Multiple sequence alignment - TraesCS5D01G055900

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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 TraesCS5D01G055900 chr5D 100.000 4053 0 0 1 4053 52274511 52278563 0.000000e+00 7485
1 TraesCS5D01G055900 chr5B 95.267 2303 97 7 164 2459 55363570 55365867 0.000000e+00 3639
2 TraesCS5D01G055900 chr5B 95.442 1448 52 9 2473 3912 55366172 55367613 0.000000e+00 2296
3 TraesCS5D01G055900 chr5B 93.333 165 10 1 3 166 55363369 55363533 4.050000e-60 243
4 TraesCS5D01G055900 chr5B 91.129 124 8 2 3900 4023 55368470 55368590 9.010000e-37 165
5 TraesCS5D01G055900 chrUn 77.439 1476 253 49 977 2402 28321326 28322771 0.000000e+00 808
6 TraesCS5D01G055900 chrUn 83.748 523 73 10 3499 4013 83219662 83219144 6.090000e-133 484
7 TraesCS5D01G055900 chr7D 88.316 582 55 11 3479 4051 592567828 592567251 0.000000e+00 686
8 TraesCS5D01G055900 chr5A 77.517 1192 214 39 1235 2402 659360880 659362041 0.000000e+00 667
9 TraesCS5D01G055900 chr5A 89.655 377 25 6 2749 3112 41419244 41419619 6.130000e-128 468
10 TraesCS5D01G055900 chr5A 88.022 359 30 8 2407 2754 41413060 41413416 2.920000e-111 412
11 TraesCS5D01G055900 chr5A 87.535 353 17 9 3118 3459 41419661 41419997 2.290000e-102 383
12 TraesCS5D01G055900 chr5A 91.787 207 17 0 2199 2405 41412798 41413004 5.130000e-74 289
13 TraesCS5D01G055900 chr1A 85.813 578 76 6 3479 4053 305605030 305605604 3.460000e-170 608
14 TraesCS5D01G055900 chr1D 85.345 580 75 10 3479 4053 240984813 240985387 3.490000e-165 592
15 TraesCS5D01G055900 chr3B 88.036 443 41 10 3480 3919 482988657 482988224 7.770000e-142 514
16 TraesCS5D01G055900 chr7B 82.906 585 83 13 3478 4051 453015946 453016524 1.000000e-140 510
17 TraesCS5D01G055900 chr4D 81.625 566 77 23 3499 4049 501043567 501043014 1.030000e-120 444
18 TraesCS5D01G055900 chr7A 80.858 606 79 30 3473 4052 65118318 65117724 3.720000e-120 442


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 TraesCS5D01G055900 chr5D 52274511 52278563 4052 False 7485.00 7485 100.00000 1 4053 1 chr5D.!!$F1 4052
1 TraesCS5D01G055900 chr5B 55363369 55368590 5221 False 1585.75 3639 93.79275 3 4023 4 chr5B.!!$F1 4020
2 TraesCS5D01G055900 chrUn 28321326 28322771 1445 False 808.00 808 77.43900 977 2402 1 chrUn.!!$F1 1425
3 TraesCS5D01G055900 chrUn 83219144 83219662 518 True 484.00 484 83.74800 3499 4013 1 chrUn.!!$R1 514
4 TraesCS5D01G055900 chr7D 592567251 592567828 577 True 686.00 686 88.31600 3479 4051 1 chr7D.!!$R1 572
