Multiple sequence alignment - TraesCS6B01G202700

Loading Multiple Alignment...

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 TraesCS6B01G202700 chr6B 100.000 7666 0 0 1 7666 248350482 248358147 0.000000e+00 14157.0
1 TraesCS6B01G202700 chr6B 76.536 179 23 12 7393 7565 91138571 91138406 6.380000e-11 80.5
2 TraesCS6B01G202700 chr6B 76.536 179 23 12 7393 7565 91168879 91168714 6.380000e-11 80.5
3 TraesCS6B01G202700 chr6A 94.688 6401 173 77 551 6888 187735827 187742123 0.000000e+00 9782.0
4 TraesCS6B01G202700 chr6A 88.070 570 32 18 1 538 187735220 187735785 1.800000e-180 643.0
5 TraesCS6B01G202700 chr6A 89.928 139 10 4 6879 7017 317609303 317609169 7.910000e-40 176.0
6 TraesCS6B01G202700 chr6A 79.231 130 14 8 7393 7516 12371673 12371551 2.290000e-10 78.7
7 TraesCS6B01G202700 chr6D 97.118 3192 66 10 3688 6876 142747244 142750412 0.000000e+00 5361.0
8 TraesCS6B01G202700 chr6D 93.477 2928 85 35 553 3432 142744375 142747244 0.000000e+00 4252.0
9 TraesCS6B01G202700 chr6D 87.370 578 32 20 1 538 142743745 142744321 6.530000e-175 625.0
10 TraesCS6B01G202700 chr6D 96.183 262 10 0 3431 3692 450529004 450529265 5.500000e-116 429.0
11 TraesCS6B01G202700 chr3A 99.361 782 4 1 6886 7666 175806224 175807005 0.000000e+00 1415.0
12 TraesCS6B01G202700 chr3A 86.598 97 13 0 3714 3810 661786321 661786417 2.930000e-19 108.0
13 TraesCS6B01G202700 chr3A 87.912 91 7 3 3712 3802 610058807 610058893 3.780000e-18 104.0
14 TraesCS6B01G202700 chr3B 97.396 768 16 3 6900 7666 103899649 103898885 0.000000e+00 1304.0
15 TraesCS6B01G202700 chr1B 98.165 654 11 1 7014 7666 650050497 650051150 0.000000e+00 1140.0
16 TraesCS6B01G202700 chr1B 75.156 640 136 21 4065 4692 598903676 598903048 5.860000e-71 279.0
17 TraesCS6B01G202700 chrUn 100.000 404 0 0 6924 7327 478282394 478282797 0.000000e+00 747.0
18 TraesCS6B01G202700 chr2A 95.149 268 13 0 3431 3698 625120490 625120223 2.560000e-114 424.0
19 TraesCS6B01G202700 chr2A 96.094 256 9 1 3431 3686 631201672 631201926 4.280000e-112 416.0
20 TraesCS6B01G202700 chr2A 93.015 272 17 2 3431 3700 578489077 578488806 5.570000e-106 396.0
21 TraesCS6B01G202700 chr2A 88.971 136 13 2 6882 7017 41150193 41150326 4.760000e-37 167.0
22 TraesCS6B01G202700 chr2D 95.019 261 13 0 3431 3691 535240032 535240292 1.990000e-110 411.0
23 TraesCS6B01G202700 chr2D 89.423 104 11 0 3712 3815 152871118 152871221 1.740000e-26 132.0
24 TraesCS6B01G202700 chr5A 94.656 262 14 0 3431 3692 684940048 684940309 2.580000e-109 407.0
25 TraesCS6B01G202700 chr5A 93.657 268 16 1 3425 3691 281122088 281122355 4.310000e-107 399.0
26 TraesCS6B01G202700 chr5A 89.167 120 11 2 6898 7017 229497053 229496936 1.720000e-31 148.0
27 TraesCS6B01G202700 chr5B 92.989 271 18 1 3422 3692 588158889 588158620 2.010000e-105 394.0
28 TraesCS6B01G202700 chr5B 76.374 182 24 12 7390 7565 184300326 184300494 6.380000e-11 80.5
29 TraesCS6B01G202700 chr1A 75.430 639 130 24 4065 4689 536936617 536937242 1.260000e-72 285.0
