Multiple sequence alignment - TraesCS5A01G273400

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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 TraesCS5A01G273400 chr5A 100.000 2981 0 0 1 2981 482620711 482623691 0.000000e+00 5505.0
1 TraesCS5A01G273400 chr5A 88.303 1915 162 36 166 2052 482532371 482534251 0.000000e+00 2239.0
2 TraesCS5A01G273400 chr5D 88.836 2087 118 54 716 2762 382267757 382269768 0.000000e+00 2457.0
3 TraesCS5A01G273400 chr5D 84.929 1128 103 40 111 1214 382199340 382200424 0.000000e+00 1079.0
4 TraesCS5A01G273400 chr5D 97.368 38 1 0 2762 2799 382269802 382269839 6.900000e-07 65.8
5 TraesCS5A01G273400 chr5B 90.632 1345 68 19 758 2087 458633759 458635060 0.000000e+00 1733.0
6 TraesCS5A01G273400 chr5B 89.823 678 32 14 2085 2741 458635090 458635751 0.000000e+00 835.0
7 TraesCS5A01G273400 chr7D 82.851 484 72 9 1194 1670 223869347 223869826 9.880000e-115 424.0
8 TraesCS5A01G273400 chr7B 82.895 456 73 4 1194 1648 176207325 176206874 3.580000e-109 405.0
9 TraesCS5A01G273400 chr6A 97.253 182 5 0 2800 2981 184791394 184791213 2.890000e-80 309.0
10 TraesCS5A01G273400 chr6B 95.082 183 9 0 2799 2981 141760839 141761021 3.760000e-74 289.0
11 TraesCS5A01G273400 chr6B 95.000 180 9 0 2802 2981 7599514 7599335 1.750000e-72 283.0
12 TraesCS5A01G273400 chr6B 93.407 182 11 1 2800 2981 686198388 686198568 4.900000e-68 268.0
13 TraesCS5A01G273400 chr4B 94.624 186 9 1 2797 2981 472424874 472424689 1.350000e-73 287.0
14 TraesCS5A01G273400 chr4B 93.333 180 12 0 2802 2981 388984251 388984072 1.760000e-67 267.0
15 TraesCS5A01G273400 chr4B 92.391 184 13 1 2797 2979 472425280 472425097 8.200000e-66 261.0
16 TraesCS5A01G273400 chr4A 93.011 186 12 1 2797 2981 646253978 646253793 1.360000e-68 270.0
17 TraesCS5A01G273400 chr2B 93.939 165 10 0 2802 2966 58277243 58277407 1.770000e-62 250.0
18 TraesCS5A01G273400 chr4D 78.095 105 18 4 116 218 497935258 497935359 8.920000e-06 62.1


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 TraesCS5A01G273400 chr5A 482620711 482623691 2980 False 5505.0 5505 100.0000 1 2981 1 chr5A.!!$F2 2980
1 TraesCS5A01G273400 chr5A 482532371 482534251 1880 False 2239.0 2239 88.3030 166 2052 1 chr5A.!!$F1 1886
2 TraesCS5A01G273400 chr5D 382267757 382269839 2082 False 1261.4 2457 93.1020 716 2799 2 chr5D.!!$F2 2083
3 TraesCS5A01G273400 chr5D 382199340 382200424 1084 False 1079.0 1079 84.9290 111 1214 1 chr5D.!!$F1 1103
4 TraesCS5A01G273400 chr5B 458633759 458635751 1992 False 1284.0 1733 90.2275 758 2741 2 chr5B.!!$F1 1983
5 TraesCS5A01G273400 chr4B 472424689 472425280 591 True 274.0 287 93.5075 2797 2981 2 chr4B.!!$R2 184

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
