Multiple sequence alignment - TraesCS7B01G112100

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 TraesCS7B01G112100 chr7B 100.000 3783 0 0 1 3783 128760564 128764346 0.000000e+00 6986
1 TraesCS7B01G112100 chr7D 90.759 3268 173 60 559 3743 165480802 165484023 0.000000e+00 4242
2 TraesCS7B01G112100 chr7D 89.606 558 44 7 2 553 165479072 165479621 0.000000e+00 697
3 TraesCS7B01G112100 chr7A 91.817 2835 145 39 1 2803 167160682 167163461 0.000000e+00 3869
4 TraesCS7B01G112100 chr7A 86.700 1015 93 18 2800 3776 167163501 167164511 0.000000e+00 1088
5 TraesCS7B01G112100 chr7A 97.101 69 2 0 2666 2734 167163270 167163338 2.390000e-22 117
6 TraesCS7B01G112100 chr6D 77.519 516 89 24 1994 2487 384294635 384294125 6.180000e-73 285
7 TraesCS7B01G112100 chr6D 75.691 543 99 28 1994 2511 384228178 384227644 1.360000e-59 241
8 TraesCS7B01G112100 chr6A 77.122 542 92 25 1994 2511 526121971 526121438 6.180000e-73 285
9 TraesCS7B01G112100 chr6A 77.316 529 90 24 1994 2498 528924193 528923671 6.180000e-73 285
10 TraesCS7B01G112100 chrUn 76.938 529 91 28 1994 2498 362046797 362047318 4.820000e-69 272


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 TraesCS7B01G112100 chr7B 128760564 128764346 3782 False 6986.000000 6986 100.000000 1 3783 1 chr7B.!!$F1 3782
1 TraesCS7B01G112100 chr7D 165479072 165484023 4951 False 2469.500000 4242 90.182500 2 3743 2 chr7D.!!$F1 3741
2 TraesCS7B01G112100 chr7A 167160682 167164511 3829 False 1691.333333 3869 91.872667 1 3776 3 chr7A.!!$F1 3775
3 TraesCS7B01G112100 chr6D 384294125 384294635 510 True 285.000000 285 77.519000 1994 2487 1 chr6D.!!$R2 493
4 TraesCS7B01G112100 chr6D 384227644 384228178 534 True 241.000000 241 75.691000 1994 2511 1 chr6D.!!$R1 517
5 TraesCS7B01G112100 chr6A 526121438 526121971 533 True 285.000000 285 77.122000 1994 2511 1 chr6A.!!$R1 517
6 TraesCS7B01G112100 chr6A 528923671 528924193 522 True 285.000000 285 77.316000 1994 2498 1 chr6A.!!$R2 504
7 TraesCS7B01G112100 chrUn 362046797 362047318 521 False 272.000000 272 76.938000 1994 2498 1 chrUn.!!$F1 504

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
966 2153 0.032540 GCCCAACAGAAGCACAAAGG 59.967 55.0 0.00 0.0 0.00 3.11 F
968 2155 0.746063 CCAACAGAAGCACAAAGGCA 59.254 50.0 0.00 0.0 35.83 4.75 F
