Multiple sequence alignment - TraesCS7B01G482200

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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 TraesCS7B01G482200 chr7B 100.000 6134 0 0 1 6134 740037881 740031748 0.000000e+00 11328.0
1 TraesCS7B01G482200 chr7B 90.995 211 19 0 3784 3994 739990323 739990113 1.010000e-72 285.0
2 TraesCS7B01G482200 chr7A 93.403 4093 192 35 1 4050 730430778 730426721 0.000000e+00 5991.0
3 TraesCS7B01G482200 chr7A 91.524 1227 80 15 4155 5368 730426631 730425416 0.000000e+00 1668.0
4 TraesCS7B01G482200 chr7A 92.999 757 24 6 3323 4050 730301114 730300358 0.000000e+00 1077.0
5 TraesCS7B01G482200 chr7A 88.627 765 54 8 5396 6133 730425100 730424342 0.000000e+00 900.0
6 TraesCS7B01G482200 chr7A 93.486 568 32 4 5569 6133 730295160 730294595 0.000000e+00 839.0
7 TraesCS7B01G482200 chr7A 93.429 487 32 0 1954 2440 730358426 730357940 0.000000e+00 723.0
8 TraesCS7B01G482200 chr7A 93.018 487 32 1 1954 2440 730311173 730310689 0.000000e+00 710.0
9 TraesCS7B01G482200 chr7A 92.678 478 24 6 4185 4653 730298664 730298189 0.000000e+00 678.0
10 TraesCS7B01G482200 chr7A 86.293 642 63 14 3274 3913 730290297 730289679 0.000000e+00 675.0
11 TraesCS7B01G482200 chr7A 89.462 446 47 0 2852 3297 730301553 730301108 1.150000e-156 564.0
12 TraesCS7B01G482200 chr7A 89.462 446 47 0 2852 3297 730349527 730349082 1.150000e-156 564.0
13 TraesCS7B01G482200 chr7A 90.864 405 30 6 2451 2851 730302331 730301930 2.520000e-148 536.0
14 TraesCS7B01G482200 chr7A 91.710 386 26 5 2470 2851 730350287 730349904 1.170000e-146 531.0
15 TraesCS7B01G482200 chr7A 95.408 196 9 0 3323 3518 730349088 730348893 4.620000e-81 313.0
16 TraesCS7B01G482200 chr7A 87.770 139 7 5 5377 5506 730296084 730295947 2.960000e-33 154.0
17 TraesCS7B01G482200 chr7A 92.105 76 3 1 5498 5570 730295258 730295183 3.020000e-18 104.0
18 TraesCS7B01G482200 chr7A 100.000 41 0 0 5466 5506 730295944 730295904 6.590000e-10 76.8
19 TraesCS7B01G482200 chr7A 97.143 35 1 0 4149 4183 730300271 730300237 6.640000e-05 60.2
20 TraesCS7B01G482200 chr7D 93.019 3982 218 30 106 4046 635584105 635588067 0.000000e+00 5758.0
21 TraesCS7B01G482200 chr7D 92.633 1276 71 13 4107 5368 635588066 635589332 0.000000e+00 1814.0
22 TraesCS7B01G482200 chr7D 93.827 567 25 7 5570 6133 635589384 635589943 0.000000e+00 845.0
23 TraesCS7B01G482200 chr7D 87.442 430 48 6 5705 6133 635637428 635637852 1.990000e-134 490.0
24 TraesCS7B01G482200 chr2D 83.126 4095 486 119 1235 5239 518265535 518269514 0.000000e+00 3544.0
25 TraesCS7B01G482200 chr2D 79.681 251 34 6 3804 4047 621083747 621083507 1.370000e-36 165.0
26 TraesCS7B01G482200 chr2B 84.156 3768 433 111 1235 4916 610416068 610419757 0.000000e+00 3500.0
27 TraesCS7B01G482200 chr2A 84.888 2905 316 81 1235 4064 662338724 662341580 0.000000e+00 2819.0
