Multiple sequence alignment - TraesCS2D01G168200

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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 TraesCS2D01G168200 chr2D 100.000 4810 0 0 1 4810 112098325 112103134 0.000000e+00 8883.0
1 TraesCS2D01G168200 chr2D 85.532 1645 164 43 628 2225 111588299 111589916 0.000000e+00 1652.0
2 TraesCS2D01G168200 chr2D 89.116 1222 77 21 1781 2984 112180287 112179104 0.000000e+00 1469.0
3 TraesCS2D01G168200 chr2D 90.807 979 65 8 726 1686 112181350 112180379 0.000000e+00 1286.0
4 TraesCS2D01G168200 chr2D 79.050 1327 164 74 2935 4205 112178883 112177615 0.000000e+00 806.0
5 TraesCS2D01G168200 chr2D 83.062 738 87 23 2277 2984 111589931 111590660 1.890000e-178 636.0
6 TraesCS2D01G168200 chr2D 84.844 640 59 26 3442 4072 111591329 111591939 1.140000e-170 610.0
7 TraesCS2D01G168200 chr2D 90.795 239 18 1 1 235 112183584 112183346 2.790000e-82 316.0
8 TraesCS2D01G168200 chr2D 81.356 413 45 18 3000 3397 111590932 111591327 1.680000e-79 307.0
9 TraesCS2D01G168200 chr2D 90.805 174 11 1 4340 4513 111592354 111592522 1.350000e-55 228.0
10 TraesCS2D01G168200 chr2D 84.862 218 31 2 593 810 112187999 112187784 8.110000e-53 219.0
11 TraesCS2D01G168200 chr2D 83.636 220 33 2 593 810 112186881 112186663 2.270000e-48 204.0
12 TraesCS2D01G168200 chr2D 88.971 136 12 2 4060 4195 111591956 111592088 1.070000e-36 165.0
13 TraesCS2D01G168200 chr2D 92.405 79 3 1 252 327 112181846 112181768 5.090000e-20 110.0
14 TraesCS2D01G168200 chr2A 91.065 1813 66 37 246 1987 112744065 112745852 0.000000e+00 2362.0
15 TraesCS2D01G168200 chr2A 86.776 2019 174 47 628 2577 111921568 111923562 0.000000e+00 2163.0
16 TraesCS2D01G168200 chr2A 88.514 1454 106 22 593 1987 113312380 113310929 0.000000e+00 1703.0
17 TraesCS2D01G168200 chr2A 93.013 873 31 13 2051 2919 113310830 113309984 0.000000e+00 1247.0
18 TraesCS2D01G168200 chr2A 90.929 893 31 24 2051 2919 112745951 112746817 0.000000e+00 1155.0
19 TraesCS2D01G168200 chr2A 82.120 1236 134 58 3000 4195 111924197 111925385 0.000000e+00 977.0
20 TraesCS2D01G168200 chr2A 87.879 627 22 19 4205 4807 112748171 112748767 0.000000e+00 688.0
21 TraesCS2D01G168200 chr2A 92.774 429 25 3 2947 3373 113309983 113309559 2.460000e-172 616.0
22 TraesCS2D01G168200 chr2A 98.214 336 6 0 3745 4080 112747521 112747856 5.360000e-164 588.0
23 TraesCS2D01G168200 chr2A 90.868 438 31 6 2944 3377 112746815 112747247 3.230000e-161 579.0
24 TraesCS2D01G168200 chr2A 87.473 455 40 8 3752 4205 113309452 113309014 4.290000e-140 508.0
25 TraesCS2D01G168200 chr2A 90.202 347 33 1 2638 2983 111923579 111923925 7.340000e-123 451.0
26 TraesCS2D01G168200 chr2A 94.776 268 14 0 1 268 112743789 112744056 7.450000e-113 418.0
27 TraesCS2D01G168200 chr2A 83.203 256 38 3 324 575 640704748 640704494 3.740000e-56 230.0
