Multiple sequence alignment - TraesCS2B01G190200

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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 TraesCS2B01G190200 chr2B 100.000 3242 0 0 1 3242 165521452 165524693 0.000000e+00 5987
1 TraesCS2B01G190200 chr2A 92.226 2161 109 28 695 2806 116452636 116454786 0.000000e+00 3005
2 TraesCS2B01G190200 chr2A 76.758 654 93 34 90 711 116450943 116451569 8.730000e-81 311
3 TraesCS2B01G190200 chr2D 95.843 1251 49 1 950 2197 115104647 115105897 0.000000e+00 2019
4 TraesCS2B01G190200 chr2D 90.704 1065 45 19 2229 3242 115105898 115106959 0.000000e+00 1369
5 TraesCS2B01G190200 chr2D 78.784 806 97 27 91 851 115103840 115104616 1.050000e-129 473


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 TraesCS2B01G190200 chr2B 165521452 165524693 3241 False 5987 5987 100.000000 1 3242 1 chr2B.!!$F1 3241
1 TraesCS2B01G190200 chr2A 116450943 116454786 3843 False 1658 3005 84.492000 90 2806 2 chr2A.!!$F1 2716
2 TraesCS2B01G190200 chr2D 115103840 115106959 3119 False 1287 2019 88.443667 91 3242 3 chr2D.!!$F1 3151

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
679 730 0.185175 AAACTGTTCACCCTCCCACC 59.815 55.0 0.0 0.0 0.00 4.61 F
919 2054 0.392060 GGTAACGAATTCCCCGTGCT 60.392 55.0 0.0 0.0 40.44 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 3355 0.449388 CTGCGGAGTTGGAATCTTGC 59.551 55.000 0.00 0.0 0.0 4.01 R
2742 3936 3.260884 TGCCATCGAAACTCCTCTTAAGT 59.739 43.478 1.63 0.0 0.0 2.24 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
41 42 9.515226 TGCAAGAAAATATAAAGTAACTCCAGT 57.485 29.630 0.00 0.00 0.00 4.00
42 43 9.774742 GCAAGAAAATATAAAGTAACTCCAGTG 57.225 33.333 0.00 0.00 0.00 3.66
54 55 9.708092 AAAGTAACTCCAGTGACTAAGAATTAC 57.292 33.333 7.62 7.62 38.78 1.89
55 56 8.418597 AGTAACTCCAGTGACTAAGAATTACA 57.581 34.615 14.47 0.00 37.96 2.41
56 57 8.867097 AGTAACTCCAGTGACTAAGAATTACAA 58.133 33.333 14.47 0.00 37.96 2.41
57 58 9.654663 GTAACTCCAGTGACTAAGAATTACAAT 57.345 33.333 9.76 0.00 0.00 2.71
82 83 9.995003 ATATATCTCTTGGAAACATCTCAAGAC 57.005 33.333 0.00 0.00 41.04 3.01
83 84 5.815233 TCTCTTGGAAACATCTCAAGACT 57.185 39.130 0.00 0.00 41.04 3.24
84 85 6.179906 TCTCTTGGAAACATCTCAAGACTT 57.820 37.500 0.00 0.00 41.04 3.01
85 86 6.226787 TCTCTTGGAAACATCTCAAGACTTC 58.773 40.000 0.00 0.00 41.04 3.01
86 87 5.928976 TCTTGGAAACATCTCAAGACTTCA 58.071 37.500 0.00 0.00 41.04 3.02
87 88 5.994054 TCTTGGAAACATCTCAAGACTTCAG 59.006 40.000 0.00 0.00 41.04 3.02
88 89 5.296151 TGGAAACATCTCAAGACTTCAGT 57.704 39.130 0.00 0.00 33.40 3.41
107 108 2.232452 AGTGAGCAGCGATACTTTCACT 59.768 45.455 5.58 5.58 42.10 3.41
131 132 3.454042 TCGCTCACACGAAATTGATTG 57.546 42.857 0.00 0.00 39.54 2.67
