Multiple sequence alignment - TraesCS3A01G028900

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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 TraesCS3A01G028900 chr3A 100.000 3143 0 0 1 3143 15313855 15316997 0.000000e+00 5805
1 TraesCS3A01G028900 chr3A 97.749 844 19 0 2300 3143 112935968 112935125 0.000000e+00 1454
2 TraesCS3A01G028900 chr3A 81.604 424 42 14 1237 1635 313184545 313184133 5.060000e-83 318
3 TraesCS3A01G028900 chr3A 91.870 123 10 0 681 803 737387921 737387799 4.170000e-39 172
4 TraesCS3A01G028900 chr3A 91.200 125 10 1 680 803 687616122 687616246 5.390000e-38 169
5 TraesCS3A01G028900 chr3A 91.525 118 10 0 686 803 716802988 716803105 2.510000e-36 163
6 TraesCS3A01G028900 chr3D 90.707 1485 71 27 870 2300 5858127 5856656 0.000000e+00 1916
7 TraesCS3A01G028900 chrUn 94.908 923 40 2 1378 2297 40589068 40589986 0.000000e+00 1437
8 TraesCS3A01G028900 chrUn 92.395 526 24 6 810 1319 40588456 40588981 0.000000e+00 736
9 TraesCS3A01G028900 chrUn 82.872 397 35 15 4 396 40587874 40588241 3.020000e-85 326
10 TraesCS3A01G028900 chrUn 90.909 198 18 0 434 631 40588242 40588439 1.860000e-67 267
11 TraesCS3A01G028900 chr7A 96.930 847 26 0 2297 3143 133663342 133662496 0.000000e+00 1421
12 TraesCS3A01G028900 chr3B 94.621 911 37 4 1378 2285 11664202 11665103 0.000000e+00 1400
13 TraesCS3A01G028900 chr3B 91.729 532 21 8 811 1319 11663585 11664116 0.000000e+00 717
14 TraesCS3A01G028900 chr3B 87.282 574 50 6 112 681 11663020 11663574 4.420000e-178 634
15 TraesCS3A01G028900 chr3B 90.244 123 12 0 681 803 507302842 507302964 9.020000e-36 161
16 TraesCS3A01G028900 chr3B 92.473 93 7 0 4 96 11662940 11663032 1.970000e-27 134
17 TraesCS3A01G028900 chr7D 96.213 845 32 0 2299 3143 19415756 19416600 0.000000e+00 1384
18 TraesCS3A01G028900 chr7D 91.870 123 10 0 681 803 93883387 93883509 4.170000e-39 172
19 TraesCS3A01G028900 chr2A 95.390 846 37 2 2298 3143 565061622 565062465 0.000000e+00 1345
20 TraesCS3A01G028900 chr2A 92.373 118 9 0 686 803 594654360 594654243 5.390000e-38 169
21 TraesCS3A01G028900 chr6D 94.706 850 38 6 2297 3140 438924549 438925397 0.000000e+00 1314
22 TraesCS3A01G028900 chr2D 91.657 839 67 3 2300 3138 315124117 315123282 0.000000e+00 1158
23 TraesCS3A01G028900 chr2D 84.471 850 98 19 2297 3127 519346732 519347566 0.000000e+00 808
24 TraesCS3A01G028900 chr6B 92.901 648 43 3 2329 2976 76189078 76189722 0.000000e+00 939
25 TraesCS3A01G028900 chr5D 85.511 842 99 17 2300 3127 510066631 510065799 0.000000e+00 857
26 TraesCS3A01G028900 chr5D 84.314 408 28 13 1217 1599 380295999 380295603 1.780000e-97 366
27 TraesCS3A01G028900 chr5D 95.536 112 5 0 685 796 246008723 246008612 2.490000e-41 180
28 TraesCS3A01G028900 chr1D 92.437 119 9 0 684 802 468747497 468747379 1.500000e-38 171
29 TraesCS3A01G028900 chr2B 92.174 115 9 0 685 799 615332461 615332347 2.510000e-36 163
30 TraesCS3A01G028900 chr1B 91.753 97 7 1 1214 1310 298764587 298764682 1.970000e-27 134
31 TraesCS3A01G028900 chr6A 92.208 77 6 0 1559 1635 354886569 354886493 3.310000e-20 110


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 TraesCS3A01G028900 chr3A 15313855 15316997 3142 False 5805.00 5805 100.00000 1 3143 1 chr3A.!!$F1 3142
1 TraesCS3A01G028900 chr3A 112935125 112935968 843 True 1454.00 1454 97.74900 2300 3143 1 chr3A.!!$R1 843
2 TraesCS3A01G028900 chr3D 5856656 5858127 1471 True 1916.00 1916 90.70700 870 2300 1 chr3D.!!$R1 1430
3 TraesCS3A01G028900 chrUn 40587874 40589986 2112 False 691.50 1437 90.27100 4 2297 4 chrUn.!!$F1 2293
4 TraesCS3A01G028900 chr7A 133662496 133663342 846 True 1421.00 1421 96.93000 2297 3143 1 chr7A.!!$R1 846
5 TraesCS3A01G028900 chr3B 11662940 11665103 2163 False 721.25 1400 91.52625 4 2285 4 chr3B.!!$F2 2281
6 TraesCS3A01G028900 chr7D 19415756 19416600 844 False 1384.00 1384 96.21300 2299 3143 1 chr7D.!!$F1 844
7 TraesCS3A01G028900 chr2A 565061622 565062465 843 False 1345.00 1345 95.39000 2298 3143 1 chr2A.!!$F1 845
8 TraesCS3A01G028900 chr6D 438924549 438925397 848 False 1314.00 1314 94.70600 2297 3140 1 chr6D.!!$F1 843
9 TraesCS3A01G028900 chr2D 315123282 315124117 835 True 1158.00 1158 91.65700 2300 3138 1 chr2D.!!$R1 838
10 TraesCS3A01G028900 chr2D 519346732 519347566 834 False 808.00 808 84.47100 2297 3127 1 chr2D.!!$F1 830
11 TraesCS3A01G028900 chr6B 76189078 76189722 644 False 939.00 939 92.90100 2329 2976 1 chr6B.!!$F1 647
12 TraesCS3A01G028900 chr5D 510065799 510066631 832 True 857.00 857 85.51100 2300 3127 1 chr5D.!!$R3 827

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
