Multiple sequence alignment - TraesCS2A01G104900

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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 TraesCS2A01G104900 chr2A 100.000 3720 0 0 1 3720 57888089 57891808 0.000000e+00 6870.0
1 TraesCS2A01G104900 chr2A 81.679 655 84 15 2099 2723 57865528 57866176 2.560000e-141 512.0
2 TraesCS2A01G104900 chr2A 94.872 78 4 0 1389 1466 57889554 57889477 5.050000e-24 122.0
3 TraesCS2A01G104900 chr2A 95.652 46 2 0 1383 1428 394582949 394582904 1.430000e-09 75.0
4 TraesCS2A01G104900 chr2B 87.757 972 65 22 2064 3009 89432519 89433462 0.000000e+00 1086.0
5 TraesCS2A01G104900 chr2B 89.762 547 39 8 695 1234 89430905 89431441 0.000000e+00 684.0
6 TraesCS2A01G104900 chr2B 82.669 652 80 16 2099 2723 89327560 89328205 7.020000e-152 547.0
7 TraesCS2A01G104900 chr2B 84.192 563 52 10 2 536 89430195 89430748 2.560000e-141 512.0
8 TraesCS2A01G104900 chr2B 86.640 247 19 3 3048 3286 89433458 89433698 1.020000e-65 261.0
9 TraesCS2A01G104900 chr2B 91.398 186 3 4 1668 1840 89432028 89432213 3.710000e-60 243.0
10 TraesCS2A01G104900 chr2B 93.878 147 7 1 523 669 89430766 89430910 1.740000e-53 220.0
11 TraesCS2A01G104900 chr2B 90.741 162 15 0 3559 3720 89433944 89434105 2.250000e-52 217.0
12 TraesCS2A01G104900 chr2B 91.057 123 4 4 1926 2046 89432418 89432535 3.850000e-35 159.0
13 TraesCS2A01G104900 chr2B 85.915 142 18 2 3559 3699 89329091 89329231 2.310000e-32 150.0
14 TraesCS2A01G104900 chr2B 84.722 72 9 2 1 70 699213420 699213349 1.850000e-08 71.3
15 TraesCS2A01G104900 chr2D 91.061 716 33 15 695 1388 56297685 56298391 0.000000e+00 939.0
16 TraesCS2A01G104900 chr2D 90.393 687 36 7 2075 2743 56446996 56447670 0.000000e+00 876.0
17 TraesCS2A01G104900 chr2D 88.295 692 48 14 1 669 56444860 56445541 0.000000e+00 798.0
18 TraesCS2A01G104900 chr2D 87.954 689 42 11 695 1350 56445536 56446216 0.000000e+00 774.0
19 TraesCS2A01G104900 chr2D 87.606 710 28 20 2064 2752 56299059 56299729 0.000000e+00 769.0
20 TraesCS2A01G104900 chr2D 87.013 693 55 15 1 669 56297009 56297690 0.000000e+00 749.0
21 TraesCS2A01G104900 chr2D 91.270 504 34 3 2785 3286 56299718 56300213 0.000000e+00 678.0
22 TraesCS2A01G104900 chr2D 92.381 420 17 7 1474 1880 56298390 56298807 5.350000e-163 584.0
23 TraesCS2A01G104900 chr2D 82.470 656 83 17 2099 2723 56255256 56255910 2.530000e-151 545.0
24 TraesCS2A01G104900 chr2D 82.059 680 82 15 2074 2723 56321366 56322035 9.090000e-151 544.0
25 TraesCS2A01G104900 chr2D 96.073 331 11 2 1491 1819 56446241 56446571 4.230000e-149 538.0
26 TraesCS2A01G104900 chr2D 83.202 506 54 10 2796 3286 56301465 56301954 5.710000e-118 435.0
27 TraesCS2A01G104900 chr2D 91.388 209 10 2 3047 3247 56450056 56450264 2.830000e-71 279.0