881 910 0.037326 CTTCAGTCCACCGCTTGCTA 60.037 55.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2799 2944 0.250945 TGCATCCAAACGCACCCTTA 60.251 50.0 0.0 0.0 31.95 2.69 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
17 18 2.809010 TCGTCCACGCAACAGACA 59.191 55.556 0.00 0.00 39.60 3.41
18 19 1.365999 TCGTCCACGCAACAGACAT 59.634 52.632 0.00 0.00 39.60 3.06
19 20 0.249699 TCGTCCACGCAACAGACATT 60.250 50.000 0.00 0.00 39.60 2.71
20 21 0.163788 CGTCCACGCAACAGACATTC 59.836 55.000 0.00 0.00 0.00 2.67
21 22 1.225855 GTCCACGCAACAGACATTCA 58.774 50.000 0.00 0.00 0.00 2.57
22 23 1.195448 GTCCACGCAACAGACATTCAG 59.805 52.381 0.00 0.00 0.00 3.02
23 24 0.110056 CCACGCAACAGACATTCAGC 60.110 55.000 0.00 0.00 0.00 4.26
25 26 1.198408 CACGCAACAGACATTCAGCAT 59.802 47.619 0.00 0.00 0.00 3.79
26 27 1.466167 ACGCAACAGACATTCAGCATC 59.534 47.619 0.00 0.00 0.00 3.91
28 29 2.222976 CGCAACAGACATTCAGCATCTC 60.223 50.000 0.00 0.00 0.00 2.75
29 30 2.222976 GCAACAGACATTCAGCATCTCG 60.223 50.000 0.00 0.00 0.00 4.04
30 31 1.649664 ACAGACATTCAGCATCTCGC 58.350 50.000 0.00 0.00 42.91 5.03
54 55 2.815647 CGGTCCCTCAGCGCTTTC 60.816 66.667 7.50 0.00 39.58 2.62
55 56 2.815647 GGTCCCTCAGCGCTTTCG 60.816 66.667 7.50 0.00 39.07 3.46
57 58 4.760047 TCCCTCAGCGCTTTCGGC 62.760 66.667 7.50 0.00 35.95 5.54
61 62 3.371097 CTCAGCGCTTTCGGCCCTA 62.371 63.158 7.50 0.00 37.74 3.53
62 63 3.195698 CAGCGCTTTCGGCCCTAC 61.196 66.667 7.50 0.00 37.74 3.18
63 64 4.814294 AGCGCTTTCGGCCCTACG 62.814 66.667 2.64 0.00 37.74 3.51
88 89 3.192230 CGACATTTGCCGGCGCTA 61.192 61.111 23.90 9.93 35.36 4.26
89 90 2.403586 GACATTTGCCGGCGCTAC 59.596 61.111 23.90 7.18 35.36 3.58
97 98 4.208686 CCGGCGCTACTGGGAGAC 62.209 72.222 7.64 0.00 41.71 3.36
99 100 3.450115 GGCGCTACTGGGAGACGT 61.450 66.667 7.64 0.00 0.00 4.34
101 102 1.805945 GCGCTACTGGGAGACGTTG 60.806 63.158 0.00 0.00 0.00 4.10
102 103 1.805945 CGCTACTGGGAGACGTTGC 60.806 63.158 0.00 0.00 0.00 4.17
103 104 1.448013 GCTACTGGGAGACGTTGCC 60.448 63.158 0.00 0.00 37.90 4.52
104 105 1.972198 CTACTGGGAGACGTTGCCA 59.028 57.895 9.46 9.62 46.23 4.92
107 108 3.805928 TGGGAGACGTTGCCATCT 58.194 55.556 9.46 0.00 43.15 2.90
108 109 1.296392 TGGGAGACGTTGCCATCTG 59.704 57.895 9.46 0.00 43.15 2.90
111 112 1.610624 GGGAGACGTTGCCATCTGAAA 60.611 52.381 9.46 0.00 37.22 2.69
112 113 2.151202 GGAGACGTTGCCATCTGAAAA 58.849 47.619 0.00 0.00 0.00 2.29
114 115 3.191371 GGAGACGTTGCCATCTGAAAAAT 59.809 43.478 0.00 0.00 0.00 1.82
115 116 4.161333 GAGACGTTGCCATCTGAAAAATG 58.839 43.478 0.00 0.00 0.00 2.32
139 140 2.353208 CGTCAAAGAGGAGGTGAAGGAG 60.353 54.545 0.00 0.00 0.00 3.69
227 228 4.757773 TCCACGACGGAGGAGATT 57.242 55.556 7.15 0.00 39.64 2.40
395 396 2.672961 TCGACCTCATCATGGACAAC 57.327 50.000 0.00 0.00 0.00 3.32
398 399 2.481969 CGACCTCATCATGGACAACGAT 60.482 50.000 0.00 0.00 0.00 3.73
