Multiple sequence alignment - TraesCS5B01G037900

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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 TraesCS5B01G037900 chr5B 100.000 3437 0 0 1 3437 42534074 42530638 0.000000e+00 6348.0
1 TraesCS5B01G037900 chr5B 81.209 1075 155 33 1326 2372 554809025 554807970 0.000000e+00 822.0
2 TraesCS5B01G037900 chr5D 92.499 2413 106 23 362 2762 44138575 44136226 0.000000e+00 3384.0
3 TraesCS5B01G037900 chr5D 81.395 1075 153 32 1326 2372 454099611 454098556 0.000000e+00 833.0
4 TraesCS5B01G037900 chr5D 95.070 284 13 1 2767 3050 44136155 44135873 2.430000e-121 446.0
5 TraesCS5B01G037900 chr5D 94.595 148 5 2 362 506 44153178 44153031 3.450000e-55 226.0
6 TraesCS5B01G037900 chr5D 93.706 143 6 3 3274 3416 44135811 44135672 9.660000e-51 211.0
7 TraesCS5B01G037900 chr5D 91.429 70 4 2 1274 1342 402723558 402723626 1.020000e-15 95.3
8 TraesCS5B01G037900 chr5A 92.281 1995 100 26 745 2719 34262053 34264013 0.000000e+00 2782.0
9 TraesCS5B01G037900 chr5A 89.416 1096 69 30 1835 2911 363860416 363861483 0.000000e+00 1338.0
10 TraesCS5B01G037900 chr5A 81.227 1076 153 34 1326 2372 573086636 573085581 0.000000e+00 822.0
11 TraesCS5B01G037900 chr5A 84.531 640 33 32 15 600 34261348 34261975 1.070000e-159 573.0
12 TraesCS5B01G037900 chr5A 83.435 658 44 26 2779 3434 34264040 34264634 5.010000e-153 551.0
13 TraesCS5B01G037900 chr5A 93.258 178 10 2 1162 1338 363859319 363859495 9.460000e-66 261.0
14 TraesCS5B01G037900 chr5A 87.766 188 17 2 195 376 34250694 34250881 7.470000e-52 215.0
15 TraesCS5B01G037900 chr5A 88.000 100 11 1 1 100 34250332 34250430 2.170000e-22 117.0
16 TraesCS5B01G037900 chr3B 90.737 1112 66 15 1835 2921 559103043 559101944 0.000000e+00 1448.0
17 TraesCS5B01G037900 chr3B 92.537 402 21 5 1352 1752 559103429 559103036 4.980000e-158 568.0
18 TraesCS5B01G037900 chr1B 90.428 1097 64 14 1835 2921 343969528 343970593 0.000000e+00 1406.0
19 TraesCS5B01G037900 chr1B 89.142 1096 73 28 1835 2911 605938708 605939776 0.000000e+00 1323.0
20 TraesCS5B01G037900 chr1B 94.521 292 16 0 1449 1740 605938405 605938696 5.230000e-123 451.0
21 TraesCS5B01G037900 chr1B 93.258 178 10 2 1162 1338 605937573 605937749 9.460000e-66 261.0
22 TraesCS5B01G037900 chr4B 89.416 1096 70 29 1835 2911 389754254 389753186 0.000000e+00 1339.0
23 TraesCS5B01G037900 chr4B 94.863 292 15 0 1449 1740 389754557 389754266 1.120000e-124 457.0
24 TraesCS5B01G037900 chr4B 92.697 178 11 2 1162 1338 389755389 389755213 4.400000e-64 255.0
25 TraesCS5B01G037900 chr7B 89.234 1096 72 27 1835 2911 60628888 60627820 0.000000e+00 1328.0
26 TraesCS5B01G037900 chr7B 94.521 292 16 0 1449 1740 60629191 60628900 5.230000e-123 451.0
27 TraesCS5B01G037900 chr7B 92.697 178 11 2 1162 1338 60630023 60629847 4.400000e-64 255.0
28 TraesCS5B01G037900 chr7B 98.214 56 1 0 1283 1338 458795895 458795950 7.850000e-17 99.0
29 TraesCS5B01G037900 chr6B 88.785 642 48 17 2275 2911 623987428 623986806 0.000000e+00 765.0
30 TraesCS5B01G037900 chr6B 93.258 178 10 2 1162 1338 623994409 623994233 9.460000e-66 261.0
31 TraesCS5B01G037900 chr1D 100.000 28 0 0 1737 1764 459818166 459818139 6.000000e-03 52.8


