Multiple sequence alignment - TraesCS7A01G116700

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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 TraesCS7A01G116700 chr7A 100.000 3591 0 0 1 3591 74641611 74645201 0.000000e+00 6632.0
1 TraesCS7A01G116700 chr7A 93.554 1117 29 14 1593 2701 70889242 70888161 0.000000e+00 1624.0
2 TraesCS7A01G116700 chr7A 91.638 873 33 14 758 1595 70890136 70889269 0.000000e+00 1171.0
3 TraesCS7A01G116700 chr7A 98.208 279 4 1 3314 3591 70887602 70887324 1.500000e-133 486.0
4 TraesCS7A01G116700 chr7A 93.769 321 20 0 2882 3202 70887981 70887661 1.940000e-132 483.0
5 TraesCS7A01G116700 chr7A 79.186 663 98 21 932 1590 70898565 70897939 1.190000e-114 424.0
6 TraesCS7A01G116700 chr7A 96.957 230 6 1 519 747 459003470 459003241 5.620000e-103 385.0
7 TraesCS7A01G116700 chr7A 93.625 251 14 2 2546 2795 71112899 71112650 1.220000e-99 374.0
8 TraesCS7A01G116700 chr7A 94.872 234 10 2 285 518 459003744 459003513 7.330000e-97 364.0
9 TraesCS7A01G116700 chr7A 77.975 395 62 18 986 1378 77915214 77915585 1.300000e-54 224.0
10 TraesCS7A01G116700 chr7A 83.333 264 19 8 4 244 70890421 70890160 1.680000e-53 220.0
11 TraesCS7A01G116700 chr7A 93.043 115 8 0 2739 2853 70888159 70888045 6.170000e-38 169.0
12 TraesCS7A01G116700 chr7A 90.517 116 9 1 861 976 47049213 47049326 6.210000e-33 152.0
13 TraesCS7A01G116700 chr7D 89.816 1522 73 23 756 2202 66416732 66415218 0.000000e+00 1877.0
14 TraesCS7A01G116700 chr7D 90.095 1474 64 30 756 2186 68983318 68984752 0.000000e+00 1838.0
15 TraesCS7A01G116700 chr7D 96.882 417 10 3 2094 2509 66415036 66414622 0.000000e+00 695.0
16 TraesCS7A01G116700 chr7D 89.175 582 17 5 2906 3463 68985372 68985931 0.000000e+00 684.0
17 TraesCS7A01G116700 chr7D 95.174 373 18 0 2500 2872 66413278 66412906 1.110000e-164 590.0
18 TraesCS7A01G116700 chr7D 89.096 376 20 5 2510 2885 68984946 68985300 7.070000e-122 448.0
19 TraesCS7A01G116700 chr7D 77.097 751 129 29 861 1595 68901803 68902526 9.340000e-106 394.0
20 TraesCS7A01G116700 chr7D 82.609 322 50 2 1688 2006 69056086 69056404 2.730000e-71 279.0
21 TraesCS7A01G116700 chr7D 88.889 225 14 5 2543 2762 68930308 68930526 2.130000e-67 267.0
22 TraesCS7A01G116700 chr7D 84.800 250 13 8 2546 2795 66506860 66506636 1.000000e-55 228.0
23 TraesCS7A01G116700 chr7D 77.722 395 63 18 986 1378 73367967 73368338 6.040000e-53 219.0
24 TraesCS7A01G116700 chr7D 84.071 226 11 14 2882 3099 66412845 66412637 1.020000e-45 195.0
25 TraesCS7A01G116700 chr7D 85.165 182 21 5 2477 2653 69057067 69057247 7.920000e-42 182.0