754 758 0.03213 AGGCCGTACATGCGTATGAG 59.968 55.0 20.86 10.35 36.84 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2462 0.101759 GGCGTTGTATCAGCCGTCTA 59.898 55.0 0.0 0.0 41.53 2.59 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
26 27 5.106118 GCCAAAGAGTCATTAACTTTCCTCC 60.106 44.000 0.00 0.00 38.74 4.30
90 91 1.473434 GCTTCGGGGTAGGTCAATCTG 60.473 57.143 0.00 0.00 0.00 2.90
98 99 3.782042 GGTCAATCTGTCGACCGC 58.218 61.111 14.12 0.00 42.19 5.68
100 101 2.158959 GTCAATCTGTCGACCGCGG 61.159 63.158 26.86 26.86 38.28 6.46
101 102 3.554692 CAATCTGTCGACCGCGGC 61.555 66.667 28.58 17.52 43.78 6.53
107 108 2.103538 GTCGACCGCGGCATTAGA 59.896 61.111 28.58 14.72 42.82 2.10
108 109 1.299926 GTCGACCGCGGCATTAGAT 60.300 57.895 28.58 2.52 42.82 1.98
109 110 0.874607 GTCGACCGCGGCATTAGATT 60.875 55.000 28.58 1.54 42.82 2.40
110 111 0.179094 TCGACCGCGGCATTAGATTT 60.179 50.000 28.58 0.57 38.28 2.17
111 112 0.655733 CGACCGCGGCATTAGATTTT 59.344 50.000 28.58 0.00 0.00 1.82
112 113 1.332904 CGACCGCGGCATTAGATTTTC 60.333 52.381 28.58 10.22 0.00 2.29
113 114 1.668751 GACCGCGGCATTAGATTTTCA 59.331 47.619 28.58 0.00 0.00 2.69
114 115 2.088423 ACCGCGGCATTAGATTTTCAA 58.912 42.857 28.58 0.00 0.00 2.69
115 116 2.490115 ACCGCGGCATTAGATTTTCAAA 59.510 40.909 28.58 0.00 0.00 2.69
116 117 2.851824 CCGCGGCATTAGATTTTCAAAC 59.148 45.455 14.67 0.00 0.00 2.93
117 118 3.427503 CCGCGGCATTAGATTTTCAAACT 60.428 43.478 14.67 0.00 0.00 2.66
118 119 4.201871 CCGCGGCATTAGATTTTCAAACTA 60.202 41.667 14.67 0.00 0.00 2.24
119 120 5.505654 CCGCGGCATTAGATTTTCAAACTAT 60.506 40.000 14.67 0.00 0.00 2.12
120 121 6.293190 CCGCGGCATTAGATTTTCAAACTATA 60.293 38.462 14.67 0.00 0.00 1.31
121 122 6.573725 CGCGGCATTAGATTTTCAAACTATAC 59.426 38.462 0.00 0.00 0.00 1.47
122 123 7.414436 GCGGCATTAGATTTTCAAACTATACA 58.586 34.615 0.00 0.00 0.00 2.29
123 124 7.376072 GCGGCATTAGATTTTCAAACTATACAC 59.624 37.037 0.00 0.00 0.00 2.90
124 125 8.612619 CGGCATTAGATTTTCAAACTATACACT 58.387 33.333 0.00 0.00 0.00 3.55
140 141 1.937899 ACACTAGTTTGTTGTGCGACC 59.062 47.619 0.00 0.00 35.33 4.79
142 143 2.032894 CACTAGTTTGTTGTGCGACCAG 60.033 50.000 0.00 0.00 0.00 4.00
154 155 1.508088 CGACCAGCCATTTCTTGCC 59.492 57.895 0.00 0.00 0.00 4.52
221 222 3.595190 CCCATAAAGTTAGGAAGGGGG 57.405 52.381 0.00 0.00 0.00 5.40
257 261 2.185004 AAATGGTGTGTCGAGGAAGG 57.815 50.000 0.00 0.00 0.00 3.46
268 272 2.928116 GTCGAGGAAGGTTAAACCATCG 59.072 50.000 0.00 0.00 41.95 3.84
287 291 1.735018 CGACCGTGGCATTACATTTCA 59.265 47.619 0.00 0.00 0.00 2.69
299 303 8.797438 TGGCATTACATTTCAAAAGTATACACA 58.203 29.630 5.50 0.00 0.00 3.72
312 316 1.064003 ATACACAAGTCTGCCCCACA 58.936 50.000 0.00 0.00 0.00 4.17
316 320 0.033601 ACAAGTCTGCCCCACAACAA 60.034 50.000 0.00 0.00 0.00 2.83
330 334 3.354089 ACAACAAGTGATTTCTTGCCG 57.646 42.857 6.38 1.55 45.86 5.69
332 336 3.243068 ACAACAAGTGATTTCTTGCCGAC 60.243 43.478 6.38 0.00 45.86 4.79
353 357 1.241315 AACCACGTGTAATGGCTGGC 61.241 55.000 15.65 0.00 41.31 4.85
357 361 0.253044 ACGTGTAATGGCTGGCTCAT 59.747 50.000 2.00 0.00 0.00 2.90
359 363 1.755179 GTGTAATGGCTGGCTCATGT 58.245 50.000 2.00 0.00 0.00 3.21
375 379 5.517770 GGCTCATGTGCAAAGAATCATTTAC 59.482 40.000 20.43 0.00 34.04 2.01
388 392 5.966935 AGAATCATTTACTTCCCTCCAGAGA 59.033 40.000 0.00 0.00 0.00 3.10
425 429 2.332063 ACTAGAAATGTGGCGGATGG 57.668 50.000 0.00 0.00 0.00 3.51
441 445 4.507869 GCGGATGGGGGTAGGTAATAAAAT 60.508 45.833 0.00 0.00 0.00 1.82
443 447 5.250982 GGATGGGGGTAGGTAATAAAATCG 58.749 45.833 0.00 0.00 0.00 3.34
446 450 4.970640 TGGGGGTAGGTAATAAAATCGACT 59.029 41.667 0.00 0.00 0.00 4.18
497 501 3.371179 GCTCCGCGTTCGTCTTAC 58.629 61.111 4.92 0.00 0.00 2.34
559 563 2.000447 GTTTCGTCCAGCTAAGCGATT 59.000 47.619 6.53 0.00 33.27 3.34
568 572 4.281941 TCCAGCTAAGCGATTGATGACTAT 59.718 41.667 0.00 0.00 0.00 2.12
603 607 1.201429 ATCACAGCTCCCCTTCCGTT 61.201 55.000 0.00 0.00 0.00 4.44
654 658 2.400911 TCGTATGCTCGACGGTCAT 58.599 52.632 9.10 1.57 40.70 3.06
659 663 3.365064 CGTATGCTCGACGGTCATATCTT 60.365 47.826 9.10 0.00 36.66 2.40
663 667 4.546570 TGCTCGACGGTCATATCTTAATG 58.453 43.478 9.10 0.00 0.00 1.90
671 675 3.412386 GTCATATCTTAATGGGCGCCTT 58.588 45.455 28.56 16.71 0.00 4.35
672 676 4.564821 GGTCATATCTTAATGGGCGCCTTA 60.565 45.833 28.56 15.53 0.00 2.69
673 677 5.186198 GTCATATCTTAATGGGCGCCTTAT 58.814 41.667 28.56 18.35 0.00 1.73
674 678 6.346096 GTCATATCTTAATGGGCGCCTTATA 58.654 40.000 28.56 13.74 0.00 0.98
675 679 6.992715 GTCATATCTTAATGGGCGCCTTATAT 59.007 38.462 28.56 15.53 0.00 0.86
676 680 7.499232 GTCATATCTTAATGGGCGCCTTATATT 59.501 37.037 28.56 21.76 0.00 1.28
