Multiple sequence alignment - TraesCS6B01G269300

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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 TraesCS6B01G269300 chr6B 100.000 4398 0 0 1 4398 484990891 484986494 0.000000e+00 8122.0
1 TraesCS6B01G269300 chr6B 83.333 114 16 3 31 142 89198015 89198127 7.780000e-18 102.0
2 TraesCS6B01G269300 chr6A 89.560 2749 155 60 212 2851 475259602 475262327 0.000000e+00 3365.0
3 TraesCS6B01G269300 chr6A 95.482 996 28 3 2938 3916 475262383 475263378 0.000000e+00 1574.0
4 TraesCS6B01G269300 chr6A 94.336 459 18 2 3943 4398 475264390 475264843 0.000000e+00 697.0
5 TraesCS6B01G269300 chr6D 96.604 1973 46 11 1977 3931 335983507 335985476 0.000000e+00 3253.0
6 TraesCS6B01G269300 chr6D 94.346 1521 50 17 485 1983 335979794 335981300 0.000000e+00 2300.0
7 TraesCS6B01G269300 chr6D 91.904 457 16 7 3943 4398 335986643 335987079 1.740000e-173 619.0
8 TraesCS6B01G269300 chr6D 93.272 327 14 6 160 480 335979366 335979690 3.980000e-130 475.0
9 TraesCS6B01G269300 chr6D 100.000 30 0 0 1 30 452308648 452308677 6.140000e-04 56.5
10 TraesCS6B01G269300 chr6D 100.000 30 0 0 1 30 471073264 471073235 6.140000e-04 56.5
11 TraesCS6B01G269300 chr7D 94.595 37 2 0 1 37 190087508 190087544 1.710000e-04 58.4
12 TraesCS6B01G269300 chr7B 96.970 33 1 0 1 33 328166392 328166360 6.140000e-04 56.5
13 TraesCS6B01G269300 chr4A 100.000 30 0 0 1 30 87968961 87968932 6.140000e-04 56.5
14 TraesCS6B01G269300 chr4B 100.000 29 0 0 2 30 342853344 342853372 2.000000e-03 54.7
15 TraesCS6B01G269300 chr1B 100.000 29 0 0 1 29 469980916 469980944 2.000000e-03 54.7
16 TraesCS6B01G269300 chr2D 100.000 28 0 0 3 30 370056678 370056651 8.000000e-03 52.8
17 TraesCS6B01G269300 chr2D 100.000 28 0 0 3 30 382129480 382129453 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G269300 chr6B 484986494 484990891 4397 True 8122.000000 8122 100.0000 1 4398 1 chr6B.!!$R1 4397
1 TraesCS6B01G269300 chr6A 475259602 475264843 5241 False 1878.666667 3365 93.1260 212 4398 3 chr6A.!!$F1 4186
2 TraesCS6B01G269300 chr6D 335979366 335987079 7713 False 1661.750000 3253 94.0315 160 4398 4 chr6D.!!$F2 4238

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
882 1030 0.036732 TCTTGATTTGTGCTCGCCCT 59.963 50.0 0.0 0.0 0.00 5.19 F
1287 1442 0.796255 AGCCCTGCTCCCCTATATCT 59.204 55.0 0.0 0.0 30.62 1.98 F
1801 1987 1.114627 TGCACTGGAGTATCGCTGAT 58.885 50.0 0.0 0.0 34.37 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 2038 4.739137 GCAAAACAACCCAGCAATGAAGTA 60.739 41.667 0.0 0.0 0.00 2.24 R
3238 5691 4.003648 AGTTCGAGATGACAAAATCACCC 58.996 43.478 0.0 0.0 41.24 4.61 R
3697 6150 1.651240 CCCAGCTCGCCAAACATCAG 61.651 60.000 0.0 0.0 0.00 2.90 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
17 18 3.411700 GGGTTTGAGGGGTCCGAT 58.588 61.111 0.00 0.00 0.00 4.18
18 19 1.689412 GGGTTTGAGGGGTCCGATT 59.311 57.895 0.00 0.00 0.00 3.34
19 20 0.679960 GGGTTTGAGGGGTCCGATTG 60.680 60.000 0.00 0.00 0.00 2.67
20 21 0.037734 GGTTTGAGGGGTCCGATTGT 59.962 55.000 0.00 0.00 0.00 2.71
21 22 1.279846 GGTTTGAGGGGTCCGATTGTA 59.720 52.381 0.00 0.00 0.00 2.41
