Multiple sequence alignment - TraesCS4D01G079600

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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 TraesCS4D01G079600 chr4D 100.000 5719 0 0 1 5719 53763534 53757816 0.000000e+00 10562.0
1 TraesCS4D01G079600 chr4D 88.679 106 12 0 2797 2902 367828011 367827906 4.650000e-26 130.0
2 TraesCS4D01G079600 chr4D 87.500 72 3 1 540 611 53775492 53775427 1.710000e-10 78.7
3 TraesCS4D01G079600 chr4D 97.368 38 1 0 534 571 53771675 53771638 1.330000e-06 65.8
4 TraesCS4D01G079600 chr4A 95.635 4559 134 31 1198 5718 543366082 543370613 0.000000e+00 7256.0
5 TraesCS4D01G079600 chr4A 86.827 539 32 15 722 1245 543365426 543365940 2.990000e-157 566.0
6 TraesCS4D01G079600 chr4A 87.500 144 14 2 1292 1434 543365944 543366084 4.580000e-36 163.0
7 TraesCS4D01G079600 chr4A 85.333 150 15 7 3397 3542 84537355 84537501 1.280000e-31 148.0
8 TraesCS4D01G079600 chr4B 94.109 4515 173 32 1260 5718 78613805 78609328 0.000000e+00 6778.0
9 TraesCS4D01G079600 chr4B 83.099 426 23 18 728 1127 78614271 78613869 5.490000e-90 342.0
10 TraesCS4D01G079600 chr4B 89.912 228 19 4 280 505 604043935 604044160 2.020000e-74 291.0
11 TraesCS4D01G079600 chr4B 93.590 78 5 0 534 611 78620612 78620535 3.620000e-22 117.0
12 TraesCS4D01G079600 chr2D 85.588 791 89 14 2282 3047 547782834 547782044 0.000000e+00 806.0
13 TraesCS4D01G079600 chr2D 85.811 148 21 0 3394 3541 122703798 122703945 2.130000e-34 158.0
14 TraesCS4D01G079600 chr5A 87.087 635 62 10 2286 2901 11212982 11212349 0.000000e+00 701.0
15 TraesCS4D01G079600 chr5A 91.463 164 13 1 2745 2907 11733462 11733625 2.070000e-54 224.0
16 TraesCS4D01G079600 chr6A 86.533 646 61 12 2282 2901 490995184 490995829 0.000000e+00 688.0
17 TraesCS4D01G079600 chr6A 82.000 200 19 4 3081 3280 490995949 490996131 2.760000e-33 154.0
18 TraesCS4D01G079600 chr1D 88.509 409 42 4 2498 2902 233393136 233392729 1.850000e-134 490.0
19 TraesCS4D01G079600 chr1D 93.182 220 13 2 296 514 465118274 465118056 7.150000e-84 322.0
20 TraesCS4D01G079600 chr7A 95.968 248 10 0 1 248 30906516 30906763 2.480000e-108 403.0
21 TraesCS4D01G079600 chr7A 90.991 111 8 2 399 509 30907046 30907154 1.280000e-31 148.0
22 TraesCS4D01G079600 chr7B 95.161 248 12 0 1 248 597249550 597249797 5.370000e-105 392.0
23 TraesCS4D01G079600 chr7B 93.574 249 7 2 270 509 597250107 597250355 4.210000e-96 363.0
24 TraesCS4D01G079600 chr1B 90.435 230 18 4 280 507 422357596 422357369 3.350000e-77 300.0
25 TraesCS4D01G079600 chr1B 84.663 163 12 8 3390 3541 424538581 424538741 3.570000e-32 150.0
26 TraesCS4D01G079600 chr6D 89.496 238 19 6 280 515 186852192 186852425 4.330000e-76 296.0
27 TraesCS4D01G079600 chr3A 87.943 141 8 6 3404 3541 416307014 416307148 2.130000e-34 158.0
28 TraesCS4D01G079600 chr3D 88.060 134 9 3 47 179 533587130 533587003 9.920000e-33 152.0
29 TraesCS4D01G079600 chr3D 86.620 142 9 7 3404 3541 313816802 313816937 1.280000e-31 148.0
30 TraesCS4D01G079600 chr3D 86.861 137 8 7 3404 3533 365519356 365519223 1.660000e-30 145.0
31 TraesCS4D01G079600 chr3B 85.417 144 11 7 3404 3542 475993832 475993694 2.150000e-29 141.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G079600 chr4D 53757816 53763534 5718 True 10562.000000 10562 100.000000 1 5719 1 chr4D.!!$R1 5718
1 TraesCS4D01G079600 chr4A 543365426 543370613 5187 False 2661.666667 7256 89.987333 722 5718 3 chr4A.!!$F2 4996
2 TraesCS4D01G079600 chr4B 78609328 78614271 4943 True 3560.000000 6778 88.604000 728 5718 2 chr4B.!!$R2 4990
3 TraesCS4D01G079600 chr2D 547782044 547782834 790 True 806.000000 806 85.588000 2282 3047 1 chr2D.!!$R1 765
4 TraesCS4D01G079600 chr5A 11212349 11212982 633 True 701.000000 701 87.087000 2286 2901 1 chr5A.!!$R1 615
5 TraesCS4D01G079600 chr6A 490995184 490996131 947 False 421.000000 688 84.266500 2282 3280 2 chr6A.!!$F1 998
6 TraesCS4D01G079600 chr7A 30906516 30907154 638 False 275.500000 403 93.479500 1 509 2 chr7A.!!$F1 508
7 TraesCS4D01G079600 chr7B 597249550 597250355 805 False 377.500000 392 94.367500 1 509 2 chr7B.!!$F1 508

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
179 180 0.031585 AGTGCTCGTCGCTGTTGTAA 59.968 50.0 0.0 0.0 40.11 2.41 F
658 956 0.106819 ACGAGGATAGTACGTGCCCT 60.107 55.0 0.0 0.0 38.79 5.19 F
986 1304 0.244994 CGCTGTTGAGCCTGACTACT 59.755 55.0 0.0 0.0 42.91 2.57 F
1223 1547 0.454600 TTAGCTGTTCTAGGCGGTCG 59.545 55.0 0.0 0.0 0.00 4.79 F
1232 1556 0.459759 CTAGGCGGTCGTTTCTTCCC 60.460 60.0 0.0 0.0 0.00 3.97 F
1993 2554 0.565674 AGGGTGGGATTGGTTTGGTT 59.434 50.0 0.0 0.0 0.00 3.67 F
1996 2570 0.755686 GTGGGATTGGTTTGGTTGCA 59.244 50.0 0.0 0.0 0.00 4.08 F
3280 3888 0.323360 TCAATAGCCCCCACTTGTGC 60.323 55.0 0.0 0.0 0.00 4.57 F
