Multiple sequence alignment - TraesCS5D01G339500

Loading Multiple Alignment...

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 TraesCS5D01G339500 chr5D 100.000 3125 0 0 1 3125 428511220 428514344 0.000000 5771.0
1 TraesCS5D01G339500 chr5D 83.683 2482 318 44 670 3125 428592700 428595120 0.000000 2259.0
2 TraesCS5D01G339500 chr5D 84.133 2168 307 18 988 3125 428670623 428672783 0.000000 2063.0
3 TraesCS5D01G339500 chr5D 84.243 2107 297 22 1038 3125 428565561 428567651 0.000000 2019.0
4 TraesCS5D01G339500 chr5D 89.286 812 71 11 66 864 428519806 428520614 0.000000 1003.0
5 TraesCS5D01G339500 chr5A 94.865 1811 55 21 1025 2811 544158572 544160368 0.000000 2795.0
6 TraesCS5D01G339500 chr5A 84.729 2161 305 18 986 3125 544452890 544455046 0.000000 2139.0
7 TraesCS5D01G339500 chr5A 82.619 1749 251 33 1016 2726 544461636 544463369 0.000000 1496.0
8 TraesCS5D01G339500 chr5A 88.315 736 84 2 2391 3125 544246354 544247088 0.000000 881.0
9 TraesCS5D01G339500 chr5A 88.790 562 36 5 1 561 544157480 544158015 0.000000 664.0
10 TraesCS5D01G339500 chr5B 83.855 2490 332 49 670 3125 517774595 517777048 0.000000 2307.0
11 TraesCS5D01G339500 chr5B 84.215 2173 303 24 986 3125 517797682 517799847 0.000000 2076.0
12 TraesCS5D01G339500 chr5B 83.603 2104 306 27 1038 3125 517694429 517696509 0.000000 1938.0
13 TraesCS5D01G339500 chr4A 91.304 46 2 1 722 767 740378083 740378040 0.000009 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G339500 chr5D 428511220 428514344 3124 False 5771.0 5771 100.0000 1 3125 1 chr5D.!!$F1 3124
1 TraesCS5D01G339500 chr5D 428592700 428595120 2420 False 2259.0 2259 83.6830 670 3125 1 chr5D.!!$F4 2455
2 TraesCS5D01G339500 chr5D 428670623 428672783 2160 False 2063.0 2063 84.1330 988 3125 1 chr5D.!!$F5 2137
3 TraesCS5D01G339500 chr5D 428565561 428567651 2090 False 2019.0 2019 84.2430 1038 3125 1 chr5D.!!$F3 2087
4 TraesCS5D01G339500 chr5D 428519806 428520614 808 False 1003.0 1003 89.2860 66 864 1 chr5D.!!$F2 798
5 TraesCS5D01G339500 chr5A 544452890 544455046 2156 False 2139.0 2139 84.7290 986 3125 1 chr5A.!!$F2 2139
6 TraesCS5D01G339500 chr5A 544157480 544160368 2888 False 1729.5 2795 91.8275 1 2811 2 chr5A.!!$F4 2810
7 TraesCS5D01G339500 chr5A 544461636 544463369 1733 False 1496.0 1496 82.6190 1016 2726 1 chr5A.!!$F3 1710
8 TraesCS5D01G339500 chr5A 544246354 544247088 734 False 881.0 881 88.3150 2391 3125 1 chr5A.!!$F1 734
