Multiple sequence alignment - TraesCS2B01G523300

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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 TraesCS2B01G523300 chr2B 100.000 2896 0 0 1 2896 717894980 717897875 0.000000e+00 5349.0
1 TraesCS2B01G523300 chr2B 82.407 432 45 15 1000 1414 717678584 717679001 5.940000e-92 348.0
2 TraesCS2B01G523300 chr2B 81.780 236 32 9 1179 1414 717237413 717237637 1.370000e-43 187.0
3 TraesCS2B01G523300 chr2B 81.498 227 20 11 1200 1424 717098221 717098427 1.780000e-37 167.0
4 TraesCS2B01G523300 chr2D 90.714 2423 120 39 11 2376 592273062 592275436 0.000000e+00 3131.0
5 TraesCS2B01G523300 chr2D 86.070 402 31 14 1016 1414 592080397 592080776 2.690000e-110 409.0
6 TraesCS2B01G523300 chr2D 86.070 402 31 14 1016 1414 592115452 592115831 2.690000e-110 409.0
7 TraesCS2B01G523300 chr2D 80.306 589 67 28 854 1414 592030972 592031539 1.620000e-107 399.0
8 TraesCS2B01G523300 chr2D 85.075 402 35 14 1016 1414 592092217 592092596 1.260000e-103 387.0
9 TraesCS2B01G523300 chr2D 92.486 173 11 2 2460 2632 592275552 592275722 2.230000e-61 246.0
10 TraesCS2B01G523300 chr2D 82.105 190 14 4 2724 2896 592275874 592276060 8.360000e-31 145.0
11 TraesCS2B01G523300 chr2A 92.626 1207 40 20 771 1959 726755778 726756953 0.000000e+00 1690.0
12 TraesCS2B01G523300 chr2A 88.280 785 79 9 4 776 726754918 726755701 0.000000e+00 928.0
13 TraesCS2B01G523300 chr2A 84.841 409 32 9 1995 2376 726756950 726757355 4.530000e-103 385.0
14 TraesCS2B01G523300 chr2A 84.826 402 36 13 1016 1414 726592736 726593115 5.860000e-102 381.0
15 TraesCS2B01G523300 chr2A 82.201 427 39 19 1000 1414 726560762 726561163 1.660000e-87 333.0
16 TraesCS2B01G523300 chr2A 90.116 172 10 3 2466 2632 726757443 726757612 1.750000e-52 217.0
17 TraesCS2B01G523300 chr2A 95.000 60 3 0 2834 2893 726757907 726757966 8.540000e-16 95.3


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 TraesCS2B01G523300 chr2B 717894980 717897875 2895 False 5349.00 5349 100.0000 1 2896 1 chr2B.!!$F4 2895
1 TraesCS2B01G523300 chr2D 592273062 592276060 2998 False 1174.00 3131 88.4350 11 2896 3 chr2D.!!$F5 2885
2 TraesCS2B01G523300 chr2D 592030972 592031539 567 False 399.00 399 80.3060 854 1414 1 chr2D.!!$F1 560
3 TraesCS2B01G523300 chr2A 726754918 726757966 3048 False 663.06 1690 90.1726 4 2893 5 chr2A.!!$F3 2889

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
218 220 0.038166 TCCAGGGCATTTGTCCAGTC 59.962 55.0 3.69 0.0 43.78 3.51 F
935 1042 0.192064 TCCATCATCTCCCTCCCTCC 59.808 60.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1797 0.030705 CAATGGAGGGAGGGAGAGGA 60.031 60.0 0.0 0.0 0.00 3.71 R
2699 2988 0.108520 CCATGATTGCTTGGTGGTGC 60.109 55.0 0.0 0.0 35.26 5.01 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
19 20 1.974265 TGTCCTCCGTCATTTTTGCA 58.026 45.000 0.00 0.00 0.00 4.08
21 22 0.881118 TCCTCCGTCATTTTTGCAGC 59.119 50.000 0.00 0.00 0.00 5.25
31 32 1.010580 TTTTTGCAGCAACGACGAGA 58.989 45.000 7.54 0.00 0.00 4.04