26 TraesCS7A01G116700 chr7D 84.024 169 14 10 834 993 66548230 66548066 2.230000e-32 150.0
27 TraesCS7A01G116700 chr7D 81.955 133 16 5 2330 2455 69056818 69056949 4.900000e-19 106.0
28 TraesCS7A01G116700 chr7D 94.000 50 3 0 2746 2795 68930563 68930612 3.840000e-10 76.8
29 TraesCS7A01G116700 chr7D 93.750 48 3 0 2746 2793 66506625 66506578 4.970000e-09 73.1
30 TraesCS7A01G116700 chr7B 94.720 625 26 3 974 1595 10559038 10559658 0.000000e+00 965.0
31 TraesCS7A01G116700 chr7B 95.066 608 24 1 988 1595 7717576 7716975 0.000000e+00 952.0
32 TraesCS7A01G116700 chr7B 84.769 801 42 28 2430 3202 10560549 10561297 0.000000e+00 730.0
33 TraesCS7A01G116700 chr7B 87.479 607 38 13 1593 2190 10559685 10560262 0.000000e+00 665.0
34 TraesCS7A01G116700 chr7B 87.231 603 38 12 1593 2190 7716948 7716380 0.000000e+00 651.0
35 TraesCS7A01G116700 chr7B 90.147 477 24 5 3120 3574 139855166 139854691 1.850000e-167 599.0
36 TraesCS7A01G116700 chr7B 77.394 1013 147 44 991 1986 10237628 10238575 8.830000e-146 527.0
37 TraesCS7A01G116700 chr7B 88.514 444 31 4 2427 2869 7716076 7715652 1.480000e-143 520.0
38 TraesCS7A01G116700 chr7B 98.655 223 3 0 756 978 10558770 10558992 2.600000e-106 396.0
39 TraesCS7A01G116700 chr7B 83.578 408 51 11 861 1265 10067527 10067921 5.660000e-98 368.0
40 TraesCS7A01G116700 chr7B 95.045 222 6 3 757 978 7717848 7717632 9.550000e-91 344.0
41 TraesCS7A01G116700 chr7B 90.800 250 17 3 2546 2795 7730560 7730317 2.670000e-86 329.0
42 TraesCS7A01G116700 chr7B 76.171 491 80 19 1000 1485 491084216 491083758 1.300000e-54 224.0
43 TraesCS7A01G116700 chr7B 90.476 147 12 2 2882 3026 7715572 7715426 3.660000e-45 193.0
44 TraesCS7A01G116700 chr7B 94.545 110 6 0 861 970 10916482 10916591 1.710000e-38 171.0
45 TraesCS7A01G116700 chr7B 83.432 169 15 9 834 993 8448767 8448603 1.040000e-30 145.0
46 TraesCS7A01G116700 chr7B 88.182 110 7 3 2330 2433 10947794 10947903 3.760000e-25 126.0
47 TraesCS7A01G116700 chr7B 91.765 85 7 0 2315 2399 7716155 7716071 6.300000e-23 119.0
48 TraesCS7A01G116700 chr7B 88.095 84 8 1 48 129 7718161 7718078 8.210000e-17 99.0
49 TraesCS7A01G116700 chr7B 90.909 66 5 1 63 127 10558582 10558647 1.780000e-13 87.9
50 TraesCS7A01G116700 chr5A 96.957 230 6 1 519 747 694506629 694506400 5.620000e-103 385.0
51 TraesCS7A01G116700 chr5A 94.348 230 13 0 289 518 694506901 694506672 1.590000e-93 353.0
52 TraesCS7A01G116700 chr5A 91.775 231 18 1 518 747 22060958 22061188 1.610000e-83 320.0
53 TraesCS7A01G116700 chr5A 92.233 206 15 1 290 495 22060588 22060792 1.260000e-74 291.0
