0.00 40.92 3.16
2699 2884 1.733360 CAATTTTGCTTCCGGCCATTG 59.267 47.619 2.24 0.00 40.92 2.82
2700 2885 0.391528 ATTTTGCTTCCGGCCATTGC 60.392 50.000 2.24 1.33 40.92 3.56
2718 2903 3.918220 CGCTTCAGCCGCATCGAC 61.918 66.667 0.00 0.00 37.91 4.20
2721 2906 4.467084 TTCAGCCGCATCGACCCC 62.467 66.667 0.00 0.00 0.00 4.95
2733 2918 3.782443 GACCCCGAGCATCCCGTT 61.782 66.667 0.00 0.00 0.00 4.44
2736 2921 4.891727 CCCGAGCATCCCGTTCCG 62.892 72.222 0.00 0.00 0.00 4.30
2741 2932 1.945354 GAGCATCCCGTTCCGTCTCA 61.945 60.000 0.00 0.00 0.00 3.27
2752 2948 3.440228 GTTCCGTCTCATCTCACTTAGC 58.560 50.000 0.00 0.00 0.00 3.09
2753 2949 3.006112 TCCGTCTCATCTCACTTAGCT 57.994 47.619 0.00 0.00 0.00 3.32
2759 2955 5.587289 GTCTCATCTCACTTAGCTTCGAAT 58.413 41.667 0.00 0.00 0.00 3.34
2760 2956 5.685511 GTCTCATCTCACTTAGCTTCGAATC 59.314 44.000 0.00 0.00 0.00 2.52
2761 2957 5.358160 TCTCATCTCACTTAGCTTCGAATCA 59.642 40.000 0.00 0.00 0.00 2.57
2762 2958 6.040278 TCTCATCTCACTTAGCTTCGAATCAT 59.960 38.462 0.00 0.00 0.00 2.45
2789 3009 2.630580 AGCCGAATAAGAGGGACAGATC 59.369 50.000 0.00 0.00 0.00 2.75
2805 3029 1.765314 AGATCTGGGGAATCAACCGAG 59.235 52.381 0.00 0.00 35.41 4.63
2810 3034 1.559065 GGGGAATCAACCGAGGACCA 61.559 60.000 0.00 0.00 0.00 4.02
2834 3058 3.541831 CGACCGGACATGCGTTCG 61.542 66.667 9.46 0.00 44.26 3.95
2874 3098 5.065704 TGTCTCATTCTTCTTCTTCTCCG 57.934 43.478 0.00 0.00 0.00 4.63
2898 3123 2.099921 CAGCTAATACTGACTGCGGACT 59.900 50.000 0.00 0.00 40.25 3.85
2950 3175 2.243264 GCTCATACGCTGCCAGCTC 61.243 63.158 15.80 0.00 39.60 4.09
3003 3230 2.360138 CACCTGGAGTGCAGACTCT 58.640 57.895 14.03 0.00 46.96 3.24
3004 3231 1.550327 CACCTGGAGTGCAGACTCTA 58.450 55.000 14.03 0.00 46.96 2.43
3007 3234 3.289797 TGGAGTGCAGACTCTAGGG 57.710 57.895 4.51 0.00 46.96 3.53
3008 3235 0.972983 TGGAGTGCAGACTCTAGGGC 60.973 60.000 4.51 0.00 46.96 5.19
3009 3236 1.681486 GGAGTGCAGACTCTAGGGCC 61.681 65.000 0.00 0.00 46.96 5.80
3010 3237 0.686112 GAGTGCAGACTCTAGGGCCT 60.686 60.000 12.58 12.58 44.73 5.19
3014 3268 1.217942 TGCAGACTCTAGGGCCTGATA 59.782 52.381 18.53 0.00 0.00 2.15
3067 3332 2.431260 GGGTTGCTTGCATGCGTG 60.431 61.111 18.54 9.29 35.36 5.34
3072 3337 0.388778 TTGCTTGCATGCGTGGAATG 60.389 50.000 13.64 8.91 35.02 2.67
