Multiple sequence alignment - TraesCS1A01G065000

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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 TraesCS1A01G065000 chr1A 100.000 4146 0 0 1 4146 47212960 47208815 0.000000e+00 7657.0
1 TraesCS1A01G065000 chr1A 81.548 1111 196 8 1312 2417 392529019 392527913 0.000000e+00 907.0
2 TraesCS1A01G065000 chr1A 80.745 1101 194 16 1312 2401 47825961 47824868 0.000000e+00 843.0
3 TraesCS1A01G065000 chr1A 83.501 497 65 10 2422 2905 47824805 47824313 8.180000e-122 448.0
4 TraesCS1A01G065000 chr1A 78.838 723 109 18 621 1306 392529811 392529096 8.180000e-122 448.0
5 TraesCS1A01G065000 chr1A 77.792 770 128 19 574 1306 47826801 47826038 6.370000e-118 435.0
6 TraesCS1A01G065000 chr1A 82.213 461 75 3 2422 2875 392527866 392527406 1.400000e-104 390.0
7 TraesCS1A01G065000 chr1A 74.566 346 59 16 3070 3406 47824188 47823863 1.560000e-24 124.0
8 TraesCS1A01G065000 chr1D 96.449 2957 70 12 1 2936 47331037 47328095 0.000000e+00 4846.0
9 TraesCS1A01G065000 chr1D 95.788 1092 40 5 3060 4146 47328096 47327006 0.000000e+00 1757.0
10 TraesCS1A01G065000 chr1D 81.818 1111 193 8 1312 2417 312972685 312971579 0.000000e+00 924.0
11 TraesCS1A01G065000 chr1D 81.256 1099 192 12 1312 2401 48023444 48022351 0.000000e+00 876.0
12 TraesCS1A01G065000 chr1D 83.702 497 64 9 2422 2905 48022288 48021796 1.760000e-123 453.0
13 TraesCS1A01G065000 chr1D 78.611 720 116 12 621 1306 312973477 312972762 3.800000e-120 442.0
14 TraesCS1A01G065000 chr1D 77.676 766 129 18 577 1306 48024280 48023521 2.960000e-116 429.0
15 TraesCS1A01G065000 chr1D 82.646 461 73 3 2422 2875 312971532 312971072 6.460000e-108 401.0
16 TraesCS1A01G065000 chr1D 94.194 155 6 3 2915 3067 162866919 162866766 2.490000e-57 233.0
17 TraesCS1A01G065000 chr1D 92.903 155 8 3 2915 3067 348291754 348291601 5.390000e-54 222.0
18 TraesCS1A01G065000 chr1D 75.145 346 57 16 3070 3406 48021750 48021425 7.230000e-28 135.0
19 TraesCS1A01G065000 chr1B 92.347 1764 75 15 1178 2935 67053886 67052177 0.000000e+00 2455.0
20 TraesCS1A01G065000 chr1B 96.083 1200 19 10 1 1179 67055239 67054047 0.000000e+00 1930.0
21 TraesCS1A01G065000 chr1B 82.009 1095 188 8 1312 2401 423209134 423208044 0.000000e+00 922.0
22 TraesCS1A01G065000 chr1B 81.488 1102 188 13 1310 2401 67682409 67681314 0.000000e+00 891.0
23 TraesCS1A01G065000 chr1B 78.750 720 115 12 621 1306 423209926 423209211 8.180000e-122 448.0
24 TraesCS1A01G065000 chr1B 77.966 767 125 20 577 1306 67683243 67682484 1.370000e-119 440.0
25 TraesCS1A01G065000 chr1B 82.868 537 37 18 3060 3586 67052179 67051688 8.230000e-117 431.0
26 TraesCS1A01G065000 chr1B 82.969 458 71 3 2422 2872 423207981 423207524 1.390000e-109 407.0
27 TraesCS1A01G065000 chr1B 93.227 251 13 3 3900 4146 67051672 67051422 2.360000e-97 366.0
