Multiple sequence alignment - TraesCS5D01G264500

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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 TraesCS5D01G264500 chr5D 100.000 3875 0 0 1 3875 369376792 369380666 0.000000e+00 7156
1 TraesCS5D01G264500 chr5D 90.442 837 80 0 1 837 286418505 286419341 0.000000e+00 1103
2 TraesCS5D01G264500 chr5D 92.973 185 12 1 2920 3104 367381118 367380935 6.380000e-68 268
3 TraesCS5D01G264500 chr5B 95.874 2036 78 4 885 2916 438167210 438169243 0.000000e+00 3290
4 TraesCS5D01G264500 chr5B 93.981 731 37 2 3105 3829 438169238 438169967 0.000000e+00 1099
5 TraesCS5D01G264500 chr5A 95.533 2037 79 7 882 2914 471904012 471906040 0.000000e+00 3247
6 TraesCS5D01G264500 chr5A 94.013 618 33 1 3105 3718 471906037 471906654 0.000000e+00 933
7 TraesCS5D01G264500 chr1B 91.548 840 70 1 1 839 688377377 688378216 0.000000e+00 1157
8 TraesCS5D01G264500 chr1B 91.282 195 12 3 2919 3109 669003485 669003678 1.070000e-65 261
9 TraesCS5D01G264500 chr7D 91.320 841 71 2 1 839 435431130 435430290 0.000000e+00 1147
10 TraesCS5D01G264500 chr7D 82.506 846 137 11 1 840 25381319 25382159 0.000000e+00 732
11 TraesCS5D01G264500 chr6D 89.786 842 79 2 4 838 18102146 18101305 0.000000e+00 1072
12 TraesCS5D01G264500 chr6D 95.187 187 9 0 2919 3105 98748641 98748827 2.930000e-76 296
13 TraesCS5D01G264500 chr2B 89.713 836 85 1 4 839 63053996 63053162 0.000000e+00 1066
14 TraesCS5D01G264500 chr2B 85.541 823 119 0 16 838 755980233 755979411 0.000000e+00 861
15 TraesCS5D01G264500 chr7A 87.097 837 106 2 1 837 33490337 33491171 0.000000e+00 946
16 TraesCS5D01G264500 chr2D 82.012 845 143 9 1 840 209116315 209117155 0.000000e+00 710
17 TraesCS5D01G264500 chr2D 86.239 545 55 5 1071 1604 2196337 2196872 1.210000e-159 573
18 TraesCS5D01G264500 chr2D 91.799 378 31 0 2539 2916 2197418 2197795 9.540000e-146 527
19 TraesCS5D01G264500 chr2D 83.384 331 49 3 1645 1969 2196874 2197204 6.290000e-78 302
20 TraesCS5D01G264500 chr1D 95.722 187 6 2 2919 3105 480625474 480625658 2.260000e-77 300
21 TraesCS5D01G264500 chr1D 95.676 185 6 2 2921 3105 480623485 480623667 2.930000e-76 296
22 TraesCS5D01G264500 chr1D 94.652 187 7 2 2919 3105 480622821 480623004 1.760000e-73 287
23 TraesCS5D01G264500 chr1D 94.118 187 10 1 2919 3105 480624143 480624328 2.280000e-72 283
24 TraesCS5D01G264500 chr1D 93.158 190 9 3 2919 3105 480624807 480624995 3.810000e-70 276
25 TraesCS5D01G264500 chr1A 93.514 185 11 1 2921 3105 577093996 577094179 1.370000e-69 274


