Multiple sequence alignment - TraesCS1D01G261200

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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 TraesCS1D01G261200 chr1D 100.000 3655 0 0 1 3655 355428660 355432314 0.000000e+00 6750.0
1 TraesCS1D01G261200 chr1D 93.000 600 36 4 3061 3655 355320623 355320025 0.000000e+00 870.0
2 TraesCS1D01G261200 chr1D 86.103 662 67 14 3001 3655 355321905 355321262 0.000000e+00 689.0
3 TraesCS1D01G261200 chr1D 82.287 621 58 30 2123 2716 434034850 434034255 1.180000e-134 490.0
4 TraesCS1D01G261200 chr1D 81.094 640 71 34 1514 2121 434035753 434035132 1.990000e-127 466.0
5 TraesCS1D01G261200 chr1D 80.938 640 72 34 1514 2121 433980767 433980146 9.250000e-126 460.0
6 TraesCS1D01G261200 chr1D 84.828 435 38 17 2123 2551 433979864 433979452 2.630000e-111 412.0
7 TraesCS1D01G261200 chr1D 86.313 358 32 10 2658 3001 355322213 355321859 1.240000e-99 374.0
8 TraesCS1D01G261200 chr1D 79.947 379 41 18 1167 1516 434036154 434035782 2.820000e-61 246.0
9 TraesCS1D01G261200 chr1D 79.683 379 42 18 1167 1516 433981168 433980796 1.310000e-59 241.0
10 TraesCS1D01G261200 chr1D 76.190 189 31 11 1 185 434074675 434074497 1.810000e-13 87.9
11 TraesCS1D01G261200 chr1B 90.806 3252 160 61 498 3655 478053425 478056631 0.000000e+00 4220.0
12 TraesCS1D01G261200 chr1B 92.845 601 36 5 3061 3655 477947767 477947168 0.000000e+00 865.0
13 TraesCS1D01G261200 chr1B 85.347 662 71 14 3001 3655 477949051 477948409 0.000000e+00 662.0
14 TraesCS1D01G261200 chr1B 78.502 721 94 36 1167 1847 587040951 587040252 2.030000e-112 416.0
15 TraesCS1D01G261200 chr1B 83.568 426 51 9 2123 2541 587526929 587526516 7.410000e-102 381.0
16 TraesCS1D01G261200 chr1B 85.475 358 34 11 2658 3001 477949358 477949005 1.250000e-94 357.0
17 TraesCS1D01G261200 chr1B 85.437 309 17 12 1 309 478052342 478052622 2.760000e-76 296.0
18 TraesCS1D01G261200 chr1B 78.772 391 49 21 710 1087 587069990 587069621 7.890000e-57 231.0
19 TraesCS1D01G261200 chr1B 78.517 391 50 21 710 1087 587048113 587047744 3.670000e-55 226.0
20 TraesCS1D01G261200 chr1B 93.137 102 7 0 1868 1969 587039775 587039674 2.270000e-32 150.0
21 TraesCS1D01G261200 chr1B 74.837 306 53 15 10 307 587053012 587052723 2.310000e-22 117.0
22 TraesCS1D01G261200 chr1B 73.881 268 51 13 10 272 587075052 587074799 5.030000e-14 89.8
23 TraesCS1D01G261200 chr1A 94.115 2124 89 16 1534 3655 455605816 455607905 0.000000e+00 3197.0
24 TraesCS1D01G261200 chr1A 86.042 960 61 18 541 1436 455604855 455605805 0.000000e+00 963.0
25 TraesCS1D01G261200 chr1A 93.162 234 16 0 315 548 455604197 455604430 9.720000e-91 344.0
26 TraesCS1D01G261200 chr1A 84.337 332 22 21 1 328 455603872 455604177 7.670000e-77 298.0
27 TraesCS1D01G261200 chr1A 82.267 344 37 10 2389 2716 532264512 532264177 3.600000e-70 276.0
