Multiple sequence alignment - TraesCS4A01G067000

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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 TraesCS4A01G067000 chr4A 100.000 3123 0 0 1 3123 64567443 64570565 0.000000e+00 5768.0
1 TraesCS4A01G067000 chr4B 93.719 3057 109 36 106 3123 506322665 506325677 0.000000e+00 4505.0
2 TraesCS4A01G067000 chr4D 92.445 2634 115 40 525 3123 409480538 409477954 0.000000e+00 3685.0
3 TraesCS4A01G067000 chr4D 86.414 449 26 10 103 537 409481010 409480583 2.840000e-125 459.0
4 TraesCS4A01G067000 chr3A 91.176 102 9 0 1 102 552301838 552301939 4.200000e-29 139.0
5 TraesCS4A01G067000 chr6A 90.385 104 10 0 1 104 21717892 21717995 1.510000e-28 137.0
6 TraesCS4A01G067000 chr6A 89.216 102 11 0 1 102 8982580 8982681 9.090000e-26 128.0
7 TraesCS4A01G067000 chr6A 80.612 98 16 3 6 102 21888732 21888637 4.320000e-09 73.1
8 TraesCS4A01G067000 chr5A 89.720 107 10 1 1 106 46666420 46666526 5.430000e-28 135.0
9 TraesCS4A01G067000 chr5A 89.524 105 11 0 1 105 699752806 699752702 1.950000e-27 134.0
10 TraesCS4A01G067000 chr5A 89.796 98 10 0 5 102 15725598 15725501 3.270000e-25 126.0
11 TraesCS4A01G067000 chr1A 89.216 102 11 0 1 102 6577310 6577209 9.090000e-26 128.0
12 TraesCS4A01G067000 chr7B 84.466 103 14 2 1 102 11231608 11231507 1.980000e-17 100.0
13 TraesCS4A01G067000 chr3D 82.955 88 11 4 2726 2811 517809464 517809549 3.340000e-10 76.8


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 TraesCS4A01G067000 chr4A 64567443 64570565 3122 False 5768 5768 100.0000 1 3123 1 chr4A.!!$F1 3122
1 TraesCS4A01G067000 chr4B 506322665 506325677 3012 False 4505 4505 93.7190 106 3123 1 chr4B.!!$F1 3017
2 TraesCS4A01G067000 chr4D 409477954 409481010 3056 True 2072 3685 89.4295 103 3123 2 chr4D.!!$R1 3020

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
72 73 0.034089 AACTAATGGGCTGGCCAGAC 60.034 55.0 37.21 34.76 37.98 3.51 F
940 1017 0.036732 AGCAACCGAATTCTGCAGGA 59.963 50.0 15.13 5.14 38.58 3.86 F
1296 1396 0.534203 TCACCGACAAGAAACCCAGC 60.534 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1845 0.798009 GCAATGCACGTGTACATGGC 60.798 55.000 18.38 17.29 36.14 4.40 R
1774 1882 1.677637 AAGCAGACTACTAGGCGGGC 61.678 60.000 0.00 0.00 0.00 6.13 R
2151 2259 3.738830 ACTACAGTACAAAAGTCGCCA 57.261 42.857 0.00 0.00 0.00 5.69 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
30 31 2.497107 GGGACGAATGCATTCATTGG 57.503 50.000 32.72 21.19 42.60 3.16
34 35 1.750778 ACGAATGCATTCATTGGTCCC 59.249 47.619 32.72 9.19 44.71 4.46
35 36 1.268692 CGAATGCATTCATTGGTCCCG 60.269 52.381 32.72 16.46 42.60 5.14
36 37 2.023673 GAATGCATTCATTGGTCCCGA 58.976 47.619 30.15 0.00 42.60 5.14
37 38 2.369983 ATGCATTCATTGGTCCCGAT 57.630 45.000 0.00 0.00 0.00 4.18
38 39 2.142356 TGCATTCATTGGTCCCGATT 57.858 45.000 0.00 0.00 0.00 3.34
39 40 2.023673 TGCATTCATTGGTCCCGATTC 58.976 47.619 0.00 0.00 0.00 2.52
40 41 1.002468 GCATTCATTGGTCCCGATTCG 60.002 52.381 0.00 0.00 0.00 3.34
41 42 2.288666 CATTCATTGGTCCCGATTCGT 58.711 47.619 5.20 0.00 0.00 3.85
42 43 1.732941 TTCATTGGTCCCGATTCGTG 58.267 50.000 5.20 0.00 0.00 4.35
43 44 0.899019 TCATTGGTCCCGATTCGTGA 59.101 50.000 5.20 0.00 0.00 4.35
