Multiple sequence alignment - TraesCS7D01G523900

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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 TraesCS7D01G523900 chr7D 100.000 3409 0 0 1 3409 620196388 620199796 0.000000e+00 6296.0
1 TraesCS7D01G523900 chr7D 83.204 774 93 20 1181 1944 620143008 620143754 0.000000e+00 675.0
2 TraesCS7D01G523900 chr7D 80.381 892 139 24 2105 2972 620143871 620144750 0.000000e+00 645.0
3 TraesCS7D01G523900 chr7D 86.193 507 67 3 1183 1688 620116240 620116744 2.310000e-151 545.0
4 TraesCS7D01G523900 chr7D 84.024 338 29 10 1764 2091 620116805 620117127 5.530000e-78 302.0
5 TraesCS7D01G523900 chr7D 89.941 169 15 2 2244 2411 638418518 638418685 2.060000e-52 217.0
6 TraesCS7D01G523900 chr7D 81.188 101 9 4 3200 3298 620146256 620146348 4.720000e-09 73.1
7 TraesCS7D01G523900 chr7A 91.208 2036 121 30 1 2015 714760886 714758888 0.000000e+00 2715.0
8 TraesCS7D01G523900 chr7A 82.750 829 97 24 1182 1995 714823204 714822407 0.000000e+00 697.0
9 TraesCS7D01G523900 chr7A 89.834 541 51 2 2153 2689 714758857 714758317 0.000000e+00 691.0
10 TraesCS7D01G523900 chr7A 83.503 394 46 9 2688 3072 714758282 714757899 1.950000e-92 350.0
11 TraesCS7D01G523900 chr7A 91.848 184 6 3 3226 3409 714757298 714757124 7.310000e-62 248.0
12 TraesCS7D01G523900 chr7B 90.022 1393 105 20 676 2053 716308741 716307368 0.000000e+00 1772.0
13 TraesCS7D01G523900 chr7B 85.476 840 81 18 2153 2968 716307349 716306527 0.000000e+00 837.0
14 TraesCS7D01G523900 chr7B 83.204 774 100 20 1182 1951 716466988 716466241 0.000000e+00 682.0
15 TraesCS7D01G523900 chr7B 80.652 889 136 24 2110 2978 717000349 717001221 0.000000e+00 656.0
16 TraesCS7D01G523900 chr7B 83.210 673 96 13 2093 2759 716315138 716314477 4.870000e-168 601.0
17 TraesCS7D01G523900 chr7B 86.406 537 69 4 1182 1716 716316037 716315503 4.900000e-163 584.0
18 TraesCS7D01G523900 chr7B 84.795 513 71 5 1181 1688 716999492 717000002 3.030000e-140 508.0
19 TraesCS7D01G523900 chr7B 87.206 383 42 5 1714 2091 716315448 716315068 2.430000e-116 429.0
20 TraesCS7D01G523900 chr7B 82.020 495 56 22 2153 2636 716369181 716368709 1.150000e-104 390.0
21 TraesCS7D01G523900 chr7B 86.400 250 32 2 1764 2012 716369508 716369260 4.330000e-69 272.0
22 TraesCS7D01G523900 chr7B 87.783 221 19 1 1764 1976 717000047 717000267 5.650000e-63 252.0
23 TraesCS7D01G523900 chr7B 79.293 396 26 22 331 683 716309277 716308895 3.420000e-55 226.0
24 TraesCS7D01G523900 chr7B 94.030 67 3 1 3200 3266 716464791 716464726 2.160000e-17 100.0
25 TraesCS7D01G523900 chr7B 82.828 99 8 4 3200 3298 716306257 716306168 2.820000e-11 80.5
26 TraesCS7D01G523900 chrUn 85.981 535 71 3 1181 1714 466806753 466807284 1.370000e-158 569.0
27 TraesCS7D01G523900 chr6D 75.875 514 94 21 2475 2967 107534913 107535417 5.690000e-58 235.0
28 TraesCS7D01G523900 chr2D 90.533 169 14 2 2244 2411 484559987 484559820 4.430000e-54 222.0
29 TraesCS7D01G523900 chr2D 89.349 169 16 2 2244 2411 379110580 379110413 9.580000e-51 211.0


