Multiple sequence alignment - TraesCS5B01G389200

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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 TraesCS5B01G389200 chr5B 100.000 3902 0 0 1 3902 568400644 568404545 0.000000e+00 7206.0
1 TraesCS5B01G389200 chr5B 96.345 684 25 0 2 685 356687774 356688457 0.000000e+00 1125.0
2 TraesCS5B01G389200 chr5B 96.302 676 24 1 1 675 463915857 463916532 0.000000e+00 1109.0
3 TraesCS5B01G389200 chr5B 98.333 60 1 0 3004 3063 568403590 568403649 5.330000e-19 106.0
4 TraesCS5B01G389200 chr5B 98.333 60 1 0 2947 3006 568403647 568403706 5.330000e-19 106.0
5 TraesCS5B01G389200 chr5B 95.000 40 2 0 3217 3256 568403819 568403858 3.250000e-06 63.9
6 TraesCS5B01G389200 chr5B 95.000 40 2 0 3176 3215 568403860 568403899 3.250000e-06 63.9
7 TraesCS5B01G389200 chr5D 95.321 2351 87 6 676 3005 462073972 462076320 0.000000e+00 3711.0
8 TraesCS5B01G389200 chr5D 94.131 903 33 5 3004 3902 462076262 462077148 0.000000e+00 1356.0
9 TraesCS5B01G389200 chr5D 81.818 99 13 4 3433 3529 255076534 255076439 1.160000e-10 78.7
10 TraesCS5B01G389200 chr5D 95.000 40 2 0 3217 3256 462076434 462076473 3.250000e-06 63.9
11 TraesCS5B01G389200 chr5A 94.079 2280 101 9 751 2997 582381352 582383630 0.000000e+00 3432.0
12 TraesCS5B01G389200 chr5A 93.148 540 25 3 3224 3756 582383761 582384295 0.000000e+00 782.0
13 TraesCS5B01G389200 chr5A 87.324 213 25 1 3004 3214 582383580 582383792 3.900000e-60 243.0
14 TraesCS5B01G389200 chr5A 95.270 148 7 0 3755 3902 582384400 582384547 6.520000e-58 235.0
15 TraesCS5B01G389200 chr5A 89.655 58 6 0 3592 3649 141880995 141881052 1.500000e-09 75.0
16 TraesCS5B01G389200 chr5A 80.808 99 14 4 3433 3529 338287883 338287788 5.410000e-09 73.1
17 TraesCS5B01G389200 chr5A 89.474 57 6 0 3591 3647 667304819 667304875 5.410000e-09 73.1
18 TraesCS5B01G389200 chr3B 96.736 674 21 1 2 675 702701854 702702526 0.000000e+00 1122.0
19 TraesCS5B01G389200 chr7B 96.439 674 24 0 1 674 4594931 4595604 0.000000e+00 1112.0
20 TraesCS5B01G389200 chr7B 96.307 677 24 1 1 676 712852729 712853405 0.000000e+00 1110.0
21 TraesCS5B01G389200 chr4B 96.439 674 24 0 1 674 7828024 7827351 0.000000e+00 1112.0
22 TraesCS5B01G389200 chr4B 96.307 677 24 1 1 676 436250764 436251440 0.000000e+00 1110.0
23 TraesCS5B01G389200 chr4B 95.894 682 28 0 1 682 67922887 67923568 0.000000e+00 1105.0
24 TraesCS5B01G389200 chr4B 95.369 691 30 2 1 689 659332758 659333448 0.000000e+00 1098.0
25 TraesCS5B01G389200 chr4B 80.576 139 17 9 3432 3565 100314579 100314712 8.920000e-17 99.0
26 TraesCS5B01G389200 chr7D 88.053 226 18 4 804 1020 21085044 21084819 3.870000e-65 259.0
27 TraesCS5B01G389200 chr7D 92.308 130 7 1 681 807 21085284 21085155 8.610000e-42 182.0
28 TraesCS5B01G389200 chr7D 80.255 157 27 3 3433 3589 175652628 175652476 8.860000e-22 115.0
