Multiple sequence alignment - TraesCS7A01G246100

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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 TraesCS7A01G246100 chr7A 100.000 3845 0 0 1 3845 224986578 224990422 0.000000e+00 7101.0
1 TraesCS7A01G246100 chr7D 96.996 2197 62 4 740 2934 213374281 213376475 0.000000e+00 3688.0
2 TraesCS7A01G246100 chr7D 92.809 737 39 11 7 739 213373523 213374249 0.000000e+00 1055.0
3 TraesCS7A01G246100 chr7D 88.636 748 32 13 3147 3845 213376712 213377455 0.000000e+00 861.0
4 TraesCS7A01G246100 chr7D 85.714 154 14 7 3000 3149 213376476 213376625 5.140000e-34 156.0
5 TraesCS7A01G246100 chr7B 96.770 2198 64 4 740 2934 188604574 188602381 0.000000e+00 3659.0
6 TraesCS7A01G246100 chr7B 91.204 739 44 8 5 739 188605326 188604605 0.000000e+00 985.0
7 TraesCS7A01G246100 chr7B 89.466 655 25 11 3147 3759 188602150 188601498 0.000000e+00 787.0
8 TraesCS7A01G246100 chr7B 100.000 57 0 0 3789 3845 188601369 188601313 5.250000e-19 106.0
9 TraesCS7A01G246100 chr5B 80.280 786 147 4 1082 1860 449752506 449751722 1.540000e-163 586.0
10 TraesCS7A01G246100 chr5D 78.141 947 181 17 1082 2006 376664380 376663438 2.580000e-161 579.0
11 TraesCS7A01G246100 chr5A 79.644 786 152 3 1082 1860 477437375 477436591 3.360000e-155 558.0
12 TraesCS7A01G246100 chr3D 94.737 38 2 0 2930 2967 179912262 179912299 4.150000e-05 60.2
13 TraesCS7A01G246100 chr3A 100.000 31 0 0 2937 2967 223522311 223522341 1.490000e-04 58.4


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 TraesCS7A01G246100 chr7A 224986578 224990422 3844 False 7101.00 7101 100.00000 1 3845 1 chr7A.!!$F1 3844
1 TraesCS7A01G246100 chr7D 213373523 213377455 3932 False 1440.00 3688 91.03875 7 3845 4 chr7D.!!$F1 3838
2 TraesCS7A01G246100 chr7B 188601313 188605326 4013 True 1384.25 3659 94.36000 5 3845 4 chr7B.!!$R1 3840
3 TraesCS7A01G246100 chr5B 449751722 449752506 784 True 586.00 586 80.28000 1082 1860 1 chr5B.!!$R1 778
4 TraesCS7A01G246100 chr5D 376663438 376664380 942 True 579.00 579 78.14100 1082 2006 1 chr5D.!!$R1 924
5 TraesCS7A01G246100 chr5A 477436591 477437375 784 True 558.00 558 79.64400 1082 1860 1 chr5A.!!$R1 778

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
834 871 0.039437 CTCACTCGCACTGTACGGTT 60.039 55.000 4.06 0.0 0.0 4.44 F
2226 2281 1.268079 GCAGAGGTTTTGAGCAACTCC 59.732 52.381 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2349 0.251916 TCCTCCATTTGTACCGGCAG 59.748 55.0 0.0 0.0 0.0 4.85 R
3135 3193 0.033504 TCTTGCAACCGACCTCACTC 59.966 55.0 0.0 0.0 0.0 3.51 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
