Multiple sequence alignment - TraesCS2A01G096900

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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 TraesCS2A01G096900 chr2A 100.000 2985 0 0 510 3494 50915700 50918684 0.000000e+00 5513.0
1 TraesCS2A01G096900 chr2A 85.101 1584 183 26 1666 3200 51540622 51539043 0.000000e+00 1568.0
2 TraesCS2A01G096900 chr2A 92.384 709 35 8 2312 3016 50923415 50924108 0.000000e+00 992.0
3 TraesCS2A01G096900 chr2A 88.529 340 38 1 1217 1555 51540998 51540659 9.030000e-111 411.0
4 TraesCS2A01G096900 chr2A 90.096 313 21 5 3012 3323 50956199 50956502 7.030000e-107 398.0
5 TraesCS2A01G096900 chr2A 100.000 205 0 0 1 205 50915191 50915395 2.550000e-101 379.0
6 TraesCS2A01G096900 chr2A 77.480 373 80 2 1282 1651 619583859 619583488 1.630000e-53 220.0
7 TraesCS2A01G096900 chr2A 86.228 167 7 7 752 902 51541207 51541041 2.160000e-37 167.0
8 TraesCS2A01G096900 chr2A 93.506 77 4 1 3191 3267 51539024 51538949 2.850000e-21 113.0
9 TraesCS2A01G096900 chr2B 93.683 2628 135 14 571 3193 75606190 75608791 0.000000e+00 3904.0
10 TraesCS2A01G096900 chr2B 89.342 1595 139 11 1243 2808 76906027 76904435 0.000000e+00 1975.0
11 TraesCS2A01G096900 chr2B 88.599 1228 107 12 1529 2727 77770843 77772066 0.000000e+00 1461.0
12 TraesCS2A01G096900 chr2B 90.247 769 61 12 2730 3494 77772100 77772858 0.000000e+00 992.0
13 TraesCS2A01G096900 chr2B 94.753 324 13 3 3171 3494 76903825 76903506 5.210000e-138 501.0
14 TraesCS2A01G096900 chr2B 90.031 321 28 2 1217 1533 77762107 77762427 2.510000e-111 412.0
15 TraesCS2A01G096900 chr2B 89.671 213 15 5 701 907 77761882 77762093 7.440000e-67 265.0
16 TraesCS2A01G096900 chr2B 95.041 121 5 1 3200 3319 75608880 75609000 4.600000e-44 189.0
17 TraesCS2A01G096900 chr2B 84.472 161 17 4 704 859 76906194 76906037 6.040000e-33 152.0
18 TraesCS2A01G096900 chr2B 82.500 160 20 7 50 205 513700076 513699921 2.190000e-27 134.0
19 TraesCS2A01G096900 chr2D 86.769 2804 231 46 701 3454 49256627 49253914 0.000000e+00 2994.0
20 TraesCS2A01G096900 chr2D 92.083 581 32 11 2651 3229 47411923 47412491 0.000000e+00 806.0
21 TraesCS2A01G096900 chr2D 95.833 144 5 1 2568 2710 47411632 47411775 7.540000e-57 231.0
22 TraesCS2A01G096900 chr2D 77.480 373 81 1 1282 1651 477053080 477052708 1.630000e-53 220.0
23 TraesCS2A01G096900 chr2D 76.944 373 83 1 1282 1651 477105362 477104990 3.530000e-50 209.0
24 TraesCS2A01G096900 chr2D 95.495 111 5 0 3213 3323 47414893 47415003 9.970000e-41 178.0
25 TraesCS2A01G096900 chr2D 98.361 61 1 0 510 570 114513208 114513268 1.330000e-19 108.0
26 TraesCS2A01G096900 chr2D 98.361 61 1 0 510 570 645008175 645008235 1.330000e-19 108.0
