Multiple sequence alignment - TraesCS6D01G039400

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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 TraesCS6D01G039400 chr6D 100.000 3800 0 0 1 3800 16233025 16236824 0.000000e+00 7018.0
1 TraesCS6D01G039400 chr6D 91.070 1467 106 13 1375 2817 16247787 16246322 0.000000e+00 1960.0
2 TraesCS6D01G039400 chr6D 87.117 163 20 1 1001 1162 16253099 16252937 2.330000e-42 183.0
3 TraesCS6D01G039400 chr6D 88.991 109 12 0 191 299 79857104 79857212 6.620000e-28 135.0
4 TraesCS6D01G039400 chr6D 85.417 96 10 2 2983 3076 16246207 16246114 3.120000e-16 97.1
5 TraesCS6D01G039400 chr6D 100.000 41 0 0 3134 3174 16246105 16246065 4.070000e-10 76.8
6 TraesCS6D01G039400 chr6A 95.254 2128 68 11 875 2973 16468421 16470544 0.000000e+00 3339.0
7 TraesCS6D01G039400 chr6A 85.880 602 37 16 1 593 16467539 16468101 7.030000e-167 597.0
8 TraesCS6D01G039400 chr6A 91.858 393 24 4 3409 3800 16471215 16471600 3.340000e-150 542.0
9 TraesCS6D01G039400 chr6A 84.599 474 37 12 2983 3421 16470691 16471163 4.510000e-119 438.0
10 TraesCS6D01G039400 chr6A 90.583 223 11 3 573 793 16468109 16468323 1.730000e-73 287.0
11 TraesCS6D01G039400 chr6A 96.774 62 2 0 819 880 16468322 16468383 1.870000e-18 104.0
12 TraesCS6D01G039400 chr6B 90.777 1312 69 15 580 1871 27966751 27968030 0.000000e+00 1705.0
13 TraesCS6D01G039400 chr6B 87.522 569 44 14 1 557 27966210 27966763 1.930000e-177 632.0
14 TraesCS6D01G039400 chr6B 86.792 583 45 10 1989 2565 27968047 27968603 4.170000e-174 621.0
15 TraesCS6D01G039400 chr6B 91.481 270 22 1 2574 2843 27989080 27989348 1.670000e-98 370.0
16 TraesCS6D01G039400 chr6B 85.204 196 16 3 2991 3174 27989528 27989722 5.010000e-44 189.0
17 TraesCS6D01G039400 chr6B 100.000 36 0 0 297 332 668262420 668262455 2.450000e-07 67.6
18 TraesCS6D01G039400 chr5D 76.413 1132 230 24 1232 2338 36178432 36179551 9.150000e-161 577.0
19 TraesCS6D01G039400 chr5D 90.909 88 6 2 3637 3723 122198429 122198515 2.400000e-22 117.0
20 TraesCS6D01G039400 chr5D 89.412 85 8 1 3640 3723 498655286 498655370 5.190000e-19 106.0
21 TraesCS6D01G039400 chr5B 75.968 1136 228 34 1232 2338 27134655 27135774 9.280000e-151 544.0
22 TraesCS6D01G039400 chr5B 92.857 84 6 0 3640 3723 134917850 134917767 5.150000e-24 122.0
23 TraesCS6D01G039400 chr5B 97.436 39 1 0 297 335 693568920 693568958 2.450000e-07 67.6
24 TraesCS6D01G039400 chr5B 97.368 38 1 0 297 334 712222708 712222671 8.810000e-07 65.8
25 TraesCS6D01G039400 chr2A 88.991 109 12 0 191 299 173127158 173127266 6.620000e-28 135.0
26 TraesCS6D01G039400 chr1A 88.496 113 12 1 187 298 427816468 427816356 6.620000e-28 135.0
27 TraesCS6D01G039400 chr5A 87.826 115 13 1 184 298 537119672 537119785 2.380000e-27 134.0
