Multiple sequence alignment - TraesCS3B01G139600

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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 TraesCS3B01G139600 chr3B 100.000 3675 0 0 1 3675 126003375 125999701 0.000000e+00 6787.0
1 TraesCS3B01G139600 chr3D 93.665 2731 119 28 12 2728 79632800 79630110 0.000000e+00 4036.0
2 TraesCS3B01G139600 chr3D 88.403 457 37 9 3191 3635 79629651 79629199 1.500000e-148 536.0
3 TraesCS3B01G139600 chr3D 94.169 343 19 1 2727 3068 79630061 79629719 4.210000e-144 521.0
4 TraesCS3B01G139600 chr3A 95.567 1737 67 5 1 1735 93897113 93895385 0.000000e+00 2772.0
5 TraesCS3B01G139600 chr3A 95.960 990 36 3 1733 2718 93895293 93894304 0.000000e+00 1604.0
6 TraesCS3B01G139600 chr3A 93.913 345 19 2 2723 3066 93894255 93893912 1.510000e-143 520.0
7 TraesCS3B01G139600 chr3A 82.237 456 40 16 3110 3555 93893912 93893488 4.510000e-94 355.0
8 TraesCS3B01G139600 chr3A 100.000 37 0 0 2984 3020 695753415 695753379 6.590000e-08 69.4
9 TraesCS3B01G139600 chr7A 83.784 222 30 5 3143 3360 136848442 136848661 4.810000e-49 206.0
10 TraesCS3B01G139600 chr6B 80.335 239 36 8 3135 3363 32704503 32704266 1.750000e-38 171.0
11 TraesCS3B01G139600 chr6B 86.916 107 14 0 1855 1961 653883209 653883103 1.790000e-23 121.0
12 TraesCS3B01G139600 chr1D 73.263 475 105 19 1863 2328 116548643 116549104 1.770000e-33 154.0
13 TraesCS3B01G139600 chr1A 73.150 473 109 17 1863 2328 127759795 127760256 1.770000e-33 154.0
14 TraesCS3B01G139600 chr6A 88.889 108 10 2 1855 1961 579146956 579146850 8.280000e-27 132.0
15 TraesCS3B01G139600 chr6A 79.137 139 14 11 3547 3675 574693115 574692982 8.460000e-12 82.4
16 TraesCS3B01G139600 chr6D 87.850 107 13 0 1855 1961 433286375 433286269 3.850000e-25 126.0
17 TraesCS3B01G139600 chr6D 86.486 111 15 0 1855 1965 433164237 433164127 4.980000e-24 122.0
18 TraesCS3B01G139600 chr6D 74.439 223 41 11 3151 3363 388533943 388534159 8.460000e-12 82.4
19 TraesCS3B01G139600 chr2D 76.543 243 41 11 3135 3365 428709916 428710154 6.450000e-23 119.0
20 TraesCS3B01G139600 chr7B 75.833 240 45 11 3135 3363 659714436 659714199 3.880000e-20 110.0
21 TraesCS3B01G139600 chr7B 75.104 241 44 12 3135 3363 662669203 662668967 8.400000e-17 99.0
22 TraesCS3B01G139600 chr5B 75.610 246 43 13 3131 3363 91204341 91204582 5.020000e-19 106.0
23 TraesCS3B01G139600 chr2B 75.417 240 45 9 3135 3363 273870006 273869770 1.810000e-18 104.0
24 TraesCS3B01G139600 chr5D 79.720 143 23 4 3225 3363 469071214 469071354 8.400000e-17 99.0
25 TraesCS3B01G139600 chr5A 78.322 143 25 4 3225 3363 589232069 589232209 1.820000e-13 87.9


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 TraesCS3B01G139600 chr3B 125999701 126003375 3674 True 6787.000000 6787 100.00000 1 3675 1 chr3B.!!$R1 3674
1 TraesCS3B01G139600 chr3D 79629199 79632800 3601 True 1697.666667 4036 92.07900 12 3635 3 chr3D.!!$R1 3623
2 TraesCS3B01G139600 chr3A 93893488 93897113 3625 True 1312.750000 2772 91.91925 1 3555 4 chr3A.!!$R2 3554

