Multiple sequence alignment - TraesCS6A01G109400

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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 TraesCS6A01G109400 chr6A 100.000 2514 0 0 1 2514 78566403 78568916 0.000000e+00 4643.0
1 TraesCS6A01G109400 chr6A 95.468 662 26 2 1853 2514 93180390 93181047 0.000000e+00 1053.0
2 TraesCS6A01G109400 chr6A 78.727 597 66 30 640 1230 78002256 78002797 2.390000e-90 342.0
3 TraesCS6A01G109400 chr6A 78.333 600 71 30 637 1230 77962786 77963332 1.440000e-87 333.0
4 TraesCS6A01G109400 chr6A 77.870 601 72 31 637 1230 78127320 78127866 1.450000e-82 316.0
5 TraesCS6A01G109400 chr6A 77.167 600 75 36 637 1230 77912228 77912771 2.450000e-75 292.0
6 TraesCS6A01G109400 chr6A 97.059 34 0 1 1611 1644 397485828 397485860 3.490000e-04 56.5
7 TraesCS6A01G109400 chr2A 95.770 662 24 2 1853 2514 744893930 744894587 0.000000e+00 1064.0
8 TraesCS6A01G109400 chr2A 95.475 663 25 2 1854 2514 81166683 81167342 0.000000e+00 1053.0
9 TraesCS6A01G109400 chr1A 95.903 659 22 3 1856 2514 98988007 98988660 0.000000e+00 1062.0
10 TraesCS6A01G109400 chr1A 92.157 51 4 0 1109 1159 8121900 8121950 3.470000e-09 73.1
11 TraesCS6A01G109400 chr4A 95.633 664 24 3 1852 2514 580287666 580287007 0.000000e+00 1061.0
12 TraesCS6A01G109400 chr4A 90.385 52 4 1 1109 1160 607759358 607759408 1.610000e-07 67.6
13 TraesCS6A01G109400 chr1B 95.751 659 24 3 1856 2513 26839781 26840436 0.000000e+00 1059.0
14 TraesCS6A01G109400 chr7A 95.613 661 26 2 1854 2514 276127634 276128291 0.000000e+00 1057.0
15 TraesCS6A01G109400 chr7A 95.345 666 28 1 1849 2514 686660037 686660699 0.000000e+00 1055.0
16 TraesCS6A01G109400 chr3A 95.606 660 25 3 1856 2514 649848539 649849195 0.000000e+00 1055.0
17 TraesCS6A01G109400 chr3A 90.566 53 4 1 1109 1161 24628144 24628195 4.490000e-08 69.4
18 TraesCS6A01G109400 chr6D 88.767 819 45 20 704 1517 61411619 61412395 0.000000e+00 959.0
19 TraesCS6A01G109400 chr6D 85.586 888 84 18 1 856 61410822 61411697 0.000000e+00 891.0
20 TraesCS6A01G109400 chr6B 91.704 675 42 9 875 1548 135360002 135360663 0.000000e+00 924.0
21 TraesCS6A01G109400 chr6B 93.413 334 17 2 1526 1856 135360671 135361002 8.080000e-135 490.0
22 TraesCS6A01G109400 chr6B 89.802 353 28 5 1 350 135357006 135357353 1.770000e-121 446.0
23 TraesCS6A01G109400 chr6B 90.400 250 16 4 405 650 135359111 135359356 3.120000e-84 322.0
24 TraesCS6A01G109400 chr6B 78.821 458 53 21 657 1113 135139047 135139461 4.120000e-68 268.0
