Multiple sequence alignment - TraesCS1D01G380400

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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 TraesCS1D01G380400 chr1D 100.000 3041 0 0 1 3041 455805509 455802469 0.000000e+00 5616.0
1 TraesCS1D01G380400 chr1D 83.010 206 18 8 519 711 455993233 455993032 1.450000e-38 171.0
2 TraesCS1D01G380400 chr1B 91.640 1591 71 29 1 1570 626252556 626251007 0.000000e+00 2145.0
3 TraesCS1D01G380400 chr1B 85.605 785 45 27 1689 2430 626250930 626250171 0.000000e+00 761.0
4 TraesCS1D01G380400 chr1B 82.051 273 16 20 522 781 626305931 626305679 5.140000e-48 202.0
5 TraesCS1D01G380400 chr1A 89.342 1201 69 31 434 1614 549524783 549523622 0.000000e+00 1454.0
6 TraesCS1D01G380400 chr1A 83.704 810 51 20 1691 2440 549523581 549522793 0.000000e+00 689.0
7 TraesCS1D01G380400 chr1A 88.494 478 31 16 2574 3041 549522738 549522275 9.520000e-155 556.0
8 TraesCS1D01G380400 chr1A 83.077 455 50 13 2 441 549525250 549524808 3.680000e-104 388.0
9 TraesCS1D01G380400 chr3B 86.709 316 32 5 86 397 139462387 139462696 2.900000e-90 342.0
10 TraesCS1D01G380400 chr3B 85.366 82 11 1 2 83 596046843 596046923 1.940000e-12 84.2
11 TraesCS1D01G380400 chr3D 85.759 316 35 5 86 397 90204501 90204810 2.920000e-85 326.0
12 TraesCS1D01G380400 chr3A 85.987 314 33 5 86 396 106543980 106544285 2.920000e-85 326.0
13 TraesCS1D01G380400 chr2B 87.952 83 8 1 1 83 470263987 470263907 2.500000e-16 97.1
14 TraesCS1D01G380400 chr5A 84.270 89 12 2 1 89 29686742 29686828 5.400000e-13 86.1
15 TraesCS1D01G380400 chr5A 81.707 82 14 1 2 83 309203001 309203081 1.960000e-07 67.6
16 TraesCS1D01G380400 chr6A 83.133 83 13 1 1 83 289776990 289777071 1.170000e-09 75.0
17 TraesCS1D01G380400 chr4B 83.333 84 11 3 1 83 102087563 102087644 1.170000e-09 75.0
18 TraesCS1D01G380400 chr5B 79.518 83 13 3 2 83 255580688 255580767 4.240000e-04 56.5


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 TraesCS1D01G380400 chr1D 455802469 455805509 3040 True 5616.00 5616 100.00000 1 3041 1 chr1D.!!$R1 3040
1 TraesCS1D01G380400 chr1B 626250171 626252556 2385 True 1453.00 2145 88.62250 1 2430 2 chr1B.!!$R2 2429
2 TraesCS1D01G380400 chr1A 549522275 549525250 2975 True 771.75 1454 86.15425 2 3041 4 chr1A.!!$R1 3039

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
971 1029 0.108424 GCGCTCACCAGATCAGAACT 60.108 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2836 3004 0.034896 AGTTTGTAGGCAGTCGGTGG 59.965 55.0 0.0 0.0 0.0 4.61 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
99 102 1.206371 GTATGAGTGGGTTACGCCTGT 59.794 52.381 0.00 0.00 37.43 4.00
104 107 0.322648 GTGGGTTACGCCTGTTAGGT 59.677 55.000 0.00 0.00 37.80 3.08
116 119 0.771127 TGTTAGGTTGGGCTGCTCTT 59.229 50.000 0.00 0.00 0.00 2.85
186 191 9.909043 AAACAATTTCACAAATAGTTTTTACGC 57.091 25.926 0.00 0.00 0.00 4.42
206 211 4.202151 ACGCAAGGAAAAGAAGCAGAAAAT 60.202 37.500 0.00 0.00 46.39 1.82
207 212 4.149396 CGCAAGGAAAAGAAGCAGAAAATG 59.851 41.667 0.00 0.00 0.00 2.32
258 263 1.584175 TTCCTACAAAAGCGCGTCAA 58.416 45.000 8.43 0.00 0.00 3.18
356 361 9.125026 CATATTTCAAAGCCTAAGACCATTACT 57.875 33.333 0.00 0.00 0.00 2.24
455 501 1.847798 TAGAGGGGCGGTGTTGCATT 61.848 55.000 0.00 0.00 36.28 3.56
485 531 2.364632 CCTGGTGAATTTGGCATCGTA 58.635 47.619 0.00 0.00 0.00 3.43
488 536 3.351740 TGGTGAATTTGGCATCGTACAT 58.648 40.909 0.00 0.00 0.00 2.29
506 554 2.056906 ATGCCGTGGATAAGCCTCCC 62.057 60.000 0.00 0.00 37.63 4.30
507 555 2.421739 CCGTGGATAAGCCTCCCG 59.578 66.667 0.00 0.00 37.63 5.14
512 560 2.070650 GGATAAGCCTCCCGGTGGT 61.071 63.158 11.67 0.00 0.00 4.16
513 561 1.632965 GGATAAGCCTCCCGGTGGTT 61.633 60.000 11.67 8.63 0.00 3.67
514 562 1.125633 GATAAGCCTCCCGGTGGTTA 58.874 55.000 11.67 10.33 0.00 2.85
515 563 1.487558 GATAAGCCTCCCGGTGGTTAA 59.512 52.381 11.67 0.00 0.00 2.01
672 721 0.729478 CACTCACAGACGCACGTAGG 60.729 60.000 0.00 0.00 0.00 3.18
674 723 0.179187 CTCACAGACGCACGTAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
730 779 7.790823 AAAAAGCATGCACAAATCTTTTACT 57.209 28.000 21.98 0.00 36.36 2.24
769 818 1.515020 CCGAGTCTTGGAGGCTCTG 59.485 63.158 15.23 5.48 44.49 3.35
934 992 4.563184 AGCGCTTATAAGTCGAGAAACTTG 59.437 41.667 24.07 0.00 39.74 3.16
967 1025 1.521010 CCAGCGCTCACCAGATCAG 60.521 63.158 7.13 0.00 0.00 2.90
968 1026 1.514553 CAGCGCTCACCAGATCAGA 59.485 57.895 7.13 0.00 0.00 3.27
