Multiple sequence alignment - TraesCS2D01G441400

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 TraesCS2D01G441400 chr2D 100.000 6150 0 0 1 6150 551894085 551887936 0.000000e+00 11358
1 TraesCS2D01G441400 chr2D 94.425 574 32 0 5577 6150 572679444 572678871 0.000000e+00 883
2 TraesCS2D01G441400 chr2D 93.031 574 38 1 5577 6150 47516594 47516023 0.000000e+00 837
3 TraesCS2D01G441400 chr2D 85.567 97 13 1 3583 3678 573957469 573957373 3.920000e-17 100
4 TraesCS2D01G441400 chr2B 94.647 2634 93 26 2961 5576 657197976 657195373 0.000000e+00 4039
5 TraesCS2D01G441400 chr2B 89.519 2223 117 42 819 2982 657200324 657198159 0.000000e+00 2708
6 TraesCS2D01G441400 chr2A 92.448 2529 129 16 759 3243 692700353 692697843 0.000000e+00 3555
7 TraesCS2D01G441400 chr2A 93.866 2380 93 18 3226 5576 692697660 692695305 0.000000e+00 3537
8 TraesCS2D01G441400 chr2A 85.567 97 13 1 3583 3678 712543617 712543521 3.920000e-17 100
9 TraesCS2D01G441400 chr5D 95.176 767 28 4 1 762 37679933 37680695 0.000000e+00 1203
10 TraesCS2D01G441400 chr5D 94.648 766 32 3 1 761 26759066 26758305 0.000000e+00 1179
11 TraesCS2D01G441400 chr1D 94.751 762 31 3 1 757 349809511 349810268 0.000000e+00 1177
12 TraesCS2D01G441400 chr7A 93.054 763 44 7 1 757 65546321 65545562 0.000000e+00 1107
13 TraesCS2D01G441400 chr7A 92.257 762 49 8 1 761 121041621 121042373 0.000000e+00 1072
14 TraesCS2D01G441400 chr7A 89.342 319 30 4 5198 5515 308027427 308027742 1.240000e-106 398
15 TraesCS2D01G441400 chr7A 89.308 318 32 2 5198 5515 620420683 620420368 1.240000e-106 398
16 TraesCS2D01G441400 chr5A 92.109 773 51 6 1 766 149337855 149337086 0.000000e+00 1081
17 TraesCS2D01G441400 chr5A 91.874 763 53 5 1 757 514781527 514780768 0.000000e+00 1057
18 TraesCS2D01G441400 chr5A 89.557 316 32 1 5197 5512 1838639 1838953 3.450000e-107 399
19 TraesCS2D01G441400 chr4B 91.525 767 53 5 1 757 625969241 625970005 0.000000e+00 1046
20 TraesCS2D01G441400 chr4B 90.988 577 51 1 5574 6150 513077352 513076777 0.000000e+00 776
21 TraesCS2D01G441400 chrUn 90.980 765 56 6 2 758 102693188 102692429 0.000000e+00 1018
22 TraesCS2D01G441400 chr4A 90.767 574 52 1 5577 6150 445033417 445033989 0.000000e+00 765
23 TraesCS2D01G441400 chr4A 90.435 575 52 3 5577 6150 646577058 646576486 0.000000e+00 754
24 TraesCS2D01G441400 chr4A 90.476 315 29 1 5197 5511 190832992 190833305 1.230000e-111 414
25 TraesCS2D01G441400 chr4A 89.969 319 29 3 5198 5515 546123531 546123847 5.740000e-110 409
26 TraesCS2D01G441400 chr4A 89.342 319 31 3 5198 5515 93621678 93621994 1.240000e-106 398
27 TraesCS2D01G441400 chr6B 89.637 579 56 4 5574 6150 213490264 213490840 0.000000e+00 734
28 TraesCS2D01G441400 chr6B 89.841 315 31 1 5198 5512 277270687 277270374 2.670000e-108 403