45 47 1.205893 GACGAGATTTCTGCCTCACCT 59.794 52.381 0.00 0.00 0.00 4.00
49 51 3.034635 GAGATTTCTGCCTCACCTCCTA 58.965 50.000 0.00 0.00 0.00 2.94
95 97 9.608617 CATATCATTGTCTATTTGTTCATGCTC 57.391 33.333 0.00 0.00 0.00 4.26
102 104 1.909700 TTTGTTCATGCTCCCTGTCC 58.090 50.000 0.00 0.00 0.00 4.02
104 106 2.109126 GTTCATGCTCCCTGTCCGC 61.109 63.158 0.00 0.00 0.00 5.54
146 148 5.009010 GCAGAAGTTTTGTTCAAGAGATGGA 59.991 40.000 0.00 0.00 0.00 3.41
164 166 2.110899 TGGATTAGCTTTGGGGTTTCCA 59.889 45.455 0.00 0.00 45.43 3.53
190 192 7.684937 TCTATAGAAGGCTTCTACGGTTATC 57.315 40.000 33.07 3.28 44.43 1.75
207 209 2.978156 ATCACTTCTTTTCCAGGGCA 57.022 45.000 0.00 0.00 0.00 5.36
210 212 3.575805 TCACTTCTTTTCCAGGGCATTT 58.424 40.909 0.00 0.00 0.00 2.32
217 219 0.482446 TTCCAGGGCATTTGTCCAGT 59.518 50.000 3.69 0.00 43.78 4.00
218 220 0.038166 TCCAGGGCATTTGTCCAGTC 59.962 55.000 3.69 0.00 43.78 3.51
260 264 4.242475 TCGACCACAAGATACAATGTCAC 58.758 43.478 0.00 0.00 0.00 3.67
263 267 3.244422 ACCACAAGATACAATGTCACGGT 60.244 43.478 0.00 0.00 0.00 4.83
267 271 1.277842 AGATACAATGTCACGGTGGCA 59.722 47.619 18.75 18.75 35.91 4.92
297 301 2.413765 CTTCCGCTAGCTCGTCCC 59.586 66.667 13.93 0.00 0.00 4.46
306 310 2.748532 GCTAGCTCGTCCCGTAGATTAT 59.251 50.000 7.70 0.00 0.00 1.28
307 311 3.190953 GCTAGCTCGTCCCGTAGATTATT 59.809 47.826 7.70 0.00 0.00 1.40
308 312 4.394300 GCTAGCTCGTCCCGTAGATTATTA 59.606 45.833 7.70 0.00 0.00 0.98
431 437 6.662865 TCAACTCTCTATTGATGAGGGATC 57.337 41.667 0.00 0.00 35.69 3.36
439 445 2.609427 TGATGAGGGATCGCAAAGAG 57.391 50.000 12.83 0.00 33.17 2.85
485 491 9.748708 CAAGGAAACATTGAACTTGATAAAGAA 57.251 29.630 0.00 0.00 40.60 2.52
634 640 5.252547 TGCATTTGGAGCACTAAATACAGA 58.747 37.500 5.23 0.00 35.56 3.41
636 642 6.208402 TGCATTTGGAGCACTAAATACAGAAA 59.792 34.615 5.23 0.00 35.56 2.52
657 663 8.928733 CAGAAATATATTTGTGGGCAATATTGC 58.071 33.333 28.68 28.68 40.95 3.56
701 712 4.744136 AGAAAGCGTACAACTTTTAGGC 57.256 40.909 11.10 1.23 37.47 3.93
740 752 7.759886 TGAACCTATCTAAGAAAATGTCGTGAG 59.240 37.037 0.00 0.00 0.00 3.51
766 779 5.582269 ACAATGATCACTAACGACCTTCATG 59.418 40.000 0.00 0.00 0.00 3.07
935 1042 0.192064 TCCATCATCTCCCTCCCTCC 59.808 60.000 0.00 0.00 0.00 4.30
936 1043 0.839853 CCATCATCTCCCTCCCTCCC 60.840 65.000 0.00 0.00 0.00 4.30
937 1044 0.193069 CATCATCTCCCTCCCTCCCT 59.807 60.000 0.00 0.00 0.00 4.20
938 1045 0.491371 ATCATCTCCCTCCCTCCCTC 59.509 60.000 0.00 0.00 0.00 4.30
939 1046 0.931250 TCATCTCCCTCCCTCCCTCA 60.931 60.000 0.00 0.00 0.00 3.86
941 1048 0.933791 ATCTCCCTCCCTCCCTCACT 60.934 60.000 0.00 0.00 0.00 3.41
945 1052 1.390125 CCTCCCTCCCTCACTCACT 59.610 63.158 0.00 0.00 0.00 3.41
947 1054 0.686112 CTCCCTCCCTCACTCACTCC 60.686 65.000 0.00 0.00 0.00 3.85
1056 1195 0.820891 AACAACAGCAGACCAGCAGG 60.821 55.000 0.00 0.00 42.21 4.85
1058 1197 3.124051 AACAGCAGACCAGCAGGCA 62.124 57.895 0.00 0.00 39.06 4.75
1059 1198 2.746671 CAGCAGACCAGCAGGCAG 60.747 66.667 0.00 0.00 39.06 4.85
