Multiple sequence alignment - TraesCS3D01G348100

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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 TraesCS3D01G348100 chr3D 100.000 3179 0 0 1 3179 459480702 459477524 0 5871
1 TraesCS3D01G348100 chr3B 89.776 3218 175 71 1 3149 607409406 607406274 0 3978
2 TraesCS3D01G348100 chr3A 88.997 3281 170 60 1 3179 601542144 601545335 0 3882


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 TraesCS3D01G348100 chr3D 459477524 459480702 3178 True 5871 5871 100.000 1 3179 1 chr3D.!!$R1 3178
1 TraesCS3D01G348100 chr3B 607406274 607409406 3132 True 3978 3978 89.776 1 3149 1 chr3B.!!$R1 3148
2 TraesCS3D01G348100 chr3A 601542144 601545335 3191 False 3882 3882 88.997 1 3179 1 chr3A.!!$F1 3178

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
542 561 0.396974 TTCCTGCAAAACCACCAGCT 60.397 50.0 0.00 0.0 0.00 4.24 F
763 782 0.397957 TACTGCAGCGGGAGGGAATA 60.398 55.0 15.27 0.0 36.68 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1578 0.445436 GAGTCCACAGCTCAATTGCG 59.555 55.0 0.0 0.0 38.13 4.85 R
2753 2864 0.663568 GTCTTGTCCTGTCACGGTCG 60.664 60.0 0.0 0.0 0.00 4.79 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
54 55 2.823924 TTGCAACGAGTAGCACCTTA 57.176 45.000 0.00 0.00 41.05 2.69
55 56 3.328382 TTGCAACGAGTAGCACCTTAT 57.672 42.857 0.00 0.00 41.05 1.73
56 57 2.616960 TGCAACGAGTAGCACCTTATG 58.383 47.619 0.00 0.00 35.51 1.90
57 58 1.933853 GCAACGAGTAGCACCTTATGG 59.066 52.381 0.00 0.00 39.83 2.74
59 60 3.429822 GCAACGAGTAGCACCTTATGGTA 60.430 47.826 0.00 0.00 46.60 3.25
60 61 4.739735 GCAACGAGTAGCACCTTATGGTAT 60.740 45.833 0.00 0.00 46.60 2.73
61 62 5.508489 GCAACGAGTAGCACCTTATGGTATA 60.508 44.000 0.00 0.00 46.60 1.47
65 66 8.053026 ACGAGTAGCACCTTATGGTATAATAG 57.947 38.462 0.00 0.41 46.60 1.73
83 97 5.514500 AATAGAAGGCCAGACAACCTTTA 57.486 39.130 5.01 0.00 46.33 1.85
137 151 2.000447 GTACGACAAGTCCTTGATGCC 59.000 52.381 13.69 0.22 42.93 4.40
214 228 1.216710 GGCACTCTCTCTTCACGGG 59.783 63.158 0.00 0.00 0.00 5.28
252 267 9.492973 AAGGTTTTTATCATCAAATTTCCACAG 57.507 29.630 0.00 0.00 0.00 3.66
253 268 8.650490 AGGTTTTTATCATCAAATTTCCACAGT 58.350 29.630 0.00 0.00 0.00 3.55
254 269 9.921637 GGTTTTTATCATCAAATTTCCACAGTA 57.078 29.630 0.00 0.00 0.00 2.74