677 681 8.052748 TCATATCTTAATGGGCGCCTTATATTT 58.947 33.333 28.56 12.98 0.00 1.40
678 682 8.686334 CATATCTTAATGGGCGCCTTATATTTT 58.314 33.333 28.56 11.61 0.00 1.82
679 683 6.325919 TCTTAATGGGCGCCTTATATTTTG 57.674 37.500 28.56 15.69 0.00 2.44
680 684 5.242838 TCTTAATGGGCGCCTTATATTTTGG 59.757 40.000 28.56 13.65 0.00 3.28
681 685 2.738587 TGGGCGCCTTATATTTTGGA 57.261 45.000 28.56 0.00 0.00 3.53
682 686 2.582052 TGGGCGCCTTATATTTTGGAG 58.418 47.619 28.56 0.00 0.00 3.86
683 687 2.092103 TGGGCGCCTTATATTTTGGAGT 60.092 45.455 28.56 0.00 0.00 3.85
684 688 2.552743 GGGCGCCTTATATTTTGGAGTC 59.447 50.000 28.56 0.00 0.00 3.36
685 689 3.211045 GGCGCCTTATATTTTGGAGTCA 58.789 45.455 22.15 0.00 0.00 3.41
686 690 3.821033 GGCGCCTTATATTTTGGAGTCAT 59.179 43.478 22.15 0.00 0.00 3.06
687 691 4.320494 GGCGCCTTATATTTTGGAGTCATG 60.320 45.833 22.15 0.00 0.00 3.07
688 692 4.787598 CGCCTTATATTTTGGAGTCATGC 58.212 43.478 0.00 0.00 0.00 4.06
689 693 4.516698 CGCCTTATATTTTGGAGTCATGCT 59.483 41.667 0.00 0.00 0.00 3.79
690 694 5.700832 CGCCTTATATTTTGGAGTCATGCTA 59.299 40.000 0.00 0.00 0.00 3.49
691 695 6.372659 CGCCTTATATTTTGGAGTCATGCTAT 59.627 38.462 0.00 0.00 0.00 2.97
692 696 7.533426 GCCTTATATTTTGGAGTCATGCTATG 58.467 38.462 0.00 0.00 0.00 2.23
693 697 7.533426 CCTTATATTTTGGAGTCATGCTATGC 58.467 38.462 0.00 0.00 0.00 3.14
694 698 7.175467 CCTTATATTTTGGAGTCATGCTATGCA 59.825 37.037 0.00 0.00 44.86 3.96
695 699 4.644103 ATTTTGGAGTCATGCTATGCAC 57.356 40.909 0.00 0.00 43.04 4.57
696 700 2.785540 TTGGAGTCATGCTATGCACA 57.214 45.000 0.00 0.00 43.04 4.57
697 701 2.028420 TGGAGTCATGCTATGCACAC 57.972 50.000 0.00 0.00 43.04 3.82
698 702 0.933097 GGAGTCATGCTATGCACACG 59.067 55.000 0.00 0.00 43.04 4.49
699 703 1.471501 GGAGTCATGCTATGCACACGA 60.472 52.381 0.00 0.00 43.04 4.35
700 704 2.477825 GAGTCATGCTATGCACACGAT 58.522 47.619 0.00 0.00 43.04 3.73
701 705 3.552890 GGAGTCATGCTATGCACACGATA 60.553 47.826 0.00 0.00 43.04 2.92
702 706 4.051237 GAGTCATGCTATGCACACGATAA 58.949 43.478 0.00 0.00 43.04 1.75
703 707 4.441792 AGTCATGCTATGCACACGATAAA 58.558 39.130 0.00 0.00 43.04 1.40
704 708 4.875536 AGTCATGCTATGCACACGATAAAA 59.124 37.500 0.00 0.00 43.04 1.52
705 709 5.528690 AGTCATGCTATGCACACGATAAAAT 59.471 36.000 0.00 0.00 43.04 1.82
706 710 5.848036 GTCATGCTATGCACACGATAAAATC 59.152 40.000 0.00 0.00 43.04 2.17
707 711 5.526846 TCATGCTATGCACACGATAAAATCA 59.473 36.000 0.00 0.00 43.04 2.57
708 712 5.408204 TGCTATGCACACGATAAAATCAG 57.592 39.130 0.00 0.00 31.71 2.90
709 713 4.273235 TGCTATGCACACGATAAAATCAGG 59.727 41.667 0.00 0.00 31.71 3.86
710 714 4.511454 GCTATGCACACGATAAAATCAGGA 59.489 41.667 0.00 0.00 0.00 3.86
711 715 4.882671 ATGCACACGATAAAATCAGGAC 57.117 40.909 0.00 0.00 0.00 3.85
712 716 2.670905 TGCACACGATAAAATCAGGACG 59.329 45.455 0.00 0.00 0.00 4.79
713 717 2.927477 GCACACGATAAAATCAGGACGA 59.073 45.455 0.00 0.00 0.00 4.20
714 718 3.555956 GCACACGATAAAATCAGGACGAT 59.444 43.478 0.00 0.00 35.12 3.73
715 719 4.034048 GCACACGATAAAATCAGGACGATT 59.966 41.667 0.00 0.00 46.70 3.34
716 720 5.728255 CACACGATAAAATCAGGACGATTC 58.272 41.667 0.00 0.00 43.83 2.52
717 721 5.290885 CACACGATAAAATCAGGACGATTCA 59.709 40.000 0.00 0.00 43.83 2.57
718 722 5.291128 ACACGATAAAATCAGGACGATTCAC 59.709 40.000 0.00 0.00 43.83 3.18
719 723 4.503007 ACGATAAAATCAGGACGATTCACG 59.497 41.667 0.00 0.00 43.83 4.35
720 724 4.085055 CGATAAAATCAGGACGATTCACGG 60.085 45.833 0.00 0.00 43.83 4.94
721 725 3.328382 AAAATCAGGACGATTCACGGA 57.672 42.857 0.00 0.00 43.83 4.69
722 726 3.328382 AAATCAGGACGATTCACGGAA 57.672 42.857 0.00 0.00 43.83 4.30
723 727 2.893637 AATCAGGACGATTCACGGAAG 58.106 47.619 0.00 0.00 40.48 3.46
724 728 2.496070 AATCAGGACGATTCACGGAAGA 59.504 45.455 0.00 0.00 40.48 2.87
725 729 3.133003 AATCAGGACGATTCACGGAAGAT 59.867 43.478 0.00 0.00 40.48 2.40
726 730 4.975432 AATCAGGACGATTCACGGAAGATG 60.975 45.833 0.00 0.00 40.48 2.90
727 731 7.918311 AATCAGGACGATTCACGGAAGATGG 62.918 48.000 0.00 0.00 40.48 3.51
733 737 5.734855 CGATTCACGGAAGATGGTTAAAT 57.265 39.130 0.00 0.00 38.46 1.40
734 738 5.738370 CGATTCACGGAAGATGGTTAAATC 58.262 41.667 0.00 0.00 38.46 2.17
735 739 5.293324 CGATTCACGGAAGATGGTTAAATCA 59.707 40.000 0.00 0.00 38.46 2.57
736 740 6.510157 CGATTCACGGAAGATGGTTAAATCAG 60.510 42.308 0.00 0.00 38.46 2.90
737 741 4.513442 TCACGGAAGATGGTTAAATCAGG 58.487 43.478 0.00 0.00 0.00 3.86
738 742 3.065371 CACGGAAGATGGTTAAATCAGGC 59.935 47.826 0.00 0.00 0.00 4.85
739 743 2.618709 CGGAAGATGGTTAAATCAGGCC 59.381 50.000 0.00 0.00 0.00 5.19
740 744 2.618709 GGAAGATGGTTAAATCAGGCCG 59.381 50.000 0.00 0.00 0.00 6.13