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 TraesCS5B01G037900 chr5B 42530638 42534074 3436 True 6348.000000 6348 100.000000 1 3437 1 chr5B.!!$R1 3436
1 TraesCS5B01G037900 chr5B 554807970 554809025 1055 True 822.000000 822 81.209000 1326 2372 1 chr5B.!!$R2 1046
2 TraesCS5B01G037900 chr5D 44135672 44138575 2903 True 1347.000000 3384 93.758333 362 3416 3 chr5D.!!$R3 3054
3 TraesCS5B01G037900 chr5D 454098556 454099611 1055 True 833.000000 833 81.395000 1326 2372 1 chr5D.!!$R2 1046
4 TraesCS5B01G037900 chr5A 34261348 34264634 3286 False 1302.000000 2782 86.749000 15 3434 3 chr5A.!!$F2 3419
5 TraesCS5B01G037900 chr5A 573085581 573086636 1055 True 822.000000 822 81.227000 1326 2372 1 chr5A.!!$R1 1046
6 TraesCS5B01G037900 chr5A 363859319 363861483 2164 False 799.500000 1338 91.337000 1162 2911 2 chr5A.!!$F3 1749
7 TraesCS5B01G037900 chr3B 559101944 559103429 1485 True 1008.000000 1448 91.637000 1352 2921 2 chr3B.!!$R1 1569
8 TraesCS5B01G037900 chr1B 343969528 343970593 1065 False 1406.000000 1406 90.428000 1835 2921 1 chr1B.!!$F1 1086
9 TraesCS5B01G037900 chr1B 605937573 605939776 2203 False 678.333333 1323 92.307000 1162 2911 3 chr1B.!!$F2 1749
10 TraesCS5B01G037900 chr4B 389753186 389755389 2203 True 683.666667 1339 92.325333 1162 2911 3 chr4B.!!$R1 1749
11 TraesCS5B01G037900 chr7B 60627820 60630023 2203 True 678.000000 1328 92.150667 1162 2911 3 chr7B.!!$R1 1749
12 TraesCS5B01G037900 chr6B 623986806 623987428 622 True 765.000000 765 88.785000 2275 2911 1 chr6B.!!$R1 636

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
944 1004 0.538746 TCTCACTGTCCGCCACTGTA 60.539 55.0 0.0 0.0 35.5 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 3225 0.323087 ATCAAGGGGTGGGCGTTAAC 60.323 55.0 0.0 0.0 0.0 2.01 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
34 35 1.228533 GGGTTTGTAAGCCGTTTCGA 58.771 50.000 0.00 0.00 39.57 3.71
75 80 3.186409 CGGTTTCTGATGATGACAACGTT 59.814 43.478 0.00 0.00 0.00 3.99
77 82 4.911610 GGTTTCTGATGATGACAACGTTTG 59.088 41.667 0.00 0.00 0.00 2.93
78 83 3.811722 TCTGATGATGACAACGTTTGC 57.188 42.857 0.00 0.00 0.00 3.68
121 126 1.611491 CGGCCAAACTCCAAAAGCTTA 59.389 47.619 2.24 0.00 0.00 3.09
122 127 2.351738 CGGCCAAACTCCAAAAGCTTAG 60.352 50.000 2.24 0.00 0.00 2.18
123 128 2.890945 GGCCAAACTCCAAAAGCTTAGA 59.109 45.455 0.00 0.00 0.00 2.10
124 129 3.057245 GGCCAAACTCCAAAAGCTTAGAG 60.057 47.826 15.79 15.79 0.00 2.43
125 130 3.570125 GCCAAACTCCAAAAGCTTAGAGT 59.430 43.478 16.81 16.81 41.25 3.24
126 131 4.320567 GCCAAACTCCAAAAGCTTAGAGTC 60.321 45.833 20.71 9.60 38.61 3.36
127 132 4.083802 CCAAACTCCAAAAGCTTAGAGTCG 60.084 45.833 20.71 16.06 38.61 4.18
128 133 4.338379 AACTCCAAAAGCTTAGAGTCGT 57.662 40.909 20.71 8.92 38.61 4.34
172 182 1.102978 GGATCCATGAACCCCGTTTG 58.897 55.000 6.95 0.00 0.00 2.93
173 183 1.102978 GATCCATGAACCCCGTTTGG 58.897 55.000 0.00 0.00 0.00 3.28
199 209 2.705371 CATGCATGCATGTACCGGA 58.295 52.632 40.30 11.51 46.20 5.14
210 230 0.594602 TGTACCGGAAGACAGTGTCG 59.405 55.000 17.40 6.37 37.67 4.35
335 363 1.196911 CCAACCAGGACCGGTACATA 58.803 55.000 21.66 0.00 38.76 2.29
