Multiple sequence alignment - TraesCS1A01G206400

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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 TraesCS1A01G206400 chr1A 100.000 3680 0 0 1 3680 368803532 368799853 0.000000e+00 6796
1 TraesCS1A01G206400 chr1D 94.262 2614 109 18 1 2601 295542605 295540020 0.000000e+00 3958
2 TraesCS1A01G206400 chr1D 86.909 550 42 12 3067 3609 295538938 295538412 1.140000e-164 590
3 TraesCS1A01G206400 chr1D 92.459 305 15 2 2758 3054 295539296 295538992 2.630000e-116 429
4 TraesCS1A01G206400 chr1D 91.573 178 10 2 2588 2761 295539508 295539332 1.320000e-59 241
5 TraesCS1A01G206400 chr1B 95.231 1929 77 7 3 1929 397058099 397056184 0.000000e+00 3038
6 TraesCS1A01G206400 chr1B 92.743 813 42 6 1965 2761 397056072 397055261 0.000000e+00 1158
7 TraesCS1A01G206400 chr1B 86.864 944 87 31 2760 3680 397055223 397054294 0.000000e+00 1022
8 TraesCS1A01G206400 chr4B 87.535 361 41 4 1216 1574 660661774 660662132 7.350000e-112 414
9 TraesCS1A01G206400 chr4B 82.900 269 41 4 1665 1933 660662534 660662797 1.710000e-58 237
10 TraesCS1A01G206400 chr5A 87.500 360 37 7 1216 1574 700663499 700663851 3.420000e-110 409
11 TraesCS1A01G206400 chr5A 84.615 260 37 2 1674 1933 700664285 700664541 4.720000e-64 255
12 TraesCS1A01G206400 chrUn 86.721 369 41 5 1209 1574 110658143 110658506 1.590000e-108 403
13 TraesCS1A01G206400 chrUn 83.206 262 41 2 1672 1933 110658907 110659165 1.710000e-58 237
14 TraesCS1A01G206400 chr5B 92.473 93 5 2 2758 2849 703484620 703484529 8.290000e-27 132


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 TraesCS1A01G206400 chr1A 368799853 368803532 3679 True 6796.000000 6796 100.000000 1 3680 1 chr1A.!!$R1 3679
1 TraesCS1A01G206400 chr1D 295538412 295542605 4193 True 1304.500000 3958 91.300750 1 3609 4 chr1D.!!$R1 3608
2 TraesCS1A01G206400 chr1B 397054294 397058099 3805 True 1739.333333 3038 91.612667 3 3680 3 chr1B.!!$R1 3677
3 TraesCS1A01G206400 chr4B 660661774 660662797 1023 False 325.500000 414 85.217500 1216 1933 2 chr4B.!!$F1 717
4 TraesCS1A01G206400 chr5A 700663499 700664541 1042 False 332.000000 409 86.057500 1216 1933 2 chr5A.!!$F1 717
5 TraesCS1A01G206400 chrUn 110658143 110659165 1022 False 320.000000 403 84.963500 1209 1933 2 chrUn.!!$F1 724

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
842 844 0.103937 CACGCATCTCCTCTCCCTTC 59.896 60.0 0.0 0.0 0.00 3.46 F
1942 2316 0.034089 AGGTAAGCATCCACTTGGCC 60.034 55.0 0.0 0.0 34.44 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2543 0.449388 CGCTTCAGATGGAACTTGCC 59.551 55.0 0.0 0.0 0.0 4.52 R
