Multiple sequence alignment - TraesCS3A01G304700

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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 TraesCS3A01G304700 chr3A 100.000 5723 0 0 1 5723 540680318 540686040 0.000000e+00 10569
1 TraesCS3A01G304700 chr3A 93.116 552 38 0 1 552 540745744 540745193 0.000000e+00 809
2 TraesCS3A01G304700 chr3A 93.223 546 37 0 4 549 47876712 47877257 0.000000e+00 804
3 TraesCS3A01G304700 chr3A 93.040 546 38 0 1 546 540672773 540673318 0.000000e+00 798
4 TraesCS3A01G304700 chr3D 96.061 2970 95 15 2742 5702 410973419 410970463 0.000000e+00 4817
5 TraesCS3A01G304700 chr3D 91.680 649 46 4 2098 2743 410974098 410973455 0.000000e+00 893
6 TraesCS3A01G304700 chr3D 93.078 549 37 1 1 549 590718871 590718324 0.000000e+00 802
7 TraesCS3A01G304700 chr3D 90.240 584 44 10 1543 2118 410980143 410979565 0.000000e+00 750
8 TraesCS3A01G304700 chr3D 81.352 917 152 13 563 1473 277068241 277069144 0.000000e+00 728
9 TraesCS3A01G304700 chr3D 79.116 905 177 10 571 1471 305882831 305883727 1.050000e-171 614
10 TraesCS3A01G304700 chr3D 78.775 914 169 22 569 1472 505053774 505054672 1.780000e-164 590
11 TraesCS3A01G304700 chr3B 96.944 2258 61 6 2878 5132 537310287 537308035 0.000000e+00 3781
12 TraesCS3A01G304700 chr3B 93.253 578 31 6 5134 5704 537301580 537301004 0.000000e+00 845
13 TraesCS3A01G304700 chr5A 93.784 547 34 0 3 549 309924175 309923629 0.000000e+00 822
14 TraesCS3A01G304700 chr2A 93.613 548 34 1 2 549 54808746 54808200 0.000000e+00 817
15 TraesCS3A01G304700 chr2A 80.571 911 161 12 569 1473 382343969 382343069 0.000000e+00 688
16 TraesCS3A01G304700 chr1A 93.248 548 34 3 1 547 154020429 154020974 0.000000e+00 804
17 TraesCS3A01G304700 chr7A 92.767 553 40 0 1 553 139609215 139608663 0.000000e+00 800
18 TraesCS3A01G304700 chr7A 82.807 855 142 3 566 1417 518551562 518552414 0.000000e+00 760
19 TraesCS3A01G304700 chr6A 92.922 551 36 3 1 549 120872172 120871623 0.000000e+00 798
20 TraesCS3A01G304700 chr7D 81.469 912 159 9 563 1473 270161564 270162466 0.000000e+00 739
21 TraesCS3A01G304700 chr7D 79.057 912 171 18 569 1473 629487109 629486211 4.900000e-170 608
22 TraesCS3A01G304700 chr2D 81.099 910 155 12 569 1473 304334703 304333806 0.000000e+00 712
23 TraesCS3A01G304700 chr2B 80.664 874 146 18 563 1426 160912686 160913546 0.000000e+00 656
24 TraesCS3A01G304700 chr2B 80.946 803 136 15 563 1355 160906881 160907676 2.270000e-173 619
25 TraesCS3A01G304700 chr2B 82.313 147 25 1 2659 2805 5364265 5364410 6.020000e-25 126
26 TraesCS3A01G304700 chr2B 83.594 128 13 7 2659 2783 69251949 69251827 4.690000e-21 113
27 TraesCS3A01G304700 chr4A 78.728 912 174 17 569 1473 678203089 678202191 4.940000e-165 592
28 TraesCS3A01G304700 chr4A 84.127 126 20 0 2663 2788 725919280 725919155 7.790000e-24 122
29 TraesCS3A01G304700 chr6D 78.633 922 166 27 563 1473 307789431 307790332 2.970000e-162 582


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 TraesCS3A01G304700 chr3A 540680318 540686040 5722 False 10569 10569 100.0000 1 5723 1 chr3A.!!$F3 5722
1 TraesCS3A01G304700 chr3A 540745193 540745744 551 True 809 809 93.1160 1 552 1 chr3A.!!$R1 551
2 TraesCS3A01G304700 chr3A 47876712 47877257 545 False 804 804 93.2230 4 549 1 chr3A.!!$F1 545
3 TraesCS3A01G304700 chr3A 540672773 540673318 545 False 798 798 93.0400 1 546 1 chr3A.!!$F2 545
4 TraesCS3A01G304700 chr3D 410970463 410974098 3635 True 2855 4817 93.8705 2098 5702 2 chr3D.!!$R3 3604
5 TraesCS3A01G304700 chr3D 590718324 590718871 547 True 802 802 93.0780 1 549 1 chr3D.!!$R2 548
6 TraesCS3A01G304700 chr3D 410979565 410980143 578 True 750 750 90.2400 1543 2118 1 chr3D.!!$R1 575
7 TraesCS3A01G304700 chr3D 277068241 277069144 903 False 728 728 81.3520 563 1473 1 chr3D.!!$F1 910
8 TraesCS3A01G304700 chr3D 305882831 305883727 896 False 614 614 79.1160 571 1471 1 chr3D.!!$F2 900
9 TraesCS3A01G304700 chr3D 505053774 505054672 898 False 590 590 78.7750 569 1472 1 chr3D.!!$F3 903
10 TraesCS3A01G304700 chr3B 537308035 537310287 2252 True 3781 3781 96.9440 2878 5132 1 chr3B.!!$R2 2254
11 TraesCS3A01G304700 chr3B 537301004 537301580 576 True 845 845 93.2530 5134 5704 1 chr3B.!!$R1 570
12 TraesCS3A01G304700 chr5A 309923629 309924175 546 True 822 822 93.7840 3 549 1 chr5A.!!$R1 546
13 TraesCS3A01G304700 chr2A 54808200 54808746 546 True 817 817 93.6130 2 549 1 chr2A.!!$R1 547
14 TraesCS3A01G304700 chr2A 382343069 382343969 900 True 688 688 80.5710 569 1473 1 chr2A.!!$R2 904
15 TraesCS3A01G304700 chr1A 154020429 154020974 545 False 804 804 93.2480 1 547 1 chr1A.!!$F1 546
16 TraesCS3A01G304700 chr7A 139608663 139609215 552 True 800 800 92.7670 1 553 1 chr7A.!!$R1 552
