Multiple sequence alignment - TraesCS7B01G310600

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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 TraesCS7B01G310600 chr7B 100.000 3435 0 0 1 3435 555654843 555658277 0.000000e+00 6344
1 TraesCS7B01G310600 chr7B 80.169 590 75 22 1242 1826 556333129 556332577 1.480000e-108 403
2 TraesCS7B01G310600 chr7B 78.197 477 66 15 674 1143 556333680 556333235 1.570000e-68 270
3 TraesCS7B01G310600 chr7D 90.999 2133 125 33 59 2134 521762841 521764963 0.000000e+00 2813
4 TraesCS7B01G310600 chr7D 83.699 730 59 26 2125 2816 521764990 521765697 4.840000e-178 634
5 TraesCS7B01G310600 chr7D 85.685 482 42 7 2959 3435 521765819 521766278 1.850000e-132 483
6 TraesCS7B01G310600 chr7D 78.488 688 84 24 1152 1829 522154542 522153909 3.210000e-105 392
7 TraesCS7B01G310600 chr7A 92.845 1216 54 6 1 1212 602098154 602099340 0.000000e+00 1733
8 TraesCS7B01G310600 chr7A 92.083 720 42 8 1239 1945 602099335 602100052 0.000000e+00 1000
9 TraesCS7B01G310600 chr7A 82.613 1087 100 37 1956 2981 602100094 602101152 0.000000e+00 878
10 TraesCS7B01G310600 chr7A 79.229 597 68 25 1242 1829 602658495 602657946 7.010000e-97 364
11 TraesCS7B01G310600 chr7A 78.571 476 53 20 674 1143 602659033 602658601 5.650000e-68 268
12 TraesCS7B01G310600 chr1D 76.812 414 49 26 148 551 37528511 37528135 4.530000e-44 189


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 TraesCS7B01G310600 chr7B 555654843 555658277 3434 False 6344.000000 6344 100.000000 1 3435 1 chr7B.!!$F1 3434
1 TraesCS7B01G310600 chr7B 556332577 556333680 1103 True 336.500000 403 79.183000 674 1826 2 chr7B.!!$R1 1152
2 TraesCS7B01G310600 chr7D 521762841 521766278 3437 False 1310.000000 2813 86.794333 59 3435 3 chr7D.!!$F1 3376
3 TraesCS7B01G310600 chr7D 522153909 522154542 633 True 392.000000 392 78.488000 1152 1829 1 chr7D.!!$R1 677
4 TraesCS7B01G310600 chr7A 602098154 602101152 2998 False 1203.666667 1733 89.180333 1 2981 3 chr7A.!!$F1 2980
5 TraesCS7B01G310600 chr7A 602657946 602659033 1087 True 316.000000 364 78.900000 674 1829 2 chr7A.!!$R1 1155

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
630 646 0.943673 CCAACGACATGCACACAGAA 59.056 50.0 0.00 0.00 0.0 3.02 F
1311 1404 0.032615 AAGAGGCTCCTGGAGATCGT 60.033 55.0 27.53 17.71 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1635 1.466856 TACTAGCACTACCACCGGTG 58.533 55.0 28.26 28.26 36.19 4.94 R
3176 3490 0.039165 CAAGGCGCAGAAGAAAACCC 60.039 55.0 10.83 0.00 0.00 4.11 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
43 46 5.007682 AGGCGCTTTTCCTTCTTGTAAATA 58.992 37.500 7.64 0.00 0.00 1.40
48 51 7.218963 GCGCTTTTCCTTCTTGTAAATATTCTG 59.781 37.037 0.00 0.00 0.00 3.02
50 53 8.028938 GCTTTTCCTTCTTGTAAATATTCTGCA 58.971 33.333 0.00 0.00 0.00 4.41
51 54 9.565213 CTTTTCCTTCTTGTAAATATTCTGCAG 57.435 33.333 7.63 7.63 0.00 4.41
52 55 8.862325 TTTCCTTCTTGTAAATATTCTGCAGA 57.138 30.769 13.74 13.74 0.00 4.26
53 56 8.862325 TTCCTTCTTGTAAATATTCTGCAGAA 57.138 30.769 30.23 30.23 38.56 3.02
