Multiple sequence alignment - TraesCS2B01G311300

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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 TraesCS2B01G311300 chr2B 100.000 3256 0 0 1 3256 445249985 445253240 0.000000e+00 6013.0
1 TraesCS2B01G311300 chr2B 95.367 518 19 2 2739 3256 10393748 10393236 0.000000e+00 819.0
2 TraesCS2B01G311300 chr2A 90.195 2774 150 55 15 2727 507427726 507430438 0.000000e+00 3504.0
3 TraesCS2B01G311300 chr2A 96.911 518 10 3 2739 3256 554447684 554448195 0.000000e+00 863.0
4 TraesCS2B01G311300 chr2D 88.992 1508 74 39 155 1613 375145187 375146651 0.000000e+00 1781.0
5 TraesCS2B01G311300 chr2D 89.096 1183 51 27 1606 2727 375146728 375147893 0.000000e+00 1399.0
6 TraesCS2B01G311300 chr6A 97.297 518 9 2 2739 3256 189424944 189425456 0.000000e+00 874.0
7 TraesCS2B01G311300 chr6A 96.573 496 12 2 2739 3234 130959145 130959635 0.000000e+00 817.0
8 TraesCS2B01G311300 chr6A 100.000 28 0 0 3229 3256 130983942 130983969 6.000000e-03 52.8
9 TraesCS2B01G311300 chr1A 97.104 518 10 2 2739 3256 522887071 522886559 0.000000e+00 869.0
10 TraesCS2B01G311300 chr7A 96.332 518 14 2 2739 3256 63477249 63476737 0.000000e+00 846.0
11 TraesCS2B01G311300 chr6B 88.417 518 53 5 2739 3256 247274910 247275420 4.620000e-173 617.0
12 TraesCS2B01G311300 chr4A 93.382 136 9 0 1523 1658 667247957 667248092 5.510000e-48 202.0
13 TraesCS2B01G311300 chr4A 93.382 136 9 0 1523 1658 667269993 667270128 5.510000e-48 202.0
14 TraesCS2B01G311300 chr4A 92.647 136 10 0 1523 1658 667293545 667293680 2.560000e-46 196.0
15 TraesCS2B01G311300 chr1B 88.095 126 11 1 1465 1590 28505584 28505705 2.620000e-31 147.0


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 TraesCS2B01G311300 chr2B 445249985 445253240 3255 False 6013 6013 100.000 1 3256 1 chr2B.!!$F1 3255
1 TraesCS2B01G311300 chr2B 10393236 10393748 512 True 819 819 95.367 2739 3256 1 chr2B.!!$R1 517
2 TraesCS2B01G311300 chr2A 507427726 507430438 2712 False 3504 3504 90.195 15 2727 1 chr2A.!!$F1 2712
3 TraesCS2B01G311300 chr2A 554447684 554448195 511 False 863 863 96.911 2739 3256 1 chr2A.!!$F2 517
4 TraesCS2B01G311300 chr2D 375145187 375147893 2706 False 1590 1781 89.044 155 2727 2 chr2D.!!$F1 2572
5 TraesCS2B01G311300 chr6A 189424944 189425456 512 False 874 874 97.297 2739 3256 1 chr6A.!!$F3 517
6 TraesCS2B01G311300 chr1A 522886559 522887071 512 True 869 869 97.104 2739 3256 1 chr1A.!!$R1 517
7 TraesCS2B01G311300 chr7A 63476737 63477249 512 True 846 846 96.332 2739 3256 1 chr7A.!!$R1 517
8 TraesCS2B01G311300 chr6B 247274910 247275420 510 False 617 617 88.417 2739 3256 1 chr6B.!!$F1 517

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
132 146 0.242825 TAAACGGCTCTGGTGTCTCG 59.757 55.0 0.0 0.0 0.0 4.04 F
1196 1253 0.040425 GGTGCCAAGTTTGCGTACAG 60.040 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1397 1454 0.035176 AGGTAAGCGGCGTTTGGTTA 59.965 50.0 19.4 0.0 0.0 2.85 R
2454 2662 0.365523 CGGACGCATTTACAGACACG 59.634 55.0 0.0 0.0 0.0 4.49 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
