Multiple sequence alignment - TraesCS3D01G142000

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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 TraesCS3D01G142000 chr3D 100.000 2710 0 0 1 2710 104016881 104014172 0.000000e+00 5005.0
1 TraesCS3D01G142000 chr3D 87.356 261 31 2 2137 2396 146723795 146723536 5.670000e-77 298.0
2 TraesCS3D01G142000 chr3B 92.254 2130 112 23 586 2710 154606637 154604556 0.000000e+00 2970.0
3 TraesCS3D01G142000 chr3B 85.429 501 56 11 2 494 154607293 154606802 3.110000e-139 505.0
4 TraesCS3D01G142000 chr3A 91.689 1853 109 20 664 2500 552306346 552308169 0.000000e+00 2527.0
5 TraesCS3D01G142000 chr3A 88.123 261 28 3 2137 2396 236603078 236603336 9.430000e-80 307.0
6 TraesCS3D01G142000 chr3A 93.182 176 11 1 2491 2665 552308187 552308362 9.630000e-65 257.0
7 TraesCS3D01G142000 chr3A 100.000 42 0 0 2647 2688 552308374 552308415 8.040000e-11 78.7
8 TraesCS3D01G142000 chr5D 87.786 262 28 4 2137 2396 177985782 177985523 1.220000e-78 303.0
9 TraesCS3D01G142000 chr6D 87.405 262 30 3 2137 2396 360671225 360670965 5.670000e-77 298.0
10 TraesCS3D01G142000 chr6D 88.306 248 26 3 2137 2382 288432702 288432456 7.340000e-76 294.0
11 TraesCS3D01G142000 chr1A 87.903 248 27 3 2137 2382 103990413 103990659 3.410000e-74 289.0
12 TraesCS3D01G142000 chr1A 86.260 262 33 3 2137 2396 217992335 217992075 5.710000e-72 281.0
13 TraesCS3D01G142000 chr7B 82.443 131 18 2 373 500 125719632 125719504 2.850000e-20 110.0
14 TraesCS3D01G142000 chr4B 86.022 93 12 1 424 515 180697876 180697784 6.180000e-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 TraesCS3D01G142000 chr3D 104014172 104016881 2709 True 5005.000000 5005 100.0000 1 2710 1 chr3D.!!$R1 2709
1 TraesCS3D01G142000 chr3B 154604556 154607293 2737 True 1737.500000 2970 88.8415 2 2710 2 chr3B.!!$R1 2708
2 TraesCS3D01G142000 chr3A 552306346 552308415 2069 False 954.233333 2527 94.9570 664 2688 3 chr3A.!!$F2 2024

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
167 169 0.378962 CTAGTCGACGAAGCCTGGAG 59.621 60.0 10.46 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2251 0.73084 GCGGAGTAAAAATGACCGGG 59.269 55.0 6.32 0.0 43.15 5.73 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
19 20 0.745845 AAGATGCAGTGTCGCCATCC 60.746 55.000 0.00 0.00 0.00 3.51
46 48 1.301423 CGTTGTCCCCGTGAGAAAAA 58.699 50.000 0.00 0.00 0.00 1.94
74 76 9.588096 AATCCTAAACCTAAATTATTAGCCAGG 57.412 33.333 0.00 0.00 37.74 4.45
95 97 3.917760 GAGGCATCGAGGTCCCCG 61.918 72.222 0.00 0.00 0.00 5.73
120 122 4.704833 CACTGGCCACCTGACCGG 62.705 72.222 0.00 0.00 38.37 5.28
144 146 1.637553 ACAGAGGTGAGGCAAATCCAT 59.362 47.619 0.00 0.00 37.29 3.41
