Multiple sequence alignment - TraesCS3A01G231900

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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 TraesCS3A01G231900 chr3A 100.000 3350 0 0 1 3350 433408078 433411427 0.000000e+00 6187.0
1 TraesCS3A01G231900 chr3D 91.917 1633 124 7 1719 3350 301848893 301847268 0.000000e+00 2278.0
2 TraesCS3A01G231900 chr3D 94.590 647 28 2 809 1455 301850196 301849557 0.000000e+00 994.0
3 TraesCS3A01G231900 chr3D 88.088 638 35 17 186 790 301850811 301850182 0.000000e+00 719.0
4 TraesCS3A01G231900 chr3D 87.455 279 22 7 1456 1721 301849249 301848971 3.250000e-80 309.0
5 TraesCS3A01G231900 chr3D 93.939 99 6 0 89 187 301850976 301850878 2.080000e-32 150.0
6 TraesCS3A01G231900 chr3B 88.107 1606 143 24 1720 3292 419122634 419124224 0.000000e+00 1864.0
7 TraesCS3A01G231900 chr3B 95.475 663 24 3 809 1471 419120034 419120690 0.000000e+00 1053.0
8 TraesCS3A01G231900 chr3B 88.748 631 37 18 186 790 419119426 419120048 0.000000e+00 741.0
9 TraesCS3A01G231900 chr3B 89.163 203 13 4 1477 1672 419121922 419122122 9.280000e-61 244.0
10 TraesCS3A01G231900 chr3B 91.398 93 8 0 95 187 419119267 419119359 9.760000e-26 128.0
11 TraesCS3A01G231900 chr4A 77.607 652 112 16 2501 3142 607311940 607312567 6.830000e-97 364.0
12 TraesCS3A01G231900 chr4A 100.000 88 0 0 3 90 602878143 602878056 2.670000e-36 163.0
13 TraesCS3A01G231900 chr4A 100.000 86 0 0 3 88 708642915 708642830 3.460000e-35 159.0
14 TraesCS3A01G231900 chr6B 77.077 650 123 19 2500 3142 518677323 518676693 5.320000e-93 351.0
15 TraesCS3A01G231900 chr6B 100.000 86 0 0 3 88 8602710 8602625 3.460000e-35 159.0
16 TraesCS3A01G231900 chr6B 72.128 531 121 20 2585 3107 569819560 569820071 5.830000e-28 135.0
17 TraesCS3A01G231900 chr7D 77.891 588 113 10 2521 3107 460527435 460528006 1.910000e-92 350.0
18 TraesCS3A01G231900 chr7D 81.250 208 37 2 2500 2705 436988137 436988344 2.070000e-37 167.0
19 TraesCS3A01G231900 chr2D 77.740 593 102 16 2564 3151 432875017 432874450 1.490000e-88 337.0
20 TraesCS3A01G231900 chr1A 78.269 543 95 9 2588 3128 296915889 296915368 8.960000e-86 327.0
21 TraesCS3A01G231900 chr1A 98.889 90 1 0 3 92 490790712 490790801 9.620000e-36 161.0
22 TraesCS3A01G231900 chr2A 80.978 368 65 5 2769 3133 536694367 536694002 1.520000e-73 287.0
23 TraesCS3A01G231900 chr1D 80.441 363 66 5 2770 3129 272537371 272537731 4.260000e-69 272.0
24 TraesCS3A01G231900 chr2B 75.325 616 119 25 2502 3110 77775335 77774746 7.130000e-67 265.0
25 TraesCS3A01G231900 chr2B 94.595 37 2 0 2654 2690 742654976 742654940 1.300000e-04 58.4
26 TraesCS3A01G231900 chr6A 97.849 93 0 1 1 91 441495538 441495630 3.460000e-35 159.0
27 TraesCS3A01G231900 chr6A 100.000 86 0 0 3 88 616607009 616607094 3.460000e-35 159.0
