Multiple sequence alignment - TraesCS3B01G244600

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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 TraesCS3B01G244600 chr3B 100.000 4121 0 0 1 4121 387193973 387198093 0.000000e+00 7611.0
1 TraesCS3B01G244600 chr3B 98.667 1050 14 0 1 1050 71363406 71364455 0.000000e+00 1862.0
2 TraesCS3B01G244600 chr3D 97.909 1148 24 0 1052 2199 293613036 293614183 0.000000e+00 1988.0
3 TraesCS3B01G244600 chr3D 96.090 1151 37 6 2219 3367 293614342 293615486 0.000000e+00 1869.0
4 TraesCS3B01G244600 chr3D 72.492 309 65 15 1052 1350 560867141 560867439 9.490000e-12 82.4
5 TraesCS3B01G244600 chr7B 98.950 1048 11 0 1 1048 697392917 697393964 0.000000e+00 1875.0
6 TraesCS3B01G244600 chr7B 94.531 128 4 1 3366 3493 389983878 389984002 1.170000e-45 195.0
7 TraesCS3B01G244600 chr1B 98.949 1047 11 0 1 1047 651489842 651490888 0.000000e+00 1873.0
8 TraesCS3B01G244600 chr2B 98.855 1048 12 0 1 1048 637045814 637044767 0.000000e+00 1869.0
9 TraesCS3B01G244600 chr2B 98.668 1051 13 1 1 1050 515467149 515466099 0.000000e+00 1862.0
10 TraesCS3B01G244600 chr2B 94.605 1075 30 2 1 1047 691197489 691196415 0.000000e+00 1639.0
11 TraesCS3B01G244600 chr2B 90.923 650 43 9 3482 4121 120560633 120559990 0.000000e+00 859.0
12 TraesCS3B01G244600 chr2B 80.114 352 42 17 3482 3810 672605824 672605478 1.910000e-58 237.0
13 TraesCS3B01G244600 chr2B 92.157 51 3 1 2199 2249 453180929 453180978 2.060000e-08 71.3
14 TraesCS3B01G244600 chr6B 98.854 1047 12 0 1 1047 711716223 711715177 0.000000e+00 1868.0
15 TraesCS3B01G244600 chr4A 98.758 1047 13 0 1 1047 707158591 707157545 0.000000e+00 1862.0
16 TraesCS3B01G244600 chr4A 89.541 784 51 12 3365 4121 541922788 541923567 0.000000e+00 965.0
17 TraesCS3B01G244600 chrUn 98.457 1037 16 0 1 1037 17568506 17567470 0.000000e+00 1827.0
18 TraesCS3B01G244600 chrUn 98.628 802 11 0 246 1047 295470307 295469506 0.000000e+00 1421.0
19 TraesCS3B01G244600 chrUn 86.156 809 63 20 3355 4120 35424820 35425622 0.000000e+00 828.0
20 TraesCS3B01G244600 chr6D 89.777 763 55 12 3372 4120 428935992 428936745 0.000000e+00 955.0
21 TraesCS3B01G244600 chr6D 94.231 52 2 1 2199 2250 10798632 10798582 1.230000e-10 78.7
22 TraesCS3B01G244600 chr4B 89.017 783 52 12 3366 4121 625378015 625377240 0.000000e+00 939.0
23 TraesCS3B01G244600 chr5B 88.761 783 50 16 3372 4121 612034370 612035147 0.000000e+00 924.0
