Multiple sequence alignment - TraesCS7D01G093400

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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 TraesCS7D01G093400 chr7D 100.000 3261 0 0 1 3261 55528338 55531598 0.000000e+00 6023
1 TraesCS7D01G093400 chr7D 94.096 1101 49 7 752 1848 55609777 55610865 0.000000e+00 1659
2 TraesCS7D01G093400 chr7D 89.469 1168 100 10 1640 2789 55487828 55488990 0.000000e+00 1454
3 TraesCS7D01G093400 chr7D 87.924 1151 77 31 1874 3018 55610857 55611951 0.000000e+00 1299
4 TraesCS7D01G093400 chr7D 83.495 824 100 16 1641 2458 54372455 54371662 0.000000e+00 736
5 TraesCS7D01G093400 chr7D 84.412 417 44 12 316 718 55601237 55601646 1.100000e-104 390
6 TraesCS7D01G093400 chr7D 88.679 318 26 4 2951 3261 55490574 55490888 2.370000e-101 379
7 TraesCS7D01G093400 chr7D 84.824 369 51 5 121 486 440201183 440201549 1.850000e-97 366
8 TraesCS7D01G093400 chr7D 84.267 375 53 6 106 478 618194730 618194360 8.600000e-96 361
9 TraesCS7D01G093400 chrUn 93.435 1767 92 11 752 2512 284724330 284726078 0.000000e+00 2599
10 TraesCS7D01G093400 chrUn 87.033 509 47 9 2514 3018 48623345 48622852 1.020000e-154 556
11 TraesCS7D01G093400 chr4A 93.435 1767 92 11 752 2512 672211875 672213623 0.000000e+00 2599
12 TraesCS7D01G093400 chr4A 89.533 984 91 8 1641 2621 672001407 672002381 0.000000e+00 1236
13 TraesCS7D01G093400 chr4A 86.823 812 88 8 1641 2444 669993050 669992250 0.000000e+00 889
14 TraesCS7D01G093400 chr4A 90.732 669 50 7 713 1371 672174188 672174854 0.000000e+00 881
15 TraesCS7D01G093400 chr4A 83.350 991 117 19 1641 2601 669920934 669919962 0.000000e+00 872
16 TraesCS7D01G093400 chr4A 88.772 668 51 18 713 1371 672265444 672266096 0.000000e+00 797
17 TraesCS7D01G093400 chr4A 87.988 641 65 9 2624 3261 672246295 672246926 0.000000e+00 747
18 TraesCS7D01G093400 chr4A 86.595 649 65 12 2626 3261 672161105 672161744 0.000000e+00 697
19 TraesCS7D01G093400 chr4A 84.602 591 77 7 1914 2494 672197348 672197934 2.820000e-160 575
20 TraesCS7D01G093400 chr4A 88.100 479 53 4 1 478 672264366 672264841 1.700000e-157 566
21 TraesCS7D01G093400 chr4A 81.499 627 72 24 125 718 672173278 672173893 2.940000e-130 475
22 TraesCS7D01G093400 chr4A 89.837 246 15 6 479 718 672264872 672265113 1.140000e-79 307
23 TraesCS7D01G093400 chr4A 78.810 420 64 17 720 1119 672246956 672247370 3.230000e-65 259
24 TraesCS7D01G093400 chr4A 90.909 88 7 1 720 807 672287292 672287378 2.060000e-22 117
25 TraesCS7D01G093400 chr4A 85.217 115 12 4 2392 2503 672275005 672275117 2.660000e-21 113
26 TraesCS7D01G093400 chr7A 83.787 993 123 17 1641 2601 57889736 57888750 0.000000e+00 907
27 TraesCS7D01G093400 chr7A 84.615 130 8 10 2366 2485 59434925 59435052 5.720000e-23 119
28 TraesCS7D01G093400 chr5A 86.877 381 46 4 100 478 443272907 443272529 1.080000e-114 424
29 TraesCS7D01G093400 chr5D 85.974 385 45 6 101 478 502182288 502182670 1.410000e-108 403
30 TraesCS7D01G093400 chr5B 85.864 382 48 4 101 478 626065635 626066014 5.070000e-108 401
