Multiple sequence alignment - TraesCS7A01G175900

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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 TraesCS7A01G175900 chr7A 100.000 3402 0 0 1 3402 128970232 128973633 0.000000e+00 6283.0
1 TraesCS7A01G175900 chr7A 80.000 225 33 5 3045 3257 711190494 711190718 4.550000e-34 156.0
2 TraesCS7A01G175900 chrUn 97.808 2555 50 3 1 2552 32408170 32405619 0.000000e+00 4403.0
3 TraesCS7A01G175900 chrUn 98.089 1727 27 4 84 1809 30197752 30199473 0.000000e+00 3001.0
4 TraesCS7A01G175900 chrUn 96.913 745 21 2 1811 2553 30199521 30200265 0.000000e+00 1247.0
5 TraesCS7A01G175900 chrUn 97.183 71 2 0 1 71 30197634 30197704 1.660000e-23 121.0
6 TraesCS7A01G175900 chr3B 96.150 1818 29 8 1 1809 15970034 15971819 0.000000e+00 2931.0
7 TraesCS7A01G175900 chr3B 96.913 745 21 2 1811 2553 15971867 15972611 0.000000e+00 1247.0
8 TraesCS7A01G175900 chr3B 87.709 358 28 7 1455 1809 513568418 513568074 1.470000e-108 403.0
9 TraesCS7A01G175900 chr3B 84.971 173 18 5 1265 1430 758407637 758407466 5.840000e-38 169.0
10 TraesCS7A01G175900 chr3B 83.582 67 5 4 263 324 47611104 47611169 1.320000e-04 58.4
11 TraesCS7A01G175900 chr7B 88.695 858 60 13 2552 3402 91250619 91251446 0.000000e+00 1013.0
12 TraesCS7A01G175900 chr7B 81.467 259 28 8 1964 2207 472332788 472333041 9.630000e-46 195.0
13 TraesCS7A01G175900 chr7B 81.467 259 28 8 1964 2207 472398269 472398522 9.630000e-46 195.0
14 TraesCS7A01G175900 chr7B 82.143 140 19 2 2419 2552 747257162 747257301 7.710000e-22 115.0
15 TraesCS7A01G175900 chr7B 100.000 29 0 0 52 80 693970888 693970916 2.000000e-03 54.7
16 TraesCS7A01G175900 chr3A 89.356 357 28 6 1455 1809 513607069 513606721 1.120000e-119 440.0
17 TraesCS7A01G175900 chr3A 83.616 177 18 3 1265 1430 646278334 646278510 4.550000e-34 156.0
18 TraesCS7A01G175900 chr3A 83.051 177 19 3 1265 1430 53329963 53329787 2.110000e-32 150.0
19 TraesCS7A01G175900 chr3A 84.672 137 16 2 3043 3179 711114909 711114778 7.660000e-27 132.0
20 TraesCS7A01G175900 chr3A 85.938 64 4 4 271 330 82906397 82906459 2.830000e-06 63.9
21 TraesCS7A01G175900 chr3A 97.059 34 0 1 366 398 546144483 546144516 4.740000e-04 56.5
22 TraesCS7A01G175900 chr6D 90.645 310 27 2 416 723 156745347 156745656 8.790000e-111 411.0
23 TraesCS7A01G175900 chr6D 91.542 201 12 2 153 350 156745130 156745328 4.330000e-69 272.0
24 TraesCS7A01G175900 chr6D 94.872 78 2 1 3321 3396 386276305 386276382 1.660000e-23 121.0
25 TraesCS7A01G175900 chr3D 86.849 365 27 10 1455 1809 393657043 393656690 4.120000e-104 388.0
