Multiple sequence alignment - TraesCS7D01G259300

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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 TraesCS7D01G259300 chr7D 100.000 5522 0 0 1 5522 234809918 234804397 0.000000e+00 10198.0
1 TraesCS7D01G259300 chr7D 85.756 344 43 4 201 538 230903662 230903319 5.260000e-95 359.0
2 TraesCS7D01G259300 chr7A 94.442 4750 166 35 836 5522 249596756 249592042 0.000000e+00 7219.0
3 TraesCS7D01G259300 chr7A 94.444 54 2 1 786 839 355689760 355689812 1.270000e-11 82.4
4 TraesCS7D01G259300 chr7B 97.224 1693 39 2 2618 4302 210862973 210861281 0.000000e+00 2859.0
5 TraesCS7D01G259300 chr7B 94.820 1699 65 9 875 2561 210864659 210862972 0.000000e+00 2628.0
6 TraesCS7D01G259300 chr7B 90.684 1170 57 11 4372 5505 210861256 210860103 0.000000e+00 1509.0
7 TraesCS7D01G259300 chr7B 87.582 459 49 5 1 454 210868252 210867797 4.900000e-145 525.0
8 TraesCS7D01G259300 chr7B 86.024 415 41 6 153 550 432594540 432594954 3.950000e-116 429.0
9 TraesCS7D01G259300 chr7B 79.902 204 30 9 1 193 456439022 456438819 7.460000e-29 139.0
10 TraesCS7D01G259300 chr7B 84.000 75 10 2 764 837 368136892 368136965 2.760000e-08 71.3
11 TraesCS7D01G259300 chr4D 84.629 553 49 16 24 550 38361816 38361274 8.200000e-143 518.0
12 TraesCS7D01G259300 chr4D 89.362 94 8 1 2064 2157 395380198 395380107 3.490000e-22 117.0
13 TraesCS7D01G259300 chr5D 83.114 533 62 13 22 527 99723717 99723186 1.400000e-125 460.0
14 TraesCS7D01G259300 chr5D 84.835 455 45 10 113 550 222523969 222523522 2.360000e-118 436.0
15 TraesCS7D01G259300 chr5D 94.118 85 5 0 2064 2148 442203727 442203811 4.490000e-26 130.0
16 TraesCS7D01G259300 chr6B 86.310 336 38 8 211 540 201108240 201107907 5.260000e-95 359.0
17 TraesCS7D01G259300 chr5B 85.507 345 44 6 208 546 376441055 376440711 6.800000e-94 355.0
18 TraesCS7D01G259300 chr5B 91.765 85 7 0 2064 2148 538397396 538397480 9.720000e-23 119.0
19 TraesCS7D01G259300 chr5A 82.697 393 47 18 161 545 255464160 255464539 4.120000e-86 329.0
20 TraesCS7D01G259300 chr5A 82.081 173 21 8 1 164 524748959 524749130 7.460000e-29 139.0
21 TraesCS7D01G259300 chr4A 78.729 362 58 13 1 344 63956348 63956708 2.000000e-54 224.0
22 TraesCS7D01G259300 chrUn 80.392 204 29 8 1 193 58402002 58401799 1.600000e-30 145.0
23 TraesCS7D01G259300 chr4B 82.081 173 22 7 1 164 596686735 596686907 7.460000e-29 139.0
24 TraesCS7D01G259300 chr4B 86.567 67 8 1 798 863 240690134 240690068 7.670000e-09 73.1
25 TraesCS7D01G259300 chr3B 79.902 204 30 8 1 193 677474878 677474675 7.460000e-29 139.0
26 TraesCS7D01G259300 chr3B 91.765 85 5 1 2064 2148 194074854 194074772 3.490000e-22 117.0
27 TraesCS7D01G259300 chr2B 79.902 204 30 9 1 193 218856889 218856686 7.460000e-29 139.0
28 TraesCS7D01G259300 chr1A 79.412 204 31 8 1 193 95206478 95206275 3.470000e-27 134.0
29 TraesCS7D01G259300 chr6D 91.765 85 7 0 2064 2148 90111817 90111901 9.720000e-23 119.0
30 TraesCS7D01G259300 chr6D 83.117 77 11 2 764 839 277256686 277256761 9.930000e-08 69.4
31 TraesCS7D01G259300 chr3A 91.765 85 7 0 2064 2148 151644768 151644684 9.720000e-23 119.0