3270 4382 0.034670 GAAGCCCAGGTCAAGCTCAT 60.035 55.0 0.0 0.0 35.3 2.90 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
34 35 3.450115 GTCCCCCGACCTGACGAG 61.450 72.222 0.00 0.00 32.40 4.18
107 108 1.672356 CGGCACCTCCACCTTGAAG 60.672 63.158 0.00 0.00 34.01 3.02
224 225 3.638484 TCACAGCATACATATTCGTCGG 58.362 45.455 0.00 0.00 0.00 4.79
271 272 4.008035 GCGATGGCTGGTACGTAC 57.992 61.111 17.56 17.56 35.83 3.67
272 273 1.942712 GCGATGGCTGGTACGTACG 60.943 63.158 18.98 15.01 35.83 3.67
273 274 1.430632 CGATGGCTGGTACGTACGT 59.569 57.895 25.98 25.98 0.00 3.57
282 283 2.002586 TGGTACGTACGTGCTAGAGAC 58.997 52.381 30.65 18.99 0.00 3.36
304 305 1.413077 AGTATAGAAGGGTTCAGGCGC 59.587 52.381 0.00 0.00 0.00 6.53
509 510 3.071479 GTCGACCAAAGACCAATTAGCA 58.929 45.455 3.51 0.00 32.78 3.49
510 511 3.125316 GTCGACCAAAGACCAATTAGCAG 59.875 47.826 3.51 0.00 32.78 4.24
556 557 3.849951 CCGGTGAGATGGGGTCGG 61.850 72.222 0.00 0.00 0.00 4.79
707 709 1.271102 CGGCAGAGTAGAATAGCCTCC 59.729 57.143 0.00 0.00 43.07 4.30
715 717 5.362430 AGAGTAGAATAGCCTCCTCTTGTTG 59.638 44.000 0.00 0.00 0.00 3.33
727 729 0.746204 TCTTGTTGCAGCCACGACAA 60.746 50.000 8.63 8.63 40.77 3.18
842 844 0.103937 CACGCATCTCCTCTCCCTTC 59.896 60.000 0.00 0.00 0.00 3.46
865 867 2.772287 CTCACTTTCCCCTCACTGTTC 58.228 52.381 0.00 0.00 0.00 3.18
1025 1027 1.076632 ATCGGACGAAGCCCTCTCT 60.077 57.895 0.00 0.00 0.00 3.10
1159 1161 3.217743 CCGTCTCCGCCTACCTCC 61.218 72.222 0.00 0.00 0.00 4.30
1602 1813 1.134401 TGCTCGATCCAACCTCCAATC 60.134 52.381 0.00 0.00 0.00 2.67
1615 1826 2.422093 CCTCCAATCCCTAGCTGTTTCC 60.422 54.545 0.00 0.00 0.00 3.13
1619 1830 1.289160 ATCCCTAGCTGTTTCCTGCA 58.711 50.000 0.00 0.00 37.95 4.41
1942 2316 0.034089 AGGTAAGCATCCACTTGGCC 60.034 55.000 0.00 0.00 34.44 5.36
1943 2317 0.323360 GGTAAGCATCCACTTGGCCA 60.323 55.000 0.00 0.00 34.44 5.36
1948 2322 1.687612 CATCCACTTGGCCAGGAGT 59.312 57.895 23.57 13.61 34.40 3.85
1963 2337 1.899814 AGGAGTACATTGCCTCACGAA 59.100 47.619 0.00 0.00 0.00 3.85
1996 2448 9.552114 CATGTTCAGAACTTCAGATAACAATTC 57.448 33.333 14.51 0.00 0.00 2.17
2007 2459 5.690409 TCAGATAACAATTCGGCTCGATTAC 59.310 40.000 0.00 0.00 35.23 1.89
2011 2463 3.448686 ACAATTCGGCTCGATTACTCAG 58.551 45.455 0.00 0.00 35.23 3.35
2090 2543 3.876198 GGCTGTATGGCCGCAACG 61.876 66.667 0.00 0.00 42.82 4.10
2390 2843 2.033602 GGAACTTGTGGGACCCCG 59.966 66.667 8.45 0.00 39.42 5.73
2537 2997 1.217244 GAGTGGTACCGTCGCCATT 59.783 57.895 7.57 0.00 37.09 3.16
2541 3001 1.520787 GGTACCGTCGCCATTCCTG 60.521 63.158 0.00 0.00 0.00 3.86
2543 3003 0.108520 GTACCGTCGCCATTCCTGAA 60.109 55.000 0.00 0.00 0.00 3.02
2559 3019 3.261897 TCCTGAATGTGAACCTCTTCTCC 59.738 47.826 0.00 0.00 0.00 3.71
