Multiple sequence alignment - TraesCS1D01G340400

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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 TraesCS1D01G340400 chr1D 100.000 7375 0 0 1 7375 430409504 430416878 0.000000e+00 13620.0
1 TraesCS1D01G340400 chr1B 96.719 4420 114 16 1 4415 581199473 581203866 0.000000e+00 7330.0
2 TraesCS1D01G340400 chr1B 92.228 2020 80 28 4589 6584 581204098 581206064 0.000000e+00 2789.0
3 TraesCS1D01G340400 chr1B 88.816 608 35 12 6630 7212 581206679 581207278 0.000000e+00 715.0
4 TraesCS1D01G340400 chr1B 95.575 113 5 0 4420 4532 581203986 581204098 1.630000e-41 182.0
5 TraesCS1D01G340400 chr1B 93.333 120 6 2 7256 7375 581207283 581207400 7.600000e-40 176.0
6 TraesCS1D01G340400 chr1A 96.085 3729 109 16 1 3726 527949592 527953286 0.000000e+00 6043.0
7 TraesCS1D01G340400 chr1A 95.196 2956 115 14 3832 6775 527953334 527956274 0.000000e+00 4647.0
8 TraesCS1D01G340400 chr1A 92.068 353 23 4 6988 7340 527956826 527957173 6.650000e-135 492.0
9 TraesCS1D01G340400 chr3B 81.615 1474 269 2 1722 3194 524453367 524451895 0.000000e+00 1219.0
10 TraesCS1D01G340400 chr3B 84.014 563 82 5 1127 1682 524453995 524453434 1.090000e-147 534.0
11 TraesCS1D01G340400 chr3A 81.559 1475 268 4 1722 3194 517665876 517664404 0.000000e+00 1214.0
12 TraesCS1D01G340400 chr3A 85.258 563 75 5 1127 1682 517666501 517665940 2.310000e-159 573.0
13 TraesCS1D01G340400 chr3D 81.369 1476 269 6 1722 3194 398406174 398404702 0.000000e+00 1197.0
14 TraesCS1D01G340400 chr3D 84.725 563 78 5 1127 1682 398406799 398406238 2.320000e-154 556.0
15 TraesCS1D01G340400 chr3D 78.804 368 58 10 4552 4900 602055132 602054766 5.760000e-56 230.0
16 TraesCS1D01G340400 chr5A 79.931 289 55 3 4036 4323 238697773 238698059 7.500000e-50 209.0
17 TraesCS1D01G340400 chr5D 79.585 289 56 3 4036 4323 204078042 204078328 3.490000e-48 204.0
18 TraesCS1D01G340400 chr5B 79.585 289 56 3 4036 4323 208261122 208261408 3.490000e-48 204.0
19 TraesCS1D01G340400 chr4D 100.000 28 0 0 6276 6303 109242438 109242465 1.300000e-02 52.8
20 TraesCS1D01G340400 chr4A 100.000 28 0 0 6276 6303 467264697 467264670 1.300000e-02 52.8


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 TraesCS1D01G340400 chr1D 430409504 430416878 7374 False 13620.000000 13620 100.000000 1 7375 1 chr1D.!!$F1 7374
1 TraesCS1D01G340400 chr1B 581199473 581207400 7927 False 2238.400000 7330 93.334200 1 7375 5 chr1B.!!$F1 7374