26 TraesCS7A01G175900 chr3D 83.122 237 32 5 2079 2310 553421174 553420941 3.440000e-50 209.0
27 TraesCS7A01G175900 chr3D 94.118 85 3 1 3320 3402 20756416 20756332 9.910000e-26 128.0
28 TraesCS7A01G175900 chr3D 83.099 71 6 5 271 336 380280444 380280375 3.670000e-05 60.2
29 TraesCS7A01G175900 chr3D 97.059 34 0 1 366 398 92391949 92391982 4.740000e-04 56.5
30 TraesCS7A01G175900 chr3D 96.875 32 1 0 400 431 175239716 175239747 2.000000e-03 54.7
31 TraesCS7A01G175900 chr2D 92.079 202 10 3 153 350 43228438 43228637 2.590000e-71 279.0
32 TraesCS7A01G175900 chr2D 93.452 168 11 0 2878 3045 482892467 482892634 2.030000e-62 250.0
33 TraesCS7A01G175900 chr2D 76.897 290 45 9 3044 3321 531440065 531439786 9.840000e-31 145.0
34 TraesCS7A01G175900 chr2D 95.238 84 2 1 3321 3402 482892625 482892708 7.660000e-27 132.0
35 TraesCS7A01G175900 chr2D 86.916 107 10 3 422 527 534330415 534330518 2.140000e-22 117.0
36 TraesCS7A01G175900 chr2D 100.000 29 0 0 370 398 7150906 7150934 2.000000e-03 54.7
37 TraesCS7A01G175900 chr2D 100.000 29 0 0 3266 3294 630166183 630166211 2.000000e-03 54.7
38 TraesCS7A01G175900 chr1D 94.643 168 8 1 2878 3045 334450109 334450275 3.370000e-65 259.0
39 TraesCS7A01G175900 chr1D 91.765 170 13 1 2877 3045 452597472 452597303 5.680000e-58 235.0
40 TraesCS7A01G175900 chr1D 95.000 80 1 2 3325 3402 334450270 334450348 4.610000e-24 122.0
41 TraesCS7A01G175900 chr1D 76.404 178 27 6 3040 3212 57945739 57945906 7.820000e-12 82.4
42 TraesCS7A01G175900 chr1D 85.915 71 10 0 3246 3316 318891078 318891148 3.640000e-10 76.8
43 TraesCS7A01G175900 chr4D 92.353 170 13 0 2876 3045 43651397 43651566 3.390000e-60 243.0
44 TraesCS7A01G175900 chr4D 79.188 197 32 5 3044 3234 17753462 17753269 9.910000e-26 128.0
45 TraesCS7A01G175900 chr6A 92.262 168 13 0 2878 3045 573193098 573192931 4.390000e-59 239.0
46 TraesCS7A01G175900 chr6A 76.863 255 46 9 3044 3294 473615112 473615357 7.660000e-27 132.0
47 TraesCS7A01G175900 chr6A 77.093 227 37 7 3048 3260 578692398 578692623 2.140000e-22 117.0
48 TraesCS7A01G175900 chr6A 78.191 188 27 8 3043 3218 433958503 433958688 1.290000e-19 108.0
49 TraesCS7A01G175900 chr1B 92.814 167 9 3 2881 3045 464151984 464151819 4.390000e-59 239.0
50 TraesCS7A01G175900 chr1B 87.200 125 13 1 1265 1386 589512353 589512477 4.580000e-29 139.0
51 TraesCS7A01G175900 chr5D 91.765 170 14 0 2876 3045 352931654 352931823 1.580000e-58 237.0
52 TraesCS7A01G175900 chr5D 93.902 82 3 1 3321 3400 242638026 242638107 4.610000e-24 122.0
53 TraesCS7A01G175900 chr5D 82.759 87 9 4 2467 2551 208538176 208538094 4.710000e-09 73.1