30 TraesCS6B01G202700 chr1A 90.909 132 10 2 6886 7017 74755121 74754992 7.910000e-40 176.0
31 TraesCS6B01G202700 chr1D 74.844 640 138 21 4065 4692 441078340 441077712 1.270000e-67 268.0
32 TraesCS6B01G202700 chr1D 85.149 101 15 0 3712 3812 188462784 188462684 3.780000e-18 104.0
33 TraesCS6B01G202700 chr4B 90.710 183 12 2 7424 7602 429272366 429272185 9.940000e-59 239.0
34 TraesCS6B01G202700 chr4A 90.769 130 10 2 6888 7017 650405050 650404923 1.020000e-38 172.0
35 TraesCS6B01G202700 chr4A 88.119 101 12 0 3712 3812 734405809 734405709 3.760000e-23 121.0
36 TraesCS6B01G202700 chr2B 90.152 132 11 2 6886 7017 771168360 771168231 3.680000e-38 171.0
37 TraesCS6B01G202700 chr7D 85.714 112 10 6 3712 3822 145831857 145831963 6.290000e-21 113.0
38 TraesCS6B01G202700 chr7D 97.059 34 1 0 7393 7426 24667203 24667236 2.990000e-04 58.4
39 TraesCS6B01G202700 chr7A 86.747 83 11 0 3728 3810 511516984 511516902 8.190000e-15 93.5
40 TraesCS6B01G202700 chr7A 78.146 151 18 10 7374 7516 171258713 171258856 1.770000e-11 82.4


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 TraesCS6B01G202700 chr6B 248350482 248358147 7665 False 14157.000000 14157 100.000 1 7666 1 chr6B.!!$F1 7665
1 TraesCS6B01G202700 chr6A 187735220 187742123 6903 False 5212.500000 9782 91.379 1 6888 2 chr6A.!!$F1 6887
2 TraesCS6B01G202700 chr6D 142743745 142750412 6667 False 3412.666667 5361 92.655 1 6876 3 chr6D.!!$F2 6875
3 TraesCS6B01G202700 chr3A 175806224 175807005 781 False 1415.000000 1415 99.361 6886 7666 1 chr3A.!!$F1 780
4 TraesCS6B01G202700 chr3B 103898885 103899649 764 True 1304.000000 1304 97.396 6900 7666 1 chr3B.!!$R1 766
5 TraesCS6B01G202700 chr1B 650050497 650051150 653 False 1140.000000 1140 98.165 7014 7666 1 chr1B.!!$F1 652
6 TraesCS6B01G202700 chr1B 598903048 598903676 628 True 279.000000 279 75.156 4065 4692 1 chr1B.!!$R1 627
7 TraesCS6B01G202700 chr1A 536936617 536937242 625 False 285.000000 285 75.430 4065 4689 1 chr1A.!!$F1 624
8 TraesCS6B01G202700 chr1D 441077712 441078340 628 True 268.000000 268 74.844 4065 4692 1 chr1D.!!$R2 627

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
485 526 0.517316 GCGAGACAAAAATCGTGGCT 59.483 50.000 0.0 0.0 40.97 4.75 F
1190 1323 0.321919 TTGCATGTCTGGTGAGAGGC 60.322 55.000 0.0 0.0 42.45 4.70 F
2671 2833 0.846015 CCATTCCCATGAGTAGGGCA 59.154 55.000 0.0 0.0 46.36 5.36 F
3778 3940 1.130561 GCCTTGAGGTGCGTTATGTTC 59.869 52.381 0.0 0.0 37.57 3.18 F
4007 4169 0.881118 TTTCTCGCCCAAGCACATTC 59.119 50.000 0.0 0.0 39.83 2.67 F
5752 5922 1.532868 CAGCGTTCAAGAAGTTCCCAG 59.467 52.381 0.0 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1928 1.195900 TCGCAAACTCATACGCAAACC 59.804 47.619 0.0 0.0 0.00 3.27 R
2888 3050 1.005394 CGTACCACAGACCCACACC 60.005 63.158 0.0 0.0 0.00 4.16 R
4007 4169 1.612676 ACATTCCCATCATGGCATCG 58.387 50.000 0.0 0.0 35.79 3.84 R
5752 5922 0.165295 GTGAGAACCCGCTTAAACGC 59.835 55.000 0.0 0.0 0.00 4.84 R