9 TraesCS5D01G339500 chr5B 517774595 517777048 2453 False 2307.0 2307 83.8550 670 3125 1 chr5B.!!$F2 2455
10 TraesCS5D01G339500 chr5B 517797682 517799847 2165 False 2076.0 2076 84.2150 986 3125 1 chr5B.!!$F3 2139
11 TraesCS5D01G339500 chr5B 517694429 517696509 2080 False 1938.0 1938 83.6030 1038 3125 1 chr5B.!!$F1 2087

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
901 1066 0.027063 AACCATATTTACGCGCGTGC 59.973 50.0 42.78 11.84 37.91 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2826 3062 1.069204 TCTGGCCAGATAGTCGATTGC 59.931 52.381 32.0 0.0 31.41 3.56 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
114 115 6.548251 AGGCCTTAGTAACAAGATAGAGAGAC 59.452 42.308 0.00 0.00 0.00 3.36
115 116 6.239092 GGCCTTAGTAACAAGATAGAGAGACC 60.239 46.154 0.00 0.00 0.00 3.85
144 146 3.753272 TGGAGAAGCTGTACTTTGAATGC 59.247 43.478 0.00 0.00 39.29 3.56
198 200 2.452600 AGGTTGAAAAGGAGGCACAA 57.547 45.000 0.00 0.00 0.00 3.33
262 264 6.287589 AGTCCAACTAATGACACTTCTAGG 57.712 41.667 0.00 0.00 0.00 3.02
263 265 4.870991 GTCCAACTAATGACACTTCTAGGC 59.129 45.833 0.00 0.00 0.00 3.93
340 343 3.305950 CCGTGGAAGAAATGGCATTTTCA 60.306 43.478 25.02 17.38 37.93 2.69
341 344 3.674753 CGTGGAAGAAATGGCATTTTCAC 59.325 43.478 25.02 24.19 37.93 3.18
342 345 4.630111 GTGGAAGAAATGGCATTTTCACA 58.370 39.130 25.02 18.04 37.93 3.58
343 346 4.448732 GTGGAAGAAATGGCATTTTCACAC 59.551 41.667 25.02 23.53 37.93 3.82
344 347 4.344679 TGGAAGAAATGGCATTTTCACACT 59.655 37.500 25.02 14.71 37.93 3.55
345 348 4.925646 GGAAGAAATGGCATTTTCACACTC 59.074 41.667 25.02 11.66 37.93 3.51
346 349 5.509501 GGAAGAAATGGCATTTTCACACTCA 60.510 40.000 25.02 0.00 37.93 3.41
347 350 5.534207 AGAAATGGCATTTTCACACTCAA 57.466 34.783 25.02 0.00 37.93 3.02
348 351 5.916318 AGAAATGGCATTTTCACACTCAAA 58.084 33.333 25.02 0.00 37.93 2.69
349 352 5.754890 AGAAATGGCATTTTCACACTCAAAC 59.245 36.000 25.02 8.95 37.93 2.93
350 353 3.077229 TGGCATTTTCACACTCAAACG 57.923 42.857 0.00 0.00 0.00 3.60
351 354 2.425312 TGGCATTTTCACACTCAAACGT 59.575 40.909 0.00 0.00 0.00 3.99
352 355 3.042887 GGCATTTTCACACTCAAACGTC 58.957 45.455 0.00 0.00 0.00 4.34
353 356 3.488384 GGCATTTTCACACTCAAACGTCA 60.488 43.478 0.00 0.00 0.00 4.35
354 357 4.101942 GCATTTTCACACTCAAACGTCAA 58.898 39.130 0.00 0.00 0.00 3.18
355 358 4.204978 GCATTTTCACACTCAAACGTCAAG 59.795 41.667 0.00 0.00 0.00 3.02
368 387 1.335964 ACGTCAAGAGTGTCCATGTCG 60.336 52.381 0.00 0.00 0.00 4.35
