Multiple sequence alignment - TraesCS6D01G068000

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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 TraesCS6D01G068000 chr6D 100.000 4417 0 0 1 4417 34298715 34294299 0.000000e+00 8157.0
1 TraesCS6D01G068000 chr6D 85.880 1204 149 15 928 2124 34306170 34304981 0.000000e+00 1262.0
2 TraesCS6D01G068000 chr6D 82.293 1186 172 32 923 2083 33312711 33311539 0.000000e+00 992.0
3 TraesCS6D01G068000 chr6D 95.072 629 29 2 46 673 464465369 464465996 0.000000e+00 989.0
4 TraesCS6D01G068000 chr6D 94.778 632 32 1 43 673 14615532 14616163 0.000000e+00 983.0
5 TraesCS6D01G068000 chr6D 94.304 632 34 2 43 673 87385652 87386282 0.000000e+00 966.0
6 TraesCS6D01G068000 chr6D 83.915 889 109 20 2125 2997 34304915 34304045 0.000000e+00 819.0
7 TraesCS6D01G068000 chr6D 80.507 867 148 16 1191 2050 33253278 33252426 0.000000e+00 645.0
8 TraesCS6D01G068000 chr6D 76.291 1181 204 53 2130 3252 33311459 33310297 1.070000e-155 560.0
9 TraesCS6D01G068000 chr6D 78.983 885 132 38 2130 2995 34322706 34321857 4.990000e-154 555.0
10 TraesCS6D01G068000 chr6D 80.997 642 105 17 2140 2769 33252280 33251644 1.100000e-135 494.0
11 TraesCS6D01G068000 chr6D 82.034 590 85 18 2125 2700 33304549 33303967 2.390000e-132 483.0
12 TraesCS6D01G068000 chr6D 77.256 554 81 29 2994 3510 34304013 34303468 2.600000e-72 283.0
13 TraesCS6D01G068000 chr6D 97.826 46 1 0 3549 3594 33249990 33249945 3.660000e-11 80.5
14 TraesCS6D01G068000 chr6A 91.833 2804 164 42 1366 4128 38447209 38444430 0.000000e+00 3849.0
15 TraesCS6D01G068000 chr6A 78.878 1586 264 50 1459 2989 38111512 38109943 0.000000e+00 1007.0
16 TraesCS6D01G068000 chr6A 82.968 1004 107 22 1055 2039 38403437 38402479 0.000000e+00 848.0
17 TraesCS6D01G068000 chr6A 79.868 909 154 18 1191 2085 37845553 37844660 4.820000e-179 638.0
18 TraesCS6D01G068000 chr6A 90.275 473 26 13 907 1370 38454397 38453936 6.320000e-168 601.0
19 TraesCS6D01G068000 chr6A 76.818 1100 216 29 1040 2125 38461763 38460689 2.290000e-162 582.0
20 TraesCS6D01G068000 chr6A 79.288 927 113 48 3133 4009 38401608 38400711 3.830000e-160 575.0
21 TraesCS6D01G068000 chr6A 80.338 651 108 19 2125 2761 37844567 37843923 4.000000e-130 475.0
22 TraesCS6D01G068000 chr6A 85.020 247 17 4 4171 4417 38444417 38444191 2.660000e-57 233.0
23 TraesCS6D01G068000 chr6B 93.075 1343 68 11 2798 4128 70755538 70754209 0.000000e+00 1941.0
24 TraesCS6D01G068000 chr6B 95.304 873 34 4 1946 2813 70756598 70755728 0.000000e+00 1378.0
25 TraesCS6D01G068000 chr6B 84.257 1029 148 11 1063 2083 70571658 70570636 0.000000e+00 990.0
26 TraesCS6D01G068000 chr6B 78.178 889 158 27 2130 2995 70570557 70569682 6.500000e-148 534.0
27 TraesCS6D01G068000 chr6B 82.857 490 74 8 2134 2615 70563576 70563089 8.780000e-117 431.0
28 TraesCS6D01G068000 chr6B 86.154 325 24 6 4093 4417 70754208 70753905 9.160000e-87 331.0
29 TraesCS6D01G068000 chr6B 84.880 291 19 10 906 1190 70756859 70756588 2.020000e-68 270.0
30 TraesCS6D01G068000 chr6B 95.652 46 2 0 3549 3594 70050450 70050405 1.700000e-09 75.0
31 TraesCS6D01G068000 chr5D 94.377 658 29 3 23 673 530488381 530487725 0.000000e+00 1003.0
32 TraesCS6D01G068000 chr7D 94.778 632 32 1 43 673 153076452 153075821 0.000000e+00 983.0
33 TraesCS6D01G068000 chr3D 94.904 628 31 1 46 673 41271941 41272567 0.000000e+00 981.0
34 TraesCS6D01G068000 chrUn 94.479 634 31 3 43 673 83929049 83928417 0.000000e+00 974.0
35 TraesCS6D01G068000 chr5B 94.462 632 33 2 43 673 680927240 680927870 0.000000e+00 972.0
36 TraesCS6D01G068000 chr5B 81.429 70 12 1 4213 4281 571817435 571817504 6.170000e-04 56.5
37 TraesCS6D01G068000 chr4D 94.295 631 35 1 43 673 47729341 47728712 0.000000e+00 965.0
38 TraesCS6D01G068000 chr2A 81.262 1062 167 18 1068 2104 766994880 766993826 0.000000e+00 830.0
39 TraesCS6D01G068000 chr2A 95.349 43 2 0 4199 4241 587344333 587344375 7.930000e-08 69.4
40 TraesCS6D01G068000 chr7A 81.806 753 114 16 2308 3046 33342097 33341354 1.050000e-170 610.0
41 TraesCS6D01G068000 chr2D 78.853 558 88 13 1583 2125 642020586 642020044 2.530000e-92 350.0
42 TraesCS6D01G068000 chr3B 83.217 143 18 5 728 865 662781281 662781422 4.640000e-25 126.0
43 TraesCS6D01G068000 chr3B 85.714 84 11 1 798 880 758431968 758432051 2.190000e-13 87.9
44 TraesCS6D01G068000 chr3B 97.561 41 1 0 4199 4239 692219112 692219072 2.200000e-08 71.3
45 TraesCS6D01G068000 chr5A 81.746 126 23 0 1249 1374 564304734 564304609 6.040000e-19 106.0
46 TraesCS6D01G068000 chr4A 76.879 173 31 7 4199 4367 709686124 709686291 6.080000e-14 89.8
47 TraesCS6D01G068000 chr3A 89.041 73 6 2 798 870 738067815 738067885 6.080000e-14 89.8
48 TraesCS6D01G068000 chr3A 92.683 41 3 0 4199 4239 673256204 673256164 4.770000e-05 60.2


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 TraesCS6D01G068000 chr6D 34294299 34298715 4416 True 8157.0 8157 100.000000 1 4417 1 chr6D.!!$R2 4416
1 TraesCS6D01G068000 chr6D 464465369 464465996 627 False 989.0 989 95.072000 46 673 1 chr6D.!!$F3 627
2 TraesCS6D01G068000 chr6D 14615532 14616163 631 False 983.0 983 94.778000 43 673 1 chr6D.!!$F1 630
3 TraesCS6D01G068000 chr6D 87385652 87386282 630 False 966.0 966 94.304000 43 673 1 chr6D.!!$F2 630
4 TraesCS6D01G068000 chr6D 34303468 34306170 2702 True 788.0 1262 82.350333 928 3510 3 chr6D.!!$R6 2582
5 TraesCS6D01G068000 chr6D 33310297 33312711 2414 True 776.0 992 79.292000 923 3252 2 chr6D.!!$R5 2329