29 TraesCS5B01G389200 chr7A 79.618 157 28 3 3433 3589 177333680 177333528 4.120000e-20 110.0
30 TraesCS5B01G389200 chr4D 87.000 100 9 3 3442 3540 486932213 486932117 4.120000e-20 110.0
31 TraesCS5B01G389200 chr4D 81.746 126 14 8 3432 3552 67791793 67791914 3.210000e-16 97.1
32 TraesCS5B01G389200 chr4D 94.545 55 3 0 3593 3647 486932157 486932211 6.950000e-13 86.1
33 TraesCS5B01G389200 chr1B 95.000 60 3 0 3591 3650 565664621 565664562 1.150000e-15 95.3
34 TraesCS5B01G389200 chr2D 93.333 60 4 0 3591 3650 394525140 394525199 5.370000e-14 89.8
35 TraesCS5B01G389200 chr2B 93.333 60 4 0 3591 3650 466165248 466165307 5.370000e-14 89.8
36 TraesCS5B01G389200 chr4A 89.062 64 6 1 3587 3650 501972654 501972592 1.160000e-10 78.7


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 TraesCS5B01G389200 chr5B 568400644 568404545 3901 False 1509.16 7206 97.333200 1 3902 5 chr5B.!!$F3 3901
1 TraesCS5B01G389200 chr5B 356687774 356688457 683 False 1125.00 1125 96.345000 2 685 1 chr5B.!!$F1 683
2 TraesCS5B01G389200 chr5B 463915857 463916532 675 False 1109.00 1109 96.302000 1 675 1 chr5B.!!$F2 674
3 TraesCS5B01G389200 chr5D 462073972 462077148 3176 False 1710.30 3711 94.817333 676 3902 3 chr5D.!!$F1 3226
4 TraesCS5B01G389200 chr5A 582381352 582384547 3195 False 1173.00 3432 92.455250 751 3902 4 chr5A.!!$F3 3151
5 TraesCS5B01G389200 chr3B 702701854 702702526 672 False 1122.00 1122 96.736000 2 675 1 chr3B.!!$F1 673
6 TraesCS5B01G389200 chr7B 4594931 4595604 673 False 1112.00 1112 96.439000 1 674 1 chr7B.!!$F1 673
7 TraesCS5B01G389200 chr7B 712852729 712853405 676 False 1110.00 1110 96.307000 1 676 1 chr7B.!!$F2 675
8 TraesCS5B01G389200 chr4B 7827351 7828024 673 True 1112.00 1112 96.439000 1 674 1 chr4B.!!$R1 673
9 TraesCS5B01G389200 chr4B 436250764 436251440 676 False 1110.00 1110 96.307000 1 676 1 chr4B.!!$F3 675
10 TraesCS5B01G389200 chr4B 67922887 67923568 681 False 1105.00 1105 95.894000 1 682 1 chr4B.!!$F1 681
11 TraesCS5B01G389200 chr4B 659332758 659333448 690 False 1098.00 1098 95.369000 1 689 1 chr4B.!!$F4 688

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
738 739 0.164002 GCGCTCGAGTCTTTGGTTTC 59.836 55.0 15.13 0.0 0.0 2.78 F
1469 1497 0.106708 TGACCTCTTGCTTTGCGTCT 59.893 50.0 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2013 0.030235 TCATCGTATCACGGGCTTCG 59.970 55.0 0.0 0.0 42.81 3.79 R
3050 3086 0.032952 TCTGGTCGTCTTTTCCGGTG 59.967 55.0 0.0 0.0 0.00 4.94 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
130 131 2.107204 AGTCTGTTCAAGCAAGGATGGT 59.893 45.455 0.00 0.00 39.43 3.55
286 287 1.691976 TCTGGAAGACGGAACATGTGT 59.308 47.619 0.00 0.00 38.67 3.72
429 430 1.272490 GGTAAGGGCTTCACTTTTGGC 59.728 52.381 0.00 0.00 0.00 4.52
528 529 1.346395 TCTTTTCTTCGGTGGCTGCTA 59.654 47.619 0.00 0.00 0.00 3.49