25 TraesCS6A01G109400 chr7D 89.831 59 4 2 1109 1166 619757900 619757843 9.640000e-10 75.0
26 TraesCS6A01G109400 chr7B 93.878 49 3 0 1109 1157 559634371 559634419 9.640000e-10 75.0
27 TraesCS6A01G109400 chr5D 93.617 47 3 0 1109 1155 446350230 446350276 1.250000e-08 71.3
28 TraesCS6A01G109400 chr2B 93.617 47 3 0 1109 1155 638002759 638002713 1.250000e-08 71.3
29 TraesCS6A01G109400 chr2B 90.196 51 4 1 1110 1160 2769055 2769104 5.800000e-07 65.8
30 TraesCS6A01G109400 chr5A 90.385 52 4 1 1109 1160 18027082 18027132 1.610000e-07 67.6


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 TraesCS6A01G109400 chr6A 78566403 78568916 2513 False 4643.0 4643 100.00000 1 2514 1 chr6A.!!$F5 2513
1 TraesCS6A01G109400 chr6A 93180390 93181047 657 False 1053.0 1053 95.46800 1853 2514 1 chr6A.!!$F6 661
2 TraesCS6A01G109400 chr6A 78002256 78002797 541 False 342.0 342 78.72700 640 1230 1 chr6A.!!$F3 590
3 TraesCS6A01G109400 chr6A 77962786 77963332 546 False 333.0 333 78.33300 637 1230 1 chr6A.!!$F2 593
4 TraesCS6A01G109400 chr6A 78127320 78127866 546 False 316.0 316 77.87000 637 1230 1 chr6A.!!$F4 593
5 TraesCS6A01G109400 chr6A 77912228 77912771 543 False 292.0 292 77.16700 637 1230 1 chr6A.!!$F1 593
6 TraesCS6A01G109400 chr2A 744893930 744894587 657 False 1064.0 1064 95.77000 1853 2514 1 chr2A.!!$F2 661
7 TraesCS6A01G109400 chr2A 81166683 81167342 659 False 1053.0 1053 95.47500 1854 2514 1 chr2A.!!$F1 660
8 TraesCS6A01G109400 chr1A 98988007 98988660 653 False 1062.0 1062 95.90300 1856 2514 1 chr1A.!!$F2 658
9 TraesCS6A01G109400 chr4A 580287007 580287666 659 True 1061.0 1061 95.63300 1852 2514 1 chr4A.!!$R1 662
10 TraesCS6A01G109400 chr1B 26839781 26840436 655 False 1059.0 1059 95.75100 1856 2513 1 chr1B.!!$F1 657
11 TraesCS6A01G109400 chr7A 276127634 276128291 657 False 1057.0 1057 95.61300 1854 2514 1 chr7A.!!$F1 660
12 TraesCS6A01G109400 chr7A 686660037 686660699 662 False 1055.0 1055 95.34500 1849 2514 1 chr7A.!!$F2 665
13 TraesCS6A01G109400 chr3A 649848539 649849195 656 False 1055.0 1055 95.60600 1856 2514 1 chr3A.!!$F2 658
14 TraesCS6A01G109400 chr6D 61410822 61412395 1573 False 925.0 959 87.17650 1 1517 2 chr6D.!!$F1 1516
15 TraesCS6A01G109400 chr6B 135357006 135361002 3996 False 545.5 924 91.32975 1 1856 4 chr6B.!!$F2 1855

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