22 23 2.629051 GTTTGAGGGGTCCGATTGTAG 58.371 52.381 0.00 0.00 0.00 2.74
23 24 2.235402 GTTTGAGGGGTCCGATTGTAGA 59.765 50.000 0.00 0.00 0.00 2.59
24 25 2.471815 TGAGGGGTCCGATTGTAGAT 57.528 50.000 0.00 0.00 0.00 1.98
25 26 2.039418 TGAGGGGTCCGATTGTAGATG 58.961 52.381 0.00 0.00 0.00 2.90
26 27 0.759346 AGGGGTCCGATTGTAGATGC 59.241 55.000 0.00 0.00 0.00 3.91
27 28 0.759346 GGGGTCCGATTGTAGATGCT 59.241 55.000 0.00 0.00 0.00 3.79
28 29 1.270358 GGGGTCCGATTGTAGATGCTC 60.270 57.143 0.00 0.00 0.00 4.26
29 30 1.689273 GGGTCCGATTGTAGATGCTCT 59.311 52.381 0.00 0.00 0.00 4.09
30 31 2.288518 GGGTCCGATTGTAGATGCTCTC 60.289 54.545 0.00 0.00 0.00 3.20
31 32 2.362397 GGTCCGATTGTAGATGCTCTCA 59.638 50.000 0.00 0.00 0.00 3.27
32 33 3.376540 GTCCGATTGTAGATGCTCTCAC 58.623 50.000 0.00 0.00 0.00 3.51
33 34 2.033424 TCCGATTGTAGATGCTCTCACG 59.967 50.000 0.00 0.00 0.00 4.35
34 35 1.783711 CGATTGTAGATGCTCTCACGC 59.216 52.381 0.00 0.00 0.00 5.34
35 36 2.796032 CGATTGTAGATGCTCTCACGCA 60.796 50.000 0.00 0.00 45.10 5.24
36 37 1.996292 TTGTAGATGCTCTCACGCAC 58.004 50.000 0.00 0.00 43.61 5.34
37 38 0.173481 TGTAGATGCTCTCACGCACC 59.827 55.000 0.00 0.00 43.61 5.01
38 39 0.457851 GTAGATGCTCTCACGCACCT 59.542 55.000 0.00 0.00 43.61 4.00
39 40 1.676529 GTAGATGCTCTCACGCACCTA 59.323 52.381 0.00 0.00 43.61 3.08
40 41 1.186200 AGATGCTCTCACGCACCTAA 58.814 50.000 0.00 0.00 43.61 2.69
41 42 1.135915 AGATGCTCTCACGCACCTAAG 59.864 52.381 0.00 0.00 43.61 2.18
42 43 0.460987 ATGCTCTCACGCACCTAAGC 60.461 55.000 0.00 0.00 43.61 3.09
43 44 1.079819 GCTCTCACGCACCTAAGCA 60.080 57.895 0.00 0.00 0.00 3.91
44 45 0.460987 GCTCTCACGCACCTAAGCAT 60.461 55.000 0.00 0.00 0.00 3.79
45 46 1.565305 CTCTCACGCACCTAAGCATC 58.435 55.000 0.00 0.00 0.00 3.91
46 47 1.135915 CTCTCACGCACCTAAGCATCT 59.864 52.381 0.00 0.00 0.00 2.90
47 48 1.550524 TCTCACGCACCTAAGCATCTT 59.449 47.619 0.00 0.00 0.00 2.40
48 49 1.929836 CTCACGCACCTAAGCATCTTC 59.070 52.381 0.00 0.00 0.00 2.87
49 50 1.009829 CACGCACCTAAGCATCTTCC 58.990 55.000 0.00 0.00 0.00 3.46
50 51 0.613260 ACGCACCTAAGCATCTTCCA 59.387 50.000 0.00 0.00 0.00 3.53
51 52 1.210478 ACGCACCTAAGCATCTTCCAT 59.790 47.619 0.00 0.00 0.00 3.41
52 53 1.600957 CGCACCTAAGCATCTTCCATG 59.399 52.381 0.00 0.00 0.00 3.66
53 54 1.336125 GCACCTAAGCATCTTCCATGC 59.664 52.381 0.00 0.00 44.85 4.06
54 55 2.646930 CACCTAAGCATCTTCCATGCA 58.353 47.619 9.16 0.00 46.77 3.96
55 56 3.018856 CACCTAAGCATCTTCCATGCAA 58.981 45.455 9.16 0.00 46.77 4.08
56 57 3.444742 CACCTAAGCATCTTCCATGCAAA 59.555 43.478 9.16 0.00 46.77 3.68
57 58 4.082081 CACCTAAGCATCTTCCATGCAAAA 60.082 41.667 9.16 0.00 46.77 2.44
58 59 4.527816 ACCTAAGCATCTTCCATGCAAAAA 59.472 37.500 9.16 0.00 46.77 1.94
119 120 9.717942 TTTAAAATTTGTTATTCACCATGGGAG 57.282 29.630 18.09 8.50 0.00 4.30
120 121 5.343307 AATTTGTTATTCACCATGGGAGC 57.657 39.130 18.09 0.00 0.00 4.70
121 122 3.448093 TTGTTATTCACCATGGGAGCA 57.552 42.857 18.09 0.00 0.00 4.26
122 123 3.003394 TGTTATTCACCATGGGAGCAG 57.997 47.619 18.09 0.24 0.00 4.24
123 124 2.575735 TGTTATTCACCATGGGAGCAGA 59.424 45.455 18.09 2.85 0.00 4.26
