Multiple sequence alignment - TraesCS7D01G364700

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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 TraesCS7D01G364700 chr7D 100.000 7765 0 0 1 7765 470893937 470886173 0.000000e+00 14340.0
1 TraesCS7D01G364700 chr7B 95.257 6747 224 42 254 6952 494588408 494581710 0.000000e+00 10599.0
2 TraesCS7D01G364700 chr7B 91.876 517 17 8 7263 7765 494581340 494580835 0.000000e+00 699.0
3 TraesCS7D01G364700 chr7B 92.835 321 17 2 6946 7265 494581683 494581368 1.970000e-125 460.0
4 TraesCS7D01G364700 chr7B 85.659 258 31 4 1 254 494588826 494588571 4.620000e-67 267.0
5 TraesCS7D01G364700 chr7A 92.433 4348 227 57 180 4482 527533804 527538094 0.000000e+00 6113.0
6 TraesCS7D01G364700 chr7A 92.903 2494 143 20 4481 6954 527538173 527540652 0.000000e+00 3594.0
7 TraesCS7D01G364700 chr7A 88.046 435 30 12 7353 7765 527541068 527541502 5.410000e-136 496.0
8 TraesCS7D01G364700 chr7A 89.506 324 27 1 6946 7262 527540677 527541000 3.370000e-108 403.0
9 TraesCS7D01G364700 chr6D 86.043 2350 246 40 3618 5938 91983 89687 0.000000e+00 2447.0
10 TraesCS7D01G364700 chr6D 91.020 1392 125 0 1772 3163 95121 93730 0.000000e+00 1879.0
11 TraesCS7D01G364700 chr6D 88.914 893 85 8 6056 6947 89637 88758 0.000000e+00 1088.0
12 TraesCS7D01G364700 chr6D 89.340 394 39 3 3200 3591 93553 93161 7.000000e-135 492.0
13 TraesCS7D01G364700 chr5D 82.160 213 27 6 7 210 486734631 486734841 1.040000e-38 172.0
14 TraesCS7D01G364700 chr5A 85.915 142 19 1 6 147 378502701 378502561 4.850000e-32 150.0
15 TraesCS7D01G364700 chr4B 81.481 162 18 8 1 151 55031787 55031947 1.060000e-23 122.0
16 TraesCS7D01G364700 chr2B 88.776 98 10 1 1 98 439922172 439922268 1.370000e-22 119.0
17 TraesCS7D01G364700 chr2D 83.019 106 15 3 1 105 368530385 368530282 8.300000e-15 93.5
18 TraesCS7D01G364700 chr1D 80.000 95 19 0 68 162 452862744 452862838 3.890000e-08 71.3


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 TraesCS7D01G364700 chr7D 470886173 470893937 7764 True 14340.00 14340 100.00000 1 7765 1 chr7D.!!$R1 7764
1 TraesCS7D01G364700 chr7B 494580835 494588826 7991 True 3006.25 10599 91.40675 1 7765 4 chr7B.!!$R1 7764
2 TraesCS7D01G364700 chr7A 527533804 527541502 7698 False 2651.50 6113 90.72200 180 7765 4 chr7A.!!$F1 7585
3 TraesCS7D01G364700 chr6D 88758 95121 6363 True 1476.50 2447 88.82925 1772 6947 4 chr6D.!!$R1 5175

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
865 1062 0.246635 AAATCCTCCGTCTGTCCGTG 59.753 55.000 0.00 0.00 0.00 4.94 F
1176 1383 0.030101 CCCGTTGCTTTGCTTTTCGA 59.970 50.000 0.00 0.00 0.00 3.71 F
1183 1400 0.704551 CTTTGCTTTTCGATGCGTGC 59.295 50.000 0.00 0.00 0.00 5.34 F
1587 1810 1.067821 CTATGGTGGACGCTCTTCTCC 59.932 57.143 0.00 0.00 0.00 3.71 F
2634 2857 1.079405 GTTCCGGAGCATGGTCGAA 60.079 57.895 18.14 13.73 0.00 3.71 F
3696 5214 1.003866 GTTCTTGTGACGCACCAAGTC 60.004 52.381 7.38 0.00 38.98 3.01 F
4309 5832 1.142748 CGCCTACCTCAGAAGCCTG 59.857 63.158 0.00 0.00 41.74 4.85 F
4333 5856 1.276421 GCTGCTACTCTGGGACTCAAA 59.724 52.381 0.00 0.00 0.00 2.69 F
4466 5993 1.615392 GTATGGCTCCCCAAATGATGC 59.385 52.381 0.00 0.00 46.14 3.91 F