29 TraesCS2D01G441400 chr6B 90.064 312 30 1 5199 5510 547713647 547713957 2.670000e-108 403
30 TraesCS2D01G441400 chr3D 90.727 550 49 2 5600 6148 96699434 96698886 0.000000e+00 732
31 TraesCS2D01G441400 chr1B 89.391 575 59 2 5577 6150 616085580 616086153 0.000000e+00 723
32 TraesCS2D01G441400 chr3B 89.217 575 60 2 5577 6150 232720925 232720352 0.000000e+00 717


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 TraesCS2D01G441400 chr2D 551887936 551894085 6149 True 11358.0 11358 100.000 1 6150 1 chr2D.!!$R2 6149
1 TraesCS2D01G441400 chr2D 572678871 572679444 573 True 883.0 883 94.425 5577 6150 1 chr2D.!!$R3 573
2 TraesCS2D01G441400 chr2D 47516023 47516594 571 True 837.0 837 93.031 5577 6150 1 chr2D.!!$R1 573
3 TraesCS2D01G441400 chr2B 657195373 657200324 4951 True 3373.5 4039 92.083 819 5576 2 chr2B.!!$R1 4757
4 TraesCS2D01G441400 chr2A 692695305 692700353 5048 True 3546.0 3555 93.157 759 5576 2 chr2A.!!$R2 4817
5 TraesCS2D01G441400 chr5D 37679933 37680695 762 False 1203.0 1203 95.176 1 762 1 chr5D.!!$F1 761
6 TraesCS2D01G441400 chr5D 26758305 26759066 761 True 1179.0 1179 94.648 1 761 1 chr5D.!!$R1 760
7 TraesCS2D01G441400 chr1D 349809511 349810268 757 False 1177.0 1177 94.751 1 757 1 chr1D.!!$F1 756
8 TraesCS2D01G441400 chr7A 65545562 65546321 759 True 1107.0 1107 93.054 1 757 1 chr7A.!!$R1 756
9 TraesCS2D01G441400 chr7A 121041621 121042373 752 False 1072.0 1072 92.257 1 761 1 chr7A.!!$F1 760
10 TraesCS2D01G441400 chr5A 149337086 149337855 769 True 1081.0 1081 92.109 1 766 1 chr5A.!!$R1 765
11 TraesCS2D01G441400 chr5A 514780768 514781527 759 True 1057.0 1057 91.874 1 757 1 chr5A.!!$R2 756
12 TraesCS2D01G441400 chr4B 625969241 625970005 764 False 1046.0 1046 91.525 1 757 1 chr4B.!!$F1 756
13 TraesCS2D01G441400 chr4B 513076777 513077352 575 True 776.0 776 90.988 5574 6150 1 chr4B.!!$R1 576
14 TraesCS2D01G441400 chrUn 102692429 102693188 759 True 1018.0 1018 90.980 2 758 1 chrUn.!!$R1 756
15 TraesCS2D01G441400 chr4A 445033417 445033989 572 False 765.0 765 90.767 5577 6150 1 chr4A.!!$F3 573
16 TraesCS2D01G441400 chr4A 646576486 646577058 572 True 754.0 754 90.435 5577 6150 1 chr4A.!!$R1 573
17 TraesCS2D01G441400 chr6B 213490264 213490840 576 False 734.0 734 89.637 5574 6150 1 chr6B.!!$F1 576
18 TraesCS2D01G441400 chr3D 96698886 96699434 548 True 732.0 732 90.727 5600 6148 1 chr3D.!!$R1 548
19 TraesCS2D01G441400 chr1B 616085580 616086153 573 False 723.0 723 89.391 5577 6150 1 chr1B.!!$F1 573
20 TraesCS2D01G441400 chr3B 232720352 232720925 573 True 717.0 717 89.217 5577 6150 1 chr3B.!!$R1 573

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
833 864 0.029567 TGTTTAACAAAGCCCGTGCG 59.970 50.000 0.00 0.00 44.33 5.34 F
1031 1064 0.108329 GGCGACGATTCTCCAAAGGA 60.108 55.000 0.00 0.00 0.00 3.36 F