54 TraesCS7A01G175900 chr5D 100.000 29 0 0 370 398 550611571 550611543 2.000000e-03 54.7
55 TraesCS7A01G175900 chr5A 91.228 171 15 0 2875 3045 708527183 708527353 2.040000e-57 233.0
56 TraesCS7A01G175900 chr5A 80.851 188 31 1 3045 3227 613460567 613460754 3.540000e-30 143.0
57 TraesCS7A01G175900 chr5A 77.459 244 40 8 3041 3271 606559449 606559690 7.660000e-27 132.0
58 TraesCS7A01G175900 chr5A 82.955 88 9 5 2467 2552 3454418 3454335 1.310000e-09 75.0
59 TraesCS7A01G175900 chr4B 84.746 177 22 4 2031 2207 434477291 434477462 4.510000e-39 172.0
60 TraesCS7A01G175900 chr4B 84.884 86 12 1 2467 2552 563994075 563993991 6.050000e-13 86.1
61 TraesCS7A01G175900 chr4B 87.671 73 9 0 2479 2551 581290993 581291065 6.050000e-13 86.1
62 TraesCS7A01G175900 chr5B 93.182 88 3 2 3318 3402 307259831 307259918 3.560000e-25 126.0
63 TraesCS7A01G175900 chr5B 89.552 67 7 0 2486 2552 53667021 53667087 6.050000e-13 86.1
64 TraesCS7A01G175900 chr5B 100.000 29 0 0 370 398 703172962 703172934 2.000000e-03 54.7
65 TraesCS7A01G175900 chr6B 94.937 79 2 1 3324 3400 397554626 397554548 4.610000e-24 122.0
66 TraesCS7A01G175900 chr6B 100.000 30 0 0 369 398 610241028 610240999 4.740000e-04 56.5
67 TraesCS7A01G175900 chr2B 90.909 88 5 2 3318 3402 506172985 506173072 7.710000e-22 115.0
68 TraesCS7A01G175900 chr4A 77.720 193 30 9 3045 3234 88712608 88712426 4.640000e-19 106.0
69 TraesCS7A01G175900 chr4A 86.207 58 4 2 271 324 740035919 740035976 3.670000e-05 60.2
70 TraesCS7A01G175900 chr4A 90.476 42 4 0 3252 3293 66806393 66806352 4.740000e-04 56.5


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 TraesCS7A01G175900 chr7A 128970232 128973633 3401 False 6283.000000 6283 100.0000 1 3402 1 chr7A.!!$F1 3401
1 TraesCS7A01G175900 chrUn 32405619 32408170 2551 True 4403.000000 4403 97.8080 1 2552 1 chrUn.!!$R1 2551
2 TraesCS7A01G175900 chrUn 30197634 30200265 2631 False 1456.333333 3001 97.3950 1 2553 3 chrUn.!!$F1 2552
3 TraesCS7A01G175900 chr3B 15970034 15972611 2577 False 2089.000000 2931 96.5315 1 2553 2 chr3B.!!$F2 2552
4 TraesCS7A01G175900 chr7B 91250619 91251446 827 False 1013.000000 1013 88.6950 2552 3402 1 chr7B.!!$F1 850
5 TraesCS7A01G175900 chr6D 156745130 156745656 526 False 341.500000 411 91.0935 153 723 2 chr6D.!!$F2 570

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
561 613 2.253610 TGTCTGACCACGGAAGGTTAT 58.746 47.619 5.17 0.0 43.38 1.89 F
2039 2142 1.797025 CCCAGACACTTCCGAAAGTC 58.203 55.000 0.00 5.6 43.99 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2146 1.740025 GGGAGTTCTTCGCCATTTCTG 59.260 52.381 0.00 0.00 37.76 3.02 R
