Multiple sequence alignment - TraesCS2D01G292800

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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 TraesCS2D01G292800 chr2D 100.000 3785 0 0 1 3785 375255231 375259015 0.000000e+00 6990.0
1 TraesCS2D01G292800 chr2A 92.865 2747 140 14 1045 3785 507603286 507605982 0.000000e+00 3936.0
2 TraesCS2D01G292800 chr2A 92.293 1038 46 16 1 1007 507602252 507603286 0.000000e+00 1443.0
3 TraesCS2D01G292800 chr2B 92.918 2104 72 29 842 2908 445496316 445498379 0.000000e+00 2988.0
4 TraesCS2D01G292800 chr2B 86.554 885 73 18 2905 3785 445498880 445499722 0.000000e+00 933.0
5 TraesCS2D01G292800 chr2B 88.592 412 20 17 1 412 445490454 445490838 3.420000e-130 475.0
6 TraesCS2D01G292800 chr2B 84.896 192 23 4 416 605 445491327 445491514 4.990000e-44 189.0
7 TraesCS2D01G292800 chr2B 91.525 118 5 2 735 852 445496186 445496298 1.410000e-34 158.0
8 TraesCS2D01G292800 chr5A 97.531 243 6 0 2105 2347 501850980 501851222 2.100000e-112 416.0
9 TraesCS2D01G292800 chr1A 97.119 243 7 0 2105 2347 540182259 540182017 9.790000e-111 411.0
10 TraesCS2D01G292800 chr1A 83.796 216 21 6 2359 2574 549330359 549330560 3.860000e-45 193.0
11 TraesCS2D01G292800 chr1A 81.988 161 23 5 2941 3098 178176754 178176911 8.530000e-27 132.0
12 TraesCS2D01G292800 chr6B 96.694 242 8 0 2106 2347 188499807 188499566 1.640000e-108 403.0
13 TraesCS2D01G292800 chr6B 82.390 159 27 1 2940 3098 430527162 430527005 1.830000e-28 137.0
14 TraesCS2D01G292800 chr3D 89.189 222 13 4 2359 2580 15994220 15994430 2.240000e-67 267.0
15 TraesCS2D01G292800 chr3D 100.000 29 0 0 2566 2594 455716763 455716791 2.000000e-03 54.7
16 TraesCS2D01G292800 chr4D 87.671 219 13 5 2362 2580 196877510 196877306 3.780000e-60 243.0
17 TraesCS2D01G292800 chr3B 85.000 220 20 6 2362 2580 709286548 709286755 1.070000e-50 211.0
18 TraesCS2D01G292800 chr3B 100.000 29 0 0 2566 2594 598990122 598990150 2.000000e-03 54.7
19 TraesCS2D01G292800 chr5D 84.513 226 20 8 2355 2580 468104617 468104827 3.830000e-50 209.0
20 TraesCS2D01G292800 chr5B 84.906 159 23 1 2940 3098 206799783 206799940 3.910000e-35 159.0
21 TraesCS2D01G292800 chr5B 85.185 81 10 2 2363 2443 457026308 457026230 8.710000e-12 82.4
22 TraesCS2D01G292800 chr4A 84.906 159 23 1 2940 3098 586680332 586680175 3.910000e-35 159.0
23 TraesCS2D01G292800 chr3A 83.099 142 24 0 2939 3080 218516542 218516401 3.070000e-26 130.0
24 TraesCS2D01G292800 chr3A 100.000 29 0 0 2566 2594 597920256 597920284 2.000000e-03 54.7
25 TraesCS2D01G292800 chr4B 77.165 127 25 3 3515 3637 58065674 58065548 1.890000e-08 71.3


