Multiple sequence alignment - TraesCS7B01G233000

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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 TraesCS7B01G233000 chr7B 100.000 3914 0 0 1 3914 436700612 436704525 0.000000e+00 7228.0
1 TraesCS7B01G233000 chr7B 90.698 43 2 2 874 915 625910517 625910476 5.460000e-04 56.5
2 TraesCS7B01G233000 chr7D 95.039 2963 124 12 957 3914 420626507 420629451 0.000000e+00 4636.0
3 TraesCS7B01G233000 chr7D 83.945 654 76 11 2 643 463975829 463976465 2.010000e-167 599.0
4 TraesCS7B01G233000 chr7D 83.513 649 76 20 2 643 571475015 571474391 9.430000e-161 577.0
5 TraesCS7B01G233000 chr7D 90.441 272 18 7 644 913 420626228 420626493 6.220000e-93 351.0
6 TraesCS7B01G233000 chr7A 94.285 2782 131 13 978 3757 512443174 512440419 0.000000e+00 4231.0
7 TraesCS7B01G233000 chr7A 84.072 609 75 5 38 644 620203508 620202920 5.680000e-158 568.0
8 TraesCS7B01G233000 chr7A 94.969 159 8 0 3756 3914 512440337 512440179 2.330000e-62 250.0
9 TraesCS7B01G233000 chr7A 75.371 337 42 23 636 967 518766766 518767066 1.480000e-24 124.0
10 TraesCS7B01G233000 chr6B 86.778 658 58 13 2 642 577462535 577461890 0.000000e+00 706.0
11 TraesCS7B01G233000 chr6B 81.579 152 18 9 646 793 711697127 711697272 2.470000e-22 117.0
12 TraesCS7B01G233000 chr6D 86.064 653 68 11 2 643 305745365 305744725 0.000000e+00 680.0
13 TraesCS7B01G233000 chr3D 85.429 652 75 6 2 644 45633863 45634503 0.000000e+00 660.0
14 TraesCS7B01G233000 chr3D 88.889 72 7 1 644 714 574233291 574233362 1.940000e-13 87.9
15 TraesCS7B01G233000 chr3D 87.273 55 3 4 859 911 29419216 29419164 4.220000e-05 60.2
16 TraesCS7B01G233000 chr5B 85.494 648 68 8 2 644 470217255 470216629 0.000000e+00 652.0
17 TraesCS7B01G233000 chr5B 86.602 515 66 3 133 644 438788935 438789449 2.040000e-157 566.0
18 TraesCS7B01G233000 chr2B 85.918 632 55 15 40 648 479890025 479890645 0.000000e+00 643.0
19 TraesCS7B01G233000 chr3A 87.873 503 59 2 143 643 418765766 418766268 1.210000e-164 590.0
20 TraesCS7B01G233000 chr3A 75.882 170 27 11 811 975 686682847 686682687 1.510000e-09 75.0
21 TraesCS7B01G233000 chr3B 82.895 152 21 3 644 793 623909807 623909955 8.820000e-27 132.0
22 TraesCS7B01G233000 chr4B 82.993 147 19 5 644 784 64788441 64788587 1.140000e-25 128.0
23 TraesCS7B01G233000 chr4B 77.401 177 29 8 809 975 492225590 492225415 1.160000e-15 95.3
24 TraesCS7B01G233000 chr4D 79.730 148 21 8 644 789 343550126 343549986 8.950000e-17 99.0
25 TraesCS7B01G233000 chr4D 78.000 150 22 7 644 789 102739680 102739822 2.510000e-12 84.2
26 TraesCS7B01G233000 chr1B 79.710 138 20 7 651 785 475282712 475282844 4.160000e-15 93.5


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 TraesCS7B01G233000 chr7B 436700612 436704525 3913 False 7228.0 7228 100.000 1 3914 1 chr7B.!!$F1 3913
1 TraesCS7B01G233000 chr7D 420626228 420629451 3223 False 2493.5 4636 92.740 644 3914 2 chr7D.!!$F2 3270