1943 3144 0.179225 TACGTAAGACCGAACGACGC 60.179 55.0 1.45 0.0 41.55 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 3093 0.108207 GGCTGATGGTCTCCATGAGG 59.892 60.0 14.81 3.66 45.26 3.86 R
2259 3465 1.431488 CGTCGATCCCTTGGCATGTG 61.431 60.0 0.00 0.00 0.00 3.21 R
3559 4872 0.460987 GGTCTGGCTCTTCATCCACG 60.461 60.0 0.00 0.00 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
92 93 9.956640 TGGAAATTTTTATAATTGGAGCATTGT 57.043 25.926 0.00 0.00 0.00 2.71
115 116 7.956558 TGTAGTTTTATTACTTTAGAGCACGC 58.043 34.615 0.00 0.00 0.00 5.34
131 132 5.577945 AGAGCACGCCATTTTTCATTATTTG 59.422 36.000 0.00 0.00 0.00 2.32
136 137 7.444245 CACGCCATTTTTCATTATTTGTACAC 58.556 34.615 0.00 0.00 0.00 2.90
140 141 9.593134 GCCATTTTTCATTATTTGTACACCATA 57.407 29.630 0.00 0.00 0.00 2.74
254 259 1.229428 TCTGCCTTTCTCAAAGCACG 58.771 50.000 0.00 0.00 37.18 5.34
313 319 2.684374 CAAATCTGCCACGATCAATCCA 59.316 45.455 0.00 0.00 0.00 3.41
414 421 6.761731 TGTTTTGATTTTTCTGTTATGGCG 57.238 33.333 0.00 0.00 0.00 5.69
434 441 5.473162 TGGCGAAGAAAATACATATCATGGG 59.527 40.000 0.00 0.00 33.60 4.00
525 532 2.686405 TGTTCGGCTCAGATACGTACAT 59.314 45.455 0.00 0.00 33.99 2.29
553 561 3.802948 TTAGCGTCTTCTTCCCTCATC 57.197 47.619 0.00 0.00 0.00 2.92
555 563 2.114616 AGCGTCTTCTTCCCTCATCAT 58.885 47.619 0.00 0.00 0.00 2.45
557 565 3.706594 AGCGTCTTCTTCCCTCATCATAA 59.293 43.478 0.00 0.00 0.00 1.90
616 1800 2.978156 ATTCTCCTTCCTTGCACCAA 57.022 45.000 0.00 0.00 0.00 3.67
626 1810 0.039618 CTTGCACCAAGGTACCCCAT 59.960 55.000 8.74 0.00 37.77 4.00
648 1835 1.784283 CCATGAAAAACCGTTTGCGAC 59.216 47.619 0.00 0.00 41.33 5.19
684 1871 1.065053 ACAACAACCACAGCTACCACA 60.065 47.619 0.00 0.00 0.00 4.17
692 1879 1.206610 CACAGCTACCACATCAGCTCT 59.793 52.381 0.00 0.00 44.83 4.09
755 1942 0.040067 CCAAGCCTTTTCTCACACGC 60.040 55.000 0.00 0.00 0.00 5.34
762 1949 1.126846 CTTTTCTCACACGCTTAGCCG 59.873 52.381 0.00 0.00 0.00 5.52
778 1965 1.888512 AGCCGTTGCAATTCAATCACT 59.111 42.857 0.59 0.00 41.13 3.41
791 1978 1.327460 CAATCACTACACCCAATCGCG 59.673 52.381 0.00 0.00 0.00 5.87
819 2006 5.171476 CAAAATTCTCTCGCTACCAGAAGA 58.829 41.667 0.00 0.00 29.78 2.87
846 2033 3.233507 ACTTGCAGGAAATGTCATGGTT 58.766 40.909 1.40 0.00 36.05 3.67
847 2034 3.642848 ACTTGCAGGAAATGTCATGGTTT 59.357 39.130 1.40 0.00 36.05 3.27
