Multiple sequence alignment - TraesCS7A01G251100

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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 TraesCS7A01G251100 chr7A 100.000 3522 0 0 1 3522 234350966 234354487 0.000000e+00 6505.0
1 TraesCS7A01G251100 chr7A 81.319 91 10 7 3270 3359 35762541 35762625 2.270000e-07 67.6
2 TraesCS7A01G251100 chr7B 91.891 2602 147 31 1 2592 176360393 176357846 0.000000e+00 3578.0
3 TraesCS7A01G251100 chr7B 92.148 2076 109 24 1 2066 176400466 176398435 0.000000e+00 2881.0
4 TraesCS7A01G251100 chr7B 81.587 315 30 14 2582 2894 176357824 176357536 5.880000e-58 235.0
5 TraesCS7A01G251100 chr7B 84.328 134 19 2 273 405 176644090 176644222 2.850000e-26 130.0
6 TraesCS7A01G251100 chr7D 91.779 1861 92 31 1074 2922 223752054 223753865 0.000000e+00 2532.0
7 TraesCS7A01G251100 chr7D 91.954 1044 58 15 2 1030 223751030 223752062 0.000000e+00 1439.0
8 TraesCS7A01G251100 chr7D 86.894 557 53 15 2975 3522 223754018 223754563 1.080000e-169 606.0
9 TraesCS7A01G251100 chr7D 81.395 86 13 3 3197 3280 534649956 534649872 2.270000e-07 67.6
10 TraesCS7A01G251100 chr5D 88.596 114 11 2 307 420 547722232 547722121 1.710000e-28 137.0
11 TraesCS7A01G251100 chr5D 86.486 111 15 0 308 418 438974599 438974709 4.770000e-24 122.0
12 TraesCS7A01G251100 chr1B 86.607 112 15 0 309 420 646131535 646131424 1.330000e-24 124.0
13 TraesCS7A01G251100 chr1B 78.378 111 18 6 3271 3380 470962794 470962689 2.270000e-07 67.6
14 TraesCS7A01G251100 chr2A 85.470 117 17 0 305 421 630462535 630462419 4.770000e-24 122.0
15 TraesCS7A01G251100 chr2D 80.405 148 25 4 280 425 630180687 630180542 3.720000e-20 110.0
16 TraesCS7A01G251100 chr3B 80.741 135 21 5 3181 3311 826660187 826660320 2.240000e-17 100.0
17 TraesCS7A01G251100 chr2B 83.750 80 7 5 3284 3362 550217552 550217626 1.750000e-08 71.3
18 TraesCS7A01G251100 chr2B 80.723 83 9 7 3269 3348 246375525 246375447 1.370000e-04 58.4
19 TraesCS7A01G251100 chr6D 81.522 92 8 7 3270 3361 25719173 25719255 2.270000e-07 67.6
20 TraesCS7A01G251100 chr5B 83.784 74 9 3 3287 3359 546089776 546089847 2.270000e-07 67.6
21 TraesCS7A01G251100 chr3D 80.000 85 14 3 3184 3266 612299840 612299757 3.800000e-05 60.2
22 TraesCS7A01G251100 chr4B 83.582 67 6 4 3284 3349 634602333 634602395 1.370000e-04 58.4


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 TraesCS7A01G251100 chr7A 234350966 234354487 3521 False 6505.000000 6505 100.000 1 3522 1 chr7A.!!$F2 3521
1 TraesCS7A01G251100 chr7B 176398435 176400466 2031 True 2881.000000 2881 92.148 1 2066 1 chr7B.!!$R1 2065
2 TraesCS7A01G251100 chr7B 176357536 176360393 2857 True 1906.500000 3578 86.739 1 2894 2 chr7B.!!$R2 2893
3 TraesCS7A01G251100 chr7D 223751030 223754563 3533 False 1525.666667 2532 90.209 2 3522 3 chr7D.!!$F1 3520

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
28 29 0.172578 CGGTACTGAATGCGGTGAGA 59.827 55.0 0.0 0.0 34.79 3.27 F
581 585 0.179000 CAGTAGACCAGTCCATGCCC 59.821 60.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2026 2.950433 ACAATGCAGCAATGCTTGTAC 58.050 42.857 4.36 0.00 36.4 2.90 R
2540 2574 0.170561 ATCACTGGTCTCGTACGCAC 59.829 55.000 11.24 9.47 0.0 5.34 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
28 29 0.172578 CGGTACTGAATGCGGTGAGA 59.827 55.000 0.00 0.00 34.79 3.27