31 TraesCS7D01G093400 chr1B 86.072 359 48 2 121 478 281089584 281089227 5.100000e-103 385
32 TraesCS7D01G093400 chr7B 85.955 356 45 5 125 478 726349644 726349292 3.070000e-100 375


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 TraesCS7D01G093400 chr7D 55528338 55531598 3260 False 6023.000000 6023 100.0000 1 3261 1 chr7D.!!$F1 3260
1 TraesCS7D01G093400 chr7D 55609777 55611951 2174 False 1479.000000 1659 91.0100 752 3018 2 chr7D.!!$F5 2266
2 TraesCS7D01G093400 chr7D 55487828 55490888 3060 False 916.500000 1454 89.0740 1640 3261 2 chr7D.!!$F4 1621
3 TraesCS7D01G093400 chr7D 54371662 54372455 793 True 736.000000 736 83.4950 1641 2458 1 chr7D.!!$R1 817
4 TraesCS7D01G093400 chrUn 284724330 284726078 1748 False 2599.000000 2599 93.4350 752 2512 1 chrUn.!!$F1 1760
5 TraesCS7D01G093400 chr4A 672211875 672213623 1748 False 2599.000000 2599 93.4350 752 2512 1 chr4A.!!$F4 1760
6 TraesCS7D01G093400 chr4A 672001407 672002381 974 False 1236.000000 1236 89.5330 1641 2621 1 chr4A.!!$F1 980
7 TraesCS7D01G093400 chr4A 669992250 669993050 800 True 889.000000 889 86.8230 1641 2444 1 chr4A.!!$R2 803
8 TraesCS7D01G093400 chr4A 669919962 669920934 972 True 872.000000 872 83.3500 1641 2601 1 chr4A.!!$R1 960
9 TraesCS7D01G093400 chr4A 672161105 672161744 639 False 697.000000 697 86.5950 2626 3261 1 chr4A.!!$F2 635
10 TraesCS7D01G093400 chr4A 672173278 672174854 1576 False 678.000000 881 86.1155 125 1371 2 chr4A.!!$F7 1246
11 TraesCS7D01G093400 chr4A 672197348 672197934 586 False 575.000000 575 84.6020 1914 2494 1 chr4A.!!$F3 580
12 TraesCS7D01G093400 chr4A 672264366 672266096 1730 False 556.666667 797 88.9030 1 1371 3 chr4A.!!$F9 1370
13 TraesCS7D01G093400 chr4A 672246295 672247370 1075 False 503.000000 747 83.3990 720 3261 2 chr4A.!!$F8 2541
14 TraesCS7D01G093400 chr7A 57888750 57889736 986 True 907.000000 907 83.7870 1641 2601 1 chr7A.!!$R1 960

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
822 1581 0.918258 TCCATCCAAGCAGCCATGTA 59.082 50.0 0.0 0.0 0.0 2.29 F
1441 2216 1.097547 CCCTTGTTAGCAGCATCCGG 61.098 60.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 2669 0.178876 TCACCAGTGGGAGGGATGAA 60.179 55.0 15.21 0.0 38.05 2.57 R
3018 5375 1.187087 CTCTTCGGCCTCAACCTAGT 58.813 55.0 0.00 0.0 0.00 2.57 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
37 38 2.159338 CCGAACCAAGCCAATGAAGATG 60.159 50.000 0.00 0.00 0.00 2.90
43 44 2.490509 CAAGCCAATGAAGATGAGCACA 59.509 45.455 0.00 0.00 0.00 4.57
61 62 5.985781 AGCACAAACATTAAGTAGACAACG 58.014 37.500 0.00 0.00 0.00 4.10
74 75 7.787823 AAGTAGACAACGTTCGTTACTAATC 57.212 36.000 10.18 6.97 0.00 1.75
76 77 8.256611 AGTAGACAACGTTCGTTACTAATCTA 57.743 34.615 10.18 9.52 0.00 1.98
79 81 7.533426 AGACAACGTTCGTTACTAATCTACAT 58.467 34.615 10.18 0.00 0.00 2.29
81 83 7.086376 ACAACGTTCGTTACTAATCTACATGT 58.914 34.615 10.18 2.69 0.00 3.21
83 85 5.961843 ACGTTCGTTACTAATCTACATGTCG 59.038 40.000 0.00 0.00 0.00 4.35
