Multiple sequence alignment - TraesCS6A01G253900

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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 TraesCS6A01G253900 chr6A 100.000 3192 0 0 1 3192 470065098 470068289 0.000000e+00 5895
1 TraesCS6A01G253900 chr6B 91.337 2655 146 46 583 3192 489832712 489835327 0.000000e+00 3552
2 TraesCS6A01G253900 chr6B 90.588 85 7 1 3042 3125 30070500 30070584 9.360000e-21 111
3 TraesCS6A01G253900 chr6D 93.767 2246 96 15 583 2807 331198503 331200725 0.000000e+00 3332
4 TraesCS6A01G253900 chr6D 87.797 590 64 5 1 589 428063998 428063416 0.000000e+00 684
5 TraesCS6A01G253900 chr6D 91.892 148 11 1 2983 3130 331201013 331201159 4.170000e-49 206
6 TraesCS6A01G253900 chr6D 90.226 133 12 1 2804 2935 331200757 331200889 4.230000e-39 172
7 TraesCS6A01G253900 chr6D 94.737 76 4 0 3040 3115 17133240 17133315 5.590000e-23 119
8 TraesCS6A01G253900 chr1D 90.018 551 53 2 1 550 310496051 310496600 0.000000e+00 712
9 TraesCS6A01G253900 chr1D 89.550 555 54 4 1 554 39686339 39685788 0.000000e+00 701
10 TraesCS6A01G253900 chr1D 88.988 563 60 2 1 562 144512678 144513239 0.000000e+00 695
11 TraesCS6A01G253900 chr5D 89.655 551 55 2 1 551 304096696 304097244 0.000000e+00 701
12 TraesCS6A01G253900 chr2B 89.046 566 60 2 1 565 435046866 435046302 0.000000e+00 701
13 TraesCS6A01G253900 chr2B 91.358 81 7 0 3048 3128 40354505 40354585 9.360000e-21 111
14 TraesCS6A01G253900 chr4A 88.988 563 60 2 4 565 462398967 462398406 0.000000e+00 695
15 TraesCS6A01G253900 chr7D 88.265 588 57 6 1 583 307385669 307386249 0.000000e+00 693
16 TraesCS6A01G253900 chr7D 88.988 563 57 4 1 562 396137420 396137978 0.000000e+00 691
17 TraesCS6A01G253900 chr7A 91.566 83 5 1 3048 3128 725436466 725436548 2.600000e-21 113
18 TraesCS6A01G253900 chr2A 92.500 80 4 2 3051 3128 775933789 775933710 2.600000e-21 113
19 TraesCS6A01G253900 chr2D 91.463 82 6 1 3048 3128 24954803 24954884 9.360000e-21 111
20 TraesCS6A01G253900 chr2D 91.250 80 7 0 3036 3115 651728593 651728672 3.370000e-20 110


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 TraesCS6A01G253900 chr6A 470065098 470068289 3191 False 5895.000000 5895 100.000000 1 3192 1 chr6A.!!$F1 3191
1 TraesCS6A01G253900 chr6B 489832712 489835327 2615 False 3552.000000 3552 91.337000 583 3192 1 chr6B.!!$F2 2609
2 TraesCS6A01G253900 chr6D 331198503 331201159 2656 False 1236.666667 3332 91.961667 583 3130 3 chr6D.!!$F2 2547
3 TraesCS6A01G253900 chr6D 428063416 428063998 582 True 684.000000 684 87.797000 1 589 1 chr6D.!!$R1 588