28 TraesCS7B01G482200 chr2A 78.553 1175 153 58 4101 5239 662341647 662342758 0.000000e+00 682.0
29 TraesCS7B01G482200 chr6D 75.714 1400 259 55 2683 4043 471919362 471920719 1.450000e-175 627.0
30 TraesCS7B01G482200 chr6D 83.772 228 37 0 2212 2439 471918865 471919092 3.720000e-52 217.0
31 TraesCS7B01G482200 chr6D 85.135 74 11 0 1031 1104 471917820 471917893 6.590000e-10 76.8
32 TraesCS7B01G482200 chr6B 75.904 996 175 44 2683 3643 716619775 716620740 3.370000e-122 449.0
33 TraesCS7B01G482200 chrUn 85.022 227 34 0 2213 2439 74820429 74820203 1.330000e-56 231.0
34 TraesCS7B01G482200 chr4D 91.000 100 9 0 1527 1626 457948 457849 1.070000e-27 135.0


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 TraesCS7B01G482200 chr7B 740031748 740037881 6133 True 11328.000000 11328 100.000000 1 6134 1 chr7B.!!$R2 6133
1 TraesCS7B01G482200 chr7A 730424342 730430778 6436 True 2853.000000 5991 91.184667 1 6133 3 chr7A.!!$R6 6132
2 TraesCS7B01G482200 chr7A 730289679 730290297 618 True 675.000000 675 86.293000 3274 3913 1 chr7A.!!$R1 639
3 TraesCS7B01G482200 chr7A 730348893 730350287 1394 True 469.333333 564 92.193333 2470 3518 3 chr7A.!!$R5 1048
4 TraesCS7B01G482200 chr7A 730294595 730302331 7736 True 454.333333 1077 92.945222 2451 6133 9 chr7A.!!$R4 3682
5 TraesCS7B01G482200 chr7D 635584105 635589943 5838 False 2805.666667 5758 93.159667 106 6133 3 chr7D.!!$F2 6027
6 TraesCS7B01G482200 chr2D 518265535 518269514 3979 False 3544.000000 3544 83.126000 1235 5239 1 chr2D.!!$F1 4004
7 TraesCS7B01G482200 chr2B 610416068 610419757 3689 False 3500.000000 3500 84.156000 1235 4916 1 chr2B.!!$F1 3681
8 TraesCS7B01G482200 chr2A 662338724 662342758 4034 False 1750.500000 2819 81.720500 1235 5239 2 chr2A.!!$F1 4004
9 TraesCS7B01G482200 chr6D 471917820 471920719 2899 False 306.933333 627 81.540333 1031 4043 3 chr6D.!!$F1 3012
10 TraesCS7B01G482200 chr6B 716619775 716620740 965 False 449.000000 449 75.904000 2683 3643 1 chr6B.!!$F1 960

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
871 900 0.178961 GGGAGGTTTTGTGCCCTCTT 60.179 55.000 5.73 0.0 45.46 2.85 F
899 929 0.322456 TGTTGTCCATAGCACCCAGC 60.322 55.000 0.00 0.0 46.19 4.85 F
2207 2292 0.458025 GCCTAACGTTCCTCCACGAG 60.458 60.000 2.82 0.0 43.15 4.18 F
2630 2759 0.110104 GCAAGGCCATCATCCTAGCT 59.890 55.000 5.01 0.0 32.65 3.32 F
4094 4733 1.213182 TGGAGTAACAAACCCAGTGCA 59.787 47.619 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2117 0.107410 TGAAGCTTGTCCACCGTGTT 60.107 50.0 2.10 0.00 0.00 3.32 R
2565 2685 1.831580 AACCCTGCTGCTTGATTCTC 58.168 50.0 0.00 0.00 0.00 2.87 R
4083 4722 0.106918 TCCGTTTCTGCACTGGGTTT 60.107 50.0 0.00 0.00 0.00 3.27 R
4099 4738 0.535797 GGTAGAGTGGGGTTTCTCCG 59.464 60.0 0.00 0.00 37.00 4.63 R
5884 10858 0.093026 GCATGTGACGTTACAGCGAC 59.907 55.0 18.52 4.47 33.44 5.19 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