24 TraesCS3B01G244600 chr2D 88.604 781 54 11 3367 4120 409597118 409596346 0.000000e+00 917.0
25 TraesCS3B01G244600 chr2D 95.652 46 2 0 2199 2244 302246944 302246899 1.590000e-09 75.0
26 TraesCS3B01G244600 chr2D 95.556 45 2 0 2196 2240 621087699 621087743 5.710000e-09 73.1
27 TraesCS3B01G244600 chr5D 88.773 766 54 16 3372 4114 378632608 378633364 0.000000e+00 909.0
28 TraesCS3B01G244600 chr5D 86.852 791 64 12 3366 4120 251828071 251828857 0.000000e+00 848.0
29 TraesCS3B01G244600 chr6A 91.549 568 44 3 3556 4121 89974659 89975224 0.000000e+00 780.0
30 TraesCS3B01G244600 chr7D 88.191 669 55 13 3468 4120 625762528 625761868 0.000000e+00 776.0
31 TraesCS3B01G244600 chr7D 85.144 801 69 29 3364 4121 9300628 9299835 0.000000e+00 774.0
32 TraesCS3B01G244600 chr7D 91.176 170 10 3 3373 3542 497899476 497899312 4.140000e-55 226.0
33 TraesCS3B01G244600 chr7D 92.969 128 5 2 3367 3493 614242879 614242755 2.530000e-42 183.0
34 TraesCS3B01G244600 chr2A 91.388 569 42 4 3556 4121 660551591 660551027 0.000000e+00 773.0
35 TraesCS3B01G244600 chr2A 90.973 565 47 2 3560 4121 58178392 58178955 0.000000e+00 758.0
36 TraesCS3B01G244600 chr2A 85.281 231 12 11 3366 3580 660551852 660551628 6.940000e-53 219.0
37 TraesCS3B01G244600 chr7A 85.233 772 87 15 3365 4121 720404789 720404030 0.000000e+00 769.0
38 TraesCS3B01G244600 chr7A 94.231 52 2 1 2193 2243 560993992 560994043 1.230000e-10 78.7
39 TraesCS3B01G244600 chr7A 97.619 42 1 0 2199 2240 6102309 6102268 5.710000e-09 73.1
40 TraesCS3B01G244600 chr5A 94.000 50 3 0 2199 2248 17241842 17241891 4.420000e-10 76.8
41 TraesCS3B01G244600 chr3A 95.745 47 1 1 2199 2244 46989973 46990019 1.590000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G244600 chr3B 387193973 387198093 4120 False 7611.0 7611 100.0000 1 4121 1 chr3B.!!$F2 4120
1 TraesCS3B01G244600 chr3B 71363406 71364455 1049 False 1862.0 1862 98.6670 1 1050 1 chr3B.!!$F1 1049
2 TraesCS3B01G244600 chr3D 293613036 293615486 2450 False 1928.5 1988 96.9995 1052 3367 2 chr3D.!!$F2 2315
3 TraesCS3B01G244600 chr7B 697392917 697393964 1047 False 1875.0 1875 98.9500 1 1048 1 chr7B.!!$F2 1047
4 TraesCS3B01G244600 chr1B 651489842 651490888 1046 False 1873.0 1873 98.9490 1 1047 1 chr1B.!!$F1 1046
5 TraesCS3B01G244600 chr2B 637044767 637045814 1047 True 1869.0 1869 98.8550 1 1048 1 chr2B.!!$R3 1047
6 TraesCS3B01G244600 chr2B 515466099 515467149 1050 True 1862.0 1862 98.6680 1 1050 1 chr2B.!!$R2 1049
