Multiple sequence alignment - TraesCS1B01G031400

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 TraesCS1B01G031400 chr1B 100.000 2198 0 0 1 2198 15420816 15423013 0.000000e+00 4060.0
1 TraesCS1B01G031400 chr1B 98.762 727 7 1 1 727 533415966 533416690 0.000000e+00 1291.0
2 TraesCS1B01G031400 chr1B 98.762 727 6 1 1 727 633166706 633167429 0.000000e+00 1290.0
3 TraesCS1B01G031400 chr1B 98.497 732 7 2 1 731 51961230 51961958 0.000000e+00 1288.0
4 TraesCS1B01G031400 chr1B 98.493 730 7 2 1 727 17478635 17477907 0.000000e+00 1284.0
5 TraesCS1B01G031400 chr1B 82.045 440 47 22 776 1198 15531145 15530721 1.620000e-91 346.0
6 TraesCS1B01G031400 chr1B 80.278 431 52 24 776 1189 15582114 15581700 5.930000e-76 294.0
7 TraesCS1B01G031400 chr1B 86.878 221 29 0 985 1205 15339953 15340173 4.690000e-62 248.0
8 TraesCS1B01G031400 chr1B 80.399 301 29 10 845 1136 15299394 15299673 3.700000e-48 202.0
9 TraesCS1B01G031400 chr1B 79.323 266 30 11 838 1091 15533490 15533238 1.750000e-36 163.0
10 TraesCS1B01G031400 chr1A 86.319 1440 122 29 793 2169 12171099 12169672 0.000000e+00 1498.0
11 TraesCS1B01G031400 chr1A 86.165 1330 104 27 793 2059 12109134 12110446 0.000000e+00 1363.0
12 TraesCS1B01G031400 chr1A 82.947 604 64 22 808 1376 12138633 12139232 1.950000e-140 508.0
13 TraesCS1B01G031400 chr1A 83.028 436 42 22 776 1198 12129403 12129819 1.240000e-97 366.0
14 TraesCS1B01G031400 chr1A 88.000 100 9 1 1605 1701 552458593 552458692 4.960000e-22 115.0
15 TraesCS1B01G031400 chr6B 98.762 727 5 2 1 727 14636651 14635929 0.000000e+00 1290.0
16 TraesCS1B01G031400 chr2A 98.762 727 6 1 1 727 745735959 745735236 0.000000e+00 1290.0
17 TraesCS1B01G031400 chr2A 77.397 584 96 16 1565 2119 21147090 21147666 4.560000e-82 315.0
18 TraesCS1B01G031400 chr2A 81.481 270 46 4 1702 1971 413181966 413181701 3.670000e-53 219.0
19 TraesCS1B01G031400 chr2A 78.983 295 34 15 1809 2095 244316690 244316964 2.240000e-40 176.0
20 TraesCS1B01G031400 chr2A 77.132 258 36 10 1464 1701 518338174 518337920 6.370000e-26 128.0
21 TraesCS1B01G031400 chr3B 98.626 728 9 1 1 727 817232152 817231425 0.000000e+00 1288.0
22 TraesCS1B01G031400 chr2B 98.624 727 9 1 1 727 496110074 496110799 0.000000e+00 1286.0
23 TraesCS1B01G031400 chr5B 98.489 728 8 2 1 728 513951607 513952331 0.000000e+00 1280.0
24 TraesCS1B01G031400 chr1D 89.709 447 27 8 775 1206 10390375 10390817 8.870000e-154 553.0
25 TraesCS1B01G031400 chr1D 80.592 304 53 4 1703 2005 26622789 26622491 1.700000e-56 230.0