388 407 4.557301 GTCGAACACAAAAAGTTTCCACAG 59.443 41.667 0.00 0.00 0.00 3.66
578 600 9.936759 TTTTAAACCAAAAATCTCTGAACAGTT 57.063 25.926 1.73 0.00 33.14 3.16
583 605 8.974060 ACCAAAAATCTCTGAACAGTTAACTA 57.026 30.769 8.04 0.00 0.00 2.24
595 617 8.400184 TGAACAGTTAACTACTCTACAAGCTA 57.600 34.615 8.04 0.00 33.85 3.32
609 631 4.494350 ACAAGCTAATGTTTGTCAGCAG 57.506 40.909 0.00 0.00 42.55 4.24
612 634 5.530915 ACAAGCTAATGTTTGTCAGCAGTAA 59.469 36.000 0.00 0.00 42.55 2.24
615 637 6.438763 AGCTAATGTTTGTCAGCAGTAAAAC 58.561 36.000 0.00 0.00 36.47 2.43
616 638 5.339611 GCTAATGTTTGTCAGCAGTAAAACG 59.660 40.000 0.00 0.00 35.71 3.60
617 639 3.684103 TGTTTGTCAGCAGTAAAACGG 57.316 42.857 0.00 0.00 35.71 4.44
637 664 1.465689 GGTTTGGTCGCACATCAATCG 60.466 52.381 0.00 0.00 0.00 3.34
647 674 3.179830 GCACATCAATCGACGTAGAAGT 58.820 45.455 1.49 0.00 0.00 3.01
653 680 4.971008 TCAATCGACGTAGAAGTTCTCTG 58.029 43.478 9.12 5.71 35.41 3.35
667 694 1.753930 TCTCTGTGCGGTTCCGTATA 58.246 50.000 12.81 5.90 0.00 1.47
808 941 1.134340 GTACAACTCACACACCACCCA 60.134 52.381 0.00 0.00 0.00 4.51
811 944 1.920734 AACTCACACACCACCCAGCA 61.921 55.000 0.00 0.00 0.00 4.41
827 975 3.498018 CCCAGCAAAAACCAAGCATAAAC 59.502 43.478 0.00 0.00 0.00 2.01
835 983 1.315257 CCAAGCATAAACGGCTGCCT 61.315 55.000 17.92 0.00 41.66 4.75
850 1002 2.556287 CCTCGTTTTGCTGTCCGC 59.444 61.111 0.00 0.00 39.77 5.54
882 1043 4.584743 TGCGCCAATCTCTCTATCTCTTTA 59.415 41.667 4.18 0.00 0.00 1.85
898 1063 4.207635 TCTCTTTAACCATATTTACGCGCG 59.792 41.667 30.96 30.96 0.00 6.86
901 1066 0.027063 AACCATATTTACGCGCGTGC 59.973 50.000 42.78 11.84 37.91 5.34
912 1077 4.627114 CGCGTGCGTGTGTGTGTC 62.627 66.667 6.00 0.00 34.35 3.67
913 1078 3.261951 GCGTGCGTGTGTGTGTCT 61.262 61.111 0.00 0.00 0.00 3.41
921 1086 2.469826 CGTGTGTGTGTCTTCTTGCTA 58.530 47.619 0.00 0.00 0.00 3.49
922 1087 2.863740 CGTGTGTGTGTCTTCTTGCTAA 59.136 45.455 0.00 0.00 0.00 3.09
923 1088 3.302480 CGTGTGTGTGTCTTCTTGCTAAC 60.302 47.826 0.00 0.00 0.00 2.34
942 1107 5.047519 GCTAACAGACTTGTGGGAGTACTTA 60.048 44.000 0.00 0.00 37.67 2.24
943 1108 6.351117 GCTAACAGACTTGTGGGAGTACTTAT 60.351 42.308 0.00 0.00 37.67 1.73
950 1115 6.161381 ACTTGTGGGAGTACTTATGTTTACG 58.839 40.000 0.00 0.00 0.00 3.18
963 1128 4.593597 ATGTTTACGTAATCACTTGGCG 57.406 40.909 18.68 0.00 0.00 5.69
973 1148 0.391130 TCACTTGGCGTATGCAGTCC 60.391 55.000 9.59 0.00 45.35 3.85
974 1149 1.447838 ACTTGGCGTATGCAGTCCG 60.448 57.895 9.59 0.00 45.35 4.79
