Multiple sequence alignment - TraesCS4A01G223800

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 TraesCS4A01G223800 chr4A 100.000 4076 0 0 1 4076 531310802 531314877 0.000000e+00 7528.0
1 TraesCS4A01G223800 chr4A 81.686 1862 235 55 1531 3316 531247715 531249546 0.000000e+00 1452.0
2 TraesCS4A01G223800 chr4A 78.695 2145 318 66 1248 3301 531326125 531328221 0.000000e+00 1301.0
3 TraesCS4A01G223800 chr4A 80.827 266 41 9 914 1177 531325845 531326102 2.480000e-47 200.0
4 TraesCS4A01G223800 chr4A 97.297 37 0 1 1304 1340 531311504 531311539 1.220000e-05 62.1
5 TraesCS4A01G223800 chr4A 100.000 33 0 0 768 800 531311535 531311567 1.220000e-05 62.1
6 TraesCS4A01G223800 chr4A 100.000 33 0 0 734 766 531311569 531311601 1.220000e-05 62.1
7 TraesCS4A01G223800 chr4A 97.297 37 0 1 703 738 531312105 531312141 1.220000e-05 62.1
8 TraesCS4A01G223800 chr4D 94.481 3225 111 13 886 4076 64617508 64614317 0.000000e+00 4907.0
9 TraesCS4A01G223800 chr4D 80.000 1540 194 56 1856 3317 64605202 64603699 0.000000e+00 1033.0
10 TraesCS4A01G223800 chr4D 87.577 652 72 6 1 648 73405831 73405185 0.000000e+00 747.0
11 TraesCS4A01G223800 chr4D 79.289 956 146 33 914 1825 64606261 64605314 4.470000e-174 621.0
12 TraesCS4A01G223800 chr4B 92.479 2061 99 25 761 2789 95218898 95216862 0.000000e+00 2896.0
13 TraesCS4A01G223800 chr4B 82.041 1832 227 45 1539 3298 95366125 95367926 0.000000e+00 1467.0
14 TraesCS4A01G223800 chr4B 78.763 1681 244 70 914 2501 95109577 95107917 0.000000e+00 1022.0
15 TraesCS4A01G223800 chr4B 82.077 1194 137 38 1537 2665 95318127 95316946 0.000000e+00 948.0
16 TraesCS4A01G223800 chr4B 91.595 583 45 3 2879 3461 95216859 95216281 0.000000e+00 802.0
17 TraesCS4A01G223800 chr4B 85.231 650 54 9 3459 4076 95204628 95203989 7.430000e-177 630.0
18 TraesCS4A01G223800 chr4B 97.297 37 0 1 703 738 95218374 95218338 1.220000e-05 62.1
19 TraesCS4A01G223800 chr1A 89.392 641 64 3 1 640 461264342 461264979 0.000000e+00 804.0
20 TraesCS4A01G223800 chr1A 85.759 646 71 11 1 627 405523720 405523077 0.000000e+00 664.0
21 TraesCS4A01G223800 chr1A 90.476 84 7 1 803 885 506544520 506544437 4.310000e-20 110.0
22 TraesCS4A01G223800 chr7D 88.957 652 63 7 1 648 605089561 605090207 0.000000e+00 797.0
23 TraesCS4A01G223800 chr6B 86.997 646 75 5 1 641 15779112 15779753 0.000000e+00 719.0
24 TraesCS4A01G223800 chr7B 76.716 335 75 3 24 357 178673633 178673301 2.500000e-42 183.0
25 TraesCS4A01G223800 chr7B 95.946 74 1 2 804 876 572400328 572400400 7.160000e-23 119.0
26 TraesCS4A01G223800 chr2D 74.464 466 88 19 27 488 610382165 610381727 5.420000e-39 172.0
27 TraesCS4A01G223800 chr2D 95.946 74 3 0 804 877 592631069 592630996 1.990000e-23 121.0
28 TraesCS4A01G223800 chr5D 94.595 74 4 0 804 877 339760804 339760877 9.260000e-22 115.0
29 TraesCS4A01G223800 chr5A 93.333 75 5 0 804 878 552100896 552100822 1.200000e-20 111.0