3183 3291 0.025641 TAACGCGCGAATACGACGTA 59.974 50.000 39.36 10.62 46.65 3.57 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
88 124 2.983592 CGGAAGGGGCGCTTGTTT 60.984 61.111 22.39 0.00 0.00 2.83
529 580 7.978975 CCAAGTGGAAAACTATTTCACTTTCAA 59.021 33.333 11.24 0.00 45.53 2.69
561 613 2.253610 TGTCTGACCACGGAAGGTTAT 58.746 47.619 5.17 0.00 43.38 1.89
1164 1219 4.558697 GGTATATGTACAGTGCTCGATGCA 60.559 45.833 0.33 5.59 39.91 3.96
1671 1728 5.926542 TGTACTTGCACATACTTGTTCTCTC 59.073 40.000 7.80 0.00 32.34 3.20
2039 2142 1.797025 CCCAGACACTTCCGAAAGTC 58.203 55.000 0.00 5.60 43.99 3.01
2043 2146 2.471743 CAGACACTTCCGAAAGTCGAAC 59.528 50.000 0.00 0.00 43.99 3.95
2064 2167 1.351017 AGAAATGGCGAAGAACTCCCA 59.649 47.619 0.00 0.00 0.00 4.37
2114 2217 2.364324 TGGGCAGCTAATCGGTTAGTAG 59.636 50.000 16.55 10.40 39.60 2.57
2172 2275 5.627182 ATTGCTAGGATTCAGAGTGACAT 57.373 39.130 0.00 0.00 0.00 3.06
2458 2564 7.159322 TGTCTTCTCACTAAACTAAGCCTAG 57.841 40.000 0.00 0.00 0.00 3.02
2462 2568 6.268825 TCTCACTAAACTAAGCCTAGTGTG 57.731 41.667 0.00 0.86 42.04 3.82
2517 2623 1.580845 GCACGCACAATCTTGCCTCT 61.581 55.000 0.00 0.00 39.53 3.69
2610 2716 0.733150 GGATTTTAGTGTCAGCCCGC 59.267 55.000 0.00 0.00 0.00 6.13
2611 2717 0.733150 GATTTTAGTGTCAGCCCGCC 59.267 55.000 0.00 0.00 0.00 6.13
2612 2718 0.679960 ATTTTAGTGTCAGCCCGCCC 60.680 55.000 0.00 0.00 0.00 6.13
2613 2719 3.599285 TTTAGTGTCAGCCCGCCCG 62.599 63.158 0.00 0.00 0.00 6.13
2649 2757 5.547465 TCCCGGCAATATACTGTAGAAATG 58.453 41.667 0.00 0.00 0.00 2.32
2650 2758 5.305902 TCCCGGCAATATACTGTAGAAATGA 59.694 40.000 0.00 0.00 0.00 2.57
2651 2759 5.639506 CCCGGCAATATACTGTAGAAATGAG 59.360 44.000 0.00 0.00 0.00 2.90
2652 2760 6.455647 CCGGCAATATACTGTAGAAATGAGA 58.544 40.000 0.00 0.00 0.00 3.27
2653 2761 7.099764 CCGGCAATATACTGTAGAAATGAGAT 58.900 38.462 0.00 0.00 0.00 2.75
2654 2762 8.251026 CCGGCAATATACTGTAGAAATGAGATA 58.749 37.037 0.00 0.00 0.00 1.98
2655 2763 9.295214 CGGCAATATACTGTAGAAATGAGATAG 57.705 37.037 0.00 0.00 0.00 2.08
2656 2764 9.092876 GGCAATATACTGTAGAAATGAGATAGC 57.907 37.037 0.00 0.00 0.00 2.97
2657 2765 9.645059 GCAATATACTGTAGAAATGAGATAGCA 57.355 33.333 0.00 0.00 0.00 3.49
2663 2771 8.659925 ACTGTAGAAATGAGATAGCAGAAATG 57.340 34.615 0.00 0.00 0.00 2.32
2664 2772 8.263640 ACTGTAGAAATGAGATAGCAGAAATGT 58.736 33.333 0.00 0.00 0.00 2.71
2665 2773 8.654230 TGTAGAAATGAGATAGCAGAAATGTC 57.346 34.615 0.00 0.00 0.00 3.06
2666 2774 6.841443 AGAAATGAGATAGCAGAAATGTCG 57.159 37.500 0.00 0.00 0.00 4.35