26 TraesCS1B01G031400 chr5D 82.100 419 69 4 1702 2119 9391782 9392195 9.650000e-94 353.0
27 TraesCS1B01G031400 chr3D 80.998 421 66 11 1702 2118 4927697 4927287 2.720000e-84 322.0
28 TraesCS1B01G031400 chr4B 78.155 412 79 9 1702 2111 627553389 627553791 3.620000e-63 252.0
29 TraesCS1B01G031400 chr2D 77.891 294 38 14 1809 2095 261732687 261732414 8.120000e-35 158.0
30 TraesCS1B01G031400 chr2D 81.203 133 23 1 1571 1701 383561647 383561515 2.980000e-19 106.0
31 TraesCS1B01G031400 chr6D 83.333 132 20 1 1572 1701 147688432 147688563 1.070000e-23 121.0
32 TraesCS1B01G031400 chr6D 80.000 125 22 2 1574 1696 420161509 420161386 3.010000e-14 89.8
33 TraesCS1B01G031400 chr4D 75.849 265 33 10 1464 1701 128909776 128909516 2.980000e-19 106.0


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 TraesCS1B01G031400 chr1B 15420816 15423013 2197 False 4060.0 4060 100.000 1 2198 1 chr1B.!!$F3 2197
1 TraesCS1B01G031400 chr1B 533415966 533416690 724 False 1291.0 1291 98.762 1 727 1 chr1B.!!$F5 726
2 TraesCS1B01G031400 chr1B 633166706 633167429 723 False 1290.0 1290 98.762 1 727 1 chr1B.!!$F6 726
3 TraesCS1B01G031400 chr1B 51961230 51961958 728 False 1288.0 1288 98.497 1 731 1 chr1B.!!$F4 730
4 TraesCS1B01G031400 chr1B 17477907 17478635 728 True 1284.0 1284 98.493 1 727 1 chr1B.!!$R2 726
5 TraesCS1B01G031400 chr1B 15530721 15533490 2769 True 254.5 346 80.684 776 1198 2 chr1B.!!$R3 422
6 TraesCS1B01G031400 chr1A 12169672 12171099 1427 True 1498.0 1498 86.319 793 2169 1 chr1A.!!$R1 1376
7 TraesCS1B01G031400 chr1A 12109134 12110446 1312 False 1363.0 1363 86.165 793 2059 1 chr1A.!!$F1 1266
8 TraesCS1B01G031400 chr1A 12138633 12139232 599 False 508.0 508 82.947 808 1376 1 chr1A.!!$F3 568
9 TraesCS1B01G031400 chr6B 14635929 14636651 722 True 1290.0 1290 98.762 1 727 1 chr6B.!!$R1 726
10 TraesCS1B01G031400 chr2A 745735236 745735959 723 True 1290.0 1290 98.762 1 727 1 chr2A.!!$R3 726
11 TraesCS1B01G031400 chr2A 21147090 21147666 576 False 315.0 315 77.397 1565 2119 1 chr2A.!!$F1 554
12 TraesCS1B01G031400 chr3B 817231425 817232152 727 True 1288.0 1288 98.626 1 727 1 chr3B.!!$R1 726
13 TraesCS1B01G031400 chr2B 496110074 496110799 725 False 1286.0 1286 98.624 1 727 1 chr2B.!!$F1 726
14 TraesCS1B01G031400 chr5B 513951607 513952331 724 False 1280.0 1280 98.489 1 728 1 chr5B.!!$F1 727

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
