Multiple sequence alignment - TraesCS2A01G504400

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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 TraesCS2A01G504400 chr2A 100.000 4244 0 0 1 4244 733290358 733286115 0.000000e+00 7838.0
1 TraesCS2A01G504400 chr2A 87.123 2454 275 31 888 3324 733344561 733342132 0.000000e+00 2743.0
2 TraesCS2A01G504400 chr2A 79.916 2370 392 59 887 3224 733349015 733346698 0.000000e+00 1663.0
3 TraesCS2A01G504400 chr2A 76.753 2211 439 49 1085 3247 666020967 666023150 0.000000e+00 1166.0
4 TraesCS2A01G504400 chr2A 82.530 166 26 3 3506 3669 703564953 703565117 4.420000e-30 143.0
5 TraesCS2A01G504400 chr2D 93.222 3408 174 19 877 4244 599104943 599101553 0.000000e+00 4961.0
6 TraesCS2A01G504400 chr2D 90.227 2374 214 9 881 3247 599154473 599152111 0.000000e+00 3083.0
7 TraesCS2A01G504400 chr2D 87.752 2384 259 21 954 3324 599111298 599108935 0.000000e+00 2754.0
8 TraesCS2A01G504400 chr2D 80.244 2374 380 59 887 3224 599220465 599218145 0.000000e+00 1703.0
9 TraesCS2A01G504400 chr2D 76.279 2365 467 58 946 3247 521568597 521566264 0.000000e+00 1173.0
10 TraesCS2A01G504400 chr2D 80.986 426 49 18 198 597 183388120 183388539 4.120000e-80 309.0
11 TraesCS2A01G504400 chr2D 89.024 164 16 2 3 164 183387953 183388116 7.200000e-48 202.0
12 TraesCS2A01G504400 chr2D 85.507 138 10 4 740 875 599105115 599104986 7.400000e-28 135.0
13 TraesCS2A01G504400 chr2D 82.443 131 20 3 3506 3634 642814534 642814405 1.250000e-20 111.0
14 TraesCS2A01G504400 chr2D 94.231 52 3 0 824 875 599111504 599111453 3.520000e-11 80.5
15 TraesCS2A01G504400 chr2B 93.234 2557 147 7 877 3424 728562347 728559808 0.000000e+00 3740.0
16 TraesCS2A01G504400 chr2B 91.838 2487 168 16 877 3358 728587174 728584718 0.000000e+00 3435.0
17 TraesCS2A01G504400 chr2B 80.794 2166 348 49 1085 3222 728611452 728609327 0.000000e+00 1633.0
18 TraesCS2A01G504400 chr2B 91.828 673 39 3 1 657 408323197 408323869 0.000000e+00 924.0
19 TraesCS2A01G504400 chr2B 93.258 623 15 10 3647 4244 728557758 728557138 0.000000e+00 893.0
20 TraesCS2A01G504400 chr2B 83.784 259 19 4 3421 3657 728559552 728559295 1.540000e-54 224.0
21 TraesCS2A01G504400 chr2B 87.121 132 10 4 746 875 728562516 728562390 4.420000e-30 143.0
22 TraesCS2A01G504400 chr2B 86.667 135 9 4 743 875 728587344 728587217 1.590000e-29 141.0
23 TraesCS2A01G504400 chr3B 91.158 2262 198 2 987 3247 60155745 60158005 0.000000e+00 3068.0
