Multiple sequence alignment - TraesCS5B01G376900

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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 TraesCS5B01G376900 chr5B 100.000 6276 0 0 1 6276 554724674 554730949 0.000000e+00 11590
1 TraesCS5B01G376900 chr5D 93.044 2746 159 16 2775 5499 453989002 453991736 0.000000e+00 3984
2 TraesCS5B01G376900 chr5D 87.441 1266 89 34 1309 2531 453987433 453988671 0.000000e+00 1393
3 TraesCS5B01G376900 chr5D 92.555 779 54 4 5499 6276 496089223 496089998 0.000000e+00 1114
4 TraesCS5B01G376900 chr5D 86.086 654 41 17 644 1268 453986714 453987346 0.000000e+00 658
5 TraesCS5B01G376900 chr5D 93.927 247 13 2 2535 2780 453988704 453988949 7.680000e-99 372
6 TraesCS5B01G376900 chr5A 91.570 2752 177 26 2775 5499 573042303 573045026 0.000000e+00 3746
7 TraesCS5B01G376900 chr5A 82.470 2008 156 79 644 2534 573039863 573041791 0.000000e+00 1578
8 TraesCS5B01G376900 chr5A 92.614 176 10 2 2605 2780 573042076 573042248 3.760000e-62 250
9 TraesCS5B01G376900 chr5A 96.721 61 1 1 2554 2613 573041905 573041965 4.000000e-17 100
10 TraesCS5B01G376900 chr3D 92.839 782 50 5 5500 6276 54376729 54377509 0.000000e+00 1129
11 TraesCS5B01G376900 chr3D 92.513 788 45 9 5500 6276 462266426 462265642 0.000000e+00 1116
12 TraesCS5B01G376900 chr3D 92.455 782 53 4 5500 6276 544590734 544591514 0.000000e+00 1112
13 TraesCS5B01G376900 chr3D 92.327 782 53 5 5500 6276 429246697 429245918 0.000000e+00 1105
14 TraesCS5B01G376900 chr1B 92.630 787 47 7 5500 6276 324343174 324343959 0.000000e+00 1122
15 TraesCS5B01G376900 chr1B 90.016 641 60 4 2 640 669509406 669508768 0.000000e+00 826
16 TraesCS5B01G376900 chr4B 92.513 788 48 5 5499 6276 109325715 109326501 0.000000e+00 1118
17 TraesCS5B01G376900 chr4B 89.638 608 58 5 36 640 46975744 46975139 0.000000e+00 769
18 TraesCS5B01G376900 chr7D 92.416 778 56 3 5500 6276 400914407 400915182 0.000000e+00 1107
19 TraesCS5B01G376900 chr6D 92.337 783 52 4 5500 6276 29108817 29108037 0.000000e+00 1107
20 TraesCS5B01G376900 chr3B 92.547 644 41 7 2 640 22882601 22883242 0.000000e+00 917
21 TraesCS5B01G376900 chr6B 92.391 644 41 8 2 640 624271781 624272421 0.000000e+00 911
22 TraesCS5B01G376900 chr1D 88.689 610 64 5 34 640 379575489 379574882 0.000000e+00 739
23 TraesCS5B01G376900 chr4D 87.889 611 69 5 34 640 483613329 483612720 0.000000e+00 713
24 TraesCS5B01G376900 chr4A 85.344 655 75 18 3 643 710817961 710818608 0.000000e+00 658
25 TraesCS5B01G376900 chr2B 85.993 614 74 9 34 640 25270196 25269588 0.000000e+00 647
26 TraesCS5B01G376900 chr2B 85.808 613 78 7 34 640 444551463 444550854 5.300000e-180 641


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 TraesCS5B01G376900 chr5B 554724674 554730949 6275 False 11590.00 11590 100.00000 1 6276 1 chr5B.!!$F1 6275
1 TraesCS5B01G376900 chr5D 453986714 453991736 5022 False 1601.75 3984 90.12450 644 5499 4 chr5D.!!$F2 4855
2 TraesCS5B01G376900 chr5D 496089223 496089998 775 False 1114.00 1114 92.55500 5499 6276 1 chr5D.!!$F1 777
3 TraesCS5B01G376900 chr5A 573039863 573045026 5163 False 1418.50 3746 90.84375 644 5499 4 chr5A.!!$F1 4855
4 TraesCS5B01G376900 chr3D 54376729 54377509 780 False 1129.00 1129 92.83900 5500 6276 1 chr3D.!!$F1 776
5 TraesCS5B01G376900 chr3D 462265642 462266426 784 True 1116.00 1116 92.51300 5500 6276 1 chr3D.!!$R2 776
6 TraesCS5B01G376900 chr3D 544590734 544591514 780 False 1112.00 1112 92.45500 5500 6276 1 chr3D.!!$F2 776
7 TraesCS5B01G376900 chr3D 429245918 429246697 779 True 1105.00 1105 92.32700 5500 6276 1 chr3D.!!$R1 776
8 TraesCS5B01G376900 chr1B 324343174 324343959 785 False 1122.00 1122 92.63000 5500 6276 1 chr1B.!!$F1 776
9 TraesCS5B01G376900 chr1B 669508768 669509406 638 True 826.00 826 90.01600 2 640 1 chr1B.!!$R1 638
10 TraesCS5B01G376900 chr4B 109325715 109326501 786 False 1118.00 1118 92.51300 5499 6276 1 chr4B.!!$F1 777
11 TraesCS5B01G376900 chr4B 46975139 46975744 605 True 769.00 769 89.63800 36 640 1 chr4B.!!$R1 604
12 TraesCS5B01G376900 chr7D 400914407 400915182 775 False 1107.00 1107 92.41600 5500 6276 1 chr7D.!!$F1 776
13 TraesCS5B01G376900 chr6D 29108037 29108817 780 True 1107.00 1107 92.33700 5500 6276 1 chr6D.!!$R1 776
14 TraesCS5B01G376900 chr3B 22882601 22883242 641 False 917.00 917 92.54700 2 640 1 chr3B.!!$F1 638
15 TraesCS5B01G376900 chr6B 624271781 624272421 640 False 911.00 911 92.39100 2 640 1 chr6B.!!$F1 638
16 TraesCS5B01G376900 chr1D 379574882 379575489 607 True 739.00 739 88.68900 34 640 1 chr1D.!!$R1 606
17 TraesCS5B01G376900 chr4D 483612720 483613329 609 True 713.00 713 87.88900 34 640 1 chr4D.!!$R1 606
18 TraesCS5B01G376900 chr4A 710817961 710818608 647 False 658.00 658 85.34400 3 643 1 chr4A.!!$F1 640