2667 2775 5.757320 AGAAATGAGATAGCAGAAATGTCGG 59.243 40.000 0.00 0.00 0.00 4.79
2668 2776 4.944619 ATGAGATAGCAGAAATGTCGGA 57.055 40.909 0.00 0.00 0.00 4.55
2669 2777 4.736126 TGAGATAGCAGAAATGTCGGAA 57.264 40.909 0.00 0.00 0.00 4.30
2670 2778 4.433615 TGAGATAGCAGAAATGTCGGAAC 58.566 43.478 0.00 0.00 0.00 3.62
2676 2784 0.328258 AGAAATGTCGGAACCAGGGG 59.672 55.000 0.00 0.00 0.00 4.79
2712 2820 8.437742 CAATGGATTACAAACTCTGCAATTTTC 58.562 33.333 0.00 0.00 0.00 2.29
2755 2863 1.568504 ATTCTCCTTGCGTACTCCCA 58.431 50.000 0.00 0.00 0.00 4.37
2756 2864 0.606604 TTCTCCTTGCGTACTCCCAC 59.393 55.000 0.00 0.00 0.00 4.61
2760 2868 1.445582 CTTGCGTACTCCCACCGAC 60.446 63.158 0.00 0.00 0.00 4.79
2796 2904 6.259346 ACGGGAGGTAGTACTACTTTATCT 57.741 41.667 27.71 17.83 36.36 1.98
2886 2994 4.858680 GCCCGCACTAAGGCCTCC 62.859 72.222 5.23 0.00 43.76 4.30
2910 3018 4.953940 TGGTTTGGAGGAATTTCAAAGG 57.046 40.909 0.00 0.00 32.03 3.11
3130 3238 1.105759 GCCTGATCTTGTCCATGGGC 61.106 60.000 10.20 10.20 0.00 5.36
3156 3264 1.298953 TGGGCCTAGATTTCAAGCCT 58.701 50.000 4.53 0.00 43.36 4.58
3194 3302 1.336609 GGGCCTGGATACGTCGTATTC 60.337 57.143 18.49 17.00 42.51 1.75
3196 3304 1.682982 CCTGGATACGTCGTATTCGC 58.317 55.000 18.49 6.67 42.51 4.70
3205 3313 0.634731 GTCGTATTCGCGCGTTAACA 59.365 50.000 30.98 6.92 36.96 2.41
3250 3363 1.032114 GGCTTTTAGCGTGATGGGCT 61.032 55.000 0.00 0.00 43.62 5.19
3260 3373 4.847367 GATGGGCTGGGCTTGGGG 62.847 72.222 0.00 0.00 0.00 4.96
3285 3398 3.603144 TTTTTGCATCGGGCTTTGG 57.397 47.368 0.00 0.00 45.15 3.28
3322 3435 2.968574 CTGACAGATGGCCAGGTATAGT 59.031 50.000 13.05 3.49 0.00 2.12
3335 3448 5.047660 GCCAGGTATAGTCTAGACTCAATGG 60.048 48.000 28.42 25.86 42.54 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 124 5.011431 CCACTCAGAGATAATCACATAGCCA 59.989 44.000 3.79 0.00 0.00 4.75
529 580 5.451937 CCGTGGTCAGACATGATATACAAGT 60.452 44.000 0.00 0.00 37.87 3.16
747 801 6.126409 ACAAAAGGATGTCAGGTAAGAAACA 58.874 36.000 0.00 0.00 0.00 2.83
748 802 6.635030 ACAAAAGGATGTCAGGTAAGAAAC 57.365 37.500 0.00 0.00 0.00 2.78
991 1046 2.160219 TCAAAGCTCGCATGTGATGAAC 59.840 45.455 9.87 0.23 0.00 3.18
1164 1219 6.909550 TCAAACATTTTAGGCCACACTAAT 57.090 33.333 5.01 0.00 33.31 1.73
1671 1728 4.301072 TTTCTGGAACAATACCCTGAGG 57.699 45.455 0.00 0.00 38.70 3.86
2039 2142 2.480419 AGTTCTTCGCCATTTCTGTTCG 59.520 45.455 0.00 0.00 0.00 3.95
2043 2146 1.740025 GGGAGTTCTTCGCCATTTCTG 59.260 52.381 0.00 0.00 37.76 3.02
2458 2564 9.624697 ACATTTGTTAACATGATTGTATCACAC 57.375 29.630 14.60 0.00 43.01 3.82
2462 2568 7.758980 TGCCACATTTGTTAACATGATTGTATC 59.241 33.333 14.60 9.01 34.06 2.24
