Multiple sequence alignment - TraesCS4B01G329600

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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 TraesCS4B01G329600 chr4B 100.000 4019 0 0 1 4019 620068936 620064918 0.000000e+00 7422.0
1 TraesCS4B01G329600 chr6B 86.267 3000 393 12 1023 4019 153391387 153388404 0.000000e+00 3240.0
2 TraesCS4B01G329600 chr6B 83.026 1031 157 12 1 1026 153393971 153392954 0.000000e+00 918.0
3 TraesCS4B01G329600 chr6D 80.821 3702 665 37 333 4016 297446334 297450008 0.000000e+00 2861.0
4 TraesCS4B01G329600 chr6D 83.722 1972 294 8 964 2928 448581693 448583644 0.000000e+00 1838.0
5 TraesCS4B01G329600 chr6D 83.791 1055 148 12 2967 4016 448583644 448584680 0.000000e+00 979.0
6 TraesCS4B01G329600 chr5D 81.696 3409 578 33 623 4016 483135340 483131963 0.000000e+00 2796.0
7 TraesCS4B01G329600 chr5D 83.175 2003 309 13 1 1991 249065547 249063561 0.000000e+00 1807.0
8 TraesCS4B01G329600 chr5D 80.660 1758 325 11 537 2291 99377037 99375292 0.000000e+00 1349.0
9 TraesCS4B01G329600 chr5D 78.868 1732 351 13 2298 4019 99357980 99356254 0.000000e+00 1157.0
10 TraesCS4B01G329600 chr5D 85.267 991 135 11 3037 4019 249041913 249040926 0.000000e+00 1011.0
11 TraesCS4B01G329600 chr5D 71.303 913 221 32 582 1476 268306133 268305244 3.170000e-46 196.0
12 TraesCS4B01G329600 chr2D 82.284 2128 358 11 1306 3427 346051381 346053495 0.000000e+00 1823.0
13 TraesCS4B01G329600 chr2D 83.122 551 92 1 3467 4016 346053508 346054058 6.000000e-138 501.0
14 TraesCS4B01G329600 chr3D 75.018 4071 911 80 3 4016 431232380 431228359 0.000000e+00 1786.0
15 TraesCS4B01G329600 chr4D 72.487 1323 308 44 580 1876 65091660 65090368 3.790000e-100 375.0
16 TraesCS4B01G329600 chr4D 72.913 539 116 24 568 1089 306370155 306369630 4.160000e-35 159.0
17 TraesCS4B01G329600 chr3A 77.080 637 139 7 888 1520 455597061 455597694 1.060000e-95 361.0
18 TraesCS4B01G329600 chr3A 70.336 654 160 28 2498 3134 13787615 13788251 7.110000e-18 102.0
19 TraesCS4B01G329600 chr7D 72.385 1329 299 56 580 1876 72274457 72275749 3.820000e-95 359.0
20 TraesCS4B01G329600 chr7D 73.585 265 66 4 3444 3706 578077789 578077527 9.190000e-17 99.0
21 TraesCS4B01G329600 chr7B 72.072 1332 312 48 573 1876 123579 124878 1.070000e-90 344.0
22 TraesCS4B01G329600 chr1B 73.961 361 82 11 3436 3790 587031664 587032018 7.010000e-28 135.0
23 TraesCS4B01G329600 chr5A 83.696 92 13 2 2615 2706 324429593 324429504 7.160000e-13 86.1
24 TraesCS4B01G329600 chr3B 92.157 51 3 1 625 674 760393945 760393995 2.000000e-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 TraesCS4B01G329600 chr4B 620064918 620068936 4018 True 7422.0 7422 100.0000 1 4019 1 chr4B.!!$R1 4018
1 TraesCS4B01G329600 chr6B 153388404 153393971 5567 True 2079.0 3240 84.6465 1 4019 2 chr6B.!!$R1 4018