53 54 2.900546 AGGGTTGTCCACAGAGTTAGAG 59.099 50.000 0.00 0.00 38.24 2.43
58 59 5.820947 GGTTGTCCACAGAGTTAGAGAAAAA 59.179 40.000 0.00 0.00 0.00 1.94
59 60 6.238402 GGTTGTCCACAGAGTTAGAGAAAAAC 60.238 42.308 0.00 0.00 0.00 2.43
60 61 6.235231 TGTCCACAGAGTTAGAGAAAAACT 57.765 37.500 0.00 0.00 39.84 2.66
62 63 7.963532 TGTCCACAGAGTTAGAGAAAAACTAT 58.036 34.615 0.00 0.00 37.31 2.12
224 228 1.827399 TTCTGGCCCGTTCTGTCTCC 61.827 60.000 0.00 0.00 0.00 3.71
419 423 0.741221 GTGGGATTGGTCTCTGTCGC 60.741 60.000 0.00 0.00 0.00 5.19
421 425 0.250513 GGGATTGGTCTCTGTCGCTT 59.749 55.000 0.00 0.00 0.00 4.68
456 460 2.472695 AGATAGTTGTTGCGCCTGAA 57.527 45.000 4.18 0.00 0.00 3.02
465 469 4.223964 GCGCCTGAATCCGTTCGC 62.224 66.667 0.00 0.00 37.15 4.70
468 472 1.447838 GCCTGAATCCGTTCGCTGA 60.448 57.895 0.00 0.00 37.15 4.26
472 476 0.527600 TGAATCCGTTCGCTGATCCG 60.528 55.000 0.00 0.00 37.15 4.18
473 477 1.215655 GAATCCGTTCGCTGATCCGG 61.216 60.000 0.00 0.00 41.75 5.14
515 519 2.803155 TTCAGATTGCCGCGCCTTCT 62.803 55.000 0.00 0.00 0.00 2.85
532 536 0.817654 TCTGCTGTCGTCGGATCATT 59.182 50.000 0.00 0.00 0.00 2.57
558 562 2.092429 TCTCTGTATTGATTGGTGGGGC 60.092 50.000 0.00 0.00 0.00 5.80
576 580 1.014564 GCTGGAAGTTCGGAACGGAG 61.015 60.000 14.70 10.18 44.46 4.63
597 601 2.290577 GGCCCCTCACATAGATTGATCC 60.291 54.545 0.00 0.00 0.00 3.36
632 636 9.261035 TCATGTTTCTAATCTTAGGTCTTCTCT 57.739 33.333 0.00 0.00 0.00 3.10
667 671 0.366871 GTAGTGATGACTTGCGCACG 59.633 55.000 11.12 12.17 36.43 5.34
705 709 7.255139 CGTCTTGGTTCCTTACAAATTTTCTCT 60.255 37.037 0.00 0.00 0.00 3.10
770 805 5.454554 GTCAGAAGAAAAGCACCGTTAAAAC 59.545 40.000 0.00 0.00 0.00 2.43
830 867 1.714794 ATTGCTCACTCGCACTGTAC 58.285 50.000 0.00 0.00 40.09 2.90
834 871 0.039437 CTCACTCGCACTGTACGGTT 60.039 55.000 4.06 0.00 0.00 4.44
843 880 3.181534 CGCACTGTACGGTTACAATTCTG 60.182 47.826 4.06 0.00 37.77 3.02
846 883 4.625742 CACTGTACGGTTACAATTCTGAGG 59.374 45.833 4.06 0.00 37.77 3.86
857 894 7.648112 GGTTACAATTCTGAGGTTGTTCTTTTC 59.352 37.037 13.32 2.85 39.18 2.29
890 927 8.350722 ACTAGCATTGCATTTTCAGATATTGAG 58.649 33.333 11.91 0.00 37.07 3.02
892 929 5.751509 GCATTGCATTTTCAGATATTGAGCA 59.248 36.000 3.15 0.00 37.07 4.26
895 932 6.270156 TGCATTTTCAGATATTGAGCACAA 57.730 33.333 0.00 0.00 37.07 3.33
901 938 7.509141 TTTCAGATATTGAGCACAACAGAAA 57.491 32.000 0.00 3.42 38.90 2.52
954 991 4.662468 TGGTGCAAAGAAAATAAGTGCA 57.338 36.364 0.00 0.00 42.62 4.57
959 996 4.507388 TGCAAAGAAAATAAGTGCAGCAAC 59.493 37.500 0.00 0.00 40.14 4.17
