Multiple sequence alignment - TraesCS2A01G187800

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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 TraesCS2A01G187800 chr2A 100.000 3287 0 0 1 3287 150125807 150122521 0.000000e+00 6071
1 TraesCS2A01G187800 chr2B 90.600 3383 151 63 1 3287 209435659 209438970 0.000000e+00 4331
2 TraesCS2A01G187800 chr2B 84.539 401 29 11 77 469 209402717 209403092 1.860000e-97 366
3 TraesCS2A01G187800 chr2B 94.737 76 4 0 1 76 209402544 209402619 5.760000e-23 119
4 TraesCS2A01G187800 chr2D 89.307 3348 130 93 1 3271 151324697 151327893 0.000000e+00 3989
5 TraesCS2A01G187800 chr1A 91.276 619 42 4 1138 1756 548995834 548995228 0.000000e+00 833
6 TraesCS2A01G187800 chr7A 91.129 620 44 3 1138 1756 465791406 465792015 0.000000e+00 830
7 TraesCS2A01G187800 chr4A 90.145 619 49 4 1138 1756 567327175 567326569 0.000000e+00 795
8 TraesCS2A01G187800 chr5B 86.334 622 39 13 1138 1756 297127731 297127153 1.290000e-178 636
9 TraesCS2A01G187800 chr3D 85.106 235 28 6 1133 1367 98871925 98872152 1.970000e-57 233
10 TraesCS2A01G187800 chr3B 85.106 235 28 6 1133 1367 149453754 149453981 1.970000e-57 233
11 TraesCS2A01G187800 chr6B 83.838 198 32 0 1170 1367 642915747 642915944 4.330000e-44 189
12 TraesCS2A01G187800 chr6A 83.838 198 32 0 1170 1367 571795532 571795729 4.330000e-44 189


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 TraesCS2A01G187800 chr2A 150122521 150125807 3286 True 6071.0 6071 100.000 1 3287 1 chr2A.!!$R1 3286
1 TraesCS2A01G187800 chr2B 209435659 209438970 3311 False 4331.0 4331 90.600 1 3287 1 chr2B.!!$F1 3286
2 TraesCS2A01G187800 chr2B 209402544 209403092 548 False 242.5 366 89.638 1 469 2 chr2B.!!$F2 468
3 TraesCS2A01G187800 chr2D 151324697 151327893 3196 False 3989.0 3989 89.307 1 3271 1 chr2D.!!$F1 3270
4 TraesCS2A01G187800 chr1A 548995228 548995834 606 True 833.0 833 91.276 1138 1756 1 chr1A.!!$R1 618
5 TraesCS2A01G187800 chr7A 465791406 465792015 609 False 830.0 830 91.129 1138 1756 1 chr7A.!!$F1 618
6 TraesCS2A01G187800 chr4A 567326569 567327175 606 True 795.0 795 90.145 1138 1756 1 chr4A.!!$R1 618
7 TraesCS2A01G187800 chr5B 297127153 297127731 578 True 636.0 636 86.334 1138 1756 1 chr5B.!!$R1 618

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
340 468 0.243907 GGGCCCGAGCTTTTTCTTTC 59.756 55.0 5.69 0.0 39.73 2.62 F
942 1115 0.391597 GACCCCACACGACAGAGAAA 59.608 55.0 0.00 0.0 0.00 2.52 F