157 159 0.389391 AATCCATGGGCTAGTCGACG 59.611 55.000 13.02 0.00 0.00 5.12
158 160 0.467474 ATCCATGGGCTAGTCGACGA 60.467 55.000 13.02 3.61 0.00 4.20
159 161 0.681887 TCCATGGGCTAGTCGACGAA 60.682 55.000 13.02 1.38 0.00 3.85
161 163 0.872021 CATGGGCTAGTCGACGAAGC 60.872 60.000 27.72 27.72 35.47 3.86
164 166 4.386245 GCTAGTCGACGAAGCCTG 57.614 61.111 26.25 6.17 0.00 4.85
165 167 1.226717 GCTAGTCGACGAAGCCTGG 60.227 63.158 26.25 6.90 0.00 4.45
166 168 1.654954 GCTAGTCGACGAAGCCTGGA 61.655 60.000 26.25 0.89 0.00 3.86
167 169 0.378962 CTAGTCGACGAAGCCTGGAG 59.621 60.000 10.46 0.00 0.00 3.86
168 170 1.030488 TAGTCGACGAAGCCTGGAGG 61.030 60.000 10.46 0.00 38.53 4.30
179 181 3.114616 CTGGAGGCGACAAGTGCG 61.115 66.667 0.00 0.00 0.00 5.34
216 218 1.071071 CGTAGGGGGAAAAGTCACACA 59.929 52.381 0.00 0.00 30.27 3.72
218 220 3.763057 GTAGGGGGAAAAGTCACACAAT 58.237 45.455 0.00 0.00 30.27 2.71
221 223 2.698274 GGGGGAAAAGTCACACAATGTT 59.302 45.455 0.00 0.00 27.34 2.71
263 266 5.794945 CGACCTTACATTGCATAAACACTTG 59.205 40.000 0.00 0.00 0.00 3.16
276 279 9.723601 TGCATAAACACTTGCTATATGATATCA 57.276 29.630 8.10 8.10 39.60 2.15
277 280 9.979270 GCATAAACACTTGCTATATGATATCAC 57.021 33.333 7.78 0.00 35.95 3.06
283 286 9.650539 ACACTTGCTATATGATATCACAATCTC 57.349 33.333 7.78 1.92 0.00 2.75
284 287 9.649167 CACTTGCTATATGATATCACAATCTCA 57.351 33.333 7.78 4.24 0.00 3.27
285 288 9.650539 ACTTGCTATATGATATCACAATCTCAC 57.349 33.333 7.78 0.00 0.00 3.51
286 289 8.693542 TTGCTATATGATATCACAATCTCACG 57.306 34.615 7.78 0.00 0.00 4.35
287 290 6.753744 TGCTATATGATATCACAATCTCACGC 59.246 38.462 7.78 2.62 0.00 5.34
303 311 4.929808 TCTCACGCCATAAGTTTCTCTTTC 59.070 41.667 0.00 0.00 37.56 2.62
326 334 5.929415 TCACAAATAAGATGACGCACTGTTA 59.071 36.000 0.00 0.00 0.00 2.41
337 345 2.030274 ACGCACTGTTATGAAAAAGGCC 60.030 45.455 0.00 0.00 0.00 5.19
340 348 4.671766 CGCACTGTTATGAAAAAGGCCTAC 60.672 45.833 5.16 0.00 0.00 3.18
347 355 8.871629 TGTTATGAAAAAGGCCTACAATCTTA 57.128 30.769 5.16 2.66 0.00 2.10
397 405 3.260380 CCAATTTGTGGCTGGATGGTTAA 59.740 43.478 0.00 0.00 41.72 2.01
398 406 4.262808 CCAATTTGTGGCTGGATGGTTAAA 60.263 41.667 0.00 0.00 41.72 1.52
400 408 4.329462 TTTGTGGCTGGATGGTTAAAAC 57.671 40.909 0.00 0.00 0.00 2.43
401 409 2.950781 TGTGGCTGGATGGTTAAAACA 58.049 42.857 0.00 0.00 0.00 2.83
403 411 3.320541 TGTGGCTGGATGGTTAAAACAAG 59.679 43.478 0.00 0.00 0.00 3.16
412 420 6.657541 TGGATGGTTAAAACAAGAGTGGTATC 59.342 38.462 0.00 0.00 0.00 2.24
413 421 6.884836 GGATGGTTAAAACAAGAGTGGTATCT 59.115 38.462 0.00 0.00 0.00 1.98
417 425 7.444183 TGGTTAAAACAAGAGTGGTATCTTCTG 59.556 37.037 0.00 0.00 37.43 3.02