2 TraesCS1D01G340400 chr1A 527949592 527957173 7581 False 3727.333333 6043 94.449667 1 7340 3 chr1A.!!$F1 7339
3 TraesCS1D01G340400 chr3B 524451895 524453995 2100 True 876.500000 1219 82.814500 1127 3194 2 chr3B.!!$R1 2067
4 TraesCS1D01G340400 chr3A 517664404 517666501 2097 True 893.500000 1214 83.408500 1127 3194 2 chr3A.!!$R1 2067
5 TraesCS1D01G340400 chr3D 398404702 398406799 2097 True 876.500000 1197 83.047000 1127 3194 2 chr3D.!!$R2 2067

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
731 736 0.802607 GGCTGATCTCGTCCGTCAAC 60.803 60.000 0.00 0.00 0.00 3.18 F
943 948 2.930562 GTGGACCAGGAGGCAGGT 60.931 66.667 0.00 0.00 41.83 4.00 F
2208 2249 1.902556 GGCAGCAATTTGAGGGCAT 59.097 52.632 0.00 0.00 0.00 4.40 F
3405 3446 1.967319 TTGTTCCTTGTCAGGCACTC 58.033 50.000 0.00 0.00 40.58 3.51 F
4218 4261 0.828762 ATGCTGACCAAGGCTTTGCA 60.829 50.000 2.41 4.13 32.79 4.08 F
4570 4727 0.179000 CACTATGGTGTGCTCCCTCC 59.821 60.000 0.13 0.00 38.54 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2249 1.093972 CACACCAAGCAACACAGTCA 58.906 50.000 0.00 0.0 0.00 3.41 R
2365 2406 1.227089 CTCAGCCCGAATGGACTCG 60.227 63.158 0.00 0.0 37.49 4.18 R
3407 3448 0.037605 AACTGGTGCGTGTAGTAGCC 60.038 55.000 0.00 0.0 31.78 3.93 R
4553 4710 1.330655 ACGGAGGGAGCACACCATAG 61.331 60.000 0.00 0.0 0.00 2.23 R
6166 6330 0.307760 GTGCACCAGTTGTCCTTTCG 59.692 55.000 5.22 0.0 0.00 3.46 R
6554 6739 0.112995 AATGGGCCTGAGTTTCAGCA 59.887 50.000 4.53 0.0 42.98 4.41 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
81 82 5.783360 TGGATTGAAGTTGAACCTACCTAGA 59.217 40.000 0.00 0.00 0.00 2.43
245 249 2.491693 GACAGAGCTAGAAGACACTGCT 59.508 50.000 0.00 0.00 36.63 4.24
247 251 2.187351 GAGCTAGAAGACACTGCTCG 57.813 55.000 0.00 0.00 40.25 5.03
295 299 1.420378 TGTCTGTCGCGCGAATTAAA 58.580 45.000 36.57 17.74 0.00 1.52
365 370 1.258445 ACCGTCTGCCTACCTGGAAG 61.258 60.000 0.00 0.00 43.26 3.46
405 410 2.725641 CACGGACGGTCACAGTCA 59.274 61.111 10.43 0.00 40.20 3.41
510 515 2.616960 CGGATCAAATTCGTGGACAGA 58.383 47.619 0.00 0.00 0.00 3.41
545 550 3.076296 GACACATCTGCAGCGTCGC 62.076 63.158 9.80 9.80 0.00 5.19
551 556 3.857854 CTGCAGCGTCGCCATCAC 61.858 66.667 14.86 0.00 0.00 3.06
674 679 1.586154 ATGAAAGCGCCGGACCAAAG 61.586 55.000 5.05 0.00 0.00 2.77
731 736 0.802607 GGCTGATCTCGTCCGTCAAC 60.803 60.000 0.00 0.00 0.00 3.18
903 908 4.344865 GCGGGTGGCAGGAAAGGA 62.345 66.667 0.00 0.00 42.87 3.36
943 948 2.930562 GTGGACCAGGAGGCAGGT 60.931 66.667 0.00 0.00 41.83 4.00
