Multiple sequence alignment - TraesCS6A01G326000

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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 TraesCS6A01G326000 chr6A 100.000 3119 0 0 1 3119 559402341 559405459 0.000000e+00 5760.0
1 TraesCS6A01G326000 chr6A 89.286 112 10 2 2809 2918 47702974 47702863 4.190000e-29 139.0
2 TraesCS6A01G326000 chr6A 92.453 53 1 3 2773 2823 559405001 559405052 4.310000e-09 73.1
3 TraesCS6A01G326000 chr6A 92.453 53 1 3 2661 2712 559405113 559405163 4.310000e-09 73.1
4 TraesCS6A01G326000 chr6B 85.481 3127 223 96 91 3119 624785067 624788060 0.000000e+00 3046.0
5 TraesCS6A01G326000 chr6B 92.308 65 4 1 10 73 624784931 624784995 1.190000e-14 91.6
6 TraesCS6A01G326000 chr6B 92.453 53 1 3 2773 2823 624787590 624787641 4.310000e-09 73.1
7 TraesCS6A01G326000 chr6B 93.478 46 3 0 2657 2702 624787698 624787743 5.580000e-08 69.4
8 TraesCS6A01G326000 chr6D 91.216 1924 100 28 775 2661 414466994 414468885 0.000000e+00 2553.0
9 TraesCS6A01G326000 chr6D 87.326 789 55 16 3 758 414466234 414467010 0.000000e+00 861.0
10 TraesCS6A01G326000 chr5D 79.484 931 116 32 1214 2126 15229540 15228667 2.680000e-165 592.0
11 TraesCS6A01G326000 chr5D 92.157 102 7 1 2806 2906 1692949 1693050 3.240000e-30 143.0
12 TraesCS6A01G326000 chr5B 93.878 98 5 1 2809 2905 692370488 692370391 2.510000e-31 147.0
13 TraesCS6A01G326000 chr5B 97.297 37 1 0 3035 3071 65492563 65492527 2.600000e-06 63.9
14 TraesCS6A01G326000 chr3D 93.000 100 6 1 2809 2907 22331253 22331352 9.020000e-31 145.0
15 TraesCS6A01G326000 chr2D 93.000 100 6 1 2807 2905 459304808 459304907 9.020000e-31 145.0
16 TraesCS6A01G326000 chr2D 92.157 102 7 1 2807 2907 107204078 107204179 3.240000e-30 143.0
17 TraesCS6A01G326000 chr2B 93.000 100 6 1 2809 2907 183513577 183513478 9.020000e-31 145.0
18 TraesCS6A01G326000 chr7B 91.429 105 7 2 2808 2911 642496237 642496134 3.240000e-30 143.0
19 TraesCS6A01G326000 chr1B 90.741 108 8 2 2805 2910 476030751 476030858 3.240000e-30 143.0
20 TraesCS6A01G326000 chr1A 97.222 36 1 0 3035 3070 463249222 463249187 9.340000e-06 62.1


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 TraesCS6A01G326000 chr6A 559402341 559405459 3118 False 1968.733333 5760 94.968667 1 3119 3 chr6A.!!$F1 3118
1 TraesCS6A01G326000 chr6B 624784931 624788060 3129 False 820.025000 3046 90.930000 10 3119 4 chr6B.!!$F1 3109
2 TraesCS6A01G326000 chr6D 414466234 414468885 2651 False 1707.000000 2553 89.271000 3 2661 2 chr6D.!!$F1 2658
3 TraesCS6A01G326000 chr5D 15228667 15229540 873 True 592.000000 592 79.484000 1214 2126 1 chr5D.!!$R1 912

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
407 464 0.672401 TGTTTCTCCCGCGGTGATTC 60.672 55.0 26.12 16.18 0.00 2.52 F
1908 2047 0.103208 GGTTCGAGGAGATGTGCGAT 59.897 55.0 0.00 0.00 32.38 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2209 0.490017 TCACCTCCCTTACCAGGTCA 59.510 55.0 0.0 0.0 41.41 4.02 R