5 TraesCS5D01G055900 chr5A 659360880 659362041 1161 False 667.00 667 77.51700 1235 2402 1 chr5A.!!$F1 1167
6 TraesCS5D01G055900 chr5A 41419244 41419997 753 False 425.50 468 88.59500 2749 3459 2 chr5A.!!$F3 710
7 TraesCS5D01G055900 chr5A 41412798 41413416 618 False 350.50 412 89.90450 2199 2754 2 chr5A.!!$F2 555
8 TraesCS5D01G055900 chr1A 305605030 305605604 574 False 608.00 608 85.81300 3479 4053 1 chr1A.!!$F1 574
9 TraesCS5D01G055900 chr1D 240984813 240985387 574 False 592.00 592 85.34500 3479 4053 1 chr1D.!!$F1 574
10 TraesCS5D01G055900 chr7B 453015946 453016524 578 False 510.00 510 82.90600 3478 4051 1 chr7B.!!$F1 573
11 TraesCS5D01G055900 chr4D 501043014 501043567 553 True 444.00 444 81.62500 3499 4049 1 chr4D.!!$R1 550
12 TraesCS5D01G055900 chr7A 65117724 65118318 594 True 442.00 442 80.85800 3473 4052 1 chr7A.!!$R1 579

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
304 347 0.032130 TGCAGAGAGGTGAACGTGTC 59.968 55.0 0.00 0.0 0.0 3.67 F
384 427 0.108945 CTCGAAACTACCGGACCACC 60.109 60.0 9.46 0.0 0.0 4.61 F
517 562 0.532196 CTAGGTTCGGGGGATTTCGC 60.532 60.0 0.00 0.0 0.0 4.70 F
2339 2445 1.026718 CCTCGATTTCGCCTGCCTTT 61.027 55.0 0.00 0.0 39.6 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1503 1.065401 GGACTGCATCGACTCTCTGAG 59.935 57.143 0.00 0.0 35.52 3.35 R
2340 2446 1.897802 CCAGGAAAGGAGCAGCAATTT 59.102 47.619 0.00 0.0 0.00 1.82 R
2463 2624 9.896645 AGTTCATGACTTCATCTACAAATGTAT 57.103 29.630 0.00 0.0 33.92 2.29 R
3496 4019 1.103803 TACCAACGGTGCAGCAAAAA 58.896 45.000 17.33 0.0 36.19 1.94 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
23 24 4.672409 GGGTGTTTCAGAAAAGTGTCTTG 58.328 43.478 0.00 0.00 0.00 3.02
32 33 2.755952 AAAGTGTCTTGGAAGGCCTT 57.244 45.000 20.65 20.65 34.31 4.35
56 57 2.619177 GCCTTCGTGAGTATCTCTAGCA 59.381 50.000 0.00 0.00 34.92 3.49
75 76 4.240096 AGCAGAATTTGAAAATGCCTTCG 58.760 39.130 8.79 0.00 0.00 3.79
109 110 5.388654 CCATCATTTTATAGGCCTTGAGGT 58.611 41.667 12.58 0.00 37.57 3.85
110 111 5.242393 CCATCATTTTATAGGCCTTGAGGTG 59.758 44.000 12.58 3.46 37.57 4.00
156 158 5.108254 CGTACGTGTTTTAGTGGTACTTCAC 60.108 44.000 7.22 0.00 37.89 3.18
187 228 8.816894 AGTGGAATTGTGTTTAGAGAGATTAGA 58.183 33.333 0.00 0.00 0.00 2.10
202 243 9.152327 AGAGAGATTAGATTGGTGATTATGTCA 57.848 33.333 0.00 0.00 0.00 3.58
211 252 7.667219 AGATTGGTGATTATGTCAAACTTCTGT 59.333 33.333 0.00 0.00 38.90 3.41
213 254 6.295249 TGGTGATTATGTCAAACTTCTGTCA 58.705 36.000 0.00 0.00 38.90 3.58
239 280 4.734398 TCTTTTGTGTTTTGCCAGTGAT 57.266 36.364 0.00 0.00 0.00 3.06