765 775 0.034059 AGCAAGTCTGAACCTGGACG 59.966 55.0 0.0 0.0 37.52 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 3539 0.171007 ACGCATGCAACCATTACAGC 59.829 50.0 19.57 0.0 0.0 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
741 751 2.282040 GTGGCCAACTGCTCAGCT 60.282 61.111 7.24 0.00 40.92 4.24
742 752 1.003355 GTGGCCAACTGCTCAGCTA 60.003 57.895 7.24 0.00 40.92 3.32
743 753 1.023513 GTGGCCAACTGCTCAGCTAG 61.024 60.000 7.24 0.00 40.92 3.42
760 770 3.051081 CTAGCAAGCAAGTCTGAACCT 57.949 47.619 0.00 0.00 0.00 3.50
761 771 1.602311 AGCAAGCAAGTCTGAACCTG 58.398 50.000 0.00 0.00 0.00 4.00
764 774 1.876156 CAAGCAAGTCTGAACCTGGAC 59.124 52.381 0.00 0.00 0.00 4.02
765 775 0.034059 AGCAAGTCTGAACCTGGACG 59.966 55.000 0.00 0.00 37.52 4.79
766 776 1.569479 GCAAGTCTGAACCTGGACGC 61.569 60.000 0.00 0.00 37.52 5.19
768 778 0.687354 AAGTCTGAACCTGGACGCAT 59.313 50.000 0.00 0.00 37.52 4.73
769 779 1.557099 AGTCTGAACCTGGACGCATA 58.443 50.000 0.00 0.00 37.52 3.14
770 780 2.111384 AGTCTGAACCTGGACGCATAT 58.889 47.619 0.00 0.00 37.52 1.78
771 781 3.296854 AGTCTGAACCTGGACGCATATA 58.703 45.455 0.00 0.00 37.52 0.86
772 782 3.068307 AGTCTGAACCTGGACGCATATAC 59.932 47.826 0.00 0.00 37.52 1.47
776 786 2.839486 ACCTGGACGCATATACATGG 57.161 50.000 0.00 0.00 32.36 3.66
777 787 2.325484 ACCTGGACGCATATACATGGA 58.675 47.619 0.00 0.00 32.36 3.41
778 788 2.037251 ACCTGGACGCATATACATGGAC 59.963 50.000 0.00 0.00 32.36 4.02
779 789 2.328473 CTGGACGCATATACATGGACG 58.672 52.381 0.00 0.00 32.36 4.79
789 2360 5.278808 GCATATACATGGACGGTCACTCTTA 60.279 44.000 10.76 0.00 32.36 2.10
790 2361 6.572509 GCATATACATGGACGGTCACTCTTAT 60.573 42.308 10.76 2.78 32.36 1.73
791 2362 3.526931 ACATGGACGGTCACTCTTATG 57.473 47.619 10.76 6.79 0.00 1.90
797 2368 4.202151 TGGACGGTCACTCTTATGATGATG 60.202 45.833 10.76 0.00 0.00 3.07
806 2377 5.007430 CACTCTTATGATGATGTTGCTGTCC 59.993 44.000 0.00 0.00 0.00 4.02
818 2389 3.198872 GTTGCTGTCCTGCTACCTAATC 58.801 50.000 0.62 0.00 33.76 1.75
876 2447 0.452184 TGACAAAACGAGGCGCAAAA 59.548 45.000 10.83 0.00 0.00 2.44
900 2471 6.417191 TTGTTTAGAAATGTACGATGGCTC 57.583 37.500 0.00 0.00 0.00 4.70
969 2566 4.013728 ACCTAGCTAGCTATCATCTTCCG 58.986 47.826 24.36 9.55 0.00 4.30
979 2576 1.874019 CATCTTCCGTCGGTGCTCG 60.874 63.158 11.88 0.00 40.90 5.03
980 2577 2.044555 ATCTTCCGTCGGTGCTCGA 61.045 57.895 11.88 2.49 46.77 4.04
1135 2743 3.675619 ATGCCCGACTACAACGCCC 62.676 63.158 0.00 0.00 0.00 6.13
1158 2766 1.421410 GCGTCCGCGTCTTCATCAAT 61.421 55.000 4.92 0.00 40.81 2.57
1266 2918 0.171231 CGCTAGCTGCTGTGACTACA 59.829 55.000 13.43 0.00 40.11 2.74