3218 3483 2.404995 GCTAGCTTGCAGCACAGGG 61.405 63.158 15.53 0.00 45.56 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.809181 CTGCAACATTGTGCTGCTG 58.191 52.632 13.14 9.59 45.17 4.41
52 56 2.049802 GCGCTGCAACATTGTGCT 60.050 55.556 0.00 0.00 45.17 4.40
53 57 3.463690 CGCGCTGCAACATTGTGC 61.464 61.111 5.56 0.00 45.15 4.57
117 139 4.470170 CATGCATGCACGCACGCT 62.470 61.111 25.37 1.29 46.56 5.07
255 292 3.133464 CATGCATGGCCGTCCGTT 61.133 61.111 19.40 0.00 34.14 4.44
266 303 1.753930 TCGGAGTCAAATGCATGCAT 58.246 45.000 27.46 27.46 38.46 3.96
267 304 1.532523 TTCGGAGTCAAATGCATGCA 58.467 45.000 25.04 25.04 0.00 3.96
268 305 2.523015 CTTTCGGAGTCAAATGCATGC 58.477 47.619 11.82 11.82 0.00 4.06
296 333 1.524008 CCGCTTTTGGGGTGGACTTC 61.524 60.000 0.00 0.00 46.26 3.01
331 368 1.154413 CGTTTGGTGATGAGTGCGC 60.154 57.895 0.00 0.00 0.00 6.09
332 369 0.586319 AACGTTTGGTGATGAGTGCG 59.414 50.000 0.00 0.00 0.00 5.34
343 380 1.852067 CTCCGGGCTGAAACGTTTGG 61.852 60.000 20.10 12.23 0.00 3.28
344 381 1.574428 CTCCGGGCTGAAACGTTTG 59.426 57.895 20.10 6.10 0.00 2.93
345 382 1.599797 CCTCCGGGCTGAAACGTTT 60.600 57.895 14.57 14.57 0.00 3.60
346 383 2.032071 CCTCCGGGCTGAAACGTT 59.968 61.111 0.00 0.00 0.00 3.99
347 384 4.016706 CCCTCCGGGCTGAAACGT 62.017 66.667 0.00 0.00 35.35 3.99
362 399 0.252197 ATTACCTCGCCAGTTCACCC 59.748 55.000 0.00 0.00 0.00 4.61
373 410 2.872858 GCCTTCCAGCTTAATTACCTCG 59.127 50.000 0.00 0.00 0.00 4.63
376 413 2.359214 GCAGCCTTCCAGCTTAATTACC 59.641 50.000 0.00 0.00 42.61 2.85
388 425 3.741476 CGCCACAAGCAGCCTTCC 61.741 66.667 0.00 0.00 44.04 3.46
416 453 2.563427 GCAGCGCCCAAAAGAGAC 59.437 61.111 2.29 0.00 0.00 3.36
483 535 6.861572 GGCGTTCAATTTAAGAGCTTACTTTT 59.138 34.615 0.00 0.00 0.00 2.27
484 536 6.379386 GGCGTTCAATTTAAGAGCTTACTTT 58.621 36.000 0.00 0.00 0.00 2.66
487 558 4.331962 CGGCGTTCAATTTAAGAGCTTAC 58.668 43.478 0.00 0.00 0.00 2.34
492 563 4.495844 GGATTCCGGCGTTCAATTTAAGAG 60.496 45.833 6.01 0.00 0.00 2.85
495 566 3.082548 TGGATTCCGGCGTTCAATTTAA 58.917 40.909 6.01 0.00 0.00 1.52
505 576 1.227556 CCTACCTTGGATTCCGGCG 60.228 63.158 0.00 0.00 0.00 6.46
508 579 0.463833 GCCACCTACCTTGGATTCCG 60.464 60.000 0.00 0.00 36.02 4.30
530 601 2.435938 GCTGCAACGGGGAATCGA 60.436 61.111 0.00 0.00 0.00 3.59