2 TraesCS4B01G329600 chr6D 297446334 297450008 3674 False 2861.0 2861 80.8210 333 4016 1 chr6D.!!$F1 3683
3 TraesCS4B01G329600 chr6D 448581693 448584680 2987 False 1408.5 1838 83.7565 964 4016 2 chr6D.!!$F2 3052
4 TraesCS4B01G329600 chr5D 483131963 483135340 3377 True 2796.0 2796 81.6960 623 4016 1 chr5D.!!$R6 3393
5 TraesCS4B01G329600 chr5D 249063561 249065547 1986 True 1807.0 1807 83.1750 1 1991 1 chr5D.!!$R4 1990
6 TraesCS4B01G329600 chr5D 99375292 99377037 1745 True 1349.0 1349 80.6600 537 2291 1 chr5D.!!$R2 1754
7 TraesCS4B01G329600 chr5D 99356254 99357980 1726 True 1157.0 1157 78.8680 2298 4019 1 chr5D.!!$R1 1721
8 TraesCS4B01G329600 chr5D 249040926 249041913 987 True 1011.0 1011 85.2670 3037 4019 1 chr5D.!!$R3 982
9 TraesCS4B01G329600 chr2D 346051381 346054058 2677 False 1162.0 1823 82.7030 1306 4016 2 chr2D.!!$F1 2710
10 TraesCS4B01G329600 chr3D 431228359 431232380 4021 True 1786.0 1786 75.0180 3 4016 1 chr3D.!!$R1 4013
11 TraesCS4B01G329600 chr4D 65090368 65091660 1292 True 375.0 375 72.4870 580 1876 1 chr4D.!!$R1 1296
12 TraesCS4B01G329600 chr3A 455597061 455597694 633 False 361.0 361 77.0800 888 1520 1 chr3A.!!$F2 632
13 TraesCS4B01G329600 chr7D 72274457 72275749 1292 False 359.0 359 72.3850 580 1876 1 chr7D.!!$F1 1296
14 TraesCS4B01G329600 chr7B 123579 124878 1299 False 344.0 344 72.0720 573 1876 1 chr7B.!!$F1 1303

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
92 93 0.039527 GATTTTGTGGCTTTCGCGGT 60.040 50.0 6.13 0.0 36.88 5.68 F
1163 2787 0.039527 GCGGGTGTGGAATGTTTCAC 60.040 55.0 0.00 0.0 34.71 3.18 F
1593 3218 0.248012 ACATCACGGTTATGGTGCGA 59.752 50.0 7.19 0.0 33.71 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 3638 0.112995 ATTGCTCCTTCCTGCCACAA 59.887 50.0 0.0 0.0 0.0 3.33 R
2251 3878 0.322975 GAGAGCAGAGAAGGCACCAA 59.677 55.0 0.0 0.0 0.0 3.67 R
3491 5180 0.253160 TTCACCCTAGCCCAGTCCAT 60.253 55.0 0.0 0.0 0.0 3.41 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
33 34 0.535102 AAGGTGAGGAAGTTGTGGCG 60.535 55.000 0.00 0.00 0.00 5.69
92 93 0.039527 GATTTTGTGGCTTTCGCGGT 60.040 50.000 6.13 0.00 36.88 5.68
124 125 2.237965 TGTGGTTAGGGCCATGGCT 61.238 57.895 34.70 19.81 41.08 4.75
180 183 2.308039 GCGTCTCGCGTTTGGAGTT 61.308 57.895 5.77 0.00 44.55 3.01
181 184 1.828331 GCGTCTCGCGTTTGGAGTTT 61.828 55.000 5.77 0.00 44.55 2.66
239 243 2.115291 GGGAGCGATCCTTTGTGCC 61.115 63.158 20.86 0.00 0.00 5.01
266 270 1.452108 GCGCTATTGCCTCCCTTGT 60.452 57.895 0.00 0.00 35.36 3.16
268 272 0.107703 CGCTATTGCCTCCCTTGTCA 60.108 55.000 0.00 0.00 35.36 3.58
277 281 1.186200 CTCCCTTGTCATCGTCAGGA 58.814 55.000 0.00 0.00 0.00 3.86
284 288 0.528017 GTCATCGTCAGGACAGAGCA 59.472 55.000 0.00 0.00 34.22 4.26
600 642 3.699538 CCTGGCTATATATGGCTACGTCA 59.300 47.826 19.13 8.50 34.40 4.35