27 TraesCS2A01G096900 chr2D 100.000 35 0 0 3460 3494 49253921 49253887 8.100000e-07 65.8
28 TraesCS2A01G096900 chr6A 93.103 261 18 0 1413 1673 613644737 613644997 1.970000e-102 383.0
29 TraesCS2A01G096900 chr6A 89.143 175 14 4 2 172 99934347 99934174 2.730000e-51 213.0
30 TraesCS2A01G096900 chr3D 84.277 159 16 8 50 203 431626910 431627064 2.810000e-31 147.0
31 TraesCS2A01G096900 chr7D 83.230 161 19 6 50 205 301331442 301331285 1.310000e-29 141.0
32 TraesCS2A01G096900 chr7D 96.721 61 2 0 510 570 437888287 437888227 6.170000e-18 102.0
33 TraesCS2A01G096900 chr7A 82.500 160 22 4 50 205 303947427 303947270 6.080000e-28 135.0
34 TraesCS2A01G096900 chr1B 75.801 281 59 6 2218 2495 630921328 630921054 2.190000e-27 134.0
35 TraesCS2A01G096900 chr1B 80.117 171 26 7 37 205 498380100 498379936 1.700000e-23 121.0
36 TraesCS2A01G096900 chr5A 75.265 283 57 11 2218 2495 16413912 16413638 4.740000e-24 122.0
37 TraesCS2A01G096900 chr5A 75.000 284 60 7 2211 2490 18680053 18680329 1.700000e-23 121.0
38 TraesCS2A01G096900 chr5A 74.912 283 58 9 2218 2495 18681338 18681612 2.200000e-22 117.0
39 TraesCS2A01G096900 chr4A 79.641 167 31 1 34 197 407483648 407483814 2.200000e-22 117.0
40 TraesCS2A01G096900 chr4A 77.674 215 31 13 1 205 403381802 403382009 7.930000e-22 115.0
41 TraesCS2A01G096900 chr4D 80.368 163 19 11 50 205 8191743 8191899 1.030000e-20 111.0
42 TraesCS2A01G096900 chr4D 96.774 62 2 0 510 571 8191981 8192042 1.720000e-18 104.0
43 TraesCS2A01G096900 chr6D 98.361 61 1 0 510 570 447401394 447401334 1.330000e-19 108.0
44 TraesCS2A01G096900 chr6B 94.203 69 3 1 510 577 135365346 135365414 1.720000e-18 104.0
45 TraesCS2A01G096900 chr1D 98.276 58 1 0 510 567 236260226 236260283 6.170000e-18 102.0
46 TraesCS2A01G096900 chr7B 95.161 62 3 0 510 571 504206806 504206745 7.980000e-17 99.0
47 TraesCS2A01G096900 chr3B 95.161 62 3 0 510 571 620855784 620855723 7.980000e-17 99.0


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 TraesCS2A01G096900 chr2A 50915191 50918684 3493 False 2946.00 5513 100.000000 1 3494 2 chr2A.!!$F3 3493
1 TraesCS2A01G096900 chr2A 50923415 50924108 693 False 992.00 992 92.384000 2312 3016 1 chr2A.!!$F1 704
2 TraesCS2A01G096900 chr2A 51538949 51541207 2258 True 564.75 1568 88.341000 752 3267 4 chr2A.!!$R2 2515
3 TraesCS2A01G096900 chr2B 75606190 75609000 2810 False 2046.50 3904 94.362000 571 3319 2 chr2B.!!$F1 2748
4 TraesCS2A01G096900 chr2B 77770843 77772858 2015 False 1226.50 1461 89.423000 1529 3494 2 chr2B.!!$F3 1965
5 TraesCS2A01G096900 chr2B 76903506 76906194 2688 True 876.00 1975 89.522333 704 3494 3 chr2B.!!$R2 2790