28 TraesCS2A01G104900 chr2D 88.272 162 9 7 1893 2046 56298916 56299075 6.340000e-43 185.0
29 TraesCS2A01G104900 chr2D 85.890 163 20 3 3559 3718 56302197 56302359 1.780000e-38 171.0
30 TraesCS2A01G104900 chr2D 93.976 83 5 0 3638 3720 56456703 56456785 3.900000e-25 126.0
31 TraesCS2A01G104900 chr2D 90.385 52 3 2 1426 1477 313224863 313224912 2.400000e-07 67.6
32 TraesCS2A01G104900 chr2D 90.000 50 5 0 1893 1942 56446872 56446921 8.620000e-07 65.8
33 TraesCS2A01G104900 chr1D 79.500 200 35 3 1041 1234 6278221 6278022 1.800000e-28 137.0
34 TraesCS2A01G104900 chr6B 86.087 115 16 0 3428 3542 477699969 477700083 1.400000e-24 124.0
35 TraesCS2A01G104900 chr3B 93.827 81 5 0 1386 1466 734140651 734140731 5.050000e-24 122.0
36 TraesCS2A01G104900 chr6A 86.111 108 15 0 3428 3535 446528111 446528218 2.350000e-22 117.0
37 TraesCS2A01G104900 chr6A 82.828 99 4 6 1380 1466 617583813 617583910 3.980000e-10 76.8
38 TraesCS2A01G104900 chr6A 97.561 41 1 0 1426 1466 617583861 617583821 1.850000e-08 71.3
39 TraesCS2A01G104900 chr6A 85.246 61 7 2 1426 1486 74162176 74162234 1.120000e-05 62.1
40 TraesCS2A01G104900 chr6D 82.828 99 17 0 3427 3525 309727967 309728065 5.120000e-14 89.8
41 TraesCS2A01G104900 chr7D 79.851 134 16 8 380 503 104945863 104945731 1.840000e-13 87.9
42 TraesCS2A01G104900 chr5B 89.855 69 5 1 3430 3496 289272013 289272081 1.840000e-13 87.9
43 TraesCS2A01G104900 chr3A 97.727 44 1 0 1382 1425 481522200 481522243 3.980000e-10 76.8
44 TraesCS2A01G104900 chr5A 95.652 46 2 0 1383 1428 635663192 635663147 1.430000e-09 75.0
45 TraesCS2A01G104900 chr3D 97.674 43 1 0 1386 1428 98597687 98597729 1.430000e-09 75.0
46 TraesCS2A01G104900 chr3D 90.741 54 4 1 1376 1428 28843816 28843763 1.850000e-08 71.3
47 TraesCS2A01G104900 chr4B 97.619 42 1 0 1384 1425 673200875 673200916 5.150000e-09 73.1
48 TraesCS2A01G104900 chrUn 97.561 41 1 0 1426 1466 51465525 51465565 1.850000e-08 71.3
49 TraesCS2A01G104900 chrUn 97.561 41 1 0 1426 1466 245959497 245959457 1.850000e-08 71.3
50 TraesCS2A01G104900 chr4A 92.000 50 3 1 1426 1475 744042559 744042511 6.670000e-08 69.4
51 TraesCS2A01G104900 chr4D 93.478 46 2 1 1426 1471 28421705 28421749 2.400000e-07 67.6
52 TraesCS2A01G104900 chr7B 97.222 36 1 0 380 415 63634824 63634789 1.120000e-05 62.1
53 TraesCS2A01G104900 chr1B 100.000 31 0 0 503 533 635155759 635155789 1.440000e-04 58.4


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 TraesCS2A01G104900 chr2A 57888089 57891808 3719 False 6870.000000 6870 100.000000 1 3720 1 chr2A.!!$F2 3719
1 TraesCS2A01G104900 chr2A 57865528 57866176 648 False 512.000000 512 81.679000 2099 2723 1 chr2A.!!$F1 624
2 TraesCS2A01G104900 chr2B 89430195 89434105 3910 False 422.750000 1086 89.428125 2 3720 8 chr2B.!!$F2 3718