6 TraesCS6D01G068000 chr6D 34321857 34322706 849 True 555.0 555 78.983000 2130 2995 1 chr6D.!!$R3 865
7 TraesCS6D01G068000 chr6D 33303967 33304549 582 True 483.0 483 82.034000 2125 2700 1 chr6D.!!$R1 575
8 TraesCS6D01G068000 chr6D 33249945 33253278 3333 True 406.5 645 86.443333 1191 3594 3 chr6D.!!$R4 2403
9 TraesCS6D01G068000 chr6A 38444191 38447209 3018 True 2041.0 3849 88.426500 1366 4417 2 chr6A.!!$R6 3051
10 TraesCS6D01G068000 chr6A 38109943 38111512 1569 True 1007.0 1007 78.878000 1459 2989 1 chr6A.!!$R1 1530
11 TraesCS6D01G068000 chr6A 38400711 38403437 2726 True 711.5 848 81.128000 1055 4009 2 chr6A.!!$R5 2954
12 TraesCS6D01G068000 chr6A 38460689 38461763 1074 True 582.0 582 76.818000 1040 2125 1 chr6A.!!$R3 1085
13 TraesCS6D01G068000 chr6A 37843923 37845553 1630 True 556.5 638 80.103000 1191 2761 2 chr6A.!!$R4 1570
14 TraesCS6D01G068000 chr6B 70753905 70756859 2954 True 980.0 1941 89.853250 906 4417 4 chr6B.!!$R4 3511
15 TraesCS6D01G068000 chr6B 70569682 70571658 1976 True 762.0 990 81.217500 1063 2995 2 chr6B.!!$R3 1932
16 TraesCS6D01G068000 chr5D 530487725 530488381 656 True 1003.0 1003 94.377000 23 673 1 chr5D.!!$R1 650
17 TraesCS6D01G068000 chr7D 153075821 153076452 631 True 983.0 983 94.778000 43 673 1 chr7D.!!$R1 630
18 TraesCS6D01G068000 chr3D 41271941 41272567 626 False 981.0 981 94.904000 46 673 1 chr3D.!!$F1 627
19 TraesCS6D01G068000 chrUn 83928417 83929049 632 True 974.0 974 94.479000 43 673 1 chrUn.!!$R1 630
20 TraesCS6D01G068000 chr5B 680927240 680927870 630 False 972.0 972 94.462000 43 673 1 chr5B.!!$F2 630
21 TraesCS6D01G068000 chr4D 47728712 47729341 629 True 965.0 965 94.295000 43 673 1 chr4D.!!$R1 630
22 TraesCS6D01G068000 chr2A 766993826 766994880 1054 True 830.0 830 81.262000 1068 2104 1 chr2A.!!$R1 1036
23 TraesCS6D01G068000 chr7A 33341354 33342097 743 True 610.0 610 81.806000 2308 3046 1 chr7A.!!$R1 738
24 TraesCS6D01G068000 chr2D 642020044 642020586 542 True 350.0 350 78.853000 1583 2125 1 chr2D.!!$R1 542

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
802 812 0.105504 GGCCTTCATTATTGCCCCCT 60.106 55.000 0.00 0.0 37.94 4.79 F
1013 1033 0.029567 GGTCAGATGAGGTACGCGAG 59.970 60.000 15.93 0.0 0.00 5.03 F
1409 1469 0.179119 CACCGACCTGGATACCGTTC 60.179 60.000 0.00 0.0 42.00 3.95 F
2596 2815 2.692557 ACTTCGCATGCTCTCTGTATCT 59.307 45.455 17.13 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2013 0.371645 GCTGCTGCAATCGTCACTAC 59.628 55.000 11.11 0.0 39.41 2.73 R
2855 3320 4.163078 CACCCTGGACTAACAGAATCAGAT 59.837 45.833 0.00 0.0 40.97 2.90 R
3190 4912 2.097825 GCTCCCAAATGAGAATGCAGT 58.902 47.619 0.00 0.0 34.11 4.40 R
3848 5696 0.386113 GCGGAGATCACTGGGAGTAC 59.614 60.000 0.94 0.0 0.00 2.73 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
123 132 2.041265 CTCTGGTGGCCCTAGGGT 59.959 66.667 28.96 0.00 37.65 4.34
209 219 2.882761 GTCTTGTTAGGGTTTGTGTCCC 59.117 50.000 0.00 0.00 44.90 4.46
308 318 1.153647 CTAGCATCGTTCGTGGGCA 60.154 57.895 0.00 0.00 0.00 5.36
317 327 3.918253 TTCGTGGGCATGTGGAGGC 62.918 63.158 0.00 0.00 0.00 4.70
345 355 1.068588 CGGCGGATCTATCTTTGGTGA 59.931 52.381 0.00 0.00 0.00 4.02
460 470 1.995376 TCTGATGCGCTGGTCCTATA 58.005 50.000 9.73 0.00 0.00 1.31
461 471 2.316108 TCTGATGCGCTGGTCCTATAA 58.684 47.619 9.73 0.00 0.00 0.98
538 548 1.391933 CGATGGAGGGGTGATGACGA 61.392 60.000 0.00 0.00 0.00 4.20
543 553 4.077184 GGGGTGATGACGACGGCA 62.077 66.667 5.51 5.51 0.00 5.69
630 640 5.927954 TTATTTCTGGTGTTCGTTGTACC 57.072 39.130 0.00 0.00 35.05 3.34
635 645 1.159098 GGTGTTCGTTGTACCGCCAA 61.159 55.000 0.00 0.00 0.00 4.52
643 653 2.224549 CGTTGTACCGCCAAGATTGAAA 59.775 45.455 0.00 0.00 0.00 2.69
674 684 9.758651 ATAGATTAAAAGTTTTTCCGCAAAAGT 57.241 25.926 6.10 0.00 39.36 2.66
676 686 9.758651 AGATTAAAAGTTTTTCCGCAAAAGTAT 57.241 25.926 6.10 0.00 37.07 2.12
687 697 8.896320 TTTCCGCAAAAGTATATATAAGAGCA 57.104 30.769 0.00 0.00 0.00 4.26
688 698 8.534333 TTCCGCAAAAGTATATATAAGAGCAG 57.466 34.615 0.00 0.00 0.00 4.24
689 699 6.590292 TCCGCAAAAGTATATATAAGAGCAGC 59.410 38.462 0.00 0.00 0.00 5.25
690 700 6.454318 CCGCAAAAGTATATATAAGAGCAGCG 60.454 42.308 14.56 14.56 37.89 5.18
691 701 6.089551 CGCAAAAGTATATATAAGAGCAGCGT 59.910 38.462 13.83 0.00 34.07 5.07
692 702 7.359264 CGCAAAAGTATATATAAGAGCAGCGTT 60.359 37.037 13.83 0.00 34.07 4.84
693 703 8.283291 GCAAAAGTATATATAAGAGCAGCGTTT 58.717 33.333 0.00 0.00 0.00 3.60
700 710 8.918961 ATATATAAGAGCAGCGTTTAGATCAC 57.081 34.615 0.00 0.00 0.00 3.06
701 711 2.301577 AGAGCAGCGTTTAGATCACC 57.698 50.000 0.00 0.00 0.00 4.02
702 712 1.550524 AGAGCAGCGTTTAGATCACCA 59.449 47.619 0.00 0.00 0.00 4.17
703 713 2.028112 AGAGCAGCGTTTAGATCACCAA 60.028 45.455 0.00 0.00 0.00 3.67
704 714 2.939103 GAGCAGCGTTTAGATCACCAAT 59.061 45.455 0.00 0.00 0.00 3.16
705 715 2.679837 AGCAGCGTTTAGATCACCAATG 59.320 45.455 0.00 0.00 0.00 2.82
706 716 2.677836 GCAGCGTTTAGATCACCAATGA 59.322 45.455 0.00 0.00 39.83 2.57
707 717 3.242543 GCAGCGTTTAGATCACCAATGAG 60.243 47.826 0.00 0.00 38.57 2.90
708 718 3.935203 CAGCGTTTAGATCACCAATGAGT 59.065 43.478 0.00 0.00 38.57 3.41
709 719 4.393062 CAGCGTTTAGATCACCAATGAGTT 59.607 41.667 0.00 0.00 38.57 3.01
710 720 5.003804 AGCGTTTAGATCACCAATGAGTTT 58.996 37.500 0.00 0.00 38.57 2.66
711 721 5.122396 AGCGTTTAGATCACCAATGAGTTTC 59.878 40.000 0.00 0.00 38.57 2.78
712 722 5.106712 GCGTTTAGATCACCAATGAGTTTCA 60.107 40.000 0.00 0.00 38.57 2.69
