Multiple sequence alignment - TraesCS7A01G313500

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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 TraesCS7A01G313500 chr7A 100.000 3818 0 0 1 3818 445629053 445625236 0.000000e+00 7051
1 TraesCS7A01G313500 chr7B 94.552 2992 110 14 858 3818 392818359 392815390 0.000000e+00 4573
2 TraesCS7A01G313500 chr7B 91.131 654 55 3 1 651 716504939 716505592 0.000000e+00 883
3 TraesCS7A01G313500 chr7D 94.578 2988 104 18 858 3818 393110089 393107133 0.000000e+00 4567
4 TraesCS7A01G313500 chr7D 97.143 70 1 1 652 721 393110619 393110551 2.410000e-22 117
5 TraesCS7A01G313500 chr1B 90.951 652 49 7 1 649 539835213 539835857 0.000000e+00 869
6 TraesCS7A01G313500 chr6A 90.426 658 58 5 5 660 190747958 190748612 0.000000e+00 861
7 TraesCS7A01G313500 chr2B 90.520 654 57 4 1 650 119206777 119206125 0.000000e+00 859
8 TraesCS7A01G313500 chr5B 88.125 640 71 4 10 648 271312847 271312212 0.000000e+00 756
9 TraesCS7A01G313500 chr6B 87.902 653 63 7 1 650 591575482 591576121 0.000000e+00 754
10 TraesCS7A01G313500 chr6D 89.626 588 59 2 1 587 395693068 395693654 0.000000e+00 747
11 TraesCS7A01G313500 chr4A 91.458 480 37 4 175 652 75219797 75220274 0.000000e+00 656
12 TraesCS7A01G313500 chr3A 92.327 391 28 2 262 651 716108363 716107974 4.310000e-154 555


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 TraesCS7A01G313500 chr7A 445625236 445629053 3817 True 7051 7051 100.0000 1 3818 1 chr7A.!!$R1 3817
1 TraesCS7A01G313500 chr7B 392815390 392818359 2969 True 4573 4573 94.5520 858 3818 1 chr7B.!!$R1 2960
2 TraesCS7A01G313500 chr7B 716504939 716505592 653 False 883 883 91.1310 1 651 1 chr7B.!!$F1 650
3 TraesCS7A01G313500 chr7D 393107133 393110619 3486 True 2342 4567 95.8605 652 3818 2 chr7D.!!$R1 3166
4 TraesCS7A01G313500 chr1B 539835213 539835857 644 False 869 869 90.9510 1 649 1 chr1B.!!$F1 648
5 TraesCS7A01G313500 chr6A 190747958 190748612 654 False 861 861 90.4260 5 660 1 chr6A.!!$F1 655
6 TraesCS7A01G313500 chr2B 119206125 119206777 652 True 859 859 90.5200 1 650 1 chr2B.!!$R1 649
7 TraesCS7A01G313500 chr5B 271312212 271312847 635 True 756 756 88.1250 10 648 1 chr5B.!!$R1 638
8 TraesCS7A01G313500 chr6B 591575482 591576121 639 False 754 754 87.9020 1 650 1 chr6B.!!$F1 649
9 TraesCS7A01G313500 chr6D 395693068 395693654 586 False 747 747 89.6260 1 587 1 chr6D.!!$F1 586

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
