Multiple sequence alignment - TraesCS4D01G081500

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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 TraesCS4D01G081500 chr4D 100.000 3062 0 0 1 3062 55252359 55249298 0.000000e+00 5655.0
1 TraesCS4D01G081500 chr4D 100.000 38 0 0 725 762 55251595 55251558 1.520000e-08 71.3
2 TraesCS4D01G081500 chr4D 100.000 38 0 0 765 802 55251635 55251598 1.520000e-08 71.3
3 TraesCS4D01G081500 chr4B 94.600 1926 79 11 765 2673 82165480 82163563 0.000000e+00 2957.0
4 TraesCS4D01G081500 chr4B 89.324 281 27 2 483 763 82165719 82165442 1.750000e-92 350.0
5 TraesCS4D01G081500 chr4B 91.111 225 14 3 2838 3062 82163207 82162989 1.780000e-77 300.0
6 TraesCS4D01G081500 chr4B 92.254 142 2 3 86 223 82171195 82171059 3.120000e-45 193.0
7 TraesCS4D01G081500 chr4B 93.548 93 6 0 3 95 82171682 82171590 4.120000e-29 139.0
8 TraesCS4D01G081500 chr4B 96.825 63 2 0 380 442 82165791 82165729 4.180000e-19 106.0
9 TraesCS4D01G081500 chr4A 90.718 1950 87 28 765 2673 541987089 541988985 0.000000e+00 2512.0
10 TraesCS4D01G081500 chr4A 88.172 465 35 9 1 461 541986247 541986695 1.250000e-148 536.0
11 TraesCS4D01G081500 chr4A 88.255 298 28 4 472 762 541986829 541987126 1.750000e-92 350.0
12 TraesCS4D01G081500 chr3D 83.544 79 11 2 312 389 9316483 9316406 4.240000e-09 73.1


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 TraesCS4D01G081500 chr4D 55249298 55252359 3061 True 1932.533333 5655 100.000000 1 3062 3 chr4D.!!$R1 3061
1 TraesCS4D01G081500 chr4B 82162989 82165791 2802 True 928.250000 2957 92.965000 380 3062 4 chr4B.!!$R1 2682
2 TraesCS4D01G081500 chr4A 541986247 541988985 2738 False 1132.666667 2512 89.048333 1 2673 3 chr4A.!!$F1 2672

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
159 160 0.034089 GGTCTTGGGTGGATCTTGGG 60.034 60.0 0.0 0.0 0.0 4.12 F
1347 1509 0.108585 TCCTCAAGCTCACCACCAAC 59.891 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 2100 0.255318 CCCCTGCTGCTTCATCTTCT 59.745 55.0 0.0 0.0 0.00 2.85 R
2938 3361 0.037590 TGGTACATGGTGTCCCTTGC 59.962 55.0 0.0 0.0 39.04 4.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.465724 GGGCTCATATTACAGGTTTACGAAG 59.534 44.000 0.00 0.00 0.00 3.79
35 36 5.050295 GGCTCATATTACAGGTTTACGAAGC 60.050 44.000 0.00 0.00 0.00 3.86
62 63 6.961554 GGTGAAAATGTCTCACGATATTTGAC 59.038 38.462 0.00 0.00 43.45 3.18
63 64 6.678663 GTGAAAATGTCTCACGATATTTGACG 59.321 38.462 0.00 0.00 39.22 4.35
64 65 6.367695 TGAAAATGTCTCACGATATTTGACGT 59.632 34.615 0.00 0.00 39.22 4.34
85 86 3.854286 AAGTTTTCGTGTACTTCGCTG 57.146 42.857 0.00 0.00 28.79 5.18
94 95 0.928229 GTACTTCGCTGCGTAATGGG 59.072 55.000 22.48 3.01 0.00 4.00
103 104 2.213499 CTGCGTAATGGGTGGATCTTC 58.787 52.381 0.00 0.00 0.00 2.87