54 57 8.862325 TCCTTCTTGTAAATATTCTGCAGAAA 57.138 30.769 31.55 20.53 37.61 2.52
55 58 8.730680 TCCTTCTTGTAAATATTCTGCAGAAAC 58.269 33.333 31.55 23.73 37.61 2.78
56 59 8.514594 CCTTCTTGTAAATATTCTGCAGAAACA 58.485 33.333 31.55 25.85 37.61 2.83
57 60 9.334693 CTTCTTGTAAATATTCTGCAGAAACAC 57.665 33.333 31.55 22.26 37.61 3.32
58 61 8.621532 TCTTGTAAATATTCTGCAGAAACACT 57.378 30.769 31.55 18.18 37.61 3.55
59 62 9.719355 TCTTGTAAATATTCTGCAGAAACACTA 57.281 29.630 31.55 19.71 37.61 2.74
60 63 9.760660 CTTGTAAATATTCTGCAGAAACACTAC 57.239 33.333 31.55 25.94 37.61 2.73
61 64 9.502091 TTGTAAATATTCTGCAGAAACACTACT 57.498 29.630 31.55 16.39 37.61 2.57
62 65 9.151471 TGTAAATATTCTGCAGAAACACTACTC 57.849 33.333 31.55 17.53 37.61 2.59
63 66 7.617041 AAATATTCTGCAGAAACACTACTCC 57.383 36.000 31.55 0.00 37.61 3.85
196 201 7.399191 AGGGTGACAAGTGATGTATCTACTTTA 59.601 37.037 0.00 0.00 44.12 1.85
284 292 4.395959 TCTCATAACCCGACAATGTACC 57.604 45.455 0.00 0.00 0.00 3.34
301 309 8.641541 ACAATGTACCATTTTCTTTCAGAATGT 58.358 29.630 0.00 0.00 33.67 2.71
359 367 7.064134 TCCTTGCTATTTTGTACTGATGTAACG 59.936 37.037 0.00 0.00 0.00 3.18
367 375 3.194116 TGTACTGATGTAACGGTTCCTCC 59.806 47.826 0.00 0.00 0.00 4.30
476 485 4.899239 CCCCTGCTGATCGGACGC 62.899 72.222 5.48 0.00 0.00 5.19
477 486 4.147449 CCCTGCTGATCGGACGCA 62.147 66.667 5.48 2.20 0.00 5.24
481 490 2.887568 GCTGATCGGACGCACCTG 60.888 66.667 5.48 0.00 36.31 4.00
553 562 2.507484 CTGCCTGTGGTCTCAAAATCA 58.493 47.619 0.00 0.00 0.00 2.57
597 613 3.252979 CACATGTGGTGGAGCATCA 57.747 52.632 18.51 0.00 44.04 3.07
607 623 2.502295 GTGGAGCATCATGGAATCTCC 58.498 52.381 13.62 13.62 42.67 3.71
630 646 0.943673 CCAACGACATGCACACAGAA 59.056 50.000 0.00 0.00 0.00 3.02
716 736 1.399440 CGGAAACATCAGTGATGCCAG 59.601 52.381 29.10 16.59 43.15 4.85
718 738 3.084039 GGAAACATCAGTGATGCCAGAA 58.916 45.455 29.10 0.00 43.15 3.02
722 742 1.404391 CATCAGTGATGCCAGAAAGCC 59.596 52.381 19.79 0.00 33.17 4.35
840 865 1.073897 GGGTGAGAAAGGCACAGCT 59.926 57.895 0.00 0.00 37.99 4.24
965 990 2.509916 GCTCTCCAGCATCCAGGG 59.490 66.667 0.00 0.00 46.06 4.45
1038 1063 0.386113 GGGCACCGAGTCTATCTCAC 59.614 60.000 0.00 0.00 42.88 3.51
1047 1072 4.454161 CCGAGTCTATCTCACGATGAAGAT 59.546 45.833 0.00 0.00 42.88 2.40
1050 1075 6.588373 CGAGTCTATCTCACGATGAAGATAGA 59.412 42.308 14.88 14.88 42.88 1.98
1197 1252 5.359576 TCAATCTCCTCTTTGCTCTCTACTC 59.640 44.000 0.00 0.00 0.00 2.59
1212 1305 8.629158 TGCTCTCTACTCTCTTCATATTTCTTC 58.371 37.037 0.00 0.00 0.00 2.87
1213 1306 8.629158 GCTCTCTACTCTCTTCATATTTCTTCA 58.371 37.037 0.00 0.00 0.00 3.02
1215 1308 9.130661 TCTCTACTCTCTTCATATTTCTTCAGG 57.869 37.037 0.00 0.00 0.00 3.86
1216 1309 8.830915 TCTACTCTCTTCATATTTCTTCAGGT 57.169 34.615 0.00 0.00 0.00 4.00
1217 1310 9.261035 TCTACTCTCTTCATATTTCTTCAGGTT 57.739 33.333 0.00 0.00 0.00 3.50
1218 1311 9.528018 CTACTCTCTTCATATTTCTTCAGGTTC 57.472 37.037 0.00 0.00 0.00 3.62
