Multiple sequence alignment - TraesCS6D01G250200

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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 TraesCS6D01G250200 chr6D 100.000 3865 0 0 1 3865 353633140 353637004 0.000000e+00 7138.0
1 TraesCS6D01G250200 chr6D 82.203 472 72 9 140 605 157997071 157997536 2.800000e-106 396.0
2 TraesCS6D01G250200 chr6D 94.444 36 1 1 3607 3641 201381973 201382008 2.000000e-03 54.7
3 TraesCS6D01G250200 chr6B 94.897 1450 55 11 1786 3221 524971070 524969626 0.000000e+00 2250.0
4 TraesCS6D01G250200 chr6B 95.765 614 20 4 728 1339 524972300 524971691 0.000000e+00 985.0
5 TraesCS6D01G250200 chr6B 88.376 628 28 18 3253 3865 524969290 524968693 0.000000e+00 713.0
6 TraesCS6D01G250200 chr6B 94.226 381 14 4 1415 1791 524971678 524971302 3.350000e-160 575.0
7 TraesCS6D01G250200 chr6B 81.800 500 75 14 2 491 43290092 43289599 4.650000e-109 405.0
8 TraesCS6D01G250200 chr6B 80.952 462 75 9 158 611 285243206 285242750 1.710000e-93 353.0
9 TraesCS6D01G250200 chr6B 87.919 149 15 2 583 731 524992064 524991919 5.130000e-39 172.0
10 TraesCS6D01G250200 chr6B 95.556 90 4 0 439 528 525060652 525060563 1.120000e-30 145.0
11 TraesCS6D01G250200 chr6A 89.096 1394 70 45 2472 3849 488612113 488610786 0.000000e+00 1657.0
12 TraesCS6D01G250200 chr6A 93.088 868 47 7 733 1597 488614802 488613945 0.000000e+00 1258.0
13 TraesCS6D01G250200 chr6A 93.721 430 21 2 2049 2473 488612703 488612275 1.170000e-179 640.0
14 TraesCS6D01G250200 chr6A 94.048 336 19 1 1786 2120 488613038 488612703 3.450000e-140 508.0
15 TraesCS6D01G250200 chr6A 93.289 149 6 2 1647 1791 488613414 488613266 2.340000e-52 217.0
16 TraesCS6D01G250200 chr6A 92.453 53 3 1 691 742 488615319 488615267 1.490000e-09 75.0
17 TraesCS6D01G250200 chr4A 86.408 515 60 8 5 514 585615384 585614875 4.360000e-154 555.0
18 TraesCS6D01G250200 chr7A 79.412 612 111 12 2 605 270647551 270648155 5.970000e-113 418.0
19 TraesCS6D01G250200 chr3D 79.134 647 96 23 2 632 508334313 508333690 9.990000e-111 411.0
20 TraesCS6D01G250200 chr3D 79.387 587 97 15 2 581 564007051 564006482 3.620000e-105 392.0
21 TraesCS6D01G250200 chr7B 78.361 610 117 13 5 608 227349651 227349051 7.840000e-102 381.0
22 TraesCS6D01G250200 chr7B 79.935 309 51 6 303 605 314278157 314278460 2.340000e-52 217.0
23 TraesCS6D01G250200 chr4D 81.220 410 67 10 5 407 491969999 491969593 4.820000e-84 322.0


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 TraesCS6D01G250200 chr6D 353633140 353637004 3864 False 7138.000000 7138 100.000000 1 3865 1 chr6D.!!$F3 3864
1 TraesCS6D01G250200 chr6B 524968693 524972300 3607 True 1130.750000 2250 93.316000 728 3865 4 chr6B.!!$R5 3137
2 TraesCS6D01G250200 chr6A 488610786 488615319 4533 True 725.833333 1657 92.615833 691 3849 6 chr6A.!!$R1 3158
3 TraesCS6D01G250200 chr4A 585614875 585615384 509 True 555.000000 555 86.408000 5 514 1 chr4A.!!$R1 509
4 TraesCS6D01G250200 chr7A 270647551 270648155 604 False 418.000000 418 79.412000 2 605 1 chr7A.!!$F1 603
5 TraesCS6D01G250200 chr3D 508333690 508334313 623 True 411.000000 411 79.134000 2 632 1 chr3D.!!$R1 630