741 745 3.279434 GAAGATGGTTAAATCAGGCCGT 58.721 45.455 0.00 0.00 0.00 5.68
742 746 4.448210 GAAGATGGTTAAATCAGGCCGTA 58.552 43.478 0.00 0.00 0.00 4.02
743 747 3.805207 AGATGGTTAAATCAGGCCGTAC 58.195 45.455 0.00 0.00 0.00 3.67
744 748 3.199071 AGATGGTTAAATCAGGCCGTACA 59.801 43.478 0.00 0.00 0.00 2.90
745 749 3.637911 TGGTTAAATCAGGCCGTACAT 57.362 42.857 0.00 0.00 0.00 2.29
746 750 3.275143 TGGTTAAATCAGGCCGTACATG 58.725 45.455 0.00 0.00 0.00 3.21
747 751 2.032924 GGTTAAATCAGGCCGTACATGC 59.967 50.000 0.00 0.00 0.00 4.06
748 752 1.577468 TAAATCAGGCCGTACATGCG 58.423 50.000 0.00 0.00 0.00 4.73
749 753 0.392461 AAATCAGGCCGTACATGCGT 60.392 50.000 0.00 0.00 0.00 5.24
750 754 0.462375 AATCAGGCCGTACATGCGTA 59.538 50.000 0.00 0.00 0.00 4.42
751 755 0.679505 ATCAGGCCGTACATGCGTAT 59.320 50.000 0.00 0.00 0.00 3.06
752 756 0.249280 TCAGGCCGTACATGCGTATG 60.249 55.000 12.28 12.28 40.24 2.39
753 757 0.249280 CAGGCCGTACATGCGTATGA 60.249 55.000 20.86 1.06 36.84 2.15
754 758 0.032130 AGGCCGTACATGCGTATGAG 59.968 55.000 20.86 10.35 36.84 2.90
755 759 0.249322 GGCCGTACATGCGTATGAGT 60.249 55.000 20.86 0.90 36.84 3.41
756 760 0.852777 GCCGTACATGCGTATGAGTG 59.147 55.000 20.86 8.33 36.84 3.51
757 761 1.535226 GCCGTACATGCGTATGAGTGA 60.535 52.381 20.86 0.00 36.84 3.41
758 762 2.804647 CCGTACATGCGTATGAGTGAA 58.195 47.619 20.86 0.00 36.84 3.18
759 763 3.183754 CCGTACATGCGTATGAGTGAAA 58.816 45.455 20.86 0.00 36.84 2.69
760 764 3.242944 CCGTACATGCGTATGAGTGAAAG 59.757 47.826 20.86 4.14 36.84 2.62
761 765 4.102649 CGTACATGCGTATGAGTGAAAGA 58.897 43.478 20.86 0.00 36.84 2.52
762 766 4.561213 CGTACATGCGTATGAGTGAAAGAA 59.439 41.667 20.86 0.00 36.84 2.52
763 767 4.928661 ACATGCGTATGAGTGAAAGAAC 57.071 40.909 20.86 0.00 37.73 3.01
764 768 3.684788 ACATGCGTATGAGTGAAAGAACC 59.315 43.478 20.86 0.00 37.73 3.62
765 769 2.695359 TGCGTATGAGTGAAAGAACCC 58.305 47.619 0.00 0.00 0.00 4.11
766 770 2.037902 TGCGTATGAGTGAAAGAACCCA 59.962 45.455 0.00 0.00 0.00 4.51
767 771 3.270877 GCGTATGAGTGAAAGAACCCAT 58.729 45.455 0.00 0.00 0.00 4.00
768 772 3.063997 GCGTATGAGTGAAAGAACCCATG 59.936 47.826 0.00 0.00 0.00 3.66
769 773 4.503910 CGTATGAGTGAAAGAACCCATGA 58.496 43.478 0.00 0.00 0.00 3.07
770 774 4.330074 CGTATGAGTGAAAGAACCCATGAC 59.670 45.833 0.00 0.00 0.00 3.06
771 775 2.766313 TGAGTGAAAGAACCCATGACG 58.234 47.619 0.00 0.00 0.00 4.35
772 776 1.464997 GAGTGAAAGAACCCATGACGC 59.535 52.381 0.00 0.00 0.00 5.19
773 777 1.072331 AGTGAAAGAACCCATGACGCT 59.928 47.619 0.00 0.00 0.00 5.07
774 778 1.197721 GTGAAAGAACCCATGACGCTG 59.802 52.381 0.00 0.00 0.00 5.18
775 779 0.804989 GAAAGAACCCATGACGCTGG 59.195 55.000 0.00 0.00 35.95 4.85
776 780 0.400213 AAAGAACCCATGACGCTGGA 59.600 50.000 0.00 0.00 38.69 3.86
777 781 0.620556 AAGAACCCATGACGCTGGAT 59.379 50.000 0.00 0.00 38.69 3.41
778 782 0.620556 AGAACCCATGACGCTGGATT 59.379 50.000 0.00 0.00 38.69 3.01
779 783 1.004745 AGAACCCATGACGCTGGATTT 59.995 47.619 0.00 0.00 38.69 2.17
780 784 2.238646 AGAACCCATGACGCTGGATTTA 59.761 45.455 0.00 0.00 38.69 1.40
781 785 2.038387 ACCCATGACGCTGGATTTAC 57.962 50.000 0.00 0.00 38.69 2.01
782 786 1.280710 ACCCATGACGCTGGATTTACA 59.719 47.619 0.00 0.00 38.69 2.41
783 787 2.092429 ACCCATGACGCTGGATTTACAT 60.092 45.455 0.00 0.00 38.69 2.29
784 788 3.135712 ACCCATGACGCTGGATTTACATA 59.864 43.478 0.00 0.00 38.69 2.29
785 789 4.202461 ACCCATGACGCTGGATTTACATAT 60.202 41.667 0.00 0.00 38.69 1.78
786 790 4.393062 CCCATGACGCTGGATTTACATATC 59.607 45.833 0.00 0.00 38.69 1.63
787 791 4.091945 CCATGACGCTGGATTTACATATCG 59.908 45.833 0.00 0.00 38.69 2.92
788 792 4.316205 TGACGCTGGATTTACATATCGT 57.684 40.909 0.00 0.00 0.00 3.73
789 793 4.048504 TGACGCTGGATTTACATATCGTG 58.951 43.478 0.00 0.00 0.00 4.35
790 794 2.800544 ACGCTGGATTTACATATCGTGC 59.199 45.455 0.00 0.00 0.00 5.34
791 795 2.799978 CGCTGGATTTACATATCGTGCA 59.200 45.455 0.00 0.00 0.00 4.57
792 796 3.362986 CGCTGGATTTACATATCGTGCAC 60.363 47.826 6.82 6.82 0.00 4.57
793 797 3.559655 GCTGGATTTACATATCGTGCACA 59.440 43.478 18.64 4.45 0.00 4.57
794 798 4.552767 GCTGGATTTACATATCGTGCACAC 60.553 45.833 18.64 0.00 0.00 3.82
804 808 4.064491 GTGCACACGTCGAGCAGC 62.064 66.667 13.17 0.00 39.21 5.25
805 809 4.284860 TGCACACGTCGAGCAGCT 62.285 61.111 0.00 0.00 33.75 4.24
806 810 3.038417 GCACACGTCGAGCAGCTT 61.038 61.111 0.00 0.00 0.00 3.74
807 811 3.004734 GCACACGTCGAGCAGCTTC 62.005 63.158 0.00 0.00 0.00 3.86
808 812 2.429236 ACACGTCGAGCAGCTTCG 60.429 61.111 0.00 5.22 41.79 3.79
827 850 4.699925 TCGTATATTTTGGGAAGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
829 852 4.347000 TCGTATATTTTGGGAAGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