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 TraesCS5D01G264500 chr5D 369376792 369380666 3874 False 7156.000000 7156 100.000000 1 3875 1 chr5D.!!$F2 3874
1 TraesCS5D01G264500 chr5D 286418505 286419341 836 False 1103.000000 1103 90.442000 1 837 1 chr5D.!!$F1 836
2 TraesCS5D01G264500 chr5B 438167210 438169967 2757 False 2194.500000 3290 94.927500 885 3829 2 chr5B.!!$F1 2944
3 TraesCS5D01G264500 chr5A 471904012 471906654 2642 False 2090.000000 3247 94.773000 882 3718 2 chr5A.!!$F1 2836
4 TraesCS5D01G264500 chr1B 688377377 688378216 839 False 1157.000000 1157 91.548000 1 839 1 chr1B.!!$F2 838
5 TraesCS5D01G264500 chr7D 435430290 435431130 840 True 1147.000000 1147 91.320000 1 839 1 chr7D.!!$R1 838
6 TraesCS5D01G264500 chr7D 25381319 25382159 840 False 732.000000 732 82.506000 1 840 1 chr7D.!!$F1 839
7 TraesCS5D01G264500 chr6D 18101305 18102146 841 True 1072.000000 1072 89.786000 4 838 1 chr6D.!!$R1 834
8 TraesCS5D01G264500 chr2B 63053162 63053996 834 True 1066.000000 1066 89.713000 4 839 1 chr2B.!!$R1 835
9 TraesCS5D01G264500 chr2B 755979411 755980233 822 True 861.000000 861 85.541000 16 838 1 chr2B.!!$R2 822
10 TraesCS5D01G264500 chr7A 33490337 33491171 834 False 946.000000 946 87.097000 1 837 1 chr7A.!!$F1 836
11 TraesCS5D01G264500 chr2D 209116315 209117155 840 False 710.000000 710 82.012000 1 840 1 chr2D.!!$F1 839
12 TraesCS5D01G264500 chr2D 2196337 2197795 1458 False 467.333333 573 87.140667 1071 2916 3 chr2D.!!$F2 1845
13 TraesCS5D01G264500 chr1D 480622821 480625658 2837 False 288.400000 300 94.665200 2919 3105 5 chr1D.!!$F1 186

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
942 963 0.032952 TCTTTTCACACGGACCCTCG 59.967 55.0 0.00 0.0 0.00 4.63 F
944 965 0.178533 TTTTCACACGGACCCTCGTT 59.821 50.0 0.00 0.0 41.86 3.85 F
945 966 0.178533 TTTCACACGGACCCTCGTTT 59.821 50.0 0.00 0.0 41.86 3.60 F
2488 2528 0.467844 TGCATGCAGTTGGGTTGAGT 60.468 50.0 18.46 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2691 2731 0.027194 CAGGCATTTCGATCAGTGCG 59.973 55.000 0.0 0.0 38.43 5.34 R
2784 2824 2.598565 ACCTCCCTTCCAAAAGCTTTC 58.401 47.619 13.1 0.0 0.00 2.62 R
2789 2829 3.031013 ACAACAACCTCCCTTCCAAAAG 58.969 45.455 0.0 0.0 0.00 2.27 R
3831 6532 0.242017 GCACAAGTCATGGCTGGAAC 59.758 55.000 9.2 0.0 0.00 3.62 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
121 123 0.959372 CTCCTGAGCTGGTTTGCTGG 60.959 60.000 0.00 0.00 44.17 4.85
150 152 2.484651 GAGGACGAGCGAGCTATTATGA 59.515 50.000 0.00 0.00 0.00 2.15
304 306 2.778299 CAAAATCCCTCGAGTGGTTCA 58.222 47.619 12.31 0.00 0.00 3.18
309 311 0.396811 CCCTCGAGTGGTTCAACCTT 59.603 55.000 12.31 0.00 39.58 3.50