36 37 2.237143 TGAATGCGGTGAGAAGGAAGAT 59.763 45.455 0.00 0.00 0.00 2.40
62 64 4.917415 GGGTTCTGAATTCAATGTGAAACG 59.083 41.667 9.88 0.00 40.12 3.60
202 204 4.735132 CCGCTTTCGACCGAGCCA 62.735 66.667 8.53 0.00 38.10 4.75
262 264 3.733960 CACCGTCTCCGCTGTCGA 61.734 66.667 0.00 0.00 38.10 4.20
336 338 5.713792 TTTTGCCACTATCAAAATTCCGA 57.286 34.783 0.00 0.00 38.17 4.55
376 379 5.405873 CACGTTTTGTAAAGTGGTGGTTTTT 59.594 36.000 0.00 0.00 39.24 1.94
380 383 5.640189 TTGTAAAGTGGTGGTTTTTCGAA 57.360 34.783 0.00 0.00 0.00 3.71
383 386 4.794278 AAAGTGGTGGTTTTTCGAAAGT 57.206 36.364 10.98 0.00 0.00 2.66
391 394 6.039941 TGGTGGTTTTTCGAAAGTTATGACAT 59.960 34.615 10.98 0.00 0.00 3.06
420 423 4.992319 TGGTGGTTCTGTGTATTTTACTCG 59.008 41.667 0.00 0.00 0.00 4.18
443 447 8.624701 TCGATTTATTTTCTACGTACCTGAAG 57.375 34.615 0.00 0.00 0.00 3.02
463 467 7.442364 CCTGAAGTTCTGAAGATTTTACACTGA 59.558 37.037 11.06 0.00 0.00 3.41
523 527 4.437390 CGTAAATCTGTTCAGGGCATTGAC 60.437 45.833 0.00 0.00 0.00 3.18
581 585 0.179000 CAGTAGACCAGTCCATGCCC 59.821 60.000 0.00 0.00 0.00 5.36
610 614 4.025401 CACTGTTGTTCGGCCGCC 62.025 66.667 23.51 14.37 0.00 6.13
660 669 3.655276 TTGACCAAGAACTACTCCGTC 57.345 47.619 0.00 0.00 0.00 4.79
664 673 2.086869 CCAAGAACTACTCCGTCCGTA 58.913 52.381 0.00 0.00 0.00 4.02
843 853 2.398554 CCGCCCTTGTGAACCATCG 61.399 63.158 0.00 0.00 0.00 3.84
911 922 2.903350 TCGACGGGCGCTGCTATA 60.903 61.111 7.64 0.00 40.61 1.31
912 923 2.201436 CTCGACGGGCGCTGCTATAT 62.201 60.000 7.64 0.00 40.61 0.86
913 924 0.956902 TCGACGGGCGCTGCTATATA 60.957 55.000 7.64 0.00 40.61 0.86
914 925 0.797249 CGACGGGCGCTGCTATATAC 60.797 60.000 7.64 0.00 0.00 1.47
921 938 3.130516 GGGCGCTGCTATATACTACATGA 59.869 47.826 7.64 0.00 0.00 3.07
1035 1053 2.493973 CAGAGCTCGCTGGAGGAC 59.506 66.667 8.37 0.00 40.80 3.85
1041 1059 4.361971 TCGCTGGAGGACCCGTCT 62.362 66.667 0.00 0.00 37.93 4.18
1071 1089 4.873129 CCGACGTCCTGGCCATCG 62.873 72.222 16.94 16.94 0.00 3.84
1378 1396 3.589654 CTGGCCGTCTTCTTCCGCA 62.590 63.158 0.00 0.00 0.00 5.69
1765 1783 2.026301 CCGCCGACGAGATCTTCC 59.974 66.667 0.00 0.00 43.93 3.46
1767 1785 1.433879 CGCCGACGAGATCTTCCTT 59.566 57.895 0.00 0.00 43.93 3.36
1926 1944 3.766691 GCCAACTCCGGCGACCTA 61.767 66.667 9.30 0.00 43.52 3.08
1968 1995 1.795525 CGTGTGTCCATCAGCGAGTAG 60.796 57.143 0.00 0.00 0.00 2.57
1969 1996 1.202582 GTGTGTCCATCAGCGAGTAGT 59.797 52.381 0.00 0.00 0.00 2.73
1970 1997 2.422479 GTGTGTCCATCAGCGAGTAGTA 59.578 50.000 0.00 0.00 0.00 1.82
1971 1998 2.422479 TGTGTCCATCAGCGAGTAGTAC 59.578 50.000 0.00 0.00 0.00 2.73
1972 1999 2.683867 GTGTCCATCAGCGAGTAGTACT 59.316 50.000 1.37 1.37 0.00 2.73
1974 2001 2.291190 GTCCATCAGCGAGTAGTACTCC 59.709 54.545 21.92 15.24 42.12 3.85
1975 2002 2.172930 TCCATCAGCGAGTAGTACTCCT 59.827 50.000 21.92 16.95 42.12 3.69
1976 2003 3.390311 TCCATCAGCGAGTAGTACTCCTA 59.610 47.826 21.92 7.63 42.12 2.94
1977 2004 3.499157 CCATCAGCGAGTAGTACTCCTAC 59.501 52.174 21.92 12.99 42.12 3.18
1988 2015 4.891992 AGTACTCCTACATGCTTGTTGT 57.108 40.909 10.85 7.78 37.28 3.32
1989 2016 5.995565 AGTACTCCTACATGCTTGTTGTA 57.004 39.130 10.85 6.93 37.28 2.41
1990 2017 6.546428 AGTACTCCTACATGCTTGTTGTAT 57.454 37.500 10.85 0.00 37.28 2.29
1991 2018 7.655521 AGTACTCCTACATGCTTGTTGTATA 57.344 36.000 10.85 0.00 37.28 1.47