2201 2429 0.531974 GGCTCGAAATGACGGCCATA 60.532 55.0 2.24 0.0 43.52 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2459 0.107017 AGTTGTGAGTGCTGGCTGTT 60.107 50.000 0.00 0.0 0.0 3.16 R
2232 2460 0.107017 AAGTTGTGAGTGCTGGCTGT 60.107 50.000 0.00 0.0 0.0 4.40 R
3123 3376 2.033194 CCGACGGGCTTCAGTTTCC 61.033 63.158 5.81 0.0 0.0 3.13 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
37 38 3.732721 GTCAGACTGAGCAAAACAATTGC 59.267 43.478 5.10 5.06 45.22 3.56
47 48 1.989430 AAACAATTGCATTACGGCCG 58.011 45.000 26.86 26.86 0.00 6.13
76 177 4.083484 GCGGTCAAAGCAACATAAGTTACT 60.083 41.667 0.00 0.00 35.85 2.24
77 178 5.121142 GCGGTCAAAGCAACATAAGTTACTA 59.879 40.000 0.00 0.00 35.85 1.82
78 179 6.531439 CGGTCAAAGCAACATAAGTTACTAC 58.469 40.000 0.00 0.00 35.85 2.73
85 186 6.464222 AGCAACATAAGTTACTACAGCAGAA 58.536 36.000 0.00 0.00 35.85 3.02
147 248 1.051812 CAGCCTCCCGTGATTAGGAT 58.948 55.000 0.00 0.00 31.64 3.24
151 252 3.910627 AGCCTCCCGTGATTAGGATTAAT 59.089 43.478 0.00 0.00 31.64 1.40
152 253 5.046591 CAGCCTCCCGTGATTAGGATTAATA 60.047 44.000 0.00 0.00 31.64 0.98
155 256 6.884836 GCCTCCCGTGATTAGGATTAATAAAT 59.115 38.462 0.00 0.00 31.64 1.40
156 257 8.044908 GCCTCCCGTGATTAGGATTAATAAATA 58.955 37.037 0.00 0.00 31.64 1.40
157 258 9.601217 CCTCCCGTGATTAGGATTAATAAATAG 57.399 37.037 0.00 0.00 31.64 1.73
208 333 3.248266 ACTAACCAGTTAATCGCGACAC 58.752 45.455 12.93 9.08 0.00 3.67
234 362 0.808755 CGTACAGCACATTTTCCCCC 59.191 55.000 0.00 0.00 0.00 5.40
241 369 1.974875 ACATTTTCCCCCGTTCCGC 60.975 57.895 0.00 0.00 0.00 5.54
335 463 2.283173 CTGGGGCCCGAGCTTTTT 60.283 61.111 22.09 0.00 39.73 1.94
336 464 2.282887 TGGGGCCCGAGCTTTTTC 60.283 61.111 19.83 0.00 39.73 2.29
337 465 2.035783 GGGGCCCGAGCTTTTTCT 59.964 61.111 17.79 0.00 39.73 2.52
339 467 1.185618 GGGGCCCGAGCTTTTTCTTT 61.186 55.000 17.79 0.00 39.73 2.52
340 468 0.243907 GGGCCCGAGCTTTTTCTTTC 59.756 55.000 5.69 0.00 39.73 2.62
341 469 1.248486 GGCCCGAGCTTTTTCTTTCT 58.752 50.000 0.00 0.00 39.73 2.52
342 470 1.613925 GGCCCGAGCTTTTTCTTTCTT 59.386 47.619 0.00 0.00 39.73 2.52
343 471 2.351835 GGCCCGAGCTTTTTCTTTCTTC 60.352 50.000 0.00 0.00 39.73 2.87
368 496 2.257286 CTTTGAGACAATGGCCGGCG 62.257 60.000 22.54 9.21 0.00 6.46
406 539 2.872858 AGTTTCTTGCACGGAGAAGTTC 59.127 45.455 0.00 0.00 34.84 3.01
420 555 1.393539 GAAGTTCGCGCATGCTCTAAA 59.606 47.619 17.13 2.15 39.65 1.85
424 559 3.430218 AGTTCGCGCATGCTCTAAATATC 59.570 43.478 17.13 0.00 39.65 1.63
