Multiple sequence alignment - TraesCS6A01G158600

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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 TraesCS6A01G158600 chr6A 100.000 4572 0 0 1 4572 150221306 150225877 0.000000e+00 8444.0
1 TraesCS6A01G158600 chr6A 100.000 31 0 0 3592 3622 150224868 150224898 1.780000e-04 58.4
2 TraesCS6A01G158600 chr6A 100.000 31 0 0 3563 3593 150224897 150224927 1.780000e-04 58.4
3 TraesCS6A01G158600 chr6D 95.831 3934 92 28 688 4572 128106289 128102379 0.000000e+00 6290.0
4 TraesCS6A01G158600 chr6D 97.063 647 19 0 1 647 128106932 128106286 0.000000e+00 1090.0
5 TraesCS6A01G158600 chr6D 95.297 404 19 0 1 404 128247557 128247154 3.860000e-180 641.0
6 TraesCS6A01G158600 chr6D 100.000 31 0 0 3563 3593 128103356 128103326 1.780000e-04 58.4
7 TraesCS6A01G158600 chr6B 93.796 3433 127 39 869 4248 227073273 227069874 0.000000e+00 5081.0
8 TraesCS6A01G158600 chr1D 92.431 436 33 0 1 436 405902437 405902872 1.400000e-174 623.0
9 TraesCS6A01G158600 chr1D 92.202 436 31 1 1 436 405813803 405814235 8.410000e-172 614.0
10 TraesCS6A01G158600 chr1D 91.917 433 35 0 4 436 278401252 278400820 1.410000e-169 606.0
11 TraesCS6A01G158600 chr7D 91.800 439 35 1 1 438 481998924 481999362 1.090000e-170 610.0
12 TraesCS6A01G158600 chr7D 91.917 433 35 0 4 436 185796857 185796425 1.410000e-169 606.0
13 TraesCS6A01G158600 chr7D 91.176 442 39 0 7 448 185787130 185786689 6.540000e-168 601.0
14 TraesCS6A01G158600 chr7D 91.705 434 34 2 4 436 227262728 227262296 6.540000e-168 601.0
15 TraesCS6A01G158600 chr3B 87.302 63 3 3 749 807 19233711 19233650 2.950000e-07 67.6
16 TraesCS6A01G158600 chr3B 86.441 59 4 2 749 803 32373349 32373407 1.370000e-05 62.1
17 TraesCS6A01G158600 chr3B 85.965 57 3 3 751 803 82825717 82825662 6.390000e-04 56.5
18 TraesCS6A01G158600 chr5D 86.667 60 4 2 749 804 344525733 344525792 3.820000e-06 63.9
19 TraesCS6A01G158600 chr5D 86.441 59 4 3 749 803 547555077 547555135 1.370000e-05 62.1
20 TraesCS6A01G158600 chr5D 84.615 65 4 4 751 811 495148907 495148969 4.940000e-05 60.2
21 TraesCS6A01G158600 chr7A 86.441 59 4 2 749 803 3260627 3260569 1.370000e-05 62.1
22 TraesCS6A01G158600 chr2A 83.333 66 5 4 749 808 10634323 10634258 6.390000e-04 56.5


