Multiple sequence alignment - TraesCS3D01G018200

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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 TraesCS3D01G018200 chr3D 100.000 4535 0 0 1 4535 6150809 6146275 0.000000e+00 8375
1 TraesCS3D01G018200 chr3D 80.317 757 125 15 62 802 179287677 179288425 6.630000e-153 551
2 TraesCS3D01G018200 chr3A 93.191 3334 147 24 848 4142 14848613 14851905 0.000000e+00 4826
3 TraesCS3D01G018200 chr3A 93.750 384 18 4 4149 4532 14860642 14861019 5.090000e-159 571
4 TraesCS3D01G018200 chr3A 92.282 298 17 1 3847 4144 14860302 14860593 7.020000e-113 418
5 TraesCS3D01G018200 chr3A 84.466 309 30 8 4144 4439 14851952 14852255 5.740000e-74 289
6 TraesCS3D01G018200 chr3B 93.869 3148 146 20 891 4016 7371172 7374294 0.000000e+00 4700
7 TraesCS3D01G018200 chr3B 82.937 504 68 12 237 731 418698883 418699377 5.390000e-119 438
8 TraesCS3D01G018200 chr5D 83.426 718 95 12 93 802 543766275 543765574 0.000000e+00 645
9 TraesCS3D01G018200 chr4D 81.782 763 120 11 48 802 111143890 111143139 4.980000e-174 621
10 TraesCS3D01G018200 chr5B 83.139 599 83 12 1 587 17686135 17686727 8.640000e-147 531
11 TraesCS3D01G018200 chr5B 82.927 287 45 4 517 802 632111742 632111459 5.820000e-64 255
12 TraesCS3D01G018200 chr7B 79.710 759 124 21 31 776 409218632 409219373 5.200000e-144 521
13 TraesCS3D01G018200 chr7B 82.712 295 46 5 517 809 165300186 165300477 1.620000e-64 257
14 TraesCS3D01G018200 chr7B 80.841 214 36 5 404 616 568778705 568778496 3.630000e-36 163
15 TraesCS3D01G018200 chr6D 79.292 763 132 18 48 801 9539971 9540716 1.130000e-140 510
16 TraesCS3D01G018200 chr6D 81.902 326 47 10 105 424 3041604 3041285 9.670000e-67 265
17 TraesCS3D01G018200 chr7D 82.234 394 49 16 48 431 12379081 12378699 2.040000e-83 320
18 TraesCS3D01G018200 chr4A 85.000 280 28 11 157 428 725803970 725804243 5.780000e-69 272
19 TraesCS3D01G018200 chr2B 82.432 296 48 4 517 811 772143158 772142866 5.820000e-64 255
20 TraesCS3D01G018200 chr2A 82.867 286 45 4 517 801 284739636 284739918 2.090000e-63 254
21 TraesCS3D01G018200 chr5A 80.608 263 41 9 382 639 622141425 622141168 1.290000e-45 195


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 TraesCS3D01G018200 chr3D 6146275 6150809 4534 True 8375.0 8375 100.0000 1 4535 1 chr3D.!!$R1 4534
1 TraesCS3D01G018200 chr3D 179287677 179288425 748 False 551.0 551 80.3170 62 802 1 chr3D.!!$F1 740
2 TraesCS3D01G018200 chr3A 14848613 14852255 3642 False 2557.5 4826 88.8285 848 4439 2 chr3A.!!$F1 3591
3 TraesCS3D01G018200 chr3A 14860302 14861019 717 False 494.5 571 93.0160 3847 4532 2 chr3A.!!$F2 685