418 426 5.948992 AAAACAAGAGTGGTATCTTCTGC 57.051 39.130 0.00 0.00 37.43 4.26
419 427 3.618690 ACAAGAGTGGTATCTTCTGCC 57.381 47.619 0.00 0.00 37.43 4.85
436 444 1.144708 TGCCCACCAGAATTCAAGTCA 59.855 47.619 8.44 0.00 0.00 3.41
454 462 4.075763 GTCACAGACTTGACATTGATGC 57.924 45.455 10.87 0.00 44.62 3.91
456 464 4.214971 GTCACAGACTTGACATTGATGCTT 59.785 41.667 10.87 0.00 44.62 3.91
458 466 3.504906 ACAGACTTGACATTGATGCTTGG 59.495 43.478 0.00 0.00 0.00 3.61
464 472 6.161381 ACTTGACATTGATGCTTGGATTTTC 58.839 36.000 0.00 0.00 0.00 2.29
465 473 5.988310 TGACATTGATGCTTGGATTTTCT 57.012 34.783 0.00 0.00 0.00 2.52
466 474 5.716094 TGACATTGATGCTTGGATTTTCTG 58.284 37.500 0.00 0.00 0.00 3.02
475 483 8.199449 TGATGCTTGGATTTTCTGGATTTATTC 58.801 33.333 0.00 0.00 0.00 1.75
476 484 6.877236 TGCTTGGATTTTCTGGATTTATTCC 58.123 36.000 0.00 0.00 45.69 3.01
504 512 3.867857 TCTGGCAATATGCGTTTAGTGA 58.132 40.909 0.00 0.00 46.21 3.41
505 513 4.257731 TCTGGCAATATGCGTTTAGTGAA 58.742 39.130 0.00 0.00 46.21 3.18
506 514 4.332543 TCTGGCAATATGCGTTTAGTGAAG 59.667 41.667 0.00 0.00 46.21 3.02
512 520 2.450609 TGCGTTTAGTGAAGGGAGAC 57.549 50.000 0.00 0.00 0.00 3.36
515 523 2.325761 CGTTTAGTGAAGGGAGACGTG 58.674 52.381 0.00 0.00 0.00 4.49
517 525 3.057734 GTTTAGTGAAGGGAGACGTGTG 58.942 50.000 0.00 0.00 0.00 3.82
518 526 1.991121 TAGTGAAGGGAGACGTGTGT 58.009 50.000 0.00 0.00 0.00 3.72
519 527 0.389391 AGTGAAGGGAGACGTGTGTG 59.611 55.000 0.00 0.00 0.00 3.82
520 528 0.600255 GTGAAGGGAGACGTGTGTGG 60.600 60.000 0.00 0.00 0.00 4.17
522 530 3.515316 AAGGGAGACGTGTGTGGCG 62.515 63.158 0.00 0.00 0.00 5.69
523 531 3.986006 GGGAGACGTGTGTGGCGA 61.986 66.667 0.00 0.00 0.00 5.54
526 534 2.016704 GAGACGTGTGTGGCGACTG 61.017 63.158 0.00 0.00 34.91 3.51
527 535 3.702555 GACGTGTGTGGCGACTGC 61.703 66.667 0.00 0.00 41.71 4.40
530 538 3.269347 GTGTGTGGCGACTGCGTT 61.269 61.111 0.00 0.00 44.10 4.84
531 539 2.964925 TGTGTGGCGACTGCGTTC 60.965 61.111 0.00 0.00 44.10 3.95
532 540 2.964925 GTGTGGCGACTGCGTTCA 60.965 61.111 0.00 0.00 44.10 3.18
533 541 2.030412 TGTGGCGACTGCGTTCAT 59.970 55.556 0.00 0.00 44.10 2.57
534 542 2.316867 TGTGGCGACTGCGTTCATG 61.317 57.895 0.00 0.00 44.10 3.07
536 544 3.499737 GGCGACTGCGTTCATGGG 61.500 66.667 0.00 0.00 44.10 4.00
537 545 2.742372 GCGACTGCGTTCATGGGT 60.742 61.111 0.00 0.00 40.36 4.51
538 546 3.027170 GCGACTGCGTTCATGGGTG 62.027 63.158 0.00 0.00 40.36 4.61
539 547 1.374125 CGACTGCGTTCATGGGTGA 60.374 57.895 0.00 0.00 0.00 4.02
542 550 0.603707 ACTGCGTTCATGGGTGAGTG 60.604 55.000 0.00 0.00 35.39 3.51
544 552 0.682292 TGCGTTCATGGGTGAGTGTA 59.318 50.000 0.00 0.00 35.39 2.90