44 45 1.276705 TCATTGGTCCCGATTCGTGAA 59.723 47.619 5.20 0.00 0.00 3.18
45 46 2.080693 CATTGGTCCCGATTCGTGAAA 58.919 47.619 5.20 0.00 0.00 2.69
46 47 1.803334 TTGGTCCCGATTCGTGAAAG 58.197 50.000 5.20 0.00 0.00 2.62
47 48 0.036765 TGGTCCCGATTCGTGAAAGG 60.037 55.000 5.20 0.00 0.00 3.11
48 49 0.248289 GGTCCCGATTCGTGAAAGGA 59.752 55.000 5.20 1.18 0.00 3.36
49 50 1.356938 GTCCCGATTCGTGAAAGGAC 58.643 55.000 13.28 13.28 34.32 3.85
50 51 0.248289 TCCCGATTCGTGAAAGGACC 59.752 55.000 5.20 0.00 0.00 4.46
51 52 1.082117 CCCGATTCGTGAAAGGACCG 61.082 60.000 5.20 0.00 0.00 4.79
52 53 1.082117 CCGATTCGTGAAAGGACCGG 61.082 60.000 0.00 0.00 0.00 5.28
53 54 0.108992 CGATTCGTGAAAGGACCGGA 60.109 55.000 9.46 0.00 0.00 5.14
54 55 1.670674 CGATTCGTGAAAGGACCGGAA 60.671 52.381 9.46 0.00 0.00 4.30
55 56 1.730612 GATTCGTGAAAGGACCGGAAC 59.269 52.381 9.46 0.00 0.00 3.62
56 57 0.754472 TTCGTGAAAGGACCGGAACT 59.246 50.000 9.46 1.76 0.00 3.01
57 58 1.619654 TCGTGAAAGGACCGGAACTA 58.380 50.000 9.46 0.00 0.00 2.24
58 59 1.962807 TCGTGAAAGGACCGGAACTAA 59.037 47.619 9.46 0.00 0.00 2.24
59 60 2.564062 TCGTGAAAGGACCGGAACTAAT 59.436 45.455 9.46 0.00 0.00 1.73
60 61 2.671396 CGTGAAAGGACCGGAACTAATG 59.329 50.000 9.46 0.00 0.00 1.90
61 62 3.007635 GTGAAAGGACCGGAACTAATGG 58.992 50.000 9.46 0.00 0.00 3.16
62 63 2.026636 TGAAAGGACCGGAACTAATGGG 60.027 50.000 9.46 0.00 0.00 4.00
63 64 0.255033 AAGGACCGGAACTAATGGGC 59.745 55.000 9.46 0.00 0.00 5.36
64 65 0.620700 AGGACCGGAACTAATGGGCT 60.621 55.000 9.46 0.00 0.00 5.19
65 66 0.463833 GGACCGGAACTAATGGGCTG 60.464 60.000 9.46 0.00 0.00 4.85
66 67 0.463833 GACCGGAACTAATGGGCTGG 60.464 60.000 9.46 0.00 0.00 4.85
67 68 1.823899 CCGGAACTAATGGGCTGGC 60.824 63.158 0.00 0.00 0.00 4.85
68 69 1.823899 CGGAACTAATGGGCTGGCC 60.824 63.158 14.23 14.23 0.00 5.36
69 70 1.306296 GGAACTAATGGGCTGGCCA 59.694 57.895 26.08 26.08 37.98 5.36
70 71 0.753111 GGAACTAATGGGCTGGCCAG 60.753 60.000 29.34 29.34 37.98 4.85
71 72 0.255890 GAACTAATGGGCTGGCCAGA 59.744 55.000 37.21 16.68 37.98 3.86
72 73 0.034089 AACTAATGGGCTGGCCAGAC 60.034 55.000 37.21 34.76 37.98 3.51
79 80 4.329545 GCTGGCCAGACCCGAACA 62.330 66.667 37.21 0.00 37.83 3.18
80 81 2.429930 CTGGCCAGACCCGAACAA 59.570 61.111 29.88 0.00 37.83 2.83
81 82 1.228124 CTGGCCAGACCCGAACAAA 60.228 57.895 29.88 0.00 37.83 2.83
82 83 0.821711 CTGGCCAGACCCGAACAAAA 60.822 55.000 29.88 0.00 37.83 2.44
83 84 0.178975 TGGCCAGACCCGAACAAAAT 60.179 50.000 0.00 0.00 37.83 1.82
84 85 0.526211 GGCCAGACCCGAACAAAATC 59.474 55.000 0.00 0.00 0.00 2.17
85 86 0.526211 GCCAGACCCGAACAAAATCC 59.474 55.000 0.00 0.00 0.00 3.01
86 87 1.173913 CCAGACCCGAACAAAATCCC 58.826 55.000 0.00 0.00 0.00 3.85
87 88 1.173913 CAGACCCGAACAAAATCCCC 58.826 55.000 0.00 0.00 0.00 4.81
88 89 1.073098 AGACCCGAACAAAATCCCCT 58.927 50.000 0.00 0.00 0.00 4.79
89 90 1.427753 AGACCCGAACAAAATCCCCTT 59.572 47.619 0.00 0.00 0.00 3.95
90 91 2.158370 AGACCCGAACAAAATCCCCTTT 60.158 45.455 0.00 0.00 0.00 3.11
91 92 2.631062 GACCCGAACAAAATCCCCTTTT 59.369 45.455 0.00 0.00 37.54 2.27
92 93 3.042682 ACCCGAACAAAATCCCCTTTTT 58.957 40.909 0.00 0.00 34.80 1.94