28 TraesCS2D01G168200 chr2A 84.091 220 32 2 593 810 113319363 113319145 4.880000e-50 209.0
29 TraesCS2D01G168200 chr2A 91.270 126 4 3 4078 4196 112747959 112748084 1.070000e-36 165.0
30 TraesCS2D01G168200 chr2A 84.884 172 6 10 3442 3607 112747275 112747432 6.450000e-34 156.0
31 TraesCS2D01G168200 chr2A 92.405 79 3 2 252 327 113312488 113312410 5.090000e-20 110.0
32 TraesCS2D01G168200 chr2A 96.610 59 2 0 4342 4400 111925514 111925572 1.100000e-16 99.0
33 TraesCS2D01G168200 chr2A 86.842 76 4 2 4448 4523 111925575 111925644 3.990000e-11 80.5
34 TraesCS2D01G168200 chr2B 95.000 1040 31 8 723 1741 162007420 162008459 0.000000e+00 1613.0
35 TraesCS2D01G168200 chr2B 88.649 1295 70 27 1769 3032 162008548 162009796 0.000000e+00 1506.0
36 TraesCS2D01G168200 chr2B 91.967 1083 18 19 3745 4810 162010684 162011714 0.000000e+00 1454.0
37 TraesCS2D01G168200 chr2B 85.610 1237 107 32 593 1820 161722022 161723196 0.000000e+00 1232.0
38 TraesCS2D01G168200 chr2B 89.875 958 77 13 742 1686 162449043 162448093 0.000000e+00 1214.0
39 TraesCS2D01G168200 chr2B 89.834 905 55 11 2085 2984 162447668 162446796 0.000000e+00 1127.0
40 TraesCS2D01G168200 chr2B 85.889 1063 121 20 1935 2984 161723299 161724345 0.000000e+00 1105.0
41 TraesCS2D01G168200 chr2B 79.983 1184 118 62 3068 4205 162446481 162445371 0.000000e+00 763.0
42 TraesCS2D01G168200 chr2B 84.052 765 74 28 3442 4195 161725016 161725743 0.000000e+00 693.0
43 TraesCS2D01G168200 chr2B 89.049 347 21 6 1 331 162006797 162007142 9.630000e-112 414.0
44 TraesCS2D01G168200 chr2B 81.598 413 46 18 3000 3397 161724617 161725014 1.000000e-81 315.0
45 TraesCS2D01G168200 chr2B 90.678 236 19 3 1 235 162479373 162479140 1.300000e-80 311.0
46 TraesCS2D01G168200 chr2B 87.288 236 13 7 1781 1999 162447995 162447760 2.220000e-63 254.0
47 TraesCS2D01G168200 chr2B 87.442 215 26 1 594 808 162496509 162496296 3.720000e-61 246.0
48 TraesCS2D01G168200 chr2B 83.203 256 38 4 325 576 413085070 413084816 3.740000e-56 230.0
49 TraesCS2D01G168200 chr2B 85.321 218 31 1 593 810 162482976 162482760 1.740000e-54 224.0
50 TraesCS2D01G168200 chr2B 88.235 153 16 2 593 744 162449304 162449153 1.060000e-41 182.0
51 TraesCS2D01G168200 chr2B 88.158 152 7 4 4372 4513 161725909 161726059 2.300000e-38 171.0
52 TraesCS2D01G168200 chr2B 84.884 172 8 7 3442 3607 162010272 162010431 1.790000e-34 158.0
53 TraesCS2D01G168200 chr2B 87.963 108 7 2 223 327 162449437 162449333 6.540000e-24 122.0
54 TraesCS2D01G168200 chr4A 84.646 254 32 6 326 574 560904121 560903870 3.720000e-61 246.0
55 TraesCS2D01G168200 chr7A 84.314 255 34 5 328 577 206757205 206757458 1.340000e-60 244.0
56 TraesCS2D01G168200 chr7A 83.137 255 38 3 326 576 595822966 595822713 1.350000e-55 228.0
57 TraesCS2D01G168200 chr3B 83.465 254 35 6 326 574 571760210 571760461 3.740000e-56 230.0
58 TraesCS2D01G168200 chr1A 83.137 255 38 4 326 576 533465007 533464754 1.350000e-55 228.0