358 386 9.893305 CATACATACGTATCTCTCATACAACAA 57.107 33.333 4.74 0.00 36.11 2.83
364 393 5.520288 CGTATCTCTCATACAACAACCCTTG 59.480 44.000 0.00 0.00 0.00 3.61
399 434 0.601046 GCTACACTGCTCACACTGCA 60.601 55.000 0.00 0.00 38.81 4.41
525 576 2.126502 CCAACCGCACGGCAAATC 60.127 61.111 9.43 0.00 39.32 2.17
594 649 3.030652 CACGCCACACCCAGTTTC 58.969 61.111 0.00 0.00 0.00 2.78
602 657 3.716601 CCACACCCAGTTTCATTTGAAC 58.283 45.455 0.00 0.00 33.13 3.18
617 672 0.670546 TGAACTAAGCTCCAGTGCGC 60.671 55.000 0.00 0.00 38.13 6.09
638 694 5.163923 GCGCAGTACGGTAAAAGTAGATTTT 60.164 40.000 0.30 0.00 42.35 1.82
640 696 6.952083 CGCAGTACGGTAAAAGTAGATTTTTC 59.048 38.462 0.00 0.00 38.97 2.29
641 697 7.148689 CGCAGTACGGTAAAAGTAGATTTTTCT 60.149 37.037 0.00 0.00 38.97 2.52
642 698 8.501580 GCAGTACGGTAAAAGTAGATTTTTCTT 58.498 33.333 0.00 0.00 41.40 2.52
652 708 8.877808 AAAGTAGATTTTTCTTTTTCTGCAGG 57.122 30.769 15.13 0.00 0.00 4.85
653 709 6.986250 AGTAGATTTTTCTTTTTCTGCAGGG 58.014 36.000 15.13 0.00 0.00 4.45
654 710 6.777580 AGTAGATTTTTCTTTTTCTGCAGGGA 59.222 34.615 15.13 0.00 0.00 4.20
655 711 6.094193 AGATTTTTCTTTTTCTGCAGGGAG 57.906 37.500 15.13 7.01 0.00 4.30
656 712 5.600069 AGATTTTTCTTTTTCTGCAGGGAGT 59.400 36.000 15.13 0.00 0.00 3.85
657 713 5.675684 TTTTTCTTTTTCTGCAGGGAGTT 57.324 34.783 15.13 0.00 0.00 3.01
658 714 4.918810 TTTCTTTTTCTGCAGGGAGTTC 57.081 40.909 15.13 0.00 0.00 3.01
659 715 2.863809 TCTTTTTCTGCAGGGAGTTCC 58.136 47.619 15.13 0.00 0.00 3.62
661 717 3.650942 TCTTTTTCTGCAGGGAGTTCCTA 59.349 43.478 15.13 0.00 46.12 2.94
662 718 3.418684 TTTTCTGCAGGGAGTTCCTAC 57.581 47.619 15.13 0.00 46.12 3.18
663 719 0.895530 TTCTGCAGGGAGTTCCTACG 59.104 55.000 15.13 0.00 46.12 3.51
664 720 0.970937 TCTGCAGGGAGTTCCTACGG 60.971 60.000 15.13 0.00 46.12 4.02
665 721 2.187163 GCAGGGAGTTCCTACGGC 59.813 66.667 0.00 0.00 46.12 5.68
666 722 2.494918 CAGGGAGTTCCTACGGCG 59.505 66.667 4.80 4.80 46.12 6.46
667 723 2.758737 AGGGAGTTCCTACGGCGG 60.759 66.667 13.24 0.00 45.98 6.13
731 787 3.069318 GGACGAGCCTCTCCCGTT 61.069 66.667 0.00 0.00 36.60 4.44
732 788 2.182030 GACGAGCCTCTCCCGTTG 59.818 66.667 0.00 0.00 36.60 4.10
733 789 3.991536 GACGAGCCTCTCCCGTTGC 62.992 68.421 0.00 0.00 36.60 4.17
734 790 4.821589 CGAGCCTCTCCCGTTGCC 62.822 72.222 0.00 0.00 0.00 4.52
735 791 3.394836 GAGCCTCTCCCGTTGCCT 61.395 66.667 0.00 0.00 0.00 4.75
736 792 3.672295 GAGCCTCTCCCGTTGCCTG 62.672 68.421 0.00 0.00 0.00 4.85
738 794 3.710722 CCTCTCCCGTTGCCTGCT 61.711 66.667 0.00 0.00 0.00 4.24
739 795 2.125350 CTCTCCCGTTGCCTGCTC 60.125 66.667 0.00 0.00 0.00 4.26
740 796 2.604686 TCTCCCGTTGCCTGCTCT 60.605 61.111 0.00 0.00 0.00 4.09
934 994 1.154450 CCGTCGTCGTCTCACTGTC 60.154 63.158 0.71 0.00 35.01 3.51
944 1004 0.538746 TCTCACTGTCCGCCACTGTA 60.539 55.000 0.00 0.00 35.50 2.74
962 1022 2.095364 TGTACGAGCGAGGAGAAAGAAC 60.095 50.000 0.00 0.00 0.00 3.01
973 1033 2.597510 AAAGAACGGTGCAGCCCC 60.598 61.111 10.90 0.00 0.00 5.80
987 1047 3.470888 CCCCGGACCAGGCTACTG 61.471 72.222 0.73 0.00 44.51 2.74
995 1055 3.583383 CAGGCTACTGGTGCTTGC 58.417 61.111 0.00 0.00 41.13 4.01
996 1056 1.002868 CAGGCTACTGGTGCTTGCT 60.003 57.895 0.00 0.00 41.13 3.91