124 125 3.202818 TGTTATTCACCATGGGAGCAGAT 59.797 43.478 18.09 3.82 0.00 2.90
125 126 2.359981 ATTCACCATGGGAGCAGATG 57.640 50.000 18.09 3.05 0.00 2.90
126 127 1.288188 TTCACCATGGGAGCAGATGA 58.712 50.000 18.09 5.73 0.00 2.92
127 128 0.835276 TCACCATGGGAGCAGATGAG 59.165 55.000 18.09 0.00 0.00 2.90
128 129 0.818445 CACCATGGGAGCAGATGAGC 60.818 60.000 18.09 0.00 0.00 4.26
135 136 2.813901 AGCAGATGAGCTCGGAGC 59.186 61.111 22.13 22.13 42.18 4.70
136 137 2.280052 GCAGATGAGCTCGGAGCC 60.280 66.667 25.49 17.13 43.77 4.70
137 138 3.086391 GCAGATGAGCTCGGAGCCA 62.086 63.158 25.49 21.72 43.77 4.75
138 139 1.519246 CAGATGAGCTCGGAGCCAA 59.481 57.895 25.49 14.88 43.77 4.52
139 140 0.107993 CAGATGAGCTCGGAGCCAAA 60.108 55.000 25.49 12.35 43.77 3.28
140 141 0.835941 AGATGAGCTCGGAGCCAAAT 59.164 50.000 25.49 16.39 43.77 2.32
141 142 2.042464 AGATGAGCTCGGAGCCAAATA 58.958 47.619 25.49 8.77 43.77 1.40
142 143 2.036992 AGATGAGCTCGGAGCCAAATAG 59.963 50.000 25.49 0.00 43.77 1.73
143 144 1.485124 TGAGCTCGGAGCCAAATAGA 58.515 50.000 25.49 0.17 43.77 1.98
144 145 1.137086 TGAGCTCGGAGCCAAATAGAC 59.863 52.381 25.49 8.31 43.77 2.59
145 146 1.137086 GAGCTCGGAGCCAAATAGACA 59.863 52.381 25.49 0.00 43.77 3.41
146 147 1.134670 AGCTCGGAGCCAAATAGACAC 60.135 52.381 25.49 0.00 43.77 3.67
147 148 1.941325 CTCGGAGCCAAATAGACACC 58.059 55.000 0.00 0.00 0.00 4.16
148 149 0.539986 TCGGAGCCAAATAGACACCC 59.460 55.000 0.00 0.00 0.00 4.61
149 150 0.541863 CGGAGCCAAATAGACACCCT 59.458 55.000 0.00 0.00 0.00 4.34
150 151 1.473434 CGGAGCCAAATAGACACCCTC 60.473 57.143 0.00 0.00 0.00 4.30
151 152 1.559682 GGAGCCAAATAGACACCCTCA 59.440 52.381 0.00 0.00 0.00 3.86
152 153 2.173569 GGAGCCAAATAGACACCCTCAT 59.826 50.000 0.00 0.00 0.00 2.90
153 154 3.391296 GGAGCCAAATAGACACCCTCATA 59.609 47.826 0.00 0.00 0.00 2.15
154 155 4.141482 GGAGCCAAATAGACACCCTCATAA 60.141 45.833 0.00 0.00 0.00 1.90
155 156 5.437060 GAGCCAAATAGACACCCTCATAAA 58.563 41.667 0.00 0.00 0.00 1.40
156 157 5.440610 AGCCAAATAGACACCCTCATAAAG 58.559 41.667 0.00 0.00 0.00 1.85
157 158 5.191722 AGCCAAATAGACACCCTCATAAAGA 59.808 40.000 0.00 0.00 0.00 2.52
158 159 6.064717 GCCAAATAGACACCCTCATAAAGAT 58.935 40.000 0.00 0.00 0.00 2.40
203 204 7.201609 GCAATTGCACTGATCATTTGATTTCAT 60.202 33.333 25.36 0.00 41.59 2.57
327 338 3.391626 CCTCCCTTGGGAATAGGAAGTAC 59.608 52.174 9.93 0.00 34.56 2.73
459 502 5.300286 GTCCTATGCCATTGTGCTAATCTTT 59.700 40.000 0.00 0.00 0.00 2.52
482 525 2.093341 GGGGCCGAAGACAATAACTACA 60.093 50.000 0.00 0.00 0.00 2.74
483 526 3.195661 GGGCCGAAGACAATAACTACAG 58.804 50.000 0.00 0.00 0.00 2.74
484 527 3.369157 GGGCCGAAGACAATAACTACAGT 60.369 47.826 0.00 0.00 0.00 3.55
485 528 4.142093 GGGCCGAAGACAATAACTACAGTA 60.142 45.833 0.00 0.00 0.00 2.74
567 709 0.601841 GCCGTGTATCAATACCGGGG 60.602 60.000 21.18 11.61 42.29 5.73
705 850 1.306141 TCTCGATTCAGGCCCAGGT 60.306 57.895 0.00 0.00 0.00 4.00
709 854 0.811281 CGATTCAGGCCCAGGTTTTC 59.189 55.000 0.00 0.00 0.00 2.29
777 924 0.690192 TTCTGGTCGATTTGAGGCCA 59.310 50.000 5.01 0.00 41.69 5.36
814 962 1.209128 CGACCCTTTGATCGAATCGG 58.791 55.000 1.76 7.93 40.86 4.18