345 362 1.065926 TGCACATCAAGGAAGCTCGAT 60.066 47.619 0.00 0.00 0.00 3.59
349 366 3.875727 CACATCAAGGAAGCTCGATCATT 59.124 43.478 0.00 0.00 0.00 2.57
355 372 7.251704 TCAAGGAAGCTCGATCATTAAAATC 57.748 36.000 0.00 0.00 0.00 2.17
363 380 6.650060 CTCGATCATTAAAATCGTGCAATG 57.350 37.500 17.85 0.00 44.81 2.82
369 386 5.515982 TCATTAAAATCGTGCAATGTCATGC 59.484 36.000 0.00 0.00 46.58 4.06
375 392 3.589579 GCAATGTCATGCGGTCCA 58.410 55.556 0.00 0.00 36.45 4.02
386 403 1.686355 TGCGGTCCATTCTTTGTTGT 58.314 45.000 0.00 0.00 0.00 3.32
388 405 3.215151 TGCGGTCCATTCTTTGTTGTTA 58.785 40.909 0.00 0.00 0.00 2.41
389 406 3.823873 TGCGGTCCATTCTTTGTTGTTAT 59.176 39.130 0.00 0.00 0.00 1.89
394 411 5.242838 GGTCCATTCTTTGTTGTTATGGTGA 59.757 40.000 0.00 0.00 37.58 4.02
395 412 6.239176 GGTCCATTCTTTGTTGTTATGGTGAA 60.239 38.462 0.00 0.00 37.58 3.18
424 443 0.447801 CCCGTCGCCTTTTTCTCATG 59.552 55.000 0.00 0.00 0.00 3.07
516 535 6.001449 TGATTTCCATTACTAGAACCCAGG 57.999 41.667 0.00 0.00 0.00 4.45
526 545 4.095211 ACTAGAACCCAGGTAGAAGTTCC 58.905 47.826 0.00 0.00 39.52 3.62
530 549 0.984230 CCCAGGTAGAAGTTCCTGCA 59.016 55.000 0.00 0.00 46.83 4.41
542 561 0.396974 TTCCTGCAAAACCACCAGCT 60.397 50.000 0.00 0.00 0.00 4.24
545 564 1.895131 CCTGCAAAACCACCAGCTTAT 59.105 47.619 0.00 0.00 0.00 1.73
546 565 2.353011 CCTGCAAAACCACCAGCTTATG 60.353 50.000 0.00 0.00 0.00 1.90
571 590 4.334552 TGGTGCATGTATTCACATCACTT 58.665 39.130 14.28 0.00 43.73 3.16
586 605 5.579904 CACATCACTTACAGTCATCTTCCTG 59.420 44.000 0.00 0.00 34.82 3.86
598 617 1.645710 TCTTCCTGACCTTCCACTCC 58.354 55.000 0.00 0.00 0.00 3.85
630 649 1.749033 GGATGTGACGGATCCCTCC 59.251 63.158 6.06 0.00 34.33 4.30
652 671 0.468226 ACGTACGCCATCCATCCAAT 59.532 50.000 16.72 0.00 0.00 3.16
653 672 0.867746 CGTACGCCATCCATCCAATG 59.132 55.000 0.52 0.00 0.00 2.82
654 673 1.540146 CGTACGCCATCCATCCAATGA 60.540 52.381 0.52 0.00 0.00 2.57
655 674 2.783135 GTACGCCATCCATCCAATGAT 58.217 47.619 0.00 0.00 0.00 2.45
657 676 1.171308 CGCCATCCATCCAATGATCC 58.829 55.000 0.00 0.00 0.00 3.36
709 728 3.150767 TGCCAAACATTAGCGGTAAACT 58.849 40.909 11.60 0.00 0.00 2.66
758 777 2.941210 TTTTTACTGCAGCGGGAGG 58.059 52.632 15.27 0.00 36.68 4.30
759 778 0.608035 TTTTTACTGCAGCGGGAGGG 60.608 55.000 15.27 0.00 36.68 4.30