28 TraesCS6D01G039400 chr5A 100.000 35 0 0 300 334 609814491 609814525 8.810000e-07 65.8
29 TraesCS6D01G039400 chr5A 93.182 44 2 1 297 339 42123662 42123619 3.170000e-06 63.9
30 TraesCS6D01G039400 chr7A 88.785 107 12 0 188 294 538102525 538102631 8.570000e-27 132.0
31 TraesCS6D01G039400 chr3A 89.423 104 11 0 191 294 482063236 482063133 8.570000e-27 132.0
32 TraesCS6D01G039400 chr7B 87.963 108 13 0 191 298 458512285 458512392 1.110000e-25 128.0
33 TraesCS6D01G039400 chr7B 86.869 99 9 4 3627 3722 725735150 725735053 1.440000e-19 108.0
34 TraesCS6D01G039400 chr1D 84.800 125 16 3 176 299 3303499 3303377 5.150000e-24 122.0
35 TraesCS6D01G039400 chr7D 92.771 83 6 0 3640 3722 463263075 463263157 1.850000e-23 121.0
36 TraesCS6D01G039400 chr7D 90.476 84 7 1 3640 3723 41146644 41146562 4.010000e-20 110.0
37 TraesCS6D01G039400 chr2D 93.590 78 5 0 3640 3717 420166159 420166236 2.400000e-22 117.0
38 TraesCS6D01G039400 chr4B 89.286 84 9 0 3640 3723 806777 806694 5.190000e-19 106.0
39 TraesCS6D01G039400 chr4A 87.500 72 8 1 88 158 606622725 606622654 8.750000e-12 82.4
40 TraesCS6D01G039400 chr3D 87.500 56 4 3 298 350 464323181 464323236 1.140000e-05 62.1
41 TraesCS6D01G039400 chr2B 88.235 51 4 2 299 347 391521867 391521917 4.100000e-05 60.2


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 TraesCS6D01G039400 chr6D 16233025 16236824 3799 False 7018.0 7018 100.000000 1 3800 1 chr6D.!!$F1 3799
1 TraesCS6D01G039400 chr6D 16246065 16247787 1722 True 711.3 1960 92.162333 1375 3174 3 chr6D.!!$R2 1799
2 TraesCS6D01G039400 chr6A 16467539 16471600 4061 False 884.5 3339 90.824667 1 3800 6 chr6A.!!$F1 3799
3 TraesCS6D01G039400 chr6B 27966210 27968603 2393 False 986.0 1705 88.363667 1 2565 3 chr6B.!!$F2 2564
4 TraesCS6D01G039400 chr6B 27989080 27989722 642 False 279.5 370 88.342500 2574 3174 2 chr6B.!!$F3 600
5 TraesCS6D01G039400 chr5D 36178432 36179551 1119 False 577.0 577 76.413000 1232 2338 1 chr5D.!!$F1 1106
6 TraesCS6D01G039400 chr5B 27134655 27135774 1119 False 544.0 544 75.968000 1232 2338 1 chr5B.!!$F1 1106

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
605 652 0.476771 TCCTTTTTCCTCCGTTGCCT 59.523 50.0 0.0 0.0 0.00 4.75 F
886 935 0.539986 TTGTGGGGAATAGAGACGCC 59.460 55.0 0.0 0.0 39.15 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 2688 0.465705 TTCACATGGCGGGATCTCTC 59.534 55.0 0.0 0.0 0.0 3.20 R
2806 2960 0.400213 TTCGCCCCTGTTGATCTGTT 59.600 50.0 0.0 0.0 0.0 3.16 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
91 92 6.526566 GACATTTAGAAAAGTCGTGTCAGT 57.473 37.500 0.00 0.00 35.72 3.41
124 125 5.879948 CACGTCTAGATATGCTTGAAGTG 57.120 43.478 0.00 13.06 45.66 3.16
174 175 7.100409 TGATTTATGCGGATATTCATACGGAA 58.900 34.615 0.00 0.00 42.60 4.30
