Multiple sequence alignment - TraesCS2B01G135700

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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 TraesCS2B01G135700 chr2B 100.000 4259 0 0 1 4259 102413810 102418068 0.000000e+00 7866.0
1 TraesCS2B01G135700 chr2B 100.000 123 0 0 1 123 443155490 443155368 1.190000e-55 228.0
2 TraesCS2B01G135700 chr2B 98.361 122 2 0 1 122 146999762 146999883 9.280000e-52 215.0
3 TraesCS2B01G135700 chr2D 93.057 3615 149 37 695 4255 67976777 67973211 0.000000e+00 5192.0
4 TraesCS2B01G135700 chr2D 84.590 597 62 13 124 702 67977396 67976812 2.220000e-157 566.0
5 TraesCS2B01G135700 chr2A 94.891 3151 126 9 819 3934 66577031 66580181 0.000000e+00 4894.0
6 TraesCS2B01G135700 chr2A 85.035 568 51 16 124 674 66576142 66576692 8.050000e-152 547.0
7 TraesCS2B01G135700 chr2A 94.118 153 6 3 4023 4173 66580178 66580329 3.310000e-56 230.0
8 TraesCS2B01G135700 chr2A 97.674 86 2 0 4164 4249 66580569 66580654 9.540000e-32 148.0
9 TraesCS2B01G135700 chr2A 100.000 29 0 0 763 791 66577000 66577028 2.000000e-03 54.7
10 TraesCS2B01G135700 chr6B 100.000 123 0 0 1 123 398851308 398851186 1.190000e-55 228.0
11 TraesCS2B01G135700 chr6B 100.000 122 0 0 1 122 720460099 720460220 4.280000e-55 226.0
12 TraesCS2B01G135700 chr6B 99.180 122 1 0 1 122 545655822 545655943 1.990000e-53 220.0
13 TraesCS2B01G135700 chr1A 98.450 129 2 0 1 129 241745958 241746086 1.190000e-55 228.0
14 TraesCS2B01G135700 chr1B 99.187 123 1 0 1 123 198646029 198645907 5.540000e-54 222.0
15 TraesCS2B01G135700 chr1B 98.361 122 2 0 1 122 284046369 284046248 9.280000e-52 215.0
16 TraesCS2B01G135700 chr1B 91.429 105 8 1 3930 4034 359902045 359902148 4.440000e-30 143.0
17 TraesCS2B01G135700 chr1B 93.684 95 6 0 3935 4029 518802089 518802183 4.440000e-30 143.0
18 TraesCS2B01G135700 chr1B 87.705 122 12 3 3921 4041 536657395 536657514 5.740000e-29 139.0
19 TraesCS2B01G135700 chr3B 98.361 122 2 0 1 122 9895836 9895715 9.280000e-52 215.0
20 TraesCS2B01G135700 chr4D 91.150 113 8 2 3925 4037 509117701 509117811 7.380000e-33 152.0
21 TraesCS2B01G135700 chr5B 90.741 108 8 2 3924 4031 580833530 580833425 4.440000e-30 143.0
22 TraesCS2B01G135700 chr5B 88.793 116 8 4 3919 4029 315893324 315893439 2.070000e-28 137.0
23 TraesCS2B01G135700 chr7D 90.654 107 9 1 3926 4032 545397640 545397535 1.600000e-29 141.0
24 TraesCS2B01G135700 chr5D 88.034 117 10 4 3924 4039 473790103 473789990 7.430000e-28 135.0


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 TraesCS2B01G135700 chr2B 102413810 102418068 4258 False 7866.00 7866 100.0000 1 4259 1 chr2B.!!$F1 4258
1 TraesCS2B01G135700 chr2D 67973211 67977396 4185 True 2879.00 5192 88.8235 124 4255 2 chr2D.!!$R1 4131
2 TraesCS2B01G135700 chr2A 66576142 66580654 4512 False 1174.74 4894 94.3436 124 4249 5 chr2A.!!$F1 4125

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
122 123 0.106708 AGCGCCTTCTTGAACAGTGA 59.893 50.000 2.29 0.0 0.00 3.41 F
583 600 0.108615 ATCTTCTCCGACCAGCAACG 60.109 55.000 0.00 0.0 0.00 4.10 F
860 1122 0.867746 CTAGCAGCACGCACTGAAAA 59.132 50.000 9.32 0.0 46.13 2.29 F
939 1224 1.820481 GACGAGGAGAGGAGACGGG 60.820 68.421 0.00 0.0 0.00 5.28 F