30 TraesCS4A01G223800 chr3A 93.333 75 5 0 804 878 378815050 378815124 1.200000e-20 111.0
31 TraesCS4A01G223800 chr2A 92.308 78 6 0 804 881 464165195 464165118 1.200000e-20 111.0
32 TraesCS4A01G223800 chr1B 93.333 75 5 0 803 877 17536151 17536225 1.200000e-20 111.0
33 TraesCS4A01G223800 chr1B 90.476 84 7 1 803 885 553144034 553143951 4.310000e-20 110.0
34 TraesCS4A01G223800 chr6D 100.000 31 0 0 3533 3563 79166718 79166688 1.580000e-04 58.4


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 TraesCS4A01G223800 chr4A 531310802 531314877 4075 False 1555.280000 7528 98.918800 1 4076 5 chr4A.!!$F2 4075
1 TraesCS4A01G223800 chr4A 531247715 531249546 1831 False 1452.000000 1452 81.686000 1531 3316 1 chr4A.!!$F1 1785
2 TraesCS4A01G223800 chr4A 531325845 531328221 2376 False 750.500000 1301 79.761000 914 3301 2 chr4A.!!$F3 2387
3 TraesCS4A01G223800 chr4D 64614317 64617508 3191 True 4907.000000 4907 94.481000 886 4076 1 chr4D.!!$R1 3190
4 TraesCS4A01G223800 chr4D 64603699 64606261 2562 True 827.000000 1033 79.644500 914 3317 2 chr4D.!!$R3 2403
5 TraesCS4A01G223800 chr4D 73405185 73405831 646 True 747.000000 747 87.577000 1 648 1 chr4D.!!$R2 647
6 TraesCS4A01G223800 chr4B 95366125 95367926 1801 False 1467.000000 1467 82.041000 1539 3298 1 chr4B.!!$F1 1759
7 TraesCS4A01G223800 chr4B 95216281 95218898 2617 True 1253.366667 2896 93.790333 703 3461 3 chr4B.!!$R4 2758
8 TraesCS4A01G223800 chr4B 95107917 95109577 1660 True 1022.000000 1022 78.763000 914 2501 1 chr4B.!!$R1 1587
9 TraesCS4A01G223800 chr4B 95316946 95318127 1181 True 948.000000 948 82.077000 1537 2665 1 chr4B.!!$R3 1128
10 TraesCS4A01G223800 chr4B 95203989 95204628 639 True 630.000000 630 85.231000 3459 4076 1 chr4B.!!$R2 617
11 TraesCS4A01G223800 chr1A 461264342 461264979 637 False 804.000000 804 89.392000 1 640 1 chr1A.!!$F1 639
12 TraesCS4A01G223800 chr1A 405523077 405523720 643 True 664.000000 664 85.759000 1 627 1 chr1A.!!$R1 626
13 TraesCS4A01G223800 chr7D 605089561 605090207 646 False 797.000000 797 88.957000 1 648 1 chr7D.!!$F1 647
14 TraesCS4A01G223800 chr6B 15779112 15779753 641 False 719.000000 719 86.997000 1 641 1 chr6B.!!$F1 640

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
651 677 0.389948 GCGTGTGGTAGGTGAGGAAG 60.390 60.0 0.00 0.0 0.0 3.46 F
1625 1697 0.318441 CGATATGGCATGGGACGTCT 59.682 55.0 16.46 0.0 0.0 4.18 F
2710 2963 0.593128 AACAACCGCACAATCTGAGC 59.407 50.0 0.00 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1817 1.066430 CCTGGAAAGTCCGAAATCCGA 60.066 52.381 0.00 0.0 40.17 4.55 R
2771 3026 0.403655 TGCAACCTAACTGGCCATGA 59.596 50.000 5.51 0.0 40.22 3.07 R
3783 4084 1.065928 GGGCACAGACTATCGTCGG 59.934 63.158 0.00 0.0 44.93 4.79 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
99 100 3.296709 GATCTGCACCACCGACGGT 62.297 63.158 15.37 15.37 41.07 4.83
150 151 0.984230 TCCTGAATCTCGCCCACTTT 59.016 50.000 0.00 0.00 0.00 2.66