28 TraesCS1A01G065000 chr1B 75.410 305 50 13 3070 3368 67680713 67680428 1.560000e-24 124.0
29 TraesCS1A01G065000 chr7B 86.084 309 37 5 3 310 493524710 493524407 1.110000e-85 327.0
30 TraesCS1A01G065000 chr5B 86.957 299 29 9 6 302 139410803 139411093 1.110000e-85 327.0
31 TraesCS1A01G065000 chr5B 86.469 303 34 6 1 302 139411650 139411946 4.000000e-85 326.0
32 TraesCS1A01G065000 chr5B 90.769 65 5 1 3747 3810 482988207 482988271 7.380000e-13 86.1
33 TraesCS1A01G065000 chr5B 91.525 59 5 0 3959 4017 482995193 482995135 9.550000e-12 82.4
34 TraesCS1A01G065000 chr7D 85.484 310 37 6 3 310 469841257 469840954 2.410000e-82 316.0
35 TraesCS1A01G065000 chr6A 85.479 303 35 8 3 301 453651691 453651394 1.450000e-79 307.0
36 TraesCS1A01G065000 chr5A 85.099 302 40 3 1 301 520723709 520723412 1.870000e-78 303.0
37 TraesCS1A01G065000 chr3B 84.295 312 42 7 1 309 404620070 404620377 8.710000e-77 298.0
38 TraesCS1A01G065000 chr3B 82.178 101 18 0 2589 2689 564320240 564320340 2.050000e-13 87.9
39 TraesCS1A01G065000 chr2A 97.183 142 2 2 2927 3067 93242235 93242375 5.360000e-59 239.0
40 TraesCS1A01G065000 chr6D 96.479 142 3 2 2927 3067 263622259 263622119 2.490000e-57 233.0
41 TraesCS1A01G065000 chr6D 96.479 142 3 2 2927 3067 299316041 299316181 2.490000e-57 233.0
42 TraesCS1A01G065000 chr4D 96.479 142 3 2 2927 3067 289405244 289405104 2.490000e-57 233.0
43 TraesCS1A01G065000 chr3A 94.194 155 6 3 2915 3067 579571030 579570877 2.490000e-57 233.0
44 TraesCS1A01G065000 chr3A 93.548 155 7 3 2915 3067 230018697 230018544 1.160000e-55 228.0
45 TraesCS1A01G065000 chr5D 93.548 155 7 3 2915 3067 54406722 54406569 1.160000e-55 228.0
46 TraesCS1A01G065000 chr3D 81.308 107 20 0 2583 2689 432136230 432136336 2.050000e-13 87.9


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 TraesCS1A01G065000 chr1A 47208815 47212960 4145 True 7657.000000 7657 100.000000 1 4146 1 chr1A.!!$R1 4145
1 TraesCS1A01G065000 chr1A 392527406 392529811 2405 True 581.666667 907 80.866333 621 2875 3 chr1A.!!$R3 2254
2 TraesCS1A01G065000 chr1A 47823863 47826801 2938 True 462.500000 843 79.151000 574 3406 4 chr1A.!!$R2 2832
3 TraesCS1A01G065000 chr1D 47327006 47331037 4031 True 3301.500000 4846 96.118500 1 4146 2 chr1D.!!$R3 4145
4 TraesCS1A01G065000 chr1D 312971072 312973477 2405 True 589.000000 924 81.025000 621 2875 3 chr1D.!!$R5 2254
5 TraesCS1A01G065000 chr1D 48021425 48024280 2855 True 473.250000 876 79.444750 577 3406 4 chr1D.!!$R4 2829
6 TraesCS1A01G065000 chr1B 67051422 67055239 3817 True 1295.500000 2455 91.131250 1 4146 4 chr1B.!!$R1 4145
7 TraesCS1A01G065000 chr1B 423207524 423209926 2402 True 592.333333 922 81.242667 621 2872 3 chr1B.!!$R3 2251
8 TraesCS1A01G065000 chr1B 67680428 67683243 2815 True 485.000000 891 78.288000 577 3368 3 chr1B.!!$R2 2791
9 TraesCS1A01G065000 chr5B 139410803 139411946 1143 False 326.500000 327 86.713000 1 302 2 chr5B.!!$F2 301