531 602 3.864686 CGCTGCAACGGGGAATCG 61.865 66.667 0.45 0.00 0.00 3.34
599 683 5.539955 TCCTCCCTTCTTTTCCATTTTTCTG 59.460 40.000 0.00 0.00 0.00 3.02
607 691 2.578021 CCATCTCCTCCCTTCTTTTCCA 59.422 50.000 0.00 0.00 0.00 3.53
608 692 2.092158 CCCATCTCCTCCCTTCTTTTCC 60.092 54.545 0.00 0.00 0.00 3.13
609 693 2.846827 TCCCATCTCCTCCCTTCTTTTC 59.153 50.000 0.00 0.00 0.00 2.29
613 697 1.344906 CCTTCCCATCTCCTCCCTTCT 60.345 57.143 0.00 0.00 0.00 2.85
650 739 0.033228 CTCTTCTCTATGCCGCCCTG 59.967 60.000 0.00 0.00 0.00 4.45
651 740 0.105964 TCTCTTCTCTATGCCGCCCT 60.106 55.000 0.00 0.00 0.00 5.19
653 742 2.604046 TTTCTCTTCTCTATGCCGCC 57.396 50.000 0.00 0.00 0.00 6.13
654 743 3.786635 TCTTTTCTCTTCTCTATGCCGC 58.213 45.455 0.00 0.00 0.00 6.53
655 744 6.591834 TCTTTTCTTTTCTCTTCTCTATGCCG 59.408 38.462 0.00 0.00 0.00 5.69
656 745 7.821846 TCTCTTTTCTTTTCTCTTCTCTATGCC 59.178 37.037 0.00 0.00 0.00 4.40
661 750 9.546428 CTCTTTCTCTTTTCTTTTCTCTTCTCT 57.454 33.333 0.00 0.00 0.00 3.10
662 751 9.541143 TCTCTTTCTCTTTTCTTTTCTCTTCTC 57.459 33.333 0.00 0.00 0.00 2.87
715 804 1.740025 GGAGAACAAGGCATCGAAAGG 59.260 52.381 0.00 0.00 0.00 3.11
774 878 4.021925 AAGCACGCAGGGACCCTC 62.022 66.667 11.23 4.95 0.00 4.30
775 879 4.335647 CAAGCACGCAGGGACCCT 62.336 66.667 7.44 7.44 0.00 4.34
778 882 1.234615 TTAAGCAAGCACGCAGGGAC 61.235 55.000 0.00 0.00 0.00 4.46
779 883 0.955428 CTTAAGCAAGCACGCAGGGA 60.955 55.000 0.00 0.00 0.00 4.20
851 960 1.807142 GAACAGAGAAAGGGAAAGCGG 59.193 52.381 0.00 0.00 0.00 5.52
853 962 2.163509 GGGAACAGAGAAAGGGAAAGC 58.836 52.381 0.00 0.00 0.00 3.51
896 1006 1.880027 TCGGCTTTCCTTTCTTCTTGC 59.120 47.619 0.00 0.00 0.00 4.01
897 1007 2.095516 GCTCGGCTTTCCTTTCTTCTTG 60.096 50.000 0.00 0.00 0.00 3.02
898 1008 2.155279 GCTCGGCTTTCCTTTCTTCTT 58.845 47.619 0.00 0.00 0.00 2.52
899 1009 1.349357 AGCTCGGCTTTCCTTTCTTCT 59.651 47.619 0.00 0.00 33.89 2.85
900 1010 1.735018 GAGCTCGGCTTTCCTTTCTTC 59.265 52.381 0.00 0.00 39.88 2.87
956 1066 1.710013 CGGTTATATAGTGGCAGGCG 58.290 55.000 0.00 0.00 0.00 5.52
1026 1149 3.587061 AGAGAGAGAGAGAGAGTGGTTGA 59.413 47.826 0.00 0.00 0.00 3.18
1040 1163 4.202315 CGGATCAGAGGTAGAAGAGAGAGA 60.202 50.000 0.00 0.00 0.00 3.10
1041 1164 4.065088 CGGATCAGAGGTAGAAGAGAGAG 58.935 52.174 0.00 0.00 0.00 3.20
