Multiple sequence alignment - TraesCS2B01G368800

Loading Multiple Alignment...

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 TraesCS2B01G368800 chr2B 100.000 2436 0 0 1 2436 526398634 526396199 0.000000e+00 4499.0
1 TraesCS2B01G368800 chr2B 94.208 587 29 2 1848 2433 736247960 736248542 0.000000e+00 891.0
2 TraesCS2B01G368800 chr2B 80.683 937 167 11 44 973 706530447 706529518 0.000000e+00 715.0
3 TraesCS2B01G368800 chr2B 90.119 506 38 6 977 1475 526524921 526524421 0.000000e+00 647.0
4 TraesCS2B01G368800 chr2B 100.000 148 0 0 2671 2818 526395964 526395817 9.950000e-70 274.0
5 TraesCS2B01G368800 chr2B 93.243 148 10 0 2671 2818 736248626 736248773 4.730000e-53 219.0
6 TraesCS2B01G368800 chr2B 88.235 187 15 4 1634 1818 526524429 526524248 1.700000e-52 217.0
7 TraesCS2B01G368800 chr5A 97.848 976 21 0 1 976 2882462 2881487 0.000000e+00 1687.0
8 TraesCS2B01G368800 chr5A 85.000 160 17 6 1475 1634 40913693 40913845 3.760000e-34 156.0
9 TraesCS2B01G368800 chr5A 86.131 137 11 7 1474 1609 90609706 90609577 1.050000e-29 141.0
10 TraesCS2B01G368800 chr3B 95.102 980 45 1 1 977 217647496 217646517 0.000000e+00 1541.0
11 TraesCS2B01G368800 chr3B 88.741 977 88 3 1 974 50396383 50397340 0.000000e+00 1175.0
12 TraesCS2B01G368800 chr3B 92.055 579 41 3 1848 2425 676888717 676888143 0.000000e+00 809.0
13 TraesCS2B01G368800 chr3B 91.837 147 12 0 2671 2817 675407009 675406863 3.680000e-49 206.0
14 TraesCS2B01G368800 chr3B 90.604 149 13 1 2671 2818 676888059 676887911 2.210000e-46 196.0
15 TraesCS2B01G368800 chr3B 93.130 131 9 0 1503 1633 194277019 194277149 2.860000e-45 193.0
16 TraesCS2B01G368800 chr3B 93.220 118 8 0 1503 1620 194276901 194277018 1.040000e-39 174.0
17 TraesCS2B01G368800 chr3B 88.722 133 11 3 1503 1633 683440596 683440466 2.910000e-35 159.0
18 TraesCS2B01G368800 chr1D 88.934 976 106 2 1 974 432368648 432367673 0.000000e+00 1203.0
19 TraesCS2B01G368800 chr5D 88.012 976 114 3 1 974 449643170 449642196 0.000000e+00 1151.0
20 TraesCS2B01G368800 chr2D 86.912 978 98 13 1 975 616427489 616428439 0.000000e+00 1070.0
21 TraesCS2B01G368800 chr2D 91.824 477 32 3 977 1450 446640985 446640513 0.000000e+00 658.0
22 TraesCS2B01G368800 chr2D 89.444 180 12 4 1641 1818 446640514 446640340 1.310000e-53 220.0
23 TraesCS2B01G368800 chr2D 91.837 147 12 0 2671 2817 522623316 522623170 3.680000e-49 206.0
24 TraesCS2B01G368800 chr2D 91.156 147 13 0 2671 2817 29143027 29142881 1.710000e-47 200.0
25 TraesCS2B01G368800 chr1B 89.808 834 80 3 149 977 507926585 507927418 0.000000e+00 1064.0
26 TraesCS2B01G368800 chr1B 93.051 590 36 3 1848 2436 453320503 453321088 0.000000e+00 857.0
27 TraesCS2B01G368800 chr6D 83.878 980 150 6 1 974 423005764 423006741 0.000000e+00 928.0
28 TraesCS2B01G368800 chr6D 89.438 587 57 3 1848 2433 65708409 65708991 0.000000e+00 736.0
29 TraesCS2B01G368800 chr5B 91.681 589 43 4 1848 2435 665829653 665829070 0.000000e+00 811.0
30 TraesCS2B01G368800 chr7B 91.356 590 42 5 1848 2436 681598174 681597593 0.000000e+00 798.0
31 TraesCS2B01G368800 chr7B 93.182 132 9 0 1503 1634 566225386 566225517 7.970000e-46 195.0
32 TraesCS2B01G368800 chr4A 90.525 591 48 6 1848 2436 698913350 698913934 0.000000e+00 774.0
33 TraesCS2B01G368800 chr4B 90.000 590 51 6 1848 2436 72172390 72171808 0.000000e+00 756.0
34 TraesCS2B01G368800 chr4B 90.184 163 8 1 1471 1633 517558849 517558695 3.680000e-49 206.0
35 TraesCS2B01G368800 chr4B 91.156 147 13 0 2671 2817 63082871 63082725 1.710000e-47 200.0
36 TraesCS2B01G368800 chr4B 91.156 147 13 0 2671 2817 546680309 546680163 1.710000e-47 200.0
37 TraesCS2B01G368800 chr4B 89.441 161 9 1 1474 1634 316520824 316520672 2.210000e-46 196.0
38 TraesCS2B01G368800 chr4B 88.750 160 6 2 1473 1632 447102088 447102235 4.790000e-43 185.0
39 TraesCS2B01G368800 chr4B 90.441 136 12 1 1503 1637 663901502 663901367 8.020000e-41 178.0
40 TraesCS2B01G368800 chr6B 89.761 586 54 4 1852 2436 96041275 96040695 0.000000e+00 745.0
41 TraesCS2B01G368800 chr2A 90.855 503 36 5 977 1475 590690557 590690061 0.000000e+00 665.0
42 TraesCS2B01G368800 chr2A 90.060 503 40 5 977 1475 590720101 590719605 0.000000e+00 643.0
43 TraesCS2B01G368800 chr2A 88.363 507 45 7 977 1475 590726230 590725730 5.200000e-167 597.0
44 TraesCS2B01G368800 chr2A 90.761 184 10 4 1637 1818 590719610 590719432 3.630000e-59 239.0
45 TraesCS2B01G368800 chr2A 89.130 184 13 4 1637 1818 590725735 590725557 3.650000e-54 222.0
46 TraesCS2B01G368800 chr2A 90.833 120 6 2 1634 1753 590690069 590689955 3.760000e-34 156.0
47 TraesCS2B01G368800 chr7D 90.476 147 14 0 2671 2817 99929001 99928855 7.970000e-46 195.0
48 TraesCS2B01G368800 chr3D 90.476 147 14 0 2671 2817 61067990 61067844 7.970000e-46 195.0
