Multiple sequence alignment - TraesCS5A01G262900

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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 TraesCS5A01G262900 chr5A 100.000 3152 0 0 1 3152 476022709 476025860 0.000000e+00 5821.0
1 TraesCS5A01G262900 chr5A 84.273 337 45 6 2306 2638 559739213 559738881 3.920000e-84 322.0
2 TraesCS5A01G262900 chr5B 93.977 2590 118 20 599 3152 445966619 445969206 0.000000e+00 3884.0
3 TraesCS5A01G262900 chr5B 80.952 336 50 7 2306 2633 539929215 539928886 1.450000e-63 254.0
4 TraesCS5A01G262900 chr5B 83.333 90 14 1 1211 1299 685238819 685238730 7.250000e-12 82.4
5 TraesCS5A01G262900 chr5D 94.968 1570 63 6 599 2153 374199636 374201204 0.000000e+00 2447.0
6 TraesCS5A01G262900 chr5D 89.833 836 56 10 2341 3152 374201197 374202027 0.000000e+00 1046.0
7 TraesCS5A01G262900 chr5D 90.591 457 41 1 148 602 374198479 374198935 3.480000e-169 604.0
8 TraesCS5A01G262900 chr5D 84.091 308 42 3 2337 2638 443498438 443498132 1.110000e-74 291.0
9 TraesCS5A01G262900 chr4B 82.540 315 50 3 2322 2632 663103350 663103663 4.010000e-69 272.0
10 TraesCS5A01G262900 chr4B 74.286 245 45 10 2336 2564 671704473 671704231 1.560000e-13 87.9
11 TraesCS5A01G262900 chr7A 82.121 330 43 8 2279 2594 216353706 216353379 5.180000e-68 268.0
12 TraesCS5A01G262900 chr7A 79.888 358 52 9 2304 2642 25338067 25337711 8.730000e-61 244.0
13 TraesCS5A01G262900 chr7A 87.821 156 13 2 1 150 650971947 650972102 8.980000e-41 178.0
14 TraesCS5A01G262900 chr7D 81.873 331 42 10 2277 2594 204256345 204256020 2.410000e-66 263.0
15 TraesCS5A01G262900 chr7D 87.821 156 12 4 1 150 37107807 37107961 3.230000e-40 176.0
16 TraesCS5A01G262900 chr1A 79.706 340 53 9 2307 2635 518769193 518769527 6.800000e-57 231.0
17 TraesCS5A01G262900 chrUn 89.610 154 9 3 1 148 243398039 243397887 4.150000e-44 189.0
18 TraesCS5A01G262900 chrUn 89.610 154 9 3 1 148 267337003 267337155 4.150000e-44 189.0
19 TraesCS5A01G262900 chrUn 89.610 154 9 3 1 148 349111660 349111508 4.150000e-44 189.0
20 TraesCS5A01G262900 chr3D 88.462 156 11 3 3 152 98885915 98886069 6.940000e-42 182.0
21 TraesCS5A01G262900 chr6A 88.235 153 12 5 1 147 593766319 593766471 8.980000e-41 178.0
22 TraesCS5A01G262900 chr6A 79.798 99 9 3 1160 1247 22807292 22807390 9.440000e-06 62.1
23 TraesCS5A01G262900 chr2A 87.821 156 13 3 1 150 55940764 55940919 8.980000e-41 178.0
24 TraesCS5A01G262900 chr2D 87.342 158 14 2 1 152 338671335 338671178 3.230000e-40 176.0