2451 2744 0.541296 ACTGCCAGGCAATGAAGCTT 60.541 50.000 17.03 0.0 38.41 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1068 1355 0.531974 TTCTGTCGAACAGGTGGTGC 60.532 55.000 12.89 0.0 45.94 5.01 R
2016 2309 0.872881 GCCGCATGCCATTGAACATC 60.873 55.000 13.15 0.0 0.00 3.06 R
2017 2310 1.142314 GCCGCATGCCATTGAACAT 59.858 52.632 13.15 0.0 0.00 2.71 R
2625 2918 1.533129 CGCACCATGTCGTCGAATAGA 60.533 52.381 0.00 0.0 0.00 1.98 R
3698 3999 0.681733 TGAGAGTCCAGTTCTGTGGC 59.318 55.000 0.00 0.0 37.53 5.01 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
23 24 2.269241 CGGAGGACCTTTCTGGGC 59.731 66.667 0.00 0.00 45.48 5.36
28 29 4.081050 GACCTTTCTGGGCGCTTT 57.919 55.556 7.64 0.00 41.11 3.51
29 30 2.341452 GACCTTTCTGGGCGCTTTT 58.659 52.632 7.64 0.00 41.11 2.27
30 31 0.241213 GACCTTTCTGGGCGCTTTTC 59.759 55.000 7.64 0.00 41.11 2.29
31 32 0.178990 ACCTTTCTGGGCGCTTTTCT 60.179 50.000 7.64 0.00 41.11 2.52
32 33 0.242017 CCTTTCTGGGCGCTTTTCTG 59.758 55.000 7.64 0.00 0.00 3.02
33 34 1.238439 CTTTCTGGGCGCTTTTCTGA 58.762 50.000 7.64 1.90 0.00 3.27
34 35 1.198637 CTTTCTGGGCGCTTTTCTGAG 59.801 52.381 7.64 0.00 0.00 3.35
35 36 1.237285 TTCTGGGCGCTTTTCTGAGC 61.237 55.000 7.64 0.00 39.29 4.26
42 43 2.388347 GCTTTTCTGAGCGCCTAGG 58.612 57.895 2.29 3.67 32.23 3.02
43 44 0.391793 GCTTTTCTGAGCGCCTAGGT 60.392 55.000 11.31 0.00 32.23 3.08
44 45 1.646189 CTTTTCTGAGCGCCTAGGTC 58.354 55.000 11.31 0.24 46.92 3.85
45 46 0.249398 TTTTCTGAGCGCCTAGGTCC 59.751 55.000 11.31 1.41 46.24 4.46
46 47 0.902984 TTTCTGAGCGCCTAGGTCCA 60.903 55.000 11.31 2.75 46.24 4.02
47 48 0.902984 TTCTGAGCGCCTAGGTCCAA 60.903 55.000 11.31 0.00 46.24 3.53
48 49 0.902984 TCTGAGCGCCTAGGTCCAAA 60.903 55.000 11.31 0.00 46.24 3.28
49 50 0.460987 CTGAGCGCCTAGGTCCAAAG 60.461 60.000 11.31 0.00 46.24 2.77
50 51 1.815840 GAGCGCCTAGGTCCAAAGC 60.816 63.158 11.31 6.97 41.28 3.51
53 54 4.522971 GCCTAGGTCCAAAGCGAG 57.477 61.111 11.31 0.00 0.00 5.03
54 55 1.153349 GCCTAGGTCCAAAGCGAGG 60.153 63.158 11.31 0.14 45.50 4.63
55 56 1.153349 CCTAGGTCCAAAGCGAGGC 60.153 63.158 0.00 0.00 38.65 4.70
56 57 1.519455 CTAGGTCCAAAGCGAGGCG 60.519 63.158 0.00 0.00 0.00 5.52
73 74 4.552365 GCTATGCCAGCGCCCAGA 62.552 66.667 2.29 0.00 41.37 3.86
74 75 2.280660 CTATGCCAGCGCCCAGAG 60.281 66.667 2.29 1.74 0.00 3.35
75 76 4.552365 TATGCCAGCGCCCAGAGC 62.552 66.667 2.29 0.00 38.52 4.09
78 79 4.473520 GCCAGCGCCCAGAGCTTA 62.474 66.667 2.29 0.00 44.06 3.09
79 80 2.268920 CCAGCGCCCAGAGCTTAA 59.731 61.111 2.29 0.00 44.06 1.85
80 81 1.817099 CCAGCGCCCAGAGCTTAAG 60.817 63.158 2.29 0.00 44.06 1.85
81 82 2.124942 AGCGCCCAGAGCTTAAGC 60.125 61.111 20.09 20.09 43.24 3.09
91 92 3.640992 GCTTAAGCGCGCCTAGGC 61.641 66.667 30.33 27.28 37.85 3.93
114 115 2.979130 GCCTAGTAGCGCCTTCTTG 58.021 57.895 2.29 1.06 0.00 3.02
115 116 0.460311 GCCTAGTAGCGCCTTCTTGA 59.540 55.000 2.29 0.00 0.00 3.02
116 117 1.134788 GCCTAGTAGCGCCTTCTTGAA 60.135 52.381 2.29 0.00 0.00 2.69
117 118 2.541556 CCTAGTAGCGCCTTCTTGAAC 58.458 52.381 2.29 0.00 0.00 3.18
118 119 2.094182 CCTAGTAGCGCCTTCTTGAACA 60.094 50.000 2.29 0.00 0.00 3.18
119 120 2.086054 AGTAGCGCCTTCTTGAACAG 57.914 50.000 2.29 0.00 0.00 3.16
120 121 1.344763 AGTAGCGCCTTCTTGAACAGT 59.655 47.619 2.29 0.00 0.00 3.55
121 122 1.461127 GTAGCGCCTTCTTGAACAGTG 59.539 52.381 2.29 0.00 0.00 3.66