111 112 2.050144 TGGGTGGATCTTCTAGGATGC 58.950 52.381 0.00 0.00 35.16 3.91
117 118 5.397334 GGTGGATCTTCTAGGATGCTTCTTT 60.397 44.000 0.00 0.00 35.53 2.52
146 147 5.551233 TCAAGTCAAACTATGAGGGTCTTG 58.449 41.667 0.00 0.00 39.19 3.02
147 148 4.559862 AGTCAAACTATGAGGGTCTTGG 57.440 45.455 0.00 0.00 39.19 3.61
148 149 3.264450 AGTCAAACTATGAGGGTCTTGGG 59.736 47.826 0.00 0.00 39.19 4.12
149 150 3.009143 GTCAAACTATGAGGGTCTTGGGT 59.991 47.826 0.00 0.00 39.19 4.51
150 151 3.009033 TCAAACTATGAGGGTCTTGGGTG 59.991 47.826 0.00 0.00 33.04 4.61
159 160 0.034089 GGTCTTGGGTGGATCTTGGG 60.034 60.000 0.00 0.00 0.00 4.12
211 212 5.086104 TGAACTTGGCCTTCATCTAGTAC 57.914 43.478 3.32 0.00 0.00 2.73
212 213 4.777896 TGAACTTGGCCTTCATCTAGTACT 59.222 41.667 3.32 0.00 0.00 2.73
213 214 5.955959 TGAACTTGGCCTTCATCTAGTACTA 59.044 40.000 3.32 1.89 0.00 1.82
214 215 5.855740 ACTTGGCCTTCATCTAGTACTAC 57.144 43.478 3.32 0.00 0.00 2.73
215 216 5.520751 ACTTGGCCTTCATCTAGTACTACT 58.479 41.667 3.32 0.00 0.00 2.57
216 217 5.958987 ACTTGGCCTTCATCTAGTACTACTT 59.041 40.000 3.32 0.00 0.00 2.24
353 358 7.439157 AAAATAAGCTTGGATTTTCTTTGGC 57.561 32.000 9.86 0.00 31.17 4.52
454 459 6.072008 TGCACAATCACATTAATACAAGCAGT 60.072 34.615 0.00 0.00 0.00 4.40
505 633 4.382114 CGCATTGCAACGCACGGA 62.382 61.111 18.56 0.00 38.71 4.69
641 775 9.249844 CGACGTATTAAACATTGCATATATGTG 57.750 33.333 14.14 7.33 36.41 3.21
708 843 7.714813 CCATTTTCCAAAAATGTAAACTGGACT 59.285 33.333 18.67 0.00 35.92 3.85
747 882 6.983906 ATCTCACCCAAAAGAACTGAAAAT 57.016 33.333 0.00 0.00 0.00 1.82
748 883 6.391227 TCTCACCCAAAAGAACTGAAAATC 57.609 37.500 0.00 0.00 0.00 2.17
749 884 5.890985 TCTCACCCAAAAGAACTGAAAATCA 59.109 36.000 0.00 0.00 0.00 2.57
763 898 4.304110 TGAAAATCAGATACGCGGATACC 58.696 43.478 12.47 0.00 30.90 2.73
764 899 4.202172 TGAAAATCAGATACGCGGATACCA 60.202 41.667 12.47 0.00 30.90 3.25
765 900 4.537135 AAATCAGATACGCGGATACCAT 57.463 40.909 12.47 0.00 30.90 3.55
766 901 3.784701 ATCAGATACGCGGATACCATC 57.215 47.619 12.47 0.00 29.21 3.51
767 902 2.791655 TCAGATACGCGGATACCATCT 58.208 47.619 12.47 0.00 0.00 2.90
768 903 2.747989 TCAGATACGCGGATACCATCTC 59.252 50.000 12.47 0.00 0.00 2.75
769 904 2.488153 CAGATACGCGGATACCATCTCA 59.512 50.000 12.47 0.00 0.00 3.27
778 913 3.118408 CGGATACCATCTCACCCAAAAGA 60.118 47.826 0.00 0.00 0.00 2.52
781 916 3.884037 ACCATCTCACCCAAAAGAACT 57.116 42.857 0.00 0.00 0.00 3.01
805 940 5.690409 TGAAAATCAGATACGCGGATAAGAC 59.310 40.000 12.47 0.00 30.90 3.01
806 941 2.963498 TCAGATACGCGGATAAGACG 57.037 50.000 12.47 0.00 0.00 4.18
837 972 8.950210 TGAATTTTCCAAACTTTTATTGTGCAA 58.050 25.926 0.00 0.00 0.00 4.08
882 1017 1.892209 ACAAGAATGTTCCACGGACC 58.108 50.000 0.00 0.00 35.91 4.46
910 1045 4.285790 ACCTCCCCTCCCCTGCAA 62.286 66.667 0.00 0.00 0.00 4.08
