Multiple sequence alignment - TraesCS5B01G000500

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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 TraesCS5B01G000500 chr5B 100.000 3446 0 0 1 3446 220359 216914 0.000000e+00 6364.0
1 TraesCS5B01G000500 chr5D 87.092 1929 140 36 907 2793 932415 934276 0.000000e+00 2082.0
2 TraesCS5B01G000500 chr5D 88.734 719 56 14 1 706 931475 932181 0.000000e+00 856.0
3 TraesCS5B01G000500 chr5D 94.781 479 16 1 2968 3446 934359 934828 0.000000e+00 737.0
4 TraesCS5B01G000500 chr5D 84.000 250 37 2 387 635 375052632 375052879 1.600000e-58 237.0
5 TraesCS5B01G000500 chr5A 88.037 652 41 6 1931 2567 646928 646299 0.000000e+00 737.0
6 TraesCS5B01G000500 chr5A 83.735 830 63 30 2645 3446 646286 645501 0.000000e+00 719.0
7 TraesCS5B01G000500 chr7D 89.017 346 34 4 368 712 465920628 465920286 3.180000e-115 425.0
8 TraesCS5B01G000500 chr7D 86.630 359 40 7 352 709 602080697 602081048 1.160000e-104 390.0
9 TraesCS5B01G000500 chr1B 89.381 339 34 2 375 712 679234344 679234007 3.180000e-115 425.0
10 TraesCS5B01G000500 chr1B 97.500 40 1 0 302 341 600668627 600668588 6.170000e-08 69.4
11 TraesCS5B01G000500 chr3B 88.506 348 35 5 363 709 480333091 480333434 1.910000e-112 416.0
12 TraesCS5B01G000500 chrUn 88.724 337 36 1 376 712 223002262 223001928 8.900000e-111 411.0
13 TraesCS5B01G000500 chr7B 88.623 334 36 2 376 709 478877876 478878207 4.140000e-109 405.0
14 TraesCS5B01G000500 chr7B 84.132 334 51 1 376 709 546383490 546383821 4.290000e-84 322.0
15 TraesCS5B01G000500 chr7B 77.261 387 50 21 482 837 52503868 52504247 3.510000e-45 193.0
16 TraesCS5B01G000500 chr4D 88.462 338 35 3 376 712 505502911 505502577 4.140000e-109 405.0
17 TraesCS5B01G000500 chr2B 86.389 360 45 4 351 709 98290795 98291151 1.160000e-104 390.0
18 TraesCS5B01G000500 chr2D 84.341 364 52 5 3003 3364 638455981 638456341 5.470000e-93 351.0
19 TraesCS5B01G000500 chr7A 98.592 71 1 0 3376 3446 728650518 728650448 3.610000e-25 126.0


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 TraesCS5B01G000500 chr5B 216914 220359 3445 True 6364 6364 100.000000 1 3446 1 chr5B.!!$R1 3445
1 TraesCS5B01G000500 chr5D 931475 934828 3353 False 1225 2082 90.202333 1 3446 3 chr5D.!!$F2 3445
2 TraesCS5B01G000500 chr5A 645501 646928 1427 True 728 737 85.886000 1931 3446 2 chr5A.!!$R1 1515

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
615 629 0.037326 TAGAAGTGCAGGCCGTTGAG 60.037 55.0 0.0 0.0 0.00 3.02 F
830 872 0.039764 AGAGATCCGAGGTCACACCA 59.960 55.0 0.0 0.0 41.95 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 1970 0.032952 AGCAGCAGCCATTGTTGTTG 59.967 50.0 0.00 0.0 43.56 3.33 R
2647 2763 0.179145 ACCATTCCATCGTCGTCGTC 60.179 55.0 1.33 0.0 38.33 4.20 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
25 26 4.866508 TGGTAGTTCGTGAAGACATTCT 57.133 40.909 0.00 0.00 36.33 2.40
42 43 7.525688 GACATTCTTGTCGAAGATAATGACA 57.474 36.000 14.94 0.00 42.66 3.58
43 44 7.295952 ACATTCTTGTCGAAGATAATGACAC 57.704 36.000 14.94 0.00 41.93 3.67
44 45 6.035005 ACATTCTTGTCGAAGATAATGACACG 59.965 38.462 14.94 0.00 41.93 4.49
45 46 5.055642 TCTTGTCGAAGATAATGACACGT 57.944 39.130 0.00 0.00 41.93 4.49
46 47 4.857037 TCTTGTCGAAGATAATGACACGTG 59.143 41.667 15.48 15.48 41.93 4.49
48 49 4.800784 TGTCGAAGATAATGACACGTGAA 58.199 39.130 25.01 10.55 40.67 3.18
50 51 4.857588 GTCGAAGATAATGACACGTGAAGT 59.142 41.667 25.01 11.74 40.67 3.01
70 71 6.373495 TGAAGTCATTCATCTGAAGTCAATGG 59.627 38.462 0.00 0.00 40.54 3.16
138 140 2.622942 AGTTGTACGAACCACCGAACTA 59.377 45.455 0.00 0.00 0.00 2.24
143 145 5.777802 TGTACGAACCACCGAACTATTAAA 58.222 37.500 0.00 0.00 0.00 1.52
150 152 4.264038 ACCACCGAACTATTAAATGGGGTT 60.264 41.667 0.00 0.00 0.00 4.11
214 216 8.555166 TCAAAGAAGTAAATTTAGTTGTTGCG 57.445 30.769 22.10 17.52 32.10 4.85
221 223 4.911514 AATTTAGTTGTTGCGGACTTGT 57.088 36.364 0.00 0.00 0.00 3.16
239 241 1.070615 TAGTGACGCAAGCTTGGCA 59.929 52.632 27.10 8.52 45.62 4.92
254 256 2.657237 GCAGTGGCCACTACGAGT 59.343 61.111 37.27 13.11 40.20 4.18
290 292 6.869206 TTACCATAAGCAGAGACTAGGTTT 57.131 37.500 0.00 0.00 0.00 3.27
402 416 2.512485 TGTAAACACCTTCTTCGCGA 57.488 45.000 3.71 3.71 0.00 5.87
412 426 5.354234 ACACCTTCTTCGCGATATCAATTTT 59.646 36.000 10.88 0.00 0.00 1.82
415 429 5.172053 CCTTCTTCGCGATATCAATTTTTGC 59.828 40.000 10.88 0.00 0.00 3.68
417 431 5.501715 TCTTCGCGATATCAATTTTTGCTC 58.498 37.500 10.88 0.00 0.00 4.26
421 435 4.728131 CGCGATATCAATTTTTGCTCGAAA 59.272 37.500 0.00 0.00 32.42 3.46
456 470 4.457257 AGACTTTGATAAAGAGGCTGCAAC 59.543 41.667 8.18 0.00 41.02 4.17
466 480 2.233431 AGAGGCTGCAACTAGACTGAAG 59.767 50.000 0.50 0.00 35.77 3.02
471 485 3.133691 CTGCAACTAGACTGAAGCAACA 58.866 45.455 0.00 0.00 0.00 3.33
478 492 7.573843 GCAACTAGACTGAAGCAACAATATTGT 60.574 37.037 15.47 15.47 44.72 2.71
