Multiple sequence alignment - TraesCS6D01G077700

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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 TraesCS6D01G077700 chr6D 100.000 3157 0 0 648 3804 41925293 41928449 0.000000e+00 5830
1 TraesCS6D01G077700 chr6D 100.000 311 0 0 1 311 41924646 41924956 3.300000e-160 575
2 TraesCS6D01G077700 chr6B 89.188 2488 149 54 651 3040 95331068 95328603 0.000000e+00 2994
3 TraesCS6D01G077700 chr6B 86.507 667 68 15 3097 3751 95328225 95327569 0.000000e+00 713
4 TraesCS6D01G077700 chr6B 87.379 309 36 3 1 307 95331394 95331087 6.050000e-93 351
5 TraesCS6D01G077700 chr6A 91.556 900 46 12 2159 3036 52396681 52397572 0.000000e+00 1214
6 TraesCS6D01G077700 chr6A 87.420 938 83 23 649 1560 52395217 52396145 0.000000e+00 1046
7 TraesCS6D01G077700 chr6A 85.211 710 60 18 3103 3802 52398031 52398705 0.000000e+00 688
8 TraesCS6D01G077700 chr6A 88.274 307 33 3 1 304 52394890 52395196 7.770000e-97 364


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 TraesCS6D01G077700 chr6D 41924646 41928449 3803 False 3202.500000 5830 100.000000 1 3804 2 chr6D.!!$F1 3803
1 TraesCS6D01G077700 chr6B 95327569 95331394 3825 True 1352.666667 2994 87.691333 1 3751 3 chr6B.!!$R1 3750
2 TraesCS6D01G077700 chr6A 52394890 52398705 3815 False 828.000000 1214 88.115250 1 3802 4 chr6A.!!$F1 3801

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
157 158 0.031585 TTCTTGTGTAGCGCTGACGT 59.968 50.0 22.90 0.00 42.83 4.34 F
229 232 0.105246 AGGCGGGATTGAGAGAGGAT 60.105 55.0 0.00 0.00 0.00 3.24 F
1601 1682 0.110283 TCGTTCGACATCGCGTGTTA 60.110 50.0 5.77 0.24 42.36 2.41 F
2176 2328 0.248289 AATGCAAAGCTCATGCCACC 59.752 50.0 18.59 0.00 43.16 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1769 0.037326 CTCTGCTTCGGCTTGTACCA 60.037 55.0 0.00 0.0 42.37 3.25 R
1669 1770 0.246635 TCTCTGCTTCGGCTTGTACC 59.753 55.0 0.00 0.0 42.37 3.34 R
2657 2828 0.175302 CCAGCCACAGCAACAAACAA 59.825 50.0 0.00 0.0 43.56 2.83 R
3415 4039 0.819259 ACAGGTTTGTGTGATGCGCT 60.819 50.0 9.73 0.0 35.83 5.92 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
45 46 4.487412 GGCTGCGATTGCCTGTGC 62.487 66.667 1.50 1.85 46.38 4.57
86 87 0.324738 TGTGGAGGAATCGGAGCTCT 60.325 55.000 14.64 0.00 0.00 4.09
151 152 0.161024 GTGTCGTTCTTGTGTAGCGC 59.839 55.000 0.00 0.00 0.00 5.92
157 158 0.031585 TTCTTGTGTAGCGCTGACGT 59.968 50.000 22.90 0.00 42.83 4.34
159 160 0.161658 CTTGTGTAGCGCTGACGTTG 59.838 55.000 22.90 6.90 42.83 4.10
180 182 3.953612 TGTTGCATTGTTGGAGTTCTTCT 59.046 39.130 0.00 0.00 0.00 2.85
209 212 3.577649 GAGACCTCAATCTCGTGACAA 57.422 47.619 0.00 0.00 36.05 3.18
210 213 3.914312 GAGACCTCAATCTCGTGACAAA 58.086 45.455 0.00 0.00 36.05 2.83
229 232 0.105246 AGGCGGGATTGAGAGAGGAT 60.105 55.000 0.00 0.00 0.00 3.24
247 250 2.417107 GGATGGATTGTGAAATTGCGCA 60.417 45.455 5.66 5.66 0.00 6.09
251 254 1.906966 GATTGTGAAATTGCGCAGACG 59.093 47.619 11.31 0.00 44.07 4.18
269 272 1.270947 ACGTCGGCTTGATTTTGGGTA 60.271 47.619 0.00 0.00 0.00 3.69