89 91 6.481134 GTTACTAATCTACATGTCGTCGTGA 58.519 40.000 0.00 0.00 34.90 4.35
103 105 1.588674 TCGTGAGCCGACATTTTGTT 58.411 45.000 0.00 0.00 41.60 2.83
104 106 2.756829 TCGTGAGCCGACATTTTGTTA 58.243 42.857 0.00 0.00 41.60 2.41
106 108 3.560481 TCGTGAGCCGACATTTTGTTAAA 59.440 39.130 0.00 0.00 41.60 1.52
200 203 6.144886 CGATTATCGTTTGGACCGATTTATCA 59.855 38.462 6.43 0.00 42.00 2.15
205 208 4.032900 CGTTTGGACCGATTTATCACTCTG 59.967 45.833 0.00 0.00 0.00 3.35
303 306 4.724303 TGTGTTTTGTGGACTTTGTTACG 58.276 39.130 0.00 0.00 0.00 3.18
314 317 7.545265 TGTGGACTTTGTTACGTAATATGTACC 59.455 37.037 11.86 11.72 0.00 3.34
445 448 5.620206 GGAACCTGGGATTTGTGAAAAATT 58.380 37.500 0.00 0.00 0.00 1.82
566 603 9.233232 GAATTGTTAACTTATTTTCTATGCGGG 57.767 33.333 7.22 0.00 0.00 6.13
599 636 2.754946 TCTACAAGAAATTCCCGCGT 57.245 45.000 4.92 0.00 0.00 6.01
721 765 2.062971 CTTGGCACTCCCATGCTAAT 57.937 50.000 0.00 0.00 43.98 1.73
722 766 2.381911 CTTGGCACTCCCATGCTAATT 58.618 47.619 0.00 0.00 43.98 1.40
723 767 2.530460 TGGCACTCCCATGCTAATTT 57.470 45.000 0.00 0.00 45.38 1.82
726 1476 1.334869 GCACTCCCATGCTAATTTCCG 59.665 52.381 0.00 0.00 42.62 4.30
733 1483 3.157087 CCATGCTAATTTCCGCCCTTAT 58.843 45.455 0.00 0.00 0.00 1.73
750 1500 7.155328 CGCCCTTATGACTAAATGACTATTCT 58.845 38.462 0.00 0.00 0.00 2.40
822 1581 0.918258 TCCATCCAAGCAGCCATGTA 59.082 50.000 0.00 0.00 0.00 2.29
904 1663 4.488126 TGAAGATCTTTCCGTGCAAAAG 57.512 40.909 9.87 3.40 35.49 2.27
981 1742 7.121315 CAGCTCACACTATATATACTAGCACCA 59.879 40.741 0.00 0.00 0.00 4.17
989 1750 4.850347 ATATACTAGCACCAACCGAGTC 57.150 45.455 0.00 0.00 0.00 3.36
1206 1977 1.956629 GAGCGGGAGACATCGGGAAA 61.957 60.000 0.00 0.00 0.00 3.13
1228 1999 2.223377 GGAACACTTGGTTTCAGCTACG 59.777 50.000 0.00 0.00 40.63 3.51
1230 2001 1.414919 ACACTTGGTTTCAGCTACGGA 59.585 47.619 0.00 0.00 0.00 4.69
1231 2002 1.798813 CACTTGGTTTCAGCTACGGAC 59.201 52.381 0.00 0.00 0.00 4.79
1234 2009 3.056749 ACTTGGTTTCAGCTACGGACTAG 60.057 47.826 0.00 0.00 0.00 2.57
1256 2031 2.190843 CGTTGTGGTGGGTGGTGA 59.809 61.111 0.00 0.00 0.00 4.02
1275 2050 1.529865 GACCTTACGTGCCAACTTGAC 59.470 52.381 0.00 0.00 0.00 3.18
1293 2068 2.027625 CGCCACGACTTTGTCCCTC 61.028 63.158 0.00 0.00 0.00 4.30
1298 2073 2.046217 GACTTTGTCCCTCGGCCC 60.046 66.667 0.00 0.00 0.00 5.80
1338 2113 6.656902 TGTCTTCTCTGCCATATTGATCTTT 58.343 36.000 0.00 0.00 0.00 2.52
1402 2177 6.068670 AGCCATGTTTGTCTAGGTTAAGTTT 58.931 36.000 0.00 0.00 0.00 2.66
1413 2188 7.097834 GTCTAGGTTAAGTTTGATGCACTAGT 58.902 38.462 0.00 0.00 0.00 2.57
1415 2190 8.467598 TCTAGGTTAAGTTTGATGCACTAGTAG 58.532 37.037 0.00 0.00 0.00 2.57
1441 2216 1.097547 CCCTTGTTAGCAGCATCCGG 61.098 60.000 0.00 0.00 0.00 5.14
1548 2323 4.683832 CTGCTACTTATCGGCAAGTTAGT 58.316 43.478 7.69 0.00 39.45 2.24
1551 2326 5.221130 GCTACTTATCGGCAAGTTAGTAGG 58.779 45.833 7.69 1.15 39.45 3.18
1566 2341 5.196165 AGTTAGTAGGGTTCCCACTCTAGAT 59.804 44.000 10.73 0.87 36.59 1.98
1714 2489 4.573201 CAGTTTCGAAACAACCTTGGTAGA 59.427 41.667 35.29 0.00 41.30 2.59