5808 5978 0.811915 ACTCCTTGATCTCGTCCACG 59.188 55.000 0.0 0.0 41.45 4.94 R
6747 6919 2.092861 TCGAAGAGAGGGAGTAGGAGTG 60.093 54.545 0.0 0.0 0.00 3.51 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
109 110 2.797074 TTGAACATGTCGTGTACGGA 57.203 45.000 0.00 0.00 41.14 4.69
190 196 1.336755 AGTGTTCAAAATGTGGGACGC 59.663 47.619 0.00 0.00 40.62 5.19
299 313 1.135431 GCCTTGCAAATGCGTGACATA 60.135 47.619 0.00 0.00 45.83 2.29
319 334 8.587608 TGACATATCAGATTGCTTTTTCCTTTT 58.412 29.630 0.00 0.00 0.00 2.27
348 363 3.057019 CAGACGGATCGAACTGAACAAA 58.943 45.455 8.69 0.00 37.15 2.83
405 420 0.666577 CTGACGAAGGGACAACGGAC 60.667 60.000 0.00 0.00 34.11 4.79
451 471 1.266867 ATCCATTTGCAAGGCCACCC 61.267 55.000 5.01 0.00 0.00 4.61
452 472 1.914764 CCATTTGCAAGGCCACCCT 60.915 57.895 5.01 0.00 45.77 4.34
471 512 1.209383 CACGAACGGAGAAGCGAGA 59.791 57.895 0.00 0.00 0.00 4.04
485 526 0.517316 GCGAGACAAAAATCGTGGCT 59.483 50.000 0.00 0.00 40.97 4.75
486 527 1.464189 GCGAGACAAAAATCGTGGCTC 60.464 52.381 0.00 0.00 46.10 4.70
548 590 4.441695 CGGCGGCTGCTCTCTTCA 62.442 66.667 18.85 0.00 42.25 3.02
680 777 3.529341 ATGCCACCGCGTGTCTTGA 62.529 57.895 4.92 0.00 38.08 3.02
681 778 2.970324 GCCACCGCGTGTCTTGAA 60.970 61.111 4.92 0.00 0.00 2.69
688 785 4.731667 CGTGTCTTGAAGCGCATG 57.268 55.556 11.47 0.00 0.00 4.06
689 786 1.133253 CGTGTCTTGAAGCGCATGG 59.867 57.895 11.47 0.00 0.00 3.66
690 787 1.154150 GTGTCTTGAAGCGCATGGC 60.154 57.895 11.47 0.00 44.05 4.40
691 788 2.334946 TGTCTTGAAGCGCATGGCC 61.335 57.895 11.47 0.00 45.17 5.36
692 789 2.033911 TCTTGAAGCGCATGGCCA 59.966 55.556 8.56 8.56 45.17 5.36
693 790 1.378911 TCTTGAAGCGCATGGCCAT 60.379 52.632 14.09 14.09 45.17 4.40
758 856 1.078426 CTCCCCCTCGCGTTTCAAT 60.078 57.895 5.77 0.00 0.00 2.57
817 924 1.006832 CGTTATCTGTTTGCCTCCCG 58.993 55.000 0.00 0.00 0.00 5.14
818 925 1.404986 CGTTATCTGTTTGCCTCCCGA 60.405 52.381 0.00 0.00 0.00 5.14
819 926 2.280628 GTTATCTGTTTGCCTCCCGAG 58.719 52.381 0.00 0.00 0.00 4.63
821 928 1.841302 ATCTGTTTGCCTCCCGAGCA 61.841 55.000 0.00 0.00 38.81 4.26
822 929 1.377725 CTGTTTGCCTCCCGAGCAT 60.378 57.895 0.00 0.00 40.59 3.79
824 931 2.751436 TTTGCCTCCCGAGCATGC 60.751 61.111 10.51 10.51 40.59 4.06
850 969 1.446272 GAAACTCCCGAGCACGAGG 60.446 63.158 4.70 4.90 42.66 4.63
1072 1198 3.321648 ATGTGAGGTGAGGCGCCA 61.322 61.111 31.54 5.56 36.32 5.69
1112 1238 3.088532 TCCCCCTCAATCAATCAAAACG 58.911 45.455 0.00 0.00 0.00 3.60
1116 1242 2.095263 CCTCAATCAATCAAAACGCCGT 60.095 45.455 0.00 0.00 0.00 5.68
1120 1246 1.154301 CAATCAAAACGCCGTCCCG 60.154 57.895 0.00 0.00 0.00 5.14
1190 1323 0.321919 TTGCATGTCTGGTGAGAGGC 60.322 55.000 0.00 0.00 42.45 4.70
1243 1376 5.106594 TGCAACTGTTCAGCTACATTACATG 60.107 40.000 4.75 0.00 0.00 3.21
1315 1450 6.204495 TCACCCTTTTGCATGCTTTTTAATTC 59.796 34.615 20.33 0.00 0.00 2.17
1361 1496 2.026822 TCAACCCTTCTGCCTCTTCATC 60.027 50.000 0.00 0.00 0.00 2.92
1373 1508 7.495901 TCTGCCTCTTCATCTTATTCTTGTAG 58.504 38.462 0.00 0.00 0.00 2.74