848 2035 3.663995 TGCAGGAAATGTCATGGTTTG 57.336 42.857 0.00 0.00 36.05 2.93
854 2041 3.319755 GAAATGTCATGGTTTGCACCTG 58.680 45.455 0.00 0.00 44.61 4.00
921 2108 0.532573 CCACTCGGTGCACACTAGAT 59.467 55.000 20.43 0.00 31.34 1.98
955 2142 0.825010 ACCAGCTTCTTGCCCAACAG 60.825 55.000 0.00 0.00 44.23 3.16
959 2146 0.038801 GCTTCTTGCCCAACAGAAGC 60.039 55.000 15.96 15.96 44.54 3.86
960 2147 1.321474 CTTCTTGCCCAACAGAAGCA 58.679 50.000 0.00 0.00 31.41 3.91
961 2148 1.000938 CTTCTTGCCCAACAGAAGCAC 60.001 52.381 0.00 0.00 35.96 4.40
962 2149 0.106769 TCTTGCCCAACAGAAGCACA 60.107 50.000 0.00 0.00 35.96 4.57
963 2150 0.746063 CTTGCCCAACAGAAGCACAA 59.254 50.000 0.00 0.00 35.96 3.33
964 2151 1.136695 CTTGCCCAACAGAAGCACAAA 59.863 47.619 0.00 0.00 35.96 2.83
965 2152 0.746063 TGCCCAACAGAAGCACAAAG 59.254 50.000 0.00 0.00 0.00 2.77
966 2153 0.032540 GCCCAACAGAAGCACAAAGG 59.967 55.000 0.00 0.00 0.00 3.11
967 2154 0.032540 CCCAACAGAAGCACAAAGGC 59.967 55.000 0.00 0.00 0.00 4.35
968 2155 0.746063 CCAACAGAAGCACAAAGGCA 59.254 50.000 0.00 0.00 35.83 4.75
969 2156 1.342174 CCAACAGAAGCACAAAGGCAT 59.658 47.619 0.00 0.00 35.83 4.40
970 2157 2.224113 CCAACAGAAGCACAAAGGCATT 60.224 45.455 0.00 0.00 35.83 3.56
1074 2261 1.150992 GGCCGGAGTAGCTCTAGGA 59.849 63.158 5.05 0.00 32.97 2.94
1075 2262 0.891904 GGCCGGAGTAGCTCTAGGAG 60.892 65.000 5.05 0.00 32.97 3.69
1113 2300 1.227556 GGCGCCGGTGATCTACATT 60.228 57.895 21.76 0.00 0.00 2.71
1407 2600 3.082548 CTCCCTGTATATGACCGACGAT 58.917 50.000 0.00 0.00 0.00 3.73
1458 2651 1.448540 CGGCGCAGGACTTCTCAAT 60.449 57.895 10.83 0.00 0.00 2.57
1502 2695 2.204237 CGATCGAGCCATGATGTTTCA 58.796 47.619 10.26 0.00 36.00 2.69
1616 2813 2.782192 GTCGTTCGACAACCAGATATCG 59.218 50.000 18.42 0.00 35.41 2.92
1622 2819 5.571784 TCGACAACCAGATATCGTACTTT 57.428 39.130 0.00 0.00 36.03 2.66
1789 2990 4.325204 GCAATGTACAAGTTGATACGACGA 59.675 41.667 10.54 0.00 0.00 4.20
1892 3093 1.519455 CGACCAGTTCATCGGCCTC 60.519 63.158 0.00 0.00 34.67 4.70
1941 3142 1.883476 GGTACGTAAGACCGAACGAC 58.117 55.000 0.00 0.00 41.55 4.34
1942 3143 1.514136 GTACGTAAGACCGAACGACG 58.486 55.000 0.00 0.00 41.55 5.12
1943 3144 0.179225 TACGTAAGACCGAACGACGC 60.179 55.000 1.45 0.00 41.55 5.19
1944 3145 2.148365 CGTAAGACCGAACGACGCC 61.148 63.158 0.00 0.00 41.55 5.68