1060 1199 4.719106 AGCAGACCAGCAGGCAGC 62.719 66.667 0.00 0.00 46.19 5.25
1126 1270 1.737735 CGCAACATCGTCTGGCTCA 60.738 57.895 0.00 0.00 0.00 4.26
1137 1281 3.630013 TGGCTCAGGCAGACGCTT 61.630 61.111 0.00 0.00 40.87 4.68
1300 1447 2.283894 TCTTCCGGGAGCTGCTCA 60.284 61.111 28.95 7.64 31.08 4.26
1446 1593 1.218316 GCGGTTCTTCACCCTCGAT 59.782 57.895 0.00 0.00 43.83 3.59
1521 1668 4.637489 CTCCTCCGCGGCATCTCG 62.637 72.222 23.51 3.31 0.00 4.04
1548 1695 1.410004 AGTTCGTCTGGTGACTCCAA 58.590 50.000 0.00 0.00 46.59 3.53
1562 1709 1.382557 TCCAATCCGAGCTAGGCCA 60.383 57.895 8.21 0.00 0.00 5.36
1736 1898 0.174389 GCGAAGTGAGATGGCTGAGA 59.826 55.000 0.00 0.00 0.00 3.27
1887 2054 8.561738 TTCTTCACTTACTGAATAATTCACCC 57.438 34.615 0.00 0.00 38.26 4.61
1975 2148 9.175312 CATTTCTACTACTACCTAGTTCTGTGA 57.825 37.037 0.00 0.00 36.95 3.58
1979 2152 9.040259 TCTACTACTACCTAGTTCTGTGAACTA 57.960 37.037 16.26 16.26 36.95 2.24
1982 2155 7.823799 ACTACTACCTAGTTCTGTGAACTACTC 59.176 40.741 14.02 0.00 37.73 2.59
1983 2156 5.945191 ACTACCTAGTTCTGTGAACTACTCC 59.055 44.000 14.02 0.00 31.13 3.85
1984 2157 5.000570 ACCTAGTTCTGTGAACTACTCCT 57.999 43.478 14.02 0.00 0.00 3.69
1993 2166 6.408035 TCTGTGAACTACTCCTAGTCAGTAG 58.592 44.000 18.38 18.38 46.15 2.57
2026 2199 6.471841 CGTTGTGTGATGTTGAGATTTCAAAA 59.528 34.615 0.00 0.00 44.49 2.44
2029 2202 8.945481 TGTGTGATGTTGAGATTTCAAAATTT 57.055 26.923 3.30 0.00 44.49 1.82
2061 2234 2.576317 GAGAGTCGTACGCACCGC 60.576 66.667 11.24 2.78 0.00 5.68
2163 2339 4.380974 GCTTGAAGAAGATTTGAACTTGCG 59.619 41.667 0.00 0.00 0.00 4.85
2166 2342 4.574421 TGAAGAAGATTTGAACTTGCGTGA 59.426 37.500 0.00 0.00 0.00 4.35
2173 2349 8.452989 AAGATTTGAACTTGCGTGATTTAATC 57.547 30.769 0.00 0.00 0.00 1.75
2175 2351 7.752239 AGATTTGAACTTGCGTGATTTAATCAG 59.248 33.333 8.00 4.29 40.53 2.90
2225 2416 4.317671 ACGGGTAGTAGAATATGTGTGC 57.682 45.455 0.00 0.00 0.00 4.57
2247 2438 2.202810 GCTGTCGCTAGGCTGGTC 60.203 66.667 0.00 0.00 0.00 4.02
2259 2450 0.590195 GGCTGGTCGCAATGATCATC 59.410 55.000 9.06 0.00 37.02 2.92
2266 2460 3.002656 GGTCGCAATGATCATCGAACAAT 59.997 43.478 22.93 0.00 38.41 2.71
2272 2466 5.851703 GCAATGATCATCGAACAATCATCTG 59.148 40.000 9.06 15.97 38.78 2.90
2294 2488 0.754217 ACCCGCTACCAGCTCGAATA 60.754 55.000 0.00 0.00 39.60 1.75
2298 2492 3.131396 CCGCTACCAGCTCGAATAATTT 58.869 45.455 0.00 0.00 39.60 1.82
2301 2495 4.318831 CGCTACCAGCTCGAATAATTTTCC 60.319 45.833 0.00 0.00 39.60 3.13
2307 2501 7.875971 ACCAGCTCGAATAATTTTCCATTATC 58.124 34.615 0.00 0.00 0.00 1.75
2363 2563 5.844004 ACATAAGTAGTAGCATTTCCCGAG 58.156 41.667 0.00 0.00 0.00 4.63
2376 2576 2.126228 CCGAGTCGCAACCGCTAA 60.126 61.111 7.12 0.00 35.30 3.09
2377 2577 2.442188 CCGAGTCGCAACCGCTAAC 61.442 63.158 7.12 0.00 35.30 2.34
2378 2578 1.443872 CGAGTCGCAACCGCTAACT 60.444 57.895 0.00 0.00 35.30 2.24
2379 2579 0.179181 CGAGTCGCAACCGCTAACTA 60.179 55.000 0.00 0.00 33.45 2.24
2380 2580 1.730121 CGAGTCGCAACCGCTAACTAA 60.730 52.381 0.00 0.00 33.45 2.24