2575 3035 0.508641 CTCCGACTTCACTTGTTGCG 59.491 55.000 0.00 0.00 0.00 4.85
2586 3046 5.029650 TCACTTGTTGCGTTGATATGTTC 57.970 39.130 0.00 0.00 0.00 3.18
2621 3609 6.263412 ACTCCCATCTCATCAGAAATGAAT 57.737 37.500 0.00 0.00 30.24 2.57
2688 3676 4.526262 AGGATCCATATCTAGCACTGACAC 59.474 45.833 15.82 0.00 32.29 3.67
2694 3682 0.881796 TCTAGCACTGACACGTCCTG 59.118 55.000 0.00 0.00 0.00 3.86
2740 3732 1.963464 GAAGGGCGGTACCGAATCCA 61.963 60.000 37.62 0.00 42.83 3.41
2756 3748 5.880332 CCGAATCCAAGGACAAAGATCTAAA 59.120 40.000 0.00 0.00 0.00 1.85
2819 3850 3.317711 ACAAGTGAATCATCGGTTGCAAA 59.682 39.130 0.00 0.00 0.00 3.68
2948 3987 1.147817 AGGCTGTTGAAATTGGTCCCT 59.852 47.619 0.00 0.00 0.00 4.20
2954 3993 3.396276 TGTTGAAATTGGTCCCTGGTAGA 59.604 43.478 0.00 0.00 0.00 2.59
2960 3999 0.617820 TGGTCCCTGGTAGAGGAAGC 60.618 60.000 0.00 0.00 46.33 3.86
3000 4066 1.974875 TACGTGCGCAGGGAAGAGA 60.975 57.895 31.09 8.67 0.00 3.10
3001 4067 1.529152 TACGTGCGCAGGGAAGAGAA 61.529 55.000 31.09 7.22 0.00 2.87
3002 4068 2.383527 CGTGCGCAGGGAAGAGAAC 61.384 63.158 21.95 0.00 0.00 3.01
3003 4069 1.301716 GTGCGCAGGGAAGAGAACA 60.302 57.895 12.22 0.00 0.00 3.18
3004 4070 1.301716 TGCGCAGGGAAGAGAACAC 60.302 57.895 5.66 0.00 0.00 3.32
3005 4071 1.301716 GCGCAGGGAAGAGAACACA 60.302 57.895 0.30 0.00 0.00 3.72
3006 4072 0.884704 GCGCAGGGAAGAGAACACAA 60.885 55.000 0.30 0.00 0.00 3.33
3007 4073 1.151668 CGCAGGGAAGAGAACACAAG 58.848 55.000 0.00 0.00 0.00 3.16
3008 4074 0.877743 GCAGGGAAGAGAACACAAGC 59.122 55.000 0.00 0.00 0.00 4.01
3009 4075 1.815408 GCAGGGAAGAGAACACAAGCA 60.815 52.381 0.00 0.00 0.00 3.91
3010 4076 2.575532 CAGGGAAGAGAACACAAGCAA 58.424 47.619 0.00 0.00 0.00 3.91
3011 4077 2.551459 CAGGGAAGAGAACACAAGCAAG 59.449 50.000 0.00 0.00 0.00 4.01
3012 4078 1.268079 GGGAAGAGAACACAAGCAAGC 59.732 52.381 0.00 0.00 0.00 4.01
3013 4079 1.949525 GGAAGAGAACACAAGCAAGCA 59.050 47.619 0.00 0.00 0.00 3.91
3014 4080 2.287248 GGAAGAGAACACAAGCAAGCAC 60.287 50.000 0.00 0.00 0.00 4.40
3015 4081 2.042686 AGAGAACACAAGCAAGCACA 57.957 45.000 0.00 0.00 0.00 4.57
3016 4082 2.368439 AGAGAACACAAGCAAGCACAA 58.632 42.857 0.00 0.00 0.00 3.33
3017 4083 2.098117 AGAGAACACAAGCAAGCACAAC 59.902 45.455 0.00 0.00 0.00 3.32
3018 4084 1.818060 AGAACACAAGCAAGCACAACA 59.182 42.857 0.00 0.00 0.00 3.33
3019 4085 1.919918 GAACACAAGCAAGCACAACAC 59.080 47.619 0.00 0.00 0.00 3.32
3020 4086 0.179166 ACACAAGCAAGCACAACACG 60.179 50.000 0.00 0.00 0.00 4.49
3021 4087 1.226660 ACAAGCAAGCACAACACGC 60.227 52.632 0.00 0.00 0.00 5.34
3022 4088 1.064621 CAAGCAAGCACAACACGCT 59.935 52.632 0.00 0.00 42.98 5.07