32 TraesCS7D01G259300 chr3A 100.000 40 0 0 800 839 696701137 696701098 2.130000e-09 75.0
33 TraesCS7D01G259300 chr3A 100.000 30 0 0 1134 1163 664683564 664683593 7.730000e-04 56.5
34 TraesCS7D01G259300 chr1D 91.765 85 7 0 2064 2148 279101376 279101460 9.720000e-23 119.0
35 TraesCS7D01G259300 chr1D 88.060 67 4 4 797 862 401160018 401159955 5.930000e-10 76.8
36 TraesCS7D01G259300 chr1B 84.416 77 10 2 763 838 32081296 32081221 2.130000e-09 75.0
37 TraesCS7D01G259300 chr6A 84.416 77 9 3 763 838 239116159 239116233 7.670000e-09 73.1
38 TraesCS7D01G259300 chr6A 84.000 75 11 1 764 837 134639 134565 2.760000e-08 71.3
39 TraesCS7D01G259300 chr3D 100.000 30 0 0 1134 1163 531043502 531043531 7.730000e-04 56.5


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 TraesCS7D01G259300 chr7D 234804397 234809918 5521 True 10198.00 10198 100.0000 1 5522 1 chr7D.!!$R2 5521
1 TraesCS7D01G259300 chr7A 249592042 249596756 4714 True 7219.00 7219 94.4420 836 5522 1 chr7A.!!$R1 4686
2 TraesCS7D01G259300 chr7B 210860103 210868252 8149 True 1880.25 2859 92.5775 1 5505 4 chr7B.!!$R2 5504
3 TraesCS7D01G259300 chr4D 38361274 38361816 542 True 518.00 518 84.6290 24 550 1 chr4D.!!$R1 526
4 TraesCS7D01G259300 chr5D 99723186 99723717 531 True 460.00 460 83.1140 22 527 1 chr5D.!!$R1 505

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
630 3435 0.250467 CCGGCCTGTAGGAATGGATG 60.250 60.0 0.00 0.00 37.39 3.51 F
680 3485 0.319211 TCGTCCAACGCGTTGAGAAT 60.319 50.0 44.26 13.70 42.93 2.40 F
2576 5410 0.039798 AAAAGATGCAGTGCGCTGTG 60.040 50.0 27.02 7.12 44.32 3.66 F
2833 5680 0.261696 AAACCTGCTTGAACCCCAGT 59.738 50.0 0.00 0.00 0.00 4.00 F
4061 6914 0.977395 CTGATAGGATCCCCGTTCCC 59.023 60.0 8.55 0.00 37.58 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 4641 0.106419 TTGAAGTCAACCCCACCACC 60.106 55.0 0.0 0.0 0.00 4.61 R
2598 5432 0.179073 TGCTAAGCTCATTCCGGCTC 60.179 55.0 0.0 0.0 37.87 4.70 R
3431 6284 0.253327 CCAGGTTGCTCCTTAGGTCC 59.747 60.0 0.0 0.0 45.67 4.46 R
4320 7173 1.002366 CAGAATCTTGGTCTTCGCCG 58.998 55.0 0.0 0.0 0.00 6.46 R
4897 7794 0.865769 GGCGAGAAAAGTCGAAGCAA 59.134 50.0 0.0 0.0 42.85 3.91 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
31 32 8.951787 ATTTATAACTTTGACGTGTGCCTATA 57.048 30.769 0.00 0.00 0.00 1.31
121 131 2.100916 TGCTACGAAGACTCTAATGCCC 59.899 50.000 0.00 0.00 0.00 5.36
122 132 2.859032 GCTACGAAGACTCTAATGCCCG 60.859 54.545 0.00 0.00 0.00 6.13
124 134 1.135083 ACGAAGACTCTAATGCCCGTG 60.135 52.381 0.00 0.00 0.00 4.94
164 175 5.767168 AGAAAATCTCTGTTGTCCAAGAAGG 59.233 40.000 0.00 0.00 33.26 3.46
175 188 6.780031 TGTTGTCCAAGAAGGGATTGATTTTA 59.220 34.615 0.00 0.00 39.62 1.52
178 191 6.953520 TGTCCAAGAAGGGATTGATTTTACAT 59.046 34.615 0.00 0.00 39.62 2.29
221 243 4.910195 TGATCCGATTGAAATATCCCCTG 58.090 43.478 0.00 0.00 0.00 4.45
251 273 8.907222 TGAATGTGATGCTTGCTATTCTTATA 57.093 30.769 0.00 0.00 0.00 0.98
294 316 5.128205 TGATGCTTATGGAGATGAACTTGG 58.872 41.667 0.00 0.00 0.00 3.61
345 367 3.066291 TGCTATTGTACCCACACTTGG 57.934 47.619 0.00 0.00 43.50 3.61
401 427 7.766219 TTATATCGGAGAAGTTTGCACTTAC 57.234 36.000 0.00 0.00 43.79 2.34
