Multiple sequence alignment - TraesCS5B01G387700

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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 TraesCS5B01G387700 chr5B 100.000 4443 0 0 1 4443 566690683 566686241 0.000000e+00 8205.0
1 TraesCS5B01G387700 chr5B 97.161 634 13 5 1 633 63843186 63843815 0.000000e+00 1066.0
2 TraesCS5B01G387700 chr5D 95.129 1971 62 14 1689 3654 460760575 460758634 0.000000e+00 3077.0
3 TraesCS5B01G387700 chr5D 97.100 793 20 1 3651 4443 460758474 460757685 0.000000e+00 1334.0
4 TraesCS5B01G387700 chr5D 89.155 1042 64 26 630 1658 460761852 460760847 0.000000e+00 1253.0
5 TraesCS5B01G387700 chr5D 97.930 628 13 0 1 628 17143566 17142939 0.000000e+00 1088.0
6 TraesCS5B01G387700 chr5A 93.935 1385 64 17 2262 3640 580948798 580947428 0.000000e+00 2074.0
7 TraesCS5B01G387700 chr5A 95.082 793 39 0 3651 4443 580947238 580946446 0.000000e+00 1249.0
8 TraesCS5B01G387700 chr5A 86.156 744 53 31 630 1365 580950493 580949792 0.000000e+00 758.0
9 TraesCS5B01G387700 chr5A 82.573 482 39 25 1789 2243 580949253 580948790 2.510000e-102 383.0
10 TraesCS5B01G387700 chr5A 90.385 260 17 4 1394 1653 580949796 580949545 7.120000e-88 335.0
11 TraesCS5B01G387700 chr5A 100.000 28 0 0 3627 3654 580947415 580947388 8.000000e-03 52.8
12 TraesCS5B01G387700 chr1B 99.048 630 5 1 1 630 33026671 33027299 0.000000e+00 1129.0
13 TraesCS5B01G387700 chr6A 98.891 631 7 0 1 631 447166425 447167055 0.000000e+00 1127.0
14 TraesCS5B01G387700 chr6A 97.297 629 17 0 1 629 397198280 397197652 0.000000e+00 1068.0
15 TraesCS5B01G387700 chr7D 97.933 629 13 0 1 629 5133449 5134077 0.000000e+00 1090.0
16 TraesCS5B01G387700 chr3B 97.627 632 13 1 1 630 672430227 672429596 0.000000e+00 1083.0
17 TraesCS5B01G387700 chr1A 98.217 617 11 0 1 617 99874595 99873979 0.000000e+00 1079.0
18 TraesCS5B01G387700 chr4A 97.615 629 12 1 1 629 591716249 591715624 0.000000e+00 1075.0


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 TraesCS5B01G387700 chr5B 566686241 566690683 4442 True 8205.000000 8205 100.000000 1 4443 1 chr5B.!!$R1 4442
1 TraesCS5B01G387700 chr5B 63843186 63843815 629 False 1066.000000 1066 97.161000 1 633 1 chr5B.!!$F1 632
2 TraesCS5B01G387700 chr5D 460757685 460761852 4167 True 1888.000000 3077 93.794667 630 4443 3 chr5D.!!$R2 3813
3 TraesCS5B01G387700 chr5D 17142939 17143566 627 True 1088.000000 1088 97.930000 1 628 1 chr5D.!!$R1 627
4 TraesCS5B01G387700 chr5A 580946446 580950493 4047 True 808.633333 2074 91.355167 630 4443 6 chr5A.!!$R1 3813
5 TraesCS5B01G387700 chr1B 33026671 33027299 628 False 1129.000000 1129 99.048000 1 630 1 chr1B.!!$F1 629
6 TraesCS5B01G387700 chr6A 447166425 447167055 630 False 1127.000000 1127 98.891000 1 631 1 chr6A.!!$F1 630
7 TraesCS5B01G387700 chr6A 397197652 397198280 628 True 1068.000000 1068 97.297000 1 629 1 chr6A.!!$R1 628
8 TraesCS5B01G387700 chr7D 5133449 5134077 628 False 1090.000000 1090 97.933000 1 629 1 chr7D.!!$F1 628