1219 1312 7.911651 ACTCTCTTCATATTTCTTCAGGTTCA 58.088 34.615 0.00 0.00 0.00 3.18
1220 1313 8.040132 ACTCTCTTCATATTTCTTCAGGTTCAG 58.960 37.037 0.00 0.00 0.00 3.02
1221 1314 6.820656 TCTCTTCATATTTCTTCAGGTTCAGC 59.179 38.462 0.00 0.00 0.00 4.26
1222 1315 5.882557 TCTTCATATTTCTTCAGGTTCAGCC 59.117 40.000 0.00 0.00 37.58 4.85
1231 1324 4.421365 GGTTCAGCCTTGCCATGA 57.579 55.556 0.00 0.00 0.00 3.07
1232 1325 2.187073 GGTTCAGCCTTGCCATGAG 58.813 57.895 0.00 0.00 0.00 2.90
1233 1326 1.318158 GGTTCAGCCTTGCCATGAGG 61.318 60.000 0.00 0.00 37.35 3.86
1251 1344 2.744741 GAGGCCAGTCTCTTACAAAAGC 59.255 50.000 5.01 0.00 32.36 3.51
1252 1345 1.464997 GGCCAGTCTCTTACAAAAGCG 59.535 52.381 0.00 0.00 32.36 4.68
1309 1402 0.106521 GCAAGAGGCTCCTGGAGATC 59.893 60.000 27.53 21.54 40.25 2.75
1311 1404 0.032615 AAGAGGCTCCTGGAGATCGT 60.033 55.000 27.53 17.71 0.00 3.73
1315 1408 1.067250 GCTCCTGGAGATCGTGAGC 59.933 63.158 27.53 6.21 41.31 4.26
1317 1410 2.069465 CTCCTGGAGATCGTGAGCCG 62.069 65.000 19.13 0.00 38.13 5.52
1422 1515 3.414700 GAACACGAGGCCGCACAG 61.415 66.667 7.44 0.00 39.95 3.66
1537 1635 7.316640 TCAGCTTCTAAAGTACTGATCTTGTC 58.683 38.462 0.00 0.00 32.65 3.18
1538 1636 7.039714 TCAGCTTCTAAAGTACTGATCTTGTCA 60.040 37.037 0.00 0.00 32.65 3.58
1540 1638 6.311690 GCTTCTAAAGTACTGATCTTGTCACC 59.688 42.308 0.00 0.00 32.22 4.02
1604 1704 9.777297 AGAAATTGTTTGCCTATAATGTTTGTT 57.223 25.926 0.00 0.00 0.00 2.83
1645 1751 9.899661 ATGTTGTTTACTGGCTAGTATTTATCA 57.100 29.630 11.07 8.63 39.08 2.15
1664 1787 3.723260 TCATGTCTGTGTGCTTCGTAAA 58.277 40.909 0.00 0.00 0.00 2.01
1725 1851 5.415077 CCGGATTATCGTCCTATAACAGTCT 59.585 44.000 0.00 0.00 36.07 3.24
1726 1852 6.315551 CGGATTATCGTCCTATAACAGTCTG 58.684 44.000 0.00 0.00 36.07 3.51
1794 1920 9.752961 CAATTGGAATTCAGACATTGCATATAA 57.247 29.630 7.93 0.00 34.78 0.98
1887 2017 2.730069 TGCAAGTCTTTGACATTTGCG 58.270 42.857 15.05 0.00 42.59 4.85
1888 2018 2.098934 TGCAAGTCTTTGACATTTGCGT 59.901 40.909 15.05 0.00 42.59 5.24
1900 2030 1.200716 CATTTGCGTGCAGAGGACAAT 59.799 47.619 0.00 0.00 0.00 2.71
1901 2031 1.317613 TTTGCGTGCAGAGGACAATT 58.682 45.000 0.00 0.00 0.00 2.32
1902 2032 1.317613 TTGCGTGCAGAGGACAATTT 58.682 45.000 0.00 0.00 0.00 1.82
1904 2034 1.680735 TGCGTGCAGAGGACAATTTTT 59.319 42.857 0.00 0.00 0.00 1.94
1936 2072 2.216898 GGAGATGCAGTATGGAAGCAC 58.783 52.381 0.00 0.00 42.43 4.40
1972 2139 6.539826 TCTTGTCATGGATGTTAGCAGTATTG 59.460 38.462 0.00 0.00 0.00 1.90
2111 2286 3.945346 GTGGGTACACACATACCAATGA 58.055 45.455 23.43 0.00 45.72 2.57
2126 2301 2.420547 CCAATGAGCAAATCGGAGAGGA 60.421 50.000 0.00 0.00 43.63 3.71
2128 2303 4.503817 CCAATGAGCAAATCGGAGAGGATA 60.504 45.833 0.00 0.00 43.63 2.59
2129 2304 4.963318 ATGAGCAAATCGGAGAGGATAA 57.037 40.909 0.00 0.00 43.63 1.75
2154 2367 6.463995 ACAAATTGTAACACACTCCACATT 57.536 33.333 0.00 0.00 0.00 2.71
2183 2396 8.208718 AGTTTTGCTAGCGATGAATTTACATA 57.791 30.769 10.77 0.00 0.00 2.29
2228 2441 8.897752 AGCATATCAGGTCATTAGAAAAAGAAC 58.102 33.333 0.00 0.00 0.00 3.01