713 723 6.567701 GCGTTTAGATCACCAATGAGTTTCAA 60.568 38.462 0.00 0.00 38.57 2.69
714 724 7.359595 CGTTTAGATCACCAATGAGTTTCAAA 58.640 34.615 0.00 0.00 38.57 2.69
715 725 7.860373 CGTTTAGATCACCAATGAGTTTCAAAA 59.140 33.333 0.00 0.00 38.57 2.44
716 726 9.185192 GTTTAGATCACCAATGAGTTTCAAAAG 57.815 33.333 0.00 0.00 38.57 2.27
717 727 6.336842 AGATCACCAATGAGTTTCAAAAGG 57.663 37.500 0.00 0.00 38.57 3.11
718 728 4.935352 TCACCAATGAGTTTCAAAAGGG 57.065 40.909 0.00 0.00 0.00 3.95
719 729 3.640967 TCACCAATGAGTTTCAAAAGGGG 59.359 43.478 0.00 0.00 0.00 4.79
720 730 3.387699 CACCAATGAGTTTCAAAAGGGGT 59.612 43.478 0.00 0.00 0.00 4.95
721 731 4.586841 CACCAATGAGTTTCAAAAGGGGTA 59.413 41.667 0.00 0.00 0.00 3.69
722 732 5.245977 CACCAATGAGTTTCAAAAGGGGTAT 59.754 40.000 0.00 0.00 0.00 2.73
723 733 5.843969 ACCAATGAGTTTCAAAAGGGGTATT 59.156 36.000 0.00 0.00 0.00 1.89
724 734 7.013834 ACCAATGAGTTTCAAAAGGGGTATTA 58.986 34.615 0.00 0.00 0.00 0.98
725 735 7.511028 ACCAATGAGTTTCAAAAGGGGTATTAA 59.489 33.333 0.00 0.00 0.00 1.40
726 736 8.371699 CCAATGAGTTTCAAAAGGGGTATTAAA 58.628 33.333 0.00 0.00 0.00 1.52
727 737 9.771534 CAATGAGTTTCAAAAGGGGTATTAAAA 57.228 29.630 0.00 0.00 0.00 1.52
729 739 9.772973 ATGAGTTTCAAAAGGGGTATTAAAAAC 57.227 29.630 0.00 0.00 0.00 2.43
730 740 8.983789 TGAGTTTCAAAAGGGGTATTAAAAACT 58.016 29.630 0.00 0.00 37.19 2.66
731 741 9.256477 GAGTTTCAAAAGGGGTATTAAAAACTG 57.744 33.333 0.00 0.00 35.30 3.16
732 742 8.983789 AGTTTCAAAAGGGGTATTAAAAACTGA 58.016 29.630 0.00 0.00 34.24 3.41
733 743 9.772973 GTTTCAAAAGGGGTATTAAAAACTGAT 57.227 29.630 0.00 0.00 0.00 2.90
747 757 5.385396 AAAACTGATAATACTACGCACGC 57.615 39.130 0.00 0.00 0.00 5.34
748 758 2.647337 ACTGATAATACTACGCACGCG 58.353 47.619 10.36 10.36 46.03 6.01
749 759 1.382419 CTGATAATACTACGCACGCGC 59.618 52.381 12.02 0.00 44.19 6.86
750 760 1.268640 TGATAATACTACGCACGCGCA 60.269 47.619 12.02 0.00 44.19 6.09
751 761 1.782569 GATAATACTACGCACGCGCAA 59.217 47.619 12.02 0.00 44.19 4.85
752 762 1.626747 TAATACTACGCACGCGCAAA 58.373 45.000 12.02 0.00 44.19 3.68
753 763 0.791422 AATACTACGCACGCGCAAAA 59.209 45.000 12.02 0.00 44.19 2.44
754 764 0.368907 ATACTACGCACGCGCAAAAG 59.631 50.000 12.02 6.73 44.19 2.27
755 765 0.940519 TACTACGCACGCGCAAAAGT 60.941 50.000 12.02 12.02 44.19 2.66
756 766 1.788203 CTACGCACGCGCAAAAGTG 60.788 57.895 12.02 8.64 44.19 3.16
757 767 2.153219 CTACGCACGCGCAAAAGTGA 62.153 55.000 15.97 0.00 44.19 3.41
758 768 2.419100 TACGCACGCGCAAAAGTGAC 62.419 55.000 15.97 7.25 44.19 3.67
759 769 3.085010 GCACGCGCAAAAGTGACG 61.085 61.111 15.97 0.00 40.56 4.35
760 770 2.425124 CACGCGCAAAAGTGACGG 60.425 61.111 5.73 0.00 40.56 4.79
761 771 2.586635 ACGCGCAAAAGTGACGGA 60.587 55.556 5.73 0.00 32.05 4.69
762 772 2.127758 CGCGCAAAAGTGACGGAC 60.128 61.111 8.75 0.00 0.00 4.79
763 773 2.594962 CGCGCAAAAGTGACGGACT 61.595 57.895 8.75 0.00 35.94 3.85
772 782 2.510768 AGTGACGGACTTTCACAGAC 57.489 50.000 5.97 0.00 45.00 3.51
773 783 1.068741 AGTGACGGACTTTCACAGACC 59.931 52.381 5.97 0.00 45.00 3.85
774 784 0.391597 TGACGGACTTTCACAGACCC 59.608 55.000 0.00 0.00 34.01 4.46
775 785 0.680061 GACGGACTTTCACAGACCCT 59.320 55.000 0.00 0.00 34.01 4.34
776 786 0.393077 ACGGACTTTCACAGACCCTG 59.607 55.000 0.00 0.00 34.01 4.45
777 787 0.951040 CGGACTTTCACAGACCCTGC 60.951 60.000 0.00 0.00 34.01 4.85
778 788 0.398318 GGACTTTCACAGACCCTGCT 59.602 55.000 0.00 0.00 34.37 4.24
779 789 1.517242 GACTTTCACAGACCCTGCTG 58.483 55.000 0.00 0.00 41.63 4.41
780 790 0.536006 ACTTTCACAGACCCTGCTGC 60.536 55.000 0.00 0.00 39.51 5.25
781 791 1.572085 CTTTCACAGACCCTGCTGCG 61.572 60.000 0.00 0.00 39.51 5.18
782 792 2.324014 TTTCACAGACCCTGCTGCGT 62.324 55.000 0.00 0.00 39.51 5.24
783 793 2.994387 TTCACAGACCCTGCTGCGTG 62.994 60.000 0.00 0.00 39.51 5.34
784 794 4.320456 ACAGACCCTGCTGCGTGG 62.320 66.667 5.79 5.79 39.51 4.94
791 801 2.749044 CTGCTGCGTGGCCTTCAT 60.749 61.111 3.32 0.00 0.00 2.57
792 802 2.282391 TGCTGCGTGGCCTTCATT 60.282 55.556 3.32 0.00 0.00 2.57
793 803 1.002746 TGCTGCGTGGCCTTCATTA 60.003 52.632 3.32 0.00 0.00 1.90
794 804 0.394216 TGCTGCGTGGCCTTCATTAT 60.394 50.000 3.32 0.00 0.00 1.28
795 805 0.740737 GCTGCGTGGCCTTCATTATT 59.259 50.000 3.32 0.00 0.00 1.40
796 806 1.534595 GCTGCGTGGCCTTCATTATTG 60.535 52.381 3.32 0.00 0.00 1.90
797 807 0.455410 TGCGTGGCCTTCATTATTGC 59.545 50.000 3.32 0.00 0.00 3.56
798 808 0.249031 GCGTGGCCTTCATTATTGCC 60.249 55.000 3.32 0.00 44.27 4.52
799 809 0.385390 CGTGGCCTTCATTATTGCCC 59.615 55.000 3.32 0.00 43.35 5.36
800 810 0.752658 GTGGCCTTCATTATTGCCCC 59.247 55.000 3.32 0.00 43.35 5.80
801 811 0.398381 TGGCCTTCATTATTGCCCCC 60.398 55.000 3.32 0.00 43.35 5.40
802 812 0.105504 GGCCTTCATTATTGCCCCCT 60.106 55.000 0.00 0.00 37.94 4.79
803 813 1.043022 GCCTTCATTATTGCCCCCTG 58.957 55.000 0.00 0.00 0.00 4.45
804 814 1.411501 GCCTTCATTATTGCCCCCTGA 60.412 52.381 0.00 0.00 0.00 3.86
805 815 2.757606 GCCTTCATTATTGCCCCCTGAT 60.758 50.000 0.00 0.00 0.00 2.90
806 816 3.580039 CCTTCATTATTGCCCCCTGATT 58.420 45.455 0.00 0.00 0.00 2.57
807 817 3.969312 CCTTCATTATTGCCCCCTGATTT 59.031 43.478 0.00 0.00 0.00 2.17
808 818 4.409901 CCTTCATTATTGCCCCCTGATTTT 59.590 41.667 0.00 0.00 0.00 1.82
809 819 5.602145 CCTTCATTATTGCCCCCTGATTTTA 59.398 40.000 0.00 0.00 0.00 1.52
810 820 6.099557 CCTTCATTATTGCCCCCTGATTTTAA 59.900 38.462 0.00 0.00 0.00 1.52
811 821 6.478512 TCATTATTGCCCCCTGATTTTAAC 57.521 37.500 0.00 0.00 0.00 2.01