854 865 2.806608 AAAAGTCGTCGAACTAGCCA 57.193 45.000 0.00 0.00 0.00 4.75
855 866 3.314541 AAAAGTCGTCGAACTAGCCAT 57.685 42.857 0.00 0.00 0.00 4.40
856 867 3.314541 AAAGTCGTCGAACTAGCCATT 57.685 42.857 0.00 0.00 0.00 3.16
857 868 3.314541 AAGTCGTCGAACTAGCCATTT 57.685 42.857 0.00 0.00 0.00 2.32
858 869 3.314541 AGTCGTCGAACTAGCCATTTT 57.685 42.857 0.00 0.00 0.00 1.82
859 870 3.251571 AGTCGTCGAACTAGCCATTTTC 58.748 45.455 0.00 0.00 0.00 2.29
860 871 2.347755 GTCGTCGAACTAGCCATTTTCC 59.652 50.000 0.00 0.00 0.00 3.13
861 872 1.664151 CGTCGAACTAGCCATTTTCCC 59.336 52.381 0.00 0.00 0.00 3.97
862 873 1.664151 GTCGAACTAGCCATTTTCCCG 59.336 52.381 0.00 0.00 0.00 5.14
863 874 1.276989 TCGAACTAGCCATTTTCCCGT 59.723 47.619 0.00 0.00 0.00 5.28
864 875 2.496871 TCGAACTAGCCATTTTCCCGTA 59.503 45.455 0.00 0.00 0.00 4.02
865 876 3.055963 TCGAACTAGCCATTTTCCCGTAA 60.056 43.478 0.00 0.00 0.00 3.18
866 877 3.685756 CGAACTAGCCATTTTCCCGTAAA 59.314 43.478 0.00 0.00 0.00 2.01
867 878 4.154556 CGAACTAGCCATTTTCCCGTAAAA 59.845 41.667 0.00 0.00 41.21 1.52
868 879 5.335035 CGAACTAGCCATTTTCCCGTAAAAA 60.335 40.000 0.00 0.00 40.37 1.94
942 963 0.032952 TCTTTTCACACGGACCCTCG 59.967 55.000 0.00 0.00 0.00 4.63
943 964 0.249741 CTTTTCACACGGACCCTCGT 60.250 55.000 0.00 0.00 44.91 4.18
944 965 0.178533 TTTTCACACGGACCCTCGTT 59.821 50.000 0.00 0.00 41.86 3.85
945 966 0.178533 TTTCACACGGACCCTCGTTT 59.821 50.000 0.00 0.00 41.86 3.60
1013 1037 0.551131 ACCTCCATGAGAAAGCCCCT 60.551 55.000 0.00 0.00 0.00 4.79
1031 1055 0.879765 CTCAAGCTTCTGCCCAACTG 59.120 55.000 0.00 0.00 40.80 3.16
1066 1090 1.125711 ACACACCAGACCCTACACCC 61.126 60.000 0.00 0.00 0.00 4.61
1379 1410 2.436646 CTCGCTCATTGCCGGGTT 60.437 61.111 2.18 0.00 38.78 4.11
1917 1957 3.784511 AAATCAGGGAGCATGATCGAT 57.215 42.857 4.63 0.00 36.38 3.59
1956 1996 5.215252 ACCGTGTGGATAATAAGGATCTG 57.785 43.478 0.00 0.00 39.21 2.90
2010 2050 2.780010 ACAATATGGACTGGGGAAGGAG 59.220 50.000 0.00 0.00 0.00 3.69
2124 2164 2.032681 GTGAAGGAGGGCAAGCGT 59.967 61.111 0.00 0.00 0.00 5.07
2363 2403 6.092807 GTCTTTGAACTTGACCCAGATGATAC 59.907 42.308 0.00 0.00 0.00 2.24
2421 2461 2.443390 GGCCAATGGGATGCTGCT 60.443 61.111 0.00 0.00 35.59 4.24
2424 2464 1.756950 CCAATGGGATGCTGCTGCT 60.757 57.895 17.00 2.26 36.78 4.24
2436 2476 1.761449 CTGCTGCTAGAGTGAGGAGA 58.239 55.000 0.00 0.00 37.07 3.71
2488 2528 0.467844 TGCATGCAGTTGGGTTGAGT 60.468 50.000 18.46 0.00 0.00 3.41
2490 2530 1.885887 GCATGCAGTTGGGTTGAGTTA 59.114 47.619 14.21 0.00 0.00 2.24
2496 2536 3.498777 GCAGTTGGGTTGAGTTAGAGAAC 59.501 47.826 0.00 0.00 35.64 3.01