630 672 4.811063 GCTGGATCCTTGTTTAGGGTTTCT 60.811 45.833 14.23 0.00 44.86 2.52
682 724 2.257409 ATTTCGCCCGCACTCTCCAT 62.257 55.000 0.00 0.00 0.00 3.41
739 782 2.124736 CGGCGGTGATGGGTGATT 60.125 61.111 0.00 0.00 0.00 2.57
743 786 1.378382 CGGTGATGGGTGATTGGCA 60.378 57.895 0.00 0.00 0.00 4.92
805 848 0.684805 GAGAAGAAGGGAGCGGGAGA 60.685 60.000 0.00 0.00 0.00 3.71
948 991 2.111384 TGGATCCAGCAGTAGGAGAAC 58.889 52.381 11.44 0.00 38.83 3.01
954 1000 0.969894 AGCAGTAGGAGAACAAGCGT 59.030 50.000 0.00 0.00 0.00 5.07
1018 1064 0.543277 CATGGAGCTGCCCAACTCTA 59.457 55.000 12.73 0.00 40.04 2.43
1163 2787 0.039527 GCGGGTGTGGAATGTTTCAC 60.040 55.000 0.00 0.00 34.71 3.18
1172 2796 2.123988 GAATGTTTCACGTGCGGCCA 62.124 55.000 11.67 5.10 0.00 5.36
1322 2947 3.870559 TCACTAGGGAGGGTTTCTTCTT 58.129 45.455 0.00 0.00 0.00 2.52
1372 2997 1.376466 GTGCCTGTGGATGAGTGGT 59.624 57.895 0.00 0.00 0.00 4.16
1478 3103 1.483415 GCATTGGGATTGGCAAGTGAT 59.517 47.619 5.96 0.00 0.00 3.06
1523 3148 0.389025 GTGGTGTTTCCTTTGGCTGG 59.611 55.000 0.00 0.00 37.07 4.85
1530 3155 3.137544 TGTTTCCTTTGGCTGGTCTCTTA 59.862 43.478 0.00 0.00 0.00 2.10
1539 3164 1.065854 GCTGGTCTCTTACACATGGCT 60.066 52.381 0.00 0.00 0.00 4.75
1565 3190 1.303155 GTGGCAAGCTCTTCCTGCT 60.303 57.895 7.24 0.00 43.32 4.24
1573 3198 1.004560 CTCTTCCTGCTCCGCAACA 60.005 57.895 0.00 0.00 38.41 3.33
1583 3208 1.227704 TCCGCAACAACATCACGGT 60.228 52.632 0.00 0.00 44.17 4.83
1586 3211 1.466950 CCGCAACAACATCACGGTTAT 59.533 47.619 0.00 0.00 39.05 1.89
1593 3218 0.248012 ACATCACGGTTATGGTGCGA 59.752 50.000 7.19 0.00 33.71 5.10
1661 3286 4.681978 GCGGCTTCACGGTGTCCT 62.682 66.667 8.17 0.00 0.00 3.85
1722 3348 4.283337 TCAAGATGTTGGGTCGACCTATA 58.717 43.478 32.52 19.45 41.11 1.31
1737 3363 3.235200 ACCTATAGTGGTGGATGAGCTC 58.765 50.000 6.82 6.82 39.17 4.09
1953 3579 1.869767 GTCAGTGACAAACCTGAGCAG 59.130 52.381 18.54 0.00 32.09 4.24
1988 3614 2.423538 GAGACAACAACAAGCAAGTGGT 59.576 45.455 0.00 0.00 0.00 4.16
1993 3619 2.374184 ACAACAAGCAAGTGGTTAGCA 58.626 42.857 0.00 0.00 33.98 3.49
2003 3629 2.834113 AGTGGTTAGCAGTCCTGGTAT 58.166 47.619 7.01 0.00 42.29 2.73
2012 3638 1.004745 CAGTCCTGGTATGGGCAAAGT 59.995 52.381 0.00 0.00 33.35 2.66
2023 3649 1.398958 GGGCAAAGTTGTGGCAGGAA 61.399 55.000 11.63 0.00 45.56 3.36
2035 3661 1.252904 GGCAGGAAGGAGCAATGCAA 61.253 55.000 8.35 0.00 38.63 4.08
2041 3667 2.494870 GGAAGGAGCAATGCAACAGATT 59.505 45.455 8.35 0.00 0.00 2.40
2065 3691 2.202743 GCGACGTGCAGATGGCTA 60.203 61.111 0.00 0.00 45.45 3.93
2148 3775 1.007387 GTTTGGTGCTTTGAGCGGG 60.007 57.895 0.00 0.00 46.26 6.13
2197 3824 4.011517 CGGTTAGTGTGCCCCCGT 62.012 66.667 0.00 0.00 34.10 5.28
2199 3826 1.678724 GGTTAGTGTGCCCCCGTTA 59.321 57.895 0.00 0.00 0.00 3.18
2242 3869 9.423061 GTGCTTTTAATGAGTATGGTTCAAATT 57.577 29.630 0.00 0.00 0.00 1.82
