Multiple sequence alignment - TraesCS3D01G504800

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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 TraesCS3D01G504800 chr3D 100.000 3573 0 0 1 3573 592323803 592320231 0.000000e+00 6599
1 TraesCS3D01G504800 chr3D 96.618 3578 107 10 1 3573 592243510 592239942 0.000000e+00 5925
2 TraesCS3D01G504800 chr3D 96.392 3575 114 7 1 3573 592275155 592271594 0.000000e+00 5873
3 TraesCS3D01G504800 chr3D 96.280 3575 116 8 1 3573 592295303 592291744 0.000000e+00 5849
4 TraesCS3D01G504800 chr3D 95.752 2660 101 5 1 2660 592356910 592354263 0.000000e+00 4276
5 TraesCS3D01G504800 chr3D 95.157 764 27 4 2820 3573 592172477 592171714 0.000000e+00 1197
6 TraesCS3D01G504800 chr3B 94.623 2455 111 10 213 2660 793614170 793611730 0.000000e+00 3783
7 TraesCS3D01G504800 chr3B 94.571 2450 117 8 213 2660 793532969 793530534 0.000000e+00 3773
8 TraesCS3D01G504800 chr3B 94.574 2451 115 10 213 2660 793670698 793668263 0.000000e+00 3773
9 TraesCS3D01G504800 chr3B 94.451 2451 119 9 213 2660 793588453 793586017 0.000000e+00 3757
10 TraesCS3D01G504800 chr3B 94.367 2450 122 8 213 2660 793560189 793557754 0.000000e+00 3746
11 TraesCS3D01G504800 chr3B 84.115 768 65 20 2820 3567 792570651 792571381 0.000000e+00 689
12 TraesCS3D01G504800 chr3B 86.242 596 36 15 2982 3567 792473623 792474182 3.950000e-169 604
13 TraesCS3D01G504800 chr3B 86.047 602 38 15 2982 3573 793478041 793477476 3.950000e-169 604
14 TraesCS3D01G504800 chr3B 85.906 596 38 15 2982 3567 792480986 792481545 8.540000e-166 593
15 TraesCS3D01G504800 chr3B 85.403 596 40 19 2982 3567 792491905 792492463 3.090000e-160 575
16 TraesCS3D01G504800 chr3B 90.244 451 29 7 3127 3567 793687770 793687325 3.090000e-160 575
17 TraesCS3D01G504800 chr3B 90.303 165 13 2 2820 2982 793557755 793557592 2.790000e-51 213
18 TraesCS3D01G504800 chr3B 89.697 165 14 2 2820 2982 792452645 792452808 1.300000e-49 207
19 TraesCS3D01G504800 chr3B 89.697 165 14 2 2820 2982 793485808 793485645 1.300000e-49 207
20 TraesCS3D01G504800 chr3A 91.781 219 18 0 1 219 99619756 99619974 4.480000e-79 305
21 TraesCS3D01G504800 chr2D 91.480 223 15 1 1 219 170439528 170439306 1.610000e-78 303
22 TraesCS3D01G504800 chr1D 90.952 210 19 0 1 210 58544135 58544344 2.100000e-72 283
23 TraesCS3D01G504800 chr6D 96.341 164 5 1 2659 2821 87478374 87478211 5.880000e-68 268
24 TraesCS3D01G504800 chr7A 95.181 166 6 2 2658 2821 34363833 34363998 9.840000e-66 261
25 TraesCS3D01G504800 chr5B 94.706 170 6 3 2658 2824 541610347 541610178 9.840000e-66 261
26 TraesCS3D01G504800 chr7D 94.118 170 8 2 2656 2823 552951511 552951680 1.270000e-64 257
27 TraesCS3D01G504800 chr7D 86.758 219 29 0 1 219 559109258 559109476 9.910000e-61 244
28 TraesCS3D01G504800 chr6A 92.090 177 11 3 2655 2828 328167590 328167414 2.760000e-61 246
29 TraesCS3D01G504800 chrUn 90.303 165 13 2 2820 2982 261906602 261906765 2.790000e-51 213