2234 2447 7.661847 TCAGGTCATTAGAAAAAGAACCTTCTC 59.338 37.037 0.00 0.00 36.28 2.87
2440 2696 8.821894 GCGGGATTTAATTGTAATAAAATGCAA 58.178 29.630 0.00 0.00 33.03 4.08
2457 2713 7.489574 AAATGCAAATAAACAATTCCAACGT 57.510 28.000 0.00 0.00 0.00 3.99
2458 2714 5.896922 TGCAAATAAACAATTCCAACGTG 57.103 34.783 0.00 0.00 0.00 4.49
2463 2719 6.464895 AATAAACAATTCCAACGTGCATTG 57.535 33.333 0.00 0.00 33.58 2.82
2638 2899 9.442047 TGATTTTAAAAGTTGACCACACATTTT 57.558 25.926 6.79 0.00 32.46 1.82
2753 3020 9.916397 AAATATCGTCATAGTTCGTGATTTTTC 57.084 29.630 0.00 0.00 0.00 2.29
2757 3024 8.523523 TCGTCATAGTTCGTGATTTTTCTAAA 57.476 30.769 0.00 0.00 0.00 1.85
2758 3025 8.980610 TCGTCATAGTTCGTGATTTTTCTAAAA 58.019 29.630 0.00 0.00 0.00 1.52
2822 3089 7.985184 ACTCATACAACTAGAAAAGTGTTCACA 59.015 33.333 0.00 0.00 38.88 3.58
3027 3337 9.634021 GGGAAAGGATAATCAGAAAATAGAACT 57.366 33.333 0.00 0.00 0.00 3.01
3086 3398 3.399181 GTCATCCTGGTCGGCCCA 61.399 66.667 2.12 0.00 42.51 5.36
3089 3401 1.825191 CATCCTGGTCGGCCCAATG 60.825 63.158 2.12 0.12 44.65 2.82
3092 3404 2.819595 CTGGTCGGCCCAATGACG 60.820 66.667 2.12 0.00 44.65 4.35
3131 3445 1.152860 TTTCACAAGAAGCGGCCCA 60.153 52.632 0.00 0.00 34.71 5.36
3138 3452 1.334869 CAAGAAGCGGCCCATAATGTC 59.665 52.381 0.00 0.00 0.00 3.06
3139 3453 0.179018 AGAAGCGGCCCATAATGTCC 60.179 55.000 0.00 0.00 0.00 4.02
3162 3476 0.843343 GTGTCTTCCCCACCCCCTTA 60.843 60.000 0.00 0.00 0.00 2.69
3163 3477 0.103823 TGTCTTCCCCACCCCCTTAA 60.104 55.000 0.00 0.00 0.00 1.85
3176 3490 1.452108 CCTTAAGGGCCGCTTGAGG 60.452 63.158 22.05 22.05 32.54 3.86
3185 3499 3.036431 CCGCTTGAGGGGTTTTCTT 57.964 52.632 5.97 0.00 42.54 2.52
3189 3503 1.270826 GCTTGAGGGGTTTTCTTCTGC 59.729 52.381 0.00 0.00 0.00 4.26
3214 3528 0.749454 GGTCCACATGATGACCTGGC 60.749 60.000 22.79 7.18 46.13 4.85
3272 3586 3.373748 TGACTAGCGTATGCATTTTGTGG 59.626 43.478 3.54 0.00 46.23 4.17
3275 3589 1.885887 AGCGTATGCATTTTGTGGTGT 59.114 42.857 3.54 0.00 46.23 4.16
3281 3595 5.404968 CGTATGCATTTTGTGGTGTTGAAAT 59.595 36.000 3.54 0.00 0.00 2.17
3299 3613 7.092891 TGTTGAAATATGAGGTCATGTAGGACT 60.093 37.037 2.56 0.00 37.91 3.85
3302 3616 8.421784 TGAAATATGAGGTCATGTAGGACTTAC 58.578 37.037 2.56 0.00 37.91 2.34
3307 3621 5.421056 TGAGGTCATGTAGGACTTACGAAAT 59.579 40.000 0.00 0.00 37.91 2.17
3332 3646 7.790823 ATGTATTCATTGTCAATCATCGTCA 57.209 32.000 0.00 0.00 0.00 4.35
3333 3647 7.003939 TGTATTCATTGTCAATCATCGTCAC 57.996 36.000 0.00 0.00 0.00 3.67
3334 3648 6.593382 TGTATTCATTGTCAATCATCGTCACA 59.407 34.615 0.00 0.00 0.00 3.58
3335 3649 6.688637 ATTCATTGTCAATCATCGTCACAT 57.311 33.333 0.00 0.00 0.00 3.21
3336 3650 5.723492 TCATTGTCAATCATCGTCACATC 57.277 39.130 0.00 0.00 0.00 3.06
3337 3651 4.268405 TCATTGTCAATCATCGTCACATCG 59.732 41.667 0.00 0.00 0.00 3.84
3338 3652 3.502191 TGTCAATCATCGTCACATCGA 57.498 42.857 0.00 0.00 43.86 3.59
3357 3671 1.876497 ATTGGTCATGCGGTGTTGGC 61.876 55.000 0.00 0.00 0.00 4.52