25 TraesCS5A01G262900 chr2B 77.982 218 34 8 2271 2476 786215499 786215714 1.190000e-24 124.0
26 TraesCS5A01G262900 chr2B 79.032 124 23 2 2306 2426 25690822 25690945 7.250000e-12 82.4
27 TraesCS5A01G262900 chr6D 86.420 81 11 0 1211 1291 24267264 24267344 4.330000e-14 89.8


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 TraesCS5A01G262900 chr5A 476022709 476025860 3151 False 5821.000000 5821 100.000000 1 3152 1 chr5A.!!$F1 3151
1 TraesCS5A01G262900 chr5B 445966619 445969206 2587 False 3884.000000 3884 93.977000 599 3152 1 chr5B.!!$F1 2553
2 TraesCS5A01G262900 chr5D 374198479 374202027 3548 False 1365.666667 2447 91.797333 148 3152 3 chr5D.!!$F1 3004

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
131 132 0.036875 AACGAAGGCCTTTCTGGAGG 59.963 55.0 21.54 5.92 39.93 4.30 F
557 560 0.099968 GTCTGCTATACGTGTCGCCA 59.900 55.0 6.36 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2471 0.173481 CGACGAGCAAGGATCCAGAA 59.827 55.0 15.82 0.0 0.00 3.02 R
2384 3118 0.108396 GGCCACCAAATTTTGCAGGT 59.892 50.0 15.24 2.9 33.91 4.00 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
19 20 4.814294 AGCGCACCGGGTTCGATC 62.814 66.667 23.05 6.08 39.00 3.69
20 21 4.814294 GCGCACCGGGTTCGATCT 62.814 66.667 23.05 0.00 39.00 2.75
21 22 2.885644 CGCACCGGGTTCGATCTG 60.886 66.667 14.10 0.00 39.00 2.90
22 23 2.511600 GCACCGGGTTCGATCTGG 60.512 66.667 6.32 11.32 39.00 3.86
23 24 2.186903 CACCGGGTTCGATCTGGG 59.813 66.667 6.32 9.47 39.00 4.45
24 25 2.284405 ACCGGGTTCGATCTGGGT 60.284 61.111 6.32 9.99 39.00 4.51
25 26 2.356780 ACCGGGTTCGATCTGGGTC 61.357 63.158 6.32 0.00 39.00 4.46
26 27 2.499685 CGGGTTCGATCTGGGTCC 59.500 66.667 0.00 0.00 39.00 4.46
27 28 2.499685 GGGTTCGATCTGGGTCCG 59.500 66.667 0.00 0.00 0.00 4.79
28 29 2.202892 GGTTCGATCTGGGTCCGC 60.203 66.667 0.00 0.00 0.00 5.54
29 30 2.202892 GTTCGATCTGGGTCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
30 31 3.833645 TTCGATCTGGGTCCGCCG 61.834 66.667 0.00 0.00 34.97 6.46
40 41 3.199891 GTCCGCCGGCGCTAAATT 61.200 61.111 42.39 0.00 38.24 1.82
41 42 2.893404 TCCGCCGGCGCTAAATTC 60.893 61.111 42.39 0.75 38.24 2.17
42 43 4.293626 CCGCCGGCGCTAAATTCG 62.294 66.667 42.39 22.74 38.24 3.34
43 44 4.293626 CGCCGGCGCTAAATTCGG 62.294 66.667 38.48 15.00 44.70 4.30
47 48 2.826738 GGCGCTAAATTCGGCCCA 60.827 61.111 7.64 0.00 45.13 5.36
48 49 2.715624 GCGCTAAATTCGGCCCAG 59.284 61.111 0.00 0.00 0.00 4.45