7 TraesCS3B01G244600 chr2B 691196415 691197489 1074 True 1639.0 1639 94.6050 1 1047 1 chr2B.!!$R5 1046
8 TraesCS3B01G244600 chr2B 120559990 120560633 643 True 859.0 859 90.9230 3482 4121 1 chr2B.!!$R1 639
9 TraesCS3B01G244600 chr6B 711715177 711716223 1046 True 1868.0 1868 98.8540 1 1047 1 chr6B.!!$R1 1046
10 TraesCS3B01G244600 chr4A 707157545 707158591 1046 True 1862.0 1862 98.7580 1 1047 1 chr4A.!!$R1 1046
11 TraesCS3B01G244600 chr4A 541922788 541923567 779 False 965.0 965 89.5410 3365 4121 1 chr4A.!!$F1 756
12 TraesCS3B01G244600 chrUn 17567470 17568506 1036 True 1827.0 1827 98.4570 1 1037 1 chrUn.!!$R1 1036
13 TraesCS3B01G244600 chrUn 295469506 295470307 801 True 1421.0 1421 98.6280 246 1047 1 chrUn.!!$R2 801
14 TraesCS3B01G244600 chrUn 35424820 35425622 802 False 828.0 828 86.1560 3355 4120 1 chrUn.!!$F1 765
15 TraesCS3B01G244600 chr6D 428935992 428936745 753 False 955.0 955 89.7770 3372 4120 1 chr6D.!!$F1 748
16 TraesCS3B01G244600 chr4B 625377240 625378015 775 True 939.0 939 89.0170 3366 4121 1 chr4B.!!$R1 755
17 TraesCS3B01G244600 chr5B 612034370 612035147 777 False 924.0 924 88.7610 3372 4121 1 chr5B.!!$F1 749
18 TraesCS3B01G244600 chr2D 409596346 409597118 772 True 917.0 917 88.6040 3367 4120 1 chr2D.!!$R2 753
19 TraesCS3B01G244600 chr5D 378632608 378633364 756 False 909.0 909 88.7730 3372 4114 1 chr5D.!!$F2 742
20 TraesCS3B01G244600 chr5D 251828071 251828857 786 False 848.0 848 86.8520 3366 4120 1 chr5D.!!$F1 754
21 TraesCS3B01G244600 chr6A 89974659 89975224 565 False 780.0 780 91.5490 3556 4121 1 chr6A.!!$F1 565
22 TraesCS3B01G244600 chr7D 625761868 625762528 660 True 776.0 776 88.1910 3468 4120 1 chr7D.!!$R4 652
23 TraesCS3B01G244600 chr7D 9299835 9300628 793 True 774.0 774 85.1440 3364 4121 1 chr7D.!!$R1 757
24 TraesCS3B01G244600 chr2A 58178392 58178955 563 False 758.0 758 90.9730 3560 4121 1 chr2A.!!$F1 561
25 TraesCS3B01G244600 chr2A 660551027 660551852 825 True 496.0 773 88.3345 3366 4121 2 chr2A.!!$R1 755
26 TraesCS3B01G244600 chr7A 720404030 720404789 759 True 769.0 769 85.2330 3365 4121 1 chr7A.!!$R2 756

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
883 912 0.777446 AGCACATAACCCCCAGTGTT 59.223 50.0 0.00 0.0 34.59 3.32 F
1050 1079 0.253160 TGGGAGCTATTCACCCCTGT 60.253 55.0 7.39 0.0 44.12 4.00 F
2938 3108 0.320508 GGAGAAACTGGTGGTCGGTC 60.321 60.0 0.00 0.0 32.92 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 2626 1.338674 ACGCACAAGAAATCCCGATCA 60.339 47.619 0.00 0.0 0.0 2.92 R
