Multiple sequence alignment - TraesCS5B01G379000

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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 TraesCS5B01G379000 chr5B 100.000 2787 0 0 1 2787 557136621 557139407 0.000000e+00 5147.0
1 TraesCS5B01G379000 chr5B 91.781 73 6 0 2440 2512 57969954 57969882 4.910000e-18 102.0
2 TraesCS5B01G379000 chr5B 94.030 67 3 1 2447 2512 591811322 591811256 1.770000e-17 100.0
3 TraesCS5B01G379000 chr4A 94.037 2465 98 15 1 2447 625864069 625861636 0.000000e+00 3692.0
4 TraesCS5B01G379000 chr4A 92.379 1509 79 17 781 2278 695911955 695913438 0.000000e+00 2117.0
5 TraesCS5B01G379000 chr4A 86.777 242 11 6 2567 2787 695913601 695913842 1.660000e-62 250.0
6 TraesCS5B01G379000 chr4A 100.000 38 0 0 2517 2554 625861635 625861598 1.380000e-08 71.3
7 TraesCS5B01G379000 chr5D 94.692 1639 78 9 808 2443 543339206 543340838 0.000000e+00 2536.0
8 TraesCS5B01G379000 chr5D 90.391 281 9 9 2517 2787 543340844 543341116 1.230000e-93 353.0
9 TraesCS5B01G379000 chr5D 75.089 562 53 44 1 504 543338443 543338975 6.130000e-42 182.0
10 TraesCS5B01G379000 chr5D 93.939 66 3 1 2008 2073 542272450 542272386 6.350000e-17 99.0
11 TraesCS5B01G379000 chr5D 93.750 64 4 0 2010 2073 491433801 491433738 2.280000e-16 97.1
12 TraesCS5B01G379000 chr1B 88.396 1465 137 12 569 2011 654923175 654921722 0.000000e+00 1733.0
13 TraesCS5B01G379000 chr1B 92.424 66 3 2 2449 2512 686830623 686830688 2.960000e-15 93.5
14 TraesCS5B01G379000 chr1D 88.390 801 80 5 998 1798 204988486 204987699 0.000000e+00 952.0
15 TraesCS5B01G379000 chr1D 92.424 66 5 0 2008 2073 442374990 442374925 8.220000e-16 95.3
16 TraesCS5B01G379000 chr7B 89.091 550 22 10 191 734 31433231 31432714 0.000000e+00 649.0
17 TraesCS5B01G379000 chr6A 78.588 425 36 26 86 504 289825867 289826242 2.160000e-56 230.0
18 TraesCS5B01G379000 chr5A 93.137 102 7 0 44 145 608938656 608938555 1.730000e-32 150.0
19 TraesCS5B01G379000 chr5A 89.041 73 8 0 2440 2512 702961841 702961769 1.060000e-14 91.6
20 TraesCS5B01G379000 chr3D 94.521 73 4 0 2440 2512 284191854 284191926 2.270000e-21 113.0
21 TraesCS5B01G379000 chr2D 94.521 73 3 1 2440 2512 52549531 52549602 8.160000e-21 111.0
22 TraesCS5B01G379000 chr2D 92.537 67 3 2 2008 2073 94386674 94386609 8.220000e-16 95.3
23 TraesCS5B01G379000 chr1A 93.939 66 4 0 2008 2073 454330747 454330812 1.770000e-17 100.0
24 TraesCS5B01G379000 chr1A 89.189 74 7 1 2440 2512 584307773 584307846 1.060000e-14 91.6
