Multiple sequence alignment - TraesCS4A01G207600

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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 TraesCS4A01G207600 chr4A 100.000 3551 0 0 1 3551 500899825 500903375 0.000000e+00 6558.0
1 TraesCS4A01G207600 chr4A 84.494 445 60 8 1888 2329 67892522 67892084 7.040000e-117 431.0
2 TraesCS4A01G207600 chr4A 89.655 116 12 0 1394 1509 67894297 67894182 7.940000e-32 148.0
3 TraesCS4A01G207600 chr4A 83.019 159 25 2 1208 1365 197971118 197971275 3.700000e-30 143.0
4 TraesCS4A01G207600 chr4A 100.000 42 0 0 3030 3071 500902813 500902854 1.060000e-10 78.7
5 TraesCS4A01G207600 chr4A 100.000 42 0 0 2989 3030 500902854 500902895 1.060000e-10 78.7
6 TraesCS4A01G207600 chr4D 92.850 3049 104 46 11 3011 88120835 88123817 0.000000e+00 4318.0
7 TraesCS4A01G207600 chr4D 93.499 523 19 6 3030 3551 88123795 88124303 0.000000e+00 763.0
8 TraesCS4A01G207600 chr4D 84.494 445 60 8 1888 2329 386436134 386435696 7.040000e-117 431.0
9 TraesCS4A01G207600 chr4D 89.655 116 12 0 1394 1509 386437956 386437841 7.940000e-32 148.0
10 TraesCS4A01G207600 chr4D 92.308 78 6 0 1718 1795 386437275 386437198 1.040000e-20 111.0
11 TraesCS4A01G207600 chr4B 92.243 2965 104 44 11 2913 124740548 124743448 0.000000e+00 4085.0
12 TraesCS4A01G207600 chr4B 84.719 445 59 8 1888 2329 473569981 473569543 1.510000e-118 436.0
13 TraesCS4A01G207600 chr4B 98.750 240 3 0 3310 3549 124743892 124744131 9.110000e-116 427.0
14 TraesCS4A01G207600 chr4B 91.034 290 17 5 3030 3317 124743451 124743733 2.000000e-102 383.0
15 TraesCS4A01G207600 chr4B 89.655 116 12 0 1394 1509 473571692 473571577 7.940000e-32 148.0
16 TraesCS4A01G207600 chr4B 100.000 28 0 0 822 849 670853525 670853552 6.000000e-03 52.8
17 TraesCS4A01G207600 chr1D 87.593 403 48 2 1394 1795 62600891 62600490 1.930000e-127 466.0
18 TraesCS4A01G207600 chr1D 84.045 445 62 8 1888 2329 374471503 374471065 1.520000e-113 420.0
19 TraesCS4A01G207600 chr1D 91.489 188 15 1 1507 1693 374473269 374473082 1.260000e-64 257.0
20 TraesCS4A01G207600 chr1D 83.246 191 28 3 1208 1396 374474030 374473842 4.710000e-39 172.0
21 TraesCS4A01G207600 chr1B 87.129 404 48 4 1394 1795 99755109 99754708 4.180000e-124 455.0
22 TraesCS4A01G207600 chr1B 84.821 448 55 9 1888 2330 99753564 99753125 4.210000e-119 438.0
23 TraesCS4A01G207600 chr1B 83.766 462 60 11 1873 2329 499469129 499468678 1.180000e-114 424.0
24 TraesCS4A01G207600 chr1B 83.770 191 27 3 1208 1396 499471527 499471339 1.010000e-40 178.0
25 TraesCS4A01G207600 chr1B 84.615 117 16 2 1394 1509 499470945 499470830 8.060000e-22 115.0
26 TraesCS4A01G207600 chr1B 100.000 29 0 0 827 855 647045145 647045173 2.000000e-03 54.7
27 TraesCS4A01G207600 chr1A 86.765 408 50 4 1390 1795 60735590 60735995 5.410000e-123 451.0
28 TraesCS4A01G207600 chr1A 84.821 448 55 9 1888 2330 60737113 60737552 4.210000e-119 438.0