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 TraesCS7D01G523900 chr7D 620196388 620199796 3408 False 6296.000000 6296 100.000000 1 3409 1 chr7D.!!$F1 3408
1 TraesCS7D01G523900 chr7D 620143008 620146348 3340 False 464.366667 675 81.591000 1181 3298 3 chr7D.!!$F4 2117
2 TraesCS7D01G523900 chr7D 620116240 620117127 887 False 423.500000 545 85.108500 1183 2091 2 chr7D.!!$F3 908
3 TraesCS7D01G523900 chr7A 714757124 714760886 3762 True 1001.000000 2715 89.098250 1 3409 4 chr7A.!!$R2 3408
4 TraesCS7D01G523900 chr7A 714822407 714823204 797 True 697.000000 697 82.750000 1182 1995 1 chr7A.!!$R1 813
5 TraesCS7D01G523900 chr7B 716306168 716309277 3109 True 728.875000 1772 84.404750 331 3298 4 chr7B.!!$R1 2967
6 TraesCS7D01G523900 chr7B 716314477 716316037 1560 True 538.000000 601 85.607333 1182 2759 3 chr7B.!!$R2 1577
7 TraesCS7D01G523900 chr7B 716999492 717001221 1729 False 472.000000 656 84.410000 1181 2978 3 chr7B.!!$F1 1797
8 TraesCS7D01G523900 chr7B 716464726 716466988 2262 True 391.000000 682 88.617000 1182 3266 2 chr7B.!!$R4 2084
9 TraesCS7D01G523900 chr7B 716368709 716369508 799 True 331.000000 390 84.210000 1764 2636 2 chr7B.!!$R3 872
10 TraesCS7D01G523900 chrUn 466806753 466807284 531 False 569.000000 569 85.981000 1181 1714 1 chrUn.!!$F1 533
11 TraesCS7D01G523900 chr6D 107534913 107535417 504 False 235.000000 235 75.875000 2475 2967 1 chr6D.!!$F1 492

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
837 1055 0.180171 TTCTATCATGCCCACCACCG 59.820 55.0 0.0 0.0 0.00 4.94 F
1364 1603 0.179026 CCTATCGACCTCTCCGACCA 60.179 60.0 0.0 0.0 38.97 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2674 0.040425 CAACAGCGTTAGTGCCAACC 60.040 55.0 0.0 0.00 34.65 3.77 R
2582 3225 0.313043 GCAATGCTCCATGGAATCGG 59.687 55.0 17.0 5.03 0.00 4.18 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 6.599356 ATTATATGTACTGCCCGTCATACA 57.401 37.500 0.00 0.00 32.38 2.29
87 88 9.515020 AATCCTGTGTAATTAATTTTATGCGTG 57.485 29.630 5.91 0.00 0.00 5.34
380 387 2.840511 TCCTATAGGCCAGGTCAAACA 58.159 47.619 14.50 0.00 34.56 2.83
429 436 8.550710 CAATTATTTTGAATTGAAGGGAGCAA 57.449 30.769 3.32 0.00 45.70 3.91
510 544 2.114670 GCTGCCCATGTATGTGCGT 61.115 57.895 0.00 0.00 33.70 5.24
516 550 0.676466 CCATGTATGTGCGTGGGTGT 60.676 55.000 1.81 0.00 40.82 4.16
524 558 1.453015 TGCGTGGGTGTCTTTGCTT 60.453 52.632 0.00 0.00 0.00 3.91
713 926 4.246458 AGCAAAGGACGAATCTTCTACAC 58.754 43.478 0.00 0.00 0.00 2.90
719 932 6.037786 AGGACGAATCTTCTACACAAATGA 57.962 37.500 0.00 0.00 0.00 2.57
720 933 6.464222 AGGACGAATCTTCTACACAAATGAA 58.536 36.000 0.00 0.00 0.00 2.57
721 934 6.369065 AGGACGAATCTTCTACACAAATGAAC 59.631 38.462 0.00 0.00 0.00 3.18
722 935 6.147164 GGACGAATCTTCTACACAAATGAACA 59.853 38.462 0.00 0.00 0.00 3.18
723 936 6.888430 ACGAATCTTCTACACAAATGAACAC 58.112 36.000 0.00 0.00 0.00 3.32
724 937 6.481976 ACGAATCTTCTACACAAATGAACACA 59.518 34.615 0.00 0.00 0.00 3.72
725 938 6.792250 CGAATCTTCTACACAAATGAACACAC 59.208 38.462 0.00 0.00 0.00 3.82
726 939 7.307396 CGAATCTTCTACACAAATGAACACACT 60.307 37.037 0.00 0.00 0.00 3.55
727 940 8.902540 AATCTTCTACACAAATGAACACACTA 57.097 30.769 0.00 0.00 0.00 2.74