3 TraesCS2A01G104900 chr2B 89327560 89329231 1671 False 348.500000 547 84.292000 2099 3699 2 chr2B.!!$F1 1600
4 TraesCS2A01G104900 chr2D 56297009 56302359 5350 False 563.750000 939 88.336875 1 3718 8 chr2D.!!$F5 3717
5 TraesCS2A01G104900 chr2D 56444860 56450264 5404 False 555.133333 876 90.683833 1 3247 6 chr2D.!!$F6 3246
6 TraesCS2A01G104900 chr2D 56255256 56255910 654 False 545.000000 545 82.470000 2099 2723 1 chr2D.!!$F1 624
7 TraesCS2A01G104900 chr2D 56321366 56322035 669 False 544.000000 544 82.059000 2074 2723 1 chr2D.!!$F2 649

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
805 871 0.244994 ATCGATCTACCATGGCGAGC 59.755 55.0 13.04 10.73 34.25 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2766 5583 0.170116 ATTGCGCCGTGTGTTAATGG 59.83 50.0 4.18 0.0 0.0 3.16 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
40 42 1.872197 GCCACAGAGACGAGCAGACT 61.872 60.000 0.00 0.00 0.00 3.24
76 78 1.608283 GGAAGGCACACGAAAGCTAGT 60.608 52.381 0.00 0.00 0.00 2.57
77 79 2.353406 GGAAGGCACACGAAAGCTAGTA 60.353 50.000 0.00 0.00 0.00 1.82
119 122 1.289109 GGCGCTGTTACGAGCTTTCA 61.289 55.000 7.64 0.00 36.77 2.69
146 149 9.198475 TCCTACTTATTACTTCTGGTCCTAAAG 57.802 37.037 0.00 0.00 0.00 1.85
181 184 5.724854 ACATTAACTAGCCCTTCTCCTAACA 59.275 40.000 0.00 0.00 0.00 2.41
194 197 2.420022 CTCCTAACATGCAAAAGACCCG 59.580 50.000 0.00 0.00 0.00 5.28
343 354 7.850193 AGGTGGATATTTTGCATGTATGTTTT 58.150 30.769 0.00 0.00 0.00 2.43
344 355 8.320617 AGGTGGATATTTTGCATGTATGTTTTT 58.679 29.630 0.00 0.00 0.00 1.94
347 358 8.316946 TGGATATTTTGCATGTATGTTTTTGGA 58.683 29.630 0.00 0.00 0.00 3.53
362 373 7.366847 TGTTTTTGGAATTGGTAAATCTCCA 57.633 32.000 0.00 0.00 34.20 3.86
377 388 6.723298 AAATCTCCATCGACTGAGACTTAT 57.277 37.500 15.71 0.70 40.23 1.73
378 389 7.825331 AAATCTCCATCGACTGAGACTTATA 57.175 36.000 15.71 0.00 40.23 0.98
613 679 6.199937 TCAACAAACGGTAGGAGTATAGTC 57.800 41.667 0.00 0.00 0.00 2.59
669 735 2.331893 CCATTTTGCGACCGAGCCA 61.332 57.895 0.00 0.00 36.02 4.75
670 736 1.154225 CATTTTGCGACCGAGCCAC 60.154 57.895 0.00 0.00 36.02 5.01
671 737 2.677003 ATTTTGCGACCGAGCCACG 61.677 57.895 0.00 0.00 42.18 4.94
672 738 4.595538 TTTGCGACCGAGCCACGT 62.596 61.111 0.00 0.00 40.78 4.49
677 743 4.736896 GACCGAGCCACGTCCCAC 62.737 72.222 0.00 0.00 40.78 4.61
689 755 3.366915 TCCCACGACGATGCACGA 61.367 61.111 14.18 0.00 45.77 4.35
690 756 2.880879 CCCACGACGATGCACGAG 60.881 66.667 14.18 10.14 45.77 4.18
691 757 2.178273 CCACGACGATGCACGAGA 59.822 61.111 14.18 0.00 45.77 4.04
692 758 1.869574 CCACGACGATGCACGAGAG 60.870 63.158 14.18 7.94 45.77 3.20
693 759 1.134694 CACGACGATGCACGAGAGA 59.865 57.895 14.18 0.00 45.77 3.10
694 760 1.128724 CACGACGATGCACGAGAGAC 61.129 60.000 14.18 2.07 45.77 3.36