2529 2569 5.981088 TGTTTGTGGCAAATGATGATACT 57.019 34.783 0.00 0.00 0.00 2.12
2558 2598 6.252281 CACGAGCGGAAGAGATATATAAGAC 58.748 44.000 0.00 0.00 0.00 3.01
2730 2770 2.294074 GCAGGGGCAACAATTCGTATA 58.706 47.619 0.00 0.00 40.72 1.47
2784 2824 5.277202 CCACTCTGCATTCAAATACATCTCG 60.277 44.000 0.00 0.00 0.00 4.04
2789 2829 5.572211 TGCATTCAAATACATCTCGAAAGC 58.428 37.500 0.00 0.00 32.52 3.51
2803 2843 1.541588 CGAAAGCTTTTGGAAGGGAGG 59.458 52.381 17.46 0.00 33.34 4.30
2885 2925 2.113860 TACTGGTGATTCTGCCAAGC 57.886 50.000 3.00 0.00 33.93 4.01
2916 2956 5.468746 GCGTTTATGAATCTACAAGGCCATA 59.531 40.000 5.01 0.00 0.00 2.74
2917 2957 6.347725 GCGTTTATGAATCTACAAGGCCATAG 60.348 42.308 5.01 3.72 0.00 2.23
3050 5741 7.315890 AGTTTAAGCAGAATATGTCCTTTTGC 58.684 34.615 0.00 0.00 0.00 3.68
3052 5743 3.026694 AGCAGAATATGTCCTTTTGCCC 58.973 45.455 0.00 0.00 0.00 5.36
3105 5796 2.743928 GTCAAGCTCCGCCACTGG 60.744 66.667 0.00 0.00 0.00 4.00
3106 5797 4.704833 TCAAGCTCCGCCACTGGC 62.705 66.667 10.35 10.35 46.75 4.85
3136 5827 2.270352 TTCAGTAACAGCCAACAGGG 57.730 50.000 0.00 0.00 40.85 4.45
3195 5886 3.188048 GCTTGATTGTCTCTGTTGACAGG 59.812 47.826 10.97 2.92 46.02 4.00
3236 5931 3.562973 CCCTGAAGATCATTTGACATCCG 59.437 47.826 0.00 0.00 0.00 4.18
3278 5973 4.699257 AGAAGACATGTGCTTTCATCCTTC 59.301 41.667 1.15 6.56 36.24 3.46
3289 5984 2.140065 TCATCCTTCTAGCGCAATCG 57.860 50.000 11.47 0.00 39.07 3.34
3290 5985 1.681264 TCATCCTTCTAGCGCAATCGA 59.319 47.619 11.47 0.00 38.10 3.59
3300 5995 6.597262 TCTAGCGCAATCGATAAAATTTCA 57.403 33.333 11.47 0.00 36.06 2.69
3301 5996 7.189693 TCTAGCGCAATCGATAAAATTTCAT 57.810 32.000 11.47 0.00 36.06 2.57
3302 5997 7.071414 TCTAGCGCAATCGATAAAATTTCATG 58.929 34.615 11.47 0.00 36.06 3.07
3310 6005 5.649557 TCGATAAAATTTCATGGGTTGCTG 58.350 37.500 0.00 0.00 0.00 4.41
3330 6025 2.095617 TGAAACAGCATCATTGTCTGCG 60.096 45.455 7.85 6.41 43.17 5.18
3344 6039 1.153289 CTGCGTGATTCCTGGGAGG 60.153 63.158 0.00 0.00 36.46 4.30
3356 6051 1.834263 CCTGGGAGGAAAGTAGACCTG 59.166 57.143 0.00 0.00 37.67 4.00
3574 6269 4.097741 TGGGTGATTTTGCTACATATGCAC 59.902 41.667 1.58 0.00 40.40 4.57
3791 6492 0.250467 ATGCGTGGTTGTTCTGCTCT 60.250 50.000 0.00 0.00 0.00 4.09
3794 6495 0.882042 CGTGGTTGTTCTGCTCTGCT 60.882 55.000 0.00 0.00 0.00 4.24
3817 6518 3.221771 CTGGAGGTGATTGTCCAACAAA 58.778 45.455 0.00 0.00 41.96 2.83
3818 6519 3.636300 CTGGAGGTGATTGTCCAACAAAA 59.364 43.478 0.00 0.00 41.96 2.44
3829 6530 4.211125 TGTCCAACAAAAGGATGCACTTA 58.789 39.130 0.00 0.00 37.52 2.24
3830 6531 4.832266 TGTCCAACAAAAGGATGCACTTAT 59.168 37.500 0.00 0.00 37.52 1.73