29 TraesCS4A01G207600 chr1A 83.893 447 59 9 1888 2329 474226181 474225743 7.090000e-112 414.0
30 TraesCS4A01G207600 chr1A 83.770 191 27 3 1208 1396 474228844 474228656 1.010000e-40 178.0
31 TraesCS4A01G207600 chr1A 82.486 177 31 0 2362 2538 60738595 60738771 4.750000e-34 156.0
32 TraesCS4A01G207600 chr3D 82.895 456 71 7 1863 2317 476553600 476554049 1.540000e-108 403.0
33 TraesCS4A01G207600 chr3D 87.931 290 33 2 1507 1795 476551514 476551802 1.220000e-89 340.0
34 TraesCS4A01G207600 chr3D 85.714 154 20 2 1208 1360 476550594 476550746 1.020000e-35 161.0
35 TraesCS4A01G207600 chr3B 83.333 444 67 7 1888 2329 635220436 635220874 1.540000e-108 403.0
36 TraesCS4A01G207600 chr3B 86.207 290 38 2 1507 1795 635218372 635218660 2.660000e-81 313.0
37 TraesCS4A01G207600 chr3B 85.714 154 20 2 1208 1360 635217462 635217614 1.020000e-35 161.0
38 TraesCS4A01G207600 chr3A 88.194 288 32 2 1507 1793 620220605 620220319 3.390000e-90 342.0
39 TraesCS4A01G207600 chr3A 82.292 192 28 5 1208 1396 620221447 620221259 1.020000e-35 161.0


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 TraesCS4A01G207600 chr4A 500899825 500903375 3550 False 2238.466667 6558 100.000000 1 3551 3 chr4A.!!$F2 3550
1 TraesCS4A01G207600 chr4A 67892084 67894297 2213 True 289.500000 431 87.074500 1394 2329 2 chr4A.!!$R1 935
2 TraesCS4A01G207600 chr4D 88120835 88124303 3468 False 2540.500000 4318 93.174500 11 3551 2 chr4D.!!$F1 3540
3 TraesCS4A01G207600 chr4D 386435696 386437956 2260 True 230.000000 431 88.819000 1394 2329 3 chr4D.!!$R1 935
4 TraesCS4A01G207600 chr4B 124740548 124744131 3583 False 1631.666667 4085 94.009000 11 3549 3 chr4B.!!$F2 3538
5 TraesCS4A01G207600 chr4B 473569543 473571692 2149 True 292.000000 436 87.187000 1394 2329 2 chr4B.!!$R1 935
6 TraesCS4A01G207600 chr1D 374471065 374474030 2965 True 283.000000 420 86.260000 1208 2329 3 chr1D.!!$R2 1121
7 TraesCS4A01G207600 chr1B 99753125 99755109 1984 True 446.500000 455 85.975000 1394 2330 2 chr1B.!!$R1 936
8 TraesCS4A01G207600 chr1B 499468678 499471527 2849 True 239.000000 424 84.050333 1208 2329 3 chr1B.!!$R2 1121
9 TraesCS4A01G207600 chr1A 60735590 60738771 3181 False 348.333333 451 84.690667 1390 2538 3 chr1A.!!$F1 1148
10 TraesCS4A01G207600 chr1A 474225743 474228844 3101 True 296.000000 414 83.831500 1208 2329 2 chr1A.!!$R1 1121
11 TraesCS4A01G207600 chr3D 476550594 476554049 3455 False 301.333333 403 85.513333 1208 2317 3 chr3D.!!$F1 1109
12 TraesCS4A01G207600 chr3B 635217462 635220874 3412 False 292.333333 403 85.084667 1208 2329 3 chr3B.!!$F1 1121
13 TraesCS4A01G207600 chr3A 620220319 620221447 1128 True 251.500000 342 85.243000 1208 1793 2 chr3A.!!$R1 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
