Multiple sequence alignment - TraesCS7A01G499500

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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 TraesCS7A01G499500 chr7A 100.000 4199 0 0 1 4199 689911662 689915860 0.000000e+00 7755.0
1 TraesCS7A01G499500 chr7A 100.000 570 0 0 4422 4991 689916083 689916652 0.000000e+00 1053.0
2 TraesCS7A01G499500 chr7A 85.446 426 45 10 4422 4837 689930071 689930489 1.280000e-115 427.0
3 TraesCS7A01G499500 chr7A 95.385 65 2 1 4122 4186 689930010 689930073 8.840000e-18 102.0
4 TraesCS7A01G499500 chr7A 93.333 45 3 0 3598 3642 492243081 492243125 3.220000e-07 67.6
5 TraesCS7A01G499500 chr7D 93.114 2033 109 16 1459 3479 596700097 596702110 0.000000e+00 2950.0
6 TraesCS7A01G499500 chr7D 90.061 986 58 18 427 1392 596699131 596700096 0.000000e+00 1242.0
7 TraesCS7A01G499500 chr7D 93.194 573 31 6 4422 4991 596702744 596703311 0.000000e+00 835.0
8 TraesCS7A01G499500 chr7D 92.029 552 37 5 3643 4188 596702198 596702748 0.000000e+00 769.0
9 TraesCS7A01G499500 chr7D 96.000 425 15 2 1 424 596698520 596698943 0.000000e+00 689.0
10 TraesCS7A01G499500 chr7D 95.238 42 1 1 3601 3642 351687529 351687489 1.160000e-06 65.8
11 TraesCS7A01G499500 chr7B 87.557 2395 161 42 734 3054 675187465 675189796 0.000000e+00 2645.0
12 TraesCS7A01G499500 chr7B 93.482 1795 77 10 2411 4182 675308883 675310660 0.000000e+00 2630.0
13 TraesCS7A01G499500 chr7B 88.112 1901 132 29 1616 3479 675211908 675213751 0.000000e+00 2172.0
14 TraesCS7A01G499500 chr7B 85.838 1038 68 43 427 1433 675210912 675211901 0.000000e+00 1029.0
15 TraesCS7A01G499500 chr7B 89.377 546 39 9 3643 4176 675190225 675190763 0.000000e+00 669.0
16 TraesCS7A01G499500 chr7B 91.322 484 38 3 3643 4123 675213839 675214321 0.000000e+00 658.0
17 TraesCS7A01G499500 chr7B 88.389 422 41 6 3 421 675186583 675186999 7.460000e-138 501.0
18 TraesCS7A01G499500 chr7B 90.541 296 28 0 2043 2338 675307710 675308005 4.680000e-105 392.0
19 TraesCS7A01G499500 chr7B 89.902 307 21 8 4651 4950 675214531 675214834 2.180000e-103 387.0
20 TraesCS7A01G499500 chr7B 83.529 340 27 10 3144 3479 675189824 675190138 1.760000e-74 291.0
21 TraesCS7A01G499500 chr7B 90.566 212 14 4 4422 4632 675214336 675214542 4.920000e-70 276.0
22 TraesCS7A01G499500 chr7B 85.496 262 32 6 4422 4678 675310656 675310916 8.240000e-68 268.0
23 TraesCS7A01G499500 chr5B 83.604 677 95 6 2367 3035 676113630 676112962 5.490000e-174 621.0