59 TraesCS2D01G168200 chr1A 83.071 254 36 6 326 574 510345796 510346047 1.740000e-54 224.0
60 TraesCS2D01G168200 chr6A 83.654 104 15 2 1394 1496 535154205 535154103 3.960000e-16 97.1
61 TraesCS2D01G168200 chr3A 100.000 42 0 0 4339 4380 23177335 23177294 1.440000e-10 78.7


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 TraesCS2D01G168200 chr2D 112098325 112103134 4809 False 8883.000000 8883 100.000000 1 4810 1 chr2D.!!$F1 4809
1 TraesCS2D01G168200 chr2D 112177615 112187999 10384 True 630.000000 1469 87.238714 1 4205 7 chr2D.!!$R1 4204
2 TraesCS2D01G168200 chr2D 111588299 111592522 4223 False 599.666667 1652 85.761667 628 4513 6 chr2D.!!$F2 3885
3 TraesCS2D01G168200 chr2A 113309014 113312488 3474 True 836.800000 1703 90.835800 252 4205 5 chr2A.!!$R3 3953
4 TraesCS2D01G168200 chr2A 112743789 112748767 4978 False 763.875000 2362 91.235625 1 4807 8 chr2A.!!$F2 4806
5 TraesCS2D01G168200 chr2A 111921568 111925644 4076 False 754.100000 2163 88.510000 628 4523 5 chr2A.!!$F1 3895
6 TraesCS2D01G168200 chr2B 162006797 162011714 4917 False 1029.000000 1613 89.909800 1 4810 5 chr2B.!!$F2 4809
7 TraesCS2D01G168200 chr2B 161722022 161726059 4037 False 703.200000 1232 85.061400 593 4513 5 chr2B.!!$F1 3920
8 TraesCS2D01G168200 chr2B 162445371 162449437 4066 True 610.333333 1214 87.196333 223 4205 6 chr2B.!!$R3 3982
9 TraesCS2D01G168200 chr2B 162479140 162482976 3836 True 267.500000 311 87.999500 1 810 2 chr2B.!!$R4 809


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
422 6334 0.964358 AGCCTGCTTCAATGGTGAGC 60.964 55.000 0.00 0.0 34.49 4.26 F
1692 10531 0.036164 ACAAGGTACATTCCAGCGCA 59.964 50.000 11.47 0.0 0.00 6.09 F
2025 11034 1.007963 TCCCCGGTTACCTCTTCTCAT 59.992 52.381 0.00 0.0 0.00 2.90 F
3351 13025 0.461961 AGACAAGCGCATCCTACTCC 59.538 55.000 11.47 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 10976 0.110486 GTCCCTGCCTTTCTGTGGAA 59.890 55.0 0.00 0.0 0.00 3.53 R
2860 11992 0.514691 GCAAGAACTTGAGAGCGTGG 59.485 55.0 17.19 0.0 42.93 4.94 R
3781 13673 0.512952 CTTTGTCCCGTTGCTCTTCG 59.487 55.0 0.00 0.0 0.00 3.79 R
4334 14513 0.180642 TTACGAACTGTTGGCACCCA 59.819 50.0 0.00 0.0 0.00 4.51 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
47 4463 2.578021 ACTTAGGGCATTGAGTGGTCAT 59.422 45.455 0.00 0.00 30.85 3.06
51 4467 4.046286 AGGGCATTGAGTGGTCATTTAA 57.954 40.909 0.00 0.00 30.85 1.52
131 4547 1.945387 ATCAAGGCATACACTCGCAG 58.055 50.000 0.00 0.00 0.00 5.18
134 4550 2.093500 TCAAGGCATACACTCGCAGATT 60.093 45.455 0.00 0.00 33.89 2.40
373 6285 2.611292 GAGGCAGATCCAACAAATCTCG 59.389 50.000 0.00 0.00 37.29 4.04
374 6286 2.237143 AGGCAGATCCAACAAATCTCGA 59.763 45.455 0.00 0.00 37.29 4.04
383 6295 7.557719 AGATCCAACAAATCTCGACCATTAAAT 59.442 33.333 0.00 0.00 0.00 1.40
386 6298 6.095440 CCAACAAATCTCGACCATTAAATCCT 59.905 38.462 0.00 0.00 0.00 3.24
