Multiple sequence alignment - TraesCS3B01G021100

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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 TraesCS3B01G021100 chr3B 100.000 3476 0 0 1 3476 8811942 8815417 0.000000e+00 6420.0
1 TraesCS3B01G021100 chr3A 90.834 3524 202 57 1 3472 13036141 13032687 0.000000e+00 4606.0
2 TraesCS3B01G021100 chr3D 92.615 3182 174 29 1 3149 7227073 7230226 0.000000e+00 4518.0
3 TraesCS3B01G021100 chr6D 76.667 180 32 7 2135 2309 472965773 472965599 1.330000e-14 91.6
4 TraesCS3B01G021100 chr6B 91.045 67 6 0 2135 2201 718327838 718327772 1.330000e-14 91.6
5 TraesCS3B01G021100 chr6A 91.045 67 6 0 2135 2201 616862630 616862696 1.330000e-14 91.6
6 TraesCS3B01G021100 chr6A 86.250 80 9 2 2123 2201 616881121 616881199 6.180000e-13 86.1
7 TraesCS3B01G021100 chr5A 81.731 104 16 3 2133 2235 664265175 664265276 2.220000e-12 84.2
8 TraesCS3B01G021100 chr4D 81.731 104 16 3 2133 2235 484045474 484045575 2.220000e-12 84.2
9 TraesCS3B01G021100 chr4B 81.731 104 16 3 2133 2235 615251957 615252058 2.220000e-12 84.2


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 TraesCS3B01G021100 chr3B 8811942 8815417 3475 False 6420 6420 100.000 1 3476 1 chr3B.!!$F1 3475
1 TraesCS3B01G021100 chr3A 13032687 13036141 3454 True 4606 4606 90.834 1 3472 1 chr3A.!!$R1 3471
2 TraesCS3B01G021100 chr3D 7227073 7230226 3153 False 4518 4518 92.615 1 3149 1 chr3D.!!$F1 3148

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
964 1003 0.036022 AGAAGCAACTCAGGGAGTGC 59.964 55.0 0.0 6.24 42.59 4.40 F
1192 1231 0.250727 CTCCTGCCGGTTCCTCAAAA 60.251 55.0 1.9 0.00 0.00 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2418 2470 0.388520 CACTGAACCGAGCGACATCA 60.389 55.0 0.0 0.0 0.0 3.07 R
2973 3036 0.250295 TGCGGTTGAAAGTCTCCAGG 60.250 55.0 0.0 0.0 0.0 4.45 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
75 76 4.082125 ACTAGATCAACAAAAGGCAAGGG 58.918 43.478 0.00 0.00 0.00 3.95
76 77 2.962859 AGATCAACAAAAGGCAAGGGT 58.037 42.857 0.00 0.00 0.00 4.34
183 187 6.753744 GCAACAGATCTGTAAATTTCCATTCC 59.246 38.462 28.10 0.00 44.13 3.01
224 229 3.657398 ATTGGGATGCATCTCTTGTGA 57.343 42.857 26.47 3.64 0.00 3.58
225 230 3.438216 TTGGGATGCATCTCTTGTGAA 57.562 42.857 26.47 9.99 0.00 3.18
226 231 3.657398 TGGGATGCATCTCTTGTGAAT 57.343 42.857 26.47 0.00 0.00 2.57
227 232 3.972133 TGGGATGCATCTCTTGTGAATT 58.028 40.909 26.47 0.00 0.00 2.17
228 233 3.697542 TGGGATGCATCTCTTGTGAATTG 59.302 43.478 26.47 0.00 0.00 2.32
229 234 3.698040 GGGATGCATCTCTTGTGAATTGT 59.302 43.478 25.28 0.00 0.00 2.71
