Multiple sequence alignment - TraesCS6D01G298500

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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 TraesCS6D01G298500 chr6D 100.000 3853 0 0 1 3853 409345689 409349541 0.000000e+00 7116
1 TraesCS6D01G298500 chr6D 92.947 1347 80 9 1533 2869 422190887 422192228 0.000000e+00 1947
2 TraesCS6D01G298500 chr6D 86.863 373 36 6 886 1245 422190511 422190883 4.640000e-109 405
3 TraesCS6D01G298500 chr6D 89.130 138 13 2 2915 3050 422192225 422192362 1.840000e-38 171
4 TraesCS6D01G298500 chr6D 88.060 134 12 4 2919 3050 422203933 422203802 5.150000e-34 156
5 TraesCS6D01G298500 chr6A 90.585 3229 195 50 1 3172 554823233 554826409 0.000000e+00 4178
6 TraesCS6D01G298500 chr6A 92.419 1517 95 17 1532 3037 564910516 564909009 0.000000e+00 2146
7 TraesCS6D01G298500 chr6A 91.906 1532 104 13 1533 3050 564974999 564976524 0.000000e+00 2124
8 TraesCS6D01G298500 chr6A 83.607 366 37 13 886 1233 564974626 564974986 4.800000e-84 322
9 TraesCS6D01G298500 chr6A 84.639 332 27 8 886 1194 564910899 564910569 3.740000e-80 309
10 TraesCS6D01G298500 chr6B 93.251 1867 92 12 1546 3400 614582279 614584123 0.000000e+00 2719
11 TraesCS6D01G298500 chr6B 94.765 1471 68 6 1546 3009 614311911 614313379 0.000000e+00 2281
12 TraesCS6D01G298500 chr6B 94.169 1475 73 9 1546 3009 614437221 614438693 0.000000e+00 2235
13 TraesCS6D01G298500 chr6B 92.947 1347 87 6 1535 2875 636491786 636493130 0.000000e+00 1954
14 TraesCS6D01G298500 chr6B 93.034 1335 85 6 1545 2873 636585725 636584393 0.000000e+00 1943
15 TraesCS6D01G298500 chr6B 88.851 1166 57 20 50 1195 614310714 614311826 0.000000e+00 1365
16 TraesCS6D01G298500 chr6B 89.530 468 21 6 3413 3853 614587992 614588458 5.590000e-158 568
17 TraesCS6D01G298500 chr6B 87.288 472 25 10 732 1195 614436692 614437136 1.240000e-139 507
18 TraesCS6D01G298500 chr6B 90.080 373 21 7 3497 3853 614686282 614686654 1.620000e-128 470
19 TraesCS6D01G298500 chr6B 85.201 473 28 14 732 1195 614581755 614582194 7.590000e-122 448
20 TraesCS6D01G298500 chr6B 87.987 308 32 3 886 1189 636586093 636585787 3.660000e-95 359
21 TraesCS6D01G298500 chr6B 85.350 314 35 4 886 1195 636491421 636491727 8.040000e-82 315
22 TraesCS6D01G298500 chr6B 89.247 186 14 4 120 304 614580779 614580959 1.080000e-55 228
23 TraesCS6D01G298500 chr6B 88.060 134 12 4 2919 3050 636584382 636584251 5.150000e-34 156
24 TraesCS6D01G298500 chr7A 88.929 280 25 5 1258 1534 175240557 175240833 1.330000e-89 340
25 TraesCS6D01G298500 chr7A 89.377 273 24 4 1258 1527 732467260 732466990 4.770000e-89 339
26 TraesCS6D01G298500 chr5A 89.925 268 22 4 1263 1527 600032913 600032648 1.330000e-89 340
27 TraesCS6D01G298500 chr3A 89.630 270 23 4 1261 1527 137605336 137605069 4.770000e-89 339