54 TraesCS7A01G116700 chr2B 79.417 583 86 21 1000 1568 135794947 135795509 7.280000e-102 381.0
55 TraesCS7A01G116700 chr2B 81.231 325 51 8 1684 2006 135795661 135795977 1.650000e-63 254.0
56 TraesCS7A01G116700 chr2B 76.737 331 60 10 986 1314 55855789 55855474 6.170000e-38 169.0
57 TraesCS7A01G116700 chr6A 96.522 230 7 1 519 747 76667565 76667794 2.620000e-101 379.0
58 TraesCS7A01G116700 chr6A 95.217 230 11 0 289 518 76667293 76667522 7.330000e-97 364.0
59 TraesCS7A01G116700 chr2A 96.522 230 7 1 519 747 613139906 613139677 2.620000e-101 379.0
60 TraesCS7A01G116700 chr2A 94.872 234 11 1 285 518 613140181 613139949 7.330000e-97 364.0
61 TraesCS7A01G116700 chr2A 92.174 230 17 1 519 747 18005235 18005006 1.240000e-84 324.0
62 TraesCS7A01G116700 chr2A 81.231 325 51 7 1684 2006 84749811 84750127 1.650000e-63 254.0
63 TraesCS7A01G116700 chr2A 74.886 438 82 21 851 1278 36411865 36411446 1.330000e-39 174.0
64 TraesCS7A01G116700 chr2D 93.133 233 15 1 286 518 407952569 407952800 1.230000e-89 340.0
65 TraesCS7A01G116700 chr2D 92.609 230 16 1 519 747 407952843 407953072 2.670000e-86 329.0
66 TraesCS7A01G116700 chr2D 80.531 226 38 5 2542 2766 326453687 326453907 6.170000e-38 169.0
67 TraesCS7A01G116700 chr2D 75.841 327 66 7 988 1314 33581039 33580726 1.730000e-33 154.0
68 TraesCS7A01G116700 chr2D 72.202 554 100 28 986 1517 33374128 33373607 1.750000e-23 121.0
69 TraesCS7A01G116700 chr4B 92.641 231 15 2 289 518 40607340 40607111 7.430000e-87 331.0
70 TraesCS7A01G116700 chr4B 90.000 230 13 4 519 747 40607068 40606848 4.540000e-74 289.0
71 TraesCS7A01G116700 chr1A 90.476 231 18 3 519 747 165194588 165194360 5.830000e-78 302.0
72 TraesCS7A01G116700 chr1A 89.076 238 24 2 283 518 165194868 165194631 9.750000e-76 294.0
73 TraesCS7A01G116700 chr1A 88.158 228 25 1 289 516 577987538 577987763 1.640000e-68 270.0
74 TraesCS7A01G116700 chr6B 79.695 197 30 8 1184 1378 521450235 521450423 2.250000e-27 134.0
75 TraesCS7A01G116700 chrUn 81.111 90 17 0 1757 1846 84529637 84529726 4.970000e-09 73.1


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 TraesCS7A01G116700 chr7A 74641611 74645201 3590 False 6632.000000 6632 100.000000 1 3591 1 chr7A.!!$F2 3590
1 TraesCS7A01G116700 chr7A 70887324 70890421 3097 True 692.166667 1624 92.257500 4 3591 6 chr7A.!!$R3 3587
2 TraesCS7A01G116700 chr7A 70897939 70898565 626 True 424.000000 424 79.186000 932 1590 1 chr7A.!!$R1 658
3 TraesCS7A01G116700 chr7A 459003241 459003744 503 True 374.500000 385 95.914500 285 747 2 chr7A.!!$R4 462