997 1057 1.023513 CAGGCTACTGGTGCTTGCTC 61.024 60.000 0.00 0.00 41.13 4.26
1611 2217 0.904865 TCGTCATGGAGTTCTGCCCT 60.905 55.000 0.00 0.00 0.00 5.19
1614 2220 0.842030 TCATGGAGTTCTGCCCTGGT 60.842 55.000 0.00 0.00 0.00 4.00
1719 2326 2.105128 GCGCTCGAGTACCTGCAT 59.895 61.111 15.13 0.00 0.00 3.96
1861 2533 4.493747 CCGTCGCCGAGGAGGAAC 62.494 72.222 8.59 0.00 45.00 3.62
1998 2678 3.973516 TGCTCGTTCGTCGGCACT 61.974 61.111 11.66 0.00 39.41 4.40
2095 2775 0.394488 CCTCTACGAGCTCCTCCACA 60.394 60.000 8.47 0.00 0.00 4.17
2732 3456 2.287915 ACTTGTCAGCAACAGCTAAACG 59.712 45.455 0.00 0.00 39.58 3.60
2756 3482 3.945285 TCGGCTTAATCACTCCATTTTCC 59.055 43.478 0.00 0.00 0.00 3.13
2764 3490 6.521151 AATCACTCCATTTTCCACTGAATC 57.479 37.500 0.00 0.00 0.00 2.52
2767 3493 5.416639 TCACTCCATTTTCCACTGAATCATG 59.583 40.000 0.00 0.00 0.00 3.07
2768 3494 5.184479 CACTCCATTTTCCACTGAATCATGT 59.816 40.000 0.00 0.00 0.00 3.21
2769 3495 5.416952 ACTCCATTTTCCACTGAATCATGTC 59.583 40.000 0.00 0.00 0.00 3.06
2971 3762 2.481795 GCTTCTGTCTCCTCTCATCTGC 60.482 54.545 0.00 0.00 0.00 4.26
3017 3808 1.406614 CCTGATGAGTTGTCTGAGCCC 60.407 57.143 0.00 0.00 0.00 5.19
3029 3820 1.821061 CTGAGCCCGAGTGAGTTGGT 61.821 60.000 0.00 0.00 0.00 3.67
3045 3836 2.758423 GTTGGTTTTGTGGAGTGGTTCT 59.242 45.455 0.00 0.00 0.00 3.01
3091 3882 0.108851 CCAACAAATGGCCGGTTAGC 60.109 55.000 1.90 0.00 43.80 3.09
3092 3883 0.600557 CAACAAATGGCCGGTTAGCA 59.399 50.000 1.90 0.00 0.00 3.49
3093 3884 1.204467 CAACAAATGGCCGGTTAGCAT 59.796 47.619 1.90 0.00 0.00 3.79
3094 3885 1.555967 ACAAATGGCCGGTTAGCATT 58.444 45.000 1.90 0.00 0.00 3.56
3095 3886 1.899142 ACAAATGGCCGGTTAGCATTT 59.101 42.857 1.90 0.00 0.00 2.32
3096 3887 2.094234 ACAAATGGCCGGTTAGCATTTC 60.094 45.455 1.90 0.00 0.00 2.17
3097 3888 0.738389 AATGGCCGGTTAGCATTTCG 59.262 50.000 1.90 0.00 0.00 3.46
3098 3889 0.393808 ATGGCCGGTTAGCATTTCGT 60.394 50.000 1.90 0.00 0.00 3.85
3099 3890 1.302383 TGGCCGGTTAGCATTTCGTG 61.302 55.000 1.90 0.00 0.00 4.35
3100 3891 1.022451 GGCCGGTTAGCATTTCGTGA 61.022 55.000 1.90 0.00 0.00 4.35
3101 3892 0.096454 GCCGGTTAGCATTTCGTGAC 59.904 55.000 1.90 0.00 0.00 3.67
3102 3893 1.434555 CCGGTTAGCATTTCGTGACA 58.565 50.000 0.00 0.00 0.00 3.58
3114 3905 2.863401 TCGTGACACATCTTATCCGG 57.137 50.000 6.37 0.00 0.00 5.14
3131 3922 1.172180 CGGCCAGAGTTTTTCCTGCA 61.172 55.000 2.24 0.00 0.00 4.41
3149 3940 2.287644 TGCACTCGTGTTTTCATGTCTG 59.712 45.455 0.00 0.00 37.97 3.51
3150 3941 2.908634 CACTCGTGTTTTCATGTCTGC 58.091 47.619 0.00 0.00 37.97 4.26
3151 3942 2.545526 CACTCGTGTTTTCATGTCTGCT 59.454 45.455 0.00 0.00 37.97 4.24
3152 3943 3.002656 CACTCGTGTTTTCATGTCTGCTT 59.997 43.478 0.00 0.00 37.97 3.91
3153 3944 3.002656 ACTCGTGTTTTCATGTCTGCTTG 59.997 43.478 0.00 0.00 37.97 4.01
3154 3945 2.046313 CGTGTTTTCATGTCTGCTTGC 58.954 47.619 0.00 0.00 32.61 4.01
3155 3946 2.397549 GTGTTTTCATGTCTGCTTGCC 58.602 47.619 0.00 0.00 0.00 4.52
3156 3947 1.001487 TGTTTTCATGTCTGCTTGCCG 60.001 47.619 0.00 0.00 0.00 5.69
3157 3948 1.001378 GTTTTCATGTCTGCTTGCCGT 60.001 47.619 0.00 0.00 0.00 5.68
3158 3949 0.592637 TTTCATGTCTGCTTGCCGTG 59.407 50.000 0.00 0.00 0.00 4.94
