Multiple sequence alignment - TraesCS7D01G392300

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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 TraesCS7D01G392300 chr7D 100.000 5628 0 0 1 5628 507243855 507249482 0.000000e+00 10394.0
1 TraesCS7D01G392300 chr7D 84.301 1051 96 39 802 1824 136248214 136247205 0.000000e+00 963.0
2 TraesCS7D01G392300 chr7D 81.427 1163 155 39 1922 3030 136246499 136245344 0.000000e+00 894.0
3 TraesCS7D01G392300 chr7D 80.458 742 78 34 3115 3827 136245313 136244610 6.510000e-139 505.0
4 TraesCS7D01G392300 chr7D 90.000 60 5 1 4577 4636 136244070 136244012 6.050000e-10 76.8
5 TraesCS7D01G392300 chr7A 93.262 3562 117 32 1 3479 577200194 577203715 0.000000e+00 5134.0
6 TraesCS7D01G392300 chr7A 85.217 1062 104 33 802 1831 135709027 135707987 0.000000e+00 1042.0
7 TraesCS7D01G392300 chr7A 93.097 536 14 9 4417 4937 577204779 577205306 0.000000e+00 763.0
8 TraesCS7D01G392300 chr7A 81.724 870 110 32 2147 2983 135707309 135706456 0.000000e+00 680.0
9 TraesCS7D01G392300 chr7A 94.146 410 21 2 3463 3870 577203854 577204262 6.190000e-174 621.0
10 TraesCS7D01G392300 chr7A 90.208 480 19 12 3853 4331 577204316 577204768 8.070000e-168 601.0
11 TraesCS7D01G392300 chr7A 78.249 754 99 36 3103 3827 135706311 135705594 1.870000e-114 424.0
12 TraesCS7D01G392300 chr7A 95.455 44 2 0 4938 4981 817847 817890 2.810000e-08 71.3
13 TraesCS7D01G392300 chr7A 93.617 47 3 0 566 612 578994253 578994299 2.810000e-08 71.3
14 TraesCS7D01G392300 chr7B 84.442 2436 215 76 749 3099 256170685 256173041 0.000000e+00 2248.0
15 TraesCS7D01G392300 chr7B 93.197 1514 64 12 650 2137 535687980 535689480 0.000000e+00 2189.0
16 TraesCS7D01G392300 chr7B 94.033 972 36 5 3391 4350 535690860 535691821 0.000000e+00 1454.0
17 TraesCS7D01G392300 chr7B 91.960 796 28 11 2123 2900 535689501 535690278 0.000000e+00 1083.0
18 TraesCS7D01G392300 chr7B 83.993 1087 106 44 802 1858 99106101 99105053 0.000000e+00 981.0
19 TraesCS7D01G392300 chr7B 93.121 596 26 7 4339 4921 535696038 535696631 0.000000e+00 859.0
20 TraesCS7D01G392300 chr7B 95.075 467 12 2 2940 3395 535690283 535690749 0.000000e+00 725.0
21 TraesCS7D01G392300 chr7B 76.942 798 95 40 2745 3515 99103161 99102426 6.890000e-99 372.0
22 TraesCS7D01G392300 chr7B 84.733 131 18 2 4538 4668 99101553 99101425 4.580000e-26 130.0
23 TraesCS7D01G392300 chr5B 82.500 2080 217 68 1102 3099 343721167 343723181 0.000000e+00 1688.0
24 TraesCS7D01G392300 chr5B 84.958 359 34 10 749 1107 343719115 343719453 4.170000e-91 346.0
25 TraesCS7D01G392300 chr5B 100.000 29 0 0 4472 4500 155713929 155713901 3.000000e-03 54.7