4 TraesCS6A01G253900 chr1D 310496051 310496600 549 False 712.000000 712 90.018000 1 550 1 chr1D.!!$F2 549
5 TraesCS6A01G253900 chr1D 39685788 39686339 551 True 701.000000 701 89.550000 1 554 1 chr1D.!!$R1 553
6 TraesCS6A01G253900 chr1D 144512678 144513239 561 False 695.000000 695 88.988000 1 562 1 chr1D.!!$F1 561
7 TraesCS6A01G253900 chr5D 304096696 304097244 548 False 701.000000 701 89.655000 1 551 1 chr5D.!!$F1 550
8 TraesCS6A01G253900 chr2B 435046302 435046866 564 True 701.000000 701 89.046000 1 565 1 chr2B.!!$R1 564
9 TraesCS6A01G253900 chr4A 462398406 462398967 561 True 695.000000 695 88.988000 4 565 1 chr4A.!!$R1 561
10 TraesCS6A01G253900 chr7D 307385669 307386249 580 False 693.000000 693 88.265000 1 583 1 chr7D.!!$F1 582
11 TraesCS6A01G253900 chr7D 396137420 396137978 558 False 691.000000 691 88.988000 1 562 1 chr7D.!!$F2 561

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
158 159 0.400213 ACCCAAAACATCCAGAGCGA 59.600 50.0 0.00 0.0 0.0 4.93 F
1117 1139 0.734889 GGCCGGACATTTCACATCTG 59.265 55.0 5.05 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1511 0.877071 AATCACTCAGCACGGCAAAG 59.123 50.0 0.0 0.0 0.00 2.77 R
2869 2960 0.179032 TCTTGAAGCAAACCGGCAGA 60.179 50.0 0.0 0.0 35.83 4.26 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
60 61 1.410153 CCATAAATTGGTGGCTGCTCC 59.590 52.381 0.00 3.54 40.99 4.70
118 119 0.742635 CCTCCGAAGCCTTTGAGAGC 60.743 60.000 6.53 0.00 0.00 4.09
149 150 2.223947 GCGAGGACAAAACCCAAAACAT 60.224 45.455 0.00 0.00 0.00 2.71
157 158 1.247567 AACCCAAAACATCCAGAGCG 58.752 50.000 0.00 0.00 0.00 5.03
158 159 0.400213 ACCCAAAACATCCAGAGCGA 59.600 50.000 0.00 0.00 0.00 4.93
171 172 3.572682 TCCAGAGCGAAAAGAGTGTTAGA 59.427 43.478 0.00 0.00 0.00 2.10
172 173 4.220821 TCCAGAGCGAAAAGAGTGTTAGAT 59.779 41.667 0.00 0.00 0.00 1.98
177 178 7.651304 CAGAGCGAAAAGAGTGTTAGATATCAT 59.349 37.037 5.32 0.00 0.00 2.45
181 182 8.058915 GCGAAAAGAGTGTTAGATATCATTGAC 58.941 37.037 5.32 0.00 0.00 3.18
184 185 9.436957 AAAAGAGTGTTAGATATCATTGACGTT 57.563 29.630 5.32 0.00 0.00 3.99
270 271 3.436704 GCGTCATGTTCTGAGAATCCAAA 59.563 43.478 0.00 0.00 33.51 3.28
286 287 3.750371 TCCAAAAGTCATTGTGGATCGT 58.250 40.909 0.00 0.00 35.22 3.73
307 308 2.567169 TCGGTGAATGGAGTCTGTGAAT 59.433 45.455 0.00 0.00 0.00 2.57
308 309 3.767131 TCGGTGAATGGAGTCTGTGAATA 59.233 43.478 0.00 0.00 0.00 1.75
312 313 6.761242 CGGTGAATGGAGTCTGTGAATATTTA 59.239 38.462 0.00 0.00 0.00 1.40
313 314 7.279981 CGGTGAATGGAGTCTGTGAATATTTAA 59.720 37.037 0.00 0.00 0.00 1.52
423 425 3.454082 AGTTCAATCTCAGCCTCCCTAAG 59.546 47.826 0.00 0.00 0.00 2.18