1281 2933 7.539712 TGTGACTACAGTACTACGGTATAAC 57.460 40.000 0.00 1.50 28.98 1.89
1300 2952 6.882458 ATAACGGAAGAATAAAGTGACGTC 57.118 37.500 9.11 9.11 32.41 4.34
1325 2977 4.211389 GTGTTTGTGCTACGTGATTTCTG 58.789 43.478 0.00 0.00 0.00 3.02
1334 2986 5.050363 TGCTACGTGATTTCTGTGAAAACTC 60.050 40.000 0.00 0.00 0.00 3.01
1411 3063 0.460722 GAGTTACGAGGGCTCCTTCC 59.539 60.000 0.00 0.00 31.76 3.46
1424 3076 0.248289 TCCTTCCGAAAACCTAGCCG 59.752 55.000 0.00 0.00 0.00 5.52
1425 3077 1.366854 CCTTCCGAAAACCTAGCCGC 61.367 60.000 0.00 0.00 0.00 6.53
1446 3098 0.179000 GCCAACATCTCCGTCTCCAT 59.821 55.000 0.00 0.00 0.00 3.41
1447 3099 1.808133 GCCAACATCTCCGTCTCCATC 60.808 57.143 0.00 0.00 0.00 3.51
1448 3100 1.482182 CCAACATCTCCGTCTCCATCA 59.518 52.381 0.00 0.00 0.00 3.07
1453 3105 3.823873 ACATCTCCGTCTCCATCATAGAC 59.176 47.826 0.00 0.00 40.01 2.59
1458 3110 2.430546 GTCTCCATCATAGACGCCAG 57.569 55.000 0.00 0.00 34.50 4.85
1459 3111 1.000283 GTCTCCATCATAGACGCCAGG 60.000 57.143 0.00 0.00 34.50 4.45
1460 3112 0.319728 CTCCATCATAGACGCCAGGG 59.680 60.000 0.00 0.00 0.00 4.45
1461 3113 0.398522 TCCATCATAGACGCCAGGGT 60.399 55.000 0.00 0.00 0.00 4.34
1462 3114 0.469917 CCATCATAGACGCCAGGGTT 59.530 55.000 0.00 0.00 0.00 4.11
1473 3145 3.010144 CAGGGTTGGAGGGATGGG 58.990 66.667 0.00 0.00 0.00 4.00
1499 3171 6.732896 ACCCGATCTATGTATGAAGTTCTT 57.267 37.500 4.17 0.08 0.00 2.52
1500 3172 7.834881 ACCCGATCTATGTATGAAGTTCTTA 57.165 36.000 4.17 0.00 0.00 2.10
1527 3200 5.133383 AGTAGTGTTTGGGTTAGGGTTTT 57.867 39.130 0.00 0.00 0.00 2.43
1528 3201 4.891168 AGTAGTGTTTGGGTTAGGGTTTTG 59.109 41.667 0.00 0.00 0.00 2.44
1531 3204 2.766828 TGTTTGGGTTAGGGTTTTGGTG 59.233 45.455 0.00 0.00 0.00 4.17
1534 3207 1.189524 GGGTTAGGGTTTTGGTGGCC 61.190 60.000 0.00 0.00 0.00 5.36
1537 3210 0.537828 TTAGGGTTTTGGTGGCCGTC 60.538 55.000 0.00 0.00 0.00 4.79
1544 3217 0.882927 TTTGGTGGCCGTCTTCTTCG 60.883 55.000 0.00 0.00 0.00 3.79
1563 3236 1.328680 CGTCTTTGAAGATGGCATCGG 59.671 52.381 21.01 8.97 38.19 4.18
1599 3287 4.933505 TCGACGACTAGATCTCCTTCTA 57.066 45.455 0.00 0.00 0.00 2.10
1736 3452 4.566759 CGTCGACAATGGTGATTCATACTT 59.433 41.667 17.16 0.00 0.00 2.24
1738 3454 6.402118 CGTCGACAATGGTGATTCATACTTTT 60.402 38.462 17.16 0.00 0.00 2.27
1745 3461 4.263905 TGGTGATTCATACTTTTGGCTCCT 60.264 41.667 0.00 0.00 0.00 3.69
1760 3476 1.741732 GCTCCTAGTGACGTCGACCTA 60.742 57.143 10.58 9.75 0.00 3.08
1767 3483 0.956633 TGACGTCGACCTAGCTGTTT 59.043 50.000 10.58 0.00 0.00 2.83