26 TraesCS7D01G392300 chr6B 93.333 645 34 3 4938 5573 142227880 142228524 0.000000e+00 944.0
27 TraesCS7D01G392300 chr6B 86.087 115 16 0 4937 5051 228234028 228233914 2.130000e-24 124.0
28 TraesCS7D01G392300 chr6B 95.652 46 2 0 566 611 232734861 232734816 2.170000e-09 75.0
29 TraesCS7D01G392300 chr6B 91.837 49 4 0 564 612 431936338 431936290 1.010000e-07 69.4
30 TraesCS7D01G392300 chr4B 93.302 642 37 1 4938 5573 69891851 69892492 0.000000e+00 942.0
31 TraesCS7D01G392300 chr4B 95.593 295 12 1 1153 1447 603017892 603017599 6.600000e-129 472.0
32 TraesCS7D01G392300 chr4B 88.983 118 13 0 4938 5055 69893040 69892923 4.540000e-31 147.0
33 TraesCS7D01G392300 chr3B 95.593 295 12 1 1153 1447 811782541 811782834 6.600000e-129 472.0
34 TraesCS7D01G392300 chr5A 77.889 199 36 6 4937 5130 547382877 547382682 3.560000e-22 117.0
35 TraesCS7D01G392300 chr5A 100.000 29 0 0 4472 4500 184233240 184233268 3.000000e-03 54.7
36 TraesCS7D01G392300 chr3D 84.615 117 18 0 4937 5053 47334936 47335052 3.560000e-22 117.0
37 TraesCS7D01G392300 chr4A 88.235 68 5 3 566 632 589023473 589023408 1.680000e-10 78.7
38 TraesCS7D01G392300 chr4A 93.878 49 2 1 563 610 80142889 80142937 7.820000e-09 73.1
39 TraesCS7D01G392300 chr4A 100.000 29 0 0 4938 4966 535864908 535864936 3.000000e-03 54.7
40 TraesCS7D01G392300 chr6D 85.507 69 6 4 566 632 467941653 467941587 1.010000e-07 69.4
41 TraesCS7D01G392300 chr6D 85.714 63 8 1 566 627 68652306 68652244 1.310000e-06 65.8
42 TraesCS7D01G392300 chr4D 90.566 53 3 2 563 614 427269559 427269508 1.010000e-07 69.4
43 TraesCS7D01G392300 chr4D 86.885 61 6 2 4472 4530 403138967 403139027 3.640000e-07 67.6
44 TraesCS7D01G392300 chrUn 81.818 77 4 5 4472 4540 99872256 99872330 7.880000e-04 56.5
45 TraesCS7D01G392300 chr3A 100.000 30 0 0 4471 4500 486046436 486046465 7.880000e-04 56.5
46 TraesCS7D01G392300 chr1A 88.889 45 5 0 4937 4981 575783303 575783259 7.880000e-04 56.5
47 TraesCS7D01G392300 chr1A 96.875 32 1 0 4468 4499 47582182 47582213 3.000000e-03 54.7
48 TraesCS7D01G392300 chr5D 100.000 29 0 0 4472 4500 138468979 138468951 3.000000e-03 54.7


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 TraesCS7D01G392300 chr7D 507243855 507249482 5627 False 10394.000000 10394 100.000000 1 5628 1 chr7D.!!$F1 5627
1 TraesCS7D01G392300 chr7D 136244012 136248214 4202 True 609.700000 963 84.046500 802 4636 4 chr7D.!!$R1 3834
2 TraesCS7D01G392300 chr7A 577200194 577205306 5112 False 1779.750000 5134 92.678250 1 4937 4 chr7A.!!$F3 4936
3 TraesCS7D01G392300 chr7A 135705594 135709027 3433 True 715.333333 1042 81.730000 802 3827 3 chr7A.!!$R1 3025