824 972 4.236416 CGAATCGGCCGCGCAAAT 62.236 61.111 23.51 5.11 0.00 2.32
872 1020 3.855379 CCGCATGTGTGATTCTTGATTTG 59.145 43.478 5.38 0.00 0.00 2.32
882 1030 0.036732 TCTTGATTTGTGCTCGCCCT 59.963 50.000 0.00 0.00 0.00 5.19
890 1038 1.295423 GTGCTCGCCCTGGTAGAAA 59.705 57.895 0.00 0.00 0.00 2.52
942 1097 1.078709 CTTCGCTCGGCAAATCTGAA 58.921 50.000 0.00 0.00 0.00 3.02
988 1143 2.941333 CTGCCATAATCCGCGCAG 59.059 61.111 8.75 0.00 42.42 5.18
1287 1442 0.796255 AGCCCTGCTCCCCTATATCT 59.204 55.000 0.00 0.00 30.62 1.98
1308 1463 5.011840 ATCTACTAAGAAGGGGATTTACGCC 59.988 44.000 0.00 0.00 41.48 5.68
1337 1492 2.213499 CCGACCTACTCCATTTGATGC 58.787 52.381 0.00 0.00 0.00 3.91
1375 1537 8.986929 AGAACTATAATCTTTTATGGCAGCTT 57.013 30.769 0.00 0.00 31.37 3.74
1376 1538 8.844244 AGAACTATAATCTTTTATGGCAGCTTG 58.156 33.333 0.00 0.00 31.37 4.01
1377 1539 8.525290 AACTATAATCTTTTATGGCAGCTTGT 57.475 30.769 0.00 0.00 31.37 3.16
1378 1540 9.627123 AACTATAATCTTTTATGGCAGCTTGTA 57.373 29.630 0.00 0.00 31.37 2.41
1379 1541 9.799106 ACTATAATCTTTTATGGCAGCTTGTAT 57.201 29.630 0.00 0.00 31.37 2.29
1391 1553 7.205737 TGGCAGCTTGTATTATTATGTCATG 57.794 36.000 0.00 0.00 0.00 3.07
1411 1573 9.810545 TGTCATGTACGTAGATGATTAATTGAA 57.189 29.630 30.83 9.21 38.11 2.69
1452 1614 4.260170 CTGGAAACTGGAGAGGATTTCTG 58.740 47.826 0.00 0.00 35.87 3.02
1501 1679 4.755123 GGTTTAGCTGTAGTTCTTGCTTGA 59.245 41.667 0.00 0.00 37.02 3.02
1510 1688 7.148853 GCTGTAGTTCTTGCTTGAAATGAATTG 60.149 37.037 3.29 0.00 0.00 2.32
1801 1987 1.114627 TGCACTGGAGTATCGCTGAT 58.885 50.000 0.00 0.00 34.37 2.90
1839 2029 7.396540 ACTCCTAAAGAACCTATTTTGCATG 57.603 36.000 0.00 0.00 0.00 4.06
2033 4441 5.189928 TGAAGTCAGCAGTTAACCTCAAAA 58.810 37.500 0.88 0.00 0.00 2.44
2190 4609 8.539117 TTTCCTCTGACACAGATCTATTATGA 57.461 34.615 0.00 0.00 39.92 2.15
2318 4738 4.153475 CCCACATTAACCGACTACAAACAG 59.847 45.833 0.00 0.00 0.00 3.16
2454 4874 7.250032 TGGGATATGGAGAGTGAATAATCTG 57.750 40.000 0.00 0.00 30.12 2.90
2699 5135 7.993867 CGTCAAGTACGTTTCTAATCATATCC 58.006 38.462 0.00 0.00 46.72 2.59
2730 5166 9.991906 GTGTACCTAGTATTCCATTATAAAGCA 57.008 33.333 0.00 0.00 0.00 3.91
2886 5322 6.636562 TCTACATTTCCTAGTCCTTCGATC 57.363 41.667 0.00 0.00 0.00 3.69
2887 5323 6.127101 TCTACATTTCCTAGTCCTTCGATCA 58.873 40.000 0.00 0.00 0.00 2.92
2895 5331 5.011125 TCCTAGTCCTTCGATCATTTCATCC 59.989 44.000 0.00 0.00 0.00 3.51
3238 5691 1.478510 AGCTGGATTCTCTACCACGTG 59.521 52.381 9.08 9.08 32.44 4.49
3340 5793 1.066303 GGTGGTTTGTGCGTTGATTCA 59.934 47.619 0.00 0.00 0.00 2.57
3352 5805 4.749598 TGCGTTGATTCAGTTGCGATATAT 59.250 37.500 0.00 0.00 0.00 0.86
3384 5837 1.132640 GGCGCGAGAACATGAACAC 59.867 57.895 12.10 0.00 0.00 3.32
3416 5869 2.751259 TGATGAGATTTTGCAGAGTGGC 59.249 45.455 0.00 0.00 0.00 5.01
3683 6136 7.484035 GGTCAATACCATCTTCATCTGTAAC 57.516 40.000 0.00 0.00 45.98 2.50
3697 6150 7.776933 TCATCTGTAACTTTCATCAGCATAC 57.223 36.000 0.00 0.00 0.00 2.39
3725 6178 2.266055 CGAGCTGGGTGTTCCTCC 59.734 66.667 0.00 0.00 36.20 4.30
3786 6256 3.881688 CCATTTGGGTTTGTTTTCATGCA 59.118 39.130 0.00 0.00 0.00 3.96