44 47 2.740714 GGAGGAACGCACGTGCATC 61.741 63.158 37.03 31.31 42.21 3.91
45 48 2.027073 GAGGAACGCACGTGCATCA 61.027 57.895 37.03 0.00 42.21 3.07
57 60 3.490896 CACGTGCATCACATATCTACACC 59.509 47.826 0.82 0.00 33.40 4.16
60 63 4.917998 CGTGCATCACATATCTACACCTAC 59.082 45.833 0.00 0.00 33.40 3.18
76 79 1.545136 CCTACATGCATGTGTGGCAAA 59.455 47.619 36.72 17.70 45.60 3.68
100 114 2.938838 AGGGAAAAATGAACACGGTGA 58.061 42.857 16.29 0.00 0.00 4.02
101 115 2.884639 AGGGAAAAATGAACACGGTGAG 59.115 45.455 16.29 0.00 0.00 3.51
117 131 3.125316 CGGTGAGACAAGGCAGAATAAAC 59.875 47.826 0.00 0.00 0.00 2.01
118 132 3.125316 GGTGAGACAAGGCAGAATAAACG 59.875 47.826 0.00 0.00 0.00 3.60
120 134 2.084546 AGACAAGGCAGAATAAACGGC 58.915 47.619 0.00 0.00 0.00 5.68
121 135 2.084546 GACAAGGCAGAATAAACGGCT 58.915 47.619 0.00 0.00 37.09 5.52
123 137 2.290323 ACAAGGCAGAATAAACGGCTCT 60.290 45.455 0.00 0.00 33.92 4.09
124 138 2.029838 AGGCAGAATAAACGGCTCTG 57.970 50.000 0.00 0.00 39.69 3.35
125 139 1.017387 GGCAGAATAAACGGCTCTGG 58.983 55.000 1.98 0.00 37.62 3.86
126 140 1.679032 GGCAGAATAAACGGCTCTGGT 60.679 52.381 1.98 0.00 37.62 4.00
127 141 1.398390 GCAGAATAAACGGCTCTGGTG 59.602 52.381 1.98 0.00 37.62 4.17
129 143 2.673368 CAGAATAAACGGCTCTGGTGTC 59.327 50.000 0.00 0.00 34.24 3.67
130 144 2.567615 AGAATAAACGGCTCTGGTGTCT 59.432 45.455 0.00 0.00 0.00 3.41
131 145 2.674796 ATAAACGGCTCTGGTGTCTC 57.325 50.000 0.00 0.00 0.00 3.36
132 146 0.242825 TAAACGGCTCTGGTGTCTCG 59.757 55.000 0.00 0.00 0.00 4.04
137 151 2.807045 CTCTGGTGTCTCGCGCAC 60.807 66.667 8.75 3.61 36.22 5.34
166 180 2.511600 GCCCCCGAAGTGATCACG 60.512 66.667 19.85 8.65 36.20 4.35
172 186 2.287668 CCCCGAAGTGATCACGATCTAC 60.288 54.545 19.85 8.18 38.60 2.59
174 188 3.066900 CCCGAAGTGATCACGATCTACTT 59.933 47.826 19.85 17.30 39.50 2.24
192 206 1.001815 CTTTTCAAAGAGCGCGGGAAA 60.002 47.619 8.83 6.33 38.28 3.13
310 330 1.303317 ACGTGGCCCAACAATCTCC 60.303 57.895 0.00 0.00 0.00 3.71
354 374 0.310543 TGCACGGTGAAATTGCTGAC 59.689 50.000 13.29 0.00 37.16 3.51
359 379 0.387239 GGTGAAATTGCTGACCACGC 60.387 55.000 0.00 0.00 0.00 5.34
430 453 1.073216 CGCACCGTAACTCTCTGCAG 61.073 60.000 7.63 7.63 0.00 4.41
471 498 3.311110 TGGCGACCTGACCTGACC 61.311 66.667 0.00 0.00 0.00 4.02
472 499 2.997897 GGCGACCTGACCTGACCT 60.998 66.667 0.00 0.00 0.00 3.85
473 500 2.262915 GCGACCTGACCTGACCTG 59.737 66.667 0.00 0.00 0.00 4.00
474 501 2.276116 GCGACCTGACCTGACCTGA 61.276 63.158 0.00 0.00 0.00 3.86
475 502 1.587054 CGACCTGACCTGACCTGAC 59.413 63.158 0.00 0.00 0.00 3.51
482 509 3.721706 CCTGACCTGACCTGCCCC 61.722 72.222 0.00 0.00 0.00 5.80
505 532 4.035324 CGCCCTGTGTATATATAGGAGACG 59.965 50.000 13.01 9.83 31.91 4.18
617 646 1.266989 GACTCACCTTTTGGAAAGGCG 59.733 52.381 17.12 9.67 44.07 5.52
626 659 0.538746 TTGGAAAGGCGGGGTTCTTC 60.539 55.000 0.00 0.00 0.00 2.87
646 679 4.250305 AGGTGACGGTGTGTGGCC 62.250 66.667 0.00 0.00 0.00 5.36
681 714 2.817258 CCTACGACCTCATCTCATCTCC 59.183 54.545 0.00 0.00 0.00 3.71
736 769 4.940046 GCATGATCTTGTGATGGGTATAGG 59.060 45.833 10.05 0.00 32.19 2.57