6 TraesCS6D01G250200 chr3D 564006482 564007051 569 True 392.000000 392 79.387000 2 581 1 chr3D.!!$R2 579
7 TraesCS6D01G250200 chr7B 227349051 227349651 600 True 381.000000 381 78.361000 5 608 1 chr7B.!!$R1 603

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
653 676 0.249741 CGGTATCTTTTCCGCCCGAT 60.25 55.0 0.0 0.0 40.28 4.18 F
1243 1744 0.110056 GATGCCGTGAGTTGCACTTG 60.11 55.0 0.0 0.0 45.49 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 3545 1.550659 CGCAGTGTTGTTGCAATGGC 61.551 55.0 0.59 0.0 41.59 4.40 R
3239 5071 2.093288 TGAGACCAGGTCATCATGAAGC 60.093 50.0 22.31 0.0 34.60 3.86 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
49 54 2.837591 ACCCAAGGCAGAAAACAAACTT 59.162 40.909 0.00 0.00 0.00 2.66
79 84 1.154150 GCACAAGAAGCATGCCGAC 60.154 57.895 15.66 6.16 33.06 4.79
87 92 3.397482 AGAAGCATGCCGACAAGATATC 58.603 45.455 15.66 0.00 0.00 1.63
90 95 1.457303 GCATGCCGACAAGATATCGAC 59.543 52.381 6.36 0.00 42.25 4.20
122 127 1.134753 TGTGTTGCAAGCTCAGTTTGG 59.865 47.619 0.00 0.00 0.00 3.28
130 135 3.460103 CAAGCTCAGTTTGGCATTGTTT 58.540 40.909 0.00 0.00 0.00 2.83
184 190 5.357878 TCCCTTTCAAATATCATGACTGCAC 59.642 40.000 0.00 0.00 0.00 4.57
187 193 5.469373 TTCAAATATCATGACTGCACGTC 57.531 39.130 0.00 8.75 43.14 4.34
190 196 5.748630 TCAAATATCATGACTGCACGTCTAC 59.251 40.000 14.60 0.00 43.25 2.59
275 283 0.603707 GTAGCTGTGTCAAGCCTGCA 60.604 55.000 0.00 0.00 44.68 4.41
323 332 7.956328 TTTCTTGAGACCTACTAGCAGATTA 57.044 36.000 0.00 0.00 0.00 1.75
325 334 7.336161 TCTTGAGACCTACTAGCAGATTAAC 57.664 40.000 0.00 0.00 0.00 2.01
333 342 6.127423 ACCTACTAGCAGATTAACGACAATGT 60.127 38.462 0.00 0.00 0.00 2.71
353 362 2.351726 GTCACACACAACCAACTCTGTC 59.648 50.000 0.00 0.00 0.00 3.51
358 367 3.249320 CACACAACCAACTCTGTCATGAG 59.751 47.826 0.00 0.00 39.78 2.90
362 371 1.067283 ACCAACTCTGTCATGAGCTCG 60.067 52.381 9.64 0.00 37.58 5.03
395 404 4.343526 AGTGGCAACTGTATGAGAGATAGG 59.656 45.833 0.00 0.00 34.48 2.57
414 423 8.788238 AGATAGGCTCCCATTTTATTCATTTT 57.212 30.769 0.00 0.00 0.00 1.82
514 525 7.382218 GGAGTTGAACATTTGTTGTAATTGAGG 59.618 37.037 0.00 0.00 37.68 3.86
515 526 7.209475 AGTTGAACATTTGTTGTAATTGAGGG 58.791 34.615 0.00 0.00 37.68 4.30
533 544 7.759489 TTGAGGGGATTATTGTATTGTATGC 57.241 36.000 0.00 0.00 0.00 3.14
534 545 5.937540 TGAGGGGATTATTGTATTGTATGCG 59.062 40.000 0.00 0.00 0.00 4.73
535 546 5.876357 AGGGGATTATTGTATTGTATGCGT 58.124 37.500 0.00 0.00 0.00 5.24
548 568 9.658475 TGTATTGTATGCGTTTCATTAATAAGC 57.342 29.630 0.00 0.00 36.63 3.09
635 658 9.897744 ATATTTAACATATGGTCTGAAATTGCG 57.102 29.630 7.80 0.00 0.00 4.85
636 659 4.637483 AACATATGGTCTGAAATTGCGG 57.363 40.909 7.80 0.00 0.00 5.69
637 660 3.620488 ACATATGGTCTGAAATTGCGGT 58.380 40.909 7.80 0.00 0.00 5.68
638 661 4.776349 ACATATGGTCTGAAATTGCGGTA 58.224 39.130 7.80 0.00 0.00 4.02
639 662 5.376625 ACATATGGTCTGAAATTGCGGTAT 58.623 37.500 7.80 0.00 0.00 2.73
640 663 5.470098 ACATATGGTCTGAAATTGCGGTATC 59.530 40.000 7.80 0.00 0.00 2.24
641 664 3.627395 TGGTCTGAAATTGCGGTATCT 57.373 42.857 0.00 0.00 0.00 1.98
642 665 3.950397 TGGTCTGAAATTGCGGTATCTT 58.050 40.909 0.00 0.00 0.00 2.40