798 1011 3.454812 ACAAGATATTCTTACCGTGCCCT 59.545 43.478 0.00 0.00 33.78 5.19
799 1012 3.753294 AGATATTCTTACCGTGCCCTG 57.247 47.619 0.00 0.00 0.00 4.45
809 1024 2.433436 ACCGTGCCCTGTTTAATTCTC 58.567 47.619 0.00 0.00 0.00 2.87
810 1025 2.224670 ACCGTGCCCTGTTTAATTCTCA 60.225 45.455 0.00 0.00 0.00 3.27
812 1027 2.420022 CGTGCCCTGTTTAATTCTCAGG 59.580 50.000 13.30 13.30 45.67 3.86
821 1039 6.200878 TGTTTAATTCTCAGGGTCCTTTCT 57.799 37.500 0.00 0.00 0.00 2.52
826 1044 6.838401 AATTCTCAGGGTCCTTTCTATCAT 57.162 37.500 0.00 0.00 0.00 2.45
835 1053 2.092429 TCCTTTCTATCATGCCCACCAC 60.092 50.000 0.00 0.00 0.00 4.16
837 1055 0.180171 TTCTATCATGCCCACCACCG 59.820 55.000 0.00 0.00 0.00 4.94
851 1069 1.830408 CACCGTGCCCCCTTTTCAA 60.830 57.895 0.00 0.00 0.00 2.69
852 1070 1.830847 ACCGTGCCCCCTTTTCAAC 60.831 57.895 0.00 0.00 0.00 3.18
867 1086 1.195115 TCAACACCCCAGCTAGCTAG 58.805 55.000 18.86 16.84 0.00 3.42
916 1139 2.112279 TACAGACCCACCAACCTTCT 57.888 50.000 0.00 0.00 0.00 2.85
920 1143 2.138453 GACCCACCAACCTTCTCCCC 62.138 65.000 0.00 0.00 0.00 4.81
923 1146 0.482887 CCACCAACCTTCTCCCCTTT 59.517 55.000 0.00 0.00 0.00 3.11
931 1154 1.846439 CCTTCTCCCCTTTCATAGCCA 59.154 52.381 0.00 0.00 0.00 4.75
939 1162 2.614057 CCCTTTCATAGCCAAGCTAACG 59.386 50.000 0.00 0.00 44.62 3.18
966 1191 0.247814 GCACATCGATCAGCAAACGG 60.248 55.000 12.41 0.00 0.00 4.44
967 1192 0.374758 CACATCGATCAGCAAACGGG 59.625 55.000 0.00 0.00 0.00 5.28
1053 1279 2.123033 GCCCTCCTCCTCCTCCTC 60.123 72.222 0.00 0.00 0.00 3.71
1126 1352 0.739112 CTGCTCCGCTCTCTCAAACC 60.739 60.000 0.00 0.00 0.00 3.27
1130 1356 1.801178 CTCCGCTCTCTCAAACCAAAC 59.199 52.381 0.00 0.00 0.00 2.93
1131 1357 0.512952 CCGCTCTCTCAAACCAAACG 59.487 55.000 0.00 0.00 0.00 3.60
1132 1358 1.497991 CGCTCTCTCAAACCAAACGA 58.502 50.000 0.00 0.00 0.00 3.85
1133 1359 1.864711 CGCTCTCTCAAACCAAACGAA 59.135 47.619 0.00 0.00 0.00 3.85
1134 1360 2.480419 CGCTCTCTCAAACCAAACGAAT 59.520 45.455 0.00 0.00 0.00 3.34
1169 1395 5.880054 ATATTAAATCCAGCGCATGTACC 57.120 39.130 11.47 0.00 0.00 3.34
1217 1444 9.377312 CCACCATTAATTAATTTTACCAAGTGG 57.623 33.333 8.01 10.44 42.17 4.00
1347 1586 4.479993 GGGCAGATGCAGTCGCCT 62.480 66.667 19.10 0.00 42.41 5.52
1364 1603 0.179026 CCTATCGACCTCTCCGACCA 60.179 60.000 0.00 0.00 38.97 4.02
1369 1608 1.377725 GACCTCTCCGACCACCGTA 60.378 63.158 0.00 0.00 36.31 4.02
1659 1898 2.125106 AGGCGCGACCATTTCCTC 60.125 61.111 9.25 0.00 43.14 3.71
1748 2058 1.823797 GGCACGGGGTTTATGTTGTA 58.176 50.000 0.00 0.00 0.00 2.41
1759 2069 7.252708 GGGGTTTATGTTGTAAAACTAATCCG 58.747 38.462 0.00 0.00 36.17 4.18
1760 2070 6.748658 GGGTTTATGTTGTAAAACTAATCCGC 59.251 38.462 0.00 0.00 36.17 5.54
1890 2200 1.271840 GGTACATGGGCTCCCTCACA 61.272 60.000 6.50 0.00 36.94 3.58
1964 2282 5.347012 ACGTTGTTAATGACTTTTACCGG 57.653 39.130 0.00 0.00 0.00 5.28
2009 2573 7.039882 TCTAAACTTACGGGAAATCAGCTTAG 58.960 38.462 0.00 0.00 0.00 2.18
2012 2576 0.546598 ACGGGAAATCAGCTTAGGGG 59.453 55.000 0.00 0.00 0.00 4.79
2015 2579 1.393603 GGAAATCAGCTTAGGGGCAC 58.606 55.000 0.00 0.00 34.17 5.01