170 171 3.880846 CGCCTGCCTTGGATTCGC 61.881 66.667 0.00 0.00 0.00 4.70
281 282 1.134699 GTGCTGGATGACCTCGATGAA 60.135 52.381 0.00 0.00 37.04 2.57
309 310 2.355363 CAGTTGTCGCGGTTCGGA 60.355 61.111 6.13 0.00 39.05 4.55
319 320 1.153628 CGGTTCGGAAATCGCTCCT 60.154 57.895 0.00 0.00 39.05 3.69
486 505 4.816109 CCCCCACCATCTCTCTCA 57.184 61.111 0.00 0.00 0.00 3.27
505 524 3.612247 CTCAACTGGCCCGTGGGAG 62.612 68.421 9.72 12.68 37.50 4.30
513 532 3.461773 CCCGTGGGAGCTGACGAT 61.462 66.667 0.00 0.00 37.81 3.73
526 545 1.447838 GACGATGAGAAGCCGCCAA 60.448 57.895 0.00 0.00 0.00 4.52
533 552 3.717294 GAAGCCGCCAAGGGAGGA 61.717 66.667 9.37 0.00 45.77 3.71
612 638 2.511373 CTGCGGCGCCATTACTCA 60.511 61.111 30.82 12.25 0.00 3.41
629 655 1.066303 CTCATGGTAGGTGAGACGAGC 59.934 57.143 0.00 0.00 44.57 5.03
648 674 2.264794 GGCGTGTGGTAGGTGAGG 59.735 66.667 0.00 0.00 0.00 3.86
649 675 2.280552 GGCGTGTGGTAGGTGAGGA 61.281 63.158 0.00 0.00 0.00 3.71
650 676 1.669440 GCGTGTGGTAGGTGAGGAA 59.331 57.895 0.00 0.00 0.00 3.36
651 677 0.389948 GCGTGTGGTAGGTGAGGAAG 60.390 60.000 0.00 0.00 0.00 3.46
652 678 0.389948 CGTGTGGTAGGTGAGGAAGC 60.390 60.000 0.00 0.00 0.00 3.86
653 679 0.977395 GTGTGGTAGGTGAGGAAGCT 59.023 55.000 0.00 0.00 40.55 3.74
654 680 1.348036 GTGTGGTAGGTGAGGAAGCTT 59.652 52.381 0.00 0.00 37.85 3.74
655 681 1.623811 TGTGGTAGGTGAGGAAGCTTC 59.376 52.381 18.54 18.54 37.85 3.86
717 743 8.145316 AGAAATGTTTGTTCAAAACATCATGG 57.855 30.769 14.80 0.00 46.62 3.66
718 744 5.927954 ATGTTTGTTCAAAACATCATGGC 57.072 34.783 9.96 0.00 44.83 4.40
719 745 5.021033 TGTTTGTTCAAAACATCATGGCT 57.979 34.783 0.00 0.00 41.79 4.75
720 746 5.426504 TGTTTGTTCAAAACATCATGGCTT 58.573 33.333 0.00 0.00 41.79 4.35
721 747 6.577103 TGTTTGTTCAAAACATCATGGCTTA 58.423 32.000 0.00 0.00 41.79 3.09
722 748 6.478344 TGTTTGTTCAAAACATCATGGCTTAC 59.522 34.615 0.00 0.00 41.79 2.34
723 749 5.132897 TGTTCAAAACATCATGGCTTACC 57.867 39.130 0.00 0.00 36.25 2.85
724 750 4.165779 GTTCAAAACATCATGGCTTACCG 58.834 43.478 0.00 0.00 39.70 4.02
725 751 3.680490 TCAAAACATCATGGCTTACCGA 58.320 40.909 0.00 0.00 39.70 4.69
726 752 3.438781 TCAAAACATCATGGCTTACCGAC 59.561 43.478 0.00 0.00 39.70 4.79
727 753 2.779755 AACATCATGGCTTACCGACA 57.220 45.000 0.00 0.00 39.70 4.35
728 754 3.281727 AACATCATGGCTTACCGACAT 57.718 42.857 0.00 0.00 44.09 3.06
738 764 5.547465 TGGCTTACCGACATGAAATATAGG 58.453 41.667 0.00 0.00 39.70 2.57
739 765 5.071250 TGGCTTACCGACATGAAATATAGGT 59.929 40.000 0.00 0.00 39.70 3.08
740 766 5.995897 GGCTTACCGACATGAAATATAGGTT 59.004 40.000 0.00 0.00 0.00 3.50
741 767 6.485648 GGCTTACCGACATGAAATATAGGTTT 59.514 38.462 0.00 0.00 0.00 3.27
742 768 7.352739 GCTTACCGACATGAAATATAGGTTTG 58.647 38.462 0.00 0.00 0.00 2.93
743 769 7.012044 GCTTACCGACATGAAATATAGGTTTGT 59.988 37.037 0.00 0.00 0.00 2.83
744 770 8.795842 TTACCGACATGAAATATAGGTTTGTT 57.204 30.769 0.00 0.00 0.00 2.83