4 TraesCS3D01G018200 chr3B 7371172 7374294 3122 False 4700.0 4700 93.8690 891 4016 1 chr3B.!!$F1 3125
5 TraesCS3D01G018200 chr5D 543765574 543766275 701 True 645.0 645 83.4260 93 802 1 chr5D.!!$R1 709
6 TraesCS3D01G018200 chr4D 111143139 111143890 751 True 621.0 621 81.7820 48 802 1 chr4D.!!$R1 754
7 TraesCS3D01G018200 chr5B 17686135 17686727 592 False 531.0 531 83.1390 1 587 1 chr5B.!!$F1 586
8 TraesCS3D01G018200 chr7B 409218632 409219373 741 False 521.0 521 79.7100 31 776 1 chr7B.!!$F2 745
9 TraesCS3D01G018200 chr6D 9539971 9540716 745 False 510.0 510 79.2920 48 801 1 chr6D.!!$F1 753

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
120 125 0.241481 TTTGTTAATCAACCCGCGGC 59.759 50.0 22.85 2.61 35.61 6.53 F
1095 1131 0.107800 CTGGCCATCTCCACTGTCAG 60.108 60.0 5.51 0.00 31.74 3.51 F
2096 2156 0.036448 CTGGATATGAGCCTGGGCAG 59.964 60.0 14.39 0.00 44.88 4.85 F
2666 2726 0.603707 ATGATATTGTCCGGCGCCAG 60.604 55.0 28.98 16.96 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2087 0.865111 CAACGTGAACTCATTCGGCA 59.135 50.0 0.00 0.00 37.69 5.69 R
2517 2577 0.461693 TCGCACATTCGATGCATCCA 60.462 50.0 20.87 5.35 43.57 3.41 R
3315 3375 0.527385 GAGCAACAGCTAGCCTCTCG 60.527 60.0 12.13 0.00 39.10 4.04 R
4200 4320 0.253044 GCTGCACTCCCATACCTTCA 59.747 55.0 0.00 0.00 0.00 3.02 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
22 23 2.818751 TTCAGAAAACACCCCACACT 57.181 45.000 0.00 0.00 0.00 3.55
29 30 0.991355 AACACCCCACACTTCCCTGA 60.991 55.000 0.00 0.00 0.00 3.86
37 38 2.226437 CCACACTTCCCTGAAATCAACG 59.774 50.000 0.00 0.00 0.00 4.10
41 42 1.879380 CTTCCCTGAAATCAACGCACA 59.121 47.619 0.00 0.00 0.00 4.57
42 43 1.974265 TCCCTGAAATCAACGCACAA 58.026 45.000 0.00 0.00 0.00 3.33
43 44 2.302260 TCCCTGAAATCAACGCACAAA 58.698 42.857 0.00 0.00 0.00 2.83
120 125 0.241481 TTTGTTAATCAACCCGCGGC 59.759 50.000 22.85 2.61 35.61 6.53
131 136 0.749091 ACCCGCGGCCCTATTTTAAC 60.749 55.000 22.85 0.00 0.00 2.01
132 137 1.449726 CCCGCGGCCCTATTTTAACC 61.450 60.000 22.85 0.00 0.00 2.85
140 145 4.450080 CGGCCCTATTTTAACCGAGAATAC 59.550 45.833 0.00 0.00 46.71 1.89
197 203 4.142425 GGTTTTGATTAATAAACCCGCCGA 60.142 41.667 17.09 0.00 44.78 5.54
214 220 5.230942 CCGCCGATCATCTAGAAAATAACT 58.769 41.667 0.00 0.00 0.00 2.24
428 444 4.841443 ACCCGAACTCCAATTTTAACAC 57.159 40.909 0.00 0.00 0.00 3.32
431 447 4.460505 CCGAACTCCAATTTTAACACGTC 58.539 43.478 0.00 0.00 0.00 4.34
530 549 6.548441 TTGTTTAGGACACAACCTTAATCG 57.452 37.500 0.00 0.00 41.00 3.34
552 571 0.396435 AGTGCATGACCCGTCTTTCA 59.604 50.000 0.00 0.00 0.00 2.69
