Multiple sequence alignment - TraesCS7D01G438200

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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 TraesCS7D01G438200 chr7D 100.000 3812 0 0 1 3812 557573819 557577630 0.000000e+00 7040.0
1 TraesCS7D01G438200 chr7A 92.416 3125 124 44 26 3096 643074823 643077888 0.000000e+00 4353.0
2 TraesCS7D01G438200 chr7A 83.196 607 42 22 3235 3809 643077904 643078482 5.690000e-138 501.0
3 TraesCS7D01G438200 chr7B 92.554 2780 146 30 629 3387 605643565 605646304 0.000000e+00 3930.0
4 TraesCS7D01G438200 chr7B 90.439 638 25 12 1 624 605642529 605643144 0.000000e+00 808.0
5 TraesCS7D01G438200 chr7B 89.427 227 14 4 3489 3712 605646572 605646791 1.040000e-70 278.0
6 TraesCS7D01G438200 chr7B 89.474 57 6 0 3445 3501 605646509 605646565 5.280000e-09 73.1
7 TraesCS7D01G438200 chr3B 86.675 803 45 23 2496 3264 607414697 607413923 0.000000e+00 833.0
8 TraesCS7D01G438200 chr5D 84.181 354 29 10 2791 3123 168233719 168233372 6.150000e-83 318.0
9 TraesCS7D01G438200 chr3D 90.361 83 8 0 1608 1690 479117462 479117380 4.030000e-20 110.0
10 TraesCS7D01G438200 chr2A 88.172 93 10 1 1599 1690 712968527 712968619 4.030000e-20 110.0


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 TraesCS7D01G438200 chr7D 557573819 557577630 3811 False 7040.000 7040 100.0000 1 3812 1 chr7D.!!$F1 3811
1 TraesCS7D01G438200 chr7A 643074823 643078482 3659 False 2427.000 4353 87.8060 26 3809 2 chr7A.!!$F1 3783
2 TraesCS7D01G438200 chr7B 605642529 605646791 4262 False 1272.275 3930 90.4735 1 3712 4 chr7B.!!$F1 3711
3 TraesCS7D01G438200 chr3B 607413923 607414697 774 True 833.000 833 86.6750 2496 3264 1 chr3B.!!$R1 768

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
22 23 0.384309 ACAACGAGCAGACGAACTCA 59.616 50.0 5.12 0.00 37.03 3.41 F
851 1302 0.809385 TAGTTGAAGCTCTCCGACGG 59.191 55.0 7.84 7.84 0.00 4.79 F
1250 1702 0.263172 GAGGATGAGGAGGAGGTGGA 59.737 60.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1460 0.463474 GTGCTGCTTCTCCCATCTCC 60.463 60.000 0.00 0.0 0.00 3.71 R
1977 2432 2.044252 ACGGCGAAGGAGGAGCTA 60.044 61.111 16.62 0.0 0.00 3.32 R
3006 3475 0.329596 ACAACCTCCAAGGGCTGATC 59.670 55.000 0.00 0.0 40.58 2.92 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
20 21 1.488527 GAACAACGAGCAGACGAACT 58.511 50.000 5.12 0.00 37.03 3.01
21 22 1.452399 GAACAACGAGCAGACGAACTC 59.548 52.381 5.12 0.00 37.03 3.01
22 23 0.384309 ACAACGAGCAGACGAACTCA 59.616 50.000 5.12 0.00 37.03 3.41