433 568 6.072286 CGCATGCTCTAAATATCTGGGAAATT 60.072 38.462 17.13 0.00 0.00 1.82
469 606 0.890996 CAGCCCTGAAGTGTGGAACC 60.891 60.000 0.00 0.00 34.36 3.62
483 629 1.133761 TGGAACCAACCACCGAATCAA 60.134 47.619 0.00 0.00 34.77 2.57
484 630 1.957877 GGAACCAACCACCGAATCAAA 59.042 47.619 0.00 0.00 0.00 2.69
485 631 2.287970 GGAACCAACCACCGAATCAAAC 60.288 50.000 0.00 0.00 0.00 2.93
487 633 0.601057 CCAACCACCGAATCAAACCC 59.399 55.000 0.00 0.00 0.00 4.11
506 654 4.320870 ACCCAGTACACGTAAAATTCTGG 58.679 43.478 0.00 11.65 40.13 3.86
511 659 3.418684 ACACGTAAAATTCTGGCCTCT 57.581 42.857 3.32 0.00 0.00 3.69
528 676 3.935828 GCCTCTGTATTCACCAGAACTTC 59.064 47.826 0.00 0.00 38.42 3.01
530 678 4.508662 CTCTGTATTCACCAGAACTTCCC 58.491 47.826 0.00 0.00 38.42 3.97
540 693 2.440409 CAGAACTTCCCTCCATTGGTG 58.560 52.381 1.86 0.00 0.00 4.17
562 715 1.322936 GTCGACGACGGTACTCTACAG 59.677 57.143 12.94 0.00 40.21 2.74
563 716 1.202348 TCGACGACGGTACTCTACAGA 59.798 52.381 7.55 0.00 40.21 3.41
646 800 5.221891 TCGTTCGTTGTGTACCTATCTAC 57.778 43.478 0.00 0.00 0.00 2.59
647 801 4.024438 CGTTCGTTGTGTACCTATCTACG 58.976 47.826 0.00 0.00 0.00 3.51
650 804 6.510157 CGTTCGTTGTGTACCTATCTACGTAT 60.510 42.308 0.00 0.00 33.69 3.06
651 805 6.291067 TCGTTGTGTACCTATCTACGTATG 57.709 41.667 0.00 0.00 33.69 2.39
652 806 5.817296 TCGTTGTGTACCTATCTACGTATGT 59.183 40.000 0.00 0.00 33.69 2.29
653 807 6.983890 TCGTTGTGTACCTATCTACGTATGTA 59.016 38.462 0.00 0.00 33.69 2.29
654 808 7.042725 TCGTTGTGTACCTATCTACGTATGTAC 60.043 40.741 0.00 4.48 33.69 2.90
655 809 7.042456 CGTTGTGTACCTATCTACGTATGTACT 60.042 40.741 0.00 0.00 31.22 2.73
656 810 9.261180 GTTGTGTACCTATCTACGTATGTACTA 57.739 37.037 0.00 0.00 31.22 1.82
657 811 9.481340 TTGTGTACCTATCTACGTATGTACTAG 57.519 37.037 0.00 0.00 31.22 2.57
789 943 1.887242 GCGCAGTTCACACTCACCA 60.887 57.895 0.30 0.00 0.00 4.17
914 1075 4.791069 TACCCTCCCCGTGAGCCC 62.791 72.222 0.00 0.00 39.98 5.19
935 1096 2.049433 CAGACGACCCCACACGAC 60.049 66.667 0.00 0.00 0.00 4.34
941 1114 1.802337 CGACCCCACACGACAGAGAA 61.802 60.000 0.00 0.00 0.00 2.87
942 1115 0.391597 GACCCCACACGACAGAGAAA 59.608 55.000 0.00 0.00 0.00 2.52
967 1160 4.314440 TCAGCACACTCCACGCCC 62.314 66.667 0.00 0.00 0.00 6.13
968 1161 4.624364 CAGCACACTCCACGCCCA 62.624 66.667 0.00 0.00 0.00 5.36
971 1164 4.624364 CACACTCCACGCCCAGCA 62.624 66.667 0.00 0.00 0.00 4.41
972 1165 4.626081 ACACTCCACGCCCAGCAC 62.626 66.667 0.00 0.00 0.00 4.40