49 TraesCS2B01G368800 chr6A 76.344 186 42 2 145 329 611906094 611906278 6.420000e-17 99.0
50 TraesCS2B01G368800 chr6A 78.571 140 30 0 145 284 125264391 125264530 2.990000e-15 93.5


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 TraesCS2B01G368800 chr2B 526395817 526398634 2817 True 2386.5 4499 100.0000 1 2818 2 chr2B.!!$R2 2817
1 TraesCS2B01G368800 chr2B 706529518 706530447 929 True 715.0 715 80.6830 44 973 1 chr2B.!!$R1 929
2 TraesCS2B01G368800 chr2B 736247960 736248773 813 False 555.0 891 93.7255 1848 2818 2 chr2B.!!$F1 970
3 TraesCS2B01G368800 chr2B 526524248 526524921 673 True 432.0 647 89.1770 977 1818 2 chr2B.!!$R3 841
4 TraesCS2B01G368800 chr5A 2881487 2882462 975 True 1687.0 1687 97.8480 1 976 1 chr5A.!!$R1 975
5 TraesCS2B01G368800 chr3B 217646517 217647496 979 True 1541.0 1541 95.1020 1 977 1 chr3B.!!$R1 976
6 TraesCS2B01G368800 chr3B 50396383 50397340 957 False 1175.0 1175 88.7410 1 974 1 chr3B.!!$F1 973
7 TraesCS2B01G368800 chr3B 676887911 676888717 806 True 502.5 809 91.3295 1848 2818 2 chr3B.!!$R4 970
8 TraesCS2B01G368800 chr1D 432367673 432368648 975 True 1203.0 1203 88.9340 1 974 1 chr1D.!!$R1 973
9 TraesCS2B01G368800 chr5D 449642196 449643170 974 True 1151.0 1151 88.0120 1 974 1 chr5D.!!$R1 973
10 TraesCS2B01G368800 chr2D 616427489 616428439 950 False 1070.0 1070 86.9120 1 975 1 chr2D.!!$F1 974
11 TraesCS2B01G368800 chr2D 446640340 446640985 645 True 439.0 658 90.6340 977 1818 2 chr2D.!!$R3 841
12 TraesCS2B01G368800 chr1B 507926585 507927418 833 False 1064.0 1064 89.8080 149 977 1 chr1B.!!$F2 828
13 TraesCS2B01G368800 chr1B 453320503 453321088 585 False 857.0 857 93.0510 1848 2436 1 chr1B.!!$F1 588
14 TraesCS2B01G368800 chr6D 423005764 423006741 977 False 928.0 928 83.8780 1 974 1 chr6D.!!$F2 973
15 TraesCS2B01G368800 chr6D 65708409 65708991 582 False 736.0 736 89.4380 1848 2433 1 chr6D.!!$F1 585
16 TraesCS2B01G368800 chr5B 665829070 665829653 583 True 811.0 811 91.6810 1848 2435 1 chr5B.!!$R1 587
17 TraesCS2B01G368800 chr7B 681597593 681598174 581 True 798.0 798 91.3560 1848 2436 1 chr7B.!!$R1 588
18 TraesCS2B01G368800 chr4A 698913350 698913934 584 False 774.0 774 90.5250 1848 2436 1 chr4A.!!$F1 588
19 TraesCS2B01G368800 chr4B 72171808 72172390 582 True 756.0 756 90.0000 1848 2436 1 chr4B.!!$R2 588
20 TraesCS2B01G368800 chr6B 96040695 96041275 580 True 745.0 745 89.7610 1852 2436 1 chr6B.!!$R1 584
21 TraesCS2B01G368800 chr2A 590719432 590720101 669 True 441.0 643 90.4105 977 1818 2 chr2A.!!$R2 841
22 TraesCS2B01G368800 chr2A 590689955 590690557 602 True 410.5 665 90.8440 977 1753 2 chr2A.!!$R1 776
23 TraesCS2B01G368800 chr2A 590725557 590726230 673 True 409.5 597 88.7465 977 1818 2 chr2A.!!$R3 841

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
913 918 1.608918 TTTGGCGCACCCCATGATT 60.609 52.632 10.83 0.0 34.21 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2107 0.035152 TTGGTGAGCGATGGAATGCT 60.035 50.0 0.0 0.0 45.9 3.79 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
234 236 1.801771 CACTTATGCGAAACCACGGAA 59.198 47.619 0.00 0.00 37.15 4.30
402 405 7.613801 ACACATCAGTTTATTGCCAGGTATTTA 59.386 33.333 0.00 0.00 0.00 1.40
446 450 2.180276 GAAGTTGGAGAGCTCTACCCA 58.820 52.381 23.55 20.52 0.00 4.51
456 460 1.613630 CTCTACCCACCAGCCCAGT 60.614 63.158 0.00 0.00 0.00 4.00
913 918 1.608918 TTTGGCGCACCCCATGATT 60.609 52.632 10.83 0.00 34.21 2.57
1027 1036 2.972713 TCCACCTCAAGTCAAGTAGCTT 59.027 45.455 0.00 0.00 0.00 3.74
1081 1094 2.016318 CGGCCACTTATCAAGCAATGA 58.984 47.619 2.24 0.00 43.67 2.57
1214 1227 2.203538 CTGCAGCCAGTGGGGTTT 60.204 61.111 12.15 0.00 44.14 3.27
1219 1232 2.203480 GCCAGTGGGGTTTCTGCA 60.203 61.111 12.15 0.00 39.65 4.41
1426 1443 8.678593 AATAGAATAAAGCTAAGTAAGTGGGC 57.321 34.615 0.00 0.00 0.00 5.36
1488 1507 2.179949 GGCTAACGAAATTGCTCTGC 57.820 50.000 0.00 0.00 0.00 4.26
1489 1508 1.468520 GGCTAACGAAATTGCTCTGCA 59.531 47.619 0.00 0.00 36.47 4.41
1490 1509 2.098117 GGCTAACGAAATTGCTCTGCAT 59.902 45.455 0.00 0.00 38.76 3.96
1491 1510 3.312421 GGCTAACGAAATTGCTCTGCATA 59.688 43.478 0.00 0.00 38.76 3.14
1492 1511 4.274865 GCTAACGAAATTGCTCTGCATAC 58.725 43.478 0.00 0.00 38.76 2.39
1493 1512 3.389687 AACGAAATTGCTCTGCATACG 57.610 42.857 0.00 0.00 38.76 3.06
1494 1513 2.616960 ACGAAATTGCTCTGCATACGA 58.383 42.857 0.00 0.00 38.76 3.43
1495 1514 3.198068 ACGAAATTGCTCTGCATACGAT 58.802 40.909 0.00 0.00 38.76 3.73
1496 1515 3.623060 ACGAAATTGCTCTGCATACGATT 59.377 39.130 0.00 0.00 38.76 3.34
1497 1516 4.094887 ACGAAATTGCTCTGCATACGATTT 59.905 37.500 8.09 8.09 38.76 2.17
1498 1517 5.030295 CGAAATTGCTCTGCATACGATTTT 58.970 37.500 9.22 0.00 38.76 1.82
1499 1518 5.512788 CGAAATTGCTCTGCATACGATTTTT 59.487 36.000 9.22 0.00 38.76 1.94
1500 1519 6.290748 CGAAATTGCTCTGCATACGATTTTTC 60.291 38.462 9.22 4.25 38.76 2.29
