Multiple sequence alignment - TraesCS3A01G472100

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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 TraesCS3A01G472100 chr3A 100.000 3251 0 0 1 3251 703305294 703302044 0.000000e+00 6004.0
1 TraesCS3A01G472100 chr3A 83.187 1249 170 27 1014 2245 655637062 655635837 0.000000e+00 1107.0
2 TraesCS3A01G472100 chr3A 82.407 1296 197 19 980 2256 703270261 703271544 0.000000e+00 1101.0
3 TraesCS3A01G472100 chr3A 79.968 1233 200 30 998 2219 703203823 703205019 0.000000e+00 865.0
4 TraesCS3A01G472100 chr3B 95.708 1398 47 7 1043 2433 757739781 757738390 0.000000e+00 2237.0
5 TraesCS3A01G472100 chr3B 85.935 1550 179 20 723 2253 757773705 757772176 0.000000e+00 1618.0
6 TraesCS3A01G472100 chr3B 83.655 1242 165 25 1014 2239 685039247 685038028 0.000000e+00 1134.0
7 TraesCS3A01G472100 chr3B 82.407 1296 202 16 977 2256 757734127 757735412 0.000000e+00 1107.0
8 TraesCS3A01G472100 chr3B 83.395 542 64 12 2463 2978 757738107 757737566 2.270000e-131 479.0
9 TraesCS3A01G472100 chr3B 81.971 477 49 15 548 1015 757740225 757739777 1.420000e-98 370.0
10 TraesCS3A01G472100 chr3D 84.388 1896 237 32 363 2226 570497034 570495166 0.000000e+00 1807.0
11 TraesCS3A01G472100 chr3D 93.503 862 24 5 1599 2457 570400565 570399733 0.000000e+00 1253.0
12 TraesCS3A01G472100 chr3D 89.489 999 71 4 548 1543 570401767 570400800 0.000000e+00 1232.0
13 TraesCS3A01G472100 chr3D 82.649 1291 202 14 977 2253 570393661 570394943 0.000000e+00 1123.0
14 TraesCS3A01G472100 chr3D 83.014 1254 173 24 1014 2250 520191904 520190674 0.000000e+00 1099.0
15 TraesCS3A01G472100 chr3D 80.870 1218 191 28 998 2206 570379585 570380769 0.000000e+00 920.0
16 TraesCS3A01G472100 chr3D 80.643 1245 185 39 992 2219 570281032 570282237 0.000000e+00 913.0
17 TraesCS3A01G472100 chr3D 91.329 346 28 2 2908 3251 570398323 570397978 3.800000e-129 472.0
18 TraesCS3A01G472100 chr3D 81.048 496 62 18 6 482 570497485 570497003 1.840000e-97 366.0
19 TraesCS3A01G472100 chr3D 95.714 140 6 0 2449 2588 570399568 570399429 3.260000e-55 226.0
20 TraesCS3A01G472100 chr3D 91.603 131 11 0 2613 2743 570398472 570398342 7.170000e-42 182.0
21 TraesCS3A01G472100 chr3D 85.833 120 17 0 557 676 2084956 2085075 9.470000e-26 128.0
22 TraesCS3A01G472100 chr3D 85.000 120 17 1 557 676 2104241 2104359 1.580000e-23 121.0
23 TraesCS3A01G472100 chr3D 84.348 115 18 0 562 676 80266331 80266445 2.650000e-21 113.0