1992 2019 8.074613 AGTACTCCTACATGCTTGTTGTATAA 57.925 34.615 10.85 0.00 37.28 0.98
1993 2020 8.198109 AGTACTCCTACATGCTTGTTGTATAAG 58.802 37.037 10.85 1.07 37.28 1.73
1994 2021 6.947464 ACTCCTACATGCTTGTTGTATAAGT 58.053 36.000 10.85 6.71 37.28 2.24
1995 2022 8.074613 ACTCCTACATGCTTGTTGTATAAGTA 57.925 34.615 10.85 0.00 37.28 2.24
1996 2023 8.537016 ACTCCTACATGCTTGTTGTATAAGTAA 58.463 33.333 10.85 0.00 37.28 2.24
2099 2126 4.457496 ATCACGCACCGAGCCCAG 62.457 66.667 0.00 0.00 41.38 4.45
2380 2414 4.867608 ACAATTAAGTTTGTTGGTGTGTGC 59.132 37.500 5.32 0.00 36.43 4.57
2529 2563 5.613329 TGTAGTTCTCTCCTAGCTACTAGC 58.387 45.833 0.00 0.00 42.84 3.42
2540 2574 4.390603 CCTAGCTACTAGCACATCGACTAG 59.609 50.000 10.73 6.32 45.56 2.57
2652 2718 6.999871 TGCTTCCTGAATAATTATGCATCAGA 59.000 34.615 20.22 10.42 39.85 3.27
2671 2737 4.213270 TCAGATTCGCGTTTTGAGTTCATT 59.787 37.500 5.77 0.00 0.00 2.57
2674 2740 2.214347 TCGCGTTTTGAGTTCATTCCA 58.786 42.857 5.77 0.00 0.00 3.53
2679 2745 3.057315 CGTTTTGAGTTCATTCCATGCCT 60.057 43.478 0.00 0.00 0.00 4.75
2727 2793 6.509656 TGCATATCTTTTCATTGATGGAAGC 58.490 36.000 0.00 0.00 0.00 3.86
2731 2797 4.578871 TCTTTTCATTGATGGAAGCGAGA 58.421 39.130 0.00 0.00 0.00 4.04
2745 2813 6.873997 TGGAAGCGAGAGAATATGAGTAAAA 58.126 36.000 0.00 0.00 0.00 1.52
2767 2835 3.446310 AGTGATACAACACACGACACA 57.554 42.857 0.00 0.00 42.45 3.72
2770 2838 4.814234 AGTGATACAACACACGACACAAAT 59.186 37.500 0.00 0.00 42.45 2.32
2794 2862 1.108776 GGTGGCATGAACATGATGCT 58.891 50.000 17.40 0.00 44.75 3.79
2816 2884 1.292242 AGAGCAGAGGGTCAAGGGATA 59.708 52.381 0.00 0.00 43.97 2.59
2846 2914 4.201970 CCCAAACAACGAATACAACACACT 60.202 41.667 0.00 0.00 0.00 3.55
2855 2923 6.940714 ACGAATACAACACACTTAAACTCAC 58.059 36.000 0.00 0.00 0.00 3.51
2896 2964 8.504815 TCTAGCACTTTAGCTATATGTAAGTCG 58.495 37.037 5.04 3.71 45.32 4.18
2897 2965 7.040473 AGCACTTTAGCTATATGTAAGTCGT 57.960 36.000 5.04 0.00 44.50 4.34
2898 2966 6.918569 AGCACTTTAGCTATATGTAAGTCGTG 59.081 38.462 5.04 0.00 44.50 4.35
2900 2968 7.222224 GCACTTTAGCTATATGTAAGTCGTGTT 59.778 37.037 5.04 0.00 0.00 3.32
2906 2974 8.798748 AGCTATATGTAAGTCGTGTTAACATC 57.201 34.615 12.26 5.99 0.00 3.06
2910 2978 6.807708 ATGTAAGTCGTGTTAACATCGATC 57.192 37.500 25.17 20.07 34.14 3.69
2913 2981 5.763444 AAGTCGTGTTAACATCGATCTTG 57.237 39.130 25.17 0.00 34.14 3.02
2922 2990 3.438297 ACATCGATCTTGGGTAAGTCG 57.562 47.619 0.00 0.00 38.06 4.18
2923 2991 3.021695 ACATCGATCTTGGGTAAGTCGA 58.978 45.455 0.00 13.03 43.51 4.20
2924 2992 3.637229 ACATCGATCTTGGGTAAGTCGAT 59.363 43.478 15.18 15.18 46.10 3.59
2925 2993 4.099573 ACATCGATCTTGGGTAAGTCGATT 59.900 41.667 16.87 10.64 44.73 3.34
2926 2994 4.730949 TCGATCTTGGGTAAGTCGATTT 57.269 40.909 0.00 0.00 39.34 2.17
2928 2996 5.107133 TCGATCTTGGGTAAGTCGATTTTC 58.893 41.667 0.00 0.00 39.34 2.29
2929 2997 4.026804 CGATCTTGGGTAAGTCGATTTTCG 60.027 45.833 0.00 0.00 38.52 3.46
2930 2998 3.592059 TCTTGGGTAAGTCGATTTTCGG 58.408 45.455 0.00 0.00 35.13 4.30
2931 2999 1.729284 TGGGTAAGTCGATTTTCGGC 58.271 50.000 0.00 0.00 46.20 5.54
2941 3009 3.791353 GTCGATTTTCGGCCATTGATTTC 59.209 43.478 2.24 0.00 38.79 2.17
2942 3010 3.694072 TCGATTTTCGGCCATTGATTTCT 59.306 39.130 2.24 0.00 40.88 2.52
2943 3011 3.792956 CGATTTTCGGCCATTGATTTCTG 59.207 43.478 2.24 0.00 36.00 3.02