19 TraesCS5B01G376900 chr2B 25269588 25270196 608 True 647.00 647 85.99300 34 640 1 chr2B.!!$R1 606
20 TraesCS5B01G376900 chr2B 444550854 444551463 609 True 641.00 641 85.80800 34 640 1 chr2B.!!$R2 606

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
880 921 0.036164 TACCACCACGCAGCAAGAAT 59.964 50.0 0.00 0.00 0.00 2.40 F
1573 1713 0.032130 TACCTCGGATCGATTGCTGC 59.968 55.0 0.00 0.00 34.61 5.25 F
2292 2453 0.039472 TTGGGATGTGGACCATGTGG 59.961 55.0 0.00 0.00 36.48 4.17 F
2633 3048 0.530744 TACATGTGGTGCTCGGAGAC 59.469 55.0 9.11 4.26 0.00 3.36 F
3642 4132 1.014352 GCGATTTAATCACCGTGCCT 58.986 50.0 5.76 0.00 0.00 4.75 F
4302 4796 0.249868 TTCCGGTCAGTGCAGTTCTG 60.250 55.0 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2447 0.109643 CATTGACGCACCACCACATG 60.110 55.000 0.00 0.0 0.00 3.21 R
2824 3299 0.326264 GGGCTTCCAGCTTCTCAAGA 59.674 55.000 0.00 0.0 41.99 3.02 R
3621 4111 1.131504 GGCACGGTGATTAAATCGCAA 59.868 47.619 13.29 0.0 41.46 4.85 R
4302 4796 1.160137 GCATGATATCCTTGTCCGCC 58.840 55.000 0.00 0.0 0.00 6.13 R
4784 5279 0.251653 ACTCCTGACCTAACTCCGCA 60.252 55.000 0.00 0.0 0.00 5.69 R
5279 5774 0.392595 CTCAGCTCTGCTTGGATGCA 60.393 55.000 0.00 0.0 36.40 3.96 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
83 86 8.992073 GGAACTCCGTTTACTAATTAGTTGAAA 58.008 33.333 22.66 14.91 37.73 2.69
348 373 6.238759 GCCAGAGCCTTTTCATATTTCGTTAT 60.239 38.462 0.00 0.00 0.00 1.89
411 437 2.543635 GGTCTCTGGTGGTAGGGTTAA 58.456 52.381 0.00 0.00 0.00 2.01
429 455 4.715130 ACAGCCTACCGCCAGGGA 62.715 66.667 3.06 0.00 43.47 4.20
499 526 2.754658 CCTCCGTCGCACCCTACT 60.755 66.667 0.00 0.00 0.00 2.57
617 648 8.366401 TCAGATCCTGAATTTGTATTGCAAAAA 58.634 29.630 1.71 0.00 41.56 1.94
640 671 3.190874 GTCAAAACACGAAATTTGGCCA 58.809 40.909 0.00 0.00 35.62 5.36
641 672 3.245048 GTCAAAACACGAAATTTGGCCAG 59.755 43.478 5.11 0.00 35.62 4.85
642 673 3.118956 TCAAAACACGAAATTTGGCCAGT 60.119 39.130 5.11 0.00 37.19 4.00
651 682 2.789409 ATTTGGCCAGTACTCCACTC 57.211 50.000 5.11 0.00 34.26 3.51
663 694 2.745968 ACTCCACTCCTCTCATTCTCC 58.254 52.381 0.00 0.00 0.00 3.71
814 852 3.281359 GAAGCAACCGCGGCCAAAT 62.281 57.895 28.58 9.40 45.49 2.32
852 890 3.048602 CGTGTCCTCCACTTCCGT 58.951 61.111 0.00 0.00 42.20 4.69
873 914 2.742372 GGCACTACCACCACGCAG 60.742 66.667 0.00 0.00 38.86 5.18
877 918 1.301716 ACTACCACCACGCAGCAAG 60.302 57.895 0.00 0.00 0.00 4.01
880 921 0.036164 TACCACCACGCAGCAAGAAT 59.964 50.000 0.00 0.00 0.00 2.40
892 933 2.172293 CAGCAAGAATAGGAGGAAGCCT 59.828 50.000 0.00 0.00 42.15 4.58
921 962 4.468689 GGGCCCCGCACACTCTAC 62.469 72.222 12.23 0.00 0.00 2.59
922 963 3.702048 GGCCCCGCACACTCTACA 61.702 66.667 0.00 0.00 0.00 2.74
923 964 2.584608 GCCCCGCACACTCTACAT 59.415 61.111 0.00 0.00 0.00 2.29
930 986 1.061566 CGCACACTCTACATACGACGA 59.938 52.381 0.00 0.00 0.00 4.20
931 987 2.438583 GCACACTCTACATACGACGAC 58.561 52.381 0.00 0.00 0.00 4.34
932 988 2.690735 CACACTCTACATACGACGACG 58.309 52.381 5.58 5.58 45.75 5.12
935 991 0.935898 CTCTACATACGACGACGCCT 59.064 55.000 7.30 0.00 43.96 5.52
948 1004 2.172483 GACGCCTCCACACTCCACAT 62.172 60.000 0.00 0.00 0.00 3.21
954 1010 1.759445 CTCCACACTCCACATCCTAGG 59.241 57.143 0.82 0.82 0.00 3.02
955 1011 1.078823 TCCACACTCCACATCCTAGGT 59.921 52.381 9.08 0.00 0.00 3.08
956 1012 2.313643 TCCACACTCCACATCCTAGGTA 59.686 50.000 9.08 0.00 0.00 3.08
957 1013 2.695666 CCACACTCCACATCCTAGGTAG 59.304 54.545 9.08 5.16 0.00 3.18
958 1014 3.627492 CCACACTCCACATCCTAGGTAGA 60.627 52.174 9.08 0.00 0.00 2.59
961 1017 3.068873 CACTCCACATCCTAGGTAGAAGC 59.931 52.174 9.08 0.00 0.00 3.86
964 1020 2.294791 CCACATCCTAGGTAGAAGCGAG 59.705 54.545 9.08 0.00 0.00 5.03
965 1021 2.952978 CACATCCTAGGTAGAAGCGAGT 59.047 50.000 9.08 0.00 0.00 4.18
966 1022 2.952978 ACATCCTAGGTAGAAGCGAGTG 59.047 50.000 9.08 0.00 0.00 3.51
967 1023 2.803030 TCCTAGGTAGAAGCGAGTGT 57.197 50.000 9.08 0.00 0.00 3.55
968 1024 2.366533 TCCTAGGTAGAAGCGAGTGTG 58.633 52.381 9.08 0.00 0.00 3.82
969 1025 2.026542 TCCTAGGTAGAAGCGAGTGTGA 60.027 50.000 9.08 0.00 0.00 3.58
970 1026 2.753452 CCTAGGTAGAAGCGAGTGTGAA 59.247 50.000 0.00 0.00 0.00 3.18
1011 1070 4.357947 GCGGAGATGGCGGCGATA 62.358 66.667 12.98 0.00 0.00 2.92
1014 1073 0.172578 CGGAGATGGCGGCGATAATA 59.827 55.000 12.98 0.00 0.00 0.98
1015 1074 1.202417 CGGAGATGGCGGCGATAATAT 60.202 52.381 12.98 0.00 0.00 1.28
1243 1330 2.778299 TGTCTTAGCGGCAAATTCTGT 58.222 42.857 1.45 0.00 0.00 3.41
1294 1397 2.741092 GGGTTCGTGTGAGCTGGA 59.259 61.111 0.00 0.00 0.00 3.86
1298 1401 1.000506 GGTTCGTGTGAGCTGGAGTTA 59.999 52.381 0.00 0.00 0.00 2.24
1305 1408 3.089284 TGTGAGCTGGAGTTATCTTCGA 58.911 45.455 0.00 0.00 0.00 3.71
