Multiple sequence alignment - TraesCS2D01G388400

Loading Multiple Alignment...

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 TraesCS2D01G388400 chr2D 100.000 6402 0 0 1 6402 494637752 494644153 0.000000e+00 11823
1 TraesCS2D01G388400 chr2D 85.060 502 51 19 191 676 574357861 574357368 2.070000e-134 490
2 TraesCS2D01G388400 chr2D 93.671 79 5 0 191 269 447928220 447928298 1.130000e-22 119
3 TraesCS2D01G388400 chr2A 96.379 5440 134 17 744 6143 639071544 639066128 0.000000e+00 8896
4 TraesCS2D01G388400 chr2A 89.710 379 12 7 1 352 639073005 639072627 5.850000e-125 459
5 TraesCS2D01G388400 chr2A 85.039 254 21 11 6134 6372 639065950 639065699 6.410000e-60 243
6 TraesCS2D01G388400 chr2B 95.395 3670 117 26 2700 6327 582299657 582303316 0.000000e+00 5794
7 TraesCS2D01G388400 chr2B 95.385 1885 67 9 825 2697 582297599 582299475 0.000000e+00 2981
8 TraesCS2D01G388400 chr2B 90.718 571 41 6 191 751 644616933 644616365 0.000000e+00 750
9 TraesCS2D01G388400 chr2B 93.204 103 7 0 640 742 364120601 364120499 1.110000e-32 152
10 TraesCS2D01G388400 chr7B 86.957 506 58 6 238 739 727390776 727390275 4.330000e-156 562
11 TraesCS2D01G388400 chr1B 86.400 500 58 5 254 743 3517117 3517616 7.300000e-149 538
12 TraesCS2D01G388400 chr1B 86.000 500 60 5 254 743 3451273 3451772 1.580000e-145 527
13 TraesCS2D01G388400 chr6A 83.066 561 67 22 191 732 578849686 578849135 9.650000e-133 484
14 TraesCS2D01G388400 chr7A 82.908 509 70 14 191 685 689536090 689535585 5.890000e-120 442
15 TraesCS2D01G388400 chr6B 81.341 552 80 18 191 732 631196110 631195572 1.650000e-115 427
16 TraesCS2D01G388400 chr1D 80.819 537 86 14 220 744 295284095 295284626 7.730000e-109 405
17 TraesCS2D01G388400 chr3D 93.229 192 11 2 1 191 348918893 348918703 1.360000e-71 281
18 TraesCS2D01G388400 chr3D 92.670 191 14 0 1 191 116074656 116074846 6.320000e-70 276
19 TraesCS2D01G388400 chr5A 82.562 281 16 15 191 470 357854514 357854266 3.890000e-52 217


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 TraesCS2D01G388400 chr2D 494637752 494644153 6401 False 11823.000000 11823 100.000 1 6402 1 chr2D.!!$F2 6401
1 TraesCS2D01G388400 chr2A 639065699 639073005 7306 True 3199.333333 8896 90.376 1 6372 3 chr2A.!!$R1 6371
2 TraesCS2D01G388400 chr2B 582297599 582303316 5717 False 4387.500000 5794 95.390 825 6327 2 chr2B.!!$F1 5502
3 TraesCS2D01G388400 chr2B 644616365 644616933 568 True 750.000000 750 90.718 191 751 1 chr2B.!!$R2 560
4 TraesCS2D01G388400 chr7B 727390275 727390776 501 True 562.000000 562 86.957 238 739 1 chr7B.!!$R1 501