271 274 1.132453 GTCGGCTTGATTTTGGGTAGC 59.868 52.381 0.00 0.00 0.00 3.58
309 313 3.866356 GTGGCGAACGTAGAACCC 58.134 61.111 0.00 0.00 0.00 4.11
697 701 2.755469 CCCGGGCTGATTTGGTGG 60.755 66.667 8.08 0.00 0.00 4.61
698 702 2.354729 CCGGGCTGATTTGGTGGA 59.645 61.111 0.00 0.00 0.00 4.02
714 718 2.691927 GTGGAACCGTTCGGTCTAAAT 58.308 47.619 17.19 1.19 37.57 1.40
739 743 1.078285 ACGTGTTTTGGTGACCCGT 60.078 52.632 0.00 0.00 0.00 5.28
766 770 1.248101 ATGCCCTAACCCGTTTGCAC 61.248 55.000 0.00 0.00 0.00 4.57
780 784 4.562394 CCGTTTGCACTATTATTTGCCAAG 59.438 41.667 0.00 0.00 38.00 3.61
835 839 4.838152 CGAGGCCCCATCCACACG 62.838 72.222 0.00 0.00 0.00 4.49
879 896 2.027837 AGCAAAAAGGCCAAGCATAAGG 60.028 45.455 5.01 0.00 0.00 2.69
919 936 0.415429 TCCAAGCCCCTCTCTCTCTT 59.585 55.000 0.00 0.00 0.00 2.85
920 937 0.829990 CCAAGCCCCTCTCTCTCTTC 59.170 60.000 0.00 0.00 0.00 2.87
1323 1358 2.852075 TGGGACCTCAGCCGGTTT 60.852 61.111 1.90 0.00 37.42 3.27
1380 1415 1.320344 TAGACGCCGGTGAGATTGCT 61.320 55.000 24.59 10.67 0.00 3.91
1445 1512 3.363627 AGTAACAGTAGACAGTAGGCCC 58.636 50.000 0.00 0.00 0.00 5.80
1447 1514 2.320681 ACAGTAGACAGTAGGCCCAA 57.679 50.000 0.00 0.00 0.00 4.12
1499 1567 1.271217 GGGGAATTACACGGGATAGCC 60.271 57.143 0.00 0.00 0.00 3.93
1517 1585 6.127952 GGATAGCCCGTCTACAAATAGAGTAG 60.128 46.154 0.00 0.00 38.14 2.57
1574 1643 1.221466 ACGATATGTTGCCGGCGATG 61.221 55.000 21.90 8.41 0.00 3.84
1575 1644 1.207593 GATATGTTGCCGGCGATGC 59.792 57.895 21.90 8.67 0.00 3.91
1576 1645 2.187599 GATATGTTGCCGGCGATGCC 62.188 60.000 21.90 7.84 46.75 4.40
1586 1655 1.745489 GGCGATGCCTCCTTTCGTT 60.745 57.895 0.00 0.00 46.69 3.85
1590 1671 1.000145 GATGCCTCCTTTCGTTCGAC 59.000 55.000 0.00 0.00 0.00 4.20
1601 1682 0.110283 TCGTTCGACATCGCGTGTTA 60.110 50.000 5.77 0.24 42.36 2.41
1610 1708 3.432782 ACATCGCGTGTTAGCTACTTAC 58.567 45.455 5.77 0.00 38.01 2.34
1633 1734 0.606604 TCGGGTTCAGTTGCTAGGAC 59.393 55.000 0.00 0.00 0.00 3.85
1634 1735 0.608640 CGGGTTCAGTTGCTAGGACT 59.391 55.000 0.00 0.00 0.00 3.85
1665 1766 4.933505 TGAGATAATGCTCAGGAGTCAG 57.066 45.455 0.00 0.00 39.84 3.51
1666 1767 3.640498 TGAGATAATGCTCAGGAGTCAGG 59.360 47.826 0.00 0.00 39.84 3.86
1667 1768 3.894427 GAGATAATGCTCAGGAGTCAGGA 59.106 47.826 0.00 0.00 35.01 3.86
1668 1769 4.491675 AGATAATGCTCAGGAGTCAGGAT 58.508 43.478 0.00 0.00 0.00 3.24
1669 1770 4.283978 AGATAATGCTCAGGAGTCAGGATG 59.716 45.833 0.00 0.00 37.54 3.51
1670 1771 1.129917 ATGCTCAGGAGTCAGGATGG 58.870 55.000 0.00 0.00 36.16 3.51
1671 1772 0.252421 TGCTCAGGAGTCAGGATGGT 60.252 55.000 0.00 0.00 36.16 3.55
1725 1853 1.815003 CTGTGCTCTCCATTGGTTTCC 59.185 52.381 1.86 0.00 0.00 3.13
1805 1933 0.515564 GCGTGTGCCGATTTAACACT 59.484 50.000 3.94 0.00 41.60 3.55
1809 1937 2.095263 GTGTGCCGATTTAACACTGCAT 60.095 45.455 0.00 0.00 40.79 3.96
1839 1974 2.697751 CCCTTTGGTGGTTCACAATGAA 59.302 45.455 0.38 0.00 35.86 2.57
1851 1986 5.279406 GGTTCACAATGAATTTCCACATCCA 60.279 40.000 0.00 0.00 38.79 3.41
1852 1987 6.400568 GTTCACAATGAATTTCCACATCCAT 58.599 36.000 0.00 0.00 38.79 3.41