993 998 4.036971 GGATATACTGTGTGCTCGTCTTCT 59.963 45.833 0.00 0.00 0.00 2.85
2208 2249 1.902556 GGCAGCAATTTGAGGGCAT 59.097 52.632 0.00 0.00 0.00 4.40
2365 2406 2.438392 ACGTGGGAAGGGAAAGGATATC 59.562 50.000 0.00 0.00 0.00 1.63
2578 2619 2.057830 TGTCTGTCGACAGGGCATT 58.942 52.632 37.82 0.00 44.85 3.56
3054 3095 7.148623 CCAGAAACCGAGTGAAGAATTAGTAAC 60.149 40.741 0.00 0.00 0.00 2.50
3279 3320 9.607333 ATTCAGACATAATAGGAATAGGAGTCA 57.393 33.333 0.00 0.00 0.00 3.41
3400 3441 5.772825 TTCTTCATTTGTTCCTTGTCAGG 57.227 39.130 0.00 0.00 42.50 3.86
3401 3442 3.569701 TCTTCATTTGTTCCTTGTCAGGC 59.430 43.478 0.00 0.00 40.58 4.85
3402 3443 2.942804 TCATTTGTTCCTTGTCAGGCA 58.057 42.857 0.00 0.00 40.58 4.75
3403 3444 2.622942 TCATTTGTTCCTTGTCAGGCAC 59.377 45.455 0.00 0.00 40.58 5.01
3404 3445 2.435372 TTTGTTCCTTGTCAGGCACT 57.565 45.000 0.00 0.00 40.58 4.40
3405 3446 1.967319 TTGTTCCTTGTCAGGCACTC 58.033 50.000 0.00 0.00 40.58 3.51
3406 3447 0.836606 TGTTCCTTGTCAGGCACTCA 59.163 50.000 0.00 0.00 40.58 3.41
3407 3448 1.202687 TGTTCCTTGTCAGGCACTCAG 60.203 52.381 0.00 0.00 40.58 3.35
3417 3458 3.742983 GGCACTCAGGCTACTACAC 57.257 57.895 0.00 0.00 40.24 2.90
3478 3519 2.614481 GGCGTCAAGTGGGAGAATAACA 60.614 50.000 0.00 0.00 0.00 2.41
3506 3547 1.557832 CGACAAAATACCCCTCCCTCA 59.442 52.381 0.00 0.00 0.00 3.86
3519 3560 2.103941 CCTCCCTCAGATCTGCTTTACC 59.896 54.545 18.36 0.00 0.00 2.85
3541 3582 6.411376 ACCGATTCACATTAATTACCTGTCA 58.589 36.000 0.00 0.00 0.00 3.58
3618 3659 1.556911 CACACTCTAGGATTGGCCAGT 59.443 52.381 5.11 1.42 40.02 4.00
3625 3666 1.136329 AGGATTGGCCAGTGTGAGGT 61.136 55.000 5.02 0.00 40.02 3.85
3737 3778 5.121811 TGAGATTCTCTCCTTAATTGCTGC 58.878 41.667 14.54 0.00 42.73 5.25
3751 3792 2.028420 TGCTGCGCTCAGAATTGTAT 57.972 45.000 8.15 0.00 42.95 2.29
3782 3823 2.037144 GGCGATTGGAGGGAGTACTTA 58.963 52.381 0.00 0.00 0.00 2.24
3827 3868 6.606395 GGAGTCAGTAATTAGGACTTGTAGGA 59.394 42.308 16.70 0.00 41.68 2.94
3832 3873 9.877222 TCAGTAATTAGGACTTGTAGGATCATA 57.123 33.333 0.00 0.00 0.00 2.15
3952 3993 8.495148 GCCCATTTCTGTTTAGTGTTTTTATTG 58.505 33.333 0.00 0.00 0.00 1.90
3983 4024 1.637338 TGGAGATCACTGCAGACTGT 58.363 50.000 23.35 2.26 39.43 3.55
4053 4096 4.497291 TGTTTCCATATGTAGGTGGACC 57.503 45.455 1.24 0.00 43.85 4.46
4113 4156 1.868713 TTGGATGGATGCAAATGGCT 58.131 45.000 0.00 0.00 45.15 4.75
4179 4222 4.111916 ACATTGAAACCAAAGAAACTGCG 58.888 39.130 0.00 0.00 0.00 5.18