49 50 2.834618 GCGCTAAATTCGGCCCAGG 61.835 63.158 0.00 0.00 0.00 4.45
50 51 2.834618 CGCTAAATTCGGCCCAGGC 61.835 63.158 0.00 0.00 41.06 4.85
61 62 3.518068 CCCAGGCCGGCGAAAATC 61.518 66.667 22.54 4.96 0.00 2.17
62 63 3.876198 CCAGGCCGGCGAAAATCG 61.876 66.667 22.54 2.78 43.89 3.34
67 68 3.573491 CCGGCGAAAATCGGGCTC 61.573 66.667 9.30 0.00 42.32 4.70
68 69 3.573491 CGGCGAAAATCGGGCTCC 61.573 66.667 0.00 0.00 40.84 4.70
69 70 2.124695 GGCGAAAATCGGGCTCCT 60.125 61.111 1.64 0.00 40.84 3.69
70 71 2.472909 GGCGAAAATCGGGCTCCTG 61.473 63.158 1.64 0.00 40.84 3.86
71 72 2.472909 GCGAAAATCGGGCTCCTGG 61.473 63.158 1.64 0.00 40.84 4.45
72 73 1.819632 CGAAAATCGGGCTCCTGGG 60.820 63.158 0.00 0.00 36.00 4.45
73 74 1.453928 GAAAATCGGGCTCCTGGGG 60.454 63.158 0.00 0.00 0.00 4.96
74 75 2.911221 GAAAATCGGGCTCCTGGGGG 62.911 65.000 0.00 0.00 0.00 5.40
82 83 4.087892 CTCCTGGGGGCACGACTG 62.088 72.222 0.00 0.00 0.00 3.51
90 91 4.778143 GGCACGACTGGGCCGATT 62.778 66.667 0.00 0.00 40.93 3.34
91 92 2.746277 GCACGACTGGGCCGATTT 60.746 61.111 0.00 0.00 0.00 2.17
92 93 2.332654 GCACGACTGGGCCGATTTT 61.333 57.895 0.00 0.00 0.00 1.82
93 94 1.862602 GCACGACTGGGCCGATTTTT 61.863 55.000 0.00 0.00 0.00 1.94
129 130 2.358322 AAAACGAAGGCCTTTCTGGA 57.642 45.000 21.54 0.00 38.35 3.86
130 131 1.897560 AAACGAAGGCCTTTCTGGAG 58.102 50.000 21.54 9.62 38.35 3.86
131 132 0.036875 AACGAAGGCCTTTCTGGAGG 59.963 55.000 21.54 5.92 39.93 4.30
138 139 4.767255 CTTTCTGGAGGCGCGGCT 62.767 66.667 36.96 36.96 0.00 5.52
162 163 4.363034 GCTCTAATAGCGGTGGCC 57.637 61.111 0.00 0.00 42.53 5.36
185 186 1.153229 GTGAACCCCGCTATCCACC 60.153 63.158 0.00 0.00 0.00 4.61
193 194 1.183030 CCGCTATCCACCCCGTCATA 61.183 60.000 0.00 0.00 0.00 2.15
196 197 1.272769 GCTATCCACCCCGTCATAGAC 59.727 57.143 0.00 0.00 0.00 2.59
266 267 3.011517 AAGACAGCCCCGGAGCAT 61.012 61.111 11.77 0.00 34.23 3.79
307 308 1.079658 ACTGAGGCCCTCTTAGTCCTT 59.920 52.381 12.94 0.00 37.75 3.36
328 329 3.839432 GAACTCGAGGAGGCGGGG 61.839 72.222 18.41 0.00 35.69 5.73
347 348 5.396884 GCGGGGATTCTAGCATCCTTAATAT 60.397 44.000 19.18 0.00 42.41 1.28
435 438 9.436957 AACATCGTTTGAATAGTTCTCTATTGT 57.563 29.630 5.40 0.00 44.08 2.71
436 439 8.873830 ACATCGTTTGAATAGTTCTCTATTGTG 58.126 33.333 5.40 0.00 44.08 3.33
466 469 6.127758 TGTTTTGTCCCTTTATGGATCATTCG 60.128 38.462 0.00 0.00 36.63 3.34
499 502 3.064207 GTTCATGAGTTGTTACGCTCCA 58.936 45.455 0.00 0.00 0.00 3.86