436 462 5.461032 TGATGGGTTGTGTTTTACCATTC 57.539 39.130 0.00 0.00 41.71 2.67
490 3280 1.589716 CTTGCTGCCCCTACTTGCAC 61.590 60.000 0.00 0.00 33.13 4.57
508 3298 5.843673 TGCACTTACTATGAGAGAGGAAG 57.156 43.478 0.00 0.00 0.00 3.46
527 3318 4.142227 GGAAGCACGTCTCACCTTTCTATA 60.142 45.833 0.00 0.00 0.00 1.31
557 3348 7.944729 AATACAATCAAATCACACTAGGCTT 57.055 32.000 0.00 0.00 0.00 4.35
573 3377 1.401905 GGCTTTGCCTCAACCTATTCG 59.598 52.381 0.73 0.00 46.69 3.34
577 3381 2.851263 TGCCTCAACCTATTCGTGTT 57.149 45.000 0.00 0.00 0.00 3.32
583 3387 5.050490 CCTCAACCTATTCGTGTTATCCTG 58.950 45.833 0.00 0.00 0.00 3.86
586 3390 2.769663 ACCTATTCGTGTTATCCTGGCA 59.230 45.455 0.00 0.00 0.00 4.92
599 3403 0.600782 CCTGGCATGCAAACACAACC 60.601 55.000 21.36 0.00 0.00 3.77
604 3409 2.617774 GGCATGCAAACACAACCAAAAT 59.382 40.909 21.36 0.00 0.00 1.82
617 3422 1.569072 ACCAAAATAATCCTCCGGCCT 59.431 47.619 0.00 0.00 0.00 5.19
621 3426 3.771577 AAATAATCCTCCGGCCTGTAG 57.228 47.619 0.00 0.00 0.00 2.74
629 3434 0.399949 TCCGGCCTGTAGGAATGGAT 60.400 55.000 0.00 0.00 37.39 3.41
630 3435 0.250467 CCGGCCTGTAGGAATGGATG 60.250 60.000 0.00 0.00 37.39 3.51
646 3451 3.164977 TGGAGACACGGCCAACCA 61.165 61.111 2.24 0.00 31.61 3.67
653 3458 2.035469 ACGGCCAACCATGATGCA 59.965 55.556 2.24 0.00 34.57 3.96
680 3485 0.319211 TCGTCCAACGCGTTGAGAAT 60.319 50.000 44.26 13.70 42.93 2.40
685 3490 2.481185 TCCAACGCGTTGAGAATAAACC 59.519 45.455 44.26 0.00 42.93 3.27
686 3491 2.482721 CCAACGCGTTGAGAATAAACCT 59.517 45.455 44.26 9.61 42.93 3.50
687 3492 3.058501 CCAACGCGTTGAGAATAAACCTT 60.059 43.478 44.26 9.12 42.93 3.50
719 3524 2.695759 CCGCAATAGCCGGCAAACA 61.696 57.895 31.54 11.15 37.52 2.83
727 3532 1.079888 GCCGGCAAACATTCCCTTG 60.080 57.895 24.80 0.00 0.00 3.61
796 3605 8.686334 ACACATGACAAAGTTTTCAGAAATACT 58.314 29.630 0.00 1.24 0.00 2.12
827 3636 5.835113 ATTGGGTCATCTATTTTGGAACG 57.165 39.130 0.00 0.00 0.00 3.95
828 3637 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
829 3638 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
830 3639 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
831 3640 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
832 3641 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
833 3642 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
834 3643 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
839 3648 1.263356 TTGGAACGGAGGGAGTACAG 58.737 55.000 0.00 0.00 0.00 2.74
947 3756 0.881159 TGTAACCCCAGCGAACGTTG 60.881 55.000 5.00 4.23 0.00 4.10
979 3791 6.386654 AGCATTACCGTTTCCTTATTGTTTG 58.613 36.000 0.00 0.00 0.00 2.93
1002 3814 2.256461 GCCACGAAGCCAAAGCAG 59.744 61.111 0.00 0.00 43.56 4.24
1094 3906 0.556380 AGAGGGAGAGAAGGGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
1263 4081 4.423209 GGGGCAGGAGGAGGAGGT 62.423 72.222 0.00 0.00 0.00 3.85
1282 4100 2.612251 GAGGAGGAGGAGGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
1283 4101 3.039526 AGGAGGAGGAGGAGGGGG 61.040 72.222 0.00 0.00 0.00 5.40
1332 4150 3.640407 GCCCTCCTGCTCACCACA 61.640 66.667 0.00 0.00 0.00 4.17
