Multiple sequence alignment - TraesCS1D01G092800

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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 TraesCS1D01G092800 chr1D 100.000 3785 0 0 1 3785 79079646 79075862 0.000000e+00 6990
1 TraesCS1D01G092800 chr1D 85.370 1702 189 38 1086 2767 79088520 79086859 0.000000e+00 1709
2 TraesCS1D01G092800 chr1D 78.220 427 73 17 1105 1521 79051030 79050614 4.850000e-64 255
3 TraesCS1D01G092800 chr1A 95.253 2212 96 5 1082 3290 96445800 96448005 0.000000e+00 3494
4 TraesCS1D01G092800 chr1A 85.805 1726 210 25 1064 2767 96438069 96439781 0.000000e+00 1797
5 TraesCS1D01G092800 chr1A 85.239 752 69 18 2822 3546 96439773 96440509 0.000000e+00 736
6 TraesCS1D01G092800 chr1A 86.765 544 67 4 69 611 96442157 96442696 5.410000e-168 601
7 TraesCS1D01G092800 chr1A 80.000 500 43 27 614 1085 96442939 96443409 2.190000e-82 316
8 TraesCS1D01G092800 chr1A 77.934 426 78 12 1104 1521 96453325 96453742 6.280000e-63 252
9 TraesCS1D01G092800 chr1A 86.170 94 13 0 3692 3785 96448280 96448373 6.690000e-18 102
10 TraesCS1D01G092800 chr1B 91.796 1548 105 14 790 2318 129513936 129512392 0.000000e+00 2135
11 TraesCS1D01G092800 chr1B 86.671 1703 190 27 1086 2767 129553336 129551650 0.000000e+00 1853
12 TraesCS1D01G092800 chr1B 91.429 910 60 12 2432 3336 129512395 129511499 0.000000e+00 1232
13 TraesCS1D01G092800 chr1B 84.413 494 55 8 3 495 129549292 129548820 2.060000e-127 466
14 TraesCS1D01G092800 chr1B 93.833 227 13 1 3318 3543 129511464 129511238 1.300000e-89 340
15 TraesCS1D01G092800 chr1B 74.393 824 177 25 1453 2259 129177218 129176412 4.720000e-84 322
16 TraesCS1D01G092800 chr1B 77.726 431 75 15 1094 1521 129177640 129177228 1.050000e-60 244
17 TraesCS1D01G092800 chr7D 99.332 449 3 0 3337 3785 412700370 412700818 0.000000e+00 813


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 TraesCS1D01G092800 chr1D 79075862 79079646 3784 True 6990.000000 6990 100.000000 1 3785 1 chr1D.!!$R2 3784
1 TraesCS1D01G092800 chr1D 79086859 79088520 1661 True 1709.000000 1709 85.370000 1086 2767 1 chr1D.!!$R3 1681
2 TraesCS1D01G092800 chr1A 96438069 96448373 10304 False 1174.333333 3494 86.538667 69 3785 6 chr1A.!!$F2 3716
3 TraesCS1D01G092800 chr1B 129511238 129513936 2698 True 1235.666667 2135 92.352667 790 3543 3 chr1B.!!$R2 2753
4 TraesCS1D01G092800 chr1B 129548820 129553336 4516 True 1159.500000 1853 85.542000 3 2767 2 chr1B.!!$R3 2764
5 TraesCS1D01G092800 chr1B 129176412 129177640 1228 True 283.000000 322 76.059500 1094 2259 2 chr1B.!!$R1 1165

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
567 4587 0.037605 ACCGCACTAGGTACTGCAAC 60.038 55.0 5.76 0.0 43.89 4.17 F
568 4588 0.037697 CCGCACTAGGTACTGCAACA 60.038 55.0 5.76 0.0 41.52 3.33 F
2010 8773 0.389948 AAGTCGGTGAGATTCCGCAC 60.390 55.0 0.00 0.0 46.49 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 8840 0.107017 AGAACACAACACCAGCAGCT 60.107 50.000 0.0 0.0 0.00 4.24 R
2159 8922 2.311688 GACGGGCAATCCTCGACCAT 62.312 60.000 0.0 0.0 32.66 3.55 R
2815 9591 1.496429 CCCCAGCCAGAATTGTATCCT 59.504 52.381 0.0 0.0 0.00 3.24 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
