Multiple sequence alignment - TraesCS2B01G013300

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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 TraesCS2B01G013300 chr2B 100.000 8575 0 0 1 8575 6404872 6413446 0.000000e+00 15836.0
1 TraesCS2B01G013300 chr2B 97.225 5729 110 14 1 5701 6375684 6381391 0.000000e+00 9653.0
2 TraesCS2B01G013300 chr2B 97.193 3456 62 6 5152 8575 6424081 6427533 0.000000e+00 5812.0
3 TraesCS2B01G013300 chr2B 92.759 2182 118 14 5931 8091 6381385 6383547 0.000000e+00 3118.0
4 TraesCS2B01G013300 chr2B 77.058 1373 274 35 3268 4619 31060158 31061510 0.000000e+00 752.0
5 TraesCS2B01G013300 chr2B 89.055 201 18 3 8106 8303 6385493 6385692 6.650000e-61 246.0
6 TraesCS2B01G013300 chr2B 79.487 234 43 3 2279 2509 653841076 653841307 2.480000e-35 161.0
7 TraesCS2B01G013300 chr2B 88.119 101 10 1 1691 1789 489879598 489879498 1.510000e-22 119.0
8 TraesCS2B01G013300 chr2B 88.119 101 10 1 1691 1789 755622397 755622297 1.510000e-22 119.0
9 TraesCS2B01G013300 chr2B 88.119 101 10 1 1691 1789 800062932 800062832 1.510000e-22 119.0
10 TraesCS2B01G013300 chr2B 86.735 98 13 0 2513 2610 34043336 34043433 9.100000e-20 110.0
11 TraesCS2B01G013300 chr2D 93.329 5202 250 36 2961 8094 4710363 4705191 0.000000e+00 7594.0
12 TraesCS2B01G013300 chr2D 93.850 5008 234 28 3133 8094 4689895 4684916 0.000000e+00 7474.0
13 TraesCS2B01G013300 chr2D 95.183 3882 135 17 3133 6979 4671768 4667904 0.000000e+00 6085.0
14 TraesCS2B01G013300 chr2D 81.245 1365 177 47 1 1340 4691974 4690664 0.000000e+00 1029.0
15 TraesCS2B01G013300 chr2D 80.998 1363 184 48 1 1340 4673744 4672434 0.000000e+00 1013.0
16 TraesCS2B01G013300 chr2D 80.733 1365 184 47 1 1340 4712138 4710828 0.000000e+00 990.0
17 TraesCS2B01G013300 chr2D 78.261 1357 255 31 3285 4624 2695843 2694510 0.000000e+00 835.0
18 TraesCS2B01G013300 chr2D 83.882 304 46 1 7276 7579 2693364 2693064 3.920000e-73 287.0
19 TraesCS2B01G013300 chr2D 87.562 201 21 3 8106 8303 4662824 4662625 6.700000e-56 230.0
20 TraesCS2B01G013300 chr2D 80.139 287 51 4 7295 7578 3453991 3454274 8.720000e-50 209.0
21 TraesCS2B01G013300 chr2D 84.247 146 19 3 4116 4258 2101410 2101554 1.160000e-28 139.0
22 TraesCS2B01G013300 chr2D 83.459 133 16 5 2386 2515 558960494 558960365 1.510000e-22 119.0
23 TraesCS2B01G013300 chr2D 97.619 42 1 0 293 334 4691660 4691619 1.190000e-08 73.1