1769 3485 0.956633 ACGTCGACCTAGCTGTTTGA 59.043 50.000 10.58 0.00 0.00 2.69
1801 3518 5.428496 TCTAGAATACCGGTGTTGATACG 57.572 43.478 22.34 5.36 0.00 3.06
1822 3539 0.801872 TTGCCGATGTTGGTCGATTG 59.198 50.000 0.00 0.00 44.06 2.67
1836 3553 2.161410 GTCGATTGCTGTAATGGTTGCA 59.839 45.455 0.00 0.00 0.00 4.08
1902 3619 4.137116 TGGAAGAATCCTCGTTGGTATG 57.863 45.455 0.00 0.00 46.70 2.39
1953 3670 4.503714 TTTTCCTATGGCTACCTTCAGG 57.496 45.455 0.00 0.00 42.17 3.86
1962 3679 2.079925 GCTACCTTCAGGAAAGCACAG 58.920 52.381 15.73 0.00 42.81 3.66
1991 3708 7.279615 TGTGTCATGGAAGAAGAAAGAGTTTA 58.720 34.615 0.00 0.00 0.00 2.01
1994 3711 9.184523 TGTCATGGAAGAAGAAAGAGTTTAAAA 57.815 29.630 0.00 0.00 0.00 1.52
2064 3781 5.076873 GGGAGTCAGCTCTTGTATCTCTAT 58.923 45.833 0.00 0.00 41.38 1.98
2141 3859 9.723601 AAAAGCAAATTATTCATGTGTTACCAT 57.276 25.926 0.00 0.00 0.00 3.55
2175 3893 8.458573 AGATTAGTTTGTTATGTGACCAAACA 57.541 30.769 14.46 6.79 46.43 2.83
2176 3894 9.077885 AGATTAGTTTGTTATGTGACCAAACAT 57.922 29.630 14.46 3.93 46.43 2.71
2177 3895 9.128107 GATTAGTTTGTTATGTGACCAAACATG 57.872 33.333 14.46 0.00 46.43 3.21
2178 3896 6.463995 AGTTTGTTATGTGACCAAACATGT 57.536 33.333 14.46 0.00 46.43 3.21
2179 3897 6.272318 AGTTTGTTATGTGACCAAACATGTG 58.728 36.000 14.46 0.00 46.43 3.21
2180 3898 4.235939 TGTTATGTGACCAAACATGTGC 57.764 40.909 0.00 0.00 40.93 4.57
2181 3899 3.005261 TGTTATGTGACCAAACATGTGCC 59.995 43.478 0.00 0.00 40.93 5.01
2182 3900 1.999648 ATGTGACCAAACATGTGCCT 58.000 45.000 0.00 0.00 39.32 4.75
2183 3901 1.317613 TGTGACCAAACATGTGCCTC 58.682 50.000 0.00 0.00 0.00 4.70
2184 3902 1.317613 GTGACCAAACATGTGCCTCA 58.682 50.000 0.00 0.00 0.00 3.86
2185 3903 1.888512 GTGACCAAACATGTGCCTCAT 59.111 47.619 0.00 0.00 37.22 2.90
2194 3912 3.646611 CATGTGCCTCATGTGAAAACA 57.353 42.857 9.80 0.00 46.18 2.83
2195 3913 3.979948 CATGTGCCTCATGTGAAAACAA 58.020 40.909 9.80 0.00 46.18 2.83
2196 3914 4.370049 CATGTGCCTCATGTGAAAACAAA 58.630 39.130 9.80 0.00 46.18 2.83
2197 3915 3.779759 TGTGCCTCATGTGAAAACAAAC 58.220 40.909 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
741 751 2.550855 CCAGGTTCAGACTTGCTTGCTA 60.551 50.000 0.00 0.00 31.94 3.49
742 752 1.602311 CAGGTTCAGACTTGCTTGCT 58.398 50.000 0.00 0.00 0.00 3.91
743 753 0.595095 CCAGGTTCAGACTTGCTTGC 59.405 55.000 0.00 0.00 31.94 4.01
746 756 0.034059 CGTCCAGGTTCAGACTTGCT 59.966 55.000 0.00 0.00 31.94 3.91
747 757 1.569479 GCGTCCAGGTTCAGACTTGC 61.569 60.000 0.00 0.00 31.94 4.01