405 406 2.606108 TCATGGACAACGATGAGAACG 58.394 47.619 0.00 0.00 36.59 3.95
419 420 4.572571 AACGGCAGGGCGTGGAAA 62.573 61.111 21.56 0.00 0.00 3.13
423 424 3.723348 GCAGGGCGTGGAAACGAC 61.723 66.667 9.49 0.00 41.09 4.34
430 431 1.655046 CGTGGAAACGACGACGACA 60.655 57.895 15.32 4.61 42.68 4.35
432 433 1.134226 GTGGAAACGACGACGACATT 58.866 50.000 15.32 5.90 42.66 2.71
474 486 9.788889 AGTTTAAGTTAAGTTTACTATGCACCT 57.211 29.630 0.00 0.00 0.00 4.00
476 488 9.781633 TTTAAGTTAAGTTTACTATGCACCTGA 57.218 29.630 0.00 0.00 0.00 3.86
511 523 9.672086 TCAACAGTTTTAAGTACATGTTAATGC 57.328 29.630 2.30 0.00 37.29 3.56
551 564 2.810439 TTTTAAATGCGTGGCTGCTT 57.190 40.000 0.00 0.00 35.36 3.91
582 597 3.411351 GCCGACACGTTGCGATGT 61.411 61.111 8.26 0.00 0.00 3.06
584 599 2.019408 CCGACACGTTGCGATGTGA 61.019 57.895 29.23 0.00 43.98 3.58
585 600 1.127817 CGACACGTTGCGATGTGAC 59.872 57.895 29.23 22.41 43.98 3.67
611 626 4.124351 GGATGCACCGACCGACGA 62.124 66.667 0.00 0.00 45.77 4.20
614 629 4.986587 TGCACCGACCGACGAACG 62.987 66.667 0.00 1.26 45.77 3.95
632 647 2.346597 GGGCAAAACCGAACATGGA 58.653 52.632 0.00 0.00 40.62 3.41
655 670 2.477375 GTCCGTTTTGTCGCTTCATACA 59.523 45.455 0.00 0.00 0.00 2.29
676 691 5.583495 ACAAATGAAATCCGAACAAAACGA 58.417 33.333 0.00 0.00 0.00 3.85
679 694 3.609475 TGAAATCCGAACAAAACGAACG 58.391 40.909 0.00 0.00 0.00 3.95
680 695 3.063725 TGAAATCCGAACAAAACGAACGT 59.936 39.130 0.00 0.00 0.00 3.99
681 696 3.678915 AATCCGAACAAAACGAACGTT 57.321 38.095 0.00 0.00 40.45 3.99
682 697 2.717524 TCCGAACAAAACGAACGTTC 57.282 45.000 18.47 18.47 37.35 3.95
727 743 5.193679 AGAGTTGGCCTAATAACCATTGAC 58.806 41.667 3.32 0.00 35.42 3.18
744 760 0.389948 GACCGAACCAGCAGACGAAT 60.390 55.000 0.00 0.00 0.00 3.34
844 866 2.814604 CGATGGATCGGGCAGTGA 59.185 61.111 0.00 0.00 45.93 3.41
845 867 1.592669 CGATGGATCGGGCAGTGAC 60.593 63.158 0.00 0.00 45.93 3.67
846 868 1.826024 GATGGATCGGGCAGTGACT 59.174 57.895 0.00 0.00 0.00 3.41
848 870 0.977627 ATGGATCGGGCAGTGACTCA 60.978 55.000 0.00 0.00 0.00 3.41
850 872 1.517257 GATCGGGCAGTGACTCACG 60.517 63.158 0.00 1.21 39.64 4.35
851 873 1.934220 GATCGGGCAGTGACTCACGA 61.934 60.000 10.75 10.75 39.64 4.35
852 874 1.532604 ATCGGGCAGTGACTCACGAA 61.533 55.000 12.00 0.00 39.64 3.85
853 875 1.734477 CGGGCAGTGACTCACGAAG 60.734 63.158 0.00 0.04 39.64 3.79
854 876 1.374758 GGGCAGTGACTCACGAAGG 60.375 63.158 0.00 0.00 39.64 3.46
855 877 1.666011 GGCAGTGACTCACGAAGGA 59.334 57.895 3.46 0.00 39.64 3.36
856 878 0.389166 GGCAGTGACTCACGAAGGAG 60.389 60.000 3.46 0.00 39.64 3.69
859 881 2.160205 CAGTGACTCACGAAGGAGGTA 58.840 52.381 3.46 0.00 39.64 3.08
873 902 0.537653 GAGGTAGCCTTCAGTCCACC 59.462 60.000 0.00 0.00 31.76 4.61
881 910 0.037326 CTTCAGTCCACCGCTTGCTA 60.037 55.000 0.00 0.00 0.00 3.49