971 1029 0.108424 GCGCTCACCAGATCAGAACT 60.108 55.000 0.00 0.00 0.00 3.01
972 1030 1.674221 GCGCTCACCAGATCAGAACTT 60.674 52.381 0.00 0.00 0.00 2.66
974 1032 2.353109 CGCTCACCAGATCAGAACTTCA 60.353 50.000 0.00 0.00 0.00 3.02
976 1034 3.056250 GCTCACCAGATCAGAACTTCAGA 60.056 47.826 0.00 0.00 0.00 3.27
980 1038 4.450419 CACCAGATCAGAACTTCAGAACAC 59.550 45.833 0.00 0.00 0.00 3.32
984 1042 3.194005 TCAGAACTTCAGAACACCACC 57.806 47.619 0.00 0.00 0.00 4.61
985 1043 2.503765 TCAGAACTTCAGAACACCACCA 59.496 45.455 0.00 0.00 0.00 4.17
991 1053 0.673985 TCAGAACACCACCACGAGAG 59.326 55.000 0.00 0.00 0.00 3.20
1147 1213 2.436824 GGAAAGGTGAGGCGCTCC 60.437 66.667 7.64 0.00 0.00 4.70
1217 1287 1.204704 TCACCTACTGACTGAATGCCG 59.795 52.381 0.00 0.00 0.00 5.69
1220 1290 1.066858 CCTACTGACTGAATGCCGTGT 60.067 52.381 0.00 0.00 0.00 4.49
1404 1474 1.213013 CTTCCTCTGGTCCGTCACG 59.787 63.158 0.00 0.00 0.00 4.35
1570 1640 2.169330 AGAAGTTCCTCTCGGTACCAC 58.831 52.381 13.54 0.00 31.44 4.16
1572 1642 1.546961 AGTTCCTCTCGGTACCACAG 58.453 55.000 13.54 7.13 31.44 3.66
1573 1643 1.203025 AGTTCCTCTCGGTACCACAGT 60.203 52.381 13.54 0.00 31.44 3.55
1574 1644 1.201880 GTTCCTCTCGGTACCACAGTC 59.798 57.143 13.54 0.00 0.00 3.51
1614 1688 2.338381 GCCCCATGCATCATCTGAC 58.662 57.895 0.00 0.00 40.77 3.51
1615 1689 0.466739 GCCCCATGCATCATCTGACA 60.467 55.000 0.00 0.00 40.77 3.58
1616 1690 1.605753 CCCCATGCATCATCTGACAG 58.394 55.000 0.00 0.00 0.00 3.51
1617 1691 1.133884 CCCCATGCATCATCTGACAGT 60.134 52.381 0.00 0.00 0.00 3.55
1618 1692 1.947456 CCCATGCATCATCTGACAGTG 59.053 52.381 0.00 0.78 0.00 3.66
1619 1693 1.333931 CCATGCATCATCTGACAGTGC 59.666 52.381 0.00 8.45 36.39 4.40
1620 1694 1.333931 CATGCATCATCTGACAGTGCC 59.666 52.381 11.89 0.00 35.03 5.01
1621 1695 0.393402 TGCATCATCTGACAGTGCCC 60.393 55.000 11.89 0.00 35.03 5.36
1622 1696 1.434622 GCATCATCTGACAGTGCCCG 61.435 60.000 1.59 0.00 0.00 6.13
1623 1697 0.812811 CATCATCTGACAGTGCCCGG 60.813 60.000 1.59 0.00 0.00 5.73
1630 1704 0.392461 TGACAGTGCCCGGCTATTTC 60.392 55.000 11.61 2.52 0.00 2.17
1632 1706 1.224592 CAGTGCCCGGCTATTTCCT 59.775 57.895 11.61 0.00 0.00 3.36
1635 1709 1.153249 TGCCCGGCTATTTCCTTCG 60.153 57.895 11.61 0.00 0.00 3.79
1637 1711 1.892391 CCCGGCTATTTCCTTCGGC 60.892 63.158 0.00 0.00 39.41 5.54
1643 1717 1.874231 GCTATTTCCTTCGGCTTAGCC 59.126 52.381 14.22 14.22 46.75 3.93
1656 1730 1.927895 CTTAGCCAAGTAGCTGACCG 58.072 55.000 0.00 0.00 44.67 4.79
1663 1737 2.366533 CAAGTAGCTGACCGTCTCCTA 58.633 52.381 0.00 0.00 0.00 2.94
1664 1738 2.952978 CAAGTAGCTGACCGTCTCCTAT 59.047 50.000 0.00 0.00 0.00 2.57
1665 1739 4.135306 CAAGTAGCTGACCGTCTCCTATA 58.865 47.826 0.00 0.00 0.00 1.31
1666 1740 4.644163 AGTAGCTGACCGTCTCCTATAT 57.356 45.455 0.00 0.00 0.00 0.86
1667 1741 4.328536 AGTAGCTGACCGTCTCCTATATG 58.671 47.826 0.00 0.00 0.00 1.78
1668 1742 2.520069 AGCTGACCGTCTCCTATATGG 58.480 52.381 0.00 0.00 37.10 2.74
1669 1743 1.067495 GCTGACCGTCTCCTATATGGC 60.067 57.143 0.00 0.00 35.26 4.40
1670 1744 2.520069 CTGACCGTCTCCTATATGGCT 58.480 52.381 0.00 0.00 35.26 4.75
1671 1745 3.687125 CTGACCGTCTCCTATATGGCTA 58.313 50.000 0.00 0.00 35.26 3.93
1672 1746 4.274147 CTGACCGTCTCCTATATGGCTAT 58.726 47.826 0.00 0.00 35.26 2.97
1673 1747 5.437946 CTGACCGTCTCCTATATGGCTATA 58.562 45.833 0.00 0.00 35.26 1.31
1674 1748 6.014771 TGACCGTCTCCTATATGGCTATAT 57.985 41.667 7.78 7.78 35.26 0.86
1675 1749 5.828328 TGACCGTCTCCTATATGGCTATATG 59.172 44.000 12.50 3.32 35.26 1.78
1676 1750 5.767670 ACCGTCTCCTATATGGCTATATGT 58.232 41.667 12.50 0.00 35.26 2.29
1677 1751 6.195700 ACCGTCTCCTATATGGCTATATGTT 58.804 40.000 12.50 0.00 35.26 2.71
1678 1752 6.321690 ACCGTCTCCTATATGGCTATATGTTC 59.678 42.308 12.50 0.00 35.26 3.18
1679 1753 6.547880 CCGTCTCCTATATGGCTATATGTTCT 59.452 42.308 12.50 0.00 35.26 3.01
1680 1754 7.068839 CCGTCTCCTATATGGCTATATGTTCTT 59.931 40.741 12.50 0.00 35.26 2.52
1681 1755 8.470805 CGTCTCCTATATGGCTATATGTTCTTT 58.529 37.037 12.50 0.00 35.26 2.52
1770 1847 2.824341 ACTCTGGTCTACGTTGGTAAGG 59.176 50.000 0.00 0.00 0.00 2.69
1781 1859 3.516300 ACGTTGGTAAGGATACATCACCA 59.484 43.478 0.00 0.00 37.50 4.17
1832 1918 4.338400 ACATGATGATCGACGAACTAAGGA 59.662 41.667 0.00 0.00 0.00 3.36
1836 1922 6.338146 TGATGATCGACGAACTAAGGATTTT 58.662 36.000 0.00 0.00 0.00 1.82
1875 1961 0.251341 GGGGTGCAGGATTCTTGTGT 60.251 55.000 0.00 0.00 0.00 3.72
