Multiple sequence alignment - TraesCS5D01G460500

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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 TraesCS5D01G460500 chr5D 100.000 4171 0 0 1 4171 504994212 504998382 0.000000e+00 7703.0
1 TraesCS5D01G460500 chr5D 76.775 521 92 21 3441 3945 197479335 197479842 8.890000e-67 265.0
2 TraesCS5D01G460500 chr5D 83.140 172 23 5 3940 4107 504997985 504998154 7.220000e-33 152.0
3 TraesCS5D01G460500 chr5D 87.736 106 11 2 457 560 518764704 518764599 5.660000e-24 122.0
4 TraesCS5D01G460500 chr5D 97.059 34 1 0 453 486 423490627 423490660 1.620000e-04 58.4
5 TraesCS5D01G460500 chr5B 92.391 4258 191 56 1 4171 634180821 634185032 0.000000e+00 5945.0
6 TraesCS5D01G460500 chr5B 90.945 508 34 5 2613 3117 634288046 634288544 0.000000e+00 673.0
7 TraesCS5D01G460500 chr5B 84.884 172 17 6 3940 4107 634184634 634184800 9.280000e-37 165.0
8 TraesCS5D01G460500 chr5B 87.903 124 10 5 3272 3393 533484122 533484242 1.560000e-29 141.0
9 TraesCS5D01G460500 chr5B 88.073 109 10 3 3288 3395 690316742 690316848 4.380000e-25 126.0
10 TraesCS5D01G460500 chr5B 90.741 54 4 1 787 839 634059963 634060016 2.080000e-08 71.3
11 TraesCS5D01G460500 chr5A 96.130 2739 69 18 525 3235 632356493 632359222 0.000000e+00 4436.0
12 TraesCS5D01G460500 chr5A 88.148 540 39 7 1 520 632355638 632356172 1.650000e-173 619.0
13 TraesCS5D01G460500 chr5A 81.099 455 66 15 3419 3855 60520446 60519994 3.090000e-91 346.0
14 TraesCS5D01G460500 chr5A 76.136 528 102 17 3419 3929 558976803 558976283 5.350000e-64 255.0
15 TraesCS5D01G460500 chr7A 83.302 533 73 9 3420 3943 565721602 565721077 1.050000e-130 477.0
16 TraesCS5D01G460500 chr7A 82.500 240 30 10 3936 4169 565721248 565721015 2.540000e-47 200.0
17 TraesCS5D01G460500 chr7A 81.328 241 34 9 3936 4171 61513318 61513552 7.120000e-43 185.0
18 TraesCS5D01G460500 chr4D 81.228 570 85 18 3389 3946 340016948 340017507 1.380000e-119 440.0
19 TraesCS5D01G460500 chr3B 79.592 539 89 15 3419 3943 279689646 279690177 2.370000e-97 366.0
20 TraesCS5D01G460500 chr3B 85.484 124 13 5 3272 3393 79952625 79952505 1.570000e-24 124.0
21 TraesCS5D01G460500 chr3B 84.921 126 14 5 3272 3395 82630890 82631012 5.660000e-24 122.0
22 TraesCS5D01G460500 chr3B 77.619 210 31 11 3419 3618 627195043 627194840 3.410000e-21 113.0
23 TraesCS5D01G460500 chr3B 83.505 97 16 0 3419 3515 614899392 614899488 1.600000e-14 91.6