1848 2658 3.432252 GGTAGACTGTTGATGGTTGAACG 59.568 47.826 0.00 0.00 0.00 3.95
1849 2659 3.469008 AGACTGTTGATGGTTGAACGA 57.531 42.857 0.00 0.00 0.00 3.85
1850 2660 4.008074 AGACTGTTGATGGTTGAACGAT 57.992 40.909 0.00 0.00 0.00 3.73
1851 2661 4.389374 AGACTGTTGATGGTTGAACGATT 58.611 39.130 0.00 0.00 0.00 3.34
1852 2662 4.821805 AGACTGTTGATGGTTGAACGATTT 59.178 37.500 0.00 0.00 0.00 2.17
1853 2663 5.995282 AGACTGTTGATGGTTGAACGATTTA 59.005 36.000 0.00 0.00 0.00 1.40
1854 2664 6.655003 AGACTGTTGATGGTTGAACGATTTAT 59.345 34.615 0.00 0.00 0.00 1.40
1855 2665 7.174946 AGACTGTTGATGGTTGAACGATTTATT 59.825 33.333 0.00 0.00 0.00 1.40
1856 2666 7.305474 ACTGTTGATGGTTGAACGATTTATTC 58.695 34.615 0.00 0.00 0.00 1.75
1868 2678 4.653806 CGATTTATTCGCTTCATCCCTC 57.346 45.455 0.00 0.00 41.69 4.30
1869 2679 3.433615 CGATTTATTCGCTTCATCCCTCC 59.566 47.826 0.00 0.00 41.69 4.30
1870 2680 2.930826 TTATTCGCTTCATCCCTCCC 57.069 50.000 0.00 0.00 0.00 4.30
1871 2681 1.801242 TATTCGCTTCATCCCTCCCA 58.199 50.000 0.00 0.00 0.00 4.37
1872 2682 0.181350 ATTCGCTTCATCCCTCCCAC 59.819 55.000 0.00 0.00 0.00 4.61
1873 2683 0.909610 TTCGCTTCATCCCTCCCACT 60.910 55.000 0.00 0.00 0.00 4.00
1874 2684 1.153289 CGCTTCATCCCTCCCACTG 60.153 63.158 0.00 0.00 0.00 3.66
1875 2685 1.225704 GCTTCATCCCTCCCACTGG 59.774 63.158 0.00 0.00 0.00 4.00
1876 2686 1.566298 GCTTCATCCCTCCCACTGGT 61.566 60.000 0.00 0.00 0.00 4.00
1877 2687 0.254178 CTTCATCCCTCCCACTGGTG 59.746 60.000 0.00 0.00 0.00 4.17
1878 2688 0.178876 TTCATCCCTCCCACTGGTGA 60.179 55.000 1.93 0.00 0.00 4.02
1879 2689 0.909610 TCATCCCTCCCACTGGTGAC 60.910 60.000 1.93 0.00 0.00 3.67
1909 2720 3.411446 TGACAATACTCAAACTGCTGGG 58.589 45.455 0.00 0.00 0.00 4.45
1910 2721 2.749621 GACAATACTCAAACTGCTGGGG 59.250 50.000 0.00 0.00 0.00 4.96
1965 2776 3.877508 CCTTACCGATGGAAAAGGATCAC 59.122 47.826 13.14 0.00 39.74 3.06
1966 2777 2.420058 ACCGATGGAAAAGGATCACC 57.580 50.000 0.00 0.00 0.00 4.02
2001 2818 0.892814 GCTCTCTTTGTTGGCCAGCT 60.893 55.000 21.11 0.00 0.00 4.24
2234 3053 2.684881 CCTGCCAAACCTATGTGATCAC 59.315 50.000 19.27 19.27 0.00 3.06
2244 3063 5.710646 ACCTATGTGATCACTCTATCAGGT 58.289 41.667 25.55 21.55 36.57 4.00
2258 3077 7.499563 CACTCTATCAGGTTGCTTACTCTACTA 59.500 40.741 0.00 0.00 0.00 1.82
2390 3214 5.239963 TGATATGTTATCGTGCGACTTAGGA 59.760 40.000 0.00 0.00 0.00 2.94
2439 3275 4.511826 GCCTGGTTCTGGTTATCTTTATCG 59.488 45.833 0.00 0.00 0.00 2.92
2495 3336 7.715249 GGAACTTCTAATTAGTATGATGGTGCA 59.285 37.037 12.19 0.00 0.00 4.57
2496 3337 8.668510 AACTTCTAATTAGTATGATGGTGCAG 57.331 34.615 12.19 0.00 0.00 4.41
2497 3338 8.023021 ACTTCTAATTAGTATGATGGTGCAGA 57.977 34.615 12.19 0.00 0.00 4.26
2516 3379 4.529897 CAGACTTCATTTCCATGGGATGA 58.470 43.478 20.91 20.91 0.00 2.92
2550 3413 7.088905 GTGCAACTTCATCTTTCATTTGAGAT 58.911 34.615 0.00 0.00 33.01 2.75
2655 3520 5.542616 CAAGTAAGCCTTGTTCTGATCAG 57.457 43.478 17.07 17.07 44.64 2.90
2678 3543 4.761975 CTTTATGGGCTACGTTACCTTCA 58.238 43.478 0.00 0.00 0.00 3.02