2517 2623 3.390521 CACCTGGTGGCGCCTCTA 61.391 66.667 29.70 21.50 38.35 2.43
2631 2737 9.645059 TGCTATCTCATTTCTACAGTATATTGC 57.355 33.333 0.00 0.00 0.00 3.56
2649 2757 3.804873 GGTTCCGACATTTCTGCTATCTC 59.195 47.826 0.00 0.00 0.00 2.75
2650 2758 3.197766 TGGTTCCGACATTTCTGCTATCT 59.802 43.478 0.00 0.00 0.00 1.98
2651 2759 3.531538 TGGTTCCGACATTTCTGCTATC 58.468 45.455 0.00 0.00 0.00 2.08
2652 2760 3.535561 CTGGTTCCGACATTTCTGCTAT 58.464 45.455 0.00 0.00 0.00 2.97
2653 2761 2.354704 CCTGGTTCCGACATTTCTGCTA 60.355 50.000 0.00 0.00 0.00 3.49
2654 2762 1.611673 CCTGGTTCCGACATTTCTGCT 60.612 52.381 0.00 0.00 0.00 4.24
2655 2763 0.804989 CCTGGTTCCGACATTTCTGC 59.195 55.000 0.00 0.00 0.00 4.26
2656 2764 1.453155 CCCTGGTTCCGACATTTCTG 58.547 55.000 0.00 0.00 0.00 3.02
2657 2765 0.328258 CCCCTGGTTCCGACATTTCT 59.672 55.000 0.00 0.00 0.00 2.52
2658 2766 1.313091 GCCCCTGGTTCCGACATTTC 61.313 60.000 0.00 0.00 0.00 2.17
2659 2767 1.304134 GCCCCTGGTTCCGACATTT 60.304 57.895 0.00 0.00 0.00 2.32
2660 2768 0.912487 TAGCCCCTGGTTCCGACATT 60.912 55.000 0.00 0.00 0.00 2.71
2661 2769 1.306654 TAGCCCCTGGTTCCGACAT 60.307 57.895 0.00 0.00 0.00 3.06
2662 2770 2.120940 TAGCCCCTGGTTCCGACA 59.879 61.111 0.00 0.00 0.00 4.35
2663 2771 1.988406 AGTAGCCCCTGGTTCCGAC 60.988 63.158 0.00 0.00 0.00 4.79
2664 2772 1.987855 CAGTAGCCCCTGGTTCCGA 60.988 63.158 0.00 0.00 0.00 4.55
2665 2773 2.584608 CAGTAGCCCCTGGTTCCG 59.415 66.667 0.00 0.00 0.00 4.30
2666 2774 1.926426 ATGCAGTAGCCCCTGGTTCC 61.926 60.000 0.00 0.00 41.13 3.62
2667 2775 0.464554 GATGCAGTAGCCCCTGGTTC 60.465 60.000 0.00 0.00 41.13 3.62
2668 2776 1.207488 TGATGCAGTAGCCCCTGGTT 61.207 55.000 0.00 0.00 41.13 3.67
2669 2777 1.207488 TTGATGCAGTAGCCCCTGGT 61.207 55.000 0.00 0.00 41.13 4.00
2670 2778 0.184451 ATTGATGCAGTAGCCCCTGG 59.816 55.000 0.00 0.00 41.13 4.45
2676 2784 5.756195 TTGTAATCCATTGATGCAGTAGC 57.244 39.130 0.00 0.00 42.57 3.58
2712 2820 4.006989 TCACGGGTGGAACAATAATTCAG 58.993 43.478 0.00 0.00 44.16 3.02
2755 2863 2.809696 CCGTCCAAAAATAAGTGTCGGT 59.190 45.455 0.00 0.00 0.00 4.69
2756 2864 2.160813 CCCGTCCAAAAATAAGTGTCGG 59.839 50.000 0.00 0.00 36.00 4.79
2760 2868 3.418047 ACCTCCCGTCCAAAAATAAGTG 58.582 45.455 0.00 0.00 0.00 3.16
2796 2904 7.915293 ACGATTGTGTTTGATGGAATAACTA 57.085 32.000 0.00 0.00 0.00 2.24
2805 2913 5.801350 ATCCACTACGATTGTGTTTGATG 57.199 39.130 0.00 0.00 33.92 3.07
2861 2969 1.647346 CTTAGTGCGGGCGATTAACA 58.353 50.000 0.00 0.00 0.00 2.41
2863 2971 0.812412 GCCTTAGTGCGGGCGATTAA 60.812 55.000 0.00 0.00 38.91 1.40