1342 1476 4.887655 TCGGCACTTCATCTTGAGATAGTA 59.112 41.667 0.00 0.00 32.63 1.82
1374 1508 3.187700 GCGAACGGAGTAATCAATCACT 58.812 45.455 0.00 0.00 45.00 3.41
1394 1528 2.153366 AAATTGGGCTTGCAGAAACG 57.847 45.000 0.00 0.00 0.00 3.60
1402 1536 2.926838 GGCTTGCAGAAACGTTTTTCAA 59.073 40.909 15.89 16.49 43.29 2.69
1408 1542 5.034152 TGCAGAAACGTTTTTCAACAGATC 58.966 37.500 15.89 0.00 43.29 2.75
1421 1555 2.743664 CAACAGATCCTCGCATGTCAAA 59.256 45.455 0.00 0.00 0.00 2.69
1431 1565 1.928503 CGCATGTCAAATTTGGGATGC 59.071 47.619 28.04 28.04 38.60 3.91
1444 1578 8.658609 CAAATTTGGGATGCTTGTTTATTACTG 58.341 33.333 10.49 0.00 0.00 2.74
1445 1579 7.716799 ATTTGGGATGCTTGTTTATTACTGA 57.283 32.000 0.00 0.00 0.00 3.41
1446 1580 6.757897 TTGGGATGCTTGTTTATTACTGAG 57.242 37.500 0.00 0.00 0.00 3.35
1447 1581 5.815581 TGGGATGCTTGTTTATTACTGAGT 58.184 37.500 0.00 0.00 0.00 3.41
1448 1582 6.953101 TGGGATGCTTGTTTATTACTGAGTA 58.047 36.000 0.00 0.00 0.00 2.59
1450 1584 7.048512 GGGATGCTTGTTTATTACTGAGTAGT 58.951 38.462 0.00 0.00 40.99 2.73
1452 1586 9.032420 GGATGCTTGTTTATTACTGAGTAGTAC 57.968 37.037 0.00 0.00 39.06 2.73
1453 1587 8.943909 ATGCTTGTTTATTACTGAGTAGTACC 57.056 34.615 0.00 0.00 39.06 3.34
1456 1590 5.894807 TGTTTATTACTGAGTAGTACCGCC 58.105 41.667 0.00 0.00 39.06 6.13
1458 1592 5.762825 TTATTACTGAGTAGTACCGCCTG 57.237 43.478 0.00 0.00 39.06 4.85
1461 1595 3.294038 ACTGAGTAGTACCGCCTGTAT 57.706 47.619 0.00 0.00 34.74 2.29
1465 1599 3.879295 TGAGTAGTACCGCCTGTATACAC 59.121 47.826 0.08 0.00 0.00 2.90
1466 1600 3.879295 GAGTAGTACCGCCTGTATACACA 59.121 47.826 0.08 0.00 0.00 3.72
1486 1620 5.643777 ACACAACTGCAGTTTCTGTATATCC 59.356 40.000 29.23 0.00 35.83 2.59
1506 1646 4.580868 TCCTAGTAGTGACAGTGACTCAG 58.419 47.826 0.00 0.00 0.00 3.35
1507 1647 4.041815 TCCTAGTAGTGACAGTGACTCAGT 59.958 45.833 0.00 0.00 0.00 3.41
1510 1650 3.954904 AGTAGTGACAGTGACTCAGTGTT 59.045 43.478 18.63 7.70 46.41 3.32
1551 1691 3.412386 AGTCTAAATCCGCACTTGCTTT 58.588 40.909 0.00 0.00 39.32 3.51
1561 1701 2.030457 CGCACTTGCTTTAATACCTCGG 59.970 50.000 0.00 0.00 39.32 4.63
1562 1702 3.267483 GCACTTGCTTTAATACCTCGGA 58.733 45.455 0.00 0.00 38.21 4.55
1563 1703 3.877508 GCACTTGCTTTAATACCTCGGAT 59.122 43.478 0.00 0.00 38.21 4.18
1564 1704 4.024809 GCACTTGCTTTAATACCTCGGATC 60.025 45.833 0.00 0.00 38.21 3.36
1565 1705 4.209288 CACTTGCTTTAATACCTCGGATCG 59.791 45.833 0.00 0.00 0.00 3.69
1566 1706 4.098960 ACTTGCTTTAATACCTCGGATCGA 59.901 41.667 0.00 0.00 0.00 3.59
1567 1707 4.866508 TGCTTTAATACCTCGGATCGAT 57.133 40.909 0.00 0.00 34.61 3.59
1568 1708 5.209818 TGCTTTAATACCTCGGATCGATT 57.790 39.130 0.00 0.00 34.61 3.34
1569 1709 4.988540 TGCTTTAATACCTCGGATCGATTG 59.011 41.667 0.00 0.00 34.61 2.67
1570 1710 4.143094 GCTTTAATACCTCGGATCGATTGC 60.143 45.833 0.00 0.00 34.61 3.56
1571 1711 4.866508 TTAATACCTCGGATCGATTGCT 57.133 40.909 0.00 0.00 34.61 3.91
1572 1712 2.732412 ATACCTCGGATCGATTGCTG 57.268 50.000 0.00 0.00 34.61 4.41
1573 1713 0.032130 TACCTCGGATCGATTGCTGC 59.968 55.000 0.00 0.00 34.61 5.25
1574 1714 1.068753 CCTCGGATCGATTGCTGCT 59.931 57.895 0.00 0.00 34.61 4.24
1575 1715 1.220169 CCTCGGATCGATTGCTGCTG 61.220 60.000 0.00 0.00 34.61 4.41
1576 1716 1.829349 CTCGGATCGATTGCTGCTGC 61.829 60.000 8.89 8.89 34.61 5.25
1591 1731 2.167693 CTGCTGCATTTGATTGGGATGT 59.832 45.455 1.31 0.00 0.00 3.06
1595 1735 3.289836 TGCATTTGATTGGGATGTCGAT 58.710 40.909 0.00 0.00 0.00 3.59
1600 1740 6.364165 GCATTTGATTGGGATGTCGATATTTG 59.636 38.462 0.00 0.00 0.00 2.32
1619 1759 9.899226 GATATTTGTTAGTGCTTTCTTTGTTCT 57.101 29.630 0.00 0.00 0.00 3.01
1625 1765 7.500892 TGTTAGTGCTTTCTTTGTTCTATTGGA 59.499 33.333 0.00 0.00 0.00 3.53
1626 1766 8.515414 GTTAGTGCTTTCTTTGTTCTATTGGAT 58.485 33.333 0.00 0.00 0.00 3.41
1633 1775 9.971922 CTTTCTTTGTTCTATTGGATGAAAAGT 57.028 29.630 0.00 0.00 0.00 2.66
1685 1837 5.657474 ACCTGCAAAATCATGCTTTCTATG 58.343 37.500 0.00 0.00 46.54 2.23
1692 1844 7.254319 GCAAAATCATGCTTTCTATGTTGATGG 60.254 37.037 0.00 0.00 43.06 3.51
1701 1853 3.457234 TCTATGTTGATGGTGCGATGAC 58.543 45.455 0.00 0.00 0.00 3.06
1778 1930 1.949525 CATCCGATTCCCATGGTGTTC 59.050 52.381 11.73 3.05 0.00 3.18
1909 2061 5.353394 TTTATCCAAGTGCTATTCGACCT 57.647 39.130 0.00 0.00 0.00 3.85
1915 2067 2.960819 AGTGCTATTCGACCTTCACAC 58.039 47.619 8.95 3.10 0.00 3.82
1965 2117 9.499585 CTTTGAGACAACTTATTTATGCTCATG 57.500 33.333 0.00 0.00 31.91 3.07
2020 2175 3.131046 CCATTGCCATCCAAAAGTCCTAC 59.869 47.826 0.00 0.00 36.92 3.18
2245 2400 6.872628 ACGAGGTATAACTTCACGATATGA 57.127 37.500 4.54 0.00 34.65 2.15
2283 2444 4.081697 GGTTTTTCCAGTATTGGGATGTGG 60.082 45.833 4.18 0.00 45.10 4.17
2284 2445 4.666412 TTTTCCAGTATTGGGATGTGGA 57.334 40.909 4.18 0.00 45.10 4.02
