Multiple sequence alignment - TraesCS7D01G260500

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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 TraesCS7D01G260500 chr7D 100.000 4244 0 0 1 4244 236185890 236181647 0.000000e+00 7838.0
1 TraesCS7D01G260500 chr7D 96.429 56 2 0 587 642 5318872 5318927 4.520000e-15 93.5
2 TraesCS7D01G260500 chr7A 92.036 3403 159 31 832 4213 251286149 251282838 0.000000e+00 4680.0
3 TraesCS7D01G260500 chr7A 97.119 590 15 1 7 594 11246777 11246188 0.000000e+00 994.0
4 TraesCS7D01G260500 chr7A 90.909 44 4 0 3600 3643 105168444 105168401 4.580000e-05 60.2
5 TraesCS7D01G260500 chr7B 93.446 2960 114 27 832 3778 212479219 212476327 0.000000e+00 4318.0
6 TraesCS7D01G260500 chr7B 86.709 316 24 7 3907 4213 212476201 212475895 6.800000e-88 335.0
7 TraesCS7D01G260500 chr7B 100.000 32 0 0 4213 4244 212475938 212475907 4.580000e-05 60.2
8 TraesCS7D01G260500 chr3B 96.661 599 18 1 1 597 31200606 31200008 0.000000e+00 994.0
9 TraesCS7D01G260500 chr3B 82.407 108 16 2 3534 3641 689513558 689513454 1.630000e-14 91.6
10 TraesCS7D01G260500 chr6A 95.805 596 23 1 1 594 329994961 329995556 0.000000e+00 961.0
11 TraesCS7D01G260500 chr3D 94.393 535 27 2 63 594 379583715 379584249 0.000000e+00 819.0
12 TraesCS7D01G260500 chr3D 84.404 109 14 2 3534 3642 523157484 523157379 2.090000e-18 104.0
13 TraesCS7D01G260500 chr6B 96.939 392 10 1 1 390 52697806 52698197 0.000000e+00 656.0
14 TraesCS7D01G260500 chr6B 95.663 392 15 1 1 390 52710199 52710590 2.790000e-176 628.0
15 TraesCS7D01G260500 chr6B 98.214 56 1 0 590 645 704174405 704174460 9.710000e-17 99.0
16 TraesCS7D01G260500 chr5D 94.915 59 3 0 587 645 283013769 283013827 4.520000e-15 93.5
17 TraesCS7D01G260500 chr5D 85.870 92 3 6 3549 3639 450670051 450670133 5.840000e-14 89.8
18 TraesCS7D01G260500 chr5D 84.091 88 4 5 3549 3635 450670129 450670051 4.550000e-10 76.8
19 TraesCS7D01G260500 chr2D 93.651 63 3 1 584 645 57100151 57100089 4.520000e-15 93.5
20 TraesCS7D01G260500 chr1D 95.000 60 1 2 587 645 480887611 480887553 4.520000e-15 93.5
21 TraesCS7D01G260500 chr1A 93.548 62 4 0 590 651 478423760 478423699 4.520000e-15 93.5
22 TraesCS7D01G260500 chr1A 96.429 56 2 0 590 645 478426875 478426820 4.520000e-15 93.5
23 TraesCS7D01G260500 chr2B 94.643 56 3 0 590 645 600086204 600086259 2.100000e-13 87.9
24 TraesCS7D01G260500 chr6D 90.323 62 6 0 584 645 30289638 30289699 9.780000e-12 82.4
25 TraesCS7D01G260500 chr5A 95.349 43 2 0 3597 3639 109277574 109277532 7.610000e-08 69.4
26 TraesCS7D01G260500 chr5A 94.872 39 2 0 3600 3638 132095767 132095729 1.270000e-05 62.1
27 TraesCS7D01G260500 chr5B 100.000 29 0 0 3558 3586 322271633 322271661 2.000000e-03 54.7


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 TraesCS7D01G260500 chr7D 236181647 236185890 4243 True 7838.000000 7838 100.000 1 4244 1 chr7D.!!$R1 4243
1 TraesCS7D01G260500 chr7A 251282838 251286149 3311 True 4680.000000 4680 92.036 832 4213 1 chr7A.!!$R3 3381
2 TraesCS7D01G260500 chr7A 11246188 11246777 589 True 994.000000 994 97.119 7 594 1 chr7A.!!$R1 587
3 TraesCS7D01G260500 chr7B 212475895 212479219 3324 True 1571.066667 4318 93.385 832 4244 3 chr7B.!!$R1 3412
4 TraesCS7D01G260500 chr3B 31200008 31200606 598 True 994.000000 994 96.661 1 597 1 chr3B.!!$R1 596
5 TraesCS7D01G260500 chr6A 329994961 329995556 595 False 961.000000 961 95.805 1 594 1 chr6A.!!$F1 593
6 TraesCS7D01G260500 chr3D 379583715 379584249 534 False 819.000000 819 94.393 63 594 1 chr3D.!!$F1 531

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
787 791 0.037232 ACGAGAGAGAAAAAGGCCGG 60.037 55.000 0.00 0.0 0.00 6.13 F
1201 1208 0.550914 TTGCCTTCTCCTTGTGGTGT 59.449 50.000 0.00 0.0 34.23 4.16 F
1868 1878 1.002033 GTTGCACTGCTCAAACTCCTG 60.002 52.381 1.98 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2228 1.200020 GCCAACAGACCATTTCCTTCG 59.800 52.381 0.00 0.0 0.00 3.79 R
3155 3176 1.542915 CACAGCTAGCCAAAACAGCAT 59.457 47.619 12.13 0.0 37.78 3.79 R
3711 3735 1.069636 GCAGGAACAGAAAACTCAGCG 60.070 52.381 0.00 0.0 0.00 5.18 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
94 95 8.328758 TCCTTTCCTACACATGATAACATTCTT 58.671 33.333 0.00 0.00 34.15 2.52
102 103 7.530010 ACACATGATAACATTCTTTCTTTCCG 58.470 34.615 0.00 0.00 34.15 4.30
200 201 5.656859 GGTAGCCCCAAATACTTTTCTGATT 59.343 40.000 0.00 0.00 0.00 2.57
429 433 4.479786 ACACTTGGAGCTCTAAAGGATC 57.520 45.455 24.28 5.33 0.00 3.36
449 453 5.515710 GGATCCCTTTATCCCCTCAATTCTC 60.516 48.000 0.00 0.00 39.74 2.87
562 566 4.018779 TCCTCTCGTTGGGATTATGGTTTT 60.019 41.667 0.00 0.00 0.00 2.43
570 574 3.829601 TGGGATTATGGTTTTGGTGACAC 59.170 43.478 0.00 0.00 42.67 3.67