25 TraesCS5B01G379000 chr3A 95.082 61 3 0 2010 2070 674751145 674751205 2.280000e-16 97.1
26 TraesCS5B01G379000 chr7A 89.189 74 7 1 2440 2512 76826999 76826926 1.060000e-14 91.6
27 TraesCS5B01G379000 chr6B 82.653 98 15 2 2 97 81732466 81732563 4.950000e-13 86.1
28 TraesCS5B01G379000 chr6B 87.838 74 7 2 2440 2512 617793217 617793289 4.950000e-13 86.1


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 TraesCS5B01G379000 chr5B 557136621 557139407 2786 False 5147.000000 5147 100.0000 1 2787 1 chr5B.!!$F1 2786
1 TraesCS5B01G379000 chr4A 625861598 625864069 2471 True 1881.650000 3692 97.0185 1 2554 2 chr4A.!!$R1 2553
2 TraesCS5B01G379000 chr4A 695911955 695913842 1887 False 1183.500000 2117 89.5780 781 2787 2 chr4A.!!$F1 2006
3 TraesCS5B01G379000 chr5D 543338443 543341116 2673 False 1023.666667 2536 86.7240 1 2787 3 chr5D.!!$F1 2786
4 TraesCS5B01G379000 chr1B 654921722 654923175 1453 True 1733.000000 1733 88.3960 569 2011 1 chr1B.!!$R1 1442
5 TraesCS5B01G379000 chr1D 204987699 204988486 787 True 952.000000 952 88.3900 998 1798 1 chr1D.!!$R1 800
6 TraesCS5B01G379000 chr7B 31432714 31433231 517 True 649.000000 649 89.0910 191 734 1 chr7B.!!$R1 543

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
146 164 0.193574 TCCTCCCTTCACCACTTCCT 59.806 55.0 0.00 0.0 0.0 3.36 F
147 165 1.068121 CCTCCCTTCACCACTTCCTT 58.932 55.0 0.00 0.0 0.0 3.36 F
1149 1327 0.254178 TCAAAGCTGGGATGCCTCTC 59.746 55.0 4.35 0.0 0.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 1198 0.250858 TTGGGCTCATGGTGAGTGTG 60.251 55.0 8.58 0.0 45.94 3.82 R
1551 1729 0.999406 GTGTCGTCGCATTAGCACAT 59.001 50.0 0.00 0.0 42.27 3.21 R
2479 2665 0.035343 GAACCAGAAGTACAGGGGCC 60.035 60.0 0.00 0.0 0.00 5.80 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
31 32 3.485431 CGCAGCGAGCCTCAACAG 61.485 66.667 9.98 0.00 41.38 3.16
145 163 1.003696 CTTCCTCCCTTCACCACTTCC 59.996 57.143 0.00 0.00 0.00 3.46
146 164 0.193574 TCCTCCCTTCACCACTTCCT 59.806 55.000 0.00 0.00 0.00 3.36
147 165 1.068121 CCTCCCTTCACCACTTCCTT 58.932 55.000 0.00 0.00 0.00 3.36
148 166 1.425448 CCTCCCTTCACCACTTCCTTT 59.575 52.381 0.00 0.00 0.00 3.11
149 167 2.158460 CCTCCCTTCACCACTTCCTTTT 60.158 50.000 0.00 0.00 0.00 2.27
150 168 2.887152 CTCCCTTCACCACTTCCTTTTG 59.113 50.000 0.00 0.00 0.00 2.44
151 169 1.963515 CCCTTCACCACTTCCTTTTGG 59.036 52.381 0.00 0.00 42.21 3.28
179 198 5.264395 CCTCCCTTTTGGATTTCAGTATGT 58.736 41.667 0.00 0.00 44.07 2.29
188 207 5.003160 TGGATTTCAGTATGTGTGTCCTTG 58.997 41.667 0.00 0.00 37.40 3.61