1501 1520 4.355543 TTGCTCTGCATACGATTTTTCC 57.644 40.909 0.00 0.00 38.76 3.13
1502 1521 3.342719 TGCTCTGCATACGATTTTTCCA 58.657 40.909 0.00 0.00 31.71 3.53
1503 1522 3.947196 TGCTCTGCATACGATTTTTCCAT 59.053 39.130 0.00 0.00 31.71 3.41
1504 1523 4.398988 TGCTCTGCATACGATTTTTCCATT 59.601 37.500 0.00 0.00 31.71 3.16
1505 1524 5.105797 TGCTCTGCATACGATTTTTCCATTT 60.106 36.000 0.00 0.00 31.71 2.32
1506 1525 5.807011 GCTCTGCATACGATTTTTCCATTTT 59.193 36.000 0.00 0.00 0.00 1.82
1507 1526 6.311200 GCTCTGCATACGATTTTTCCATTTTT 59.689 34.615 0.00 0.00 0.00 1.94
1508 1527 7.463251 GCTCTGCATACGATTTTTCCATTTTTC 60.463 37.037 0.00 0.00 0.00 2.29
1509 1528 6.811170 TCTGCATACGATTTTTCCATTTTTCC 59.189 34.615 0.00 0.00 0.00 3.13
1510 1529 6.459066 TGCATACGATTTTTCCATTTTTCCA 58.541 32.000 0.00 0.00 0.00 3.53
1511 1530 7.102346 TGCATACGATTTTTCCATTTTTCCAT 58.898 30.769 0.00 0.00 0.00 3.41
1512 1531 7.064371 TGCATACGATTTTTCCATTTTTCCATG 59.936 33.333 0.00 0.00 0.00 3.66
1513 1532 7.064490 GCATACGATTTTTCCATTTTTCCATGT 59.936 33.333 0.00 0.00 0.00 3.21
1514 1533 9.579768 CATACGATTTTTCCATTTTTCCATGTA 57.420 29.630 0.00 0.00 0.00 2.29
1515 1534 7.883229 ACGATTTTTCCATTTTTCCATGTAC 57.117 32.000 0.00 0.00 0.00 2.90
1516 1535 7.437748 ACGATTTTTCCATTTTTCCATGTACA 58.562 30.769 0.00 0.00 0.00 2.90
1517 1536 7.928706 ACGATTTTTCCATTTTTCCATGTACAA 59.071 29.630 0.00 0.00 0.00 2.41
1518 1537 8.934825 CGATTTTTCCATTTTTCCATGTACAAT 58.065 29.630 0.00 0.00 0.00 2.71
1522 1541 8.970859 TTTCCATTTTTCCATGTACAATTTGT 57.029 26.923 7.30 7.30 0.00 2.83
1523 1542 8.600449 TTCCATTTTTCCATGTACAATTTGTC 57.400 30.769 5.07 0.00 0.00 3.18
1524 1543 7.158021 TCCATTTTTCCATGTACAATTTGTCC 58.842 34.615 5.07 0.00 0.00 4.02
1525 1544 6.090628 CCATTTTTCCATGTACAATTTGTCCG 59.909 38.462 5.07 0.00 0.00 4.79
1526 1545 6.392625 TTTTTCCATGTACAATTTGTCCGA 57.607 33.333 5.07 0.00 0.00 4.55
1527 1546 5.365403 TTTCCATGTACAATTTGTCCGAC 57.635 39.130 5.07 0.00 0.00 4.79
1528 1547 3.340034 TCCATGTACAATTTGTCCGACC 58.660 45.455 5.07 0.00 0.00 4.79
1529 1548 3.078097 CCATGTACAATTTGTCCGACCA 58.922 45.455 5.07 0.00 0.00 4.02
1530 1549 3.504134 CCATGTACAATTTGTCCGACCAA 59.496 43.478 5.07 0.00 0.00 3.67
1531 1550 4.379394 CCATGTACAATTTGTCCGACCAAG 60.379 45.833 5.07 0.00 0.00 3.61
1532 1551 3.811083 TGTACAATTTGTCCGACCAAGT 58.189 40.909 5.07 0.00 0.00 3.16
1533 1552 3.562141 TGTACAATTTGTCCGACCAAGTG 59.438 43.478 5.07 10.32 0.00 3.16
1534 1553 2.925724 ACAATTTGTCCGACCAAGTGA 58.074 42.857 16.89 0.00 0.00 3.41
1535 1554 3.486383 ACAATTTGTCCGACCAAGTGAT 58.514 40.909 16.89 2.29 0.00 3.06
1536 1555 3.502211 ACAATTTGTCCGACCAAGTGATC 59.498 43.478 16.89 0.00 0.00 2.92
1537 1556 2.920724 TTTGTCCGACCAAGTGATCA 57.079 45.000 0.00 0.00 0.00 2.92
1538 1557 3.417069 TTTGTCCGACCAAGTGATCAT 57.583 42.857 0.00 0.00 0.00 2.45
1539 1558 4.545208 TTTGTCCGACCAAGTGATCATA 57.455 40.909 0.00 0.00 0.00 2.15
1540 1559 3.520290 TGTCCGACCAAGTGATCATAC 57.480 47.619 0.00 0.00 0.00 2.39
1541 1560 2.167693 TGTCCGACCAAGTGATCATACC 59.832 50.000 0.00 0.00 0.00 2.73
1542 1561 2.167693 GTCCGACCAAGTGATCATACCA 59.832 50.000 0.00 0.00 0.00 3.25
1543 1562 3.038280 TCCGACCAAGTGATCATACCAT 58.962 45.455 0.00 0.00 0.00 3.55
1544 1563 3.454447 TCCGACCAAGTGATCATACCATT 59.546 43.478 0.00 0.00 0.00 3.16
1545 1564 3.561310 CCGACCAAGTGATCATACCATTG 59.439 47.826 0.00 0.05 0.00 2.82
1546 1565 3.002656 CGACCAAGTGATCATACCATTGC 59.997 47.826 0.00 0.00 0.00 3.56
1547 1566 3.290710 ACCAAGTGATCATACCATTGCC 58.709 45.455 0.00 0.00 0.00 4.52
1548 1567 2.291465 CCAAGTGATCATACCATTGCCG 59.709 50.000 0.00 0.00 0.00 5.69
1549 1568 2.945008 CAAGTGATCATACCATTGCCGT 59.055 45.455 0.00 0.00 0.00 5.68
1550 1569 3.281727 AGTGATCATACCATTGCCGTT 57.718 42.857 0.00 0.00 0.00 4.44
1551 1570 2.945008 AGTGATCATACCATTGCCGTTG 59.055 45.455 0.00 0.00 0.00 4.10
1552 1571 2.682856 GTGATCATACCATTGCCGTTGT 59.317 45.455 0.00 0.00 0.00 3.32
1553 1572 3.128589 GTGATCATACCATTGCCGTTGTT 59.871 43.478 0.00 0.00 0.00 2.83
1554 1573 3.128415 TGATCATACCATTGCCGTTGTTG 59.872 43.478 0.00 0.00 0.00 3.33
1555 1574 1.201181 TCATACCATTGCCGTTGTTGC 59.799 47.619 0.00 0.00 0.00 4.17
1556 1575 1.067985 CATACCATTGCCGTTGTTGCA 60.068 47.619 0.00 0.00 36.84 4.08
1557 1576 1.252175 TACCATTGCCGTTGTTGCAT 58.748 45.000 0.00 0.00 38.76 3.96
1558 1577 1.252175 ACCATTGCCGTTGTTGCATA 58.748 45.000 0.00 0.00 38.76 3.14
1559 1578 1.202114 ACCATTGCCGTTGTTGCATAG 59.798 47.619 0.00 0.00 38.76 2.23
1560 1579 1.472082 CCATTGCCGTTGTTGCATAGA 59.528 47.619 0.00 0.00 38.76 1.98
1561 1580 2.099592 CCATTGCCGTTGTTGCATAGAT 59.900 45.455 0.00 0.00 38.76 1.98
1562 1581 3.429272 CCATTGCCGTTGTTGCATAGATT 60.429 43.478 0.00 0.00 38.76 2.40
1563 1582 3.932545 TTGCCGTTGTTGCATAGATTT 57.067 38.095 0.00 0.00 38.76 2.17