2285 2446 3.644966 TTCCAGTATTGGGATGTGGAC 57.355 47.619 4.18 0.00 45.10 4.02
2286 2447 1.843851 TCCAGTATTGGGATGTGGACC 59.156 52.381 4.18 0.00 45.10 4.46
2287 2448 1.563879 CCAGTATTGGGATGTGGACCA 59.436 52.381 0.00 0.00 41.05 4.02
2288 2449 2.175499 CCAGTATTGGGATGTGGACCAT 59.825 50.000 0.00 0.00 41.05 3.55
2289 2450 3.216800 CAGTATTGGGATGTGGACCATG 58.783 50.000 0.00 0.00 36.48 3.66
2290 2451 2.852449 AGTATTGGGATGTGGACCATGT 59.148 45.455 0.00 0.00 36.48 3.21
2291 2452 2.148446 ATTGGGATGTGGACCATGTG 57.852 50.000 0.00 0.00 36.48 3.21
2292 2453 0.039472 TTGGGATGTGGACCATGTGG 59.961 55.000 0.00 0.00 36.48 4.17
2349 2541 6.519043 GCATCTGTAGCATATTCTGTTCCCTA 60.519 42.308 0.00 0.00 0.00 3.53
2353 2545 7.177568 TCTGTAGCATATTCTGTTCCCTAGATC 59.822 40.741 0.00 0.00 0.00 2.75
2369 2561 3.814005 AGATCGCCCGTTAACTGTTAT 57.186 42.857 3.71 0.00 0.00 1.89
2370 2562 4.924305 AGATCGCCCGTTAACTGTTATA 57.076 40.909 3.71 0.00 0.00 0.98
2381 2573 6.036844 CCGTTAACTGTTATAAGGCTTCTTCC 59.963 42.308 1.30 0.00 32.23 3.46
2386 2578 6.311735 ACTGTTATAAGGCTTCTTCCCAAAA 58.688 36.000 1.30 0.00 32.23 2.44
2388 2580 7.454694 ACTGTTATAAGGCTTCTTCCCAAAAAT 59.545 33.333 1.30 0.00 32.23 1.82
2536 2769 6.711277 AGAGGAAAGCATCACATAACAGTAA 58.289 36.000 0.00 0.00 0.00 2.24
2567 2862 5.332707 GTGTCACAAGTCAAAAGTTCCTTC 58.667 41.667 0.00 0.00 0.00 3.46
2625 3040 2.711542 ACTTAAGCCTACATGTGGTGC 58.288 47.619 9.11 11.28 0.00 5.01
2633 3048 0.530744 TACATGTGGTGCTCGGAGAC 59.469 55.000 9.11 4.26 0.00 3.36
2647 3062 1.942657 CGGAGACATACCCATGCTTTG 59.057 52.381 0.00 0.00 35.39 2.77
2666 3081 1.915489 TGGTATGATGGTGTTGCTCCT 59.085 47.619 0.00 0.00 0.00 3.69
2677 3092 4.020218 TGGTGTTGCTCCTAGATATATGCC 60.020 45.833 0.00 0.00 0.00 4.40
2824 3299 5.421693 TCTTGGCAAATGCAGTGGTTAATAT 59.578 36.000 7.80 0.00 44.36 1.28
2863 3338 4.402474 GCCCATTAATGCCTACTTTTGTCT 59.598 41.667 10.11 0.00 0.00 3.41
2930 3405 2.120909 CCATGGTCGGACATTGGGC 61.121 63.158 16.62 0.00 0.00 5.36
2933 3408 2.359478 GGTCGGACATTGGGCGTT 60.359 61.111 10.76 0.00 0.00 4.84
3049 3524 9.556030 GTTGGAGAAAATCTTTAAAGGTATTCG 57.444 33.333 15.13 0.00 0.00 3.34
3068 3551 2.100418 TCGATCCATTGAGCTCTGTCAG 59.900 50.000 16.19 0.00 0.00 3.51
3071 3554 2.820178 TCCATTGAGCTCTGTCAGGTA 58.180 47.619 16.19 0.00 30.88 3.08
3077 3560 1.896465 GAGCTCTGTCAGGTACCAACT 59.104 52.381 15.94 0.00 30.88 3.16
3194 3677 1.133976 CAAGGAGAAGCTGGGGTATGG 60.134 57.143 0.00 0.00 0.00 2.74
3212 3695 6.354130 GGTATGGATCTTTAAGTTACTGGCA 58.646 40.000 0.00 0.00 0.00 4.92
3217 3707 8.189119 TGGATCTTTAAGTTACTGGCATTTTT 57.811 30.769 0.00 0.00 0.00 1.94
3253 3743 4.164221 TCCTCCCTTGCTAGTTATTTCCTG 59.836 45.833 0.00 0.00 0.00 3.86
3254 3744 4.080299 CCTCCCTTGCTAGTTATTTCCTGT 60.080 45.833 0.00 0.00 0.00 4.00
3261 3751 9.372369 CCTTGCTAGTTATTTCCTGTATATAGC 57.628 37.037 0.00 0.00 34.98 2.97
3352 3842 7.633789 AGAATTTAATGGACTGGAAGAGCTTA 58.366 34.615 0.00 0.00 37.43 3.09
3441 3931 5.013861 TCGAGCACATTTTCGAACTTAAC 57.986 39.130 0.00 0.00 42.27 2.01
3448 3938 6.470877 GCACATTTTCGAACTTAACTGTCAAA 59.529 34.615 0.00 0.00 0.00 2.69
3454 3944 6.312399 TCGAACTTAACTGTCAAAATGCAT 57.688 33.333 0.00 0.00 0.00 3.96
3464 3954 4.746729 TGTCAAAATGCATTAGATGTGGC 58.253 39.130 13.39 8.26 0.00 5.01
3487 3977 6.473455 GGCAGCAATAAAATGATCAACAGTAC 59.527 38.462 0.00 0.00 0.00 2.73
3519 4009 7.605410 ATCTTGCAAAATGGAAAGCAAATAG 57.395 32.000 0.00 0.00 45.18 1.73
3566 4056 7.739444 TGGATAGACTTATGACATTAGGGGAAT 59.261 37.037 6.42 0.00 0.00 3.01
3588 4078 2.624838 CCTTTCATTGCACACTGTCCTT 59.375 45.455 0.00 0.00 0.00 3.36
3596 4086 5.940192 TTGCACACTGTCCTTGTTTATAG 57.060 39.130 0.00 0.00 0.00 1.31
3621 4111 2.950309 GCAAGTGATCAGATCCAAGCAT 59.050 45.455 8.00 0.00 0.00 3.79
3642 4132 1.014352 GCGATTTAATCACCGTGCCT 58.986 50.000 5.76 0.00 0.00 4.75
3647 4137 4.084013 CGATTTAATCACCGTGCCTTATCC 60.084 45.833 5.76 0.00 0.00 2.59
3648 4138 4.497291 TTTAATCACCGTGCCTTATCCT 57.503 40.909 0.00 0.00 0.00 3.24
3650 4140 5.617528 TTAATCACCGTGCCTTATCCTTA 57.382 39.130 0.00 0.00 0.00 2.69
3658 4152 5.240844 ACCGTGCCTTATCCTTAATTATTGC 59.759 40.000 0.00 0.00 0.00 3.56
3661 4155 6.857964 CGTGCCTTATCCTTAATTATTGCAAG 59.142 38.462 4.94 0.00 0.00 4.01
3664 4158 7.078228 GCCTTATCCTTAATTATTGCAAGACG 58.922 38.462 4.94 0.00 0.00 4.18
3802 4296 7.923414 AAAAGACAGGGCTAGTTTTACTATG 57.077 36.000 0.00 0.00 29.08 2.23
4100 4594 9.616156 TCTTTTCTGATACTCTCTACGTATCTT 57.384 33.333 0.00 0.00 42.23 2.40
4139 4633 1.125711 ACCTGGTGGTGAGGTGGTAC 61.126 60.000 0.00 0.00 46.51 3.34
4178 4672 3.272574 TCTACTACACGAGTACCTGGG 57.727 52.381 0.00 0.00 39.81 4.45
4208 4702 7.716123 TGAGGTTTTCGTTTTGTTCTAGGATAA 59.284 33.333 0.00 0.00 0.00 1.75