643 666 4.331968 TGGTCTGAAATTGCGGTATCTTT 58.668 39.130 0.00 0.00 0.00 2.52
644 667 4.764823 TGGTCTGAAATTGCGGTATCTTTT 59.235 37.500 0.00 0.00 0.00 2.27
645 668 5.106317 TGGTCTGAAATTGCGGTATCTTTTC 60.106 40.000 0.00 0.00 0.00 2.29
646 669 5.332707 GTCTGAAATTGCGGTATCTTTTCC 58.667 41.667 0.00 0.00 0.00 3.13
651 674 3.713963 CGGTATCTTTTCCGCCCG 58.286 61.111 0.00 0.00 40.28 6.13
652 675 1.142314 CGGTATCTTTTCCGCCCGA 59.858 57.895 0.00 0.00 40.28 5.14
653 676 0.249741 CGGTATCTTTTCCGCCCGAT 60.250 55.000 0.00 0.00 40.28 4.18
654 677 1.226746 GGTATCTTTTCCGCCCGATG 58.773 55.000 0.00 0.00 0.00 3.84
655 678 1.474498 GGTATCTTTTCCGCCCGATGT 60.474 52.381 0.00 0.00 0.00 3.06
656 679 1.865340 GTATCTTTTCCGCCCGATGTC 59.135 52.381 0.00 0.00 0.00 3.06
657 680 0.810031 ATCTTTTCCGCCCGATGTCG 60.810 55.000 0.00 0.00 39.44 4.35
658 681 3.095898 CTTTTCCGCCCGATGTCGC 62.096 63.158 0.00 0.00 38.18 5.19
683 706 5.435820 GGTACCACAAATACGTTTTTGGA 57.564 39.130 27.52 12.53 44.37 3.53
684 707 5.214417 GGTACCACAAATACGTTTTTGGAC 58.786 41.667 27.52 20.07 44.37 4.02
685 708 4.985538 ACCACAAATACGTTTTTGGACA 57.014 36.364 27.52 0.00 44.37 4.02
686 709 5.326200 ACCACAAATACGTTTTTGGACAA 57.674 34.783 27.52 0.00 44.37 3.18
687 710 5.344884 ACCACAAATACGTTTTTGGACAAG 58.655 37.500 27.52 16.45 44.37 3.16
688 711 4.208253 CCACAAATACGTTTTTGGACAAGC 59.792 41.667 27.52 0.00 44.37 4.01
689 712 4.208253 CACAAATACGTTTTTGGACAAGCC 59.792 41.667 27.52 0.00 40.20 4.35
699 722 2.335316 TGGACAAGCCGTAAACTGTT 57.665 45.000 0.00 0.00 40.66 3.16
796 1295 1.517832 CTCCCTCGGCACCACTAAG 59.482 63.158 0.00 0.00 0.00 2.18
930 1431 1.834822 GGATCTAGCGCCCTCACCT 60.835 63.158 2.29 0.00 0.00 4.00
931 1432 0.539901 GGATCTAGCGCCCTCACCTA 60.540 60.000 2.29 0.00 0.00 3.08
934 1435 0.752009 TCTAGCGCCCTCACCTACAG 60.752 60.000 2.29 0.00 0.00 2.74
1178 1679 0.179000 GGTGAGTACATCCTGGCCTG 59.821 60.000 3.32 2.54 0.00 4.85
1193 1694 2.170187 TGGCCTGCAAACTGAAATTGTT 59.830 40.909 3.32 0.00 0.00 2.83
1194 1695 3.205338 GGCCTGCAAACTGAAATTGTTT 58.795 40.909 0.00 0.00 38.04 2.83
1230 1731 0.523968 CAATGTCCAAAGCGATGCCG 60.524 55.000 0.00 0.00 39.16 5.69
1239 1740 3.422303 GCGATGCCGTGAGTTGCA 61.422 61.111 0.00 0.00 42.52 4.08
1240 1741 2.476051 CGATGCCGTGAGTTGCAC 59.524 61.111 0.00 0.00 40.88 4.57
1241 1742 2.029288 CGATGCCGTGAGTTGCACT 61.029 57.895 0.00 0.00 45.49 4.40
1242 1743 1.568612 CGATGCCGTGAGTTGCACTT 61.569 55.000 0.00 0.00 45.49 3.16
1243 1744 0.110056 GATGCCGTGAGTTGCACTTG 60.110 55.000 0.00 0.00 45.49 3.16
1244 1745 2.050985 GCCGTGAGTTGCACTTGC 60.051 61.111 0.00 0.00 45.49 4.01
1267 1774 3.570550 ACCGAGATGACAGGATAGTAAGC 59.429 47.826 0.00 0.00 0.00 3.09
1285 1792 3.366052 AGCTCCAACGGGAATTGTTAT 57.634 42.857 0.00 0.00 44.38 1.89
1361 1868 5.899299 AGATTTCTTATTGCTCAATGGTGC 58.101 37.500 5.43 0.00 32.50 5.01
1362 1869 5.419788 AGATTTCTTATTGCTCAATGGTGCA 59.580 36.000 5.43 0.00 41.39 4.57
1397 1904 2.162408 GCAACTCCTGTGCTACCAATTC 59.838 50.000 0.00 0.00 0.00 2.17
1413 1920 3.124636 CCAATTCGTAACCTTGACGGAAG 59.875 47.826 0.00 0.00 40.70 3.46