450 456 4.195416 TGTACAATTGTCACAGCAACTGA 58.805 39.130 15.85 0.00 35.18 3.41
477 483 4.262617 GGTCTACCAAATCCTTGTCTTCC 58.737 47.826 0.00 0.00 35.64 3.46
478 484 4.019231 GGTCTACCAAATCCTTGTCTTCCT 60.019 45.833 0.00 0.00 35.64 3.36
501 507 7.182206 TCCTCAAGCTACTAGTTTTATCCCTTT 59.818 37.037 0.00 0.00 0.00 3.11
508 518 9.021807 GCTACTAGTTTTATCCCTTTCCTTTTT 57.978 33.333 0.00 0.00 0.00 1.94
551 561 2.276732 AGTCTTTGCTTGCTTGCCTA 57.723 45.000 0.00 0.00 0.00 3.93
555 565 2.493278 TCTTTGCTTGCTTGCCTAATCC 59.507 45.455 0.00 0.00 0.00 3.01
562 572 4.621274 GCTTGCTTGCCTAATCCATTTGAA 60.621 41.667 0.00 0.00 0.00 2.69
565 575 6.052405 TGCTTGCCTAATCCATTTGAATTT 57.948 33.333 0.00 0.00 0.00 1.82
566 576 5.875910 TGCTTGCCTAATCCATTTGAATTTG 59.124 36.000 0.00 0.00 0.00 2.32
567 577 6.108015 GCTTGCCTAATCCATTTGAATTTGA 58.892 36.000 0.00 0.00 0.00 2.69
568 578 6.036408 GCTTGCCTAATCCATTTGAATTTGAC 59.964 38.462 0.00 0.00 0.00 3.18
569 579 6.855763 TGCCTAATCCATTTGAATTTGACT 57.144 33.333 0.00 0.00 0.00 3.41
570 580 7.243604 TGCCTAATCCATTTGAATTTGACTT 57.756 32.000 0.00 0.00 0.00 3.01
571 581 7.678837 TGCCTAATCCATTTGAATTTGACTTT 58.321 30.769 0.00 0.00 0.00 2.66
572 582 8.811017 TGCCTAATCCATTTGAATTTGACTTTA 58.189 29.630 0.00 0.00 0.00 1.85
573 583 9.087424 GCCTAATCCATTTGAATTTGACTTTAC 57.913 33.333 0.00 0.00 0.00 2.01
578 588 9.807649 ATCCATTTGAATTTGACTTTACTATGC 57.192 29.630 0.00 0.00 0.00 3.14
579 589 8.801299 TCCATTTGAATTTGACTTTACTATGCA 58.199 29.630 0.00 0.00 0.00 3.96
580 590 9.421806 CCATTTGAATTTGACTTTACTATGCAA 57.578 29.630 0.00 0.00 0.00 4.08
597 607 1.701704 CAAAGGCGATTGGAAAGTGC 58.298 50.000 0.00 0.00 0.00 4.40
598 608 1.270550 CAAAGGCGATTGGAAAGTGCT 59.729 47.619 0.00 0.00 31.40 4.40
626 643 2.092375 GGGAAGAGGAAATGTGGGTAGG 60.092 54.545 0.00 0.00 0.00 3.18
633 650 2.225167 GGAAATGTGGGTAGGGTTTCCA 60.225 50.000 9.60 0.00 44.45 3.53
635 652 2.053747 ATGTGGGTAGGGTTTCCAGA 57.946 50.000 0.00 0.00 34.83 3.86
643 660 4.038633 GGTAGGGTTTCCAGATCTTACCT 58.961 47.826 8.21 5.64 34.83 3.08
644 661 4.141688 GGTAGGGTTTCCAGATCTTACCTG 60.142 50.000 8.21 0.00 34.83 4.00
648 665 4.518249 GGTTTCCAGATCTTACCTGAAGG 58.482 47.826 0.00 0.00 42.17 3.46
701 720 1.647545 AACATCATCGCAACGGGCAG 61.648 55.000 2.26 0.00 45.17 4.85
702 721 3.204827 ATCATCGCAACGGGCAGC 61.205 61.111 2.26 0.00 45.17 5.25
703 722 3.974835 ATCATCGCAACGGGCAGCA 62.975 57.895 0.00 0.00 45.17 4.41
771 790 5.948742 ACCCTCAATCAAGAAACCAAAAA 57.051 34.783 0.00 0.00 0.00 1.94
772 791 5.917462 ACCCTCAATCAAGAAACCAAAAAG 58.083 37.500 0.00 0.00 0.00 2.27
776 795 6.698766 CCTCAATCAAGAAACCAAAAAGACAG 59.301 38.462 0.00 0.00 0.00 3.51