2688 3553 5.009811 GCTACGTTACCTTCAGACTATGGAT 59.990 44.000 0.00 0.00 0.00 3.41
2723 3602 6.575162 ACTCAACAATCCTTTATTGACCAC 57.425 37.500 4.82 0.00 46.81 4.16
2732 3611 8.739039 CAATCCTTTATTGACCACAAACTATGA 58.261 33.333 0.00 0.00 46.81 2.15
2737 3616 9.702726 CTTTATTGACCACAAACTATGATTACG 57.297 33.333 0.00 0.00 39.54 3.18
2753 3632 9.442033 CTATGATTACGTCGTTTATGAGTACAA 57.558 33.333 1.78 0.00 0.00 2.41
2817 3696 2.852449 GGGTCCTCTAGCCAATTTAGC 58.148 52.381 0.00 0.00 45.71 3.09
2843 3722 4.439700 GCTAGCTCACGAGGTACACAATTA 60.440 45.833 7.70 0.00 40.09 1.40
2847 3726 4.267928 GCTCACGAGGTACACAATTATGTC 59.732 45.833 0.00 0.00 37.82 3.06
2851 3730 3.134081 CGAGGTACACAATTATGTCCCCT 59.866 47.826 7.53 7.53 37.82 4.79
2877 3756 6.627395 AACAATGTTCGAAAACCACATAGA 57.373 33.333 0.00 0.00 34.28 1.98
2878 3757 6.817765 ACAATGTTCGAAAACCACATAGAT 57.182 33.333 0.00 0.00 34.28 1.98
2903 5260 3.862877 TCACAAGCCATATGGTAGCAT 57.137 42.857 22.79 12.78 37.57 3.79
2907 5264 1.813513 AGCCATATGGTAGCATTCGC 58.186 50.000 22.79 11.82 37.57 4.70
2929 5286 3.980775 CCAAAAATAACAGCCACAACTCG 59.019 43.478 0.00 0.00 0.00 4.18
2955 5312 1.361204 TCAACCTCCAGCCTTGATGA 58.639 50.000 0.00 0.00 0.00 2.92
2975 5332 5.319140 TGATTTCGTCGACCTCAAGATTA 57.681 39.130 10.58 0.00 0.00 1.75
2976 5333 5.902681 TGATTTCGTCGACCTCAAGATTAT 58.097 37.500 10.58 0.00 0.00 1.28
2977 5334 5.977725 TGATTTCGTCGACCTCAAGATTATC 59.022 40.000 10.58 7.72 0.00 1.75
3009 5366 4.864916 ATAATTAGTCAGTTGCACGCAG 57.135 40.909 0.00 0.00 0.00 5.18
3035 5392 2.376109 TCTACTAGGTTGAGGCCGAAG 58.624 52.381 0.00 0.00 0.00 3.79
3060 5417 0.526524 CGCTAGAGCTTTCTCGGTGG 60.527 60.000 0.00 0.00 44.02 4.61
3108 5465 7.065324 TCGTTTTCATGGATAAGTGTAACCATC 59.935 37.037 0.00 0.00 40.07 3.51
3111 5468 6.806668 TCATGGATAAGTGTAACCATCAGA 57.193 37.500 0.00 0.00 40.07 3.27
3117 5480 7.126573 TGGATAAGTGTAACCATCAGAATACCA 59.873 37.037 0.00 0.00 37.80 3.25
3136 5499 8.868522 AATACCAATATCCATATCCACACTTG 57.131 34.615 0.00 0.00 0.00 3.16
3149 5513 5.452078 TCCACACTTGCTTTAAAATCCAG 57.548 39.130 0.00 0.00 0.00 3.86
3252 5616 8.844244 AGTTGATTGCCATATAGACATTTTCTC 58.156 33.333 0.00 0.00 35.55 2.87
3253 5617 8.623903 GTTGATTGCCATATAGACATTTTCTCA 58.376 33.333 0.00 0.00 35.55 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.749076 TCATCTTCATTGGCTTGGTTCG 59.251 45.455 0.00 0.00 0.00 3.95
18 19 3.428589 GCTCATCTTCATTGGCTTGGTTC 60.429 47.826 0.00 0.00 0.00 3.62
21 22 2.097036 TGCTCATCTTCATTGGCTTGG 58.903 47.619 0.00 0.00 0.00 3.61
37 38 6.071463 CGTTGTCTACTTAATGTTTGTGCTC 58.929 40.000 0.00 0.00 0.00 4.26
43 44 6.833342 ACGAACGTTGTCTACTTAATGTTT 57.167 33.333 5.00 0.00 36.46 2.83
61 62 6.138236 CGACGACATGTAGATTAGTAACGAAC 59.862 42.308 13.30 1.75 0.00 3.95
74 75 2.945315 GGCTCACGACGACATGTAG 58.055 57.895 0.00 0.00 0.00 2.74
76 77 2.622962 TCGGCTCACGACGACATGT 61.623 57.895 0.00 0.00 45.00 3.21
205 208 7.669641 CGATAGATTTCCGATAAATCGCTTGTC 60.670 40.741 6.84 3.20 44.14 3.18