978 1171 4.767255 CACGCCCAGCACCCTCTC 62.767 72.222 0.00 0.00 0.00 3.20
1044 1245 2.031120 CTAGGCCAAGTGGAGAGAGAG 58.969 57.143 5.01 0.00 37.39 3.20
1202 1422 2.556287 CGGGAGAACAACAAGCGC 59.444 61.111 0.00 0.00 0.00 5.92
1274 1494 1.790387 GCTCGGCAACTACAAGCTG 59.210 57.895 0.00 0.00 38.47 4.24
1415 1635 4.726351 GGGATCGAGATCGCCCGC 62.726 72.222 16.36 0.00 42.75 6.13
1416 1636 3.675563 GGATCGAGATCGCCCGCT 61.676 66.667 6.96 0.00 38.69 5.52
1417 1637 2.126657 GATCGAGATCGCCCGCTC 60.127 66.667 0.00 0.00 39.60 5.03
1418 1638 3.618710 GATCGAGATCGCCCGCTCC 62.619 68.421 0.00 0.00 39.60 4.70
1479 1707 1.741706 CTAGGCTTGCTTGGATGTGTG 59.258 52.381 0.00 0.00 0.00 3.82
1932 2160 3.733960 CCGGAGTGCGACGAGTCA 61.734 66.667 5.27 0.00 0.00 3.41
1983 2211 1.751927 CAGCTTCCAGATGGCCACC 60.752 63.158 8.16 0.00 34.44 4.61
2201 2429 0.531974 GGCTCGAAATGACGGCCATA 60.532 55.000 2.24 0.00 43.52 2.74
2231 2459 3.840831 GCACTGGCACTCACAGATA 57.159 52.632 0.00 0.00 40.72 1.98
2232 2460 2.099141 GCACTGGCACTCACAGATAA 57.901 50.000 0.00 0.00 40.72 1.75
2240 2468 2.005451 CACTCACAGATAACAGCCAGC 58.995 52.381 0.00 0.00 0.00 4.85
2241 2469 1.625315 ACTCACAGATAACAGCCAGCA 59.375 47.619 0.00 0.00 0.00 4.41
2242 2470 2.005451 CTCACAGATAACAGCCAGCAC 58.995 52.381 0.00 0.00 0.00 4.40
2243 2471 1.625315 TCACAGATAACAGCCAGCACT 59.375 47.619 0.00 0.00 0.00 4.40
2244 2472 2.005451 CACAGATAACAGCCAGCACTC 58.995 52.381 0.00 0.00 0.00 3.51
2245 2473 1.625315 ACAGATAACAGCCAGCACTCA 59.375 47.619 0.00 0.00 0.00 3.41
2246 2474 2.005451 CAGATAACAGCCAGCACTCAC 58.995 52.381 0.00 0.00 0.00 3.51
2388 2616 3.453353 TCGTTCATTCTAGGTTTAGGGGG 59.547 47.826 0.00 0.00 0.00 5.40
2522 2750 2.502130 GCTAGTAGCTGGGTTCCTCTTT 59.498 50.000 15.16 0.00 38.45 2.52
2523 2751 3.055021 GCTAGTAGCTGGGTTCCTCTTTT 60.055 47.826 15.16 0.00 38.45 2.27
2524 2752 4.565861 GCTAGTAGCTGGGTTCCTCTTTTT 60.566 45.833 15.16 0.00 38.45 1.94
2525 2753 4.022413 AGTAGCTGGGTTCCTCTTTTTC 57.978 45.455 0.00 0.00 0.00 2.29
2526 2754 2.294449 AGCTGGGTTCCTCTTTTTCC 57.706 50.000 0.00 0.00 0.00 3.13
2527 2755 1.783365 AGCTGGGTTCCTCTTTTTCCT 59.217 47.619 0.00 0.00 0.00 3.36
2528 2756 2.163509 GCTGGGTTCCTCTTTTTCCTC 58.836 52.381 0.00 0.00 0.00 3.71
2609 2837 0.405585 ATGTGGGGGAAAGTCCAGTG 59.594 55.000 0.00 0.00 38.64 3.66
2660 2888 2.639065 TGCCGTGACCTGAATTAATCC 58.361 47.619 0.00 0.00 0.00 3.01