4 TraesCS7A01G116700 chr7D 68983318 68985931 2613 False 990.000000 1838 89.455333 756 3463 3 chr7D.!!$F4 2707
5 TraesCS7A01G116700 chr7D 66412637 66416732 4095 True 839.250000 1877 91.485750 756 3099 4 chr7D.!!$R2 2343
6 TraesCS7A01G116700 chr7D 68901803 68902526 723 False 394.000000 394 77.097000 861 1595 1 chr7D.!!$F1 734
7 TraesCS7A01G116700 chr7B 10558582 10561297 2715 False 568.780000 965 91.306400 63 3202 5 chr7B.!!$F5 3139
8 TraesCS7A01G116700 chr7B 10237628 10238575 947 False 527.000000 527 77.394000 991 1986 1 chr7B.!!$F2 995
9 TraesCS7A01G116700 chr7B 7715426 7718161 2735 True 411.142857 952 90.884571 48 3026 7 chr7B.!!$R5 2978
10 TraesCS7A01G116700 chr5A 694506400 694506901 501 True 369.000000 385 95.652500 289 747 2 chr5A.!!$R1 458
11 TraesCS7A01G116700 chr5A 22060588 22061188 600 False 305.500000 320 92.004000 290 747 2 chr5A.!!$F1 457
12 TraesCS7A01G116700 chr2B 135794947 135795977 1030 False 317.500000 381 80.324000 1000 2006 2 chr2B.!!$F1 1006
13 TraesCS7A01G116700 chr6A 76667293 76667794 501 False 371.500000 379 95.869500 289 747 2 chr6A.!!$F1 458
14 TraesCS7A01G116700 chr2A 613139677 613140181 504 True 371.500000 379 95.697000 285 747 2 chr2A.!!$R3 462
15 TraesCS7A01G116700 chr2D 407952569 407953072 503 False 334.500000 340 92.871000 286 747 2 chr2D.!!$F2 461
16 TraesCS7A01G116700 chr1A 165194360 165194868 508 True 298.000000 302 89.776000 283 747 2 chr1A.!!$R1 464

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
749 948 0.755698 GATCCAGTGGCGGAGGTCTA 60.756 60.0 3.51 0.0 38.83 2.59 F
1026 1342 0.105453 ATCTCCAGGACGGCCACTAT 60.105 55.0 11.69 0.0 36.29 2.12 F
1678 2125 0.256752 TTGATCTCCTGGGTGGCATG 59.743 55.0 0.00 0.0 35.26 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2561 0.171455 CACGAGGCAGACAGTACTCC 59.829 60.000 0.0 0.0 0.00 3.85 R
2083 2568 0.179234 TTTCCAACACGAGGCAGACA 59.821 50.000 0.0 0.0 0.00 3.41 R
2741 4922 1.280998 AGGTTTCCTACATTGTCCGGG 59.719 52.381 0.0 0.0 28.47 5.73 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
23 24 6.639632 AAGACAACTTGTATGCTTTGATGT 57.360 33.333 0.00 0.0 34.80 3.06
36 37 3.855950 GCTTTGATGTGCATGAAACTAGC 59.144 43.478 0.00 0.0 0.00 3.42
137 155 7.121759 AGCATAGAAAAACATGACAAGCATAGT 59.878 33.333 0.00 0.0 34.82 2.12
359 410 9.981460 ATTTACAGGGATAAAATTCAAGTCTCT 57.019 29.630 0.00 0.0 0.00 3.10
366 417 6.353082 GGATAAAATTCAAGTCTCTGGGGAGA 60.353 42.308 0.00 0.0 45.30 3.71
439 491 3.126001 TGTGAGCCTCGAAATTTGAGT 57.874 42.857 9.22 0.0 0.00 3.41