3032 3238 0.040958 CGACAAGTTCAAGCACCAGC 60.041 55.0 0.0 0.0 42.56 4.85 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
30 31 3.073678 TGTTTCCATGGATTCAGACGTG 58.926 45.455 17.06 0.00 0.00 4.49
87 113 4.263506 GGCAAGGTATATTCTGCACCCTAT 60.264 45.833 0.00 0.00 32.43 2.57
90 116 6.520061 GCAAGGTATATTCTGCACCCTATACA 60.520 42.308 13.02 0.00 31.58 2.29
91 117 6.607004 AGGTATATTCTGCACCCTATACAC 57.393 41.667 13.02 6.35 31.58 2.90
100 157 3.641436 TGCACCCTATACACCTCATACAG 59.359 47.826 0.00 0.00 0.00 2.74
107 164 5.986135 CCTATACACCTCATACAGCACTTTC 59.014 44.000 0.00 0.00 0.00 2.62
135 192 6.855836 TGAAAATCATAACCATGTGCTTCTC 58.144 36.000 0.00 0.00 33.57 2.87
181 238 2.033141 TGCCTGAGGAAGCTGCAC 59.967 61.111 0.65 0.00 0.00 4.57
254 311 2.677979 GCGAGGAAAACCGACCAGC 61.678 63.158 0.00 0.00 0.00 4.85
284 341 1.618640 GCTCTTCGACACGTCAAGCC 61.619 60.000 0.00 0.00 0.00 4.35
298 355 1.378250 AAGCCTGGTGCATCTGCTC 60.378 57.895 13.76 0.00 44.83 4.26
336 393 2.171489 AAGCGAGCGAGCGTTTTTCC 62.171 55.000 0.00 0.00 43.00 3.13
347 404 5.744490 CGAGCGTTTTTCCTTTCTCTTTTA 58.256 37.500 0.00 0.00 0.00 1.52
393 450 1.853319 CTGCGACGACCTGTGTTTC 59.147 57.895 0.00 0.00 0.00 2.78
407 464 0.672401 TGTTTCTCCCGCGGTGATTC 60.672 55.000 26.12 16.18 0.00 2.52
470 530 9.599056 ATCTATGAGAGATAGAAGACCAATGAA 57.401 33.333 0.00 0.00 43.54 2.57
472 532 9.474920 CTATGAGAGATAGAAGACCAATGAAAC 57.525 37.037 0.00 0.00 0.00 2.78
577 645 4.245660 ACAACGTTGAATGATCGATCTGT 58.754 39.130 33.66 14.69 0.00 3.41
578 646 4.327357 ACAACGTTGAATGATCGATCTGTC 59.673 41.667 33.66 20.55 0.00 3.51
587 656 3.969899 TGATCGATCTGTCAGGATTTCG 58.030 45.455 25.02 4.81 0.00 3.46
632 708 2.749621 GGCTGGACTGAATGTTTACTGG 59.250 50.000 0.00 0.00 0.00 4.00
636 712 3.181445 TGGACTGAATGTTTACTGGTGCT 60.181 43.478 0.00 0.00 0.00 4.40
637 713 3.821033 GGACTGAATGTTTACTGGTGCTT 59.179 43.478 0.00 0.00 0.00 3.91
673 749 2.435805 ACTTCTCCAGCTTGTGAGTGAA 59.564 45.455 4.97 0.00 0.00 3.18
679 755 2.935201 CCAGCTTGTGAGTGAATCTAGC 59.065 50.000 0.00 0.00 0.00 3.42
752 846 2.441410 CTGTGAGTGAGTCTAGCCAGA 58.559 52.381 0.00 0.00 0.00 3.86
753 847 2.822561 CTGTGAGTGAGTCTAGCCAGAA 59.177 50.000 0.00 0.00 30.85 3.02
754 848 3.230976 TGTGAGTGAGTCTAGCCAGAAA 58.769 45.455 0.00 0.00 30.85 2.52
755 849 3.256879 TGTGAGTGAGTCTAGCCAGAAAG 59.743 47.826 0.00 0.00 30.85 2.62
756 850 3.508012 GTGAGTGAGTCTAGCCAGAAAGA 59.492 47.826 0.00 0.00 30.85 2.52
757 851 4.159506 GTGAGTGAGTCTAGCCAGAAAGAT 59.840 45.833 0.00 0.00 30.85 2.40
758 852 4.774726 TGAGTGAGTCTAGCCAGAAAGATT 59.225 41.667 0.00 0.00 30.85 2.40
759 853 5.247110 TGAGTGAGTCTAGCCAGAAAGATTT 59.753 40.000 0.00 0.00 30.85 2.17
760 854 6.120507 AGTGAGTCTAGCCAGAAAGATTTT 57.879 37.500 0.00 0.00 30.85 1.82
761 855 6.538263 AGTGAGTCTAGCCAGAAAGATTTTT 58.462 36.000 0.00 0.00 30.85 1.94
794 888 5.241662 ACAAGTCTAGCCAGAAAGATGAAC 58.758 41.667 0.00 0.00 30.85 3.18
805 899 2.010145 AAGATGAACGATGGACCGTG 57.990 50.000 0.00 0.00 42.54 4.94