1042 1165 3.456644 ACGGATCAGAGGTAGAAGAGAGA 59.543 47.826 0.00 0.00 0.00 3.10
1043 1166 3.813166 GACGGATCAGAGGTAGAAGAGAG 59.187 52.174 0.00 0.00 0.00 3.20
1044 1167 3.433882 GGACGGATCAGAGGTAGAAGAGA 60.434 52.174 0.00 0.00 0.00 3.10
1045 1168 2.882137 GGACGGATCAGAGGTAGAAGAG 59.118 54.545 0.00 0.00 0.00 2.85
1046 1169 2.510382 AGGACGGATCAGAGGTAGAAGA 59.490 50.000 0.00 0.00 0.00 2.87
1047 1170 2.882137 GAGGACGGATCAGAGGTAGAAG 59.118 54.545 0.00 0.00 0.00 2.85
1053 1176 0.678395 CATGGAGGACGGATCAGAGG 59.322 60.000 0.00 0.00 0.00 3.69
1091 1214 3.181462 ACATGCAAGTCAGACTCAACTCA 60.181 43.478 2.72 0.00 0.00 3.41
1092 1215 3.186001 CACATGCAAGTCAGACTCAACTC 59.814 47.826 2.72 0.00 0.00 3.01
1093 1216 3.136763 CACATGCAAGTCAGACTCAACT 58.863 45.455 2.72 0.00 0.00 3.16
1094 1217 3.133691 TCACATGCAAGTCAGACTCAAC 58.866 45.455 2.72 0.00 0.00 3.18
1095 1218 3.396560 CTCACATGCAAGTCAGACTCAA 58.603 45.455 2.72 0.00 0.00 3.02
1118 1241 2.097038 GTGTGCTCGCTGTAGGCTG 61.097 63.158 0.00 0.00 39.13 4.85
1129 1252 2.650813 CTAGGATGGGCCGTGTGCTC 62.651 65.000 1.02 0.00 43.43 4.26
1146 1277 5.030147 ACTTCCTCTCTCTCTCTCTGTCTA 58.970 45.833 0.00 0.00 0.00 2.59
1201 1332 0.529833 CACACACAAAGCACAACCCA 59.470 50.000 0.00 0.00 0.00 4.51
1202 1333 0.805711 GCACACACAAAGCACAACCC 60.806 55.000 0.00 0.00 0.00 4.11
1203 1334 1.139226 CGCACACACAAAGCACAACC 61.139 55.000 0.00 0.00 0.00 3.77
1204 1335 0.455972 ACGCACACACAAAGCACAAC 60.456 50.000 0.00 0.00 0.00 3.32
1205 1336 0.179176 GACGCACACACAAAGCACAA 60.179 50.000 0.00 0.00 0.00 3.33
1206 1337 1.024046 AGACGCACACACAAAGCACA 61.024 50.000 0.00 0.00 0.00 4.57
1207 1338 0.934496 TAGACGCACACACAAAGCAC 59.066 50.000 0.00 0.00 0.00 4.40
1208 1339 1.530720 CATAGACGCACACACAAAGCA 59.469 47.619 0.00 0.00 0.00 3.91
1209 1340 1.135972 CCATAGACGCACACACAAAGC 60.136 52.381 0.00 0.00 0.00 3.51
1466 1601 1.204941 AGCTCCGTTGGTCAGTGATAC 59.795 52.381 0.00 0.00 0.00 2.24
1785 1928 4.021925 GCGTGGAGGCTCTTGGGT 62.022 66.667 15.23 0.00 0.00 4.51
1786 1929 4.785453 GGCGTGGAGGCTCTTGGG 62.785 72.222 15.23 2.93 42.90 4.12
1962 2111 1.112113 GGTTAGAGGCGGTCTCATCA 58.888 55.000 12.80 0.00 44.81 3.07
1984 2133 2.731348 CTAATCCTCTCGCCGCGC 60.731 66.667 8.21 0.00 0.00 6.86