812 822 6.201591 TCATTATTGCCCCCTGATTTTAACT 58.798 36.000 0.00 0.00 0.00 2.24
813 823 5.930837 TTATTGCCCCCTGATTTTAACTG 57.069 39.130 0.00 0.00 0.00 3.16
814 824 2.230130 TGCCCCCTGATTTTAACTGG 57.770 50.000 0.00 0.00 0.00 4.00
815 825 1.431243 TGCCCCCTGATTTTAACTGGT 59.569 47.619 0.00 0.00 0.00 4.00
816 826 1.824852 GCCCCCTGATTTTAACTGGTG 59.175 52.381 0.00 0.00 0.00 4.17
817 827 2.456577 CCCCCTGATTTTAACTGGTGG 58.543 52.381 0.00 0.00 0.00 4.61
818 828 2.456577 CCCCTGATTTTAACTGGTGGG 58.543 52.381 0.00 0.00 0.00 4.61
819 829 1.824852 CCCTGATTTTAACTGGTGGGC 59.175 52.381 0.00 0.00 0.00 5.36
820 830 1.824852 CCTGATTTTAACTGGTGGGCC 59.175 52.381 0.00 0.00 0.00 5.80
821 831 1.824852 CTGATTTTAACTGGTGGGCCC 59.175 52.381 17.59 17.59 0.00 5.80
822 832 0.815095 GATTTTAACTGGTGGGCCCG 59.185 55.000 19.37 4.81 35.15 6.13
823 833 1.254975 ATTTTAACTGGTGGGCCCGC 61.255 55.000 28.23 28.23 35.15 6.13
824 834 3.871850 TTTAACTGGTGGGCCCGCC 62.872 63.158 42.66 42.66 46.15 6.13
831 841 3.712907 GTGGGCCCGCCTCACTTA 61.713 66.667 25.93 0.00 35.69 2.24
832 842 2.931105 TGGGCCCGCCTCACTTAA 60.931 61.111 19.37 0.00 36.10 1.85
833 843 2.305607 TGGGCCCGCCTCACTTAAT 61.306 57.895 19.37 0.00 36.10 1.40
834 844 1.076995 GGGCCCGCCTCACTTAATT 60.077 57.895 5.69 0.00 36.10 1.40
835 845 0.181824 GGGCCCGCCTCACTTAATTA 59.818 55.000 5.69 0.00 36.10 1.40
836 846 1.409101 GGGCCCGCCTCACTTAATTAA 60.409 52.381 5.69 0.00 36.10 1.40
837 847 2.371306 GGCCCGCCTCACTTAATTAAA 58.629 47.619 0.00 0.00 0.00 1.52
838 848 2.956333 GGCCCGCCTCACTTAATTAAAT 59.044 45.455 0.00 0.00 0.00 1.40
839 849 3.004419 GGCCCGCCTCACTTAATTAAATC 59.996 47.826 0.00 0.00 0.00 2.17
840 850 3.883489 GCCCGCCTCACTTAATTAAATCT 59.117 43.478 0.00 0.00 0.00 2.40
841 851 5.061179 GCCCGCCTCACTTAATTAAATCTA 58.939 41.667 0.00 0.00 0.00 1.98
842 852 5.529800 GCCCGCCTCACTTAATTAAATCTAA 59.470 40.000 0.00 0.00 0.00 2.10
843 853 6.293462 GCCCGCCTCACTTAATTAAATCTAAG 60.293 42.308 0.00 0.00 0.00 2.18
844 854 6.293462 CCCGCCTCACTTAATTAAATCTAAGC 60.293 42.308 0.00 0.00 0.00 3.09
845 855 6.483640 CCGCCTCACTTAATTAAATCTAAGCT 59.516 38.462 0.00 0.00 0.00 3.74
846 856 7.656137 CCGCCTCACTTAATTAAATCTAAGCTA 59.344 37.037 0.00 0.00 0.00 3.32
847 857 9.042008 CGCCTCACTTAATTAAATCTAAGCTAA 57.958 33.333 0.00 0.00 0.00 3.09
863 873 9.794719 ATCTAAGCTAATTAAATCCTAACCACC 57.205 33.333 0.00 0.00 0.00 4.61
864 874 8.215736 TCTAAGCTAATTAAATCCTAACCACCC 58.784 37.037 0.00 0.00 0.00 4.61
865 875 6.335781 AGCTAATTAAATCCTAACCACCCA 57.664 37.500 0.00 0.00 0.00 4.51
866 876 6.365520 AGCTAATTAAATCCTAACCACCCAG 58.634 40.000 0.00 0.00 0.00 4.45
867 877 6.069029 AGCTAATTAAATCCTAACCACCCAGT 60.069 38.462 0.00 0.00 0.00 4.00
868 878 7.128263 AGCTAATTAAATCCTAACCACCCAGTA 59.872 37.037 0.00 0.00 0.00 2.74
869 879 7.776500 GCTAATTAAATCCTAACCACCCAGTAA 59.224 37.037 0.00 0.00 0.00 2.24
870 880 9.689501 CTAATTAAATCCTAACCACCCAGTAAA 57.310 33.333 0.00 0.00 0.00 2.01
871 881 8.959676 AATTAAATCCTAACCACCCAGTAAAA 57.040 30.769 0.00 0.00 0.00 1.52
872 882 7.764141 TTAAATCCTAACCACCCAGTAAAAC 57.236 36.000 0.00 0.00 0.00 2.43
873 883 5.327737 AATCCTAACCACCCAGTAAAACA 57.672 39.130 0.00 0.00 0.00 2.83
874 884 4.089408 TCCTAACCACCCAGTAAAACAC 57.911 45.455 0.00 0.00 0.00 3.32
875 885 3.717913 TCCTAACCACCCAGTAAAACACT 59.282 43.478 0.00 0.00 38.32 3.55
890 900 8.788325 AGTAAAACACTGTAATCCTAACCATC 57.212 34.615 0.00 0.00 35.62 3.51
891 901 8.603304 AGTAAAACACTGTAATCCTAACCATCT 58.397 33.333 0.00 0.00 35.62 2.90
892 902 7.923414 AAAACACTGTAATCCTAACCATCTC 57.077 36.000 0.00 0.00 0.00 2.75
893 903 6.875972 AACACTGTAATCCTAACCATCTCT 57.124 37.500 0.00 0.00 0.00 3.10
894 904 6.472686 ACACTGTAATCCTAACCATCTCTC 57.527 41.667 0.00 0.00 0.00 3.20
895 905 6.198639 ACACTGTAATCCTAACCATCTCTCT 58.801 40.000 0.00 0.00 0.00 3.10
896 906 6.670027 ACACTGTAATCCTAACCATCTCTCTT 59.330 38.462 0.00 0.00 0.00 2.85
897 907 7.181125 ACACTGTAATCCTAACCATCTCTCTTT 59.819 37.037 0.00 0.00 0.00 2.52
898 908 8.696374 CACTGTAATCCTAACCATCTCTCTTTA 58.304 37.037 0.00 0.00 0.00 1.85
899 909 9.268282 ACTGTAATCCTAACCATCTCTCTTTAA 57.732 33.333 0.00 0.00 0.00 1.52
900 910 9.535878 CTGTAATCCTAACCATCTCTCTTTAAC 57.464 37.037 0.00 0.00 0.00 2.01
901 911 9.042450 TGTAATCCTAACCATCTCTCTTTAACA 57.958 33.333 0.00 0.00 0.00 2.41
902 912 9.886132 GTAATCCTAACCATCTCTCTTTAACAA 57.114 33.333 0.00 0.00 0.00 2.83
904 914 9.620259 AATCCTAACCATCTCTCTTTAACAATC 57.380 33.333 0.00 0.00 0.00 2.67
911 921 2.603560 CTCTCTTTAACAATCGACCGCC 59.396 50.000 0.00 0.00 0.00 6.13
920 930 2.711311 TCGACCGCCGACGAATAG 59.289 61.111 0.00 0.00 43.23 1.73
921 931 2.108514 TCGACCGCCGACGAATAGT 61.109 57.895 0.00 0.00 43.23 2.12
922 932 1.226491 CGACCGCCGACGAATAGTT 60.226 57.895 0.00 0.00 43.93 2.24
923 933 0.799534 CGACCGCCGACGAATAGTTT 60.800 55.000 0.00 0.00 43.93 2.66
924 934 0.919300 GACCGCCGACGAATAGTTTC 59.081 55.000 0.00 0.00 43.93 2.78
927 937 1.468565 CCGCCGACGAATAGTTTCAGA 60.469 52.381 0.00 0.00 43.93 3.27
928 938 2.256174 CGCCGACGAATAGTTTCAGAA 58.744 47.619 0.00 0.00 43.93 3.02
929 939 2.664568 CGCCGACGAATAGTTTCAGAAA 59.335 45.455 0.00 0.00 43.93 2.52
930 940 3.241678 CGCCGACGAATAGTTTCAGAAAG 60.242 47.826 0.00 0.00 43.93 2.62
931 941 3.062234 GCCGACGAATAGTTTCAGAAAGG 59.938 47.826 0.00 0.00 0.00 3.11
1001 1011 3.665675 GACTTGCCGGCGGTCAGAT 62.666 63.158 33.03 16.22 0.00 2.90
1002 1012 3.197790 CTTGCCGGCGGTCAGATG 61.198 66.667 28.82 14.61 0.00 2.90