2049 2139 2.027192 GCACTTCCACTAGGGTTCATCA 60.027 50.000 0.00 0.00 38.11 3.07
2052 2142 5.629133 GCACTTCCACTAGGGTTCATCAATA 60.629 44.000 0.00 0.00 38.11 1.90
2053 2143 6.595682 CACTTCCACTAGGGTTCATCAATAT 58.404 40.000 0.00 0.00 38.11 1.28
2056 2146 9.615660 ACTTCCACTAGGGTTCATCAATATATA 57.384 33.333 0.00 0.00 38.11 0.86
2092 2186 2.031870 CAGGAGGTCGTGATGGTGATA 58.968 52.381 0.00 0.00 33.92 2.15
2137 2234 1.347062 GGTTTCAGGGGAAATGGCAA 58.653 50.000 0.00 0.00 44.32 4.52
2187 2288 1.134640 AGTCGTGGCAAAGTGTGTGTA 60.135 47.619 0.00 0.00 0.00 2.90
2327 2474 2.885266 GTCCCCCTTCTCAAAGTGAAAC 59.115 50.000 0.00 0.00 0.00 2.78
2348 2495 0.528249 AAACGCAGTGCCAAGCAAAG 60.528 50.000 10.11 0.00 45.00 2.77
2382 2529 0.251564 AAATGGGAATGGACGCCACA 60.252 50.000 0.50 0.00 35.80 4.17
2383 2530 0.680921 AATGGGAATGGACGCCACAG 60.681 55.000 0.50 0.00 35.80 3.66
2415 2562 3.560302 CCATGTCATGGGCATAGGGCA 62.560 57.143 22.45 0.00 46.86 5.36
2424 2571 1.146041 GCATAGGGCACGATCACCA 59.854 57.895 0.00 0.00 43.97 4.17
2427 2574 0.465705 ATAGGGCACGATCACCACTG 59.534 55.000 0.00 0.00 0.00 3.66
2455 2602 4.496336 GCGCCATCCAGCCTTCCT 62.496 66.667 0.00 0.00 0.00 3.36
2456 2603 2.203126 CGCCATCCAGCCTTCCTC 60.203 66.667 0.00 0.00 0.00 3.71
2457 2604 2.739996 CGCCATCCAGCCTTCCTCT 61.740 63.158 0.00 0.00 0.00 3.69
2458 2605 1.148048 GCCATCCAGCCTTCCTCTC 59.852 63.158 0.00 0.00 0.00 3.20
2459 2606 1.835693 CCATCCAGCCTTCCTCTCC 59.164 63.158 0.00 0.00 0.00 3.71
2460 2607 1.445095 CATCCAGCCTTCCTCTCCG 59.555 63.158 0.00 0.00 0.00 4.63
2461 2608 1.045350 CATCCAGCCTTCCTCTCCGA 61.045 60.000 0.00 0.00 0.00 4.55
2462 2609 1.045911 ATCCAGCCTTCCTCTCCGAC 61.046 60.000 0.00 0.00 0.00 4.79
2463 2610 2.492090 CAGCCTTCCTCTCCGACG 59.508 66.667 0.00 0.00 0.00 5.12
2464 2611 2.756283 AGCCTTCCTCTCCGACGG 60.756 66.667 7.84 7.84 0.00 4.79
2465 2612 4.516195 GCCTTCCTCTCCGACGGC 62.516 72.222 9.66 0.00 39.66 5.68
2466 2613 3.839432 CCTTCCTCTCCGACGGCC 61.839 72.222 9.66 0.00 0.00 6.13
2467 2614 3.839432 CTTCCTCTCCGACGGCCC 61.839 72.222 9.66 0.00 0.00 5.80
2477 2624 4.041762 GACGGCCCCCATCCACAA 62.042 66.667 0.00 0.00 0.00 3.33
2478 2625 3.577334 GACGGCCCCCATCCACAAA 62.577 63.158 0.00 0.00 0.00 2.83
2479 2626 3.068064 CGGCCCCCATCCACAAAC 61.068 66.667 0.00 0.00 0.00 2.93
2480 2627 2.683572 GGCCCCCATCCACAAACC 60.684 66.667 0.00 0.00 0.00 3.27
2481 2628 2.119391 GCCCCCATCCACAAACCA 59.881 61.111 0.00 0.00 0.00 3.67
2482 2629 1.535202 GCCCCCATCCACAAACCAA 60.535 57.895 0.00 0.00 0.00 3.67
2483 2630 1.826340 GCCCCCATCCACAAACCAAC 61.826 60.000 0.00 0.00 0.00 3.77
2484 2631 0.470833 CCCCCATCCACAAACCAACA 60.471 55.000 0.00 0.00 0.00 3.33
2485 2632 1.643310 CCCCATCCACAAACCAACAT 58.357 50.000 0.00 0.00 0.00 2.71
2486 2633 1.550072 CCCCATCCACAAACCAACATC 59.450 52.381 0.00 0.00 0.00 3.06
2487 2634 1.202114 CCCATCCACAAACCAACATCG 59.798 52.381 0.00 0.00 0.00 3.84
2488 2635 1.402720 CCATCCACAAACCAACATCGC 60.403 52.381 0.00 0.00 0.00 4.58
2489 2636 1.269174 CATCCACAAACCAACATCGCA 59.731 47.619 0.00 0.00 0.00 5.10
2490 2637 1.614996 TCCACAAACCAACATCGCAT 58.385 45.000 0.00 0.00 0.00 4.73
2491 2638 2.784347 TCCACAAACCAACATCGCATA 58.216 42.857 0.00 0.00 0.00 3.14
2492 2639 3.351740 TCCACAAACCAACATCGCATAT 58.648 40.909 0.00 0.00 0.00 1.78
2493 2640 3.128415 TCCACAAACCAACATCGCATATG 59.872 43.478 0.00 0.00 0.00 1.78
2494 2641 3.119531 CCACAAACCAACATCGCATATGT 60.120 43.478 4.29 0.00 0.00 2.29
2495 2642 4.097714 CACAAACCAACATCGCATATGTC 58.902 43.478 4.29 0.00 0.00 3.06
2496 2643 3.755905 ACAAACCAACATCGCATATGTCA 59.244 39.130 4.29 0.00 0.00 3.58
2497 2644 4.142622 ACAAACCAACATCGCATATGTCAG 60.143 41.667 4.29 0.00 0.00 3.51
2498 2645 2.564771 ACCAACATCGCATATGTCAGG 58.435 47.619 4.29 14.25 34.95 3.86
2499 2646 1.265095 CCAACATCGCATATGTCAGGC 59.735 52.381 4.29 0.00 0.00 4.85
2500 2647 1.265095 CAACATCGCATATGTCAGGCC 59.735 52.381 4.29 0.00 0.00 5.19
2501 2648 0.761187 ACATCGCATATGTCAGGCCT 59.239 50.000 0.00 0.00 0.00 5.19
2502 2649 1.141657 ACATCGCATATGTCAGGCCTT 59.858 47.619 0.00 0.00 0.00 4.35
2503 2650 1.802960 CATCGCATATGTCAGGCCTTC 59.197 52.381 0.00 0.00 0.00 3.46
2504 2651 1.123077 TCGCATATGTCAGGCCTTCT 58.877 50.000 0.00 0.00 0.00 2.85
2505 2652 2.316108 TCGCATATGTCAGGCCTTCTA 58.684 47.619 0.00 0.00 0.00 2.10
2506 2653 2.035961 TCGCATATGTCAGGCCTTCTAC 59.964 50.000 0.00 1.99 0.00 2.59