737 770 5.494724 CATGATCTTGTGATGGGTATAGGG 58.505 45.833 0.44 0.00 32.19 3.53
738 771 4.826616 TGATCTTGTGATGGGTATAGGGA 58.173 43.478 0.00 0.00 32.19 4.20
739 772 5.223655 TGATCTTGTGATGGGTATAGGGAA 58.776 41.667 0.00 0.00 32.19 3.97
740 773 5.851693 TGATCTTGTGATGGGTATAGGGAAT 59.148 40.000 0.00 0.00 32.19 3.01
741 774 5.825593 TCTTGTGATGGGTATAGGGAATC 57.174 43.478 0.00 0.00 0.00 2.52
742 775 4.283467 TCTTGTGATGGGTATAGGGAATCG 59.717 45.833 0.00 0.00 0.00 3.34
743 776 2.301870 TGTGATGGGTATAGGGAATCGC 59.698 50.000 0.00 0.00 0.00 4.58
901 934 3.591196 TCACAATGCCACAATTAAGCC 57.409 42.857 0.00 0.00 0.00 4.35
902 935 2.233431 TCACAATGCCACAATTAAGCCC 59.767 45.455 0.00 0.00 0.00 5.19
903 936 1.554617 ACAATGCCACAATTAAGCCCC 59.445 47.619 0.00 0.00 0.00 5.80
904 937 1.554160 CAATGCCACAATTAAGCCCCA 59.446 47.619 0.00 0.00 0.00 4.96
905 938 2.171027 CAATGCCACAATTAAGCCCCAT 59.829 45.455 0.00 0.00 0.00 4.00
906 939 1.484038 TGCCACAATTAAGCCCCATC 58.516 50.000 0.00 0.00 0.00 3.51
907 940 1.006998 TGCCACAATTAAGCCCCATCT 59.993 47.619 0.00 0.00 0.00 2.90
908 941 2.243478 TGCCACAATTAAGCCCCATCTA 59.757 45.455 0.00 0.00 0.00 1.98
909 942 3.117169 TGCCACAATTAAGCCCCATCTAT 60.117 43.478 0.00 0.00 0.00 1.98
910 943 3.507622 GCCACAATTAAGCCCCATCTATC 59.492 47.826 0.00 0.00 0.00 2.08
911 944 4.751028 GCCACAATTAAGCCCCATCTATCT 60.751 45.833 0.00 0.00 0.00 1.98
912 945 5.514834 GCCACAATTAAGCCCCATCTATCTA 60.515 44.000 0.00 0.00 0.00 1.98
913 946 6.725364 CCACAATTAAGCCCCATCTATCTAT 58.275 40.000 0.00 0.00 0.00 1.98
914 947 6.825721 CCACAATTAAGCCCCATCTATCTATC 59.174 42.308 0.00 0.00 0.00 2.08
915 948 7.311549 CCACAATTAAGCCCCATCTATCTATCT 60.312 40.741 0.00 0.00 0.00 1.98
916 949 8.762645 CACAATTAAGCCCCATCTATCTATCTA 58.237 37.037 0.00 0.00 0.00 1.98
917 950 9.512748 ACAATTAAGCCCCATCTATCTATCTAT 57.487 33.333 0.00 0.00 0.00 1.98
918 951 9.995003 CAATTAAGCCCCATCTATCTATCTATC 57.005 37.037 0.00 0.00 0.00 2.08
919 952 9.965983 AATTAAGCCCCATCTATCTATCTATCT 57.034 33.333 0.00 0.00 0.00 1.98
952 989 6.681729 TCTATCCGCTCCCTATTTATTTGT 57.318 37.500 0.00 0.00 0.00 2.83
977 1025 1.897133 TCTACCTGCGGCTTAACTTCA 59.103 47.619 0.00 0.00 0.00 3.02
981 1032 1.068541 CCTGCGGCTTAACTTCAAACC 60.069 52.381 0.00 0.00 0.00 3.27
1004 1055 1.213678 CCCATTGCAGGAGAAGATGGA 59.786 52.381 12.02 0.00 39.66 3.41
1005 1056 2.295885 CCATTGCAGGAGAAGATGGAC 58.704 52.381 5.54 0.00 39.66 4.02
1006 1057 1.938577 CATTGCAGGAGAAGATGGACG 59.061 52.381 0.00 0.00 0.00 4.79
1063 1120 2.174349 GCGCTTGCTTTCTCACCG 59.826 61.111 0.00 0.00 35.07 4.94
1097 1154 4.619760 TGACAGCAGTACGTTAATTCTTCG 59.380 41.667 0.00 0.00 0.00 3.79
1190 1247 3.502237 CAGATGGTGCCAAGTTTGC 57.498 52.632 0.00 0.00 0.00 3.68
1196 1253 0.040425 GGTGCCAAGTTTGCGTACAG 60.040 55.000 0.00 0.00 0.00 2.74
1247 1304 3.047877 GGACCCCAACTTCACGCG 61.048 66.667 3.53 3.53 0.00 6.01
1248 1305 3.723348 GACCCCAACTTCACGCGC 61.723 66.667 5.73 0.00 0.00 6.86
1397 1454 2.747446 ACATCGCGGTAATTTTGCTCTT 59.253 40.909 6.13 0.00 0.00 2.85
1427 1484 2.754995 GCTTACCTGCCTTCTGCGC 61.755 63.158 0.00 0.00 45.60 6.09