489 503 6.672147 AGCAACAATATTGTCACTCTTTCAC 58.328 36.000 21.02 0.00 41.31 3.18
526 540 6.515272 ACCAATAATGATTTCTGAAAGCGT 57.485 33.333 13.04 10.27 0.00 5.07
530 544 8.397906 CCAATAATGATTTCTGAAAGCGTCTTA 58.602 33.333 12.91 10.61 0.00 2.10
571 585 2.945008 TGGGAAGCATTGATCGATGAAC 59.055 45.455 24.63 14.15 0.00 3.18
612 626 1.374252 CGTAGAAGTGCAGGCCGTT 60.374 57.895 0.00 0.00 0.00 4.44
615 629 0.037326 TAGAAGTGCAGGCCGTTGAG 60.037 55.000 0.00 0.00 0.00 3.02
636 650 5.899547 TGAGTCACTATATCTTCACCATGGT 59.100 40.000 13.00 13.00 0.00 3.55
639 653 5.986135 GTCACTATATCTTCACCATGGTGTC 59.014 44.000 37.49 8.19 45.55 3.67
648 662 3.684908 TCACCATGGTGTCGATGAAAAT 58.315 40.909 37.49 0.45 45.55 1.82
649 663 4.078537 TCACCATGGTGTCGATGAAAATT 58.921 39.130 37.49 0.00 45.55 1.82
650 664 4.522405 TCACCATGGTGTCGATGAAAATTT 59.478 37.500 37.49 0.00 45.55 1.82
651 665 5.010516 TCACCATGGTGTCGATGAAAATTTT 59.989 36.000 37.49 2.28 45.55 1.82
652 666 5.345741 CACCATGGTGTCGATGAAAATTTTC 59.654 40.000 32.94 21.60 40.91 2.29
653 667 7.009670 CACCATGGTGTCGATGAAAATTTTCA 61.010 38.462 32.94 30.27 44.14 2.69
665 679 6.537453 TGAAAATTTTCACCTCCACAAAGA 57.463 33.333 26.01 2.56 41.88 2.52
666 680 6.940739 TGAAAATTTTCACCTCCACAAAGAA 58.059 32.000 26.01 2.15 41.88 2.52
667 681 7.563906 TGAAAATTTTCACCTCCACAAAGAAT 58.436 30.769 26.01 0.00 41.88 2.40
668 682 7.710475 TGAAAATTTTCACCTCCACAAAGAATC 59.290 33.333 26.01 0.00 41.88 2.52
669 683 6.729690 AATTTTCACCTCCACAAAGAATCA 57.270 33.333 0.00 0.00 0.00 2.57
670 684 6.729690 ATTTTCACCTCCACAAAGAATCAA 57.270 33.333 0.00 0.00 0.00 2.57
671 685 6.537453 TTTTCACCTCCACAAAGAATCAAA 57.463 33.333 0.00 0.00 0.00 2.69
672 686 5.514274 TTCACCTCCACAAAGAATCAAAC 57.486 39.130 0.00 0.00 0.00 2.93
673 687 3.888930 TCACCTCCACAAAGAATCAAACC 59.111 43.478 0.00 0.00 0.00 3.27
674 688 3.636300 CACCTCCACAAAGAATCAAACCA 59.364 43.478 0.00 0.00 0.00 3.67
675 689 4.099266 CACCTCCACAAAGAATCAAACCAA 59.901 41.667 0.00 0.00 0.00 3.67
682 696 7.118971 TCCACAAAGAATCAAACCAACAAAAAG 59.881 33.333 0.00 0.00 0.00 2.27
686 700 7.848223 AAGAATCAAACCAACAAAAAGAAGG 57.152 32.000 0.00 0.00 0.00 3.46
695 709 4.864247 CCAACAAAAAGAAGGTTGACACAG 59.136 41.667 5.40 0.00 43.41 3.66
708 722 5.168526 GTTGACACAGCAACATAAACTCA 57.831 39.130 0.00 0.00 45.65 3.41
709 723 5.577835 GTTGACACAGCAACATAAACTCAA 58.422 37.500 0.00 0.00 45.65 3.02
714 756 6.393990 ACACAGCAACATAAACTCAACAAAA 58.606 32.000 0.00 0.00 0.00 2.44
726 768 5.405331 ACTCAACAAAAACTCTCTAACGC 57.595 39.130 0.00 0.00 0.00 4.84
751 793 3.715628 GCACTGCCAAAAGAAGAAGAA 57.284 42.857 0.00 0.00 0.00 2.52
752 794 4.045636 GCACTGCCAAAAGAAGAAGAAA 57.954 40.909 0.00 0.00 0.00 2.52
753 795 4.432712 GCACTGCCAAAAGAAGAAGAAAA 58.567 39.130 0.00 0.00 0.00 2.29
754 796 5.052481 GCACTGCCAAAAGAAGAAGAAAAT 58.948 37.500 0.00 0.00 0.00 1.82
755 797 5.525012 GCACTGCCAAAAGAAGAAGAAAATT 59.475 36.000 0.00 0.00 0.00 1.82
757 799 7.224557 GCACTGCCAAAAGAAGAAGAAAATTTA 59.775 33.333 0.00 0.00 0.00 1.40
759 801 9.836864 ACTGCCAAAAGAAGAAGAAAATTTATT 57.163 25.926 0.00 0.00 0.00 1.40
780 822 8.620116 TTATTCTCACAAAACTGTGATGATCA 57.380 30.769 8.31 0.00 46.24 2.92
796 838 7.246311 GTGATGATCACAAAGTATTGACCAAG 58.754 38.462 19.96 0.00 46.22 3.61
799 841 8.585471 ATGATCACAAAGTATTGACCAAGAAT 57.415 30.769 0.00 0.00 38.94 2.40
815 857 7.893124 ACCAAGAATATAAAGGTCGTAGAGA 57.107 36.000 0.00 0.00 36.95 3.10
817 859 8.578151 ACCAAGAATATAAAGGTCGTAGAGATC 58.422 37.037 0.00 0.00 36.95 2.75
820 862 7.166851 AGAATATAAAGGTCGTAGAGATCCGA 58.833 38.462 0.00 0.00 36.95 4.55
822 864 1.970092 AAGGTCGTAGAGATCCGAGG 58.030 55.000 0.00 0.00 36.95 4.63
823 865 0.838608 AGGTCGTAGAGATCCGAGGT 59.161 55.000 0.00 0.00 36.95 3.85
824 866 1.202675 AGGTCGTAGAGATCCGAGGTC 60.203 57.143 0.00 0.00 36.95 3.85
825 867 1.474677 GGTCGTAGAGATCCGAGGTCA 60.475 57.143 0.00 0.00 36.95 4.02
826 868 1.598601 GTCGTAGAGATCCGAGGTCAC 59.401 57.143 0.00 0.00 36.95 3.67
827 869 1.208776 TCGTAGAGATCCGAGGTCACA 59.791 52.381 0.00 0.00 0.00 3.58
828 870 1.331138 CGTAGAGATCCGAGGTCACAC 59.669 57.143 0.00 0.00 0.00 3.82
829 871 1.677052 GTAGAGATCCGAGGTCACACC 59.323 57.143 0.00 0.00 38.99 4.16
830 872 0.039764 AGAGATCCGAGGTCACACCA 59.960 55.000 0.00 0.00 41.95 4.17
831 873 0.173708 GAGATCCGAGGTCACACCAC 59.826 60.000 0.00 0.00 41.95 4.16
832 874 1.218316 GATCCGAGGTCACACCACC 59.782 63.158 0.00 0.00 41.95 4.61
839 881 2.818751 AGGTCACACCACCTTCAAAA 57.181 45.000 0.00 0.00 45.24 2.44
840 882 3.094484 AGGTCACACCACCTTCAAAAA 57.906 42.857 0.00 0.00 45.24 1.94
903 950 0.963355 GTGAGAGGCTGAGTCGGTCT 60.963 60.000 5.56 5.56 0.00 3.85
904 951 0.678366 TGAGAGGCTGAGTCGGTCTC 60.678 60.000 23.59 23.59 41.35 3.36
905 952 1.688811 AGAGGCTGAGTCGGTCTCT 59.311 57.895 27.16 27.16 45.67 3.10