24 TraesCS2A01G504400 chr3B 79.487 195 37 3 3514 3706 76491526 76491719 7.400000e-28 135.0
25 TraesCS2A01G504400 chr4A 94.526 749 34 2 1 743 154934613 154933866 0.000000e+00 1149.0
26 TraesCS2A01G504400 chr4A 79.114 158 30 3 3481 3635 546389033 546389190 5.800000e-19 106.0
27 TraesCS2A01G504400 chr6B 90.638 737 50 2 1 720 459794289 459793555 0.000000e+00 961.0
28 TraesCS2A01G504400 chr6B 79.279 222 37 8 3488 3706 693053774 693053559 3.420000e-31 147.0
29 TraesCS2A01G504400 chr1A 91.852 675 35 6 84 741 426928180 426928851 0.000000e+00 924.0
30 TraesCS2A01G504400 chr1A 93.439 442 22 4 305 740 38154756 38155196 0.000000e+00 649.0
31 TraesCS2A01G504400 chr1A 92.152 446 33 2 185 630 38154304 38154747 2.790000e-176 628.0
32 TraesCS2A01G504400 chr7A 83.662 355 42 10 198 539 315283503 315283854 1.900000e-83 320.0
33 TraesCS2A01G504400 chr4D 82.955 352 46 7 198 538 30900947 30901295 5.330000e-79 305.0
34 TraesCS2A01G504400 chr4D 88.415 164 17 2 3 164 361603059 361603222 3.350000e-46 196.0
35 TraesCS2A01G504400 chr4D 87.805 164 18 2 3 164 30900780 30900943 1.560000e-44 191.0
36 TraesCS2A01G504400 chr5D 89.024 164 16 2 3 164 27452342 27452505 7.200000e-48 202.0
37 TraesCS2A01G504400 chr5B 87.273 165 18 2 3 164 24238360 24238524 7.250000e-43 185.0
38 TraesCS2A01G504400 chr7D 78.894 199 39 3 3506 3701 397381003 397380805 9.570000e-27 132.0
39 TraesCS2A01G504400 chr7D 79.333 150 29 2 3504 3652 471058776 471058628 2.090000e-18 104.0
40 TraesCS2A01G504400 chr1D 79.605 152 26 5 3516 3664 112625774 112625923 2.090000e-18 104.0


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 TraesCS2A01G504400 chr2A 733286115 733290358 4243 True 7838.000 7838 100.00000 1 4244 1 chr2A.!!$R1 4243
1 TraesCS2A01G504400 chr2A 733342132 733349015 6883 True 2203.000 2743 83.51950 887 3324 2 chr2A.!!$R2 2437
2 TraesCS2A01G504400 chr2A 666020967 666023150 2183 False 1166.000 1166 76.75300 1085 3247 1 chr2A.!!$F1 2162
3 TraesCS2A01G504400 chr2D 599152111 599154473 2362 True 3083.000 3083 90.22700 881 3247 1 chr2D.!!$R2 2366
4 TraesCS2A01G504400 chr2D 599101553 599111504 9951 True 1982.625 4961 90.17800 740 4244 4 chr2D.!!$R5 3504
5 TraesCS2A01G504400 chr2D 599218145 599220465 2320 True 1703.000 1703 80.24400 887 3224 1 chr2D.!!$R3 2337
6 TraesCS2A01G504400 chr2D 521566264 521568597 2333 True 1173.000 1173 76.27900 946 3247 1 chr2D.!!$R1 2301
7 TraesCS2A01G504400 chr2D 183387953 183388539 586 False 255.500 309 85.00500 3 597 2 chr2D.!!$F1 594