9 TraesCS5B01G387700 chr3B 672429596 672430227 631 True 1083.000000 1083 97.627000 1 630 1 chr3B.!!$R1 629
10 TraesCS5B01G387700 chr1A 99873979 99874595 616 True 1079.000000 1079 98.217000 1 617 1 chr1A.!!$R1 616
11 TraesCS5B01G387700 chr4A 591715624 591716249 625 True 1075.000000 1075 97.615000 1 629 1 chr4A.!!$R1 628

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
758 764 0.179000 AAACGGCCCACATTTTTGCA 59.821 45.0 0.0 0.0 0.00 4.08 F
1012 1038 0.034059 ACAGCACACGGAAAGAGAGG 59.966 55.0 0.0 0.0 0.00 3.69 F
1013 1039 0.318441 CAGCACACGGAAAGAGAGGA 59.682 55.0 0.0 0.0 0.00 3.71 F
1558 1584 0.375106 GAGCTTTCCGGCGATTTCTG 59.625 55.0 9.3 0.0 37.29 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2361 0.823356 GGCTGGCTGACAAGGAACAA 60.823 55.0 0.00 0.0 0.0 2.83 R
2531 2884 1.120437 GAGCGCAAAGACAAAAACCG 58.880 50.0 11.47 0.0 0.0 4.44 R
2533 2886 1.822581 ACGAGCGCAAAGACAAAAAC 58.177 45.0 11.47 0.0 0.0 2.43 R
3479 3832 0.883833 GGTGGTGGCATCAGAGTTTG 59.116 55.0 0.00 0.0 0.0 2.93 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
95 96 3.025978 CAGGATTACCACATGGCACAAT 58.974 45.455 0.00 0.00 39.91 2.71
235 238 0.819259 TTTTGCAGCTCAAGTCGCCT 60.819 50.000 0.00 0.00 35.84 5.52
747 752 8.258708 AGATAATCTACAGATAATAAACGGCCC 58.741 37.037 0.00 0.00 33.73 5.80
750 756 3.637911 ACAGATAATAAACGGCCCACA 57.362 42.857 0.00 0.00 0.00 4.17
755 761 6.071051 ACAGATAATAAACGGCCCACATTTTT 60.071 34.615 0.00 0.00 0.00 1.94
756 762 6.255453 CAGATAATAAACGGCCCACATTTTTG 59.745 38.462 0.00 0.00 0.00 2.44
757 763 2.156343 TAAACGGCCCACATTTTTGC 57.844 45.000 0.00 0.00 0.00 3.68
758 764 0.179000 AAACGGCCCACATTTTTGCA 59.821 45.000 0.00 0.00 0.00 4.08
760 766 0.396060 ACGGCCCACATTTTTGCATT 59.604 45.000 0.00 0.00 0.00 3.56
762 768 1.338011 CGGCCCACATTTTTGCATTCT 60.338 47.619 0.00 0.00 0.00 2.40
784 790 5.059404 TCTGCGATTTTTCCTGGATTTTC 57.941 39.130 0.00 0.00 0.00 2.29
799 808 7.278424 TCCTGGATTTTCTACGGTTTATTTACG 59.722 37.037 0.00 0.00 0.00 3.18
800 809 7.278424 CCTGGATTTTCTACGGTTTATTTACGA 59.722 37.037 0.00 0.00 0.00 3.43
819 828 2.941064 CGATCCACGTAGTAGAGACCAA 59.059 50.000 0.00 0.00 41.61 3.67
820 829 3.242673 CGATCCACGTAGTAGAGACCAAC 60.243 52.174 0.00 0.00 41.61 3.77
822 831 3.079578 TCCACGTAGTAGAGACCAACAG 58.920 50.000 0.00 0.00 41.61 3.16
823 832 2.415625 CCACGTAGTAGAGACCAACAGC 60.416 54.545 0.00 0.00 41.61 4.40
825 834 2.488545 ACGTAGTAGAGACCAACAGCAG 59.511 50.000 0.00 0.00 41.94 4.24
826 835 2.159366 CGTAGTAGAGACCAACAGCAGG 60.159 54.545 0.00 0.00 0.00 4.85
827 836 2.310779 AGTAGAGACCAACAGCAGGA 57.689 50.000 0.00 0.00 0.00 3.86
828 837 2.826488 AGTAGAGACCAACAGCAGGAT 58.174 47.619 0.00 0.00 0.00 3.24
829 838 3.982516 AGTAGAGACCAACAGCAGGATA 58.017 45.455 0.00 0.00 0.00 2.59
830 839 3.702045 AGTAGAGACCAACAGCAGGATAC 59.298 47.826 0.00 0.00 0.00 2.24
831 840 2.540383 AGAGACCAACAGCAGGATACA 58.460 47.619 0.00 0.00 41.41 2.29
851 862 2.093537 GAAAACCATTGGCGGCCACA 62.094 55.000 23.78 13.59 30.78 4.17
862 873 1.903404 CGGCCACAAGAAAAGCCCT 60.903 57.895 2.24 0.00 42.66 5.19