24 TraesCS7A01G499500 chr5B 80.615 423 66 11 3643 4055 544487481 544487897 3.750000e-81 313.0
25 TraesCS7A01G499500 chr5B 95.238 42 1 1 3600 3641 522024505 522024465 1.160000e-06 65.8
26 TraesCS7A01G499500 chr4A 82.260 699 104 15 2351 3035 637164904 637164212 2.000000e-163 586.0
27 TraesCS7A01G499500 chr1B 95.455 44 1 1 3597 3640 95245670 95245712 8.970000e-08 69.4
28 TraesCS7A01G499500 chr2B 97.059 34 1 0 3612 3645 53404053 53404020 1.940000e-04 58.4


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 TraesCS7A01G499500 chr7A 689911662 689916652 4990 False 4404.000000 7755 100.000000 1 4991 2 chr7A.!!$F2 4990
1 TraesCS7A01G499500 chr7D 596698520 596703311 4791 False 1297.000000 2950 92.879600 1 4991 5 chr7D.!!$F1 4990
2 TraesCS7A01G499500 chr7B 675307710 675310916 3206 False 1096.666667 2630 89.839667 2043 4678 3 chr7B.!!$F3 2635
3 TraesCS7A01G499500 chr7B 675186583 675190763 4180 False 1026.500000 2645 87.213000 3 4176 4 chr7B.!!$F1 4173
4 TraesCS7A01G499500 chr7B 675210912 675214834 3922 False 904.400000 2172 89.148000 427 4950 5 chr7B.!!$F2 4523
5 TraesCS7A01G499500 chr5B 676112962 676113630 668 True 621.000000 621 83.604000 2367 3035 1 chr5B.!!$R2 668
6 TraesCS7A01G499500 chr4A 637164212 637164904 692 True 586.000000 586 82.260000 2351 3035 1 chr4A.!!$R1 684

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
202 205 0.177141 TCCCTAATGTCGGGCTTTCG 59.823 55.0 0.00 0.00 41.69 3.46 F
242 245 0.751643 GCTTTACCGTGGGGCATGAT 60.752 55.0 0.00 0.00 36.48 2.45 F
1077 1320 0.172352 CTCTCTTCGTCCTGCTGGTC 59.828 60.0 9.73 3.01 34.23 4.02 F
1091 1334 0.886490 CTGGTCAGCAAGAAACGCCT 60.886 55.0 0.00 0.00 0.00 5.52 F
2372 2679 0.813184 CCTGGTGATTGTCATGTGCC 59.187 55.0 0.00 0.00 0.00 5.01 F
3121 4311 0.397564 TCAGGTCAGAGCAATGCACA 59.602 50.0 8.35 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 1303 0.108898 CTGACCAGCAGGACGAAGAG 60.109 60.000 0.35 0.0 41.07 2.85 R
1327 1580 0.618968 AGGGAGGAAGGAAGCGACAT 60.619 55.000 0.00 0.0 0.00 3.06 R
2362 2669 0.036022 TCACCATTCGGCACATGACA 59.964 50.000 0.00 0.0 34.57 3.58 R
2731 3870 0.313043 CTGCAAGAACACAAGCTGGG 59.687 55.000 0.00 0.0 34.07 4.45 R
3509 4717 1.006086 TGTGCGTGTGAGTTTGACTG 58.994 50.000 0.00 0.0 0.00 3.51 R
4824 6066 1.939934 CACTAGAGAGAGACCGAGCTG 59.060 57.143 0.00 0.0 0.00 4.24 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
202 205 0.177141 TCCCTAATGTCGGGCTTTCG 59.823 55.000 0.00 0.00 41.69 3.46