400 6312 9.675464 ACCATTAAATCCTTGTAATCTAACGAA 57.325 29.630 0.00 0.00 0.00 3.85
422 6334 0.964358 AGCCTGCTTCAATGGTGAGC 60.964 55.000 0.00 0.00 34.49 4.26
423 6335 1.941999 GCCTGCTTCAATGGTGAGCC 61.942 60.000 0.00 0.00 34.49 4.70
439 6351 1.398390 GAGCCCTCAACACATTTAGCG 59.602 52.381 0.00 0.00 0.00 4.26
525 6437 8.922931 TTCATACCTAACATATGCATGTCATT 57.077 30.769 10.16 2.08 44.83 2.57
1149 8827 1.070445 CATGGATCTCGCCACCTCC 59.930 63.158 0.00 0.00 41.56 4.30
1362 10180 2.125912 CAGGAGAAGCACCCGTCG 60.126 66.667 0.00 0.00 0.00 5.12
1653 10487 1.525077 GCATTTCCCGACCGCCATA 60.525 57.895 0.00 0.00 0.00 2.74
1692 10531 0.036164 ACAAGGTACATTCCAGCGCA 59.964 50.000 11.47 0.00 0.00 6.09
1774 10680 1.039856 TGCTTTCTTGGTTCCTTGCC 58.960 50.000 0.00 0.00 0.00 4.52
1862 10785 1.131826 GCGTGATTTTCACCGTCCG 59.868 57.895 2.26 0.00 44.20 4.79
1932 10855 4.641541 ACGCTATACACACACCAGTACATA 59.358 41.667 0.00 0.00 0.00 2.29
1933 10856 5.301045 ACGCTATACACACACCAGTACATAT 59.699 40.000 0.00 0.00 0.00 1.78
1937 10938 6.724893 ATACACACACCAGTACATATAGCA 57.275 37.500 0.00 0.00 0.00 3.49
1939 10940 5.419542 ACACACACCAGTACATATAGCAAG 58.580 41.667 0.00 0.00 0.00 4.01
1975 10976 2.803030 TCCTCGCAGTAGTACTTCCT 57.197 50.000 0.00 0.00 0.00 3.36
2025 11034 1.007963 TCCCCGGTTACCTCTTCTCAT 59.992 52.381 0.00 0.00 0.00 2.90
2028 11037 3.453353 CCCCGGTTACCTCTTCTCATTTA 59.547 47.826 0.00 0.00 0.00 1.40
2034 11043 6.750963 CGGTTACCTCTTCTCATTTACAGTAC 59.249 42.308 0.00 0.00 0.00 2.73
2109 11165 3.242413 GCAATATGTACGCAGGTGTTCAG 60.242 47.826 0.00 0.00 0.00 3.02
2266 11322 8.328758 TCTTGACTTATTCTCTCTCTCTCTCTT 58.671 37.037 0.00 0.00 0.00 2.85
2304 11385 3.222603 GAAAGAGACTTTTCCTTGGCCA 58.777 45.455 0.00 0.00 32.22 5.36
2312 11397 7.016563 AGAGACTTTTCCTTGGCCATAATTTTT 59.983 33.333 6.09 0.00 0.00 1.94
2589 11719 6.757237 TGCTACTAGTACACCTAGCTACTAG 58.243 44.000 14.75 14.75 46.10 2.57
2636 11768 2.731976 GTGTGGCTCGGATCGATTAATC 59.268 50.000 5.30 5.30 34.61 1.75
2645 11777 2.481952 GGATCGATTAATCTGCAGGTGC 59.518 50.000 15.13 0.00 42.50 5.01
2716 11848 3.381590 AGAACAACAAGTTTTGCCTCTCC 59.618 43.478 0.00 0.00 41.51 3.71
2767 11899 4.459089 GACGCTCTGGGCAGGGAC 62.459 72.222 0.00 0.00 41.91 4.46
2831 11963 1.331399 GGGGAGAAAGGTCCTCGAGG 61.331 65.000 26.32 26.32 36.75 4.63
2860 11992 2.471255 CATCGAGTGGAACAAGGGC 58.529 57.895 0.00 0.00 44.16 5.19
2945 12081 0.946528 ACGGTGGCGGTTTCTTTAAC 59.053 50.000 0.00 0.00 35.94 2.01
3055 12586 5.049474 TGCATGTCTTGTTAGTTACTTGCTG 60.049 40.000 11.72 0.00 41.19 4.41
3079 12610 9.722056 CTGCATAAATATTCACACTAGGTTTTC 57.278 33.333 0.00 0.00 0.00 2.29
3085 12618 4.345859 TTCACACTAGGTTTTCGGATGT 57.654 40.909 0.00 0.00 0.00 3.06
3086 12619 4.345859 TCACACTAGGTTTTCGGATGTT 57.654 40.909 0.00 0.00 0.00 2.71
3119 12652 1.153568 GGCTATGCAGAGCGTGTCA 60.154 57.895 25.76 0.00 43.83 3.58