2055 2643 7.976734 CCCCGATATTCTCTAACAATAGTGATC 59.023 40.741 0.00 0.00 33.09 2.92
2102 2690 1.868997 CAGGTTGGCACTAACGCTG 59.131 57.895 0.00 2.67 0.00 5.18
2231 2822 9.321590 GTCCATGACGTAATTAAGTTGTTAAAC 57.678 33.333 5.50 0.00 31.81 2.01
2233 2824 9.325150 CCATGACGTAATTAAGTTGTTAAACTG 57.675 33.333 5.50 0.00 46.15 3.16
2254 2870 9.971922 AAACTGATTAACTTCTCCAATCTTTTG 57.028 29.630 0.00 0.00 31.37 2.44
2265 2881 4.858935 TCCAATCTTTTGTCAAGAAAGCG 58.141 39.130 0.00 0.00 34.80 4.68
2468 3092 6.847792 CAGCATGCGTGTTAATGTAAGATAAG 59.152 38.462 13.01 0.00 0.00 1.73
2472 3096 5.522460 TGCGTGTTAATGTAAGATAAGCTCC 59.478 40.000 0.00 0.00 0.00 4.70
2492 3120 7.630082 AGCTCCTTACATACCTTAATTTGACA 58.370 34.615 0.00 0.00 0.00 3.58
2582 3225 2.220363 GGAAACCACGAAGAAGAACGAC 59.780 50.000 0.00 0.00 0.00 4.34
2583 3226 1.861971 AACCACGAAGAAGAACGACC 58.138 50.000 0.00 0.00 0.00 4.79
2616 3259 0.992072 ATTGCAACGATCGTGACTCG 59.008 50.000 23.51 9.32 41.77 4.18
2624 3267 0.669318 GATCGTGACTCGGCACCAAA 60.669 55.000 0.00 0.00 40.32 3.28
2636 3280 1.068541 GGCACCAAACGGAGATGTTTC 60.069 52.381 0.00 0.00 39.94 2.78
2724 3421 5.355071 TCTTCAATACTTGGATGACATGTGC 59.645 40.000 1.15 0.00 37.91 4.57
2725 3422 4.847198 TCAATACTTGGATGACATGTGCT 58.153 39.130 1.15 0.00 37.91 4.40
2740 3437 3.150848 TGTGCTCAATCTAGTACGCTG 57.849 47.619 0.00 0.00 35.12 5.18
2750 3447 7.768240 TCAATCTAGTACGCTGTCTTATTTGA 58.232 34.615 0.00 0.00 0.00 2.69
2759 3456 6.659776 ACGCTGTCTTATTTGAGTTTTCTTC 58.340 36.000 0.00 0.00 0.00 2.87
2760 3457 6.483640 ACGCTGTCTTATTTGAGTTTTCTTCT 59.516 34.615 0.00 0.00 0.00 2.85
2800 3497 2.046023 TGCCTCAATCACGGCTGG 60.046 61.111 0.00 0.00 46.42 4.85
2801 3498 2.045926 GCCTCAATCACGGCTGGT 60.046 61.111 0.00 0.00 42.98 4.00
2802 3499 1.675641 GCCTCAATCACGGCTGGTT 60.676 57.895 0.00 0.00 42.98 3.67
2803 3500 1.926511 GCCTCAATCACGGCTGGTTG 61.927 60.000 0.00 0.00 42.98 3.77
2818 3515 0.675633 GGTTGTGCCATCTTGTTGCT 59.324 50.000 0.00 0.00 37.17 3.91
2833 3530 4.736126 TGTTGCTAAGATGTGCTAGCTA 57.264 40.909 17.23 5.45 36.58 3.32
2887 3600 9.730705 TCAGATCCAATCCATCTTATTATGTTC 57.269 33.333 0.00 0.00 0.00 3.18
2968 3687 5.295292 TCTTCTTCTTCAAGAAAGTGTGCTG 59.705 40.000 0.48 0.00 46.03 4.41
2972 3691 0.664761 TCAAGAAAGTGTGCTGCAGC 59.335 50.000 31.89 31.89 42.50 5.25
3037 4952 6.513180 TCTTCCTTCTTTACCGCACTATATG 58.487 40.000 0.00 0.00 0.00 1.78
3053 4968 1.960040 TATGCACCTGCTAGCACGCT 61.960 55.000 14.93 9.18 44.49 5.07
3059 4974 1.080995 CCTGCTAGCACGCTCAGTTC 61.081 60.000 14.93 0.00 0.00 3.01
3063 4978 1.344458 CTAGCACGCTCAGTTCAGTG 58.656 55.000 0.00 0.00 37.63 3.66
3064 4979 0.958822 TAGCACGCTCAGTTCAGTGA 59.041 50.000 0.00 0.00 36.79 3.41
3066 4981 0.319040 GCACGCTCAGTTCAGTGAGA 60.319 55.000 14.75 0.00 46.02 3.27
3067 4982 1.671261 GCACGCTCAGTTCAGTGAGAT 60.671 52.381 14.75 0.32 46.02 2.75
3068 4983 2.416027 GCACGCTCAGTTCAGTGAGATA 60.416 50.000 14.75 0.00 46.02 1.98
3069 4984 3.175152 CACGCTCAGTTCAGTGAGATAC 58.825 50.000 14.75 0.00 46.02 2.24
3090 5009 5.350504 ACTGAGATAGTGCTATGCTTGTT 57.649 39.130 0.00 0.00 38.49 2.83