147 148 4.789012 TGATTGCCAATGAAGGTTTCTC 57.211 40.909 0.00 0.00 0.00 2.87
159 162 1.034292 GGTTTCTCAGCCCCATGAGC 61.034 60.000 0.00 0.00 45.25 4.26
170 173 2.124983 CATGAGCCGTCCACCCAG 60.125 66.667 0.00 0.00 0.00 4.45
172 175 1.918293 ATGAGCCGTCCACCCAGAA 60.918 57.895 0.00 0.00 0.00 3.02
176 179 1.201429 AGCCGTCCACCCAGAAAGAT 61.201 55.000 0.00 0.00 0.00 2.40
192 195 0.622665 AGATGGGAAGCCTTGAGTGG 59.377 55.000 0.00 0.00 0.00 4.00
218 221 4.498241 GCTGGGATGAACCTTTGAAAATC 58.502 43.478 0.00 0.00 38.98 2.17
220 223 5.717119 CTGGGATGAACCTTTGAAAATCTG 58.283 41.667 0.00 0.00 38.98 2.90
223 226 5.011023 GGGATGAACCTTTGAAAATCTGTGT 59.989 40.000 0.00 0.00 38.98 3.72
233 236 2.386661 AAATCTGTGTCGCCGAATCT 57.613 45.000 0.00 0.00 0.00 2.40
234 237 2.386661 AATCTGTGTCGCCGAATCTT 57.613 45.000 0.00 0.00 0.00 2.40
235 238 1.645034 ATCTGTGTCGCCGAATCTTG 58.355 50.000 0.00 0.00 0.00 3.02
236 239 0.317160 TCTGTGTCGCCGAATCTTGT 59.683 50.000 0.00 0.00 0.00 3.16
295 298 7.765307 ACTCCACACATAATCAAATCAATGAC 58.235 34.615 0.00 0.00 30.82 3.06
300 303 9.194271 CACACATAATCAAATCAATGACAACAA 57.806 29.630 0.00 0.00 30.82 2.83
308 311 6.974048 TCAAATCAATGACAACAACTTGACAG 59.026 34.615 0.00 0.00 35.86 3.51
314 317 8.344831 TCAATGACAACAACTTGACAGAATAAG 58.655 33.333 0.00 0.00 35.86 1.73
344 348 3.006940 TCACCGAGTAATTGAATGTGCC 58.993 45.455 0.00 0.00 0.00 5.01
348 352 3.689161 CCGAGTAATTGAATGTGCCAGAA 59.311 43.478 0.00 0.00 0.00 3.02
350 354 5.335583 CCGAGTAATTGAATGTGCCAGAAAA 60.336 40.000 0.00 0.00 0.00 2.29
376 380 1.202533 TCTCTAGCTTTATGGCACCGC 60.203 52.381 0.00 0.00 34.17 5.68
436 442 4.868450 TGTTCACTAAACACCAACGAAG 57.132 40.909 0.00 0.00 42.95 3.79
438 444 4.936411 TGTTCACTAAACACCAACGAAGAA 59.064 37.500 0.00 0.00 42.95 2.52
439 445 5.163834 TGTTCACTAAACACCAACGAAGAAC 60.164 40.000 0.00 0.00 42.95 3.01
468 477 6.455690 AAACTCCTAAAATCAGAAGACCCT 57.544 37.500 0.00 0.00 0.00 4.34
470 479 7.569599 AACTCCTAAAATCAGAAGACCCTAA 57.430 36.000 0.00 0.00 0.00 2.69
472 481 6.500751 ACTCCTAAAATCAGAAGACCCTAACA 59.499 38.462 0.00 0.00 0.00 2.41
474 483 6.500751 TCCTAAAATCAGAAGACCCTAACACT 59.499 38.462 0.00 0.00 0.00 3.55
482 491 4.527427 AGAAGACCCTAACACTAAGGTGAC 59.473 45.833 3.06 0.00 45.61 3.67
483 492 4.129317 AGACCCTAACACTAAGGTGACT 57.871 45.455 3.06 0.00 45.61 3.41
488 497 1.045407 AACACTAAGGTGACTGCCGA 58.955 50.000 3.06 0.00 45.61 5.54
514 523 3.243873 CGAGGGAAGCAGAAGTATATGCA 60.244 47.826 0.00 0.00 45.01 3.96
520 529 0.786581 CAGAAGTATATGCAGCGGCG 59.213 55.000 0.51 0.51 45.35 6.46
523 532 3.777925 GTATATGCAGCGGCGGCG 61.778 66.667 28.70 28.70 46.35 6.46
552 562 4.838423 TCTCTCAAGAAACCCTCATGTACA 59.162 41.667 0.00 0.00 0.00 2.90
556 566 7.500992 TCTCAAGAAACCCTCATGTACATATC 58.499 38.462 8.32 0.00 0.00 1.63