1855 1990 8.672007 TTCACAATGAATTTCCACATCCATGGA 61.672 37.037 18.88 18.88 37.99 3.41
1932 2067 7.391620 AGTGTTATTAGATGGAAAGGTTCGAA 58.608 34.615 0.00 0.00 0.00 3.71
1933 2068 7.549488 AGTGTTATTAGATGGAAAGGTTCGAAG 59.451 37.037 0.00 0.00 0.00 3.79
1943 2078 0.319641 AGGTTCGAAGACTTGACCGC 60.320 55.000 0.00 0.00 34.32 5.68
1948 2083 1.344942 CGAAGACTTGACCGCTTCCG 61.345 60.000 0.00 0.00 35.73 4.30
2018 2163 4.580580 ACTTTAGTTGGAACTGGCTTCAAG 59.419 41.667 2.14 0.00 40.07 3.02
2046 2191 9.605275 TTCAAATCCACATATCTTCTGAACTAG 57.395 33.333 0.00 0.00 0.00 2.57
2047 2192 8.762645 TCAAATCCACATATCTTCTGAACTAGT 58.237 33.333 0.00 0.00 0.00 2.57
2094 2241 6.148811 GCCAGCTGTTTTACATTTCTGTAGTA 59.851 38.462 13.81 0.00 39.00 1.82
2115 2262 7.832503 AGTATTTTTGCATGAATTAACCTGC 57.167 32.000 0.00 0.00 35.21 4.85
2116 2263 7.385267 AGTATTTTTGCATGAATTAACCTGCA 58.615 30.769 0.00 0.00 42.48 4.41
2117 2264 5.921004 TTTTTGCATGAATTAACCTGCAC 57.079 34.783 0.00 0.00 43.74 4.57
2151 2298 0.620030 TGTGGCATGTGACTGGCTAT 59.380 50.000 9.23 0.00 41.93 2.97
2156 2303 2.533266 GCATGTGACTGGCTATTTTGC 58.467 47.619 0.00 0.00 0.00 3.68
2157 2304 2.094597 GCATGTGACTGGCTATTTTGCA 60.095 45.455 0.00 0.00 34.04 4.08
2159 2306 4.751060 CATGTGACTGGCTATTTTGCAAT 58.249 39.130 0.00 0.00 34.04 3.56
2160 2307 4.177165 TGTGACTGGCTATTTTGCAATG 57.823 40.909 0.00 0.00 34.04 2.82
2176 2328 0.248289 AATGCAAAGCTCATGCCACC 59.752 50.000 18.59 0.00 43.16 4.61
2230 2382 3.284617 TGCATTCCTGACAATCTGATGG 58.715 45.455 0.00 0.00 0.00 3.51
2378 2530 1.452108 CAAGCGGTTCCATCTCCCC 60.452 63.158 0.00 0.00 0.00 4.81
2477 2643 3.088259 GGCGGTATGGCATTGTACA 57.912 52.632 4.78 0.00 44.08 2.90
2497 2663 8.902540 TGTACAGAAAGAACAGTACATTCATT 57.097 30.769 11.26 6.42 41.13 2.57
2533 2704 5.705609 TTGGCCTTTTCACATCTTCTAAC 57.294 39.130 3.32 0.00 0.00 2.34
2534 2705 4.985538 TGGCCTTTTCACATCTTCTAACT 58.014 39.130 3.32 0.00 0.00 2.24
2535 2706 5.385198 TGGCCTTTTCACATCTTCTAACTT 58.615 37.500 3.32 0.00 0.00 2.66
2537 2708 6.152379 GGCCTTTTCACATCTTCTAACTTTG 58.848 40.000 0.00 0.00 0.00 2.77
2657 2828 3.018423 ACTTCTTCTGCAAAACCCTGT 57.982 42.857 0.00 0.00 0.00 4.00
2728 2899 4.825422 TCGACAATCTGAAGAAGCTCATT 58.175 39.130 0.00 0.00 0.00 2.57
2806 2977 1.005450 TCCGGGCCAAAGAAATAGCTT 59.995 47.619 4.39 0.00 0.00 3.74
2807 2978 1.134946 CCGGGCCAAAGAAATAGCTTG 59.865 52.381 4.39 0.00 0.00 4.01
2833 3004 0.881118 GAATTTTGCGGTGGCTGAGA 59.119 50.000 0.00 0.00 40.82 3.27
2836 3007 3.551496 TTTGCGGTGGCTGAGAGGG 62.551 63.158 0.00 0.00 40.82 4.30
2839 3010 4.087892 CGGTGGCTGAGAGGGGTG 62.088 72.222 0.00 0.00 0.00 4.61
2840 3011 2.607750 GGTGGCTGAGAGGGGTGA 60.608 66.667 0.00 0.00 0.00 4.02
2841 3012 1.997874 GGTGGCTGAGAGGGGTGAT 60.998 63.158 0.00 0.00 0.00 3.06
2843 3014 2.191641 GGCTGAGAGGGGTGATGC 59.808 66.667 0.00 0.00 0.00 3.91
2845 3016 1.153208 GCTGAGAGGGGTGATGCAG 60.153 63.158 0.00 0.00 0.00 4.41
2846 3017 1.620739 GCTGAGAGGGGTGATGCAGA 61.621 60.000 0.00 0.00 0.00 4.26
2847 3018 0.177604 CTGAGAGGGGTGATGCAGAC 59.822 60.000 0.00 0.00 0.00 3.51