588 592 4.819630 TGACACCATGGTTGACTTTAACTC 59.180 41.667 16.84 3.03 0.00 3.01
594 598 7.709182 CACCATGGTTGACTTTAACTCGATATA 59.291 37.037 16.84 0.00 0.00 0.86
621 625 7.650834 TTTTATTATGTTTGAGGTGCTTTGC 57.349 32.000 0.00 0.00 0.00 3.68
622 626 4.870123 ATTATGTTTGAGGTGCTTTGCA 57.130 36.364 0.00 0.00 35.60 4.08
645 649 6.980051 ACTTCCGGTGAACTTTGATAATAC 57.020 37.500 0.00 0.00 0.00 1.89
646 650 6.708285 ACTTCCGGTGAACTTTGATAATACT 58.292 36.000 0.00 0.00 0.00 2.12
647 651 7.166167 ACTTCCGGTGAACTTTGATAATACTT 58.834 34.615 0.00 0.00 0.00 2.24
648 652 7.333672 ACTTCCGGTGAACTTTGATAATACTTC 59.666 37.037 0.00 0.00 0.00 3.01
649 653 6.942976 TCCGGTGAACTTTGATAATACTTCT 58.057 36.000 0.00 0.00 0.00 2.85
650 654 8.070034 TCCGGTGAACTTTGATAATACTTCTA 57.930 34.615 0.00 0.00 0.00 2.10
651 655 8.701895 TCCGGTGAACTTTGATAATACTTCTAT 58.298 33.333 0.00 0.00 0.00 1.98
652 656 9.976511 CCGGTGAACTTTGATAATACTTCTATA 57.023 33.333 0.00 0.00 0.00 1.31
698 702 1.017387 GTCATCACGATGGCTTTCCC 58.983 55.000 4.38 0.00 40.13 3.97
699 703 0.107214 TCATCACGATGGCTTTCCCC 60.107 55.000 7.17 0.00 39.24 4.81
700 704 0.394216 CATCACGATGGCTTTCCCCA 60.394 55.000 0.00 0.00 39.65 4.96
701 705 0.331278 ATCACGATGGCTTTCCCCAA 59.669 50.000 0.00 0.00 38.61 4.12
702 706 0.111446 TCACGATGGCTTTCCCCAAA 59.889 50.000 0.00 0.00 38.61 3.28
703 707 0.965439 CACGATGGCTTTCCCCAAAA 59.035 50.000 0.00 0.00 38.61 2.44
704 708 1.067635 CACGATGGCTTTCCCCAAAAG 60.068 52.381 0.00 0.00 46.05 2.27
705 709 1.203001 ACGATGGCTTTCCCCAAAAGA 60.203 47.619 1.85 0.00 46.18 2.52
706 710 2.102578 CGATGGCTTTCCCCAAAAGAT 58.897 47.619 1.85 0.00 46.18 2.40
707 711 3.287222 CGATGGCTTTCCCCAAAAGATA 58.713 45.455 1.85 0.00 46.18 1.98
708 712 3.316308 CGATGGCTTTCCCCAAAAGATAG 59.684 47.826 1.85 0.00 46.18 2.08
709 713 4.536765 GATGGCTTTCCCCAAAAGATAGA 58.463 43.478 1.85 0.00 46.18 1.98
710 714 4.396357 TGGCTTTCCCCAAAAGATAGAA 57.604 40.909 1.85 0.00 46.18 2.10
711 715 4.746466 TGGCTTTCCCCAAAAGATAGAAA 58.254 39.130 1.85 0.00 46.18 2.52
712 716 5.151454 TGGCTTTCCCCAAAAGATAGAAAA 58.849 37.500 1.85 0.00 46.18 2.29
713 717 5.245977 TGGCTTTCCCCAAAAGATAGAAAAG 59.754 40.000 1.85 0.00 46.18 2.27
714 718 5.480422 GGCTTTCCCCAAAAGATAGAAAAGA 59.520 40.000 1.85 0.00 46.18 2.52
715 719 6.014584 GGCTTTCCCCAAAAGATAGAAAAGAA 60.015 38.462 1.85 0.00 46.18 2.52
716 720 7.441836 GCTTTCCCCAAAAGATAGAAAAGAAA 58.558 34.615 1.85 0.00 46.18 2.52
717 721 7.600375 GCTTTCCCCAAAAGATAGAAAAGAAAG 59.400 37.037 0.00 0.00 46.18 2.62
718 722 8.776061 TTTCCCCAAAAGATAGAAAAGAAAGA 57.224 30.769 0.00 0.00 0.00 2.52
719 723 8.956446 TTCCCCAAAAGATAGAAAAGAAAGAT 57.044 30.769 0.00 0.00 0.00 2.40
720 724 8.956446 TCCCCAAAAGATAGAAAAGAAAGATT 57.044 30.769 0.00 0.00 0.00 2.40
721 725 9.379770 TCCCCAAAAGATAGAAAAGAAAGATTT 57.620 29.630 0.00 0.00 0.00 2.17
722 726 9.428097 CCCCAAAAGATAGAAAAGAAAGATTTG 57.572 33.333 0.00 0.00 0.00 2.32
723 727 9.987272 CCCAAAAGATAGAAAAGAAAGATTTGT 57.013 29.630 0.00 0.00 0.00 2.83
732 736 8.722480 AGAAAAGAAAGATTTGTTTTTGAGGG 57.278 30.769 12.64 0.00 41.72 4.30
733 737 7.770433 AGAAAAGAAAGATTTGTTTTTGAGGGG 59.230 33.333 12.64 0.00 41.72 4.79
734 738 6.560003 AAGAAAGATTTGTTTTTGAGGGGT 57.440 33.333 0.00 0.00 0.00 4.95
735 739 7.669089 AAGAAAGATTTGTTTTTGAGGGGTA 57.331 32.000 0.00 0.00 0.00 3.69
736 740 7.050970 AGAAAGATTTGTTTTTGAGGGGTAC 57.949 36.000 0.00 0.00 0.00 3.34
737 741 6.609616 AGAAAGATTTGTTTTTGAGGGGTACA 59.390 34.615 0.00 0.00 0.00 2.90
738 742 6.800072 AAGATTTGTTTTTGAGGGGTACAA 57.200 33.333 0.00 0.00 0.00 2.41
739 743 6.800072 AGATTTGTTTTTGAGGGGTACAAA 57.200 33.333 0.00 0.00 41.32 2.83
740 744 7.189079 AGATTTGTTTTTGAGGGGTACAAAA 57.811 32.000 0.00 0.00 42.72 2.44
762 766 6.959671 AAAACAAAAGATGAAACGCAAAGA 57.040 29.167 0.00 0.00 0.00 2.52
763 767 6.573617 AAACAAAAGATGAAACGCAAAGAG 57.426 33.333 0.00 0.00 0.00 2.85
764 768 4.610945 ACAAAAGATGAAACGCAAAGAGG 58.389 39.130 0.00 0.00 0.00 3.69
765 769 4.338118 ACAAAAGATGAAACGCAAAGAGGA 59.662 37.500 0.00 0.00 0.00 3.71
766 770 5.163561 ACAAAAGATGAAACGCAAAGAGGAA 60.164 36.000 0.00 0.00 0.00 3.36
767 771 5.514274 AAAGATGAAACGCAAAGAGGAAA 57.486 34.783 0.00 0.00 0.00 3.13
768 772 5.514274 AAGATGAAACGCAAAGAGGAAAA 57.486 34.783 0.00 0.00 0.00 2.29
769 773 4.860072 AGATGAAACGCAAAGAGGAAAAC 58.140 39.130 0.00 0.00 0.00 2.43
770 774 3.059634 TGAAACGCAAAGAGGAAAACG 57.940 42.857 0.00 0.00 0.00 3.60
771 775 2.678836 TGAAACGCAAAGAGGAAAACGA 59.321 40.909 0.00 0.00 0.00 3.85
772 776 3.242608 TGAAACGCAAAGAGGAAAACGAG 60.243 43.478 0.00 0.00 0.00 4.18
773 777 2.234300 ACGCAAAGAGGAAAACGAGA 57.766 45.000 0.00 0.00 0.00 4.04