262 299 2.669569 TTGGACCAGCGCTTCAGC 60.670 61.111 7.50 0.00 37.78 4.26
303 346 3.567164 GCCACTCATTTCGGATGATCAAT 59.433 43.478 0.00 0.00 0.00 2.57
304 347 4.556104 GCCACTCATTTCGGATGATCAATG 60.556 45.833 0.00 0.00 0.00 2.82
305 348 4.818005 CCACTCATTTCGGATGATCAATGA 59.182 41.667 0.00 2.28 32.87 2.57
306 349 5.277683 CCACTCATTTCGGATGATCAATGAC 60.278 44.000 0.00 0.00 31.37 3.06
325 368 4.148079 TGACTGACTGACTGACTTCTCAT 58.852 43.478 0.00 0.00 0.00 2.90
453 527 2.094894 CAGGAAATTGCTAGCTCGTGTG 59.905 50.000 17.23 1.25 0.00 3.82
669 823 4.332819 GTGTGTCATAGTAAGGGATGCAAC 59.667 45.833 0.00 0.00 0.00 4.17
707 865 3.473367 CTGCAAAACTCGTCAATCTTCG 58.527 45.455 0.00 0.00 0.00 3.79
720 878 7.255569 TCGTCAATCTTCGTTTAGTACATCAT 58.744 34.615 0.00 0.00 0.00 2.45
787 955 4.444022 CCTGCTTGCATCCTTAGTCATAGT 60.444 45.833 0.00 0.00 0.00 2.12
820 992 6.238320 GCTGTCAGTTTATTCAGGAATGCTAG 60.238 42.308 4.81 0.00 32.50 3.42
826 998 8.341173 CAGTTTATTCAGGAATGCTAGTTCATC 58.659 37.037 4.81 0.00 32.50 2.92
1020 1198 1.161563 TGTTCCGACGCCTTTCCAAC 61.162 55.000 0.00 0.00 0.00 3.77
1149 1327 0.254178 TCAAAGCTGGGATGCCTCTC 59.746 55.000 4.35 0.00 0.00 3.20
1173 1351 2.037649 CGTAGCGTCATAGCGAAGAAG 58.962 52.381 0.00 0.00 43.00 2.85
1285 1463 3.945285 GTCTGAAGTCCTCTACTCCTCTG 59.055 52.174 0.00 0.00 37.50 3.35
1527 1705 1.612726 GCTGACAGTTGAAGATGGCCT 60.613 52.381 3.32 0.00 0.00 5.19
1551 1729 3.741075 CGTCTTGCCATAGAATACAGCCA 60.741 47.826 0.00 0.00 0.00 4.75
1716 1894 1.817520 TGGCAACACTCACACCACG 60.818 57.895 0.00 0.00 46.17 4.94
1896 2079 3.431486 GGCCTCTGTCTAGGTTTGATGAG 60.431 52.174 0.00 0.00 39.02 2.90
1900 2085 5.163499 CCTCTGTCTAGGTTTGATGAGTACC 60.163 48.000 0.00 0.00 31.46 3.34
1984 2169 5.065914 GCAAGATCCTGCCATGTTATTCTA 58.934 41.667 4.87 0.00 36.25 2.10
2159 2344 1.180456 TGCAAGACCCTGCCATGTTG 61.180 55.000 0.00 0.00 41.90 3.33
2197 2382 6.844696 TTCTACTTCAGTTTTGCTGTGTAG 57.155 37.500 15.93 15.93 45.23 2.74
2220 2405 9.265901 GTAGTAGTGCATCTTGATATCATGTTT 57.734 33.333 15.93 5.19 0.00 2.83
2223 2408 7.634671 AGTGCATCTTGATATCATGTTTGAA 57.365 32.000 15.93 8.83 34.96 2.69
2278 2463 3.628942 TGCTTATGCTGAAAGTATGCTGG 59.371 43.478 1.96 0.00 40.42 4.85
2287 2472 2.420058 AAGTATGCTGGCAGGGTTAC 57.580 50.000 17.64 0.00 0.00 2.50
2371 2556 9.841295 TCAGTCTGTTAAGTAATTACCTTGTTT 57.159 29.630 12.05 2.49 0.00 2.83
2417 2602 1.221566 GGGGCATTTTGGGACATGC 59.778 57.895 0.00 0.00 44.39 4.06
2447 2633 8.032952 TGCAACTGAAAGAACTATGTTATCTG 57.967 34.615 0.00 0.00 37.43 2.90