17 TraesCS3A01G304700 chr7A 518551562 518552414 852 False 760 760 82.8070 566 1417 1 chr7A.!!$F1 851
18 TraesCS3A01G304700 chr6A 120871623 120872172 549 True 798 798 92.9220 1 549 1 chr6A.!!$R1 548
19 TraesCS3A01G304700 chr7D 270161564 270162466 902 False 739 739 81.4690 563 1473 1 chr7D.!!$F1 910
20 TraesCS3A01G304700 chr7D 629486211 629487109 898 True 608 608 79.0570 569 1473 1 chr7D.!!$R1 904
21 TraesCS3A01G304700 chr2D 304333806 304334703 897 True 712 712 81.0990 569 1473 1 chr2D.!!$R1 904
22 TraesCS3A01G304700 chr2B 160912686 160913546 860 False 656 656 80.6640 563 1426 1 chr2B.!!$F3 863
23 TraesCS3A01G304700 chr2B 160906881 160907676 795 False 619 619 80.9460 563 1355 1 chr2B.!!$F2 792
24 TraesCS3A01G304700 chr4A 678202191 678203089 898 True 592 592 78.7280 569 1473 1 chr4A.!!$R1 904
25 TraesCS3A01G304700 chr6D 307789431 307790332 901 False 582 582 78.6330 563 1473 1 chr6D.!!$F1 910

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
113 114 0.036306 CTTTAGGGTCCGTGCAAGGT 59.964 55.000 18.61 1.49 0.00 3.50 F
1078 1102 0.179100 CGCAGAGTGTACCTGGGATG 60.179 60.000 8.40 0.00 44.33 3.51 F
1344 1372 0.320771 CTCCCCACGTTGTCTCCAAG 60.321 60.000 0.00 0.00 0.00 3.61 F
1478 1506 0.465705 GTTGGAGATGCCCTCGATGA 59.534 55.000 0.00 0.00 42.89 2.92 F
2901 2981 0.391130 TCAAGCGAACCCTTCCATCG 60.391 55.000 0.00 0.00 39.47 3.84 F
3563 3643 1.174783 CGGGGGATCGAGGTGTATAG 58.825 60.000 0.00 0.00 0.00 1.31 F
3948 4028 1.301401 TGCACACGCTGGGTTAGTC 60.301 57.895 0.00 0.00 39.64 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1372 0.041576 GACGTGTTTTCTCCCGCAAC 60.042 55.000 0.00 0.0 0.00 4.17 R
2876 2956 0.179018 AAGGGTTCGCTTGAGCAACT 60.179 50.000 3.65 0.0 42.21 3.16 R
2899 2979 2.300723 AGCTGGTAAATACACACACCGA 59.699 45.455 0.00 0.0 33.55 4.69 R
3376 3456 2.434359 CGAGCCAAACCCGAGGAC 60.434 66.667 0.00 0.0 0.00 3.85 R
3948 4028 0.107508 AAGCATCACGACCCTCCATG 60.108 55.000 0.00 0.0 0.00 3.66 R
4522 4602 0.846015 AGCCCATATGCTACTGCCAA 59.154 50.000 0.00 0.0 40.56 4.52 R
5358 5446 0.867746 GCATGATAATTCTCCGCGCA 59.132 50.000 8.75 0.0 0.00 6.09 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
113 114 0.036306 CTTTAGGGTCCGTGCAAGGT 59.964 55.000 18.61 1.49 0.00 3.50
129 130 1.150536 GGTCCAAGTGTTGAGCCCA 59.849 57.895 0.00 0.00 0.00 5.36
138 139 1.069090 GTTGAGCCCACGACAGACA 59.931 57.895 0.00 0.00 0.00 3.41
234 237 1.743958 CGAATAGACACCTCCACTCGT 59.256 52.381 0.00 0.00 0.00 4.18
250 253 2.314647 CGTCGCCGGTTGTGTGATT 61.315 57.895 1.90 0.00 0.00 2.57
257 260 0.874390 CGGTTGTGTGATTGGACCTG 59.126 55.000 0.00 0.00 0.00 4.00
259 262 1.202879 GGTTGTGTGATTGGACCTGGA 60.203 52.381 0.00 0.00 0.00 3.86
525 529 9.187455 GTAGGAAAATTTTAATTTGCAGTCGAA 57.813 29.630 2.75 0.00 38.53 3.71
553 557 4.155280 CCTACCGTAGAACCCAACAAAATG 59.845 45.833 7.16 0.00 0.00 2.32
554 558 2.888414 ACCGTAGAACCCAACAAAATGG 59.112 45.455 0.00 0.00 40.35 3.16
555 559 2.888414 CCGTAGAACCCAACAAAATGGT 59.112 45.455 0.00 0.00 38.91 3.55
556 560 3.057806 CCGTAGAACCCAACAAAATGGTC 60.058 47.826 0.00 0.00 38.91 4.02
557 561 3.566322 CGTAGAACCCAACAAAATGGTCA 59.434 43.478 0.00 0.00 38.91 4.02
558 562 4.320202 CGTAGAACCCAACAAAATGGTCAG 60.320 45.833 0.00 0.00 38.91 3.51
559 563 3.642141 AGAACCCAACAAAATGGTCAGT 58.358 40.909 0.00 0.00 38.91 3.41
560 564 3.384467 AGAACCCAACAAAATGGTCAGTG 59.616 43.478 0.00 0.00 38.91 3.66
561 565 2.038659 ACCCAACAAAATGGTCAGTGG 58.961 47.619 0.00 0.00 38.91 4.00
567 571 4.307032 ACAAAATGGTCAGTGGCTATCT 57.693 40.909 0.00 0.00 0.00 1.98
574 578 2.290323 GGTCAGTGGCTATCTTGTGGTT 60.290 50.000 0.00 0.00 0.00 3.67
610 617 1.501741 CGGGCTACACAATGTGCAC 59.498 57.895 14.01 10.75 36.98 4.57
743 759 3.735820 CGTTATAGAACTTGGTGGCGCTA 60.736 47.826 7.64 0.00 33.01 4.26
765 781 3.566322 AGTCTGGATAGCGTATCAGTGAC 59.434 47.826 0.00 9.66 36.91 3.67
784 800 5.877012 AGTGACATGATAACAACCTCACATC 59.123 40.000 0.00 0.00 33.79 3.06
785 801 5.877012 GTGACATGATAACAACCTCACATCT 59.123 40.000 0.00 0.00 32.70 2.90
793 810 2.299013 ACAACCTCACATCTCGTTGCTA 59.701 45.455 0.00 0.00 39.33 3.49
798 815 3.310774 CCTCACATCTCGTTGCTAAATGG 59.689 47.826 0.00 0.00 0.00 3.16
803 820 5.294306 CACATCTCGTTGCTAAATGGTGTAT 59.706 40.000 0.00 0.00 0.00 2.29
807 824 5.465390 TCTCGTTGCTAAATGGTGTATATGC 59.535 40.000 0.00 0.00 0.00 3.14
813 830 7.014988 TGCTAAATGGTGTATATGCCATAGA 57.985 36.000 10.28 3.27 44.03 1.98
816 833 3.981071 TGGTGTATATGCCATAGAGCC 57.019 47.619 0.00 0.00 0.00 4.70
817 834 3.520696 TGGTGTATATGCCATAGAGCCT 58.479 45.455 0.00 0.00 0.00 4.58
882 902 1.305718 GTCCTCCCTCTGCTCCTGT 60.306 63.158 0.00 0.00 0.00 4.00
958 979 3.120105 CGAGTAGCTCGCCATCCA 58.880 61.111 5.60 0.00 46.75 3.41