240 281 4.681744 TCTTTTGTGTTTTGCCAGTGATC 58.318 39.130 0.00 0.00 0.00 2.92
241 282 2.772568 TTGTGTTTTGCCAGTGATCG 57.227 45.000 0.00 0.00 0.00 3.69
242 283 0.310543 TGTGTTTTGCCAGTGATCGC 59.689 50.000 0.00 0.00 0.00 4.58
243 284 0.593128 GTGTTTTGCCAGTGATCGCT 59.407 50.000 2.02 2.02 0.00 4.93
244 285 0.592637 TGTTTTGCCAGTGATCGCTG 59.407 50.000 26.21 26.21 36.31 5.18
247 288 1.855213 TTTGCCAGTGATCGCTGTGC 61.855 55.000 29.40 28.81 34.84 4.57
248 289 2.435586 GCCAGTGATCGCTGTGCT 60.436 61.111 29.40 0.00 34.84 4.40
249 290 1.153568 GCCAGTGATCGCTGTGCTA 60.154 57.895 29.40 0.00 34.84 3.49
250 291 1.424493 GCCAGTGATCGCTGTGCTAC 61.424 60.000 29.40 13.15 34.84 3.58
251 292 0.807667 CCAGTGATCGCTGTGCTACC 60.808 60.000 29.40 0.00 34.84 3.18
252 293 0.807667 CAGTGATCGCTGTGCTACCC 60.808 60.000 25.11 0.00 0.00 3.69
253 294 1.218047 GTGATCGCTGTGCTACCCA 59.782 57.895 0.00 0.00 0.00 4.51
254 295 0.807667 GTGATCGCTGTGCTACCCAG 60.808 60.000 0.00 0.00 0.00 4.45
301 344 0.032678 CTGTGCAGAGAGGTGAACGT 59.967 55.000 4.50 0.00 0.00 3.99
302 345 0.249447 TGTGCAGAGAGGTGAACGTG 60.249 55.000 0.00 0.00 0.00 4.49
304 347 0.032130 TGCAGAGAGGTGAACGTGTC 59.968 55.000 0.00 0.00 0.00 3.67
333 376 1.618837 ACGTCTCAATGCACTACAGGT 59.381 47.619 0.00 0.00 0.00 4.00
375 418 2.884207 CCGGCGGCTCGAAACTAC 60.884 66.667 15.42 0.00 0.00 2.73
384 427 0.108945 CTCGAAACTACCGGACCACC 60.109 60.000 9.46 0.00 0.00 4.61
392 435 4.400251 CCGGACCACCCTCCTCCT 62.400 72.222 0.00 0.00 0.00 3.69
393 436 3.077556 CGGACCACCCTCCTCCTG 61.078 72.222 0.00 0.00 0.00 3.86
404 447 1.908340 CTCCTCCTGTGGCTCCTTGG 61.908 65.000 0.00 0.00 0.00 3.61
419 462 0.535797 CTTGGTACGGGACTCCTTCC 59.464 60.000 0.00 0.00 45.00 3.46
431 476 3.154473 CCTTCCCGGGCGATCAGA 61.154 66.667 18.49 0.00 0.00 3.27
440 485 2.279120 GCGATCAGACTCGGCTGG 60.279 66.667 0.00 0.00 39.05 4.85
441 486 3.069980 GCGATCAGACTCGGCTGGT 62.070 63.158 0.00 0.00 39.05 4.00
454 499 4.351938 CTGGTCCGTCCGCGTTCA 62.352 66.667 4.92 0.00 39.52 3.18
456 501 2.433664 GGTCCGTCCGCGTTCATT 60.434 61.111 4.92 0.00 36.15 2.57
467 512 2.574212 GTTCATTTCAGCGGCGCG 60.574 61.111 27.59 20.84 0.00 6.86
508 553 4.570663 CTCGCCGCTAGGTTCGGG 62.571 72.222 9.01 0.85 46.51 5.14
517 562 0.532196 CTAGGTTCGGGGGATTTCGC 60.532 60.000 0.00 0.00 0.00 4.70
553 598 2.029964 GGAACAACCAGACGGCGA 59.970 61.111 16.62 0.00 38.79 5.54
554 599 2.315386 GGAACAACCAGACGGCGAC 61.315 63.158 16.62 7.87 38.79 5.19
567 612 1.451387 GGCGACGGTGGATTGGATT 60.451 57.895 0.00 0.00 0.00 3.01
594 639 2.897969 CGGTCCTTATACATAGCCTGGT 59.102 50.000 0.00 0.00 0.00 4.00