1945 3146 1.081242 GTAAGACCGAACGACGCCA 60.081 57.895 0.00 0.00 41.07 5.69
1946 3147 1.069378 GTAAGACCGAACGACGCCAG 61.069 60.000 0.00 0.00 41.07 4.85
1947 3148 1.518056 TAAGACCGAACGACGCCAGT 61.518 55.000 0.00 0.00 41.07 4.00
1950 3151 1.069378 GACCGAACGACGCCAGTAAG 61.069 60.000 0.00 0.00 41.07 2.34
1951 3152 2.442188 CCGAACGACGCCAGTAAGC 61.442 63.158 0.00 0.00 41.07 3.09
1952 3153 1.443872 CGAACGACGCCAGTAAGCT 60.444 57.895 0.00 0.00 34.51 3.74
1956 3162 0.599558 ACGACGCCAGTAAGCTGTAA 59.400 50.000 0.00 0.00 41.02 2.41
1957 3163 1.269166 CGACGCCAGTAAGCTGTAAG 58.731 55.000 0.00 0.00 41.02 2.34
1962 3168 3.119566 ACGCCAGTAAGCTGTAAGAGTAC 60.120 47.826 0.00 0.00 41.02 2.73
1971 3177 2.476854 GCTGTAAGAGTACCACGTACCG 60.477 54.545 0.00 6.25 39.58 4.02
1975 3181 1.896220 AGAGTACCACGTACCGTTGA 58.104 50.000 0.00 0.00 39.58 3.18
2001 3207 7.040686 ACGTAATTATTTTGTTTCTGCAGAGGT 60.041 33.333 17.43 0.00 0.00 3.85
2112 3318 0.249911 GTGCCTGGAAGACGTGAACT 60.250 55.000 0.00 0.00 34.07 3.01
2113 3319 0.468226 TGCCTGGAAGACGTGAACTT 59.532 50.000 0.00 0.00 34.07 2.66
2725 3954 3.281359 GAATGGCAACGGCACCACC 62.281 63.158 0.00 0.00 41.84 4.61
2966 4255 0.388778 TTGCGTCGGCTTTATCGTGA 60.389 50.000 0.00 0.00 40.82 4.35
2969 4258 0.921347 CGTCGGCTTTATCGTGAAGG 59.079 55.000 0.00 0.00 0.00 3.46
2975 4264 3.608506 CGGCTTTATCGTGAAGGATATCG 59.391 47.826 0.00 0.00 0.00 2.92
2986 4275 0.822532 AGGATATCGCGTTCCCGTCT 60.823 55.000 17.60 2.63 36.15 4.18
2996 4285 2.636830 CGTTCCCGTCTAGGTCTTCTA 58.363 52.381 0.00 0.00 38.74 2.10
3016 4305 1.939785 GAGACGGCGTATCAGCACG 60.940 63.158 27.71 0.00 44.71 5.34
3038 4327 3.863424 GCATCTCCGACTCGATTTACAAA 59.137 43.478 0.00 0.00 0.00 2.83
3042 4331 1.657094 CCGACTCGATTTACAAACGGG 59.343 52.381 0.00 0.00 36.27 5.28
3043 4332 2.331194 CGACTCGATTTACAAACGGGT 58.669 47.619 0.00 0.00 43.43 5.28
3044 4333 2.733026 CGACTCGATTTACAAACGGGTT 59.267 45.455 0.00 0.00 40.83 4.11
3045 4334 3.919804 CGACTCGATTTACAAACGGGTTA 59.080 43.478 0.00 0.00 40.83 2.85
3046 4335 4.385447 CGACTCGATTTACAAACGGGTTAA 59.615 41.667 0.00 0.00 40.83 2.01
3049 4338 4.640364 TCGATTTACAAACGGGTTAACCT 58.360 39.130 23.69 5.84 36.97 3.50
3057 4346 2.014335 ACGGGTTAACCTGAATACGC 57.986 50.000 35.20 11.29 45.36 4.42