2944 3012 2.652941 TTTCGGCCATTGATTTCTGC 57.347 45.000 2.24 0.00 0.00 4.26
2946 3014 1.766494 TCGGCCATTGATTTCTGCAT 58.234 45.000 2.24 0.00 0.00 3.96
2947 3015 2.101783 TCGGCCATTGATTTCTGCATT 58.898 42.857 2.24 0.00 0.00 3.56
2949 3017 3.698539 TCGGCCATTGATTTCTGCATTAA 59.301 39.130 2.24 0.00 0.00 1.40
2951 3019 4.869297 CGGCCATTGATTTCTGCATTAAAA 59.131 37.500 2.24 0.00 0.00 1.52
2953 3021 6.037391 CGGCCATTGATTTCTGCATTAAAATT 59.963 34.615 2.24 0.00 0.00 1.82
2954 3022 7.412063 GGCCATTGATTTCTGCATTAAAATTC 58.588 34.615 0.00 0.00 0.00 2.17
2955 3023 7.121272 GCCATTGATTTCTGCATTAAAATTCG 58.879 34.615 0.00 0.00 0.00 3.34
2956 3024 7.201548 GCCATTGATTTCTGCATTAAAATTCGT 60.202 33.333 0.00 0.00 0.00 3.85
2957 3025 8.111836 CCATTGATTTCTGCATTAAAATTCGTG 58.888 33.333 0.00 0.00 0.00 4.35
2958 3026 6.630676 TGATTTCTGCATTAAAATTCGTGC 57.369 33.333 0.00 0.00 38.05 5.34
2960 3028 6.867816 TGATTTCTGCATTAAAATTCGTGCTT 59.132 30.769 0.00 0.00 38.37 3.91
2961 3029 7.384660 TGATTTCTGCATTAAAATTCGTGCTTT 59.615 29.630 0.00 0.00 38.37 3.51
2962 3030 7.475771 TTTCTGCATTAAAATTCGTGCTTTT 57.524 28.000 0.00 0.00 38.37 2.27
2963 3031 7.475771 TTCTGCATTAAAATTCGTGCTTTTT 57.524 28.000 0.00 0.00 38.37 1.94
2964 3032 7.104326 TCTGCATTAAAATTCGTGCTTTTTC 57.896 32.000 0.00 0.00 38.37 2.29
2965 3033 6.145371 TCTGCATTAAAATTCGTGCTTTTTCC 59.855 34.615 0.00 0.00 38.37 3.13
2966 3034 5.178438 TGCATTAAAATTCGTGCTTTTTCCC 59.822 36.000 0.00 0.00 38.37 3.97
2983 3151 6.896021 TTTTCCCACGGTAATGAATTGTTA 57.104 33.333 0.00 0.00 0.00 2.41
2984 3152 5.883503 TTCCCACGGTAATGAATTGTTAC 57.116 39.130 0.00 0.00 0.00 2.50
2988 3156 3.685756 CACGGTAATGAATTGTTACGGGT 59.314 43.478 15.92 9.41 36.96 5.28
3001 3169 4.208746 TGTTACGGGTTGGTTCTTTTGAT 58.791 39.130 0.00 0.00 0.00 2.57
3006 3174 3.067461 CGGGTTGGTTCTTTTGATTGACA 59.933 43.478 0.00 0.00 0.00 3.58
3018 3186 3.399440 TGATTGACAACCAATTTGGGC 57.601 42.857 19.39 6.64 45.00 5.36
3022 3190 1.337118 GACAACCAATTTGGGCCAGA 58.663 50.000 19.39 1.42 43.37 3.86
3032 3200 3.534357 TTTGGGCCAGACAATTCCTTA 57.466 42.857 6.23 0.00 0.00 2.69
3042 3210 4.276926 CAGACAATTCCTTAATGGGCTAGC 59.723 45.833 6.04 6.04 31.29 3.42
3044 3212 4.210331 ACAATTCCTTAATGGGCTAGCTG 58.790 43.478 15.72 2.37 36.20 4.24
3056 3224 1.598882 GCTAGCTGAAGCCCATTACC 58.401 55.000 7.70 0.00 43.38 2.85
3066 3234 2.045438 CCATTACCTGTGCGGCCA 60.045 61.111 2.24 0.00 35.61 5.36
3067 3235 2.114670 CCATTACCTGTGCGGCCAG 61.115 63.158 2.24 10.38 35.61 4.85
3078 3246 4.041762 CGGCCAGGCAAACCCCTA 62.042 66.667 15.19 0.00 36.11 3.53
3084 3252 1.216990 CAGGCAAACCCCTATCTCCT 58.783 55.000 0.00 0.00 36.11 3.69
3094 3262 7.323420 CAAACCCCTATCTCCTTTTGATTTTC 58.677 38.462 0.00 0.00 0.00 2.29
3097 3265 7.248976 ACCCCTATCTCCTTTTGATTTTCTTT 58.751 34.615 0.00 0.00 0.00 2.52
3098 3266 7.734865 ACCCCTATCTCCTTTTGATTTTCTTTT 59.265 33.333 0.00 0.00 0.00 2.27
3100 3268 8.253810 CCCTATCTCCTTTTGATTTTCTTTTCC 58.746 37.037 0.00 0.00 0.00 3.13
3143 3316 9.950496 TGCTCTTGATCTTTTCTTTATTAGTCT 57.050 29.630 0.00 0.00 0.00 3.24
3168 3341 5.606348 TTTGGGTATATTTGGGATGTTGC 57.394 39.130 0.00 0.00 0.00 4.17
3169 3342 3.218453 TGGGTATATTTGGGATGTTGCG 58.782 45.455 0.00 0.00 0.00 4.85
3254 3427 7.894376 ACAAATTAATGGAATTTCAGTGCAG 57.106 32.000 0.00 0.00 44.35 4.41
3267 3440 2.044551 TGCAGGGTTGTGTGCACA 60.045 55.556 17.42 17.42 44.70 4.57
