Multiple sequence alignment - TraesCS2D01G229900

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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 TraesCS2D01G229900 chr2D 100.000 4222 0 0 1 4222 200772865 200777086 0.000000e+00 7797.0
1 TraesCS2D01G229900 chr2D 89.751 361 16 8 1986 2328 200774366 200774723 3.870000e-120 442.0
2 TraesCS2D01G229900 chr2D 89.751 361 16 8 1502 1859 200774850 200775192 3.870000e-120 442.0
3 TraesCS2D01G229900 chr2D 96.774 62 2 0 2328 2389 200774791 200774852 2.080000e-18 104.0
4 TraesCS2D01G229900 chr2D 96.774 62 2 0 1927 1988 200775192 200775253 2.080000e-18 104.0
5 TraesCS2D01G229900 chr2B 94.272 2898 58 26 607 3455 377098442 377101280 0.000000e+00 4333.0
6 TraesCS2D01G229900 chr2B 91.602 512 21 3 3711 4222 377101575 377102064 0.000000e+00 688.0
7 TraesCS2D01G229900 chr2B 94.966 437 19 2 1 434 377053395 377053831 0.000000e+00 682.0
8 TraesCS2D01G229900 chr2B 93.417 319 18 2 1502 1819 377099822 377100138 1.780000e-128 470.0
9 TraesCS2D01G229900 chr2B 90.808 359 17 5 1986 2328 377099339 377099697 2.300000e-127 466.0
10 TraesCS2D01G229900 chr2B 84.302 172 8 4 438 607 377098260 377098414 2.630000e-32 150.0
11 TraesCS2D01G229900 chr2B 83.007 153 7 5 3539 3691 377101307 377101440 2.060000e-23 121.0
12 TraesCS2D01G229900 chr2B 96.774 62 2 0 2328 2389 377099763 377099824 2.080000e-18 104.0
13 TraesCS2D01G229900 chr2B 96.774 62 2 0 1927 1988 377100154 377100215 2.080000e-18 104.0
14 TraesCS2D01G229900 chr2A 90.605 958 53 18 605 1556 221199224 221200150 0.000000e+00 1236.0
15 TraesCS2D01G229900 chr2A 94.993 739 20 6 2328 3063 221200566 221201290 0.000000e+00 1144.0
16 TraesCS2D01G229900 chr2A 93.924 576 14 11 3060 3620 221201412 221201981 0.000000e+00 850.0
17 TraesCS2D01G229900 chr2A 90.300 433 35 2 1 433 221196317 221196742 1.030000e-155 560.0
18 TraesCS2D01G229900 chr2A 91.373 255 18 3 1736 1988 221200375 221200627 3.120000e-91 346.0
19 TraesCS2D01G229900 chr2A 96.386 166 4 1 4057 4222 221202320 221202483 5.380000e-69 272.0
20 TraesCS2D01G229900 chr2A 94.444 126 6 1 2204 2328 221200375 221200500 4.310000e-45 193.0
21 TraesCS2D01G229900 chr2A 88.272 162 7 5 1553 1711 221200230 221200382 2.590000e-42 183.0
22 TraesCS2D01G229900 chr2A 83.871 155 13 7 2037 2181 221200230 221200382 2.050000e-28 137.0
23 TraesCS2D01G229900 chr2A 83.784 74 1 6 534 607 221199135 221199197 4.560000e-05 60.2
24 TraesCS2D01G229900 chr6B 98.305 59 1 0 2392 2450 289381851 289381909 2.080000e-18 104.0
25 TraesCS2D01G229900 chr6B 100.000 45 0 0 993 1037 289381807 289381851 2.710000e-12 84.2
26 TraesCS2D01G229900 chr6B 94.444 54 3 0 2529 2582 289381903 289381956 2.710000e-12 84.2
27 TraesCS2D01G229900 chr1B 96.721 61 2 0 2390 2450 439169491 439169551 7.470000e-18 102.0
28 TraesCS2D01G229900 chr1B 96.721 61 2 0 2529 2589 439169545 439169605 7.470000e-18 102.0
29 TraesCS2D01G229900 chr1B 100.000 40 0 0 993 1032 439169449 439169488 1.630000e-09 75.0