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
428 449 5.046376 TGAGCTTAATCCAGATGAAGTCACA 60.046 40.0 6.61 2.46 32.82 3.58 F
1674 1972 0.528924 TCGCGAGGCAGCTACTTTTA 59.471 50.0 3.71 0.00 34.40 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2370 0.588252 CAAAAGCAGACGTGTGGAGG 59.412 55.0 15.19 0.0 0.0 4.30 R
3170 3863 0.034670 AGAGCTCAACATGGAAGGGC 60.035 55.0 17.77 0.0 0.0 5.19 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
351 354 6.305272 TGATAAGAGAACTGGAGAAAGCAT 57.695 37.500 0.00 0.00 0.00 3.79
398 419 8.491958 CCACAACCTAGTAGGGTTAATCTTATT 58.508 37.037 20.54 0.00 46.58 1.40
428 449 5.046376 TGAGCTTAATCCAGATGAAGTCACA 60.046 40.000 6.61 2.46 32.82 3.58
663 684 5.300752 CAATCTATGGACGGCAATCTTAGT 58.699 41.667 0.00 0.00 0.00 2.24
789 820 5.462398 GTCTAGAACGGTTGCTGGTATTATG 59.538 44.000 0.00 0.00 0.00 1.90
1040 1093 4.506039 TGCAGTGCAGCAAGGAAT 57.494 50.000 15.37 0.00 42.46 3.01
1434 1732 6.039829 TCTGATGATGCGAACTCTAGTGTAAT 59.960 38.462 0.00 0.00 0.00 1.89
1500 1798 3.666374 GCTGCTCGAAACTCTGTTGAATG 60.666 47.826 0.00 0.00 0.00 2.67
1520 1818 5.579753 ATGAAGAGGGTTATCATGAGCAT 57.420 39.130 0.09 0.00 32.77 3.79
1674 1972 0.528924 TCGCGAGGCAGCTACTTTTA 59.471 50.000 3.71 0.00 34.40 1.52
1768 2066 6.537355 TCTTGGTCAACTCAATGAAAGATCT 58.463 36.000 0.00 0.00 0.00 2.75
1876 2174 2.683211 ACAAATGCAAACCTCCCTCT 57.317 45.000 0.00 0.00 0.00 3.69
1890 2190 4.785376 ACCTCCCTCTTATCATGACTGTTT 59.215 41.667 0.00 0.00 0.00 2.83
2066 2370 2.289565 GCTGGTACTACCCATTTGAGC 58.710 52.381 2.59 0.51 37.50 4.26
2093 2397 2.351418 CACGTCTGCTTTTGAAGTGTCA 59.649 45.455 0.00 0.00 38.47 3.58
2134 2666 5.772825 AGCAACATAGCTGAAACTTCAAA 57.227 34.783 0.00 0.00 44.66 2.69
2151 2683 5.823045 ACTTCAAACATTATAGGCCAGCTAC 59.177 40.000 5.01 0.00 0.00 3.58
2182 2714 5.707298 GGATCATGAAAAGACTGAACCTGAA 59.293 40.000 0.00 0.00 31.26 3.02
2304 2844 2.662006 ACTCTGATGTGATGTCCGTG 57.338 50.000 0.00 0.00 0.00 4.94
2388 2928 9.502091 AGTTCTACTGTACATGAAAAAGCAATA 57.498 29.630 0.00 0.00 0.00 1.90
2508 3090 0.313672 TTTGCCGTGCCATTGAAGAC 59.686 50.000 0.00 0.00 0.00 3.01
2587 3174 0.687354 AATGCTTCACCGGTCTGTCT 59.313 50.000 2.59 0.00 0.00 3.41
2775 3365 4.444449 GGAATATTTGAGGCTTACTCCGGT 60.444 45.833 0.00 0.00 46.01 5.28
2843 3437 4.156556 GCAAGCCATCTATTTCAGTTCACA 59.843 41.667 0.00 0.00 0.00 3.58
2932 3528 7.733047 GGGTATTATGTTTTCCCCCTTATCATT 59.267 37.037 0.00 0.00 32.66 2.57
2940 3536 6.713731 TTTCCCCCTTATCATTATACTCCC 57.286 41.667 0.00 0.00 0.00 4.30
2941 3537 5.650167 TCCCCCTTATCATTATACTCCCT 57.350 43.478 0.00 0.00 0.00 4.20
2942 3538 5.600749 TCCCCCTTATCATTATACTCCCTC 58.399 45.833 0.00 0.00 0.00 4.30
2943 3539 4.722279 CCCCCTTATCATTATACTCCCTCC 59.278 50.000 0.00 0.00 0.00 4.30
2945 3541 5.024118 CCCTTATCATTATACTCCCTCCGT 58.976 45.833 0.00 0.00 0.00 4.69