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
224 227 0.321564 CGGACAGCCAGGTGAATTGA 60.322 55.0 3.46 0.00 0.00 2.57 F
1071 1075 0.179111 GGAATGATCTGACGTCGCCA 60.179 55.0 11.62 6.28 0.00 5.69 F
2006 2109 0.754472 ACGTTCCTTTCACCTCGGAA 59.246 50.0 0.00 0.00 34.61 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2085 0.818040 AGGTGAAAGGAACGTGCCAC 60.818 55.0 16.99 3.43 0.0 5.01 R
2638 2742 0.602905 CGTCGCCTCTTTCCCTGTTT 60.603 55.0 0.00 0.00 0.0 2.83 R
3583 3750 0.104882 TGTGGTTCAGGTGGGGTCTA 60.105 55.0 0.00 0.00 0.0 2.59 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
20 21 1.599797 CCTCCGAGTTTGCCGGTTT 60.600 57.895 1.90 0.00 46.53 3.27
40 41 1.734388 GCGTTCAGGGTTTGCTGGTT 61.734 55.000 0.00 0.00 0.00 3.67
50 52 3.501950 GGTTTGCTGGTTCGATTGAATC 58.498 45.455 0.00 0.00 36.29 2.52
63 65 3.426859 CGATTGAATCGCTGTGATCTACC 59.573 47.826 15.04 0.00 46.55 3.18
66 68 0.389391 AATCGCTGTGATCTACCGGG 59.611 55.000 6.32 0.00 35.84 5.73
86 89 3.243401 GGGTTGATCTTGTGGTTGTGTTC 60.243 47.826 0.00 0.00 0.00 3.18
91 94 1.680735 TCTTGTGGTTGTGTTCATGCC 59.319 47.619 0.00 0.00 0.00 4.40
100 103 4.104776 GTTGTGTTCATGCCGAATATTGG 58.895 43.478 0.00 0.00 35.63 3.16
104 107 5.126869 TGTGTTCATGCCGAATATTGGATTT 59.873 36.000 0.00 0.00 35.63 2.17
105 108 6.042143 GTGTTCATGCCGAATATTGGATTTT 58.958 36.000 0.00 0.00 35.63 1.82
138 141 2.019984 GTTGGGTTGAGATGGATGCTC 58.980 52.381 0.00 0.00 0.00 4.26
142 145 2.570135 GGTTGAGATGGATGCTCCTTC 58.430 52.381 8.93 8.93 40.06 3.46
148 151 4.888326 AGATGGATGCTCCTTCTATGAC 57.112 45.455 14.75 0.00 45.77 3.06
182 185 1.272212 CGTTGGATTTGGTTTCCCTGG 59.728 52.381 0.00 0.00 31.87 4.45
184 187 2.008242 TGGATTTGGTTTCCCTGGTG 57.992 50.000 0.00 0.00 31.87 4.17
206 209 1.280886 GCTGCTCTCCATGCGTATCG 61.281 60.000 0.00 0.00 0.00 2.92
210 213 0.668535 CTCTCCATGCGTATCGGACA 59.331 55.000 1.64 0.00 0.00 4.02
220 223 0.535335 GTATCGGACAGCCAGGTGAA 59.465 55.000 3.46 0.00 0.00 3.18
224 227 0.321564 CGGACAGCCAGGTGAATTGA 60.322 55.000 3.46 0.00 0.00 2.57
244 247 1.017387 GGGAATGGTGAGCGTTGATC 58.983 55.000 0.00 0.00 0.00 2.92
304 307 4.155826 TCCTCCGTTTTCATTGTAATGCTG 59.844 41.667 0.00 0.00 36.36 4.41
322 325 5.710513 TGCTGATTTGAGCTAAATGTGTT 57.289 34.783 6.06 0.00 39.06 3.32
327 330 3.536158 TTGAGCTAAATGTGTTGACGC 57.464 42.857 0.00 0.00 0.00 5.19
399 402 4.638865 GGGTTGGTAGATGTTACATTGGAC 59.361 45.833 0.00 0.00 0.00 4.02
540 543 1.350684 TGGTCAAGCTGTAGGATTGCA 59.649 47.619 0.00 0.00 40.70 4.08
544 547 3.944015 GTCAAGCTGTAGGATTGCAGAAT 59.056 43.478 0.00 0.00 40.70 2.40
547 550 4.760530 AGCTGTAGGATTGCAGAATACA 57.239 40.909 0.00 0.00 39.14 2.29
675 678 5.126067 TCTTTCATAAAGTCAGGCTATGGC 58.874 41.667 0.00 0.00 39.52 4.40
704 707 5.580691 CCTTCAAGTGCAATCGTGTCTATTA 59.419 40.000 0.00 0.00 0.00 0.98
751 755 8.082242 ACAAAGGCTTTCATAATTTAGTGACAC 58.918 33.333 10.08 0.00 0.00 3.67
928 932 0.606401 TGTCAAGCTAAGGTGCTGGC 60.606 55.000 0.00 0.00 43.24 4.85
956 960 1.376037 AGTTTACAGCCGCTCCTGC 60.376 57.895 0.00 0.00 36.29 4.85