3058 4347 1.292992 CGGGTTAACCTGAATACGCC 58.707 55.000 26.83 4.74 45.36 5.68
3059 4348 1.405797 CGGGTTAACCTGAATACGCCA 60.406 52.381 26.83 0.00 45.36 5.69
3060 4349 2.743838 CGGGTTAACCTGAATACGCCAT 60.744 50.000 26.83 0.00 45.36 4.40
3065 4356 6.315393 GGGTTAACCTGAATACGCCATATATG 59.685 42.308 23.69 5.68 35.85 1.78
3090 4381 0.333993 AGAGTACCGGCTTCCCTGTA 59.666 55.000 0.00 0.00 30.60 2.74
3100 4391 3.738281 CGGCTTCCCTGTAGTTGATACTG 60.738 52.174 0.00 0.00 35.78 2.74
3106 4400 7.769044 GCTTCCCTGTAGTTGATACTGAAAATA 59.231 37.037 0.00 0.00 35.84 1.40
3117 4421 6.216569 TGATACTGAAAATATCTGCGTCTCC 58.783 40.000 0.00 0.00 31.43 3.71
3163 4467 3.333189 CACCGGCGCGATGATGAG 61.333 66.667 12.10 0.00 0.00 2.90
3185 4489 3.006728 TTCTTCGGGCCGGTGGAT 61.007 61.111 27.98 0.00 0.00 3.41
3201 4505 1.186267 GGATGGGGTACTAGGCCTCG 61.186 65.000 9.68 5.28 0.00 4.63
3219 4523 0.739462 CGTAATGGCGTGGCTTCTGA 60.739 55.000 0.00 0.00 0.00 3.27
3225 4529 0.674895 GGCGTGGCTTCTGATCTTGT 60.675 55.000 0.00 0.00 0.00 3.16
3250 4554 0.696501 ATTGTGGGGTTCTTAGCGGT 59.303 50.000 0.00 0.00 0.00 5.68
3254 4558 2.306512 TGTGGGGTTCTTAGCGGTAATT 59.693 45.455 7.64 0.00 0.00 1.40
3260 4564 4.186159 GGTTCTTAGCGGTAATTGCAGTA 58.814 43.478 7.64 0.00 33.85 2.74
3489 4802 2.420890 CGATCTGCCTGGAGGAGC 59.579 66.667 0.00 0.00 37.39 4.70
3506 4819 3.007920 CTCCAGCAGGGACAGGCT 61.008 66.667 0.00 0.00 42.15 4.58
3573 4886 2.125512 ACGCGTGGATGAAGAGCC 60.126 61.111 12.93 0.00 0.00 4.70
3669 4982 1.421485 CTTAGCGCGCAAAGAGGTG 59.579 57.895 35.10 9.98 0.00 4.00
3704 5018 6.203723 GCTGATATGTTCTTTTAGCCGATCTT 59.796 38.462 0.00 0.00 0.00 2.40
3751 5068 6.235231 AGTGTTTACAGGTACATAGATGGG 57.765 41.667 0.00 0.00 0.00 4.00
3758 5075 8.736097 TTACAGGTACATAGATGGGTTCATAT 57.264 34.615 0.00 0.00 32.98 1.78
3761 5078 7.099764 CAGGTACATAGATGGGTTCATATGTC 58.900 42.308 1.90 0.00 35.43 3.06
3776 5093 7.495606 GGTTCATATGTCATGTCAAGTCATACA 59.504 37.037 1.90 0.00 0.00 2.29
3777 5094 9.049523 GTTCATATGTCATGTCAAGTCATACAT 57.950 33.333 1.90 0.00 36.78 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 7.063780 GGCGTGCTCTAAAGTAATAAAACTACA 59.936 37.037 0.00 0.00 0.00 2.74
92 93 7.098477 TGGCGTGCTCTAAAGTAATAAAACTA 58.902 34.615 0.00 0.00 0.00 2.24
103 104 4.159377 TGAAAAATGGCGTGCTCTAAAG 57.841 40.909 0.00 0.00 0.00 1.85