230 235 4.439700 GGGATGCATCTCTTGTGAATTGTG 60.440 45.833 25.28 0.00 0.00 3.33
323 328 5.254339 ACAGAAGCTTTTTGAAGAAGTGG 57.746 39.130 16.11 0.00 0.00 4.00
365 379 4.222145 TGGGCTACTAAAAGTACCACTGAG 59.778 45.833 0.00 0.00 26.25 3.35
553 567 5.412594 CACCTAACATATCAACTGTTGCACT 59.587 40.000 15.52 5.64 37.41 4.40
554 568 5.412594 ACCTAACATATCAACTGTTGCACTG 59.587 40.000 15.52 13.24 37.41 3.66
555 569 5.643348 CCTAACATATCAACTGTTGCACTGA 59.357 40.000 15.52 0.00 37.41 3.41
562 576 4.058124 TCAACTGTTGCACTGATGTAGAC 58.942 43.478 15.52 0.00 0.00 2.59
586 603 3.021356 CCCTGACCTGGGGTATCAA 57.979 57.895 0.00 0.00 43.45 2.57
703 737 8.345565 TCTGTTTTCTGCACTAGATTTTCTTTC 58.654 33.333 0.00 0.00 34.80 2.62
707 741 3.407698 TGCACTAGATTTTCTTTCGGCA 58.592 40.909 0.00 0.00 0.00 5.69
718 752 1.130373 TCTTTCGGCATGTCGAATTGC 59.870 47.619 33.15 11.39 46.50 3.56
720 754 0.447406 TTCGGCATGTCGAATTGCTG 59.553 50.000 29.85 18.89 43.12 4.41
727 761 0.512518 TGTCGAATTGCTGCGAGTTG 59.487 50.000 0.00 0.00 37.18 3.16
753 787 6.377996 TGAAAAGGTATGTTCTCCATGATTGG 59.622 38.462 0.00 0.00 45.15 3.16
763 801 1.776667 TCCATGATTGGGTCATCTCCC 59.223 52.381 0.00 0.00 45.76 4.30
766 804 3.373438 CCATGATTGGGTCATCTCCCTTT 60.373 47.826 0.00 0.00 45.76 3.11
768 806 3.373438 ATGATTGGGTCATCTCCCTTTGG 60.373 47.826 3.40 0.00 44.23 3.28
769 807 5.878879 ATGATTGGGTCATCTCCCTTTGGT 61.879 45.833 3.40 0.00 44.23 3.67
796 835 4.537135 ATCTGCTACTTTTTGTCTCGGA 57.463 40.909 0.00 0.00 0.00 4.55
835 874 2.711009 CCACCCAATCTATTCTAGGGCA 59.289 50.000 0.00 0.00 43.47 5.36
929 968 6.116806 TGTTTGAACTAACAGAGCAGGTTAA 58.883 36.000 0.00 0.00 33.31 2.01
930 969 6.260050 TGTTTGAACTAACAGAGCAGGTTAAG 59.740 38.462 0.00 0.00 33.31 1.85
931 970 5.801531 TGAACTAACAGAGCAGGTTAAGA 57.198 39.130 0.00 0.00 30.92 2.10
932 971 6.169557 TGAACTAACAGAGCAGGTTAAGAA 57.830 37.500 0.00 0.00 30.92 2.52
964 1003 0.036022 AGAAGCAACTCAGGGAGTGC 59.964 55.000 0.00 6.24 42.59 4.40
1169 1208 1.067060 TGGCGTGTCGATGAATAGAGG 59.933 52.381 0.00 0.00 0.00 3.69
1189 1228 3.706373 GCTCCTGCCGGTTCCTCA 61.706 66.667 1.90 0.00 0.00 3.86
1191 1230 1.374947 CTCCTGCCGGTTCCTCAAA 59.625 57.895 1.90 0.00 0.00 2.69
1192 1231 0.250727 CTCCTGCCGGTTCCTCAAAA 60.251 55.000 1.90 0.00 0.00 2.44
1229 1281 7.929785 TCGGTTCAGTTCTAAGTTCATTTACTT 59.070 33.333 0.00 0.00 41.13 2.24
1379 1431 2.789491 TCAGATGTATGCGAGCTGAG 57.211 50.000 0.00 0.00 32.36 3.35
1435 1487 3.908712 ATTGCCCTCCTCCACCCCA 62.909 63.158 0.00 0.00 0.00 4.96
1436 1488 4.608514 TGCCCTCCTCCACCCCAA 62.609 66.667 0.00 0.00 0.00 4.12