23 24 1.202371 ACAACGAGCAGACGAACTCAA 60.202 47.619 5.12 0.00 37.03 3.02
24 25 1.453524 CAACGAGCAGACGAACTCAAG 59.546 52.381 5.12 0.00 37.03 3.02
55 56 3.966543 AGGGCGAGTTGGTTGGGG 61.967 66.667 0.00 0.00 0.00 4.96
157 170 2.050714 CACTGGCTTTGCACTGCG 60.051 61.111 4.34 0.00 0.00 5.18
275 300 3.576982 CTCAGGGAAAGGTACACACACTA 59.423 47.826 0.00 0.00 0.00 2.74
305 330 1.003580 TGCCCTCACAGATCCTGAAAC 59.996 52.381 0.45 0.00 35.18 2.78
342 367 4.705023 GTGCATAATCACCAACCCTTAACT 59.295 41.667 0.00 0.00 0.00 2.24
397 429 4.590222 TGATCTCAGGCATATGTTCAGCTA 59.410 41.667 4.29 0.00 0.00 3.32
570 604 2.649312 TGGACATGGAGATTTTGGAGGT 59.351 45.455 0.00 0.00 0.00 3.85
575 609 2.205342 TGGAGATTTTGGAGGTAGGGG 58.795 52.381 0.00 0.00 0.00 4.79
636 1083 2.156098 AGCAAGTTGGGGCAGGAGA 61.156 57.895 4.75 0.00 0.00 3.71
637 1084 1.676967 GCAAGTTGGGGCAGGAGAG 60.677 63.158 4.75 0.00 0.00 3.20
639 1086 1.151810 AAGTTGGGGCAGGAGAGGA 60.152 57.895 0.00 0.00 0.00 3.71
668 1117 2.374184 AGAAGACAGATCAGAGACGGG 58.626 52.381 0.00 0.00 0.00 5.28
669 1118 2.096248 GAAGACAGATCAGAGACGGGT 58.904 52.381 0.00 0.00 0.00 5.28
670 1119 1.468985 AGACAGATCAGAGACGGGTG 58.531 55.000 0.00 0.00 0.00 4.61
671 1120 1.004862 AGACAGATCAGAGACGGGTGA 59.995 52.381 0.00 0.00 0.00 4.02
796 1246 1.545582 CCTGCATGGGTACAAAACTGG 59.454 52.381 0.00 0.00 0.00 4.00
851 1302 0.809385 TAGTTGAAGCTCTCCGACGG 59.191 55.000 7.84 7.84 0.00 4.79
868 1319 2.284405 GGTTCCCTCCCACTCCGA 60.284 66.667 0.00 0.00 0.00 4.55
869 1320 2.359967 GGTTCCCTCCCACTCCGAG 61.360 68.421 0.00 0.00 0.00 4.63
903 1355 2.820197 GCACCAGCATCATCATCATCAT 59.180 45.455 0.00 0.00 41.58 2.45
904 1356 3.119814 GCACCAGCATCATCATCATCATC 60.120 47.826 0.00 0.00 41.58 2.92
905 1357 4.072131 CACCAGCATCATCATCATCATCA 58.928 43.478 0.00 0.00 0.00 3.07
973 1425 1.918800 GTACAGGGCTGGGGAGTGT 60.919 63.158 0.00 0.00 34.19 3.55
993 1445 2.101380 GCGCGTGTGTGTTGGTTT 59.899 55.556 8.43 0.00 0.00 3.27
1031 1483 4.021925 GGGAGAAGCAGCACCGGT 62.022 66.667 0.00 0.00 0.00 5.28
1044 1496 1.602237 ACCGGTAGCAATGGTGGAG 59.398 57.895 4.49 0.00 33.91 3.86
1119 1571 1.153997 GACTCTGGCGTCGTCTTCC 60.154 63.158 0.00 0.00 0.00 3.46
1247 1699 0.560688 GAGGAGGATGAGGAGGAGGT 59.439 60.000 0.00 0.00 0.00 3.85
1248 1700 0.264359 AGGAGGATGAGGAGGAGGTG 59.736 60.000 0.00 0.00 0.00 4.00
1249 1701 0.762461 GGAGGATGAGGAGGAGGTGG 60.762 65.000 0.00 0.00 0.00 4.61
1250 1702 0.263172 GAGGATGAGGAGGAGGTGGA 59.737 60.000 0.00 0.00 0.00 4.02