987 1024 0.468029 GGAGGAGGAGGAGCAGAGAG 60.468 65.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 8312 1.201758 GCGCACAAACACACAAAACAC 60.202 47.619 0.3 0.0 0.0 3.32 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
75 76 5.700402 AGTACTATGAATGCCCTGTTCTT 57.300 39.130 0.00 0.00 0.00 2.52
92 114 7.278646 CCCTGTTCTTTTTCTTTTTCTTTCCAG 59.721 37.037 0.00 0.00 0.00 3.86
195 217 2.886604 CTGCGCTGCTGCTCTCTC 60.887 66.667 9.73 0.00 36.97 3.20
196 218 3.359515 CTGCGCTGCTGCTCTCTCT 62.360 63.158 9.73 0.00 36.97 3.10
238 260 3.214696 AGGGCTTACATATGAAGGTGC 57.785 47.619 10.38 6.12 0.00 5.01
304 326 7.069208 AGGAAATCTGATCTCTTAATTTTGCCC 59.931 37.037 0.00 0.00 0.00 5.36
392 415 9.391006 CTATTACAACATTCACCTTAAAGCCTA 57.609 33.333 0.00 0.00 0.00 3.93
393 416 7.681939 TTACAACATTCACCTTAAAGCCTAG 57.318 36.000 0.00 0.00 0.00 3.02
394 417 5.876357 ACAACATTCACCTTAAAGCCTAGA 58.124 37.500 0.00 0.00 0.00 2.43
395 418 6.303839 ACAACATTCACCTTAAAGCCTAGAA 58.696 36.000 0.00 0.00 0.00 2.10
423 454 6.850555 ACTCCTAACTACACATTACGAACTC 58.149 40.000 0.00 0.00 0.00 3.01
460 491 3.623060 AGTGGACATCATATTTGTGCGAC 59.377 43.478 0.00 3.60 38.16 5.19
465 496 5.484173 ACATCATATTTGTGCGACGAAAT 57.516 34.783 0.00 0.00 0.00 2.17
466 497 5.879237 ACATCATATTTGTGCGACGAAATT 58.121 33.333 0.00 0.00 0.00 1.82
467 498 7.010697 ACATCATATTTGTGCGACGAAATTA 57.989 32.000 0.00 0.00 0.00 1.40
468 499 7.468441 ACATCATATTTGTGCGACGAAATTAA 58.532 30.769 0.00 0.00 0.00 1.40
481 512 6.513317 CGACGAAATTAAACCTTTTGATTGC 58.487 36.000 0.00 0.00 0.00 3.56
494 528 3.340727 GATTGCACAATCAGCAGCC 57.659 52.632 16.57 0.00 44.89 4.85
516 550 4.651503 CCAGCTATCTCTAAACCTCCAAGA 59.348 45.833 0.00 0.00 0.00 3.02
539 573 3.149005 TGATGGGTTTGTACAAGGACC 57.851 47.619 17.72 17.72 0.00 4.46
566 600 4.418401 CCAACGTTGCATGGGCCG 62.418 66.667 22.93 2.62 40.13 6.13
580 614 2.247437 GGCCGCTAAGCTCCAATCG 61.247 63.158 0.00 0.00 0.00 3.34
640 675 6.116126 ACCCATGTTTAGAGATCTTTGCTAC 58.884 40.000 0.00 0.00 0.00 3.58
679 714 2.851195 ACAATACATTCGCCCATCTCC 58.149 47.619 0.00 0.00 0.00 3.71
710 747 2.941333 CTGAACAGCCGCTGTGTG 59.059 61.111 26.37 14.99 44.62 3.82
711 748 1.889105 CTGAACAGCCGCTGTGTGT 60.889 57.895 26.37 11.39 44.62 3.72
712 749 2.109538 CTGAACAGCCGCTGTGTGTG 62.110 60.000 26.37 13.01 44.62 3.82
713 750 2.124736 AACAGCCGCTGTGTGTGT 60.125 55.556 26.37 7.83 44.62 3.72
714 751 0.878523 GAACAGCCGCTGTGTGTGTA 60.879 55.000 26.37 0.00 44.62 2.90
729 766 4.510340 GTGTGTGTAGTGTACCAAAGGAAG 59.490 45.833 0.00 0.00 0.00 3.46
732 769 3.072038 GTGTAGTGTACCAAAGGAAGGGT 59.928 47.826 0.00 0.00 41.21 4.34
771 808 6.153340 AGAGGAGAGAAGAGAAAGATCACAAG 59.847 42.308 0.00 0.00 0.00 3.16
778 815 7.096551 AGAAGAGAAAGATCACAAGCTAGTTC 58.903 38.462 0.00 0.00 0.00 3.01
917 954 3.735029 GCTGCTTGCTTGCTCGCT 61.735 61.111 0.00 0.00 38.95 4.93
918 955 2.479650 CTGCTTGCTTGCTCGCTC 59.520 61.111 3.47 0.00 0.00 5.03
919 956 3.364249 CTGCTTGCTTGCTCGCTCG 62.364 63.158 3.47 0.00 0.00 5.03