303 306 9.101655 ACAAAATAGGACAACGGTACATATTAC 57.898 33.333 0.00 0.00 0.00 1.89
314 317 6.695278 ACAATGACAAACAAAATAGGACAACG 59.305 34.615 0.00 0.00 0.00 4.10
349 352 4.522789 TGTTACCTTGATTCCTTGCCTTTC 59.477 41.667 0.00 0.00 0.00 2.62
427 430 3.432933 CGGCAATTTTTCACAAATCCCAG 59.567 43.478 0.00 0.00 0.00 4.45
430 433 5.861222 AATCGGCAATTTTTCACAAATCC 57.139 34.783 0.00 0.00 0.00 3.01
438 441 6.745907 GGTTGACTACTAATCGGCAATTTTTC 59.254 38.462 0.00 0.00 0.00 2.29
445 448 2.093890 TCGGTTGACTACTAATCGGCA 58.906 47.619 0.00 0.00 32.78 5.69
473 476 0.248949 GTCTCGGTCGGCTGGTAATC 60.249 60.000 0.00 0.00 0.00 1.75
599 636 4.695993 TGATGCCCTGCGCGTTGA 62.696 61.111 8.43 0.00 42.08 3.18
608 645 6.839657 ACACTATAGTAACTAGTTGATGCCCT 59.160 38.462 18.56 6.67 0.00 5.19
649 690 3.951775 AGTCAGTCACTCAGGATTCAC 57.048 47.619 0.00 0.00 0.00 3.18
718 762 7.227910 GTCATTTAGTCATAAGGGCGGAAATTA 59.772 37.037 0.00 0.00 0.00 1.40
721 765 4.879545 GTCATTTAGTCATAAGGGCGGAAA 59.120 41.667 0.00 0.00 0.00 3.13
722 766 4.163458 AGTCATTTAGTCATAAGGGCGGAA 59.837 41.667 0.00 0.00 0.00 4.30
723 767 3.709653 AGTCATTTAGTCATAAGGGCGGA 59.290 43.478 0.00 0.00 0.00 5.54
726 1476 8.910351 AAGAATAGTCATTTAGTCATAAGGGC 57.090 34.615 0.00 0.00 0.00 5.19
765 1515 4.589374 ACCCTCTTCTATACCCGAATTCTG 59.411 45.833 3.52 0.00 0.00 3.02
822 1581 8.086522 TGAAATAAGTAGTAGAACGAAACAGCT 58.913 33.333 0.00 0.00 0.00 4.24
981 1742 3.446516 GGGTGTATAGAACAGACTCGGTT 59.553 47.826 0.00 0.00 39.29 4.44
989 1750 6.127338 TGACTCATCAAGGGTGTATAGAACAG 60.127 42.308 0.00 0.00 39.29 3.16
1073 1843 5.102953 TCTCAAACATGGGGAGAACATAG 57.897 43.478 9.84 0.00 34.91 2.23
1166 1937 6.370166 CGCTCTCAAACTAAAATCTCTTTCCT 59.630 38.462 0.00 0.00 0.00 3.36
1179 1950 1.919240 TGTCTCCCGCTCTCAAACTA 58.081 50.000 0.00 0.00 0.00 2.24
1189 1960 1.521681 CTTTCCCGATGTCTCCCGC 60.522 63.158 0.00 0.00 0.00 6.13
1206 1977 2.736670 AGCTGAAACCAAGTGTTCCT 57.263 45.000 0.00 0.00 35.67 3.36
1228 1999 2.132762 CACCACAACGTTCACTAGTCC 58.867 52.381 0.00 0.00 0.00 3.85
1230 2001 1.202604 CCCACCACAACGTTCACTAGT 60.203 52.381 0.00 0.00 0.00 2.57
1231 2002 1.202604 ACCCACCACAACGTTCACTAG 60.203 52.381 0.00 0.00 0.00 2.57
1234 2009 1.720694 CCACCCACCACAACGTTCAC 61.721 60.000 0.00 0.00 0.00 3.18
1256 2031 1.589803 GTCAAGTTGGCACGTAAGGT 58.410 50.000 1.68 0.00 46.39 3.50
1275 2050 2.027625 GAGGGACAAAGTCGTGGCG 61.028 63.158 0.00 0.00 32.65 5.69
1402 2177 2.504175 GGGTTTCCCTACTAGTGCATCA 59.496 50.000 5.39 0.00 41.34 3.07
1441 2216 0.105039 ACGCTGCTAGAGGGCATAAC 59.895 55.000 0.00 0.00 41.63 1.89
1458 2233 4.821412 CGGCGCGCGAGTTAAACG 62.821 66.667 37.18 19.93 0.00 3.60
1551 2326 6.299436 CTAGCAGCATCTAGAGTGGGAACC 62.299 54.167 0.00 0.00 43.35 3.62
1566 2341 2.251818 AGTCAGAGGAAACTAGCAGCA 58.748 47.619 0.00 0.00 44.43 4.41
1596 2371 1.012841 GCAGCATCTTACAGACCTGC 58.987 55.000 10.68 10.68 42.02 4.85
1597 2372 2.093816 TCTGCAGCATCTTACAGACCTG 60.094 50.000 9.47 0.00 34.35 4.00
1613 2388 0.969149 AGTGATTCTCCACGTCTGCA 59.031 50.000 0.00 0.00 41.67 4.41