5656 7317 0.741221 GTCTCGTTGATCCTGTGGGC 60.741 60.000 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2378 0.171455 ACGAGCTTGATGACGAGGAC 59.829 55.000 8.31 0.00 0.00 3.85 R
2784 3007 0.320771 CCAAGACCGTGAAGAGGGTG 60.321 60.000 0.00 0.00 40.57 4.61 R
2835 3058 3.729108 TGTCAGGATCTCAGGAAGGAAT 58.271 45.455 0.00 0.00 0.00 3.01 R
3503 3867 0.338814 AAGGGTCGTCCAGGAGGTAT 59.661 55.000 9.04 0.00 38.24 2.73 R
4450 5977 0.176449 GTTGCATCATTTGGGGAGCC 59.824 55.000 0.00 0.00 0.00 4.70 R
5521 7182 1.400494 AGAACAAGTGGTGTGTTTCGC 59.600 47.619 0.00 0.00 40.60 4.70 R
5530 7191 4.580580 GTGATTCCTTTGAGAACAAGTGGT 59.419 41.667 0.00 0.00 37.32 4.16 R
5656 7317 5.277857 AGTTGTCAATAAGTATCCTCCCG 57.722 43.478 0.00 0.00 0.00 5.14 R
6201 7870 7.449086 TCATTTTAACCTTCCGGTAACTCAAAT 59.551 33.333 0.00 0.00 44.73 2.32 R
6978 8686 1.353022 AGTCTTGGAGGACTCGAGTCT 59.647 52.381 36.98 25.73 42.15 3.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 8.763356 CAAATATTTGTTATTTACATGCGGCAT 58.237 29.630 18.32 10.23 38.23 4.40
68 69 8.885494 AATATTTGTTATTTACATGCGGCATT 57.115 26.923 13.81 7.72 36.44 3.56
69 70 6.586868 ATTTGTTATTTACATGCGGCATTG 57.413 33.333 13.81 11.32 36.44 2.82
70 71 4.039151 TGTTATTTACATGCGGCATTGG 57.961 40.909 13.81 5.71 0.00 3.16
71 72 2.791383 TATTTACATGCGGCATTGGC 57.209 45.000 13.81 0.00 40.13 4.52
109 114 4.409901 TGCATGGATTTGAGAGTCCAGATA 59.590 41.667 0.00 0.00 46.87 1.98
124 129 3.935315 CCAGATATGAGGTATGTGGCTG 58.065 50.000 0.00 0.00 44.44 4.85
125 130 3.326006 CCAGATATGAGGTATGTGGCTGT 59.674 47.826 0.00 0.00 44.44 4.40
129 134 1.521681 GAGGTATGTGGCTGTCGGC 60.522 63.158 0.00 0.00 40.90 5.54
148 153 1.004044 GCCATGAGATATGAGGGGTGG 59.996 57.143 0.00 0.00 0.00 4.61
151 156 3.246301 CATGAGATATGAGGGGTGGTCT 58.754 50.000 0.00 0.00 0.00 3.85
155 160 1.694696 GATATGAGGGGTGGTCTGGAC 59.305 57.143 0.00 0.00 0.00 4.02
157 162 4.083862 GAGGGGTGGTCTGGACGC 62.084 72.222 0.00 0.00 0.00 5.19
160 165 4.736896 GGGTGGTCTGGACGCGTC 62.737 72.222 30.67 30.67 0.00 5.19
175 180 3.900855 GTCCGCAGACGTAGAGGA 58.099 61.111 8.55 8.55 37.70 3.71
176 181 2.177950 GTCCGCAGACGTAGAGGAA 58.822 57.895 13.23 0.00 37.70 3.36
178 183 1.226717 CCGCAGACGTAGAGGAAGC 60.227 63.158 4.53 0.00 37.70 3.86
277 445 6.670233 TGGTACGTAAAACAAAATAAGCAGG 58.330 36.000 0.00 0.00 0.00 4.85
325 493 8.339247 TGATCTCTCCTCCCAAGAATAAATTTT 58.661 33.333 0.00 0.00 0.00 1.82
378 550 9.008965 TCATGTTTTAATGGCGCTATACATTAT 57.991 29.630 14.88 0.00 38.80 1.28
398 570 9.921637 ACATTATTTCCTTATTTTTGCGAAAGA 57.078 25.926 0.00 0.00 0.00 2.52
435 607 1.612991 CCCCACACGATCATGGACAAA 60.613 52.381 8.83 0.00 38.34 2.83
466 643 8.879342 CTCCACAAGAGGTAAGAGTAATATTG 57.121 38.462 0.00 0.00 39.13 1.90
467 644 8.375493 TCCACAAGAGGTAAGAGTAATATTGT 57.625 34.615 0.00 0.00 0.00 2.71
468 645 9.483489 TCCACAAGAGGTAAGAGTAATATTGTA 57.517 33.333 0.00 0.00 0.00 2.41
469 646 9.530633 CCACAAGAGGTAAGAGTAATATTGTAC 57.469 37.037 0.00 0.00 0.00 2.90
470 647 9.530633 CACAAGAGGTAAGAGTAATATTGTACC 57.469 37.037 0.00 2.78 32.77 3.34
471 648 8.702819 ACAAGAGGTAAGAGTAATATTGTACCC 58.297 37.037 0.00 0.00 32.98 3.69