2848 3019 0.252421 TGAGAGGGGTGATGCAGACT 60.252 55.000 0.00 0.00 0.00 3.24
2849 3020 0.908198 GAGAGGGGTGATGCAGACTT 59.092 55.000 0.00 0.00 0.00 3.01
2850 3021 1.280421 GAGAGGGGTGATGCAGACTTT 59.720 52.381 0.00 0.00 0.00 2.66
2851 3022 1.280421 AGAGGGGTGATGCAGACTTTC 59.720 52.381 0.00 0.00 0.00 2.62
2856 3027 2.501723 GGGTGATGCAGACTTTCTCCTA 59.498 50.000 0.00 0.00 0.00 2.94
2869 3040 7.760340 CAGACTTTCTCCTACTTATGTTGTACC 59.240 40.741 0.00 0.00 0.00 3.34
2870 3041 7.453752 AGACTTTCTCCTACTTATGTTGTACCA 59.546 37.037 0.00 0.00 0.00 3.25
2933 3108 5.560966 ATGCCATCTTGTAAAAAGTACGG 57.439 39.130 0.00 0.00 0.00 4.02
3040 3215 8.739972 AGGGTTATGATACAAAATCTTGTTGTC 58.260 33.333 0.00 0.00 43.45 3.18
3041 3216 8.519526 GGGTTATGATACAAAATCTTGTTGTCA 58.480 33.333 0.00 0.00 43.45 3.58
3042 3217 9.559958 GGTTATGATACAAAATCTTGTTGTCAG 57.440 33.333 0.00 0.00 43.45 3.51
3043 3218 9.559958 GTTATGATACAAAATCTTGTTGTCAGG 57.440 33.333 0.00 0.00 43.45 3.86
3054 3544 7.741027 ATCTTGTTGTCAGGATTATAGCATG 57.259 36.000 0.00 0.00 37.12 4.06
3058 3548 6.532826 TGTTGTCAGGATTATAGCATGCATA 58.467 36.000 21.98 12.53 0.00 3.14
3077 3570 4.731720 CATATGCACTGGAGATCTAGTCG 58.268 47.826 0.00 0.00 35.39 4.18
3092 3585 9.575783 GAGATCTAGTCGGGATTATAATTTCAC 57.424 37.037 0.00 0.00 0.00 3.18
3095 3588 8.025270 TCTAGTCGGGATTATAATTTCACCAA 57.975 34.615 0.00 0.00 0.00 3.67
3097 3590 7.568199 AGTCGGGATTATAATTTCACCAAAG 57.432 36.000 0.00 0.00 0.00 2.77
3109 3602 3.749665 TCACCAAAGCAAATCCCAAAG 57.250 42.857 0.00 0.00 0.00 2.77
3115 3608 4.383173 CAAAGCAAATCCCAAAGAAAGCT 58.617 39.130 0.00 0.00 33.08 3.74
3116 3609 3.672767 AGCAAATCCCAAAGAAAGCTG 57.327 42.857 0.00 0.00 31.27 4.24
3139 3760 9.141400 GCTGTATAAGAAGTTATCTAATTCCCG 57.859 37.037 0.00 0.00 37.42 5.14
3176 3797 1.067565 GCTTAGCAAGGTTTCAAGGGC 60.068 52.381 0.00 0.00 0.00 5.19
3190 3811 0.475828 AAGGGCTACAGGTTCAGGGT 60.476 55.000 0.00 0.00 0.00 4.34
3220 3841 7.554476 GCTCCCAAAGAAGAATGAAATAGTACT 59.446 37.037 0.00 0.00 0.00 2.73
3221 3842 9.103861 CTCCCAAAGAAGAATGAAATAGTACTC 57.896 37.037 0.00 0.00 0.00 2.59
3234 3855 8.856153 TGAAATAGTACTCCAAAACTAATGCA 57.144 30.769 0.00 0.00 32.24 3.96
3272 3894 6.165577 GGATAATGTCCACAAAATTGCACTT 58.834 36.000 0.00 0.00 46.96 3.16
3273 3895 6.091169 GGATAATGTCCACAAAATTGCACTTG 59.909 38.462 0.00 0.00 46.96 3.16
3287 3909 4.267349 TGCACTTGAGTTTCCCTAGTAC 57.733 45.455 0.00 0.00 0.00 2.73
3300 3922 9.054580 AGTTTCCCTAGTACTTAATACATTGGT 57.945 33.333 0.00 0.00 36.09 3.67
3306 3928 6.183810 AGTACTTAATACATTGGTAGCCCC 57.816 41.667 0.00 0.00 36.09 5.80
3348 3970 3.267860 CCTCGCAGCGATTCAGCC 61.268 66.667 19.91 0.00 38.01 4.85
3384 4008 8.756486 TGATGATGGTATGAAATCAGATGTTT 57.244 30.769 0.00 0.00 36.31 2.83
3394 4018 6.554419 TGAAATCAGATGTTTTAAGCCATCG 58.446 36.000 9.49 6.46 41.81 3.84
3415 4039 7.862372 CCATCGAAGAAAGTTCAATTCTGAAAA 59.138 33.333 0.00 0.00 41.51 2.29
3418 4042 6.129613 CGAAGAAAGTTCAATTCTGAAAAGCG 60.130 38.462 0.00 0.00 43.18 4.68