561 595 8.964533 AGAAACCCTCATGTACATATCTAGAT 57.035 34.615 8.32 10.73 0.00 1.98
622 661 5.410439 GTGCCGAGAAAAGAAAATAGGTACA 59.590 40.000 0.00 0.00 34.15 2.90
623 662 5.410439 TGCCGAGAAAAGAAAATAGGTACAC 59.590 40.000 0.00 0.00 0.00 2.90
624 663 5.163784 GCCGAGAAAAGAAAATAGGTACACC 60.164 44.000 0.00 0.00 0.00 4.16
636 687 3.309600 AGGTACACCTAATACTCGGCT 57.690 47.619 0.00 0.00 46.48 5.52
677 728 0.476771 GGAAACTGTTCACCCTCCCA 59.523 55.000 0.00 0.00 35.25 4.37
678 729 1.605753 GAAACTGTTCACCCTCCCAC 58.394 55.000 0.00 0.00 33.61 4.61
679 730 0.185175 AAACTGTTCACCCTCCCACC 59.815 55.000 0.00 0.00 0.00 4.61
680 731 0.991355 AACTGTTCACCCTCCCACCA 60.991 55.000 0.00 0.00 0.00 4.17
681 732 1.376466 CTGTTCACCCTCCCACCAG 59.624 63.158 0.00 0.00 0.00 4.00
734 1868 6.789268 TCCTTCACTGAAATAAAATCCCTCA 58.211 36.000 0.00 0.00 0.00 3.86
764 1898 1.075698 TCTTGTCTCCTCTCTCCCGTT 59.924 52.381 0.00 0.00 0.00 4.44
768 1902 2.510382 TGTCTCCTCTCTCCCGTTCTAT 59.490 50.000 0.00 0.00 0.00 1.98
812 1947 3.125316 GCTCACCACAAGAAATTAGACGG 59.875 47.826 0.00 0.00 0.00 4.79
835 1970 4.688413 GCCTCTACAATCCGATCAGAATTC 59.312 45.833 0.00 0.00 0.00 2.17
836 1971 4.920340 CCTCTACAATCCGATCAGAATTCG 59.080 45.833 0.00 0.00 36.38 3.34
853 1988 2.787473 TCGGCTTCAACCTGATTGAT 57.213 45.000 0.00 0.00 46.80 2.57
855 1990 1.328680 CGGCTTCAACCTGATTGATCG 59.671 52.381 0.00 0.00 46.80 3.69
859 1994 3.060003 GCTTCAACCTGATTGATCGATCG 60.060 47.826 20.03 9.36 46.80 3.69
861 1996 4.590850 TCAACCTGATTGATCGATCGAT 57.409 40.909 29.76 29.76 42.62 3.59
862 1997 4.984785 TTCAACCTGATTGATCGATCGATC 59.015 41.667 38.90 38.90 46.80 3.69
863 1998 5.221322 TTCAACCTGATTGATCGATCGATCT 60.221 40.000 41.82 30.61 46.80 2.75
864 1999 6.016276 TTCAACCTGATTGATCGATCGATCTA 60.016 38.462 41.82 37.75 46.80 1.98
905 2040 2.436115 GCGTCCCTGGCAGGTAAC 60.436 66.667 30.68 25.08 31.93 2.50
913 2048 1.379527 CTGGCAGGTAACGAATTCCC 58.620 55.000 6.61 0.00 46.39 3.97
919 2054 0.392060 GGTAACGAATTCCCCGTGCT 60.392 55.000 0.00 0.00 40.44 4.40
921 2056 2.484241 GGTAACGAATTCCCCGTGCTAT 60.484 50.000 0.00 0.00 40.44 2.97
922 2057 1.949465 AACGAATTCCCCGTGCTATC 58.051 50.000 0.00 0.00 40.44 2.08
925 2060 0.472471 GAATTCCCCGTGCTATCCCA 59.528 55.000 0.00 0.00 0.00 4.37
926 2061 0.474184 AATTCCCCGTGCTATCCCAG 59.526 55.000 0.00 0.00 0.00 4.45
956 2091 1.467875 CAGTAGCTCATACGCGTCAC 58.532 55.000 18.63 1.29 39.55 3.67
1014 2154 1.454479 CGCCATGGAATTGGAGGCT 60.454 57.895 18.40 0.00 43.07 4.58
1020 2160 0.619255 TGGAATTGGAGGCTCCGGTA 60.619 55.000 27.58 16.15 40.17 4.02
1128 2271 3.747579 CTCCTGCCCTGCCCCAAT 61.748 66.667 0.00 0.00 0.00 3.16
1478 2621 1.824329 TCGAGGAGATGGAGGCGAC 60.824 63.158 0.00 0.00 0.00 5.19