472 649 8.701895 CAAGAGGTAAGAGTAATATTGTACCCA 58.298 37.037 0.00 0.00 32.98 4.51
473 650 8.849543 AGAGGTAAGAGTAATATTGTACCCAA 57.150 34.615 0.00 0.00 32.98 4.12
474 651 9.448587 AGAGGTAAGAGTAATATTGTACCCAAT 57.551 33.333 0.00 0.00 43.62 3.16
523 701 0.452987 CACATCGATTTGGTGCCAGG 59.547 55.000 3.53 0.00 0.00 4.45
527 705 1.978617 CGATTTGGTGCCAGGCCTT 60.979 57.895 9.64 0.00 0.00 4.35
696 874 4.363990 AGCGTGCGACCTCACCTG 62.364 66.667 0.00 0.00 33.57 4.00
706 884 0.980423 ACCTCACCTGCTCTTCTTCC 59.020 55.000 0.00 0.00 0.00 3.46
865 1062 0.246635 AAATCCTCCGTCTGTCCGTG 59.753 55.000 0.00 0.00 0.00 4.94
923 1126 2.398588 ACTGGGCTAGTGCTGCTATAA 58.601 47.619 1.44 0.00 38.49 0.98
941 1144 8.842358 TGCTATAATACTATAAACAAGTGGCC 57.158 34.615 0.00 0.00 0.00 5.36
1070 1277 0.100861 CTCGGTAAGGAGGAAGACGC 59.899 60.000 0.00 0.00 0.00 5.19
1071 1278 0.609957 TCGGTAAGGAGGAAGACGCA 60.610 55.000 0.00 0.00 0.00 5.24
1072 1279 0.458025 CGGTAAGGAGGAAGACGCAC 60.458 60.000 0.00 0.00 0.00 5.34
1073 1280 0.458025 GGTAAGGAGGAAGACGCACG 60.458 60.000 0.00 0.00 0.00 5.34
1157 1364 2.800544 TCCAGCTTCGCTTAATTATCGC 59.199 45.455 0.00 1.25 36.40 4.58
1172 1379 1.805428 ATCGCCCGTTGCTTTGCTTT 61.805 50.000 0.00 0.00 38.05 3.51
1173 1380 1.591327 CGCCCGTTGCTTTGCTTTT 60.591 52.632 0.00 0.00 38.05 2.27
1174 1381 1.548132 CGCCCGTTGCTTTGCTTTTC 61.548 55.000 0.00 0.00 38.05 2.29
1175 1382 1.548132 GCCCGTTGCTTTGCTTTTCG 61.548 55.000 0.00 0.00 36.87 3.46
1176 1383 0.030101 CCCGTTGCTTTGCTTTTCGA 59.970 50.000 0.00 0.00 0.00 3.71
1183 1400 0.704551 CTTTGCTTTTCGATGCGTGC 59.295 50.000 0.00 0.00 0.00 5.34
1498 1721 2.995574 CTTCCGTCGTCAGGGGGT 60.996 66.667 0.00 0.00 0.00 4.95
1587 1810 1.067821 CTATGGTGGACGCTCTTCTCC 59.932 57.143 0.00 0.00 0.00 3.71
1647 1870 3.825833 CTATGGGCTCGACGTCGCC 62.826 68.421 32.19 26.66 45.55 5.54
1695 1918 4.834453 CTCCTGCTCTGCGCCCTG 62.834 72.222 4.18 0.00 38.05 4.45
1836 2059 2.992689 TCGTGGCTGAACCCGCTA 60.993 61.111 0.00 0.00 37.83 4.26
1989 2212 1.880340 GAGATCCAACAGGCTCGCG 60.880 63.158 0.00 0.00 0.00 5.87
2214 2437 2.028112 CCATTGGTTCTTCGACTCCAGA 60.028 50.000 0.00 0.00 0.00 3.86
2634 2857 1.079405 GTTCCGGAGCATGGTCGAA 60.079 57.895 18.14 13.73 0.00 3.71
3189 3419 8.021973 GCTCTTTATGCAGATGGAATGATTAAG 58.978 37.037 0.00 0.00 0.00 1.85
3195 3425 6.124340 TGCAGATGGAATGATTAAGTCATGT 58.876 36.000 0.00 0.00 46.80 3.21
3198 3561 7.646314 CAGATGGAATGATTAAGTCATGTTCC 58.354 38.462 0.00 10.36 46.80 3.62
3211 3574 5.634118 AGTCATGTTCCTTTCTCCATTTCA 58.366 37.500 0.00 0.00 0.00 2.69
3212 3575 5.709164 AGTCATGTTCCTTTCTCCATTTCAG 59.291 40.000 0.00 0.00 0.00 3.02
3395 3759 7.094377 TGTGCTTTGGACAAGGATATAGAAAAC 60.094 37.037 0.00 0.00 0.00 2.43
3473 3837 3.126686 GTCAGAAGCAAAGGATTCAGCTC 59.873 47.826 0.00 0.00 41.82 4.09
3503 3867 7.341512 AGAGCTGTCTATAGCAATGCAGATATA 59.658 37.037 8.35 0.29 46.07 0.86
3512 3876 5.987098 AGCAATGCAGATATATACCTCCTG 58.013 41.667 8.35 0.00 0.00 3.86
3610 3977 2.295349 CAGACAGCTTGTTTTCTGCCAT 59.705 45.455 0.00 0.00 33.80 4.40
3611 3978 2.295349 AGACAGCTTGTTTTCTGCCATG 59.705 45.455 0.00 0.00 33.80 3.66
3616 5134 2.613133 GCTTGTTTTCTGCCATGCAAAA 59.387 40.909 0.00 0.00 38.41 2.44