24 TraesCS5D01G460500 chr3B 100.000 30 0 0 453 482 113918859 113918888 5.830000e-04 56.5
25 TraesCS5D01G460500 chr3B 96.774 31 1 0 453 483 260865203 260865233 8.000000e-03 52.8
26 TraesCS5D01G460500 chr1A 76.427 543 96 22 3420 3945 515140751 515141278 8.890000e-67 265.0
27 TraesCS5D01G460500 chr1A 76.471 527 93 21 3420 3930 514884561 514885072 1.490000e-64 257.0
28 TraesCS5D01G460500 chr3A 83.333 240 32 8 3936 4170 585575518 585575282 9.080000e-52 215.0
29 TraesCS5D01G460500 chr3A 86.310 168 23 0 3774 3941 585575515 585575348 2.560000e-42 183.0
30 TraesCS5D01G460500 chr3A 100.000 31 0 0 453 483 80092651 80092681 1.620000e-04 58.4
31 TraesCS5D01G460500 chr7D 84.456 193 24 5 3757 3945 45579305 45579495 7.120000e-43 185.0
32 TraesCS5D01G460500 chr2D 80.500 200 30 9 3935 4129 393208483 393208678 1.210000e-30 145.0
33 TraesCS5D01G460500 chr2B 79.602 201 28 11 3935 4129 464919568 464919761 9.410000e-27 132.0
34 TraesCS5D01G460500 chr2B 86.290 124 12 5 3272 3393 753770253 753770373 3.380000e-26 130.0
35 TraesCS5D01G460500 chr4B 77.500 240 39 14 3926 4155 1870930 1871164 3.380000e-26 130.0
36 TraesCS5D01G460500 chr1D 78.281 221 32 7 3523 3734 80016616 80016403 1.220000e-25 128.0
37 TraesCS5D01G460500 chr1D 84.328 134 15 6 3272 3402 476220298 476220168 4.380000e-25 126.0
38 TraesCS5D01G460500 chr1D 82.432 148 17 8 3252 3399 288899192 288899330 2.040000e-23 121.0
39 TraesCS5D01G460500 chr2A 88.571 105 9 3 3290 3393 715207315 715207417 1.570000e-24 124.0


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 TraesCS5D01G460500 chr5D 504994212 504998382 4170 False 3927.5 7703 91.5700 1 4171 2 chr5D.!!$F3 4170
1 TraesCS5D01G460500 chr5D 197479335 197479842 507 False 265.0 265 76.7750 3441 3945 1 chr5D.!!$F1 504
2 TraesCS5D01G460500 chr5B 634180821 634185032 4211 False 3055.0 5945 88.6375 1 4171 2 chr5B.!!$F5 4170
3 TraesCS5D01G460500 chr5A 632355638 632359222 3584 False 2527.5 4436 92.1390 1 3235 2 chr5A.!!$F1 3234
4 TraesCS5D01G460500 chr5A 558976283 558976803 520 True 255.0 255 76.1360 3419 3929 1 chr5A.!!$R2 510
5 TraesCS5D01G460500 chr7A 565721015 565721602 587 True 338.5 477 82.9010 3420 4169 2 chr7A.!!$R1 749
6 TraesCS5D01G460500 chr4D 340016948 340017507 559 False 440.0 440 81.2280 3389 3946 1 chr4D.!!$F1 557
7 TraesCS5D01G460500 chr3B 279689646 279690177 531 False 366.0 366 79.5920 3419 3943 1 chr3B.!!$F4 524
8 TraesCS5D01G460500 chr1A 515140751 515141278 527 False 265.0 265 76.4270 3420 3945 1 chr1A.!!$F2 525