2381 2581 2.537401 GAGTCGCAACCGCTAACTAAT 58.463 47.619 0.00 0.00 33.45 1.73
2382 2582 3.699067 GAGTCGCAACCGCTAACTAATA 58.301 45.455 0.00 0.00 33.45 0.98
2383 2583 3.703420 AGTCGCAACCGCTAACTAATAG 58.297 45.455 0.00 0.00 32.05 1.73
2410 2610 3.884900 GCGGTGCGGTCAACTATT 58.115 55.556 0.00 0.00 0.00 1.73
2412 2612 0.519961 GCGGTGCGGTCAACTATTTT 59.480 50.000 0.00 0.00 0.00 1.82
2431 2639 2.094100 TTTGGTTTCATTCCTGCCCA 57.906 45.000 0.00 0.00 0.00 5.36
2438 2646 4.098501 GGTTTCATTCCTGCCCAAGATTAG 59.901 45.833 0.00 0.00 0.00 1.73
2439 2647 4.860802 TTCATTCCTGCCCAAGATTAGA 57.139 40.909 0.00 0.00 0.00 2.10
2440 2648 4.860802 TCATTCCTGCCCAAGATTAGAA 57.139 40.909 0.00 0.00 0.00 2.10
2441 2649 4.785301 TCATTCCTGCCCAAGATTAGAAG 58.215 43.478 0.00 0.00 0.00 2.85
2442 2650 4.228210 TCATTCCTGCCCAAGATTAGAAGT 59.772 41.667 0.00 0.00 0.00 3.01
2443 2651 3.634397 TCCTGCCCAAGATTAGAAGTG 57.366 47.619 0.00 0.00 0.00 3.16
2444 2652 3.181329 TCCTGCCCAAGATTAGAAGTGA 58.819 45.455 0.00 0.00 0.00 3.41
2446 2654 3.198635 CCTGCCCAAGATTAGAAGTGAGA 59.801 47.826 0.00 0.00 0.00 3.27
2447 2655 4.440880 CTGCCCAAGATTAGAAGTGAGAG 58.559 47.826 0.00 0.00 0.00 3.20
2448 2656 3.202097 GCCCAAGATTAGAAGTGAGAGC 58.798 50.000 0.00 0.00 0.00 4.09
2449 2657 3.118445 GCCCAAGATTAGAAGTGAGAGCT 60.118 47.826 0.00 0.00 0.00 4.09
2450 2658 4.100189 GCCCAAGATTAGAAGTGAGAGCTA 59.900 45.833 0.00 0.00 0.00 3.32
2451 2659 5.596845 CCCAAGATTAGAAGTGAGAGCTAC 58.403 45.833 0.00 0.00 0.00 3.58
2452 2660 5.362430 CCCAAGATTAGAAGTGAGAGCTACT 59.638 44.000 0.00 0.00 0.00 2.57
2454 2662 7.232534 CCCAAGATTAGAAGTGAGAGCTACTAT 59.767 40.741 0.00 0.00 0.00 2.12
2455 2663 8.296713 CCAAGATTAGAAGTGAGAGCTACTATC 58.703 40.741 0.00 0.00 0.00 2.08
2456 2664 7.996098 AGATTAGAAGTGAGAGCTACTATCC 57.004 40.000 0.00 0.00 0.00 2.59
2458 2666 4.528076 AGAAGTGAGAGCTACTATCCCA 57.472 45.455 0.00 0.00 0.00 4.37
2489 2739 2.443958 TCTGGAGAGATCACCGTCAT 57.556 50.000 0.00 0.00 0.00 3.06
2496 2746 0.749649 AGATCACCGTCATGCTCTCC 59.250 55.000 0.00 0.00 0.00 3.71
2506 2756 2.485814 GTCATGCTCTCCCAAAAGTGTC 59.514 50.000 0.00 0.00 0.00 3.67
2552 2807 1.067060 TGTATGGAATCCTGACGAGCG 59.933 52.381 0.00 0.00 0.00 5.03
2568 2823 1.735559 GCGTAACGTCGGCCTTTCT 60.736 57.895 0.00 0.00 0.00 2.52
2604 2859 3.058160 CGCAGCCACTTTCTGGGG 61.058 66.667 0.00 0.00 43.81 4.96
2605 2860 2.116125 GCAGCCACTTTCTGGGGT 59.884 61.111 0.00 0.00 42.62 4.95
2606 2861 4.085876 CAGCCACTTTCTGGGGTG 57.914 61.111 0.00 0.00 45.11 4.61
2663 2944 3.474570 CTTCTCCCTCCCTGGCCG 61.475 72.222 0.00 0.00 0.00 6.13
2674 2963 1.228063 CCTGGCCGGAGATTGGATG 60.228 63.158 15.09 0.00 33.16 3.51
2678 2967 1.410850 GGCCGGAGATTGGATGAGGA 61.411 60.000 5.05 0.00 0.00 3.71
2680 2969 1.902508 GCCGGAGATTGGATGAGGATA 59.097 52.381 5.05 0.00 0.00 2.59
2681 2970 2.093764 GCCGGAGATTGGATGAGGATAG 60.094 54.545 5.05 0.00 0.00 2.08
2682 2971 2.093764 CCGGAGATTGGATGAGGATAGC 60.094 54.545 0.00 0.00 0.00 2.97
2698 2987 0.692476 TAGCAGCAGCCTGGAAAGAA 59.308 50.000 0.00 0.00 43.56 2.52