1497 1549 1.816961 GCGAGGAAGAATGATGGCCAT 60.817 52.381 20.96 20.96 36.99 4.40
1599 1651 2.125912 CCAGCGGTGGTCTTCTCG 60.126 66.667 25.51 0.00 39.30 4.04
1705 1757 1.227943 GTGCACCTCCTTGTCAGCA 60.228 57.895 5.22 0.00 0.00 4.41
1713 1765 3.726517 CTTGTCAGCAACGCCCCG 61.727 66.667 0.00 0.00 0.00 5.73
1735 1787 0.865769 GTGGTGGCTTGACAAGTACG 59.134 55.000 16.39 0.00 0.00 3.67
1793 1845 0.955428 GACATGGACAGGCAAAGCGA 60.955 55.000 0.00 0.00 0.00 4.93
1862 1914 1.948145 GGAGATGAGTATCGACACCGT 59.052 52.381 0.00 0.00 38.61 4.83
1893 1945 1.922881 TGGGCACTACTCCATGGCA 60.923 57.895 6.96 0.00 42.93 4.92
2115 2167 2.659610 GAGCAGCACTCGGACCTT 59.340 61.111 0.00 0.00 35.18 3.50
2147 2199 3.414700 GCTGGTGAACTCGTGCGG 61.415 66.667 0.00 0.00 0.00 5.69
2270 2322 3.308705 GGGGGACGACTTCGGTGT 61.309 66.667 3.30 0.00 44.95 4.16
2316 2368 2.509336 GTGCAGTACGGCATCGCT 60.509 61.111 23.39 0.00 46.92 4.93
2418 2470 2.665185 GGCCAGAACGTCACGCTT 60.665 61.111 0.00 0.00 0.00 4.68
2471 2523 3.432517 CTCTGGAGCTTCTTCACCG 57.567 57.895 0.00 0.00 0.00 4.94
2479 2531 3.254892 GAGCTTCTTCACCGTTAGAAGG 58.745 50.000 16.47 0.00 44.76 3.46
2594 2646 2.094659 GGATCGCTGTCACACGGTG 61.095 63.158 6.58 6.58 36.36 4.94
2600 2652 0.032130 GCTGTCACACGGTGAGAAGA 59.968 55.000 16.29 4.35 43.57 2.87
2622 2674 6.879400 AGACAAATTCGAAGGCTAATCTAGT 58.121 36.000 3.35 0.00 0.00 2.57
2630 2682 7.584122 TCGAAGGCTAATCTAGTGACTAAAT 57.416 36.000 0.00 0.00 0.00 1.40
2720 2772 6.352516 ACCAAGGTTGAATCACATATCTCTC 58.647 40.000 0.00 0.00 0.00 3.20
2740 2792 8.134202 TCTCTCCAGATTTTACTATTGTGTCA 57.866 34.615 0.00 0.00 0.00 3.58
2802 2855 8.097078 TGCATATAATTTTATTTTGGCATGGC 57.903 30.769 13.29 13.29 0.00 4.40
2844 2897 7.221259 GTGAAAAAGGTGTGTAAAGCGTAATTT 59.779 33.333 0.00 0.00 0.00 1.82
2867 2920 8.980481 TTTGTTTAGAAAGATTTCTCTCCTGT 57.020 30.769 10.97 0.00 43.72 4.00
2868 2921 8.980481 TTGTTTAGAAAGATTTCTCTCCTGTT 57.020 30.769 10.97 0.00 43.72 3.16
2906 2959 5.835113 ACACTTCAATATGTAACCATGCC 57.165 39.130 0.00 0.00 32.29 4.40
2909 2962 4.574828 ACTTCAATATGTAACCATGCCGTC 59.425 41.667 0.00 0.00 32.29 4.79
2973 3036 9.148104 CTGGTACTCCTTTATACTGTAACAAAC 57.852 37.037 0.00 0.00 31.61 2.93
3017 3080 4.960938 TGCACAATAATGCTACTCCTAGG 58.039 43.478 0.82 0.82 46.28 3.02
3063 3126 6.529125 GGTGAGACACATAATTTGCTTCATTG 59.471 38.462 0.00 0.00 35.86 2.82
3127 3198 8.530311 CACTGAGATGCATAATCTATTCTAGGT 58.470 37.037 0.00 0.00 46.12 3.08
3161 3232 6.620877 ATTATCCTGTTGTTGACTCCTACA 57.379 37.500 0.00 0.00 0.00 2.74
3162 3233 4.974645 ATCCTGTTGTTGACTCCTACAA 57.025 40.909 0.00 0.00 36.08 2.41