441 493 3.882888 TGTGAGCCTCGAAATTTGAGTTT 59.117 39.130 9.22 0.0 0.00 2.66
676 873 5.221925 CCAGCCACATCCCTACATATTACTT 60.222 44.000 0.00 0.0 0.00 2.24
693 890 8.649841 CATATTACTTCAACTGCACCAAATTTG 58.350 33.333 11.40 11.4 0.00 2.32
722 921 3.492421 ACAGCGGCATCAACATTAAAG 57.508 42.857 1.45 0.0 0.00 1.85
747 946 2.359169 TGATCCAGTGGCGGAGGTC 61.359 63.158 3.51 0.0 38.83 3.85
748 947 2.039624 ATCCAGTGGCGGAGGTCT 59.960 61.111 3.51 0.0 38.83 3.85
749 948 0.755698 GATCCAGTGGCGGAGGTCTA 60.756 60.000 3.51 0.0 38.83 2.59
751 950 1.682684 CCAGTGGCGGAGGTCTAGT 60.683 63.158 0.00 0.0 0.00 2.57
752 951 1.258445 CCAGTGGCGGAGGTCTAGTT 61.258 60.000 0.00 0.0 0.00 2.24
754 953 2.032620 CAGTGGCGGAGGTCTAGTTAT 58.967 52.381 0.00 0.0 0.00 1.89
761 979 4.461781 GGCGGAGGTCTAGTTATATAGCAA 59.538 45.833 0.00 0.0 0.00 3.91
978 1243 1.768077 CCATCCTCCCCACCTCTCC 60.768 68.421 0.00 0.0 0.00 3.71
979 1244 1.003442 CATCCTCCCCACCTCTCCA 59.997 63.158 0.00 0.0 0.00 3.86
980 1245 1.003573 ATCCTCCCCACCTCTCCAC 59.996 63.158 0.00 0.0 0.00 4.02
982 1247 3.077556 CTCCCCACCTCTCCACCG 61.078 72.222 0.00 0.0 0.00 4.94
1026 1342 0.105453 ATCTCCAGGACGGCCACTAT 60.105 55.000 11.69 0.0 36.29 2.12
1216 1532 3.974835 TACGGCCGCTACCTCGTCA 62.975 63.158 28.58 0.0 37.10 4.35
1461 1821 1.581934 CCTTCGACAACTTCAGCACA 58.418 50.000 0.00 0.0 0.00 4.57
1462 1822 1.528586 CCTTCGACAACTTCAGCACAG 59.471 52.381 0.00 0.0 0.00 3.66
1549 1912 2.997315 TCAGGGTGAGTCCGCCAG 60.997 66.667 0.00 0.0 44.70 4.85
1595 1988 2.251642 GCGCGACTTGGGTTCTTGT 61.252 57.895 12.10 0.0 0.00 3.16
1671 2118 3.127548 CGTGTTTGATTTGATCTCCTGGG 59.872 47.826 0.00 0.0 0.00 4.45
1672 2119 4.082125 GTGTTTGATTTGATCTCCTGGGT 58.918 43.478 0.00 0.0 0.00 4.51
1673 2120 4.081406 TGTTTGATTTGATCTCCTGGGTG 58.919 43.478 0.00 0.0 0.00 4.61
1674 2121 3.370840 TTGATTTGATCTCCTGGGTGG 57.629 47.619 0.00 0.0 37.10 4.61
1678 2125 0.256752 TTGATCTCCTGGGTGGCATG 59.743 55.000 0.00 0.0 35.26 4.06
1829 2294 1.977544 CGTGTTCGAGGGGAGGTCT 60.978 63.158 0.00 0.0 39.71 3.85
1853 2318 0.391597 TCGACCTGAGGAAAACGCTT 59.608 50.000 4.99 0.0 0.00 4.68
2012 2477 2.526873 ACGCCAGGTGAACCCTCT 60.527 61.111 7.13 0.0 43.86 3.69
2066 2551 4.016444 TGCCATGATCTTTTGGGTTCTAC 58.984 43.478 0.00 0.0 33.40 2.59
2068 2553 5.045213 TGCCATGATCTTTTGGGTTCTACTA 60.045 40.000 0.00 0.0 33.40 1.82
2070 2555 6.547510 GCCATGATCTTTTGGGTTCTACTATT 59.452 38.462 0.00 0.0 33.40 1.73
2071 2556 7.068716 GCCATGATCTTTTGGGTTCTACTATTT 59.931 37.037 0.00 0.0 33.40 1.40
2080 2565 9.816787 TTTTGGGTTCTACTATTTTAATGGAGT 57.183 29.630 0.00 0.0 0.00 3.85
