Multiple sequence alignment - TraesCS3A01G525800

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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 TraesCS3A01G525800 chr3A 100.000 3370 0 0 1 3370 739668339 739664970 0.000000e+00 6224.0
1 TraesCS3A01G525800 chr3A 90.975 277 21 1 2094 2370 739613995 739613723 1.480000e-98 370.0
2 TraesCS3A01G525800 chr3A 79.492 590 64 28 1466 2020 739614683 739614116 1.910000e-97 366.0
3 TraesCS3A01G525800 chr3A 80.345 290 45 6 2082 2363 739567988 739567703 3.410000e-50 209.0
4 TraesCS3A01G525800 chr3D 95.981 1045 25 3 1770 2798 607225321 607224278 0.000000e+00 1681.0
5 TraesCS3A01G525800 chr3D 96.048 582 15 3 2795 3370 607212818 607212239 0.000000e+00 941.0
6 TraesCS3A01G525800 chr3D 85.275 910 41 30 844 1737 607226243 607225411 0.000000e+00 852.0
7 TraesCS3A01G525800 chr3D 83.753 437 39 8 382 807 607226854 607226439 5.270000e-103 385.0
8 TraesCS3A01G525800 chr3D 79.666 359 34 20 3 327 607227442 607227089 4.380000e-54 222.0
9 TraesCS3A01G525800 chr3B 82.683 1409 106 46 22 1364 816615204 816613868 0.000000e+00 1123.0
10 TraesCS3A01G525800 chr3B 92.470 664 27 10 2602 3244 816612903 816612242 0.000000e+00 928.0
11 TraesCS3A01G525800 chr3B 93.136 641 22 5 1788 2407 816613562 816612923 0.000000e+00 920.0
12 TraesCS3A01G525800 chr3B 79.494 356 53 12 2022 2363 816608505 816608156 5.620000e-58 235.0
13 TraesCS3A01G525800 chr3B 87.234 141 15 1 2657 2794 816607755 816607615 1.250000e-34 158.0
14 TraesCS3A01G525800 chr3B 93.137 102 4 1 1401 1499 816613672 816613571 2.710000e-31 147.0
15 TraesCS3A01G525800 chr3B 89.256 121 2 7 3259 3370 816612252 816612134 1.260000e-29 141.0
16 TraesCS3A01G525800 chr3B 94.737 57 3 0 3130 3186 618549331 618549387 4.630000e-14 89.8
17 TraesCS3A01G525800 chr5A 84.034 119 16 3 3072 3188 411083548 411083665 9.880000e-21 111.0
18 TraesCS3A01G525800 chr6D 79.310 116 17 3 3130 3238 328829665 328829780 1.300000e-09 75.0


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 TraesCS3A01G525800 chr3A 739664970 739668339 3369 True 6224.000000 6224 100.000000 1 3370 1 chr3A.!!$R2 3369
1 TraesCS3A01G525800 chr3A 739613723 739614683 960 True 368.000000 370 85.233500 1466 2370 2 chr3A.!!$R3 904
2 TraesCS3A01G525800 chr3D 607212239 607212818 579 True 941.000000 941 96.048000 2795 3370 1 chr3D.!!$R1 575
3 TraesCS3A01G525800 chr3D 607224278 607227442 3164 True 785.000000 1681 86.168750 3 2798 4 chr3D.!!$R2 2795