29 30 9.989296 ATGATCTACCTCTAGCATCTTTATAGT 57.011 33.333 0.00 0.00 0.00 2.12
30 31 9.237187 TGATCTACCTCTAGCATCTTTATAGTG 57.763 37.037 0.00 0.00 0.00 2.74
31 32 9.238368 GATCTACCTCTAGCATCTTTATAGTGT 57.762 37.037 0.00 0.00 0.00 3.55
32 33 8.998277 TCTACCTCTAGCATCTTTATAGTGTT 57.002 34.615 0.00 0.00 0.00 3.32
34 35 7.056844 ACCTCTAGCATCTTTATAGTGTTCC 57.943 40.000 0.00 0.00 0.00 3.62
35 36 6.841755 ACCTCTAGCATCTTTATAGTGTTCCT 59.158 38.462 0.00 0.00 0.00 3.36
36 37 7.151308 CCTCTAGCATCTTTATAGTGTTCCTG 58.849 42.308 0.00 0.00 0.00 3.86
38 39 5.041191 AGCATCTTTATAGTGTTCCTGGG 57.959 43.478 0.00 0.00 0.00 4.45
39 40 4.475016 AGCATCTTTATAGTGTTCCTGGGT 59.525 41.667 0.00 0.00 0.00 4.51
40 41 4.576463 GCATCTTTATAGTGTTCCTGGGTG 59.424 45.833 0.00 0.00 0.00 4.61
41 42 5.745227 CATCTTTATAGTGTTCCTGGGTGT 58.255 41.667 0.00 0.00 0.00 4.16
42 43 5.160607 TCTTTATAGTGTTCCTGGGTGTG 57.839 43.478 0.00 0.00 0.00 3.82
43 44 4.595781 TCTTTATAGTGTTCCTGGGTGTGT 59.404 41.667 0.00 0.00 0.00 3.72
44 45 5.781306 TCTTTATAGTGTTCCTGGGTGTGTA 59.219 40.000 0.00 0.00 0.00 2.90
45 46 6.270463 TCTTTATAGTGTTCCTGGGTGTGTAA 59.730 38.462 0.00 0.00 0.00 2.41
46 47 2.930826 AGTGTTCCTGGGTGTGTAAG 57.069 50.000 0.00 0.00 0.00 2.34
48 49 3.311091 AGTGTTCCTGGGTGTGTAAGTA 58.689 45.455 0.00 0.00 0.00 2.24
51 52 3.649023 TGTTCCTGGGTGTGTAAGTACAT 59.351 43.478 0.00 0.00 38.63 2.29
52 53 3.973206 TCCTGGGTGTGTAAGTACATG 57.027 47.619 0.00 0.00 38.63 3.21
53 54 2.027561 TCCTGGGTGTGTAAGTACATGC 60.028 50.000 0.00 0.00 38.63 4.06
54 55 1.999735 CTGGGTGTGTAAGTACATGCG 59.000 52.381 0.00 0.00 38.63 4.73
55 56 1.338294 TGGGTGTGTAAGTACATGCGG 60.338 52.381 0.00 0.00 38.63 5.69
56 57 1.338389 GGGTGTGTAAGTACATGCGGT 60.338 52.381 0.00 0.00 38.63 5.68
58 59 3.184541 GGTGTGTAAGTACATGCGGTAG 58.815 50.000 0.00 0.00 38.63 3.18
59 60 3.119388 GGTGTGTAAGTACATGCGGTAGA 60.119 47.826 0.00 0.00 38.63 2.59
61 62 5.107133 GTGTGTAAGTACATGCGGTAGATT 58.893 41.667 0.00 0.00 38.63 2.40
62 63 5.579511 GTGTGTAAGTACATGCGGTAGATTT 59.420 40.000 0.00 0.00 38.63 2.17
64 65 6.651643 TGTGTAAGTACATGCGGTAGATTTTT 59.348 34.615 0.00 0.00 38.63 1.94
87 88 7.814264 TTTTTATTTTGTACTACGTTCCCCA 57.186 32.000 0.00 0.00 0.00 4.96
88 89 7.814264 TTTTATTTTGTACTACGTTCCCCAA 57.186 32.000 0.00 0.00 0.00 4.12
89 90 6.799926 TTATTTTGTACTACGTTCCCCAAC 57.200 37.500 0.00 0.00 0.00 3.77
91 92 3.389925 TTGTACTACGTTCCCCAACTG 57.610 47.619 0.00 0.00 0.00 3.16
92 93 2.318908 TGTACTACGTTCCCCAACTGT 58.681 47.619 0.00 0.00 0.00 3.55
93 94 2.036217 TGTACTACGTTCCCCAACTGTG 59.964 50.000 0.00 0.00 0.00 3.66
94 95 0.395312 ACTACGTTCCCCAACTGTGG 59.605 55.000 0.00 0.00 45.53 4.17
121 4141 3.285484 TCCATGAGAACTAGGACGTACC 58.715 50.000 0.00 0.00 39.35 3.34
122 4142 2.033049 CCATGAGAACTAGGACGTACCG 59.967 54.545 0.00 0.00 44.74 4.02
170 4190 2.228480 GGGGGTGGTGCTCCAAGTA 61.228 63.158 9.53 0.00 46.15 2.24
182 4202 0.340908 TCCAAGTAGGGGTAGGGTCC 59.659 60.000 0.00 0.00 38.24 4.46
187 4207 0.566679 GTAGGGGTAGGGTCCAGGAT 59.433 60.000 0.00 0.00 0.00 3.24
202 4222 1.879380 CAGGATGGCGAACAAGTTCAA 59.121 47.619 12.86 0.00 39.46 2.69