911 1046 2.941025 CCTCCCCTCCCCTGCAAA 60.941 66.667 0.00 0.00 0.00 3.68
913 1048 2.451493 TCCCCTCCCCTGCAAACA 60.451 61.111 0.00 0.00 0.00 2.83
998 1142 1.475213 GCTCCTTTGTATTCCCCTCCG 60.475 57.143 0.00 0.00 0.00 4.63
1067 1220 0.871057 GGAAGAGCACACAGACAAGC 59.129 55.000 0.00 0.00 0.00 4.01
1224 1378 3.564218 ATCCATCCTCAGCCGCCC 61.564 66.667 0.00 0.00 0.00 6.13
1287 1449 2.362889 CCCCAGCACCACCATTCC 60.363 66.667 0.00 0.00 0.00 3.01
1295 1457 1.547675 GCACCACCATTCCTTCCTCAA 60.548 52.381 0.00 0.00 0.00 3.02
1301 1463 2.158475 ACCATTCCTTCCTCAACAGCAA 60.158 45.455 0.00 0.00 0.00 3.91
1346 1508 0.397941 CTCCTCAAGCTCACCACCAA 59.602 55.000 0.00 0.00 0.00 3.67
1347 1509 0.108585 TCCTCAAGCTCACCACCAAC 59.891 55.000 0.00 0.00 0.00 3.77
1348 1510 0.179020 CCTCAAGCTCACCACCAACA 60.179 55.000 0.00 0.00 0.00 3.33
1349 1511 1.233019 CTCAAGCTCACCACCAACAG 58.767 55.000 0.00 0.00 0.00 3.16
1350 1512 0.819259 TCAAGCTCACCACCAACAGC 60.819 55.000 0.00 0.00 0.00 4.40
1351 1513 1.102809 CAAGCTCACCACCAACAGCA 61.103 55.000 0.00 0.00 34.08 4.41
1355 1517 0.751277 CTCACCACCAACAGCACCAA 60.751 55.000 0.00 0.00 0.00 3.67
1374 1545 1.444895 CGCCAGCAACAGCATTTCC 60.445 57.895 0.00 0.00 0.00 3.13
1509 1680 4.486503 CTCCTGGGCCAGCAGCTC 62.487 72.222 28.51 0.00 45.08 4.09
1545 1716 4.778415 CAGGCCGACGAGACCACG 62.778 72.222 0.00 0.00 39.31 4.94
1947 2118 2.015587 GAAGAAGATGAAGCAGCAGGG 58.984 52.381 0.00 0.00 0.00 4.45
2089 2260 1.990563 GCAAGTTTGTGATGATGCTGC 59.009 47.619 0.00 0.00 0.00 5.25
2141 2313 4.281525 TGTTTCTGTAGTTCGTTTTGGC 57.718 40.909 0.00 0.00 0.00 4.52
2147 2319 4.396790 TCTGTAGTTCGTTTTGGCTGTTTT 59.603 37.500 0.00 0.00 0.00 2.43
2165 2337 4.744137 TGTTTTTGTACTGAACATGCATGC 59.256 37.500 26.53 11.82 38.10 4.06
2228 2402 4.315588 GCTGCTTGCTCTGGACAT 57.684 55.556 0.00 0.00 38.95 3.06
2231 2405 1.001764 TGCTTGCTCTGGACATGGG 60.002 57.895 0.00 0.00 0.00 4.00
2292 2480 9.994432 AAGCTAAAATATGTTCTCTTTTCATCG 57.006 29.630 0.00 0.00 0.00 3.84
2299 2487 4.693283 TGTTCTCTTTTCATCGGCGATAT 58.307 39.130 23.53 0.00 0.00 1.63
2443 2631 7.177216 TGCTGATGAATCTTTAAAACCTGATGT 59.823 33.333 0.00 0.00 0.00 3.06
2446 2634 8.733458 TGATGAATCTTTAAAACCTGATGTGAG 58.267 33.333 0.00 0.00 0.00 3.51
2494 2682 6.481644 CCTCTCTTATGACTGCCACTATTTTC 59.518 42.308 0.00 0.00 0.00 2.29
2673 2861 4.523173 CACTCTTAGACCTGTCCAGTACAA 59.477 45.833 0.00 0.00 37.74 2.41
2674 2862 4.523558 ACTCTTAGACCTGTCCAGTACAAC 59.476 45.833 0.00 0.00 37.74 3.32
2675 2863 4.476297 TCTTAGACCTGTCCAGTACAACA 58.524 43.478 0.00 0.00 37.74 3.33
2676 2864 5.084519 TCTTAGACCTGTCCAGTACAACAT 58.915 41.667 0.00 0.00 37.74 2.71
2677 2865 3.963428 AGACCTGTCCAGTACAACATC 57.037 47.619 0.00 0.00 37.74 3.06