3831 6532 5.163513 GTCCAACAAAAGGATGCACTTATG 58.836 41.667 0.00 0.00 37.52 1.90
3832 6533 4.832266 TCCAACAAAAGGATGCACTTATGT 59.168 37.500 0.00 0.00 0.00 2.29
3833 6534 5.304101 TCCAACAAAAGGATGCACTTATGTT 59.696 36.000 0.00 0.00 0.00 2.71
3834 6535 5.634859 CCAACAAAAGGATGCACTTATGTTC 59.365 40.000 0.00 0.00 0.00 3.18
3835 6536 5.391312 ACAAAAGGATGCACTTATGTTCC 57.609 39.130 0.00 0.00 33.00 3.62
3836 6537 4.832266 ACAAAAGGATGCACTTATGTTCCA 59.168 37.500 3.24 0.00 34.43 3.53
3837 6538 5.047802 ACAAAAGGATGCACTTATGTTCCAG 60.048 40.000 3.24 0.00 34.43 3.86
3838 6539 2.648059 AGGATGCACTTATGTTCCAGC 58.352 47.619 3.24 0.00 34.43 4.85
3839 6540 1.678101 GGATGCACTTATGTTCCAGCC 59.322 52.381 0.00 0.00 33.05 4.85
3840 6541 2.368439 GATGCACTTATGTTCCAGCCA 58.632 47.619 0.00 0.00 0.00 4.75
3841 6542 2.512692 TGCACTTATGTTCCAGCCAT 57.487 45.000 0.00 0.00 0.00 4.40
3842 6543 2.093890 TGCACTTATGTTCCAGCCATG 58.906 47.619 0.00 0.00 0.00 3.66
3843 6544 2.290832 TGCACTTATGTTCCAGCCATGA 60.291 45.455 0.00 0.00 0.00 3.07
3844 6545 2.098117 GCACTTATGTTCCAGCCATGAC 59.902 50.000 0.00 0.00 0.00 3.06
3845 6546 3.614092 CACTTATGTTCCAGCCATGACT 58.386 45.455 0.00 0.00 0.00 3.41
3846 6547 4.012374 CACTTATGTTCCAGCCATGACTT 58.988 43.478 0.00 0.00 0.00 3.01
3847 6548 4.012374 ACTTATGTTCCAGCCATGACTTG 58.988 43.478 0.00 0.00 0.00 3.16
3848 6549 2.592102 ATGTTCCAGCCATGACTTGT 57.408 45.000 0.00 0.00 0.00 3.16
3849 6550 1.608055 TGTTCCAGCCATGACTTGTG 58.392 50.000 0.00 0.00 0.00 3.33
3850 6551 0.242017 GTTCCAGCCATGACTTGTGC 59.758 55.000 0.00 0.00 0.00 4.57
3851 6552 0.895100 TTCCAGCCATGACTTGTGCC 60.895 55.000 0.00 0.00 0.00 5.01
3852 6553 2.693762 CCAGCCATGACTTGTGCCG 61.694 63.158 0.00 0.00 0.00 5.69
3853 6554 1.672030 CAGCCATGACTTGTGCCGA 60.672 57.895 0.00 0.00 0.00 5.54
3854 6555 1.073025 AGCCATGACTTGTGCCGAA 59.927 52.632 0.00 0.00 0.00 4.30
3855 6556 0.537143 AGCCATGACTTGTGCCGAAA 60.537 50.000 0.00 0.00 0.00 3.46
3856 6557 0.527565 GCCATGACTTGTGCCGAAAT 59.472 50.000 0.00 0.00 0.00 2.17
3857 6558 1.733389 GCCATGACTTGTGCCGAAATG 60.733 52.381 0.00 0.00 0.00 2.32
3858 6559 1.541147 CCATGACTTGTGCCGAAATGT 59.459 47.619 0.00 0.00 0.00 2.71
3859 6560 2.746904 CCATGACTTGTGCCGAAATGTA 59.253 45.455 0.00 0.00 0.00 2.29
3860 6561 3.378112 CCATGACTTGTGCCGAAATGTAT 59.622 43.478 0.00 0.00 0.00 2.29
3861 6562 4.574421 CCATGACTTGTGCCGAAATGTATA 59.426 41.667 0.00 0.00 0.00 1.47
3862 6563 5.501715 CATGACTTGTGCCGAAATGTATAC 58.498 41.667 0.00 0.00 0.00 1.47
3863 6564 4.827692 TGACTTGTGCCGAAATGTATACT 58.172 39.130 4.17 0.00 0.00 2.12
3864 6565 5.968254 TGACTTGTGCCGAAATGTATACTA 58.032 37.500 4.17 0.00 0.00 1.82