970 991 2.552743 TCGCCATCCATCGTACTCTAAG 59.447 50.000 0.00 0.00 0.00 2.18
976 998 6.516718 CCATCCATCGTACTCTAAGAAATGT 58.483 40.000 0.00 0.00 0.00 2.71
1013 1036 1.188863 AGCTCAATGGCATTTGACCC 58.811 50.000 10.65 4.30 32.39 4.46
1054 1077 0.824109 CTGCCATGGAGGTCGTCTAA 59.176 55.000 18.40 0.00 40.61 2.10
1059 1083 0.831307 ATGGAGGTCGTCTAAAGGGC 59.169 55.000 0.00 0.00 0.00 5.19
1076 1100 2.646175 GCGCAGAGTGTACCTGGGA 61.646 63.158 15.63 0.00 44.33 4.37
1078 1102 0.179100 CGCAGAGTGTACCTGGGATG 60.179 60.000 8.40 0.00 44.33 3.51
1083 1107 2.375174 AGAGTGTACCTGGGATGCAAAA 59.625 45.455 0.00 0.00 0.00 2.44
1111 1135 0.461339 GGTGGACAATGTCGCCGTAT 60.461 55.000 7.35 0.00 32.65 3.06
1158 1182 1.718757 GCAGATGTCCGACAATGCCC 61.719 60.000 22.55 5.40 38.30 5.36
1164 1188 1.148273 TCCGACAATGCCCCTATGC 59.852 57.895 0.00 0.00 0.00 3.14
1243 1268 3.457749 GAGGAGAAGGGATTGAGTGGAAT 59.542 47.826 0.00 0.00 0.00 3.01
1302 1329 3.190744 GTGTCGGAGTCTTACATGTCTGA 59.809 47.826 0.00 0.00 0.00 3.27
1344 1372 0.320771 CTCCCCACGTTGTCTCCAAG 60.321 60.000 0.00 0.00 0.00 3.61
1365 1393 1.301479 GCGGGAGAAAACACGTCCT 60.301 57.895 0.00 0.00 39.03 3.85
1391 1419 3.522808 GGCGGACCGATACAGACT 58.477 61.111 20.50 0.00 0.00 3.24
1426 1454 4.268939 ACGGTCCGAACAACGCGA 62.269 61.111 20.51 0.00 41.07 5.87
1473 1501 1.817099 CAGCGTTGGAGATGCCCTC 60.817 63.158 0.00 0.00 41.38 4.30
1474 1502 2.892425 GCGTTGGAGATGCCCTCG 60.892 66.667 0.00 0.00 42.89 4.63
1475 1503 2.892640 CGTTGGAGATGCCCTCGA 59.107 61.111 0.00 0.00 42.89 4.04
1476 1504 1.443407 CGTTGGAGATGCCCTCGAT 59.557 57.895 0.00 0.00 42.89 3.59
1477 1505 0.877649 CGTTGGAGATGCCCTCGATG 60.878 60.000 0.00 0.00 42.89 3.84
1478 1506 0.465705 GTTGGAGATGCCCTCGATGA 59.534 55.000 0.00 0.00 42.89 2.92
1479 1507 1.134401 GTTGGAGATGCCCTCGATGAA 60.134 52.381 0.00 0.00 42.89 2.57
1480 1508 0.465705 TGGAGATGCCCTCGATGAAC 59.534 55.000 0.00 0.00 42.89 3.18
1481 1509 0.465705 GGAGATGCCCTCGATGAACA 59.534 55.000 0.00 0.00 42.89 3.18
1482 1510 1.134401 GGAGATGCCCTCGATGAACAA 60.134 52.381 0.00 0.00 42.89 2.83
1483 1511 2.632377 GAGATGCCCTCGATGAACAAA 58.368 47.619 0.00 0.00 31.32 2.83
1484 1512 3.009723 GAGATGCCCTCGATGAACAAAA 58.990 45.455 0.00 0.00 31.32 2.44
1485 1513 3.624777 AGATGCCCTCGATGAACAAAAT 58.375 40.909 0.00 0.00 0.00 1.82
1486 1514 4.780815 AGATGCCCTCGATGAACAAAATA 58.219 39.130 0.00 0.00 0.00 1.40
1487 1515 4.576463 AGATGCCCTCGATGAACAAAATAC 59.424 41.667 0.00 0.00 0.00 1.89
1488 1516 3.680490 TGCCCTCGATGAACAAAATACA 58.320 40.909 0.00 0.00 0.00 2.29
1489 1517 4.075682 TGCCCTCGATGAACAAAATACAA 58.924 39.130 0.00 0.00 0.00 2.41
1490 1518 4.704540 TGCCCTCGATGAACAAAATACAAT 59.295 37.500 0.00 0.00 0.00 2.71
1491 1519 5.184864 TGCCCTCGATGAACAAAATACAATT 59.815 36.000 0.00 0.00 0.00 2.32
1492 1520 5.516339 GCCCTCGATGAACAAAATACAATTG 59.484 40.000 3.24 3.24 0.00 2.32
1493 1521 6.624861 GCCCTCGATGAACAAAATACAATTGA 60.625 38.462 13.59 0.00 0.00 2.57
1494 1522 6.968904 CCCTCGATGAACAAAATACAATTGAG 59.031 38.462 13.59 0.00 0.00 3.02
1495 1523 7.148255 CCCTCGATGAACAAAATACAATTGAGA 60.148 37.037 13.59 0.00 0.00 3.27
1496 1524 7.693951 CCTCGATGAACAAAATACAATTGAGAC 59.306 37.037 13.59 0.00 0.00 3.36
1497 1525 7.526608 TCGATGAACAAAATACAATTGAGACC 58.473 34.615 13.59 0.00 0.00 3.85
1498 1526 7.390440 TCGATGAACAAAATACAATTGAGACCT 59.610 33.333 13.59 0.00 0.00 3.85
1499 1527 8.023128 CGATGAACAAAATACAATTGAGACCTT 58.977 33.333 13.59 0.00 0.00 3.50
1502 1530 8.573035 TGAACAAAATACAATTGAGACCTTACC 58.427 33.333 13.59 0.00 0.00 2.85
1503 1531 8.472007 AACAAAATACAATTGAGACCTTACCA 57.528 30.769 13.59 0.00 0.00 3.25
1504 1532 8.650143 ACAAAATACAATTGAGACCTTACCAT 57.350 30.769 13.59 0.00 0.00 3.55
1505 1533 9.088987 ACAAAATACAATTGAGACCTTACCATT 57.911 29.630 13.59 0.00 0.00 3.16
1506 1534 9.573133 CAAAATACAATTGAGACCTTACCATTC 57.427 33.333 13.59 0.00 0.00 2.67
1507 1535 8.877864 AAATACAATTGAGACCTTACCATTCA 57.122 30.769 13.59 0.00 0.00 2.57
1508 1536 9.479549 AAATACAATTGAGACCTTACCATTCAT 57.520 29.630 13.59 0.00 0.00 2.57
1509 1537 8.682936 ATACAATTGAGACCTTACCATTCATC 57.317 34.615 13.59 0.00 0.00 2.92
1510 1538 6.484288 ACAATTGAGACCTTACCATTCATCA 58.516 36.000 13.59 0.00 0.00 3.07
1511 1539 6.947733 ACAATTGAGACCTTACCATTCATCAA 59.052 34.615 13.59 0.00 0.00 2.57
1512 1540 7.451255 ACAATTGAGACCTTACCATTCATCAAA 59.549 33.333 13.59 0.00 0.00 2.69
1513 1541 6.817765 TTGAGACCTTACCATTCATCAAAC 57.182 37.500 0.00 0.00 0.00 2.93
1514 1542 4.935205 TGAGACCTTACCATTCATCAAACG 59.065 41.667 0.00 0.00 0.00 3.60
1515 1543 5.160607 AGACCTTACCATTCATCAAACGA 57.839 39.130 0.00 0.00 0.00 3.85
1516 1544 5.745227 AGACCTTACCATTCATCAAACGAT 58.255 37.500 0.00 0.00 0.00 3.73