28 TraesCS3A01G231900 chr1B 100.000 86 0 0 3 88 148128300 148128215 3.460000e-35 159.0
29 TraesCS3A01G231900 chr1B 100.000 86 0 0 3 88 560501932 560501847 3.460000e-35 159.0
30 TraesCS3A01G231900 chr4B 94.898 98 3 2 3 99 69586384 69586480 5.790000e-33 152.0
31 TraesCS3A01G231900 chr4B 100.000 34 0 0 2647 2680 568404531 568404498 2.790000e-06 63.9


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 TraesCS3A01G231900 chr3A 433408078 433411427 3349 False 6187 6187 100.0000 1 3350 1 chr3A.!!$F1 3349
1 TraesCS3A01G231900 chr3D 301847268 301850976 3708 True 890 2278 91.1978 89 3350 5 chr3D.!!$R1 3261
2 TraesCS3A01G231900 chr3B 419119267 419124224 4957 False 806 1864 90.5782 95 3292 5 chr3B.!!$F1 3197
3 TraesCS3A01G231900 chr4A 607311940 607312567 627 False 364 364 77.6070 2501 3142 1 chr4A.!!$F1 641
4 TraesCS3A01G231900 chr6B 518676693 518677323 630 True 351 351 77.0770 2500 3142 1 chr6B.!!$R2 642
5 TraesCS3A01G231900 chr7D 460527435 460528006 571 False 350 350 77.8910 2521 3107 1 chr7D.!!$F2 586
6 TraesCS3A01G231900 chr2D 432874450 432875017 567 True 337 337 77.7400 2564 3151 1 chr2D.!!$R1 587
7 TraesCS3A01G231900 chr1A 296915368 296915889 521 True 327 327 78.2690 2588 3128 1 chr1A.!!$R1 540
8 TraesCS3A01G231900 chr2B 77774746 77775335 589 True 265 265 75.3250 2502 3110 1 chr2B.!!$R1 608

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
393 468 0.036388 GTGATCCTCTTGTTCCGGCA 60.036 55.0 0.0 0.0 0.00 5.69 F
960 1067 0.036671 GGCACTACCACCACCAGTAC 60.037 60.0 0.0 0.0 38.86 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 4384 1.612442 CCTCCCGGACCTTCTCCAA 60.612 63.158 0.73 0.0 39.39 3.53 R
2820 4980 0.653897 CGGATCTAGTCGTCGTTCGC 60.654 60.000 0.00 0.0 39.67 4.70 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
17 18 3.469370 ATCCTCTAGGGGTGGCCT 58.531 61.111 8.98 0.00 35.41 5.19
18 19 2.673023 ATCCTCTAGGGGTGGCCTA 58.327 57.895 8.98 0.00 35.41 3.93
19 20 1.180803 ATCCTCTAGGGGTGGCCTAT 58.819 55.000 8.98 0.00 35.41 2.57
20 21 0.487772 TCCTCTAGGGGTGGCCTATC 59.512 60.000 8.98 0.00 35.41 2.08
21 22 0.191064 CCTCTAGGGGTGGCCTATCA 59.809 60.000 3.32 0.00 0.00 2.15
22 23 1.343069 CTCTAGGGGTGGCCTATCAC 58.657 60.000 3.32 0.00 36.95 3.06
23 24 0.639943 TCTAGGGGTGGCCTATCACA 59.360 55.000 3.32 0.00 39.27 3.58
24 25 1.223077 TCTAGGGGTGGCCTATCACAT 59.777 52.381 3.32 0.00 39.27 3.21
25 26 2.453212 TCTAGGGGTGGCCTATCACATA 59.547 50.000 3.32 0.00 39.27 2.29
26 27 2.440494 AGGGGTGGCCTATCACATAT 57.560 50.000 3.32 0.00 39.27 1.78
27 28 3.577968 AGGGGTGGCCTATCACATATA 57.422 47.619 3.32 0.00 39.27 0.86
28 29 4.094216 AGGGGTGGCCTATCACATATAT 57.906 45.455 3.32 0.00 39.27 0.86
29 30 5.235003 AGGGGTGGCCTATCACATATATA 57.765 43.478 3.32 0.00 39.27 0.86