1251 1703 0.264359 AGGATGAGGAGGAGGTGGAG 59.736 60.000 0.00 0.00 0.00 3.86
1252 1704 0.762461 GGATGAGGAGGAGGTGGAGG 60.762 65.000 0.00 0.00 0.00 4.30
1253 1705 0.762461 GATGAGGAGGAGGTGGAGGG 60.762 65.000 0.00 0.00 0.00 4.30
1269 1724 2.597903 GGGGGAGAAGGGCATCAC 59.402 66.667 0.00 0.00 0.00 3.06
1284 1739 0.671781 ATCACGTGCTGGCTCAGTTC 60.672 55.000 11.67 0.00 33.43 3.01
1290 1745 2.331132 GCTGGCTCAGTTCCTGCAC 61.331 63.158 6.11 0.00 44.71 4.57
1397 1852 2.509336 CGACATGGACGGCCTGAC 60.509 66.667 9.82 3.90 34.31 3.51
1758 2213 2.821366 GGCTCCGACTCGTACCGA 60.821 66.667 0.00 0.00 0.00 4.69
1770 2225 1.521681 GTACCGAGGCATGCTGGTC 60.522 63.158 25.70 16.04 35.93 4.02
2025 2480 1.194781 TGAGCAGGGTGGAGGAAGTC 61.195 60.000 0.00 0.00 0.00 3.01
2094 2549 0.179089 CGCAGAAGATGGAGGAGGTG 60.179 60.000 0.00 0.00 0.00 4.00
2487 2942 4.699522 AAGTCCTTCCGGGTGCGC 62.700 66.667 0.00 0.00 36.25 6.09
2550 3005 1.668419 GGAACCGGGTCATCTTCATG 58.332 55.000 23.64 0.00 0.00 3.07
2838 3299 2.307686 TCCCTGACACCCATTTCTTACC 59.692 50.000 0.00 0.00 0.00 2.85
2844 3305 4.044065 TGACACCCATTTCTTACCCAGATT 59.956 41.667 0.00 0.00 0.00 2.40
2845 3306 4.600062 ACACCCATTTCTTACCCAGATTC 58.400 43.478 0.00 0.00 0.00 2.52
2894 3363 9.642327 TTAGCGTTAGTAGTACATTTGATTTGA 57.358 29.630 2.52 0.00 0.00 2.69
2916 3385 6.233434 TGATGTCCATAGTTTCTGCATATCC 58.767 40.000 0.00 0.00 0.00 2.59
2924 3393 4.458397 AGTTTCTGCATATCCACATCCAG 58.542 43.478 0.00 0.00 0.00 3.86
2932 3401 2.581216 ATCCACATCCAGCCATCATC 57.419 50.000 0.00 0.00 0.00 2.92
2952 3421 2.002586 CGTGATTCCCTTGTGCTGTAG 58.997 52.381 0.00 0.00 0.00 2.74
2953 3422 2.612972 CGTGATTCCCTTGTGCTGTAGT 60.613 50.000 0.00 0.00 0.00 2.73
2954 3423 3.368013 CGTGATTCCCTTGTGCTGTAGTA 60.368 47.826 0.00 0.00 0.00 1.82
2955 3424 4.680708 CGTGATTCCCTTGTGCTGTAGTAT 60.681 45.833 0.00 0.00 0.00 2.12
2973 3442 8.479313 TGTAGTATATTGCAACTTCAGTGAAG 57.521 34.615 27.66 27.66 44.37 3.02
2985 3454 5.938883 CTTCAGTGAAGTTCAAGTTTTGC 57.061 39.130 22.48 0.00 35.21 3.68
2998 3467 4.402155 TCAAGTTTTGCCATCAGTCTTGTT 59.598 37.500 0.00 0.00 34.43 2.83
3000 3469 5.343307 AGTTTTGCCATCAGTCTTGTTTT 57.657 34.783 0.00 0.00 0.00 2.43
3001 3470 5.111293 AGTTTTGCCATCAGTCTTGTTTTG 58.889 37.500 0.00 0.00 0.00 2.44
3006 3475 4.232221 GCCATCAGTCTTGTTTTGTGATG 58.768 43.478 4.04 4.04 42.72 3.07
3020 3489 1.211212 TGTGATGATCAGCCCTTGGAG 59.789 52.381 8.78 0.00 0.00 3.86
3030 3499 2.755103 CAGCCCTTGGAGGTTGTAAATC 59.245 50.000 0.00 0.00 33.71 2.17