2055 2204 6.038161 CCACATTAGCAGATCCACGAATTAAA 59.962 38.462 0.00 0.00 0.00 1.52
2065 2214 5.279056 GGACTAGTACCACATTAGCAGATCC 60.279 48.000 0.00 0.00 0.00 3.36
2070 2219 3.359033 ACGGACTAGTACCACATTAGCA 58.641 45.455 0.00 0.00 0.00 3.49
2083 2232 2.290464 ACTGCTGCTACTACGGACTAG 58.710 52.381 0.00 0.00 0.00 2.57
2084 2233 2.414994 ACTGCTGCTACTACGGACTA 57.585 50.000 0.00 0.00 0.00 2.59
2086 2235 2.015587 ACTACTGCTGCTACTACGGAC 58.984 52.381 0.00 0.00 0.00 4.79
2088 2237 4.275196 TGATTACTACTGCTGCTACTACGG 59.725 45.833 0.00 0.00 0.00 4.02
2089 2238 5.419760 TGATTACTACTGCTGCTACTACG 57.580 43.478 0.00 0.00 0.00 3.51
2090 2239 6.971602 TGATGATTACTACTGCTGCTACTAC 58.028 40.000 0.00 0.00 0.00 2.73
2091 2240 6.294231 GCTGATGATTACTACTGCTGCTACTA 60.294 42.308 0.00 0.00 0.00 1.82
2092 2241 5.508825 GCTGATGATTACTACTGCTGCTACT 60.509 44.000 0.00 0.00 0.00 2.57
2093 2242 4.683781 GCTGATGATTACTACTGCTGCTAC 59.316 45.833 0.00 0.00 0.00 3.58
2094 2243 4.262207 GGCTGATGATTACTACTGCTGCTA 60.262 45.833 0.00 0.00 0.00 3.49
2095 2244 3.494048 GGCTGATGATTACTACTGCTGCT 60.494 47.826 0.00 0.00 0.00 4.24
2096 2245 2.805099 GGCTGATGATTACTACTGCTGC 59.195 50.000 0.00 0.00 0.00 5.25
2097 2246 3.397482 GGGCTGATGATTACTACTGCTG 58.603 50.000 0.00 0.00 0.00 4.41
2098 2247 2.370189 GGGGCTGATGATTACTACTGCT 59.630 50.000 0.00 0.00 0.00 4.24
2100 2249 4.130118 GTTGGGGCTGATGATTACTACTG 58.870 47.826 0.00 0.00 0.00 2.74
2116 2265 4.301072 TGTTTCTCCTGATAAGTTGGGG 57.699 45.455 0.00 0.00 0.00 4.96
2141 2290 0.800631 TTGCTGATTGCTTGAGCTCG 59.199 50.000 9.64 0.00 43.37 5.03
2213 2362 4.039609 TCTTTGATTCACAGTGAGCTCTCA 59.960 41.667 16.19 4.56 37.24 3.27
2250 2401 5.339611 CGAGCAAAAGAACTCCAATTTAACG 59.660 40.000 0.00 0.00 0.00 3.18
2258 2409 2.613026 TCACGAGCAAAAGAACTCCA 57.387 45.000 0.00 0.00 0.00 3.86
2300 2463 7.009357 CGCTACCTAGTTCATTCTTTACTTGTC 59.991 40.741 0.00 0.00 0.00 3.18
2350 2513 1.071385 CTTTCTCTGCACCACCTCTGT 59.929 52.381 0.00 0.00 0.00 3.41
2351 2514 1.805869 CTTTCTCTGCACCACCTCTG 58.194 55.000 0.00 0.00 0.00 3.35
2354 2520 0.250640 CTGCTTTCTCTGCACCACCT 60.251 55.000 0.00 0.00 36.37 4.00
2357 2523 1.073722 CCCTGCTTTCTCTGCACCA 59.926 57.895 0.00 0.00 36.37 4.17
2360 2526 1.303074 CTGCCCTGCTTTCTCTGCA 60.303 57.895 0.00 0.00 38.81 4.41