774 778 2.135933 ACGCAAAGAGGAAAACGAGAG 58.864 47.619 0.00 0.00 0.00 3.20
775 779 2.223971 ACGCAAAGAGGAAAACGAGAGA 60.224 45.455 0.00 0.00 0.00 3.10
776 780 2.410053 CGCAAAGAGGAAAACGAGAGAG 59.590 50.000 0.00 0.00 0.00 3.20
777 781 3.654414 GCAAAGAGGAAAACGAGAGAGA 58.346 45.455 0.00 0.00 0.00 3.10
778 782 4.058817 GCAAAGAGGAAAACGAGAGAGAA 58.941 43.478 0.00 0.00 0.00 2.87
779 783 4.511826 GCAAAGAGGAAAACGAGAGAGAAA 59.488 41.667 0.00 0.00 0.00 2.52
780 784 5.007724 GCAAAGAGGAAAACGAGAGAGAAAA 59.992 40.000 0.00 0.00 0.00 2.29
781 785 6.458342 GCAAAGAGGAAAACGAGAGAGAAAAA 60.458 38.462 0.00 0.00 0.00 1.94
782 786 6.852858 AAGAGGAAAACGAGAGAGAAAAAG 57.147 37.500 0.00 0.00 0.00 2.27
783 787 5.301555 AGAGGAAAACGAGAGAGAAAAAGG 58.698 41.667 0.00 0.00 0.00 3.11
784 788 3.815962 AGGAAAACGAGAGAGAAAAAGGC 59.184 43.478 0.00 0.00 0.00 4.35
785 789 3.058155 GGAAAACGAGAGAGAAAAAGGCC 60.058 47.826 0.00 0.00 0.00 5.19
786 790 1.797025 AACGAGAGAGAAAAAGGCCG 58.203 50.000 0.00 0.00 0.00 6.13
787 791 0.037232 ACGAGAGAGAAAAAGGCCGG 60.037 55.000 0.00 0.00 0.00 6.13
788 792 0.741221 CGAGAGAGAAAAAGGCCGGG 60.741 60.000 2.18 0.00 0.00 5.73
789 793 1.002011 AGAGAGAAAAAGGCCGGGC 60.002 57.895 22.67 22.67 0.00 6.13
1027 1033 2.026905 GCCTCGTCCCTCTCTTCTCAT 61.027 57.143 0.00 0.00 0.00 2.90
1083 1089 0.654683 GACATCCTCGCTGTTGCATC 59.345 55.000 0.00 0.00 39.64 3.91
1145 1151 5.087323 ACCAAGTGTAAGATCTCTCTTCCA 58.913 41.667 0.00 0.00 40.92 3.53
1158 1164 1.761784 CTCTTCCATCTGTCCCCTCAG 59.238 57.143 0.00 0.00 36.85 3.35
1201 1208 0.550914 TTGCCTTCTCCTTGTGGTGT 59.449 50.000 0.00 0.00 34.23 4.16
1380 1387 5.872635 TCTTGTCAATTTTCATGCGATCTC 58.127 37.500 0.00 0.00 0.00 2.75
1411 1418 3.014623 GGGTTAGGGAGTGTACAAATGC 58.985 50.000 0.00 0.00 0.00 3.56
1428 1435 3.976793 ATGCCGTCATGAATGATTGAC 57.023 42.857 0.00 0.00 39.30 3.18
1463 1470 7.842982 ACCTAAAGAGTAAAGGTTCTGATCTC 58.157 38.462 0.00 0.00 40.82 2.75
1692 1702 2.545946 GCTTAAGTATGCTGCTGCTACC 59.454 50.000 17.00 4.23 40.48 3.18
1713 1723 7.870445 GCTACCTTATCCTTCTCATTTCTGTAG 59.130 40.741 0.00 0.00 0.00 2.74
1766 1776 7.925703 TTTGCACATTAAATTTTGGCAAATG 57.074 28.000 14.29 10.25 42.65 2.32
1815 1825 1.308047 TTGCTGTGTTCATTGCTCGT 58.692 45.000 0.00 0.00 0.00 4.18
1868 1878 1.002033 GTTGCACTGCTCAAACTCCTG 60.002 52.381 1.98 0.00 0.00 3.86
1927 1943 5.045286 ACATTGTTTAGAAGATCCTGGCTCT 60.045 40.000 0.00 0.00 0.00 4.09
1939 1955 3.114606 TCCTGGCTCTGATGTATCCAAA 58.885 45.455 0.00 0.00 0.00 3.28
1982 1998 8.814931 AGAAGATTCTTGGTCTGATATATCCTG 58.185 37.037 10.25 3.72 32.55 3.86
2008 2026 6.774354 AGTTTCGTTTACGTTGTGTGATAT 57.226 33.333 0.00 0.00 40.80 1.63
2018 2036 3.924073 CGTTGTGTGATATCTTTCCGTCA 59.076 43.478 3.98 0.00 0.00 4.35
2085 2103 6.536941 AGTTATGAACACGCCAAATTTTTGTT 59.463 30.769 2.63 4.65 36.45 2.83
2089 2107 4.053469 ACACGCCAAATTTTTGTTAGCT 57.947 36.364 0.00 0.00 36.45 3.32
2210 2228 7.308049 GCTTCTTAGGGCTAATAATGTGTAAGC 60.308 40.741 0.00 0.00 0.00 3.09
2257 2275 5.817296 GGAATCTTTTTCTGCCAGTTTTTGT 59.183 36.000 0.00 0.00 0.00 2.83
2320 2338 1.134753 TGCCAGCACAGTTGTTTCTTG 59.865 47.619 0.00 0.00 0.00 3.02
2321 2339 1.134946 GCCAGCACAGTTGTTTCTTGT 59.865 47.619 0.00 0.00 0.00 3.16
2322 2340 2.796032 GCCAGCACAGTTGTTTCTTGTC 60.796 50.000 0.00 0.00 0.00 3.18
2376 2394 7.171508 AGTCGCATCATTGTCAAATCGTTATAT 59.828 33.333 0.00 0.00 0.00 0.86
2377 2395 7.475565 GTCGCATCATTGTCAAATCGTTATATC 59.524 37.037 0.00 0.00 0.00 1.63
2378 2396 7.384932 TCGCATCATTGTCAAATCGTTATATCT 59.615 33.333 0.00 0.00 0.00 1.98
2379 2397 8.011673 CGCATCATTGTCAAATCGTTATATCTT 58.988 33.333 0.00 0.00 0.00 2.40
2380 2398 9.322776 GCATCATTGTCAAATCGTTATATCTTC 57.677 33.333 0.00 0.00 0.00 2.87
2660 2681 2.963854 CGCTGAGGTATGCTGCGG 60.964 66.667 0.00 0.00 45.76 5.69
2661 2682 3.275338 GCTGAGGTATGCTGCGGC 61.275 66.667 11.65 11.65 39.26 6.53
2679 2700 2.880890 CGGCTGCTGCTATTTTATCCTT 59.119 45.455 15.64 0.00 39.59 3.36
2680 2701 3.058639 CGGCTGCTGCTATTTTATCCTTC 60.059 47.826 15.64 0.00 39.59 3.46
2681 2702 4.140536 GGCTGCTGCTATTTTATCCTTCT 58.859 43.478 15.64 0.00 39.59 2.85
2734 2755 7.995463 TGAGCATTTGTTTTGGTTAACTTAC 57.005 32.000 5.42 0.02 0.00 2.34
2842 2863 1.143969 GCCGTACATACCGTGCTCAC 61.144 60.000 0.00 0.00 0.00 3.51
3005 3026 2.237392 GCCTGTGAAGAAGGAGGTATGT 59.763 50.000 0.00 0.00 36.91 2.29
3030 3051 9.909043 GTTCGTTTTATGCATTTGTTTTAGTTT 57.091 25.926 3.54 0.00 0.00 2.66
3077 3098 8.593945 ATTTGTCCAATATTTCTAGCTTCCAA 57.406 30.769 0.00 0.00 0.00 3.53
3078 3099 7.630242 TTGTCCAATATTTCTAGCTTCCAAG 57.370 36.000 0.00 0.00 0.00 3.61
3079 3100 6.957631 TGTCCAATATTTCTAGCTTCCAAGA 58.042 36.000 0.00 0.00 0.00 3.02