556 557 2.063979 CGGAGGTAGGTGATGGGCA 61.064 63.158 0.00 0.00 0.00 5.36
738 739 0.164002 GCGCTCGAGTCTTTGGTTTC 59.836 55.000 15.13 0.00 0.00 2.78
749 750 3.020984 TCTTTGGTTTCCTCGCAAAACT 58.979 40.909 6.95 0.00 36.93 2.66
847 862 1.457643 CTGTCCCCCATCGCCTCTA 60.458 63.158 0.00 0.00 0.00 2.43
960 978 1.004440 GCAGTCCACCAGAGACCAC 60.004 63.158 0.00 0.00 34.67 4.16
1067 1092 2.106683 GCCGACGGTGGATCTTTGG 61.107 63.158 16.73 0.00 0.00 3.28
1077 1102 1.074405 TGGATCTTTGGCTGCTCTTGT 59.926 47.619 0.00 0.00 0.00 3.16
1122 1150 2.103042 GCTCGACGAATTGCCTGCT 61.103 57.895 0.00 0.00 0.00 4.24
1200 1228 2.821366 CTGTGCTCCGGCCACATC 60.821 66.667 22.49 6.18 37.74 3.06
1280 1308 0.608308 GGAACCCAAAGAAGGACGGG 60.608 60.000 0.00 0.00 44.88 5.28
1327 1355 1.328680 CGAATTTGTGCTCCCGATCAG 59.671 52.381 0.00 0.00 0.00 2.90
1331 1359 1.899437 TTGTGCTCCCGATCAGGTCC 61.899 60.000 0.00 0.00 38.74 4.46
1332 1360 2.038813 TGCTCCCGATCAGGTCCA 59.961 61.111 0.00 0.00 38.74 4.02
1349 1377 1.295423 CAATCCCGTGGAGGAACGT 59.705 57.895 0.00 0.00 45.00 3.99
1351 1379 1.138266 CAATCCCGTGGAGGAACGTAT 59.862 52.381 0.00 0.00 45.00 3.06
1380 1408 1.607756 AGCTCCAAGCCTCTGTCGA 60.608 57.895 0.00 0.00 43.77 4.20
1469 1497 0.106708 TGACCTCTTGCTTTGCGTCT 59.893 50.000 0.00 0.00 0.00 4.18
1556 1584 0.328258 TCCTAAGGAGGTTTGGCAGC 59.672 55.000 0.00 0.00 44.19 5.25
1790 1818 0.687354 GGTGGACCGATGCCATAGAT 59.313 55.000 0.00 0.00 37.81 1.98
1895 1923 2.049063 GTGAAGCGTGCGAGAGGT 60.049 61.111 0.00 0.00 0.00 3.85
1985 2013 0.659957 GCAAGGCGAGGATGATGAAC 59.340 55.000 0.00 0.00 0.00 3.18
2226 2254 6.575244 TGGATATATTTGACAAGGTGAGGT 57.425 37.500 0.00 0.00 0.00 3.85
2228 2256 5.239525 GGATATATTTGACAAGGTGAGGTGC 59.760 44.000 0.00 0.00 0.00 5.01
2234 2262 1.003355 CAAGGTGAGGTGCGATGGT 60.003 57.895 0.00 0.00 0.00 3.55
2270 2298 5.348164 GCTTCCTTCTACAACTCTCTCATC 58.652 45.833 0.00 0.00 0.00 2.92
2280 2308 8.487028 TCTACAACTCTCTCATCTACATACTCA 58.513 37.037 0.00 0.00 0.00 3.41
2555 2583 5.707298 CCACATGTTTAGAAAGGACATCACT 59.293 40.000 0.00 0.00 32.01 3.41
2690 2718 5.811399 AAGAAACGTTTGATCTTGTGACA 57.189 34.783 20.10 0.00 32.42 3.58
2846 2882 1.594862 CTGTCAAGCGCTTATGGCTAC 59.405 52.381 24.55 13.88 40.53 3.58
2987 3023 9.261180 TGTTGCTCTGCTACATTTAACTATATC 57.739 33.333 3.03 0.00 39.07 1.63
2997 3033 5.235616 ACATTTAACTATATCCGCAACACCG 59.764 40.000 0.00 0.00 0.00 4.94
3005 3041 4.914291 CGCAACACCGGAAAAGAC 57.086 55.556 9.46 0.00 0.00 3.01
3006 3042 1.281656 CGCAACACCGGAAAAGACC 59.718 57.895 9.46 0.00 0.00 3.85
3007 3043 1.164041 CGCAACACCGGAAAAGACCT 61.164 55.000 9.46 0.00 0.00 3.85
3008 3044 0.310854 GCAACACCGGAAAAGACCTG 59.689 55.000 9.46 0.00 0.00 4.00
3009 3045 1.675552 CAACACCGGAAAAGACCTGT 58.324 50.000 9.46 0.00 0.00 4.00
3010 3046 2.021457 CAACACCGGAAAAGACCTGTT 58.979 47.619 9.46 2.04 31.52 3.16