28 TraesCS6D01G298500 chr3A 87.591 274 26 6 1258 1527 566936176 566935907 1.040000e-80 311
29 TraesCS6D01G298500 chr1D 87.847 288 27 6 1245 1527 397084322 397084038 7.980000e-87 331
30 TraesCS6D01G298500 chr1A 88.519 270 26 4 1261 1527 497195417 497195150 4.800000e-84 322
31 TraesCS6D01G298500 chr5B 86.620 284 28 8 1247 1527 128360660 128360936 4.840000e-79 305


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 TraesCS6D01G298500 chr6D 409345689 409349541 3852 False 7116.000000 7116 100.000000 1 3853 1 chr6D.!!$F1 3852
1 TraesCS6D01G298500 chr6D 422190511 422192362 1851 False 841.000000 1947 89.646667 886 3050 3 chr6D.!!$F2 2164
2 TraesCS6D01G298500 chr6A 554823233 554826409 3176 False 4178.000000 4178 90.585000 1 3172 1 chr6A.!!$F1 3171
3 TraesCS6D01G298500 chr6A 564909009 564910899 1890 True 1227.500000 2146 88.529000 886 3037 2 chr6A.!!$R1 2151
4 TraesCS6D01G298500 chr6A 564974626 564976524 1898 False 1223.000000 2124 87.756500 886 3050 2 chr6A.!!$F2 2164
5 TraesCS6D01G298500 chr6B 614310714 614313379 2665 False 1823.000000 2281 91.808000 50 3009 2 chr6B.!!$F2 2959
6 TraesCS6D01G298500 chr6B 614436692 614438693 2001 False 1371.000000 2235 90.728500 732 3009 2 chr6B.!!$F3 2277
7 TraesCS6D01G298500 chr6B 636491421 636493130 1709 False 1134.500000 1954 89.148500 886 2875 2 chr6B.!!$F5 1989
8 TraesCS6D01G298500 chr6B 614580779 614588458 7679 False 990.750000 2719 89.307250 120 3853 4 chr6B.!!$F4 3733
9 TraesCS6D01G298500 chr6B 636584251 636586093 1842 True 819.333333 1943 89.693667 886 3050 3 chr6B.!!$R1 2164

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
44 45 0.320421 TCCTACTCTTGTTGTGCGCC 60.320 55.0 4.18 0.00 0.00 6.53 F
45 46 0.320771 CCTACTCTTGTTGTGCGCCT 60.321 55.0 4.18 0.00 0.00 5.52 F
724 815 0.389426 CTTGGCTTGGATGCTGTTGC 60.389 55.0 0.00 0.00 40.20 4.17 F
725 816 0.828762 TTGGCTTGGATGCTGTTGCT 60.829 50.0 0.00 0.00 40.48 3.91 F
2127 2745 0.874607 ATTTACATCGACCGCTCGGC 60.875 55.0 8.41 0.68 40.58 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 2133 0.182775 ACAACTCAAAGTTCCGGCCT 59.817 50.000 0.00 0.00 36.03 5.19 R
1528 2139 1.466855 GCACGCACAACTCAAAGTTC 58.533 50.000 0.00 0.00 36.03 3.01 R
2648 3283 0.984230 GGGTCCTGATTGACACCAGA 59.016 55.000 5.78 0.00 36.97 3.86 R
2715 3350 3.621558 TCTCAGCGAGATAAAGGTCAGA 58.378 45.455 4.47 0.00 33.35 3.27 R
3073 3722 0.179119 ATGCAGCCGTACGAGTTACC 60.179 55.000 18.76 0.32 0.00 2.85 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
39 40 8.375493 TGGTTATAGAATCCTACTCTTGTTGT 57.625 34.615 0.00 0.00 0.00 3.32
40 41 8.258007 TGGTTATAGAATCCTACTCTTGTTGTG 58.742 37.037 0.00 0.00 0.00 3.33
41 42 7.224949 GGTTATAGAATCCTACTCTTGTTGTGC 59.775 40.741 0.00 0.00 0.00 4.57