179 180 5.996219 TGCGGATATTCATACGGAATTTTG 58.004 37.500 0.00 0.00 43.76 2.44
181 182 6.077838 GCGGATATTCATACGGAATTTTGTC 58.922 40.000 0.00 0.00 43.76 3.18
258 270 8.560576 ACAGAACATAAAACAGTTCAATTTCG 57.439 30.769 7.88 0.00 44.94 3.46
277 289 6.730960 TTTCGGCTGTCTTAAACGATTTAT 57.269 33.333 0.00 0.00 33.26 1.40
282 294 8.885722 TCGGCTGTCTTAAACGATTTATAAAAT 58.114 29.630 1.21 0.00 0.00 1.82
294 306 6.546034 ACGATTTATAAAATTGGTCAGAGGGG 59.454 38.462 1.21 0.00 0.00 4.79
313 325 4.230502 AGGGGGTATGTTTGATTGAGTCAT 59.769 41.667 0.00 0.00 36.54 3.06
456 473 6.365970 AGAACATTAAAGCAGAGAGAGGAA 57.634 37.500 0.00 0.00 0.00 3.36
481 498 0.875059 GGAACACTTTCGGCTTCCTG 59.125 55.000 0.00 0.00 31.78 3.86
495 512 4.821589 CCTGAACGGAGCCGGAGC 62.822 72.222 5.05 0.00 44.69 4.70
551 568 2.438868 AAAAGCGCTGGGAAATCAAC 57.561 45.000 12.58 0.00 0.00 3.18
605 652 0.476771 TCCTTTTTCCTCCGTTGCCT 59.523 50.000 0.00 0.00 0.00 4.75
630 677 3.009115 CCGGAGCCAGAGGGGAAA 61.009 66.667 0.00 0.00 40.01 3.13
631 678 2.602676 CCGGAGCCAGAGGGGAAAA 61.603 63.158 0.00 0.00 40.01 2.29
632 679 1.377333 CGGAGCCAGAGGGGAAAAC 60.377 63.158 0.00 0.00 40.01 2.43
633 680 1.000771 GGAGCCAGAGGGGAAAACC 60.001 63.158 0.00 0.00 40.01 3.27
651 698 1.149627 CGGAAAAGTCCACCCACCA 59.850 57.895 0.00 0.00 45.26 4.17
692 739 4.802051 GCCGCCATTCCTGCTCCA 62.802 66.667 0.00 0.00 0.00 3.86
764 813 1.471327 GCCTCAGATCTGTCAGTCAGC 60.471 57.143 21.92 11.38 43.32 4.26
815 864 3.009143 GGGGAATAAACAGGTCAGTCAGT 59.991 47.826 0.00 0.00 0.00 3.41
848 897 5.762045 CTTCCAACCCTATTTGCGATTATG 58.238 41.667 0.00 0.00 0.00 1.90
880 929 4.380843 TTTGCTTCTTGTGGGGAATAGA 57.619 40.909 0.00 0.00 0.00 1.98
881 930 3.634397 TGCTTCTTGTGGGGAATAGAG 57.366 47.619 0.00 0.00 0.00 2.43
883 932 3.055094 TGCTTCTTGTGGGGAATAGAGAC 60.055 47.826 0.00 0.00 0.00 3.36
885 934 1.480954 TCTTGTGGGGAATAGAGACGC 59.519 52.381 0.00 0.00 0.00 5.19
886 935 0.539986 TTGTGGGGAATAGAGACGCC 59.460 55.000 0.00 0.00 39.15 5.68
887 936 1.067582 GTGGGGAATAGAGACGCCG 59.932 63.158 0.00 0.00 41.11 6.46
949 1039 6.148480 ACTGAACTTTCATAACTCATGCTCAC 59.852 38.462 0.00 0.00 36.46 3.51
950 1040 5.412594 TGAACTTTCATAACTCATGCTCACC 59.587 40.000 0.00 0.00 34.35 4.02
1149 1250 4.202202 TGTTAAGATTGCACACCCTTTTGG 60.202 41.667 0.00 0.00 41.37 3.28
1362 1466 1.265905 CTAAGTTTCAACGGTGCCCAC 59.734 52.381 0.00 0.00 0.00 4.61
1440 1556 0.887387 GGAAGCACCGTGGCAAGTTA 60.887 55.000 0.00 0.00 35.83 2.24
1448 1564 1.068474 CGTGGCAAGTTAGTCGAAGG 58.932 55.000 0.00 0.00 0.00 3.46
1525 1641 4.863131 GGATTAGGTTTGCTATATCGTCCG 59.137 45.833 0.00 0.00 0.00 4.79
1577 1693 2.368221 CCTCATCCAATCTCCTGAGACC 59.632 54.545 0.00 0.00 40.75 3.85
1824 1949 1.203287 CACCTGAACGATGAGCTGAGA 59.797 52.381 0.00 0.00 0.00 3.27