83 84 6.092670 CACCAATACTCGATGTGTGATTCTTT 59.907 38.462 0.00 0.00 0.00 2.52
260 261 5.365133 CAAACTTATGTGCGCAAATTTCAC 58.635 37.500 20.15 0.94 0.00 3.18
412 415 7.226720 TCGAGTTTTTGAAATAAAGAGCTCAGT 59.773 33.333 17.77 5.38 0.00 3.41
417 420 9.683069 TTTTTGAAATAAAGAGCTCAGTTCATC 57.317 29.630 17.77 7.94 0.00 2.92
709 738 4.414337 AGCCATGAGGAATCTTACAGTC 57.586 45.455 0.00 0.00 36.89 3.51
710 739 3.135530 AGCCATGAGGAATCTTACAGTCC 59.864 47.826 0.00 0.00 36.89 3.85
718 747 3.817647 GGAATCTTACAGTCCCATGATGC 59.182 47.826 0.00 0.00 0.00 3.91
742 771 1.372128 CGCCTTTCTTGCCTTGTGC 60.372 57.895 0.00 0.00 41.77 4.57
871 900 0.178961 GGGAGGTTTTGTGCCCTCTT 60.179 55.000 5.73 0.00 45.46 2.85
899 929 0.322456 TGTTGTCCATAGCACCCAGC 60.322 55.000 0.00 0.00 46.19 4.85
944 976 6.538263 ACATTCTTTCTTAGTTGCTTCTCCT 58.462 36.000 0.00 0.00 0.00 3.69
959 991 6.180472 TGCTTCTCCTAAAATAGTTCTTGGG 58.820 40.000 0.00 0.00 0.00 4.12
965 997 7.236847 TCTCCTAAAATAGTTCTTGGGTCTTCA 59.763 37.037 0.00 0.00 0.00 3.02
977 1009 1.605753 GGTCTTCACCACCCAGTTTC 58.394 55.000 0.00 0.00 43.17 2.78
978 1010 1.133915 GGTCTTCACCACCCAGTTTCA 60.134 52.381 0.00 0.00 43.17 2.69
998 1030 2.054799 ACAAGCCTGGTAGTCTTCCAA 58.945 47.619 0.00 0.00 34.35 3.53
1109 1141 6.831976 AGAGGTGCTTCCAAAGGTAATATAG 58.168 40.000 1.79 0.00 39.02 1.31
1189 1222 5.579511 GCATCAAGAAATATTTGCTGCTGTT 59.420 36.000 5.17 0.00 41.77 3.16
1211 1245 6.183360 TGTTGAAGCTTTGTCATCCTGAAATT 60.183 34.615 0.00 0.00 0.00 1.82
1212 1246 5.775686 TGAAGCTTTGTCATCCTGAAATTG 58.224 37.500 0.00 0.00 0.00 2.32
1217 1251 3.370840 TGTCATCCTGAAATTGGGGAG 57.629 47.619 0.00 0.00 32.28 4.30
1219 1253 3.333381 TGTCATCCTGAAATTGGGGAGAA 59.667 43.478 0.00 0.00 32.28 2.87
1362 1399 6.392354 TCTCGGTTACATTATTTGTTCGACT 58.608 36.000 0.00 0.00 39.87 4.18
1373 1410 9.490663 CATTATTTGTTCGACTCAGGTTATTTC 57.509 33.333 0.00 0.00 0.00 2.17
1374 1412 8.610248 TTATTTGTTCGACTCAGGTTATTTCA 57.390 30.769 0.00 0.00 0.00 2.69
1492 1557 2.159382 CTACCACCATTCGTTGCCTTT 58.841 47.619 0.00 0.00 0.00 3.11
1582 1647 5.726793 AGGAATTACACCATCAGAGTACCTT 59.273 40.000 0.00 0.00 0.00 3.50
1656 1721 8.974238 ACCAAATATCATGTGATCTTTGACATT 58.026 29.630 24.00 7.06 44.51 2.71
1680 1745 8.743085 TTGATCAGAGAGCTAATTTAATGCTT 57.257 30.769 0.00 0.00 37.16 3.91
1743 1812 3.011144 TGTGAATTTCAGGGCCAAGGATA 59.989 43.478 6.18 0.00 0.00 2.59
1975 2049 9.521503 CTCGTATCAGAAGATCAGAATTAACAA 57.478 33.333 0.00 0.00 35.67 2.83
1981 2055 9.559732 TCAGAAGATCAGAATTAACAAACTGAA 57.440 29.630 0.00 0.00 41.57 3.02
2031 2113 3.739300 AGAAACTGATGGTTAACGACACG 59.261 43.478 0.00 0.00 37.12 4.49
2035 2117 3.057104 ACTGATGGTTAACGACACGATCA 60.057 43.478 0.00 0.21 0.00 2.92
2207 2292 0.458025 GCCTAACGTTCCTCCACGAG 60.458 60.000 2.82 0.00 43.15 4.18
2429 2530 1.622607 TAGGATTGCCAGACACCGGG 61.623 60.000 6.32 0.00 36.29 5.73