2676 2904 0.674895 ATCCCTCTTTGACGCAGCAC 60.675 55.000 0.00 0.00 0.00 4.40
2687 2915 1.204062 CGCAGCACGTAAACCAGTG 59.796 57.895 0.00 0.00 41.01 3.66
2703 2937 0.460311 AGTGCGTACATGGAGCTACC 59.540 55.000 6.38 0.00 39.54 3.18
2720 2954 3.620821 GCTACCAGCAAGTTCATCTCTTC 59.379 47.826 0.00 0.00 41.89 2.87
2852 3086 2.297597 GAGGATTTGTCCGATCGGAGAT 59.702 50.000 36.38 27.56 46.16 2.75
2869 3103 4.495422 GGAGATCACTGTCGTTGTTGTAT 58.505 43.478 0.00 0.00 0.00 2.29
2910 3145 1.662876 CGTTGGAAAGAACGTGGCATG 60.663 52.381 4.87 4.87 42.99 4.06
2970 3205 1.283029 TCAGAAATCTTCAGCCCTGGG 59.717 52.381 8.86 8.86 0.00 4.45
3042 3277 8.567948 CAAAACTCCAATTAACACTCTGTATGT 58.432 33.333 0.00 0.00 0.00 2.29
3056 3291 3.936453 TCTGTATGTGGTACGGAAAATGC 59.064 43.478 0.00 0.00 43.92 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 253 9.978044 GGACCTTCGATTATACTGTAACTATTT 57.022 33.333 0.00 0.00 0.00 1.40
155 256 7.994911 TCTGGACCTTCGATTATACTGTAACTA 59.005 37.037 0.00 0.00 0.00 2.24
156 257 6.832384 TCTGGACCTTCGATTATACTGTAACT 59.168 38.462 0.00 0.00 0.00 2.24
157 258 6.916932 GTCTGGACCTTCGATTATACTGTAAC 59.083 42.308 0.00 0.00 0.00 2.50
158 259 7.035840 GTCTGGACCTTCGATTATACTGTAA 57.964 40.000 0.00 0.00 0.00 2.41
241 369 5.390613 GTTCACACCAATCATTTTCTACCG 58.609 41.667 0.00 0.00 0.00 4.02
290 418 2.267961 GTGGAGTTGTAGCCCCCG 59.732 66.667 0.00 0.00 0.00 5.73
335 463 9.793252 CATTGTCTCAAAGAAAAAGAAGAAAGA 57.207 29.630 0.00 0.00 0.00 2.52
336 464 9.028185 CCATTGTCTCAAAGAAAAAGAAGAAAG 57.972 33.333 0.00 0.00 0.00 2.62
337 465 7.492344 GCCATTGTCTCAAAGAAAAAGAAGAAA 59.508 33.333 0.00 0.00 0.00 2.52
339 467 6.461509 GGCCATTGTCTCAAAGAAAAAGAAGA 60.462 38.462 0.00 0.00 0.00 2.87
340 468 5.693555 GGCCATTGTCTCAAAGAAAAAGAAG 59.306 40.000 0.00 0.00 0.00 2.85
341 469 5.600696 GGCCATTGTCTCAAAGAAAAAGAA 58.399 37.500 0.00 0.00 0.00 2.52
342 470 4.261572 CGGCCATTGTCTCAAAGAAAAAGA 60.262 41.667 2.24 0.00 0.00 2.52
343 471 3.983344 CGGCCATTGTCTCAAAGAAAAAG 59.017 43.478 2.24 0.00 0.00 2.27
368 496 0.108138 ACTCCACCTAACATGCTCGC 60.108 55.000 0.00 0.00 0.00 5.03
406 539 2.093310 CCAGATATTTAGAGCATGCGCG 59.907 50.000 16.01 0.00 45.49 6.86
420 555 3.325716 GGCATGGCAAATTTCCCAGATAT 59.674 43.478 15.47 0.00 34.01 1.63
424 559 0.614294 TGGCATGGCAAATTTCCCAG 59.386 50.000 21.13 0.60 34.01 4.45
433 568 1.736365 CTGTGTGTGTGGCATGGCAA 61.736 55.000 25.11 11.55 0.00 4.52
439 574 3.807839 AGGGCTGTGTGTGTGGCA 61.808 61.111 0.00 0.00 0.00 4.92