5 TraesCS2D01G388400 chr6A 578849135 578849686 551 True 484.000000 484 83.066 191 732 1 chr6A.!!$R1 541
6 TraesCS2D01G388400 chr7A 689535585 689536090 505 True 442.000000 442 82.908 191 685 1 chr7A.!!$R1 494
7 TraesCS2D01G388400 chr6B 631195572 631196110 538 True 427.000000 427 81.341 191 732 1 chr6B.!!$R1 541
8 TraesCS2D01G388400 chr1D 295284095 295284626 531 False 405.000000 405 80.819 220 744 1 chr1D.!!$F1 524

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
26 27 0.108041 GGCGTTAGGGGATGACGAAA 60.108 55.000 0.00 0.00 43.16 3.46 F
739 1349 1.251527 ACTCCCACTGTGGCTAGTCG 61.252 60.000 21.47 6.74 35.79 4.18 F
1375 2147 0.044244 CTCCCCCTAAGGTGGAGGAA 59.956 60.000 12.10 0.00 42.57 3.36 F
1384 2156 1.376037 GGTGGAGGAACAGAAGCCG 60.376 63.158 0.00 0.00 0.00 5.52 F
1989 2763 2.106511 TGGTGGGCTAGATAAAGATGCC 59.893 50.000 0.00 0.00 42.56 4.40 F
2096 2870 3.825160 AAGGCTTCGCGTTCCTGCA 62.825 57.895 5.77 0.00 30.62 4.41 F
3543 4499 1.933021 CCCCCAGGTGCGTATAGATA 58.067 55.000 0.00 0.00 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 1935 1.242076 CAAACCACCAGAAGAGCAGG 58.758 55.000 0.00 0.00 0.00 4.85 R
2085 2859 1.258982 GTCTCATATTGCAGGAACGCG 59.741 52.381 3.53 3.53 33.35 6.01 R
2781 3737 1.153409 CTAGCAGCTGCCAGAGTGG 60.153 63.158 34.39 14.36 43.38 4.00 R
3377 4333 3.373130 CGAGTATCAGGTCGTACAAGACA 59.627 47.826 3.73 0.00 37.76 3.41 R
3445 4401 3.961408 ACATAACAGGGCGTCTATCTCTT 59.039 43.478 0.00 0.00 0.00 2.85 R
4043 5006 0.638746 GACGAACGCTAATGTCGTGG 59.361 55.000 2.27 0.00 40.36 4.94 R
5505 6482 0.605083 AGAGAACAGATGCAGCGTGA 59.395 50.000 8.13 0.00 0.00 4.35 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
26 27 0.108041 GGCGTTAGGGGATGACGAAA 60.108 55.000 0.00 0.00 43.16 3.46
30 31 2.864343 CGTTAGGGGATGACGAAATGTC 59.136 50.000 0.00 0.00 43.16 3.06
43 44 3.257393 CGAAATGTCCCAACTCTCTCTG 58.743 50.000 0.00 0.00 0.00 3.35
153 154 1.915614 GCTTGTCTGTCACCATGGCG 61.916 60.000 13.04 1.26 0.00 5.69
229 254 9.129532 GGGTAGTAACATAGACTAGTAACATGT 57.870 37.037 0.00 3.02 30.08 3.21
381 564 4.650131 ACTAGCTATGTACCACTTTCCTCC 59.350 45.833 0.00 0.00 0.00 4.30
382 566 3.450904 AGCTATGTACCACTTTCCTCCA 58.549 45.455 0.00 0.00 0.00 3.86
555 1043 6.929606 CCTCAATAGTGGGTAGTAACATAAGC 59.070 42.308 0.00 0.00 0.00 3.09
584 1072 8.807581 GGTAACATGCAAAGCTTCATTTATTAC 58.192 33.333 0.00 8.32 0.00 1.89
697 1307 6.264832 CACATAAGCAAAACTGTTGAGTTGA 58.735 36.000 7.44 0.00 41.87 3.18
739 1349 1.251527 ACTCCCACTGTGGCTAGTCG 61.252 60.000 21.47 6.74 35.79 4.18