3011 3047 3.207778 CAACACCGGAAAAGACCTGTTA 58.792 45.455 9.46 0.00 30.69 2.41
3012 3048 2.842457 ACACCGGAAAAGACCTGTTAC 58.158 47.619 9.46 0.00 0.00 2.50
3013 3049 2.171027 ACACCGGAAAAGACCTGTTACA 59.829 45.455 9.46 0.00 0.00 2.41
3014 3050 3.207778 CACCGGAAAAGACCTGTTACAA 58.792 45.455 9.46 0.00 0.00 2.41
3015 3051 3.818773 CACCGGAAAAGACCTGTTACAAT 59.181 43.478 9.46 0.00 0.00 2.71
3016 3052 4.277423 CACCGGAAAAGACCTGTTACAATT 59.723 41.667 9.46 0.00 0.00 2.32
3017 3053 4.517832 ACCGGAAAAGACCTGTTACAATTC 59.482 41.667 9.46 0.00 0.00 2.17
3018 3054 4.760204 CCGGAAAAGACCTGTTACAATTCT 59.240 41.667 0.00 0.00 0.00 2.40
3019 3055 5.334879 CCGGAAAAGACCTGTTACAATTCTG 60.335 44.000 0.00 0.00 0.00 3.02
3020 3056 5.238650 CGGAAAAGACCTGTTACAATTCTGT 59.761 40.000 0.00 0.00 39.75 3.41
3021 3057 6.238648 CGGAAAAGACCTGTTACAATTCTGTT 60.239 38.462 0.00 0.00 36.96 3.16
3022 3058 6.918022 GGAAAAGACCTGTTACAATTCTGTTG 59.082 38.462 3.76 0.00 36.96 3.33
3023 3059 5.438761 AAGACCTGTTACAATTCTGTTGC 57.561 39.130 0.00 0.00 36.96 4.17
3024 3060 4.718961 AGACCTGTTACAATTCTGTTGCT 58.281 39.130 0.00 0.00 36.96 3.91
3025 3061 4.757149 AGACCTGTTACAATTCTGTTGCTC 59.243 41.667 0.00 0.00 36.96 4.26
3026 3062 4.718961 ACCTGTTACAATTCTGTTGCTCT 58.281 39.130 0.00 0.00 36.96 4.09
3027 3063 4.516698 ACCTGTTACAATTCTGTTGCTCTG 59.483 41.667 0.00 0.00 36.96 3.35
3028 3064 4.470462 CTGTTACAATTCTGTTGCTCTGC 58.530 43.478 0.00 0.00 36.96 4.26
3029 3065 4.136796 TGTTACAATTCTGTTGCTCTGCT 58.863 39.130 0.00 0.00 36.96 4.24
3030 3066 5.304778 TGTTACAATTCTGTTGCTCTGCTA 58.695 37.500 0.00 0.00 36.96 3.49
3031 3067 5.179368 TGTTACAATTCTGTTGCTCTGCTAC 59.821 40.000 0.00 0.00 36.96 3.58
3032 3068 3.743521 ACAATTCTGTTGCTCTGCTACA 58.256 40.909 6.65 6.65 41.31 2.74
3033 3069 4.330250 ACAATTCTGTTGCTCTGCTACAT 58.670 39.130 7.20 0.00 42.40 2.29
3034 3070 4.763793 ACAATTCTGTTGCTCTGCTACATT 59.236 37.500 7.20 0.00 42.40 2.71
3035 3071 5.242393 ACAATTCTGTTGCTCTGCTACATTT 59.758 36.000 7.20 1.07 42.40 2.32
3036 3072 6.430925 ACAATTCTGTTGCTCTGCTACATTTA 59.569 34.615 7.20 0.00 42.40 1.40
3037 3073 7.040478 ACAATTCTGTTGCTCTGCTACATTTAA 60.040 33.333 7.20 4.11 42.40 1.52
3038 3074 5.862924 TCTGTTGCTCTGCTACATTTAAC 57.137 39.130 7.20 0.00 42.40 2.01
3039 3075 5.551233 TCTGTTGCTCTGCTACATTTAACT 58.449 37.500 7.20 0.00 42.40 2.24
3040 3076 6.697395 TCTGTTGCTCTGCTACATTTAACTA 58.303 36.000 7.20 0.00 42.40 2.24
3041 3077 7.331026 TCTGTTGCTCTGCTACATTTAACTAT 58.669 34.615 7.20 0.00 42.40 2.12
3042 3078 8.474831 TCTGTTGCTCTGCTACATTTAACTATA 58.525 33.333 7.20 0.00 42.40 1.31
3043 3079 9.265901 CTGTTGCTCTGCTACATTTAACTATAT 57.734 33.333 7.20 0.00 42.40 0.86
3044 3080 9.261180 TGTTGCTCTGCTACATTTAACTATATC 57.739 33.333 3.03 0.00 39.07 1.63
3045 3081 8.713271 GTTGCTCTGCTACATTTAACTATATCC 58.287 37.037 0.00 0.00 34.70 2.59