1064 1068 4.747108 CGACATACCAAGGAATGATCTGAC 59.253 45.833 0.00 0.00 0.00 3.51
1071 1075 0.179111 GGAATGATCTGACGTCGCCA 60.179 55.000 11.62 6.28 0.00 5.69
1350 1354 3.190849 CATCCACGCGCTCCACTG 61.191 66.667 5.73 0.00 0.00 3.66
1504 1508 3.942829 TCCGAGTCTGATTCTTTTGCAT 58.057 40.909 0.00 0.00 0.00 3.96
1518 1522 5.785243 TCTTTTGCATCAATTTCATCTGCA 58.215 33.333 0.00 0.00 40.79 4.41
1650 1654 1.070134 CTTCGACTGAACCACCTCCAA 59.930 52.381 0.00 0.00 0.00 3.53
1724 1728 7.974504 AGAGTAAACATTAGGTCTTTCAGGAA 58.025 34.615 0.00 0.00 0.00 3.36
1781 1879 3.058293 TGGATGAGATGCAACGTTTTGAC 60.058 43.478 0.00 0.00 34.24 3.18
1982 2085 1.960763 TGTTGCTAGGTGCTGTGCG 60.961 57.895 0.00 0.00 43.37 5.34
1985 2088 3.121030 GCTAGGTGCTGTGCGTGG 61.121 66.667 0.00 0.00 38.95 4.94
2006 2109 0.754472 ACGTTCCTTTCACCTCGGAA 59.246 50.000 0.00 0.00 34.61 4.30
2022 2126 4.275936 CCTCGGAATACCTTGCTTATTTGG 59.724 45.833 0.00 0.00 0.00 3.28
2029 2133 8.474831 GGAATACCTTGCTTATTTGGTTGTAAT 58.525 33.333 0.00 0.00 34.33 1.89
2283 2387 2.276740 GGGGTTCTGGCATCTGGG 59.723 66.667 0.00 0.00 0.00 4.45
2346 2450 1.623163 TCCCACCCGTTTTCCATTTC 58.377 50.000 0.00 0.00 0.00 2.17
2393 2497 3.119424 TGCTCATGCATACACATTTGTGG 60.119 43.478 14.71 0.00 46.28 4.17
2395 2499 6.692286 GCTCATGCATACACATTTGTGGCA 62.692 45.833 14.71 13.82 45.60 4.92
2420 2524 1.756375 CGCGATTAGCTGACACCTGC 61.756 60.000 0.00 0.00 45.59 4.85
2458 2562 3.485394 TCAGGTTTGCTGCATCTGTTTA 58.515 40.909 19.85 6.20 0.00 2.01
2470 2574 5.559770 TGCATCTGTTTATCAAGGTTCTCA 58.440 37.500 0.00 0.00 0.00 3.27
2521 2625 1.021390 GGCACGTCTTCCACATGGAG 61.021 60.000 0.00 0.00 46.36 3.86
2563 2667 4.626081 AACGCGCTGTGCCCTCTT 62.626 61.111 5.73 0.00 42.08 2.85
2638 2742 1.686052 GGCCAACACCAACAGAATGAA 59.314 47.619 0.00 0.00 39.69 2.57
2648 2752 4.714308 ACCAACAGAATGAAAACAGGGAAA 59.286 37.500 0.00 0.00 39.69 3.13
2718 2826 0.251653 GCATGGGCATGAGGATGGAT 60.252 55.000 0.00 0.00 41.20 3.41
2719 2827 1.545841 CATGGGCATGAGGATGGATG 58.454 55.000 0.00 0.00 41.20 3.51
2720 2828 0.408309 ATGGGCATGAGGATGGATGG 59.592 55.000 0.00 0.00 0.00 3.51
2721 2829 0.698542 TGGGCATGAGGATGGATGGA 60.699 55.000 0.00 0.00 0.00 3.41
2722 2830 0.479815 GGGCATGAGGATGGATGGAA 59.520 55.000 0.00 0.00 0.00 3.53
2815 2969 3.515502 TCACACCTGCTTAGCTAGTGATT 59.484 43.478 25.53 8.63 36.38 2.57
2848 3002 2.314246 TGTCAAATGTGGCATTCACCA 58.686 42.857 0.00 0.00 45.48 4.17
2867 3021 2.233271 CAGAAACAGTGGTTGGAGCAT 58.767 47.619 0.00 0.00 37.30 3.79
2877 3031 2.299582 TGGTTGGAGCATTGGAATTGTG 59.700 45.455 0.00 0.00 0.00 3.33
2947 3101 5.293814 CAGAAAGCTCATGATCCTGTAACTG 59.706 44.000 0.00 1.72 0.00 3.16
2956 3110 7.512130 TCATGATCCTGTAACTGATTAATGCT 58.488 34.615 0.00 0.00 0.00 3.79
2981 3136 3.442273 ACTTGAGTCCATTCGAGAGTCTC 59.558 47.826 10.33 10.33 35.19 3.36
3026 3182 8.451908 ACTTTGTATTACTCAAATATCTGGGC 57.548 34.615 0.00 0.00 34.88 5.36
3076 3232 5.042463 CCACATCTGGTCTAGAGTCTAGA 57.958 47.826 23.38 23.38 39.20 2.43
3077 3233 4.819630 CCACATCTGGTCTAGAGTCTAGAC 59.180 50.000 36.94 36.94 42.28 2.59