122 123 0.106708 AGCGCCTTCTTGAACAGTGA 59.893 50.000 2.29 0.00 0.00 3.41
140 141 0.749454 GATCAAGACTGGCGGCCAAT 60.749 55.000 23.94 14.27 30.80 3.16
145 146 1.675641 GACTGGCGGCCAATGAACT 60.676 57.895 23.94 0.97 30.80 3.01
160 161 2.243810 TGAACTATGCCCAAAACCACC 58.756 47.619 0.00 0.00 0.00 4.61
180 181 1.295423 GTGGGCGTCCTAGCTTCAA 59.705 57.895 7.97 0.00 37.29 2.69
203 204 2.225019 CCCAATCGTGCAGAGAATATGC 59.775 50.000 0.00 0.00 44.11 3.14
357 358 2.370189 AGAATAAGCCTCCATCTTCCCG 59.630 50.000 0.00 0.00 0.00 5.14
404 405 1.153349 GGGAGCTTTCGCCGAATCT 60.153 57.895 0.00 0.70 36.60 2.40
406 407 0.741221 GGAGCTTTCGCCGAATCTGT 60.741 55.000 0.00 0.00 36.60 3.41
429 430 1.004745 CCTGTAGTTGCCCTTCACCAT 59.995 52.381 0.00 0.00 0.00 3.55
430 431 2.086869 CTGTAGTTGCCCTTCACCATG 58.913 52.381 0.00 0.00 0.00 3.66
457 458 1.152756 AAGCTTTGGAGGCGGTTGT 60.153 52.632 0.00 0.00 34.52 3.32
458 459 1.455383 AAGCTTTGGAGGCGGTTGTG 61.455 55.000 0.00 0.00 34.52 3.33
461 462 3.723097 TTTGGAGGCGGTTGTGGCA 62.723 57.895 0.00 0.00 36.77 4.92
479 480 2.016318 GCATCCACCGAATGTTGATCA 58.984 47.619 0.00 0.00 27.22 2.92
489 490 5.882557 ACCGAATGTTGATCATTAGCTCTTT 59.117 36.000 0.00 0.00 45.49 2.52
504 521 2.347731 CTCTTTAGACGCCAAACTCCC 58.652 52.381 0.00 0.00 0.00 4.30
505 522 1.975680 TCTTTAGACGCCAAACTCCCT 59.024 47.619 0.00 0.00 0.00 4.20
550 567 2.536066 ACTATGTACAGGAGTGCACCA 58.464 47.619 14.63 2.29 43.19 4.17
552 569 1.644509 ATGTACAGGAGTGCACCAGA 58.355 50.000 14.63 0.00 43.19 3.86
562 579 2.930562 GCACCAGACTCCACCCCT 60.931 66.667 0.00 0.00 0.00 4.79
563 580 2.529744 GCACCAGACTCCACCCCTT 61.530 63.158 0.00 0.00 0.00 3.95
583 600 0.108615 ATCTTCTCCGACCAGCAACG 60.109 55.000 0.00 0.00 0.00 4.10
604 621 2.161609 GCCGACAACAAAATCGAGGATT 59.838 45.455 0.00 0.00 40.86 3.01
606 623 3.426159 CCGACAACAAAATCGAGGATTGG 60.426 47.826 10.99 0.00 40.86 3.16
615 632 1.529244 CGAGGATTGGGGATTGGGC 60.529 63.158 0.00 0.00 0.00 5.36
640 657 2.808543 GCCCAAGCTCATCGTATTTAGG 59.191 50.000 0.00 0.00 35.50 2.69
641 658 3.403038 CCCAAGCTCATCGTATTTAGGG 58.597 50.000 0.00 0.00 0.00 3.53
664 683 4.213564 TCAAAGGAGGCTTGAGAAGATC 57.786 45.455 0.00 0.00 0.00 2.75
671 690 2.028130 GGCTTGAGAAGATCGAGAGGA 58.972 52.381 0.00 0.00 41.48 3.71
675 694 4.328712 GCTTGAGAAGATCGAGAGGAAAAC 59.671 45.833 0.00 0.00 41.48 2.43
681 706 2.098443 AGATCGAGAGGAAAACGAGCTC 59.902 50.000 2.73 2.73 46.85 4.09
684 709 2.159366 TCGAGAGGAAAACGAGCTCATC 60.159 50.000 15.40 5.93 0.00 2.92
687 712 3.791245 AGAGGAAAACGAGCTCATCATC 58.209 45.455 15.40 12.47 0.00 2.92
690 715 4.125703 AGGAAAACGAGCTCATCATCATC 58.874 43.478 15.40 2.20 0.00 2.92
693 718 5.333952 GGAAAACGAGCTCATCATCATCATC 60.334 44.000 15.40 0.00 0.00 2.92
699 724 6.757478 ACGAGCTCATCATCATCATCATTATC 59.243 38.462 15.40 0.00 0.00 1.75
702 727 8.669946 AGCTCATCATCATCATCATTATCATC 57.330 34.615 0.00 0.00 0.00 2.92
703 728 8.490311 AGCTCATCATCATCATCATTATCATCT 58.510 33.333 0.00 0.00 0.00 2.90
704 729 8.769891 GCTCATCATCATCATCATTATCATCTC 58.230 37.037 0.00 0.00 0.00 2.75
720 790 4.058124 TCATCTCTCGACAACAAACAAGG 58.942 43.478 0.00 0.00 0.00 3.61
722 792 3.454375 TCTCTCGACAACAAACAAGGAC 58.546 45.455 0.00 0.00 0.00 3.85
723 793 3.118920 TCTCTCGACAACAAACAAGGACA 60.119 43.478 0.00 0.00 0.00 4.02