956 985 5.036117 ACACCACTATCTCTCTCTCTCTC 57.964 47.826 0.00 0.00 0.00 3.20
959 990 3.394274 CCACTATCTCTCTCTCTCTCCCA 59.606 52.174 0.00 0.00 0.00 4.37
962 993 0.544223 TCTCTCTCTCTCTCCCACCG 59.456 60.000 0.00 0.00 0.00 4.94
982 1017 1.948144 GCCTCAGCTTCAACTCCCTTC 60.948 57.143 0.00 0.00 35.50 3.46
983 1018 1.339535 CCTCAGCTTCAACTCCCTTCC 60.340 57.143 0.00 0.00 0.00 3.46
984 1019 0.693049 TCAGCTTCAACTCCCTTCCC 59.307 55.000 0.00 0.00 0.00 3.97
985 1020 0.322906 CAGCTTCAACTCCCTTCCCC 60.323 60.000 0.00 0.00 0.00 4.81
986 1021 1.000771 GCTTCAACTCCCTTCCCCC 60.001 63.158 0.00 0.00 0.00 5.40
987 1022 1.789576 GCTTCAACTCCCTTCCCCCA 61.790 60.000 0.00 0.00 0.00 4.96
988 1023 0.329596 CTTCAACTCCCTTCCCCCAG 59.670 60.000 0.00 0.00 0.00 4.45
989 1024 1.789576 TTCAACTCCCTTCCCCCAGC 61.790 60.000 0.00 0.00 0.00 4.85
990 1025 2.211279 AACTCCCTTCCCCCAGCT 59.789 61.111 0.00 0.00 0.00 4.24
991 1026 1.925972 AACTCCCTTCCCCCAGCTC 60.926 63.158 0.00 0.00 0.00 4.09
992 1027 2.285668 CTCCCTTCCCCCAGCTCA 60.286 66.667 0.00 0.00 0.00 4.26
993 1028 2.285668 TCCCTTCCCCCAGCTCAG 60.286 66.667 0.00 0.00 0.00 3.35
994 1029 4.120755 CCCTTCCCCCAGCTCAGC 62.121 72.222 0.00 0.00 0.00 4.26
995 1030 3.013932 CCTTCCCCCAGCTCAGCT 61.014 66.667 0.00 0.00 40.77 4.24
996 1031 2.588989 CTTCCCCCAGCTCAGCTC 59.411 66.667 0.00 0.00 36.40 4.09
997 1032 2.203983 TTCCCCCAGCTCAGCTCA 60.204 61.111 0.00 0.00 36.40 4.26
1008 1043 4.284490 CCAGCTCAGCTCACCCTATATAAA 59.716 45.833 0.00 0.00 36.40 1.40
1036 1071 1.005569 TCCACGGACAGGTAGACAGAT 59.994 52.381 0.00 0.00 0.00 2.90
1109 1160 0.318529 CAGGAGCCATCGATCGACAG 60.319 60.000 22.06 15.64 0.00 3.51
1110 1161 0.466372 AGGAGCCATCGATCGACAGA 60.466 55.000 22.06 0.00 0.00 3.41
1111 1162 0.039617 GGAGCCATCGATCGACAGAG 60.040 60.000 22.06 10.37 0.00 3.35
1152 1204 3.555518 GCTTACGCTTTCTTGGTTCTTG 58.444 45.455 0.00 0.00 0.00 3.02
1185 1237 3.821995 TCGTCTGCCGATCGATCA 58.178 55.556 24.40 12.91 41.60 2.92
1233 1285 3.247424 GGACCTCATCCTGATCCCA 57.753 57.895 0.00 0.00 45.22 4.37
1491 1543 1.518133 GCTCAGCAGCACCTACTCG 60.518 63.158 0.00 0.00 46.06 4.18
1587 1639 1.815613 CTGCTCGTCTTCCTCTTCTCA 59.184 52.381 0.00 0.00 0.00 3.27
1983 2035 1.092348 GCTGCATGCAAGTCTGATCA 58.908 50.000 22.88 0.00 42.31 2.92
2008 2060 1.014044 TGATCGTCGGAAGCAAGTGC 61.014 55.000 0.00 0.00 42.49 4.40
2061 2114 1.478137 CGTTTCGATCAGTCCGATCC 58.522 55.000 0.00 0.00 46.85 3.36
2169 2257 3.335786 TCTCTGAACCTGGGAAGGTACTA 59.664 47.826 0.00 0.00 42.20 1.82
2170 2258 3.438183 TCTGAACCTGGGAAGGTACTAC 58.562 50.000 0.00 0.00 42.20 2.73
2171 2259 3.077088 TCTGAACCTGGGAAGGTACTACT 59.923 47.826 0.00 0.00 42.20 2.57
2172 2260 4.293102 TCTGAACCTGGGAAGGTACTACTA 59.707 45.833 0.00 0.00 42.20 1.82
2173 2261 4.607239 TGAACCTGGGAAGGTACTACTAG 58.393 47.826 0.00 0.00 42.20 2.57