6 TraesCS2A01G096900 chr2B 77761882 77762427 545 False 338.50 412 89.851000 701 1533 2 chr2B.!!$F2 832
7 TraesCS2A01G096900 chr2D 49253887 49256627 2740 True 1529.90 2994 93.384500 701 3494 2 chr2D.!!$R3 2793
8 TraesCS2A01G096900 chr2D 47411632 47415003 3371 False 405.00 806 94.470333 2568 3323 3 chr2D.!!$F3 755

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
610 613 0.955428 TCCAATCAGGTCAACGCTGC 60.955 55.000 0.00 0.0 39.02 5.25 F
1344 1406 0.631753 TCGAGATCCCTGACCTCCTT 59.368 55.000 0.00 0.0 0.00 3.36 F
1746 1808 1.078988 GGTTTACGGTCCGCCATCA 60.079 57.895 12.28 0.0 34.09 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2101 0.252103 AAACCGGTCCTCAGGCTCTA 60.252 55.0 8.04 0.00 32.18 2.43 R
2286 2360 1.089920 CATGGTTTCCCTTGAGAGCG 58.910 55.0 0.00 0.00 37.97 5.03 R
3456 6780 0.469070 GGCTCACAGATGCTGGATCT 59.531 55.0 5.79 5.79 42.70 2.75 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
26 27 6.263516 TCTGAATTCCAGAGCATTTTTCTG 57.736 37.500 2.27 0.00 46.38 3.02
27 28 5.771666 TCTGAATTCCAGAGCATTTTTCTGT 59.228 36.000 2.27 0.00 46.38 3.41
28 29 6.942005 TCTGAATTCCAGAGCATTTTTCTGTA 59.058 34.615 2.27 0.00 46.38 2.74
29 30 7.448161 TCTGAATTCCAGAGCATTTTTCTGTAA 59.552 33.333 2.27 0.00 46.38 2.41
30 31 8.125978 TGAATTCCAGAGCATTTTTCTGTAAT 57.874 30.769 2.27 0.00 40.32 1.89
31 32 8.246180 TGAATTCCAGAGCATTTTTCTGTAATC 58.754 33.333 2.27 0.00 40.32 1.75
32 33 7.707624 ATTCCAGAGCATTTTTCTGTAATCA 57.292 32.000 2.05 0.00 40.32 2.57
33 34 7.707624 TTCCAGAGCATTTTTCTGTAATCAT 57.292 32.000 2.05 0.00 40.32 2.45
34 35 7.092137 TCCAGAGCATTTTTCTGTAATCATG 57.908 36.000 2.05 0.00 40.32 3.07
35 36 6.885918 TCCAGAGCATTTTTCTGTAATCATGA 59.114 34.615 0.00 0.00 40.32 3.07
36 37 7.558807 TCCAGAGCATTTTTCTGTAATCATGAT 59.441 33.333 1.18 1.18 40.32 2.45
37 38 8.195436 CCAGAGCATTTTTCTGTAATCATGATT 58.805 33.333 23.75 23.75 40.32 2.57
38 39 9.582431 CAGAGCATTTTTCTGTAATCATGATTT 57.418 29.630 25.26 10.37 37.79 2.17
72 73 9.604626 TTGTGAACATTTTTCAATTTCACAAAC 57.395 25.926 20.26 0.00 44.52 2.93
73 74 8.777413 TGTGAACATTTTTCAATTTCACAAACA 58.223 25.926 11.90 0.00 41.37 2.83
74 75 9.771915 GTGAACATTTTTCAATTTCACAAACAT 57.228 25.926 7.68 0.00 38.56 2.71
110 111 9.689976 ATCGTGAACATTGTTTTAAATTCATGA 57.310 25.926 17.67 17.67 0.00 3.07
111 112 9.521503 TCGTGAACATTGTTTTAAATTCATGAA 57.478 25.926 11.26 11.26 0.00 2.57
112 113 9.566624 CGTGAACATTGTTTTAAATTCATGAAC 57.433 29.630 11.07 0.00 0.00 3.18
162 163 8.843885 TTGCCAAATCATGATTGTTTTATTCA 57.156 26.923 21.39 8.48 0.00 2.57
163 164 8.843885 TGCCAAATCATGATTGTTTTATTCAA 57.156 26.923 21.39 0.00 0.00 2.69
164 165 9.281371 TGCCAAATCATGATTGTTTTATTCAAA 57.719 25.926 21.39 0.00 0.00 2.69