522 525 3.198872 GGCTATGACTAGTCTTTGTGGC 58.801 50.000 23.01 17.47 0.00 5.01
529 532 4.696877 TGACTAGTCTTTGTGGCATTCATG 59.303 41.667 23.01 0.00 0.00 3.07
530 533 4.012374 ACTAGTCTTTGTGGCATTCATGG 58.988 43.478 0.00 0.00 0.00 3.66
537 540 5.246656 TCTTTGTGGCATTCATGGAAAGAAT 59.753 36.000 0.00 0.00 36.19 2.40
548 551 7.792374 TTCATGGAAAGAATGTCTGCTATAC 57.208 36.000 0.00 0.00 0.00 1.47
553 556 5.232414 GGAAAGAATGTCTGCTATACGTGTC 59.768 44.000 0.00 0.00 0.00 3.67
557 560 0.099968 GTCTGCTATACGTGTCGCCA 59.900 55.000 6.36 0.00 0.00 5.69
559 562 1.407618 TCTGCTATACGTGTCGCCAAT 59.592 47.619 6.36 0.00 0.00 3.16
561 564 3.067040 TCTGCTATACGTGTCGCCAATAA 59.933 43.478 6.36 0.00 0.00 1.40
575 578 8.583765 GTGTCGCCAATAAATTGATTAACTTTC 58.416 33.333 4.25 0.00 40.14 2.62
613 1320 6.142798 CGTGTTTTGTGATCCTTGAAGAAATG 59.857 38.462 0.00 0.00 0.00 2.32
620 1327 4.935205 TGATCCTTGAAGAAATGTACCACG 59.065 41.667 0.00 0.00 0.00 4.94
684 1391 1.089920 GCGAATGGTGAAGCTCATGT 58.910 50.000 0.00 0.00 0.00 3.21
688 1395 1.171308 ATGGTGAAGCTCATGTGTGC 58.829 50.000 0.00 0.00 35.00 4.57
718 1425 1.416401 TCTTCCTCGCTTGAGTTTGGT 59.584 47.619 0.00 0.00 38.10 3.67
829 1537 8.294577 CCCTAAAAATAACTAAGTGTGTTGGTC 58.705 37.037 0.00 0.00 0.00 4.02
850 1558 5.334337 GGTCCGGTCATTAATTATAAACGGC 60.334 44.000 0.00 8.30 38.72 5.68
856 1564 8.380644 CGGTCATTAATTATAAACGGCTATCTG 58.619 37.037 0.00 0.00 0.00 2.90
1088 1805 4.509122 GGATAACATGGGCAATATGGAGGT 60.509 45.833 0.00 0.00 0.00 3.85
1089 1806 5.280985 GGATAACATGGGCAATATGGAGGTA 60.281 44.000 0.00 0.00 0.00 3.08
1103 1820 3.170717 TGGAGGTAGAGATGGTTTTCGT 58.829 45.455 0.00 0.00 0.00 3.85
1123 1840 3.005261 CGTGAGAGATAGATGGTTCCCTG 59.995 52.174 0.00 0.00 0.00 4.45
1270 2000 7.591006 TCTACAAGAACACCATTTTACGATC 57.409 36.000 0.00 0.00 0.00 3.69
1354 2086 4.006319 GACAGCTCAAAGAAAGGCTACAT 58.994 43.478 0.00 0.00 33.43 2.29
1552 2284 6.539173 TGTAGTGACATGGTGGTTATTTTCT 58.461 36.000 0.00 0.00 0.00 2.52
1556 2288 7.913789 AGTGACATGGTGGTTATTTTCTACTA 58.086 34.615 0.00 0.00 0.00 1.82
1739 2471 3.369546 GCATTATTGCGCCAATACCTT 57.630 42.857 4.18 0.00 39.49 3.50
1791 2523 2.158986 AGAAGTGGATCAAGCTCATCCG 60.159 50.000 16.36 0.00 42.69 4.18
1812 2544 1.818642 GTGCCAGTTCTCTTCATGCT 58.181 50.000 0.00 0.00 0.00 3.79
1820 2552 1.056700 TCTCTTCATGCTAGGGGCCC 61.057 60.000 17.12 17.12 40.92 5.80
1861 2593 7.883311 AGAGCAGTTAACTACATATGTTGGTTT 59.117 33.333 22.72 12.57 0.00 3.27