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 TraesCS2D01G292800 chr2D 375255231 375259015 3784 False 6990.000000 6990 100.000000 1 3785 1 chr2D.!!$F1 3784
1 TraesCS2D01G292800 chr2A 507602252 507605982 3730 False 2689.500000 3936 92.579000 1 3785 2 chr2A.!!$F1 3784
2 TraesCS2D01G292800 chr2B 445496186 445499722 3536 False 1359.666667 2988 90.332333 735 3785 3 chr2B.!!$F2 3050
3 TraesCS2D01G292800 chr2B 445490454 445491514 1060 False 332.000000 475 86.744000 1 605 2 chr2B.!!$F1 604

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
249 250 0.036388 TGAATCTGGGGCGAGTGAAC 60.036 55.0 0.0 0.00 0.0 3.18 F
402 404 0.110238 TTGAATCGCTTGCGTGCTTC 60.110 50.0 14.7 14.92 0.0 3.86 F
1649 2254 0.179009 CCGGCATGGAGGTGATCAAT 60.179 55.0 0.0 0.00 42.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1942 0.391661 GGAGCTTGGACGAGATGCAA 60.392 55.000 0.0 0.0 36.08 4.08 R
2093 2698 1.222936 CTGCTTGGGCTTCTCGGAT 59.777 57.895 0.0 0.0 39.59 4.18 R
3403 4526 0.043637 AAGAAGGGGACGGGGATACA 59.956 55.000 0.0 0.0 39.74 2.29 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
249 250 0.036388 TGAATCTGGGGCGAGTGAAC 60.036 55.000 0.00 0.00 0.00 3.18
329 330 0.978146 CGGTTCTGGGTCTGGGAGAT 60.978 60.000 0.00 0.00 0.00 2.75
390 392 0.729140 GCGGTGCTTGGTTTGAATCG 60.729 55.000 0.00 0.00 0.00 3.34
402 404 0.110238 TTGAATCGCTTGCGTGCTTC 60.110 50.000 14.70 14.92 0.00 3.86
412 414 2.328099 GCGTGCTTCAGGAACAGGG 61.328 63.158 0.00 0.00 0.00 4.45
413 415 1.672356 CGTGCTTCAGGAACAGGGG 60.672 63.158 0.00 0.00 0.00 4.79
433 920 2.226437 GGGCAGTTGTGTACACATCTTG 59.774 50.000 28.83 24.75 41.52 3.02
441 928 6.701841 AGTTGTGTACACATCTTGAGTTGTAG 59.298 38.462 28.35 0.00 41.52 2.74
442 929 6.156748 TGTGTACACATCTTGAGTTGTAGT 57.843 37.500 24.62 0.62 36.21 2.73
544 1036 0.309612 CGCCCGTGCTAAACAAAACT 59.690 50.000 0.00 0.00 34.43 2.66
622 1121 6.547880 ACAGCTAGTAGTAGTATCATTGTGCT 59.452 38.462 6.47 0.00 0.00 4.40
644 1143 5.746721 GCTAAATCGGTGTTTGACTTTTGTT 59.253 36.000 0.00 0.00 0.00 2.83
645 1144 6.913673 GCTAAATCGGTGTTTGACTTTTGTTA 59.086 34.615 0.00 0.00 0.00 2.41
646 1145 7.593644 GCTAAATCGGTGTTTGACTTTTGTTAT 59.406 33.333 0.00 0.00 0.00 1.89
648 1147 8.791355 AAATCGGTGTTTGACTTTTGTTATAC 57.209 30.769 0.00 0.00 0.00 1.47
649 1148 7.739498 ATCGGTGTTTGACTTTTGTTATACT 57.261 32.000 0.00 0.00 0.00 2.12
673 1182 3.575687 CTCTTTCTTTGGGGCACAATCTT 59.424 43.478 1.47 0.00 39.21 2.40
682 1191 1.599542 GGGCACAATCTTATCACTCGC 59.400 52.381 0.00 0.00 0.00 5.03
732 1241 6.014499 GGCAATGTGTACTACTCCTATATGGT 60.014 42.308 0.00 0.00 37.07 3.55