3372 3686 2.643272 GGCGTGAGACGTGTGAGA 59.357 61.111 0.00 0.00 44.73 3.27
3381 3695 5.798434 CGTGAGACGTGTGAGAAATAATGTA 59.202 40.000 0.00 0.00 36.74 2.29
3396 3710 6.506538 AATAATGTAGATCTGGCTCTTGGT 57.493 37.500 5.18 0.00 0.00 3.67
3401 3715 4.402793 TGTAGATCTGGCTCTTGGTTCTAC 59.597 45.833 5.18 0.00 36.32 2.59
3409 3723 4.141482 TGGCTCTTGGTTCTACAACTCTTT 60.141 41.667 0.00 0.00 32.50 2.52
3414 3728 6.110707 TCTTGGTTCTACAACTCTTTCGTTT 58.889 36.000 0.00 0.00 32.50 3.60
3431 3746 5.607119 TCGTTTTATGGCTTCTTCTTCAC 57.393 39.130 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.565213 CTGCAGAATATTTACAAGAAGGAAAAG 57.435 33.333 8.42 0.00 0.00 2.27
26 27 9.295825 TCTGCAGAATATTTACAAGAAGGAAAA 57.704 29.630 15.67 0.00 0.00 2.29
43 46 4.623932 TGGAGTAGTGTTTCTGCAGAAT 57.376 40.909 28.89 16.79 33.54 2.40
48 51 1.443802 GGCTGGAGTAGTGTTTCTGC 58.556 55.000 0.00 0.00 0.00 4.26
50 53 1.625818 CTGGGCTGGAGTAGTGTTTCT 59.374 52.381 0.00 0.00 0.00 2.52
51 54 1.623811 TCTGGGCTGGAGTAGTGTTTC 59.376 52.381 0.00 0.00 0.00 2.78
52 55 1.729586 TCTGGGCTGGAGTAGTGTTT 58.270 50.000 0.00 0.00 0.00 2.83
53 56 1.729586 TTCTGGGCTGGAGTAGTGTT 58.270 50.000 0.00 0.00 0.00 3.32
54 57 1.729586 TTTCTGGGCTGGAGTAGTGT 58.270 50.000 0.00 0.00 0.00 3.55
55 58 4.192317 GTTATTTCTGGGCTGGAGTAGTG 58.808 47.826 0.00 0.00 0.00 2.74
56 59 3.118738 CGTTATTTCTGGGCTGGAGTAGT 60.119 47.826 0.00 0.00 0.00 2.73
57 60 3.118738 ACGTTATTTCTGGGCTGGAGTAG 60.119 47.826 0.00 0.00 0.00 2.57
58 61 2.835764 ACGTTATTTCTGGGCTGGAGTA 59.164 45.455 0.00 0.00 0.00 2.59
59 62 1.628846 ACGTTATTTCTGGGCTGGAGT 59.371 47.619 0.00 0.00 0.00 3.85
60 63 2.280628 GACGTTATTTCTGGGCTGGAG 58.719 52.381 0.00 0.00 0.00 3.86
61 64 1.065709 GGACGTTATTTCTGGGCTGGA 60.066 52.381 0.00 0.00 0.00 3.86
62 65 1.339631 TGGACGTTATTTCTGGGCTGG 60.340 52.381 0.00 0.00 0.00 4.85
63 66 1.737793 GTGGACGTTATTTCTGGGCTG 59.262 52.381 0.00 0.00 0.00 4.85
249 257 7.123098 TCGGGTTATGAGAAGTTTGTACAGATA 59.877 37.037 0.00 0.00 0.00 1.98
301 309 7.594758 GCTGCATCAGTAAAAACAATTCTTACA 59.405 33.333 0.00 0.00 33.43 2.41
342 350 5.613329 AGGAACCGTTACATCAGTACAAAA 58.387 37.500 0.00 0.00 0.00 2.44
359 367 0.171231 GCATTTTCTGCGGAGGAACC 59.829 55.000 3.37 0.00 41.97 3.62
476 485 2.089980 CTCCTCCATGAAAAGCAGGTG 58.910 52.381 0.00 0.00 0.00 4.00
477 486 1.988107 TCTCCTCCATGAAAAGCAGGT 59.012 47.619 0.00 0.00 0.00 4.00
481 490 4.148128 TCTCATCTCCTCCATGAAAAGC 57.852 45.455 0.00 0.00 29.74 3.51
597 613 1.819632 GTTGGCGCGGAGATTCCAT 60.820 57.895 8.83 0.00 35.91 3.41
716 736 2.882927 ACTTTTGTTTCGGGGCTTTC 57.117 45.000 0.00 0.00 0.00 2.62
840 865 1.537397 AGCTGGAGAGGTGCCTTGA 60.537 57.895 0.00 0.00 0.00 3.02
965 990 4.422840 GAGGCTCGTCTAGTCTTTTAACC 58.577 47.826 0.00 0.00 41.43 2.85
1011 1036 2.046892 CTCGGTGCCCAACAGAGG 60.047 66.667 0.00 0.00 44.62 3.69
1038 1063 2.873609 CGAGGGCATCTATCTTCATCG 58.126 52.381 0.00 0.00 0.00 3.84
1047 1072 1.323412 GAAGAGAGCGAGGGCATCTA 58.677 55.000 0.00 0.00 43.41 1.98
1050 1075 1.382420 AGGAAGAGAGCGAGGGCAT 60.382 57.895 0.00 0.00 43.41 4.40