4302 4796 0.249868 TTCCGGTCAGTGCAGTTCTG 60.250 55.000 0.00 0.00 0.00 3.02
4308 4802 2.031163 AGTGCAGTTCTGGCGGAC 59.969 61.111 0.00 0.00 0.00 4.79
4335 4829 1.655484 TCATGCTGTGTATCAAGCCG 58.345 50.000 0.00 0.00 0.00 5.52
4379 4873 8.499162 TGAACCACTGTTAATTTTGTTTGTTTG 58.501 29.630 0.00 0.00 33.97 2.93
4436 4931 6.942532 TTCAGTTTTGTCTTTAGTGAGCAT 57.057 33.333 0.00 0.00 0.00 3.79
4545 5040 6.993786 TCAGTGTTCTTTTTGTGTATGTCA 57.006 33.333 0.00 0.00 0.00 3.58
4784 5279 3.512724 ACCATTTGCTTAATTGCAGAGCT 59.487 39.130 12.53 0.00 44.27 4.09
4823 5318 5.820947 GGAGTTCAGAGACCAGTTACAAAAA 59.179 40.000 0.00 0.00 0.00 1.94
4843 5338 5.485662 AAAGTTCAACAGAAGTTTCCTCG 57.514 39.130 5.46 0.00 39.50 4.63
4901 5396 2.275318 GCAGTAGACCTAAGCAGCAAG 58.725 52.381 0.00 0.00 0.00 4.01
5009 5504 1.545651 CGATTAGCCCCTCCCATTTCC 60.546 57.143 0.00 0.00 0.00 3.13
5087 5582 3.769739 AGTCTGCATTTACTGACACCA 57.230 42.857 4.57 0.00 40.02 4.17
5101 5596 4.991056 ACTGACACCATATTATGTGATCGC 59.009 41.667 0.00 0.00 0.00 4.58
5116 5611 0.577269 ATCGCGTTCGCTTGCTAATC 59.423 50.000 14.92 0.00 35.26 1.75
5227 5722 2.399916 AGCAGATCAAGAAGCCAGAC 57.600 50.000 0.00 0.00 0.00 3.51
5241 5736 1.826385 CCAGACTCGGAGGCAAAAAT 58.174 50.000 14.42 0.00 0.00 1.82
5251 5746 3.421844 GGAGGCAAAAATACCAGTCTGT 58.578 45.455 0.00 0.00 0.00 3.41
5279 5774 1.071228 GCGGTCGGGATTTATAAGGGT 59.929 52.381 0.00 0.00 0.00 4.34
5280 5775 2.762745 CGGTCGGGATTTATAAGGGTG 58.237 52.381 0.00 0.00 0.00 4.61
5286 5788 3.497763 CGGGATTTATAAGGGTGCATCCA 60.498 47.826 20.62 0.00 38.11 3.41
5294 5796 2.413142 GGGTGCATCCAAGCAGAGC 61.413 63.158 12.38 0.00 46.69 4.09
5321 5823 3.213206 ACCAGCAATTTCAGAGACACA 57.787 42.857 0.00 0.00 0.00 3.72
5323 5825 3.316308 ACCAGCAATTTCAGAGACACAAC 59.684 43.478 0.00 0.00 0.00 3.32
5327 5829 4.044426 GCAATTTCAGAGACACAACAACC 58.956 43.478 0.00 0.00 0.00 3.77
5382 5886 2.514510 ATACCGCACCATGTCGCACA 62.515 55.000 4.67 0.00 0.00 4.57
5403 5907 2.549754 ACTCTGTTCAGAAAATGTGCCG 59.450 45.455 4.09 0.00 0.00 5.69
5576 6081 6.573664 ATCATGACTACAGTAGCAGAGATC 57.426 41.667 7.57 0.00 0.00 2.75
5615 6120 6.172136 ACTAGCATAGCAGATGAACAGATT 57.828 37.500 2.96 0.00 44.39 2.40
5628 6133 5.894298 TGAACAGATTACATCTAGGGCAT 57.106 39.130 0.00 0.00 37.58 4.40
5771 6276 0.830866 AGGTCGGGGAAGAAGTCGTT 60.831 55.000 0.00 0.00 0.00 3.85
5809 6314 2.355126 CAGCAGTCGCACGAGTGT 60.355 61.111 24.22 11.78 44.85 3.55
5913 6418 0.322456 CACGCCAAAAGGAGGGATGA 60.322 55.000 0.00 0.00 0.00 2.92
5919 6424 3.359950 CCAAAAGGAGGGATGAAGAAGG 58.640 50.000 0.00 0.00 0.00 3.46
5920 6425 3.245407 CCAAAAGGAGGGATGAAGAAGGT 60.245 47.826 0.00 0.00 0.00 3.50
5927 6432 4.567747 GGAGGGATGAAGAAGGTTTGCTTA 60.568 45.833 0.00 0.00 0.00 3.09
5948 6453 1.089112 CAGCGCAATGATCTGGAACA 58.911 50.000 11.47 0.00 0.00 3.18
5990 6495 2.117156 GCGACGGCTAGGGTAGACA 61.117 63.158 0.00 0.00 31.54 3.41
5995 6500 1.214673 ACGGCTAGGGTAGACATCTGA 59.785 52.381 0.00 0.00 31.54 3.27
6057 6562 1.514228 CACGTCCGAGTCATCACGG 60.514 63.158 9.54 0.00 46.29 4.94
6168 6673 2.878406 AGACAACGTGCATAGCTTTGTT 59.122 40.909 6.03 0.00 31.03 2.83
6234 6763 4.541648 GGCGGGCCTAGGAGGAGA 62.542 72.222 14.75 0.00 37.67 3.71
6270 6799 4.527816 GGTCTCCTCTTCTCATGCTCATAT 59.472 45.833 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.882415 ACAGAGTTCAACTAATTAGAAAACGA 57.118 30.769 19.38 5.02 0.00 3.85
83 86 6.042143 AGTGCAAAGAACATTTCAAACGAAT 58.958 32.000 0.00 0.00 0.00 3.34
275 298 1.078426 GGCGGTAGGCTGTGTGATT 60.078 57.895 0.00 0.00 42.94 2.57
312 337 1.522569 GCTCTGGCGGTAGGTTCAT 59.477 57.895 0.00 0.00 0.00 2.57
393 419 3.581332 CTGTTTAACCCTACCACCAGAGA 59.419 47.826 0.00 0.00 0.00 3.10
411 437 3.717294 CCCTGGCGGTAGGCTGTT 61.717 66.667 0.00 0.00 44.18 3.16
429 455 1.875488 AAGTACCCTACCGCCAGATT 58.125 50.000 0.00 0.00 0.00 2.40
590 621 7.649533 TTGCAATACAAATTCAGGATCTGAT 57.350 32.000 0.00 0.00 36.41 2.90
617 648 3.453424 GCCAAATTTCGTGTTTTGACCT 58.547 40.909 7.82 0.00 35.34 3.85
640 671 4.532834 GAGAATGAGAGGAGTGGAGTACT 58.467 47.826 0.00 0.00 44.02 2.73
641 672 3.634910 GGAGAATGAGAGGAGTGGAGTAC 59.365 52.174 0.00 0.00 0.00 2.73
642 673 3.373220 GGGAGAATGAGAGGAGTGGAGTA 60.373 52.174 0.00 0.00 0.00 2.59
651 682 0.758123 GGCAGAGGGAGAATGAGAGG 59.242 60.000 0.00 0.00 0.00 3.69
663 694 1.439679 GTTACGGAACAAGGCAGAGG 58.560 55.000 5.39 0.00 35.48 3.69
726 757 2.202892 GAATGGGGCGGAGTCGAC 60.203 66.667 7.70 7.70 45.30 4.20
727 758 3.467226 GGAATGGGGCGGAGTCGA 61.467 66.667 0.00 0.00 39.00 4.20
728 759 4.891727 CGGAATGGGGCGGAGTCG 62.892 72.222 0.00 0.00 39.81 4.18
750 781 1.725557 GCTCACGGCGTCTCTGGATA 61.726 60.000 10.85 0.00 0.00 2.59
852 890 2.745037 GTGGTGGTAGTGCCGGAA 59.255 61.111 5.05 0.00 41.21 4.30