2946 3542 5.127356 CCCTTATCATTATACTCCCTCCGTC 59.873 48.000 0.00 0.00 0.00 4.79
2947 3543 5.127356 CCTTATCATTATACTCCCTCCGTCC 59.873 48.000 0.00 0.00 0.00 4.79
2948 3544 2.885616 TCATTATACTCCCTCCGTCCC 58.114 52.381 0.00 0.00 0.00 4.46
2950 3546 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2951 3547 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2952 3548 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2953 3549 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2954 3550 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2955 3551 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2957 3553 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2958 3554 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2959 3555 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2961 3557 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2962 3558 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2963 3559 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2964 3560 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2965 3561 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2966 3562 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2967 3563 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2968 3564 7.335924 CCGTCCCAAAATTCTTGTCTTAGATTA 59.664 37.037 0.00 0.00 0.00 1.75
2969 3565 8.391106 CGTCCCAAAATTCTTGTCTTAGATTAG 58.609 37.037 0.00 0.00 0.00 1.73
2970 3566 9.232473 GTCCCAAAATTCTTGTCTTAGATTAGT 57.768 33.333 0.00 0.00 0.00 2.24
2971 3567 9.449719 TCCCAAAATTCTTGTCTTAGATTAGTC 57.550 33.333 0.00 0.00 0.00 2.59
2972 3568 9.454859 CCCAAAATTCTTGTCTTAGATTAGTCT 57.545 33.333 0.00 0.00 38.52 3.24
2980 3576 9.491675 TCTTGTCTTAGATTAGTCTAGATACCG 57.508 37.037 0.00 0.00 38.17 4.02
2981 3577 9.491675 CTTGTCTTAGATTAGTCTAGATACCGA 57.508 37.037 0.00 0.00 38.17 4.69
2983 3579 9.438228 TGTCTTAGATTAGTCTAGATACCGATG 57.562 37.037 0.00 0.00 38.17 3.84
2984 3580 9.439500 GTCTTAGATTAGTCTAGATACCGATGT 57.561 37.037 0.00 0.00 38.17 3.06
3002 3598 8.792831 ACCGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
3003 3599 8.623903 ACCGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
3004 3600 8.899776 CCGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
3005 3601 8.899776 CGATGTATCTAATACTAAAACGTGACC 58.100 37.037 0.00 0.00 36.70 4.02
3006 3602 9.962783 GATGTATCTAATACTAAAACGTGACCT 57.037 33.333 0.00 0.00 36.70 3.85
3007 3603 9.745880 ATGTATCTAATACTAAAACGTGACCTG 57.254 33.333 0.00 0.00 36.70 4.00
3008 3604 8.959548 TGTATCTAATACTAAAACGTGACCTGA 58.040 33.333 0.00 0.00 36.70 3.86
3009 3605 9.962783 GTATCTAATACTAAAACGTGACCTGAT 57.037 33.333 0.00 0.00 33.00 2.90
3011 3607 9.962783 ATCTAATACTAAAACGTGACCTGATAC 57.037 33.333 0.00 0.00 0.00 2.24
3012 3608 8.959548 TCTAATACTAAAACGTGACCTGATACA 58.040 33.333 0.00 0.00 0.00 2.29