779 798 2.492019 AGAAACCAAAAAGACAGCGC 57.508 45.000 0.00 0.00 0.00 5.92
842 861 2.595172 TTTCCCCCGTTTCACGCC 60.595 61.111 0.00 0.00 40.91 5.68
981 1003 1.338389 GCAAAACCCTAGCTCCGTACA 60.338 52.381 0.00 0.00 0.00 2.90
987 1009 4.525576 TAGCTCCGTACACGCGCG 62.526 66.667 30.96 30.96 38.59 6.86
1054 1076 1.069935 GGCAGGTAAGATCTCCGCC 59.930 63.158 15.46 15.46 36.73 6.13
1059 1081 2.432510 CAGGTAAGATCTCCGCCTCTTT 59.567 50.000 9.05 0.00 33.83 2.52
1060 1082 2.696187 AGGTAAGATCTCCGCCTCTTTC 59.304 50.000 0.00 0.00 33.83 2.62
1117 1139 0.734889 GGCCGGACATTTCACATCTG 59.265 55.000 5.05 0.00 0.00 2.90
1128 1154 5.470098 ACATTTCACATCTGTGTAGGTTGTC 59.530 40.000 9.96 0.00 45.76 3.18
1139 1165 2.104111 TGTAGGTTGTCTGACTGGTTGG 59.896 50.000 9.51 0.00 0.00 3.77
1271 1297 2.741759 GCTCTCTAGCCCTGCTATTC 57.258 55.000 0.00 0.00 43.40 1.75
1304 1330 6.959639 GATCTCCAGATCTGTTCTACTTCT 57.040 41.667 21.11 0.00 45.60 2.85
1316 1342 6.258727 TCTGTTCTACTTCTTGTTCAGCTTTG 59.741 38.462 0.00 0.00 0.00 2.77
1433 1459 1.302192 GCCAACGTGAGCCACCTTA 60.302 57.895 0.00 0.00 0.00 2.69
1435 1461 0.953960 CCAACGTGAGCCACCTTACC 60.954 60.000 0.00 0.00 0.00 2.85
1446 1472 2.557056 GCCACCTTACCCTGTTTTCTTC 59.443 50.000 0.00 0.00 0.00 2.87
1480 1506 6.499172 TCTTCGCTTGTATAGACATCTCAAG 58.501 40.000 0.00 5.03 38.60 3.02
1485 1511 4.327982 TGTATAGACATCTCAAGCTGCC 57.672 45.455 0.00 0.00 0.00 4.85
1565 1591 3.262660 TCTGATGAGGTGAGTGCATCTTT 59.737 43.478 0.00 0.00 35.04 2.52
1604 1631 6.264292 GTCTCTGCATAGATCTTTCCTAGTGA 59.736 42.308 0.00 0.00 31.21 3.41
1626 1653 7.924947 AGTGAACTTACCTGTTACTGTACTTTC 59.075 37.037 0.00 0.00 0.00 2.62
1676 1703 9.630098 ATTACAGCTTTTGTTCTTCAATGTATG 57.370 29.630 0.00 0.00 41.29 2.39
1774 1804 0.105224 CGTTACCGGGTGGCATGATA 59.895 55.000 10.66 0.00 39.70 2.15
1923 1955 0.664761 GGGATCATGGTGCATGTTCG 59.335 55.000 0.00 0.00 41.98 3.95
1964 1996 7.908193 ACAAAGTTTTAGTGCTAATTTGACG 57.092 32.000 16.76 0.00 31.83 4.35
2073 2106 5.408604 GGGTAGCGATGAGGTATAAACATTG 59.591 44.000 0.00 0.00 35.06 2.82
2088 2121 9.369904 GTATAAACATTGAGCATTTTGGTTGAT 57.630 29.630 0.00 0.00 0.00 2.57
2089 2122 6.548441 AAACATTGAGCATTTTGGTTGATG 57.452 33.333 0.00 0.00 31.41 3.07
2090 2123 4.571919 ACATTGAGCATTTTGGTTGATGG 58.428 39.130 0.00 0.00 30.23 3.51
2091 2124 4.040706 ACATTGAGCATTTTGGTTGATGGT 59.959 37.500 0.00 0.00 36.76 3.55
2134 2167 2.018542 TGATGTTTACCCGCTAGTGC 57.981 50.000 0.00 0.00 0.00 4.40
2205 2238 9.553418 CGATGATGAGTAAATAGTGTATCAGAG 57.447 37.037 0.00 0.00 0.00 3.35
2502 2535 3.569250 TTGGCTCTTGGTTAATTTCGC 57.431 42.857 0.00 0.00 0.00 4.70