3696 5214 1.003866 GTTCTTGTGACGCACCAAGTC 60.004 52.381 7.38 0.00 38.98 3.01
3746 5264 6.672266 TCTGGTAAGTTGATCTTCTGAACT 57.328 37.500 0.00 0.00 37.56 3.01
3748 5266 8.190326 TCTGGTAAGTTGATCTTCTGAACTTA 57.810 34.615 9.93 9.93 39.86 2.24
3826 5349 5.055265 TGTTTCAACAGGTAATGGAAGGA 57.945 39.130 0.00 0.00 34.30 3.36
3877 5400 2.669133 CCTGCTGGAATCCGGGACA 61.669 63.158 10.56 0.00 34.57 4.02
4144 5667 2.649816 AGTCTCCAAGGGCATTTTACCT 59.350 45.455 0.00 0.00 39.21 3.08
4271 5794 2.657237 GGGCATACTCGGGGATCG 59.343 66.667 0.00 0.00 40.90 3.69
4309 5832 1.142748 CGCCTACCTCAGAAGCCTG 59.857 63.158 0.00 0.00 41.74 4.85
4333 5856 1.276421 GCTGCTACTCTGGGACTCAAA 59.724 52.381 0.00 0.00 0.00 2.69
4354 5877 3.766545 AGCCTCCAAAGCATTCTTTACA 58.233 40.909 0.00 0.00 40.35 2.41
4450 5977 8.044908 ACAAGGGTATGGTTACTTTACTGTATG 58.955 37.037 0.00 0.00 0.00 2.39
4457 5984 4.449131 GTTACTTTACTGTATGGCTCCCC 58.551 47.826 0.00 0.00 0.00 4.81
4461 5988 4.017499 ACTTTACTGTATGGCTCCCCAAAT 60.017 41.667 0.00 0.00 46.14 2.32
4462 5989 2.442236 ACTGTATGGCTCCCCAAATG 57.558 50.000 0.00 0.00 46.14 2.32
4465 5992 2.889045 CTGTATGGCTCCCCAAATGATG 59.111 50.000 0.00 0.00 46.14 3.07
4466 5993 1.615392 GTATGGCTCCCCAAATGATGC 59.385 52.381 0.00 0.00 46.14 3.91
4566 6207 6.992063 TCAGATTTAAGCATTCTGGACTTC 57.008 37.500 0.00 0.00 37.93 3.01
4653 6294 3.073209 TCATGGGTACTGTAACTTGGCAA 59.927 43.478 2.46 0.00 0.00 4.52
4713 6354 6.039047 TGGTATATGTTCAGGTAAGTCGTCTC 59.961 42.308 0.00 0.00 0.00 3.36
5055 6702 7.344612 TGGATTCTTATAAGAGTGGAAGCACTA 59.655 37.037 14.60 0.00 36.22 2.74
5412 7070 4.547671 CACAGGAGGGAAGAATAGACCTA 58.452 47.826 0.00 0.00 32.42 3.08
5460 7121 5.964758 TCCTTTGCACATAATCATGGAAAC 58.035 37.500 0.00 0.00 36.39 2.78
5463 7124 4.987408 TGCACATAATCATGGAAACTGG 57.013 40.909 0.00 0.00 36.39 4.00
5521 7182 6.677781 TTTTCTGAGCAGATTAAATACCGG 57.322 37.500 0.00 0.00 37.29 5.28
5523 7184 2.476619 CTGAGCAGATTAAATACCGGCG 59.523 50.000 0.00 0.00 0.00 6.46
5530 7191 4.093703 CAGATTAAATACCGGCGAAACACA 59.906 41.667 9.30 0.00 0.00 3.72
5656 7317 0.741221 GTCTCGTTGATCCTGTGGGC 60.741 60.000 0.00 0.00 0.00 5.36
5770 7431 1.571460 CAGAGGAACTGTGCGCAAC 59.429 57.895 14.00 7.43 44.43 4.17
6199 7868 9.643693 CAGAACAAAAGAATTACCATAGCAAAT 57.356 29.630 0.00 0.00 0.00 2.32
6366 8035 2.890474 GCAACGGCGTCCATCGAT 60.890 61.111 15.17 0.00 42.86 3.59
6444 8113 4.256110 CAGTGATAACCATTGCTCACAGA 58.744 43.478 4.56 0.00 40.32 3.41
6464 8133 1.837439 AGTCCCAACTGTGACAGACAA 59.163 47.619 20.97 0.00 35.18 3.18
6489 8158 4.371681 ACAGGGTCATGGTACTTTCCTAT 58.628 43.478 0.00 0.00 0.00 2.57
6548 8221 6.566079 AGTGATGAAATCTCTGGTCCATTA 57.434 37.500 0.00 0.00 44.73 1.90
6805 8478 2.735663 GGCATGATAGACAAGATGAGCG 59.264 50.000 0.00 0.00 0.00 5.03
6816 8489 5.645067 AGACAAGATGAGCGATTCAATCAAA 59.355 36.000 0.00 0.00 39.77 2.69
6817 8490 5.877031 ACAAGATGAGCGATTCAATCAAAG 58.123 37.500 0.00 0.00 39.77 2.77
6818 8491 5.645067 ACAAGATGAGCGATTCAATCAAAGA 59.355 36.000 0.00 0.00 39.77 2.52
6819 8492 6.318144 ACAAGATGAGCGATTCAATCAAAGAT 59.682 34.615 0.00 0.00 39.77 2.40
6944 8619 3.308438 AGAAGGCATCAACAACAATGC 57.692 42.857 0.00 0.00 45.96 3.56