4 TraesCS3A01G525800 chr3B 816607615 816615204 7589 True 521.714286 1123 88.201429 22 3370 7 chr3B.!!$R1 3348

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
975 1426 0.038166 TTGATCAACAGGGACAGGGC 59.962 55.000 3.38 0.0 0.0 5.19 F
976 1427 1.077429 GATCAACAGGGACAGGGCC 60.077 63.158 0.00 0.0 0.0 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 3013 0.392863 TGTATGTGCGCAGATTGCCT 60.393 50.000 26.08 3.83 41.12 4.75 R
2970 3797 1.379443 ACACAGAGATACCGGCCGA 60.379 57.895 30.73 8.21 0.00 5.54 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
72 73 0.609131 ATGCTGAGGGACAAAACGGG 60.609 55.000 0.00 0.00 0.00 5.28
80 101 0.326927 GGACAAAACGGGGAGATCCA 59.673 55.000 0.47 0.00 37.91 3.41
104 131 5.288015 TCGGCACATTTTATATGCAAATGG 58.712 37.500 19.03 12.44 43.27 3.16
263 310 2.095438 CTATAGCCGACCCCCTCCCT 62.095 65.000 0.00 0.00 0.00 4.20
330 577 1.192146 AAGCCTGCCTCCGTCACTAA 61.192 55.000 0.00 0.00 0.00 2.24
369 616 4.123545 GGGGTGGGGGTGGAATCG 62.124 72.222 0.00 0.00 0.00 3.34
370 617 4.123545 GGGTGGGGGTGGAATCGG 62.124 72.222 0.00 0.00 0.00 4.18
371 618 3.012722 GGTGGGGGTGGAATCGGA 61.013 66.667 0.00 0.00 0.00 4.55
372 619 2.383601 GGTGGGGGTGGAATCGGAT 61.384 63.158 0.00 0.00 0.00 4.18
373 620 1.613061 GTGGGGGTGGAATCGGATT 59.387 57.895 2.19 2.19 0.00 3.01
374 621 0.751643 GTGGGGGTGGAATCGGATTG 60.752 60.000 8.18 0.00 0.00 2.67
375 622 0.916845 TGGGGGTGGAATCGGATTGA 60.917 55.000 8.18 0.00 0.00 2.57
376 623 0.478507 GGGGGTGGAATCGGATTGAT 59.521 55.000 8.18 0.00 39.67 2.57
377 624 1.609208 GGGGTGGAATCGGATTGATG 58.391 55.000 8.18 0.00 37.39 3.07
378 625 1.133792 GGGGTGGAATCGGATTGATGT 60.134 52.381 8.18 0.00 37.39 3.06
379 626 2.105821 GGGGTGGAATCGGATTGATGTA 59.894 50.000 8.18 0.00 37.39 2.29
380 627 3.244911 GGGGTGGAATCGGATTGATGTAT 60.245 47.826 8.18 0.00 37.39 2.29
381 628 4.019681 GGGGTGGAATCGGATTGATGTATA 60.020 45.833 8.18 0.00 37.39 1.47
382 629 5.339200 GGGGTGGAATCGGATTGATGTATAT 60.339 44.000 8.18 0.00 37.39 0.86
383 630 5.817816 GGGTGGAATCGGATTGATGTATATC 59.182 44.000 8.18 0.00 37.39 1.63
508 760 3.984732 GAAGGTGCCCTTGGGCCT 61.985 66.667 26.03 14.87 44.82 5.19
523 775 2.743928 CCTTGGCCAGCGTGACTC 60.744 66.667 5.11 0.00 0.00 3.36
602 866 4.217983 CGATCCCGGCTATATATACCTTCC 59.782 50.000 0.00 0.38 0.00 3.46
603 867 3.919834 TCCCGGCTATATATACCTTCCC 58.080 50.000 0.00 0.00 0.00 3.97
604 868 2.970640 CCCGGCTATATATACCTTCCCC 59.029 54.545 0.00 0.00 0.00 4.81
605 869 2.970640 CCGGCTATATATACCTTCCCCC 59.029 54.545 0.00 0.00 0.00 5.40