1875 2000 7.065324 CACTACTTGAAGGTTGTTTACTGTGAA 59.935 37.037 0.00 0.00 0.00 3.18
2131 2258 5.886960 AGTAAGGATTTAGCTTGTGCAAG 57.113 39.130 7.51 7.51 42.74 4.01
2313 2445 1.308069 TGCTCCGCTCATTGAAAGGC 61.308 55.000 3.00 0.00 0.00 4.35
2410 2561 2.134346 ACCGTTGCATGCATTTTGAAC 58.866 42.857 23.37 14.44 0.00 3.18
2418 2569 4.993584 TGCATGCATTTTGAACGGTATTTT 59.006 33.333 18.46 0.00 0.00 1.82
2534 2688 0.905357 AATGAGGGACCTTCCAGACG 59.095 55.000 0.38 0.00 38.64 4.18
2547 2701 2.121538 CAGACGAGAGATCCCGCCA 61.122 63.158 0.00 0.00 0.00 5.69
2572 2726 5.732288 GTGAATACACGCATCTGAAGAATC 58.268 41.667 0.00 0.00 37.28 2.52
2583 2737 3.421844 TCTGAAGAATCTCCGTGTCTCA 58.578 45.455 0.00 0.00 0.00 3.27
2773 2927 3.686760 TGCTCGACAGACTCCCAG 58.313 61.111 0.00 0.00 0.00 4.45
2774 2928 1.228583 TGCTCGACAGACTCCCAGT 60.229 57.895 0.00 0.00 0.00 4.00
2788 2942 1.662044 CCAGTGGGTGCAAAGCTTC 59.338 57.895 0.00 0.00 0.00 3.86
2794 2948 1.143684 TGGGTGCAAAGCTTCTTCTCT 59.856 47.619 0.00 0.00 0.00 3.10
2806 2960 3.618507 GCTTCTTCTCTCTTAAGGCAGCA 60.619 47.826 1.85 0.00 33.91 4.41
2808 2962 3.931578 TCTTCTCTCTTAAGGCAGCAAC 58.068 45.455 1.85 0.00 0.00 4.17
2882 3059 1.281925 ATTGGTGTGCCTAGGGGGAG 61.282 60.000 11.72 0.00 37.23 4.30
2889 3066 2.884980 GCCTAGGGGGAGCGATTCC 61.885 68.421 11.72 0.00 46.00 3.01
2895 3072 1.821332 GGGGAGCGATTCCTTGCTG 60.821 63.158 0.00 0.00 45.98 4.41
2899 3076 1.078143 AGCGATTCCTTGCTGGACC 60.078 57.895 0.00 0.00 46.14 4.46
2904 3081 1.488705 ATTCCTTGCTGGACCGGTGA 61.489 55.000 14.63 0.00 46.14 4.02
2915 3092 0.868406 GACCGGTGAAGTTCTTGCAG 59.132 55.000 14.63 0.00 0.00 4.41
2929 3106 1.798223 CTTGCAGAATCGTTTCGGTGA 59.202 47.619 7.94 0.00 36.93 4.02
2931 3108 1.270094 TGCAGAATCGTTTCGGTGACT 60.270 47.619 7.94 0.00 36.93 3.41
2942 3119 0.174845 TCGGTGACTTAGGGCGAATG 59.825 55.000 0.00 0.00 0.00 2.67
2952 3129 1.378514 GGGCGAATGGGCTTCTTGA 60.379 57.895 0.00 0.00 41.87 3.02
2980 3157 1.901464 GGAGCTCCAAAAACCCGCA 60.901 57.895 28.43 0.00 35.64 5.69
2981 3158 1.285950 GAGCTCCAAAAACCCGCAC 59.714 57.895 0.87 0.00 0.00 5.34
2988 3306 1.151908 AAAAACCCGCACAGGCCTA 59.848 52.632 3.98 0.00 39.21 3.93
2989 3307 0.468400 AAAAACCCGCACAGGCCTAA 60.468 50.000 3.98 0.00 39.21 2.69
3029 3347 4.142600 GGTGGATGTTGTTAGATGAGTTGC 60.143 45.833 0.00 0.00 0.00 4.17
3058 3382 2.949177 TGATGTAGGTGCAGTTGGTT 57.051 45.000 0.00 0.00 0.00 3.67
3070 3396 3.187637 TGCAGTTGGTTCGTTTATAGCAC 59.812 43.478 0.00 0.00 0.00 4.40
3110 3445 1.350193 CCTGTGCTGTACAAGTAGCG 58.650 55.000 0.00 0.00 42.74 4.26
3111 3446 1.350193 CTGTGCTGTACAAGTAGCGG 58.650 55.000 0.00 0.00 42.74 5.52
3197 3532 3.205338 CCAAGTGTGTGTGAGTGATTGA 58.795 45.455 0.00 0.00 0.00 2.57