3268 3441 1.455402 TGCAGGGTTGTGTGCACAT 60.455 52.632 24.69 1.98 44.70 3.21
3306 3479 7.784470 TTTAAAAGGTAATACCAATGCCACT 57.216 32.000 12.54 0.00 41.95 4.00
3308 3481 8.880991 TTAAAAGGTAATACCAATGCCACTAA 57.119 30.769 12.54 0.00 41.95 2.24
3310 3483 7.971368 AAAGGTAATACCAATGCCACTAATT 57.029 32.000 12.54 0.00 41.95 1.40
3311 3484 7.582667 AAGGTAATACCAATGCCACTAATTC 57.417 36.000 12.54 0.00 41.95 2.17
3312 3485 6.668645 AGGTAATACCAATGCCACTAATTCA 58.331 36.000 12.54 0.00 41.95 2.57
3313 3486 7.297614 AGGTAATACCAATGCCACTAATTCAT 58.702 34.615 12.54 0.00 41.95 2.57
3314 3487 7.231317 AGGTAATACCAATGCCACTAATTCATG 59.769 37.037 12.54 0.00 41.95 3.07
3335 3508 8.741101 TCATGTTGTTGCATATTAAACTTCAC 57.259 30.769 0.00 0.00 0.00 3.18
3460 3636 8.814038 ACCAATGCTAGTAATTCATTCTTTCT 57.186 30.769 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.172578 TCTCACCGCATTCAGTACCG 59.827 55.000 0.00 0.00 0.00 4.02
28 29 5.014544 TGAATTCAGAACCCTCATCTTCCTT 59.985 40.000 3.38 0.00 0.00 3.36
36 37 4.984295 TCACATTGAATTCAGAACCCTCA 58.016 39.130 8.41 0.00 0.00 3.86
62 64 4.832608 CGTAGCCCTGGCCGTTCC 62.833 72.222 4.13 0.00 43.17 3.62
278 280 4.988540 AGAAATGATCTCGTTTTGACGTGA 59.011 37.500 0.00 6.23 39.41 4.35
333 335 2.157668 GTGACACTTTGTACTGCATCGG 59.842 50.000 0.00 0.00 0.00 4.18
336 338 2.833794 ACGTGACACTTTGTACTGCAT 58.166 42.857 3.68 0.00 0.00 3.96
376 379 5.995282 ACCACTTTCATGTCATAACTTTCGA 59.005 36.000 0.00 0.00 0.00 3.71
380 383 5.385198 ACCACCACTTTCATGTCATAACTT 58.615 37.500 0.00 0.00 0.00 2.66
383 386 5.473162 CAGAACCACCACTTTCATGTCATAA 59.527 40.000 0.00 0.00 0.00 1.90
391 394 2.799126 ACACAGAACCACCACTTTCA 57.201 45.000 0.00 0.00 0.00 2.69
435 439 8.429641 AGTGTAAAATCTTCAGAACTTCAGGTA 58.570 33.333 0.00 0.00 0.00 3.08
485 489 5.287274 CAGATTTACGCAACAACAACAACAA 59.713 36.000 0.00 0.00 0.00 2.83
486 490 4.795795 CAGATTTACGCAACAACAACAACA 59.204 37.500 0.00 0.00 0.00 3.33
487 491 4.796312 ACAGATTTACGCAACAACAACAAC 59.204 37.500 0.00 0.00 0.00 3.32
488 492 4.987832 ACAGATTTACGCAACAACAACAA 58.012 34.783 0.00 0.00 0.00 2.83
489 493 4.624336 ACAGATTTACGCAACAACAACA 57.376 36.364 0.00 0.00 0.00 3.33
523 527 2.431419 AGCTCTGTCCATGTGATCTGAG 59.569 50.000 0.00 4.77 0.00 3.35
581 585 0.664761 CAACAGTGTTGGAGCACCTG 59.335 55.000 25.45 0.00 40.04 4.00
610 614 3.645975 GTGTCAACGTGTGGCGGG 61.646 66.667 0.00 0.00 46.52 6.13
611 615 2.177580 AAGTGTCAACGTGTGGCGG 61.178 57.895 0.00 0.00 46.52 6.13
613 617 0.027586 GTCAAGTGTCAACGTGTGGC 59.972 55.000 0.00 0.00 37.13 5.01
614 618 1.062002 GTGTCAAGTGTCAACGTGTGG 59.938 52.381 0.00 0.00 37.13 4.17
660 669 2.742372 GCCTGTGGCTGTGTACGG 60.742 66.667 0.73 0.00 46.69 4.02
843 853 3.462678 GGGAGGGGAGCTCGTGAC 61.463 72.222 7.83 0.00 0.00 3.67
911 922 1.366366 GGCCCGCGTCATGTAGTAT 59.634 57.895 4.92 0.00 0.00 2.12
912 923 1.605971 TTGGCCCGCGTCATGTAGTA 61.606 55.000 4.92 0.00 0.00 1.82
913 924 2.949909 TTGGCCCGCGTCATGTAGT 61.950 57.895 4.92 0.00 0.00 2.73
914 925 2.125310 TTGGCCCGCGTCATGTAG 60.125 61.111 4.92 0.00 0.00 2.74
937 955 0.248539 CGCTACTAACTCCGCTGACC 60.249 60.000 0.00 0.00 0.00 4.02
942 960 0.317687 GTAGGCGCTACTAACTCCGC 60.318 60.000 7.64 0.00 45.15 5.54
1053 1071 4.530857 GATGGCCAGGACGTCGGG 62.531 72.222 13.05 17.83 0.00 5.14
1242 1260 2.997315 CGGAGGGAGGCTGTGACA 60.997 66.667 0.00 0.00 0.00 3.58