842 936 1.224592 GTGGACATGGGCCTGGTAG 59.775 63.158 4.53 0.00 0.00 3.18
898 997 1.279271 AGGGAGTACGCTGATGCTTTT 59.721 47.619 0.00 0.00 37.89 2.27
1351 1478 1.201429 GGAAGAGGAGCCCACCAAGA 61.201 60.000 0.00 0.00 0.00 3.02
1361 1488 4.760047 CACCAAGACGGCCCCTCG 62.760 72.222 0.00 0.00 39.03 4.63
1377 1504 2.510238 CGCTCCGCTCCCAAGAAG 60.510 66.667 0.00 0.00 0.00 2.85
1386 1513 3.983420 CCCAAGAAGCAGCCCCCA 61.983 66.667 0.00 0.00 0.00 4.96
1542 1681 2.665603 GCCGAGACCAAGAAGCCT 59.334 61.111 0.00 0.00 0.00 4.58
1680 1819 2.434359 GGGAAGCTCGACAACCGG 60.434 66.667 0.00 0.00 39.14 5.28
1714 1853 2.285743 AGCTCCAGGGGAAGGTCC 60.286 66.667 0.00 0.00 35.23 4.46
1722 1861 3.412408 GGGAAGGTCCTGGCCCTC 61.412 72.222 18.81 0.00 36.57 4.30
1829 1968 4.778143 GGAAGGCGGCGACATGGT 62.778 66.667 18.30 0.00 0.00 3.55
1855 1994 2.033757 CAGCTGCCTCTGCCAAGT 59.966 61.111 0.00 0.00 36.33 3.16
1908 2047 0.103208 GGTTCGAGGAGATGTGCGAT 59.897 55.000 0.00 0.00 32.38 4.58
1998 2137 0.178961 TCGGGATGATGGACGAGGAT 60.179 55.000 0.00 0.00 0.00 3.24
2035 2174 1.134848 ACGAGAAGATCAAGAGGCAGC 60.135 52.381 0.00 0.00 0.00 5.25
2107 2246 0.179000 GACCAAGGCCATCATCGACT 59.821 55.000 5.01 0.00 0.00 4.18
2240 2410 2.225382 TTGGTGTCTCGGATGGTCTA 57.775 50.000 0.00 0.00 0.00 2.59
2326 2507 4.162131 TGTGACCAGAGCATGCTAGAATTA 59.838 41.667 22.74 3.49 0.00 1.40
2327 2508 5.163269 TGTGACCAGAGCATGCTAGAATTAT 60.163 40.000 22.74 2.36 0.00 1.28
2355 2536 2.879103 AGGGGTGTCTTTATGGTGTG 57.121 50.000 0.00 0.00 0.00 3.82
2356 2537 2.344592 AGGGGTGTCTTTATGGTGTGA 58.655 47.619 0.00 0.00 0.00 3.58
2357 2538 2.305927 AGGGGTGTCTTTATGGTGTGAG 59.694 50.000 0.00 0.00 0.00 3.51
2358 2539 2.084546 GGGTGTCTTTATGGTGTGAGC 58.915 52.381 0.00 0.00 0.00 4.26
2359 2540 2.552155 GGGTGTCTTTATGGTGTGAGCA 60.552 50.000 0.00 0.00 0.00 4.26
2360 2541 3.347216 GGTGTCTTTATGGTGTGAGCAT 58.653 45.455 0.00 0.00 39.88 3.79
2361 2542 3.127548 GGTGTCTTTATGGTGTGAGCATG 59.872 47.826 0.00 0.00 36.89 4.06
2429 2610 2.949447 AGAATGTTTTCCTGTGTGGCT 58.051 42.857 0.00 0.00 35.26 4.75
2440 2621 3.093057 CCTGTGTGGCTAGAGAAGTACT 58.907 50.000 0.00 0.00 0.00 2.73
2493 2683 0.516877 CGCGAATCTTTCTTGCCACA 59.483 50.000 0.00 0.00 0.00 4.17
2515 2705 2.615493 GGTTCCATCGATTGTGTGAGGT 60.615 50.000 0.00 0.00 0.00 3.85
2516 2706 3.074412 GTTCCATCGATTGTGTGAGGTT 58.926 45.455 0.00 0.00 0.00 3.50
2546 2737 3.059461 TGAAACGGTCGCTGAATTTGTAC 60.059 43.478 0.00 0.00 0.00 2.90
2592 2784 3.878103 TGTTAGTTTTGGCAGCTCGTTTA 59.122 39.130 0.00 0.00 0.00 2.01
2641 2833 0.260230 TTTCAGGGTTTGGGTGCAGA 59.740 50.000 0.00 0.00 0.00 4.26
2663 2855 4.079970 ACTGGAGTCGTGAGTCTGAATTA 58.920 43.478 4.80 0.00 0.00 1.40
2671 2863 7.551585 AGTCGTGAGTCTGAATTAGATGAATT 58.448 34.615 0.00 0.00 40.62 2.17
2732 2924 5.385509 TCTGCTGTTTAATTTAACCAGCC 57.614 39.130 26.25 14.51 34.33 4.85
2756 2948 4.896562 TTATACTTGCGTGACTGTTTCG 57.103 40.909 2.22 2.22 0.00 3.46