2699 2988 0.608582 AGCAGCAGCCTGGAAAGAAG 60.609 55.000 0.00 0.00 43.56 2.85
2702 2991 0.892814 AGCAGCCTGGAAAGAAGCAC 60.893 55.000 0.00 0.00 0.00 4.40
2713 3002 1.708341 AAGAAGCACCACCAAGCAAT 58.292 45.000 0.00 0.00 0.00 3.56
2714 3003 1.251251 AGAAGCACCACCAAGCAATC 58.749 50.000 0.00 0.00 0.00 2.67
2715 3004 0.961019 GAAGCACCACCAAGCAATCA 59.039 50.000 0.00 0.00 0.00 2.57
2716 3005 1.547372 GAAGCACCACCAAGCAATCAT 59.453 47.619 0.00 0.00 0.00 2.45
2717 3006 0.892755 AGCACCACCAAGCAATCATG 59.107 50.000 0.00 0.00 0.00 3.07
2718 3007 0.108520 GCACCACCAAGCAATCATGG 60.109 55.000 0.00 0.00 42.60 3.66
2719 3008 0.533491 CACCACCAAGCAATCATGGG 59.467 55.000 0.00 0.00 41.17 4.00
2720 3009 0.409092 ACCACCAAGCAATCATGGGA 59.591 50.000 0.00 0.00 41.17 4.37
2721 3010 1.108776 CCACCAAGCAATCATGGGAG 58.891 55.000 0.00 0.00 41.17 4.30
2722 3011 1.108776 CACCAAGCAATCATGGGAGG 58.891 55.000 0.00 0.00 41.17 4.30
2725 3044 0.685131 CAAGCAATCATGGGAGGGCA 60.685 55.000 0.00 0.00 0.00 5.36
2782 3101 5.464965 AACGTCGTAATAAAGCCTCAATG 57.535 39.130 0.00 0.00 0.00 2.82
2783 3102 4.501071 ACGTCGTAATAAAGCCTCAATGT 58.499 39.130 0.00 0.00 0.00 2.71
2784 3103 4.565564 ACGTCGTAATAAAGCCTCAATGTC 59.434 41.667 0.00 0.00 0.00 3.06
2789 3108 5.463724 CGTAATAAAGCCTCAATGTCCTCTC 59.536 44.000 0.00 0.00 0.00 3.20
2814 3158 0.780637 ACAGAGAGAGTCCCAGGTGA 59.219 55.000 0.00 0.00 0.00 4.02
2818 3162 1.079438 GAGAGTCCCAGGTGACCCT 59.921 63.158 0.00 0.00 44.02 4.34
2819 3163 0.973496 GAGAGTCCCAGGTGACCCTC 60.973 65.000 0.00 0.00 39.89 4.30
2820 3164 1.990614 GAGTCCCAGGTGACCCTCC 60.991 68.421 0.00 0.00 39.89 4.30
2821 3165 3.009714 GTCCCAGGTGACCCTCCC 61.010 72.222 0.00 0.00 39.89 4.30
2823 3167 2.531685 CCCAGGTGACCCTCCCAA 60.532 66.667 0.00 0.00 39.89 4.12
2824 3168 2.606587 CCCAGGTGACCCTCCCAAG 61.607 68.421 0.00 0.00 39.89 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.879380 CTGCAAAAATGACGGAGGACA 59.121 47.619 0.00 0.00 0.00 4.02
1 2 1.401539 GCTGCAAAAATGACGGAGGAC 60.402 52.381 0.00 0.00 0.00 3.85
2 3 0.881118 GCTGCAAAAATGACGGAGGA 59.119 50.000 0.00 0.00 0.00 3.71
8 9 1.447938 CGTCGTTGCTGCAAAAATGAC 59.552 47.619 17.80 18.99 38.42 3.06
9 10 1.332065 TCGTCGTTGCTGCAAAAATGA 59.668 42.857 17.80 14.99 0.00 2.57
19 20 1.071605 GCAGAAATCTCGTCGTTGCT 58.928 50.000 0.00 0.00 0.00 3.91
21 22 1.656095 GAGGCAGAAATCTCGTCGTTG 59.344 52.381 0.00 0.00 0.00 4.10
31 32 2.122768 CCTAGGAGGTGAGGCAGAAAT 58.877 52.381 1.05 0.00 0.00 2.17
95 97 3.814268 CATTTGCGGCGGACAGGG 61.814 66.667 9.78 0.00 0.00 4.45
102 104 0.634731 CAATTTCGTCATTTGCGGCG 59.365 50.000 0.51 0.51 0.00 6.46
104 106 0.991344 GCCAATTTCGTCATTTGCGG 59.009 50.000 0.00 0.00 0.00 5.69
164 166 6.980416 AACCGTAGAAGCCTTCTATAGATT 57.020 37.500 16.78 5.72 43.59 2.40
170 172 5.198965 AGTGATAACCGTAGAAGCCTTCTA 58.801 41.667 10.13 10.13 41.14 2.10
190 192 3.070015 ACAAATGCCCTGGAAAAGAAGTG 59.930 43.478 0.00 0.00 0.00 3.16
217 219 0.454600 GTCATCGTGCTAAGGTCCGA 59.545 55.000 0.00 0.00 0.00 4.55