975 1150 1.447838 CTTGGCGTATGCAGTCCGT 60.448 57.895 9.59 0.00 45.35 4.69
977 1152 1.295357 TTGGCGTATGCAGTCCGTTG 61.295 55.000 9.59 0.00 45.35 4.10
982 1157 1.094785 GTATGCAGTCCGTTGCCATT 58.905 50.000 0.00 0.00 43.43 3.16
983 1158 1.093972 TATGCAGTCCGTTGCCATTG 58.906 50.000 0.00 0.00 43.43 2.82
984 1159 2.126346 GCAGTCCGTTGCCATTGC 60.126 61.111 0.00 0.00 38.13 3.56
1006 1187 4.018609 GTCGTGAGATCATGGCGG 57.981 61.111 0.00 0.00 45.19 6.13
1021 1202 2.198287 GCGGATTCCATGCTGCCAT 61.198 57.895 3.09 0.00 0.00 4.40
1026 1207 1.692173 ATTCCATGCTGCCATTGCCC 61.692 55.000 0.00 0.00 36.33 5.36
1028 1209 3.857038 CATGCTGCCATTGCCCCC 61.857 66.667 0.00 0.00 36.33 5.40
1036 1217 3.463585 CATTGCCCCCGCTGCATT 61.464 61.111 0.00 0.00 38.76 3.56
1058 1240 2.347490 GGCTCTCTCGTTTGCCCA 59.653 61.111 0.00 0.00 39.49 5.36
1062 1244 1.004560 TCTCTCGTTTGCCCAGCTG 60.005 57.895 6.78 6.78 0.00 4.24
1127 1339 3.625897 ACCAGCAGCACGGCACTA 61.626 61.111 0.00 0.00 35.83 2.74
1182 1394 4.842574 TCCACTGGAAATCATCAATCGAA 58.157 39.130 0.00 0.00 0.00 3.71
1185 1397 7.226441 TCCACTGGAAATCATCAATCGAATAT 58.774 34.615 0.00 0.00 0.00 1.28
1190 1402 8.462589 TGGAAATCATCAATCGAATATTCCAA 57.537 30.769 9.87 0.00 0.00 3.53
1239 1457 1.064003 TGTACCCATGCAACTGGACT 58.936 50.000 7.97 0.00 38.69 3.85
1269 1494 2.046892 GGTGACACTCGGCTGCAT 60.047 61.111 5.39 0.00 0.00 3.96
1310 1538 4.568592 GGTCATCAGAGGAATTTCCCTTGT 60.569 45.833 11.92 0.00 37.19 3.16
1374 1602 2.093658 GTCGCTCCCTTACCTCATCAAA 60.094 50.000 0.00 0.00 0.00 2.69
1445 1673 1.815003 CGGCTCTCTTTCCATGCTTTT 59.185 47.619 0.00 0.00 0.00 2.27
1545 1773 2.354259 GACCTCTCCAGCAACAATCTG 58.646 52.381 0.00 0.00 0.00 2.90
2095 2326 5.551233 AGTTTGGAAATCTCGTGAATCTGA 58.449 37.500 0.00 0.00 0.00 3.27
2147 2379 1.641577 GACCAGTGCCGTCAAGTATC 58.358 55.000 0.00 0.00 0.00 2.24
2273 2505 0.955905 ACGAAAACCAATTGTCCGGG 59.044 50.000 0.00 0.00 0.00 5.73
2826 3062 5.942826 GCCTCTATTGGATGGATTTAGGAAG 59.057 44.000 0.00 0.00 0.00 3.46
2985 3221 8.046708 ACATATGAATAACAACAGCCTTAGTGA 58.953 33.333 10.38 0.00 0.00 3.41
3022 3258 0.709992 TGGGCCATTTAGCTTCCCTT 59.290 50.000 0.00 0.00 37.83 3.95
3064 3300 4.580995 AGTATGAATAGTCTCAGTGGACCG 59.419 45.833 7.80 0.00 36.95 4.79
3088 3324 2.154462 CCATCGGAACTCAGCAAACTT 58.846 47.619 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 4.984006 AAGTACAGCTTCTCCAACAGTTGG 60.984 45.833 24.73 24.73 42.17 3.77