545 553 1.277842 TGCGTTCATGGGTGAGTGTAT 59.722 47.619 0.00 0.00 35.39 2.29
547 555 1.665679 CGTTCATGGGTGAGTGTATGC 59.334 52.381 0.00 0.00 35.39 3.14
548 556 2.677902 CGTTCATGGGTGAGTGTATGCT 60.678 50.000 0.00 0.00 35.39 3.79
550 558 4.513442 GTTCATGGGTGAGTGTATGCTTA 58.487 43.478 0.00 0.00 35.39 3.09
555 609 5.018539 TGGGTGAGTGTATGCTTATGTAC 57.981 43.478 0.00 0.00 0.00 2.90
560 614 5.977725 GTGAGTGTATGCTTATGTACGTGAT 59.022 40.000 0.00 0.00 0.00 3.06
561 615 6.142480 GTGAGTGTATGCTTATGTACGTGATC 59.858 42.308 0.00 0.00 0.00 2.92
562 616 5.212934 AGTGTATGCTTATGTACGTGATCG 58.787 41.667 0.00 0.00 43.34 3.69
567 621 4.348656 TGCTTATGTACGTGATCGACTTC 58.651 43.478 0.00 0.00 40.62 3.01
601 683 4.105486 GTCAAAGAAGAAACACCACAAGC 58.895 43.478 0.00 0.00 0.00 4.01
655 737 7.125659 CCACCACCTATTAAATTTGAATTCCCT 59.874 37.037 2.27 0.00 0.00 4.20
789 871 3.120304 GCACCTTTTCGTAAGCTAGTTGG 60.120 47.826 0.00 0.00 37.18 3.77
875 957 6.182627 TGAGCAGAAAACTACCAATCATCAT 58.817 36.000 0.00 0.00 0.00 2.45
877 959 6.182627 AGCAGAAAACTACCAATCATCATCA 58.817 36.000 0.00 0.00 0.00 3.07
906 988 5.742063 TCTCTCGATCCGCCTATAAATAGA 58.258 41.667 0.00 0.00 32.05 1.98
949 1035 5.529791 CATCATATTCCCTTCGACGTACTT 58.470 41.667 0.00 0.00 0.00 2.24
963 1049 8.888332 TTCGACGTACTTAATTACATTACGAA 57.112 30.769 19.22 12.44 39.04 3.85
996 1083 1.674221 GGACTACTTGAGGTGCAGCAG 60.674 57.143 19.63 9.44 0.00 4.24
1008 1095 3.190849 CAGCAGGACATGGCGACG 61.191 66.667 0.00 0.00 34.54 5.12
1032 1119 0.238289 AAAGCAAATCGACAGCACCG 59.762 50.000 8.09 0.00 0.00 4.94
1099 1186 8.472413 CACATCAAATTCTCTACCCAAATGAAT 58.528 33.333 0.00 0.00 0.00 2.57
1137 1224 7.974675 AGCAATTTACATACTCATGTGTGTAC 58.025 34.615 10.62 0.00 45.77 2.90
1141 1228 8.624701 ATTTACATACTCATGTGTGTACGTAC 57.375 34.615 18.90 18.90 45.77 3.67
1151 1238 1.864082 TGTGTACGTACGTCGACTCAA 59.136 47.619 26.53 1.73 42.86 3.02
1160 1255 3.152261 ACGTCGACTCAATTCTCATCC 57.848 47.619 14.70 0.00 0.00 3.51
1184 1282 3.244353 TGTTTCAGAAGGAGGAGCAAGAG 60.244 47.826 0.00 0.00 0.00 2.85
1229 1327 1.446907 CGAGCAACATGGAGAAGCTT 58.553 50.000 0.00 0.00 35.36 3.74
1423 1521 2.892640 CGTGAAGGAGCGGATGGA 59.107 61.111 0.00 0.00 0.00 3.41
1679 1777 1.810030 GTTCCTGGCGGACGTGATC 60.810 63.158 0.00 0.00 39.60 2.92
2069 2170 2.409975 TCGGAACTTGGTCGTGAAATC 58.590 47.619 0.00 0.00 0.00 2.17
2125 2226 2.893215 TCGGTCTCTAGGGAACAAGA 57.107 50.000 8.74 0.00 0.00 3.02
2143 2251 7.362660 GGAACAAGACAATAAACATTACTCCCC 60.363 40.741 0.00 0.00 0.00 4.81
2171 2279 7.568861 CGGTCATTTTTACTCCGCATATAAGAC 60.569 40.741 0.00 0.00 35.01 3.01
2187 2295 8.171840 GCATATAAGACTTGTCTGAAGTCAAAC 58.828 37.037 15.11 0.00 46.78 2.93