3424 4048 3.825308 TCAATTCTGAAAAGCGCATCAC 58.175 40.909 11.47 0.00 0.00 3.06
3555 4179 0.875059 GACCTGCAAAGGTAGCACAC 59.125 55.000 0.00 0.00 43.24 3.82
3559 4183 2.297033 CCTGCAAAGGTAGCACACAAAT 59.703 45.455 0.00 0.00 37.02 2.32
3575 4199 6.682441 GCACACAAATTTAAACTTTCTGTTGC 59.318 34.615 0.00 1.94 39.13 4.17
3595 4219 2.483876 CTGCATCGGGGTAACTATGTG 58.516 52.381 0.00 0.00 0.00 3.21
3645 4270 8.856247 GGTAACAACTTTACAAAACAAACTGAG 58.144 33.333 0.00 0.00 0.00 3.35
3679 4304 2.436417 TGCAGCTGAAGGGAATAACAC 58.564 47.619 20.43 0.00 0.00 3.32
3684 4309 3.260884 AGCTGAAGGGAATAACACGAGAA 59.739 43.478 0.00 0.00 0.00 2.87
3689 4314 4.635699 AGGGAATAACACGAGAAAGGTT 57.364 40.909 0.00 0.00 0.00 3.50
3690 4315 4.324267 AGGGAATAACACGAGAAAGGTTG 58.676 43.478 0.00 0.00 0.00 3.77
3691 4316 3.439129 GGGAATAACACGAGAAAGGTTGG 59.561 47.826 0.00 0.00 0.00 3.77
3721 4349 2.230508 CTGTAACCTGCTAGACCGAACA 59.769 50.000 0.00 0.00 0.00 3.18
3748 4376 6.653526 TTCATGACATCTTCACACCAAAAT 57.346 33.333 0.00 0.00 36.92 1.82
3749 4377 7.757941 TTCATGACATCTTCACACCAAAATA 57.242 32.000 0.00 0.00 36.92 1.40
3751 4379 7.819644 TCATGACATCTTCACACCAAAATAAG 58.180 34.615 0.00 0.00 36.92 1.73
3753 4381 7.815840 TGACATCTTCACACCAAAATAAGAA 57.184 32.000 0.00 0.00 30.56 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.892914 CCGTGTTGGTGTCGCACA 60.893 61.111 11.20 0.00 35.86 4.57
78 79 1.064946 CGCTTAGGACAGAGCTCCG 59.935 63.158 10.93 1.77 36.76 4.63
151 152 2.118683 CCAACAATGCAACAACGTCAG 58.881 47.619 0.00 0.00 0.00 3.51
157 158 4.402155 AGAAGAACTCCAACAATGCAACAA 59.598 37.500 0.00 0.00 0.00 2.83
159 160 4.574599 AGAAGAACTCCAACAATGCAAC 57.425 40.909 0.00 0.00 0.00 4.17
180 182 2.093075 AGATTGAGGTCTCGTCGGACTA 60.093 50.000 6.57 0.00 36.55 2.59
209 212 0.325671 TCCTCTCTCAATCCCGCCTT 60.326 55.000 0.00 0.00 0.00 4.35
210 213 0.105246 ATCCTCTCTCAATCCCGCCT 60.105 55.000 0.00 0.00 0.00 5.52
229 232 1.885233 TCTGCGCAATTTCACAATCCA 59.115 42.857 13.05 0.00 0.00 3.41
247 250 1.156736 CCAAAATCAAGCCGACGTCT 58.843 50.000 14.70 0.00 0.00 4.18
251 254 1.132453 GCTACCCAAAATCAAGCCGAC 59.868 52.381 0.00 0.00 0.00 4.79
260 263 2.644798 ACAGTCAGGAGCTACCCAAAAT 59.355 45.455 0.00 0.00 40.05 1.82
269 272 1.617850 CAACTCTGACAGTCAGGAGCT 59.382 52.381 27.15 13.42 44.39 4.09
683 687 1.595093 CGGTTCCACCAAATCAGCCC 61.595 60.000 0.00 0.00 38.47 5.19
685 689 0.958822 AACGGTTCCACCAAATCAGC 59.041 50.000 0.00 0.00 38.47 4.26
710 714 6.418226 GTCACCAAAACACGTGCAAATATTTA 59.582 34.615 17.22 0.00 0.00 1.40
714 718 3.489398 GGTCACCAAAACACGTGCAAATA 60.489 43.478 17.22 0.00 0.00 1.40
739 743 0.623723 GGGTTAGGGCATCTCCAACA 59.376 55.000 0.00 0.00 36.21 3.33
766 770 7.814107 ACACAACACATTCTTGGCAAATAATAG 59.186 33.333 0.00 3.80 0.00 1.73
780 784 1.358402 TGGCGCACACAACACATTC 59.642 52.632 10.83 0.00 0.00 2.67
896 913 1.614824 AGAGAGGGGCTTGGACAGG 60.615 63.158 0.00 0.00 0.00 4.00
897 914 0.617249 AGAGAGAGGGGCTTGGACAG 60.617 60.000 0.00 0.00 0.00 3.51
919 936 4.541705 CCTTTGAGGATAGAGTGAGAGGA 58.458 47.826 0.00 0.00 37.67 3.71