2448 2634 7.661437 TGCAACTGAAAGAACTATGTTATCTGT 59.339 33.333 0.00 0.00 37.43 3.41
2449 2635 7.959651 GCAACTGAAAGAACTATGTTATCTGTG 59.040 37.037 0.00 0.00 37.43 3.66
2450 2636 8.993121 CAACTGAAAGAACTATGTTATCTGTGT 58.007 33.333 0.00 0.00 37.43 3.72
2451 2637 8.539770 ACTGAAAGAACTATGTTATCTGTGTG 57.460 34.615 0.00 0.00 37.43 3.82
2452 2638 8.150945 ACTGAAAGAACTATGTTATCTGTGTGT 58.849 33.333 0.00 0.00 37.43 3.72
2453 2639 8.902540 TGAAAGAACTATGTTATCTGTGTGTT 57.097 30.769 0.00 0.00 0.00 3.32
2454 2640 8.773645 TGAAAGAACTATGTTATCTGTGTGTTG 58.226 33.333 0.00 0.00 0.00 3.33
2455 2641 8.677148 AAAGAACTATGTTATCTGTGTGTTGT 57.323 30.769 0.00 0.00 0.00 3.32
2456 2642 8.677148 AAGAACTATGTTATCTGTGTGTTGTT 57.323 30.769 0.00 0.00 0.00 2.83
2457 2643 8.087982 AGAACTATGTTATCTGTGTGTTGTTG 57.912 34.615 0.00 0.00 0.00 3.33
2458 2644 7.715249 AGAACTATGTTATCTGTGTGTTGTTGT 59.285 33.333 0.00 0.00 0.00 3.32
2459 2645 7.189693 ACTATGTTATCTGTGTGTTGTTGTG 57.810 36.000 0.00 0.00 0.00 3.33
2460 2646 4.285807 TGTTATCTGTGTGTTGTTGTGC 57.714 40.909 0.00 0.00 0.00 4.57
2461 2647 3.944650 TGTTATCTGTGTGTTGTTGTGCT 59.055 39.130 0.00 0.00 0.00 4.40
2462 2648 4.397730 TGTTATCTGTGTGTTGTTGTGCTT 59.602 37.500 0.00 0.00 0.00 3.91
2463 2649 5.105957 TGTTATCTGTGTGTTGTTGTGCTTT 60.106 36.000 0.00 0.00 0.00 3.51
2464 2650 6.094186 TGTTATCTGTGTGTTGTTGTGCTTTA 59.906 34.615 0.00 0.00 0.00 1.85
2465 2651 5.772825 ATCTGTGTGTTGTTGTGCTTTAT 57.227 34.783 0.00 0.00 0.00 1.40
2466 2652 5.574891 TCTGTGTGTTGTTGTGCTTTATT 57.425 34.783 0.00 0.00 0.00 1.40
2467 2653 5.960113 TCTGTGTGTTGTTGTGCTTTATTT 58.040 33.333 0.00 0.00 0.00 1.40
2468 2654 6.033341 TCTGTGTGTTGTTGTGCTTTATTTC 58.967 36.000 0.00 0.00 0.00 2.17
2469 2655 5.960113 TGTGTGTTGTTGTGCTTTATTTCT 58.040 33.333 0.00 0.00 0.00 2.52
2470 2656 6.033341 TGTGTGTTGTTGTGCTTTATTTCTC 58.967 36.000 0.00 0.00 0.00 2.87
2471 2657 5.458779 GTGTGTTGTTGTGCTTTATTTCTCC 59.541 40.000 0.00 0.00 0.00 3.71
2472 2658 5.359576 TGTGTTGTTGTGCTTTATTTCTCCT 59.640 36.000 0.00 0.00 0.00 3.69
2473 2659 6.127479 TGTGTTGTTGTGCTTTATTTCTCCTT 60.127 34.615 0.00 0.00 0.00 3.36
2474 2660 6.417930 GTGTTGTTGTGCTTTATTTCTCCTTC 59.582 38.462 0.00 0.00 0.00 3.46
2475 2661 5.705609 TGTTGTGCTTTATTTCTCCTTCC 57.294 39.130 0.00 0.00 0.00 3.46
2476 2662 4.522789 TGTTGTGCTTTATTTCTCCTTCCC 59.477 41.667 0.00 0.00 0.00 3.97
2477 2663 3.343617 TGTGCTTTATTTCTCCTTCCCG 58.656 45.455 0.00 0.00 0.00 5.14
2478 2664 3.244770 TGTGCTTTATTTCTCCTTCCCGT 60.245 43.478 0.00 0.00 0.00 5.28