3571 4182 2.795175 ATCTAGGTTGCGGACATACG 57.205 50.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1160 1484 0.322098 CCAACCAATACACGGCCAGA 60.322 55.000 2.24 0.00 0.00 3.86 R
1834 2394 0.537371 AAAGAACAACCTCAGCCCCG 60.537 55.000 0.00 0.00 0.00 5.73 R
1993 2554 1.497286 AGGAGTAAAGGTGGGTTTGCA 59.503 47.619 0.00 0.00 0.00 4.08 R
2107 2681 4.135306 TCTGTTGGCAAAAATGTACCGTA 58.865 39.130 0.00 0.00 0.00 4.02 R
2509 3097 4.639334 ACAGCAGAGCATATAACTGGATG 58.361 43.478 0.00 0.00 33.00 3.51 R
2893 3494 7.655732 AGTTGGTAATTAAATGTTGAAACTGGC 59.344 33.333 0.00 0.00 0.00 4.85 R
4299 4910 4.833478 AAAATAGGAGCTCTCTGCAGAA 57.167 40.909 18.85 8.05 45.94 3.02 R
4625 5238 1.305623 CTGGCCAGATGCTCCCTTT 59.694 57.895 29.88 0.00 40.92 3.11 R
5619 6245 3.685139 TTCTGGCTGAAGAACTACTGG 57.315 47.619 2.37 0.00 31.19 4.00 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
83 84 1.946081 TCACAGATGAAGCGCAACAAA 59.054 42.857 11.47 0.00 0.00 2.83
122 123 4.237724 TCGAGATAGTTGCACAACAAGAG 58.762 43.478 15.40 2.71 43.47 2.85
179 180 0.031585 AGTGCTCGTCGCTGTTGTAA 59.968 50.000 0.00 0.00 40.11 2.41
237 238 4.592936 CTCGTCGCCGTCGCCTAG 62.593 72.222 0.00 0.00 35.26 3.02
278 567 1.192146 CGTGAAGGAGAGGGGTTGGA 61.192 60.000 0.00 0.00 0.00 3.53
301 598 2.997897 GGAGGTGAGTGCGAGGGT 60.998 66.667 0.00 0.00 0.00 4.34
444 742 3.232213 ACATACTGAACGCGAGAATGT 57.768 42.857 15.93 10.51 0.00 2.71
451 749 2.745884 CGCGAGAATGTGGCCCAA 60.746 61.111 0.00 0.00 0.00 4.12
481 779 2.185310 GACCCGTGACATTCCAGCCT 62.185 60.000 0.00 0.00 0.00 4.58
492 790 0.538057 TTCCAGCCTGTTCCTGCAAG 60.538 55.000 0.00 0.00 0.00 4.01
509 807 2.100749 GCAAGCAAACACACCCTTAAGT 59.899 45.455 0.97 0.00 0.00 2.24
510 808 3.705604 CAAGCAAACACACCCTTAAGTG 58.294 45.455 0.97 0.00 43.65 3.16
511 809 3.290948 AGCAAACACACCCTTAAGTGA 57.709 42.857 0.97 0.00 40.34 3.41
512 810 2.949644 AGCAAACACACCCTTAAGTGAC 59.050 45.455 0.97 0.00 40.34 3.67
513 811 2.034179 GCAAACACACCCTTAAGTGACC 59.966 50.000 0.97 0.00 40.34 4.02
514 812 2.621526 CAAACACACCCTTAAGTGACCC 59.378 50.000 0.97 0.00 40.34 4.46
515 813 1.815757 ACACACCCTTAAGTGACCCT 58.184 50.000 0.97 0.00 40.34 4.34
516 814 2.980548 ACACACCCTTAAGTGACCCTA 58.019 47.619 0.97 0.00 40.34 3.53
517 815 2.636403 ACACACCCTTAAGTGACCCTAC 59.364 50.000 0.97 0.00 40.34 3.18
518 816 2.027469 CACACCCTTAAGTGACCCTACC 60.027 54.545 0.97 0.00 40.34 3.18
519 817 1.558294 CACCCTTAAGTGACCCTACCC 59.442 57.143 0.97 0.00 40.34 3.69
520 818 1.210538 CCCTTAAGTGACCCTACCCC 58.789 60.000 0.97 0.00 0.00 4.95
521 819 0.828677 CCTTAAGTGACCCTACCCCG 59.171 60.000 0.97 0.00 0.00 5.73
522 820 0.828677 CTTAAGTGACCCTACCCCGG 59.171 60.000 0.00 0.00 0.00 5.73
523 821 1.266867 TTAAGTGACCCTACCCCGGC 61.267 60.000 0.00 0.00 0.00 6.13
524 822 2.172229 TAAGTGACCCTACCCCGGCT 62.172 60.000 0.00 0.00 0.00 5.52
525 823 3.468140 GTGACCCTACCCCGGCTC 61.468 72.222 0.00 0.00 0.00 4.70
564 862 4.863925 GAGGCAGCGCTCGACCTC 62.864 72.222 26.33 26.33 41.81 3.85
573 871 2.192443 CTCGACCTCCGCCTCCTA 59.808 66.667 0.00 0.00 38.37 2.94
574 872 2.124403 TCGACCTCCGCCTCCTAC 60.124 66.667 0.00 0.00 38.37 3.18
575 873 3.217743 CGACCTCCGCCTCCTACC 61.218 72.222 0.00 0.00 0.00 3.18
576 874 2.838693 GACCTCCGCCTCCTACCC 60.839 72.222 0.00 0.00 0.00 3.69
577 875 4.477119 ACCTCCGCCTCCTACCCC 62.477 72.222 0.00 0.00 0.00 4.95
579 877 4.475444 CTCCGCCTCCTACCCCCA 62.475 72.222 0.00 0.00 0.00 4.96
580 878 4.791069 TCCGCCTCCTACCCCCAC 62.791 72.222 0.00 0.00 0.00 4.61
583 881 4.752594 GCCTCCTACCCCCACCCA 62.753 72.222 0.00 0.00 0.00 4.51
584 882 2.691252 CCTCCTACCCCCACCCAC 60.691 72.222 0.00 0.00 0.00 4.61
585 883 2.124085 CTCCTACCCCCACCCACA 59.876 66.667 0.00 0.00 0.00 4.17
586 884 2.204029 TCCTACCCCCACCCACAC 60.204 66.667 0.00 0.00 0.00 3.82
587 885 2.204090 CCTACCCCCACCCACACT 60.204 66.667 0.00 0.00 0.00 3.55
588 886 2.602676 CCTACCCCCACCCACACTG 61.603 68.421 0.00 0.00 0.00 3.66
589 887 3.253838 TACCCCCACCCACACTGC 61.254 66.667 0.00 0.00 0.00 4.40
590 888 3.803311 TACCCCCACCCACACTGCT 62.803 63.158 0.00 0.00 0.00 4.24
591 889 4.666253 CCCCCACCCACACTGCTG 62.666 72.222 0.00 0.00 0.00 4.41
592 890 4.666253 CCCCACCCACACTGCTGG 62.666 72.222 0.00 0.00 0.00 4.85
624 922 4.410400 CTCCCCCGGCCAACACTC 62.410 72.222 2.24 0.00 0.00 3.51
627 925 4.278513 CCCCGGCCAACACTCCAA 62.279 66.667 2.24 0.00 0.00 3.53
628 926 2.672996 CCCGGCCAACACTCCAAG 60.673 66.667 2.24 0.00 0.00 3.61
629 927 2.429930 CCGGCCAACACTCCAAGA 59.570 61.111 2.24 0.00 0.00 3.02
630 928 1.228124 CCGGCCAACACTCCAAGAA 60.228 57.895 2.24 0.00 0.00 2.52
631 929 1.515521 CCGGCCAACACTCCAAGAAC 61.516 60.000 2.24 0.00 0.00 3.01
632 930 0.817634 CGGCCAACACTCCAAGAACA 60.818 55.000 2.24 0.00 0.00 3.18
633 931 0.954452 GGCCAACACTCCAAGAACAG 59.046 55.000 0.00 0.00 0.00 3.16
634 932 1.680338 GCCAACACTCCAAGAACAGT 58.320 50.000 0.00 0.00 0.00 3.55