3031 3500 2.378547 AGCCCTTGGAGGTTGTAAATCA 59.621 45.455 0.00 0.00 31.93 2.57
3032 3501 2.755103 GCCCTTGGAGGTTGTAAATCAG 59.245 50.000 0.00 0.00 31.93 2.90
3123 3613 7.342799 AGCAAATATATCCAAACACACTCCATT 59.657 33.333 0.00 0.00 0.00 3.16
3125 3615 7.587037 AATATATCCAAACACACTCCATTGG 57.413 36.000 0.00 0.00 42.92 3.16
3126 3616 2.746279 TCCAAACACACTCCATTGGT 57.254 45.000 1.86 0.00 42.32 3.67
3168 3665 3.072476 GCAGAGAGCAAGTGGGGA 58.928 61.111 0.00 0.00 44.79 4.81
3180 3677 2.954318 CAAGTGGGGATTATGAGCAAGG 59.046 50.000 0.00 0.00 0.00 3.61
3181 3678 1.496429 AGTGGGGATTATGAGCAAGGG 59.504 52.381 0.00 0.00 0.00 3.95
3191 3688 1.398692 TGAGCAAGGGGACAAACAAC 58.601 50.000 0.00 0.00 0.00 3.32
3273 3777 6.407202 ACAAGAACATGTTGTCCTACTATCC 58.593 40.000 17.58 0.00 32.53 2.59
3274 3778 5.263968 AGAACATGTTGTCCTACTATCCG 57.736 43.478 17.58 0.00 0.00 4.18
3336 3845 1.210234 TCCCGTGATGCATCAAGATGT 59.790 47.619 34.90 0.00 40.80 3.06
3362 3871 1.000396 AACCTCTCCAGCAATGGCC 60.000 57.895 0.00 0.00 42.56 5.36
3416 4087 5.684704 CTCTGTGGCTCAAATTTATCCCTA 58.315 41.667 0.00 0.00 0.00 3.53
3431 4102 0.598680 CCCTAGAGCCAAAGCGATCG 60.599 60.000 11.69 11.69 46.67 3.69
3432 4103 0.385751 CCTAGAGCCAAAGCGATCGA 59.614 55.000 21.57 0.00 46.67 3.59
3481 4154 7.609056 AGCAATGCTGAATTAGTGAATTTTCT 58.391 30.769 7.07 0.00 37.57 2.52
3487 4179 7.121168 TGCTGAATTAGTGAATTTTCTAGTGGG 59.879 37.037 0.00 0.00 35.33 4.61
3494 4186 6.133356 AGTGAATTTTCTAGTGGGTTTGGAA 58.867 36.000 0.00 0.00 0.00 3.53
3520 4216 4.469657 TGCTTACTTGGTCCATCTTTTGT 58.530 39.130 0.00 0.00 0.00 2.83
3528 4224 5.413309 TGGTCCATCTTTTGTTTGTTGTT 57.587 34.783 0.00 0.00 0.00 2.83
3529 4225 5.174395 TGGTCCATCTTTTGTTTGTTGTTG 58.826 37.500 0.00 0.00 0.00 3.33
3530 4226 5.175127 GGTCCATCTTTTGTTTGTTGTTGT 58.825 37.500 0.00 0.00 0.00 3.32
3537 4233 9.687717 CATCTTTTGTTTGTTGTTGTTAATGAC 57.312 29.630 0.00 0.00 0.00 3.06
3577 4273 6.289834 TCATTTGCAGTGAACATCCATTTTT 58.710 32.000 0.00 0.00 0.00 1.94
3643 4340 1.006220 TGCAGCACTGGACGTACTG 60.006 57.895 2.65 2.65 39.55 2.74
3668 4367 9.511272 TGTAGTACAGAGTCTGAAAATACAGTA 57.489 33.333 26.86 9.00 38.79 2.74
3669 4368 9.991388 GTAGTACAGAGTCTGAAAATACAGTAG 57.009 37.037 26.86 0.00 38.79 2.57
3670 4369 8.638629 AGTACAGAGTCTGAAAATACAGTAGT 57.361 34.615 26.86 5.28 38.79 2.73
3671 4370 9.736414 AGTACAGAGTCTGAAAATACAGTAGTA 57.264 33.333 26.86 0.80 38.79 1.82
3712 4411 6.017109 GTCTGCTGAAACAATGACTAGGAAAA 60.017 38.462 0.00 0.00 0.00 2.29