93 94 3.070446 ACCCGAACAAAATCCCCTTTTTC 59.930 43.478 0.00 0.00 34.80 2.29
94 95 3.323691 CCCGAACAAAATCCCCTTTTTCT 59.676 43.478 0.00 0.00 34.80 2.52
95 96 4.525100 CCCGAACAAAATCCCCTTTTTCTA 59.475 41.667 0.00 0.00 34.80 2.10
96 97 5.466819 CCGAACAAAATCCCCTTTTTCTAC 58.533 41.667 0.00 0.00 34.80 2.59
97 98 5.243060 CCGAACAAAATCCCCTTTTTCTACT 59.757 40.000 0.00 0.00 34.80 2.57
98 99 6.431852 CCGAACAAAATCCCCTTTTTCTACTA 59.568 38.462 0.00 0.00 34.80 1.82
99 100 7.361799 CCGAACAAAATCCCCTTTTTCTACTAG 60.362 40.741 0.00 0.00 34.80 2.57
100 101 7.174426 CGAACAAAATCCCCTTTTTCTACTAGT 59.826 37.037 0.00 0.00 34.80 2.57
101 102 7.761038 ACAAAATCCCCTTTTTCTACTAGTG 57.239 36.000 5.39 0.00 34.80 2.74
102 103 6.719829 ACAAAATCCCCTTTTTCTACTAGTGG 59.280 38.462 5.39 1.87 34.80 4.00
103 104 5.452341 AATCCCCTTTTTCTACTAGTGGG 57.548 43.478 5.39 5.39 0.00 4.61
104 105 4.150516 TCCCCTTTTTCTACTAGTGGGA 57.849 45.455 12.64 10.74 38.46 4.37
131 132 7.040409 GGTTCATTTTCAGTACTTCACCATTCT 60.040 37.037 0.00 0.00 0.00 2.40
160 161 2.408050 CGCATGAGTATTGAGTAGCCC 58.592 52.381 0.00 0.00 0.00 5.19
486 498 6.017275 GCCATCGCTTTCTTCTACTAGTACTA 60.017 42.308 1.89 1.89 0.00 1.82
497 509 7.982919 TCTTCTACTAGTACTAGCTCTGTGAAG 59.017 40.741 26.54 24.44 36.66 3.02
498 510 7.185318 TCTACTAGTACTAGCTCTGTGAAGT 57.815 40.000 26.54 10.70 36.66 3.01
499 511 7.042950 TCTACTAGTACTAGCTCTGTGAAGTG 58.957 42.308 26.54 3.00 36.66 3.16
500 512 5.562635 ACTAGTACTAGCTCTGTGAAGTGT 58.437 41.667 26.54 3.61 36.66 3.55
501 513 4.775058 AGTACTAGCTCTGTGAAGTGTG 57.225 45.455 0.00 0.00 0.00 3.82
502 514 4.399219 AGTACTAGCTCTGTGAAGTGTGA 58.601 43.478 0.00 0.00 0.00 3.58
503 515 4.827835 AGTACTAGCTCTGTGAAGTGTGAA 59.172 41.667 0.00 0.00 0.00 3.18
568 639 0.329261 ACTAGCTTGGCTGCCATTGA 59.671 50.000 24.03 6.80 40.10 2.57
624 701 0.179108 GGCTCGTGTACTCATCACCC 60.179 60.000 0.00 0.00 32.86 4.61
628 705 0.460284 CGTGTACTCATCACCCTGGC 60.460 60.000 0.00 0.00 32.86 4.85
684 761 2.893637 AGCTACGAAGTGCTAACCATG 58.106 47.619 0.00 0.00 45.73 3.66
698 775 4.496341 GCTAACCATGATGGACATTTGTCG 60.496 45.833 20.11 0.00 45.65 4.35
763 840 5.515626 GCCAGTTTGTAATCTCGTACTGTAG 59.484 44.000 0.00 0.00 33.04 2.74
764 841 6.618811 CCAGTTTGTAATCTCGTACTGTAGT 58.381 40.000 0.00 0.00 33.04 2.73
765 842 7.627088 GCCAGTTTGTAATCTCGTACTGTAGTA 60.627 40.741 0.00 0.00 33.04 1.82
779 856 6.315891 CGTACTGTAGTACTAGCCTTTCTTCT 59.684 42.308 17.33 0.00 46.43 2.85
926 1003 2.675056 CGACAGGCAGCAGAGCAAC 61.675 63.158 0.00 0.00 35.83 4.17
933 1010 0.179179 GCAGCAGAGCAACCGAATTC 60.179 55.000 0.00 0.00 0.00 2.17
937 1014 1.159285 CAGAGCAACCGAATTCTGCA 58.841 50.000 17.45 0.00 38.58 4.41
938 1015 1.129998 CAGAGCAACCGAATTCTGCAG 59.870 52.381 17.45 7.63 38.58 4.41
940 1017 0.036732 AGCAACCGAATTCTGCAGGA 59.963 50.000 15.13 5.14 38.58 3.86
945 1022 4.380444 GCAACCGAATTCTGCAGGATTAAA 60.380 41.667 20.48 3.55 36.09 1.52
946 1023 5.708948 CAACCGAATTCTGCAGGATTAAAA 58.291 37.500 20.48 2.76 0.00 1.52
947 1024 6.332630 CAACCGAATTCTGCAGGATTAAAAT 58.667 36.000 20.48 5.23 0.00 1.82
948 1025 6.530019 ACCGAATTCTGCAGGATTAAAATT 57.470 33.333 20.48 13.63 0.00 1.82
949 1026 6.332630 ACCGAATTCTGCAGGATTAAAATTG 58.667 36.000 20.48 7.89 0.00 2.32