945 1019 6.072119 GGTGGTGAGATAAAAATCCGTTCTTT 60.072 38.462 0.00 0.00 0.00 2.52
956 1030 1.597027 CGTTCTTTGTCCCGTGCCT 60.597 57.895 0.00 0.00 0.00 4.75
957 1031 1.164041 CGTTCTTTGTCCCGTGCCTT 61.164 55.000 0.00 0.00 0.00 4.35
958 1032 0.591659 GTTCTTTGTCCCGTGCCTTC 59.408 55.000 0.00 0.00 0.00 3.46
959 1033 0.536460 TTCTTTGTCCCGTGCCTTCC 60.536 55.000 0.00 0.00 0.00 3.46
960 1034 1.971695 CTTTGTCCCGTGCCTTCCC 60.972 63.158 0.00 0.00 0.00 3.97
961 1035 3.835790 TTTGTCCCGTGCCTTCCCG 62.836 63.158 0.00 0.00 0.00 5.14
963 1037 3.782443 GTCCCGTGCCTTCCCGAT 61.782 66.667 0.00 0.00 0.00 4.18
964 1038 3.467226 TCCCGTGCCTTCCCGATC 61.467 66.667 0.00 0.00 0.00 3.69
995 1069 0.607112 TCTGCTCTGCTCTGGAGTTG 59.393 55.000 0.00 0.00 33.73 3.16
1010 1084 3.070018 GGAGTTGATCAATGGCGGATAG 58.930 50.000 12.12 0.00 0.00 2.08
1025 1099 1.474879 GGATAGATACCGAGCAGGAGC 59.525 57.143 5.19 0.00 45.00 4.70
1026 1100 2.163509 GATAGATACCGAGCAGGAGCA 58.836 52.381 5.19 0.00 45.00 4.26
1027 1101 1.610363 TAGATACCGAGCAGGAGCAG 58.390 55.000 5.19 0.00 45.00 4.24
1028 1102 1.112315 AGATACCGAGCAGGAGCAGG 61.112 60.000 5.19 0.00 45.00 4.85
1029 1103 2.093537 GATACCGAGCAGGAGCAGGG 62.094 65.000 5.19 0.00 45.00 4.45
1050 1124 1.695597 AGGGGAGGGGAAGCAGATG 60.696 63.158 0.00 0.00 0.00 2.90
1052 1126 1.694169 GGGAGGGGAAGCAGATGGA 60.694 63.158 0.00 0.00 0.00 3.41
1069 1155 2.770048 AGGATCGGGCCAAGAGGG 60.770 66.667 4.39 0.00 40.85 4.30
1078 1164 3.322466 CCAAGAGGGCGGTGGAGT 61.322 66.667 0.00 0.00 34.05 3.85
1079 1165 2.046892 CAAGAGGGCGGTGGAGTG 60.047 66.667 0.00 0.00 0.00 3.51
1130 1216 3.673484 CTGCCACCGCAACCCAAG 61.673 66.667 0.00 0.00 46.66 3.61
1294 1380 2.198287 GCCCGGATGCGAGGTACTA 61.198 63.158 8.71 0.00 41.55 1.82
1295 1381 1.658673 CCCGGATGCGAGGTACTAC 59.341 63.158 8.71 0.00 41.55 2.73
1308 1394 1.338105 GGTACTACCCACCACGAAACC 60.338 57.143 0.00 0.00 36.01 3.27
1319 1405 0.461339 CACGAAACCCCGATCCGATT 60.461 55.000 0.00 0.00 0.00 3.34
1329 1415 1.401670 CCGATCCGATTCCGATCAGTC 60.402 57.143 13.18 0.00 38.22 3.51
1372 1470 2.794621 CATCTGCTGCTGCTGCTG 59.205 61.111 27.67 26.32 40.48 4.41
1395 1493 4.416533 CTGGAGATCAGCTGCGAC 57.583 61.111 9.47 2.59 37.86 5.19
1404 1502 3.973516 AGCTGCGACACGACGGAA 61.974 61.111 0.00 0.00 32.77 4.30
1405 1503 3.470567 GCTGCGACACGACGGAAG 61.471 66.667 0.00 0.00 32.77 3.46
1406 1504 3.470567 CTGCGACACGACGGAAGC 61.471 66.667 0.00 0.00 32.77 3.86
1409 1507 2.126071 CGACACGACGGAAGCCAT 60.126 61.111 0.00 0.00 0.00 4.40
1410 1508 2.158959 CGACACGACGGAAGCCATC 61.159 63.158 0.00 0.00 0.00 3.51
1411 1509 2.126071 ACACGACGGAAGCCATCG 60.126 61.111 0.00 0.00 41.60 3.84
1412 1510 2.180769 CACGACGGAAGCCATCGA 59.819 61.111 9.02 0.00 39.16 3.59
1413 1511 1.874019 CACGACGGAAGCCATCGAG 60.874 63.158 9.02 0.00 39.16 4.04
1414 1512 2.278857 CGACGGAAGCCATCGAGG 60.279 66.667 0.00 0.00 38.10 4.63
1415 1513 2.771639 CGACGGAAGCCATCGAGGA 61.772 63.158 0.00 0.00 41.22 3.71
1416 1514 1.066587 GACGGAAGCCATCGAGGAG 59.933 63.158 0.00 0.00 41.22 3.69
1417 1515 2.279784 CGGAAGCCATCGAGGAGC 60.280 66.667 0.00 0.00 41.22 4.70
1420 1518 1.227497 GAAGCCATCGAGGAGCAGG 60.227 63.158 11.95 0.00 41.22 4.85
1426 1524 1.152567 ATCGAGGAGCAGGAGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
1428 1526 1.380515 CGAGGAGCAGGAGGAGGAA 60.381 63.158 0.00 0.00 0.00 3.36
1689 1787 4.847444 GGCGGCAGGCTCTTCTCC 62.847 72.222 3.07 0.00 42.94 3.71
1718 1816 2.124983 CGGGTGGGTCATGCTCAG 60.125 66.667 0.00 0.00 0.00 3.35
1719 1817 2.439156 GGGTGGGTCATGCTCAGC 60.439 66.667 9.76 9.76 44.92 4.26
1725 1823 3.503363 GTCATGCTCAGCACGCCC 61.503 66.667 0.00 0.00 43.04 6.13
1726 1824 4.019312 TCATGCTCAGCACGCCCA 62.019 61.111 0.00 0.00 43.04 5.36
1810 1908 2.351276 GCGACCAGGGGTTCATGT 59.649 61.111 0.00 0.00 35.25 3.21
1814 1912 0.678048 GACCAGGGGTTCATGTGCTC 60.678 60.000 0.00 0.00 35.25 4.26
1859 1960 0.176680 AATGGCCGCAACAACAACAA 59.823 45.000 0.00 0.00 0.00 2.83
1861 1962 1.153745 GGCCGCAACAACAACAACA 60.154 52.632 0.00 0.00 0.00 3.33
1862 1963 0.737715 GGCCGCAACAACAACAACAA 60.738 50.000 0.00 0.00 0.00 2.83
1867 1968 2.472861 CGCAACAACAACAACAACAACA 59.527 40.909 0.00 0.00 0.00 3.33
1868 1969 3.060272 CGCAACAACAACAACAACAACAA 60.060 39.130 0.00 0.00 0.00 2.83
1869 1970 4.207599 GCAACAACAACAACAACAACAAC 58.792 39.130 0.00 0.00 0.00 3.32
1870 1971 4.260375 GCAACAACAACAACAACAACAACA 60.260 37.500 0.00 0.00 0.00 3.33
1871 1972 5.727791 GCAACAACAACAACAACAACAACAA 60.728 36.000 0.00 0.00 0.00 2.83
1872 1973 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1873 1974 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1874 1975 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1878 1979 6.037610 ACAACAACAACAACAACAACAACAAT 59.962 30.769 0.00 0.00 0.00 2.71
1880 1981 5.049818 ACAACAACAACAACAACAACAATGG 60.050 36.000 0.00 0.00 0.00 3.16