595 640 3.306088 CGGTCCTTATACATAGCCTGGTG 60.306 52.174 0.00 0.00 0.00 4.17
599 644 3.307059 CCTTATACATAGCCTGGTGGAGC 60.307 52.174 0.00 0.00 34.57 4.70
627 672 4.946157 TGCTTTCCTCATGATTCCTTTCTC 59.054 41.667 0.00 0.00 0.00 2.87
647 692 1.355916 CGAGTCCGATCCGAGTTCC 59.644 63.158 0.00 0.00 38.22 3.62
656 701 1.272554 ATCCGAGTTCCTTCCCACCC 61.273 60.000 0.00 0.00 0.00 4.61
674 719 2.098770 ACCCGTCTAGTTTATCGTCAGC 59.901 50.000 0.00 0.00 0.00 4.26
677 722 3.548415 CCGTCTAGTTTATCGTCAGCTCC 60.548 52.174 0.00 0.00 0.00 4.70
735 780 2.158579 ACCTCTCTTCCTCCGTATCTCC 60.159 54.545 0.00 0.00 0.00 3.71
745 790 3.861689 CCTCCGTATCTCCAACGTTTTAC 59.138 47.826 0.00 0.00 38.67 2.01
763 808 6.747280 CGTTTTACAGGTTTCATTCATCATCC 59.253 38.462 0.00 0.00 0.00 3.51
1138 1192 6.252599 TGGACTCATGCCAAGTTATAATCT 57.747 37.500 0.00 0.00 31.13 2.40
1139 1193 7.373617 TGGACTCATGCCAAGTTATAATCTA 57.626 36.000 0.00 0.00 31.13 1.98
1140 1194 7.445121 TGGACTCATGCCAAGTTATAATCTAG 58.555 38.462 0.00 0.00 31.13 2.43
2119 2203 1.308998 CACCGAGTCAAAGGTTTGCT 58.691 50.000 0.00 0.00 39.00 3.91
2339 2445 1.026718 CCTCGATTTCGCCTGCCTTT 61.027 55.000 0.00 0.00 39.60 3.11
2340 2446 1.651987 CTCGATTTCGCCTGCCTTTA 58.348 50.000 0.00 0.00 39.60 1.85
2463 2624 8.950007 AATAAAGGGGAAACAGTCTTCAAATA 57.050 30.769 0.00 0.00 0.00 1.40
2566 3017 4.760204 GTGGAATAAACAGGGCGCTATTAT 59.240 41.667 7.64 8.87 0.00 1.28
2567 3018 5.935789 GTGGAATAAACAGGGCGCTATTATA 59.064 40.000 7.64 4.56 0.00 0.98
2706 3167 6.073440 TGCGTAAAAAGTAGTCACATTCTTCC 60.073 38.462 0.00 0.00 0.00 3.46
2755 3216 1.279271 GAGCATCCAAGGTACACCACT 59.721 52.381 0.38 0.00 38.89 4.00
2821 3282 0.389817 TCAGGCTGGTCGAAATCACG 60.390 55.000 15.73 0.00 0.00 4.35
2824 3285 1.079405 GCTGGTCGAAATCACGGGA 60.079 57.895 0.00 0.00 0.00 5.14
2935 3399 0.693049 CCCCTGCAGTAGTTGGTTCT 59.307 55.000 13.81 0.00 0.00 3.01
2965 3429 1.301954 GCTGGGATGTACGGGGTTT 59.698 57.895 0.00 0.00 0.00 3.27
2966 3430 1.029947 GCTGGGATGTACGGGGTTTG 61.030 60.000 0.00 0.00 0.00 2.93
3058 3526 2.828520 TGTCCTAGAACCTTGAGCTCAG 59.171 50.000 17.43 9.03 0.00 3.35
3102 3576 2.027605 CTCTCACACACACGCCGT 59.972 61.111 0.00 0.00 0.00 5.68
3495 4018 2.880443 TGTACTAGAAGGGTTGGACGT 58.120 47.619 0.00 0.00 0.00 4.34
3496 4019 3.233507 TGTACTAGAAGGGTTGGACGTT 58.766 45.455 0.00 0.00 0.00 3.99
3497 4020 3.642848 TGTACTAGAAGGGTTGGACGTTT 59.357 43.478 0.00 0.00 0.00 3.60
3515 4038 1.103803 TTTTTGCTGCACCGTTGGTA 58.896 45.000 0.00 0.00 32.11 3.25
3942 5360 2.102070 TCCGTCGTGGTTGCATTTAT 57.898 45.000 0.00 0.00 39.52 1.40