232 235 1.378514 CCATGCCCAGCTTTACCGT 60.379 57.895 0.00 0.00 0.00 4.83
242 245 0.751643 GCTTTACCGTGGGGCATGAT 60.752 55.000 0.00 0.00 36.48 2.45
313 317 5.405935 AAAGGTTGCTTTCCATCCAATAC 57.594 39.130 0.00 0.00 36.03 1.89
508 708 2.025156 CCCGTACGATCCGAACCG 59.975 66.667 18.76 0.00 0.00 4.44
563 772 8.788806 ACTCGTGGATTTTTCACATATGTTTTA 58.211 29.630 5.37 0.00 35.03 1.52
633 842 0.807496 GGCCAGAGTGAAACATGAGC 59.193 55.000 0.00 0.00 41.43 4.26
654 868 3.676873 GCTCCTGCCAAACCAAACATATG 60.677 47.826 0.00 0.00 0.00 1.78
757 973 4.927425 TCTACTTGTGATTTTACAGCCGTC 59.073 41.667 0.00 0.00 0.00 4.79
810 1034 2.060050 AGAGGGAGGAGATACACACG 57.940 55.000 0.00 0.00 0.00 4.49
817 1048 2.291190 GAGGAGATACACACGGTAGAGC 59.709 54.545 0.00 0.00 34.92 4.09
978 1210 2.214920 ACCCACTCCGTTCCACTCC 61.215 63.158 0.00 0.00 0.00 3.85
1009 1251 4.545706 GGCGCCGGATGGACATGA 62.546 66.667 12.58 0.00 37.49 3.07
1072 1315 0.739112 CAAGCCTCTCTTCGTCCTGC 60.739 60.000 0.00 0.00 31.27 4.85
1077 1320 0.172352 CTCTCTTCGTCCTGCTGGTC 59.828 60.000 9.73 3.01 34.23 4.02
1091 1334 0.886490 CTGGTCAGCAAGAAACGCCT 60.886 55.000 0.00 0.00 0.00 5.52
1347 1600 1.258445 TGTCGCTTCCTTCCTCCCTC 61.258 60.000 0.00 0.00 0.00 4.30
1365 1628 1.135915 CTCCCTTCCGATGTCTGTCTG 59.864 57.143 0.00 0.00 0.00 3.51
1381 1644 2.806818 TGTCTGTCTGTACTCTGTCGTC 59.193 50.000 0.00 0.00 0.00 4.20
1386 1649 3.437049 TGTCTGTACTCTGTCGTCATGAG 59.563 47.826 0.00 7.27 0.00 2.90
1436 1699 8.514594 TCAGAATCTCGCTGAAAAATAATGTTT 58.485 29.630 0.00 0.00 39.29 2.83
1443 1706 6.143118 TCGCTGAAAAATAATGTTTGGTTTCG 59.857 34.615 0.00 0.00 0.00 3.46
1444 1707 6.074569 CGCTGAAAAATAATGTTTGGTTTCGT 60.075 34.615 0.00 0.00 0.00 3.85
1452 1715 3.202829 TGTTTGGTTTCGTTCTAGCCT 57.797 42.857 0.00 0.00 0.00 4.58
1467 1730 2.413142 GCCTTGGTGCCTGATGCTC 61.413 63.158 0.00 0.00 42.00 4.26
1503 1767 7.363268 GGCAAAGTTCAGATTTATGAGTCCATT 60.363 37.037 0.00 0.00 34.31 3.16
1522 1786 2.391926 TAATATCAGGGAGACGGGCA 57.608 50.000 0.00 0.00 0.00 5.36
1594 1863 7.727181 AGTTCAGTTCACATACAGAAACTAGT 58.273 34.615 0.00 0.00 0.00 2.57
1612 1881 9.983804 GAAACTAGTATTTTACCTGCAATGTAC 57.016 33.333 0.00 0.00 0.00 2.90
2070 2370 9.787435 TGTCTCTAAATAACCAAGTGTACATTT 57.213 29.630 0.00 0.00 0.00 2.32
2169 2470 1.841302 TTGAAGCTCCTGATGGCCGT 61.841 55.000 0.00 0.00 0.00 5.68
2277 2578 2.158519 ACAAAACTCCTCCATCCGGTTT 60.159 45.455 0.00 0.00 0.00 3.27