695 761 1.930188 CGACGATGCACGAGAGACG 60.930 63.158 14.18 0.00 45.77 4.18
696 762 1.424240 GACGATGCACGAGAGACGA 59.576 57.895 14.18 0.00 45.77 4.20
697 763 0.587737 GACGATGCACGAGAGACGAG 60.588 60.000 14.18 0.00 45.77 4.18
702 768 4.838486 CACGAGAGACGAGCCGGC 62.838 72.222 21.89 21.89 45.77 6.13
704 770 4.544689 CGAGAGACGAGCCGGCAG 62.545 72.222 31.54 24.30 45.77 4.85
705 771 4.863925 GAGAGACGAGCCGGCAGC 62.864 72.222 31.54 19.39 37.34 5.25
803 869 1.000274 CACATCGATCTACCATGGCGA 60.000 52.381 13.04 12.90 35.32 5.54
805 871 0.244994 ATCGATCTACCATGGCGAGC 59.755 55.000 13.04 10.73 34.25 5.03
809 875 2.972589 ATCTACCATGGCGAGCCCCT 62.973 60.000 13.04 0.00 34.56 4.79
838 911 2.183555 CCGTAGCTCCACGTTCCC 59.816 66.667 8.15 0.00 40.31 3.97
885 958 1.517475 GTCTCGCTCGCCTTTCTCC 60.517 63.158 0.00 0.00 0.00 3.71
890 963 1.355066 CGCTCGCCTTTCTCCAACTC 61.355 60.000 0.00 0.00 0.00 3.01
901 974 1.978580 TCTCCAACTCTTCCTCCCAAC 59.021 52.381 0.00 0.00 0.00 3.77
912 985 1.738099 CTCCCAACTTCTCACCGCG 60.738 63.158 0.00 0.00 0.00 6.46
975 1048 1.130054 AGCAAGCCCTGTTCTCCAGA 61.130 55.000 0.00 0.00 44.49 3.86
983 1056 2.383855 CCTGTTCTCCAGACCCTCTAG 58.616 57.143 0.00 0.00 44.49 2.43
1130 1207 2.147387 AGGGGTCGCCAAGAGTGTT 61.147 57.895 8.89 0.00 0.00 3.32
1201 1278 1.019278 CGCTATGTCGGTGTTTGGCT 61.019 55.000 0.00 0.00 0.00 4.75
1230 1310 2.932234 CGGTGTGGAGGCGTCTTCT 61.932 63.158 6.34 0.00 0.00 2.85
1250 1357 2.102925 CTGGGAGGAAGAAGAGATCAGC 59.897 54.545 0.00 0.00 0.00 4.26
1388 1542 9.654663 AAATTATTATCGCCTCCAACTATCTAC 57.345 33.333 0.00 0.00 0.00 2.59
1390 1544 5.961396 TTATCGCCTCCAACTATCTACTC 57.039 43.478 0.00 0.00 0.00 2.59
1391 1545 2.584236 TCGCCTCCAACTATCTACTCC 58.416 52.381 0.00 0.00 0.00 3.85
1393 1547 2.753507 CGCCTCCAACTATCTACTCCCT 60.754 54.545 0.00 0.00 0.00 4.20
1394 1548 2.894765 GCCTCCAACTATCTACTCCCTC 59.105 54.545 0.00 0.00 0.00 4.30
1395 1549 3.502356 CCTCCAACTATCTACTCCCTCC 58.498 54.545 0.00 0.00 0.00 4.30
1396 1550 3.150767 CTCCAACTATCTACTCCCTCCG 58.849 54.545 0.00 0.00 0.00 4.63
1397 1551 2.512896 TCCAACTATCTACTCCCTCCGT 59.487 50.000 0.00 0.00 0.00 4.69
1398 1552 3.053095 TCCAACTATCTACTCCCTCCGTT 60.053 47.826 0.00 0.00 0.00 4.44
1399 1553 3.705072 CCAACTATCTACTCCCTCCGTTT 59.295 47.826 0.00 0.00 0.00 3.60
1400 1554 4.441634 CCAACTATCTACTCCCTCCGTTTG 60.442 50.000 0.00 0.00 0.00 2.93
1401 1555 3.297736 ACTATCTACTCCCTCCGTTTGG 58.702 50.000 0.00 0.00 0.00 3.28
1402 1556 2.544844 ATCTACTCCCTCCGTTTGGA 57.455 50.000 0.00 0.00 43.88 3.53
1403 1557 2.314071 TCTACTCCCTCCGTTTGGAA 57.686 50.000 0.00 0.00 45.87 3.53
1404 1558 2.829023 TCTACTCCCTCCGTTTGGAAT 58.171 47.619 0.00 0.00 45.87 3.01
1405 1559 3.178865 TCTACTCCCTCCGTTTGGAATT 58.821 45.455 0.00 0.00 45.87 2.17