3081 3102 8.055181 TGTCCAATATTTCTAGCTTCCAAGATT 58.945 33.333 0.00 0.00 0.00 2.40
3082 3103 8.563732 GTCCAATATTTCTAGCTTCCAAGATTC 58.436 37.037 0.00 0.00 0.00 2.52
3084 3105 9.129532 CCAATATTTCTAGCTTCCAAGATTCTT 57.870 33.333 0.00 0.00 0.00 2.52
3126 3147 5.124297 CAGTCTTACATCAATCACATTGCCA 59.876 40.000 0.00 0.00 40.05 4.92
3127 3148 5.711506 AGTCTTACATCAATCACATTGCCAA 59.288 36.000 0.00 0.00 40.05 4.52
3128 3149 5.801947 GTCTTACATCAATCACATTGCCAAC 59.198 40.000 0.00 0.00 40.05 3.77
3129 3150 3.220507 ACATCAATCACATTGCCAACG 57.779 42.857 0.00 0.00 40.05 4.10
3130 3151 2.557924 ACATCAATCACATTGCCAACGT 59.442 40.909 0.00 0.00 40.05 3.99
3131 3152 3.005684 ACATCAATCACATTGCCAACGTT 59.994 39.130 0.00 0.00 40.05 3.99
3132 3153 3.281341 TCAATCACATTGCCAACGTTC 57.719 42.857 0.00 0.00 40.05 3.95
3133 3154 2.884012 TCAATCACATTGCCAACGTTCT 59.116 40.909 0.00 0.00 40.05 3.01
3134 3155 3.317711 TCAATCACATTGCCAACGTTCTT 59.682 39.130 0.00 0.00 40.05 2.52
3135 3156 4.517075 TCAATCACATTGCCAACGTTCTTA 59.483 37.500 0.00 0.00 40.05 2.10
3136 3157 5.182950 TCAATCACATTGCCAACGTTCTTAT 59.817 36.000 0.00 0.00 40.05 1.73
3137 3158 6.372937 TCAATCACATTGCCAACGTTCTTATA 59.627 34.615 0.00 0.00 40.05 0.98
3167 3188 6.030228 GTCTGTTCTTATATGCTGTTTTGGC 58.970 40.000 0.00 0.00 0.00 4.52
3184 3205 2.752030 TGGCTAGCTGTGTCTCCTAAT 58.248 47.619 15.72 0.00 0.00 1.73
3213 3234 2.551270 TGTCTCCTTTGGTAGGCTGAT 58.449 47.619 0.00 0.00 44.37 2.90
3348 3369 7.560368 TCCTTGATGTTTTTGTTACCAACATT 58.440 30.769 6.25 0.00 40.46 2.71
3437 3458 7.337689 ACAGTTTCAGATATTTGAGCATTAGCA 59.662 33.333 0.00 0.00 45.49 3.49
3479 3500 2.436824 GCTGGTCCTTTCGGGCTC 60.437 66.667 0.00 0.00 34.49 4.70
3526 3547 5.801350 TTTTAGTTGCTCTGAATGATCCG 57.199 39.130 0.00 0.00 0.00 4.18
3595 3616 3.701241 TGTTTTGGCAGTTCGATTTCAC 58.299 40.909 0.00 0.00 0.00 3.18
3596 3617 3.129462 TGTTTTGGCAGTTCGATTTCACA 59.871 39.130 0.00 0.00 0.00 3.58
3654 3675 9.322773 GGTAGTACTTCCTATTGGTCATAAAAC 57.677 37.037 11.11 0.00 34.23 2.43
3661 3682 5.424252 TCCTATTGGTCATAAAACTCCTCGT 59.576 40.000 0.00 0.00 34.23 4.18
3672 3693 1.339097 ACTCCTCGTTGGCTTACTGT 58.661 50.000 0.00 0.00 35.26 3.55
3711 3735 2.425592 GTTGCCCCTTGGTTTGCC 59.574 61.111 0.00 0.00 0.00 4.52
3785 3812 9.233232 GTGCCGAACATTTTCTTTATAATTAGG 57.767 33.333 0.00 0.00 0.00 2.69
3787 3814 7.381408 GCCGAACATTTTCTTTATAATTAGGGC 59.619 37.037 0.00 0.00 0.00 5.19
3788 3815 7.589954 CCGAACATTTTCTTTATAATTAGGGCG 59.410 37.037 0.00 0.00 0.00 6.13
3789 3816 8.339714 CGAACATTTTCTTTATAATTAGGGCGA 58.660 33.333 0.00 0.00 0.00 5.54
3921 3984 7.065443 GTCAAACCGTTAAAGCACCTATATTCT 59.935 37.037 0.00 0.00 0.00 2.40
3944 4007 3.308866 GTGGCTGTATACGGTCAAATCAC 59.691 47.826 20.30 4.44 38.75 3.06
3945 4008 2.870411 GGCTGTATACGGTCAAATCACC 59.130 50.000 11.51 0.00 0.00 4.02
3947 4010 4.202182 GGCTGTATACGGTCAAATCACCTA 60.202 45.833 11.51 0.00 33.77 3.08
3949 4012 5.462398 GCTGTATACGGTCAAATCACCTAAG 59.538 44.000 13.23 0.00 33.77 2.18
3950 4013 6.534475 TGTATACGGTCAAATCACCTAAGT 57.466 37.500 0.00 0.00 33.77 2.24
3951 4014 6.334989 TGTATACGGTCAAATCACCTAAGTG 58.665 40.000 0.00 0.00 46.00 3.16
4014 4079 5.985781 AGTTGTACTAACAAATTGTCAGCG 58.014 37.500 0.00 0.00 46.84 5.18
4051 4117 4.610605 TTCGGGATGAACAGTAAACTCA 57.389 40.909 0.00 0.00 0.00 3.41
4052 4118 4.819105 TCGGGATGAACAGTAAACTCAT 57.181 40.909 0.00 0.00 32.49 2.90
4054 4120 5.902681 TCGGGATGAACAGTAAACTCATAG 58.097 41.667 0.00 0.00 29.97 2.23
4200 4271 4.648762 TCACTCCAAGATGCCTTTGAAAAA 59.351 37.500 0.00 0.00 0.00 1.94
4226 4297 7.967890 ACATTTTTGGAAAAATCATCACTCC 57.032 32.000 7.04 0.00 44.38 3.85
4227 4298 7.507829 ACATTTTTGGAAAAATCATCACTCCA 58.492 30.769 7.04 0.00 44.38 3.86
4228 4299 7.992033 ACATTTTTGGAAAAATCATCACTCCAA 59.008 29.630 7.04 0.00 44.38 3.53
4229 4300 8.500773 CATTTTTGGAAAAATCATCACTCCAAG 58.499 33.333 7.04 0.00 44.38 3.61
4230 4301 6.975196 TTTGGAAAAATCATCACTCCAAGA 57.025 33.333 2.41 0.00 44.68 3.02
4231 4302 7.543359 TTTGGAAAAATCATCACTCCAAGAT 57.457 32.000 2.41 0.00 44.68 2.40
4232 4303 6.519679 TGGAAAAATCATCACTCCAAGATG 57.480 37.500 0.00 0.00 43.25 2.90
4233 4304 5.105635 TGGAAAAATCATCACTCCAAGATGC 60.106 40.000 0.00 0.00 41.98 3.91
4234 4305 4.996788 AAAATCATCACTCCAAGATGCC 57.003 40.909 0.00 0.00 41.98 4.40
4235 4306 3.947612 AATCATCACTCCAAGATGCCT 57.052 42.857 0.00 0.00 41.98 4.75
4236 4307 3.947612 ATCATCACTCCAAGATGCCTT 57.052 42.857 0.00 0.00 41.98 4.35
4237 4308 3.726557 TCATCACTCCAAGATGCCTTT 57.273 42.857 0.00 0.00 41.98 3.11
4238 4309 3.349927 TCATCACTCCAAGATGCCTTTG 58.650 45.455 0.00 0.00 41.98 2.77
4239 4310 3.009363 TCATCACTCCAAGATGCCTTTGA 59.991 43.478 0.00 0.00 41.98 2.69