2082 2567 9.895138 TTGGGTTCTACTATTTTAATGGAGTAC 57.105 33.333 0.00 0.0 0.00 2.73
2083 2568 9.275572 TGGGTTCTACTATTTTAATGGAGTACT 57.724 33.333 0.00 0.0 0.00 2.73
2099 2591 0.317160 TACTGTCTGCCTCGTGTTGG 59.683 55.000 0.00 0.0 0.00 3.77
2122 2626 7.032580 TGGAAAACAGTGTACTGAATTTGTTG 58.967 34.615 18.18 0.0 46.59 3.33
2421 3235 1.003580 AGGCTGTATCCCACAACACTG 59.996 52.381 0.00 0.0 36.48 3.66
2463 3277 5.070313 ACATTGCCTTCAGGTTTTGTACATT 59.930 36.000 0.00 0.0 37.57 2.71
2537 4704 1.067071 CCTCCTCACCGTTCCTTGTAC 60.067 57.143 0.00 0.0 0.00 2.90
2557 4724 2.016318 CATTCTATTTCAGCCCACGCA 58.984 47.619 0.00 0.0 37.52 5.24
2609 4789 2.178580 AGAGAAAGACCAGAGCAGGAG 58.821 52.381 0.00 0.0 0.00 3.69
2655 4835 1.007734 GTTCAGAGTGTCGCCGTCA 60.008 57.895 0.00 0.0 0.00 4.35
2717 4898 3.866883 ACCCAGAAGTTGTTGTGTTTG 57.133 42.857 0.00 0.0 0.00 2.93
2719 4900 4.337145 ACCCAGAAGTTGTTGTGTTTGTA 58.663 39.130 0.00 0.0 0.00 2.41
2722 4903 5.105917 CCCAGAAGTTGTTGTGTTTGTACTT 60.106 40.000 0.00 0.0 0.00 2.24
2741 4922 1.886886 TGCTAAACTTGGTCCGTTCC 58.113 50.000 0.00 0.0 0.00 3.62
2744 4925 0.035176 TAAACTTGGTCCGTTCCCCG 59.965 55.000 0.00 0.0 0.00 5.73
2784 4965 7.231317 ACCTATTTGCTGTTCTCAAATTCAGAA 59.769 33.333 6.32 0.0 42.27 3.02
2885 5082 5.459536 TCTACCTATAGCAGAGCATGTTG 57.540 43.478 0.00 0.0 0.00 3.33
2886 5083 3.482156 ACCTATAGCAGAGCATGTTGG 57.518 47.619 0.00 0.0 0.00 3.77
2889 5086 1.386533 ATAGCAGAGCATGTTGGCAC 58.613 50.000 5.75 0.0 35.83 5.01
2890 5087 0.325933 TAGCAGAGCATGTTGGCACT 59.674 50.000 5.75 0.0 34.98 4.40
2891 5088 0.538977 AGCAGAGCATGTTGGCACTT 60.539 50.000 5.75 0.0 32.20 3.16
2990 5259 3.305335 CCCTGTCTTGGTTATGTGCAAAC 60.305 47.826 0.00 0.0 0.00 2.93
3220 5526 2.491693 GCCATTTTAGCTAACCTGTGCA 59.508 45.455 5.45 0.0 0.00 4.57
3279 5585 3.055819 AGCAAGCCTGAAACGAATCTCTA 60.056 43.478 0.00 0.0 0.00 2.43
3280 5586 3.684788 GCAAGCCTGAAACGAATCTCTAA 59.315 43.478 0.00 0.0 0.00 2.10
3281 5587 4.201763 GCAAGCCTGAAACGAATCTCTAAG 60.202 45.833 0.00 0.0 0.00 2.18
3282 5588 5.171476 CAAGCCTGAAACGAATCTCTAAGA 58.829 41.667 0.00 0.0 0.00 2.10
3283 5589 5.004922 AGCCTGAAACGAATCTCTAAGAG 57.995 43.478 0.00 0.0 0.00 2.85
3284 5590 4.707448 AGCCTGAAACGAATCTCTAAGAGA 59.293 41.667 0.00 0.0 43.20 3.10
3356 5665 4.991776 TCGATCTCCCTTATGACTCTCAT 58.008 43.478 0.00 0.0 40.72 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.618489 GCACATCAAAGCATACAAGTTGTC 59.382 41.667 12.82 0.00 0.00 3.18
23 24 9.071221 CATAAAAATAAACGCTAGTTTCATGCA 57.929 29.630 0.00 0.00 46.73 3.96