920 957 3.114616 GCTTGCTTGCTCGCTCGA 61.115 61.111 0.00 0.00 0.00 4.04
921 958 2.459442 GCTTGCTTGCTCGCTCGAT 61.459 57.895 0.00 0.00 0.00 3.59
922 959 1.635281 CTTGCTTGCTCGCTCGATC 59.365 57.895 0.00 0.00 0.00 3.69
923 960 1.760268 CTTGCTTGCTCGCTCGATCC 61.760 60.000 0.00 0.00 0.00 3.36
924 961 2.105930 GCTTGCTCGCTCGATCCT 59.894 61.111 0.00 0.00 0.00 3.24
966 1003 0.762082 TGCCATAGCAGGGGAGAGAG 60.762 60.000 0.00 0.00 46.52 3.20
967 1004 0.470833 GCCATAGCAGGGGAGAGAGA 60.471 60.000 0.00 0.00 39.53 3.10
968 1005 1.631405 CCATAGCAGGGGAGAGAGAG 58.369 60.000 0.00 0.00 0.00 3.20
969 1006 1.631405 CATAGCAGGGGAGAGAGAGG 58.369 60.000 0.00 0.00 0.00 3.69
970 1007 1.146774 CATAGCAGGGGAGAGAGAGGA 59.853 57.143 0.00 0.00 0.00 3.71
987 1024 0.468029 GGAGGAGGAGGAGCAGAGAG 60.468 65.000 0.00 0.00 0.00 3.20
988 1025 0.468029 GAGGAGGAGGAGCAGAGAGG 60.468 65.000 0.00 0.00 0.00 3.69
990 1027 1.457455 GAGGAGGAGCAGAGAGGGG 60.457 68.421 0.00 0.00 0.00 4.79
1370 1407 2.747855 CAAGGAGCGGGACAAGGC 60.748 66.667 0.00 0.00 0.00 4.35
1848 4238 8.417176 GTGTAGTAATTTTGCATGTTTTTCGAG 58.583 33.333 0.00 0.00 0.00 4.04
1953 6515 1.227380 CTACCTCATGGCCACGCTC 60.227 63.158 8.16 0.00 36.63 5.03
2564 8137 6.152831 CCAAGGCACTAATTACCTAGCTTTTT 59.847 38.462 0.00 0.00 38.49 1.94
2726 8307 6.820470 TGTTTTTGAATTTTGATCGTGTCC 57.180 33.333 0.00 0.00 0.00 4.02
2731 8312 5.107109 TGAATTTTGATCGTGTCCTGTTG 57.893 39.130 0.00 0.00 0.00 3.33
2749 8330 3.246226 TGTTGTGTTTTGTGTGTTTGTGC 59.754 39.130 0.00 0.00 0.00 4.57
2751 8332 1.063806 TGTTTTGTGTGTTTGTGCGC 58.936 45.000 0.00 0.00 0.00 6.09
2753 8334 1.678269 TTTTGTGTGTTTGTGCGCGC 61.678 50.000 27.26 27.26 0.00 6.86
2754 8335 4.544689 TGTGTGTTTGTGCGCGCC 62.545 61.111 30.77 20.33 0.00 6.53
2755 8336 4.544689 GTGTGTTTGTGCGCGCCA 62.545 61.111 30.77 22.86 0.00 5.69
2759 8351 2.354539 GTTTGTGCGCGCCATGTT 60.355 55.556 30.77 0.00 0.00 2.71
2763 8355 1.786049 TTGTGCGCGCCATGTTTGTA 61.786 50.000 30.77 2.53 0.00 2.41
2766 8358 0.242286 TGCGCGCCATGTTTGTAATT 59.758 45.000 30.77 0.00 0.00 1.40
2767 8359 0.913876 GCGCGCCATGTTTGTAATTC 59.086 50.000 23.24 0.00 0.00 2.17
2804 8413 3.624410 TCATGAGAACTGTATGCATGTGC 59.376 43.478 10.16 0.00 37.98 4.57
2874 8488 0.687354 TTCCGCTCTTTGCTTCTCCT 59.313 50.000 0.00 0.00 40.11 3.69
2891 8505 8.198109 TGCTTCTCCTATCTATAAAGTTCACAC 58.802 37.037 0.00 0.00 0.00 3.82
2903 8517 1.140816 GTTCACACGCAGTTCTCCTC 58.859 55.000 0.00 0.00 41.61 3.71
2904 8518 0.033504 TTCACACGCAGTTCTCCTCC 59.966 55.000 0.00 0.00 41.61 4.30
2913 8527 2.159043 GCAGTTCTCCTCCATGATTCGA 60.159 50.000 0.00 0.00 0.00 3.71
2914 8528 3.679917 GCAGTTCTCCTCCATGATTCGAA 60.680 47.826 0.00 0.00 0.00 3.71
2915 8529 4.507710 CAGTTCTCCTCCATGATTCGAAA 58.492 43.478 0.00 0.00 0.00 3.46
2916 8530 4.937620 CAGTTCTCCTCCATGATTCGAAAA 59.062 41.667 0.00 0.00 0.00 2.29