760 779 1.485294 TTTTACTGCAGCGGGAGGGA 61.485 55.000 15.27 0.00 36.68 4.20
761 780 1.485294 TTTACTGCAGCGGGAGGGAA 61.485 55.000 15.27 0.71 36.68 3.97
762 781 1.271840 TTACTGCAGCGGGAGGGAAT 61.272 55.000 15.27 0.00 36.68 3.01
763 782 0.397957 TACTGCAGCGGGAGGGAATA 60.398 55.000 15.27 0.00 36.68 1.75
764 783 1.070445 CTGCAGCGGGAGGGAATAG 59.930 63.158 0.00 0.00 0.00 1.73
827 860 1.795768 TGCACAACAGCACTACTAGC 58.204 50.000 0.00 0.00 40.11 3.42
828 861 1.344438 TGCACAACAGCACTACTAGCT 59.656 47.619 0.00 0.00 44.62 3.32
868 924 1.692519 CCCAGACCCTTCTTATACCCG 59.307 57.143 0.00 0.00 0.00 5.28
871 927 0.749049 GACCCTTCTTATACCCGCGT 59.251 55.000 4.92 0.00 0.00 6.01
903 965 1.101049 ACCTCCCAGCAAAACACACG 61.101 55.000 0.00 0.00 0.00 4.49
946 1008 2.343426 GCTAAAGGCACCCACAGGC 61.343 63.158 0.00 0.00 41.35 4.85
1086 1152 3.227276 CCGACCCTGATCCCTCGG 61.227 72.222 3.84 3.84 39.78 4.63
1179 1254 4.233635 CCGCCGTCGTCCTACTCG 62.234 72.222 0.00 0.00 0.00 4.18
1186 1261 2.021106 CGTCCTACTCGTCGTCGC 59.979 66.667 0.00 0.00 36.96 5.19
1187 1262 2.451167 CGTCCTACTCGTCGTCGCT 61.451 63.158 0.00 0.00 36.96 4.93
1188 1263 1.347907 GTCCTACTCGTCGTCGCTC 59.652 63.158 0.00 0.00 36.96 5.03
1189 1264 1.812922 TCCTACTCGTCGTCGCTCC 60.813 63.158 0.00 0.00 36.96 4.70
1190 1265 2.104859 CCTACTCGTCGTCGCTCCA 61.105 63.158 0.00 0.00 36.96 3.86
1191 1266 1.348938 CTACTCGTCGTCGCTCCAG 59.651 63.158 0.00 0.00 36.96 3.86
1192 1267 1.360194 CTACTCGTCGTCGCTCCAGT 61.360 60.000 0.00 0.00 36.96 4.00
1193 1268 1.357258 TACTCGTCGTCGCTCCAGTC 61.357 60.000 0.00 0.00 36.96 3.51
1194 1269 3.703939 CTCGTCGTCGCTCCAGTCG 62.704 68.421 0.00 0.00 36.96 4.18
1195 1270 4.086178 CGTCGTCGCTCCAGTCGT 62.086 66.667 0.00 0.00 0.00 4.34
1196 1271 2.202324 GTCGTCGCTCCAGTCGTC 60.202 66.667 0.00 0.00 0.00 4.20
1197 1272 3.785499 TCGTCGCTCCAGTCGTCG 61.785 66.667 0.00 0.00 39.15 5.12
1198 1273 4.086178 CGTCGCTCCAGTCGTCGT 62.086 66.667 0.00 0.00 34.78 4.34
1199 1274 2.733671 CGTCGCTCCAGTCGTCGTA 61.734 63.158 0.00 0.00 34.78 3.43
1200 1275 1.225963 GTCGCTCCAGTCGTCGTAC 60.226 63.158 0.00 0.00 0.00 3.67
1204 1279 1.081892 GCTCCAGTCGTCGTACTACA 58.918 55.000 0.00 0.00 0.00 2.74
1215 1293 3.362831 CGTCGTACTACAACAACATCCAC 59.637 47.826 0.00 0.00 0.00 4.02