3087 3243 6.186234 GTCTAGAGTCTAGACCCTAACCAAA 58.814 44.000 35.69 10.05 38.33 3.28
3088 3244 6.095300 GTCTAGAGTCTAGACCCTAACCAAAC 59.905 46.154 35.69 16.61 38.33 2.93
3089 3245 4.748701 AGAGTCTAGACCCTAACCAAACA 58.251 43.478 19.38 0.00 0.00 2.83
3090 3246 4.527427 AGAGTCTAGACCCTAACCAAACAC 59.473 45.833 19.38 0.00 0.00 3.32
3091 3247 4.228824 AGTCTAGACCCTAACCAAACACA 58.771 43.478 19.38 0.00 0.00 3.72
3092 3248 4.844655 AGTCTAGACCCTAACCAAACACAT 59.155 41.667 19.38 0.00 0.00 3.21
3093 3249 5.046520 AGTCTAGACCCTAACCAAACACATC 60.047 44.000 19.38 0.00 0.00 3.06
3094 3250 5.046520 GTCTAGACCCTAACCAAACACATCT 60.047 44.000 12.13 0.00 0.00 2.90
3096 3252 3.081804 GACCCTAACCAAACACATCTGG 58.918 50.000 0.00 0.00 38.77 3.86
3099 3255 3.244911 CCCTAACCAAACACATCTGGTCT 60.245 47.826 0.00 0.00 45.39 3.85
3100 3256 4.019681 CCCTAACCAAACACATCTGGTCTA 60.020 45.833 0.00 0.00 45.39 2.59
3104 3260 4.505039 AACCAAACACATCTGGTCTAGACC 60.505 45.833 31.61 31.61 45.39 3.85
3137 3293 4.438145 CGATAGTGCGTTTCTGACATCTAC 59.562 45.833 0.00 0.00 0.00 2.59
3174 3330 0.913924 GGACCCCCTCGTATTTTGGA 59.086 55.000 0.00 0.00 0.00 3.53
3176 3332 2.486727 GGACCCCCTCGTATTTTGGATC 60.487 54.545 0.00 0.00 0.00 3.36
3179 3335 3.010808 ACCCCCTCGTATTTTGGATCAAA 59.989 43.478 0.00 0.00 0.00 2.69
3259 3421 7.069208 GGATTCATATTTGAAAGAGCTTTCCCT 59.931 37.037 17.57 7.18 46.15 4.20
3260 3422 9.125026 GATTCATATTTGAAAGAGCTTTCCCTA 57.875 33.333 17.57 8.76 46.15 3.53
3263 3428 8.906867 TCATATTTGAAAGAGCTTTCCCTAATG 58.093 33.333 17.57 15.18 46.15 1.90
3266 3431 7.448748 TTTGAAAGAGCTTTCCCTAATGTAC 57.551 36.000 17.57 0.00 46.15 2.90
3269 3434 6.655003 TGAAAGAGCTTTCCCTAATGTACTTG 59.345 38.462 17.57 0.00 46.15 3.16
3324 3489 6.575162 ACTTTATGGTCAAACTTTAGCCTG 57.425 37.500 0.00 0.00 0.00 4.85
3353 3518 2.631545 AGGGGTCTAATAAATCCGGACG 59.368 50.000 6.12 0.00 0.00 4.79
3364 3529 3.409201 TCCGGACGGAGGTAGTATG 57.591 57.895 9.76 0.00 39.76 2.39
3372 3537 3.698040 GACGGAGGTAGTATGGAAGTTCA 59.302 47.826 5.01 0.00 0.00 3.18
3381 3546 5.767816 AGTATGGAAGTTCACCAACAAAC 57.232 39.130 5.01 0.00 40.93 2.93
3399 3565 4.082787 ACAAACGGCTTACATGATTTGAGG 60.083 41.667 0.00 0.00 32.63 3.86
3419 3585 3.318275 AGGTCGACGCACATGAGTAATAT 59.682 43.478 9.92 0.00 0.00 1.28
3464 3630 5.964758 TCACTTTTATTTCATCCACCATGC 58.035 37.500 0.00 0.00 31.70 4.06
3473 3639 3.281158 TCATCCACCATGCAAGTGTATG 58.719 45.455 15.49 15.49 37.79 2.39
3527 3693 7.243604 AGATTAAATGCTTCCAAACAATCCA 57.756 32.000 0.00 0.00 0.00 3.41
3534 3700 3.119352 GCTTCCAAACAATCCATCTCCAC 60.119 47.826 0.00 0.00 0.00 4.02
3543 3709 4.018141 ACAATCCATCTCCACCAGAATTGA 60.018 41.667 0.00 0.00 33.62 2.57
3558 3725 6.183347 CCAGAATTGAGAAATTACCCAGACT 58.817 40.000 0.00 0.00 0.00 3.24
3572 3739 2.030007 CCCAGACTTAAACCACGTACGA 60.030 50.000 24.41 0.00 0.00 3.43
3573 3740 3.240069 CCAGACTTAAACCACGTACGAG 58.760 50.000 24.41 14.76 0.00 4.18
3580 3747 0.807496 AACCACGTACGAGTAGCCTC 59.193 55.000 24.41 0.00 0.00 4.70