869 880 2.232208 CACAAGAAAAGCCCTGGGAATC 59.768 50.000 19.27 8.11 0.00 2.52
923 934 2.258109 GAAACCGAGCCCCCTATATCT 58.742 52.381 0.00 0.00 0.00 1.98
1012 1038 0.034059 ACAGCACACGGAAAGAGAGG 59.966 55.000 0.00 0.00 0.00 3.69
1013 1039 0.318441 CAGCACACGGAAAGAGAGGA 59.682 55.000 0.00 0.00 0.00 3.71
1014 1040 0.605589 AGCACACGGAAAGAGAGGAG 59.394 55.000 0.00 0.00 0.00 3.69
1015 1041 0.603569 GCACACGGAAAGAGAGGAGA 59.396 55.000 0.00 0.00 0.00 3.71
1016 1042 1.403514 GCACACGGAAAGAGAGGAGAG 60.404 57.143 0.00 0.00 0.00 3.20
1017 1043 2.163509 CACACGGAAAGAGAGGAGAGA 58.836 52.381 0.00 0.00 0.00 3.10
1018 1044 2.163412 CACACGGAAAGAGAGGAGAGAG 59.837 54.545 0.00 0.00 0.00 3.20
1019 1045 1.748493 CACGGAAAGAGAGGAGAGAGG 59.252 57.143 0.00 0.00 0.00 3.69
1020 1046 1.341581 ACGGAAAGAGAGGAGAGAGGG 60.342 57.143 0.00 0.00 0.00 4.30
1021 1047 1.788229 GGAAAGAGAGGAGAGAGGGG 58.212 60.000 0.00 0.00 0.00 4.79
1022 1048 1.289530 GGAAAGAGAGGAGAGAGGGGA 59.710 57.143 0.00 0.00 0.00 4.81
1311 1337 1.451927 CCGCCAGCCTTGCTCAATA 60.452 57.895 0.00 0.00 36.40 1.90
1312 1338 1.031571 CCGCCAGCCTTGCTCAATAA 61.032 55.000 0.00 0.00 36.40 1.40
1313 1339 1.027357 CGCCAGCCTTGCTCAATAAT 58.973 50.000 0.00 0.00 36.40 1.28
1314 1340 2.221169 CGCCAGCCTTGCTCAATAATA 58.779 47.619 0.00 0.00 36.40 0.98
1315 1341 2.031682 CGCCAGCCTTGCTCAATAATAC 60.032 50.000 0.00 0.00 36.40 1.89
1316 1342 3.217626 GCCAGCCTTGCTCAATAATACT 58.782 45.455 0.00 0.00 36.40 2.12
1317 1343 3.004106 GCCAGCCTTGCTCAATAATACTG 59.996 47.826 0.00 0.00 36.40 2.74
1318 1344 4.202441 CCAGCCTTGCTCAATAATACTGT 58.798 43.478 0.00 0.00 36.40 3.55
1319 1345 5.368145 CCAGCCTTGCTCAATAATACTGTA 58.632 41.667 0.00 0.00 36.40 2.74
1320 1346 5.237344 CCAGCCTTGCTCAATAATACTGTAC 59.763 44.000 0.00 0.00 36.40 2.90
1340 1366 2.223665 ACAATACTACGAGTAAGCCGGC 60.224 50.000 21.89 21.89 33.89 6.13
1362 1388 3.044305 GCAGTGCTGTCGGGTGAC 61.044 66.667 8.18 0.00 45.71 3.67
1382 1408 2.127232 GAAAGCTGCGCCGTGTTC 60.127 61.111 4.18 2.82 0.00 3.18
1393 1419 2.544359 CGTGTTCACGCCTTCACG 59.456 61.111 12.19 8.76 45.10 4.35
1434 1460 2.668550 GCTTCGCCGGGACTTTGT 60.669 61.111 2.18 0.00 0.00 2.83
1435 1461 2.258726 GCTTCGCCGGGACTTTGTT 61.259 57.895 2.18 0.00 0.00 2.83
1436 1462 1.574428 CTTCGCCGGGACTTTGTTG 59.426 57.895 2.18 0.00 0.00 3.33
1478 1504 1.335496 CGGAGATCTCCCTTTCTCGTC 59.665 57.143 31.77 7.14 46.96 4.20
1496 1522 4.344865 TGGTTTCTCCGGGCCAGC 62.345 66.667 4.39 0.00 39.52 4.85
1508 1534 2.503546 GCCAGCCCAGCTAGAGAC 59.496 66.667 0.00 0.00 36.40 3.36
1522 1548 2.355717 AGAGACGTAGCTTTCAGTGC 57.644 50.000 0.00 0.00 0.00 4.40
1534 1560 1.723608 TTCAGTGCCGTGCTGGTTTG 61.724 55.000 0.00 0.00 41.21 2.93
1535 1561 2.906897 AGTGCCGTGCTGGTTTGG 60.907 61.111 0.00 0.00 41.21 3.28
1536 1562 3.977244 GTGCCGTGCTGGTTTGGG 61.977 66.667 0.00 0.00 41.21 4.12
1558 1584 0.375106 GAGCTTTCCGGCGATTTCTG 59.625 55.000 9.30 0.00 37.29 3.02
1563 1589 1.187974 TTCCGGCGATTTCTGGTCTA 58.812 50.000 9.30 0.00 34.12 2.59