24 TraesCS3A01G472100 chr3D 97.674 43 1 0 2586 2628 570398528 570398486 1.250000e-09 75.0
25 TraesCS3A01G472100 chrUn 87.395 119 14 1 557 674 42855187 42855069 5.660000e-28 135.0
26 TraesCS3A01G472100 chrUn 89.552 67 7 0 557 623 303775289 303775355 5.780000e-13 86.1
27 TraesCS3A01G472100 chr5A 86.555 119 16 0 558 676 598076809 598076691 7.320000e-27 132.0
28 TraesCS3A01G472100 chr1D 79.389 131 24 3 107 235 16269078 16268949 4.470000e-14 89.8
29 TraesCS3A01G472100 chr1D 89.474 57 6 0 2518 2574 407162322 407162378 4.500000e-09 73.1


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 TraesCS3A01G472100 chr3A 703302044 703305294 3250 True 6004.000000 6004 100.000000 1 3251 1 chr3A.!!$R2 3250
1 TraesCS3A01G472100 chr3A 655635837 655637062 1225 True 1107.000000 1107 83.187000 1014 2245 1 chr3A.!!$R1 1231
2 TraesCS3A01G472100 chr3A 703270261 703271544 1283 False 1101.000000 1101 82.407000 980 2256 1 chr3A.!!$F2 1276
3 TraesCS3A01G472100 chr3A 703203823 703205019 1196 False 865.000000 865 79.968000 998 2219 1 chr3A.!!$F1 1221
4 TraesCS3A01G472100 chr3B 757772176 757773705 1529 True 1618.000000 1618 85.935000 723 2253 1 chr3B.!!$R2 1530
5 TraesCS3A01G472100 chr3B 685038028 685039247 1219 True 1134.000000 1134 83.655000 1014 2239 1 chr3B.!!$R1 1225
6 TraesCS3A01G472100 chr3B 757734127 757735412 1285 False 1107.000000 1107 82.407000 977 2256 1 chr3B.!!$F1 1279
7 TraesCS3A01G472100 chr3B 757737566 757740225 2659 True 1028.666667 2237 87.024667 548 2978 3 chr3B.!!$R3 2430
8 TraesCS3A01G472100 chr3D 570393661 570394943 1282 False 1123.000000 1123 82.649000 977 2253 1 chr3D.!!$F6 1276
9 TraesCS3A01G472100 chr3D 520190674 520191904 1230 True 1099.000000 1099 83.014000 1014 2250 1 chr3D.!!$R1 1236
10 TraesCS3A01G472100 chr3D 570495166 570497485 2319 True 1086.500000 1807 82.718000 6 2226 2 chr3D.!!$R3 2220
11 TraesCS3A01G472100 chr3D 570379585 570380769 1184 False 920.000000 920 80.870000 998 2206 1 chr3D.!!$F5 1208
12 TraesCS3A01G472100 chr3D 570281032 570282237 1205 False 913.000000 913 80.643000 992 2219 1 chr3D.!!$F4 1227
13 TraesCS3A01G472100 chr3D 570397978 570401767 3789 True 573.333333 1253 93.218667 548 3251 6 chr3D.!!$R2 2703

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
700 819 0.106819 ATGCATGGAGAAGGGAGCAC 60.107 55.0 0.0 0.0 34.54 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2370 2732 0.313987 GACTTGCACGAAAAAGGGGG 59.686 55.0 0.0 0.0 0.0 5.4 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