42 43 3.589988 AGAATCCTACTCTTGTTGTGCG 58.410 45.455 0.00 0.00 0.00 5.34
43 44 1.726853 ATCCTACTCTTGTTGTGCGC 58.273 50.000 0.00 0.00 0.00 6.09
44 45 0.320421 TCCTACTCTTGTTGTGCGCC 60.320 55.000 4.18 0.00 0.00 6.53
45 46 0.320771 CCTACTCTTGTTGTGCGCCT 60.321 55.000 4.18 0.00 0.00 5.52
46 47 1.071605 CTACTCTTGTTGTGCGCCTC 58.928 55.000 4.18 0.00 0.00 4.70
47 48 0.391228 TACTCTTGTTGTGCGCCTCA 59.609 50.000 4.18 0.67 0.00 3.86
48 49 1.160329 ACTCTTGTTGTGCGCCTCAC 61.160 55.000 4.18 0.00 45.82 3.51
49 50 1.845809 CTCTTGTTGTGCGCCTCACC 61.846 60.000 4.18 0.00 45.03 4.02
50 51 1.893808 CTTGTTGTGCGCCTCACCT 60.894 57.895 4.18 0.00 45.03 4.00
51 52 2.121564 CTTGTTGTGCGCCTCACCTG 62.122 60.000 4.18 0.00 45.03 4.00
123 130 1.067743 CTCTGCGTAGAGTGCACACG 61.068 60.000 21.04 20.60 44.43 4.49
146 153 2.198406 TCCGTTTGTTCTGTTGAGTCG 58.802 47.619 0.00 0.00 0.00 4.18
223 234 2.493278 CTGCTTATCCCACCCAAAGTTG 59.507 50.000 0.00 0.00 0.00 3.16
224 235 2.158385 TGCTTATCCCACCCAAAGTTGT 60.158 45.455 0.00 0.00 0.00 3.32
225 236 2.897326 GCTTATCCCACCCAAAGTTGTT 59.103 45.455 0.00 0.00 0.00 2.83
269 283 0.597568 TGGTACGGAAATGACGTCGT 59.402 50.000 11.62 7.97 44.37 4.34
310 375 4.202050 CGGAATTCCTTGGGATGAACAATC 60.202 45.833 22.05 0.00 34.19 2.67
311 376 4.958581 GGAATTCCTTGGGATGAACAATCT 59.041 41.667 17.73 0.00 35.43 2.40
312 377 6.129179 GGAATTCCTTGGGATGAACAATCTA 58.871 40.000 17.73 0.00 35.43 1.98
313 378 6.779539 GGAATTCCTTGGGATGAACAATCTAT 59.220 38.462 17.73 0.00 35.43 1.98
314 379 7.944554 GGAATTCCTTGGGATGAACAATCTATA 59.055 37.037 17.73 0.00 35.43 1.31
315 380 9.525826 GAATTCCTTGGGATGAACAATCTATAT 57.474 33.333 0.00 0.00 35.43 0.86
316 381 9.887862 AATTCCTTGGGATGAACAATCTATATT 57.112 29.630 0.00 0.00 35.43 1.28
317 382 9.887862 ATTCCTTGGGATGAACAATCTATATTT 57.112 29.630 0.00 0.00 35.43 1.40
318 383 9.713684 TTCCTTGGGATGAACAATCTATATTTT 57.286 29.630 0.00 0.00 35.43 1.82
319 384 9.354673 TCCTTGGGATGAACAATCTATATTTTC 57.645 33.333 0.00 0.00 35.43 2.29
320 385 9.359653 CCTTGGGATGAACAATCTATATTTTCT 57.640 33.333 0.00 0.00 35.43 2.52
323 388 8.632679 TGGGATGAACAATCTATATTTTCTTGC 58.367 33.333 0.00 0.00 35.43 4.01
324 389 8.084684 GGGATGAACAATCTATATTTTCTTGCC 58.915 37.037 0.00 0.00 35.43 4.52
325 390 8.632679 GGATGAACAATCTATATTTTCTTGCCA 58.367 33.333 0.00 0.00 35.43 4.92
326 391 9.455847 GATGAACAATCTATATTTTCTTGCCAC 57.544 33.333 0.00 0.00 32.01 5.01
327 392 8.347004 TGAACAATCTATATTTTCTTGCCACA 57.653 30.769 0.00 0.00 0.00 4.17
328 393 8.970020 TGAACAATCTATATTTTCTTGCCACAT 58.030 29.630 0.00 0.00 0.00 3.21
376 441 5.232202 GCTCATCGAACGAATGAATACTTGA 59.768 40.000 0.12 0.00 0.00 3.02
408 473 8.400947 TGTTTTGATCTCTTCAGACAGAAAAAG 58.599 33.333 0.00 0.00 35.40 2.27