2507 2654 2.224042 CGCATATGTCAGGCCTTCTACA 60.224 50.000 0.00 8.87 0.00 2.74
2508 2655 3.555795 CGCATATGTCAGGCCTTCTACAT 60.556 47.826 22.37 22.37 36.56 2.29
2509 2656 3.999663 GCATATGTCAGGCCTTCTACATC 59.000 47.826 22.39 9.90 34.54 3.06
2510 2657 2.898729 ATGTCAGGCCTTCTACATCG 57.101 50.000 16.10 0.00 0.00 3.84
2511 2658 0.824109 TGTCAGGCCTTCTACATCGG 59.176 55.000 0.00 0.00 0.00 4.18
2512 2659 0.530870 GTCAGGCCTTCTACATCGGC 60.531 60.000 0.00 0.00 43.03 5.54
2513 2660 1.592669 CAGGCCTTCTACATCGGCG 60.593 63.158 0.00 0.00 44.68 6.46
2514 2661 2.280186 GGCCTTCTACATCGGCGG 60.280 66.667 7.21 0.00 44.68 6.13
2515 2662 2.499685 GCCTTCTACATCGGCGGT 59.500 61.111 7.21 0.00 33.64 5.68
2516 2663 1.883084 GCCTTCTACATCGGCGGTG 60.883 63.158 20.23 20.23 33.64 4.94
2517 2664 1.883084 CCTTCTACATCGGCGGTGC 60.883 63.158 21.87 0.00 0.00 5.01
2518 2665 1.153647 CTTCTACATCGGCGGTGCA 60.154 57.895 21.87 6.45 0.00 4.57
2519 2666 0.530650 CTTCTACATCGGCGGTGCAT 60.531 55.000 21.87 3.96 0.00 3.96
2520 2667 0.529773 TTCTACATCGGCGGTGCATC 60.530 55.000 21.87 0.00 0.00 3.91
2521 2668 1.956170 CTACATCGGCGGTGCATCC 60.956 63.158 21.87 0.00 0.00 3.51
2574 2721 1.302511 ACCATTGCGACCGAGCTTT 60.303 52.632 0.00 0.00 38.13 3.51
2575 2722 1.298859 ACCATTGCGACCGAGCTTTC 61.299 55.000 0.00 0.00 38.13 2.62
2576 2723 1.298157 CCATTGCGACCGAGCTTTCA 61.298 55.000 0.00 0.00 38.13 2.69
2577 2724 0.516877 CATTGCGACCGAGCTTTCAA 59.483 50.000 0.00 0.00 38.13 2.69
2578 2725 0.798776 ATTGCGACCGAGCTTTCAAG 59.201 50.000 0.00 0.00 38.13 3.02
2579 2726 0.249699 TTGCGACCGAGCTTTCAAGA 60.250 50.000 0.00 0.00 38.13 3.02
2580 2727 0.667487 TGCGACCGAGCTTTCAAGAG 60.667 55.000 0.00 0.00 38.13 2.85
2613 2780 7.880195 ACAACTAATTTCTCTCAAGTAGCACAT 59.120 33.333 0.00 0.00 29.15 3.21
2615 2782 9.593134 AACTAATTTCTCTCAAGTAGCACATAG 57.407 33.333 0.00 0.00 29.15 2.23
2712 2879 4.283212 CCCATGGTACTTGTGGAATTTTGT 59.717 41.667 11.73 0.00 34.94 2.83
2766 2933 0.259938 ATGGATCAAGGACAAGCCCC 59.740 55.000 0.00 0.00 37.37 5.80
2768 2935 0.332972 GGATCAAGGACAAGCCCCTT 59.667 55.000 0.00 0.00 44.36 3.95
2769 2936 1.683319 GGATCAAGGACAAGCCCCTTC 60.683 57.143 0.00 0.00 41.79 3.46
2770 2937 0.035056 ATCAAGGACAAGCCCCTTCG 60.035 55.000 0.00 0.00 41.79 3.79
2771 2938 1.125093 TCAAGGACAAGCCCCTTCGA 61.125 55.000 0.00 0.00 41.79 3.71
2772 2939 0.035056 CAAGGACAAGCCCCTTCGAT 60.035 55.000 0.00 0.00 41.79 3.59
2774 2941 1.153147 GGACAAGCCCCTTCGATCC 60.153 63.158 0.00 0.00 0.00 3.36
2775 2942 1.602237 GACAAGCCCCTTCGATCCA 59.398 57.895 0.00 0.00 0.00 3.41
2803 2971 2.452105 GCTAACACTCGACGGAATCTC 58.548 52.381 0.00 0.00 0.00 2.75
2823 2991 3.745803 GCTTGCAGCAGAGCACCC 61.746 66.667 18.96 0.00 45.61 4.61
2825 2993 1.900016 CTTGCAGCAGAGCACCCAA 60.900 57.895 0.00 0.00 45.61 4.12
2827 2995 1.737355 TTGCAGCAGAGCACCCAAAC 61.737 55.000 0.00 0.00 45.61 2.93
2834 3002 1.682854 CAGAGCACCCAAACACACAAT 59.317 47.619 0.00 0.00 0.00 2.71
2835 3003 1.956477 AGAGCACCCAAACACACAATC 59.044 47.619 0.00 0.00 0.00 2.67
2836 3004 1.000274 GAGCACCCAAACACACAATCC 60.000 52.381 0.00 0.00 0.00 3.01
2837 3005 0.033366 GCACCCAAACACACAATCCC 59.967 55.000 0.00 0.00 0.00 3.85
2838 3006 1.407936 CACCCAAACACACAATCCCA 58.592 50.000 0.00 0.00 0.00 4.37
2839 3007 1.068434 CACCCAAACACACAATCCCAC 59.932 52.381 0.00 0.00 0.00 4.61
2840 3008 0.678950 CCCAAACACACAATCCCACC 59.321 55.000 0.00 0.00 0.00 4.61
2841 3009 0.313672 CCAAACACACAATCCCACCG 59.686 55.000 0.00 0.00 0.00 4.94
2842 3010 1.313772 CAAACACACAATCCCACCGA 58.686 50.000 0.00 0.00 0.00 4.69
2843 3011 1.001815 CAAACACACAATCCCACCGAC 60.002 52.381 0.00 0.00 0.00 4.79
2844 3012 0.472471 AACACACAATCCCACCGACT 59.528 50.000 0.00 0.00 0.00 4.18
2878 3046 8.632906 ACTCAAATTCAGAATTCTCATTCACT 57.367 30.769 4.57 0.00 41.37 3.41
2886 3054 7.642669 TCAGAATTCTCATTCACTTTCACAAC 58.357 34.615 4.57 0.00 41.37 3.32
2890 3058 5.657470 TCTCATTCACTTTCACAACGAAG 57.343 39.130 0.00 0.00 34.32 3.79
2913 3081 8.887264 AAGATGTGGGGATACTTATACTAGAG 57.113 38.462 0.00 0.00 0.00 2.43
2915 3083 5.331069 TGTGGGGATACTTATACTAGAGGC 58.669 45.833 0.00 0.00 0.00 4.70
2916 3084 5.162914 TGTGGGGATACTTATACTAGAGGCA 60.163 44.000 0.00 0.00 0.00 4.75
2931 3106 3.281332 GGCACATAGGCTTGGGAAA 57.719 52.632 0.00 0.00 40.24 3.13
2933 3108 1.204704 GGCACATAGGCTTGGGAAAAC 59.795 52.381 0.00 0.00 40.24 2.43
2934 3109 2.171003 GCACATAGGCTTGGGAAAACT 58.829 47.619 0.00 0.00 0.00 2.66