4025 5455 4.696455 CAGGATTGATGTTTTAATGGCCC 58.304 43.478 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.943033 AGACACTTTTCTGAAACACCCG 59.057 45.455 1.58 0.00 0.00 5.28
1 2 4.440112 CCAAGACACTTTTCTGAAACACCC 60.440 45.833 1.58 0.00 0.00 4.61
32 33 4.440250 GCTAGAGATACTCACGAAGGCAAA 60.440 45.833 0.00 0.00 32.06 3.68
41 42 8.709386 TTTCAAATTCTGCTAGAGATACTCAC 57.291 34.615 0.00 0.00 32.06 3.51
45 46 7.859875 GGCATTTTCAAATTCTGCTAGAGATAC 59.140 37.037 0.00 0.00 0.00 2.24
56 57 6.458210 ACATTCGAAGGCATTTTCAAATTCT 58.542 32.000 10.18 0.00 0.00 2.40
75 76 7.148171 GCCTATAAAATGATGGCCTAGACATTC 60.148 40.741 3.32 0.00 37.81 2.67
109 110 3.485394 TGTTAGCAGGCATTCTCAAACA 58.515 40.909 0.00 0.00 0.00 2.83
110 111 3.671702 GCTGTTAGCAGGCATTCTCAAAC 60.672 47.826 8.78 0.00 41.89 2.93
156 158 7.819415 TCTCTCTAAACACAATTCCACTACATG 59.181 37.037 0.00 0.00 0.00 3.21
187 228 7.448161 TGACAGAAGTTTGACATAATCACCAAT 59.552 33.333 0.00 0.00 36.92 3.16
189 230 6.295249 TGACAGAAGTTTGACATAATCACCA 58.705 36.000 0.00 0.00 36.92 4.17
191 232 7.810658 ACATGACAGAAGTTTGACATAATCAC 58.189 34.615 0.00 0.00 36.92 3.06
201 242 7.329226 ACACAAAAGAAACATGACAGAAGTTTG 59.671 33.333 0.00 3.91 35.77 2.93
202 243 7.378181 ACACAAAAGAAACATGACAGAAGTTT 58.622 30.769 0.00 3.87 38.10 2.66
208 249 6.242829 GCAAAACACAAAAGAAACATGACAG 58.757 36.000 0.00 0.00 0.00 3.51
211 252 5.240891 TGGCAAAACACAAAAGAAACATGA 58.759 33.333 0.00 0.00 0.00 3.07
213 254 5.122082 CACTGGCAAAACACAAAAGAAACAT 59.878 36.000 0.00 0.00 0.00 2.71
239 280 0.970640 TTAACTGGGTAGCACAGCGA 59.029 50.000 9.46 0.00 39.55 4.93
240 281 1.665679 CATTAACTGGGTAGCACAGCG 59.334 52.381 9.46 0.00 39.55 5.18
241 282 2.017049 CCATTAACTGGGTAGCACAGC 58.983 52.381 9.46 0.00 41.82 4.40
242 283 3.627395 TCCATTAACTGGGTAGCACAG 57.373 47.619 8.34 8.34 45.98 3.66
243 284 3.073209 TGTTCCATTAACTGGGTAGCACA 59.927 43.478 0.00 0.00 45.98 4.57
244 285 3.681593 TGTTCCATTAACTGGGTAGCAC 58.318 45.455 0.00 0.00 45.98 4.40
247 288 7.012421 GCTTAATCTGTTCCATTAACTGGGTAG 59.988 40.741 4.69 0.00 45.98 3.18
248 289 6.826741 GCTTAATCTGTTCCATTAACTGGGTA 59.173 38.462 4.69 0.00 45.98 3.69
249 290 5.652452 GCTTAATCTGTTCCATTAACTGGGT 59.348 40.000 4.69 0.00 45.98 4.51
250 291 5.888161 AGCTTAATCTGTTCCATTAACTGGG 59.112 40.000 4.69 0.00 45.98 4.45
251 292 6.183360 CCAGCTTAATCTGTTCCATTAACTGG 60.183 42.308 5.64 13.42 37.87 4.00
252 293 6.375455 ACCAGCTTAATCTGTTCCATTAACTG 59.625 38.462 5.64 0.00 38.99 3.16
253 294 6.485171 ACCAGCTTAATCTGTTCCATTAACT 58.515 36.000 5.64 0.00 38.99 2.24