867 1247 0.033366 AAAAAGGCCGTTGCACCATC 59.967 50.0 4.14 0.00 40.13 3.51 F
1484 1876 0.394488 CCTGAGAGACCGGTCAGCTA 60.394 60.0 35.00 17.69 39.16 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 2934 0.031585 GGCTGGAAAACGACAAACCC 59.968 55.0 0.00 0.0 0.00 4.11 R
3399 3809 0.178967 TGGCAAATGGCAGAACTGGA 60.179 50.0 5.46 0.0 46.12 3.86 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
65 66 0.105964 TCTGTTCGCCATATTCGGGG 59.894 55.000 0.00 0.00 40.29 5.73
84 85 1.573108 GGGATCTCACAGTCCTGGAA 58.427 55.000 0.00 0.00 34.84 3.53
87 88 3.054065 GGGATCTCACAGTCCTGGAAATT 60.054 47.826 0.00 0.00 34.84 1.82
124 125 1.072965 CCATCCTTCTAGGTCATGGGC 59.927 57.143 5.82 0.00 36.56 5.36
144 145 4.699522 AGACCGCCCGAACTTGGC 62.700 66.667 0.00 0.00 45.70 4.52
323 326 2.168728 GGGAGTCCTATTCGCAAGTCTT 59.831 50.000 9.58 0.00 39.48 3.01
344 347 2.200081 AGGGGCTACTCACATGTGATT 58.800 47.619 28.00 24.14 39.13 2.57
357 360 3.181465 ACATGTGATTATGGAGACGGACC 60.181 47.826 0.00 0.00 32.32 4.46
399 402 0.865769 GAACGATCGCCACAACACTT 59.134 50.000 16.60 0.00 0.00 3.16
423 426 2.682856 TCGATTGTGGCTCCTATTTTGC 59.317 45.455 0.00 0.00 0.00 3.68
493 500 8.812972 TCACATGTAAGTAGGACAACTAATCTT 58.187 33.333 0.00 0.00 32.37 2.40
499 506 1.134788 AGGACAACTAATCTTCCGGCG 60.135 52.381 0.00 0.00 32.97 6.46
506 513 0.825410 TAATCTTCCGGCGCACCTAA 59.175 50.000 10.83 0.00 0.00 2.69
531 538 1.084370 AAGCGTGCCTGCTCGATTAC 61.084 55.000 14.29 0.00 46.60 1.89
583 590 1.371558 GTTCCTGGTCACGAGCCTT 59.628 57.895 0.00 0.00 0.00 4.35
629 636 7.811713 GCTCTTTTGTTTGAATAAAGCTCTCAT 59.188 33.333 0.00 0.00 0.00 2.90
643 650 2.094854 GCTCTCATGTTTCCCTGCAAAG 60.095 50.000 0.00 0.00 0.00 2.77
710 717 3.430453 TCAGCCCCCATTCTTTTTACAG 58.570 45.455 0.00 0.00 0.00 2.74
721 728 4.098914 TCTTTTTACAGTCCATGGCACT 57.901 40.909 6.96 8.93 0.00 4.40
722 729 5.235850 TCTTTTTACAGTCCATGGCACTA 57.764 39.130 6.96 0.00 0.00 2.74
723 730 5.245531 TCTTTTTACAGTCCATGGCACTAG 58.754 41.667 6.96 8.94 0.00 2.57
724 731 4.901197 TTTTACAGTCCATGGCACTAGA 57.099 40.909 6.96 0.68 0.00 2.43
725 732 4.471904 TTTACAGTCCATGGCACTAGAG 57.528 45.455 6.96 3.17 0.00 2.43
726 733 2.238084 ACAGTCCATGGCACTAGAGA 57.762 50.000 6.96 0.00 0.00 3.10
727 734 2.540383 ACAGTCCATGGCACTAGAGAA 58.460 47.619 6.96 0.00 0.00 2.87
728 735 2.906389 ACAGTCCATGGCACTAGAGAAA 59.094 45.455 6.96 0.00 0.00 2.52
729 736 3.055530 ACAGTCCATGGCACTAGAGAAAG 60.056 47.826 6.96 1.18 0.00 2.62