559 578 4.096382 GCATGACCCGTCTTTCATTTGTAT 59.904 41.667 0.00 0.00 29.64 2.29
576 595 2.224281 TGTATTGGTGCCGATCCAGATC 60.224 50.000 0.00 0.00 36.28 2.75
632 651 5.008811 AGACGAAAGAGACCATCTATAACCG 59.991 44.000 0.00 0.00 37.23 4.44
633 652 3.982058 CGAAAGAGACCATCTATAACCGC 59.018 47.826 0.00 0.00 37.23 5.68
640 659 2.143122 CCATCTATAACCGCGCATGTT 58.857 47.619 15.52 15.52 0.00 2.71
659 678 0.886043 TCGTCGACGAGGGTGAGAAA 60.886 55.000 34.97 10.59 44.22 2.52
716 737 5.638596 ATTGAAATAAAGAACGTGGACCC 57.361 39.130 0.00 0.00 0.00 4.46
717 738 3.068560 TGAAATAAAGAACGTGGACCCG 58.931 45.455 0.00 1.36 0.00 5.28
784 807 0.890542 TTTCTCCTGTTGCAGCGCAT 60.891 50.000 11.47 0.00 38.76 4.73
786 809 2.281692 TCCTGTTGCAGCGCATGT 60.282 55.556 11.47 0.00 38.76 3.21
794 817 1.513586 GCAGCGCATGTGCTCTTTC 60.514 57.895 30.27 15.58 45.23 2.62
795 818 1.871077 CAGCGCATGTGCTCTTTCA 59.129 52.632 30.27 0.00 45.23 2.69
802 825 3.926527 CGCATGTGCTCTTTCACTAGTAA 59.073 43.478 0.00 0.00 39.32 2.24
803 826 4.388773 CGCATGTGCTCTTTCACTAGTAAA 59.611 41.667 0.00 0.00 39.32 2.01
804 827 5.107104 CGCATGTGCTCTTTCACTAGTAAAA 60.107 40.000 0.00 0.00 39.32 1.52
805 828 6.565811 CGCATGTGCTCTTTCACTAGTAAAAA 60.566 38.462 0.00 0.00 39.32 1.94
848 871 9.747898 TTTTGAGGCAAAAGAATAAGGTATAGA 57.252 29.630 1.51 0.00 38.24 1.98
849 872 9.920946 TTTGAGGCAAAAGAATAAGGTATAGAT 57.079 29.630 0.00 0.00 29.89 1.98
850 873 8.908786 TGAGGCAAAAGAATAAGGTATAGATG 57.091 34.615 0.00 0.00 0.00 2.90
851 874 7.939039 TGAGGCAAAAGAATAAGGTATAGATGG 59.061 37.037 0.00 0.00 0.00 3.51
852 875 8.045720 AGGCAAAAGAATAAGGTATAGATGGA 57.954 34.615 0.00 0.00 0.00 3.41
853 876 8.673251 AGGCAAAAGAATAAGGTATAGATGGAT 58.327 33.333 0.00 0.00 0.00 3.41
854 877 9.301897 GGCAAAAGAATAAGGTATAGATGGATT 57.698 33.333 0.00 0.00 0.00 3.01
904 930 3.330405 AGCACCAAATGGGCCTTTAAATT 59.670 39.130 4.53 0.00 42.05 1.82
908 934 2.677337 CAAATGGGCCTTTAAATTGCCG 59.323 45.455 17.80 5.16 46.31 5.69
914 940 2.750712 GGCCTTTAAATTGCCGTGTCTA 59.249 45.455 11.76 0.00 35.08 2.59
928 954 2.165641 CGTGTCTATTGGGCACTACAGA 59.834 50.000 3.20 0.00 0.00 3.41
991 1024 9.813446 GGATAGATTAGAGTACTACTAGCTCTC 57.187 40.741 0.00 0.00 39.87 3.20
997 1033 4.885325 AGAGTACTACTAGCTCTCAAAGGC 59.115 45.833 0.00 0.00 34.86 4.35
1024 1060 2.103094 CGCACCCTTATCTCATCTTCCA 59.897 50.000 0.00 0.00 0.00 3.53
1064 1100 0.754957 AGATCCCCTCGCTCTCACAG 60.755 60.000 0.00 0.00 0.00 3.66
1095 1131 0.107800 CTGGCCATCTCCACTGTCAG 60.108 60.000 5.51 0.00 31.74 3.51
1339 1399 1.153958 GCAGCGGAAAATGGCAGAC 60.154 57.895 0.00 0.00 0.00 3.51