2174 2262 4.045079 TGAACCTGGGAAGGTACTACTAGT 59.955 45.833 0.00 0.00 42.20 2.57
2252 2345 0.036952 TCTGGCTTGTCAGTAGCTGC 60.037 55.000 0.00 0.00 38.67 5.25
2413 2517 2.421073 CAGTGTGACAATGTATGCCTGG 59.579 50.000 4.66 0.00 0.00 4.45
2503 2609 1.812571 CCCGCTTATTTTGACACTGCT 59.187 47.619 0.00 0.00 0.00 4.24
2584 2695 5.202004 TGTAACACCCCTAACAAACACAAT 58.798 37.500 0.00 0.00 0.00 2.71
2611 2722 6.625873 AAGAGAGTCCAAACATTTCTGTTC 57.374 37.500 0.00 0.00 44.83 3.18
2745 2856 5.723295 GCTTTCTGCCCATTTCATTAAGAA 58.277 37.500 0.00 0.00 35.15 2.52
2791 2936 4.287067 AGAGGGAGTACATGAGAAAAGCAA 59.713 41.667 0.00 0.00 0.00 3.91
2799 2944 9.468532 GAGTACATGAGAAAAGCAAAAAGAAAT 57.531 29.630 0.00 0.00 0.00 2.17
2855 3000 7.812690 AGTTTTTCTAGAATACCGTGGTTTT 57.187 32.000 5.89 0.00 0.00 2.43
2934 3079 8.575649 AAGTTTTGTAAACCATAGTATCCCAG 57.424 34.615 0.00 0.00 0.00 4.45
2940 3085 5.789574 AAACCATAGTATCCCAGAAACCA 57.210 39.130 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.249699 AATGTCTGTTGCGTGGACGA 60.250 50.000 2.73 0.00 43.02 4.20
1 2 0.163788 GAATGTCTGTTGCGTGGACG 59.836 55.000 0.00 0.00 43.27 4.79
2 3 1.195448 CTGAATGTCTGTTGCGTGGAC 59.805 52.381 0.00 0.00 0.00 4.02
3 4 1.511850 CTGAATGTCTGTTGCGTGGA 58.488 50.000 0.00 0.00 0.00 4.02
4 5 0.110056 GCTGAATGTCTGTTGCGTGG 60.110 55.000 0.00 0.00 0.00 4.94
5 6 0.587768 TGCTGAATGTCTGTTGCGTG 59.412 50.000 0.00 0.00 0.00 5.34
7 8 1.736126 AGATGCTGAATGTCTGTTGCG 59.264 47.619 0.00 0.00 0.00 4.85
9 10 2.222976 GCGAGATGCTGAATGTCTGTTG 60.223 50.000 0.00 0.00 41.73 3.33
10 11 2.005451 GCGAGATGCTGAATGTCTGTT 58.995 47.619 0.00 0.00 41.73 3.16
11 12 1.649664 GCGAGATGCTGAATGTCTGT 58.350 50.000 0.00 0.00 41.73 3.41
37 38 2.815647 GAAAGCGCTGAGGGACCG 60.816 66.667 12.58 0.00 0.00 4.79
38 39 2.815647 CGAAAGCGCTGAGGGACC 60.816 66.667 12.58 0.00 0.00 4.46
39 40 2.815647 CCGAAAGCGCTGAGGGAC 60.816 66.667 12.58 0.00 35.83 4.46
71 72 3.192230 TAGCGCCGGCAAATGTCG 61.192 61.111 28.98 9.29 43.41 4.35
72 73 2.106683 AGTAGCGCCGGCAAATGTC 61.107 57.895 28.98 11.07 43.41 3.06
73 74 2.046314 AGTAGCGCCGGCAAATGT 60.046 55.556 28.98 7.77 43.41 2.71
74 75 2.404789 CAGTAGCGCCGGCAAATG 59.595 61.111 28.98 16.51 43.41 2.32
75 76 2.824041 CCAGTAGCGCCGGCAAAT 60.824 61.111 28.98 13.98 43.41 2.32
80 81 4.208686 GTCTCCCAGTAGCGCCGG 62.209 72.222 2.29 0.00 0.00 6.13
81 82 4.554363 CGTCTCCCAGTAGCGCCG 62.554 72.222 2.29 0.00 0.00 6.46
82 83 3.003113 AACGTCTCCCAGTAGCGCC 62.003 63.158 2.29 0.00 0.00 6.53
83 84 1.805945 CAACGTCTCCCAGTAGCGC 60.806 63.158 0.00 0.00 0.00 5.92
85 86 1.448013 GGCAACGTCTCCCAGTAGC 60.448 63.158 0.00 0.00 0.00 3.58
86 87 0.537188 ATGGCAACGTCTCCCAGTAG 59.463 55.000 0.00 0.00 42.51 2.57
88 89 3.483587 ATGGCAACGTCTCCCAGT 58.516 55.556 0.00 0.00 42.51 4.00