2479 2665 3.127030 GTGCTTTATTTCTCCTTCCCGTG 59.873 47.826 0.00 0.00 0.00 4.94
2480 2666 2.683362 GCTTTATTTCTCCTTCCCGTGG 59.317 50.000 0.00 0.00 0.00 4.94
2481 2667 2.413310 TTATTTCTCCTTCCCGTGGC 57.587 50.000 0.00 0.00 0.00 5.01
2482 2668 0.544697 TATTTCTCCTTCCCGTGGCC 59.455 55.000 0.00 0.00 0.00 5.36
2483 2669 2.211468 ATTTCTCCTTCCCGTGGCCC 62.211 60.000 0.00 0.00 0.00 5.80
2488 2674 3.006728 CTTCCCGTGGCCCCTGTA 61.007 66.667 0.00 0.00 0.00 2.74
2489 2675 3.324108 TTCCCGTGGCCCCTGTAC 61.324 66.667 0.00 0.00 0.00 2.90
2490 2676 3.857521 TTCCCGTGGCCCCTGTACT 62.858 63.158 0.00 0.00 0.00 2.73
2491 2677 3.327404 CCCGTGGCCCCTGTACTT 61.327 66.667 0.00 0.00 0.00 2.24
2492 2678 2.267961 CCGTGGCCCCTGTACTTC 59.732 66.667 0.00 0.00 0.00 3.01
2493 2679 2.291043 CCGTGGCCCCTGTACTTCT 61.291 63.158 0.00 0.00 0.00 2.85
2494 2680 1.079127 CGTGGCCCCTGTACTTCTG 60.079 63.158 0.00 0.00 0.00 3.02
2495 2681 1.299976 GTGGCCCCTGTACTTCTGG 59.700 63.158 0.00 0.00 35.32 3.86
2496 2682 1.151899 TGGCCCCTGTACTTCTGGT 60.152 57.895 0.00 0.00 33.97 4.00
2497 2683 0.770557 TGGCCCCTGTACTTCTGGTT 60.771 55.000 0.00 0.00 33.97 3.67
2498 2684 0.035343 GGCCCCTGTACTTCTGGTTC 60.035 60.000 0.00 0.00 33.97 3.62
2499 2685 0.690762 GCCCCTGTACTTCTGGTTCA 59.309 55.000 0.00 0.00 33.97 3.18
2500 2686 1.610886 GCCCCTGTACTTCTGGTTCAC 60.611 57.143 0.00 0.00 33.97 3.18
2501 2687 1.978580 CCCCTGTACTTCTGGTTCACT 59.021 52.381 0.00 0.00 33.97 3.41
2502 2688 2.372172 CCCCTGTACTTCTGGTTCACTT 59.628 50.000 0.00 0.00 33.97 3.16
2503 2689 3.403038 CCCTGTACTTCTGGTTCACTTG 58.597 50.000 0.00 0.00 33.97 3.16
2504 2690 3.071023 CCCTGTACTTCTGGTTCACTTGA 59.929 47.826 0.00 0.00 33.97 3.02
2505 2691 4.444306 CCCTGTACTTCTGGTTCACTTGAA 60.444 45.833 0.00 0.00 33.97 2.69
2554 2740 9.268282 TGAACCCTTTCTAGAATAGTAATCTGT 57.732 33.333 5.89 0.00 40.38 3.41
2555 2741 9.535878 GAACCCTTTCTAGAATAGTAATCTGTG 57.464 37.037 5.89 0.00 40.38 3.66
2556 2742 8.611051 ACCCTTTCTAGAATAGTAATCTGTGT 57.389 34.615 5.89 0.00 40.38 3.72
2619 2826 6.795144 TGTTTTCATATGCCCTCAATGATT 57.205 33.333 0.00 0.00 30.17 2.57
2628 2835 4.870636 TGCCCTCAATGATTATTTCCTGT 58.129 39.130 0.00 0.00 0.00 4.00
2643 2850 2.550175 TCCTGTGGGATCTGATTGTCA 58.450 47.619 0.00 0.00 36.57 3.58
2669 2879 3.981071 ACCTAGCTTTGCTGTGTCATA 57.019 42.857 0.00 0.00 40.10 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 198 5.560722 TTTCTGAGATTACCAAGGACACA 57.439 39.130 0.00 0.00 0.00 3.72