254 295 6.759497 ACCAGCTTAATCTGTTCCATTAAC 57.241 37.500 5.64 0.00 38.67 2.01
301 344 2.785713 TGAGACGTTTCACATCGACA 57.214 45.000 4.39 0.00 0.00 4.35
302 345 3.722082 GCATTGAGACGTTTCACATCGAC 60.722 47.826 8.51 0.00 0.00 4.20
304 347 2.157474 TGCATTGAGACGTTTCACATCG 59.843 45.455 8.51 0.00 0.00 3.84
333 376 0.685131 TCCGCGGGATTCTCCTAACA 60.685 55.000 27.83 0.00 36.57 2.41
361 404 2.884207 CCGGTAGTTTCGAGCCGC 60.884 66.667 0.00 0.00 42.54 6.53
362 405 1.515736 GTCCGGTAGTTTCGAGCCG 60.516 63.158 0.00 0.00 43.40 5.52
368 411 0.248565 GAGGGTGGTCCGGTAGTTTC 59.751 60.000 0.00 0.00 41.52 2.78
369 412 1.196766 GGAGGGTGGTCCGGTAGTTT 61.197 60.000 0.00 0.00 41.52 2.66
375 418 4.400251 AGGAGGAGGGTGGTCCGG 62.400 72.222 0.00 0.00 42.05 5.14
384 427 1.614824 AAGGAGCCACAGGAGGAGG 60.615 63.158 0.00 0.00 0.00 4.30
392 435 2.589157 CCCGTACCAAGGAGCCACA 61.589 63.158 0.00 0.00 0.00 4.17
393 436 2.267961 CCCGTACCAAGGAGCCAC 59.732 66.667 0.00 0.00 0.00 5.01
419 462 4.271816 CCGAGTCTGATCGCCCGG 62.272 72.222 0.00 0.00 41.37 5.73
420 463 4.933064 GCCGAGTCTGATCGCCCG 62.933 72.222 0.00 0.00 41.37 6.13
422 465 2.279120 CAGCCGAGTCTGATCGCC 60.279 66.667 0.00 0.00 41.37 5.54
424 467 1.064946 GACCAGCCGAGTCTGATCG 59.935 63.158 0.00 3.54 42.36 3.69
438 483 2.718747 AAATGAACGCGGACGGACCA 62.719 55.000 12.47 0.00 46.04 4.02
440 485 1.286354 TGAAATGAACGCGGACGGAC 61.286 55.000 12.47 0.00 46.04 4.79
441 486 1.005984 TGAAATGAACGCGGACGGA 60.006 52.632 12.47 0.00 46.04 4.69
447 492 2.574212 GCCGCTGAAATGAACGCG 60.574 61.111 3.53 3.53 44.69 6.01
450 495 2.574212 CGCGCCGCTGAAATGAAC 60.574 61.111 7.78 0.00 0.00 3.18
497 542 0.532196 CGAAATCCCCCGAACCTAGC 60.532 60.000 0.00 0.00 0.00 3.42
505 550 2.361865 TTTGGGCGAAATCCCCCG 60.362 61.111 0.00 0.00 45.97 5.73
507 552 2.058001 CCCTTTGGGCGAAATCCCC 61.058 63.158 0.00 0.00 45.97 4.81
508 553 3.616086 CCCTTTGGGCGAAATCCC 58.384 61.111 0.00 0.00 46.73 3.85
520 565 3.970842 TGTTCCAACAAGTGTACCCTTT 58.029 40.909 0.00 0.00 35.67 3.11
547 592 4.752879 CCAATCCACCGTCGCCGT 62.753 66.667 0.00 0.00 0.00 5.68
549 594 1.029947 AAATCCAATCCACCGTCGCC 61.030 55.000 0.00 0.00 0.00 5.54
553 598 2.711542 GAGACAAATCCAATCCACCGT 58.288 47.619 0.00 0.00 0.00 4.83
554 599 1.665679 CGAGACAAATCCAATCCACCG 59.334 52.381 0.00 0.00 0.00 4.94
567 612 4.280174 GGCTATGTATAAGGACCGAGACAA 59.720 45.833 1.67 0.00 0.00 3.18
599 644 1.386533 ATCATGAGGAAAGCAAGGCG 58.613 50.000 0.09 0.00 0.00 5.52
606 651 4.034975 GCGAGAAAGGAATCATGAGGAAAG 59.965 45.833 0.09 0.00 0.00 2.62