30 31 5.804013 AGGGGTGGCCTATCACATATATAT 58.196 41.667 3.32 0.00 39.27 0.86
31 32 6.945371 AGGGGTGGCCTATCACATATATATA 58.055 40.000 3.32 0.00 39.27 0.86
32 33 7.557283 AGGGGTGGCCTATCACATATATATAT 58.443 38.462 3.32 0.00 39.27 0.86
33 34 8.697529 AGGGGTGGCCTATCACATATATATATA 58.302 37.037 3.32 4.92 39.27 0.86
34 35 9.507381 GGGGTGGCCTATCACATATATATATAT 57.493 37.037 3.32 9.12 39.27 0.86
59 60 9.918630 ATATAATGAGGTGGTATACAACGTTAC 57.081 33.333 7.03 0.00 43.31 2.50
60 61 5.664294 ATGAGGTGGTATACAACGTTACA 57.336 39.130 7.03 2.59 43.31 2.41
61 62 5.465532 TGAGGTGGTATACAACGTTACAA 57.534 39.130 7.03 0.00 43.31 2.41
62 63 6.040209 TGAGGTGGTATACAACGTTACAAT 57.960 37.500 7.03 0.00 43.31 2.71
63 64 7.167924 TGAGGTGGTATACAACGTTACAATA 57.832 36.000 7.03 0.00 43.31 1.90
64 65 7.784037 TGAGGTGGTATACAACGTTACAATAT 58.216 34.615 7.03 0.00 43.31 1.28
65 66 8.911965 TGAGGTGGTATACAACGTTACAATATA 58.088 33.333 7.03 0.00 43.31 0.86
66 67 9.185192 GAGGTGGTATACAACGTTACAATATAC 57.815 37.037 7.03 10.70 43.31 1.47
67 68 8.694540 AGGTGGTATACAACGTTACAATATACA 58.305 33.333 20.89 12.28 43.31 2.29
68 69 8.755018 GGTGGTATACAACGTTACAATATACAC 58.245 37.037 20.89 18.40 32.62 2.90
69 70 9.299963 GTGGTATACAACGTTACAATATACACA 57.700 33.333 20.89 16.35 32.62 3.72
93 94 8.628882 CATGTAAATACAGTCTAACATGTCGA 57.371 34.615 0.00 0.00 39.39 4.20
118 119 1.802960 CGTCTCATGCCCTATCAATGC 59.197 52.381 0.00 0.00 0.00 3.56
170 171 3.190849 CGGAGTCTGTGCATGCCG 61.191 66.667 16.68 4.66 0.00 5.69
171 172 2.265739 GGAGTCTGTGCATGCCGA 59.734 61.111 16.68 6.28 0.00 5.54
249 318 1.439228 CGTCCTGATCATGCTCCGT 59.561 57.895 0.00 0.00 0.00 4.69
292 361 0.522180 TGAGCTTCCTCGTCGTCTTC 59.478 55.000 0.00 0.00 41.13 2.87
315 384 2.747855 CACGAAAGGGCTGAGGGC 60.748 66.667 0.00 0.00 40.90 5.19
393 468 0.036388 GTGATCCTCTTGTTCCGGCA 60.036 55.000 0.00 0.00 0.00 5.69
527 602 7.202047 GGATATTAATATGGGAGCTAGGGTCTG 60.202 44.444 12.74 0.00 0.00 3.51
529 604 1.241485 TATGGGAGCTAGGGTCTGGA 58.759 55.000 0.00 0.00 0.00 3.86
568 643 2.366916 GACACCTCGGGATCAGATGAAT 59.633 50.000 0.00 0.00 0.00 2.57
629 714 4.611581 GCAGAAGAGGTTGAAAGCTTAACG 60.612 45.833 0.00 0.00 36.78 3.18
637 722 3.713826 TGAAAGCTTAACGGAATCCCT 57.286 42.857 0.00 0.00 0.00 4.20
638 723 3.606687 TGAAAGCTTAACGGAATCCCTC 58.393 45.455 0.00 0.00 0.00 4.30
640 725 0.179081 AGCTTAACGGAATCCCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
641 726 1.158484 GCTTAACGGAATCCCTCGCC 61.158 60.000 0.00 0.00 0.00 5.54
642 727 0.464452 CTTAACGGAATCCCTCGCCT 59.536 55.000 0.00 0.00 0.00 5.52
644 729 0.974010 TAACGGAATCCCTCGCCTGT 60.974 55.000 0.00 0.00 0.00 4.00
645 730 2.202932 CGGAATCCCTCGCCTGTG 60.203 66.667 0.00 0.00 0.00 3.66
672 779 4.421479 CGTTCGGCTGGCTCGTCT 62.421 66.667 0.00 0.00 0.00 4.18