3163 3234 4.336889 TCCTGTTGTTGACTCCTACAAG 57.663 45.455 0.00 0.00 38.35 3.16
3164 3235 3.964688 TCCTGTTGTTGACTCCTACAAGA 59.035 43.478 0.00 0.00 38.35 3.02
3165 3236 4.593206 TCCTGTTGTTGACTCCTACAAGAT 59.407 41.667 0.00 0.00 38.35 2.40
3166 3237 4.932200 CCTGTTGTTGACTCCTACAAGATC 59.068 45.833 0.00 0.00 38.35 2.75
3167 3238 5.279708 CCTGTTGTTGACTCCTACAAGATCT 60.280 44.000 0.00 0.00 38.35 2.75
3168 3239 5.784177 TGTTGTTGACTCCTACAAGATCTC 58.216 41.667 0.00 0.00 38.35 2.75
3169 3240 5.172205 GTTGTTGACTCCTACAAGATCTCC 58.828 45.833 0.00 0.00 38.35 3.71
3170 3241 3.769844 TGTTGACTCCTACAAGATCTCCC 59.230 47.826 0.00 0.00 0.00 4.30
3171 3242 3.757947 TGACTCCTACAAGATCTCCCA 57.242 47.619 0.00 0.00 0.00 4.37
3172 3243 4.061131 TGACTCCTACAAGATCTCCCAA 57.939 45.455 0.00 0.00 0.00 4.12
3173 3244 3.769844 TGACTCCTACAAGATCTCCCAAC 59.230 47.826 0.00 0.00 0.00 3.77
3174 3245 3.769844 GACTCCTACAAGATCTCCCAACA 59.230 47.826 0.00 0.00 0.00 3.33
3175 3246 4.366267 ACTCCTACAAGATCTCCCAACAT 58.634 43.478 0.00 0.00 0.00 2.71
3176 3247 4.163078 ACTCCTACAAGATCTCCCAACATG 59.837 45.833 0.00 0.00 0.00 3.21
3180 3251 6.615316 TCCTACAAGATCTCCCAACATGATAA 59.385 38.462 0.00 0.00 0.00 1.75
3200 3271 2.769209 AGTGGGCTGTTGGATCTCTAT 58.231 47.619 0.00 0.00 0.00 1.98
3218 3289 5.001237 TCTATCGCACGGTAAAAATCTGA 57.999 39.130 0.00 0.00 0.00 3.27
3242 3313 2.998316 AATCCAGTGGCTAAGCTCTC 57.002 50.000 3.51 0.00 0.00 3.20
3258 3329 5.581126 AGCTCTCACTCAACTGAGAATAG 57.419 43.478 13.61 7.37 44.87 1.73
3275 3346 8.908786 TGAGAATAGCAATTCCATAAGGTAAG 57.091 34.615 0.00 0.00 42.20 2.34
3277 3348 9.343539 GAGAATAGCAATTCCATAAGGTAAGTT 57.656 33.333 0.00 0.00 42.20 2.66
3282 3353 7.830739 AGCAATTCCATAAGGTAAGTTTTCAG 58.169 34.615 0.00 0.00 35.89 3.02
3311 3382 9.583530 TTTACTATCGTGTTGTTTTGATTTACG 57.416 29.630 0.00 0.00 0.00 3.18
3316 3387 6.968585 TCGTGTTGTTTTGATTTACGTTTTG 58.031 32.000 0.00 0.00 0.00 2.44
3319 3390 7.503165 GTGTTGTTTTGATTTACGTTTTGTGT 58.497 30.769 0.00 0.00 0.00 3.72
3335 3411 1.542472 TGTGTGCATCATGCTTTCTGG 59.458 47.619 11.84 0.00 45.31 3.86
3342 3418 5.528690 GTGCATCATGCTTTCTGGTATAGAA 59.471 40.000 11.84 0.00 45.31 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 1.335145 GACCCGGGGAAAGATCGATA 58.665 55.000 27.92 0.00 0.00 2.92
100 101 1.408453 GGACCCGGGGAAAGATCGAT 61.408 60.000 27.92 0.00 0.00 3.59
101 102 2.062177 GGACCCGGGGAAAGATCGA 61.062 63.158 27.92 0.00 0.00 3.59
113 117 1.202582 CAACTACTCTGACAGGACCCG 59.797 57.143 1.81 0.00 0.00 5.28
157 161 6.839124 ATGGAAATTTACAGATCTGTTGCA 57.161 33.333 32.14 24.02 41.83 4.08