1406 1560 4.355549 TCTACTCCCTCCGTTTGGAATTA 58.644 43.478 0.00 0.00 45.87 1.40
1407 1561 3.345508 ACTCCCTCCGTTTGGAATTAC 57.654 47.619 0.00 0.00 45.87 1.89
1408 1562 2.910977 ACTCCCTCCGTTTGGAATTACT 59.089 45.455 0.00 0.00 45.87 2.24
1409 1563 3.329814 ACTCCCTCCGTTTGGAATTACTT 59.670 43.478 0.00 0.00 45.87 2.24
1410 1564 3.681593 TCCCTCCGTTTGGAATTACTTG 58.318 45.455 0.00 0.00 45.87 3.16
1411 1565 3.073356 TCCCTCCGTTTGGAATTACTTGT 59.927 43.478 0.00 0.00 45.87 3.16
1412 1566 3.439129 CCCTCCGTTTGGAATTACTTGTC 59.561 47.826 0.00 0.00 45.87 3.18
1413 1567 3.124636 CCTCCGTTTGGAATTACTTGTCG 59.875 47.826 0.00 0.00 45.87 4.35
1414 1568 2.481185 TCCGTTTGGAATTACTTGTCGC 59.519 45.455 0.00 0.00 42.85 5.19
1415 1569 2.492001 CGTTTGGAATTACTTGTCGCG 58.508 47.619 0.00 0.00 0.00 5.87
1416 1570 2.723618 CGTTTGGAATTACTTGTCGCGG 60.724 50.000 6.13 0.00 0.00 6.46
1417 1571 2.459060 TTGGAATTACTTGTCGCGGA 57.541 45.000 6.13 0.00 0.00 5.54
1418 1572 2.459060 TGGAATTACTTGTCGCGGAA 57.541 45.000 6.13 0.00 0.00 4.30
1419 1573 2.768698 TGGAATTACTTGTCGCGGAAA 58.231 42.857 6.13 0.00 0.00 3.13
1420 1574 3.340034 TGGAATTACTTGTCGCGGAAAT 58.660 40.909 6.13 0.00 0.00 2.17
1421 1575 3.126171 TGGAATTACTTGTCGCGGAAATG 59.874 43.478 6.13 0.00 0.00 2.32
1422 1576 3.486875 GGAATTACTTGTCGCGGAAATGG 60.487 47.826 6.13 0.00 0.00 3.16
1423 1577 2.459060 TTACTTGTCGCGGAAATGGA 57.541 45.000 6.13 0.00 0.00 3.41
1424 1578 2.684001 TACTTGTCGCGGAAATGGAT 57.316 45.000 6.13 0.00 0.00 3.41
1425 1579 2.684001 ACTTGTCGCGGAAATGGATA 57.316 45.000 6.13 0.00 0.00 2.59
1426 1580 3.194005 ACTTGTCGCGGAAATGGATAT 57.806 42.857 6.13 0.00 0.00 1.63
1427 1581 4.330944 ACTTGTCGCGGAAATGGATATA 57.669 40.909 6.13 0.00 0.00 0.86
1428 1582 4.056050 ACTTGTCGCGGAAATGGATATAC 58.944 43.478 6.13 0.00 0.00 1.47
1429 1583 3.737032 TGTCGCGGAAATGGATATACA 57.263 42.857 6.13 0.00 0.00 2.29
1430 1584 4.265904 TGTCGCGGAAATGGATATACAT 57.734 40.909 6.13 0.00 0.00 2.29
1431 1585 4.242475 TGTCGCGGAAATGGATATACATC 58.758 43.478 6.13 0.00 0.00 3.06
1443 1597 4.842139 GATATACATCCATTTCCGCGAC 57.158 45.455 8.23 0.00 0.00 5.19
1444 1598 2.613026 ATACATCCATTTCCGCGACA 57.387 45.000 8.23 0.00 0.00 4.35
1445 1599 2.388310 TACATCCATTTCCGCGACAA 57.612 45.000 8.23 0.00 0.00 3.18
1446 1600 1.086696 ACATCCATTTCCGCGACAAG 58.913 50.000 8.23 0.00 0.00 3.16
1447 1601 1.086696 CATCCATTTCCGCGACAAGT 58.913 50.000 8.23 0.00 0.00 3.16
1448 1602 2.276201 CATCCATTTCCGCGACAAGTA 58.724 47.619 8.23 0.00 0.00 2.24
1449 1603 2.459060 TCCATTTCCGCGACAAGTAA 57.541 45.000 8.23 0.00 0.00 2.24
1450 1604 2.980568 TCCATTTCCGCGACAAGTAAT 58.019 42.857 8.23 0.00 0.00 1.89
1451 1605 3.340034 TCCATTTCCGCGACAAGTAATT 58.660 40.909 8.23 0.00 0.00 1.40