1569 1595 3.736252 CGGCGATTTCTGGTCTATAGTTG 59.264 47.826 0.00 0.00 0.00 3.16
1605 1631 3.490078 CGTGAATTCTAGGCCAGACTCTC 60.490 52.174 5.01 5.71 31.12 3.20
1650 1676 4.464069 TGTGACATCACCATTATGACGA 57.536 40.909 9.48 0.00 45.88 4.20
1671 1731 4.038522 CGAGTATGTTCAGATCCTGTCCAT 59.961 45.833 0.00 0.00 32.61 3.41
1676 1736 8.589338 AGTATGTTCAGATCCTGTCCATATTAC 58.411 37.037 0.00 0.00 32.60 1.89
1677 1737 6.174720 TGTTCAGATCCTGTCCATATTACC 57.825 41.667 0.00 0.00 32.61 2.85
1679 1739 6.329986 TGTTCAGATCCTGTCCATATTACCAT 59.670 38.462 0.00 0.00 32.61 3.55
1680 1740 7.147320 TGTTCAGATCCTGTCCATATTACCATT 60.147 37.037 0.00 0.00 32.61 3.16
1681 1741 8.375506 GTTCAGATCCTGTCCATATTACCATTA 58.624 37.037 0.00 0.00 32.61 1.90
1682 1742 7.907389 TCAGATCCTGTCCATATTACCATTAC 58.093 38.462 0.00 0.00 32.61 1.89
1684 1744 6.792473 AGATCCTGTCCATATTACCATTACCA 59.208 38.462 0.00 0.00 0.00 3.25
1686 1746 7.401060 TCCTGTCCATATTACCATTACCATT 57.599 36.000 0.00 0.00 0.00 3.16
1720 2013 4.946157 CAGTCAAGATCCAGCTTACCATTT 59.054 41.667 0.00 0.00 0.00 2.32
1738 2031 4.458295 CCATTTGAGCTGTTGAGACTGATT 59.542 41.667 0.00 0.00 0.00 2.57
1739 2032 5.048224 CCATTTGAGCTGTTGAGACTGATTT 60.048 40.000 0.00 0.00 0.00 2.17
1741 2034 5.679734 TTGAGCTGTTGAGACTGATTTTC 57.320 39.130 0.00 0.00 0.00 2.29
1787 2080 6.619801 AAGTTGAAACTTCACACTGGTATC 57.380 37.500 2.56 0.00 45.65 2.24
1896 2189 5.044846 AGTCTTGCCTGAACCCTTTATGTAT 60.045 40.000 0.00 0.00 0.00 2.29
1897 2190 6.157994 AGTCTTGCCTGAACCCTTTATGTATA 59.842 38.462 0.00 0.00 0.00 1.47
1898 2191 6.483640 GTCTTGCCTGAACCCTTTATGTATAG 59.516 42.308 0.00 0.00 0.00 1.31
1899 2192 6.385759 TCTTGCCTGAACCCTTTATGTATAGA 59.614 38.462 0.00 0.00 0.00 1.98
1900 2193 6.763715 TGCCTGAACCCTTTATGTATAGAT 57.236 37.500 0.00 0.00 0.00 1.98
1940 2233 5.365403 TTTTCCCTACACTATGTTTTGCG 57.635 39.130 0.00 0.00 0.00 4.85
1944 2237 2.347452 CCTACACTATGTTTTGCGTCCG 59.653 50.000 0.00 0.00 0.00 4.79
2025 2347 6.703607 CACATGTCCATCTTACCTTGATACTC 59.296 42.308 0.00 0.00 0.00 2.59
2055 2377 2.942804 TCAATTGTTCCTTGTCAGCCA 58.057 42.857 5.13 0.00 0.00 4.75
2183 2529 8.918116 ACTAACTCATAAGTGAAGATGATAGCA 58.082 33.333 0.00 0.00 35.36 3.49
2184 2530 9.755804 CTAACTCATAAGTGAAGATGATAGCAA 57.244 33.333 0.00 0.00 35.36 3.91
2245 2592 9.095065 TCGATAGGAAGCAACTTTTACTTATTC 57.905 33.333 0.00 0.00 0.00 1.75
2336 2685 1.838112 TGGGCTGCCAACTTGAATAG 58.162 50.000 22.05 0.00 0.00 1.73
2497 2849 7.043059 CGACTAGTGCTCCTGAGAATTATTTTC 60.043 40.741 0.00 0.00 0.00 2.29
2531 2884 8.561738 TTCTTGAAATATGTTAACCTGACTCC 57.438 34.615 2.48 0.00 0.00 3.85
2532 2885 6.816640 TCTTGAAATATGTTAACCTGACTCCG 59.183 38.462 2.48 0.00 0.00 4.63
2533 2886 5.424757 TGAAATATGTTAACCTGACTCCGG 58.575 41.667 2.48 0.00 0.00 5.14
2577 2930 3.004734 CCAGGATGTTTGGTTCTGTGAAC 59.995 47.826 2.16 2.16 0.00 3.18
2601 2954 3.515104 ACATATTTTGCCTGTTCCAAGGG 59.485 43.478 0.00 0.00 37.84 3.95
2757 3110 2.158813 TCTCAGTGGAAGGTTCGCTTTT 60.159 45.455 0.00 0.00 0.00 2.27
2837 3190 9.612066 ATCTCTCTTCTGAAAGGATGTAAATTC 57.388 33.333 0.00 0.00 33.03 2.17