24 TraesCS2B01G013300 chr2D 97.619 42 1 0 293 334 4711824 4711783 1.190000e-08 73.1
25 TraesCS2B01G013300 chr2D 88.679 53 6 0 2609 2661 73822115 73822063 2.000000e-06 65.8
26 TraesCS2B01G013300 chr2D 88.679 53 6 0 2609 2661 557285167 557285115 2.000000e-06 65.8
27 TraesCS2B01G013300 chrUn 100.000 391 0 0 2308 2698 479899615 479899225 0.000000e+00 723.0
28 TraesCS2B01G013300 chrUn 93.659 410 22 2 7189 7598 477374847 477375252 2.050000e-170 610.0
29 TraesCS2B01G013300 chrUn 88.889 54 6 0 2609 2662 384619897 384619844 5.560000e-07 67.6
30 TraesCS2B01G013300 chr4D 84.466 206 29 2 2723 2926 298611736 298611532 5.250000e-47 200.0
31 TraesCS2B01G013300 chr4D 83.654 104 17 0 2507 2610 331420054 331420157 1.970000e-16 99.0
32 TraesCS2B01G013300 chr7B 84.817 191 27 1 2723 2911 209151480 209151290 3.160000e-44 191.0
33 TraesCS2B01G013300 chr7B 83.582 67 11 0 2609 2675 719065173 719065107 7.190000e-06 63.9
34 TraesCS2B01G013300 chr7B 94.118 34 2 0 401 434 689687791 689687758 1.600000e-02 52.8
35 TraesCS2B01G013300 chr3D 82.888 187 30 1 2720 2904 169553020 169553206 5.320000e-37 167.0
36 TraesCS2B01G013300 chr3D 78.899 218 24 12 2645 2842 470722039 470721824 2.510000e-25 128.0
37 TraesCS2B01G013300 chr3D 88.889 54 6 0 2609 2662 1386026 1385973 5.560000e-07 67.6
38 TraesCS2B01G013300 chr6B 78.926 242 49 2 2276 2515 239359008 239358767 6.890000e-36 163.0
39 TraesCS2B01G013300 chr6B 86.607 112 11 2 1676 1783 280210371 280210482 4.200000e-23 121.0
40 TraesCS2B01G013300 chr6B 84.000 100 11 4 2511 2610 123378660 123378566 3.300000e-14 91.6
41 TraesCS2B01G013300 chr6B 97.143 35 1 0 768 802 92462932 92462898 9.300000e-05 60.2
42 TraesCS2B01G013300 chr1D 74.537 432 78 17 38 439 361133074 361133503 8.910000e-35 159.0
43 TraesCS2B01G013300 chr2A 86.301 146 16 3 4116 4258 1978591 1978735 1.150000e-33 156.0
44 TraesCS2B01G013300 chr2A 86.301 146 16 3 4116 4258 2016611 2016755 1.150000e-33 156.0
45 TraesCS2B01G013300 chr2A 86.301 146 16 3 4116 4258 2053589 2053733 1.150000e-33 156.0
46 TraesCS2B01G013300 chr2A 83.486 109 18 0 2819 2927 559069979 559070087 1.520000e-17 102.0
47 TraesCS2B01G013300 chr2A 83.951 81 5 3 2659 2731 592468924 592468844 4.290000e-08 71.3
48 TraesCS2B01G013300 chr6D 78.333 240 47 3 2279 2515 1784239 1784476 5.360000e-32 150.0
49 TraesCS2B01G013300 chr6D 90.566 53 5 0 2609 2661 351958703 351958651 4.290000e-08 71.3