161 165 8.526147 CAAAGGAATGGAAATTTACAGATCTGT 58.474 33.333 30.11 30.11 46.87 3.41
183 187 7.225538 CCCAATAGCAGAGAATGTACTACAAAG 59.774 40.741 0.00 0.00 0.00 2.77
224 229 8.836268 TTGTTAAACGTAGGAGTATCACAATT 57.164 30.769 0.00 0.00 36.25 2.32
225 230 9.444600 AATTGTTAAACGTAGGAGTATCACAAT 57.555 29.630 0.00 0.00 36.25 2.71
226 231 8.836268 AATTGTTAAACGTAGGAGTATCACAA 57.164 30.769 0.00 0.00 36.25 3.33
227 232 8.836268 AAATTGTTAAACGTAGGAGTATCACA 57.164 30.769 0.00 0.00 36.25 3.58
297 302 7.128976 CACTTCTTCAAAAAGCTTCTGTAGAC 58.871 38.462 13.88 0.00 32.18 2.59
301 306 4.949856 TCCACTTCTTCAAAAAGCTTCTGT 59.050 37.500 0.00 0.00 32.18 3.41
365 379 2.802816 CAGGCGACATATTGAGTTAGGC 59.197 50.000 0.00 0.00 0.00 3.93
553 567 3.773119 GGTCAGGGTAAAGGTCTACATCA 59.227 47.826 0.00 0.00 0.00 3.07
554 568 4.031611 AGGTCAGGGTAAAGGTCTACATC 58.968 47.826 0.00 0.00 0.00 3.06
555 569 3.775316 CAGGTCAGGGTAAAGGTCTACAT 59.225 47.826 0.00 0.00 0.00 2.29
586 603 0.185901 AACTTGGTGCTGGTGGACAT 59.814 50.000 0.00 0.00 36.16 3.06
703 737 1.584483 GCAGCAATTCGACATGCCG 60.584 57.895 15.85 8.78 43.57 5.69
707 741 1.129251 CAACTCGCAGCAATTCGACAT 59.871 47.619 0.00 0.00 0.00 3.06
718 752 3.498397 ACATACCTTTTCACAACTCGCAG 59.502 43.478 0.00 0.00 0.00 5.18
720 754 4.213482 AGAACATACCTTTTCACAACTCGC 59.787 41.667 0.00 0.00 0.00 5.03
727 761 7.253422 CAATCATGGAGAACATACCTTTTCAC 58.747 38.462 0.00 0.00 37.84 3.18
753 787 7.229506 CAGATAAATAACCAAAGGGAGATGACC 59.770 40.741 0.00 0.00 38.05 4.02
766 804 9.515226 AGACAAAAAGTAGCAGATAAATAACCA 57.485 29.630 0.00 0.00 0.00 3.67
768 806 9.690434 CGAGACAAAAAGTAGCAGATAAATAAC 57.310 33.333 0.00 0.00 0.00 1.89
769 807 8.879759 CCGAGACAAAAAGTAGCAGATAAATAA 58.120 33.333 0.00 0.00 0.00 1.40
796 835 4.581409 GGGTGGTGTTGTGTAAAGTGTATT 59.419 41.667 0.00 0.00 0.00 1.89
835 874 5.102953 TCACCAACAGAATAAGCAGCTAT 57.897 39.130 0.00 0.00 0.00 2.97
929 968 9.487790 GAGTTGCTTCTATGCTTATATTCTTCT 57.512 33.333 0.00 0.00 0.00 2.85
930 969 9.265901 TGAGTTGCTTCTATGCTTATATTCTTC 57.734 33.333 0.00 0.00 0.00 2.87
931 970 9.270640 CTGAGTTGCTTCTATGCTTATATTCTT 57.729 33.333 0.00 0.00 0.00 2.52
932 971 7.877097 CCTGAGTTGCTTCTATGCTTATATTCT 59.123 37.037 0.00 0.00 0.00 2.40
964 1003 1.833630 TCCTCACAGGAGTAGCAATGG 59.166 52.381 0.00 0.00 40.06 3.16
1196 1235 8.932791 TGAACTTAGAACTGAACCGAAATAATC 58.067 33.333 0.00 0.00 0.00 1.75
1198 1237 8.842358 ATGAACTTAGAACTGAACCGAAATAA 57.158 30.769 0.00 0.00 0.00 1.40
1199 1238 8.842358 AATGAACTTAGAACTGAACCGAAATA 57.158 30.769 0.00 0.00 0.00 1.40