2447 2548 3.307480 CCGGGGGTCAGGTATCAATATTC 60.307 52.174 0.00 0.00 0.00 1.75
2467 2570 8.854614 ATATTCTTCAAATAGTAGGACATGGC 57.145 34.615 0.00 0.00 0.00 4.40
2468 2571 5.692115 TCTTCAAATAGTAGGACATGGCA 57.308 39.130 0.00 0.00 0.00 4.92
2488 2593 4.445448 GGCAACTCTGATCAGGTTATCCAT 60.445 45.833 22.42 1.25 35.89 3.41
2489 2594 5.221722 GGCAACTCTGATCAGGTTATCCATA 60.222 44.000 22.42 0.00 35.89 2.74
2491 2596 6.939163 GCAACTCTGATCAGGTTATCCATATT 59.061 38.462 22.42 0.00 35.89 1.28
2565 2685 1.449956 GGAAGAGGAGCTGCTGCAG 60.450 63.158 24.80 24.80 42.74 4.41
2612 2732 3.733443 AACACCAAAGATTCTTGTGGC 57.267 42.857 19.19 0.00 34.27 5.01
2630 2759 0.110104 GCAAGGCCATCATCCTAGCT 59.890 55.000 5.01 0.00 32.65 3.32
2719 2852 4.627255 CTGATACCAGATTCCAAAGGCACT 60.627 45.833 0.00 0.00 43.02 4.40
2887 3398 7.538678 CAGGTTTGTCAGCTGTCAATTATTAAC 59.461 37.037 23.76 17.58 44.77 2.01
2896 3407 8.615211 CAGCTGTCAATTATTAACTATCAGCAA 58.385 33.333 5.25 0.00 45.12 3.91
3016 3542 3.008923 TCATTGGCAACTACACTGATGGA 59.991 43.478 0.00 0.00 37.61 3.41
3067 3593 2.750350 GGAGTCACACAGGTGGGG 59.250 66.667 1.24 0.00 45.32 4.96
3089 3616 7.944554 TGGGGAAATGTCTAATCAAATAGGATC 59.055 37.037 0.00 0.00 0.00 3.36
3095 3622 7.878621 TGTCTAATCAAATAGGATCCCTCAT 57.121 36.000 8.55 0.00 34.61 2.90
3103 3632 6.440010 TCAAATAGGATCCCTCATGATCTCTC 59.560 42.308 8.55 0.00 40.80 3.20
3138 3667 6.582636 TCACAGTTGATATGACATCCCTAAC 58.417 40.000 0.00 0.00 0.00 2.34
3213 3745 3.450457 AGAACTCAGATGCTAAGTGGAGG 59.550 47.826 0.00 0.00 0.00 4.30
4083 4722 7.069877 ACTAACTGTATGGTTTGGAGTAACA 57.930 36.000 0.00 0.00 0.00 2.41
4093 4732 1.975660 TGGAGTAACAAACCCAGTGC 58.024 50.000 0.00 0.00 0.00 4.40
4094 4733 1.213182 TGGAGTAACAAACCCAGTGCA 59.787 47.619 0.00 0.00 0.00 4.57
4097 4736 3.211045 GAGTAACAAACCCAGTGCAGAA 58.789 45.455 0.00 0.00 0.00 3.02
4098 4737 3.626930 AGTAACAAACCCAGTGCAGAAA 58.373 40.909 0.00 0.00 0.00 2.52
4099 4738 2.959507 AACAAACCCAGTGCAGAAAC 57.040 45.000 0.00 0.00 0.00 2.78
4100 4739 0.738389 ACAAACCCAGTGCAGAAACG 59.262 50.000 0.00 0.00 0.00 3.60
4101 4740 0.030638 CAAACCCAGTGCAGAAACGG 59.969 55.000 0.00 0.00 0.00 4.44
4102 4741 0.106918 AAACCCAGTGCAGAAACGGA 60.107 50.000 0.00 0.00 0.00 4.69
4103 4742 0.535102 AACCCAGTGCAGAAACGGAG 60.535 55.000 0.00 0.00 0.00 4.63
4106 4745 1.593196 CCAGTGCAGAAACGGAGAAA 58.407 50.000 0.00 0.00 0.00 2.52
4228 6442 2.125512 GAGGCGATGAACTGCGGT 60.126 61.111 0.00 0.00 0.00 5.68
4444 6658 3.242291 CCGACCCCTATCCTGCCC 61.242 72.222 0.00 0.00 0.00 5.36
4488 6714 5.011635 CCTACCTGGTGCAAAAATTTAACCT 59.988 40.000 10.23 0.00 31.05 3.50
4490 6716 5.364778 ACCTGGTGCAAAAATTTAACCTTC 58.635 37.500 0.00 0.00 31.05 3.46
4493 6719 6.227298 TGGTGCAAAAATTTAACCTTCTGA 57.773 33.333 11.39 0.00 31.05 3.27
4553 6782 4.666512 ACTAAAGTGCTGAACATGGGATT 58.333 39.130 0.00 0.00 0.00 3.01