50 TraesCS2B01G013300 chr1B 81.522 184 22 6 2745 2928 666850132 666850303 3.230000e-29 141.0
51 TraesCS2B01G013300 chr1B 87.500 112 10 2 1676 1783 33564036 33564147 9.040000e-25 126.0
52 TraesCS2B01G013300 chr1B 80.247 162 32 0 2354 2515 354580558 354580397 1.170000e-23 122.0
53 TraesCS2B01G013300 chr7D 78.241 216 47 0 2300 2515 126988082 126988297 1.160000e-28 139.0
54 TraesCS2B01G013300 chr7D 77.778 189 41 1 2278 2465 616706636 616706824 1.960000e-21 115.0
55 TraesCS2B01G013300 chr7D 78.107 169 22 11 2690 2845 72953309 72953143 9.170000e-15 93.5
56 TraesCS2B01G013300 chr7D 85.938 64 9 0 2547 2610 617085040 617084977 1.540000e-07 69.4
57 TraesCS2B01G013300 chr5B 88.679 106 10 2 2513 2617 474772888 474772784 2.510000e-25 128.0
58 TraesCS2B01G013300 chr5B 87.037 54 7 0 2609 2662 565531782 565531729 2.580000e-05 62.1
59 TraesCS2B01G013300 chr4A 89.109 101 9 1 1691 1789 585692282 585692182 3.250000e-24 124.0
60 TraesCS2B01G013300 chr3A 87.736 106 11 1 1688 1791 501866570 501866675 1.170000e-23 122.0
61 TraesCS2B01G013300 chr3A 77.778 117 22 3 2766 2880 627949100 627949214 1.540000e-07 69.4
62 TraesCS2B01G013300 chr3B 88.889 99 7 3 1691 1786 183601201 183601104 1.510000e-22 119.0
63 TraesCS2B01G013300 chr6A 83.784 111 11 4 2513 2619 588015344 588015451 1.970000e-16 99.0
64 TraesCS2B01G013300 chr6A 84.946 93 10 1 2511 2599 127187252 127187344 3.300000e-14 91.6
65 TraesCS2B01G013300 chr5D 74.872 195 37 7 2321 2515 434700792 434700974 2.570000e-10 78.7
66 TraesCS2B01G013300 chr5A 94.595 37 0 2 380 414 4277648 4277684 1.000000e-03 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 TraesCS2B01G013300 chr2B 6404872 6413446 8574 False 15836.0 15836 100.000000 1 8575 1 chr2B.!!$F1 8574
1 TraesCS2B01G013300 chr2B 6424081 6427533 3452 False 5812.0 5812 97.193000 5152 8575 1 chr2B.!!$F2 3423
2 TraesCS2B01G013300 chr2B 6375684 6385692 10008 False 4339.0 9653 93.013000 1 8303 3 chr2B.!!$F6 8302
3 TraesCS2B01G013300 chr2B 31060158 31061510 1352 False 752.0 752 77.058000 3268 4619 1 chr2B.!!$F3 1351
4 TraesCS2B01G013300 chr2D 4667904 4673744 5840 True 3549.0 6085 88.090500 1 6979 2 chr2D.!!$R6 6978
5 TraesCS2B01G013300 chr2D 4705191 4712138 6947 True 2885.7 7594 90.560333 1 8094 3 chr2D.!!$R8 8093
6 TraesCS2B01G013300 chr2D 4684916 4691974 7058 True 2858.7 7474 90.904667 1 8094 3 chr2D.!!$R7 8093