3582 3749 1.028330 CCACGTACGAGTAGCCTCCA 61.028 60.000 24.41 0.00 33.93 3.86
3583 3750 1.022735 CACGTACGAGTAGCCTCCAT 58.977 55.000 24.41 0.00 33.93 3.41
3584 3751 2.216046 CACGTACGAGTAGCCTCCATA 58.784 52.381 24.41 0.00 33.93 2.74
3585 3752 2.223611 CACGTACGAGTAGCCTCCATAG 59.776 54.545 24.41 0.00 33.93 2.23
3586 3753 2.103771 ACGTACGAGTAGCCTCCATAGA 59.896 50.000 24.41 0.00 33.93 1.98
3589 3758 1.249407 CGAGTAGCCTCCATAGACCC 58.751 60.000 0.00 0.00 33.93 4.46
3593 3762 0.105142 TAGCCTCCATAGACCCCACC 60.105 60.000 0.00 0.00 0.00 4.61
3601 3770 1.065418 CATAGACCCCACCTGAACCAC 60.065 57.143 0.00 0.00 0.00 4.16
3647 3818 9.871238 TTTGTTCTATACCTAATGACAACTCTC 57.129 33.333 0.00 0.00 0.00 3.20
3648 3819 8.824756 TGTTCTATACCTAATGACAACTCTCT 57.175 34.615 0.00 0.00 0.00 3.10
3649 3820 9.256228 TGTTCTATACCTAATGACAACTCTCTT 57.744 33.333 0.00 0.00 0.00 2.85
3650 3821 9.522804 GTTCTATACCTAATGACAACTCTCTTG 57.477 37.037 0.00 0.00 0.00 3.02
3651 3822 8.824756 TCTATACCTAATGACAACTCTCTTGT 57.175 34.615 0.00 0.00 34.97 3.16
3652 3823 9.916360 TCTATACCTAATGACAACTCTCTTGTA 57.084 33.333 0.00 0.00 31.96 2.41
3653 3824 9.953697 CTATACCTAATGACAACTCTCTTGTAC 57.046 37.037 0.00 0.00 31.96 2.90
3654 3825 6.665992 ACCTAATGACAACTCTCTTGTACA 57.334 37.500 0.00 0.00 31.96 2.90
3655 3826 7.246171 ACCTAATGACAACTCTCTTGTACAT 57.754 36.000 0.00 0.00 31.96 2.29
3656 3827 7.680730 ACCTAATGACAACTCTCTTGTACATT 58.319 34.615 0.00 0.00 35.91 2.71
3657 3828 7.819900 ACCTAATGACAACTCTCTTGTACATTC 59.180 37.037 0.00 0.00 34.83 2.67
3658 3829 8.037758 CCTAATGACAACTCTCTTGTACATTCT 58.962 37.037 0.00 0.00 34.83 2.40
3659 3830 9.429359 CTAATGACAACTCTCTTGTACATTCTT 57.571 33.333 0.00 0.00 34.83 2.52
3660 3831 8.682936 AATGACAACTCTCTTGTACATTCTTT 57.317 30.769 0.00 0.00 31.26 2.52
3661 3832 9.778741 AATGACAACTCTCTTGTACATTCTTTA 57.221 29.630 0.00 0.00 31.26 1.85
3662 3833 9.950496 ATGACAACTCTCTTGTACATTCTTTAT 57.050 29.630 0.00 0.00 31.96 1.40
3663 3834 9.424319 TGACAACTCTCTTGTACATTCTTTATC 57.576 33.333 0.00 0.00 31.96 1.75
3664 3835 9.646427 GACAACTCTCTTGTACATTCTTTATCT 57.354 33.333 0.00 0.00 31.96 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.426752 CGCAAACCGGCAAACTCG 60.427 61.111 0.00 0.00 0.00 4.18
8 9 1.065109 GAACGCAAACCGGCAAACT 59.935 52.632 0.00 0.00 42.52 2.66
15 16 0.593773 CAAACCCTGAACGCAAACCG 60.594 55.000 0.00 0.00 44.21 4.44
17 18 0.102300 AGCAAACCCTGAACGCAAAC 59.898 50.000 0.00 0.00 0.00 2.93
20 21 2.192861 CCAGCAAACCCTGAACGCA 61.193 57.895 0.00 0.00 34.77 5.24
50 52 0.806102 CAACCCGGTAGATCACAGCG 60.806 60.000 0.00 10.83 36.69 5.18
52 54 2.695666 AGATCAACCCGGTAGATCACAG 59.304 50.000 22.31 0.00 40.39 3.66
58 60 1.553248 CCACAAGATCAACCCGGTAGA 59.447 52.381 0.00 0.00 0.00 2.59
63 65 1.266718 CACAACCACAAGATCAACCCG 59.733 52.381 0.00 0.00 0.00 5.28
66 68 4.630894 TGAACACAACCACAAGATCAAC 57.369 40.909 0.00 0.00 0.00 3.18
86 89 6.583806 GCTAAGAAAATCCAATATTCGGCATG 59.416 38.462 0.00 0.00 0.00 4.06
91 94 7.026631 TGTGGCTAAGAAAATCCAATATTCG 57.973 36.000 0.00 0.00 0.00 3.34