96 97 2.627699 ACCATTTTTCAGATGGCAACGT 59.372 40.909 0.00 0.00 46.43 3.99
97 98 3.244976 GACCATTTTTCAGATGGCAACG 58.755 45.455 0.00 0.00 46.43 4.10
99 100 2.890311 ACGACCATTTTTCAGATGGCAA 59.110 40.909 0.00 0.00 46.43 4.52
101 102 2.487762 TGACGACCATTTTTCAGATGGC 59.512 45.455 3.16 0.00 46.43 4.40
103 104 6.000891 TCTTTGACGACCATTTTTCAGATG 57.999 37.500 0.00 0.00 0.00 2.90
104 105 5.182001 CCTCTTTGACGACCATTTTTCAGAT 59.818 40.000 0.00 0.00 0.00 2.90
105 106 4.515191 CCTCTTTGACGACCATTTTTCAGA 59.485 41.667 0.00 0.00 0.00 3.27
106 107 4.515191 TCCTCTTTGACGACCATTTTTCAG 59.485 41.667 0.00 0.00 0.00 3.02
107 108 4.456535 TCCTCTTTGACGACCATTTTTCA 58.543 39.130 0.00 0.00 0.00 2.69
108 109 4.083271 CCTCCTCTTTGACGACCATTTTTC 60.083 45.833 0.00 0.00 0.00 2.29
111 112 2.372172 ACCTCCTCTTTGACGACCATTT 59.628 45.455 0.00 0.00 0.00 2.32
112 113 1.978580 ACCTCCTCTTTGACGACCATT 59.021 47.619 0.00 0.00 0.00 3.16
114 115 0.679505 CACCTCCTCTTTGACGACCA 59.320 55.000 0.00 0.00 0.00 4.02
115 116 0.966920 TCACCTCCTCTTTGACGACC 59.033 55.000 0.00 0.00 0.00 4.79
139 140 1.990614 GGACTCCTCCACCACCTCC 60.991 68.421 0.00 0.00 36.42 4.30
162 163 1.375523 GCGGGTTCCACTTGTCGAT 60.376 57.895 0.00 0.00 0.00 3.59
265 266 4.309950 GCTCCGGTGAACGTGGGT 62.310 66.667 7.92 0.00 42.24 4.51
296 297 4.341783 GCCTGCACCACCTCTGCT 62.342 66.667 0.00 0.00 35.53 4.24
395 396 2.892425 GCCCTGCCGTTCTCATCG 60.892 66.667 0.00 0.00 0.00 3.84
398 399 4.680237 CACGCCCTGCCGTTCTCA 62.680 66.667 0.00 0.00 39.83 3.27
562 577 2.032634 ATCGCAACGTGTCGGCATT 61.033 52.632 0.00 0.00 0.00 3.56
567 582 1.127817 GTCACATCGCAACGTGTCG 59.872 57.895 0.00 0.00 34.66 4.35
614 629 0.894835 ATCCATGTTCGGTTTTGCCC 59.105 50.000 0.00 0.00 0.00 5.36
629 644 0.250124 AGCGACAAAACGGACATCCA 60.250 50.000 0.00 0.00 35.14 3.41
632 647 1.588674 TGAAGCGACAAAACGGACAT 58.411 45.000 0.00 0.00 0.00 3.06
655 670 5.172411 CGTTCGTTTTGTTCGGATTTCATTT 59.828 36.000 0.00 0.00 0.00 2.32
679 694 1.459592 CATGACTCCAAACGGACGAAC 59.540 52.381 0.00 0.00 0.00 3.95
680 695 1.790755 CATGACTCCAAACGGACGAA 58.209 50.000 0.00 0.00 0.00 3.85
681 696 0.669318 GCATGACTCCAAACGGACGA 60.669 55.000 0.00 0.00 0.00 4.20
682 697 1.787847 GCATGACTCCAAACGGACG 59.212 57.895 0.00 0.00 0.00 4.79
683 698 0.949105 ACGCATGACTCCAAACGGAC 60.949 55.000 0.00 0.00 0.00 4.79
691 706 2.271800 CCAACTCTAACGCATGACTCC 58.728 52.381 0.00 0.00 0.00 3.85
693 708 1.676014 GGCCAACTCTAACGCATGACT 60.676 52.381 0.00 0.00 0.00 3.41
727 743 0.389817 TCATTCGTCTGCTGGTTCGG 60.390 55.000 0.00 0.00 0.00 4.30
744 760 1.501741 GTACGTACGTCGCCCTTCA 59.498 57.895 26.53 0.85 44.19 3.02
775 791 4.747810 ACAAAAAGAATGCCAATCGATCC 58.252 39.130 0.00 0.00 0.00 3.36
782 798 5.221422 CCCAGACTAACAAAAAGAATGCCAA 60.221 40.000 0.00 0.00 0.00 4.52