4680 6909 2.172679 TCTACGGTGTATCAGGTGCAA 58.827 47.619 0.00 0.00 0.00 4.08
4878 8124 3.838795 GTGTGCGCGCTCTTACGG 61.839 66.667 33.29 0.00 0.00 4.02
4994 8936 0.754217 CGGAACCGGATCCAGAGGTA 60.754 60.000 28.26 0.00 39.61 3.08
5074 9020 4.910195 TGCTGATCACTGGTTATGTTTCT 58.090 39.130 0.00 0.00 0.00 2.52
5075 9021 5.316167 TGCTGATCACTGGTTATGTTTCTT 58.684 37.500 0.00 0.00 0.00 2.52
5213 9171 5.886474 TCAGTTCGTTCTATCAGTACCAGAT 59.114 40.000 4.13 4.13 0.00 2.90
5224 9182 4.883083 TCAGTACCAGATTGTGAAGTGAC 58.117 43.478 0.00 0.00 0.00 3.67
5243 9201 3.077359 GACTGGTGTTGAGGATTGGAAG 58.923 50.000 0.00 0.00 0.00 3.46
5244 9202 2.711009 ACTGGTGTTGAGGATTGGAAGA 59.289 45.455 0.00 0.00 0.00 2.87
5247 9205 4.335416 TGGTGTTGAGGATTGGAAGATTC 58.665 43.478 0.00 0.00 0.00 2.52
5325 9283 0.536006 GGCAGCAAGTGTGTCTTCCT 60.536 55.000 0.00 0.00 33.63 3.36
5328 9286 2.775890 CAGCAAGTGTGTCTTCCTGAT 58.224 47.619 0.00 0.00 42.74 2.90
5366 9324 9.678260 ATCTTATAAGAACTTGCATGAGACTTT 57.322 29.630 18.79 0.00 38.77 2.66
5367 9325 8.939929 TCTTATAAGAACTTGCATGAGACTTTG 58.060 33.333 12.87 2.25 30.73 2.77
5368 9326 3.911661 AGAACTTGCATGAGACTTTGC 57.088 42.857 6.60 4.78 39.33 3.68
5369 9327 2.225019 AGAACTTGCATGAGACTTTGCG 59.775 45.455 6.60 0.00 41.80 4.85
5370 9328 1.597742 ACTTGCATGAGACTTTGCGT 58.402 45.000 6.60 0.00 41.80 5.24
5371 9329 1.949525 ACTTGCATGAGACTTTGCGTT 59.050 42.857 6.60 0.00 41.80 4.84
5414 9659 1.259316 GCCGAATTTGCGTTGATCAC 58.741 50.000 0.00 0.00 0.00 3.06
5440 9686 8.746751 CGTATGCATATAAAGGATGAATAGACG 58.253 37.037 10.16 0.94 27.37 4.18
5453 9699 2.400467 ATAGACGATACAAGGGCCCT 57.600 50.000 22.28 22.28 0.00 5.19
5456 9702 0.179081 GACGATACAAGGGCCCTGTC 60.179 60.000 29.50 23.06 0.00 3.51
5546 10491 4.224594 ACAGCTATATGTCATCCCTCATGG 59.775 45.833 0.00 0.00 32.64 3.66
5550 10498 5.658634 GCTATATGTCATCCCTCATGGTCTA 59.341 44.000 0.00 0.00 32.64 2.59
5605 10577 5.741011 TGTGTTTCTCTTGGTAGAACTTGT 58.259 37.500 0.00 0.00 35.25 3.16
5606 10578 6.177610 TGTGTTTCTCTTGGTAGAACTTGTT 58.822 36.000 0.00 0.00 35.25 2.83
5615 10587 7.024768 TCTTGGTAGAACTTGTTTTTGTTTCG 58.975 34.615 0.00 0.00 0.00 3.46
5624 10596 1.262950 GTTTTTGTTTCGCCATTGCCC 59.737 47.619 0.00 0.00 0.00 5.36
5634 10606 1.601759 CCATTGCCCCCGCTCATAG 60.602 63.158 0.00 0.00 35.36 2.23
5650 10624 3.664107 TCATAGTGTGAACCAGCTTGAC 58.336 45.455 0.00 0.00 32.78 3.18
5767 10741 7.692291 CGTTGCGAAGTCTACATTCATAAAATT 59.308 33.333 0.00 0.00 0.00 1.82
5912 10886 3.722555 AACGTCACATGCAATTCTACG 57.277 42.857 9.49 9.49 35.17 3.51
5948 10922 7.769220 AGTTCTTGATGAAATATGCTCAAAGG 58.231 34.615 0.00 0.00 36.30 3.11
5967 10941 1.396653 GGGCTCAAATGATGACCAGG 58.603 55.000 0.00 0.00 33.44 4.45
6009 10983 9.630098 TTCTCAATTCTTGATGCAAAATAGTTC 57.370 29.630 0.00 0.00 39.30 3.01
6030 11004 5.159273 TCTATCACATGTGCACCTACAAA 57.841 39.130 21.38 0.43 33.69 2.83