205 4225 1.200020 GATGGCGAACAAGTTCAAGGG 59.800 52.381 12.86 0.00 39.46 3.95
211 4231 1.734388 AACAAGTTCAAGGGCGTGGC 61.734 55.000 0.00 0.00 0.00 5.01
214 4234 3.365265 GTTCAAGGGCGTGGCAGG 61.365 66.667 2.14 2.14 0.00 4.85
233 4253 2.191375 CTCCAGGTGGCGCATGAT 59.809 61.111 15.08 0.00 34.44 2.45
234 4254 2.124612 TCCAGGTGGCGCATGATG 60.125 61.111 15.08 1.91 34.44 3.07
258 4278 3.414272 GCGCAGGCTGGACAATAG 58.586 61.111 17.64 0.00 35.83 1.73
260 4280 0.744414 GCGCAGGCTGGACAATAGAA 60.744 55.000 17.64 0.00 35.83 2.10
277 4297 8.558973 ACAATAGAAATGAGGAGAAGAACAAG 57.441 34.615 0.00 0.00 0.00 3.16
282 4302 3.558931 TGAGGAGAAGAACAAGTTGCA 57.441 42.857 1.81 0.00 0.00 4.08
286 4306 2.952310 GGAGAAGAACAAGTTGCAGGTT 59.048 45.455 1.81 0.00 0.00 3.50
301 4321 1.888512 CAGGTTGATTTGGTGGGAGTG 59.111 52.381 0.00 0.00 0.00 3.51
303 4323 1.203001 GGTTGATTTGGTGGGAGTGGA 60.203 52.381 0.00 0.00 0.00 4.02
344 4364 3.989056 TCCTATGTGGTGGACATGTCTA 58.011 45.455 24.50 17.03 45.43 2.59
349 4369 1.135083 GTGGTGGACATGTCTAGACGG 60.135 57.143 24.50 14.45 0.00 4.79
376 4396 1.598962 CCGCCTGACATATGGGCTG 60.599 63.158 16.45 8.63 43.29 4.85
389 4409 4.717313 GGCTGGGTTGGGACGGTC 62.717 72.222 0.00 0.00 0.00 4.79
390 4410 4.717313 GCTGGGTTGGGACGGTCC 62.717 72.222 19.06 19.06 35.23 4.46
399 4419 1.221021 GGGACGGTCCAGACAATCC 59.779 63.158 27.32 4.86 38.64 3.01
409 4429 4.559153 GTCCAGACAATCCAAACAAATGG 58.441 43.478 0.00 0.00 42.12 3.16
410 4430 3.577848 TCCAGACAATCCAAACAAATGGG 59.422 43.478 0.00 0.00 41.05 4.00
419 4439 3.640967 TCCAAACAAATGGGAGAGGTTTG 59.359 43.478 0.00 0.00 44.71 2.93
426 4446 0.402861 TGGGAGAGGTTTGGGAAGGT 60.403 55.000 0.00 0.00 0.00 3.50
482 4502 1.108132 GGGTTCGAGCGACCTCCTAT 61.108 60.000 4.81 0.00 34.49 2.57
492 4512 2.166664 GCGACCTCCTATTTGACACTCT 59.833 50.000 0.00 0.00 0.00 3.24
496 4516 5.348997 CGACCTCCTATTTGACACTCTTTTC 59.651 44.000 0.00 0.00 0.00 2.29
513 4533 3.383698 TTTCCGTCAGATAGGAGAGGT 57.616 47.619 0.00 0.00 37.88 3.85
514 4534 2.350057 TCCGTCAGATAGGAGAGGTG 57.650 55.000 0.00 0.00 31.95 4.00
515 4535 1.564818 TCCGTCAGATAGGAGAGGTGT 59.435 52.381 0.00 0.00 31.95 4.16
525 4545 2.448542 AGAGGTGTGCACAGGGGT 60.449 61.111 22.40 4.68 0.00 4.95
558 4578 0.249322 CGACCCATTACCGCACTAGG 60.249 60.000 0.00 0.00 37.30 3.02
564 4584 2.470821 CATTACCGCACTAGGTACTGC 58.529 52.381 0.00 0.00 45.59 4.40
567 4587 0.037605 ACCGCACTAGGTACTGCAAC 60.038 55.000 5.76 0.00 43.89 4.17
568 4588 0.037697 CCGCACTAGGTACTGCAACA 60.038 55.000 5.76 0.00 41.52 3.33
574 4594 3.741344 CACTAGGTACTGCAACAACTCAC 59.259 47.826 0.00 0.00 41.52 3.51
643 4904 8.647143 TTGTTTTCATTGATTTTCCAGAGAAC 57.353 30.769 0.00 0.00 0.00 3.01
648 4909 7.528996 TCATTGATTTTCCAGAGAACACAAT 57.471 32.000 0.00 0.00 33.49 2.71
683 4945 9.270640 TCATGAATTGAACCCTTTTAAAATGTG 57.729 29.630 0.09 0.00 0.00 3.21
684 4946 9.270640 CATGAATTGAACCCTTTTAAAATGTGA 57.729 29.630 0.09 0.00 0.00 3.58
685 4947 9.844257 ATGAATTGAACCCTTTTAAAATGTGAA 57.156 25.926 0.09 0.90 0.00 3.18
686 4948 9.672673 TGAATTGAACCCTTTTAAAATGTGAAA 57.327 25.926 0.09 2.12 0.00 2.69
726 4988 9.627395 TTGAAAGAAAATAAAACGTTTGTGAGA 57.373 25.926 15.46 0.00 0.00 3.27
