Multiple sequence alignment - TraesCS3A01G343400

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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 TraesCS3A01G343400 chr3A 100.000 3133 0 0 1 3133 591693581 591690449 0.000000e+00 5786.0
1 TraesCS3A01G343400 chr3A 88.278 691 42 23 936 1621 577563694 577563038 0.000000e+00 791.0
2 TraesCS3A01G343400 chr3A 87.561 611 60 13 1873 2472 603855065 603854460 0.000000e+00 693.0
3 TraesCS3A01G343400 chr3A 86.207 145 20 0 97 241 676852861 676853005 1.160000e-34 158.0
4 TraesCS3A01G343400 chr6A 96.283 2152 72 7 324 2472 165816466 165818612 0.000000e+00 3524.0
5 TraesCS3A01G343400 chr6A 95.548 292 13 0 1 292 165816187 165816478 4.730000e-128 468.0
6 TraesCS3A01G343400 chr6A 85.784 204 26 2 406 609 603277416 603277616 2.450000e-51 213.0
7 TraesCS3A01G343400 chr6A 89.404 151 16 0 97 247 89283986 89283836 1.150000e-44 191.0
8 TraesCS3A01G343400 chr6A 93.939 99 6 0 1 99 592798152 592798250 1.950000e-32 150.0
9 TraesCS3A01G343400 chr4B 92.956 866 42 7 1625 2473 662859113 662859976 0.000000e+00 1243.0
10 TraesCS3A01G343400 chr4B 87.975 815 82 12 1669 2472 395553410 395554219 0.000000e+00 948.0
11 TraesCS3A01G343400 chr5D 96.380 663 22 2 2473 3133 338417707 338418369 0.000000e+00 1090.0
12 TraesCS3A01G343400 chr5D 96.078 663 22 3 2473 3133 124588718 124589378 0.000000e+00 1077.0
13 TraesCS3A01G343400 chr5D 96.084 664 21 5 2473 3133 500905420 500904759 0.000000e+00 1077.0
14 TraesCS3A01G343400 chr5D 96.073 662 24 2 2473 3133 513494283 513493623 0.000000e+00 1077.0
15 TraesCS3A01G343400 chr5D 87.158 366 30 8 1256 1621 561348647 561348299 1.750000e-107 399.0
16 TraesCS3A01G343400 chr5D 80.702 228 33 7 939 1163 495402517 495402298 1.930000e-37 167.0
17 TraesCS3A01G343400 chr3D 96.380 663 21 3 2473 3133 523667218 523667879 0.000000e+00 1088.0
18 TraesCS3A01G343400 chr3D 96.078 663 23 3 2473 3133 414865765 414866426 0.000000e+00 1077.0
19 TraesCS3A01G343400 chr3D 90.061 815 49 13 1669 2472 3893400 3892607 0.000000e+00 1027.0
20 TraesCS3A01G343400 chr3D 91.760 716 29 14 915 1621 438608335 438607641 0.000000e+00 968.0
21 TraesCS3A01G343400 chr3D 82.787 122 18 3 122 242 74455306 74455187 4.270000e-19 106.0
22 TraesCS3A01G343400 chr4D 96.229 663 23 2 2473 3133 109687304 109687966 0.000000e+00 1085.0
23 TraesCS3A01G343400 chr4D 86.111 144 17 2 97 240 104639988 104640128 5.410000e-33 152.0
24 TraesCS3A01G343400 chr2D 96.235 664 21 4 2473 3133 150318352 150319014 0.000000e+00 1085.0
25 TraesCS3A01G343400 chr2D 89.323 871 48 16 1625 2472 490511234 490512082 0.000000e+00 1051.0
26 TraesCS3A01G343400 chr2D 89.865 148 15 0 98 245 420178821 420178674 1.150000e-44 191.0