3091 5010 5.114780 ACTGAGATAGTGCTATGCTTGTTG 58.885 41.667 0.00 0.00 38.49 3.33
3119 5053 1.882623 TGCATGGCATGTACGTTTTCA 59.117 42.857 26.94 12.00 31.71 2.69
3120 5054 2.095314 TGCATGGCATGTACGTTTTCAG 60.095 45.455 26.94 0.00 31.71 3.02
3121 5055 2.731968 GCATGGCATGTACGTTTTCAGG 60.732 50.000 26.94 0.00 0.00 3.86
3145 5086 8.375506 AGGTAAGTCTTGACACTTATGAATTGA 58.624 33.333 3.49 0.00 40.25 2.57
3146 5087 8.660373 GGTAAGTCTTGACACTTATGAATTGAG 58.340 37.037 3.49 0.00 40.25 3.02
3171 5116 1.069432 GCATGATGCATGTGATCGACC 60.069 52.381 13.36 0.00 44.26 4.79
3178 5123 1.153289 ATGTGATCGACCAGGCAGC 60.153 57.895 0.00 0.00 0.00 5.25
3209 5637 0.324943 AAACCGTCCATGACAGGAGG 59.675 55.000 0.00 0.00 41.92 4.30
3260 5697 1.257750 GGGGCCCTTGTCAATTGTCC 61.258 60.000 24.38 0.00 0.00 4.02
3261 5698 1.257750 GGGCCCTTGTCAATTGTCCC 61.258 60.000 17.04 2.86 0.00 4.46
3262 5699 0.251787 GGCCCTTGTCAATTGTCCCT 60.252 55.000 5.13 0.00 0.00 4.20
3263 5700 1.005450 GGCCCTTGTCAATTGTCCCTA 59.995 52.381 5.13 0.00 0.00 3.53
3264 5701 2.358195 GGCCCTTGTCAATTGTCCCTAT 60.358 50.000 5.13 0.00 0.00 2.57
3265 5702 2.952310 GCCCTTGTCAATTGTCCCTATC 59.048 50.000 5.13 0.00 0.00 2.08
3266 5703 3.206150 CCCTTGTCAATTGTCCCTATCG 58.794 50.000 5.13 0.00 0.00 2.92
3267 5704 3.206150 CCTTGTCAATTGTCCCTATCGG 58.794 50.000 5.13 0.00 0.00 4.18
3298 5735 0.460811 GGCTGCGAGACATCACATGA 60.461 55.000 0.00 0.00 0.00 3.07
3316 5753 7.132863 TCACATGAAATTATACGAGAGAGACG 58.867 38.462 0.00 0.00 0.00 4.18
3328 5765 2.101380 GAGACGGAGACAGAGCGC 59.899 66.667 0.00 0.00 0.00 5.92
3344 5781 3.120041 GAGCGCCAAGAAGTCTAGATTC 58.880 50.000 2.29 1.46 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 9.282247 CATTTACAAAGAATCTGTCTAATGCAC 57.718 33.333 0.00 0.00 34.56 4.57
190 193 9.429109 TCCCTTCCTATTAACTTTGTTTTCTTT 57.571 29.630 0.00 0.00 0.00 2.52
205 208 9.743581 TTAGATTTTACGTTTTCCCTTCCTATT 57.256 29.630 0.00 0.00 0.00 1.73
345 352 8.390143 TGGCCTATAGGAAAATCTGCAAATATA 58.610 33.333 23.61 0.00 37.39 0.86
510 544 2.451490 TGAAACAAGCAAAGACACCCA 58.549 42.857 0.00 0.00 0.00 4.51
516 550 6.696411 TCCTTCTTTTTGAAACAAGCAAAGA 58.304 32.000 0.00 0.00 36.68 2.52
524 558 6.925165 GCATGAATCTCCTTCTTTTTGAAACA 59.075 34.615 0.00 0.00 34.75 2.83
601 651 7.383687 ACGTCAATTGACTATTAGGTTTCTCA 58.616 34.615 30.45 0.00 42.66 3.27
635 685 3.478780 AGCAAAGTGGCTCCCGTA 58.521 55.556 0.00 0.00 41.05 4.02
672 885 3.704566 TGCTCTAACATCACGGTAAGGAT 59.295 43.478 0.00 0.00 0.00 3.24
674 887 3.520290 TGCTCTAACATCACGGTAAGG 57.480 47.619 0.00 0.00 0.00 2.69
713 926 7.769272 ACCAACAAATTAGTGTGTTCATTTG 57.231 32.000 0.00 0.00 35.81 2.32
719 932 4.641094 TCGGAACCAACAAATTAGTGTGTT 59.359 37.500 0.00 0.00 38.49 3.32
720 933 4.200874 TCGGAACCAACAAATTAGTGTGT 58.799 39.130 0.00 0.00 0.00 3.72
721 934 4.822036 TCGGAACCAACAAATTAGTGTG 57.178 40.909 0.00 0.00 0.00 3.82
722 935 5.221165 CCTTTCGGAACCAACAAATTAGTGT 60.221 40.000 0.00 0.00 0.00 3.55
723 936 5.219633 CCTTTCGGAACCAACAAATTAGTG 58.780 41.667 0.00 0.00 0.00 2.74
724 937 4.279922 CCCTTTCGGAACCAACAAATTAGT 59.720 41.667 0.00 0.00 0.00 2.24