1008 1028 1.065928 CGGCGGTCAGATGAGGTAC 59.934 63.158 0.00 0.00 0.00 3.34
1013 1033 0.029567 GGTCAGATGAGGTACGCGAG 59.970 60.000 15.93 0.00 0.00 5.03
1409 1469 0.179119 CACCGACCTGGATACCGTTC 60.179 60.000 0.00 0.00 42.00 3.95
1824 1899 3.508762 CTTTGCTTGAAGACATGGCATC 58.491 45.455 0.00 0.00 36.01 3.91
1884 1959 7.092079 TGCAAAGATGTCTGTTTGAATTATGG 58.908 34.615 0.00 0.00 37.73 2.74
1938 2013 5.964958 ACATGTAAGAATTGTGTTCCTGG 57.035 39.130 0.00 0.00 0.00 4.45
2052 2143 8.911918 TGCCACTTGTCTTTAACTTCTTTATA 57.088 30.769 0.00 0.00 0.00 0.98
2522 2731 5.058613 GTGATGTGATCGACGAGATAATTCG 59.941 44.000 3.01 0.00 45.70 3.34
2550 2768 5.577945 AGTTTTGAAGTTCTTGTGTGCATTG 59.422 36.000 4.17 0.00 0.00 2.82
2596 2815 2.692557 ACTTCGCATGCTCTCTGTATCT 59.307 45.455 17.13 0.00 0.00 1.98
2855 3320 6.016108 GTGGTTTTTGGGTACTAGCACAAATA 60.016 38.462 0.00 0.00 37.23 1.40
2902 4557 8.349983 GTGGTTGTACAATATCTTCACTTGTTT 58.650 33.333 12.26 0.00 35.00 2.83
3229 4951 5.763698 GGGAGCAGTTTAACTAGTTGTTCTT 59.236 40.000 18.56 0.00 39.89 2.52
3520 5337 1.202651 CCAACTCAGAGGAACGGTGTT 60.203 52.381 1.53 0.00 32.61 3.32
3522 5339 0.393077 ACTCAGAGGAACGGTGTTGG 59.607 55.000 1.53 0.00 0.00 3.77
3523 5340 0.393077 CTCAGAGGAACGGTGTTGGT 59.607 55.000 0.00 0.00 0.00 3.67
3524 5341 0.105964 TCAGAGGAACGGTGTTGGTG 59.894 55.000 0.00 0.00 0.00 4.17
3525 5342 0.179056 CAGAGGAACGGTGTTGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
3526 5343 1.069513 CAGAGGAACGGTGTTGGTGTA 59.930 52.381 0.00 0.00 0.00 2.90
3528 5345 1.342174 GAGGAACGGTGTTGGTGTAGA 59.658 52.381 0.00 0.00 0.00 2.59
3531 5348 3.579586 AGGAACGGTGTTGGTGTAGAATA 59.420 43.478 0.00 0.00 0.00 1.75
3532 5349 4.224370 AGGAACGGTGTTGGTGTAGAATAT 59.776 41.667 0.00 0.00 0.00 1.28
3535 5352 6.594937 GGAACGGTGTTGGTGTAGAATATTAA 59.405 38.462 0.00 0.00 0.00 1.40
3536 5353 7.201582 GGAACGGTGTTGGTGTAGAATATTAAG 60.202 40.741 0.00 0.00 0.00 1.85
3537 5354 5.583457 ACGGTGTTGGTGTAGAATATTAAGC 59.417 40.000 0.00 0.00 0.00 3.09
3538 5355 5.583061 CGGTGTTGGTGTAGAATATTAAGCA 59.417 40.000 0.00 0.00 0.00 3.91
3539 5356 6.260050 CGGTGTTGGTGTAGAATATTAAGCAT 59.740 38.462 0.00 0.00 0.00 3.79
3540 5357 7.518370 CGGTGTTGGTGTAGAATATTAAGCATC 60.518 40.741 0.00 0.00 0.00 3.91
3541 5358 7.499232 GGTGTTGGTGTAGAATATTAAGCATCT 59.501 37.037 0.00 0.00 0.00 2.90
3542 5359 8.893727 GTGTTGGTGTAGAATATTAAGCATCTT 58.106 33.333 0.00 0.00 0.00 2.40
3596 5413 5.417580 GCTGGACTTGGTTTTATGGTATTCA 59.582 40.000 0.00 0.00 0.00 2.57
3618 5445 3.003378 AGTTGCACCTAAGCGTTTCTTTC 59.997 43.478 0.00 0.00 36.25 2.62
3625 5452 5.642063 CACCTAAGCGTTTCTTTCTTGGATA 59.358 40.000 0.00 0.00 36.25 2.59
3804 5650 3.319972 AGAAAGCTGAAAATGAGCTGCAA 59.680 39.130 1.02 0.00 46.32 4.08
3810 5656 2.555325 TGAAAATGAGCTGCAACTCTGG 59.445 45.455 17.56 0.00 37.58 3.86
3854 5702 1.767088 GGATACCCCAGTTGGTACTCC 59.233 57.143 0.00 0.00 43.45 3.85
3855 5703 1.767088 GATACCCCAGTTGGTACTCCC 59.233 57.143 0.00 0.00 43.45 4.30
3889 5737 3.321682 CCACCCATTTTCGCATCCATATT 59.678 43.478 0.00 0.00 0.00 1.28
3983 5831 0.179124 CTCCTACTCAAGTCGCAGGC 60.179 60.000 0.00 0.00 0.00 4.85
4006 5854 3.186001 CGATGCCAATGCTTGTATCTCTC 59.814 47.826 0.00 0.00 38.71 3.20
4015 5864 0.027716 TTGTATCTCTCGCTCGACGC 59.972 55.000 0.00 0.40 43.23 5.19
4040 5889 1.320507 GTAGCTAGGGTTCCCTCTCG 58.679 60.000 14.24 5.65 37.64 4.04
4052 5901 2.654079 CCTCTCGCTCCCTTGTGCT 61.654 63.158 0.00 0.00 0.00 4.40
4086 5935 4.467795 TGGGAGGTCTTCAGATTTGTAGAG 59.532 45.833 0.00 0.00 32.27 2.43
4089 5938 5.317733 AGGTCTTCAGATTTGTAGAGACG 57.682 43.478 0.00 0.00 32.27 4.18
4142 6027 4.623932 TCAGATGGAGAATTATTCCCCG 57.376 45.455 0.78 0.00 33.62 5.73
4145 6030 1.217916 TGGAGAATTATTCCCCGGCA 58.782 50.000 0.00 0.00 33.62 5.69
4155 6040 1.414158 TTCCCCGGCAAACATTTTGA 58.586 45.000 0.00 0.00 0.00 2.69
4197 6082 7.503230 TCTCTTTGATGCTTCATTATAATGGCA 59.497 33.333 23.17 23.17 37.75 4.92
4214 6099 0.322456 GCAACATGAGCCACCCTACA 60.322 55.000 0.00 0.00 0.00 2.74
4247 6132 3.440173 CCATATGATGTAATTCCCACGGC 59.560 47.826 3.65 0.00 0.00 5.68
4345 6230 3.981071 TTCCTGTCCGATTCATCAGTT 57.019 42.857 0.00 0.00 0.00 3.16
4383 6268 7.514721 AGTTTAGATGTCTCACCAAGGTTAAA 58.485 34.615 0.00 0.00 0.00 1.52
4384 6269 8.164070 AGTTTAGATGTCTCACCAAGGTTAAAT 58.836 33.333 0.00 0.00 0.00 1.40
4387 6272 7.839680 AGATGTCTCACCAAGGTTAAATTTT 57.160 32.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.885922 TGGTATTTTTATGGACTGTTGCTCTTA 59.114 33.333 0.00 0.00 0.00 2.10
8 9 6.719370 TGGTATTTTTATGGACTGTTGCTCTT 59.281 34.615 0.00 0.00 0.00 2.85
10 11 6.404734 CCTGGTATTTTTATGGACTGTTGCTC 60.405 42.308 0.00 0.00 0.00 4.26
13 14 5.184864 TGCCTGGTATTTTTATGGACTGTTG 59.815 40.000 0.00 0.00 0.00 3.33
14 15 5.329399 TGCCTGGTATTTTTATGGACTGTT 58.671 37.500 0.00 0.00 0.00 3.16
15 16 4.929479 TGCCTGGTATTTTTATGGACTGT 58.071 39.130 0.00 0.00 0.00 3.55
16 17 5.913137 TTGCCTGGTATTTTTATGGACTG 57.087 39.130 0.00 0.00 0.00 3.51
17 18 5.777732 TGTTTGCCTGGTATTTTTATGGACT 59.222 36.000 0.00 0.00 0.00 3.85
18 19 5.867174 GTGTTTGCCTGGTATTTTTATGGAC 59.133 40.000 0.00 0.00 0.00 4.02
19 20 5.046950 GGTGTTTGCCTGGTATTTTTATGGA 60.047 40.000 0.00 0.00 0.00 3.41
20 21 5.046663 AGGTGTTTGCCTGGTATTTTTATGG 60.047 40.000 0.00 0.00 37.50 2.74
21 22 6.036577 AGGTGTTTGCCTGGTATTTTTATG 57.963 37.500 0.00 0.00 37.50 1.90
209 219 0.318529 CCGTCTCATCATCCTGAGCG 60.319 60.000 9.41 9.41 42.00 5.03