4240 4311 3.507162 TCACTCCAAGATGCCTTTGAA 57.493 42.857 0.00 0.00 0.00 2.69
4241 4312 3.831323 TCACTCCAAGATGCCTTTGAAA 58.169 40.909 0.00 0.00 0.00 2.69
4242 4313 4.214310 TCACTCCAAGATGCCTTTGAAAA 58.786 39.130 0.00 0.00 0.00 2.29
4243 4314 4.834496 TCACTCCAAGATGCCTTTGAAAAT 59.166 37.500 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 7.174946 ACGGAAAGAAAGAATGTTATCATGTGT 59.825 33.333 0.00 0.00 34.19 3.72
94 95 3.824443 GGAAAATTCAGGGACGGAAAGAA 59.176 43.478 0.00 0.00 46.79 2.52
102 103 6.368805 AGAATATGGAGGAAAATTCAGGGAC 58.631 40.000 0.00 0.00 32.04 4.46
200 201 4.020218 CCTCCAAGTGAGTAATGAGACCAA 60.020 45.833 0.00 0.00 39.65 3.67
429 433 5.394562 AAGAGAATTGAGGGGATAAAGGG 57.605 43.478 0.00 0.00 0.00 3.95
494 498 9.638239 TTGTCACCTTATCTTTTTATCATTTGC 57.362 29.630 0.00 0.00 0.00 3.68
570 574 8.657074 TTATATCGAGTTAAAGTCAACCATGG 57.343 34.615 11.19 11.19 0.00 3.66
597 601 7.212976 TGCAAAGCACCTCAAACATAATAAAA 58.787 30.769 0.00 0.00 31.71 1.52
598 602 6.753180 TGCAAAGCACCTCAAACATAATAAA 58.247 32.000 0.00 0.00 31.71 1.40
599 603 6.338214 TGCAAAGCACCTCAAACATAATAA 57.662 33.333 0.00 0.00 31.71 1.40
600 604 5.973899 TGCAAAGCACCTCAAACATAATA 57.026 34.783 0.00 0.00 31.71 0.98
601 605 4.870123 TGCAAAGCACCTCAAACATAAT 57.130 36.364 0.00 0.00 31.71 1.28
614 618 0.749818 TTCACCGGAAGTGCAAAGCA 60.750 50.000 9.46 0.00 46.81 3.91
615 619 0.317854 GTTCACCGGAAGTGCAAAGC 60.318 55.000 9.46 0.00 46.81 3.51
616 620 1.308998 AGTTCACCGGAAGTGCAAAG 58.691 50.000 9.46 0.00 46.81 2.77
617 621 1.757682 AAGTTCACCGGAAGTGCAAA 58.242 45.000 9.46 0.00 46.81 3.68
618 622 1.403679 CAAAGTTCACCGGAAGTGCAA 59.596 47.619 9.46 0.00 46.81 4.08
619 623 1.021202 CAAAGTTCACCGGAAGTGCA 58.979 50.000 9.46 0.00 46.81 4.57
620 624 1.305201 TCAAAGTTCACCGGAAGTGC 58.695 50.000 9.46 0.00 46.81 4.40
622 626 6.708285 AGTATTATCAAAGTTCACCGGAAGT 58.292 36.000 9.46 0.00 38.32 3.01
623 627 7.549488 AGAAGTATTATCAAAGTTCACCGGAAG 59.451 37.037 9.46 0.00 32.62 3.46
624 628 7.391620 AGAAGTATTATCAAAGTTCACCGGAA 58.608 34.615 9.46 0.00 0.00 4.30
625 629 6.942976 AGAAGTATTATCAAAGTTCACCGGA 58.057 36.000 9.46 0.00 0.00 5.14
626 630 8.888579 ATAGAAGTATTATCAAAGTTCACCGG 57.111 34.615 0.00 0.00 0.00 5.28
667 671 9.337396 AGCCATCGTGATGACTTTATTTATTTA 57.663 29.630 11.35 0.00 41.20 1.40
668 672 8.225603 AGCCATCGTGATGACTTTATTTATTT 57.774 30.769 11.35 0.00 41.20 1.40
669 673 7.807977 AGCCATCGTGATGACTTTATTTATT 57.192 32.000 11.35 0.00 41.20 1.40
670 674 7.807977 AAGCCATCGTGATGACTTTATTTAT 57.192 32.000 11.35 0.00 38.13 1.40
671 675 7.201696 GGAAAGCCATCGTGATGACTTTATTTA 60.202 37.037 19.63 0.00 46.56 1.40
672 676 6.404734 GGAAAGCCATCGTGATGACTTTATTT 60.405 38.462 19.63 3.11 46.56 1.40
673 677 5.066505 GGAAAGCCATCGTGATGACTTTATT 59.933 40.000 19.63 3.42 46.56 1.40
674 678 4.576463 GGAAAGCCATCGTGATGACTTTAT 59.424 41.667 19.63 4.03 46.56 1.40
675 679 3.938963 GGAAAGCCATCGTGATGACTTTA 59.061 43.478 19.63 0.00 46.56 1.85
677 681 2.359900 GGAAAGCCATCGTGATGACTT 58.640 47.619 11.35 8.39 42.12 3.01
678 682 1.407437 GGGAAAGCCATCGTGATGACT 60.407 52.381 11.35 1.98 41.20 3.41
679 683 1.017387 GGGAAAGCCATCGTGATGAC 58.983 55.000 11.35 0.00 41.20 3.06
680 684 0.107214 GGGGAAAGCCATCGTGATGA 60.107 55.000 11.35 0.00 41.20 2.92
681 685 0.394216 TGGGGAAAGCCATCGTGATG 60.394 55.000 2.81 2.81 38.51 3.07
682 686 0.331278 TTGGGGAAAGCCATCGTGAT 59.669 50.000 0.00 0.00 35.15 3.06
683 687 0.111446 TTTGGGGAAAGCCATCGTGA 59.889 50.000 0.00 0.00 35.15 4.35
684 688 0.965439 TTTTGGGGAAAGCCATCGTG 59.035 50.000 0.00 0.00 35.15 4.35
685 689 1.203001 TCTTTTGGGGAAAGCCATCGT 60.203 47.619 0.00 0.00 43.61 3.73
686 690 1.544724 TCTTTTGGGGAAAGCCATCG 58.455 50.000 0.00 0.00 43.61 3.84
687 691 4.536765 TCTATCTTTTGGGGAAAGCCATC 58.463 43.478 0.00 0.00 43.61 3.51
688 692 4.608170 TCTATCTTTTGGGGAAAGCCAT 57.392 40.909 0.00 0.00 43.61 4.40
689 693 4.396357 TTCTATCTTTTGGGGAAAGCCA 57.604 40.909 0.00 0.00 43.61 4.75
690 694 5.480422 TCTTTTCTATCTTTTGGGGAAAGCC 59.520 40.000 0.00 0.00 43.61 4.35
691 695 6.590234 TCTTTTCTATCTTTTGGGGAAAGC 57.410 37.500 0.00 0.00 43.61 3.51
692 696 8.860088 TCTTTCTTTTCTATCTTTTGGGGAAAG 58.140 33.333 0.00 0.00 44.99 2.62
693 697 8.776061 TCTTTCTTTTCTATCTTTTGGGGAAA 57.224 30.769 0.00 0.00 0.00 3.13
694 698 8.956446 ATCTTTCTTTTCTATCTTTTGGGGAA 57.044 30.769 0.00 0.00 0.00 3.97
695 699 8.956446 AATCTTTCTTTTCTATCTTTTGGGGA 57.044 30.769 0.00 0.00 0.00 4.81
696 700 9.428097 CAAATCTTTCTTTTCTATCTTTTGGGG 57.572 33.333 0.00 0.00 0.00 4.96
697 701 9.987272 ACAAATCTTTCTTTTCTATCTTTTGGG 57.013 29.630 0.00 0.00 0.00 4.12
706 710 9.816354 CCCTCAAAAACAAATCTTTCTTTTCTA 57.184 29.630 0.00 0.00 0.00 2.10