1266 1344 3.023949 GCTCCACATCCAGCTCGGT 62.024 63.158 2.68 0.00 35.57 4.69
1269 1347 0.977627 TCCACATCCAGCTCGGTGAT 60.978 55.000 0.00 0.00 35.57 3.06
1309 1387 1.746220 CATTCTTCTCGTCCTCGTCCT 59.254 52.381 0.00 0.00 38.33 3.85
1338 1416 1.900016 CCAGCAGCTGTCTTTGCCA 60.900 57.895 21.26 0.00 41.17 4.92
1395 1473 1.629013 TGTACGATTTCAGCAGCTCG 58.371 50.000 0.00 0.00 37.17 5.03
1442 1524 2.331805 CGGCGATCTCCAGGTACG 59.668 66.667 0.00 0.00 0.00 3.67
1449 1531 4.514577 CTCCAGGTACGGCGCCAG 62.515 72.222 28.98 21.29 0.00 4.85
1452 1534 2.186903 CAGGTACGGCGCCAGAAT 59.813 61.111 28.98 11.13 0.00 2.40
1496 1578 0.316841 GATCGGGCTGTCTGGAGATC 59.683 60.000 0.00 0.00 0.00 2.75
1510 1592 1.329906 GGAGATCGCAATTGAGCTGTG 59.670 52.381 10.34 0.00 34.13 3.66
1515 1598 0.445436 CGCAATTGAGCTGTGGACTC 59.555 55.000 10.34 0.00 34.62 3.36
1567 1650 1.198094 TGAAGCAGGGGATGAACGGA 61.198 55.000 0.00 0.00 0.00 4.69
1741 1824 3.949754 TCACCGTAAGTACCATCTCGATT 59.050 43.478 0.00 0.00 0.00 3.34
1833 1917 1.080705 GTACGCGTGCAGGAAGTCT 60.081 57.895 24.59 0.00 0.00 3.24
1941 2025 1.064296 CAGCTACGACTACTGCGGG 59.936 63.158 0.00 0.00 0.00 6.13
2155 2239 4.033776 CCACCCTGGGCGACATGT 62.034 66.667 14.08 0.00 32.67 3.21
2436 2534 3.156288 TCGGAGACAAAAGGAGAGAGA 57.844 47.619 0.00 0.00 0.00 3.10
2437 2535 3.085533 TCGGAGACAAAAGGAGAGAGAG 58.914 50.000 0.00 0.00 0.00 3.20
2581 2679 1.270358 GCTCCTCTGTCGTCCAAAACT 60.270 52.381 0.00 0.00 0.00 2.66
2583 2681 2.035961 CTCCTCTGTCGTCCAAAACTCA 59.964 50.000 0.00 0.00 0.00 3.41
2591 2700 3.564225 GTCGTCCAAAACTCACCTGAATT 59.436 43.478 0.00 0.00 0.00 2.17
2603 2712 1.350351 ACCTGAATTCTCAGTGCTGCT 59.650 47.619 7.05 0.00 46.71 4.24
2640 2749 0.041312 CCTTCCGTGCTCGTTTTGTG 60.041 55.000 7.47 0.00 35.01 3.33
2662 2771 1.005924 TGCCCATTTTCCTTCTCCTCC 59.994 52.381 0.00 0.00 0.00 4.30
2756 2867 2.821366 CCATGGCCAGTCAGCGAC 60.821 66.667 13.05 1.15 0.00 5.19
2807 2918 4.525576 CATGCAGTTCGCGCGCAT 62.526 61.111 32.61 19.46 46.98 4.73
2808 2919 3.803082 ATGCAGTTCGCGCGCATT 61.803 55.556 32.61 8.74 43.67 3.56
2809 2920 3.326889 ATGCAGTTCGCGCGCATTT 62.327 52.632 32.61 10.40 43.67 2.32
2810 2921 3.233345 GCAGTTCGCGCGCATTTC 61.233 61.111 32.61 17.33 0.00 2.17
2826 2937 4.435253 CGCATTTCTTTCAGCTCACACTAG 60.435 45.833 0.00 0.00 0.00 2.57