3230 12883 0.734253 GCGCGCTATCGATCCAATCT 60.734 55.000 26.67 0.00 38.10 2.40
3351 13025 0.461961 AGACAAGCGCATCCTACTCC 59.538 55.000 11.47 0.00 0.00 3.85
3450 13147 5.388786 CGTATACAGTGATGCATGCATGTAC 60.389 44.000 36.73 30.30 36.70 2.90
3550 13249 7.836479 ATACCTAGGTACCTAAAGCAACTAG 57.164 40.000 24.07 9.10 33.01 2.57
3553 13258 6.832900 ACCTAGGTACCTAAAGCAACTAGTAG 59.167 42.308 22.00 7.69 0.00 2.57
3554 13259 6.832900 CCTAGGTACCTAAAGCAACTAGTAGT 59.167 42.308 22.00 0.00 0.00 2.73
3556 13261 7.637631 AGGTACCTAAAGCAACTAGTAGTAC 57.362 40.000 14.41 0.00 0.00 2.73
3557 13262 6.605194 AGGTACCTAAAGCAACTAGTAGTACC 59.395 42.308 14.41 7.30 34.01 3.34
3558 13263 5.573337 ACCTAAAGCAACTAGTAGTACCG 57.427 43.478 2.50 0.00 0.00 4.02
3559 13264 5.012893 ACCTAAAGCAACTAGTAGTACCGT 58.987 41.667 2.50 0.00 0.00 4.83
3560 13265 5.105997 ACCTAAAGCAACTAGTAGTACCGTG 60.106 44.000 2.50 0.00 0.00 4.94
3607 13312 1.134280 AGCTAGCAGTTAGGTGCATGG 60.134 52.381 18.83 0.00 46.60 3.66
3617 13322 5.871524 CAGTTAGGTGCATGGCATATACTAG 59.128 44.000 0.00 0.00 41.91 2.57
3618 13323 5.544176 AGTTAGGTGCATGGCATATACTAGT 59.456 40.000 0.00 0.00 41.91 2.57
3641 13346 1.748500 GCTCTTGAGCTGCTTCCCC 60.749 63.158 14.65 0.00 0.00 4.81
3665 13370 8.462016 CCCATAAAGTTGATTGTTAGGAGAAAG 58.538 37.037 0.00 0.00 0.00 2.62
3688 13393 5.414454 AGAAAGCAATGAAATGTTAGGCGTA 59.586 36.000 0.00 0.00 0.00 4.42
3691 13396 4.275936 AGCAATGAAATGTTAGGCGTATCC 59.724 41.667 0.00 0.00 0.00 2.59
3707 13412 5.116882 GCGTATCCCTTTTCTTGTAGTCAT 58.883 41.667 0.00 0.00 0.00 3.06
3708 13413 5.006746 GCGTATCCCTTTTCTTGTAGTCATG 59.993 44.000 0.00 0.00 0.00 3.07
3709 13414 5.523916 CGTATCCCTTTTCTTGTAGTCATGG 59.476 44.000 0.00 0.00 0.00 3.66
3711 13416 3.330701 TCCCTTTTCTTGTAGTCATGGCT 59.669 43.478 4.63 4.63 0.00 4.75
3713 13418 5.013704 TCCCTTTTCTTGTAGTCATGGCTTA 59.986 40.000 4.49 0.00 0.00 3.09
3714 13419 5.710099 CCCTTTTCTTGTAGTCATGGCTTAA 59.290 40.000 4.49 0.44 0.00 1.85
3718 13586 9.346725 CTTTTCTTGTAGTCATGGCTTAATTTC 57.653 33.333 4.49 0.00 0.00 2.17
4196 14286 6.393171 TGATGTGATCTCTGTTGACAAGTAG 58.607 40.000 0.00 0.00 0.00 2.57
4197 14287 4.560128 TGTGATCTCTGTTGACAAGTAGC 58.440 43.478 0.00 0.00 0.00 3.58
4198 14288 4.281941 TGTGATCTCTGTTGACAAGTAGCT 59.718 41.667 0.00 0.00 0.00 3.32
4199 14289 5.476945 TGTGATCTCTGTTGACAAGTAGCTA 59.523 40.000 0.00 0.00 0.00 3.32
4200 14290 6.153510 TGTGATCTCTGTTGACAAGTAGCTAT 59.846 38.462 0.00 0.00 0.00 2.97
4202 14292 8.191446 GTGATCTCTGTTGACAAGTAGCTATAA 58.809 37.037 0.00 0.00 0.00 0.98
4203 14293 8.409371 TGATCTCTGTTGACAAGTAGCTATAAG 58.591 37.037 0.00 0.00 0.00 1.73
4290 14469 8.792633 CAATCAAGGGAGAACTTAAACAACATA 58.207 33.333 0.00 0.00 0.00 2.29
4291 14470 8.934023 ATCAAGGGAGAACTTAAACAACATAA 57.066 30.769 0.00 0.00 0.00 1.90
4303 14482 5.484173 AAACAACATAACATGCGATCGAT 57.516 34.783 21.57 0.00 0.00 3.59