2950 8564 8.729756 CCATGTCTGATTTATACAAAGTTCACA 58.270 33.333 0.00 0.00 0.00 3.58
2953 8567 9.283768 TGTCTGATTTATACAAAGTTCACATGT 57.716 29.630 0.00 0.00 0.00 3.21
3007 8621 8.950007 TTGTTCTCCCTGGTTTTTAATTAGAT 57.050 30.769 0.00 0.00 0.00 1.98
3011 8625 6.603201 TCTCCCTGGTTTTTAATTAGATGCAG 59.397 38.462 0.00 0.00 0.00 4.41
3012 8626 6.489603 TCCCTGGTTTTTAATTAGATGCAGA 58.510 36.000 0.00 0.00 0.00 4.26
3013 8627 6.603201 TCCCTGGTTTTTAATTAGATGCAGAG 59.397 38.462 0.00 0.00 0.00 3.35
3014 8628 6.268566 CCTGGTTTTTAATTAGATGCAGAGC 58.731 40.000 0.00 0.00 0.00 4.09
3015 8629 6.127647 CCTGGTTTTTAATTAGATGCAGAGCA 60.128 38.462 0.00 0.00 44.86 4.26
3032 8646 7.885297 TGCAGAGCATTTTTAATATGTATCCC 58.115 34.615 0.00 0.00 31.71 3.85
3033 8647 7.725397 TGCAGAGCATTTTTAATATGTATCCCT 59.275 33.333 0.00 0.00 31.71 4.20
3034 8648 8.025445 GCAGAGCATTTTTAATATGTATCCCTG 58.975 37.037 0.00 0.00 0.00 4.45
3035 8649 8.517878 CAGAGCATTTTTAATATGTATCCCTGG 58.482 37.037 0.00 0.00 0.00 4.45
3036 8650 8.227507 AGAGCATTTTTAATATGTATCCCTGGT 58.772 33.333 0.00 0.00 0.00 4.00
3037 8651 8.782137 AGCATTTTTAATATGTATCCCTGGTT 57.218 30.769 0.00 0.00 0.00 3.67
3038 8652 9.212593 AGCATTTTTAATATGTATCCCTGGTTT 57.787 29.630 0.00 0.00 0.00 3.27
3039 8653 9.830975 GCATTTTTAATATGTATCCCTGGTTTT 57.169 29.630 0.00 0.00 0.00 2.43
3050 8664 8.232913 TGTATCCCTGGTTTTTAATTAGATGC 57.767 34.615 0.00 0.00 0.00 3.91
3051 8665 7.836685 TGTATCCCTGGTTTTTAATTAGATGCA 59.163 33.333 0.00 0.00 0.00 3.96
3052 8666 6.773976 TCCCTGGTTTTTAATTAGATGCAG 57.226 37.500 0.00 0.00 0.00 4.41
3053 8667 6.489603 TCCCTGGTTTTTAATTAGATGCAGA 58.510 36.000 0.00 0.00 0.00 4.26
3054 8668 6.603201 TCCCTGGTTTTTAATTAGATGCAGAG 59.397 38.462 0.00 0.00 0.00 3.35
3055 8669 6.268566 CCTGGTTTTTAATTAGATGCAGAGC 58.731 40.000 0.00 0.00 0.00 4.09
3056 8670 6.127647 CCTGGTTTTTAATTAGATGCAGAGCA 60.128 38.462 0.00 0.00 44.86 4.26
3201 8817 1.778334 TGTGCTGCTACACTACAACG 58.222 50.000 0.00 0.00 41.30 4.10
3210 8826 2.743636 ACACTACAACGGTGGAGATG 57.256 50.000 22.46 16.13 38.04 2.90
3215 8831 5.046878 ACACTACAACGGTGGAGATGATTTA 60.047 40.000 22.46 0.00 38.04 1.40
3218 8834 7.169308 CACTACAACGGTGGAGATGATTTATAC 59.831 40.741 22.46 0.00 38.04 1.47
3229 8845 8.623903 TGGAGATGATTTATACAGATTTTGTGC 58.376 33.333 0.00 0.00 41.10 4.57
3292 8909 6.012157 CCCTCCCTGATAATCAATTACTCCAT 60.012 42.308 0.00 0.00 0.00 3.41
3354 9137 4.036941 GAGGGTCCTACCATCTACTAGG 57.963 54.545 3.58 0.00 45.03 3.02
3393 9183 1.609208 CATCCCCTTCATAAAGCGGG 58.391 55.000 0.00 0.00 41.14 6.13
3416 9206 4.634883 GCATCCTATGGTGATGATGATGAC 59.365 45.833 10.37 0.00 41.72 3.06
3476 9266 7.040062 CCACAGGACAACTAAATAATTTCACCA 60.040 37.037 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.884814 GTGATAGGGGATCTATGGTACTATAAT 57.115 37.037 0.26 0.00 38.71 1.28
4 5 9.081508 AGTGATAGGGGATCTATGGTACTATAA 57.918 37.037 0.26 0.00 38.71 0.98