3013 3609 9.745880 CTAATACTAAAACGTGACCTGATACAT 57.254 33.333 0.00 0.00 0.00 2.29
3014 3610 8.644318 AATACTAAAACGTGACCTGATACATC 57.356 34.615 0.00 0.00 0.00 3.06
3015 3611 5.416947 ACTAAAACGTGACCTGATACATCC 58.583 41.667 0.00 0.00 0.00 3.51
3016 3612 2.579207 AACGTGACCTGATACATCCG 57.421 50.000 0.00 0.00 0.00 4.18
3019 3615 3.220110 ACGTGACCTGATACATCCGTAT 58.780 45.455 0.00 0.00 41.16 3.06
3020 3616 3.635373 ACGTGACCTGATACATCCGTATT 59.365 43.478 0.00 0.00 38.48 1.89
3025 3621 6.862090 GTGACCTGATACATCCGTATTTAGAC 59.138 42.308 0.00 0.00 38.48 2.59
3026 3622 6.548251 TGACCTGATACATCCGTATTTAGACA 59.452 38.462 0.00 0.00 38.48 3.41
3030 3626 8.926710 CCTGATACATCCGTATTTAGACAAATC 58.073 37.037 0.00 0.00 38.48 2.17
3036 3632 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
3039 3635 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
3048 3644 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3049 3645 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3051 3647 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3052 3648 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3053 3649 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3054 3650 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3055 3651 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3056 3652 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3057 3653 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3058 3654 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3066 3662 3.660959 TGGGACGGAGGGAGTATTTATT 58.339 45.455 0.00 0.00 0.00 1.40
3170 3863 6.753180 TCTCAAAAGATCTATTCAGGATCCG 58.247 40.000 5.98 1.36 40.07 4.18
3215 3909 3.375299 GCGAGTGCCTTAATTCTGACAAT 59.625 43.478 0.00 0.00 33.98 2.71
3345 4043 8.439971 TCTTTTGTGGATATATATGCCAAGTCT 58.560 33.333 11.30 0.00 32.68 3.24
3527 4230 4.235360 CTGATTAACGTTGTCCTCGACTT 58.765 43.478 11.99 0.00 33.15 3.01
3576 4279 0.993746 GCTCGTCTTGTTGCTTTGCG 60.994 55.000 0.00 0.00 0.00 4.85
3824 4528 6.018994 GCCACTTTGTAGGTGATATTAGAACG 60.019 42.308 0.00 0.00 36.89 3.95
3876 4581 8.255905 ACGGTTAGTAGCAAGTATAATCTGTTT 58.744 33.333 0.00 0.00 0.00 2.83
3878 4583 9.043079 GGTTAGTAGCAAGTATAATCTGTTTCC 57.957 37.037 0.00 0.00 0.00 3.13
3912 4619 1.136828 TTCCACCTTGTACTGCTGGT 58.863 50.000 0.00 0.00 0.00 4.00
4127 4836 3.811497 CGTGATATGTGCCACAATCTGAT 59.189 43.478 0.00 0.00 33.13 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
304 307 8.766476 TCAATCAAACTCTCCTCATCTTATCTT 58.234 33.333 0.00 0.00 0.00 2.40
309 312 8.766476 TCTTATCAATCAAACTCTCCTCATCTT 58.234 33.333 0.00 0.00 0.00 2.40
351 354 3.128242 GGAAGTGCTACTTGTACTCGCTA 59.872 47.826 6.31 0.00 40.73 4.26
398 419 6.499106 TCATCTGGATTAAGCTCACCATTA 57.501 37.500 0.00 0.00 0.00 1.90
403 424 5.293079 GTGACTTCATCTGGATTAAGCTCAC 59.707 44.000 15.44 15.44 32.70 3.51