2764 2956 0.234884 GTGACTGTTTCGGGCTTTCG 59.765 55.000 0.00 0.00 0.00 3.46
2765 2957 1.206831 GACTGTTTCGGGCTTTCGC 59.793 57.895 0.00 0.00 0.00 4.70
2769 2961 2.593148 TTTCGGGCTTTCGCTGCA 60.593 55.556 0.00 0.00 36.09 4.41
2776 2968 0.659957 GGCTTTCGCTGCAGGATTAG 59.340 55.000 17.12 11.74 36.09 1.73
2817 3009 1.705873 CGCTGGGTTATACTCCCTCT 58.294 55.000 11.93 0.00 44.84 3.69
2821 3013 3.200165 GCTGGGTTATACTCCCTCTGTTT 59.800 47.826 11.93 0.00 44.84 2.83
2825 3017 5.311121 TGGGTTATACTCCCTCTGTTTCAAA 59.689 40.000 11.93 0.00 44.84 2.69
2826 3018 6.183361 TGGGTTATACTCCCTCTGTTTCAAAA 60.183 38.462 11.93 0.00 44.84 2.44
2827 3019 6.890268 GGGTTATACTCCCTCTGTTTCAAAAT 59.110 38.462 5.24 0.00 41.58 1.82
2828 3020 8.050930 GGGTTATACTCCCTCTGTTTCAAAATA 58.949 37.037 5.24 0.00 41.58 1.40
2829 3021 9.110502 GGTTATACTCCCTCTGTTTCAAAATAG 57.889 37.037 0.00 0.00 0.00 1.73
2830 3022 9.886132 GTTATACTCCCTCTGTTTCAAAATAGA 57.114 33.333 2.56 2.56 35.32 1.98
2832 3024 8.970859 ATACTCCCTCTGTTTCAAAATAGATG 57.029 34.615 2.91 1.27 35.92 2.90
2837 3029 6.881065 CCCTCTGTTTCAAAATAGATGACTCA 59.119 38.462 2.91 0.00 35.92 3.41
2838 3030 7.391554 CCCTCTGTTTCAAAATAGATGACTCAA 59.608 37.037 2.91 0.00 35.92 3.02
2840 3032 8.908786 TCTGTTTCAAAATAGATGACTCAACT 57.091 30.769 0.00 0.00 32.24 3.16
2842 3034 9.956720 CTGTTTCAAAATAGATGACTCAACTTT 57.043 29.630 0.00 0.00 29.67 2.66
2881 3073 9.826574 ATACAAAGTTAGTACAAAGTTGAGACA 57.173 29.630 0.00 0.00 0.00 3.41
2882 3074 8.732746 ACAAAGTTAGTACAAAGTTGAGACAT 57.267 30.769 0.00 0.00 0.00 3.06
2883 3075 8.827677 ACAAAGTTAGTACAAAGTTGAGACATC 58.172 33.333 0.00 0.00 0.00 3.06
2910 3103 3.760684 TGAAACGGAGGGAGTACTACTTC 59.239 47.826 8.73 8.73 0.00 3.01
2914 3107 4.036518 ACGGAGGGAGTACTACTTCTCTA 58.963 47.826 16.21 0.00 32.88 2.43
3004 3210 4.803098 TGTTTAGAGGGAGTGCTACTTC 57.197 45.455 0.00 0.00 0.00 3.01
3014 3220 3.249917 GAGTGCTACTTCTCTGCTGTTC 58.750 50.000 0.00 0.00 0.00 3.18
3020 3226 6.147821 GTGCTACTTCTCTGCTGTTCAATTTA 59.852 38.462 0.00 0.00 0.00 1.40
3023 3229 7.118390 GCTACTTCTCTGCTGTTCAATTTAGAA 59.882 37.037 0.00 0.00 0.00 2.10
3028 3234 8.539770 TCTCTGCTGTTCAATTTAGAAGTAAG 57.460 34.615 0.00 0.00 0.00 2.34
3030 3236 9.424319 CTCTGCTGTTCAATTTAGAAGTAAGTA 57.576 33.333 0.00 0.00 0.00 2.24
3032 3238 8.014322 TGCTGTTCAATTTAGAAGTAAGTACG 57.986 34.615 0.00 0.00 0.00 3.67
3034 3240 7.148623 GCTGTTCAATTTAGAAGTAAGTACGCT 60.149 37.037 0.00 0.00 0.00 5.07
3044 3252 2.036733 AGTAAGTACGCTGGTGCTTGAA 59.963 45.455 7.66 0.00 46.61 2.69
3047 3255 1.202651 AGTACGCTGGTGCTTGAACTT 60.203 47.619 0.00 0.00 35.39 2.66
3050 3258 0.040958 CGCTGGTGCTTGAACTTGTC 60.041 55.000 0.00 0.00 36.97 3.18
3051 3259 0.040958 GCTGGTGCTTGAACTTGTCG 60.041 55.000 0.00 0.00 36.03 4.35
3062 3270 3.738982 TGAACTTGTCGTGGATGTTCAT 58.261 40.909 0.00 0.00 41.02 2.57
3069 3277 5.605564 TGTCGTGGATGTTCATTTTAGTG 57.394 39.130 0.00 0.00 0.00 2.74
3073 3281 5.935206 TCGTGGATGTTCATTTTAGTGCTTA 59.065 36.000 0.00 0.00 0.00 3.09