3016 3369 1.847328 CCATTCCCCAAAGGTACACC 58.153 55.000 0.00 0.00 36.75 4.16
3048 3401 1.900981 TTGCCACGGTTCACCCATG 60.901 57.895 0.00 0.00 0.00 3.66
3078 3431 7.717875 TCTTTGTTTGTATCCCTATAATTCGGG 59.282 37.037 1.84 1.84 42.05 5.14
3081 3434 6.099990 TGTTTGTATCCCTATAATTCGGGTGA 59.900 38.462 7.13 0.00 41.40 4.02
3115 3468 6.481976 TCATCTTGACACTACATTTTCGTTGT 59.518 34.615 0.00 0.00 0.00 3.32
3400 3753 7.782242 TGCATTTTATTTTTGAGCAGTTTACG 58.218 30.769 0.00 0.00 0.00 3.18
3479 3832 5.228843 GCTGTAAGTTTACCGATACTCGAAC 59.771 44.000 0.00 0.00 38.18 3.95
3521 3874 2.504175 GGTGGTAGAGGTTTATCAGCCA 59.496 50.000 0.00 0.00 0.00 4.75
3537 3891 4.017126 TCAGCCACCCTATATATGTCTCG 58.983 47.826 0.00 0.00 0.00 4.04
3584 3938 9.296400 GCTTAGTTTGTTTTGTCTTTTGTATCA 57.704 29.630 0.00 0.00 0.00 2.15
3613 3993 3.084070 GCTTGCAGCTAGTGTTTTTGT 57.916 42.857 5.72 0.00 38.45 2.83
3624 4004 6.040247 GCTAGTGTTTTTGTTTTAGGCAGTT 58.960 36.000 0.00 0.00 0.00 3.16
3625 4005 6.198403 GCTAGTGTTTTTGTTTTAGGCAGTTC 59.802 38.462 0.00 0.00 0.00 3.01
3821 4364 6.427853 CCTTCACGATTATATGGAAATGCTGA 59.572 38.462 0.00 0.00 0.00 4.26
3823 4366 5.409520 TCACGATTATATGGAAATGCTGAGC 59.590 40.000 0.00 0.00 0.00 4.26
3868 4411 9.476928 AGGGCCAAGTACTTGTATATAGTATAG 57.523 37.037 29.05 13.43 38.85 1.31
4016 4559 1.034292 GCCTGAAATCCTGGTGCTCC 61.034 60.000 0.00 0.00 36.37 4.70
4028 4574 1.559682 TGGTGCTCCTGTAAATCCTCC 59.440 52.381 6.34 0.00 34.23 4.30
4029 4575 1.840635 GGTGCTCCTGTAAATCCTCCT 59.159 52.381 0.00 0.00 0.00 3.69
4030 4576 2.158885 GGTGCTCCTGTAAATCCTCCTC 60.159 54.545 0.00 0.00 0.00 3.71
4196 4742 1.352156 GGCACTTGTAGAGGAACGCG 61.352 60.000 3.53 3.53 0.00 6.01
4199 4745 2.607187 CACTTGTAGAGGAACGCGAAT 58.393 47.619 15.93 0.00 0.00 3.34
4385 4931 5.491070 CGATGCCCAGATATGATTTTAGGA 58.509 41.667 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 4.587976 AACACTCCTACTCCTGTAGCTA 57.412 45.455 0.00 0.00 43.51 3.32
213 214 1.002468 GCGACTTGAGCTGCAAAAAGA 60.002 47.619 13.58 0.00 35.74 2.52
235 238 4.167113 AGGCCTAGAGATCTGAAGTCTACA 59.833 45.833 1.29 0.00 0.00 2.74
650 653 1.288335 AGTCCCAGAGGTCTTATCCGT 59.712 52.381 0.00 0.00 0.00 4.69
651 654 2.074729 AGTCCCAGAGGTCTTATCCG 57.925 55.000 0.00 0.00 0.00 4.18
653 656 4.146564 GTCCTAGTCCCAGAGGTCTTATC 58.853 52.174 0.00 0.00 33.25 1.75
654 657 3.117054 GGTCCTAGTCCCAGAGGTCTTAT 60.117 52.174 0.00 0.00 33.25 1.73
655 658 2.244252 GGTCCTAGTCCCAGAGGTCTTA 59.756 54.545 0.00 0.00 33.25 2.10
657 660 0.632294 GGTCCTAGTCCCAGAGGTCT 59.368 60.000 0.00 0.00 35.54 3.85
658 661 0.752376 CGGTCCTAGTCCCAGAGGTC 60.752 65.000 0.00 0.00 34.20 3.85
659 662 1.306970 CGGTCCTAGTCCCAGAGGT 59.693 63.158 0.00 0.00 34.20 3.85
662 666 1.002069 TAACCGGTCCTAGTCCCAGA 58.998 55.000 8.04 0.00 0.00 3.86
664 668 2.555732 AATAACCGGTCCTAGTCCCA 57.444 50.000 8.04 0.00 0.00 4.37
757 763 3.691118 TCCAGGAAAAATCGCAGAGAATG 59.309 43.478 0.00 0.00 43.63 2.67
758 764 3.955471 TCCAGGAAAAATCGCAGAGAAT 58.045 40.909 0.00 0.00 43.63 2.40