745 771 9.887629 TTACCGACATGAAATATAGGTTTGTTA 57.112 29.630 0.00 0.00 0.00 2.41
746 772 8.795842 ACCGACATGAAATATAGGTTTGTTAA 57.204 30.769 0.00 0.00 0.00 2.01
747 773 9.233649 ACCGACATGAAATATAGGTTTGTTAAA 57.766 29.630 0.00 0.00 0.00 1.52
748 774 9.498307 CCGACATGAAATATAGGTTTGTTAAAC 57.502 33.333 0.00 0.00 40.65 2.01
757 783 9.734984 AATATAGGTTTGTTAAACACTAGCACT 57.265 29.630 6.74 0.00 43.15 4.40
758 784 7.668525 ATAGGTTTGTTAAACACTAGCACTC 57.331 36.000 6.74 0.00 43.15 3.51
759 785 4.820173 AGGTTTGTTAAACACTAGCACTCC 59.180 41.667 6.74 0.00 43.15 3.85
760 786 4.023450 GGTTTGTTAAACACTAGCACTCCC 60.023 45.833 6.74 0.00 43.15 4.30
761 787 3.412237 TGTTAAACACTAGCACTCCCC 57.588 47.619 0.00 0.00 0.00 4.81
762 788 2.039348 TGTTAAACACTAGCACTCCCCC 59.961 50.000 0.00 0.00 0.00 5.40
763 789 2.305052 GTTAAACACTAGCACTCCCCCT 59.695 50.000 0.00 0.00 0.00 4.79
764 790 0.693049 AAACACTAGCACTCCCCCTG 59.307 55.000 0.00 0.00 0.00 4.45
775 801 3.308904 GCACTCCCCCTGTTTATAGGTTT 60.309 47.826 0.00 0.00 36.02 3.27
788 814 9.821662 CTGTTTATAGGTTTGTTAAACACTAGC 57.178 33.333 6.74 0.00 43.15 3.42
795 821 3.412237 TGTTAAACACTAGCACTCCCC 57.588 47.619 0.00 0.00 0.00 4.81
799 825 0.473886 AACACTAGCACTCCCCCTGT 60.474 55.000 0.00 0.00 0.00 4.00
800 826 0.412244 ACACTAGCACTCCCCCTGTA 59.588 55.000 0.00 0.00 0.00 2.74
801 827 1.203262 ACACTAGCACTCCCCCTGTAA 60.203 52.381 0.00 0.00 0.00 2.41
802 828 1.906574 CACTAGCACTCCCCCTGTAAA 59.093 52.381 0.00 0.00 0.00 2.01
956 982 7.383687 CCTTGTTTTGATATATCCGTAGCCTA 58.616 38.462 10.25 0.00 0.00 3.93
991 1017 9.152595 CACATCCATTACTTCTCATATCATCAG 57.847 37.037 0.00 0.00 0.00 2.90
1008 1044 9.961264 ATATCATCAGCATCAGAAATGAATACT 57.039 29.630 0.00 0.00 30.76 2.12
1101 1137 2.232452 AGATCAGTTCTCAGACAACCGG 59.768 50.000 0.00 0.00 0.00 5.28
1162 1199 6.974622 GGTATGTTCATGCCTTACATTTTCTG 59.025 38.462 11.61 0.00 36.64 3.02
1169 1206 4.819769 TGCCTTACATTTTCTGCCATTTC 58.180 39.130 0.00 0.00 0.00 2.17
1179 1216 2.582052 TCTGCCATTTCGAAAAGTGGT 58.418 42.857 24.43 4.07 42.66 4.16
1205 1250 7.607607 TGCATATTTCTGAATAAGTGTCTGTGT 59.392 33.333 0.00 0.00 31.82 3.72
1208 1253 3.664107 TCTGAATAAGTGTCTGTGTGGC 58.336 45.455 0.00 0.00 0.00 5.01
1286 1331 2.546321 GCCGATTGCACGCGATAG 59.454 61.111 15.93 2.87 40.77 2.08
1431 1476 5.169295 GCAGATGTTTACGAAGGTCTACTT 58.831 41.667 0.00 0.00 43.65 2.24
1625 1697 0.318441 CGATATGGCATGGGACGTCT 59.682 55.000 16.46 0.00 0.00 4.18
1682 1754 9.508567 GTTTACATTTTCTTCATAGCATTCCTC 57.491 33.333 0.00 0.00 0.00 3.71
1744 1816 5.178623 GGATGATAACATGACGCCGAAAATA 59.821 40.000 0.00 0.00 36.82 1.40
1745 1817 6.128282 GGATGATAACATGACGCCGAAAATAT 60.128 38.462 0.00 0.00 36.82 1.28
1826 1900 6.747414 ATGTTGTGGGATCATAGTAAGCTA 57.253 37.500 0.00 0.00 0.00 3.32
2256 2459 2.910688 AGAGTGTGTGGACGTTGATT 57.089 45.000 0.00 0.00 0.00 2.57
2710 2963 0.593128 AACAACCGCACAATCTGAGC 59.407 50.000 0.00 0.00 0.00 4.26