4599 14819 3.575805 GATCCAGGAAGAGAGATCTGGT 58.424 50.000 0.00 0.00 45.07 4.00
4681 14905 2.186644 CATGGATGGACGGACGCA 59.813 61.111 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 6115 8.138365 ACTATGCACATTATACCTTTAACGTG 57.862 34.615 0.00 0.00 30.56 4.49
343 6255 4.202567 TGTTGGATCTGCCTCTTTAGGTTT 60.203 41.667 0.00 0.00 45.64 3.27
344 6256 3.330701 TGTTGGATCTGCCTCTTTAGGTT 59.669 43.478 0.00 0.00 45.64 3.50
346 6258 3.634397 TGTTGGATCTGCCTCTTTAGG 57.366 47.619 0.00 0.00 46.76 2.69
347 6259 5.884792 AGATTTGTTGGATCTGCCTCTTTAG 59.115 40.000 0.00 0.00 37.63 1.85
350 6262 4.268359 GAGATTTGTTGGATCTGCCTCTT 58.732 43.478 0.00 0.00 34.13 2.85
351 6263 3.681034 CGAGATTTGTTGGATCTGCCTCT 60.681 47.826 0.00 0.00 34.13 3.69
352 6264 2.611292 CGAGATTTGTTGGATCTGCCTC 59.389 50.000 0.00 0.00 34.13 4.70
353 6265 2.237143 TCGAGATTTGTTGGATCTGCCT 59.763 45.455 0.00 0.00 34.13 4.75
354 6266 2.352960 GTCGAGATTTGTTGGATCTGCC 59.647 50.000 0.00 0.00 34.13 4.85
355 6267 2.352960 GGTCGAGATTTGTTGGATCTGC 59.647 50.000 0.00 0.00 34.13 4.26
356 6268 3.599343 TGGTCGAGATTTGTTGGATCTG 58.401 45.455 0.00 0.00 34.13 2.90
357 6269 3.981071 TGGTCGAGATTTGTTGGATCT 57.019 42.857 0.00 0.00 36.60 2.75
358 6270 6.677781 TTAATGGTCGAGATTTGTTGGATC 57.322 37.500 0.00 0.00 0.00 3.36
362 6274 7.088589 AGGATTTAATGGTCGAGATTTGTTG 57.911 36.000 0.00 0.00 0.00 3.33
373 6285 9.321562 TCGTTAGATTACAAGGATTTAATGGTC 57.678 33.333 0.00 0.00 0.00 4.02
374 6286 9.675464 TTCGTTAGATTACAAGGATTTAATGGT 57.325 29.630 0.00 0.00 0.00 3.55
383 6295 5.128827 AGGCTGATTCGTTAGATTACAAGGA 59.871 40.000 0.00 0.00 0.00 3.36
386 6298 4.570772 GCAGGCTGATTCGTTAGATTACAA 59.429 41.667 20.86 0.00 0.00 2.41
400 6312 1.005097 TCACCATTGAAGCAGGCTGAT 59.995 47.619 20.86 9.84 0.00 2.90
404 6316 1.509923 GCTCACCATTGAAGCAGGC 59.490 57.895 0.00 0.00 0.00 4.85
422 6334 1.135689 GCACGCTAAATGTGTTGAGGG 60.136 52.381 0.00 0.00 39.53 4.30
423 6335 1.535028 TGCACGCTAAATGTGTTGAGG 59.465 47.619 0.00 0.00 39.53 3.86
465 6377 5.050490 ACTTATGTGATTAGCGCTCGAATT 58.950 37.500 16.34 0.00 0.00 2.17
472 6384 9.710979 TTATTTGTTTACTTATGTGATTAGCGC 57.289 29.630 0.00 0.00 0.00 5.92
525 6437 9.660180 TGCACGTTGATATTAGGCATTATATTA 57.340 29.630 0.00 0.00 0.00 0.98
557 6469 8.851960 TTGCTGATAACTAGTAAATCTGTACG 57.148 34.615 18.31 0.00 0.00 3.67
563 6475 9.262472 CGTGTTTTTGCTGATAACTAGTAAATC 57.738 33.333 0.00 3.49 31.48 2.17
588 6500 1.640428 AATCGCATGACCACACTACG 58.360 50.000 0.00 0.00 0.00 3.51
1362 10180 1.026718 CCTCGAACCACTCCAATGCC 61.027 60.000 0.00 0.00 0.00 4.40
1599 10433 3.728474 GCATCCCTCATCTGCGTG 58.272 61.111 0.00 0.00 0.00 5.34
1653 10487 1.193323 CTCTGCATCTCCCACTCACT 58.807 55.000 0.00 0.00 0.00 3.41
1692 10531 8.312669 AGAAAGTAGCACTAGAGGATATGTTT 57.687 34.615 0.00 0.00 0.00 2.83
1743 10587 9.267084 GGAACCAAGAAAGCAACAAAATTATAA 57.733 29.630 0.00 0.00 0.00 0.98