5 6 8.654751 AGTGATAGGGGATCTATGGTACTATA 57.345 38.462 0.00 0.00 38.71 1.31
6 7 7.547177 AGTGATAGGGGATCTATGGTACTAT 57.453 40.000 0.00 0.00 38.71 2.12
7 8 6.989709 AGTGATAGGGGATCTATGGTACTA 57.010 41.667 0.00 0.00 38.71 1.82
8 9 5.887480 AGTGATAGGGGATCTATGGTACT 57.113 43.478 0.00 0.00 38.71 2.73
9 10 9.134055 GTTATAGTGATAGGGGATCTATGGTAC 57.866 40.741 0.00 0.00 38.71 3.34
154 176 0.816018 TTAGTTGGCACACGTGTGGG 60.816 55.000 40.73 23.49 45.72 4.61
195 217 8.240682 CCCTAAGATCGACAAGAATATCAGTAG 58.759 40.741 0.00 0.00 0.00 2.57
196 218 7.309255 GCCCTAAGATCGACAAGAATATCAGTA 60.309 40.741 0.00 0.00 0.00 2.74
318 341 9.838163 GTATTTTATTTTGTTCACACGGAAAAC 57.162 29.630 0.00 0.00 37.23 2.43
351 374 6.435904 TGTTGTAATAGCTTGGCAATTAACCT 59.564 34.615 0.00 0.00 0.00 3.50
392 415 8.457261 CGTAATGTGTAGTTAGGAGTACTTTCT 58.543 37.037 0.00 0.69 33.64 2.52
393 416 8.454106 TCGTAATGTGTAGTTAGGAGTACTTTC 58.546 37.037 0.00 0.00 33.64 2.62
394 417 8.340618 TCGTAATGTGTAGTTAGGAGTACTTT 57.659 34.615 0.00 0.00 33.64 2.66
395 418 7.928307 TCGTAATGTGTAGTTAGGAGTACTT 57.072 36.000 0.00 0.00 33.64 2.24
460 491 7.171447 TGTGCAATCAAAAGGTTTAATTTCG 57.829 32.000 0.00 0.00 0.00 3.46
494 528 5.860941 TCTTGGAGGTTTAGAGATAGCTG 57.139 43.478 0.00 0.00 0.00 4.24
516 550 4.526650 GGTCCTTGTACAAACCCATCATTT 59.473 41.667 15.82 0.00 0.00 2.32
566 600 1.876322 AGATGCGATTGGAGCTTAGC 58.124 50.000 0.00 0.00 35.28 3.09
597 632 1.014044 TCCGACTGTGATCTTTGCGC 61.014 55.000 0.00 0.00 0.00 6.09
679 714 3.799420 GCTGTTCAGCGAATAGTAAGAGG 59.201 47.826 9.04 0.00 34.13 3.69
708 745 4.062991 CCTTCCTTTGGTACACTACACAC 58.937 47.826 0.00 0.00 39.29 3.82
710 747 3.072038 ACCCTTCCTTTGGTACACTACAC 59.928 47.826 0.00 0.00 39.29 2.90
711 748 3.320129 ACCCTTCCTTTGGTACACTACA 58.680 45.455 0.00 0.00 39.29 2.74
712 749 5.488262 TTACCCTTCCTTTGGTACACTAC 57.512 43.478 0.00 0.00 39.29 2.73
713 750 5.013391 CCTTTACCCTTCCTTTGGTACACTA 59.987 44.000 0.00 0.00 39.29 2.74
714 751 4.202535 CCTTTACCCTTCCTTTGGTACACT 60.203 45.833 0.00 0.00 39.29 3.55
729 766 3.332783 TCCTCTCCCTTTTTCCTTTACCC 59.667 47.826 0.00 0.00 0.00 3.69
732 769 5.412384 TCTCTCCTCTCCCTTTTTCCTTTA 58.588 41.667 0.00 0.00 0.00 1.85
771 808 2.103042 CACCAGCTGGCGAACTAGC 61.103 63.158 33.06 0.00 39.32 3.42
916 953 6.824196 TGCAGTACTATATAGGAAGGATCGAG 59.176 42.308 14.25 0.00 0.00 4.04
917 954 6.718294 TGCAGTACTATATAGGAAGGATCGA 58.282 40.000 14.25 0.00 0.00 3.59
918 955 6.459024 GCTGCAGTACTATATAGGAAGGATCG 60.459 46.154 16.64 0.00 0.00 3.69
919 956 6.183360 GGCTGCAGTACTATATAGGAAGGATC 60.183 46.154 16.64 0.00 0.00 3.36
920 957 5.659079 GGCTGCAGTACTATATAGGAAGGAT 59.341 44.000 16.64 0.00 0.00 3.24
921 958 5.017490 GGCTGCAGTACTATATAGGAAGGA 58.983 45.833 16.64 2.68 0.00 3.36
922 959 5.020132 AGGCTGCAGTACTATATAGGAAGG 58.980 45.833 16.64 2.62 0.00 3.46
923 960 5.949354 AGAGGCTGCAGTACTATATAGGAAG 59.051 44.000 16.64 3.33 0.00 3.46