2717 2970 2.032550 CCGCACAATCTGAGCATTAAGG 59.967 50.000 0.00 0.00 33.49 2.69
2760 3015 5.066893 GTGATGTTACCTGATGCATTCACAT 59.933 40.000 14.45 6.57 0.00 3.21
2771 3026 3.623703 TGCATTCACATTATCTGCCTGT 58.376 40.909 0.00 0.00 31.89 4.00
2890 3153 6.425210 TCTAGGAGGGAACATAATCACATG 57.575 41.667 0.00 0.00 0.00 3.21
2900 3163 4.928601 ACATAATCACATGTGCATGCTTC 58.071 39.130 21.38 12.47 42.39 3.86
2966 3230 9.998106 AGTGTAGATTTTTCACTGTTACTATGT 57.002 29.630 0.00 0.00 40.29 2.29
3072 3340 1.497278 CACCACTTCCATGCGAACG 59.503 57.895 0.00 0.00 0.00 3.95
3083 3351 1.393539 CATGCGAACGTGAAACTAGGG 59.606 52.381 0.00 0.00 34.49 3.53
3340 3609 4.337555 CCAGTTGATCAAACATGAGATCCC 59.662 45.833 10.35 11.99 41.61 3.85
3341 3610 5.191426 CAGTTGATCAAACATGAGATCCCT 58.809 41.667 10.35 13.34 41.61 4.20
3449 3718 2.826136 TAGGGCTCCTTTACGGGCCA 62.826 60.000 4.39 0.00 45.64 5.36
3472 3741 6.458210 CAAATTCCCTAGCTTGTTTGTGATT 58.542 36.000 0.00 0.00 0.00 2.57
3572 3862 2.203938 AGGAAACCTCGGCCCTCA 60.204 61.111 0.00 0.00 0.00 3.86
3638 3928 2.163613 CCCCATTGGCGTTTTTCTCTAC 59.836 50.000 0.00 0.00 0.00 2.59
3652 3942 1.899814 TCTCTACTGGTTCGGCACATT 59.100 47.619 0.00 0.00 0.00 2.71
3706 3996 3.428532 AGCATTCTCTTGTGGAAAGCAT 58.571 40.909 6.47 0.00 39.08 3.79
3739 4029 7.496920 TGATGAAGATCAAGATTTTCGTATGCT 59.503 33.333 7.72 0.00 35.55 3.79
3783 4084 1.907807 TGGCCAAACAGCATGGACC 60.908 57.895 0.61 0.00 46.07 4.46
3830 4131 0.685131 TGTCCCCGATTTCGAGGCTA 60.685 55.000 0.67 0.00 43.02 3.93
3845 4146 5.411781 TCGAGGCTAACATTTTCTTCTCTC 58.588 41.667 0.00 0.00 0.00 3.20
3872 4173 1.593196 TGTTCACTTCCTTTGGAGCG 58.407 50.000 0.00 0.00 31.21 5.03
3916 4217 0.674895 GTGGCAGGCTCTGTACTTGG 60.675 60.000 0.00 0.00 33.43 3.61
3936 4237 3.073798 TGGGTGAGTTATTGGAAGCTCAA 59.926 43.478 0.00 0.00 39.33 3.02
3980 4281 2.482839 GGCATCTCTTCTGGCTAGTGTC 60.483 54.545 0.00 0.00 36.34 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.829388 TCCCCTGAATCGTGGGAT 57.171 55.556 11.83 0.00 46.15 3.85
15 16 1.993391 GGTCCCCTGAATCGTGGGA 60.993 63.158 11.83 8.82 46.15 4.37
99 100 2.264480 CGACTCAACATCCGGCCA 59.736 61.111 2.24 0.00 0.00 5.36
170 171 1.760086 ATCCAGGAGGCGGAGTCAG 60.760 63.158 0.00 0.00 35.56 3.51
260 261 0.176449 CATCGAGGTCATCCAGCACA 59.824 55.000 0.00 0.00 35.89 4.57
281 282 1.736032 GCGACAACTGGCTAACGATCT 60.736 52.381 0.00 0.00 0.00 2.75
287 288 0.947180 GAACCGCGACAACTGGCTAA 60.947 55.000 8.23 0.00 0.00 3.09
289 290 2.665185 GAACCGCGACAACTGGCT 60.665 61.111 8.23 0.00 0.00 4.75
309 310 1.079127 CGTGGTGGAGGAGCGATTT 60.079 57.895 0.00 0.00 0.00 2.17
319 320 2.047655 GATGGTTCGCGTGGTGGA 60.048 61.111 5.77 0.00 0.00 4.02
486 505 3.953775 CCCACGGGCCAGTTGAGT 61.954 66.667 5.51 0.00 0.00 3.41
505 524 2.520904 GCGGCTTCTCATCGTCAGC 61.521 63.158 0.00 0.00 0.00 4.26
513 532 2.927856 TCCCTTGGCGGCTTCTCA 60.928 61.111 11.43 0.00 0.00 3.27