2935 3110 2.094545 GCACATAGGCTTGGGAAAACTG 60.095 50.000 0.00 0.00 0.00 3.16
2958 3133 7.737972 TGAAAAACAGAGGATTAATTCGTGA 57.262 32.000 6.23 0.00 0.00 4.35
2972 3147 2.595124 TCGTGAGAAACAAGCTGTGA 57.405 45.000 0.00 0.00 37.03 3.58
2996 3171 3.461843 GCAAACTTGCGGAGTCTTG 57.538 52.632 0.00 3.00 45.11 3.02
3001 3176 1.302033 CTTGCGGAGTCTTGGCAGT 60.302 57.895 4.70 0.00 38.04 4.40
3004 3179 0.037326 TGCGGAGTCTTGGCAGTAAG 60.037 55.000 0.00 0.00 32.07 2.34
3008 3183 3.251571 CGGAGTCTTGGCAGTAAGTAAC 58.748 50.000 0.00 0.00 0.00 2.50
3012 3187 5.279556 GGAGTCTTGGCAGTAAGTAACTCTT 60.280 44.000 12.14 0.00 35.76 2.85
3015 3190 3.695830 TGGCAGTAAGTAACTCTTGGG 57.304 47.619 0.00 0.00 35.76 4.12
3023 3198 1.674322 TAACTCTTGGGCCGCTTGC 60.674 57.895 0.00 0.00 40.16 4.01
3025 3200 2.753043 CTCTTGGGCCGCTTGCAT 60.753 61.111 0.00 0.00 43.89 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.317391 TCAAAAATACTTTGGCCCTTGTTTTG 59.683 34.615 0.00 8.30 35.68 2.44
74 75 2.416431 GCGTAACCCACTCATACGTCTT 60.416 50.000 0.00 0.00 43.12 3.01
99 102 1.705186 AGAAAGAGCAGCCCAACCTAA 59.295 47.619 0.00 0.00 0.00 2.69
104 107 0.767375 AGACAGAAAGAGCAGCCCAA 59.233 50.000 0.00 0.00 0.00 4.12
170 175 8.192110 TCTTTTCCTTGCGTAAAAACTATTTGT 58.808 29.630 0.00 0.00 0.00 2.83
185 190 5.052481 ACATTTTCTGCTTCTTTTCCTTGC 58.948 37.500 0.00 0.00 0.00 4.01
186 191 6.865205 CCTACATTTTCTGCTTCTTTTCCTTG 59.135 38.462 0.00 0.00 0.00 3.61
206 211 9.581289 TCTTTCATCTCAAATTAAAACCCTACA 57.419 29.630 0.00 0.00 0.00 2.74
250 255 0.384974 TTCCATTTCGTTTGACGCGC 60.385 50.000 5.73 0.00 42.21 6.86
251 256 1.314581 GTTCCATTTCGTTTGACGCG 58.685 50.000 3.53 3.53 42.21 6.01
258 263 4.380867 GCCTTCATCATGTTCCATTTCGTT 60.381 41.667 0.00 0.00 0.00 3.85
280 285 2.548480 ACTTAGTTTTCTGCACCTTCGC 59.452 45.455 0.00 0.00 0.00 4.70
321 326 5.793817 AGGCTTTGAAATATGTTTCCAACC 58.206 37.500 11.86 10.65 42.44 3.77
322 327 8.303876 TCTTAGGCTTTGAAATATGTTTCCAAC 58.696 33.333 11.86 3.65 42.44 3.77
324 329 7.093945 GGTCTTAGGCTTTGAAATATGTTTCCA 60.094 37.037 11.86 0.00 42.44 3.53
418 431 5.598830 CCCTCTACCTGATAACTAGCTGAAA 59.401 44.000 0.00 0.00 0.00 2.69
455 501 6.112058 GCCAAATTCACCAGGCATTAAAATA 58.888 36.000 0.00 0.00 46.26 1.40
485 531 0.179045 GAGGCTTATCCACGGCATGT 60.179 55.000 0.00 0.00 37.29 3.21
488 536 2.742116 GGGAGGCTTATCCACGGCA 61.742 63.158 0.00 0.00 41.52 5.69
506 554 8.259049 TGTTCTTCAGTTATAATTAACCACCG 57.741 34.615 0.00 0.00 38.81 4.94
609 657 0.534203 TTGCTTGGACGAAGGGTGTC 60.534 55.000 0.00 0.00 35.60 3.67
612 660 0.182775 ACTTTGCTTGGACGAAGGGT 59.817 50.000 0.00 0.00 35.65 4.34
616 664 4.320202 GCATTTCTACTTTGCTTGGACGAA 60.320 41.667 0.00 0.00 33.61 3.85
660 709 2.273179 TTGGCTCCTACGTGCGTCT 61.273 57.895 0.00 0.00 0.00 4.18
672 721 1.689959 CGTTTGCATCTTGTTGGCTC 58.310 50.000 0.00 0.00 0.00 4.70
674 723 2.144362 GCGTTTGCATCTTGTTGGC 58.856 52.632 0.00 0.00 42.15 4.52
730 779 1.123861 AGCCAGCCAACTCTCTCACA 61.124 55.000 0.00 0.00 0.00 3.58
807 856 1.604593 GGGCAAGAGGCTTGCTTCA 60.605 57.895 25.62 0.00 44.36 3.02
843 901 1.823899 GGATAGCTTTGTGCCGGGG 60.824 63.158 2.18 0.00 44.23 5.73
906 964 3.106672 CTCGACTTATAAGCGCTTCGTT 58.893 45.455 28.82 15.25 0.00 3.85
934 992 2.282391 TGGGCATGCAGGTCACAC 60.282 61.111 21.36 0.00 0.00 3.82
961 1019 4.503991 GGTGGTGTTCTGAAGTTCTGATCT 60.504 45.833 12.62 0.00 0.00 2.75
967 1025 1.597663 CGTGGTGGTGTTCTGAAGTTC 59.402 52.381 0.00 0.00 0.00 3.01
968 1026 1.208535 TCGTGGTGGTGTTCTGAAGTT 59.791 47.619 0.00 0.00 0.00 2.66
971 1029 1.068588 CTCTCGTGGTGGTGTTCTGAA 59.931 52.381 0.00 0.00 0.00 3.02
972 1030 0.673985 CTCTCGTGGTGGTGTTCTGA 59.326 55.000 0.00 0.00 0.00 3.27
974 1032 1.367840 GCTCTCGTGGTGGTGTTCT 59.632 57.895 0.00 0.00 0.00 3.01
976 1034 2.029073 CGCTCTCGTGGTGGTGTT 59.971 61.111 0.00 0.00 0.00 3.32
984 1042 4.862092 ATCGCTGCCGCTCTCGTG 62.862 66.667 0.00 0.00 0.00 4.35
985 1043 4.862092 CATCGCTGCCGCTCTCGT 62.862 66.667 0.00 0.00 0.00 4.18
1168 1235 1.216710 GGTGCGGTTCTCAGAGGAG 59.783 63.158 0.00 0.00 42.80 3.69
1169 1236 2.636412 CGGTGCGGTTCTCAGAGGA 61.636 63.158 0.00 0.00 0.00 3.71
1217 1287 2.213499 CCAACAGTTCAGAGACCACAC 58.787 52.381 0.00 0.00 0.00 3.82
1220 1290 0.836606 TGCCAACAGTTCAGAGACCA 59.163 50.000 0.00 0.00 0.00 4.02
1374 1444 1.122227 AGAGGAAGAGCAGGAGCATC 58.878 55.000 0.00 0.00 45.49 3.91