1897 2629 9.443323 TTCATTTTTAACTACATCATCTTCCGA 57.557 29.630 0.00 0.00 0.00 4.55
2253 2986 3.239587 TCAAATGTTGCCATGCATCAG 57.760 42.857 0.00 0.00 40.75 2.90
2259 2992 2.826725 TGTTGCCATGCATCAGAATCAA 59.173 40.909 0.00 0.00 38.76 2.57
2318 3051 2.151202 CACACTACACCCATGACCAAC 58.849 52.381 0.00 0.00 0.00 3.77
2320 3053 2.224523 ACACTACACCCATGACCAACAG 60.225 50.000 0.00 0.00 0.00 3.16
2433 3167 2.093973 TCCGAGGAGCTCTGAATTTGTC 60.094 50.000 14.64 0.00 0.00 3.18
2454 3188 5.046663 TGTCTCCTCAAATGTATGTGCACTA 60.047 40.000 19.41 4.84 0.00 2.74
2563 3297 5.879237 TCATAATCAATGCCACGAAGTTTC 58.121 37.500 0.00 0.00 34.83 2.78
2618 3352 2.135903 ATCATGGGGTGCACCGAACA 62.136 55.000 29.08 25.73 41.60 3.18
2646 3380 1.961394 AGCCACTACGTTCTCAGTCAA 59.039 47.619 0.00 0.00 0.00 3.18
2760 3504 6.073314 TCTACCTAATACTAACCGAATGCCT 58.927 40.000 0.00 0.00 0.00 4.75
2839 3583 9.529325 AATTCAGAAATATGCATTGAACATGAG 57.471 29.630 3.54 0.00 31.34 2.90
2861 3605 6.493115 TGAGATCATGTGGTTTTTGTTATGGT 59.507 34.615 0.00 0.00 0.00 3.55
2870 3614 7.140048 GTGGTTTTTGTTATGGTAATCGTCAA 58.860 34.615 0.00 0.00 0.00 3.18
2939 3683 3.287222 CTCACTCCTACTTCCTCTCCAG 58.713 54.545 0.00 0.00 0.00 3.86
2963 3707 8.258007 CAGTCTCCACCTACATTATTTTCACTA 58.742 37.037 0.00 0.00 0.00 2.74
2987 3731 2.104111 TCTGAGCCCTCTTTTCGAAACA 59.896 45.455 10.79 1.77 0.00 2.83
2992 3736 3.636764 AGCCCTCTTTTCGAAACATTGTT 59.363 39.130 10.79 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.814294 GATCGAACCCGGTGCGCT 62.814 66.667 13.69 2.95 34.09 5.92
3 4 4.814294 AGATCGAACCCGGTGCGC 62.814 66.667 13.69 0.00 34.09 6.09
4 5 2.885644 CAGATCGAACCCGGTGCG 60.886 66.667 12.22 12.22 35.64 5.34
5 6 2.511600 CCAGATCGAACCCGGTGC 60.512 66.667 0.00 0.00 36.24 5.01
6 7 2.186903 CCCAGATCGAACCCGGTG 59.813 66.667 0.00 0.00 36.24 4.94
7 8 2.284405 ACCCAGATCGAACCCGGT 60.284 61.111 0.00 0.00 36.24 5.28
8 9 2.499685 GACCCAGATCGAACCCGG 59.500 66.667 0.00 0.00 36.24 5.73
9 10 2.499685 GGACCCAGATCGAACCCG 59.500 66.667 0.00 0.00 37.07 5.28
10 11 2.499685 CGGACCCAGATCGAACCC 59.500 66.667 0.00 0.00 0.00 4.11
11 12 2.202892 GCGGACCCAGATCGAACC 60.203 66.667 0.00 0.00 0.00 3.62
12 13 2.202892 GGCGGACCCAGATCGAAC 60.203 66.667 0.00 0.00 0.00 3.95
13 14 3.833645 CGGCGGACCCAGATCGAA 61.834 66.667 0.00 0.00 0.00 3.71
23 24 3.164390 GAATTTAGCGCCGGCGGAC 62.164 63.158 45.81 31.88 46.35 4.79
24 25 2.893404 GAATTTAGCGCCGGCGGA 60.893 61.111 45.81 14.61 46.35 5.54