2 TraesCS7B01G233000 chr7D 463975829 463976465 636 False 599.0 599 83.945 2 643 1 chr7D.!!$F1 641
3 TraesCS7B01G233000 chr7D 571474391 571475015 624 True 577.0 577 83.513 2 643 1 chr7D.!!$R1 641
4 TraesCS7B01G233000 chr7A 512440179 512443174 2995 True 2240.5 4231 94.627 978 3914 2 chr7A.!!$R2 2936
5 TraesCS7B01G233000 chr7A 620202920 620203508 588 True 568.0 568 84.072 38 644 1 chr7A.!!$R1 606
6 TraesCS7B01G233000 chr6B 577461890 577462535 645 True 706.0 706 86.778 2 642 1 chr6B.!!$R1 640
7 TraesCS7B01G233000 chr6D 305744725 305745365 640 True 680.0 680 86.064 2 643 1 chr6D.!!$R1 641
8 TraesCS7B01G233000 chr3D 45633863 45634503 640 False 660.0 660 85.429 2 644 1 chr3D.!!$F1 642
9 TraesCS7B01G233000 chr5B 470216629 470217255 626 True 652.0 652 85.494 2 644 1 chr5B.!!$R1 642
10 TraesCS7B01G233000 chr5B 438788935 438789449 514 False 566.0 566 86.602 133 644 1 chr5B.!!$F1 511
11 TraesCS7B01G233000 chr2B 479890025 479890645 620 False 643.0 643 85.918 40 648 1 chr2B.!!$F1 608
12 TraesCS7B01G233000 chr3A 418765766 418766268 502 False 590.0 590 87.873 143 643 1 chr3A.!!$F1 500

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
217 237 0.104120 CCGTGGATGAATCTACCGCA 59.896 55.0 1.70 0.0 35.16 5.69 F
395 448 0.400594 GGGGCGGTGAGGCTAATAAT 59.599 55.0 0.00 0.0 45.89 1.28 F
2295 2355 0.474184 AGGGGATGCCTATCAAACCG 59.526 55.0 2.19 0.0 34.90 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1731 0.036671 CCACAGCATCTCTCACAGCA 60.037 55.000 0.00 0.0 0.0 4.41 R
2304 2364 0.106708 TGAGAAGCGCACCCCATATC 59.893 55.000 11.47 0.0 0.0 1.63 R
3873 4032 4.927425 GTCGATAAACTACTGACAAGCCAA 59.073 41.667 0.00 0.0 0.0 4.52 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
77 85 3.491766 ATCCCTCTTCTACTCCAACCA 57.508 47.619 0.00 0.00 0.00 3.67
100 108 6.015010 CCACATCTACCTCTATTCCGATCTTT 60.015 42.308 0.00 0.00 0.00 2.52
117 135 7.921214 TCCGATCTTTCATGAACTACTATGAAC 59.079 37.037 7.89 0.00 41.51 3.18
118 136 7.923344 CCGATCTTTCATGAACTACTATGAACT 59.077 37.037 7.89 0.00 41.51 3.01
119 137 8.963130 CGATCTTTCATGAACTACTATGAACTC 58.037 37.037 7.89 0.00 41.51 3.01
120 138 9.255304 GATCTTTCATGAACTACTATGAACTCC 57.745 37.037 7.89 0.00 41.51 3.85
121 139 8.367660 TCTTTCATGAACTACTATGAACTCCT 57.632 34.615 7.89 0.00 41.51 3.69
122 140 9.475620 TCTTTCATGAACTACTATGAACTCCTA 57.524 33.333 7.89 0.00 41.51 2.94
125 143 8.768501 TCATGAACTACTATGAACTCCTATGT 57.231 34.615 0.00 0.00 30.84 2.29
126 144 9.862149 TCATGAACTACTATGAACTCCTATGTA 57.138 33.333 0.00 0.00 30.84 2.29
217 237 0.104120 CCGTGGATGAATCTACCGCA 59.896 55.000 1.70 0.00 35.16 5.69
265 287 5.023533 TGACAAACAGAGAAGTGCTTACT 57.976 39.130 0.00 0.00 0.00 2.24
295 318 1.043816 CTGGCTAGGTGATGATCCGT 58.956 55.000 0.00 0.00 0.00 4.69
297 320 1.837439 TGGCTAGGTGATGATCCGTTT 59.163 47.619 0.00 0.00 0.00 3.60
320 343 0.693049 GGTGATGGAGTCTGGTGGTT 59.307 55.000 0.00 0.00 0.00 3.67