3159 3950 0.534877 TTCATGTCTGCTTGCCGTGT 60.535 50.000 0.00 0.00 0.00 4.49
3160 3951 0.534877 TCATGTCTGCTTGCCGTGTT 60.535 50.000 0.00 0.00 0.00 3.32
3161 3952 0.311790 CATGTCTGCTTGCCGTGTTT 59.688 50.000 0.00 0.00 0.00 2.83
3162 3953 1.032014 ATGTCTGCTTGCCGTGTTTT 58.968 45.000 0.00 0.00 0.00 2.43
3163 3954 0.380378 TGTCTGCTTGCCGTGTTTTC 59.620 50.000 0.00 0.00 0.00 2.29
3164 3955 0.657368 GTCTGCTTGCCGTGTTTTCG 60.657 55.000 0.00 0.00 0.00 3.46
3165 3956 1.092921 TCTGCTTGCCGTGTTTTCGT 61.093 50.000 0.00 0.00 0.00 3.85
3166 3957 0.929824 CTGCTTGCCGTGTTTTCGTG 60.930 55.000 0.00 0.00 0.00 4.35
3172 3963 0.306533 GCCGTGTTTTCGTGACACAT 59.693 50.000 6.37 0.00 45.88 3.21
3188 3979 7.390440 TCGTGACACATTCTTTTTATCCAAGAT 59.610 33.333 6.37 0.00 30.26 2.40
3251 4042 6.272318 TGATTTGATTGGAACACACTGTTTC 58.728 36.000 0.00 0.00 41.28 2.78
3253 4044 4.898829 TGATTGGAACACACTGTTTCTG 57.101 40.909 0.00 0.00 41.28 3.02
3254 4045 4.269183 TGATTGGAACACACTGTTTCTGT 58.731 39.130 0.00 0.00 41.28 3.41
3271 4062 0.392706 TGTCTGCGTGTGGAGATGTT 59.607 50.000 0.00 0.00 44.90 2.71
3292 4083 0.108615 CTGAGTGTAGTCCCCGCTTG 60.109 60.000 0.00 0.00 0.00 4.01
3366 4157 2.425773 CGCACGCACAGAGTTTGC 60.426 61.111 0.00 0.00 36.57 3.68
3425 4216 4.609018 AAGTGCACGGCGTCAGCT 62.609 61.111 20.69 11.51 44.37 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.683867 CAAACCCACGTTACCAAACTGA 59.316 45.455 0.00 0.00 33.15 3.41
1 2 2.424246 ACAAACCCACGTTACCAAACTG 59.576 45.455 0.00 0.00 33.15 3.16
2 3 2.725637 ACAAACCCACGTTACCAAACT 58.274 42.857 0.00 0.00 33.15 2.66
3 4 4.600032 CTTACAAACCCACGTTACCAAAC 58.400 43.478 0.00 0.00 0.00 2.93
4 5 3.066481 GCTTACAAACCCACGTTACCAAA 59.934 43.478 0.00 0.00 0.00 3.28
5 6 2.617774 GCTTACAAACCCACGTTACCAA 59.382 45.455 0.00 0.00 0.00 3.67
6 7 2.220313 GCTTACAAACCCACGTTACCA 58.780 47.619 0.00 0.00 0.00 3.25
8 9 1.195222 CGGCTTACAAACCCACGTTAC 59.805 52.381 0.00 0.00 0.00 2.50
9 10 1.202627 ACGGCTTACAAACCCACGTTA 60.203 47.619 0.00 0.00 0.00 3.18
10 11 0.464193 ACGGCTTACAAACCCACGTT 60.464 50.000 0.00 0.00 0.00 3.99
11 12 0.464193 AACGGCTTACAAACCCACGT 60.464 50.000 0.00 0.00 34.25 4.49
12 13 0.664224 AAACGGCTTACAAACCCACG 59.336 50.000 0.00 0.00 0.00 4.94
13 14 1.334329 CGAAACGGCTTACAAACCCAC 60.334 52.381 0.00 0.00 0.00 4.61
75 80 4.606961 GTGTTTTCATTCCGAGAAAGCAA 58.393 39.130 6.74 0.00 44.10 3.91
77 82 3.226347 CGTGTTTTCATTCCGAGAAAGC 58.774 45.455 0.00 0.00 36.45 3.51
78 83 4.455124 GACGTGTTTTCATTCCGAGAAAG 58.545 43.478 0.00 0.00 36.45 2.62
121 126 0.535780 TGGTGGTACGACACGACTCT 60.536 55.000 10.36 0.00 42.23 3.24
122 127 0.386478 GTGGTGGTACGACACGACTC 60.386 60.000 10.36 0.00 43.81 3.36
123 128 1.656441 GTGGTGGTACGACACGACT 59.344 57.895 10.36 0.00 43.81 4.18
124 129 1.372128 GGTGGTGGTACGACACGAC 60.372 63.158 10.36 9.18 45.61 4.34
125 130 2.906939 CGGTGGTGGTACGACACGA 61.907 63.158 10.36 0.00 42.23 4.35
126 131 2.429571 CGGTGGTGGTACGACACG 60.430 66.667 10.36 7.36 42.23 4.49
127 132 2.048877 CCGGTGGTGGTACGACAC 60.049 66.667 10.36 7.41 40.60 3.67
128 133 2.521465 ACCGGTGGTGGTACGACA 60.521 61.111 6.12 0.00 41.55 4.35
148 153 2.783510 ACGGGGTTCATGGATCCTATTT 59.216 45.455 14.23 0.00 0.00 1.40