2533 2579 3.131577 TGTCGTGGTTACTTCTTCTGTGT 59.868 43.478 0.00 0.00 0.00 3.72
2537 2583 4.628074 GTGGTTACTTCTTCTGTGTGCTA 58.372 43.478 0.00 0.00 0.00 3.49
2606 2652 6.705302 TGAATTCTTAGCTGTGACTTCATCT 58.295 36.000 14.75 0.00 30.55 2.90
2661 2707 3.964688 TGGGATTATTTCCGAGCTACAGA 59.035 43.478 0.00 0.00 46.52 3.41
2746 2792 0.958822 GTTTGAGAATTGGCCGGTGT 59.041 50.000 1.90 0.00 0.00 4.16
2750 2796 1.228552 AGAATTGGCCGGTGTTGCT 60.229 52.632 1.90 0.00 0.00 3.91
2756 2802 1.600916 GGCCGGTGTTGCTCTTTCT 60.601 57.895 1.90 0.00 0.00 2.52
2770 2816 3.498397 GCTCTTTCTGGACGACATTTCAA 59.502 43.478 0.00 0.00 0.00 2.69
2839 2929 5.046014 TGGTAACTGCATTTTTGGGCAATAT 60.046 36.000 0.00 0.00 39.93 1.28
2847 2938 4.470334 TTTTTGGGCAATATGAGAAGCC 57.530 40.909 0.00 0.00 46.28 4.35
2917 3008 4.811024 TCTATTTGTTGATCTCGTCATGGC 59.189 41.667 0.00 0.00 36.54 4.40
2994 3172 0.176680 ATGCTGGTTAGGAGACGCAG 59.823 55.000 0.00 0.00 0.00 5.18
3044 3222 3.242543 ACGCGATTTATAACTCGTCGTCT 60.243 43.478 25.91 14.64 40.67 4.18
3147 3325 5.878406 TTTGGCCTCAAGATTTTGGTAAA 57.122 34.783 3.32 0.00 34.97 2.01
3149 3327 3.831911 TGGCCTCAAGATTTTGGTAAAGG 59.168 43.478 3.32 0.00 34.97 3.11
3151 3329 4.283467 GGCCTCAAGATTTTGGTAAAGGTT 59.717 41.667 0.00 0.00 34.97 3.50
3153 3331 5.243954 GCCTCAAGATTTTGGTAAAGGTTCT 59.756 40.000 0.00 0.00 34.97 3.01
3155 3333 6.717084 CCTCAAGATTTTGGTAAAGGTTCTCT 59.283 38.462 0.00 0.00 34.97 3.10
3156 3334 7.094592 CCTCAAGATTTTGGTAAAGGTTCTCTC 60.095 40.741 0.00 0.00 34.97 3.20
3157 3335 6.715264 TCAAGATTTTGGTAAAGGTTCTCTCC 59.285 38.462 0.00 0.00 34.97 3.71
3158 3336 5.571285 AGATTTTGGTAAAGGTTCTCTCCC 58.429 41.667 0.00 0.00 0.00 4.30
3159 3337 3.801307 TTTGGTAAAGGTTCTCTCCCC 57.199 47.619 0.00 0.00 0.00 4.81
3160 3338 2.735259 TGGTAAAGGTTCTCTCCCCT 57.265 50.000 0.00 0.00 0.00 4.79
3161 3339 2.999928 TGGTAAAGGTTCTCTCCCCTT 58.000 47.619 0.00 0.00 42.88 3.95
3162 3340 2.910977 TGGTAAAGGTTCTCTCCCCTTC 59.089 50.000 0.00 0.00 40.17 3.46
3163 3341 2.093606 GGTAAAGGTTCTCTCCCCTTCG 60.094 54.545 0.00 0.00 40.17 3.79
3169 3347 1.619332 GTTCTCTCCCCTTCGTTCAGT 59.381 52.381 0.00 0.00 0.00 3.41
3171 3349 0.533032 CTCTCCCCTTCGTTCAGTCC 59.467 60.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.538449 ACAAAAGTCGTGCACTAACTCG 59.462 45.455 16.19 11.94 32.30 4.18
139 140 0.400213 TCGCTCTGGATGTTTTGGGT 59.600 50.000 0.00 0.00 0.00 4.51
149 150 2.910688 AACACTCTTTTCGCTCTGGA 57.089 45.000 0.00 0.00 0.00 3.86
157 158 9.088512 ACGTCAATGATATCTAACACTCTTTTC 57.911 33.333 3.98 0.00 0.00 2.29
158 159 9.436957 AACGTCAATGATATCTAACACTCTTTT 57.563 29.630 3.98 0.00 0.00 2.27