635 933 2.024414 GCCAACACTCCAAGAACAGTT 58.976 47.619 0.00 0.00 0.00 3.16
636 934 2.033424 GCCAACACTCCAAGAACAGTTC 59.967 50.000 5.00 5.00 0.00 3.01
637 935 2.618709 CCAACACTCCAAGAACAGTTCC 59.381 50.000 9.85 0.00 0.00 3.62
638 936 2.618709 CAACACTCCAAGAACAGTTCCC 59.381 50.000 9.85 0.00 0.00 3.97
639 937 1.843851 ACACTCCAAGAACAGTTCCCA 59.156 47.619 9.85 0.00 0.00 4.37
640 938 2.222027 CACTCCAAGAACAGTTCCCAC 58.778 52.381 9.85 0.00 0.00 4.61
641 939 1.202651 ACTCCAAGAACAGTTCCCACG 60.203 52.381 9.85 0.00 0.00 4.94
642 940 1.070134 CTCCAAGAACAGTTCCCACGA 59.930 52.381 9.85 0.43 0.00 4.35
643 941 1.070134 TCCAAGAACAGTTCCCACGAG 59.930 52.381 9.85 0.00 0.00 4.18
644 942 1.512926 CAAGAACAGTTCCCACGAGG 58.487 55.000 9.85 0.00 0.00 4.63
645 943 1.070134 CAAGAACAGTTCCCACGAGGA 59.930 52.381 9.85 0.00 45.68 3.71
646 944 1.645710 AGAACAGTTCCCACGAGGAT 58.354 50.000 9.85 0.00 46.94 3.24
647 945 2.816411 AGAACAGTTCCCACGAGGATA 58.184 47.619 9.85 0.00 46.94 2.59
648 946 2.761208 AGAACAGTTCCCACGAGGATAG 59.239 50.000 9.85 0.00 46.94 2.08
649 947 2.233305 ACAGTTCCCACGAGGATAGT 57.767 50.000 0.00 0.00 46.94 2.12
650 948 3.377253 ACAGTTCCCACGAGGATAGTA 57.623 47.619 0.00 0.00 46.94 1.82
651 949 3.022406 ACAGTTCCCACGAGGATAGTAC 58.978 50.000 0.00 0.00 46.94 2.73
652 950 2.033049 CAGTTCCCACGAGGATAGTACG 59.967 54.545 0.00 0.00 46.94 3.67
653 951 2.019984 GTTCCCACGAGGATAGTACGT 58.980 52.381 0.00 0.00 46.94 3.57
654 952 2.019249 TTCCCACGAGGATAGTACGTG 58.981 52.381 0.00 0.00 46.94 4.49
657 955 2.412605 ACGAGGATAGTACGTGCCC 58.587 57.895 0.00 0.00 38.79 5.36
658 956 0.106819 ACGAGGATAGTACGTGCCCT 60.107 55.000 0.00 0.00 38.79 5.19
659 957 0.592148 CGAGGATAGTACGTGCCCTC 59.408 60.000 14.53 14.53 39.88 4.30
660 958 1.688772 GAGGATAGTACGTGCCCTCA 58.311 55.000 18.03 0.00 42.15 3.86
661 959 1.337387 GAGGATAGTACGTGCCCTCAC 59.663 57.143 18.03 0.00 42.15 3.51
662 960 1.063867 AGGATAGTACGTGCCCTCACT 60.064 52.381 0.00 0.00 40.99 3.41
663 961 1.337387 GGATAGTACGTGCCCTCACTC 59.663 57.143 0.00 0.00 40.99 3.51
664 962 2.299521 GATAGTACGTGCCCTCACTCT 58.700 52.381 0.00 0.00 40.99 3.24
665 963 1.747709 TAGTACGTGCCCTCACTCTC 58.252 55.000 0.00 0.00 40.99 3.20
666 964 1.136984 GTACGTGCCCTCACTCTCG 59.863 63.158 0.00 0.00 40.99 4.04
667 965 2.044555 TACGTGCCCTCACTCTCGG 61.045 63.158 0.00 0.00 40.99 4.63
668 966 2.473891 TACGTGCCCTCACTCTCGGA 62.474 60.000 0.00 0.00 40.99 4.55
669 967 2.574399 GTGCCCTCACTCTCGGAC 59.426 66.667 0.00 0.00 40.03 4.79
670 968 1.979693 GTGCCCTCACTCTCGGACT 60.980 63.158 0.00 0.00 40.03 3.85
671 969 1.679305 TGCCCTCACTCTCGGACTC 60.679 63.158 0.00 0.00 0.00 3.36
672 970 2.766400 GCCCTCACTCTCGGACTCG 61.766 68.421 0.00 0.00 37.82 4.18
673 971 1.078356 CCCTCACTCTCGGACTCGA 60.078 63.158 0.00 0.00 43.86 4.04
674 972 0.677098 CCCTCACTCTCGGACTCGAA 60.677 60.000 0.00 0.00 45.47 3.71
675 973 1.166129 CCTCACTCTCGGACTCGAAA 58.834 55.000 0.00 0.00 45.47 3.46
676 974 1.135632 CCTCACTCTCGGACTCGAAAC 60.136 57.143 0.00 0.00 45.47 2.78
677 975 1.535896 CTCACTCTCGGACTCGAAACA 59.464 52.381 0.00 0.00 45.47 2.83
678 976 2.160205 TCACTCTCGGACTCGAAACAT 58.840 47.619 0.00 0.00 45.47 2.71
679 977 2.161808 TCACTCTCGGACTCGAAACATC 59.838 50.000 0.00 0.00 45.47 3.06
680 978 1.130749 ACTCTCGGACTCGAAACATCG 59.869 52.381 0.00 0.00 45.47 3.84
681 979 0.450583 TCTCGGACTCGAAACATCGG 59.549 55.000 0.00 0.00 45.47 4.18
682 980 1.140407 CTCGGACTCGAAACATCGGC 61.140 60.000 0.00 0.00 45.47 5.54
683 981 2.165301 CGGACTCGAAACATCGGCC 61.165 63.158 0.00 0.00 39.00 6.13
684 982 1.814169 GGACTCGAAACATCGGCCC 60.814 63.158 0.00 0.00 0.00 5.80
685 983 2.125673 ACTCGAAACATCGGCCCG 60.126 61.111 0.00 0.00 0.00 6.13
686 984 3.564027 CTCGAAACATCGGCCCGC 61.564 66.667 0.00 0.00 0.00 6.13
687 985 4.077184 TCGAAACATCGGCCCGCT 62.077 61.111 0.00 0.00 0.00 5.52
688 986 3.864686 CGAAACATCGGCCCGCTG 61.865 66.667 5.26 5.26 0.00 5.18
689 987 2.435938 GAAACATCGGCCCGCTGA 60.436 61.111 14.77 3.99 35.60 4.26
690 988 2.746277 AAACATCGGCCCGCTGAC 60.746 61.111 14.77 0.00 33.73 3.51
691 989 3.545124 AAACATCGGCCCGCTGACA 62.545 57.895 14.77 0.00 33.73 3.58
692 990 3.958147 AACATCGGCCCGCTGACAG 62.958 63.158 14.77 0.00 33.73 3.51
712 1010 2.842936 CGCCCCCTCCGACCTTAT 60.843 66.667 0.00 0.00 0.00 1.73
713 1011 2.440817 CGCCCCCTCCGACCTTATT 61.441 63.158 0.00 0.00 0.00 1.40
714 1012 1.920532 GCCCCCTCCGACCTTATTT 59.079 57.895 0.00 0.00 0.00 1.40
715 1013 1.134228 GCCCCCTCCGACCTTATTTA 58.866 55.000 0.00 0.00 0.00 1.40
716 1014 1.202734 GCCCCCTCCGACCTTATTTAC 60.203 57.143 0.00 0.00 0.00 2.01
717 1015 1.419012 CCCCCTCCGACCTTATTTACC 59.581 57.143 0.00 0.00 0.00 2.85
718 1016 2.121129 CCCCTCCGACCTTATTTACCA 58.879 52.381 0.00 0.00 0.00 3.25
719 1017 2.506644 CCCCTCCGACCTTATTTACCAA 59.493 50.000 0.00 0.00 0.00 3.67