606 870 2.626743 CGGCTATATATACCTTCCCCCG 59.373 54.545 8.70 0.00 0.00 5.73
607 871 2.970640 GGCTATATATACCTTCCCCCGG 59.029 54.545 0.00 0.00 0.00 5.73
608 872 2.367894 GCTATATATACCTTCCCCCGGC 59.632 54.545 0.00 0.00 0.00 6.13
609 873 1.889174 ATATATACCTTCCCCCGGCC 58.111 55.000 0.00 0.00 0.00 6.13
610 874 0.615544 TATATACCTTCCCCCGGCCG 60.616 60.000 21.04 21.04 0.00 6.13
644 920 0.390735 CCCGGCCGTATATAAGCACC 60.391 60.000 26.12 3.11 0.00 5.01
657 933 7.117812 CGTATATAAGCACCCAGATTCGAATTT 59.882 37.037 12.81 3.29 0.00 1.82
679 955 4.779733 GCTCCTCCTCCCCGTCCA 62.780 72.222 0.00 0.00 0.00 4.02
680 956 2.760385 CTCCTCCTCCCCGTCCAC 60.760 72.222 0.00 0.00 0.00 4.02
681 957 4.753662 TCCTCCTCCCCGTCCACG 62.754 72.222 0.00 0.00 39.44 4.94
735 1016 1.154688 AAGCAAGCTCCAAGGCCTT 59.845 52.632 13.78 13.78 0.00 4.35
852 1296 0.309612 TTTCTTCGCGGTTGCTTTCC 59.690 50.000 6.13 0.00 39.65 3.13
859 1304 2.114411 GGTTGCTTTCCGGGTGGA 59.886 61.111 0.00 0.00 44.61 4.02
878 1323 4.002506 GGCTTTTGGTTGCCGGGG 62.003 66.667 2.18 0.00 39.71 5.73
905 1350 1.673009 GGTTGATTGGTTCGGCGGA 60.673 57.895 7.21 0.00 0.00 5.54
907 1352 1.376683 TTGATTGGTTCGGCGGAGG 60.377 57.895 7.21 0.00 0.00 4.30
975 1426 0.038166 TTGATCAACAGGGACAGGGC 59.962 55.000 3.38 0.00 0.00 5.19
976 1427 1.077429 GATCAACAGGGACAGGGCC 60.077 63.158 0.00 0.00 0.00 5.80
977 1428 1.852157 ATCAACAGGGACAGGGCCA 60.852 57.895 6.18 0.00 0.00 5.36
978 1429 2.142292 ATCAACAGGGACAGGGCCAC 62.142 60.000 6.18 0.00 0.00 5.01
979 1430 3.580319 AACAGGGACAGGGCCACC 61.580 66.667 6.18 6.06 0.00 4.61
1069 1520 2.596338 TCACCGAGACGCTGGACA 60.596 61.111 0.00 0.00 0.00 4.02
1140 1591 1.671379 GCAGTTCGACAAGGTCCCC 60.671 63.158 0.00 0.00 0.00 4.81
1141 1592 2.058675 CAGTTCGACAAGGTCCCCT 58.941 57.895 0.00 0.00 33.87 4.79
1144 1595 1.916777 TTCGACAAGGTCCCCTCCC 60.917 63.158 0.00 0.00 30.89 4.30
1145 1596 2.284699 CGACAAGGTCCCCTCCCT 60.285 66.667 0.00 0.00 30.89 4.20
1146 1597 2.359967 CGACAAGGTCCCCTCCCTC 61.360 68.421 0.00 0.00 30.89 4.30
1147 1598 1.996187 GACAAGGTCCCCTCCCTCC 60.996 68.421 0.00 0.00 30.89 4.30
1153 1604 4.038804 TCCCCTCCCTCCCCCTTG 62.039 72.222 0.00 0.00 0.00 3.61
1157 1608 4.120755 CTCCCTCCCCCTTGCTGC 62.121 72.222 0.00 0.00 0.00 5.25
1159 1610 4.120755 CCCTCCCCCTTGCTGCTC 62.121 72.222 0.00 0.00 0.00 4.26
1162 1613 3.333219 TCCCCCTTGCTGCTCCTG 61.333 66.667 0.00 0.00 0.00 3.86
1181 1632 7.137426 GCTCCTGCAATAAACTTATCAATCAG 58.863 38.462 0.00 0.00 39.41 2.90