9 TraesCS5D01G460500 chr1A 514884561 514885072 511 False 257.0 257 76.4710 3420 3930 1 chr1A.!!$F1 510

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
960 1324 1.145377 GGACACACCACAAGGACGT 59.855 57.895 0.0 0.0 38.69 4.34 F
2046 2436 1.136197 CGCGTTGCCGAAGAATTACAA 60.136 47.619 0.0 0.0 35.63 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2506 0.373370 CGCCGTACATGGTGATGTTG 59.627 55.0 0.0 0.0 40.05 3.33 R
3529 3955 0.694444 GGGTGGGAGGAGGATAAGCA 60.694 60.0 0.0 0.0 0.00 3.91 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
49 50 9.074576 TGCATCTTATATCAGCAATTCAGATTT 57.925 29.630 0.00 0.00 31.42 2.17
73 74 9.846248 TTTTATCTCTTAAATTCTTGCTTGCTC 57.154 29.630 0.00 0.00 30.03 4.26
140 141 7.121168 CAGTGGTATCAACATTGTCAATAACCT 59.879 37.037 0.00 0.00 0.00 3.50
278 315 3.880174 TTTGGAATCAAAGGGGGCA 57.120 47.368 0.00 0.00 37.89 5.36
282 319 1.607801 GGAATCAAAGGGGGCAGTGC 61.608 60.000 6.55 6.55 0.00 4.40
428 465 2.892025 GCTCCATGCAGGGAATGTT 58.108 52.632 22.26 0.00 42.31 2.71
446 483 7.254898 GGGAATGTTGTATATGATGTGACACAG 60.255 40.741 14.66 0.00 0.00 3.66
447 484 7.280876 GGAATGTTGTATATGATGTGACACAGT 59.719 37.037 14.66 5.40 0.00 3.55
501 540 4.555906 GCAACAAGCGTATGTTAGTGGTTT 60.556 41.667 7.49 0.00 41.44 3.27
516 555 9.959749 TGTTAGTGGTTTAAAATCAATCTTGTC 57.040 29.630 0.00 0.00 0.00 3.18
650 1006 9.589111 GTTAATACAAGACCTGTTTTGGAAAAA 57.411 29.630 5.66 0.00 39.64 1.94
738 1094 3.006859 CCAAGGAACATGGGAGGAAAAAC 59.993 47.826 0.00 0.00 44.48 2.43
743 1100 1.203174 ACATGGGAGGAAAAACCAGGG 60.203 52.381 0.00 0.00 40.16 4.45
960 1324 1.145377 GGACACACCACAAGGACGT 59.855 57.895 0.00 0.00 38.69 4.34
976 1340 2.350484 GGACGTAGCAAAGAAACCAAGC 60.350 50.000 0.00 0.00 0.00 4.01
1750 2116 2.599597 GCCATCATCCAGCAGGGT 59.400 61.111 0.00 0.00 38.11 4.34
1838 2228 1.808945 ACGACGACAAAGACGATACCT 59.191 47.619 0.00 0.00 33.85 3.08
1886 2276 1.606601 CTCCAGGAGTCCGTGTCCA 60.607 63.158 8.54 0.00 36.43 4.02
2046 2436 1.136197 CGCGTTGCCGAAGAATTACAA 60.136 47.619 0.00 0.00 35.63 2.41
2116 2506 4.296265 GTCACCAACGGGATGTCC 57.704 61.111 0.00 0.00 38.05 4.02
2505 2914 3.362399 CTGCATCGTCTCCGGCACT 62.362 63.158 0.00 0.00 30.01 4.40
2631 3040 4.008933 GACCGGCAGCAGACCACT 62.009 66.667 0.00 0.00 0.00 4.00
2999 3408 2.359169 TGAGGCTAGGGCTGTTCGG 61.359 63.158 0.00 0.00 38.98 4.30
3000 3409 3.741830 GAGGCTAGGGCTGTTCGGC 62.742 68.421 0.00 0.00 38.98 5.54
3001 3410 3.787001 GGCTAGGGCTGTTCGGCT 61.787 66.667 3.62 0.00 38.73 5.52