730 737 3.196469 CAGTCCATGGCACTAGAGAAAGA 59.804 47.826 6.96 0.00 0.00 2.52
731 738 3.840666 AGTCCATGGCACTAGAGAAAGAA 59.159 43.478 6.96 0.00 0.00 2.52
732 739 4.287067 AGTCCATGGCACTAGAGAAAGAAA 59.713 41.667 6.96 0.00 0.00 2.52
733 740 4.393371 GTCCATGGCACTAGAGAAAGAAAC 59.607 45.833 6.96 0.00 0.00 2.78
734 741 3.372206 CCATGGCACTAGAGAAAGAAACG 59.628 47.826 0.00 0.00 0.00 3.60
735 742 2.413837 TGGCACTAGAGAAAGAAACGC 58.586 47.619 0.00 0.00 0.00 4.84
736 743 2.224185 TGGCACTAGAGAAAGAAACGCA 60.224 45.455 0.00 0.00 0.00 5.24
737 744 2.157863 GGCACTAGAGAAAGAAACGCAC 59.842 50.000 0.00 0.00 0.00 5.34
746 753 6.097356 AGAGAAAGAAACGCACAATACGATA 58.903 36.000 0.00 0.00 0.00 2.92
754 761 9.472361 AGAAACGCACAATACGATACTTAATAT 57.528 29.630 0.00 0.00 0.00 1.28
789 796 8.763049 TTTCAGTCTATATGCTCAATATTCCG 57.237 34.615 0.00 0.00 33.35 4.30
790 797 7.468141 TCAGTCTATATGCTCAATATTCCGT 57.532 36.000 0.00 0.00 33.35 4.69
791 798 7.896811 TCAGTCTATATGCTCAATATTCCGTT 58.103 34.615 0.00 0.00 33.35 4.44
792 799 8.029522 TCAGTCTATATGCTCAATATTCCGTTC 58.970 37.037 0.00 0.00 33.35 3.95
795 802 2.684001 TGCTCAATATTCCGTTCCGT 57.316 45.000 0.00 0.00 0.00 4.69
800 807 1.330521 CAATATTCCGTTCCGTGCTGG 59.669 52.381 0.00 0.00 40.09 4.85
808 815 0.390472 GTTCCGTGCTGGGAGAGAAG 60.390 60.000 0.00 0.00 37.40 2.85
840 1185 4.160329 ACGGATGAGGCCTAATATCTTCA 58.840 43.478 4.42 0.00 0.00 3.02
842 1187 4.932200 CGGATGAGGCCTAATATCTTCAAC 59.068 45.833 4.42 0.00 0.00 3.18
843 1188 5.511373 CGGATGAGGCCTAATATCTTCAACA 60.511 44.000 4.42 0.00 0.00 3.33
845 1190 6.205658 GGATGAGGCCTAATATCTTCAACAAC 59.794 42.308 4.42 0.00 0.00 3.32
867 1247 0.033366 AAAAAGGCCGTTGCACCATC 59.967 50.000 4.14 0.00 40.13 3.51
994 1374 1.079405 TCCATCGCAGGAAACGACC 60.079 57.895 0.00 0.00 43.23 4.79
995 1375 1.375396 CCATCGCAGGAAACGACCA 60.375 57.895 0.00 0.00 43.23 4.02
1363 1755 1.200716 CTGCATGCATCCAGTTCGTTT 59.799 47.619 22.97 0.00 0.00 3.60
1378 1770 6.788930 CCAGTTCGTTTCGTTTCTGTTATAAC 59.211 38.462 8.75 8.75 0.00 1.89
1457 1849 4.659111 TCTAATGCTGGAATTGCAATGG 57.341 40.909 13.82 5.26 44.01 3.16
1475 1867 3.208747 TGGTTTGTTTCCTGAGAGACC 57.791 47.619 0.00 0.00 0.00 3.85
1476 1868 2.143925 GGTTTGTTTCCTGAGAGACCG 58.856 52.381 0.00 0.00 0.00 4.79
1482 1874 1.251527 TTCCTGAGAGACCGGTCAGC 61.252 60.000 35.00 25.42 39.16 4.26
1484 1876 0.394488 CCTGAGAGACCGGTCAGCTA 60.394 60.000 35.00 17.69 39.16 3.32
1492 1884 1.476891 GACCGGTCAGCTAAGATGTGA 59.523 52.381 29.75 0.00 0.00 3.58