725 795 4.196193 TCTCGACAACAAACAAGGACAAT 58.804 39.130 0.00 0.00 0.00 2.71
727 797 5.995282 TCTCGACAACAAACAAGGACAATAT 59.005 36.000 0.00 0.00 0.00 1.28
729 799 6.664515 TCGACAACAAACAAGGACAATATTC 58.335 36.000 0.00 0.00 0.00 1.75
730 800 5.856455 CGACAACAAACAAGGACAATATTCC 59.144 40.000 0.00 0.00 35.66 3.01
732 802 7.118496 ACAACAAACAAGGACAATATTCCAA 57.882 32.000 0.00 0.00 38.25 3.53
733 803 6.983890 ACAACAAACAAGGACAATATTCCAAC 59.016 34.615 0.00 0.00 38.25 3.77
744 823 4.020307 ACAATATTCCAACAAAGGGCAAGG 60.020 41.667 0.00 0.00 0.00 3.61
791 1051 2.187707 CTATTGCGCAGTTTTCATGGC 58.812 47.619 11.77 0.00 0.00 4.40
860 1122 0.867746 CTAGCAGCACGCACTGAAAA 59.132 50.000 9.32 0.00 46.13 2.29
939 1224 1.820481 GACGAGGAGAGGAGACGGG 60.820 68.421 0.00 0.00 0.00 5.28
1084 1371 2.279851 CGCACCACCTGTTCGACA 60.280 61.111 0.00 0.00 35.51 4.35
1124 1417 3.205395 CAGGACGCCTCTCTCCTG 58.795 66.667 3.39 3.39 45.97 3.86
1313 1606 3.009714 GACCGGCTCCTTCCCCTT 61.010 66.667 0.00 0.00 0.00 3.95
1317 1610 4.448976 GGCTCCTTCCCCTTGGCC 62.449 72.222 0.00 0.00 0.00 5.36
1383 1676 2.434884 ACCATGCTCTCCGCGTTG 60.435 61.111 4.92 0.00 43.27 4.10
1514 1807 4.956932 GGGCGGCCTTGGGATAGC 62.957 72.222 22.87 0.00 0.00 2.97
1596 1889 2.799371 CTCGTCACGGCCTACTCC 59.201 66.667 0.00 0.00 0.00 3.85
1731 2024 2.358737 GTGGTCCGGCTGTTCCTG 60.359 66.667 0.00 0.00 0.00 3.86
1921 2214 3.523087 TACAAGTGCGGCGCTCCAA 62.523 57.895 33.26 9.91 0.00 3.53
2451 2744 0.541296 ACTGCCAGGCAATGAAGCTT 60.541 50.000 17.03 0.00 38.41 3.74
2472 2765 4.271816 CTCGGCGCCAGCGAGTAT 62.272 66.667 28.98 0.00 46.35 2.12
2534 2827 2.039137 GGAGGAGTCCGGGAAGGT 59.961 66.667 0.00 0.00 41.99 3.50
2628 2921 2.767445 CGACGCCGTCATGGGTCTA 61.767 63.158 18.40 0.00 36.39 2.59
2733 3026 2.908015 GGCACCGGCAAGGAGATA 59.092 61.111 0.00 0.00 45.00 1.98
2741 3034 2.224066 CCGGCAAGGAGATATTCGACTT 60.224 50.000 0.00 0.00 45.00 3.01
2856 3149 0.885150 AGCTCATGATGCAGATGCCG 60.885 55.000 16.20 0.00 41.18 5.69
2958 3251 0.312102 CTGACGTGCTGACAGAGTCA 59.688 55.000 20.15 20.15 42.03 3.41
3033 3326 4.424711 GATTGGGGAGGCGTGGCA 62.425 66.667 0.00 0.00 0.00 4.92
3162 3461 2.126618 GACGACACGACGCATCCA 60.127 61.111 0.00 0.00 36.70 3.41
3309 3610 5.423886 TGTTTGACCATCAAAAAGGAAACC 58.576 37.500 5.59 0.00 46.53 3.27
3349 3650 1.992667 CAACTCGCATCGCTTTACTCA 59.007 47.619 0.00 0.00 0.00 3.41
3377 3678 3.497262 GGTGGTGCTACAAAGTACAGAAC 59.503 47.826 0.00 0.00 39.87 3.01
3420 3721 3.119316 TCTGCAAAACGTTGTTGGTCAAT 60.119 39.130 18.37 0.00 38.38 2.57
3463 3764 8.948631 TTAACATAAGCAACCAAATGTGAAAA 57.051 26.923 0.00 0.00 33.04 2.29
3507 3808 2.178912 TGACTAAAACTTGGCCGGAG 57.821 50.000 5.05 0.43 0.00 4.63
3515 3816 4.344865 TTGGCCGGAGTCCAAGCC 62.345 66.667 26.59 26.59 42.29 4.35
3698 3999 3.736252 CAGTGTCGGTACTTCAACAAGAG 59.264 47.826 0.00 0.00 33.34 2.85
3873 4183 3.132646 ACAAGAGATTGGCTGAGAGCTAG 59.867 47.826 0.00 0.00 41.99 3.42
3886 4196 0.610687 GAGCTAGGTGACAGCCTTGT 59.389 55.000 0.00 0.00 39.99 3.16
3946 4260 3.735720 ATATAGTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
3950 4264 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3961 4275 2.671396 CCGTCCCAAAATAAGTGTCTCG 59.329 50.000 0.00 0.00 0.00 4.04