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 TraesCS6A01G158600 chr6A 150221306 150225877 4571 False 2853.600000 8444 100.000000 1 4572 3 chr6A.!!$F1 4571
1 TraesCS6A01G158600 chr6D 128102379 128106932 4553 True 2479.466667 6290 97.631333 1 4572 3 chr6D.!!$R2 4571
2 TraesCS6A01G158600 chr6B 227069874 227073273 3399 True 5081.000000 5081 93.796000 869 4248 1 chr6B.!!$R1 3379

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
55 56 0.741221 GAGACAGGGGCACGATGTTC 60.741 60.0 0.0 0.0 0.00 3.18 F
1030 1037 0.326713 GAGGAGGGCTAGGGTTTCCT 60.327 60.0 0.0 0.0 46.96 3.36 F
1149 1159 0.106894 CCTAGGGCTTCGGATTCCAC 59.893 60.0 0.0 0.0 0.00 4.02 F
2617 2675 0.321919 TGCTCCATGCCAGTGAGAAC 60.322 55.0 0.0 0.0 42.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1148 1158 0.108992 TTCGATCAAACGCTAGCGGT 60.109 50.000 37.66 32.16 44.69 5.68 R
2617 2675 0.887933 AGCAAATGGGCAACGTAAGG 59.112 50.000 0.00 0.00 37.87 2.69 R
3110 3171 5.164051 CGGTAAGATAATTGCGCATACAGAG 60.164 44.000 12.75 0.81 0.00 3.35 R
3639 3701 1.202927 CCAGTCCACTCAACACCCATT 60.203 52.381 0.00 0.00 0.00 3.16 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
55 56 0.741221 GAGACAGGGGCACGATGTTC 60.741 60.000 0.00 0.00 0.00 3.18
101 102 6.556644 TGGAGGTAATACCCTACTTCCTAT 57.443 41.667 13.63 0.00 44.50 2.57
206 207 6.712095 GGTGATTGATTATGATTGCCTCTACA 59.288 38.462 0.00 0.00 0.00 2.74
270 271 3.495753 GGTTGTACAAGGTCGGTTTACAG 59.504 47.826 8.98 0.00 0.00 2.74
273 274 1.426751 ACAAGGTCGGTTTACAGGGA 58.573 50.000 0.00 0.00 0.00 4.20
283 284 3.252458 CGGTTTACAGGGAAAGGAAACTG 59.748 47.826 0.00 0.00 42.68 3.16
342 343 2.758327 CCCATCCGGACACGAGGA 60.758 66.667 6.12 0.00 44.60 3.71
369 370 6.652900 AGATCTTCGATCTCATATCTTCACGA 59.347 38.462 0.67 0.00 0.00 4.35
380 381 1.924731 TCTTCACGACCCATCAGTCT 58.075 50.000 0.00 0.00 34.46 3.24
422 423 2.123382 CCCGAGGACCCCCTAGTC 60.123 72.222 0.00 0.00 44.53 2.59
423 424 2.702302 CCCGAGGACCCCCTAGTCT 61.702 68.421 0.00 0.00 44.53 3.24
455 456 2.146779 TGGGAACAACCGACCATGA 58.853 52.632 0.00 0.00 40.11 3.07
567 568 3.211288 GCCTGCGAGCCTCTTCTA 58.789 61.111 0.00 0.00 0.00 2.10
580 581 3.931468 GCCTCTTCTAAGGTCGTTTTACC 59.069 47.826 0.00 0.00 38.79 2.85
595 596 6.755141 GTCGTTTTACCTCTGTAATAGATGCA 59.245 38.462 0.00 0.00 36.84 3.96
662 663 5.109662 GGACAAACCTTTAGTCTCTTTGC 57.890 43.478 0.00 0.00 35.41 3.68