184 185 9.768662 ATTCAAAATTAGCAACTTTTCTGACAT 57.231 25.926 0.00 0.00 0.00 3.06
185 186 9.598517 TTCAAAATTAGCAACTTTTCTGACATT 57.401 25.926 0.00 0.00 0.00 2.71
186 187 9.598517 TCAAAATTAGCAACTTTTCTGACATTT 57.401 25.926 0.00 0.00 0.00 2.32
189 190 9.696917 AAATTAGCAACTTTTCTGACATTTAGG 57.303 29.630 0.00 0.00 0.00 2.69
190 191 8.635765 ATTAGCAACTTTTCTGACATTTAGGA 57.364 30.769 0.00 0.00 0.00 2.94
191 192 6.319141 AGCAACTTTTCTGACATTTAGGAC 57.681 37.500 0.00 0.00 0.00 3.85
192 193 5.241728 AGCAACTTTTCTGACATTTAGGACC 59.758 40.000 0.00 0.00 0.00 4.46
193 194 5.241728 GCAACTTTTCTGACATTTAGGACCT 59.758 40.000 0.00 0.00 0.00 3.85
194 195 6.239036 GCAACTTTTCTGACATTTAGGACCTT 60.239 38.462 0.00 0.00 0.00 3.50
195 196 7.684428 GCAACTTTTCTGACATTTAGGACCTTT 60.684 37.037 0.00 0.00 0.00 3.11
196 197 7.898014 ACTTTTCTGACATTTAGGACCTTTT 57.102 32.000 0.00 0.00 0.00 2.27
197 198 8.306313 ACTTTTCTGACATTTAGGACCTTTTT 57.694 30.769 0.00 0.00 0.00 1.94
198 199 8.414003 ACTTTTCTGACATTTAGGACCTTTTTC 58.586 33.333 0.00 0.00 0.00 2.29
199 200 7.889873 TTTCTGACATTTAGGACCTTTTTCA 57.110 32.000 0.00 0.00 0.00 2.69
200 201 8.477419 TTTCTGACATTTAGGACCTTTTTCAT 57.523 30.769 0.00 0.00 0.00 2.57
201 202 9.581289 TTTCTGACATTTAGGACCTTTTTCATA 57.419 29.630 0.00 0.00 0.00 2.15
202 203 9.753674 TTCTGACATTTAGGACCTTTTTCATAT 57.246 29.630 0.00 0.00 0.00 1.78
203 204 9.396022 TCTGACATTTAGGACCTTTTTCATATC 57.604 33.333 0.00 0.00 0.00 1.63
204 205 8.519799 TGACATTTAGGACCTTTTTCATATCC 57.480 34.615 0.00 0.00 0.00 2.59
548 549 3.121030 CTTCCTTCCCAGCGCGTG 61.121 66.667 8.43 4.73 0.00 5.34
562 563 2.356313 CGTGCTGCGCCCTATAGG 60.356 66.667 12.27 12.27 39.47 2.57
608 611 1.813513 CTTCCAATCAGGTCAACGCT 58.186 50.000 0.00 0.00 39.02 5.07
609 612 1.466167 CTTCCAATCAGGTCAACGCTG 59.534 52.381 0.00 0.00 39.02 5.18
610 613 0.955428 TCCAATCAGGTCAACGCTGC 60.955 55.000 0.00 0.00 39.02 5.25
611 614 1.133253 CAATCAGGTCAACGCTGCG 59.867 57.895 21.91 21.91 0.00 5.18
612 615 2.034879 AATCAGGTCAACGCTGCGG 61.035 57.895 26.95 9.56 0.00 5.69
791 803 4.495422 GATTCTGAGAAGCAAACCGAGTA 58.505 43.478 5.45 0.00 0.00 2.59
881 906 2.572191 TCGCGTATTCGAATCAGGTT 57.428 45.000 15.25 0.00 39.71 3.50
951 1004 6.209391 CCTCTGTTTCCATCCAAAGTTGTAAT 59.791 38.462 0.00 0.00 0.00 1.89
1033 1087 2.059541 GTACGCCTGAGAATAATCGGC 58.940 52.381 0.00 0.00 37.40 5.54
1035 1089 1.862806 GCCTGAGAATAATCGGCGC 59.137 57.895 0.00 0.00 0.00 6.53
1062 1116 2.356135 GAAGCTGCGTATTTTCCTCCA 58.644 47.619 0.00 0.00 0.00 3.86
1063 1117 2.489938 AGCTGCGTATTTTCCTCCAA 57.510 45.000 0.00 0.00 0.00 3.53
1152 1206 4.141846 TGGACAATGAGCTTATGGAGTCTC 60.142 45.833 14.42 0.00 32.53 3.36