115 116 3.733337 AGTACAGCTTCTCCAACAGTTG 58.267 45.455 6.28 6.28 0.00 3.16
130 131 4.346734 AGCAATCGCATTCAAAGTACAG 57.653 40.909 0.00 0.00 42.27 2.74
144 146 4.647424 AAGAGGAGAGAGTAAGCAATCG 57.353 45.455 0.00 0.00 0.00 3.34
198 200 4.054359 ACTGACTTCCAGAGGTAGTGAT 57.946 45.455 0.00 0.00 45.78 3.06
262 264 6.012658 TGTTCAAACAGAGGAAATGTATGC 57.987 37.500 0.00 0.00 34.30 3.14
342 345 2.167693 TGGACACTCTTGACGTTTGAGT 59.832 45.455 11.49 11.49 41.15 3.41
343 346 2.821546 TGGACACTCTTGACGTTTGAG 58.178 47.619 10.46 10.46 0.00 3.02
344 347 2.971660 TGGACACTCTTGACGTTTGA 57.028 45.000 0.00 0.00 0.00 2.69
345 348 2.872245 ACATGGACACTCTTGACGTTTG 59.128 45.455 0.00 0.00 0.00 2.93
346 349 3.131396 GACATGGACACTCTTGACGTTT 58.869 45.455 0.00 0.00 0.00 3.60
347 350 2.755650 GACATGGACACTCTTGACGTT 58.244 47.619 0.00 0.00 0.00 3.99
348 351 1.335964 CGACATGGACACTCTTGACGT 60.336 52.381 0.00 0.00 0.00 4.34
349 352 1.068541 TCGACATGGACACTCTTGACG 60.069 52.381 0.00 0.00 33.85 4.35
350 353 2.724977 TCGACATGGACACTCTTGAC 57.275 50.000 0.00 0.00 0.00 3.18
351 354 2.364002 TGTTCGACATGGACACTCTTGA 59.636 45.455 0.00 0.00 0.00 3.02
352 355 2.476619 GTGTTCGACATGGACACTCTTG 59.523 50.000 9.53 0.00 40.28 3.02
353 356 2.102420 TGTGTTCGACATGGACACTCTT 59.898 45.455 16.04 0.00 43.03 2.85
354 357 1.686587 TGTGTTCGACATGGACACTCT 59.313 47.619 16.04 0.00 43.03 3.24
355 358 2.148916 TGTGTTCGACATGGACACTC 57.851 50.000 16.04 0.00 43.03 3.51
368 387 6.866248 TCTTTCTGTGGAAACTTTTTGTGTTC 59.134 34.615 0.00 0.00 36.63 3.18
388 407 7.707035 TCAAGTGAACTTAACTGTCTCTCTTTC 59.293 37.037 0.00 0.00 34.28 2.62
569 588 7.371936 AGCTTGTAGAGTAGTTAACTGTTCAG 58.628 38.462 18.56 9.30 39.07 3.02
570 589 7.286215 AGCTTGTAGAGTAGTTAACTGTTCA 57.714 36.000 18.56 6.11 39.07 3.18
578 600 9.635520 GACAAACATTAGCTTGTAGAGTAGTTA 57.364 33.333 0.00 0.00 34.39 2.24
583 605 5.409826 GCTGACAAACATTAGCTTGTAGAGT 59.590 40.000 0.00 0.00 34.39 3.24
595 617 4.499019 CCCGTTTTACTGCTGACAAACATT 60.499 41.667 16.45 0.00 0.00 2.71
609 631 0.662085 TGCGACCAAACCCGTTTTAC 59.338 50.000 0.00 0.00 0.00 2.01
612 634 1.104577 ATGTGCGACCAAACCCGTTT 61.105 50.000 0.00 0.00 0.00 3.60
615 637 1.511318 TTGATGTGCGACCAAACCCG 61.511 55.000 0.00 0.00 0.00 5.28
616 638 0.887933 ATTGATGTGCGACCAAACCC 59.112 50.000 0.00 0.00 0.00 4.11
617 639 1.465689 CGATTGATGTGCGACCAAACC 60.466 52.381 0.00 0.00 0.00 3.27