188 207 4.636249 AGGCATCGATTTCTGAGATTACC 58.364 43.478 0.00 0.00 0.00 2.85
262 299 3.943381 TGGCAGTCAAGCATCAATCTAAG 59.057 43.478 0.00 0.00 35.83 2.18
303 346 3.555966 TGAGAAGTCAGTCAGTCAGTCA 58.444 45.455 0.00 0.00 0.00 3.41
304 347 4.782019 ATGAGAAGTCAGTCAGTCAGTC 57.218 45.455 0.00 0.00 35.66 3.51
305 348 5.321102 ACTATGAGAAGTCAGTCAGTCAGT 58.679 41.667 0.00 0.00 35.66 3.41
306 349 5.895636 ACTATGAGAAGTCAGTCAGTCAG 57.104 43.478 0.00 0.00 35.66 3.51
368 431 2.866762 GGCATCGGATGAACAGAACTAC 59.133 50.000 21.69 0.00 0.00 2.73
369 432 2.766263 AGGCATCGGATGAACAGAACTA 59.234 45.455 21.69 0.00 0.00 2.24
370 433 1.556911 AGGCATCGGATGAACAGAACT 59.443 47.619 21.69 4.56 0.00 3.01
371 434 2.029838 AGGCATCGGATGAACAGAAC 57.970 50.000 21.69 1.83 0.00 3.01
453 527 1.767759 AACCTTACATGGCAGCATCC 58.232 50.000 0.00 0.00 0.00 3.51
555 657 4.461431 TGCAACCGTAATACTCTGAAGAGA 59.539 41.667 14.20 0.00 44.74 3.10
557 659 4.219944 ACTGCAACCGTAATACTCTGAAGA 59.780 41.667 0.00 0.00 0.00 2.87
610 757 6.886459 ACATGAACTAGAATTGTAGCAACCAT 59.114 34.615 9.45 5.49 0.00 3.55
787 955 5.069318 TGAATAAACTGACAGCAATCACCA 58.931 37.500 1.25 0.00 0.00 4.17
820 992 5.008415 CCTTACATGGAAGCATCAGATGAAC 59.992 44.000 15.12 4.24 0.00 3.18
826 998 6.757897 TTTAACCTTACATGGAAGCATCAG 57.242 37.500 12.63 0.68 0.00 2.90
1020 1198 0.250858 TTGGGCTCATGGTGAGTGTG 60.251 55.000 8.58 0.00 45.94 3.82
1039 1217 1.674651 CAGATGCCAGTGCTGCTGT 60.675 57.895 0.00 0.00 43.55 4.40
1149 1327 2.011349 CGCTATGACGCTACGCCTG 61.011 63.158 0.00 0.00 0.00 4.85
1527 1705 3.457234 CTGTATTCTATGGCAAGACGCA 58.543 45.455 0.00 0.00 45.17 5.24
1551 1729 0.999406 GTGTCGTCGCATTAGCACAT 59.001 50.000 0.00 0.00 42.27 3.21
1711 1889 4.410883 TCAATATACCCTTCAATCCGTGGT 59.589 41.667 0.00 0.00 0.00 4.16
1716 1894 7.684428 GCACCTTTTCAATATACCCTTCAATCC 60.684 40.741 0.00 0.00 0.00 3.01
1896 2079 5.959618 AAGACCAAAATAGCACAAGGTAC 57.040 39.130 0.00 0.00 0.00 3.34
2159 2344 5.986135 TGAAGTAGAAAAGCTCAGTCAGAAC 59.014 40.000 0.00 0.00 0.00 3.01
2197 2382 8.146479 TCAAACATGATATCAAGATGCACTAC 57.854 34.615 14.59 0.00 0.00 2.73
2220 2405 8.250332 GGGAAATACATTAATGCTTTCAGTTCA 58.750 33.333 27.91 4.49 35.84 3.18
2223 2408 7.961326 AGGGAAATACATTAATGCTTTCAGT 57.039 32.000 27.91 18.89 35.84 3.41
2278 2463 4.017126 AGCCATTTTTCTAGTAACCCTGC 58.983 43.478 0.00 0.00 0.00 4.85
2371 2556 1.535028 CATGCTCACCGCTGTTTAACA 59.465 47.619 0.00 0.00 40.11 2.41
2384 2569 3.518766 CCCCTATTTGGCATGCTCA 57.481 52.632 18.92 11.22 0.00 4.26