1209 1263 1.375098 GAGCTTTGCCTAGGCTGCTG 61.375 60.000 35.83 24.28 40.48 4.41
1238 1297 6.122277 TCACTCCAAGTTCACTGAAGAAATT 58.878 36.000 0.00 0.00 36.37 1.82
1239 1298 6.038603 TCACTCCAAGTTCACTGAAGAAATTG 59.961 38.462 15.34 15.34 46.99 2.32
1240 1299 5.888161 ACTCCAAGTTCACTGAAGAAATTGT 59.112 36.000 18.37 5.80 46.40 2.71
1241 1300 6.135290 TCCAAGTTCACTGAAGAAATTGTG 57.865 37.500 18.37 13.15 46.40 3.33
1342 1404 0.825840 CCTCGAGATCCCTGACCTCC 60.826 65.000 15.71 0.00 0.00 4.30
1344 1406 0.631753 TCGAGATCCCTGACCTCCTT 59.368 55.000 0.00 0.00 0.00 3.36
1356 1418 4.069232 CTCCTTCGTGCCGGCTCA 62.069 66.667 29.70 12.08 0.00 4.26
1392 1454 3.127352 CTCCGCGTACTCCAGGCTC 62.127 68.421 4.92 0.00 35.84 4.70
1416 1478 2.357034 CTTGGGCACTACACGCGT 60.357 61.111 5.58 5.58 0.00 6.01
1443 1505 2.893398 CCGTGCCTCCTCTACACC 59.107 66.667 0.00 0.00 0.00 4.16
1495 1557 1.377366 CTACAGCCTCGCGGAGAAGA 61.377 60.000 6.13 0.00 0.00 2.87
1510 1572 3.065648 GGAGAAGAGGACGTACAAGCTAG 59.934 52.174 0.00 0.00 0.00 3.42
1515 1577 1.746220 AGGACGTACAAGCTAGCTCTG 59.254 52.381 19.65 19.33 0.00 3.35
1563 1625 1.299976 GATTGGGTCCTCGCAAGGT 59.700 57.895 0.00 0.00 46.55 3.50
1590 1652 5.409520 GCTTGTTACAGTTGATGACAGATCA 59.590 40.000 0.00 0.00 39.83 2.92
1712 1774 5.737860 TCTTCACCAGTACGAGTACTCATA 58.262 41.667 22.37 9.26 43.98 2.15
1727 1789 3.686016 ACTCATACCACTCCGCAAAAAT 58.314 40.909 0.00 0.00 0.00 1.82
1746 1808 1.078988 GGTTTACGGTCCGCCATCA 60.079 57.895 12.28 0.00 34.09 3.07
1749 1811 1.741145 GTTTACGGTCCGCCATCAATT 59.259 47.619 12.28 0.00 34.09 2.32
1965 2036 1.238439 ACGCAGTCACTTCATTTGGG 58.762 50.000 0.00 0.00 29.74 4.12
2027 2101 5.609423 GATGAAGATGATTACACAGGAGCT 58.391 41.667 0.00 0.00 0.00 4.09
2064 2138 6.370718 ACCGGTTTCTGAATACTTACATTGTC 59.629 38.462 0.00 0.00 0.00 3.18
2105 2179 8.396390 CAATCTTCTTCAAGTGTGGAGATTATG 58.604 37.037 8.91 0.20 39.26 1.90
2286 2360 4.939271 GTCTTACTGCTCAAGACTATCCC 58.061 47.826 14.51 0.00 45.50 3.85
2344 2418 0.467290 TGTGCTTTGGACAAGGGGAC 60.467 55.000 0.00 1.70 0.00 4.46
2409 2483 2.755952 ACAGCAGGGAGGAACTTTTT 57.244 45.000 0.00 0.00 41.55 1.94
3080 3440 7.044181 TCTTTGCTGATGTAGAAGATAAGTGG 58.956 38.462 0.00 0.00 0.00 4.00
3084 3444 7.847096 TGCTGATGTAGAAGATAAGTGGTAAA 58.153 34.615 0.00 0.00 0.00 2.01
3097 3464 9.046296 AGATAAGTGGTAAAATTTGCGATAGAG 57.954 33.333 0.00 0.00 39.76 2.43
3098 3465 5.485662 AGTGGTAAAATTTGCGATAGAGC 57.514 39.130 0.00 0.00 39.76 4.09
3110 3477 3.636764 TGCGATAGAGCAGGATGAAAGTA 59.363 43.478 0.00 0.00 42.92 2.24
3116 3483 4.789807 AGAGCAGGATGAAAGTATGCATT 58.210 39.130 3.54 0.00 39.69 3.56
3117 3484 4.579340 AGAGCAGGATGAAAGTATGCATTG 59.421 41.667 3.54 0.00 39.69 2.82