3046 3082 7.090808 TGCTCTGCTACATTTAACTATATCCG 58.909 38.462 0.00 0.00 0.00 4.18
3047 3083 6.035112 GCTCTGCTACATTTAACTATATCCGC 59.965 42.308 0.00 0.00 0.00 5.54
3048 3084 6.988522 TCTGCTACATTTAACTATATCCGCA 58.011 36.000 0.00 0.00 0.00 5.69
3049 3085 7.438564 TCTGCTACATTTAACTATATCCGCAA 58.561 34.615 0.00 0.00 0.00 4.85
3050 3086 7.384115 TCTGCTACATTTAACTATATCCGCAAC 59.616 37.037 0.00 0.00 0.00 4.17
3051 3087 6.987404 TGCTACATTTAACTATATCCGCAACA 59.013 34.615 0.00 0.00 0.00 3.33
3052 3088 7.042321 TGCTACATTTAACTATATCCGCAACAC 60.042 37.037 0.00 0.00 0.00 3.32
3053 3089 6.613755 ACATTTAACTATATCCGCAACACC 57.386 37.500 0.00 0.00 0.00 4.16
3054 3090 5.235616 ACATTTAACTATATCCGCAACACCG 59.764 40.000 0.00 0.00 0.00 4.94
3062 3098 4.914291 CGCAACACCGGAAAAGAC 57.086 55.556 9.46 0.00 0.00 3.01
3085 3121 4.434520 GACCAGAAGTTCCATAGCAGTAC 58.565 47.826 0.00 0.00 0.00 2.73
3108 3144 3.244770 GGACATTGGTCAAGTCCCTTACA 60.245 47.826 15.24 0.00 46.17 2.41
3250 3286 6.545504 AGCATATATAAACAGTTTCCTGCG 57.454 37.500 0.48 0.00 42.81 5.18
3255 3291 1.507141 AAACAGTTTCCTGCGAGCCG 61.507 55.000 0.00 0.00 42.81 5.52
3343 3379 7.225784 TCACAAAATCAGCAGCCTTATTTAA 57.774 32.000 0.00 0.00 27.74 1.52
3350 3386 1.957177 GCAGCCTTATTTAAGCTCCCC 59.043 52.381 0.00 0.00 32.02 4.81
3418 3455 4.685169 AGAGTTACACGCATGGAAATTG 57.315 40.909 0.00 0.00 27.33 2.32
3428 3465 2.599973 GCATGGAAATTGTCGTCATTGC 59.400 45.455 0.00 0.00 0.00 3.56
3439 3476 3.386402 TGTCGTCATTGCATATACTCCCA 59.614 43.478 0.00 0.00 0.00 4.37
3483 3520 7.454225 AGTTCTAGCTTTGTCCTAAGTCAAAT 58.546 34.615 0.00 0.00 31.96 2.32
3647 3686 9.914131 AAGCTAGAACTTCAAATAATTTGGAAC 57.086 29.630 0.00 0.00 40.98 3.62
3652 3691 6.642707 ACTTCAAATAATTTGGAACGGTGA 57.357 33.333 0.00 0.00 40.98 4.02
3690 3729 1.251251 GTTCTTCATGCCTGCACCTT 58.749 50.000 0.00 0.00 0.00 3.50
3691 3730 1.068055 GTTCTTCATGCCTGCACCTTG 60.068 52.381 0.00 0.00 0.00 3.61
3694 3733 0.467844 TTCATGCCTGCACCTTGTGT 60.468 50.000 0.00 0.00 35.75 3.72
3711 3750 9.959749 CACCTTGTGTTTTTACTTGTAATGTAT 57.040 29.630 0.00 0.00 0.00 2.29
3773 3925 8.484214 AAGAGCTAGTACAAATCTGATGGATA 57.516 34.615 0.00 0.00 33.71 2.59
3857 4009 3.129638 GCGAGTCCAAGTAGATCTTCTGT 59.870 47.826 0.00 0.00 33.63 3.41
3888 4040 1.063912 TCATTTTATCGCTGCTTGCCG 59.936 47.619 0.00 0.00 38.78 5.69
3894 4046 4.170062 CGCTGCTTGCCGGTGATG 62.170 66.667 1.90 0.00 38.78 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
286 287 1.524165 CCACGAACCACGAACCCAA 60.524 57.895 0.00 0.00 45.77 4.12
528 529 2.363276 TACCTCCGGCACCACGAT 60.363 61.111 0.00 0.00 35.47 3.73
544 545 0.998928 ACACCAATGCCCATCACCTA 59.001 50.000 0.00 0.00 0.00 3.08
556 557 3.008813 ACATCTCTGAGCTTGACACCAAT 59.991 43.478 12.47 0.00 0.00 3.16
700 701 5.783111 AGCGCCAAAATTTACTCAAAGATT 58.217 33.333 2.29 0.00 0.00 2.40