6066 11040 1.539157 TAACCATTTGCGCCATGACA 58.461 45.000 16.28 0.91 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.536460 GCCAGAACCAGGAAACGGAA 60.536 55.000 0.00 0.00 0.00 4.30
186 187 4.573201 AGAAAACATTCCGACACGAAAAGA 59.427 37.500 0.00 0.00 0.00 2.52
690 719 3.455910 TGGGACTGTAAGATTCCTCATGG 59.544 47.826 0.00 0.00 37.43 3.66
709 738 2.028484 GCGGCATTGCATCATGGG 59.972 61.111 11.39 0.00 34.15 4.00
710 739 2.023414 AAGGCGGCATTGCATCATGG 62.023 55.000 13.08 0.00 36.28 3.66
718 747 1.446618 GGCAAGAAAGGCGGCATTG 60.447 57.895 13.08 11.44 0.00 2.82
742 771 5.472137 TGGGAGAAGTTATTCCAAAGAAACG 59.528 40.000 0.00 0.00 35.94 3.60
871 900 6.770785 GGGTGCTATGGACAACAATTTATAGA 59.229 38.462 0.00 0.00 0.00 1.98
899 929 2.358957 TGCGGAGAAGATTGTGATTGG 58.641 47.619 0.00 0.00 0.00 3.16
944 976 6.713450 GTGGTGAAGACCCAAGAACTATTTTA 59.287 38.462 0.00 0.00 42.34 1.52
959 991 1.947456 GTGAAACTGGGTGGTGAAGAC 59.053 52.381 0.00 0.00 0.00 3.01
965 997 0.755327 GGCTTGTGAAACTGGGTGGT 60.755 55.000 0.00 0.00 38.04 4.16
977 1009 1.347707 TGGAAGACTACCAGGCTTGTG 59.652 52.381 0.00 0.00 45.32 3.33
978 1010 1.729586 TGGAAGACTACCAGGCTTGT 58.270 50.000 0.00 0.00 45.32 3.16
998 1030 1.302285 CTGAGCTTGGAGGCCATGT 59.698 57.895 5.01 0.00 31.53 3.21
1362 1399 6.661805 GGGGAATGTAAAGTGAAATAACCTGA 59.338 38.462 0.00 0.00 0.00 3.86
1373 1410 4.352893 AGGGAATTGGGGAATGTAAAGTG 58.647 43.478 0.00 0.00 0.00 3.16
1374 1412 4.692523 AGGGAATTGGGGAATGTAAAGT 57.307 40.909 0.00 0.00 0.00 2.66
1492 1557 3.282021 GCCAGGATTCATTCTAACAGCA 58.718 45.455 0.00 0.00 0.00 4.41
1656 1721 7.989170 TCAAGCATTAAATTAGCTCTCTGATCA 59.011 33.333 0.00 0.00 37.70 2.92
1698 1764 8.298854 CACATGAACAGACCATATTTTTCAGAA 58.701 33.333 0.00 0.00 0.00 3.02
1743 1812 6.257630 CCAAAATCAACTTCCAACGAATTGTT 59.742 34.615 0.00 0.00 43.09 2.83
1811 1880 1.213296 ACTGCATCCCGTTCCCTATT 58.787 50.000 0.00 0.00 0.00 1.73
1990 2064 8.074370 CAGTTTCTGCATGTTCATAAGGATATG 58.926 37.037 0.00 0.00 40.29 1.78
2031 2113 0.517316 GCTTGTCCACCGTGTTGATC 59.483 55.000 0.00 0.00 0.00 2.92
2035 2117 0.107410 TGAAGCTTGTCCACCGTGTT 60.107 50.000 2.10 0.00 0.00 3.32
2207 2292 3.316308 ACTCCTGAAATCTGCAACACAAC 59.684 43.478 0.00 0.00 0.00 3.32
2429 2530 8.697507 ATTTGAAGAATATTGATACCTGACCC 57.302 34.615 0.00 0.00 0.00 4.46
2447 2548 5.882557 AGTTGCCATGTCCTACTATTTGAAG 59.117 40.000 0.00 0.00 0.00 3.02
2465 2568 3.118261 TGGATAACCTGATCAGAGTTGCC 60.118 47.826 26.67 25.42 37.04 4.52
2466 2569 4.142609 TGGATAACCTGATCAGAGTTGC 57.857 45.455 26.67 20.66 37.04 4.17
2467 2570 8.915057 AAATATGGATAACCTGATCAGAGTTG 57.085 34.615 26.67 14.57 37.04 3.16
2491 2596 8.974060 ACCTGTTACAGAGAAAGAAATGTTAA 57.026 30.769 14.66 0.00 32.44 2.01
2493 2598 7.339466 ACAACCTGTTACAGAGAAAGAAATGTT 59.661 33.333 14.66 2.49 32.44 2.71