725 938 4.521256 TCCCTTTCGGAACCAACAAATTAG 59.479 41.667 0.00 0.00 37.88 1.73
726 939 4.471548 TCCCTTTCGGAACCAACAAATTA 58.528 39.130 0.00 0.00 37.88 1.40
727 940 3.301274 TCCCTTTCGGAACCAACAAATT 58.699 40.909 0.00 0.00 37.88 1.82
754 967 3.019799 CTCCTGTAGAGGGTTAGCTGA 57.980 52.381 6.00 0.00 40.25 4.26
768 981 5.069251 CGGTAAGAATATCTTGTCCTCCTGT 59.931 44.000 2.94 0.00 37.29 4.00
782 995 3.706600 AAACAGGGCACGGTAAGAATA 57.293 42.857 0.00 0.00 0.00 1.75
798 1011 6.200878 AGAAAGGACCCTGAGAATTAAACA 57.799 37.500 0.00 0.00 0.00 2.83
799 1012 8.047310 TGATAGAAAGGACCCTGAGAATTAAAC 58.953 37.037 0.00 0.00 0.00 2.01
809 1024 2.487986 GGGCATGATAGAAAGGACCCTG 60.488 54.545 0.00 0.00 33.11 4.45
810 1025 1.777272 GGGCATGATAGAAAGGACCCT 59.223 52.381 0.00 0.00 33.11 4.34
812 1027 2.576615 GTGGGCATGATAGAAAGGACC 58.423 52.381 0.00 0.00 0.00 4.46
815 1033 2.301346 GTGGTGGGCATGATAGAAAGG 58.699 52.381 0.00 0.00 0.00 3.11
821 1039 1.223211 CACGGTGGTGGGCATGATA 59.777 57.895 0.00 0.00 40.58 2.15
835 1053 1.830408 TGTTGAAAAGGGGGCACGG 60.830 57.895 0.00 0.00 0.00 4.94
837 1055 1.745890 GGTGTTGAAAAGGGGGCAC 59.254 57.895 0.00 0.00 0.00 5.01
851 1069 1.617947 GCACTAGCTAGCTGGGGTGT 61.618 60.000 28.58 15.39 37.91 4.16
852 1070 1.144936 GCACTAGCTAGCTGGGGTG 59.855 63.158 28.58 28.00 37.91 4.61
867 1086 0.043053 CGCGCACACTATACATGCAC 60.043 55.000 8.75 0.00 39.39 4.57
916 1139 1.298953 AGCTTGGCTATGAAAGGGGA 58.701 50.000 0.00 0.00 36.99 4.81
920 1143 3.001736 GCTCGTTAGCTTGGCTATGAAAG 59.998 47.826 0.00 0.00 45.85 2.62
923 1146 2.225068 GCTCGTTAGCTTGGCTATGA 57.775 50.000 0.00 1.97 45.85 2.15
939 1162 2.392821 CTGATCGATGTGCTACTGCTC 58.607 52.381 0.54 0.00 40.48 4.26
1169 1395 8.552034 GGTGGAAGAATTAATCGAGAAATACAG 58.448 37.037 0.00 0.00 0.00 2.74
1213 1440 4.346127 TGCATGCAAGAGATATACTCCACT 59.654 41.667 20.30 0.00 45.96 4.00
1214 1441 4.635223 TGCATGCAAGAGATATACTCCAC 58.365 43.478 20.30 0.00 45.96 4.02
1215 1442 4.590222 TCTGCATGCAAGAGATATACTCCA 59.410 41.667 22.88 0.00 45.96 3.86
1216 1443 4.928615 GTCTGCATGCAAGAGATATACTCC 59.071 45.833 22.88 2.99 45.96 3.85
1217 1444 4.620609 CGTCTGCATGCAAGAGATATACTC 59.379 45.833 22.88 6.07 45.22 2.59
1256 1495 1.956629 CTTGGACCCGCGGATGTAGT 61.957 60.000 30.73 16.30 0.00 2.73
1326 1565 2.900273 GACTGCATCTGCCCGGTA 59.100 61.111 0.00 0.00 41.18 4.02
1334 1573 2.720659 TCGATAGGCGACTGCATCT 58.279 52.632 0.00 0.00 45.59 2.90
1347 1586 0.465097 GGTGGTCGGAGAGGTCGATA 60.465 60.000 0.00 0.00 36.95 2.92
1521 1760 2.930019 CTGGGGGAGTGCCAGTGA 60.930 66.667 1.97 0.00 35.15 3.41
1557 1796 2.985282 TCGAGGTTGTACCGGCGT 60.985 61.111 6.01 0.00 44.90 5.68
1659 1898 9.884653 GTTAGAGAAACCTAACGTACCTCGTGG 62.885 48.148 0.99 0.99 41.02 4.94
1736 2046 7.483691 CAGCGGATTAGTTTTACAACATAAACC 59.516 37.037 0.00 0.00 35.39 3.27
1740 2050 6.402766 GCACAGCGGATTAGTTTTACAACATA 60.403 38.462 0.00 0.00 35.05 2.29
1742 2052 4.319911 GCACAGCGGATTAGTTTTACAACA 60.320 41.667 0.00 0.00 35.05 3.33
1748 2058 1.200020 GCTGCACAGCGGATTAGTTTT 59.800 47.619 6.92 0.00 45.29 2.43
1760 2070 1.623359 GTAAGACTCGAGCTGCACAG 58.377 55.000 13.61 0.00 0.00 3.66