748 758 0.249868 TGCGTCCAGGTTCAGACTTG 60.250 55.000 0.00 0.00 33.00 3.16
751 761 2.604046 ATATGCGTCCAGGTTCAGAC 57.396 50.000 0.00 0.00 0.00 3.51
753 763 3.452755 TGTATATGCGTCCAGGTTCAG 57.547 47.619 0.00 0.00 0.00 3.02
754 764 3.494223 CCATGTATATGCGTCCAGGTTCA 60.494 47.826 0.00 0.00 32.79 3.18
755 765 3.067106 CCATGTATATGCGTCCAGGTTC 58.933 50.000 0.00 0.00 32.79 3.62
759 769 2.328473 CGTCCATGTATATGCGTCCAG 58.672 52.381 0.00 0.00 32.79 3.86
760 770 1.000394 CCGTCCATGTATATGCGTCCA 60.000 52.381 0.00 0.00 32.79 4.02
761 771 1.000506 ACCGTCCATGTATATGCGTCC 59.999 52.381 0.00 0.00 32.79 4.79
764 774 2.058798 GTGACCGTCCATGTATATGCG 58.941 52.381 0.00 0.00 32.79 4.73
765 775 3.005897 AGAGTGACCGTCCATGTATATGC 59.994 47.826 0.00 0.00 32.79 3.14
766 776 4.855715 AGAGTGACCGTCCATGTATATG 57.144 45.455 0.00 0.00 0.00 1.78
768 778 6.066032 TCATAAGAGTGACCGTCCATGTATA 58.934 40.000 0.00 0.00 0.00 1.47
769 779 4.893524 TCATAAGAGTGACCGTCCATGTAT 59.106 41.667 0.00 0.00 0.00 2.29
770 780 4.274978 TCATAAGAGTGACCGTCCATGTA 58.725 43.478 0.00 0.00 0.00 2.29
771 781 3.096852 TCATAAGAGTGACCGTCCATGT 58.903 45.455 0.00 0.00 0.00 3.21
772 782 3.801114 TCATAAGAGTGACCGTCCATG 57.199 47.619 0.00 0.00 0.00 3.66
776 786 4.938080 ACATCATCATAAGAGTGACCGTC 58.062 43.478 0.00 0.00 0.00 4.79
777 787 5.111989 CAACATCATCATAAGAGTGACCGT 58.888 41.667 0.00 0.00 0.00 4.83
778 788 4.025396 GCAACATCATCATAAGAGTGACCG 60.025 45.833 0.00 0.00 0.00 4.79
779 789 5.007430 CAGCAACATCATCATAAGAGTGACC 59.993 44.000 0.00 0.00 0.00 4.02
789 2360 2.022195 GCAGGACAGCAACATCATCAT 58.978 47.619 0.00 0.00 0.00 2.45
790 2361 1.003928 AGCAGGACAGCAACATCATCA 59.996 47.619 0.00 0.00 36.85 3.07
791 2362 1.747709 AGCAGGACAGCAACATCATC 58.252 50.000 0.00 0.00 36.85 2.92
797 2368 2.762535 TTAGGTAGCAGGACAGCAAC 57.237 50.000 0.00 0.00 36.85 4.17
806 2377 1.371558 GGGCGGGATTAGGTAGCAG 59.628 63.158 0.00 0.00 0.00 4.24
876 2447 6.597672 TGAGCCATCGTACATTTCTAAACAAT 59.402 34.615 0.00 0.00 0.00 2.71
900 2471 5.013079 TGGTGTATTTATAGGGAGAGCCATG 59.987 44.000 0.00 0.00 35.15 3.66
945 2520 5.295787 CGGAAGATGATAGCTAGCTAGGTAG 59.704 48.000 30.29 22.09 39.36 3.18
979 2576 0.747255 TTGGGAGCTAGCTCGTGATC 59.253 55.000 32.78 20.79 43.59 2.92
980 2577 0.749649 CTTGGGAGCTAGCTCGTGAT 59.250 55.000 32.78 5.04 43.59 3.06
981 2578 0.323451 TCTTGGGAGCTAGCTCGTGA 60.323 55.000 32.78 24.28 43.59 4.35
982 2579 0.749649 ATCTTGGGAGCTAGCTCGTG 59.250 55.000 32.78 22.75 43.59 4.35
1266 2918 8.677148 TTATTCTTCCGTTATACCGTAGTACT 57.323 34.615 0.00 0.00 0.00 2.73