2868 2979 0.765903 TACGTGGTTGGGTGGGGTTA 60.766 55.000 0.00 0.00 0.00 2.85
2876 2991 4.442454 GGTGGGGTTAGGCTGGCC 62.442 72.222 3.00 3.00 0.00 5.36
2941 3076 1.005867 TCAAAGGGGTACGTGCGTC 60.006 57.895 0.00 0.00 0.00 5.19
2970 3113 3.209812 CCGTCTCATCGCCGGAGA 61.210 66.667 11.31 11.31 44.41 3.71
2971 3114 2.329690 CGTCTCATCGCCGGAGAG 59.670 66.667 14.81 10.36 41.77 3.20
2972 3115 2.026879 GTCTCATCGCCGGAGAGC 59.973 66.667 14.81 3.75 41.77 4.09
3111 3264 0.107456 GCATGTGATCAGTCCCCGAT 59.893 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 6.465894 GGTTGTCTGGCCTTCTATTATACCAT 60.466 42.308 3.32 0.00 0.00 3.55
55 56 5.163237 GGTTGTCTGGCCTTCTATTATACCA 60.163 44.000 3.32 0.00 0.00 3.25
56 57 5.071923 AGGTTGTCTGGCCTTCTATTATACC 59.928 44.000 3.32 0.11 0.00 2.73
57 58 6.176014 AGGTTGTCTGGCCTTCTATTATAC 57.824 41.667 3.32 0.00 0.00 1.47
59 60 5.717119 AAGGTTGTCTGGCCTTCTATTAT 57.283 39.130 3.32 0.00 40.81 1.28
60 61 5.514500 AAAGGTTGTCTGGCCTTCTATTA 57.486 39.130 3.32 0.00 43.66 0.98
61 62 4.388577 AAAGGTTGTCTGGCCTTCTATT 57.611 40.909 3.32 0.00 43.66 1.73
65 66 4.200092 CCTATAAAGGTTGTCTGGCCTTC 58.800 47.826 3.32 0.00 43.66 3.46
83 97 3.264450 GTGCCATAGCCAATAGTCCCTAT 59.736 47.826 0.00 0.00 38.69 2.57
137 151 2.232452 ACAAGATCGTCCAGACTGAAGG 59.768 50.000 3.32 0.00 0.00 3.46
345 362 5.515982 GCATGACATTGCACGATTTTAATGA 59.484 36.000 0.00 0.00 42.31 2.57
349 366 3.424487 CGCATGACATTGCACGATTTTA 58.576 40.909 0.00 0.00 42.91 1.52
355 372 1.226101 GACCGCATGACATTGCACG 60.226 57.895 0.00 1.75 42.91 5.34
363 380 1.812571 ACAAAGAATGGACCGCATGAC 59.187 47.619 0.00 0.00 0.00 3.06
369 386 4.217550 ACCATAACAACAAAGAATGGACCG 59.782 41.667 6.65 0.00 39.60 4.79
370 387 5.242838 TCACCATAACAACAAAGAATGGACC 59.757 40.000 6.65 0.00 39.60 4.46
372 389 6.968263 TTCACCATAACAACAAAGAATGGA 57.032 33.333 6.65 0.00 39.60 3.41
441 460 1.524621 CAACTATGCGGAGGCTGGG 60.525 63.158 0.00 0.00 40.82 4.45
444 463 3.694364 CATCAACTATGCGGAGGCT 57.306 52.632 0.00 0.00 40.82 4.58
467 486 3.812156 AAACCCCGTTTTCTCCAAAAG 57.188 42.857 0.00 0.00 31.10 2.27
492 511 6.011981 ACCTGGGTTCTAGTAATGGAAATCAA 60.012 38.462 0.00 0.00 0.00 2.57
516 535 3.004419 GGTGGTTTTGCAGGAACTTCTAC 59.996 47.826 12.83 8.35 34.60 2.59