2960 3130 0.461548 GCACGTCTCATCATCCTCCA 59.538 55.000 0.00 0.0 0.0 3.86 R
4094 4475 1.523154 TTCCAAAATCTTGCGCGGCT 61.523 50.000 8.83 0.0 0.0 5.52 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
130 131 6.146047 TCTCCTTCATGATCTCCAATTCCTA 58.854 40.000 0.00 0.00 0.00 2.94
645 674 2.285368 AGGCCACAGATCGGGGAA 60.285 61.111 5.01 0.00 0.00 3.97
883 912 0.777446 AGCACATAACCCCCAGTGTT 59.223 50.000 0.00 0.00 34.59 3.32
942 971 1.729517 CGTAAATGGTGTGTCGCATGA 59.270 47.619 0.00 0.00 0.00 3.07
1008 1037 0.452184 AACGACGTCGCATGAGAGAT 59.548 50.000 35.92 12.02 44.43 2.75
1050 1079 0.253160 TGGGAGCTATTCACCCCTGT 60.253 55.000 7.39 0.00 44.12 4.00
1068 1097 1.074850 TATCATCGCCTCCCACCCA 60.075 57.895 0.00 0.00 0.00 4.51
1199 1228 3.966543 CAACAGGCCGTTCCCCCT 61.967 66.667 9.57 0.00 34.86 4.79
1372 1401 1.528776 GCCGGGGAGATCGAGTACT 60.529 63.158 2.18 0.00 0.00 2.73
1421 1450 1.413382 CTCGCGATTATCCTCAGCAC 58.587 55.000 10.36 0.00 0.00 4.40
1498 1527 0.729116 GATGTCCATGGCACGTGAAG 59.271 55.000 22.23 4.83 0.00 3.02
1632 1661 1.980052 CGTCCTGGGCTACTTGGAA 59.020 57.895 0.00 0.00 0.00 3.53
1686 1715 1.134670 GTCATCCAGGTGTCCTAGTGC 60.135 57.143 0.00 0.00 29.64 4.40
1704 1733 1.901464 CTCCCTAGCTCTCCTCCGC 60.901 68.421 0.00 0.00 0.00 5.54
1743 1772 5.480772 ACCACTACATAGTATACCATGGCTC 59.519 44.000 13.04 0.00 34.13 4.70
1852 1881 2.890945 GGCTAACATGGTTCCAAGTGTT 59.109 45.455 13.14 13.14 38.28 3.32
1864 1893 6.268847 TGGTTCCAAGTGTTAAAATATTGGCT 59.731 34.615 7.43 0.00 40.19 4.75
1867 1896 8.495148 GTTCCAAGTGTTAAAATATTGGCTTTG 58.505 33.333 7.43 0.00 40.19 2.77
1981 2010 6.426646 AGAAATACACATACTCCATCCTCC 57.573 41.667 0.00 0.00 0.00 4.30
2130 2159 5.892160 GCATGTTCATGCTCCATATACAT 57.108 39.130 24.69 0.00 43.79 2.29
2140 2169 5.131784 TGCTCCATATACATGTTTCATGCA 58.868 37.500 2.30 4.20 0.00 3.96
2167 2196 5.725110 AATATGTCGTTCATGCTTCAGAC 57.275 39.130 6.22 0.00 37.91 3.51
2302 2471 8.065473 TGTAACAAGGAACAAATATGCATCAT 57.935 30.769 0.19 0.00 0.00 2.45
2350 2519 7.230849 TGATCTGGCTTGTTTGATAAAATGT 57.769 32.000 0.00 0.00 0.00 2.71
2391 2560 5.009310 ACTTTTAGTTGGTCATCCGAAAACC 59.991 40.000 0.00 0.00 36.30 3.27
2396 2565 2.785562 TGGTCATCCGAAAACCGAAAT 58.214 42.857 0.00 0.00 41.76 2.17
2397 2566 3.150767 TGGTCATCCGAAAACCGAAATT 58.849 40.909 0.00 0.00 41.76 1.82
2405 2574 5.593010 TCCGAAAACCGAAATTTGTTCATT 58.407 33.333 0.00 0.00 41.76 2.57