3139 3506 6.586868 TGTTGTTCTTTCAAAATGCACATC 57.413 33.333 0.00 0.00 0.00 3.06
3168 4003 7.412672 GCTTGTTTAAGTATACTGTACAGTGGC 60.413 40.741 33.77 23.05 37.96 5.01
3169 4004 6.995364 TGTTTAAGTATACTGTACAGTGGCA 58.005 36.000 33.77 17.93 42.52 4.92
3377 6701 8.911247 AAATAAAATAAGATGTGTCCTTTCGC 57.089 30.769 0.00 0.00 0.00 4.70
3379 6703 3.914426 ATAAGATGTGTCCTTTCGCCT 57.086 42.857 0.00 0.00 0.00 5.52
3392 6716 3.525537 CTTTCGCCTATCTTTGAGCAGA 58.474 45.455 0.00 0.00 0.00 4.26
3446 6770 1.846439 CCCCATCTGACCTGGTATGTT 59.154 52.381 0.00 0.00 31.44 2.71
3447 6771 2.242196 CCCCATCTGACCTGGTATGTTT 59.758 50.000 0.00 0.00 31.44 2.83
3448 6772 3.545703 CCCATCTGACCTGGTATGTTTC 58.454 50.000 0.00 0.00 31.44 2.78
3449 6773 3.054434 CCCATCTGACCTGGTATGTTTCA 60.054 47.826 0.00 0.00 31.44 2.69
3450 6774 4.194640 CCATCTGACCTGGTATGTTTCAG 58.805 47.826 0.00 1.64 35.93 3.02
3451 6775 3.334583 TCTGACCTGGTATGTTTCAGC 57.665 47.619 0.00 0.00 34.82 4.26
3452 6776 2.637382 TCTGACCTGGTATGTTTCAGCA 59.363 45.455 0.00 0.00 34.82 4.41
3453 6777 3.264193 TCTGACCTGGTATGTTTCAGCAT 59.736 43.478 0.00 0.00 34.82 3.79
3454 6778 4.469586 TCTGACCTGGTATGTTTCAGCATA 59.530 41.667 0.00 0.00 34.82 3.14
3455 6779 4.513442 TGACCTGGTATGTTTCAGCATAC 58.487 43.478 0.00 5.47 46.23 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.523293 TTACAGAAAAATGCTCTGGAATTCA 57.477 32.000 7.93 0.00 43.88 2.57
9 10 7.394077 TCATGATTACAGAAAAATGCTCTGGAA 59.606 33.333 0.45 0.45 45.59 3.53
10 11 6.885918 TCATGATTACAGAAAAATGCTCTGGA 59.114 34.615 5.07 0.00 43.88 3.86
11 12 7.092137 TCATGATTACAGAAAAATGCTCTGG 57.908 36.000 5.07 0.00 43.88 3.86
12 13 9.582431 AAATCATGATTACAGAAAAATGCTCTG 57.418 29.630 21.00 0.00 44.90 3.35
48 49 9.771915 ATGTTTGTGAAATTGAAAAATGTTCAC 57.228 25.926 7.68 7.68 45.28 3.18
84 85 9.689976 TCATGAATTTAAAACAATGTTCACGAT 57.310 25.926 0.00 0.00 0.00 3.73
85 86 9.521503 TTCATGAATTTAAAACAATGTTCACGA 57.478 25.926 3.38 0.00 0.00 4.35
86 87 9.566624 GTTCATGAATTTAAAACAATGTTCACG 57.433 29.630 12.12 0.00 0.00 4.35
136 137 9.281371 TGAATAAAACAATCATGATTTGGCAAA 57.719 25.926 18.41 16.01 34.00 3.68
137 138 8.843885 TGAATAAAACAATCATGATTTGGCAA 57.156 26.923 18.41 0.00 34.00 4.52
138 139 8.843885 TTGAATAAAACAATCATGATTTGGCA 57.156 26.923 18.41 3.89 34.00 4.92
158 159 9.768662 ATGTCAGAAAAGTTGCTAATTTTGAAT 57.231 25.926 10.85 0.00 0.00 2.57
159 160 9.598517 AATGTCAGAAAAGTTGCTAATTTTGAA 57.401 25.926 10.85 0.00 0.00 2.69
160 161 9.598517 AAATGTCAGAAAAGTTGCTAATTTTGA 57.401 25.926 10.85 1.73 0.00 2.69
163 164 9.696917 CCTAAATGTCAGAAAAGTTGCTAATTT 57.303 29.630 0.00 0.00 0.00 1.82