1495 1887 3.898123 ACCGGTCAGCTAAGATGTGATAT 59.102 43.478 0.00 0.00 0.00 1.63
1496 1888 5.077564 ACCGGTCAGCTAAGATGTGATATA 58.922 41.667 0.00 0.00 0.00 0.86
1526 1918 8.731591 AGGATATGATATTTCTGCCCAATTTT 57.268 30.769 0.00 0.00 0.00 1.82
1528 1920 9.211485 GGATATGATATTTCTGCCCAATTTTTG 57.789 33.333 0.00 0.00 0.00 2.44
1534 1926 4.953940 TTCTGCCCAATTTTTGTTAGCT 57.046 36.364 0.00 0.00 0.00 3.32
1586 1978 2.290367 ACATTGGTGTGAATGTGTCGTG 59.710 45.455 0.00 0.00 43.45 4.35
1638 2030 3.006752 GCTCTCCTCTATGGATTCCAGTG 59.993 52.174 11.78 6.48 45.16 3.66
1676 2068 3.153919 GTCAGGCTTGTCCATGGTAAAA 58.846 45.455 12.58 4.09 37.29 1.52
1725 2117 5.866633 GTCTCTCTGCCTATGTATGTTATGC 59.133 44.000 0.00 0.00 0.00 3.14
1761 2153 5.527951 CAAGCTAAGCACCATTGTTTGTTA 58.472 37.500 0.00 0.00 0.00 2.41
1865 2257 6.249035 TCTTCTTGCATAAGGGTTTTAACG 57.751 37.500 8.89 0.00 34.59 3.18
1943 2338 6.165577 TGGGCTCATTTTTCTTCTTTAATGC 58.834 36.000 0.00 0.00 0.00 3.56
1966 2361 4.817517 TGTTTTCTAATCCGAGGAGTCAC 58.182 43.478 0.00 0.00 0.00 3.67
1995 2390 7.067737 TCCAAAATTCACCCTCGGAATATTTAC 59.932 37.037 0.00 0.00 34.02 2.01
2117 2512 4.631813 ACAAAAGTGTGTCTCAGAACTGTC 59.368 41.667 1.73 0.00 36.31 3.51
2215 2610 6.511416 TGCATGCTTGTTGTTTACTTACATT 58.489 32.000 20.33 0.00 0.00 2.71
2244 2639 8.755018 CAACATTCTCATTTCTGTTTTGGTAAC 58.245 33.333 0.00 0.00 29.74 2.50
2276 2671 2.476854 GGTTTGATCAAGCGCATCTGAC 60.477 50.000 11.47 7.02 0.00 3.51
2278 2673 2.320745 TGATCAAGCGCATCTGACAT 57.679 45.000 11.47 0.00 0.00 3.06
2539 2934 2.773993 AACACTGGGTGGTATTACGG 57.226 50.000 2.75 0.00 37.94 4.02
2540 2935 0.906775 ACACTGGGTGGTATTACGGG 59.093 55.000 2.75 0.00 37.94 5.28
2573 2968 1.002468 CCAGCCTTGCGTGTATATTGC 60.002 52.381 0.00 0.00 0.00 3.56
2574 2969 1.002468 CAGCCTTGCGTGTATATTGCC 60.002 52.381 0.00 0.00 0.00 4.52
2639 3044 7.332182 AGACAAAAACGCCTACAAATTGAAAAA 59.668 29.630 0.00 0.00 0.00 1.94
2734 3141 7.733773 TGGTTTCTGATATTCAGTAAGGAGA 57.266 36.000 4.56 0.00 44.58 3.71
2778 3185 6.974622 TCTTCTCATTGAGCTTTGTTGTTTTC 59.025 34.615 8.89 0.00 0.00 2.29
2871 3278 3.378512 ACAGCACTCAGGATGGATCTTA 58.621 45.455 0.00 0.00 36.16 2.10
2877 3284 8.316946 CAGCACTCAGGATGGATCTTATTTATA 58.683 37.037 0.00 0.00 36.16 0.98
2880 3287 9.107177 CACTCAGGATGGATCTTATTTATATGC 57.893 37.037 0.00 0.00 36.16 3.14
2980 3389 3.271153 AACTAGTAGGGTTCTGGTGGT 57.729 47.619 0.00 0.00 0.00 4.16