764 1504 3.004524 GTCTTAGTCCCACTATGGCTACG 59.995 52.174 0.00 0.00 35.79 3.51
955 1695 1.386533 GGAGAATACGACTCGACCCA 58.613 55.000 5.20 0.00 35.49 4.51
1163 1935 1.426041 TTCGCTTCCGCTAATTCCGC 61.426 55.000 0.00 0.00 0.00 5.54
1375 2147 0.044244 CTCCCCCTAAGGTGGAGGAA 59.956 60.000 12.10 0.00 42.57 3.36
1384 2156 1.376037 GGTGGAGGAACAGAAGCCG 60.376 63.158 0.00 0.00 0.00 5.52
1429 2201 4.400961 GCCGCTGAGGTGAAGGCT 62.401 66.667 0.00 0.00 44.06 4.58
1537 2309 3.305403 GCTTATAGATCTGTGCTACGCCA 60.305 47.826 5.18 0.00 0.00 5.69
1561 2335 3.483421 CCGTTTTTCCTTACTTGGGACT 58.517 45.455 0.00 0.00 31.94 3.85
1573 2347 6.321435 CCTTACTTGGGACTTCTTGTCTTTTT 59.679 38.462 0.00 0.00 44.74 1.94
1575 2349 4.645136 ACTTGGGACTTCTTGTCTTTTTCC 59.355 41.667 0.00 0.00 44.74 3.13
1576 2350 4.519906 TGGGACTTCTTGTCTTTTTCCT 57.480 40.909 0.00 0.00 44.74 3.36
1577 2351 5.640158 TGGGACTTCTTGTCTTTTTCCTA 57.360 39.130 0.00 0.00 44.74 2.94
1578 2352 6.200878 TGGGACTTCTTGTCTTTTTCCTAT 57.799 37.500 0.00 0.00 44.74 2.57
1579 2353 7.324388 TGGGACTTCTTGTCTTTTTCCTATA 57.676 36.000 0.00 0.00 44.74 1.31
1580 2354 7.928873 TGGGACTTCTTGTCTTTTTCCTATAT 58.071 34.615 0.00 0.00 44.74 0.86
1581 2355 9.053472 TGGGACTTCTTGTCTTTTTCCTATATA 57.947 33.333 0.00 0.00 44.74 0.86
1596 2370 8.997621 TTTCCTATATATAAATGTGCGAGGAC 57.002 34.615 0.00 0.00 30.41 3.85
1602 2376 2.254546 AAATGTGCGAGGACTTGACA 57.745 45.000 0.00 0.00 0.00 3.58
1713 2487 2.125350 GAAGAGGAGCCTGCCGTG 60.125 66.667 0.00 0.00 0.00 4.94
1774 2548 4.162690 AGGACGGCGATGAAGGGC 62.163 66.667 16.62 0.00 0.00 5.19
1842 2616 2.439507 TGAGGAGGAACTGGATAATGGC 59.560 50.000 0.00 0.00 41.55 4.40
1989 2763 2.106511 TGGTGGGCTAGATAAAGATGCC 59.893 50.000 0.00 0.00 42.56 4.40
2085 2859 7.360575 TGTTACGAAGAAGAATAAAGGCTTC 57.639 36.000 0.00 0.00 40.54 3.86
2088 2862 3.929414 GAAGAAGAATAAAGGCTTCGCG 58.071 45.455 0.00 0.00 43.94 5.87
2096 2870 3.825160 AAGGCTTCGCGTTCCTGCA 62.825 57.895 5.77 0.00 30.62 4.41
2473 3250 4.141287 ACTGAAGATCTATGAGGTCGAGG 58.859 47.826 0.00 0.00 0.00 4.63
2481 3258 6.496565 AGATCTATGAGGTCGAGGATTTTGAT 59.503 38.462 0.00 0.00 0.00 2.57
2713 3669 6.791303 TGTTTTCTGCAGTAGTTTTAAGTGG 58.209 36.000 14.67 0.00 0.00 4.00
2723 3679 6.691388 CAGTAGTTTTAAGTGGCACTGTTTTC 59.309 38.462 22.83 11.99 0.00 2.29
3444 4400 4.968719 TCCACTGAAGAGGCCAATAGATAA 59.031 41.667 5.01 0.00 0.00 1.75
3445 4401 5.428457 TCCACTGAAGAGGCCAATAGATAAA 59.572 40.000 5.01 0.00 0.00 1.40
3469 4425 2.293677 AGATAGACGCCCTGTTATGTCG 59.706 50.000 0.00 0.00 36.49 4.35