1714 2489 7.655328 TCAATTACGCATTTGATCTTTGGTTTT 59.345 29.630 0.00 0.00 0.00 2.43
1848 2658 3.753797 GGGAGGGATGAAGCGAATAAATC 59.246 47.826 0.00 0.00 0.00 2.17
1849 2659 3.138283 TGGGAGGGATGAAGCGAATAAAT 59.862 43.478 0.00 0.00 0.00 1.40
1850 2660 2.507886 TGGGAGGGATGAAGCGAATAAA 59.492 45.455 0.00 0.00 0.00 1.40
1851 2661 2.123589 TGGGAGGGATGAAGCGAATAA 58.876 47.619 0.00 0.00 0.00 1.40
1852 2662 1.416401 GTGGGAGGGATGAAGCGAATA 59.584 52.381 0.00 0.00 0.00 1.75
1853 2663 0.181350 GTGGGAGGGATGAAGCGAAT 59.819 55.000 0.00 0.00 0.00 3.34
1854 2664 0.909610 AGTGGGAGGGATGAAGCGAA 60.910 55.000 0.00 0.00 0.00 4.70
1855 2665 1.306141 AGTGGGAGGGATGAAGCGA 60.306 57.895 0.00 0.00 0.00 4.93
1856 2666 1.153289 CAGTGGGAGGGATGAAGCG 60.153 63.158 0.00 0.00 0.00 4.68
1857 2667 1.225704 CCAGTGGGAGGGATGAAGC 59.774 63.158 0.00 0.00 35.59 3.86
1858 2668 0.254178 CACCAGTGGGAGGGATGAAG 59.746 60.000 15.21 0.00 38.05 3.02
1859 2669 0.178876 TCACCAGTGGGAGGGATGAA 60.179 55.000 15.21 0.00 38.05 2.57
1860 2670 0.909610 GTCACCAGTGGGAGGGATGA 60.910 60.000 15.21 3.79 38.05 2.92
1861 2671 1.200760 TGTCACCAGTGGGAGGGATG 61.201 60.000 15.21 1.04 38.05 3.51
1862 2672 0.475632 TTGTCACCAGTGGGAGGGAT 60.476 55.000 15.21 0.00 38.05 3.85
1863 2673 0.475632 ATTGTCACCAGTGGGAGGGA 60.476 55.000 15.21 2.47 38.05 4.20
1864 2674 1.285280 TATTGTCACCAGTGGGAGGG 58.715 55.000 15.21 0.00 38.05 4.30
1865 2675 2.774234 AGATATTGTCACCAGTGGGAGG 59.226 50.000 15.21 2.55 38.05 4.30
1866 2676 4.494091 AAGATATTGTCACCAGTGGGAG 57.506 45.455 15.21 5.78 38.05 4.30
1867 2677 4.288366 TCAAAGATATTGTCACCAGTGGGA 59.712 41.667 15.21 5.13 38.05 4.37
1868 2678 4.396166 GTCAAAGATATTGTCACCAGTGGG 59.604 45.833 15.21 2.47 41.29 4.61
1869 2679 5.003160 TGTCAAAGATATTGTCACCAGTGG 58.997 41.667 7.91 7.91 0.00 4.00
1870 2680 6.558771 TTGTCAAAGATATTGTCACCAGTG 57.441 37.500 0.00 0.00 0.00 3.66
1871 2681 8.103305 AGTATTGTCAAAGATATTGTCACCAGT 58.897 33.333 0.00 0.00 0.00 4.00
1872 2682 8.498054 AGTATTGTCAAAGATATTGTCACCAG 57.502 34.615 0.00 0.00 0.00 4.00
1873 2683 8.100164 TGAGTATTGTCAAAGATATTGTCACCA 58.900 33.333 0.00 0.00 0.00 4.17
1874 2684 8.492673 TGAGTATTGTCAAAGATATTGTCACC 57.507 34.615 0.00 0.00 0.00 4.02
1879 2689 9.282247 GCAGTTTGAGTATTGTCAAAGATATTG 57.718 33.333 0.00 0.00 45.00 1.90
1909 2720 0.954452 CTGCCTCAAGGACAACAACC 59.046 55.000 0.00 0.00 37.39 3.77
1910 2721 1.604278 GTCTGCCTCAAGGACAACAAC 59.396 52.381 0.00 0.00 37.39 3.32
1965 2776 2.040544 GCATGTCCACCCAACTCGG 61.041 63.158 0.00 0.00 0.00 4.63
1966 2777 1.003355 AGCATGTCCACCCAACTCG 60.003 57.895 0.00 0.00 0.00 4.18
2001 2818 1.376466 GGCAGAGACTTGGAGCCAA 59.624 57.895 1.47 1.47 44.59 4.52
2212 3031 2.575735 TGATCACATAGGTTTGGCAGGA 59.424 45.455 0.00 0.00 0.00 3.86
2219 3038 6.613271 ACCTGATAGAGTGATCACATAGGTTT 59.387 38.462 27.02 4.86 30.42 3.27
2234 3053 6.952773 AGTAGAGTAAGCAACCTGATAGAG 57.047 41.667 0.00 0.00 0.00 2.43
2244 3063 9.938280 TCATAAAAGCTTTAGTAGAGTAAGCAA 57.062 29.630 13.10 0.00 45.08 3.91