25 26 4.293626 CGAATTTAGCGCCGGCGG 62.294 66.667 45.81 29.29 46.35 6.13
26 27 4.293626 CCGAATTTAGCGCCGGCG 62.294 66.667 43.13 43.13 46.35 6.46
28 29 3.949047 GGCCGAATTTAGCGCCGG 61.949 66.667 15.00 15.00 44.34 6.13
29 30 3.949047 GGGCCGAATTTAGCGCCG 61.949 66.667 2.29 0.00 36.04 6.46
30 31 2.826738 TGGGCCGAATTTAGCGCC 60.827 61.111 2.29 9.32 40.93 6.53
31 32 2.715624 CTGGGCCGAATTTAGCGC 59.284 61.111 0.00 0.00 41.90 5.92
32 33 2.834618 GCCTGGGCCGAATTTAGCG 61.835 63.158 0.00 0.00 34.56 4.26
33 34 3.120105 GCCTGGGCCGAATTTAGC 58.880 61.111 0.00 0.00 34.56 3.09
44 45 3.518068 GATTTTCGCCGGCCTGGG 61.518 66.667 23.46 6.82 38.63 4.45
45 46 3.876198 CGATTTTCGCCGGCCTGG 61.876 66.667 23.46 7.26 42.50 4.45
46 47 3.876198 CCGATTTTCGCCGGCCTG 61.876 66.667 23.46 8.15 38.82 4.85
50 51 3.573491 GAGCCCGATTTTCGCCGG 61.573 66.667 0.00 0.00 44.94 6.13
51 52 3.573491 GGAGCCCGATTTTCGCCG 61.573 66.667 0.00 0.00 38.82 6.46
52 53 2.124695 AGGAGCCCGATTTTCGCC 60.125 61.111 0.00 0.00 38.82 5.54
53 54 2.472909 CCAGGAGCCCGATTTTCGC 61.473 63.158 0.00 0.00 38.82 4.70
54 55 1.819632 CCCAGGAGCCCGATTTTCG 60.820 63.158 0.00 0.00 40.07 3.46
55 56 1.453928 CCCCAGGAGCCCGATTTTC 60.454 63.158 0.00 0.00 0.00 2.29
56 57 2.683475 CCCCAGGAGCCCGATTTT 59.317 61.111 0.00 0.00 0.00 1.82
57 58 3.420482 CCCCCAGGAGCCCGATTT 61.420 66.667 0.00 0.00 33.47 2.17
65 66 4.087892 CAGTCGTGCCCCCAGGAG 62.088 72.222 0.00 0.00 36.62 3.69
73 74 4.778143 AATCGGCCCAGTCGTGCC 62.778 66.667 0.00 0.00 44.41 5.01
74 75 1.862602 AAAAATCGGCCCAGTCGTGC 61.863 55.000 0.00 0.00 30.45 5.34
75 76 2.253513 AAAAATCGGCCCAGTCGTG 58.746 52.632 0.00 0.00 30.45 4.35
76 77 4.813346 AAAAATCGGCCCAGTCGT 57.187 50.000 0.00 0.00 30.45 4.34
109 110 2.623416 CTCCAGAAAGGCCTTCGTTTTT 59.377 45.455 20.79 0.44 39.22 1.94
110 111 2.230660 CTCCAGAAAGGCCTTCGTTTT 58.769 47.619 20.79 1.36 39.22 2.43
111 112 1.545651 CCTCCAGAAAGGCCTTCGTTT 60.546 52.381 20.79 1.84 39.22 3.60
112 113 0.036875 CCTCCAGAAAGGCCTTCGTT 59.963 55.000 20.79 2.31 39.22 3.85
113 114 1.679898 CCTCCAGAAAGGCCTTCGT 59.320 57.895 20.79 3.24 39.22 3.85
114 115 4.625800 CCTCCAGAAAGGCCTTCG 57.374 61.111 20.79 10.49 39.22 3.79
121 122 4.767255 AGCCGCGCCTCCAGAAAG 62.767 66.667 0.00 0.00 0.00 2.62
146 147 0.039074 CGAGGCCACCGCTATTAGAG 60.039 60.000 5.01 0.00 34.44 2.43
179 180 1.414158 CTGTCTATGACGGGGTGGAT 58.586 55.000 0.00 0.00 35.49 3.41
185 186 1.360551 CTCGGCTGTCTATGACGGG 59.639 63.158 8.38 0.00 39.16 5.28