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 TraesCS2D01G229900 chr2D 200772865 200777086 4221 False 1777.80 7797 94.6100 1 4222 5 chr2D.!!$F1 4221
1 TraesCS2D01G229900 chr2B 377098260 377102064 3804 False 804.50 4333 91.3695 438 4222 8 chr2B.!!$F2 3784
2 TraesCS2D01G229900 chr2A 221196317 221202483 6166 False 498.12 1236 90.7952 1 4222 10 chr2A.!!$F1 4221

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
840 3168 0.315568 CTCGATCAATCTCGTCCCCC 59.684 60.000 0.0 0.0 39.62 5.40 F
1705 4123 1.398390 CGCCTTCTGTCTTATTGGTGC 59.602 52.381 0.0 0.0 0.00 5.01 F
2169 4605 2.084546 GTTTGGCGCCTTCTGTCTTAT 58.915 47.619 29.7 0.0 0.00 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 4746 0.100503 AGCAGTGCAAAACGGAACAC 59.899 50.0 19.2 0.0 0.0 3.32 R
3121 5688 0.250252 TGACATCAACGAAGCTGCCA 60.250 50.0 0.0 0.0 0.0 4.92 R
3252 5823 0.670546 CGTCGCAACCTGAACATCCT 60.671 55.0 0.0 0.0 0.0 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
48 49 5.106555 CCACTAGGAGTTGTGTGCTATTTTG 60.107 44.000 0.00 0.00 36.89 2.44
51 52 3.891366 AGGAGTTGTGTGCTATTTTGCTT 59.109 39.130 0.00 0.00 0.00 3.91
83 84 5.810587 TGTAACCGCTTATGAATCAAGAGAC 59.189 40.000 0.00 0.00 0.00 3.36
84 85 3.448686 ACCGCTTATGAATCAAGAGACG 58.551 45.455 0.00 0.00 0.00 4.18
103 104 5.529791 AGACGGGAAGATCAATGTTATACG 58.470 41.667 0.00 0.00 0.00 3.06
105 106 5.287226 ACGGGAAGATCAATGTTATACGAC 58.713 41.667 0.00 0.00 0.00 4.34
114 115 8.647796 AGATCAATGTTATACGACCTTTCCATA 58.352 33.333 0.00 0.00 0.00 2.74
155 156 8.091385 TGAATCAAATCATCCATTAGATCACG 57.909 34.615 0.00 0.00 30.59 4.35
157 158 7.664082 ATCAAATCATCCATTAGATCACGTC 57.336 36.000 0.00 0.00 30.59 4.34
168 169 6.585702 CCATTAGATCACGTCATTTTGCAAAA 59.414 34.615 25.76 25.76 0.00 2.44
176 177 3.061831 CGTCATTTTGCAAAACAGCACAA 59.938 39.130 26.05 2.38 45.61 3.33
179 180 5.678047 GTCATTTTGCAAAACAGCACAATTC 59.322 36.000 26.05 5.32 45.61 2.17
227 228 1.867233 GAACATTGTCGTGTGCAGAGT 59.133 47.619 0.00 0.00 31.49 3.24
231 232 2.882927 TTGTCGTGTGCAGAGTAGTT 57.117 45.000 0.00 0.00 0.00 2.24
340 341 2.588856 ATACCCTTTGCTCGCGGGAC 62.589 60.000 12.03 0.62 40.55 4.46
360 361 0.527817 CCGAAGGCACCGAGTGATAC 60.528 60.000 8.04 0.00 46.14 2.24
371 372 2.889045 CCGAGTGATACGATTTCCCCTA 59.111 50.000 0.00 0.00 0.00 3.53
378 379 2.544844 ACGATTTCCCCTACCTCTCA 57.455 50.000 0.00 0.00 0.00 3.27
402 403 4.899239 CCGCCATCAGTCCGCCTC 62.899 72.222 0.00 0.00 0.00 4.70
408 409 0.803768 CATCAGTCCGCCTCGTCTTG 60.804 60.000 0.00 0.00 0.00 3.02
413 414 0.454600 GTCCGCCTCGTCTTGTATGA 59.545 55.000 0.00 0.00 0.00 2.15
427 428 4.840680 TCTTGTATGATCCTAGGACCATGG 59.159 45.833 26.83 11.19 29.83 3.66
446 447 1.005450 GGAAACACATCCCTAAGGCCA 59.995 52.381 5.01 0.00 33.05 5.36
463 464 1.369625 CCAGGACTAATGGACGCAAC 58.630 55.000 0.00 0.00 40.51 4.17
500 2557 2.796383 CGAGACGACTGATTCACATCCC 60.796 54.545 0.00 0.00 0.00 3.85
502 2559 1.482593 GACGACTGATTCACATCCCCT 59.517 52.381 0.00 0.00 0.00 4.79
508 2565 2.981784 CTGATTCACATCCCCTATCCCA 59.018 50.000 0.00 0.00 0.00 4.37