695 2675 0.612744 GAGGCTATCTCATCTGCCCC 59.387 60.0 0.0 0.0 45.94 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 4415 0.179134 CGCCGGGATATAGCTAGTGC 60.179 60.0 2.18 0.0 40.05 4.4 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
78 79 1.741706 CATGTCATGAACTGTCCTGGC 59.258 52.381 7.04 0.00 0.00 4.85
79 80 1.059098 TGTCATGAACTGTCCTGGCT 58.941 50.000 0.00 0.00 0.00 4.75
115 116 2.563427 GTCCTCTTGCAAAGGCGC 59.437 61.111 17.77 0.00 46.24 6.53
129 130 2.826738 GCGCGGGGCAAATTCCTA 60.827 61.111 8.83 0.00 42.87 2.94
151 152 2.142356 TCCGAAATCCATGCAACCAT 57.858 45.000 0.00 0.00 0.00 3.55
166 167 2.692557 CAACCATGTGTCTTCCCAACAA 59.307 45.455 0.00 0.00 0.00 2.83
172 173 3.082548 TGTGTCTTCCCAACAAAACGAA 58.917 40.909 0.00 0.00 0.00 3.85
202 203 2.008242 TCCCCCACATCCACAAAAAG 57.992 50.000 0.00 0.00 0.00 2.27
233 234 2.361085 ACTCCCCCAAGGTCTAACAT 57.639 50.000 0.00 0.00 36.75 2.71
235 236 2.576648 ACTCCCCCAAGGTCTAACATTC 59.423 50.000 0.00 0.00 36.75 2.67
299 302 4.526970 TCAACCATCTGAAATTAGGGAGC 58.473 43.478 0.00 0.00 0.00 4.70
323 327 1.299648 CTCGCCAGTCCATTTGGGA 59.700 57.895 0.00 0.00 45.89 4.37
341 345 9.452287 CATTTGGGAAAATTTTCAACCATCTAT 57.548 29.630 27.53 17.17 38.92 1.98
451 2160 1.562008 TGGGTGTTCACTCAACTTGGA 59.438 47.619 2.80 0.00 35.79 3.53
459 2168 5.124776 TGTTCACTCAACTTGGACGAAAAAT 59.875 36.000 0.00 0.00 35.79 1.82
473 2186 6.039270 TGGACGAAAAATTCACTTTGATCACT 59.961 34.615 0.00 0.00 0.00 3.41
487 2200 7.920151 CACTTTGATCACTGGACTTAGAGATAG 59.080 40.741 0.00 0.00 29.84 2.08
488 2201 7.617723 ACTTTGATCACTGGACTTAGAGATAGT 59.382 37.037 0.00 0.00 29.84 2.12
489 2202 9.126151 CTTTGATCACTGGACTTAGAGATAGTA 57.874 37.037 0.00 0.00 29.84 1.82
506 2226 6.335777 AGATAGTACATTGTTTACGGTCACC 58.664 40.000 0.00 0.00 0.00 4.02
533 2253 6.605594 AGGTGGTTTTATTGAACAGAACTTGA 59.394 34.615 0.00 0.00 0.00 3.02
564 2284 4.437682 TCAAAGATGAACTCCACCAACT 57.562 40.909 0.00 0.00 30.99 3.16
565 2285 4.136796 TCAAAGATGAACTCCACCAACTG 58.863 43.478 0.00 0.00 30.99 3.16
605 2327 3.240069 CGACCGGTGTTGAACTACTAAG 58.760 50.000 14.63 0.00 0.00 2.18
606 2328 3.582780 GACCGGTGTTGAACTACTAAGG 58.417 50.000 14.63 2.58 0.00 2.69
653 2633 5.331607 GCGCGATCAATTAACTAGTACACTG 60.332 44.000 12.10 0.00 0.00 3.66
673 2653 6.258727 ACACTGATAAAGGCAAGACATAATCG 59.741 38.462 0.00 0.00 0.00 3.34
695 2675 0.612744 GAGGCTATCTCATCTGCCCC 59.387 60.000 0.00 0.00 45.94 5.80
746 2924 8.732531 ACATGAAGATAAAAATGGGCAAAATTG 58.267 29.630 0.00 0.00 0.00 2.32