1281 2933 4.625742 ACATGACGTCACTTTATTCTTCCG 59.374 41.667 22.71 0.00 0.00 4.30
1300 2952 3.811722 ATCACGTAGCACAAACACATG 57.188 42.857 0.00 0.00 0.00 3.21
1325 2977 6.007677 CACGAATAGTTTAGCGAGTTTTCAC 58.992 40.000 0.00 0.00 0.00 3.18
1334 2986 2.997986 ACAACCCACGAATAGTTTAGCG 59.002 45.455 0.00 0.00 0.00 4.26
1372 3024 3.386486 TCACGTTCTGGTACACATGAAC 58.614 45.455 0.00 2.74 35.61 3.18
1400 3052 1.134438 AGGTTTTCGGAAGGAGCCCT 61.134 55.000 0.00 0.00 33.87 5.19
1401 3053 0.616891 TAGGTTTTCGGAAGGAGCCC 59.383 55.000 0.00 0.00 0.00 5.19
1402 3054 2.012554 GCTAGGTTTTCGGAAGGAGCC 61.013 57.143 0.00 0.00 0.00 4.70
1403 3055 1.370609 GCTAGGTTTTCGGAAGGAGC 58.629 55.000 0.00 0.00 0.00 4.70
1404 3056 1.739371 CGGCTAGGTTTTCGGAAGGAG 60.739 57.143 0.00 0.00 0.00 3.69
1405 3057 0.248289 CGGCTAGGTTTTCGGAAGGA 59.752 55.000 0.00 0.00 0.00 3.36
1406 3058 1.366854 GCGGCTAGGTTTTCGGAAGG 61.367 60.000 0.00 0.00 0.00 3.46
1407 3059 1.366854 GGCGGCTAGGTTTTCGGAAG 61.367 60.000 0.00 0.00 0.00 3.46
1411 3063 3.861263 GCGGCGGCTAGGTTTTCG 61.861 66.667 9.78 0.00 35.83 3.46
1424 3076 3.195698 GACGGAGATGTTGGCGGC 61.196 66.667 0.00 0.00 0.00 6.53
1425 3077 1.519455 GAGACGGAGATGTTGGCGG 60.519 63.158 0.00 0.00 0.00 6.13
1440 3092 1.332195 CCTGGCGTCTATGATGGAGA 58.668 55.000 0.00 0.00 0.00 3.71
1446 3098 0.616395 TCCAACCCTGGCGTCTATGA 60.616 55.000 0.00 0.00 43.17 2.15
1447 3099 0.179073 CTCCAACCCTGGCGTCTATG 60.179 60.000 0.00 0.00 43.17 2.23
1448 3100 1.338136 CCTCCAACCCTGGCGTCTAT 61.338 60.000 0.00 0.00 43.17 1.98
1453 3105 3.411517 ATCCCTCCAACCCTGGCG 61.412 66.667 0.00 0.00 43.17 5.69
1454 3106 2.276740 CATCCCTCCAACCCTGGC 59.723 66.667 0.00 0.00 43.17 4.85
1455 3107 2.693871 CCCATCCCTCCAACCCTGG 61.694 68.421 0.00 0.00 45.08 4.45
1456 3108 2.693871 CCCCATCCCTCCAACCCTG 61.694 68.421 0.00 0.00 0.00 4.45
1457 3109 2.287194 CCCCATCCCTCCAACCCT 60.287 66.667 0.00 0.00 0.00 4.34
1458 3110 1.933812 TTCCCCATCCCTCCAACCC 60.934 63.158 0.00 0.00 0.00 4.11
1459 3111 1.306633 GTTCCCCATCCCTCCAACC 59.693 63.158 0.00 0.00 0.00 3.77
1460 3112 1.306633 GGTTCCCCATCCCTCCAAC 59.693 63.158 0.00 0.00 0.00 3.77
1461 3113 1.933812 GGGTTCCCCATCCCTCCAA 60.934 63.158 0.00 0.00 44.65 3.53
1462 3114 2.286885 GGGTTCCCCATCCCTCCA 60.287 66.667 0.00 0.00 44.65 3.86
1473 3145 5.470047 ACTTCATACATAGATCGGGTTCC 57.530 43.478 0.00 0.00 0.00 3.62
1492 3164 9.636789 ACCCAAACACTACTTTATTAAGAACTT 57.363 29.630 0.00 0.00 35.30 2.66