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 TraesCS3D01G504800 chr3D 592320231 592323803 3572 True 6599.0 6599 100.000 1 3573 1 chr3D.!!$R5 3572
1 TraesCS3D01G504800 chr3D 592239942 592243510 3568 True 5925.0 5925 96.618 1 3573 1 chr3D.!!$R2 3572
2 TraesCS3D01G504800 chr3D 592271594 592275155 3561 True 5873.0 5873 96.392 1 3573 1 chr3D.!!$R3 3572
3 TraesCS3D01G504800 chr3D 592291744 592295303 3559 True 5849.0 5849 96.280 1 3573 1 chr3D.!!$R4 3572
4 TraesCS3D01G504800 chr3D 592354263 592356910 2647 True 4276.0 4276 95.752 1 2660 1 chr3D.!!$R6 2659
5 TraesCS3D01G504800 chr3D 592171714 592172477 763 True 1197.0 1197 95.157 2820 3573 1 chr3D.!!$R1 753
6 TraesCS3D01G504800 chr3B 793611730 793614170 2440 True 3783.0 3783 94.623 213 2660 1 chr3B.!!$R5 2447
7 TraesCS3D01G504800 chr3B 793530534 793532969 2435 True 3773.0 3773 94.571 213 2660 1 chr3B.!!$R3 2447
8 TraesCS3D01G504800 chr3B 793668263 793670698 2435 True 3773.0 3773 94.574 213 2660 1 chr3B.!!$R6 2447
9 TraesCS3D01G504800 chr3B 793586017 793588453 2436 True 3757.0 3757 94.451 213 2660 1 chr3B.!!$R4 2447
10 TraesCS3D01G504800 chr3B 793557592 793560189 2597 True 1979.5 3746 92.335 213 2982 2 chr3B.!!$R8 2769
11 TraesCS3D01G504800 chr3B 792570651 792571381 730 False 689.0 689 84.115 2820 3567 1 chr3B.!!$F5 747
12 TraesCS3D01G504800 chr3B 792473623 792474182 559 False 604.0 604 86.242 2982 3567 1 chr3B.!!$F2 585
13 TraesCS3D01G504800 chr3B 793477476 793478041 565 True 604.0 604 86.047 2982 3573 1 chr3B.!!$R1 591
14 TraesCS3D01G504800 chr3B 792480986 792481545 559 False 593.0 593 85.906 2982 3567 1 chr3B.!!$F3 585
15 TraesCS3D01G504800 chr3B 792491905 792492463 558 False 575.0 575 85.403 2982 3567 1 chr3B.!!$F4 585

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
32 33 1.153549 CTAGTGGTCTCGGCCAAGC 60.154 63.158 2.24 0.0 40.68 4.01 F
1430 1435 0.319555 CACGAAAGGCGGACTCTTCA 60.320 55.000 0.00 0.0 46.49 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 1957 0.253610 ACCTTGTTCACGGTGTCCAA 59.746 50.0 8.17 10.71 30.9 3.53 R
3359 3544 0.719015 AGGAAGGGAGAGGATGTGGA 59.281 55.0 0.00 0.00 0.0 4.02 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
32 33 1.153549 CTAGTGGTCTCGGCCAAGC 60.154 63.158 2.24 0.00 40.68 4.01
91 92 3.181329 TCCTCCCTCAACTGCATCTTTA 58.819 45.455 0.00 0.00 0.00 1.85
509 511 2.279741 GTGCGTTCATAAGGATGAGCA 58.720 47.619 3.25 1.31 43.03 4.26
542 544 5.324784 TGTATGAGTGCTTTCGTCTGTAT 57.675 39.130 0.00 0.00 0.00 2.29
809 811 9.366216 ACACTAGTCTTTTTCATTTTTGGAAAC 57.634 29.630 0.00 0.00 34.23 2.78
1088 1093 3.402681 CTCGGCCATCCACCACCT 61.403 66.667 2.24 0.00 0.00 4.00
1100 1105 3.798515 TCCACCACCTACCTGAAACTAT 58.201 45.455 0.00 0.00 0.00 2.12
1186 1191 0.742505 TCCTCGCAACGGACGATATT 59.257 50.000 0.00 0.00 39.12 1.28
1371 1376 1.065126 CCTCCTCCGCAAGAAAATCCT 60.065 52.381 0.00 0.00 43.02 3.24
1430 1435 0.319555 CACGAAAGGCGGACTCTTCA 60.320 55.000 0.00 0.00 46.49 3.02