1452 1606 3.372822 TCCATTTCCGCGACAAGTAATTC 59.627 43.478 8.23 0.00 0.00 2.17
1453 1607 3.486875 CCATTTCCGCGACAAGTAATTCC 60.487 47.826 8.23 0.00 0.00 3.01
1454 1608 2.459060 TTCCGCGACAAGTAATTCCA 57.541 45.000 8.23 0.00 0.00 3.53
1455 1609 2.459060 TCCGCGACAAGTAATTCCAA 57.541 45.000 8.23 0.00 0.00 3.53
1456 1610 2.768698 TCCGCGACAAGTAATTCCAAA 58.231 42.857 8.23 0.00 0.00 3.28
1457 1611 2.481185 TCCGCGACAAGTAATTCCAAAC 59.519 45.455 8.23 0.00 0.00 2.93
1458 1612 2.492001 CGCGACAAGTAATTCCAAACG 58.508 47.619 0.00 0.00 0.00 3.60
1459 1613 2.156117 CGCGACAAGTAATTCCAAACGA 59.844 45.455 0.00 0.00 0.00 3.85
1460 1614 3.363182 CGCGACAAGTAATTCCAAACGAA 60.363 43.478 0.00 0.00 34.14 3.85
1461 1615 4.148891 GCGACAAGTAATTCCAAACGAAG 58.851 43.478 0.00 0.00 32.78 3.79
1462 1616 4.708601 CGACAAGTAATTCCAAACGAAGG 58.291 43.478 0.00 0.00 32.78 3.46
1463 1617 4.378046 CGACAAGTAATTCCAAACGAAGGG 60.378 45.833 0.00 0.00 32.78 3.95
1464 1618 4.721132 ACAAGTAATTCCAAACGAAGGGA 58.279 39.130 0.00 0.00 32.78 4.20
1465 1619 4.760204 ACAAGTAATTCCAAACGAAGGGAG 59.240 41.667 0.00 0.00 34.02 4.30
1466 1620 3.951663 AGTAATTCCAAACGAAGGGAGG 58.048 45.455 0.00 0.00 34.02 4.30
1467 1621 2.215942 AATTCCAAACGAAGGGAGGG 57.784 50.000 0.00 0.00 34.02 4.30
1468 1622 1.368374 ATTCCAAACGAAGGGAGGGA 58.632 50.000 0.00 0.00 34.02 4.20
1469 1623 0.690762 TTCCAAACGAAGGGAGGGAG 59.309 55.000 0.00 0.00 34.02 4.30
1470 1624 0.473117 TCCAAACGAAGGGAGGGAGT 60.473 55.000 0.00 0.00 0.00 3.85
1471 1625 1.203212 TCCAAACGAAGGGAGGGAGTA 60.203 52.381 0.00 0.00 0.00 2.59
1472 1626 1.207329 CCAAACGAAGGGAGGGAGTAG 59.793 57.143 0.00 0.00 0.00 2.57
1473 1627 1.900486 CAAACGAAGGGAGGGAGTAGT 59.100 52.381 0.00 0.00 0.00 2.73
1474 1628 3.094572 CAAACGAAGGGAGGGAGTAGTA 58.905 50.000 0.00 0.00 0.00 1.82
1475 1629 3.684408 AACGAAGGGAGGGAGTAGTAT 57.316 47.619 0.00 0.00 0.00 2.12
1476 1630 3.684408 ACGAAGGGAGGGAGTAGTATT 57.316 47.619 0.00 0.00 0.00 1.89
1477 1631 3.991683 ACGAAGGGAGGGAGTAGTATTT 58.008 45.455 0.00 0.00 0.00 1.40
1478 1632 4.359996 ACGAAGGGAGGGAGTAGTATTTT 58.640 43.478 0.00 0.00 0.00 1.82
1479 1633 5.522641 ACGAAGGGAGGGAGTAGTATTTTA 58.477 41.667 0.00 0.00 0.00 1.52
1480 1634 6.141790 ACGAAGGGAGGGAGTAGTATTTTAT 58.858 40.000 0.00 0.00 0.00 1.40
1512 1666 3.146847 ACTATTAATTTGGCGGCCTAGC 58.853 45.455 21.46 0.00 0.00 3.42
1543 1697 1.033746 AAGCGCCAATGATCAGTGGG 61.034 55.000 35.87 27.36 45.92 4.61
1613 1770 5.772825 TTTTGTCAAAAGTAGATGCTGCT 57.227 34.783 6.65 0.00 0.00 4.24
1724 2062 2.275318 GTCGAAGAGCCCTTTCATCAG 58.725 52.381 0.00 0.00 36.95 2.90
1849 2311 5.466058 TCTGTTGTGCTGCAAATTAATTTGG 59.534 36.000 31.89 21.45 45.44 3.28
1853 2315 4.996122 TGTGCTGCAAATTAATTTGGAAGG 59.004 37.500 31.89 22.74 45.29 3.46