3962 4276 2.671396 CGTCCCAAAATAAGTGTCTCGG 59.329 50.000 0.00 0.00 0.00 4.63
3965 4279 2.618045 CCCAAAATAAGTGTCTCGGCCT 60.618 50.000 0.00 0.00 0.00 5.19
3971 4285 5.927281 AATAAGTGTCTCGGCCTTAGTAA 57.073 39.130 0.00 0.00 0.00 2.24
3978 4292 5.237996 GTGTCTCGGCCTTAGTAAAACTTTT 59.762 40.000 0.00 0.00 0.00 2.27
3979 4293 5.467735 TGTCTCGGCCTTAGTAAAACTTTTC 59.532 40.000 0.00 0.00 0.00 2.29
4022 4336 4.360951 AGACACTTATTTTGGGACGGAA 57.639 40.909 0.00 0.00 0.00 4.30
4256 4820 9.282247 CAGAACAATTGATGAACTAAATACTGC 57.718 33.333 13.59 0.00 0.00 4.40
4257 4821 9.236006 AGAACAATTGATGAACTAAATACTGCT 57.764 29.630 13.59 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.836400 AGAAAGGTCCTCCGGCAAGA 60.836 55.000 0.00 0.00 39.05 3.02
1 2 0.674895 CAGAAAGGTCCTCCGGCAAG 60.675 60.000 0.00 0.00 39.05 4.01
2 3 1.374947 CAGAAAGGTCCTCCGGCAA 59.625 57.895 0.00 0.00 39.05 4.52
3 4 2.592993 CCAGAAAGGTCCTCCGGCA 61.593 63.158 0.00 0.00 39.05 5.69
4 5 2.269241 CCAGAAAGGTCCTCCGGC 59.731 66.667 0.00 0.00 39.05 6.13
5 6 2.990479 CCCAGAAAGGTCCTCCGG 59.010 66.667 0.00 0.00 39.05 5.14
6 7 2.269241 GCCCAGAAAGGTCCTCCG 59.731 66.667 0.00 0.00 39.05 4.63
7 8 2.269241 CGCCCAGAAAGGTCCTCC 59.731 66.667 0.00 0.00 34.66 4.30
8 9 2.436824 GCGCCCAGAAAGGTCCTC 60.437 66.667 0.00 0.00 34.66 3.71
9 10 2.069165 AAAGCGCCCAGAAAGGTCCT 62.069 55.000 2.29 0.00 34.66 3.85
10 11 1.179174 AAAAGCGCCCAGAAAGGTCC 61.179 55.000 2.29 0.00 34.66 4.46
11 12 0.241213 GAAAAGCGCCCAGAAAGGTC 59.759 55.000 2.29 0.00 34.66 3.85
12 13 0.178990 AGAAAAGCGCCCAGAAAGGT 60.179 50.000 2.29 0.00 34.66 3.50
13 14 0.242017 CAGAAAAGCGCCCAGAAAGG 59.758 55.000 2.29 0.00 37.03 3.11
14 15 1.198637 CTCAGAAAAGCGCCCAGAAAG 59.801 52.381 2.29 0.00 0.00 2.62
15 16 1.238439 CTCAGAAAAGCGCCCAGAAA 58.762 50.000 2.29 0.00 0.00 2.52
16 17 1.237285 GCTCAGAAAAGCGCCCAGAA 61.237 55.000 2.29 0.00 31.56 3.02
17 18 1.672356 GCTCAGAAAAGCGCCCAGA 60.672 57.895 2.29 0.00 31.56 3.86
18 19 2.873288 GCTCAGAAAAGCGCCCAG 59.127 61.111 2.29 0.00 31.56 4.45
24 25 0.391793 ACCTAGGCGCTCAGAAAAGC 60.392 55.000 9.30 0.00 38.97 3.51
25 26 1.646189 GACCTAGGCGCTCAGAAAAG 58.354 55.000 9.30 0.00 0.00 2.27
26 27 0.249398 GGACCTAGGCGCTCAGAAAA 59.751 55.000 9.30 0.00 0.00 2.29
27 28 0.902984 TGGACCTAGGCGCTCAGAAA 60.903 55.000 9.30 0.00 0.00 2.52
28 29 0.902984 TTGGACCTAGGCGCTCAGAA 60.903 55.000 9.30 0.00 0.00 3.02
29 30 0.902984 TTTGGACCTAGGCGCTCAGA 60.903 55.000 9.30 0.00 0.00 3.27
30 31 0.460987 CTTTGGACCTAGGCGCTCAG 60.461 60.000 9.30 4.41 0.00 3.35
31 32 1.596934 CTTTGGACCTAGGCGCTCA 59.403 57.895 9.30 0.00 0.00 4.26
32 33 1.815840 GCTTTGGACCTAGGCGCTC 60.816 63.158 9.30 0.00 0.00 5.03
33 34 2.269241 GCTTTGGACCTAGGCGCT 59.731 61.111 9.30 0.00 0.00 5.92
34 35 3.195698 CGCTTTGGACCTAGGCGC 61.196 66.667 18.28 0.00 39.42 6.53
35 36 1.519455 CTCGCTTTGGACCTAGGCG 60.519 63.158 22.90 22.90 45.93 5.52
36 37 1.153349 CCTCGCTTTGGACCTAGGC 60.153 63.158 9.30 1.17 0.00 3.93
37 38 1.153349 GCCTCGCTTTGGACCTAGG 60.153 63.158 7.41 7.41 0.00 3.02
38 39 1.519455 CGCCTCGCTTTGGACCTAG 60.519 63.158 0.00 0.00 0.00 3.02
39 40 2.577059 CGCCTCGCTTTGGACCTA 59.423 61.111 0.00 0.00 0.00 3.08
57 58 2.280660 CTCTGGGCGCTGGCATAG 60.281 66.667 7.64 0.00 42.47 2.23