509 2566 3.590630 CTGATTCACATCCCCTATCCCAT 59.409 47.826 0.00 0.00 0.00 4.00
510 2567 3.331591 TGATTCACATCCCCTATCCCATG 59.668 47.826 0.00 0.00 0.00 3.66
514 2571 2.986019 CACATCCCCTATCCCATGGTAA 59.014 50.000 11.73 0.00 0.00 2.85
637 2964 2.674084 GCGAAACCGTGTGGCCTAC 61.674 63.158 3.32 1.99 39.70 3.18
840 3168 0.315568 CTCGATCAATCTCGTCCCCC 59.684 60.000 0.00 0.00 39.62 5.40
912 3240 2.923020 CGGCCAAATTTCGGAGAATTTG 59.077 45.455 19.86 19.86 45.90 2.32
1052 3381 1.425448 CCTGGGTTTGTTCCTTCTCCT 59.575 52.381 0.00 0.00 0.00 3.69
1053 3382 2.508526 CTGGGTTTGTTCCTTCTCCTG 58.491 52.381 0.00 0.00 0.00 3.86
1057 3386 2.576615 GTTTGTTCCTTCTCCTGTGCT 58.423 47.619 0.00 0.00 0.00 4.40
1073 3402 3.706594 CTGTGCTCCTCTCCCTGTTAATA 59.293 47.826 0.00 0.00 0.00 0.98
1306 3636 3.629855 TCCCATATGCCGTTGTTACATTG 59.370 43.478 0.00 0.00 0.00 2.82
1309 3639 4.142491 CCATATGCCGTTGTTACATTGTGT 60.142 41.667 0.00 0.00 0.00 3.72
1559 3892 8.484641 TCATCTTGCAATAGAGTTTACTTCTG 57.515 34.615 0.00 0.00 0.00 3.02
1560 3893 8.314021 TCATCTTGCAATAGAGTTTACTTCTGA 58.686 33.333 0.00 0.00 0.00 3.27
1561 3894 8.602328 CATCTTGCAATAGAGTTTACTTCTGAG 58.398 37.037 0.00 0.00 0.00 3.35
1562 3895 7.896811 TCTTGCAATAGAGTTTACTTCTGAGA 58.103 34.615 0.00 0.00 0.00 3.27
1563 3896 7.815068 TCTTGCAATAGAGTTTACTTCTGAGAC 59.185 37.037 0.00 0.00 0.00 3.36
1624 4042 8.417106 TGGATGCTTTTGTACAATTCTTGTTAA 58.583 29.630 9.56 0.00 42.22 2.01
1651 4069 8.561738 TCAGGTTCATAAGATTCTGTTTTACC 57.438 34.615 0.00 0.00 0.00 2.85
1705 4123 1.398390 CGCCTTCTGTCTTATTGGTGC 59.602 52.381 0.00 0.00 0.00 5.01
1718 4136 9.936759 TGTCTTATTGGTGCGATTGAATATATA 57.063 29.630 0.00 0.00 0.00 0.86
1873 4293 2.168106 TGCACTGGTTGATGCTTTTGTT 59.832 40.909 0.00 0.00 42.55 2.83
1874 4294 3.382865 TGCACTGGTTGATGCTTTTGTTA 59.617 39.130 0.00 0.00 42.55 2.41
1914 4334 8.598041 ACTGTCTCCACTAAAAACTCTAATGAT 58.402 33.333 0.00 0.00 0.00 2.45
1915 4335 9.442047 CTGTCTCCACTAAAAACTCTAATGATT 57.558 33.333 0.00 0.00 0.00 2.57
1964 4384 7.672983 TCCAGTGTCAAGTTATTTTCATCTC 57.327 36.000 0.00 0.00 0.00 2.75
2097 4517 3.648339 TGCTTTCTGGATGCTTTTGTC 57.352 42.857 0.00 0.00 0.00 3.18
2105 4525 6.748333 TCTGGATGCTTTTGTCTAATTCTG 57.252 37.500 0.00 0.00 0.00 3.02
2115 4535 8.178313 GCTTTTGTCTAATTCTGGTTAGATCAC 58.822 37.037 0.00 0.00 41.34 3.06
2116 4536 7.827819 TTTGTCTAATTCTGGTTAGATCACG 57.172 36.000 0.00 0.00 41.34 4.35
2155 4591 3.011949 ACAATGTTGTGATCGTTTGGC 57.988 42.857 0.00 0.00 40.49 4.52
2169 4605 2.084546 GTTTGGCGCCTTCTGTCTTAT 58.915 47.619 29.70 0.00 0.00 1.73
2237 4673 4.108501 AGTATTCCCCCGTTTTTGAACT 57.891 40.909 0.00 0.00 0.00 3.01
2254 4690 8.810990 TTTTGAACTGACCTTAGGTTTAAGAA 57.189 30.769 4.99 0.00 38.88 2.52
2288 4724 8.695456 ACAAATGGTCTCAAGTATTTCTTTTGT 58.305 29.630 0.00 0.00 33.63 2.83
2289 4725 9.533253 CAAATGGTCTCAAGTATTTCTTTTGTT 57.467 29.630 0.00 0.00 33.63 2.83
2293 4729 8.339714 TGGTCTCAAGTATTTCTTTTGTTAACG 58.660 33.333 0.26 0.00 33.63 3.18