720 1018 3.433173 CCCCTCCGACCTTATTTACCAAG 60.433 52.174 0.00 0.00 0.00 3.61
724 1022 2.943033 CCGACCTTATTTACCAAGCCTG 59.057 50.000 0.00 0.00 0.00 4.85
726 1024 3.621558 GACCTTATTTACCAAGCCTGCT 58.378 45.455 0.00 0.00 0.00 4.24
766 1067 1.610554 CCTACCCAATCCACGACCGT 61.611 60.000 0.00 0.00 0.00 4.83
782 1083 3.550656 GTGAGAAACGGCGGTCAG 58.449 61.111 13.24 0.00 0.00 3.51
783 1084 1.006571 GTGAGAAACGGCGGTCAGA 60.007 57.895 13.24 0.00 0.00 3.27
784 1085 1.009389 GTGAGAAACGGCGGTCAGAG 61.009 60.000 13.24 0.00 0.00 3.35
785 1086 2.048127 AGAAACGGCGGTCAGAGC 60.048 61.111 13.24 0.00 0.00 4.09
786 1087 2.048127 GAAACGGCGGTCAGAGCT 60.048 61.111 13.24 0.00 34.52 4.09
787 1088 2.048127 AAACGGCGGTCAGAGCTC 60.048 61.111 13.24 5.27 34.52 4.09
788 1089 2.765250 GAAACGGCGGTCAGAGCTCA 62.765 60.000 17.77 0.00 34.52 4.26
789 1090 2.377628 AAACGGCGGTCAGAGCTCAA 62.378 55.000 17.77 0.00 34.52 3.02
809 1110 2.197324 GACCACCAACCAAGCCCA 59.803 61.111 0.00 0.00 0.00 5.36
879 1197 1.452025 CGAGGTGCATTTATACGCTCG 59.548 52.381 0.00 0.00 34.16 5.03
920 1238 1.337823 TGTAACTCCCGCTTTCAGCTC 60.338 52.381 0.00 0.00 39.60 4.09
926 1244 2.097038 CCGCTTTCAGCTCACTCCG 61.097 63.158 0.00 0.00 39.60 4.63
979 1297 2.345244 CAGGTCGCTGTTGAGCCT 59.655 61.111 0.00 0.00 42.91 4.58
986 1304 0.244994 CGCTGTTGAGCCTGACTACT 59.755 55.000 0.00 0.00 42.91 2.57
1073 1391 3.119096 GGTGACGCCCGCTCTTTC 61.119 66.667 0.00 0.00 0.00 2.62
1079 1397 2.358247 GCCCGCTCTTTCGTTCCA 60.358 61.111 0.00 0.00 0.00 3.53
1088 1412 4.566759 CGCTCTTTCGTTCCATTTCTATCA 59.433 41.667 0.00 0.00 0.00 2.15
1147 1471 1.671379 GCCTGAGTTGGTTCGGACC 60.671 63.158 5.70 5.70 46.71 4.46
1160 1484 2.426023 GGACCGTGTTGACCAGCT 59.574 61.111 0.00 0.00 0.00 4.24
1214 1538 3.008049 AGTTGAACCCGATTAGCTGTTCT 59.992 43.478 12.07 0.00 38.29 3.01
1215 1539 4.222145 AGTTGAACCCGATTAGCTGTTCTA 59.778 41.667 12.07 3.87 38.29 2.10
1216 1540 4.386867 TGAACCCGATTAGCTGTTCTAG 57.613 45.455 12.07 0.00 38.29 2.43
1217 1541 3.132289 TGAACCCGATTAGCTGTTCTAGG 59.868 47.826 12.07 7.61 38.29 3.02
1218 1542 1.413077 ACCCGATTAGCTGTTCTAGGC 59.587 52.381 0.00 0.00 0.00 3.93
1219 1543 1.603172 CCCGATTAGCTGTTCTAGGCG 60.603 57.143 0.00 0.00 0.00 5.52
1220 1544 1.603172 CCGATTAGCTGTTCTAGGCGG 60.603 57.143 0.00 0.00 38.50 6.13
1221 1545 1.067212 CGATTAGCTGTTCTAGGCGGT 59.933 52.381 0.00 0.00 0.00 5.68
1222 1546 2.745102 GATTAGCTGTTCTAGGCGGTC 58.255 52.381 0.00 0.00 0.00 4.79
1223 1547 0.454600 TTAGCTGTTCTAGGCGGTCG 59.545 55.000 0.00 0.00 0.00 4.79
1224 1548 0.679002 TAGCTGTTCTAGGCGGTCGT 60.679 55.000 0.00 0.00 0.00 4.34
1225 1549 1.080025 GCTGTTCTAGGCGGTCGTT 60.080 57.895 0.00 0.00 0.00 3.85
1226 1550 0.669625 GCTGTTCTAGGCGGTCGTTT 60.670 55.000 0.00 0.00 0.00 3.60
1227 1551 1.347320 CTGTTCTAGGCGGTCGTTTC 58.653 55.000 0.00 0.00 0.00 2.78
1228 1552 0.963962 TGTTCTAGGCGGTCGTTTCT 59.036 50.000 0.00 0.00 0.00 2.52
1229 1553 1.342174 TGTTCTAGGCGGTCGTTTCTT 59.658 47.619 0.00 0.00 0.00 2.52
1230 1554 1.991264 GTTCTAGGCGGTCGTTTCTTC 59.009 52.381 0.00 0.00 0.00 2.87
1231 1555 0.529378 TCTAGGCGGTCGTTTCTTCC 59.471 55.000 0.00 0.00 0.00 3.46
1232 1556 0.459759 CTAGGCGGTCGTTTCTTCCC 60.460 60.000 0.00 0.00 0.00 3.97
1233 1557 1.891722 TAGGCGGTCGTTTCTTCCCC 61.892 60.000 0.00 0.00 0.00 4.81
1234 1558 2.745100 GCGGTCGTTTCTTCCCCC 60.745 66.667 0.00 0.00 0.00 5.40
1272 1812 6.203915 TGTGTAATAAACATATGCCCTAAGCG 59.796 38.462 1.58 0.00 42.43 4.68
1274 1814 6.203915 TGTAATAAACATATGCCCTAAGCGTG 59.796 38.462 1.58 0.00 37.49 5.34
1275 1815 7.902527 TGTAATAAACATATGCCCTAAGCGTGA 60.903 37.037 1.58 0.00 37.49 4.35
1337 1894 2.419667 GCTTCGGTACCAGTAAGCAAA 58.580 47.619 26.78 6.14 43.00 3.68
1377 1934 8.051535 ACTGAAATGTCTGAGAATGGTATGATT 58.948 33.333 0.00 0.00 0.00 2.57
1394 1951 6.930722 GGTATGATTGCATCTTTTAAATGGGG 59.069 38.462 0.00 0.00 35.94 4.96
1396 1953 6.811634 TGATTGCATCTTTTAAATGGGGAT 57.188 33.333 0.00 0.00 0.00 3.85
1399 1956 8.587608 TGATTGCATCTTTTAAATGGGGATATC 58.412 33.333 0.00 0.00 0.00 1.63
1415 1972 5.279556 GGGGATATCAACTGTACCTTAGAGC 60.280 48.000 4.83 0.00 0.00 4.09
1416 1973 5.279556 GGGATATCAACTGTACCTTAGAGCC 60.280 48.000 4.83 0.00 0.00 4.70
1421 1978 2.890814 ACTGTACCTTAGAGCCAGTGT 58.109 47.619 0.00 0.00 35.20 3.55
1445 2002 1.003928 GGTCATAACGGGTGGTCCTTT 59.996 52.381 0.00 0.00 0.00 3.11
1463 2020 1.175983 TTTGACCCAACCGTGGCATC 61.176 55.000 0.00 0.00 44.46 3.91
1481 2038 0.810648 TCGTTCCAGCAATTGCATCC 59.189 50.000 30.89 13.13 45.16 3.51
1482 2039 0.813184 CGTTCCAGCAATTGCATCCT 59.187 50.000 30.89 8.70 45.16 3.24
1483 2040 1.468565 CGTTCCAGCAATTGCATCCTG 60.469 52.381 30.89 19.80 45.16 3.86
1484 2041 1.547372 GTTCCAGCAATTGCATCCTGT 59.453 47.619 30.89 7.52 45.16 4.00
1485 2042 1.927487 TCCAGCAATTGCATCCTGTT 58.073 45.000 30.89 6.74 45.16 3.16