3865 6566 5.808540 TGACTTGTGCCGAAATGTATACTAC 59.191 40.000 4.17 0.00 0.00 2.73
3866 6567 4.802039 ACTTGTGCCGAAATGTATACTACG 59.198 41.667 4.17 4.83 0.00 3.51
3867 6568 4.374843 TGTGCCGAAATGTATACTACGT 57.625 40.909 4.17 0.00 0.00 3.57
3868 6569 5.497635 TGTGCCGAAATGTATACTACGTA 57.502 39.130 4.17 0.00 0.00 3.57
3869 6570 5.273170 TGTGCCGAAATGTATACTACGTAC 58.727 41.667 4.17 6.78 0.00 3.67
3870 6571 5.066375 TGTGCCGAAATGTATACTACGTACT 59.934 40.000 4.17 0.00 0.00 2.73
3871 6572 5.622856 GTGCCGAAATGTATACTACGTACTC 59.377 44.000 4.17 0.00 0.00 2.59
3872 6573 5.149977 GCCGAAATGTATACTACGTACTCC 58.850 45.833 4.17 0.00 0.00 3.85
3873 6574 5.377358 CCGAAATGTATACTACGTACTCCG 58.623 45.833 4.17 0.00 44.03 4.63
3874 6575 4.842911 CGAAATGTATACTACGTACTCCGC 59.157 45.833 4.17 0.00 41.42 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 152 4.230502 CCATAAGGCATATAACCCCTGGAT 59.769 45.833 0.00 0.00 0.00 3.41
590 599 1.156095 TCCCAGCACTGAGAGGTCA 59.844 57.895 0.00 0.00 0.00 4.02
599 608 0.977627 TGATCATCGGTCCCAGCACT 60.978 55.000 0.00 0.00 0.00 4.40
756 767 9.087424 CGAAATAATGTGAAGAATACAGTCTGA 57.913 33.333 6.91 0.00 0.00 3.27
840 851 2.613691 GGAAAATGGCTAGTTCGACGA 58.386 47.619 0.00 0.00 0.00 4.20
841 852 1.664151 GGGAAAATGGCTAGTTCGACG 59.336 52.381 0.00 0.00 0.00 5.12
842 853 1.664151 CGGGAAAATGGCTAGTTCGAC 59.336 52.381 0.00 0.00 0.00 4.20
843 854 1.276989 ACGGGAAAATGGCTAGTTCGA 59.723 47.619 0.00 0.00 0.00 3.71
844 855 1.734163 ACGGGAAAATGGCTAGTTCG 58.266 50.000 0.00 0.00 0.00 3.95
845 856 5.632244 TTTTACGGGAAAATGGCTAGTTC 57.368 39.130 0.00 0.00 31.90 3.01
912 928 3.059597 CGTGTGAAAAGAACAGCGAGAAT 60.060 43.478 0.00 0.00 0.00 2.40
927 943 0.249573 GAAACGAGGGTCCGTGTGAA 60.250 55.000 0.00 0.00 42.54 3.18
931 947 0.317479 AGAAGAAACGAGGGTCCGTG 59.683 55.000 0.00 0.00 42.54 4.94
942 963 1.351153 CCGAGAAGGCGAGAAGAAAC 58.649 55.000 0.00 0.00 0.00 2.78
943 964 0.246635 CCCGAGAAGGCGAGAAGAAA 59.753 55.000 0.00 0.00 39.21 2.52
944 965 0.611062 TCCCGAGAAGGCGAGAAGAA 60.611 55.000 0.00 0.00 39.21 2.52
945 966 1.001269 TCCCGAGAAGGCGAGAAGA 60.001 57.895 0.00 0.00 39.21 2.87
988 1009 0.911769 TTTCTCATGGAGGTGGCGAT 59.088 50.000 0.00 0.00 0.00 4.58
1013 1037 1.174712 GCAGTTGGGCAGAAGCTTGA 61.175 55.000 2.10 0.00 41.70 3.02
1031 1055 0.456628 GTGTCGGTAGAGGAGAAGGC 59.543 60.000 0.00 0.00 0.00 4.35
1158 1186 2.190981 GCGGTTATGAACGAGTGGTAG 58.809 52.381 0.00 0.00 0.00 3.18
1379 1410 3.478394 GCATGTCGTTCTGCGCGA 61.478 61.111 12.10 0.00 41.07 5.87
1739 1774 0.889186 ATGTGTCGCCTCAAACCCAC 60.889 55.000 0.00 0.00 0.00 4.61