2294 4730 8.553696 GGTCTCAAGTATTTCTTTTGTTAACGA 58.446 33.333 0.26 0.00 33.63 3.85
2297 4733 9.878599 CTCAAGTATTTCTTTTGTTAACGATGT 57.121 29.630 0.26 0.00 33.63 3.06
2307 4743 9.917129 TCTTTTGTTAACGATGTACTATCTTGA 57.083 29.630 0.26 0.00 0.00 3.02
2309 4745 9.701098 TTTTGTTAACGATGTACTATCTTGAGT 57.299 29.630 0.26 0.00 0.00 3.41
2310 4746 8.683550 TTGTTAACGATGTACTATCTTGAGTG 57.316 34.615 0.26 0.00 0.00 3.51
2311 4747 7.823665 TGTTAACGATGTACTATCTTGAGTGT 58.176 34.615 0.26 0.00 0.00 3.55
2649 5088 5.516339 ACGAGCAGTTCTTTTCATTGTTTTG 59.484 36.000 0.00 0.00 0.00 2.44
2727 5166 7.337436 ACTTGCCAATATTTCATTTCCATTTGG 59.663 33.333 0.00 0.00 36.34 3.28
2772 5211 5.769662 TGTTATGTTTGGATGTGCTCTCTTT 59.230 36.000 0.00 0.00 0.00 2.52
2867 5306 7.912250 GCTGTTCATGTTTGGAATCTGTATTAG 59.088 37.037 0.00 0.00 0.00 1.73
2869 5308 9.952030 TGTTCATGTTTGGAATCTGTATTAGTA 57.048 29.630 0.00 0.00 0.00 1.82
3215 5782 1.627550 GCGAGAACACTTTCGGCTCC 61.628 60.000 0.00 0.00 36.78 4.70
3251 5822 3.181501 GCGCTGCCACTGTAAATAAATGA 60.182 43.478 0.00 0.00 0.00 2.57
3252 5823 4.674101 GCGCTGCCACTGTAAATAAATGAA 60.674 41.667 0.00 0.00 0.00 2.57
3253 5824 5.030295 CGCTGCCACTGTAAATAAATGAAG 58.970 41.667 0.00 0.00 0.00 3.02
3310 5881 2.158755 ACTAGTATGCTGGTGGATTGCC 60.159 50.000 0.00 0.00 35.02 4.52
3378 5949 3.487120 AGAACGGCCTGTAAAACTCTT 57.513 42.857 0.00 0.00 0.00 2.85
3379 5950 4.612264 AGAACGGCCTGTAAAACTCTTA 57.388 40.909 0.00 0.00 0.00 2.10
3380 5951 5.161943 AGAACGGCCTGTAAAACTCTTAT 57.838 39.130 0.00 0.00 0.00 1.73
3381 5952 5.176592 AGAACGGCCTGTAAAACTCTTATC 58.823 41.667 0.00 0.00 0.00 1.75
3385 5956 6.885922 ACGGCCTGTAAAACTCTTATCTATT 58.114 36.000 0.00 0.00 0.00 1.73
3386 5957 8.015185 ACGGCCTGTAAAACTCTTATCTATTA 57.985 34.615 0.00 0.00 0.00 0.98
3387 5958 7.924947 ACGGCCTGTAAAACTCTTATCTATTAC 59.075 37.037 0.00 0.00 0.00 1.89
3440 6035 6.272318 TGGGATGATTTCAATCGCAAATTAC 58.728 36.000 1.20 0.00 38.26 1.89
3623 6218 2.359478 ATGTTTCCGGCGACACCC 60.359 61.111 9.30 0.00 33.26 4.61
3703 6539 1.154016 CGTACCGTGAGCCTGTCTG 60.154 63.158 0.00 0.00 0.00 3.51
3709 6545 3.305516 TGAGCCTGTCTGCGCTGA 61.306 61.111 13.46 13.46 34.84 4.26
3710 6546 2.813042 GAGCCTGTCTGCGCTGAC 60.813 66.667 32.92 32.92 34.84 3.51
3713 6549 2.356313 CCTGTCTGCGCTGACGTT 60.356 61.111 33.02 0.00 42.83 3.99
3764 6600 1.459450 GCCGGGCAGATACAGAAAAA 58.541 50.000 15.62 0.00 0.00 1.94
3794 6630 1.359459 GCTAAGAAACCGTGGAGGCG 61.359 60.000 0.00 0.00 46.52 5.52
3811 6647 3.000727 AGGCGCATAGTAAGTGTTTGAC 58.999 45.455 10.83 0.00 0.00 3.18
3828 6664 1.594833 ACGAAGTGGAGGCGCATAA 59.405 52.632 10.83 0.00 42.51 1.90
3830 6666 1.299541 CGAAGTGGAGGCGCATAATT 58.700 50.000 10.83 0.00 0.00 1.40
3831 6667 2.159014 ACGAAGTGGAGGCGCATAATTA 60.159 45.455 10.83 0.00 42.51 1.40
3842 6678 4.574828 AGGCGCATAATTAAAGTGTTCGAT 59.425 37.500 10.83 0.00 0.00 3.59
3843 6679 4.670621 GGCGCATAATTAAAGTGTTCGATG 59.329 41.667 10.83 0.00 0.00 3.84
3852 6688 7.745022 ATTAAAGTGTTCGATGAAATGCATG 57.255 32.000 0.00 0.00 37.34 4.06