3074 3282 6.021596 CGTGGATGTTCATTTTAGTGCTTAC 58.978 40.000 0.00 0.00 0.00 2.34
3083 3291 6.800543 TCATTTTAGTGCTTACAGTTGCAAA 58.199 32.000 0.00 0.00 41.10 3.68
3098 3306 6.128309 ACAGTTGCAAATGGTTTCAAAACTTC 60.128 34.615 28.40 0.00 38.89 3.01
3099 3307 5.936956 AGTTGCAAATGGTTTCAAAACTTCA 59.063 32.000 0.00 0.00 38.89 3.02
3100 3308 5.793026 TGCAAATGGTTTCAAAACTTCAC 57.207 34.783 5.66 0.00 38.89 3.18
3101 3309 5.240891 TGCAAATGGTTTCAAAACTTCACA 58.759 33.333 5.66 0.00 38.89 3.58
3102 3310 5.879223 TGCAAATGGTTTCAAAACTTCACAT 59.121 32.000 5.66 0.00 38.89 3.21
3103 3311 6.183360 TGCAAATGGTTTCAAAACTTCACATG 60.183 34.615 5.66 0.00 38.89 3.21
3104 3312 5.989551 AATGGTTTCAAAACTTCACATGC 57.010 34.783 5.66 0.00 38.89 4.06
3105 3313 3.443037 TGGTTTCAAAACTTCACATGCG 58.557 40.909 5.66 0.00 38.89 4.73
3107 3315 1.752753 TTCAAAACTTCACATGCGCG 58.247 45.000 0.00 0.00 0.00 6.86
3109 3317 1.867865 TCAAAACTTCACATGCGCGTA 59.132 42.857 8.43 2.40 0.00 4.42
3111 3319 2.594529 AAACTTCACATGCGCGTAAG 57.405 45.000 8.43 5.34 43.44 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 113 6.599356 TTAGAAAGTGCTGTATGAGGTGTA 57.401 37.500 0.00 0.00 0.00 2.90
90 116 6.299805 TCATTAGAAAGTGCTGTATGAGGT 57.700 37.500 0.00 0.00 0.00 3.85
91 117 7.615582 TTTCATTAGAAAGTGCTGTATGAGG 57.384 36.000 0.00 0.00 38.76 3.86
100 157 9.807649 ATGGTTATGATTTTCATTAGAAAGTGC 57.192 29.630 0.00 0.00 44.03 4.40
107 164 9.241317 GAAGCACATGGTTATGATTTTCATTAG 57.759 33.333 0.00 0.00 38.26 1.73
181 238 2.743928 GAGGACAGGCGCCACTTG 60.744 66.667 31.54 21.18 0.00 3.16
254 311 0.173481 TCGAAGAGCTCCATGAACCG 59.827 55.000 10.93 4.05 0.00 4.44
284 341 3.200593 GGCGAGCAGATGCACCAG 61.201 66.667 7.68 0.00 45.16 4.00
298 355 1.291184 TTCATCAACACTGCGAGGCG 61.291 55.000 0.00 0.00 0.00 5.52
336 393 3.003480 CGGGACAGGCTAAAAGAGAAAG 58.997 50.000 0.00 0.00 0.00 2.62
347 404 3.474570 GCAGGATCGGGACAGGCT 61.475 66.667 0.00 0.00 0.00 4.58
393 450 1.811266 CTGTGAATCACCGCGGGAG 60.811 63.158 31.76 21.75 32.73 4.30
458 515 5.940470 AGGAGTACATGTTTCATTGGTCTTC 59.060 40.000 2.30 0.00 0.00 2.87
470 530 8.408043 TTTTGATCATTCAAGGAGTACATGTT 57.592 30.769 2.30 0.00 42.60 2.71
514 578 5.231357 TGCGAGAATAACGATAATGTGTCAC 59.769 40.000 0.00 0.00 0.00 3.67
543 611 7.484975 TCATTCAACGTTGTTCTACCATTTTT 58.515 30.769 26.47 0.00 0.00 1.94
544 612 7.033530 TCATTCAACGTTGTTCTACCATTTT 57.966 32.000 26.47 0.00 0.00 1.82
545 613 6.627395 TCATTCAACGTTGTTCTACCATTT 57.373 33.333 26.47 0.00 0.00 2.32
546 614 6.402118 CGATCATTCAACGTTGTTCTACCATT 60.402 38.462 26.47 5.52 0.00 3.16
547 615 5.063438 CGATCATTCAACGTTGTTCTACCAT 59.937 40.000 26.47 11.27 0.00 3.55
558 626 4.108336 CTGACAGATCGATCATTCAACGT 58.892 43.478 26.47 11.34 0.00 3.99
560 628 4.686972 TCCTGACAGATCGATCATTCAAC 58.313 43.478 26.47 11.81 0.00 3.18
577 645 5.753438 CGAAATAACATCTCCGAAATCCTGA 59.247 40.000 0.00 0.00 0.00 3.86