4218 4261 0.828762 ATGCTGACCAAGGCTTTGCA 60.829 50.000 2.41 4.13 32.79 4.08
4386 4429 5.127519 CCAATTTTTGTGCCATCCATAGAGA 59.872 40.000 0.00 0.00 0.00 3.10
4387 4430 6.270815 CAATTTTTGTGCCATCCATAGAGAG 58.729 40.000 0.00 0.00 0.00 3.20
4415 4458 3.244976 CGCACATGATTTTTCCCTTCAC 58.755 45.455 0.00 0.00 0.00 3.18
4470 4627 1.479389 GCATTTAGCTGGTGCCCCTAT 60.479 52.381 0.00 0.00 41.15 2.57
4496 4653 3.871594 AGGTTCGCATAATACTTCTGTGC 59.128 43.478 0.00 0.00 0.00 4.57
4551 4708 8.893727 ACATTACTTCAGGTTAATGTGATTAGC 58.106 33.333 6.25 0.00 40.39 3.09
4570 4727 0.179000 CACTATGGTGTGCTCCCTCC 59.821 60.000 0.13 0.00 38.54 4.30
4574 4731 3.311110 GGTGTGCTCCCTCCGTCA 61.311 66.667 0.00 0.00 0.00 4.35
4624 4781 3.202906 GCATGCCCGTAATTCTAAGTCA 58.797 45.455 6.36 0.00 0.00 3.41
4708 4865 4.517075 GTGAATTAATTAGCCAGAGGAGCC 59.483 45.833 0.00 0.00 0.00 4.70
4920 5079 0.454957 CAATCTCAGCGTTTTGGCCG 60.455 55.000 0.00 0.00 0.00 6.13
4922 5081 0.392998 ATCTCAGCGTTTTGGCCGAT 60.393 50.000 0.00 0.00 0.00 4.18
4925 5084 2.282180 AGCGTTTTGGCCGATGGT 60.282 55.556 0.00 0.00 0.00 3.55
4941 5100 4.076394 CGATGGTCCTTTTAAACCCAGAA 58.924 43.478 0.00 0.00 34.47 3.02
5056 5215 5.746721 GTGAATGCCTTTCAGTTTTACGTTT 59.253 36.000 0.00 0.00 44.89 3.60
5215 5377 8.364894 AGTTGTTTACATGAGTACTGTCATACA 58.635 33.333 0.00 0.00 35.30 2.29
5244 5406 3.293311 GCATCATATTGCATCCACCAC 57.707 47.619 0.00 0.00 42.31 4.16
5577 5739 3.795877 CATTGTTGCTCCAAAAACACCT 58.204 40.909 0.00 0.00 36.08 4.00
5590 5752 3.441496 AAACACCTCTGTTTGCATGTG 57.559 42.857 0.00 0.00 46.79 3.21
5812 5974 3.877559 CCTGGAACTGAATCTGCATACA 58.122 45.455 0.00 0.00 0.00 2.29
6047 6211 2.166664 ACAATAGCCTCGTTCCTCAGTC 59.833 50.000 0.00 0.00 0.00 3.51
6135 6299 4.594920 TCCCATGTTTCTCTTCTGTTCTCT 59.405 41.667 0.00 0.00 0.00 3.10
6166 6330 7.859325 TGGAGAATATTAGTGTTAAACCTGC 57.141 36.000 0.00 0.00 0.00 4.85
6185 6350 0.307760 CGAAAGGACAACTGGTGCAC 59.692 55.000 8.80 8.80 40.89 4.57
6268 6433 1.156736 GTAATGTTGCGCAGGTGTCT 58.843 50.000 11.31 0.00 0.00 3.41
6335 6500 5.090845 TGTGCACCCTTATATCTGGCTATA 58.909 41.667 15.69 0.00 0.00 1.31
6353 6518 9.555727 CTGGCTATATTTTACCTTAGTTTGCTA 57.444 33.333 0.00 0.00 0.00 3.49
6391 6556 9.325198 CATAATGCCATGAACTTACAGTAGTTA 57.675 33.333 0.00 0.00 38.43 2.24
6410 6575 9.148879 AGTAGTTAGTATTGCTGATTATCACCT 57.851 33.333 0.00 0.00 0.00 4.00
6468 6645 3.251729 ACTGCTATGCTATGCCAATTTCG 59.748 43.478 0.00 0.00 0.00 3.46