1581 1716 1.132643 CCGCTATAGATGCTCCGGTAC 59.867 57.143 3.21 0.00 0.00 3.34
1649 1784 5.597813 TCTCTTGCTCGACTTTCAATTTC 57.402 39.130 0.00 0.00 0.00 2.17
1650 1785 4.452455 TCTCTTGCTCGACTTTCAATTTCC 59.548 41.667 0.00 0.00 0.00 3.13
1651 1786 3.502211 TCTTGCTCGACTTTCAATTTCCC 59.498 43.478 0.00 0.00 0.00 3.97
1724 1859 7.574592 GCCAAAGTGCTAATCATCCTATCATTC 60.575 40.741 0.00 0.00 0.00 2.67
1793 1928 3.243201 GGCTTATTTCCCGAATCAAGCAG 60.243 47.826 17.99 0.00 36.79 4.24
1927 2062 8.032952 TGATAAGTCAACACTAATTGCTGAAG 57.967 34.615 0.00 0.00 32.01 3.02
2047 2183 2.493278 ACAGGTATGCATGCAAAACTCC 59.507 45.455 26.68 20.26 0.00 3.85
2391 2529 8.344939 TGTTTATGGACCTAATTATCCCTTCT 57.655 34.615 3.21 0.00 33.69 2.85
2619 2781 5.247507 TGTGGCATCCAAAAAGAATATCG 57.752 39.130 0.00 0.00 34.18 2.92
2620 2782 4.044426 GTGGCATCCAAAAAGAATATCGC 58.956 43.478 0.00 0.00 34.18 4.58
2671 2833 0.846015 CCATTCCCATGAGTAGGGCA 59.154 55.000 0.00 0.00 46.36 5.36
3034 3196 4.701171 TGGGGTTAGCGAACGAAAAATTAT 59.299 37.500 3.50 0.00 36.32 1.28
3059 3221 5.656213 CGTATTTATAGGAACGGAGGGAT 57.344 43.478 0.00 0.00 0.00 3.85
3288 3450 5.826208 AGTCCGAAGAAAACCTAACACATTT 59.174 36.000 0.00 0.00 0.00 2.32
3448 3610 9.866655 TTATCTACTACTCCCTCCGTTTTTATA 57.133 33.333 0.00 0.00 0.00 0.98
3455 3617 6.510536 ACTCCCTCCGTTTTTATATACTTCG 58.489 40.000 0.00 0.00 0.00 3.79
3686 3848 5.553123 TGCAGAGTAAATAAAAACGGAGGA 58.447 37.500 0.00 0.00 0.00 3.71
3778 3940 1.130561 GCCTTGAGGTGCGTTATGTTC 59.869 52.381 0.00 0.00 37.57 3.18
3907 4069 6.264518 GGTGTACCTTGAAATTCCTCTTTTCA 59.735 38.462 0.00 0.00 40.37 2.69
4007 4169 0.881118 TTTCTCGCCCAAGCACATTC 59.119 50.000 0.00 0.00 39.83 2.67
4379 4542 5.499334 CGAGACAAGCGTCAAGAAATCATAC 60.499 44.000 0.00 0.00 45.23 2.39
5015 5183 4.040047 TCAATTAGATGGAGAGAGGCCAA 58.960 43.478 5.01 0.00 39.21 4.52
5308 5476 9.493206 TTGAAACGTAAAGAACAGAACAATTAC 57.507 29.630 0.00 0.00 0.00 1.89
5358 5526 6.804677 TGTCATGCACTAACATCTTGTTTTT 58.195 32.000 0.00 0.00 41.45 1.94
5480 5650 4.209080 CGAATTCCTTGACTTTGCCAAAAC 59.791 41.667 0.00 0.00 0.00 2.43
5521 5691 4.323417 ACTGATCGAGATAGAGGTAGCAG 58.677 47.826 0.00 0.00 0.00 4.24
5540 5710 5.869579 AGCAGATCCTTTTCACTGAAGTTA 58.130 37.500 0.00 0.00 32.90 2.24
5541 5711 5.703130 AGCAGATCCTTTTCACTGAAGTTAC 59.297 40.000 0.00 0.00 32.90 2.50
5709 5879 1.882912 AGCAGCAAGTGTTCATCGAA 58.117 45.000 0.00 0.00 0.00 3.71
5752 5922 1.532868 CAGCGTTCAAGAAGTTCCCAG 59.467 52.381 0.00 0.00 0.00 4.45
5814 5984 2.747686 TCCAAGCCTTCCGTGGAC 59.252 61.111 0.00 0.00 45.44 4.02
5837 6007 1.064654 GATCAAGGAGTTTGCGGATGC 59.935 52.381 0.00 0.00 43.20 3.91
6003 6173 2.496899 ACTTTGCTGATCCGATGGTT 57.503 45.000 0.00 0.00 0.00 3.67
6111 6281 2.223112 CCTGTTTGACGCTATGCACATC 60.223 50.000 0.00 0.00 0.00 3.06
6385 6556 4.357279 GCACCCTTGCTGGAGCCT 62.357 66.667 0.00 0.00 46.17 4.58
6555 6726 0.764271 TCGGGCTGCCATTGATCATA 59.236 50.000 22.05 0.00 0.00 2.15
6588 6759 4.854173 TGGCATTGTACTACCACATGATT 58.146 39.130 0.00 0.00 0.00 2.57