3023 4089 1.064621 AAGCAAGCACAACACGCTG 59.935 52.632 0.00 0.00 40.35 5.18
3024 4090 2.340453 AAGCAAGCACAACACGCTGG 62.340 55.000 0.00 0.00 40.35 4.85
3025 4091 2.833533 GCAAGCACAACACGCTGGA 61.834 57.895 0.00 0.00 40.35 3.86
3026 4092 1.280746 CAAGCACAACACGCTGGAG 59.719 57.895 0.00 0.00 40.35 3.86
3041 4107 0.177836 TGGAGGTGACATACGGCATG 59.822 55.000 0.00 0.00 40.78 4.06
3048 4114 1.206745 GACATACGGCATGGTCGTCG 61.207 60.000 0.00 0.00 40.97 5.12
3157 4265 3.782244 CAAGCTCTCACGCCGTGC 61.782 66.667 13.39 0.00 32.98 5.34
3268 4380 2.720605 GACGCCGGTAGGAGCTAC 59.279 66.667 1.90 0.00 41.37 3.58
3270 4382 2.898840 CGCCGGTAGGAGCTACGA 60.899 66.667 1.90 0.00 41.02 3.43
3290 4405 1.376466 GAGCTTGACCTGGGCTTCA 59.624 57.895 0.00 0.00 36.37 3.02
3298 4413 2.237143 TGACCTGGGCTTCAGTAAGATG 59.763 50.000 0.00 0.00 41.83 2.90
3305 4420 3.536570 GGCTTCAGTAAGATGGAAGTCC 58.463 50.000 0.00 0.00 40.06 3.85
3332 4447 0.395862 CAGGTCGCTCTTCCTCCCTA 60.396 60.000 0.00 0.00 30.91 3.53
3358 4473 3.753272 TCCTGAGAAAAGATTTTCCTGCG 59.247 43.478 13.12 1.83 45.84 5.18
3368 4483 2.035237 TTTTCCTGCGGACGAGGTGT 62.035 55.000 0.00 0.00 31.85 4.16
3407 4522 3.131933 CAGCACTGAATAGTAGCAGGAGT 59.868 47.826 7.49 0.00 34.74 3.85
3409 4524 3.868077 GCACTGAATAGTAGCAGGAGTTG 59.132 47.826 7.49 0.00 34.74 3.16
3410 4525 4.437239 CACTGAATAGTAGCAGGAGTTGG 58.563 47.826 7.49 0.00 34.74 3.77
3411 4526 4.081420 CACTGAATAGTAGCAGGAGTTGGT 60.081 45.833 7.49 0.00 41.25 3.67
3412 4527 4.081420 ACTGAATAGTAGCAGGAGTTGGTG 60.081 45.833 7.49 0.00 38.18 4.17
3413 4528 3.197766 TGAATAGTAGCAGGAGTTGGTGG 59.802 47.826 0.00 0.00 38.18 4.61
3414 4529 0.902531 TAGTAGCAGGAGTTGGTGGC 59.097 55.000 0.00 0.00 38.18 5.01
3415 4530 0.838122 AGTAGCAGGAGTTGGTGGCT 60.838 55.000 0.00 0.00 38.18 4.75
3416 4531 0.674895 GTAGCAGGAGTTGGTGGCTG 60.675 60.000 0.00 0.00 38.18 4.85
3417 4532 0.835971 TAGCAGGAGTTGGTGGCTGA 60.836 55.000 0.00 0.00 38.18 4.26
3418 4533 1.673665 GCAGGAGTTGGTGGCTGAG 60.674 63.158 0.00 0.00 0.00 3.35
3419 4534 1.002868 CAGGAGTTGGTGGCTGAGG 60.003 63.158 0.00 0.00 0.00 3.86
3420 4535 2.360475 GGAGTTGGTGGCTGAGGC 60.360 66.667 0.00 0.00 37.82 4.70
3421 4536 2.753029 GAGTTGGTGGCTGAGGCT 59.247 61.111 7.74 0.00 38.73 4.58
3422 4537 1.673665 GAGTTGGTGGCTGAGGCTG 60.674 63.158 7.74 0.00 38.73 4.85
3447 4570 2.680577 CAAGTTGCTTCTGAAATGGCC 58.319 47.619 0.00 0.00 0.00 5.36
3448 4571 2.298163 CAAGTTGCTTCTGAAATGGCCT 59.702 45.455 3.32 0.00 0.00 5.19
3455 4578 3.507622 GCTTCTGAAATGGCCTAGTGTTT 59.492 43.478 3.32 0.00 0.00 2.83
3472 4597 3.630312 GTGTTTGGGAGCTCACTGTTTAA 59.370 43.478 18.70 0.00 0.00 1.52
3475 4600 5.221224 TGTTTGGGAGCTCACTGTTTAATTG 60.221 40.000 18.70 0.00 0.00 2.32