1433 1490 1.588824 CCTGCCTTCTGCGCATTCAA 61.589 55.000 12.24 3.20 45.60 2.69
1490 1576 3.802139 GTGTTCTTGTTCTGTGTGATCGA 59.198 43.478 0.00 0.00 0.00 3.59
1712 1882 1.559682 GACCCTTTCCTCATGCAGGTA 59.440 52.381 0.00 0.29 43.95 3.08
1729 1899 5.241506 TGCAGGTAAGTTTTGATCCTCAAAG 59.758 40.000 2.88 0.00 45.77 2.77
1750 1922 5.102953 AGAGTTTATATGCCTTGACTGCA 57.897 39.130 0.00 0.00 43.97 4.41
1768 1940 9.671279 TTGACTGCAGATTCATTTCTAGATTTA 57.329 29.630 23.35 0.00 0.00 1.40
1772 1944 8.806429 TGCAGATTCATTTCTAGATTTAACCA 57.194 30.769 0.00 0.00 0.00 3.67
1862 2034 1.910580 GAAAGGTGCTCCGATCCCCA 61.911 60.000 0.00 0.00 39.05 4.96
1870 2042 2.123597 CCGATCCCCACCGGAGTA 60.124 66.667 9.46 0.00 46.60 2.59
1873 2045 0.179009 CGATCCCCACCGGAGTAGTA 60.179 60.000 9.46 0.00 46.60 1.82
1884 2056 2.354303 CCGGAGTAGTAAACATGTGGCA 60.354 50.000 0.00 0.00 0.00 4.92
2013 2188 2.074576 GCCTCCGAACCAGTTAACTTC 58.925 52.381 5.07 0.25 0.00 3.01
2038 2226 9.216117 TCTTTTACTTTCGAAAAGGAGGATTAG 57.784 33.333 12.41 0.00 41.96 1.73
2040 2228 4.262617 ACTTTCGAAAAGGAGGATTAGCC 58.737 43.478 12.41 0.00 0.00 3.93
2070 2258 2.517321 GCTTGTGCTCTGAATTCGTC 57.483 50.000 0.04 0.00 36.03 4.20
2309 2497 3.403968 AGATGATGATGATGCTGCAGTC 58.596 45.455 16.64 6.47 0.00 3.51
2333 2521 0.671796 TCGTCTTTGCTCTCGGTTCA 59.328 50.000 0.00 0.00 0.00 3.18
2337 2525 1.000955 TCTTTGCTCTCGGTTCAGGAC 59.999 52.381 0.00 0.00 0.00 3.85
2388 2592 4.444720 GCAAGTCGTGTTAGCATATAGGTC 59.555 45.833 0.00 0.00 0.00 3.85
2397 2601 8.027189 CGTGTTAGCATATAGGTCTGCTTTATA 58.973 37.037 3.99 0.00 46.22 0.98
2398 2602 9.360093 GTGTTAGCATATAGGTCTGCTTTATAG 57.640 37.037 3.99 0.00 46.22 1.31
2399 2603 8.531982 TGTTAGCATATAGGTCTGCTTTATAGG 58.468 37.037 3.99 0.00 46.22 2.57
2400 2604 8.532819 GTTAGCATATAGGTCTGCTTTATAGGT 58.467 37.037 3.99 0.00 46.22 3.08
2401 2605 7.560796 AGCATATAGGTCTGCTTTATAGGTT 57.439 36.000 0.00 0.00 46.22 3.50
2402 2606 7.978925 AGCATATAGGTCTGCTTTATAGGTTT 58.021 34.615 0.00 0.00 46.22 3.27
2403 2607 7.880195 AGCATATAGGTCTGCTTTATAGGTTTG 59.120 37.037 0.00 0.00 46.22 2.93
2404 2608 7.361286 GCATATAGGTCTGCTTTATAGGTTTGC 60.361 40.741 0.00 0.00 35.49 3.68
2405 2609 4.576330 AGGTCTGCTTTATAGGTTTGCT 57.424 40.909 0.00 0.00 0.00 3.91
2406 2610 4.923415 AGGTCTGCTTTATAGGTTTGCTT 58.077 39.130 0.00 0.00 0.00 3.91
2407 2611 5.325239 AGGTCTGCTTTATAGGTTTGCTTT 58.675 37.500 0.00 0.00 0.00 3.51
2408 2612 6.481643 AGGTCTGCTTTATAGGTTTGCTTTA 58.518 36.000 0.00 0.00 0.00 1.85
2409 2613 7.119387 AGGTCTGCTTTATAGGTTTGCTTTAT 58.881 34.615 0.00 0.00 0.00 1.40
2410 2614 7.283354 AGGTCTGCTTTATAGGTTTGCTTTATC 59.717 37.037 0.00 0.00 0.00 1.75
2411 2615 7.126398 GTCTGCTTTATAGGTTTGCTTTATCG 58.874 38.462 0.00 0.00 0.00 2.92
2412 2616 5.816919 TGCTTTATAGGTTTGCTTTATCGC 58.183 37.500 0.00 0.00 0.00 4.58
2413 2617 5.588648 TGCTTTATAGGTTTGCTTTATCGCT 59.411 36.000 0.00 0.00 0.00 4.93
2414 2618 6.094881 TGCTTTATAGGTTTGCTTTATCGCTT 59.905 34.615 0.00 0.00 0.00 4.68
2415 2619 7.281324 TGCTTTATAGGTTTGCTTTATCGCTTA 59.719 33.333 0.00 0.00 0.00 3.09