164 165 9.077885 TCCTAAATGTCAGAAAAGTTGCTAATT 57.922 29.630 0.00 0.00 0.00 1.40
165 166 8.515414 GTCCTAAATGTCAGAAAAGTTGCTAAT 58.485 33.333 0.00 0.00 0.00 1.73
166 167 7.040686 GGTCCTAAATGTCAGAAAAGTTGCTAA 60.041 37.037 0.00 0.00 0.00 3.09
167 168 6.430000 GGTCCTAAATGTCAGAAAAGTTGCTA 59.570 38.462 0.00 0.00 0.00 3.49
168 169 5.241728 GGTCCTAAATGTCAGAAAAGTTGCT 59.758 40.000 0.00 0.00 0.00 3.91
169 170 5.241728 AGGTCCTAAATGTCAGAAAAGTTGC 59.758 40.000 0.00 0.00 0.00 4.17
170 171 6.884280 AGGTCCTAAATGTCAGAAAAGTTG 57.116 37.500 0.00 0.00 0.00 3.16
171 172 7.898014 AAAGGTCCTAAATGTCAGAAAAGTT 57.102 32.000 0.00 0.00 0.00 2.66
172 173 7.898014 AAAAGGTCCTAAATGTCAGAAAAGT 57.102 32.000 0.00 0.00 0.00 2.66
173 174 8.413229 TGAAAAAGGTCCTAAATGTCAGAAAAG 58.587 33.333 0.00 0.00 0.00 2.27
174 175 8.299990 TGAAAAAGGTCCTAAATGTCAGAAAA 57.700 30.769 0.00 0.00 0.00 2.29
175 176 7.889873 TGAAAAAGGTCCTAAATGTCAGAAA 57.110 32.000 0.00 0.00 0.00 2.52
176 177 9.753674 ATATGAAAAAGGTCCTAAATGTCAGAA 57.246 29.630 0.00 0.00 0.00 3.02
177 178 9.396022 GATATGAAAAAGGTCCTAAATGTCAGA 57.604 33.333 0.00 0.00 0.00 3.27
178 179 8.624776 GGATATGAAAAAGGTCCTAAATGTCAG 58.375 37.037 0.00 0.00 0.00 3.51
179 180 8.519799 GGATATGAAAAAGGTCCTAAATGTCA 57.480 34.615 0.00 0.00 0.00 3.58
531 532 3.121030 CACGCGCTGGGAAGGAAG 61.121 66.667 5.73 0.00 0.00 3.46
554 555 3.003763 GGGGGAGCGCCTATAGGG 61.004 72.222 20.58 11.34 33.42 3.53
555 556 3.382832 CGGGGGAGCGCCTATAGG 61.383 72.222 15.01 15.01 34.08 2.57
556 557 4.070552 GCGGGGGAGCGCCTATAG 62.071 72.222 2.29 0.00 34.08 1.31
881 906 4.819105 ATAGATCACAAACGGAGGACAA 57.181 40.909 0.00 0.00 0.00 3.18
1017 1071 0.880278 TGCGCCGATTATTCTCAGGC 60.880 55.000 4.18 0.00 44.00 4.85
1041 1095 1.671328 GGAGGAAAATACGCAGCTTCC 59.329 52.381 2.70 2.70 38.09 3.46
1048 1102 2.070783 TGACGTTGGAGGAAAATACGC 58.929 47.619 0.00 0.00 35.77 4.42
1062 1116 1.686355 TGCAAAGACCCAATGACGTT 58.314 45.000 0.00 0.00 0.00 3.99
1063 1117 1.686355 TTGCAAAGACCCAATGACGT 58.314 45.000 0.00 0.00 0.00 4.34
1152 1206 3.515630 CAGATATGCTGGGTGTATAGCG 58.484 50.000 0.00 0.00 42.74 4.26
1209 1263 1.301716 TGAACTTGGAGTGAGGCGC 60.302 57.895 0.00 0.00 0.00 6.53
1238 1297 0.607217 CAGTGGAGGATGCTTGCACA 60.607 55.000 0.00 0.00 39.09 4.57
1239 1298 0.321919 TCAGTGGAGGATGCTTGCAC 60.322 55.000 0.00 0.00 37.18 4.57
1240 1299 0.622136 ATCAGTGGAGGATGCTTGCA 59.378 50.000 0.00 0.00 0.00 4.08
1241 1300 1.307097 GATCAGTGGAGGATGCTTGC 58.693 55.000 0.00 0.00 0.00 4.01
1356 1418 3.073735 CGCCAGGAGGAGCAGACT 61.074 66.667 0.00 0.00 36.89 3.24
1443 1505 1.591059 CTCGCCGGCAGATTCAGAG 60.591 63.158 28.98 18.52 0.00 3.35
1495 1557 1.746220 CAGAGCTAGCTTGTACGTCCT 59.254 52.381 20.42 5.54 0.00 3.85