781 1290 2.051692 TCTCACCGGGAAGAAAAAGGA 58.948 47.619 6.32 0.00 0.00 3.36
787 1296 3.136992 ACCGGGAAGAAAAAGGAACTACA 59.863 43.478 6.32 0.00 38.49 2.74
788 1297 3.751698 CCGGGAAGAAAAAGGAACTACAG 59.248 47.826 0.00 0.00 38.49 2.74
789 1298 4.386711 CGGGAAGAAAAAGGAACTACAGT 58.613 43.478 0.00 0.00 38.49 3.55
791 1300 5.407691 CGGGAAGAAAAAGGAACTACAGTAC 59.592 44.000 0.00 0.00 38.49 2.73
792 1301 5.407691 GGGAAGAAAAAGGAACTACAGTACG 59.592 44.000 0.00 0.00 38.49 3.67
793 1302 5.407691 GGAAGAAAAAGGAACTACAGTACGG 59.592 44.000 0.00 0.00 38.49 4.02
794 1303 5.541953 AGAAAAAGGAACTACAGTACGGT 57.458 39.130 3.62 3.62 38.49 4.83
925 1463 3.146828 AACCCAACCCAGTGAGGCC 62.147 63.158 0.00 0.00 35.39 5.19
942 1480 3.801997 CGGAGAGGCCAGCCCAAT 61.802 66.667 5.01 0.00 35.94 3.16
949 1487 0.186873 AGGCCAGCCCAATCCAATAG 59.813 55.000 5.01 0.00 36.58 1.73
1015 1562 1.734748 TTTTTCGGTTTGCGGACCC 59.265 52.632 3.01 0.00 36.28 4.46
1016 1563 0.752376 TTTTTCGGTTTGCGGACCCT 60.752 50.000 3.01 0.00 36.28 4.34
1017 1564 1.167781 TTTTCGGTTTGCGGACCCTC 61.168 55.000 3.01 0.00 36.28 4.30
1018 1565 3.540367 TTCGGTTTGCGGACCCTCC 62.540 63.158 3.01 0.00 36.28 4.30
1019 1566 4.016706 CGGTTTGCGGACCCTCCT 62.017 66.667 3.01 0.00 36.28 3.69
1020 1567 2.046217 GGTTTGCGGACCCTCCTC 60.046 66.667 0.00 0.00 33.30 3.71
1021 1568 2.593956 GGTTTGCGGACCCTCCTCT 61.594 63.158 0.00 0.00 33.30 3.69
1022 1569 1.375326 GTTTGCGGACCCTCCTCTT 59.625 57.895 0.00 0.00 33.30 2.85
1023 1570 0.673956 GTTTGCGGACCCTCCTCTTC 60.674 60.000 0.00 0.00 33.30 2.87
1024 1571 0.836400 TTTGCGGACCCTCCTCTTCT 60.836 55.000 0.00 0.00 33.30 2.85
1025 1572 1.258445 TTGCGGACCCTCCTCTTCTC 61.258 60.000 0.00 0.00 33.30 2.87
1026 1573 1.380650 GCGGACCCTCCTCTTCTCT 60.381 63.158 0.00 0.00 33.30 3.10
1027 1574 1.671901 GCGGACCCTCCTCTTCTCTG 61.672 65.000 0.00 0.00 33.30 3.35
1028 1575 1.040339 CGGACCCTCCTCTTCTCTGG 61.040 65.000 0.00 0.00 33.30 3.86
1029 1576 1.334384 GGACCCTCCTCTTCTCTGGC 61.334 65.000 0.00 0.00 32.53 4.85
1030 1577 1.671901 GACCCTCCTCTTCTCTGGCG 61.672 65.000 0.00 0.00 0.00 5.69
1031 1578 2.498726 CCTCCTCTTCTCTGGCGC 59.501 66.667 0.00 0.00 0.00 6.53
1032 1579 2.103934 CTCCTCTTCTCTGGCGCG 59.896 66.667 0.00 0.00 0.00 6.86
1033 1580 3.423162 CTCCTCTTCTCTGGCGCGG 62.423 68.421 8.83 0.00 0.00 6.46
1034 1581 4.521062 CCTCTTCTCTGGCGCGGG 62.521 72.222 8.83 0.00 0.00 6.13
1053 1648 2.204151 ACCAACCCTCTCCCCCAG 60.204 66.667 0.00 0.00 0.00 4.45
1299 1904 4.421479 AGTGCTTCTCCGTCGCCG 62.421 66.667 0.00 0.00 0.00 6.46
1301 1906 3.057548 TGCTTCTCCGTCGCCGTA 61.058 61.111 0.00 0.00 0.00 4.02