1197 1252 6.038050 GGCTGAACCTGAAGAAATATGAAGAG 59.962 42.308 0.00 0.00 34.51 2.85
1214 1307 1.318158 CCTCATGGCAAGGCTGAACC 61.318 60.000 0.00 0.00 39.61 3.62
1215 1308 2.187073 CCTCATGGCAAGGCTGAAC 58.813 57.895 0.00 0.00 0.00 3.18
1216 1309 4.749323 CCTCATGGCAAGGCTGAA 57.251 55.556 0.00 0.00 0.00 3.02
1226 1319 1.833630 TGTAAGAGACTGGCCTCATGG 59.166 52.381 3.32 0.00 35.68 3.66
1227 1320 3.616956 TTGTAAGAGACTGGCCTCATG 57.383 47.619 3.32 0.00 35.68 3.07
1228 1321 4.583871 CTTTTGTAAGAGACTGGCCTCAT 58.416 43.478 3.32 0.00 35.68 2.90
1229 1322 3.807209 GCTTTTGTAAGAGACTGGCCTCA 60.807 47.826 3.32 0.00 35.68 3.86
1230 1323 2.744741 GCTTTTGTAAGAGACTGGCCTC 59.255 50.000 3.32 0.00 32.92 4.70
1231 1324 2.784347 GCTTTTGTAAGAGACTGGCCT 58.216 47.619 3.32 0.00 32.92 5.19
1232 1325 1.464997 CGCTTTTGTAAGAGACTGGCC 59.535 52.381 0.00 0.00 33.52 5.36
1233 1326 2.143925 ACGCTTTTGTAAGAGACTGGC 58.856 47.619 0.00 0.00 35.44 4.85
1234 1327 3.186613 GGAACGCTTTTGTAAGAGACTGG 59.813 47.826 0.00 0.00 35.44 4.00
1235 1328 4.058817 AGGAACGCTTTTGTAAGAGACTG 58.941 43.478 0.00 0.00 35.44 3.51
1236 1329 4.058817 CAGGAACGCTTTTGTAAGAGACT 58.941 43.478 0.00 0.00 35.44 3.24
1237 1330 3.186613 CCAGGAACGCTTTTGTAAGAGAC 59.813 47.826 0.00 0.00 35.44 3.36
1238 1331 3.070446 TCCAGGAACGCTTTTGTAAGAGA 59.930 43.478 0.00 0.00 35.44 3.10
1239 1332 3.399330 TCCAGGAACGCTTTTGTAAGAG 58.601 45.455 0.00 0.00 37.23 2.85
1240 1333 3.478857 TCCAGGAACGCTTTTGTAAGA 57.521 42.857 0.00 0.00 32.92 2.10
1241 1334 3.564225 AGTTCCAGGAACGCTTTTGTAAG 59.436 43.478 24.13 0.00 45.96 2.34
1242 1335 3.314080 CAGTTCCAGGAACGCTTTTGTAA 59.686 43.478 24.13 0.00 45.96 2.41
1243 1336 2.875933 CAGTTCCAGGAACGCTTTTGTA 59.124 45.455 24.13 0.00 45.96 2.41
1251 1344 3.423154 GCGGCAGTTCCAGGAACG 61.423 66.667 24.13 19.49 45.96 3.95
1252 1345 0.321298 TAAGCGGCAGTTCCAGGAAC 60.321 55.000 23.26 23.26 42.25 3.62
1317 1410 2.598394 TGTGCCCAAGCTTCCTGC 60.598 61.111 0.00 0.00 40.80 4.85
1537 1635 1.466856 TACTAGCACTACCACCGGTG 58.533 55.000 28.26 28.26 36.19 4.94
1538 1636 2.091994 AGATACTAGCACTACCACCGGT 60.092 50.000 0.00 0.00 40.16 5.28
1540 1638 2.950309 ACAGATACTAGCACTACCACCG 59.050 50.000 0.00 0.00 0.00 4.94
1604 1704 7.926018 AGTAAACAACATATCAGCACGATATCA 59.074 33.333 3.12 0.00 44.10 2.15
1645 1751 4.997395 AGAATTTACGAAGCACACAGACAT 59.003 37.500 0.00 0.00 0.00 3.06
1697 1823 6.240894 TGTTATAGGACGATAATCCGGTACT 58.759 40.000 0.00 0.00 44.22 2.73
1725 1851 8.139350 CGATTCCTTGGTGTACATACTTATACA 58.861 37.037 0.00 0.00 0.00 2.29
1726 1852 8.355169 TCGATTCCTTGGTGTACATACTTATAC 58.645 37.037 0.00 0.00 0.00 1.47
1794 1920 5.014858 GGATGCCAGGATATGTCATTTCAT 58.985 41.667 5.75 0.00 0.00 2.57
1874 2004 2.313234 CTCTGCACGCAAATGTCAAAG 58.687 47.619 0.00 0.00 0.00 2.77
1904 2034 8.415553 CCATACTGCATCTCCATAATTCAAAAA 58.584 33.333 0.00 0.00 0.00 1.94
1911 2041 5.221986 TGCTTCCATACTGCATCTCCATAAT 60.222 40.000 0.00 0.00 0.00 1.28