3481 4606 6.543831 GGGAGCTCACTGTTTAATTGACATAT 59.456 38.462 17.19 0.00 0.00 1.78
3484 4609 9.846248 GAGCTCACTGTTTAATTGACATATTTT 57.154 29.630 9.40 0.00 0.00 1.82
3498 4623 8.934023 TTGACATATTTTCCTTTCTGGTAGTT 57.066 30.769 0.00 0.00 37.07 2.24
3507 4632 7.654022 TTCCTTTCTGGTAGTTGAATTTGTT 57.346 32.000 0.00 0.00 37.07 2.83
3509 4634 6.017440 TCCTTTCTGGTAGTTGAATTTGTTCG 60.017 38.462 0.00 0.00 37.07 3.95
3516 4641 6.762187 TGGTAGTTGAATTTGTTCGTCAAGTA 59.238 34.615 0.00 0.00 37.35 2.24
3519 4644 6.715464 AGTTGAATTTGTTCGTCAAGTAGTG 58.285 36.000 0.00 0.00 37.35 2.74
3599 4724 5.509972 CGAACTGAAAACGACACAAATTCAA 59.490 36.000 0.00 0.00 30.37 2.69
3606 4731 2.050691 CGACACAAATTCAAAAGGCCG 58.949 47.619 0.00 0.00 0.00 6.13
3626 4751 2.731654 CGTGCCAATCGAAATTGATGCA 60.732 45.455 0.26 0.00 44.25 3.96
3632 4757 5.610975 CCAATCGAAATTGATGCACAAAAC 58.389 37.500 0.26 1.69 44.25 2.43
3634 4759 3.304257 TCGAAATTGATGCACAAAACCG 58.696 40.909 5.94 8.79 42.03 4.44
3656 4781 4.495844 CGTTCCTCTTTCACAACTTGTTCC 60.496 45.833 0.00 0.00 0.00 3.62
3670 4795 2.083167 TGTTCCCAATTACGTCGACC 57.917 50.000 10.58 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 4.755507 ACGGACGAGGAGGGGGTC 62.756 72.222 0.00 0.00 0.00 4.46
197 198 5.466728 ACGAATATGTATGCTGTGATGGTTC 59.533 40.000 0.00 0.00 0.00 3.62
200 201 4.090498 CGACGAATATGTATGCTGTGATGG 59.910 45.833 0.00 0.00 0.00 3.51
250 251 2.109181 GTACCAGCCATCGCTCCC 59.891 66.667 0.00 0.00 43.95 4.30
270 271 5.297278 CCTTCTATACTTGTCTCTAGCACGT 59.703 44.000 0.00 0.00 0.00 4.49
271 272 5.278071 CCCTTCTATACTTGTCTCTAGCACG 60.278 48.000 0.00 0.00 0.00 5.34
272 273 5.595133 ACCCTTCTATACTTGTCTCTAGCAC 59.405 44.000 0.00 0.00 0.00 4.40
273 274 5.767670 ACCCTTCTATACTTGTCTCTAGCA 58.232 41.667 0.00 0.00 0.00 3.49
282 283 3.458189 CGCCTGAACCCTTCTATACTTG 58.542 50.000 0.00 0.00 0.00 3.16
472 473 0.250234 CGACAATGGCTTGGAGGAGA 59.750 55.000 0.00 0.00 36.64 3.71
509 510 0.683973 CCATTCCATCGAGCTAGCCT 59.316 55.000 12.13 0.00 0.00 4.58
510 511 0.681733 TCCATTCCATCGAGCTAGCC 59.318 55.000 12.13 1.79 0.00 3.93
569 570 4.196826 GCGCGCTAGCTTGACACG 62.197 66.667 26.67 7.82 42.32 4.49
707 709 1.159713 TGTCGTGGCTGCAACAAGAG 61.160 55.000 8.09 0.00 0.00 2.85
715 717 4.012895 CGGTGTTGTCGTGGCTGC 62.013 66.667 0.00 0.00 0.00 5.25
778 780 3.799755 CGTAAGCTGTTGGGCCGC 61.800 66.667 0.00 0.00 0.00 6.53
781 783 2.038837 GGACCGTAAGCTGTTGGGC 61.039 63.158 0.00 0.00 0.00 5.36
842 844 1.376037 GTGAGGGGAAAGTGAGCGG 60.376 63.158 0.00 0.00 0.00 5.52
865 867 3.006752 ACTCTTGGAGTTGAGAAGCTGAG 59.993 47.826 0.00 0.00 40.28 3.35
1025 1027 1.667154 CTTCGGGTCTCTCATGGCGA 61.667 60.000 0.00 0.00 0.00 5.54