1647 1707 4.148825 ACCTGGACGGCGCTGATC 62.149 66.667 25.98 16.13 35.61 2.92
1665 1725 3.713248 TGATCACAGGCCATACTCTGAAT 59.287 43.478 5.01 0.00 35.20 2.57
1717 1777 3.805891 GAGATGCTCGAGCTGGGGC 62.806 68.421 35.27 14.54 42.66 5.80
1830 1890 2.611224 GGTTAAGTATGGGGCCGATACG 60.611 54.545 26.55 0.00 32.46 3.06
1873 1933 4.393062 CACTTTGTAGGATGTACTGCAAGG 59.607 45.833 4.12 4.12 42.53 3.61
1878 1938 0.749454 GGATGTACTGCAAGGCTGGG 60.749 60.000 0.00 0.00 39.30 4.45
2027 2087 2.444895 GCTCGAGGGAGGGGTGAT 60.445 66.667 15.58 0.00 40.80 3.06
2087 2147 1.735920 GCGCGAGGCTGGATATGAG 60.736 63.158 12.10 0.00 39.11 2.90
2096 2156 0.036448 CTGGATATGAGCCTGGGCAG 59.964 60.000 14.39 0.00 44.88 4.85
2235 2295 2.364970 AGAGATGGACAGCAGCAGTATC 59.635 50.000 0.00 0.00 0.00 2.24
2259 2319 1.935873 ACGTGGAATGCAATGATCTCG 59.064 47.619 0.00 0.44 0.00 4.04
2283 2343 4.454678 GGTATGCTCAAATCATGGACTCA 58.545 43.478 0.00 0.00 0.00 3.41
2394 2454 3.582647 TGTTCACCTTCTCAAGCATCCTA 59.417 43.478 0.00 0.00 0.00 2.94
2517 2577 5.220970 GCTGGTAAACATGTACAACAAGTGT 60.221 40.000 0.00 0.00 44.82 3.55
2529 2589 2.183478 ACAAGTGTGGATGCATCGAA 57.817 45.000 20.15 8.55 0.00 3.71
2655 2715 5.821470 ACAGCTCTTTGAGGACATGATATTG 59.179 40.000 0.00 0.00 0.00 1.90
2666 2726 0.603707 ATGATATTGTCCGGCGCCAG 60.604 55.000 28.98 16.96 0.00 4.85
2820 2880 1.206578 GGTTGACATGTTCGTGCGG 59.793 57.895 0.00 0.00 0.00 5.69
2901 2961 1.538047 CCATCTGGTCCAGTTTGGTG 58.462 55.000 24.35 14.92 39.03 4.17
2943 3003 4.706962 GGGAACATGGAACTTGCTTTCTAT 59.293 41.667 0.00 0.00 0.00 1.98
3024 3084 2.649331 ACATGTACGTGTCTACTGGC 57.351 50.000 15.10 0.00 0.00 4.85
3039 3099 2.742372 GGCAGATGGCGTGACGTT 60.742 61.111 6.91 0.00 46.16 3.99
3051 3111 3.488090 GACGTTGCTAGGGTGCGC 61.488 66.667 0.00 0.00 35.36 6.09
3265 3325 0.913451 ATCTGACAGCAAGGAGGGCT 60.913 55.000 0.00 0.00 43.77 5.19
3315 3375 4.379499 GGTTCACTAATAAAGCACCACAGC 60.379 45.833 0.00 0.00 0.00 4.40
3322 3382 3.890936 AAGCACCACAGCGAGAGGC 62.891 63.158 0.00 0.00 44.05 4.70
3420 3480 2.548875 GACTGCCACAGCTCTATCAAG 58.451 52.381 0.00 0.00 40.80 3.02
3553 3613 2.754002 TGATGCCGAAAAATCTCATGCA 59.246 40.909 0.00 0.00 0.00 3.96
3554 3614 3.382227 TGATGCCGAAAAATCTCATGCAT 59.618 39.130 0.00 0.00 36.62 3.96
3555 3615 3.153676 TGCCGAAAAATCTCATGCATG 57.846 42.857 21.07 21.07 0.00 4.06
3556 3616 1.856597 GCCGAAAAATCTCATGCATGC 59.143 47.619 22.25 11.82 0.00 4.06
3584 3644 5.988561 CCCTGCTATTCTATTCTGAGAACAC 59.011 44.000 0.00 0.00 38.25 3.32
3616 3678 5.033589 TGCATTGGAAACAGGTTTGATTT 57.966 34.783 1.52 0.00 44.54 2.17