50 51 7.599630 AAAATGGCAGCAACATATTAAACAG 57.400 32.000 0.00 0.00 0.00 3.16
53 54 4.522405 TGGCAGCAACATATTAAACAGTGT 59.478 37.500 0.00 0.00 0.00 3.55
158 160 3.886549 TGTATTTGGCAAAACGTTACCG 58.113 40.909 17.70 0.00 40.83 4.02
267 271 8.470805 TCCATGTGTGTGTTAAAAATGTACTTT 58.529 29.630 0.00 0.00 0.00 2.66
268 272 8.538856 CCATGTGTGTGTTAAAAATGTACTTTG 58.461 33.333 0.00 0.00 0.00 2.77
269 273 9.081997 CATGTGTGTGTTAAAAATGTACTTTGT 57.918 29.630 0.00 0.00 0.00 2.83
321 325 5.952698 AACAAAATTGGTTAAAACGGACG 57.047 34.783 0.00 0.00 0.00 4.79
323 327 5.834169 ACAAAATTGGTTAAAACGGACGAT 58.166 33.333 0.00 0.00 0.00 3.73
366 383 9.418045 ACGAAAAATGAAGAAAGAAACAAAAGA 57.582 25.926 0.00 0.00 0.00 2.52
523 621 1.086696 GCGACTGCTCTAATTTGCCA 58.913 50.000 0.00 0.00 38.39 4.92
528 626 2.562738 ACTGCTCTAATTTGCCAAACCC 59.437 45.455 0.00 0.00 0.00 4.11
554 662 3.136750 TTGCCACGCCAGCAAAAT 58.863 50.000 5.01 0.00 46.71 1.82
580 693 6.043243 ACTCTCAAGGTTCAAAATAGACCAGA 59.957 38.462 0.00 0.00 0.00 3.86
581 694 6.837312 TCTCAAGGTTCAAAATAGACCAGAA 58.163 36.000 0.00 0.00 0.00 3.02
582 695 7.461749 TCTCAAGGTTCAAAATAGACCAGAAT 58.538 34.615 0.00 0.00 0.00 2.40
583 696 7.944554 TCTCAAGGTTCAAAATAGACCAGAATT 59.055 33.333 0.00 0.00 0.00 2.17
584 697 9.231297 CTCAAGGTTCAAAATAGACCAGAATTA 57.769 33.333 0.00 0.00 0.00 1.40
598 711 6.497259 AGACCAGAATTAGAGAGTTTGGTGTA 59.503 38.462 0.00 0.00 37.56 2.90
628 741 5.477510 TCAGAGATTGAAAGCTCAGAGTTC 58.522 41.667 10.65 0.00 43.60 3.01
636 755 4.627467 TGAAAGCTCAGAGTTCGATTTAGC 59.373 41.667 0.00 0.00 0.00 3.09
667 786 3.881089 ACGAGTCTAAGGTTTGTTTTGGG 59.119 43.478 0.00 0.00 0.00 4.12
700 819 0.106819 ATGCATGGAGAAGGGAGCAC 60.107 55.000 0.00 0.00 34.54 4.40
716 838 4.082136 GGGAGCACGAGGGATATTAGTTAG 60.082 50.000 0.00 0.00 0.00 2.34
721 843 8.418597 AGCACGAGGGATATTAGTTAGAATTA 57.581 34.615 0.00 0.00 0.00 1.40
748 870 7.063074 CGACTTCGTCTTAAACAGTTTATCCAT 59.937 37.037 6.58 0.00 34.11 3.41
821 951 6.742718 CGCCACATAGAACAAGAATTTAACTG 59.257 38.462 0.00 0.00 0.00 3.16
844 974 1.523711 CAGCACACTGGTCACCGTT 60.524 57.895 0.00 0.00 40.48 4.44
917 1047 3.130516 TGCTCCGGAAGACACTGTATAAG 59.869 47.826 5.23 0.00 0.00 1.73
972 1128 1.221840 CCCCACCTGATCGACCTTG 59.778 63.158 0.00 0.00 0.00 3.61
994 1150 3.429141 CTCTGGCAGTTGGCGCAG 61.429 66.667 15.27 0.00 46.16 5.18
1119 1286 1.379977 CTCCCTCTACACGCTCCCA 60.380 63.158 0.00 0.00 0.00 4.37
1560 1727 3.009143 AGAAGGTCGCCAATAAGTTCCTT 59.991 43.478 0.00 0.00 36.67 3.36