2884 2992 4.551671 TGAAATTCCTCCAAACCAAAGGA 58.448 39.130 0.00 0.00 37.42 3.36
2885 2993 4.953940 TGAAATTCCTCCAAACCAAAGG 57.046 40.909 0.00 0.00 0.00 3.11
2886 2994 5.759763 CCTTTGAAATTCCTCCAAACCAAAG 59.240 40.000 0.00 0.00 39.03 2.77
2941 3049 6.712276 TGAACCAAAGGGCTTTAAAGAAAAA 58.288 32.000 19.48 0.00 37.90 1.94
2945 3053 5.714806 CCTATGAACCAAAGGGCTTTAAAGA 59.285 40.000 19.48 0.00 37.90 2.52
2946 3054 5.714806 TCCTATGAACCAAAGGGCTTTAAAG 59.285 40.000 11.02 11.02 37.90 1.85
2947 3055 5.646215 TCCTATGAACCAAAGGGCTTTAAA 58.354 37.500 0.00 0.00 37.90 1.52
2948 3056 5.263872 TCCTATGAACCAAAGGGCTTTAA 57.736 39.130 0.00 0.00 37.90 1.52
2949 3057 4.938575 TCCTATGAACCAAAGGGCTTTA 57.061 40.909 0.00 0.00 37.90 1.85
3012 3120 8.445493 GGCTCATGTTTATTTTCCTTTGAAATG 58.555 33.333 0.00 0.00 40.08 2.32
3069 3177 3.812019 CCGAGTCAGGTCGACCGG 61.812 72.222 28.26 27.42 46.69 5.28
3076 3184 2.047213 TTTTTCGGGCCGAGTCAGGT 62.047 55.000 29.30 0.00 37.14 4.00
3079 3187 1.964373 GCTTTTTCGGGCCGAGTCA 60.964 57.895 29.30 12.26 37.14 3.41
3080 3188 1.636570 GAGCTTTTTCGGGCCGAGTC 61.637 60.000 29.30 16.25 37.14 3.36
3083 3191 2.740826 CGAGCTTTTTCGGGCCGA 60.741 61.111 27.46 27.46 36.95 5.54
3117 3225 3.727258 CCCGGCCCATGGACAAGA 61.727 66.667 15.22 0.00 0.00 3.02
3137 3245 1.064463 CAGGCTTGAAATCTAGGCCCA 60.064 52.381 13.19 0.00 43.16 5.36
3174 3282 0.677842 AATACGACGTATCCAGGCCC 59.322 55.000 20.15 0.00 0.00 5.80
3183 3291 0.025641 TAACGCGCGAATACGACGTA 59.974 50.000 39.36 10.62 46.65 3.57
3194 3302 1.509162 GCCTCTTTGTTAACGCGCG 60.509 57.895 30.96 30.96 0.00 6.86
3196 3304 1.500396 GGGCCTCTTTGTTAACGCG 59.500 57.895 3.53 3.53 0.00 6.01
3226 3334 2.609459 CCATCACGCTAAAAGCCTACTG 59.391 50.000 0.00 0.00 38.18 2.74
3227 3335 2.420129 CCCATCACGCTAAAAGCCTACT 60.420 50.000 0.00 0.00 38.18 2.57
3228 3336 1.940613 CCCATCACGCTAAAAGCCTAC 59.059 52.381 0.00 0.00 38.18 3.18
3229 3337 1.745827 GCCCATCACGCTAAAAGCCTA 60.746 52.381 0.00 0.00 38.18 3.93
3230 3338 1.032114 GCCCATCACGCTAAAAGCCT 61.032 55.000 0.00 0.00 38.18 4.58
3231 3339 1.032114 AGCCCATCACGCTAAAAGCC 61.032 55.000 0.00 0.00 38.18 4.35
3241 3354 2.757099 CCAAGCCCAGCCCATCAC 60.757 66.667 0.00 0.00 0.00 3.06
3250 3363 2.310930 AAAACTGAGCCCCAAGCCCA 62.311 55.000 0.00 0.00 45.47 5.36
3292 3405 1.269958 CCATCTGTCAGGTCAGGTCA 58.730 55.000 0.00 0.00 36.25 4.02
3294 3407 1.557269 GGCCATCTGTCAGGTCAGGT 61.557 60.000 0.00 0.00 36.25 4.00
3304 3417 3.336509 AGACTATACCTGGCCATCTGT 57.663 47.619 5.51 6.94 0.00 3.41
3335 3448 9.874205 TCATTTGGTTCATCATAGGAATTTTTC 57.126 29.630 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.