2349 2458 6.273071 GTTGGTCAAACTTTATGAAGCTTGT 58.727 36.000 2.10 0.00 39.10 3.16
2477 2586 0.750546 GCCCCCGAGATACAAAACCC 60.751 60.000 0.00 0.00 0.00 4.11
2600 2737 3.644884 ATGCGAACCGTCTAAGATAGG 57.355 47.619 0.00 0.00 0.00 2.57
2684 2852 0.396811 GGCCCGCTAGTGATACCAAT 59.603 55.000 4.44 0.00 0.00 3.16
2685 2853 1.621814 GGCCCGCTAGTGATACCAATA 59.378 52.381 4.44 0.00 0.00 1.90
2698 2866 6.099701 AGTGATACCAATACACATCTTAGGCA 59.900 38.462 0.00 0.00 37.05 4.75
2701 2869 3.947834 ACCAATACACATCTTAGGCAAGC 59.052 43.478 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 4.899457 GGCCCTGGCTAATAATTTAGGTTT 59.101 41.667 8.29 0.00 41.60 3.27
74 76 4.593864 GACCTCGATGCCTCGGCC 62.594 72.222 11.57 0.00 45.10 6.13
120 122 0.250467 TTTGCCTCACCTCTGTCTGC 60.250 55.000 0.00 0.00 0.00 4.26
144 146 2.707849 GGCTTCGTCGACTAGCCCA 61.708 63.158 32.30 3.67 46.94 5.36
161 163 2.743928 GCACTTGTCGCCTCCAGG 60.744 66.667 0.00 0.00 38.53 4.45
162 164 3.114616 CGCACTTGTCGCCTCCAG 61.115 66.667 0.00 0.00 0.00 3.86
169 171 2.730672 GCACCTAGCGCACTTGTCG 61.731 63.158 11.47 0.00 0.00 4.35
170 172 3.169198 GCACCTAGCGCACTTGTC 58.831 61.111 11.47 0.00 0.00 3.18
179 181 2.434359 GTGACCGTGGCACCTAGC 60.434 66.667 12.86 0.00 44.65 3.42
193 195 1.345415 GTGACTTTTCCCCCTACGTGA 59.655 52.381 0.00 0.00 0.00 4.35
216 218 4.162651 AGAAGGATGCAAAGGGAAACATT 58.837 39.130 0.00 0.00 34.57 2.71
218 220 3.157087 GAGAAGGATGCAAAGGGAAACA 58.843 45.455 0.00 0.00 0.00 2.83
221 223 1.628340 TCGAGAAGGATGCAAAGGGAA 59.372 47.619 0.00 0.00 0.00 3.97
263 266 6.199908 GGCGTGAGATTGTGATATCATATAGC 59.800 42.308 9.02 5.64 36.05 2.97
273 276 4.142609 ACTTATGGCGTGAGATTGTGAT 57.857 40.909 5.40 0.00 0.00 3.06
274 277 3.610040 ACTTATGGCGTGAGATTGTGA 57.390 42.857 5.40 0.00 0.00 3.58
275 278 4.393062 AGAAACTTATGGCGTGAGATTGTG 59.607 41.667 5.40 0.00 0.00 3.33
276 279 4.579869 AGAAACTTATGGCGTGAGATTGT 58.420 39.130 5.40 0.00 0.00 2.71
277 280 4.872691 AGAGAAACTTATGGCGTGAGATTG 59.127 41.667 5.40 0.00 0.00 2.67
278 281 5.091261 AGAGAAACTTATGGCGTGAGATT 57.909 39.130 5.40 0.00 0.00 2.40
281 284 4.690748 TGAAAGAGAAACTTATGGCGTGAG 59.309 41.667 0.00 0.00 37.93 3.51
282 285 4.451096 GTGAAAGAGAAACTTATGGCGTGA 59.549 41.667 0.00 0.00 37.93 4.35
283 286 4.213270 TGTGAAAGAGAAACTTATGGCGTG 59.787 41.667 0.00 0.00 37.93 5.34
284 287 4.385825 TGTGAAAGAGAAACTTATGGCGT 58.614 39.130 0.00 0.00 37.93 5.68
285 288 5.356882 TTGTGAAAGAGAAACTTATGGCG 57.643 39.130 0.00 0.00 37.93 5.69
286 289 9.346725 CTTATTTGTGAAAGAGAAACTTATGGC 57.653 33.333 0.00 0.00 37.93 4.40
303 311 4.668576 ACAGTGCGTCATCTTATTTGTG 57.331 40.909 0.00 0.00 0.00 3.33
317 325 2.228822 AGGCCTTTTTCATAACAGTGCG 59.771 45.455 0.00 0.00 0.00 5.34