1082 1084 1.680651 CTGAGCCTGTCGAGGAGGT 60.681 63.158 11.27 0.00 42.93 3.85
1144 1146 1.829096 GGAGGAGGTAGGCGGAGAC 60.829 68.421 0.00 0.00 0.00 3.36
1486 1488 0.745845 CGGTTCCAGAAGGGCATCTG 60.746 60.000 11.39 11.39 45.19 2.90
1575 1577 2.942796 TTGGATCGAGCAGCGGTGT 61.943 57.895 17.07 2.78 41.33 4.16
1576 1578 2.125552 TTGGATCGAGCAGCGGTG 60.126 61.111 10.98 10.98 41.33 4.94
1577 1579 2.125512 GTTGGATCGAGCAGCGGT 60.126 61.111 1.84 0.00 41.33 5.68
1578 1580 2.892425 GGTTGGATCGAGCAGCGG 60.892 66.667 1.84 0.00 41.33 5.52
1602 1813 0.326264 ACTGCAGGAAACAGCTAGGG 59.674 55.000 19.93 0.00 44.30 3.53
1631 1947 1.725641 AATCAGACGCGAGAATGCAA 58.274 45.000 15.93 0.00 34.15 4.08
1640 1956 0.179181 ATGCAGCAAAATCAGACGCG 60.179 50.000 3.53 3.53 0.00 6.01
1642 1958 4.039703 CCATTATGCAGCAAAATCAGACG 58.960 43.478 0.00 0.00 0.00 4.18
1763 2137 2.673200 ATGCTCCACGTCCTGGCAT 61.673 57.895 8.40 8.40 40.39 4.40
1853 2227 1.394917 CGGAAGAAGGCAAAGATGTCG 59.605 52.381 0.00 0.00 35.88 4.35
1942 2316 1.204704 TCGTGAGGCAATGTACTCCTG 59.795 52.381 0.00 0.00 32.80 3.86
1943 2317 1.557099 TCGTGAGGCAATGTACTCCT 58.443 50.000 0.00 0.00 32.80 3.69
1948 2322 4.940654 TGATGAATTTCGTGAGGCAATGTA 59.059 37.500 0.00 0.00 0.00 2.29
1963 2337 7.991084 TCTGAAGTTCTGAACATGATGAATT 57.009 32.000 21.50 5.35 0.00 2.17
1996 2448 0.525668 AACGCTGAGTAATCGAGCCG 60.526 55.000 8.37 6.85 0.00 5.52
2007 2459 2.639751 GTTGTAAACTGCAACGCTGAG 58.360 47.619 0.00 0.00 45.32 3.35
2090 2543 0.449388 CGCTTCAGATGGAACTTGCC 59.551 55.000 0.00 0.00 0.00 4.52
2150 2603 2.270205 CGGGCAGAGGCAGAACAT 59.730 61.111 0.00 0.00 43.71 2.71
2194 2647 2.361357 AGGACCGACTCCACGAGG 60.361 66.667 0.00 0.00 42.46 4.63
2378 2831 2.833227 CTTCACGGGGTCCCACAA 59.167 61.111 10.98 0.00 35.37 3.33
2537 2997 3.261897 GGAGAAGAGGTTCACATTCAGGA 59.738 47.826 0.00 0.00 34.82 3.86
2541 3001 3.056465 AGTCGGAGAAGAGGTTCACATTC 60.056 47.826 0.00 0.00 39.69 2.67
2543 3003 2.530701 AGTCGGAGAAGAGGTTCACAT 58.469 47.619 0.00 0.00 39.69 3.21
2559 3019 1.326245 TCAACGCAACAAGTGAAGTCG 59.674 47.619 0.00 0.00 0.00 4.18
2575 3035 8.824159 AGTAGAGCACATATGAACATATCAAC 57.176 34.615 10.38 0.00 42.54 3.18
2586 3046 4.525874 TGAGATGGGAGTAGAGCACATATG 59.474 45.833 0.00 0.00 0.00 1.78
2740 3732 8.166726 AGATGAAAGGTTTAGATCTTTGTCCTT 58.833 33.333 0.00 7.83 33.85 3.36
2756 3748 2.300152 TCACTTCGCTCAGATGAAAGGT 59.700 45.455 0.00 0.00 0.00 3.50
2819 3850 1.515088 CGATCGCTTGCTCTCGTGT 60.515 57.895 0.26 0.00 0.00 4.49
2898 3929 9.401058 CTCTAGTGACCTTTTATTCCAAATGAT 57.599 33.333 0.00 0.00 0.00 2.45
2899 3930 7.336931 GCTCTAGTGACCTTTTATTCCAAATGA 59.663 37.037 0.00 0.00 0.00 2.57