803 5066 8.870160 TTTGTGAACATTTTTCTAACATCCTG 57.130 30.769 0.00 0.00 0.00 3.86
804 5067 6.980593 TGTGAACATTTTTCTAACATCCTGG 58.019 36.000 0.00 0.00 0.00 4.45
867 5136 9.786224 ATTTTTAACGTAATGTGAATTTTTCGC 57.214 25.926 0.00 0.00 40.51 4.70
904 5181 3.744238 AAGACAAAAATGAAACCCCCG 57.256 42.857 0.00 0.00 0.00 5.73
921 5198 3.340928 CCCCGGAGAAAAACGAAACTAT 58.659 45.455 0.73 0.00 0.00 2.12
1024 5311 0.740737 GCTCTCTCACTCTCCTCTGC 59.259 60.000 0.00 0.00 0.00 4.26
1079 5370 4.742201 CCCAGGTGCGTCACTCCG 62.742 72.222 9.31 0.00 37.00 4.63
1636 8396 0.808453 CGGTATGCATTTCCCGACGT 60.808 55.000 21.03 0.00 43.01 4.34
1697 8460 4.680537 AGCTCCGGTGGGACGACT 62.681 66.667 0.00 0.00 37.43 4.18
1927 8690 2.009774 GTGCTCACTATGCGTGGATTT 58.990 47.619 0.00 0.00 43.94 2.17
2010 8773 0.389948 AAGTCGGTGAGATTCCGCAC 60.390 55.000 0.00 0.00 46.49 5.34
2045 8808 4.260784 CGATGATTGGTTCGGATCCTTTTC 60.261 45.833 10.75 0.00 0.00 2.29
2159 8922 2.723273 TGAAGATGACGAGGCTGTCTA 58.277 47.619 14.98 5.63 39.64 2.59
2163 8926 1.683917 GATGACGAGGCTGTCTATGGT 59.316 52.381 14.98 0.00 39.64 3.55
2168 8931 0.671251 GAGGCTGTCTATGGTCGAGG 59.329 60.000 0.00 0.00 0.00 4.63
2214 8977 1.744320 TACACGATAGCATGGCCGCT 61.744 55.000 10.20 10.20 46.26 5.52
2215 8978 2.280389 ACGATAGCATGGCCGCTG 60.280 61.111 14.75 8.02 43.68 5.18
2357 9128 8.804912 TTAAACCAAACAGTTCAGTTAACCTA 57.195 30.769 0.88 0.00 39.03 3.08
2359 9130 5.747342 ACCAAACAGTTCAGTTAACCTACA 58.253 37.500 0.88 0.00 39.03 2.74
2384 9155 9.012448 CAGCCATTCAAAATTTTCTTTTTGTTC 57.988 29.630 0.00 0.00 43.71 3.18
2564 9337 1.714794 CGAACCTGCTCTAGTTGTGG 58.285 55.000 0.00 0.00 0.00 4.17
2574 9347 6.480320 CCTGCTCTAGTTGTGGTTATATGTTC 59.520 42.308 0.00 0.00 0.00 3.18
2580 9353 5.681639 AGTTGTGGTTATATGTTCTAGCCC 58.318 41.667 0.00 0.00 0.00 5.19
2815 9591 4.783055 TGGTGCTTAACTTAAGGTTGTCA 58.217 39.130 7.53 0.00 38.75 3.58
2865 9641 1.273267 TGGCTCCTCTGGTACTGATGT 60.273 52.381 0.00 0.00 35.31 3.06
2919 9696 3.575256 TGGCATGCTCAATGAAGAAACTT 59.425 39.130 18.92 0.00 38.72 2.66
3146 10025 7.930325 TGAGATTTCTGAGATAGGTTATGCTTG 59.070 37.037 0.00 0.00 0.00 4.01
3336 10278 1.405526 GCCGTTATGAGGTGAAGCTGA 60.406 52.381 0.00 0.00 0.00 4.26
3407 10350 3.895820 TTTTGGGACATGCCGGGGG 62.896 63.158 2.18 0.00 39.30 5.40
3441 10384 2.290323 CCCTCAAGTTACTCTGGGGTTG 60.290 54.545 10.82 0.00 31.42 3.77
3499 10442 4.393062 ACAAATACACTGATTTCGCAGAGG 59.607 41.667 0.00 0.00 38.43 3.69
3579 10536 5.465056 TGCTATTTTTGTTAAAACTGCTGCC 59.535 36.000 0.00 0.00 36.15 4.85
3583 10540 3.552604 TTGTTAAAACTGCTGCCGATC 57.447 42.857 0.00 0.00 0.00 3.69
3588 10545 0.036732 AAACTGCTGCCGATCTTCCA 59.963 50.000 0.00 0.00 0.00 3.53
3614 10571 1.147817 AGGTGCCATTTCTCCCTTTGT 59.852 47.619 0.00 0.00 0.00 2.83
3620 10577 2.684881 CCATTTCTCCCTTTGTCATCGG 59.315 50.000 0.00 0.00 0.00 4.18
3637 10595 0.468648 CGGTGTTTCCCCCTCTATCC 59.531 60.000 0.00 0.00 0.00 2.59
3645 10603 1.145325 TCCCCCTCTATCCTCTCGAAC 59.855 57.143 0.00 0.00 0.00 3.95
3656 10614 4.585955 TCCTCTCGAACCTAATATGCAC 57.414 45.455 0.00 0.00 0.00 4.57
3665 10623 5.451381 CGAACCTAATATGCACTCACCACTA 60.451 44.000 0.00 0.00 0.00 2.74