1508 4326 0.320596 CAATGCGGTGCCAAATGGTT 60.321 50.000 0.71 0.00 37.57 3.67
1692 4510 8.041323 TCTTCAAATTTAGGAGAAGCTTATCGT 58.959 33.333 19.03 19.03 37.86 3.73
1702 4520 5.320549 AGAAGCTTATCGTTTTCCGTAGA 57.679 39.130 0.00 0.00 37.94 2.59
1770 4588 2.363306 TTGTGGGTCCATGCCATATC 57.637 50.000 0.00 0.00 0.00 1.63
1771 4589 0.478072 TGTGGGTCCATGCCATATCC 59.522 55.000 0.00 0.00 0.00 2.59
1796 4614 1.891150 CTCAGTTCTTGCATTTGGGCT 59.109 47.619 0.00 0.00 34.04 5.19
1823 4641 2.666619 GCGCAATCTCAAGAGTTTGGTG 60.667 50.000 17.76 9.55 38.13 4.17
1824 4642 2.095567 CGCAATCTCAAGAGTTTGGTGG 60.096 50.000 17.76 0.00 38.13 4.61
1825 4643 2.887152 GCAATCTCAAGAGTTTGGTGGT 59.113 45.455 17.76 0.00 38.13 4.16
1826 4644 3.304928 GCAATCTCAAGAGTTTGGTGGTG 60.305 47.826 17.76 0.00 38.13 4.17
1827 4645 2.638480 TCTCAAGAGTTTGGTGGTGG 57.362 50.000 0.00 0.00 34.97 4.61
1866 4684 8.917088 CAATATGGTTCAGGGAATTATTTGAGT 58.083 33.333 0.00 0.00 0.00 3.41
1914 4732 7.061441 CGGCAATCTTGATGTTATTAATGCATC 59.939 37.037 19.46 19.46 39.37 3.91
1972 4790 9.103861 GGACACAATTTTGATTTAACTTTGGAA 57.896 29.630 0.00 0.00 0.00 3.53
2380 5210 4.770010 GTGGTCCTTGGTTCCATTTATTCA 59.230 41.667 8.76 0.00 33.68 2.57
2421 5251 7.512297 CAGGATGTGTTGTTTTTAATGCATTC 58.488 34.615 16.86 1.25 0.00 2.67
2447 5277 0.549950 CAGGATGGGCTCAATCTGGT 59.450 55.000 10.64 0.00 0.00 4.00
2485 5319 8.553459 AACTTCATTATCTAACAGTCCAACAG 57.447 34.615 0.00 0.00 0.00 3.16
2555 5389 0.179056 AGTGAAGTGGTTCGTGTGGG 60.179 55.000 0.00 0.00 35.17 4.61
2568 5402 1.608590 CGTGTGGGAAAAAGATGCAGT 59.391 47.619 0.00 0.00 0.00 4.40
2569 5403 2.605338 CGTGTGGGAAAAAGATGCAGTG 60.605 50.000 0.00 0.00 0.00 3.66
2570 5404 1.340889 TGTGGGAAAAAGATGCAGTGC 59.659 47.619 8.58 8.58 0.00 4.40
2571 5405 0.597568 TGGGAAAAAGATGCAGTGCG 59.402 50.000 11.20 0.00 0.00 5.34
2572 5406 0.733909 GGGAAAAAGATGCAGTGCGC 60.734 55.000 11.20 0.00 42.89 6.09
2573 5407 0.242017 GGAAAAAGATGCAGTGCGCT 59.758 50.000 9.73 7.58 43.06 5.92
2574 5408 1.334054 GAAAAAGATGCAGTGCGCTG 58.666 50.000 23.02 23.02 45.23 5.18
2575 5409 0.670162 AAAAAGATGCAGTGCGCTGT 59.330 45.000 27.02 9.68 44.32 4.40
2576 5410 0.039798 AAAAGATGCAGTGCGCTGTG 60.040 50.000 27.02 7.12 44.32 3.66
2577 5411 2.467946 AAAGATGCAGTGCGCTGTGC 62.468 55.000 27.02 22.76 44.32 4.57
2597 5431 2.843077 CACGCATTCTTTGTGCTACTG 58.157 47.619 0.00 0.00 40.37 2.74
2598 5432 1.806542 ACGCATTCTTTGTGCTACTGG 59.193 47.619 0.00 0.00 40.37 4.00
2619 5453 1.094785 GCCGGAATGAGCTTAGCAAA 58.905 50.000 5.05 0.00 0.00 3.68
2768 5615 2.501723 ACAATAGTCGGGCTTGATGTCT 59.498 45.455 0.00 0.00 0.00 3.41
2791 5638 1.596727 GATGAAGGCTCAGATTCGCAC 59.403 52.381 0.00 0.00 34.23 5.34
2833 5680 0.261696 AAACCTGCTTGAACCCCAGT 59.738 50.000 0.00 0.00 0.00 4.00
3073 5920 1.531264 GCTTCTGCATCATCAACTGCG 60.531 52.381 0.00 0.00 41.32 5.18
3214 6064 2.486918 CCTGCACGATTGATATCTGCA 58.513 47.619 13.92 13.92 39.93 4.41
3215 6065 3.790212 CTGCACGATTGATATCTGCAG 57.210 47.619 22.16 22.16 45.45 4.41
3216 6066 1.869132 TGCACGATTGATATCTGCAGC 59.131 47.619 9.47 5.75 38.65 5.25
3217 6067 1.869132 GCACGATTGATATCTGCAGCA 59.131 47.619 9.47 0.00 36.14 4.41