4 TraesCS7D01G392300 chr7B 256170685 256173041 2356 False 2248.000000 2248 84.442000 749 3099 1 chr7B.!!$F1 2350
5 TraesCS7D01G392300 chr7B 535687980 535691821 3841 False 1362.750000 2189 93.566250 650 4350 4 chr7B.!!$F3 3700
6 TraesCS7D01G392300 chr7B 535696038 535696631 593 False 859.000000 859 93.121000 4339 4921 1 chr7B.!!$F2 582
7 TraesCS7D01G392300 chr7B 99101425 99106101 4676 True 494.333333 981 81.889333 802 4668 3 chr7B.!!$R1 3866
8 TraesCS7D01G392300 chr5B 343719115 343723181 4066 False 1017.000000 1688 83.729000 749 3099 2 chr5B.!!$F1 2350
9 TraesCS7D01G392300 chr6B 142227880 142228524 644 False 944.000000 944 93.333000 4938 5573 1 chr6B.!!$F1 635
10 TraesCS7D01G392300 chr4B 69891851 69892492 641 False 942.000000 942 93.302000 4938 5573 1 chr4B.!!$F1 635

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
380 383 0.966179 TTTAGCGACAGGAGAGCACA 59.034 50.000 0.00 0.0 0.00 4.57 F
1044 1066 1.079336 GGTGGAGTACAACCCGCTC 60.079 63.158 10.81 0.0 33.65 5.03 F
1440 3182 1.295792 TTCTGTCGAACACCTTGCAC 58.704 50.000 0.00 0.0 0.00 4.57 F
1680 3458 2.159071 TGTAGCGTTACCTGTGTTGTGT 60.159 45.455 6.98 0.0 0.00 3.72 F
3442 7062 3.244596 GCTCCAATAGTTCCTGGGTATCC 60.245 52.174 0.00 0.0 33.19 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 3243 1.058404 GACGACGTAAGCAACTGTCC 58.942 55.000 0.00 0.00 45.62 4.02 R
2365 5596 3.537580 CCTAAAATGCATGCAGCCAAAT 58.462 40.909 26.69 4.78 44.83 2.32 R
2615 5938 4.481368 AATCATGGAACGCTTACCTACA 57.519 40.909 0.00 0.00 0.00 2.74 R
3521 7333 3.365264 CGCAAGCAGAAAGAAATGCACTA 60.365 43.478 0.00 0.00 45.01 2.74 R
5396 9377 0.181350 CCTCCTTCTCCAAATCCGGG 59.819 60.000 0.00 0.00 0.00 5.73 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
266 268 3.247442 GTGATGTGACATTGTTGCATGG 58.753 45.455 0.00 0.00 0.00 3.66
281 283 4.137116 TGCATGGATAGTGAGGTACAAC 57.863 45.455 0.00 0.00 0.00 3.32
286 288 6.425114 GCATGGATAGTGAGGTACAACTATTG 59.575 42.308 13.31 10.24 0.00 1.90
345 347 3.627577 AGGCGATGCAACTTTTATACCTG 59.372 43.478 0.00 0.00 0.00 4.00
370 372 1.074084 TGGGGAAATGGTTTAGCGACA 59.926 47.619 0.00 0.00 0.00 4.35
380 383 0.966179 TTTAGCGACAGGAGAGCACA 59.034 50.000 0.00 0.00 0.00 4.57
399 402 4.304110 CACATTGAGAGCAAGCAATTTGT 58.696 39.130 0.00 0.00 39.08 2.83
615 619 6.936968 AGGAATGGAGGGAGTACATATTAC 57.063 41.667 0.00 0.00 0.00 1.89
774 782 1.594293 CCCCGCACTATAGCAACGG 60.594 63.158 17.42 17.42 43.44 4.44
1044 1066 1.079336 GGTGGAGTACAACCCGCTC 60.079 63.158 10.81 0.00 33.65 5.03
1440 3182 1.295792 TTCTGTCGAACACCTTGCAC 58.704 50.000 0.00 0.00 0.00 4.57
1458 3214 4.712873 GCGTGCGCGTTGTGTACC 62.713 66.667 22.18 0.00 40.81 3.34