100 103 5.170748 CCCAACAATGTGGCTAAGAAAATC 58.829 41.667 0.00 0.00 37.34 2.17
104 107 3.237268 ACCCAACAATGTGGCTAAGAA 57.763 42.857 0.00 0.00 37.34 2.52
105 108 2.890311 CAACCCAACAATGTGGCTAAGA 59.110 45.455 0.00 0.00 37.34 2.10
138 141 6.402222 GGGCATTACTCATAGTCATAGAAGG 58.598 44.000 0.00 0.00 0.00 3.46
142 145 5.392767 ACGGGCATTACTCATAGTCATAG 57.607 43.478 0.00 0.00 0.00 2.23
143 146 5.510690 CCAACGGGCATTACTCATAGTCATA 60.511 44.000 0.00 0.00 0.00 2.15
144 147 4.380531 CAACGGGCATTACTCATAGTCAT 58.619 43.478 0.00 0.00 0.00 3.06
145 148 3.431626 CCAACGGGCATTACTCATAGTCA 60.432 47.826 0.00 0.00 0.00 3.41
146 149 3.131396 CCAACGGGCATTACTCATAGTC 58.869 50.000 0.00 0.00 0.00 2.59
147 150 2.769663 TCCAACGGGCATTACTCATAGT 59.230 45.455 0.00 0.00 0.00 2.12
148 151 3.469008 TCCAACGGGCATTACTCATAG 57.531 47.619 0.00 0.00 0.00 2.23
182 185 2.762234 GCATGGAGAGCAGCAGCAC 61.762 63.158 3.17 0.00 45.49 4.40
184 187 2.913054 TACGCATGGAGAGCAGCAGC 62.913 60.000 0.00 0.00 42.56 5.25
206 209 1.457346 CTCAATTCACCTGGCTGTCC 58.543 55.000 0.00 0.00 0.00 4.02
210 213 1.075601 TTCCCTCAATTCACCTGGCT 58.924 50.000 0.00 0.00 0.00 4.75
220 223 0.620556 ACGCTCACCATTCCCTCAAT 59.379 50.000 0.00 0.00 0.00 2.57
224 227 0.620556 ATCAACGCTCACCATTCCCT 59.379 50.000 0.00 0.00 0.00 4.20
304 307 4.554973 GCGTCAACACATTTAGCTCAAATC 59.445 41.667 0.00 0.00 34.49 2.17
322 325 1.279527 CTAGTTCAAACGCCGCGTCA 61.280 55.000 20.46 3.31 39.99 4.35
327 330 3.306166 CCAAGATACTAGTTCAAACGCCG 59.694 47.826 0.00 0.00 0.00 6.46
399 402 5.539193 ACTTAGGAACGATAGGATTAGTGGG 59.461 44.000 0.00 0.00 43.77 4.61
540 543 8.641498 ATCAACCTTTTCATCAACTGTATTCT 57.359 30.769 0.00 0.00 0.00 2.40
544 547 9.739276 ATAGAATCAACCTTTTCATCAACTGTA 57.261 29.630 0.00 0.00 0.00 2.74
675 678 2.554032 ACGATTGCACTTGAAGGAAAGG 59.446 45.455 0.00 0.00 0.00 3.11
751 755 4.825546 ACTTCAGTTCACTGCAAATCTG 57.174 40.909 1.74 0.00 43.46 2.90
845 849 2.509052 TTCTCACACACTCTGAACCG 57.491 50.000 0.00 0.00 0.00 4.44
846 850 4.060038 TCTTTCTCACACACTCTGAACC 57.940 45.455 0.00 0.00 0.00 3.62
928 932 2.031157 CGGCTGTAAACTGGAAACCAAG 60.031 50.000 0.00 0.00 30.80 3.61
1064 1068 2.525248 CGGGATGTTGATGGCGACG 61.525 63.158 0.00 0.00 0.00 5.12
1071 1075 4.043859 TCCGGACGGGATGTTGAT 57.956 55.556 11.27 0.00 40.94 2.57
1350 1354 1.111277 AGCCAACAACCCACTCAAAC 58.889 50.000 0.00 0.00 0.00 2.93
1518 1522 3.125829 CGTTTACAGCTTCTGATGCATGT 59.874 43.478 16.56 17.19 35.18 3.21
1650 1654 4.927978 ATCGTCATAGCTAAACTGCTCT 57.072 40.909 0.00 0.00 42.97 4.09
1724 1728 9.592196 AGTAAAATGATCTAATGTATTGGGCAT 57.408 29.630 0.00 0.00 0.00 4.40
1781 1879 8.306680 TCGTAACTTTAAACATCAGGAAGAAG 57.693 34.615 0.00 0.00 0.00 2.85
1818 1916 5.221501 TGCGTAGACCCTACAAGTAAAAAGT 60.222 40.000 5.17 0.00 0.00 2.66
1819 1917 5.232463 TGCGTAGACCCTACAAGTAAAAAG 58.768 41.667 5.17 0.00 0.00 2.27
1982 2085 0.818040 AGGTGAAAGGAACGTGCCAC 60.818 55.000 16.99 3.43 0.00 5.01
1985 2088 1.566018 CCGAGGTGAAAGGAACGTGC 61.566 60.000 0.00 0.00 0.00 5.34