770 3015 7.109501 TGATTCTACTAAAGTATTTGCCAGCA 58.890 34.615 0.00 0.00 39.63 4.41
773 3018 2.161609 ACTAAAGTATTTGCCAGCACGC 59.838 45.455 0.00 0.00 39.63 5.34
787 3032 1.017387 GCACGCTGATAAGGAAAGGG 58.983 55.000 0.00 0.00 0.00 3.95
812 3057 8.903820 GGTAAATACATGAAGATATAATGGGCC 58.096 37.037 0.00 0.00 0.00 5.80
850 3098 4.938832 ACTATTTGCCAGCACGTTAATACA 59.061 37.500 0.00 0.00 0.00 2.29
851 3099 3.822594 TTTGCCAGCACGTTAATACAG 57.177 42.857 0.00 0.00 0.00 2.74
852 3100 1.732941 TGCCAGCACGTTAATACAGG 58.267 50.000 0.00 0.00 0.00 4.00
853 3101 1.276705 TGCCAGCACGTTAATACAGGA 59.723 47.619 0.00 0.00 0.00 3.86
854 3102 2.289756 TGCCAGCACGTTAATACAGGAA 60.290 45.455 0.00 0.00 0.00 3.36
855 3103 2.745281 GCCAGCACGTTAATACAGGAAA 59.255 45.455 0.00 0.00 0.00 3.13
856 3104 3.377172 GCCAGCACGTTAATACAGGAAAT 59.623 43.478 0.00 0.00 0.00 2.17
857 3105 4.573201 GCCAGCACGTTAATACAGGAAATA 59.427 41.667 0.00 0.00 0.00 1.40
858 3106 5.503520 GCCAGCACGTTAATACAGGAAATAC 60.504 44.000 0.00 0.00 0.00 1.89
859 3107 5.815740 CCAGCACGTTAATACAGGAAATACT 59.184 40.000 0.00 0.00 0.00 2.12
860 3108 6.982141 CCAGCACGTTAATACAGGAAATACTA 59.018 38.462 0.00 0.00 0.00 1.82
861 3109 7.042925 CCAGCACGTTAATACAGGAAATACTAC 60.043 40.741 0.00 0.00 0.00 2.73
862 3110 6.982724 AGCACGTTAATACAGGAAATACTACC 59.017 38.462 0.00 0.00 0.00 3.18
863 3111 6.982724 GCACGTTAATACAGGAAATACTACCT 59.017 38.462 0.00 0.00 36.92 3.08
864 3112 7.168804 GCACGTTAATACAGGAAATACTACCTC 59.831 40.741 0.00 0.00 33.91 3.85
865 3113 7.377928 CACGTTAATACAGGAAATACTACCTCG 59.622 40.741 0.00 0.00 33.91 4.63
866 3114 6.361748 CGTTAATACAGGAAATACTACCTCGC 59.638 42.308 0.00 0.00 33.91 5.03
867 3115 5.864418 AATACAGGAAATACTACCTCGCA 57.136 39.130 0.00 0.00 33.91 5.10
868 3116 5.864418 ATACAGGAAATACTACCTCGCAA 57.136 39.130 0.00 0.00 33.91 4.85
869 3117 4.546829 ACAGGAAATACTACCTCGCAAA 57.453 40.909 0.00 0.00 33.91 3.68
870 3118 4.901868 ACAGGAAATACTACCTCGCAAAA 58.098 39.130 0.00 0.00 33.91 2.44
871 3119 5.310451 ACAGGAAATACTACCTCGCAAAAA 58.690 37.500 0.00 0.00 33.91 1.94
961 3209 1.298413 CCGGTGACATCGTCGCTAG 60.298 63.158 7.44 3.06 42.03 3.42
962 3210 1.298413 CGGTGACATCGTCGCTAGG 60.298 63.158 0.00 0.00 42.03 3.02
973 3221 2.050350 TCGCTAGGGAAGGACACCG 61.050 63.158 7.09 0.00 0.00 4.94
994 3242 3.060363 CGACGGTACAAAGAAAAGGATCG 59.940 47.826 0.00 0.00 0.00 3.69
1023 3271 2.607892 GCGCACCAGAGACAACACC 61.608 63.158 0.30 0.00 0.00 4.16