2495 2600 7.227512 AGACAACCTGTTACAGAGAAAGAAATG 59.772 37.037 14.66 2.22 32.44 2.32
2497 2602 6.650120 AGACAACCTGTTACAGAGAAAGAAA 58.350 36.000 14.66 0.00 32.44 2.52
2498 2603 6.235231 AGACAACCTGTTACAGAGAAAGAA 57.765 37.500 14.66 0.00 32.44 2.52
2499 2604 5.871396 AGACAACCTGTTACAGAGAAAGA 57.129 39.130 14.66 0.00 32.44 2.52
2500 2605 6.513180 TGTAGACAACCTGTTACAGAGAAAG 58.487 40.000 14.66 0.00 32.44 2.62
2565 2685 1.831580 AACCCTGCTGCTTGATTCTC 58.168 50.000 0.00 0.00 0.00 2.87
2612 2732 3.996921 ATAGCTAGGATGATGGCCTTG 57.003 47.619 3.32 0.00 36.96 3.61
2621 2750 5.186603 TGACATAGCAGGAATAGCTAGGATG 59.813 44.000 12.92 4.73 46.14 3.51
2630 2759 8.486210 AGTTCTACAAATGACATAGCAGGAATA 58.514 33.333 0.00 0.00 0.00 1.75
2719 2852 4.873827 GGTTCGAGCTCCACATTACATTTA 59.126 41.667 8.47 0.00 0.00 1.40
2887 3398 5.173664 TCACTCACACAAGATTGCTGATAG 58.826 41.667 0.00 0.00 0.00 2.08
2896 3407 4.887748 ACGAAAGATCACTCACACAAGAT 58.112 39.130 0.00 0.00 0.00 2.40
2905 3424 8.388853 GGGATAAAACTTTACGAAAGATCACTC 58.611 37.037 12.35 0.00 41.02 3.51
3016 3542 3.175710 AGGGACGCCACCAGGTTT 61.176 61.111 0.00 0.00 37.19 3.27
3067 3593 9.225436 GAGGGATCCTATTTGATTAGACATTTC 57.775 37.037 12.58 0.00 31.76 2.17
3089 3616 3.323403 GGTGGTAAGAGAGATCATGAGGG 59.677 52.174 0.09 0.00 0.00 4.30
3095 3622 4.777366 TGTGATTGGTGGTAAGAGAGATCA 59.223 41.667 0.00 0.00 0.00 2.92
3103 3632 6.823182 TCATATCAACTGTGATTGGTGGTAAG 59.177 38.462 0.00 0.00 42.03 2.34
3138 3667 2.656947 TTCCCTGTCAGGAAAACCAG 57.343 50.000 21.23 1.46 43.02 4.00
3213 3745 2.802719 TGGTATTTTTGGTCCAGCTCC 58.197 47.619 0.00 0.00 0.00 4.70
3574 4115 4.348461 TCAATCTGTGGGTGTAAACCTGTA 59.652 41.667 1.05 0.00 0.00 2.74
4083 4722 0.106918 TCCGTTTCTGCACTGGGTTT 60.107 50.000 0.00 0.00 0.00 3.27
4088 4727 1.264288 GGTTTCTCCGTTTCTGCACTG 59.736 52.381 0.00 0.00 0.00 3.66
4089 4728 1.594331 GGTTTCTCCGTTTCTGCACT 58.406 50.000 0.00 0.00 0.00 4.40
4090 4729 0.591659 GGGTTTCTCCGTTTCTGCAC 59.408 55.000 0.00 0.00 37.00 4.57
4091 4730 0.536460 GGGGTTTCTCCGTTTCTGCA 60.536 55.000 0.00 0.00 37.00 4.41
4093 4732 1.202770 AGTGGGGTTTCTCCGTTTCTG 60.203 52.381 0.00 0.00 37.00 3.02
4094 4733 1.071857 GAGTGGGGTTTCTCCGTTTCT 59.928 52.381 0.00 0.00 37.00 2.52
4097 4736 1.622312 GTAGAGTGGGGTTTCTCCGTT 59.378 52.381 0.00 0.00 37.00 4.44
4098 4737 1.264295 GTAGAGTGGGGTTTCTCCGT 58.736 55.000 0.00 0.00 37.00 4.69
4099 4738 0.535797 GGTAGAGTGGGGTTTCTCCG 59.464 60.000 0.00 0.00 37.00 4.63
4100 4739 0.910338 GGGTAGAGTGGGGTTTCTCC 59.090 60.000 0.00 0.00 0.00 3.71
4101 4740 1.954035 AGGGTAGAGTGGGGTTTCTC 58.046 55.000 0.00 0.00 0.00 2.87
4102 4741 2.435203 AAGGGTAGAGTGGGGTTTCT 57.565 50.000 0.00 0.00 0.00 2.52
4103 4742 3.074094 AGAAAAGGGTAGAGTGGGGTTTC 59.926 47.826 0.00 0.00 0.00 2.78
4106 4745 2.435203 AGAAAAGGGTAGAGTGGGGT 57.565 50.000 0.00 0.00 0.00 4.95