28 TraesCS1D01G261200 chr7A 89.583 192 20 0 3437 3628 645029917 645029726 1.010000e-60 244.0
29 TraesCS1D01G261200 chrUn 78.307 378 52 20 2245 2603 42301267 42300901 2.210000e-52 217.0
30 TraesCS1D01G261200 chrUn 78.307 378 52 18 2245 2603 319476816 319477182 2.210000e-52 217.0
31 TraesCS1D01G261200 chr7B 88.679 159 12 4 3503 3655 52983772 52983614 4.820000e-44 189.0
32 TraesCS1D01G261200 chr7B 100.000 31 0 0 417 447 3887439 3887409 1.420000e-04 58.4
33 TraesCS1D01G261200 chr4A 88.679 159 12 4 3503 3655 67514716 67514558 4.820000e-44 189.0
34 TraesCS1D01G261200 chr5A 100.000 32 0 0 417 448 203096939 203096908 3.940000e-05 60.2
35 TraesCS1D01G261200 chr3D 90.909 44 2 2 413 455 561709066 561709024 1.420000e-04 58.4
36 TraesCS1D01G261200 chr3B 100.000 31 0 0 417 447 40227138 40227108 1.420000e-04 58.4
37 TraesCS1D01G261200 chr3B 92.308 39 2 1 416 454 777570868 777570831 2.000000e-03 54.7
38 TraesCS1D01G261200 chr2D 97.059 34 0 1 315 347 9885200 9885167 5.100000e-04 56.5
39 TraesCS1D01G261200 chr5B 90.476 42 3 1 417 457 197204073 197204032 2.000000e-03 54.7
40 TraesCS1D01G261200 chr4B 96.970 33 0 1 417 449 588198602 588198633 2.000000e-03 54.7
41 TraesCS1D01G261200 chr2B 96.970 33 0 1 417 448 743344684 743344716 2.000000e-03 54.7


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 TraesCS1D01G261200 chr1D 355428660 355432314 3654 False 6750.000000 6750 100.000000 1 3655 1 chr1D.!!$F1 3654
1 TraesCS1D01G261200 chr1D 355320025 355322213 2188 True 644.333333 870 88.472000 2658 3655 3 chr1D.!!$R2 997
2 TraesCS1D01G261200 chr1D 434034255 434036154 1899 True 400.666667 490 81.109333 1167 2716 3 chr1D.!!$R4 1549
3 TraesCS1D01G261200 chr1D 433979452 433981168 1716 True 371.000000 460 81.816333 1167 2551 3 chr1D.!!$R3 1384
4 TraesCS1D01G261200 chr1B 478052342 478056631 4289 False 2258.000000 4220 88.121500 1 3655 2 chr1B.!!$F1 3654
5 TraesCS1D01G261200 chr1B 477947168 477949358 2190 True 628.000000 865 87.889000 2658 3655 3 chr1B.!!$R6 997
6 TraesCS1D01G261200 chr1B 587039674 587040951 1277 True 283.000000 416 85.819500 1167 1969 2 chr1B.!!$R7 802
7 TraesCS1D01G261200 chr1A 455603872 455607905 4033 False 1200.500000 3197 89.414000 1 3655 4 chr1A.!!$F1 3654

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
956 2105 0.320421 CCCCTTTCTGCGAAAGACGA 60.320 55.0 23.56 0.0 45.77 4.20 F
1005 2154 1.195115 GTGAGCTGGTCTGTATGGGA 58.805 55.0 8.47 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 4254 0.865111 TGCATGAACGACCAGTTTCG 59.135 50.0 0.0 0.0 44.35 3.46 R
2911 4999 1.832883 ATTCGCCTGTAAATGCACCA 58.167 45.0 0.0 0.0 0.00 4.17 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
67 68 4.318121 GCTTTTGATAGATACAAGCCGACG 60.318 45.833 0.00 0.00 0.00 5.12