1113 3361 7.335171 GGTACGTACTCCCTATTTTCACAAATT 59.665 37.037 24.07 0.00 34.29 1.82
1115 3363 7.590279 ACGTACTCCCTATTTTCACAAATTTG 58.410 34.615 16.67 16.67 34.29 2.32
1117 3365 8.293867 CGTACTCCCTATTTTCACAAATTTGAA 58.706 33.333 24.64 8.72 34.29 2.69
1118 3366 9.406828 GTACTCCCTATTTTCACAAATTTGAAC 57.593 33.333 24.64 0.00 35.18 3.18
1130 3378 9.493206 TTCACAAATTTGAACTAAAACTACGAC 57.507 29.630 24.64 0.00 30.29 4.34
1131 3379 7.847078 TCACAAATTTGAACTAAAACTACGACG 59.153 33.333 24.64 0.00 0.00 5.12
1132 3380 7.847078 CACAAATTTGAACTAAAACTACGACGA 59.153 33.333 24.64 0.00 0.00 4.20
1133 3381 8.060090 ACAAATTTGAACTAAAACTACGACGAG 58.940 33.333 24.64 0.00 0.00 4.18
1135 3383 8.801715 AATTTGAACTAAAACTACGACGAGTA 57.198 30.769 0.00 0.00 0.00 2.59
1136 3384 8.801715 ATTTGAACTAAAACTACGACGAGTAA 57.198 30.769 0.00 0.00 34.45 2.24
1139 3387 8.801715 TGAACTAAAACTACGACGAGTAATTT 57.198 30.769 0.00 2.73 36.45 1.82
1140 3388 9.891828 TGAACTAAAACTACGACGAGTAATTTA 57.108 29.630 0.00 3.67 34.13 1.40
1146 3394 7.982371 AACTACGACGAGTAATTTAGAATGG 57.018 36.000 0.00 0.00 34.45 3.16
1147 3395 7.325660 ACTACGACGAGTAATTTAGAATGGA 57.674 36.000 0.00 0.00 34.45 3.41
1148 3396 7.416022 ACTACGACGAGTAATTTAGAATGGAG 58.584 38.462 0.00 0.00 34.45 3.86
1152 3400 6.853872 CGACGAGTAATTTAGAATGGAGAGAG 59.146 42.308 0.00 0.00 0.00 3.20
1164 3413 7.482169 AGAATGGAGAGAGTACATACAAACA 57.518 36.000 0.00 0.00 0.00 2.83
1171 3420 8.999431 GGAGAGAGTACATACAAACAAAATGAA 58.001 33.333 0.00 0.00 0.00 2.57
1298 3549 3.513515 GTCCCCAGGTGATTTATTTTGCA 59.486 43.478 0.00 0.00 0.00 4.08
1330 3581 4.225042 TGAGTATTATGTGCTGACTGGGTT 59.775 41.667 0.00 0.00 0.00 4.11
1331 3582 5.423931 TGAGTATTATGTGCTGACTGGGTTA 59.576 40.000 0.00 0.00 0.00 2.85
1332 3583 6.099701 TGAGTATTATGTGCTGACTGGGTTAT 59.900 38.462 0.00 0.00 0.00 1.89
1333 3584 6.291377 AGTATTATGTGCTGACTGGGTTATG 58.709 40.000 0.00 0.00 0.00 1.90
1334 3585 1.755179 ATGTGCTGACTGGGTTATGC 58.245 50.000 0.00 0.00 0.00 3.14
1335 3586 0.399833 TGTGCTGACTGGGTTATGCA 59.600 50.000 0.00 0.00 0.00 3.96
1341 3592 2.691526 CTGACTGGGTTATGCATGCATT 59.308 45.455 36.23 18.06 37.82 3.56
1374 3625 3.244284 GGTACCACCAAGATGTGTGTACA 60.244 47.826 7.15 0.00 40.62 2.90
1524 3775 4.272018 CGTGAGGAAATAATTGAGAGCTGG 59.728 45.833 0.00 0.00 0.00 4.85
1539 3790 5.645067 TGAGAGCTGGAAATGTTAAGTCATG 59.355 40.000 0.00 0.00 0.00 3.07
1540 3791 5.564550 AGAGCTGGAAATGTTAAGTCATGT 58.435 37.500 0.00 0.00 0.00 3.21