2250 3877 8.877864 ATGAGTATGGTTCAAATTTGGAGTTA 57.122 30.769 17.90 0.00 0.00 2.24
2251 3878 8.877864 TGAGTATGGTTCAAATTTGGAGTTAT 57.122 30.769 17.90 6.77 0.00 1.89
2252 3879 9.308000 TGAGTATGGTTCAAATTTGGAGTTATT 57.692 29.630 17.90 0.00 0.00 1.40
2281 3908 0.251354 TCTGCTCTCTGACCCAATGC 59.749 55.000 0.00 0.00 0.00 3.56
2292 3919 1.302285 CCCAATGCTGCTGGAGACT 59.698 57.895 9.32 0.00 35.85 3.24
2316 3955 2.359169 GGCCCAGGTGATCTCGTCA 61.359 63.158 0.00 0.00 0.00 4.35
2355 3999 3.554960 CCGACTCTGGATGTGTTCTGAAA 60.555 47.826 0.00 0.00 0.00 2.69
2356 4000 4.058124 CGACTCTGGATGTGTTCTGAAAA 58.942 43.478 0.00 0.00 0.00 2.29
2445 4089 1.378762 GGCAGGCAGGAAACCTACA 59.621 57.895 0.00 0.00 35.10 2.74
2495 4139 1.607612 CTTCTATGGGGTTGGGCGT 59.392 57.895 0.00 0.00 0.00 5.68
2604 4249 2.668632 CGGTCCAAGGCCAAGCTA 59.331 61.111 5.01 0.00 0.00 3.32
2679 4324 3.792114 TGGAGACCTCAGGTAATCCTCTA 59.208 47.826 22.72 9.96 43.07 2.43
2691 4336 4.648307 GGTAATCCTCTACCTTCCTTTCGA 59.352 45.833 0.00 0.00 38.69 3.71
2710 4355 3.941483 TCGAATTCTCAATGCTTTCTCCC 59.059 43.478 3.52 0.00 0.00 4.30
2769 4414 0.601841 CGGTTTCGGCCAGTAGTGTT 60.602 55.000 2.24 0.00 0.00 3.32
2789 4434 6.549364 AGTGTTGATGTTATTTCTTTGGTCCA 59.451 34.615 0.00 0.00 0.00 4.02
2810 4455 4.115199 GCGGGAAGAGGGCCATGT 62.115 66.667 6.18 0.00 0.00 3.21
2884 4529 0.396974 AACAGCAGGGAAAGTTGCCA 60.397 50.000 1.21 0.00 41.75 4.92
2906 4551 1.078426 CCGTGCCCGAAAAGGAGAT 60.078 57.895 0.00 0.00 45.00 2.75
2939 4623 4.281941 GGATGCCTCTGTTTTTCCTTCTTT 59.718 41.667 0.00 0.00 0.00 2.52
3008 4692 1.056660 GGAGTTCACCTCAGGAACCA 58.943 55.000 0.00 0.00 44.40 3.67
3046 4730 1.265635 CCTGTTTTGAAACATCCGCGA 59.734 47.619 8.23 0.00 46.71 5.87
3151 4835 7.930217 ACGATCAAAACAGATTTCTCTTTCAA 58.070 30.769 0.00 0.00 0.00 2.69
3188 4872 8.500773 TCGTTAGATCCTTTACAATGTTTTGAC 58.499 33.333 0.00 0.00 36.64 3.18
3210 4894 2.933287 AATGGGTGCCGTCCTCCA 60.933 61.111 0.00 0.00 0.00 3.86
3218 4902 4.277552 CCGTCCTCCAGGCTATCA 57.722 61.111 0.00 0.00 34.44 2.15
3219 4906 2.751991 CCGTCCTCCAGGCTATCAT 58.248 57.895 0.00 0.00 34.44 2.45
3230 4918 3.138283 CCAGGCTATCATGGGGTCTTTTA 59.862 47.826 0.00 0.00 32.63 1.52
3236 4924 4.898014 ATCATGGGGTCTTTTATTGGGA 57.102 40.909 0.00 0.00 0.00 4.37
3246 4934 5.826208 GGTCTTTTATTGGGATGTAATCGGT 59.174 40.000 0.00 0.00 46.86 4.69
3256 4944 5.186992 TGGGATGTAATCGGTATATCTGTGG 59.813 44.000 4.61 0.00 46.86 4.17
3291 4980 1.036707 CCGGGGTGTGTTTTCATTGT 58.963 50.000 0.00 0.00 0.00 2.71
3295 4984 1.137872 GGGTGTGTTTTCATTGTGGCA 59.862 47.619 0.00 0.00 0.00 4.92
3308 4997 2.566833 TGTGGCAACTATCAAGCACT 57.433 45.000 0.00 0.00 37.61 4.40
3346 5035 7.148689 CGTTCTTGGGTAGTGATGTTAGTTTAC 60.149 40.741 0.00 0.00 0.00 2.01
3372 5061 2.050269 CTGACCACTCCCGTTCAGT 58.950 57.895 0.00 0.00 0.00 3.41