1890 1991 0.754472 ACAACAATGGCTGCTGCTTT 59.246 45.000 15.64 6.97 39.59 3.51
1984 2085 3.768922 GCGTGGAGGAGCAGAGCT 61.769 66.667 0.00 0.00 43.88 4.09
2080 2181 3.613689 GGGTCTACGATCCCGGCC 61.614 72.222 0.00 0.00 40.78 6.13
2142 2243 0.802607 CGGAGCTCGCCTACAAGAAC 60.803 60.000 7.83 0.00 0.00 3.01
2286 2387 3.431725 GGCCGCTCCCTTTTCACG 61.432 66.667 0.00 0.00 0.00 4.35
2289 2390 2.746277 CGCTCCCTTTTCACGGGG 60.746 66.667 0.00 0.00 42.23 5.73
2424 2525 2.047179 GGCCGCCTCTTCTTCGTT 60.047 61.111 0.71 0.00 0.00 3.85
2425 2526 2.391389 GGCCGCCTCTTCTTCGTTG 61.391 63.158 0.71 0.00 0.00 4.10
2426 2527 1.668151 GCCGCCTCTTCTTCGTTGT 60.668 57.895 0.00 0.00 0.00 3.32
2427 2528 0.389426 GCCGCCTCTTCTTCGTTGTA 60.389 55.000 0.00 0.00 0.00 2.41
2428 2529 1.938016 GCCGCCTCTTCTTCGTTGTAA 60.938 52.381 0.00 0.00 0.00 2.41
2429 2530 2.409975 CCGCCTCTTCTTCGTTGTAAA 58.590 47.619 0.00 0.00 0.00 2.01
2430 2531 2.803956 CCGCCTCTTCTTCGTTGTAAAA 59.196 45.455 0.00 0.00 0.00 1.52
2613 2729 0.248565 CCTCGCCGGATGATGATGAT 59.751 55.000 5.05 0.00 33.16 2.45
2619 2735 3.542648 GCCGGATGATGATGATGATGAT 58.457 45.455 5.05 0.00 0.00 2.45
2625 2741 6.708054 CGGATGATGATGATGATGATGATGAT 59.292 38.462 0.00 0.00 0.00 2.45
2631 2747 7.849804 TGATGATGATGATGATGATGATGAC 57.150 36.000 0.00 0.00 0.00 3.06
2637 2753 5.867716 TGATGATGATGATGATGACGATGAC 59.132 40.000 0.00 0.00 0.00 3.06
2638 2754 4.232221 TGATGATGATGATGACGATGACG 58.768 43.478 0.00 0.00 45.75 4.35
2639 2755 3.988379 TGATGATGATGACGATGACGA 57.012 42.857 0.00 0.00 42.66 4.20
2640 2756 3.632189 TGATGATGATGACGATGACGAC 58.368 45.455 0.00 0.00 42.66 4.34
2641 2757 2.105323 TGATGATGACGATGACGACG 57.895 50.000 0.00 0.00 42.66 5.12
2642 2758 1.668751 TGATGATGACGATGACGACGA 59.331 47.619 0.00 0.00 42.66 4.20
2643 2759 2.037649 GATGATGACGATGACGACGAC 58.962 52.381 0.00 0.00 42.66 4.34
2644 2760 0.247537 TGATGACGATGACGACGACG 60.248 55.000 5.58 5.58 42.66 5.12
2645 2761 0.025898 GATGACGATGACGACGACGA 59.974 55.000 15.32 0.00 42.66 4.20
2646 2762 0.247576 ATGACGATGACGACGACGAC 60.248 55.000 15.32 8.68 42.66 4.34
2647 2763 1.922220 GACGATGACGACGACGACG 60.922 63.158 17.60 17.60 42.66 5.12
2648 2764 2.271024 GACGATGACGACGACGACGA 62.271 60.000 25.15 5.17 41.06 4.20
2649 2765 1.922220 CGATGACGACGACGACGAC 60.922 63.158 25.15 19.21 41.06 4.34
2937 3109 9.770097 TCTATGATGATGATGATGATGATGATG 57.230 33.333 0.00 0.00 0.00 3.07
2938 3110 9.770097 CTATGATGATGATGATGATGATGATGA 57.230 33.333 0.00 0.00 0.00 2.92
2940 3112 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
2941 3113 8.267183 TGATGATGATGATGATGATGATGATGA 58.733 33.333 0.00 0.00 0.00 2.92
2942 3114 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
2943 3115 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
2944 3116 8.267183 TGATGATGATGATGATGATGATGATGA 58.733 33.333 0.00 0.00 0.00 2.92
2945 3117 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
2946 3118 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
2947 3119 8.267183 TGATGATGATGATGATGATGATGATGA 58.733 33.333 0.00 0.00 0.00 2.92
2948 3120 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
2949 3121 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
2950 3122 8.267183 TGATGATGATGATGATGATGATGATGA 58.733 33.333 0.00 0.00 0.00 2.92
2951 3123 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
2952 3124 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
2953 3125 8.267183 TGATGATGATGATGATGATGATGATGA 58.733 33.333 0.00 0.00 0.00 2.92
2988 3165 6.476053 TGATGATGATGTTGTTGTTGTTGTTG 59.524 34.615 0.00 0.00 0.00 3.33
2989 3166 5.958955 TGATGATGTTGTTGTTGTTGTTGA 58.041 33.333 0.00 0.00 0.00 3.18
2990 3167 6.571605 TGATGATGTTGTTGTTGTTGTTGAT 58.428 32.000 0.00 0.00 0.00 2.57
2991 3168 6.476053 TGATGATGTTGTTGTTGTTGTTGATG 59.524 34.615 0.00 0.00 0.00 3.07
2992 3169 5.958955 TGATGTTGTTGTTGTTGTTGATGA 58.041 33.333 0.00 0.00 0.00 2.92
2993 3170 6.393171 TGATGTTGTTGTTGTTGTTGATGAA 58.607 32.000 0.00 0.00 0.00 2.57
2994 3171 7.040494 TGATGTTGTTGTTGTTGTTGATGAAT 58.960 30.769 0.00 0.00 0.00 2.57
2995 3172 7.548427 TGATGTTGTTGTTGTTGTTGATGAATT 59.452 29.630 0.00 0.00 0.00 2.17
2996 3173 7.058298 TGTTGTTGTTGTTGTTGATGAATTG 57.942 32.000 0.00 0.00 0.00 2.32
2997 3174 6.648310 TGTTGTTGTTGTTGTTGATGAATTGT 59.352 30.769 0.00 0.00 0.00 2.71
2998 3175 6.884096 TGTTGTTGTTGTTGATGAATTGTC 57.116 33.333 0.00 0.00 0.00 3.18
3010 3187 1.782569 TGAATTGTCGTCGTTGTCGTC 59.217 47.619 0.00 0.00 38.33 4.20
3357 3534 4.379221 CGTAGTAGACGCTGGTGC 57.621 61.111 0.00 0.00 46.27 5.01
3360 3537 1.794437 CGTAGTAGACGCTGGTGCTTC 60.794 57.143 0.00 0.00 46.27 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.800784 TCACGTGTCATTATCTTCGACAA 58.199 39.130 16.51 0.00 41.08 3.18
29 30 4.857037 TGACTTCACGTGTCATTATCTTCG 59.143 41.667 16.51 0.00 39.23 3.79