920 937 3.640967 CCCTTTGAGGATAGAGTGAGAGG 59.359 52.174 0.00 0.00 37.67 3.69
1397 1434 1.002087 CAGAAGCGTGAAACCCCTAGT 59.998 52.381 0.00 0.00 0.00 2.57
1400 1437 1.600916 GCAGAAGCGTGAAACCCCT 60.601 57.895 0.00 0.00 0.00 4.79
1445 1512 7.933396 TCCAGATAAAATGCTGTGATATGTTG 58.067 34.615 0.00 0.00 0.00 3.33
1447 1514 7.392673 GGATCCAGATAAAATGCTGTGATATGT 59.607 37.037 6.95 0.00 0.00 2.29
1499 1567 4.097437 TGCACCTACTCTATTTGTAGACGG 59.903 45.833 0.00 0.00 39.61 4.79
1574 1643 1.000145 GATGTCGAACGAAAGGAGGC 59.000 55.000 0.00 0.00 0.00 4.70
1575 1644 1.269166 CGATGTCGAACGAAAGGAGG 58.731 55.000 0.00 0.00 43.02 4.30
1576 1645 0.640768 GCGATGTCGAACGAAAGGAG 59.359 55.000 6.60 0.00 43.02 3.69
1577 1646 1.068832 CGCGATGTCGAACGAAAGGA 61.069 55.000 0.00 0.00 43.02 3.36
1578 1647 1.340465 CGCGATGTCGAACGAAAGG 59.660 57.895 0.00 0.00 43.02 3.11
1583 1652 0.290840 CTAACACGCGATGTCGAACG 59.709 55.000 15.93 3.87 42.31 3.95
1586 1655 0.728542 TAGCTAACACGCGATGTCGA 59.271 50.000 15.93 4.81 42.31 4.20
1590 1671 2.787680 GGTAAGTAGCTAACACGCGATG 59.212 50.000 15.93 10.38 34.40 3.84
1633 1734 6.221659 TGAGCATTATCTCATCAAGCACTAG 58.778 40.000 0.00 0.00 38.11 2.57
1634 1735 6.165700 TGAGCATTATCTCATCAAGCACTA 57.834 37.500 0.00 0.00 38.11 2.74
1661 1762 0.535335 TCGGCTTGTACCATCCTGAC 59.465 55.000 0.00 0.00 0.00 3.51
1662 1763 1.207089 CTTCGGCTTGTACCATCCTGA 59.793 52.381 0.00 0.00 0.00 3.86
1663 1764 1.656652 CTTCGGCTTGTACCATCCTG 58.343 55.000 0.00 0.00 0.00 3.86
1664 1765 0.107654 GCTTCGGCTTGTACCATCCT 60.108 55.000 0.00 0.00 38.08 3.24
1665 1766 0.392461 TGCTTCGGCTTGTACCATCC 60.392 55.000 0.00 0.00 42.37 3.51
1666 1767 1.009829 CTGCTTCGGCTTGTACCATC 58.990 55.000 0.00 0.00 42.37 3.51
1667 1768 0.613260 TCTGCTTCGGCTTGTACCAT 59.387 50.000 0.00 0.00 42.37 3.55
1668 1769 0.037326 CTCTGCTTCGGCTTGTACCA 60.037 55.000 0.00 0.00 42.37 3.25
1669 1770 0.246635 TCTCTGCTTCGGCTTGTACC 59.753 55.000 0.00 0.00 42.37 3.34
1670 1771 1.202582 TCTCTCTGCTTCGGCTTGTAC 59.797 52.381 0.00 0.00 42.37 2.90
1671 1772 1.545841 TCTCTCTGCTTCGGCTTGTA 58.454 50.000 0.00 0.00 42.37 2.41
1709 1837 1.467920 CCTGGAAACCAATGGAGAGC 58.532 55.000 6.16 0.00 30.80 4.09
1791 1919 1.135431 GCATGCAGTGTTAAATCGGCA 60.135 47.619 14.21 7.97 38.81 5.69
1805 1933 0.685131 CAAAGGGGAGGATGCATGCA 60.685 55.000 25.04 25.04 0.00 3.96
1809 1937 1.383799 CACCAAAGGGGAGGATGCA 59.616 57.895 0.00 0.00 41.15 3.96
1932 2067 1.289380 GACGGAAGCGGTCAAGTCT 59.711 57.895 8.42 0.00 34.47 3.24
1933 2068 2.087009 CGACGGAAGCGGTCAAGTC 61.087 63.158 0.00 0.00 34.13 3.01
1948 2083 8.385858 GTTTACATAAAGTAGTGATTTCCCGAC 58.614 37.037 0.00 0.00 33.43 4.79
1998 2143 4.431416 TCTTGAAGCCAGTTCCAACTAA 57.569 40.909 0.00 0.00 37.08 2.24
1999 2144 4.640771 ATCTTGAAGCCAGTTCCAACTA 57.359 40.909 0.00 0.00 37.08 2.24
2018 2163 9.118300 AGTTCAGAAGATATGTGGATTTGAATC 57.882 33.333 0.00 0.00 34.66 2.52
2046 2191 5.106277 GCAGGGTAGTTCAGTTTGGAATTAC 60.106 44.000 0.00 0.00 38.51 1.89
2047 2192 5.007682 GCAGGGTAGTTCAGTTTGGAATTA 58.992 41.667 0.00 0.00 0.00 1.40