663 664 4.578928 GGACAAACCTTTAGTCTCTTTGCA 59.421 41.667 0.00 0.00 35.41 4.08
664 665 5.278022 GGACAAACCTTTAGTCTCTTTGCAG 60.278 44.000 0.00 0.00 35.41 4.41
665 666 4.036852 ACAAACCTTTAGTCTCTTTGCAGC 59.963 41.667 0.00 0.00 0.00 5.25
666 667 3.778954 ACCTTTAGTCTCTTTGCAGCT 57.221 42.857 0.00 0.00 0.00 4.24
667 668 3.669536 ACCTTTAGTCTCTTTGCAGCTC 58.330 45.455 0.00 0.00 0.00 4.09
668 669 3.326297 ACCTTTAGTCTCTTTGCAGCTCT 59.674 43.478 0.00 0.00 0.00 4.09
669 670 3.932089 CCTTTAGTCTCTTTGCAGCTCTC 59.068 47.826 0.00 0.00 0.00 3.20
670 671 4.562347 CCTTTAGTCTCTTTGCAGCTCTCA 60.562 45.833 0.00 0.00 0.00 3.27
671 672 4.815533 TTAGTCTCTTTGCAGCTCTCAT 57.184 40.909 0.00 0.00 0.00 2.90
672 673 3.699411 AGTCTCTTTGCAGCTCTCATT 57.301 42.857 0.00 0.00 0.00 2.57
673 674 4.815533 AGTCTCTTTGCAGCTCTCATTA 57.184 40.909 0.00 0.00 0.00 1.90
674 675 4.757594 AGTCTCTTTGCAGCTCTCATTAG 58.242 43.478 0.00 0.00 0.00 1.73
675 676 4.222588 AGTCTCTTTGCAGCTCTCATTAGT 59.777 41.667 0.00 0.00 0.00 2.24
676 677 4.934602 GTCTCTTTGCAGCTCTCATTAGTT 59.065 41.667 0.00 0.00 0.00 2.24
677 678 5.411053 GTCTCTTTGCAGCTCTCATTAGTTT 59.589 40.000 0.00 0.00 0.00 2.66
678 679 5.410746 TCTCTTTGCAGCTCTCATTAGTTTG 59.589 40.000 0.00 0.00 0.00 2.93
679 680 3.837213 TTGCAGCTCTCATTAGTTTGC 57.163 42.857 0.00 0.00 32.96 3.68
680 681 2.086869 TGCAGCTCTCATTAGTTTGCC 58.913 47.619 0.00 0.00 32.01 4.52
681 682 2.290514 TGCAGCTCTCATTAGTTTGCCT 60.291 45.455 0.00 0.00 32.01 4.75
682 683 3.055167 TGCAGCTCTCATTAGTTTGCCTA 60.055 43.478 0.00 0.00 32.01 3.93
683 684 4.133078 GCAGCTCTCATTAGTTTGCCTAT 58.867 43.478 0.00 0.00 0.00 2.57
684 685 4.024218 GCAGCTCTCATTAGTTTGCCTATG 60.024 45.833 0.00 0.00 0.00 2.23
685 686 4.024218 CAGCTCTCATTAGTTTGCCTATGC 60.024 45.833 0.00 0.00 38.26 3.14
686 687 3.059325 GCTCTCATTAGTTTGCCTATGCG 60.059 47.826 0.00 0.00 41.78 4.73
1030 1037 0.326713 GAGGAGGGCTAGGGTTTCCT 60.327 60.000 0.00 0.00 46.96 3.36
1122 1132 3.559069 CCTCTACGAGGTAATACCACCA 58.441 50.000 12.54 0.00 44.25 4.17
1148 1158 1.054406 CCCTAGGGCTTCGGATTCCA 61.054 60.000 16.90 0.00 0.00 3.53
1149 1159 0.106894 CCTAGGGCTTCGGATTCCAC 59.893 60.000 0.00 0.00 0.00 4.02
1170 1181 1.137153 CGCTAGCGTTTGATCGAATCG 60.137 52.381 28.66 0.00 34.35 3.34
1174 1185 0.914996 GCGTTTGATCGAATCGTGCG 60.915 55.000 1.52 8.27 0.00 5.34
1184 1195 0.648441 GAATCGTGCGCGGATGTTTA 59.352 50.000 21.04 0.48 38.89 2.01