2372 2679 0.813184 CCTGGTGATTGTCATGTGCC 59.187 55.000 0.00 0.00 0.00 5.01
2407 2977 3.505464 ATTAGGACCTTCAAGTCGTCG 57.495 47.619 0.00 0.00 37.66 5.12
2422 3534 2.097056 GTCGTCGAGTGCTTTTGGTAAC 60.097 50.000 0.00 0.00 0.00 2.50
2731 3870 9.262358 GACCGATCCATAGGCTATTAATTAATC 57.738 37.037 13.95 1.52 0.00 1.75
2804 3971 2.119495 GAGGGGATAACTGAAGCTCCA 58.881 52.381 0.00 0.00 0.00 3.86
2840 4007 5.118990 GCCCATAGCAACGACATGATATAT 58.881 41.667 0.00 0.00 42.97 0.86
2889 4056 6.549736 TGACGATCAAGTAATCCTCCAATCTA 59.450 38.462 0.00 0.00 0.00 1.98
3062 4252 3.712881 GAAGGCCGTCGTGCACAC 61.713 66.667 18.64 12.88 0.00 3.82
3120 4310 1.747709 ATCAGGTCAGAGCAATGCAC 58.252 50.000 8.35 0.00 0.00 4.57
3121 4311 0.397564 TCAGGTCAGAGCAATGCACA 59.602 50.000 8.35 0.00 0.00 4.57
3139 4329 2.817844 CACAGCTGCCATATATGTGCAT 59.182 45.455 21.58 10.87 35.35 3.96
3140 4330 3.254903 CACAGCTGCCATATATGTGCATT 59.745 43.478 21.58 13.97 35.35 3.56
3141 4331 3.504906 ACAGCTGCCATATATGTGCATTC 59.495 43.478 21.58 17.39 34.88 2.67
3142 4332 3.087031 AGCTGCCATATATGTGCATTCC 58.913 45.455 21.58 15.35 34.88 3.01
3147 4337 5.005740 TGCCATATATGTGCATTCCTTCTC 58.994 41.667 19.01 0.00 31.96 2.87
3180 4370 5.333046 CACATTTTGGATGACTTTTGTGC 57.667 39.130 0.00 0.00 0.00 4.57
3202 4392 4.216257 GCTCATTGTGTGAACACCATAAGT 59.784 41.667 10.92 0.00 45.88 2.24
3493 4701 1.975660 TGTCACCCCACTACTTTTGC 58.024 50.000 0.00 0.00 0.00 3.68
3524 4732 4.335082 TTCAAACAGTCAAACTCACACG 57.665 40.909 0.00 0.00 0.00 4.49
3600 4808 3.733443 ATGCGCAGTTTTCTTCCTTTT 57.267 38.095 18.32 0.00 0.00 2.27
3605 4813 3.972502 CGCAGTTTTCTTCCTTTTTACCG 59.027 43.478 0.00 0.00 0.00 4.02
3608 4816 5.758924 CAGTTTTCTTCCTTTTTACCGGAG 58.241 41.667 9.46 0.00 0.00 4.63
3680 4888 2.023673 GCGGAATGAACCATTGATCCA 58.976 47.619 0.00 0.00 33.90 3.41
3792 5000 4.154347 CTCCGCCTCCTGCTGGAC 62.154 72.222 8.48 0.00 37.61 4.02
3818 5026 0.257039 GACAGGGATTGGGACTGCAT 59.743 55.000 0.00 0.00 35.70 3.96
4011 5223 5.545588 TGAGAGAGTTTGACTGAAGAATGG 58.454 41.667 0.00 0.00 0.00 3.16
4035 5251 3.570540 TGATGCTAGATAGAGCCTGTGT 58.429 45.455 0.00 0.00 42.11 3.72
4057 5279 4.466726 GTCTAACTGATGGACCCTACACTT 59.533 45.833 0.00 0.00 33.65 3.16
4069 5291 2.039084 CCCTACACTTTTGCTGACTCCT 59.961 50.000 0.00 0.00 0.00 3.69
4130 5352 2.875672 GCAGCCACCTCATGAACAACTA 60.876 50.000 0.00 0.00 0.00 2.24
4168 5391 5.826737 AGTGATGATTCAGATTTCCACCATC 59.173 40.000 0.00 0.00 30.85 3.51