2948 3987 1.833630 CACTGATGGCTTCCTCTACCA 59.166 52.381 0.00 0.00 37.99 3.25
3000 4066 1.732077 CGTGTTGTGCTTGCTTGTGTT 60.732 47.619 0.00 0.00 0.00 3.32
3001 4067 0.179166 CGTGTTGTGCTTGCTTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
3002 4068 1.473857 GCGTGTTGTGCTTGCTTGTG 61.474 55.000 0.00 0.00 0.00 3.33
3003 4069 1.226660 GCGTGTTGTGCTTGCTTGT 60.227 52.632 0.00 0.00 0.00 3.16
3004 4070 1.064621 AGCGTGTTGTGCTTGCTTG 59.935 52.632 0.00 0.00 40.48 4.01
3005 4071 1.064621 CAGCGTGTTGTGCTTGCTT 59.935 52.632 0.00 0.00 41.72 3.91
3006 4072 2.717485 CAGCGTGTTGTGCTTGCT 59.283 55.556 0.00 0.00 41.72 3.91
3007 4073 2.353839 CCAGCGTGTTGTGCTTGC 60.354 61.111 0.00 0.00 41.72 4.01
3008 4074 1.280746 CTCCAGCGTGTTGTGCTTG 59.719 57.895 0.00 0.00 41.72 4.01
3009 4075 1.893808 CCTCCAGCGTGTTGTGCTT 60.894 57.895 0.00 0.00 41.72 3.91
3010 4076 2.281070 CCTCCAGCGTGTTGTGCT 60.281 61.111 0.00 0.00 45.31 4.40
3011 4077 2.591715 ACCTCCAGCGTGTTGTGC 60.592 61.111 0.00 0.00 0.00 4.57
3012 4078 1.227527 TCACCTCCAGCGTGTTGTG 60.228 57.895 0.00 0.00 32.86 3.33
3013 4079 1.227556 GTCACCTCCAGCGTGTTGT 60.228 57.895 0.00 0.00 32.86 3.32
3014 4080 0.603707 ATGTCACCTCCAGCGTGTTG 60.604 55.000 0.00 0.00 32.86 3.33
3015 4081 0.973632 TATGTCACCTCCAGCGTGTT 59.026 50.000 0.00 0.00 32.86 3.32
3016 4082 0.246635 GTATGTCACCTCCAGCGTGT 59.753 55.000 0.00 0.00 32.86 4.49
3017 4083 0.802222 CGTATGTCACCTCCAGCGTG 60.802 60.000 0.00 0.00 0.00 5.34
3018 4084 1.511305 CGTATGTCACCTCCAGCGT 59.489 57.895 0.00 0.00 0.00 5.07
3019 4085 1.226974 CCGTATGTCACCTCCAGCG 60.227 63.158 0.00 0.00 0.00 5.18
3020 4086 1.521681 GCCGTATGTCACCTCCAGC 60.522 63.158 0.00 0.00 0.00 4.85
3021 4087 0.465705 ATGCCGTATGTCACCTCCAG 59.534 55.000 0.00 0.00 0.00 3.86
3022 4088 0.177836 CATGCCGTATGTCACCTCCA 59.822 55.000 0.00 0.00 31.92 3.86
3023 4089 0.532862 CCATGCCGTATGTCACCTCC 60.533 60.000 0.00 0.00 34.87 4.30
3024 4090 0.178068 ACCATGCCGTATGTCACCTC 59.822 55.000 0.00 0.00 34.87 3.85
3025 4091 0.178068 GACCATGCCGTATGTCACCT 59.822 55.000 0.00 0.00 34.87 4.00
3026 4092 1.151777 CGACCATGCCGTATGTCACC 61.152 60.000 0.00 0.00 34.87 4.02
3105 4212 1.528129 GCAACAAGACTTCCTCCTGG 58.472 55.000 0.00 0.00 0.00 4.45
3157 4265 4.786609 GCTCGGAACTTTCAACAGAAACAG 60.787 45.833 0.00 0.00 0.00 3.16
3221 4329 0.759346 AAGAACACCTTCCTGCGACT 59.241 50.000 0.00 0.00 0.00 4.18
3268 4380 1.817099 GCCCAGGTCAAGCTCATCG 60.817 63.158 0.00 0.00 0.00 3.84
3270 4382 0.034670 GAAGCCCAGGTCAAGCTCAT 60.035 55.000 0.00 0.00 35.30 2.90
3281 4396 7.879957 GGACTTCCATCTTACTGAAGCCCAG 62.880 52.000 0.00 2.49 38.21 4.45