27 TraesCS3A01G343400 chr2D 83.893 149 19 4 105 250 44732695 44732841 1.520000e-28 137.0
28 TraesCS3A01G343400 chr6D 95.934 664 24 3 2473 3133 79753506 79754169 0.000000e+00 1074.0
29 TraesCS3A01G343400 chr6D 81.016 374 40 12 406 771 456553118 456553468 5.150000e-68 268.0
30 TraesCS3A01G343400 chr5B 89.171 868 71 9 1625 2472 441749943 441749079 0.000000e+00 1061.0
31 TraesCS3A01G343400 chr5B 88.736 870 75 9 1625 2472 569823602 569824470 0.000000e+00 1042.0
32 TraesCS3A01G343400 chr2B 87.945 871 80 11 1625 2472 38674227 38673359 0.000000e+00 1003.0
33 TraesCS3A01G343400 chr2B 85.737 624 74 12 1864 2476 506803356 506802737 0.000000e+00 645.0
34 TraesCS3A01G343400 chr2B 92.655 177 13 0 1256 1432 411179910 411180086 4.010000e-64 255.0
35 TraesCS3A01G343400 chr2B 84.722 144 18 3 105 246 237753150 237753291 1.170000e-29 141.0
36 TraesCS3A01G343400 chr1A 87.875 866 72 14 1625 2472 242067954 242067104 0.000000e+00 987.0
37 TraesCS3A01G343400 chr1A 88.251 366 26 8 1256 1621 346785341 346785689 3.740000e-114 422.0
38 TraesCS3A01G343400 chr3B 86.134 714 43 16 915 1621 574681794 574681130 0.000000e+00 719.0
39 TraesCS3A01G343400 chr2A 88.496 565 53 10 1913 2472 777178759 777179316 0.000000e+00 673.0
40 TraesCS3A01G343400 chr2A 89.071 366 23 6 1256 1621 272967808 272967460 3.710000e-119 438.0
41 TraesCS3A01G343400 chr2A 88.798 366 24 8 1256 1621 272956440 272956788 1.730000e-117 433.0
42 TraesCS3A01G343400 chr2A 97.368 76 2 0 780 855 484994788 484994713 2.540000e-26 130.0
43 TraesCS3A01G343400 chr2A 97.015 67 2 0 851 917 484994680 484994614 2.550000e-21 113.0
44 TraesCS3A01G343400 chr7D 84.308 701 48 24 936 1621 70220000 70220653 2.050000e-176 628.0
45 TraesCS3A01G343400 chr7D 88.798 366 23 8 1256 1621 556663310 556662963 1.730000e-117 433.0
46 TraesCS3A01G343400 chr7D 85.714 140 16 3 105 242 9111943 9111806 9.060000e-31 145.0
47 TraesCS3A01G343400 chr7D 89.524 105 11 0 140 244 608192606 608192502 1.960000e-27 134.0
48 TraesCS3A01G343400 chr7A 90.654 214 14 4 919 1126 199441055 199440842 2.380000e-71 279.0
49 TraesCS3A01G343400 chrUn 93.785 177 11 0 919 1095 295945426 295945250 1.850000e-67 267.0
50 TraesCS3A01G343400 chrUn 86.127 173 12 5 1449 1621 67153738 67153898 3.210000e-40 176.0
51 TraesCS3A01G343400 chrUn 96.842 95 3 0 925 1019 67446077 67445983 3.230000e-35 159.0
52 TraesCS3A01G343400 chrUn 96.842 95 3 0 925 1019 337804729 337804823 3.230000e-35 159.0
53 TraesCS3A01G343400 chrUn 95.238 63 3 0 1256 1318 67152860 67152922 1.990000e-17 100.0
54 TraesCS3A01G343400 chr4A 93.785 177 11 0 919 1095 611288032 611288208 1.850000e-67 267.0