2416 2620 8.290325 GCTTTATAGGTTTGCTTTATCGCTTAT 58.710 33.333 0.00 0.00 0.00 1.73
2454 2662 8.626526 TGAATTTGGTTAAGTGTTAGGTCTTTC 58.373 33.333 0.00 0.00 0.00 2.62
2468 2676 3.746492 AGGTCTTTCGTGTCTGTAAATGC 59.254 43.478 0.00 0.00 0.00 3.56
2473 2681 0.365523 CGTGTCTGTAAATGCGTCCG 59.634 55.000 0.00 0.00 0.00 4.79
2545 2754 8.401490 AGCTAATCAAGAAAGTTTCACTTCAT 57.599 30.769 17.65 2.41 37.47 2.57
2550 2759 5.009010 TCAAGAAAGTTTCACTTCATGAGCC 59.991 40.000 17.65 0.00 37.47 4.70
2583 2792 1.160329 AACACTGTGCGTCTTGCTCC 61.160 55.000 7.90 0.00 46.63 4.70
2612 2841 2.343843 CAGAGACGTTGAAAGAGCATCG 59.656 50.000 0.00 0.00 42.67 3.84
2623 2852 4.349503 AGCATCGGGCCAGTTGCA 62.350 61.111 31.71 3.14 46.50 4.08
2650 2879 5.044698 TGGTAACGAGAAATTCCCCCTAAAT 60.045 40.000 0.00 0.00 42.51 1.40
2652 2881 6.709397 GGTAACGAGAAATTCCCCCTAAATAG 59.291 42.308 0.00 0.00 0.00 1.73
2653 2882 5.970501 ACGAGAAATTCCCCCTAAATAGT 57.029 39.130 0.00 0.00 0.00 2.12
2654 2883 7.441903 AACGAGAAATTCCCCCTAAATAGTA 57.558 36.000 0.00 0.00 0.00 1.82
2655 2884 7.441903 ACGAGAAATTCCCCCTAAATAGTAA 57.558 36.000 0.00 0.00 0.00 2.24
2656 2885 8.042286 ACGAGAAATTCCCCCTAAATAGTAAT 57.958 34.615 0.00 0.00 0.00 1.89
2733 2981 5.976865 CGTACTTATGCGCTCTTATGTAG 57.023 43.478 9.73 0.00 0.00 2.74
2734 2982 5.450171 CGTACTTATGCGCTCTTATGTAGT 58.550 41.667 9.73 4.82 0.00 2.73
2735 2983 5.913514 CGTACTTATGCGCTCTTATGTAGTT 59.086 40.000 9.73 0.00 0.00 2.24
2736 2984 6.417044 CGTACTTATGCGCTCTTATGTAGTTT 59.583 38.462 9.73 0.00 0.00 2.66
2737 2985 7.043590 CGTACTTATGCGCTCTTATGTAGTTTT 60.044 37.037 9.73 0.00 0.00 2.43
2942 3190 8.258007 TCTGATATGGTCGTCAAATAAAGAACT 58.742 33.333 0.00 0.00 0.00 3.01
2987 3235 1.028330 AGTGTGCGATTGCCAGGATG 61.028 55.000 1.50 0.00 41.78 3.51
3064 3312 1.202758 TGGATTCGTGGTTGAAGTGCT 60.203 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.147865 GTCGTCAATGTCTACATATCTCCG 58.852 45.833 0.00 0.00 35.10 4.63
1 2 5.147865 CGTCGTCAATGTCTACATATCTCC 58.852 45.833 0.00 0.00 35.10 3.71
2 3 4.613448 GCGTCGTCAATGTCTACATATCTC 59.387 45.833 0.00 0.00 35.10 2.75
3 4 4.537965 GCGTCGTCAATGTCTACATATCT 58.462 43.478 0.00 0.00 35.10 1.98
4 5 3.358115 CGCGTCGTCAATGTCTACATATC 59.642 47.826 0.00 0.00 35.10 1.63
5 6 3.297472 CGCGTCGTCAATGTCTACATAT 58.703 45.455 0.00 0.00 35.10 1.78
6 7 2.540157 CCGCGTCGTCAATGTCTACATA 60.540 50.000 4.92 0.00 35.10 2.29
7 8 1.545759 CGCGTCGTCAATGTCTACAT 58.454 50.000 0.00 0.00 38.41 2.29
8 9 0.455464 CCGCGTCGTCAATGTCTACA 60.455 55.000 4.92 0.00 0.00 2.74
9 10 0.179181 TCCGCGTCGTCAATGTCTAC 60.179 55.000 4.92 0.00 0.00 2.59
10 11 0.098200 CTCCGCGTCGTCAATGTCTA 59.902 55.000 4.92 0.00 0.00 2.59
11 12 1.154016 CTCCGCGTCGTCAATGTCT 60.154 57.895 4.92 0.00 0.00 3.41
12 13 2.158959 CCTCCGCGTCGTCAATGTC 61.159 63.158 4.92 0.00 0.00 3.06
13 14 2.126071 CCTCCGCGTCGTCAATGT 60.126 61.111 4.92 0.00 0.00 2.71
44 47 6.146673 CACATGCATGTAGGTGTAGATATGTG 59.853 42.308 30.92 11.44 39.39 3.21
45 48 6.183361 ACACATGCATGTAGGTGTAGATATGT 60.183 38.462 28.68 16.88 42.97 2.29