58 59 4.552365 GCTCTGGGCGCTGGCATA 62.552 66.667 7.64 0.00 42.47 3.14
67 68 3.567797 CGCGCTTAAGCTCTGGGC 61.568 66.667 24.33 18.01 39.32 5.36
68 69 3.567797 GCGCGCTTAAGCTCTGGG 61.568 66.667 26.67 17.41 39.32 4.45
69 70 2.629050 TAGGCGCGCTTAAGCTCTGG 62.629 60.000 32.29 10.49 39.32 3.86
70 71 1.211818 CTAGGCGCGCTTAAGCTCTG 61.212 60.000 32.29 10.83 39.32 3.35
71 72 1.066587 CTAGGCGCGCTTAAGCTCT 59.933 57.895 32.29 19.48 39.32 4.09
72 73 1.951631 CCTAGGCGCGCTTAAGCTC 60.952 63.158 32.29 16.34 39.32 4.09
73 74 2.107141 CCTAGGCGCGCTTAAGCT 59.893 61.111 32.29 21.01 39.32 3.74
74 75 3.640992 GCCTAGGCGCGCTTAAGC 61.641 66.667 32.29 28.27 37.78 3.09
96 97 0.460311 TCAAGAAGGCGCTACTAGGC 59.540 55.000 7.64 0.00 0.00 3.93
97 98 2.094182 TGTTCAAGAAGGCGCTACTAGG 60.094 50.000 7.64 1.39 0.00 3.02
98 99 3.182967 CTGTTCAAGAAGGCGCTACTAG 58.817 50.000 7.64 0.00 0.00 2.57
99 100 2.561419 ACTGTTCAAGAAGGCGCTACTA 59.439 45.455 7.64 0.00 0.00 1.82
100 101 1.344763 ACTGTTCAAGAAGGCGCTACT 59.655 47.619 7.64 1.07 0.00 2.57
101 102 1.461127 CACTGTTCAAGAAGGCGCTAC 59.539 52.381 7.64 0.00 0.00 3.58
102 103 1.343142 TCACTGTTCAAGAAGGCGCTA 59.657 47.619 7.64 0.00 0.00 4.26
103 104 0.106708 TCACTGTTCAAGAAGGCGCT 59.893 50.000 7.64 0.00 0.00 5.92
104 105 1.129437 GATCACTGTTCAAGAAGGCGC 59.871 52.381 0.00 0.00 0.00 6.53
105 106 2.416747 TGATCACTGTTCAAGAAGGCG 58.583 47.619 0.00 0.00 0.00 5.52
112 113 3.141398 GCCAGTCTTGATCACTGTTCAA 58.859 45.455 10.06 3.13 39.84 2.69
113 114 2.771089 GCCAGTCTTGATCACTGTTCA 58.229 47.619 10.06 0.00 39.84 3.18
114 115 1.728971 CGCCAGTCTTGATCACTGTTC 59.271 52.381 10.06 2.63 39.84 3.18
115 116 1.609061 CCGCCAGTCTTGATCACTGTT 60.609 52.381 10.06 0.00 39.84 3.16
116 117 0.036952 CCGCCAGTCTTGATCACTGT 60.037 55.000 10.06 0.00 39.84 3.55
117 118 1.364626 GCCGCCAGTCTTGATCACTG 61.365 60.000 0.00 0.00 40.96 3.66
118 119 1.078848 GCCGCCAGTCTTGATCACT 60.079 57.895 0.00 0.00 0.00 3.41
119 120 2.109126 GGCCGCCAGTCTTGATCAC 61.109 63.158 3.91 0.00 0.00 3.06
120 121 2.123248 TTGGCCGCCAGTCTTGATCA 62.123 55.000 12.95 0.00 33.81 2.92
121 122 0.749454 ATTGGCCGCCAGTCTTGATC 60.749 55.000 12.95 0.00 33.81 2.92
122 123 1.033746 CATTGGCCGCCAGTCTTGAT 61.034 55.000 12.95 0.00 33.81 2.57
140 141 2.243810 GGTGGTTTTGGGCATAGTTCA 58.756 47.619 0.00 0.00 0.00 3.18
145 146 0.896019 CACCGGTGGTTTTGGGCATA 60.896 55.000 27.57 0.00 31.02 3.14
160 161 3.718210 GAAGCTAGGACGCCCACCG 62.718 68.421 0.00 0.00 44.21 4.94
171 172 2.289002 GCACGATTGGGATTGAAGCTAG 59.711 50.000 0.00 0.00 0.00 3.42
180 181 4.321718 CATATTCTCTGCACGATTGGGAT 58.678 43.478 0.00 0.00 0.00 3.85
271 272 1.404315 GGAGCGTCCAACTTCTACAGG 60.404 57.143 0.00 0.00 36.28 4.00
357 358 4.554036 GTGGGGCGGCTGGATCTC 62.554 72.222 9.56 0.00 0.00 2.75
404 405 1.764571 AAGGGCAACTACAGGCGACA 61.765 55.000 0.00 0.00 0.00 4.35
406 407 1.295423 GAAGGGCAACTACAGGCGA 59.705 57.895 0.00 0.00 0.00 5.54
429 430 0.257328 TCCAAAGCTTGTCACCCACA 59.743 50.000 0.00 0.00 0.00 4.17
430 431 0.954452 CTCCAAAGCTTGTCACCCAC 59.046 55.000 0.00 0.00 0.00 4.61
457 458 0.037447 TCAACATTCGGTGGATGCCA 59.963 50.000 0.00 0.00 0.00 4.92
458 459 1.334869 GATCAACATTCGGTGGATGCC 59.665 52.381 0.00 0.00 40.39 4.40
461 462 4.516698 GCTAATGATCAACATTCGGTGGAT 59.483 41.667 0.00 0.00 44.77 3.41