39 40 4.237724 TCAGATGAATGACTTCACGTGTC 58.762 43.478 16.51 6.57 43.92 3.67
40 41 4.257267 TCAGATGAATGACTTCACGTGT 57.743 40.909 16.51 0.00 43.92 4.49
41 42 4.687948 ACTTCAGATGAATGACTTCACGTG 59.312 41.667 9.94 9.94 43.92 4.49
42 43 4.887748 ACTTCAGATGAATGACTTCACGT 58.112 39.130 0.00 0.00 43.92 4.49
43 44 4.925646 TGACTTCAGATGAATGACTTCACG 59.074 41.667 0.00 0.00 43.92 4.35
44 45 6.791887 TTGACTTCAGATGAATGACTTCAC 57.208 37.500 0.00 0.00 43.92 3.18
45 46 6.373495 CCATTGACTTCAGATGAATGACTTCA 59.627 38.462 0.00 0.00 45.15 3.02
46 47 6.596888 TCCATTGACTTCAGATGAATGACTTC 59.403 38.462 0.00 0.00 33.01 3.01
48 49 6.058553 TCCATTGACTTCAGATGAATGACT 57.941 37.500 0.00 0.00 33.01 3.41
50 51 5.434408 CCTCCATTGACTTCAGATGAATGA 58.566 41.667 0.00 0.00 33.01 2.57
93 95 9.408648 ACTCAGGAAAGAAGAAAATGAAACTAA 57.591 29.630 0.00 0.00 0.00 2.24
113 115 1.792006 GGTGGTTCGTACAACTCAGG 58.208 55.000 0.00 0.00 0.00 3.86
115 117 1.031235 TCGGTGGTTCGTACAACTCA 58.969 50.000 0.00 0.00 0.00 3.41
116 118 1.788886 GTTCGGTGGTTCGTACAACTC 59.211 52.381 0.00 0.00 32.13 3.01
214 216 0.790814 GCTTGCGTCACTACAAGTCC 59.209 55.000 8.69 0.00 44.12 3.85
221 223 0.950555 CTGCCAAGCTTGCGTCACTA 60.951 55.000 21.43 0.80 0.00 2.74
239 241 1.045407 TTGAACTCGTAGTGGCCACT 58.955 50.000 38.92 38.92 45.02 4.00
246 248 2.719739 TCCGGAGATTGAACTCGTAGT 58.280 47.619 0.00 0.00 37.74 2.73
254 256 5.163248 TGCTTATGGTAATCCGGAGATTGAA 60.163 40.000 11.34 0.00 42.78 2.69
371 385 8.384607 AGAAGGTGTTTACAAGAGATTTTCTC 57.615 34.615 0.00 0.00 43.70 2.87
395 409 4.373961 CGAGCAAAAATTGATATCGCGAAG 59.626 41.667 15.24 0.00 0.00 3.79
429 443 5.620879 GCAGCCTCTTTATCAAAGTCTTTGG 60.621 44.000 22.23 8.45 40.98 3.28
439 453 4.467795 AGTCTAGTTGCAGCCTCTTTATCA 59.532 41.667 0.00 0.00 0.00 2.15
441 455 4.467795 TCAGTCTAGTTGCAGCCTCTTTAT 59.532 41.667 0.00 0.00 0.00 1.40
446 460 2.615869 CTTCAGTCTAGTTGCAGCCTC 58.384 52.381 0.00 0.00 0.00 4.70
456 470 7.332926 AGTGACAATATTGTTGCTTCAGTCTAG 59.667 37.037 21.63 0.00 42.43 2.43
466 480 5.858581 GGTGAAAGAGTGACAATATTGTTGC 59.141 40.000 21.63 16.41 42.43 4.17
471 485 3.689649 GCGGGTGAAAGAGTGACAATATT 59.310 43.478 0.00 0.00 0.00 1.28
478 492 1.300620 CGTGCGGGTGAAAGAGTGA 60.301 57.895 0.00 0.00 0.00 3.41
489 503 1.091537 ATTGGTAATGTTCGTGCGGG 58.908 50.000 0.00 0.00 0.00 6.13
526 540 4.954202 TCTTTCTAGATGGGCGACTTAAGA 59.046 41.667 10.09 0.00 0.00 2.10
551 565 2.032549 CGTTCATCGATCAATGCTTCCC 60.033 50.000 0.00 0.00 42.86 3.97
571 585 3.476419 ATCCCCGGCCCAAGTACG 61.476 66.667 0.00 0.00 0.00 3.67
612 626 5.899547 ACCATGGTGAAGATATAGTGACTCA 59.100 40.000 18.99 0.00 0.00 3.41
648 662 6.337356 GTTTGATTCTTTGTGGAGGTGAAAA 58.663 36.000 0.00 0.00 0.00 2.29
649 663 5.163457 GGTTTGATTCTTTGTGGAGGTGAAA 60.163 40.000 0.00 0.00 0.00 2.69
650 664 4.340950 GGTTTGATTCTTTGTGGAGGTGAA 59.659 41.667 0.00 0.00 0.00 3.18
651 665 3.888930 GGTTTGATTCTTTGTGGAGGTGA 59.111 43.478 0.00 0.00 0.00 4.02
652 666 3.636300 TGGTTTGATTCTTTGTGGAGGTG 59.364 43.478 0.00 0.00 0.00 4.00
653 667 3.909732 TGGTTTGATTCTTTGTGGAGGT 58.090 40.909 0.00 0.00 0.00 3.85
655 669 5.261209 TGTTGGTTTGATTCTTTGTGGAG 57.739 39.130 0.00 0.00 0.00 3.86
656 670 5.667539 TTGTTGGTTTGATTCTTTGTGGA 57.332 34.783 0.00 0.00 0.00 4.02
657 671 6.734104 TTTTGTTGGTTTGATTCTTTGTGG 57.266 33.333 0.00 0.00 0.00 4.17
658 672 8.027440 TCTTTTTGTTGGTTTGATTCTTTGTG 57.973 30.769 0.00 0.00 0.00 3.33
659 673 8.614469 TTCTTTTTGTTGGTTTGATTCTTTGT 57.386 26.923 0.00 0.00 0.00 2.83
664 678 7.333174 TCAACCTTCTTTTTGTTGGTTTGATTC 59.667 33.333 0.00 0.00 38.76 2.52
665 679 7.119116 GTCAACCTTCTTTTTGTTGGTTTGATT 59.881 33.333 0.00 0.00 38.76 2.57
666 680 6.593770 GTCAACCTTCTTTTTGTTGGTTTGAT 59.406 34.615 0.00 0.00 38.76 2.57
667 681 5.929415 GTCAACCTTCTTTTTGTTGGTTTGA 59.071 36.000 0.00 0.00 38.76 2.69
668 682 5.698545 TGTCAACCTTCTTTTTGTTGGTTTG 59.301 36.000 0.00 0.00 38.76 2.93
669 683 5.699001 GTGTCAACCTTCTTTTTGTTGGTTT 59.301 36.000 0.00 0.00 38.76 3.27
670 684 5.221541 TGTGTCAACCTTCTTTTTGTTGGTT 60.222 36.000 0.00 0.00 41.12 3.67
671 685 4.282195 TGTGTCAACCTTCTTTTTGTTGGT 59.718 37.500 0.00 0.00 39.77 3.67
672 686 4.815269 TGTGTCAACCTTCTTTTTGTTGG 58.185 39.130 0.00 0.00 39.77 3.77
673 687 4.327087 GCTGTGTCAACCTTCTTTTTGTTG 59.673 41.667 0.00 0.00 40.48 3.33
674 688 4.021544 TGCTGTGTCAACCTTCTTTTTGTT 60.022 37.500 0.00 0.00 0.00 2.83
675 689 3.509575 TGCTGTGTCAACCTTCTTTTTGT 59.490 39.130 0.00 0.00 0.00 2.83
682 696 4.829064 TTATGTTGCTGTGTCAACCTTC 57.171 40.909 4.46 0.00 44.15 3.46
686 700 5.168526 TGAGTTTATGTTGCTGTGTCAAC 57.831 39.130 0.14 0.14 44.80 3.18
695 709 7.702348 AGAGAGTTTTTGTTGAGTTTATGTTGC 59.298 33.333 0.00 0.00 0.00 4.17
706 720 4.193090 TGGCGTTAGAGAGTTTTTGTTGA 58.807 39.130 0.00 0.00 0.00 3.18
708 722 4.023193 CCATGGCGTTAGAGAGTTTTTGTT 60.023 41.667 0.00 0.00 0.00 2.83