7 TraesCS2B01G013300 chr2D 2693064 2695843 2779 True 561.0 835 81.071500 3285 7579 2 chr2D.!!$R5 4294

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
102 103 0.320374 CCTCAAGTGGTGTAGGCGAA 59.680 55.000 0.00 0.0 0.00 4.70 F
169 170 0.453282 CATTGGTGTCGCTTGCTTCG 60.453 55.000 0.00 0.0 0.00 3.79 F
247 248 0.958822 GTTTGGTTGGACTCGGCAAT 59.041 50.000 0.00 0.0 0.00 3.56 F
1863 1909 0.539438 TGCCCGTTCTTCTTTGCCAT 60.539 50.000 0.00 0.0 0.00 4.40 F
2738 2786 1.556911 GGATGAGACAGAAGGGAAGCA 59.443 52.381 0.00 0.0 0.00 3.91 F
3992 4202 1.070758 TCCAGAGTGTCCACTTGAAGC 59.929 52.381 0.79 0.0 42.66 3.86 F
4915 5751 1.110442 CACCAGAACCACAAGCCAAA 58.890 50.000 0.00 0.0 0.00 3.28 F
5688 6524 2.762327 GTGGCATGGGAAGAAACATCAT 59.238 45.455 0.00 0.0 0.00 2.45 F
7371 8272 1.003118 AGGTCGCCTTTGCTGTAATCA 59.997 47.619 0.00 0.0 34.43 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 1826 4.935205 ACTTCGCTGCTCACATACATTTAA 59.065 37.500 0.00 0.00 0.00 1.52 R
1863 1909 5.118990 GTTGACCTCAGAGCAAATATAGCA 58.881 41.667 0.00 0.00 0.00 3.49 R
2698 2746 7.619965 TCATCCAACTCGGCATGAATATAATA 58.380 34.615 0.00 0.00 33.14 0.98 R
2757 2805 0.750850 TTGGAGTCCGTGCTATAGCC 59.249 55.000 21.84 12.00 41.18 3.93 R
5006 5842 0.035458 CCCACTCGAGTGCTCCTTTT 59.965 55.000 35.09 0.00 44.34 2.27 R
5009 5845 3.386237 GCCCACTCGAGTGCTCCT 61.386 66.667 35.09 2.23 44.34 3.69 R
6914 7803 2.288640 AAACTGCCTCTGCAATTTGCTC 60.289 45.455 21.19 6.98 44.51 4.26 R
7558 8459 0.178970 TAGCTAGACGGGGATGGGTC 60.179 60.000 0.00 0.00 0.00 4.46 R
8314 11149 2.798976 ACATGTTGCGCAAAATGACT 57.201 40.000 44.51 28.60 38.08 3.41 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
36 37 5.582550 TCTGATATGTTCTTACAGTGCTCG 58.417 41.667 0.00 0.00 37.77 5.03
53 54 2.362397 GCTCGGATCTAGTGTGGATGAA 59.638 50.000 0.00 0.00 0.00 2.57
69 70 2.594592 AACTGACCCTGGTTGCGC 60.595 61.111 0.00 0.00 0.00 6.09
102 103 0.320374 CCTCAAGTGGTGTAGGCGAA 59.680 55.000 0.00 0.00 0.00 4.70
107 108 2.109425 AGTGGTGTAGGCGAATTTCC 57.891 50.000 0.00 0.00 0.00 3.13
151 152 3.071837 TAGCGATGACGGCACCCA 61.072 61.111 0.00 0.00 40.15 4.51
169 170 0.453282 CATTGGTGTCGCTTGCTTCG 60.453 55.000 0.00 0.00 0.00 3.79
197 198 2.799917 CGTCGTCATGGATCTTCCCTTC 60.800 54.545 0.00 0.00 35.03 3.46
200 201 2.169352 CGTCATGGATCTTCCCTTCTGT 59.831 50.000 0.00 0.00 35.03 3.41