1734 1798 0.727398 GATTTGTAGCAGGGTCGTGC 59.273 55.000 7.47 7.47 44.35 5.34 F
2851 2951 1.134280 CCCATGTCTAAGCCTCCACTG 60.134 57.143 0.00 0.00 0.00 3.66 F
4090 4606 0.997196 CCTTTTGAGTAGGCGCGTAC 59.003 55.000 28.08 28.08 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2793 2893 3.191162 CCACGACATTCAACATTCACCAT 59.809 43.478 0.00 0.0 0.00 3.55 R
2836 2936 0.321671 TGCACAGTGGAGGCTTAGAC 59.678 55.000 1.84 0.0 0.00 2.59 R
2917 3017 3.119531 CGCCAATTGTTTCCATGAAGCTA 60.120 43.478 4.43 0.0 0.00 3.32 R
4652 5173 2.497273 TCGATCTGGAAGCATCAGTGAA 59.503 45.455 0.00 0.0 34.15 3.18 R
6048 6595 0.250597 GGGGCGGAAACTTACTGTGT 60.251 55.000 0.00 0.0 0.00 3.72 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
35 36 4.514441 ACAAGCTTGTCTCTATATGCATGC 59.486 41.667 26.36 11.82 36.50 4.06
138 139 4.439860 ACAATTCTTCCCCTACCTCTCTT 58.560 43.478 0.00 0.00 0.00 2.85
215 216 7.038659 ACATCCGATTTTTGTGTTTTTCTTGA 58.961 30.769 0.00 0.00 0.00 3.02
229 230 9.853921 GTGTTTTTCTTGATGACAATTTGATTC 57.146 29.630 2.79 0.00 35.37 2.52
239 240 5.147032 TGACAATTTGATTCCTTGGTCCTT 58.853 37.500 2.79 0.00 0.00 3.36
260 261 2.651382 AAAAGGCAGGTAACCGTCTT 57.349 45.000 0.00 0.00 37.17 3.01
405 408 9.936759 TGTGATAACATCTCAGTTGTTTACATA 57.063 29.630 6.43 4.01 38.26 2.29
612 617 1.067582 CGAGCCTCCCGTTGATACC 59.932 63.158 0.00 0.00 0.00 2.73
616 621 2.777972 CCTCCCGTTGATACCGCGA 61.778 63.158 8.23 0.00 0.00 5.87
686 692 7.559170 AGTCGTATTGTAATAGGTCTAGTTGGT 59.441 37.037 4.76 0.00 0.00 3.67
797 822 2.069273 GTCAGATATGGAATTCGGGCG 58.931 52.381 0.00 0.00 0.00 6.13
833 864 0.029567 TGTTTAACAAAGCCCGTGCG 59.970 50.000 0.00 0.00 44.33 5.34
834 865 1.008309 TTTAACAAAGCCCGTGCGC 60.008 52.632 0.00 0.00 44.33 6.09
843 874 4.170062 CCCGTGCGCTGCTGATTG 62.170 66.667 9.73 0.00 0.00 2.67
870 901 2.591429 TGGTCACTTGCACAGCCG 60.591 61.111 0.00 0.00 0.00 5.52
987 1020 0.819582 GAAATAGTCCCGTCCCGTGA 59.180 55.000 0.00 0.00 0.00 4.35
1031 1064 0.108329 GGCGACGATTCTCCAAAGGA 60.108 55.000 0.00 0.00 0.00 3.36
1041 1074 3.373565 CCAAAGGAGGTTGGGCGC 61.374 66.667 0.00 0.00 43.79 6.53
1066 1099 3.755628 GCAGACCTCGGCGTGGTA 61.756 66.667 30.90 0.00 38.03 3.25
1070 1103 2.282674 ACCTCGGCGTGGTAGTGA 60.283 61.111 30.01 0.00 35.80 3.41
1425 1459 1.352622 TTGACAAGGTGAGGGCTGGT 61.353 55.000 0.00 0.00 0.00 4.00
1428 1462 3.260100 AAGGTGAGGGCTGGTGGG 61.260 66.667 0.00 0.00 0.00 4.61
1485 1519 1.916181 CACTATGACCCCAAGGACCTT 59.084 52.381 0.00 0.00 36.73 3.50
1514 1548 1.555075 AGAGGCAAGCGGATTCTGTAA 59.445 47.619 0.00 0.00 0.00 2.41
1515 1549 1.666189 GAGGCAAGCGGATTCTGTAAC 59.334 52.381 0.00 0.00 0.00 2.50
1516 1550 1.279271 AGGCAAGCGGATTCTGTAACT 59.721 47.619 0.00 0.00 0.00 2.24
1518 1552 2.488153 GGCAAGCGGATTCTGTAACTTT 59.512 45.455 0.00 0.00 0.00 2.66