3414 5103 6.593807 TGCTTAGTTTTGTAGGGACTAAACA 58.406 36.000 14.45 0.00 46.98 2.83
3428 5117 2.224548 ACTAAACAAGCGCTCCTCCTTT 60.225 45.455 12.06 6.67 0.00 3.11
3469 5158 1.815421 CAACTTGATCCGCTCGGGG 60.815 63.158 8.59 0.00 36.01 5.73
3471 5160 3.470888 CTTGATCCGCTCGGGGGT 61.471 66.667 8.59 0.00 36.95 4.95
3491 5180 6.126409 GGGGTGGACAAGAATAATGACAATA 58.874 40.000 0.00 0.00 0.00 1.90
3670 5359 3.446873 TGTTCTTCCATCTCTGCTCTCTC 59.553 47.826 0.00 0.00 0.00 3.20
3681 5370 2.485795 GCTCTCTCGTGGCGGAGAT 61.486 63.158 8.30 0.00 41.92 2.75
3722 5411 3.633690 CCTCCCCCTCATCTTTTCCTCTA 60.634 52.174 0.00 0.00 0.00 2.43
3727 5416 4.657969 CCCCTCATCTTTTCCTCTAGTGAT 59.342 45.833 0.00 0.00 0.00 3.06
3792 5481 2.543031 GGTTTGAAGTCGAGGGTTTTGC 60.543 50.000 0.00 0.00 0.00 3.68
3827 5516 3.433319 GCTGGGCGTCTATCTCGA 58.567 61.111 0.00 0.00 0.00 4.04
3832 5521 0.454600 GGGCGTCTATCTCGACACAA 59.545 55.000 0.00 0.00 38.15 3.33
3836 5525 2.159558 GCGTCTATCTCGACACAACTCA 60.160 50.000 0.00 0.00 33.54 3.41
3983 5674 1.577922 CAGCGTTGCATGCTCAAGT 59.422 52.632 20.33 0.00 38.65 3.16
3993 5684 3.007290 TGCATGCTCAAGTTGACTCTAGT 59.993 43.478 20.33 0.00 0.00 2.57
4016 5707 1.003580 GATGGCTGAAAGTGAGTGGGA 59.996 52.381 0.00 0.00 35.30 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.735358 GCCGGTTTCCACTCCCCC 62.735 72.222 1.90 0.00 0.00 5.40
63 64 0.950836 CCACAAAATCGCACACCAGA 59.049 50.000 0.00 0.00 0.00 3.86
64 65 0.664166 GCCACAAAATCGCACACCAG 60.664 55.000 0.00 0.00 0.00 4.00
106 107 2.237965 AGCCATGGCCCTAACCACA 61.238 57.895 33.14 0.00 44.17 4.17
124 125 4.293671 CCCCGGGGCAAAACTCCA 62.294 66.667 31.01 0.00 0.00 3.86
149 152 3.458163 GACGCCACCGATCTGGGA 61.458 66.667 3.36 0.00 44.64 4.37
180 183 1.984570 CGCTCCCAGGAGAGGACAA 60.985 63.158 18.08 0.00 44.53 3.18
181 184 2.363018 CGCTCCCAGGAGAGGACA 60.363 66.667 18.08 0.00 44.53 4.02
224 227 1.377725 CAGGGCACAAAGGATCGCT 60.378 57.895 0.00 0.00 0.00 4.93
253 257 0.620556 ACGATGACAAGGGAGGCAAT 59.379 50.000 0.00 0.00 0.00 3.56
266 270 1.203287 CTTGCTCTGTCCTGACGATGA 59.797 52.381 0.00 0.00 0.00 2.92
268 272 0.534412 CCTTGCTCTGTCCTGACGAT 59.466 55.000 0.00 0.00 0.00 3.73
277 281 2.753029 GGCCACTCCTTGCTCTGT 59.247 61.111 0.00 0.00 0.00 3.41
362 366 1.614824 CCTGGACCAGCTCCTCCTT 60.615 63.158 16.72 0.00 40.26 3.36
453 466 1.538876 AGCCCCTACAGTTCTGCCA 60.539 57.895 0.00 0.00 0.00 4.92
454 467 1.078143 CAGCCCCTACAGTTCTGCC 60.078 63.158 0.00 0.00 0.00 4.85
457 470 0.687354 CACACAGCCCCTACAGTTCT 59.313 55.000 0.00 0.00 0.00 3.01
459 472 0.108585 CACACACAGCCCCTACAGTT 59.891 55.000 0.00 0.00 0.00 3.16
460 473 1.754745 CACACACAGCCCCTACAGT 59.245 57.895 0.00 0.00 0.00 3.55
494 507 3.953775 CACCGACACCTGGGCCTT 61.954 66.667 4.53 0.00 0.00 4.35
600 642 2.610859 AAGGATCCAGCACCCCGT 60.611 61.111 15.82 0.00 0.00 5.28