1745 10589 7.508687 AGGAACCAAGAAAGCAACAAAATTAT 58.491 30.769 0.00 0.00 0.00 1.28
1774 10680 2.273449 GGAGCCATGGTGTGAGGG 59.727 66.667 14.67 0.00 0.00 4.30
1891 10814 0.737715 GTCTAGGTTCACGCCTGCAG 60.738 60.000 6.78 6.78 39.60 4.41
1932 10855 3.374058 ACGCTCATAAAAACGCTTGCTAT 59.626 39.130 0.00 0.00 0.00 2.97
1933 10856 2.739913 ACGCTCATAAAAACGCTTGCTA 59.260 40.909 0.00 0.00 0.00 3.49
1937 10938 3.252458 AGGAAACGCTCATAAAAACGCTT 59.748 39.130 0.00 0.00 0.00 4.68
1939 10940 3.161306 GAGGAAACGCTCATAAAAACGC 58.839 45.455 0.00 0.00 0.00 4.84
1975 10976 0.110486 GTCCCTGCCTTTCTGTGGAA 59.890 55.000 0.00 0.00 0.00 3.53
2025 11034 4.970472 CGTAGGCAAAACGTACTGTAAA 57.030 40.909 0.00 0.00 37.46 2.01
2109 11165 1.268079 GCTCCTCCAGTTTCACAAAGC 59.732 52.381 0.00 0.00 0.00 3.51
2266 11322 4.395625 TCTTTCACGAGGACTGTAGAGAA 58.604 43.478 0.00 0.00 0.00 2.87
2312 11397 3.436359 GCGACTTAATTACCGGGAACAAA 59.564 43.478 0.00 0.00 0.00 2.83
2589 11719 9.282247 CTTGTCAGCAAATCATTTACATTCTAC 57.718 33.333 0.00 0.00 33.73 2.59
2645 11777 0.737367 TTCGCCGTCAGCTTCTCATG 60.737 55.000 0.00 0.00 40.39 3.07
2767 11899 2.031012 TCCAGCACTGCCTTCACG 59.969 61.111 0.00 0.00 0.00 4.35
2831 11963 3.917760 CTCGATGGAGGGCCGGAC 61.918 72.222 5.05 0.00 36.61 4.79
2860 11992 0.514691 GCAAGAACTTGAGAGCGTGG 59.485 55.000 17.19 0.00 42.93 4.94
2945 12081 3.089784 CTGCCCCGTCGATTTTCG 58.910 61.111 0.00 0.00 42.10 3.46
3055 12586 7.855904 CCGAAAACCTAGTGTGAATATTTATGC 59.144 37.037 0.00 0.00 0.00 3.14
3145 12678 3.052620 ATCCTCGTCTGTGCGGTCG 62.053 63.158 0.00 0.00 0.00 4.79
3230 12883 4.640771 AAGTAAAGGGCTCAGTTCATCA 57.359 40.909 0.00 0.00 0.00 3.07
3351 13025 4.383861 TCAGCAGGCTCACGCAGG 62.384 66.667 0.00 0.00 38.10 4.85
3424 13116 3.123050 TGCATGCATCACTGTATACGTC 58.877 45.455 18.46 0.00 0.00 4.34
3426 13118 3.495753 ACATGCATGCATCACTGTATACG 59.504 43.478 30.07 16.64 33.90 3.06
3427 13119 5.466393 TGTACATGCATGCATCACTGTATAC 59.534 40.000 30.07 20.48 33.90 1.47
3432 13129 3.550030 CCATGTACATGCATGCATCACTG 60.550 47.826 30.07 22.27 43.46 3.66
3439 13136 6.499234 TTATACATCCATGTACATGCATGC 57.501 37.500 31.03 11.82 45.11 4.06
3450 13147 5.220989 GGCATGCAGCTATTATACATCCATG 60.221 44.000 21.36 0.00 44.79 3.66
3527 13226 6.735556 ACTAGTTGCTTTAGGTACCTAGGTA 58.264 40.000 20.79 18.10 0.00 3.08
3528 13227 5.587861 ACTAGTTGCTTTAGGTACCTAGGT 58.412 41.667 20.57 20.57 0.00 3.08
3529 13228 6.832900 ACTACTAGTTGCTTTAGGTACCTAGG 59.167 42.308 20.79 17.74 0.00 3.02
3530 13229 7.878547 ACTACTAGTTGCTTTAGGTACCTAG 57.121 40.000 20.79 13.94 0.00 3.02
3531 13230 7.775561 GGTACTACTAGTTGCTTTAGGTACCTA 59.224 40.741 18.10 18.10 41.66 3.08
3532 13231 6.605194 GGTACTACTAGTTGCTTTAGGTACCT 59.395 42.308 20.57 20.57 41.66 3.08
3533 13232 6.458888 CGGTACTACTAGTTGCTTTAGGTACC 60.459 46.154 2.73 2.73 41.55 3.34
3534 13233 6.094186 ACGGTACTACTAGTTGCTTTAGGTAC 59.906 42.308 0.00 2.90 0.00 3.34