80 81 2.726633 AGCCGACGTTGACAATTTTTG 58.273 42.857 3.74 0.00 0.00 2.44
84 85 4.087930 GCCGACGTTGACAATTTTTGTATG 59.912 41.667 3.74 0.00 45.52 2.39
95 96 6.677913 ACAATTTTTGTATGGAGCAGTACAC 58.322 36.000 0.00 0.00 43.27 2.90
111 112 5.651530 CAGTACACCTCATGGTAGTTGTAG 58.348 45.833 0.00 0.00 46.60 2.74
112 113 5.185249 CAGTACACCTCATGGTAGTTGTAGT 59.815 44.000 0.00 0.00 46.60 2.73
113 114 4.803098 ACACCTCATGGTAGTTGTAGTC 57.197 45.455 0.00 0.00 46.60 2.59
114 115 4.417437 ACACCTCATGGTAGTTGTAGTCT 58.583 43.478 0.00 0.00 46.60 3.24
115 116 4.838986 ACACCTCATGGTAGTTGTAGTCTT 59.161 41.667 0.00 0.00 46.60 3.01
116 117 5.171476 CACCTCATGGTAGTTGTAGTCTTG 58.829 45.833 0.00 0.00 46.60 3.02
117 118 4.838986 ACCTCATGGTAGTTGTAGTCTTGT 59.161 41.667 0.00 0.00 46.43 3.16
118 119 6.014647 ACCTCATGGTAGTTGTAGTCTTGTA 58.985 40.000 0.00 0.00 46.43 2.41
119 120 6.153000 ACCTCATGGTAGTTGTAGTCTTGTAG 59.847 42.308 0.00 0.00 46.43 2.74
160 162 2.403252 AGCCTAGCGTACAAGCAATT 57.597 45.000 0.00 0.00 40.15 2.32
161 163 3.536956 AGCCTAGCGTACAAGCAATTA 57.463 42.857 0.00 0.00 40.15 1.40
162 164 3.195661 AGCCTAGCGTACAAGCAATTAC 58.804 45.455 0.00 0.00 40.15 1.89
163 165 2.034001 GCCTAGCGTACAAGCAATTACG 60.034 50.000 6.65 6.65 43.18 3.18
164 166 3.441163 CCTAGCGTACAAGCAATTACGA 58.559 45.455 13.31 0.00 43.01 3.43
165 167 3.486108 CCTAGCGTACAAGCAATTACGAG 59.514 47.826 13.31 4.68 43.01 4.18
226 232 7.280205 ACGTAATTCTTTCTCTCTCTCTCTCTC 59.720 40.741 0.00 0.00 0.00 3.20
227 233 7.495934 CGTAATTCTTTCTCTCTCTCTCTCTCT 59.504 40.741 0.00 0.00 0.00 3.10
228 234 7.872113 AATTCTTTCTCTCTCTCTCTCTCTC 57.128 40.000 0.00 0.00 0.00 3.20
229 235 6.627087 TTCTTTCTCTCTCTCTCTCTCTCT 57.373 41.667 0.00 0.00 0.00 3.10
230 236 6.227298 TCTTTCTCTCTCTCTCTCTCTCTC 57.773 45.833 0.00 0.00 0.00 3.20
231 237 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
232 238 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
233 239 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
234 240 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
235 241 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
236 242 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
237 243 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
238 244 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
321 447 4.021229 AGTTCCTCCGTTCCAAAACTTTT 58.979 39.130 0.00 0.00 32.95 2.27
322 448 4.464951 AGTTCCTCCGTTCCAAAACTTTTT 59.535 37.500 0.00 0.00 32.95 1.94
384 950 5.825593 TCCACAACCTCAAATACTCTCTT 57.174 39.130 0.00 0.00 0.00 2.85
386 952 4.627467 CCACAACCTCAAATACTCTCTTCG 59.373 45.833 0.00 0.00 0.00 3.79
399 965 3.377798 ACTCTCTTCGTCCGGAAATACTC 59.622 47.826 5.23 0.00 33.34 2.59
405 971 0.453390 GTCCGGAAATACTCGTCGGT 59.547 55.000 5.23 0.00 41.27 4.69