1517 1545 6.884832 AGACCTTACCATTCATCAAACGATA 58.115 36.000 0.00 0.00 0.00 2.92
1518 1546 7.509546 AGACCTTACCATTCATCAAACGATAT 58.490 34.615 0.00 0.00 0.00 1.63
1519 1547 7.993183 AGACCTTACCATTCATCAAACGATATT 59.007 33.333 0.00 0.00 0.00 1.28
1520 1548 8.519799 ACCTTACCATTCATCAAACGATATTT 57.480 30.769 0.00 0.00 0.00 1.40
1521 1549 8.966868 ACCTTACCATTCATCAAACGATATTTT 58.033 29.630 0.00 0.00 0.00 1.82
1522 1550 9.450807 CCTTACCATTCATCAAACGATATTTTC 57.549 33.333 0.00 0.00 0.00 2.29
1673 1701 0.887933 GGGCGTGAAACCATGTTCAT 59.112 50.000 2.44 0.00 39.61 2.57
1676 1704 2.030363 GGCGTGAAACCATGTTCATCAA 60.030 45.455 2.44 0.00 39.61 2.57
1679 1707 4.324402 GCGTGAAACCATGTTCATCAAATC 59.676 41.667 2.44 0.00 39.61 2.17
1682 1710 4.522405 TGAAACCATGTTCATCAAATCCGT 59.478 37.500 0.00 0.00 32.56 4.69
1701 1729 2.783135 GTGTCTGTGTCCATGTCCAAT 58.217 47.619 0.00 0.00 0.00 3.16
1707 1735 2.374839 TGTGTCCATGTCCAATGAAGGA 59.625 45.455 0.00 0.00 34.64 3.36
1730 1758 5.979288 ACCACCTAGTAAGTGTTGACTAG 57.021 43.478 2.68 2.68 43.20 2.57
1823 1855 1.551329 CCTATCTAGGTCCAGCCCTCC 60.551 61.905 0.00 0.00 38.69 4.30
1842 1874 3.216800 TCCTCTGCATTTATGTCATGGC 58.783 45.455 0.00 0.00 0.00 4.40
1860 1892 2.178521 GAGTCGCGTCGTCACCAT 59.821 61.111 5.77 0.00 0.00 3.55
1900 1932 1.517694 CGGTCGGTTATGGTGTCCG 60.518 63.158 0.00 0.00 44.76 4.79
1912 1944 0.532573 GGTGTCCGATCTTGAGCTCA 59.467 55.000 13.74 13.74 0.00 4.26
1914 1946 2.419297 GGTGTCCGATCTTGAGCTCAAT 60.419 50.000 28.57 15.83 35.02 2.57
1915 1947 2.863137 GTGTCCGATCTTGAGCTCAATC 59.137 50.000 28.57 22.01 35.02 2.67
1918 1950 2.123342 CCGATCTTGAGCTCAATCGTC 58.877 52.381 33.65 26.26 36.92 4.20
1920 1952 1.520590 GATCTTGAGCTCAATCGTCGC 59.479 52.381 28.57 11.80 35.02 5.19
1937 1969 1.719709 GCCTAATTCAACCGGCGAC 59.280 57.895 9.30 0.00 32.22 5.19
1948 1980 1.321074 ACCGGCGACCCAAACAAAAA 61.321 50.000 9.30 0.00 0.00 1.94
1980 2012 2.774351 CTCCCTCCCCATCACCCC 60.774 72.222 0.00 0.00 0.00 4.95
2024 2057 5.461032 ACTCTCTTTCATCGTTGTCTCTT 57.539 39.130 0.00 0.00 0.00 2.85
2031 2064 8.507524 TCTTTCATCGTTGTCTCTTCTATAGA 57.492 34.615 0.00 0.00 0.00 1.98
2061 2094 7.120432 ACTGAGAAAATAGTTGCTTGAGGAATC 59.880 37.037 0.00 0.00 0.00 2.52
2124 2157 2.305009 GATGGAAGGGCATCTCCAAAG 58.695 52.381 7.05 0.00 35.71 2.77
2132 2165 1.546029 GGCATCTCCAAAGAAACCACC 59.454 52.381 0.00 0.00 34.49 4.61
2139 2172 2.432510 TCCAAAGAAACCACCGCATTTT 59.567 40.909 0.00 0.00 0.00 1.82
2140 2173 3.118592 TCCAAAGAAACCACCGCATTTTT 60.119 39.130 0.00 0.00 0.00 1.94
2158 2191 4.681074 TTTTTCATTTTCTGGGGACACC 57.319 40.909 0.00 0.00 40.81 4.16
2181 2214 6.388689 ACCTTATACCATGGTATCCAAGTGAA 59.611 38.462 35.39 22.38 41.12 3.18
2186 2219 3.141398 CATGGTATCCAAGTGAATCCCG 58.859 50.000 0.00 0.00 36.95 5.14
2187 2220 2.193127 TGGTATCCAAGTGAATCCCGT 58.807 47.619 0.00 0.00 0.00 5.28
2199 2232 2.093500 TGAATCCCGTCTTGTCCATCAG 60.093 50.000 0.00 0.00 0.00 2.90
2208 2241 5.339990 CGTCTTGTCCATCAGTTTTGTTTT 58.660 37.500 0.00 0.00 0.00 2.43
2243 2276 7.744087 TTTCAGTATATTTGATCCATTCCCG 57.256 36.000 0.00 0.00 0.00 5.14
2338 2371 2.605837 TAGCGTTCCAAGTTCACACA 57.394 45.000 0.00 0.00 0.00 3.72
2340 2373 2.088423 AGCGTTCCAAGTTCACACAAA 58.912 42.857 0.00 0.00 0.00 2.83
2351 2384 7.277539 TCCAAGTTCACACAAATTGAATCAAAC 59.722 33.333 0.00 0.00 35.47 2.93
2438 2471 3.133901 TGGTACGCACAGTATTGATCCAT 59.866 43.478 0.00 0.00 37.69 3.41
2455 2488 3.963129 TCCATTTCTATTGGTTCGCCTT 58.037 40.909 0.00 0.00 38.36 4.35
2461 2494 4.422073 TCTATTGGTTCGCCTTCATGAT 57.578 40.909 0.00 0.00 38.36 2.45
2462 2495 4.129380 TCTATTGGTTCGCCTTCATGATG 58.871 43.478 0.00 0.00 38.36 3.07
2463 2496 1.462616 TTGGTTCGCCTTCATGATGG 58.537 50.000 20.70 20.70 38.36 3.51
2474 2507 2.584492 TCATGATGGTGCTAGTGTCG 57.416 50.000 0.00 0.00 0.00 4.35
2486 2519 2.928116 GCTAGTGTCGGTAAACATGACC 59.072 50.000 0.00 0.00 0.00 4.02
2501 2534 4.256920 ACATGACCTTTGAAATCCTCGAG 58.743 43.478 5.13 5.13 0.00 4.04
2502 2535 4.020218 ACATGACCTTTGAAATCCTCGAGA 60.020 41.667 15.71 0.00 0.00 4.04
2516 2549 1.001406 CTCGAGAAACCTTGTGAGCCT 59.999 52.381 6.58 0.00 0.00 4.58
2519 2552 2.028930 CGAGAAACCTTGTGAGCCTAGT 60.029 50.000 0.00 0.00 0.00 2.57
2545 2578 1.754226 TGGTCTTTGTTGCCTTTCACC 59.246 47.619 0.00 0.00 0.00 4.02
2556 2589 1.002792 GCCTTTCACCTCAACGACAAC 60.003 52.381 0.00 0.00 0.00 3.32
2585 2618 3.202151 TCTCTCTCTCCCTCTTTCTCTCC 59.798 52.174 0.00 0.00 0.00 3.71
2587 2620 3.023832 CTCTCTCCCTCTTTCTCTCCAC 58.976 54.545 0.00 0.00 0.00 4.02
2601 2634 3.769844 TCTCTCCACTTGGGTTGTATCTC 59.230 47.826 0.00 0.00 38.11 2.75
2611 2644 2.548067 GGGTTGTATCTCCATGTAGCCG 60.548 54.545 0.00 0.00 0.00 5.52