2249 2871 2.352814 CCTTCCACGTTTCGATCACTCT 60.353 50.000 0.00 0.00 0.00 3.24
2320 2942 1.698165 TCAGCTTCACGTCGATCAAC 58.302 50.000 0.00 0.00 0.00 3.18
2526 3178 1.891178 CAGCTCGTCGACGTTATTGA 58.109 50.000 34.40 15.60 40.80 2.57
2529 3181 1.730121 GCTCGTCGACGTTATTGACCA 60.730 52.381 34.40 13.41 38.38 4.02
2627 3303 4.083862 GCTTCCCTTCCTCGCCGT 62.084 66.667 0.00 0.00 0.00 5.68
2628 3304 2.184579 CTTCCCTTCCTCGCCGTC 59.815 66.667 0.00 0.00 0.00 4.79
2629 3305 3.701604 CTTCCCTTCCTCGCCGTCG 62.702 68.421 0.00 0.00 0.00 5.12
2682 3358 1.043022 GGGGGCTCATTTGGCAATAG 58.957 55.000 0.00 0.38 0.00 1.73
2793 5610 1.733758 CACGGCGCAATTTGCATGT 60.734 52.632 20.56 12.20 45.36 3.21
2794 5611 1.444212 ACGGCGCAATTTGCATGTC 60.444 52.632 20.56 6.51 45.36 3.06
2965 5822 7.121611 CCAGTACGACCTTAAATTATGGGTTTT 59.878 37.037 9.36 0.00 31.60 2.43
3118 6106 9.986833 AAAAGCTTTGCAATTTTTACTGTTAAG 57.013 25.926 13.54 0.00 0.00 1.85
3159 6319 9.302345 TCGTAATCTATCTCAATCAACAACTTC 57.698 33.333 0.00 0.00 0.00 3.01
3254 6416 4.853007 AGCAGGAGCACTTGAATTCTATT 58.147 39.130 7.05 0.00 45.49 1.73
3270 6432 7.616935 TGAATTCTATTGAAAAGGAGAATGGCT 59.383 33.333 7.05 0.00 39.90 4.75
3286 6448 9.822185 GGAGAATGGCTTTATTTATGACAAAAT 57.178 29.630 0.00 0.00 33.69 1.82
3290 6452 9.737844 AATGGCTTTATTTATGACAAAATTGGT 57.262 25.926 0.00 0.00 31.63 3.67
3291 6453 9.737844 ATGGCTTTATTTATGACAAAATTGGTT 57.262 25.926 0.00 0.00 31.63 3.67
3365 6638 4.625311 CGGACCAAAGGCATTACAAATTTC 59.375 41.667 0.00 0.00 0.00 2.17
3372 6645 9.007901 CCAAAGGCATTACAAATTTCCAATTTA 57.992 29.630 0.00 0.00 0.00 1.40
3408 6681 7.311408 AGCTTGATCTCAGCAAGATTTAAAAC 58.689 34.615 16.82 0.00 45.06 2.43
3409 6682 6.529477 GCTTGATCTCAGCAAGATTTAAAACC 59.471 38.462 5.71 0.00 45.06 3.27
3418 6691 9.303116 TCAGCAAGATTTAAAACCCATACTTTA 57.697 29.630 0.00 0.00 0.00 1.85
3464 6737 8.706322 AAATCACTTCCATTACTTAAACAGGT 57.294 30.769 0.00 0.00 0.00 4.00
3465 6738 8.706322 AATCACTTCCATTACTTAAACAGGTT 57.294 30.769 0.00 0.00 0.00 3.50
3466 6739 7.739498 TCACTTCCATTACTTAAACAGGTTC 57.261 36.000 0.00 0.00 0.00 3.62
3467 6740 7.284074 TCACTTCCATTACTTAAACAGGTTCA 58.716 34.615 0.00 0.00 0.00 3.18
3468 6741 7.942341 TCACTTCCATTACTTAAACAGGTTCAT 59.058 33.333 0.00 0.00 0.00 2.57
3469 6742 8.576442 CACTTCCATTACTTAAACAGGTTCATT 58.424 33.333 0.00 0.00 0.00 2.57
3470 6743 9.802039 ACTTCCATTACTTAAACAGGTTCATTA 57.198 29.630 0.00 0.00 0.00 1.90
3472 6745 9.575868 TTCCATTACTTAAACAGGTTCATTACA 57.424 29.630 0.00 0.00 0.00 2.41
3473 6746 9.226606 TCCATTACTTAAACAGGTTCATTACAG 57.773 33.333 0.00 0.00 0.00 2.74
3474 6747 9.010029 CCATTACTTAAACAGGTTCATTACAGT 57.990 33.333 0.00 0.00 0.00 3.55
3476 6749 8.611654 TTACTTAAACAGGTTCATTACAGTCC 57.388 34.615 0.00 0.00 0.00 3.85