412 978 3.308866 GGAAATACTCGTCGGTGAAATGG 59.691 47.826 0.00 0.00 0.00 3.16
427 993 8.240682 TCGGTGAAATGGATTACAAGTATTTTG 58.759 33.333 0.00 0.00 0.00 2.44
491 1057 8.568676 TTGAAATATTTGAAACGGATGGAGTA 57.431 30.769 5.17 0.00 0.00 2.59
536 1221 5.221185 CCATAGTGAAAAGAGGGAATGCATG 60.221 44.000 0.00 0.00 0.00 4.06
539 1224 3.703052 GTGAAAAGAGGGAATGCATGGAT 59.297 43.478 0.00 0.00 0.00 3.41
544 1229 2.445905 AGAGGGAATGCATGGATGTGAT 59.554 45.455 0.00 0.00 0.00 3.06
605 1722 3.955551 TGTGTTGTCACCTGTCAGTACTA 59.044 43.478 0.00 0.00 43.26 1.82
655 1776 2.337532 CCTGTTGGCTGTTGCTGC 59.662 61.111 0.00 0.00 39.59 5.25
677 1798 3.424302 CGCACGCGCATAAATATATGGTT 60.424 43.478 5.73 0.00 39.49 3.67
707 1828 1.870941 TAGCTCCTCCTTCCCCGTCA 61.871 60.000 0.00 0.00 0.00 4.35
765 1912 4.154195 GTGTGGATCGAACAAAGCATAAGT 59.846 41.667 1.74 0.00 0.00 2.24
830 1977 3.586470 TTCCCTGTTGTTTCTTGGCTA 57.414 42.857 0.00 0.00 0.00 3.93
918 2066 3.392882 CAATGTCTTTGCCCTTTTGTCC 58.607 45.455 0.00 0.00 0.00 4.02
956 2105 0.320421 CCCCTTTCTGCGAAAGACGA 60.320 55.000 23.56 0.00 45.77 4.20
1005 2154 1.195115 GTGAGCTGGTCTGTATGGGA 58.805 55.000 8.47 0.00 0.00 4.37
1010 2159 1.959042 CTGGTCTGTATGGGATGTGC 58.041 55.000 0.00 0.00 0.00 4.57
1102 2260 4.737279 GTGAGCTTCTGTTTTTCTTTCTGC 59.263 41.667 0.00 0.00 0.00 4.26
1109 2267 7.649306 GCTTCTGTTTTTCTTTCTGCTGATTTA 59.351 33.333 0.00 0.00 0.00 1.40
1110 2268 9.688592 CTTCTGTTTTTCTTTCTGCTGATTTAT 57.311 29.630 0.00 0.00 0.00 1.40
1165 2329 3.537580 TCCGCTGCCGTTTAATTTCTAT 58.462 40.909 0.00 0.00 0.00 1.98
1184 2348 5.129634 TCTATTAATTTCTTCCCGCATGCA 58.870 37.500 19.57 0.00 0.00 3.96
1185 2349 4.942761 ATTAATTTCTTCCCGCATGCAT 57.057 36.364 19.57 0.00 0.00 3.96
1186 2350 2.589798 AATTTCTTCCCGCATGCATG 57.410 45.000 22.70 22.70 0.00 4.06
1279 2443 3.883489 GGATGGGCTTATTCACAAGGTAC 59.117 47.826 0.00 0.00 0.00 3.34
1312 2476 7.663081 TGTCTTGCTCATCATCTTCTTTTAGTT 59.337 33.333 0.00 0.00 0.00 2.24
1317 2496 6.765512 GCTCATCATCTTCTTTTAGTTAGGCT 59.234 38.462 0.00 0.00 0.00 4.58
1328 2507 4.678509 TTAGTTAGGCTGCAAATTCACG 57.321 40.909 0.50 0.00 0.00 4.35
1481 2686 3.741344 CCGAATAGCTGTAATTTCTCGGG 59.259 47.826 10.25 0.00 33.92 5.14
1483 2688 2.218953 TAGCTGTAATTTCTCGGGCG 57.781 50.000 0.00 0.00 0.00 6.13
1501 2706 2.094906 GGCGATTTGGGTGTCCTTTAAC 60.095 50.000 0.00 0.00 0.00 2.01
1526 2772 3.861569 GCGTGACAGCCTGAATATTAC 57.138 47.619 0.00 0.00 0.00 1.89
1530 2776 3.561725 GTGACAGCCTGAATATTACCTGC 59.438 47.826 0.00 0.00 0.00 4.85
1531 2777 3.142174 GACAGCCTGAATATTACCTGCC 58.858 50.000 0.00 0.00 0.00 4.85
1579 2825 4.371786 TGCACAAATATCTCGGATCAGAC 58.628 43.478 0.00 0.00 0.00 3.51
1594 2848 5.855045 GGATCAGACCGACCTGTTTATATT 58.145 41.667 0.00 0.00 35.71 1.28
1601 2855 8.889717 CAGACCGACCTGTTTATATTTGTATTT 58.110 33.333 0.00 0.00 0.00 1.40