3668 11042 5.366768 ACCTAATATGCACTCACCACTATGT 59.633 40.000 0.00 0.00 0.00 2.29
3677 11051 3.753272 ACTCACCACTATGTTCATTGCAC 59.247 43.478 0.00 0.00 0.00 4.57
3685 11059 7.340232 ACCACTATGTTCATTGCACATAATTCT 59.660 33.333 9.82 0.00 36.81 2.40
3688 11062 9.394767 ACTATGTTCATTGCACATAATTCTACA 57.605 29.630 9.82 0.00 36.81 2.74
3691 11065 8.054152 TGTTCATTGCACATAATTCTACATGT 57.946 30.769 2.69 2.69 35.79 3.21
3692 11066 8.183536 TGTTCATTGCACATAATTCTACATGTC 58.816 33.333 0.00 0.00 33.12 3.06
3733 11107 9.546428 AACAAGGAGAATTTAAATCCACAAAAG 57.454 29.630 0.10 0.00 35.45 2.27
3735 11109 9.933723 CAAGGAGAATTTAAATCCACAAAAGAT 57.066 29.630 0.10 0.00 35.45 2.40
3743 11117 8.810652 TTTAAATCCACAAAAGATAGTGCAAC 57.189 30.769 0.00 0.00 34.48 4.17
3744 11118 5.391312 AATCCACAAAAGATAGTGCAACC 57.609 39.130 0.00 0.00 37.80 3.77
3756 11130 6.860080 AGATAGTGCAACCAGAAAATGAATG 58.140 36.000 0.00 0.00 37.80 2.67
3774 11148 5.229423 TGAATGCATTTGTAAACAGCCTTC 58.771 37.500 14.33 0.00 32.66 3.46
3776 11150 2.881513 TGCATTTGTAAACAGCCTTCGA 59.118 40.909 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.989296 ACTATAAAGATGCTAGAGGTAGATCAT 57.011 33.333 0.00 0.00 0.00 2.45
4 5 9.237187 CACTATAAAGATGCTAGAGGTAGATCA 57.763 37.037 0.00 0.00 0.00 2.92
5 6 9.238368 ACACTATAAAGATGCTAGAGGTAGATC 57.762 37.037 0.00 0.00 0.00 2.75
6 7 9.594936 AACACTATAAAGATGCTAGAGGTAGAT 57.405 33.333 0.00 0.00 0.00 1.98
7 8 8.998277 AACACTATAAAGATGCTAGAGGTAGA 57.002 34.615 0.00 0.00 0.00 2.59
9 10 8.005388 AGGAACACTATAAAGATGCTAGAGGTA 58.995 37.037 0.00 0.00 0.00 3.08
10 11 6.841755 AGGAACACTATAAAGATGCTAGAGGT 59.158 38.462 0.00 0.00 0.00 3.85
13 14 6.042093 CCCAGGAACACTATAAAGATGCTAGA 59.958 42.308 0.00 0.00 0.00 2.43
14 15 6.183361 ACCCAGGAACACTATAAAGATGCTAG 60.183 42.308 0.00 0.00 0.00 3.42
15 16 5.665812 ACCCAGGAACACTATAAAGATGCTA 59.334 40.000 0.00 0.00 0.00 3.49
16 17 4.475016 ACCCAGGAACACTATAAAGATGCT 59.525 41.667 0.00 0.00 0.00 3.79
19 20 5.250774 ACACACCCAGGAACACTATAAAGAT 59.749 40.000 0.00 0.00 0.00 2.40
22 23 4.986054 ACACACCCAGGAACACTATAAA 57.014 40.909 0.00 0.00 0.00 1.40
23 24 5.544948 ACTTACACACCCAGGAACACTATAA 59.455 40.000 0.00 0.00 0.00 0.98
24 25 5.088730 ACTTACACACCCAGGAACACTATA 58.911 41.667 0.00 0.00 0.00 1.31
25 26 3.908103 ACTTACACACCCAGGAACACTAT 59.092 43.478 0.00 0.00 0.00 2.12
26 27 3.311091 ACTTACACACCCAGGAACACTA 58.689 45.455 0.00 0.00 0.00 2.74
28 29 2.632987 ACTTACACACCCAGGAACAC 57.367 50.000 0.00 0.00 0.00 3.32
29 30 3.039743 TGTACTTACACACCCAGGAACA 58.960 45.455 0.00 0.00 0.00 3.18
30 31 3.756933 TGTACTTACACACCCAGGAAC 57.243 47.619 0.00 0.00 0.00 3.62
31 32 3.558321 GCATGTACTTACACACCCAGGAA 60.558 47.826 0.00 0.00 39.30 3.36
32 33 2.027561 GCATGTACTTACACACCCAGGA 60.028 50.000 0.00 0.00 39.30 3.86
34 35 1.999735 CGCATGTACTTACACACCCAG 59.000 52.381 0.00 0.00 39.30 4.45
35 36 1.338294 CCGCATGTACTTACACACCCA 60.338 52.381 0.00 0.00 39.30 4.51
36 37 1.338389 ACCGCATGTACTTACACACCC 60.338 52.381 0.00 0.00 39.30 4.61
38 39 4.100707 TCTACCGCATGTACTTACACAC 57.899 45.455 0.00 0.00 39.30 3.82
39 40 4.994907 ATCTACCGCATGTACTTACACA 57.005 40.909 0.00 0.00 39.30 3.72