637 664 2.243407 CGCACAGAGAACTTCTACGTC 58.757 52.381 0.00 0.00 33.83 4.34
647 674 0.892755 ATACGGAACCGCACAGAGAA 59.107 50.000 13.32 0.00 44.19 2.87
653 680 5.464389 ACATAATTTCTATACGGAACCGCAC 59.536 40.000 13.32 0.00 44.19 5.34
667 694 6.116126 GTCCAAGTCTGGCTACATAATTTCT 58.884 40.000 0.00 0.00 43.17 2.52
718 835 1.946768 ACACGCATACACACTTGCTTT 59.053 42.857 0.00 0.00 36.71 3.51
808 941 3.389221 CCGTTTATGCTTGGTTTTTGCT 58.611 40.909 0.00 0.00 0.00 3.91
811 944 3.389221 CAGCCGTTTATGCTTGGTTTTT 58.611 40.909 0.00 0.00 36.81 1.94
827 975 3.357079 AGCAAAACGAGGCAGCCG 61.357 61.111 5.55 0.00 0.00 5.52
853 1011 0.747255 GAGAGATTGGCGCACCTCTA 59.253 55.000 10.83 0.00 36.25 2.43
882 1043 0.027063 GCACGCGCGTAAATATGGTT 59.973 50.000 37.24 5.61 0.00 3.67
898 1063 1.006832 AAGAAGACACACACACGCAC 58.993 50.000 0.00 0.00 0.00 5.34
901 1066 1.290203 AGCAAGAAGACACACACACG 58.710 50.000 0.00 0.00 0.00 4.49
907 1072 4.672587 AGTCTGTTAGCAAGAAGACACA 57.327 40.909 10.88 0.00 41.22 3.72
908 1073 4.811557 ACAAGTCTGTTAGCAAGAAGACAC 59.188 41.667 10.88 0.00 41.22 3.67
909 1074 4.811024 CACAAGTCTGTTAGCAAGAAGACA 59.189 41.667 10.88 0.00 41.22 3.41
910 1075 4.212214 CCACAAGTCTGTTAGCAAGAAGAC 59.788 45.833 0.00 0.00 39.47 3.01
911 1076 4.380531 CCACAAGTCTGTTAGCAAGAAGA 58.619 43.478 0.00 0.00 31.64 2.87
912 1077 3.499918 CCCACAAGTCTGTTAGCAAGAAG 59.500 47.826 0.00 0.00 31.64 2.85
913 1078 3.135712 TCCCACAAGTCTGTTAGCAAGAA 59.864 43.478 0.00 0.00 31.64 2.52
921 1086 5.307196 ACATAAGTACTCCCACAAGTCTGTT 59.693 40.000 0.00 0.00 31.64 3.16
922 1087 4.838986 ACATAAGTACTCCCACAAGTCTGT 59.161 41.667 0.00 0.00 35.63 3.41
923 1088 5.407407 ACATAAGTACTCCCACAAGTCTG 57.593 43.478 0.00 0.00 0.00 3.51
942 1107 3.998341 ACGCCAAGTGATTACGTAAACAT 59.002 39.130 19.44 3.99 34.79 2.71
943 1108 3.391965 ACGCCAAGTGATTACGTAAACA 58.608 40.909 12.81 13.24 34.79 2.83
950 1115 2.936498 ACTGCATACGCCAAGTGATTAC 59.064 45.455 0.00 0.00 37.32 1.89
963 1128 1.094785 AATGGCAACGGACTGCATAC 58.905 50.000 8.40 0.00 44.52 2.39
974 1149 1.296056 ACGACGTAGGCAATGGCAAC 61.296 55.000 10.05 0.00 43.71 4.17
975 1150 1.004320 ACGACGTAGGCAATGGCAA 60.004 52.632 10.05 0.00 43.71 4.52
977 1152 1.421410 CTCACGACGTAGGCAATGGC 61.421 60.000 0.00 0.00 40.13 4.40
982 1157 1.065551 CATGATCTCACGACGTAGGCA 59.934 52.381 0.00 2.58 0.00 4.75
983 1158 1.600663 CCATGATCTCACGACGTAGGC 60.601 57.143 0.00 0.00 0.00 3.93
984 1159 1.600663 GCCATGATCTCACGACGTAGG 60.601 57.143 0.00 0.00 0.00 3.18