331 354 2.952310 GTCTGGTGGTTTTCTTGCTCTT 59.048 45.455 0.00 0.00 0.00 2.85
395 448 0.400594 GGGGCGGTGAGGCTAATAAT 59.599 55.000 0.00 0.00 45.89 1.28
472 526 4.634703 AACGCCCACATGCACCGA 62.635 61.111 0.00 0.00 0.00 4.69
547 603 4.036380 CCCAAGAGTGCTTTAAAGTTCGTT 59.964 41.667 16.38 6.78 30.14 3.85
924 981 3.235369 GTCCATCTGGAGCTCCCC 58.765 66.667 29.95 7.49 46.49 4.81
925 982 2.444706 TCCATCTGGAGCTCCCCG 60.445 66.667 29.95 20.19 39.78 5.73
926 983 2.444706 CCATCTGGAGCTCCCCGA 60.445 66.667 29.95 24.54 37.39 5.14
927 984 2.801631 CCATCTGGAGCTCCCCGAC 61.802 68.421 29.95 5.05 37.39 4.79
928 985 2.835431 ATCTGGAGCTCCCCGACG 60.835 66.667 29.95 12.74 30.65 5.12
931 988 4.435970 TGGAGCTCCCCGACGCTA 62.436 66.667 29.95 5.60 36.45 4.26
932 989 3.597728 GGAGCTCCCCGACGCTAG 61.598 72.222 23.19 0.00 36.45 3.42
933 990 2.516460 GAGCTCCCCGACGCTAGA 60.516 66.667 0.87 0.00 36.45 2.43
934 991 2.517402 AGCTCCCCGACGCTAGAG 60.517 66.667 0.00 0.00 34.11 2.43
935 992 4.273257 GCTCCCCGACGCTAGAGC 62.273 72.222 13.73 13.73 44.36 4.09
936 993 2.517402 CTCCCCGACGCTAGAGCT 60.517 66.667 0.00 0.00 39.32 4.09
937 994 2.044252 TCCCCGACGCTAGAGCTT 60.044 61.111 0.00 0.00 39.32 3.74
938 995 2.065906 CTCCCCGACGCTAGAGCTTC 62.066 65.000 0.00 0.00 39.32 3.86
939 996 2.413765 CCCGACGCTAGAGCTTCC 59.586 66.667 0.00 0.00 36.13 3.46
940 997 2.413765 CCGACGCTAGAGCTTCCC 59.586 66.667 0.00 0.00 36.13 3.97
941 998 2.122167 CCGACGCTAGAGCTTCCCT 61.122 63.158 0.00 0.00 36.13 4.20
942 999 1.357334 CGACGCTAGAGCTTCCCTC 59.643 63.158 0.00 0.00 41.07 4.30
949 1006 2.498726 GAGCTTCCCTCTGCCTCG 59.501 66.667 0.00 0.00 37.60 4.63
950 1007 3.731653 GAGCTTCCCTCTGCCTCGC 62.732 68.421 0.00 0.00 37.60 5.03
951 1008 4.087892 GCTTCCCTCTGCCTCGCA 62.088 66.667 0.00 0.00 36.92 5.10
952 1009 2.665000 CTTCCCTCTGCCTCGCAA 59.335 61.111 0.00 0.00 38.41 4.85
953 1010 1.743252 CTTCCCTCTGCCTCGCAAC 60.743 63.158 0.00 0.00 38.41 4.17
954 1011 2.454832 CTTCCCTCTGCCTCGCAACA 62.455 60.000 0.00 0.00 38.41 3.33
955 1012 2.032528 CCCTCTGCCTCGCAACAA 59.967 61.111 0.00 0.00 38.41 2.83
990 1048 2.660802 CCAGTTAACCGCCTCCGT 59.339 61.111 0.88 0.00 0.00 4.69
1141 1201 0.821517 CATTGCAGCATCACCACCAT 59.178 50.000 0.00 0.00 0.00 3.55
1180 1240 1.343075 ACCTCGCTTCTTCCCCTCATA 60.343 52.381 0.00 0.00 0.00 2.15
1298 1358 1.227853 GCCCTGACACGGTCTTGTT 60.228 57.895 5.77 0.00 33.15 2.83
1320 1380 5.939764 TCACCAAGCTAGTTGATCTGTAT 57.060 39.130 0.00 0.00 38.60 2.29
1494 1554 1.066430 GTGGAGCCGGATAACTTCACA 60.066 52.381 5.05 0.00 41.32 3.58
1605 1665 2.401592 GACGTGTTTGTGTGCGCA 59.598 55.556 5.66 5.66 0.00 6.09
1609 1669 1.767127 CGTGTTTGTGTGCGCAGGTA 61.767 55.000 12.22 0.00 0.00 3.08
1623 1683 3.312421 GCGCAGGTATTGTTGACATGTAT 59.688 43.478 0.30 0.00 31.37 2.29
1645 1705 3.037686 AAGTGCGGGTGTGTGGACA 62.038 57.895 0.00 0.00 0.00 4.02