317 327 1.516365 ATAGATCCGCCGGAGACACG 61.516 60.000 13.12 0.00 34.05 4.49
345 355 1.135083 ACGACGAGATCCGAGCAAATT 60.135 47.619 0.00 0.00 41.76 1.82
460 470 1.080025 GTCGTCGTGCTAAGGCCTT 60.080 57.895 24.18 24.18 37.74 4.35
461 471 1.533469 AAGTCGTCGTGCTAAGGCCT 61.533 55.000 0.00 0.00 37.74 5.19
630 640 9.734620 TTAATCTATTCATTTTCAATCTTGGCG 57.265 29.630 0.00 0.00 0.00 5.69
643 653 9.921637 TGCGGAAAAACTTTTAATCTATTCATT 57.078 25.926 0.00 0.00 0.00 2.57
675 685 7.976734 GGTGATCTAAACGCTGCTCTTATATAT 59.023 37.037 0.00 0.00 0.00 0.86
676 686 7.039993 TGGTGATCTAAACGCTGCTCTTATATA 60.040 37.037 0.00 0.00 0.00 0.86
677 687 6.159988 GGTGATCTAAACGCTGCTCTTATAT 58.840 40.000 0.00 0.00 0.00 0.86
678 688 5.068591 TGGTGATCTAAACGCTGCTCTTATA 59.931 40.000 0.00 0.00 0.00 0.98
679 689 4.141937 TGGTGATCTAAACGCTGCTCTTAT 60.142 41.667 0.00 0.00 0.00 1.73
680 690 3.194755 TGGTGATCTAAACGCTGCTCTTA 59.805 43.478 0.00 0.00 0.00 2.10
681 691 2.028112 TGGTGATCTAAACGCTGCTCTT 60.028 45.455 0.00 0.00 0.00 2.85
682 692 1.550524 TGGTGATCTAAACGCTGCTCT 59.449 47.619 0.00 0.00 0.00 4.09
683 693 2.010145 TGGTGATCTAAACGCTGCTC 57.990 50.000 0.00 0.00 0.00 4.26
684 694 2.472695 TTGGTGATCTAAACGCTGCT 57.527 45.000 0.00 0.00 0.00 4.24
685 695 2.677836 TCATTGGTGATCTAAACGCTGC 59.322 45.455 0.00 0.00 0.00 5.25
686 696 3.935203 ACTCATTGGTGATCTAAACGCTG 59.065 43.478 0.00 0.00 32.98 5.18
687 697 4.207891 ACTCATTGGTGATCTAAACGCT 57.792 40.909 0.00 0.00 32.98 5.07
688 698 4.946784 AACTCATTGGTGATCTAAACGC 57.053 40.909 0.00 0.00 32.98 4.84
689 699 6.480524 TGAAACTCATTGGTGATCTAAACG 57.519 37.500 0.00 0.00 32.98 3.60
690 700 9.185192 CTTTTGAAACTCATTGGTGATCTAAAC 57.815 33.333 0.00 0.00 32.98 2.01
691 701 8.359642 CCTTTTGAAACTCATTGGTGATCTAAA 58.640 33.333 0.00 0.00 32.98 1.85
692 702 7.039784 CCCTTTTGAAACTCATTGGTGATCTAA 60.040 37.037 0.00 0.00 32.98 2.10
693 703 6.434028 CCCTTTTGAAACTCATTGGTGATCTA 59.566 38.462 0.00 0.00 32.98 1.98
694 704 5.244626 CCCTTTTGAAACTCATTGGTGATCT 59.755 40.000 0.00 0.00 32.98 2.75
695 705 5.473039 CCCTTTTGAAACTCATTGGTGATC 58.527 41.667 0.00 0.00 32.98 2.92
696 706 4.284234 CCCCTTTTGAAACTCATTGGTGAT 59.716 41.667 0.00 0.00 32.98 3.06
697 707 3.640967 CCCCTTTTGAAACTCATTGGTGA 59.359 43.478 0.00 0.00 0.00 4.02
698 708 3.387699 ACCCCTTTTGAAACTCATTGGTG 59.612 43.478 0.00 0.00 0.00 4.17
699 709 3.653164 ACCCCTTTTGAAACTCATTGGT 58.347 40.909 0.00 0.00 0.00 3.67
700 710 6.358974 AATACCCCTTTTGAAACTCATTGG 57.641 37.500 0.00 0.00 0.00 3.16
701 711 9.771534 TTTTAATACCCCTTTTGAAACTCATTG 57.228 29.630 0.00 0.00 0.00 2.82
703 713 9.772973 GTTTTTAATACCCCTTTTGAAACTCAT 57.227 29.630 0.00 0.00 0.00 2.90
704 714 8.983789 AGTTTTTAATACCCCTTTTGAAACTCA 58.016 29.630 0.00 0.00 31.37 3.41
705 715 9.256477 CAGTTTTTAATACCCCTTTTGAAACTC 57.744 33.333 0.00 0.00 33.87 3.01
706 716 8.983789 TCAGTTTTTAATACCCCTTTTGAAACT 58.016 29.630 0.00 0.00 35.80 2.66
707 717 9.772973 ATCAGTTTTTAATACCCCTTTTGAAAC 57.227 29.630 0.00 0.00 0.00 2.78
721 731 8.060090 GCGTGCGTAGTATTATCAGTTTTTAAT 58.940 33.333 0.00 0.00 0.00 1.40
722 732 7.393327 GCGTGCGTAGTATTATCAGTTTTTAA 58.607 34.615 0.00 0.00 0.00 1.52
723 733 6.291217 CGCGTGCGTAGTATTATCAGTTTTTA 60.291 38.462 6.00 0.00 34.35 1.52
724 734 5.499652 CGCGTGCGTAGTATTATCAGTTTTT 60.500 40.000 6.00 0.00 34.35 1.94
725 735 4.027132 CGCGTGCGTAGTATTATCAGTTTT 60.027 41.667 6.00 0.00 34.35 2.43
726 736 3.484649 CGCGTGCGTAGTATTATCAGTTT 59.515 43.478 6.00 0.00 34.35 2.66
727 737 3.040795 CGCGTGCGTAGTATTATCAGTT 58.959 45.455 6.00 0.00 34.35 3.16
728 738 2.647337 CGCGTGCGTAGTATTATCAGT 58.353 47.619 6.00 0.00 34.35 3.41
729 739 1.382419 GCGCGTGCGTAGTATTATCAG 59.618 52.381 16.27 0.00 42.09 2.90
730 740 1.401530 GCGCGTGCGTAGTATTATCA 58.598 50.000 16.27 0.00 42.09 2.15
742 752 3.085010 CGTCACTTTTGCGCGTGC 61.085 61.111 15.48 15.48 43.20 5.34
743 753 2.425124 CCGTCACTTTTGCGCGTG 60.425 61.111 8.43 4.67 0.00 5.34
744 754 2.586635 TCCGTCACTTTTGCGCGT 60.587 55.556 8.43 0.00 0.00 6.01
745 755 2.101209 AAGTCCGTCACTTTTGCGCG 62.101 55.000 0.00 0.00 43.38 6.86
746 756 1.647084 AAGTCCGTCACTTTTGCGC 59.353 52.632 0.00 0.00 43.38 6.09
753 763 1.068741 GGTCTGTGAAAGTCCGTCACT 59.931 52.381 6.17 0.00 44.70 3.41
754 764 1.499049 GGTCTGTGAAAGTCCGTCAC 58.501 55.000 0.00 0.00 44.67 3.67
755 765 0.391597 GGGTCTGTGAAAGTCCGTCA 59.608 55.000 0.00 0.00 35.13 4.35
756 766 0.680061 AGGGTCTGTGAAAGTCCGTC 59.320 55.000 0.00 0.00 35.13 4.79
757 767 0.393077 CAGGGTCTGTGAAAGTCCGT 59.607 55.000 0.00 0.00 35.13 4.69
758 768 0.951040 GCAGGGTCTGTGAAAGTCCG 60.951 60.000 0.00 0.00 35.13 4.79
759 769 0.398318 AGCAGGGTCTGTGAAAGTCC 59.602 55.000 0.00 0.00 33.43 3.85
760 770 1.517242 CAGCAGGGTCTGTGAAAGTC 58.483 55.000 0.00 0.00 33.43 3.01
761 771 0.536006 GCAGCAGGGTCTGTGAAAGT 60.536 55.000 0.00 0.00 36.49 2.66
762 772 1.572085 CGCAGCAGGGTCTGTGAAAG 61.572 60.000 0.00 0.00 44.89 2.62
763 773 1.597854 CGCAGCAGGGTCTGTGAAA 60.598 57.895 0.00 0.00 44.89 2.69
764 774 2.031012 CGCAGCAGGGTCTGTGAA 59.969 61.111 0.00 0.00 44.89 3.18
765 775 3.233980 ACGCAGCAGGGTCTGTGA 61.234 61.111 10.77 0.00 44.89 3.58
766 776 3.046087 CACGCAGCAGGGTCTGTG 61.046 66.667 0.00 3.13 46.79 3.66
767 777 4.320456 CCACGCAGCAGGGTCTGT 62.320 66.667 0.00 0.00 39.11 3.41
774 784 1.026182 TAATGAAGGCCACGCAGCAG 61.026 55.000 5.01 0.00 0.00 4.24
775 785 0.394216 ATAATGAAGGCCACGCAGCA 60.394 50.000 5.01 0.00 0.00 4.41
776 786 0.740737 AATAATGAAGGCCACGCAGC 59.259 50.000 5.01 0.00 0.00 5.25