3713 4412 6.205464 TCTGCTGAAACAATGACTAGGAAAAG 59.795 38.462 0.00 0.00 0.00 2.27
3714 4413 5.241506 TGCTGAAACAATGACTAGGAAAAGG 59.758 40.000 0.00 0.00 0.00 3.11
3715 4414 5.473504 GCTGAAACAATGACTAGGAAAAGGA 59.526 40.000 0.00 0.00 0.00 3.36
3717 4416 6.837312 TGAAACAATGACTAGGAAAAGGAGA 58.163 36.000 0.00 0.00 0.00 3.71
3718 4417 7.287061 TGAAACAATGACTAGGAAAAGGAGAA 58.713 34.615 0.00 0.00 0.00 2.87
3726 4443 9.844257 ATGACTAGGAAAAGGAGAATATTTCAG 57.156 33.333 0.00 0.00 35.32 3.02
3732 4449 6.350445 GGAAAAGGAGAATATTTCAGCAAGCA 60.350 38.462 0.00 0.00 35.32 3.91
3735 4452 6.388435 AGGAGAATATTTCAGCAAGCATTC 57.612 37.500 0.00 0.00 0.00 2.67
3744 4461 2.429971 TCAGCAAGCATTCCAAACAACA 59.570 40.909 0.00 0.00 0.00 3.33
3745 4462 3.118847 TCAGCAAGCATTCCAAACAACAA 60.119 39.130 0.00 0.00 0.00 2.83
3758 4475 6.503524 TCCAAACAACAAAAGAGCAGAATAC 58.496 36.000 0.00 0.00 0.00 1.89
3761 4478 3.826729 ACAACAAAAGAGCAGAATACCCC 59.173 43.478 0.00 0.00 0.00 4.95
3784 4501 1.262950 TGCAAACAACAGGATTCGTCG 59.737 47.619 0.00 0.00 0.00 5.12
3801 4518 0.522180 TCGAAGGACGCAGAGAGAAC 59.478 55.000 0.00 0.00 42.26 3.01
3802 4519 0.794981 CGAAGGACGCAGAGAGAACG 60.795 60.000 0.00 0.00 34.51 3.95
3809 4526 1.332178 CGCAGAGAGAACGAACAGAC 58.668 55.000 0.00 0.00 0.00 3.51
3810 4527 1.068885 CGCAGAGAGAACGAACAGACT 60.069 52.381 0.00 0.00 0.00 3.24
3811 4528 2.159824 CGCAGAGAGAACGAACAGACTA 59.840 50.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.677199 TCATGACTTGAGTTCGTCTGC 58.323 47.619 0.00 0.00 0.00 4.26
20 21 2.169978 CCCTGCTCTGATCATGACTTGA 59.830 50.000 0.00 0.00 39.12 3.02
21 22 2.562635 CCCTGCTCTGATCATGACTTG 58.437 52.381 0.00 0.00 0.00 3.16
22 23 1.134159 GCCCTGCTCTGATCATGACTT 60.134 52.381 0.00 0.00 0.00 3.01
23 24 0.469070 GCCCTGCTCTGATCATGACT 59.531 55.000 0.00 0.00 0.00 3.41
24 25 0.879400 CGCCCTGCTCTGATCATGAC 60.879 60.000 0.00 0.00 0.00 3.06
157 170 1.065928 GATGCATGGAAGCTGCTGC 59.934 57.895 2.46 7.62 40.34 5.25
275 300 0.904649 TGTGAGGGCATCATCGAGTT 59.095 50.000 4.69 0.00 40.92 3.01
305 330 7.796622 GTGATTATGCACTAGCCCATTATGGG 61.797 46.154 25.23 25.23 46.52 4.00
397 429 2.178764 TGGGAGCTAGTGATCAGGAGAT 59.821 50.000 0.00 0.00 37.13 2.75
526 560 6.096036 CACAACCACAACTTGTTTACATCAA 58.904 36.000 0.00 0.00 29.02 2.57
531 565 4.082679 TGTCCACAACCACAACTTGTTTAC 60.083 41.667 0.00 0.00 29.02 2.01
532 566 4.079970 TGTCCACAACCACAACTTGTTTA 58.920 39.130 0.00 0.00 29.02 2.01
533 567 2.894126 TGTCCACAACCACAACTTGTTT 59.106 40.909 0.00 0.00 29.02 2.83