1199 1210 4.752101 GGATGTTTAGGATTCGTGGATGAG 59.248 45.833 0.00 0.00 0.00 2.90
1206 1217 3.126831 GGATTCGTGGATGAGCAGTAAG 58.873 50.000 0.00 0.00 0.00 2.34
1207 1218 2.672961 TTCGTGGATGAGCAGTAAGG 57.327 50.000 0.00 0.00 0.00 2.69
1208 1219 0.824109 TCGTGGATGAGCAGTAAGGG 59.176 55.000 0.00 0.00 0.00 3.95
1209 1220 0.811616 CGTGGATGAGCAGTAAGGGC 60.812 60.000 0.00 0.00 0.00 5.19
1210 1221 0.811616 GTGGATGAGCAGTAAGGGCG 60.812 60.000 0.00 0.00 36.08 6.13
1244 1255 1.018226 GCTTGTCTGATGTCGCTGCT 61.018 55.000 0.00 0.00 0.00 4.24
1252 1267 2.021068 GATGTCGCTGCTCAGGGCTA 62.021 60.000 8.83 1.76 42.39 3.93
1362 1382 0.534877 AAACATGCGCACACAGGAGA 60.535 50.000 14.90 0.00 0.00 3.71
1403 1430 4.079096 AGTCCTATGACCTAGTTACCTGCT 60.079 45.833 0.00 0.00 42.81 4.24
1432 1460 2.024369 ACCTGGACACATATTTTCCCCC 60.024 50.000 0.00 0.00 0.00 5.40
1692 1723 5.510520 GGATCTGCTGGGCTGCTATATATAC 60.511 48.000 0.00 0.00 0.00 1.47
2617 2675 0.321919 TGCTCCATGCCAGTGAGAAC 60.322 55.000 0.00 0.00 42.00 3.01
3110 3171 0.536460 TCAACCGGCTCCTCAAAACC 60.536 55.000 0.00 0.00 0.00 3.27
3182 3243 2.159627 GTCCACCAAAGTGTATGCGAAG 59.840 50.000 0.00 0.00 42.88 3.79
3197 3258 3.153919 TGCGAAGTGGGCTAAAAAGATT 58.846 40.909 0.00 0.00 0.00 2.40
3285 3347 4.387026 TCCATCCCTTGAAACACTTCAT 57.613 40.909 0.00 0.00 41.22 2.57
3333 3395 3.133003 AGTCGCTATCACCTGCTTATGTT 59.867 43.478 0.00 0.00 0.00 2.71
3780 3844 1.004918 GTGGAAGTGTCCTGTCCCG 60.005 63.158 0.00 0.00 45.22 5.14
3842 3906 5.745294 GGTGATAGTCTGTTTAATTCGCGTA 59.255 40.000 5.77 0.00 0.00 4.42
4085 4149 7.062322 TGGATGTTGATTAATCAAGCTGGTAT 58.938 34.615 27.26 15.66 46.44 2.73
4323 4389 5.752098 CTGACGGAGCAAATTTTCATTTC 57.248 39.130 0.00 0.00 29.41 2.17
4440 4509 0.976963 CGCAAACATTTACAGCGCTG 59.023 50.000 34.89 34.89 41.95 5.18
4442 4511 1.929926 GCAAACATTTACAGCGCTGCA 60.930 47.619 36.28 23.13 0.00 4.41
4447 4516 2.223688 ACATTTACAGCGCTGCAAACAA 60.224 40.909 32.28 20.22 29.60 2.83
4457 4526 2.548875 GCTGCAAACAACCATTGACAA 58.451 42.857 0.00 0.00 0.00 3.18
4482 4551 1.595993 ATGGAGGACGTCGTGGACAG 61.596 60.000 16.63 0.00 32.09 3.51
4505 4574 6.038714 CAGCCTAGGATTAAGTTTTGGATGAC 59.961 42.308 14.75 0.00 32.24 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.455872 TCCTGTTACCTTCGATCCTAAGAT 58.544 41.667 4.42 0.00 34.57 2.40