2678 2866 3.239449 AGACCTGTCCAGTACAACATCA 58.761 45.455 0.00 0.00 37.74 3.07
2679 2867 3.259374 AGACCTGTCCAGTACAACATCAG 59.741 47.826 0.00 0.00 37.74 2.90
2681 2869 2.027745 CCTGTCCAGTACAACATCAGCT 60.028 50.000 0.00 0.00 37.74 4.24
2682 2870 3.195610 CCTGTCCAGTACAACATCAGCTA 59.804 47.826 0.00 0.00 37.74 3.32
2683 2871 4.141846 CCTGTCCAGTACAACATCAGCTAT 60.142 45.833 0.00 0.00 37.74 2.97
2684 2872 4.758688 TGTCCAGTACAACATCAGCTATG 58.241 43.478 0.00 0.00 35.87 2.23
2696 2884 5.384063 CATCAGCTATGTACACTCCTAGG 57.616 47.826 0.82 0.82 0.00 3.02
2719 3142 3.181440 CCCTAGCCAAGATCCAAATGCTA 60.181 47.826 0.00 0.00 0.00 3.49
2723 3146 5.743636 AGCCAAGATCCAAATGCTAAAAA 57.256 34.783 0.00 0.00 0.00 1.94
2791 3214 0.743688 GGTGTTGTGTGTCAATGGCA 59.256 50.000 0.00 0.00 38.38 4.92
2807 3230 3.183793 TGGCACATGATAGTACAGCAG 57.816 47.619 0.00 0.00 0.00 4.24
2808 3231 2.158914 TGGCACATGATAGTACAGCAGG 60.159 50.000 0.00 0.00 0.00 4.85
2809 3232 2.158900 GGCACATGATAGTACAGCAGGT 60.159 50.000 0.00 0.00 38.24 4.00
2810 3233 3.126831 GCACATGATAGTACAGCAGGTC 58.873 50.000 0.00 0.00 34.90 3.85
2811 3234 3.722147 CACATGATAGTACAGCAGGTCC 58.278 50.000 0.00 0.00 34.90 4.46
2812 3235 2.700897 ACATGATAGTACAGCAGGTCCC 59.299 50.000 0.00 0.00 30.41 4.46
2813 3236 2.543037 TGATAGTACAGCAGGTCCCA 57.457 50.000 0.00 0.00 0.00 4.37
2814 3237 3.046283 TGATAGTACAGCAGGTCCCAT 57.954 47.619 0.00 0.00 0.00 4.00
2815 3238 3.384168 TGATAGTACAGCAGGTCCCATT 58.616 45.455 0.00 0.00 0.00 3.16
2816 3239 3.388024 TGATAGTACAGCAGGTCCCATTC 59.612 47.826 0.00 0.00 0.00 2.67
2817 3240 1.958288 AGTACAGCAGGTCCCATTCT 58.042 50.000 0.00 0.00 0.00 2.40
2818 3241 1.834263 AGTACAGCAGGTCCCATTCTC 59.166 52.381 0.00 0.00 0.00 2.87
2819 3242 1.555075 GTACAGCAGGTCCCATTCTCA 59.445 52.381 0.00 0.00 0.00 3.27
2820 3243 0.326264 ACAGCAGGTCCCATTCTCAC 59.674 55.000 0.00 0.00 0.00 3.51
2821 3244 0.393537 CAGCAGGTCCCATTCTCACC 60.394 60.000 0.00 0.00 0.00 4.02
2822 3245 0.842030 AGCAGGTCCCATTCTCACCA 60.842 55.000 0.00 0.00 31.99 4.17
2823 3246 0.038166 GCAGGTCCCATTCTCACCAA 59.962 55.000 0.00 0.00 31.99 3.67
2824 3247 1.547675 GCAGGTCCCATTCTCACCAAA 60.548 52.381 0.00 0.00 31.99 3.28
2825 3248 2.885554 GCAGGTCCCATTCTCACCAAAT 60.886 50.000 0.00 0.00 31.99 2.32
2826 3249 3.019564 CAGGTCCCATTCTCACCAAATC 58.980 50.000 0.00 0.00 31.99 2.17
2827 3250 2.649312 AGGTCCCATTCTCACCAAATCA 59.351 45.455 0.00 0.00 31.99 2.57
2828 3251 3.075882 AGGTCCCATTCTCACCAAATCAA 59.924 43.478 0.00 0.00 31.99 2.57
2829 3252 3.831911 GGTCCCATTCTCACCAAATCAAA 59.168 43.478 0.00 0.00 0.00 2.69
2830 3253 4.467438 GGTCCCATTCTCACCAAATCAAAT 59.533 41.667 0.00 0.00 0.00 2.32
2831 3254 5.656416 GGTCCCATTCTCACCAAATCAAATA 59.344 40.000 0.00 0.00 0.00 1.40
2832 3255 6.154363 GGTCCCATTCTCACCAAATCAAATAA 59.846 38.462 0.00 0.00 0.00 1.40