6589 6760 5.995446 TGGCATTGTACTACCACATGATTA 58.005 37.500 0.00 0.00 0.00 1.75
6590 6761 6.600388 TGGCATTGTACTACCACATGATTAT 58.400 36.000 0.00 0.00 0.00 1.28
6592 6763 6.149474 GGCATTGTACTACCACATGATTATCC 59.851 42.308 0.00 0.00 0.00 2.59
6593 6764 6.936900 GCATTGTACTACCACATGATTATCCT 59.063 38.462 0.00 0.00 0.00 3.24
6594 6765 7.118390 GCATTGTACTACCACATGATTATCCTC 59.882 40.741 0.00 0.00 0.00 3.71
6622 6793 1.577736 CTCCTCCTCACACCCTGAAT 58.422 55.000 0.00 0.00 0.00 2.57
6662 6833 8.547967 TTGCTGTTTAAAGTAGATACTTCCTG 57.452 34.615 5.75 1.74 45.17 3.86
6667 6838 8.311836 TGTTTAAAGTAGATACTTCCTGACCAG 58.688 37.037 5.75 0.00 45.17 4.00
6713 6884 4.081862 CAGAAAGTTTCATCCCATGCATGT 60.082 41.667 24.58 4.09 0.00 3.21
6747 6919 4.762251 ACTCTCAAATGTTTAGGGAACTGC 59.238 41.667 0.00 0.00 43.88 4.40
6751 6923 4.518970 TCAAATGTTTAGGGAACTGCACTC 59.481 41.667 0.00 0.00 43.88 3.51
6752 6924 2.561478 TGTTTAGGGAACTGCACTCC 57.439 50.000 1.92 1.92 43.88 3.85
6791 6963 3.365472 GGAAGGCACTGGAATTTACCAT 58.635 45.455 0.00 0.00 40.86 3.55
6792 6964 3.381590 GGAAGGCACTGGAATTTACCATC 59.618 47.826 0.00 0.00 40.86 3.51
6793 6965 4.273318 GAAGGCACTGGAATTTACCATCT 58.727 43.478 0.00 0.00 40.86 2.90
6794 6966 4.322057 AGGCACTGGAATTTACCATCTT 57.678 40.909 0.00 0.00 39.34 2.40
6820 6995 7.653713 TCTGAAGTAAAAACAGCAAACAAAACA 59.346 29.630 0.00 0.00 0.00 2.83
6821 6996 7.791949 TGAAGTAAAAACAGCAAACAAAACAG 58.208 30.769 0.00 0.00 0.00 3.16
6822 6997 7.439655 TGAAGTAAAAACAGCAAACAAAACAGT 59.560 29.630 0.00 0.00 0.00 3.55
6823 6998 8.819643 AAGTAAAAACAGCAAACAAAACAGTA 57.180 26.923 0.00 0.00 0.00 2.74
6824 6999 8.234887 AGTAAAAACAGCAAACAAAACAGTAC 57.765 30.769 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.652507 CCAGGTTTCTAATACTCCGTTTAGATC 59.347 40.741 0.00 0.00 35.11 2.75
109 110 5.240844 TCATTCATACATACAGACCGACGAT 59.759 40.000 0.00 0.00 0.00 3.73
190 196 3.566322 TGTTCTATTCAAACAACCGGGTG 59.434 43.478 20.60 20.60 33.86 4.61
222 228 7.502226 ACAGATTTCTTCAACTACATGGACAAA 59.498 33.333 0.00 0.00 0.00 2.83
224 230 6.533730 ACAGATTTCTTCAACTACATGGACA 58.466 36.000 0.00 0.00 0.00 4.02
256 262 9.412460 AGGCATGTTTCTTTCTTCATTCATATA 57.588 29.630 0.00 0.00 0.00 0.86
299 313 5.280164 GGGGAAAAGGAAAAAGCAATCTGAT 60.280 40.000 0.00 0.00 0.00 2.90
319 334 2.833582 GATCCGTCTGCGAGGGGA 60.834 66.667 14.35 8.39 41.33 4.81
348 363 5.148651 AGTCGGCTAGTAATTCAACAACT 57.851 39.130 0.00 0.00 0.00 3.16
422 437 1.259840 GCAAATGGATGGTGCCACCT 61.260 55.000 16.23 0.00 41.56 4.00
451 471 0.794981 CTCGCTTCTCCGTTCGTGAG 60.795 60.000 0.00 0.00 0.00 3.51
452 472 1.209383 CTCGCTTCTCCGTTCGTGA 59.791 57.895 0.00 0.00 0.00 4.35
471 512 3.214328 ACTCTTGAGCCACGATTTTTGT 58.786 40.909 0.00 0.00 0.00 2.83
485 526 2.225017 GGATTTGGGGGTGAACTCTTGA 60.225 50.000 0.00 0.00 0.00 3.02
486 527 2.171003 GGATTTGGGGGTGAACTCTTG 58.829 52.381 0.00 0.00 0.00 3.02
534 576 2.507992 CCGTGAAGAGAGCAGCCG 60.508 66.667 0.00 0.00 0.00 5.52