709 723 3.502211 CCATGGCGTTAGAGAGTTTTTGT 59.498 43.478 0.00 0.00 0.00 2.83
714 756 0.613260 TGCCATGGCGTTAGAGAGTT 59.387 50.000 30.87 0.00 45.51 3.01
773 815 7.615582 TCTTGGTCAATACTTTGTGATCATC 57.384 36.000 0.00 0.00 34.91 2.92
774 816 8.585471 ATTCTTGGTCAATACTTTGTGATCAT 57.415 30.769 0.00 0.00 34.91 2.45
784 826 8.483758 ACGACCTTTATATTCTTGGTCAATACT 58.516 33.333 10.46 0.00 45.25 2.12
785 827 8.658499 ACGACCTTTATATTCTTGGTCAATAC 57.342 34.615 10.46 0.00 45.25 1.89
787 829 8.701895 TCTACGACCTTTATATTCTTGGTCAAT 58.298 33.333 10.46 1.56 45.25 2.57
788 830 8.070034 TCTACGACCTTTATATTCTTGGTCAA 57.930 34.615 10.46 0.00 45.25 3.18
789 831 7.558807 TCTCTACGACCTTTATATTCTTGGTCA 59.441 37.037 10.46 0.00 45.25 4.02
790 832 7.938715 TCTCTACGACCTTTATATTCTTGGTC 58.061 38.462 0.00 0.00 42.53 4.02
791 833 7.893124 TCTCTACGACCTTTATATTCTTGGT 57.107 36.000 0.00 0.00 0.00 3.67
792 834 8.030106 GGATCTCTACGACCTTTATATTCTTGG 58.970 40.741 0.00 0.00 0.00 3.61
793 835 7.751348 CGGATCTCTACGACCTTTATATTCTTG 59.249 40.741 0.00 0.00 0.00 3.02
796 838 7.375106 TCGGATCTCTACGACCTTTATATTC 57.625 40.000 0.00 0.00 33.69 1.75
799 841 5.221803 ACCTCGGATCTCTACGACCTTTATA 60.222 44.000 0.00 0.00 35.04 0.98
802 844 2.299521 CCTCGGATCTCTACGACCTTT 58.700 52.381 0.00 0.00 35.04 3.11
804 846 0.838608 ACCTCGGATCTCTACGACCT 59.161 55.000 0.00 0.00 35.04 3.85
805 847 1.228533 GACCTCGGATCTCTACGACC 58.771 60.000 0.00 0.00 35.04 4.79
806 848 1.598601 GTGACCTCGGATCTCTACGAC 59.401 57.143 0.00 0.00 35.04 4.34
807 849 1.208776 TGTGACCTCGGATCTCTACGA 59.791 52.381 0.00 0.00 37.56 3.43
810 852 1.283905 TGGTGTGACCTCGGATCTCTA 59.716 52.381 0.00 0.00 39.58 2.43
813 855 1.258445 GGTGGTGTGACCTCGGATCT 61.258 60.000 0.00 0.00 39.58 2.75
815 857 0.836400 AAGGTGGTGTGACCTCGGAT 60.836 55.000 0.00 0.00 46.29 4.18
817 859 1.004918 GAAGGTGGTGTGACCTCGG 60.005 63.158 0.00 0.00 46.29 4.63
882 929 1.214062 CCGACTCAGCCTCTCACAC 59.786 63.158 0.00 0.00 0.00 3.82
903 950 2.239654 CCACCAGATTTAAGGCCAGAGA 59.760 50.000 5.01 0.00 0.00 3.10
904 951 2.025887 ACCACCAGATTTAAGGCCAGAG 60.026 50.000 5.01 0.00 0.00 3.35
905 952 1.992557 ACCACCAGATTTAAGGCCAGA 59.007 47.619 5.01 0.00 0.00 3.86
956 1030 0.750850 GACTCCAATCGGATCGGGAA 59.249 55.000 11.19 0.00 41.79 3.97
957 1031 0.106167 AGACTCCAATCGGATCGGGA 60.106 55.000 10.01 10.01 41.79 5.14
958 1032 0.315568 GAGACTCCAATCGGATCGGG 59.684 60.000 0.00 0.00 41.79 5.14
959 1033 1.000827 CAGAGACTCCAATCGGATCGG 60.001 57.143 0.00 0.00 41.79 4.18
960 1034 1.601663 GCAGAGACTCCAATCGGATCG 60.602 57.143 0.00 0.00 41.79 3.69
961 1035 1.686052 AGCAGAGACTCCAATCGGATC 59.314 52.381 0.00 0.00 41.79 3.36
962 1036 1.686052 GAGCAGAGACTCCAATCGGAT 59.314 52.381 0.00 0.00 41.79 4.18
963 1037 1.107114 GAGCAGAGACTCCAATCGGA 58.893 55.000 0.00 0.00 39.79 4.55
964 1038 1.110442 AGAGCAGAGACTCCAATCGG 58.890 55.000 0.00 0.00 37.39 4.18
995 1069 3.130516 TCGGTATCTATCCGCCATTGATC 59.869 47.826 0.00 0.00 46.49 2.92
1010 1084 1.365633 CCTGCTCCTGCTCGGTATC 59.634 63.158 0.00 0.00 40.48 2.24
1016 1090 4.486503 CTGCCCCTGCTCCTGCTC 62.487 72.222 0.00 0.00 40.48 4.26
1050 1124 2.812619 CCTCTTGGCCCGATCCTCC 61.813 68.421 0.00 0.00 0.00 4.30
1052 1126 2.770048 CCCTCTTGGCCCGATCCT 60.770 66.667 0.00 0.00 0.00 3.24
1293 1379 2.881528 CGGGGTTTCGTGGTGGGTA 61.882 63.158 0.00 0.00 0.00 3.69
1294 1380 4.259131 CGGGGTTTCGTGGTGGGT 62.259 66.667 0.00 0.00 0.00 4.51
1295 1381 3.262448 ATCGGGGTTTCGTGGTGGG 62.262 63.158 0.00 0.00 0.00 4.61
1308 1394 0.109086 CTGATCGGAATCGGATCGGG 60.109 60.000 23.84 15.90 40.23 5.14
1336 1422 1.826921 CAGAGCCATGGGGTGATGC 60.827 63.158 15.13 0.00 36.17 3.91
1337 1423 1.826921 GCAGAGCCATGGGGTGATG 60.827 63.158 15.13 2.92 36.17 3.07
1338 1424 1.652187 ATGCAGAGCCATGGGGTGAT 61.652 55.000 15.13 0.00 36.17 3.06
1339 1425 2.274948 GATGCAGAGCCATGGGGTGA 62.275 60.000 15.13 0.00 36.17 4.02
1368 1466 0.906282 TGATCTCCAGTCCTGCAGCA 60.906 55.000 8.66 0.00 0.00 4.41
1369 1467 0.179078 CTGATCTCCAGTCCTGCAGC 60.179 60.000 8.66 0.00 38.10 5.25
1370 1468 0.179078 GCTGATCTCCAGTCCTGCAG 60.179 60.000 6.78 6.78 44.71 4.41
1371 1469 0.616964 AGCTGATCTCCAGTCCTGCA 60.617 55.000 0.00 0.00 44.71 4.41
1372 1470 0.179078 CAGCTGATCTCCAGTCCTGC 60.179 60.000 8.42 0.00 44.71 4.85
1373 1471 0.179078 GCAGCTGATCTCCAGTCCTG 60.179 60.000 20.43 0.00 44.71 3.86
1404 1502 2.042537 TCCTGCTCCTCGATGGCT 60.043 61.111 0.00 0.00 35.26 4.75
1405 1503 2.420890 CTCCTGCTCCTCGATGGC 59.579 66.667 0.00 0.00 35.26 4.40
1406 1504 1.456518 TCCTCCTGCTCCTCGATGG 60.457 63.158 0.00 0.00 37.10 3.51
1407 1505 1.462731 CCTCCTCCTGCTCCTCGATG 61.463 65.000 0.00 0.00 0.00 3.84
1408 1506 1.152567 CCTCCTCCTGCTCCTCGAT 60.153 63.158 0.00 0.00 0.00 3.59
1409 1507 1.864263 TTCCTCCTCCTGCTCCTCGA 61.864 60.000 0.00 0.00 0.00 4.04