1756 3018 3.510459 CCCTTTTCCTCCCAATGTTCTT 58.490 45.455 0.00 0.00 0.00 2.52
1759 3021 5.299949 CCTTTTCCTCCCAATGTTCTTTTG 58.700 41.667 0.00 0.00 0.00 2.44
1766 3028 4.019858 TCCCAATGTTCTTTTGTGTGTGA 58.980 39.130 0.00 0.00 0.00 3.58
1797 3059 7.599998 GTGAATGTTTTAAGAAATGACTGGCAT 59.400 33.333 0.00 0.00 39.43 4.40
1798 3060 8.801299 TGAATGTTTTAAGAAATGACTGGCATA 58.199 29.630 0.00 0.00 35.78 3.14
1811 3073 9.768662 AAATGACTGGCATATTTCATAAATTCC 57.231 29.630 0.00 0.00 35.78 3.01
1817 3079 5.010617 GGCATATTTCATAAATTCCGGGTGT 59.989 40.000 0.00 0.00 32.38 4.16
1818 3080 5.920273 GCATATTTCATAAATTCCGGGTGTG 59.080 40.000 0.00 0.00 32.38 3.82
1969 3705 1.865865 TTGAACGTGAAGAGGTCTGC 58.134 50.000 0.00 0.00 0.00 4.26
2006 3743 9.661187 CTGAACTGAATTATTCTGCACATAATC 57.339 33.333 10.97 3.37 32.51 1.75
2011 3748 9.661187 CTGAATTATTCTGCACATAATCTTGTC 57.339 33.333 6.50 3.22 0.00 3.18
2012 3749 9.399797 TGAATTATTCTGCACATAATCTTGTCT 57.600 29.630 6.50 0.00 0.00 3.41
2060 3824 8.649591 TGTTTTTAACATACTACCAGTCTACCA 58.350 33.333 0.00 0.00 36.25 3.25
2142 4191 6.936279 TCACTGGAAAAATAACACAAAACCA 58.064 32.000 0.00 0.00 0.00 3.67
2178 4228 2.295253 ATAGCACGCACACTACCTTC 57.705 50.000 0.00 0.00 0.00 3.46
2204 4254 4.893424 TTTGACAGTTTGAGCACTTACC 57.107 40.909 0.00 0.00 0.00 2.85
2340 4390 1.469703 TCCAGATGAAATGTTGCTGCG 59.530 47.619 0.00 0.00 0.00 5.18
2352 4402 0.385849 TTGCTGCGCAAGAATCGTTG 60.386 50.000 13.05 0.00 43.99 4.10
2361 4411 3.612423 CGCAAGAATCGTTGACACTATGA 59.388 43.478 0.00 0.00 43.02 2.15
2364 4414 5.961843 GCAAGAATCGTTGACACTATGAATG 59.038 40.000 0.00 0.00 0.00 2.67
2497 4547 2.886081 CTGAAGAACATGACTCTCCCG 58.114 52.381 0.00 0.00 0.00 5.14
2669 4738 1.489481 TGTAGCAGTAGCAGCCATCT 58.511 50.000 0.00 0.00 45.49 2.90
2832 4920 4.460948 CTCAACAGCTGGGCAATTTATT 57.539 40.909 19.93 0.00 0.00 1.40
2858 4946 0.179000 GTCACCGAATGGGCTGATCT 59.821 55.000 0.00 0.00 40.62 2.75
2867 4955 4.617995 CGAATGGGCTGATCTCTCTCATAC 60.618 50.000 0.00 0.00 0.00 2.39
2879 4967 7.924947 TGATCTCTCTCATACTTACATTTGCAG 59.075 37.037 0.00 0.00 0.00 4.41
2911 4999 7.293073 ACAGTTTGGCCATATAGATTCTTCAT 58.707 34.615 6.09 0.00 0.00 2.57
3031 5119 6.611613 TGACTATTGAACTCCATGACTCTT 57.388 37.500 0.00 0.00 0.00 2.85
3034 5122 6.402222 ACTATTGAACTCCATGACTCTTGAC 58.598 40.000 0.00 0.00 0.00 3.18
3376 6693 3.840437 GCAGTTGCAAGTCCACCA 58.160 55.556 3.08 0.00 41.59 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.247894 GACGCGTGCTGTTTTGTTCA 60.248 50.000 20.70 0.00 0.00 3.18
19 20 0.247894 TGACGCGTGCTGTTTTGTTC 60.248 50.000 20.70 0.00 0.00 3.18
67 68 6.215845 ACTGCTCCATACAAAAATTGTCAAC 58.784 36.000 0.00 0.00 44.12 3.18
80 81 3.493350 CCATGAGGTGTACTGCTCCATAC 60.493 52.174 0.00 0.00 33.35 2.39
84 85 3.768633 CCATGAGGTGTACTGCTCC 57.231 57.895 0.00 0.00 0.00 4.70