2416 2583 4.398549 TCACAAAATTCGTGAATCCGTC 57.601 40.909 7.92 0.00 40.34 4.79
2545 2716 3.083997 GGCATCTCCGGACTGGGT 61.084 66.667 0.00 0.00 38.76 4.51
2547 2718 0.462759 GAAAGGCATCTCCGGACTGG 60.463 60.000 0.00 0.00 40.77 4.00
2662 2834 1.208009 TTGTTCGTTCGTTCGACCGG 61.208 55.000 11.56 0.00 39.58 5.28
2664 2836 2.936050 AATTGTTCGTTCGTTCGACC 57.064 45.000 4.50 0.00 39.58 4.79
2666 2838 3.030441 GCAAAATTGTTCGTTCGTTCGA 58.970 40.909 1.29 1.29 38.08 3.71
2701 2886 3.918220 GTCGATGCGGCTGAAGCG 61.918 66.667 4.30 4.30 43.26 4.68
2702 2887 3.567797 GGTCGATGCGGCTGAAGC 61.568 66.667 0.00 0.00 41.14 3.86
2703 2888 2.892425 GGGTCGATGCGGCTGAAG 60.892 66.667 0.00 0.00 0.00 3.02
2704 2889 4.467084 GGGGTCGATGCGGCTGAA 62.467 66.667 0.00 0.00 0.00 3.02
2718 2903 4.547367 GGAACGGGATGCTCGGGG 62.547 72.222 0.00 0.00 0.00 5.73
2733 2918 3.006112 AGCTAAGTGAGATGAGACGGA 57.994 47.619 0.00 0.00 0.00 4.69
2736 2921 4.624336 TCGAAGCTAAGTGAGATGAGAC 57.376 45.455 0.00 0.00 0.00 3.36
2741 2932 7.026562 CGATATGATTCGAAGCTAAGTGAGAT 58.973 38.462 15.31 0.00 41.62 2.75
2759 2955 4.082190 CCCTCTTATTCGGCTTCGATATGA 60.082 45.833 0.00 0.00 42.93 2.15
2760 2956 4.082190 TCCCTCTTATTCGGCTTCGATATG 60.082 45.833 0.00 0.00 42.93 1.78
2761 2957 4.082136 GTCCCTCTTATTCGGCTTCGATAT 60.082 45.833 0.00 0.00 42.93 1.63
2762 2958 3.255149 GTCCCTCTTATTCGGCTTCGATA 59.745 47.826 0.00 0.00 42.93 2.92
2770 2990 3.006323 CCAGATCTGTCCCTCTTATTCGG 59.994 52.174 21.11 0.00 0.00 4.30
2780 3000 1.511613 TGATTCCCCAGATCTGTCCC 58.488 55.000 21.11 5.17 0.00 4.46
2789 3009 0.107654 GTCCTCGGTTGATTCCCCAG 60.108 60.000 0.00 0.00 0.00 4.45
2805 3029 2.572284 CGGTCGAGGTCTTGGTCC 59.428 66.667 0.00 0.00 0.00 4.46
2810 3034 1.890894 CATGTCCGGTCGAGGTCTT 59.109 57.895 0.00 0.00 0.00 3.01
2874 3098 1.587547 GCAGTCAGTATTAGCTGCCC 58.412 55.000 0.00 0.00 45.96 5.36
2898 3123 1.940752 GCCACTACCGCCGAAAAAGTA 60.941 52.381 0.00 0.00 0.00 2.24
2923 3148 2.546494 GCGTATGAGCCATGGCCAC 61.546 63.158 33.14 25.86 43.17 5.01
2950 3175 3.306019 GGCAACCCACATACAGAAAAAGG 60.306 47.826 0.00 0.00 0.00 3.11
2992 3219 0.975040 CAGGCCCTAGAGTCTGCACT 60.975 60.000 1.86 0.00 34.57 4.40
2993 3220 0.972983 TCAGGCCCTAGAGTCTGCAC 60.973 60.000 0.09 0.00 0.00 4.57