3874 6710 8.578769 GCATGAGCTAAATTTTCTTTTACTTCG 58.421 33.333 0.00 0.00 37.91 3.79
3887 6723 6.819284 TCTTTTACTTCGTTAACTTCAGGGA 58.181 36.000 3.71 0.00 0.00 4.20
3889 6725 7.769970 TCTTTTACTTCGTTAACTTCAGGGAAA 59.230 33.333 3.71 0.00 0.00 3.13
3908 6744 2.450609 ACGGCTAGACACGACAAAAT 57.549 45.000 0.00 0.00 0.00 1.82
3959 6795 8.430063 CGACGTTTACTCTGCTAAAATTTAGAA 58.570 33.333 16.22 5.10 0.00 2.10
3960 6796 9.742552 GACGTTTACTCTGCTAAAATTTAGAAG 57.257 33.333 16.22 14.76 0.00 2.85
3965 6801 7.778470 ACTCTGCTAAAATTTAGAAGATCGG 57.222 36.000 20.48 13.20 29.35 4.18
3969 6805 7.653713 TCTGCTAAAATTTAGAAGATCGGCTAG 59.346 37.037 17.28 2.51 0.00 3.42
4017 6853 3.190118 ACTTCACTAGGGTTTACTCGACG 59.810 47.826 0.00 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.923017 AGCAAAATAGCACACAACTCC 57.077 42.857 0.00 0.00 36.85 3.85
48 49 0.733150 GCGGTTACATTGGGAGAAGC 59.267 55.000 0.00 0.00 0.00 3.86
51 52 3.452990 TCATAAGCGGTTACATTGGGAGA 59.547 43.478 9.61 0.00 0.00 3.71
83 84 4.684703 GGTCGTATAACATTGATCTTCCCG 59.315 45.833 0.00 0.00 0.00 5.14
84 85 5.855045 AGGTCGTATAACATTGATCTTCCC 58.145 41.667 0.00 0.00 0.00 3.97
150 151 3.490526 GCTGTTTTGCAAAATGACGTGAT 59.509 39.130 26.24 0.00 0.00 3.06
155 156 4.596801 TTGTGCTGTTTTGCAAAATGAC 57.403 36.364 26.24 18.92 45.12 3.06
157 158 5.570344 TGAATTGTGCTGTTTTGCAAAATG 58.430 33.333 26.24 21.36 46.61 2.32
168 169 3.221771 TGCCTACTTTGAATTGTGCTGT 58.778 40.909 0.00 0.00 0.00 4.40
212 213 2.882927 AACTACTCTGCACACGACAA 57.117 45.000 0.00 0.00 0.00 3.18
214 215 1.714460 CGAAACTACTCTGCACACGAC 59.286 52.381 0.00 0.00 0.00 4.34
217 218 3.284323 TCTCGAAACTACTCTGCACAC 57.716 47.619 0.00 0.00 0.00 3.82
219 220 3.119459 TCCATCTCGAAACTACTCTGCAC 60.119 47.826 0.00 0.00 0.00 4.57
227 228 3.197766 AGTGGCATTCCATCTCGAAACTA 59.802 43.478 0.00 0.00 45.62 2.24
231 232 1.407299 CCAGTGGCATTCCATCTCGAA 60.407 52.381 0.00 0.00 45.62 3.71
340 341 1.672854 TATCACTCGGTGCCTTCGGG 61.673 60.000 0.00 0.00 32.98 5.14
342 343 0.866061 CGTATCACTCGGTGCCTTCG 60.866 60.000 0.00 0.00 32.98 3.79
349 350 1.411612 GGGGAAATCGTATCACTCGGT 59.588 52.381 0.00 0.00 0.00 4.69
351 352 3.305199 GGTAGGGGAAATCGTATCACTCG 60.305 52.174 0.00 0.00 0.00 4.18
360 361 1.413077 GGTGAGAGGTAGGGGAAATCG 59.587 57.143 0.00 0.00 0.00 3.34
392 393 0.456221 ATACAAGACGAGGCGGACTG 59.544 55.000 0.00 0.00 0.00 3.51
397 398 1.338337 AGGATCATACAAGACGAGGCG 59.662 52.381 0.00 0.00 0.00 5.52
402 403 3.889538 TGGTCCTAGGATCATACAAGACG 59.110 47.826 21.38 0.00 29.14 4.18
408 409 5.071788 TGTTTCCATGGTCCTAGGATCATAC 59.928 44.000 32.59 26.48 43.40 2.39
413 414 3.189606 TGTGTTTCCATGGTCCTAGGAT 58.810 45.455 16.27 0.00 0.00 3.24
427 428 2.369394 CTGGCCTTAGGGATGTGTTTC 58.631 52.381 3.32 0.00 33.58 2.78
433 434 2.103153 TAGTCCTGGCCTTAGGGATG 57.897 55.000 9.21 0.00 38.42 3.51
434 435 2.889522 TTAGTCCTGGCCTTAGGGAT 57.110 50.000 9.21 1.46 38.42 3.85
435 436 2.408565 CATTAGTCCTGGCCTTAGGGA 58.591 52.381 9.21 6.30 38.42 4.20
436 437 1.421646 CCATTAGTCCTGGCCTTAGGG 59.578 57.143 9.21 4.04 38.42 3.53