719 826 1.523758 GTGGTTTACACTCCAGGCTG 58.476 55.000 7.75 7.75 46.72 4.85
720 827 1.071699 GTGGTTTACACTCCAGGCTGA 59.928 52.381 17.94 0.95 46.72 4.26
721 828 1.071699 TGGTTTACACTCCAGGCTGAC 59.928 52.381 17.94 2.88 0.00 3.51
722 829 1.348036 GGTTTACACTCCAGGCTGACT 59.652 52.381 17.94 0.00 0.00 3.41
765 872 5.059587 CGTCTCGTGCACTTTTATTTACGTA 59.940 40.000 16.19 0.00 33.68 3.57
768 875 6.807720 TCTCGTGCACTTTTATTTACGTATGA 59.192 34.615 16.19 0.00 33.68 2.15
775 882 9.783256 GCACTTTTATTTACGTATGATTTTCCT 57.217 29.630 0.00 0.00 0.00 3.36
786 893 8.425577 ACGTATGATTTTCCTCACTAATCTTG 57.574 34.615 0.00 0.00 31.25 3.02
787 894 8.041323 ACGTATGATTTTCCTCACTAATCTTGT 58.959 33.333 0.00 0.00 31.25 3.16
788 895 8.883731 CGTATGATTTTCCTCACTAATCTTGTT 58.116 33.333 0.00 0.00 31.25 2.83
832 939 9.846248 AATCACTAATCTTGTTTGAAATACAGC 57.154 29.630 0.00 0.00 0.00 4.40
919 1026 2.734079 GAGAAGAGTCAAGAAAGCCACG 59.266 50.000 0.00 0.00 0.00 4.94
960 1067 0.036671 GGCACTACCACCACCAGTAC 60.037 60.000 0.00 0.00 38.86 2.73
961 1068 0.682852 GCACTACCACCACCAGTACA 59.317 55.000 0.00 0.00 0.00 2.90
984 1091 1.807573 CCAGCTTCTCGGTTCTCGC 60.808 63.158 0.00 0.00 39.05 5.03
1062 1169 3.745797 GCCTTACTCCTGCTAGAAATGGG 60.746 52.174 0.00 0.00 0.00 4.00
1066 1173 1.451927 CCTGCTAGAAATGGGCGCA 60.452 57.895 10.83 5.70 0.00 6.09
1150 1257 2.170166 AGGAATCATTTTTGCGGCTCA 58.830 42.857 0.00 0.00 0.00 4.26
1151 1258 2.762327 AGGAATCATTTTTGCGGCTCAT 59.238 40.909 0.00 0.00 0.00 2.90
1270 1377 4.393062 CGATGTGTCTCTTTTGTATGCCTT 59.607 41.667 0.00 0.00 0.00 4.35
1411 1518 2.684038 GCAAAGGGAGGGAACATCCTAC 60.684 54.545 0.00 0.00 37.25 3.18
1414 1521 3.151542 AGGGAGGGAACATCCTACAAT 57.848 47.619 0.00 0.00 39.56 2.71
1447 1554 6.589907 ACTGATTCCTGTGTTTTTGTTTTGAC 59.410 34.615 0.00 0.00 0.00 3.18
1451 1558 4.565022 CCTGTGTTTTTGTTTTGACAGGT 58.435 39.130 0.00 0.00 43.65 4.00
1473 1887 5.582665 GGTTGAATGAGTAGCTTGGTAAGAG 59.417 44.000 0.00 0.00 0.00 2.85
1475 3114 6.360370 TGAATGAGTAGCTTGGTAAGAGTT 57.640 37.500 0.00 0.00 0.00 3.01
1499 3138 5.401550 TGTAAATCCTGTACGTACTTTCCG 58.598 41.667 25.12 9.00 0.00 4.30
1532 3171 0.183492 GCAGATCCCCAGCCAACATA 59.817 55.000 0.00 0.00 0.00 2.29
1551 3191 8.633561 CCAACATACTAGATCTTCACTCATACA 58.366 37.037 0.00 0.00 0.00 2.29
1598 3245 5.515534 GGATGTTCCATGGCACTCCTTATAT 60.516 44.000 15.79 0.00 36.28 0.86
1599 3246 6.296432 GGATGTTCCATGGCACTCCTTATATA 60.296 42.308 15.79 0.00 36.28 0.86
1600 3247 6.508030 TGTTCCATGGCACTCCTTATATAA 57.492 37.500 15.79 0.00 0.00 0.98
1601 3248 6.533730 TGTTCCATGGCACTCCTTATATAAG 58.466 40.000 15.79 14.56 0.00 1.73
1602 3249 6.101150 TGTTCCATGGCACTCCTTATATAAGT 59.899 38.462 15.79 1.17 0.00 2.24