55 TraesCS3A01G343400 chr4A 84.677 124 17 2 124 246 735492901 735493023 4.240000e-24 122.0
56 TraesCS3A01G343400 chr6B 77.330 397 52 23 406 771 694399553 694399942 1.910000e-47 200.0
57 TraesCS3A01G343400 chr5A 85.816 141 16 3 105 243 567936762 567936900 2.520000e-31 147.0
58 TraesCS3A01G343400 chr1D 85.366 123 15 2 122 243 395812078 395812198 1.180000e-24 124.0
59 TraesCS3A01G343400 chr7B 97.183 71 2 0 847 917 684163403 684163473 1.530000e-23 121.0
60 TraesCS3A01G343400 chr7B 96.875 32 1 0 1362 1393 697407291 697407322 2.000000e-03 54.7
61 TraesCS3A01G343400 chr1B 97.059 68 2 0 850 917 558598519 558598452 7.100000e-22 115.0


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 TraesCS3A01G343400 chr3A 591690449 591693581 3132 True 5786 5786 100.0000 1 3133 1 chr3A.!!$R2 3132
1 TraesCS3A01G343400 chr3A 577563038 577563694 656 True 791 791 88.2780 936 1621 1 chr3A.!!$R1 685
2 TraesCS3A01G343400 chr3A 603854460 603855065 605 True 693 693 87.5610 1873 2472 1 chr3A.!!$R3 599
3 TraesCS3A01G343400 chr6A 165816187 165818612 2425 False 1996 3524 95.9155 1 2472 2 chr6A.!!$F3 2471
4 TraesCS3A01G343400 chr4B 662859113 662859976 863 False 1243 1243 92.9560 1625 2473 1 chr4B.!!$F2 848
5 TraesCS3A01G343400 chr4B 395553410 395554219 809 False 948 948 87.9750 1669 2472 1 chr4B.!!$F1 803
6 TraesCS3A01G343400 chr5D 338417707 338418369 662 False 1090 1090 96.3800 2473 3133 1 chr5D.!!$F2 660
7 TraesCS3A01G343400 chr5D 124588718 124589378 660 False 1077 1077 96.0780 2473 3133 1 chr5D.!!$F1 660
8 TraesCS3A01G343400 chr5D 500904759 500905420 661 True 1077 1077 96.0840 2473 3133 1 chr5D.!!$R2 660
9 TraesCS3A01G343400 chr5D 513493623 513494283 660 True 1077 1077 96.0730 2473 3133 1 chr5D.!!$R3 660
10 TraesCS3A01G343400 chr3D 523667218 523667879 661 False 1088 1088 96.3800 2473 3133 1 chr3D.!!$F2 660
11 TraesCS3A01G343400 chr3D 414865765 414866426 661 False 1077 1077 96.0780 2473 3133 1 chr3D.!!$F1 660
12 TraesCS3A01G343400 chr3D 3892607 3893400 793 True 1027 1027 90.0610 1669 2472 1 chr3D.!!$R1 803
13 TraesCS3A01G343400 chr3D 438607641 438608335 694 True 968 968 91.7600 915 1621 1 chr3D.!!$R3 706
14 TraesCS3A01G343400 chr4D 109687304 109687966 662 False 1085 1085 96.2290 2473 3133 1 chr4D.!!$F2 660
15 TraesCS3A01G343400 chr2D 150318352 150319014 662 False 1085 1085 96.2350 2473 3133 1 chr2D.!!$F2 660
16 TraesCS3A01G343400 chr2D 490511234 490512082 848 False 1051 1051 89.3230 1625 2472 1 chr2D.!!$F3 847
17 TraesCS3A01G343400 chr6D 79753506 79754169 663 False 1074 1074 95.9340 2473 3133 1 chr6D.!!$F1 660
18 TraesCS3A01G343400 chr5B 441749079 441749943 864 True 1061 1061 89.1710 1625 2472 1 chr5B.!!$R1 847