526 545 2.353011 CCATAAGCTGGTGGTTTTGCAG 60.353 50.000 9.03 0.00 40.49 4.41
528 547 2.368655 CCATAAGCTGGTGGTTTTGC 57.631 50.000 9.03 0.00 40.49 3.68
542 561 5.012893 TGTGAATACATGCACCAACCATAA 58.987 37.500 0.00 0.00 34.19 1.90
545 564 2.868899 TGTGAATACATGCACCAACCA 58.131 42.857 0.00 0.00 34.19 3.67
586 605 3.074788 ACTGGAGGAGTGGAAGGTC 57.925 57.895 0.00 0.00 31.75 3.85
598 617 0.326618 ACATCCCCCTACCACTGGAG 60.327 60.000 0.71 0.00 0.00 3.86
630 649 0.597637 GGATGGATGGCGTACGTGAG 60.598 60.000 17.90 0.00 0.00 3.51
652 671 2.435437 TCGAATCATCAGGCTTGGATCA 59.565 45.455 0.00 0.00 0.00 2.92
653 672 2.805099 GTCGAATCATCAGGCTTGGATC 59.195 50.000 0.00 0.00 0.00 3.36
654 673 2.437281 AGTCGAATCATCAGGCTTGGAT 59.563 45.455 0.00 0.00 0.00 3.41
655 674 1.833630 AGTCGAATCATCAGGCTTGGA 59.166 47.619 0.00 0.00 0.00 3.53
657 676 1.329906 GCAGTCGAATCATCAGGCTTG 59.670 52.381 0.00 0.00 0.00 4.01
747 766 1.689233 ACTATTCCCTCCCGCTGCA 60.689 57.895 0.00 0.00 0.00 4.41
748 767 1.227674 CACTATTCCCTCCCGCTGC 60.228 63.158 0.00 0.00 0.00 5.25
749 768 1.227674 GCACTATTCCCTCCCGCTG 60.228 63.158 0.00 0.00 0.00 5.18
750 769 2.797278 CGCACTATTCCCTCCCGCT 61.797 63.158 0.00 0.00 0.00 5.52
751 770 2.280186 CGCACTATTCCCTCCCGC 60.280 66.667 0.00 0.00 0.00 6.13
752 771 2.280186 GCGCACTATTCCCTCCCG 60.280 66.667 0.30 0.00 0.00 5.14
753 772 2.280186 CGCGCACTATTCCCTCCC 60.280 66.667 8.75 0.00 0.00 4.30
754 773 1.883084 CACGCGCACTATTCCCTCC 60.883 63.158 5.73 0.00 0.00 4.30
755 774 1.141019 TCACGCGCACTATTCCCTC 59.859 57.895 5.73 0.00 0.00 4.30
756 775 1.153628 GTCACGCGCACTATTCCCT 60.154 57.895 5.73 0.00 0.00 4.20
757 776 2.171725 GGTCACGCGCACTATTCCC 61.172 63.158 5.73 0.00 0.00 3.97
758 777 2.171725 GGGTCACGCGCACTATTCC 61.172 63.158 5.73 1.25 0.00 3.01
759 778 0.101759 TAGGGTCACGCGCACTATTC 59.898 55.000 5.73 0.00 0.00 1.75
760 779 0.179119 GTAGGGTCACGCGCACTATT 60.179 55.000 5.73 0.00 0.00 1.73
761 780 1.436336 GTAGGGTCACGCGCACTAT 59.564 57.895 5.73 0.00 0.00 2.12
762 781 2.703798 GGTAGGGTCACGCGCACTA 61.704 63.158 5.73 0.00 0.00 2.74
763 782 4.065281 GGTAGGGTCACGCGCACT 62.065 66.667 5.73 0.00 0.00 4.40
821 854 2.862536 CGCGTACACTACAGAGCTAGTA 59.137 50.000 0.00 0.00 0.00 1.82
824 857 0.376152 GCGCGTACACTACAGAGCTA 59.624 55.000 8.43 0.00 0.00 3.32