1523 1557 6.469275 GCAAGCGGATTCTGTAACTTTTAATC 59.531 38.462 0.00 0.00 0.00 1.75
1528 1562 6.183360 CGGATTCTGTAACTTTTAATCGCAGT 60.183 38.462 0.00 0.00 0.00 4.40
1584 1618 8.572185 TCAGATGTTATCTTAGACTCTATGCAC 58.428 37.037 0.00 0.00 37.58 4.57
1586 1620 7.507277 AGATGTTATCTTAGACTCTATGCACCA 59.493 37.037 0.00 0.00 35.76 4.17
1588 1622 8.023021 TGTTATCTTAGACTCTATGCACCAAT 57.977 34.615 0.00 0.00 0.00 3.16
1589 1623 8.144478 TGTTATCTTAGACTCTATGCACCAATC 58.856 37.037 0.00 0.00 0.00 2.67
1640 1704 3.186001 CCTATCAAGCGCATGATGAAGTC 59.814 47.826 32.10 0.00 40.21 3.01
1690 1754 4.336993 CCTGCCAGTAGTTAGTAGACTCTG 59.663 50.000 0.00 0.00 0.00 3.35
1697 1761 8.358148 CCAGTAGTTAGTAGACTCTGTTTTTGA 58.642 37.037 0.00 0.00 0.00 2.69
1698 1762 9.745880 CAGTAGTTAGTAGACTCTGTTTTTGAA 57.254 33.333 0.00 0.00 0.00 2.69
1719 1783 7.962964 TGAAACTGAACTCTGATTACGATTT 57.037 32.000 0.00 0.00 0.00 2.17
1734 1798 0.727398 GATTTGTAGCAGGGTCGTGC 59.273 55.000 7.47 7.47 44.35 5.34
1774 1838 1.827399 AACAGGGCCGAGTAGTGGTG 61.827 60.000 5.10 0.00 0.00 4.17
1843 1907 8.512138 CAATCGATTAAAAGTTTGTTCCCTACT 58.488 33.333 10.97 0.00 0.00 2.57
1874 1938 8.730680 ACAGTTATACTTGATGGTTGATGTTTC 58.269 33.333 0.00 0.00 0.00 2.78
2239 2328 7.505258 AGCTGGTTTGGTTGTTGTATTATTTT 58.495 30.769 0.00 0.00 0.00 1.82
2272 2361 2.225382 TCATCTCCGGGTCTTACACA 57.775 50.000 0.00 0.00 0.00 3.72
2448 2537 6.785337 TCGATAGACCAGAGTTTCCATTAA 57.215 37.500 0.00 0.00 42.67 1.40
2678 2777 7.475015 TGACACTGATAGTTTATGTACGGTAC 58.525 38.462 11.33 11.33 0.00 3.34
2679 2778 7.121020 TGACACTGATAGTTTATGTACGGTACA 59.879 37.037 22.05 22.05 43.80 2.90
2745 2845 6.044054 GGGGTAAATGTAAGCTATAGGGACTT 59.956 42.308 1.04 0.00 41.75 3.01
2748 2848 8.312564 GGTAAATGTAAGCTATAGGGACTTAGG 58.687 40.741 1.04 0.00 41.75 2.69
2793 2893 4.832823 TGATGTGTTAGAGAGAGGTGTCAA 59.167 41.667 0.00 0.00 0.00 3.18
2836 2936 3.368739 GGAAAATTGGTTGCTCTCCCATG 60.369 47.826 0.00 0.00 0.00 3.66
2851 2951 1.134280 CCCATGTCTAAGCCTCCACTG 60.134 57.143 0.00 0.00 0.00 3.66
2903 3003 3.244044 GGATGCTCTGGAAGGACTGTATC 60.244 52.174 0.00 0.00 0.00 2.24
2907 3007 3.431486 GCTCTGGAAGGACTGTATCTTGG 60.431 52.174 1.38 0.00 0.00 3.61
2917 3017 5.070685 GGACTGTATCTTGGACTTGGTTTT 58.929 41.667 0.00 0.00 0.00 2.43
2946 3046 4.360936 TGGAAACAATTGGCGTTGTGCA 62.361 45.455 10.83 0.00 41.22 4.57
3076 3380 6.266330 TCTGATATGGTAGAAGTGTCATCTGG 59.734 42.308 0.00 0.00 0.00 3.86
3263 3769 9.336171 AGGAAAATCTAATGCTATTGTCTCTTC 57.664 33.333 0.00 0.00 0.00 2.87
3314 3828 4.590400 TTGGCGTTTGTTTGTTCATTTG 57.410 36.364 0.00 0.00 0.00 2.32
3490 4004 3.919804 CACGGTAAGAATTTGCCATTGTG 59.080 43.478 0.00 0.00 38.84 3.33
3519 4035 1.531739 TTTTGGGGACGAGCCATTGC 61.532 55.000 0.00 0.00 38.95 3.56
3574 4090 9.635520 ATTTCTGCAAAGATATTAATGCTATGC 57.364 29.630 0.00 3.56 39.49 3.14