6963 8671 1.734465 GCAAGGTTGATGGAGAGAACG 59.266 52.381 0.00 0.00 0.00 3.95
6978 8686 3.382865 AGAGAACGAGCTCAAGATGCATA 59.617 43.478 15.40 0.00 37.37 3.14
6997 8705 1.828979 AGACTCGAGTCCTCCAAGAC 58.171 55.000 35.83 13.69 45.85 3.01
7075 8783 7.656137 CACCTTTAGTGTGATATATGGTACACC 59.344 40.741 15.53 0.00 43.23 4.16
7109 8817 7.171508 TGAGTTCTACTGTTGAATAACAAGCAG 59.828 37.037 7.87 0.00 45.53 4.24
7140 8855 3.624861 GTGTCAAGATGCCAGTAGATTGG 59.375 47.826 0.00 0.00 41.35 3.16
7195 8910 4.983671 CCTTGTCCTAAATAAGGTTGGC 57.016 45.455 0.00 0.00 46.62 4.52
7224 8939 1.317613 TGGAAGTGCATGTTGTCCAC 58.682 50.000 0.00 0.00 33.43 4.02
7486 9234 3.879295 CCATACCTCAAATGATTGCGAGT 59.121 43.478 0.00 0.00 36.45 4.18
7583 9349 5.227152 CAAGCCACCAAACCAGTTTATTAC 58.773 41.667 0.00 0.00 0.00 1.89
7591 9357 5.220970 CCAAACCAGTTTATTACGGGCATAG 60.221 44.000 0.00 0.00 45.00 2.23
7674 9453 9.950680 AACATGAACAAGTGACAAATAGTAAAG 57.049 29.630 0.00 0.00 0.00 1.85
7751 9531 8.550376 ACAACGAATTTCTGAAATTTGGAATTG 58.450 29.630 31.62 28.08 43.51 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 8.885494 ATGCCGCATGTAAATAACAAATATTT 57.115 26.923 4.68 0.00 44.48 1.40
60 61 0.750911 TCATACATGCCAATGCCGCA 60.751 50.000 0.00 0.00 41.28 5.69
61 62 0.599558 ATCATACATGCCAATGCCGC 59.400 50.000 0.00 0.00 37.29 6.53
62 63 1.881324 TCATCATACATGCCAATGCCG 59.119 47.619 0.00 0.00 37.29 5.69
63 64 3.645884 GTTCATCATACATGCCAATGCC 58.354 45.455 0.00 0.00 37.29 4.40
67 68 2.097304 GCACGTTCATCATACATGCCAA 59.903 45.455 0.00 0.00 0.00 4.52
68 69 1.670295 GCACGTTCATCATACATGCCA 59.330 47.619 0.00 0.00 0.00 4.92
69 70 1.670295 TGCACGTTCATCATACATGCC 59.330 47.619 0.00 0.00 0.00 4.40
70 71 3.294102 CATGCACGTTCATCATACATGC 58.706 45.455 0.00 0.00 0.00 4.06
71 72 3.560896 TCCATGCACGTTCATCATACATG 59.439 43.478 0.00 0.00 34.60 3.21
105 110 3.256879 CGACAGCCACATACCTCATATCT 59.743 47.826 0.00 0.00 0.00 1.98
109 114 0.465705 CCGACAGCCACATACCTCAT 59.534 55.000 0.00 0.00 0.00 2.90
122 127 2.353505 CCTCATATCTCATGGCCGACAG 60.354 54.545 0.00 0.00 0.00 3.51
124 129 1.066573 CCCTCATATCTCATGGCCGAC 60.067 57.143 0.00 0.00 0.00 4.79
125 130 1.269958 CCCTCATATCTCATGGCCGA 58.730 55.000 0.00 0.00 0.00 5.54
129 134 2.304180 GACCACCCCTCATATCTCATGG 59.696 54.545 0.00 0.00 0.00 3.66
132 137 2.682594 CAGACCACCCCTCATATCTCA 58.317 52.381 0.00 0.00 0.00 3.27
160 165 1.226717 GCTTCCTCTACGTCTGCGG 60.227 63.158 0.00 0.00 43.45 5.69
164 169 0.106619 ATCCGGCTTCCTCTACGTCT 60.107 55.000 0.00 0.00 0.00 4.18
165 170 0.745468 AATCCGGCTTCCTCTACGTC 59.255 55.000 0.00 0.00 0.00 4.34
168 173 1.134371 AGCAAATCCGGCTTCCTCTAC 60.134 52.381 0.00 0.00 38.81 2.59
175 180 1.751437 GGACTTAGCAAATCCGGCTT 58.249 50.000 0.00 0.00 42.62 4.35
176 181 3.478540 GGACTTAGCAAATCCGGCT 57.521 52.632 0.00 0.00 45.18 5.52
215 220 3.819564 TTACCCTCAATCGATCCACTG 57.180 47.619 0.00 0.00 0.00 3.66
216 221 5.373812 AAATTACCCTCAATCGATCCACT 57.626 39.130 0.00 0.00 0.00 4.00
273 441 8.371699 ACTAAATCTACCAAGAATATCTCCTGC 58.628 37.037 0.00 0.00 34.73 4.85
325 493 8.816894 AGGCGAATAAGGAAAGATATATCAAGA 58.183 33.333 15.08 0.00 0.00 3.02