3012 3421 5.997746 TCCTTTTCTCTGTATCAACTGTTGG 59.002 40.000 19.55 4.25 0.00 3.77
3016 3425 5.808366 TCTCTGTATCAACTGTTGGTCTT 57.192 39.130 19.55 6.16 0.00 3.01
3088 3497 4.533707 AGTTTCTCCTTCATCCTGATCACA 59.466 41.667 0.00 0.00 0.00 3.58
3109 3518 2.936498 ACGTTCACCTCACTCTTTGTTG 59.064 45.455 0.00 0.00 0.00 3.33
3289 3699 2.033448 TTTGCCGGCCTACCTGTG 59.967 61.111 26.77 0.00 0.00 3.66
3309 3719 3.496130 GTGCCCTCACATCGAATCAATAG 59.504 47.826 0.00 0.00 42.66 1.73
3323 3733 6.373216 TCGAATCAATAGTCCGTCCAAATTTT 59.627 34.615 0.00 0.00 0.00 1.82
3328 3738 2.514803 AGTCCGTCCAAATTTTCCCAG 58.485 47.619 0.00 0.00 0.00 4.45
3367 3777 4.142730 CGCGGTACTACTTAAGAAGTGAGT 60.143 45.833 10.09 6.71 42.84 3.41
3378 3788 8.779354 ACTTAAGAAGTGAGTTGATACATTCC 57.221 34.615 10.09 0.00 41.01 3.01
3396 3806 6.281405 ACATTCCCTTATCTTTACGTGCTAG 58.719 40.000 0.00 0.00 0.00 3.42
3399 3809 4.404715 TCCCTTATCTTTACGTGCTAGCTT 59.595 41.667 17.23 2.72 0.00 3.74
3403 3813 3.232213 TCTTTACGTGCTAGCTTCCAG 57.768 47.619 17.23 4.73 0.00 3.86
3420 3830 1.276989 CCAGTTCTGCCATTTGCCAAT 59.723 47.619 0.00 0.00 40.16 3.16
3422 3832 3.404899 CAGTTCTGCCATTTGCCAATTT 58.595 40.909 0.00 0.00 40.16 1.82
3426 3836 2.027929 TCTGCCATTTGCCAATTTCCAG 60.028 45.455 0.00 0.00 40.16 3.86
3427 3837 1.698532 TGCCATTTGCCAATTTCCAGT 59.301 42.857 0.00 0.00 40.16 4.00
3428 3838 2.902486 TGCCATTTGCCAATTTCCAGTA 59.098 40.909 0.00 0.00 40.16 2.74
3429 3839 3.055963 TGCCATTTGCCAATTTCCAGTAG 60.056 43.478 0.00 0.00 40.16 2.57
3430 3840 3.055891 GCCATTTGCCAATTTCCAGTAGT 60.056 43.478 0.00 0.00 0.00 2.73
3431 3841 4.497300 CCATTTGCCAATTTCCAGTAGTG 58.503 43.478 0.00 0.00 0.00 2.74
3432 3842 4.021192 CCATTTGCCAATTTCCAGTAGTGT 60.021 41.667 0.00 0.00 0.00 3.55
3433 3843 4.582701 TTTGCCAATTTCCAGTAGTGTG 57.417 40.909 0.00 0.00 0.00 3.82
3434 3844 1.885887 TGCCAATTTCCAGTAGTGTGC 59.114 47.619 0.00 0.00 0.00 4.57
3435 3845 2.162681 GCCAATTTCCAGTAGTGTGCT 58.837 47.619 0.00 0.00 0.00 4.40
3436 3846 2.162408 GCCAATTTCCAGTAGTGTGCTC 59.838 50.000 0.00 0.00 0.00 4.26
3437 3847 2.749621 CCAATTTCCAGTAGTGTGCTCC 59.250 50.000 0.00 0.00 0.00 4.70
3438 3848 2.386661 ATTTCCAGTAGTGTGCTCCG 57.613 50.000 0.00 0.00 0.00 4.63
3473 3883 1.808945 CAAGATCACAGGAACAGCCAC 59.191 52.381 0.00 0.00 40.02 5.01
3502 3912 5.574891 TCTCTTCATCTTCTTCTCCTTCG 57.425 43.478 0.00 0.00 0.00 3.79
3609 4019 2.067013 GGTAACGCTTCCTTCAGTGTC 58.933 52.381 0.00 0.00 36.46 3.67