231 236 4.625028 GTGCTTTGAGAAAGGCAGAAAAT 58.375 39.130 0.00 0.00 38.93 1.82
466 473 4.646492 AGCCCATTTTCCTGTGATATCAAC 59.354 41.667 7.07 2.82 0.00 3.18
469 476 5.859205 AAAGCCCATTTTCCTGTGATATC 57.141 39.130 0.00 0.00 0.00 1.63
472 479 4.980339 AAAAAGCCCATTTTCCTGTGAT 57.020 36.364 0.00 0.00 40.27 3.06
553 561 6.334202 GGGAGCGATAGAAATAGGACTTATG 58.666 44.000 0.00 0.00 39.76 1.90
555 563 4.458295 CGGGAGCGATAGAAATAGGACTTA 59.542 45.833 0.00 0.00 39.76 2.24
557 565 2.820787 CGGGAGCGATAGAAATAGGACT 59.179 50.000 0.00 0.00 39.76 3.85
582 1766 2.417243 GGAGAATTTGGTTGGAATGCGG 60.417 50.000 0.00 0.00 0.00 5.69
618 1802 2.093711 GGTTTTTCATGGCATGGGGTAC 60.094 50.000 26.15 17.99 0.00 3.34
626 1810 1.576356 GCAAACGGTTTTTCATGGCA 58.424 45.000 2.79 0.00 0.00 4.92
648 1835 2.542178 TGTTGTGGAAATGTCGTTCTCG 59.458 45.455 0.00 0.00 38.55 4.04
684 1871 0.108898 GTGTCGTGAGCAGAGCTGAT 60.109 55.000 0.85 0.00 39.88 2.90
692 1879 0.885879 AATCGGTAGTGTCGTGAGCA 59.114 50.000 0.00 0.00 0.00 4.26
755 1942 3.853671 GTGATTGAATTGCAACGGCTAAG 59.146 43.478 0.00 0.00 39.78 2.18
762 1949 4.022416 TGGGTGTAGTGATTGAATTGCAAC 60.022 41.667 0.00 0.00 39.78 4.17
791 1978 1.168714 AGCGAGAGAATTTTGTGCCC 58.831 50.000 0.00 0.00 0.00 5.36
819 2006 2.365293 GACATTTCCTGCAAGTTTGGGT 59.635 45.455 0.00 0.00 0.00 4.51
915 2102 4.141620 GGTGGTGATTGGTGATGATCTAGT 60.142 45.833 0.00 0.00 0.00 2.57
921 2108 1.614051 GCTGGTGGTGATTGGTGATGA 60.614 52.381 0.00 0.00 0.00 2.92
955 2142 1.666888 CGGTGAATGCCTTTGTGCTTC 60.667 52.381 0.00 0.00 0.00 3.86
959 2146 0.523072 CCTCGGTGAATGCCTTTGTG 59.477 55.000 0.00 0.00 0.00 3.33
960 2147 0.400213 TCCTCGGTGAATGCCTTTGT 59.600 50.000 0.00 0.00 0.00 2.83
961 2148 1.089920 CTCCTCGGTGAATGCCTTTG 58.910 55.000 0.00 0.00 0.00 2.77
962 2149 0.035056 CCTCCTCGGTGAATGCCTTT 60.035 55.000 0.00 0.00 0.00 3.11
963 2150 0.909610 TCCTCCTCGGTGAATGCCTT 60.910 55.000 0.00 0.00 0.00 4.35
964 2151 0.909610 TTCCTCCTCGGTGAATGCCT 60.910 55.000 0.00 0.00 0.00 4.75
965 2152 0.035439 TTTCCTCCTCGGTGAATGCC 60.035 55.000 0.00 0.00 0.00 4.40
966 2153 1.373570 CTTTCCTCCTCGGTGAATGC 58.626 55.000 0.00 0.00 0.00 3.56
967 2154 1.065854 AGCTTTCCTCCTCGGTGAATG 60.066 52.381 0.00 0.00 0.00 2.67
968 2155 1.065854 CAGCTTTCCTCCTCGGTGAAT 60.066 52.381 0.00 0.00 0.00 2.57