1914 3057 2.105128 CGCCTGCTCCTTAGTCCG 59.895 66.667 0.00 0.00 0.00 4.79
1995 3139 4.578928 GTGTCCATCTCCTCTCTTCTACTC 59.421 50.000 0.00 0.00 0.00 2.59
2040 3184 9.810545 TGCTTAATTTATTGGTAAAATACTGGC 57.189 29.630 0.00 0.00 33.76 4.85
2203 3347 2.221981 GGAGACGACAACAAAGAAGCAG 59.778 50.000 0.00 0.00 0.00 4.24
2211 3355 1.283793 CAAAGAAGCAGTGCCCACG 59.716 57.895 12.58 0.00 36.20 4.94
2261 3405 2.026822 AGTTTCGTTCCCTGATGCAGAT 60.027 45.455 0.00 0.00 32.44 2.90
2262 3406 2.749621 GTTTCGTTCCCTGATGCAGATT 59.250 45.455 0.00 0.00 32.44 2.40
2432 3601 3.831715 AGCGTTGTCCTTTTATTCAGC 57.168 42.857 0.00 0.00 0.00 4.26
2497 3666 3.190535 AGCAGTTTATACAAGGTTTGCGG 59.809 43.478 0.00 0.00 35.59 5.69
2614 3793 6.822667 TTGATGACATCAAGTAGCATTGTT 57.177 33.333 23.89 0.00 43.84 2.83
2616 3795 5.706833 TGATGACATCAAGTAGCATTGTTGT 59.293 36.000 15.83 10.83 42.76 3.32
2617 3796 6.207221 TGATGACATCAAGTAGCATTGTTGTT 59.793 34.615 15.83 1.75 41.09 2.83
2620 3799 6.147864 ACATCAAGTAGCATTGTTGTTGTT 57.852 33.333 7.03 0.00 39.08 2.83
2674 3865 5.078949 TCATCCAAGAAATGACCATGTTGT 58.921 37.500 0.00 0.00 0.00 3.32
2709 3900 3.573967 CCTTCCATTAGGCTTGTTGTTGT 59.426 43.478 0.00 0.00 33.74 3.32
2711 3902 4.846779 TCCATTAGGCTTGTTGTTGTTC 57.153 40.909 0.00 0.00 33.74 3.18
2712 3903 4.211125 TCCATTAGGCTTGTTGTTGTTCA 58.789 39.130 0.00 0.00 33.74 3.18
2713 3904 4.037446 TCCATTAGGCTTGTTGTTGTTCAC 59.963 41.667 0.00 0.00 33.74 3.18
2714 3905 4.037923 CCATTAGGCTTGTTGTTGTTCACT 59.962 41.667 0.00 0.00 0.00 3.41
2742 3936 0.243636 TCATTCTTCGAGCGAGCACA 59.756 50.000 0.00 0.00 0.00 4.57
2744 3938 0.244994 ATTCTTCGAGCGAGCACACT 59.755 50.000 0.00 0.00 0.00 3.55
2853 4053 2.742053 TGCCGTAGATTTTTGCACTCTC 59.258 45.455 0.00 0.00 0.00 3.20
2920 4120 0.673644 CTGATCGGCGGTCCAAGTTT 60.674 55.000 18.78 0.00 0.00 2.66
2927 4127 3.055963 TCGGCGGTCCAAGTTTTATTCTA 60.056 43.478 7.21 0.00 0.00 2.10
2930 4130 4.698780 GGCGGTCCAAGTTTTATTCTAACT 59.301 41.667 0.00 0.00 37.43 2.24
3024 4227 3.125146 CGCTGTATTGTGTGTTGTATGCT 59.875 43.478 0.00 0.00 0.00 3.79
3082 4285 2.489329 CACACAATCCATCCTTGGTGTC 59.511 50.000 0.00 0.00 44.06 3.67
3086 4289 0.994247 ATCCATCCTTGGTGTCTGCA 59.006 50.000 0.00 0.00 44.06 4.41
3100 4303 4.531332 GTGTCTGCACTGAGTTGAATTTC 58.469 43.478 0.00 0.00 42.13 2.17
3113 4316 3.639716 TGAATTTCACGAAAGCATGCA 57.360 38.095 21.98 0.00 33.32 3.96
3119 4322 1.675483 TCACGAAAGCATGCACAAAGT 59.325 42.857 21.98 10.09 0.00 2.66
3126 4329 2.494059 AGCATGCACAAAGTAAGACGT 58.506 42.857 21.98 0.00 0.00 4.34
3161 4364 4.569676 TTCCATGGATAGGAGGGAACTA 57.430 45.455 17.06 0.00 44.43 2.24
3168 4372 8.224720 CCATGGATAGGAGGGAACTAATTTTTA 58.775 37.037 5.56 0.00 44.43 1.52
3187 4391 5.777850 TTTATCTTGTGGATCCATGCATG 57.222 39.130 19.62 20.19 35.98 4.06