1533 2041 6.607735 TTTAAAAACGAGACACCTAGGTTG 57.392 37.500 13.15 10.64 0.00 3.77
1552 2060 4.684242 GGTTGTTTGCCAATTAGCTTGTAC 59.316 41.667 0.00 0.00 35.02 2.90
1553 2061 4.513198 TGTTTGCCAATTAGCTTGTACC 57.487 40.909 0.00 0.00 32.61 3.34
1605 2113 3.846360 ACGTGTACTCCTTATGCAAGTC 58.154 45.455 0.00 0.00 0.00 3.01
1705 2694 4.460382 CCAGCTTATGTTCTCCACATGTTT 59.540 41.667 0.00 0.00 46.37 2.83
1759 2752 6.604396 TGGACTCGATATTGTACTGAGGTAAA 59.396 38.462 0.00 0.00 0.00 2.01
1787 2780 3.491766 TTCTACCTCCTCCCACTTCAT 57.508 47.619 0.00 0.00 0.00 2.57
1840 3070 9.156156 CAACTAGAAGTATCAGTTACGTATTCG 57.844 37.037 0.00 0.00 35.84 3.34
1856 3086 6.567050 ACGTATTCGCCAAGAAACTATTAGA 58.433 36.000 0.00 0.00 42.91 2.10
2063 3295 3.516615 GCACAGGTCTATGAGAAGTCAC 58.483 50.000 0.00 0.00 34.75 3.67
2242 3545 1.142060 TGGGCCAATCCTACATTACCG 59.858 52.381 2.13 0.00 34.39 4.02
2384 3692 9.469097 AATTATACTAATTGCTTGTAACACCCA 57.531 29.630 0.00 0.00 0.00 4.51
2502 3973 7.063544 AGCTCAGTACAAGATTTATGTTCGAAC 59.936 37.037 21.42 21.42 32.27 3.95
2523 3994 4.783055 ACCACCACAACATTTGTAGTACA 58.217 39.130 0.00 0.00 43.23 2.90
2883 4355 3.680937 GTGACGATTCACCCGTAAATGAA 59.319 43.478 0.00 0.00 45.77 2.57
2903 4375 6.702972 TGAAATTTGCGACACCATAATTTG 57.297 33.333 0.00 0.00 30.85 2.32
2966 4439 3.847671 TGAATTGACACACCCTACACA 57.152 42.857 0.00 0.00 0.00 3.72
3020 4493 5.104109 TGGTATAGGCTTGCACCTTTCTTAT 60.104 40.000 0.51 0.00 41.50 1.73
3021 4494 6.100569 TGGTATAGGCTTGCACCTTTCTTATA 59.899 38.462 0.51 0.00 41.50 0.98
3022 4495 7.168905 GGTATAGGCTTGCACCTTTCTTATAT 58.831 38.462 0.51 0.00 41.50 0.86
3023 4496 8.319146 GGTATAGGCTTGCACCTTTCTTATATA 58.681 37.037 0.51 0.00 41.50 0.86
3024 4497 9.892130 GTATAGGCTTGCACCTTTCTTATATAT 57.108 33.333 0.51 0.00 41.50 0.86
3111 4609 1.149101 GGGAATAGAATGCCCCCTCA 58.851 55.000 0.00 0.00 35.76 3.86
3122 4628 1.061735 TGCCCCCTCACAGATATACCA 60.062 52.381 0.00 0.00 0.00 3.25
3189 4696 6.953101 TGTAAGTTCCAGCCACATTCTATTA 58.047 36.000 0.00 0.00 0.00 0.98
3207 4714 8.876275 TTCTATTAGTAAGTGTTGTGTCGTTT 57.124 30.769 0.00 0.00 0.00 3.60
3233 5065 4.513442 ACTTTTATCATGCCTCGTTGCTA 58.487 39.130 0.00 0.00 0.00 3.49
3234 5066 4.572389 ACTTTTATCATGCCTCGTTGCTAG 59.428 41.667 0.00 0.00 0.00 3.42
3235 5067 2.154854 TATCATGCCTCGTTGCTAGC 57.845 50.000 8.10 8.10 0.00 3.42
3236 5068 0.533755 ATCATGCCTCGTTGCTAGCC 60.534 55.000 13.29 0.00 0.00 3.93
3237 5069 1.153289 CATGCCTCGTTGCTAGCCT 60.153 57.895 13.29 0.00 0.00 4.58
3238 5070 0.104855 CATGCCTCGTTGCTAGCCTA 59.895 55.000 13.29 0.00 0.00 3.93
3239 5071 0.390860 ATGCCTCGTTGCTAGCCTAG 59.609 55.000 13.29 3.05 0.00 3.02
3252 5084 2.926778 AGCCTAGCTTCATGATGACC 57.073 50.000 12.54 0.00 33.89 4.02
3253 5085 2.406559 AGCCTAGCTTCATGATGACCT 58.593 47.619 12.54 0.00 33.89 3.85
3256 5088 2.437281 CCTAGCTTCATGATGACCTGGT 59.563 50.000 12.54 0.00 0.00 4.00
3266 5098 4.371624 TGATGACCTGGTCTCAAATGTT 57.628 40.909 26.03 2.78 33.15 2.71
3326 5158 9.594936 TTTTTGATAACAGGGGAAGAAGAATTA 57.405 29.630 0.00 0.00 0.00 1.40
3487 5325 1.765657 AAAAAGCCCAGGCCTGCAA 60.766 52.632 28.39 0.00 43.17 4.08
3641 5493 1.007842 AGAGGAGAGGGGGAGAAGAAC 59.992 57.143 0.00 0.00 0.00 3.01