969 2156 0.321671 CAGCTTTCCTCCTCGGTGAA 59.678 55.000 0.00 0.00 0.00 3.18
970 2157 0.541998 TCAGCTTTCCTCCTCGGTGA 60.542 55.000 0.00 0.00 0.00 4.02
1054 2241 0.540830 CCTAGAGCTACTCCGGCCAT 60.541 60.000 2.24 0.00 0.00 4.40
1085 2272 3.431725 CCGGCGCCTTCTTTGTCC 61.432 66.667 26.68 0.00 0.00 4.02
1113 2300 4.470876 GACATCGAGTCGCCGAAA 57.529 55.556 7.92 0.00 42.22 3.46
1446 2639 1.827969 CCGGTCTCATTGAGAAGTCCT 59.172 52.381 17.73 0.00 40.59 3.85
1458 2651 1.274167 ACGAAGTAAATGCCGGTCTCA 59.726 47.619 1.90 0.00 41.94 3.27
1502 2695 4.832248 TCTGCAACAATTAACGAGGAGAT 58.168 39.130 0.00 0.00 0.00 2.75
1616 2813 4.434857 GCGTTCTTGATCTGCTCAAAGTAC 60.435 45.833 0.00 0.00 43.20 2.73
1622 2819 0.321346 TGGCGTTCTTGATCTGCTCA 59.679 50.000 0.00 0.00 0.00 4.26
1743 2940 1.683943 CGGGGCAACTGATTGATCAT 58.316 50.000 0.00 0.00 38.15 2.45
1892 3093 0.108207 GGCTGATGGTCTCCATGAGG 59.892 60.000 14.81 3.66 45.26 3.86
1909 3110 2.815647 GTACCGTGAGCTGCTGGC 60.816 66.667 7.01 0.00 42.19 4.85
1934 3135 1.443872 AGCTTACTGGCGTCGTTCG 60.444 57.895 0.00 0.00 43.12 3.95
1936 3137 4.261888 CAGCTTACTGGCGTCGTT 57.738 55.556 0.00 0.00 40.48 3.85
1943 3144 9.679721 GTACGTGGTACTCTTACAGCTTACTGG 62.680 48.148 0.00 0.00 40.65 4.00
1944 3145 6.891884 GTACGTGGTACTCTTACAGCTTACTG 60.892 46.154 0.00 0.00 41.34 2.74
1945 3146 4.077822 ACGTGGTACTCTTACAGCTTACT 58.922 43.478 0.00 0.00 0.00 2.24
1946 3147 4.431661 ACGTGGTACTCTTACAGCTTAC 57.568 45.455 0.00 0.00 0.00 2.34
1947 3148 4.396166 GGTACGTGGTACTCTTACAGCTTA 59.604 45.833 0.00 0.00 38.85 3.09
1950 3151 3.142404 GGTACGTGGTACTCTTACAGC 57.858 52.381 0.00 0.00 38.85 4.40
1971 3177 8.276060 TGCAGAAACAAAATAATTACGTCAAC 57.724 30.769 0.00 0.00 0.00 3.18
1975 3181 7.040686 ACCTCTGCAGAAACAAAATAATTACGT 60.041 33.333 18.85 0.00 0.00 3.57
2112 3318 2.215196 GTTGAACTGAAGGGCGTACAA 58.785 47.619 0.00 0.00 0.00 2.41
2113 3319 1.870580 CGTTGAACTGAAGGGCGTACA 60.871 52.381 0.00 0.00 0.00 2.90
2257 3463 1.750018 CGATCCCTTGGCATGTGCA 60.750 57.895 7.36 0.00 44.36 4.57
2258 3464 1.451927 TCGATCCCTTGGCATGTGC 60.452 57.895 0.00 0.00 41.14 4.57
2259 3465 1.431488 CGTCGATCCCTTGGCATGTG 61.431 60.000 0.00 0.00 0.00 3.21
2519 3748 2.668550 GACGGTGGTGTTGCCCTC 60.669 66.667 0.00 0.00 36.04 4.30
2695 3924 2.270205 CCATTCACAGGCCTCGCT 59.730 61.111 0.00 0.00 0.00 4.93