8 TraesCS2A01G504400 chr2B 728584718 728587344 2626 True 1788.000 3435 89.25250 743 3358 2 chr2B.!!$R3 2615
9 TraesCS2A01G504400 chr2B 728609327 728611452 2125 True 1633.000 1633 80.79400 1085 3222 1 chr2B.!!$R1 2137
10 TraesCS2A01G504400 chr2B 728557138 728562516 5378 True 1250.000 3740 89.34925 746 4244 4 chr2B.!!$R2 3498
11 TraesCS2A01G504400 chr2B 408323197 408323869 672 False 924.000 924 91.82800 1 657 1 chr2B.!!$F1 656
12 TraesCS2A01G504400 chr3B 60155745 60158005 2260 False 3068.000 3068 91.15800 987 3247 1 chr3B.!!$F1 2260
13 TraesCS2A01G504400 chr4A 154933866 154934613 747 True 1149.000 1149 94.52600 1 743 1 chr4A.!!$R1 742
14 TraesCS2A01G504400 chr6B 459793555 459794289 734 True 961.000 961 90.63800 1 720 1 chr6B.!!$R1 719
15 TraesCS2A01G504400 chr1A 426928180 426928851 671 False 924.000 924 91.85200 84 741 1 chr1A.!!$F1 657
16 TraesCS2A01G504400 chr1A 38154304 38155196 892 False 638.500 649 92.79550 185 740 2 chr1A.!!$F2 555
17 TraesCS2A01G504400 chr4D 30900780 30901295 515 False 248.000 305 85.38000 3 538 2 chr4D.!!$F2 535

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
827 1219 0.034616 GACACTCTTGCTGGCACTCT 59.965 55.0 0.0 0.0 0.0 3.24 F
828 1220 0.471617 ACACTCTTGCTGGCACTCTT 59.528 50.0 0.0 0.0 0.0 2.85 F
882 1274 0.618458 TTCCCAAGCTATCGCCACTT 59.382 50.0 0.0 0.0 36.6 3.16 F
2068 9995 0.250295 CTTCCAGCCCGACAACTCAA 60.250 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 9978 0.321564 CATTGAGTTGTCGGGCTGGA 60.322 55.0 0.0 0.00 0.00 3.86 R
2068 9995 0.325296 TAGACCAACGAGGCCTCCAT 60.325 55.0 27.2 12.92 43.14 3.41 R
2241 10177 2.008242 AAAGCTGGTTGCCCACAATA 57.992 45.0 0.0 0.00 44.23 1.90 R
3628 11873 0.610174 CCTAGACTTGGCACTGCTGA 59.390 55.0 0.0 0.00 0.00 4.26 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
32 34 3.440173 TCAACCGATGAATTTGAAGCCTC 59.560 43.478 0.00 0.00 34.30 4.70
127 131 1.086696 GCATAACGGCGGCATATCAT 58.913 50.000 13.24 0.00 0.00 2.45
218 222 1.476891 GATGGACTGCAGACCGTCTTA 59.523 52.381 35.52 18.95 40.87 2.10
226 230 1.669211 GCAGACCGTCTTAGGTGACAC 60.669 57.143 0.00 0.00 46.09 3.67
329 338 1.573108 ACCACGACCTCATCTTCCAT 58.427 50.000 0.00 0.00 0.00 3.41
697 1083 1.140052 TGCCGATCGTATGTGGGAAAT 59.860 47.619 15.09 0.00 0.00 2.17
750 1142 8.922058 TTTAATAGTAGAGATGACGGTTCAAC 57.078 34.615 0.00 0.00 34.61 3.18
754 1146 6.525578 AGTAGAGATGACGGTTCAACAATA 57.474 37.500 0.00 0.00 34.61 1.90