57 60 3.129813 AGATTTGCCACACATGCATGTAG 59.870 43.478 30.92 24.85 39.39 2.74
60 63 2.665649 AGATTTGCCACACATGCATG 57.334 45.000 25.09 25.09 38.76 4.06
76 79 4.700213 CACCGTGTTCATTTTTCCCTAGAT 59.300 41.667 0.00 0.00 0.00 1.98
100 114 2.084546 GCCGTTTATTCTGCCTTGTCT 58.915 47.619 0.00 0.00 0.00 3.41
101 115 2.084546 AGCCGTTTATTCTGCCTTGTC 58.915 47.619 0.00 0.00 0.00 3.18
120 134 2.807045 GTGCGCGAGACACCAGAG 60.807 66.667 12.10 0.00 33.85 3.35
141 155 2.747855 CTTCGGGGGCAGACAAGC 60.748 66.667 0.00 0.00 0.00 4.01
142 156 1.672356 CACTTCGGGGGCAGACAAG 60.672 63.158 0.00 0.00 0.00 3.16
143 157 1.488705 ATCACTTCGGGGGCAGACAA 61.489 55.000 0.00 0.00 0.00 3.18
145 159 1.153349 GATCACTTCGGGGGCAGAC 60.153 63.158 0.00 0.00 0.00 3.51
147 161 1.450312 GTGATCACTTCGGGGGCAG 60.450 63.158 18.83 0.00 0.00 4.85
148 162 2.668632 GTGATCACTTCGGGGGCA 59.331 61.111 18.83 0.00 0.00 5.36
149 163 2.311688 ATCGTGATCACTTCGGGGGC 62.312 60.000 22.95 0.00 0.00 5.80
150 164 0.249489 GATCGTGATCACTTCGGGGG 60.249 60.000 22.95 6.32 37.74 5.40
151 165 0.747255 AGATCGTGATCACTTCGGGG 59.253 55.000 22.95 7.03 40.22 5.73
152 166 2.619177 AGTAGATCGTGATCACTTCGGG 59.381 50.000 22.95 7.75 40.22 5.14
153 167 3.972950 AGTAGATCGTGATCACTTCGG 57.027 47.619 22.95 8.12 40.22 4.30
166 180 3.242123 CCGCGCTCTTTGAAAAGTAGATC 60.242 47.826 5.56 0.00 37.31 2.75
172 186 0.591170 TTCCCGCGCTCTTTGAAAAG 59.409 50.000 5.56 0.00 37.36 2.27
174 188 1.025812 TTTTCCCGCGCTCTTTGAAA 58.974 45.000 5.56 4.30 0.00 2.69
192 206 3.967332 CCCTTTGGCAGACATCAATTT 57.033 42.857 0.00 0.00 0.00 1.82
227 243 2.031807 CCACGTCGTGTATACTCCAGAG 59.968 54.545 23.01 0.37 0.00 3.35
228 244 2.011947 CCACGTCGTGTATACTCCAGA 58.988 52.381 23.01 0.00 0.00 3.86
229 245 2.011947 TCCACGTCGTGTATACTCCAG 58.988 52.381 23.01 5.49 0.00 3.86
230 246 2.011947 CTCCACGTCGTGTATACTCCA 58.988 52.381 23.01 0.00 0.00 3.86
231 247 1.332997 CCTCCACGTCGTGTATACTCC 59.667 57.143 23.01 0.00 0.00 3.85
232 248 2.031437 GTCCTCCACGTCGTGTATACTC 59.969 54.545 23.01 6.34 0.00 2.59
233 249 2.012673 GTCCTCCACGTCGTGTATACT 58.987 52.381 23.01 0.00 0.00 2.12
234 250 1.267732 CGTCCTCCACGTCGTGTATAC 60.268 57.143 23.01 14.00 44.07 1.47
235 251 1.009078 CGTCCTCCACGTCGTGTATA 58.991 55.000 23.01 8.17 44.07 1.47
279 299 2.657237 CACGTCCTCCACACCCTC 59.343 66.667 0.00 0.00 0.00 4.30
373 396 0.467844 TAGTGCTCCCCGCGGTAATA 60.468 55.000 26.12 5.03 43.27 0.98
482 509 4.035324 CGTCTCCTATATATACACAGGGCG 59.965 50.000 6.91 6.24 0.00 6.13
592 621 0.032952 TCCAAAAGGTGAGTCGTCGG 59.967 55.000 0.00 0.00 0.00 4.79
617 646 0.037232 CGTCACCTCAGAAGAACCCC 60.037 60.000 0.00 0.00 0.00 4.95
626 659 1.300931 CCACACACCGTCACCTCAG 60.301 63.158 0.00 0.00 0.00 3.35
646 679 1.302033 GTAGGCCGGGATGCTGATG 60.302 63.158 2.18 0.00 0.00 3.07
681 714 0.536687 AATCATGCAGGGCCTCGATG 60.537 55.000 0.95 9.15 0.00 3.84
743 776 1.521681 GGAAGGTGAGGCGATTCGG 60.522 63.158 8.34 0.00 0.00 4.30
914 947 9.817809 GGAGCGGATAGATAGATAGATAGATAG 57.182 40.741 0.00 0.00 0.00 2.08
915 948 8.764558 GGGAGCGGATAGATAGATAGATAGATA 58.235 40.741 0.00 0.00 0.00 1.98