1486 2043 2.250031 TCCAGCAATTGCATCCTGTTT 58.750 42.857 30.89 5.95 45.16 2.83
1527 2085 6.489127 TGCTTATTTTTAACTTGAGCGCTA 57.511 33.333 11.50 0.00 0.00 4.26
1529 2087 7.364200 TGCTTATTTTTAACTTGAGCGCTAAA 58.636 30.769 11.50 9.01 0.00 1.85
1530 2088 7.863375 TGCTTATTTTTAACTTGAGCGCTAAAA 59.137 29.630 11.50 12.35 0.00 1.52
1531 2089 8.154038 GCTTATTTTTAACTTGAGCGCTAAAAC 58.846 33.333 11.50 0.00 0.00 2.43
1545 2104 7.073342 AGCGCTAAAACGATTTCTTATTTCT 57.927 32.000 8.99 0.00 34.06 2.52
1610 2169 5.393678 GGTGGTTTCAAGCTCAAAACAACTA 60.394 40.000 21.63 7.70 38.69 2.24
1616 2175 8.395633 GTTTCAAGCTCAAAACAACTACTAAGA 58.604 33.333 15.41 0.00 35.83 2.10
1670 2230 7.817418 AAGATTTGTTTGTGTAGTGTGGTAT 57.183 32.000 0.00 0.00 0.00 2.73
1731 2291 2.746472 GCTCTTCAGTTTGTGTGAGGGT 60.746 50.000 0.00 0.00 32.35 4.34
1775 2335 7.657761 CACAAAAACAGTACTCTCCTAAGACAT 59.342 37.037 0.00 0.00 0.00 3.06
1834 2394 1.272769 CTAGGAGCCAGCGGTTATACC 59.727 57.143 0.00 0.00 34.05 2.73
1855 2415 1.613925 GGGGCTGAGGTTGTTCTTTTC 59.386 52.381 0.00 0.00 0.00 2.29
1898 2458 3.519107 TGTTGACTGCTTATCATCCAGGA 59.481 43.478 0.00 0.00 0.00 3.86
1905 2465 2.412591 CTTATCATCCAGGACCAGGGT 58.587 52.381 2.58 0.00 0.00 4.34
1922 2482 3.062122 GGGTTAGATTGTTTCACCCGA 57.938 47.619 0.00 0.00 37.93 5.14
1969 2530 4.714308 TCTTGGCCCCTATTACCAAAAATG 59.286 41.667 0.00 0.00 42.65 2.32
1985 2546 0.615544 AATGTGGCAGGGTGGGATTG 60.616 55.000 0.00 0.00 0.00 2.67
1993 2554 0.565674 AGGGTGGGATTGGTTTGGTT 59.434 50.000 0.00 0.00 0.00 3.67
1996 2570 0.755686 GTGGGATTGGTTTGGTTGCA 59.244 50.000 0.00 0.00 0.00 4.08
2019 2593 2.916934 ACCCACCTTTACTCCTATGCAA 59.083 45.455 0.00 0.00 0.00 4.08
2026 2600 7.721399 CCACCTTTACTCCTATGCAATTATCTT 59.279 37.037 0.00 0.00 0.00 2.40
2027 2601 8.778358 CACCTTTACTCCTATGCAATTATCTTC 58.222 37.037 0.00 0.00 0.00 2.87
2054 2628 2.557924 TGCTTTTCCGATGCAACATTCT 59.442 40.909 0.00 0.00 35.69 2.40
2068 2642 4.521146 CAACATTCTGGTGCTAGGATTCT 58.479 43.478 0.00 0.00 0.00 2.40
2090 2664 8.627208 TTCTGATATTTTGATCCTCTTATGGC 57.373 34.615 0.00 0.00 0.00 4.40
2107 2681 4.844349 ATGGCTCAGTTACTAATGTGGT 57.156 40.909 0.00 0.00 0.00 4.16
2279 2853 3.627123 CCTCCACATTTGATGCGTCATTA 59.373 43.478 9.96 1.41 33.56 1.90
2288 2862 3.954999 TGATGCGTCATTATTGTGCATG 58.045 40.909 18.07 0.00 42.14 4.06
2325 2899 3.425359 CCTTTCAGCAGTAGCACATTTCG 60.425 47.826 0.00 0.00 45.49 3.46
2330 2904 3.001634 CAGCAGTAGCACATTTCGGTATG 59.998 47.826 0.00 0.00 45.49 2.39
2337 2924 4.905429 AGCACATTTCGGTATGGCATATA 58.095 39.130 10.92 0.00 0.00 0.86
2381 2968 2.595386 GACCTGCCAAATTTAGTTGCG 58.405 47.619 0.00 0.00 0.00 4.85
2509 3097 5.098211 GTCAATTGCTGAACTTATGAAGGC 58.902 41.667 0.00 0.00 35.22 4.35
2576 3164 2.417933 CTGGACACACTAAGAGCAATGC 59.582 50.000 0.00 0.00 0.00 3.56
2752 3345 1.295792 GCAGGATTTCCGATTGCGTA 58.704 50.000 0.00 0.00 42.08 4.42
2893 3494 4.380531 TGAAGCTACCAAGTTCTGAAGTG 58.619 43.478 0.00 0.00 0.00 3.16
3280 3888 0.323360 TCAATAGCCCCCACTTGTGC 60.323 55.000 0.00 0.00 0.00 4.57
3360 3971 8.579850 TTTGTCAAAATATTCTGCCTAGTCAT 57.420 30.769 0.00 0.00 0.00 3.06
3503 4114 9.342308 ACACAAATATACATCCGATTCAGAAAT 57.658 29.630 0.00 0.00 0.00 2.17
3561 4172 9.059260 GGAGTAGTCTTCTTAGTATCTAGGTTG 57.941 40.741 0.00 0.00 0.00 3.77
3571 4182 2.795175 ATCTAGGTTGCGGACATACG 57.205 50.000 0.00 0.00 0.00 3.06
4298 4909 9.029368 TGTTTGACCATGTGGATTAAATTATCA 57.971 29.630 5.96 0.00 38.94 2.15
4520 5133 4.033990 TCATCATCTCTGTCGTAAGTGC 57.966 45.455 0.00 0.00 39.48 4.40
4565 5178 3.347216 AGGTTAGCGAAATGTTGCAGAT 58.653 40.909 0.00 0.00 0.00 2.90
4625 5238 6.286240 ACACTGCAGATAGACAATCTTGTA 57.714 37.500 23.35 0.00 42.62 2.41
4872 5485 6.208988 TGTGCTGGTGTAGTATTTAGAGAG 57.791 41.667 0.00 0.00 0.00 3.20
4933 5546 3.153919 GGCTTGGTGTAATGAAAGTCCA 58.846 45.455 0.00 0.00 0.00 4.02
5278 5892 3.780804 TGGTAAAGCTCCAGCAGTTAA 57.219 42.857 0.48 0.00 45.16 2.01
5442 6061 4.081697 TGTGTAGATGCATCGAAAGAGGAA 60.082 41.667 20.67 0.00 46.52 3.36
5488 6107 4.536090 TCCCATTGTTCTTCTATGTCTGGT 59.464 41.667 0.00 0.00 0.00 4.00
5587 6213 4.284490 AGCCTGTCATGAACTCTGAACTTA 59.716 41.667 0.00 0.00 0.00 2.24
5619 6245 8.956426 TGATTTTAGAAATGTATGGTCAGGTTC 58.044 33.333 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 1.412710 TCGAGGTCAACAGCAAGAGTT 59.587 47.619 0.00 0.00 0.00 3.01
122 123 2.043953 GGGATGGACAGGGGTTGC 60.044 66.667 0.00 0.00 0.00 4.17
179 180 1.595993 CGACCTGATCTGACGTGGGT 61.596 60.000 0.00 0.00 0.00 4.51
237 238 1.204467 CTCTCTCTCCACTTGGTCTGC 59.796 57.143 0.00 0.00 36.34 4.26
278 567 1.680651 CGCACTCACCTCCTCTCCT 60.681 63.158 0.00 0.00 0.00 3.69
301 598 2.354401 CCTCGCCTGCTTCCTCTCA 61.354 63.158 0.00 0.00 0.00 3.27
481 779 1.135141 GTGTGTTTGCTTGCAGGAACA 60.135 47.619 0.00 8.29 0.00 3.18
492 790 2.034179 GGTCACTTAAGGGTGTGTTTGC 59.966 50.000 4.27 0.00 38.28 3.68