3425 6278 1.326213 ACGAGATCCAGCCTCACAGG 61.326 60.000 0.00 0.00 38.80 4.00
3579 6432 3.819564 TTCAGATGAATCACGGGTAGG 57.180 47.619 0.00 0.00 0.00 3.18
4059 6912 1.718280 ACCTGATAGGATCCCCGTTC 58.282 55.000 8.55 0.94 37.67 3.95
4061 6914 0.977395 CTGATAGGATCCCCGTTCCC 59.023 60.000 8.55 0.00 37.58 3.97
4087 6940 8.049655 TCTCTCCAGATCATACAAAGATATCG 57.950 38.462 0.00 0.00 0.00 2.92
4093 6946 7.010275 CCAGATCATACAAAGATATCGCATCTG 59.990 40.741 0.00 6.66 35.38 2.90
4221 7074 7.986085 TTAGCTAGCATATTCCCATCTTTTC 57.014 36.000 18.83 0.00 0.00 2.29
4320 7173 1.198637 GTTGAGTGTTGAGGATGCTGC 59.801 52.381 0.00 0.00 0.00 5.25
4398 7259 4.444022 GCAATCAGACCTGTATCATCACCT 60.444 45.833 0.00 0.00 0.00 4.00
4414 7275 7.669089 TCATCACCTACATTGTTATCCTGTA 57.331 36.000 0.00 0.00 0.00 2.74
4505 7366 7.514784 TTTTCCATATGCATCCTGTTCTATG 57.485 36.000 0.19 0.00 0.00 2.23
4531 7392 1.518325 TGTATGTTCAACCCACTGCG 58.482 50.000 0.00 0.00 0.00 5.18
4897 7794 1.940242 AACGGGTTGGTTCCCCTTGT 61.940 55.000 0.00 0.00 44.32 3.16
4912 7809 2.618709 CCCTTGTTGCTTCGACTTTTCT 59.381 45.455 0.00 0.00 0.00 2.52
5042 7940 3.371063 GTCCGACGACCTGCTCCA 61.371 66.667 0.00 0.00 32.40 3.86
5189 8093 4.779733 GGGAGGCAGTCGAGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
5325 8229 1.135333 GCCGAGTTCGAGATCCTCTTT 59.865 52.381 2.59 0.00 43.02 2.52
5379 8283 1.115930 AGGATCTCGTAAGCCCGCAT 61.116 55.000 0.00 0.00 37.18 4.73
5395 8299 1.745264 CATCCCTCTCGCCTTCTCC 59.255 63.158 0.00 0.00 0.00 3.71
5414 8318 1.154301 CCCCGTTGAACATTTCGCG 60.154 57.895 0.00 0.00 0.00 5.87
5415 8319 1.572447 CCCGTTGAACATTTCGCGT 59.428 52.632 5.77 0.00 0.00 6.01
5424 8328 3.427528 TGAACATTTCGCGTCTGACTAAC 59.572 43.478 5.77 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.859325 ATAGGCACACGTCAAAGTTATAAAT 57.141 32.000 0.00 0.00 0.00 1.40
8 9 8.774890 TTTATAGGCACACGTCAAAGTTATAA 57.225 30.769 0.00 0.00 0.00 0.98
10 11 7.675962 TTTTATAGGCACACGTCAAAGTTAT 57.324 32.000 0.00 0.00 0.00 1.89
11 12 7.675962 ATTTTATAGGCACACGTCAAAGTTA 57.324 32.000 0.00 0.00 0.00 2.24
12 13 6.569179 ATTTTATAGGCACACGTCAAAGTT 57.431 33.333 0.00 0.00 0.00 2.66
13 14 6.378582 CAATTTTATAGGCACACGTCAAAGT 58.621 36.000 0.00 0.00 0.00 2.66
14 15 5.286082 GCAATTTTATAGGCACACGTCAAAG 59.714 40.000 0.00 0.00 0.00 2.77
16 17 4.457603 AGCAATTTTATAGGCACACGTCAA 59.542 37.500 0.00 0.00 0.00 3.18
17 18 4.006989 AGCAATTTTATAGGCACACGTCA 58.993 39.130 0.00 0.00 0.00 4.35
18 19 4.342772 CAGCAATTTTATAGGCACACGTC 58.657 43.478 0.00 0.00 0.00 4.34
19 20 3.427503 GCAGCAATTTTATAGGCACACGT 60.428 43.478 0.00 0.00 0.00 4.49
20 21 3.108144 GCAGCAATTTTATAGGCACACG 58.892 45.455 0.00 0.00 0.00 4.49
105 109 1.135083 ACACGGGCATTAGAGTCTTCG 60.135 52.381 0.00 0.00 0.00 3.79
205 218 7.587037 TTCATCAACAGGGGATATTTCAATC 57.413 36.000 0.00 0.00 0.00 2.67
221 243 4.106029 AGCAAGCATCACATTCATCAAC 57.894 40.909 0.00 0.00 0.00 3.18
251 273 8.758829 AGCATCATTAATATTGGCATCATGATT 58.241 29.630 5.16 0.00 29.37 2.57
253 275 7.712204 AGCATCATTAATATTGGCATCATGA 57.288 32.000 0.00 0.00 0.00 3.07
367 393 6.884832 ACTTCTCCGATATAATGTTGTTGGA 58.115 36.000 0.00 0.00 0.00 3.53