201 202 3.369892 CGTCATGGATCTTCCCTTCTGTT 60.370 47.826 0.00 0.00 35.03 3.16
227 228 3.586892 CTCCGGGTGAAAACTCTAGTTC 58.413 50.000 0.00 0.00 37.25 3.01
247 248 0.958822 GTTTGGTTGGACTCGGCAAT 59.041 50.000 0.00 0.00 0.00 3.56
250 251 1.303317 GGTTGGACTCGGCAATGGT 60.303 57.895 0.00 0.00 0.00 3.55
259 260 1.140161 CGGCAATGGTGATGCTTGG 59.860 57.895 0.00 0.00 43.34 3.61
261 262 1.592743 GCAATGGTGATGCTTGGCA 59.407 52.632 0.00 0.00 44.86 4.92
359 386 2.891191 TTGTAAATGGTCCTCCCCAC 57.109 50.000 0.00 0.00 37.31 4.61
364 391 5.482580 TGTAAATGGTCCTCCCCACTATAT 58.517 41.667 0.00 0.00 37.31 0.86
371 398 5.091552 GGTCCTCCCCACTATATTGTATCA 58.908 45.833 0.00 0.00 0.00 2.15
581 610 9.235537 GACTATTAGTTTATCACCGACTTTCTC 57.764 37.037 0.00 0.00 0.00 2.87
582 611 8.746530 ACTATTAGTTTATCACCGACTTTCTCA 58.253 33.333 0.00 0.00 0.00 3.27
583 612 9.582431 CTATTAGTTTATCACCGACTTTCTCAA 57.418 33.333 0.00 0.00 0.00 3.02
584 613 8.842358 ATTAGTTTATCACCGACTTTCTCAAA 57.158 30.769 0.00 0.00 0.00 2.69
585 614 8.665643 TTAGTTTATCACCGACTTTCTCAAAA 57.334 30.769 0.00 0.00 0.00 2.44
606 635 9.057089 TCAAAACAAAACAAAACAATAACACCT 57.943 25.926 0.00 0.00 0.00 4.00
658 687 9.495382 AAAATTAGACATCTAGAGTACTCCCTT 57.505 33.333 19.38 3.77 0.00 3.95
660 689 4.710324 AGACATCTAGAGTACTCCCTTCG 58.290 47.826 19.38 8.28 0.00 3.79
727 757 4.652421 AGTAATTATCCGGTACTGCCTTCA 59.348 41.667 0.00 0.00 34.25 3.02
743 773 6.438425 ACTGCCTTCATTCCAAAATGTAAGAT 59.562 34.615 9.73 0.00 42.46 2.40
831 863 5.348997 ACCGACTTACTTACGTGTACTAGTC 59.651 44.000 0.00 5.17 31.78 2.59
1737 1783 8.119226 GTGTGAATCTACACTCTAAAATGCATC 58.881 37.037 0.00 0.00 45.70 3.91
1863 1909 0.539438 TGCCCGTTCTTCTTTGCCAT 60.539 50.000 0.00 0.00 0.00 4.40
2698 2746 9.975218 ATAAGGTACATTCAGTTGGATTAAACT 57.025 29.630 0.00 0.00 41.08 2.66
2738 2786 1.556911 GGATGAGACAGAAGGGAAGCA 59.443 52.381 0.00 0.00 0.00 3.91
2757 2805 2.460918 CAGACGGTAGATTAACAGCCG 58.539 52.381 0.00 0.00 46.83 5.52
2761 2809 1.338973 CGGTAGATTAACAGCCGGCTA 59.661 52.381 32.30 15.12 38.86 3.93
2767 2815 2.234300 TTAACAGCCGGCTATAGCAC 57.766 50.000 32.30 14.24 44.36 4.40
2777 2825 1.269831 GGCTATAGCACGGACTCCAAG 60.270 57.143 25.53 0.00 44.36 3.61
2855 2903 8.853469 AGAAACTAGCTATTATACGTGTTGAC 57.147 34.615 0.00 0.00 0.00 3.18
2882 2930 6.908870 TTGCTTGACTATATGTGACATGTC 57.091 37.500 19.27 19.27 0.00 3.06