1680 3458 2.159071 TGTAGCGTTACCTGTGTTGTGT 60.159 45.455 6.98 0.00 0.00 3.72
1692 3471 4.634004 CCTGTGTTGTGTTTTGACTGTAGA 59.366 41.667 0.00 0.00 0.00 2.59
1722 3501 6.866010 TCATGTTTCACATATATCACCTGC 57.134 37.500 0.00 0.00 36.53 4.85
1808 3596 4.293662 AGCCTCTTTTACCTTCCTTCTG 57.706 45.455 0.00 0.00 0.00 3.02
1862 4504 8.870160 TTTGTTCTCTTCAACATTTTGTATGG 57.130 30.769 0.00 0.00 36.16 2.74
2615 5938 7.608376 GCTCTTTCAGGGTTTAATTTCTACTCT 59.392 37.037 0.00 0.00 0.00 3.24
2622 5945 8.755977 CAGGGTTTAATTTCTACTCTGTAGGTA 58.244 37.037 5.10 0.00 36.00 3.08
2726 6060 5.248705 GCTTACATACTATCCCTAGCCCTTT 59.751 44.000 0.00 0.00 0.00 3.11
2902 6297 6.295916 CCTCCTCAGTCAACCTTTTACATAGT 60.296 42.308 0.00 0.00 0.00 2.12
3077 6560 6.624423 AGCATGGTTTCATTTGTCATAACTC 58.376 36.000 0.00 0.00 0.00 3.01
3197 6683 5.582269 TGCATATCTTTCGAGGAAGAGTTTG 59.418 40.000 5.82 4.62 38.90 2.93
3399 7019 6.349033 GGGCACAAGTTTTGTAAGTACATAGG 60.349 42.308 0.00 0.00 43.23 2.57
3442 7062 3.244596 GCTCCAATAGTTCCTGGGTATCC 60.245 52.174 0.00 0.00 33.19 2.59
3478 7252 7.062749 TCTAATTGCCCATACTGTTACCTAG 57.937 40.000 0.00 0.00 0.00 3.02
3705 7519 8.664798 TGCATGAAATTCACTACACATACTTAC 58.335 33.333 0.00 0.00 0.00 2.34
3713 7527 8.503458 TTCACTACACATACTTACCTCTAGTC 57.497 38.462 0.00 0.00 0.00 2.59
3714 7528 7.859540 TCACTACACATACTTACCTCTAGTCT 58.140 38.462 0.00 0.00 0.00 3.24
3870 7694 7.774625 TGGTGATGTTTAGATGCAATATTCTCA 59.225 33.333 0.00 0.00 0.00 3.27
3947 7842 4.076394 TGCGGGTGCTATTTCTAGTTTTT 58.924 39.130 0.00 0.00 43.34 1.94
4072 7999 6.954352 AAGGAAAAACATACTACTCCCTCT 57.046 37.500 0.00 0.00 0.00 3.69
4121 8059 5.934935 AACCACGTCAACTATTTTCGAAT 57.065 34.783 0.00 0.00 0.00 3.34
4184 8122 0.470833 AGGTGCTCCTCGGCATATCT 60.471 55.000 0.18 0.00 44.34 1.98
4207 8146 1.760613 GTCATTCATGGTAGGTCGGGA 59.239 52.381 0.00 0.00 0.00 5.14
4270 8209 6.952358 TCCCATCTTAGTCACTTGTTAGTAGT 59.048 38.462 0.00 0.00 31.96 2.73
4278 8221 5.182760 AGTCACTTGTTAGTAGTACCGGAAG 59.817 44.000 9.46 0.00 31.96 3.46
4378 8333 9.353999 AGTAATTTGGTTTATGCTCGAATTTTC 57.646 29.630 0.00 0.00 0.00 2.29
4406 8361 1.520342 GACCAGGCTCTCGTGATGC 60.520 63.158 0.00 0.00 0.00 3.91
4501 8457 5.104109 TCCCTCCGATCCAAATTAATTGAGT 60.104 40.000 0.39 0.00 41.85 3.41
4543 8499 2.829720 GGGGGTATGAGTTTGTTTTCCC 59.170 50.000 0.00 0.00 0.00 3.97
4557 8515 3.328343 TGTTTTCCCCCTCGTGAATTCTA 59.672 43.478 7.05 0.00 0.00 2.10
4568 8526 6.238759 CCCTCGTGAATTCTAAATGGAAATCC 60.239 42.308 7.05 0.00 0.00 3.01
4573 8531 7.859377 CGTGAATTCTAAATGGAAATCCTGATG 59.141 37.037 7.05 0.00 36.82 3.07
4630 8588 2.989639 CCCCAGGCTTCGTGATCA 59.010 61.111 0.00 0.00 0.00 2.92