534 568 2.520069 TGTCCACAACCACAACTTGTT 58.480 42.857 0.00 0.00 29.02 2.83
535 569 2.208132 TGTCCACAACCACAACTTGT 57.792 45.000 0.00 0.00 31.80 3.16
536 570 2.223782 CCATGTCCACAACCACAACTTG 60.224 50.000 0.00 0.00 0.00 3.16
537 571 2.031120 CCATGTCCACAACCACAACTT 58.969 47.619 0.00 0.00 0.00 2.66
538 572 1.214175 TCCATGTCCACAACCACAACT 59.786 47.619 0.00 0.00 0.00 3.16
539 573 1.608590 CTCCATGTCCACAACCACAAC 59.391 52.381 0.00 0.00 0.00 3.32
540 574 1.492599 TCTCCATGTCCACAACCACAA 59.507 47.619 0.00 0.00 0.00 3.33
541 575 1.135960 TCTCCATGTCCACAACCACA 58.864 50.000 0.00 0.00 0.00 4.17
542 576 2.496899 ATCTCCATGTCCACAACCAC 57.503 50.000 0.00 0.00 0.00 4.16
543 577 3.524095 AAATCTCCATGTCCACAACCA 57.476 42.857 0.00 0.00 0.00 3.67
544 578 3.056607 CCAAAATCTCCATGTCCACAACC 60.057 47.826 0.00 0.00 0.00 3.77
570 604 2.610546 TTGCTGCCTGCTCCCCTA 60.611 61.111 0.00 0.00 43.37 3.53
575 609 0.679002 TGGAATCTTGCTGCCTGCTC 60.679 55.000 0.00 0.00 43.37 4.26
636 1083 3.511477 TCTGTCTTCTTGTTAGCCTCCT 58.489 45.455 0.00 0.00 0.00 3.69
637 1084 3.963428 TCTGTCTTCTTGTTAGCCTCC 57.037 47.619 0.00 0.00 0.00 4.30
639 1086 4.774726 TCTGATCTGTCTTCTTGTTAGCCT 59.225 41.667 0.00 0.00 0.00 4.58
668 1117 1.373497 CGCACCTGTCCTCACTCAC 60.373 63.158 0.00 0.00 0.00 3.51
669 1118 2.574018 CCGCACCTGTCCTCACTCA 61.574 63.158 0.00 0.00 0.00 3.41
670 1119 2.262915 CCGCACCTGTCCTCACTC 59.737 66.667 0.00 0.00 0.00 3.51
671 1120 3.314331 CCCGCACCTGTCCTCACT 61.314 66.667 0.00 0.00 0.00 3.41
815 1266 2.572290 ACTATTAATGGAGGCGTTGGC 58.428 47.619 5.74 0.00 38.90 4.52
862 1313 0.181824 GAGTAGGAGGAGCTCGGAGT 59.818 60.000 7.83 0.00 0.00 3.85
864 1315 1.146485 CGAGTAGGAGGAGCTCGGA 59.854 63.158 7.83 0.00 45.60 4.55
868 1319 1.755008 GGTGCGAGTAGGAGGAGCT 60.755 63.158 0.00 0.00 0.00 4.09
869 1320 2.010582 CTGGTGCGAGTAGGAGGAGC 62.011 65.000 0.00 0.00 0.00 4.70
903 1355 0.670546 GCTCGCAGCTAACCAACTGA 60.671 55.000 0.00 0.00 38.45 3.41
904 1356 1.790387 GCTCGCAGCTAACCAACTG 59.210 57.895 0.00 0.00 38.45 3.16
905 1357 4.285851 GCTCGCAGCTAACCAACT 57.714 55.556 0.00 0.00 38.45 3.16
981 1433 0.960861 TGGCGACAAACCAACACACA 60.961 50.000 0.00 0.00 37.44 3.72
1008 1460 0.463474 GTGCTGCTTCTCCCATCTCC 60.463 60.000 0.00 0.00 0.00 3.71
1031 1483 0.543277 CTCTGCCTCCACCATTGCTA 59.457 55.000 0.00 0.00 0.00 3.49
1236 1688 2.780693 CCCTCCACCTCCTCCTCA 59.219 66.667 0.00 0.00 0.00 3.86
1252 1704 2.597903 GTGATGCCCTTCTCCCCC 59.402 66.667 0.00 0.00 0.00 5.40