399 571 2.562738 GTGGGGCTAGCATGAACTTTTT 59.437 45.455 18.24 0.00 0.00 1.94
403 575 0.035056 GTGTGGGGCTAGCATGAACT 60.035 55.000 18.24 0.00 0.00 3.01
406 578 1.337384 ATCGTGTGGGGCTAGCATGA 61.337 55.000 18.24 6.71 33.42 3.07
410 582 0.882042 CATGATCGTGTGGGGCTAGC 60.882 60.000 6.04 6.04 0.00 3.42
435 607 6.257586 ACTCTTACCTCTTGTGGAGTAAGAT 58.742 40.000 10.83 1.74 40.06 2.40
466 643 7.542534 TCACGAACAATACAATATTGGGTAC 57.457 36.000 19.37 3.92 33.56 3.34
467 644 8.563123 TTTCACGAACAATACAATATTGGGTA 57.437 30.769 19.37 4.47 33.56 3.69
468 645 7.455641 TTTCACGAACAATACAATATTGGGT 57.544 32.000 19.37 9.00 33.56 4.51
469 646 8.749841 TTTTTCACGAACAATACAATATTGGG 57.250 30.769 19.37 8.42 33.56 4.12
474 651 9.108449 CGTCAATTTTTCACGAACAATACAATA 57.892 29.630 0.00 0.00 35.49 1.90
475 652 7.114247 CCGTCAATTTTTCACGAACAATACAAT 59.886 33.333 0.00 0.00 35.49 2.71
476 653 6.415280 CCGTCAATTTTTCACGAACAATACAA 59.585 34.615 0.00 0.00 35.49 2.41
477 654 5.910166 CCGTCAATTTTTCACGAACAATACA 59.090 36.000 0.00 0.00 35.49 2.29
478 655 5.164225 GCCGTCAATTTTTCACGAACAATAC 60.164 40.000 0.00 0.00 35.49 1.89
479 656 4.912766 GCCGTCAATTTTTCACGAACAATA 59.087 37.500 0.00 0.00 35.49 1.90
480 657 3.733727 GCCGTCAATTTTTCACGAACAAT 59.266 39.130 0.00 0.00 35.49 2.71
481 658 3.109619 GCCGTCAATTTTTCACGAACAA 58.890 40.909 0.00 0.00 35.49 2.83
482 659 2.356382 AGCCGTCAATTTTTCACGAACA 59.644 40.909 0.00 0.00 35.49 3.18
483 660 2.971261 GAGCCGTCAATTTTTCACGAAC 59.029 45.455 0.00 0.00 35.49 3.95
484 661 2.614520 TGAGCCGTCAATTTTTCACGAA 59.385 40.909 0.00 0.00 35.49 3.85
523 701 1.741770 CGTGGCTACTGGTCAAGGC 60.742 63.158 0.00 0.00 38.68 4.35
527 705 2.632544 CCGTCGTGGCTACTGGTCA 61.633 63.158 0.00 0.00 0.00 4.02
573 751 2.443390 GGAAGGCTGGCATGGCAT 60.443 61.111 23.59 7.72 34.73 4.40
691 869 1.206849 GAGGAGGAAGAAGAGCAGGTG 59.793 57.143 0.00 0.00 0.00 4.00
692 870 1.567357 GAGGAGGAAGAAGAGCAGGT 58.433 55.000 0.00 0.00 0.00 4.00
693 871 0.829990 GGAGGAGGAAGAAGAGCAGG 59.170 60.000 0.00 0.00 0.00 4.85
696 874 0.618968 TGGGGAGGAGGAAGAAGAGC 60.619 60.000 0.00 0.00 0.00 4.09
706 884 1.592223 GAACTCGTGTGGGGAGGAG 59.408 63.158 0.00 0.00 35.82 3.69
793 985 4.704833 CTCCGGGCTGTGGTGTGG 62.705 72.222 0.00 0.00 0.00 4.17
794 986 3.941188 ACTCCGGGCTGTGGTGTG 61.941 66.667 0.00 0.00 32.31 3.82
795 987 3.941188 CACTCCGGGCTGTGGTGT 61.941 66.667 0.00 1.58 33.69 4.16
865 1062 2.851104 GTATATTCGCACGCGGGC 59.149 61.111 26.66 26.66 40.25 6.13
923 1126 4.975794 AGGGAGGCCACTTGTTTATAGTAT 59.024 41.667 5.01 0.00 0.00 2.12
941 1144 1.152839 GGAGACGAGGAGGAGGGAG 60.153 68.421 0.00 0.00 0.00 4.30
1157 1364 0.030101 TCGAAAAGCAAAGCAACGGG 59.970 50.000 0.00 0.00 0.00 5.28
1172 1379 3.410516 CCACACGCACGCATCGAA 61.411 61.111 0.00 0.00 0.00 3.71
1175 1382 4.450122 CTGCCACACGCACGCATC 62.450 66.667 0.00 0.00 44.64 3.91
1183 1400 3.345808 CGACCAACCTGCCACACG 61.346 66.667 0.00 0.00 0.00 4.49
1482 1705 2.524887 AACCCCCTGACGACGGAA 60.525 61.111 0.00 0.00 0.00 4.30
1498 1721 4.885270 CACGGCCACCCACACCAA 62.885 66.667 2.24 0.00 0.00 3.67
1569 1792 1.617947 GGGAGAAGAGCGTCCACCAT 61.618 60.000 0.00 0.00 34.14 3.55
1587 1810 1.878522 GTACGCGGTGATGAGCAGG 60.879 63.158 12.47 0.00 0.00 4.85