149 154 2.418669 ACGGGGTTCATGGATCCTATT 58.581 47.619 14.23 0.00 0.00 1.73
150 155 2.118403 ACGGGGTTCATGGATCCTAT 57.882 50.000 14.23 1.95 0.00 2.57
151 156 1.887797 AACGGGGTTCATGGATCCTA 58.112 50.000 14.23 0.00 0.00 2.94
152 157 0.999712 AAACGGGGTTCATGGATCCT 59.000 50.000 14.23 0.00 0.00 3.24
172 182 1.269723 CATGCATGCATGTGGATCTCC 59.730 52.381 40.30 8.94 46.20 3.71
173 183 2.706555 CATGCATGCATGTGGATCTC 57.293 50.000 40.30 9.65 46.20 2.75
193 203 1.582968 GCGACACTGTCTTCCGGTA 59.417 57.895 0.00 0.00 0.00 4.02
195 205 2.432628 GGCGACACTGTCTTCCGG 60.433 66.667 7.58 0.00 0.00 5.14
196 206 2.338620 TGGCGACACTGTCTTCCG 59.661 61.111 7.58 0.00 33.40 4.30
210 230 1.527370 GTGTGGGGTCTAGGATGGC 59.473 63.158 0.00 0.00 0.00 4.40
312 336 4.263572 CCGGTCCTGGTTGGTGCA 62.264 66.667 0.00 0.00 37.07 4.57
335 363 7.201145 GGTTGTTGTATGAGAGATACGTATGT 58.799 38.462 13.97 9.25 0.00 2.29
356 384 0.675633 CTTGCTGGTTCCAAGGGTTG 59.324 55.000 0.00 0.00 36.82 3.77
358 386 4.929807 CTTGCTGGTTCCAAGGGT 57.070 55.556 0.00 0.00 36.82 4.34
364 393 4.043200 GCGTGCCTTGCTGGTTCC 62.043 66.667 0.00 0.00 38.35 3.62
399 434 1.879796 GCTGCTAGTGCTGGTCAAGTT 60.880 52.381 0.00 0.00 40.48 2.66
533 584 2.122413 AGACAGCCACCCACTGGA 60.122 61.111 0.00 0.00 43.95 3.86
594 649 3.425359 CGCACTGGAGCTTAGTTCAAATG 60.425 47.826 2.16 0.00 0.00 2.32
602 657 0.173481 TACTGCGCACTGGAGCTTAG 59.827 55.000 5.66 0.00 40.21 2.18
638 694 3.117512 AGGAACTCCCTGCAGAAAAAGAA 60.118 43.478 17.39 0.00 45.61 2.52
640 696 2.868899 AGGAACTCCCTGCAGAAAAAG 58.131 47.619 17.39 9.03 45.61 2.27
641 697 3.805807 CGTAGGAACTCCCTGCAGAAAAA 60.806 47.826 17.39 0.00 46.67 1.94
642 698 2.289444 CGTAGGAACTCCCTGCAGAAAA 60.289 50.000 17.39 0.00 46.67 2.29
643 699 1.275291 CGTAGGAACTCCCTGCAGAAA 59.725 52.381 17.39 1.00 46.67 2.52
644 700 0.895530 CGTAGGAACTCCCTGCAGAA 59.104 55.000 17.39 1.42 46.67 3.02
645 701 2.579878 CGTAGGAACTCCCTGCAGA 58.420 57.895 17.39 0.00 46.67 4.26
659 715 1.807981 TCATTTCGCACCGCCGTAG 60.808 57.895 0.00 0.00 0.00 3.51
660 716 2.095847 GTCATTTCGCACCGCCGTA 61.096 57.895 0.00 0.00 0.00 4.02
661 717 3.419759 GTCATTTCGCACCGCCGT 61.420 61.111 0.00 0.00 0.00 5.68
662 718 4.499023 CGTCATTTCGCACCGCCG 62.499 66.667 0.00 0.00 0.00 6.46
663 719 4.160635 CCGTCATTTCGCACCGCC 62.161 66.667 0.00 0.00 0.00 6.13
664 720 4.160635 CCCGTCATTTCGCACCGC 62.161 66.667 0.00 0.00 0.00 5.68
665 721 4.160635 GCCCGTCATTTCGCACCG 62.161 66.667 0.00 0.00 0.00 4.94
666 722 2.406616 ATGCCCGTCATTTCGCACC 61.407 57.895 0.00 0.00 33.31 5.01
667 723 1.226379 CATGCCCGTCATTTCGCAC 60.226 57.895 0.00 0.00 33.31 5.34
726 782 4.711949 AGCAGAGCAGGCAACGGG 62.712 66.667 0.00 0.00 46.39 5.28
727 783 3.123620 GAGCAGAGCAGGCAACGG 61.124 66.667 0.00 0.00 46.39 4.44
728 784 3.123620 GGAGCAGAGCAGGCAACG 61.124 66.667 0.00 0.00 46.39 4.10
729 785 1.378250 ATGGAGCAGAGCAGGCAAC 60.378 57.895 0.00 0.00 0.00 4.17
730 786 1.378119 CATGGAGCAGAGCAGGCAA 60.378 57.895 0.00 0.00 0.00 4.52
731 787 2.271173 CATGGAGCAGAGCAGGCA 59.729 61.111 0.00 0.00 0.00 4.75
732 788 3.210528 GCATGGAGCAGAGCAGGC 61.211 66.667 0.00 0.00 44.79 4.85