2637 2673 3.833732 ACCTTTCACCCTTCTTTTCCTC 58.166 45.455 0.00 0.00 0.00 3.71
2656 2692 3.198635 CCTCCCTCTCTTATTGCACTTGA 59.801 47.826 0.00 0.00 0.00 3.02
2821 2901 9.887862 ATTCCATACATCTTATTGAAATTCCCT 57.112 29.630 0.00 0.00 0.00 4.20
2869 2949 2.162681 GTTCACCATGTTGAGAAGGGG 58.837 52.381 0.00 0.00 0.00 4.79
2876 2956 5.307976 CACCATGTTGAGAAGGGGATATCTA 59.692 44.000 2.05 0.00 0.00 1.98
2899 2979 0.678048 GCTCAAGCGAACCCTTCCAT 60.678 55.000 0.00 0.00 0.00 3.41
2901 2981 0.391130 TCAAGCGAACCCTTCCATCG 60.391 55.000 0.00 0.00 39.47 3.84
2962 3042 6.975196 TTCAATTCCTCAATTCAGTTCCAA 57.025 33.333 0.00 0.00 28.97 3.53
3214 3294 2.549611 CTTCTCCTCCCTCACGCGTG 62.550 65.000 32.76 32.76 0.00 5.34
3376 3456 4.794439 TCCACGCGCACTCCATCG 62.794 66.667 5.73 0.00 0.00 3.84
3487 3567 4.504097 TGTTCGATGCAATTCGTGATAGAG 59.496 41.667 9.37 0.00 40.03 2.43
3495 3575 4.201724 GCAATTCGTGATAGAGGTGTTGTC 60.202 45.833 0.00 0.00 0.00 3.18
3563 3643 1.174783 CGGGGGATCGAGGTGTATAG 58.825 60.000 0.00 0.00 0.00 1.31
3948 4028 1.301401 TGCACACGCTGGGTTAGTC 60.301 57.895 0.00 0.00 39.64 2.59
3971 4051 1.610624 GGAGGGTCGTGATGCTTTTGA 60.611 52.381 0.00 0.00 0.00 2.69
3972 4052 1.464997 GAGGGTCGTGATGCTTTTGAC 59.535 52.381 0.00 0.00 0.00 3.18
4197 4277 2.299993 AGCGATTGATTGCTCTCGAA 57.700 45.000 0.00 0.00 44.00 3.71
4290 4370 5.429762 TGAGAAGGTGAGGAATACCATGATT 59.570 40.000 0.00 0.00 40.74 2.57
4522 4602 8.454106 GTGCACTTAGATATCACAGTGAAAAAT 58.546 33.333 26.84 1.72 39.25 1.82
4647 4727 0.247460 TGTCAGCTGTGGAGAATCGG 59.753 55.000 14.67 0.00 34.37 4.18
4704 4784 6.041979 ACCATTTTAAAGATGGCAAGTGTTCT 59.958 34.615 20.31 0.00 46.43 3.01
4780 4863 9.661563 CTGGTAATAGTCACCAACAAAATAGTA 57.338 33.333 0.00 0.00 45.27 1.82
4838 4921 2.041485 TGTCCTGGAATTCTGCCATCAA 59.959 45.455 5.23 0.00 34.33 2.57
5007 5090 8.634335 TCTCATTTTTCTGAACATCCACAATA 57.366 30.769 0.00 0.00 0.00 1.90
5160 5243 6.134535 TCCAAGTACCATTCTTATGTGGTT 57.865 37.500 2.02 0.00 46.22 3.67
5358 5446 4.847198 TGATTATGTGCCTGACTCATTGT 58.153 39.130 0.00 0.00 34.43 2.71
5379 5467 1.136141 GCGCGGAGAATTATCATGCAG 60.136 52.381 8.83 9.33 0.00 4.41
5387 5475 5.994054 GGAGAATTATCATGCAGAAGCTGTA 59.006 40.000 1.97 0.00 42.74 2.74
5410 5498 9.419297 TGTATATAATCGACTACATTTGAAGCC 57.581 33.333 0.00 0.00 0.00 4.35
5489 5578 7.640630 CGTGTGTAAGTTTGTAAATTGCAACTA 59.359 33.333 0.00 0.00 0.00 2.24
5509 5598 3.870633 ACTAAACGGCCAAGACTAGAG 57.129 47.619 2.24 0.00 0.00 2.43
5540 5629 7.447374 TGAGTTCCATGTACCAAACTTTATG 57.553 36.000 0.00 0.00 32.34 1.90
5545 5634 6.307776 TCCATGTACCAAACTTTATGTTCCA 58.692 36.000 0.00 0.00 38.03 3.53
5581 5670 7.094508 TGAGCAAAATACACTTCACTTCAAA 57.905 32.000 0.00 0.00 0.00 2.69
5589 5678 4.137543 ACACTTCACTTCAAATGGAGACC 58.862 43.478 0.00 0.00 0.00 3.85
5610 5699 0.947244 CCCTTGTGACTTGTGAGCAC 59.053 55.000 0.00 0.00 33.41 4.40
5639 5728 3.815401 ACTTTGTCATTGTCCTTTCGGAG 59.185 43.478 0.00 0.00 40.84 4.63
5663 5752 7.283329 AGGTACATTATCCTTGATTCCTTGTC 58.717 38.462 0.00 0.00 0.00 3.18
5699 5788 4.438880 CCAGCTTTCATCAGAGCAAATCAG 60.439 45.833 0.00 0.00 41.31 2.90
5702 5791 2.048444 TCATCAGAGCAAATCAGGGC 57.952 50.000 0.00 0.00 0.00 5.19
5703 5792 1.282738 TCATCAGAGCAAATCAGGGCA 59.717 47.619 0.00 0.00 0.00 5.36
5704 5793 2.092049 TCATCAGAGCAAATCAGGGCAT 60.092 45.455 0.00 0.00 0.00 4.40
5705 5794 1.758936 TCAGAGCAAATCAGGGCATG 58.241 50.000 0.00 0.00 0.00 4.06
5706 5795 0.102481 CAGAGCAAATCAGGGCATGC 59.898 55.000 9.90 9.90 39.06 4.06
5707 5796 1.041447 AGAGCAAATCAGGGCATGCC 61.041 55.000 29.47 29.47 39.59 4.40
5717 5806 2.517875 GGCATGCCCAGCAGGTAG 60.518 66.667 27.24 0.00 43.65 3.18
5718 5807 3.214845 GCATGCCCAGCAGGTAGC 61.215 66.667 6.36 0.00 43.65 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 1.227823 CGTGGGCTCAACACTTGGA 60.228 57.895 0.00 0.00 36.71 3.53
129 130 5.889853 TCCACTTTATATAGGTGTCTGTCGT 59.110 40.000 13.30 0.00 0.00 4.34
138 139 3.323979 CGGCACCTCCACTTTATATAGGT 59.676 47.826 0.00 0.00 41.24 3.08
234 237 1.963855 CCAATCACACAACCGGCGA 60.964 57.895 9.30 0.00 0.00 5.54
257 260 1.513586 CGTCGTGTAGCGGACTTCC 60.514 63.158 0.00 0.00 41.72 3.46
259 262 0.166814 GTACGTCGTGTAGCGGACTT 59.833 55.000 8.47 0.00 38.75 3.01
525 529 0.974525 GGGTTCTACGGTAGGGTGCT 60.975 60.000 14.82 0.00 0.00 4.40
553 557 1.279271 ACCACAAGATAGCCACTGACC 59.721 52.381 0.00 0.00 0.00 4.02
554 558 2.770164 ACCACAAGATAGCCACTGAC 57.230 50.000 0.00 0.00 0.00 3.51
555 559 2.637382 TGAACCACAAGATAGCCACTGA 59.363 45.455 0.00 0.00 0.00 3.41
556 560 3.057969 TGAACCACAAGATAGCCACTG 57.942 47.619 0.00 0.00 0.00 3.66
557 561 3.264193 TGATGAACCACAAGATAGCCACT 59.736 43.478 0.00 0.00 0.00 4.00