3814 6284 9.702494 CAGCTTGAATGTATGAGAATGATACTA 57.298 33.333 0.00 0.00 36.09 1.82
3820 6290 6.208988 TGTATGAGAATGATACTATCGGGC 57.791 41.667 0.00 0.00 36.09 6.13
3872 6342 0.919289 ACCTTGGGATCGGGGACATT 60.919 55.000 0.00 0.00 0.00 2.71
3885 6355 3.619487 CGGGGACATTTTTGCCATCAAAT 60.619 43.478 0.00 0.00 41.37 2.32
4028 7687 9.772973 ACTAAACACAGAACAAACATATACTCA 57.227 29.630 0.00 0.00 0.00 3.41
4030 7689 8.445275 AAACACAGAACAAACATATACTCACA 57.555 30.769 0.00 0.00 0.00 3.58
4064 7723 3.249080 ACACTCATTCCGGTTAACAAACG 59.751 43.478 8.10 1.81 42.36 3.60
4072 7731 0.248134 GGTTAACAAACGCACGCACA 60.248 50.000 8.10 0.00 0.00 4.57
4073 7732 1.109296 GTTAACAAACGCACGCACAG 58.891 50.000 0.00 0.00 0.00 3.66
4142 7801 1.829533 GGGGCATGCTACACCATGG 60.830 63.158 18.92 11.19 42.18 3.66
4207 7867 7.038659 ACTCTTCAAGTCAGATTATGCTACAC 58.961 38.462 0.00 0.00 30.02 2.90
4261 7921 3.681593 TCACATAACCACAAACTAGGGC 58.318 45.455 0.00 0.00 0.00 5.19
4334 7994 4.084849 CGAAATACATCGGAGTTGCTGATC 60.085 45.833 0.00 0.00 40.68 2.92
4359 8019 4.736793 CGGCACAATCAAGATTTAAGATGC 59.263 41.667 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.679960 CAATCGGACCCCTCAAACCC 60.680 60.000 0.00 0.00 0.00 4.11
1 2 0.037734 ACAATCGGACCCCTCAAACC 59.962 55.000 0.00 0.00 0.00 3.27
2 3 2.235402 TCTACAATCGGACCCCTCAAAC 59.765 50.000 0.00 0.00 0.00 2.93
3 4 2.542550 TCTACAATCGGACCCCTCAAA 58.457 47.619 0.00 0.00 0.00 2.69
4 5 2.241281 TCTACAATCGGACCCCTCAA 57.759 50.000 0.00 0.00 0.00 3.02
5 6 2.039418 CATCTACAATCGGACCCCTCA 58.961 52.381 0.00 0.00 0.00 3.86
6 7 1.270358 GCATCTACAATCGGACCCCTC 60.270 57.143 0.00 0.00 0.00 4.30
7 8 0.759346 GCATCTACAATCGGACCCCT 59.241 55.000 0.00 0.00 0.00 4.79
8 9 0.759346 AGCATCTACAATCGGACCCC 59.241 55.000 0.00 0.00 0.00 4.95
9 10 2.156343 GAGCATCTACAATCGGACCC 57.844 55.000 0.00 0.00 0.00 4.46
24 25 1.079819 GCTTAGGTGCGTGAGAGCA 60.080 57.895 0.00 0.00 45.96 4.26
25 26 0.460987 ATGCTTAGGTGCGTGAGAGC 60.461 55.000 0.00 0.00 35.36 4.09
26 27 1.135915 AGATGCTTAGGTGCGTGAGAG 59.864 52.381 0.00 0.00 35.36 3.20
27 28 1.186200 AGATGCTTAGGTGCGTGAGA 58.814 50.000 0.00 0.00 35.36 3.27
28 29 1.929836 GAAGATGCTTAGGTGCGTGAG 59.070 52.381 0.00 0.00 35.36 3.51
29 30 1.405526 GGAAGATGCTTAGGTGCGTGA 60.406 52.381 0.00 0.00 35.36 4.35
30 31 1.009829 GGAAGATGCTTAGGTGCGTG 58.990 55.000 0.00 0.00 35.36 5.34
31 32 0.613260 TGGAAGATGCTTAGGTGCGT 59.387 50.000 0.00 0.00 35.36 5.24
32 33 1.600957 CATGGAAGATGCTTAGGTGCG 59.399 52.381 0.00 0.00 35.36 5.34
33 34 1.336125 GCATGGAAGATGCTTAGGTGC 59.664 52.381 0.00 0.00 41.52 5.01
34 35 2.646930 TGCATGGAAGATGCTTAGGTG 58.353 47.619 8.05 0.00 44.79 4.00
35 36 3.370840 TTGCATGGAAGATGCTTAGGT 57.629 42.857 8.05 0.00 44.79 3.08
36 37 4.724074 TTTTGCATGGAAGATGCTTAGG 57.276 40.909 0.00 0.00 44.79 2.69
93 94 9.717942 CTCCCATGGTGAATAACAAATTTTAAA 57.282 29.630 11.73 0.00 0.00 1.52
94 95 7.821846 GCTCCCATGGTGAATAACAAATTTTAA 59.178 33.333 11.73 0.00 0.00 1.52
95 96 7.038729 TGCTCCCATGGTGAATAACAAATTTTA 60.039 33.333 11.73 0.00 0.00 1.52
96 97 6.172630 GCTCCCATGGTGAATAACAAATTTT 58.827 36.000 11.73 0.00 0.00 1.82