4183 5406 3.137176 CCACCATCTCTCTCTCTCTCTCT 59.863 52.174 0.00 0.00 0.00 3.10
4184 5407 4.384056 CACCATCTCTCTCTCTCTCTCTC 58.616 52.174 0.00 0.00 0.00 3.20
4185 5408 4.102210 CACCATCTCTCTCTCTCTCTCTCT 59.898 50.000 0.00 0.00 0.00 3.10
4186 5409 4.346418 ACCATCTCTCTCTCTCTCTCTCTC 59.654 50.000 0.00 0.00 0.00 3.20
4187 5410 4.592351 CCATCTCTCTCTCTCTCTCTCTCT 59.408 50.000 0.00 0.00 0.00 3.10
4188 5411 5.279406 CCATCTCTCTCTCTCTCTCTCTCTC 60.279 52.000 0.00 0.00 0.00 3.20
4189 5412 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
4190 5413 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4191 5414 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4192 5415 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4193 5416 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4194 5417 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4195 5418 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4196 5419 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4197 5420 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4198 5421 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4498 5724 2.183679 CTTCTTCAGCTGGGACTAGGT 58.816 52.381 15.13 0.00 0.00 3.08
4503 5729 0.674895 CAGCTGGGACTAGGTTGTGC 60.675 60.000 5.57 0.00 0.00 4.57
4602 5830 1.734465 AGTAGATGCGCAAAAGAGCAC 59.266 47.619 17.11 5.85 46.83 4.40
4649 5886 1.858091 CACTCAAGTCTGCGTTCACT 58.142 50.000 0.00 0.00 0.00 3.41
4685 5922 2.814805 AAGGGTCCCAGATGATGTTG 57.185 50.000 11.55 0.00 0.00 3.33
4686 5923 1.673767 AGGGTCCCAGATGATGTTGT 58.326 50.000 11.55 0.00 0.00 3.32
4782 6021 2.809309 TCCCTTCTCCTTATACCCCC 57.191 55.000 0.00 0.00 0.00 5.40
4824 6066 6.575942 CCGTGTAAAAATGCAGTAACAGTAAC 59.424 38.462 0.00 0.00 0.00 2.50
4866 6108 2.294791 AGCAGCTCATCACCTCGTATAC 59.705 50.000 0.00 0.00 0.00 1.47
4871 6114 5.755375 CAGCTCATCACCTCGTATACAATTT 59.245 40.000 3.32 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 138 5.337009 CCCAAAAGAGTGAAATGAGGGATTG 60.337 44.000 0.00 0.00 35.81 2.67
153 155 3.146847 ACCTCGCTTTTCTACCCAAAAG 58.853 45.455 1.98 1.98 43.52 2.27
232 235 1.900254 TTAGGGTGTATCATGCCCCA 58.100 50.000 1.98 0.00 43.32 4.96
313 317 3.570125 GGTTTTGTCTTGAAGAAGGGAGG 59.430 47.826 0.00 0.00 0.00 4.30
370 375 6.007076 TGTGATGTAAAAAGGAGCATAACCA 58.993 36.000 0.00 0.00 0.00 3.67
508 708 3.345508 AGGTATTGAAAGTTCGGGTCC 57.654 47.619 0.00 0.00 0.00 4.46