682 724 1.073706 GGGAGGAGGGGGCAAGATA 60.074 63.158 0.00 0.00 0.00 1.98
707 750 2.342279 CCGTCGCAAAGGAGACCA 59.658 61.111 0.00 0.00 40.30 4.02
709 752 3.479269 CGCCGTCGCAAAGGAGAC 61.479 66.667 0.00 0.00 40.05 3.36
739 782 4.020617 CCTCTTGTCCGCCTGCCA 62.021 66.667 0.00 0.00 0.00 4.92
784 827 0.252284 TCCCGCTCCCTTCTTCTCTT 60.252 55.000 0.00 0.00 0.00 2.85
805 848 3.434319 CTTGGCCTTGTCGCGCAT 61.434 61.111 8.75 0.00 0.00 4.73
825 868 3.718210 CTAACGGCCCCGAGCAGAC 62.718 68.421 14.44 0.00 46.50 3.51
836 879 4.878682 CGCGGTACCCCTAACGGC 62.879 72.222 6.25 0.56 39.15 5.68
841 884 2.713967 GCTTGTCGCGGTACCCCTA 61.714 63.158 6.13 0.00 0.00 3.53
940 983 5.336531 CCTTCTTCTTACGCTTGTTCTCCTA 60.337 44.000 0.00 0.00 0.00 2.94
948 991 0.095417 GCGCCTTCTTCTTACGCTTG 59.905 55.000 0.00 0.00 45.71 4.01
954 1000 1.021390 GCTGCTGCGCCTTCTTCTTA 61.021 55.000 4.18 0.00 0.00 2.10
976 1022 4.819761 GTGCTCCAGATCGCGGCA 62.820 66.667 6.13 2.40 0.00 5.69
984 1030 1.634973 TCCATGGATTTGTGCTCCAGA 59.365 47.619 11.44 0.00 45.64 3.86
1018 1064 1.697754 GATCCCCATGTCCCCCACT 60.698 63.158 0.00 0.00 0.00 4.00
1148 2772 1.753956 GCACGTGAAACATTCCACAC 58.246 50.000 22.23 0.00 35.74 3.82
1163 2787 3.585990 GATCCCAATGGCCGCACG 61.586 66.667 0.00 0.00 0.00 5.34
1172 2796 6.646267 CATTTGGACTGAAAATGATCCCAAT 58.354 36.000 3.36 0.00 44.30 3.16
1178 2802 4.529377 AGGTGCATTTGGACTGAAAATGAT 59.471 37.500 11.91 0.00 44.30 2.45
1322 2947 1.405463 CATCATCGTCGAACTGGAGGA 59.595 52.381 0.00 0.00 35.54 3.71
1372 2997 2.508439 GATGGCCGAGTTCGCGAA 60.508 61.111 19.38 19.38 38.18 4.70
1405 3030 4.400961 GCGGAGGGACAGCTTGCT 62.401 66.667 0.00 0.00 36.79 3.91
1452 3077 3.903282 CAATCCCAATGCCCCGCG 61.903 66.667 0.00 0.00 0.00 6.46
1459 3084 3.196039 TGAATCACTTGCCAATCCCAATG 59.804 43.478 0.00 0.00 0.00 2.82
1478 3103 1.774254 AGTCATTGTCACCCACCTGAA 59.226 47.619 0.00 0.00 0.00 3.02
1523 3148 5.348986 TCGATTTAGCCATGTGTAAGAGAC 58.651 41.667 0.00 0.00 0.00 3.36
1530 3155 2.632377 CCACTCGATTTAGCCATGTGT 58.368 47.619 0.00 0.00 0.00 3.72
1539 3164 3.262420 GAAGAGCTTGCCACTCGATTTA 58.738 45.455 0.00 0.00 39.23 1.40
1565 3190 0.816018 AACCGTGATGTTGTTGCGGA 60.816 50.000 8.31 0.00 44.57 5.54
1573 3198 1.083489 CGCACCATAACCGTGATGTT 58.917 50.000 0.00 0.00 32.77 2.71
1583 3208 1.655484 CAGCATGTCTCGCACCATAA 58.345 50.000 0.00 0.00 0.00 1.90
1586 3211 2.743538 GCAGCATGTCTCGCACCA 60.744 61.111 0.00 0.00 39.31 4.17
1593 3218 2.484742 TCACTTCATGCAGCATGTCT 57.515 45.000 30.38 14.12 41.98 3.41
1656 3281 0.179234 TGCGGTGTTTCTTCAGGACA 59.821 50.000 0.00 0.00 0.00 4.02
1657 3282 0.868406 CTGCGGTGTTTCTTCAGGAC 59.132 55.000 0.00 0.00 0.00 3.85
1661 3286 0.181587 TTCCCTGCGGTGTTTCTTCA 59.818 50.000 0.00 0.00 0.00 3.02
1722 3348 1.006998 AGAGAGAGCTCATCCACCACT 59.993 52.381 17.77 1.84 43.81 4.00