841 897 1.937899 CTCCGGGCGTTTTATACCAAG 59.062 52.381 0.00 0.00 0.00 3.61
934 994 4.111016 TCGCTCGTACAGTGGCGG 62.111 66.667 15.08 3.23 46.31 6.13
944 1004 0.109689 CGTTCTTTCTCCTCGCTCGT 60.110 55.000 0.00 0.00 0.00 4.18
978 1038 1.002868 AGCAAGCACCAGTAGCCTG 60.003 57.895 0.00 0.00 38.50 4.85
979 1039 1.197430 AGAGCAAGCACCAGTAGCCT 61.197 55.000 0.00 0.00 0.00 4.58
980 1040 1.023513 CAGAGCAAGCACCAGTAGCC 61.024 60.000 0.00 0.00 0.00 3.93
981 1041 0.036952 TCAGAGCAAGCACCAGTAGC 60.037 55.000 0.00 0.00 0.00 3.58
982 1042 2.277969 CATCAGAGCAAGCACCAGTAG 58.722 52.381 0.00 0.00 0.00 2.57
983 1043 1.065926 CCATCAGAGCAAGCACCAGTA 60.066 52.381 0.00 0.00 0.00 2.74
984 1044 0.322277 CCATCAGAGCAAGCACCAGT 60.322 55.000 0.00 0.00 0.00 4.00
985 1045 0.322277 ACCATCAGAGCAAGCACCAG 60.322 55.000 0.00 0.00 0.00 4.00
986 1046 0.607217 CACCATCAGAGCAAGCACCA 60.607 55.000 0.00 0.00 0.00 4.17
987 1047 1.310933 CCACCATCAGAGCAAGCACC 61.311 60.000 0.00 0.00 0.00 5.01
988 1048 1.930908 GCCACCATCAGAGCAAGCAC 61.931 60.000 0.00 0.00 0.00 4.40
989 1049 1.676635 GCCACCATCAGAGCAAGCA 60.677 57.895 0.00 0.00 0.00 3.91
990 1050 2.413142 GGCCACCATCAGAGCAAGC 61.413 63.158 0.00 0.00 0.00 4.01
991 1051 2.110967 CGGCCACCATCAGAGCAAG 61.111 63.158 2.24 0.00 0.00 4.01
992 1052 2.046023 CGGCCACCATCAGAGCAA 60.046 61.111 2.24 0.00 0.00 3.91
993 1053 4.783621 GCGGCCACCATCAGAGCA 62.784 66.667 2.24 0.00 0.00 4.26
1076 1136 3.062466 TCTCCAGGTCCGACAGCG 61.062 66.667 0.00 0.00 37.24 5.18
1860 2532 4.379243 CGCGGCTCCTCCTGTTGT 62.379 66.667 0.00 0.00 0.00 3.32
1883 2555 0.968901 ACGTATCGGGAAGCAGGACA 60.969 55.000 0.00 0.00 0.00 4.02
2228 2911 2.529744 GGGTCCTTGGTGAGCAGGT 61.530 63.158 0.00 0.00 34.46 4.00
2451 3151 3.217743 GACTCGGGGAGGCTACGG 61.218 72.222 6.00 0.00 34.31 4.02
2521 3221 3.113979 GGGTGGGCGTTAACGTCG 61.114 66.667 27.28 4.71 46.26 5.12
2522 3222 2.736579 AAGGGGTGGGCGTTAACGTC 62.737 60.000 27.28 25.67 44.28 4.34
2523 3223 2.821518 AAGGGGTGGGCGTTAACGT 61.822 57.895 27.28 3.79 42.22 3.99
2524 3224 2.032987 AAGGGGTGGGCGTTAACG 59.967 61.111 23.40 23.40 43.27 3.18
2525 3225 0.323087 ATCAAGGGGTGGGCGTTAAC 60.323 55.000 0.00 0.00 0.00 2.01
2526 3226 1.287217 TATCAAGGGGTGGGCGTTAA 58.713 50.000 0.00 0.00 0.00 2.01
2527 3227 1.287217 TTATCAAGGGGTGGGCGTTA 58.713 50.000 0.00 0.00 0.00 3.18
2532 3232 3.053077 TGGTAGATTATCAAGGGGTGGG 58.947 50.000 0.00 0.00 0.00 4.61
2533 3233 3.716872 AGTGGTAGATTATCAAGGGGTGG 59.283 47.826 0.00 0.00 0.00 4.61
2534 3234 4.202367 GGAGTGGTAGATTATCAAGGGGTG 60.202 50.000 0.00 0.00 0.00 4.61
2661 3377 1.530013 AAGCACTGGCACATGGAAGC 61.530 55.000 0.00 0.00 44.61 3.86
2732 3456 2.246719 ATGGAGTGATTAAGCCGAGC 57.753 50.000 0.00 0.00 0.00 5.03
2756 3482 1.662629 GCACTCCGACATGATTCAGTG 59.337 52.381 0.00 7.43 35.39 3.66
2764 3490 1.662629 GATTCACTGCACTCCGACATG 59.337 52.381 0.00 0.00 0.00 3.21
2767 3493 1.662629 CATGATTCACTGCACTCCGAC 59.337 52.381 0.00 0.00 0.00 4.79
2768 3494 1.276138 ACATGATTCACTGCACTCCGA 59.724 47.619 0.00 0.00 0.00 4.55
2769 3495 1.662629 GACATGATTCACTGCACTCCG 59.337 52.381 0.00 0.00 0.00 4.63
2841 3632 2.491693 CCACCACATCATTAACACACCC 59.508 50.000 0.00 0.00 0.00 4.61