3627 3689 6.874288 ACAGGTTTGATTTCTCTGAAGAAG 57.126 37.500 0.00 0.00 42.36 2.85
3717 3789 3.386402 TCAGTCGGCATTGGTGACATATA 59.614 43.478 0.00 0.00 42.32 0.86
3718 3790 4.040339 TCAGTCGGCATTGGTGACATATAT 59.960 41.667 0.00 0.00 42.32 0.86
3719 3791 4.152938 CAGTCGGCATTGGTGACATATATG 59.847 45.833 11.29 11.29 42.32 1.78
3720 3792 3.436704 GTCGGCATTGGTGACATATATGG 59.563 47.826 16.96 0.00 42.32 2.74
3756 3828 4.403432 CCATGCATAAACCCAGTCAGATTT 59.597 41.667 0.00 0.00 0.00 2.17
3757 3829 5.450965 CCATGCATAAACCCAGTCAGATTTC 60.451 44.000 0.00 0.00 0.00 2.17
3758 3830 4.922206 TGCATAAACCCAGTCAGATTTCT 58.078 39.130 0.00 0.00 0.00 2.52
3759 3831 4.701651 TGCATAAACCCAGTCAGATTTCTG 59.298 41.667 0.97 0.97 45.08 3.02
3798 3874 2.895404 TCCTTAGCACTGTAGAACGGTT 59.105 45.455 0.00 0.00 35.04 4.44
3799 3875 3.057033 TCCTTAGCACTGTAGAACGGTTC 60.057 47.826 12.91 12.91 35.04 3.62
3805 3881 6.216801 AGCACTGTAGAACGGTTCAATATA 57.783 37.500 21.86 3.80 35.04 0.86
3830 3906 2.704725 AACTGTTGTAAATGCTGGCG 57.295 45.000 0.00 0.00 0.00 5.69
3857 3933 8.664669 ATTAGGGTCAGGTTTCATTGTTTTAT 57.335 30.769 0.00 0.00 0.00 1.40
3942 4018 6.851609 TGTGTACCATATGAAACAAATCTGC 58.148 36.000 3.65 0.00 0.00 4.26
4054 4130 1.453155 GGTGTAGTTGCTCCCATGTG 58.547 55.000 0.00 0.00 0.00 3.21
4055 4131 1.271379 GGTGTAGTTGCTCCCATGTGT 60.271 52.381 0.00 0.00 0.00 3.72
4056 4132 1.806542 GTGTAGTTGCTCCCATGTGTG 59.193 52.381 0.00 0.00 0.00 3.82
4057 4133 1.419762 TGTAGTTGCTCCCATGTGTGT 59.580 47.619 0.00 0.00 0.00 3.72
4058 4134 2.158682 TGTAGTTGCTCCCATGTGTGTT 60.159 45.455 0.00 0.00 0.00 3.32
4059 4135 2.071778 AGTTGCTCCCATGTGTGTTT 57.928 45.000 0.00 0.00 0.00 2.83
4100 4176 5.016831 TCTTCAGTCTCATAGCACTTGGTA 58.983 41.667 0.00 0.00 0.00 3.25
4144 4220 1.208293 AGAAGAAAGATGGGGCTCGAC 59.792 52.381 0.00 0.00 0.00 4.20
4145 4221 0.984230 AAGAAAGATGGGGCTCGACA 59.016 50.000 0.00 0.00 0.00 4.35
4146 4222 0.539051 AGAAAGATGGGGCTCGACAG 59.461 55.000 0.00 0.00 0.00 3.51
4213 4334 2.373502 GGAAGGGATGAAGGTATGGGAG 59.626 54.545 0.00 0.00 0.00 4.30
4281 4402 3.553095 GAGGAAGGTTGCGGTGGCT 62.553 63.158 0.00 0.00 40.82 4.75
4284 4405 4.586235 AAGGTTGCGGTGGCTGCT 62.586 61.111 0.00 0.00 40.82 4.24
4364 4497 1.879575 CCTCCCATCTTCCAGGTACA 58.120 55.000 0.00 0.00 0.00 2.90
4379 4512 0.763035 GTACACCCTGTCCCTGTTGT 59.237 55.000 0.00 0.00 0.00 3.32
4380 4513 1.142262 GTACACCCTGTCCCTGTTGTT 59.858 52.381 0.00 0.00 0.00 2.83
4381 4514 0.106719 ACACCCTGTCCCTGTTGTTG 60.107 55.000 0.00 0.00 0.00 3.33
4470 4603 0.584396 CTGCCGTAGTCGCAAAAACA 59.416 50.000 0.00 0.00 35.54 2.83
4532 4665 5.920193 TTGATTTGATCCTGGAATGGAAC 57.080 39.130 0.00 0.00 39.85 3.62