1737 3363 0.179936 GCCCCAACCTGATGAGAGAG 59.820 60.000 0.00 0.00 0.00 3.20
1876 3502 2.236223 CTCAGAGCGCCACCATCACT 62.236 60.000 2.29 0.00 0.00 3.41
1934 3560 1.486310 ACTGCTCAGGTTTGTCACTGA 59.514 47.619 1.66 0.00 41.13 3.41
1935 3561 1.959042 ACTGCTCAGGTTTGTCACTG 58.041 50.000 1.66 0.00 36.07 3.66
1936 3562 2.292267 CAACTGCTCAGGTTTGTCACT 58.708 47.619 1.66 0.00 0.00 3.41
1953 3579 1.003233 GTCTCCCTGCTGTCCCAAC 60.003 63.158 0.00 0.00 0.00 3.77
1988 3614 0.837272 GCCCATACCAGGACTGCTAA 59.163 55.000 0.00 0.00 0.00 3.09
1993 3619 1.372501 ACTTTGCCCATACCAGGACT 58.627 50.000 0.00 0.00 0.00 3.85
2003 3629 2.132996 CCTGCCACAACTTTGCCCA 61.133 57.895 0.00 0.00 0.00 5.36
2012 3638 0.112995 ATTGCTCCTTCCTGCCACAA 59.887 50.000 0.00 0.00 0.00 3.33
2023 3649 1.741706 CGAATCTGTTGCATTGCTCCT 59.258 47.619 10.49 0.00 0.00 3.69
2041 3667 4.717629 CTGCACGTCGCCCTTCGA 62.718 66.667 7.38 0.00 46.29 3.71
2065 3691 3.843027 TCTTCAAGCTCCTCTTCCTGATT 59.157 43.478 0.00 0.00 31.27 2.57
2133 3760 4.659172 CCCCCGCTCAAAGCACCA 62.659 66.667 0.00 0.00 42.58 4.17
2148 3775 2.750237 GCCACAATCCGTGTCCCC 60.750 66.667 0.00 0.00 44.78 4.81
2156 3783 3.499737 CCTGCGTCGCCACAATCC 61.500 66.667 15.88 0.00 0.00 3.01
2160 3787 4.961511 GTGTCCTGCGTCGCCACA 62.962 66.667 15.88 11.91 0.00 4.17
2224 3851 7.781324 ACTCCAAATTTGAACCATACTCATT 57.219 32.000 19.86 0.00 0.00 2.57
2242 3869 3.330701 AGAGAAGGCACCAATAACTCCAA 59.669 43.478 0.00 0.00 0.00 3.53
2250 3877 0.990374 AGAGCAGAGAAGGCACCAAT 59.010 50.000 0.00 0.00 0.00 3.16
2251 3878 0.322975 GAGAGCAGAGAAGGCACCAA 59.677 55.000 0.00 0.00 0.00 3.67
2252 3879 0.543883 AGAGAGCAGAGAAGGCACCA 60.544 55.000 0.00 0.00 0.00 4.17
2355 3999 1.228154 GGTCGCACCAGTCCCTTTT 60.228 57.895 1.01 0.00 38.42 2.27
2356 4000 2.430367 GGTCGCACCAGTCCCTTT 59.570 61.111 1.01 0.00 38.42 3.11
2396 4040 1.459348 TGTCTGCCTGACCCACTCA 60.459 57.895 0.00 0.00 44.75 3.41
2478 4122 1.301623 CACGCCCAACCCCATAGAA 59.698 57.895 0.00 0.00 0.00 2.10
2590 4235 2.677228 GCCTAGCTTGGCCTTGGA 59.323 61.111 26.55 0.00 46.82 3.53
2604 4249 3.001514 ATGGAAGACATGCCGCCT 58.998 55.556 0.00 0.00 38.70 5.52
2679 4324 4.156739 GCATTGAGAATTCGAAAGGAAGGT 59.843 41.667 0.00 0.00 38.24 3.50
2691 4336 3.441572 CGTGGGAGAAAGCATTGAGAATT 59.558 43.478 0.00 0.00 0.00 2.17
2769 4414 5.392919 CGCATGGACCAAAGAAATAACATCA 60.393 40.000 0.00 0.00 0.00 3.07
2808 4453 1.672030 CGCCTCAGCCAACATGACA 60.672 57.895 0.00 0.00 34.57 3.58
2810 4455 2.046023 CCGCCTCAGCCAACATGA 60.046 61.111 0.00 0.00 34.57 3.07
2875 4520 2.193536 GCACGGGACTGGCAACTTT 61.194 57.895 0.00 0.00 37.61 2.66
2877 4522 4.643387 GGCACGGGACTGGCAACT 62.643 66.667 0.00 0.00 36.71 3.16
2884 4529 2.032071 CTTTTCGGGCACGGGACT 59.968 61.111 9.32 0.00 41.39 3.85
2956 4640 1.721487 CCTTAGCCATGCGTTTCCG 59.279 57.895 0.00 0.00 37.07 4.30