1917 1957 1.305201 GGTCAAACACCTTTCTCGCA 58.695 50.000 0.00 0.00 42.84 5.10
1956 1996 3.568007 TGAGCATTGTGTTCCAAGTAACC 59.432 43.478 0.00 0.00 36.25 2.85
2010 2050 0.462759 CCTCGAAATGGGAGACTGCC 60.463 60.000 5.96 5.96 33.27 4.85
2025 2065 2.547642 GCCAGATTTCCTCATCTCCTCG 60.548 54.545 0.00 0.00 30.50 4.63
2124 2164 8.092068 TCGTACTCCTTCATCATTTCAAAGTAA 58.908 33.333 0.00 0.00 0.00 2.24
2303 2343 5.351458 CAAATTGCCCTACTTTAGCATTCC 58.649 41.667 0.00 0.00 36.20 3.01
2363 2403 0.250467 CAACAGGACAGGTGGACCAG 60.250 60.000 0.00 0.00 38.89 4.00
2421 2461 4.540715 TCATCATTCTCCTCACTCTAGCA 58.459 43.478 0.00 0.00 0.00 3.49
2424 2464 6.190587 TGTCTTCATCATTCTCCTCACTCTA 58.809 40.000 0.00 0.00 0.00 2.43
2436 2476 4.717877 TCACACCAGTTGTCTTCATCATT 58.282 39.130 0.00 0.00 35.67 2.57
2488 2528 4.607293 ACATGTGCACAGAGTTCTCTAA 57.393 40.909 25.84 0.00 0.00 2.10
2490 2530 3.482156 AACATGTGCACAGAGTTCTCT 57.518 42.857 25.97 11.36 0.00 3.10
2496 2536 1.601162 GCCACAAACATGTGCACAGAG 60.601 52.381 25.84 21.25 38.40 3.35
2529 2569 0.679960 TCTCTTCCGCTCGTGGATGA 60.680 55.000 12.67 12.67 39.21 2.92
2558 2598 1.207089 TCTTGCTTATCTCACCCCACG 59.793 52.381 0.00 0.00 0.00 4.94
2691 2731 0.027194 CAGGCATTTCGATCAGTGCG 59.973 55.000 0.00 0.00 38.43 5.34
2730 2770 9.127560 TCCCCACATATCCTAATATTCTTCATT 57.872 33.333 0.00 0.00 0.00 2.57
2784 2824 2.598565 ACCTCCCTTCCAAAAGCTTTC 58.401 47.619 13.10 0.00 0.00 2.62
2789 2829 3.031013 ACAACAACCTCCCTTCCAAAAG 58.969 45.455 0.00 0.00 0.00 2.27
2885 2925 7.254117 CCTTGTAGATTCATAAACGCACTACAG 60.254 40.741 0.00 0.00 39.39 2.74
2916 2956 4.400961 GAAGCTCCGCCACTGCCT 62.401 66.667 0.00 0.00 0.00 4.75
2917 2957 4.704833 TGAAGCTCCGCCACTGCC 62.705 66.667 0.00 0.00 0.00 4.85
3032 5723 2.101415 GGGGCAAAAGGACATATTCTGC 59.899 50.000 0.00 0.00 0.00 4.26
3052 5743 1.384222 GCAAAGCCGAGTTATGGGGG 61.384 60.000 0.00 0.00 0.00 5.40
3105 5796 4.035675 GCTGTTACTGAATCAACCTATGGC 59.964 45.833 0.00 0.00 0.00 4.40
3106 5797 4.576463 GGCTGTTACTGAATCAACCTATGG 59.424 45.833 0.00 0.00 0.00 2.74
3107 5798 5.185454 TGGCTGTTACTGAATCAACCTATG 58.815 41.667 0.00 0.00 0.00 2.23
3108 5799 5.435686 TGGCTGTTACTGAATCAACCTAT 57.564 39.130 0.00 0.00 0.00 2.57
3109 5800 4.901197 TGGCTGTTACTGAATCAACCTA 57.099 40.909 0.00 0.00 0.00 3.08
3110 5801 3.788227 TGGCTGTTACTGAATCAACCT 57.212 42.857 0.00 0.00 0.00 3.50
3136 5827 6.183360 GCCCTTTATCAGTCCATAAAAAGGTC 60.183 42.308 9.96 0.00 40.77 3.85
3195 5886 4.389576 CGGAGCGTGCTGTTTGCC 62.390 66.667 0.00 0.00 42.00 4.52
3209 5900 0.918983 AAATGATCTTCAGGGCCGGA 59.081 50.000 5.05 0.91 0.00 5.14