924 961 5.712446 CAGAGGCTGCAGTACTATATAGGAA 59.288 44.000 16.64 0.00 0.00 3.36
966 1003 0.468029 CTCTGCTCCTCCTCCTCCTC 60.468 65.000 0.00 0.00 0.00 3.71
967 1004 0.923729 TCTCTGCTCCTCCTCCTCCT 60.924 60.000 0.00 0.00 0.00 3.69
968 1005 0.468029 CTCTCTGCTCCTCCTCCTCC 60.468 65.000 0.00 0.00 0.00 4.30
969 1006 0.468029 CCTCTCTGCTCCTCCTCCTC 60.468 65.000 0.00 0.00 0.00 3.71
970 1007 1.620259 CCTCTCTGCTCCTCCTCCT 59.380 63.158 0.00 0.00 0.00 3.69
987 1024 1.059006 ATGCCATCCTCACTCTCCCC 61.059 60.000 0.00 0.00 0.00 4.81
988 1025 0.396060 GATGCCATCCTCACTCTCCC 59.604 60.000 0.00 0.00 0.00 4.30
990 1027 0.033228 CCGATGCCATCCTCACTCTC 59.967 60.000 0.00 0.00 0.00 3.20
1173 1210 4.729856 AACCACGCGTCGTAGGCC 62.730 66.667 9.86 0.00 38.32 5.19
1176 1213 2.434134 GCTGAACCACGCGTCGTAG 61.434 63.158 9.86 5.47 38.32 3.51
1819 3188 9.171701 GAAAAACATGCAAAATTACTACACGTA 57.828 29.630 0.00 0.00 0.00 3.57
1822 3191 8.276060 TCGAAAAACATGCAAAATTACTACAC 57.724 30.769 0.00 0.00 0.00 2.90
1848 4238 1.595466 CAAGATCCATGAGCAGGAGC 58.405 55.000 0.00 0.00 41.78 4.70
1882 5686 1.397343 GTGCATGATCTCACTGTGCAG 59.603 52.381 2.12 2.16 45.32 4.41
2400 7973 4.823419 TTGGCGGCGTACATCCCG 62.823 66.667 9.37 11.10 46.94 5.14
2726 8307 4.608000 GCACAAACACACAAAACACAACAG 60.608 41.667 0.00 0.00 0.00 3.16
2731 8312 1.201758 GCGCACAAACACACAAAACAC 60.202 47.619 0.30 0.00 0.00 3.32
2749 8330 2.542766 AGAATTACAAACATGGCGCG 57.457 45.000 0.00 0.00 0.00 6.86
2751 8332 7.810766 AATTACAAGAATTACAAACATGGCG 57.189 32.000 0.00 0.00 0.00 5.69
2864 8478 8.758829 TGTGAACTTTATAGATAGGAGAAGCAA 58.241 33.333 0.00 0.00 0.00 3.91
2866 8480 7.380065 CGTGTGAACTTTATAGATAGGAGAAGC 59.620 40.741 0.00 0.00 0.00 3.86
2874 8488 7.544622 AGAACTGCGTGTGAACTTTATAGATA 58.455 34.615 0.00 0.00 0.00 1.98
2891 8505 2.208431 GAATCATGGAGGAGAACTGCG 58.792 52.381 0.00 0.00 41.01 5.18
2946 8560 8.568794 GCAGATCAATACTACTACTACATGTGA 58.431 37.037 9.11 0.00 0.00 3.58
2947 8561 8.572185 AGCAGATCAATACTACTACTACATGTG 58.428 37.037 9.11 0.93 0.00 3.21
2950 8564 9.581289 AAGAGCAGATCAATACTACTACTACAT 57.419 33.333 0.00 0.00 0.00 2.29
2951 8565 8.841300 CAAGAGCAGATCAATACTACTACTACA 58.159 37.037 0.00 0.00 0.00 2.74
2952 8566 8.842280 ACAAGAGCAGATCAATACTACTACTAC 58.158 37.037 0.00 0.00 0.00 2.73
2953 8567 8.982091 ACAAGAGCAGATCAATACTACTACTA 57.018 34.615 0.00 0.00 0.00 1.82
2954 8568 7.889873 ACAAGAGCAGATCAATACTACTACT 57.110 36.000 0.00 0.00 0.00 2.57
2955 8569 8.934507 AAACAAGAGCAGATCAATACTACTAC 57.065 34.615 0.00 0.00 0.00 2.73
2956 8570 9.944376 AAAAACAAGAGCAGATCAATACTACTA 57.056 29.630 0.00 0.00 0.00 1.82
2957 8571 8.854614 AAAAACAAGAGCAGATCAATACTACT 57.145 30.769 0.00 0.00 0.00 2.57
2991 8605 6.855836 TGCTCTGCATCTAATTAAAAACCAG 58.144 36.000 0.00 0.00 31.71 4.00
3007 8621 7.725397 AGGGATACATATTAAAAATGCTCTGCA 59.275 33.333 0.00 0.00 40.80 4.41