1304 1909 2.749044 TTCTCCGTCGCCGTAGCT 60.749 61.111 0.00 0.00 36.60 3.32
1314 1919 4.849329 CCGTAGCTGTCGCCGTCC 62.849 72.222 0.00 0.00 36.60 4.79
1316 1921 4.509737 GTAGCTGTCGCCGTCCCC 62.510 72.222 0.00 0.00 36.60 4.81
1604 2209 2.031465 GTCCCGGACGCCAAGAAA 59.969 61.111 0.73 0.00 0.00 2.52
1649 2254 0.179009 CCGGCATGGAGGTGATCAAT 60.179 55.000 0.00 0.00 42.00 2.57
2093 2698 0.327924 ACATCAAGCGGGTGATTGGA 59.672 50.000 0.00 0.00 41.75 3.53
2548 3153 3.905678 CGGCGAGCGGAAGGAGAT 61.906 66.667 0.00 0.00 0.00 2.75
2561 3166 2.660064 GGAGATGGTCCAGTGCGGT 61.660 63.158 0.00 0.00 46.10 5.68
2612 3217 0.879400 CCATCTGCTCGTGATGAGGC 60.879 60.000 3.55 0.00 45.38 4.70
2613 3218 1.067084 ATCTGCTCGTGATGAGGCG 59.933 57.895 3.55 0.00 45.38 5.52
2615 3220 4.819761 TGCTCGTGATGAGGCGGC 62.820 66.667 0.00 0.00 45.38 6.53
2617 3222 2.584418 CTCGTGATGAGGCGGCAG 60.584 66.667 13.08 0.00 41.29 4.85
2618 3223 4.819761 TCGTGATGAGGCGGCAGC 62.820 66.667 13.08 0.00 44.18 5.25
2619 3224 4.827087 CGTGATGAGGCGGCAGCT 62.827 66.667 13.08 0.00 44.37 4.24
2620 3225 3.200593 GTGATGAGGCGGCAGCTG 61.201 66.667 13.08 10.11 44.37 4.24
2621 3226 3.709633 TGATGAGGCGGCAGCTGT 61.710 61.111 16.64 0.00 44.37 4.40
2712 3323 1.741706 AGGCTCTGATTTTGCGATGTG 59.258 47.619 0.00 0.00 0.00 3.21
2719 3330 4.215185 TCTGATTTTGCGATGTGCTTGTTA 59.785 37.500 0.00 0.00 46.63 2.41
2757 3374 6.072397 TGCTAATTAAACACCTGTAATGCGTT 60.072 34.615 0.00 0.00 0.00 4.84
2775 3392 3.603857 GCGTTCCCGTTCATATTGATTCG 60.604 47.826 0.00 0.00 36.15 3.34
2776 3393 3.554324 CGTTCCCGTTCATATTGATTCGT 59.446 43.478 0.00 0.00 0.00 3.85
2777 3394 4.741185 CGTTCCCGTTCATATTGATTCGTA 59.259 41.667 0.00 0.00 0.00 3.43
2778 3395 5.332055 CGTTCCCGTTCATATTGATTCGTAC 60.332 44.000 0.00 0.00 0.00 3.67
2779 3396 5.524971 TCCCGTTCATATTGATTCGTACT 57.475 39.130 0.00 0.00 0.00 2.73
2898 3516 7.210873 AGACATCCAAATAACGTCTTAGATCC 58.789 38.462 0.00 0.00 33.20 3.36
2912 4034 2.510768 AGATCCGATCACTAAACGCC 57.489 50.000 11.01 0.00 0.00 5.68
2915 4037 1.219664 CCGATCACTAAACGCCCCA 59.780 57.895 0.00 0.00 0.00 4.96
2952 4074 2.302517 ATAGGTAGGGCCCGTTCGGA 62.303 60.000 18.44 1.34 38.26 4.55
2997 4119 1.197430 AGCTGAAGTGGTGGAGAGGG 61.197 60.000 0.00 0.00 0.00 4.30
3000 4122 3.316573 GAAGTGGTGGAGAGGGGCG 62.317 68.421 0.00 0.00 0.00 6.13
3005 4127 4.864334 GTGGAGAGGGGCGGCATG 62.864 72.222 12.47 0.00 0.00 4.06
3019 4141 2.406130 CGGCATGCAGTTCATTTTTGT 58.594 42.857 21.36 0.00 31.79 2.83
3028 4150 2.036346 AGTTCATTTTTGTGGAGCAGCC 59.964 45.455 0.00 0.00 37.10 4.85
3037 4159 2.068915 TGGAGCAGCCATTCTGTCA 58.931 52.632 0.00 0.00 43.33 3.58