40 41 6.657836 AAAATCTACCGCATGTACTTACAC 57.342 37.500 0.00 0.00 39.30 2.90
64 65 7.501892 AGTTGGGGAACGTAGTACAAAATAAAA 59.498 33.333 0.38 0.00 45.00 1.52
65 66 6.997476 AGTTGGGGAACGTAGTACAAAATAAA 59.003 34.615 0.38 0.00 45.00 1.40
66 67 6.427547 CAGTTGGGGAACGTAGTACAAAATAA 59.572 38.462 0.38 0.00 45.00 1.40
67 68 5.933463 CAGTTGGGGAACGTAGTACAAAATA 59.067 40.000 0.38 0.00 45.00 1.40
68 69 4.758165 CAGTTGGGGAACGTAGTACAAAAT 59.242 41.667 0.38 0.00 45.00 1.82
69 70 4.128643 CAGTTGGGGAACGTAGTACAAAA 58.871 43.478 0.38 0.00 45.00 2.44
70 71 3.134442 ACAGTTGGGGAACGTAGTACAAA 59.866 43.478 0.38 0.00 45.00 2.83
71 72 2.699846 ACAGTTGGGGAACGTAGTACAA 59.300 45.455 0.38 0.00 45.00 2.41
72 73 2.036217 CACAGTTGGGGAACGTAGTACA 59.964 50.000 0.38 0.00 45.00 2.90
73 74 2.611224 CCACAGTTGGGGAACGTAGTAC 60.611 54.545 0.00 0.00 42.67 2.73
74 75 1.619827 CCACAGTTGGGGAACGTAGTA 59.380 52.381 0.00 0.00 42.67 1.82
75 76 0.395312 CCACAGTTGGGGAACGTAGT 59.605 55.000 0.00 0.00 42.67 2.73
76 77 0.953960 GCCACAGTTGGGGAACGTAG 60.954 60.000 4.17 0.00 42.67 3.51
77 78 1.071814 GCCACAGTTGGGGAACGTA 59.928 57.895 4.17 0.00 42.67 3.57
78 79 2.203294 GCCACAGTTGGGGAACGT 60.203 61.111 4.17 0.00 42.67 3.99
79 80 1.826054 TTGCCACAGTTGGGGAACG 60.826 57.895 4.17 0.00 42.67 3.95
80 81 1.739667 GTTGCCACAGTTGGGGAAC 59.260 57.895 4.17 6.45 46.97 3.62
81 82 0.105760 ATGTTGCCACAGTTGGGGAA 60.106 50.000 4.17 0.00 42.67 3.97
82 83 0.539438 GATGTTGCCACAGTTGGGGA 60.539 55.000 4.17 0.00 42.67 4.81
83 84 1.535204 GGATGTTGCCACAGTTGGGG 61.535 60.000 0.00 0.00 44.15 4.96
84 85 0.827089 TGGATGTTGCCACAGTTGGG 60.827 55.000 0.00 0.00 44.15 4.12
86 87 1.887854 TCATGGATGTTGCCACAGTTG 59.112 47.619 0.00 0.00 41.56 3.16
87 88 2.165167 CTCATGGATGTTGCCACAGTT 58.835 47.619 0.00 0.00 41.56 3.16
88 89 1.352017 TCTCATGGATGTTGCCACAGT 59.648 47.619 0.00 0.00 41.56 3.55
89 90 2.118313 TCTCATGGATGTTGCCACAG 57.882 50.000 0.00 0.00 41.56 3.66
91 92 2.440409 AGTTCTCATGGATGTTGCCAC 58.560 47.619 0.00 0.00 41.56 5.01
92 93 2.885135 AGTTCTCATGGATGTTGCCA 57.115 45.000 0.00 0.00 43.23 4.92
93 94 3.118261 TCCTAGTTCTCATGGATGTTGCC 60.118 47.826 0.00 0.00 0.00 4.52
94 95 3.873952 GTCCTAGTTCTCATGGATGTTGC 59.126 47.826 0.00 0.00 0.00 4.17
135 4155 3.406361 CGAGCACAGTCGTGGCAC 61.406 66.667 7.79 7.79 43.81 5.01
138 4158 4.742201 CCCCGAGCACAGTCGTGG 62.742 72.222 0.00 0.00 43.81 4.94
170 4190 1.318380 CATCCTGGACCCTACCCCT 59.682 63.158 0.00 0.00 0.00 4.79
182 4202 1.522668 TGAACTTGTTCGCCATCCTG 58.477 50.000 8.68 0.00 0.00 3.86
187 4207 1.452145 GCCCTTGAACTTGTTCGCCA 61.452 55.000 8.68 0.00 0.00 5.69
189 4209 1.082104 CGCCCTTGAACTTGTTCGC 60.082 57.895 8.68 5.35 0.00 4.70
190 4210 0.041312 CACGCCCTTGAACTTGTTCG 60.041 55.000 8.68 0.00 0.00 3.95
220 4240 4.511246 CCCCATCATGCGCCACCT 62.511 66.667 4.18 0.00 0.00 4.00
248 4268 6.882656 TCTTCTCCTCATTTCTATTGTCCAG 58.117 40.000 0.00 0.00 0.00 3.86
252 4272 8.160106 ACTTGTTCTTCTCCTCATTTCTATTGT 58.840 33.333 0.00 0.00 0.00 2.71
258 4278 5.009010 TGCAACTTGTTCTTCTCCTCATTTC 59.991 40.000 0.00 0.00 0.00 2.17
260 4280 4.464008 TGCAACTTGTTCTTCTCCTCATT 58.536 39.130 0.00 0.00 0.00 2.57