1671 1731 1.463674 GAGCGGTGTTTGATGGGATT 58.536 50.000 0.00 0.00 0.00 3.01
1674 1734 1.176527 CGGTGTTTGATGGGATTGCT 58.823 50.000 0.00 0.00 0.00 3.91
1683 1743 2.775960 TGATGGGATTGCTGTGAGAGAT 59.224 45.455 0.00 0.00 0.00 2.75
1689 1749 1.804601 TTGCTGTGAGAGATGCTGTG 58.195 50.000 0.00 0.00 0.00 3.66
1729 1789 0.557238 TGCATATGGGCAGAATGGGT 59.443 50.000 4.56 0.00 39.25 4.51
1731 1791 1.624336 CATATGGGCAGAATGGGTGG 58.376 55.000 0.00 0.00 35.86 4.61
1750 1810 2.409870 CCCATGGAGGCGCTTTCAC 61.410 63.158 15.22 0.00 35.39 3.18
1777 1837 0.747644 CGACATGGCTGCCAATGGTA 60.748 55.000 27.24 0.00 36.95 3.25
1791 1851 2.504996 CAATGGTATTGGGCCCACAATT 59.495 45.455 28.70 16.18 41.12 2.32
1863 1923 1.002662 AGGGAGAGAGCTGCATGGA 59.997 57.895 1.02 0.00 33.56 3.41
1869 1929 1.030457 GAGAGCTGCATGGATTTGGG 58.970 55.000 1.02 0.00 0.00 4.12
1891 1951 4.522975 GGAGGGGATTTGGGCGGG 62.523 72.222 0.00 0.00 0.00 6.13
1956 2016 4.329545 TGGGTTCAGGTGGCTCGC 62.330 66.667 0.00 0.00 0.00 5.03
1957 2017 4.329545 GGGTTCAGGTGGCTCGCA 62.330 66.667 0.00 0.00 0.00 5.10
1982 2042 7.426929 TTCTCTTTGAGCAACTTATGAAGAC 57.573 36.000 0.00 0.00 0.00 3.01
1989 2049 4.246458 AGCAACTTATGAAGACGGAACTC 58.754 43.478 0.00 0.00 0.00 3.01
2085 2145 2.550277 TGAGGGGAGATGCTCAAGTA 57.450 50.000 0.00 0.00 31.08 2.24
2086 2146 3.051940 TGAGGGGAGATGCTCAAGTAT 57.948 47.619 0.00 0.00 31.08 2.12
2160 2220 5.010282 GGGATGGTAGAAGAAGCAAAAGAA 58.990 41.667 0.00 0.00 0.00 2.52
2168 2228 8.352942 GGTAGAAGAAGCAAAAGAATTCTTTGA 58.647 33.333 29.31 6.98 44.69 2.69
2178 2238 7.063074 GCAAAAGAATTCTTTGATCTGATGGTG 59.937 37.037 29.31 20.56 44.69 4.17
2196 2256 4.156455 GGTGGATGTGTACTCCATCAAT 57.844 45.455 20.43 0.00 44.34 2.57
2202 2262 3.595173 TGTGTACTCCATCAATCCAACG 58.405 45.455 0.00 0.00 0.00 4.10
2271 2331 5.619220 AGGTTTGAGGAAGCATATGATCTC 58.381 41.667 6.97 4.81 38.21 2.75
2274 2334 6.149142 GGTTTGAGGAAGCATATGATCTCATC 59.851 42.308 11.76 10.47 35.58 2.92
2280 2340 4.571369 AGCATATGATCTCATCAAGGGG 57.429 45.455 6.97 0.00 43.50 4.79
2295 2355 0.474184 AGGGGATGCCTATCAAACCG 59.526 55.000 2.19 0.00 34.90 4.44
2304 2364 2.851195 CCTATCAAACCGGATTCAGGG 58.149 52.381 9.46 0.00 0.00 4.45
2313 2373 1.362224 CGGATTCAGGGATATGGGGT 58.638 55.000 0.00 0.00 0.00 4.95
2316 2376 0.401738 ATTCAGGGATATGGGGTGCG 59.598 55.000 0.00 0.00 0.00 5.34
2364 2424 5.695851 AAAATGTTGAACTAGGTGAGCTG 57.304 39.130 0.00 0.00 0.00 4.24
2388 2448 2.818432 CCTGCAGAAGTTGATTGAGCTT 59.182 45.455 17.39 0.00 0.00 3.74
2415 2475 5.278169 GCCTGAAGATGCTGGTAATTATGTG 60.278 44.000 0.00 0.00 0.00 3.21
2457 2517 3.760684 CTCAGTCTGGGAAATGGGAAAAG 59.239 47.826 0.00 0.00 0.00 2.27
2487 2547 3.440522 GGGTGAGAAAGCTAATGACCAAC 59.559 47.826 4.27 0.00 0.00 3.77
2634 2694 1.209019 GGTCTCATGAGTGATGCTGGT 59.791 52.381 21.92 0.00 32.98 4.00
2838 2898 0.516877 TTTCAAAGATCGTGCAGCGG 59.483 50.000 8.46 0.00 41.72 5.52
2937 2997 8.220755 AGCTTTCACAGTGAATAAACAAGTTA 57.779 30.769 16.89 0.00 36.11 2.24