218 220 0.456221 AGTCATCGTGCTAAGGTCCG 59.544 55.000 0.00 0.00 0.00 4.79
244 248 3.334691 CCACCGTGACATTGTATCTTGT 58.665 45.455 0.00 0.00 0.00 3.16
260 264 2.405892 GCAAGCTAATATTGCCACCG 57.594 50.000 0.00 0.00 45.79 4.94
297 301 9.716507 CCAGTGAACCAAAAATAATAATCTACG 57.283 33.333 0.00 0.00 0.00 3.51
345 351 8.503428 AGACTTCCAAGGATATATGACATTCT 57.497 34.615 0.00 0.00 0.00 2.40
360 366 9.760660 CTCGATTTTGTATTAAAGACTTCCAAG 57.239 33.333 0.00 0.00 0.00 3.61
396 402 8.795513 TCAATAGAGAGTTGATGAATTTTTGCA 58.204 29.630 0.00 0.00 31.07 4.08
439 445 1.127951 GTGTATGTGCACGCCAAGTAC 59.872 52.381 13.13 8.50 0.00 2.73
701 712 5.486526 AGATAGGTTCAGCAGACTTTGAAG 58.513 41.667 0.49 0.00 34.25 3.02
740 752 5.637810 TGAAGGTCGTTAGTGATCATTGTTC 59.362 40.000 0.00 0.00 0.00 3.18
852 955 1.911766 TGTGAAGGGGACGGGACTC 60.912 63.158 0.00 0.00 0.00 3.36
935 1042 0.686112 GAGGGAGGGAGTGAGTGAGG 60.686 65.000 0.00 0.00 0.00 3.86
936 1043 0.686112 GGAGGGAGGGAGTGAGTGAG 60.686 65.000 0.00 0.00 0.00 3.51
937 1044 1.388531 GGAGGGAGGGAGTGAGTGA 59.611 63.158 0.00 0.00 0.00 3.41
938 1045 1.687493 GGGAGGGAGGGAGTGAGTG 60.687 68.421 0.00 0.00 0.00 3.51
939 1046 1.864559 AGGGAGGGAGGGAGTGAGT 60.865 63.158 0.00 0.00 0.00 3.41
941 1048 2.637640 GGAGGGAGGGAGGGAGTGA 61.638 68.421 0.00 0.00 0.00 3.41
945 1052 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
947 1054 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1058 1197 2.281345 GGACTGTGCTGCTGTGCT 60.281 61.111 0.00 0.00 35.21 4.40
1059 1198 3.360340 GGGACTGTGCTGCTGTGC 61.360 66.667 0.00 2.78 36.82 4.57
1060 1199 1.670406 GAGGGACTGTGCTGCTGTG 60.670 63.158 0.00 0.00 41.55 3.66
1061 1200 1.699054 TTGAGGGACTGTGCTGCTGT 61.699 55.000 0.00 0.00 41.55 4.40
1063 1202 1.072159 GTTGAGGGACTGTGCTGCT 59.928 57.895 0.00 0.00 41.55 4.24
1064 1203 1.072159 AGTTGAGGGACTGTGCTGC 59.928 57.895 0.00 0.00 41.55 5.25
1065 1204 1.233285 GCAGTTGAGGGACTGTGCTG 61.233 60.000 6.85 0.00 46.81 4.41
1066 1205 1.072159 GCAGTTGAGGGACTGTGCT 59.928 57.895 6.85 0.00 46.81 4.40
1067 1206 1.968540 GGCAGTTGAGGGACTGTGC 60.969 63.158 6.85 0.00 46.81 4.57
1068 1207 1.669115 CGGCAGTTGAGGGACTGTG 60.669 63.158 6.85 0.00 46.81 3.66
1069 1208 1.194781 ATCGGCAGTTGAGGGACTGT 61.195 55.000 6.85 0.00 46.81 3.55
1446 1593 2.815211 GCGCCGCTCTTGATGTCA 60.815 61.111 0.00 0.00 0.00 3.58
1588 1741 1.902918 GCCACCACCAGCACAATGA 60.903 57.895 0.00 0.00 0.00 2.57
1620 1774 5.067413 AGGGAGAGGAAAACGAAAAAGAAAC 59.933 40.000 0.00 0.00 0.00 2.78
1630 1792 0.537653 GAGGGAGGGAGAGGAAAACG 59.462 60.000 0.00 0.00 0.00 3.60
1635 1797 0.030705 CAATGGAGGGAGGGAGAGGA 60.031 60.000 0.00 0.00 0.00 3.71
1874 2041 9.778741 CTAGCTATTTACAGGGTGAATTATTCA 57.221 33.333 3.20 3.20 37.33 2.57
1887 2054 2.135933 GCACGGGCTAGCTATTTACAG 58.864 52.381 15.72 0.00 36.96 2.74
1961 2132 6.137104 AGGAGTAGTTCACAGAACTAGGTA 57.863 41.667 17.27 0.00 33.81 3.08
1962 2133 5.000570 AGGAGTAGTTCACAGAACTAGGT 57.999 43.478 17.27 9.69 33.81 3.08
1963 2134 6.181908 ACTAGGAGTAGTTCACAGAACTAGG 58.818 44.000 17.27 8.28 35.88 3.02