2994 3221 0.031716 ATCAGGCCCTAGAGTCTGCA 60.032 55.000 0.09 0.00 0.00 4.41
2995 3222 2.002505 TATCAGGCCCTAGAGTCTGC 57.997 55.000 0.09 0.00 0.00 4.26
2996 3223 3.763360 CTGATATCAGGCCCTAGAGTCTG 59.237 52.174 22.89 0.00 40.20 3.51
2997 3224 3.660177 TCTGATATCAGGCCCTAGAGTCT 59.340 47.826 28.30 0.00 43.91 3.24
2998 3225 4.040936 TCTGATATCAGGCCCTAGAGTC 57.959 50.000 28.30 0.00 43.91 3.36
2999 3226 4.477536 TTCTGATATCAGGCCCTAGAGT 57.522 45.455 28.30 0.00 43.91 3.24
3000 3227 5.815233 TTTTCTGATATCAGGCCCTAGAG 57.185 43.478 28.30 4.86 43.91 2.43
3001 3228 6.466326 CCAATTTTCTGATATCAGGCCCTAGA 60.466 42.308 28.30 8.46 43.91 2.43
3002 3229 5.709164 CCAATTTTCTGATATCAGGCCCTAG 59.291 44.000 28.30 16.10 43.91 3.02
3003 3230 5.458069 CCCAATTTTCTGATATCAGGCCCTA 60.458 44.000 28.30 9.60 43.91 3.53
3004 3231 4.477249 CCAATTTTCTGATATCAGGCCCT 58.523 43.478 28.30 11.66 43.91 5.19
3005 3232 3.575687 CCCAATTTTCTGATATCAGGCCC 59.424 47.826 28.30 0.00 43.91 5.80
3006 3233 4.218312 ACCCAATTTTCTGATATCAGGCC 58.782 43.478 28.30 0.00 43.91 5.19
3007 3234 6.716628 TCATACCCAATTTTCTGATATCAGGC 59.283 38.462 28.30 0.00 43.91 4.85
3008 3235 8.737175 CATCATACCCAATTTTCTGATATCAGG 58.263 37.037 28.30 15.47 43.91 3.86
3009 3236 8.242053 GCATCATACCCAATTTTCTGATATCAG 58.758 37.037 24.32 24.32 45.08 2.90
3010 3237 7.724951 TGCATCATACCCAATTTTCTGATATCA 59.275 33.333 5.07 5.07 0.00 2.15
3014 3268 5.303589 CCTGCATCATACCCAATTTTCTGAT 59.696 40.000 0.00 0.00 0.00 2.90
3067 3332 3.056313 GCAGCCGCTCAACCATTCC 62.056 63.158 0.00 0.00 34.30 3.01
3168 3433 1.133363 CAACACAACAGTGCACGCAC 61.133 55.000 14.28 14.28 46.50 5.34
3169 3434 1.136356 CAACACAACAGTGCACGCA 59.864 52.632 12.01 0.00 36.74 5.24
3170 3435 1.586042 CCAACACAACAGTGCACGC 60.586 57.895 12.01 0.00 36.74 5.34
3171 3436 0.027979 CTCCAACACAACAGTGCACG 59.972 55.000 12.01 9.15 36.74 5.34
3172 3437 1.064060 GTCTCCAACACAACAGTGCAC 59.936 52.381 9.40 9.40 36.74 4.57
3173 3438 1.339535 TGTCTCCAACACAACAGTGCA 60.340 47.619 0.00 0.00 36.74 4.57
3174 3439 1.331756 CTGTCTCCAACACAACAGTGC 59.668 52.381 0.00 0.00 36.74 4.40
3207 3472 3.002583 TCCGATCCCTGTGCTGCA 61.003 61.111 0.00 0.00 0.00 4.41
3210 3475 4.148825 GCGTCCGATCCCTGTGCT 62.149 66.667 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.