270 271 1.275291 ACCGACGATCCACAATGACTT 59.725 47.619 0.00 0.00 0.00 3.01
286 287 1.627864 TCACAGACTCCATTCACCGA 58.372 50.000 0.00 0.00 0.00 4.69
367 368 4.597507 TGTCTTCACCTTATTCCCTTGAGT 59.402 41.667 0.00 0.00 0.00 3.41
423 425 6.147821 AGTTGCTGTGACAATTGTACATCTAC 59.852 38.462 11.95 15.95 0.00 2.59
477 483 7.496263 GGAAAGGGATAAAACTAGTAGCTTGAG 59.504 40.741 0.00 0.00 0.00 3.02
478 484 7.182206 AGGAAAGGGATAAAACTAGTAGCTTGA 59.818 37.037 0.00 0.00 0.00 3.02
508 518 8.402472 ACTTCACGAAGACAAATTGAAATGTAA 58.598 29.630 13.60 0.00 40.79 2.41
509 519 7.925993 ACTTCACGAAGACAAATTGAAATGTA 58.074 30.769 13.60 0.00 40.79 2.29
518 528 4.576463 AGCAAAGACTTCACGAAGACAAAT 59.424 37.500 13.60 0.00 40.79 2.32
562 572 5.414454 TCGCCTTTGCATAGTAAAGTCAAAT 59.586 36.000 3.39 0.00 37.32 2.32
565 575 3.932822 TCGCCTTTGCATAGTAAAGTCA 58.067 40.909 3.39 0.00 37.32 3.41
566 576 5.266242 CAATCGCCTTTGCATAGTAAAGTC 58.734 41.667 3.39 0.00 37.32 3.01
567 577 4.096382 CCAATCGCCTTTGCATAGTAAAGT 59.904 41.667 3.39 0.00 37.32 2.66
568 578 4.335315 TCCAATCGCCTTTGCATAGTAAAG 59.665 41.667 3.39 1.31 37.32 1.85
569 579 4.265893 TCCAATCGCCTTTGCATAGTAAA 58.734 39.130 3.39 0.00 37.32 2.01
570 580 3.879998 TCCAATCGCCTTTGCATAGTAA 58.120 40.909 3.39 0.00 37.32 2.24
571 581 3.552132 TCCAATCGCCTTTGCATAGTA 57.448 42.857 3.39 0.00 37.32 1.82
572 582 2.418368 TCCAATCGCCTTTGCATAGT 57.582 45.000 3.39 0.00 37.32 2.12
573 583 3.129287 ACTTTCCAATCGCCTTTGCATAG 59.871 43.478 0.00 0.00 37.32 2.23
574 584 3.088532 ACTTTCCAATCGCCTTTGCATA 58.911 40.909 0.00 0.00 37.32 3.14
575 585 1.895131 ACTTTCCAATCGCCTTTGCAT 59.105 42.857 0.00 0.00 37.32 3.96
576 586 1.000385 CACTTTCCAATCGCCTTTGCA 60.000 47.619 0.00 0.00 37.32 4.08
577 587 1.701704 CACTTTCCAATCGCCTTTGC 58.298 50.000 0.00 0.00 0.00 3.68
578 588 1.270550 AGCACTTTCCAATCGCCTTTG 59.729 47.619 0.00 0.00 0.00 2.77
579 589 1.620822 AGCACTTTCCAATCGCCTTT 58.379 45.000 0.00 0.00 0.00 3.11
580 590 2.084546 GTAGCACTTTCCAATCGCCTT 58.915 47.619 0.00 0.00 0.00 4.35
581 591 1.739067 GTAGCACTTTCCAATCGCCT 58.261 50.000 0.00 0.00 0.00 5.52
597 607 3.197983 ACATTTCCTCTTCCCTTCCGTAG 59.802 47.826 0.00 0.00 0.00 3.51
598 608 3.055385 CACATTTCCTCTTCCCTTCCGTA 60.055 47.826 0.00 0.00 0.00 4.02
626 643 4.225267 TCCTTCAGGTAAGATCTGGAAACC 59.775 45.833 0.00 2.29 37.38 3.27
633 650 5.740290 TTTCGTTCCTTCAGGTAAGATCT 57.260 39.130 0.00 0.00 37.38 2.75
681 700 1.240641 TGCCCGTTGCGATGATGTTT 61.241 50.000 0.00 0.00 45.60 2.83
701 720 1.270971 CGCACAACCAAAGCATATGC 58.729 50.000 20.36 20.36 42.49 3.14