1916 2052 2.216898 GTGCTTCCATACTGCATCTCC 58.783 52.381 0.00 0.00 39.00 3.71
1925 2061 3.815401 ACTGTTCAGTTGTGCTTCCATAC 59.185 43.478 0.00 0.00 0.00 2.39
1936 2072 4.129380 TCCATGACAAGACTGTTCAGTTG 58.871 43.478 6.91 5.22 35.30 3.16
1972 2139 8.045176 ACTTAGAAAATCTGACATAAGTTGGC 57.955 34.615 0.00 0.00 31.25 4.52
2066 2241 9.703892 CACTGAGCATATTCTAAGTTAGCTAAT 57.296 33.333 9.88 3.91 0.00 1.73
2104 2279 2.636830 CTCTCCGATTTGCTCATTGGT 58.363 47.619 2.80 0.00 0.00 3.67
2106 2281 2.910199 TCCTCTCCGATTTGCTCATTG 58.090 47.619 0.00 0.00 0.00 2.82
2111 2286 4.843728 TGTTTTATCCTCTCCGATTTGCT 58.156 39.130 0.00 0.00 0.00 3.91
2126 2301 8.470805 TGTGGAGTGTGTTACAATTTGTTTTAT 58.529 29.630 7.45 0.00 0.00 1.40
2128 2303 6.692486 TGTGGAGTGTGTTACAATTTGTTTT 58.308 32.000 7.45 0.00 0.00 2.43
2129 2304 6.274157 TGTGGAGTGTGTTACAATTTGTTT 57.726 33.333 7.45 0.00 0.00 2.83
2183 2396 6.664428 ATGCTATTTGGTGTGTTTAAAGGT 57.336 33.333 0.00 0.00 0.00 3.50
2228 2441 5.468072 CAGTTCCAATATCAATCCGAGAAGG 59.532 44.000 0.00 0.00 42.97 3.46
2234 2447 7.483307 ACAATTTCAGTTCCAATATCAATCCG 58.517 34.615 0.00 0.00 0.00 4.18
2440 2696 6.219473 TCAATGCACGTTGGAATTGTTTATT 58.781 32.000 6.51 0.00 0.00 1.40
2457 2713 7.714377 TCTTTCTAAAAATGGCTTTTCAATGCA 59.286 29.630 0.00 0.00 38.26 3.96
2458 2714 8.086851 TCTTTCTAAAAATGGCTTTTCAATGC 57.913 30.769 0.00 0.00 38.26 3.56
2608 2869 6.020995 GTGTGGTCAACTTTTAAAATCACACG 60.021 38.462 14.40 0.68 41.51 4.49
2760 3027 8.503196 TGCGCGATGACTATTTAAATAAATGAT 58.497 29.630 12.10 1.06 36.62 2.45
2761 3028 7.856556 TGCGCGATGACTATTTAAATAAATGA 58.143 30.769 12.10 0.00 36.62 2.57
2762 3029 8.659569 ATGCGCGATGACTATTTAAATAAATG 57.340 30.769 12.10 1.15 36.62 2.32
2767 3034 9.509855 TTTTAAATGCGCGATGACTATTTAAAT 57.490 25.926 22.28 5.89 40.20 1.40
2797 3064 8.365399 TGTGAACACTTTTCTAGTTGTATGAG 57.635 34.615 6.51 0.00 33.85 2.90
2888 3156 8.981647 ACATTTTGAAAGATGCATGAAGTTTAC 58.018 29.630 2.46 0.00 0.00 2.01
2893 3161 8.529102 CGATAACATTTTGAAAGATGCATGAAG 58.471 33.333 2.46 0.00 0.00 3.02
2903 3171 9.726034 GCAAAATACACGATAACATTTTGAAAG 57.274 29.630 18.02 0.00 45.03 2.62
2907 3175 9.855361 TTTTGCAAAATACACGATAACATTTTG 57.145 25.926 20.46 12.12 45.02 2.44
3013 3323 9.573166 TCATTTTTCTCCAGTTCTATTTTCTGA 57.427 29.630 0.00 0.00 0.00 3.27
3027 3337 3.387374 TGCTGGCTTTTCATTTTTCTCCA 59.613 39.130 0.00 0.00 0.00 3.86
3028 3338 3.993920 TGCTGGCTTTTCATTTTTCTCC 58.006 40.909 0.00 0.00 0.00 3.71
3092 3404 4.962122 CATATTGGCCGCACGCGC 62.962 66.667 5.73 0.00 38.94 6.86
3094 3406 1.157870 ACTACATATTGGCCGCACGC 61.158 55.000 0.00 0.00 0.00 5.34
3102 3416 6.250819 CGCTTCTTGTGAAACTACATATTGG 58.749 40.000 0.00 0.00 38.04 3.16
3131 3445 2.420129 GGGAAGACACTGCGGACATTAT 60.420 50.000 0.00 0.00 0.00 1.28
3138 3452 2.358737 GTGGGGAAGACACTGCGG 60.359 66.667 0.00 0.00 35.98 5.69
3139 3453 2.358737 GGTGGGGAAGACACTGCG 60.359 66.667 0.00 0.00 38.83 5.18
3176 3490 0.039165 CAAGGCGCAGAAGAAAACCC 60.039 55.000 10.83 0.00 0.00 4.11