951 1028 6.813152 CCGAATTCTGCAGGATTAAAATTGTT 59.187 34.615 20.48 0.00 0.00 2.83
953 1030 7.009540 CGAATTCTGCAGGATTAAAATTGTTCC 59.990 37.037 20.48 3.19 0.00 3.62
954 1031 6.916360 TTCTGCAGGATTAAAATTGTTCCT 57.084 33.333 15.13 0.00 39.18 3.36
957 1034 6.603201 TCTGCAGGATTAAAATTGTTCCTAGG 59.397 38.462 15.13 0.82 36.45 3.02
958 1035 6.252995 TGCAGGATTAAAATTGTTCCTAGGT 58.747 36.000 9.08 0.00 36.45 3.08
959 1036 6.152661 TGCAGGATTAAAATTGTTCCTAGGTG 59.847 38.462 9.08 0.00 36.45 4.00
961 1038 7.093945 GCAGGATTAAAATTGTTCCTAGGTGAA 60.094 37.037 9.08 0.46 36.45 3.18
962 1039 8.244113 CAGGATTAAAATTGTTCCTAGGTGAAC 58.756 37.037 9.08 7.54 43.90 3.18
963 1040 8.170730 AGGATTAAAATTGTTCCTAGGTGAACT 58.829 33.333 9.08 0.00 43.96 3.01
973 1067 5.019657 TCCTAGGTGAACTAAAAGGAGGA 57.980 43.478 9.08 0.00 0.00 3.71
991 1091 1.335182 GGAAGCTGTGATCGATCGAGA 59.665 52.381 23.84 9.72 0.00 4.04
1149 1249 3.528370 ATCCTCTCGCCGTTCCCG 61.528 66.667 0.00 0.00 0.00 5.14
1254 1354 1.227946 GTCCCGCTACTCCTCCTCT 59.772 63.158 0.00 0.00 0.00 3.69
1290 1390 2.037251 CTCCTTCCTCACCGACAAGAAA 59.963 50.000 0.00 0.00 0.00 2.52
1295 1395 1.512926 CTCACCGACAAGAAACCCAG 58.487 55.000 0.00 0.00 0.00 4.45
1296 1396 0.534203 TCACCGACAAGAAACCCAGC 60.534 55.000 0.00 0.00 0.00 4.85
1297 1397 1.597027 ACCGACAAGAAACCCAGCG 60.597 57.895 0.00 0.00 0.00 5.18
1509 1612 1.083209 CGTCTTCGTCGTCGTCACA 60.083 57.895 1.33 0.00 38.33 3.58
1511 1614 1.043224 GTCTTCGTCGTCGTCACAAG 58.957 55.000 1.33 0.00 38.33 3.16
1717 1820 2.328099 GGCCACTTCACCTTCGCAG 61.328 63.158 0.00 0.00 0.00 5.18
1742 1845 1.131771 CAGCAGGTACGCATACATCG 58.868 55.000 0.00 0.00 32.40 3.84
2063 2171 2.275748 TCAGGAGGAGATCGCCGT 59.724 61.111 10.07 0.00 40.51 5.68
2133 2241 7.595130 CGCAGCAACTCTATAAATCATACTACA 59.405 37.037 0.00 0.00 0.00 2.74
2154 2262 6.743575 ACATGTACTACTCATCTTTTTGGC 57.256 37.500 0.00 0.00 0.00 4.52
2155 2263 5.351465 ACATGTACTACTCATCTTTTTGGCG 59.649 40.000 0.00 0.00 0.00 5.69
2156 2264 5.142061 TGTACTACTCATCTTTTTGGCGA 57.858 39.130 0.00 0.00 0.00 5.54
2157 2265 4.927425 TGTACTACTCATCTTTTTGGCGAC 59.073 41.667 0.00 0.00 0.00 5.19
2158 2266 4.273148 ACTACTCATCTTTTTGGCGACT 57.727 40.909 0.00 0.00 0.00 4.18
2261 2377 5.632959 CAGTTCAGTTTTTACGTGTGGAAA 58.367 37.500 0.00 0.00 0.00 3.13
2266 2382 4.973663 CAGTTTTTACGTGTGGAAATGGAC 59.026 41.667 0.00 0.00 0.00 4.02
2323 2439 8.840833 TTGTGCAAATTGTCTACTGAGTAATA 57.159 30.769 0.00 0.00 0.00 0.98
2324 2440 8.251750 TGTGCAAATTGTCTACTGAGTAATAC 57.748 34.615 0.00 0.00 0.00 1.89
2325 2441 7.875554 TGTGCAAATTGTCTACTGAGTAATACA 59.124 33.333 3.99 3.99 0.00 2.29
2326 2442 8.383619 GTGCAAATTGTCTACTGAGTAATACAG 58.616 37.037 7.31 0.00 40.68 2.74
2407 2524 3.004944 TCCCATGGACAAAAGCGTTTAAC 59.995 43.478 15.22 0.00 0.00 2.01
2440 2557 0.108615 CCGAAGTGCCAGAGTAGGTG 60.109 60.000 0.00 0.00 0.00 4.00
2450 2567 1.741770 GAGTAGGTGGTTGGCGCTG 60.742 63.158 7.64 0.00 0.00 5.18
2871 2988 3.640000 CGATGTTCCGGGCGATGC 61.640 66.667 0.00 0.00 0.00 3.91
2873 2990 2.203070 ATGTTCCGGGCGATGCTC 60.203 61.111 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.076533 CATTCGTCCCGGTTCGTGAG 61.077 60.000 13.60 3.53 0.00 3.51