3211 4415 2.173519 CATCATGGCTTCCCACACTTT 58.826 47.619 0.00 0.00 45.77 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.515226 ACTGGAGTTACTTTATATTTTCTTGCA 57.485 29.630 0.00 0.00 0.00 4.08
16 17 9.774742 CACTGGAGTTACTTTATATTTTCTTGC 57.225 33.333 0.00 0.00 0.00 4.01
28 29 9.708092 GTAATTCTTAGTCACTGGAGTTACTTT 57.292 33.333 14.78 0.00 34.63 2.66
29 30 8.867097 TGTAATTCTTAGTCACTGGAGTTACTT 58.133 33.333 19.02 3.88 34.63 2.24
30 31 8.418597 TGTAATTCTTAGTCACTGGAGTTACT 57.581 34.615 19.02 0.00 36.55 2.24
31 32 9.654663 ATTGTAATTCTTAGTCACTGGAGTTAC 57.345 33.333 15.00 15.00 34.08 2.50
56 57 9.995003 GTCTTGAGATGTTTCCAAGAGATATAT 57.005 33.333 0.00 0.00 44.54 0.86
57 58 9.206690 AGTCTTGAGATGTTTCCAAGAGATATA 57.793 33.333 0.00 0.00 44.54 0.86
58 59 8.088463 AGTCTTGAGATGTTTCCAAGAGATAT 57.912 34.615 0.00 0.00 44.54 1.63
59 60 7.487822 AGTCTTGAGATGTTTCCAAGAGATA 57.512 36.000 0.00 0.00 44.54 1.98
60 61 6.371595 AGTCTTGAGATGTTTCCAAGAGAT 57.628 37.500 0.00 0.00 44.54 2.75
61 62 5.815233 AGTCTTGAGATGTTTCCAAGAGA 57.185 39.130 0.00 0.00 44.54 3.10
62 63 5.994054 TGAAGTCTTGAGATGTTTCCAAGAG 59.006 40.000 0.00 0.00 44.54 2.85
63 64 5.928976 TGAAGTCTTGAGATGTTTCCAAGA 58.071 37.500 0.00 0.00 42.55 3.02
64 65 5.762218 ACTGAAGTCTTGAGATGTTTCCAAG 59.238 40.000 6.02 0.00 38.79 3.61
65 66 5.528690 CACTGAAGTCTTGAGATGTTTCCAA 59.471 40.000 6.02 0.00 0.00 3.53
66 67 5.059161 CACTGAAGTCTTGAGATGTTTCCA 58.941 41.667 6.02 0.00 0.00 3.53
67 68 5.300752 TCACTGAAGTCTTGAGATGTTTCC 58.699 41.667 6.02 0.00 0.00 3.13
68 69 5.107143 GCTCACTGAAGTCTTGAGATGTTTC 60.107 44.000 6.02 0.00 39.36 2.78
69 70 4.754114 GCTCACTGAAGTCTTGAGATGTTT 59.246 41.667 6.02 0.00 39.36 2.83
70 71 4.202295 TGCTCACTGAAGTCTTGAGATGTT 60.202 41.667 6.02 0.00 39.36 2.71
71 72 3.323115 TGCTCACTGAAGTCTTGAGATGT 59.677 43.478 6.02 0.00 39.36 3.06
72 73 3.922910 TGCTCACTGAAGTCTTGAGATG 58.077 45.455 6.02 1.42 39.36 2.90
73 74 3.617045 GCTGCTCACTGAAGTCTTGAGAT 60.617 47.826 6.02 0.00 39.36 2.75
74 75 2.288702 GCTGCTCACTGAAGTCTTGAGA 60.289 50.000 6.02 0.00 39.36 3.27
75 76 2.067766 GCTGCTCACTGAAGTCTTGAG 58.932 52.381 0.00 0.00 39.89 3.02
76 77 1.603931 CGCTGCTCACTGAAGTCTTGA 60.604 52.381 0.00 0.00 0.00 3.02
77 78 0.788995 CGCTGCTCACTGAAGTCTTG 59.211 55.000 0.00 0.00 0.00 3.02
78 79 0.676184 TCGCTGCTCACTGAAGTCTT 59.324 50.000 0.00 0.00 0.00 3.01
79 80 0.894141 ATCGCTGCTCACTGAAGTCT 59.106 50.000 0.00 0.00 0.00 3.24
80 81 2.159310 AGTATCGCTGCTCACTGAAGTC 60.159 50.000 0.00 0.00 0.00 3.01
81 82 1.821753 AGTATCGCTGCTCACTGAAGT 59.178 47.619 0.00 0.00 0.00 3.01
82 83 2.575694 AGTATCGCTGCTCACTGAAG 57.424 50.000 0.00 0.00 0.00 3.02
83 84 3.254060 GAAAGTATCGCTGCTCACTGAA 58.746 45.455 0.00 0.00 0.00 3.02