1564 1583 3.214697 TGCCGTTGTTGCATAGATTTG 57.785 42.857 0.00 0.00 32.85 2.32
1565 1584 2.816672 TGCCGTTGTTGCATAGATTTGA 59.183 40.909 0.00 0.00 32.85 2.69
1566 1585 3.443329 TGCCGTTGTTGCATAGATTTGAT 59.557 39.130 0.00 0.00 32.85 2.57
1567 1586 4.037690 GCCGTTGTTGCATAGATTTGATC 58.962 43.478 0.00 0.00 0.00 2.92
1568 1587 4.274069 CCGTTGTTGCATAGATTTGATCG 58.726 43.478 0.00 0.00 0.00 3.69
1569 1588 4.274069 CGTTGTTGCATAGATTTGATCGG 58.726 43.478 0.00 0.00 0.00 4.18
1570 1589 4.033932 CGTTGTTGCATAGATTTGATCGGA 59.966 41.667 0.00 0.00 0.00 4.55
1571 1590 5.505286 GTTGTTGCATAGATTTGATCGGAG 58.495 41.667 0.00 0.00 0.00 4.63
1572 1591 4.129380 TGTTGCATAGATTTGATCGGAGG 58.871 43.478 0.00 0.00 0.00 4.30
1573 1592 3.407424 TGCATAGATTTGATCGGAGGG 57.593 47.619 0.00 0.00 0.00 4.30
1574 1593 2.705658 TGCATAGATTTGATCGGAGGGT 59.294 45.455 0.00 0.00 0.00 4.34
1575 1594 3.070018 GCATAGATTTGATCGGAGGGTG 58.930 50.000 0.00 0.00 0.00 4.61
1576 1595 3.244215 GCATAGATTTGATCGGAGGGTGA 60.244 47.826 0.00 0.00 0.00 4.02
1577 1596 4.564406 GCATAGATTTGATCGGAGGGTGAT 60.564 45.833 0.00 0.00 0.00 3.06
1578 1597 5.555017 CATAGATTTGATCGGAGGGTGATT 58.445 41.667 0.00 0.00 0.00 2.57
1579 1598 3.813443 AGATTTGATCGGAGGGTGATTG 58.187 45.455 0.00 0.00 0.00 2.67
1580 1599 3.455910 AGATTTGATCGGAGGGTGATTGA 59.544 43.478 0.00 0.00 0.00 2.57
1581 1600 2.988010 TTGATCGGAGGGTGATTGAG 57.012 50.000 0.00 0.00 0.00 3.02
1582 1601 0.465705 TGATCGGAGGGTGATTGAGC 59.534 55.000 0.00 0.00 0.00 4.26
1583 1602 0.465705 GATCGGAGGGTGATTGAGCA 59.534 55.000 0.00 0.00 0.00 4.26
1584 1603 0.467384 ATCGGAGGGTGATTGAGCAG 59.533 55.000 0.00 0.00 0.00 4.24
1585 1604 0.904865 TCGGAGGGTGATTGAGCAGT 60.905 55.000 0.00 0.00 0.00 4.40
1586 1605 0.742281 CGGAGGGTGATTGAGCAGTG 60.742 60.000 0.00 0.00 0.00 3.66
1587 1606 0.326264 GGAGGGTGATTGAGCAGTGT 59.674 55.000 0.00 0.00 0.00 3.55
1588 1607 1.271597 GGAGGGTGATTGAGCAGTGTT 60.272 52.381 0.00 0.00 0.00 3.32
1589 1608 2.079925 GAGGGTGATTGAGCAGTGTTC 58.920 52.381 0.00 0.00 0.00 3.18
1590 1609 0.798776 GGGTGATTGAGCAGTGTTCG 59.201 55.000 2.32 0.00 0.00 3.95
1591 1610 1.512926 GGTGATTGAGCAGTGTTCGT 58.487 50.000 2.32 0.00 0.00 3.85
1592 1611 2.611971 GGGTGATTGAGCAGTGTTCGTA 60.612 50.000 2.32 0.00 0.00 3.43
1593 1612 2.412089 GGTGATTGAGCAGTGTTCGTAC 59.588 50.000 2.32 0.00 0.00 3.67
1594 1613 3.057019 GTGATTGAGCAGTGTTCGTACA 58.943 45.455 2.32 0.00 0.00 2.90
1595 1614 3.493129 GTGATTGAGCAGTGTTCGTACAA 59.507 43.478 0.00 0.00 35.69 2.41
1596 1615 3.493129 TGATTGAGCAGTGTTCGTACAAC 59.507 43.478 0.00 0.00 35.69 3.32
1597 1616 1.483316 TGAGCAGTGTTCGTACAACG 58.517 50.000 0.00 0.00 44.19 4.10
1598 1617 1.202325 TGAGCAGTGTTCGTACAACGT 60.202 47.619 0.00 0.00 43.14 3.99
1599 1618 1.450905 GAGCAGTGTTCGTACAACGTC 59.549 52.381 0.00 0.00 43.14 4.34
1600 1619 0.158096 GCAGTGTTCGTACAACGTCG 59.842 55.000 0.00 0.00 43.14 5.12
1601 1620 1.469917 CAGTGTTCGTACAACGTCGT 58.530 50.000 0.00 0.00 43.14 4.34
1602 1621 2.638673 CAGTGTTCGTACAACGTCGTA 58.361 47.619 0.00 0.00 43.14 3.43
1603 1622 3.228749 CAGTGTTCGTACAACGTCGTAT 58.771 45.455 0.00 0.00 43.14 3.06
1604 1623 4.393934 CAGTGTTCGTACAACGTCGTATA 58.606 43.478 0.00 0.00 43.14 1.47
1605 1624 4.845598 CAGTGTTCGTACAACGTCGTATAA 59.154 41.667 0.00 0.00 43.14 0.98
1606 1625 5.339348 CAGTGTTCGTACAACGTCGTATAAA 59.661 40.000 0.00 0.00 43.14 1.40
1607 1626 5.912396 AGTGTTCGTACAACGTCGTATAAAA 59.088 36.000 0.00 0.00 43.14 1.52
1608 1627 6.582295 AGTGTTCGTACAACGTCGTATAAAAT 59.418 34.615 0.00 0.00 43.14 1.82
1609 1628 7.114811 AGTGTTCGTACAACGTCGTATAAAATT 59.885 33.333 0.00 0.00 43.14 1.82
1610 1629 7.735586 GTGTTCGTACAACGTCGTATAAAATTT 59.264 33.333 0.00 0.00 43.14 1.82
1611 1630 7.735156 TGTTCGTACAACGTCGTATAAAATTTG 59.265 33.333 0.00 0.00 43.14 2.32
1612 1631 7.559835 TCGTACAACGTCGTATAAAATTTGA 57.440 32.000 0.00 0.00 43.14 2.69
1613 1632 8.172159 TCGTACAACGTCGTATAAAATTTGAT 57.828 30.769 0.00 0.00 43.14 2.57
1614 1633 9.283420 TCGTACAACGTCGTATAAAATTTGATA 57.717 29.630 0.00 0.00 43.14 2.15
1615 1634 9.546098 CGTACAACGTCGTATAAAATTTGATAG 57.454 33.333 0.00 0.00 36.74 2.08
1619 1638 9.546098 CAACGTCGTATAAAATTTGATAGTACG 57.454 33.333 19.17 19.17 35.94 3.67
1620 1639 7.767860 ACGTCGTATAAAATTTGATAGTACGC 58.232 34.615 20.02 9.63 34.96 4.42
1621 1640 7.096477 ACGTCGTATAAAATTTGATAGTACGCC 60.096 37.037 20.02 5.40 34.96 5.68
1622 1641 7.113965 CGTCGTATAAAATTTGATAGTACGCCT 59.886 37.037 13.05 0.00 34.96 5.52
1623 1642 9.398170 GTCGTATAAAATTTGATAGTACGCCTA 57.602 33.333 4.93 0.00 34.96 3.93
1624 1643 9.616634 TCGTATAAAATTTGATAGTACGCCTAG 57.383 33.333 4.93 0.00 34.96 3.02
1625 1644 8.371053 CGTATAAAATTTGATAGTACGCCTAGC 58.629 37.037 0.00 0.00 32.52 3.42
1626 1645 9.199982 GTATAAAATTTGATAGTACGCCTAGCA 57.800 33.333 0.00 0.00 40.20 3.49