1492 1497 2.124901 CCTTTCACGGGCGCCATA 60.125 61.111 30.85 7.00 0.00 2.74
1519 1524 3.688414 GCTTCAAGGTGCCTATACCCATT 60.688 47.826 0.00 0.00 41.83 3.16
1662 1667 1.132527 TGGAGAAGGGGAGTTCAGGAA 60.133 52.381 0.00 0.00 0.00 3.36
1708 1713 4.084328 CGTCACAAGAACTTGACATCCTTC 60.084 45.833 19.35 0.00 41.98 3.46
1726 1731 2.717485 GCAGGCGGCATGTACATG 59.283 61.111 28.07 28.07 43.97 3.21
1947 1955 1.815421 GCATGCCGGTGGTCTACAG 60.815 63.158 6.36 0.00 0.00 2.74
1948 1956 1.596934 CATGCCGGTGGTCTACAGT 59.403 57.895 1.90 0.00 0.00 3.55
1949 1957 0.036388 CATGCCGGTGGTCTACAGTT 60.036 55.000 1.90 0.00 0.00 3.16
2375 2389 5.663106 AGAGAAGATCTAATGCACCACCTTA 59.337 40.000 0.00 0.00 36.10 2.69
2376 2390 6.156949 AGAGAAGATCTAATGCACCACCTTAA 59.843 38.462 0.00 0.00 36.10 1.85
2377 2391 6.352516 AGAAGATCTAATGCACCACCTTAAG 58.647 40.000 0.00 0.00 0.00 1.85
2378 2392 4.455606 AGATCTAATGCACCACCTTAAGC 58.544 43.478 0.00 0.00 0.00 3.09
2379 2393 4.164988 AGATCTAATGCACCACCTTAAGCT 59.835 41.667 0.00 0.00 0.00 3.74
2380 2394 4.301072 TCTAATGCACCACCTTAAGCTT 57.699 40.909 3.48 3.48 0.00 3.74
2471 2485 3.181458 TGGCCTATCCGTGGAATTACTTC 60.181 47.826 3.32 0.00 37.80 3.01
2502 2516 8.594550 AGCTTTGTGAGGAGTTCTATAACTTTA 58.405 33.333 0.00 0.00 46.09 1.85
2589 2603 9.733556 ACTACATAAAACATATTCACTGGTTCA 57.266 29.630 0.00 0.00 0.00 3.18
2643 2657 2.101582 AGAGGCTATTGCTACCAGTTCG 59.898 50.000 0.00 0.00 39.59 3.95
2657 2671 0.526662 AGTTCGACCGGTGAGTCATC 59.473 55.000 14.63 0.00 36.52 2.92
2658 2672 0.526662 GTTCGACCGGTGAGTCATCT 59.473 55.000 14.63 0.00 36.52 2.90
2659 2673 1.741706 GTTCGACCGGTGAGTCATCTA 59.258 52.381 14.63 0.00 36.52 1.98
2660 2674 1.376543 TCGACCGGTGAGTCATCTAC 58.623 55.000 14.63 0.00 36.52 2.59
2661 2675 1.065636 TCGACCGGTGAGTCATCTACT 60.066 52.381 14.63 0.00 42.80 2.57
2670 2684 2.830651 AGTCATCTACTCCCTCCGTT 57.169 50.000 0.00 0.00 30.33 4.44
2671 2685 2.657143 AGTCATCTACTCCCTCCGTTC 58.343 52.381 0.00 0.00 30.33 3.95
2672 2686 1.682323 GTCATCTACTCCCTCCGTTCC 59.318 57.143 0.00 0.00 0.00 3.62
2673 2687 1.569548 TCATCTACTCCCTCCGTTCCT 59.430 52.381 0.00 0.00 0.00 3.36
2674 2688 2.781757 TCATCTACTCCCTCCGTTCCTA 59.218 50.000 0.00 0.00 0.00 2.94
2675 2689 3.203710 TCATCTACTCCCTCCGTTCCTAA 59.796 47.826 0.00 0.00 0.00 2.69
2676 2690 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2677 2691 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2678 2692 3.958798 TCTACTCCCTCCGTTCCTAAATG 59.041 47.826 0.00 0.00 0.00 2.32
2679 2693 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2680 2694 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2681 2695 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2682 2696 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2683 2697 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2684 2698 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2685 2699 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2686 2700 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2687 2701 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2688 2702 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