707 711 7.770433 CCCCTCAAAAACAAATCTTTCTTTTCT 59.230 33.333 0.00 0.00 0.00 2.52
708 712 7.552687 ACCCCTCAAAAACAAATCTTTCTTTTC 59.447 33.333 0.00 0.00 0.00 2.29
709 713 7.402054 ACCCCTCAAAAACAAATCTTTCTTTT 58.598 30.769 0.00 0.00 0.00 2.27
710 714 6.957631 ACCCCTCAAAAACAAATCTTTCTTT 58.042 32.000 0.00 0.00 0.00 2.52
711 715 6.560003 ACCCCTCAAAAACAAATCTTTCTT 57.440 33.333 0.00 0.00 0.00 2.52
712 716 6.609616 TGTACCCCTCAAAAACAAATCTTTCT 59.390 34.615 0.00 0.00 0.00 2.52
713 717 6.811954 TGTACCCCTCAAAAACAAATCTTTC 58.188 36.000 0.00 0.00 0.00 2.62
714 718 6.800072 TGTACCCCTCAAAAACAAATCTTT 57.200 33.333 0.00 0.00 0.00 2.52
715 719 6.800072 TTGTACCCCTCAAAAACAAATCTT 57.200 33.333 0.00 0.00 0.00 2.40
716 720 6.800072 TTTGTACCCCTCAAAAACAAATCT 57.200 33.333 0.00 0.00 35.69 2.40
717 721 7.851387 TTTTTGTACCCCTCAAAAACAAATC 57.149 32.000 10.95 0.00 44.37 2.17
738 742 7.357951 TCTTTGCGTTTCATCTTTTGTTTTT 57.642 28.000 0.00 0.00 0.00 1.94
739 743 6.035975 CCTCTTTGCGTTTCATCTTTTGTTTT 59.964 34.615 0.00 0.00 0.00 2.43
740 744 5.519927 CCTCTTTGCGTTTCATCTTTTGTTT 59.480 36.000 0.00 0.00 0.00 2.83
741 745 5.043248 CCTCTTTGCGTTTCATCTTTTGTT 58.957 37.500 0.00 0.00 0.00 2.83
742 746 4.338118 TCCTCTTTGCGTTTCATCTTTTGT 59.662 37.500 0.00 0.00 0.00 2.83
743 747 4.858935 TCCTCTTTGCGTTTCATCTTTTG 58.141 39.130 0.00 0.00 0.00 2.44
744 748 5.514274 TTCCTCTTTGCGTTTCATCTTTT 57.486 34.783 0.00 0.00 0.00 2.27
745 749 5.514274 TTTCCTCTTTGCGTTTCATCTTT 57.486 34.783 0.00 0.00 0.00 2.52
746 750 5.281727 GTTTTCCTCTTTGCGTTTCATCTT 58.718 37.500 0.00 0.00 0.00 2.40
747 751 4.554723 CGTTTTCCTCTTTGCGTTTCATCT 60.555 41.667 0.00 0.00 0.00 2.90
748 752 3.664025 CGTTTTCCTCTTTGCGTTTCATC 59.336 43.478 0.00 0.00 0.00 2.92
749 753 3.314080 TCGTTTTCCTCTTTGCGTTTCAT 59.686 39.130 0.00 0.00 0.00 2.57
750 754 2.678836 TCGTTTTCCTCTTTGCGTTTCA 59.321 40.909 0.00 0.00 0.00 2.69
751 755 3.001939 TCTCGTTTTCCTCTTTGCGTTTC 59.998 43.478 0.00 0.00 0.00 2.78
752 756 2.940410 TCTCGTTTTCCTCTTTGCGTTT 59.060 40.909 0.00 0.00 0.00 3.60
753 757 2.544267 CTCTCGTTTTCCTCTTTGCGTT 59.456 45.455 0.00 0.00 0.00 4.84
754 758 2.135933 CTCTCGTTTTCCTCTTTGCGT 58.864 47.619 0.00 0.00 0.00 5.24
755 759 2.404215 TCTCTCGTTTTCCTCTTTGCG 58.596 47.619 0.00 0.00 0.00 4.85
756 760 3.654414 TCTCTCTCGTTTTCCTCTTTGC 58.346 45.455 0.00 0.00 0.00 3.68
757 761 6.604735 TTTTCTCTCTCGTTTTCCTCTTTG 57.395 37.500 0.00 0.00 0.00 2.77
758 762 6.261158 CCTTTTTCTCTCTCGTTTTCCTCTTT 59.739 38.462 0.00 0.00 0.00 2.52
759 763 5.760743 CCTTTTTCTCTCTCGTTTTCCTCTT 59.239 40.000 0.00 0.00 0.00 2.85
760 764 5.301555 CCTTTTTCTCTCTCGTTTTCCTCT 58.698 41.667 0.00 0.00 0.00 3.69
761 765 4.083749 GCCTTTTTCTCTCTCGTTTTCCTC 60.084 45.833 0.00 0.00 0.00 3.71
762 766 3.815962 GCCTTTTTCTCTCTCGTTTTCCT 59.184 43.478 0.00 0.00 0.00 3.36
763 767 3.058155 GGCCTTTTTCTCTCTCGTTTTCC 60.058 47.826 0.00 0.00 0.00 3.13
764 768 3.364068 CGGCCTTTTTCTCTCTCGTTTTC 60.364 47.826 0.00 0.00 0.00 2.29
765 769 2.548480 CGGCCTTTTTCTCTCTCGTTTT 59.452 45.455 0.00 0.00 0.00 2.43
766 770 2.143925 CGGCCTTTTTCTCTCTCGTTT 58.856 47.619 0.00 0.00 0.00 3.60
767 771 1.608283 CCGGCCTTTTTCTCTCTCGTT 60.608 52.381 0.00 0.00 0.00 3.85
768 772 0.037232 CCGGCCTTTTTCTCTCTCGT 60.037 55.000 0.00 0.00 0.00 4.18
769 773 0.741221 CCCGGCCTTTTTCTCTCTCG 60.741 60.000 0.00 0.00 0.00 4.04
770 774 1.027255 GCCCGGCCTTTTTCTCTCTC 61.027 60.000 0.00 0.00 0.00 3.20
771 775 1.002011 GCCCGGCCTTTTTCTCTCT 60.002 57.895 0.00 0.00 0.00 3.10
772 776 2.046864 GGCCCGGCCTTTTTCTCTC 61.047 63.158 22.31 0.00 46.69 3.20
773 777 2.035783 GGCCCGGCCTTTTTCTCT 59.964 61.111 22.31 0.00 46.69 3.10
805 809 9.722056 GCGTATTTGGATTATCATTATGGAATC 57.278 33.333 10.33 10.33 0.00 2.52
806 810 8.397906 CGCGTATTTGGATTATCATTATGGAAT 58.602 33.333 0.00 0.00 0.00 3.01
807 811 7.604545 TCGCGTATTTGGATTATCATTATGGAA 59.395 33.333 5.77 0.00 0.00 3.53
808 812 7.100409 TCGCGTATTTGGATTATCATTATGGA 58.900 34.615 5.77 0.00 0.00 3.41
809 813 7.277760 TCTCGCGTATTTGGATTATCATTATGG 59.722 37.037 5.77 0.00 0.00 2.74
810 814 8.110612 GTCTCGCGTATTTGGATTATCATTATG 58.889 37.037 5.77 0.00 0.00 1.90
811 815 7.817478 TGTCTCGCGTATTTGGATTATCATTAT 59.183 33.333 5.77 0.00 0.00 1.28
812 816 7.149307 TGTCTCGCGTATTTGGATTATCATTA 58.851 34.615 5.77 0.00 0.00 1.90
813 817 5.989168 TGTCTCGCGTATTTGGATTATCATT 59.011 36.000 5.77 0.00 0.00 2.57
814 818 5.538118 TGTCTCGCGTATTTGGATTATCAT 58.462 37.500 5.77 0.00 0.00 2.45
815 819 4.939271 TGTCTCGCGTATTTGGATTATCA 58.061 39.130 5.77 0.00 0.00 2.15
816 820 6.299604 CAATGTCTCGCGTATTTGGATTATC 58.700 40.000 5.77 0.00 0.00 1.75
817 821 5.179368 CCAATGTCTCGCGTATTTGGATTAT 59.821 40.000 17.63 3.03 0.00 1.28