1792 2015 2.948720 GCTGGCTGAAGAGTCCGGT 61.949 63.158 0.00 0.00 0.00 5.28
1797 2020 2.264166 GCGAGCTGGCTGAAGAGT 59.736 61.111 14.13 0.00 0.00 3.24
1914 2137 1.480954 GCCTCGGAGAACCTATGTGAA 59.519 52.381 6.58 0.00 34.09 3.18
1989 2212 2.959357 GCACTTGCACAGGACGAGC 61.959 63.158 0.00 0.00 41.59 5.03
2131 2354 2.357034 GACGAGCGACAGGCCAAA 60.357 61.111 5.01 0.00 45.17 3.28
2155 2378 0.171455 ACGAGCTTGATGACGAGGAC 59.829 55.000 8.31 0.00 0.00 3.85
2214 2437 3.757248 GATGCGCATCCCGGTCCTT 62.757 63.158 35.11 5.74 37.44 3.36
2624 2847 0.465705 TCTGAGGGATTCGACCATGC 59.534 55.000 0.00 0.00 0.00 4.06
2784 3007 0.320771 CCAAGACCGTGAAGAGGGTG 60.321 60.000 0.00 0.00 40.57 4.61
2835 3058 3.729108 TGTCAGGATCTCAGGAAGGAAT 58.271 45.455 0.00 0.00 0.00 3.01
3189 3419 5.707298 TCTGAAATGGAGAAAGGAACATGAC 59.293 40.000 0.00 0.00 0.00 3.06
3395 3759 5.982356 TCTGTAAGGTCTCCATGATTGAAG 58.018 41.667 0.00 0.00 0.00 3.02
3473 3837 3.906014 TTGCTATAGACAGCTCTAGCG 57.094 47.619 3.21 0.00 45.05 4.26
3492 3856 5.127845 CGTCCAGGAGGTATATATCTGCATT 59.872 44.000 15.98 0.00 35.89 3.56
3503 3867 0.338814 AAGGGTCGTCCAGGAGGTAT 59.661 55.000 9.04 0.00 38.24 2.73
3616 5134 9.911788 ATCCTGTAAGAACATTGACATTAGAAT 57.088 29.630 0.00 0.00 34.07 2.40
3636 5154 3.753272 GTGCTGTCATTACACAATCCTGT 59.247 43.478 0.00 0.00 35.63 4.00
3746 5264 6.491394 ATTTTACGAAATTATGCGCAGCTAA 58.509 32.000 18.32 11.36 43.35 3.09
3748 5266 4.920376 ATTTTACGAAATTATGCGCAGCT 58.080 34.783 18.32 1.49 43.35 4.24
3826 5349 3.117663 TCCCTTGCTGTTTAACTTGACCT 60.118 43.478 0.00 0.00 0.00 3.85
3877 5400 4.155644 GCTGAAACTAGCTTCTCAAATGCT 59.844 41.667 7.37 0.00 40.52 3.79
4144 5667 1.555075 GCTGTAACCATCCCACAGAGA 59.445 52.381 5.19 0.00 41.80 3.10
4271 5794 2.799371 GCAGCAGCTGAAGATGGC 59.201 61.111 27.39 4.57 37.91 4.40
4309 5832 0.458716 GTCCCAGAGTAGCAGCGAAC 60.459 60.000 0.00 0.00 0.00 3.95
4333 5856 3.760684 CTGTAAAGAATGCTTTGGAGGCT 59.239 43.478 9.11 0.00 43.84 4.58
4450 5977 0.176449 GTTGCATCATTTGGGGAGCC 59.824 55.000 0.00 0.00 0.00 4.70
4457 5984 3.554324 GCTTGCTATGGTTGCATCATTTG 59.446 43.478 8.11 4.45 40.34 2.32
4461 5988 2.133281 AGCTTGCTATGGTTGCATCA 57.867 45.000 0.00 0.00 40.34 3.07
4462 5989 4.637483 TTTAGCTTGCTATGGTTGCATC 57.363 40.909 2.99 0.00 40.34 3.91
4465 5992 4.376340 ACATTTAGCTTGCTATGGTTGC 57.624 40.909 2.99 0.00 0.00 4.17
4466 5993 8.931385 AAATTACATTTAGCTTGCTATGGTTG 57.069 30.769 2.99 2.63 0.00 3.77
4492 6103 5.305644 GGTCAGGGATTCATCAGTACTACAT 59.694 44.000 0.00 0.00 0.00 2.29
4494 6105 4.261656 CGGTCAGGGATTCATCAGTACTAC 60.262 50.000 0.00 0.00 0.00 2.73
4502 6113 1.486726 ACCTTCGGTCAGGGATTCATC 59.513 52.381 1.91 0.00 38.42 2.92
4503 6114 1.584724 ACCTTCGGTCAGGGATTCAT 58.415 50.000 1.91 0.00 38.42 2.57
4566 6207 2.365617 AGCCATGGAGTAAGGTATGTCG 59.634 50.000 18.40 0.00 0.00 4.35
4653 6294 4.532521 ACTGGGATTGCTACAACTAAGACT 59.467 41.667 0.00 0.00 0.00 3.24
4713 6354 4.676196 GCTTGGATCAATGTACAGCAAAGG 60.676 45.833 0.33 0.00 0.00 3.11
4884 6531 3.208594 TGATGCATAGTTCATGACAGGC 58.791 45.455 0.00 0.00 36.69 4.85
5055 6702 5.948162 AGATGTGAATATGGTCAAGCTTTGT 59.052 36.000 0.00 0.00 0.00 2.83