558 562 3.375299 GTGATGAACCACAAGATAGCCAC 59.625 47.826 0.00 0.00 37.04 5.01
559 563 3.609853 GTGATGAACCACAAGATAGCCA 58.390 45.455 0.00 0.00 37.04 4.75
560 564 2.609459 CGTGATGAACCACAAGATAGCC 59.391 50.000 0.00 0.00 36.89 3.93
561 565 2.609459 CCGTGATGAACCACAAGATAGC 59.391 50.000 0.00 0.00 36.89 2.97
567 571 1.514678 GCTGCCGTGATGAACCACAA 61.515 55.000 0.00 0.00 36.89 3.33
610 617 3.961477 TTCGTTCACTCAATGTTGGTG 57.039 42.857 7.57 7.57 33.50 4.17
648 663 8.145767 TGAGATCGTAAGTTTTGTTTCCTCTTA 58.854 33.333 0.00 0.00 39.48 2.10
657 672 6.102663 CAGAGGATGAGATCGTAAGTTTTGT 58.897 40.000 0.00 0.00 39.48 2.83
743 759 3.566322 GTCACTGATACGCTATCCAGACT 59.434 47.826 0.00 0.00 34.26 3.24
765 781 5.111989 ACGAGATGTGAGGTTGTTATCATG 58.888 41.667 0.00 0.00 0.00 3.07
784 800 5.334105 GGCATATACACCATTTAGCAACGAG 60.334 44.000 0.00 0.00 0.00 4.18
785 801 4.513692 GGCATATACACCATTTAGCAACGA 59.486 41.667 0.00 0.00 0.00 3.85
793 810 5.014544 AGGCTCTATGGCATATACACCATTT 59.985 40.000 7.81 0.00 44.37 2.32
798 815 6.536582 CACATTAGGCTCTATGGCATATACAC 59.463 42.308 7.81 0.00 44.55 2.90
803 820 3.584406 AGCACATTAGGCTCTATGGCATA 59.416 43.478 7.06 7.06 44.55 3.14
807 824 3.496130 CGAAAGCACATTAGGCTCTATGG 59.504 47.826 12.47 4.82 41.66 2.74
813 830 0.804989 GCACGAAAGCACATTAGGCT 59.195 50.000 0.00 0.00 45.15 4.58
882 902 4.439057 GCCGTATCCACAGATTTTGTAGA 58.561 43.478 0.00 0.00 38.16 2.59
958 979 7.941919 TGCTATGACATTTCTTAGAGTACGAT 58.058 34.615 6.08 0.00 33.24 3.73
970 991 8.685536 GCTTATTTTCGAATGCTATGACATTTC 58.314 33.333 0.00 0.00 40.31 2.17
976 998 7.552458 TTGAGCTTATTTTCGAATGCTATGA 57.448 32.000 0.00 0.00 0.00 2.15
1013 1036 3.716006 CACGCTCGGCAGGTGTTG 61.716 66.667 0.00 0.00 0.00 3.33
1032 1055 2.202797 CGACCTCCATGGCAGACG 60.203 66.667 6.96 9.01 40.22 4.18
1054 1077 1.913762 AGGTACACTCTGCGCCCTT 60.914 57.895 4.18 0.00 0.00 3.95
1059 1083 0.179100 CATCCCAGGTACACTCTGCG 60.179 60.000 0.00 0.00 0.00 5.18
1076 1100 0.901580 CACCCTGGAGCCTTTTGCAT 60.902 55.000 0.00 0.00 44.83 3.96
1078 1102 2.278330 CCACCCTGGAGCCTTTTGC 61.278 63.158 0.00 0.00 40.96 3.68
1111 1135 3.315949 AACACCCCGGCTCGCTAA 61.316 61.111 0.00 0.00 0.00 3.09
1120 1144 1.072505 AACTAGCACCAACACCCCG 59.927 57.895 0.00 0.00 0.00 5.73
1158 1182 4.301027 GTCTCCGGCCGGCATAGG 62.301 72.222 39.89 26.67 34.68 2.57
1178 1203 2.709475 CTCCGTTGCCGCTATTGC 59.291 61.111 0.00 0.00 0.00 3.56
1182 1207 2.102109 TTTCACCTCCGTTGCCGCTA 62.102 55.000 0.00 0.00 0.00 4.26
1222 1247 2.649742 TCCACTCAATCCCTTCTCCT 57.350 50.000 0.00 0.00 0.00 3.69
1243 1268 0.698238 CCCCTCACAGTCCCATTTCA 59.302 55.000 0.00 0.00 0.00 2.69
1276 1303 0.113776 TGTAAGACTCCGACACCCCT 59.886 55.000 0.00 0.00 0.00 4.79
1322 1349 2.928396 AGACAACGTGGGGAGGGG 60.928 66.667 0.00 0.00 0.00 4.79
1323 1350 2.663196 GAGACAACGTGGGGAGGG 59.337 66.667 0.00 0.00 0.00 4.30
1344 1372 0.041576 GACGTGTTTTCTCCCGCAAC 60.042 55.000 0.00 0.00 0.00 4.17
1391 1419 1.302112 TGAAAGCCATCCAACGCGA 60.302 52.632 15.93 0.00 0.00 5.87
1441 1469 1.448540 CGCTGATCCTCAAACCGCT 60.449 57.895 0.00 0.00 0.00 5.52
1456 1484 2.586792 GAGGGCATCTCCAACGCT 59.413 61.111 0.00 0.00 36.52 5.07
1473 1501 7.530010 AGGTCTCAATTGTATTTTGTTCATCG 58.470 34.615 5.13 0.00 0.00 3.84
1476 1504 8.573035 GGTAAGGTCTCAATTGTATTTTGTTCA 58.427 33.333 5.13 0.00 0.00 3.18
1477 1505 8.573035 TGGTAAGGTCTCAATTGTATTTTGTTC 58.427 33.333 5.13 0.00 0.00 3.18
1478 1506 8.472007 TGGTAAGGTCTCAATTGTATTTTGTT 57.528 30.769 5.13 0.00 0.00 2.83
1479 1507 8.650143 ATGGTAAGGTCTCAATTGTATTTTGT 57.350 30.769 5.13 0.00 0.00 2.83
1480 1508 9.573133 GAATGGTAAGGTCTCAATTGTATTTTG 57.427 33.333 5.13 0.00 0.00 2.44
1481 1509 9.308000 TGAATGGTAAGGTCTCAATTGTATTTT 57.692 29.630 5.13 0.00 0.00 1.82
1482 1510 8.877864 TGAATGGTAAGGTCTCAATTGTATTT 57.122 30.769 5.13 0.00 0.00 1.40
1483 1511 9.125026 GATGAATGGTAAGGTCTCAATTGTATT 57.875 33.333 5.13 0.00 0.00 1.89
1484 1512 8.274322 TGATGAATGGTAAGGTCTCAATTGTAT 58.726 33.333 5.13 0.00 0.00 2.29
1485 1513 7.629157 TGATGAATGGTAAGGTCTCAATTGTA 58.371 34.615 5.13 0.00 0.00 2.41
1486 1514 6.484288 TGATGAATGGTAAGGTCTCAATTGT 58.516 36.000 5.13 0.00 0.00 2.71
1487 1515 7.395190 TTGATGAATGGTAAGGTCTCAATTG 57.605 36.000 0.00 0.00 0.00 2.32
1488 1516 7.362056 CGTTTGATGAATGGTAAGGTCTCAATT 60.362 37.037 0.00 0.00 0.00 2.32
1489 1517 6.094048 CGTTTGATGAATGGTAAGGTCTCAAT 59.906 38.462 0.00 0.00 0.00 2.57
1490 1518 5.411361 CGTTTGATGAATGGTAAGGTCTCAA 59.589 40.000 0.00 0.00 0.00 3.02
1491 1519 4.935205 CGTTTGATGAATGGTAAGGTCTCA 59.065 41.667 0.00 0.00 0.00 3.27
1492 1520 5.175859 TCGTTTGATGAATGGTAAGGTCTC 58.824 41.667 0.00 0.00 0.00 3.36
1493 1521 5.160607 TCGTTTGATGAATGGTAAGGTCT 57.839 39.130 0.00 0.00 0.00 3.85