3070 4192 1.696832 GCGTTGAGCGGAATGGAGTC 61.697 60.000 0.00 0.00 41.69 3.36
3071 4193 0.389817 CGTTGAGCGGAATGGAGTCA 60.390 55.000 0.00 0.00 36.85 3.41
3073 4195 0.389817 TTGAGCGGAATGGAGTCACG 60.390 55.000 0.00 0.00 0.00 4.35
3075 4197 2.511600 GCGGAATGGAGTCACGGG 60.512 66.667 0.00 0.00 0.00 5.28
3111 4233 3.660865 GAACAGGCCCGTAGTATTATGG 58.339 50.000 0.00 0.00 35.96 2.74
3139 4261 5.570320 TCCATAAACTTGAGGAAGAAAGGG 58.430 41.667 0.00 0.00 32.98 3.95
3239 4361 7.042187 GCTCTCAGATCATCATCATTTTTACGT 60.042 37.037 0.00 0.00 0.00 3.57
3250 4372 3.430895 TCATTTTTACGTTCGAGTCTGGC 59.569 43.478 0.00 0.00 0.00 4.85
3282 4404 4.831674 TCTCTGAGCATTGGATCTTCAA 57.168 40.909 0.00 0.00 0.00 2.69
3292 4414 5.565439 GCATTGGATCTTCAATTAATCCCGG 60.565 44.000 0.00 0.00 38.56 5.73
3299 4421 4.966805 TCTTCAATTAATCCCGGTACTCCT 59.033 41.667 0.00 0.00 0.00 3.69
3329 4451 8.370182 ACAAAATCCTTGATTTGCTGTTAATCT 58.630 29.630 3.03 0.00 40.77 2.40
3403 4526 4.207891 AGAAACACAATGCGACCTCTAT 57.792 40.909 0.00 0.00 0.00 1.98
3404 4527 3.935203 AGAAACACAATGCGACCTCTATG 59.065 43.478 0.00 0.00 0.00 2.23
3433 4556 0.401738 CCCCTTCTTCCACTCTTGCA 59.598 55.000 0.00 0.00 0.00 4.08
3446 4569 4.507710 CACTCTTGCACTAAGCCTAATCA 58.492 43.478 0.00 0.00 44.83 2.57
3511 4634 1.403814 CTCCTAGCGACCTGGATCAA 58.596 55.000 0.00 0.00 0.00 2.57
3524 4647 0.679640 GGATCAACGCCATGGAACCA 60.680 55.000 18.40 0.00 0.00 3.67
3552 4675 0.856982 TCCCTTCCCCAAGCTTGAAA 59.143 50.000 28.05 16.41 0.00 2.69
3651 4774 1.333791 CGTCGCCAAGGTTGAAAAGAC 60.334 52.381 0.00 0.00 0.00 3.01
3657 4780 3.507622 GCCAAGGTTGAAAAGACTGCTAT 59.492 43.478 0.00 0.00 0.00 2.97
3699 4822 4.537433 GCCCAGCGCCCTAGACTG 62.537 72.222 2.29 0.00 0.00 3.51
3700 4823 4.537433 CCCAGCGCCCTAGACTGC 62.537 72.222 2.29 0.00 0.00 4.40
3738 4861 7.597743 AGACGTAAATATAGTTTTGGCTATCGG 59.402 37.037 0.00 0.00 34.00 4.18
3752 4875 6.037786 TGGCTATCGGAGTATATTTGGAAG 57.962 41.667 0.00 0.00 0.00 3.46
3763 4886 7.541437 GGAGTATATTTGGAAGACTATACGTGC 59.459 40.741 0.00 0.00 34.01 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.863346 CGACACCTTCGGGGACACA 61.863 63.158 2.52 0.00 44.60 3.72
360 361 2.898920 AAGCACCGCCCATCTCCATG 62.899 60.000 0.00 0.00 0.00 3.66
390 392 1.081840 GTTCCTGAAGCACGCAAGC 60.082 57.895 0.00 0.00 45.62 4.01
402 404 1.604593 CAACTGCCCCCTGTTCCTG 60.605 63.158 0.00 0.00 31.71 3.86
412 414 2.185004 AGATGTGTACACAACTGCCC 57.815 50.000 30.98 16.85 45.41 5.36
413 415 3.138304 TCAAGATGTGTACACAACTGCC 58.862 45.455 31.83 18.77 42.50 4.85
433 920 2.726760 CACGCAAGACTCACTACAACTC 59.273 50.000 0.00 0.00 43.62 3.01