3646 5498 2.372172 GAGAGGGGGAGAAGAACAACAA 59.628 50.000 0.00 0.00 0.00 2.83
3648 5500 1.850345 AGGGGGAGAAGAACAACAACA 59.150 47.619 0.00 0.00 0.00 3.33
3649 5501 1.954382 GGGGGAGAAGAACAACAACAC 59.046 52.381 0.00 0.00 0.00 3.32
3650 5502 1.954382 GGGGAGAAGAACAACAACACC 59.046 52.381 0.00 0.00 0.00 4.16
3651 5503 2.422945 GGGGAGAAGAACAACAACACCT 60.423 50.000 0.00 0.00 0.00 4.00
3652 5504 2.879026 GGGAGAAGAACAACAACACCTC 59.121 50.000 0.00 0.00 0.00 3.85
3653 5505 2.879026 GGAGAAGAACAACAACACCTCC 59.121 50.000 0.00 0.00 33.17 4.30
3654 5506 2.544267 GAGAAGAACAACAACACCTCCG 59.456 50.000 0.00 0.00 0.00 4.63
3655 5507 2.169769 AGAAGAACAACAACACCTCCGA 59.830 45.455 0.00 0.00 0.00 4.55
3656 5508 2.930826 AGAACAACAACACCTCCGAT 57.069 45.000 0.00 0.00 0.00 4.18
3657 5509 4.039973 AGAAGAACAACAACACCTCCGATA 59.960 41.667 0.00 0.00 0.00 2.92
3658 5510 3.926616 AGAACAACAACACCTCCGATAG 58.073 45.455 0.00 0.00 0.00 2.08
3666 5522 1.143277 ACACCTCCGATAGTCCGATCT 59.857 52.381 0.00 0.00 0.00 2.75
3855 5711 2.023673 CACAAGGTGAGCAGAAACCAA 58.976 47.619 0.00 0.00 39.05 3.67
3859 5715 1.177401 GGTGAGCAGAAACCAATCCC 58.823 55.000 0.00 0.00 36.41 3.85
3862 5718 3.561313 GGTGAGCAGAAACCAATCCCTAA 60.561 47.826 0.00 0.00 36.41 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.433186 TTATCTTCACAAATGTTGCCCG 57.567 40.909 0.00 0.00 0.00 6.13
19 20 7.005296 TGTTTTCTGCCTTGGGTTACTAATTA 58.995 34.615 0.00 0.00 0.00 1.40
79 84 5.007039 CACCAAATGTCCTGTCGATATCTTG 59.993 44.000 0.34 0.00 0.00 3.02
87 92 1.593196 ACACACCAAATGTCCTGTCG 58.407 50.000 0.00 0.00 40.64 4.35
90 95 1.408340 TGCAACACACCAAATGTCCTG 59.592 47.619 0.00 0.00 40.64 3.86
122 127 1.079612 GCAGGGCCTCAAACAATGC 60.080 57.895 0.95 0.00 0.00 3.56
130 135 4.087892 GAAGCGAGCAGGGCCTCA 62.088 66.667 0.95 0.00 0.00 3.86
184 190 7.346208 TGATCATGTTGTGTAAAAGTAGACG 57.654 36.000 0.00 0.00 0.00 4.18
187 193 8.185003 TCGATGATCATGTTGTGTAAAAGTAG 57.815 34.615 14.30 0.00 0.00 2.57
190 196 6.313658 TCCTCGATGATCATGTTGTGTAAAAG 59.686 38.462 14.30 0.00 0.00 2.27
275 283 4.205587 GCAGTGATTCATCTGGATTCCTT 58.794 43.478 3.95 0.00 32.94 3.36
323 332 2.096819 GGTTGTGTGTGACATTGTCGTT 59.903 45.455 11.97 0.00 34.95 3.85
325 334 1.668237 TGGTTGTGTGTGACATTGTCG 59.332 47.619 11.97 0.00 34.95 4.35
333 342 2.027653 TGACAGAGTTGGTTGTGTGTGA 60.028 45.455 0.00 0.00 0.00 3.58
362 371 1.103398 AGTTGCCACTGGTGCTCAAC 61.103 55.000 19.33 19.33 39.99 3.18
387 396 6.770286 TGAATAAAATGGGAGCCTATCTCT 57.230 37.500 0.00 0.00 41.60 3.10
491 500 6.423604 CCCCTCAATTACAACAAATGTTCAAC 59.576 38.462 0.00 0.00 43.63 3.18
514 525 7.644490 TGAAACGCATACAATACAATAATCCC 58.356 34.615 0.00 0.00 0.00 3.85
515 526 9.677567 AATGAAACGCATACAATACAATAATCC 57.322 29.630 0.00 0.00 35.78 3.01
611 632 7.147915 ACCGCAATTTCAGACCATATGTTAAAT 60.148 33.333 1.24 0.00 0.00 1.40
612 633 6.151985 ACCGCAATTTCAGACCATATGTTAAA 59.848 34.615 1.24 0.00 0.00 1.52
613 634 5.650266 ACCGCAATTTCAGACCATATGTTAA 59.350 36.000 1.24 0.00 0.00 2.01
615 636 4.016444 ACCGCAATTTCAGACCATATGTT 58.984 39.130 1.24 0.00 0.00 2.71