1302 1320 4.025401 GTGGCCACGCGGTTGAAG 62.025 66.667 22.49 0.00 33.28 3.02
1765 1783 3.869272 GATGCGGCGGTGCTCAAG 61.869 66.667 9.78 0.00 35.36 3.02
1968 1995 7.980099 ACTTATACAACAAGCATGTAGGAGTAC 59.020 37.037 0.00 0.00 39.40 2.73
1969 1996 8.074613 ACTTATACAACAAGCATGTAGGAGTA 57.925 34.615 0.00 0.00 39.40 2.59
1970 1997 6.947464 ACTTATACAACAAGCATGTAGGAGT 58.053 36.000 0.00 0.81 39.40 3.85
1971 1998 8.942338 TTACTTATACAACAAGCATGTAGGAG 57.058 34.615 0.00 0.27 39.40 3.69
1988 2015 8.988934 GCAGCAATGCTTGTACTATTACTTATA 58.011 33.333 4.36 0.00 36.40 0.98
1989 2016 7.498900 TGCAGCAATGCTTGTACTATTACTTAT 59.501 33.333 4.36 0.00 36.40 1.73
1990 2017 6.821160 TGCAGCAATGCTTGTACTATTACTTA 59.179 34.615 4.36 0.00 36.40 2.24
1991 2018 5.647658 TGCAGCAATGCTTGTACTATTACTT 59.352 36.000 4.36 0.00 36.40 2.24
1992 2019 5.185454 TGCAGCAATGCTTGTACTATTACT 58.815 37.500 4.36 0.00 36.40 2.24
1993 2020 5.484173 TGCAGCAATGCTTGTACTATTAC 57.516 39.130 4.36 0.00 36.40 1.89
1994 2021 6.095300 ACAATGCAGCAATGCTTGTACTATTA 59.905 34.615 4.36 0.00 36.40 0.98
1995 2022 5.105635 ACAATGCAGCAATGCTTGTACTATT 60.106 36.000 4.36 0.00 36.40 1.73
1996 2023 4.400251 ACAATGCAGCAATGCTTGTACTAT 59.600 37.500 4.36 0.00 36.40 2.12
1999 2026 2.950433 ACAATGCAGCAATGCTTGTAC 58.050 42.857 4.36 0.00 36.40 2.90
2078 2105 2.125512 GCTCGGTGCGTGATCCTT 60.126 61.111 0.00 0.00 0.00 3.36
2357 2391 4.867608 GCACACACCAACAAACTTAATTGT 59.132 37.500 0.00 0.00 45.12 2.71
2358 2392 5.108517 AGCACACACCAACAAACTTAATTG 58.891 37.500 0.00 0.00 36.37 2.32
2359 2393 5.105554 TGAGCACACACCAACAAACTTAATT 60.106 36.000 0.00 0.00 0.00 1.40
2360 2394 4.400884 TGAGCACACACCAACAAACTTAAT 59.599 37.500 0.00 0.00 0.00 1.40
2361 2395 3.759086 TGAGCACACACCAACAAACTTAA 59.241 39.130 0.00 0.00 0.00 1.85
2362 2396 3.348119 TGAGCACACACCAACAAACTTA 58.652 40.909 0.00 0.00 0.00 2.24
2363 2397 2.164219 CTGAGCACACACCAACAAACTT 59.836 45.455 0.00 0.00 0.00 2.66
2364 2398 1.745087 CTGAGCACACACCAACAAACT 59.255 47.619 0.00 0.00 0.00 2.66
2365 2399 1.472480 ACTGAGCACACACCAACAAAC 59.528 47.619 0.00 0.00 0.00 2.93
2366 2400 1.472082 CACTGAGCACACACCAACAAA 59.528 47.619 0.00 0.00 0.00 2.83
2367 2401 1.093972 CACTGAGCACACACCAACAA 58.906 50.000 0.00 0.00 0.00 2.83
2368 2402 0.251634 TCACTGAGCACACACCAACA 59.748 50.000 0.00 0.00 0.00 3.33
2369 2403 0.657840 GTCACTGAGCACACACCAAC 59.342 55.000 0.00 0.00 0.00 3.77
2380 2414 0.388649 GCCACAGGTACGTCACTGAG 60.389 60.000 21.80 15.28 38.09 3.35
2529 2563 1.061566 TCGTACGCACTAGTCGATGTG 59.938 52.381 11.24 10.47 37.26 3.21
2540 2574 0.170561 ATCACTGGTCTCGTACGCAC 59.829 55.000 11.24 9.47 0.00 5.34
2644 2710 1.803555 TCAAAACGCGAATCTGATGCA 59.196 42.857 15.93 0.00 0.00 3.96
2652 2718 3.252215 TGGAATGAACTCAAAACGCGAAT 59.748 39.130 15.93 0.00 0.00 3.34
2690 2756 9.378551 TGAAAAGATATGCAGACTTTACGTATT 57.621 29.630 13.25 1.24 34.18 1.89
2691 2757 8.942338 TGAAAAGATATGCAGACTTTACGTAT 57.058 30.769 13.25 1.78 34.18 3.06
2692 2758 8.942338 ATGAAAAGATATGCAGACTTTACGTA 57.058 30.769 13.25 0.00 34.18 3.57
2700 2766 7.268199 TCCATCAATGAAAAGATATGCAGAC 57.732 36.000 0.00 0.00 0.00 3.51
2701 2767 7.469594 GCTTCCATCAATGAAAAGATATGCAGA 60.470 37.037 0.00 0.00 0.00 4.26
2706 2772 6.994496 TCTCGCTTCCATCAATGAAAAGATAT 59.006 34.615 7.34 0.00 0.00 1.63