2962 3022 8.469309 AATTTTGCTCATATATGGTGCTAGTT 57.531 30.769 22.57 14.86 0.00 2.24
2974 3034 5.244785 TGGTGCTAGTTGTATTAGTCTCG 57.755 43.478 0.00 0.00 0.00 4.04
3036 3096 4.081752 TCAGCCAAAAAGAAAACAGCTCAA 60.082 37.500 0.00 0.00 0.00 3.02
3156 3217 1.134753 CCAGCACAGAGTTGCAAAACA 59.865 47.619 0.00 0.00 45.62 2.83
3197 3258 7.154656 TGATATGGAGCACTTCATGTATGTAC 58.845 38.462 1.45 0.00 0.00 2.90
3198 3259 4.817318 TGGAGCACTTCATGTATGTACA 57.183 40.909 0.00 0.00 40.98 2.90
3200 3261 6.478512 TGGAGCACTTCATGTATGTACATA 57.521 37.500 11.62 11.62 44.57 2.29
3330 3391 2.103941 GGTTGGCCTTCATGGTTTCAAA 59.896 45.455 3.32 0.00 38.35 2.69
3331 3392 3.432890 GGTTGGCCTTCATGGTTTCAAAA 60.433 43.478 3.32 0.00 38.35 2.44
3332 3393 4.388485 GTTGGCCTTCATGGTTTCAAAAT 58.612 39.130 3.32 0.00 38.35 1.82
3333 3394 4.005487 TGGCCTTCATGGTTTCAAAATG 57.995 40.909 3.32 0.00 38.35 2.32
3334 3395 3.244491 TGGCCTTCATGGTTTCAAAATGG 60.244 43.478 3.32 0.00 38.35 3.16
3335 3396 3.244526 GGCCTTCATGGTTTCAAAATGGT 60.245 43.478 0.00 0.00 38.35 3.55
3336 3397 4.020662 GGCCTTCATGGTTTCAAAATGGTA 60.021 41.667 0.00 0.00 38.35 3.25
3337 3398 5.512232 GGCCTTCATGGTTTCAAAATGGTAA 60.512 40.000 0.00 0.00 38.35 2.85
3338 3399 5.639082 GCCTTCATGGTTTCAAAATGGTAAG 59.361 40.000 0.00 0.00 38.35 2.34
3339 3400 5.639082 CCTTCATGGTTTCAAAATGGTAAGC 59.361 40.000 0.00 0.00 0.00 3.09
3340 3401 5.798125 TCATGGTTTCAAAATGGTAAGCA 57.202 34.783 0.00 0.00 33.22 3.91
3341 3402 6.166984 TCATGGTTTCAAAATGGTAAGCAA 57.833 33.333 0.00 0.00 32.55 3.91
3342 3403 6.767456 TCATGGTTTCAAAATGGTAAGCAAT 58.233 32.000 0.00 0.00 32.55 3.56
3618 3694 6.344572 TGTTCGATCTATTGTGTTGCATAC 57.655 37.500 0.00 0.00 0.00 2.39
3638 3714 7.510685 TGCATACCTATCCTATTCTTCTGTCTT 59.489 37.037 0.00 0.00 0.00 3.01
3835 3994 8.417780 TGATTTGGTGTTAACATCTTTTTGTG 57.582 30.769 19.28 0.00 0.00 3.33
3841 4000 6.691388 GGTGTTAACATCTTTTTGTGTGAGTC 59.309 38.462 12.26 0.00 0.00 3.36
3858 4017 6.371548 GTGTGAGTCATTATGGAGTAGCAAAA 59.628 38.462 0.00 0.00 0.00 2.44
3873 4032 7.145932 AGTAGCAAAACTTTGATTAAGCGAT 57.854 32.000 6.37 0.00 40.55 4.58
3894 4053 5.276395 CGATTGGCTTGTCAGTAGTTTATCG 60.276 44.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.430765 CTGGCTAACCGCGACCGT 62.431 66.667 8.23 0.00 40.44 4.83
23 24 1.525718 TACACACTGGCTAACCGCGA 61.526 55.000 8.23 0.00 40.44 5.87
77 85 6.778069 TGAAAGATCGGAATAGAGGTAGATGT 59.222 38.462 0.00 0.00 0.00 3.06
100 108 8.768501 ACATAGGAGTTCATAGTAGTTCATGA 57.231 34.615 0.00 0.00 0.00 3.07
117 135 7.966246 ACTAGTTCATACGAGTACATAGGAG 57.034 40.000 0.00 0.00 38.29 3.69
118 136 9.433153 CATACTAGTTCATACGAGTACATAGGA 57.567 37.037 0.00 0.00 42.66 2.94
119 137 9.433153 TCATACTAGTTCATACGAGTACATAGG 57.567 37.037 0.00 0.00 42.66 2.57
122 140 9.339850 AGTTCATACTAGTTCATACGAGTACAT 57.660 33.333 0.00 0.00 42.66 2.29