2833 3256 7.310361 GGTCCCATTCTCACCAAATCAAATAAA 60.310 37.037 0.00 0.00 0.00 1.40
2834 3257 7.761249 GTCCCATTCTCACCAAATCAAATAAAG 59.239 37.037 0.00 0.00 0.00 1.85
2835 3258 7.673504 TCCCATTCTCACCAAATCAAATAAAGA 59.326 33.333 0.00 0.00 0.00 2.52
2836 3259 7.977853 CCCATTCTCACCAAATCAAATAAAGAG 59.022 37.037 0.00 0.00 0.00 2.85
2837 3260 8.742777 CCATTCTCACCAAATCAAATAAAGAGA 58.257 33.333 0.00 0.00 0.00 3.10
3004 3427 0.179059 ACCACGCCATCGATTATGCA 60.179 50.000 0.00 0.00 39.41 3.96
3038 3461 2.351276 GGGGACAGTTGCGGACAT 59.649 61.111 0.00 0.00 0.00 3.06
3042 3465 1.335872 GGGACAGTTGCGGACATTTTG 60.336 52.381 0.00 0.00 0.00 2.44
3052 3475 3.252215 TGCGGACATTTTGGAGTTAGTTG 59.748 43.478 0.00 0.00 0.00 3.16
3059 3482 8.237267 GGACATTTTGGAGTTAGTTGACTATTG 58.763 37.037 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.952460 TCGTAAACCTGTAATATGAGCCC 58.048 43.478 0.00 0.00 0.00 5.19
34 35 2.143122 TCGTGAGACATTTTCACCTGC 58.857 47.619 0.29 0.00 41.43 4.85
35 36 6.668541 AATATCGTGAGACATTTTCACCTG 57.331 37.500 0.29 0.00 46.97 4.00
62 63 3.423206 AGCGAAGTACACGAAAACTTACG 59.577 43.478 14.74 3.32 36.10 3.18
63 64 4.685020 CAGCGAAGTACACGAAAACTTAC 58.315 43.478 14.74 0.00 36.10 2.34
64 65 3.182972 GCAGCGAAGTACACGAAAACTTA 59.817 43.478 14.74 0.00 36.10 2.24
73 74 1.323534 CCATTACGCAGCGAAGTACAC 59.676 52.381 24.65 0.00 0.00 2.90
79 80 1.743623 CCACCCATTACGCAGCGAA 60.744 57.895 24.65 11.95 0.00 4.70
81 82 1.498865 GATCCACCCATTACGCAGCG 61.499 60.000 14.82 14.82 0.00 5.18
85 86 2.622064 AGAAGATCCACCCATTACGC 57.378 50.000 0.00 0.00 0.00 4.42
94 95 4.953940 AGAAGCATCCTAGAAGATCCAC 57.046 45.455 0.00 0.00 0.00 4.02
103 104 8.273780 ACTTGAATAACAAAGAAGCATCCTAG 57.726 34.615 0.00 0.00 38.08 3.02
117 118 7.458397 ACCCTCATAGTTTGACTTGAATAACA 58.542 34.615 0.00 0.00 0.00 2.41
146 147 1.863155 TTGAGGCCCAAGATCCACCC 61.863 60.000 0.00 0.00 0.00 4.61
147 148 0.259938 ATTGAGGCCCAAGATCCACC 59.740 55.000 0.00 0.00 38.31 4.61
148 149 1.341383 ACATTGAGGCCCAAGATCCAC 60.341 52.381 0.00 0.00 38.31 4.02
149 150 1.002069 ACATTGAGGCCCAAGATCCA 58.998 50.000 0.00 0.00 38.31 3.41
150 151 2.149973 AACATTGAGGCCCAAGATCC 57.850 50.000 0.00 0.00 38.31 3.36
244 249 3.909258 GAACGAAGCACTCCGCCGA 62.909 63.158 0.00 0.00 44.04 5.54
330 335 6.532826 TGCCAAAGAAAATCCAAGCTTATTT 58.467 32.000 0.00 0.00 0.00 1.40
336 341 2.481568 GCTTGCCAAAGAAAATCCAAGC 59.518 45.455 7.31 7.31 45.29 4.01
341 346 5.934043 ACTTATTGGCTTGCCAAAGAAAATC 59.066 36.000 27.66 0.00 35.19 2.17
346 351 3.495331 TCACTTATTGGCTTGCCAAAGA 58.505 40.909 27.66 17.23 35.19 2.52
387 392 9.750783 ACCCGCGATATACCTATCTAAATATAT 57.249 33.333 8.23 0.00 32.98 0.86
416 421 9.709495 AATGTGATTGTGCAAATAAATGTTACT 57.291 25.926 0.00 0.00 0.00 2.24