2722 2788 7.772332 TTTTTACTCATATTCTCTCGCTTCC 57.228 36.000 0.00 0.00 0.00 3.46
2745 2813 4.185394 TGTGTCGTGTGTTGTATCACTTT 58.815 39.130 0.00 0.00 38.90 2.66
2747 2815 3.446310 TGTGTCGTGTGTTGTATCACT 57.554 42.857 0.00 0.00 38.90 3.41
2751 2819 5.743026 TTCATTTGTGTCGTGTGTTGTAT 57.257 34.783 0.00 0.00 0.00 2.29
2761 2829 1.336440 TGCCACCTTTCATTTGTGTCG 59.664 47.619 0.00 0.00 0.00 4.35
2767 2835 4.283978 TCATGTTCATGCCACCTTTCATTT 59.716 37.500 7.80 0.00 0.00 2.32
2770 2838 2.874014 TCATGTTCATGCCACCTTTCA 58.126 42.857 7.80 0.00 0.00 2.69
2794 2862 1.078823 TCCCTTGACCCTCTGCTCTAA 59.921 52.381 0.00 0.00 0.00 2.10
2816 2884 0.106918 TTCGTTGTTTGGGGCTGAGT 60.107 50.000 0.00 0.00 0.00 3.41
2846 2914 8.836413 AGAAATTTCAGACAATCGTGAGTTTAA 58.164 29.630 19.99 0.00 0.00 1.52
2855 2923 6.414408 AGTGCTAGAAATTTCAGACAATCG 57.586 37.500 19.99 0.00 0.00 3.34
2896 2964 5.873164 ACTTACCCAAGATCGATGTTAACAC 59.127 40.000 11.22 4.38 35.60 3.32
2897 2965 6.045072 ACTTACCCAAGATCGATGTTAACA 57.955 37.500 11.41 11.41 35.60 2.41
2898 2966 5.231568 CGACTTACCCAAGATCGATGTTAAC 59.768 44.000 7.56 0.00 37.42 2.01
2900 2968 4.641541 TCGACTTACCCAAGATCGATGTTA 59.358 41.667 7.56 0.00 38.35 2.41
2903 2971 3.710326 TCGACTTACCCAAGATCGATG 57.290 47.619 0.54 0.00 38.35 3.84
2906 2974 4.026804 CGAAAATCGACTTACCCAAGATCG 60.027 45.833 0.00 0.00 43.74 3.69
2910 2978 2.095372 GCCGAAAATCGACTTACCCAAG 59.905 50.000 0.58 0.00 43.74 3.61
2913 2981 1.012086 GGCCGAAAATCGACTTACCC 58.988 55.000 0.58 0.00 43.74 3.69
2922 2990 3.553105 GCAGAAATCAATGGCCGAAAATC 59.447 43.478 0.00 0.00 0.00 2.17
2923 2991 3.055963 TGCAGAAATCAATGGCCGAAAAT 60.056 39.130 0.00 0.00 0.00 1.82
2924 2992 2.298446 TGCAGAAATCAATGGCCGAAAA 59.702 40.909 0.00 0.00 0.00 2.29
2925 2993 1.891811 TGCAGAAATCAATGGCCGAAA 59.108 42.857 0.00 0.00 0.00 3.46
2926 2994 1.543607 TGCAGAAATCAATGGCCGAA 58.456 45.000 0.00 0.00 0.00 4.30
2928 2996 2.589798 AATGCAGAAATCAATGGCCG 57.410 45.000 0.00 0.00 0.00 6.13
2929 2997 6.930667 ATTTTAATGCAGAAATCAATGGCC 57.069 33.333 0.00 0.00 0.00 5.36
2930 2998 7.121272 CGAATTTTAATGCAGAAATCAATGGC 58.879 34.615 0.00 0.00 0.00 4.40
2931 2999 8.111836 CACGAATTTTAATGCAGAAATCAATGG 58.888 33.333 0.00 0.00 0.00 3.16
2933 3001 7.546667 AGCACGAATTTTAATGCAGAAATCAAT 59.453 29.630 0.00 0.00 40.63 2.57
2934 3002 6.867816 AGCACGAATTTTAATGCAGAAATCAA 59.132 30.769 0.00 0.00 40.63 2.57
2935 3003 6.389091 AGCACGAATTTTAATGCAGAAATCA 58.611 32.000 0.00 0.00 40.63 2.57
2936 3004 6.875926 AGCACGAATTTTAATGCAGAAATC 57.124 33.333 0.00 0.00 40.63 2.17
2937 3005 7.656707 AAAGCACGAATTTTAATGCAGAAAT 57.343 28.000 0.00 0.00 40.63 2.17
2941 3009 6.298853 GGAAAAAGCACGAATTTTAATGCAG 58.701 36.000 0.00 0.00 40.63 4.41
2942 3010 5.178438 GGGAAAAAGCACGAATTTTAATGCA 59.822 36.000 0.00 0.00 40.63 3.96
2943 3011 5.178438 TGGGAAAAAGCACGAATTTTAATGC 59.822 36.000 0.00 0.00 38.39 3.56
2944 3012 6.589454 GTGGGAAAAAGCACGAATTTTAATG 58.411 36.000 0.00 0.00 29.93 1.90
2946 3014 4.740695 CGTGGGAAAAAGCACGAATTTTAA 59.259 37.500 0.00 0.00 42.84 1.52
2947 3015 4.291783 CGTGGGAAAAAGCACGAATTTTA 58.708 39.130 0.00 0.00 42.84 1.52
2949 3017 2.544903 CCGTGGGAAAAAGCACGAATTT 60.545 45.455 0.00 0.00 42.84 1.82
2951 3019 0.596082 CCGTGGGAAAAAGCACGAAT 59.404 50.000 0.00 0.00 42.84 3.34
2953 3021 0.106335 TACCGTGGGAAAAAGCACGA 59.894 50.000 0.00 0.00 42.84 4.35