2016 2374 2.582978 GAGGGCGGGGTGAACTAC 59.417 66.667 0.00 0.00 0.00 2.73
2154 2512 1.676014 GGGTTCCAGATGGAGAACGTG 60.676 57.143 1.13 0.00 46.36 4.49
2263 2625 3.946558 GACCGGCTAGACTTTCTCTTCTA 59.053 47.826 0.00 0.00 0.00 2.10
2361 2723 5.407407 ACATTTGTCGTGAGGTTCTATCT 57.593 39.130 0.00 0.00 0.00 1.98
2370 2732 4.859798 CGTGAGGTTCTATCTTGTCAAGAC 59.140 45.833 17.49 5.22 41.01 3.01
2409 2771 6.009115 AGTCCATTTGTCACGGTTAATTTC 57.991 37.500 0.00 0.00 0.00 2.17
2446 3042 5.121611 TGTGTGTTGTTCAGACAAGTAACAG 59.878 40.000 0.00 0.00 45.20 3.16
2537 3306 2.582052 GGACCCACATGTCAGTGAAAA 58.418 47.619 0.00 0.00 42.05 2.29
2580 3349 0.980231 AGGATCCTCCTCCACTGCAC 60.980 60.000 9.02 0.00 45.66 4.57
2588 3357 1.956170 CTCCACTGCACGGTGTGTC 60.956 63.158 10.24 0.00 35.75 3.67
2633 4334 4.040339 TCAGCTCTTGTTCCATCTTGTACA 59.960 41.667 0.00 0.00 0.00 2.90
2656 4357 3.004734 CCCGAGTTGCAAAAATGAAGTCT 59.995 43.478 0.00 0.00 0.00 3.24
2657 4358 3.976942 CCGAGTTGCAAAAATGAAGTCTG 59.023 43.478 0.00 0.00 0.00 3.51
2677 4378 2.364324 TGCTTTGGTGACTTCTCTACGT 59.636 45.455 0.00 0.00 0.00 3.57
2707 4408 1.591703 CTGCGAAGTCTGTAGGGCA 59.408 57.895 0.00 0.00 0.00 5.36
2773 4476 3.243201 CCTCTCAGTTGCAAGGTGTTTTC 60.243 47.826 0.00 0.00 0.00 2.29
2774 4477 3.351740 TCTCAGTTGCAAGGTGTTTTCA 58.648 40.909 0.00 0.00 0.00 2.69
2782 4485 2.806382 GCAAGGTGTTTTCATGGTTGGG 60.806 50.000 0.00 0.00 0.00 4.12
2785 4488 1.047801 GTGTTTTCATGGTTGGGGCT 58.952 50.000 0.00 0.00 0.00 5.19
2793 4496 2.181975 CATGGTTGGGGCTGAAGAATT 58.818 47.619 0.00 0.00 0.00 2.17
2798 4501 0.776810 TGGGGCTGAAGAATTGGTGA 59.223 50.000 0.00 0.00 0.00 4.02
2813 4516 0.758734 GGTGATGGACCATCCGATCA 59.241 55.000 28.01 11.02 45.34 2.92
2827 4530 0.994241 CGATCAATCGGCTCGTCGAG 60.994 60.000 18.08 18.08 45.93 4.04
2863 4566 2.096218 GTCACTTGTCCACTTTGCGATC 60.096 50.000 0.00 0.00 0.00 3.69
2864 4567 1.872952 CACTTGTCCACTTTGCGATCA 59.127 47.619 0.00 0.00 0.00 2.92
2865 4568 2.096069 CACTTGTCCACTTTGCGATCAG 60.096 50.000 0.00 0.00 0.00 2.90
2866 4569 1.466167 CTTGTCCACTTTGCGATCAGG 59.534 52.381 0.00 0.00 0.00 3.86
2867 4570 0.396435 TGTCCACTTTGCGATCAGGT 59.604 50.000 0.00 0.00 0.00 4.00
2868 4571 1.202758 TGTCCACTTTGCGATCAGGTT 60.203 47.619 0.00 0.00 0.00 3.50
2869 4572 1.464997 GTCCACTTTGCGATCAGGTTC 59.535 52.381 0.00 0.00 0.00 3.62
2870 4573 0.804989 CCACTTTGCGATCAGGTTCC 59.195 55.000 0.00 0.00 0.00 3.62
2871 4574 0.443869 CACTTTGCGATCAGGTTCCG 59.556 55.000 0.00 0.00 0.00 4.30