1183 1634 6.602803 TCCTGCAATAAACTTATCAATCAGCA 59.397 34.615 0.00 0.00 0.00 4.41
1184 1635 7.286087 TCCTGCAATAAACTTATCAATCAGCAT 59.714 33.333 0.00 0.00 0.00 3.79
1185 1636 7.381408 CCTGCAATAAACTTATCAATCAGCATG 59.619 37.037 0.00 0.00 37.54 4.06
1188 1639 7.380602 GCAATAAACTTATCAATCAGCATGTCC 59.619 37.037 0.00 0.00 37.40 4.02
1205 1656 3.976169 TGTCCTGCAATAAACAAACTGC 58.024 40.909 0.00 0.00 35.32 4.40
1206 1657 3.382865 TGTCCTGCAATAAACAAACTGCA 59.617 39.130 0.00 0.00 42.28 4.41
1207 1658 4.039004 TGTCCTGCAATAAACAAACTGCAT 59.961 37.500 0.00 0.00 43.42 3.96
1208 1659 4.386652 GTCCTGCAATAAACAAACTGCATG 59.613 41.667 0.00 0.00 43.42 4.06
1209 1660 3.123959 CCTGCAATAAACAAACTGCATGC 59.876 43.478 11.82 11.82 43.42 4.06
1210 1661 3.725490 TGCAATAAACAAACTGCATGCA 58.275 36.364 21.29 21.29 39.77 3.96
1211 1662 4.316645 TGCAATAAACAAACTGCATGCAT 58.683 34.783 22.97 3.95 39.77 3.96
1212 1663 4.152580 TGCAATAAACAAACTGCATGCATG 59.847 37.500 22.97 22.70 39.77 4.06
1374 2017 7.672240 TGTGATTGTCATGTAGTACAGGTTTA 58.328 34.615 14.17 2.26 30.95 2.01
1375 2018 8.151596 TGTGATTGTCATGTAGTACAGGTTTAA 58.848 33.333 14.17 8.70 30.95 1.52
1399 2042 6.418057 TTTGTTTCAAGGGAATAATGCACT 57.582 33.333 0.00 0.00 31.93 4.40
1462 2108 5.300969 TGCAGATCAGCTACACATTTTTC 57.699 39.130 11.68 0.00 34.99 2.29
1555 2204 7.593273 TGCGTGTTATTTTCCAGTTCTTTATTG 59.407 33.333 0.00 0.00 0.00 1.90
1567 2216 6.376581 CCAGTTCTTTATTGAGGAGCAGATTT 59.623 38.462 0.00 0.00 0.00 2.17
1568 2217 7.554118 CCAGTTCTTTATTGAGGAGCAGATTTA 59.446 37.037 0.00 0.00 0.00 1.40
1569 2218 9.118300 CAGTTCTTTATTGAGGAGCAGATTTAT 57.882 33.333 0.00 0.00 0.00 1.40
1604 2264 4.669197 CGGAAAAAGATACCTGAACTTGCG 60.669 45.833 0.00 0.00 0.00 4.85
1613 2273 1.217001 CTGAACTTGCGTGTGTGCTA 58.783 50.000 0.00 0.00 35.36 3.49
1614 2274 1.193203 CTGAACTTGCGTGTGTGCTAG 59.807 52.381 0.00 0.00 42.32 3.42
1696 2356 2.489722 GGAGATCTGTTTGCTTTGGTCC 59.510 50.000 0.00 0.00 0.00 4.46
1738 2441 7.538303 TGTAACTGTATATGTGCTCATGTTG 57.462 36.000 11.46 2.38 35.70 3.33
1808 2544 6.625267 ACTTATATCTGGACCTACTGGATGT 58.375 40.000 0.00 0.00 37.04 3.06
1933 2669 3.508402 TCCACTGTATTAGCGACACAAGA 59.492 43.478 0.00 0.00 0.00 3.02
2017 2762 2.218953 CATGTTTCTGGCATGCCATC 57.781 50.000 38.47 26.38 46.15 3.51
2018 2763 1.754803 CATGTTTCTGGCATGCCATCT 59.245 47.619 38.47 16.85 46.15 2.90
2019 2764 2.804986 TGTTTCTGGCATGCCATCTA 57.195 45.000 38.47 23.91 46.15 1.98