3543 4499 1.933021 CCCCCAGGTGCGTATAGATA 58.067 55.000 0.00 0.00 0.00 1.98
3580 4536 5.222079 TGTAGAACATTCAACTGTAGCCA 57.778 39.130 0.00 0.00 0.00 4.75
3952 4914 7.181305 TGTTGAGATGGTGAGGGTAGTTTAATA 59.819 37.037 0.00 0.00 0.00 0.98
3996 4959 6.054035 GCACTAGCAGTTTATTCCTCAATC 57.946 41.667 0.00 0.00 41.58 2.67
4043 5006 1.664321 ATGACGTGCCTCCTCGGTAC 61.664 60.000 0.00 0.00 44.13 3.34
4140 5103 3.198872 GCTTATACTGAGAGGTTGGTGC 58.801 50.000 0.00 0.00 0.00 5.01
4164 5127 7.012327 TGCATATTTAGTAACATGCAGTCCTTC 59.988 37.037 20.06 0.07 46.46 3.46
4209 5172 6.969828 AGAGAACGTCTTGGTATTTGATTC 57.030 37.500 0.00 0.00 27.07 2.52
4218 5181 9.098355 CGTCTTGGTATTTGATTCTAATCTCAA 57.902 33.333 4.45 3.64 36.39 3.02
4358 5322 4.462834 TGGAGGTATATACTCTTGATGCCG 59.537 45.833 12.54 0.00 35.34 5.69
4515 5489 5.746245 CGTGGATCTGATGTAAGTCTTCTTC 59.254 44.000 0.00 0.00 35.36 2.87
4656 5633 7.085746 TCAACAACATCAAATTGATACTGCTG 58.914 34.615 8.29 9.96 34.28 4.41
4792 5769 0.030235 CATCGCATTACTCGGGTCGA 59.970 55.000 0.00 0.00 0.00 4.20
4888 5865 9.586435 AATCAGTTTCAGTTTTCCTTTAGTTTG 57.414 29.630 0.00 0.00 0.00 2.93
4911 5888 5.701290 TGATTGCATTGCACATGAATTTTGA 59.299 32.000 11.66 0.00 38.71 2.69
5049 6026 7.894753 TTTAATGATACAGATTTGGCATCCA 57.105 32.000 0.00 0.00 0.00 3.41
5505 6482 5.449553 ACTTCTGAAACCTTTGGTTCAGAT 58.550 37.500 20.20 7.14 46.20 2.90
5627 6604 3.742433 AAATCGGATTTGTTGGTTGCA 57.258 38.095 14.83 0.00 0.00 4.08
5659 6636 5.532779 GGGAGAAACCTTTTATATGGCTCAG 59.467 44.000 0.00 0.00 38.98 3.35
5662 6639 5.888161 AGAAACCTTTTATATGGCTCAGGTG 59.112 40.000 0.00 0.00 34.76 4.00
5785 6762 4.021104 GCATAGAGTACATGGCACCAGATA 60.021 45.833 0.00 0.00 0.00 1.98
5873 6851 5.048224 GGAGCATGGATCAATACATCTTTGG 60.048 44.000 0.00 0.00 0.00 3.28
6110 7115 3.158676 CGGGGGTTGATGGTTTTAGAAA 58.841 45.455 0.00 0.00 0.00 2.52
6212 7408 7.569297 TGCGTCTACAAGTTTATAAACAACAG 58.431 34.615 26.06 17.42 41.30 3.16
6267 7469 7.763985 TGTCATGTGCTAATTCGAAGAAATAGA 59.236 33.333 3.35 0.00 45.90 1.98
6282 7484 9.190858 CGAAGAAATAGATAGGTGAAAGAGATG 57.809 37.037 0.00 0.00 0.00 2.90
6340 7543 4.485163 GCAATAAGGCTTACCAAACTGTG 58.515 43.478 9.55 0.00 39.06 3.66
6353 7560 8.611654 TTACCAAACTGTGTTAATACCTTCTC 57.388 34.615 0.00 0.00 0.00 2.87
6356 7563 6.710744 CCAAACTGTGTTAATACCTTCTCTGT 59.289 38.462 0.00 0.00 0.00 3.41
6361 7568 4.093556 GTGTTAATACCTTCTCTGTGCTGC 59.906 45.833 0.00 0.00 0.00 5.25
6372 7579 1.439353 CTGTGCTGCAACAACGAGGT 61.439 55.000 2.77 0.00 0.00 3.85