1688 3344 1.594833 GGGACAGTACGCCATGACA 59.405 57.895 0.00 0.00 0.00 3.58
1758 3878 5.733226 TGTATGGTGCGTATTCATTTGAG 57.267 39.130 0.00 0.00 0.00 3.02
1912 4056 6.824553 TCTAGTCCTGCTTTATCTCTACGTA 58.175 40.000 0.00 0.00 0.00 3.57
1918 4062 7.491696 GTCCTGCTTTATCTCTACGTAAATTGT 59.508 37.037 0.00 0.00 0.00 2.71
1963 4107 1.211703 TCACACTTGGACTGAAGCCAA 59.788 47.619 0.00 0.00 42.81 4.52
1967 4111 3.706086 ACACTTGGACTGAAGCCAATTTT 59.294 39.130 0.00 0.00 43.90 1.82
2001 4145 5.934625 ACAGAGTTATCATGTCAAGGTTGTC 59.065 40.000 0.00 0.00 0.00 3.18
2051 4199 1.707632 CTCTGTCGAGGCTTGAACTG 58.292 55.000 5.89 5.61 33.51 3.16
2121 4269 0.543749 AAGTAGCCAGCAGGACATCC 59.456 55.000 0.00 0.00 36.89 3.51
2128 4276 2.202987 GCAGGACATCCCGCAGAG 60.203 66.667 1.04 0.00 40.87 3.35
2129 4277 2.725312 GCAGGACATCCCGCAGAGA 61.725 63.158 1.04 0.00 40.87 3.10
2202 4350 2.093235 ACATGCTGAAGCTAGAACCTCC 60.093 50.000 3.61 0.00 42.66 4.30
2236 4384 6.441088 ACAAGAGGAAAGTAATGGAGAAGT 57.559 37.500 0.00 0.00 0.00 3.01
2330 4478 4.828072 ACTTGTTGATCCCTCCTACTTC 57.172 45.455 0.00 0.00 0.00 3.01
2360 4509 3.001736 GCTTACATCTGAAAGGCATCGTC 59.998 47.826 0.00 0.00 0.00 4.20
2372 4521 3.187700 AGGCATCGTCTCGTTGTAAATC 58.812 45.455 0.00 0.00 0.00 2.17
2487 4642 3.567530 CTCGCTGCATTGTTTTTCATGA 58.432 40.909 0.00 0.00 0.00 3.07
2490 4645 4.215185 TCGCTGCATTGTTTTTCATGACTA 59.785 37.500 0.00 0.00 0.00 2.59
2559 4717 8.171196 CGATAATGGCAGTATAATGAACATCAC 58.829 37.037 7.53 3.03 0.00 3.06
2616 4775 4.703575 ACATAGCGAGGACTACAAACACTA 59.296 41.667 0.00 0.00 0.00 2.74
2624 4783 4.038883 AGGACTACAAACACTAAAGCGAGT 59.961 41.667 0.00 0.00 0.00 4.18
2657 4816 2.359169 CGCTGTAGCCCCTTCCTCA 61.359 63.158 0.00 0.00 37.91 3.86
2683 4842 2.763448 AGCCAGGCAAAACTTGTTGTAA 59.237 40.909 15.80 0.00 0.00 2.41
2686 4845 5.245977 AGCCAGGCAAAACTTGTTGTAATAT 59.754 36.000 15.80 0.00 0.00 1.28
2820 4980 5.263968 ACCTGAAGACACACGAATATAGG 57.736 43.478 0.00 0.00 0.00 2.57
2906 5067 1.592110 CCATTGACGATGCTAAACGCG 60.592 52.381 3.53 3.53 43.27 6.01
3050 5211 2.353323 CTTCTACCGGCAAGGGTTAAC 58.647 52.381 0.00 0.00 46.96 2.01
3071 5232 4.415150 CACTGCGTCCCCATGGCT 62.415 66.667 6.09 0.00 0.00 4.75
3156 5317 7.904558 AATCTTTCTTTGAAGAGGAACCTTT 57.095 32.000 0.00 0.00 38.90 3.11
3227 5388 7.094205 CCCTTGATACATACAAGAACAAAAGCT 60.094 37.037 0.00 0.00 44.92 3.74
3330 5491 8.627208 TTTGAGAGAAGAAAGCATATTTGAGT 57.373 30.769 0.00 0.00 0.00 3.41
3331 5492 7.606858 TGAGAGAAGAAAGCATATTTGAGTG 57.393 36.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.673023 TAGGCCACCCCTAGAGGAT 58.327 57.895 5.01 0.00 44.08 3.24
8 9 7.814693 ATATATATATGTGATAGGCCACCCC 57.185 40.000 5.01 0.00 36.26 4.95
33 34 9.918630 GTAACGTTGTATACCACCTCATTATAT 57.081 33.333 11.99 0.00 0.00 0.86