818 822 4.509970 CCAATGTCTCGCGTATTTGGATTA 59.490 41.667 17.63 0.00 0.00 1.75
819 823 3.312421 CCAATGTCTCGCGTATTTGGATT 59.688 43.478 17.63 3.51 0.00 3.01
820 824 2.872245 CCAATGTCTCGCGTATTTGGAT 59.128 45.455 17.63 0.00 0.00 3.41
821 825 2.276201 CCAATGTCTCGCGTATTTGGA 58.724 47.619 17.63 3.07 0.00 3.53
822 826 1.330521 CCCAATGTCTCGCGTATTTGG 59.669 52.381 5.77 13.06 0.00 3.28
823 827 1.268032 GCCCAATGTCTCGCGTATTTG 60.268 52.381 5.77 4.65 0.00 2.32
824 828 1.014352 GCCCAATGTCTCGCGTATTT 58.986 50.000 5.77 0.00 0.00 1.40
825 829 0.814010 GGCCCAATGTCTCGCGTATT 60.814 55.000 5.77 0.31 0.00 1.89
826 830 1.227556 GGCCCAATGTCTCGCGTAT 60.228 57.895 5.77 0.00 0.00 3.06
827 831 2.185867 GGCCCAATGTCTCGCGTA 59.814 61.111 5.77 0.00 0.00 4.42
829 833 3.709880 TACGGCCCAATGTCTCGCG 62.710 63.158 0.00 0.00 0.00 5.87
830 834 1.429148 CTTACGGCCCAATGTCTCGC 61.429 60.000 0.00 0.00 0.00 5.03
1027 1033 1.065926 CAGCAGGCAGAGGATTGTACA 60.066 52.381 0.00 0.00 0.00 2.90
1083 1089 0.456312 GAGTACTTCACCTGCGACGG 60.456 60.000 0.00 0.00 0.00 4.79
1145 1151 4.664688 AAAAATCACTGAGGGGACAGAT 57.335 40.909 0.00 0.00 40.63 2.90
1201 1208 3.608241 GCACGAAACATCGGATCAAAACA 60.608 43.478 3.12 0.00 37.45 2.83
1322 1329 2.499197 TCAATCAACCAGTAGCGCAAA 58.501 42.857 11.47 0.00 0.00 3.68
1380 1387 4.189231 CACTCCCTAACCCTAAATCAACG 58.811 47.826 0.00 0.00 0.00 4.10
1428 1435 9.503399 ACCTTTACTCTTTAGGTTTATCACAAG 57.497 33.333 0.00 0.00 39.19 3.16
1463 1470 2.608752 GGGAACTGTGCATGCAAAGAAG 60.609 50.000 38.53 26.03 34.97 2.85
1692 1702 9.995003 ATTAGCTACAGAAATGAGAAGGATAAG 57.005 33.333 0.00 0.00 0.00 1.73
1713 1723 5.574443 GGACTTCAAAATTGCAGACATTAGC 59.426 40.000 0.00 0.00 0.00 3.09
1868 1878 2.626840 GGGCAAAGATCACTGAGACTC 58.373 52.381 0.00 0.00 0.00 3.36
1904 1915 5.296283 CAGAGCCAGGATCTTCTAAACAATG 59.704 44.000 3.79 0.00 0.00 2.82
1939 1955 8.368668 AGAATCTTCTAAACGATTAATCCCGAT 58.631 33.333 9.87 0.00 35.34 4.18
1982 1998 6.201556 TCACACAACGTAAACGAAACTATC 57.798 37.500 9.86 0.00 43.02 2.08
1996 2012 3.924073 TGACGGAAAGATATCACACAACG 59.076 43.478 5.32 4.49 0.00 4.10
2008 2026 3.936372 AGAAACGAGATGACGGAAAGA 57.064 42.857 0.00 0.00 37.61 2.52
2069 2087 4.760683 CAAGCTAACAAAAATTTGGCGTG 58.239 39.130 10.38 8.41 42.34 5.34
2085 2103 9.672673 ACAGAAAAGAATAAATAGAGCAAGCTA 57.327 29.630 0.00 0.00 0.00 3.32
2100 2118 7.390718 GGTATACACACCTCAACAGAAAAGAAT 59.609 37.037 5.01 0.00 35.55 2.40
2118 2136 3.941483 AGTGAGCAATGCTTGGTATACAC 59.059 43.478 9.91 10.88 42.23 2.90
2144 2162 6.725834 ACATGGGATATTTTTCACCAAGTTCT 59.274 34.615 0.00 0.00 34.45 3.01
2210 2228 1.200020 GCCAACAGACCATTTCCTTCG 59.800 52.381 0.00 0.00 0.00 3.79
2316 2334 5.525745 TCAATCTAGCACAAAAACGACAAGA 59.474 36.000 0.00 0.00 0.00 3.02
2320 2338 7.962918 ACATTATCAATCTAGCACAAAAACGAC 59.037 33.333 0.00 0.00 0.00 4.34
2321 2339 8.039603 ACATTATCAATCTAGCACAAAAACGA 57.960 30.769 0.00 0.00 0.00 3.85
2322 2340 8.577939 CAACATTATCAATCTAGCACAAAAACG 58.422 33.333 0.00 0.00 0.00 3.60
2376 2394 5.815740 AGTTAGCGAAACAAACAAGAGAAGA 59.184 36.000 7.58 0.00 40.83 2.87
2377 2395 6.049263 AGTTAGCGAAACAAACAAGAGAAG 57.951 37.500 7.58 0.00 40.83 2.85
2378 2396 6.255215 CAAGTTAGCGAAACAAACAAGAGAA 58.745 36.000 7.58 0.00 40.83 2.87
2379 2397 5.729454 GCAAGTTAGCGAAACAAACAAGAGA 60.729 40.000 7.58 0.00 40.83 3.10
2380 2398 4.437820 GCAAGTTAGCGAAACAAACAAGAG 59.562 41.667 7.58 0.00 40.83 2.85
2659 2680 4.140536 AGAAGGATAAAATAGCAGCAGCC 58.859 43.478 0.00 0.00 43.56 4.85
2660 2681 4.818546 TGAGAAGGATAAAATAGCAGCAGC 59.181 41.667 0.00 0.00 42.56 5.25
2661 2682 7.444792 AGAATGAGAAGGATAAAATAGCAGCAG 59.555 37.037 0.00 0.00 0.00 4.24
2709 2730 8.421002 AGTAAGTTAACCAAAACAAATGCTCAT 58.579 29.630 0.88 0.00 0.00 2.90
2734 2755 7.254319 CCTTTAACCTATGTACGCAACACATAG 60.254 40.741 16.74 16.74 42.09 2.23
2842 2863 1.556564 ACTTACGATTGATGCGTCCG 58.443 50.000 2.83 2.40 42.62 4.79
3030 3051 7.775053 AATTTACAAGTTCCAGATAGGCAAA 57.225 32.000 0.00 0.00 37.29 3.68
3075 3096 8.783833 TTAGAAGGTGAATCTGAAGAATCTTG 57.216 34.615 0.00 0.00 0.00 3.02
3077 3098 8.766476 TGATTAGAAGGTGAATCTGAAGAATCT 58.234 33.333 0.00 0.00 33.92 2.40
3078 3099 8.954950 TGATTAGAAGGTGAATCTGAAGAATC 57.045 34.615 0.00 0.00 33.92 2.52
3079 3100 8.547173 ACTGATTAGAAGGTGAATCTGAAGAAT 58.453 33.333 8.05 0.00 35.63 2.40
3081 3102 7.398618 AGACTGATTAGAAGGTGAATCTGAAGA 59.601 37.037 8.05 0.00 35.63 2.87
3082 3103 7.555087 AGACTGATTAGAAGGTGAATCTGAAG 58.445 38.462 8.05 0.00 35.63 3.02
3084 3105 7.487822 AAGACTGATTAGAAGGTGAATCTGA 57.512 36.000 8.05 0.00 35.63 3.27
3085 3106 8.253810 TGTAAGACTGATTAGAAGGTGAATCTG 58.746 37.037 0.00 0.00 37.17 2.90