326 334 7.400052 ACCAATAAGATTGTAGGCCTTTTTCAT 59.600 33.333 12.58 0.00 0.00 2.57
379 387 3.706594 TGTTTTAACCATCCAGCCACAAA 59.293 39.130 0.00 0.00 0.00 2.83
380 388 3.300388 TGTTTTAACCATCCAGCCACAA 58.700 40.909 0.00 0.00 0.00 3.33
382 390 3.572255 TCTTGTTTTAACCATCCAGCCAC 59.428 43.478 0.00 0.00 0.00 5.01
385 393 4.321230 CCACTCTTGTTTTAACCATCCAGC 60.321 45.833 0.00 0.00 0.00 4.85
386 394 4.827284 ACCACTCTTGTTTTAACCATCCAG 59.173 41.667 0.00 0.00 0.00 3.86
388 396 6.884836 AGATACCACTCTTGTTTTAACCATCC 59.115 38.462 0.00 0.00 0.00 3.51
397 405 4.327680 GGCAGAAGATACCACTCTTGTTT 58.672 43.478 0.00 0.00 35.63 2.83
398 406 3.307762 GGGCAGAAGATACCACTCTTGTT 60.308 47.826 0.00 0.00 35.63 2.83
400 408 2.237143 TGGGCAGAAGATACCACTCTTG 59.763 50.000 0.00 0.00 35.63 3.02
401 409 2.551270 TGGGCAGAAGATACCACTCTT 58.449 47.619 0.00 0.00 38.18 2.85
412 420 2.205022 TGAATTCTGGTGGGCAGAAG 57.795 50.000 7.05 0.00 41.31 2.85
413 421 2.158475 ACTTGAATTCTGGTGGGCAGAA 60.158 45.455 7.05 0.00 42.08 3.02
417 425 1.541588 GTGACTTGAATTCTGGTGGGC 59.458 52.381 7.05 0.00 0.00 5.36
418 426 2.816087 CTGTGACTTGAATTCTGGTGGG 59.184 50.000 7.05 0.00 0.00 4.61
419 427 3.499918 GTCTGTGACTTGAATTCTGGTGG 59.500 47.826 7.05 0.00 0.00 4.61
436 444 3.504906 CCAAGCATCAATGTCAAGTCTGT 59.495 43.478 0.00 0.00 0.00 3.41
485 493 3.376859 CCTTCACTAAACGCATATTGCCA 59.623 43.478 0.00 0.00 41.12 4.92
489 497 5.116882 GTCTCCCTTCACTAAACGCATATT 58.883 41.667 0.00 0.00 0.00 1.28
494 502 1.336609 ACGTCTCCCTTCACTAAACGC 60.337 52.381 0.00 0.00 32.25 4.84
496 504 3.057734 CACACGTCTCCCTTCACTAAAC 58.942 50.000 0.00 0.00 0.00 2.01
497 505 2.696707 ACACACGTCTCCCTTCACTAAA 59.303 45.455 0.00 0.00 0.00 1.85
499 507 1.611977 CACACACGTCTCCCTTCACTA 59.388 52.381 0.00 0.00 0.00 2.74
504 512 2.426023 GCCACACACGTCTCCCTT 59.574 61.111 0.00 0.00 0.00 3.95
505 513 3.991051 CGCCACACACGTCTCCCT 61.991 66.667 0.00 0.00 0.00 4.20
506 514 3.986006 TCGCCACACACGTCTCCC 61.986 66.667 0.00 0.00 0.00 4.30
515 523 2.317609 ATGAACGCAGTCGCCACAC 61.318 57.895 0.00 0.00 45.00 3.82
517 525 2.476051 CATGAACGCAGTCGCCAC 59.524 61.111 0.00 0.00 45.00 5.01
518 526 2.741985 CCATGAACGCAGTCGCCA 60.742 61.111 0.00 0.00 45.00 5.69
519 527 3.499737 CCCATGAACGCAGTCGCC 61.500 66.667 0.00 0.00 45.00 5.54
520 528 2.742372 ACCCATGAACGCAGTCGC 60.742 61.111 0.00 0.00 45.00 5.19
522 530 0.320771 ACTCACCCATGAACGCAGTC 60.321 55.000 0.00 0.00 45.00 3.51
526 534 1.665679 CATACACTCACCCATGAACGC 59.334 52.381 0.00 0.00 33.30 4.84
527 535 1.665679 GCATACACTCACCCATGAACG 59.334 52.381 0.00 0.00 33.30 3.95
528 536 2.991250 AGCATACACTCACCCATGAAC 58.009 47.619 0.00 0.00 33.30 3.18