377 403 7.553334 AGTAAGTGCAAACTTCTCCGATATAA 58.447 34.615 0.00 0.00 0.00 0.98
490 3280 4.336993 ACGTGCTTCCTCTCTCATAGTAAG 59.663 45.833 0.00 0.00 0.00 2.34
508 3298 6.043411 AGAAATATAGAAAGGTGAGACGTGC 58.957 40.000 0.00 0.00 0.00 5.34
541 3332 3.221964 GGCAAAGCCTAGTGTGATTTG 57.778 47.619 0.00 4.45 46.69 2.32
557 3348 2.851263 ACACGAATAGGTTGAGGCAA 57.149 45.000 0.00 0.00 0.00 4.52
562 3366 4.682320 GCCAGGATAACACGAATAGGTTGA 60.682 45.833 0.00 0.00 0.00 3.18
565 3369 2.769663 TGCCAGGATAACACGAATAGGT 59.230 45.455 0.00 0.00 0.00 3.08
569 3373 1.949525 GCATGCCAGGATAACACGAAT 59.050 47.619 6.36 0.00 0.00 3.34
573 3377 2.230992 TGTTTGCATGCCAGGATAACAC 59.769 45.455 16.68 0.00 0.00 3.32
577 3381 2.212812 TGTGTTTGCATGCCAGGATA 57.787 45.000 16.68 0.00 0.00 2.59
583 3387 1.661341 TTTGGTTGTGTTTGCATGCC 58.339 45.000 16.68 0.00 0.00 4.40
586 3390 6.532826 AGGATTATTTTGGTTGTGTTTGCAT 58.467 32.000 0.00 0.00 0.00 3.96
617 3422 2.430694 CGTGTCTCCATCCATTCCTACA 59.569 50.000 0.00 0.00 0.00 2.74
621 3426 0.815615 GCCGTGTCTCCATCCATTCC 60.816 60.000 0.00 0.00 0.00 3.01
629 3434 2.525124 ATGGTTGGCCGTGTCTCCA 61.525 57.895 0.00 0.30 37.67 3.86
630 3435 2.040544 CATGGTTGGCCGTGTCTCC 61.041 63.158 0.00 0.00 44.71 3.71
642 3447 2.352030 CGAAAAGCTGTGCATCATGGTT 60.352 45.455 0.00 0.00 0.00 3.67
645 3450 2.512885 GACGAAAAGCTGTGCATCATG 58.487 47.619 0.00 0.00 0.00 3.07
646 3451 1.470098 GGACGAAAAGCTGTGCATCAT 59.530 47.619 0.00 0.00 0.00 2.45
653 3458 1.647084 GCGTTGGACGAAAAGCTGT 59.353 52.632 4.46 0.00 46.05 4.40
698 3503 3.613877 TTGCCGGCTATTGCGGTCA 62.614 57.895 29.70 0.00 40.82 4.02
727 3532 6.585416 AGAAATGTTTGCAAATATCATCCCC 58.415 36.000 20.02 9.48 0.00 4.81
801 3610 8.247562 CGTTCCAAAATAGATGACCCAATTTTA 58.752 33.333 0.00 0.00 31.97 1.52
802 3611 7.096551 CGTTCCAAAATAGATGACCCAATTTT 58.903 34.615 0.00 0.00 33.07 1.82
803 3612 6.350949 CCGTTCCAAAATAGATGACCCAATTT 60.351 38.462 0.00 0.00 0.00 1.82
804 3613 5.127031 CCGTTCCAAAATAGATGACCCAATT 59.873 40.000 0.00 0.00 0.00 2.32
805 3614 4.644685 CCGTTCCAAAATAGATGACCCAAT 59.355 41.667 0.00 0.00 0.00 3.16
806 3615 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
807 3616 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
808 3617 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
809 3618 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
810 3619 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
811 3620 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
812 3621 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
813 3622 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
814 3623 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
815 3624 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
816 3625 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
817 3626 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
818 3627 2.038033 CTGTACTCCCTCCGTTCCAAAA 59.962 50.000 0.00 0.00 0.00 2.44
819 3628 1.621814 CTGTACTCCCTCCGTTCCAAA 59.378 52.381 0.00 0.00 0.00 3.28
820 3629 1.263356 CTGTACTCCCTCCGTTCCAA 58.737 55.000 0.00 0.00 0.00 3.53