6373 7580 1.009675 GTGCTGCAACAACGAGGTG 60.010 57.895 2.77 0.00 38.24 4.00
6374 7581 1.451207 TGCTGCAACAACGAGGTGT 60.451 52.632 0.00 0.00 37.23 4.16
6375 7582 1.029408 TGCTGCAACAACGAGGTGTT 61.029 50.000 0.00 0.00 42.48 3.32
6388 7595 1.579429 GGTGTTGTGAATCACCCGC 59.421 57.895 11.24 7.90 45.70 6.13
6389 7596 1.169661 GGTGTTGTGAATCACCCGCA 61.170 55.000 11.24 4.40 45.70 5.69
6390 7597 0.040425 GTGTTGTGAATCACCCGCAC 60.040 55.000 11.24 12.44 32.73 5.34
6391 7598 0.179032 TGTTGTGAATCACCCGCACT 60.179 50.000 11.24 0.00 32.73 4.40
6392 7599 1.070914 TGTTGTGAATCACCCGCACTA 59.929 47.619 11.24 0.00 32.73 2.74
6393 7600 2.147958 GTTGTGAATCACCCGCACTAA 58.852 47.619 11.24 0.00 32.73 2.24
6394 7601 1.803334 TGTGAATCACCCGCACTAAC 58.197 50.000 11.24 0.00 32.73 2.34
6395 7602 1.346395 TGTGAATCACCCGCACTAACT 59.654 47.619 11.24 0.00 32.73 2.24
6396 7603 2.224426 TGTGAATCACCCGCACTAACTT 60.224 45.455 11.24 0.00 32.73 2.66
6397 7604 2.159627 GTGAATCACCCGCACTAACTTG 59.840 50.000 1.10 0.00 0.00 3.16
6398 7605 1.737793 GAATCACCCGCACTAACTTGG 59.262 52.381 0.00 0.00 0.00 3.61
6399 7606 0.981183 ATCACCCGCACTAACTTGGA 59.019 50.000 0.00 0.00 0.00 3.53
6400 7607 0.759959 TCACCCGCACTAACTTGGAA 59.240 50.000 0.00 0.00 0.00 3.53
6401 7608 1.349688 TCACCCGCACTAACTTGGAAT 59.650 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.908198 GGCAGAGAGAGTTGGGACAT 59.092 55.000 0.00 0.00 39.30 3.06
30 31 2.575805 AAAAGGCAGAGAGAGTTGGG 57.424 50.000 0.00 0.00 0.00 4.12
143 144 2.265739 GCTCTGACGCCATGGTGA 59.734 61.111 31.66 9.48 0.00 4.02
181 182 2.363795 TGGCTAGTCCCAGACCGG 60.364 66.667 0.00 0.00 32.18 5.28
252 277 7.013274 CACATGTTAATCCCCACTATAAAGGTG 59.987 40.741 0.00 0.00 34.78 4.00
381 564 6.369340 TGTGGCAAGCAATAAATGAAGAAATG 59.631 34.615 0.00 0.00 0.00 2.32
382 566 6.465948 TGTGGCAAGCAATAAATGAAGAAAT 58.534 32.000 0.00 0.00 0.00 2.17
459 935 4.763355 TCCATTATGGCTAGTCTACCCAT 58.237 43.478 6.33 10.87 41.88 4.00
522 1010 4.996788 ACCCACTATTGAGGTAGTAACG 57.003 45.455 0.00 0.00 33.29 3.18
555 1043 2.031245 TGAAGCTTTGCATGTTACCACG 60.031 45.455 0.00 0.00 0.00 4.94
584 1072 6.873605 TCCCAATGCAATATGAGTCTATAACG 59.126 38.462 0.00 0.00 0.00 3.18
659 1269 7.637631 TTGCTTATGTGGCAATGAGTTAATA 57.362 32.000 0.00 0.00 43.50 0.98
686 1296 5.692204 AGTAACATCGAGTTCAACTCAACAG 59.308 40.000 17.81 6.55 45.30 3.16
697 1307 5.382618 AACTTCGGTAGTAACATCGAGTT 57.617 39.130 0.00 0.00 44.27 3.01
739 1349 4.216708 AGCCATAGTGGGACTAAGACTAC 58.783 47.826 0.00 0.00 38.19 2.73
764 1504 2.202623 CGACGTCAGGCTAGCCAC 60.203 66.667 34.70 23.42 38.92 5.01