123 141 8.728337 AGTTCATACTAGTTCATACGAGTACA 57.272 34.615 0.00 0.00 42.66 2.90
126 144 8.961294 AGTAGTTCATACTAGTTCATACGAGT 57.039 34.615 0.00 0.00 43.17 4.18
158 177 4.727507 ATAGAGGTAGATAAGCATGGCG 57.272 45.455 0.00 0.00 0.00 5.69
217 237 5.277828 GCACTACTTTTTCGTGTTTGATCCT 60.278 40.000 0.00 0.00 0.00 3.24
281 304 1.472552 CGGCAAACGGATCATCACCTA 60.473 52.381 0.00 0.00 39.42 3.08
295 318 0.321564 CAGACTCCATCACCGGCAAA 60.322 55.000 0.00 0.00 0.00 3.68
297 320 2.659063 CCAGACTCCATCACCGGCA 61.659 63.158 0.00 0.00 0.00 5.69
320 343 3.997021 GTGGATCGAAGAAGAGCAAGAAA 59.003 43.478 0.00 0.00 43.58 2.52
331 354 4.508128 GCGGCGGTGGATCGAAGA 62.508 66.667 9.78 0.00 45.75 2.87
455 509 3.918253 ATCGGTGCATGTGGGCGTT 62.918 57.895 0.00 0.00 36.28 4.84
456 510 4.408821 ATCGGTGCATGTGGGCGT 62.409 61.111 0.00 0.00 36.28 5.68
464 518 4.552365 CAGGCCCGATCGGTGCAT 62.552 66.667 33.72 28.86 34.56 3.96
514 569 1.159664 ACTCTTGGGTCTGGCTCCT 59.840 57.895 0.00 0.00 0.00 3.69
547 603 4.776322 CTGTTCGGCCCGCATGGA 62.776 66.667 0.00 0.00 37.49 3.41
796 853 8.879227 ACTTCCAAATATTCTTCCCATCAAAAA 58.121 29.630 0.00 0.00 0.00 1.94
900 957 4.731853 TCCAGATGGACCGGCCCA 62.732 66.667 13.59 13.59 39.78 5.36
901 958 3.866582 CTCCAGATGGACCGGCCC 61.867 72.222 0.00 0.00 39.78 5.80
903 960 3.453070 GAGCTCCAGATGGACCGGC 62.453 68.421 0.00 0.35 39.78 6.13
914 971 4.435970 TAGCGTCGGGGAGCTCCA 62.436 66.667 33.29 11.43 43.44 3.86
928 985 1.048160 AGGCAGAGGGAAGCTCTAGC 61.048 60.000 0.00 0.00 42.49 3.42
929 986 1.039856 GAGGCAGAGGGAAGCTCTAG 58.960 60.000 0.00 0.00 0.00 2.43
930 987 0.753479 CGAGGCAGAGGGAAGCTCTA 60.753 60.000 0.00 0.00 0.00 2.43
931 988 2.057408 CGAGGCAGAGGGAAGCTCT 61.057 63.158 0.00 0.00 0.00 4.09
932 989 2.498726 CGAGGCAGAGGGAAGCTC 59.501 66.667 0.00 0.00 0.00 4.09
933 990 3.780173 GCGAGGCAGAGGGAAGCT 61.780 66.667 0.00 0.00 0.00 3.74
934 991 3.612247 TTGCGAGGCAGAGGGAAGC 62.612 63.158 0.00 0.00 40.61 3.86
935 992 1.743252 GTTGCGAGGCAGAGGGAAG 60.743 63.158 0.00 0.00 40.61 3.46
936 993 2.050836 TTGTTGCGAGGCAGAGGGAA 62.051 55.000 0.00 0.00 40.61 3.97
937 994 2.454832 CTTGTTGCGAGGCAGAGGGA 62.455 60.000 0.00 0.00 40.61 4.20
938 995 2.032528 TTGTTGCGAGGCAGAGGG 59.967 61.111 0.00 0.00 40.61 4.30
939 996 2.684843 GCTTGTTGCGAGGCAGAGG 61.685 63.158 0.00 0.00 40.61 3.69
940 997 2.866028 GCTTGTTGCGAGGCAGAG 59.134 61.111 0.00 0.00 40.61 3.35
949 1006 1.009829 CCCTATGTCTCGCTTGTTGC 58.990 55.000 0.00 0.00 38.57 4.17
950 1007 2.271800 GTCCCTATGTCTCGCTTGTTG 58.728 52.381 0.00 0.00 0.00 3.33
951 1008 1.135083 CGTCCCTATGTCTCGCTTGTT 60.135 52.381 0.00 0.00 0.00 2.83
952 1009 0.456221 CGTCCCTATGTCTCGCTTGT 59.544 55.000 0.00 0.00 0.00 3.16
953 1010 0.872021 GCGTCCCTATGTCTCGCTTG 60.872 60.000 0.00 0.00 42.88 4.01
954 1011 1.437986 GCGTCCCTATGTCTCGCTT 59.562 57.895 0.00 0.00 42.88 4.68
955 1012 2.491022 GGCGTCCCTATGTCTCGCT 61.491 63.158 7.69 0.00 45.01 4.93