760 766 3.634397 ATCCAGGAAAAATCGCAGAGA 57.366 42.857 0.00 0.00 43.63 3.10
762 768 4.766891 AGAAAATCCAGGAAAAATCGCAGA 59.233 37.500 0.00 0.00 45.75 4.26
784 790 5.550701 CGTGGATCGTAAATAAACCGTAG 57.449 43.478 0.00 0.00 34.52 3.51
799 808 3.693085 TGTTGGTCTCTACTACGTGGATC 59.307 47.826 5.70 0.00 0.00 3.36
800 809 3.693807 TGTTGGTCTCTACTACGTGGAT 58.306 45.455 5.70 0.00 0.00 3.41
810 819 3.701542 CTGTATCCTGCTGTTGGTCTCTA 59.298 47.826 0.00 0.00 0.00 2.43
811 820 2.499289 CTGTATCCTGCTGTTGGTCTCT 59.501 50.000 0.00 0.00 0.00 3.10
812 821 2.497675 TCTGTATCCTGCTGTTGGTCTC 59.502 50.000 0.00 0.00 0.00 3.36
814 823 3.334583 TTCTGTATCCTGCTGTTGGTC 57.665 47.619 0.00 0.00 0.00 4.02
816 825 3.191371 GGTTTTCTGTATCCTGCTGTTGG 59.809 47.826 0.00 0.00 0.00 3.77
817 826 3.820467 TGGTTTTCTGTATCCTGCTGTTG 59.180 43.478 0.00 0.00 0.00 3.33
819 828 3.788227 TGGTTTTCTGTATCCTGCTGT 57.212 42.857 0.00 0.00 0.00 4.40
820 829 4.142315 CCAATGGTTTTCTGTATCCTGCTG 60.142 45.833 0.00 0.00 0.00 4.41
822 831 3.429410 GCCAATGGTTTTCTGTATCCTGC 60.429 47.826 0.00 0.00 0.00 4.85
823 832 3.181497 CGCCAATGGTTTTCTGTATCCTG 60.181 47.826 0.00 0.00 0.00 3.86
825 834 2.099098 CCGCCAATGGTTTTCTGTATCC 59.901 50.000 0.00 0.00 0.00 2.59
826 835 2.479560 GCCGCCAATGGTTTTCTGTATC 60.480 50.000 0.00 0.00 0.00 2.24
827 836 1.476488 GCCGCCAATGGTTTTCTGTAT 59.524 47.619 0.00 0.00 0.00 2.29
828 837 0.885196 GCCGCCAATGGTTTTCTGTA 59.115 50.000 0.00 0.00 0.00 2.74
829 838 1.665442 GCCGCCAATGGTTTTCTGT 59.335 52.632 0.00 0.00 0.00 3.41
830 839 1.079888 GGCCGCCAATGGTTTTCTG 60.080 57.895 3.91 0.00 0.00 3.02
831 840 1.532794 TGGCCGCCAATGGTTTTCT 60.533 52.632 10.50 0.00 0.00 2.52
851 862 2.291865 GGAGATTCCCAGGGCTTTTCTT 60.292 50.000 0.00 0.00 0.00 2.52
869 880 3.307906 TCGGTCGGTTGGTGGGAG 61.308 66.667 0.00 0.00 0.00 4.30
913 924 3.393800 CGCAAGTCAACAGATATAGGGG 58.606 50.000 0.00 0.00 0.00 4.79
923 934 2.904866 GGCCACCGCAAGTCAACA 60.905 61.111 0.00 0.00 36.38 3.33
955 966 1.079543 GTGCTGCGGTGTGATCTCT 60.080 57.895 0.00 0.00 0.00 3.10
1012 1038 1.271379 CCGATCTCTCTCCCCTCTCTC 60.271 61.905 0.00 0.00 0.00 3.20
1013 1039 0.771127 CCGATCTCTCTCCCCTCTCT 59.229 60.000 0.00 0.00 0.00 3.10
1014 1040 0.768622 TCCGATCTCTCTCCCCTCTC 59.231 60.000 0.00 0.00 0.00 3.20
1015 1041 0.771127 CTCCGATCTCTCTCCCCTCT 59.229 60.000 0.00 0.00 0.00 3.69
1016 1042 0.768622 TCTCCGATCTCTCTCCCCTC 59.231 60.000 0.00 0.00 0.00 4.30
1017 1043 0.771127 CTCTCCGATCTCTCTCCCCT 59.229 60.000 0.00 0.00 0.00 4.79
1018 1044 0.251165 CCTCTCCGATCTCTCTCCCC 60.251 65.000 0.00 0.00 0.00 4.81
1019 1045 0.476771 ACCTCTCCGATCTCTCTCCC 59.523 60.000 0.00 0.00 0.00 4.30
1020 1046 1.142060 TCACCTCTCCGATCTCTCTCC 59.858 57.143 0.00 0.00 0.00 3.71
1021 1047 2.218603 GTCACCTCTCCGATCTCTCTC 58.781 57.143 0.00 0.00 0.00 3.20
1022 1048 1.133915 GGTCACCTCTCCGATCTCTCT 60.134 57.143 0.00 0.00 0.00 3.10
1297 1323 5.817296 TGTACAGTATTATTGAGCAAGGCTG 59.183 40.000 0.00 0.00 39.88 4.85