1627 1646 5.986004 AAATTTGATAGTACGCCTAGCAC 57.014 39.130 0.64 0.00 41.57 4.40
1628 1647 4.939052 ATTTGATAGTACGCCTAGCACT 57.061 40.909 0.64 0.00 41.57 4.40
1629 1648 3.710326 TTGATAGTACGCCTAGCACTG 57.290 47.619 0.64 0.00 41.57 3.66
1630 1649 1.337071 TGATAGTACGCCTAGCACTGC 59.663 52.381 0.00 0.00 37.14 4.40
1631 1650 1.609555 GATAGTACGCCTAGCACTGCT 59.390 52.381 8.95 8.95 43.41 4.24
1632 1651 1.022735 TAGTACGCCTAGCACTGCTC 58.977 55.000 6.86 0.00 40.44 4.26
1692 1711 2.473816 CAGAGCAGTGTTGTCGAGAAA 58.526 47.619 0.00 0.00 0.00 2.52
1693 1712 2.866156 CAGAGCAGTGTTGTCGAGAAAA 59.134 45.455 0.00 0.00 0.00 2.29
1694 1713 3.309682 CAGAGCAGTGTTGTCGAGAAAAA 59.690 43.478 0.00 0.00 0.00 1.94
1695 1714 3.309954 AGAGCAGTGTTGTCGAGAAAAAC 59.690 43.478 0.00 0.00 0.00 2.43
1716 1735 2.418628 CGAAATAAGCCACGGACAACAT 59.581 45.455 0.00 0.00 0.00 2.71
1717 1736 3.619483 CGAAATAAGCCACGGACAACATA 59.381 43.478 0.00 0.00 0.00 2.29
1814 1835 2.965671 TACTACCGCCTAGCCTACAT 57.034 50.000 0.00 0.00 0.00 2.29
1818 1839 4.158015 ACTACCGCCTAGCCTACATAAAT 58.842 43.478 0.00 0.00 0.00 1.40
1819 1840 5.327732 ACTACCGCCTAGCCTACATAAATA 58.672 41.667 0.00 0.00 0.00 1.40
1820 1841 4.532314 ACCGCCTAGCCTACATAAATAC 57.468 45.455 0.00 0.00 0.00 1.89
1821 1842 3.260128 ACCGCCTAGCCTACATAAATACC 59.740 47.826 0.00 0.00 0.00 2.73
1822 1843 3.259876 CCGCCTAGCCTACATAAATACCA 59.740 47.826 0.00 0.00 0.00 3.25
1823 1844 4.262721 CCGCCTAGCCTACATAAATACCAA 60.263 45.833 0.00 0.00 0.00 3.67
1824 1845 4.929808 CGCCTAGCCTACATAAATACCAAG 59.070 45.833 0.00 0.00 0.00 3.61
1825 1846 5.510861 CGCCTAGCCTACATAAATACCAAGT 60.511 44.000 0.00 0.00 0.00 3.16
1826 1847 5.701290 GCCTAGCCTACATAAATACCAAGTG 59.299 44.000 0.00 0.00 0.00 3.16
1827 1848 6.231211 CCTAGCCTACATAAATACCAAGTGG 58.769 44.000 0.00 0.00 42.17 4.00
1828 1849 5.968676 AGCCTACATAAATACCAAGTGGA 57.031 39.130 3.83 0.00 38.94 4.02
1829 1850 6.321821 AGCCTACATAAATACCAAGTGGAA 57.678 37.500 3.83 0.00 38.94 3.53
1830 1851 6.357367 AGCCTACATAAATACCAAGTGGAAG 58.643 40.000 3.83 0.00 38.94 3.46
1831 1852 6.157994 AGCCTACATAAATACCAAGTGGAAGA 59.842 38.462 3.83 0.00 38.94 2.87
1832 1853 6.826741 GCCTACATAAATACCAAGTGGAAGAA 59.173 38.462 3.83 0.00 38.94 2.52
1833 1854 7.201705 GCCTACATAAATACCAAGTGGAAGAAC 60.202 40.741 3.83 0.00 38.94 3.01
1834 1855 7.282450 CCTACATAAATACCAAGTGGAAGAACC 59.718 40.741 3.83 0.00 38.94 3.62
1880 1901 3.617263 GTCCTTGGTGAGTATTACTTGCG 59.383 47.826 0.00 0.00 0.00 4.85
1887 1908 3.991773 GTGAGTATTACTTGCGTGTGGAA 59.008 43.478 0.00 0.00 0.00 3.53
2058 2079 2.550208 GGTGGTCGGAGAGTTGAACATT 60.550 50.000 0.00 0.00 36.95 2.71
2086 2107 0.109532 TCCGAACCAAGTGCATCCAA 59.890 50.000 0.00 0.00 0.00 3.53
2120 2141 0.455633 ACCAACTAACGCGCGTCTAG 60.456 55.000 37.77 33.78 0.00 2.43
2121 2142 1.624323 CAACTAACGCGCGTCTAGC 59.376 57.895 37.77 0.00 43.95 3.42
2122 2143 0.797249 CAACTAACGCGCGTCTAGCT 60.797 55.000 37.77 24.63 45.59 3.32
2123 2144 0.729116 AACTAACGCGCGTCTAGCTA 59.271 50.000 37.77 22.74 45.59 3.32
2220 2241 3.381949 GTGAGATATTGTACGGCCAGTC 58.618 50.000 2.24 0.00 0.00 3.51
2327 2349 0.539051 CGTTCTCATCAGCCCCTTCT 59.461 55.000 0.00 0.00 0.00 2.85
2365 2387 2.504175 TGGTCTTATGGTAACCTGAGCC 59.496 50.000 0.00 0.00 34.05 4.70
2732 2754 2.727123 TCTGACTGCCAAAAGAACCA 57.273 45.000 0.00 0.00 0.00 3.67
2757 2779 7.736447 AGATCTGAAGAAATCAAGTCGTTTT 57.264 32.000 0.00 0.00 37.67 2.43
2771 2794 2.097954 GTCGTTTTTGAACCCCTTTCGT 59.902 45.455 0.00 0.00 36.97 3.85
2777 2800 6.291902 CGTTTTTGAACCCCTTTCGTAATTTG 60.292 38.462 0.00 0.00 36.97 2.32
2801 2824 8.920509 TGAAAGAACGATAATAGAAACATCGA 57.079 30.769 9.89 0.00 43.20 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 236 2.552315 CAACCATTGTTTCGCACTAGGT 59.448 45.455 0.00 0.00 30.42 3.08
402 405 2.528564 GGCAGGAGCTCTAGATCATCT 58.471 52.381 14.64 0.00 41.70 2.90
411 414 0.902516 ACTTCTTCGGCAGGAGCTCT 60.903 55.000 14.64 0.00 41.70 4.09
446 450 0.779997 AATTCTTCCACTGGGCTGGT 59.220 50.000 0.00 0.00 32.50 4.00
456 460 1.651737 TGGGACGGAGAATTCTTCCA 58.348 50.000 21.06 15.16 31.01 3.53
913 918 2.932855 TGGTGTGGGATACAAAACGA 57.067 45.000 0.00 0.00 41.89 3.85
1027 1036 1.077140 TCCTGCTGTTGTGTGGCAA 60.077 52.632 0.00 0.00 35.49 4.52
1081 1094 3.799753 CGGCATCGCTAGCTTTGT 58.200 55.556 13.93 0.00 0.00 2.83
1103 1116 0.596600 GAGTGTCAGGAACGTCGCAA 60.597 55.000 0.00 0.00 0.00 4.85
1189 1202 2.191513 ACTGGCTGCAGCACAAGTG 61.192 57.895 37.63 22.17 44.36 3.16
1190 1203 2.191513 CACTGGCTGCAGCACAAGT 61.192 57.895 37.63 31.20 44.36 3.16
1192 1205 2.908428 CCACTGGCTGCAGCACAA 60.908 61.111 37.63 22.16 44.36 3.33
1219 1232 3.391382 GTAGTCTGGGCCCGTGCT 61.391 66.667 19.37 16.65 37.74 4.40
1335 1348 1.980052 CACCCACGTCACCTATGGT 59.020 57.895 0.00 0.00 35.62 3.55