758 1150 5.869888 AGAGATGACGGTTCAACAATACTTC 59.130 40.000 0.00 0.00 34.61 3.01
771 1163 4.072131 ACAATACTTCGCATGGTTGTCTT 58.928 39.130 0.00 0.00 0.00 3.01
806 1198 4.463050 AAAAATCCCTGTCCAACCTACA 57.537 40.909 0.00 0.00 0.00 2.74
807 1199 4.675063 AAAATCCCTGTCCAACCTACAT 57.325 40.909 0.00 0.00 0.00 2.29
808 1200 3.652057 AATCCCTGTCCAACCTACATG 57.348 47.619 0.00 0.00 0.00 3.21
809 1201 2.335681 TCCCTGTCCAACCTACATGA 57.664 50.000 0.00 0.00 0.00 3.07
810 1202 1.906574 TCCCTGTCCAACCTACATGAC 59.093 52.381 0.00 0.00 0.00 3.06
811 1203 1.628340 CCCTGTCCAACCTACATGACA 59.372 52.381 0.00 0.00 36.40 3.58
812 1204 2.615493 CCCTGTCCAACCTACATGACAC 60.615 54.545 0.00 0.00 34.30 3.67
813 1205 2.303022 CCTGTCCAACCTACATGACACT 59.697 50.000 0.00 0.00 34.30 3.55
814 1206 3.589988 CTGTCCAACCTACATGACACTC 58.410 50.000 0.00 0.00 34.30 3.51
815 1207 3.239449 TGTCCAACCTACATGACACTCT 58.761 45.455 0.00 0.00 33.09 3.24
816 1208 3.646162 TGTCCAACCTACATGACACTCTT 59.354 43.478 0.00 0.00 33.09 2.85
817 1209 3.997021 GTCCAACCTACATGACACTCTTG 59.003 47.826 0.00 0.00 0.00 3.02
818 1210 2.744202 CCAACCTACATGACACTCTTGC 59.256 50.000 0.00 0.00 0.00 4.01
819 1211 3.557898 CCAACCTACATGACACTCTTGCT 60.558 47.826 0.00 0.00 0.00 3.91
820 1212 3.325293 ACCTACATGACACTCTTGCTG 57.675 47.619 0.00 0.00 0.00 4.41
821 1213 2.027745 ACCTACATGACACTCTTGCTGG 60.028 50.000 0.00 0.00 0.00 4.85
822 1214 2.005451 CTACATGACACTCTTGCTGGC 58.995 52.381 0.00 0.00 0.00 4.85
823 1215 0.109153 ACATGACACTCTTGCTGGCA 59.891 50.000 0.00 0.00 0.00 4.92
824 1216 0.520404 CATGACACTCTTGCTGGCAC 59.480 55.000 0.00 0.00 26.12 5.01
825 1217 0.399454 ATGACACTCTTGCTGGCACT 59.601 50.000 0.00 0.00 26.12 4.40
826 1218 0.250038 TGACACTCTTGCTGGCACTC 60.250 55.000 0.00 0.00 0.00 3.51
827 1219 0.034616 GACACTCTTGCTGGCACTCT 59.965 55.000 0.00 0.00 0.00 3.24
828 1220 0.471617 ACACTCTTGCTGGCACTCTT 59.528 50.000 0.00 0.00 0.00 2.85
829 1221 1.155042 CACTCTTGCTGGCACTCTTC 58.845 55.000 0.00 0.00 0.00 2.87
872 1264 1.534729 GGAACGTCAATTCCCAAGCT 58.465 50.000 0.00 0.00 42.16 3.74
875 1267 3.312697 GGAACGTCAATTCCCAAGCTATC 59.687 47.826 0.00 0.00 42.16 2.08
877 1269 1.261619 CGTCAATTCCCAAGCTATCGC 59.738 52.381 0.00 0.00 0.00 4.58
878 1270 1.604278 GTCAATTCCCAAGCTATCGCC 59.396 52.381 0.00 0.00 36.60 5.54
879 1271 1.211703 TCAATTCCCAAGCTATCGCCA 59.788 47.619 0.00 0.00 36.60 5.69
881 1273 0.839946 ATTCCCAAGCTATCGCCACT 59.160 50.000 0.00 0.00 36.60 4.00