3002 3411 2.512515 GCTAGGGCTGTTCGGCTG 60.513 66.667 3.62 0.00 38.46 4.85
3003 3412 3.019003 GCTAGGGCTGTTCGGCTGA 62.019 63.158 0.00 0.00 38.46 4.26
3004 3413 1.142748 CTAGGGCTGTTCGGCTGAG 59.857 63.158 0.00 0.00 38.46 3.35
3005 3414 1.608717 CTAGGGCTGTTCGGCTGAGT 61.609 60.000 0.00 0.00 38.46 3.41
3006 3415 1.605058 TAGGGCTGTTCGGCTGAGTC 61.605 60.000 0.00 0.00 38.46 3.36
3007 3416 2.343758 GGCTGTTCGGCTGAGTCA 59.656 61.111 0.00 0.00 34.85 3.41
3138 3547 4.838986 ACCTCAAAAGAGAAGTGCCTACTA 59.161 41.667 0.00 0.00 35.69 1.82
3149 3558 1.134560 GTGCCTACTACGTGAAGAGGG 59.865 57.143 0.00 0.00 0.00 4.30
3225 3640 1.514678 AACCGTGCGTGCACATGAAT 61.515 50.000 23.26 7.12 46.47 2.57
3267 3688 3.711704 GGATGGAACTGGATCCTCTAACA 59.288 47.826 14.23 7.35 40.35 2.41
3268 3689 4.349342 GGATGGAACTGGATCCTCTAACAT 59.651 45.833 14.23 11.83 40.35 2.71
3269 3690 5.544176 GGATGGAACTGGATCCTCTAACATA 59.456 44.000 14.23 0.00 40.35 2.29
3270 3691 5.871396 TGGAACTGGATCCTCTAACATAC 57.129 43.478 14.23 0.00 40.35 2.39
3282 3703 9.469807 GATCCTCTAACATACAACATACAGAAG 57.530 37.037 0.00 0.00 0.00 2.85
3306 3727 8.950208 AGAAAAGTTAGAGATGCTACAATACC 57.050 34.615 0.00 0.00 0.00 2.73
3314 3735 7.056844 AGAGATGCTACAATACCCTAACTTC 57.943 40.000 0.00 0.00 0.00 3.01
3315 3736 6.042208 AGAGATGCTACAATACCCTAACTTCC 59.958 42.308 0.00 0.00 0.00 3.46
3316 3737 4.765813 TGCTACAATACCCTAACTTCCC 57.234 45.455 0.00 0.00 0.00 3.97
3317 3738 4.368067 TGCTACAATACCCTAACTTCCCT 58.632 43.478 0.00 0.00 0.00 4.20
3318 3739 4.786454 TGCTACAATACCCTAACTTCCCTT 59.214 41.667 0.00 0.00 0.00 3.95
3319 3740 5.104652 TGCTACAATACCCTAACTTCCCTTC 60.105 44.000 0.00 0.00 0.00 3.46
3320 3741 5.130643 GCTACAATACCCTAACTTCCCTTCT 59.869 44.000 0.00 0.00 0.00 2.85
3321 3742 6.352823 GCTACAATACCCTAACTTCCCTTCTT 60.353 42.308 0.00 0.00 0.00 2.52
3322 3743 6.464530 ACAATACCCTAACTTCCCTTCTTT 57.535 37.500 0.00 0.00 0.00 2.52
3323 3744 6.482524 ACAATACCCTAACTTCCCTTCTTTC 58.517 40.000 0.00 0.00 0.00 2.62
3324 3745 6.045106 ACAATACCCTAACTTCCCTTCTTTCA 59.955 38.462 0.00 0.00 0.00 2.69
3325 3746 6.713731 ATACCCTAACTTCCCTTCTTTCAA 57.286 37.500 0.00 0.00 0.00 2.69
3326 3747 5.600669 ACCCTAACTTCCCTTCTTTCAAT 57.399 39.130 0.00 0.00 0.00 2.57
3327 3748 5.571285 ACCCTAACTTCCCTTCTTTCAATC 58.429 41.667 0.00 0.00 0.00 2.67
3328 3749 4.950475 CCCTAACTTCCCTTCTTTCAATCC 59.050 45.833 0.00 0.00 0.00 3.01
3329 3750 5.516591 CCCTAACTTCCCTTCTTTCAATCCA 60.517 44.000 0.00 0.00 0.00 3.41