6486 6663 2.173669 GTCGCCATGTCCATGTCCG 61.174 63.158 6.53 8.39 37.11 4.79
6554 6739 7.201418 GCTTTTAACGTCGCTATTTCTTAGACT 60.201 37.037 0.00 0.00 0.00 3.24
6587 6772 2.630580 GGCCCATTTGTTTTCCACAGTA 59.369 45.455 0.00 0.00 36.48 2.74
6662 7417 6.544928 TTTCCTAGCTGATGATACTTGACA 57.455 37.500 0.00 0.00 0.00 3.58
6669 7424 4.428209 CTGATGATACTTGACACTCGCTT 58.572 43.478 0.00 0.00 0.00 4.68
6709 7464 2.368655 AATGTTTTGCCCGAATGAGC 57.631 45.000 0.00 0.00 0.00 4.26
6731 7487 1.986575 GCACAGCGCAGGGAGATTTC 61.987 60.000 11.47 0.00 41.79 2.17
6780 7730 7.780271 AGGGAGATTGACATAAACCTATTTTCC 59.220 37.037 0.00 0.00 0.00 3.13
6781 7731 7.255139 GGGAGATTGACATAAACCTATTTTCCG 60.255 40.741 0.00 0.00 0.00 4.30
6782 7732 7.282450 GGAGATTGACATAAACCTATTTTCCGT 59.718 37.037 0.00 0.00 0.00 4.69
6799 7749 7.539712 TTTTCCGTCATCATCATTAGAACTC 57.460 36.000 0.00 0.00 0.00 3.01
6803 7753 3.426859 GTCATCATCATTAGAACTCGGCG 59.573 47.826 0.00 0.00 0.00 6.46
6826 7776 6.509677 GCGCGATTATTATCATTAGCTTACCC 60.510 42.308 12.10 0.00 0.00 3.69
6836 7786 6.824958 TCATTAGCTTACCCCAACTCTTAT 57.175 37.500 0.00 0.00 0.00 1.73
6849 7799 6.243900 CCCAACTCTTATGGCTGATGATAAT 58.756 40.000 0.00 0.00 36.58 1.28
6850 7800 7.397221 CCCAACTCTTATGGCTGATGATAATA 58.603 38.462 0.00 0.00 36.58 0.98
6851 7801 7.884877 CCCAACTCTTATGGCTGATGATAATAA 59.115 37.037 0.00 0.00 36.58 1.40
6940 7892 5.751028 CACGAGTCTGGGAAAGAATAGATTC 59.249 44.000 0.00 0.00 36.40 2.52
6976 7928 6.255453 GTGCTACTCTGCTAGAAAGATTCAAG 59.745 42.308 0.00 0.00 0.00 3.02
6978 7930 6.406400 GCTACTCTGCTAGAAAGATTCAAGGA 60.406 42.308 0.00 0.00 0.00 3.36
7087 8191 4.611355 CGCTGATACTGACAACCAAGTTTG 60.611 45.833 0.00 0.00 0.00 2.93
7136 8240 2.398036 GCCAATGGCGAACGTACG 59.602 61.111 15.01 15.01 39.62 3.67
7151 8257 6.422223 CGAACGTACGGACTACTGTTATAAT 58.578 40.000 21.06 0.00 36.89 1.28
7152 8258 7.564128 CGAACGTACGGACTACTGTTATAATA 58.436 38.462 21.06 0.00 36.89 0.98
7153 8259 7.527516 CGAACGTACGGACTACTGTTATAATAC 59.472 40.741 21.06 0.00 36.89 1.89
7175 8281 3.469008 ACAAGATGAACAACACCTCGA 57.531 42.857 0.00 0.00 0.00 4.04
7212 8318 1.935199 TCACTCCGAAAACCGAAACAC 59.065 47.619 0.00 0.00 41.76 3.32
7213 8319 1.937899 CACTCCGAAAACCGAAACACT 59.062 47.619 0.00 0.00 41.76 3.55
7225 8331 3.243336 CCGAAACACTACAGCTACTGAC 58.757 50.000 0.78 0.00 35.18 3.51
7313 8419 8.135529 CGAAGGTCTCATCAGTACAATAATACA 58.864 37.037 0.00 0.00 0.00 2.29
7341 8447 3.135225 TGGTACACAACACTGTACATGC 58.865 45.455 10.73 0.00 45.76 4.06