1494 1522 7.730364 ATATCGTTTGATGAATGGTAAGGTC 57.270 36.000 0.00 0.00 35.99 3.85
1495 1523 8.519799 AAATATCGTTTGATGAATGGTAAGGT 57.480 30.769 0.00 0.00 35.99 3.50
1496 1524 9.450807 GAAAATATCGTTTGATGAATGGTAAGG 57.549 33.333 0.00 0.00 35.99 2.69
1546 1574 7.305533 GCTTTAGTTTCGCGTGATGTTTAAAAA 60.306 33.333 5.77 0.00 0.00 1.94
1547 1575 6.141053 GCTTTAGTTTCGCGTGATGTTTAAAA 59.859 34.615 5.77 0.00 0.00 1.52
1548 1576 5.622041 GCTTTAGTTTCGCGTGATGTTTAAA 59.378 36.000 5.77 2.93 0.00 1.52
1549 1577 5.141568 GCTTTAGTTTCGCGTGATGTTTAA 58.858 37.500 5.77 0.00 0.00 1.52
1550 1578 4.664640 CGCTTTAGTTTCGCGTGATGTTTA 60.665 41.667 5.77 0.00 41.78 2.01
1559 1587 1.056750 CGACCGCTTTAGTTTCGCG 59.943 57.895 0.00 0.00 45.86 5.87
1563 1591 4.184079 ACATAGTCGACCGCTTTAGTTT 57.816 40.909 13.01 0.00 0.00 2.66
1565 1593 4.337555 ACATACATAGTCGACCGCTTTAGT 59.662 41.667 13.01 1.28 0.00 2.24
1632 1660 8.294577 CGCCCACCCTTTATAAATAGTAAATTC 58.705 37.037 0.00 0.00 0.00 2.17
1644 1672 2.618559 GGTTTCACGCCCACCCTTTATA 60.619 50.000 0.00 0.00 0.00 0.98
1649 1677 2.840753 ATGGTTTCACGCCCACCCT 61.841 57.895 0.00 0.00 32.49 4.34
1673 1701 1.414550 TGGACACAGACACGGATTTGA 59.585 47.619 0.00 0.00 0.00 2.69
1676 1704 1.347707 ACATGGACACAGACACGGATT 59.652 47.619 0.00 0.00 0.00 3.01
1679 1707 0.670546 GGACATGGACACAGACACGG 60.671 60.000 0.00 0.00 0.00 4.94
1682 1710 2.371510 TCATTGGACATGGACACAGACA 59.628 45.455 0.00 0.00 0.00 3.41
1701 1729 4.228824 ACACTTACTAGGTGGTTCCTTCA 58.771 43.478 3.58 0.00 45.67 3.02
1707 1735 6.073314 TCTAGTCAACACTTACTAGGTGGTT 58.927 40.000 9.06 0.00 43.51 3.67
1720 1748 9.567848 TTCATTTTCAACTTTTCTAGTCAACAC 57.432 29.630 0.00 0.00 35.54 3.32
1805 1836 1.429687 GAGGAGGGCTGGACCTAGATA 59.570 57.143 0.00 0.00 42.10 1.98
1817 1848 2.225467 GACATAAATGCAGAGGAGGGC 58.775 52.381 0.00 0.00 0.00 5.19
1823 1855 2.874086 TCGCCATGACATAAATGCAGAG 59.126 45.455 0.00 0.00 0.00 3.35
1842 1874 3.662623 ATGGTGACGACGCGACTCG 62.663 63.158 15.93 16.22 45.38 4.18
1877 1909 0.461163 CACCATAACCGACCGCATCA 60.461 55.000 0.00 0.00 0.00 3.07
1900 1932 1.520590 GCGACGATTGAGCTCAAGATC 59.479 52.381 31.14 24.76 39.47 2.75
1901 1933 1.565305 GCGACGATTGAGCTCAAGAT 58.435 50.000 31.14 19.90 39.47 2.40
1912 1944 1.931172 CGGTTGAATTAGGCGACGATT 59.069 47.619 0.00 0.00 0.00 3.34
1914 1946 0.458889 CCGGTTGAATTAGGCGACGA 60.459 55.000 0.00 0.00 0.00 4.20
1915 1947 2.003672 CCGGTTGAATTAGGCGACG 58.996 57.895 0.00 0.00 0.00 5.12
1920 1952 1.093496 GGGTCGCCGGTTGAATTAGG 61.093 60.000 1.90 0.00 0.00 2.69
1948 1980 1.619669 GGAGGGTGGGGGTGAGATT 60.620 63.158 0.00 0.00 0.00 2.40
1980 2012 3.354678 CAACCCGGGTTGCTTCAG 58.645 61.111 44.61 26.08 46.92 3.02
2000 2033 6.189677 AGAGACAACGATGAAAGAGAGTAG 57.810 41.667 0.00 0.00 0.00 2.57
2031 2064 8.734386 CCTCAAGCAACTATTTTCTCAGTTTAT 58.266 33.333 0.00 0.00 32.72 1.40
2036 2069 6.808008 TTCCTCAAGCAACTATTTTCTCAG 57.192 37.500 0.00 0.00 0.00 3.35
2094 2127 0.618458 CCCTTCCATCCCGAACTTCA 59.382 55.000 0.00 0.00 0.00 3.02
2095 2128 0.748367 GCCCTTCCATCCCGAACTTC 60.748 60.000 0.00 0.00 0.00 3.01
2108 2141 2.493675 GGTTTCTTTGGAGATGCCCTTC 59.506 50.000 0.00 0.00 34.97 3.46
2139 2172 3.611025 AGGTGTCCCCAGAAAATGAAA 57.389 42.857 0.00 0.00 34.66 2.69
2140 2173 3.611025 AAGGTGTCCCCAGAAAATGAA 57.389 42.857 0.00 0.00 34.66 2.57
2141 2174 4.946160 ATAAGGTGTCCCCAGAAAATGA 57.054 40.909 0.00 0.00 34.66 2.57
2148 2181 2.106511 CCATGGTATAAGGTGTCCCCAG 59.893 54.545 2.57 0.00 34.66 4.45
2153 2186 5.818678 TGGATACCATGGTATAAGGTGTC 57.181 43.478 32.68 20.76 40.93 3.67
2154 2187 5.670361 ACTTGGATACCATGGTATAAGGTGT 59.330 40.000 32.26 24.97 40.93 4.16
2155 2188 5.997746 CACTTGGATACCATGGTATAAGGTG 59.002 44.000 32.26 30.58 40.93 4.00
2156 2189 5.908831 TCACTTGGATACCATGGTATAAGGT 59.091 40.000 32.26 26.80 40.93 3.50
2157 2190 6.433847 TCACTTGGATACCATGGTATAAGG 57.566 41.667 32.26 26.34 40.93 2.69
2158 2191 7.607991 GGATTCACTTGGATACCATGGTATAAG 59.392 40.741 32.68 31.02 40.93 1.73
2181 2214 1.573108 ACTGATGGACAAGACGGGAT 58.427 50.000 0.00 0.00 0.00 3.85
2186 2219 8.871686 ATTAAAACAAAACTGATGGACAAGAC 57.128 30.769 0.00 0.00 0.00 3.01
2221 2254 5.245531 GCGGGAATGGATCAAATATACTGA 58.754 41.667 0.00 0.00 0.00 3.41
2226 2259 3.524095 TGGCGGGAATGGATCAAATAT 57.476 42.857 0.00 0.00 0.00 1.28
2233 2266 3.772025 TGTTTTATTTGGCGGGAATGGAT 59.228 39.130 0.00 0.00 0.00 3.41
2240 2273 3.983741 TCAAGTTGTTTTATTTGGCGGG 58.016 40.909 2.11 0.00 0.00 6.13
2297 2330 7.798052 CGCTATGTTGCTTGCTTTTTAAAAATT 59.202 29.630 13.55 0.00 0.00 1.82
2298 2331 7.042119 ACGCTATGTTGCTTGCTTTTTAAAAAT 60.042 29.630 13.55 0.00 0.00 1.82
2304 2337 3.369546 ACGCTATGTTGCTTGCTTTTT 57.630 38.095 0.00 0.00 0.00 1.94