2689 2703 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
2690 2704 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
2691 2705 9.211485 TCCGTTCCTAAATGTAAGTCTTTTTAG 57.789 33.333 7.75 7.75 0.00 1.85
2692 2706 9.211485 CCGTTCCTAAATGTAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 0.00 2.10
2705 2719 8.593492 AAGTCTTTTTAGACATTTCAAATGGC 57.407 30.769 14.70 11.66 41.02 4.40
2706 2720 7.725251 AGTCTTTTTAGACATTTCAAATGGCA 58.275 30.769 18.54 1.52 41.02 4.92
2707 2721 8.203485 AGTCTTTTTAGACATTTCAAATGGCAA 58.797 29.630 18.54 7.61 41.02 4.52
2708 2722 8.275632 GTCTTTTTAGACATTTCAAATGGCAAC 58.724 33.333 18.54 5.01 38.59 4.17
2760 2774 9.944376 TTAGAGTGTAGATTCACTTATTTTGCT 57.056 29.630 0.98 0.00 46.81 3.91
2761 2775 8.485976 AGAGTGTAGATTCACTTATTTTGCTC 57.514 34.615 0.98 0.00 46.81 4.26
2762 2776 7.550906 AGAGTGTAGATTCACTTATTTTGCTCC 59.449 37.037 0.98 0.00 46.81 4.70
2763 2777 6.313905 AGTGTAGATTCACTTATTTTGCTCCG 59.686 38.462 0.00 0.00 44.92 4.63
2764 2778 6.092259 GTGTAGATTCACTTATTTTGCTCCGT 59.908 38.462 0.00 0.00 35.68 4.69
2765 2779 7.277098 GTGTAGATTCACTTATTTTGCTCCGTA 59.723 37.037 0.00 0.00 35.68 4.02
2766 2780 7.985184 TGTAGATTCACTTATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
2767 2781 7.251704 AGATTCACTTATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
2768 2782 6.823689 AGATTCACTTATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
2769 2783 7.985184 AGATTCACTTATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
2770 2784 7.534085 TTCACTTATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
2771 2785 6.636705 TCACTTATTTTGCTCCGTATGTAGT 58.363 36.000 0.00 0.00 0.00 2.73
2772 2786 6.755141 TCACTTATTTTGCTCCGTATGTAGTC 59.245 38.462 0.00 0.00 0.00 2.59
2773 2787 6.533723 CACTTATTTTGCTCCGTATGTAGTCA 59.466 38.462 0.00 0.00 0.00 3.41
2774 2788 7.224753 CACTTATTTTGCTCCGTATGTAGTCAT 59.775 37.037 0.00 0.00 38.00 3.06
2775 2789 7.769044 ACTTATTTTGCTCCGTATGTAGTCATT 59.231 33.333 0.00 0.00 35.70 2.57
2776 2790 8.500753 TTATTTTGCTCCGTATGTAGTCATTT 57.499 30.769 0.00 0.00 35.70 2.32
2777 2791 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
2778 2792 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
2779 2793 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
2780 2794 5.968254 TGCTCCGTATGTAGTCATTTGTTA 58.032 37.500 0.00 0.00 35.70 2.41
2781 2795 6.040247 TGCTCCGTATGTAGTCATTTGTTAG 58.960 40.000 0.00 0.00 35.70 2.34
2782 2796 6.127563 TGCTCCGTATGTAGTCATTTGTTAGA 60.128 38.462 0.00 0.00 35.70 2.10
2783 2797 6.755141 GCTCCGTATGTAGTCATTTGTTAGAA 59.245 38.462 0.00 0.00 35.70 2.10
2784 2798 7.438459 GCTCCGTATGTAGTCATTTGTTAGAAT 59.562 37.037 0.00 0.00 35.70 2.40