84 85 2.231235 TGAAAGTATCGCTGCTCACTGA 59.769 45.455 0.00 0.00 0.00 3.41
85 86 2.346847 GTGAAAGTATCGCTGCTCACTG 59.653 50.000 8.22 0.00 37.64 3.66
86 87 2.232452 AGTGAAAGTATCGCTGCTCACT 59.768 45.455 11.29 11.29 46.99 3.41
87 88 2.611518 AGTGAAAGTATCGCTGCTCAC 58.388 47.619 7.59 7.59 46.99 3.51
131 132 1.203287 GGCTGAGAAACCTTCATTGGC 59.797 52.381 0.00 0.00 0.00 4.52
147 148 4.864334 GGACGGCTCATGGGGCTG 62.864 72.222 18.14 16.53 41.39 4.85
159 162 0.392998 CCATCTTTCTGGGTGGACGG 60.393 60.000 0.00 0.00 33.53 4.79
170 173 2.751806 CACTCAAGGCTTCCCATCTTTC 59.248 50.000 0.00 0.00 0.00 2.62
172 175 1.005215 CCACTCAAGGCTTCCCATCTT 59.995 52.381 0.00 0.00 0.00 2.40
192 195 0.613012 AAAGGTTCATCCCAGCCAGC 60.613 55.000 0.00 0.00 36.75 4.85
194 197 0.776810 TCAAAGGTTCATCCCAGCCA 59.223 50.000 0.00 0.00 36.75 4.75
218 221 0.439985 CACAAGATTCGGCGACACAG 59.560 55.000 10.16 6.29 0.00 3.66
220 223 1.324736 GATCACAAGATTCGGCGACAC 59.675 52.381 10.16 6.76 33.72 3.67
223 226 2.094234 TGAAGATCACAAGATTCGGCGA 60.094 45.455 4.99 4.99 33.72 5.54
236 239 6.796785 TCCTCAACATCATAGTGAAGATCA 57.203 37.500 0.00 0.00 0.00 2.92
288 291 6.698008 ATTCTGTCAAGTTGTTGTCATTGA 57.302 33.333 2.11 0.00 32.33 2.57
314 317 9.817365 CATTCAATTACTCGGTGATGAATTATC 57.183 33.333 0.00 0.00 36.29 1.75
348 352 4.950475 GCCATAAAGCTAGAGAGGGTTTTT 59.050 41.667 0.00 0.00 36.15 1.94
350 354 3.523564 TGCCATAAAGCTAGAGAGGGTTT 59.476 43.478 0.00 0.00 37.92 3.27
353 357 2.224402 GGTGCCATAAAGCTAGAGAGGG 60.224 54.545 0.00 0.00 0.00 4.30
379 383 7.225011 AGAATAAAGTTCCTCTCGTCCTTTTT 58.775 34.615 0.00 0.00 0.00 1.94
422 428 9.881529 GTTTTATATGTTCTTCGTTGGTGTTTA 57.118 29.630 0.00 0.00 0.00 2.01
425 431 7.094933 GGAGTTTTATATGTTCTTCGTTGGTGT 60.095 37.037 0.00 0.00 0.00 4.16
426 432 7.119262 AGGAGTTTTATATGTTCTTCGTTGGTG 59.881 37.037 0.00 0.00 0.00 4.17
428 434 7.611213 AGGAGTTTTATATGTTCTTCGTTGG 57.389 36.000 0.00 0.00 0.00 3.77
459 468 4.527427 GTCACCTTAGTGTTAGGGTCTTCT 59.473 45.833 0.00 0.00 44.83 2.85
464 473 2.302157 GCAGTCACCTTAGTGTTAGGGT 59.698 50.000 0.00 0.00 44.83 4.34
468 477 2.241160 TCGGCAGTCACCTTAGTGTTA 58.759 47.619 0.00 0.00 44.83 2.41
470 479 1.000955 CTTCGGCAGTCACCTTAGTGT 59.999 52.381 0.00 0.00 44.83 3.55
472 481 0.608640 CCTTCGGCAGTCACCTTAGT 59.391 55.000 0.00 0.00 0.00 2.24
488 497 1.298014 CTTCTGCTTCCCTCGCCTT 59.702 57.895 0.00 0.00 0.00 4.35
498 507 2.487934 CCGCTGCATATACTTCTGCTT 58.512 47.619 0.00 0.00 39.16 3.91
500 509 0.514691 GCCGCTGCATATACTTCTGC 59.485 55.000 0.00 0.00 38.87 4.26
520 529 0.608640 TTCTTGAGAGAAGGACCGCC 59.391 55.000 0.00 0.00 36.99 6.13
523 532 2.640332 AGGGTTTCTTGAGAGAAGGACC 59.360 50.000 2.75 2.75 42.55 4.46
526 536 4.260170 CATGAGGGTTTCTTGAGAGAAGG 58.740 47.826 0.00 0.00 42.55 3.46