95 96 5.407407 ACAAGACTACAACTACCATGAGG 57.593 43.478 0.00 0.00 42.21 3.86
111 112 4.141914 CCCTACCCAAGATGTCTACAAGAC 60.142 50.000 0.01 0.01 45.26 3.01
112 113 4.030913 CCCTACCCAAGATGTCTACAAGA 58.969 47.826 0.00 0.00 0.00 3.02
113 114 4.030913 TCCCTACCCAAGATGTCTACAAG 58.969 47.826 0.00 0.00 0.00 3.16
114 115 4.030913 CTCCCTACCCAAGATGTCTACAA 58.969 47.826 0.00 0.00 0.00 2.41
115 116 3.630054 CCTCCCTACCCAAGATGTCTACA 60.630 52.174 0.00 0.00 0.00 2.74
116 117 2.966516 CCTCCCTACCCAAGATGTCTAC 59.033 54.545 0.00 0.00 0.00 2.59
117 118 2.693074 GCCTCCCTACCCAAGATGTCTA 60.693 54.545 0.00 0.00 0.00 2.59
118 119 1.972207 GCCTCCCTACCCAAGATGTCT 60.972 57.143 0.00 0.00 0.00 3.41
119 120 0.470341 GCCTCCCTACCCAAGATGTC 59.530 60.000 0.00 0.00 0.00 3.06
184 188 8.707938 AGAATTACGTATACCACTGTTAAACC 57.292 34.615 0.00 0.00 0.00 3.27
193 197 8.623030 AGAGAGAGAAAGAATTACGTATACCAC 58.377 37.037 0.00 0.00 0.00 4.16
201 205 7.495934 AGAGAGAGAGAGAGAGAAAGAATTACG 59.504 40.741 0.00 0.00 0.00 3.18
222 226 5.124457 CCACAAAAGAGAGAGAGAGAGAGAG 59.876 48.000 0.00 0.00 0.00 3.20
226 232 5.467035 AACCACAAAAGAGAGAGAGAGAG 57.533 43.478 0.00 0.00 0.00 3.20
227 233 4.022762 CGAACCACAAAAGAGAGAGAGAGA 60.023 45.833 0.00 0.00 0.00 3.10
228 234 4.022762 TCGAACCACAAAAGAGAGAGAGAG 60.023 45.833 0.00 0.00 0.00 3.20
229 235 3.889538 TCGAACCACAAAAGAGAGAGAGA 59.110 43.478 0.00 0.00 0.00 3.10
230 236 3.984633 GTCGAACCACAAAAGAGAGAGAG 59.015 47.826 0.00 0.00 0.00 3.20
231 237 3.383505 TGTCGAACCACAAAAGAGAGAGA 59.616 43.478 0.00 0.00 0.00 3.10
232 238 3.717707 TGTCGAACCACAAAAGAGAGAG 58.282 45.455 0.00 0.00 0.00 3.20
233 239 3.132289 ACTGTCGAACCACAAAAGAGAGA 59.868 43.478 0.00 0.00 0.00 3.10
234 240 3.246226 CACTGTCGAACCACAAAAGAGAG 59.754 47.826 0.00 0.00 0.00 3.20
235 241 3.194861 CACTGTCGAACCACAAAAGAGA 58.805 45.455 0.00 0.00 0.00 3.10
236 242 2.287915 CCACTGTCGAACCACAAAAGAG 59.712 50.000 0.00 0.00 0.00 2.85
237 243 2.285083 CCACTGTCGAACCACAAAAGA 58.715 47.619 0.00 0.00 0.00 2.52
238 244 2.014128 ACCACTGTCGAACCACAAAAG 58.986 47.619 0.00 0.00 0.00 2.27
370 936 3.377485 TCCGGACGAAGAGAGTATTTGAG 59.623 47.826 0.00 0.00 0.00 3.02
384 950 0.374758 CGACGAGTATTTCCGGACGA 59.625 55.000 15.79 3.01 34.06 4.20
386 952 0.453390 ACCGACGAGTATTTCCGGAC 59.547 55.000 1.83 0.00 42.49 4.79
399 965 3.682858 ACTTGTAATCCATTTCACCGACG 59.317 43.478 0.00 0.00 0.00 5.12
405 971 8.527810 GTCCCAAAATACTTGTAATCCATTTCA 58.472 33.333 0.00 0.00 0.00 2.69
412 978 5.296035 CCTCCGTCCCAAAATACTTGTAATC 59.704 44.000 0.00 0.00 0.00 1.75
427 993 2.305858 ATATGTACTCCCTCCGTCCC 57.694 55.000 0.00 0.00 0.00 4.46
491 1057 7.814693 ATGGAATACAGGCCATATAAGTAGT 57.185 36.000 5.01 0.00 42.86 2.73
536 1221 2.294979 TGCAGCAAGATCATCACATCC 58.705 47.619 0.00 0.00 0.00 3.51