3008 4692 5.546621 ACAGGTACCGCATTAGATAATGT 57.453 39.130 6.18 0.00 43.72 2.71
3046 4730 4.740822 GCCCCAGGTGTCCGCAAT 62.741 66.667 0.00 0.00 0.00 3.56
3135 4819 5.574970 AGGTCCTTGAAAGAGAAATCTGT 57.425 39.130 0.00 0.00 0.00 3.41
3151 4835 2.168728 GGATCTAACGAAGCAAGGTCCT 59.831 50.000 0.00 0.00 39.11 3.85
3210 4894 5.388654 CAATAAAAGACCCCATGATAGCCT 58.611 41.667 0.00 0.00 0.00 4.58
3215 4899 4.898014 TCCCAATAAAAGACCCCATGAT 57.102 40.909 0.00 0.00 0.00 2.45
3218 4902 4.625225 ACATCCCAATAAAAGACCCCAT 57.375 40.909 0.00 0.00 0.00 4.00
3219 4906 5.538082 TTACATCCCAATAAAAGACCCCA 57.462 39.130 0.00 0.00 0.00 4.96
3230 4918 7.331026 CACAGATATACCGATTACATCCCAAT 58.669 38.462 0.00 0.00 0.00 3.16
3236 4924 6.665992 ACACCACAGATATACCGATTACAT 57.334 37.500 0.00 0.00 0.00 2.29
3246 4934 4.502431 CCACGCCAATACACCACAGATATA 60.502 45.833 0.00 0.00 0.00 0.86
3256 4944 2.104253 CGGTCCCACGCCAATACAC 61.104 63.158 0.00 0.00 0.00 2.90
3291 4980 2.153645 CACAGTGCTTGATAGTTGCCA 58.846 47.619 0.00 0.00 0.00 4.92
3295 4984 4.281941 TCTGAGACACAGTGCTTGATAGTT 59.718 41.667 0.00 0.00 45.86 2.24
3308 4997 2.029020 CCCAAGAACGATCTGAGACACA 60.029 50.000 0.00 0.00 35.59 3.72
3414 5103 0.980423 AAGAGAAAGGAGGAGCGCTT 59.020 50.000 13.26 0.00 0.00 4.68
3428 5117 2.961536 TCCCCTCCCACAATAAGAGA 57.038 50.000 0.00 0.00 0.00 3.10
3469 5158 7.502226 TCCATATTGTCATTATTCTTGTCCACC 59.498 37.037 0.00 0.00 0.00 4.61
3471 5160 8.274322 AGTCCATATTGTCATTATTCTTGTCCA 58.726 33.333 0.00 0.00 0.00 4.02
3491 5180 0.253160 TTCACCCTAGCCCAGTCCAT 60.253 55.000 0.00 0.00 0.00 3.41
3606 5295 1.261480 CACCCTGTCTAGCACACTCT 58.739 55.000 0.00 0.00 0.00 3.24
3650 5339 2.687425 CGAGAGAGCAGAGATGGAAGAA 59.313 50.000 0.00 0.00 0.00 2.52
3657 5346 1.723608 CGCCACGAGAGAGCAGAGAT 61.724 60.000 0.00 0.00 34.42 2.75
3670 5359 0.729478 CTATACGCATCTCCGCCACG 60.729 60.000 0.00 0.00 0.00 4.94
3681 5370 0.457035 GTGGTCCGAACCTATACGCA 59.543 55.000 0.00 0.00 46.60 5.24
3722 5411 1.204704 TCTCCGCAACGAATCATCACT 59.795 47.619 0.00 0.00 0.00 3.41
3727 5416 3.194861 CCTATTTCTCCGCAACGAATCA 58.805 45.455 0.00 0.00 0.00 2.57
3792 5481 1.574428 CGCTCCCGAACCAAAAGTG 59.426 57.895 0.00 0.00 36.29 3.16
3824 5513 0.757561 TGGGGTCTGAGTTGTGTCGA 60.758 55.000 0.00 0.00 0.00 4.20
3827 5516 0.179056 CGTTGGGGTCTGAGTTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
3853 5542 1.340889 GCCACTGTCCAAAATTCAGCA 59.659 47.619 0.00 0.00 33.12 4.41
3973 5664 4.180057 GGACTAGAGTCAACTTGAGCATG 58.820 47.826 11.64 0.00 46.47 4.06
3978 5669 3.444034 CCATCGGACTAGAGTCAACTTGA 59.556 47.826 11.64 2.11 46.47 3.02
3983 5674 1.751351 CAGCCATCGGACTAGAGTCAA 59.249 52.381 11.64 0.00 46.47 3.18
3993 5684 0.976641 ACTCACTTTCAGCCATCGGA 59.023 50.000 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.