571 780 9.933723 CATTTCATTCATTTTAGGGAAAAGAGT 57.066 29.630 0.00 0.00 37.94 3.24
572 781 8.876790 GCATTTCATTCATTTTAGGGAAAAGAG 58.123 33.333 0.00 0.00 37.94 2.85
633 842 3.511146 ACATATGTTTGGTTTGGCAGGAG 59.489 43.478 1.41 0.00 0.00 3.69
654 868 6.425114 TCTTCTCACTTAGCTCATGTTTCAAC 59.575 38.462 0.00 0.00 0.00 3.18
664 878 5.337578 AGGAACATCTTCTCACTTAGCTC 57.662 43.478 0.00 0.00 0.00 4.09
665 879 7.430760 AATAGGAACATCTTCTCACTTAGCT 57.569 36.000 0.00 0.00 0.00 3.32
666 880 8.417884 AGTAATAGGAACATCTTCTCACTTAGC 58.582 37.037 0.00 0.00 0.00 3.09
671 885 7.717568 TGCTAGTAATAGGAACATCTTCTCAC 58.282 38.462 0.00 0.00 0.00 3.51
757 973 2.744709 CCAAGTACCCAACGCCCG 60.745 66.667 0.00 0.00 0.00 6.13
810 1034 0.100861 GTGACCGCTAGTGCTCTACC 59.899 60.000 0.00 0.00 36.97 3.18
817 1048 2.809601 GGCACGTGACCGCTAGTG 60.810 66.667 22.23 0.00 37.70 2.74
958 1189 1.755393 GAGTGGAACGGAGTGGGTGT 61.755 60.000 0.00 0.00 45.00 4.16
962 1193 2.663196 GGGAGTGGAACGGAGTGG 59.337 66.667 0.00 0.00 45.00 4.00
1009 1251 1.067354 CGTACCTTGGTTAGCTCCGTT 60.067 52.381 0.00 0.00 0.00 4.44
1058 1301 0.172352 GACCAGCAGGACGAAGAGAG 59.828 60.000 0.35 0.00 38.69 3.20
1059 1302 0.539669 TGACCAGCAGGACGAAGAGA 60.540 55.000 0.35 0.00 38.69 3.10
1060 1303 0.108898 CTGACCAGCAGGACGAAGAG 60.109 60.000 0.35 0.00 41.07 2.85
1061 1304 1.967535 CTGACCAGCAGGACGAAGA 59.032 57.895 0.35 0.00 41.07 2.87
1062 1305 4.586618 CTGACCAGCAGGACGAAG 57.413 61.111 0.35 0.00 41.07 3.79
1072 1315 0.886490 AGGCGTTTCTTGCTGACCAG 60.886 55.000 0.00 0.00 0.00 4.00
1077 1320 1.517242 AAGAGAGGCGTTTCTTGCTG 58.483 50.000 11.02 0.00 32.65 4.41
1106 1351 3.058914 ACAGCCGTGAGAAAAATCGAAAG 60.059 43.478 0.00 0.00 0.00 2.62
1214 1467 0.742281 CTCCACCACTCGCATTCCTG 60.742 60.000 0.00 0.00 0.00 3.86
1327 1580 0.618968 AGGGAGGAAGGAAGCGACAT 60.619 55.000 0.00 0.00 0.00 3.06
1328 1581 1.229209 AGGGAGGAAGGAAGCGACA 60.229 57.895 0.00 0.00 0.00 4.35
1347 1600 0.898320 ACAGACAGACATCGGAAGGG 59.102 55.000 0.00 0.00 0.00 3.95
1365 1628 3.685272 TCTCATGACGACAGAGTACAGAC 59.315 47.826 0.00 0.00 0.00 3.51
1381 1644 4.711355 ACCCCAACCAACATTATTCTCATG 59.289 41.667 0.00 0.00 0.00 3.07
1386 1649 5.423931 ACCATTACCCCAACCAACATTATTC 59.576 40.000 0.00 0.00 0.00 1.75
1436 1699 1.418637 ACCAAGGCTAGAACGAAACCA 59.581 47.619 0.00 0.00 0.00 3.67
1467 1730 5.443185 TCTGAACTTTGCCAAGAATGAAG 57.557 39.130 4.25 0.00 33.72 3.02