441 506 3.433615 CGCTAGAAAGTTTCTGAACCTGG 59.566 47.826 25.27 4.15 40.94 4.45
442 507 4.642429 GCTAGAAAGTTTCTGAACCTGGA 58.358 43.478 25.27 4.58 40.94 3.86
492 557 1.476833 CCACATCCGGGTTATTCAGGG 60.477 57.143 0.00 0.00 0.00 4.45
496 571 3.720002 ACATCCGGGTTATTCAGGGTAAT 59.280 43.478 0.00 0.00 0.00 1.89
571 646 2.036256 ATCCTGCCCACTTGCCAC 59.964 61.111 0.00 0.00 0.00 5.01
601 676 4.178540 CGCTGATCTTTTACGAAGGGTTA 58.821 43.478 0.00 0.00 0.00 2.85
603 678 4.032558 GCTGATCTTTTACGAAGGGTTACG 59.967 45.833 0.00 0.00 0.00 3.18
720 811 3.604875 ATTTTCTTGGCTTGGATGCTG 57.395 42.857 0.00 0.00 0.00 4.41
721 812 1.999648 TTTCTTGGCTTGGATGCTGT 58.000 45.000 0.00 0.00 0.00 4.40
722 813 1.999648 TTCTTGGCTTGGATGCTGTT 58.000 45.000 0.00 0.00 0.00 3.16
724 815 0.389426 CTTGGCTTGGATGCTGTTGC 60.389 55.000 0.00 0.00 40.20 4.17
725 816 0.828762 TTGGCTTGGATGCTGTTGCT 60.829 50.000 0.00 0.00 40.48 3.91
787 1318 7.218614 TCCATGAAAAATGCTCAAATGTTCTT 58.781 30.769 0.00 0.00 0.00 2.52
788 1319 7.385752 TCCATGAAAAATGCTCAAATGTTCTTC 59.614 33.333 0.00 0.00 0.00 2.87
789 1320 7.171848 CCATGAAAAATGCTCAAATGTTCTTCA 59.828 33.333 0.00 0.00 0.00 3.02
790 1321 8.717821 CATGAAAAATGCTCAAATGTTCTTCAT 58.282 29.630 0.00 0.00 38.57 2.57
791 1322 8.301730 TGAAAAATGCTCAAATGTTCTTCATC 57.698 30.769 0.00 0.00 35.48 2.92
792 1323 7.927092 TGAAAAATGCTCAAATGTTCTTCATCA 59.073 29.630 0.00 0.00 35.48 3.07
794 1325 8.665643 AAAATGCTCAAATGTTCTTCATCAAA 57.334 26.923 0.00 0.00 35.48 2.69
795 1326 7.884816 AATGCTCAAATGTTCTTCATCAAAG 57.115 32.000 0.00 0.00 35.48 2.77
796 1327 6.395426 TGCTCAAATGTTCTTCATCAAAGT 57.605 33.333 0.00 0.00 35.48 2.66
797 1328 6.808829 TGCTCAAATGTTCTTCATCAAAGTT 58.191 32.000 0.00 0.00 35.48 2.66
1003 1565 1.606885 AAGTTGCAATCCCGGCATGG 61.607 55.000 0.59 0.00 41.58 3.66
1081 1643 1.528129 GTCCTCTTCCAAAGCACAGG 58.472 55.000 0.00 0.00 0.00 4.00
1250 1847 2.959030 GTTTTCTTTTGGACTGGCCTCT 59.041 45.455 3.32 0.00 37.63 3.69
1269 1866 5.243954 GCCTCTTTTGGTTTGTAGGAATCTT 59.756 40.000 0.00 0.00 0.00 2.40
1276 1873 9.681062 TTTTGGTTTGTAGGAATCTTATAGGAG 57.319 33.333 0.00 0.00 0.00 3.69
1277 1874 7.374975 TGGTTTGTAGGAATCTTATAGGAGG 57.625 40.000 0.00 0.00 0.00 4.30
1278 1875 7.136885 TGGTTTGTAGGAATCTTATAGGAGGA 58.863 38.462 0.00 0.00 0.00 3.71
1310 1921 6.136857 GGAAAAATTCCTATAGAGCCCCTTT 58.863 40.000 0.00 0.00 46.57 3.11
1311 1922 6.040955 GGAAAAATTCCTATAGAGCCCCTTTG 59.959 42.308 0.00 0.00 46.57 2.77
1317 1928 3.202151 CCTATAGAGCCCCTTTGGTTTGA 59.798 47.826 0.00 0.00 36.04 2.69
1319 1930 2.001076 AGAGCCCCTTTGGTTTGAAG 57.999 50.000 0.00 0.00 36.04 3.02
1324 1935 2.289631 GCCCCTTTGGTTTGAAGGAATG 60.290 50.000 4.52 0.00 45.25 2.67