873 914 2.844946 GAGGCTTCCTCCTATTCTTGC 58.155 52.381 1.44 0.00 44.36 4.01
915 956 0.654683 GGCGTCGTCGTATGTAGAGT 59.345 55.000 3.66 0.00 39.49 3.24
916 957 0.935898 AGGCGTCGTCGTATGTAGAG 59.064 55.000 3.66 0.00 39.49 2.43
917 958 0.933097 GAGGCGTCGTCGTATGTAGA 59.067 55.000 3.66 0.00 39.49 2.59
919 960 0.744057 TGGAGGCGTCGTCGTATGTA 60.744 55.000 3.66 0.00 39.49 2.29
920 961 2.042259 TGGAGGCGTCGTCGTATGT 61.042 57.895 3.66 0.00 39.49 2.29
921 962 1.585521 GTGGAGGCGTCGTCGTATG 60.586 63.158 3.66 0.00 39.49 2.39
922 963 2.042259 TGTGGAGGCGTCGTCGTAT 61.042 57.895 3.66 0.00 39.49 3.06
923 964 2.669229 TGTGGAGGCGTCGTCGTA 60.669 61.111 3.66 0.00 39.49 3.43
930 986 2.172483 GATGTGGAGTGTGGAGGCGT 62.172 60.000 0.00 0.00 0.00 5.68
931 987 1.448540 GATGTGGAGTGTGGAGGCG 60.449 63.158 0.00 0.00 0.00 5.52
932 988 1.078143 GGATGTGGAGTGTGGAGGC 60.078 63.158 0.00 0.00 0.00 4.70
935 991 1.078823 ACCTAGGATGTGGAGTGTGGA 59.921 52.381 17.98 0.00 0.00 4.02
948 1004 2.026542 TCACACTCGCTTCTACCTAGGA 60.027 50.000 17.98 0.00 0.00 2.94
954 1010 0.985549 CGCTTCACACTCGCTTCTAC 59.014 55.000 0.00 0.00 0.00 2.59
955 1011 0.732880 GCGCTTCACACTCGCTTCTA 60.733 55.000 0.00 0.00 44.79 2.10
956 1012 2.024319 GCGCTTCACACTCGCTTCT 61.024 57.895 0.00 0.00 44.79 2.85
957 1013 2.472049 GCGCTTCACACTCGCTTC 59.528 61.111 0.00 0.00 44.79 3.86
958 1014 3.406361 CGCGCTTCACACTCGCTT 61.406 61.111 5.56 0.00 45.87 4.68
1009 1068 1.079405 CACCCCGCCGCGATATTAT 60.079 57.895 15.93 0.00 0.00 1.28
1010 1069 2.340809 CACCCCGCCGCGATATTA 59.659 61.111 15.93 0.00 0.00 0.98
1269 1372 1.000060 CTCACACGAACCCGAACCTAA 60.000 52.381 0.00 0.00 39.50 2.69
1271 1374 1.366366 CTCACACGAACCCGAACCT 59.634 57.895 0.00 0.00 39.50 3.50
1298 1401 7.872993 TGCCGAAGAAGAATATAAATCGAAGAT 59.127 33.333 0.00 0.00 45.12 2.40
1305 1408 8.682936 ATGAAGTGCCGAAGAAGAATATAAAT 57.317 30.769 0.00 0.00 0.00 1.40
1355 1489 8.122952 CCAATTTAGTGATTGATTACTCCGTTC 58.877 37.037 0.00 0.00 38.93 3.95
1357 1491 6.542370 CCCAATTTAGTGATTGATTACTCCGT 59.458 38.462 0.00 0.00 38.93 4.69
1368 1502 4.088634 TCTGCAAGCCCAATTTAGTGATT 58.911 39.130 0.00 0.00 0.00 2.57
1374 1508 2.625790 ACGTTTCTGCAAGCCCAATTTA 59.374 40.909 0.00 0.00 0.00 1.40
1394 1528 3.896648 TGCGAGGATCTGTTGAAAAAC 57.103 42.857 0.00 0.00 0.00 2.43
1402 1536 2.768253 TTTGACATGCGAGGATCTGT 57.232 45.000 0.00 0.00 0.00 3.41
1408 1542 1.818060 TCCCAAATTTGACATGCGAGG 59.182 47.619 19.86 9.33 0.00 4.63
1421 1555 7.397192 ACTCAGTAATAAACAAGCATCCCAAAT 59.603 33.333 0.00 0.00 0.00 2.32
1431 1565 6.474751 GGCGGTACTACTCAGTAATAAACAAG 59.525 42.308 0.00 0.00 38.98 3.16
1444 1578 3.879295 TGTGTATACAGGCGGTACTACTC 59.121 47.826 5.62 6.20 34.07 2.59
1445 1579 3.889815 TGTGTATACAGGCGGTACTACT 58.110 45.455 5.62 0.00 34.07 2.57
1446 1580 4.096984 AGTTGTGTATACAGGCGGTACTAC 59.903 45.833 5.62 5.32 38.23 2.73
1447 1581 4.096833 CAGTTGTGTATACAGGCGGTACTA 59.903 45.833 5.62 0.00 38.23 1.82
1448 1582 3.094572 AGTTGTGTATACAGGCGGTACT 58.905 45.455 5.62 1.34 38.23 2.73
1450 1584 2.417651 GCAGTTGTGTATACAGGCGGTA 60.418 50.000 5.62 0.00 38.23 4.02
1452 1586 1.006832 GCAGTTGTGTATACAGGCGG 58.993 55.000 5.62 1.86 38.23 6.13
1453 1587 1.660607 CTGCAGTTGTGTATACAGGCG 59.339 52.381 5.62 0.00 38.23 5.52
1456 1590 5.466728 ACAGAAACTGCAGTTGTGTATACAG 59.533 40.000 31.83 18.49 38.44 2.74
1458 1592 5.924475 ACAGAAACTGCAGTTGTGTATAC 57.076 39.130 31.83 18.78 38.44 1.47
1461 1595 6.816640 GGATATACAGAAACTGCAGTTGTGTA 59.183 38.462 34.77 34.77 40.00 2.90
1465 1599 7.268586 ACTAGGATATACAGAAACTGCAGTTG 58.731 38.462 31.73 22.42 38.44 3.16
1466 1600 7.425224 ACTAGGATATACAGAAACTGCAGTT 57.575 36.000 26.36 26.36 40.50 3.16
1486 1620 4.757657 ACACTGAGTCACTGTCACTACTAG 59.242 45.833 0.04 0.00 0.00 2.57
1506 1646 1.062880 TCGAAACAAAGGCGACAACAC 59.937 47.619 0.00 0.00 0.00 3.32
1507 1647 1.370609 TCGAAACAAAGGCGACAACA 58.629 45.000 0.00 0.00 0.00 3.33
1509 1649 2.011222 AGTTCGAAACAAAGGCGACAA 58.989 42.857 0.00 0.00 33.33 3.18
1510 1650 1.658994 AGTTCGAAACAAAGGCGACA 58.341 45.000 0.00 0.00 33.33 4.35
1551 1691 3.614150 GCAGCAATCGATCCGAGGTATTA 60.614 47.826 0.00 0.00 39.91 0.98
1569 1709 0.533491 TCCCAATCAAATGCAGCAGC 59.467 50.000 0.00 0.00 42.57 5.25
1570 1710 2.167693 ACATCCCAATCAAATGCAGCAG 59.832 45.455 0.00 0.00 0.00 4.24
1571 1711 2.166870 GACATCCCAATCAAATGCAGCA 59.833 45.455 0.00 0.00 0.00 4.41
1572 1712 2.797087 CGACATCCCAATCAAATGCAGC 60.797 50.000 0.00 0.00 0.00 5.25
1573 1713 2.684374 TCGACATCCCAATCAAATGCAG 59.316 45.455 0.00 0.00 0.00 4.41
1574 1714 2.720915 TCGACATCCCAATCAAATGCA 58.279 42.857 0.00 0.00 0.00 3.96
1575 1715 3.996150 ATCGACATCCCAATCAAATGC 57.004 42.857 0.00 0.00 0.00 3.56