3753 4163 3.626670 CCAGCTTCTCCTTCATCATCAAC 59.373 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.277557 GCTCCTTCTCATGTGTCCACT 59.722 52.381 0.00 0.00 0.00 4.00
41 42 3.243434 CCGAATATGGCGAACAGACTACT 60.243 47.826 0.00 0.00 0.00 2.57
43 44 2.035449 CCCGAATATGGCGAACAGACTA 59.965 50.000 0.00 0.00 0.00 2.59
65 66 1.573108 TTCCAGGACTGTGAGATCCC 58.427 55.000 0.00 0.00 35.38 3.85
84 85 2.620115 GGATGCATCGACACATGGAATT 59.380 45.455 20.15 0.00 0.00 2.17
87 88 0.540923 TGGATGCATCGACACATGGA 59.459 50.000 20.15 0.00 0.00 3.41
144 145 6.493116 GCCATCAGTATTGATCTTGACAAAG 58.507 40.000 0.00 0.00 42.12 2.77
258 260 1.140161 CGAGCGGGTCGGTAATTCA 59.860 57.895 20.92 0.00 45.58 2.57
323 326 2.543037 TCACATGTGAGTAGCCCCTA 57.457 50.000 24.56 0.00 34.14 3.53
399 402 1.123077 ATAGGAGCCACAATCGAGCA 58.877 50.000 0.00 0.00 0.00 4.26
423 426 5.362430 ACAAGGTAAGCTCTCCAATCTCTAG 59.638 44.000 9.34 0.00 0.00 2.43
527 534 2.897969 ACCAACTCTCAGTCACCGTAAT 59.102 45.455 0.00 0.00 0.00 1.89
531 538 1.502231 CAACCAACTCTCAGTCACCG 58.498 55.000 0.00 0.00 0.00 4.94
583 590 0.252761 TCCTGCGATCATCTGCCAAA 59.747 50.000 0.00 0.00 0.00 3.28
589 596 1.412079 AAGAGCTCCTGCGATCATCT 58.588 50.000 10.93 0.00 45.42 2.90
680 687 1.600058 ATGGGGGCTGAAGATTCTGA 58.400 50.000 3.89 0.00 0.00 3.27
710 717 3.895232 TCTTTCTCTAGTGCCATGGAC 57.105 47.619 18.40 11.05 0.00 4.02
721 728 5.463286 TCGTATTGTGCGTTTCTTTCTCTA 58.537 37.500 0.00 0.00 0.00 2.43
722 729 4.304110 TCGTATTGTGCGTTTCTTTCTCT 58.696 39.130 0.00 0.00 0.00 3.10
723 730 4.640805 TCGTATTGTGCGTTTCTTTCTC 57.359 40.909 0.00 0.00 0.00 2.87
724 731 5.867716 AGTATCGTATTGTGCGTTTCTTTCT 59.132 36.000 0.00 0.00 0.00 2.52
725 732 6.091123 AGTATCGTATTGTGCGTTTCTTTC 57.909 37.500 0.00 0.00 0.00 2.62
726 733 6.476243 AAGTATCGTATTGTGCGTTTCTTT 57.524 33.333 0.00 0.00 0.00 2.52
727 734 7.585286 TTAAGTATCGTATTGTGCGTTTCTT 57.415 32.000 0.00 0.00 0.00 2.52
728 735 7.766219 ATTAAGTATCGTATTGTGCGTTTCT 57.234 32.000 0.00 0.00 0.00 2.52
731 738 9.472361 AGAATATTAAGTATCGTATTGTGCGTT 57.528 29.630 0.00 0.00 0.00 4.84
732 739 8.912658 CAGAATATTAAGTATCGTATTGTGCGT 58.087 33.333 0.00 0.00 0.00 5.24
733 740 8.912658 ACAGAATATTAAGTATCGTATTGTGCG 58.087 33.333 0.00 0.00 33.55 5.34
763 770 9.208022 CGGAATATTGAGCATATAGACTGAAAA 57.792 33.333 0.00 0.00 0.00 2.29
764 771 8.367911 ACGGAATATTGAGCATATAGACTGAAA 58.632 33.333 0.00 0.00 0.00 2.69
765 772 7.896811 ACGGAATATTGAGCATATAGACTGAA 58.103 34.615 0.00 0.00 0.00 3.02