984 1021 6.222038 TGAGTAGGGTGATGTTATTGAGTC 57.778 41.667 0.00 0.00 0.00 3.36
1035 1072 1.927895 CTATTGTCGCGAAGGAGCTT 58.072 50.000 12.06 0.00 34.40 3.74
1101 1138 4.218417 TCTGAGAATGATGTCAGTGACGAA 59.782 41.667 18.17 6.79 44.95 3.85
1755 1798 1.541588 GTGATCAAACACTTGGCTCCC 59.458 52.381 0.00 0.00 37.73 4.30
1927 1976 3.655777 TGACCTAGGGGACAAAAATGAGT 59.344 43.478 14.81 0.00 34.62 3.41
2100 2155 2.841442 AACGCTCTACTCAAAGGCTT 57.159 45.000 0.00 0.00 0.00 4.35
2123 2178 9.368674 GCTTCCTAGTACTAAGGAAACTAAAAG 57.631 37.037 22.98 15.57 42.68 2.27
2204 2259 9.527157 TGAAGGAACACAAAGGAATGATAATAA 57.473 29.630 0.00 0.00 0.00 1.40
2224 2279 2.057137 TGCAGAGGTTTTGAGCAACT 57.943 45.000 0.00 0.00 31.42 3.16
2226 2281 1.268079 GCAGAGGTTTTGAGCAACTCC 59.732 52.381 0.00 0.00 0.00 3.85
2294 2349 1.200020 CCCGTTGACAAGCTTCAATCC 59.800 52.381 4.22 0.00 37.80 3.01
2517 2572 3.991121 GTCTTGGATCTATCGGCTTTAGC 59.009 47.826 0.00 0.00 41.14 3.09
2562 2617 1.672363 TCTGCTGCAAAACACTCAGTG 59.328 47.619 2.22 2.22 39.75 3.66
2571 2626 3.769739 AAACACTCAGTGCCACTATCA 57.230 42.857 4.13 0.00 36.98 2.15
2572 2627 3.325293 AACACTCAGTGCCACTATCAG 57.675 47.619 4.13 0.00 36.98 2.90
2626 2681 5.050023 GGAGCTTTGAACAGTTCTTACAGTC 60.050 44.000 14.51 4.65 0.00 3.51
2627 2682 5.428253 AGCTTTGAACAGTTCTTACAGTCA 58.572 37.500 14.51 0.00 0.00 3.41
2628 2683 6.058183 AGCTTTGAACAGTTCTTACAGTCAT 58.942 36.000 14.51 0.00 0.00 3.06
2655 2713 2.092323 GCAGGTAGTGGGAATTCAACC 58.908 52.381 7.93 6.44 0.00 3.77
2678 2736 2.477176 TTGCTGGTGACACGCAACC 61.477 57.895 14.52 0.00 44.10 3.77
2751 2809 4.651045 AGTTCTTTTGATGGACTGCCTTTT 59.349 37.500 0.00 0.00 34.31 2.27
2787 2845 8.218488 GGTATTAATAGTCCAATTCCTGACCTT 58.782 37.037 0.00 0.00 31.76 3.50
2820 2878 3.959293 TGAACTGCTGGATGACAATGAT 58.041 40.909 0.00 0.00 0.00 2.45
2926 2984 9.226606 TGGATGTACCTTTTCTTAATACAGTTG 57.773 33.333 0.00 0.00 39.86 3.16
2937 2995 8.685838 TTCTTAATACAGTTGCAATATACCCC 57.314 34.615 0.59 0.00 0.00 4.95
2938 2996 7.228590 TCTTAATACAGTTGCAATATACCCCC 58.771 38.462 0.59 0.00 0.00 5.40
2939 2997 5.663158 AATACAGTTGCAATATACCCCCT 57.337 39.130 0.59 0.00 0.00 4.79
2940 2998 5.663158 ATACAGTTGCAATATACCCCCTT 57.337 39.130 0.59 0.00 0.00 3.95
2941 2999 4.331159 ACAGTTGCAATATACCCCCTTT 57.669 40.909 0.59 0.00 0.00 3.11
2942 3000 4.023291 ACAGTTGCAATATACCCCCTTTG 58.977 43.478 0.59 0.00 0.00 2.77
2943 3001 4.023291 CAGTTGCAATATACCCCCTTTGT 58.977 43.478 0.59 0.00 0.00 2.83
2944 3002 4.466015 CAGTTGCAATATACCCCCTTTGTT 59.534 41.667 0.59 0.00 0.00 2.83