663 684 2.345880 GATCGCCTTCCGCTACCGAA 62.346 60.000 0.00 0.00 36.29 4.30
789 820 4.742438 TGTGTCCAACGAATTCTTAAGC 57.258 40.909 3.52 0.00 0.00 3.09
1040 1093 2.246588 ACATACCCCAGCACCTCTAGTA 59.753 50.000 0.00 0.00 0.00 1.82
1434 1732 6.294473 TGGCCTTTTCAATGAAGCATTAAAA 58.706 32.000 3.32 0.00 32.35 1.52
1500 1798 3.501445 GCATGCTCATGATAACCCTCTTC 59.499 47.826 11.37 0.00 41.20 2.87
1520 1818 0.817229 TGTTCCGCACATTGTCAGCA 60.817 50.000 0.77 0.00 0.00 4.41
1641 1939 0.957888 TCGCGACAATGCCAATCCAA 60.958 50.000 3.71 0.00 0.00 3.53
1674 1972 6.408662 GGACCTTCAAGGATAGAGCTAAATGT 60.409 42.308 11.59 0.00 37.67 2.71
1730 2028 4.245660 TGACCAAGAAATCAAGTCTAGCG 58.754 43.478 0.00 0.00 0.00 4.26
1768 2066 5.824097 GTGGAGACTTTTACCTGGTTGTTTA 59.176 40.000 3.84 0.00 0.00 2.01
1805 2103 0.598065 AAAGCTCAAACATCCACCGC 59.402 50.000 0.00 0.00 0.00 5.68
1876 2174 6.611613 ACTCTCCAGAAACAGTCATGATAA 57.388 37.500 0.00 0.00 0.00 1.75
1890 2190 7.776618 TTGAAACATCTTACTACTCTCCAGA 57.223 36.000 0.00 0.00 0.00 3.86
2066 2370 0.588252 CAAAAGCAGACGTGTGGAGG 59.412 55.000 15.19 0.00 0.00 4.30
2093 2397 7.168219 TGTTGCTAACTCTCATAACCTCATTT 58.832 34.615 0.00 0.00 0.00 2.32
2134 2666 2.963101 TGACGTAGCTGGCCTATAATGT 59.037 45.455 3.32 0.00 0.00 2.71
2151 2683 2.939103 GTCTTTTCATGATCCCCTGACG 59.061 50.000 0.00 0.00 0.00 4.35
2182 2714 8.870116 AGGCAAGAGTATTTGGAGTTAAAAATT 58.130 29.630 0.00 0.00 0.00 1.82
2304 2844 3.272574 TGATCAGCAGTCTGGGAAATC 57.727 47.619 1.14 0.00 40.69 2.17
2440 3022 6.672593 TGGAGCATATTTGGTATTCTTCCTT 58.327 36.000 0.00 0.00 32.62 3.36
2587 3174 4.038271 AGCATGAGAAAATTGGAGGTCA 57.962 40.909 0.00 0.00 0.00 4.02
2775 3365 6.486657 GCTTTTCCTTCATACCATGCAGTATA 59.513 38.462 0.00 0.00 31.66 1.47
2932 3528 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
2934 3530 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2935 3531 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2938 3534 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2940 3536 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2941 3537 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2942 3538 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2943 3539 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2945 3541 9.449719 GACTAATCTAAGACAAGAATTTTGGGA 57.550 33.333 5.68 0.00 0.00 4.37
2946 3542 9.454859 AGACTAATCTAAGACAAGAATTTTGGG 57.545 33.333 5.68 0.00 31.46 4.12
2954 3550 9.491675 CGGTATCTAGACTAATCTAAGACAAGA 57.508 37.037 0.00 0.00 36.98 3.02
2955 3551 9.491675 TCGGTATCTAGACTAATCTAAGACAAG 57.508 37.037 0.00 0.00 36.98 3.16
2957 3553 9.438228 CATCGGTATCTAGACTAATCTAAGACA 57.562 37.037 0.00 0.00 36.98 3.41
2958 3554 9.439500 ACATCGGTATCTAGACTAATCTAAGAC 57.561 37.037 0.00 0.00 36.98 3.01
2976 3572 9.882996 CACGTTTTAGTATTAGATACATCGGTA 57.117 33.333 0.00 0.00 38.21 4.02