701 702 5.391312 AGCGCCAAAATTTACTCAAAGAT 57.609 34.783 2.29 0.00 0.00 2.40
738 739 2.604614 CCCGAAGAAAAGTTTTGCGAGG 60.605 50.000 5.36 4.33 0.00 4.63
749 750 3.830755 AGTACTAGAGCACCCGAAGAAAA 59.169 43.478 0.00 0.00 0.00 2.29
823 838 4.176752 GATGGGGGACAGGGCGAC 62.177 72.222 0.00 0.00 0.00 5.19
830 845 1.457643 CTAGAGGCGATGGGGGACA 60.458 63.158 0.00 0.00 0.00 4.02
843 858 1.367102 GCTGGGCTGCTAGCTAGAG 59.633 63.158 25.15 17.95 41.99 2.43
847 862 3.324930 TGTGCTGGGCTGCTAGCT 61.325 61.111 17.23 0.00 41.99 3.32
946 964 0.105709 TGTGAGTGGTCTCTGGTGGA 60.106 55.000 0.00 0.00 40.98 4.02
1038 1063 4.564116 CGTCGGCGCTAATCGGGT 62.564 66.667 7.64 0.00 38.94 5.28
1040 1065 4.564116 ACCGTCGGCGCTAATCGG 62.564 66.667 23.29 23.29 45.53 4.18
1059 1084 1.471684 CCACAAGAGCAGCCAAAGATC 59.528 52.381 0.00 0.00 0.00 2.75
1060 1085 1.542492 CCACAAGAGCAGCCAAAGAT 58.458 50.000 0.00 0.00 0.00 2.40
1063 1088 1.455402 TGCCACAAGAGCAGCCAAA 60.455 52.632 0.00 0.00 34.69 3.28
1095 1123 0.603569 ATTCGTCGAGCACCTTGTCT 59.396 50.000 0.00 0.00 0.00 3.41
1280 1308 4.133078 GGTCATCATCATCAAAGGAGTCC 58.867 47.826 0.00 0.00 0.00 3.85
1327 1355 1.559065 TTCCTCCACGGGATTGGACC 61.559 60.000 0.00 0.00 41.00 4.46
1331 1359 0.533491 TACGTTCCTCCACGGGATTG 59.467 55.000 0.00 0.00 44.82 2.67
1332 1360 1.411612 GATACGTTCCTCCACGGGATT 59.588 52.381 0.00 0.00 44.82 3.01
1469 1497 1.152631 TATCACGATGGCCTCCGGA 60.153 57.895 18.70 2.93 0.00 5.14
1556 1584 3.039202 GAACGCAGCCACCCAATCG 62.039 63.158 0.00 0.00 0.00 3.34
1568 1596 1.801771 CACATAAAGAACCCGAACGCA 59.198 47.619 0.00 0.00 0.00 5.24
1712 1740 2.904866 GCCAGCGACACCAAACCA 60.905 61.111 0.00 0.00 0.00 3.67
1790 1818 1.339610 CGGTCCATTTTGTTGAAGGCA 59.660 47.619 0.00 0.00 0.00 4.75
1895 1923 0.250295 CCCTCAACTCTTGGAACGCA 60.250 55.000 0.00 0.00 0.00 5.24
1985 2013 0.030235 TCATCGTATCACGGGCTTCG 59.970 55.000 0.00 0.00 42.81 3.79
2226 2254 4.277009 TGGGGCACAACCATCGCA 62.277 61.111 0.00 0.00 42.05 5.10
2228 2256 2.040544 GTCTGGGGCACAACCATCG 61.041 63.158 0.00 0.00 42.05 3.84
2234 2262 2.281484 GAAGCGTCTGGGGCACAA 60.281 61.111 0.00 0.00 0.00 3.33
2270 2298 2.035704 CCCTGCTCTGCTGAGTATGTAG 59.964 54.545 20.24 11.38 42.13 2.74
2280 2308 1.988956 CCAGTCTCCCTGCTCTGCT 60.989 63.158 0.00 0.00 40.06 4.24
2313 2341 2.623416 TGCTGGACATCTTATCGACGAT 59.377 45.455 15.74 15.74 0.00 3.73
2555 2583 4.298626 AGGTATAGGTGCTGAAATCAGGA 58.701 43.478 12.09 6.54 43.94 3.86
2690 2718 3.895232 TTCGCCTTATCAAGCTTCTCT 57.105 42.857 0.00 0.00 0.00 3.10
2839 2875 2.463752 TGTCCTAAGGTTCGTAGCCAT 58.536 47.619 0.00 0.00 0.00 4.40
2846 2882 3.343941 TCCCATTTGTCCTAAGGTTCG 57.656 47.619 0.00 0.00 0.00 3.95
2900 2936 4.127171 CCATTTCGATGAACGGATAGGTT 58.873 43.478 0.00 0.00 42.82 3.50
2987 3023 1.281656 GTCTTTTCCGGTGTTGCGG 59.718 57.895 0.00 0.00 0.00 5.69