2945 3003 4.709886 AGTTGCAATATACCCCCTTTGTTC 59.290 41.667 0.59 0.00 0.00 3.18
2946 3004 3.637769 TGCAATATACCCCCTTTGTTCC 58.362 45.455 0.00 0.00 0.00 3.62
2947 3005 3.011821 TGCAATATACCCCCTTTGTTCCA 59.988 43.478 0.00 0.00 0.00 3.53
2948 3006 4.027437 GCAATATACCCCCTTTGTTCCAA 58.973 43.478 0.00 0.00 0.00 3.53
2949 3007 4.468153 GCAATATACCCCCTTTGTTCCAAA 59.532 41.667 0.00 0.00 0.00 3.28
2950 3008 5.046231 GCAATATACCCCCTTTGTTCCAAAA 60.046 40.000 0.00 0.00 0.00 2.44
2951 3009 6.352651 GCAATATACCCCCTTTGTTCCAAAAT 60.353 38.462 0.00 0.00 0.00 1.82
2952 3010 7.147637 GCAATATACCCCCTTTGTTCCAAAATA 60.148 37.037 0.00 0.00 0.00 1.40
2953 3011 8.763601 CAATATACCCCCTTTGTTCCAAAATAA 58.236 33.333 0.00 0.00 0.00 1.40
2954 3012 6.867519 ATACCCCCTTTGTTCCAAAATAAG 57.132 37.500 0.00 0.00 0.00 1.73
2955 3013 4.562767 ACCCCCTTTGTTCCAAAATAAGT 58.437 39.130 0.00 0.00 0.00 2.24
2956 3014 4.346709 ACCCCCTTTGTTCCAAAATAAGTG 59.653 41.667 0.00 0.00 0.00 3.16
2957 3015 4.346709 CCCCCTTTGTTCCAAAATAAGTGT 59.653 41.667 0.00 0.00 0.00 3.55
2958 3016 5.510690 CCCCCTTTGTTCCAAAATAAGTGTC 60.511 44.000 0.00 0.00 0.00 3.67
2959 3017 5.219633 CCCTTTGTTCCAAAATAAGTGTCG 58.780 41.667 0.00 0.00 0.00 4.35
2960 3018 5.221165 CCCTTTGTTCCAAAATAAGTGTCGT 60.221 40.000 0.00 0.00 0.00 4.34
2961 3019 5.685511 CCTTTGTTCCAAAATAAGTGTCGTG 59.314 40.000 0.00 0.00 0.00 4.35
2962 3020 4.822036 TGTTCCAAAATAAGTGTCGTGG 57.178 40.909 0.00 0.00 0.00 4.94
2963 3021 4.200874 TGTTCCAAAATAAGTGTCGTGGT 58.799 39.130 0.00 0.00 0.00 4.16
2964 3022 4.641094 TGTTCCAAAATAAGTGTCGTGGTT 59.359 37.500 0.00 0.00 0.00 3.67
2965 3023 5.125739 TGTTCCAAAATAAGTGTCGTGGTTT 59.874 36.000 0.00 0.00 0.00 3.27
2966 3024 5.838531 TCCAAAATAAGTGTCGTGGTTTT 57.161 34.783 0.00 0.00 0.00 2.43
2967 3025 6.939132 TCCAAAATAAGTGTCGTGGTTTTA 57.061 33.333 0.00 0.00 0.00 1.52
2968 3026 7.330900 TCCAAAATAAGTGTCGTGGTTTTAA 57.669 32.000 0.00 0.00 0.00 1.52
2969 3027 7.194962 TCCAAAATAAGTGTCGTGGTTTTAAC 58.805 34.615 0.00 0.00 0.00 2.01
3020 3078 6.538742 GGAGTATGTAATAGTGCTTGCTTCAA 59.461 38.462 0.00 0.00 37.56 2.69
3027 3085 3.205784 AGTGCTTGCTTCAACTCTCTT 57.794 42.857 0.00 0.00 0.00 2.85
3050 3108 9.778741 TCTTTGTGGGCAATTATATCTAGTTAG 57.221 33.333 0.00 0.00 34.18 2.34
3056 3114 9.111519 TGGGCAATTATATCTAGTTAGAATCCA 57.888 33.333 2.06 3.31 35.69 3.41
3093 3151 1.903183 AGAGGTGAGGTTGGTTAGAGC 59.097 52.381 0.00 0.00 0.00 4.09
3107 3165 5.607477 TGGTTAGAGCCAAATTATCTACCG 58.393 41.667 0.00 0.00 35.25 4.02
3110 3168 6.867293 GGTTAGAGCCAAATTATCTACCGTAG 59.133 42.308 0.00 0.00 0.00 3.51