34 35 8.911965 TGTAACGTTGTATACCACCTCATTATA 58.088 33.333 11.99 0.00 0.00 0.98
35 36 7.784037 TGTAACGTTGTATACCACCTCATTAT 58.216 34.615 11.99 0.00 0.00 1.28
36 37 7.167924 TGTAACGTTGTATACCACCTCATTA 57.832 36.000 11.99 0.00 0.00 1.90
37 38 6.040209 TGTAACGTTGTATACCACCTCATT 57.960 37.500 11.99 0.00 0.00 2.57
38 39 5.664294 TGTAACGTTGTATACCACCTCAT 57.336 39.130 11.99 0.00 0.00 2.90
39 40 5.465532 TTGTAACGTTGTATACCACCTCA 57.534 39.130 11.99 0.00 0.00 3.86
40 41 9.185192 GTATATTGTAACGTTGTATACCACCTC 57.815 37.037 11.99 0.00 0.00 3.85
41 42 8.694540 TGTATATTGTAACGTTGTATACCACCT 58.305 33.333 11.99 0.00 30.78 4.00
42 43 8.755018 GTGTATATTGTAACGTTGTATACCACC 58.245 37.037 11.99 6.07 30.78 4.61
43 44 9.299963 TGTGTATATTGTAACGTTGTATACCAC 57.700 33.333 11.99 14.15 30.78 4.16
68 69 8.628882 TCGACATGTTAGACTGTATTTACATG 57.371 34.615 19.70 19.70 45.03 3.21
69 70 9.647797 TTTCGACATGTTAGACTGTATTTACAT 57.352 29.630 0.00 0.00 35.36 2.29
70 71 9.135843 CTTTCGACATGTTAGACTGTATTTACA 57.864 33.333 0.00 0.00 34.56 2.41
71 72 8.592998 CCTTTCGACATGTTAGACTGTATTTAC 58.407 37.037 0.00 0.00 0.00 2.01
72 73 7.277098 GCCTTTCGACATGTTAGACTGTATTTA 59.723 37.037 0.00 0.00 0.00 1.40
73 74 6.092259 GCCTTTCGACATGTTAGACTGTATTT 59.908 38.462 0.00 0.00 0.00 1.40
74 75 5.581085 GCCTTTCGACATGTTAGACTGTATT 59.419 40.000 0.00 0.00 0.00 1.89
75 76 5.109903 GCCTTTCGACATGTTAGACTGTAT 58.890 41.667 0.00 0.00 0.00 2.29
76 77 4.491676 GCCTTTCGACATGTTAGACTGTA 58.508 43.478 0.00 0.00 0.00 2.74
77 78 3.326747 GCCTTTCGACATGTTAGACTGT 58.673 45.455 0.00 0.00 0.00 3.55
78 79 2.345641 CGCCTTTCGACATGTTAGACTG 59.654 50.000 0.00 0.00 41.67 3.51
79 80 2.029290 ACGCCTTTCGACATGTTAGACT 60.029 45.455 0.00 0.00 41.67 3.24
80 81 2.334838 ACGCCTTTCGACATGTTAGAC 58.665 47.619 0.00 0.00 41.67 2.59
81 82 2.230508 AGACGCCTTTCGACATGTTAGA 59.769 45.455 0.00 0.00 41.67 2.10
82 83 2.599082 GAGACGCCTTTCGACATGTTAG 59.401 50.000 0.00 0.00 41.67 2.34
83 84 2.029739 TGAGACGCCTTTCGACATGTTA 60.030 45.455 0.00 0.00 41.67 2.41
84 85 1.270094 TGAGACGCCTTTCGACATGTT 60.270 47.619 0.00 0.00 41.67 2.71
85 86 0.317160 TGAGACGCCTTTCGACATGT 59.683 50.000 0.00 0.00 41.67 3.21
86 87 1.325640 CATGAGACGCCTTTCGACATG 59.674 52.381 0.00 0.00 41.67 3.21
87 88 1.645034 CATGAGACGCCTTTCGACAT 58.355 50.000 0.00 0.00 41.67 3.06
118 119 2.998668 CGTTCTTCGGAATTCGGATG 57.001 50.000 15.56 16.78 39.77 3.51
228 297 1.596477 GAGCATGATCAGGACGGCC 60.596 63.158 12.39 0.00 0.00 6.13
239 308 2.162208 GCAAAAGATTCACGGAGCATGA 59.838 45.455 0.00 0.00 0.00 3.07
249 318 0.796312 GCCGTCGAGCAAAAGATTCA 59.204 50.000 0.00 0.00 0.00 2.57
292 361 2.358737 AGCCCTTTCGTGAAGCCG 60.359 61.111 0.00 0.00 33.84 5.52
346 421 4.815108 GTCAATCCCCGCCCACCC 62.815 72.222 0.00 0.00 0.00 4.61