1499 3171 7.987820 ACCCTAACCCAAACACTACTTTATTA 58.012 34.615 0.00 0.00 0.00 0.98
1500 3172 6.855667 ACCCTAACCCAAACACTACTTTATT 58.144 36.000 0.00 0.00 0.00 1.40
1527 3200 2.342279 CGAAGAAGACGGCCACCA 59.658 61.111 2.24 0.00 0.00 4.17
1528 3201 1.737008 GACGAAGAAGACGGCCACC 60.737 63.158 2.24 0.00 32.13 4.61
1531 3204 0.790814 CAAAGACGAAGAAGACGGCC 59.209 55.000 0.00 0.00 39.85 6.13
1544 3217 1.064654 GCCGATGCCATCTTCAAAGAC 59.935 52.381 2.75 0.00 37.98 3.01
1563 3236 2.354773 CGATCGAAGGGCCGTAGC 60.355 66.667 10.26 0.00 38.76 3.58
1586 3274 3.859061 TGACGCCTAGAAGGAGATCTA 57.141 47.619 3.57 0.00 37.36 1.98
1599 3287 1.228245 AACACCAGCATTGACGCCT 60.228 52.632 0.00 0.00 0.00 5.52
1669 3357 7.630026 CGACGATGAGAAATTATCCAAAATCA 58.370 34.615 0.00 0.00 0.00 2.57
1704 3393 4.035684 CACCATTGTCGACGACATAGTAG 58.964 47.826 29.60 18.56 42.40 2.57
1714 3430 6.422776 AAAGTATGAATCACCATTGTCGAC 57.577 37.500 9.11 9.11 0.00 4.20
1736 3452 0.242825 CGACGTCACTAGGAGCCAAA 59.757 55.000 17.16 0.00 0.00 3.28
1738 3454 1.002990 TCGACGTCACTAGGAGCCA 60.003 57.895 17.16 0.00 0.00 4.75
1745 3461 1.338484 ACAGCTAGGTCGACGTCACTA 60.338 52.381 15.00 12.96 0.00 2.74
1781 3497 3.633525 AGCGTATCAACACCGGTATTCTA 59.366 43.478 6.87 0.00 0.00 2.10
1782 3498 2.429610 AGCGTATCAACACCGGTATTCT 59.570 45.455 6.87 0.00 0.00 2.40
1797 3514 0.392461 ACCAACATCGGCAAGCGTAT 60.392 50.000 0.00 0.00 0.00 3.06
1801 3518 1.369091 ATCGACCAACATCGGCAAGC 61.369 55.000 0.00 0.00 42.50 4.01
1822 3539 0.171007 ACGCATGCAACCATTACAGC 59.829 50.000 19.57 0.00 0.00 4.40
1836 3553 0.744414 AAAGGCTACGATGCACGCAT 60.744 50.000 3.71 3.71 46.94 4.73
1861 3578 5.277825 TCCATAATTTTAATTTGAGCCGCG 58.722 37.500 0.00 0.00 0.00 6.46
1902 3619 9.046296 CAAAGATATCAAACCATAGACCTGTAC 57.954 37.037 5.32 0.00 0.00 2.90
1940 3657 1.064003 TGCTTTCCTGAAGGTAGCCA 58.936 50.000 17.55 8.11 40.56 4.75
1962 3679 5.707298 TCTTTCTTCTTCCATGACACAATCC 59.293 40.000 0.00 0.00 0.00 3.01
1991 3708 4.003648 ACGAGCCATTCTTCGAGATTTTT 58.996 39.130 0.51 0.00 0.00 1.94
1994 3711 2.969628 ACGAGCCATTCTTCGAGATT 57.030 45.000 0.51 0.00 0.00 2.40
2041 3758 3.295973 AGAGATACAAGAGCTGACTCCC 58.704 50.000 0.00 0.00 44.65 4.30
2163 3881 1.888512 GAGGCACATGTTTGGTCACAT 59.111 47.619 0.00 0.00 37.93 3.21
2175 3893 4.370917 GTTTGTTTTCACATGAGGCACAT 58.629 39.130 0.00 0.00 40.17 3.21
2176 3894 3.779759 GTTTGTTTTCACATGAGGCACA 58.220 40.909 0.00 0.00 31.06 4.57


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

AutoCloner maintained by Alex Coulton.