97 98 5.248020 TGCTCCCATGGTGAATAACAAATTT 59.752 36.000 11.73 0.00 0.00 1.82
98 99 4.776837 TGCTCCCATGGTGAATAACAAATT 59.223 37.500 11.73 0.00 0.00 1.82
99 100 4.352009 TGCTCCCATGGTGAATAACAAAT 58.648 39.130 11.73 0.00 0.00 2.32
100 101 3.763360 CTGCTCCCATGGTGAATAACAAA 59.237 43.478 11.73 0.00 0.00 2.83
101 102 3.010027 TCTGCTCCCATGGTGAATAACAA 59.990 43.478 11.73 0.00 0.00 2.83
102 103 2.575735 TCTGCTCCCATGGTGAATAACA 59.424 45.455 11.73 3.56 0.00 2.41
103 104 3.281727 TCTGCTCCCATGGTGAATAAC 57.718 47.619 11.73 0.00 0.00 1.89
104 105 3.459227 TCATCTGCTCCCATGGTGAATAA 59.541 43.478 11.73 0.00 0.00 1.40
105 106 3.047857 TCATCTGCTCCCATGGTGAATA 58.952 45.455 11.73 0.00 0.00 1.75
106 107 1.848388 TCATCTGCTCCCATGGTGAAT 59.152 47.619 11.73 0.00 0.00 2.57
107 108 1.211212 CTCATCTGCTCCCATGGTGAA 59.789 52.381 11.73 0.00 0.00 3.18
108 109 0.835276 CTCATCTGCTCCCATGGTGA 59.165 55.000 11.73 6.87 0.00 4.02
109 110 0.818445 GCTCATCTGCTCCCATGGTG 60.818 60.000 11.73 4.22 0.00 4.17
110 111 0.987081 AGCTCATCTGCTCCCATGGT 60.987 55.000 11.73 0.00 39.34 3.55
111 112 1.837789 AGCTCATCTGCTCCCATGG 59.162 57.895 4.14 4.14 39.34 3.66
119 120 2.280052 GGCTCCGAGCTCATCTGC 60.280 66.667 19.68 11.50 41.99 4.26
120 121 0.107993 TTTGGCTCCGAGCTCATCTG 60.108 55.000 19.68 1.62 41.99 2.90
121 122 0.835941 ATTTGGCTCCGAGCTCATCT 59.164 50.000 19.68 4.62 41.99 2.90
122 123 2.036475 TCTATTTGGCTCCGAGCTCATC 59.964 50.000 19.68 4.00 41.99 2.92
123 124 2.042464 TCTATTTGGCTCCGAGCTCAT 58.958 47.619 19.68 11.42 41.99 2.90
124 125 1.137086 GTCTATTTGGCTCCGAGCTCA 59.863 52.381 19.68 12.94 41.99 4.26
125 126 1.137086 TGTCTATTTGGCTCCGAGCTC 59.863 52.381 19.68 2.73 41.99 4.09
126 127 1.134670 GTGTCTATTTGGCTCCGAGCT 60.135 52.381 19.68 2.77 41.99 4.09
127 128 1.291132 GTGTCTATTTGGCTCCGAGC 58.709 55.000 12.27 12.27 41.46 5.03
128 129 1.473434 GGGTGTCTATTTGGCTCCGAG 60.473 57.143 0.00 0.00 34.95 4.63
129 130 0.539986 GGGTGTCTATTTGGCTCCGA 59.460 55.000 0.00 0.00 34.95 4.55
130 131 0.541863 AGGGTGTCTATTTGGCTCCG 59.458 55.000 0.00 0.00 34.95 4.63
131 132 1.559682 TGAGGGTGTCTATTTGGCTCC 59.440 52.381 0.00 0.00 33.48 4.70
132 133 3.567478 ATGAGGGTGTCTATTTGGCTC 57.433 47.619 0.00 0.00 0.00 4.70
133 134 5.191722 TCTTTATGAGGGTGTCTATTTGGCT 59.808 40.000 0.00 0.00 0.00 4.75
134 135 5.437060 TCTTTATGAGGGTGTCTATTTGGC 58.563 41.667 0.00 0.00 0.00 4.52
135 136 8.432805 ACTATCTTTATGAGGGTGTCTATTTGG 58.567 37.037 0.00 0.00 0.00 3.28
136 137 9.838339 AACTATCTTTATGAGGGTGTCTATTTG 57.162 33.333 0.00 0.00 0.00 2.32
138 139 9.440761 AGAACTATCTTTATGAGGGTGTCTATT 57.559 33.333 0.00 0.00 29.15 1.73
139 140 9.440761 AAGAACTATCTTTATGAGGGTGTCTAT 57.559 33.333 0.00 0.00 43.43 1.98
140 141 8.840200 AAGAACTATCTTTATGAGGGTGTCTA 57.160 34.615 0.00 0.00 43.43 2.59
141 142 7.741554 AAGAACTATCTTTATGAGGGTGTCT 57.258 36.000 0.00 0.00 43.43 3.41
155 156 4.457257 GCCAGCTGAAACAAAGAACTATCT 59.543 41.667 17.39 0.00 37.57 1.98
156 157 4.216257 TGCCAGCTGAAACAAAGAACTATC 59.784 41.667 17.39 0.00 0.00 2.08
157 158 4.144297 TGCCAGCTGAAACAAAGAACTAT 58.856 39.130 17.39 0.00 0.00 2.12