1515 1585 1.589196 GGCGATGTCGTAGAGCACC 60.589 63.158 4.20 0.00 42.22 5.01
1570 1640 2.810852 GCAAACAAGGGAGAAGAGACTG 59.189 50.000 0.00 0.00 0.00 3.51
1572 1642 2.550180 GTGCAAACAAGGGAGAAGAGAC 59.450 50.000 0.00 0.00 0.00 3.36
1573 1643 2.806745 CGTGCAAACAAGGGAGAAGAGA 60.807 50.000 0.00 0.00 0.00 3.10
1574 1644 1.532868 CGTGCAAACAAGGGAGAAGAG 59.467 52.381 0.00 0.00 0.00 2.85
1614 1688 0.394352 AAGGAAATAGCCGGGCACTG 60.394 55.000 23.09 0.00 0.00 3.66
1615 1689 0.107165 GAAGGAAATAGCCGGGCACT 60.107 55.000 23.09 3.52 0.00 4.40
1616 1690 1.436983 CGAAGGAAATAGCCGGGCAC 61.437 60.000 23.09 6.70 0.00 5.01
1617 1691 1.153249 CGAAGGAAATAGCCGGGCA 60.153 57.895 23.09 7.74 0.00 5.36
1618 1692 3.732470 CGAAGGAAATAGCCGGGC 58.268 61.111 12.11 12.11 0.00 6.13
1637 1711 1.204941 ACGGTCAGCTACTTGGCTAAG 59.795 52.381 8.47 8.47 41.00 2.18
1643 1717 1.178276 AGGAGACGGTCAGCTACTTG 58.822 55.000 11.27 0.00 0.00 3.16
1646 1720 3.440872 CCATATAGGAGACGGTCAGCTAC 59.559 52.174 11.27 0.00 41.22 3.58
1649 1723 1.067495 GCCATATAGGAGACGGTCAGC 60.067 57.143 11.27 1.69 41.22 4.26
1652 1726 5.828859 ACATATAGCCATATAGGAGACGGTC 59.171 44.000 0.00 0.00 41.22 4.79
1654 1728 6.547880 AGAACATATAGCCATATAGGAGACGG 59.452 42.308 0.00 0.00 41.22 4.79
1663 1737 7.988937 TGGAGGAAAAGAACATATAGCCATAT 58.011 34.615 0.00 0.00 0.00 1.78
1664 1738 7.387265 TGGAGGAAAAGAACATATAGCCATA 57.613 36.000 0.00 0.00 0.00 2.74
1665 1739 6.266131 TGGAGGAAAAGAACATATAGCCAT 57.734 37.500 0.00 0.00 0.00 4.40
1666 1740 5.708736 TGGAGGAAAAGAACATATAGCCA 57.291 39.130 0.00 0.00 0.00 4.75
1667 1741 5.048434 GCATGGAGGAAAAGAACATATAGCC 60.048 44.000 0.00 0.00 0.00 3.93
1668 1742 5.532406 TGCATGGAGGAAAAGAACATATAGC 59.468 40.000 0.00 0.00 0.00 2.97
1669 1743 7.255381 CCTTGCATGGAGGAAAAGAACATATAG 60.255 40.741 13.33 0.00 36.33 1.31
1670 1744 6.547141 CCTTGCATGGAGGAAAAGAACATATA 59.453 38.462 13.33 0.00 36.33 0.86
1671 1745 5.361857 CCTTGCATGGAGGAAAAGAACATAT 59.638 40.000 13.33 0.00 36.33 1.78
1672 1746 4.706476 CCTTGCATGGAGGAAAAGAACATA 59.294 41.667 13.33 0.00 36.33 2.29
1673 1747 3.512724 CCTTGCATGGAGGAAAAGAACAT 59.487 43.478 13.33 0.00 36.33 2.71
1674 1748 2.892852 CCTTGCATGGAGGAAAAGAACA 59.107 45.455 13.33 0.00 36.33 3.18
1675 1749 2.893489 ACCTTGCATGGAGGAAAAGAAC 59.107 45.455 24.48 0.00 37.72 3.01
1676 1750 2.892852 CACCTTGCATGGAGGAAAAGAA 59.107 45.455 24.48 0.00 37.72 2.52
1677 1751 2.108075 TCACCTTGCATGGAGGAAAAGA 59.892 45.455 24.48 6.79 37.72 2.52
1678 1752 2.517959 TCACCTTGCATGGAGGAAAAG 58.482 47.619 24.48 4.73 37.72 2.27
1679 1753 2.673775 TCACCTTGCATGGAGGAAAA 57.326 45.000 24.48 0.00 37.72 2.29
1680 1754 2.827322 CAATCACCTTGCATGGAGGAAA 59.173 45.455 24.48 5.21 37.72 3.13
1681 1755 2.449464 CAATCACCTTGCATGGAGGAA 58.551 47.619 24.48 5.55 37.72 3.36
1805 1883 2.125461 TCGTCGATCATCATGTCTGC 57.875 50.000 0.00 0.00 0.00 4.26
1806 1884 3.700154 AGTTCGTCGATCATCATGTCTG 58.300 45.455 6.12 0.00 0.00 3.51
1836 1922 4.177026 CCCAACGAACAACAAATCACAAA 58.823 39.130 0.00 0.00 0.00 2.83
1896 1982 0.744414 CCGTCCCGTACCTCTCGTAA 60.744 60.000 0.00 0.00 0.00 3.18
1954 2040 3.578716 TCCACCTTCCTGTAGAACTTCTG 59.421 47.826 1.17 0.00 0.00 3.02
2049 2139 9.219603 CCTGAAATCAACCACGATGTATATATT 57.780 33.333 0.00 0.00 0.00 1.28
2052 2142 6.826668 TCCTGAAATCAACCACGATGTATAT 58.173 36.000 0.00 0.00 0.00 0.86
2053 2143 6.228616 TCCTGAAATCAACCACGATGTATA 57.771 37.500 0.00 0.00 0.00 1.47
2056 2146 3.338249 CTCCTGAAATCAACCACGATGT 58.662 45.455 0.00 0.00 0.00 3.06
2107 2204 1.241165 CCTGAAACCAAACCCCGTAC 58.759 55.000 0.00 0.00 0.00 3.67
2155 2256 0.597637 CCACGACTCGCAACTGAACT 60.598 55.000 0.00 0.00 0.00 3.01
2187 2288 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
2327 2474 0.805322 TTGCTTGGCACTGCGTTTTG 60.805 50.000 7.09 0.00 38.71 2.44
2415 2562 0.608640 GGGAAGACAGTGGTGATCGT 59.391 55.000 0.00 0.00 0.00 3.73
2440 2587 1.148048 GAGAGGAAGGCTGGATGGC 59.852 63.158 0.00 0.00 42.15 4.40
2442 2589 1.045350 TCGGAGAGGAAGGCTGGATG 61.045 60.000 0.00 0.00 0.00 3.51
2444 2591 1.682684 GTCGGAGAGGAAGGCTGGA 60.683 63.158 0.00 0.00 36.95 3.86
2445 2592 2.896443 GTCGGAGAGGAAGGCTGG 59.104 66.667 0.00 0.00 36.95 4.85
2446 2593 2.492090 CGTCGGAGAGGAAGGCTG 59.508 66.667 0.00 0.00 46.48 4.85
2447 2594 2.756283 CCGTCGGAGAGGAAGGCT 60.756 66.667 4.91 0.00 46.48 4.58
2449 2596 3.839432 GGCCGTCGGAGAGGAAGG 61.839 72.222 17.49 0.00 46.48 3.46