463 468 9.653067 CGATGTAGATGTTCTAGTAAGTTACTG 57.347 37.037 23.14 13.87 39.81 2.74
469 474 7.358765 GCAATGCGATGTAGATGTTCTAGTAAG 60.359 40.741 0.00 0.00 28.01 2.34
470 475 6.420903 GCAATGCGATGTAGATGTTCTAGTAA 59.579 38.462 0.00 0.00 28.01 2.24
485 613 2.490443 CGTGCGTTGCAATGCGATG 61.490 57.895 32.28 23.26 43.79 3.84
573 704 2.294074 TCCACTTGGACTTTGGTTTCG 58.706 47.619 0.00 0.00 39.78 3.46
641 775 4.384056 CTCTACATCATGGATGGTTGGAC 58.616 47.826 10.64 0.00 43.60 4.02
697 832 0.796927 GCCGCTTCAGTCCAGTTTAC 59.203 55.000 0.00 0.00 0.00 2.01
698 833 0.685097 AGCCGCTTCAGTCCAGTTTA 59.315 50.000 0.00 0.00 0.00 2.01
708 843 1.045350 AGATAGCTCCAGCCGCTTCA 61.045 55.000 0.00 0.00 43.38 3.02
747 882 2.747989 GAGATGGTATCCGCGTATCTGA 59.252 50.000 4.92 0.00 0.00 3.27
748 883 2.488153 TGAGATGGTATCCGCGTATCTG 59.512 50.000 4.92 0.00 0.00 2.90
749 884 2.488545 GTGAGATGGTATCCGCGTATCT 59.511 50.000 4.92 4.26 0.00 1.98
750 885 2.415625 GGTGAGATGGTATCCGCGTATC 60.416 54.545 4.92 0.00 0.00 2.24
751 886 1.544691 GGTGAGATGGTATCCGCGTAT 59.455 52.381 4.92 0.00 0.00 3.06
752 887 0.956633 GGTGAGATGGTATCCGCGTA 59.043 55.000 4.92 0.00 0.00 4.42
753 888 1.740285 GGTGAGATGGTATCCGCGT 59.260 57.895 4.92 0.00 0.00 6.01
754 889 1.006102 GGGTGAGATGGTATCCGCG 60.006 63.158 0.00 0.00 0.00 6.46
755 890 0.468226 TTGGGTGAGATGGTATCCGC 59.532 55.000 0.00 0.00 0.00 5.54
756 891 3.118408 TCTTTTGGGTGAGATGGTATCCG 60.118 47.826 0.00 0.00 0.00 4.18
757 892 4.503714 TCTTTTGGGTGAGATGGTATCC 57.496 45.455 0.00 0.00 0.00 2.59
758 893 5.355350 CAGTTCTTTTGGGTGAGATGGTATC 59.645 44.000 0.00 0.00 0.00 2.24
759 894 5.014123 TCAGTTCTTTTGGGTGAGATGGTAT 59.986 40.000 0.00 0.00 0.00 2.73
760 895 4.349636 TCAGTTCTTTTGGGTGAGATGGTA 59.650 41.667 0.00 0.00 0.00 3.25
761 896 3.138283 TCAGTTCTTTTGGGTGAGATGGT 59.862 43.478 0.00 0.00 0.00 3.55
762 897 3.754965 TCAGTTCTTTTGGGTGAGATGG 58.245 45.455 0.00 0.00 0.00 3.51
763 898 5.772825 TTTCAGTTCTTTTGGGTGAGATG 57.227 39.130 0.00 0.00 0.00 2.90
764 899 6.550854 TGATTTTCAGTTCTTTTGGGTGAGAT 59.449 34.615 0.00 0.00 0.00 2.75
765 900 5.890985 TGATTTTCAGTTCTTTTGGGTGAGA 59.109 36.000 0.00 0.00 0.00 3.27
766 901 6.039717 TCTGATTTTCAGTTCTTTTGGGTGAG 59.960 38.462 4.56 0.00 44.58 3.51
767 902 5.890985 TCTGATTTTCAGTTCTTTTGGGTGA 59.109 36.000 4.56 0.00 44.58 4.02
768 903 6.147864 TCTGATTTTCAGTTCTTTTGGGTG 57.852 37.500 4.56 0.00 44.58 4.61
769 904 6.983906 ATCTGATTTTCAGTTCTTTTGGGT 57.016 33.333 4.56 0.00 44.58 4.51
778 913 3.857052 TCCGCGTATCTGATTTTCAGTT 58.143 40.909 4.92 0.00 44.58 3.16
781 916 5.690409 GTCTTATCCGCGTATCTGATTTTCA 59.310 40.000 4.92 0.00 0.00 2.69
805 940 9.980780 AATAAAAGTTTGGAAAATTCAACAACG 57.019 25.926 0.00 0.00 0.00 4.10
837 972 4.389890 TTCTGCTGCTTCATTTTGTTGT 57.610 36.364 0.00 0.00 0.00 3.32