535 577 2.125350 CCCGTGAAGAGAGCAGCC 60.125 66.667 0.00 0.00 0.00 4.85
537 579 1.153667 GAGCCCGTGAAGAGAGCAG 60.154 63.158 0.00 0.00 0.00 4.24
538 580 2.650116 GGAGCCCGTGAAGAGAGCA 61.650 63.158 0.00 0.00 0.00 4.26
540 582 2.726351 GGGGAGCCCGTGAAGAGAG 61.726 68.421 0.00 0.00 36.85 3.20
541 583 2.683933 GGGGAGCCCGTGAAGAGA 60.684 66.667 0.00 0.00 36.85 3.10
542 584 3.787001 GGGGGAGCCCGTGAAGAG 61.787 72.222 0.00 0.00 46.66 2.85
561 643 1.600638 CCCCGGTAGTGGAAGGTTC 59.399 63.158 0.00 0.00 0.00 3.62
673 770 2.334946 GGCCATGCGCTTCAAGACA 61.335 57.895 9.73 0.00 37.74 3.41
689 786 2.895372 CGTAACTCCGCCCATGGC 60.895 66.667 6.09 0.58 46.75 4.40
690 787 1.227263 CTCGTAACTCCGCCCATGG 60.227 63.158 4.14 4.14 0.00 3.66
691 788 1.227263 CCTCGTAACTCCGCCCATG 60.227 63.158 0.00 0.00 0.00 3.66
692 789 1.684734 ACCTCGTAACTCCGCCCAT 60.685 57.895 0.00 0.00 0.00 4.00
693 790 2.283388 ACCTCGTAACTCCGCCCA 60.283 61.111 0.00 0.00 0.00 5.36
749 847 2.077413 TGCCATGGAAATTGAAACGC 57.923 45.000 18.40 0.00 0.00 4.84
758 856 3.055240 CCTGCCTTAAAATGCCATGGAAA 60.055 43.478 18.40 2.28 0.00 3.13
817 924 3.366781 GGAGTTTCTTTCTTGGCATGCTC 60.367 47.826 18.92 8.46 0.00 4.26
818 925 2.560105 GGAGTTTCTTTCTTGGCATGCT 59.440 45.455 18.92 0.00 0.00 3.79
819 926 2.353109 GGGAGTTTCTTTCTTGGCATGC 60.353 50.000 9.90 9.90 0.00 4.06
821 928 2.162681 CGGGAGTTTCTTTCTTGGCAT 58.837 47.619 0.00 0.00 0.00 4.40
822 929 1.142060 TCGGGAGTTTCTTTCTTGGCA 59.858 47.619 0.00 0.00 0.00 4.92
824 931 1.807142 GCTCGGGAGTTTCTTTCTTGG 59.193 52.381 0.00 0.00 0.00 3.61
850 969 1.819903 CCCCGTCTATCTAGCTAAGCC 59.180 57.143 0.00 0.00 0.00 4.35
1092 1218 2.417243 GCGTTTTGATTGATTGAGGGGG 60.417 50.000 0.00 0.00 0.00 5.40
1093 1219 2.417243 GGCGTTTTGATTGATTGAGGGG 60.417 50.000 0.00 0.00 0.00 4.79
1116 1242 3.583086 AGAAGAAGATTGAAGGAACGGGA 59.417 43.478 0.00 0.00 0.00 5.14
1120 1246 7.361628 CCAAGCTAAGAAGAAGATTGAAGGAAC 60.362 40.741 2.86 0.00 41.69 3.62
1123 1249 5.356470 CCCAAGCTAAGAAGAAGATTGAAGG 59.644 44.000 2.86 0.00 41.69 3.46
1124 1250 6.176183 TCCCAAGCTAAGAAGAAGATTGAAG 58.824 40.000 2.86 0.00 41.69 3.02
1228 1361 7.129457 AGGAAAGATCATGTAATGTAGCTGA 57.871 36.000 0.00 0.00 46.80 4.26
1243 1376 5.289083 AGGATCTGCTACAAGGAAAGATC 57.711 43.478 0.00 0.00 41.58 2.75
1378 1513 9.632807 AAGAGATATATCTATGCACTCGAAAAC 57.367 33.333 15.31 0.00 37.25 2.43
1581 1716 2.775911 TCCAGAGTCTGCCATTTCTG 57.224 50.000 15.10 0.00 37.41 3.02
1651 1786 2.032860 AATGCTCGATCGAGTGGGGG 62.033 60.000 37.59 19.01 43.70 5.40
1793 1928 1.195900 TCGCAAACTCATACGCAAACC 59.804 47.619 0.00 0.00 0.00 3.27
1927 2062 5.370679 TGTTTTGTCCTTCTTAGGGTACAC 58.629 41.667 0.00 0.00 42.26 2.90
1950 2085 8.494433 TGAATATCTTCTAAACCCAGCTTGTAT 58.506 33.333 0.00 0.00 32.29 2.29
2047 2183 2.842208 TTGCAGTTCAAACGGTTCAG 57.158 45.000 0.00 0.00 0.00 3.02
2328 2466 7.383102 ACATGAACAAGAACTTGCTATAAGG 57.617 36.000 13.50 0.36 44.03 2.69
2391 2529 8.837788 AGCATATATGAAAGATCGTTGATTGA 57.162 30.769 17.10 0.00 0.00 2.57