3202 3537 3.063452 GTGTGTGTGAGTGATTGAAACGT 59.937 43.478 0.00 0.00 0.00 3.99
3240 3575 9.429359 TCAGTTGTGAAATTTATTGTTGTGTTT 57.571 25.926 0.00 0.00 0.00 2.83
3242 3577 8.174422 AGTTGTGAAATTTATTGTTGTGTTTGC 58.826 29.630 0.00 0.00 0.00 3.68
3247 3582 2.672188 TATTGTTGTGTTTGCGGACG 57.328 45.000 0.00 0.00 0.00 4.79
3299 3634 2.500509 TCCAAACACGCATTTTGTCC 57.499 45.000 4.00 0.00 32.92 4.02
3343 3684 1.697982 AGAACCAACTCCAGGGTACAC 59.302 52.381 0.00 0.00 36.05 2.90
3369 3710 2.158813 ACTCAAGGAAGCAAAGAACCGA 60.159 45.455 0.00 0.00 0.00 4.69
3381 3738 2.770164 AGAACCGAACAAGGATCAGG 57.230 50.000 0.00 0.00 35.77 3.86
3446 3867 3.947196 TGCAGGCAAGTTTATACATCCAG 59.053 43.478 0.00 0.00 0.00 3.86
3502 3924 8.807581 CAAAATTTCTGAAGAACCAACAACTAC 58.192 33.333 0.00 0.00 33.13 2.73
3522 3944 8.559536 CAACTACACACATATCTCACAGTTTTT 58.440 33.333 0.00 0.00 0.00 1.94
3551 3973 0.756903 AGCCAACTCCACACGTTAGT 59.243 50.000 0.00 0.00 0.00 2.24
3583 4005 8.204583 AGTGGTATATCACTAGCATTGGCTCC 62.205 46.154 17.22 0.00 45.18 4.70
3597 4019 1.750780 GCTCCTAGGTTTGCCAGGC 60.751 63.158 9.08 3.66 34.86 4.85
3643 4065 6.183361 TGCCATCAGATTACATTGTATCTCCA 60.183 38.462 0.00 0.00 0.00 3.86
3647 4069 7.616528 TCAGATTACATTGTATCTCCATCCA 57.383 36.000 0.00 0.00 0.00 3.41
3665 4087 6.042437 TCCATCCATCCCATAATATGAGATCG 59.958 42.308 1.10 0.00 0.00 3.69
3711 4133 8.684386 TGCAAAACGATCTTATATTATGGGAA 57.316 30.769 0.00 0.00 0.00 3.97
3724 4146 9.852784 TTATATTATGGGAAGGAGGAAGTATCA 57.147 33.333 0.00 0.00 0.00 2.15
3727 4149 1.769465 GGGAAGGAGGAAGTATCACCC 59.231 57.143 0.00 0.00 0.00 4.61
3730 4152 2.661176 AGGAGGAAGTATCACCCCAA 57.339 50.000 0.00 0.00 0.00 4.12
3733 4155 2.844348 GGAGGAAGTATCACCCCAAGAA 59.156 50.000 0.00 0.00 0.00 2.52
3736 4158 5.221742 GGAGGAAGTATCACCCCAAGAATAG 60.222 48.000 0.00 0.00 0.00 1.73
3749 4171 8.816894 CACCCCAAGAATAGTATACATCTGTAT 58.183 37.037 5.50 7.88 43.15 2.29
3769 4191 6.743110 TGTATGCATGTTTAACAGCAAGAAA 58.257 32.000 19.76 8.76 36.43 2.52
3770 4192 7.205992 TGTATGCATGTTTAACAGCAAGAAAA 58.794 30.769 19.76 7.17 36.43 2.29
3773 4195 6.047870 TGCATGTTTAACAGCAAGAAAATGT 58.952 32.000 15.78 0.00 32.32 2.71
3774 4196 6.538021 TGCATGTTTAACAGCAAGAAAATGTT 59.462 30.769 15.78 0.00 40.17 2.71
3775 4197 6.847289 GCATGTTTAACAGCAAGAAAATGTTG 59.153 34.615 3.63 0.00 37.69 3.33
3776 4198 7.254387 GCATGTTTAACAGCAAGAAAATGTTGA 60.254 33.333 3.63 0.00 37.69 3.18
3777 4199 8.767085 CATGTTTAACAGCAAGAAAATGTTGAT 58.233 29.630 3.63 0.00 37.69 2.57
3778 4200 8.351495 TGTTTAACAGCAAGAAAATGTTGATC 57.649 30.769 0.00 0.00 37.69 2.92
3786 4208 5.594926 CAAGAAAATGTTGATCCCTATGCC 58.405 41.667 0.00 0.00 0.00 4.40
3792 4214 1.072965 GTTGATCCCTATGCCCCTGAG 59.927 57.143 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.226859 GATCGTGATCGTGCGGGAA 60.227 57.895 0.00 0.00 38.33 3.97