19 TraesCS3A01G343400 chr5B 569823602 569824470 868 False 1042 1042 88.7360 1625 2472 1 chr5B.!!$F1 847
20 TraesCS3A01G343400 chr2B 38673359 38674227 868 True 1003 1003 87.9450 1625 2472 1 chr2B.!!$R1 847
21 TraesCS3A01G343400 chr2B 506802737 506803356 619 True 645 645 85.7370 1864 2476 1 chr2B.!!$R2 612
22 TraesCS3A01G343400 chr1A 242067104 242067954 850 True 987 987 87.8750 1625 2472 1 chr1A.!!$R1 847
23 TraesCS3A01G343400 chr3B 574681130 574681794 664 True 719 719 86.1340 915 1621 1 chr3B.!!$R1 706
24 TraesCS3A01G343400 chr2A 777178759 777179316 557 False 673 673 88.4960 1913 2472 1 chr2A.!!$F2 559
25 TraesCS3A01G343400 chr7D 70220000 70220653 653 False 628 628 84.3080 936 1621 1 chr7D.!!$F1 685

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
252 253 0.036875 AACAGCCCCTTAGTGACAGC 59.963 55.0 0.00 0.0 0.0 4.40 F
309 310 0.390340 TCCTGTCACGATGCTTCAGC 60.390 55.0 0.08 0.0 42.5 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1208 1224 4.286297 AGACGAGGGAAACATCAATCAA 57.714 40.909 0.0 0.0 42.48 2.57 R
2155 2234 4.420522 AATTCAGCCCATTTGTTGTTGT 57.579 36.364 0.0 0.0 0.00 3.32 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
57 58 4.690184 TGCATAGCATTCAAACTGACAG 57.310 40.909 0.00 0.00 31.71 3.51
117 118 2.880890 ACAGAGTGTGGCAAGAAATCAC 59.119 45.455 0.00 0.00 0.00 3.06
172 173 2.286365 CCTTAGGAGGCAACCAAACA 57.714 50.000 0.00 0.00 35.94 2.83
173 174 2.593026 CCTTAGGAGGCAACCAAACAA 58.407 47.619 0.00 0.00 35.94 2.83
174 175 2.296190 CCTTAGGAGGCAACCAAACAAC 59.704 50.000 0.00 0.00 35.94 3.32
176 177 0.106918 AGGAGGCAACCAAACAACGA 60.107 50.000 0.00 0.00 37.17 3.85
252 253 0.036875 AACAGCCCCTTAGTGACAGC 59.963 55.000 0.00 0.00 0.00 4.40
270 271 2.227388 CAGCAATCTGACCTGTTTGGAC 59.773 50.000 0.00 0.00 42.95 4.02
287 288 8.463930 TGTTTGGACAGAATAAAACTCAGATT 57.536 30.769 0.00 0.00 34.39 2.40
288 289 8.567948 TGTTTGGACAGAATAAAACTCAGATTC 58.432 33.333 0.00 0.00 34.39 2.52
289 290 8.567948 GTTTGGACAGAATAAAACTCAGATTCA 58.432 33.333 0.00 0.00 32.96 2.57
290 291 8.868522 TTGGACAGAATAAAACTCAGATTCAT 57.131 30.769 0.00 0.00 32.96 2.57
291 292 8.498054 TGGACAGAATAAAACTCAGATTCATC 57.502 34.615 0.00 0.00 32.96 2.92
292 293 7.554118 TGGACAGAATAAAACTCAGATTCATCC 59.446 37.037 0.00 0.00 37.49 3.51
293 294 7.772757 GGACAGAATAAAACTCAGATTCATCCT 59.227 37.037 0.00 0.00 35.85 3.24
294 295 8.503458 ACAGAATAAAACTCAGATTCATCCTG 57.497 34.615 0.00 0.00 32.96 3.86
295 296 8.105829 ACAGAATAAAACTCAGATTCATCCTGT 58.894 33.333 0.00 0.00 32.96 4.00
296 297 8.610896 CAGAATAAAACTCAGATTCATCCTGTC 58.389 37.037 0.00 0.00 32.96 3.51
297 298 8.324306 AGAATAAAACTCAGATTCATCCTGTCA 58.676 33.333 0.00 0.00 32.96 3.58