4768 8740 2.988010 TTCTCGGAACATGCTATGCT 57.012 45.000 0.00 0.00 0.00 3.79
4807 8779 6.263617 GGTGTTGATTTTACAACCCTGTTCTA 59.736 38.462 0.00 0.00 46.32 2.10
4926 8898 4.875536 TGCTGTAATCATGTTCGTAGCATT 59.124 37.500 10.88 0.00 35.27 3.56
4992 8964 6.392354 CACCGAAGTCTAATGTACAACCTTA 58.608 40.000 0.00 0.00 0.00 2.69
5004 8976 8.936070 AATGTACAACCTTAAACTTCAAAACC 57.064 30.769 0.00 0.00 0.00 3.27
5021 8993 1.362355 CCGTCTGTTTTGCAACCCC 59.638 57.895 0.00 0.00 31.02 4.95
5028 9000 1.135333 TGTTTTGCAACCCCGAACTTC 59.865 47.619 0.00 0.00 31.02 3.01
5038 9010 2.332654 CCGAACTTCCAAAGCCGGG 61.333 63.158 2.18 0.00 41.43 5.73
5148 9121 1.136891 GCATGGGCACTAAACCAATCC 59.863 52.381 0.00 0.00 40.73 3.01
5166 9139 5.365025 CCAATCCCATCTCTTTCTCTCTGTA 59.635 44.000 0.00 0.00 0.00 2.74
5235 9210 2.443390 CTGGTACCCCGTCCCGAT 60.443 66.667 10.07 0.00 0.00 4.18
5363 9338 1.124297 CGTTGTCCGAGTCATTGAACG 59.876 52.381 7.30 7.30 39.56 3.95
5396 9377 1.154197 GTTCACGGCTGTTACCTTCC 58.846 55.000 0.00 0.00 0.00 3.46
5574 9555 2.887568 GCTGGACAGCGGACGATG 60.888 66.667 8.72 8.54 45.29 3.84
5575 9556 2.887568 CTGGACAGCGGACGATGC 60.888 66.667 10.09 3.12 34.49 3.91
5576 9557 4.794439 TGGACAGCGGACGATGCG 62.794 66.667 10.09 0.00 34.49 4.73
5583 9564 3.257561 CGGACGATGCGCTCAAGG 61.258 66.667 9.73 0.00 0.00 3.61
5584 9565 2.892425 GGACGATGCGCTCAAGGG 60.892 66.667 9.73 0.00 0.00 3.95
5585 9566 2.184322 GACGATGCGCTCAAGGGA 59.816 61.111 9.73 0.00 0.00 4.20
5586 9567 1.880340 GACGATGCGCTCAAGGGAG 60.880 63.158 9.73 0.00 44.33 4.30
5587 9568 2.284798 GACGATGCGCTCAAGGGAGA 62.285 60.000 9.73 0.00 44.26 3.71
5588 9569 1.068753 CGATGCGCTCAAGGGAGAT 59.931 57.895 9.73 0.00 44.26 2.75
5589 9570 1.220169 CGATGCGCTCAAGGGAGATG 61.220 60.000 9.73 0.00 44.26 2.90
5590 9571 0.883814 GATGCGCTCAAGGGAGATGG 60.884 60.000 9.73 0.00 44.26 3.51
5591 9572 2.899339 GCGCTCAAGGGAGATGGC 60.899 66.667 0.00 0.00 44.26 4.40
5592 9573 2.203126 CGCTCAAGGGAGATGGCC 60.203 66.667 0.00 0.00 44.26 5.36
5593 9574 2.739996 CGCTCAAGGGAGATGGCCT 61.740 63.158 3.32 0.00 44.26 5.19
5594 9575 1.153005 GCTCAAGGGAGATGGCCTG 60.153 63.158 3.32 0.00 44.26 4.85
5595 9576 1.530771 CTCAAGGGAGATGGCCTGG 59.469 63.158 3.32 0.00 44.26 4.45
5596 9577 1.992519 CTCAAGGGAGATGGCCTGGG 61.993 65.000 3.32 0.00 44.26 4.45
5597 9578 3.424105 AAGGGAGATGGCCTGGGC 61.424 66.667 14.23 14.23 41.06 5.36
5598 9579 4.765970 AGGGAGATGGCCTGGGCA 62.766 66.667 26.08 26.08 44.11 5.36
5599 9580 4.512914 GGGAGATGGCCTGGGCAC 62.513 72.222 26.41 18.26 41.84 5.01
5600 9581 4.864334 GGAGATGGCCTGGGCACG 62.864 72.222 26.41 0.00 41.84 5.34
5613 9594 2.890474 GCACGCCGTCCGATGAAT 60.890 61.111 0.00 0.00 41.02 2.57