998 1142 1.182667 GGTTTTGTAGGGGTGCATCC 58.817 55.000 7.76 7.76 0.00 3.51
1287 1449 0.954452 GGGTGTTGCTGTTGAGGAAG 59.046 55.000 0.00 0.00 28.76 3.46
1295 1457 2.587753 CGTCGTGGGTGTTGCTGT 60.588 61.111 0.00 0.00 0.00 4.40
1346 1508 4.873810 TGCTGGCGTTGGTGCTGT 62.874 61.111 0.00 0.00 34.52 4.40
1347 1509 3.594775 TTGCTGGCGTTGGTGCTG 61.595 61.111 0.00 0.00 34.52 4.41
1348 1510 3.595758 GTTGCTGGCGTTGGTGCT 61.596 61.111 0.00 0.00 34.52 4.40
1349 1511 3.829272 CTGTTGCTGGCGTTGGTGC 62.829 63.158 0.00 0.00 0.00 5.01
1350 1512 2.332514 CTGTTGCTGGCGTTGGTG 59.667 61.111 0.00 0.00 0.00 4.17
1351 1513 3.595758 GCTGTTGCTGGCGTTGGT 61.596 61.111 0.00 0.00 36.03 3.67
1355 1517 1.286880 GAAATGCTGTTGCTGGCGT 59.713 52.632 0.00 0.00 40.48 5.68
1548 1719 2.835431 AGGACGATGAGGAGGGCG 60.835 66.667 0.00 0.00 0.00 6.13
1809 1980 0.526524 GCTCCCAGATGAACTCGTCG 60.527 60.000 0.00 0.00 36.99 5.12
1881 2052 3.760035 TTCTCCAGGAGCCGCGTC 61.760 66.667 12.26 0.00 0.00 5.19
1929 2100 0.255318 CCCCTGCTGCTTCATCTTCT 59.745 55.000 0.00 0.00 0.00 2.85
1935 2106 2.609534 ATCTGCCCCTGCTGCTTCA 61.610 57.895 0.00 0.00 38.71 3.02
1947 2118 1.145819 GTCAGCCTCCTCATCTGCC 59.854 63.158 0.00 0.00 0.00 4.85
2089 2260 1.779221 TAAAATCAGCTGCCCCATGG 58.221 50.000 9.47 4.14 0.00 3.66
2115 2287 6.238374 CCAAAACGAACTACAGAAACATGACT 60.238 38.462 0.00 0.00 0.00 3.41
2141 2313 5.107760 GCATGCATGTTCAGTACAAAAACAG 60.108 40.000 26.79 0.00 40.89 3.16
2147 2319 4.581077 TTTGCATGCATGTTCAGTACAA 57.419 36.364 26.79 17.04 40.89 2.41
2189 2363 8.883731 GCAGCTTCTCAAACACTTATCTTTATA 58.116 33.333 0.00 0.00 0.00 0.98
2190 2364 7.609532 AGCAGCTTCTCAAACACTTATCTTTAT 59.390 33.333 0.00 0.00 0.00 1.40
2246 2420 5.636543 AGCTTTGCAGTTTATCTTTTGCATC 59.363 36.000 0.00 0.00 44.99 3.91
2299 2487 0.958091 CACCGAGTTTCCAAATGGCA 59.042 50.000 0.00 0.00 34.44 4.92
2494 2682 0.950836 TTGTGCATGAAACGGTGGAG 59.049 50.000 0.00 0.00 0.00 3.86
2674 2862 4.321601 GCCTAGGAGTGTACATAGCTGATG 60.322 50.000 14.75 0.00 41.79 3.07
2675 2863 3.829601 GCCTAGGAGTGTACATAGCTGAT 59.170 47.826 14.75 0.00 0.00 2.90
2676 2864 3.223435 GCCTAGGAGTGTACATAGCTGA 58.777 50.000 14.75 0.00 0.00 4.26
2677 2865 2.297597 GGCCTAGGAGTGTACATAGCTG 59.702 54.545 14.75 0.00 0.00 4.24
2678 2866 2.599677 GGCCTAGGAGTGTACATAGCT 58.400 52.381 14.75 0.00 0.00 3.32
2679 2867 1.619332 GGGCCTAGGAGTGTACATAGC 59.381 57.143 14.75 0.00 0.00 2.97
2681 2869 3.499926 GCTAGGGCCTAGGAGTGTACATA 60.500 52.174 35.37 3.15 34.88 2.29
2682 2870 2.756919 GCTAGGGCCTAGGAGTGTACAT 60.757 54.545 35.37 0.27 34.88 2.29
2683 2871 1.411216 GCTAGGGCCTAGGAGTGTACA 60.411 57.143 35.37 3.91 34.88 2.90
2684 2872 1.330234 GCTAGGGCCTAGGAGTGTAC 58.670 60.000 35.37 17.36 34.88 2.90