616 637 3.620488 ACCGCAATTTCAGACCATATGT 58.380 40.909 1.24 0.00 0.00 2.29
617 638 5.702670 AGATACCGCAATTTCAGACCATATG 59.297 40.000 0.00 0.00 0.00 1.78
618 639 5.869579 AGATACCGCAATTTCAGACCATAT 58.130 37.500 0.00 0.00 0.00 1.78
619 640 5.290493 AGATACCGCAATTTCAGACCATA 57.710 39.130 0.00 0.00 0.00 2.74
625 648 4.342772 CGGAAAAGATACCGCAATTTCAG 58.657 43.478 0.00 0.00 42.55 3.02
635 658 1.226746 CATCGGGCGGAAAAGATACC 58.773 55.000 0.00 0.00 0.00 2.73
636 659 1.865340 GACATCGGGCGGAAAAGATAC 59.135 52.381 0.00 0.00 0.00 2.24
637 660 1.537348 CGACATCGGGCGGAAAAGATA 60.537 52.381 0.00 0.00 35.37 1.98
638 661 0.810031 CGACATCGGGCGGAAAAGAT 60.810 55.000 0.00 0.00 35.37 2.40
639 662 1.447140 CGACATCGGGCGGAAAAGA 60.447 57.895 0.00 0.00 35.37 2.52
640 663 3.089784 CGACATCGGGCGGAAAAG 58.910 61.111 0.00 0.00 35.37 2.27
641 664 3.122323 GCGACATCGGGCGGAAAA 61.122 61.111 3.08 0.00 40.23 2.29
650 673 3.829044 TGGTACCCCGCGACATCG 61.829 66.667 8.23 0.00 43.27 3.84
651 674 2.202837 GTGGTACCCCGCGACATC 60.203 66.667 8.23 0.00 0.00 3.06
652 675 2.114488 TTTGTGGTACCCCGCGACAT 62.114 55.000 8.23 0.00 44.67 3.06
653 676 2.114488 ATTTGTGGTACCCCGCGACA 62.114 55.000 8.23 3.41 44.67 4.35
654 677 0.108233 TATTTGTGGTACCCCGCGAC 60.108 55.000 8.23 0.31 44.67 5.19
655 678 0.108233 GTATTTGTGGTACCCCGCGA 60.108 55.000 8.23 0.00 44.67 5.87
656 679 1.422950 CGTATTTGTGGTACCCCGCG 61.423 60.000 10.07 0.00 44.67 6.46
657 680 0.391528 ACGTATTTGTGGTACCCCGC 60.392 55.000 10.07 0.03 41.91 6.13
658 681 2.097680 AACGTATTTGTGGTACCCCG 57.902 50.000 10.07 2.93 0.00 5.73
659 682 4.548494 CAAAAACGTATTTGTGGTACCCC 58.452 43.478 10.07 0.00 35.93 4.95
660 683 4.548494 CCAAAAACGTATTTGTGGTACCC 58.452 43.478 10.07 1.05 45.17 3.69
666 689 4.208253 GGCTTGTCCAAAAACGTATTTGTG 59.792 41.667 0.00 0.00 38.37 3.33
667 690 4.364860 GGCTTGTCCAAAAACGTATTTGT 58.635 39.130 0.00 0.00 38.37 2.83
668 691 3.423867 CGGCTTGTCCAAAAACGTATTTG 59.576 43.478 0.00 0.00 39.47 2.32
669 692 3.067040 ACGGCTTGTCCAAAAACGTATTT 59.933 39.130 0.00 0.00 34.01 1.40
670 693 2.619646 ACGGCTTGTCCAAAAACGTATT 59.380 40.909 0.00 0.00 34.01 1.89
671 694 2.223745 ACGGCTTGTCCAAAAACGTAT 58.776 42.857 0.00 0.00 34.01 3.06
672 695 1.666054 ACGGCTTGTCCAAAAACGTA 58.334 45.000 0.00 0.00 34.01 3.57
673 696 1.666054 TACGGCTTGTCCAAAAACGT 58.334 45.000 0.00 0.00 36.93 3.99
674 697 2.759538 TTACGGCTTGTCCAAAAACG 57.240 45.000 0.00 0.00 34.01 3.60
675 698 3.794564 CAGTTTACGGCTTGTCCAAAAAC 59.205 43.478 0.00 0.00 38.45 2.43
676 699 3.444388 ACAGTTTACGGCTTGTCCAAAAA 59.556 39.130 0.00 0.00 34.01 1.94
677 700 3.018149 ACAGTTTACGGCTTGTCCAAAA 58.982 40.909 0.00 0.00 34.01 2.44
678 701 2.645802 ACAGTTTACGGCTTGTCCAAA 58.354 42.857 0.00 0.00 34.01 3.28
679 702 2.335316 ACAGTTTACGGCTTGTCCAA 57.665 45.000 0.00 0.00 34.01 3.53
680 703 2.335316 AACAGTTTACGGCTTGTCCA 57.665 45.000 0.00 0.00 34.01 4.02
681 704 3.703286 AAAACAGTTTACGGCTTGTCC 57.297 42.857 0.00 0.00 0.00 4.02
699 722 1.464997 GCAAAAACGTGTGCCCAAAAA 59.535 42.857 7.68 0.00 34.58 1.94
704 727 2.656973 CCGCAAAAACGTGTGCCC 60.657 61.111 12.07 0.00 37.47 5.36
711 734 2.159627 AGTTAGAGATGCCGCAAAAACG 59.840 45.455 0.00 0.00 0.00 3.60