821 3630 0.613853 CCTGTACTCCCTCCGTTCCA 60.614 60.000 0.00 0.00 0.00 3.53
822 3631 0.324091 TCCTGTACTCCCTCCGTTCC 60.324 60.000 0.00 0.00 0.00 3.62
823 3632 0.816373 GTCCTGTACTCCCTCCGTTC 59.184 60.000 0.00 0.00 0.00 3.95
824 3633 0.113776 TGTCCTGTACTCCCTCCGTT 59.886 55.000 0.00 0.00 0.00 4.44
825 3634 0.113776 TTGTCCTGTACTCCCTCCGT 59.886 55.000 0.00 0.00 0.00 4.69
826 3635 1.263356 TTTGTCCTGTACTCCCTCCG 58.737 55.000 0.00 0.00 0.00 4.63
827 3636 4.302559 AAATTTGTCCTGTACTCCCTCC 57.697 45.455 0.00 0.00 0.00 4.30
828 3637 5.313712 TCAAAATTTGTCCTGTACTCCCTC 58.686 41.667 5.56 0.00 0.00 4.30
829 3638 5.319043 TCAAAATTTGTCCTGTACTCCCT 57.681 39.130 5.56 0.00 0.00 4.20
830 3639 5.476945 ACATCAAAATTTGTCCTGTACTCCC 59.523 40.000 5.56 0.00 0.00 4.30
831 3640 6.206634 TCACATCAAAATTTGTCCTGTACTCC 59.793 38.462 5.56 0.00 0.00 3.85
832 3641 7.202016 TCACATCAAAATTTGTCCTGTACTC 57.798 36.000 5.56 0.00 0.00 2.59
833 3642 7.581213 TTCACATCAAAATTTGTCCTGTACT 57.419 32.000 5.56 0.00 0.00 2.73
834 3643 8.816640 ATTTCACATCAAAATTTGTCCTGTAC 57.183 30.769 5.56 0.00 0.00 2.90
947 3756 3.242518 GAAACGGTAATGCTTTTCAGCC 58.757 45.455 0.00 0.00 46.74 4.85
1242 4054 3.093172 CCTCCTCCTGCCCCTTCC 61.093 72.222 0.00 0.00 0.00 3.46
1263 4081 2.328589 CCCTCCTCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
1427 4245 1.404986 CGAGCAATGTCTTCGGGGTTA 60.405 52.381 0.00 0.00 0.00 2.85
1692 4510 4.929808 GCAACTGAGAATCTCTACGGAAAA 59.070 41.667 11.92 0.00 34.92 2.29
1702 4520 3.418995 ACAGCATTGCAACTGAGAATCT 58.581 40.909 20.45 3.19 37.35 2.40
1770 4588 1.813513 ATGCAAGAACTGAGGAACGG 58.186 50.000 0.00 0.00 0.00 4.44
1771 4589 3.558505 CAAATGCAAGAACTGAGGAACG 58.441 45.455 0.00 0.00 0.00 3.95
1796 4614 2.497675 ACTCTTGAGATTGCGCCTTCTA 59.502 45.455 4.18 0.00 0.00 2.10
1823 4641 0.106419 TTGAAGTCAACCCCACCACC 60.106 55.000 0.00 0.00 0.00 4.61
1824 4642 1.995376 ATTGAAGTCAACCCCACCAC 58.005 50.000 0.00 0.00 38.86 4.16
1825 4643 3.563261 CCATATTGAAGTCAACCCCACCA 60.563 47.826 0.00 0.00 38.86 4.17
1826 4644 3.023832 CCATATTGAAGTCAACCCCACC 58.976 50.000 0.00 0.00 38.86 4.61
1827 4645 3.697166 ACCATATTGAAGTCAACCCCAC 58.303 45.455 0.00 0.00 38.86 4.61
1866 4684 4.935205 CGAGGTCCATAATCACAAGACAAA 59.065 41.667 0.00 0.00 0.00 2.83
1914 4732 3.305094 CGTACGGTTGCTACAATAACTGG 59.695 47.826 7.57 0.00 37.46 4.00
1957 4775 8.366401 TGCATTTGATCTTCCAAAGTTAAATCA 58.634 29.630 0.00 0.00 39.13 2.57
1963 4781 5.163322 TGGTTGCATTTGATCTTCCAAAGTT 60.163 36.000 0.00 0.00 39.13 2.66
1972 4790 1.077663 ACCCCTGGTTGCATTTGATCT 59.922 47.619 0.00 0.00 27.29 2.75
2143 4969 6.314400 GGTGCGAACATTCTTATTTGGTACTA 59.686 38.462 0.00 0.00 0.00 1.82
2380 5210 1.522355 CTGCGCCCATGAATCGAGT 60.522 57.895 4.18 0.00 0.00 4.18
2421 5251 2.795231 TGAGCCCATCCTGAGAAAAG 57.205 50.000 0.00 0.00 0.00 2.27
2465 5295 4.870426 ACGCTGTTGGACTGTTAGATAATG 59.130 41.667 0.00 0.00 0.00 1.90
2485 5319 7.617533 ATTCATACAACAAAGTTACAAACGC 57.382 32.000 0.00 0.00 36.23 4.84
2570 5404 1.081906 AAAGAATGCGTGCACAGCG 60.082 52.632 18.64 3.96 37.44 5.18
2571 5405 0.318107 ACAAAGAATGCGTGCACAGC 60.318 50.000 18.64 20.34 0.00 4.40