2048 2193 3.826729 GCAGGGTAGTTCAGTTTGGAATT 59.173 43.478 0.00 0.00 0.00 2.17
2049 2194 3.421844 GCAGGGTAGTTCAGTTTGGAAT 58.578 45.455 0.00 0.00 0.00 3.01
2050 2195 2.488347 GGCAGGGTAGTTCAGTTTGGAA 60.488 50.000 0.00 0.00 0.00 3.53
2115 2262 3.303990 GCCACATGTGTACAAACTCTGTG 60.304 47.826 23.79 10.21 39.20 3.66
2116 2263 2.878406 GCCACATGTGTACAAACTCTGT 59.122 45.455 23.79 0.00 42.47 3.41
2117 2264 2.877786 TGCCACATGTGTACAAACTCTG 59.122 45.455 23.79 6.11 0.00 3.35
2156 2303 1.355971 GTGGCATGAGCTTTGCATTG 58.644 50.000 20.18 3.09 41.95 2.82
2157 2304 0.248289 GGTGGCATGAGCTTTGCATT 59.752 50.000 20.18 0.00 41.95 3.56
2159 2306 1.228644 AGGTGGCATGAGCTTTGCA 60.229 52.632 20.18 0.64 41.95 4.08
2160 2307 1.214589 CAGGTGGCATGAGCTTTGC 59.785 57.895 12.76 12.76 41.70 3.68
2176 2328 1.232119 TCACTGCAGCACATCAACAG 58.768 50.000 15.27 0.00 0.00 3.16
2230 2382 1.188863 ACAAAGATGCCATTCAGCCC 58.811 50.000 0.00 0.00 0.00 5.19
2378 2530 1.594862 CCATTTAGCTTCTCGGCTTCG 59.405 52.381 0.00 0.00 42.97 3.79
2474 2640 9.778741 AGAAATGAATGTACTGTTCTTTCTGTA 57.221 29.630 20.93 0.00 34.96 2.74
2475 2641 8.682936 AGAAATGAATGTACTGTTCTTTCTGT 57.317 30.769 20.93 8.64 34.96 3.41
2497 2663 5.514500 AAAGGCCAAAGGTGTATCTAGAA 57.486 39.130 5.01 0.00 0.00 2.10
2502 2668 3.572255 TGTGAAAAGGCCAAAGGTGTATC 59.428 43.478 5.01 0.00 0.00 2.24
2503 2669 3.571590 TGTGAAAAGGCCAAAGGTGTAT 58.428 40.909 5.01 0.00 0.00 2.29
2513 2679 5.966742 AAGTTAGAAGATGTGAAAAGGCC 57.033 39.130 0.00 0.00 0.00 5.19
2533 2704 5.677091 GCCTGCATAGACATTGGTTACAAAG 60.677 44.000 0.00 0.00 40.55 2.77
2534 2705 4.157656 GCCTGCATAGACATTGGTTACAAA 59.842 41.667 0.00 0.00 40.55 2.83
2535 2706 3.694072 GCCTGCATAGACATTGGTTACAA 59.306 43.478 0.00 0.00 41.59 2.41
2537 2708 2.618709 GGCCTGCATAGACATTGGTTAC 59.381 50.000 0.00 0.00 0.00 2.50
2657 2828 0.175302 CCAGCCACAGCAACAAACAA 59.825 50.000 0.00 0.00 43.56 2.83
2728 2899 1.866601 TCGTAGAACGTTGACTCGTCA 59.133 47.619 5.00 0.00 43.38 4.35
2806 2977 2.223923 CCACCGCAAAATTCAACTTCCA 60.224 45.455 0.00 0.00 0.00 3.53
2807 2978 2.403259 CCACCGCAAAATTCAACTTCC 58.597 47.619 0.00 0.00 0.00 3.46
2833 3004 1.280421 GAGAAAGTCTGCATCACCCCT 59.720 52.381 0.00 0.00 0.00 4.79
2836 3007 2.777832 AGGAGAAAGTCTGCATCACC 57.222 50.000 0.00 0.00 37.29 4.02
2838 3009 6.155221 ACATAAGTAGGAGAAAGTCTGCATCA 59.845 38.462 0.00 0.00 37.29 3.07
2839 3010 6.578023 ACATAAGTAGGAGAAAGTCTGCATC 58.422 40.000 0.00 0.00 37.29 3.91
2840 3011 6.552445 ACATAAGTAGGAGAAAGTCTGCAT 57.448 37.500 0.00 0.00 37.29 3.96
2841 3012 6.166279 CAACATAAGTAGGAGAAAGTCTGCA 58.834 40.000 0.00 0.00 37.29 4.41
2843 3014 7.760340 GGTACAACATAAGTAGGAGAAAGTCTG 59.240 40.741 0.00 0.00 0.00 3.51
2845 3016 7.609056 TGGTACAACATAAGTAGGAGAAAGTC 58.391 38.462 0.00 0.00 31.92 3.01
2846 3017 7.549147 TGGTACAACATAAGTAGGAGAAAGT 57.451 36.000 0.00 0.00 31.92 2.66
2931 3106 3.793801 GCTCTAGCACATAACTGAGTCCG 60.794 52.174 0.00 0.00 41.59 4.79
2933 3108 3.383185 AGGCTCTAGCACATAACTGAGTC 59.617 47.826 4.07 0.00 44.36 3.36