298 299 7.856145 ATAAAACTCAGATTCATCCTGTCAC 57.144 36.000 0.00 0.00 33.57 3.67
299 300 3.516981 ACTCAGATTCATCCTGTCACG 57.483 47.619 0.00 0.00 33.57 4.35
300 301 3.092301 ACTCAGATTCATCCTGTCACGA 58.908 45.455 0.00 0.00 33.57 4.35
301 302 3.703556 ACTCAGATTCATCCTGTCACGAT 59.296 43.478 0.00 0.00 33.57 3.73
302 303 4.049869 CTCAGATTCATCCTGTCACGATG 58.950 47.826 5.68 5.68 38.79 3.84
303 304 2.543012 CAGATTCATCCTGTCACGATGC 59.457 50.000 6.88 0.00 37.60 3.91
304 305 2.433604 AGATTCATCCTGTCACGATGCT 59.566 45.455 6.88 0.00 37.60 3.79
305 306 2.768253 TTCATCCTGTCACGATGCTT 57.232 45.000 6.88 0.00 37.60 3.91
306 307 2.299993 TCATCCTGTCACGATGCTTC 57.700 50.000 6.88 0.00 37.60 3.86
307 308 1.550072 TCATCCTGTCACGATGCTTCA 59.450 47.619 6.88 0.00 37.60 3.02
308 309 1.931841 CATCCTGTCACGATGCTTCAG 59.068 52.381 0.08 0.00 31.37 3.02
309 310 0.390340 TCCTGTCACGATGCTTCAGC 60.390 55.000 0.08 0.00 42.50 4.26
321 322 2.563297 CTTCAGCAGCATGGCTTCA 58.437 52.632 0.00 0.00 42.71 3.02
322 323 1.103803 CTTCAGCAGCATGGCTTCAT 58.896 50.000 0.00 0.00 42.71 2.57
323 324 2.294979 CTTCAGCAGCATGGCTTCATA 58.705 47.619 0.00 0.00 42.71 2.15
324 325 1.671979 TCAGCAGCATGGCTTCATAC 58.328 50.000 0.00 0.00 42.71 2.39
325 326 1.211212 TCAGCAGCATGGCTTCATACT 59.789 47.619 0.00 0.00 42.71 2.12
326 327 1.602851 CAGCAGCATGGCTTCATACTC 59.397 52.381 0.00 0.00 42.71 2.59
357 358 4.098960 TCGCTAAGTTACCTTGGTATCCTG 59.901 45.833 0.00 0.00 32.14 3.86
489 490 3.640498 TGATGCAGTTGGATTGGTTTTCA 59.360 39.130 0.00 0.00 0.00 2.69
490 491 3.731652 TGCAGTTGGATTGGTTTTCAG 57.268 42.857 0.00 0.00 0.00 3.02
531 532 6.822667 ACTGCATGTACATCATTTCTTTCA 57.177 33.333 5.07 0.00 34.09 2.69
532 533 6.615088 ACTGCATGTACATCATTTCTTTCAC 58.385 36.000 5.07 0.00 34.09 3.18
534 535 6.614160 TGCATGTACATCATTTCTTTCACTG 58.386 36.000 5.07 0.00 34.09 3.66
581 582 2.544486 GCTTTGTTTTCCTGGTCAGCTG 60.544 50.000 7.63 7.63 0.00 4.24
654 655 3.738982 CCACATGTTACTTCCAGTGACA 58.261 45.455 0.00 4.19 46.49 3.58
662 663 5.353123 TGTTACTTCCAGTGACACTTTTGAC 59.647 40.000 5.04 0.00 39.39 3.18
743 744 6.078456 ACTGGATATTTCTCATGTTTGGGA 57.922 37.500 0.00 0.00 0.00 4.37
816 817 7.492344 CACATGACTACTACATCTGTTATGCAA 59.508 37.037 0.00 0.00 32.13 4.08
818 819 6.930731 TGACTACTACATCTGTTATGCAACA 58.069 36.000 0.00 0.00 42.39 3.33
819 820 6.811665 TGACTACTACATCTGTTATGCAACAC 59.188 38.462 0.00 0.00 39.75 3.32
820 821 6.697395 ACTACTACATCTGTTATGCAACACA 58.303 36.000 0.00 0.00 39.75 3.72
969 971 6.704937 TGAATGATTTCATCTTGATCTCCGAG 59.295 38.462 0.00 0.00 36.94 4.63
1111 1119 2.095212 TCCTCAGATCACAAGAACGACG 60.095 50.000 0.00 0.00 0.00 5.12
1153 1163 9.826574 AACTTCAGACTTTTACATACTACACAA 57.173 29.630 0.00 0.00 0.00 3.33