3715 4231 4.935808 GGAGTTTTGTCCTCGTATGAATGT 59.064 41.667 0.00 0.00 33.30 2.71
3873 4389 8.222138 TCCCTTATTTCTTTAACCCAGTCTAA 57.778 34.615 0.00 0.00 0.00 2.10
3912 4428 5.105513 TGTCATTCTTGCTATACCGTCTGAA 60.106 40.000 0.00 0.00 0.00 3.02
3926 4442 4.827284 ACCGTCTGAAAGGTTGATTTTCAT 59.173 37.500 1.40 0.00 41.98 2.57
3991 4507 2.716424 TCCTGGATTTTGGAACTGGACT 59.284 45.455 0.00 0.00 0.00 3.85
4000 4516 3.502123 TGGAACTGGACTTTTACCCTG 57.498 47.619 0.00 0.00 0.00 4.45
4060 4576 4.142249 CGTAATTGGAGGGGAATTGGTTTC 60.142 45.833 0.00 0.00 0.00 2.78
4086 4602 1.739067 ATGTCCTTTTGAGTAGGCGC 58.261 50.000 0.00 0.00 32.59 6.53
4090 4606 0.997196 CCTTTTGAGTAGGCGCGTAC 59.003 55.000 28.08 28.08 0.00 3.67
4130 4646 9.439500 AAGGAAATTCATTATGGAATGTGTTTG 57.561 29.630 0.00 0.00 42.71 2.93
4144 4660 6.074088 GGAATGTGTTTGATAGATGTCTAGCG 60.074 42.308 1.39 0.00 37.65 4.26
4149 4665 5.515270 TGTTTGATAGATGTCTAGCGAAACG 59.485 40.000 9.00 0.00 39.22 3.60
4160 4676 6.558009 TGTCTAGCGAAACGTAATCAGTAAT 58.442 36.000 0.00 0.00 0.00 1.89
4161 4677 6.471198 TGTCTAGCGAAACGTAATCAGTAATG 59.529 38.462 0.00 0.00 0.00 1.90
4183 4699 3.963428 AAGCTAACGATCCACACTCTT 57.037 42.857 0.00 0.00 0.00 2.85
4195 4711 6.693545 CGATCCACACTCTTATCACTAAGAAC 59.306 42.308 0.00 0.00 42.11 3.01
4279 4795 7.059788 TGGACACATAATTATAGCATGGTTGT 58.940 34.615 1.12 0.00 0.00 3.32
4283 4799 9.402320 ACACATAATTATAGCATGGTTGTACAA 57.598 29.630 3.59 3.59 0.00 2.41
4345 4863 1.019805 GCCTGTAGAAAGGACGTGGC 61.020 60.000 0.00 0.00 40.02 5.01
4347 4865 1.673033 CCTGTAGAAAGGACGTGGCTG 60.673 57.143 0.00 0.00 40.02 4.85
4350 4868 1.272769 GTAGAAAGGACGTGGCTGACT 59.727 52.381 0.00 0.00 0.00 3.41
4372 4890 5.129485 ACTGAGGAGTAATGACCGATCAATT 59.871 40.000 0.00 0.00 38.69 2.32
4584 5102 1.463444 GGCGCGTTTCAGTTTCTGTAT 59.537 47.619 8.43 0.00 32.61 2.29
4652 5173 7.201821 CCTTTAAACTGGTCTCAAACTCACATT 60.202 37.037 0.00 0.00 0.00 2.71
4805 5327 6.127897 GCATGCATACCTTACTTCAGTTTTCT 60.128 38.462 14.21 0.00 0.00 2.52
5050 5577 1.148273 ACTGTCGCCACACCATTGT 59.852 52.632 0.00 0.00 35.84 2.71
5155 5696 1.016130 AGGTTTGACAGCTCGCATCG 61.016 55.000 0.00 0.00 0.00 3.84
5172 5713 0.392998 TCGAATTCCCTGCTGCCTTC 60.393 55.000 0.00 0.00 0.00 3.46
5228 5772 6.296145 CCTCCTTTGGTTCATAGGATAGGATC 60.296 46.154 7.38 0.00 39.94 3.36
5287 5831 9.311916 GTGACATATATCTCAAATCCTATGAGC 57.688 37.037 0.00 0.00 43.19 4.26
5303 5847 6.777782 CCTATGAGCAGGAATAGGAAAAGAT 58.222 40.000 3.09 0.00 45.72 2.40
5446 5991 5.155161 ACCAAAGGGCTCTAAAGGAAAAAT 58.845 37.500 5.94 0.00 37.90 1.82
5449 5994 6.014242 CCAAAGGGCTCTAAAGGAAAAATTCT 60.014 38.462 0.00 0.00 0.00 2.40
5644 6189 5.934402 ACGGTCACTGAACTTAGGAATAT 57.066 39.130 0.00 0.00 0.00 1.28