777 787 1.534595 GCAATAATGAAGGCCACGCAG 60.535 52.381 5.01 0.00 0.00 5.18
778 788 0.455410 GCAATAATGAAGGCCACGCA 59.545 50.000 5.01 0.00 0.00 5.24
779 789 0.249031 GGCAATAATGAAGGCCACGC 60.249 55.000 5.01 0.00 45.70 5.34
780 790 3.944871 GGCAATAATGAAGGCCACG 57.055 52.632 5.01 0.00 45.70 4.94
783 793 0.105504 AGGGGGCAATAATGAAGGCC 60.106 55.000 0.00 0.00 46.34 5.19
784 794 1.043022 CAGGGGGCAATAATGAAGGC 58.957 55.000 0.00 0.00 0.00 4.35
785 795 2.754012 TCAGGGGGCAATAATGAAGG 57.246 50.000 0.00 0.00 0.00 3.46
786 796 5.619132 AAAATCAGGGGGCAATAATGAAG 57.381 39.130 0.00 0.00 0.00 3.02
787 797 6.671779 AGTTAAAATCAGGGGGCAATAATGAA 59.328 34.615 0.00 0.00 0.00 2.57
788 798 6.098124 CAGTTAAAATCAGGGGGCAATAATGA 59.902 38.462 0.00 0.00 0.00 2.57
789 799 6.282930 CAGTTAAAATCAGGGGGCAATAATG 58.717 40.000 0.00 0.00 0.00 1.90
790 800 5.366477 CCAGTTAAAATCAGGGGGCAATAAT 59.634 40.000 0.00 0.00 0.00 1.28
791 801 4.714308 CCAGTTAAAATCAGGGGGCAATAA 59.286 41.667 0.00 0.00 0.00 1.40
792 802 4.264623 ACCAGTTAAAATCAGGGGGCAATA 60.265 41.667 0.00 0.00 0.00 1.90
793 803 3.106827 CCAGTTAAAATCAGGGGGCAAT 58.893 45.455 0.00 0.00 0.00 3.56
794 804 2.158234 ACCAGTTAAAATCAGGGGGCAA 60.158 45.455 0.00 0.00 0.00 4.52
795 805 1.431243 ACCAGTTAAAATCAGGGGGCA 59.569 47.619 0.00 0.00 0.00 5.36
796 806 1.824852 CACCAGTTAAAATCAGGGGGC 59.175 52.381 0.00 0.00 0.00 5.80
797 807 2.456577 CCACCAGTTAAAATCAGGGGG 58.543 52.381 0.00 0.00 36.42 5.40
798 808 2.456577 CCCACCAGTTAAAATCAGGGG 58.543 52.381 0.00 0.00 0.00 4.79
799 809 1.824852 GCCCACCAGTTAAAATCAGGG 59.175 52.381 0.00 0.00 38.10 4.45
800 810 1.824852 GGCCCACCAGTTAAAATCAGG 59.175 52.381 0.00 0.00 35.26 3.86
801 811 1.824852 GGGCCCACCAGTTAAAATCAG 59.175 52.381 19.95 0.00 39.85 2.90
802 812 1.888826 CGGGCCCACCAGTTAAAATCA 60.889 52.381 24.92 0.00 40.22 2.57
803 813 0.815095 CGGGCCCACCAGTTAAAATC 59.185 55.000 24.92 0.00 40.22 2.17
804 814 1.254975 GCGGGCCCACCAGTTAAAAT 61.255 55.000 24.92 0.00 40.22 1.82
805 815 1.904378 GCGGGCCCACCAGTTAAAA 60.904 57.895 24.92 0.00 40.22 1.52
806 816 2.282603 GCGGGCCCACCAGTTAAA 60.283 61.111 24.92 0.00 40.22 1.52
807 817 4.354162 GGCGGGCCCACCAGTTAA 62.354 66.667 24.82 0.00 40.22 2.01
814 824 2.552231 ATTAAGTGAGGCGGGCCCAC 62.552 60.000 24.92 13.23 37.46 4.61
815 825 1.858739 AATTAAGTGAGGCGGGCCCA 61.859 55.000 24.92 0.00 36.58 5.36
816 826 0.181824 TAATTAAGTGAGGCGGGCCC 59.818 55.000 13.57 13.57 36.58 5.80
817 827 2.047002 TTAATTAAGTGAGGCGGGCC 57.953 50.000 0.18 0.18 0.00 5.80
818 828 3.883489 AGATTTAATTAAGTGAGGCGGGC 59.117 43.478 0.00 0.00 0.00 6.13
819 829 6.293462 GCTTAGATTTAATTAAGTGAGGCGGG 60.293 42.308 0.00 0.00 31.16 6.13
820 830 6.483640 AGCTTAGATTTAATTAAGTGAGGCGG 59.516 38.462 0.00 0.00 31.16 6.13
821 831 7.484035 AGCTTAGATTTAATTAAGTGAGGCG 57.516 36.000 0.00 0.00 31.16 5.52
837 847 9.794719 GGTGGTTAGGATTTAATTAGCTTAGAT 57.205 33.333 0.00 0.00 0.00 1.98
838 848 8.215736 GGGTGGTTAGGATTTAATTAGCTTAGA 58.784 37.037 0.00 0.00 0.00 2.10
839 849 7.996644 TGGGTGGTTAGGATTTAATTAGCTTAG 59.003 37.037 0.00 0.00 0.00 2.18
840 850 7.874252 TGGGTGGTTAGGATTTAATTAGCTTA 58.126 34.615 0.00 0.00 0.00 3.09
841 851 6.737608 TGGGTGGTTAGGATTTAATTAGCTT 58.262 36.000 0.00 0.00 0.00 3.74
842 852 6.069029 ACTGGGTGGTTAGGATTTAATTAGCT 60.069 38.462 0.00 0.00 0.00 3.32
843 853 6.127101 ACTGGGTGGTTAGGATTTAATTAGC 58.873 40.000 0.00 0.00 0.00 3.09
844 854 9.689501 TTTACTGGGTGGTTAGGATTTAATTAG 57.310 33.333 0.00 0.00 0.00 1.73
846 856 8.809066 GTTTTACTGGGTGGTTAGGATTTAATT 58.191 33.333 0.00 0.00 0.00 1.40
847 857 7.951245 TGTTTTACTGGGTGGTTAGGATTTAAT 59.049 33.333 0.00 0.00 0.00 1.40
848 858 7.231115 GTGTTTTACTGGGTGGTTAGGATTTAA 59.769 37.037 0.00 0.00 0.00 1.52
849 859 6.716173 GTGTTTTACTGGGTGGTTAGGATTTA 59.284 38.462 0.00 0.00 0.00 1.40
850 860 5.537295 GTGTTTTACTGGGTGGTTAGGATTT 59.463 40.000 0.00 0.00 0.00 2.17
851 861 5.074804 GTGTTTTACTGGGTGGTTAGGATT 58.925 41.667 0.00 0.00 0.00 3.01
852 862 4.352893 AGTGTTTTACTGGGTGGTTAGGAT 59.647 41.667 0.00 0.00 38.49 3.24
853 863 3.717913 AGTGTTTTACTGGGTGGTTAGGA 59.282 43.478 0.00 0.00 38.49 2.94
854 864 4.094830 AGTGTTTTACTGGGTGGTTAGG 57.905 45.455 0.00 0.00 38.49 2.69
865 875 8.603304 AGATGGTTAGGATTACAGTGTTTTACT 58.397 33.333 0.00 0.00 41.36 2.24
866 876 8.788325 AGATGGTTAGGATTACAGTGTTTTAC 57.212 34.615 0.00 0.00 0.00 2.01
867 877 8.822805 AGAGATGGTTAGGATTACAGTGTTTTA 58.177 33.333 0.00 0.00 0.00 1.52
868 878 7.690256 AGAGATGGTTAGGATTACAGTGTTTT 58.310 34.615 0.00 0.00 0.00 2.43
869 879 7.181125 AGAGAGATGGTTAGGATTACAGTGTTT 59.819 37.037 0.00 0.00 0.00 2.83
870 880 6.670027 AGAGAGATGGTTAGGATTACAGTGTT 59.330 38.462 0.00 0.00 0.00 3.32
871 881 6.198639 AGAGAGATGGTTAGGATTACAGTGT 58.801 40.000 0.00 0.00 0.00 3.55
872 882 6.723298 AGAGAGATGGTTAGGATTACAGTG 57.277 41.667 0.00 0.00 0.00 3.66
873 883 7.741554 AAAGAGAGATGGTTAGGATTACAGT 57.258 36.000 0.00 0.00 0.00 3.55
874 884 9.535878 GTTAAAGAGAGATGGTTAGGATTACAG 57.464 37.037 0.00 0.00 0.00 2.74
875 885 9.042450 TGTTAAAGAGAGATGGTTAGGATTACA 57.958 33.333 0.00 0.00 0.00 2.41
876 886 9.886132 TTGTTAAAGAGAGATGGTTAGGATTAC 57.114 33.333 0.00 0.00 0.00 1.89
878 888 9.620259 GATTGTTAAAGAGAGATGGTTAGGATT 57.380 33.333 0.00 0.00 0.00 3.01
879 889 7.928706 CGATTGTTAAAGAGAGATGGTTAGGAT 59.071 37.037 0.00 0.00 0.00 3.24
880 890 7.123697 TCGATTGTTAAAGAGAGATGGTTAGGA 59.876 37.037 0.00 0.00 0.00 2.94