2497 2659 7.131565 CACATTAAACAAAATGACCCTTTTGC 58.868 34.615 8.71 0.00 45.66 3.68
2619 2781 7.906160 ACACGTTATGTAAAGATAACATCAGC 58.094 34.615 9.76 0.00 40.88 4.26
2695 2857 1.898574 ACCCTGCGCCTTGTTCAAG 60.899 57.895 4.18 5.66 0.00 3.02
2874 3036 3.716006 CACCCACACAGCGCTTCG 61.716 66.667 7.50 3.72 0.00 3.79
2875 3037 2.591715 ACACCCACACAGCGCTTC 60.592 61.111 7.50 0.00 0.00 3.86
2876 3038 2.901840 CACACCCACACAGCGCTT 60.902 61.111 7.50 0.00 0.00 4.68
2877 3039 4.935495 CCACACCCACACAGCGCT 62.935 66.667 2.64 2.64 0.00 5.92
2879 3041 4.562425 ACCCACACCCACACAGCG 62.562 66.667 0.00 0.00 0.00 5.18
2880 3042 2.594592 GACCCACACCCACACAGC 60.595 66.667 0.00 0.00 0.00 4.40
2881 3043 1.227943 CAGACCCACACCCACACAG 60.228 63.158 0.00 0.00 0.00 3.66
2882 3044 1.998438 ACAGACCCACACCCACACA 60.998 57.895 0.00 0.00 0.00 3.72
2883 3045 1.525995 CACAGACCCACACCCACAC 60.526 63.158 0.00 0.00 0.00 3.82
2884 3046 2.751731 CCACAGACCCACACCCACA 61.752 63.158 0.00 0.00 0.00 4.17
2885 3047 1.412453 TACCACAGACCCACACCCAC 61.412 60.000 0.00 0.00 0.00 4.61
2886 3048 1.074395 TACCACAGACCCACACCCA 60.074 57.895 0.00 0.00 0.00 4.51
2887 3049 1.373812 GTACCACAGACCCACACCC 59.626 63.158 0.00 0.00 0.00 4.61
2888 3050 1.005394 CGTACCACAGACCCACACC 60.005 63.158 0.00 0.00 0.00 4.16
2965 3127 2.111384 GACCCATGCTACTCCTGAGAA 58.889 52.381 0.22 0.00 0.00 2.87
2966 3128 1.007118 TGACCCATGCTACTCCTGAGA 59.993 52.381 0.22 0.00 0.00 3.27
2973 3135 1.623811 ACGAAACTGACCCATGCTACT 59.376 47.619 0.00 0.00 0.00 2.57
3059 3221 8.956533 TGTTGATATATTGTGTTAGCTGCTAA 57.043 30.769 17.67 17.67 0.00 3.09
3230 3392 3.438781 CCGTGTGCCATTAGTAACACATT 59.561 43.478 7.76 0.00 44.17 2.71
3298 3460 4.233789 GGATTCACGATTAGCTAGCTCAG 58.766 47.826 23.26 13.29 0.00 3.35
3299 3461 3.636764 TGGATTCACGATTAGCTAGCTCA 59.363 43.478 23.26 11.58 0.00 4.26
3418 3580 4.659835 ACGGAGGGAGTAGTAGATAAGAGT 59.340 45.833 0.00 0.00 0.00 3.24
3434 3596 5.051816 TGCGAAGTATATAAAAACGGAGGG 58.948 41.667 0.00 0.00 0.00 4.30
3448 3610 8.500753 TTGACCAAAACTAATATGCGAAGTAT 57.499 30.769 0.00 0.00 36.38 2.12
3455 3617 7.062255 GCTTGACTTTGACCAAAACTAATATGC 59.938 37.037 0.00 0.00 0.00 3.14
3686 3848 7.233553 TGCTCCACTATGACTAGCATTATACTT 59.766 37.037 5.22 0.00 38.22 2.24
3778 3940 5.244178 CCATAGTGGGAGTAACTTAGCTAGG 59.756 48.000 0.48 0.48 32.67 3.02
3907 4069 8.872845 CAACAACAAAAGTTTCAGAAGCTAAAT 58.127 29.630 0.00 0.00 0.00 1.40
4007 4169 1.612676 ACATTCCCATCATGGCATCG 58.387 50.000 0.00 0.00 35.79 3.84
4152 4314 8.140677 TGCAAAAGGAAACATGAACTTTATTG 57.859 30.769 0.00 2.43 33.21 1.90
4346 4509 2.334838 ACGCTTGTCTCGGTAACATTC 58.665 47.619 0.00 0.00 0.00 2.67
4379 4542 9.875675 GATTTCAGATCTTTCAATATTTCTCCG 57.124 33.333 0.00 0.00 0.00 4.63
4953 5121 8.084684 TCAATCGTAGGATGATGATGAGTTAAG 58.915 37.037 0.00 0.00 31.83 1.85
5358 5526 3.264947 CTCGGCTGATCAGATGAACAAA 58.735 45.455 27.04 0.46 0.00 2.83
5359 5527 2.897436 CTCGGCTGATCAGATGAACAA 58.103 47.619 27.04 2.94 0.00 2.83