3111 3169 7.432059 GTTAGAGCCAAATTATCTACCGTAGT 58.568 38.462 5.46 0.00 0.00 2.73
3112 3170 6.481434 AGAGCCAAATTATCTACCGTAGTT 57.519 37.500 5.46 0.22 0.00 2.24
3113 3171 7.592885 AGAGCCAAATTATCTACCGTAGTTA 57.407 36.000 5.46 0.00 0.00 2.24
3114 3172 8.015185 AGAGCCAAATTATCTACCGTAGTTAA 57.985 34.615 10.24 10.24 0.00 2.01
3115 3173 8.480501 AGAGCCAAATTATCTACCGTAGTTAAA 58.519 33.333 11.40 3.83 0.00 1.52
3118 3176 9.874215 GCCAAATTATCTACCGTAGTTAAAATC 57.126 33.333 11.40 0.62 0.00 2.17
3135 3193 9.784531 AGTTAAAATCTATCCATACATGTGAGG 57.215 33.333 9.11 10.31 0.00 3.86
3136 3194 9.778741 GTTAAAATCTATCCATACATGTGAGGA 57.221 33.333 19.47 19.47 34.12 3.71
3144 3202 3.181471 CCATACATGTGAGGAGTGAGGTC 60.181 52.174 9.11 0.00 0.00 3.85
3174 3324 7.039784 TGCAAGAATTACTCCTGCTGTTATTTT 60.040 33.333 0.00 0.00 34.54 1.82
3188 3338 6.714810 TGCTGTTATTTTCCAGTGTCTTACAT 59.285 34.615 0.00 0.00 0.00 2.29
3263 3413 3.119388 GCTTATTCTGTTGATTGCAGCCA 60.119 43.478 0.00 0.00 34.21 4.75
3264 3414 4.418392 CTTATTCTGTTGATTGCAGCCAC 58.582 43.478 0.00 0.00 34.21 5.01
3359 3511 5.067936 GTGCTAATCCTGCTACAGTAGAGAA 59.932 44.000 12.15 0.00 0.00 2.87
3381 3533 9.766277 GAGAATGATGTATTGTGTCTCTTTTTC 57.234 33.333 0.00 0.00 0.00 2.29
3494 3648 3.178267 GCGTCTGATGAAGAGAACTGAG 58.822 50.000 0.00 0.00 34.84 3.35
3561 3720 1.168714 GTTGTCATGCCCTCTTGGAC 58.831 55.000 0.00 0.00 35.39 4.02
3730 3929 1.865865 TCGTGACTTTCAGTTCTGGC 58.134 50.000 0.00 0.00 0.00 4.85
3759 3958 2.543861 CGTCTCTCAATGTCATACCCCG 60.544 54.545 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 6.235231 AGTTTTTCTCTAACTCTGTGGACA 57.765 37.500 0.00 0.00 30.20 4.02
53 54 8.660373 CCGGATTATGAGATGCTATAGTTTTTC 58.340 37.037 0.00 0.00 0.00 2.29
58 59 4.959210 AGCCGGATTATGAGATGCTATAGT 59.041 41.667 5.05 0.00 0.00 2.12
59 60 5.288015 CAGCCGGATTATGAGATGCTATAG 58.712 45.833 5.05 0.00 0.00 1.31
60 61 4.442052 GCAGCCGGATTATGAGATGCTATA 60.442 45.833 5.05 0.00 0.00 1.31
62 63 2.354103 GCAGCCGGATTATGAGATGCTA 60.354 50.000 5.05 0.00 0.00 3.49
202 206 2.045926 CAGAACGGGCCAGAAGGG 60.046 66.667 10.86 0.00 40.85 3.95
205 209 1.671742 GAGACAGAACGGGCCAGAA 59.328 57.895 10.86 0.00 0.00 3.02
224 228 1.339644 TTAATTCGGGGGACGGGGAG 61.340 60.000 0.00 0.00 44.45 4.30
387 391 3.430651 CCAATCCCACCAAAAATCCATCG 60.431 47.826 0.00 0.00 0.00 3.84
390 394 2.903135 GACCAATCCCACCAAAAATCCA 59.097 45.455 0.00 0.00 0.00 3.41
465 469 1.838077 ACCCTAGAAAACCCGGATCAG 59.162 52.381 0.73 0.00 0.00 2.90
468 472 2.882643 GCAAACCCTAGAAAACCCGGAT 60.883 50.000 0.73 0.00 0.00 4.18