1329 1940 5.934043 CCCTTTGGTTTGAAGGAATGAATTC 59.066 40.000 0.00 0.00 45.25 2.17
1352 1963 6.195700 TCCTATTGCTATGTAGGATAGGGTC 58.804 44.000 7.62 0.00 41.09 4.46
1368 1979 3.434309 AGGGTCCAATCCTTCACATTTG 58.566 45.455 0.00 0.00 0.00 2.32
1373 1984 5.473039 GTCCAATCCTTCACATTTGAAAGG 58.527 41.667 0.00 9.01 41.34 3.11
1467 2078 8.929260 TTATAGGAATTCAGATGCATGTCATT 57.071 30.769 2.46 0.09 35.05 2.57
1474 2085 5.970317 TCAGATGCATGTCATTTCACTTT 57.030 34.783 2.46 0.00 35.05 2.66
1475 2086 6.335471 TCAGATGCATGTCATTTCACTTTT 57.665 33.333 2.46 0.00 35.05 2.27
1527 2138 2.017049 CCTATGAACCAAAGAAGGCCG 58.983 52.381 0.00 0.00 0.00 6.13
1528 2139 2.017049 CTATGAACCAAAGAAGGCCGG 58.983 52.381 0.00 0.00 0.00 6.13
1660 2278 2.997315 CACGTCTGGCTCCCTCCA 60.997 66.667 0.00 0.00 34.42 3.86
1993 2611 2.656069 CCCCGACATCGACCACCTT 61.656 63.158 2.09 0.00 43.02 3.50
2042 2660 1.073722 TGGCTCAACTGGCTCAAGG 59.926 57.895 0.00 0.00 0.00 3.61
2127 2745 0.874607 ATTTACATCGACCGCTCGGC 60.875 55.000 8.41 0.68 40.58 5.54
2266 2884 4.043100 AAAGGCCCCGCTACCACC 62.043 66.667 0.00 0.00 0.00 4.61
2269 2887 4.043100 GGCCCCGCTACCACCTTT 62.043 66.667 0.00 0.00 0.00 3.11
2473 3091 2.355513 GCAGGGATATGCCTACATCCTG 60.356 54.545 16.36 3.76 43.69 3.86
2715 3350 3.806380 CTGCAAATCATAGAGGCTGACT 58.194 45.455 0.00 0.00 0.00 3.41
2837 3472 1.002142 CATGGCAATGACTATGCGGTG 60.002 52.381 0.00 0.00 44.75 4.94
3038 3681 5.337578 TTTTTGCACTCTTGGCTTACTTT 57.662 34.783 0.00 0.00 0.00 2.66
3058 3701 5.641636 ACTTTGTGTTGGTTGAATGAAAACC 59.358 36.000 0.00 0.00 46.13 3.27
3076 3725 3.755628 GAGCAGCCACGACCGGTA 61.756 66.667 7.34 0.00 0.00 4.02
3077 3726 3.291101 GAGCAGCCACGACCGGTAA 62.291 63.158 7.34 0.00 0.00 2.85
3078 3727 3.116531 GCAGCCACGACCGGTAAC 61.117 66.667 7.34 0.00 0.00 2.50
3088 3737 3.190878 CCGGTAACTCGTACGGCT 58.809 61.111 16.52 2.65 39.85 5.52
3114 3763 2.241685 ACCGGAGTAGTGGTAGACTCAT 59.758 50.000 9.46 0.00 43.28 2.90
3125 3774 2.673368 GGTAGACTCATGAGCGTTTTGG 59.327 50.000 22.83 0.00 0.00 3.28
3157 3806 1.001282 TTACGGGGGCTGGGTTTAAT 58.999 50.000 0.00 0.00 0.00 1.40
3218 3867 8.464770 TTTTTGTTCAGTCACTTTTTCATCTG 57.535 30.769 0.00 0.00 0.00 2.90
3219 3868 5.173774 TGTTCAGTCACTTTTTCATCTGC 57.826 39.130 0.00 0.00 0.00 4.26
3229 3878 7.806014 GTCACTTTTTCATCTGCCGTTAAATTA 59.194 33.333 0.00 0.00 0.00 1.40
3239 3888 8.943925 CATCTGCCGTTAAATTAAGATTAAACG 58.056 33.333 0.00 0.00 0.00 3.60
3240 3889 8.031848 TCTGCCGTTAAATTAAGATTAAACGT 57.968 30.769 0.00 0.00 0.00 3.99
3242 3891 9.925268 CTGCCGTTAAATTAAGATTAAACGTAT 57.075 29.630 0.00 0.00 0.00 3.06
3310 3959 3.744238 TCAGTCGAATTCCTCACACAA 57.256 42.857 0.00 0.00 0.00 3.33
3395 4045 1.284657 CTGATGCAGCCTACAAGACG 58.715 55.000 0.00 0.00 0.00 4.18