882 1274 0.618458 TTCCCAAGCTATCGCCACTT 59.382 50.000 0.00 0.00 36.60 3.16
884 1276 1.004277 TCCCAAGCTATCGCCACTTTT 59.996 47.619 0.00 0.00 36.60 2.27
885 1277 1.401905 CCCAAGCTATCGCCACTTTTC 59.598 52.381 0.00 0.00 36.60 2.29
897 1377 1.226746 CACTTTTCCCTCGACCACAC 58.773 55.000 0.00 0.00 0.00 3.82
899 1379 0.949105 CTTTTCCCTCGACCACACCG 60.949 60.000 0.00 0.00 0.00 4.94
908 8800 1.518572 GACCACACCGATGCCTACG 60.519 63.158 0.00 0.00 0.00 3.51
1125 9040 1.987855 CCAGGAGGACCGCCAGTTA 60.988 63.158 17.44 0.00 41.83 2.24
1173 9088 1.920835 GCACCAGTCCTTCCTCCCT 60.921 63.158 0.00 0.00 0.00 4.20
1287 9202 3.861263 GGGTTTGTCGCCGCGATC 61.861 66.667 20.03 12.92 38.42 3.69
1931 9858 2.202932 CAACTCCGGCCCGATCAG 60.203 66.667 3.71 0.00 0.00 2.90
1938 9865 3.934962 GGCCCGATCAGCTCCTCC 61.935 72.222 0.00 0.00 0.00 4.30
2067 9994 1.118965 TCTTCCAGCCCGACAACTCA 61.119 55.000 0.00 0.00 0.00 3.41
2068 9995 0.250295 CTTCCAGCCCGACAACTCAA 60.250 55.000 0.00 0.00 0.00 3.02
2386 10322 2.135933 CGACGGCAAATATCTCCTTCC 58.864 52.381 0.00 0.00 0.00 3.46
2387 10323 2.224066 CGACGGCAAATATCTCCTTCCT 60.224 50.000 0.00 0.00 0.00 3.36
2388 10324 3.394719 GACGGCAAATATCTCCTTCCTC 58.605 50.000 0.00 0.00 0.00 3.71
2679 10624 1.141881 GTCCGCCATCATGACGACT 59.858 57.895 0.00 0.00 0.00 4.18
2813 10758 4.218312 GGCCTGATATTTGACATTTCCCT 58.782 43.478 0.00 0.00 0.00 4.20
2815 10760 4.646492 GCCTGATATTTGACATTTCCCTGT 59.354 41.667 0.00 0.00 0.00 4.00
2961 10906 1.826487 GGTGTTGTTCCCGCCAACT 60.826 57.895 5.07 0.00 42.09 3.16
3006 10951 2.809601 GAGCGCACGGTGTCGAAT 60.810 61.111 22.56 13.13 40.11 3.34
3112 11063 2.816012 TGTTCACCGAGGCGAACA 59.184 55.556 18.49 18.49 46.91 3.18
3135 11086 7.220030 ACAAGGTGCAGAAATTCGATATAGAT 58.780 34.615 0.00 0.00 0.00 1.98
3144 11095 4.744795 ATTCGATATAGATGTGGAGGCC 57.255 45.455 0.00 0.00 0.00 5.19
3225 11179 1.486726 GTGAGGATCCCAATCTCGGTT 59.513 52.381 8.55 0.00 32.12 4.44
3237 11191 2.736682 CTCGGTTACCTTTGCGGCG 61.737 63.158 0.51 0.51 35.61 6.46
3519 11756 3.610040 TGAAATACTGAGCGGACACAT 57.390 42.857 0.00 0.00 0.00 3.21
3531 11768 5.028549 AGCGGACACATCATCTTAAGATT 57.971 39.130 15.49 0.00 31.21 2.40
3532 11769 4.813161 AGCGGACACATCATCTTAAGATTG 59.187 41.667 15.49 14.26 31.21 2.67
3551 11788 3.108521 ACGAAGTCATCACAGACGC 57.891 52.632 0.00 0.00 43.24 5.19
3597 11842 4.811555 TCAACTGAAAGAACATTGTCGG 57.188 40.909 0.00 0.00 37.43 4.79
3607 11852 2.403252 ACATTGTCGGAAAGCCTAGG 57.597 50.000 3.67 3.67 0.00 3.02