547 845 4.863925 GAGGTCGAGCGCTGCCTC 62.864 72.222 26.25 26.25 40.39 4.70
556 854 2.188161 GTAGGAGGCGGAGGTCGAG 61.188 68.421 0.00 0.00 42.43 4.04
557 855 2.124403 GTAGGAGGCGGAGGTCGA 60.124 66.667 0.00 0.00 42.43 4.20
558 856 3.217743 GGTAGGAGGCGGAGGTCG 61.218 72.222 0.00 0.00 42.76 4.79
559 857 2.838693 GGGTAGGAGGCGGAGGTC 60.839 72.222 0.00 0.00 0.00 3.85
560 858 4.477119 GGGGTAGGAGGCGGAGGT 62.477 72.222 0.00 0.00 0.00 3.85
562 860 4.475444 TGGGGGTAGGAGGCGGAG 62.475 72.222 0.00 0.00 0.00 4.63
563 861 4.791069 GTGGGGGTAGGAGGCGGA 62.791 72.222 0.00 0.00 0.00 5.54
566 864 4.752594 TGGGTGGGGGTAGGAGGC 62.753 72.222 0.00 0.00 0.00 4.70
567 865 2.691252 GTGGGTGGGGGTAGGAGG 60.691 72.222 0.00 0.00 0.00 4.30
568 866 2.124085 TGTGGGTGGGGGTAGGAG 59.876 66.667 0.00 0.00 0.00 3.69
569 867 2.204029 GTGTGGGTGGGGGTAGGA 60.204 66.667 0.00 0.00 0.00 2.94
570 868 2.204090 AGTGTGGGTGGGGGTAGG 60.204 66.667 0.00 0.00 0.00 3.18
571 869 3.077907 CAGTGTGGGTGGGGGTAG 58.922 66.667 0.00 0.00 0.00 3.18
572 870 3.253838 GCAGTGTGGGTGGGGGTA 61.254 66.667 0.00 0.00 0.00 3.69
574 872 4.666253 CAGCAGTGTGGGTGGGGG 62.666 72.222 0.00 0.00 32.80 5.40
607 905 4.410400 GAGTGTTGGCCGGGGGAG 62.410 72.222 2.18 0.00 0.00 4.30
610 908 4.278513 TTGGAGTGTTGGCCGGGG 62.279 66.667 2.18 0.00 0.00 5.73
611 909 2.672996 CTTGGAGTGTTGGCCGGG 60.673 66.667 2.18 0.00 0.00 5.73
612 910 1.228124 TTCTTGGAGTGTTGGCCGG 60.228 57.895 0.00 0.00 0.00 6.13
613 911 0.817634 TGTTCTTGGAGTGTTGGCCG 60.818 55.000 0.00 0.00 0.00 6.13
614 912 0.954452 CTGTTCTTGGAGTGTTGGCC 59.046 55.000 0.00 0.00 0.00 5.36
615 913 1.680338 ACTGTTCTTGGAGTGTTGGC 58.320 50.000 0.00 0.00 0.00 4.52
616 914 2.618709 GGAACTGTTCTTGGAGTGTTGG 59.381 50.000 19.05 0.00 0.00 3.77
617 915 2.618709 GGGAACTGTTCTTGGAGTGTTG 59.381 50.000 19.05 0.00 0.00 3.33
618 916 2.241176 TGGGAACTGTTCTTGGAGTGTT 59.759 45.455 19.05 0.00 0.00 3.32
619 917 1.843851 TGGGAACTGTTCTTGGAGTGT 59.156 47.619 19.05 0.00 0.00 3.55
620 918 2.222027 GTGGGAACTGTTCTTGGAGTG 58.778 52.381 19.05 0.00 0.00 3.51
621 919 1.202651 CGTGGGAACTGTTCTTGGAGT 60.203 52.381 19.05 0.00 0.00 3.85
622 920 1.070134 TCGTGGGAACTGTTCTTGGAG 59.930 52.381 19.05 8.38 0.00 3.86
623 921 1.070134 CTCGTGGGAACTGTTCTTGGA 59.930 52.381 19.05 10.87 0.00 3.53
624 922 1.512926 CTCGTGGGAACTGTTCTTGG 58.487 55.000 19.05 7.56 0.00 3.61
625 923 1.070134 TCCTCGTGGGAACTGTTCTTG 59.930 52.381 19.05 7.74 41.91 3.02
626 924 1.420430 TCCTCGTGGGAACTGTTCTT 58.580 50.000 19.05 0.00 41.91 2.52
627 925 3.143010 TCCTCGTGGGAACTGTTCT 57.857 52.632 19.05 0.00 41.91 3.01
639 937 0.106819 AGGGCACGTACTATCCTCGT 60.107 55.000 0.00 0.00 38.34 4.18
640 938 0.592148 GAGGGCACGTACTATCCTCG 59.408 60.000 0.00 0.00 35.30 4.63
641 939 1.337387 GTGAGGGCACGTACTATCCTC 59.663 57.143 12.12 12.12 43.06 3.71
642 940 1.400737 GTGAGGGCACGTACTATCCT 58.599 55.000 0.00 0.00 34.94 3.24
643 941 3.961576 GTGAGGGCACGTACTATCC 57.038 57.895 0.00 0.00 34.94 2.59
652 950 1.939769 GAGTCCGAGAGTGAGGGCAC 61.940 65.000 0.00 0.00 45.49 5.01
653 951 1.679305 GAGTCCGAGAGTGAGGGCA 60.679 63.158 0.00 0.00 33.85 5.36
654 952 2.766400 CGAGTCCGAGAGTGAGGGC 61.766 68.421 0.00 0.00 38.22 5.19
655 953 0.677098 TTCGAGTCCGAGAGTGAGGG 60.677 60.000 0.00 0.00 46.39 4.30
656 954 1.135632 GTTTCGAGTCCGAGAGTGAGG 60.136 57.143 0.00 0.00 46.39 3.86
657 955 1.535896 TGTTTCGAGTCCGAGAGTGAG 59.464 52.381 0.00 0.00 46.39 3.51
658 956 1.601166 TGTTTCGAGTCCGAGAGTGA 58.399 50.000 0.00 0.00 46.39 3.41
659 957 2.520979 GATGTTTCGAGTCCGAGAGTG 58.479 52.381 0.00 0.00 46.39 3.51
660 958 2.923605 GATGTTTCGAGTCCGAGAGT 57.076 50.000 0.00 0.00 46.39 3.24
671 969 3.864686 CAGCGGGCCGATGTTTCG 61.865 66.667 34.17 10.30 45.08 3.46
672 970 2.435938 TCAGCGGGCCGATGTTTC 60.436 61.111 38.92 17.11 43.92 2.78
673 971 2.746277 GTCAGCGGGCCGATGTTT 60.746 61.111 38.92 12.35 43.92 2.83
674 972 3.958147 CTGTCAGCGGGCCGATGTT 62.958 63.158 38.92 14.92 43.92 2.71
675 973 4.457496 CTGTCAGCGGGCCGATGT 62.457 66.667 38.92 16.77 43.92 3.06
695 993 1.979619 AAATAAGGTCGGAGGGGGCG 61.980 60.000 0.00 0.00 0.00 6.13
696 994 1.134228 TAAATAAGGTCGGAGGGGGC 58.866 55.000 0.00 0.00 0.00 5.80
697 995 1.419012 GGTAAATAAGGTCGGAGGGGG 59.581 57.143 0.00 0.00 0.00 5.40
698 996 2.121129 TGGTAAATAAGGTCGGAGGGG 58.879 52.381 0.00 0.00 0.00 4.79
699 997 3.805207 CTTGGTAAATAAGGTCGGAGGG 58.195 50.000 0.00 0.00 0.00 4.30
700 998 3.203716 GCTTGGTAAATAAGGTCGGAGG 58.796 50.000 0.00 0.00 0.00 4.30
701 999 3.118371 AGGCTTGGTAAATAAGGTCGGAG 60.118 47.826 0.00 0.00 0.00 4.63
702 1000 2.841881 AGGCTTGGTAAATAAGGTCGGA 59.158 45.455 0.00 0.00 0.00 4.55
703 1001 2.943033 CAGGCTTGGTAAATAAGGTCGG 59.057 50.000 0.00 0.00 0.00 4.79
704 1002 2.354821 GCAGGCTTGGTAAATAAGGTCG 59.645 50.000 0.00 0.00 0.00 4.79