1410 1508 1.380515 TTCCTCCTCCTGCTCCTCG 60.381 63.158 0.00 0.00 0.00 4.63
1411 1509 1.048160 CCTTCCTCCTCCTGCTCCTC 61.048 65.000 0.00 0.00 0.00 3.71
1412 1510 1.002792 CCTTCCTCCTCCTGCTCCT 59.997 63.158 0.00 0.00 0.00 3.69
1413 1511 2.069430 CCCTTCCTCCTCCTGCTCC 61.069 68.421 0.00 0.00 0.00 4.70
1414 1512 2.741055 GCCCTTCCTCCTCCTGCTC 61.741 68.421 0.00 0.00 0.00 4.26
1415 1513 2.690510 GCCCTTCCTCCTCCTGCT 60.691 66.667 0.00 0.00 0.00 4.24
1416 1514 3.803162 GGCCCTTCCTCCTCCTGC 61.803 72.222 0.00 0.00 0.00 4.85
1417 1515 3.474570 CGGCCCTTCCTCCTCCTG 61.475 72.222 0.00 0.00 0.00 3.86
1420 1518 3.471806 GTCCGGCCCTTCCTCCTC 61.472 72.222 0.00 0.00 0.00 3.71
1637 1735 3.839432 CGGCGAGGAGGAAGGTCC 61.839 72.222 0.00 0.00 36.58 4.46
1669 1767 3.130160 GAAGAGCCTGCCGCCTTG 61.130 66.667 0.00 0.00 38.78 3.61
1671 1769 3.780173 GAGAAGAGCCTGCCGCCT 61.780 66.667 0.00 0.00 38.78 5.52
1741 1839 2.266055 GTCCAGGAGGTTGGCGAG 59.734 66.667 0.00 0.00 38.16 5.03
1793 1891 2.040544 CACATGAACCCCTGGTCGC 61.041 63.158 0.00 0.00 33.12 5.19
1797 1895 1.379044 GGAGCACATGAACCCCTGG 60.379 63.158 0.00 0.00 0.00 4.45
1799 1897 2.671070 CGGAGCACATGAACCCCT 59.329 61.111 0.00 0.00 0.00 4.79
1826 1924 2.668212 CATTGTCGTGGCCGTGGT 60.668 61.111 0.00 0.00 35.01 4.16
1834 1932 2.126888 GTTGCGGCCATTGTCGTG 60.127 61.111 2.24 0.00 42.91 4.35
1835 1933 2.190170 TTGTTGCGGCCATTGTCGT 61.190 52.632 2.24 0.00 42.91 4.34
1859 1960 3.434984 GCCATTGTTGTTGTTGTTGTTGT 59.565 39.130 0.00 0.00 0.00 3.32
1861 1962 3.683822 CAGCCATTGTTGTTGTTGTTGTT 59.316 39.130 0.00 0.00 0.00 2.83
1862 1963 3.260740 CAGCCATTGTTGTTGTTGTTGT 58.739 40.909 0.00 0.00 0.00 3.32
1867 1968 1.807377 GCAGCAGCCATTGTTGTTGTT 60.807 47.619 0.00 0.00 39.89 2.83
1868 1969 0.249573 GCAGCAGCCATTGTTGTTGT 60.250 50.000 0.00 0.00 39.89 3.32
1869 1970 0.032952 AGCAGCAGCCATTGTTGTTG 59.967 50.000 0.00 0.00 43.56 3.33
1870 1971 0.754472 AAGCAGCAGCCATTGTTGTT 59.246 45.000 0.00 0.00 43.56 2.83
1871 1972 0.754472 AAAGCAGCAGCCATTGTTGT 59.246 45.000 0.00 0.00 43.56 3.32
1872 1973 1.144969 CAAAGCAGCAGCCATTGTTG 58.855 50.000 0.00 0.00 43.56 3.33
1873 1974 1.042229 TCAAAGCAGCAGCCATTGTT 58.958 45.000 14.19 0.00 43.56 2.83
1874 1975 0.316204 GTCAAAGCAGCAGCCATTGT 59.684 50.000 14.19 0.00 43.56 2.71
1878 1979 2.203195 ACGTCAAAGCAGCAGCCA 60.203 55.556 0.00 0.00 43.56 4.75
1880 1981 0.658536 GAACACGTCAAAGCAGCAGC 60.659 55.000 0.00 0.00 42.56 5.25
1912 2013 1.383799 CCCTGATGGTGCCCAAGAA 59.616 57.895 0.00 0.00 36.95 2.52
1913 2014 3.089838 CCCTGATGGTGCCCAAGA 58.910 61.111 0.00 0.00 36.95 3.02
1924 2025 1.760086 CCCAGCTCTCGACCCTGAT 60.760 63.158 4.31 0.00 0.00 2.90
1949 2050 3.997064 CTCTTCCAGACGCTGCCGG 62.997 68.421 0.00 0.00 39.22 6.13
1954 2055 2.259818 CACGCTCTTCCAGACGCT 59.740 61.111 0.00 0.00 0.00 5.07
1958 2059 0.967887 CTCCTCCACGCTCTTCCAGA 60.968 60.000 0.00 0.00 0.00 3.86
1984 2085 1.339438 GCAGCAGGACATTCTGAAGGA 60.339 52.381 9.26 0.00 36.93 3.36
1985 2086 1.093159 GCAGCAGGACATTCTGAAGG 58.907 55.000 0.00 0.00 36.93 3.46
1986 2087 1.738350 CAGCAGCAGGACATTCTGAAG 59.262 52.381 0.00 0.00 36.93 3.02
2324 2425 1.439353 CTTGTCGGCCATGGATTCGG 61.439 60.000 18.40 2.23 0.00 4.30
2403 2504 1.524849 GAAGAAGAGGCGGCCATCC 60.525 63.158 23.09 9.83 0.00 3.51
2443 2544 0.833287 GATCCCTGTTGCTCCTGCTA 59.167 55.000 0.00 0.00 40.48 3.49
2607 2723 6.535150 CGTCATCATCATCATCATCATCATCA 59.465 38.462 0.00 0.00 0.00 3.07
2613 2729 5.867716 GTCATCGTCATCATCATCATCATCA 59.132 40.000 0.00 0.00 0.00 3.07
2619 2735 3.632189 GTCGTCATCGTCATCATCATCA 58.368 45.455 0.00 0.00 38.33 3.07
2625 2741 0.247537 CGTCGTCGTCATCGTCATCA 60.248 55.000 0.00 0.00 38.33 3.07
2631 2747 1.922220 GTCGTCGTCGTCGTCATCG 60.922 63.158 11.41 4.14 38.33 3.84
2637 2753 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
2638 2754 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
2639 2755 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
2640 2756 3.397649 ATCGTCGTCGTCGTCGTCG 62.398 63.158 20.39 20.39 45.27 5.12
2641 2757 1.922220 CATCGTCGTCGTCGTCGTC 60.922 63.158 18.44 5.52 45.27 4.20
2642 2758 2.095282 CATCGTCGTCGTCGTCGT 59.905 61.111 18.44 6.36 45.27 4.34
2643 2759 2.552918 TTCCATCGTCGTCGTCGTCG 62.553 60.000 14.18 14.18 46.06 5.12
2644 2760 0.247974 ATTCCATCGTCGTCGTCGTC 60.248 55.000 11.41 0.00 38.33 4.20
2645 2761 0.522705 CATTCCATCGTCGTCGTCGT 60.523 55.000 11.41 0.00 38.33 4.34
2646 2762 1.200474 CCATTCCATCGTCGTCGTCG 61.200 60.000 5.50 5.50 38.33 5.12
2647 2763 0.179145 ACCATTCCATCGTCGTCGTC 60.179 55.000 1.33 0.00 38.33 4.20
2648 2764 0.245539 AACCATTCCATCGTCGTCGT 59.754 50.000 1.33 0.00 38.33 4.34
2649 2765 2.197792 TAACCATTCCATCGTCGTCG 57.802 50.000 0.00 0.00 38.55 5.12
2650 2766 4.916249 GTCTATAACCATTCCATCGTCGTC 59.084 45.833 0.00 0.00 0.00 4.20