441 928 0.040958 CCAAAGCACGCAAGACTCAC 60.041 55.000 0.00 0.00 43.62 3.51
442 929 0.463654 ACCAAAGCACGCAAGACTCA 60.464 50.000 0.00 0.00 43.62 3.41
544 1036 3.066064 GCACGAGAGAAGATCAGAGCTTA 59.934 47.826 0.00 0.00 0.00 3.09
622 1121 9.881529 GTATAACAAAAGTCAAACACCGATTTA 57.118 29.630 0.00 0.00 0.00 1.40
644 1143 5.486063 TGTGCCCCAAAGAAAGAGTAGTATA 59.514 40.000 0.00 0.00 0.00 1.47
645 1144 4.288626 TGTGCCCCAAAGAAAGAGTAGTAT 59.711 41.667 0.00 0.00 0.00 2.12
646 1145 3.649023 TGTGCCCCAAAGAAAGAGTAGTA 59.351 43.478 0.00 0.00 0.00 1.82
647 1146 2.441750 TGTGCCCCAAAGAAAGAGTAGT 59.558 45.455 0.00 0.00 0.00 2.73
648 1147 3.140325 TGTGCCCCAAAGAAAGAGTAG 57.860 47.619 0.00 0.00 0.00 2.57
649 1148 3.586470 TTGTGCCCCAAAGAAAGAGTA 57.414 42.857 0.00 0.00 0.00 2.59
673 1182 0.733150 CGACCAGTGAGCGAGTGATA 59.267 55.000 0.00 0.00 0.00 2.15
781 1290 4.099881 TCTTTGACCAACCGTACTGTAGTT 59.900 41.667 0.00 0.00 0.00 2.24
787 1296 1.682854 TCGTCTTTGACCAACCGTACT 59.317 47.619 0.00 0.00 0.00 2.73
788 1297 2.138596 TCGTCTTTGACCAACCGTAC 57.861 50.000 0.00 0.00 0.00 3.67
789 1298 2.472816 GTTCGTCTTTGACCAACCGTA 58.527 47.619 0.00 0.00 29.77 4.02
791 1300 0.231279 CGTTCGTCTTTGACCAACCG 59.769 55.000 3.42 0.00 31.74 4.44
792 1301 0.041576 GCGTTCGTCTTTGACCAACC 60.042 55.000 3.42 0.00 31.74 3.77
793 1302 0.382636 CGCGTTCGTCTTTGACCAAC 60.383 55.000 0.00 0.00 32.02 3.77
794 1303 1.492319 CCGCGTTCGTCTTTGACCAA 61.492 55.000 4.92 0.00 0.00 3.67
925 1463 3.764160 GATTGGGCTGGCCTCTCCG 62.764 68.421 21.72 0.00 37.80 4.63
942 1480 0.245266 TTGAGTCGCGCACTATTGGA 59.755 50.000 8.75 0.00 34.41 3.53
949 1487 1.472276 CTATCCGTTGAGTCGCGCAC 61.472 60.000 8.75 4.91 0.00 5.34
1006 1553 1.229209 AGAAGAGGAGGGTCCGCAA 60.229 57.895 0.00 0.00 42.75 4.85
1007 1554 1.682684 GAGAAGAGGAGGGTCCGCA 60.683 63.158 0.00 0.00 42.75 5.69
1008 1555 1.380650 AGAGAAGAGGAGGGTCCGC 60.381 63.158 0.00 0.00 42.75 5.54
1009 1556 1.040339 CCAGAGAAGAGGAGGGTCCG 61.040 65.000 0.00 0.00 42.75 4.79
1010 1557 1.334384 GCCAGAGAAGAGGAGGGTCC 61.334 65.000 0.00 0.00 36.58 4.46
1011 1558 1.671901 CGCCAGAGAAGAGGAGGGTC 61.672 65.000 0.00 0.00 0.00 4.46
1012 1559 1.684049 CGCCAGAGAAGAGGAGGGT 60.684 63.158 0.00 0.00 0.00 4.34
1013 1560 3.087666 GCGCCAGAGAAGAGGAGGG 62.088 68.421 0.00 0.00 0.00 4.30
1014 1561 2.498726 GCGCCAGAGAAGAGGAGG 59.501 66.667 0.00 0.00 0.00 4.30
1015 1562 2.103934 CGCGCCAGAGAAGAGGAG 59.896 66.667 0.00 0.00 0.00 3.69
1016 1563 3.452786 CCGCGCCAGAGAAGAGGA 61.453 66.667 0.00 0.00 0.00 3.71
1017 1564 4.521062 CCCGCGCCAGAGAAGAGG 62.521 72.222 0.00 0.00 0.00 3.69