3414 6107 6.052405 AGACGGTAACCCATAACAACATAA 57.948 37.500 0.00 0.00 0.00 1.90
3415 6108 6.474630 AGACGGTAACCCATAACAACATAAA 58.525 36.000 0.00 0.00 0.00 1.40
3416 6109 6.941436 AGACGGTAACCCATAACAACATAAAA 59.059 34.615 0.00 0.00 0.00 1.52
3417 6110 7.447853 AGACGGTAACCCATAACAACATAAAAA 59.552 33.333 0.00 0.00 0.00 1.94
3502 8009 4.161942 GCATGGATGGAGCTAGATGAGTAT 59.838 45.833 0.00 0.00 0.00 2.12
3505 8012 7.232330 GCATGGATGGAGCTAGATGAGTATATA 59.768 40.741 0.00 0.00 0.00 0.86
3506 8013 8.575589 CATGGATGGAGCTAGATGAGTATATAC 58.424 40.741 4.60 4.60 0.00 1.47
3568 8086 7.831690 TGATTAAATTTGTACATAGGTGCTCCA 59.168 33.333 7.70 0.00 35.89 3.86
3582 8100 6.229936 AGGTGCTCCAAAAACGAGTATATA 57.770 37.500 7.70 0.00 35.89 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.641645 TGGCAACCAGGTGAGGCG 62.642 66.667 12.56 0.00 0.00 5.52
50 51 2.784356 GCACAACTGCTGGCAACCA 61.784 57.895 0.00 0.00 40.63 3.67
51 52 2.028043 GCACAACTGCTGGCAACC 59.972 61.111 0.00 0.00 40.63 3.77
116 123 1.649390 AACAAACGGAAGCGTGTGCA 61.649 50.000 0.00 0.00 46.23 4.57
123 130 2.354821 ACTCAACAGAACAAACGGAAGC 59.645 45.455 0.00 0.00 0.00 3.86
146 153 0.686789 AGGCCAAAGCAAATCCAACC 59.313 50.000 5.01 0.00 42.56 3.77
269 283 0.893270 CGAATGGGGGTTGCAACTCA 60.893 55.000 29.75 22.85 0.00 3.41
310 375 9.209175 GTAGGAGTATGTGGCAAGAAAATATAG 57.791 37.037 0.00 0.00 0.00 1.31
311 376 8.154856 GGTAGGAGTATGTGGCAAGAAAATATA 58.845 37.037 0.00 0.00 0.00 0.86
312 377 6.998673 GGTAGGAGTATGTGGCAAGAAAATAT 59.001 38.462 0.00 0.00 0.00 1.28
313 378 6.354130 GGTAGGAGTATGTGGCAAGAAAATA 58.646 40.000 0.00 0.00 0.00 1.40
314 379 5.193679 GGTAGGAGTATGTGGCAAGAAAAT 58.806 41.667 0.00 0.00 0.00 1.82
315 380 4.566907 GGGTAGGAGTATGTGGCAAGAAAA 60.567 45.833 0.00 0.00 0.00 2.29
316 381 3.054655 GGGTAGGAGTATGTGGCAAGAAA 60.055 47.826 0.00 0.00 0.00 2.52
317 382 2.504175 GGGTAGGAGTATGTGGCAAGAA 59.496 50.000 0.00 0.00 0.00 2.52
318 383 2.116238 GGGTAGGAGTATGTGGCAAGA 58.884 52.381 0.00 0.00 0.00 3.02
319 384 2.103263 GAGGGTAGGAGTATGTGGCAAG 59.897 54.545 0.00 0.00 0.00 4.01
320 385 2.116238 GAGGGTAGGAGTATGTGGCAA 58.884 52.381 0.00 0.00 0.00 4.52
321 386 1.007842 TGAGGGTAGGAGTATGTGGCA 59.992 52.381 0.00 0.00 0.00 4.92
322 387 1.413077 GTGAGGGTAGGAGTATGTGGC 59.587 57.143 0.00 0.00 0.00 5.01
323 388 1.681793 CGTGAGGGTAGGAGTATGTGG 59.318 57.143 0.00 0.00 0.00 4.17
324 389 2.651455 TCGTGAGGGTAGGAGTATGTG 58.349 52.381 0.00 0.00 0.00 3.21
325 390 3.377253 TTCGTGAGGGTAGGAGTATGT 57.623 47.619 0.00 0.00 0.00 2.29
326 391 4.341235 TCATTTCGTGAGGGTAGGAGTATG 59.659 45.833 0.00 0.00 31.80 2.39
327 392 4.543689 TCATTTCGTGAGGGTAGGAGTAT 58.456 43.478 0.00 0.00 31.80 2.12
328 393 3.972133 TCATTTCGTGAGGGTAGGAGTA 58.028 45.455 0.00 0.00 31.80 2.59