2651 2767 4.583489 AGTCTATAACCATTCCATCGTCGT 59.417 41.667 0.00 0.00 0.00 4.34
2652 2768 4.917998 CAGTCTATAACCATTCCATCGTCG 59.082 45.833 0.00 0.00 0.00 5.12
2653 2769 5.921408 GTCAGTCTATAACCATTCCATCGTC 59.079 44.000 0.00 0.00 0.00 4.20
2654 2770 5.221461 GGTCAGTCTATAACCATTCCATCGT 60.221 44.000 0.00 0.00 33.11 3.73
2655 2771 5.230942 GGTCAGTCTATAACCATTCCATCG 58.769 45.833 0.00 0.00 33.11 3.84
2818 2946 9.405587 GACATGCTCTAGTAAGTAGAATGAATC 57.594 37.037 3.85 0.00 37.32 2.52
2821 2949 9.278978 CTAGACATGCTCTAGTAAGTAGAATGA 57.721 37.037 17.40 0.00 42.68 2.57
2822 2950 8.511321 CCTAGACATGCTCTAGTAAGTAGAATG 58.489 40.741 21.01 0.00 45.24 2.67
2825 2953 7.376335 TCCTAGACATGCTCTAGTAAGTAGA 57.624 40.000 21.01 12.63 45.24 2.59
2826 2954 7.880713 TCATCCTAGACATGCTCTAGTAAGTAG 59.119 40.741 21.01 11.27 45.24 2.57
2827 2955 7.662258 GTCATCCTAGACATGCTCTAGTAAGTA 59.338 40.741 21.01 9.27 45.24 2.24
2828 2956 6.488683 GTCATCCTAGACATGCTCTAGTAAGT 59.511 42.308 21.01 9.07 45.24 2.24
2829 2957 6.348132 CGTCATCCTAGACATGCTCTAGTAAG 60.348 46.154 21.01 14.11 45.24 2.34
2848 2988 3.921677 TGTTAGAACAACTCCCGTCATC 58.078 45.455 0.00 0.00 35.67 2.92
2849 2989 4.202326 ACTTGTTAGAACAACTCCCGTCAT 60.202 41.667 3.71 0.00 43.45 3.06
2850 2990 3.133362 ACTTGTTAGAACAACTCCCGTCA 59.867 43.478 3.71 0.00 43.45 4.35
2851 2991 3.725490 ACTTGTTAGAACAACTCCCGTC 58.275 45.455 3.71 0.00 43.45 4.79
2852 2992 3.832615 ACTTGTTAGAACAACTCCCGT 57.167 42.857 3.71 0.00 43.45 5.28
2853 2993 6.164176 AGATTACTTGTTAGAACAACTCCCG 58.836 40.000 3.71 0.00 43.45 5.14
2854 2994 7.981102 AAGATTACTTGTTAGAACAACTCCC 57.019 36.000 3.71 0.00 43.45 4.30
2879 3019 8.479689 TCAATTCTCCATTCATATTGCAACAAT 58.520 29.630 0.00 0.00 0.00 2.71
2915 3087 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2916 3088 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2917 3089 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2918 3090 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2919 3091 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2920 3092 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2921 3093 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2922 3094 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2923 3095 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2924 3096 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2925 3097 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2926 3098 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2927 3099 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2928 3100 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2929 3101 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2930 3102 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2931 3103 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2932 3104 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2933 3105 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2934 3106 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2935 3107 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2936 3108 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2937 3109 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2938 3110 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2939 3111 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2940 3112 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2941 3113 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2942 3114 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2943 3115 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2944 3116 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2945 3117 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
2946 3118 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2947 3119 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
2948 3120 8.049117 ACATCATCATCATCATCATCATCATCA 58.951 33.333 0.00 0.00 0.00 3.07
2949 3121 8.443953 ACATCATCATCATCATCATCATCATC 57.556 34.615 0.00 0.00 0.00 2.92
2950 3122 8.680903 CAACATCATCATCATCATCATCATCAT 58.319 33.333 0.00 0.00 0.00 2.45
2951 3123 7.665559 ACAACATCATCATCATCATCATCATCA 59.334 33.333 0.00 0.00 0.00 3.07
2952 3124 8.045176 ACAACATCATCATCATCATCATCATC 57.955 34.615 0.00 0.00 0.00 2.92
2953 3125 8.299570 CAACAACATCATCATCATCATCATCAT 58.700 33.333 0.00 0.00 0.00 2.45
2988 3165 2.407361 ACGACAACGACGACAATTCATC 59.593 45.455 0.00 0.00 42.66 2.92
2989 3166 2.400399 ACGACAACGACGACAATTCAT 58.600 42.857 0.00 0.00 42.66 2.57
2990 3167 1.782569 GACGACAACGACGACAATTCA 59.217 47.619 0.00 0.00 42.66 2.57
2991 3168 2.466210 GACGACAACGACGACAATTC 57.534 50.000 0.00 0.00 42.66 2.17
3010 3187 4.099170 ACCTCCGCTTCGACGACG 62.099 66.667 0.00 0.00 41.26 5.12


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

AutoCloner maintained by Alex Coulton.