2572 5406 1.401530 CACAAAGAATGCGTGCACAG 58.598 50.000 18.64 10.86 0.00 3.66
2573 5407 3.548201 CACAAAGAATGCGTGCACA 57.452 47.368 18.64 0.00 0.00 4.57
2580 5414 3.754188 CTCCAGTAGCACAAAGAATGC 57.246 47.619 0.00 0.00 43.74 3.56
2597 5431 0.882484 GCTAAGCTCATTCCGGCTCC 60.882 60.000 0.00 0.00 37.87 4.70
2598 5432 0.179073 TGCTAAGCTCATTCCGGCTC 60.179 55.000 0.00 0.00 37.87 4.70
2602 5436 5.053145 AGAGTATTTGCTAAGCTCATTCCG 58.947 41.667 14.13 0.00 0.00 4.30
2619 5453 7.676683 TGCTCCTCCAAAGTAAATAGAGTAT 57.323 36.000 0.00 0.00 0.00 2.12
2768 5615 2.910199 CGAATCTGAGCCTTCATCCAA 58.090 47.619 0.00 0.00 31.68 3.53
2833 5680 1.493022 ACTGTACTGCCAAGGTCCAAA 59.507 47.619 0.00 0.00 0.00 3.28
3073 5920 2.372264 TCCATCTTTGATGCAAGGAGC 58.628 47.619 0.00 0.00 45.96 4.70
3205 6052 1.863454 CGTTGTCCTGCTGCAGATATC 59.137 52.381 30.10 16.32 32.44 1.63
3214 6064 1.583054 GTTCACTTCGTTGTCCTGCT 58.417 50.000 0.00 0.00 0.00 4.24
3215 6065 0.586802 GGTTCACTTCGTTGTCCTGC 59.413 55.000 0.00 0.00 0.00 4.85
3216 6066 2.240493 AGGTTCACTTCGTTGTCCTG 57.760 50.000 0.00 0.00 0.00 3.86
3217 6067 2.835027 GAAGGTTCACTTCGTTGTCCT 58.165 47.619 0.00 0.00 45.51 3.85
3425 6278 2.901042 CTCCTTAGGTCCGGGCAC 59.099 66.667 9.07 0.00 0.00 5.01
3431 6284 0.253327 CCAGGTTGCTCCTTAGGTCC 59.747 60.000 0.00 0.00 45.67 4.46
3556 6409 2.711542 ACCCGTGATTCATCTGAAACC 58.288 47.619 0.00 0.00 37.61 3.27
3579 6432 1.456732 GCAGTTGATTCGCGCATTAC 58.543 50.000 8.75 0.00 0.00 1.89
4059 6912 4.898265 TCTTTGTATGATCTGGAGAGAGGG 59.102 45.833 0.00 0.00 0.00 4.30
4061 6914 8.183536 CGATATCTTTGTATGATCTGGAGAGAG 58.816 40.741 0.34 0.00 0.00 3.20
4087 6940 2.960819 ACTGACTAAACCGACAGATGC 58.039 47.619 0.00 0.00 34.88 3.91
4221 7074 6.985059 GGTTTTACCCTACAGAGTAAGCATAG 59.015 42.308 0.00 0.00 30.04 2.23
4320 7173 1.002366 CAGAATCTTGGTCTTCGCCG 58.998 55.000 0.00 0.00 0.00 6.46
4391 7252 7.041780 GCTTACAGGATAACAATGTAGGTGATG 60.042 40.741 0.00 0.00 31.30 3.07
4398 7259 5.601583 TCGGCTTACAGGATAACAATGTA 57.398 39.130 0.00 0.00 0.00 2.29
4414 7275 2.380081 CCGTTCGCTTATTCGGCTT 58.620 52.632 0.00 0.00 36.68 4.35
4505 7366 3.190535 GTGGGTTGAACATACATCACCAC 59.809 47.826 0.00 0.00 0.00 4.16
4679 7544 3.815401 GCTCTTCTAGTCCAGTGCAAAAA 59.185 43.478 0.00 0.00 31.24 1.94
4849 7739 1.396301 CAGCTCAGCGAGTCCAAATTC 59.604 52.381 0.00 0.00 31.39 2.17
4897 7794 0.865769 GGCGAGAAAAGTCGAAGCAA 59.134 50.000 0.00 0.00 42.85 3.91
4912 7809 2.071844 GATCTTGGATCGGACGGCGA 62.072 60.000 16.62 0.00 0.00 5.54
4986 7883 2.579738 GAGAGGGTGGGTTCGAGC 59.420 66.667 0.00 0.00 0.00 5.03
4988 7885 2.678934 CGGAGAGGGTGGGTTCGA 60.679 66.667 0.00 0.00 0.00 3.71
5325 8229 1.478510 GCGATGAGGAAGAAGAGGACA 59.521 52.381 0.00 0.00 0.00 4.02
5379 8283 2.042843 GGGAGAAGGCGAGAGGGA 60.043 66.667 0.00 0.00 0.00 4.20
5395 8299 1.211709 GCGAAATGTTCAACGGGGG 59.788 57.895 0.00 0.00 0.00 5.40
5414 8318 2.806608 TTGACCCGTGTTAGTCAGAC 57.193 50.000 0.00 0.00 43.48 3.51
5415 8319 3.823281 TTTTGACCCGTGTTAGTCAGA 57.177 42.857 0.00 0.00 43.48 3.27
5424 8328 1.335872 GCACCAGAATTTTGACCCGTG 60.336 52.381 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.