3335 3756 7.589993 ACTTCCCTTCTTTCAATCCATATGAT 58.410 34.615 3.65 0.00 34.22 2.45
3338 3759 9.934784 TTCCCTTCTTTCAATCCATATGATTAA 57.065 29.630 3.65 0.00 41.85 1.40
3339 3760 9.934784 TCCCTTCTTTCAATCCATATGATTAAA 57.065 29.630 3.65 0.00 41.85 1.52
3521 3947 4.853924 ATTTGAATACGGCATTCCATCC 57.146 40.909 8.89 0.00 42.17 3.51
3529 3955 1.315257 GGCATTCCATCCGTGTTGCT 61.315 55.000 0.00 0.00 0.00 3.91
3577 4008 0.682209 ATGGCCTGCTCACACAATCC 60.682 55.000 3.32 0.00 0.00 3.01
3615 4057 4.201970 GGTCAATCCTAAGACGTCTCTCTG 60.202 50.000 20.33 10.56 35.63 3.35
3616 4058 4.396790 GTCAATCCTAAGACGTCTCTCTGT 59.603 45.833 20.33 5.11 0.00 3.41
3628 4070 3.498777 CGTCTCTCTGTCCGCATAAGATA 59.501 47.826 0.00 0.00 0.00 1.98
3676 4118 1.197721 GAGGTTTTGCTGATGTGTCCG 59.802 52.381 0.00 0.00 0.00 4.79
3702 4144 8.609176 GTGCGTTGGTATAGATAATTTCTTTCA 58.391 33.333 0.00 0.00 35.79 2.69
3960 4576 9.111519 TGATATGGACTATTTATTAAGGCTCCA 57.888 33.333 0.00 0.00 0.00 3.86
3961 4577 9.384764 GATATGGACTATTTATTAAGGCTCCAC 57.615 37.037 0.00 0.00 29.44 4.02
3962 4578 5.937111 TGGACTATTTATTAAGGCTCCACC 58.063 41.667 0.00 0.00 39.61 4.61
3963 4579 5.163131 TGGACTATTTATTAAGGCTCCACCC 60.163 44.000 0.00 0.00 40.58 4.61
3964 4580 5.073280 GGACTATTTATTAAGGCTCCACCCT 59.927 44.000 0.00 0.00 40.58 4.34
3965 4581 6.271624 GGACTATTTATTAAGGCTCCACCCTA 59.728 42.308 0.00 0.00 40.58 3.53
3966 4582 7.202158 GGACTATTTATTAAGGCTCCACCCTAA 60.202 40.741 0.00 0.00 40.58 2.69
3967 4583 8.109560 ACTATTTATTAAGGCTCCACCCTAAA 57.890 34.615 0.00 0.00 40.58 1.85
3968 4584 8.733808 ACTATTTATTAAGGCTCCACCCTAAAT 58.266 33.333 0.00 0.00 40.58 1.40
3971 4587 8.756486 TTTATTAAGGCTCCACCCTAAATAAC 57.244 34.615 0.00 0.00 40.58 1.89
3972 4588 5.782677 TTAAGGCTCCACCCTAAATAACA 57.217 39.130 0.00 0.00 40.58 2.41
3973 4589 4.881157 AAGGCTCCACCCTAAATAACAT 57.119 40.909 0.00 0.00 40.58 2.71
3974 4590 4.881157 AGGCTCCACCCTAAATAACATT 57.119 40.909 0.00 0.00 40.58 2.71
3975 4591 5.206905 AGGCTCCACCCTAAATAACATTT 57.793 39.130 0.00 0.00 40.58 2.32
3976 4592 5.589831 AGGCTCCACCCTAAATAACATTTT 58.410 37.500 0.00 0.00 40.58 1.82
3977 4593 6.737608 AGGCTCCACCCTAAATAACATTTTA 58.262 36.000 0.00 0.00 40.58 1.52
3978 4594 7.186268 AGGCTCCACCCTAAATAACATTTTAA 58.814 34.615 0.00 0.00 40.58 1.52
3979 4595 7.676468 AGGCTCCACCCTAAATAACATTTTAAA 59.324 33.333 0.00 0.00 40.58 1.52
3980 4596 8.315482 GGCTCCACCCTAAATAACATTTTAAAA 58.685 33.333 2.51 2.51 0.00 1.52