469 606 1.269448 CTGGGTTTGATTCGGTGGTTG 59.731 52.381 0.00 0.00 0.00 3.77
483 629 4.758165 CCAGAATTTTACGTGTACTGGGTT 59.242 41.667 0.00 0.00 39.47 4.11
484 630 4.320870 CCAGAATTTTACGTGTACTGGGT 58.679 43.478 0.00 0.00 39.47 4.51
485 631 3.126343 GCCAGAATTTTACGTGTACTGGG 59.874 47.826 19.27 6.45 42.20 4.45
487 633 4.000988 AGGCCAGAATTTTACGTGTACTG 58.999 43.478 5.01 0.00 0.00 2.74
506 654 3.618690 AGTTCTGGTGAATACAGAGGC 57.381 47.619 0.00 0.00 44.91 4.70
511 659 3.263425 GGAGGGAAGTTCTGGTGAATACA 59.737 47.826 2.25 0.00 34.40 2.29
540 693 0.460284 TAGAGTACCGTCGTCGACCC 60.460 60.000 19.29 5.49 39.71 4.46
542 695 1.322936 CTGTAGAGTACCGTCGTCGAC 59.677 57.143 15.51 15.51 39.71 4.20
562 715 1.058404 GTGCGTGGTAGAAACTCGTC 58.942 55.000 0.00 0.00 0.00 4.20
563 716 0.662374 CGTGCGTGGTAGAAACTCGT 60.662 55.000 0.00 0.00 0.00 4.18
602 756 0.034059 AGTATCTATGGGTGCTGCGC 59.966 55.000 0.00 0.00 0.00 6.09
604 758 1.974236 AGGAGTATCTATGGGTGCTGC 59.026 52.381 0.00 0.00 33.73 5.25
606 760 2.158445 ACGAGGAGTATCTATGGGTGCT 60.158 50.000 0.00 0.00 33.73 4.40
607 761 2.240279 ACGAGGAGTATCTATGGGTGC 58.760 52.381 0.00 0.00 33.73 5.01
608 762 3.058155 CGAACGAGGAGTATCTATGGGTG 60.058 52.174 0.00 0.00 33.73 4.61
610 764 3.147629 ACGAACGAGGAGTATCTATGGG 58.852 50.000 0.14 0.00 33.73 4.00
611 765 4.036498 ACAACGAACGAGGAGTATCTATGG 59.964 45.833 0.14 0.00 33.73 2.74
612 766 4.970611 CACAACGAACGAGGAGTATCTATG 59.029 45.833 0.14 0.00 33.73 2.23
613 767 4.639310 ACACAACGAACGAGGAGTATCTAT 59.361 41.667 0.14 0.00 33.73 1.98
646 800 7.816513 TGGCAGTATAGTCTACTAGTACATACG 59.183 40.741 0.00 3.77 0.00 3.06
647 801 9.153721 CTGGCAGTATAGTCTACTAGTACATAC 57.846 40.741 6.28 5.13 0.00 2.39
650 804 5.996513 GCTGGCAGTATAGTCTACTAGTACA 59.003 44.000 17.16 0.00 0.00 2.90
651 805 5.996513 TGCTGGCAGTATAGTCTACTAGTAC 59.003 44.000 17.16 0.00 0.00 2.73
652 806 5.996513 GTGCTGGCAGTATAGTCTACTAGTA 59.003 44.000 17.16 1.89 0.00 1.82
653 807 4.822896 GTGCTGGCAGTATAGTCTACTAGT 59.177 45.833 17.16 0.00 0.00 2.57
654 808 4.083749 CGTGCTGGCAGTATAGTCTACTAG 60.084 50.000 17.16 0.00 0.00 2.57
655 809 3.813724 CGTGCTGGCAGTATAGTCTACTA 59.186 47.826 17.16 0.00 0.00 1.82
656 810 2.619177 CGTGCTGGCAGTATAGTCTACT 59.381 50.000 17.16 0.00 0.00 2.57
657 811 2.617308 TCGTGCTGGCAGTATAGTCTAC 59.383 50.000 17.16 0.00 0.00 2.59
766 920 3.050275 GTGTGAACTGCGCCCTCC 61.050 66.667 4.18 0.00 0.00 4.30
767 921 2.029844 GAGTGTGAACTGCGCCCTC 61.030 63.158 4.18 0.00 0.00 4.30