3615 11860 5.365619 TGTCGGAAAGCCTAGGATAATTTC 58.634 41.667 14.75 15.23 0.00 2.17
3618 11863 5.365605 TCGGAAAGCCTAGGATAATTTCAGA 59.634 40.000 14.75 17.49 33.65 3.27
3628 11873 8.571336 CCTAGGATAATTTCAGAAAAATGCGAT 58.429 33.333 1.05 0.00 0.00 4.58
3657 13449 4.647399 GTGCCAAGTCTAGGTCTTAGATCT 59.353 45.833 0.00 0.00 40.42 2.75
3701 13493 8.402472 CACAACAAACTTAACCATCTGAGTTAA 58.598 33.333 3.26 3.26 37.35 2.01
3722 13514 2.171448 AGCTCCATTCGCCTTGACTAAT 59.829 45.455 0.00 0.00 0.00 1.73
4045 13862 3.565214 TGGAGGTTTGGGCGCTGA 61.565 61.111 7.64 0.00 0.00 4.26
4199 14018 2.565841 GTTGCTAGCCTTGTATCTGGG 58.434 52.381 13.29 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 5.551760 TTCTTCGAGGCTTCAAATTCATC 57.448 39.130 0.00 0.00 0.00 2.92
32 34 3.685836 ACCGTGTTTCCTTTTTCTTCG 57.314 42.857 0.00 0.00 0.00 3.79
218 222 0.178958 ACCTTCTCCTCGTGTCACCT 60.179 55.000 0.00 0.00 0.00 4.00
226 230 4.821589 GGGCGCACCTTCTCCTCG 62.822 72.222 10.83 0.00 35.85 4.63
362 371 0.253868 TGGGAGAGAGAGGGAGGAGA 60.254 60.000 0.00 0.00 0.00 3.71
429 441 2.201921 TCTAAGTGAGGCGTGTCTCT 57.798 50.000 2.84 0.00 34.98 3.10
697 1083 0.172578 CGTGATGGTTCGACCTGCTA 59.827 55.000 5.77 0.00 39.58 3.49
750 1142 4.685169 AAGACAACCATGCGAAGTATTG 57.315 40.909 0.00 0.00 0.00 1.90
754 1146 5.508200 TTTTTAAGACAACCATGCGAAGT 57.492 34.783 0.00 0.00 0.00 3.01
785 1177 4.463050 TGTAGGTTGGACAGGGATTTTT 57.537 40.909 0.00 0.00 0.00 1.94
786 1178 4.044065 TCATGTAGGTTGGACAGGGATTTT 59.956 41.667 0.00 0.00 0.00 1.82
787 1179 3.591527 TCATGTAGGTTGGACAGGGATTT 59.408 43.478 0.00 0.00 0.00 2.17
788 1180 3.054361 GTCATGTAGGTTGGACAGGGATT 60.054 47.826 0.00 0.00 0.00 3.01
791 1183 1.628340 TGTCATGTAGGTTGGACAGGG 59.372 52.381 0.00 0.00 35.51 4.45
804 1196 0.109153 TGCCAGCAAGAGTGTCATGT 59.891 50.000 0.00 0.00 0.00 3.21
805 1197 0.520404 GTGCCAGCAAGAGTGTCATG 59.480 55.000 0.00 0.00 0.00 3.07
806 1198 0.399454 AGTGCCAGCAAGAGTGTCAT 59.601 50.000 0.00 0.00 0.00 3.06
807 1199 0.250038 GAGTGCCAGCAAGAGTGTCA 60.250 55.000 0.00 0.00 0.00 3.58
808 1200 0.034616 AGAGTGCCAGCAAGAGTGTC 59.965 55.000 0.00 0.00 0.00 3.67
809 1201 0.471617 AAGAGTGCCAGCAAGAGTGT 59.528 50.000 0.00 0.00 0.00 3.55
810 1202 1.155042 GAAGAGTGCCAGCAAGAGTG 58.845 55.000 0.00 0.00 0.00 3.51
811 1203 0.320247 CGAAGAGTGCCAGCAAGAGT 60.320 55.000 0.00 0.00 0.00 3.24
812 1204 1.633852 GCGAAGAGTGCCAGCAAGAG 61.634 60.000 0.00 0.00 0.00 2.85
813 1205 1.669115 GCGAAGAGTGCCAGCAAGA 60.669 57.895 0.00 0.00 0.00 3.02