158 159 3.550820 TGCCAGCTGAAACAAAGAACTA 58.449 40.909 17.39 0.00 0.00 2.24
174 175 3.520290 AATGATCAGTGCAATTGCCAG 57.480 42.857 26.94 16.31 41.18 4.85
277 279 7.593644 GCCGCTATTGAACCGATAAAATTTATT 59.406 33.333 0.00 0.00 0.00 1.40
278 280 7.081976 GCCGCTATTGAACCGATAAAATTTAT 58.918 34.615 0.00 0.00 0.00 1.40
294 305 1.097547 CAAGGGAGGTGCCGCTATTG 61.098 60.000 0.00 0.00 37.63 1.90
327 338 9.507280 TGGATTAAGTTCGAATTTAGTACTACG 57.493 33.333 15.86 3.18 0.00 3.51
356 399 5.733091 GCGGATTTGATTCGATTGGATTTGA 60.733 40.000 0.00 0.00 0.00 2.69
472 515 8.241367 GGGTCCAATTGTTTACTGTAGTTATTG 58.759 37.037 4.43 0.00 0.00 1.90
482 525 3.319689 CCGTTTGGGTCCAATTGTTTACT 59.680 43.478 4.43 0.00 35.70 2.24
483 526 3.644823 CCGTTTGGGTCCAATTGTTTAC 58.355 45.455 4.43 0.00 35.70 2.01
484 527 2.036089 GCCGTTTGGGTCCAATTGTTTA 59.964 45.455 4.43 0.00 38.44 2.01
485 528 1.202592 GCCGTTTGGGTCCAATTGTTT 60.203 47.619 4.43 0.00 38.44 2.83
697 842 0.544120 TTGATGGGAAAACCTGGGCC 60.544 55.000 0.00 0.00 41.11 5.80
824 972 4.142491 CCAAATTACAGCCGAATACAAGCA 60.142 41.667 0.00 0.00 0.00 3.91
872 1020 0.741221 CTTTCTACCAGGGCGAGCAC 60.741 60.000 0.00 0.00 0.00 4.40
955 1110 1.302033 CAGCCTTCCTTGCAGACGT 60.302 57.895 0.00 0.00 0.00 4.34
988 1143 2.629051 CGTCCCCATCTAAGACCAAAC 58.371 52.381 0.00 0.00 0.00 2.93
1287 1442 3.389002 GGGCGTAAATCCCCTTCTTAGTA 59.611 47.826 0.00 0.00 38.30 1.82
1337 1492 7.949434 AGATTATAGTTCTACCTTTGTACCGG 58.051 38.462 0.00 0.00 0.00 5.28
1384 1546 9.981114 TCAATTAATCATCTACGTACATGACAT 57.019 29.630 14.67 9.95 31.80 3.06
1385 1547 9.810545 TTCAATTAATCATCTACGTACATGACA 57.189 29.630 14.67 4.66 31.80 3.58
1411 1573 7.956328 TTCCAGTATTAGCCGATATATCTGT 57.044 36.000 10.93 0.00 0.00 3.41
1420 1582 3.101437 TCCAGTTTCCAGTATTAGCCGA 58.899 45.455 0.00 0.00 0.00 5.54
1421 1583 3.132289 TCTCCAGTTTCCAGTATTAGCCG 59.868 47.826 0.00 0.00 0.00 5.52
1423 1585 4.406003 TCCTCTCCAGTTTCCAGTATTAGC 59.594 45.833 0.00 0.00 0.00 3.09
1424 1586 6.739331 ATCCTCTCCAGTTTCCAGTATTAG 57.261 41.667 0.00 0.00 0.00 1.73
1472 1634 6.621596 GCAAGAACTACAGCTAAACCAATCAG 60.622 42.308 0.00 0.00 0.00 2.90
1479 1641 5.924475 TCAAGCAAGAACTACAGCTAAAC 57.076 39.130 0.00 0.00 36.07 2.01
1483 1645 5.065914 TCATTTCAAGCAAGAACTACAGCT 58.934 37.500 0.00 0.00 39.37 4.24
1501 1679 6.991531 TGCCTTTTAAGCAGAACAATTCATTT 59.008 30.769 0.00 0.00 34.69 2.32
1510 1688 3.726291 TGGTTGCCTTTTAAGCAGAAC 57.274 42.857 0.00 0.00 42.17 3.01
1537 1715 2.292569 CGATCCAGAATTCCTGCCATTG 59.707 50.000 0.65 0.00 41.57 2.82
1539 1717 1.770658 TCGATCCAGAATTCCTGCCAT 59.229 47.619 0.65 0.00 41.57 4.40
1541 1719 1.414181 TCTCGATCCAGAATTCCTGCC 59.586 52.381 0.65 0.00 41.57 4.85
1608 1786 6.540083 TCTTCGGTCATCTATACCTGTGATA 58.460 40.000 0.00 0.00 34.66 2.15
1848 2038 4.739137 GCAAAACAACCCAGCAATGAAGTA 60.739 41.667 0.00 0.00 0.00 2.24
1923 2118 5.063017 AGCCTAACCAGCTACAGAGTATA 57.937 43.478 0.00 0.00 39.29 1.47
2011 4419 5.751243 TTTTGAGGTTAACTGCTGACTTC 57.249 39.130 5.42 0.00 0.00 3.01
2033 4441 6.171921 TGCAAAATTAGCAACATTTAGGCAT 58.828 32.000 3.25 0.00 39.39 4.40