5729 6274 1.292061 GTACAGCGTTGTTGACCACA 58.708 50.000 11.04 0.00 38.76 4.17
5770 6315 2.280592 GTGGCGAAACGTGGAGGT 60.281 61.111 0.00 0.00 0.00 3.85
5882 6428 1.198759 TAGAAACAGGGGAGCGGCTT 61.199 55.000 2.97 0.00 0.00 4.35
5895 6441 4.787871 GGCTTCTGCATAGGCGAT 57.212 55.556 6.76 0.00 45.35 4.58
6131 6679 1.818674 CTCCTTTTAAGGCCGCATTGT 59.181 47.619 0.00 0.00 46.06 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 5.416013 TGATTATAGTGAGGTATGCGAGGAG 59.584 44.000 0.00 0.00 0.00 3.69
138 139 1.679153 TCTGCATCAGAATACGCGGTA 59.321 47.619 12.47 0.25 37.57 4.02
201 202 8.768957 TCAAATTGTCATCAAGAAAAACACAA 57.231 26.923 0.00 0.00 36.97 3.33
215 216 5.336102 AGGACCAAGGAATCAAATTGTCAT 58.664 37.500 0.00 0.00 0.00 3.06
239 240 3.775261 AGACGGTTACCTGCCTTTTTA 57.225 42.857 0.00 0.00 0.00 1.52
260 261 4.116328 CTTCAGCGGACGAGCGGA 62.116 66.667 0.00 0.00 43.00 5.54
297 300 1.081892 CCGTATCAGCCATAGCATGC 58.918 55.000 10.51 10.51 43.56 4.06
304 307 1.050988 AGCCAGACCGTATCAGCCAT 61.051 55.000 0.00 0.00 30.93 4.40
405 408 1.633432 TGTTGAACAGGATTCCCGGAT 59.367 47.619 0.73 0.00 37.58 4.18
612 617 1.315690 TAGTCTAACATCCCCTCGCG 58.684 55.000 0.00 0.00 0.00 5.87
616 621 5.071923 GCCAAGTAATAGTCTAACATCCCCT 59.928 44.000 0.00 0.00 0.00 4.79
686 692 9.999009 CGAGCGGTATATATAAGAGATTACAAA 57.001 33.333 0.00 0.00 0.00 2.83
807 832 2.030274 GGGCTTTGTTAAACATCGCACT 60.030 45.455 0.00 0.00 28.50 4.40
811 836 2.580589 CACGGGCTTTGTTAAACATCG 58.419 47.619 0.00 0.00 0.00 3.84
815 840 1.272784 GCGCACGGGCTTTGTTAAAC 61.273 55.000 8.62 0.00 38.10 2.01
840 871 0.682209 GTGACCAGCCCTGCATCAAT 60.682 55.000 0.00 0.00 0.00 2.57
842 873 1.782201 AAGTGACCAGCCCTGCATCA 61.782 55.000 0.00 0.00 0.00 3.07
843 874 1.001641 AAGTGACCAGCCCTGCATC 60.002 57.895 0.00 0.00 0.00 3.91
1174 1208 4.717313 GGAACCCCTGACGTGGCC 62.717 72.222 0.00 0.00 0.00 5.36
1245 1279 1.965754 GCTCCTCGATCCACAGCCTT 61.966 60.000 0.00 0.00 0.00 4.35
1485 1519 1.040646 CGCTTGCCTCTAGGTATGGA 58.959 55.000 0.00 0.00 37.57 3.41
1514 1548 7.477494 ACAAGTAACAAACTGCGATTAAAAGT 58.523 30.769 0.00 0.00 38.88 2.66
1515 1549 7.908193 ACAAGTAACAAACTGCGATTAAAAG 57.092 32.000 0.00 0.00 38.88 2.27
1516 1550 8.614346 ACTACAAGTAACAAACTGCGATTAAAA 58.386 29.630 0.00 0.00 38.88 1.52
1518 1552 7.718272 ACTACAAGTAACAAACTGCGATTAA 57.282 32.000 0.00 0.00 38.88 1.40
1523 1557 4.746115 TGGTACTACAAGTAACAAACTGCG 59.254 41.667 2.38 0.00 44.69 5.18
1584 1618 7.012421 CCTCTTCCGTTATCTAAAAAGGATTGG 59.988 40.741 0.00 0.00 36.97 3.16
1586 1620 7.858498 TCCTCTTCCGTTATCTAAAAAGGATT 58.142 34.615 0.00 0.00 36.97 3.01
1588 1622 6.862469 TCCTCTTCCGTTATCTAAAAAGGA 57.138 37.500 0.00 0.00 35.56 3.36
1589 1623 7.148289 GGTTTCCTCTTCCGTTATCTAAAAAGG 60.148 40.741 0.00 0.00 0.00 3.11
1625 1689 2.119801 AAAGGACTTCATCATGCGCT 57.880 45.000 9.73 0.00 0.00 5.92