1426 1443 3.719173 GCTACACTTAGCTCCCAGTAG 57.281 52.381 0.00 0.36 46.47 2.57
1466 1485 2.927477 CAGAGCAATTTCGTTAGCCGTA 59.073 45.455 0.00 0.00 37.94 4.02
1467 1486 1.732259 CAGAGCAATTTCGTTAGCCGT 59.268 47.619 0.00 0.00 37.94 5.68
1468 1487 1.529826 GCAGAGCAATTTCGTTAGCCG 60.530 52.381 0.00 0.00 38.13 5.52
1469 1488 1.468520 TGCAGAGCAATTTCGTTAGCC 59.531 47.619 0.00 0.00 34.76 3.93
1470 1489 2.900122 TGCAGAGCAATTTCGTTAGC 57.100 45.000 0.00 0.00 34.76 3.09
1471 1490 4.267690 TCGTATGCAGAGCAATTTCGTTAG 59.732 41.667 0.00 0.00 43.62 2.34
1472 1491 4.177783 TCGTATGCAGAGCAATTTCGTTA 58.822 39.130 0.00 0.00 43.62 3.18
1473 1492 3.000041 TCGTATGCAGAGCAATTTCGTT 59.000 40.909 0.00 0.00 43.62 3.85
1474 1493 2.616960 TCGTATGCAGAGCAATTTCGT 58.383 42.857 0.00 0.00 43.62 3.85
1475 1494 3.867055 ATCGTATGCAGAGCAATTTCG 57.133 42.857 0.00 0.00 43.62 3.46
1476 1495 6.020360 GGAAAAATCGTATGCAGAGCAATTTC 60.020 38.462 0.00 0.00 43.62 2.17
1477 1496 5.807011 GGAAAAATCGTATGCAGAGCAATTT 59.193 36.000 0.00 0.00 43.62 1.82
1478 1497 5.105797 TGGAAAAATCGTATGCAGAGCAATT 60.106 36.000 0.00 0.00 43.62 2.32
1479 1498 4.398988 TGGAAAAATCGTATGCAGAGCAAT 59.601 37.500 0.00 0.00 43.62 3.56
1480 1499 3.755905 TGGAAAAATCGTATGCAGAGCAA 59.244 39.130 0.00 0.00 43.62 3.91
1481 1500 3.342719 TGGAAAAATCGTATGCAGAGCA 58.657 40.909 0.00 0.00 44.86 4.26
1482 1501 4.558538 ATGGAAAAATCGTATGCAGAGC 57.441 40.909 0.00 0.00 0.00 4.09
1483 1502 7.009540 GGAAAAATGGAAAAATCGTATGCAGAG 59.990 37.037 0.00 0.00 0.00 3.35
1484 1503 6.811170 GGAAAAATGGAAAAATCGTATGCAGA 59.189 34.615 0.00 0.00 0.00 4.26
1485 1504 6.589523 TGGAAAAATGGAAAAATCGTATGCAG 59.410 34.615 0.00 0.00 0.00 4.41
1486 1505 6.459066 TGGAAAAATGGAAAAATCGTATGCA 58.541 32.000 0.00 0.00 0.00 3.96
1487 1506 6.959671 TGGAAAAATGGAAAAATCGTATGC 57.040 33.333 0.00 0.00 0.00 3.14
1488 1507 8.477984 ACATGGAAAAATGGAAAAATCGTATG 57.522 30.769 0.00 0.00 31.46 2.39
1489 1508 9.581099 GTACATGGAAAAATGGAAAAATCGTAT 57.419 29.630 0.00 0.00 31.46 3.06
1490 1509 8.577296 TGTACATGGAAAAATGGAAAAATCGTA 58.423 29.630 0.00 0.00 31.46 3.43
1491 1510 7.437748 TGTACATGGAAAAATGGAAAAATCGT 58.562 30.769 0.00 0.00 31.46 3.73
1492 1511 7.881643 TGTACATGGAAAAATGGAAAAATCG 57.118 32.000 0.00 0.00 31.46 3.34
1496 1515 9.401058 ACAAATTGTACATGGAAAAATGGAAAA 57.599 25.926 0.00 0.00 31.46 2.29
1497 1516 8.970859 ACAAATTGTACATGGAAAAATGGAAA 57.029 26.923 0.00 0.00 31.46 3.13
1498 1517 7.659390 GGACAAATTGTACATGGAAAAATGGAA 59.341 33.333 2.98 0.00 29.61 3.53
1499 1518 7.158021 GGACAAATTGTACATGGAAAAATGGA 58.842 34.615 2.98 0.00 29.61 3.41
1500 1519 6.090628 CGGACAAATTGTACATGGAAAAATGG 59.909 38.462 9.24 0.00 27.91 3.16
1501 1520 6.865726 TCGGACAAATTGTACATGGAAAAATG 59.134 34.615 9.24 0.00 27.91 2.32
1502 1521 6.866248 GTCGGACAAATTGTACATGGAAAAAT 59.134 34.615 9.24 0.00 27.91 1.82
1503 1522 6.210078 GTCGGACAAATTGTACATGGAAAAA 58.790 36.000 9.24 0.00 27.91 1.94
1504 1523 5.278561 GGTCGGACAAATTGTACATGGAAAA 60.279 40.000 9.24 0.00 27.91 2.29
1505 1524 4.216687 GGTCGGACAAATTGTACATGGAAA 59.783 41.667 9.24 0.00 27.91 3.13
1506 1525 3.754323 GGTCGGACAAATTGTACATGGAA 59.246 43.478 9.24 0.00 27.91 3.53
1507 1526 3.244596 TGGTCGGACAAATTGTACATGGA 60.245 43.478 9.24 0.00 27.91 3.41
1508 1527 3.078097 TGGTCGGACAAATTGTACATGG 58.922 45.455 9.24 0.00 27.91 3.66
1509 1528 4.215399 ACTTGGTCGGACAAATTGTACATG 59.785 41.667 9.24 0.00 27.91 3.21
1510 1529 4.215399 CACTTGGTCGGACAAATTGTACAT 59.785 41.667 9.24 0.00 27.91 2.29
1511 1530 3.562141 CACTTGGTCGGACAAATTGTACA 59.438 43.478 9.24 0.00 27.91 2.90
1512 1531 3.810941 TCACTTGGTCGGACAAATTGTAC 59.189 43.478 13.38 0.00 0.00 2.90
1513 1532 4.074627 TCACTTGGTCGGACAAATTGTA 57.925 40.909 13.38 1.33 0.00 2.41
1514 1533 2.925724 TCACTTGGTCGGACAAATTGT 58.074 42.857 13.38 0.00 0.00 2.71
1515 1534 3.501828 TGATCACTTGGTCGGACAAATTG 59.498 43.478 10.76 9.67 0.00 2.32
1516 1535 3.750371 TGATCACTTGGTCGGACAAATT 58.250 40.909 10.76 0.00 0.00 1.82
1517 1536 3.417069 TGATCACTTGGTCGGACAAAT 57.583 42.857 10.76 0.00 0.00 2.32
1518 1537 2.920724 TGATCACTTGGTCGGACAAA 57.079 45.000 10.76 3.91 0.00 2.83
1519 1538 3.369052 GGTATGATCACTTGGTCGGACAA 60.369 47.826 10.76 0.00 0.00 3.18
1520 1539 2.167693 GGTATGATCACTTGGTCGGACA 59.832 50.000 10.76 0.00 0.00 4.02
1521 1540 2.167693 TGGTATGATCACTTGGTCGGAC 59.832 50.000 0.00 0.00 0.00 4.79
1522 1541 2.462723 TGGTATGATCACTTGGTCGGA 58.537 47.619 0.00 0.00 0.00 4.55
1523 1542 2.979814 TGGTATGATCACTTGGTCGG 57.020 50.000 0.00 0.00 0.00 4.79
1524 1543 3.002656 GCAATGGTATGATCACTTGGTCG 59.997 47.826 0.00 0.00 0.00 4.79
1525 1544 3.316308 GGCAATGGTATGATCACTTGGTC 59.684 47.826 0.00 0.00 0.00 4.02
1526 1545 3.290710 GGCAATGGTATGATCACTTGGT 58.709 45.455 0.00 0.00 0.00 3.67
1527 1546 2.291465 CGGCAATGGTATGATCACTTGG 59.709 50.000 0.00 0.00 0.00 3.61