526 545 0.252284 ACCACATCGTCTTCCTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
533 552 1.553690 CCCCCTCACCACATCGTCTT 61.554 60.000 0.00 0.00 0.00 3.01
563 586 2.335369 CGCGCGGGCTTATCTAGT 59.665 61.111 24.84 0.00 36.88 2.57
612 638 1.384989 CCGCTCGTCTCACCTACCAT 61.385 60.000 0.00 0.00 0.00 3.55
629 655 3.642778 CTCACCTACCACACGCCCG 62.643 68.421 0.00 0.00 0.00 6.13
635 661 1.623811 GAAGCTTCCTCACCTACCACA 59.376 52.381 15.97 0.00 0.00 4.17
697 723 5.021033 AGCCATGATGTTTTGAACAAACA 57.979 34.783 2.78 2.78 45.86 2.83
698 724 5.989551 AAGCCATGATGTTTTGAACAAAC 57.010 34.783 0.00 0.00 45.86 2.93
699 725 5.988561 GGTAAGCCATGATGTTTTGAACAAA 59.011 36.000 0.00 0.00 38.75 2.83
700 726 5.537188 GGTAAGCCATGATGTTTTGAACAA 58.463 37.500 0.00 0.00 38.75 2.83
701 727 4.320861 CGGTAAGCCATGATGTTTTGAACA 60.321 41.667 0.00 0.00 39.26 3.18
702 728 4.083003 TCGGTAAGCCATGATGTTTTGAAC 60.083 41.667 0.00 0.00 34.09 3.18
703 729 4.075682 TCGGTAAGCCATGATGTTTTGAA 58.924 39.130 0.00 0.00 34.09 2.69
704 730 3.438781 GTCGGTAAGCCATGATGTTTTGA 59.561 43.478 0.00 0.00 34.09 2.69
705 731 3.190327 TGTCGGTAAGCCATGATGTTTTG 59.810 43.478 0.00 0.00 34.09 2.44
706 732 3.417101 TGTCGGTAAGCCATGATGTTTT 58.583 40.909 0.00 0.00 34.09 2.43
707 733 3.066291 TGTCGGTAAGCCATGATGTTT 57.934 42.857 0.00 0.00 34.09 2.83
708 734 2.779755 TGTCGGTAAGCCATGATGTT 57.220 45.000 0.00 0.00 34.09 2.71
709 735 2.170397 TCATGTCGGTAAGCCATGATGT 59.830 45.455 0.00 0.00 39.87 3.06
710 736 2.837498 TCATGTCGGTAAGCCATGATG 58.163 47.619 0.00 0.00 39.87 3.07
711 737 3.558931 TTCATGTCGGTAAGCCATGAT 57.441 42.857 0.00 0.00 43.12 2.45
712 738 3.342377 TTTCATGTCGGTAAGCCATGA 57.658 42.857 0.00 0.00 42.25 3.07
713 739 5.947228 ATATTTCATGTCGGTAAGCCATG 57.053 39.130 0.00 0.00 37.82 3.66
714 740 6.173339 CCTATATTTCATGTCGGTAAGCCAT 58.827 40.000 0.00 0.00 34.09 4.40
715 741 5.071250 ACCTATATTTCATGTCGGTAAGCCA 59.929 40.000 0.00 0.00 34.09 4.75
716 742 5.548406 ACCTATATTTCATGTCGGTAAGCC 58.452 41.667 0.00 0.00 0.00 4.35
717 743 7.012044 ACAAACCTATATTTCATGTCGGTAAGC 59.988 37.037 0.00 0.00 0.00 3.09
718 744 8.433421 ACAAACCTATATTTCATGTCGGTAAG 57.567 34.615 0.00 0.00 0.00 2.34
719 745 8.795842 AACAAACCTATATTTCATGTCGGTAA 57.204 30.769 0.00 0.00 0.00 2.85
720 746 9.887629 TTAACAAACCTATATTTCATGTCGGTA 57.112 29.630 0.00 0.00 0.00 4.02
721 747 8.795842 TTAACAAACCTATATTTCATGTCGGT 57.204 30.769 0.00 0.00 0.00 4.69
722 748 9.498307 GTTTAACAAACCTATATTTCATGTCGG 57.502 33.333 0.00 0.00 35.35 4.79
731 757 9.734984 AGTGCTAGTGTTTAACAAACCTATATT 57.265 29.630 0.00 0.00 40.67 1.28
732 758 9.379791 GAGTGCTAGTGTTTAACAAACCTATAT 57.620 33.333 0.00 0.00 40.67 0.86
733 759 7.820872 GGAGTGCTAGTGTTTAACAAACCTATA 59.179 37.037 0.00 0.00 40.67 1.31
734 760 6.653740 GGAGTGCTAGTGTTTAACAAACCTAT 59.346 38.462 0.00 0.00 40.67 2.57
735 761 5.993441 GGAGTGCTAGTGTTTAACAAACCTA 59.007 40.000 0.00 0.00 40.67 3.08
736 762 4.820173 GGAGTGCTAGTGTTTAACAAACCT 59.180 41.667 0.00 0.00 40.67 3.50