2883 2931 5.043248 TGCTTGACTATATGTGACATGTCG 58.957 41.667 20.54 7.19 0.00 4.35
3992 4202 1.070758 TCCAGAGTGTCCACTTGAAGC 59.929 52.381 0.79 0.00 42.66 3.86
4534 4794 3.582647 TCTGATGTGCTTTAGGGAGTTCA 59.417 43.478 0.00 0.00 0.00 3.18
4915 5751 1.110442 CACCAGAACCACAAGCCAAA 58.890 50.000 0.00 0.00 0.00 3.28
5120 5956 8.733458 TCATCTAAAGTACGTACACACTTATGT 58.267 33.333 26.55 2.81 40.80 2.29
5198 6034 9.476202 TCAAGTATTTATTAGATCATGACCACG 57.524 33.333 0.00 0.00 0.00 4.94
5278 6114 8.683550 TTATCGAAACAATATCTACGCCTATG 57.316 34.615 0.00 0.00 0.00 2.23
5688 6524 2.762327 GTGGCATGGGAAGAAACATCAT 59.238 45.455 0.00 0.00 0.00 2.45
5876 6726 4.518970 GCTGGTCCTTCAACATAAAACTCA 59.481 41.667 0.00 0.00 0.00 3.41
5883 6733 9.237846 GTCCTTCAACATAAAACTCAAGAAAAG 57.762 33.333 0.00 0.00 0.00 2.27
6012 6862 5.163395 GGGACACAAATACAAAAACCTTGGA 60.163 40.000 0.00 0.00 0.00 3.53
6632 7520 3.248888 AGCTCAAACTAAGTACTGGGGT 58.751 45.455 0.00 0.00 0.00 4.95
6914 7803 2.311124 GGGAAGTGAACCCATAGACG 57.689 55.000 0.00 0.00 46.05 4.18
7097 7986 6.912426 AGACCTCATAGTGGAGAGTACATTA 58.088 40.000 0.00 0.00 37.05 1.90
7371 8272 1.003118 AGGTCGCCTTTGCTGTAATCA 59.997 47.619 0.00 0.00 34.43 2.57
7522 8423 3.014304 AGATGCCTTCACATTCAGCAT 57.986 42.857 0.00 0.00 46.35 3.79
7556 8457 3.247173 GCATTATCAAGAGCCTCTTCGTG 59.753 47.826 3.39 0.00 33.78 4.35
7558 8459 2.957491 ATCAAGAGCCTCTTCGTGAG 57.043 50.000 3.39 0.00 38.60 3.51
7559 8460 1.911057 TCAAGAGCCTCTTCGTGAGA 58.089 50.000 3.39 0.00 45.39 3.27
8013 8914 1.461127 GCACAAGCCTCGTGTCTTTAG 59.539 52.381 0.00 0.00 36.71 1.85
8022 8923 5.185249 AGCCTCGTGTCTTTAGTTATCTTCA 59.815 40.000 0.00 0.00 0.00 3.02
8268 11103 4.397420 AGCACCATTCAACATGTACTCAA 58.603 39.130 0.00 0.00 0.00 3.02
8312 11147 4.529109 TCTGTGTGACATAATCGGACAA 57.471 40.909 0.00 0.00 0.00 3.18
8314 11149 5.301555 TCTGTGTGACATAATCGGACAAAA 58.698 37.500 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.303078 AGATCCGAGCACTGTAAGAACATAT 59.697 40.000 0.00 0.00 37.43 1.78
36 37 4.442192 GGTCAGTTCATCCACACTAGATCC 60.442 50.000 0.00 0.00 0.00 3.36
53 54 3.560251 AGCGCAACCAGGGTCAGT 61.560 61.111 11.47 0.00 0.00 3.41
151 152 0.884704 ACGAAGCAAGCGACACCAAT 60.885 50.000 0.00 0.00 0.00 3.16
169 170 2.993899 AGATCCATGACGACGTTTTCAC 59.006 45.455 0.13 0.00 0.00 3.18
197 198 1.550130 TTCACCCGGAGCCCTAACAG 61.550 60.000 0.73 0.00 0.00 3.16