1640 1704 8.262715 GAGTTTTCTCTTCCATTCTCTAAAGG 57.737 38.462 0.00 0.00 43.12 3.11
1690 1754 8.120465 TCGTAATCAGAGTTCAGTTTCAAAAAC 58.880 33.333 0.00 0.00 0.00 2.43
1697 1761 7.730364 ACAAATCGTAATCAGAGTTCAGTTT 57.270 32.000 0.00 0.00 0.00 2.66
1698 1762 7.063544 GCTACAAATCGTAATCAGAGTTCAGTT 59.936 37.037 0.00 0.00 0.00 3.16
1719 1783 4.063967 CCGCACGACCCTGCTACA 62.064 66.667 0.00 0.00 34.77 2.74
1734 1798 3.869065 TCAGCTAACCTACAAATTCCCG 58.131 45.455 0.00 0.00 0.00 5.14
1774 1838 4.956075 ACCCCCAGAAATATTCATTCACAC 59.044 41.667 0.00 0.00 0.00 3.82
1843 1907 7.390823 TCAACCATCAAGTATAACTGTAAGCA 58.609 34.615 0.00 0.00 37.60 3.91
1882 1946 3.743521 TCAGCACATTGAAACAGCTACT 58.256 40.909 0.00 0.00 33.59 2.57
2239 2328 4.081807 CCGGAGATGAAGCATAGATGATGA 60.082 45.833 0.00 0.00 37.82 2.92
2272 2361 6.822676 TGGCATTGAAAAAGAAACAAGTCAAT 59.177 30.769 0.00 0.00 36.42 2.57
2448 2537 3.307762 GGTGTTCTTCAGCATAGGAAGGT 60.308 47.826 0.00 0.00 41.59 3.50
2488 2577 6.863126 GTCCAACCAAAAGATCACAACAATAG 59.137 38.462 0.00 0.00 0.00 1.73
2586 2678 9.122613 GAAAATAAGAGAAGCAATCACAGAAAC 57.877 33.333 0.00 0.00 0.00 2.78
2590 2682 6.835914 ACGAAAATAAGAGAAGCAATCACAG 58.164 36.000 0.00 0.00 0.00 3.66
2678 2777 8.458843 AGGAAATATTTCAAGATTTACACCGTG 58.541 33.333 25.55 0.00 33.83 4.94
2679 2778 8.575649 AGGAAATATTTCAAGATTTACACCGT 57.424 30.769 25.55 0.00 33.83 4.83
2745 2845 5.528600 TTTTCCCATGTCTCCATTTCCTA 57.471 39.130 0.00 0.00 0.00 2.94
2748 2848 5.653769 TCAGATTTTCCCATGTCTCCATTTC 59.346 40.000 0.00 0.00 0.00 2.17
2793 2893 3.191162 CCACGACATTCAACATTCACCAT 59.809 43.478 0.00 0.00 0.00 3.55
2836 2936 0.321671 TGCACAGTGGAGGCTTAGAC 59.678 55.000 1.84 0.00 0.00 2.59
2851 2951 8.425577 AACTACTCAATATGATAACACTGCAC 57.574 34.615 0.00 0.00 0.00 4.57
2903 3003 5.464168 CATGAAGCTAAAACCAAGTCCAAG 58.536 41.667 0.00 0.00 0.00 3.61
2907 3007 5.705609 TTCCATGAAGCTAAAACCAAGTC 57.294 39.130 0.00 0.00 0.00 3.01
2917 3017 3.119531 CGCCAATTGTTTCCATGAAGCTA 60.120 43.478 4.43 0.00 0.00 3.32
3058 3362 5.023452 ACATACCAGATGACACTTCTACCA 58.977 41.667 0.00 0.00 0.00 3.25
3171 3475 5.798132 TCATAACTGATCAAGACAGCAAGT 58.202 37.500 0.00 0.00 38.74 3.16
3574 4090 3.560068 GCGGACCTGAACCAAATAGTATG 59.440 47.826 0.00 0.00 0.00 2.39
3715 4231 5.939764 ACTTCATCAGCAGTATTCCTGTA 57.060 39.130 0.00 0.00 43.55 2.74
3873 4389 7.148340 GCAAGAATGACAGCTACATAAAGAACT 60.148 37.037 6.10 0.00 0.00 3.01
3912 4428 6.986231 GGACAAACAAGATGAAAATCAACCTT 59.014 34.615 0.00 0.00 0.00 3.50
3991 4507 8.648698 TTTCATCTTCATCAATCAGGGTAAAA 57.351 30.769 0.00 0.00 0.00 1.52
4000 4516 7.201496 GCCAACACATTTTCATCTTCATCAATC 60.201 37.037 0.00 0.00 0.00 2.67
4060 4576 5.109903 CCTACTCAAAAGGACATTACCTCG 58.890 45.833 0.00 0.00 39.62 4.63