529 537 3.719268 AAGCATACACTCACCCATGAA 57.281 42.857 0.00 0.00 33.30 2.57
530 538 4.164030 ACATAAGCATACACTCACCCATGA 59.836 41.667 0.00 0.00 0.00 3.07
531 539 4.454678 ACATAAGCATACACTCACCCATG 58.545 43.478 0.00 0.00 0.00 3.66
532 540 4.778213 ACATAAGCATACACTCACCCAT 57.222 40.909 0.00 0.00 0.00 4.00
533 541 4.440940 CGTACATAAGCATACACTCACCCA 60.441 45.833 0.00 0.00 0.00 4.51
534 542 4.049186 CGTACATAAGCATACACTCACCC 58.951 47.826 0.00 0.00 0.00 4.61
536 544 5.337554 TCACGTACATAAGCATACACTCAC 58.662 41.667 0.00 0.00 0.00 3.51
537 545 5.570234 TCACGTACATAAGCATACACTCA 57.430 39.130 0.00 0.00 0.00 3.41
538 546 5.339875 CGATCACGTACATAAGCATACACTC 59.660 44.000 0.00 0.00 34.56 3.51
539 547 5.008316 TCGATCACGTACATAAGCATACACT 59.992 40.000 0.00 0.00 40.69 3.55
542 550 5.450171 AGTCGATCACGTACATAAGCATAC 58.550 41.667 0.00 0.00 40.69 2.39
544 552 4.569761 AGTCGATCACGTACATAAGCAT 57.430 40.909 0.00 0.00 40.69 3.79
545 553 4.348656 GAAGTCGATCACGTACATAAGCA 58.651 43.478 0.00 0.00 40.69 3.91
547 555 4.829808 TCGAAGTCGATCACGTACATAAG 58.170 43.478 0.00 0.00 44.22 1.73
548 556 4.863152 TCGAAGTCGATCACGTACATAA 57.137 40.909 0.00 0.00 44.22 1.90
561 615 9.447040 TTCTTTGACATAGTATAATCGAAGTCG 57.553 33.333 16.34 0.00 34.88 4.18
572 626 7.936847 TGTGGTGTTTCTTCTTTGACATAGTAT 59.063 33.333 0.00 0.00 0.00 2.12
576 630 6.459573 GCTTGTGGTGTTTCTTCTTTGACATA 60.460 38.462 0.00 0.00 0.00 2.29
581 635 4.107622 CAGCTTGTGGTGTTTCTTCTTTG 58.892 43.478 0.00 0.00 36.97 2.77
619 701 0.834687 TAGGTGGTGGCCTCGAACTT 60.835 55.000 12.83 5.99 39.94 2.66
668 750 8.910351 ATAGGAGGAGCTATGTTCAAATTAAC 57.090 34.615 0.00 0.00 0.00 2.01
789 871 3.850010 GCAACTTGAACCGCTTTTCTCTC 60.850 47.826 0.00 0.00 0.00 3.20
906 988 1.331756 GCCGCGTGATGATCAAATCTT 59.668 47.619 4.92 0.00 0.00 2.40
949 1035 6.101332 AGTTCTGCCGTTCGTAATGTAATTA 58.899 36.000 0.00 0.00 37.87 1.40
963 1049 0.320697 GTAGTCCCAAGTTCTGCCGT 59.679 55.000 0.00 0.00 0.00 5.68
996 1083 0.742990 TTTGGATCGTCGCCATGTCC 60.743 55.000 0.00 0.00 34.90 4.02
1008 1095 2.162208 TGCTGTCGATTTGCTTTGGATC 59.838 45.455 8.31 0.00 0.00 3.36
1032 1119 2.415090 CCTGCTTGCAGTAACAGATTGC 60.415 50.000 19.49 0.00 41.07 3.56
1117 1204 6.742264 CGTACGTACACACATGAGTATGTAAA 59.258 38.462 24.50 3.00 45.53 2.01
1119 1206 5.351189 ACGTACGTACACACATGAGTATGTA 59.649 40.000 21.41 14.01 45.53 2.29
1120 1207 8.771100 CGACGTACGTACACACATGAGTATGT 62.771 46.154 22.87 15.56 41.70 2.29
1121 1208 4.655027 ACGTACGTACACACATGAGTATG 58.345 43.478 21.41 7.46 40.24 2.39
1122 1209 4.493057 CGACGTACGTACACACATGAGTAT 60.493 45.833 22.87 0.00 37.22 2.12
1123 1210 3.181531 CGACGTACGTACACACATGAGTA 60.182 47.826 22.87 0.00 37.22 2.59