814 1206 2.866028 GCGAAGAGTGCCAGCAAG 59.134 61.111 0.00 0.00 0.00 4.01
821 1213 0.235926 GACAAACTGGCGAAGAGTGC 59.764 55.000 0.00 0.00 0.00 4.40
822 1214 1.871080 AGACAAACTGGCGAAGAGTG 58.129 50.000 0.00 0.00 0.00 3.51
823 1215 2.614057 CAAAGACAAACTGGCGAAGAGT 59.386 45.455 0.00 0.00 0.00 3.24
824 1216 2.603173 GCAAAGACAAACTGGCGAAGAG 60.603 50.000 0.00 0.00 0.00 2.85
825 1217 1.333619 GCAAAGACAAACTGGCGAAGA 59.666 47.619 0.00 0.00 0.00 2.87
826 1218 1.065401 TGCAAAGACAAACTGGCGAAG 59.935 47.619 0.00 0.00 34.04 3.79
827 1219 1.098869 TGCAAAGACAAACTGGCGAA 58.901 45.000 0.00 0.00 34.04 4.70
828 1220 1.001487 CATGCAAAGACAAACTGGCGA 60.001 47.619 0.00 0.00 34.04 5.54
829 1221 1.411394 CATGCAAAGACAAACTGGCG 58.589 50.000 0.00 0.00 34.04 5.69
872 1264 1.134907 GTCGAGGGAAAAGTGGCGATA 60.135 52.381 0.00 0.00 0.00 2.92
875 1267 2.033194 GGTCGAGGGAAAAGTGGCG 61.033 63.158 0.00 0.00 0.00 5.69
877 1269 0.107831 TGTGGTCGAGGGAAAAGTGG 59.892 55.000 0.00 0.00 0.00 4.00
878 1270 1.226746 GTGTGGTCGAGGGAAAAGTG 58.773 55.000 0.00 0.00 0.00 3.16
879 1271 0.108019 GGTGTGGTCGAGGGAAAAGT 59.892 55.000 0.00 0.00 0.00 2.66
881 1273 1.070105 CGGTGTGGTCGAGGGAAAA 59.930 57.895 0.00 0.00 0.00 2.29
882 1274 1.189524 ATCGGTGTGGTCGAGGGAAA 61.190 55.000 0.00 0.00 40.09 3.13
884 1276 2.036731 ATCGGTGTGGTCGAGGGA 59.963 61.111 0.00 0.00 40.09 4.20
885 1277 2.184322 CATCGGTGTGGTCGAGGG 59.816 66.667 0.00 0.00 40.09 4.30
897 1377 0.949397 TAGCTGTACGTAGGCATCGG 59.051 55.000 18.56 4.36 0.00 4.18
899 1379 3.066342 TGTTCTAGCTGTACGTAGGCATC 59.934 47.826 18.56 1.98 0.00 3.91
908 8800 3.678548 CCCGTTTCTTGTTCTAGCTGTAC 59.321 47.826 0.00 0.00 0.00 2.90
972 8868 3.678289 TCACTTGCTCTGGTACGTAGTA 58.322 45.455 0.00 0.00 45.11 1.82
974 8870 3.128764 TGATCACTTGCTCTGGTACGTAG 59.871 47.826 0.00 0.00 0.00 3.51
977 8873 2.534298 CTGATCACTTGCTCTGGTACG 58.466 52.381 0.00 0.00 0.00 3.67
978 8874 2.275318 GCTGATCACTTGCTCTGGTAC 58.725 52.381 0.00 0.00 0.00 3.34
1078 8993 2.028130 GGATGACGTACGTCCCGAT 58.972 57.895 37.57 27.24 46.05 4.18
1098 9013 4.980592 TCCTCCTGGGGCTGCACA 62.981 66.667 3.46 0.00 35.33 4.57
1125 9040 3.060000 TCGTCATCGGTCGTGCCT 61.060 61.111 0.00 0.00 37.69 4.75
1173 9088 2.685017 AGGAGACGGCCATGCTCA 60.685 61.111 15.77 0.00 0.00 4.26
1285 9200 0.106369 TGGTAGATCACGTCCGGGAT 60.106 55.000 3.73 3.73 41.59 3.85
1287 9202 0.032130 CATGGTAGATCACGTCCGGG 59.968 60.000 0.00 0.00 0.00 5.73