277 4297 1.270252 CCCACCAAATCAACCTGCAAC 60.270 52.381 0.00 0.00 0.00 4.17
282 4302 1.203050 CCACTCCCACCAAATCAACCT 60.203 52.381 0.00 0.00 0.00 3.50
286 4306 1.073763 CACTCCACTCCCACCAAATCA 59.926 52.381 0.00 0.00 0.00 2.57
301 4321 2.171635 GGCAAACCGACATCACTCC 58.828 57.895 0.00 0.00 0.00 3.85
376 4396 2.926242 TCTGGACCGTCCCAACCC 60.926 66.667 15.24 0.00 35.03 4.11
387 4407 4.559153 CCATTTGTTTGGATTGTCTGGAC 58.441 43.478 0.00 0.00 39.25 4.02
388 4408 3.577848 CCCATTTGTTTGGATTGTCTGGA 59.422 43.478 0.00 0.00 39.25 3.86
389 4409 3.577848 TCCCATTTGTTTGGATTGTCTGG 59.422 43.478 0.00 0.00 39.25 3.86
390 4410 4.523943 TCTCCCATTTGTTTGGATTGTCTG 59.476 41.667 0.00 0.00 39.25 3.51
399 4419 3.244181 CCCAAACCTCTCCCATTTGTTTG 60.244 47.826 0.00 0.00 43.21 2.93
409 4429 0.328592 GGACCTTCCCAAACCTCTCC 59.671 60.000 0.00 0.00 0.00 3.71
410 4430 3.959433 GGACCTTCCCAAACCTCTC 57.041 57.895 0.00 0.00 0.00 3.20
435 4455 0.105453 TGCCCAGCCTAAAAACCCAA 60.105 50.000 0.00 0.00 0.00 4.12
472 4492 4.457834 AAGAGTGTCAAATAGGAGGTCG 57.542 45.455 0.00 0.00 0.00 4.79
482 4502 4.131649 TCTGACGGAAAAGAGTGTCAAA 57.868 40.909 0.00 0.00 40.50 2.69
492 4512 3.447586 CACCTCTCCTATCTGACGGAAAA 59.552 47.826 0.00 0.00 0.00 2.29
496 4516 1.678627 CACACCTCTCCTATCTGACGG 59.321 57.143 0.00 0.00 0.00 4.79
537 4557 1.678598 TAGTGCGGTAATGGGTCGGG 61.679 60.000 0.00 0.00 0.00 5.14
542 4562 2.037144 AGTACCTAGTGCGGTAATGGG 58.963 52.381 0.00 0.00 40.99 4.00
558 4578 2.198406 TCACGTGAGTTGTTGCAGTAC 58.802 47.619 15.76 0.00 46.40 2.73
564 4584 2.095853 ACTTGCTTCACGTGAGTTGTTG 59.904 45.455 19.11 10.94 46.40 3.33
567 4587 1.933181 TCACTTGCTTCACGTGAGTTG 59.067 47.619 19.11 13.66 46.40 3.16
568 4588 2.309528 TCACTTGCTTCACGTGAGTT 57.690 45.000 19.11 0.00 46.40 3.01
618 4879 8.256605 TGTTCTCTGGAAAATCAATGAAAACAA 58.743 29.630 0.00 0.00 32.81 2.83
758 5020 9.790389 TCACAAAAGTTTAAAATATGTTCACGT 57.210 25.926 4.77 0.00 0.00 4.49
778 5040 7.925483 CCAGGATGTTAGAAAAATGTTCACAAA 59.075 33.333 0.00 0.00 0.00 2.83
848 5111 6.638873 TCATTTGCGAAAAATTCACATTACGT 59.361 30.769 0.00 0.00 0.00 3.57
849 5112 7.032168 TCATTTGCGAAAAATTCACATTACG 57.968 32.000 0.00 0.00 0.00 3.18
850 5113 9.810231 AAATCATTTGCGAAAAATTCACATTAC 57.190 25.926 0.00 0.00 0.00 1.89
879 5148 6.708502 CGGGGGTTTCATTTTTGTCTTTAAAT 59.291 34.615 0.00 0.00 0.00 1.40
894 5171 1.694844 GTTTTTCTCCGGGGGTTTCA 58.305 50.000 0.00 0.00 0.00 2.69
899 5176 0.594602 GTTTCGTTTTTCTCCGGGGG 59.405 55.000 0.00 0.00 0.00 5.40
904 5181 7.361542 GGAAGGGTTATAGTTTCGTTTTTCTCC 60.362 40.741 0.00 0.00 0.00 3.71
921 5198 2.735259 AGGAGGTTCTGGAAGGGTTA 57.265 50.000 0.00 0.00 0.00 2.85
964 5243 3.004862 GGCATTCATTTTTGGGAAGCTG 58.995 45.455 0.00 0.00 0.00 4.24
1024 5311 0.920664 TAATGTGTCGAGCAATCGCG 59.079 50.000 0.00 0.00 45.49 5.87
1636 8396 1.071987 CAGCTCTGTGGTTCCAGCA 59.928 57.895 0.00 0.00 34.08 4.41
1927 8690 0.953471 CGACCCAAACCTCGATGCAA 60.953 55.000 0.00 0.00 31.24 4.08
2010 8773 2.109538 AATCATCGCTTGCATCGCCG 62.110 55.000 4.25 0.00 0.00 6.46
2018 8781 1.368641 TCCGAACCAATCATCGCTTG 58.631 50.000 0.00 0.00 37.73 4.01