561 595 9.997482 GTAAGATGCTTAATAAAATGAACCGAA 57.003 29.630 0.00 0.00 0.00 4.30
582 616 5.361571 TCTCGGCACCTTGTATAATGTAAGA 59.638 40.000 0.00 0.00 0.00 2.10
586 620 4.481368 TTCTCGGCACCTTGTATAATGT 57.519 40.909 0.00 0.00 0.00 2.71
591 625 3.695830 TCTTTTCTCGGCACCTTGTAT 57.304 42.857 0.00 0.00 0.00 2.29
601 635 6.171213 AGGTGTACCTATTTTCTTTTCTCGG 58.829 40.000 0.72 0.00 46.48 4.63
622 661 0.753262 CCTGCAGCCGAGTATTAGGT 59.247 55.000 8.66 0.00 0.00 3.08
623 662 1.000283 CTCCTGCAGCCGAGTATTAGG 60.000 57.143 8.66 0.00 0.00 2.69
624 663 1.957177 TCTCCTGCAGCCGAGTATTAG 59.043 52.381 8.66 0.00 0.00 1.73
626 665 0.749649 CTCTCCTGCAGCCGAGTATT 59.250 55.000 8.66 0.00 0.00 1.89
629 668 3.768922 GCTCTCCTGCAGCCGAGT 61.769 66.667 23.16 0.00 0.00 4.18
630 669 2.590391 AATGCTCTCCTGCAGCCGAG 62.590 60.000 20.12 20.12 46.71 4.63
631 670 2.189191 AAATGCTCTCCTGCAGCCGA 62.189 55.000 8.66 5.58 46.71 5.54
636 687 6.782558 CCTATTCGGAAATGCTCTCCTGCA 62.783 50.000 0.00 0.00 40.59 4.41
677 728 0.535102 CTTTGTTCCGCTGGTCTGGT 60.535 55.000 0.00 0.00 0.00 4.00
678 729 1.237285 CCTTTGTTCCGCTGGTCTGG 61.237 60.000 0.00 0.00 0.00 3.86
679 730 0.250295 TCCTTTGTTCCGCTGGTCTG 60.250 55.000 0.00 0.00 0.00 3.51
680 731 0.472471 TTCCTTTGTTCCGCTGGTCT 59.528 50.000 0.00 0.00 0.00 3.85
681 732 1.314730 TTTCCTTTGTTCCGCTGGTC 58.685 50.000 0.00 0.00 0.00 4.02
711 762 7.559170 AGATGAGGGATTTTATTTCAGTGAAGG 59.441 37.037 5.56 0.00 0.00 3.46
712 763 8.517062 AGATGAGGGATTTTATTTCAGTGAAG 57.483 34.615 5.56 0.00 0.00 3.02
734 1868 7.093509 GGAGAGAGGAGACAAGAAAAGTAAGAT 60.094 40.741 0.00 0.00 0.00 2.40
764 1898 4.597004 ACTAAGTCAACTCACGGGATAGA 58.403 43.478 0.00 0.00 0.00 1.98
768 1902 4.124238 CAAAACTAAGTCAACTCACGGGA 58.876 43.478 0.00 0.00 0.00 5.14
812 1947 3.735237 TTCTGATCGGATTGTAGAGGC 57.265 47.619 4.74 0.00 0.00 4.70
853 1988 2.333417 GCCGGCCTAGATCGATCGA 61.333 63.158 21.86 21.86 0.00 3.59
855 1990 0.963355 AGAGCCGGCCTAGATCGATC 60.963 60.000 26.15 17.91 0.00 3.69
859 1994 3.372123 GGAGAGCCGGCCTAGATC 58.628 66.667 26.15 14.34 0.00 2.75
905 2040 0.602905 GGGATAGCACGGGGAATTCG 60.603 60.000 0.00 0.00 0.00 3.34
919 2054 2.101783 CTGCAAACAATGGCTGGGATA 58.898 47.619 0.00 0.00 0.00 2.59
921 2056 0.469705 ACTGCAAACAATGGCTGGGA 60.470 50.000 0.00 0.00 33.82 4.37
922 2057 1.203052 CTACTGCAAACAATGGCTGGG 59.797 52.381 0.00 0.00 33.82 4.45
925 2060 1.815003 GAGCTACTGCAAACAATGGCT 59.185 47.619 0.00 0.00 42.74 4.75
926 2061 1.541147 TGAGCTACTGCAAACAATGGC 59.459 47.619 0.00 0.00 42.74 4.40
991 2131 4.910722 CAATTCCATGGCGCGGCG 62.911 66.667 28.22 19.62 0.00 6.46
1014 2154 1.022735 GATCTGCTTCGACTACCGGA 58.977 55.000 9.46 0.00 39.14 5.14
1020 2160 2.427245 CCCCGGATCTGCTTCGACT 61.427 63.158 0.73 0.00 0.00 4.18