437 438 2.104963 GTCCATTAGTCCTGGCCTTAGG 59.895 54.545 3.32 2.86 39.29 2.69
438 439 2.224066 CGTCCATTAGTCCTGGCCTTAG 60.224 54.545 3.32 0.00 33.56 2.18
439 440 1.760613 CGTCCATTAGTCCTGGCCTTA 59.239 52.381 3.32 0.00 33.56 2.69
440 441 0.541863 CGTCCATTAGTCCTGGCCTT 59.458 55.000 3.32 0.00 33.56 4.35
442 443 1.523938 GCGTCCATTAGTCCTGGCC 60.524 63.158 0.00 0.00 33.56 5.36
446 447 0.739813 GCGTTGCGTCCATTAGTCCT 60.740 55.000 0.00 0.00 0.00 3.85
463 464 2.153219 CTCGAGATCGACGGAGAGCG 62.153 65.000 6.58 0.00 44.22 5.03
500 2557 3.832490 TCAGATCGTTACCATGGGATAGG 59.168 47.826 18.09 6.54 0.00 2.57
502 2559 4.480115 ACTCAGATCGTTACCATGGGATA 58.520 43.478 18.09 0.00 0.00 2.59
508 2565 2.481449 GCCGAACTCAGATCGTTACCAT 60.481 50.000 3.42 0.00 38.60 3.55
509 2566 1.135199 GCCGAACTCAGATCGTTACCA 60.135 52.381 3.42 0.00 38.60 3.25
510 2567 1.557651 GCCGAACTCAGATCGTTACC 58.442 55.000 3.42 0.00 38.60 2.85
514 2571 0.965866 TCTGGCCGAACTCAGATCGT 60.966 55.000 3.42 0.00 38.60 3.73
561 2857 7.688372 TCCTCATTAACTTACGTAGTACTTCG 58.312 38.462 18.88 18.88 45.76 3.79
563 2859 7.121759 TGCTCCTCATTAACTTACGTAGTACTT 59.878 37.037 0.00 0.00 45.76 2.24
564 2860 6.600822 TGCTCCTCATTAACTTACGTAGTACT 59.399 38.462 0.00 0.00 45.76 2.73
565 2861 6.789262 TGCTCCTCATTAACTTACGTAGTAC 58.211 40.000 0.00 0.00 45.76 2.73
566 2862 7.423199 CATGCTCCTCATTAACTTACGTAGTA 58.577 38.462 0.00 0.00 35.82 1.82
567 2863 6.273825 CATGCTCCTCATTAACTTACGTAGT 58.726 40.000 0.00 0.00 37.76 2.73
568 2864 5.175856 GCATGCTCCTCATTAACTTACGTAG 59.824 44.000 11.37 0.00 31.79 3.51
637 2964 1.530720 TGTATTGCGTGCACAACTCTG 59.469 47.619 18.64 0.00 31.03 3.35
697 3024 3.132160 GCGGCTATTTAAGAGGACCTTC 58.868 50.000 0.00 0.00 36.34 3.46
912 3240 2.202892 GAGCGGACGATGAACCCC 60.203 66.667 0.00 0.00 0.00 4.95
1052 3381 2.024176 TTAACAGGGAGAGGAGCACA 57.976 50.000 0.00 0.00 0.00 4.57
1053 3382 4.591072 AGATATTAACAGGGAGAGGAGCAC 59.409 45.833 0.00 0.00 0.00 4.40
1057 3386 7.749377 TTGAAAGATATTAACAGGGAGAGGA 57.251 36.000 0.00 0.00 0.00 3.71
1073 3402 7.836183 ACCATGTAAGAGCCTAAATTGAAAGAT 59.164 33.333 0.00 0.00 0.00 2.40
1092 3421 4.811908 TCGATCAGACGAAAAACCATGTA 58.188 39.130 0.00 0.00 39.34 2.29
1306 3636 1.739067 GACAACCATCTGCCCTACAC 58.261 55.000 0.00 0.00 0.00 2.90
1309 3639 1.904771 CCGACAACCATCTGCCCTA 59.095 57.895 0.00 0.00 0.00 3.53
1406 3736 7.604164 TGAATTGATGAACTAAGTCTTCTGGAC 59.396 37.037 0.00 0.00 44.80 4.02
1409 3739 8.545229 ACTGAATTGATGAACTAAGTCTTCTG 57.455 34.615 0.00 0.00 0.00 3.02
1423 3756 8.777413 TGAAAAACAGAGACTACTGAATTGATG 58.223 33.333 0.00 0.00 40.63 3.07
1527 3860 6.851222 ACTCTATTGCAAGATGATAAACCG 57.149 37.500 4.94 0.00 0.00 4.44
1651 4069 8.039603 TCACATAATTGCTGGTTACTTAACTG 57.960 34.615 0.00 0.00 36.47 3.16
1718 4136 4.591321 TCCATAGGAGAAGCCAAACAAT 57.409 40.909 0.00 0.00 40.02 2.71
1719 4137 4.591321 ATCCATAGGAGAAGCCAAACAA 57.409 40.909 0.00 0.00 40.02 2.83
1720 4138 4.272489 CAATCCATAGGAGAAGCCAAACA 58.728 43.478 0.00 0.00 40.02 2.83