362 437 2.190756 GGATCACGTCCTCTTCGGT 58.809 57.895 0.00 0.00 44.16 4.69
527 602 0.391263 AAACGGTCCGCTGATCTTCC 60.391 55.000 12.28 0.00 0.00 3.46
529 604 0.320374 TCAAACGGTCCGCTGATCTT 59.680 50.000 12.28 0.00 0.00 2.40
629 714 2.514824 GCACAGGCGAGGGATTCC 60.515 66.667 0.00 0.00 0.00 3.01
717 824 1.211969 GTTGCCATGCTGCAGTCAG 59.788 57.895 16.64 5.03 43.21 3.51
718 825 2.619165 CGTTGCCATGCTGCAGTCA 61.619 57.895 16.64 14.12 43.21 3.41
719 826 2.177531 CGTTGCCATGCTGCAGTC 59.822 61.111 16.64 8.39 43.21 3.51
720 827 2.595463 ACGTTGCCATGCTGCAGT 60.595 55.556 16.64 0.00 43.21 4.40
721 828 2.126618 CACGTTGCCATGCTGCAG 60.127 61.111 10.11 10.11 43.21 4.41
722 829 3.672447 CCACGTTGCCATGCTGCA 61.672 61.111 4.13 4.13 40.07 4.41
788 895 6.877236 AGTGATTCAGGCAAGAAAAGAAAAA 58.123 32.000 0.00 0.00 0.00 1.94
789 896 6.469782 AGTGATTCAGGCAAGAAAAGAAAA 57.530 33.333 0.00 0.00 0.00 2.29
790 897 7.581213 TTAGTGATTCAGGCAAGAAAAGAAA 57.419 32.000 0.00 0.00 0.00 2.52
791 898 7.667219 AGATTAGTGATTCAGGCAAGAAAAGAA 59.333 33.333 0.00 0.00 0.00 2.52
792 899 7.170965 AGATTAGTGATTCAGGCAAGAAAAGA 58.829 34.615 0.00 0.00 0.00 2.52
793 900 7.388460 AGATTAGTGATTCAGGCAAGAAAAG 57.612 36.000 0.00 0.00 0.00 2.27
794 901 7.231317 ACAAGATTAGTGATTCAGGCAAGAAAA 59.769 33.333 0.00 0.00 0.00 2.29
795 902 6.716628 ACAAGATTAGTGATTCAGGCAAGAAA 59.283 34.615 0.00 0.00 0.00 2.52
796 903 6.240894 ACAAGATTAGTGATTCAGGCAAGAA 58.759 36.000 0.00 0.00 0.00 2.52
797 904 5.809001 ACAAGATTAGTGATTCAGGCAAGA 58.191 37.500 0.00 0.00 0.00 3.02
798 905 6.506500 AACAAGATTAGTGATTCAGGCAAG 57.493 37.500 0.00 0.00 0.00 4.01
799 906 6.489700 TCAAACAAGATTAGTGATTCAGGCAA 59.510 34.615 0.00 0.00 0.00 4.52
800 907 6.003326 TCAAACAAGATTAGTGATTCAGGCA 58.997 36.000 0.00 0.00 0.00 4.75
801 908 6.500684 TCAAACAAGATTAGTGATTCAGGC 57.499 37.500 0.00 0.00 0.00 4.85
806 913 9.846248 GCTGTATTTCAAACAAGATTAGTGATT 57.154 29.630 0.00 0.00 0.00 2.57
807 914 8.177663 CGCTGTATTTCAAACAAGATTAGTGAT 58.822 33.333 0.00 0.00 0.00 3.06
832 939 4.634004 TGACAAATAAGACCCTGCATTACG 59.366 41.667 0.00 0.00 0.00 3.18
863 970 1.594293 ACTGGAGGACAAACGCACG 60.594 57.895 0.00 0.00 0.00 5.34
893 1000 4.576463 GGCTTTCTTGACTCTTCTCAACAA 59.424 41.667 0.00 0.00 0.00 2.83
919 1026 0.962855 GGAAGGCAAGTGCTTCCTCC 60.963 60.000 19.06 8.23 41.17 4.30
984 1091 1.474077 GCCATTGTTGTTGCTCCTAGG 59.526 52.381 0.82 0.82 0.00 3.02
1066 1173 4.619227 CCGTGACCTTGTGCGGGT 62.619 66.667 0.00 0.00 40.45 5.28
1150 1257 9.113838 GTGTTCATGTGGTAGAATAATTCTGAT 57.886 33.333 0.00 0.00 40.94 2.90
1151 1258 8.100164 TGTGTTCATGTGGTAGAATAATTCTGA 58.900 33.333 0.00 0.00 40.94 3.27
1270 1377 3.751246 GCGGCAGCCAATCAAGCA 61.751 61.111 13.30 0.00 37.42 3.91
1411 1518 7.678947 ACACAGGAATCAGTAGAGAAAATTG 57.321 36.000 0.00 0.00 0.00 2.32