64 67 8.629986 CATGCTTTACTAAAAACAATGTTCTCG 58.370 33.333 0.00 0.00 0.00 4.04
359 410 0.490017 TGTCTGGTTAGGTCTCCCCA 59.510 55.000 0.00 0.00 34.66 4.96
366 417 2.654877 CGCCGTGTCTGGTTAGGT 59.345 61.111 0.00 0.00 0.00 3.08
396 448 0.036483 TCGCTAGGCATGCACTTTCA 60.036 50.000 21.36 0.00 0.00 2.69
441 493 9.638239 GCTTGTAATTTTGTCCATGAATTTAGA 57.362 29.630 0.00 0.00 0.00 2.10
480 532 8.396272 TCGTACATGAAATCATAGAGAGATCA 57.604 34.615 0.00 0.00 34.26 2.92
676 873 2.975732 TGCAAATTTGGTGCAGTTGA 57.024 40.000 19.47 0.00 46.76 3.18
693 890 0.730494 GATGCCGCTGTTTCAAGTGC 60.730 55.000 0.00 0.00 0.00 4.40
722 921 1.626654 CGCCACTGGATCACGTGAAC 61.627 60.000 24.13 20.16 33.04 3.18
748 947 9.674068 TGTCCACAACAAATTGCTATATAACTA 57.326 29.630 0.00 0.00 39.66 2.24
749 948 8.574251 TGTCCACAACAAATTGCTATATAACT 57.426 30.769 0.00 0.00 39.66 2.24
754 953 8.673711 GTCTAATGTCCACAACAAATTGCTATA 58.326 33.333 0.00 0.00 42.37 1.31
761 979 4.320202 GCACGTCTAATGTCCACAACAAAT 60.320 41.667 0.00 0.00 42.37 2.32
1461 1821 1.681666 CACCACCCAGTGCATCTCT 59.318 57.895 0.00 0.00 31.34 3.10
1462 1822 1.377725 CCACCACCCAGTGCATCTC 60.378 63.158 0.00 0.00 36.38 2.75
1549 1912 1.134371 ACAAGAATCTAGAAGCGGGCC 60.134 52.381 0.00 0.00 0.00 5.80
1595 1988 5.328691 GCGAATGGAATTAACACGATTTGA 58.671 37.500 0.00 0.00 36.07 2.69
1671 2118 3.615496 GCAAAGAAACATCATCATGCCAC 59.385 43.478 0.00 0.00 32.57 5.01
1672 2119 3.673866 CGCAAAGAAACATCATCATGCCA 60.674 43.478 0.00 0.00 32.57 4.92
1673 2120 2.855963 CGCAAAGAAACATCATCATGCC 59.144 45.455 0.00 0.00 32.57 4.40
1674 2121 3.545078 GTCGCAAAGAAACATCATCATGC 59.455 43.478 0.00 0.00 32.57 4.06
1678 2125 4.668576 TGAGTCGCAAAGAAACATCATC 57.331 40.909 0.00 0.00 0.00 2.92
1829 2294 2.557317 GTTTTCCTCAGGTCGAACACA 58.443 47.619 1.87 0.00 0.00 3.72
1925 2390 2.362120 ACGACGAGTGGGGTAGGG 60.362 66.667 0.00 0.00 0.00 3.53
2012 2477 1.646447 AGGGTGATCAGTAGGGAGACA 59.354 52.381 0.00 0.00 0.00 3.41
2066 2551 7.275920 AGGCAGACAGTACTCCATTAAAATAG 58.724 38.462 0.00 0.00 0.00 1.73
2068 2553 6.067217 AGGCAGACAGTACTCCATTAAAAT 57.933 37.500 0.00 0.00 0.00 1.82
2070 2555 4.381612 CGAGGCAGACAGTACTCCATTAAA 60.382 45.833 0.00 0.00 0.00 1.52
2071 2556 3.130516 CGAGGCAGACAGTACTCCATTAA 59.869 47.826 0.00 0.00 0.00 1.40
2073 2558 1.478510 CGAGGCAGACAGTACTCCATT 59.521 52.381 0.00 0.00 0.00 3.16
2074 2559 1.107114 CGAGGCAGACAGTACTCCAT 58.893 55.000 0.00 0.00 0.00 3.41
2075 2560 0.251209 ACGAGGCAGACAGTACTCCA 60.251 55.000 0.00 0.00 0.00 3.86
2076 2561 0.171455 CACGAGGCAGACAGTACTCC 59.829 60.000 0.00 0.00 0.00 3.85