1721 4139 3.067320 GCAATCCATAGGAGAAGCCAAAC 59.933 47.826 0.00 0.00 40.02 2.93
1873 4293 7.505923 AGTGGAGACAGTAACTGTGCATATATA 59.494 37.037 0.00 0.00 45.44 0.86
1874 4294 6.325028 AGTGGAGACAGTAACTGTGCATATAT 59.675 38.462 0.00 0.00 45.44 0.86
1932 4352 6.808008 ATAACTTGACACTGGAAGAACATG 57.192 37.500 0.00 0.00 37.43 3.21
2051 4471 9.597681 AAGGCATTCAGGAATATGAATAAAGAT 57.402 29.630 1.90 0.00 45.83 2.40
2052 4472 8.853126 CAAGGCATTCAGGAATATGAATAAAGA 58.147 33.333 1.90 0.00 45.83 2.52
2097 4517 9.529325 TTATGAACGTGATCTAACCAGAATTAG 57.471 33.333 0.00 0.00 33.50 1.73
2105 4525 7.707035 ACAGAATCTTATGAACGTGATCTAACC 59.293 37.037 0.00 0.00 0.00 2.85
2115 4535 9.825972 ACATTGTAAAACAGAATCTTATGAACG 57.174 29.630 0.00 0.00 0.00 3.95
2155 4591 1.398390 GCACCAATAAGACAGAAGGCG 59.602 52.381 0.00 0.00 0.00 5.52
2288 4724 7.823665 ACACACTCAAGATAGTACATCGTTAA 58.176 34.615 0.00 0.00 0.00 2.01
2289 4725 7.387119 ACACACTCAAGATAGTACATCGTTA 57.613 36.000 0.00 0.00 0.00 3.18
2290 4726 6.268825 ACACACTCAAGATAGTACATCGTT 57.731 37.500 0.00 0.00 0.00 3.85
2291 4727 5.899120 ACACACTCAAGATAGTACATCGT 57.101 39.130 0.00 0.00 0.00 3.73
2292 4728 5.744345 GGAACACACTCAAGATAGTACATCG 59.256 44.000 0.00 0.00 0.00 3.84
2293 4729 5.744345 CGGAACACACTCAAGATAGTACATC 59.256 44.000 0.00 0.00 0.00 3.06
2294 4730 5.185249 ACGGAACACACTCAAGATAGTACAT 59.815 40.000 0.00 0.00 0.00 2.29
2295 4731 4.521639 ACGGAACACACTCAAGATAGTACA 59.478 41.667 0.00 0.00 0.00 2.90
2296 4732 5.056894 ACGGAACACACTCAAGATAGTAC 57.943 43.478 0.00 0.00 0.00 2.73
2297 4733 5.717078 AACGGAACACACTCAAGATAGTA 57.283 39.130 0.00 0.00 0.00 1.82
2298 4734 4.602340 AACGGAACACACTCAAGATAGT 57.398 40.909 0.00 0.00 0.00 2.12
2299 4735 5.679906 CAAAACGGAACACACTCAAGATAG 58.320 41.667 0.00 0.00 0.00 2.08
2300 4736 4.024387 GCAAAACGGAACACACTCAAGATA 60.024 41.667 0.00 0.00 0.00 1.98
2301 4737 3.243068 GCAAAACGGAACACACTCAAGAT 60.243 43.478 0.00 0.00 0.00 2.40
2302 4738 2.096819 GCAAAACGGAACACACTCAAGA 59.903 45.455 0.00 0.00 0.00 3.02
2303 4739 2.159448 TGCAAAACGGAACACACTCAAG 60.159 45.455 0.00 0.00 0.00 3.02
2304 4740 1.813178 TGCAAAACGGAACACACTCAA 59.187 42.857 0.00 0.00 0.00 3.02
2305 4741 1.131504 GTGCAAAACGGAACACACTCA 59.868 47.619 0.00 0.00 33.23 3.41
2306 4742 1.400494 AGTGCAAAACGGAACACACTC 59.600 47.619 0.00 0.00 33.25 3.51
2307 4743 1.132262 CAGTGCAAAACGGAACACACT 59.868 47.619 0.00 0.00 38.84 3.55
2308 4744 1.544686 CAGTGCAAAACGGAACACAC 58.455 50.000 0.00 0.00 35.47 3.82
2309 4745 0.179150 GCAGTGCAAAACGGAACACA 60.179 50.000 11.09 0.00 35.47 3.72
2310 4746 0.100503 AGCAGTGCAAAACGGAACAC 59.899 50.000 19.20 0.00 0.00 3.32
2311 4747 0.814457 AAGCAGTGCAAAACGGAACA 59.186 45.000 19.20 0.00 0.00 3.18
2500 4939 5.762179 TGACCACAGAACTCAATTAGGAT 57.238 39.130 0.00 0.00 0.00 3.24
2626 5065 5.516339 ACAAAACAATGAAAAGAACTGCTCG 59.484 36.000 0.00 0.00 0.00 5.03
2649 5088 2.753029 AGCAGAGCTCAACCCCAC 59.247 61.111 17.77 0.00 30.62 4.61
2727 5166 5.418676 ACAAATTGTTATGGGCATACAAGC 58.581 37.500 0.00 0.00 0.00 4.01