990 1048 2.359850 GGAAGCATCGTGTGGCCA 60.360 61.111 0.00 0.00 0.00 5.36
1070 1130 1.813862 CGAGCGAAGAGGAGAGGAGAT 60.814 57.143 0.00 0.00 0.00 2.75
1141 1201 1.059584 TGGGAGTTGGTGCTTGGAGA 61.060 55.000 0.00 0.00 0.00 3.71
1180 1240 1.551791 GGAGGTGTAGTGGTGGTAGGT 60.552 57.143 0.00 0.00 0.00 3.08
1298 1358 5.664457 CATACAGATCAACTAGCTTGGTGA 58.336 41.667 18.19 18.19 0.00 4.02
1308 1368 2.915349 CAGGCAGCATACAGATCAACT 58.085 47.619 0.00 0.00 0.00 3.16
1311 1371 0.531311 CGCAGGCAGCATACAGATCA 60.531 55.000 1.96 0.00 46.13 2.92
1314 1374 2.187685 CCGCAGGCAGCATACAGA 59.812 61.111 1.96 0.00 46.14 3.41
1359 1419 3.864686 CGCTTGGGCATTCCGTCG 61.865 66.667 0.00 0.00 38.76 5.12
1470 1530 0.907704 AGTTATCCGGCTCCACACCA 60.908 55.000 0.00 0.00 0.00 4.17
1473 1533 1.066430 GTGAAGTTATCCGGCTCCACA 60.066 52.381 0.00 0.00 0.00 4.17
1534 1594 2.283809 CTCCCTCCCGGTCTCCAT 59.716 66.667 0.00 0.00 0.00 3.41
1590 1650 1.767127 TACCTGCGCACACAAACACG 61.767 55.000 5.66 0.00 0.00 4.49
1605 1665 4.854173 TGGCATACATGTCAACAATACCT 58.146 39.130 0.00 0.00 39.82 3.08
1609 1669 4.618927 GCACTTGGCATACATGTCAACAAT 60.619 41.667 0.00 0.00 46.34 2.71
1623 1683 4.497984 ACACACCCGCACTTGGCA 62.498 61.111 0.00 0.00 45.17 4.92
1645 1705 0.602638 TCAAACACCGCTCGAGCATT 60.603 50.000 34.69 19.31 42.21 3.56
1671 1731 0.036671 CCACAGCATCTCTCACAGCA 60.037 55.000 0.00 0.00 0.00 4.41
1674 1734 1.051008 ACACCACAGCATCTCTCACA 58.949 50.000 0.00 0.00 0.00 3.58
1683 1743 0.107643 TCGAATTCCACACCACAGCA 59.892 50.000 0.00 0.00 0.00 4.41
1689 1749 2.684881 AGCAATCATCGAATTCCACACC 59.315 45.455 0.00 0.00 0.00 4.16
1768 1828 1.382420 TGGGCCCAATACCATTGGC 60.382 57.895 26.33 7.76 43.26 4.52
1770 1830 1.566211 TTGTGGGCCCAATACCATTG 58.434 50.000 30.64 0.00 39.30 2.82
1777 1837 1.194218 GTAGCAATTGTGGGCCCAAT 58.806 50.000 30.64 15.85 36.62 3.16
1863 1923 0.254299 ATCCCCTCCTCCACCCAAAT 60.254 55.000 0.00 0.00 0.00 2.32
1869 1929 1.615262 CCCAAATCCCCTCCTCCAC 59.385 63.158 0.00 0.00 0.00 4.02
1891 1951 4.849518 AGGGAAGTTTTCAGCTTATCCTC 58.150 43.478 0.00 0.00 29.65 3.71
1956 2016 7.961827 GTCTTCATAAGTTGCTCAAAGAGAATG 59.038 37.037 0.00 0.00 0.00 2.67
1957 2017 7.148507 CGTCTTCATAAGTTGCTCAAAGAGAAT 60.149 37.037 0.00 0.00 0.00 2.40
1982 2042 2.412847 GCATTCCAAGAAACGAGTTCCG 60.413 50.000 0.00 0.00 45.44 4.30
2051 2111 5.534654 TCTCCCCTCATTTTGTTAAACAGTG 59.465 40.000 0.00 0.00 0.00 3.66
2085 2145 5.380043 ACAAAAGTGATGTTGTCAGGAGAT 58.620 37.500 0.00 0.00 37.56 2.75
2086 2146 4.780815 ACAAAAGTGATGTTGTCAGGAGA 58.219 39.130 0.00 0.00 37.56 3.71
2160 2220 5.593095 CACATCCACCATCAGATCAAAGAAT 59.407 40.000 0.00 0.00 0.00 2.40
2168 2228 3.389329 GGAGTACACATCCACCATCAGAT 59.611 47.826 0.00 0.00 36.79 2.90
2178 2238 4.422073 TGGATTGATGGAGTACACATCC 57.578 45.455 20.90 11.81 43.10 3.51
2196 2256 0.250510 TGTAATGCTGCACCGTTGGA 60.251 50.000 3.57 0.00 0.00 3.53
2202 2262 0.109132 GGCAAGTGTAATGCTGCACC 60.109 55.000 3.57 0.00 43.34 5.01