2902 4605 2.238942 TCACCTATTAGTGGCATGCG 57.761 50.000 12.44 0.00 38.34 4.73
2993 4721 4.152759 CCGCGTAAAAGAAAACATCTACCA 59.847 41.667 4.92 0.00 37.42 3.25
2994 4722 5.334260 CCGCGTAAAAGAAAACATCTACCAA 60.334 40.000 4.92 0.00 37.42 3.67
3002 4730 5.630121 AGAAAACATCTACCAACCATCACA 58.370 37.500 0.00 0.00 36.32 3.58
3010 4738 1.006281 ACCAACCATCACATGCCTCAT 59.994 47.619 0.00 0.00 0.00 2.90
3033 4762 0.467290 TTGGGAACTGTGGAAGCACC 60.467 55.000 0.00 0.00 39.54 5.01
3039 4768 0.107410 ACTGTGGAAGCACCGAAACA 60.107 50.000 0.00 0.00 42.61 2.83
3044 4773 1.072489 TGGAAGCACCGAAACACCATA 59.928 47.619 0.00 0.00 42.61 2.74
3064 4793 5.004345 CCATAATTTTCGACAACGCAAATCC 59.996 40.000 0.00 0.00 42.29 3.01
3071 4800 1.169661 ACAACGCAAATCCCGCAGAA 61.170 50.000 0.00 0.00 0.00 3.02
3088 4817 3.004944 GCAGAACGGCTAGCTAGTCTTAT 59.995 47.826 22.42 10.55 0.00 1.73
3117 4846 1.136329 TCTTGGAGGAAGGCAAGGCT 61.136 55.000 0.00 0.00 31.85 4.58
3118 4847 0.251519 CTTGGAGGAAGGCAAGGCTT 60.252 55.000 8.74 8.74 0.00 4.35
3150 4879 1.831106 GGGCTTTTAAAGGGGACATGG 59.169 52.381 6.84 0.00 0.00 3.66
3178 4908 9.747898 ACCTTTCTTCCACATTTGTATATGTTA 57.252 29.630 0.00 0.00 36.64 2.41
3194 4924 9.487442 TGTATATGTTATGTAGGCAGGATATGA 57.513 33.333 0.00 0.00 0.00 2.15
3198 4928 7.078249 TGTTATGTAGGCAGGATATGAATGT 57.922 36.000 0.00 0.00 0.00 2.71
3203 4933 4.630644 AGGCAGGATATGAATGTGTAGG 57.369 45.455 0.00 0.00 0.00 3.18
3206 4936 3.499918 GCAGGATATGAATGTGTAGGCAC 59.500 47.826 0.00 0.00 45.44 5.01
3208 4938 3.716353 AGGATATGAATGTGTAGGCACCA 59.284 43.478 0.00 0.00 44.65 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.451064 AAACAATTCAGAAAGTTTCGGACT 57.549 33.333 16.66 9.88 41.47 3.85
1 2 7.520119 AAAAACAATTCAGAAAGTTTCGGAC 57.480 32.000 16.66 0.00 33.64 4.79
2 3 9.640963 TTTAAAAACAATTCAGAAAGTTTCGGA 57.359 25.926 13.56 13.56 33.45 4.55
8 9 9.171877 TGCCATTTTAAAAACAATTCAGAAAGT 57.828 25.926 4.44 0.00 0.00 2.66
9 10 9.654417 CTGCCATTTTAAAAACAATTCAGAAAG 57.346 29.630 4.44 0.00 0.00 2.62
129 131 5.692654 ACGTTTTGCCAAATACATGTTTACC 59.307 36.000 2.30 0.00 0.00 2.85
130 132 6.757026 ACGTTTTGCCAAATACATGTTTAC 57.243 33.333 2.30 0.00 0.00 2.01
242 246 8.538856 CAAAGTACATTTTTAACACACACATGG 58.461 33.333 0.00 0.00 0.00 3.66
267 271 7.814587 CACATGTCTAATTTCTCTCAGTACACA 59.185 37.037 0.00 0.00 0.00 3.72
268 272 7.815068 ACACATGTCTAATTTCTCTCAGTACAC 59.185 37.037 0.00 0.00 0.00 2.90
269 273 7.896811 ACACATGTCTAATTTCTCTCAGTACA 58.103 34.615 0.00 0.00 0.00 2.90