2450 2597 3.839432 GGGCCGTCGGAGAGGAAG 61.839 72.222 17.49 0.00 46.48 3.46
2460 2607 3.577334 TTTGTGGATGGGGGCCGTC 62.577 63.158 0.00 0.00 38.72 4.79
2461 2608 3.585428 TTTGTGGATGGGGGCCGT 61.585 61.111 0.00 0.00 0.00 5.68
2462 2609 3.068064 GTTTGTGGATGGGGGCCG 61.068 66.667 0.00 0.00 0.00 6.13
2463 2610 2.683572 GGTTTGTGGATGGGGGCC 60.684 66.667 0.00 0.00 0.00 5.80
2464 2611 1.535202 TTGGTTTGTGGATGGGGGC 60.535 57.895 0.00 0.00 0.00 5.80
2465 2612 0.470833 TGTTGGTTTGTGGATGGGGG 60.471 55.000 0.00 0.00 0.00 5.40
2466 2613 1.550072 GATGTTGGTTTGTGGATGGGG 59.450 52.381 0.00 0.00 0.00 4.96
2467 2614 1.202114 CGATGTTGGTTTGTGGATGGG 59.798 52.381 0.00 0.00 0.00 4.00
2468 2615 1.402720 GCGATGTTGGTTTGTGGATGG 60.403 52.381 0.00 0.00 0.00 3.51
2469 2616 1.269174 TGCGATGTTGGTTTGTGGATG 59.731 47.619 0.00 0.00 0.00 3.51
2470 2617 1.614996 TGCGATGTTGGTTTGTGGAT 58.385 45.000 0.00 0.00 0.00 3.41
2471 2618 1.614996 ATGCGATGTTGGTTTGTGGA 58.385 45.000 0.00 0.00 0.00 4.02
2472 2619 3.119531 ACATATGCGATGTTGGTTTGTGG 60.120 43.478 1.58 0.00 0.00 4.17
2473 2620 4.095410 ACATATGCGATGTTGGTTTGTG 57.905 40.909 1.58 0.00 0.00 3.33
2474 2621 3.755905 TGACATATGCGATGTTGGTTTGT 59.244 39.130 1.58 0.00 31.52 2.83
2475 2622 4.345288 CTGACATATGCGATGTTGGTTTG 58.655 43.478 1.58 0.00 31.52 2.93
2476 2623 3.378112 CCTGACATATGCGATGTTGGTTT 59.622 43.478 1.58 0.00 31.52 3.27
2477 2624 2.945008 CCTGACATATGCGATGTTGGTT 59.055 45.455 1.58 0.00 31.52 3.67
2478 2625 2.564771 CCTGACATATGCGATGTTGGT 58.435 47.619 1.58 0.00 31.52 3.67
2479 2626 1.265095 GCCTGACATATGCGATGTTGG 59.735 52.381 1.58 14.62 31.52 3.77
2480 2627 1.265095 GGCCTGACATATGCGATGTTG 59.735 52.381 1.58 3.08 31.52 3.33
2481 2628 1.141657 AGGCCTGACATATGCGATGTT 59.858 47.619 3.11 0.00 31.52 2.71
2482 2629 0.761187 AGGCCTGACATATGCGATGT 59.239 50.000 3.11 3.84 34.52 3.06
2483 2630 1.802960 GAAGGCCTGACATATGCGATG 59.197 52.381 5.69 0.00 0.00 3.84
2484 2631 1.696336 AGAAGGCCTGACATATGCGAT 59.304 47.619 5.69 0.00 0.00 4.58
2485 2632 1.123077 AGAAGGCCTGACATATGCGA 58.877 50.000 5.69 0.00 0.00 5.10
2486 2633 2.224042 TGTAGAAGGCCTGACATATGCG 60.224 50.000 5.69 0.00 0.00 4.73
2487 2634 3.475566 TGTAGAAGGCCTGACATATGC 57.524 47.619 5.69 0.00 0.00 3.14
2488 2635 4.240888 CGATGTAGAAGGCCTGACATATG 58.759 47.826 21.98 15.80 32.75 1.78
2489 2636 3.259374 CCGATGTAGAAGGCCTGACATAT 59.741 47.826 21.98 9.35 32.75 1.78
2490 2637 2.628178 CCGATGTAGAAGGCCTGACATA 59.372 50.000 21.98 5.19 32.75 2.29
2491 2638 1.414181 CCGATGTAGAAGGCCTGACAT 59.586 52.381 22.07 22.07 35.26 3.06
2492 2639 0.824109 CCGATGTAGAAGGCCTGACA 59.176 55.000 5.69 12.28 0.00 3.58
2493 2640 0.530870 GCCGATGTAGAAGGCCTGAC 60.531 60.000 5.69 5.81 44.80 3.51
2494 2641 1.823295 GCCGATGTAGAAGGCCTGA 59.177 57.895 5.69 0.00 44.80 3.86
2495 2642 4.445699 GCCGATGTAGAAGGCCTG 57.554 61.111 5.69 0.00 44.80 4.85
2498 2645 1.883084 CACCGCCGATGTAGAAGGC 60.883 63.158 0.37 0.37 46.88 4.35
2499 2646 1.883084 GCACCGCCGATGTAGAAGG 60.883 63.158 0.00 0.00 0.00 3.46
2500 2647 0.530650 ATGCACCGCCGATGTAGAAG 60.531 55.000 0.00 0.00 0.00 2.85
2501 2648 0.529773 GATGCACCGCCGATGTAGAA 60.530 55.000 0.00 0.00 0.00 2.10
2502 2649 1.067416 GATGCACCGCCGATGTAGA 59.933 57.895 0.00 0.00 0.00 2.59
2503 2650 1.956170 GGATGCACCGCCGATGTAG 60.956 63.158 0.00 0.00 0.00 2.74
2504 2651 2.108157 GGATGCACCGCCGATGTA 59.892 61.111 0.00 0.00 0.00 2.29
2530 2677 4.363999 CGACATCAGGGCTAAACTCTTAG 58.636 47.826 0.00 0.00 38.06 2.18
2531 2678 3.132289 CCGACATCAGGGCTAAACTCTTA 59.868 47.826 0.00 0.00 0.00 2.10
2532 2679 2.093447 CCGACATCAGGGCTAAACTCTT 60.093 50.000 0.00 0.00 0.00 2.85
2533 2680 1.482593 CCGACATCAGGGCTAAACTCT 59.517 52.381 0.00 0.00 0.00 3.24
2534 2681 1.473434 CCCGACATCAGGGCTAAACTC 60.473 57.143 0.00 0.00 42.77 3.01
2535 2682 0.541863 CCCGACATCAGGGCTAAACT 59.458 55.000 0.00 0.00 42.77 2.66
2536 2683 3.080647 CCCGACATCAGGGCTAAAC 57.919 57.895 0.00 0.00 42.77 2.01
2542 2689 2.556840 AATGGTGCCCGACATCAGGG 62.557 60.000 0.00 0.00 44.40 4.45
2543 2690 1.077501 AATGGTGCCCGACATCAGG 60.078 57.895 0.00 0.00 44.40 3.86
2558 2705 0.516877 TTGAAAGCTCGGTCGCAATG 59.483 50.000 0.00 0.00 0.00 2.82
2570 2717 0.670162 TGTTGCTGCCTCTTGAAAGC 59.330 50.000 0.00 0.00 36.18 3.51
2574 2721 2.928801 TAGTTGTTGCTGCCTCTTGA 57.071 45.000 0.00 0.00 0.00 3.02
2575 2722 4.510038 AATTAGTTGTTGCTGCCTCTTG 57.490 40.909 0.00 0.00 0.00 3.02