3550 13249 4.082571 AGTGACCACAATACACGGTACTAC 60.083 45.833 2.78 0.00 39.19 2.73
3553 13258 2.991190 CAGTGACCACAATACACGGTAC 59.009 50.000 2.78 0.00 39.19 3.34
3554 13259 2.629137 ACAGTGACCACAATACACGGTA 59.371 45.455 0.00 0.00 39.99 4.02
3556 13261 2.163818 ACAGTGACCACAATACACGG 57.836 50.000 0.00 0.00 39.19 4.94
3557 13262 2.349438 GCAACAGTGACCACAATACACG 60.349 50.000 0.00 0.00 39.19 4.49
3558 13263 2.616376 TGCAACAGTGACCACAATACAC 59.384 45.455 0.00 0.00 35.15 2.90
3559 13264 2.877786 CTGCAACAGTGACCACAATACA 59.122 45.455 0.00 0.00 0.00 2.29
3560 13265 2.878406 ACTGCAACAGTGACCACAATAC 59.122 45.455 0.00 0.00 43.63 1.89
3628 13333 1.635487 ACTTTATGGGGAAGCAGCTCA 59.365 47.619 0.00 0.00 0.00 4.26
3631 13336 2.446435 TCAACTTTATGGGGAAGCAGC 58.554 47.619 0.00 0.00 0.00 5.25
3665 13370 4.485163 ACGCCTAACATTTCATTGCTTTC 58.515 39.130 0.00 0.00 0.00 2.62
3688 13393 4.018050 AGCCATGACTACAAGAAAAGGGAT 60.018 41.667 0.00 0.00 0.00 3.85
3691 13396 6.817765 TTAAGCCATGACTACAAGAAAAGG 57.182 37.500 0.00 0.00 0.00 3.11
3707 13412 5.471797 TCATGTCAAACTCGAAATTAAGCCA 59.528 36.000 0.00 0.00 0.00 4.75
3708 13413 5.938322 TCATGTCAAACTCGAAATTAAGCC 58.062 37.500 0.00 0.00 0.00 4.35
3709 13414 7.851822 TTTCATGTCAAACTCGAAATTAAGC 57.148 32.000 0.00 0.00 0.00 3.09
3781 13673 0.512952 CTTTGTCCCGTTGCTCTTCG 59.487 55.000 0.00 0.00 0.00 3.79
4215 14383 2.499289 AGCAGTGACAACTAGCATAGCT 59.501 45.455 0.00 0.00 44.39 3.32
4290 14469 3.170791 ACAGAGAATCGATCGCATGTT 57.829 42.857 11.09 2.39 42.67 2.71
4291 14470 2.862536 CAACAGAGAATCGATCGCATGT 59.137 45.455 11.09 5.64 42.67 3.21
4330 14509 0.883833 GAACTGTTGGCACCCATCTG 59.116 55.000 0.00 0.00 31.53 2.90
4331 14510 0.606401 CGAACTGTTGGCACCCATCT 60.606 55.000 0.00 0.00 31.53 2.90
4333 14512 0.398696 TACGAACTGTTGGCACCCAT 59.601 50.000 0.00 0.00 31.53 4.00
4334 14513 0.180642 TTACGAACTGTTGGCACCCA 59.819 50.000 0.00 0.00 0.00 4.51
4335 14514 1.310904 TTTACGAACTGTTGGCACCC 58.689 50.000 0.00 0.00 0.00 4.61
4651 14871 0.888619 ATCCATGCATGCATAGCAGC 59.111 50.000 31.73 13.17 46.36 5.25
4652 14872 1.202348 CCATCCATGCATGCATAGCAG 59.798 52.381 31.73 19.29 46.36 4.24
4654 14874 1.201647 GTCCATCCATGCATGCATAGC 59.798 52.381 31.73 8.74 34.91 2.97
4655 14875 1.467342 CGTCCATCCATGCATGCATAG 59.533 52.381 31.73 25.08 34.91 2.23
4656 14876 1.525941 CGTCCATCCATGCATGCATA 58.474 50.000 31.73 18.79 34.91 3.14
4681 14905 1.829533 GCGCCACCCCATTGATGAT 60.830 57.895 0.00 0.00 0.00 2.45
4744 14968 0.184692 AGTAGTAGGAGTACCCGGCC 59.815 60.000 0.00 0.00 40.87 6.13
4745 14969 1.680207 CAAGTAGTAGGAGTACCCGGC 59.320 57.143 0.00 0.00 40.87 6.13
4746 14970 2.092212 TCCAAGTAGTAGGAGTACCCGG 60.092 54.545 0.00 0.00 40.87 5.73
4747 14971 3.287867 TCCAAGTAGTAGGAGTACCCG 57.712 52.381 0.00 0.00 40.87 5.28



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

AutoCloner maintained by Alex Coulton.