7370 8476 1.133790 GTAAGAGAAGAACCGCGGCTA 59.866 52.381 28.58 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 4.912395 TGCCCTTTGCCGTTGCCT 62.912 61.111 0.00 0.00 40.16 4.75
245 249 0.596577 AACAGCTAGCGAACAGACGA 59.403 50.000 9.55 0.00 35.09 4.20
247 251 2.135933 ACAAACAGCTAGCGAACAGAC 58.864 47.619 9.55 0.00 0.00 3.51
365 370 4.593864 GTCGCCCTCGGATGCTCC 62.594 72.222 0.00 0.00 36.13 4.70
491 496 3.600388 ACTCTGTCCACGAATTTGATCC 58.400 45.455 0.00 0.00 0.00 3.36
510 515 2.261671 CCGTGACTAGGCGCAACT 59.738 61.111 10.83 0.00 0.00 3.16
674 679 2.598565 GATAAAGAATTCCCCAGGCCC 58.401 52.381 0.00 0.00 0.00 5.80
893 898 2.363018 GGGCCCTTCCTTTCCTGC 60.363 66.667 17.04 0.00 34.39 4.85
900 905 3.090532 GACCGATGGGCCCTTCCT 61.091 66.667 27.49 15.47 36.48 3.36
971 976 5.176407 AGAAGACGAGCACACAGTATATC 57.824 43.478 0.00 0.00 0.00 1.63
1013 1018 3.021263 AGTTCGGGGGAATGGGGG 61.021 66.667 0.00 0.00 0.00 5.40
1116 1124 2.757124 ATGGCTGAATCCCCCGGAC 61.757 63.158 0.73 0.00 32.98 4.79
2208 2249 1.093972 CACACCAAGCAACACAGTCA 58.906 50.000 0.00 0.00 0.00 3.41
2365 2406 1.227089 CTCAGCCCGAATGGACTCG 60.227 63.158 0.00 0.00 37.49 4.18
2578 2619 1.468985 GTGCAGACTCAGAGCTAGGA 58.531 55.000 0.00 0.00 0.00 2.94
3054 3095 5.104941 TCCGAGCATAGGGTATTAATGATGG 60.105 44.000 0.00 0.00 0.00 3.51
3400 3441 0.802607 GCGTGTAGTAGCCTGAGTGC 60.803 60.000 0.00 0.00 0.00 4.40
3401 3442 0.526211 TGCGTGTAGTAGCCTGAGTG 59.474 55.000 0.00 0.00 0.00 3.51
3402 3443 0.526662 GTGCGTGTAGTAGCCTGAGT 59.473 55.000 0.00 0.00 0.00 3.41
3403 3444 0.179134 GGTGCGTGTAGTAGCCTGAG 60.179 60.000 0.00 0.00 0.00 3.35
3404 3445 0.896479 TGGTGCGTGTAGTAGCCTGA 60.896 55.000 0.00 0.00 31.78 3.86
3405 3446 0.458543 CTGGTGCGTGTAGTAGCCTG 60.459 60.000 0.00 0.00 31.78 4.85
3406 3447 0.898789 ACTGGTGCGTGTAGTAGCCT 60.899 55.000 0.00 0.00 31.78 4.58
3407 3448 0.037605 AACTGGTGCGTGTAGTAGCC 60.038 55.000 0.00 0.00 31.78 3.93
3417 3458 1.276415 CCAAACAAACAACTGGTGCG 58.724 50.000 0.00 0.00 0.00 5.34
3478 3519 2.423577 GGGTATTTTGTCGAGCACTGT 58.576 47.619 0.00 0.00 0.00 3.55
3506 3547 4.471904 TGTGAATCGGTAAAGCAGATCT 57.528 40.909 0.00 0.00 30.83 2.75
3519 3560 7.401860 CAGTGACAGGTAATTAATGTGAATCG 58.598 38.462 8.84 0.00 0.00 3.34
3618 3659 5.364778 CATCCGTTTAATATGGACCTCACA 58.635 41.667 0.00 0.00 44.72 3.58
3625 3666 7.758076 CGATAACTAGCATCCGTTTAATATGGA 59.242 37.037 0.00 0.00 45.96 3.41