1576 1716 7.428020 ACAAATATCGACATCCCAATCAAATG 58.572 34.615 0.00 0.00 0.00 2.32
1591 1731 8.094798 ACAAAGAAAGCACTAACAAATATCGA 57.905 30.769 0.00 0.00 0.00 3.59
1600 1740 7.871853 TCCAATAGAACAAAGAAAGCACTAAC 58.128 34.615 0.00 0.00 0.00 2.34
1651 1793 6.279513 TGATTTTGCAGGTAATTCGGAAAT 57.720 33.333 0.00 0.00 0.00 2.17
1653 1795 5.649557 CATGATTTTGCAGGTAATTCGGAA 58.350 37.500 0.00 0.00 0.00 4.30
1656 1798 4.675510 AGCATGATTTTGCAGGTAATTCG 58.324 39.130 0.00 0.00 45.23 3.34
1685 1837 0.676466 TGGGTCATCGCACCATCAAC 60.676 55.000 1.14 0.00 38.32 3.18
1692 1844 3.689649 ACTAGAAATTTGGGTCATCGCAC 59.310 43.478 0.00 0.00 36.27 5.34
1778 1930 0.464554 GCGATCCTTCCCCTTTGGAG 60.465 60.000 0.00 0.00 46.24 3.86
1793 1945 4.323792 CCTTCAGGGTCCAATATATGCGAT 60.324 45.833 0.00 0.00 0.00 4.58
1904 2056 2.080286 ATTCCGAAGTGTGAAGGTCG 57.920 50.000 0.00 0.00 0.00 4.79
1909 2061 4.513692 CACCAACTAATTCCGAAGTGTGAA 59.486 41.667 0.00 0.00 0.00 3.18
1915 2067 2.811431 TGCACACCAACTAATTCCGAAG 59.189 45.455 0.00 0.00 0.00 3.79
1965 2117 7.824672 AGAGAATTGACAAACCAAGATCATTC 58.175 34.615 0.00 0.00 0.00 2.67
2020 2175 3.114809 CTGCTTGTTCTATCAGAGCTCG 58.885 50.000 8.37 3.55 34.56 5.03
2245 2400 9.541884 ACTGGAAAAACCCTAATAAACATGTAT 57.458 29.630 0.00 0.00 38.00 2.29
2253 2408 7.710579 TCCCAATACTGGAAAAACCCTAATAA 58.289 34.615 0.00 0.00 46.92 1.40
2286 2447 0.109643 CATTGACGCACCACCACATG 60.110 55.000 0.00 0.00 0.00 3.21
2287 2448 1.243342 CCATTGACGCACCACCACAT 61.243 55.000 0.00 0.00 0.00 3.21
2288 2449 1.896183 CCATTGACGCACCACCACA 60.896 57.895 0.00 0.00 0.00 4.17
2289 2450 0.960364 ATCCATTGACGCACCACCAC 60.960 55.000 0.00 0.00 0.00 4.16
2290 2451 0.251121 AATCCATTGACGCACCACCA 60.251 50.000 0.00 0.00 0.00 4.17
2291 2452 0.887933 AAATCCATTGACGCACCACC 59.112 50.000 0.00 0.00 0.00 4.61
2292 2453 1.812571 AGAAATCCATTGACGCACCAC 59.187 47.619 0.00 0.00 0.00 4.16
2299 2460 5.669477 AGTCAGAGCTAGAAATCCATTGAC 58.331 41.667 0.00 0.00 34.24 3.18
2349 2541 3.814005 ATAACAGTTAACGGGCGATCT 57.186 42.857 10.55 0.00 0.00 2.75
2353 2545 2.286025 GCCTTATAACAGTTAACGGGCG 59.714 50.000 10.55 0.00 0.00 6.13
2395 2587 8.679100 CATCCGGGACAGTGTTATTTTTATTTA 58.321 33.333 0.00 0.00 0.00 1.40
2398 2590 6.419791 TCATCCGGGACAGTGTTATTTTTAT 58.580 36.000 0.00 0.00 0.00 1.40
2399 2591 5.806818 TCATCCGGGACAGTGTTATTTTTA 58.193 37.500 0.00 0.00 0.00 1.52
2400 2592 4.658063 TCATCCGGGACAGTGTTATTTTT 58.342 39.130 0.00 0.00 0.00 1.94
2401 2593 4.295141 TCATCCGGGACAGTGTTATTTT 57.705 40.909 0.00 0.00 0.00 1.82
2402 2594 3.992943 TCATCCGGGACAGTGTTATTT 57.007 42.857 0.00 0.00 0.00 1.40
2405 2597 2.462723 TCATCATCCGGGACAGTGTTA 58.537 47.619 0.00 0.00 0.00 2.41
2406 2598 1.275666 TCATCATCCGGGACAGTGTT 58.724 50.000 0.00 0.00 0.00 3.32
2415 2616 4.199310 ACTAACCAAACATCATCATCCGG 58.801 43.478 0.00 0.00 0.00 5.14
2449 2650 8.867097 AGGATATATTTGCTTGCTTGATTGATT 58.133 29.630 0.00 0.00 0.00 2.57
2450 2651 8.418597 AGGATATATTTGCTTGCTTGATTGAT 57.581 30.769 0.00 0.00 0.00 2.57
2451 2652 7.828508 AGGATATATTTGCTTGCTTGATTGA 57.171 32.000 0.00 0.00 0.00 2.57
2452 2653 9.970395 TTTAGGATATATTTGCTTGCTTGATTG 57.030 29.630 0.00 0.00 0.00 2.67
2536 2769 5.866335 TTTGACTTGTGACACGTTTACTT 57.134 34.783 0.22 0.00 0.00 2.24
2567 2862 5.335127 CGCTTATTTTGAAGATGTTGGAGG 58.665 41.667 0.00 0.00 0.00 4.30
2625 3040 1.043816 AGCATGGGTATGTCTCCGAG 58.956 55.000 0.00 0.00 36.65 4.63
2647 3062 2.717639 AGGAGCAACACCATCATACC 57.282 50.000 0.00 0.00 0.00 2.73
2652 3067 5.814705 GCATATATCTAGGAGCAACACCATC 59.185 44.000 0.00 0.00 0.00 3.51
2677 3092 8.954350 CAGGATATCCAGATAAAATAAGCAAGG 58.046 37.037 23.81 0.00 38.89 3.61
2824 3299 0.326264 GGGCTTCCAGCTTCTCAAGA 59.674 55.000 0.00 0.00 41.99 3.02
2850 3325 6.206829 ACTCCAAACATTAGACAAAAGTAGGC 59.793 38.462 0.00 0.00 0.00 3.93
2863 3338 3.640967 AGCCTGCAAAACTCCAAACATTA 59.359 39.130 0.00 0.00 0.00 1.90
2930 3405 5.175090 TGTCACAGCTCATAGAGATAACG 57.825 43.478 0.00 0.00 0.00 3.18
2933 3408 6.966534 TCATTGTCACAGCTCATAGAGATA 57.033 37.500 0.00 0.00 0.00 1.98
3049 3524 2.170187 ACCTGACAGAGCTCAATGGATC 59.830 50.000 17.77 4.39 0.00 3.36
3071 3554 9.982651 CACTAATAACAGTAGCATATAGTTGGT 57.017 33.333 0.00 0.00 0.00 3.67
3235 3725 9.372369 GCTATATACAGGAAATAACTAGCAAGG 57.628 37.037 0.00 0.00 31.65 3.61
3261 3751 8.307582 TCAACTAGGGGAGAATTAGTTTCTAG 57.692 38.462 0.00 0.00 44.88 2.43
3420 3910 4.840772 CAGTTAAGTTCGAAAATGTGCTCG 59.159 41.667 0.00 0.00 36.39 5.03
3433 3923 9.846248 ATCTAATGCATTTTGACAGTTAAGTTC 57.154 29.630 18.75 0.00 0.00 3.01
3435 3925 8.796475 ACATCTAATGCATTTTGACAGTTAAGT 58.204 29.630 18.75 4.05 0.00 2.24
3441 3931 4.802039 GCCACATCTAATGCATTTTGACAG 59.198 41.667 18.75 8.55 0.00 3.51
3448 3938 2.380941 TGCTGCCACATCTAATGCATT 58.619 42.857 17.56 17.56 32.53 3.56