1982 2155 5.645497 ACAACGGTTAGTACTACTGACTAGG 59.355 44.000 0.91 4.37 35.35 3.02
1983 2156 6.148480 ACACAACGGTTAGTACTACTGACTAG 59.852 42.308 0.91 7.83 35.35 2.57
1984 2157 5.997746 ACACAACGGTTAGTACTACTGACTA 59.002 40.000 0.91 0.00 35.35 2.59
1993 2166 4.746115 TCAACATCACACAACGGTTAGTAC 59.254 41.667 0.00 0.00 0.00 2.73
1998 2171 2.912771 TCTCAACATCACACAACGGTT 58.087 42.857 0.00 0.00 0.00 4.44
2026 2199 5.136105 ACTCTCTGCAGAAACCAAGAAAAT 58.864 37.500 18.85 0.00 0.00 1.82
2029 2202 3.733337 GACTCTCTGCAGAAACCAAGAA 58.267 45.455 18.85 0.00 0.00 2.52
2061 2234 8.735315 TGAGTAGAATACAGTTTTCTCAGAGAG 58.265 37.037 9.32 0.00 46.26 3.20
2163 2339 3.447229 CCAACCCCCACTGATTAAATCAC 59.553 47.826 0.00 0.00 35.06 3.06
2166 2342 3.881713 GCTCCAACCCCCACTGATTAAAT 60.882 47.826 0.00 0.00 0.00 1.40
2173 2349 0.404040 TTAAGCTCCAACCCCCACTG 59.596 55.000 0.00 0.00 0.00 3.66
2175 2351 0.404426 ACTTAAGCTCCAACCCCCAC 59.596 55.000 1.29 0.00 0.00 4.61
2247 2438 4.199840 TGATTGTTCGATGATCATTGCG 57.800 40.909 17.01 13.28 0.00 4.85
2259 2450 0.734889 GGGTGGCAGATGATTGTTCG 59.265 55.000 0.00 0.00 0.00 3.95
2294 2488 8.141268 ACGAATTATTGCCGATAATGGAAAATT 58.859 29.630 0.00 0.00 39.47 1.82
2298 2492 5.180492 GGACGAATTATTGCCGATAATGGAA 59.820 40.000 0.00 0.00 39.47 3.53
2301 2495 5.621422 CAGGACGAATTATTGCCGATAATG 58.379 41.667 0.00 0.00 39.47 1.90
2307 2501 1.013596 TGCAGGACGAATTATTGCCG 58.986 50.000 0.00 0.00 33.98 5.69
2393 2593 0.519961 AAAATAGTTGACCGCACCGC 59.480 50.000 0.00 0.00 0.00 5.68
2394 2594 2.981400 AAAAATAGTTGACCGCACCG 57.019 45.000 0.00 0.00 0.00 4.94
2410 2610 2.774234 TGGGCAGGAATGAAACCAAAAA 59.226 40.909 0.00 0.00 0.00 1.94
2412 2612 2.094100 TGGGCAGGAATGAAACCAAA 57.906 45.000 0.00 0.00 0.00 3.28
2415 2615 1.923356 TCTTGGGCAGGAATGAAACC 58.077 50.000 0.00 0.00 0.00 3.27
2416 2616 4.949856 TCTAATCTTGGGCAGGAATGAAAC 59.050 41.667 0.00 0.00 0.00 2.78
2421 2629 4.228210 TCACTTCTAATCTTGGGCAGGAAT 59.772 41.667 0.00 0.00 0.00 3.01
2422 2630 3.587061 TCACTTCTAATCTTGGGCAGGAA 59.413 43.478 0.00 0.00 0.00 3.36
2431 2639 7.450323 GGGATAGTAGCTCTCACTTCTAATCTT 59.550 40.741 0.00 0.00 0.00 2.40
2438 2646 3.005367 GCTGGGATAGTAGCTCTCACTTC 59.995 52.174 0.00 0.00 36.99 3.01
2439 2647 2.962421 GCTGGGATAGTAGCTCTCACTT 59.038 50.000 0.00 0.00 36.99 3.16
2440 2648 2.593026 GCTGGGATAGTAGCTCTCACT 58.407 52.381 0.00 0.00 36.99 3.41
2441 2649 1.616374 GGCTGGGATAGTAGCTCTCAC 59.384 57.143 0.00 0.00 39.80 3.51
2442 2650 1.501170 AGGCTGGGATAGTAGCTCTCA 59.499 52.381 0.00 0.00 39.80 3.27
2443 2651 2.167662 GAGGCTGGGATAGTAGCTCTC 58.832 57.143 0.00 0.00 39.80 3.20
2444 2652 1.786441 AGAGGCTGGGATAGTAGCTCT 59.214 52.381 0.00 0.00 39.80 4.09
2446 2654 1.786441 AGAGAGGCTGGGATAGTAGCT 59.214 52.381 0.00 0.00 39.80 3.32
2447 2655 2.167662 GAGAGAGGCTGGGATAGTAGC 58.832 57.143 0.00 0.00 39.17 3.58
2448 2656 3.806949 AGAGAGAGGCTGGGATAGTAG 57.193 52.381 0.00 0.00 0.00 2.57
2449 2657 4.169068 AGAAAGAGAGAGGCTGGGATAGTA 59.831 45.833 0.00 0.00 0.00 1.82