387 452 6.179906 ACCTTTTTCTGTCTGAAGAGATCA 57.820 37.500 0.00 0.00 35.89 2.92
401 466 2.952310 AGCGAGCTTCAAACCTTTTTCT 59.048 40.909 0.00 0.00 0.00 2.52
404 469 3.740115 TCTAGCGAGCTTCAAACCTTTT 58.260 40.909 1.86 0.00 0.00 2.27
408 473 3.067833 ACTTTCTAGCGAGCTTCAAACC 58.932 45.455 1.86 0.00 0.00 3.27
416 481 3.123790 GGTTCAGAAACTTTCTAGCGAGC 59.876 47.826 3.64 0.78 38.11 5.03
441 506 4.433615 TCGATGCAGATAAAACTGGACTC 58.566 43.478 0.00 0.00 40.64 3.36
442 507 4.160439 TCTCGATGCAGATAAAACTGGACT 59.840 41.667 0.00 0.00 40.64 3.85
492 557 8.462016 ACAGAAATCCAGTCAGCAAATTATTAC 58.538 33.333 0.00 0.00 0.00 1.89
496 571 6.899393 AACAGAAATCCAGTCAGCAAATTA 57.101 33.333 0.00 0.00 0.00 1.40
571 646 0.883833 AAAAGATCAGCGGCAACTGG 59.116 50.000 1.45 0.00 38.26 4.00
622 699 1.355971 TCGCGCACTAAAATGAGGTC 58.644 50.000 8.75 0.00 0.00 3.85
717 808 1.229428 TCTACTGCAACAGCAACAGC 58.771 50.000 0.00 0.00 37.91 4.40
720 811 2.095567 CACCATCTACTGCAACAGCAAC 60.096 50.000 0.00 0.00 37.91 4.17
721 812 2.153645 CACCATCTACTGCAACAGCAA 58.846 47.619 0.00 0.00 37.91 3.91
722 813 1.347378 TCACCATCTACTGCAACAGCA 59.653 47.619 0.00 0.00 34.37 4.41
724 815 4.456911 ACAAATCACCATCTACTGCAACAG 59.543 41.667 0.00 0.00 37.52 3.16
725 816 4.397420 ACAAATCACCATCTACTGCAACA 58.603 39.130 0.00 0.00 0.00 3.33
739 1268 3.315191 ACAGTGCTGTGGTTACAAATCAC 59.685 43.478 3.80 0.00 43.11 3.06
787 1318 5.551305 TCTGAACCTCTGAACTTTGATGA 57.449 39.130 0.00 0.00 0.00 2.92
788 1319 6.814506 ATTCTGAACCTCTGAACTTTGATG 57.185 37.500 0.00 0.00 37.20 3.07
789 1320 8.160106 AGTTATTCTGAACCTCTGAACTTTGAT 58.840 33.333 0.00 0.00 37.20 2.57
790 1321 7.442364 CAGTTATTCTGAACCTCTGAACTTTGA 59.558 37.037 10.11 0.00 46.27 2.69
791 1322 7.579726 CAGTTATTCTGAACCTCTGAACTTTG 58.420 38.462 10.11 0.00 46.27 2.77
792 1323 7.736447 CAGTTATTCTGAACCTCTGAACTTT 57.264 36.000 10.11 0.00 46.27 2.66
1003 1565 4.273480 CCAGGTATTTATACTGTGCTGCAC 59.727 45.833 25.15 25.15 33.81 4.57
1081 1643 0.450983 GCCATGTTCTTCAGCTCTGC 59.549 55.000 0.00 0.00 0.00 4.26
1250 1847 9.681062 CTCCTATAAGATTCCTACAAACCAAAA 57.319 33.333 0.00 0.00 0.00 2.44
1300 1911 1.481242 CCTTCAAACCAAAGGGGCTCT 60.481 52.381 0.00 0.00 42.05 4.09
1329 1940 5.364157 GGACCCTATCCTACATAGCAATAGG 59.636 48.000 13.62 13.62 45.22 2.57
1352 1963 5.726980 TCCTTTCAAATGTGAAGGATTGG 57.273 39.130 9.26 3.96 44.49 3.16
1440 2051 8.750515 TGACATGCATCTGAATTCCTATAAAA 57.249 30.769 2.27 0.00 0.00 1.52
1448 2059 6.561614 AGTGAAATGACATGCATCTGAATTC 58.438 36.000 0.00 0.00 35.78 2.17
1503 2114 5.445964 GGCCTTCTTTGGTTCATAGGATAA 58.554 41.667 0.00 0.00 0.00 1.75
1522 2133 0.182775 ACAACTCAAAGTTCCGGCCT 59.817 50.000 0.00 0.00 36.03 5.19
1527 2138 1.859998 GCACGCACAACTCAAAGTTCC 60.860 52.381 0.00 0.00 36.03 3.62