768 922 2.031163 GAGTGTGAACTGCGCCCT 59.969 61.111 4.18 0.00 0.00 5.19
769 923 2.280797 TGAGTGTGAACTGCGCCC 60.281 61.111 4.18 0.00 0.00 6.13
770 924 2.607892 GGTGAGTGTGAACTGCGCC 61.608 63.158 4.18 0.00 0.00 6.53
789 943 1.077429 GGGCTCGGCTTTTGAGGAT 60.077 57.895 0.00 0.00 33.99 3.24
874 1035 1.227468 GACCCCCGTCCGCTTTATC 60.227 63.158 0.00 0.00 32.40 1.75
935 1096 1.337917 TGCTGAGCTGAGCTTTCTCTG 60.338 52.381 25.74 0.95 39.88 3.35
941 1114 0.320596 GAGTGTGCTGAGCTGAGCTT 60.321 55.000 25.74 9.04 39.88 3.74
942 1115 1.292860 GAGTGTGCTGAGCTGAGCT 59.707 57.895 25.74 6.69 43.88 4.09
967 1160 2.664081 GGACTGGGAGAGGGTGCTG 61.664 68.421 0.00 0.00 0.00 4.41
968 1161 2.284995 GGACTGGGAGAGGGTGCT 60.285 66.667 0.00 0.00 0.00 4.40
970 1163 0.031111 TATGGGACTGGGAGAGGGTG 60.031 60.000 0.00 0.00 0.00 4.61
971 1164 0.031010 GTATGGGACTGGGAGAGGGT 60.031 60.000 0.00 0.00 0.00 4.34
972 1165 0.266152 AGTATGGGACTGGGAGAGGG 59.734 60.000 0.00 0.00 36.87 4.30
973 1166 3.957188 AGTATGGGACTGGGAGAGG 57.043 57.895 0.00 0.00 36.87 3.69
981 1174 1.497161 GGGTGCTACAGTATGGGACT 58.503 55.000 0.00 0.00 43.62 3.85
1044 1245 1.152839 CTCTCTCCGTCCCCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
1088 1300 3.230245 CTAGCTCCCCTGCTCCGG 61.230 72.222 0.00 0.00 42.97 5.14
1089 1301 3.922640 GCTAGCTCCCCTGCTCCG 61.923 72.222 7.70 0.00 42.97 4.63
1274 1494 3.286751 TTGTCGCAGTGCTTGGGC 61.287 61.111 14.33 0.00 39.45 5.36
1414 1634 0.332972 AAGAAACATGGGAGGGGAGC 59.667 55.000 0.00 0.00 0.00 4.70
1415 1635 1.918957 AGAAGAAACATGGGAGGGGAG 59.081 52.381 0.00 0.00 0.00 4.30
1416 1636 1.916181 GAGAAGAAACATGGGAGGGGA 59.084 52.381 0.00 0.00 0.00 4.81
1417 1637 1.064389 GGAGAAGAAACATGGGAGGGG 60.064 57.143 0.00 0.00 0.00 4.79
1418 1638 1.064389 GGGAGAAGAAACATGGGAGGG 60.064 57.143 0.00 0.00 0.00 4.30
1419 1639 1.064389 GGGGAGAAGAAACATGGGAGG 60.064 57.143 0.00 0.00 0.00 4.30
1420 1640 1.064389 GGGGGAGAAGAAACATGGGAG 60.064 57.143 0.00 0.00 0.00 4.30
1421 1641 0.999712 GGGGGAGAAGAAACATGGGA 59.000 55.000 0.00 0.00 0.00 4.37
1425 1645 0.912486 CGGAGGGGGAGAAGAAACAT 59.088 55.000 0.00 0.00 0.00 2.71
1479 1707 2.972625 TCGAACCACACAATCAGATCC 58.027 47.619 0.00 0.00 0.00 3.36
1932 2160 2.114625 TCCACCGTGGAGACGTCT 59.885 61.111 20.18 20.18 42.67 4.18
1995 2223 4.430765 AGGTTGTACGCGGGCGAG 62.431 66.667 20.98 0.00 42.83 5.03
2085 2313 4.384599 TCGAACTCGAACTCCGGA 57.615 55.556 2.93 2.93 46.30 5.14