2045 8808 1.153369 CGCCCTGTGGAGTATGGTG 60.153 63.158 0.00 0.00 0.00 4.17
2077 8840 0.107017 AGAACACAACACCAGCAGCT 60.107 50.000 0.00 0.00 0.00 4.24
2105 8868 3.698539 TGAATGGAGAACAAACAACTGCA 59.301 39.130 0.00 0.00 36.55 4.41
2114 8877 5.248640 GGTCTCAAGATGAATGGAGAACAA 58.751 41.667 0.00 0.00 42.32 2.83
2159 8922 2.311688 GACGGGCAATCCTCGACCAT 62.312 60.000 0.00 0.00 32.66 3.55
2163 8926 2.423898 GGAGACGGGCAATCCTCGA 61.424 63.158 0.00 0.00 32.66 4.04
2384 9155 3.477899 GAAGAATTCACCCAAGAAGCG 57.522 47.619 8.44 0.00 46.62 4.68
2564 9337 6.276832 TGATACGGGGCTAGAACATATAAC 57.723 41.667 0.00 0.00 0.00 1.89
2574 9347 6.282199 ACTAATTACATGATACGGGGCTAG 57.718 41.667 0.00 0.00 0.00 3.42
2580 9353 6.844696 AGCACAACTAATTACATGATACGG 57.155 37.500 0.00 0.00 0.00 4.02
2758 9534 5.758296 GCCGGATGAACTGATACAGAAATTA 59.242 40.000 5.05 0.00 35.18 1.40
2815 9591 1.496429 CCCCAGCCAGAATTGTATCCT 59.504 52.381 0.00 0.00 0.00 3.24
2865 9641 2.959030 AGTAGACTATCCAGCATTCGCA 59.041 45.455 0.00 0.00 42.27 5.10
2919 9696 7.175104 ACATTAGGCCAAATTCTTCAGTCTTA 58.825 34.615 5.01 0.00 0.00 2.10
3336 10278 7.294017 AGACCAATTGACAGAACAAATGATT 57.706 32.000 7.12 0.00 33.95 2.57
3407 10350 2.360475 GAGGGTTGAGGCTGCCAC 60.360 66.667 22.65 15.93 0.00 5.01
3441 10384 5.768164 TCCAACCCAGATAAACTCAAGAAAC 59.232 40.000 0.00 0.00 0.00 2.78
3499 10442 7.802738 TGCATACATAAATAAGGATAACGTGC 58.197 34.615 0.00 0.00 0.00 5.34
3574 10531 1.602311 ATCATTGGAAGATCGGCAGC 58.398 50.000 0.00 0.00 0.00 5.25
3579 10536 3.070018 GGCACCTATCATTGGAAGATCG 58.930 50.000 0.00 0.00 0.00 3.69
3583 10540 4.891756 AGAAATGGCACCTATCATTGGAAG 59.108 41.667 0.00 0.00 34.28 3.46
3588 10545 3.464833 AGGGAGAAATGGCACCTATCATT 59.535 43.478 0.00 0.00 35.37 2.57
3620 10577 2.701423 GAGAGGATAGAGGGGGAAACAC 59.299 54.545 0.00 0.00 0.00 3.32
3637 10595 4.979197 GTGAGTGCATATTAGGTTCGAGAG 59.021 45.833 0.00 0.00 0.00 3.20
3645 10603 5.858381 ACATAGTGGTGAGTGCATATTAGG 58.142 41.667 0.00 0.00 0.00 2.69
3656 10614 3.752747 TGTGCAATGAACATAGTGGTGAG 59.247 43.478 0.00 0.00 0.00 3.51
3665 10623 8.689061 ACATGTAGAATTATGTGCAATGAACAT 58.311 29.630 12.10 12.10 41.14 2.71
3668 11042 8.510243 AGACATGTAGAATTATGTGCAATGAA 57.490 30.769 0.00 0.00 37.63 2.57
3685 11059 9.990360 TTGTTTTCATACTTCAGTAGACATGTA 57.010 29.630 0.00 0.00 33.52 2.29
3688 11062 8.375506 TCCTTGTTTTCATACTTCAGTAGACAT 58.624 33.333 0.00 0.00 33.52 3.06
3690 11064 8.088981 TCTCCTTGTTTTCATACTTCAGTAGAC 58.911 37.037 0.00 0.00 33.52 2.59
3691 11065 8.190326 TCTCCTTGTTTTCATACTTCAGTAGA 57.810 34.615 0.00 0.00 33.52 2.59
3692 11066 8.833231 TTCTCCTTGTTTTCATACTTCAGTAG 57.167 34.615 0.00 0.00 33.52 2.57
3721 11095 5.304101 TGGTTGCACTATCTTTTGTGGATTT 59.696 36.000 0.00 0.00 34.69 2.17
3725 11099 3.820467 TCTGGTTGCACTATCTTTTGTGG 59.180 43.478 0.00 0.00 34.99 4.17
3726 11100 5.437289 TTCTGGTTGCACTATCTTTTGTG 57.563 39.130 0.00 0.00 37.26 3.33
3733 11107 5.517770 GCATTCATTTTCTGGTTGCACTATC 59.482 40.000 0.00 0.00 34.92 2.08
3735 11109 4.280425 TGCATTCATTTTCTGGTTGCACTA 59.720 37.500 0.00 0.00 37.86 2.74
3756 11130 3.552604 TCGAAGGCTGTTTACAAATGC 57.447 42.857 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.