539 1224 1.404035 GCATGCAGCAAGATCATCACA 59.596 47.619 14.21 0.00 44.79 3.58
605 1722 2.113860 AGTGCGGCACAGAATATTGT 57.886 45.000 32.29 7.86 36.74 2.71
677 1798 2.313342 AGGAGGAGCTAGAAGAAGGACA 59.687 50.000 0.00 0.00 0.00 4.02
707 1828 0.253327 GGTGGCTCGGGAGAAAGATT 59.747 55.000 0.00 0.00 39.18 2.40
765 1912 5.069781 CCTGGGAAACAACAAACAAAGGATA 59.930 40.000 0.00 0.00 0.00 2.59
883 2031 6.478344 GCAAAGACATTGGTATCAACACAAAA 59.522 34.615 0.00 0.00 39.54 2.44
895 2043 2.771372 ACAAAAGGGCAAAGACATTGGT 59.229 40.909 0.00 0.00 39.54 3.67
918 2066 4.010349 GGGGATGAAGAAAACACACCTAG 58.990 47.826 0.00 0.00 0.00 3.02
983 2132 2.625737 CCATACAGACCAGCTCACAAG 58.374 52.381 0.00 0.00 0.00 3.16
1005 2154 3.508402 TGAACTGCTTTGATGATGCACAT 59.492 39.130 0.00 0.00 42.47 3.21
1010 2159 3.681417 TCGTCTGAACTGCTTTGATGATG 59.319 43.478 0.00 0.00 0.00 3.07
1017 2166 1.606737 GGAGCTCGTCTGAACTGCTTT 60.607 52.381 7.83 0.00 34.49 3.51
1102 2260 9.588774 CATTTTTGCACTGAACAAATAAATCAG 57.411 29.630 0.00 0.00 44.77 2.90
1109 2267 4.512571 GGCTCATTTTTGCACTGAACAAAT 59.487 37.500 0.00 0.00 36.91 2.32
1110 2268 3.870419 GGCTCATTTTTGCACTGAACAAA 59.130 39.130 0.00 0.00 35.30 2.83
1111 2269 3.456280 GGCTCATTTTTGCACTGAACAA 58.544 40.909 0.00 0.00 0.00 2.83
1112 2270 2.224018 GGGCTCATTTTTGCACTGAACA 60.224 45.455 0.00 0.00 0.00 3.18
1165 2329 3.698539 TCATGCATGCGGGAAGAAATTAA 59.301 39.130 22.25 0.00 0.00 1.40
1184 2348 5.009010 ACTTCATTCAAAGAAACTGCGTCAT 59.991 36.000 0.00 0.00 0.00 3.06
1185 2349 4.335315 ACTTCATTCAAAGAAACTGCGTCA 59.665 37.500 0.00 0.00 0.00 4.35
1186 2350 4.672413 CACTTCATTCAAAGAAACTGCGTC 59.328 41.667 0.00 0.00 0.00 5.19
1279 2443 5.856156 AGATGATGAGCAAGACAAGATAGG 58.144 41.667 0.00 0.00 0.00 2.57
1312 2476 2.419673 CACATCGTGAATTTGCAGCCTA 59.580 45.455 0.00 0.00 35.23 3.93
1317 2496 2.225467 TGACCACATCGTGAATTTGCA 58.775 42.857 0.00 0.00 35.23 4.08
1328 2507 3.184986 GCAGTTTGCAAATTGACCACATC 59.815 43.478 31.67 12.98 44.26 3.06
1442 2647 1.961277 GGAGCGTTGGAGTGGTGTG 60.961 63.158 0.00 0.00 0.00 3.82
1481 2686 2.817844 AGTTAAAGGACACCCAAATCGC 59.182 45.455 0.00 0.00 33.88 4.58
1483 2688 5.538118 CCAAAGTTAAAGGACACCCAAATC 58.462 41.667 0.00 0.00 33.88 2.17
1526 2772 4.321230 GGAACAATTTTACAGTCAGGCAGG 60.321 45.833 0.00 0.00 0.00 4.85
1579 2825 8.889717 AGTCAAATACAAATATAAACAGGTCGG 58.110 33.333 0.00 0.00 0.00 4.79
1594 2848 9.665719 TCAAATATCTGCACTAGTCAAATACAA 57.334 29.630 0.00 0.00 0.00 2.41
1756 3018 3.755905 ACATTCACACACTCACACACAAA 59.244 39.130 0.00 0.00 0.00 2.83
1759 3021 4.355543 AAACATTCACACACTCACACAC 57.644 40.909 0.00 0.00 0.00 3.82
1766 3028 8.686334 AGTCATTTCTTAAAACATTCACACACT 58.314 29.630 0.00 0.00 0.00 3.55
1797 3059 7.558081 TGAATCACACCCGGAATTTATGAAATA 59.442 33.333 0.73 0.00 0.00 1.40