1414 1521 8.405531 CAAAAACACAGGAATCAGTAGAGAAAA 58.594 33.333 0.00 0.00 0.00 2.29
1447 1554 3.679389 ACCAAGCTACTCATTCAACCTG 58.321 45.455 0.00 0.00 0.00 4.00
1451 1558 6.360370 ACTCTTACCAAGCTACTCATTCAA 57.640 37.500 0.00 0.00 0.00 2.69
1473 1887 7.513132 GGAAAGTACGTACAGGATTTACAAAC 58.487 38.462 26.55 6.82 0.00 2.93
1475 3114 5.863397 CGGAAAGTACGTACAGGATTTACAA 59.137 40.000 26.55 0.00 0.00 2.41
1499 3138 2.224402 GGATCTGCTGGAGGACCAATAC 60.224 54.545 0.00 0.00 46.32 1.89
1532 3171 7.343057 TGGACATTGTATGAGTGAAGATCTAGT 59.657 37.037 0.00 0.00 0.00 2.57
1551 3191 6.954684 TCCTAGAAGTTTCTCTACTGGACATT 59.045 38.462 0.00 0.00 38.70 2.71
1556 3196 6.783708 ACATCCTAGAAGTTTCTCTACTGG 57.216 41.667 0.00 0.00 38.70 4.00
1758 3878 3.243636 TGAAGAGTTCGTTCACACTACCC 60.244 47.826 0.00 0.00 0.00 3.69
1863 4007 5.647589 TCGAAGTTTTGATGCTCTATACGT 58.352 37.500 0.00 0.00 0.00 3.57
1912 4056 8.862325 TGACAGGATACACATCTTAACAATTT 57.138 30.769 0.00 0.00 41.41 1.82
1967 4111 7.611855 TGACATGATAACTCTGTCTACAAGAGA 59.388 37.037 0.00 0.00 39.94 3.10
2051 4199 4.575236 GCTAAACTGATAAGTAACAGGGGC 59.425 45.833 0.00 0.00 38.30 5.80
2121 4269 1.762522 ATGCCAGGGTATCTCTGCGG 61.763 60.000 0.00 0.00 0.00 5.69
2124 4272 4.630644 AATGTATGCCAGGGTATCTCTG 57.369 45.455 0.00 0.00 0.00 3.35
2128 4276 3.740115 ACGAAATGTATGCCAGGGTATC 58.260 45.455 0.00 0.00 0.00 2.24
2129 4277 3.391296 AGACGAAATGTATGCCAGGGTAT 59.609 43.478 0.00 0.00 0.00 2.73
2202 4350 5.363939 ACTTTCCTCTTGTTCTCTTGTCTG 58.636 41.667 0.00 0.00 0.00 3.51
2236 4384 1.612442 CCTCCCGGACCTTCTCCAA 60.612 63.158 0.73 0.00 39.39 3.53
2534 4692 9.002600 TGTGATGTTCATTATACTGCCATTATC 57.997 33.333 0.00 0.00 0.00 1.75
2572 4731 9.862371 CTATGTGGTCTAAGGATATGAATGTAC 57.138 37.037 0.00 0.00 0.00 2.90
2581 4740 4.079970 CCTCGCTATGTGGTCTAAGGATA 58.920 47.826 0.00 0.00 0.00 2.59
2616 4775 1.560860 GCACGCTCTCAACTCGCTTT 61.561 55.000 0.00 0.00 0.00 3.51
2642 4801 1.987855 CGGTGAGGAAGGGGCTACA 60.988 63.158 0.00 0.00 0.00 2.74
2657 4816 2.597510 GTTTTGCCTGGCTCCGGT 60.598 61.111 21.03 0.00 0.00 5.28
2683 4842 3.698040 ACGACGACTTCCCAACTGTATAT 59.302 43.478 0.00 0.00 0.00 0.86
2686 4845 1.001048 CACGACGACTTCCCAACTGTA 60.001 52.381 0.00 0.00 0.00 2.74
2820 4980 0.653897 CGGATCTAGTCGTCGTTCGC 60.654 60.000 0.00 0.00 39.67 4.70
2832 4992 6.258727 GTCTTTGATGAATTTGCTCGGATCTA 59.741 38.462 0.00 0.00 0.00 1.98
2906 5067 3.218386 TAGCCCCCACCTTGTTGGC 62.218 63.158 0.00 0.00 42.48 4.52
2930 5091 8.940397 TTTCTGAAGATGGAATAAGGTTCTTT 57.060 30.769 0.00 0.00 0.00 2.52
3071 5232 0.039180 TCGTCTCTGGTGGCCTTAGA 59.961 55.000 3.32 4.08 0.00 2.10
3227 5388 7.904558 AACTAGATCAACTCCATGTCTATCA 57.095 36.000 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.