4533 4666 3.947196 TGATTTGATCCTGGAATGGAACG 59.053 43.478 0.00 0.00 39.85 3.95
4534 4667 3.433306 TTTGATCCTGGAATGGAACGT 57.567 42.857 0.00 0.00 39.85 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.650322 GAAGTGTGGGGTGTTTTCTGA 58.350 47.619 0.00 0.00 0.00 3.27
13 14 1.075536 GATTTCAGGGAAGTGTGGGGT 59.924 52.381 0.00 0.00 0.00 4.95
14 15 1.075374 TGATTTCAGGGAAGTGTGGGG 59.925 52.381 0.00 0.00 0.00 4.96
15 16 2.558359 GTTGATTTCAGGGAAGTGTGGG 59.442 50.000 0.00 0.00 0.00 4.61
22 23 1.974265 TGTGCGTTGATTTCAGGGAA 58.026 45.000 0.00 0.00 0.00 3.97
29 30 7.902403 CACTTTAAAATGTTTGTGCGTTGATTT 59.098 29.630 0.00 0.00 0.00 2.17
37 38 9.677567 TCTATTCTCACTTTAAAATGTTTGTGC 57.322 29.630 0.00 0.00 0.00 4.57
74 76 2.962859 AGGAGGGTTTCTGCAAAACAT 58.037 42.857 19.25 11.29 36.17 2.71
120 125 9.730420 CATTTTGTATTCTCGGTTAAAATAGGG 57.270 33.333 0.00 0.00 0.00 3.53
131 136 8.574196 AAAAGTGAAACATTTTGTATTCTCGG 57.426 30.769 0.00 0.00 33.41 4.63
181 187 4.906618 AGATGATCGGCGGGTTTATTAAT 58.093 39.130 7.21 0.00 0.00 1.40
505 524 6.854381 CGATTAAGGTTGTGTCCTAAACAAAC 59.146 38.462 0.00 0.00 44.03 2.93
506 525 6.016943 CCGATTAAGGTTGTGTCCTAAACAAA 60.017 38.462 0.00 0.00 40.31 2.83
530 549 0.249398 AAGACGGGTCATGCACTACC 59.751 55.000 10.26 10.26 34.85 3.18
552 571 2.951642 CTGGATCGGCACCAATACAAAT 59.048 45.455 0.00 0.00 36.95 2.32
576 595 3.624326 TTGCTGAGGTGTTCATTTTCG 57.376 42.857 0.00 0.00 34.68 3.46
632 651 3.169924 TCGTCGACGAACATGCGC 61.170 61.111 36.25 0.00 46.30 6.09
655 674 4.583073 AGTGTTGCCGTTTATCCTTTTTCT 59.417 37.500 0.00 0.00 0.00 2.52
659 678 3.482436 TCAGTGTTGCCGTTTATCCTTT 58.518 40.909 0.00 0.00 0.00 3.11
694 713 4.155280 CGGGTCCACGTTCTTTATTTCAAT 59.845 41.667 0.00 0.00 0.00 2.57
716 737 1.002134 ATGGCTCAAGACCCCAACG 60.002 57.895 0.00 0.00 31.43 4.10
717 738 0.967380 CCATGGCTCAAGACCCCAAC 60.967 60.000 0.00 0.00 31.43 3.77
822 845 9.747898 TCTATACCTTATTCTTTTGCCTCAAAA 57.252 29.630 4.87 4.87 40.41 2.44
823 846 9.920946 ATCTATACCTTATTCTTTTGCCTCAAA 57.079 29.630 0.00 0.00 0.00 2.69
824 847 9.342308 CATCTATACCTTATTCTTTTGCCTCAA 57.658 33.333 0.00 0.00 0.00 3.02
825 848 7.939039 CCATCTATACCTTATTCTTTTGCCTCA 59.061 37.037 0.00 0.00 0.00 3.86
826 849 8.157476 TCCATCTATACCTTATTCTTTTGCCTC 58.843 37.037 0.00 0.00 0.00 4.70
827 850 8.045720 TCCATCTATACCTTATTCTTTTGCCT 57.954 34.615 0.00 0.00 0.00 4.75
828 851 8.870075 ATCCATCTATACCTTATTCTTTTGCC 57.130 34.615 0.00 0.00 0.00 4.52
882 905 2.022718 TTAAAGGCCCATTTGGTGCT 57.977 45.000 0.00 0.00 36.04 4.40
883 906 2.849294 TTTAAAGGCCCATTTGGTGC 57.151 45.000 0.00 0.00 36.04 5.01