1253 1705 2.190578 CGTGATGCCCTTCTCCCC 59.809 66.667 0.00 0.00 0.00 4.81
1269 1724 2.345244 AGGAACTGAGCCAGCACG 59.655 61.111 2.50 0.00 37.18 5.34
1323 1778 4.994471 CTGCACTGCGAGGCCACA 62.994 66.667 5.01 0.00 0.00 4.17
1509 1964 2.047179 AAGAACCGCTTCTCGCCC 60.047 61.111 0.00 0.00 35.52 6.13
1756 2211 2.110967 CCTTGACCAGCATGCCTCG 61.111 63.158 15.66 4.23 31.97 4.63
1758 2213 2.362120 GCCTTGACCAGCATGCCT 60.362 61.111 15.66 0.00 31.97 4.75
1977 2432 2.044252 ACGGCGAAGGAGGAGCTA 60.044 61.111 16.62 0.00 0.00 3.32
2019 2474 3.441572 CCACCATGAACATCTTGACTTCC 59.558 47.826 0.00 0.00 0.00 3.46
2025 2480 2.422479 CTGCTCCACCATGAACATCTTG 59.578 50.000 0.00 0.00 0.00 3.02
2550 3005 4.681978 AGGTTGTCGCCGTCCTGC 62.682 66.667 0.00 0.00 0.00 4.85
2590 3045 4.016706 CTTGCCCTCGGACGGGTT 62.017 66.667 12.27 0.00 46.47 4.11
2838 3299 4.948004 GGGGTGTTTAGTAAAGGAATCTGG 59.052 45.833 0.00 0.00 0.00 3.86
2844 3305 5.649970 TCAAAGGGGTGTTTAGTAAAGGA 57.350 39.130 0.00 0.00 0.00 3.36
2845 3306 6.911250 AATCAAAGGGGTGTTTAGTAAAGG 57.089 37.500 0.00 0.00 0.00 3.11
2894 3363 6.000219 GTGGATATGCAGAAACTATGGACAT 59.000 40.000 0.00 0.00 0.00 3.06
2916 3385 0.942252 CACGATGATGGCTGGATGTG 59.058 55.000 0.00 0.00 0.00 3.21
2924 3393 1.605710 CAAGGGAATCACGATGATGGC 59.394 52.381 0.00 0.00 37.15 4.40
2932 3401 2.002586 CTACAGCACAAGGGAATCACG 58.997 52.381 0.00 0.00 0.00 4.35
2973 3442 4.574599 AGACTGATGGCAAAACTTGAAC 57.425 40.909 0.00 0.00 0.00 3.18
2985 3454 5.694231 TCATCACAAAACAAGACTGATGG 57.306 39.130 6.19 0.00 39.06 3.51
2998 3467 2.041485 TCCAAGGGCTGATCATCACAAA 59.959 45.455 0.97 0.00 0.00 2.83
3000 3469 1.211212 CTCCAAGGGCTGATCATCACA 59.789 52.381 0.97 0.00 0.00 3.58
3001 3470 1.476471 CCTCCAAGGGCTGATCATCAC 60.476 57.143 0.00 0.00 0.00 3.06
3006 3475 0.329596 ACAACCTCCAAGGGCTGATC 59.670 55.000 0.00 0.00 40.58 2.92
3020 3489 4.584327 AACAAGCACCTGATTTACAACC 57.416 40.909 0.00 0.00 0.00 3.77
3030 3499 3.144506 AGATGTCTGAAACAAGCACCTG 58.855 45.455 0.00 0.00 42.37 4.00
3031 3500 3.498774 AGATGTCTGAAACAAGCACCT 57.501 42.857 0.00 0.00 42.37 4.00
3032 3501 3.854784 GCAAGATGTCTGAAACAAGCACC 60.855 47.826 0.00 0.00 42.37 5.01
3125 3615 5.992217 AGTCTTGACAAAACTGGTGAGATAC 59.008 40.000 0.00 0.00 0.00 2.24
3126 3616 5.991606 CAGTCTTGACAAAACTGGTGAGATA 59.008 40.000 12.98 0.00 37.38 1.98
3168 3665 4.046286 TGTTTGTCCCCTTGCTCATAAT 57.954 40.909 0.00 0.00 0.00 1.28
3180 3677 4.154737 GGTAGTTAATCCGTTGTTTGTCCC 59.845 45.833 0.00 0.00 0.00 4.46