837 860 2.292061 TGGGAAGGAGGGAGTACTGTAC 60.292 54.545 9.93 9.93 0.00 2.90
866 895 1.812922 CTAGCAAGACGGGCAGCAG 60.813 63.158 0.00 0.00 0.00 4.24
916 945 1.336887 CCGTTCCACTGTACTCCACTG 60.337 57.143 0.00 0.00 0.00 3.66
1029 1063 0.178990 AGGACAAGAGGTGTTTGCCC 60.179 55.000 0.00 0.00 41.96 5.36
1031 1065 1.692411 GACAAGAGGTGTTTGCCCTT 58.308 50.000 0.00 0.00 41.96 3.95
1319 1374 1.167851 GTACGCCATGGCATGCATAT 58.832 50.000 34.93 10.48 42.06 1.78
1322 1377 3.280197 ACGCCATGGCATGCATATATA 57.720 42.857 34.93 0.00 42.06 0.86
1323 1378 3.208594 ACGCCATGGCATGCATATATAG 58.791 45.455 34.93 16.82 42.06 1.31
1328 1383 6.213677 GCCATGGCATGCATATATAGATTTG 58.786 40.000 32.08 4.26 41.49 2.32
1353 1408 9.733556 TGTTTCCAGATTATTACTACAACACAT 57.266 29.630 0.00 0.00 0.00 3.21
1354 1409 9.988350 GTTTCCAGATTATTACTACAACACATG 57.012 33.333 0.00 0.00 0.00 3.21
1358 1432 9.161629 CCAGATTATTACTACAACACATGAACA 57.838 33.333 0.00 0.00 0.00 3.18
1909 1996 1.511305 GGCGACAAGGACGAGATGA 59.489 57.895 0.00 0.00 0.00 2.92
1920 2007 2.028294 GGACGAGATGATCATGATGGCT 60.028 50.000 14.30 7.09 0.00 4.75
1923 2010 2.666994 CGAGATGATCATGATGGCTTCG 59.333 50.000 14.30 12.89 0.00 3.79
2139 2241 0.178992 CAACAACCAGGAGGCTCCAA 60.179 55.000 33.86 0.00 39.61 3.53
2144 2246 1.225704 CCAGGAGGCTCCAATGACC 59.774 63.158 33.86 7.21 39.61 4.02
2184 2289 6.890979 TGATGATGTTGTGTATGTTTTGGA 57.109 33.333 0.00 0.00 0.00 3.53
2201 2306 8.545229 TGTTTTGGATTTAAATGGCATGTTAG 57.455 30.769 5.17 0.00 0.00 2.34
2269 2379 5.070180 TGTGTCCAAAACCAATCATGTCAAT 59.930 36.000 0.00 0.00 0.00 2.57
2274 2384 9.050601 GTCCAAAACCAATCATGTCAATTTTTA 57.949 29.630 0.00 0.00 0.00 1.52
2427 2545 2.622470 CACAACCACCATGACAACATCA 59.378 45.455 0.00 0.00 43.13 3.07
2495 2614 1.447643 GGACACAGAGCACACAGGT 59.552 57.895 0.00 0.00 0.00 4.00
2665 2784 1.704641 TGATGGAGTACATAGCGCCT 58.295 50.000 2.29 0.00 40.72 5.52
2791 2915 2.046892 CAAGCACCTAGGCAGCGT 60.047 61.111 18.10 13.73 35.83 5.07
3000 3128 1.067749 CATCTCCGGAGCTCAGCAG 59.932 63.158 27.39 7.35 0.00 4.24
3054 3183 1.381872 ATCACCGTGGAGAGGGGAG 60.382 63.158 0.00 0.00 45.50 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.241728 AGGAAAGTTAATGACTCTTTGGCAC 59.758 40.000 0.00 0.00 37.72 5.01
1 2 5.385198 AGGAAAGTTAATGACTCTTTGGCA 58.615 37.500 0.00 0.00 37.72 4.92
2 3 5.106118 GGAGGAAAGTTAATGACTCTTTGGC 60.106 44.000 0.00 0.00 37.72 4.52
26 27 1.354368 TCAGCCCCCTTCCTAAGTTTG 59.646 52.381 0.00 0.00 0.00 2.93
64 65 1.227263 CCTACCCCGAAGCATCACG 60.227 63.158 0.00 0.00 0.00 4.35
68 69 1.141053 GATTGACCTACCCCGAAGCAT 59.859 52.381 0.00 0.00 0.00 3.79
90 91 0.874607 AATCTAATGCCGCGGTCGAC 60.875 55.000 28.70 7.13 38.10 4.20
96 97 3.758300 AGTTTGAAAATCTAATGCCGCG 58.242 40.909 0.00 0.00 0.00 6.46
97 98 7.376072 GTGTATAGTTTGAAAATCTAATGCCGC 59.624 37.037 0.00 0.00 32.38 6.53
98 99 8.612619 AGTGTATAGTTTGAAAATCTAATGCCG 58.387 33.333 0.00 0.00 32.38 5.69
113 114 6.702723 TCGCACAACAAACTAGTGTATAGTTT 59.297 34.615 0.00 7.10 45.47 2.66
114 115 6.145048 GTCGCACAACAAACTAGTGTATAGTT 59.855 38.462 0.00 0.00 39.24 2.24
115 116 5.632347 GTCGCACAACAAACTAGTGTATAGT 59.368 40.000 0.00 0.00 35.75 2.12
116 117 5.061808 GGTCGCACAACAAACTAGTGTATAG 59.938 44.000 0.00 0.00 35.75 1.31
117 118 4.925054 GGTCGCACAACAAACTAGTGTATA 59.075 41.667 0.00 0.00 35.75 1.47
118 119 3.744426 GGTCGCACAACAAACTAGTGTAT 59.256 43.478 0.00 0.00 35.75 2.29
119 120 3.125316 GGTCGCACAACAAACTAGTGTA 58.875 45.455 0.00 0.00 35.75 2.90
120 121 1.937899 GGTCGCACAACAAACTAGTGT 59.062 47.619 0.00 0.00 35.75 3.55
121 122 1.937223 TGGTCGCACAACAAACTAGTG 59.063 47.619 0.00 0.00 36.39 2.74
122 123 2.210116 CTGGTCGCACAACAAACTAGT 58.790 47.619 0.00 0.00 0.00 2.57
123 124 1.069906 GCTGGTCGCACAACAAACTAG 60.070 52.381 0.00 0.00 38.92 2.57
124 125 0.941542 GCTGGTCGCACAACAAACTA 59.058 50.000 0.00 0.00 38.92 2.24
131 132 0.537143 AGAAATGGCTGGTCGCACAA 60.537 50.000 0.00 0.00 41.67 3.33
154 155 3.370978 AGCCGTTACTCGTGATTCAATTG 59.629 43.478 0.00 0.00 37.94 2.32
199 200 2.177016 CCCCTTCCTAACTTTATGGGGG 59.823 54.545 6.30 0.00 46.71 5.40
204 205 3.822880 TCCACCCCCTTCCTAACTTTAT 58.177 45.455 0.00 0.00 0.00 1.40
246 250 3.615592 CGATGGTTTAACCTTCCTCGACA 60.616 47.826 19.87 0.00 38.74 4.35
251 255 2.354403 CGGTCGATGGTTTAACCTTCCT 60.354 50.000 19.87 2.43 38.74 3.36
253 257 2.414138 CACGGTCGATGGTTTAACCTTC 59.586 50.000 15.68 16.43 39.58 3.46
257 261 0.445043 GCCACGGTCGATGGTTTAAC 59.555 55.000 5.48 0.00 39.63 2.01
268 272 3.840890 TTGAAATGTAATGCCACGGTC 57.159 42.857 0.00 0.00 0.00 4.79