1193 1694 9.513906 TGGACATTGTTCTCTGTCATAAAATAA 57.486 29.630 5.20 0.00 42.83 1.40
1194 1695 9.513906 TTGGACATTGTTCTCTGTCATAAAATA 57.486 29.630 5.20 0.00 42.83 1.40
1201 1702 3.565482 GCTTTGGACATTGTTCTCTGTCA 59.435 43.478 5.20 0.00 42.83 3.58
1202 1703 3.364366 CGCTTTGGACATTGTTCTCTGTC 60.364 47.826 0.00 0.00 40.82 3.51
1239 1740 0.036952 CCTGTCATCTCGGTGCAAGT 60.037 55.000 0.00 0.00 0.00 3.16
1240 1741 0.247460 TCCTGTCATCTCGGTGCAAG 59.753 55.000 0.00 0.00 0.00 4.01
1241 1742 0.904649 ATCCTGTCATCTCGGTGCAA 59.095 50.000 0.00 0.00 0.00 4.08
1242 1743 1.683385 CTATCCTGTCATCTCGGTGCA 59.317 52.381 0.00 0.00 0.00 4.57
1243 1744 1.683917 ACTATCCTGTCATCTCGGTGC 59.316 52.381 0.00 0.00 0.00 5.01
1244 1745 4.557695 GCTTACTATCCTGTCATCTCGGTG 60.558 50.000 0.00 0.00 0.00 4.94
1267 1774 4.881273 TCATGATAACAATTCCCGTTGGAG 59.119 41.667 0.00 0.00 43.07 3.86
1285 1792 7.068226 TGTTAGGAGAGTAATTGTCGATCATGA 59.932 37.037 0.00 0.00 0.00 3.07
1397 1904 4.151157 CCTAAAACTTCCGTCAAGGTTACG 59.849 45.833 0.00 0.00 41.57 3.18
1413 1920 7.547227 AGATTGCAATGTGTTATCCCTAAAAC 58.453 34.615 18.59 0.00 0.00 2.43
1533 2041 4.783764 AGGTACAAGCTAATTGGCAAAC 57.216 40.909 16.72 7.75 43.68 2.93
1585 2093 3.859961 CAGACTTGCATAAGGAGTACACG 59.140 47.826 0.00 0.00 38.26 4.49
1605 2113 4.703575 AGATTGGATGGTGTGTTTCATCAG 59.296 41.667 0.00 0.00 40.76 2.90
1725 2714 6.716934 ACAATATCGAGTCCAGATACAAGT 57.283 37.500 0.00 0.00 33.92 3.16
1759 2752 4.470304 GTGGGAGGAGGTAGAATGTTTAGT 59.530 45.833 0.00 0.00 0.00 2.24
1856 3086 7.998383 TGGGCAGTATGATTACATAAAGACAAT 59.002 33.333 0.00 0.00 40.13 2.71
1916 3148 3.535561 CTCCTGCGGAAGTAACATGAAT 58.464 45.455 0.00 0.00 0.00 2.57
1925 3157 1.689233 TATGCCCTCCTGCGGAAGT 60.689 57.895 0.00 0.00 0.00 3.01
2063 3295 3.623906 ACTGACCTCCACATGAATCAG 57.376 47.619 0.00 5.52 40.08 2.90
2110 3343 2.825861 ACTGGAATTGCTTGCAAAGG 57.174 45.000 12.17 4.10 46.35 3.11
2120 3423 5.163513 GTGTCATAGGCAAAACTGGAATTG 58.836 41.667 0.00 0.00 0.00 2.32
2135 3438 8.840321 CCTAAAAAGGTATCATTGGTGTCATAG 58.160 37.037 0.00 0.00 0.00 2.23
2242 3545 1.550659 CGCAGTGTTGTTGCAATGGC 61.551 55.000 0.59 0.00 41.59 4.40
2384 3692 5.241506 CGGGACCATTGCAAAATATCTACAT 59.758 40.000 1.71 0.00 0.00 2.29
2466 3774 9.900710 AAATCTTGTACTGAGCTATATAGAACG 57.099 33.333 14.16 1.27 0.00 3.95
2523 3994 9.965824 AGTTTTCGTTCTATGATGAACAAAAAT 57.034 25.926 8.71 9.22 41.63 1.82
2660 4132 9.830975 TGCAAGAATATAGCAATTAAGTACTCA 57.169 29.630 0.00 0.00 34.97 3.41
2883 4355 4.564041 TGCAAATTATGGTGTCGCAAATT 58.436 34.783 0.00 0.00 0.00 1.82
2889 4361 4.154015 TCAGAGTTGCAAATTATGGTGTCG 59.846 41.667 0.00 0.00 0.00 4.35
2898 4370 6.889301 TCAAGATCTTCAGAGTTGCAAATT 57.111 33.333 4.57 0.00 0.00 1.82
2899 4371 6.263842 TGTTCAAGATCTTCAGAGTTGCAAAT 59.736 34.615 4.57 0.00 0.00 2.32
2903 4375 5.629097 CATGTTCAAGATCTTCAGAGTTGC 58.371 41.667 4.57 0.00 0.00 4.17
2966 4439 4.551702 AAAAGTTTCTGGCAAAACAGGT 57.448 36.364 19.83 8.22 40.77 4.00
3091 4589 3.703492 AGGGGGCATTCTATTCCCT 57.297 52.632 0.00 0.00 42.74 4.20
3111 4609 5.602561 TCACAGCCTTACATGGTATATCTGT 59.397 40.000 0.00 0.46 33.13 3.41