3181 3678 4.756135 TGGTAGTTAATCCGTTGTTTGTCC 59.244 41.667 0.00 0.00 0.00 4.02
3191 3688 1.931172 CCGCAGTTGGTAGTTAATCCG 59.069 52.381 0.00 0.00 0.00 4.18
3273 3777 6.339587 AGATAAAGAAGGAATCTCTAGGCG 57.660 41.667 0.00 0.00 37.42 5.52
3274 3778 7.659799 GGAAAGATAAAGAAGGAATCTCTAGGC 59.340 40.741 0.00 0.00 37.42 3.93
3336 3845 1.367471 CTGGAGAGGTTCACGTGCA 59.633 57.895 11.67 0.00 0.00 4.57
3362 3871 4.125703 CAAACAGCTAGAAGCCTGGATAG 58.874 47.826 0.00 0.00 43.77 2.08
3416 4087 0.531532 CCATCGATCGCTTTGGCTCT 60.532 55.000 11.09 0.00 36.09 4.09
3431 4102 2.673368 GACACGTGAACCAAGATCCATC 59.327 50.000 25.01 0.00 0.00 3.51
3432 4103 2.303022 AGACACGTGAACCAAGATCCAT 59.697 45.455 25.01 0.00 0.00 3.41
3481 4154 3.737559 AGCATGATTCCAAACCCACTA 57.262 42.857 0.00 0.00 0.00 2.74
3487 4179 5.391312 ACCAAGTAAGCATGATTCCAAAC 57.609 39.130 0.00 0.00 0.00 2.93
3494 4186 4.785346 AGATGGACCAAGTAAGCATGAT 57.215 40.909 0.00 0.00 0.00 2.45
3537 4233 6.157904 TGCAAATGAATATGGACAAGTGTTG 58.842 36.000 0.00 0.00 0.00 3.33
3623 4320 2.048222 TACGTCCAGTGCTGCAGC 60.048 61.111 31.89 31.89 42.50 5.25
3643 4340 9.991388 CTACTGTATTTTCAGACTCTGTACTAC 57.009 37.037 5.94 5.58 38.63 2.73
3668 4367 5.068460 GCAGACATGTCCTCTGTTAGATACT 59.932 44.000 22.21 0.00 37.96 2.12
3669 4368 5.068460 AGCAGACATGTCCTCTGTTAGATAC 59.932 44.000 22.21 0.46 37.96 2.24
3670 4369 5.068329 CAGCAGACATGTCCTCTGTTAGATA 59.932 44.000 25.29 0.00 37.96 1.98
3671 4370 4.029520 AGCAGACATGTCCTCTGTTAGAT 58.970 43.478 22.21 0.00 37.96 1.98
3684 4383 4.761235 AGTCATTGTTTCAGCAGACATG 57.239 40.909 0.00 0.00 0.00 3.21
3712 4411 5.301298 GGAATGCTTGCTGAAATATTCTCCT 59.699 40.000 0.00 0.00 0.00 3.69
3713 4412 5.068198 TGGAATGCTTGCTGAAATATTCTCC 59.932 40.000 0.00 0.00 0.00 3.71
3714 4413 6.140303 TGGAATGCTTGCTGAAATATTCTC 57.860 37.500 0.00 0.00 0.00 2.87
3715 4414 6.534475 TTGGAATGCTTGCTGAAATATTCT 57.466 33.333 0.00 0.00 0.00 2.40
3717 4416 6.465948 TGTTTGGAATGCTTGCTGAAATATT 58.534 32.000 0.00 0.00 0.00 1.28
3718 4417 6.040209 TGTTTGGAATGCTTGCTGAAATAT 57.960 33.333 0.00 0.00 0.00 1.28
3726 4443 4.332268 TCTTTTGTTGTTTGGAATGCTTGC 59.668 37.500 0.00 0.00 0.00 4.01
3732 4449 5.596836 TCTGCTCTTTTGTTGTTTGGAAT 57.403 34.783 0.00 0.00 0.00 3.01
3735 4452 5.691754 GGTATTCTGCTCTTTTGTTGTTTGG 59.308 40.000 0.00 0.00 0.00 3.28
3781 4498 0.522180 TTCTCTCTGCGTCCTTCGAC 59.478 55.000 0.00 0.00 42.86 4.20
3784 4501 0.522180 TCGTTCTCTCTGCGTCCTTC 59.478 55.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.