3185 3499 2.894257 ATGTGGACCAAGGCGCAGA 61.894 57.895 10.83 0.00 0.00 4.26
3189 3503 0.392863 TCATCATGTGGACCAAGGCG 60.393 55.000 0.00 0.00 0.00 5.52
3212 3526 0.878523 GGCCAAACAAAAGGAACGCC 60.879 55.000 0.00 0.00 0.00 5.68
3214 3528 0.461961 TGGGCCAAACAAAAGGAACG 59.538 50.000 2.13 0.00 0.00 3.95
3253 3567 3.126858 ACACCACAAAATGCATACGCTAG 59.873 43.478 0.00 0.00 39.64 3.42
3254 3568 3.078097 ACACCACAAAATGCATACGCTA 58.922 40.909 0.00 0.00 39.64 4.26
3255 3569 1.885887 ACACCACAAAATGCATACGCT 59.114 42.857 0.00 0.00 39.64 5.07
3256 3570 2.346099 ACACCACAAAATGCATACGC 57.654 45.000 0.00 0.00 39.24 4.42
3257 3571 3.894920 TCAACACCACAAAATGCATACG 58.105 40.909 0.00 0.00 0.00 3.06
3258 3572 6.783892 ATTTCAACACCACAAAATGCATAC 57.216 33.333 0.00 0.00 0.00 2.39
3259 3573 8.309656 TCATATTTCAACACCACAAAATGCATA 58.690 29.630 0.00 0.00 0.00 3.14
3260 3574 7.160049 TCATATTTCAACACCACAAAATGCAT 58.840 30.769 0.00 0.00 0.00 3.96
3261 3575 6.519382 TCATATTTCAACACCACAAAATGCA 58.481 32.000 0.00 0.00 0.00 3.96
3272 3586 7.011482 GTCCTACATGACCTCATATTTCAACAC 59.989 40.741 0.00 0.00 34.26 3.32
3275 3589 7.437713 AGTCCTACATGACCTCATATTTCAA 57.562 36.000 0.00 0.00 35.83 2.69
3281 3595 5.687780 TCGTAAGTCCTACATGACCTCATA 58.312 41.667 0.00 0.00 35.83 2.15
3307 3621 8.764287 GTGACGATGATTGACAATGAATACATA 58.236 33.333 5.14 0.00 35.50 2.29
3327 3641 2.539476 CATGACCAATCGATGTGACGA 58.461 47.619 0.00 0.00 46.04 4.20
3328 3642 1.004610 GCATGACCAATCGATGTGACG 60.005 52.381 0.00 0.00 0.00 4.35
3329 3643 1.004610 CGCATGACCAATCGATGTGAC 60.005 52.381 0.00 0.00 31.20 3.67
3330 3644 1.289276 CGCATGACCAATCGATGTGA 58.711 50.000 0.00 0.00 31.20 3.58
3331 3645 0.305617 CCGCATGACCAATCGATGTG 59.694 55.000 0.00 0.00 0.00 3.21
3332 3646 0.107703 ACCGCATGACCAATCGATGT 60.108 50.000 0.00 0.00 0.00 3.06
3333 3647 0.305617 CACCGCATGACCAATCGATG 59.694 55.000 0.00 0.00 0.00 3.84
3334 3648 0.107703 ACACCGCATGACCAATCGAT 60.108 50.000 0.00 0.00 0.00 3.59
3335 3649 0.321210 AACACCGCATGACCAATCGA 60.321 50.000 0.00 0.00 0.00 3.59
3336 3650 0.179192 CAACACCGCATGACCAATCG 60.179 55.000 0.00 0.00 0.00 3.34
3337 3651 0.171007 CCAACACCGCATGACCAATC 59.829 55.000 0.00 0.00 0.00 2.67
3338 3652 1.876497 GCCAACACCGCATGACCAAT 61.876 55.000 0.00 0.00 0.00 3.16
3339 3653 2.560119 GCCAACACCGCATGACCAA 61.560 57.895 0.00 0.00 0.00 3.67
3365 3679 6.989169 AGCCAGATCTACATTATTTCTCACAC 59.011 38.462 0.00 0.00 0.00 3.82
3367 3681 7.441017 AGAGCCAGATCTACATTATTTCTCAC 58.559 38.462 0.00 0.00 0.00 3.51
3372 3686 6.904626 ACCAAGAGCCAGATCTACATTATTT 58.095 36.000 0.00 0.00 0.00 1.40
3381 3695 3.445008 TGTAGAACCAAGAGCCAGATCT 58.555 45.455 0.00 0.00 0.00 2.75
3396 3710 6.708949 AGCCATAAAACGAAAGAGTTGTAGAA 59.291 34.615 0.00 0.00 34.14 2.10
3401 3715 6.002062 AGAAGCCATAAAACGAAAGAGTTG 57.998 37.500 0.00 0.00 34.14 3.16
3409 3723 4.151689 CGTGAAGAAGAAGCCATAAAACGA 59.848 41.667 0.00 0.00 0.00 3.85
3414 3728 3.695830 ACCGTGAAGAAGAAGCCATAA 57.304 42.857 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.