3454 3944 6.772360 TCATTTTATTGCTGCCACATCTAA 57.228 33.333 0.00 0.00 0.00 2.10
3464 3954 8.969121 TTGTACTGTTGATCATTTTATTGCTG 57.031 30.769 0.00 0.00 0.00 4.41
3487 3977 9.925268 GCTTTCCATTTTGCAAGATTATTATTG 57.075 29.630 0.00 0.00 0.00 1.90
3566 4056 2.158623 AGGACAGTGTGCAATGAAAGGA 60.159 45.455 17.69 0.00 0.00 3.36
3588 4078 8.969260 ATCTGATCACTTGCAATCTATAAACA 57.031 30.769 0.00 0.00 0.00 2.83
3596 4086 4.497674 GCTTGGATCTGATCACTTGCAATC 60.498 45.833 18.64 5.98 0.00 2.67
3621 4111 1.131504 GGCACGGTGATTAAATCGCAA 59.868 47.619 13.29 0.00 41.46 4.85
3636 4126 6.312399 TGCAATAATTAAGGATAAGGCACG 57.688 37.500 0.00 0.00 0.00 5.34
3642 4132 8.500753 ACACGTCTTGCAATAATTAAGGATAA 57.499 30.769 0.00 0.00 0.00 1.75
3650 4140 7.931407 TCCAGATATACACGTCTTGCAATAATT 59.069 33.333 0.00 0.00 0.00 1.40
3802 4296 1.750778 CAGGCACCATAAATGTCACCC 59.249 52.381 0.00 0.00 0.00 4.61
3854 4348 5.591877 AGAAAAATGGTAGCATCAGGACATC 59.408 40.000 8.07 1.13 0.00 3.06
3891 4385 3.648339 ACACGAATTTGCAGCAGAATT 57.352 38.095 12.57 12.57 0.00 2.17
3898 4392 7.352739 GGATTATTACCTACACGAATTTGCAG 58.647 38.462 0.00 0.00 0.00 4.41
3934 4428 7.749570 CACAAATCTCTGACAGCTTTCAAATAG 59.250 37.037 3.79 2.63 0.00 1.73
4100 4594 3.057456 GGTACTTGTGAAGCGAGAAGAGA 60.057 47.826 0.00 0.00 32.82 3.10
4139 4633 9.010029 GTAGTAGAAGAGGAGATAAATGGAGAG 57.990 40.741 0.00 0.00 0.00 3.20
4178 4672 1.752498 ACAAAACGAAAACCTCACCCC 59.248 47.619 0.00 0.00 0.00 4.95
4208 4702 7.624360 TGTCAAAAATCAGAACTGTAGTTGT 57.376 32.000 1.35 0.00 38.56 3.32
4302 4796 1.160137 GCATGATATCCTTGTCCGCC 58.840 55.000 0.00 0.00 0.00 6.13
4308 4802 6.348295 GCTTGATACACAGCATGATATCCTTG 60.348 42.308 0.00 0.00 39.69 3.61
4335 4829 1.351017 TCACACCTTCCATGTTCTCCC 59.649 52.381 0.00 0.00 0.00 4.30
4379 4873 7.653311 ACATTTAACTTGCTTTGGAATGAACTC 59.347 33.333 0.00 0.00 0.00 3.01
4453 4948 4.056050 GTGTGATGGTCAAAACTAGACGT 58.944 43.478 0.00 0.00 36.87 4.34
4569 5064 6.484977 TGTACTGCATTTGATCAAGTGTAACA 59.515 34.615 26.05 21.14 41.43 2.41
4585 5080 3.258123 GGTTTCCACCAAATGTACTGCAT 59.742 43.478 0.00 0.00 43.61 3.96
4784 5279 0.251653 ACTCCTGACCTAACTCCGCA 60.252 55.000 0.00 0.00 0.00 5.69
4823 5318 4.138487 ACGAGGAAACTTCTGTTGAACT 57.862 40.909 0.00 0.00 44.43 3.01
4843 5338 6.014840 TCTCCCACGTATTTCCCTGATAATAC 60.015 42.308 0.00 0.00 35.09 1.89
4901 5396 1.270571 GCAGAAGCAGGGTATAGAGCC 60.271 57.143 0.00 0.00 44.20 4.70
5009 5504 2.624838 GGCAAATGGGTCATACCTGATG 59.375 50.000 0.00 0.00 38.64 3.07
5087 5582 3.972706 GCGAACGCGATCACATAATAT 57.027 42.857 15.93 0.00 40.82 1.28
5101 5596 0.742990 TGGGGATTAGCAAGCGAACG 60.743 55.000 0.00 0.00 0.00 3.95
5227 5722 2.678336 GACTGGTATTTTTGCCTCCGAG 59.322 50.000 0.00 0.00 0.00 4.63
5241 5736 1.749063 CGCACCTATCACAGACTGGTA 59.251 52.381 7.51 0.00 0.00 3.25
5251 5746 1.046472 AATCCCGACCGCACCTATCA 61.046 55.000 0.00 0.00 0.00 2.15
5279 5774 0.392595 CTCAGCTCTGCTTGGATGCA 60.393 55.000 0.00 0.00 36.40 3.96
5280 5775 1.096386 CCTCAGCTCTGCTTGGATGC 61.096 60.000 0.00 0.00 36.40 3.91
5286 5788 0.901124 CTGGTACCTCAGCTCTGCTT 59.099 55.000 14.36 0.00 36.40 3.91
5294 5796 3.937706 CTCTGAAATTGCTGGTACCTCAG 59.062 47.826 14.36 15.08 37.79 3.35
5382 5886 2.549754 CGGCACATTTTCTGAACAGAGT 59.450 45.455 4.72 0.00 38.88 3.24
5576 6081 5.469373 TGCTAGTTTGCATGATTAGTTCG 57.531 39.130 0.00 0.00 38.12 3.95
5615 6120 9.769677 ATGTTTCTAGTATATGCCCTAGATGTA 57.230 33.333 8.54 0.00 39.40 2.29
5663 6168 7.834881 ACCGTATGTGATTCTATCTTTCCTA 57.165 36.000 0.00 0.00 0.00 2.94
5718 6223 2.024868 CGACGACATGGGCGACAAA 61.025 57.895 15.69 0.00 0.00 2.83
5771 6276 1.590525 AGCGACGACTTTGCGAACA 60.591 52.632 0.00 0.00 40.01 3.18
5809 6314 1.886222 CGATCAGGTTTTTGGGGAGCA 60.886 52.381 0.00 0.00 0.00 4.26
5900 6405 4.749048 AACCTTCTTCATCCCTCCTTTT 57.251 40.909 0.00 0.00 0.00 2.27
5927 6432 0.393402 TTCCAGATCATTGCGCTGCT 60.393 50.000 9.73 0.00 0.00 4.24
5966 6471 3.896133 CCTAGCCGTCGCCGCTTA 61.896 66.667 1.26 0.00 34.57 3.09
5990 6495 5.394663 GCCCGCATTATATAGTCAGTCAGAT 60.395 44.000 0.00 0.00 0.00 2.90
5995 6500 2.094182 CGGCCCGCATTATATAGTCAGT 60.094 50.000 0.00 0.00 0.00 3.41
6057 6562 3.497262 AGTCGTTTCCGATTCTTTTGGAC 59.503 43.478 0.00 0.00 46.30 4.02
6168 6673 2.786495 GGATTGAGCCGAGCCGAGA 61.786 63.158 0.00 0.00 0.00 4.04
6221 6726 3.133946 CGCTTCTCCTCCTAGGCC 58.866 66.667 2.96 0.00 34.61 5.19
6225 6730 3.889044 CGCGCGCTTCTCCTCCTA 61.889 66.667 30.48 0.00 0.00 2.94
6234 6763 2.048503 AGACCTAAACGCGCGCTT 60.049 55.556 32.58 27.35 0.00 4.68
6244 6773 3.957497 GAGCATGAGAAGAGGAGACCTAA 59.043 47.826 0.00 0.00 31.76 2.69


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

AutoCloner maintained by Alex Coulton.