1503 1767 2.391926 TGCCCGTCTCCCTGATATTA 57.608 50.000 0.00 0.00 0.00 0.98
1505 1769 1.734655 AATGCCCGTCTCCCTGATAT 58.265 50.000 0.00 0.00 0.00 1.63
1511 1775 1.143073 AGGAAATAATGCCCGTCTCCC 59.857 52.381 0.00 0.00 0.00 4.30
1522 1786 7.069208 GCTGAAATCCCAGAGAAAGGAAATAAT 59.931 37.037 0.00 0.00 35.30 1.28
1594 1863 9.325198 CATCTACAGTACATTGCAGGTAAAATA 57.675 33.333 0.00 0.00 0.00 1.40
1612 1881 2.095567 GCGCCATATTTGCCATCTACAG 60.096 50.000 0.00 0.00 0.00 2.74
1631 1900 0.965439 TCAGACAAATTTTGGGGGCG 59.035 50.000 13.42 0.00 34.12 6.13
1804 2104 9.931698 TCCACTACTCTATAGTCCTATCAAAAA 57.068 33.333 0.00 0.00 37.15 1.94
1811 2111 9.216148 GGATATCTCCACTACTCTATAGTCCTA 57.784 40.741 2.05 0.00 41.64 2.94
2070 2370 1.293498 GCGCTGTCCAAGGAGAAGA 59.707 57.895 0.00 0.00 0.00 2.87
2169 2470 4.354893 ACCGATTTTAACAGGGTACACA 57.645 40.909 0.00 0.00 0.00 3.72
2277 2578 0.759812 TGGAGTTCCCACGGTACACA 60.760 55.000 0.00 0.00 40.82 3.72
2362 2669 0.036022 TCACCATTCGGCACATGACA 59.964 50.000 0.00 0.00 34.57 3.58
2372 2679 4.332819 GGTCCTAATTGACTTCACCATTCG 59.667 45.833 0.00 0.00 35.54 3.34
2407 2977 3.349488 AAAGCGTTACCAAAAGCACTC 57.651 42.857 0.00 0.00 41.86 3.51
2422 3534 6.313905 AGAGTGTTATAACCATCAGAAAAGCG 59.686 38.462 13.01 0.00 0.00 4.68
2469 3581 2.439156 GCAGGATCAGGCACCACC 60.439 66.667 0.00 0.00 39.61 4.61
2583 3710 3.679389 ACGAAATTCAGACCTCATGCTT 58.321 40.909 0.00 0.00 0.00 3.91
2731 3870 0.313043 CTGCAAGAACACAAGCTGGG 59.687 55.000 0.00 0.00 34.07 4.45
2804 3971 2.692041 GCTATGGGCTTTGAGCTGAATT 59.308 45.455 0.00 0.00 41.99 2.17
2840 4007 1.226916 CTTGCTTGCGCCAACAACA 60.227 52.632 4.18 0.00 34.43 3.33
2889 4056 6.998074 TGACCATCTACAAAATGACTCAACTT 59.002 34.615 0.00 0.00 0.00 2.66
3062 4252 1.221466 TTGAAGCCGTGTTCTGAGCG 61.221 55.000 0.00 0.00 0.00 5.03
3120 4310 3.119602 GGAATGCACATATATGGCAGCTG 60.120 47.826 23.93 10.11 37.38 4.24
3121 4311 3.087031 GGAATGCACATATATGGCAGCT 58.913 45.455 23.93 17.23 37.38 4.24
3139 4329 5.047566 TGTGGTGAAATGAAGAGAAGGAA 57.952 39.130 0.00 0.00 0.00 3.36
3140 4330 4.705110 TGTGGTGAAATGAAGAGAAGGA 57.295 40.909 0.00 0.00 0.00 3.36
3141 4331 5.972107 AATGTGGTGAAATGAAGAGAAGG 57.028 39.130 0.00 0.00 0.00 3.46
3142 4332 6.643770 CCAAAATGTGGTGAAATGAAGAGAAG 59.356 38.462 0.00 0.00 43.20 2.85
3202 4392 5.774690 AGTCCTGAAAAACATTCCATGCTTA 59.225 36.000 0.00 0.00 0.00 3.09
3493 4701 3.358775 TGACTGTTTGAAAACGCAATCG 58.641 40.909 1.76 0.00 41.74 3.34