916 949 7.461043 AGGGAGCGGATAGATAGATAGATAGAT 59.539 40.741 0.00 0.00 0.00 1.98
917 950 6.790461 AGGGAGCGGATAGATAGATAGATAGA 59.210 42.308 0.00 0.00 0.00 1.98
918 951 7.016153 AGGGAGCGGATAGATAGATAGATAG 57.984 44.000 0.00 0.00 0.00 2.08
919 952 8.688222 ATAGGGAGCGGATAGATAGATAGATA 57.312 38.462 0.00 0.00 0.00 1.98
920 953 5.922960 AGGGAGCGGATAGATAGATAGAT 57.077 43.478 0.00 0.00 0.00 1.98
921 954 7.395525 AATAGGGAGCGGATAGATAGATAGA 57.604 40.000 0.00 0.00 0.00 1.98
934 971 2.948979 TGCACAAATAAATAGGGAGCGG 59.051 45.455 0.00 0.00 0.00 5.52
938 975 7.502226 CAGGTAGAATGCACAAATAAATAGGGA 59.498 37.037 0.00 0.00 0.00 4.20
977 1025 0.542702 CTCCTGCAATGGGTGGGTTT 60.543 55.000 0.00 0.00 0.00 3.27
981 1032 0.329261 TCTTCTCCTGCAATGGGTGG 59.671 55.000 0.00 0.00 0.00 4.61
1063 1120 2.209064 CTGCTGTCACATGCAAGGGC 62.209 60.000 0.00 0.00 38.81 5.19
1113 1170 5.576447 AAAAACACAGTGAAATCCGAACT 57.424 34.783 7.81 0.00 0.00 3.01
1137 1194 5.492162 AGGATGGTTGGGCATATCATACATA 59.508 40.000 0.00 0.00 0.00 2.29
1190 1247 1.153823 CCAAGAGGACCGCTGTACG 60.154 63.158 0.00 0.00 38.36 3.67
1248 1305 4.155733 TACGTCCCCATGGCGCAG 62.156 66.667 10.83 0.00 35.45 5.18
1315 1372 2.673523 CCTGTGAAGAGGCCCCAG 59.326 66.667 0.00 0.00 0.00 4.45
1397 1454 0.035176 AGGTAAGCGGCGTTTGGTTA 59.965 50.000 19.40 0.00 0.00 2.85
1427 1484 4.148696 GGATGAAACGCAAACTGTTGAATG 59.851 41.667 0.00 0.00 36.83 2.67
1433 1490 2.808543 GAGAGGATGAAACGCAAACTGT 59.191 45.455 0.00 0.00 0.00 3.55
1490 1576 2.605101 GCATCGCAGCTGCATCGAT 61.605 57.895 36.03 26.63 42.82 3.59
1729 1899 5.118990 TCTGCAGTCAAGGCATATAAACTC 58.881 41.667 14.67 0.00 41.06 3.01
1772 1944 2.378038 CCATCCATCAACGGACCAAAT 58.622 47.619 0.00 0.00 38.07 2.32
1862 2034 2.354403 GCCACATGTTTACTACTCCGGT 60.354 50.000 0.00 0.00 0.00 5.28
1870 2042 0.883833 GCAGCTGCCACATGTTTACT 59.116 50.000 28.76 0.00 34.31 2.24
1873 2045 2.646719 CGCAGCTGCCACATGTTT 59.353 55.556 32.07 0.00 37.91 2.83
1999 2174 8.606602 TCGAAAGTAAAAGAAGTTAACTGGTTC 58.393 33.333 9.34 3.16 0.00 3.62
2013 2188 7.963465 GCTAATCCTCCTTTTCGAAAGTAAAAG 59.037 37.037 10.98 5.18 41.51 2.27
2038 2226 2.042831 ACAAGCTGCGATTCAGGGC 61.043 57.895 0.00 0.00 43.06 5.19
2040 2228 1.136147 GCACAAGCTGCGATTCAGG 59.864 57.895 0.00 0.00 43.06 3.86
2070 2258 3.423539 TCTCCCAGGTTCAAACATCAG 57.576 47.619 0.00 0.00 0.00 2.90
2309 2497 1.202132 CCGAGAGCAAAGACGAGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
2361 2549 2.455674 TGCTAACACGACTTGCAGAT 57.544 45.000 0.00 0.00 0.00 2.90
2362 2550 2.455674 ATGCTAACACGACTTGCAGA 57.544 45.000 0.00 0.00 37.07 4.26
2388 2592 5.909610 GCGATAAAGCAAACCTATAAAGCAG 59.090 40.000 0.00 0.00 37.05 4.24
2397 2601 3.560068 CCGATAAGCGATAAAGCAAACCT 59.440 43.478 0.00 0.00 44.57 3.50
2398 2602 3.311596 ACCGATAAGCGATAAAGCAAACC 59.688 43.478 0.00 0.00 44.57 3.27
2399 2603 4.270325 AGACCGATAAGCGATAAAGCAAAC 59.730 41.667 0.00 0.00 44.57 2.93
2400 2604 4.439057 AGACCGATAAGCGATAAAGCAAA 58.561 39.130 0.00 0.00 44.57 3.68
2401 2605 4.054780 AGACCGATAAGCGATAAAGCAA 57.945 40.909 0.00 0.00 44.57 3.91