1128 2271 1.302431 CACCACCTGGATGTCGCAA 60.302 57.895 0.00 0.00 38.94 4.85
1289 2432 3.237741 CCTGATCCTCCTCCGCCC 61.238 72.222 0.00 0.00 0.00 6.13
1302 2445 2.552819 GCGGTCGATCGGATCCTGA 61.553 63.158 21.29 9.41 0.00 3.86
1303 2446 2.049985 GCGGTCGATCGGATCCTG 60.050 66.667 21.29 12.05 0.00 3.86
1914 3057 1.555741 GATCAGCGCCGATCTTGCTC 61.556 60.000 23.35 3.48 39.02 4.26
1995 3139 9.846248 ATTAAGCAAGCAATGTTAGAAAACTAG 57.154 29.630 0.00 0.00 36.51 2.57
2040 3184 8.654230 ACATACATAGAGTAGCATCAGTTTTG 57.346 34.615 0.00 0.00 35.85 2.44
2211 3355 0.449388 CTGCGGAGTTGGAATCTTGC 59.551 55.000 0.00 0.00 0.00 4.01
2277 3421 7.012989 AGGGAGTATATACGAAACAAAAATGCC 59.987 37.037 7.23 1.26 0.00 4.40
2343 3494 4.196193 CCTCCGTACCATTAGCAATTCAA 58.804 43.478 0.00 0.00 0.00 2.69
2344 3495 3.433031 CCCTCCGTACCATTAGCAATTCA 60.433 47.826 0.00 0.00 0.00 2.57
2404 3573 3.423154 GGACAACGCTTCTGCCGG 61.423 66.667 0.00 0.00 35.36 6.13
2471 3640 6.858993 CGCAAACCTTGTATAAACTGCTTAAA 59.141 34.615 0.00 0.00 0.00 1.52
2497 3666 6.148976 CCCTAGGTTGTAGCACTTAAACTTTC 59.851 42.308 8.29 0.00 0.00 2.62
2614 3793 9.248291 GAAAATGCTAGAATTTTCTGAACAACA 57.752 29.630 30.20 0.67 46.24 3.33
2692 3883 5.186996 AGTGAACAACAACAAGCCTAATG 57.813 39.130 0.00 0.00 0.00 1.90
2709 3900 6.172630 TCGAAGAATGATGGATCAAAGTGAA 58.827 36.000 0.00 0.00 40.69 3.18
2711 3902 5.503683 GCTCGAAGAATGATGGATCAAAGTG 60.504 44.000 0.00 0.00 40.69 3.16
2712 3903 4.574013 GCTCGAAGAATGATGGATCAAAGT 59.426 41.667 0.00 0.00 40.69 2.66
2713 3904 4.318618 CGCTCGAAGAATGATGGATCAAAG 60.319 45.833 0.00 0.00 40.69 2.77
2714 3905 3.557185 CGCTCGAAGAATGATGGATCAAA 59.443 43.478 0.00 0.00 40.69 2.69
2742 3936 3.260884 TGCCATCGAAACTCCTCTTAAGT 59.739 43.478 1.63 0.00 0.00 2.24
2744 3938 3.973206 TGCCATCGAAACTCCTCTTAA 57.027 42.857 0.00 0.00 0.00 1.85
2920 4120 8.032451 GCCAACCTTTTTGCATAGTTAGAATAA 58.968 33.333 0.00 0.00 0.00 1.40
2927 4127 3.401033 GGCCAACCTTTTTGCATAGTT 57.599 42.857 0.00 0.00 0.00 2.24
3000 4203 0.591170 ACAACACACAATACAGCGGC 59.409 50.000 0.00 0.00 0.00 6.53
3024 4227 0.601558 GTCACTACTCGGAAGCCACA 59.398 55.000 0.00 0.00 0.00 4.17
3082 4285 3.248363 TCGTGAAATTCAACTCAGTGCAG 59.752 43.478 0.00 0.00 0.00 4.41
3086 4289 4.335315 TGCTTTCGTGAAATTCAACTCAGT 59.665 37.500 0.00 0.00 0.00 3.41
3100 4303 2.124011 ACTTTGTGCATGCTTTCGTG 57.876 45.000 20.33 7.37 0.00 4.35
3161 4364 7.185318 TGCATGGATCCACAAGATAAAAATT 57.815 32.000 18.99 0.00 34.42 1.82
3168 4372 3.588210 TCATGCATGGATCCACAAGAT 57.412 42.857 25.97 4.01 38.17 2.40
3187 4391 1.133699 TGTGGGAAGCCATGATGGATC 60.134 52.381 17.22 12.13 40.96 3.36
3211 4415 2.305927 GTCTCACTGGGGAAGAATTGGA 59.694 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.