737 763 4.023450 GGGAGTGCTAGTGTTTAACAAACC 60.023 45.833 0.00 0.00 40.67 3.27
738 764 4.023450 GGGGAGTGCTAGTGTTTAACAAAC 60.023 45.833 0.00 0.00 41.73 2.93
739 765 4.139038 GGGGAGTGCTAGTGTTTAACAAA 58.861 43.478 0.00 0.00 0.00 2.83
740 766 3.497227 GGGGGAGTGCTAGTGTTTAACAA 60.497 47.826 0.00 0.00 0.00 2.83
741 767 2.039348 GGGGGAGTGCTAGTGTTTAACA 59.961 50.000 0.00 0.00 0.00 2.41
742 768 2.305052 AGGGGGAGTGCTAGTGTTTAAC 59.695 50.000 0.00 0.00 0.00 2.01
743 769 2.304761 CAGGGGGAGTGCTAGTGTTTAA 59.695 50.000 0.00 0.00 0.00 1.52
744 770 1.906574 CAGGGGGAGTGCTAGTGTTTA 59.093 52.381 0.00 0.00 0.00 2.01
745 771 0.693049 CAGGGGGAGTGCTAGTGTTT 59.307 55.000 0.00 0.00 0.00 2.83
746 772 0.473886 ACAGGGGGAGTGCTAGTGTT 60.474 55.000 0.00 0.00 0.00 3.32
747 773 0.473886 AACAGGGGGAGTGCTAGTGT 60.474 55.000 0.00 0.00 0.00 3.55
748 774 0.693049 AAACAGGGGGAGTGCTAGTG 59.307 55.000 0.00 0.00 0.00 2.74
749 775 2.337359 TAAACAGGGGGAGTGCTAGT 57.663 50.000 0.00 0.00 0.00 2.57
750 776 3.325135 CCTATAAACAGGGGGAGTGCTAG 59.675 52.174 0.00 0.00 31.47 3.42
751 777 3.311103 ACCTATAAACAGGGGGAGTGCTA 60.311 47.826 0.00 0.00 40.29 3.49
752 778 2.127708 CCTATAAACAGGGGGAGTGCT 58.872 52.381 0.00 0.00 31.47 4.40
753 779 1.844497 ACCTATAAACAGGGGGAGTGC 59.156 52.381 0.00 0.00 40.29 4.40
754 780 4.263771 ACAAACCTATAAACAGGGGGAGTG 60.264 45.833 0.00 0.00 40.29 3.51
755 781 3.920841 ACAAACCTATAAACAGGGGGAGT 59.079 43.478 0.00 0.00 40.29 3.85
756 782 4.586306 ACAAACCTATAAACAGGGGGAG 57.414 45.455 0.00 0.00 40.29 4.30
757 783 6.466009 TTAACAAACCTATAAACAGGGGGA 57.534 37.500 0.00 0.00 40.29 4.81
758 784 6.494146 TGTTTAACAAACCTATAAACAGGGGG 59.506 38.462 0.00 0.00 41.84 5.40
759 785 7.231925 AGTGTTTAACAAACCTATAAACAGGGG 59.768 37.037 0.00 0.00 45.17 4.79
760 786 8.173542 AGTGTTTAACAAACCTATAAACAGGG 57.826 34.615 0.00 0.00 45.17 4.45
762 788 9.821662 GCTAGTGTTTAACAAACCTATAAACAG 57.178 33.333 0.00 2.29 45.17 3.16
763 789 9.339850 TGCTAGTGTTTAACAAACCTATAAACA 57.660 29.630 0.00 6.30 43.47 2.83
764 790 9.603298 GTGCTAGTGTTTAACAAACCTATAAAC 57.397 33.333 0.00 0.00 40.67 2.01
775 801 2.039348 GGGGGAGTGCTAGTGTTTAACA 59.961 50.000 0.00 0.00 0.00 2.41
788 814 8.996651 ATATTTCTTTATTTACAGGGGGAGTG 57.003 34.615 0.00 0.00 0.00 3.51
867 893 7.735321 AGTAAAGCCATAACATATACTCCCTCT 59.265 37.037 0.00 0.00 0.00 3.69
877 903 9.109393 GAGAAACATGAGTAAAGCCATAACATA 57.891 33.333 0.00 0.00 0.00 2.29
956 982 7.994911 TGAGAAGTAATGGATGTGAATTGCTAT 59.005 33.333 0.00 0.00 29.90 2.97
991 1017 8.068977 GTCATCTTCAGTATTCATTTCTGATGC 58.931 37.037 0.00 0.00 37.91 3.91
1008 1044 3.758755 ACAGTCTGCTTGTCATCTTCA 57.241 42.857 0.00 0.00 0.00 3.02
1101 1137 4.439563 CCAAATGCACCTTTACCGATAACC 60.440 45.833 0.00 0.00 0.00 2.85
1162 1199 1.269517 TGCACCACTTTTCGAAATGGC 60.270 47.619 24.10 18.02 35.49 4.40
1169 1206 5.295431 TCAGAAATATGCACCACTTTTCG 57.705 39.130 0.00 0.00 32.84 3.46