2318 4738 7.285401 AGAGAACCTCTTCTGTTGATCTATCTC 59.715 40.741 0.00 0.00 37.60 2.75
2693 5114 7.122948 GGAATACTAGGTACACTCCAGGATATG 59.877 44.444 0.00 0.00 0.00 1.78
2699 5135 6.732896 AATGGAATACTAGGTACACTCCAG 57.267 41.667 0.00 0.00 32.18 3.86
2730 5166 9.926158 TGCAAGAAAACATCAATACATACAAAT 57.074 25.926 0.00 0.00 0.00 2.32
2877 5313 5.357742 TGAAGGATGAAATGATCGAAGGA 57.642 39.130 0.00 0.00 0.00 3.36
3238 5691 4.003648 AGTTCGAGATGACAAAATCACCC 58.996 43.478 0.00 0.00 41.24 4.61
3340 5793 3.323979 ACCCTTTCGGATATATCGCAACT 59.676 43.478 6.64 0.00 34.64 3.16
3384 5837 5.503031 GCAAAATCTCATCACATGTAGACCG 60.503 44.000 0.00 0.00 0.00 4.79
3420 5873 4.284860 TCGTGTCGCTGCAGCACT 62.285 61.111 36.03 0.00 42.21 4.40
3566 6019 4.267341 ACCTCCCTAGCTGTGTAACTAT 57.733 45.455 0.00 0.00 38.04 2.12
3697 6150 1.651240 CCCAGCTCGCCAAACATCAG 61.651 60.000 0.00 0.00 0.00 2.90
3725 6178 2.554806 TATAATCATAGGGCGACGCG 57.445 50.000 14.61 3.53 0.00 6.01
3763 6218 3.304592 GCATGAAAACAAACCCAAATGGC 60.305 43.478 0.00 0.00 37.83 4.40
3786 6256 9.217278 GTATCATTCTCATACATTCAAGCTGAT 57.783 33.333 0.00 0.00 0.00 2.90
3814 6284 1.671979 CACATCAACATCAGCCCGAT 58.328 50.000 0.00 0.00 33.27 4.18
3820 6290 1.931841 CTCCGAGCACATCAACATCAG 59.068 52.381 0.00 0.00 0.00 2.90
3857 6327 1.846007 CAAAAATGTCCCCGATCCCA 58.154 50.000 0.00 0.00 0.00 4.37
3872 6342 8.442632 TGTATTCAACAAATTTGATGGCAAAA 57.557 26.923 24.64 12.77 40.23 2.44
3931 6429 1.981256 AAGTGGAAGCAACCAATCGT 58.019 45.000 3.52 0.00 41.87 3.73
3932 6430 2.554032 AGAAAGTGGAAGCAACCAATCG 59.446 45.455 3.52 0.00 41.87 3.34
3934 6432 3.319122 GTGAGAAAGTGGAAGCAACCAAT 59.681 43.478 3.52 0.04 41.87 3.16
3936 6434 2.297701 GTGAGAAAGTGGAAGCAACCA 58.702 47.619 0.00 0.00 37.63 3.67
3938 6436 2.291741 CAGGTGAGAAAGTGGAAGCAAC 59.708 50.000 0.00 0.00 0.00 4.17
3940 6438 1.202806 CCAGGTGAGAAAGTGGAAGCA 60.203 52.381 0.00 0.00 31.04 3.91
3941 6439 1.528129 CCAGGTGAGAAAGTGGAAGC 58.472 55.000 0.00 0.00 31.04 3.86
4026 7685 7.926018 GGAATGAGTGTATGTATGTGTATGTGA 59.074 37.037 0.00 0.00 0.00 3.58
4027 7686 7.096065 CGGAATGAGTGTATGTATGTGTATGTG 60.096 40.741 0.00 0.00 0.00 3.21
4028 7687 6.923508 CGGAATGAGTGTATGTATGTGTATGT 59.076 38.462 0.00 0.00 0.00 2.29
4029 7688 6.366061 CCGGAATGAGTGTATGTATGTGTATG 59.634 42.308 0.00 0.00 0.00 2.39
4030 7689 6.041637 ACCGGAATGAGTGTATGTATGTGTAT 59.958 38.462 9.46 0.00 0.00 2.29
4064 7723 2.501223 TAGTGGTAGGCTGTGCGTGC 62.501 60.000 0.00 0.00 0.00 5.34
4072 7731 3.635510 GGCTGCTAGTGGTAGGCT 58.364 61.111 10.67 0.00 46.50 4.58
4111 7770 1.576368 ATGCCCCATGGAACGGGTTA 61.576 55.000 15.22 0.00 42.77 2.85
4142 7801 6.932356 TGATCATAATCCTCTCAAAACTGC 57.068 37.500 0.00 0.00 0.00 4.40
4207 7867 1.277273 TGATCTGAGAGCCCTGTTGTG 59.723 52.381 0.00 0.00 0.00 3.33
4261 7921 2.669434 GCAATTTTATGTGTGCCTGCAG 59.331 45.455 6.78 6.78 0.00 4.41
4334 7994 5.295431 TCTTAAATCTTGATTGTGCCGTG 57.705 39.130 0.00 0.00 0.00 4.94
4359 8019 0.252479 ATCTGCCTGAGCTGTTCCAG 59.748 55.000 0.00 0.00 40.80 3.86


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

AutoCloner maintained by Alex Coulton.