491 495 2.485122 GCGGCAATCTGAAACCCG 59.515 61.111 0.00 8.33 41.72 5.28
515 519 0.460109 CCAATGATCCGACGACAGCA 60.460 55.000 0.00 0.00 0.00 4.41
518 522 1.518352 CGCCAATGATCCGACGACA 60.518 57.895 0.00 0.00 0.00 4.35
532 536 2.236146 ACCAATCAATACAGAGACGCCA 59.764 45.455 0.00 0.00 0.00 5.69
558 562 0.389948 CCTCCGTTCCGAACTTCCAG 60.390 60.000 9.55 0.44 0.00 3.86
576 580 2.290577 GGATCAATCTATGTGAGGGGCC 60.291 54.545 0.00 0.00 0.00 5.80
632 636 9.056005 GTCATCACTACATTATCAAAGCCAATA 57.944 33.333 0.00 0.00 0.00 1.90
667 671 3.009714 AAGACGGCCCTTCTCCCC 61.010 66.667 0.00 0.00 0.00 4.81
677 681 1.886886 TTGTAAGGAACCAAGACGGC 58.113 50.000 0.00 0.00 39.03 5.68
678 682 5.447624 AAATTTGTAAGGAACCAAGACGG 57.552 39.130 0.00 0.00 42.50 4.79
679 683 6.735130 AGAAAATTTGTAAGGAACCAAGACG 58.265 36.000 0.00 0.00 0.00 4.18
770 805 4.899502 AGCGACTTATCCCAATTCTATGG 58.100 43.478 0.00 0.00 40.35 2.74
830 867 4.755123 AGAACAACCTCAGAATTGTAACCG 59.245 41.667 1.03 0.00 38.08 4.44
834 871 6.831353 TGGAAAAGAACAACCTCAGAATTGTA 59.169 34.615 1.03 0.00 38.08 2.41
843 880 4.640647 AGTCAACTGGAAAAGAACAACCTC 59.359 41.667 0.00 0.00 0.00 3.85
846 883 5.065988 TGCTAGTCAACTGGAAAAGAACAAC 59.934 40.000 0.00 0.00 0.00 3.32
857 894 4.445452 AAATGCAATGCTAGTCAACTGG 57.555 40.909 6.82 0.00 0.00 4.00
890 927 3.197265 ACCTGCAAAATTTCTGTTGTGC 58.803 40.909 3.80 3.80 0.00 4.57
892 929 3.622612 GCAACCTGCAAAATTTCTGTTGT 59.377 39.130 14.30 0.81 44.26 3.32
954 991 2.639839 ACATCACCCTACTCAAGTTGCT 59.360 45.455 0.00 0.00 0.00 3.91
959 996 6.644347 ACTCAATAACATCACCCTACTCAAG 58.356 40.000 0.00 0.00 0.00 3.02
984 1021 7.701539 ATCCATCATCTCTAGTGCTTACTAG 57.298 40.000 7.91 7.91 40.66 2.57
1035 1072 3.073678 CTCAAAATCCGACACATCACCA 58.926 45.455 0.00 0.00 0.00 4.17
1101 1138 0.823356 GCTCCTCAGCCTCGATCTCT 60.823 60.000 0.00 0.00 40.14 3.10
1631 1674 0.326264 AGCAATCCACCACTCCTCAC 59.674 55.000 0.00 0.00 0.00 3.51
1927 1976 2.837532 TCACAGCTGCTGTATGAACA 57.162 45.000 32.51 11.41 43.43 3.18
2072 2127 6.703607 CCTTTGAGTAGAGCGTTTATCATGAT 59.296 38.462 13.81 13.81 0.00 2.45
2100 2155 9.029368 GGTCTTTTAGTTTCCTTAGTACTAGGA 57.971 37.037 13.32 13.61 0.00 2.94
2123 2178 1.531578 GTCTTCTTCGCTTTGGTGGTC 59.468 52.381 0.00 0.00 0.00 4.02
2163 2218 1.065126 CCTTCAACCTCAGACCCATCC 60.065 57.143 0.00 0.00 0.00 3.51
2204 2259 2.555757 GAGTTGCTCAAAACCTCTGCAT 59.444 45.455 0.00 0.00 33.50 3.96
2205 2260 1.949525 GAGTTGCTCAAAACCTCTGCA 59.050 47.619 0.00 0.00 0.00 4.41
2206 2261 1.268079 GGAGTTGCTCAAAACCTCTGC 59.732 52.381 0.00 0.00 31.08 4.26