2444 2630 5.574891 AATAAAGCACAACAACACACAGA 57.425 34.783 0.00 0.00 0.00 3.41
2447 2633 5.458779 GGAGAAATAAAGCACAACAACACAC 59.541 40.000 0.00 0.00 0.00 3.82
2448 2634 5.359576 AGGAGAAATAAAGCACAACAACACA 59.640 36.000 0.00 0.00 0.00 3.72
2449 2635 5.831997 AGGAGAAATAAAGCACAACAACAC 58.168 37.500 0.00 0.00 0.00 3.32
2450 2636 6.460953 GGAAGGAGAAATAAAGCACAACAACA 60.461 38.462 0.00 0.00 0.00 3.33
2451 2637 5.920840 GGAAGGAGAAATAAAGCACAACAAC 59.079 40.000 0.00 0.00 0.00 3.32
2452 2638 5.010617 GGGAAGGAGAAATAAAGCACAACAA 59.989 40.000 0.00 0.00 0.00 2.83
2453 2639 4.522789 GGGAAGGAGAAATAAAGCACAACA 59.477 41.667 0.00 0.00 0.00 3.33
2454 2640 4.379499 CGGGAAGGAGAAATAAAGCACAAC 60.379 45.833 0.00 0.00 0.00 3.32
2455 2641 3.756434 CGGGAAGGAGAAATAAAGCACAA 59.244 43.478 0.00 0.00 0.00 3.33
2456 2642 3.244770 ACGGGAAGGAGAAATAAAGCACA 60.245 43.478 0.00 0.00 0.00 4.57
2457 2643 3.127030 CACGGGAAGGAGAAATAAAGCAC 59.873 47.826 0.00 0.00 0.00 4.40
2458 2644 3.343617 CACGGGAAGGAGAAATAAAGCA 58.656 45.455 0.00 0.00 0.00 3.91
2459 2645 2.683362 CCACGGGAAGGAGAAATAAAGC 59.317 50.000 0.00 0.00 0.00 3.51
2460 2646 2.683362 GCCACGGGAAGGAGAAATAAAG 59.317 50.000 0.00 0.00 0.00 1.85
2461 2647 2.619590 GGCCACGGGAAGGAGAAATAAA 60.620 50.000 0.00 0.00 0.00 1.40
2462 2648 1.064979 GGCCACGGGAAGGAGAAATAA 60.065 52.381 0.00 0.00 0.00 1.40
2463 2649 0.544697 GGCCACGGGAAGGAGAAATA 59.455 55.000 0.00 0.00 0.00 1.40
2464 2650 1.303282 GGCCACGGGAAGGAGAAAT 59.697 57.895 0.00 0.00 0.00 2.17
2465 2651 2.754375 GGCCACGGGAAGGAGAAA 59.246 61.111 0.00 0.00 0.00 2.52
2466 2652 3.327404 GGGCCACGGGAAGGAGAA 61.327 66.667 4.39 0.00 0.00 2.87
2471 2657 3.006728 TACAGGGGCCACGGGAAG 61.007 66.667 10.79 0.00 0.00 3.46
2472 2658 3.324108 GTACAGGGGCCACGGGAA 61.324 66.667 10.79 0.00 0.00 3.97
2473 2659 3.857521 AAGTACAGGGGCCACGGGA 62.858 63.158 10.79 0.00 0.00 5.14
2474 2660 3.325201 GAAGTACAGGGGCCACGGG 62.325 68.421 10.79 3.77 0.00 5.28
2475 2661 2.267961 GAAGTACAGGGGCCACGG 59.732 66.667 2.52 2.52 0.00 4.94
2476 2662 1.079127 CAGAAGTACAGGGGCCACG 60.079 63.158 4.39 0.00 0.00 4.94
2477 2663 1.299976 CCAGAAGTACAGGGGCCAC 59.700 63.158 4.39 0.00 0.00 5.01
2478 2664 0.770557 AACCAGAAGTACAGGGGCCA 60.771 55.000 4.39 0.00 0.00 5.36
2479 2665 0.035343 GAACCAGAAGTACAGGGGCC 60.035 60.000 0.00 0.00 0.00 5.80
2480 2666 0.690762 TGAACCAGAAGTACAGGGGC 59.309 55.000 0.00 0.00 0.00 5.80
2481 2667 1.978580 AGTGAACCAGAAGTACAGGGG 59.021 52.381 0.00 0.00 0.00 4.79
2482 2668 3.071023 TCAAGTGAACCAGAAGTACAGGG 59.929 47.826 0.00 0.00 0.00 4.45