471 472 5.520288 GCGTCTAAAGAGCTAATGATCAACA 59.480 40.000 0.00 0.00 0.00 3.33
479 480 4.833390 AGTTTGGCGTCTAAAGAGCTAAT 58.167 39.130 0.00 0.00 31.75 1.73
489 490 2.235402 CCTTAAGGGAGTTTGGCGTCTA 59.765 50.000 14.25 0.00 37.23 2.59
504 521 6.946583 AGCTTTAGGTTTAGGGTTTCCTTAAG 59.053 38.462 0.00 0.00 41.56 1.85
505 522 6.855667 AGCTTTAGGTTTAGGGTTTCCTTAA 58.144 36.000 0.00 0.00 41.56 1.85
550 567 3.631346 GGAGAAGATAAGGGGTGGAGTCT 60.631 52.174 0.00 0.00 0.00 3.24
552 569 2.765502 GGAGAAGATAAGGGGTGGAGT 58.234 52.381 0.00 0.00 0.00 3.85
562 579 2.416836 CGTTGCTGGTCGGAGAAGATAA 60.417 50.000 0.00 0.00 39.69 1.75
563 580 1.134367 CGTTGCTGGTCGGAGAAGATA 59.866 52.381 0.00 0.00 39.69 1.98
583 600 1.153353 TCCTCGATTTTGTTGTCGGC 58.847 50.000 0.00 0.00 38.34 5.54
640 657 0.326264 TCTCAAGCCTCCTTTGAGCC 59.674 55.000 9.50 0.00 37.29 4.70
641 658 2.083002 CTTCTCAAGCCTCCTTTGAGC 58.917 52.381 9.50 0.00 37.29 4.26
660 679 2.096248 AGCTCGTTTTCCTCTCGATCT 58.904 47.619 0.00 0.00 33.26 2.75
664 683 2.189342 GATGAGCTCGTTTTCCTCTCG 58.811 52.381 10.42 0.00 0.00 4.04
671 690 5.121105 TGATGATGATGATGAGCTCGTTTT 58.879 37.500 10.42 0.24 0.00 2.43
675 694 6.757010 TGATAATGATGATGATGATGAGCTCG 59.243 38.462 9.64 0.00 0.00 5.03
681 706 8.973378 CGAGAGATGATAATGATGATGATGATG 58.027 37.037 0.00 0.00 0.00 3.07
684 709 7.974501 TGTCGAGAGATGATAATGATGATGATG 59.025 37.037 0.00 0.00 45.19 3.07
687 712 7.597743 TGTTGTCGAGAGATGATAATGATGATG 59.402 37.037 0.00 0.00 45.19 3.07
690 715 7.704789 TTGTTGTCGAGAGATGATAATGATG 57.295 36.000 0.00 0.00 45.19 3.07
693 718 7.294676 TGTTTGTTGTCGAGAGATGATAATG 57.705 36.000 0.00 0.00 45.19 1.90
699 724 4.058124 TCCTTGTTTGTTGTCGAGAGATG 58.942 43.478 0.00 0.00 45.19 2.90
702 727 3.194861 TGTCCTTGTTTGTTGTCGAGAG 58.805 45.455 0.00 0.00 0.00 3.20
703 728 3.254470 TGTCCTTGTTTGTTGTCGAGA 57.746 42.857 0.00 0.00 0.00 4.04
704 729 4.552166 ATTGTCCTTGTTTGTTGTCGAG 57.448 40.909 0.00 0.00 0.00 4.04
720 790 4.799564 TGCCCTTTGTTGGAATATTGTC 57.200 40.909 0.00 0.00 0.00 3.18
722 792 4.222588 TCCTTGCCCTTTGTTGGAATATTG 59.777 41.667 0.00 0.00 0.00 1.90
723 793 4.424842 TCCTTGCCCTTTGTTGGAATATT 58.575 39.130 0.00 0.00 0.00 1.28
725 795 3.430453 CTCCTTGCCCTTTGTTGGAATA 58.570 45.455 0.00 0.00 0.00 1.75
727 797 1.703411 CTCCTTGCCCTTTGTTGGAA 58.297 50.000 0.00 0.00 0.00 3.53
729 799 0.178964 TCCTCCTTGCCCTTTGTTGG 60.179 55.000 0.00 0.00 0.00 3.77
730 800 0.961753 GTCCTCCTTGCCCTTTGTTG 59.038 55.000 0.00 0.00 0.00 3.33
732 802 0.555769 TTGTCCTCCTTGCCCTTTGT 59.444 50.000 0.00 0.00 0.00 2.83
733 803 0.961753 GTTGTCCTCCTTGCCCTTTG 59.038 55.000 0.00 0.00 0.00 2.77
744 823 7.678947 ATAGCAATAGCAATATGTTGTCCTC 57.321 36.000 4.00 0.00 45.49 3.71
791 1051 2.014857 TCTGTTCGTCGGAGGATGTAG 58.985 52.381 0.69 1.55 0.00 2.74
860 1122 2.429250 TGCTGCAGATATGCTTGCAAAT 59.571 40.909 23.56 0.00 39.99 2.32
884 1151 4.261801 TGGTTTGAATTGCTACTAGCCTC 58.738 43.478 5.58 1.13 41.51 4.70
975 1260 2.623502 GGTGGAGAGACTAGCAGGGTAA 60.624 54.545 0.00 0.00 0.00 2.85
1068 1355 0.531974 TTCTGTCGAACAGGTGGTGC 60.532 55.000 12.89 0.00 45.94 5.01
1084 1371 2.592308 GCTTGGGCGAGGGATTCT 59.408 61.111 0.00 0.00 0.00 2.40
1110 1397 3.844090 GGGCAGGAGAGAGGCGTC 61.844 72.222 0.00 0.00 0.00 5.19