297 301 6.589139 TCGTCCGTTTTAACCAATTTTGTTTT 59.411 30.769 0.00 0.00 0.00 2.43
299 303 5.648572 TCGTCCGTTTTAACCAATTTTGTT 58.351 33.333 0.00 0.00 0.00 2.83
300 304 5.246145 TCGTCCGTTTTAACCAATTTTGT 57.754 34.783 0.00 0.00 0.00 2.83
301 305 5.915758 TCATCGTCCGTTTTAACCAATTTTG 59.084 36.000 0.00 0.00 0.00 2.44
307 311 3.875727 TGTTTCATCGTCCGTTTTAACCA 59.124 39.130 0.00 0.00 0.00 3.67
308 312 4.471157 TGTTTCATCGTCCGTTTTAACC 57.529 40.909 0.00 0.00 0.00 2.85
347 364 9.927668 TCAGTTTTCTTTTGTTTCTTTCTTCAT 57.072 25.926 0.00 0.00 0.00 2.57
366 383 9.793259 TTCCATCTCAGTTATACTTTCAGTTTT 57.207 29.630 0.00 0.00 0.00 2.43
371 388 9.010029 GGTTTTTCCATCTCAGTTATACTTTCA 57.990 33.333 0.00 0.00 35.97 2.69
372 389 9.010029 TGGTTTTTCCATCTCAGTTATACTTTC 57.990 33.333 0.00 0.00 41.93 2.62
377 394 9.753674 ATCTTTGGTTTTTCCATCTCAGTTATA 57.246 29.630 0.00 0.00 46.60 0.98
383 400 9.231297 CTAGTTATCTTTGGTTTTTCCATCTCA 57.769 33.333 0.00 0.00 46.60 3.27
384 401 9.232473 ACTAGTTATCTTTGGTTTTTCCATCTC 57.768 33.333 0.00 0.00 46.60 2.75
388 405 8.215050 TCTCACTAGTTATCTTTGGTTTTTCCA 58.785 33.333 0.00 0.00 45.60 3.53
389 406 8.617290 TCTCACTAGTTATCTTTGGTTTTTCC 57.383 34.615 0.00 0.00 0.00 3.13
480 576 1.032114 GCGCCCTCTGCTATGGTTTT 61.032 55.000 0.00 0.00 38.05 2.43
523 621 1.123928 TGGCAAATCAAACCGGGTTT 58.876 45.000 19.22 19.22 36.05 3.27
528 626 1.732683 GGCGTGGCAAATCAAACCG 60.733 57.895 0.00 0.00 0.00 4.44
554 662 7.234782 TCTGGTCTATTTTGAACCTTGAGAGTA 59.765 37.037 0.00 0.00 0.00 2.59
580 693 9.220767 GAAATCAGTACACCAAACTCTCTAATT 57.779 33.333 0.00 0.00 0.00 1.40
581 694 8.375506 TGAAATCAGTACACCAAACTCTCTAAT 58.624 33.333 0.00 0.00 0.00 1.73
582 695 7.732025 TGAAATCAGTACACCAAACTCTCTAA 58.268 34.615 0.00 0.00 0.00 2.10
583 696 7.232737 TCTGAAATCAGTACACCAAACTCTCTA 59.767 37.037 10.06 0.00 44.12 2.43
584 697 6.042093 TCTGAAATCAGTACACCAAACTCTCT 59.958 38.462 10.06 0.00 44.12 3.10
619 732 4.859798 ACGAAAGCTAAATCGAACTCTGAG 59.140 41.667 19.45 2.45 41.43 3.35
624 737 4.792189 CGTAGACGAAAGCTAAATCGAACT 59.208 41.667 19.45 17.90 41.43 3.01
674 793 1.779025 CTTCTCCATGCATTCGCGGG 61.779 60.000 6.13 0.00 42.97 6.13
678 797 1.590932 CTCCCTTCTCCATGCATTCG 58.409 55.000 0.00 0.00 0.00 3.34
700 819 8.728833 AGTCGTAATTCTAACTAATATCCCTCG 58.271 37.037 0.00 0.00 0.00 4.63
728 850 6.021596 GTGCATGGATAAACTGTTTAAGACG 58.978 40.000 16.14 6.45 0.00 4.18
748 870 1.934849 GCGAGTCATGTACAGTGTGCA 60.935 52.381 16.69 16.69 32.05 4.57