2785 2799 8.867112 TCCGTATGTAGTCATTTGTTAGAATC 57.133 34.615 0.00 0.00 35.70 2.52
2786 2800 8.692710 TCCGTATGTAGTCATTTGTTAGAATCT 58.307 33.333 0.00 0.00 35.70 2.40
2787 2801 8.969267 CCGTATGTAGTCATTTGTTAGAATCTC 58.031 37.037 0.00 0.00 35.70 2.75
2788 2802 9.737427 CGTATGTAGTCATTTGTTAGAATCTCT 57.263 33.333 0.00 0.00 35.70 3.10
2868 3044 6.267928 AGAGATAATGTGCCTTTACCGTAGAT 59.732 38.462 0.00 0.00 0.00 1.98
2878 3054 6.183360 TGCCTTTACCGTAGATCATGATTACA 60.183 38.462 10.14 0.00 0.00 2.41
3029 3207 3.947910 TTGATAGAAAACGACGAGGGT 57.052 42.857 0.00 0.00 0.00 4.34
3339 3524 3.426615 ACCTATCCCGCATTCTCTAGAG 58.573 50.000 13.98 13.98 0.00 2.43
3359 3544 0.395312 AACTCCCAATTGTCGGTCGT 59.605 50.000 4.43 0.00 0.00 4.34
3423 3608 2.181196 ACTTTCCTCCCAATTTTCCCCA 59.819 45.455 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.520536 AAGCTTGGCCGAGACCACT 61.521 57.895 25.25 8.15 40.19 4.00
32 33 1.882912 TGCTGCAGTTGTACCTCAAG 58.117 50.000 16.64 0.00 36.66 3.02
509 511 2.923655 GCACTCATACATACGCGCATAT 59.076 45.455 5.73 0.00 0.00 1.78
542 544 4.039245 TGTCAAGTTTGGTTTTGAACACCA 59.961 37.500 0.00 0.00 42.90 4.17
647 649 6.499106 TCAGACTGCATTCCTATTCCATTA 57.501 37.500 0.00 0.00 0.00 1.90
727 729 4.647424 ACTTTCCAAAACTGAAATCGCA 57.353 36.364 0.00 0.00 31.75 5.10
809 811 2.680913 GCATGCCCGGCGCTATTAG 61.681 63.158 6.36 0.00 38.78 1.73
910 913 7.809546 TGTGTGAATACATACAAGGTTTGAA 57.190 32.000 0.00 0.00 43.15 2.69
1075 1080 1.224592 CAGGTAGGTGGTGGATGGC 59.775 63.158 0.00 0.00 0.00 4.40
1088 1093 3.452990 TCCGCCATGAATAGTTTCAGGTA 59.547 43.478 0.00 0.00 44.75 3.08
1100 1105 2.063015 AACACCAGGTCCGCCATGAA 62.063 55.000 0.00 0.00 37.19 2.57
1186 1191 0.535335 GGAAGGCGACATAGTGGTCA 59.465 55.000 0.00 0.00 37.66 4.02
1519 1524 0.315251 CGACAGAGCTCACCTGTTCA 59.685 55.000 17.77 0.00 44.14 3.18
1662 1667 1.003312 CCAAAGCCCCAATCCCCAT 59.997 57.895 0.00 0.00 0.00 4.00
1708 1713 2.896854 ATGTACATGCCGCCTGCG 60.897 61.111 7.78 4.20 45.60 5.18
1947 1955 1.064952 CCTTGTTCACGGTGTCCAAAC 59.935 52.381 8.17 5.81 0.00 2.93
1948 1956 1.340211 ACCTTGTTCACGGTGTCCAAA 60.340 47.619 8.17 0.00 30.90 3.28
1949 1957 0.253610 ACCTTGTTCACGGTGTCCAA 59.746 50.000 8.17 10.71 30.90 3.53
2033 2041 0.249155 TTGGACTTCGTGGTGTCGAC 60.249 55.000 9.11 9.11 39.58 4.20
2312 2320 1.740380 CGCAGATCACTCGGTGGATTT 60.740 52.381 0.00 0.00 33.87 2.17
2502 2516 6.744112 TGAGAAAAACAAACAAGGCGATTAT 58.256 32.000 0.00 0.00 0.00 1.28
2563 2577 9.733556 TGAACCAGTGAATATGTTTTATGTAGT 57.266 29.630 0.00 0.00 0.00 2.73
2589 2603 2.549754 CGTCCACTTCTCACTTTTGCAT 59.450 45.455 0.00 0.00 0.00 3.96
2657 2671 3.705072 ACATTTAGGAACGGAGGGAGTAG 59.295 47.826 0.00 0.00 0.00 2.57
2658 2672 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
2659 2673 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