702 721 1.270971 GCGCACAACCAAAGCATATG 58.729 50.000 0.30 0.00 0.00 1.78
703 722 0.887247 TGCGCACAACCAAAGCATAT 59.113 45.000 5.66 0.00 32.43 1.78
747 766 7.508977 TCTTTTTGGTTTCTTGATTGAGGGTAT 59.491 33.333 0.00 0.00 0.00 2.73
807 826 2.124695 GGGGACAGCGATGGGTTC 60.125 66.667 5.32 0.00 0.00 3.62
958 980 1.298667 GGAGCTAGGGTTTTGCGGA 59.701 57.895 0.00 0.00 0.00 5.54
987 1009 1.450312 CTTCATGGTGGAGGTCGCC 60.450 63.158 0.00 0.00 46.03 5.54
991 1013 1.434513 TTGCCCTTCATGGTGGAGGT 61.435 55.000 3.70 0.00 0.00 3.85
1054 1076 0.985549 CTCGCGGAGTTTCGAAAGAG 59.014 55.000 11.66 9.33 43.69 2.85
1059 1081 1.211969 CTTCCTCGCGGAGTTTCGA 59.788 57.895 6.13 0.00 41.25 3.71
1060 1082 1.805945 CCTTCCTCGCGGAGTTTCG 60.806 63.158 6.13 0.00 41.25 3.46
1117 1139 3.131396 CAACCAGTCAGACAACCTACAC 58.869 50.000 2.66 0.00 0.00 2.90
1128 1154 1.605710 CTGCAAGAACCAACCAGTCAG 59.394 52.381 0.00 0.00 34.07 3.51
1139 1165 1.583477 GCCTTGAGCCTGCAAGAAC 59.417 57.895 11.78 2.38 46.31 3.01
1218 1244 2.603776 ACGAAGAAGGCGGAGGGT 60.604 61.111 0.00 0.00 0.00 4.34
1259 1285 1.063183 GGAGATGGAATAGCAGGGCT 58.937 55.000 0.00 0.00 43.41 5.19
1271 1297 2.395336 TCTGGAGATCTGGGAGATGG 57.605 55.000 0.00 0.00 34.53 3.51
1302 1328 2.435372 ACCACCAAAGCTGAACAAGA 57.565 45.000 0.00 0.00 0.00 3.02
1303 1329 3.447742 GAAACCACCAAAGCTGAACAAG 58.552 45.455 0.00 0.00 0.00 3.16
1304 1330 2.159310 CGAAACCACCAAAGCTGAACAA 60.159 45.455 0.00 0.00 0.00 2.83
1316 1342 1.509644 GAAACCCGGACGAAACCACC 61.510 60.000 0.73 0.00 0.00 4.61
1433 1459 7.290813 AGATAAAAGTGAGAAGAAAACAGGGT 58.709 34.615 0.00 0.00 0.00 4.34
1435 1461 8.012241 CGAAGATAAAAGTGAGAAGAAAACAGG 58.988 37.037 0.00 0.00 0.00 4.00
1446 1472 8.747666 GTCTATACAAGCGAAGATAAAAGTGAG 58.252 37.037 0.00 0.00 0.00 3.51
1480 1506 4.712425 CAGCACGGCAAAGGCAGC 62.712 66.667 0.00 0.00 43.71 5.25
1485 1511 0.877071 AATCACTCAGCACGGCAAAG 59.123 50.000 0.00 0.00 0.00 2.77
1565 1591 2.810274 GCAGAGACTGTTTGAGCATTGA 59.190 45.455 0.00 0.00 33.43 2.57
1626 1653 5.824904 ATGTGCAGCTTAGGAATGTTTAG 57.175 39.130 0.00 0.00 0.00 1.85
1676 1703 4.275936 ACAACAGAGCCACTTCACATAAAC 59.724 41.667 0.00 0.00 0.00 2.01
1923 1955 6.144078 ACTTTGTAACCTTCACAATTGGAC 57.856 37.500 10.83 0.00 35.89 4.02
1964 1996 6.419413 CGCACTCTCCTGAAAGAATTAGATAC 59.581 42.308 0.00 0.00 34.07 2.24
2073 2106 3.244181 ACCAACCATCAACCAAAATGCTC 60.244 43.478 0.00 0.00 0.00 4.26
2088 2121 3.304794 GCGCTACAAACATAAACCAACCA 60.305 43.478 0.00 0.00 0.00 3.67
2089 2122 3.239254 GCGCTACAAACATAAACCAACC 58.761 45.455 0.00 0.00 0.00 3.77
2090 2123 3.239254 GGCGCTACAAACATAAACCAAC 58.761 45.455 7.64 0.00 0.00 3.77