3981 4597 9.713713 GCTCCACCCTAAATAACATTTTAAAAA 57.286 29.630 4.44 0.00 0.00 1.94
3995 4611 9.620259 AACATTTTAAAAATGGTTAAGAGCCAA 57.380 25.926 4.44 0.00 39.72 4.52
3996 4612 9.620259 ACATTTTAAAAATGGTTAAGAGCCAAA 57.380 25.926 4.44 0.00 39.72 3.28
4003 4619 9.435688 AAAAATGGTTAAGAGCCAAATAACATC 57.564 29.630 0.00 0.00 39.72 3.06
4004 4620 7.716799 AATGGTTAAGAGCCAAATAACATCA 57.283 32.000 0.00 0.00 39.72 3.07
4005 4621 7.902920 ATGGTTAAGAGCCAAATAACATCAT 57.097 32.000 0.00 0.00 39.72 2.45
4006 4622 8.995027 ATGGTTAAGAGCCAAATAACATCATA 57.005 30.769 0.00 0.00 39.72 2.15
4007 4623 8.995027 TGGTTAAGAGCCAAATAACATCATAT 57.005 30.769 0.00 0.00 32.47 1.78
4008 4624 9.420118 TGGTTAAGAGCCAAATAACATCATATT 57.580 29.630 0.00 0.00 32.47 1.28
4009 4625 9.899226 GGTTAAGAGCCAAATAACATCATATTC 57.101 33.333 0.00 0.00 32.47 1.75
4012 4628 8.985315 AAGAGCCAAATAACATCATATTCAGA 57.015 30.769 0.00 0.00 0.00 3.27
4013 4629 9.584008 AAGAGCCAAATAACATCATATTCAGAT 57.416 29.630 0.00 0.00 0.00 2.90
4014 4630 9.584008 AGAGCCAAATAACATCATATTCAGATT 57.416 29.630 0.00 0.00 0.00 2.40
4015 4631 9.837525 GAGCCAAATAACATCATATTCAGATTC 57.162 33.333 0.00 0.00 0.00 2.52
4016 4632 9.584008 AGCCAAATAACATCATATTCAGATTCT 57.416 29.630 0.00 0.00 0.00 2.40
4024 4640 9.896645 AACATCATATTCAGATTCTACACACTT 57.103 29.630 0.00 0.00 0.00 3.16
4025 4641 9.896645 ACATCATATTCAGATTCTACACACTTT 57.103 29.630 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.798859 AGAGCAAGCAAGAATTTAAGAGATAA 57.201 30.769 0.00 0.00 0.00 1.75
73 74 2.097629 CCATCTCTGCATGCAACTGAAG 59.902 50.000 22.88 15.27 0.00 3.02
140 141 0.758123 AAACCAAGTCCGGTCGGTAA 59.242 50.000 9.36 0.00 38.76 2.85
314 351 5.559427 TGTTACGAACTAACGTATAGGCA 57.441 39.130 0.00 0.00 45.70 4.75
428 465 9.744468 GTATGTTACTGTGTCACATCATATACA 57.256 33.333 6.03 6.13 33.31 2.29
446 483 7.439381 TGGGCAATTAGCTAGTAGTATGTTAC 58.561 38.462 0.00 0.00 44.79 2.50
447 484 7.606135 TGGGCAATTAGCTAGTAGTATGTTA 57.394 36.000 0.00 0.00 44.79 2.41
453 490 3.744660 GCATGGGCAATTAGCTAGTAGT 58.255 45.455 0.00 0.00 44.79 2.73
738 1094 3.650950 CTCCACCACCCACCCTGG 61.651 72.222 0.00 0.00 37.25 4.45
743 1100 4.699522 GTCGCCTCCACCACCCAC 62.700 72.222 0.00 0.00 0.00 4.61
960 1324 2.264005 TCGGCTTGGTTTCTTTGCTA 57.736 45.000 0.00 0.00 0.00 3.49
976 1340 0.040425 CCACTGCGGAAGTTTTTCGG 60.040 55.000 0.00 0.00 36.83 4.30
1966 2356 1.301087 CTTGGCCACCGTCACGTTA 60.301 57.895 3.88 0.00 0.00 3.18