200 201 0.037160 GTTTTCACCCGGAGCCCTAA 59.963 55.000 0.73 0.00 0.00 2.69
201 202 0.838987 AGTTTTCACCCGGAGCCCTA 60.839 55.000 0.73 0.00 0.00 3.53
227 228 1.440938 TTGCCGAGTCCAACCAAACG 61.441 55.000 0.00 0.00 0.00 3.60
278 279 2.427453 CACCTAGCTCCACGATAACACT 59.573 50.000 0.00 0.00 0.00 3.55
349 376 5.780793 AGTGATACAATATAGTGGGGAGGAC 59.219 44.000 5.03 0.00 0.00 3.85
359 386 5.998553 ACACGACCGAGTGATACAATATAG 58.001 41.667 11.50 0.00 44.43 1.31
364 391 3.076621 AGTACACGACCGAGTGATACAA 58.923 45.455 11.50 0.00 44.43 2.41
371 398 2.877043 AACAAAGTACACGACCGAGT 57.123 45.000 0.00 0.00 0.00 4.18
415 442 1.550976 CTCGAACTAGGCTTTCACCCT 59.449 52.381 0.00 0.00 36.47 4.34
450 477 8.509690 CAGATCAATTAATCAACAGTGTCAAGT 58.490 33.333 0.00 0.00 0.00 3.16
553 582 7.657023 AAGTCGGTGATAAACTAATAGTCCT 57.343 36.000 0.00 0.00 0.00 3.85
583 612 9.490379 TGTAGGTGTTATTGTTTTGTTTTGTTT 57.510 25.926 0.00 0.00 0.00 2.83
584 613 9.145865 CTGTAGGTGTTATTGTTTTGTTTTGTT 57.854 29.630 0.00 0.00 0.00 2.83
585 614 7.762159 CCTGTAGGTGTTATTGTTTTGTTTTGT 59.238 33.333 0.00 0.00 0.00 2.83
606 635 1.775459 TGTTGCCCCTTACAACCTGTA 59.225 47.619 4.35 0.00 45.42 2.74
698 728 3.887716 AGTACCGGATAATTACTGCTCGT 59.112 43.478 9.46 0.00 0.00 4.18
703 733 4.602340 AGGCAGTACCGGATAATTACTG 57.398 45.455 19.72 19.72 46.52 2.74
768 799 8.356000 TCCGTCCCAAAATATAAGATGTTTTT 57.644 30.769 0.00 0.00 32.31 1.94
774 805 6.101296 ACTCCTTCCGTCCCAAAATATAAGAT 59.899 38.462 0.00 0.00 0.00 2.40
831 863 8.400947 CCTACAATATTTTGTCTTCCAGTGATG 58.599 37.037 4.71 0.00 42.43 3.07
1780 1826 4.935205 ACTTCGCTGCTCACATACATTTAA 59.065 37.500 0.00 0.00 0.00 1.52
1863 1909 5.118990 GTTGACCTCAGAGCAAATATAGCA 58.881 41.667 0.00 0.00 0.00 3.49
2698 2746 7.619965 TCATCCAACTCGGCATGAATATAATA 58.380 34.615 0.00 0.00 33.14 0.98
2711 2759 2.417924 CCTTCTGTCTCATCCAACTCGG 60.418 54.545 0.00 0.00 0.00 4.63
2715 2763 3.604582 CTTCCCTTCTGTCTCATCCAAC 58.395 50.000 0.00 0.00 0.00 3.77
2738 2786 1.407979 CCGGCTGTTAATCTACCGTCT 59.592 52.381 0.00 0.00 42.29 4.18
2757 2805 0.750850 TTGGAGTCCGTGCTATAGCC 59.249 55.000 21.84 12.00 41.18 3.93
2761 2809 2.301870 TGTTTCTTGGAGTCCGTGCTAT 59.698 45.455 4.30 0.00 0.00 2.97
2767 2815 5.419542 TCTCATAATGTTTCTTGGAGTCCG 58.580 41.667 4.30 0.00 0.00 4.79
2777 2825 6.036517 CCTGCAGTACACTCTCATAATGTTTC 59.963 42.308 13.81 0.00 0.00 2.78