2997 3033 6.635030 ACAGAATTGTAACAGGTCTTTTCC 57.365 37.500 0.00 0.00 35.25 3.13
2998 3034 6.417930 GCAACAGAATTGTAACAGGTCTTTTC 59.582 38.462 0.00 0.00 36.23 2.29
3001 3037 5.133221 AGCAACAGAATTGTAACAGGTCTT 58.867 37.500 0.00 0.00 36.23 3.01
3002 3038 4.718961 AGCAACAGAATTGTAACAGGTCT 58.281 39.130 0.00 0.00 36.23 3.85
3003 3039 4.757149 AGAGCAACAGAATTGTAACAGGTC 59.243 41.667 0.00 0.00 36.23 3.85
3004 3040 4.516698 CAGAGCAACAGAATTGTAACAGGT 59.483 41.667 0.00 0.00 36.23 4.00
3005 3041 4.614535 GCAGAGCAACAGAATTGTAACAGG 60.615 45.833 0.00 0.00 36.23 4.00
3006 3042 4.214971 AGCAGAGCAACAGAATTGTAACAG 59.785 41.667 0.00 0.00 36.23 3.16
3007 3043 4.136796 AGCAGAGCAACAGAATTGTAACA 58.863 39.130 0.00 0.00 36.23 2.41
3008 3044 4.756084 AGCAGAGCAACAGAATTGTAAC 57.244 40.909 0.00 0.00 36.23 2.50
3009 3045 5.304778 TGTAGCAGAGCAACAGAATTGTAA 58.695 37.500 0.00 0.00 36.23 2.41
3010 3046 4.893608 TGTAGCAGAGCAACAGAATTGTA 58.106 39.130 0.00 0.00 36.23 2.41
3011 3047 3.743521 TGTAGCAGAGCAACAGAATTGT 58.256 40.909 0.00 0.00 39.87 2.71
3012 3048 4.959596 ATGTAGCAGAGCAACAGAATTG 57.040 40.909 0.00 0.00 0.00 2.32
3013 3049 5.972107 AAATGTAGCAGAGCAACAGAATT 57.028 34.783 0.00 0.00 0.00 2.17
3014 3050 6.656693 AGTTAAATGTAGCAGAGCAACAGAAT 59.343 34.615 0.00 0.00 0.00 2.40
3015 3051 5.997746 AGTTAAATGTAGCAGAGCAACAGAA 59.002 36.000 0.00 0.00 0.00 3.02
3016 3052 5.551233 AGTTAAATGTAGCAGAGCAACAGA 58.449 37.500 0.00 0.00 0.00 3.41
3017 3053 5.869753 AGTTAAATGTAGCAGAGCAACAG 57.130 39.130 0.00 0.00 0.00 3.16
3018 3054 9.261180 GATATAGTTAAATGTAGCAGAGCAACA 57.739 33.333 0.00 0.00 0.00 3.33
3019 3055 8.713271 GGATATAGTTAAATGTAGCAGAGCAAC 58.287 37.037 0.00 0.00 0.00 4.17
3020 3056 7.598869 CGGATATAGTTAAATGTAGCAGAGCAA 59.401 37.037 0.00 0.00 0.00 3.91
3021 3057 7.090808 CGGATATAGTTAAATGTAGCAGAGCA 58.909 38.462 0.00 0.00 0.00 4.26
3022 3058 6.035112 GCGGATATAGTTAAATGTAGCAGAGC 59.965 42.308 0.00 0.00 0.00 4.09
3023 3059 7.090808 TGCGGATATAGTTAAATGTAGCAGAG 58.909 38.462 0.00 0.00 0.00 3.35
3024 3060 6.988522 TGCGGATATAGTTAAATGTAGCAGA 58.011 36.000 0.00 0.00 0.00 4.26
3025 3061 7.170828 TGTTGCGGATATAGTTAAATGTAGCAG 59.829 37.037 0.00 0.00 0.00 4.24
3026 3062 6.987404 TGTTGCGGATATAGTTAAATGTAGCA 59.013 34.615 0.00 0.00 0.00 3.49
3027 3063 7.288672 GTGTTGCGGATATAGTTAAATGTAGC 58.711 38.462 0.00 0.00 0.00 3.58
3028 3064 7.358931 CGGTGTTGCGGATATAGTTAAATGTAG 60.359 40.741 0.00 0.00 0.00 2.74
3029 3065 6.421501 CGGTGTTGCGGATATAGTTAAATGTA 59.578 38.462 0.00 0.00 0.00 2.29
3030 3066 5.235616 CGGTGTTGCGGATATAGTTAAATGT 59.764 40.000 0.00 0.00 0.00 2.71
3031 3067 5.333798 CCGGTGTTGCGGATATAGTTAAATG 60.334 44.000 0.00 0.00 0.00 2.32
3032 3068 4.753107 CCGGTGTTGCGGATATAGTTAAAT 59.247 41.667 0.00 0.00 0.00 1.40
3033 3069 4.121317 CCGGTGTTGCGGATATAGTTAAA 58.879 43.478 0.00 0.00 0.00 1.52