1311 1337 8.348507 GGCTTACTCGTAGTATTGTACAGTATT 58.651 37.037 1.03 0.12 29.64 1.89
1312 1338 7.307632 CGGCTTACTCGTAGTATTGTACAGTAT 60.308 40.741 1.03 0.00 29.64 2.12
1313 1339 6.018751 CGGCTTACTCGTAGTATTGTACAGTA 60.019 42.308 0.00 0.00 29.64 2.74
1314 1340 5.220739 CGGCTTACTCGTAGTATTGTACAGT 60.221 44.000 0.00 0.00 29.64 3.55
1315 1341 5.203370 CGGCTTACTCGTAGTATTGTACAG 58.797 45.833 0.00 0.00 29.64 2.74
1316 1342 4.035558 CCGGCTTACTCGTAGTATTGTACA 59.964 45.833 0.00 0.00 29.64 2.90
1317 1343 4.531332 CCGGCTTACTCGTAGTATTGTAC 58.469 47.826 0.00 0.00 29.64 2.90
1318 1344 3.003689 GCCGGCTTACTCGTAGTATTGTA 59.996 47.826 22.15 0.00 29.64 2.41
1319 1345 2.223665 GCCGGCTTACTCGTAGTATTGT 60.224 50.000 22.15 0.00 29.64 2.71
1320 1346 2.391879 GCCGGCTTACTCGTAGTATTG 58.608 52.381 22.15 0.00 29.64 1.90
1340 1366 4.081030 CCGACAGCACTGCAAGCG 62.081 66.667 3.30 3.34 37.60 4.68
1346 1372 2.734723 CGTCACCCGACAGCACTG 60.735 66.667 0.00 0.00 42.74 3.66
1424 1450 1.235724 GAACCTCCAACAAAGTCCCG 58.764 55.000 0.00 0.00 0.00 5.14
1478 1504 2.045926 CTGGCCCGGAGAAACCAG 60.046 66.667 0.73 8.05 43.45 4.00
1496 1522 3.103637 AGCTACGTCTCTAGCTGGG 57.896 57.895 9.71 0.00 46.40 4.45
1502 1528 2.163815 GGCACTGAAAGCTACGTCTCTA 59.836 50.000 0.00 0.00 37.60 2.43
1508 1534 1.781555 CACGGCACTGAAAGCTACG 59.218 57.895 0.00 0.00 37.60 3.51
1522 1548 3.294493 CCACCCAAACCAGCACGG 61.294 66.667 0.00 0.00 42.50 4.94
1535 1561 3.682292 ATCGCCGGAAAGCTCCACC 62.682 63.158 5.05 0.00 42.58 4.61
1536 1562 1.305930 AAATCGCCGGAAAGCTCCAC 61.306 55.000 5.05 0.00 42.58 4.02
1586 1612 3.034635 TGGAGAGTCTGGCCTAGAATTC 58.965 50.000 3.32 0.00 37.12 2.17
1605 1631 7.228108 ACATAACTTATGTTGCAGATCTGATGG 59.772 37.037 27.04 10.18 46.69 3.51
1636 1662 6.096282 TCTGAACATACTCGTCATAATGGTGA 59.904 38.462 0.00 0.00 0.00 4.02
1650 1676 7.623999 AATATGGACAGGATCTGAACATACT 57.376 36.000 13.65 5.66 36.91 2.12
1676 1736 6.848451 ACTGTTTAAACGCTAATGGTAATGG 58.152 36.000 13.45 0.00 0.00 3.16
1677 1737 7.523219 TGACTGTTTAAACGCTAATGGTAATG 58.477 34.615 13.45 0.00 0.00 1.90
1679 1739 7.441760 TCTTGACTGTTTAAACGCTAATGGTAA 59.558 33.333 13.45 0.00 0.00 2.85
1680 1740 6.930164 TCTTGACTGTTTAAACGCTAATGGTA 59.070 34.615 13.45 0.00 0.00 3.25
1681 1741 5.761234 TCTTGACTGTTTAAACGCTAATGGT 59.239 36.000 13.45 3.96 0.00 3.55
1682 1742 6.236017 TCTTGACTGTTTAAACGCTAATGG 57.764 37.500 13.45 2.11 0.00 3.16
1684 1744 6.653320 TGGATCTTGACTGTTTAAACGCTAAT 59.347 34.615 13.45 1.37 0.00 1.73
1686 1746 5.543714 TGGATCTTGACTGTTTAAACGCTA 58.456 37.500 13.45 2.57 0.00 4.26
1720 2013 4.965814 AGAAAATCAGTCTCAACAGCTCA 58.034 39.130 0.00 0.00 0.00 4.26
1738 2031 4.464008 ACAGCAGGAATCAAGACAAGAAA 58.536 39.130 0.00 0.00 0.00 2.52
1739 2032 4.090761 ACAGCAGGAATCAAGACAAGAA 57.909 40.909 0.00 0.00 0.00 2.52
1741 2034 3.817084 TGAACAGCAGGAATCAAGACAAG 59.183 43.478 0.00 0.00 0.00 3.16
1787 2080 3.117550 TGGATAACATGATTGGACCCAGG 60.118 47.826 0.00 0.00 0.00 4.45
1940 2233 1.725164 GACGAATCTTTGGACACGGAC 59.275 52.381 0.00 0.00 0.00 4.79