840 1580 1.296649 GCTTCCGACGCAATAACGC 60.297 57.895 0.00 0.00 36.19 4.84
955 1695 2.764547 GTTAGCCTCCCCGCTCCT 60.765 66.667 0.00 0.00 40.39 3.69
1163 1935 1.242076 CAAACCACCAGAAGAGCAGG 58.758 55.000 0.00 0.00 0.00 4.85
1537 2309 2.560981 CCCAAGTAAGGAAAAACGGCAT 59.439 45.455 0.00 0.00 0.00 4.40
1573 2347 7.956328 AGTCCTCGCACATTTATATATAGGA 57.044 36.000 0.00 0.00 0.00 2.94
1575 2349 9.077674 GTCAAGTCCTCGCACATTTATATATAG 57.922 37.037 0.00 0.00 0.00 1.31
1576 2350 8.581578 TGTCAAGTCCTCGCACATTTATATATA 58.418 33.333 0.00 0.00 0.00 0.86
1577 2351 7.441836 TGTCAAGTCCTCGCACATTTATATAT 58.558 34.615 0.00 0.00 0.00 0.86
1578 2352 6.811954 TGTCAAGTCCTCGCACATTTATATA 58.188 36.000 0.00 0.00 0.00 0.86
1579 2353 5.670485 TGTCAAGTCCTCGCACATTTATAT 58.330 37.500 0.00 0.00 0.00 0.86
1580 2354 5.079689 TGTCAAGTCCTCGCACATTTATA 57.920 39.130 0.00 0.00 0.00 0.98
1581 2355 3.937814 TGTCAAGTCCTCGCACATTTAT 58.062 40.909 0.00 0.00 0.00 1.40
1590 2364 8.425577 AAAATTACATAGATGTCAAGTCCTCG 57.574 34.615 0.00 0.00 41.97 4.63
1713 2487 3.436496 CAAATCCTTCTCGTCGTAGTCC 58.564 50.000 0.00 0.00 0.00 3.85
1774 2548 5.447954 CGACTACATCTTCAGTGTACTCCAG 60.448 48.000 0.00 0.00 0.00 3.86
1842 2616 4.320456 CCCTCGCCATCATCCCCG 62.320 72.222 0.00 0.00 0.00 5.73
2085 2859 1.258982 GTCTCATATTGCAGGAACGCG 59.741 52.381 3.53 3.53 33.35 6.01
2088 2862 3.624861 CCACAGTCTCATATTGCAGGAAC 59.375 47.826 0.00 0.00 0.00 3.62
2096 2870 3.054875 TGCTTGCTCCACAGTCTCATATT 60.055 43.478 0.00 0.00 0.00 1.28
2244 3021 8.836413 CACCTACAGAATTTCAGAAACAGTTAA 58.164 33.333 0.00 0.00 0.00 2.01
2481 3258 9.639563 TTGCTATCCTCAACCAATATTAAATCA 57.360 29.630 0.00 0.00 0.00 2.57
2781 3737 1.153409 CTAGCAGCTGCCAGAGTGG 60.153 63.158 34.39 14.36 43.38 4.00
3377 4333 3.373130 CGAGTATCAGGTCGTACAAGACA 59.627 47.826 3.73 0.00 37.76 3.41
3444 4400 4.406003 ACATAACAGGGCGTCTATCTCTTT 59.594 41.667 0.00 0.00 0.00 2.52
3445 4401 3.961408 ACATAACAGGGCGTCTATCTCTT 59.039 43.478 0.00 0.00 0.00 2.85
3469 4425 5.708877 AACGCCTAACTCTATCTGGTATC 57.291 43.478 0.00 0.00 0.00 2.24
3543 4499 8.706322 AATGTTCTACAAAAAGAATGGGTACT 57.294 30.769 0.00 0.00 37.78 2.73
3580 4536 9.458727 ACAGATGAAGTATGAGAAATTTGATGT 57.541 29.630 0.00 0.00 0.00 3.06
3978 4940 5.416952 CAGGTTGATTGAGGAATAAACTGCT 59.583 40.000 0.00 0.00 34.39 4.24
3996 4959 7.087409 TGCATCATTAACAATAGTCAGGTTG 57.913 36.000 0.00 0.00 0.00 3.77
4043 5006 0.638746 GACGAACGCTAATGTCGTGG 59.361 55.000 2.27 0.00 40.36 4.94
4140 5103 8.554528 CAGAAGGACTGCATGTTACTAAATATG 58.445 37.037 0.00 0.00 39.86 1.78