2226 2281 4.999311 TGATTGCTCTTCATATCCGGAATG 59.001 41.667 9.01 13.85 0.00 2.67
2294 2349 0.251916 TCCTCCATTTGTACCGGCAG 59.748 55.000 0.00 0.00 0.00 4.85
2508 2563 2.688507 TGTGAAGAAGAGCTAAAGCCG 58.311 47.619 0.00 0.00 43.38 5.52
2517 2572 6.638610 AGACTGGTAATCATGTGAAGAAGAG 58.361 40.000 0.00 0.00 0.00 2.85
2626 2681 2.639347 TCCCACTACCTGCCATATGATG 59.361 50.000 3.65 0.00 0.00 3.07
2627 2682 2.990195 TCCCACTACCTGCCATATGAT 58.010 47.619 3.65 0.00 0.00 2.45
2628 2683 2.487746 TCCCACTACCTGCCATATGA 57.512 50.000 3.65 0.00 0.00 2.15
2655 2713 1.835483 GCGTGTCACCAGCAACAGAG 61.835 60.000 0.00 0.00 0.00 3.35
2678 2736 9.326339 CAATATAAAAAGCATCACTCATGATCG 57.674 33.333 0.00 0.00 44.13 3.69
2724 2782 2.229784 CAGTCCATCAAAAGAACTGCCC 59.770 50.000 0.00 0.00 0.00 5.36
2778 2836 2.525368 TCGAGTTCATCAAGGTCAGGA 58.475 47.619 0.00 0.00 0.00 3.86
2787 2845 3.256558 CAGCAGTTCATCGAGTTCATCA 58.743 45.455 0.00 0.00 0.00 3.07
2820 2878 4.269183 ACGTTCCCAGATATTGCATCAAA 58.731 39.130 0.00 0.00 0.00 2.69
2926 2984 3.637769 TGGAACAAAGGGGGTATATTGC 58.362 45.455 0.00 0.00 31.92 3.56
2941 2999 4.200874 ACCACGACACTTATTTTGGAACA 58.799 39.130 0.00 0.00 0.00 3.18
2942 3000 4.823790 ACCACGACACTTATTTTGGAAC 57.176 40.909 0.00 0.00 0.00 3.62
2943 3001 5.838531 AAACCACGACACTTATTTTGGAA 57.161 34.783 0.00 0.00 0.00 3.53
2944 3002 5.838531 AAAACCACGACACTTATTTTGGA 57.161 34.783 0.00 0.00 0.00 3.53
2945 3003 7.384358 GTTAAAACCACGACACTTATTTTGG 57.616 36.000 0.00 0.00 0.00 3.28
2981 3039 1.732117 TACTCCCTCCGTCCCAAAAA 58.268 50.000 0.00 0.00 0.00 1.94
2982 3040 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
2983 3041 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
2984 3042 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2985 3043 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
2986 3044 2.077687 TTACATACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
2987 3045 4.217983 CACTATTACATACTCCCTCCGTCC 59.782 50.000 0.00 0.00 0.00 4.79
2988 3046 4.321082 GCACTATTACATACTCCCTCCGTC 60.321 50.000 0.00 0.00 0.00 4.79
2989 3047 3.573110 GCACTATTACATACTCCCTCCGT 59.427 47.826 0.00 0.00 0.00 4.69
2990 3048 3.827302 AGCACTATTACATACTCCCTCCG 59.173 47.826 0.00 0.00 0.00 4.63
2991 3049 5.542779 CAAGCACTATTACATACTCCCTCC 58.457 45.833 0.00 0.00 0.00 4.30
2992 3050 4.991687 GCAAGCACTATTACATACTCCCTC 59.008 45.833 0.00 0.00 0.00 4.30
2993 3051 4.656112 AGCAAGCACTATTACATACTCCCT 59.344 41.667 0.00 0.00 0.00 4.20
2994 3052 4.962155 AGCAAGCACTATTACATACTCCC 58.038 43.478 0.00 0.00 0.00 4.30
2995 3053 6.049149 TGAAGCAAGCACTATTACATACTCC 58.951 40.000 0.00 0.00 0.00 3.85