3009 3184 7.902920 AGATTTTGTATCATAACCCTGCAAT 57.097 32.000 0.00 0.00 0.00 3.56
3021 3196 8.408043 AATCCTGACAACAAGATTTTGTATCA 57.592 30.769 1.50 8.53 46.54 2.15
3054 3544 4.493547 GACTAGATCTCCAGTGCATATGC 58.506 47.826 21.09 21.09 42.50 3.14
3058 3548 1.959985 CCGACTAGATCTCCAGTGCAT 59.040 52.381 0.00 0.00 0.00 3.96
3061 3551 2.350057 TCCCGACTAGATCTCCAGTG 57.650 55.000 0.00 0.00 0.00 3.66
3063 3553 7.889873 ATTATAATCCCGACTAGATCTCCAG 57.110 40.000 0.00 0.00 0.00 3.86
3065 3555 8.750298 TGAAATTATAATCCCGACTAGATCTCC 58.250 37.037 0.00 0.00 0.00 3.71
3077 3570 8.962884 ATTTGCTTTGGTGAAATTATAATCCC 57.037 30.769 0.00 0.00 0.00 3.85
3092 3585 3.499537 GCTTTCTTTGGGATTTGCTTTGG 59.500 43.478 0.00 0.00 0.00 3.28
3095 3588 3.389002 ACAGCTTTCTTTGGGATTTGCTT 59.611 39.130 0.00 0.00 0.00 3.91
3097 3590 3.391506 ACAGCTTTCTTTGGGATTTGC 57.608 42.857 0.00 0.00 0.00 3.68
3136 3757 2.598589 CTGATGCAAAACATTGTCGGG 58.401 47.619 0.00 0.00 39.84 5.14
3139 3760 4.325472 GCTAAGCTGATGCAAAACATTGTC 59.675 41.667 0.00 0.00 39.84 3.18
3140 3761 4.240096 GCTAAGCTGATGCAAAACATTGT 58.760 39.130 0.00 0.00 39.84 2.71
3143 3764 4.491676 CTTGCTAAGCTGATGCAAAACAT 58.508 39.130 17.75 0.00 44.49 2.71
3176 3797 1.625818 AGCTTCACCCTGAACCTGTAG 59.374 52.381 0.00 0.00 32.21 2.74
3190 3811 4.371624 TCATTCTTCTTTGGGAGCTTCA 57.628 40.909 0.00 0.00 0.00 3.02
3220 3841 6.265196 AGTGAAGAATGTGCATTAGTTTTGGA 59.735 34.615 0.00 0.00 0.00 3.53
3221 3842 6.449698 AGTGAAGAATGTGCATTAGTTTTGG 58.550 36.000 0.00 0.00 0.00 3.28
3234 3855 5.359194 ACATTATCCCGAGTGAAGAATGT 57.641 39.130 0.00 0.00 33.48 2.71
3273 3895 9.543783 CCAATGTATTAAGTACTAGGGAAACTC 57.456 37.037 0.00 0.00 34.27 3.01
3287 3909 4.039973 TCGAGGGGCTACCAATGTATTAAG 59.960 45.833 0.97 0.00 43.89 1.85
3300 3922 3.568443 TGTGTGTATATTCGAGGGGCTA 58.432 45.455 0.00 0.00 0.00 3.93
3306 3928 5.047021 AGGGGATCATGTGTGTATATTCGAG 60.047 44.000 0.00 0.00 0.00 4.04
3376 4000 5.801350 TCTTCGATGGCTTAAAACATCTG 57.199 39.130 13.87 9.36 40.93 2.90
3381 4005 6.435428 TGAACTTTCTTCGATGGCTTAAAAC 58.565 36.000 0.00 0.00 0.00 2.43
3384 4008 6.817765 ATTGAACTTTCTTCGATGGCTTAA 57.182 33.333 0.00 0.00 0.00 1.85
3394 4018 6.345329 GCGCTTTTCAGAATTGAACTTTCTTC 60.345 38.462 0.00 0.00 42.79 2.87
3415 4039 0.819259 ACAGGTTTGTGTGATGCGCT 60.819 50.000 9.73 0.00 35.83 5.92
3555 4179 7.002816 TGCAGCAACAGAAAGTTTAAATTTG 57.997 32.000 0.00 0.00 38.74 2.32
3559 4183 4.975502 CGATGCAGCAACAGAAAGTTTAAA 59.024 37.500 1.53 0.00 38.74 1.52
3575 4199 2.102420 TCACATAGTTACCCCGATGCAG 59.898 50.000 0.00 0.00 0.00 4.41
3595 4219 5.446473 CGCTTTCTCTGATGTGGTGTAATTC 60.446 44.000 0.00 0.00 0.00 2.17
3645 4270 3.253188 TCAGCTGCAAAATGGTTGTACTC 59.747 43.478 9.47 0.00 0.00 2.59
3679 4304 4.627467 CAGTTATCTGTCCAACCTTTCTCG 59.373 45.833 0.00 0.00 36.97 4.04
3712 4340 6.586344 AGATGTCATGAAATATGTTCGGTCT 58.414 36.000 0.00 0.00 0.00 3.85
3721 4349 7.943079 TTGGTGTGAAGATGTCATGAAATAT 57.057 32.000 0.00 0.00 38.90 1.28


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

AutoCloner maintained by Alex Coulton.