837 859 0.389166 CTCCTTCGTGAGTCACTGCC 60.389 60.000 20.64 0.00 31.34 4.85
838 860 0.389166 CCTCCTTCGTGAGTCACTGC 60.389 60.000 20.64 0.00 31.34 4.40
843 865 0.456628 GGCTACCTCCTTCGTGAGTC 59.543 60.000 0.00 0.00 0.00 3.36
844 866 0.039911 AGGCTACCTCCTTCGTGAGT 59.960 55.000 0.00 0.00 30.82 3.41
845 867 1.187087 AAGGCTACCTCCTTCGTGAG 58.813 55.000 0.00 0.00 42.55 3.51
846 868 3.376082 AAGGCTACCTCCTTCGTGA 57.624 52.632 0.00 0.00 42.55 4.35
852 874 0.413832 TGGACTGAAGGCTACCTCCT 59.586 55.000 0.00 0.00 38.31 3.69
853 875 0.537653 GTGGACTGAAGGCTACCTCC 59.462 60.000 0.00 0.00 30.89 4.30
854 876 0.537653 GGTGGACTGAAGGCTACCTC 59.462 60.000 11.29 0.00 30.89 3.85
855 877 1.258445 CGGTGGACTGAAGGCTACCT 61.258 60.000 15.89 0.00 33.87 3.08
856 878 1.218316 CGGTGGACTGAAGGCTACC 59.782 63.158 8.62 8.62 0.00 3.18
859 881 2.520536 AAGCGGTGGACTGAAGGCT 61.521 57.895 0.00 0.00 0.00 4.58
865 894 0.320771 AAGTAGCAAGCGGTGGACTG 60.321 55.000 0.00 0.00 0.00 3.51
873 902 1.432514 TCAGCTGAAAGTAGCAAGCG 58.567 50.000 15.67 0.00 46.07 4.68
881 910 2.158623 TGGTGGTCAATCAGCTGAAAGT 60.159 45.455 22.50 6.29 36.25 2.66
956 985 3.551496 TTGAAGCTGAGGCGGTGGG 62.551 63.158 0.00 0.00 44.37 4.61
959 990 1.004440 GAGTTGAAGCTGAGGCGGT 60.004 57.895 0.00 0.00 44.37 5.68
962 993 0.037447 AAGGGAGTTGAAGCTGAGGC 59.963 55.000 0.00 0.00 39.06 4.70
982 1017 4.106925 GGTGAGCTGAGCTGGGGG 62.107 72.222 13.71 0.00 39.88 5.40
983 1018 4.106925 GGGTGAGCTGAGCTGGGG 62.107 72.222 13.71 0.00 39.88 4.96
984 1019 1.053264 ATAGGGTGAGCTGAGCTGGG 61.053 60.000 13.71 0.00 39.88 4.45
985 1020 1.709578 TATAGGGTGAGCTGAGCTGG 58.290 55.000 13.71 0.00 39.88 4.85
986 1021 5.474578 TTTATATAGGGTGAGCTGAGCTG 57.525 43.478 13.71 0.00 39.88 4.24
987 1022 4.020662 GCTTTATATAGGGTGAGCTGAGCT 60.021 45.833 6.69 6.69 43.88 4.09
988 1023 4.249661 GCTTTATATAGGGTGAGCTGAGC 58.750 47.826 0.00 0.00 0.00 4.26
989 1024 5.233988 GTGCTTTATATAGGGTGAGCTGAG 58.766 45.833 0.00 0.00 0.00 3.35
990 1025 4.040461 GGTGCTTTATATAGGGTGAGCTGA 59.960 45.833 0.00 0.00 0.00 4.26
991 1026 4.319177 GGTGCTTTATATAGGGTGAGCTG 58.681 47.826 0.00 0.00 0.00 4.24
992 1027 3.328050 GGGTGCTTTATATAGGGTGAGCT 59.672 47.826 0.00 0.00 0.00 4.09
993 1028 3.072476 TGGGTGCTTTATATAGGGTGAGC 59.928 47.826 0.00 0.00 0.00 4.26
994 1029 4.974645 TGGGTGCTTTATATAGGGTGAG 57.025 45.455 0.00 0.00 0.00 3.51
995 1030 4.288626 GGATGGGTGCTTTATATAGGGTGA 59.711 45.833 0.00 0.00 0.00 4.02
996 1031 4.042809 TGGATGGGTGCTTTATATAGGGTG 59.957 45.833 0.00 0.00 0.00 4.61
997 1032 4.042934 GTGGATGGGTGCTTTATATAGGGT 59.957 45.833 0.00 0.00 0.00 4.34
1008 1043 2.927856 TGTCCGTGGATGGGTGCT 60.928 61.111 0.00 0.00 0.00 4.40
1036 1071 2.167398 GAACCGTGTGGAGCTGGCTA 62.167 60.000 0.00 0.00 39.21 3.93
1109 1160 1.079819 TGGCACTAGCACGCTTCTC 60.080 57.895 0.00 0.00 44.61 2.87