1869 2179 1.760875 GAGGGAGCCCATGTACCGA 60.761 63.158 8.53 0.00 38.92 4.69
2009 2573 2.868253 GTTAGTGACCATGTGCCCC 58.132 57.895 0.00 0.00 0.00 5.80
2062 2650 7.393234 ACCTGCAAAAGCATGTATCTACTTTAA 59.607 33.333 0.00 0.00 32.28 1.52
2063 2651 6.884295 ACCTGCAAAAGCATGTATCTACTTTA 59.116 34.615 0.00 0.00 32.28 1.85
2064 2652 5.711976 ACCTGCAAAAGCATGTATCTACTTT 59.288 36.000 0.00 0.00 33.92 2.66
2065 2653 5.256474 ACCTGCAAAAGCATGTATCTACTT 58.744 37.500 0.00 0.00 0.00 2.24
2066 2654 4.848357 ACCTGCAAAAGCATGTATCTACT 58.152 39.130 0.00 0.00 0.00 2.57
2067 2655 5.335127 CAACCTGCAAAAGCATGTATCTAC 58.665 41.667 0.00 0.00 0.00 2.59
2068 2656 4.398988 CCAACCTGCAAAAGCATGTATCTA 59.601 41.667 0.00 0.00 0.00 1.98
2069 2657 3.194116 CCAACCTGCAAAAGCATGTATCT 59.806 43.478 0.00 0.00 0.00 1.98
2070 2658 3.514645 CCAACCTGCAAAAGCATGTATC 58.485 45.455 0.00 0.00 0.00 2.24
2071 2659 2.354003 GCCAACCTGCAAAAGCATGTAT 60.354 45.455 0.00 0.00 0.00 2.29
2072 2660 1.000731 GCCAACCTGCAAAAGCATGTA 59.999 47.619 0.00 0.00 0.00 2.29
2073 2661 0.249996 GCCAACCTGCAAAAGCATGT 60.250 50.000 0.00 0.00 0.00 3.21
2074 2662 0.249953 TGCCAACCTGCAAAAGCATG 60.250 50.000 0.00 0.00 38.56 4.06
2075 2663 0.249996 GTGCCAACCTGCAAAAGCAT 60.250 50.000 0.00 0.00 44.11 3.79
2076 2664 1.143620 GTGCCAACCTGCAAAAGCA 59.856 52.632 0.00 0.00 44.11 3.91
2077 2665 0.673437 TAGTGCCAACCTGCAAAAGC 59.327 50.000 0.00 0.00 44.11 3.51
2078 2666 2.742774 GTTAGTGCCAACCTGCAAAAG 58.257 47.619 0.00 0.00 44.11 2.27
2079 2667 1.066303 CGTTAGTGCCAACCTGCAAAA 59.934 47.619 0.00 0.00 44.11 2.44
2080 2668 0.665835 CGTTAGTGCCAACCTGCAAA 59.334 50.000 0.00 0.00 44.11 3.68
2081 2669 1.791103 GCGTTAGTGCCAACCTGCAA 61.791 55.000 0.00 0.00 44.11 4.08
2082 2670 2.258013 GCGTTAGTGCCAACCTGCA 61.258 57.895 0.00 0.00 39.37 4.41
2083 2671 1.966451 AGCGTTAGTGCCAACCTGC 60.966 57.895 0.00 0.00 34.65 4.85
2084 2672 0.884704 ACAGCGTTAGTGCCAACCTG 60.885 55.000 0.00 0.00 35.04 4.00
2085 2673 0.179029 AACAGCGTTAGTGCCAACCT 60.179 50.000 0.00 0.00 34.65 3.50
2086 2674 0.040425 CAACAGCGTTAGTGCCAACC 60.040 55.000 0.00 0.00 34.65 3.77
2087 2675 0.941542 TCAACAGCGTTAGTGCCAAC 59.058 50.000 0.00 0.00 34.65 3.77
2088 2676 1.890876 ATCAACAGCGTTAGTGCCAA 58.109 45.000 0.00 0.00 34.65 4.52
2089 2677 2.753055 TATCAACAGCGTTAGTGCCA 57.247 45.000 0.00 0.00 34.65 4.92
2090 2678 3.871594 AGAATATCAACAGCGTTAGTGCC 59.128 43.478 0.00 0.00 34.65 5.01
2091 2679 4.806247 AGAGAATATCAACAGCGTTAGTGC 59.194 41.667 0.00 0.00 0.00 4.40
2228 2819 9.971922 CAAAAGATTGGAGAAGTTAATCAGTTT 57.028 29.630 0.00 0.00 34.18 2.66
2229 2820 9.136323 ACAAAAGATTGGAGAAGTTAATCAGTT 57.864 29.630 0.00 0.00 41.01 3.16
2231 2822 8.786898 TGACAAAAGATTGGAGAAGTTAATCAG 58.213 33.333 0.00 0.00 41.01 2.90
2233 2824 9.617975 CTTGACAAAAGATTGGAGAAGTTAATC 57.382 33.333 0.00 0.00 41.01 1.75
2239 2855 6.640092 GCTTTCTTGACAAAAGATTGGAGAAG 59.360 38.462 4.17 0.00 41.01 2.85
2254 2870 2.977405 ATGCACTTCGCTTTCTTGAC 57.023 45.000 0.00 0.00 43.06 3.18
2414 3038 3.189287 CCTCACGCTTGCTGAAGTTTAAT 59.811 43.478 0.00 0.00 0.00 1.40
2468 3092 7.859325 TGTCAAATTAAGGTATGTAAGGAGC 57.141 36.000 0.00 0.00 0.00 4.70