1350 1643 1.419381 TGGTGTTGTAGGAGCTGACA 58.581 50.000 0.00 0.00 0.00 3.58
1453 1746 2.380410 GCGCGACGGTGAAAGTGAT 61.380 57.895 12.10 0.00 0.00 3.06
1731 2024 3.838271 TCGTCCCTGAGCATCCGC 61.838 66.667 0.00 0.00 38.99 5.54
1873 2166 2.434185 GAGCACGTTGCCGATGGA 60.434 61.111 6.39 0.00 46.52 3.41
1965 2258 2.672961 TGATTGTGGTCCACGAGATC 57.327 50.000 17.19 18.12 37.14 2.75
2016 2309 0.872881 GCCGCATGCCATTGAACATC 60.873 55.000 13.15 0.00 0.00 3.06
2017 2310 1.142314 GCCGCATGCCATTGAACAT 59.858 52.632 13.15 0.00 0.00 2.71
2385 2678 4.773117 GTCTCGACGCCGGTGACC 62.773 72.222 24.59 11.93 35.42 4.02
2472 2765 2.284625 ATGAGGGTGCCGGAGACA 60.285 61.111 5.05 0.00 0.00 3.41
2527 2820 2.047560 CCCGTCGAACACCTTCCC 60.048 66.667 0.00 0.00 0.00 3.97
2589 2882 3.041940 CTCCCGTGCTTCGCGTTT 61.042 61.111 5.77 0.00 38.35 3.60
2625 2918 1.533129 CGCACCATGTCGTCGAATAGA 60.533 52.381 0.00 0.00 0.00 1.98
2628 2921 2.452813 GCGCACCATGTCGTCGAAT 61.453 57.895 0.30 0.00 0.00 3.34
2661 2954 4.681978 AGGAGCACAACGCCGTCC 62.682 66.667 0.00 0.00 44.30 4.79
2729 3022 2.868044 GCGGCCATCAAGTCGAATATCT 60.868 50.000 2.24 0.00 0.00 1.98
2733 3026 1.819632 GGCGGCCATCAAGTCGAAT 60.820 57.895 15.62 0.00 0.00 3.34
2823 3116 3.731766 GAGCTCCTCGGCCTCCTCT 62.732 68.421 0.87 0.00 0.00 3.69
2856 3149 2.413765 GAGATGCTCGGTCCGGAC 59.586 66.667 27.04 27.04 0.00 4.79
3018 3311 4.211330 TTTGCCACGCCTCCCCAA 62.211 61.111 0.00 0.00 0.00 4.12
3033 3326 2.026449 CCTCATCTGCCTTCTCACCTTT 60.026 50.000 0.00 0.00 0.00 3.11
3123 3422 2.408050 GACGAGAACTTGTGCAGATGT 58.592 47.619 0.00 0.00 0.00 3.06
3162 3461 3.147629 CCTGTATATCTCTTCCGTCCGT 58.852 50.000 0.00 0.00 0.00 4.69
3309 3610 1.002033 GCTGCCTTTTCTCACTGTGTG 60.002 52.381 7.79 5.56 34.45 3.82
3349 3650 2.306847 CTTTGTAGCACCACCCAGTTT 58.693 47.619 0.00 0.00 0.00 2.66
3377 3678 6.783162 CAGAATGCAAGATAAACCTTCTCTG 58.217 40.000 0.00 0.00 0.00 3.35
3436 3737 6.686630 TCACATTTGGTTGCTTATGTTAAGG 58.313 36.000 0.00 0.00 0.00 2.69
3485 3786 1.396996 CCGGCCAAGTTTTAGTCATCG 59.603 52.381 2.24 0.00 0.00 3.84
3507 3808 7.553044 ACATGTATAACTCTAAAAGGCTTGGAC 59.447 37.037 0.00 0.00 0.00 4.02
3698 3999 0.681733 TGAGAGTCCAGTTCTGTGGC 59.318 55.000 0.00 0.00 37.53 5.01
3873 4183 3.733443 AATTTTCACAAGGCTGTCACC 57.267 42.857 0.00 0.00 31.64 4.02
3886 4196 2.029470 CCGCCTTGTTGCCTAATTTTCA 60.029 45.455 0.00 0.00 0.00 2.69
3933 4247 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3934 4248 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3935 4249 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3936 4250 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3937 4251 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3938 4252 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3939 4253 3.615592 CGAGACACTTATTTTGGGACGGA 60.616 47.826 0.00 0.00 0.00 4.69
3946 4260 4.935808 ACTAAGGCCGAGACACTTATTTTG 59.064 41.667 14.03 0.00 0.00 2.44
3950 4264 5.927281 TTTACTAAGGCCGAGACACTTAT 57.073 39.130 14.03 0.00 0.00 1.73
3961 4275 9.976511 ATTTTAGTGAAAAGTTTTACTAAGGCC 57.023 29.630 16.16 0.00 44.56 5.19
3997 4311 5.702209 TCCGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
4045 4359 0.955428 GGAATGCTTGCTCCGTGTCA 60.955 55.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.