2685 2873 3.844161 GCTAGGGCCTAGGAGTGTA 57.156 57.895 35.37 5.44 34.88 2.90
2686 2874 4.709690 GCTAGGGCCTAGGAGTGT 57.290 61.111 35.37 2.61 34.88 3.55
2696 2884 1.959282 CATTTGGATCTTGGCTAGGGC 59.041 52.381 0.00 0.00 37.82 5.19
2719 3142 3.818210 TGCCACACGACATATCAGTTTTT 59.182 39.130 0.00 0.00 0.00 1.94
2723 3146 1.824852 TCTGCCACACGACATATCAGT 59.175 47.619 0.00 0.00 0.00 3.41
2772 3195 0.743688 TGCCATTGACACACAACACC 59.256 50.000 0.00 0.00 41.52 4.16
2791 3214 2.700897 GGGACCTGCTGTACTATCATGT 59.299 50.000 0.00 0.00 0.00 3.21
2795 3218 3.643792 AGAATGGGACCTGCTGTACTATC 59.356 47.826 0.00 0.00 25.02 2.08
2796 3219 3.643792 GAGAATGGGACCTGCTGTACTAT 59.356 47.826 0.00 0.00 28.33 2.12
2797 3220 3.031736 GAGAATGGGACCTGCTGTACTA 58.968 50.000 0.00 0.00 0.00 1.82
2798 3221 1.834263 GAGAATGGGACCTGCTGTACT 59.166 52.381 0.00 0.00 0.00 2.73
2799 3222 1.555075 TGAGAATGGGACCTGCTGTAC 59.445 52.381 0.00 0.00 0.00 2.90
2800 3223 1.555075 GTGAGAATGGGACCTGCTGTA 59.445 52.381 0.00 0.00 0.00 2.74
2801 3224 0.326264 GTGAGAATGGGACCTGCTGT 59.674 55.000 0.00 0.00 0.00 4.40
2802 3225 0.393537 GGTGAGAATGGGACCTGCTG 60.394 60.000 0.00 0.00 0.00 4.41
2803 3226 0.842030 TGGTGAGAATGGGACCTGCT 60.842 55.000 0.00 0.00 0.00 4.24
2804 3227 0.038166 TTGGTGAGAATGGGACCTGC 59.962 55.000 0.00 0.00 0.00 4.85
2805 3228 2.584835 TTTGGTGAGAATGGGACCTG 57.415 50.000 0.00 0.00 0.00 4.00
2806 3229 2.649312 TGATTTGGTGAGAATGGGACCT 59.351 45.455 0.00 0.00 0.00 3.85
2807 3230 3.085952 TGATTTGGTGAGAATGGGACC 57.914 47.619 0.00 0.00 0.00 4.46
2808 3231 5.665916 ATTTGATTTGGTGAGAATGGGAC 57.334 39.130 0.00 0.00 0.00 4.46
2809 3232 7.673504 TCTTTATTTGATTTGGTGAGAATGGGA 59.326 33.333 0.00 0.00 0.00 4.37
2810 3233 7.839907 TCTTTATTTGATTTGGTGAGAATGGG 58.160 34.615 0.00 0.00 0.00 4.00
2811 3234 8.742777 TCTCTTTATTTGATTTGGTGAGAATGG 58.257 33.333 0.00 0.00 0.00 3.16
2817 3240 9.973661 TCCTTATCTCTTTATTTGATTTGGTGA 57.026 29.630 0.00 0.00 0.00 4.02
2819 3242 9.190317 GGTCCTTATCTCTTTATTTGATTTGGT 57.810 33.333 0.00 0.00 0.00 3.67
2820 3243 9.413734 AGGTCCTTATCTCTTTATTTGATTTGG 57.586 33.333 0.00 0.00 0.00 3.28
2832 3255 9.731001 TCTTCCTAAATAAGGTCCTTATCTCTT 57.269 33.333 22.01 15.66 46.62 2.85
2833 3256 9.731001 TTCTTCCTAAATAAGGTCCTTATCTCT 57.269 33.333 22.01 13.17 46.62 3.10
2924 3347 5.046807 GTGTCCCTTGCCTAAGAAACTAGTA 60.047 44.000 0.00 0.00 35.92 1.82
2925 3348 3.908103 TGTCCCTTGCCTAAGAAACTAGT 59.092 43.478 0.00 0.00 35.92 2.57
2926 3349 4.254492 GTGTCCCTTGCCTAAGAAACTAG 58.746 47.826 0.00 0.00 35.92 2.57
2938 3361 0.037590 TGGTACATGGTGTCCCTTGC 59.962 55.000 0.00 0.00 39.04 4.01
2956 3379 3.204306 TGGAGAGGCTATGATGCTTTG 57.796 47.619 0.00 0.00 0.00 2.77
3015 3438 0.251916 CCGCAACTGTCCCCATCTAA 59.748 55.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.