1997 2387 1.880027 GGCCGAGATGTTTGTGAAGTT 59.120 47.619 0.00 0.00 0.00 2.66
2116 2506 0.373370 CGCCGTACATGGTGATGTTG 59.627 55.000 0.00 0.00 40.05 3.33
2185 2575 1.066430 GCGGTTCTCCACATCCTTACA 60.066 52.381 0.00 0.00 0.00 2.41
2477 2886 2.104928 CGATGCAGCTGCGGTAGA 59.895 61.111 32.11 16.16 45.83 2.59
2505 2914 0.389817 CGCCGAAGATGAAGTCCACA 60.390 55.000 0.00 0.00 0.00 4.17
2559 2968 3.319198 GGGAGCGGGTCCTTGACA 61.319 66.667 24.13 0.00 46.06 3.58
2631 3040 4.680237 CGGTGCAGGACGAAGCCA 62.680 66.667 0.00 0.00 0.00 4.75
2952 3361 2.031360 CGTCTCCGGTATCCACTCC 58.969 63.158 0.00 0.00 0.00 3.85
3000 3409 6.349528 CCATCTGTATATCTCAGCTGACTCAG 60.350 46.154 13.74 13.77 32.83 3.35
3001 3410 5.476254 CCATCTGTATATCTCAGCTGACTCA 59.524 44.000 13.74 0.00 32.83 3.41
3002 3411 5.105797 CCCATCTGTATATCTCAGCTGACTC 60.106 48.000 13.74 0.60 32.83 3.36
3003 3412 4.771577 CCCATCTGTATATCTCAGCTGACT 59.228 45.833 13.74 5.77 32.83 3.41
3004 3413 4.526262 ACCCATCTGTATATCTCAGCTGAC 59.474 45.833 13.74 2.83 32.83 3.51
3005 3414 4.525874 CACCCATCTGTATATCTCAGCTGA 59.474 45.833 17.19 17.19 32.83 4.26
3006 3415 4.322574 CCACCCATCTGTATATCTCAGCTG 60.323 50.000 7.63 7.63 33.48 4.24
3007 3416 3.837146 CCACCCATCTGTATATCTCAGCT 59.163 47.826 3.76 0.00 33.48 4.24
3138 3547 4.630069 CGACATTAATTTCCCTCTTCACGT 59.370 41.667 0.00 0.00 0.00 4.49
3225 3640 3.395630 GGGGCTCCGTTGGTCTTA 58.604 61.111 0.00 0.00 0.00 2.10
3245 3666 3.711704 TGTTAGAGGATCCAGTTCCATCC 59.288 47.826 15.82 0.00 38.32 3.51
3282 3703 7.988028 AGGGTATTGTAGCATCTCTAACTTTTC 59.012 37.037 0.00 0.00 0.00 2.29
3293 3714 5.071923 AGGGAAGTTAGGGTATTGTAGCATC 59.928 44.000 0.00 0.00 0.00 3.91
3295 3716 4.368067 AGGGAAGTTAGGGTATTGTAGCA 58.632 43.478 0.00 0.00 0.00 3.49
3306 3727 5.570320 TGGATTGAAAGAAGGGAAGTTAGG 58.430 41.667 0.00 0.00 0.00 2.69
3407 3828 3.699779 TGCAACGCACAAACTCATTAA 57.300 38.095 0.00 0.00 31.71 1.40
3408 3829 3.367607 GTTGCAACGCACAAACTCATTA 58.632 40.909 14.90 0.00 38.71 1.90
3521 3947 1.009829 GGAGGATAAGCAGCAACACG 58.990 55.000 0.00 0.00 0.00 4.49
3529 3955 0.694444 GGGTGGGAGGAGGATAAGCA 60.694 60.000 0.00 0.00 0.00 3.91
3577 4008 3.428746 TTGACCACATTCAAACGTTGG 57.571 42.857 0.00 0.00 32.42 3.77
3615 4057 5.698545 AGCAGATTTCTTATCTTATGCGGAC 59.301 40.000 0.00 0.00 0.00 4.79
3616 4058 5.858381 AGCAGATTTCTTATCTTATGCGGA 58.142 37.500 0.00 0.00 0.00 5.54
3652 4094 3.225104 ACACATCAGCAAAACCTCACAT 58.775 40.909 0.00 0.00 0.00 3.21
3676 4118 8.609176 TGAAAGAAATTATCTATACCAACGCAC 58.391 33.333 0.00 0.00 37.42 5.34