2 3 1.080366 CATTCGTCCCGGTTCGTGA 60.080 57.895 13.60 6.24 0.00 4.35
3 4 2.736682 GCATTCGTCCCGGTTCGTG 61.737 63.158 13.60 8.10 0.00 4.35
4 5 2.433664 GCATTCGTCCCGGTTCGT 60.434 61.111 13.60 0.00 0.00 3.85
5 6 1.366111 AATGCATTCGTCCCGGTTCG 61.366 55.000 5.99 4.79 0.00 3.95
6 7 0.377203 GAATGCATTCGTCCCGGTTC 59.623 55.000 22.90 0.00 0.00 3.62
7 8 0.322098 TGAATGCATTCGTCCCGGTT 60.322 50.000 29.23 0.00 39.62 4.44
8 9 0.107214 ATGAATGCATTCGTCCCGGT 60.107 50.000 29.23 10.23 39.62 5.28
9 10 1.024271 AATGAATGCATTCGTCCCGG 58.976 50.000 29.50 0.00 40.65 5.73
10 11 1.268692 CCAATGAATGCATTCGTCCCG 60.269 52.381 29.50 21.02 42.66 5.14
11 12 1.750778 ACCAATGAATGCATTCGTCCC 59.249 47.619 29.50 10.87 42.66 4.46
12 13 3.070429 GACCAATGAATGCATTCGTCC 57.930 47.619 29.50 17.09 42.90 4.79
13 14 2.223572 GGGACCAATGAATGCATTCGTC 60.224 50.000 29.50 27.01 45.84 4.20
14 15 1.750778 GGGACCAATGAATGCATTCGT 59.249 47.619 29.23 27.32 42.66 3.85
15 16 1.268692 CGGGACCAATGAATGCATTCG 60.269 52.381 29.23 19.31 42.66 3.34
16 17 2.023673 TCGGGACCAATGAATGCATTC 58.976 47.619 28.83 28.83 42.66 2.67
17 18 2.142356 TCGGGACCAATGAATGCATT 57.858 45.000 12.83 12.83 45.33 3.56
18 19 2.369983 ATCGGGACCAATGAATGCAT 57.630 45.000 0.00 0.00 35.92 3.96
19 20 2.023673 GAATCGGGACCAATGAATGCA 58.976 47.619 0.00 0.00 0.00 3.96
20 21 1.002468 CGAATCGGGACCAATGAATGC 60.002 52.381 0.00 0.00 0.00 3.56
21 22 2.032054 CACGAATCGGGACCAATGAATG 59.968 50.000 7.80 0.00 28.17 2.67
22 23 2.093181 TCACGAATCGGGACCAATGAAT 60.093 45.455 2.35 0.00 32.99 2.57
23 24 1.276705 TCACGAATCGGGACCAATGAA 59.723 47.619 2.35 0.00 32.99 2.57
24 25 0.899019 TCACGAATCGGGACCAATGA 59.101 50.000 2.35 0.00 32.99 2.57
25 26 1.732941 TTCACGAATCGGGACCAATG 58.267 50.000 7.27 0.00 39.70 2.82
26 27 2.356135 CTTTCACGAATCGGGACCAAT 58.644 47.619 7.27 0.00 39.70 3.16
27 28 1.609580 CCTTTCACGAATCGGGACCAA 60.610 52.381 7.27 0.00 39.70 3.67
28 29 0.036765 CCTTTCACGAATCGGGACCA 60.037 55.000 7.27 0.00 39.70 4.02
29 30 0.248289 TCCTTTCACGAATCGGGACC 59.752 55.000 7.27 0.00 39.70 4.46
30 31 1.356938 GTCCTTTCACGAATCGGGAC 58.643 55.000 7.27 9.69 39.70 4.46
31 32 0.248289 GGTCCTTTCACGAATCGGGA 59.752 55.000 2.35 2.35 37.57 5.14
32 33 1.082117 CGGTCCTTTCACGAATCGGG 61.082 60.000 7.80 1.97 0.00 5.14
33 34 1.082117 CCGGTCCTTTCACGAATCGG 61.082 60.000 7.80 0.00 0.00 4.18
34 35 0.108992 TCCGGTCCTTTCACGAATCG 60.109 55.000 0.00 0.00 0.00 3.34
35 36 1.730612 GTTCCGGTCCTTTCACGAATC 59.269 52.381 0.00 0.00 0.00 2.52
36 37 1.346722 AGTTCCGGTCCTTTCACGAAT 59.653 47.619 0.00 0.00 0.00 3.34
37 38 0.754472 AGTTCCGGTCCTTTCACGAA 59.246 50.000 0.00 0.00 0.00 3.85
38 39 1.619654 TAGTTCCGGTCCTTTCACGA 58.380 50.000 0.00 0.00 0.00 4.35
39 40 2.443887 TTAGTTCCGGTCCTTTCACG 57.556 50.000 0.00 0.00 0.00 4.35
40 41 3.007635 CCATTAGTTCCGGTCCTTTCAC 58.992 50.000 0.00 0.00 0.00 3.18
41 42 2.026636 CCCATTAGTTCCGGTCCTTTCA 60.027 50.000 0.00 0.00 0.00 2.69
42 43 2.640184 CCCATTAGTTCCGGTCCTTTC 58.360 52.381 0.00 0.00 0.00 2.62
43 44 1.340697 GCCCATTAGTTCCGGTCCTTT 60.341 52.381 0.00 0.00 0.00 3.11
44 45 0.255033 GCCCATTAGTTCCGGTCCTT 59.745 55.000 0.00 0.00 0.00 3.36