1944 2237 4.690748 TCTTCATGACGAATCTTTGGACAC 59.309 41.667 0.00 0.00 31.69 3.67
2025 2347 9.619316 TGACAAGGAACAATTGATTAATTAACG 57.381 29.630 13.59 0.00 34.81 3.18
2039 2361 0.823356 GGCTGGCTGACAAGGAACAA 60.823 55.000 0.00 0.00 0.00 2.83
2191 2537 8.689972 AGAAAAATTGATCTTCACTTGTGACTT 58.310 29.630 2.62 0.00 0.00 3.01
2193 2539 8.862550 AAGAAAAATTGATCTTCACTTGTGAC 57.137 30.769 2.62 0.00 30.16 3.67
2197 2543 8.786937 TCGAAAGAAAAATTGATCTTCACTTG 57.213 30.769 6.49 0.00 34.90 3.16
2264 2611 7.977789 TGTCAGCAAACATGATCTTTAAGTA 57.022 32.000 0.00 0.00 0.00 2.24
2272 2619 6.187125 AGTATGTTGTCAGCAAACATGATC 57.813 37.500 11.10 0.00 36.22 2.92
2336 2685 6.788243 TGAGTCACATCAATGTTCATTATGC 58.212 36.000 0.00 0.00 39.39 3.14
2508 2860 6.037172 CCGGAGTCAGGTTAACATATTTCAAG 59.963 42.308 8.10 0.00 0.00 3.02
2531 2884 1.120437 GAGCGCAAAGACAAAAACCG 58.880 50.000 11.47 0.00 0.00 4.44
2532 2885 1.120437 CGAGCGCAAAGACAAAAACC 58.880 50.000 11.47 0.00 0.00 3.27
2533 2886 1.822581 ACGAGCGCAAAGACAAAAAC 58.177 45.000 11.47 0.00 0.00 2.43
2577 2930 4.414852 CTTGGAACAGGCAAAATATGTCG 58.585 43.478 0.00 0.00 42.39 4.35
2837 3190 9.840427 CAAAACCATATTCAACTACAGGTTAAG 57.160 33.333 0.00 0.00 36.92 1.85
3016 3369 4.216963 GCAACGCTGCTCTTTGTG 57.783 55.556 2.93 0.00 45.74 3.33
3037 3390 3.157087 ACAAAGATGACATGGGTGAACC 58.843 45.455 0.00 0.00 40.81 3.62
3076 3429 3.706594 TCAAGATGATGAGTACCTCACCC 59.293 47.826 0.00 0.00 43.63 4.61
3078 3431 5.105554 AGTGTCAAGATGATGAGTACCTCAC 60.106 44.000 0.00 0.00 43.63 3.51
3081 3434 5.952347 TGTAGTGTCAAGATGATGAGTACCT 59.048 40.000 0.00 0.00 0.00 3.08
3115 3468 2.355108 GGTGTAGAAGCAGCCTGATGAA 60.355 50.000 0.00 0.00 0.00 2.57
3306 3659 3.073062 ACAACAAGGGTCATCAAGCTAGT 59.927 43.478 0.00 0.00 0.00 2.57
3400 3753 2.285827 ACAGCATTGTCTAGAGCGTC 57.714 50.000 0.00 0.00 29.46 5.19
3479 3832 0.883833 GGTGGTGGCATCAGAGTTTG 59.116 55.000 0.00 0.00 0.00 2.93
3613 3993 7.817418 AGTACATGAAAAGAACTGCCTAAAA 57.183 32.000 0.00 0.00 0.00 1.52
3661 4204 6.971527 TTGATCATGAAACAAAATGGATGC 57.028 33.333 13.69 0.00 0.00 3.91
3821 4364 0.325933 TCTATGTGGTTGCTGCTGCT 59.674 50.000 17.00 0.00 40.48 4.24
3823 4366 1.736126 CTGTCTATGTGGTTGCTGCTG 59.264 52.381 0.00 0.00 0.00 4.41
3831 4374 0.620556 CTTGGCCCTGTCTATGTGGT 59.379 55.000 0.00 0.00 0.00 4.16
3875 4418 8.612145 ACCTACTGTTCTATTTAGGAATTGGTT 58.388 33.333 0.49 0.00 35.56 3.67
4016 4559 4.672587 TCCATTCGAGGAGGATTTACAG 57.327 45.455 0.00 0.00 32.77 2.74
4028 4574 2.691409 TACCCAAGCTTCCATTCGAG 57.309 50.000 0.00 0.00 0.00 4.04
4029 4575 2.421388 CCATACCCAAGCTTCCATTCGA 60.421 50.000 0.00 0.00 0.00 3.71
4030 4576 1.949525 CCATACCCAAGCTTCCATTCG 59.050 52.381 0.00 0.00 0.00 3.34
4196 4742 0.745845 AGTGCATCGTCCAGGCATTC 60.746 55.000 0.00 0.00 40.05 2.67
4199 4745 2.046988 CAGTGCATCGTCCAGGCA 60.047 61.111 0.00 0.00 34.70 4.75
4361 4907 4.637534 CCTAAAATCATATCTGGGCATCGG 59.362 45.833 0.00 0.00 0.00 4.18
4385 4931 1.380302 GGATCCCAAGTGTGTGCCT 59.620 57.895 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.