2977 3573 8.623903 TCACGTTTTAGTATTAGATACATCGGT 58.376 33.333 0.00 0.00 38.21 4.69
2978 3574 8.899776 GTCACGTTTTAGTATTAGATACATCGG 58.100 37.037 0.00 0.00 38.21 4.18
2979 3575 8.899776 GGTCACGTTTTAGTATTAGATACATCG 58.100 37.037 0.00 0.00 38.21 3.84
2980 3576 9.962783 AGGTCACGTTTTAGTATTAGATACATC 57.037 33.333 0.00 0.00 38.21 3.06
2981 3577 9.745880 CAGGTCACGTTTTAGTATTAGATACAT 57.254 33.333 0.00 0.00 38.21 2.29
2982 3578 8.959548 TCAGGTCACGTTTTAGTATTAGATACA 58.040 33.333 0.00 0.00 38.21 2.29
2983 3579 9.962783 ATCAGGTCACGTTTTAGTATTAGATAC 57.037 33.333 0.00 0.00 35.99 2.24
2985 3581 9.962783 GTATCAGGTCACGTTTTAGTATTAGAT 57.037 33.333 0.00 0.00 0.00 1.98
2986 3582 8.959548 TGTATCAGGTCACGTTTTAGTATTAGA 58.040 33.333 0.00 0.00 0.00 2.10
2987 3583 9.745880 ATGTATCAGGTCACGTTTTAGTATTAG 57.254 33.333 0.00 0.00 0.00 1.73
2988 3584 9.740239 GATGTATCAGGTCACGTTTTAGTATTA 57.260 33.333 0.00 0.00 0.00 0.98
2989 3585 7.709613 GGATGTATCAGGTCACGTTTTAGTATT 59.290 37.037 0.00 0.00 0.00 1.89
2990 3586 7.208080 GGATGTATCAGGTCACGTTTTAGTAT 58.792 38.462 0.00 0.00 0.00 2.12
2991 3587 6.567050 GGATGTATCAGGTCACGTTTTAGTA 58.433 40.000 0.00 0.00 0.00 1.82
2992 3588 5.416947 GGATGTATCAGGTCACGTTTTAGT 58.583 41.667 0.00 0.00 0.00 2.24
2993 3589 4.503007 CGGATGTATCAGGTCACGTTTTAG 59.497 45.833 0.00 0.00 0.00 1.85
2994 3590 4.082081 ACGGATGTATCAGGTCACGTTTTA 60.082 41.667 0.00 0.00 0.00 1.52
2995 3591 3.259064 CGGATGTATCAGGTCACGTTTT 58.741 45.455 0.00 0.00 0.00 2.43
2996 3592 2.232941 ACGGATGTATCAGGTCACGTTT 59.767 45.455 0.00 0.00 0.00 3.60
2997 3593 1.822990 ACGGATGTATCAGGTCACGTT 59.177 47.619 0.00 0.00 0.00 3.99
2998 3594 1.471119 ACGGATGTATCAGGTCACGT 58.529 50.000 0.00 0.00 0.00 4.49
2999 3595 3.917329 ATACGGATGTATCAGGTCACG 57.083 47.619 0.00 0.00 36.56 4.35
3000 3596 6.862090 GTCTAAATACGGATGTATCAGGTCAC 59.138 42.308 0.00 0.00 40.42 3.67
3001 3597 6.548251 TGTCTAAATACGGATGTATCAGGTCA 59.452 38.462 0.00 0.00 40.42 4.02
3002 3598 6.978338 TGTCTAAATACGGATGTATCAGGTC 58.022 40.000 0.00 0.00 40.42 3.85
3003 3599 6.971726 TGTCTAAATACGGATGTATCAGGT 57.028 37.500 0.00 0.00 40.42 4.00
3004 3600 8.833231 ATTTGTCTAAATACGGATGTATCAGG 57.167 34.615 0.00 0.00 40.42 3.86
3005 3601 9.698309 AGATTTGTCTAAATACGGATGTATCAG 57.302 33.333 0.00 0.00 40.42 2.90
3010 3606 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
3011 3607 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
3013 3609 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
3014 3610 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
3025 3621 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3026 3622 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3030 3626 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3034 3630 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3036 3632 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3038 3634 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3039 3635 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3044 3640 1.961133 AAATACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