1110 1161 1.374758 GTGGCACTAGCACGCTTCT 60.375 57.895 11.13 0.00 44.61 2.85
1111 1162 1.667830 TGTGGCACTAGCACGCTTC 60.668 57.895 19.83 0.00 44.61 3.86
1152 1204 0.589229 ACGACGATGATCGAGCGAAC 60.589 55.000 29.24 11.82 45.13 3.95
1185 1237 1.077501 CCTCCACGCCACCATGATT 60.078 57.895 0.00 0.00 0.00 2.57
1233 1285 4.423209 GGGAGGAGGAGCCCCAGT 62.423 72.222 0.00 0.00 39.89 4.00
1491 1543 2.394563 GCTCAGCGGCTTCTTCACC 61.395 63.158 0.00 0.00 0.00 4.02
1587 1639 0.842030 TGAGGGTGTGGCAGAGGAAT 60.842 55.000 0.00 0.00 0.00 3.01
1904 1956 2.182030 CCTTCGTCCCTCTGTCGC 59.818 66.667 0.00 0.00 0.00 5.19
1914 1966 2.386660 GCTGCTGTGCTCCTTCGTC 61.387 63.158 0.00 0.00 0.00 4.20
1983 2035 1.067060 TGCTTCCGACGATCATCGATT 59.933 47.619 15.60 0.00 45.13 3.34
1997 2049 1.285023 CTGCACTGCACTTGCTTCC 59.715 57.895 14.97 0.00 40.86 3.46
2008 2060 2.614446 GGCTGACTGCACTGCACTG 61.614 63.158 0.00 0.00 45.15 3.66
2061 2114 2.034124 CATCATGTAAAAGGGGCAGGG 58.966 52.381 0.00 0.00 0.00 4.45
2169 2257 8.135382 TGGATGAAAAGAAAGCTAGTACTAGT 57.865 34.615 26.76 13.66 35.65 2.57
2170 2258 8.470805 TCTGGATGAAAAGAAAGCTAGTACTAG 58.529 37.037 23.25 23.25 36.29 2.57
2171 2259 8.251721 GTCTGGATGAAAAGAAAGCTAGTACTA 58.748 37.037 1.89 1.89 0.00 1.82
2172 2260 7.100409 GTCTGGATGAAAAGAAAGCTAGTACT 58.900 38.462 0.00 0.00 0.00 2.73
2173 2261 6.874134 TGTCTGGATGAAAAGAAAGCTAGTAC 59.126 38.462 0.00 0.00 0.00 2.73
2174 2262 7.004555 TGTCTGGATGAAAAGAAAGCTAGTA 57.995 36.000 0.00 0.00 0.00 1.82
2192 2280 2.660064 CCCCTCCCGACTTGTCTGG 61.660 68.421 5.07 5.07 0.00 3.86
2252 2345 4.934942 TCCACACGACACGCACCG 62.935 66.667 0.00 0.00 0.00 4.94
2318 2411 3.676324 GCCCGTACCATCTGCTATGATAC 60.676 52.174 1.67 0.00 0.00 2.24
2321 2414 0.679505 GCCCGTACCATCTGCTATGA 59.320 55.000 1.67 0.00 0.00 2.15
2424 2528 1.112113 CCTACAGATACACGCCCTGT 58.888 55.000 0.00 0.00 42.94 4.00
2584 2695 7.054124 ACAGAAATGTTTGGACTCTCTTACAA 58.946 34.615 0.00 0.00 0.00 2.41
2694 2805 2.033372 TCCCGTCAAAAGAAAAACCCC 58.967 47.619 0.00 0.00 0.00 4.95
2756 2867 1.577729 ACTCCCTCTGATCCAGGATCA 59.422 52.381 27.64 27.64 45.35 2.92
2791 2936 4.342665 TCCAAACGCACCCTTATTTCTTTT 59.657 37.500 0.00 0.00 0.00 2.27
2799 2944 0.250945 TGCATCCAAACGCACCCTTA 60.251 50.000 0.00 0.00 31.95 2.69
2800 2945 1.112315 TTGCATCCAAACGCACCCTT 61.112 50.000 0.00 0.00 38.00 3.95
2866 3011 8.877779 CAAACACATCAAAGTATTCAAAACCAA 58.122 29.630 0.00 0.00 0.00 3.67
2908 3053 8.570068 TGGGATACTATGGTTTACAAAACTTC 57.430 34.615 2.84 0.00 0.00 3.01
2913 3058 7.612633 GGTTTCTGGGATACTATGGTTTACAAA 59.387 37.037 0.00 0.00 0.00 2.83
2926 3071 7.123547 TCAAAAATACCATGGTTTCTGGGATAC 59.876 37.037 25.38 0.00 36.23 2.24


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

AutoCloner maintained by Alex Coulton.