2274 2334 2.310538 GGTTTGATAGGCATCCCCTTG 58.689 52.381 0.00 0.00 43.06 3.61
2280 2340 3.476552 TGAATCCGGTTTGATAGGCATC 58.523 45.455 1.57 0.00 0.00 3.91
2284 2344 2.438021 TCCCTGAATCCGGTTTGATAGG 59.562 50.000 1.57 7.50 0.00 2.57
2295 2355 1.272147 GCACCCCATATCCCTGAATCC 60.272 57.143 0.00 0.00 0.00 3.01
2304 2364 0.106708 TGAGAAGCGCACCCCATATC 59.893 55.000 11.47 0.00 0.00 1.63
2313 2373 2.177394 TACAACCATTGAGAAGCGCA 57.823 45.000 11.47 0.00 0.00 6.09
2316 2376 4.943705 TGGATCTTACAACCATTGAGAAGC 59.056 41.667 0.00 0.00 31.66 3.86
2364 2424 0.529378 CAATCAACTTCTGCAGGGCC 59.471 55.000 15.13 0.00 0.00 5.80
2388 2448 1.571955 TACCAGCATCTTCAGGCTCA 58.428 50.000 0.00 0.00 38.56 4.26
2415 2475 8.945481 ACTGAGCATAGATATTTGATAGATGC 57.055 34.615 0.00 0.00 38.75 3.91
2457 2517 1.871126 GCTTTCTCACCCTTGCAGCC 61.871 60.000 0.00 0.00 0.00 4.85
2838 2898 8.499162 CGGTTAACATCTCTTATGATGATTTCC 58.501 37.037 8.10 7.22 44.71 3.13
2937 2997 8.355169 CAACTAGCACCATATATGAGCAAAATT 58.645 33.333 23.29 13.46 33.19 1.82
2951 3011 5.360144 ACGAGACTAATACAACTAGCACCAT 59.640 40.000 0.00 0.00 0.00 3.55
2952 3012 4.703575 ACGAGACTAATACAACTAGCACCA 59.296 41.667 0.00 0.00 0.00 4.17
2962 3022 6.101997 TCTTCTGTCGTACGAGACTAATACA 58.898 40.000 20.18 10.01 41.47 2.29
2974 3034 3.851976 AGACCACATCTTCTGTCGTAC 57.148 47.619 0.00 0.00 35.29 3.67
3036 3096 6.486657 TCCAGTCACTTTCGAATTCTCAAAAT 59.513 34.615 0.00 0.00 0.00 1.82
3156 3217 6.484288 TCCATATCAAAGTCATCACCTTTGT 58.516 36.000 11.38 4.02 45.67 2.83
3200 3261 9.239551 TCATGTTTCTTCATCTCTGAATGATTT 57.760 29.630 0.00 0.00 40.52 2.17
3330 3391 7.949696 TCCCCCATTATATATTGCTTACCATT 58.050 34.615 0.00 0.00 0.00 3.16
3331 3392 7.538327 TCCCCCATTATATATTGCTTACCAT 57.462 36.000 0.00 0.00 0.00 3.55
3332 3393 6.979018 TCCCCCATTATATATTGCTTACCA 57.021 37.500 0.00 0.00 0.00 3.25
3333 3394 8.658840 TTTTCCCCCATTATATATTGCTTACC 57.341 34.615 0.00 0.00 0.00 2.85
3336 3397 9.259832 GAGATTTTCCCCCATTATATATTGCTT 57.740 33.333 0.00 0.00 0.00 3.91
3337 3398 7.557719 CGAGATTTTCCCCCATTATATATTGCT 59.442 37.037 0.00 0.00 0.00 3.91
3338 3399 7.339466 ACGAGATTTTCCCCCATTATATATTGC 59.661 37.037 0.00 0.00 0.00 3.56
3339 3400 8.807948 ACGAGATTTTCCCCCATTATATATTG 57.192 34.615 0.00 0.00 0.00 1.90
3340 3401 9.462606 GAACGAGATTTTCCCCCATTATATATT 57.537 33.333 0.00 0.00 0.00 1.28
3341 3402 8.836735 AGAACGAGATTTTCCCCCATTATATAT 58.163 33.333 0.00 0.00 0.00 0.86
3342 3403 8.100791 CAGAACGAGATTTTCCCCCATTATATA 58.899 37.037 0.00 0.00 0.00 0.86
3618 3694 6.463614 CCCACAAGACAGAAGAATAGGATAGG 60.464 46.154 0.00 0.00 0.00 2.57
3638 3714 4.975147 ACAGTAGGATGGATATTTCCCACA 59.025 41.667 0.00 0.00 41.83 4.17
3835 3994 6.595716 AGTTTTGCTACTCCATAATGACTCAC 59.404 38.462 0.00 0.00 0.00 3.51
3873 4032 4.927425 GTCGATAAACTACTGACAAGCCAA 59.073 41.667 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.