578 646 5.753438 TCGAAATAACATCTCCGAAATCCTG 59.247 40.000 0.00 0.00 0.00 3.86
587 656 5.973565 CCAGCATTTTCGAAATAACATCTCC 59.026 40.000 12.12 0.00 0.00 3.71
632 708 7.694886 AGAAGTAGTTAGTTGTCAAAAAGCAC 58.305 34.615 0.00 0.00 0.00 4.40
636 712 7.012044 GCTGGAGAAGTAGTTAGTTGTCAAAAA 59.988 37.037 6.30 0.00 32.34 1.94
637 713 6.482308 GCTGGAGAAGTAGTTAGTTGTCAAAA 59.518 38.462 6.30 0.00 32.34 2.44
728 822 2.357637 GGCTAGACTCACTCACAGCTAG 59.642 54.545 0.00 0.00 32.37 3.42
729 823 2.290960 TGGCTAGACTCACTCACAGCTA 60.291 50.000 0.00 0.00 32.37 3.32
763 857 5.290493 TCTGGCTAGACTTGTCTCAAAAA 57.710 39.130 6.55 0.00 0.00 1.94
764 858 4.955811 TCTGGCTAGACTTGTCTCAAAA 57.044 40.909 6.55 0.00 0.00 2.44
765 859 4.955811 TTCTGGCTAGACTTGTCTCAAA 57.044 40.909 6.55 0.00 31.21 2.69
766 860 4.588951 TCTTTCTGGCTAGACTTGTCTCAA 59.411 41.667 6.55 0.00 31.21 3.02
767 861 4.152647 TCTTTCTGGCTAGACTTGTCTCA 58.847 43.478 6.55 0.00 31.21 3.27
768 862 4.792521 TCTTTCTGGCTAGACTTGTCTC 57.207 45.455 6.55 0.00 31.21 3.36
769 863 4.774726 TCATCTTTCTGGCTAGACTTGTCT 59.225 41.667 0.00 8.41 31.21 3.41
770 864 5.078411 TCATCTTTCTGGCTAGACTTGTC 57.922 43.478 0.00 0.00 31.21 3.18
771 865 5.241662 GTTCATCTTTCTGGCTAGACTTGT 58.758 41.667 0.00 0.00 31.21 3.16
772 866 4.328440 CGTTCATCTTTCTGGCTAGACTTG 59.672 45.833 0.00 0.00 31.21 3.16
773 867 4.220821 TCGTTCATCTTTCTGGCTAGACTT 59.779 41.667 0.00 0.00 31.21 3.01
774 868 3.764434 TCGTTCATCTTTCTGGCTAGACT 59.236 43.478 0.00 0.00 31.21 3.24
775 869 4.111375 TCGTTCATCTTTCTGGCTAGAC 57.889 45.455 0.00 0.00 31.21 2.59
776 870 4.442052 CCATCGTTCATCTTTCTGGCTAGA 60.442 45.833 0.00 0.00 0.00 2.43
777 871 3.806521 CCATCGTTCATCTTTCTGGCTAG 59.193 47.826 0.00 0.00 0.00 3.42
778 872 3.450817 TCCATCGTTCATCTTTCTGGCTA 59.549 43.478 0.00 0.00 0.00 3.93
779 873 2.237143 TCCATCGTTCATCTTTCTGGCT 59.763 45.455 0.00 0.00 0.00 4.75
780 874 2.352960 GTCCATCGTTCATCTTTCTGGC 59.647 50.000 0.00 0.00 0.00 4.85
781 875 2.939103 GGTCCATCGTTCATCTTTCTGG 59.061 50.000 0.00 0.00 0.00 3.86
782 876 2.604914 CGGTCCATCGTTCATCTTTCTG 59.395 50.000 0.00 0.00 0.00 3.02
783 877 2.233922 ACGGTCCATCGTTCATCTTTCT 59.766 45.455 0.00 0.00 40.85 2.52
784 878 2.348666 CACGGTCCATCGTTCATCTTTC 59.651 50.000 0.00 0.00 41.86 2.62
794 888 1.520787 GGCCTTACACGGTCCATCG 60.521 63.158 0.00 0.00 0.00 3.84
865 964 4.844998 GTACTCCCTACGATAACCCTTC 57.155 50.000 0.00 0.00 0.00 3.46
893 992 4.404715 GGGGTTTATTAGGGGAAGAAAAGC 59.595 45.833 0.00 0.00 30.31 3.51
898 997 3.239508 TGGGGGTTTATTAGGGGAAGA 57.760 47.619 0.00 0.00 0.00 2.87
968 1068 2.192263 AGCTAGGGTTTGGGAGAAGAG 58.808 52.381 0.00 0.00 0.00 2.85
1096 1202 2.490685 GGCGTCTTCGTCCTCCTC 59.509 66.667 0.00 0.00 39.49 3.71
1097 1203 3.441290 CGGCGTCTTCGTCCTCCT 61.441 66.667 0.00 0.00 38.56 3.69
1098 1204 3.398353 CTCGGCGTCTTCGTCCTCC 62.398 68.421 6.85 0.00 38.56 4.30
1099 1205 2.100603 CTCGGCGTCTTCGTCCTC 59.899 66.667 6.85 0.00 38.56 3.71
1100 1206 2.672307 ACTCGGCGTCTTCGTCCT 60.672 61.111 6.85 0.00 38.56 3.85