2867 5306 9.922305 GTACAGAGCAAGACAATAAATCAATAC 57.078 33.333 0.00 0.00 0.00 1.89
2869 5308 8.565896 TGTACAGAGCAAGACAATAAATCAAT 57.434 30.769 0.00 0.00 0.00 2.57
2870 5309 7.977789 TGTACAGAGCAAGACAATAAATCAA 57.022 32.000 0.00 0.00 0.00 2.57
2872 5311 9.282247 CAATTGTACAGAGCAAGACAATAAATC 57.718 33.333 0.00 0.00 40.68 2.17
2873 5312 8.796475 ACAATTGTACAGAGCAAGACAATAAAT 58.204 29.630 9.97 0.00 40.68 1.40
2874 5313 8.165239 ACAATTGTACAGAGCAAGACAATAAA 57.835 30.769 9.97 0.00 40.68 1.40
2875 5314 7.744087 ACAATTGTACAGAGCAAGACAATAA 57.256 32.000 9.97 0.00 40.68 1.40
2876 5315 7.744087 AACAATTGTACAGAGCAAGACAATA 57.256 32.000 12.39 0.00 40.68 1.90
2877 5316 6.639632 AACAATTGTACAGAGCAAGACAAT 57.360 33.333 12.39 0.00 42.76 2.71
3120 5687 0.874390 GACATCAACGAAGCTGCCAA 59.126 50.000 0.00 0.00 0.00 4.52
3121 5688 0.250252 TGACATCAACGAAGCTGCCA 60.250 50.000 0.00 0.00 0.00 4.92
3251 5822 1.523758 GTCGCAACCTGAACATCCTT 58.476 50.000 0.00 0.00 0.00 3.36
3252 5823 0.670546 CGTCGCAACCTGAACATCCT 60.671 55.000 0.00 0.00 0.00 3.24
3253 5824 0.949105 ACGTCGCAACCTGAACATCC 60.949 55.000 0.00 0.00 0.00 3.51
3310 5881 7.329226 CACACTTAAAAGCATTAAACCATGAGG 59.671 37.037 0.00 0.00 42.21 3.86
3385 5956 8.502860 ATGAGGAACATAAACCAGACGAGAGTA 61.503 40.741 0.00 0.00 40.52 2.59
3386 5957 7.757279 ATGAGGAACATAAACCAGACGAGAGT 61.757 42.308 0.00 0.00 42.32 3.24
3387 5958 4.082190 TGAGGAACATAAACCAGACGAGAG 60.082 45.833 0.00 0.00 0.00 3.20
3440 6035 0.886490 AAACTCGGTTCTGCTGCCAG 60.886 55.000 0.00 0.00 40.54 4.85
3590 6185 3.671008 AACATGGCGAGTAAGTGTACA 57.329 42.857 0.00 0.00 32.12 2.90
3764 6600 6.316390 CCACGGTTTCTTAGCAATCTCTAAAT 59.684 38.462 0.00 0.00 0.00 1.40
3794 6630 5.389516 CCACTTCGTCAAACACTTACTATGC 60.390 44.000 0.00 0.00 0.00 3.14
3811 6647 1.299541 AATTATGCGCCTCCACTTCG 58.700 50.000 4.18 0.00 0.00 3.79
3818 6654 4.033587 TCGAACACTTTAATTATGCGCCTC 59.966 41.667 4.18 0.00 0.00 4.70
3828 6664 7.537715 TCATGCATTTCATCGAACACTTTAAT 58.462 30.769 0.00 0.00 31.79 1.40
3830 6666 6.493449 TCATGCATTTCATCGAACACTTTA 57.507 33.333 0.00 0.00 31.79 1.85
3831 6667 5.375417 TCATGCATTTCATCGAACACTTT 57.625 34.783 0.00 0.00 31.79 2.66
3842 6678 8.836268 AAAGAAAATTTAGCTCATGCATTTCA 57.164 26.923 0.00 0.00 42.74 2.69
3874 6710 2.501261 AGCCGTTTCCCTGAAGTTAAC 58.499 47.619 0.00 0.00 0.00 2.01
3887 6723 2.228138 TTTGTCGTGTCTAGCCGTTT 57.772 45.000 0.00 0.00 0.00 3.60
3889 6725 2.450609 ATTTTGTCGTGTCTAGCCGT 57.549 45.000 0.00 0.00 0.00 5.68
3959 6795 6.575162 AATTTTGTTGTTTCTAGCCGATCT 57.425 33.333 0.00 0.00 0.00 2.75
3960 6796 8.234546 TCTAAATTTTGTTGTTTCTAGCCGATC 58.765 33.333 0.00 0.00 0.00 3.69
4050 6886 3.514309 ACGTTTACAGGCTTAGACCATCT 59.486 43.478 0.00 0.00 0.00 2.90
4133 6969 1.228552 AAGCGTGCTCACCCCAAAT 60.229 52.632 0.00 0.00 0.00 2.32
4138 6974 3.357079 CACCAAGCGTGCTCACCC 61.357 66.667 0.00 0.00 35.18 4.61


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

AutoCloner maintained by Alex Coulton.