4228 6442 2.357034 GTCGCGAAGGTTGGCAGA 60.357 61.111 12.06 0.00 31.76 4.26
4434 6648 2.211250 CCATTCATGGGGCAGGATAG 57.789 55.000 0.00 0.00 44.31 2.08
4482 6708 7.744733 TGCCATCATGTATATCAGAAGGTTAA 58.255 34.615 0.00 0.00 0.00 2.01
4488 6714 5.494390 AGCTGCCATCATGTATATCAGAA 57.506 39.130 0.00 0.00 0.00 3.02
4490 6716 5.579904 GTGTAGCTGCCATCATGTATATCAG 59.420 44.000 0.00 0.00 0.00 2.90
4493 6719 5.488262 TGTGTAGCTGCCATCATGTATAT 57.512 39.130 0.00 0.00 0.00 0.86
4553 6782 2.435805 GTCCTCCAGAAGCCATACATCA 59.564 50.000 0.00 0.00 0.00 3.07
4680 6909 2.262292 GCATTGTGCATTGGCCGT 59.738 55.556 0.00 0.00 44.26 5.68
4731 7061 6.209361 GGTCTTCACCTGAATGAAAGAAAAC 58.791 40.000 0.00 0.00 40.00 2.43
4878 8124 4.159879 TCCCGGTCTCTCTTGAGTAAATTC 59.840 45.833 0.00 0.00 40.98 2.17
4994 8936 1.622312 GGGAGGTAGAACCGAACACTT 59.378 52.381 0.00 0.00 44.90 3.16
5074 9020 3.503363 GTCATCATCCTGAGCACACAAAA 59.497 43.478 0.00 0.00 0.00 2.44
5075 9021 3.076621 GTCATCATCCTGAGCACACAAA 58.923 45.455 0.00 0.00 0.00 2.83
5124 9080 7.823799 TCATGTAGCTGTTCTGATCATTTGTTA 59.176 33.333 0.00 0.00 0.00 2.41
5213 9171 3.270027 CTCAACACCAGTCACTTCACAA 58.730 45.455 0.00 0.00 0.00 3.33
5224 9182 3.423539 TCTTCCAATCCTCAACACCAG 57.576 47.619 0.00 0.00 0.00 4.00
5243 9201 8.555166 TCAACAACGAACACAATAAAAGAATC 57.445 30.769 0.00 0.00 0.00 2.52
5355 9313 0.730494 GGCAACGCAAAGTCTCATGC 60.730 55.000 0.00 1.41 39.17 4.06
5414 9659 8.746751 CGTCTATTCATCCTTTATATGCATACG 58.253 37.037 8.99 0.22 0.00 3.06
5440 9686 0.759346 ATCGACAGGGCCCTTGTATC 59.241 55.000 26.10 16.51 0.00 2.24
5453 9699 5.789521 TGATCTCACCAAAGTTTATCGACA 58.210 37.500 0.00 0.00 0.00 4.35
5456 9702 8.236586 TCAAATTGATCTCACCAAAGTTTATCG 58.763 33.333 0.00 0.00 0.00 2.92
5546 10491 7.396055 ACTCATCTGCTAGAGGGAATATTAGAC 59.604 40.741 0.00 0.00 36.20 2.59
5550 10498 7.125507 CCATACTCATCTGCTAGAGGGAATATT 59.874 40.741 0.00 0.00 36.20 1.28
5605 10577 1.587547 GGGCAATGGCGAAACAAAAA 58.412 45.000 0.00 0.00 42.47 1.94
5606 10578 0.250081 GGGGCAATGGCGAAACAAAA 60.250 50.000 0.00 0.00 42.47 2.44
5615 10587 3.790416 TATGAGCGGGGGCAATGGC 62.790 63.158 0.00 0.00 40.13 4.40
5624 10596 0.249120 TGGTTCACACTATGAGCGGG 59.751 55.000 0.00 0.00 39.36 6.13
5634 10606 1.279840 GCGTCAAGCTGGTTCACAC 59.720 57.895 0.00 0.00 44.04 3.82
5650 10624 7.743838 CCAAATAACACCATTTTTATTGTTGCG 59.256 33.333 0.00 0.00 34.15 4.85
5767 10741 9.140874 TGTGTGCATTCCCATGATATAATTTTA 57.859 29.630 0.00 0.00 31.07 1.52
5884 10858 0.093026 GCATGTGACGTTACAGCGAC 59.907 55.000 18.52 4.47 33.44 5.19
5933 10907 3.290710 TGAGCCCCTTTGAGCATATTTC 58.709 45.455 0.00 0.00 0.00 2.17
5967 10941 4.081322 TGAGAAGGTAAACTGGTGAACC 57.919 45.455 0.00 0.00 0.00 3.62
6009 10983 5.878332 TTTTGTAGGTGCACATGTGATAG 57.122 39.130 29.80 2.96 0.00 2.08


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

AutoCloner maintained by Alex Coulton.