705 1003 3.378427 CAGCAGGCTTGGTAAATAAGGTC 59.622 47.826 0.00 0.00 32.80 3.85
706 1004 3.356290 CAGCAGGCTTGGTAAATAAGGT 58.644 45.455 0.00 0.00 32.80 3.50
707 1005 2.099756 GCAGCAGGCTTGGTAAATAAGG 59.900 50.000 0.00 0.00 40.25 2.69
708 1006 2.099756 GGCAGCAGGCTTGGTAAATAAG 59.900 50.000 0.00 0.00 44.01 1.73
709 1007 2.099405 GGCAGCAGGCTTGGTAAATAA 58.901 47.619 0.00 0.00 44.01 1.40
710 1008 1.684869 GGGCAGCAGGCTTGGTAAATA 60.685 52.381 0.00 0.00 44.01 1.40
711 1009 0.972471 GGGCAGCAGGCTTGGTAAAT 60.972 55.000 0.00 0.00 44.01 1.40
712 1010 1.606313 GGGCAGCAGGCTTGGTAAA 60.606 57.895 0.00 0.00 44.01 2.01
713 1011 2.035626 GGGCAGCAGGCTTGGTAA 59.964 61.111 0.00 0.00 44.01 2.85
714 1012 3.256178 TGGGCAGCAGGCTTGGTA 61.256 61.111 0.00 0.00 44.01 3.25
715 1013 4.982701 GTGGGCAGCAGGCTTGGT 62.983 66.667 1.94 0.00 44.01 3.67
717 1015 4.980702 TGGTGGGCAGCAGGCTTG 62.981 66.667 1.94 0.00 44.01 4.01
766 1067 1.289066 CTCTGACCGCCGTTTCTCA 59.711 57.895 0.00 0.00 0.00 3.27
770 1071 2.048127 GAGCTCTGACCGCCGTTT 60.048 61.111 6.43 0.00 0.00 3.60
778 1079 1.011451 GTGGTCGCTTGAGCTCTGAC 61.011 60.000 16.19 15.96 40.76 3.51
780 1081 1.739562 GGTGGTCGCTTGAGCTCTG 60.740 63.158 16.19 9.02 40.76 3.35
781 1082 1.758440 TTGGTGGTCGCTTGAGCTCT 61.758 55.000 16.19 0.00 40.76 4.09
782 1083 1.301716 TTGGTGGTCGCTTGAGCTC 60.302 57.895 6.82 6.82 40.76 4.09
783 1084 1.598130 GTTGGTGGTCGCTTGAGCT 60.598 57.895 1.07 0.00 40.76 4.09
784 1085 2.617274 GGTTGGTGGTCGCTTGAGC 61.617 63.158 0.00 0.00 40.54 4.26
785 1086 0.817634 TTGGTTGGTGGTCGCTTGAG 60.818 55.000 0.00 0.00 0.00 3.02
786 1087 0.817634 CTTGGTTGGTGGTCGCTTGA 60.818 55.000 0.00 0.00 0.00 3.02
787 1088 1.654220 CTTGGTTGGTGGTCGCTTG 59.346 57.895 0.00 0.00 0.00 4.01
788 1089 2.193536 GCTTGGTTGGTGGTCGCTT 61.194 57.895 0.00 0.00 0.00 4.68
789 1090 2.594592 GCTTGGTTGGTGGTCGCT 60.595 61.111 0.00 0.00 0.00 4.93
850 1168 2.075355 AATGCACCTCGTGGGGGAAA 62.075 55.000 3.44 0.00 41.57 3.13
853 1171 0.106719 ATAAATGCACCTCGTGGGGG 60.107 55.000 8.06 1.27 42.69 5.40
879 1197 1.230324 GAAGTGTCAGGAAGGTGTGC 58.770 55.000 0.00 0.00 0.00 4.57
920 1238 3.060003 GCAAATCGAGATTGATCGGAGTG 60.060 47.826 15.66 0.00 42.93 3.51
926 1244 2.031333 GGCTGGCAAATCGAGATTGATC 60.031 50.000 15.66 8.49 0.00 2.92
968 1286 1.404851 GGAGTAGTCAGGCTCAACAGC 60.405 57.143 0.00 0.00 46.06 4.40
969 1287 1.205893 GGGAGTAGTCAGGCTCAACAG 59.794 57.143 0.00 0.00 33.66 3.16
970 1288 1.267121 GGGAGTAGTCAGGCTCAACA 58.733 55.000 0.00 0.00 33.66 3.33
971 1289 0.537653 GGGGAGTAGTCAGGCTCAAC 59.462 60.000 0.00 0.00 33.66 3.18
972 1290 0.970937 CGGGGAGTAGTCAGGCTCAA 60.971 60.000 0.00 0.00 33.66 3.02
973 1291 1.379977 CGGGGAGTAGTCAGGCTCA 60.380 63.158 0.00 0.00 33.66 4.26
1073 1391 4.880886 TGCACATGATAGAAATGGAACG 57.119 40.909 0.00 0.00 0.00 3.95
1079 1397 5.434408 TCAGAGCTTGCACATGATAGAAAT 58.566 37.500 0.00 0.00 0.00 2.17
1147 1471 3.957260 CCAGAGCTGGTCAACACG 58.043 61.111 9.78 0.00 45.53 4.49
1160 1484 0.322098 CCAACCAATACACGGCCAGA 60.322 55.000 2.24 0.00 0.00 3.86
1214 1538 1.593265 GGGAAGAAACGACCGCCTA 59.407 57.895 0.00 0.00 0.00 3.93
1215 1539 2.346365 GGGAAGAAACGACCGCCT 59.654 61.111 0.00 0.00 0.00 5.52
1216 1540 2.745100 GGGGAAGAAACGACCGCC 60.745 66.667 0.00 0.00 0.00 6.13
1217 1541 2.745100 GGGGGAAGAAACGACCGC 60.745 66.667 0.00 0.00 36.19 5.68
1231 1555 0.467384 CACATGCTCTACAGAGGGGG 59.533 60.000 8.29 0.00 42.29 5.40
1232 1556 1.198713 ACACATGCTCTACAGAGGGG 58.801 55.000 8.29 0.00 42.29 4.79
1233 1557 4.679373 ATTACACATGCTCTACAGAGGG 57.321 45.455 8.29 0.00 42.29 4.30
1234 1558 7.041721 TGTTTATTACACATGCTCTACAGAGG 58.958 38.462 8.29 0.00 42.29 3.69
1235 1559 8.654230 ATGTTTATTACACATGCTCTACAGAG 57.346 34.615 1.68 1.68 41.40 3.35
1245 1569 8.023128 GCTTAGGGCATATGTTTATTACACATG 58.977 37.037 4.29 0.00 43.15 3.21
1246 1570 7.094805 CGCTTAGGGCATATGTTTATTACACAT 60.095 37.037 4.29 1.42 39.34 3.21
1266 1806 4.250464 TGTAATTCCCTTGTCACGCTTAG 58.750 43.478 0.00 0.00 0.00 2.18
1267 1807 4.274602 TGTAATTCCCTTGTCACGCTTA 57.725 40.909 0.00 0.00 0.00 3.09
1272 1812 4.935808 AGTTCGATGTAATTCCCTTGTCAC 59.064 41.667 0.00 0.00 0.00 3.67
1274 1814 6.258068 CCTTAGTTCGATGTAATTCCCTTGTC 59.742 42.308 0.00 0.00 0.00 3.18
1275 1815 6.113411 CCTTAGTTCGATGTAATTCCCTTGT 58.887 40.000 0.00 0.00 0.00 3.16
1278 1818 5.952347 ACCTTAGTTCGATGTAATTCCCT 57.048 39.130 0.00 0.00 0.00 4.20
1337 1894 9.199982 CAGACATTTCAGTTAGCAAATTCAAAT 57.800 29.630 0.00 0.00 0.00 2.32
1377 1934 7.564660 AGTTGATATCCCCATTTAAAAGATGCA 59.435 33.333 0.00 0.00 0.00 3.96
1394 1951 6.041069 ACTGGCTCTAAGGTACAGTTGATATC 59.959 42.308 0.00 0.00 39.16 1.63
1396 1953 5.127194 CACTGGCTCTAAGGTACAGTTGATA 59.873 44.000 0.00 0.00 40.14 2.15
1399 1956 3.006967 ACACTGGCTCTAAGGTACAGTTG 59.993 47.826 0.00 0.00 40.14 3.16