825 858 1.136984 GCGCGTACACTACAGAGCT 59.863 57.895 8.43 0.00 0.00 4.09
826 859 1.872679 GGCGCGTACACTACAGAGC 60.873 63.158 8.43 0.00 0.00 4.09
827 860 0.109458 TTGGCGCGTACACTACAGAG 60.109 55.000 8.43 0.00 0.00 3.35
828 861 0.109458 CTTGGCGCGTACACTACAGA 60.109 55.000 8.43 0.00 0.00 3.41
851 907 1.038280 CGCGGGTATAAGAAGGGTCT 58.962 55.000 0.00 0.00 34.72 3.85
868 924 1.671379 GGTTGAAGTGGAGGGACGC 60.671 63.158 0.00 0.00 0.00 5.19
871 927 0.840722 GGGAGGTTGAAGTGGAGGGA 60.841 60.000 0.00 0.00 0.00 4.20
903 965 3.649986 GGGACTGTGTGCGTGTGC 61.650 66.667 0.00 0.00 43.20 4.57
946 1008 1.199097 CCGGACGTGGAAATGAAAAGG 59.801 52.381 0.00 0.00 0.00 3.11
989 1055 3.822192 GGAACATTTCCGGCCGGC 61.822 66.667 39.89 22.83 40.59 6.13
1179 1254 2.202324 GACGACTGGAGCGACGAC 60.202 66.667 0.00 0.00 0.00 4.34
1186 1261 2.481568 TGTTGTAGTACGACGACTGGAG 59.518 50.000 22.35 0.00 35.23 3.86
1187 1262 2.493035 TGTTGTAGTACGACGACTGGA 58.507 47.619 22.35 4.88 35.23 3.86
1188 1263 2.975410 TGTTGTAGTACGACGACTGG 57.025 50.000 22.35 0.00 35.23 4.00
1189 1264 3.620761 TGTTGTTGTAGTACGACGACTG 58.379 45.455 29.44 0.00 44.00 3.51
1190 1265 3.969117 TGTTGTTGTAGTACGACGACT 57.031 42.857 29.44 3.47 44.00 4.18
1191 1266 3.605486 GGATGTTGTTGTAGTACGACGAC 59.395 47.826 25.58 25.58 43.95 4.34
1192 1267 3.252944 TGGATGTTGTTGTAGTACGACGA 59.747 43.478 14.64 10.79 35.23 4.20
1193 1268 3.362831 GTGGATGTTGTTGTAGTACGACG 59.637 47.826 14.64 0.00 35.23 5.12
1194 1269 4.300803 TGTGGATGTTGTTGTAGTACGAC 58.699 43.478 13.05 13.05 33.08 4.34
1195 1270 4.552355 CTGTGGATGTTGTTGTAGTACGA 58.448 43.478 0.00 0.00 0.00 3.43
1196 1271 3.678072 CCTGTGGATGTTGTTGTAGTACG 59.322 47.826 0.00 0.00 0.00 3.67
1197 1272 4.890088 TCCTGTGGATGTTGTTGTAGTAC 58.110 43.478 0.00 0.00 0.00 2.73
1198 1273 4.562757 GCTCCTGTGGATGTTGTTGTAGTA 60.563 45.833 0.00 0.00 0.00 1.82
1199 1274 3.807209 GCTCCTGTGGATGTTGTTGTAGT 60.807 47.826 0.00 0.00 0.00 2.73
1200 1275 2.744202 GCTCCTGTGGATGTTGTTGTAG 59.256 50.000 0.00 0.00 0.00 2.74
1204 1279 2.224843 TGATGCTCCTGTGGATGTTGTT 60.225 45.455 0.00 0.00 0.00 2.83
1266 1344 1.448893 GCCGCCGTTGAGGTTATCA 60.449 57.895 0.00 0.00 43.70 2.15
1269 1347 4.745751 CCGCCGCCGTTGAGGTTA 62.746 66.667 0.00 0.00 43.70 2.85
1287 1365 0.888619 ACGAGGACGAGAAGAATGCA 59.111 50.000 0.00 0.00 42.66 3.96