4086 4602 5.295431 TCCTTCAAATGCATGAAAGTACG 57.705 39.130 0.00 0.00 38.75 3.67
4090 4606 7.661127 TGAATTTCCTTCAAATGCATGAAAG 57.339 32.000 0.00 4.51 40.92 2.62
4130 4646 7.076362 TGATTACGTTTCGCTAGACATCTATC 58.924 38.462 0.00 0.00 0.00 2.08
4144 4660 9.897349 GTTAGCTTACATTACTGATTACGTTTC 57.103 33.333 0.00 0.00 0.00 2.78
4149 4665 8.913656 GGATCGTTAGCTTACATTACTGATTAC 58.086 37.037 3.47 0.00 0.00 1.89
4160 4676 3.762288 AGAGTGTGGATCGTTAGCTTACA 59.238 43.478 3.47 0.00 0.00 2.41
4161 4677 4.373348 AGAGTGTGGATCGTTAGCTTAC 57.627 45.455 0.00 0.00 0.00 2.34
4195 4711 8.822652 TGTCAAGCAATAGTATCACATCATAG 57.177 34.615 0.00 0.00 0.00 2.23
4279 4795 6.288294 CACTCGGAAAAGATATGGGATTGTA 58.712 40.000 0.00 0.00 0.00 2.41
4283 4799 3.136443 TGCACTCGGAAAAGATATGGGAT 59.864 43.478 0.00 0.00 0.00 3.85
4284 4800 2.503765 TGCACTCGGAAAAGATATGGGA 59.496 45.455 0.00 0.00 0.00 4.37
4285 4801 2.917933 TGCACTCGGAAAAGATATGGG 58.082 47.619 0.00 0.00 0.00 4.00
4286 4802 5.505173 AAATGCACTCGGAAAAGATATGG 57.495 39.130 0.00 0.00 0.00 2.74
4345 4863 3.017442 TCGGTCATTACTCCTCAGTCAG 58.983 50.000 0.00 0.00 33.62 3.51
4347 4865 3.632604 TGATCGGTCATTACTCCTCAGTC 59.367 47.826 0.00 0.00 33.62 3.51
4350 4868 5.614324 AATTGATCGGTCATTACTCCTCA 57.386 39.130 0.00 0.00 33.56 3.86
4372 4890 7.415541 GCTGCAATGAGATACAACCAAAGATAA 60.416 37.037 0.00 0.00 0.00 1.75
4652 5173 2.497273 TCGATCTGGAAGCATCAGTGAA 59.503 45.455 0.00 0.00 34.15 3.18
4805 5327 7.981789 GTGAATCTATCCAGACAAGTCAATGTA 59.018 37.037 2.72 0.00 32.25 2.29
5050 5577 4.926832 CACGGTACACTTGTGTAATGATCA 59.073 41.667 14.23 0.00 0.00 2.92
5082 5609 1.686052 ACCAAGTACGGTCACGGTAAA 59.314 47.619 0.00 0.00 46.48 2.01
5155 5696 0.813821 GTGAAGGCAGCAGGGAATTC 59.186 55.000 0.00 0.00 0.00 2.17
5172 5713 4.124910 ACACTGGCAGTTCGTGTG 57.875 55.556 19.43 9.17 40.11 3.82
5242 5786 6.126409 TGTCACCTCATTTCCTACAAGTTTT 58.874 36.000 0.00 0.00 0.00 2.43
5303 5847 5.885352 CCTATGGTGTGAACCAAATGACATA 59.115 40.000 0.99 0.00 43.83 2.29
5368 5912 6.381133 GGATTGGTTCCTATTCTCCACATTTT 59.619 38.462 0.00 0.00 41.78 1.82
5588 6133 5.405269 CGATCGCAACTATAATGACCATGAA 59.595 40.000 0.26 0.00 0.00 2.57
5644 6189 4.556699 CGTATTGAGTGACCATATCGAGCA 60.557 45.833 0.00 0.00 0.00 4.26
5761 6306 2.901292 GACGACGACACCTCCACGT 61.901 63.158 0.00 0.00 42.84 4.49
5770 6315 1.545614 GCAAAAGAGCGACGACGACA 61.546 55.000 12.29 0.00 42.66 4.35
5921 6468 4.079850 CCTCAGCTCGCCTGCACT 62.080 66.667 0.00 0.00 41.50 4.40
5979 6526 0.596577 CCTCCGACGAGAAGAACACA 59.403 55.000 0.00 0.00 38.52 3.72
6048 6595 0.250597 GGGGCGGAAACTTACTGTGT 60.251 55.000 0.00 0.00 0.00 3.72
6049 6596 0.958876 GGGGGCGGAAACTTACTGTG 60.959 60.000 0.00 0.00 0.00 3.66
6120 6668 1.486310 TCTAAGATGACAATGCGGCCT 59.514 47.619 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.