287 291 4.202524 TGGGGCAGACTTGTGTATACTTTT 60.203 41.667 4.17 0.00 0.00 2.27
299 303 0.258774 ACTTGTTGTGGGGCAGACTT 59.741 50.000 0.00 0.00 0.00 3.01
304 308 1.686052 GAAATCACTTGTTGTGGGGCA 59.314 47.619 0.00 0.00 46.20 5.36
312 316 2.032030 CGTCGGCAAGAAATCACTTGTT 60.032 45.455 0.00 0.00 45.98 2.83
316 320 1.798813 GTTCGTCGGCAAGAAATCACT 59.201 47.619 0.00 0.00 0.00 3.41
319 323 1.136057 GTGGTTCGTCGGCAAGAAATC 60.136 52.381 0.00 0.00 0.00 2.17
332 336 0.442310 CAGCCATTACACGTGGTTCG 59.558 55.000 21.57 5.42 46.00 3.95
348 352 0.599558 TTCTTTGCACATGAGCCAGC 59.400 50.000 12.78 2.70 0.00 4.85
353 357 7.487189 GGAAGTAAATGATTCTTTGCACATGAG 59.513 37.037 0.00 0.00 0.00 2.90
357 361 5.774690 AGGGAAGTAAATGATTCTTTGCACA 59.225 36.000 0.00 0.00 0.00 4.57
359 363 5.418840 GGAGGGAAGTAAATGATTCTTTGCA 59.581 40.000 0.00 0.00 0.00 4.08
388 392 1.228306 TTTTGACGCCCGTTCCCAT 60.228 52.632 0.00 0.00 0.00 4.00
425 429 6.016276 TCGTAGTCGATTTTATTACCTACCCC 60.016 42.308 0.00 0.00 41.35 4.95
443 447 7.744715 ACAATTTGAAAATCGAATGTCGTAGTC 59.255 33.333 2.79 0.00 41.35 2.59
446 450 8.496751 TGTACAATTTGAAAATCGAATGTCGTA 58.503 29.630 2.79 0.00 41.35 3.43
450 454 7.356540 TCGTGTACAATTTGAAAATCGAATGT 58.643 30.769 2.79 0.00 31.15 2.71
495 499 2.285024 CCCTCCGTCCGGGTTTGTA 61.285 63.158 0.00 0.00 36.91 2.41
496 500 3.633116 CCCTCCGTCCGGGTTTGT 61.633 66.667 0.00 0.00 36.91 2.83
497 501 3.310860 CTCCCTCCGTCCGGGTTTG 62.311 68.421 0.00 0.00 42.56 2.93
559 563 7.989947 AACCCCTAAGTTTAGATAGTCATCA 57.010 36.000 0.51 0.00 33.21 3.07
568 572 5.724854 AGCTGTGATAACCCCTAAGTTTAGA 59.275 40.000 0.51 0.00 32.47 2.10
603 607 2.234414 ACGGCAAGAAACGGGTTCTATA 59.766 45.455 9.03 0.00 46.36 1.31
649 653 2.084546 GGCGCCCATTAAGATATGACC 58.915 52.381 18.11 0.00 0.00 4.02
654 658 7.122055 CCAAAATATAAGGCGCCCATTAAGATA 59.878 37.037 26.15 10.58 0.00 1.98
659 663 4.730966 TCCAAAATATAAGGCGCCCATTA 58.269 39.130 26.15 17.11 0.00 1.90
663 667 2.552743 GACTCCAAAATATAAGGCGCCC 59.447 50.000 26.15 5.07 0.00 6.13
671 675 6.997476 TGTGCATAGCATGACTCCAAAATATA 59.003 34.615 0.00 0.00 41.91 0.86
672 676 5.829391 TGTGCATAGCATGACTCCAAAATAT 59.171 36.000 0.00 0.00 41.91 1.28
673 677 5.066375 GTGTGCATAGCATGACTCCAAAATA 59.934 40.000 0.00 0.00 41.91 1.40
674 678 4.018490 TGTGCATAGCATGACTCCAAAAT 58.982 39.130 0.00 0.00 41.91 1.82
675 679 3.191162 GTGTGCATAGCATGACTCCAAAA 59.809 43.478 0.00 0.00 41.91 2.44
676 680 2.749076 GTGTGCATAGCATGACTCCAAA 59.251 45.455 0.00 0.00 41.91 3.28
677 681 2.358957 GTGTGCATAGCATGACTCCAA 58.641 47.619 0.00 0.00 41.91 3.53
678 682 1.740043 CGTGTGCATAGCATGACTCCA 60.740 52.381 0.00 0.00 41.91 3.86
679 683 0.933097 CGTGTGCATAGCATGACTCC 59.067 55.000 0.00 0.00 41.91 3.85
680 684 1.926561 TCGTGTGCATAGCATGACTC 58.073 50.000 0.00 0.00 41.91 3.36
681 685 2.609427 ATCGTGTGCATAGCATGACT 57.391 45.000 0.00 0.00 41.91 3.41
682 686 4.794248 TTTATCGTGTGCATAGCATGAC 57.206 40.909 0.00 0.00 41.91 3.06
683 687 5.526846 TGATTTTATCGTGTGCATAGCATGA 59.473 36.000 0.00 0.00 41.91 3.07
684 688 5.750650 TGATTTTATCGTGTGCATAGCATG 58.249 37.500 0.00 0.00 41.91 4.06
685 689 5.049198 CCTGATTTTATCGTGTGCATAGCAT 60.049 40.000 0.00 0.00 41.91 3.79
686 690 4.273235 CCTGATTTTATCGTGTGCATAGCA 59.727 41.667 0.00 0.00 35.60 3.49
687 691 4.511454 TCCTGATTTTATCGTGTGCATAGC 59.489 41.667 0.00 0.00 0.00 2.97
688 692 5.332581 CGTCCTGATTTTATCGTGTGCATAG 60.333 44.000 0.00 0.00 0.00 2.23
689 693 4.506288 CGTCCTGATTTTATCGTGTGCATA 59.494 41.667 0.00 0.00 0.00 3.14
690 694 3.309682 CGTCCTGATTTTATCGTGTGCAT 59.690 43.478 0.00 0.00 0.00 3.96
691 695 2.670905 CGTCCTGATTTTATCGTGTGCA 59.329 45.455 0.00 0.00 0.00 4.57
692 696 2.927477 TCGTCCTGATTTTATCGTGTGC 59.073 45.455 0.00 0.00 0.00 4.57
693 697 5.718649 AATCGTCCTGATTTTATCGTGTG 57.281 39.130 0.00 0.00 45.06 3.82
704 708 2.100197 TCTTCCGTGAATCGTCCTGAT 58.900 47.619 0.00 0.00 39.67 2.90
705 709 1.541379 TCTTCCGTGAATCGTCCTGA 58.459 50.000 0.00 0.00 37.94 3.86
706 710 2.196749 CATCTTCCGTGAATCGTCCTG 58.803 52.381 0.00 0.00 37.94 3.86
707 711 1.137086 CCATCTTCCGTGAATCGTCCT 59.863 52.381 0.00 0.00 37.94 3.85
708 712 1.134788 ACCATCTTCCGTGAATCGTCC 60.135 52.381 0.00 0.00 37.94 4.79
709 713 2.295253 ACCATCTTCCGTGAATCGTC 57.705 50.000 0.00 0.00 37.94 4.20
710 714 2.762535 AACCATCTTCCGTGAATCGT 57.237 45.000 0.00 0.00 37.94 3.73
711 715 5.293324 TGATTTAACCATCTTCCGTGAATCG 59.707 40.000 0.00 0.00 39.52 3.34
712 716 6.238484 CCTGATTTAACCATCTTCCGTGAATC 60.238 42.308 0.00 0.00 0.00 2.52
713 717 5.590259 CCTGATTTAACCATCTTCCGTGAAT 59.410 40.000 0.00 0.00 0.00 2.57
714 718 4.941263 CCTGATTTAACCATCTTCCGTGAA 59.059 41.667 0.00 0.00 0.00 3.18