5614 9595 3.005898 CACGCCGTCCGATGAATG 58.994 61.111 0.00 0.00 41.02 2.67
5615 9596 2.890474 ACGCCGTCCGATGAATGC 60.890 61.111 0.00 0.00 41.02 3.56
5616 9597 2.586079 CGCCGTCCGATGAATGCT 60.586 61.111 0.00 0.00 40.02 3.79
5617 9598 2.173669 CGCCGTCCGATGAATGCTT 61.174 57.895 0.00 0.00 40.02 3.91
5618 9599 1.353103 GCCGTCCGATGAATGCTTG 59.647 57.895 0.00 0.00 0.00 4.01
5619 9600 1.089481 GCCGTCCGATGAATGCTTGA 61.089 55.000 0.00 0.00 0.00 3.02
5620 9601 1.586422 CCGTCCGATGAATGCTTGAT 58.414 50.000 0.00 0.00 0.00 2.57
5621 9602 1.942657 CCGTCCGATGAATGCTTGATT 59.057 47.619 0.00 0.00 0.00 2.57
5622 9603 2.286595 CCGTCCGATGAATGCTTGATTG 60.287 50.000 0.00 0.00 0.00 2.67
5623 9604 2.724349 GTCCGATGAATGCTTGATTGC 58.276 47.619 0.00 0.00 0.00 3.56
5624 9605 1.331447 TCCGATGAATGCTTGATTGCG 59.669 47.619 0.00 0.00 35.36 4.85
5625 9606 1.331447 CCGATGAATGCTTGATTGCGA 59.669 47.619 0.00 0.00 35.36 5.10
5626 9607 2.031420 CCGATGAATGCTTGATTGCGAT 60.031 45.455 0.00 0.00 35.36 4.58
5627 9608 3.549423 CCGATGAATGCTTGATTGCGATT 60.549 43.478 0.00 0.00 35.36 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.593263 GTAGAACGCACGGGGTATCG 60.593 60.000 0.00 0.00 0.00 2.92
173 175 2.479566 AACATGCAACCTCATCGACT 57.520 45.000 0.00 0.00 0.00 4.18
228 230 6.427853 TCACATCACCAAGTTATGCATATAGC 59.572 38.462 7.36 1.51 45.96 2.97
266 268 7.584122 TCCTCAATAGTTGTACCTCACTATC 57.416 40.000 8.97 0.00 0.00 2.08
286 288 8.581578 CCTTGTTCTAGGTATTCTCTATTCCTC 58.418 40.741 0.00 0.00 35.76 3.71
345 347 2.094906 GCTAAACCATTTCCCCACGTTC 60.095 50.000 0.00 0.00 0.00 3.95
370 372 1.273759 TGCTCTCAATGTGCTCTCCT 58.726 50.000 0.00 0.00 36.27 3.69
380 383 6.930667 AAAAACAAATTGCTTGCTCTCAAT 57.069 29.167 0.00 0.00 38.75 2.57
446 449 8.020819 TCGCATAAAGAGAAACATAAAAAGGTG 58.979 33.333 0.00 0.00 0.00 4.00
582 586 9.322769 GTACTCCCTCCATTCCTAAATATAAGA 57.677 37.037 0.00 0.00 0.00 2.10
688 696 6.263168 CCATTCACATAGGTATGAGGTTTTCC 59.737 42.308 3.96 0.00 37.15 3.13
1458 3214 1.803334 TGTTTGGACGAGGGATTTCG 58.197 50.000 0.00 0.00 45.70 3.46
1487 3243 1.058404 GACGACGTAAGCAACTGTCC 58.942 55.000 0.00 0.00 45.62 4.02
1722 3501 6.868339 TCCAGCATACATAGACAAATATGACG 59.132 38.462 0.97 0.00 36.76 4.35
1808 3596 7.169645 ACACAATGTTAGCAATGTTTGATGAAC 59.830 33.333 0.00 0.00 36.67 3.18
1862 4504 5.482908 CAGACCAGCTATATAATCACCCAC 58.517 45.833 0.00 0.00 0.00 4.61
2033 4704 4.394920 CACAGTACACCTTGACAAACAGTT 59.605 41.667 0.00 0.00 0.00 3.16
2076 4747 7.971183 TGCACATAAATAGTACACTTTGACA 57.029 32.000 0.00 0.00 0.00 3.58
2365 5596 3.537580 CCTAAAATGCATGCAGCCAAAT 58.462 40.909 26.69 4.78 44.83 2.32