1178 1287 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1179 1288 1.293683 ACTCCTCCTCCTCCTCCTCC 61.294 65.000 0.00 0.00 0.00 4.30
1180 1289 0.185175 GACTCCTCCTCCTCCTCCTC 59.815 65.000 0.00 0.00 0.00 3.71
1314 1426 1.098712 CCTCCTCCTCGTCGGAAGAG 61.099 65.000 13.15 13.15 46.03 2.85
1604 1743 1.959085 CCGTGCTGCTTTTGGTGAT 59.041 52.632 0.00 0.00 0.00 3.06
1665 1804 3.119096 GCCCGGTTGTCGAGCTTC 61.119 66.667 0.00 0.00 39.59 3.86
1722 1861 4.849329 GCGAGGTACCGACGCCTG 62.849 72.222 33.06 12.38 45.35 4.85
1740 1879 2.046892 TCGCCCTTCTTGCTGAGC 60.047 61.111 0.00 0.00 0.00 4.26
1851 1990 3.793144 GCCGCCTTCGCAGACTTG 61.793 66.667 0.00 0.00 34.32 3.16
1855 1994 2.359850 ATTTGCCGCCTTCGCAGA 60.360 55.556 0.00 0.00 34.03 4.26
1932 2071 1.078918 CGCATCCAGCTCCTTCACA 60.079 57.895 0.00 0.00 42.61 3.58
1965 2104 0.762418 TCCCGAACTGCCTCTTGAAA 59.238 50.000 0.00 0.00 0.00 2.69
2035 2174 3.197790 CTTCATCTGCGCCACCCG 61.198 66.667 4.18 0.00 40.75 5.28
2070 2209 0.490017 TCACCTCCCTTACCAGGTCA 59.510 55.000 0.00 0.00 41.41 4.02
2107 2246 1.596934 GCTCCCATCAGTCGACCAA 59.403 57.895 13.01 0.08 0.00 3.67
2240 2410 4.018960 AGTTCCAGCATAGGTCTCATGTTT 60.019 41.667 0.00 0.00 0.00 2.83
2300 2479 1.374631 GCATGCTCTGGTCACACGA 60.375 57.895 11.37 0.00 0.00 4.35
2326 2507 6.777580 CCATAAAGACACCCCTAATTTGCTAT 59.222 38.462 0.00 0.00 0.00 2.97
2327 2508 6.126409 CCATAAAGACACCCCTAATTTGCTA 58.874 40.000 0.00 0.00 0.00 3.49
2355 2536 2.835027 TGTCTCATCATGCTCATGCTC 58.165 47.619 5.04 0.00 38.65 4.26
2356 2537 3.142174 CATGTCTCATCATGCTCATGCT 58.858 45.455 5.04 0.00 38.65 3.79
2357 2538 2.879026 ACATGTCTCATCATGCTCATGC 59.121 45.455 12.93 0.00 46.15 4.06
2358 2539 3.304057 GCACATGTCTCATCATGCTCATG 60.304 47.826 0.00 12.00 46.15 3.07
2359 2540 2.879026 GCACATGTCTCATCATGCTCAT 59.121 45.455 0.00 0.00 46.15 2.90
2360 2541 2.093128 AGCACATGTCTCATCATGCTCA 60.093 45.455 0.00 0.00 46.15 4.26
2361 2542 2.288186 CAGCACATGTCTCATCATGCTC 59.712 50.000 12.28 0.27 46.15 4.26
2429 2610 6.534436 CAGTTCTAGCGTACAGTACTTCTCTA 59.466 42.308 9.10 4.53 0.00 2.43
2440 2621 2.823924 TTTGCCAGTTCTAGCGTACA 57.176 45.000 0.00 0.00 0.00 2.90
2468 2652 2.236690 CAAGAAAGATTCGCGCAACAG 58.763 47.619 8.75 0.00 34.02 3.16
2493 2683 2.355108 CCTCACACAATCGATGGAACCT 60.355 50.000 6.84 0.00 0.00 3.50
2515 2705 4.930405 TCAGCGACCGTTTCATACATAAAA 59.070 37.500 0.00 0.00 0.00 1.52
2516 2706 4.496360 TCAGCGACCGTTTCATACATAAA 58.504 39.130 0.00 0.00 0.00 1.40
2546 2737 6.136541 ACAGAAAAGCTTTACTGAACCAAG 57.863 37.500 13.10 0.00 34.88 3.61
2592 2784 1.378250 GCAAGACCAGCCTCTGCAT 60.378 57.895 0.00 0.00 41.13 3.96
2641 2833 1.982660 TTCAGACTCACGACTCCAGT 58.017 50.000 0.00 0.00 0.00 4.00
2663 2855 3.962718 CCATGCCCTGGTAAAATTCATCT 59.037 43.478 0.00 0.00 40.49 2.90
2764 2956 5.049129 GGTAACATTCATCTAATCCTGCAGC 60.049 44.000 8.66 0.00 0.00 5.25
2765 2957 6.057533 TGGTAACATTCATCTAATCCTGCAG 58.942 40.000 6.78 6.78 46.17 4.41