2660 2674 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2661 2675 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2662 2676 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2663 2677 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2664 2678 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
2665 2679 9.211485 CTAAAAAGACTTACATTTAGGAACGGA 57.789 33.333 8.91 0.00 33.69 4.69
2666 2680 9.211485 TCTAAAAAGACTTACATTTAGGAACGG 57.789 33.333 13.94 0.00 36.48 4.44
2679 2693 9.691362 GCCATTTGAAATGTCTAAAAAGACTTA 57.309 29.630 15.93 0.00 39.41 2.24
2680 2694 8.203485 TGCCATTTGAAATGTCTAAAAAGACTT 58.797 29.630 15.93 0.00 39.41 3.01
2681 2695 7.725251 TGCCATTTGAAATGTCTAAAAAGACT 58.275 30.769 15.93 0.00 39.41 3.24
2682 2696 7.945033 TGCCATTTGAAATGTCTAAAAAGAC 57.055 32.000 15.93 0.00 39.15 3.01
2683 2697 7.984050 TGTTGCCATTTGAAATGTCTAAAAAGA 59.016 29.630 15.93 0.00 0.00 2.52
2684 2698 8.140677 TGTTGCCATTTGAAATGTCTAAAAAG 57.859 30.769 15.93 0.50 0.00 2.27
2685 2699 8.394121 GTTGTTGCCATTTGAAATGTCTAAAAA 58.606 29.630 15.93 7.17 0.00 1.94
2686 2700 7.550551 TGTTGTTGCCATTTGAAATGTCTAAAA 59.449 29.630 15.93 0.00 0.00 1.52
2687 2701 7.044181 TGTTGTTGCCATTTGAAATGTCTAAA 58.956 30.769 15.93 3.18 0.00 1.85
2688 2702 6.577103 TGTTGTTGCCATTTGAAATGTCTAA 58.423 32.000 15.93 6.02 0.00 2.10
2689 2703 6.154203 TGTTGTTGCCATTTGAAATGTCTA 57.846 33.333 15.93 0.00 0.00 2.59
2690 2704 5.021033 TGTTGTTGCCATTTGAAATGTCT 57.979 34.783 15.93 0.00 0.00 3.41
2691 2705 5.927954 ATGTTGTTGCCATTTGAAATGTC 57.072 34.783 15.93 4.58 0.00 3.06
2692 2706 6.286758 TGTATGTTGTTGCCATTTGAAATGT 58.713 32.000 15.93 0.00 0.00 2.71
2693 2707 6.645827 TCTGTATGTTGTTGCCATTTGAAATG 59.354 34.615 10.84 10.84 0.00 2.32
2694 2708 6.757237 TCTGTATGTTGTTGCCATTTGAAAT 58.243 32.000 0.00 0.00 0.00 2.17
2695 2709 6.154203 TCTGTATGTTGTTGCCATTTGAAA 57.846 33.333 0.00 0.00 0.00 2.69
2696 2710 5.781210 TCTGTATGTTGTTGCCATTTGAA 57.219 34.783 0.00 0.00 0.00 2.69
2697 2711 5.243507 ACATCTGTATGTTGTTGCCATTTGA 59.756 36.000 0.00 0.00 44.07 2.69
2698 2712 5.472148 ACATCTGTATGTTGTTGCCATTTG 58.528 37.500 0.00 0.00 44.07 2.32
2699 2713 5.726980 ACATCTGTATGTTGTTGCCATTT 57.273 34.783 0.00 0.00 44.07 2.32
2739 2753 6.092259 ACGGAGCAAAATAAGTGAATCTACAC 59.908 38.462 0.00 0.00 40.60 2.90
2740 2754 6.170506 ACGGAGCAAAATAAGTGAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
2741 2755 6.663944 ACGGAGCAAAATAAGTGAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
2742 2756 7.985184 ACATACGGAGCAAAATAAGTGAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
2743 2757 6.823689 ACATACGGAGCAAAATAAGTGAATCT 59.176 34.615 0.00 0.00 0.00 2.40
2744 2758 7.016361 ACATACGGAGCAAAATAAGTGAATC 57.984 36.000 0.00 0.00 0.00 2.52
2745 2759 7.769044 ACTACATACGGAGCAAAATAAGTGAAT 59.231 33.333 0.00 0.00 0.00 2.57
2746 2760 7.101054 ACTACATACGGAGCAAAATAAGTGAA 58.899 34.615 0.00 0.00 0.00 3.18
2747 2761 6.636705 ACTACATACGGAGCAAAATAAGTGA 58.363 36.000 0.00 0.00 0.00 3.41
2748 2762 6.533723 TGACTACATACGGAGCAAAATAAGTG 59.466 38.462 0.00 0.00 0.00 3.16