1033 1580 4.048470 GGGGAGAGGGTTGGTGCC 62.048 72.222 0.00 0.00 0.00 5.01
1034 1581 4.048470 GGGGGAGAGGGTTGGTGC 62.048 72.222 0.00 0.00 0.00 5.01
1035 1582 2.531685 TGGGGGAGAGGGTTGGTG 60.532 66.667 0.00 0.00 0.00 4.17
1036 1583 2.204151 CTGGGGGAGAGGGTTGGT 60.204 66.667 0.00 0.00 0.00 3.67
1037 1584 2.204151 ACTGGGGGAGAGGGTTGG 60.204 66.667 0.00 0.00 0.00 3.77
1038 1585 2.660064 CGACTGGGGGAGAGGGTTG 61.660 68.421 0.00 0.00 0.00 3.77
1039 1586 2.182858 ATCGACTGGGGGAGAGGGTT 62.183 60.000 0.00 0.00 0.00 4.11
1040 1587 2.182858 AATCGACTGGGGGAGAGGGT 62.183 60.000 0.00 0.00 0.00 4.34
1041 1588 1.383248 AATCGACTGGGGGAGAGGG 60.383 63.158 0.00 0.00 0.00 4.30
1042 1589 1.739338 CGAATCGACTGGGGGAGAGG 61.739 65.000 0.00 0.00 0.00 3.69
1043 1590 0.752009 TCGAATCGACTGGGGGAGAG 60.752 60.000 0.00 0.00 0.00 3.20
1299 1904 4.509737 GGGGACGGCGACAGCTAC 62.510 72.222 16.62 0.00 44.37 3.58
1337 1942 0.391661 GGAGCTTGGACGAGATGCAA 60.392 55.000 0.00 0.00 36.08 4.08
1427 2032 1.616628 GGTGGTGGAGGTGAGGGAT 60.617 63.158 0.00 0.00 0.00 3.85
1493 2098 4.432741 GGCAGGTCCTTGGCTCCC 62.433 72.222 1.50 0.00 40.23 4.30
1629 2234 1.561769 TTGATCACCTCCATGCCGGT 61.562 55.000 1.90 0.00 35.57 5.28
1649 2254 2.190313 GCCATGATCTCCCACGCA 59.810 61.111 0.00 0.00 0.00 5.24
1793 2398 2.592993 CGGGCTGTTCTCCTTCCCA 61.593 63.158 0.00 0.00 36.79 4.37
2093 2698 1.222936 CTGCTTGGGCTTCTCGGAT 59.777 57.895 0.00 0.00 39.59 4.18
2548 3153 2.842462 ACTCACCGCACTGGACCA 60.842 61.111 0.00 0.00 42.00 4.02
2561 3166 1.954146 GCCGTTCTCGTTGCACTCA 60.954 57.895 0.00 0.00 35.01 3.41
2612 3217 1.033746 AATCCAATCCACAGCTGCCG 61.034 55.000 15.27 5.03 0.00 5.69
2613 3218 0.458669 CAATCCAATCCACAGCTGCC 59.541 55.000 15.27 0.00 0.00 4.85
2615 3220 3.581755 CAAACAATCCAATCCACAGCTG 58.418 45.455 13.48 13.48 0.00 4.24
2617 3222 2.299867 ACCAAACAATCCAATCCACAGC 59.700 45.455 0.00 0.00 0.00 4.40
2618 3223 3.321682 ACACCAAACAATCCAATCCACAG 59.678 43.478 0.00 0.00 0.00 3.66
2619 3224 3.303938 ACACCAAACAATCCAATCCACA 58.696 40.909 0.00 0.00 0.00 4.17
2620 3225 4.335400 AACACCAAACAATCCAATCCAC 57.665 40.909 0.00 0.00 0.00 4.02
2621 3226 4.895889 TGTAACACCAAACAATCCAATCCA 59.104 37.500 0.00 0.00 0.00 3.41
2712 3323 0.110192 GGTTGCAGAGCGTAACAAGC 60.110 55.000 0.00 0.00 41.59 4.01
2757 3374 5.163488 ACAGTACGAATCAATATGAACGGGA 60.163 40.000 12.26 0.00 35.66 5.14
2898 3516 1.663695 AATGGGGCGTTTAGTGATCG 58.336 50.000 0.00 0.00 0.00 3.69
2934 4056 2.442643 CCGAACGGGCCCTACCTA 60.443 66.667 22.43 0.00 39.10 3.08
2952 4074 1.228154 GTTGGGAGCCGGAGTGTTT 60.228 57.895 5.05 0.00 0.00 2.83