885 908 3.561097 GGCAATTTAAAGGCCCATTTGGT 60.561 43.478 18.40 0.00 41.90 3.67
886 909 3.016031 GGCAATTTAAAGGCCCATTTGG 58.984 45.455 18.40 0.00 41.90 3.28
887 910 2.677337 CGGCAATTTAAAGGCCCATTTG 59.323 45.455 21.52 8.90 44.90 2.32
888 911 2.304470 ACGGCAATTTAAAGGCCCATTT 59.696 40.909 21.52 0.00 44.90 2.32
889 912 1.905894 ACGGCAATTTAAAGGCCCATT 59.094 42.857 21.52 0.00 44.90 3.16
908 934 3.887621 TCTGTAGTGCCCAATAGACAC 57.112 47.619 0.00 0.00 34.48 3.67
954 982 9.921637 GTACTCTAATCTATCCCAAAAGATCTG 57.078 37.037 0.00 0.00 31.20 2.90
985 1018 1.379576 GCATGGGCCTTTGAGAGCT 60.380 57.895 4.53 0.00 0.00 4.09
991 1024 4.440127 GGTGCGCATGGGCCTTTG 62.440 66.667 29.42 3.64 36.38 2.77
997 1033 0.886490 GAGATAAGGGTGCGCATGGG 60.886 60.000 15.91 5.19 0.00 4.00
1024 1060 1.895020 TTTGGGTCGAGTATGCGGCT 61.895 55.000 0.00 0.00 35.93 5.52
1088 1124 3.240134 ATTGGCGCGGTCTGACAGT 62.240 57.895 8.83 0.00 0.00 3.55
1262 1321 9.558396 AATATGCAATGGTGAAAGAAAAAGAAA 57.442 25.926 0.00 0.00 0.00 2.52
1339 1399 3.535962 GGGGCTCTCGCTCTCCAG 61.536 72.222 0.00 0.00 36.65 3.86
1647 1707 3.875727 CAGAATTCAGAGTATGGCCTGTG 59.124 47.826 8.44 0.00 0.00 3.66
1665 1725 2.669569 GCCAGCACCGCTTCAGAA 60.670 61.111 0.00 0.00 36.40 3.02
1830 1890 1.002033 GAATTGCCCATGCTCGTGATC 60.002 52.381 0.00 0.00 38.71 2.92
1873 1933 1.298014 CAGACTCCAAGTCCCCAGC 59.702 63.158 3.54 0.00 46.18 4.85
1878 1938 1.194781 TCAGGCCAGACTCCAAGTCC 61.195 60.000 5.01 0.00 46.18 3.85
1993 2053 3.868888 GAGCATATCGAGAAACAAGCC 57.131 47.619 0.00 0.00 0.00 4.35
2027 2087 0.865111 CAACGTGAACTCATTCGGCA 59.135 50.000 0.00 0.00 37.69 5.69
2096 2156 1.676967 CAGAAAGCCTGGACCTGCC 60.677 63.158 0.00 0.00 39.23 4.85
2199 2259 3.495193 CATCTCTTCAAACAACCGCATG 58.505 45.455 0.00 0.00 0.00 4.06
2235 2295 3.314357 AGATCATTGCATTCCACGTGATG 59.686 43.478 19.30 14.84 32.30 3.07
2259 2319 2.887152 GTCCATGATTTGAGCATACCCC 59.113 50.000 0.00 0.00 0.00 4.95
2394 2454 1.818363 CATGGCGCTGCAGACTGAT 60.818 57.895 20.43 0.00 0.00 2.90
2472 2532 1.662360 CGCTGTTCACAACAACATCG 58.338 50.000 0.00 0.00 41.61 3.84
2517 2577 0.461693 TCGCACATTCGATGCATCCA 60.462 50.000 20.87 5.35 43.57 3.41
2529 2589 1.577328 CGAAGGCTTTGGTCGCACAT 61.577 55.000 6.59 0.00 0.00 3.21
2666 2726 2.993899 ACGAATGTGATCTCGTTTGGTC 59.006 45.455 17.32 0.73 45.58 4.02
2721 2781 4.200283 CGCTCAGCCTCCTCGACC 62.200 72.222 0.00 0.00 0.00 4.79
2781 2841 2.104253 GCACCCGTAATGGTCCACG 61.104 63.158 0.00 0.00 36.12 4.94
2820 2880 3.721370 ATCATCCAGCCGGCCCAAC 62.721 63.158 26.15 0.00 0.00 3.77