2020 2765 3.084536 TGTTTCTGGCATGCCATCTAA 57.915 42.857 38.47 27.73 46.15 2.10
2073 2890 8.950208 ATAGCTTAACTCAAATAGTTCACCTC 57.050 34.615 0.00 0.00 45.64 3.85
2095 2916 6.758886 CCTCGCTAGTATTTCAGTCAATTTCT 59.241 38.462 0.00 0.00 0.00 2.52
2126 2947 5.112220 TGTCTTCACAATGTTGCAATCTC 57.888 39.130 0.59 0.00 0.00 2.75
2192 3013 1.328279 TCCTCTTGTCTTGACAGCGA 58.672 50.000 3.61 4.60 0.00 4.93
2407 3228 2.119029 GGCGCCATCCCCAAACTAC 61.119 63.158 24.80 0.00 0.00 2.73
2447 3268 3.338249 GCAACTTCCATTGTGCTAGAGA 58.662 45.455 0.00 0.00 31.83 3.10
2508 3329 3.485877 GGAATGATGGTTTCGCTCTTTCG 60.486 47.826 0.00 0.00 0.00 3.46
2541 3362 6.049149 ACATAACTTATGGATGAGTGGAACG 58.951 40.000 12.48 0.00 40.65 3.95
2556 3377 3.924686 GTGGAACGACGAATAGAATGTGT 59.075 43.478 0.00 0.00 0.00 3.72
2727 3548 1.940613 GTGGAACTTGAGCTCGTTGTT 59.059 47.619 11.18 13.50 0.00 2.83
2804 3625 2.413453 GACTTGGAGAATGACTGAACGC 59.587 50.000 0.00 0.00 0.00 4.84
2844 3670 2.676342 GCGTGTTGGGAAACATAGTAGG 59.324 50.000 0.00 0.00 34.86 3.18
2848 3674 5.470777 CGTGTTGGGAAACATAGTAGGAAAA 59.529 40.000 0.00 0.00 34.86 2.29
2909 3736 2.778299 GGAAGATGTGTTGGTGTAGCA 58.222 47.619 0.00 0.00 0.00 3.49
2935 3762 4.470304 GGTACAGATTCCTTACAACCTCCT 59.530 45.833 0.00 0.00 0.00 3.69
2936 3763 5.659971 GGTACAGATTCCTTACAACCTCCTA 59.340 44.000 0.00 0.00 0.00 2.94
2970 3797 7.678837 AGAATTTTCTCTCACAATCTCTCTGT 58.321 34.615 0.00 0.00 29.94 3.41
2998 3837 3.058914 GGTATCTCTGTGTGTGTTTGTGC 60.059 47.826 0.00 0.00 0.00 4.57
3017 3856 1.375908 GGGTGCGCATGAGTGAGAA 60.376 57.895 15.91 0.00 0.00 2.87
3028 3867 3.003763 GTGAGAAGGAGGGCGGGT 61.004 66.667 0.00 0.00 0.00 5.28
3358 4207 6.737254 ACTTGGTGTTTATTATTCCACTCG 57.263 37.500 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.428045 CCATTGGAAGAAGGCATTCGAAC 60.428 47.826 5.31 0.47 40.58 3.95
1 2 2.754552 CCATTGGAAGAAGGCATTCGAA 59.245 45.455 5.31 0.00 40.58 3.71
2 3 2.026356 TCCATTGGAAGAAGGCATTCGA 60.026 45.455 1.94 0.00 40.58 3.71
3 4 2.368439 TCCATTGGAAGAAGGCATTCG 58.632 47.619 1.94 0.00 40.58 3.34
4 5 3.004106 CGATCCATTGGAAGAAGGCATTC 59.996 47.826 9.98 2.10 34.34 2.67
5 6 2.954318 CGATCCATTGGAAGAAGGCATT 59.046 45.455 9.98 0.00 34.34 3.56
72 73 1.972872 AAATGTGCCGATGGATCTCC 58.027 50.000 0.00 0.00 0.00 3.71
80 101 5.927689 CCATTTGCATATAAAATGTGCCGAT 59.072 36.000 16.22 0.00 45.45 4.18
104 131 1.343506 CCGTTCTGTTACCGTGCTAC 58.656 55.000 0.00 0.00 0.00 3.58
173 215 2.525105 TAAATTCTTGGGTGGGCCTC 57.475 50.000 4.53 0.00 34.45 4.70