2971 3762 0.250038 CATATGGACACGCCCAGAGG 60.250 60.000 0.00 0.00 39.97 3.69
3017 3808 2.285083 TCCACAAAACCAACTCACTCG 58.715 47.619 0.00 0.00 0.00 4.18
3029 3820 2.426738 CAAGCAGAACCACTCCACAAAA 59.573 45.455 0.00 0.00 0.00 2.44
3045 3836 1.271840 ACTTATCTCCCCGGCAAGCA 61.272 55.000 0.00 0.00 0.00 3.91
3090 3881 4.550831 CGGATAAGATGTGTCACGAAATGC 60.551 45.833 0.00 0.00 0.00 3.56
3091 3882 4.025730 CCGGATAAGATGTGTCACGAAATG 60.026 45.833 0.00 0.00 0.00 2.32
3092 3883 4.119862 CCGGATAAGATGTGTCACGAAAT 58.880 43.478 0.00 0.00 0.00 2.17
3093 3884 3.517602 CCGGATAAGATGTGTCACGAAA 58.482 45.455 0.00 0.00 0.00 3.46
3094 3885 2.737359 GCCGGATAAGATGTGTCACGAA 60.737 50.000 5.05 0.00 0.00 3.85
3095 3886 1.202371 GCCGGATAAGATGTGTCACGA 60.202 52.381 5.05 0.00 0.00 4.35
3096 3887 1.209128 GCCGGATAAGATGTGTCACG 58.791 55.000 5.05 0.00 0.00 4.35
3097 3888 1.134521 TGGCCGGATAAGATGTGTCAC 60.135 52.381 5.05 0.00 0.00 3.67
3098 3889 1.138859 CTGGCCGGATAAGATGTGTCA 59.861 52.381 5.28 0.00 0.00 3.58
3099 3890 1.412710 TCTGGCCGGATAAGATGTGTC 59.587 52.381 11.27 0.00 0.00 3.67
3100 3891 1.414181 CTCTGGCCGGATAAGATGTGT 59.586 52.381 16.52 0.00 0.00 3.72
3101 3892 1.414181 ACTCTGGCCGGATAAGATGTG 59.586 52.381 16.52 2.89 0.00 3.21
3102 3893 1.794714 ACTCTGGCCGGATAAGATGT 58.205 50.000 16.52 5.28 0.00 3.06
3114 3905 1.268079 GAGTGCAGGAAAAACTCTGGC 59.732 52.381 0.00 0.00 37.84 4.85
3131 3922 2.838736 AGCAGACATGAAAACACGAGT 58.161 42.857 0.00 0.00 0.00 4.18
3149 3940 0.928451 GTCACGAAAACACGGCAAGC 60.928 55.000 0.00 0.00 37.61 4.01
3150 3941 0.375454 TGTCACGAAAACACGGCAAG 59.625 50.000 0.00 0.00 37.61 4.01
3151 3942 0.097325 GTGTCACGAAAACACGGCAA 59.903 50.000 0.00 0.00 37.83 4.52
3152 3943 1.716760 GTGTCACGAAAACACGGCA 59.283 52.632 0.00 0.00 37.83 5.69
3153 3944 4.582452 GTGTCACGAAAACACGGC 57.418 55.556 0.00 0.00 37.83 5.68
3156 3947 6.626199 AAAAAGAATGTGTCACGAAAACAC 57.374 33.333 11.10 11.10 45.74 3.32
3157 3948 7.646130 GGATAAAAAGAATGTGTCACGAAAACA 59.354 33.333 0.00 0.00 0.00 2.83
3158 3949 7.646130 TGGATAAAAAGAATGTGTCACGAAAAC 59.354 33.333 0.00 0.00 0.00 2.43
3159 3950 7.708051 TGGATAAAAAGAATGTGTCACGAAAA 58.292 30.769 0.00 0.00 0.00 2.29
3160 3951 7.265647 TGGATAAAAAGAATGTGTCACGAAA 57.734 32.000 0.00 0.00 0.00 3.46
3161 3952 6.869315 TGGATAAAAAGAATGTGTCACGAA 57.131 33.333 0.00 0.00 0.00 3.85
3162 3953 6.708502 TCTTGGATAAAAAGAATGTGTCACGA 59.291 34.615 0.00 0.00 30.79 4.35
3163 3954 6.898041 TCTTGGATAAAAAGAATGTGTCACG 58.102 36.000 0.00 0.00 30.79 4.35
3164 3955 9.696917 AAATCTTGGATAAAAAGAATGTGTCAC 57.303 29.630 0.00 0.00 37.22 3.67
3172 3963 9.586732 TCCTGAGAAAATCTTGGATAAAAAGAA 57.413 29.630 0.00 0.00 37.22 2.52
3251 4042 0.037882 ACATCTCCACACGCAGACAG 60.038 55.000 0.00 0.00 0.00 3.51
3253 4044 1.461127 GAAACATCTCCACACGCAGAC 59.539 52.381 0.00 0.00 0.00 3.51
3254 4045 1.344438 AGAAACATCTCCACACGCAGA 59.656 47.619 0.00 0.00 0.00 4.26
3271 4062 0.251653 AGCGGGGACTACACTCAGAA 60.252 55.000 0.00 0.00 0.00 3.02
3292 4083 4.208686 CGGGCTCGCCTCACCTAC 62.209 72.222 8.00 0.00 36.10 3.18
3360 4151 0.594796 CGCGCAAAAGGAAGCAAACT 60.595 50.000 8.75 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.