2405 5639 9.959721 AAATAAATAACTGATACCACAGACAGT 57.040 29.630 0.00 0.00 43.92 3.55
2594 5917 8.319146 CCTACAGAGTAGAAATTAAACCCTGAA 58.681 37.037 5.78 0.00 0.00 3.02
2615 5938 4.481368 AATCATGGAACGCTTACCTACA 57.519 40.909 0.00 0.00 0.00 2.74
2622 5945 4.631813 GTCTAGACAAATCATGGAACGCTT 59.368 41.667 18.20 0.00 0.00 4.68
2902 6297 9.871175 AAAGGTGTTCCTAAAAAGGTAAGAATA 57.129 29.630 0.00 0.00 44.35 1.75
3176 6662 5.983540 AGCAAACTCTTCCTCGAAAGATAT 58.016 37.500 0.16 0.00 40.84 1.63
3442 7062 9.136952 GTATGGGCAATTAGAAAGTACGTATAG 57.863 37.037 0.00 0.00 0.00 1.31
3521 7333 3.365264 CGCAAGCAGAAAGAAATGCACTA 60.365 43.478 0.00 0.00 45.01 2.74
3681 7495 9.383519 AGGTAAGTATGTGTAGTGAATTTCATG 57.616 33.333 1.78 0.00 0.00 3.07
3705 7519 0.396974 AGGCTGGCAGAGACTAGAGG 60.397 60.000 20.86 0.00 38.86 3.69
3832 7656 8.870160 TCTAAACATCACCAAAATGAAAAGTG 57.130 30.769 0.00 0.00 30.82 3.16
3870 7694 8.026026 CGTGACTGCATATGACTTAGATATCTT 58.974 37.037 11.25 0.00 0.00 2.40
3947 7842 8.304596 GTCCATGGTATCATCGAGACTATAAAA 58.695 37.037 12.58 0.00 0.00 1.52
3959 7854 4.696899 CATGCATGTCCATGGTATCATC 57.303 45.455 18.91 9.60 39.08 2.92
4072 7999 7.548196 AGTTCAAGTCAACTATTTTCGAACA 57.452 32.000 0.00 0.00 34.70 3.18
4121 8059 9.613428 CAATCTTGTAAATATGTACTTCCTCCA 57.387 33.333 4.68 0.00 0.00 3.86
4184 8122 1.470805 CGACCTACCATGAATGACGCA 60.471 52.381 0.00 0.00 0.00 5.24
4215 8154 4.884744 ACAAGCAACCTAAACATGTGTACA 59.115 37.500 0.00 0.00 0.00 2.90
4270 8209 2.762327 GTGATCCTACCAACTTCCGGTA 59.238 50.000 0.00 0.00 37.99 4.02
4278 8221 2.304761 TCCACCTTGTGATCCTACCAAC 59.695 50.000 0.00 0.00 35.23 3.77
4322 8267 9.745018 ATCACATATATTTCAGTCCCATAAAGG 57.255 33.333 0.00 0.00 37.03 3.11
4378 8333 4.396166 ACGAGAGCCTGGTCAATTTAATTG 59.604 41.667 11.12 11.12 41.57 2.32
4406 8361 1.008194 CATGCATCCAAATCGCCCG 60.008 57.895 0.00 0.00 0.00 6.13
4411 8366 6.431198 AAAATTCAAGCATGCATCCAAATC 57.569 33.333 21.98 0.00 0.00 2.17
4501 8457 7.901861 ACCCCCTCCAATACAAATTAATTAACA 59.098 33.333 0.01 0.00 0.00 2.41
4515 8471 4.116113 ACAAACTCATACCCCCTCCAATA 58.884 43.478 0.00 0.00 0.00 1.90
4518 8474 2.053747 ACAAACTCATACCCCCTCCA 57.946 50.000 0.00 0.00 0.00 3.86
4543 8499 6.238759 GGATTTCCATTTAGAATTCACGAGGG 60.239 42.308 8.44 3.96 35.64 4.30
4568 8526 7.029563 GGCTGGAAAGTAAAAACATACATCAG 58.970 38.462 0.00 0.00 0.00 2.90
4573 8531 7.430441 TCTTTGGCTGGAAAGTAAAAACATAC 58.570 34.615 0.00 0.00 34.95 2.39
4588 8546 1.589716 CCTCGGCTTTCTTTGGCTGG 61.590 60.000 0.00 0.00 35.72 4.85
4630 8588 1.977129 AGACTGAAAGAGCTCTGCCTT 59.023 47.619 19.06 8.07 37.43 4.35
4740 8712 4.214332 AGCATGTTCCGAGAAAAGAGAAAC 59.786 41.667 0.00 0.00 0.00 2.78