1566 3848 0.393448 TGGTGTTACCGCTTACTGCA 59.607 50.000 0.00 0.00 42.58 4.41
1569 3851 1.664151 GTGTTACCGCTTACTGCATCC 59.336 52.381 0.00 0.00 43.06 3.51
1589 3871 6.127897 GCATCCAAATATGTATTACCTCTGCC 60.128 42.308 0.00 0.00 0.00 4.85
1591 3873 5.010282 CCAAATATGTATTACCTCTGCCCC 58.990 45.833 0.00 0.00 0.00 5.80
1606 3888 5.452356 CCTCTGCCCCAAATTATTTGTCATC 60.452 44.000 15.40 3.97 38.98 2.92
1612 3894 6.207810 GCCCCAAATTATTTGTCATCCGTATA 59.792 38.462 15.40 0.00 38.98 1.47
1741 4023 1.609932 GTGAAACATGCATGCAGTCG 58.390 50.000 26.69 18.40 36.32 4.18
1773 4055 7.127801 TCCCATGATTTCTTTTATCCTCAGAGA 59.872 37.037 0.00 0.00 0.00 3.10
1774 4056 7.444792 CCCATGATTTCTTTTATCCTCAGAGAG 59.555 40.741 0.00 0.00 0.00 3.20
1775 4057 7.041235 CCATGATTTCTTTTATCCTCAGAGAGC 60.041 40.741 0.00 0.00 0.00 4.09
1826 4108 5.864418 ATATCTGTTGCCTTTTCATGCAT 57.136 34.783 0.00 0.00 37.33 3.96
1864 4149 2.431057 CACGTACCTCTAAGGGCATCTT 59.569 50.000 0.00 0.00 40.58 2.40
2091 4381 3.973472 AAGTCAAGGTTTTCTTCCCCT 57.027 42.857 0.00 0.00 32.41 4.79
2325 4618 2.964978 GCGTTTTGCCTGCCTCAT 59.035 55.556 0.00 0.00 37.76 2.90
2326 4619 1.153958 GCGTTTTGCCTGCCTCATC 60.154 57.895 0.00 0.00 37.76 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 2.563427 GCGCCTTTGCAAGAGGAC 59.437 61.111 23.58 16.05 36.33 3.85
107 108 3.588057 AATTTGCCCCGCGCCTTTG 62.588 57.895 0.00 0.00 36.24 2.77
115 116 1.878102 CGGATCTAGGAATTTGCCCCG 60.878 57.143 0.00 0.00 0.00 5.73
129 130 2.301346 GGTTGCATGGATTTCGGATCT 58.699 47.619 0.00 0.00 0.00 2.75
151 152 2.712709 TCGTTTTGTTGGGAAGACACA 58.287 42.857 0.00 0.00 0.00 3.72
166 167 3.626475 GGGGGATGGTAAATCCTTCGTTT 60.626 47.826 4.46 0.00 40.14 3.60
172 173 1.994399 TGTGGGGGATGGTAAATCCT 58.006 50.000 4.46 0.00 38.26 3.24
233 234 2.347490 GCTGCGGGGAACTGAGAA 59.653 61.111 0.00 0.00 39.98 2.87
235 236 1.971505 TATGGCTGCGGGGAACTGAG 61.972 60.000 0.00 0.00 39.98 3.35
259 262 2.548875 TGAACATTGCTTTTGGTGTGC 58.451 42.857 0.00 0.00 0.00 4.57
299 302 2.826777 AATGGACTGGCGAGCTTGGG 62.827 60.000 2.37 0.00 0.00 4.12
306 309 0.111446 TTTCCCAAATGGACTGGCGA 59.889 50.000 0.00 0.00 45.11 5.54
341 345 8.192774 GGCATGTTTAGAATCATGAAGATTTCA 58.807 33.333 14.63 0.00 46.76 2.69
364 385 8.303876 GGTCAAAAATTTTGTCTATTAGAGGCA 58.696 33.333 16.83 0.00 38.28 4.75
374 395 7.616313 TGTTGTAAGGGTCAAAAATTTTGTCT 58.384 30.769 16.83 10.77 0.00 3.41
385 406 8.983702 AGTAAGTTAATTGTTGTAAGGGTCAA 57.016 30.769 0.00 0.00 0.00 3.18