105 106 4.442733 GCGACACTTCAAGCATATCTAGAC 59.557 45.833 0.00 0.00 0.00 2.59
124 125 3.756069 ACATAGAACTTAGACGTGCGAC 58.244 45.455 0.00 0.00 0.00 5.19
157 158 5.997385 ACAAAATTCCGTATGAATATCCGC 58.003 37.500 0.00 0.00 42.97 5.54
198 208 9.710979 TCTAAAACGTCTTACAAAAATGAACAG 57.289 29.630 0.00 0.00 0.00 3.16
277 289 4.542525 ACATACCCCCTCTGACCAATTTTA 59.457 41.667 0.00 0.00 0.00 1.52
282 294 2.041081 CAAACATACCCCCTCTGACCAA 59.959 50.000 0.00 0.00 0.00 3.67
285 297 3.933861 ATCAAACATACCCCCTCTGAC 57.066 47.619 0.00 0.00 0.00 3.51
286 298 3.849574 TCAATCAAACATACCCCCTCTGA 59.150 43.478 0.00 0.00 0.00 3.27
289 301 4.200092 GACTCAATCAAACATACCCCCTC 58.800 47.826 0.00 0.00 0.00 4.30
292 304 6.530019 AAATGACTCAATCAAACATACCCC 57.470 37.500 0.00 0.00 41.93 4.95
294 306 9.941664 CATCTAAATGACTCAATCAAACATACC 57.058 33.333 0.00 0.00 41.93 2.73
431 444 7.106439 TCCTCTCTCTGCTTTAATGTTCTAG 57.894 40.000 0.00 0.00 0.00 2.43
434 447 7.622893 AATTCCTCTCTCTGCTTTAATGTTC 57.377 36.000 0.00 0.00 0.00 3.18
436 449 6.314896 CGAAATTCCTCTCTCTGCTTTAATGT 59.685 38.462 0.00 0.00 0.00 2.71
437 450 6.238320 CCGAAATTCCTCTCTCTGCTTTAATG 60.238 42.308 0.00 0.00 0.00 1.90
438 451 5.819901 CCGAAATTCCTCTCTCTGCTTTAAT 59.180 40.000 0.00 0.00 0.00 1.40
456 473 0.879090 GCCGAAAGTGTTCCCGAAAT 59.121 50.000 0.00 0.00 0.00 2.17
551 568 5.835113 TTCAGTCTTGACAAAGAAAAGGG 57.165 39.130 3.49 0.00 44.01 3.95
626 673 1.338973 GGTGGACTTTTCCGGTTTTCC 59.661 52.381 0.00 2.31 46.37 3.13
627 674 1.338973 GGGTGGACTTTTCCGGTTTTC 59.661 52.381 0.00 0.00 46.37 2.29
628 675 1.342175 TGGGTGGACTTTTCCGGTTTT 60.342 47.619 0.00 0.00 46.37 2.43
629 676 0.259356 TGGGTGGACTTTTCCGGTTT 59.741 50.000 0.00 0.00 46.37 3.27
630 677 0.466739 GTGGGTGGACTTTTCCGGTT 60.467 55.000 0.00 0.00 46.37 4.44
631 678 1.149854 GTGGGTGGACTTTTCCGGT 59.850 57.895 0.00 0.00 46.37 5.28
632 679 1.602605 GGTGGGTGGACTTTTCCGG 60.603 63.158 0.00 0.00 46.37 5.14
633 680 1.149627 TGGTGGGTGGACTTTTCCG 59.850 57.895 0.00 0.00 46.37 4.30
815 864 0.827507 GGGTTGGAAGCAGAGGCAAA 60.828 55.000 0.00 0.00 44.61 3.68
848 897 1.902938 AGAAGCAAAACAGAGGAGGC 58.097 50.000 0.00 0.00 0.00 4.70
880 929 3.810941 TGTAAACTCAATTTTCGGCGTCT 59.189 39.130 6.85 0.00 0.00 4.18
881 930 3.904234 GTGTAAACTCAATTTTCGGCGTC 59.096 43.478 6.85 0.00 0.00 5.19
883 932 3.879427 TGTGTAAACTCAATTTTCGGCG 58.121 40.909 0.00 0.00 0.00 6.46
885 934 5.460646 AGCATGTGTAAACTCAATTTTCGG 58.539 37.500 0.00 0.00 0.00 4.30
886 935 7.269084 CAGTAGCATGTGTAAACTCAATTTTCG 59.731 37.037 0.00 0.00 0.00 3.46
887 936 8.076178 ACAGTAGCATGTGTAAACTCAATTTTC 58.924 33.333 0.00 0.00 30.46 2.29
949 1039 4.841422 ACATCAGAGAAACAAGAGGATGG 58.159 43.478 0.00 0.00 36.02 3.51