3290 4405 2.108970 GACGGGGACTTCCATCTTACT 58.891 52.381 0.00 0.00 37.91 2.24
3298 4413 4.452733 CTGGCGACGGGGACTTCC 62.453 72.222 0.00 0.00 0.00 3.46
3332 4447 6.239148 GCAGGAAAATCTTTTCTCAGGAAACT 60.239 38.462 13.46 0.00 44.49 2.66
3358 4473 3.343788 CTCGCCAGACACCTCGTCC 62.344 68.421 0.00 0.00 46.69 4.79
3393 4508 2.092914 GCCACCAACTCCTGCTACTATT 60.093 50.000 0.00 0.00 0.00 1.73
3407 4522 3.177884 ACCAGCCTCAGCCACCAA 61.178 61.111 0.00 0.00 41.25 3.67
3409 4524 4.729918 CCACCAGCCTCAGCCACC 62.730 72.222 0.00 0.00 41.25 4.61
3412 4527 4.666253 TTGCCACCAGCCTCAGCC 62.666 66.667 0.00 0.00 42.71 4.85
3413 4528 3.060615 CTTGCCACCAGCCTCAGC 61.061 66.667 0.00 0.00 42.71 4.26
3414 4529 1.228367 AACTTGCCACCAGCCTCAG 60.228 57.895 0.00 0.00 42.71 3.35
3415 4530 1.529010 CAACTTGCCACCAGCCTCA 60.529 57.895 0.00 0.00 42.71 3.86
3416 4531 2.924105 GCAACTTGCCACCAGCCTC 61.924 63.158 1.95 0.00 42.71 4.70
3417 4532 2.914097 GCAACTTGCCACCAGCCT 60.914 61.111 1.95 0.00 42.71 4.58
3418 4533 2.426122 GAAGCAACTTGCCACCAGCC 62.426 60.000 10.25 0.00 46.52 4.85
3419 4534 1.006922 GAAGCAACTTGCCACCAGC 60.007 57.895 10.25 0.00 46.52 4.85
3420 4535 0.313043 CAGAAGCAACTTGCCACCAG 59.687 55.000 10.25 0.00 46.52 4.00
3421 4536 0.106769 TCAGAAGCAACTTGCCACCA 60.107 50.000 10.25 0.00 46.52 4.17
3422 4537 1.032014 TTCAGAAGCAACTTGCCACC 58.968 50.000 10.25 0.35 46.52 4.61
3447 4570 2.037772 ACAGTGAGCTCCCAAACACTAG 59.962 50.000 12.15 5.32 40.84 2.57
3448 4571 2.047061 ACAGTGAGCTCCCAAACACTA 58.953 47.619 12.15 0.00 40.84 2.74
3455 4578 4.072131 GTCAATTAAACAGTGAGCTCCCA 58.928 43.478 12.15 0.00 27.51 4.37
3472 4597 9.533831 AACTACCAGAAAGGAAAATATGTCAAT 57.466 29.630 0.00 0.00 41.22 2.57
3475 4600 8.561738 TCAACTACCAGAAAGGAAAATATGTC 57.438 34.615 0.00 0.00 41.22 3.06
3481 4606 8.073467 ACAAATTCAACTACCAGAAAGGAAAA 57.927 30.769 0.00 0.00 41.22 2.29
3484 4609 6.017440 CGAACAAATTCAACTACCAGAAAGGA 60.017 38.462 0.00 0.00 36.23 3.36
3498 4623 6.314152 TGAACACTACTTGACGAACAAATTCA 59.686 34.615 0.00 0.00 38.08 2.57
3507 4632 5.001237 TCAAAGTGAACACTACTTGACGA 57.999 39.130 14.23 0.00 41.58 4.20
3509 4634 4.570772 TGCTCAAAGTGAACACTACTTGAC 59.429 41.667 14.23 12.32 41.58 3.18
3606 4731 2.599973 GTGCATCAATTTCGATTGGCAC 59.400 45.455 13.60 13.60 40.07 5.01
3626 4751 3.349022 TGTGAAAGAGGAACGGTTTTGT 58.651 40.909 0.00 0.00 0.00 2.83
3632 4757 2.943033 ACAAGTTGTGAAAGAGGAACGG 59.057 45.455 7.96 0.00 0.00 4.44
3634 4759 4.202020 GGGAACAAGTTGTGAAAGAGGAAC 60.202 45.833 9.79 0.00 0.00 3.62
3656 4781 1.087771 GGCCTGGTCGACGTAATTGG 61.088 60.000 9.92 6.16 0.00 3.16


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

AutoCloner maintained by Alex Coulton.