2576 2723 4.829492 AGAAATTAGTTGTTGCTGCCTCTT 59.171 37.500 0.00 0.00 0.00 2.85
2577 2724 4.401925 AGAAATTAGTTGTTGCTGCCTCT 58.598 39.130 0.00 0.00 0.00 3.69
2578 2725 4.457257 AGAGAAATTAGTTGTTGCTGCCTC 59.543 41.667 0.00 0.00 0.00 4.70
2579 2726 4.401925 AGAGAAATTAGTTGTTGCTGCCT 58.598 39.130 0.00 0.00 0.00 4.75
2580 2727 4.216257 TGAGAGAAATTAGTTGTTGCTGCC 59.784 41.667 0.00 0.00 0.00 4.85
2613 2780 1.901833 TGAGAGTGGTTCATGCTGCTA 59.098 47.619 0.00 0.00 0.00 3.49
2615 2782 1.085091 CTGAGAGTGGTTCATGCTGC 58.915 55.000 0.00 0.00 0.00 5.25
2621 2788 4.284490 AGCAGTAAATCTGAGAGTGGTTCA 59.716 41.667 0.00 0.00 46.27 3.18
2753 2920 0.035056 ATCGAAGGGGCTTGTCCTTG 60.035 55.000 0.00 0.00 43.98 3.61
2766 2933 0.670546 AGCCGTTGTGTGGATCGAAG 60.671 55.000 0.00 0.00 0.00 3.79
2768 2935 0.604073 TTAGCCGTTGTGTGGATCGA 59.396 50.000 0.00 0.00 0.00 3.59
2769 2936 0.719465 GTTAGCCGTTGTGTGGATCG 59.281 55.000 0.00 0.00 0.00 3.69
2770 2937 1.463444 GTGTTAGCCGTTGTGTGGATC 59.537 52.381 0.00 0.00 0.00 3.36
2771 2938 1.071699 AGTGTTAGCCGTTGTGTGGAT 59.928 47.619 0.00 0.00 0.00 3.41
2772 2939 0.466543 AGTGTTAGCCGTTGTGTGGA 59.533 50.000 0.00 0.00 0.00 4.02
2774 2941 0.506932 CGAGTGTTAGCCGTTGTGTG 59.493 55.000 0.00 0.00 0.00 3.82
2775 2942 0.386476 TCGAGTGTTAGCCGTTGTGT 59.614 50.000 0.00 0.00 0.00 3.72
2816 2984 1.000274 GGATTGTGTGTTTGGGTGCTC 60.000 52.381 0.00 0.00 0.00 4.26
2823 2991 1.001815 GTCGGTGGGATTGTGTGTTTG 60.002 52.381 0.00 0.00 0.00 2.93
2825 2993 0.472471 AGTCGGTGGGATTGTGTGTT 59.528 50.000 0.00 0.00 0.00 3.32
2827 2995 1.577328 GCAGTCGGTGGGATTGTGTG 61.577 60.000 0.00 0.00 35.01 3.82
2834 3002 1.122632 TTTGTAGGCAGTCGGTGGGA 61.123 55.000 0.00 0.00 0.00 4.37
2835 3003 0.953960 GTTTGTAGGCAGTCGGTGGG 60.954 60.000 0.00 0.00 0.00 4.61
2836 3004 0.034896 AGTTTGTAGGCAGTCGGTGG 59.965 55.000 0.00 0.00 0.00 4.61
2837 3005 1.270094 TGAGTTTGTAGGCAGTCGGTG 60.270 52.381 0.00 0.00 0.00 4.94
2838 3006 1.045407 TGAGTTTGTAGGCAGTCGGT 58.955 50.000 0.00 0.00 0.00 4.69
2839 3007 2.163818 TTGAGTTTGTAGGCAGTCGG 57.836 50.000 0.00 0.00 0.00 4.79
2840 3008 4.213270 TGAATTTGAGTTTGTAGGCAGTCG 59.787 41.667 0.00 0.00 0.00 4.18
2841 3009 5.470098 TCTGAATTTGAGTTTGTAGGCAGTC 59.530 40.000 0.00 0.00 0.00 3.51
2842 3010 5.376625 TCTGAATTTGAGTTTGTAGGCAGT 58.623 37.500 0.00 0.00 0.00 4.40
2843 3011 5.947228 TCTGAATTTGAGTTTGTAGGCAG 57.053 39.130 0.00 0.00 0.00 4.85
2844 3012 6.899393 ATTCTGAATTTGAGTTTGTAGGCA 57.101 33.333 0.00 0.00 0.00 4.75
2878 3046 2.158740 TCCCCACATCTTCGTTGTGAAA 60.159 45.455 5.43 0.00 45.83 2.69
2886 3054 6.591750 AGTATAAGTATCCCCACATCTTCG 57.408 41.667 0.00 0.00 0.00 3.79
2890 3058 6.097129 GCCTCTAGTATAAGTATCCCCACATC 59.903 46.154 0.00 0.00 0.00 3.06
2897 3065 7.201839 GCCTATGTGCCTCTAGTATAAGTATCC 60.202 44.444 0.00 0.00 0.00 2.59
2913 3081 1.204704 GTTTTCCCAAGCCTATGTGCC 59.795 52.381 0.00 0.00 0.00 5.01
2915 3083 3.420893 TCAGTTTTCCCAAGCCTATGTG 58.579 45.455 0.00 0.00 0.00 3.21
2916 3084 3.806949 TCAGTTTTCCCAAGCCTATGT 57.193 42.857 0.00 0.00 0.00 2.29
2927 3102 9.764363 AATTAATCCTCTGTTTTTCAGTTTTCC 57.236 29.630 0.00 0.00 43.97 3.13
2929 3104 9.463443 CGAATTAATCCTCTGTTTTTCAGTTTT 57.537 29.630 0.00 0.00 43.97 2.43
2931 3106 8.076178 CACGAATTAATCCTCTGTTTTTCAGTT 58.924 33.333 0.00 0.00 43.97 3.16
2933 3108 7.806690 TCACGAATTAATCCTCTGTTTTTCAG 58.193 34.615 0.00 0.00 44.85 3.02
2934 3109 7.659799 TCTCACGAATTAATCCTCTGTTTTTCA 59.340 33.333 0.00 0.00 0.00 2.69
2935 3110 8.029642 TCTCACGAATTAATCCTCTGTTTTTC 57.970 34.615 0.00 0.00 0.00 2.29
2943 3118 6.092807 AGCTTGTTTCTCACGAATTAATCCTC 59.907 38.462 0.00 0.00 0.00 3.71
2954 3129 3.548587 CATTCACAGCTTGTTTCTCACG 58.451 45.455 0.00 0.00 0.00 4.35
2958 3133 2.555757 GCTCCATTCACAGCTTGTTTCT 59.444 45.455 0.00 0.00 32.48 2.52
2961 3136 1.985473 TGCTCCATTCACAGCTTGTT 58.015 45.000 0.00 0.00 36.53 2.83
2996 3171 2.357075 GCCCAAGAGTTACTTACTGCC 58.643 52.381 0.00 0.00 37.17 4.85
3001 3176 1.272807 AGCGGCCCAAGAGTTACTTA 58.727 50.000 0.00 0.00 37.03 2.24
3004 3179 1.923227 GCAAGCGGCCCAAGAGTTAC 61.923 60.000 0.00 0.00 36.11 2.50
3008 3183 2.753043 ATGCAAGCGGCCCAAGAG 60.753 61.111 0.00 0.00 43.89 2.85
3012 3187 4.675161 TTCCATGCAAGCGGCCCA 62.675 61.111 0.00 0.00 43.89 5.36
3015 3190 1.698714 GCAATTTCCATGCAAGCGGC 61.699 55.000 0.00 0.00 43.29 6.53


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

AutoCloner maintained by Alex Coulton.