2006 2109 8.588290 TGATTACAACCAAATAAGCAAGGTAT 57.412 30.769 0.00 0.00 33.15 2.73
2022 2126 6.215845 ACACAGCCTGAAAAATGATTACAAC 58.784 36.000 0.00 0.00 0.00 3.32
2029 2133 6.237901 ACACTATACACAGCCTGAAAAATGA 58.762 36.000 0.00 0.00 0.00 2.57
2283 2387 1.310933 TAGTCCGCTCCTTGTCGGTC 61.311 60.000 0.47 0.00 45.44 4.79
2370 2474 4.487019 CACAAATGTGTATGCATGAGCAA 58.513 39.130 10.16 0.00 46.57 3.91
2393 2497 2.644707 GCTAATCGCGCAACGTGC 60.645 61.111 8.75 1.57 44.19 5.34
2395 2499 1.445410 TCAGCTAATCGCGCAACGT 60.445 52.632 8.75 0.00 45.59 3.99
2405 2509 1.676014 GGTTCGCAGGTGTCAGCTAAT 60.676 52.381 3.79 0.00 0.00 1.73
2458 2562 5.123227 TCTTCGTTGTTTGAGAACCTTGAT 58.877 37.500 0.00 0.00 34.80 2.57
2470 2574 2.989840 CTCTCGCAGATCTTCGTTGTTT 59.010 45.455 14.37 0.00 33.89 2.83
2521 2625 0.950555 TGAGCCACTTGTCGATGCAC 60.951 55.000 0.00 0.00 0.00 4.57
2563 2667 2.032528 CCCAGCTCGGACTTGCAA 59.967 61.111 0.00 0.00 36.56 4.08
2596 2700 4.475135 GGGCCAGCCTCGGAAGAC 62.475 72.222 4.39 0.00 35.39 3.01
2638 2742 0.602905 CGTCGCCTCTTTCCCTGTTT 60.603 55.000 0.00 0.00 0.00 2.83
2648 2752 2.358369 TGACTCGACGTCGCCTCT 60.358 61.111 32.19 14.01 45.87 3.69
2718 2826 3.065786 CGTCCTACTTATAGCGTGTTCCA 59.934 47.826 0.00 0.00 0.00 3.53
2719 2827 3.625938 CGTCCTACTTATAGCGTGTTCC 58.374 50.000 0.00 0.00 0.00 3.62
2720 2828 3.041492 GCGTCCTACTTATAGCGTGTTC 58.959 50.000 0.00 0.00 0.00 3.18
2721 2829 2.424601 TGCGTCCTACTTATAGCGTGTT 59.575 45.455 0.00 0.00 0.00 3.32
2722 2830 2.019249 TGCGTCCTACTTATAGCGTGT 58.981 47.619 0.00 0.00 0.00 4.49
2724 2832 2.686915 ACTTGCGTCCTACTTATAGCGT 59.313 45.455 0.00 0.00 0.00 5.07
2815 2969 7.826744 TGCCACATTTGACAAATACTGAGTATA 59.173 33.333 12.98 0.00 0.00 1.47
2848 3002 2.624838 CAATGCTCCAACCACTGTTTCT 59.375 45.455 0.00 0.00 30.42 2.52
2877 3031 4.255833 TCAATTTCTGCATGGTTTGGAC 57.744 40.909 0.00 0.00 0.00 4.02
2884 3038 5.291178 TGAAACAGTTCAATTTCTGCATGG 58.709 37.500 0.00 0.00 40.87 3.66
2937 3091 4.635765 GTGCAGCATTAATCAGTTACAGGA 59.364 41.667 0.00 0.00 0.00 3.86
2947 3101 3.691118 TGGACTCAAGTGCAGCATTAATC 59.309 43.478 0.00 0.00 41.48 1.75
3022 3178 2.167693 CTGTAACGAGGAATGTAGCCCA 59.832 50.000 0.00 0.00 0.00 5.36
3026 3182 3.416119 TCGCTGTAACGAGGAATGTAG 57.584 47.619 0.00 0.00 37.09 2.74
3068 3224 4.282703 TGTGTTTGGTTAGGGTCTAGACTC 59.717 45.833 21.88 18.89 0.00 3.36
3069 3225 4.228824 TGTGTTTGGTTAGGGTCTAGACT 58.771 43.478 21.88 6.36 0.00 3.24
3070 3226 4.612264 TGTGTTTGGTTAGGGTCTAGAC 57.388 45.455 14.87 14.87 0.00 2.59
3071 3227 5.046591 CAGATGTGTTTGGTTAGGGTCTAGA 60.047 44.000 0.00 0.00 0.00 2.43
3072 3228 5.178797 CAGATGTGTTTGGTTAGGGTCTAG 58.821 45.833 0.00 0.00 0.00 2.43
3073 3229 4.019681 CCAGATGTGTTTGGTTAGGGTCTA 60.020 45.833 0.00 0.00 0.00 2.59
3074 3230 3.244911 CCAGATGTGTTTGGTTAGGGTCT 60.245 47.826 0.00 0.00 0.00 3.85
3076 3232 2.445525 ACCAGATGTGTTTGGTTAGGGT 59.554 45.455 0.00 0.00 45.16 4.34
3077 3233 3.154827 ACCAGATGTGTTTGGTTAGGG 57.845 47.619 0.00 0.00 45.16 3.53