1528 1547 2.945008 ACGGCAATGGTATGATCACTTG 59.055 45.455 0.00 0.00 0.00 3.16
1529 1548 3.281727 ACGGCAATGGTATGATCACTT 57.718 42.857 0.00 0.00 0.00 3.16
1530 1549 2.945008 CAACGGCAATGGTATGATCACT 59.055 45.455 0.00 0.00 0.00 3.41
1531 1550 2.682856 ACAACGGCAATGGTATGATCAC 59.317 45.455 0.00 0.00 0.00 3.06
1532 1551 2.997980 ACAACGGCAATGGTATGATCA 58.002 42.857 0.00 0.00 0.00 2.92
1533 1552 3.694734 CAACAACGGCAATGGTATGATC 58.305 45.455 0.00 0.00 0.00 2.92
1534 1553 2.159254 GCAACAACGGCAATGGTATGAT 60.159 45.455 0.00 0.00 0.00 2.45
1535 1554 1.201181 GCAACAACGGCAATGGTATGA 59.799 47.619 0.00 0.00 0.00 2.15
1536 1555 1.067985 TGCAACAACGGCAATGGTATG 60.068 47.619 0.00 0.00 38.54 2.39
1537 1556 1.252175 TGCAACAACGGCAATGGTAT 58.748 45.000 0.00 0.00 38.54 2.73
1538 1557 1.252175 ATGCAACAACGGCAATGGTA 58.748 45.000 0.00 0.00 45.60 3.25
1539 1558 1.202114 CTATGCAACAACGGCAATGGT 59.798 47.619 0.00 0.00 45.60 3.55
1540 1559 1.472082 TCTATGCAACAACGGCAATGG 59.528 47.619 0.00 0.00 45.60 3.16
1541 1560 2.917701 TCTATGCAACAACGGCAATG 57.082 45.000 0.00 0.00 45.60 2.82
1542 1561 4.082300 TCAAATCTATGCAACAACGGCAAT 60.082 37.500 0.00 0.00 45.60 3.56
1543 1562 3.254411 TCAAATCTATGCAACAACGGCAA 59.746 39.130 0.00 0.00 45.60 4.52
1544 1563 2.816672 TCAAATCTATGCAACAACGGCA 59.183 40.909 0.00 0.00 46.66 5.69
1545 1564 3.485947 TCAAATCTATGCAACAACGGC 57.514 42.857 0.00 0.00 0.00 5.68
1546 1565 4.274069 CGATCAAATCTATGCAACAACGG 58.726 43.478 0.00 0.00 0.00 4.44
1547 1566 4.033932 TCCGATCAAATCTATGCAACAACG 59.966 41.667 0.00 0.00 0.00 4.10
1548 1567 5.484173 TCCGATCAAATCTATGCAACAAC 57.516 39.130 0.00 0.00 0.00 3.32
1549 1568 4.576053 CCTCCGATCAAATCTATGCAACAA 59.424 41.667 0.00 0.00 0.00 2.83
1550 1569 4.129380 CCTCCGATCAAATCTATGCAACA 58.871 43.478 0.00 0.00 0.00 3.33
1551 1570 3.499918 CCCTCCGATCAAATCTATGCAAC 59.500 47.826 0.00 0.00 0.00 4.17
1552 1571 3.136443 ACCCTCCGATCAAATCTATGCAA 59.864 43.478 0.00 0.00 0.00 4.08
1553 1572 2.705658 ACCCTCCGATCAAATCTATGCA 59.294 45.455 0.00 0.00 0.00 3.96
1554 1573 3.070018 CACCCTCCGATCAAATCTATGC 58.930 50.000 0.00 0.00 0.00 3.14
1555 1574 4.607293 TCACCCTCCGATCAAATCTATG 57.393 45.455 0.00 0.00 0.00 2.23
1556 1575 5.307976 TCAATCACCCTCCGATCAAATCTAT 59.692 40.000 0.00 0.00 0.00 1.98
1557 1576 4.653801 TCAATCACCCTCCGATCAAATCTA 59.346 41.667 0.00 0.00 0.00 1.98
1558 1577 3.455910 TCAATCACCCTCCGATCAAATCT 59.544 43.478 0.00 0.00 0.00 2.40
1559 1578 3.808728 TCAATCACCCTCCGATCAAATC 58.191 45.455 0.00 0.00 0.00 2.17
1560 1579 3.813443 CTCAATCACCCTCCGATCAAAT 58.187 45.455 0.00 0.00 0.00 2.32
1561 1580 2.680805 GCTCAATCACCCTCCGATCAAA 60.681 50.000 0.00 0.00 0.00 2.69
1562 1581 1.134401 GCTCAATCACCCTCCGATCAA 60.134 52.381 0.00 0.00 0.00 2.57
1563 1582 0.465705 GCTCAATCACCCTCCGATCA 59.534 55.000 0.00 0.00 0.00 2.92
1564 1583 0.465705 TGCTCAATCACCCTCCGATC 59.534 55.000 0.00 0.00 0.00 3.69
1565 1584 0.467384 CTGCTCAATCACCCTCCGAT 59.533 55.000 0.00 0.00 0.00 4.18
1566 1585 0.904865 ACTGCTCAATCACCCTCCGA 60.905 55.000 0.00 0.00 0.00 4.55
1567 1586 0.742281 CACTGCTCAATCACCCTCCG 60.742 60.000 0.00 0.00 0.00 4.63
1568 1587 0.326264 ACACTGCTCAATCACCCTCC 59.674 55.000 0.00 0.00 0.00 4.30
1569 1588 2.079925 GAACACTGCTCAATCACCCTC 58.920 52.381 0.00 0.00 0.00 4.30
1570 1589 1.609061 CGAACACTGCTCAATCACCCT 60.609 52.381 0.00 0.00 0.00 4.34
1571 1590 0.798776 CGAACACTGCTCAATCACCC 59.201 55.000 0.00 0.00 0.00 4.61
1572 1591 1.512926 ACGAACACTGCTCAATCACC 58.487 50.000 0.00 0.00 0.00 4.02
1573 1592 3.057019 TGTACGAACACTGCTCAATCAC 58.943 45.455 0.00 0.00 0.00 3.06
1574 1593 3.378911 TGTACGAACACTGCTCAATCA 57.621 42.857 0.00 0.00 0.00 2.57
1575 1594 3.421826 CGTTGTACGAACACTGCTCAATC 60.422 47.826 0.00 0.00 46.05 2.67
1576 1595 2.475111 CGTTGTACGAACACTGCTCAAT 59.525 45.455 0.00 0.00 46.05 2.57
1577 1596 1.855978 CGTTGTACGAACACTGCTCAA 59.144 47.619 0.00 0.00 46.05 3.02
1578 1597 1.202325 ACGTTGTACGAACACTGCTCA 60.202 47.619 6.19 0.00 46.05 4.26
1579 1598 1.450905 GACGTTGTACGAACACTGCTC 59.549 52.381 6.19 0.00 46.05 4.26
1580 1599 1.484356 GACGTTGTACGAACACTGCT 58.516 50.000 6.19 0.00 46.05 4.24
1581 1600 0.158096 CGACGTTGTACGAACACTGC 59.842 55.000 6.19 0.00 46.05 4.40
1582 1601 1.469917 ACGACGTTGTACGAACACTG 58.530 50.000 6.67 0.00 46.05 3.66
1583 1602 3.542712 ATACGACGTTGTACGAACACT 57.457 42.857 17.85 0.00 46.05 3.55
1584 1603 5.723319 TTTATACGACGTTGTACGAACAC 57.277 39.130 17.85 0.00 46.05 3.32
1585 1604 6.926280 ATTTTATACGACGTTGTACGAACA 57.074 33.333 17.85 8.84 46.05 3.18
1586 1605 7.944120 TCAAATTTTATACGACGTTGTACGAAC 59.056 33.333 17.85 0.00 46.05 3.95
1587 1606 8.001358 TCAAATTTTATACGACGTTGTACGAA 57.999 30.769 17.85 12.03 46.05 3.85
1588 1607 7.559835 TCAAATTTTATACGACGTTGTACGA 57.440 32.000 17.85 6.55 46.05 3.43