101 102 7.775093 CCCCTATACTCATCAAAGTCAATCAAA 59.225 37.037 0.00 0.00 0.00 2.69
155 156 6.176014 AGACATCTAGGGTTTAGCCATTAC 57.824 41.667 0.26 0.00 39.65 1.89
270 271 2.158579 TGGGTGTACAGTTTCCTTTCCC 60.159 50.000 0.00 0.01 0.00 3.97
273 274 3.379057 CGTTTGGGTGTACAGTTTCCTTT 59.621 43.478 0.00 0.00 0.00 3.11
283 284 1.589803 AGCTTGACGTTTGGGTGTAC 58.410 50.000 0.00 0.00 0.00 2.90
342 343 7.807433 CGTGAAGATATGAGATCGAAGATCTTT 59.193 37.037 9.87 7.55 45.12 2.52
369 370 2.204136 TGGGCCAGACTGATGGGT 60.204 61.111 0.00 0.00 40.97 4.51
380 381 0.546122 GGACTATGTGATGTGGGCCA 59.454 55.000 0.00 0.00 0.00 5.36
449 450 0.698818 GGTGGTTCTCCCTTCATGGT 59.301 55.000 0.00 0.00 0.00 3.55
455 456 3.833559 ATTCAATGGTGGTTCTCCCTT 57.166 42.857 0.00 0.00 0.00 3.95
510 511 1.507140 ACCCTGAGAACACCACTTGA 58.493 50.000 0.00 0.00 0.00 3.02
580 581 5.618863 CGCCTAGTCTGCATCTATTACAGAG 60.619 48.000 0.00 0.00 40.91 3.35
643 644 4.276926 AGCTGCAAAGAGACTAAAGGTTTG 59.723 41.667 1.02 0.00 0.00 2.93
644 645 4.464947 AGCTGCAAAGAGACTAAAGGTTT 58.535 39.130 1.02 0.00 0.00 3.27
645 646 4.068599 GAGCTGCAAAGAGACTAAAGGTT 58.931 43.478 1.02 0.00 0.00 3.50
646 647 3.326297 AGAGCTGCAAAGAGACTAAAGGT 59.674 43.478 1.02 0.00 0.00 3.50
647 648 3.932089 GAGAGCTGCAAAGAGACTAAAGG 59.068 47.826 1.02 0.00 0.00 3.11
648 649 4.564041 TGAGAGCTGCAAAGAGACTAAAG 58.436 43.478 1.02 0.00 0.00 1.85
649 650 4.607293 TGAGAGCTGCAAAGAGACTAAA 57.393 40.909 1.02 0.00 0.00 1.85
650 651 4.815533 ATGAGAGCTGCAAAGAGACTAA 57.184 40.909 1.02 0.00 0.00 2.24
651 652 4.815533 AATGAGAGCTGCAAAGAGACTA 57.184 40.909 1.02 0.00 0.00 2.59
652 653 3.699411 AATGAGAGCTGCAAAGAGACT 57.301 42.857 1.02 0.00 0.00 3.24
653 654 4.502962 ACTAATGAGAGCTGCAAAGAGAC 58.497 43.478 1.02 0.00 0.00 3.36
654 655 4.815533 ACTAATGAGAGCTGCAAAGAGA 57.184 40.909 1.02 0.00 0.00 3.10
655 656 5.629097 CAAACTAATGAGAGCTGCAAAGAG 58.371 41.667 1.02 0.00 0.00 2.85
656 657 4.083110 GCAAACTAATGAGAGCTGCAAAGA 60.083 41.667 1.02 0.00 0.00 2.52
657 658 4.164294 GCAAACTAATGAGAGCTGCAAAG 58.836 43.478 1.02 0.00 0.00 2.77
658 659 3.057315 GGCAAACTAATGAGAGCTGCAAA 60.057 43.478 1.02 0.00 31.17 3.68
659 660 2.489329 GGCAAACTAATGAGAGCTGCAA 59.511 45.455 1.02 0.00 31.17 4.08
660 661 2.086869 GGCAAACTAATGAGAGCTGCA 58.913 47.619 1.02 0.00 31.17 4.41