3024 3084 0.735978 TAGCAACGTCACGCCATCTG 60.736 55.000 0.00 0.00 0.00 2.90
3039 3099 1.965930 CAGTTTGCGCACCCTAGCA 60.966 57.895 11.12 0.00 42.15 3.49
3051 3111 3.731652 TCTTCATGTTTGGCCAGTTTG 57.268 42.857 5.11 2.99 0.00 2.93
3219 3279 0.811616 CAGGAGCATTCTGGTACGGC 60.812 60.000 0.00 0.00 33.02 5.68
3265 3325 0.740868 GCAGCAGGCTTGTCGTCATA 60.741 55.000 0.00 0.00 40.25 2.15
3288 3348 3.181510 GGTGCTTTATTAGTGAACCTGCG 60.182 47.826 0.00 0.00 0.00 5.18
3315 3375 0.527385 GAGCAACAGCTAGCCTCTCG 60.527 60.000 12.13 0.00 39.10 4.04
3322 3382 1.451028 GCCCCAGAGCAACAGCTAG 60.451 63.158 0.00 0.00 39.10 3.42
3333 3393 0.823356 GTGTTTTGAGCAGCCCCAGA 60.823 55.000 0.00 0.00 0.00 3.86
3420 3480 5.862323 TCTGTTTGCGAGTAATGAGAAGTAC 59.138 40.000 0.00 0.00 0.00 2.73
3556 3616 8.621304 TTCTCAGAATAGAATAGCAGGGTGCG 62.621 46.154 0.00 0.00 38.29 5.34
3562 3622 6.416455 GTCGTGTTCTCAGAATAGAATAGCAG 59.584 42.308 0.00 0.00 37.78 4.24
3563 3623 6.127730 TGTCGTGTTCTCAGAATAGAATAGCA 60.128 38.462 0.00 0.00 37.78 3.49
3584 3644 5.401033 TGTTTCCAATGCAAAAATTGTCG 57.599 34.783 0.00 0.00 36.06 4.35
3616 3678 5.670485 TGCAGTAAACAACTTCTTCAGAGA 58.330 37.500 0.00 0.00 35.76 3.10
3627 3689 4.517453 TCATGGTACCTTGCAGTAAACAAC 59.483 41.667 20.39 0.00 0.00 3.32
3717 3789 6.836714 ATGCATGGTCATATATACTCCCAT 57.163 37.500 0.00 3.99 33.06 4.00
3718 3790 7.747809 TTATGCATGGTCATATATACTCCCA 57.252 36.000 10.16 0.10 0.00 4.37
3719 3791 7.499232 GGTTTATGCATGGTCATATATACTCCC 59.501 40.741 10.16 0.00 0.00 4.30
3720 3792 7.499232 GGGTTTATGCATGGTCATATATACTCC 59.501 40.741 10.16 0.00 0.00 3.85
3805 3881 5.564651 GCCAGCATTTACAACAGTTACACAT 60.565 40.000 0.00 0.00 0.00 3.21
3830 3906 7.462571 AAACAATGAAACCTGACCCTAATAC 57.537 36.000 0.00 0.00 0.00 1.89
3857 3933 5.771153 TTGAGTCAGCATTGTGAATGAAA 57.229 34.783 0.40 0.00 41.46 2.69
4144 4220 2.743928 GACAGGGAACAGCGGCTG 60.744 66.667 27.43 27.43 37.52 4.85
4145 4221 4.379243 CGACAGGGAACAGCGGCT 62.379 66.667 0.00 0.00 0.00 5.52
4200 4320 0.253044 GCTGCACTCCCATACCTTCA 59.747 55.000 0.00 0.00 0.00 3.02
4239 4360 4.016706 CCGACACCGCCCTCCTTT 62.017 66.667 0.00 0.00 0.00 3.11
4364 4497 1.286305 ACCAACAACAGGGACAGGGT 61.286 55.000 0.00 0.00 0.00 4.34
4379 4512 2.224185 ACAGCACGTACAGATGAACCAA 60.224 45.455 7.46 0.00 0.00 3.67
4380 4513 1.343142 ACAGCACGTACAGATGAACCA 59.657 47.619 7.46 0.00 0.00 3.67
4381 4514 2.080286 ACAGCACGTACAGATGAACC 57.920 50.000 7.46 0.00 0.00 3.62
4494 4627 8.976986 ATCAAATCAATAACTGAGTTTTGCTC 57.023 30.769 1.97 0.00 39.25 4.26


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

AutoCloner maintained by Alex Coulton.