1515 1577 4.828296 CTGATGGGTGGCCCTGGC 62.828 72.222 0.00 0.00 45.70 4.85
1563 1625 5.588246 TCTGTCATCAACTGTAACAAGCAAA 59.412 36.000 0.00 0.00 0.00 3.68
1590 1652 2.356535 GGGATTGACAAGGTGCATCTCT 60.357 50.000 0.00 0.00 0.00 3.10
1651 1713 2.821969 AGATGGGTTTCACATGCTCAAC 59.178 45.455 0.00 0.00 0.00 3.18
1712 1774 1.408969 AACCATTTTTGCGGAGTGGT 58.591 45.000 0.00 0.00 44.62 4.16
1727 1789 1.078988 GATGGCGGACCGTAAACCA 60.079 57.895 16.73 14.40 39.70 3.67
1794 1856 4.794762 CCATTGCATGTATCAGAAAACACG 59.205 41.667 0.00 0.00 0.00 4.49
1965 2036 3.122937 AGATCGAAAGCGTGAATTTGC 57.877 42.857 0.00 0.00 38.98 3.68
2027 2101 0.252103 AAACCGGTCCTCAGGCTCTA 60.252 55.000 8.04 0.00 32.18 2.43
2064 2138 1.382146 ATTGCCCCATGGAGCTTGG 60.382 57.895 19.99 9.69 0.00 3.61
2105 2179 3.437049 GGGTTCTAAATCACAGTGCTCAC 59.563 47.826 0.00 0.00 0.00 3.51
2286 2360 1.089920 CATGGTTTCCCTTGAGAGCG 58.910 55.000 0.00 0.00 37.97 5.03
2344 2418 2.472695 TCACGGGGATTGTTCTTGAG 57.527 50.000 0.00 0.00 0.00 3.02
2476 2550 6.698766 GCTAAAACCTATTCATTGAATGCCAG 59.301 38.462 19.81 10.49 33.95 4.85
3046 3406 6.935167 TCTACATCAGCAAAGAGACAATACA 58.065 36.000 0.00 0.00 0.00 2.29
3080 3440 5.734855 TCCTGCTCTATCGCAAATTTTAC 57.265 39.130 0.00 0.00 39.80 2.01
3084 3444 4.077300 TCATCCTGCTCTATCGCAAATT 57.923 40.909 0.00 0.00 39.80 1.82
3090 3450 4.624882 GCATACTTTCATCCTGCTCTATCG 59.375 45.833 0.00 0.00 0.00 2.92
3097 3464 4.644103 ACAATGCATACTTTCATCCTGC 57.356 40.909 0.00 0.00 0.00 4.85
3098 3465 5.957798 ACAACAATGCATACTTTCATCCTG 58.042 37.500 0.00 0.00 0.00 3.86
3101 3468 8.524870 AAAGAACAACAATGCATACTTTCATC 57.475 30.769 0.00 0.00 0.00 2.92
3110 3477 6.038382 TGCATTTTGAAAGAACAACAATGCAT 59.962 30.769 22.78 0.00 45.14 3.96
3116 3483 6.256104 CAGATGTGCATTTTGAAAGAACAACA 59.744 34.615 0.00 0.00 0.00 3.33
3117 3484 6.292488 CCAGATGTGCATTTTGAAAGAACAAC 60.292 38.462 0.00 0.00 0.00 3.32
3139 3506 7.817962 ACTGTACAGTATACTTAAACAAGCCAG 59.182 37.037 26.91 3.42 40.43 4.85
3392 6716 3.623453 GCAACAAGGAGGGAATTAGAGCT 60.623 47.826 0.00 0.00 0.00 4.09
3446 6770 3.390311 AGATGCTGGATCTGTATGCTGAA 59.610 43.478 11.10 0.00 40.19 3.02
3447 6771 2.970640 AGATGCTGGATCTGTATGCTGA 59.029 45.455 11.10 0.00 40.19 4.26
3448 6772 3.404224 AGATGCTGGATCTGTATGCTG 57.596 47.619 11.10 0.00 40.19 4.41
3456 6780 0.469070 GGCTCACAGATGCTGGATCT 59.531 55.000 5.79 5.79 42.70 2.75
3457 6781 0.879400 CGGCTCACAGATGCTGGATC 60.879 60.000 0.29 0.29 35.51 3.36
3458 6782 1.145598 CGGCTCACAGATGCTGGAT 59.854 57.895 0.00 0.00 35.51 3.41


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

AutoCloner maintained by Alex Coulton.