3667 3708 2.645730 TGAAAAGCGCCGCAAAATAT 57.354 40.000 13.36 0.00 0.00 1.28
3737 3778 1.869767 GAGGGCATACAATTCTGAGCG 59.130 52.381 0.00 0.00 0.00 5.03
3768 3809 6.154021 GTCATTACAGTTAAGTACTCCCTCCA 59.846 42.308 0.00 0.00 33.85 3.86
3782 3823 3.259876 TCCGCTAGTTGGTCATTACAGTT 59.740 43.478 3.50 0.00 0.00 3.16
3832 3873 8.635765 ACATGAGTTTAATGAACATAAGGTGT 57.364 30.769 0.00 0.00 44.84 4.16
3952 3993 0.399833 GATCTCCATTCTCCCCAGGC 59.600 60.000 0.00 0.00 0.00 4.85
3983 4024 9.519191 TTCTCTAGTGATTCCAAAAATCATGAA 57.481 29.630 0.00 2.97 38.71 2.57
4053 4096 3.760151 TGGTTTGCCATTCTTCATCTCTG 59.240 43.478 0.00 0.00 40.46 3.35
4113 4156 6.888105 TGTATAAAGATTCATCACTGGCTCA 58.112 36.000 0.00 0.00 0.00 4.26
4218 4261 3.684981 GCATCTCCTTTGCCTGAGAAGAT 60.685 47.826 0.00 0.00 40.75 2.40
4386 4429 5.278463 GGGAAAAATCATGTGCGCATATACT 60.278 40.000 19.76 7.04 33.30 2.12
4387 4430 4.917415 GGGAAAAATCATGTGCGCATATAC 59.083 41.667 19.76 3.81 33.30 1.47
4470 4627 5.127194 ACAGAAGTATTATGCGAACCTCAGA 59.873 40.000 0.00 0.00 41.97 3.27
4496 4653 3.731089 ACAAAATGGCTTGTGTGATTGG 58.269 40.909 0.00 0.00 38.12 3.16
4553 4710 1.330655 ACGGAGGGAGCACACCATAG 61.331 60.000 0.00 0.00 0.00 2.23
4570 4727 1.539827 CTGGCCTTTTAAACCCTGACG 59.460 52.381 3.32 0.00 0.00 4.35
4574 4731 1.482365 CCCACTGGCCTTTTAAACCCT 60.482 52.381 3.32 0.00 0.00 4.34
4920 5079 4.462834 CCTTCTGGGTTTAAAAGGACCATC 59.537 45.833 0.00 0.00 40.63 3.51
4922 5081 3.464080 TCCTTCTGGGTTTAAAAGGACCA 59.536 43.478 0.76 2.09 41.74 4.02
4941 5100 4.258457 AGCCTAGTGACTACTTCATCCT 57.742 45.455 0.00 0.00 38.36 3.24
5177 5339 8.458573 TCATGTAAACAACTAAACAAGGACAT 57.541 30.769 0.00 0.00 0.00 3.06
5215 5377 3.364889 GCAATATGATGCATGCACTGT 57.635 42.857 25.37 13.89 45.70 3.55
5242 5404 5.495640 AGCATCTAAAGAGGGAAAGAAGTG 58.504 41.667 0.00 0.00 0.00 3.16
5243 5405 5.770685 AGCATCTAAAGAGGGAAAGAAGT 57.229 39.130 0.00 0.00 0.00 3.01
5244 5406 8.567285 TTAAAGCATCTAAAGAGGGAAAGAAG 57.433 34.615 0.00 0.00 0.00 2.85
5363 5525 2.667473 AATGGAAATTCAGCAGCAGC 57.333 45.000 0.00 0.00 42.56 5.25
5577 5739 0.669619 CCACAGCACATGCAAACAGA 59.330 50.000 6.64 0.00 45.16 3.41
5590 5752 3.365265 CGGTTTCTGCCCCACAGC 61.365 66.667 0.00 0.00 46.76 4.40
5812 5974 7.516198 AGTTTTAGTGAGTCAAAGCATCATT 57.484 32.000 0.00 0.00 0.00 2.57
5850 6012 2.031012 CACTGCTCCACCGCTTCA 59.969 61.111 0.00 0.00 0.00 3.02
6047 6211 2.491693 ACCCATTGAAATGCAGTAACCG 59.508 45.455 0.00 0.00 35.08 4.44