950 1040 5.350914 GTGACATCAGAGAAACAAGAGGATG 59.649 44.000 0.00 0.00 37.33 3.51
999 1096 2.615912 GCTTGTCAGATAGTTGCCCATC 59.384 50.000 0.00 0.00 0.00 3.51
1093 1190 6.710744 TCTGGAAGGTCTTGAAGTTTAATGTC 59.289 38.462 0.00 0.00 0.00 3.06
1362 1466 2.892334 CTGTTTCACCCCGTGCGTG 61.892 63.158 0.00 0.00 32.98 5.34
1368 1472 2.568090 GCATGCTGTTTCACCCCG 59.432 61.111 11.37 0.00 0.00 5.73
1448 1564 8.932791 TCTCAAACATAAATTTAACCTCGAGAC 58.067 33.333 15.71 0.00 0.00 3.36
1525 1641 3.821033 TCAAAAGCTAGCTTCTTTGTCCC 59.179 43.478 29.42 0.00 34.84 4.46
1577 1693 2.481449 GGGAACGTGTAGTGATAGCCAG 60.481 54.545 0.00 0.00 0.00 4.85
1824 1949 1.660575 CGACAACGGCTGAACGACT 60.661 57.895 0.00 0.00 37.61 4.18
1875 2000 5.104900 AGCGTGGAACTCTATCTTGGTTATT 60.105 40.000 0.00 0.00 24.30 1.40
2313 2445 7.657761 GGGAATATTACTCACATGTACTTCCAG 59.342 40.741 0.00 0.00 32.77 3.86
2396 2547 5.107143 ACAAAATACCGTTCAAAATGCATGC 60.107 36.000 11.82 11.82 0.00 4.06
2410 2561 8.125728 AGAAACAATGTTTGAACAAAATACCG 57.874 30.769 16.78 0.00 43.03 4.02
2418 2569 5.357878 AGCAGAGAGAAACAATGTTTGAACA 59.642 36.000 16.78 0.00 44.06 3.18
2534 2688 0.465705 TTCACATGGCGGGATCTCTC 59.534 55.000 0.00 0.00 0.00 3.20
2547 2701 4.758688 TCTTCAGATGCGTGTATTCACAT 58.241 39.130 3.25 0.00 44.02 3.21
2572 2726 1.613925 TCTGAAACCTGAGACACGGAG 59.386 52.381 0.00 0.00 0.00 4.63
2583 2737 1.229209 TCTCGCCCCTCTGAAACCT 60.229 57.895 0.00 0.00 0.00 3.50
2773 2927 1.268079 GAGAAGAAGCTTTGCACCCAC 59.732 52.381 0.00 0.00 0.00 4.61
2774 2928 1.143684 AGAGAAGAAGCTTTGCACCCA 59.856 47.619 0.00 0.00 0.00 4.51
2788 2942 3.668447 TGTTGCTGCCTTAAGAGAGAAG 58.332 45.455 3.36 0.00 0.00 2.85
2794 2948 3.701205 TGATCTGTTGCTGCCTTAAGA 57.299 42.857 3.36 0.00 0.00 2.10
2806 2960 0.400213 TTCGCCCCTGTTGATCTGTT 59.600 50.000 0.00 0.00 0.00 3.16
2808 2962 1.372087 GCTTCGCCCCTGTTGATCTG 61.372 60.000 0.00 0.00 0.00 2.90
2889 3066 0.535102 AACTTCACCGGTCCAGCAAG 60.535 55.000 2.59 4.66 0.00 4.01
2895 3072 0.534203 TGCAAGAACTTCACCGGTCC 60.534 55.000 2.59 0.00 0.00 4.46
2915 3092 2.928116 CCCTAAGTCACCGAAACGATTC 59.072 50.000 0.00 0.00 0.00 2.52
2929 3106 0.107165 GAAGCCCATTCGCCCTAAGT 60.107 55.000 0.00 0.00 0.00 2.24
2931 3108 0.623723 AAGAAGCCCATTCGCCCTAA 59.376 50.000 0.00 0.00 43.16 2.69
2942 3119 1.676967 CCAGCCTGTCAAGAAGCCC 60.677 63.158 0.00 0.00 0.00 5.19
2973 3150 0.251608 AAATTAGGCCTGTGCGGGTT 60.252 50.000 17.99 0.00 38.85 4.11
2974 3151 0.679960 GAAATTAGGCCTGTGCGGGT 60.680 55.000 17.99 0.00 38.85 5.28
2975 3152 1.714899 CGAAATTAGGCCTGTGCGGG 61.715 60.000 17.99 0.00 38.85 6.13
2976 3153 1.714899 CCGAAATTAGGCCTGTGCGG 61.715 60.000 17.99 16.57 38.85 5.69
2980 3157 2.741878 CGATGACCGAAATTAGGCCTGT 60.742 50.000 17.99 1.46 41.76 4.00