2450 2658 3.052186 AGAAAGAGAGAGGCTGGGATAGT 60.052 47.826 0.00 0.00 0.00 2.12
2451 2659 3.321682 CAGAAAGAGAGAGGCTGGGATAG 59.678 52.174 0.00 0.00 0.00 2.08
2452 2660 3.303938 CAGAAAGAGAGAGGCTGGGATA 58.696 50.000 0.00 0.00 0.00 2.59
2454 2662 1.566211 CAGAAAGAGAGAGGCTGGGA 58.434 55.000 0.00 0.00 0.00 4.37
2455 2663 0.540923 CCAGAAAGAGAGAGGCTGGG 59.459 60.000 0.00 0.00 41.81 4.45
2456 2664 1.481772 CTCCAGAAAGAGAGAGGCTGG 59.518 57.143 0.00 0.00 45.77 4.85
2458 2666 2.917713 TCTCCAGAAAGAGAGAGGCT 57.082 50.000 0.00 0.00 37.98 4.58
2489 2739 0.250295 CGGACACTTTTGGGAGAGCA 60.250 55.000 0.00 0.00 0.00 4.26
2496 2746 1.503818 CGGTGACCGGACACTTTTGG 61.504 60.000 30.85 14.80 44.15 3.28
2552 2807 2.352503 TGTAGAAAGGCCGACGTTAC 57.647 50.000 0.00 0.00 0.00 2.50
2568 2823 2.735478 CGTGGTCGGCGCTTTGTA 60.735 61.111 7.64 0.00 0.00 2.41
2604 2859 5.111293 CCTAAAAATGTCATCCATTGCCAC 58.889 41.667 0.00 0.00 43.04 5.01
2605 2860 4.161942 CCCTAAAAATGTCATCCATTGCCA 59.838 41.667 0.00 0.00 43.04 4.92
2606 2861 4.443315 CCCCTAAAAATGTCATCCATTGCC 60.443 45.833 0.00 0.00 43.04 4.52
2632 2887 6.126623 GGGAGGGAGAAGATAGAAAGATGTTT 60.127 42.308 0.00 0.00 0.00 2.83
2633 2888 5.368230 GGGAGGGAGAAGATAGAAAGATGTT 59.632 44.000 0.00 0.00 0.00 2.71
2634 2889 4.904853 GGGAGGGAGAAGATAGAAAGATGT 59.095 45.833 0.00 0.00 0.00 3.06
2663 2944 3.619487 GCTGCTATCCTCATCCAATCTCC 60.619 52.174 0.00 0.00 0.00 3.71
2674 2963 1.071128 CCAGGCTGCTGCTATCCTC 59.929 63.158 15.64 0.00 39.59 3.71
2678 2967 0.914644 TCTTTCCAGGCTGCTGCTAT 59.085 50.000 15.64 1.80 39.59 2.97
2680 2969 0.608582 CTTCTTTCCAGGCTGCTGCT 60.609 55.000 15.64 0.00 39.59 4.24
2681 2970 1.881602 CTTCTTTCCAGGCTGCTGC 59.118 57.895 9.56 7.10 38.76 5.25
2682 2971 0.892358 TGCTTCTTTCCAGGCTGCTG 60.892 55.000 9.56 0.00 0.00 4.41
2698 2987 0.892755 CATGATTGCTTGGTGGTGCT 59.107 50.000 0.00 0.00 0.00 4.40
2699 2988 0.108520 CCATGATTGCTTGGTGGTGC 60.109 55.000 0.00 0.00 35.26 5.01
2702 2991 1.108776 CTCCCATGATTGCTTGGTGG 58.891 55.000 0.00 0.00 37.57 4.61
2713 3002 3.731728 GCCACTGCCCTCCCATGA 61.732 66.667 0.00 0.00 0.00 3.07
2725 3044 1.214305 TTGGATTAGCAGGGGCCACT 61.214 55.000 0.00 0.00 42.56 4.00
2789 3108 2.752354 CTGGGACTCTCTCTGTACACAG 59.248 54.545 2.84 2.84 45.08 3.66
2814 3158 2.640332 GAGAGAAAGAACTTGGGAGGGT 59.360 50.000 0.00 0.00 0.00 4.34
2818 3162 4.464597 GCTAGAGAGAGAAAGAACTTGGGA 59.535 45.833 0.00 0.00 0.00 4.37
2819 3163 4.221703 TGCTAGAGAGAGAAAGAACTTGGG 59.778 45.833 0.00 0.00 0.00 4.12
2820 3164 5.398603 TGCTAGAGAGAGAAAGAACTTGG 57.601 43.478 0.00 0.00 0.00 3.61
2821 3165 5.047377 ACCTGCTAGAGAGAGAAAGAACTTG 60.047 44.000 0.00 0.00 0.00 3.16
2823 3167 4.462483 CACCTGCTAGAGAGAGAAAGAACT 59.538 45.833 0.00 0.00 0.00 3.01
2824 3168 4.743493 CACCTGCTAGAGAGAGAAAGAAC 58.257 47.826 0.00 0.00 0.00 3.01
2853 3208 1.248101 CCGGCCCACAGTAAAAAGGG 61.248 60.000 0.00 0.00 44.37 3.95


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

AutoCloner maintained by Alex Coulton.