1415 1972 3.202906 CCCGTTATGACCAATACACTGG 58.797 50.000 0.00 0.00 42.68 4.00
1416 1973 3.621268 CACCCGTTATGACCAATACACTG 59.379 47.826 0.00 0.00 0.00 3.66
1421 1978 2.171027 GGACCACCCGTTATGACCAATA 59.829 50.000 0.00 0.00 0.00 1.90
1445 2002 1.602323 GATGCCACGGTTGGGTCAA 60.602 57.895 0.00 0.00 44.15 3.18
1455 2012 1.647545 ATTGCTGGAACGATGCCACG 61.648 55.000 0.00 0.00 39.31 4.94
1463 2020 0.813184 AGGATGCAATTGCTGGAACG 59.187 50.000 29.37 0.00 42.66 3.95
1481 2038 6.345250 GCAATTTCATGACGAAACAGAAACAG 60.345 38.462 0.00 0.00 46.22 3.16
1482 2039 5.458452 GCAATTTCATGACGAAACAGAAACA 59.542 36.000 0.00 0.00 46.22 2.83
1483 2040 5.687285 AGCAATTTCATGACGAAACAGAAAC 59.313 36.000 0.00 0.00 46.22 2.78
1484 2041 5.830912 AGCAATTTCATGACGAAACAGAAA 58.169 33.333 0.00 0.00 46.22 2.52
1485 2042 5.437289 AGCAATTTCATGACGAAACAGAA 57.563 34.783 0.00 0.00 46.22 3.02
1486 2043 5.437289 AAGCAATTTCATGACGAAACAGA 57.563 34.783 0.00 0.00 46.22 3.41
1520 2078 7.180748 AGAAATAAGAAATCGTTTTAGCGCTC 58.819 34.615 16.34 0.00 0.00 5.03
1527 2085 9.199982 TCTACACGAGAAATAAGAAATCGTTTT 57.800 29.630 0.00 0.00 43.51 2.43
1529 2087 8.027771 ACTCTACACGAGAAATAAGAAATCGTT 58.972 33.333 0.00 0.00 43.51 3.85
1530 2088 7.485277 CACTCTACACGAGAAATAAGAAATCGT 59.515 37.037 0.00 0.00 46.63 3.73
1531 2089 7.043986 CCACTCTACACGAGAAATAAGAAATCG 60.044 40.741 0.00 0.00 42.62 3.34
1545 2104 2.160205 CAAGGACTCCACTCTACACGA 58.840 52.381 0.00 0.00 0.00 4.35
1554 2113 4.223032 TGAAAGTAGATCCAAGGACTCCAC 59.777 45.833 0.00 0.00 0.00 4.02
1610 2169 6.567602 AGAGGGCATAAAACTCATCTTAGT 57.432 37.500 0.00 0.00 33.76 2.24
1616 2175 8.829373 AGAAAATAAGAGGGCATAAAACTCAT 57.171 30.769 0.00 0.00 33.76 2.90
1688 2248 3.432252 CGTCCAACCTTCAATGTAGACAC 59.568 47.826 0.00 0.00 0.00 3.67
1731 2291 4.299586 TGTGGTGAAGAAGCAATGGATA 57.700 40.909 0.00 0.00 38.21 2.59
1775 2335 2.239654 CCTCCCCTGATTTAACTGCTGA 59.760 50.000 0.00 0.00 0.00 4.26
1810 2370 4.537433 CCGCTGGCTCCTAGCACC 62.537 72.222 0.78 0.00 44.75 5.01
1834 2394 0.537371 AAAGAACAACCTCAGCCCCG 60.537 55.000 0.00 0.00 0.00 5.73
1855 2415 4.281688 ACACAAATGGAAAATGACAGGGAG 59.718 41.667 0.00 0.00 0.00 4.30
1898 2458 3.499745 GGGTGAAACAATCTAACCCTGGT 60.500 47.826 1.85 0.00 39.98 4.00
1905 2465 3.816523 GGTTGTCGGGTGAAACAATCTAA 59.183 43.478 0.00 0.00 39.98 2.10
1922 2482 4.411927 TGTGCCCTTGTTTATATGGTTGT 58.588 39.130 0.00 0.00 0.00 3.32
1954 2515 4.141959 CCCTGCCACATTTTTGGTAATAGG 60.142 45.833 0.00 0.00 39.09 2.57
1955 2516 4.466015 ACCCTGCCACATTTTTGGTAATAG 59.534 41.667 0.00 0.00 39.09 1.73
1969 2530 2.362889 CCAATCCCACCCTGCCAC 60.363 66.667 0.00 0.00 0.00 5.01
1993 2554 1.497286 AGGAGTAAAGGTGGGTTTGCA 59.503 47.619 0.00 0.00 0.00 4.08
1996 2570 3.332485 TGCATAGGAGTAAAGGTGGGTTT 59.668 43.478 0.00 0.00 0.00 3.27
2054 2628 6.899089 TCAAAATATCAGAATCCTAGCACCA 58.101 36.000 0.00 0.00 0.00 4.17
2090 2664 5.320549 ACCGTACCACATTAGTAACTGAG 57.679 43.478 0.00 0.00 0.00 3.35
2107 2681 4.135306 TCTGTTGGCAAAAATGTACCGTA 58.865 39.130 0.00 0.00 0.00 4.02
2247 2821 5.047566 TCAAATGTGGAGGAAGTGAAGAA 57.952 39.130 0.00 0.00 0.00 2.52
2279 2853 6.327934 GTTCAGCTAATTCTTCATGCACAAT 58.672 36.000 0.00 0.00 0.00 2.71
2325 2899 8.814038 AAAAGAGGATCAATATATGCCATACC 57.186 34.615 0.00 0.00 37.82 2.73
2337 2924 8.854117 GTCCTGCAATATTAAAAGAGGATCAAT 58.146 33.333 0.00 0.00 37.82 2.57
2381 2968 9.798994 ACATCTGAAAAATCTGCATCTTTAATC 57.201 29.630 0.00 0.00 0.00 1.75
2486 3074 5.098211 GCCTTCATAAGTTCAGCAATTGAC 58.902 41.667 10.34 0.30 34.94 3.18
2509 3097 4.639334 ACAGCAGAGCATATAACTGGATG 58.361 43.478 0.00 0.00 33.00 3.51
2752 3345 4.880120 CCACTCAGCATACTCATTGATGTT 59.120 41.667 0.00 0.00 32.49 2.71
2893 3494 7.655732 AGTTGGTAATTAAATGTTGAAACTGGC 59.344 33.333 0.00 0.00 0.00 4.85
4298 4909 5.370875 AAAATAGGAGCTCTCTGCAGAAT 57.629 39.130 18.85 2.44 45.94 2.40
4299 4910 4.833478 AAAATAGGAGCTCTCTGCAGAA 57.167 40.909 18.85 8.05 45.94 3.02
4497 5110 5.046529 GCACTTACGACAGAGATGATGATT 58.953 41.667 0.00 0.00 0.00 2.57
4520 5133 6.856135 TGAGCAACTTATAGATTGATGCAG 57.144 37.500 0.00 0.00 34.89 4.41
4625 5238 1.305623 CTGGCCAGATGCTCCCTTT 59.694 57.895 29.88 0.00 40.92 3.11
4872 5485 4.503741 TTCAACTGCTAATTGTTGCTCC 57.496 40.909 0.00 0.00 42.11 4.70
4933 5546 8.686739 ATCCACTGTAGGATATAATAGCCTTT 57.313 34.615 9.18 0.00 43.21 3.11
5086 5699 8.967218 CGTCACACAAGATAAAATTTGACAAAT 58.033 29.630 7.62 7.62 33.27 2.32
5278 5892 6.070881 TGCAAGCCCATTTACATTAACAGAAT 60.071 34.615 0.00 0.00 0.00 2.40
5442 6061 9.166222 GGGAAATAAAAATAATAATCCCTGGGT 57.834 33.333 13.56 0.00 41.66 4.51
5488 6107 5.335583 CCCAACAGCATAACGAAAGAATCAA 60.336 40.000 0.00 0.00 0.00 2.57
5619 6245 3.685139 TTCTGGCTGAAGAACTACTGG 57.315 47.619 2.37 0.00 31.19 4.00


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

AutoCloner maintained by Alex Coulton.