2091 2124 2.229302 GGGCGCTACAAACATAAACCAA 59.771 45.455 7.64 0.00 0.00 3.67
2134 2167 9.443283 CAGAAAAATCAAGAGTGTCACTAAAAG 57.557 33.333 5.21 0.00 0.00 2.27
2173 2206 5.853810 CACTATTTACTCATCATCGTCCTCG 59.146 44.000 0.00 0.00 38.55 4.63
2205 2238 4.270008 ACACCCAATTTGCTACCTCATAC 58.730 43.478 0.00 0.00 0.00 2.39
2206 2239 4.584638 ACACCCAATTTGCTACCTCATA 57.415 40.909 0.00 0.00 0.00 2.15
2502 2535 7.198306 AGAAGTAACCACGACAAATTTAAGG 57.802 36.000 0.00 0.00 0.00 2.69
2533 2579 5.360999 AGCAGATAGATTACACACAGTAGCA 59.639 40.000 0.00 0.00 33.43 3.49
2537 2583 5.105716 ACGAAGCAGATAGATTACACACAGT 60.106 40.000 0.00 0.00 0.00 3.55
2606 2652 1.480212 ATCACCAACAGACTCGGGCA 61.480 55.000 0.00 0.00 0.00 5.36
2746 2792 2.839486 ATGTCGTCCAGAAAGAGCAA 57.161 45.000 0.00 0.00 0.00 3.91
2750 2796 5.304778 TCATTGAAATGTCGTCCAGAAAGA 58.695 37.500 3.10 0.00 37.65 2.52
2756 2802 3.127376 CAGCATCATTGAAATGTCGTCCA 59.873 43.478 3.10 0.00 37.65 4.02
2770 2816 2.124570 GTCCCGTGCCAGCATCAT 60.125 61.111 0.00 0.00 0.00 2.45
2869 2960 0.179032 TCTTGAAGCAAACCGGCAGA 60.179 50.000 0.00 0.00 35.83 4.26
2917 3008 0.525668 CCGCTACCTGCAGTTAGACG 60.526 60.000 21.36 20.64 43.06 4.18
2994 3172 3.248029 CGCATTATCCTGAGCGGC 58.752 61.111 0.00 0.00 45.83 6.53
3138 3316 3.725267 AGGGGAGAGAACCTTTACCAAAA 59.275 43.478 0.00 0.00 31.68 2.44
3139 3317 3.332968 AGGGGAGAGAACCTTTACCAAA 58.667 45.455 0.00 0.00 31.68 3.28
3147 3325 1.268066 GAACGAAGGGGAGAGAACCT 58.732 55.000 0.00 0.00 39.21 3.50
3149 3327 1.619332 ACTGAACGAAGGGGAGAGAAC 59.381 52.381 0.00 0.00 0.00 3.01
3151 3329 1.546961 GACTGAACGAAGGGGAGAGA 58.453 55.000 0.00 0.00 0.00 3.10
3153 3331 0.114560 AGGACTGAACGAAGGGGAGA 59.885 55.000 0.00 0.00 0.00 3.71
3155 3333 1.553706 GTAGGACTGAACGAAGGGGA 58.446 55.000 0.00 0.00 0.00 4.81
3156 3334 0.172803 CGTAGGACTGAACGAAGGGG 59.827 60.000 0.00 0.00 41.55 4.79
3157 3335 0.458025 GCGTAGGACTGAACGAAGGG 60.458 60.000 0.00 0.00 41.55 3.95
3158 3336 0.526662 AGCGTAGGACTGAACGAAGG 59.473 55.000 0.00 0.00 41.55 3.46
3159 3337 2.349297 AAGCGTAGGACTGAACGAAG 57.651 50.000 0.00 0.00 41.55 3.79
3160 3338 2.608752 GGAAAGCGTAGGACTGAACGAA 60.609 50.000 0.00 0.00 41.55 3.85
3161 3339 1.068055 GGAAAGCGTAGGACTGAACGA 60.068 52.381 0.00 0.00 41.55 3.85
3162 3340 1.067776 AGGAAAGCGTAGGACTGAACG 60.068 52.381 0.00 0.00 41.92 3.95
3163 3341 2.231721 AGAGGAAAGCGTAGGACTGAAC 59.768 50.000 0.00 0.00 0.00 3.18
3169 3347 2.100989 GAGGAAGAGGAAAGCGTAGGA 58.899 52.381 0.00 0.00 0.00 2.94
3171 3349 3.430333 GAGAGGAAGAGGAAAGCGTAG 57.570 52.381 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.