1528 2139 1.466855 GCACGCACAACTCAAAGTTC 58.533 50.000 0.00 0.00 36.03 3.01
1993 2611 3.636313 CTTCTGGACGCGCGGGTTA 62.636 63.158 35.22 20.02 0.00 2.85
2266 2884 1.956477 CCCTTGGTGGTGAAGTCAAAG 59.044 52.381 0.00 0.00 0.00 2.77
2269 2887 1.150536 GCCCTTGGTGGTGAAGTCA 59.849 57.895 0.00 0.00 0.00 3.41
2558 3192 3.566322 TCATCATTTCGGTCGTGGTTTTT 59.434 39.130 0.00 0.00 0.00 1.94
2574 3208 8.681486 TGGAGAATCACGATTATTTTCATCAT 57.319 30.769 0.00 0.00 36.25 2.45
2648 3283 0.984230 GGGTCCTGATTGACACCAGA 59.016 55.000 5.78 0.00 36.97 3.86
2715 3350 3.621558 TCTCAGCGAGATAAAGGTCAGA 58.378 45.455 4.47 0.00 33.35 3.27
2837 3472 7.706607 GGTAATTTTGCTCATATTTTCTCCCAC 59.293 37.037 0.00 0.00 0.00 4.61
3038 3681 3.444034 TCGGTTTTCATTCAACCAACACA 59.556 39.130 2.90 0.00 43.59 3.72
3073 3722 0.179119 ATGCAGCCGTACGAGTTACC 60.179 55.000 18.76 0.32 0.00 2.85
3074 3723 2.114825 GTATGCAGCCGTACGAGTTAC 58.885 52.381 18.76 6.00 0.00 2.50
3075 3724 1.066002 GGTATGCAGCCGTACGAGTTA 59.934 52.381 18.76 0.00 34.85 2.24
3076 3725 0.179119 GGTATGCAGCCGTACGAGTT 60.179 55.000 18.76 1.74 34.85 3.01
3077 3726 1.436336 GGTATGCAGCCGTACGAGT 59.564 57.895 18.76 0.00 34.85 4.18
3078 3727 1.657487 CGGTATGCAGCCGTACGAG 60.657 63.158 18.76 8.15 43.84 4.18
3088 3737 2.092267 TCTACCACTACTCCGGTATGCA 60.092 50.000 0.00 0.00 37.15 3.96
3114 3763 2.172851 ATTCCGTACCAAAACGCTCA 57.827 45.000 0.00 0.00 41.51 4.26
3125 3774 2.001872 CCCCGTAACACAATTCCGTAC 58.998 52.381 0.00 0.00 0.00 3.67
3157 3806 9.750783 AGTAACTAGACTATTAGTTTGTCTCCA 57.249 33.333 0.00 0.00 40.11 3.86
3199 3848 3.250762 CGGCAGATGAAAAAGTGACTGAA 59.749 43.478 0.00 0.00 0.00 3.02
3200 3849 2.807967 CGGCAGATGAAAAAGTGACTGA 59.192 45.455 0.00 0.00 0.00 3.41
3207 3856 8.964420 TCTTAATTTAACGGCAGATGAAAAAG 57.036 30.769 0.00 0.00 0.00 2.27
3208 3857 9.921637 AATCTTAATTTAACGGCAGATGAAAAA 57.078 25.926 0.00 0.00 0.00 1.94
3212 3861 9.997482 GTTTAATCTTAATTTAACGGCAGATGA 57.003 29.630 0.00 0.00 28.26 2.92
3213 3862 8.943925 CGTTTAATCTTAATTTAACGGCAGATG 58.056 33.333 12.15 0.00 46.32 2.90
3350 4000 1.362355 GGTGTTTTTGGGCCTCACG 59.638 57.895 4.53 0.00 0.00 4.35
3478 7985 1.274447 TCATCTAGCTCCATCCATGCG 59.726 52.381 0.00 0.00 0.00 4.73
3502 8009 7.386573 CCATATGGTTTAACAGATGTGCGTATA 59.613 37.037 14.09 0.00 38.15 1.47
3505 8012 4.335315 CCATATGGTTTAACAGATGTGCGT 59.665 41.667 14.09 0.00 38.15 5.24
3506 8013 4.847633 CCATATGGTTTAACAGATGTGCG 58.152 43.478 14.09 0.00 38.15 5.34
3560 8078 8.773404 ATATATATACTCGTTTTTGGAGCACC 57.227 34.615 0.00 0.00 34.87 5.01
3749 8282 1.540707 TCATGCTTGCGCTGAATTCAA 59.459 42.857 9.73 0.00 36.97 2.69


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

AutoCloner maintained by Alex Coulton.