232 277 5.238868 GGGTCGGCTATAGAATTTCTTTTCC 59.761 44.000 3.21 1.91 0.00 3.13
233 278 5.238868 GGGGTCGGCTATAGAATTTCTTTTC 59.761 44.000 3.21 0.00 0.00 2.29
263 310 9.935682 GCGAATTATGAAATCTTAATGTTGAGA 57.064 29.630 0.00 0.00 0.00 3.27
369 616 7.909777 CGTACATACGGATATACATCAATCC 57.090 40.000 3.47 0.00 45.30 3.01
457 704 5.004726 CGTTTCCAGTTTCTTTTTCTTGCAG 59.995 40.000 0.00 0.00 0.00 4.41
469 720 2.225727 GACCCATCACGTTTCCAGTTTC 59.774 50.000 0.00 0.00 0.00 2.78
508 760 4.680237 CCGAGTCACGCTGGCCAA 62.680 66.667 7.01 0.00 41.07 4.52
523 775 2.361104 TTTTGCCCCTGCTAGCCG 60.361 61.111 13.29 5.57 38.71 5.52
577 841 2.230750 GGTATATATAGCCGGGATCGCC 59.769 54.545 2.18 0.00 34.56 5.54
578 842 3.155501 AGGTATATATAGCCGGGATCGC 58.844 50.000 16.49 0.00 34.56 4.58
585 849 2.626743 CGGGGGAAGGTATATATAGCCG 59.373 54.545 16.49 9.24 0.00 5.52
644 920 0.316196 GCGGCGAAATTCGAATCTGG 60.316 55.000 20.38 0.00 43.74 3.86
753 1038 2.498941 TAGCCGCTTCGGATCTGGG 61.499 63.158 9.70 0.00 44.45 4.45
761 1046 1.226888 GGTACTGGTAGCCGCTTCG 60.227 63.158 0.00 0.00 0.00 3.79
829 1120 2.561373 CAACCGCGAAGAAAGGCC 59.439 61.111 8.23 0.00 0.00 5.19
852 1296 2.676471 CCAAAAGCCCTCCACCCG 60.676 66.667 0.00 0.00 0.00 5.28
862 1307 4.002506 CCCCCGGCAACCAAAAGC 62.003 66.667 0.00 0.00 0.00 3.51
882 1327 2.696759 CGAACCAATCAACCCCCGC 61.697 63.158 0.00 0.00 0.00 6.13
883 1328 2.043980 CCGAACCAATCAACCCCCG 61.044 63.158 0.00 0.00 0.00 5.73
979 1430 4.075793 TCCTCCCCTGACCTCCGG 62.076 72.222 0.00 0.00 0.00 5.14
980 1431 2.443016 CTCCTCCCCTGACCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
981 1432 2.041405 CCTCCTCCCCTGACCTCC 60.041 72.222 0.00 0.00 0.00 4.30
982 1433 1.967343 ATCCCTCCTCCCCTGACCTC 61.967 65.000 0.00 0.00 0.00 3.85
983 1434 1.949449 ATCCCTCCTCCCCTGACCT 60.949 63.158 0.00 0.00 0.00 3.85
984 1435 1.768077 CATCCCTCCTCCCCTGACC 60.768 68.421 0.00 0.00 0.00 4.02
1017 1468 1.065928 CGACTGCCGGTACATCTCC 59.934 63.158 1.90 0.00 33.91 3.71
1069 1520 2.437359 GCCGCTGCTCACCATCTT 60.437 61.111 0.00 0.00 33.53 2.40
1140 1591 4.120755 GCAGCAAGGGGGAGGGAG 62.121 72.222 0.00 0.00 0.00 4.30
1141 1592 4.682714 AGCAGCAAGGGGGAGGGA 62.683 66.667 0.00 0.00 0.00 4.20
1144 1595 3.013932 AGGAGCAGCAAGGGGGAG 61.014 66.667 0.00 0.00 0.00 4.30
1145 1596 3.333219 CAGGAGCAGCAAGGGGGA 61.333 66.667 0.00 0.00 0.00 4.81
1157 1608 7.137426 GCTGATTGATAAGTTTATTGCAGGAG 58.863 38.462 0.00 0.00 0.00 3.69
1159 1610 6.798482 TGCTGATTGATAAGTTTATTGCAGG 58.202 36.000 0.00 0.00 0.00 4.85