45 46 0.620700 AGCCCATTAGTTCCGGTCCT 60.621 55.000 0.00 0.45 0.00 3.85
46 47 0.463833 CAGCCCATTAGTTCCGGTCC 60.464 60.000 0.00 0.00 0.00 4.46
47 48 0.463833 CCAGCCCATTAGTTCCGGTC 60.464 60.000 0.00 0.00 0.00 4.79
48 49 1.607612 CCAGCCCATTAGTTCCGGT 59.392 57.895 0.00 0.00 0.00 5.28
49 50 1.823899 GCCAGCCCATTAGTTCCGG 60.824 63.158 0.00 0.00 0.00 5.14
50 51 1.823899 GGCCAGCCCATTAGTTCCG 60.824 63.158 0.00 0.00 0.00 4.30
51 52 0.753111 CTGGCCAGCCCATTAGTTCC 60.753 60.000 22.33 0.00 44.33 3.62
52 53 0.255890 TCTGGCCAGCCCATTAGTTC 59.744 55.000 28.91 0.00 44.33 3.01
53 54 0.034089 GTCTGGCCAGCCCATTAGTT 60.034 55.000 28.91 0.00 44.33 2.24
54 55 1.609783 GTCTGGCCAGCCCATTAGT 59.390 57.895 28.91 0.00 44.33 2.24
55 56 1.152881 GGTCTGGCCAGCCCATTAG 60.153 63.158 27.97 2.58 44.33 1.73
56 57 2.689691 GGGTCTGGCCAGCCCATTA 61.690 63.158 39.21 19.80 44.33 1.90
57 58 4.066139 GGGTCTGGCCAGCCCATT 62.066 66.667 39.21 0.00 44.33 3.16
62 63 3.842925 TTGTTCGGGTCTGGCCAGC 62.843 63.158 28.91 21.69 39.65 4.85
63 64 0.821711 TTTTGTTCGGGTCTGGCCAG 60.822 55.000 27.87 27.87 39.65 4.85
64 65 0.178975 ATTTTGTTCGGGTCTGGCCA 60.179 50.000 4.71 4.71 39.65 5.36
65 66 0.526211 GATTTTGTTCGGGTCTGGCC 59.474 55.000 0.00 0.00 0.00 5.36
66 67 0.526211 GGATTTTGTTCGGGTCTGGC 59.474 55.000 0.00 0.00 0.00 4.85
67 68 1.173913 GGGATTTTGTTCGGGTCTGG 58.826 55.000 0.00 0.00 0.00 3.86
68 69 1.173913 GGGGATTTTGTTCGGGTCTG 58.826 55.000 0.00 0.00 0.00 3.51
69 70 1.073098 AGGGGATTTTGTTCGGGTCT 58.927 50.000 0.00 0.00 0.00 3.85
70 71 1.919240 AAGGGGATTTTGTTCGGGTC 58.081 50.000 0.00 0.00 0.00 4.46
71 72 2.391926 AAAGGGGATTTTGTTCGGGT 57.608 45.000 0.00 0.00 0.00 5.28
72 73 3.323691 AGAAAAAGGGGATTTTGTTCGGG 59.676 43.478 0.00 0.00 40.27 5.14
73 74 4.600692 AGAAAAAGGGGATTTTGTTCGG 57.399 40.909 0.00 0.00 40.27 4.30
74 75 6.327279 AGTAGAAAAAGGGGATTTTGTTCG 57.673 37.500 0.00 0.00 40.27 3.95
75 76 8.297426 CACTAGTAGAAAAAGGGGATTTTGTTC 58.703 37.037 3.59 0.00 40.27 3.18
76 77 7.232737 CCACTAGTAGAAAAAGGGGATTTTGTT 59.767 37.037 3.59 0.00 40.27 2.83
77 78 6.719829 CCACTAGTAGAAAAAGGGGATTTTGT 59.280 38.462 3.59 0.00 40.27 2.83
78 79 6.152831 CCCACTAGTAGAAAAAGGGGATTTTG 59.847 42.308 3.59 0.00 40.27 2.44
79 80 6.046286 TCCCACTAGTAGAAAAAGGGGATTTT 59.954 38.462 8.84 0.00 43.04 1.82
80 81 5.554350 TCCCACTAGTAGAAAAAGGGGATTT 59.446 40.000 8.84 0.00 38.38 2.17
81 82 5.105853 TCCCACTAGTAGAAAAAGGGGATT 58.894 41.667 8.84 0.00 38.38 3.01
82 83 4.706616 TCCCACTAGTAGAAAAAGGGGAT 58.293 43.478 8.84 0.00 38.38 3.85
83 84 4.101856 CTCCCACTAGTAGAAAAAGGGGA 58.898 47.826 11.67 11.67 40.90 4.81
84 85 3.200165 CCTCCCACTAGTAGAAAAAGGGG 59.800 52.174 11.26 8.06 35.52 4.79
85 86 3.844804 ACCTCCCACTAGTAGAAAAAGGG 59.155 47.826 3.59 5.95 36.15 3.95
86 87 5.012768 TGAACCTCCCACTAGTAGAAAAAGG 59.987 44.000 3.59 7.83 0.00 3.11
87 88 6.110411 TGAACCTCCCACTAGTAGAAAAAG 57.890 41.667 3.59 0.00 0.00 2.27
88 89 6.697641 ATGAACCTCCCACTAGTAGAAAAA 57.302 37.500 3.59 0.00 0.00 1.94
89 90 6.697641 AATGAACCTCCCACTAGTAGAAAA 57.302 37.500 3.59 0.00 0.00 2.29
90 91 6.697641 AAATGAACCTCCCACTAGTAGAAA 57.302 37.500 3.59 0.00 0.00 2.52
91 92 6.271391 TGAAAATGAACCTCCCACTAGTAGAA 59.729 38.462 3.59 0.00 0.00 2.10