3045 3641 2.852714 TAAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
3046 3642 4.141551 ACAAATAAATACTCCCTCCGTCCC 60.142 45.833 0.00 0.00 0.00 4.46
3047 3643 5.032327 ACAAATAAATACTCCCTCCGTCC 57.968 43.478 0.00 0.00 0.00 4.79
3048 3644 5.667466 TGACAAATAAATACTCCCTCCGTC 58.333 41.667 0.00 0.00 0.00 4.79
3049 3645 5.396436 CCTGACAAATAAATACTCCCTCCGT 60.396 44.000 0.00 0.00 0.00 4.69
3051 3647 5.132144 TCCCTGACAAATAAATACTCCCTCC 59.868 44.000 0.00 0.00 0.00 4.30
3052 3648 6.248569 TCCCTGACAAATAAATACTCCCTC 57.751 41.667 0.00 0.00 0.00 4.30
3053 3649 6.389869 TCATCCCTGACAAATAAATACTCCCT 59.610 38.462 0.00 0.00 0.00 4.20
3054 3650 6.601332 TCATCCCTGACAAATAAATACTCCC 58.399 40.000 0.00 0.00 0.00 4.30
3055 3651 7.509546 TCTCATCCCTGACAAATAAATACTCC 58.490 38.462 0.00 0.00 0.00 3.85
3056 3652 8.207545 ACTCTCATCCCTGACAAATAAATACTC 58.792 37.037 0.00 0.00 0.00 2.59
3057 3653 7.989741 CACTCTCATCCCTGACAAATAAATACT 59.010 37.037 0.00 0.00 0.00 2.12
3058 3654 7.770897 ACACTCTCATCCCTGACAAATAAATAC 59.229 37.037 0.00 0.00 0.00 1.89
3066 3662 2.300152 GTCACACTCTCATCCCTGACAA 59.700 50.000 0.00 0.00 0.00 3.18
3110 3803 3.181482 CCAAGTATGTCTGCGAGATCACT 60.181 47.826 0.00 0.00 0.00 3.41
3140 3833 7.566509 TCCTGAATAGATCTTTTGAGATCAGGA 59.433 37.037 20.73 20.73 45.20 3.86
3141 3834 7.733969 TCCTGAATAGATCTTTTGAGATCAGG 58.266 38.462 17.98 17.98 45.20 3.86
3159 3852 0.988145 TGGAAGGGCGGATCCTGAAT 60.988 55.000 10.75 0.00 37.20 2.57
3170 3863 0.034670 AGAGCTCAACATGGAAGGGC 60.035 55.000 17.77 0.00 0.00 5.19
3215 3909 2.632377 GATGCGATTTCCCTGACTTCA 58.368 47.619 0.00 0.00 0.00 3.02
3300 3998 0.034896 AAACCTTCGTCACAGCCGAT 59.965 50.000 0.00 0.00 33.81 4.18
3345 4043 1.902938 TCATTCATCCGTGGCAAACA 58.097 45.000 0.00 0.00 0.00 2.83
3527 4230 2.486592 CAGCAGCACAGATGATTCAACA 59.513 45.455 0.00 0.00 0.00 3.33
3576 4279 2.169352 ACTGGATGAGCACCTGACATAC 59.831 50.000 0.00 0.00 0.00 2.39
3824 4528 6.092807 GTCTCCCTTGACATATTGAACAGAAC 59.907 42.308 0.00 0.00 36.97 3.01
3876 4581 4.385825 GTGGAATACAAGTTGTCTGTGGA 58.614 43.478 12.82 0.00 0.00 4.02
3878 4583 4.389374 AGGTGGAATACAAGTTGTCTGTG 58.611 43.478 12.82 0.00 0.00 3.66
3912 4619 6.929625 TGGAGAATCAACTCAAACAAAAACA 58.070 32.000 0.00 0.00 38.51 2.83
4033 4742 9.890629 AGTGCTTATGAGATTAAACAATGACTA 57.109 29.630 0.00 0.00 0.00 2.59
4040 4749 8.565896 AACATGAGTGCTTATGAGATTAAACA 57.434 30.769 10.33 0.00 31.82 2.83
4044 4753 8.144478 GGACTAACATGAGTGCTTATGAGATTA 58.856 37.037 10.33 0.16 35.10 1.75


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

AutoCloner maintained by Alex Coulton.