2976 4098 0.108898 CTCTCCACCACTTCAGCTCG 60.109 60.000 0.00 0.00 0.00 5.03
2997 4119 0.390209 AAAATGAACTGCATGCCGCC 60.390 50.000 16.68 5.21 41.33 6.13
3000 4122 2.481185 CCACAAAAATGAACTGCATGCC 59.519 45.455 16.68 0.00 37.28 4.40
3004 4126 2.429971 TGCTCCACAAAAATGAACTGCA 59.570 40.909 0.00 0.00 0.00 4.41
3005 4127 3.054878 CTGCTCCACAAAAATGAACTGC 58.945 45.455 0.00 0.00 0.00 4.40
3028 4150 4.582869 TGGAAATGAGGAGTGACAGAATG 58.417 43.478 0.00 0.00 46.00 2.67
3037 4159 1.347707 TCAACGCTGGAAATGAGGAGT 59.652 47.619 0.00 0.00 0.00 3.85
3064 4186 1.906824 GACCACTCCCGTGACTCCA 60.907 63.158 0.00 0.00 43.97 3.86
3075 4197 1.671379 GTTCGGCAAGGGACCACTC 60.671 63.158 0.00 0.00 0.00 3.51
3089 4211 3.314553 CATAATACTACGGGCCTGTTCG 58.685 50.000 25.37 16.90 0.00 3.95
3098 4220 4.866508 TGGAAGCTCCATAATACTACGG 57.133 45.455 1.25 0.00 42.67 4.02
3111 4233 5.809719 CTTCCTCAAGTTTATGGAAGCTC 57.190 43.478 12.54 0.00 45.73 4.09
3134 4256 6.739331 TTAAACATCAACAACCATCCCTTT 57.261 33.333 0.00 0.00 0.00 3.11
3139 4261 8.514594 TCTTCTCATTAAACATCAACAACCATC 58.485 33.333 0.00 0.00 0.00 3.51
3213 4335 7.042187 ACGTAAAAATGATGATGATCTGAGAGC 60.042 37.037 0.00 0.00 0.00 4.09
3239 4361 1.480954 GACCATAAGGCCAGACTCGAA 59.519 52.381 5.01 0.00 39.06 3.71
3250 4372 4.620589 ATGCTCAGAGATGACCATAAGG 57.379 45.455 0.00 0.00 42.21 2.69
3282 4404 3.387050 GTCACAGGAGTACCGGGATTAAT 59.613 47.826 6.32 0.00 41.83 1.40
3292 4414 5.305585 TCAAGGATTTTGTCACAGGAGTAC 58.694 41.667 0.00 0.00 0.00 2.73
3299 4421 5.163426 ACAGCAAATCAAGGATTTTGTCACA 60.163 36.000 1.63 0.00 39.82 3.58
3403 4526 0.043637 AAGAAGGGGACGGGGATACA 59.956 55.000 0.00 0.00 39.74 2.29
3404 4527 0.757512 GAAGAAGGGGACGGGGATAC 59.242 60.000 0.00 0.00 0.00 2.24
3433 4556 1.134491 GGTGCGGTGATTAGGCTTAGT 60.134 52.381 0.00 0.00 0.00 2.24
3511 4634 3.055719 CGCTTGGTTCCATGGCGT 61.056 61.111 21.68 0.00 40.78 5.68
3552 4675 1.741770 GTGGCCTTTGTCGCTCGAT 60.742 57.895 3.32 0.00 0.00 3.59
3682 4805 4.537433 CAGTCTAGGGCGCTGGGC 62.537 72.222 14.51 12.67 42.51 5.36
3700 4823 1.940883 TTACGTCTAGGCTGCACCCG 61.941 60.000 0.50 0.00 40.58 5.28
3701 4824 0.248289 TTTACGTCTAGGCTGCACCC 59.752 55.000 0.50 0.00 40.58 4.61
3702 4825 2.311124 ATTTACGTCTAGGCTGCACC 57.689 50.000 0.50 0.00 39.61 5.01
3703 4826 5.770417 ACTATATTTACGTCTAGGCTGCAC 58.230 41.667 0.50 0.00 0.00 4.57
3738 4861 8.080417 TGCACGTATAGTCTTCCAAATATACTC 58.920 37.037 0.00 0.00 31.73 2.59
3752 4875 7.742019 AATCAATATCGATGCACGTATAGTC 57.258 36.000 8.54 0.00 43.13 2.59


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

AutoCloner maintained by Alex Coulton.