92 93 5.783360 TGAAAATGAACCTCCCACTAGTAGA 59.217 40.000 3.59 0.00 0.00 2.59
93 94 6.049955 TGAAAATGAACCTCCCACTAGTAG 57.950 41.667 0.00 0.00 0.00 2.57
94 95 5.546499 ACTGAAAATGAACCTCCCACTAGTA 59.454 40.000 0.00 0.00 0.00 1.82
95 96 4.351111 ACTGAAAATGAACCTCCCACTAGT 59.649 41.667 0.00 0.00 0.00 2.57
96 97 4.911390 ACTGAAAATGAACCTCCCACTAG 58.089 43.478 0.00 0.00 0.00 2.57
97 98 4.993705 ACTGAAAATGAACCTCCCACTA 57.006 40.909 0.00 0.00 0.00 2.74
98 99 3.884037 ACTGAAAATGAACCTCCCACT 57.116 42.857 0.00 0.00 0.00 4.00
99 100 4.652822 AGTACTGAAAATGAACCTCCCAC 58.347 43.478 0.00 0.00 0.00 4.61
100 101 4.993705 AGTACTGAAAATGAACCTCCCA 57.006 40.909 0.00 0.00 0.00 4.37
101 102 5.181433 GTGAAGTACTGAAAATGAACCTCCC 59.819 44.000 0.00 0.00 0.00 4.30
102 103 5.181433 GGTGAAGTACTGAAAATGAACCTCC 59.819 44.000 0.00 0.00 0.00 4.30
103 104 5.763204 TGGTGAAGTACTGAAAATGAACCTC 59.237 40.000 0.00 0.00 0.00 3.85
104 105 5.690865 TGGTGAAGTACTGAAAATGAACCT 58.309 37.500 0.00 0.00 0.00 3.50
262 266 7.043192 GCACATGGCAATTATCAAATACAAGAC 60.043 37.037 0.00 0.00 43.97 3.01
333 337 1.860641 AGGGTGATGGTACGATGACA 58.139 50.000 9.45 0.00 0.00 3.58
337 341 3.308035 TCACTAGGGTGATGGTACGAT 57.692 47.619 0.00 0.00 46.19 3.73
378 382 3.999663 CAGAAGCCAAAAGGTACTCTGAG 59.000 47.826 2.45 2.45 38.49 3.35
468 472 8.609176 CACAGAGCTAGTACTAGTAGAAGAAAG 58.391 40.741 26.76 12.30 35.65 2.62
486 498 3.827008 TTCTTCACACTTCACAGAGCT 57.173 42.857 0.00 0.00 0.00 4.09
498 510 9.162764 GCCTAAACACTCTTATATTTCTTCACA 57.837 33.333 0.00 0.00 0.00 3.58
499 511 9.384764 AGCCTAAACACTCTTATATTTCTTCAC 57.615 33.333 0.00 0.00 0.00 3.18
500 512 9.601217 GAGCCTAAACACTCTTATATTTCTTCA 57.399 33.333 0.00 0.00 0.00 3.02
501 513 9.601217 TGAGCCTAAACACTCTTATATTTCTTC 57.399 33.333 0.00 0.00 0.00 2.87
502 514 9.384764 GTGAGCCTAAACACTCTTATATTTCTT 57.615 33.333 0.00 0.00 34.65 2.52
503 515 8.763601 AGTGAGCCTAAACACTCTTATATTTCT 58.236 33.333 0.00 0.00 42.61 2.52
523 535 5.938125 TCCCACTTCAAATTAAGTAGTGAGC 59.062 40.000 14.91 0.00 37.61 4.26
568 639 7.247456 TGCATGCATGGATGGATTAATAATT 57.753 32.000 27.34 0.00 36.67 1.40
624 701 2.219325 GAGAGTGTGAGTCGGGCCAG 62.219 65.000 4.39 0.00 0.00 4.85
628 705 0.523966 GAGTGAGAGTGTGAGTCGGG 59.476 60.000 0.00 0.00 0.00 5.14
684 761 3.376859 TGGCATTACGACAAATGTCCATC 59.623 43.478 7.91 0.00 40.08 3.51
763 840 5.423704 AAAGGGAGAAGAAAGGCTAGTAC 57.576 43.478 0.00 0.00 0.00 2.73
764 841 7.750947 AATAAAGGGAGAAGAAAGGCTAGTA 57.249 36.000 0.00 0.00 0.00 1.82
765 842 6.644308 AATAAAGGGAGAAGAAAGGCTAGT 57.356 37.500 0.00 0.00 0.00 2.57
779 856 4.367166 GGGAAAATGGGGAAATAAAGGGA 58.633 43.478 0.00 0.00 0.00 4.20
856 933 0.178973 AAAAGGGGTCGAGGTTTGGG 60.179 55.000 0.00 0.00 0.00 4.12
926 1003 6.332630 ACAATTTTAATCCTGCAGAATTCGG 58.667 36.000 17.39 0.69 0.00 4.30
933 1010 6.378280 ACCTAGGAACAATTTTAATCCTGCAG 59.622 38.462 17.98 6.78 42.20 4.41
937 1014 8.349568 GTTCACCTAGGAACAATTTTAATCCT 57.650 34.615 17.98 0.00 45.07 3.24
949 1026 5.247792 TCCTCCTTTTAGTTCACCTAGGAAC 59.752 44.000 17.98 10.64 45.87 3.62
951 1028 5.019657 TCCTCCTTTTAGTTCACCTAGGA 57.980 43.478 17.98 0.00 0.00 2.94