766 773 7.468141 ACGGAATATTGAGCATATAGACTGA 57.532 36.000 0.00 0.00 0.00 3.41
767 774 7.276658 GGAACGGAATATTGAGCATATAGACTG 59.723 40.741 0.00 0.00 0.00 3.51
768 775 7.324178 GGAACGGAATATTGAGCATATAGACT 58.676 38.462 0.00 0.00 0.00 3.24
769 776 7.527084 GGAACGGAATATTGAGCATATAGAC 57.473 40.000 0.00 0.00 0.00 2.59
789 796 0.390472 CTTCTCTCCCAGCACGGAAC 60.390 60.000 0.00 0.00 36.56 3.62
790 797 0.541998 TCTTCTCTCCCAGCACGGAA 60.542 55.000 0.00 0.00 36.56 4.30
791 798 0.541998 TTCTTCTCTCCCAGCACGGA 60.542 55.000 0.00 0.00 36.56 4.69
792 799 0.321671 TTTCTTCTCTCCCAGCACGG 59.678 55.000 0.00 0.00 0.00 4.94
820 827 5.869579 TGTTGAAGATATTAGGCCTCATCC 58.130 41.667 9.68 0.00 0.00 3.51
822 829 6.662755 TGTTGTTGAAGATATTAGGCCTCAT 58.337 36.000 9.68 6.60 0.00 2.90
867 1247 2.362077 GGCTATAATGGCCCAAACACTG 59.638 50.000 0.00 0.00 43.49 3.66
894 1274 0.322008 CAGGGCCTTGAGTGGACTTC 60.322 60.000 9.80 0.00 34.90 3.01
1363 1755 6.170506 AGGCATTCAGTTATAACAGAAACGA 58.829 36.000 22.44 5.32 37.83 3.85
1378 1770 2.736978 CTAGCACGACTAGGCATTCAG 58.263 52.381 0.00 0.00 44.14 3.02
1457 1849 2.143925 CCGGTCTCTCAGGAAACAAAC 58.856 52.381 0.00 0.00 33.18 2.93
1475 1867 7.542890 AGAATATATCACATCTTAGCTGACCG 58.457 38.462 0.00 0.00 0.00 4.79
1495 1887 9.506042 TGGGCAGAAATATCATATCCTAGAATA 57.494 33.333 0.00 0.00 0.00 1.75
1496 1888 8.397951 TGGGCAGAAATATCATATCCTAGAAT 57.602 34.615 0.00 0.00 0.00 2.40
1519 1911 3.362888 GCGCACAAGCTAACAAAAATTGG 60.363 43.478 0.30 0.00 39.10 3.16
1526 1918 3.070748 TCTTATGCGCACAAGCTAACAA 58.929 40.909 23.35 2.10 39.10 2.83
1528 1920 3.951979 ATCTTATGCGCACAAGCTAAC 57.048 42.857 23.35 0.00 39.10 2.34
1534 1926 9.435688 AACTAATGATATATCTTATGCGCACAA 57.564 29.630 14.90 6.58 0.00 3.33
1574 1966 2.238942 ACAGCTTCACGACACATTCA 57.761 45.000 0.00 0.00 0.00 2.57
1586 1978 8.082242 ACATAAACTGATAAAACCAACAGCTTC 58.918 33.333 0.00 0.00 34.25 3.86
1638 2030 1.000396 ACAATGCTCTCCAAGGCCC 60.000 57.895 0.00 0.00 0.00 5.80
1725 2117 4.229876 GCTTAGCTTGCCAAGTACAAAAG 58.770 43.478 6.28 4.60 0.00 2.27
1761 2153 6.770746 ATTGATCATTTGCTCTTACTTGCT 57.229 33.333 0.00 0.00 0.00 3.91
1891 2283 2.291741 CTGCAACCTTGTCTTCTCCAAC 59.708 50.000 0.00 0.00 0.00 3.77
1943 2338 4.865365 GTGACTCCTCGGATTAGAAAACAG 59.135 45.833 0.00 0.00 0.00 3.16
1966 2361 3.153919 TCCGAGGGTGAATTTTGGAAAG 58.846 45.455 0.00 0.00 0.00 2.62
1995 2390 7.734924 TTCATATAGCAAAACTGGATAGCTG 57.265 36.000 0.00 0.00 36.80 4.24