614 659 2.482142 GGACTCGCGAGAAAGGAATCAT 60.482 50.000 40.58 15.73 41.32 2.45
627 672 2.968330 GAACTCGGATCGGACTCGCG 62.968 65.000 0.00 0.00 36.13 5.87
647 692 3.490419 CGATAAACTAGACGGGTGGGAAG 60.490 52.174 0.00 0.00 0.00 3.46
656 701 3.619729 GGAGCTGACGATAAACTAGACG 58.380 50.000 0.00 0.00 0.00 4.18
706 751 1.826096 GAGGAAGAGAGGTGTGGGTAC 59.174 57.143 0.00 0.00 0.00 3.34
707 752 1.273098 GGAGGAAGAGAGGTGTGGGTA 60.273 57.143 0.00 0.00 0.00 3.69
711 756 1.835494 TACGGAGGAAGAGAGGTGTG 58.165 55.000 0.00 0.00 0.00 3.82
735 780 6.915300 TGATGAATGAAACCTGTAAAACGTTG 59.085 34.615 0.00 0.00 0.00 4.10
745 790 4.201950 GGAACGGATGATGAATGAAACCTG 60.202 45.833 0.00 0.00 0.00 4.00
763 808 3.801698 AGGACATGATGAATCTGGAACG 58.198 45.455 0.00 0.00 0.00 3.95
895 940 6.989169 GCTCAACATCTCACCTGATATTACTT 59.011 38.462 0.00 0.00 0.00 2.24
1138 1192 8.534954 AGGAAAGCACACTGATATAGTTACTA 57.465 34.615 0.00 0.00 37.60 1.82
1139 1193 7.425224 AGGAAAGCACACTGATATAGTTACT 57.575 36.000 0.00 0.00 37.60 2.24
1140 1194 8.494016 AAAGGAAAGCACACTGATATAGTTAC 57.506 34.615 0.00 0.00 37.60 2.50
1438 1503 1.065401 GGACTGCATCGACTCTCTGAG 59.935 57.143 0.00 0.00 35.52 3.35
1568 1633 7.989826 AGAAATCAAATATAAGCTGTTTCGCT 58.010 30.769 0.00 0.00 43.31 4.93
2119 2203 5.687166 ACTGGAAATAGGAACGGTGAATA 57.313 39.130 0.00 0.00 0.00 1.75
2339 2445 3.091545 CCAGGAAAGGAGCAGCAATTTA 58.908 45.455 0.00 0.00 0.00 1.40
2340 2446 1.897802 CCAGGAAAGGAGCAGCAATTT 59.102 47.619 0.00 0.00 0.00 1.82
2463 2624 9.896645 AGTTCATGACTTCATCTACAAATGTAT 57.103 29.630 0.00 0.00 33.92 2.29
2566 3017 5.921962 AGACATCGGATTGCTGCTATATA 57.078 39.130 0.00 0.00 0.00 0.86
2567 3018 4.815533 AGACATCGGATTGCTGCTATAT 57.184 40.909 0.00 0.00 0.00 0.86
2706 3167 5.512788 CGCAGCACCATCTGTAAATAAAAAG 59.487 40.000 0.00 0.00 36.49 2.27
2755 3216 4.757773 CGTAGGTCTCCCTGGTCA 57.242 61.111 0.00 0.00 42.67 4.02
2821 3282 1.749063 CCTTTCCAGCCGTAAAATCCC 59.251 52.381 0.00 0.00 0.00 3.85
2824 3285 3.081804 CTGACCTTTCCAGCCGTAAAAT 58.918 45.455 0.00 0.00 0.00 1.82
2935 3399 2.025037 ACATCCCAGCAGCCTAAAATCA 60.025 45.455 0.00 0.00 0.00 2.57
3102 3576 0.895530 CGCTGGTCTGGAGGAAGTTA 59.104 55.000 0.00 0.00 0.00 2.24
3286 3805 7.630242 TGAACAGATAAGGGAAAATCATCAC 57.370 36.000 0.00 0.00 0.00 3.06
3496 4019 1.103803 TACCAACGGTGCAGCAAAAA 58.896 45.000 17.33 0.00 36.19 1.94
3497 4020 1.323412 ATACCAACGGTGCAGCAAAA 58.677 45.000 17.33 0.00 36.19 2.44
4025 5455 1.394572 TCGAATCAATCAGCAGCAACG 59.605 47.619 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.