2979 4268 1.833630 TCGTAGAAGACCTAGACGGGA 59.166 52.381 0.00 0.00 36.97 5.14
2986 4275 1.661341 GCCGTCTCGTAGAAGACCTA 58.339 55.000 0.00 0.00 34.09 3.08
2996 4285 2.404186 TGCTGATACGCCGTCTCGT 61.404 57.895 0.00 0.00 45.49 4.18
3016 4305 3.079960 TGTAAATCGAGTCGGAGATGC 57.920 47.619 13.54 1.56 40.67 3.91
3038 4327 1.405933 GGCGTATTCAGGTTAACCCGT 60.406 52.381 21.30 7.39 38.74 5.28
3042 4331 7.303634 CCATATATGGCGTATTCAGGTTAAC 57.696 40.000 18.77 0.00 41.75 2.01
3058 4347 4.929808 GCCGGTACTCTGTTTCCATATATG 59.070 45.833 1.90 5.68 0.00 1.78
3059 4348 4.838986 AGCCGGTACTCTGTTTCCATATAT 59.161 41.667 1.90 0.00 0.00 0.86
3060 4349 4.220724 AGCCGGTACTCTGTTTCCATATA 58.779 43.478 1.90 0.00 0.00 0.86
3065 4356 1.675116 GGAAGCCGGTACTCTGTTTCC 60.675 57.143 1.90 8.69 0.00 3.13
3072 4363 0.745468 CTACAGGGAAGCCGGTACTC 59.255 60.000 1.90 0.00 0.00 2.59
3090 4381 7.268586 AGACGCAGATATTTTCAGTATCAACT 58.731 34.615 0.00 0.00 35.91 3.16
3100 4391 3.531538 TGTGGGAGACGCAGATATTTTC 58.468 45.455 0.00 0.00 33.95 2.29
3106 4400 0.977627 TGGATGTGGGAGACGCAGAT 60.978 55.000 0.00 0.00 43.91 2.90
3117 4421 3.244976 GCTTGTCGATTTTTGGATGTGG 58.755 45.455 0.00 0.00 0.00 4.17
3148 4452 4.957684 AGCTCATCATCGCGCCGG 62.958 66.667 0.00 0.00 0.00 6.13
3185 4489 0.630673 TTACGAGGCCTAGTACCCCA 59.369 55.000 23.68 8.03 0.00 4.96
3201 4505 1.599542 GATCAGAAGCCACGCCATTAC 59.400 52.381 0.00 0.00 0.00 1.89
3489 4802 2.600729 AAGCCTGTCCCTGCTGGAG 61.601 63.158 11.88 0.28 46.38 3.86
3546 4859 3.545481 CCACGCGTCGATGCAGTC 61.545 66.667 27.92 0.09 34.15 3.51
3559 4872 0.460987 GGTCTGGCTCTTCATCCACG 60.461 60.000 0.00 0.00 0.00 4.94
3573 4886 2.669569 CAACGGGCAGGTGGTCTG 60.670 66.667 0.00 0.00 46.03 3.51
3588 4901 2.689083 CGATATTCCGCCTGCACAA 58.311 52.632 0.00 0.00 0.00 3.33
3607 4920 4.796231 CTCGTTCTGACCCGGCCG 62.796 72.222 21.04 21.04 0.00 6.13
3669 4982 3.254657 AGAACATATCAGCGCCTCTAGAC 59.745 47.826 2.29 0.00 0.00 2.59
3724 5038 9.477484 CCATCTATGTACCTGTAAACACTATTC 57.523 37.037 0.00 0.00 0.00 1.75
3749 5066 5.185454 TGACTTGACATGACATATGAACCC 58.815 41.667 10.38 0.00 0.00 4.11
3751 5068 8.424274 TGTATGACTTGACATGACATATGAAC 57.576 34.615 10.38 3.82 0.00 3.18


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

AutoCloner maintained by Alex Coulton.