2258 3077 5.198602 ACCCCTCTGATCATAAAAGCTTT 57.801 39.130 5.69 5.69 0.00 3.51
2356 3180 7.252897 CGCACGATAACATATCACTACGATAAC 60.253 40.741 0.00 0.00 40.04 1.89
2439 3275 5.913514 CAGACGGTACATAACATAGCACTAC 59.086 44.000 0.00 0.00 0.00 2.73
2495 3336 4.868172 TCATCCCATGGAAATGAAGTCT 57.132 40.909 21.01 0.00 34.34 3.24
2496 3337 6.475596 AATTCATCCCATGGAAATGAAGTC 57.524 37.500 30.01 0.00 35.19 3.01
2497 3338 5.068198 CGAATTCATCCCATGGAAATGAAGT 59.932 40.000 30.01 29.02 35.19 3.01
2516 3379 4.012374 AGATGAAGTTGCACATCCGAATT 58.988 39.130 10.50 0.00 42.38 2.17
2566 3429 5.067283 GCCTTCAGAGGTGAAAAGTTTGTTA 59.933 40.000 0.00 0.00 45.44 2.41
2644 3509 3.054139 AGCCCATAAAGCTGATCAGAACA 60.054 43.478 27.04 7.97 39.69 3.18
2651 3516 3.560636 AACGTAGCCCATAAAGCTGAT 57.439 42.857 0.00 0.00 41.71 2.90
2655 3520 3.189618 AGGTAACGTAGCCCATAAAGC 57.810 47.619 4.88 0.00 46.39 3.51
2709 3588 8.877864 AATCATAGTTTGTGGTCAATAAAGGA 57.122 30.769 0.00 0.00 33.32 3.36
2723 3602 8.804743 ACTCATAAACGACGTAATCATAGTTTG 58.195 33.333 0.00 0.00 34.29 2.93
2732 3611 6.855836 TCCTTGTACTCATAAACGACGTAAT 58.144 36.000 0.00 0.00 0.00 1.89
2737 3616 6.978659 TGATCATCCTTGTACTCATAAACGAC 59.021 38.462 0.00 0.00 0.00 4.34
2771 3650 5.036117 TGTAATAGCTGGATGGAAGAACC 57.964 43.478 0.00 0.00 39.54 3.62
2817 3696 2.288458 GTGTACCTCGTGAGCTAGCTAG 59.712 54.545 19.38 16.84 0.00 3.42
2833 3712 8.967664 TTGTTATAGGGGACATAATTGTGTAC 57.032 34.615 8.98 8.98 35.79 2.90
2843 3722 5.623956 TCGAACATTGTTATAGGGGACAT 57.376 39.130 1.15 0.00 0.00 3.06
2847 3726 5.416326 TGGTTTTCGAACATTGTTATAGGGG 59.584 40.000 1.15 0.00 0.00 4.79
2851 3730 9.438228 TCTATGTGGTTTTCGAACATTGTTATA 57.562 29.630 1.15 0.00 36.08 0.98
2877 3756 6.777091 TGCTACCATATGGCTTGTGAATTTAT 59.223 34.615 22.18 0.00 39.32 1.40
2878 3757 6.125719 TGCTACCATATGGCTTGTGAATTTA 58.874 36.000 22.18 1.66 39.32 1.40
2903 5260 2.362397 TGTGGCTGTTATTTTTGGCGAA 59.638 40.909 0.00 0.00 0.00 4.70
2907 5264 3.980775 CGAGTTGTGGCTGTTATTTTTGG 59.019 43.478 0.00 0.00 0.00 3.28
2955 5312 5.902681 TGATAATCTTGAGGTCGACGAAAT 58.097 37.500 9.92 0.00 0.00 2.17
3006 5363 3.926616 TCAACCTAGTAGAAACTGCTGC 58.073 45.455 0.00 0.00 36.36 5.25
3009 5366 3.263261 GCCTCAACCTAGTAGAAACTGC 58.737 50.000 0.00 0.00 36.36 4.40
3018 5375 1.187087 CTCTTCGGCCTCAACCTAGT 58.813 55.000 0.00 0.00 0.00 2.57
3060 5417 3.872409 ATGTTTGCACGAACGCGCC 62.872 57.895 5.73 0.00 42.48 6.53
3071 5428 4.922692 TCCATGAAAACGATTGATGTTTGC 59.077 37.500 0.00 0.00 39.36 3.68
3108 5465 8.324306 AGTGTGGATATGGATATTGGTATTCTG 58.676 37.037 0.00 0.00 0.00 3.02
3111 5468 7.394359 GCAAGTGTGGATATGGATATTGGTATT 59.606 37.037 0.00 0.00 0.00 1.89
3117 5480 8.995027 TTAAAGCAAGTGTGGATATGGATATT 57.005 30.769 0.00 0.00 0.00 1.28
3216 5580 7.849804 ATATGGCAATCAACTATTCGTATCC 57.150 36.000 0.00 0.00 0.00 2.59
3227 5591 8.623903 TGAGAAAATGTCTATATGGCAATCAAC 58.376 33.333 0.00 0.00 36.41 3.18


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

AutoCloner maintained by Alex Coulton.