953 1030 5.046231 AGCTTCCTCCTTTTAGTTCACCTAG 60.046 44.000 0.00 0.00 0.00 3.02
954 1031 4.844655 AGCTTCCTCCTTTTAGTTCACCTA 59.155 41.667 0.00 0.00 0.00 3.08
957 1034 4.214332 CACAGCTTCCTCCTTTTAGTTCAC 59.786 45.833 0.00 0.00 0.00 3.18
958 1035 4.102524 TCACAGCTTCCTCCTTTTAGTTCA 59.897 41.667 0.00 0.00 0.00 3.18
959 1036 4.642429 TCACAGCTTCCTCCTTTTAGTTC 58.358 43.478 0.00 0.00 0.00 3.01
961 1038 4.621747 CGATCACAGCTTCCTCCTTTTAGT 60.622 45.833 0.00 0.00 0.00 2.24
962 1039 3.868077 CGATCACAGCTTCCTCCTTTTAG 59.132 47.826 0.00 0.00 0.00 1.85
963 1040 3.513912 TCGATCACAGCTTCCTCCTTTTA 59.486 43.478 0.00 0.00 0.00 1.52
973 1067 2.792890 CGTTCTCGATCGATCACAGCTT 60.793 50.000 24.40 0.00 39.71 3.74
991 1091 1.667830 CTGGTGCCATGACGACGTT 60.668 57.895 0.13 0.00 0.00 3.99
1050 1150 3.142838 TAGTAGGCGCACGGGGAC 61.143 66.667 10.83 0.00 0.00 4.46
1254 1354 2.357034 GAGTTGTTGGAGCCGCGA 60.357 61.111 8.23 0.00 0.00 5.87
1677 1780 3.558411 GACATGTCGAGCAGCGGC 61.558 66.667 10.69 0.00 46.88 6.53
1717 1820 2.815647 GCGTACCTGCTGTGAGGC 60.816 66.667 0.00 0.00 36.46 4.70
1742 1845 0.798009 GCAATGCACGTGTACATGGC 60.798 55.000 18.38 17.29 36.14 4.40
1773 1881 3.130227 CAGACTACTAGGCGGGCC 58.870 66.667 0.18 0.18 0.00 5.80
1774 1882 1.677637 AAGCAGACTACTAGGCGGGC 61.678 60.000 0.00 0.00 0.00 6.13
1849 1957 4.849329 CTCACCGTCGTAGCGCCC 62.849 72.222 2.29 0.00 0.00 6.13
2000 2108 2.890371 GTACGTGAGCCGGACCAT 59.110 61.111 5.05 0.00 45.06 3.55
2133 2241 5.581085 GTCGCCAAAAAGATGAGTAGTACAT 59.419 40.000 2.52 0.00 0.00 2.29
2137 2245 4.273148 AGTCGCCAAAAAGATGAGTAGT 57.727 40.909 0.00 0.00 0.00 2.73
2139 2247 5.298276 ACAAAAGTCGCCAAAAAGATGAGTA 59.702 36.000 0.00 0.00 0.00 2.59
2140 2248 4.097892 ACAAAAGTCGCCAAAAAGATGAGT 59.902 37.500 0.00 0.00 0.00 3.41
2141 2249 4.610945 ACAAAAGTCGCCAAAAAGATGAG 58.389 39.130 0.00 0.00 0.00 2.90
2143 2251 5.399301 CAGTACAAAAGTCGCCAAAAAGATG 59.601 40.000 0.00 0.00 0.00 2.90
2144 2252 5.067283 ACAGTACAAAAGTCGCCAAAAAGAT 59.933 36.000 0.00 0.00 0.00 2.40
2145 2253 4.396790 ACAGTACAAAAGTCGCCAAAAAGA 59.603 37.500 0.00 0.00 0.00 2.52
2148 2256 4.877251 ACTACAGTACAAAAGTCGCCAAAA 59.123 37.500 0.00 0.00 0.00 2.44
2149 2257 4.444536 ACTACAGTACAAAAGTCGCCAAA 58.555 39.130 0.00 0.00 0.00 3.28
2150 2258 4.062677 ACTACAGTACAAAAGTCGCCAA 57.937 40.909 0.00 0.00 0.00 4.52
2151 2259 3.738830 ACTACAGTACAAAAGTCGCCA 57.261 42.857 0.00 0.00 0.00 5.69
2174 2282 7.765819 TGAGAATTCGAGATGTACATGAACAAT 59.234 33.333 14.43 3.70 32.02 2.71
2175 2283 7.096551 TGAGAATTCGAGATGTACATGAACAA 58.903 34.615 14.43 1.33 32.02 2.83
2176 2284 6.630071 TGAGAATTCGAGATGTACATGAACA 58.370 36.000 14.43 2.72 0.00 3.18
2177 2285 7.525688 TTGAGAATTCGAGATGTACATGAAC 57.474 36.000 14.43 0.00 0.00 3.18
2178 2286 7.168135 CGATTGAGAATTCGAGATGTACATGAA 59.832 37.037 14.43 11.11 0.00 2.57
2179 2287 6.638468 CGATTGAGAATTCGAGATGTACATGA 59.362 38.462 14.43 1.24 0.00 3.07
2180 2288 6.638468 TCGATTGAGAATTCGAGATGTACATG 59.362 38.462 14.43 0.00 0.00 3.21
2261 2377 9.421399 TCTATATATAATCACATCCGTGTCCAT 57.579 33.333 0.00 0.00 44.02 3.41


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

AutoCloner maintained by Alex Coulton.