2201 2429 3.425713 CAGTGCAATGCTCCGCGT 61.426 61.111 6.82 0.00 0.00 6.01
2228 2456 2.099141 TGTGAGTGCTGGCTGTTATC 57.901 50.000 0.00 0.00 0.00 1.75
2231 2459 0.107017 AGTTGTGAGTGCTGGCTGTT 60.107 50.000 0.00 0.00 0.00 3.16
2232 2460 0.107017 AAGTTGTGAGTGCTGGCTGT 60.107 50.000 0.00 0.00 0.00 4.40
2240 2468 2.639286 GCCGGCAAGTTGTGAGTG 59.361 61.111 24.80 0.00 0.00 3.51
2241 2469 2.594592 GGCCGGCAAGTTGTGAGT 60.595 61.111 30.85 0.00 0.00 3.41
2242 2470 2.594303 TGGCCGGCAAGTTGTGAG 60.594 61.111 30.85 0.00 0.00 3.51
2243 2471 2.594303 CTGGCCGGCAAGTTGTGA 60.594 61.111 30.85 0.00 0.00 3.58
2244 2472 2.906897 ACTGGCCGGCAAGTTGTG 60.907 61.111 31.52 8.23 0.00 3.33
2245 2473 2.697147 ATCACTGGCCGGCAAGTTGT 62.697 55.000 34.43 21.87 0.00 3.32
2246 2474 1.926511 GATCACTGGCCGGCAAGTTG 61.927 60.000 34.43 26.45 0.00 3.16
2388 2616 2.076100 TCGAACAACAGATGCATCCAC 58.924 47.619 23.06 0.00 0.00 4.02
2463 2691 7.257003 TGAATGAATAATGAAACAATCCGTGG 58.743 34.615 0.00 0.00 0.00 4.94
2522 2750 7.112779 ACACAAAGAGAAAGAAGAAGAGGAAA 58.887 34.615 0.00 0.00 0.00 3.13
2523 2751 6.653989 ACACAAAGAGAAAGAAGAAGAGGAA 58.346 36.000 0.00 0.00 0.00 3.36
2524 2752 6.240549 ACACAAAGAGAAAGAAGAAGAGGA 57.759 37.500 0.00 0.00 0.00 3.71
2525 2753 6.765512 AGAACACAAAGAGAAAGAAGAAGAGG 59.234 38.462 0.00 0.00 0.00 3.69
2526 2754 7.784633 AGAACACAAAGAGAAAGAAGAAGAG 57.215 36.000 0.00 0.00 0.00 2.85
2527 2755 7.414540 GCAAGAACACAAAGAGAAAGAAGAAGA 60.415 37.037 0.00 0.00 0.00 2.87
2528 2756 6.690528 GCAAGAACACAAAGAGAAAGAAGAAG 59.309 38.462 0.00 0.00 0.00 2.85
2609 2837 3.017442 GCTCCATCCACCTTTTTACTCC 58.983 50.000 0.00 0.00 0.00 3.85
2660 2888 2.856032 CGTGCTGCGTCAAAGAGG 59.144 61.111 0.00 0.00 35.54 3.69
2676 2904 1.392168 CCATGTACGCACTGGTTTACG 59.608 52.381 0.00 0.00 0.00 3.18
2687 2915 0.876342 GCTGGTAGCTCCATGTACGC 60.876 60.000 5.50 2.56 46.12 4.42
2703 2937 3.672808 AGTGGAAGAGATGAACTTGCTG 58.327 45.455 0.00 0.00 36.81 4.41
2720 2954 1.856265 GCTCCCGCTGTCAAAAGTGG 61.856 60.000 0.00 0.00 45.75 4.00
2823 3057 1.696832 GGACAAATCCTCGTGCTCGC 61.697 60.000 2.69 0.00 42.45 5.03
2852 3086 4.939271 TCAGAATACAACAACGACAGTGA 58.061 39.130 0.00 0.00 0.00 3.41
3042 3277 2.392181 CGGCGCATTTTCCGTACCA 61.392 57.895 10.83 0.00 40.72 3.25
3077 3330 3.918220 CGAGCGTGCCGATTCTGC 61.918 66.667 0.00 0.00 0.00 4.26
3123 3376 2.033194 CCGACGGGCTTCAGTTTCC 61.033 63.158 5.81 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.