3210 5901 1.027357 CAAATGATCTTCAGGGCCGG 58.973 55.000 0.00 0.00 0.00 6.13
3278 5973 6.303970 CCATGAAATTTTATCGATTGCGCTAG 59.696 38.462 9.73 0.00 37.46 3.42
3289 5984 7.387397 TGTTTCAGCAACCCATGAAATTTTATC 59.613 33.333 0.00 0.00 44.65 1.75
3290 5985 7.222872 TGTTTCAGCAACCCATGAAATTTTAT 58.777 30.769 0.00 0.00 44.65 1.40
3310 6005 2.095567 ACGCAGACAATGATGCTGTTTC 60.096 45.455 11.84 0.00 40.34 2.78
3344 6039 3.691609 CCTCCAAATGCAGGTCTACTTTC 59.308 47.826 0.00 0.00 0.00 2.62
3356 6051 2.573941 GAGATTGTGCCTCCAAATGC 57.426 50.000 0.00 0.00 0.00 3.56
3547 6242 1.202989 TGTAGCAAAATCACCCAGCCA 60.203 47.619 0.00 0.00 0.00 4.75
3574 6269 1.750193 ATACCCTGAAATGCACACCG 58.250 50.000 0.00 0.00 0.00 4.94
3622 6317 1.340889 AGCAAAATCACCGTGCATTGT 59.659 42.857 0.00 0.00 40.83 2.71
3791 6492 1.555075 GGACAATCACCTCCAGTAGCA 59.445 52.381 0.00 0.00 0.00 3.49
3794 6495 2.976185 TGTTGGACAATCACCTCCAGTA 59.024 45.455 0.00 0.00 37.85 2.74
3817 6518 3.019564 GCTGGAACATAAGTGCATCCTT 58.980 45.455 0.00 0.00 38.20 3.36
3818 6519 2.648059 GCTGGAACATAAGTGCATCCT 58.352 47.619 0.00 0.00 38.20 3.24
3829 6530 2.165167 CACAAGTCATGGCTGGAACAT 58.835 47.619 9.20 0.00 38.20 2.71
3830 6531 1.608055 CACAAGTCATGGCTGGAACA 58.392 50.000 9.20 0.00 0.00 3.18
3831 6532 0.242017 GCACAAGTCATGGCTGGAAC 59.758 55.000 9.20 0.00 0.00 3.62
3832 6533 0.895100 GGCACAAGTCATGGCTGGAA 60.895 55.000 9.20 0.00 39.45 3.53
3833 6534 1.303561 GGCACAAGTCATGGCTGGA 60.304 57.895 9.20 0.00 39.45 3.86
3834 6535 2.693762 CGGCACAAGTCATGGCTGG 61.694 63.158 0.00 0.00 40.35 4.85
3835 6536 1.236616 TTCGGCACAAGTCATGGCTG 61.237 55.000 0.00 0.00 40.35 4.85
3836 6537 0.537143 TTTCGGCACAAGTCATGGCT 60.537 50.000 0.00 0.00 40.35 4.75
3837 6538 0.527565 ATTTCGGCACAAGTCATGGC 59.472 50.000 0.00 0.00 39.18 4.40
3838 6539 1.541147 ACATTTCGGCACAAGTCATGG 59.459 47.619 0.00 0.00 0.00 3.66
3839 6540 2.995466 ACATTTCGGCACAAGTCATG 57.005 45.000 0.00 0.00 0.00 3.07
3840 6541 5.428253 AGTATACATTTCGGCACAAGTCAT 58.572 37.500 5.50 0.00 0.00 3.06
3841 6542 4.827692 AGTATACATTTCGGCACAAGTCA 58.172 39.130 5.50 0.00 0.00 3.41
3842 6543 5.051907 CGTAGTATACATTTCGGCACAAGTC 60.052 44.000 5.50 0.00 43.24 3.01
3843 6544 4.802039 CGTAGTATACATTTCGGCACAAGT 59.198 41.667 5.50 0.00 43.24 3.16
3844 6545 4.802039 ACGTAGTATACATTTCGGCACAAG 59.198 41.667 5.50 0.00 43.24 3.16
3845 6546 4.746729 ACGTAGTATACATTTCGGCACAA 58.253 39.130 5.50 0.00 43.24 3.33
3846 6547 4.374843 ACGTAGTATACATTTCGGCACA 57.625 40.909 5.50 0.00 43.24 4.57


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

AutoCloner maintained by Alex Coulton.