3503 4711 3.425625 GCGTGTGAGTTTGACTGTTTGAA 60.426 43.478 0.00 0.00 0.00 2.69
3504 4712 2.095213 GCGTGTGAGTTTGACTGTTTGA 59.905 45.455 0.00 0.00 0.00 2.69
3505 4713 2.159585 TGCGTGTGAGTTTGACTGTTTG 60.160 45.455 0.00 0.00 0.00 2.93
3506 4714 2.080693 TGCGTGTGAGTTTGACTGTTT 58.919 42.857 0.00 0.00 0.00 2.83
3508 4716 1.006832 GTGCGTGTGAGTTTGACTGT 58.993 50.000 0.00 0.00 0.00 3.55
3509 4717 1.006086 TGTGCGTGTGAGTTTGACTG 58.994 50.000 0.00 0.00 0.00 3.51
3510 4718 1.953559 ATGTGCGTGTGAGTTTGACT 58.046 45.000 0.00 0.00 0.00 3.41
3524 4732 3.356290 AGGTGAGAAATGGGTTATGTGC 58.644 45.455 0.00 0.00 0.00 4.57
3579 4787 3.733443 AAAGGAAGAAAACTGCGCATT 57.267 38.095 12.24 0.75 0.00 3.56
3583 4791 3.972502 CGGTAAAAAGGAAGAAAACTGCG 59.027 43.478 0.00 0.00 0.00 5.18
3587 4795 6.381481 TTCTCCGGTAAAAAGGAAGAAAAC 57.619 37.500 0.00 0.00 35.90 2.43
3600 4808 2.088950 CGAAAGCCTTTCTCCGGTAA 57.911 50.000 14.82 0.00 37.52 2.85
3680 4888 2.033550 GTCAGATACGACGATCAGCCTT 59.966 50.000 0.00 0.00 0.00 4.35
3792 5000 2.885644 CAATCCCTGTCGTCGCCG 60.886 66.667 0.00 0.00 0.00 6.46
3818 5026 2.978156 AGATTTCCTCAAGCCCAACA 57.022 45.000 0.00 0.00 0.00 3.33
4011 5223 2.094078 CAGGCTCTATCTAGCATCAGGC 60.094 54.545 0.00 0.00 44.64 4.85
4035 5251 4.332683 AGTGTAGGGTCCATCAGTTAGA 57.667 45.455 0.00 0.00 0.00 2.10
4057 5279 2.928801 TAGCACAAGGAGTCAGCAAA 57.071 45.000 0.00 0.00 0.00 3.68
4069 5291 2.754552 GGGATCAGCAACAATAGCACAA 59.245 45.455 0.00 0.00 0.00 3.33
4155 5377 4.882559 AGAGAGAGAGATGGTGGAAATCT 58.117 43.478 0.00 0.00 37.09 2.40
4168 5391 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4632 5869 5.403897 TTTTTAGTGAACGCAGACTTGAG 57.596 39.130 0.00 0.00 0.00 3.02
4692 5929 8.603181 GCGGATGTTTTGCATTTAAAATCTTAT 58.397 29.630 0.00 0.00 38.06 1.73
4694 5931 6.128309 GGCGGATGTTTTGCATTTAAAATCTT 60.128 34.615 0.00 0.00 38.06 2.40
4696 5933 5.121454 TGGCGGATGTTTTGCATTTAAAATC 59.879 36.000 0.00 0.00 38.06 2.17
4782 6021 1.953686 ACGGAACCTGTTTTCCATGTG 59.046 47.619 2.95 0.00 44.87 3.21
4801 6043 7.112984 GCTGTTACTGTTACTGCATTTTTACAC 59.887 37.037 19.33 0.00 39.41 2.90
4824 6066 1.939934 CACTAGAGAGAGACCGAGCTG 59.060 57.143 0.00 0.00 0.00 4.24
4866 6108 9.906660 TTGCCAAATACTTACAGTAGAAAATTG 57.093 29.630 0.00 0.00 33.66 2.32
4871 6114 7.602644 CAGTCTTGCCAAATACTTACAGTAGAA 59.397 37.037 0.00 0.00 33.66 2.10


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

AutoCloner maintained by Alex Coulton.