2492 3120 8.604035 CAACTATGTATCGACAACAATAAGCTT 58.396 33.333 3.48 3.48 39.59 3.74
2534 3162 6.549736 ACAACTAAGGGCATGGGAAAATATAC 59.450 38.462 0.00 0.00 0.00 1.47
2582 3225 0.313043 GCAATGCTCCATGGAATCGG 59.687 55.000 17.00 5.03 0.00 4.18
2583 3226 1.026584 TGCAATGCTCCATGGAATCG 58.973 50.000 17.00 5.43 0.00 3.34
2616 3259 0.958822 AAACATCTCCGTTTGGTGCC 59.041 50.000 0.00 0.00 37.69 5.01
2624 3267 2.289694 CCAAGACCAGAAACATCTCCGT 60.290 50.000 0.00 0.00 0.00 4.69
2636 3280 1.101049 AACAACCGTGCCAAGACCAG 61.101 55.000 0.00 0.00 0.00 4.00
2724 3421 7.915923 TCAAATAAGACAGCGTACTAGATTGAG 59.084 37.037 0.00 0.00 0.00 3.02
2725 3422 7.768240 TCAAATAAGACAGCGTACTAGATTGA 58.232 34.615 0.00 0.00 0.00 2.57
2773 3470 5.469479 CCGTGATTGAGGCACTTTTTATTT 58.531 37.500 0.00 0.00 41.55 1.40
2789 3486 2.268076 GGCACAACCAGCCGTGATT 61.268 57.895 0.00 0.00 43.15 2.57
2802 3499 3.689347 ATCTTAGCAACAAGATGGCACA 58.311 40.909 7.25 0.00 42.38 4.57
2810 3507 3.937706 AGCTAGCACATCTTAGCAACAAG 59.062 43.478 18.83 0.00 37.97 3.16
2833 3530 9.321562 GTGCAATGATGAAGAAATAAATCCATT 57.678 29.630 0.00 0.00 0.00 3.16
2992 3711 9.547753 GGAAGAGCAACAAATATAGATCTGTAA 57.452 33.333 5.18 0.00 0.00 2.41
2995 3714 8.674263 AAGGAAGAGCAACAAATATAGATCTG 57.326 34.615 5.18 0.00 0.00 2.90
3011 4923 1.732809 GTGCGGTAAAGAAGGAAGAGC 59.267 52.381 0.00 0.00 0.00 4.09
3037 4952 3.191539 GAGCGTGCTAGCAGGTGC 61.192 66.667 31.55 26.89 40.15 5.01
3041 4956 0.389037 TGAACTGAGCGTGCTAGCAG 60.389 55.000 20.03 13.40 40.15 4.24
3063 4978 6.757897 AGCATAGCACTATCTCAGTATCTC 57.242 41.667 0.00 0.00 34.98 2.75
3064 4979 6.493115 ACAAGCATAGCACTATCTCAGTATCT 59.507 38.462 0.00 0.00 34.98 1.98
3066 4981 6.662865 ACAAGCATAGCACTATCTCAGTAT 57.337 37.500 0.00 0.00 34.98 2.12
3067 4982 6.127338 ACAACAAGCATAGCACTATCTCAGTA 60.127 38.462 0.00 0.00 34.98 2.74
3068 4983 5.114780 CAACAAGCATAGCACTATCTCAGT 58.885 41.667 0.00 0.00 38.32 3.41
3069 4984 5.114780 ACAACAAGCATAGCACTATCTCAG 58.885 41.667 0.00 0.00 0.00 3.35
3105 5039 4.689345 AGACTTACCTGAAAACGTACATGC 59.311 41.667 0.00 0.00 0.00 4.06
3110 5044 5.750067 GTGTCAAGACTTACCTGAAAACGTA 59.250 40.000 1.53 0.00 0.00 3.57
3119 5053 8.375506 TCAATTCATAAGTGTCAAGACTTACCT 58.624 33.333 2.24 0.00 40.41 3.08
3120 5054 8.547967 TCAATTCATAAGTGTCAAGACTTACC 57.452 34.615 2.24 0.00 40.41 2.85
3121 5055 8.171840 GCTCAATTCATAAGTGTCAAGACTTAC 58.828 37.037 2.24 0.00 40.41 2.34
3178 5123 1.798813 GGACGGTTTACAGTGCAGAAG 59.201 52.381 0.00 0.00 33.17 2.85
3189 5180 1.553248 CCTCCTGTCATGGACGGTTTA 59.447 52.381 4.65 0.00 37.24 2.01
3191 5198 0.544357 TCCTCCTGTCATGGACGGTT 60.544 55.000 4.65 0.00 37.24 4.44
3298 5735 5.821470 TGTCTCCGTCTCTCTCGTATAATTT 59.179 40.000 0.00 0.00 0.00 1.82
3316 5753 0.739112 CTTCTTGGCGCTCTGTCTCC 60.739 60.000 7.64 0.00 0.00 3.71
3328 5765 8.253810 TGTATCAAGTGAATCTAGACTTCTTGG 58.746 37.037 19.29 7.70 33.85 3.61
3344 5781 3.627577 GGTAGGCACCAATGTATCAAGTG 59.372 47.826 1.86 0.00 45.04 3.16


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

AutoCloner maintained by Alex Coulton.