4768 8740 2.107378 TCAACACCAAATGGGCTACTCA 59.893 45.455 4.17 0.00 42.05 3.41
4807 8779 3.469008 TGGTTCACAGTTGATCGTTCT 57.531 42.857 0.00 0.00 0.00 3.01
4926 8898 6.672266 ATGGACTTCTCTCTGTTGAAACTA 57.328 37.500 0.00 0.00 0.00 2.24
5004 8976 1.008995 CGGGGTTGCAAAACAGACG 60.009 57.895 0.00 0.17 32.77 4.18
5021 8993 2.978018 GCCCGGCTTTGGAAGTTCG 61.978 63.158 0.71 0.00 0.00 3.95
5028 9000 1.596752 GGTTTTTGCCCGGCTTTGG 60.597 57.895 11.61 0.00 0.00 3.28
5038 9010 2.483013 GGTGAAGAGGGTTGGTTTTTGC 60.483 50.000 0.00 0.00 0.00 3.68
5148 9121 5.913137 ACTGTACAGAGAGAAAGAGATGG 57.087 43.478 29.30 0.00 0.00 3.51
5166 9139 2.928396 CGGGTGGGGAGGAACTGT 60.928 66.667 0.00 0.00 41.55 3.55
5295 9270 2.108568 GTCCTCCTACTCGGACAGC 58.891 63.158 3.72 0.00 46.98 4.40
5363 9338 1.382419 CGTGAACTCAATGTCGTCGTC 59.618 52.381 0.00 0.00 0.00 4.20
5396 9377 0.181350 CCTCCTTCTCCAAATCCGGG 59.819 60.000 0.00 0.00 0.00 5.73
5573 9554 2.586245 CCATCTCCCTTGAGCGCA 59.414 61.111 11.47 0.00 38.58 6.09
5574 9555 2.899339 GCCATCTCCCTTGAGCGC 60.899 66.667 0.00 0.00 38.58 5.92
5575 9556 2.203126 GGCCATCTCCCTTGAGCG 60.203 66.667 0.00 0.00 38.58 5.03
5576 9557 1.153005 CAGGCCATCTCCCTTGAGC 60.153 63.158 5.01 0.00 38.58 4.26
5577 9558 1.530771 CCAGGCCATCTCCCTTGAG 59.469 63.158 5.01 0.00 40.17 3.02
5578 9559 2.002977 CCCAGGCCATCTCCCTTGA 61.003 63.158 5.01 0.00 0.00 3.02
5579 9560 2.599597 CCCAGGCCATCTCCCTTG 59.400 66.667 5.01 0.00 0.00 3.61
5580 9561 3.424105 GCCCAGGCCATCTCCCTT 61.424 66.667 5.01 0.00 34.56 3.95
5581 9562 4.765970 TGCCCAGGCCATCTCCCT 62.766 66.667 5.01 0.00 41.09 4.20
5582 9563 4.512914 GTGCCCAGGCCATCTCCC 62.513 72.222 5.01 0.00 41.09 4.30
5583 9564 4.864334 CGTGCCCAGGCCATCTCC 62.864 72.222 5.01 0.00 41.09 3.71
5596 9577 2.890474 ATTCATCGGACGGCGTGC 60.890 61.111 21.19 21.74 0.00 5.34
5597 9578 3.005898 CATTCATCGGACGGCGTG 58.994 61.111 21.19 3.53 0.00 5.34
5598 9579 2.852495 AAGCATTCATCGGACGGCGT 62.852 55.000 14.65 14.65 0.00 5.68
5599 9580 2.173669 AAGCATTCATCGGACGGCG 61.174 57.895 4.80 4.80 0.00 6.46
5600 9581 1.089481 TCAAGCATTCATCGGACGGC 61.089 55.000 0.00 0.00 0.00 5.68
5601 9582 1.586422 ATCAAGCATTCATCGGACGG 58.414 50.000 0.00 0.00 0.00 4.79
5602 9583 2.852143 GCAATCAAGCATTCATCGGACG 60.852 50.000 0.00 0.00 0.00 4.79
5603 9584 2.724349 GCAATCAAGCATTCATCGGAC 58.276 47.619 0.00 0.00 0.00 4.79
5604 9585 1.331447 CGCAATCAAGCATTCATCGGA 59.669 47.619 0.00 0.00 0.00 4.55
5605 9586 1.331447 TCGCAATCAAGCATTCATCGG 59.669 47.619 0.00 0.00 0.00 4.18
5606 9587 2.742954 TCGCAATCAAGCATTCATCG 57.257 45.000 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.