2408 2577 7.064728 TCCGAAAACCGAAATTTGTTCATTTTT 59.935 29.630 0.00 0.00 41.76 1.94
2468 2637 5.041191 AGATAAGCTGTTGATCGGGATTT 57.959 39.130 0.00 0.00 0.00 2.17
2766 2936 2.100418 TCAGTCCGATGAAGCTGATGAG 59.900 50.000 0.00 0.00 33.62 2.90
2775 2945 2.673523 GCTGATGAGCCCAGTGGT 59.326 61.111 8.74 0.00 39.57 4.16
2925 3095 4.464008 AGAGAACACAAATGCTGGAGAAA 58.536 39.130 0.00 0.00 0.00 2.52
2936 3106 0.320771 CTGGAGAAACTGGTGGTCGG 60.321 60.000 0.00 0.00 0.00 4.79
2938 3108 0.320508 GGAGAAACTGGTGGTCGGTC 60.321 60.000 0.00 0.00 32.92 4.79
2942 3112 1.342672 AAACTGGTGGTCGGTCTGGT 61.343 55.000 0.00 0.00 32.92 4.00
2958 3128 1.069090 GGTCAACGGAGACACTGCA 59.931 57.895 10.94 0.00 40.29 4.41
2960 3130 1.512926 GTCAACGGAGACACTGCATT 58.487 50.000 4.84 0.00 38.40 3.56
2980 3150 0.461548 GGAGGATGATGAGACGTGCA 59.538 55.000 0.00 0.00 0.00 4.57
3014 3184 0.704076 TTGGCTATGGCAAGAAGGGT 59.296 50.000 2.58 0.00 42.98 4.34
3048 3218 2.125065 ACGGTGTTGGTTGTCGCA 60.125 55.556 0.00 0.00 0.00 5.10
3150 3320 4.937620 TGGTCAGTTTCATGCTTCAGTATC 59.062 41.667 0.00 0.00 0.00 2.24
3166 3336 7.169982 GCTTCAGTATCCACATGAGTAACATAC 59.830 40.741 0.00 0.00 37.46 2.39
3187 3357 3.517500 ACCACTCCCTCTTTCAGATCTTC 59.482 47.826 0.00 0.00 0.00 2.87
3188 3358 3.774216 CCACTCCCTCTTTCAGATCTTCT 59.226 47.826 0.00 0.00 0.00 2.85
3189 3359 4.224818 CCACTCCCTCTTTCAGATCTTCTT 59.775 45.833 0.00 0.00 0.00 2.52
3190 3360 5.280419 CCACTCCCTCTTTCAGATCTTCTTT 60.280 44.000 0.00 0.00 0.00 2.52
3191 3361 6.237154 CACTCCCTCTTTCAGATCTTCTTTT 58.763 40.000 0.00 0.00 0.00 2.27
3245 3415 7.390027 AGTTCTGCTTGATACAGTTAACATCT 58.610 34.615 8.61 0.00 36.50 2.90
3253 3423 2.960819 ACAGTTAACATCTGCGAGGAC 58.039 47.619 8.61 0.00 36.50 3.85
3260 3430 3.382803 ATCTGCGAGGACTGGCTGC 62.383 63.158 7.79 0.00 35.25 5.25
3302 3472 3.235157 AGCAAGCCGTGTATTTACGTA 57.765 42.857 0.00 0.00 42.24 3.57
3310 3480 5.009410 AGCCGTGTATTTACGTAGCTAGATT 59.991 40.000 0.00 0.00 38.93 2.40
3447 3619 6.573434 CCTTCATTAAAAAGGGTAGGATTGC 58.427 40.000 10.72 0.00 39.75 3.56
3504 3741 1.431036 GCTGTACGTCGACTACCCC 59.569 63.158 14.70 5.50 0.00 4.95
3916 4297 4.752879 GGCGGCGGTAGCTTGTGA 62.753 66.667 9.78 0.00 44.37 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 3.379372 CGATTTTGCAGATGTTGATCCCT 59.621 43.478 0.00 0.00 0.00 4.20
645 674 1.632965 GCCCGAAACCCTAGTCCCAT 61.633 60.000 0.00 0.00 0.00 4.00
717 746 0.472471 TCTCCGGCAGTGGTTTCTTT 59.528 50.000 0.00 0.00 0.00 2.52