881 891 7.222999 GTCGATTGTTAAAGAGAGATGGTTAGG 59.777 40.741 0.00 0.00 0.00 2.69
882 892 7.222999 GGTCGATTGTTAAAGAGAGATGGTTAG 59.777 40.741 0.00 0.00 0.00 2.34
883 893 7.039882 GGTCGATTGTTAAAGAGAGATGGTTA 58.960 38.462 0.00 0.00 0.00 2.85
884 894 5.875359 GGTCGATTGTTAAAGAGAGATGGTT 59.125 40.000 0.00 0.00 0.00 3.67
885 895 5.420409 GGTCGATTGTTAAAGAGAGATGGT 58.580 41.667 0.00 0.00 0.00 3.55
886 896 4.504461 CGGTCGATTGTTAAAGAGAGATGG 59.496 45.833 0.00 0.00 0.00 3.51
887 897 4.026475 GCGGTCGATTGTTAAAGAGAGATG 60.026 45.833 0.00 0.00 0.00 2.90
888 898 4.113354 GCGGTCGATTGTTAAAGAGAGAT 58.887 43.478 0.00 0.00 0.00 2.75
889 899 3.508762 GCGGTCGATTGTTAAAGAGAGA 58.491 45.455 0.00 0.00 0.00 3.10
890 900 2.603560 GGCGGTCGATTGTTAAAGAGAG 59.396 50.000 0.00 0.00 0.00 3.20
891 901 2.613691 GGCGGTCGATTGTTAAAGAGA 58.386 47.619 0.00 0.00 0.00 3.10
892 902 1.323534 CGGCGGTCGATTGTTAAAGAG 59.676 52.381 0.00 0.00 42.43 2.85
893 903 1.067706 TCGGCGGTCGATTGTTAAAGA 60.068 47.619 7.21 0.00 43.74 2.52
894 904 1.352114 TCGGCGGTCGATTGTTAAAG 58.648 50.000 7.21 0.00 43.74 1.85
895 905 3.511182 TCGGCGGTCGATTGTTAAA 57.489 47.368 7.21 0.00 43.74 1.52
903 913 1.647545 AACTATTCGTCGGCGGTCGA 61.648 55.000 10.62 19.62 46.77 4.20
904 914 0.799534 AAACTATTCGTCGGCGGTCG 60.800 55.000 10.62 12.96 38.89 4.79
911 921 6.462073 TTTCCTTTCTGAAACTATTCGTCG 57.538 37.500 0.00 0.00 38.46 5.12
919 929 2.158667 TCCCGCTTTCCTTTCTGAAACT 60.159 45.455 0.00 0.00 31.28 2.66
920 930 2.226674 CTCCCGCTTTCCTTTCTGAAAC 59.773 50.000 0.00 0.00 31.28 2.78
921 931 2.158667 ACTCCCGCTTTCCTTTCTGAAA 60.159 45.455 2.44 2.44 33.42 2.69
922 932 1.420138 ACTCCCGCTTTCCTTTCTGAA 59.580 47.619 0.00 0.00 0.00 3.02
923 933 1.002087 GACTCCCGCTTTCCTTTCTGA 59.998 52.381 0.00 0.00 0.00 3.27
924 934 1.443802 GACTCCCGCTTTCCTTTCTG 58.556 55.000 0.00 0.00 0.00 3.02
985 995 3.197790 CATCTGACCGCCGGCAAG 61.198 66.667 28.98 19.90 0.00 4.01
996 1006 1.725557 GCCTCGCGTACCTCATCTGA 61.726 60.000 5.77 0.00 0.00 3.27
1435 1510 1.040646 TCACATAGGGCTCGTCATCC 58.959 55.000 0.00 0.00 0.00 3.51
1506 1581 3.444703 ACTCAAGCTCGTCATGGATAC 57.555 47.619 0.00 0.00 0.00 2.24
1824 1899 0.723414 CACACATGCGGCTTCTAGTG 59.277 55.000 0.00 5.53 0.00 2.74
1844 1919 5.221891 TCTTTGCATTCAACGCTAAGATC 57.778 39.130 0.00 0.00 43.19 2.75
1884 1959 1.876156 CTCCACAGAAAACACCAGAGC 59.124 52.381 0.00 0.00 0.00 4.09
1938 2013 0.371645 GCTGCTGCAATCGTCACTAC 59.628 55.000 11.11 0.00 39.41 2.73
2052 2143 4.307032 ACAACACAGAAAGGGATAGCAT 57.693 40.909 0.00 0.00 0.00 3.79
2522 2731 6.584563 TGCACACAAGAACTTCAAAACTTTAC 59.415 34.615 0.00 0.00 0.00 2.01
2635 2861 4.447724 TCAGAAGTTTCGTATTGACTGCAC 59.552 41.667 0.00 0.00 0.00 4.57
2855 3320 4.163078 CACCCTGGACTAACAGAATCAGAT 59.837 45.833 0.00 0.00 40.97 2.90
2907 4562 5.122519 TGCATTTGAGTTACTGTTCACTGA 58.877 37.500 0.00 0.00 0.00 3.41
3184 4906 5.127519 TCCCAAATGAGAATGCAGTAAATGG 59.872 40.000 0.00 0.00 0.00 3.16
3190 4912 2.097825 GCTCCCAAATGAGAATGCAGT 58.902 47.619 0.00 0.00 34.11 4.40
3537 5354 7.798596 AGAGTTCATAAGTTGGCATAAGATG 57.201 36.000 0.00 0.00 0.00 2.90
3538 5355 8.928448 TCTAGAGTTCATAAGTTGGCATAAGAT 58.072 33.333 0.00 0.00 0.00 2.40
3539 5356 8.198109 GTCTAGAGTTCATAAGTTGGCATAAGA 58.802 37.037 0.00 0.00 0.00 2.10
3540 5357 7.439655 GGTCTAGAGTTCATAAGTTGGCATAAG 59.560 40.741 0.00 0.00 0.00 1.73
3541 5358 7.093068 TGGTCTAGAGTTCATAAGTTGGCATAA 60.093 37.037 0.00 0.00 0.00 1.90
3542 5359 6.382859 TGGTCTAGAGTTCATAAGTTGGCATA 59.617 38.462 0.00 0.00 0.00 3.14
3543 5360 5.189736 TGGTCTAGAGTTCATAAGTTGGCAT 59.810 40.000 0.00 0.00 0.00 4.40
3544 5361 4.530553 TGGTCTAGAGTTCATAAGTTGGCA 59.469 41.667 0.00 0.00 0.00 4.92
3545 5362 5.086104 TGGTCTAGAGTTCATAAGTTGGC 57.914 43.478 0.00 0.00 0.00 4.52
3546 5363 7.118496 AGATGGTCTAGAGTTCATAAGTTGG 57.882 40.000 0.00 0.00 0.00 3.77
3596 5413 2.256117 AGAAACGCTTAGGTGCAACT 57.744 45.000 10.34 10.34 36.74 3.16
3618 5445 1.143813 AGTCATGGGCCCTATCCAAG 58.856 55.000 25.70 0.00 37.87 3.61
3625 5452 1.136329 ACAGAACAGTCATGGGCCCT 61.136 55.000 25.70 5.48 0.00 5.19
3848 5696 0.386113 GCGGAGATCACTGGGAGTAC 59.614 60.000 0.94 0.00 0.00 2.73
3854 5702 2.187946 GGTGGCGGAGATCACTGG 59.812 66.667 0.94 0.00 34.60 4.00
3855 5703 1.976132 ATGGGTGGCGGAGATCACTG 61.976 60.000 0.00 0.00 34.60 3.66
3913 5761 2.818751 TGAAGACAACAACAACCCCT 57.181 45.000 0.00 0.00 0.00 4.79
3955 5803 2.685897 ACTTGAGTAGGAGATGTCGCTC 59.314 50.000 0.00 0.00 0.00 5.03
4015 5864 0.745468 GGAACCCTAGCTACACCTCG 59.255 60.000 0.00 0.00 0.00 4.63
4040 5889 0.957888 GACCAGAAGCACAAGGGAGC 60.958 60.000 0.00 0.00 0.00 4.70
4052 5901 1.150135 AGACCTCCCAAGAGACCAGAA 59.850 52.381 0.00 0.00 43.39 3.02
4086 5935 1.149148 GGGAACTTGAGCAAGACGTC 58.851 55.000 16.47 7.70 40.79 4.34
4089 5938 1.594331 AACGGGAACTTGAGCAAGAC 58.406 50.000 16.47 9.61 40.79 3.01
4142 6027 6.070829 GCGACTTTTATTCAAAATGTTTGCC 58.929 36.000 0.00 0.00 33.27 4.52
4145 6030 7.171337 AGCATGCGACTTTTATTCAAAATGTTT 59.829 29.630 13.01 0.00 33.27 2.83
4155 6040 5.412594 TCAAAGAGAGCATGCGACTTTTATT 59.587 36.000 25.13 14.60 0.00 1.40
4197 6082 1.915489 TCATGTAGGGTGGCTCATGTT 59.085 47.619 0.00 0.00 38.78 2.71
4207 6092 6.273026 TCATATGGATCACAATCATGTAGGGT 59.727 38.462 2.13 0.00 37.82 4.34
4247 6132 7.799784 TGTTCATCACATAGCAATATGATTCG 58.200 34.615 2.41 0.00 29.25 3.34
4345 6230 9.102757 GAGACATCTAAACTAGCAAATGAATGA 57.897 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.