661 662 2.363683 AGGCAAACTAATGAGAGCTGC 58.636 47.619 0.00 0.00 0.00 5.25
662 663 4.024218 GCATAGGCAAACTAATGAGAGCTG 60.024 45.833 0.00 0.00 40.72 4.24
663 664 4.133078 GCATAGGCAAACTAATGAGAGCT 58.867 43.478 0.00 0.00 40.72 4.09
664 665 3.059325 CGCATAGGCAAACTAATGAGAGC 60.059 47.826 0.00 0.00 41.24 4.09
665 666 3.059325 GCGCATAGGCAAACTAATGAGAG 60.059 47.826 0.30 0.00 41.24 3.20
666 667 2.872245 GCGCATAGGCAAACTAATGAGA 59.128 45.455 0.30 0.00 41.24 3.27
667 668 2.613595 TGCGCATAGGCAAACTAATGAG 59.386 45.455 5.66 0.00 40.59 2.90
668 669 2.637947 TGCGCATAGGCAAACTAATGA 58.362 42.857 5.66 0.00 40.59 2.57
677 678 1.141449 GGCATTTTGCGCATAGGCA 59.859 52.632 24.41 3.40 46.21 4.75
678 679 1.945662 CGGCATTTTGCGCATAGGC 60.946 57.895 12.75 16.08 46.21 3.93
679 680 0.311790 ATCGGCATTTTGCGCATAGG 59.688 50.000 12.75 5.52 46.21 2.57
680 681 2.046313 GAATCGGCATTTTGCGCATAG 58.954 47.619 12.75 2.33 46.21 2.23
681 682 1.675483 AGAATCGGCATTTTGCGCATA 59.325 42.857 12.75 2.60 46.21 3.14
682 683 0.457035 AGAATCGGCATTTTGCGCAT 59.543 45.000 12.75 0.00 46.21 4.73
683 684 0.456482 CAGAATCGGCATTTTGCGCA 60.456 50.000 5.66 5.66 46.21 6.09
684 685 1.745768 GCAGAATCGGCATTTTGCGC 61.746 55.000 0.00 0.00 46.21 6.09
685 686 2.281359 GCAGAATCGGCATTTTGCG 58.719 52.632 0.00 0.00 46.21 4.85
686 687 1.133790 AGAGCAGAATCGGCATTTTGC 59.866 47.619 8.26 13.44 46.10 3.68
803 810 8.524487 GGTGAACAGGGAGATAATACTAGTATG 58.476 40.741 16.11 4.66 0.00 2.39
805 812 7.008941 GGGTGAACAGGGAGATAATACTAGTA 58.991 42.308 4.77 4.77 0.00 1.82
807 814 5.246429 GGGGTGAACAGGGAGATAATACTAG 59.754 48.000 0.00 0.00 0.00 2.57
810 817 3.072622 GGGGGTGAACAGGGAGATAATAC 59.927 52.174 0.00 0.00 0.00 1.89
1119 1129 1.384643 GCCCTAGGGTCTGGATGGT 60.385 63.158 28.96 0.00 37.65 3.55
1122 1132 0.760945 CGAAGCCCTAGGGTCTGGAT 60.761 60.000 28.96 11.50 37.65 3.41
1148 1158 0.108992 TTCGATCAAACGCTAGCGGT 60.109 50.000 37.66 32.16 44.69 5.68
1149 1159 1.190323 GATTCGATCAAACGCTAGCGG 59.810 52.381 37.66 22.04 44.69 5.52
1170 1181 1.003866 GAATCCTAAACATCCGCGCAC 60.004 52.381 8.75 0.00 0.00 5.34
1174 1185 1.597663 CCACGAATCCTAAACATCCGC 59.402 52.381 0.00 0.00 0.00 5.54
1184 1195 1.198713 ACTGCTCATCCACGAATCCT 58.801 50.000 0.00 0.00 0.00 3.24
1206 1217 3.903282 TACATACGACGCCCGCCC 61.903 66.667 0.00 0.00 43.32 6.13
1207 1218 2.656328 GTACATACGACGCCCGCC 60.656 66.667 0.00 0.00 43.32 6.13