451 2160 6.039270 TCCAGTGATCAAAGTGAATTTTTCGT 59.961 34.615 0.00 0.00 0.00 3.85
459 2168 6.267699 TCTCTAAGTCCAGTGATCAAAGTGAA 59.732 38.462 0.00 0.00 0.00 3.18
487 2200 4.083696 CCTTGGTGACCGTAAACAATGTAC 60.084 45.833 0.00 0.00 0.00 2.90
488 2201 4.066490 CCTTGGTGACCGTAAACAATGTA 58.934 43.478 0.00 0.00 0.00 2.29
489 2202 2.882137 CCTTGGTGACCGTAAACAATGT 59.118 45.455 0.00 0.00 0.00 2.71
506 2226 6.805713 AGTTCTGTTCAATAAAACCACCTTG 58.194 36.000 0.00 0.00 0.00 3.61
564 2284 6.148315 CGGTCGTGTCTACCATATAATAGTCA 59.852 42.308 0.00 0.00 36.78 3.41
565 2285 6.402983 CCGGTCGTGTCTACCATATAATAGTC 60.403 46.154 0.00 0.00 36.78 2.59
629 2351 4.738740 AGTGTACTAGTTAATTGATCGCGC 59.261 41.667 0.00 0.00 0.00 6.86
635 2357 9.595823 GCCTTTATCAGTGTACTAGTTAATTGA 57.404 33.333 0.00 2.95 0.00 2.57
653 2633 6.223852 TCCTCGATTATGTCTTGCCTTTATC 58.776 40.000 0.00 0.00 0.00 1.75
673 2653 1.550072 GGCAGATGAGATAGCCTCCTC 59.450 57.143 0.00 0.00 43.70 3.71
734 2714 8.366359 ACTTTAGTAGAATCAATTTTGCCCAT 57.634 30.769 0.00 0.00 0.00 4.00
746 2924 7.410485 GTGCTGGCAAATACTTTAGTAGAATC 58.590 38.462 0.00 0.00 33.52 2.52
770 3015 4.563140 TTTACCCTTTCCTTATCAGCGT 57.437 40.909 0.00 0.00 0.00 5.07
773 3018 9.627123 TTCATGTATTTACCCTTTCCTTATCAG 57.373 33.333 0.00 0.00 0.00 2.90
787 3032 9.461312 TGGCCCATTATATCTTCATGTATTTAC 57.539 33.333 0.00 0.00 0.00 2.01
828 3076 5.478233 TGTATTAACGTGCTGGCAAATAG 57.522 39.130 0.00 0.00 0.00 1.73
961 3209 1.978617 TACCGTCGGTGTCCTTCCC 60.979 63.158 27.20 0.00 36.19 3.97
962 3210 1.213799 GTACCGTCGGTGTCCTTCC 59.786 63.158 27.20 2.25 36.19 3.46
973 3221 3.181523 GCGATCCTTTTCTTTGTACCGTC 60.182 47.826 0.00 0.00 0.00 4.79
994 3242 4.759096 GGTGCGCGTCATGTTGGC 62.759 66.667 8.43 0.00 0.00 4.52
1023 3271 0.167470 CCATCAAGCACAGAACTGCG 59.833 55.000 1.46 0.00 42.42 5.18
1113 3361 8.801715 AATTACTCGTCGTAGTTTTAGTTCAA 57.198 30.769 3.29 0.00 0.00 2.69
1121 3369 8.246180 TCCATTCTAAATTACTCGTCGTAGTTT 58.754 33.333 10.79 10.79 40.05 2.66
1122 3370 7.765307 TCCATTCTAAATTACTCGTCGTAGTT 58.235 34.615 3.29 0.00 30.27 2.24
1123 3371 7.281774 TCTCCATTCTAAATTACTCGTCGTAGT 59.718 37.037 0.00 0.00 0.00 2.73
1124 3372 7.637229 TCTCCATTCTAAATTACTCGTCGTAG 58.363 38.462 0.00 0.00 0.00 3.51
1126 3374 6.318144 TCTCTCCATTCTAAATTACTCGTCGT 59.682 38.462 0.00 0.00 0.00 4.34
1127 3375 6.726230 TCTCTCCATTCTAAATTACTCGTCG 58.274 40.000 0.00 0.00 0.00 5.12