4164 5127 8.134895 TCTCTAAAACAAACAAATACCAAGCAG 58.865 33.333 0.00 0.00 0.00 4.24
4218 5181 9.401058 CTTCAAGGATGGATATTTGTAAGAACT 57.599 33.333 0.00 0.00 0.00 3.01
4354 5318 2.916640 TCATGACAAATAGCATCGGCA 58.083 42.857 0.00 0.00 44.61 5.69
4358 5322 8.388484 AGAAAGGTATCATGACAAATAGCATC 57.612 34.615 0.00 0.00 0.00 3.91
4610 5584 5.324409 TGATGCTGGTAGTTTTTCCTTCAT 58.676 37.500 0.00 0.00 0.00 2.57
4656 5633 6.397272 TGGAAGTGCATTTTATGTTGAATCC 58.603 36.000 0.00 0.00 0.00 3.01
4792 5769 0.884704 CACTGCTGCTACCCGTGTTT 60.885 55.000 0.00 0.00 0.00 2.83
4888 5865 6.171932 TCAAAATTCATGTGCAATGCAATC 57.828 33.333 10.44 0.00 41.47 2.67
5049 6026 2.702592 TCTGTTCCACAAAGACGGTT 57.297 45.000 0.00 0.00 0.00 4.44
5076 6053 2.116238 GCCTACACCAACCTCCTATGA 58.884 52.381 0.00 0.00 0.00 2.15
5505 6482 0.605083 AGAGAACAGATGCAGCGTGA 59.395 50.000 8.13 0.00 0.00 4.35
5611 6588 1.068434 ACCTTGCAACCAACAAATCCG 59.932 47.619 0.00 0.00 0.00 4.18
5627 6604 3.973472 AAAGGTTTCTCCCAGAACCTT 57.027 42.857 13.22 13.22 42.26 3.50
5662 6639 4.948847 AGAAATTGCTTGGTGAAAGAACC 58.051 39.130 0.00 0.00 38.24 3.62
5785 6762 9.979578 TCAGTGTTGATAATGCTTGTTAAATTT 57.020 25.926 0.00 0.00 0.00 1.82
5873 6851 3.299503 ACCATCCAACAGATATTTGGCC 58.700 45.455 0.00 0.00 42.96 5.36
6267 7469 9.178758 GTATTTTCAACCATCTCTTTCACCTAT 57.821 33.333 0.00 0.00 0.00 2.57
6329 7532 7.876068 CAGAGAAGGTATTAACACAGTTTGGTA 59.124 37.037 0.00 0.00 0.00 3.25
6340 7543 4.253685 TGCAGCACAGAGAAGGTATTAAC 58.746 43.478 0.00 0.00 0.00 2.01
6353 7560 1.280746 CCTCGTTGTTGCAGCACAG 59.719 57.895 1.37 0.00 0.00 3.66
6356 7563 1.029408 AACACCTCGTTGTTGCAGCA 61.029 50.000 0.00 0.00 38.31 4.41
6372 7579 0.179032 AGTGCGGGTGATTCACAACA 60.179 50.000 18.09 9.78 38.06 3.33
6373 7580 1.803334 TAGTGCGGGTGATTCACAAC 58.197 50.000 18.09 9.43 35.86 3.32
6374 7581 2.147958 GTTAGTGCGGGTGATTCACAA 58.852 47.619 18.09 0.00 35.86 3.33
6375 7582 1.346395 AGTTAGTGCGGGTGATTCACA 59.654 47.619 18.09 0.00 35.86 3.58
6376 7583 2.094762 AGTTAGTGCGGGTGATTCAC 57.905 50.000 8.34 8.34 0.00 3.18
6377 7584 2.422597 CAAGTTAGTGCGGGTGATTCA 58.577 47.619 0.00 0.00 0.00 2.57
6378 7585 1.737793 CCAAGTTAGTGCGGGTGATTC 59.262 52.381 0.00 0.00 0.00 2.52
6379 7586 1.349688 TCCAAGTTAGTGCGGGTGATT 59.650 47.619 0.00 0.00 0.00 2.57
6380 7587 0.981183 TCCAAGTTAGTGCGGGTGAT 59.019 50.000 0.00 0.00 0.00 3.06
6381 7588 0.759959 TTCCAAGTTAGTGCGGGTGA 59.240 50.000 0.00 0.00 0.00 4.02
6382 7589 1.821216 ATTCCAAGTTAGTGCGGGTG 58.179 50.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.