6153 6317 2.876550 GTCCTTTCGCAGGTTTAACACT 59.123 45.455 0.00 0.00 44.37 3.55
6166 6330 0.307760 GTGCACCAGTTGTCCTTTCG 59.692 55.000 5.22 0.00 0.00 3.46
6180 6345 2.607892 GCCGACAGACAAGGTGCAC 61.608 63.158 8.80 8.80 0.00 4.57
6185 6350 1.813513 AATCAAGCCGACAGACAAGG 58.186 50.000 0.00 0.00 0.00 3.61
6268 6433 9.117183 CATTTGAATCTCATCCTTGATAGTCAA 57.883 33.333 1.70 1.70 39.64 3.18
6453 6629 0.376852 GCGACGAAATTGGCATAGCA 59.623 50.000 0.00 0.00 0.00 3.49
6554 6739 0.112995 AATGGGCCTGAGTTTCAGCA 59.887 50.000 4.53 0.00 42.98 4.41
6587 6772 4.389374 AGTCAATCGGTGTCTCAATTTGT 58.611 39.130 0.00 0.00 0.00 2.83
6662 7417 4.760204 AGCAAAAACTAATACCAAGCGAGT 59.240 37.500 0.00 0.00 0.00 4.18
6731 7487 4.567558 TGTGCTGCACTTGAAAATGAAAAG 59.432 37.500 30.43 0.00 35.11 2.27
6780 7730 3.426859 GCCGAGTTCTAATGATGATGACG 59.573 47.826 0.00 0.00 0.00 4.35
6781 7731 3.426859 CGCCGAGTTCTAATGATGATGAC 59.573 47.826 0.00 0.00 0.00 3.06
6782 7732 3.642705 CGCCGAGTTCTAATGATGATGA 58.357 45.455 0.00 0.00 0.00 2.92
6799 7749 3.551890 AGCTAATGATAATAATCGCGCCG 59.448 43.478 0.00 0.00 34.60 6.46
6803 7753 6.821665 TGGGGTAAGCTAATGATAATAATCGC 59.178 38.462 0.00 0.00 34.60 4.58
6826 7776 8.853077 TTATTATCATCAGCCATAAGAGTTGG 57.147 34.615 0.00 0.00 37.31 3.77
6836 7786 7.624549 GGAGACCTTATTATTATCATCAGCCA 58.375 38.462 0.00 0.00 0.00 4.75
6895 7845 7.671827 TCGTGATGAATAATCAGTAAAACACG 58.328 34.615 0.00 0.00 46.09 4.49
6976 7928 7.609532 TCTTCCTAACTGTTACAGTACTACTCC 59.390 40.741 18.93 0.00 44.62 3.85
6978 7930 7.611079 CCTCTTCCTAACTGTTACAGTACTACT 59.389 40.741 18.93 5.17 44.62 2.57
7087 8191 6.813649 TCAGTTCAGTAGTACAGATCATTTGC 59.186 38.462 2.52 0.00 0.00 3.68
7151 8257 5.242171 TCGAGGTGTTGTTCATCTTGTAGTA 59.758 40.000 0.00 0.00 37.67 1.82
7152 8258 4.038763 TCGAGGTGTTGTTCATCTTGTAGT 59.961 41.667 0.00 0.00 37.67 2.73
7153 8259 4.556233 TCGAGGTGTTGTTCATCTTGTAG 58.444 43.478 0.00 0.00 37.67 2.74
7175 8281 4.102367 GGAGTGAATAAGAGCATCCTCCTT 59.898 45.833 0.00 0.00 38.96 3.36
7225 8331 1.153667 GAGTTCAGGAGGAGCAGCG 60.154 63.158 0.00 0.00 0.00 5.18
7313 8419 4.013728 ACAGTGTTGTGTACCATGTGTTT 58.986 39.130 0.00 0.00 35.83 2.83
7341 8447 5.154932 CGGTTCTTCTCTTACTGTACTGTG 58.845 45.833 15.01 0.19 0.00 3.66
7346 8452 2.163010 CCGCGGTTCTTCTCTTACTGTA 59.837 50.000 19.50 0.00 0.00 2.74
7352 8458 0.108756 GTAGCCGCGGTTCTTCTCTT 60.109 55.000 28.70 3.94 0.00 2.85


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

AutoCloner maintained by Alex Coulton.