2749 2763 6.636705 TGACTACATACGGAGCAAAATAAGT 58.363 36.000 0.00 0.00 0.00 2.24
2750 2764 7.715265 ATGACTACATACGGAGCAAAATAAG 57.285 36.000 0.00 0.00 34.71 1.73
2751 2765 8.394877 CAAATGACTACATACGGAGCAAAATAA 58.605 33.333 0.00 0.00 35.50 1.40
2752 2766 7.551262 ACAAATGACTACATACGGAGCAAAATA 59.449 33.333 0.00 0.00 35.50 1.40
2753 2767 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
2754 2768 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
2755 2769 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
2756 2770 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
2757 2771 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
2758 2772 6.270815 TCTAACAAATGACTACATACGGAGC 58.729 40.000 0.00 0.00 35.50 4.70
2759 2773 8.873215 ATTCTAACAAATGACTACATACGGAG 57.127 34.615 0.00 0.00 35.50 4.63
2760 2774 8.692710 AGATTCTAACAAATGACTACATACGGA 58.307 33.333 0.00 0.00 35.50 4.69
2761 2775 8.873215 AGATTCTAACAAATGACTACATACGG 57.127 34.615 0.00 0.00 35.50 4.02
2762 2776 9.737427 AGAGATTCTAACAAATGACTACATACG 57.263 33.333 0.00 0.00 35.50 3.06
2793 2807 9.900112 ACTCCCTCTGTTCCTAAATATAAGTAT 57.100 33.333 0.00 0.00 0.00 2.12
2795 2809 9.369672 CTACTCCCTCTGTTCCTAAATATAAGT 57.630 37.037 0.00 0.00 0.00 2.24
2796 2810 9.369672 ACTACTCCCTCTGTTCCTAAATATAAG 57.630 37.037 0.00 0.00 0.00 1.73
2797 2811 9.725206 AACTACTCCCTCTGTTCCTAAATATAA 57.275 33.333 0.00 0.00 0.00 0.98
2799 2813 9.725206 TTAACTACTCCCTCTGTTCCTAAATAT 57.275 33.333 0.00 0.00 0.00 1.28
2800 2814 9.725206 ATTAACTACTCCCTCTGTTCCTAAATA 57.275 33.333 0.00 0.00 0.00 1.40
2801 2815 8.625467 ATTAACTACTCCCTCTGTTCCTAAAT 57.375 34.615 0.00 0.00 0.00 1.40
2802 2816 9.725206 ATATTAACTACTCCCTCTGTTCCTAAA 57.275 33.333 0.00 0.00 0.00 1.85
2805 2819 8.512813 ACTATATTAACTACTCCCTCTGTTCCT 58.487 37.037 0.00 0.00 0.00 3.36
2806 2820 8.709272 ACTATATTAACTACTCCCTCTGTTCC 57.291 38.462 0.00 0.00 0.00 3.62
2807 2821 8.795513 GGACTATATTAACTACTCCCTCTGTTC 58.204 40.741 0.00 0.00 0.00 3.18
2808 2822 8.287350 TGGACTATATTAACTACTCCCTCTGTT 58.713 37.037 0.00 0.00 0.00 3.16
2809 2823 7.724951 GTGGACTATATTAACTACTCCCTCTGT 59.275 40.741 0.00 0.00 0.00 3.41
2810 2824 7.945664 AGTGGACTATATTAACTACTCCCTCTG 59.054 40.741 0.00 0.00 0.00 3.35
2811 2825 8.059565 AGTGGACTATATTAACTACTCCCTCT 57.940 38.462 0.00 0.00 0.00 3.69
2812 2826 8.709272 AAGTGGACTATATTAACTACTCCCTC 57.291 38.462 0.00 0.00 0.00 4.30
2878 3054 7.607250 GCTGACTAGCTACCATTGAAGTATAT 58.393 38.462 0.00 0.00 46.57 0.86
2896 3072 5.946486 TCATTCCTCAGATCTAGCTGACTA 58.054 41.667 0.00 0.00 39.84 2.59
3029 3207 9.338622 TCTCGACTCTATATTTACAGATCACAA 57.661 33.333 0.00 0.00 0.00 3.33
3339 3524 1.076332 CGACCGACAATTGGGAGTTC 58.924 55.000 10.83 0.00 0.00 3.01
3359 3544 0.719015 AGGAAGGGAGAGGATGTGGA 59.281 55.000 0.00 0.00 0.00 4.02
3512 3697 0.336737 GTGGAGGAGGAGGAGGAGAA 59.663 60.000 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.