3096 3252 4.732672 ATCGTTTGGTTAGGGTCTAGAC 57.267 45.455 14.87 14.87 0.00 2.59
3099 3255 4.142093 GCACTATCGTTTGGTTAGGGTCTA 60.142 45.833 0.00 0.00 0.00 2.59
3100 3256 3.369157 GCACTATCGTTTGGTTAGGGTCT 60.369 47.826 0.00 0.00 0.00 3.85
3104 3260 2.613691 ACGCACTATCGTTTGGTTAGG 58.386 47.619 0.00 0.00 40.07 2.69
3137 3293 1.557832 TCCAATAAACCCGGACAGAGG 59.442 52.381 0.73 0.00 0.00 3.69
3164 3320 7.881643 TGGTCAAAATTTGATCCAAAATACG 57.118 32.000 19.93 0.00 40.09 3.06
3308 3473 7.362142 CCTCTTATTTCAGGCTAAAGTTTGACC 60.362 40.741 0.00 0.00 0.00 4.02
3309 3474 7.362142 CCCTCTTATTTCAGGCTAAAGTTTGAC 60.362 40.741 0.00 0.00 0.00 3.18
3324 3489 7.606839 CCGGATTTATTAGACCCCTCTTATTTC 59.393 40.741 0.00 0.00 0.00 2.17
3353 3518 3.773119 TGGTGAACTTCCATACTACCTCC 59.227 47.826 0.00 0.00 0.00 4.30
3363 3528 1.746220 CCGTTTGTTGGTGAACTTCCA 59.254 47.619 0.00 0.00 32.79 3.53
3364 3529 1.535226 GCCGTTTGTTGGTGAACTTCC 60.535 52.381 0.00 0.00 32.79 3.46
3372 3537 2.577700 TCATGTAAGCCGTTTGTTGGT 58.422 42.857 0.00 0.00 0.00 3.67
3381 3546 2.285220 CGACCTCAAATCATGTAAGCCG 59.715 50.000 0.00 0.00 0.00 5.52
3399 3565 5.913514 ACTTATATTACTCATGTGCGTCGAC 59.086 40.000 5.18 5.18 0.00 4.20
3419 3585 5.046878 TGAAGCTGGAGGAACGAAATACTTA 60.047 40.000 0.00 0.00 0.00 2.24
3464 3630 7.043788 CGACACTGATAGATCAACATACACTTG 60.044 40.741 0.00 0.00 36.18 3.16
3527 3693 6.830838 GGTAATTTCTCAATTCTGGTGGAGAT 59.169 38.462 0.00 0.00 36.39 2.75
3534 3700 6.183347 AGTCTGGGTAATTTCTCAATTCTGG 58.817 40.000 0.00 0.00 34.29 3.86
3543 3709 5.704053 CGTGGTTTAAGTCTGGGTAATTTCT 59.296 40.000 0.00 0.00 0.00 2.52
3558 3725 2.819608 AGGCTACTCGTACGTGGTTTAA 59.180 45.455 20.21 4.22 0.00 1.52
3572 3739 0.941963 TGGGGTCTATGGAGGCTACT 59.058 55.000 0.00 0.00 0.00 2.57
3573 3740 1.049402 GTGGGGTCTATGGAGGCTAC 58.951 60.000 0.00 0.00 0.00 3.58
3580 3747 0.546598 GGTTCAGGTGGGGTCTATGG 59.453 60.000 0.00 0.00 0.00 2.74
3582 3749 1.286248 GTGGTTCAGGTGGGGTCTAT 58.714 55.000 0.00 0.00 0.00 1.98
3583 3750 0.104882 TGTGGTTCAGGTGGGGTCTA 60.105 55.000 0.00 0.00 0.00 2.59
3584 3751 1.385347 TGTGGTTCAGGTGGGGTCT 60.385 57.895 0.00 0.00 0.00 3.85
3585 3752 1.228154 GTGTGGTTCAGGTGGGGTC 60.228 63.158 0.00 0.00 0.00 4.46
3586 3753 1.286305 AAGTGTGGTTCAGGTGGGGT 61.286 55.000 0.00 0.00 0.00 4.95
3589 3758 2.719376 CCAAGTGTGGTTCAGGTGG 58.281 57.895 0.00 0.00 40.42 4.61
3601 3770 1.986882 AAAAGAGGCCTGACCAAGTG 58.013 50.000 12.00 0.00 43.14 3.16
3627 3798 9.953697 GTACAAGAGAGTTGTCATTAGGTATAG 57.046 37.037 0.00 0.00 34.11 1.31
3631 3802 6.665992 TGTACAAGAGAGTTGTCATTAGGT 57.334 37.500 0.00 0.00 34.11 3.08
3635 3806 8.682936 AAAGAATGTACAAGAGAGTTGTCATT 57.317 30.769 0.00 11.76 35.25 2.57
3636 3807 9.950496 ATAAAGAATGTACAAGAGAGTTGTCAT 57.050 29.630 0.00 0.00 34.11 3.06
3637 3808 9.424319 GATAAAGAATGTACAAGAGAGTTGTCA 57.576 33.333 0.00 0.00 34.11 3.58
3638 3809 9.646427 AGATAAAGAATGTACAAGAGAGTTGTC 57.354 33.333 0.00 0.00 34.11 3.18


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

AutoCloner maintained by Alex Coulton.