1179 1216 7.607607 ACACAGACACTTATTCAGAAATATGCA 59.392 33.333 0.00 0.00 0.00 3.96
1205 1250 1.340017 GCATAGTTCCCTGTTCAGCCA 60.340 52.381 0.00 0.00 0.00 4.75
1208 1253 2.237143 TCAGGCATAGTTCCCTGTTCAG 59.763 50.000 6.57 0.00 46.83 3.02
1431 1476 9.603921 CTTCCCTTAGGTAAATATTCGTAACAA 57.396 33.333 0.00 0.00 0.00 2.83
1625 1697 7.394359 GCATATCCCCTTAATTATCTTGAAGCA 59.606 37.037 0.00 0.00 0.00 3.91
1744 1816 2.420129 CCTGGAAAGTCCGAAATCCGAT 60.420 50.000 0.00 0.00 40.17 4.18
1745 1817 1.066430 CCTGGAAAGTCCGAAATCCGA 60.066 52.381 0.00 0.00 40.17 4.55
1826 1900 5.104610 ACAGAATATCATGACAGCTCCAGTT 60.105 40.000 0.00 0.00 0.00 3.16
1838 1912 9.537192 AAATGCAATTAACCACAGAATATCATG 57.463 29.630 0.00 0.00 33.67 3.07
1988 2157 1.994507 CTCGCCAGTGGTAGTCTCGG 61.995 65.000 11.74 0.00 0.00 4.63
2568 2813 2.808919 TCTCGATCCCATCCATAGTCC 58.191 52.381 0.00 0.00 0.00 3.85
2688 2941 3.705604 CTCAGATTGTGCGGTTGTTTTT 58.294 40.909 0.00 0.00 0.00 1.94
2710 2963 6.438763 AGAAAAAGTTCGCAGAACCTTAATG 58.561 36.000 14.85 0.00 45.90 1.90
2717 2970 3.000925 TCACGAGAAAAAGTTCGCAGAAC 59.999 43.478 11.79 11.79 45.90 3.01
2771 3026 0.403655 TGCAACCTAACTGGCCATGA 59.596 50.000 5.51 0.00 40.22 3.07
2890 3153 1.666888 CCAAAGGAACGAAGCATGCAC 60.667 52.381 21.98 12.47 0.00 4.57
2900 3163 2.456010 CCGACAAAAACCAAAGGAACG 58.544 47.619 0.00 0.00 0.00 3.95
3016 3281 9.747898 TTTTGTAGAGGATATGTTACCAACAAT 57.252 29.630 0.00 0.00 45.86 2.71
3072 3340 7.556844 TCATCAATAGAAGACCCTAGTTTCAC 58.443 38.462 0.00 0.00 0.00 3.18
3083 3351 5.882557 TGCCCTTCTTTCATCAATAGAAGAC 59.117 40.000 11.53 5.34 44.82 3.01
3162 3431 4.670621 GTGACGTGACAACACAAATGATTC 59.329 41.667 0.00 0.00 46.20 2.52
3319 3588 5.191323 AGAGGGATCTCATGTTTGATCAACT 59.809 40.000 7.89 17.03 42.34 3.16
3322 3591 4.718276 TCAGAGGGATCTCATGTTTGATCA 59.282 41.667 19.41 0.00 42.34 2.92
3340 3609 5.634439 GGATCTCATGTTTGATCGATCAGAG 59.366 44.000 25.95 25.34 39.77 3.35
3341 3610 5.069516 TGGATCTCATGTTTGATCGATCAGA 59.930 40.000 25.95 20.28 39.77 3.27
3449 3718 6.670695 AATCACAAACAAGCTAGGGAATTT 57.329 33.333 0.00 0.00 0.00 1.82
3472 3741 1.422531 AAAGCATTGGGTCCAAGCAA 58.577 45.000 18.86 5.13 39.47 3.91
3510 3779 3.324556 CAGGATGTTCCAAACCCAATTGT 59.675 43.478 4.43 0.00 39.61 2.71
3580 3870 5.184479 CACAACATCCAAAGATCCTGACAAT 59.816 40.000 0.00 0.00 0.00 2.71
3638 3928 2.993471 GCCCAATGTGCCGAACCAG 61.993 63.158 0.00 0.00 0.00 4.00
3652 3942 1.302949 GCAGACCACATAAGGCCCA 59.697 57.895 0.00 0.00 0.00 5.36
3783 4084 1.065928 GGGCACAGACTATCGTCGG 59.934 63.158 0.00 0.00 44.93 4.79
3872 4173 2.514458 ACCCAGACCATCATGGAAAC 57.486 50.000 11.90 1.29 40.96 2.78
3916 4217 4.082733 GGTTTGAGCTTCCAATAACTCACC 60.083 45.833 0.00 0.00 38.81 4.02
3936 4237 3.118038 TCCTCTTACTTGCACAGTTGGTT 60.118 43.478 6.82 0.00 36.88 3.67


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

AutoCloner maintained by Alex Coulton.