3122 4628 2.816087 CTGCAAAGTCACAGCCTTACAT 59.184 45.455 0.00 0.00 0.00 2.29
3189 4696 5.870978 AGTAACAAACGACACAACACTTACT 59.129 36.000 0.00 0.00 0.00 2.24
3207 4714 5.391523 GCAACGAGGCATGATAAAAGTAACA 60.392 40.000 0.00 0.00 0.00 2.41
3233 5065 2.104451 CAGGTCATCATGAAGCTAGGCT 59.896 50.000 0.00 0.00 42.56 4.58
3234 5066 2.492012 CAGGTCATCATGAAGCTAGGC 58.508 52.381 0.00 0.00 0.00 3.93
3235 5067 2.437281 ACCAGGTCATCATGAAGCTAGG 59.563 50.000 0.00 6.53 0.00 3.02
3236 5068 3.387374 AGACCAGGTCATCATGAAGCTAG 59.613 47.826 22.31 0.00 34.60 3.42
3237 5069 3.378512 AGACCAGGTCATCATGAAGCTA 58.621 45.455 22.31 0.00 34.60 3.32
3238 5070 2.170187 GAGACCAGGTCATCATGAAGCT 59.830 50.000 22.31 0.00 34.60 3.74
3239 5071 2.093288 TGAGACCAGGTCATCATGAAGC 60.093 50.000 22.31 0.00 34.60 3.86
3240 5072 3.900966 TGAGACCAGGTCATCATGAAG 57.099 47.619 22.31 0.00 34.60 3.02
3241 5073 4.639078 TTTGAGACCAGGTCATCATGAA 57.361 40.909 22.31 10.97 34.60 2.57
3242 5074 4.019051 ACATTTGAGACCAGGTCATCATGA 60.019 41.667 22.31 12.96 34.60 3.07
3243 5075 4.267536 ACATTTGAGACCAGGTCATCATG 58.732 43.478 22.31 17.88 34.60 3.07
3244 5076 4.581309 ACATTTGAGACCAGGTCATCAT 57.419 40.909 22.31 0.00 34.60 2.45
3245 5077 4.371624 AACATTTGAGACCAGGTCATCA 57.628 40.909 22.31 17.73 34.60 3.07
3246 5078 4.636206 GGTAACATTTGAGACCAGGTCATC 59.364 45.833 22.31 15.51 34.60 2.92
3247 5079 4.042809 TGGTAACATTTGAGACCAGGTCAT 59.957 41.667 22.31 6.81 46.17 3.06
3248 5080 3.392947 TGGTAACATTTGAGACCAGGTCA 59.607 43.478 22.31 0.55 46.17 4.02
3249 5081 4.015872 TGGTAACATTTGAGACCAGGTC 57.984 45.455 12.25 12.25 46.17 3.85
3266 5098 2.054799 ACAGCAGTTTTCCCTCTGGTA 58.945 47.619 0.00 0.00 39.82 3.25
3396 5229 6.364701 TCGATGTATTCCTGGGAAATTTCAT 58.635 36.000 19.49 6.16 37.69 2.57
3401 5234 4.655963 CCATCGATGTATTCCTGGGAAAT 58.344 43.478 23.27 0.00 37.69 2.17
3469 5307 1.765657 TTGCAGGCCTGGGCTTTTT 60.766 52.632 33.46 0.00 41.60 1.94
3584 5436 9.974980 ATTCTCCGCTGTTTATTTTTAAGAAAA 57.025 25.926 0.00 0.00 38.96 2.29
3629 5481 1.954382 GTGTTGTTGTTCTTCTCCCCC 59.046 52.381 0.00 0.00 0.00 5.40
3641 5493 2.618053 GGACTATCGGAGGTGTTGTTG 58.382 52.381 0.00 0.00 0.00 3.33
3646 5498 1.143277 AGATCGGACTATCGGAGGTGT 59.857 52.381 0.00 0.00 0.00 4.16
3648 5500 1.420514 TGAGATCGGACTATCGGAGGT 59.579 52.381 0.00 0.00 0.00 3.85
3649 5501 1.807742 GTGAGATCGGACTATCGGAGG 59.192 57.143 0.00 0.00 0.00 4.30
3650 5502 2.224549 GTGTGAGATCGGACTATCGGAG 59.775 54.545 0.00 0.00 0.00 4.63
3651 5503 2.219458 GTGTGAGATCGGACTATCGGA 58.781 52.381 0.00 0.00 0.00 4.55
3652 5504 1.267261 GGTGTGAGATCGGACTATCGG 59.733 57.143 0.00 0.00 0.00 4.18
3653 5505 1.267261 GGGTGTGAGATCGGACTATCG 59.733 57.143 0.00 0.00 0.00 2.92
3654 5506 2.034812 GTGGGTGTGAGATCGGACTATC 59.965 54.545 0.00 0.00 0.00 2.08
3655 5507 2.032620 GTGGGTGTGAGATCGGACTAT 58.967 52.381 0.00 0.00 0.00 2.12
3656 5508 1.471119 GTGGGTGTGAGATCGGACTA 58.529 55.000 0.00 0.00 0.00 2.59
3657 5509 1.258445 GGTGGGTGTGAGATCGGACT 61.258 60.000 0.00 0.00 0.00 3.85
3658 5510 1.218316 GGTGGGTGTGAGATCGGAC 59.782 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.