806 936 5.067674 TGCTGCTCACAGTTAAATTCTTGTT 59.932 36.000 0.00 0.00 46.30 2.83
821 951 1.227645 TGACCAGTGTGCTGCTCAC 60.228 57.895 23.17 23.17 45.82 3.51
917 1047 6.293462 GGTTTGTCAGTTTGGAACATCTCTAC 60.293 42.308 0.00 0.00 39.30 2.59
972 1128 1.009829 CGCCAACTGCCAGAGATTAC 58.990 55.000 0.00 0.00 36.24 1.89
994 1150 2.535012 GCTACTAGTGCCATCTTCCC 57.465 55.000 5.39 0.00 0.00 3.97
2008 2363 1.918609 GCCGTTCATCGAGTAGTTCAC 59.081 52.381 0.00 0.00 42.86 3.18
2016 2374 0.459237 AGAGCAAGCCGTTCATCGAG 60.459 55.000 0.00 0.00 42.86 4.04
2077 2435 0.546747 TTCACCCCCTTCATCTCCGT 60.547 55.000 0.00 0.00 0.00 4.69
2154 2512 1.021390 CCATGTCGAACTCCAGCACC 61.021 60.000 0.00 0.00 0.00 5.01
2285 2647 7.117812 GCAGTAGAGAACTAGCTAGAGATACAG 59.882 44.444 27.45 16.86 35.76 2.74
2293 2655 5.816919 GTTCAGCAGTAGAGAACTAGCTAG 58.183 45.833 19.44 19.44 39.21 3.42
2294 2656 5.821516 GTTCAGCAGTAGAGAACTAGCTA 57.178 43.478 0.00 0.00 39.21 3.32
2295 2657 4.712122 GTTCAGCAGTAGAGAACTAGCT 57.288 45.455 0.00 0.00 40.77 3.32
2322 2684 7.241042 ACAAATGTAGCATATATCCCGTAGT 57.759 36.000 0.00 0.00 0.00 2.73
2361 2723 2.303175 CGAAAAAGGGGGTCTTGACAA 58.697 47.619 3.08 0.00 35.55 3.18
2370 2732 0.313987 GACTTGCACGAAAAAGGGGG 59.686 55.000 0.00 0.00 0.00 5.40
2409 2771 3.119990 ACAACACACAAACAAGTTCGAGG 60.120 43.478 0.00 0.00 0.00 4.63
2440 3036 8.623030 CAGAGTAATAGTTCTCCTACCTGTTAC 58.377 40.741 0.00 0.00 34.75 2.50
2446 3042 4.023021 CGGCAGAGTAATAGTTCTCCTACC 60.023 50.000 0.00 0.00 0.00 3.18
2492 3261 0.467290 GAACCTGGCCCACTTGTCAA 60.467 55.000 0.00 0.00 0.00 3.18
2498 3267 1.456287 GTTGAGAACCTGGCCCACT 59.544 57.895 0.00 0.00 0.00 4.00
2580 3349 1.665916 CCTCTGCAGTGACACACCG 60.666 63.158 17.19 0.00 34.49 4.94
2588 3357 1.162698 CATGTGAACCCTCTGCAGTG 58.837 55.000 14.67 11.58 0.00 3.66
2633 4334 2.693074 ACTTCATTTTTGCAACTCGGGT 59.307 40.909 0.00 0.00 0.00 5.28
2656 4357 2.364324 ACGTAGAGAAGTCACCAAAGCA 59.636 45.455 0.00 0.00 0.00 3.91
2657 4358 2.731976 CACGTAGAGAAGTCACCAAAGC 59.268 50.000 0.00 0.00 0.00 3.51
2707 4408 1.647545 CGCCGCAAGATCATGTTGGT 61.648 55.000 11.32 0.00 43.02 3.67
2758 4459 3.177997 ACCATGAAAACACCTTGCAAC 57.822 42.857 0.00 0.00 0.00 4.17
2759 4460 3.529533 CAACCATGAAAACACCTTGCAA 58.470 40.909 0.00 0.00 0.00 4.08
2773 4476 1.856629 ATTCTTCAGCCCCAACCATG 58.143 50.000 0.00 0.00 0.00 3.66
2774 4477 2.181975 CAATTCTTCAGCCCCAACCAT 58.818 47.619 0.00 0.00 0.00 3.55
2782 4485 2.424956 GTCCATCACCAATTCTTCAGCC 59.575 50.000 0.00 0.00 0.00 4.85