1187 1201 6.632909 TCTTCAGATGTATTTGCCATTTTGG 58.367 36.000 0.00 0.00 41.55 3.28
1208 1224 0.179073 AAAGCAGCGAGTCTGTGTGT 60.179 50.000 0.00 0.00 44.66 3.72
1346 1370 4.435436 CCGCCGCTGCTGTCTACA 62.435 66.667 0.00 0.00 34.43 2.74
1447 1475 5.237127 GCTGATGTAAGCTATACATGCACAA 59.763 40.000 19.60 5.97 40.20 3.33
1505 1548 4.624364 CAGGGGCACGCACTGACA 62.624 66.667 7.04 0.00 46.88 3.58
1510 1553 1.079543 GGCACGCACTGACAGAGAT 60.080 57.895 10.08 0.00 0.00 2.75
1517 1560 2.103373 GCACTGACAGAGATGACCCTA 58.897 52.381 10.08 0.00 0.00 3.53
1691 1748 7.011389 GCACTGCTGTTGTTATTCACTATATCA 59.989 37.037 0.00 0.00 0.00 2.15
2031 2098 6.165577 CAAACCAGAATCGAAAATTTGGGAT 58.834 36.000 9.57 0.00 0.00 3.85
2109 2183 3.410631 ACCCAAAAATAAAAAGGCCGG 57.589 42.857 0.00 0.00 0.00 6.13
2562 2662 0.043334 AGATGTAGCTGGTGGGTCCT 59.957 55.000 0.00 0.00 37.07 3.85
2727 2829 1.317431 TACAGTCCACGTCCGATGGG 61.317 60.000 0.00 0.00 37.85 4.00
2753 2855 0.762418 TCCTTGACCACGTTGACCAT 59.238 50.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.755591 TGCAAGAGAGCAGAAAAATAATGTAG 58.244 34.615 0.00 0.00 40.11 2.74
57 58 4.202050 ACTCACAAAAACTGAGCATTCACC 60.202 41.667 0.00 0.00 39.08 4.02
117 118 3.994392 ACATGCGTAGTGTCTTTTGTAGG 59.006 43.478 0.00 0.00 0.00 3.18
270 271 8.503458 ACAGGATGAATCTGAGTTTTATTCTG 57.497 34.615 12.33 12.33 39.69 3.02
283 284 2.433604 AGCATCGTGACAGGATGAATCT 59.566 45.455 32.13 20.60 41.57 2.40
284 285 2.831333 AGCATCGTGACAGGATGAATC 58.169 47.619 32.13 19.09 41.57 2.52
285 286 2.996249 AGCATCGTGACAGGATGAAT 57.004 45.000 32.13 20.57 41.57 2.57
286 287 2.028203 TGAAGCATCGTGACAGGATGAA 60.028 45.455 32.13 16.45 41.57 2.57
287 288 1.550072 TGAAGCATCGTGACAGGATGA 59.450 47.619 32.13 15.09 41.57 2.92
288 289 1.931841 CTGAAGCATCGTGACAGGATG 59.068 52.381 26.49 26.49 41.85 3.51
289 290 1.741732 GCTGAAGCATCGTGACAGGAT 60.742 52.381 4.80 4.80 41.59 3.24
290 291 0.390340 GCTGAAGCATCGTGACAGGA 60.390 55.000 0.00 0.00 41.59 3.86
291 292 2.084844 GCTGAAGCATCGTGACAGG 58.915 57.895 0.00 0.00 41.59 4.00
303 304 1.103803 ATGAAGCCATGCTGCTGAAG 58.896 50.000 0.00 0.00 41.80 3.02
304 305 2.019249 GTATGAAGCCATGCTGCTGAA 58.981 47.619 0.00 0.00 41.80 3.02
305 306 1.211212 AGTATGAAGCCATGCTGCTGA 59.789 47.619 0.00 0.00 42.82 4.26
306 307 1.602851 GAGTATGAAGCCATGCTGCTG 59.397 52.381 0.00 0.00 44.13 4.41
307 308 1.476471 GGAGTATGAAGCCATGCTGCT 60.476 52.381 0.00 0.00 45.45 4.24
308 309 0.950116 GGAGTATGAAGCCATGCTGC 59.050 55.000 0.93 0.00 44.13 5.25
309 310 1.202568 TCGGAGTATGAAGCCATGCTG 60.203 52.381 0.93 0.00 44.13 4.41
310 311 1.123077 TCGGAGTATGAAGCCATGCT 58.877 50.000 0.00 0.00 46.24 3.79