1124 1211 2.411935 CGACGTACGTACACACATGAGT 60.412 50.000 22.87 11.79 37.22 3.41
1125 1212 2.159801 TCGACGTACGTACACACATGAG 60.160 50.000 22.87 8.72 43.13 2.90
1126 1213 1.797635 TCGACGTACGTACACACATGA 59.202 47.619 22.87 10.46 43.13 3.07
1127 1214 1.900603 GTCGACGTACGTACACACATG 59.099 52.381 22.87 10.10 43.13 3.21
1128 1215 1.800586 AGTCGACGTACGTACACACAT 59.199 47.619 22.87 2.47 43.13 3.21
1129 1216 1.192312 GAGTCGACGTACGTACACACA 59.808 52.381 22.87 3.61 43.13 3.72
1134 1221 3.996032 AGAATTGAGTCGACGTACGTAC 58.004 45.455 22.87 16.93 43.13 3.67
1137 1224 3.113325 TGAGAATTGAGTCGACGTACG 57.887 47.619 15.01 15.01 44.09 3.67
1141 1228 2.112522 CGGATGAGAATTGAGTCGACG 58.887 52.381 10.46 0.00 0.00 5.12
1151 1238 4.020218 TCCTTCTGAAACACGGATGAGAAT 60.020 41.667 0.00 0.00 33.54 2.40
1160 1255 1.270305 TGCTCCTCCTTCTGAAACACG 60.270 52.381 0.00 0.00 0.00 4.49
1229 1327 3.037833 CTGCTGCTTGCGACGACA 61.038 61.111 0.00 0.00 46.63 4.35
1278 1376 2.258591 CTCCACCTCCGACACGTG 59.741 66.667 15.48 15.48 0.00 4.49
1283 1381 2.675772 ACCGTCTCCACCTCCGAC 60.676 66.667 0.00 0.00 0.00 4.79
1772 1870 7.070074 ACGATACTCCTAGATGGATGTCTTTTT 59.930 37.037 0.00 0.00 45.16 1.94
1867 1967 1.202463 ACATCGATGCCACAGAGTAGC 60.202 52.381 25.11 0.00 0.00 3.58
1972 2073 1.135315 CCCACGTGCATCAAAGGAATG 60.135 52.381 10.91 0.00 0.00 2.67
2040 2141 3.495377 CGACCAAGTTCCGAAACATGTTA 59.505 43.478 12.39 0.00 37.88 2.41
2051 2152 4.766404 AATGATTTCACGACCAAGTTCC 57.234 40.909 0.00 0.00 0.00 3.62
2109 2210 7.159372 TGTTTATTGTCTTGTTCCCTAGAGAC 58.841 38.462 0.00 0.00 39.11 3.36
2143 2251 0.730840 GCGGAGTAAAAATGACCGGG 59.269 55.000 6.32 0.00 43.15 5.73
2150 2258 8.732746 ACAAGTCTTATATGCGGAGTAAAAAT 57.267 30.769 0.00 0.00 0.00 1.82
2254 2362 9.906660 TTAGTTGCGTCATGAATTTAATTTTCT 57.093 25.926 0.00 0.00 0.00 2.52
2370 2479 3.461831 TCCCTTCTCTCCTTTTTGTTCCA 59.538 43.478 0.00 0.00 0.00 3.53
2371 2480 4.075682 CTCCCTTCTCTCCTTTTTGTTCC 58.924 47.826 0.00 0.00 0.00 3.62
2375 2484 9.771534 CTATAATACTCCCTTCTCTCCTTTTTG 57.228 37.037 0.00 0.00 0.00 2.44
2451 2560 2.037144 TGTATCTCGGGGGCTCTTTAC 58.963 52.381 0.00 0.00 0.00 2.01
2570 2707 4.062991 AGACGGTTCGCATAAAAAGTCTT 58.937 39.130 0.00 0.00 34.50 3.01
2583 2720 5.526846 AGAGTTACCTATCTTAGACGGTTCG 59.473 44.000 9.77 0.00 0.00 3.95
2600 2737 2.082354 GCTTGCCGCTGAGAGTTAC 58.918 57.895 0.00 0.00 35.14 2.50
2684 2852 4.826274 AAGAGCTTGCCTAAGATGTGTA 57.174 40.909 0.00 0.00 35.92 2.90
2685 2853 3.710209 AAGAGCTTGCCTAAGATGTGT 57.290 42.857 0.00 0.00 35.92 3.72


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

AutoCloner maintained by Alex Coulton.