2981 3158 1.867233 CGATGACCGAAATTAGGCCTG 59.133 52.381 17.99 0.00 41.76 4.85
3029 3347 7.167924 ACTGCACCTACATCATCATATAGAG 57.832 40.000 0.00 0.00 0.00 2.43
3070 3396 4.628333 AGGGACACAATACAAACGTTATCG 59.372 41.667 0.00 0.00 43.34 2.92
3110 3445 8.974408 GGTGTACAAAAGAACAACATTAAATCC 58.026 33.333 0.00 0.00 33.40 3.01
3111 3446 9.744468 AGGTGTACAAAAGAACAACATTAAATC 57.256 29.630 0.00 0.00 35.71 2.17
3197 3532 9.210329 TCACAACTGATGTATATTAACACGTTT 57.790 29.630 0.00 0.00 41.46 3.60
3226 3561 3.064958 TCGTCCGCAAACACAACAATAAA 59.935 39.130 0.00 0.00 0.00 1.40
3227 3562 2.612672 TCGTCCGCAAACACAACAATAA 59.387 40.909 0.00 0.00 0.00 1.40
3228 3563 2.210961 TCGTCCGCAAACACAACAATA 58.789 42.857 0.00 0.00 0.00 1.90
3230 3565 0.803117 TTCGTCCGCAAACACAACAA 59.197 45.000 0.00 0.00 0.00 2.83
3231 3566 1.018148 ATTCGTCCGCAAACACAACA 58.982 45.000 0.00 0.00 0.00 3.33
3240 3575 1.872388 TTCTCAACAATTCGTCCGCA 58.128 45.000 0.00 0.00 0.00 5.69
3265 3600 6.858993 GCGTGTTTGGAATACAACAAATCTTA 59.141 34.615 0.00 0.00 39.19 2.10
3288 3623 3.536158 TTTCTTCTCGGACAAAATGCG 57.464 42.857 0.00 0.00 44.87 4.73
3343 3684 5.291858 GGTTCTTTGCTTCCTTGAGTTTTTG 59.708 40.000 0.00 0.00 0.00 2.44
3369 3710 3.636764 GTCAAAACCACCTGATCCTTGTT 59.363 43.478 0.00 0.00 0.00 2.83
3502 3924 7.747799 GTGATCAAAAACTGTGAGATATGTGTG 59.252 37.037 0.00 0.00 0.00 3.82
3522 3944 0.036732 GGAGTTGGCTGTGGTGATCA 59.963 55.000 0.00 0.00 0.00 2.92
3551 3973 5.600898 TGCTAGTGATATACCACTGCCTTTA 59.399 40.000 10.25 0.00 46.00 1.85
3583 4005 1.589716 GCACAGCCTGGCAAACCTAG 61.590 60.000 22.65 4.30 36.63 3.02
3591 4013 2.541547 TAGTGGATGCACAGCCTGGC 62.542 60.000 20.21 11.65 37.85 4.85
3618 4040 6.183361 TGGAGATACAATGTAATCTGATGGCA 60.183 38.462 0.00 0.00 32.60 4.92
3711 4133 2.045885 TCTTGGGGTGATACTTCCTCCT 59.954 50.000 0.00 0.00 0.00 3.69
3724 4146 8.816894 CATACAGATGTATACTATTCTTGGGGT 58.183 37.037 5.21 2.03 39.06 4.95
3727 4149 9.881649 ATGCATACAGATGTATACTATTCTTGG 57.118 33.333 0.00 0.00 39.06 3.61
3749 4171 6.047870 ACATTTTCTTGCTGTTAAACATGCA 58.952 32.000 0.00 0.00 33.01 3.96
3755 4177 6.928492 GGGATCAACATTTTCTTGCTGTTAAA 59.072 34.615 0.00 0.00 32.14 1.52
3769 4191 2.146998 AGGGGCATAGGGATCAACATT 58.853 47.619 0.00 0.00 0.00 2.71
3770 4192 1.426598 CAGGGGCATAGGGATCAACAT 59.573 52.381 0.00 0.00 0.00 2.71
3773 4195 1.438469 CTCAGGGGCATAGGGATCAA 58.562 55.000 0.00 0.00 0.00 2.57
3774 4196 1.130054 GCTCAGGGGCATAGGGATCA 61.130 60.000 0.00 0.00 0.00 2.92
3775 4197 1.682257 GCTCAGGGGCATAGGGATC 59.318 63.158 0.00 0.00 0.00 3.36
3776 4198 2.219875 CGCTCAGGGGCATAGGGAT 61.220 63.158 0.00 0.00 0.00 3.85
3777 4199 2.844362 CGCTCAGGGGCATAGGGA 60.844 66.667 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.