238 239 2.805353 CTGTCTTCGTGCCGTCCG 60.805 66.667 0.00 0.00 0.00 4.79
284 285 2.180276 GACTAAGAGGGCCTCAGTGAA 58.820 52.381 33.86 13.65 32.06 3.18
289 290 1.078823 TCAAGGACTAAGAGGGCCTCA 59.921 52.381 33.86 14.72 32.06 3.86
307 308 2.687805 CGCCTCCTCGAGTTCGTCA 61.688 63.158 12.31 0.00 40.80 4.35
353 356 9.570488 TTGTGGTAATTTGTGTTTAACTTGTAC 57.430 29.630 0.00 0.00 0.00 2.90
391 394 1.034356 TTCGTTGGGAACTGTCGAGA 58.966 50.000 0.00 0.00 32.39 4.04
435 438 6.307776 TCCATAAAGGGACAAAACACATACA 58.692 36.000 0.00 0.00 38.24 2.29
436 439 6.827586 TCCATAAAGGGACAAAACACATAC 57.172 37.500 0.00 0.00 38.24 2.39
492 495 1.615883 CTAGTCATAGCCATGGAGCGT 59.384 52.381 18.40 0.00 38.01 5.07
499 502 4.684485 GCCACAAAGACTAGTCATAGCCAT 60.684 45.833 24.44 0.00 31.66 4.40
529 532 5.109903 ACACGTATAGCAGACATTCTTTCC 58.890 41.667 0.00 0.00 0.00 3.13
530 533 5.052304 CGACACGTATAGCAGACATTCTTTC 60.052 44.000 0.00 0.00 0.00 2.62
537 540 0.099968 GGCGACACGTATAGCAGACA 59.900 55.000 0.40 0.00 0.00 3.41
548 551 6.255215 AGTTAATCAATTTATTGGCGACACG 58.745 36.000 0.00 0.00 42.67 4.49
553 556 8.909708 TCAGAAAGTTAATCAATTTATTGGCG 57.090 30.769 2.85 0.00 38.30 5.69
575 578 4.853196 CACAAAACACGCCTAATGAATCAG 59.147 41.667 0.00 0.00 0.00 2.90
583 586 3.134574 AGGATCACAAAACACGCCTAA 57.865 42.857 0.00 0.00 0.00 2.69
613 1320 0.971386 TGAACTCCTTCCCGTGGTAC 59.029 55.000 0.00 0.00 0.00 3.34
620 1327 0.680061 ACGTCAGTGAACTCCTTCCC 59.320 55.000 0.00 0.00 0.00 3.97
684 1391 0.889186 GGAAGAAGCCTTTCCGCACA 60.889 55.000 0.00 0.00 33.64 4.57
688 1395 1.362406 GCGAGGAAGAAGCCTTTCCG 61.362 60.000 6.00 0.00 38.73 4.30
718 1425 1.809547 CAAACCACACATACATGCCGA 59.190 47.619 0.00 0.00 0.00 5.54
829 1537 5.934935 AGCCGTTTATAATTAATGACCGG 57.065 39.130 0.00 0.00 0.00 5.28
850 1558 2.611473 CGGTATGCTCCAAGGCAGATAG 60.611 54.545 0.00 0.00 45.75 2.08
856 1564 2.124736 TGCGGTATGCTCCAAGGC 60.125 61.111 0.00 0.00 46.63 4.35
1088 1805 7.054751 TCTATCTCTCACGAAAACCATCTCTA 58.945 38.462 0.00 0.00 0.00 2.43
1089 1806 5.888724 TCTATCTCTCACGAAAACCATCTCT 59.111 40.000 0.00 0.00 0.00 3.10
1158 1876 8.576442 GCATATGCCACTATTTAAAACTATGGT 58.424 33.333 17.26 0.00 34.31 3.55
1179 1897 3.583086 AGGACTACCGCTATTTGGCATAT 59.417 43.478 0.00 0.00 41.83 1.78
1195 1913 4.101119 GGCTATAGCTGTTTTGGAGGACTA 59.899 45.833 23.53 0.00 41.70 2.59
1270 2000 0.468226 TATAGCGGTTTGAGCAGGGG 59.532 55.000 0.00 0.00 37.01 4.79