2798 4501 2.462456 CGATTGATCGGATGGTCCAT 57.538 50.000 3.26 3.26 45.93 3.41
2813 4516 2.799371 GTCCTCGACGAGCCGATT 59.201 61.111 19.55 0.00 37.96 3.34
2827 4530 2.501610 GACCTGATGAGGGCGTCC 59.498 66.667 0.00 0.00 44.84 4.79
2863 4566 0.037590 TCCACCATTTCCGGAACCTG 59.962 55.000 18.64 16.93 0.00 4.00
2864 4567 0.999712 ATCCACCATTTCCGGAACCT 59.000 50.000 18.64 4.25 31.18 3.50
2865 4568 1.340600 TGATCCACCATTTCCGGAACC 60.341 52.381 18.64 0.00 31.18 3.62
2866 4569 1.743394 GTGATCCACCATTTCCGGAAC 59.257 52.381 18.64 2.21 31.18 3.62
2867 4570 2.122783 GTGATCCACCATTTCCGGAA 57.877 50.000 14.35 14.35 31.18 4.30
2868 4571 3.873781 GTGATCCACCATTTCCGGA 57.126 52.632 0.00 0.00 0.00 5.14
2890 4593 0.461870 CCACTAGCGCATGCCACTAA 60.462 55.000 13.15 0.00 44.31 2.24
2891 4594 1.143838 CCACTAGCGCATGCCACTA 59.856 57.895 13.15 13.06 44.31 2.74
2892 4595 2.124983 CCACTAGCGCATGCCACT 60.125 61.111 13.15 12.57 44.31 4.00
2902 4605 0.464554 GGAGGGTGAATGCCACTAGC 60.465 60.000 0.00 0.00 45.03 3.42
2971 4699 5.272167 TGGTAGATGTTTTCTTTTACGCG 57.728 39.130 3.53 3.53 35.79 6.01
2993 4721 5.163385 CCAAATTATGAGGCATGTGATGGTT 60.163 40.000 0.00 0.00 0.00 3.67
2994 4722 4.342951 CCAAATTATGAGGCATGTGATGGT 59.657 41.667 0.00 0.00 0.00 3.55
3002 4730 4.403432 CACAGTTCCCAAATTATGAGGCAT 59.597 41.667 0.00 0.00 0.00 4.40
3010 4738 3.572255 GTGCTTCCACAGTTCCCAAATTA 59.428 43.478 0.00 0.00 41.67 1.40
3039 4768 4.491234 TTGCGTTGTCGAAAATTATGGT 57.509 36.364 0.00 0.00 39.71 3.55
3052 4781 1.169661 TTCTGCGGGATTTGCGTTGT 61.170 50.000 0.00 0.00 34.24 3.32
3071 4800 7.125507 TCCTAGTATATAAGACTAGCTAGCCGT 59.874 40.741 20.91 10.73 43.40 5.68
3088 4817 5.162870 TGCCTTCCTCCAAGATCCTAGTATA 60.163 44.000 0.00 0.00 33.29 1.47
3117 4846 1.917872 AAAGCCCTAATGAACCGCAA 58.082 45.000 0.00 0.00 0.00 4.85
3118 4847 1.917872 AAAAGCCCTAATGAACCGCA 58.082 45.000 0.00 0.00 0.00 5.69
3150 4879 8.739972 ACATATACAAATGTGGAAGAAAGGTTC 58.260 33.333 0.00 0.00 38.65 3.62
3178 4908 5.573380 ACACATTCATATCCTGCCTACAT 57.427 39.130 0.00 0.00 0.00 2.29
3198 4928 5.384063 CACAATTAAATGTGGTGCCTACA 57.616 39.130 14.73 0.00 45.47 2.74
3208 4938 7.330262 CAAATAGGCCTTCCACAATTAAATGT 58.670 34.615 12.58 0.00 33.74 2.71
3217 4947 1.339631 CGACCAAATAGGCCTTCCACA 60.340 52.381 12.58 0.00 43.14 4.17
3223 4953 1.628846 ACAACTCGACCAAATAGGCCT 59.371 47.619 11.78 11.78 43.14 5.19


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

AutoCloner maintained by Alex Coulton.