1128 3376 7.708998 ACTCTCTCCATTCTAAATTACTCGTC 58.291 38.462 0.00 0.00 0.00 4.20
1130 3378 8.622157 TGTACTCTCTCCATTCTAAATTACTCG 58.378 37.037 0.00 0.00 0.00 4.18
1139 3387 8.589701 TGTTTGTATGTACTCTCTCCATTCTA 57.410 34.615 0.00 0.00 0.00 2.10
1140 3388 7.482169 TGTTTGTATGTACTCTCTCCATTCT 57.518 36.000 0.00 0.00 0.00 2.40
1142 3390 8.918202 TTTTGTTTGTATGTACTCTCTCCATT 57.082 30.769 0.00 0.00 0.00 3.16
1143 3391 8.950210 CATTTTGTTTGTATGTACTCTCTCCAT 58.050 33.333 0.00 0.00 0.00 3.41
1144 3392 8.154203 TCATTTTGTTTGTATGTACTCTCTCCA 58.846 33.333 0.00 0.00 0.00 3.86
1145 3393 8.547967 TCATTTTGTTTGTATGTACTCTCTCC 57.452 34.615 0.00 0.00 0.00 3.71
1162 3411 8.994429 TTACTGTGTTTGTTCATTCATTTTGT 57.006 26.923 0.00 0.00 0.00 2.83
1171 3420 7.012515 TGGACGTATTTTACTGTGTTTGTTCAT 59.987 33.333 0.00 0.00 0.00 2.57
1231 3482 5.011840 GTCACCCCCTTCACTATTATAGGAC 59.988 48.000 4.15 0.00 0.00 3.85
1307 3558 3.774766 ACCCAGTCAGCACATAATACTCA 59.225 43.478 0.00 0.00 0.00 3.41
1330 3581 9.093970 GTACCTATTTATACGAATGCATGCATA 57.906 33.333 32.36 17.99 35.31 3.14
1331 3582 7.065803 GGTACCTATTTATACGAATGCATGCAT 59.934 37.037 27.46 27.46 38.46 3.96
1332 3583 6.370442 GGTACCTATTTATACGAATGCATGCA 59.630 38.462 25.04 25.04 0.00 3.96
1333 3584 6.370442 TGGTACCTATTTATACGAATGCATGC 59.630 38.462 11.82 11.82 0.00 4.06
1334 3585 7.148474 GGTGGTACCTATTTATACGAATGCATG 60.148 40.741 14.36 0.00 34.73 4.06
1335 3586 6.877322 GGTGGTACCTATTTATACGAATGCAT 59.123 38.462 14.36 0.00 34.73 3.96
1341 3592 7.288389 ACATCTTGGTGGTACCTATTTATACGA 59.712 37.037 14.36 0.00 39.58 3.43
1566 3848 6.485171 GGGCAGAGGTAATACATATTTGGAT 58.515 40.000 0.00 0.00 0.00 3.41
1569 3851 5.630121 TGGGGCAGAGGTAATACATATTTG 58.370 41.667 0.00 0.00 0.00 2.32
1589 3871 8.792633 ACATATACGGATGACAAATAATTTGGG 58.207 33.333 0.00 0.00 44.81 4.12
1628 3910 7.310361 CCCTCCATCCTAAATTGCTTGTTTTAA 60.310 37.037 0.00 0.00 0.00 1.52
1642 3924 5.476950 TTGTAGTACTCCCTCCATCCTAA 57.523 43.478 0.00 0.00 0.00 2.69
1648 3930 4.899457 CCACATATTGTAGTACTCCCTCCA 59.101 45.833 0.00 0.00 0.00 3.86
1741 4023 6.039829 GGATAAAAGAAATCATGGGAGTGACC 59.960 42.308 0.00 0.00 38.08 4.02
1826 4108 7.802117 AGGTACGTGGTAGGTAGTACTATTTA 58.198 38.462 5.75 0.00 39.33 1.40
2124 4415 0.179134 CGCCGGGATATAGCTAGTGC 60.179 60.000 2.18 0.00 40.05 4.40
2334 4627 1.680735 CTCTTCCTCCTCATCCGAGTG 59.319 57.143 0.00 0.00 37.59 3.51


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

AutoCloner maintained by Alex Coulton.