1162 1613 7.380602 GGACATGCTGATTGATAAGTTTATTGC 59.619 37.037 0.00 0.00 0.00 3.56
1163 1614 8.627403 AGGACATGCTGATTGATAAGTTTATTG 58.373 33.333 0.00 0.00 0.00 1.90
1164 1615 8.627403 CAGGACATGCTGATTGATAAGTTTATT 58.373 33.333 0.00 0.00 0.00 1.40
1165 1616 8.162878 CAGGACATGCTGATTGATAAGTTTAT 57.837 34.615 0.00 0.00 0.00 1.40
1166 1617 7.558161 CAGGACATGCTGATTGATAAGTTTA 57.442 36.000 0.00 0.00 0.00 2.01
1183 1634 4.039004 TGCAGTTTGTTTATTGCAGGACAT 59.961 37.500 0.00 0.00 41.23 3.06
1184 1635 3.382865 TGCAGTTTGTTTATTGCAGGACA 59.617 39.130 0.00 0.00 41.23 4.02
1185 1636 3.976169 TGCAGTTTGTTTATTGCAGGAC 58.024 40.909 0.00 0.00 41.23 3.85
1205 1656 1.135053 TCAAAACATCCGGCATGCATG 60.135 47.619 22.70 22.70 35.65 4.06
1206 1657 1.184431 TCAAAACATCCGGCATGCAT 58.816 45.000 21.36 0.85 35.65 3.96
1207 1658 1.134753 GATCAAAACATCCGGCATGCA 59.865 47.619 21.36 0.00 35.65 3.96
1208 1659 1.536709 GGATCAAAACATCCGGCATGC 60.537 52.381 9.90 9.90 35.65 4.06
1209 1660 2.026641 AGGATCAAAACATCCGGCATG 58.973 47.619 0.00 4.32 46.43 4.06
1210 1661 2.026641 CAGGATCAAAACATCCGGCAT 58.973 47.619 0.00 0.00 46.43 4.40
1211 1662 1.462616 CAGGATCAAAACATCCGGCA 58.537 50.000 0.00 0.00 46.43 5.69
1212 1663 0.740737 CCAGGATCAAAACATCCGGC 59.259 55.000 0.00 0.00 46.43 6.13
1213 1664 2.017049 GACCAGGATCAAAACATCCGG 58.983 52.381 0.00 0.00 46.43 5.14
1214 1665 2.991250 AGACCAGGATCAAAACATCCG 58.009 47.619 0.00 0.00 46.43 4.18
1215 1666 4.082125 ACAAGACCAGGATCAAAACATCC 58.918 43.478 0.00 0.00 42.68 3.51
1216 1667 5.010012 ACAACAAGACCAGGATCAAAACATC 59.990 40.000 0.00 0.00 0.00 3.06
1217 1668 4.895297 ACAACAAGACCAGGATCAAAACAT 59.105 37.500 0.00 0.00 0.00 2.71
1374 2017 7.452562 AGTGCATTATTCCCTTGAAACAAATT 58.547 30.769 0.00 0.00 33.32 1.82
1375 2018 7.008021 AGTGCATTATTCCCTTGAAACAAAT 57.992 32.000 0.00 0.00 33.32 2.32
1569 2218 9.597681 AGGTATCTTTTTCCGGAGAAGTATATA 57.402 33.333 21.88 13.55 32.35 0.86
1570 2219 8.368668 CAGGTATCTTTTTCCGGAGAAGTATAT 58.631 37.037 21.88 14.26 32.35 0.86
1613 2273 5.938125 ACAAACTGTCGTAATTTGGCTATCT 59.062 36.000 0.00 0.00 37.59 1.98
1614 2274 6.178239 ACAAACTGTCGTAATTTGGCTATC 57.822 37.500 0.00 0.00 37.59 2.08
1710 2370 9.177608 ACATGAGCACATATACAGTTACATTTT 57.822 29.630 0.00 0.00 35.09 1.82
1711 2371 8.737168 ACATGAGCACATATACAGTTACATTT 57.263 30.769 0.00 0.00 35.09 2.32
1712 2372 8.615211 CAACATGAGCACATATACAGTTACATT 58.385 33.333 0.00 0.00 35.09 2.71