715 719 4.513442 CCTGATTTAACCATCTTCCGTGA 58.487 43.478 0.00 0.00 0.00 4.35
716 720 3.065371 GCCTGATTTAACCATCTTCCGTG 59.935 47.826 0.00 0.00 0.00 4.94
717 721 3.279434 GCCTGATTTAACCATCTTCCGT 58.721 45.455 0.00 0.00 0.00 4.69
718 722 2.618709 GGCCTGATTTAACCATCTTCCG 59.381 50.000 0.00 0.00 0.00 4.30
719 723 2.618709 CGGCCTGATTTAACCATCTTCC 59.381 50.000 0.00 0.00 0.00 3.46
720 724 3.279434 ACGGCCTGATTTAACCATCTTC 58.721 45.455 0.00 0.00 0.00 2.87
721 725 3.366052 ACGGCCTGATTTAACCATCTT 57.634 42.857 0.00 0.00 0.00 2.40
722 726 3.199071 TGTACGGCCTGATTTAACCATCT 59.801 43.478 0.00 0.00 0.00 2.90
723 727 3.537580 TGTACGGCCTGATTTAACCATC 58.462 45.455 0.00 0.00 0.00 3.51
724 728 3.637911 TGTACGGCCTGATTTAACCAT 57.362 42.857 0.00 0.00 0.00 3.55
725 729 3.275143 CATGTACGGCCTGATTTAACCA 58.725 45.455 0.00 0.00 0.00 3.67
726 730 2.032924 GCATGTACGGCCTGATTTAACC 59.967 50.000 0.00 0.00 0.00 2.85
727 731 2.286184 CGCATGTACGGCCTGATTTAAC 60.286 50.000 0.00 0.00 0.00 2.01
728 732 1.937223 CGCATGTACGGCCTGATTTAA 59.063 47.619 0.00 0.00 0.00 1.52
729 733 1.134640 ACGCATGTACGGCCTGATTTA 60.135 47.619 0.00 0.00 37.37 1.40
730 734 0.392461 ACGCATGTACGGCCTGATTT 60.392 50.000 0.00 0.00 37.37 2.17
731 735 0.462375 TACGCATGTACGGCCTGATT 59.538 50.000 0.00 0.00 37.37 2.57
732 736 0.679505 ATACGCATGTACGGCCTGAT 59.320 50.000 0.00 0.00 37.37 2.90
733 737 0.249280 CATACGCATGTACGGCCTGA 60.249 55.000 0.00 0.00 37.37 3.86
734 738 0.249280 TCATACGCATGTACGGCCTG 60.249 55.000 0.00 0.00 37.37 4.85
735 739 0.032130 CTCATACGCATGTACGGCCT 59.968 55.000 0.00 0.00 37.37 5.19
736 740 0.249322 ACTCATACGCATGTACGGCC 60.249 55.000 0.00 0.00 37.37 6.13
737 741 0.852777 CACTCATACGCATGTACGGC 59.147 55.000 0.00 0.00 37.37 5.68
738 742 2.485266 TCACTCATACGCATGTACGG 57.515 50.000 0.00 0.00 37.37 4.02
739 743 4.102649 TCTTTCACTCATACGCATGTACG 58.897 43.478 0.00 0.00 39.50 3.67
740 744 5.220416 GGTTCTTTCACTCATACGCATGTAC 60.220 44.000 0.00 0.00 32.26 2.90
741 745 4.868171 GGTTCTTTCACTCATACGCATGTA 59.132 41.667 0.00 0.00 33.57 2.29
742 746 3.684788 GGTTCTTTCACTCATACGCATGT 59.315 43.478 0.00 0.00 33.57 3.21
743 747 3.063997 GGGTTCTTTCACTCATACGCATG 59.936 47.826 0.00 0.00 0.00 4.06
744 748 3.270877 GGGTTCTTTCACTCATACGCAT 58.729 45.455 0.00 0.00 0.00 4.73
745 749 2.037902 TGGGTTCTTTCACTCATACGCA 59.962 45.455 0.00 0.00 0.00 5.24
746 750 2.695359 TGGGTTCTTTCACTCATACGC 58.305 47.619 0.00 0.00 0.00 4.42
747 751 4.330074 GTCATGGGTTCTTTCACTCATACG 59.670 45.833 0.00 0.00 35.52 3.06
748 752 4.330074 CGTCATGGGTTCTTTCACTCATAC 59.670 45.833 0.00 0.00 35.52 2.39
749 753 4.503910 CGTCATGGGTTCTTTCACTCATA 58.496 43.478 0.00 0.00 35.52 2.15
750 754 3.338249 CGTCATGGGTTCTTTCACTCAT 58.662 45.455 0.00 0.00 38.50 2.90
751 755 2.766313 CGTCATGGGTTCTTTCACTCA 58.234 47.619 0.00 0.00 0.00 3.41
752 756 1.464997 GCGTCATGGGTTCTTTCACTC 59.535 52.381 0.00 0.00 0.00 3.51
753 757 1.072331 AGCGTCATGGGTTCTTTCACT 59.928 47.619 0.00 0.00 0.00 3.41
754 758 1.197721 CAGCGTCATGGGTTCTTTCAC 59.802 52.381 0.00 0.00 0.00 3.18
755 759 1.522668 CAGCGTCATGGGTTCTTTCA 58.477 50.000 0.00 0.00 0.00 2.69
756 760 0.804989 CCAGCGTCATGGGTTCTTTC 59.195 55.000 0.00 0.00 36.64 2.62
757 761 0.400213 TCCAGCGTCATGGGTTCTTT 59.600 50.000 0.00 0.00 41.01 2.52
758 762 0.620556 ATCCAGCGTCATGGGTTCTT 59.379 50.000 0.00 0.00 41.01 2.52
759 763 0.620556 AATCCAGCGTCATGGGTTCT 59.379 50.000 0.00 0.00 39.59 3.01
760 764 1.463674 AAATCCAGCGTCATGGGTTC 58.536 50.000 2.99 0.00 43.05 3.62
761 765 2.290641 TGTAAATCCAGCGTCATGGGTT 60.291 45.455 0.00 0.65 45.88 4.11
762 766 1.280710 TGTAAATCCAGCGTCATGGGT 59.719 47.619 0.00 0.00 41.01 4.51
763 767 2.036958 TGTAAATCCAGCGTCATGGG 57.963 50.000 0.00 0.00 41.01 4.00
764 768 4.091945 CGATATGTAAATCCAGCGTCATGG 59.908 45.833 0.00 0.00 42.11 3.66
765 769 4.686091 ACGATATGTAAATCCAGCGTCATG 59.314 41.667 0.00 0.00 0.00 3.07
766 770 4.686091 CACGATATGTAAATCCAGCGTCAT 59.314 41.667 0.00 0.00 0.00 3.06
767 771 4.048504 CACGATATGTAAATCCAGCGTCA 58.951 43.478 0.00 0.00 0.00 4.35
768 772 3.120991 GCACGATATGTAAATCCAGCGTC 60.121 47.826 0.00 0.00 0.00 5.19
769 773 2.800544 GCACGATATGTAAATCCAGCGT 59.199 45.455 0.00 0.00 0.00 5.07
770 774 2.799978 TGCACGATATGTAAATCCAGCG 59.200 45.455 0.00 0.00 0.00 5.18
771 775 3.559655 TGTGCACGATATGTAAATCCAGC 59.440 43.478 13.13 0.00 0.00 4.85
772 776 5.083136 GTGTGCACGATATGTAAATCCAG 57.917 43.478 13.13 0.00 0.00 3.86
787 791 4.064491 GCTGCTCGACGTGTGCAC 62.064 66.667 10.75 10.75 41.83 4.57
788 792 3.790334 AAGCTGCTCGACGTGTGCA 62.790 57.895 1.00 3.60 44.29 4.57
789 793 3.004734 GAAGCTGCTCGACGTGTGC 62.005 63.158 1.00 0.00 37.59 4.57