1200 1239 7.745620 AATGAACTTAGAACTGAACCGAAAT 57.254 32.000 0.00 0.00 0.00 2.17
1201 1240 7.562454 AAATGAACTTAGAACTGAACCGAAA 57.438 32.000 0.00 0.00 0.00 3.46
1204 1243 7.653767 AGTAAATGAACTTAGAACTGAACCG 57.346 36.000 0.00 0.00 0.00 4.44
1229 1281 6.892658 ACCTCACTGCAAAACACATAATAA 57.107 33.333 0.00 0.00 0.00 1.40
1234 1286 2.481795 GCAACCTCACTGCAAAACACAT 60.482 45.455 0.00 0.00 39.69 3.21
1239 1291 1.473258 ACAGCAACCTCACTGCAAAA 58.527 45.000 0.00 0.00 42.48 2.44
1379 1431 2.726822 GATTACCCGGACATCGCCCC 62.727 65.000 0.73 0.00 37.59 5.80
1435 1487 1.078848 GGCGCCTCACAGAGACATT 60.079 57.895 22.15 0.00 0.00 2.71
1436 1488 2.581354 GGCGCCTCACAGAGACAT 59.419 61.111 22.15 0.00 0.00 3.06
1497 1549 3.422303 GTGACATTGGCGAGCGCA 61.422 61.111 17.16 0.00 44.11 6.09
1584 1636 2.600769 ACCGAGAAGACCACCGCT 60.601 61.111 0.00 0.00 0.00 5.52
1767 1819 0.729116 GCCTGTCCATGTCAATGACG 59.271 55.000 9.00 0.00 35.67 4.35
1793 1845 1.552792 GAGGGTAGCAGAGCACTTCTT 59.447 52.381 0.00 0.00 32.41 2.52
1862 1914 2.137528 TGCCCACCGACAGTCTTCA 61.138 57.895 0.00 0.00 0.00 3.02
1893 1945 2.985847 GCAAGGCGGGCAAAGTCT 60.986 61.111 3.78 0.00 0.00 3.24
1959 2011 1.860950 CTCTTGATATTGTCACCGCCG 59.139 52.381 0.00 0.00 36.32 6.46
1963 2015 2.213499 CGGGCTCTTGATATTGTCACC 58.787 52.381 0.00 0.00 36.32 4.02
2254 2306 2.048503 CACACCGAAGTCGTCCCC 60.049 66.667 0.00 0.00 37.74 4.81
2316 2368 2.203640 AGTGTGCTCTCCCCGACA 60.204 61.111 0.00 0.00 0.00 4.35
2418 2470 0.388520 CACTGAACCGAGCGACATCA 60.389 55.000 0.00 0.00 0.00 3.07
2471 2523 1.339151 CCCTGTGGAGTGCCTTCTAAC 60.339 57.143 0.00 0.00 34.31 2.34
2479 2531 1.961180 ATCTACGCCCTGTGGAGTGC 61.961 60.000 0.00 0.00 45.12 4.40
2594 2646 6.536941 AGATTAGCCTTCGAATTTGTCTTCTC 59.463 38.462 0.00 0.00 0.00 2.87
2600 2652 6.535508 GTCACTAGATTAGCCTTCGAATTTGT 59.464 38.462 0.00 0.00 0.00 2.83
2622 2674 8.307483 CCTTAGTTGAGTGAGAGAATTTAGTCA 58.693 37.037 0.00 0.00 0.00 3.41
2630 2682 6.437477 TGCTAATCCTTAGTTGAGTGAGAGAA 59.563 38.462 0.00 0.00 35.66 2.87
2802 2855 5.437289 TTTTCACAGCTCATAACAACTGG 57.563 39.130 0.00 0.00 34.40 4.00
2844 2897 8.980481 AAACAGGAGAGAAATCTTTCTAAACA 57.020 30.769 5.21 0.00 46.84 2.83
2863 2916 5.409826 GTGTATCCTCTGACAGAAAAACAGG 59.590 44.000 6.61 3.30 33.19 4.00
2867 2920 6.826668 TGAAGTGTATCCTCTGACAGAAAAA 58.173 36.000 6.61 0.00 0.00 1.94
2868 2921 6.419484 TGAAGTGTATCCTCTGACAGAAAA 57.581 37.500 6.61 0.00 0.00 2.29
2906 2959 7.957484 CCATTATTTACAGTGAAAAGTGAGACG 59.043 37.037 0.00 0.00 0.00 4.18
2909 2962 9.994432 GATCCATTATTTACAGTGAAAAGTGAG 57.006 33.333 0.00 0.00 0.00 3.51