2954 3022 0.945813 TTACCGTGGGAAAAAGCACG 59.054 50.000 0.00 0.00 40.30 5.34
2955 3023 2.554893 TCATTACCGTGGGAAAAAGCAC 59.445 45.455 0.00 0.00 0.00 4.40
2956 3024 2.865079 TCATTACCGTGGGAAAAAGCA 58.135 42.857 0.00 0.00 0.00 3.91
2957 3025 3.926821 TTCATTACCGTGGGAAAAAGC 57.073 42.857 0.00 0.00 0.00 3.51
2958 3026 5.778862 ACAATTCATTACCGTGGGAAAAAG 58.221 37.500 0.00 0.00 0.00 2.27
2960 3028 5.793030 AACAATTCATTACCGTGGGAAAA 57.207 34.783 0.00 0.00 0.00 2.29
2961 3029 5.106634 CGTAACAATTCATTACCGTGGGAAA 60.107 40.000 0.00 0.00 30.16 3.13
2962 3030 4.392445 CGTAACAATTCATTACCGTGGGAA 59.608 41.667 4.33 0.00 30.16 3.97
2963 3031 3.933955 CGTAACAATTCATTACCGTGGGA 59.066 43.478 4.33 0.00 30.16 4.37
2964 3032 3.064271 CCGTAACAATTCATTACCGTGGG 59.936 47.826 4.33 0.00 30.16 4.61
2965 3033 3.064271 CCCGTAACAATTCATTACCGTGG 59.936 47.826 4.33 0.00 30.16 4.94
2966 3034 3.685756 ACCCGTAACAATTCATTACCGTG 59.314 43.478 4.33 0.00 30.16 4.94
2969 3137 4.460034 ACCAACCCGTAACAATTCATTACC 59.540 41.667 4.33 0.00 30.16 2.85
2972 3140 4.830600 AGAACCAACCCGTAACAATTCATT 59.169 37.500 0.00 0.00 0.00 2.57
2973 3141 4.403734 AGAACCAACCCGTAACAATTCAT 58.596 39.130 0.00 0.00 0.00 2.57
2983 3151 3.067601 GTCAATCAAAAGAACCAACCCGT 59.932 43.478 0.00 0.00 0.00 5.28
2984 3152 3.067461 TGTCAATCAAAAGAACCAACCCG 59.933 43.478 0.00 0.00 0.00 5.28
2988 3156 5.667539 TGGTTGTCAATCAAAAGAACCAA 57.332 34.783 0.00 0.00 43.48 3.67
3001 3169 1.415659 CTGGCCCAAATTGGTTGTCAA 59.584 47.619 11.52 0.00 40.01 3.18
3006 3174 1.799933 TTGTCTGGCCCAAATTGGTT 58.200 45.000 11.52 0.00 35.17 3.67
3018 3186 3.635591 AGCCCATTAAGGAATTGTCTGG 58.364 45.455 0.00 0.00 41.22 3.86
3022 3190 4.079787 TCAGCTAGCCCATTAAGGAATTGT 60.080 41.667 12.13 0.00 41.22 2.71
3056 3224 4.347453 GTTTGCCTGGCCGCACAG 62.347 66.667 17.53 0.00 38.83 3.66
3066 3234 1.987080 AAGGAGATAGGGGTTTGCCT 58.013 50.000 0.00 0.00 34.45 4.75
3067 3235 2.760650 CAAAAGGAGATAGGGGTTTGCC 59.239 50.000 0.00 0.00 0.00 4.52
3070 3238 7.248976 AGAAAATCAAAAGGAGATAGGGGTTT 58.751 34.615 0.00 0.00 0.00 3.27
3144 3317 6.410540 GCAACATCCCAAATATACCCAAAAA 58.589 36.000 0.00 0.00 0.00 1.94
3228 3401 9.590451 CTGCACTGAAATTCCATTAATTTGTAT 57.410 29.630 0.71 0.00 45.70 2.29
3231 3404 6.314400 CCCTGCACTGAAATTCCATTAATTTG 59.686 38.462 0.71 0.00 45.70 2.32
3235 3408 4.415596 ACCCTGCACTGAAATTCCATTAA 58.584 39.130 0.00 0.00 0.00 1.40
3238 3411 2.564062 CAACCCTGCACTGAAATTCCAT 59.436 45.455 0.00 0.00 0.00 3.41
3241 3414 2.362077 ACACAACCCTGCACTGAAATTC 59.638 45.455 0.00 0.00 0.00 2.17
3280 3453 8.821817 AGTGGCATTGGTATTACCTTTTAAAAT 58.178 29.630 13.90 1.83 39.58 1.82
3290 3463 7.940850 ACATGAATTAGTGGCATTGGTATTAC 58.059 34.615 0.00 0.00 0.00 1.89
3302 3475 9.800433 TTAATATGCAACAACATGAATTAGTGG 57.200 29.630 0.00 0.00 0.00 4.00
3308 3481 9.926158 TGAAGTTTAATATGCAACAACATGAAT 57.074 25.926 0.00 0.00 0.00 2.57
3310 3483 8.575589 AGTGAAGTTTAATATGCAACAACATGA 58.424 29.630 0.00 0.00 0.00 3.07
3311 3484 8.746922 AGTGAAGTTTAATATGCAACAACATG 57.253 30.769 0.00 0.00 0.00 3.21
3370 3546 8.237811 ACAAACAATCACCAAATTAGAGAAGT 57.762 30.769 0.00 0.00 0.00 3.01
3450 3626 8.980481 AGTGAAGTTTCCTAAAGAAAGAATGA 57.020 30.769 0.00 0.00 45.11 2.57


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

AutoCloner maintained by Alex Coulton.