2855 2903 9.049523 ACATGTCACATATAGTCAAGCAAATAG 57.950 33.333 0.00 0.00 0.00 1.73
2882 2930 5.789710 AAACAACCGGTTATATGAAGTCG 57.210 39.130 21.79 5.94 39.29 4.18
2883 2931 7.838771 AGTAAACAACCGGTTATATGAAGTC 57.161 36.000 21.79 4.88 39.29 3.01
3958 4168 4.846940 ACACTCTGGAGGAGGTTAAATTCT 59.153 41.667 2.58 0.00 45.83 2.40
4460 4720 1.679139 CACAAGGGAAACAGCACTCA 58.321 50.000 0.00 0.00 0.00 3.41
4534 4794 5.880901 ACCATTAAGTGTCAACTCATCCTT 58.119 37.500 0.00 0.00 34.77 3.36
4915 5751 6.660949 AGCCAGATGCAGTTTATCTTTAAAGT 59.339 34.615 14.74 5.49 44.83 2.66
4962 5798 3.317149 ACCATCGTATACACACATAGCGT 59.683 43.478 3.32 0.00 0.00 5.07
5006 5842 0.035458 CCCACTCGAGTGCTCCTTTT 59.965 55.000 35.09 0.00 44.34 2.27
5009 5845 3.386237 GCCCACTCGAGTGCTCCT 61.386 66.667 35.09 2.23 44.34 3.69
5198 6034 3.681897 ACATGTTCTCAAGCGAAGTGATC 59.318 43.478 0.00 0.00 0.00 2.92
6012 6862 7.891498 TTCTTTTCTAACCTTGGTAAGCTTT 57.109 32.000 3.20 0.00 0.00 3.51
6406 7294 5.222547 ACCCCTCTTCCATTATTCCAAGTTT 60.223 40.000 0.00 0.00 0.00 2.66
6581 7469 7.854337 TCTTCCTTAGTATTATTGGACGGTTT 58.146 34.615 0.00 0.00 0.00 3.27
6632 7520 5.412594 GTGCATTGTGACAATAAGGAGAAGA 59.587 40.000 10.89 0.00 0.00 2.87
6832 7720 6.289834 TGCCACAACATTTCATCATTTCTTT 58.710 32.000 0.00 0.00 0.00 2.52
6914 7803 2.288640 AAACTGCCTCTGCAATTTGCTC 60.289 45.455 21.19 6.98 44.51 4.26
7097 7986 3.057596 GCTGCTAGATCTACTTCAGCGAT 60.058 47.826 21.36 0.00 40.83 4.58
7371 8272 7.295322 TCCATTCATCTTCTATCATCGAGTT 57.705 36.000 0.00 0.00 0.00 3.01
7454 8355 6.402222 CAGGCTGAGACTAAAGTTGATAACT 58.598 40.000 9.42 0.00 45.46 2.24
7522 8423 2.916640 TGATAATGCCGTCAAGATGCA 58.083 42.857 0.00 0.00 39.68 3.96
7556 8457 1.465200 GCTAGACGGGGATGGGTCTC 61.465 65.000 0.00 0.00 42.27 3.36
7558 8459 0.178970 TAGCTAGACGGGGATGGGTC 60.179 60.000 0.00 0.00 0.00 4.46
7559 8460 0.469518 GTAGCTAGACGGGGATGGGT 60.470 60.000 0.00 0.00 0.00 4.51
7983 8884 0.751643 AGGCTTGTGCGGTGAAAACT 60.752 50.000 0.00 0.00 40.82 2.66
8254 11089 2.810852 TGCGCAATTGAGTACATGTTGA 59.189 40.909 8.16 0.00 0.00 3.18
8268 11103 5.497635 TCATAATGTACATGTTGCGCAAT 57.502 34.783 27.79 12.95 0.00 3.56
8312 11147 3.456280 ACATGTTGCGCAAAATGACTTT 58.544 36.364 44.51 27.66 38.08 2.66
8314 11149 2.798976 ACATGTTGCGCAAAATGACT 57.201 40.000 44.51 28.60 38.08 3.41


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

AutoCloner maintained by Alex Coulton.