2075 2470 8.023128 ACTTTTGTTCATCATTACACAGCATAC 58.977 33.333 0.00 0.00 0.00 2.39
2196 2591 8.865001 TGTTGAAAATGTAAGTAAACAACAAGC 58.135 29.630 0.00 0.00 41.63 4.01
2215 2610 8.040132 ACCAAAACAGAAATGAGAATGTTGAAA 58.960 29.630 0.00 0.00 36.09 2.69
2276 2671 2.838736 ACATTACGCTCCTAGCCAATG 58.161 47.619 14.57 14.57 41.83 2.82
2278 2673 2.235155 TCAACATTACGCTCCTAGCCAA 59.765 45.455 0.00 0.00 38.18 4.52
2539 2934 0.031585 GGCTGGAAAACGACAAACCC 59.968 55.000 0.00 0.00 0.00 4.11
2540 2935 1.029681 AGGCTGGAAAACGACAAACC 58.970 50.000 0.00 0.00 0.00 3.27
2573 2968 8.408601 CACATAAGATGAATTTAAAGACCCAGG 58.591 37.037 0.00 0.00 0.00 4.45
2574 2969 8.960591 ACACATAAGATGAATTTAAAGACCCAG 58.039 33.333 0.00 0.00 0.00 4.45
2639 3044 3.611766 CGTAGGATTTTGACCTGGACT 57.388 47.619 0.00 0.00 38.31 3.85
2734 3141 8.428063 TGAGAAGAGAAGAAGAAAAAGAGATGT 58.572 33.333 0.00 0.00 0.00 3.06
2778 3185 7.201266 GCAAAGTCTAATGCGTTGTATCAAAAG 60.201 37.037 0.08 0.00 32.17 2.27
2880 3287 1.953138 CGCCAAGCCGAGCATCTAG 60.953 63.158 0.00 0.00 0.00 2.43
2980 3389 8.567948 GTTGATACAGAGAAAAGGACATTTCAA 58.432 33.333 3.31 0.00 40.89 2.69
3012 3421 4.937620 TCATGTTCAGATTAGGCACAAGAC 59.062 41.667 0.00 0.00 0.00 3.01
3016 3425 4.558226 ACTCATGTTCAGATTAGGCACA 57.442 40.909 0.00 0.00 0.00 4.57
3088 3497 2.936498 CAACAAAGAGTGAGGTGAACGT 59.064 45.455 0.00 0.00 0.00 3.99
3289 3699 3.733337 ACTATTGATTCGATGTGAGGGC 58.267 45.455 0.00 0.00 0.00 5.19
3309 3719 2.235891 ACTGGGAAAATTTGGACGGAC 58.764 47.619 0.00 0.00 0.00 4.79
3323 3733 1.132527 TCCTTCCTTCTCCAACTGGGA 60.133 52.381 0.00 0.00 45.89 4.37
3328 3738 1.014564 CGCGTCCTTCCTTCTCCAAC 61.015 60.000 0.00 0.00 0.00 3.77
3367 3777 7.225931 GCACGTAAAGATAAGGGAATGTATCAA 59.774 37.037 0.00 0.00 0.00 2.57
3378 3788 4.745620 GGAAGCTAGCACGTAAAGATAAGG 59.254 45.833 18.83 0.00 0.00 2.69
3396 3806 1.670967 GCAAATGGCAGAACTGGAAGC 60.671 52.381 3.99 0.00 43.97 3.86
3399 3809 0.178967 TGGCAAATGGCAGAACTGGA 60.179 50.000 5.46 0.00 46.12 3.86
3420 3830 0.320374 CCGGAGCACACTACTGGAAA 59.680 55.000 0.00 0.00 0.00 3.13
3422 3832 2.646175 GCCGGAGCACACTACTGGA 61.646 63.158 5.05 0.00 39.53 3.86
3473 3883 5.421277 AGAAGAAGATGAAGAGAGCACATG 58.579 41.667 0.00 0.00 0.00 3.21
3609 4019 1.821241 CGCTAATGTCGATGTGCCCG 61.821 60.000 0.00 0.00 0.00 6.13
3753 4163 2.270986 GCTGCTGTTGGACTTGGGG 61.271 63.158 0.00 0.00 0.00 4.96
3789 4199 1.680249 GGGTAGCTGGCAAGGAAGAAG 60.680 57.143 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.