1928 9855 5.224821 CTCATTCAATATGGAGGAGCTGA 57.775 43.478 0.00 0.00 0.00 4.26
1938 9865 2.094906 CCATGGCGCCTCATTCAATATG 60.095 50.000 29.70 18.42 0.00 1.78
2051 9978 0.321564 CATTGAGTTGTCGGGCTGGA 60.322 55.000 0.00 0.00 0.00 3.86
2067 9994 1.201429 AGACCAACGAGGCCTCCATT 61.201 55.000 27.20 18.28 43.14 3.16
2068 9995 0.325296 TAGACCAACGAGGCCTCCAT 60.325 55.000 27.20 12.92 43.14 3.41
2154 10087 3.181486 CGCAGAGCACTATCTTGTCCTTA 60.181 47.826 0.00 0.00 0.00 2.69
2208 10144 4.828925 GCTCTCAGCACCTCGGCC 62.829 72.222 0.00 0.00 41.89 6.13
2241 10177 2.008242 AAAGCTGGTTGCCCACAATA 57.992 45.000 0.00 0.00 44.23 1.90
2257 10193 2.009774 CGTGATGTAGCCCTCCAAAAG 58.990 52.381 0.00 0.00 0.00 2.27
2961 10906 2.990977 TGGAGGATTCGAGCTCCAA 58.009 52.632 8.47 1.12 42.32 3.53
3001 10946 1.154093 GCACGTCTCCGACATTCGA 60.154 57.895 0.00 0.00 43.74 3.71
3075 11026 4.907879 CAAGAGCTTGTCTGGAAAAACT 57.092 40.909 2.11 0.00 34.84 2.66
3112 11063 7.172190 CACATCTATATCGAATTTCTGCACCTT 59.828 37.037 0.00 0.00 0.00 3.50
3135 11086 1.228245 GCTGTTCTTGGCCTCCACA 60.228 57.895 3.32 0.57 30.78 4.17
3144 11095 2.253452 GTGGCGCTGCTGTTCTTG 59.747 61.111 7.64 0.00 0.00 3.02
3216 11170 1.734163 CCGCAAAGGTAACCGAGATT 58.266 50.000 0.00 0.00 34.51 2.40
3225 11179 1.447140 CTAGTGCGCCGCAAAGGTA 60.447 57.895 15.84 2.26 41.47 3.08
3237 11191 1.407258 CAGTAGACTGGGCTCTAGTGC 59.593 57.143 8.29 8.29 37.37 4.40
3262 11216 3.612423 CGATTGACGTTGCAGAAGATGTA 59.388 43.478 0.00 0.00 37.22 2.29
3519 11756 7.489435 GTGATGACTTCGTCAATCTTAAGATGA 59.511 37.037 18.61 14.30 45.96 2.92
3531 11768 1.666023 GCGTCTGTGATGACTTCGTCA 60.666 52.381 0.00 0.00 46.90 4.35
3532 11769 0.985549 GCGTCTGTGATGACTTCGTC 59.014 55.000 0.00 0.00 35.00 4.20
3576 11821 4.447290 TCCGACAATGTTCTTTCAGTTGA 58.553 39.130 0.00 0.00 0.00 3.18
3578 11823 5.733373 GCTTTCCGACAATGTTCTTTCAGTT 60.733 40.000 0.00 0.00 0.00 3.16
3607 11852 7.433131 TGCTGATCGCATTTTTCTGAAATTATC 59.567 33.333 3.31 2.84 45.47 1.75
3628 11873 0.610174 CCTAGACTTGGCACTGCTGA 59.390 55.000 0.00 0.00 0.00 4.26
3657 13449 4.688770 GTGGAACCAACCCACCAA 57.311 55.556 0.00 0.00 46.30 3.67
3701 13493 1.195115 TAGTCAAGGCGAATGGAGCT 58.805 50.000 0.00 0.00 34.52 4.09
3722 13514 7.389803 TCAAAGTTCAGAATGTTTCAAGTGA 57.610 32.000 0.00 0.00 37.40 3.41
4199 14018 4.462483 TCCAAGAGGCAACCAATTGTATTC 59.538 41.667 4.43 0.00 38.17 1.75


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

AutoCloner maintained by Alex Coulton.