883 912 4.382685 CCGTTAGGCTGAGATTTGGTTAGA 60.383 45.833 0.00 0.00 0.00 2.10
917 946 2.248274 GACACACCATTTACGCGGCC 62.248 60.000 12.47 0.00 0.00 6.13
960 989 1.171308 AGCTTGCATGCGACATCTTT 58.829 45.000 17.83 0.00 38.13 2.52
1008 1037 1.597690 CGACGTCGTTGGTGTGAACTA 60.598 52.381 29.08 0.00 34.11 2.24
1050 1079 1.074850 TGGGTGGGAGGCGATGATA 60.075 57.895 0.00 0.00 0.00 2.15
1080 1109 2.047844 CAGGTGAGGTGGACGCAG 60.048 66.667 0.00 0.00 0.00 5.18
1199 1228 2.747460 CGGGGAGGTACACGTCGA 60.747 66.667 0.00 0.00 0.00 4.20
1305 1334 3.400054 CGGAGGTGGGGGAAGACC 61.400 72.222 0.00 0.00 39.11 3.85
1372 1401 2.954684 CGGGGCTACACTGGAGCAA 61.955 63.158 15.44 0.00 41.98 3.91
1421 1450 0.037232 GACGTGAGAGGAAGGGTTGG 60.037 60.000 0.00 0.00 0.00 3.77
1491 1520 2.105528 ACAACGGCGACTTCACGT 59.894 55.556 16.62 0.00 43.43 4.49
1627 1656 0.878416 GCGTGTATGCTTGGTTCCAA 59.122 50.000 4.17 4.17 0.00 3.53
1632 1661 0.806102 CTAGCGCGTGTATGCTTGGT 60.806 55.000 8.43 0.00 42.48 3.67
1686 1715 1.901464 GCGGAGGAGAGCTAGGGAG 60.901 68.421 0.00 0.00 0.00 4.30
1704 1733 5.830912 TGTAGTGGTGAAAAATTCAAGCAG 58.169 37.500 0.00 0.00 42.15 4.24
1743 1772 3.041211 TCAAGGGGGACACATATCTCTG 58.959 50.000 0.00 0.00 0.00 3.35
1852 1881 6.682746 TCGCACTTTCAAAGCCAATATTTTA 58.317 32.000 0.00 0.00 0.00 1.52
1864 1893 4.555262 GGATTCCAAATCGCACTTTCAAA 58.445 39.130 0.00 0.00 0.00 2.69
1867 1896 2.785679 CGGATTCCAAATCGCACTTTC 58.214 47.619 3.09 0.00 0.00 2.62
1955 1984 7.873505 GGAGGATGGAGTATGTGTATTTCTTAC 59.126 40.741 0.00 0.00 0.00 2.34
1981 2010 6.156083 AGGTTATCTCAAGAAAGGAGAAGGAG 59.844 42.308 0.00 0.00 44.01 3.69
2039 2068 5.106197 CGATGAAACAAATTGGATCTGGACA 60.106 40.000 0.00 0.00 0.00 4.02
2130 2159 6.676950 ACGACATATTTTTCTGCATGAAACA 58.323 32.000 0.00 5.69 43.55 2.83
2140 2169 7.119699 TCTGAAGCATGAACGACATATTTTTCT 59.880 33.333 0.00 0.00 37.46 2.52
2167 2196 1.543429 GGAGCATGATAAACGAGGGGG 60.543 57.143 0.00 0.00 0.00 5.40
2240 2408 6.624423 AGTAAAAGGCATGCTCATTACAAAG 58.376 36.000 26.43 0.00 0.00 2.77
2381 2550 5.189659 TGAACAAATTTCGGTTTTCGGAT 57.810 34.783 0.00 0.00 39.77 4.18
2408 2577 8.694540 ACAAGCATTATATTTTACTGCCATGAA 58.305 29.630 0.00 0.00 33.34 2.57
2453 2622 3.426695 GCACAAGAAATCCCGATCAACAG 60.427 47.826 0.00 0.00 0.00 3.16
2457 2626 1.338674 ACGCACAAGAAATCCCGATCA 60.339 47.619 0.00 0.00 0.00 2.92
2628 2797 8.634444 CATCCAGCACTAACTAGTAACTAAGAT 58.366 37.037 0.00 0.00 34.13 2.40