2996 3054 7.278868 AGTTGAAGCAAGCACTATTACATACTC 59.721 37.037 0.00 0.00 0.00 2.59
2997 3055 7.106239 AGTTGAAGCAAGCACTATTACATACT 58.894 34.615 0.00 0.00 0.00 2.12
2998 3056 7.278868 AGAGTTGAAGCAAGCACTATTACATAC 59.721 37.037 0.00 0.00 0.00 2.39
3020 3078 6.904626 AGATATAATTGCCCACAAAGAGAGT 58.095 36.000 0.00 0.00 39.77 3.24
3050 3108 7.484140 TCTCGCATGTATGACTATATGGATTC 58.516 38.462 0.00 0.00 29.68 2.52
3056 3114 5.946377 TCACCTCTCGCATGTATGACTATAT 59.054 40.000 0.00 0.00 0.00 0.86
3104 3162 9.706691 CATGTATGGATAGATTTTAACTACGGT 57.293 33.333 0.00 0.00 0.00 4.83
3105 3163 9.706691 ACATGTATGGATAGATTTTAACTACGG 57.293 33.333 0.00 0.00 0.00 4.02
3110 3168 9.778741 TCCTCACATGTATGGATAGATTTTAAC 57.221 33.333 13.15 0.00 0.00 2.01
3112 3170 9.159254 ACTCCTCACATGTATGGATAGATTTTA 57.841 33.333 16.34 0.00 0.00 1.52
3113 3171 7.935755 CACTCCTCACATGTATGGATAGATTTT 59.064 37.037 16.34 0.00 0.00 1.82
3114 3172 7.290948 TCACTCCTCACATGTATGGATAGATTT 59.709 37.037 16.34 0.00 0.00 2.17
3115 3173 6.784473 TCACTCCTCACATGTATGGATAGATT 59.216 38.462 16.34 1.25 0.00 2.40
3118 3176 5.047448 CCTCACTCCTCACATGTATGGATAG 60.047 48.000 16.34 13.79 0.00 2.08
3128 3186 0.251832 ACCGACCTCACTCCTCACAT 60.252 55.000 0.00 0.00 0.00 3.21
3135 3193 0.033504 TCTTGCAACCGACCTCACTC 59.966 55.000 0.00 0.00 0.00 3.51
3136 3194 0.468226 TTCTTGCAACCGACCTCACT 59.532 50.000 0.00 0.00 0.00 3.41
3144 3202 3.747099 CAGGAGTAATTCTTGCAACCG 57.253 47.619 0.00 0.00 0.00 4.44
3174 3324 4.466015 TGCATAGACATGTAAGACACTGGA 59.534 41.667 0.00 0.00 34.40 3.86
3188 3338 5.151297 TGAGAACAAGACATGCATAGACA 57.849 39.130 0.00 0.00 0.00 3.41
3263 3413 0.456221 CTCAGCGATCAACTACCGGT 59.544 55.000 13.98 13.98 34.15 5.28
3264 3414 0.738975 TCTCAGCGATCAACTACCGG 59.261 55.000 0.00 0.00 0.00 5.28
3359 3511 7.672983 ACGAAAAAGAGACACAATACATCAT 57.327 32.000 0.00 0.00 0.00 2.45
3381 3533 3.261981 AGGGGCACTCTACAAATTACG 57.738 47.619 0.00 0.00 0.00 3.18
3515 3674 4.378149 GCATGCATCACGATTCATCTTAGG 60.378 45.833 14.21 0.00 0.00 2.69
3577 3736 5.360714 AGCAAAATTCAGGACAGACAGAAAA 59.639 36.000 0.00 0.00 0.00 2.29
3581 3740 3.611057 GCAGCAAAATTCAGGACAGACAG 60.611 47.826 0.00 0.00 0.00 3.51
3730 3929 0.179089 CATTGAGAGACGAGGCCCAG 60.179 60.000 0.00 0.00 0.00 4.45
3738 3937 2.543861 CGGGGTATGACATTGAGAGACG 60.544 54.545 0.00 0.00 0.00 4.18
3759 3958 3.551890 CGATCATAGTGTTGCCACAGTAC 59.448 47.826 7.58 0.00 44.39 2.73
3776 4066 4.448732 CAGAATTATGAATGCCGTCGATCA 59.551 41.667 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.