2402 2606 3.728076 AGACCGATAAGCGATAAAGCA 57.272 42.857 0.00 0.00 44.57 3.91
2403 2607 5.221130 AGTAAGACCGATAAGCGATAAAGC 58.779 41.667 0.00 0.00 44.57 3.51
2404 2608 6.579292 CAGAGTAAGACCGATAAGCGATAAAG 59.421 42.308 0.00 0.00 44.57 1.85
2405 2609 6.261603 TCAGAGTAAGACCGATAAGCGATAAA 59.738 38.462 0.00 0.00 44.57 1.40
2406 2610 5.761726 TCAGAGTAAGACCGATAAGCGATAA 59.238 40.000 0.00 0.00 44.57 1.75
2407 2611 5.303165 TCAGAGTAAGACCGATAAGCGATA 58.697 41.667 0.00 0.00 44.57 2.92
2408 2612 4.135306 TCAGAGTAAGACCGATAAGCGAT 58.865 43.478 0.00 0.00 44.57 4.58
2409 2613 3.538591 TCAGAGTAAGACCGATAAGCGA 58.461 45.455 0.00 0.00 44.57 4.93
2410 2614 3.965292 TCAGAGTAAGACCGATAAGCG 57.035 47.619 0.00 0.00 40.47 4.68
2411 2615 6.018669 CCAAATTCAGAGTAAGACCGATAAGC 60.019 42.308 0.00 0.00 0.00 3.09
2412 2616 7.042335 ACCAAATTCAGAGTAAGACCGATAAG 58.958 38.462 0.00 0.00 0.00 1.73
2413 2617 6.942976 ACCAAATTCAGAGTAAGACCGATAA 58.057 36.000 0.00 0.00 0.00 1.75
2414 2618 6.540438 ACCAAATTCAGAGTAAGACCGATA 57.460 37.500 0.00 0.00 0.00 2.92
2415 2619 5.422214 ACCAAATTCAGAGTAAGACCGAT 57.578 39.130 0.00 0.00 0.00 4.18
2416 2620 4.884668 ACCAAATTCAGAGTAAGACCGA 57.115 40.909 0.00 0.00 0.00 4.69
2454 2662 0.365523 CGGACGCATTTACAGACACG 59.634 55.000 0.00 0.00 0.00 4.49
2468 2676 2.186903 CATCAACCCTCCCGGACG 59.813 66.667 0.73 0.00 34.64 4.79
2473 2681 0.830648 TCGATCACATCAACCCTCCC 59.169 55.000 0.00 0.00 0.00 4.30
2514 2723 9.952188 GTGAAACTTTCTTGATTAGCTTAACTT 57.048 29.630 0.00 0.00 0.00 2.66
2562 2771 0.378257 AGCAAGACGCACAGTGTTTG 59.622 50.000 1.61 0.00 46.13 2.93
2563 2772 0.657840 GAGCAAGACGCACAGTGTTT 59.342 50.000 1.61 0.00 46.13 2.83
2566 2775 2.661566 CGGAGCAAGACGCACAGTG 61.662 63.158 0.00 0.00 46.13 3.66
2583 2792 0.385598 TCAACGTCTCTGCGAAGTCG 60.386 55.000 0.00 0.00 43.27 4.18
2623 2852 3.560668 GGGGGAATTTCTCGTTACCAGTT 60.561 47.826 0.00 0.00 30.68 3.16
2627 2856 4.492494 TTAGGGGGAATTTCTCGTTACC 57.508 45.455 0.00 0.00 0.00 2.85
2650 2879 7.118680 GGTTTCATCCAAGACGTCAAATTACTA 59.881 37.037 19.50 0.00 0.00 1.82
2652 2881 6.084277 GGTTTCATCCAAGACGTCAAATTAC 58.916 40.000 19.50 3.78 0.00 1.89
2653 2882 5.182380 GGGTTTCATCCAAGACGTCAAATTA 59.818 40.000 19.50 0.00 0.00 1.40
2654 2883 4.022329 GGGTTTCATCCAAGACGTCAAATT 60.022 41.667 19.50 0.00 0.00 1.82
2655 2884 3.506067 GGGTTTCATCCAAGACGTCAAAT 59.494 43.478 19.50 0.00 0.00 2.32
2656 2885 2.882137 GGGTTTCATCCAAGACGTCAAA 59.118 45.455 19.50 4.57 0.00 2.69
2716 2964 9.459640 CTAGTAAAACTACATAAGAGCGCATAA 57.540 33.333 11.47 0.00 0.00 1.90
2772 3020 9.803130 GACAATGATATTCATTCTGATAACACG 57.197 33.333 0.00 0.00 43.03 4.49
2942 3190 8.212312 TCCAAGTTAACAGTGAGGTAATTACAA 58.788 33.333 17.16 0.00 30.78 2.41
2950 3198 3.454812 ACACTCCAAGTTAACAGTGAGGT 59.545 43.478 23.31 14.19 38.90 3.85
3002 3250 3.057736 CCAGCAACAGAAATGTTCTCAGG 60.058 47.826 0.00 0.00 38.11 3.86
3064 3312 2.019249 GCAGCCAAGTCAATGATGCTA 58.981 47.619 0.00 0.00 33.04 3.49


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

AutoCloner maintained by Alex Coulton.