2766 2936 1.524008 GGTTGCACTTACCACTGGGC 61.524 60.000 0.98 0.00 37.90 5.36
2775 2945 3.476552 CCAGAACTTGAGGTTGCACTTA 58.523 45.455 0.00 0.00 38.41 2.24
2925 3095 2.122989 ACCAGACCGACCACCAGT 60.123 61.111 0.00 0.00 0.00 4.00
2936 3106 0.674534 AGTGTCTCCGTTGACCAGAC 59.325 55.000 3.19 0.00 37.63 3.51
2938 3108 0.946221 GCAGTGTCTCCGTTGACCAG 60.946 60.000 0.00 0.00 36.21 4.00
2942 3112 1.511850 CAATGCAGTGTCTCCGTTGA 58.488 50.000 5.87 0.00 0.00 3.18
2958 3128 2.484417 GCACGTCTCATCATCCTCCAAT 60.484 50.000 0.00 0.00 0.00 3.16
2960 3130 0.461548 GCACGTCTCATCATCCTCCA 59.538 55.000 0.00 0.00 0.00 3.86
2993 3163 1.753073 CCCTTCTTGCCATAGCCAAAG 59.247 52.381 0.00 0.00 38.69 2.77
3014 3184 1.816537 GTCATAGGGCACTCGCTGA 59.183 57.895 0.00 0.00 38.60 4.26
3075 3245 1.865970 GAAAGATCAGATGCTCTGCGG 59.134 52.381 7.94 0.00 43.95 5.69
3124 3294 2.821378 TGAAGCATGAAACTGACCATGG 59.179 45.455 11.19 11.19 40.22 3.66
3150 3320 4.442706 GGAGTGGTATGTTACTCATGTGG 58.557 47.826 0.00 0.00 43.91 4.17
3187 3357 5.666969 TTGTCGTAACTGTCCATGAAAAG 57.333 39.130 0.00 0.00 0.00 2.27
3188 3358 6.627395 AATTGTCGTAACTGTCCATGAAAA 57.373 33.333 0.00 0.00 0.00 2.29
3189 3359 7.604545 TCATAATTGTCGTAACTGTCCATGAAA 59.395 33.333 0.00 0.00 0.00 2.69
3190 3360 7.100409 TCATAATTGTCGTAACTGTCCATGAA 58.900 34.615 0.00 0.00 0.00 2.57
3191 3361 6.635755 TCATAATTGTCGTAACTGTCCATGA 58.364 36.000 0.00 0.00 0.00 3.07
3230 3400 4.740695 GTCCTCGCAGATGTTAACTGTATC 59.259 45.833 7.22 1.86 37.64 2.24
3245 3415 0.755327 TATAGCAGCCAGTCCTCGCA 60.755 55.000 0.00 0.00 0.00 5.10
3260 3430 6.861572 TGCTACGCTAGTTTTACATGCTATAG 59.138 38.462 0.00 0.00 0.00 1.31
3284 3454 3.184541 AGCTACGTAAATACACGGCTTG 58.815 45.455 0.00 0.00 46.12 4.01
3302 3472 8.011844 TGTGAGTGATATGTGTAAATCTAGCT 57.988 34.615 0.00 0.00 0.00 3.32
3447 3619 0.173255 CGGCTTTTTATGTGCTGGGG 59.827 55.000 0.00 0.00 0.00 4.96
3478 3715 2.401766 CGACGTACAGCCCCGTAGT 61.402 63.158 0.00 0.00 37.44 2.73
3479 3716 2.108514 TCGACGTACAGCCCCGTAG 61.109 63.158 0.00 0.00 37.44 3.51
3480 3717 2.046411 TCGACGTACAGCCCCGTA 60.046 61.111 0.00 0.00 37.44 4.02
3603 3932 2.595095 CACACATCGCGTCGTGTAATTA 59.405 45.455 27.10 0.00 44.34 1.40
3607 3945 1.443025 CCACACATCGCGTCGTGTA 60.443 57.895 27.10 0.69 44.34 2.90
3941 4322 2.492090 ACGGATGAGCTCGTCTGC 59.508 61.111 34.85 19.71 40.95 4.26
4094 4475 1.523154 TTCCAAAATCTTGCGCGGCT 61.523 50.000 8.83 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.