1309 1387 2.997315 CTGCTGGTGAGGGGACGA 60.997 66.667 0.00 0.00 0.00 4.20
1338 1416 2.042930 GGGGAGGAGGACATGGGT 59.957 66.667 0.00 0.00 0.00 4.51
1374 1452 2.028523 CGAGCTGCTGAAATCGTACAAG 59.971 50.000 7.01 0.00 0.00 3.16
1375 1453 1.992667 CGAGCTGCTGAAATCGTACAA 59.007 47.619 7.01 0.00 0.00 2.41
1442 1524 2.178235 GTTACCGGATTCTGGCGCC 61.178 63.158 22.73 22.73 0.00 6.53
1449 1531 4.165779 CAATTGTGCAAGTTACCGGATTC 58.834 43.478 9.46 0.00 0.00 2.52
1496 1578 0.445436 GAGTCCACAGCTCAATTGCG 59.555 55.000 0.00 0.00 38.13 4.85
1510 1592 2.587522 AGGCAAGGAAAACAAGAGTCC 58.412 47.619 0.00 0.00 0.00 3.85
1515 1598 3.950087 GCAAAAGGCAAGGAAAACAAG 57.050 42.857 0.00 0.00 43.97 3.16
1736 1819 2.093500 CAGGGTGTTGATGGAGAATCGA 60.093 50.000 0.00 0.00 38.22 3.59
1741 1824 0.770499 TTGCAGGGTGTTGATGGAGA 59.230 50.000 0.00 0.00 0.00 3.71
1941 2025 2.047274 TTGCTGGGCTCGCTGTAC 60.047 61.111 2.27 0.00 0.00 2.90
2155 2239 2.112297 GGCCAGGTTCACGGACAA 59.888 61.111 0.00 0.00 0.00 3.18
2225 2312 1.076632 ACGGAGCCCACCAAAAACA 60.077 52.632 0.00 0.00 0.00 2.83
2434 2532 1.076632 AGGAAGGCGATCGGTCTCT 60.077 57.895 18.30 0.00 0.00 3.10
2435 2533 1.360911 GAGGAAGGCGATCGGTCTC 59.639 63.158 18.30 0.00 0.00 3.36
2436 2534 2.482333 CGAGGAAGGCGATCGGTCT 61.482 63.158 18.30 1.18 32.93 3.85
2437 2535 2.026301 CGAGGAAGGCGATCGGTC 59.974 66.667 18.30 0.00 32.93 4.79
2640 2749 2.493675 GAGGAGAAGGAAAATGGGCAAC 59.506 50.000 0.00 0.00 0.00 4.17
2662 2771 2.719556 CGACAACAGTTGAGTGTAGTCG 59.280 50.000 20.56 12.31 41.00 4.18
2703 2814 3.129638 TGGACTTTGTTACAAACAGGTGC 59.870 43.478 6.41 9.37 43.27 5.01
2753 2864 0.663568 GTCTTGTCCTGTCACGGTCG 60.664 60.000 0.00 0.00 0.00 4.79
2756 2867 0.939577 CGTGTCTTGTCCTGTCACGG 60.940 60.000 7.89 0.00 44.92 4.94
2807 2918 3.059884 CGCTAGTGTGAGCTGAAAGAAA 58.940 45.455 0.00 0.00 40.51 2.52
2808 2919 2.610479 CCGCTAGTGTGAGCTGAAAGAA 60.610 50.000 1.99 0.00 40.51 2.52
2809 2920 1.067565 CCGCTAGTGTGAGCTGAAAGA 60.068 52.381 1.99 0.00 40.51 2.52
2810 2921 1.354040 CCGCTAGTGTGAGCTGAAAG 58.646 55.000 1.99 0.00 40.51 2.62
3111 3264 1.262151 GCGAACGAACAGCTAACCAAA 59.738 47.619 0.00 0.00 0.00 3.28
3159 3316 2.919666 CCCGGTGAAATTCATGTGTC 57.080 50.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.