1354 2086 9.890629 AGACATGCAACTTCTATTTACTCATTA 57.109 29.630 0.00 0.00 0.00 1.90
1378 2110 9.069082 GCCTTGTAGACTCAATAGTTAGATAGA 57.931 37.037 0.00 0.00 35.56 1.98
1385 2117 5.700402 ATGGCCTTGTAGACTCAATAGTT 57.300 39.130 3.32 0.00 35.56 2.24
1552 2284 4.094294 GTGCGGCACAAATCTTTGATAGTA 59.906 41.667 27.10 0.00 40.55 1.82
1556 2288 1.401409 CGTGCGGCACAAATCTTTGAT 60.401 47.619 30.23 0.00 40.55 2.57
1739 2471 0.173481 CGACGAGCAAGGATCCAGAA 59.827 55.000 15.82 0.00 0.00 3.02
1791 2523 0.445436 CATGAAGAGAACTGGCACGC 59.555 55.000 0.00 0.00 0.00 5.34
1820 2552 1.307097 GCTCTAGCTGGAGGCATTTG 58.693 55.000 26.35 2.67 44.79 2.32
1861 2593 8.239038 TGTAGTTAAAAATGAATCCCAACACA 57.761 30.769 0.00 0.00 0.00 3.72
1897 2629 1.615392 GCCCACAACTCTTTGCATCTT 59.385 47.619 0.00 0.00 36.00 2.40
2015 2748 2.349755 CGAACCCCACCCGTTGAT 59.650 61.111 0.00 0.00 0.00 2.57
2021 2754 2.168666 GAGACAGACGAACCCCACCC 62.169 65.000 0.00 0.00 0.00 4.61
2124 2857 6.123045 ACTAGTACCACAAAACTAAGCCAT 57.877 37.500 0.00 0.00 0.00 4.40
2164 2897 1.299648 TGCTCGGCTGGTAGCAAAT 59.700 52.632 6.46 0.00 45.36 2.32
2171 2904 1.904287 TAAAATGTTGCTCGGCTGGT 58.096 45.000 0.00 0.00 0.00 4.00
2205 2938 7.254852 CACAAATAACTTTGGTACAGTGTTGT 58.745 34.615 0.00 0.00 44.97 3.32
2211 2944 7.447374 TGATCCACAAATAACTTTGGTACAG 57.553 36.000 0.00 0.00 44.97 2.74
2275 3008 1.061735 TGCATCCACCCTGGGTATAGA 60.062 52.381 20.09 15.88 38.32 1.98
2384 3118 0.108396 GGCCACCAAATTTTGCAGGT 59.892 50.000 15.24 2.90 33.91 4.00
2386 3120 1.964552 TTGGCCACCAAATTTTGCAG 58.035 45.000 3.88 0.00 40.92 4.41
2433 3167 6.932356 AATAGTGCACATACATTTGAGGAG 57.068 37.500 21.04 0.00 0.00 3.69
2735 3479 6.724905 AGGCATTCGGTTAGTATTAGGTAGAT 59.275 38.462 0.00 0.00 0.00 1.98
2760 3504 3.691609 TCGTATTTATGTGGCAATGCACA 59.308 39.130 7.79 10.10 35.65 4.57
2839 3583 9.301153 GATTACCATAACAAAAACCACATGATC 57.699 33.333 0.00 0.00 0.00 2.92
2861 3605 4.811969 TGGTTAAGGAGCTTGACGATTA 57.188 40.909 0.00 0.00 31.92 1.75
2870 3614 4.589908 CAAGGTACAATGGTTAAGGAGCT 58.410 43.478 0.00 0.00 0.00 4.09
2919 3663 2.650322 ACTGGAGAGGAAGTAGGAGTGA 59.350 50.000 0.00 0.00 0.00 3.41
2939 3683 9.046296 CATAGTGAAAATAATGTAGGTGGAGAC 57.954 37.037 0.00 0.00 0.00 3.36
2963 3707 1.902508 TCGAAAAGAGGGCTCAGACAT 59.097 47.619 0.00 0.00 0.00 3.06
3057 3801 8.833231 TTACAACTCTGGAAGATTTAACTGAG 57.167 34.615 0.00 0.00 45.62 3.35


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

AutoCloner maintained by Alex Coulton.