2973 3036 0.250295 TGCGGTTGAAAGTCTCCAGG 60.250 55.000 0.00 0.00 0.00 4.45
3063 3126 1.144298 ACACCACCAGGGAAAGTAACC 59.856 52.381 0.00 0.00 41.15 2.85
3131 3202 7.390718 GGAGTCAACAACAGGATAATAAACTGT 59.609 37.037 0.00 0.00 46.59 3.55
3132 3203 7.607991 AGGAGTCAACAACAGGATAATAAACTG 59.392 37.037 0.00 0.00 38.19 3.16
3161 3232 5.398353 CCCACTTATCATGTTGGGAGATCTT 60.398 44.000 0.00 0.00 38.82 2.40
3162 3233 4.103785 CCCACTTATCATGTTGGGAGATCT 59.896 45.833 0.00 0.00 38.82 2.75
3163 3234 4.392940 CCCACTTATCATGTTGGGAGATC 58.607 47.826 11.37 0.00 38.82 2.75
3164 3235 3.435601 GCCCACTTATCATGTTGGGAGAT 60.436 47.826 17.61 0.00 38.82 2.75
3165 3236 2.092429 GCCCACTTATCATGTTGGGAGA 60.092 50.000 17.61 0.00 38.82 3.71
3166 3237 2.092212 AGCCCACTTATCATGTTGGGAG 60.092 50.000 17.61 3.98 38.82 4.30
3167 3238 1.922447 AGCCCACTTATCATGTTGGGA 59.078 47.619 17.61 0.00 38.82 4.37
3168 3239 2.026641 CAGCCCACTTATCATGTTGGG 58.973 52.381 12.09 12.09 39.47 4.12
3169 3240 2.726821 ACAGCCCACTTATCATGTTGG 58.273 47.619 0.00 0.00 0.00 3.77
3170 3241 3.119388 CCAACAGCCCACTTATCATGTTG 60.119 47.826 8.50 8.50 44.34 3.33
3171 3242 3.091545 CCAACAGCCCACTTATCATGTT 58.908 45.455 0.00 0.00 0.00 2.71
3172 3243 2.308570 TCCAACAGCCCACTTATCATGT 59.691 45.455 0.00 0.00 0.00 3.21
3173 3244 3.003394 TCCAACAGCCCACTTATCATG 57.997 47.619 0.00 0.00 0.00 3.07
3174 3245 3.461085 AGATCCAACAGCCCACTTATCAT 59.539 43.478 0.00 0.00 0.00 2.45
3175 3246 2.846206 AGATCCAACAGCCCACTTATCA 59.154 45.455 0.00 0.00 0.00 2.15
3176 3247 3.135530 AGAGATCCAACAGCCCACTTATC 59.864 47.826 0.00 0.00 0.00 1.75
3180 3251 2.254152 TAGAGATCCAACAGCCCACT 57.746 50.000 0.00 0.00 0.00 4.00
3200 3271 2.343101 CCTCAGATTTTTACCGTGCGA 58.657 47.619 0.00 0.00 0.00 5.10
3218 3289 1.141858 GCTTAGCCACTGGATTAGCCT 59.858 52.381 12.41 0.00 37.72 4.58
3242 3313 5.645067 TGGAATTGCTATTCTCAGTTGAGTG 59.355 40.000 18.26 0.00 42.60 3.51
3258 3329 7.826690 TCTGAAAACTTACCTTATGGAATTGC 58.173 34.615 0.81 0.00 37.04 3.56
3309 3380 1.769733 GCATGATGCACACAAAACGT 58.230 45.000 13.36 0.00 44.26 3.99
3316 3387 8.803579 TTCTATACCAGAAAGCATGATGCACAC 61.804 40.741 20.71 9.62 41.27 3.82
3319 3390 5.683681 TTCTATACCAGAAAGCATGATGCA 58.316 37.500 20.71 0.00 41.27 3.96
3335 3411 7.424803 TGCACATGCCAACATAAATTCTATAC 58.575 34.615 0.49 0.00 41.18 1.47
3342 3418 5.247084 ACAATTGCACATGCCAACATAAAT 58.753 33.333 5.05 0.00 41.18 1.40
3443 3525 8.219660 AGCAACCTGGTTATATATATTGAGGT 57.780 34.615 12.53 9.68 33.94 3.85


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

AutoCloner maintained by Alex Coulton.