5480 5650 6.641169 TCAGTATACCAGAGACATTGCTAG 57.359 41.667 0.00 0.00 0.00 3.42
5540 5710 5.133221 GGGGATAACATGAGCAAATAGTGT 58.867 41.667 0.00 0.00 0.00 3.55
5541 5711 4.214119 CGGGGATAACATGAGCAAATAGTG 59.786 45.833 0.00 0.00 0.00 2.74
5709 5879 1.209990 AGTACGGAGGAGTCGTCTGAT 59.790 52.381 24.77 13.15 41.38 2.90
5752 5922 0.165295 GTGAGAACCCGCTTAAACGC 59.835 55.000 0.00 0.00 0.00 4.84
5808 5978 0.811915 ACTCCTTGATCTCGTCCACG 59.188 55.000 0.00 0.00 41.45 4.94
5814 5984 1.002366 CCGCAAACTCCTTGATCTCG 58.998 55.000 0.00 0.00 37.17 4.04
5837 6007 2.815211 CGCGGGTCACCATCACTG 60.815 66.667 0.00 0.00 36.13 3.66
6003 6173 3.251972 CAGCAGAGTATGTAGCGATCTCA 59.748 47.826 0.00 0.00 0.00 3.27
6041 6211 0.246635 AGGGAACTCGGTCACAATCG 59.753 55.000 0.00 0.00 32.90 3.34
6042 6212 1.726853 CAGGGAACTCGGTCACAATC 58.273 55.000 0.00 0.00 40.21 2.67
6111 6281 2.225019 AGCTGCAATCTGAAACTGTTCG 59.775 45.455 1.02 0.00 36.46 3.95
6232 6403 5.279106 CCCTGCAATTCATTCAGACAAAGAA 60.279 40.000 0.00 0.00 0.00 2.52
6235 6406 4.151121 TCCCTGCAATTCATTCAGACAAA 58.849 39.130 0.00 0.00 0.00 2.83
6588 6759 5.136220 TGAGGAGGAGGAAACATAGAGGATA 59.864 44.000 0.00 0.00 0.00 2.59
6589 6760 4.078336 TGAGGAGGAGGAAACATAGAGGAT 60.078 45.833 0.00 0.00 0.00 3.24
6590 6761 3.272285 TGAGGAGGAGGAAACATAGAGGA 59.728 47.826 0.00 0.00 0.00 3.71
6592 6763 4.026744 TGTGAGGAGGAGGAAACATAGAG 58.973 47.826 0.00 0.00 0.00 2.43
6593 6764 3.769844 GTGTGAGGAGGAGGAAACATAGA 59.230 47.826 0.00 0.00 0.00 1.98
6594 6765 3.118592 GGTGTGAGGAGGAGGAAACATAG 60.119 52.174 0.00 0.00 0.00 2.23
6662 6833 3.065371 GTGTAATTATGTGCAGGCTGGTC 59.935 47.826 17.64 0.29 0.00 4.02
6667 6838 3.016736 AGGTGTGTAATTATGTGCAGGC 58.983 45.455 0.00 0.00 0.00 4.85
6747 6919 2.092861 TCGAAGAGAGGGAGTAGGAGTG 60.093 54.545 0.00 0.00 0.00 3.51
6771 6943 4.273318 AGATGGTAAATTCCAGTGCCTTC 58.727 43.478 0.00 0.00 41.05 3.46
6772 6944 4.322057 AGATGGTAAATTCCAGTGCCTT 57.678 40.909 0.00 0.00 41.05 4.35
6773 6945 4.018050 AGAAGATGGTAAATTCCAGTGCCT 60.018 41.667 0.00 0.00 41.05 4.75
6774 6946 4.096984 CAGAAGATGGTAAATTCCAGTGCC 59.903 45.833 0.00 0.00 41.05 5.01
6775 6947 4.943705 TCAGAAGATGGTAAATTCCAGTGC 59.056 41.667 0.00 0.00 41.05 4.40
6791 6963 7.151999 TGTTTGCTGTTTTTACTTCAGAAGA 57.848 32.000 17.56 0.00 0.00 2.87
6792 6964 7.810766 TTGTTTGCTGTTTTTACTTCAGAAG 57.189 32.000 8.77 8.77 0.00 2.85
6793 6965 8.491950 GTTTTGTTTGCTGTTTTTACTTCAGAA 58.508 29.630 0.00 0.00 0.00 3.02
6794 6966 7.653713 TGTTTTGTTTGCTGTTTTTACTTCAGA 59.346 29.630 0.00 0.00 0.00 3.27
6884 7059 8.926710 CGTGCTTTATTAGTAGGGAAAGATATG 58.073 37.037 0.00 0.00 31.83 1.78
6888 7063 5.422970 TCCGTGCTTTATTAGTAGGGAAAGA 59.577 40.000 2.51 0.00 46.26 2.52
6889 7064 5.667466 TCCGTGCTTTATTAGTAGGGAAAG 58.333 41.667 2.51 0.00 46.26 2.62
6890 7065 5.680594 TCCGTGCTTTATTAGTAGGGAAA 57.319 39.130 2.51 0.00 46.26 3.13


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

AutoCloner maintained by Alex Coulton.