1593 1612 9.546098 CGTACTATCAAATTTTATACGACGTTG 57.454 33.333 5.50 0.00 36.85 4.10
1594 1613 8.261908 GCGTACTATCAAATTTTATACGACGTT 58.738 33.333 5.50 0.00 36.85 3.99
1595 1614 7.096477 GGCGTACTATCAAATTTTATACGACGT 60.096 37.037 5.52 5.52 36.85 4.34
1596 1615 7.113965 AGGCGTACTATCAAATTTTATACGACG 59.886 37.037 15.27 13.92 45.06 5.12
1597 1616 8.290663 AGGCGTACTATCAAATTTTATACGAC 57.709 34.615 15.27 13.45 41.71 4.34
1598 1617 9.616634 CTAGGCGTACTATCAAATTTTATACGA 57.383 33.333 15.27 0.66 36.85 3.43
1599 1618 8.371053 GCTAGGCGTACTATCAAATTTTATACG 58.629 37.037 10.07 10.07 37.56 3.06
1600 1619 9.199982 TGCTAGGCGTACTATCAAATTTTATAC 57.800 33.333 0.00 0.00 0.00 1.47
1601 1620 9.199982 GTGCTAGGCGTACTATCAAATTTTATA 57.800 33.333 0.00 0.00 30.25 0.98
1602 1621 7.931948 AGTGCTAGGCGTACTATCAAATTTTAT 59.068 33.333 0.00 0.00 36.76 1.40
1603 1622 7.223971 CAGTGCTAGGCGTACTATCAAATTTTA 59.776 37.037 0.00 0.00 36.35 1.52
1604 1623 6.037172 CAGTGCTAGGCGTACTATCAAATTTT 59.963 38.462 0.00 0.00 36.35 1.82
1605 1624 5.523916 CAGTGCTAGGCGTACTATCAAATTT 59.476 40.000 0.00 0.00 36.35 1.82
1606 1625 5.050490 CAGTGCTAGGCGTACTATCAAATT 58.950 41.667 0.00 0.00 36.35 1.82
1607 1626 4.621991 CAGTGCTAGGCGTACTATCAAAT 58.378 43.478 0.00 0.00 36.35 2.32
1608 1627 3.737047 GCAGTGCTAGGCGTACTATCAAA 60.737 47.826 8.18 0.00 36.35 2.69
1609 1628 2.223735 GCAGTGCTAGGCGTACTATCAA 60.224 50.000 8.18 0.00 36.35 2.57
1610 1629 1.337071 GCAGTGCTAGGCGTACTATCA 59.663 52.381 8.18 0.00 36.35 2.15
1611 1630 1.609555 AGCAGTGCTAGGCGTACTATC 59.390 52.381 18.11 0.00 36.35 2.08
1612 1631 1.609555 GAGCAGTGCTAGGCGTACTAT 59.390 52.381 19.77 0.00 39.88 2.12
1613 1632 1.022735 GAGCAGTGCTAGGCGTACTA 58.977 55.000 19.77 0.00 39.88 1.82
1614 1633 0.681564 AGAGCAGTGCTAGGCGTACT 60.682 55.000 19.77 5.98 39.88 2.73
1615 1634 1.022735 TAGAGCAGTGCTAGGCGTAC 58.977 55.000 19.77 3.33 39.88 3.67
1616 1635 1.022735 GTAGAGCAGTGCTAGGCGTA 58.977 55.000 19.77 2.15 39.88 4.42
1617 1636 1.810532 GTAGAGCAGTGCTAGGCGT 59.189 57.895 19.77 3.16 39.88 5.68
1618 1637 1.298713 CGTAGAGCAGTGCTAGGCG 60.299 63.158 19.77 17.69 39.88 5.52
1619 1638 1.066587 CCGTAGAGCAGTGCTAGGC 59.933 63.158 19.77 5.83 39.88 3.93
1620 1639 1.066587 GCCGTAGAGCAGTGCTAGG 59.933 63.158 19.77 19.01 39.88 3.02
1621 1640 1.309950 TAGCCGTAGAGCAGTGCTAG 58.690 55.000 19.77 9.83 39.88 3.42
1622 1641 1.758936 TTAGCCGTAGAGCAGTGCTA 58.241 50.000 19.77 0.00 39.88 3.49
1623 1642 1.115467 ATTAGCCGTAGAGCAGTGCT 58.885 50.000 19.86 19.86 43.88 4.40
1624 1643 2.395654 GTATTAGCCGTAGAGCAGTGC 58.604 52.381 7.13 7.13 34.23 4.40
1625 1644 2.033049 ACGTATTAGCCGTAGAGCAGTG 59.967 50.000 0.00 0.00 36.65 3.66
1626 1645 2.295885 ACGTATTAGCCGTAGAGCAGT 58.704 47.619 0.00 0.00 36.65 4.40
1627 1646 3.364764 GGTACGTATTAGCCGTAGAGCAG 60.365 52.174 0.00 0.00 41.04 4.24
1628 1647 2.549754 GGTACGTATTAGCCGTAGAGCA 59.450 50.000 0.00 0.00 41.04 4.26
1629 1648 3.194581 GGTACGTATTAGCCGTAGAGC 57.805 52.381 0.00 0.00 41.04 4.09
1692 1711 2.496111 TGTCCGTGGCTTATTTCGTTT 58.504 42.857 0.00 0.00 0.00 3.60
1693 1712 2.172851 TGTCCGTGGCTTATTTCGTT 57.827 45.000 0.00 0.00 0.00 3.85
1694 1713 1.802365 GTTGTCCGTGGCTTATTTCGT 59.198 47.619 0.00 0.00 0.00 3.85
1695 1714 1.801771 TGTTGTCCGTGGCTTATTTCG 59.198 47.619 0.00 0.00 0.00 3.46
1761 1782 9.253832 AGTGTAATTTATGATGGATCCAAAACA 57.746 29.630 20.67 18.73 0.00 2.83
1842 1863 9.308000 TCACCAAGGACAACTTAATCAAAATAT 57.692 29.630 0.00 0.00 37.29 1.28
1843 1864 8.698973 TCACCAAGGACAACTTAATCAAAATA 57.301 30.769 0.00 0.00 37.29 1.40
1844 1865 7.287696 ACTCACCAAGGACAACTTAATCAAAAT 59.712 33.333 0.00 0.00 37.29 1.82
1845 1866 6.605594 ACTCACCAAGGACAACTTAATCAAAA 59.394 34.615 0.00 0.00 37.29 2.44
1846 1867 6.126409 ACTCACCAAGGACAACTTAATCAAA 58.874 36.000 0.00 0.00 37.29 2.69
1887 1908 8.085296 TGCGTATCAAAAATTTTATGTGGTTCT 58.915 29.630 3.34 0.00 0.00 3.01
2058 2079 3.599343 CACTTGGTTCGGAGATTGATCA 58.401 45.455 0.00 0.00 35.04 2.92
2086 2107 0.035152 TTGGTGAGCGATGGAATGCT 60.035 50.000 0.00 0.00 45.90 3.79
2120 2141 8.225603 TGATTCCCTTGAATATTCAGTTTAGC 57.774 34.615 17.28 7.77 41.30 3.09
2123 2144 9.880157 CAAATGATTCCCTTGAATATTCAGTTT 57.120 29.630 17.28 6.99 41.30 2.66
2220 2241 0.964358 ACGTGGTTAGGGGAGACTCG 60.964 60.000 0.00 0.00 34.16 4.18
2327 2349 1.899814 ACCAACTGACTCGCCATTCTA 59.100 47.619 0.00 0.00 0.00 2.10
2685 2707 1.471119 AGAGGAAATACCGTCTCGCA 58.529 50.000 0.00 0.00 44.74 5.10
2732 2754 7.736447 AAACGACTTGATTTCTTCAGATCTT 57.264 32.000 0.00 0.00 35.27 2.40
2757 2779 6.321690 TCTTTCAAATTACGAAAGGGGTTCAA 59.678 34.615 21.35 6.18 46.11 2.69
2777 2800 8.804743 TGTCGATGTTTCTATTATCGTTCTTTC 58.195 33.333 0.00 0.00 42.96 2.62


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

AutoCloner maintained by Alex Coulton.