1226 1237 0.997932 GAGCAGCGACATCAGACAAG 59.002 55.000 0.00 0.00 0.00 3.16
1231 1242 1.521010 CCCTGAGCAGCGACATCAG 60.521 63.158 2.94 2.94 40.13 2.90
1244 1255 2.835764 ACTTAACAACGGATAGCCCTGA 59.164 45.455 0.95 0.00 0.00 3.86
1252 1267 2.038557 AGCACCTGACTTAACAACGGAT 59.961 45.455 0.00 0.00 0.00 4.18
1309 1327 5.783875 ACCCAAATACTACTAACACCTGAGT 59.216 40.000 0.00 0.00 0.00 3.41
1362 1382 3.100671 GACTCCATATCTCGGGGCTAAT 58.899 50.000 0.00 0.00 0.00 1.73
1403 1430 8.962679 GGAAAATATGTGTCCAGGTTTATACAA 58.037 33.333 0.00 0.00 0.00 2.41
1692 1723 1.407618 TGGTATGTTCCTGGATCGACG 59.592 52.381 0.00 0.00 0.00 5.12
1721 1752 6.710744 ACTTACAGGACAATTGACACCTTTAG 59.289 38.462 13.59 14.06 0.00 1.85
2617 2675 0.887933 AGCAAATGGGCAACGTAAGG 59.112 50.000 0.00 0.00 37.87 2.69
3110 3171 5.164051 CGGTAAGATAATTGCGCATACAGAG 60.164 44.000 12.75 0.81 0.00 3.35
3182 3243 6.765915 ATCTCAGAAATCTTTTTAGCCCAC 57.234 37.500 0.00 0.00 0.00 4.61
3197 3258 3.516586 TGTGGGTGGTTCTATCTCAGAA 58.483 45.455 0.00 0.00 41.10 3.02
3333 3395 4.127171 GGAGACAAAACAGTGCAGACTTA 58.873 43.478 0.00 0.00 0.00 2.24
3639 3701 1.202927 CCAGTCCACTCAACACCCATT 60.203 52.381 0.00 0.00 0.00 3.16
3656 3718 1.376466 CACAACCCCTCCACTCCAG 59.624 63.158 0.00 0.00 0.00 3.86
3780 3844 4.142403 TGCCGAGGATTTCATTTCATTCAC 60.142 41.667 0.00 0.00 0.00 3.18
4301 4367 5.221880 TGAAATGAAAATTTGCTCCGTCAG 58.778 37.500 0.00 0.00 0.00 3.51
4302 4368 5.193663 TGAAATGAAAATTTGCTCCGTCA 57.806 34.783 0.00 0.00 0.00 4.35
4323 4389 7.547370 CCTCTGTAAAACTCCTCTCACTTATTG 59.453 40.741 0.00 0.00 0.00 1.90
4440 4509 3.123050 GTCCTTGTCAATGGTTGTTTGC 58.877 45.455 0.00 0.00 0.00 3.68
4442 4511 3.370104 TGGTCCTTGTCAATGGTTGTTT 58.630 40.909 0.00 0.00 0.00 2.83
4447 4516 1.710244 TCCATGGTCCTTGTCAATGGT 59.290 47.619 12.58 0.00 0.00 3.55
4457 4526 2.052690 CGACGTCCTCCATGGTCCT 61.053 63.158 12.58 0.00 37.07 3.85
4482 4551 5.007724 CGTCATCCAAAACTTAATCCTAGGC 59.992 44.000 2.96 0.00 0.00 3.93
4505 4574 1.721257 CGTGTTCTTCGTCTAGCGCG 61.721 60.000 0.00 0.00 41.07 6.86
4515 4584 9.445786 TTTAATTCTGAATTGAACGTGTTCTTC 57.554 29.630 22.47 10.08 40.14 2.87
4521 4590 8.236586 TCATCCTTTAATTCTGAATTGAACGTG 58.763 33.333 22.47 15.96 32.38 4.49


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

AutoCloner maintained by Alex Coulton.