790 794 2.710971 CGAAGCTGCTCGACGTGTG 61.711 63.158 1.00 0.00 41.44 3.82
791 795 1.848932 TACGAAGCTGCTCGACGTGT 61.849 55.000 26.66 13.38 41.44 4.49
792 796 0.523546 ATACGAAGCTGCTCGACGTG 60.524 55.000 26.66 9.36 41.44 4.49
793 797 1.012086 TATACGAAGCTGCTCGACGT 58.988 50.000 23.94 23.94 41.44 4.34
794 798 2.317679 ATATACGAAGCTGCTCGACG 57.682 50.000 21.95 19.62 41.44 5.12
795 799 4.318121 CCAAAATATACGAAGCTGCTCGAC 60.318 45.833 21.95 9.17 41.44 4.20
796 800 3.802139 CCAAAATATACGAAGCTGCTCGA 59.198 43.478 21.95 10.42 41.44 4.04
797 801 3.059597 CCCAAAATATACGAAGCTGCTCG 60.060 47.826 16.18 16.18 44.50 5.03
798 802 4.127171 TCCCAAAATATACGAAGCTGCTC 58.873 43.478 1.00 0.00 0.00 4.26
799 803 4.150897 TCCCAAAATATACGAAGCTGCT 57.849 40.909 0.00 0.00 0.00 4.24
800 804 4.261197 CCTTCCCAAAATATACGAAGCTGC 60.261 45.833 0.00 0.00 30.75 5.25
801 805 5.123227 TCCTTCCCAAAATATACGAAGCTG 58.877 41.667 0.00 0.00 30.75 4.24
802 806 5.367945 TCCTTCCCAAAATATACGAAGCT 57.632 39.130 0.00 0.00 30.75 3.74
803 807 4.515567 CCTCCTTCCCAAAATATACGAAGC 59.484 45.833 0.00 0.00 30.75 3.86
804 808 5.063880 CCCTCCTTCCCAAAATATACGAAG 58.936 45.833 0.00 0.00 0.00 3.79
805 809 4.722781 TCCCTCCTTCCCAAAATATACGAA 59.277 41.667 0.00 0.00 0.00 3.85
806 810 4.300345 TCCCTCCTTCCCAAAATATACGA 58.700 43.478 0.00 0.00 0.00 3.43
807 811 4.102681 ACTCCCTCCTTCCCAAAATATACG 59.897 45.833 0.00 0.00 0.00 3.06
808 812 5.648330 ACTCCCTCCTTCCCAAAATATAC 57.352 43.478 0.00 0.00 0.00 1.47
827 850 9.539825 TGCTAGTACTATACTTGTACAGTACTC 57.460 37.037 25.68 17.10 46.72 2.59
837 860 5.759963 CCCGTCTTGCTAGTACTATACTTG 58.240 45.833 2.33 0.00 40.14 3.16
848 871 1.812922 CTGCTGCCCGTCTTGCTAG 60.813 63.158 0.00 0.00 0.00 3.42
849 872 2.230994 CTCTGCTGCCCGTCTTGCTA 62.231 60.000 0.00 0.00 0.00 3.49
852 875 2.435586 CCTCTGCTGCCCGTCTTG 60.436 66.667 0.00 0.00 0.00 3.02
866 895 2.433318 GAGACTGCACCGTGCCTC 60.433 66.667 20.67 15.30 44.23 4.70
874 903 1.226435 CCGCTACGAGAGACTGCAC 60.226 63.158 0.00 0.00 0.00 4.57
875 904 0.958876 TTCCGCTACGAGAGACTGCA 60.959 55.000 0.00 0.00 0.00 4.41
879 908 1.064458 GGCTTCCGCTACGAGAGAC 59.936 63.158 0.00 0.00 36.09 3.36
1029 1063 3.736100 TTGCACGCCGGCATCAAG 61.736 61.111 28.98 12.44 44.48 3.02
1121 1155 2.443016 CCCACTCCTCCTCCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
1305 1360 7.342769 ACAAATCTATATATGCATGCCATGG 57.657 36.000 16.68 7.63 35.34 3.66
1328 1383 9.988350 CATGTGTTGTAGTAATAATCTGGAAAC 57.012 33.333 0.00 0.00 0.00 2.78
1344 1399 4.320129 CGGCAAGATTGTTCATGTGTTGTA 60.320 41.667 0.00 0.00 0.00 2.41
1346 1401 2.981805 CGGCAAGATTGTTCATGTGTTG 59.018 45.455 0.00 0.00 0.00 3.33
1347 1402 2.622942 ACGGCAAGATTGTTCATGTGTT 59.377 40.909 0.00 0.00 0.00 3.32
1348 1403 2.229792 ACGGCAAGATTGTTCATGTGT 58.770 42.857 0.00 0.00 0.00 3.72
1349 1404 2.981805 CAACGGCAAGATTGTTCATGTG 59.018 45.455 0.00 0.00 0.00 3.21
1350 1405 2.607771 GCAACGGCAAGATTGTTCATGT 60.608 45.455 0.00 0.00 40.72 3.21
1351 1406 1.987770 GCAACGGCAAGATTGTTCATG 59.012 47.619 0.00 0.00 40.72 3.07
1353 1408 0.313672 GGCAACGGCAAGATTGTTCA 59.686 50.000 0.00 0.00 43.71 3.18
1354 1409 3.107017 GGCAACGGCAAGATTGTTC 57.893 52.632 0.00 0.00 43.71 3.18
1965 2052 1.750399 CAAGAACATCCCCTGGCCG 60.750 63.158 0.00 0.00 0.00 6.13
1968 2055 1.750399 CGCCAAGAACATCCCCTGG 60.750 63.158 0.00 0.00 0.00 4.45
1996 2083 2.024868 CGTCGCCGGACATCAACAA 61.025 57.895 5.05 0.00 43.61 2.83
1997 2084 2.431771 CGTCGCCGGACATCAACA 60.432 61.111 5.05 0.00 43.61 3.33
2019 2106 3.974835 AATGCGGACGCTGATGGCA 62.975 57.895 18.04 0.00 42.51 4.92
2107 2203 0.811281 GTTGTTGTCCTAGCATGGGC 59.189 55.000 0.00 0.00 36.20 5.36
2139 2241 3.172339 AGAAGAAGAGCAGAGTGGTCAT 58.828 45.455 8.69 0.00 46.52 3.06
2144 2246 4.818642 TCATCAAGAAGAAGAGCAGAGTG 58.181 43.478 0.00 0.00 0.00 3.51
2184 2289 6.094881 ACGTACTGCTAACATGCCATTTAAAT 59.905 34.615 0.00 0.00 0.00 1.40
2352 2462 0.101759 GGCGTTGTATCAGCCGTCTA 59.898 55.000 0.00 0.00 41.53 2.59
2427 2545 0.539669 GGGCAAGGGTGTTAGTTGCT 60.540 55.000 6.27 0.00 44.87 3.91
2665 2784 0.612744 TTGTGGACATGAGCATCCGA 59.387 50.000 0.00 0.00 37.87 4.55
2762 2886 2.040544 GTGCTTGGGGTGTCATCCG 61.041 63.158 0.00 0.00 0.00 4.18
2766 2890 1.488705 CCTAGGTGCTTGGGGTGTCA 61.489 60.000 0.00 0.00 0.00 3.58
2791 2915 2.291043 GCCGTCCCCTTCTTGGAGA 61.291 63.158 0.00 0.00 38.35 3.71
3000 3128 0.110486 TTTGCCTCCCACTTCCAGTC 59.890 55.000 0.00 0.00 0.00 3.51
3068 3198 4.408821 GGTCTGCGGATGGTGGCA 62.409 66.667 0.00 0.00 37.63 4.92


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

AutoCloner maintained by Alex Coulton.