2309 2342 3.312709 GGAACGCTATGTTGCTTGC 57.687 52.632 0.00 0.00 44.71 4.01
2322 2355 4.667262 TCAATTTGTGTGAACTTGGAACG 58.333 39.130 0.00 0.00 0.00 3.95
2351 2384 9.926751 CAAATTGTGCTTGATTACTAGACTATG 57.073 33.333 0.00 0.00 0.00 2.23
2360 2393 6.709145 TGCAATCAAATTGTGCTTGATTAC 57.291 33.333 9.71 6.22 46.70 1.89
2367 2400 5.079689 TGATCATGCAATCAAATTGTGCT 57.920 34.783 9.45 0.00 42.20 4.40
2438 2471 4.584874 TCATGAAGGCGAACCAATAGAAA 58.415 39.130 0.00 0.00 39.06 2.52
2455 2488 1.136891 CCGACACTAGCACCATCATGA 59.863 52.381 0.00 0.00 0.00 3.07
2461 2494 1.687660 TGTTTACCGACACTAGCACCA 59.312 47.619 0.00 0.00 0.00 4.17
2462 2495 2.443887 TGTTTACCGACACTAGCACC 57.556 50.000 0.00 0.00 0.00 5.01
2463 2496 3.367025 GTCATGTTTACCGACACTAGCAC 59.633 47.826 0.00 0.00 31.30 4.40
2474 2507 6.590234 AGGATTTCAAAGGTCATGTTTACC 57.410 37.500 0.00 0.00 37.27 2.85
2486 2519 5.239525 ACAAGGTTTCTCGAGGATTTCAAAG 59.760 40.000 13.56 0.00 0.00 2.77
2501 2534 3.304726 GCAAACTAGGCTCACAAGGTTTC 60.305 47.826 0.00 0.00 0.00 2.78
2502 2535 2.623416 GCAAACTAGGCTCACAAGGTTT 59.377 45.455 0.00 0.00 0.00 3.27
2516 2549 3.181480 GGCAACAAAGACCAAGCAAACTA 60.181 43.478 0.00 0.00 0.00 2.24
2519 2552 1.830477 AGGCAACAAAGACCAAGCAAA 59.170 42.857 0.00 0.00 41.41 3.68
2585 2618 3.955471 ACATGGAGATACAACCCAAGTG 58.045 45.455 0.00 0.00 31.59 3.16
2587 2620 4.130118 GCTACATGGAGATACAACCCAAG 58.870 47.826 9.87 0.00 33.15 3.61
2601 2634 3.754323 TGAAAGGTTTAACGGCTACATGG 59.246 43.478 0.00 0.00 0.00 3.66
2611 2644 6.097839 AGGAAAAGAAGGGTGAAAGGTTTAAC 59.902 38.462 0.00 0.00 0.00 2.01
2637 2673 4.187694 GTCTCAAGTGCAATAAGAGAGGG 58.812 47.826 16.50 0.00 36.15 4.30
2656 2692 5.426185 ACAAATATTTTCCCATGCATGGTCT 59.574 36.000 37.30 21.50 46.65 3.85
2848 2928 2.162681 CCCTTCTCAACATGGTGAACC 58.837 52.381 15.67 0.00 0.00 3.62
2869 2949 4.446051 GGTTCGCTTGAGCAACTAGATATC 59.554 45.833 0.00 0.00 42.21 1.63
2876 2956 0.179018 AAGGGTTCGCTTGAGCAACT 60.179 50.000 3.65 0.00 42.21 3.16
2899 2979 2.300723 AGCTGGTAAATACACACACCGA 59.699 45.455 0.00 0.00 33.55 4.69
2901 2981 3.007635 GGAGCTGGTAAATACACACACC 58.992 50.000 0.00 0.00 0.00 4.16
3376 3456 2.434359 CGAGCCAAACCCGAGGAC 60.434 66.667 0.00 0.00 0.00 3.85
3487 3567 1.278637 CGTTCCAAGCGACAACACC 59.721 57.895 0.00 0.00 0.00 4.16
3507 3587 4.755411 TCTGTTCGTACCCAGAAATCATC 58.245 43.478 2.90 0.00 34.88 2.92
3948 4028 0.107508 AAGCATCACGACCCTCCATG 60.108 55.000 0.00 0.00 0.00 3.66
3971 4051 4.040217 GTCCATAGATCCTCTTCATGCAGT 59.960 45.833 0.00 0.00 0.00 4.40
3972 4052 4.283978 AGTCCATAGATCCTCTTCATGCAG 59.716 45.833 0.00 0.00 0.00 4.41
4157 4237 2.840753 GCCACCTCCACCCCAAGAA 61.841 63.158 0.00 0.00 0.00 2.52
4197 4277 3.421394 TGGTAGGATGGATTCTCAGGT 57.579 47.619 0.00 0.00 0.00 4.00
4290 4370 8.420222 CCTATCTGCTTCTTCAATCTTCTCTTA 58.580 37.037 0.00 0.00 0.00 2.10
4522 4602 0.846015 AGCCCATATGCTACTGCCAA 59.154 50.000 0.00 0.00 40.56 4.52
4647 4727 3.879892 GCTTATCCCTGACAACAATCTCC 59.120 47.826 0.00 0.00 0.00 3.71
4704 4784 7.942341 AGAGTTTGTTACCAATATTCCAGACAA 59.058 33.333 0.00 0.00 0.00 3.18
4782 4865 8.628630 TGTGAATGTAGTTGTTCATTTCCATA 57.371 30.769 0.00 0.00 36.79 2.74
4783 4866 7.523293 TGTGAATGTAGTTGTTCATTTCCAT 57.477 32.000 0.00 0.00 36.79 3.41
4838 4921 9.884814 AGGTTATCTTCTAGTACTGGTGATAAT 57.115 33.333 24.24 15.27 30.87 1.28
4903 4986 7.301868 TGCAATATCAGGACTATGTATCACA 57.698 36.000 0.00 0.00 0.00 3.58
5007 5090 3.704566 TCAGAAATATGTAGGTCGCTGGT 59.295 43.478 0.00 0.00 0.00 4.00
5160 5243 6.206634 ACAGAATTATCGAAAGCAAAAGTCCA 59.793 34.615 0.00 0.00 0.00 4.02
5358 5446 0.867746 GCATGATAATTCTCCGCGCA 59.132 50.000 8.75 0.00 0.00 6.09
5387 5475 8.993121 CAAGGCTTCAAATGTAGTCGATTATAT 58.007 33.333 0.00 0.00 0.00 0.86
5410 5498 2.886523 TGTGGGCAATCTTCAGAACAAG 59.113 45.455 0.00 0.00 0.00 3.16
5489 5578 2.496470 CCTCTAGTCTTGGCCGTTTAGT 59.504 50.000 0.00 0.00 0.00 2.24
5509 5598 7.339466 AGTTTGGTACATGGAACTCAATAATCC 59.661 37.037 0.00 0.00 32.16 3.01
5545 5634 9.193806 AGTGTATTTTGCTCATTATTCCTCAAT 57.806 29.630 0.00 0.00 0.00 2.57
5581 5670 1.918293 TCACAAGGGCGGTCTCCAT 60.918 57.895 0.00 0.00 0.00 3.41
5589 5678 1.845809 GCTCACAAGTCACAAGGGCG 61.846 60.000 0.00 0.00 0.00 6.13
5610 5699 4.315803 AGGACAATGACAAAGTAAGTCCG 58.684 43.478 0.00 0.00 46.46 4.79
5639 5728 7.012421 GTGACAAGGAATCAAGGATAATGTACC 59.988 40.741 0.00 0.00 0.00 3.34
5663 5752 1.171308 AAGCTGGTAGCATGCAAGTG 58.829 50.000 21.98 6.90 45.56 3.16
5702 5791 2.517875 GGCTACCTGCTGGGCATG 60.518 66.667 14.82 2.27 42.39 4.06
5703 5792 3.813724 GGGCTACCTGCTGGGCAT 61.814 66.667 14.82 0.00 42.39 4.40


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

AutoCloner maintained by Alex Coulton.