3946 4562 8.337739 TGTTATTTAGGGTGGAGCCTTAATAAA 58.662 33.333 21.70 10.35 38.40 1.40
3947 4563 7.874252 TGTTATTTAGGGTGGAGCCTTAATAA 58.126 34.615 18.42 18.42 38.40 1.40
3948 4564 7.454553 TGTTATTTAGGGTGGAGCCTTAATA 57.545 36.000 10.74 10.74 38.40 0.98
3949 4565 6.335781 TGTTATTTAGGGTGGAGCCTTAAT 57.664 37.500 12.37 12.37 38.40 1.40
3950 4566 5.782677 TGTTATTTAGGGTGGAGCCTTAA 57.217 39.130 2.03 0.48 37.07 1.85
3951 4567 5.987019 ATGTTATTTAGGGTGGAGCCTTA 57.013 39.130 2.03 0.00 37.43 2.69
3952 4568 4.881157 ATGTTATTTAGGGTGGAGCCTT 57.119 40.909 2.03 0.00 37.43 4.35
3953 4569 4.881157 AATGTTATTTAGGGTGGAGCCT 57.119 40.909 2.37 2.37 37.43 4.58
3954 4570 5.932619 AAAATGTTATTTAGGGTGGAGCC 57.067 39.130 0.00 0.00 0.00 4.70
3955 4571 9.713713 TTTTTAAAATGTTATTTAGGGTGGAGC 57.286 29.630 0.55 0.00 0.00 4.70
3969 4585 9.620259 TTGGCTCTTAACCATTTTTAAAATGTT 57.380 25.926 23.46 19.37 36.96 2.71
3970 4586 9.620259 TTTGGCTCTTAACCATTTTTAAAATGT 57.380 25.926 23.46 12.34 36.96 2.71
3977 4593 9.435688 GATGTTATTTGGCTCTTAACCATTTTT 57.564 29.630 0.00 0.00 36.96 1.94
3978 4594 8.592809 TGATGTTATTTGGCTCTTAACCATTTT 58.407 29.630 0.00 0.00 36.96 1.82
3979 4595 8.133024 TGATGTTATTTGGCTCTTAACCATTT 57.867 30.769 0.00 0.00 36.96 2.32
3980 4596 7.716799 TGATGTTATTTGGCTCTTAACCATT 57.283 32.000 0.00 0.00 36.96 3.16
3981 4597 7.902920 ATGATGTTATTTGGCTCTTAACCAT 57.097 32.000 0.00 0.00 36.96 3.55
3982 4598 8.995027 ATATGATGTTATTTGGCTCTTAACCA 57.005 30.769 0.00 0.00 34.65 3.67
3983 4599 9.899226 GAATATGATGTTATTTGGCTCTTAACC 57.101 33.333 0.00 0.00 0.00 2.85
3987 4603 8.985315 TCTGAATATGATGTTATTTGGCTCTT 57.015 30.769 0.00 0.00 0.00 2.85
3988 4604 9.584008 AATCTGAATATGATGTTATTTGGCTCT 57.416 29.630 0.00 0.00 0.00 4.09
3989 4605 9.837525 GAATCTGAATATGATGTTATTTGGCTC 57.162 33.333 0.00 0.00 0.00 4.70
3990 4606 9.584008 AGAATCTGAATATGATGTTATTTGGCT 57.416 29.630 0.00 0.00 0.00 4.75
3998 4614 9.896645 AAGTGTGTAGAATCTGAATATGATGTT 57.103 29.630 0.00 0.00 0.00 2.71
3999 4615 9.896645 AAAGTGTGTAGAATCTGAATATGATGT 57.103 29.630 0.00 0.00 0.00 3.06
4049 4665 9.878599 CTTTCGAACTGTAACTTCAATTAACAT 57.121 29.630 0.00 0.00 0.00 2.71
4050 4666 9.100554 TCTTTCGAACTGTAACTTCAATTAACA 57.899 29.630 0.00 0.00 0.00 2.41
4055 4671 9.653287 TCATATCTTTCGAACTGTAACTTCAAT 57.347 29.630 0.00 0.00 0.00 2.57
4056 4672 8.922676 GTCATATCTTTCGAACTGTAACTTCAA 58.077 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.