3011 8625 8.409358 ACCAGGGATACATATTAAAAATGCTC 57.591 34.615 0.00 0.70 39.74 4.26
3012 8626 8.782137 AACCAGGGATACATATTAAAAATGCT 57.218 30.769 0.00 0.00 39.74 3.79
3013 8627 9.830975 AAAACCAGGGATACATATTAAAAATGC 57.169 29.630 0.00 0.00 39.74 3.56
3024 8638 8.860088 GCATCTAATTAAAAACCAGGGATACAT 58.140 33.333 0.00 0.00 39.74 2.29
3025 8639 7.836685 TGCATCTAATTAAAAACCAGGGATACA 59.163 33.333 0.00 0.00 39.74 2.29
3026 8640 8.232913 TGCATCTAATTAAAAACCAGGGATAC 57.767 34.615 0.00 0.00 0.00 2.24
3027 8641 8.278639 TCTGCATCTAATTAAAAACCAGGGATA 58.721 33.333 0.00 0.00 0.00 2.59
3028 8642 7.125391 TCTGCATCTAATTAAAAACCAGGGAT 58.875 34.615 0.00 0.00 0.00 3.85
3029 8643 6.489603 TCTGCATCTAATTAAAAACCAGGGA 58.510 36.000 0.00 0.00 0.00 4.20
3030 8644 6.681368 GCTCTGCATCTAATTAAAAACCAGGG 60.681 42.308 0.00 0.00 0.00 4.45
3031 8645 6.127647 TGCTCTGCATCTAATTAAAAACCAGG 60.128 38.462 0.00 0.00 31.71 4.45
3032 8646 6.855836 TGCTCTGCATCTAATTAAAAACCAG 58.144 36.000 0.00 0.00 31.71 4.00
3033 8647 6.832520 TGCTCTGCATCTAATTAAAAACCA 57.167 33.333 0.00 0.00 31.71 3.67
3062 8676 7.724506 TCTCGGGTTCTGAACTCTATACATATT 59.275 37.037 17.63 0.00 0.00 1.28
3064 8678 6.598503 TCTCGGGTTCTGAACTCTATACATA 58.401 40.000 17.63 0.00 0.00 2.29
3067 8681 5.124645 TCTCTCGGGTTCTGAACTCTATAC 58.875 45.833 17.63 1.75 0.00 1.47
3069 8683 4.204012 CTCTCTCGGGTTCTGAACTCTAT 58.796 47.826 17.63 0.00 0.00 1.98
3125 8741 8.630054 ATTAAGCTAAATAAACACCTCACACA 57.370 30.769 0.00 0.00 0.00 3.72
3126 8742 9.341899 CAATTAAGCTAAATAAACACCTCACAC 57.658 33.333 0.00 0.00 0.00 3.82
3127 8743 9.073475 ACAATTAAGCTAAATAAACACCTCACA 57.927 29.630 0.00 0.00 0.00 3.58
3128 8744 9.908152 AACAATTAAGCTAAATAAACACCTCAC 57.092 29.630 0.00 0.00 0.00 3.51
3129 8745 9.906660 CAACAATTAAGCTAAATAAACACCTCA 57.093 29.630 0.00 0.00 0.00 3.86
3131 8747 7.540745 CGCAACAATTAAGCTAAATAAACACCT 59.459 33.333 0.00 0.00 0.00 4.00
3201 8817 9.125026 ACAAAATCTGTATAAATCATCTCCACC 57.875 33.333 0.00 0.00 36.10 4.61
3229 8845 4.290711 TGCATATATGGACAGGACATGG 57.709 45.455 14.51 0.00 0.00 3.66
3292 8909 4.141937 CCAGGAGTATGTGAAGATCCGAAA 60.142 45.833 0.00 0.00 35.13 3.46
3349 9132 3.528078 TCATCACCACTCCTAGTCCTAGT 59.472 47.826 0.96 0.00 0.00 2.57
3350 9133 4.171878 TCATCACCACTCCTAGTCCTAG 57.828 50.000 0.00 0.00 0.00 3.02
3351 9134 4.447908 GGATCATCACCACTCCTAGTCCTA 60.448 50.000 0.00 0.00 0.00 2.94
3352 9135 3.571590 GATCATCACCACTCCTAGTCCT 58.428 50.000 0.00 0.00 0.00 3.85
3353 9136 2.630580 GGATCATCACCACTCCTAGTCC 59.369 54.545 0.00 0.00 0.00 3.85
3354 9137 3.300388 TGGATCATCACCACTCCTAGTC 58.700 50.000 0.00 0.00 32.03 2.59
3393 9183 4.634883 GTCATCATCATCACCATAGGATGC 59.365 45.833 0.00 0.00 41.46 3.91
3476 9266 2.034179 TGTCACACGTGATTCTTCGACT 59.966 45.455 25.01 0.00 42.18 4.18


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

AutoCloner maintained by Alex Coulton.