2483 2669 4.336889 TCAAGTGAACCAGAAGTACAGG 57.663 45.455 0.00 0.00 0.00 4.00
2484 2670 5.659048 GTTCAAGTGAACCAGAAGTACAG 57.341 43.478 12.29 0.00 46.42 2.74
2496 2682 6.661805 GGGATGTTAAATAGGGTTCAAGTGAA 59.338 38.462 0.00 0.00 0.00 3.18
2497 2683 6.184789 GGGATGTTAAATAGGGTTCAAGTGA 58.815 40.000 0.00 0.00 0.00 3.41
2498 2684 5.359860 GGGGATGTTAAATAGGGTTCAAGTG 59.640 44.000 0.00 0.00 0.00 3.16
2499 2685 5.015817 TGGGGATGTTAAATAGGGTTCAAGT 59.984 40.000 0.00 0.00 0.00 3.16
2500 2686 5.359860 GTGGGGATGTTAAATAGGGTTCAAG 59.640 44.000 0.00 0.00 0.00 3.02
2501 2687 5.265989 GTGGGGATGTTAAATAGGGTTCAA 58.734 41.667 0.00 0.00 0.00 2.69
2502 2688 4.325501 GGTGGGGATGTTAAATAGGGTTCA 60.326 45.833 0.00 0.00 0.00 3.18
2503 2689 4.079385 AGGTGGGGATGTTAAATAGGGTTC 60.079 45.833 0.00 0.00 0.00 3.62
2504 2690 3.862309 AGGTGGGGATGTTAAATAGGGTT 59.138 43.478 0.00 0.00 0.00 4.11
2505 2691 3.462205 GAGGTGGGGATGTTAAATAGGGT 59.538 47.826 0.00 0.00 0.00 4.34
2506 2692 3.722101 AGAGGTGGGGATGTTAAATAGGG 59.278 47.826 0.00 0.00 0.00 3.53
2507 2693 4.412199 TCAGAGGTGGGGATGTTAAATAGG 59.588 45.833 0.00 0.00 0.00 2.57
2508 2694 5.630415 TCAGAGGTGGGGATGTTAAATAG 57.370 43.478 0.00 0.00 0.00 1.73
2509 2695 5.339695 GGTTCAGAGGTGGGGATGTTAAATA 60.340 44.000 0.00 0.00 0.00 1.40
2510 2696 4.569865 GGTTCAGAGGTGGGGATGTTAAAT 60.570 45.833 0.00 0.00 0.00 1.40
2511 2697 3.245122 GGTTCAGAGGTGGGGATGTTAAA 60.245 47.826 0.00 0.00 0.00 1.52
2512 2698 2.307686 GGTTCAGAGGTGGGGATGTTAA 59.692 50.000 0.00 0.00 0.00 2.01
2513 2699 1.913419 GGTTCAGAGGTGGGGATGTTA 59.087 52.381 0.00 0.00 0.00 2.41
2514 2700 0.698818 GGTTCAGAGGTGGGGATGTT 59.301 55.000 0.00 0.00 0.00 2.71
2515 2701 1.208165 GGGTTCAGAGGTGGGGATGT 61.208 60.000 0.00 0.00 0.00 3.06
2554 2740 3.699038 AGCAAAAACAAGAGGCTGTAACA 59.301 39.130 0.00 0.00 32.76 2.41
2555 2741 4.044426 CAGCAAAAACAAGAGGCTGTAAC 58.956 43.478 0.00 0.00 45.11 2.50
2556 2742 4.305989 CAGCAAAAACAAGAGGCTGTAA 57.694 40.909 0.00 0.00 45.11 2.41
2558 2744 2.877043 CAGCAAAAACAAGAGGCTGT 57.123 45.000 0.00 0.00 45.11 4.40
2560 2746 2.101415 GGAACAGCAAAAACAAGAGGCT 59.899 45.455 0.00 0.00 34.64 4.58
2561 2747 2.101415 AGGAACAGCAAAAACAAGAGGC 59.899 45.455 0.00 0.00 0.00 4.70
2628 2835 5.014123 AGGTACTTTTGACAATCAGATCCCA 59.986 40.000 0.00 0.00 27.25 4.37
2643 2850 4.461198 ACACAGCAAAGCTAGGTACTTTT 58.539 39.130 0.00 0.00 41.75 2.27


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

AutoCloner maintained by Alex Coulton.