311 312 1.202580 AGTCGGAGTATGAAGCCATGC 60.203 52.381 0.00 0.00 35.90 4.06
312 313 2.101415 TGAGTCGGAGTATGAAGCCATG 59.899 50.000 0.00 0.00 34.31 3.66
313 314 2.388735 TGAGTCGGAGTATGAAGCCAT 58.611 47.619 0.00 0.00 36.81 4.40
314 315 1.847328 TGAGTCGGAGTATGAAGCCA 58.153 50.000 0.00 0.00 0.00 4.75
315 316 2.605823 CGATGAGTCGGAGTATGAAGCC 60.606 54.545 0.00 0.00 44.00 4.35
316 317 2.656085 CGATGAGTCGGAGTATGAAGC 58.344 52.381 0.00 0.00 44.00 3.86
341 342 6.887626 TCAAAAACAGGATACCAAGGTAAC 57.112 37.500 2.62 0.31 33.99 2.50
376 377 4.588528 ACATGTGTGGCTCAATTAAACCTT 59.411 37.500 0.00 0.00 0.00 3.50
489 490 4.323562 GCAGTATGGTTCTGGAAGTTACCT 60.324 45.833 0.00 0.00 39.40 3.08
490 491 3.939592 GCAGTATGGTTCTGGAAGTTACC 59.060 47.826 0.00 0.00 39.21 2.85
684 685 7.560991 TGAGAAACCGGTAACTATATTAGTCCA 59.439 37.037 8.00 0.00 38.26 4.02
743 744 4.964593 TGTGTACTATGAGATGCATGCAT 58.035 39.130 32.66 32.66 37.87 3.96
816 817 6.542370 ACTGAAGTTAGCTAAACATGTTGTGT 59.458 34.615 12.82 0.00 44.84 3.72
818 819 8.671384 TTACTGAAGTTAGCTAAACATGTTGT 57.329 30.769 12.82 5.25 40.83 3.32
1111 1119 6.647481 GTCTGAAGTTCTTCTTTTACCTCCTC 59.353 42.308 12.74 0.00 36.40 3.71
1153 1163 8.697846 CAAATACATCTGAAGAATTTGCATGT 57.302 30.769 0.00 0.00 32.61 3.21
1208 1224 4.286297 AGACGAGGGAAACATCAATCAA 57.714 40.909 0.00 0.00 42.48 2.57
1447 1475 6.701145 TTCAAGCTACGAGAGATTCAGTAT 57.299 37.500 0.00 0.00 28.88 2.12
1505 1548 4.964897 TCATCACACAATAGGGTCATCTCT 59.035 41.667 0.00 0.00 0.00 3.10
1510 1553 5.434182 TCAATCATCACACAATAGGGTCA 57.566 39.130 0.00 0.00 0.00 4.02
1517 1560 5.953548 TCCCTGAAATCAATCATCACACAAT 59.046 36.000 0.00 0.00 0.00 2.71
1691 1748 4.498009 CCAACAAGAAAACAGAACAGCGAT 60.498 41.667 0.00 0.00 0.00 4.58
1799 1859 6.344500 AGAGTTCACAATGCCTAGATAACTG 58.656 40.000 0.00 0.00 0.00 3.16
1800 1860 6.552445 AGAGTTCACAATGCCTAGATAACT 57.448 37.500 0.00 0.00 0.00 2.24
1808 1868 6.240894 TGAAATTCTAGAGTTCACAATGCCT 58.759 36.000 13.99 0.00 0.00 4.75
2031 2098 5.762179 ATTGTCAGGTTCTGATAAGTGGA 57.238 39.130 11.52 0.00 42.85 4.02
2155 2234 4.420522 AATTCAGCCCATTTGTTGTTGT 57.579 36.364 0.00 0.00 0.00 3.32
2394 2489 6.487689 TTGTTTTTCATTTGCGACCTTTTT 57.512 29.167 0.00 0.00 0.00 1.94
2562 2662 0.834687 ACGTTTCCCCCTGACTGCTA 60.835 55.000 0.00 0.00 0.00 3.49
2669 2771 1.302192 GGTCCACGGCTACAGCAAA 60.302 57.895 3.24 0.00 44.36 3.68
2727 2829 2.027625 CGTGGTCAAGGAACGGCTC 61.028 63.158 0.00 0.00 33.77 4.70
2895 2997 1.449601 CCCTGTTATTCTGCGGCGT 60.450 57.895 9.37 0.00 0.00 5.68
2998 3101 3.073735 CCTCGTGCTCCTGCCTCT 61.074 66.667 0.00 0.00 38.71 3.69


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

AutoCloner maintained by Alex Coulton.