1713 2373 7.986889 TCAACATGAGCACATATACAGTTACAT 59.013 33.333 0.00 0.00 35.09 2.29
1714 2374 7.327214 TCAACATGAGCACATATACAGTTACA 58.673 34.615 0.00 0.00 35.09 2.41
1715 2375 7.770801 TCAACATGAGCACATATACAGTTAC 57.229 36.000 0.00 0.00 35.09 2.50
1716 2376 8.829612 CAATCAACATGAGCACATATACAGTTA 58.170 33.333 0.00 0.00 35.09 2.24
1717 2377 7.680350 GCAATCAACATGAGCACATATACAGTT 60.680 37.037 0.00 0.00 35.09 3.16
1718 2378 6.238566 GCAATCAACATGAGCACATATACAGT 60.239 38.462 0.00 0.00 35.09 3.55
1719 2379 6.017357 AGCAATCAACATGAGCACATATACAG 60.017 38.462 0.00 0.00 35.09 2.74
1720 2380 5.824097 AGCAATCAACATGAGCACATATACA 59.176 36.000 0.00 0.00 35.09 2.29
1721 2381 6.309712 AGCAATCAACATGAGCACATATAC 57.690 37.500 0.00 0.00 35.09 1.47
1722 2382 6.947644 AAGCAATCAACATGAGCACATATA 57.052 33.333 0.00 0.00 35.09 0.86
1738 2441 5.799827 ACCCTCTGATAGTCTAAGCAATC 57.200 43.478 0.00 0.00 0.00 2.67
1875 2611 0.457853 TCGGAAACTCGATCGGCAAG 60.458 55.000 16.41 8.06 33.92 4.01
2019 2764 9.167311 CCATGTAGAAAAGTATAGCTTTCTGTT 57.833 33.333 14.95 0.00 45.91 3.16
2020 2765 7.281100 GCCATGTAGAAAAGTATAGCTTTCTGT 59.719 37.037 14.95 3.74 45.91 3.41
2073 2890 7.525688 TCAGAAATTGACTGAAATACTAGCG 57.474 36.000 11.53 0.00 40.70 4.26
2095 2916 7.924947 TGCAACATTGTGAAGACAAAATATTCA 59.075 29.630 0.00 0.00 45.23 2.57
2192 3013 0.392863 TGTATGTGCGCAGATTGCCT 60.393 50.000 26.08 3.83 41.12 4.75
2337 3158 4.399303 GCACTGATGGCAAGTAATAGGTTT 59.601 41.667 0.00 0.00 0.00 3.27
2541 3362 7.063426 TCACAAAGATGACACATTCTATTCGTC 59.937 37.037 0.00 0.00 0.00 4.20
2727 3548 3.242608 GCAGTTCGTGTTACAAAGCTTCA 60.243 43.478 0.00 0.00 0.00 3.02
2804 3625 1.404851 GCCGGAAGAACAGGAGAGAAG 60.405 57.143 5.05 0.00 35.91 2.85
2848 3674 6.773976 TTGATTCATAGGGCGATTCTTTTT 57.226 33.333 0.00 0.00 0.00 1.94
2856 3683 2.158813 GGGAGTTTGATTCATAGGGCGA 60.159 50.000 0.00 0.00 0.00 5.54
2887 3714 2.870435 GCTACACCAACACATCTTCCGT 60.870 50.000 0.00 0.00 0.00 4.69
2909 3736 6.388619 AGGTTGTAAGGAATCTGTACCAAT 57.611 37.500 0.00 0.00 0.00 3.16
2970 3797 1.379443 ACACAGAGATACCGGCCGA 60.379 57.895 30.73 8.21 0.00 5.54
2998 3837 3.190849 CTCACTCATGCGCACCCG 61.191 66.667 14.90 6.12 37.57 5.28
3017 3856 3.670629 CTCTCTCACCCGCCCTCCT 62.671 68.421 0.00 0.00 0.00 3.69
3028 3867 3.368501 CCCCCTCCCCCTCTCTCA 61.369 72.222 0.00 0.00 0.00 3.27
3263 4104 8.551682 TCTTATTTTCCTGATTATGGCCATTT 57.448 30.769 26.37 12.42 0.00 2.32


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

AutoCloner maintained by Alex Coulton.