2817 3009 9.734620 CAAAGTTGAGTCATCTATTTTGAAACA 57.265 29.630 4.14 0.00 38.91 2.83
2821 3013 9.778741 AGTACAAAGTTGAGTCATCTATTTTGA 57.221 29.630 15.99 3.46 38.91 2.69
2857 3049 8.732746 ATGTCTCAACTTTGTACTAACTTTGT 57.267 30.769 0.00 0.00 0.00 2.83
2868 3060 8.070171 CGTTTCAAATAGATGTCTCAACTTTGT 58.930 33.333 0.00 0.00 0.00 2.83
2869 3061 7.535258 CCGTTTCAAATAGATGTCTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2873 3065 6.183360 CCTCCGTTTCAAATAGATGTCTCAAC 60.183 42.308 0.00 0.00 0.00 3.18
2874 3066 5.874810 CCTCCGTTTCAAATAGATGTCTCAA 59.125 40.000 0.00 0.00 0.00 3.02
2875 3067 5.419542 CCTCCGTTTCAAATAGATGTCTCA 58.580 41.667 0.00 0.00 0.00 3.27
2876 3068 4.811557 CCCTCCGTTTCAAATAGATGTCTC 59.188 45.833 0.00 0.00 0.00 3.36
2877 3069 4.469945 TCCCTCCGTTTCAAATAGATGTCT 59.530 41.667 0.00 0.00 0.00 3.41
2881 3073 5.661759 AGTACTCCCTCCGTTTCAAATAGAT 59.338 40.000 0.00 0.00 0.00 1.98
2882 3074 5.021458 AGTACTCCCTCCGTTTCAAATAGA 58.979 41.667 0.00 0.00 0.00 1.98
2883 3075 5.340439 AGTACTCCCTCCGTTTCAAATAG 57.660 43.478 0.00 0.00 0.00 1.73
2886 3078 4.154942 AGTAGTACTCCCTCCGTTTCAAA 58.845 43.478 0.00 0.00 0.00 2.69
2887 3079 3.771216 AGTAGTACTCCCTCCGTTTCAA 58.229 45.455 0.00 0.00 0.00 2.69
2893 3086 3.564053 AGAGAAGTAGTACTCCCTCCG 57.436 52.381 20.39 0.00 32.02 4.63
2910 3103 8.047310 ACAAAGGAGTATAACCCAACAATAGAG 58.953 37.037 0.00 0.00 0.00 2.43
2914 3107 7.392393 GTGTACAAAGGAGTATAACCCAACAAT 59.608 37.037 0.00 0.00 0.00 2.71
2948 3142 9.240159 ACGTTAAATGAAACTACAAAAACATCC 57.760 29.630 0.00 0.00 0.00 3.51
2969 3163 8.537728 TCCCTCTAAACAAATATAGGACGTTA 57.462 34.615 0.00 0.00 0.00 3.18
2979 3183 6.869206 AGTAGCACTCCCTCTAAACAAATA 57.131 37.500 0.00 0.00 0.00 1.40
3004 3210 8.316640 ACTTACTTCTAAATTGAACAGCAGAG 57.683 34.615 0.00 0.00 0.00 3.35
3014 3220 6.672357 GCACCAGCGTACTTACTTCTAAATTG 60.672 42.308 0.00 0.00 0.00 2.32
3020 3226 2.365408 GCACCAGCGTACTTACTTCT 57.635 50.000 0.00 0.00 0.00 2.85
3032 3238 0.040958 CGACAAGTTCAAGCACCAGC 60.041 55.000 0.00 0.00 42.56 4.85
3034 3240 1.013596 CACGACAAGTTCAAGCACCA 58.986 50.000 0.00 0.00 0.00 4.17
3044 3252 5.763204 ACTAAAATGAACATCCACGACAAGT 59.237 36.000 0.00 0.00 0.00 3.16
3047 3255 4.083537 GCACTAAAATGAACATCCACGACA 60.084 41.667 0.00 0.00 0.00 4.35
3050 3258 4.685169 AGCACTAAAATGAACATCCACG 57.315 40.909 0.00 0.00 0.00 4.94
3051 3259 6.908825 TGTAAGCACTAAAATGAACATCCAC 58.091 36.000 0.00 0.00 0.00 4.02
3062 3270 5.982516 CCATTTGCAACTGTAAGCACTAAAA 59.017 36.000 14.83 1.16 41.05 1.52
3069 3277 4.367450 TGAAACCATTTGCAACTGTAAGC 58.633 39.130 14.83 3.73 37.60 3.09
3073 3281 5.244755 AGTTTTGAAACCATTTGCAACTGT 58.755 33.333 14.83 2.77 39.71 3.55
3074 3282 5.799681 AGTTTTGAAACCATTTGCAACTG 57.200 34.783 9.70 9.70 39.71 3.16
3083 3291 4.050553 CGCATGTGAAGTTTTGAAACCAT 58.949 39.130 0.00 0.00 39.71 3.55


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

AutoCloner maintained by Alex Coulton.