3126 3147 6.874134 AGAACAGACAGCATTATAAGAACGTT 59.126 34.615 0.00 0.00 0.00 3.99
3127 3148 6.398918 AGAACAGACAGCATTATAAGAACGT 58.601 36.000 0.00 0.00 0.00 3.99
3128 3149 6.893958 AGAACAGACAGCATTATAAGAACG 57.106 37.500 0.00 0.00 0.00 3.95
3134 3155 9.428097 CAGCATATAAGAACAGACAGCATTATA 57.572 33.333 0.00 0.00 0.00 0.98
3135 3156 7.935755 ACAGCATATAAGAACAGACAGCATTAT 59.064 33.333 0.00 0.00 0.00 1.28
3136 3157 7.275183 ACAGCATATAAGAACAGACAGCATTA 58.725 34.615 0.00 0.00 0.00 1.90
3137 3158 6.118170 ACAGCATATAAGAACAGACAGCATT 58.882 36.000 0.00 0.00 0.00 3.56
3155 3176 1.542915 CACAGCTAGCCAAAACAGCAT 59.457 47.619 12.13 0.00 37.78 3.79
3167 3188 3.808466 TGCATTAGGAGACACAGCTAG 57.192 47.619 0.00 0.00 0.00 3.42
3213 3234 1.372004 CCTTGGTGCGACGACGTTA 60.372 57.895 9.33 0.00 41.98 3.18
3253 3274 2.019249 CTGTTGGACGAATGCATCCAT 58.981 47.619 7.58 0.00 44.49 3.41
3257 3278 2.479566 AGACTGTTGGACGAATGCAT 57.520 45.000 0.00 0.00 0.00 3.96
3271 3292 8.138712 ACTTGAGAAGAACTACAACTAAGACTG 58.861 37.037 0.00 0.00 0.00 3.51
3273 3294 9.396938 GTACTTGAGAAGAACTACAACTAAGAC 57.603 37.037 0.00 0.00 0.00 3.01
3348 3369 7.094377 GCATCAACCTTAACAAATCCTTACTCA 60.094 37.037 0.00 0.00 0.00 3.41
3638 3659 5.671493 ACGAGGAGTTTTATGACCAATAGG 58.329 41.667 0.00 0.00 42.21 2.57
3654 3675 2.457366 AACAGTAAGCCAACGAGGAG 57.543 50.000 2.86 0.00 41.22 3.69
3661 3682 6.404074 CCAAAAATTGCAAAACAGTAAGCCAA 60.404 34.615 1.71 0.00 0.00 4.52
3699 3720 2.597217 TCAGCGGCAAACCAAGGG 60.597 61.111 1.45 0.00 34.57 3.95
3711 3735 1.069636 GCAGGAACAGAAAACTCAGCG 60.070 52.381 0.00 0.00 0.00 5.18
3714 3738 2.092429 AGTGGCAGGAACAGAAAACTCA 60.092 45.455 0.00 0.00 0.00 3.41
3778 3805 5.916318 TCGGTAAAAGATTCGCCCTAATTA 58.084 37.500 0.00 0.00 0.00 1.40
3779 3806 4.773013 TCGGTAAAAGATTCGCCCTAATT 58.227 39.130 0.00 0.00 0.00 1.40
3780 3807 4.411256 TCGGTAAAAGATTCGCCCTAAT 57.589 40.909 0.00 0.00 0.00 1.73
3781 3808 3.891422 TCGGTAAAAGATTCGCCCTAA 57.109 42.857 0.00 0.00 0.00 2.69
3782 3809 5.733620 ATATCGGTAAAAGATTCGCCCTA 57.266 39.130 0.00 0.00 0.00 3.53
3783 3810 4.618920 ATATCGGTAAAAGATTCGCCCT 57.381 40.909 0.00 0.00 0.00 5.19
3785 3812 4.024387 TGCAATATCGGTAAAAGATTCGCC 60.024 41.667 0.00 0.00 0.00 5.54
3787 3814 5.140177 GCTGCAATATCGGTAAAAGATTCG 58.860 41.667 0.00 0.00 0.00 3.34
3788 3815 5.008613 TGGCTGCAATATCGGTAAAAGATTC 59.991 40.000 0.50 0.00 0.00 2.52
3789 3816 4.887071 TGGCTGCAATATCGGTAAAAGATT 59.113 37.500 0.50 0.00 0.00 2.40
3790 3817 4.460263 TGGCTGCAATATCGGTAAAAGAT 58.540 39.130 0.50 0.00 0.00 2.40
3791 3818 3.876914 CTGGCTGCAATATCGGTAAAAGA 59.123 43.478 0.50 0.00 0.00 2.52
3826 3856 4.722700 AGGTCCATGCGCACCACC 62.723 66.667 14.90 19.15 34.80 4.61
3837 3867 1.448497 GAACACCGGTGAAGGTCCA 59.552 57.895 40.21 0.00 43.89 4.02
3911 3942 5.185249 CCGTATACAGCCACAGAATATAGGT 59.815 44.000 3.32 0.00 0.00 3.08
3921 3984 3.055747 TGATTTGACCGTATACAGCCACA 60.056 43.478 3.32 0.00 0.00 4.17
3944 4007 7.811236 TCGTTGTTTGTTCTACTATCACTTAGG 59.189 37.037 0.00 0.00 31.68 2.69
3945 4008 8.738199 TCGTTGTTTGTTCTACTATCACTTAG 57.262 34.615 0.00 0.00 0.00 2.18
3947 4010 7.709613 ACTTCGTTGTTTGTTCTACTATCACTT 59.290 33.333 0.00 0.00 0.00 3.16
3949 4012 7.404139 ACTTCGTTGTTTGTTCTACTATCAC 57.596 36.000 0.00 0.00 0.00 3.06
3950 4013 8.332464 CAAACTTCGTTGTTTGTTCTACTATCA 58.668 33.333 19.78 0.00 46.73 2.15
3951 4014 8.695355 CAAACTTCGTTGTTTGTTCTACTATC 57.305 34.615 19.78 0.00 46.73 2.08
4014 4079 2.412089 CCCGAACTTGTCTCGTCATTTC 59.588 50.000 0.00 0.00 34.46 2.17
4092 4158 8.704234 TCAAAAACTGTTGTCAATGTTTGTAAC 58.296 29.630 15.57 0.00 33.61 2.50
4143 4212 2.749621 GCCACCACTTCCAAGAATGTAG 59.250 50.000 0.00 0.00 0.00 2.74
4144 4213 2.107378 TGCCACCACTTCCAAGAATGTA 59.893 45.455 0.00 0.00 0.00 2.29
4200 4271 8.839343 GGAGTGATGATTTTTCCAAAAATGTTT 58.161 29.630 13.50 0.55 45.70 2.83
4213 4284 4.607239 AGGCATCTTGGAGTGATGATTTT 58.393 39.130 7.77 0.00 42.68 1.82
4214 4285 4.246712 AGGCATCTTGGAGTGATGATTT 57.753 40.909 7.77 0.00 42.68 2.17
4215 4286 3.947612 AGGCATCTTGGAGTGATGATT 57.052 42.857 7.77 0.00 42.68 2.57
4216 4287 3.947612 AAGGCATCTTGGAGTGATGAT 57.052 42.857 7.77 0.00 42.68 2.45
4217 4288 3.009363 TCAAAGGCATCTTGGAGTGATGA 59.991 43.478 7.77 0.00 42.68 2.92
4218 4289 3.349927 TCAAAGGCATCTTGGAGTGATG 58.650 45.455 0.00 0.00 42.86 3.07
4219 4290 3.726557 TCAAAGGCATCTTGGAGTGAT 57.273 42.857 0.00 0.00 32.75 3.06
4220 4291 3.507162 TTCAAAGGCATCTTGGAGTGA 57.493 42.857 0.00 0.00 34.65 3.41
4221 4292 4.589216 TTTTCAAAGGCATCTTGGAGTG 57.411 40.909 0.00 0.00 34.65 3.51


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

AutoCloner maintained by Alex Coulton.