1798 3060 6.379703 TGAATCACACCCGGAATTTATGAAAT 59.620 34.615 0.73 0.00 0.00 2.17
1811 3073 1.066858 ACTGCTACTGAATCACACCCG 60.067 52.381 0.00 0.00 0.00 5.28
1817 3079 2.432146 CCAGGCTACTGCTACTGAATCA 59.568 50.000 0.00 0.00 43.53 2.57
1818 3080 2.432510 ACCAGGCTACTGCTACTGAATC 59.567 50.000 0.00 0.00 43.53 2.52
2006 3743 9.347934 CTTGAAGTAGTATGTTCAGTAGACAAG 57.652 37.037 0.00 0.00 34.25 3.16
2009 3746 9.509855 CATCTTGAAGTAGTATGTTCAGTAGAC 57.490 37.037 0.00 0.00 34.25 2.59
2011 3748 9.862371 AACATCTTGAAGTAGTATGTTCAGTAG 57.138 33.333 4.68 0.00 36.33 2.57
2053 3817 2.412089 GCAAATCGAGTGTGTGGTAGAC 59.588 50.000 0.00 0.00 0.00 2.59
2054 3818 2.611971 GGCAAATCGAGTGTGTGGTAGA 60.612 50.000 0.00 0.00 0.00 2.59
2055 3819 1.732259 GGCAAATCGAGTGTGTGGTAG 59.268 52.381 0.00 0.00 0.00 3.18
2056 3820 1.803334 GGCAAATCGAGTGTGTGGTA 58.197 50.000 0.00 0.00 0.00 3.25
2057 3821 1.227999 CGGCAAATCGAGTGTGTGGT 61.228 55.000 0.00 0.00 0.00 4.16
2058 3822 0.948623 TCGGCAAATCGAGTGTGTGG 60.949 55.000 0.00 0.00 34.82 4.17
2059 3823 1.078709 ATCGGCAAATCGAGTGTGTG 58.921 50.000 0.00 0.00 42.69 3.82
2060 3824 1.808411 AATCGGCAAATCGAGTGTGT 58.192 45.000 0.00 0.00 42.69 3.72
2142 4191 6.128282 GCGTGCTATACTTGGTGCATATAATT 60.128 38.462 0.00 0.00 37.76 1.40
2178 4228 4.675510 AGTGCTCAAACTGTCAAATTGTG 58.324 39.130 0.00 0.00 0.00 3.33
2204 4254 0.865111 TGCATGAACGACCAGTTTCG 59.135 50.000 0.00 0.00 44.35 3.46
2340 4390 5.530519 TTCATAGTGTCAACGATTCTTGC 57.469 39.130 0.00 0.00 0.00 4.01
2381 4431 5.366829 TGCTTGAATGTCTGTCAGAATTG 57.633 39.130 3.51 0.00 0.00 2.32
2382 4432 4.458295 CCTGCTTGAATGTCTGTCAGAATT 59.542 41.667 3.51 6.99 0.00 2.17
2789 4877 3.064545 GCTGATGTGTACCATTTCTCAGC 59.935 47.826 15.55 15.55 39.22 4.26
2830 4918 4.466015 AGCCCATTCGGTGACAAAATAAAT 59.534 37.500 0.00 0.00 0.00 1.40
2831 4919 3.829601 AGCCCATTCGGTGACAAAATAAA 59.170 39.130 0.00 0.00 0.00 1.40
2832 4920 3.192422 CAGCCCATTCGGTGACAAAATAA 59.808 43.478 0.00 0.00 0.00 1.40
2858 4946 8.918116 AGATACTGCAAATGTAAGTATGAGAGA 58.082 33.333 12.59 0.00 37.27 3.10
2867 4955 9.546909 CAAACTGTTAGATACTGCAAATGTAAG 57.453 33.333 0.00 0.00 0.00 2.34
2879 4967 9.726438 AATCTATATGGCCAAACTGTTAGATAC 57.274 33.333 10.96 0.00 0.00 2.24
2911 4999 1.832883 ATTCGCCTGTAAATGCACCA 58.167 45.000 0.00 0.00 0.00 4.17
3031 5119 2.159028 TCGGACAGTGAAATGTGTGTCA 60.159 45.455 0.00 0.00 40.96 3.58
3034 5122 2.476619 GAGTCGGACAGTGAAATGTGTG 59.523 50.000 11.27 0.00 32.25 3.82
3369 6686 5.774498 AAGTCTTCTCATTTTTGGTGGAC 57.226 39.130 0.00 0.00 0.00 4.02
3376 6693 6.299141 TGGAGTGCTAAGTCTTCTCATTTTT 58.701 36.000 0.00 0.00 0.00 1.94
3440 6760 8.482429 GCATCATTAGTACTGCATTTAAATTGC 58.518 33.333 5.39 12.76 34.77 3.56


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

AutoCloner maintained by Alex Coulton.