1006 1187 0.249741 GGCAATGGCAGCATGGAATC 60.250 55.000 0.58 0.00 43.71 2.52
1028 1209 4.189188 GAGCCAGGCAATGCAGCG 62.189 66.667 15.80 0.00 34.64 5.18
1036 1217 1.004560 CAAACGAGAGAGCCAGGCA 60.005 57.895 15.80 0.00 0.00 4.75
1043 1224 1.018226 CAGCTGGGCAAACGAGAGAG 61.018 60.000 5.57 0.00 0.00 3.20
1062 1244 0.392193 TAAGGAGAAGCAGCAGCAGC 60.392 55.000 3.17 0.46 45.49 5.25
1103 1297 2.987547 GTGCTGCTGGTGTGGCAT 60.988 61.111 0.00 0.00 39.07 4.40
1111 1311 3.121030 GTAGTGCCGTGCTGCTGG 61.121 66.667 0.00 4.05 0.00 4.85
1122 1334 2.189342 GATCTCAGCGAAGTGTAGTGC 58.811 52.381 0.00 0.00 0.00 4.40
1126 1338 1.847328 TGGGATCTCAGCGAAGTGTA 58.153 50.000 0.00 0.00 0.00 2.90
1127 1339 0.976641 TTGGGATCTCAGCGAAGTGT 59.023 50.000 0.00 0.00 0.00 3.55
1149 1361 2.352805 CAGTGGAGAAGCACCCCC 59.647 66.667 0.00 0.00 0.00 5.40
1154 1366 3.009363 TGATGATTTCCAGTGGAGAAGCA 59.991 43.478 19.99 19.99 31.21 3.91
1182 1394 3.052642 AGGTTCCCATGTGCTTGGAATAT 60.053 43.478 4.03 0.00 40.11 1.28
1185 1397 0.482446 AGGTTCCCATGTGCTTGGAA 59.518 50.000 5.77 0.00 39.25 3.53
1190 1402 0.842030 TCTCCAGGTTCCCATGTGCT 60.842 55.000 0.00 0.00 0.00 4.40
1269 1494 1.752198 CTTCACCGTGGTTCCTCCA 59.248 57.895 0.00 0.00 45.01 3.86
1310 1538 3.682885 CTGCAATGCCGGCACCAA 61.683 61.111 35.50 16.99 36.11 3.67
1330 1558 2.040412 GGAATCTCAGGGTGTCCAGTTT 59.960 50.000 0.00 0.00 34.83 2.66
1374 1602 0.171455 GATTGTCGCTGAGGTCGAGT 59.829 55.000 0.00 0.00 36.56 4.18
1445 1673 1.694150 CACCAGAGAAGTTGAGGGTGA 59.306 52.381 2.56 0.00 46.67 4.02
1545 1773 2.442830 GGAGGGATTTGGCCAGCC 60.443 66.667 5.11 9.28 0.00 4.85
2095 2326 7.506938 TGAAATTTTCAGAGAGGTCAAGGATTT 59.493 33.333 7.74 0.00 34.08 2.17
2147 2379 3.927142 GTCTAAGTGAAGACATGTTCCCG 59.073 47.826 0.00 0.00 44.41 5.14
2273 2505 5.527214 CCAATTTTCCAAAACTTTGAGGGAC 59.473 40.000 3.72 0.00 40.55 4.46
2826 3062 1.069204 TCTGGCCAGATAGTCGATTGC 59.931 52.381 32.00 0.00 31.41 3.56
2935 3171 8.409371 TGTAATGACTGCAGTTTCAAACAATTA 58.591 29.630 22.65 7.51 0.00 1.40
2985 3221 3.750922 GCCCAAACTACCAGGAAGACTTT 60.751 47.826 0.00 0.00 0.00 2.66
3022 3258 7.049754 TCATACTAAGATCAAGCATGCTTTGA 58.950 34.615 30.07 26.88 33.42 2.69
3064 3300 2.890808 TGCTGAGTTCCGATGGTATC 57.109 50.000 0.00 0.00 0.00 2.24
3088 3324 4.392047 AGTTCACAAACATCAGCATCTCA 58.608 39.130 0.00 0.00 37.88 3.27


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

AutoCloner maintained by Alex Coulton.