3034 3070 3.384146 TCCGGTGTTGCGGATATAGTTAA 59.616 43.478 0.00 0.00 0.00 2.01
3035 3071 2.957680 TCCGGTGTTGCGGATATAGTTA 59.042 45.455 0.00 0.00 0.00 2.24
3036 3072 1.758280 TCCGGTGTTGCGGATATAGTT 59.242 47.619 0.00 0.00 0.00 2.24
3037 3073 1.405872 TCCGGTGTTGCGGATATAGT 58.594 50.000 0.00 0.00 0.00 2.12
3038 3074 2.519377 TTCCGGTGTTGCGGATATAG 57.481 50.000 0.00 0.00 33.97 1.31
3039 3075 2.983907 TTTCCGGTGTTGCGGATATA 57.016 45.000 0.00 0.00 33.97 0.86
3040 3076 2.014128 CTTTTCCGGTGTTGCGGATAT 58.986 47.619 0.00 0.00 33.97 1.63
3041 3077 1.002201 TCTTTTCCGGTGTTGCGGATA 59.998 47.619 0.00 0.00 33.97 2.59
3042 3078 0.250553 TCTTTTCCGGTGTTGCGGAT 60.251 50.000 0.00 0.00 33.97 4.18
3043 3079 1.146485 TCTTTTCCGGTGTTGCGGA 59.854 52.632 0.00 0.00 0.00 5.54
3044 3080 1.281656 GTCTTTTCCGGTGTTGCGG 59.718 57.895 0.00 0.00 0.00 5.69
3045 3081 1.083015 CGTCTTTTCCGGTGTTGCG 60.083 57.895 0.00 0.00 0.00 4.85
3046 3082 0.041576 GTCGTCTTTTCCGGTGTTGC 60.042 55.000 0.00 0.00 0.00 4.17
3047 3083 0.584876 GGTCGTCTTTTCCGGTGTTG 59.415 55.000 0.00 0.00 0.00 3.33
3048 3084 0.178533 TGGTCGTCTTTTCCGGTGTT 59.821 50.000 0.00 0.00 0.00 3.32
3049 3085 0.249741 CTGGTCGTCTTTTCCGGTGT 60.250 55.000 0.00 0.00 0.00 4.16
3050 3086 0.032952 TCTGGTCGTCTTTTCCGGTG 59.967 55.000 0.00 0.00 0.00 4.94
3051 3087 0.754472 TTCTGGTCGTCTTTTCCGGT 59.246 50.000 0.00 0.00 0.00 5.28
3052 3088 1.270147 ACTTCTGGTCGTCTTTTCCGG 60.270 52.381 0.00 0.00 0.00 5.14
3053 3089 2.150397 ACTTCTGGTCGTCTTTTCCG 57.850 50.000 0.00 0.00 0.00 4.30
3054 3090 2.806818 GGAACTTCTGGTCGTCTTTTCC 59.193 50.000 0.00 0.00 0.00 3.13
3062 3098 2.093973 ACTGCTATGGAACTTCTGGTCG 60.094 50.000 0.00 0.00 0.00 4.79
3104 3140 4.947388 AGGAATAAAATCGGCAGCTTGTAA 59.053 37.500 0.00 0.00 0.00 2.41
3108 3144 5.047377 TGAAAAGGAATAAAATCGGCAGCTT 60.047 36.000 0.00 0.00 0.00 3.74
3250 3286 1.000506 TGAACAACCTCTGTACGGCTC 59.999 52.381 0.00 0.00 37.23 4.70
3255 3291 5.440685 CATTTTCGTGAACAACCTCTGTAC 58.559 41.667 0.00 0.00 37.23 2.90
3343 3379 2.279173 ACTGTTGGAAATAGGGGAGCT 58.721 47.619 0.00 0.00 39.63 4.09
3350 3386 5.687285 GTGTTTGCTCAACTGTTGGAAATAG 59.313 40.000 19.55 10.60 41.28 1.73
3418 3455 3.741344 GTGGGAGTATATGCAATGACGAC 59.259 47.826 0.00 0.00 0.00 4.34
3428 3465 8.884124 ATAATTTGGAATGGTGGGAGTATATG 57.116 34.615 0.00 0.00 0.00 1.78
3493 3530 8.006741 CACATTTTGCTTTAGACATGGTAAAC 57.993 34.615 0.00 0.00 0.00 2.01
3647 3686 4.418013 TTTGTCATATTGCAGTTCACCG 57.582 40.909 0.00 0.00 0.00 4.94
3652 3691 6.594788 AGAACCATTTGTCATATTGCAGTT 57.405 33.333 0.00 0.00 0.00 3.16
3773 3925 7.226441 TGTGGCAGCACATAATATTATTCTCT 58.774 34.615 5.18 0.76 0.00 3.10
3857 4009 3.435327 GCGATAAAATGACACCTGTGTGA 59.565 43.478 7.81 0.00 45.76 3.58


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

AutoCloner maintained by Alex Coulton.