5112 6759 5.239525 GGTTATGCAGATACCTGGTGAAATC 59.760 44.000 10.23 4.73 40.72 2.17
5521 7182 1.400494 AGAACAAGTGGTGTGTTTCGC 59.600 47.619 0.00 0.00 40.60 4.70
5523 7184 4.695217 TTGAGAACAAGTGGTGTGTTTC 57.305 40.909 0.00 0.00 40.60 2.78
5530 7191 4.580580 GTGATTCCTTTGAGAACAAGTGGT 59.419 41.667 0.00 0.00 37.32 4.16
5656 7317 5.277857 AGTTGTCAATAAGTATCCTCCCG 57.722 43.478 0.00 0.00 0.00 5.14
5948 7609 7.816995 TCTGTCTTTAAGAAAAGCTCAGATCTC 59.183 37.037 14.96 0.00 41.98 2.75
6199 7868 8.688747 TTTTAACCTTCCGGTAACTCAAATTA 57.311 30.769 0.00 0.00 44.73 1.40
6201 7870 7.449086 TCATTTTAACCTTCCGGTAACTCAAAT 59.551 33.333 0.00 0.00 44.73 2.32
6489 8158 8.359642 ACTGAACTGTTTAAGTATAACGTACCA 58.640 33.333 7.74 0.00 38.56 3.25
6636 8309 5.683509 GCTTACCTGTAGAAGTCATCAGCAT 60.684 44.000 0.00 0.00 0.00 3.79
6816 8489 8.697507 ACAATCTTTCAGTACCTCAAAAATCT 57.302 30.769 0.00 0.00 0.00 2.40
6944 8619 3.257393 CTCGTTCTCTCCATCAACCTTG 58.743 50.000 0.00 0.00 0.00 3.61
6963 8671 3.004210 TCGAGTCTATGCATCTTGAGCTC 59.996 47.826 6.82 6.82 0.00 4.09
6978 8686 1.353022 AGTCTTGGAGGACTCGAGTCT 59.647 52.381 36.98 25.73 42.15 3.24
6997 8705 6.988580 TCTCAATATCCTTGTTGACATGCTAG 59.011 38.462 0.00 0.00 30.78 3.42
6998 8706 6.888105 TCTCAATATCCTTGTTGACATGCTA 58.112 36.000 0.00 0.00 30.78 3.49
7084 8792 7.385205 TCTGCTTGTTATTCAACAGTAGAACTC 59.615 37.037 0.00 0.00 45.17 3.01
7109 8817 3.569701 TGGCATCTTGACACTTCCTTTTC 59.430 43.478 0.00 0.00 24.43 2.29
7140 8855 2.237393 TTTTTGTCACATGCCTTGGC 57.763 45.000 4.43 4.43 0.00 4.52
7195 8910 2.380410 GCACTTCCACGCGGTACAG 61.380 63.158 12.47 3.33 0.00 2.74
7224 8939 4.946157 AGGTTCTTGGCACTATCTTCATTG 59.054 41.667 0.00 0.00 0.00 2.82
7287 9034 6.429692 TGATAGTAATGTTTTGTGTGACCCAG 59.570 38.462 0.00 0.00 0.00 4.45
7517 9270 2.110578 TGCTATGCTCTAAGGCACTGA 58.889 47.619 0.00 0.00 45.36 3.41
7522 9275 3.003068 CACATGTTGCTATGCTCTAAGGC 59.997 47.826 0.00 0.00 0.00 4.35
7583 9349 4.058817 GGAGAAATCTGTAACTATGCCCG 58.941 47.826 0.00 0.00 0.00 6.13
7634 9400 5.283294 TGTTCATGTTCAGCATTTCTGTTG 58.717 37.500 0.00 0.00 43.32 3.33
7635 9401 5.518848 TGTTCATGTTCAGCATTTCTGTT 57.481 34.783 0.00 0.00 43.32 3.16
7636 9402 5.068198 ACTTGTTCATGTTCAGCATTTCTGT 59.932 36.000 0.00 0.00 43.32 3.41
7637 9403 5.401376 CACTTGTTCATGTTCAGCATTTCTG 59.599 40.000 0.00 0.00 44.21 3.02
7638 9404 5.300034 TCACTTGTTCATGTTCAGCATTTCT 59.700 36.000 0.00 0.00 35.19 2.52
7639 9405 5.400485 GTCACTTGTTCATGTTCAGCATTTC 59.600 40.000 0.00 0.00 35.19 2.17
7640 9406 5.163530 TGTCACTTGTTCATGTTCAGCATTT 60.164 36.000 0.00 0.00 35.19 2.32
7641 9407 4.338964 TGTCACTTGTTCATGTTCAGCATT 59.661 37.500 0.00 0.00 35.19 3.56
7642 9408 3.884693 TGTCACTTGTTCATGTTCAGCAT 59.115 39.130 0.00 0.00 38.60 3.79
7643 9409 3.277715 TGTCACTTGTTCATGTTCAGCA 58.722 40.909 0.00 0.00 0.00 4.41
7644 9410 3.969117 TGTCACTTGTTCATGTTCAGC 57.031 42.857 0.00 0.00 0.00 4.26
7647 9413 9.944663 TTTACTATTTGTCACTTGTTCATGTTC 57.055 29.630 0.00 0.00 0.00 3.18
7652 9418 7.066404 TGCACTTTACTATTTGTCACTTGTTCA 59.934 33.333 0.00 0.00 0.00 3.18
7674 9453 3.811722 TGAAACGTGAAGATGATGCAC 57.188 42.857 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.