2077 2562 0.882474 ACACGAGGCAGACAGTACTC 59.118 55.000 0.00 0.00 0.00 2.59
2078 2563 1.000163 CAACACGAGGCAGACAGTACT 60.000 52.381 0.00 0.00 0.00 2.73
2079 2564 1.419374 CAACACGAGGCAGACAGTAC 58.581 55.000 0.00 0.00 0.00 2.73
2080 2565 0.317160 CCAACACGAGGCAGACAGTA 59.683 55.000 0.00 0.00 0.00 2.74
2081 2566 1.069765 CCAACACGAGGCAGACAGT 59.930 57.895 0.00 0.00 0.00 3.55
2082 2567 0.249868 TTCCAACACGAGGCAGACAG 60.250 55.000 0.00 0.00 0.00 3.51
2083 2568 0.179234 TTTCCAACACGAGGCAGACA 59.821 50.000 0.00 0.00 0.00 3.41
2099 2591 6.529829 TGCAACAAATTCAGTACACTGTTTTC 59.470 34.615 9.11 1.62 44.12 2.29
2122 2626 4.094887 TCAGTGAACTGTTTTTCAGACTGC 59.905 41.667 10.14 0.00 46.27 4.40
2421 3235 6.476706 GGCAATGTAGAAACTAATTTCCATGC 59.523 38.462 0.00 0.00 44.66 4.06
2463 3277 9.996554 TCAATAACAAGATCAAGAAGACAGTTA 57.003 29.630 0.00 0.00 0.00 2.24
2537 4704 2.016318 TGCGTGGGCTGAAATAGAATG 58.984 47.619 0.00 0.00 40.82 2.67
2609 4789 1.733399 GTGAAGCGACGGTCAGGAC 60.733 63.158 9.10 0.00 0.00 3.85
2655 4835 6.347696 TCACTGCAAAAAGTTTTGGATTCAT 58.652 32.000 16.17 0.34 45.29 2.57
2717 4898 3.396560 ACGGACCAAGTTTAGCAAGTAC 58.603 45.455 0.00 0.00 0.00 2.73
2719 4900 2.632987 ACGGACCAAGTTTAGCAAGT 57.367 45.000 0.00 0.00 0.00 3.16
2722 4903 1.543871 GGGAACGGACCAAGTTTAGCA 60.544 52.381 0.00 0.00 31.14 3.49
2741 4922 1.280998 AGGTTTCCTACATTGTCCGGG 59.719 52.381 0.00 0.00 28.47 5.73
2744 4925 5.652452 AGCAAATAGGTTTCCTACATTGTCC 59.348 40.000 16.94 0.00 39.10 4.02
2784 4965 4.615912 GCATCGTTGTTCCAGCAGTTAATT 60.616 41.667 0.00 0.00 0.00 1.40
2885 5082 4.911514 TTGGACTGAAACTTTAAGTGCC 57.088 40.909 7.82 4.92 31.87 5.01
2886 5083 5.891451 AGTTTGGACTGAAACTTTAAGTGC 58.109 37.500 0.00 3.97 42.33 4.40
2913 5180 7.770201 TGTGAAAACACAAATTCATTCTCTCA 58.230 30.769 0.00 0.00 37.82 3.27
2914 5181 8.807667 ATGTGAAAACACAAATTCATTCTCTC 57.192 30.769 7.12 0.00 37.82 3.20
2990 5259 4.250080 GCTTCGGCCTGCAAAAAG 57.750 55.556 0.00 0.00 34.32 2.27
3156 5441 6.169094 CGCCTCCAGATCATTTATGTATTCT 58.831 40.000 0.00 0.00 0.00 2.40
3220 5526 4.163078 ACAACATAGCAGTAATGGAGAGCT 59.837 41.667 0.00 0.00 39.22 4.09
3238 5544 4.503741 GCTCTTTTAGCCATGAACAACA 57.496 40.909 0.00 0.00 46.25 3.33
3253 5559 1.967319 TCGTTTCAGGCTTGCTCTTT 58.033 45.000 0.00 0.00 0.00 2.52
3292 5598 9.567776 TGGAGTTTGTTGTATGATTTTTAGAGA 57.432 29.630 0.00 0.00 0.00 3.10
3311 5617 3.694566 GTCGGCCAAGAATTATGGAGTTT 59.305 43.478 12.76 0.00 40.56 2.66
3565 5875 5.428253 GCCAGGTATAGTCTCACATGAAAA 58.572 41.667 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.