3477 6750 6.838382 ACTTAAACAGGTTCATTACAGTCCT 58.162 36.000 0.00 0.00 0.00 3.85
3479 6752 3.059352 ACAGGTTCATTACAGTCCTGC 57.941 47.619 9.07 0.00 46.49 4.85
3480 6753 2.639839 ACAGGTTCATTACAGTCCTGCT 59.360 45.455 9.07 0.00 46.49 4.24
3481 6754 3.557898 ACAGGTTCATTACAGTCCTGCTG 60.558 47.826 9.07 0.00 46.49 4.41
3508 6781 6.536731 CAGCATGTTAATCTCATCAGGTAC 57.463 41.667 0.00 0.00 0.00 3.34
3509 6782 6.051074 CAGCATGTTAATCTCATCAGGTACA 58.949 40.000 0.00 0.00 0.00 2.90
3510 6783 6.018425 CAGCATGTTAATCTCATCAGGTACAC 60.018 42.308 0.00 0.00 0.00 2.90
3511 6784 5.237344 GCATGTTAATCTCATCAGGTACACC 59.763 44.000 0.00 0.00 0.00 4.16
3513 6786 6.222038 TGTTAATCTCATCAGGTACACCTC 57.778 41.667 0.00 0.00 46.65 3.85
3514 6787 5.958380 TGTTAATCTCATCAGGTACACCTCT 59.042 40.000 0.00 0.00 46.65 3.69
3515 6788 6.440647 TGTTAATCTCATCAGGTACACCTCTT 59.559 38.462 0.00 0.00 46.65 2.85
3516 6789 7.618117 TGTTAATCTCATCAGGTACACCTCTTA 59.382 37.037 0.00 0.00 46.65 2.10
3517 6790 8.475639 GTTAATCTCATCAGGTACACCTCTTAA 58.524 37.037 0.00 0.00 46.65 1.85
3518 6791 5.916661 TCTCATCAGGTACACCTCTTAAC 57.083 43.478 0.00 0.00 46.65 2.01
3519 6792 4.710375 TCTCATCAGGTACACCTCTTAACC 59.290 45.833 0.00 0.00 46.65 2.85
3520 6793 4.422057 TCATCAGGTACACCTCTTAACCA 58.578 43.478 0.00 0.00 46.65 3.67
3521 6794 4.222145 TCATCAGGTACACCTCTTAACCAC 59.778 45.833 0.00 0.00 46.65 4.16
3522 6795 3.578978 TCAGGTACACCTCTTAACCACA 58.421 45.455 0.00 0.00 46.65 4.17
3523 6796 3.322828 TCAGGTACACCTCTTAACCACAC 59.677 47.826 0.00 0.00 46.65 3.82
3524 6797 3.070446 CAGGTACACCTCTTAACCACACA 59.930 47.826 0.00 0.00 46.65 3.72
3525 6798 3.323979 AGGTACACCTCTTAACCACACAG 59.676 47.826 0.00 0.00 44.77 3.66
3526 6799 2.256117 ACACCTCTTAACCACACAGC 57.744 50.000 0.00 0.00 0.00 4.40
3527 6800 1.488812 ACACCTCTTAACCACACAGCA 59.511 47.619 0.00 0.00 0.00 4.41
3528 6801 2.146342 CACCTCTTAACCACACAGCAG 58.854 52.381 0.00 0.00 0.00 4.24
3529 6802 1.768870 ACCTCTTAACCACACAGCAGT 59.231 47.619 0.00 0.00 0.00 4.40
3530 6803 2.172717 ACCTCTTAACCACACAGCAGTT 59.827 45.455 0.00 0.00 0.00 3.16
3531 6804 3.214328 CCTCTTAACCACACAGCAGTTT 58.786 45.455 0.00 0.00 0.00 2.66
3532 6805 3.632145 CCTCTTAACCACACAGCAGTTTT 59.368 43.478 0.00 0.00 0.00 2.43
3533 6806 4.819630 CCTCTTAACCACACAGCAGTTTTA 59.180 41.667 0.00 0.00 0.00 1.52
3534 6807 5.049405 CCTCTTAACCACACAGCAGTTTTAG 60.049 44.000 0.00 0.00 0.00 1.85
3535 6808 4.819630 TCTTAACCACACAGCAGTTTTAGG 59.180 41.667 0.00 0.00 0.00 2.69
3536 6809 3.290948 AACCACACAGCAGTTTTAGGA 57.709 42.857 0.00 0.00 0.00 2.94
3537 6810 3.290948 ACCACACAGCAGTTTTAGGAA 57.709 42.857 0.00 0.00 0.00 3.36
3538 6811 3.214328 ACCACACAGCAGTTTTAGGAAG 58.786 45.455 0.00 0.00 0.00 3.46
3539 6812 3.118038 ACCACACAGCAGTTTTAGGAAGA 60.118 43.478 0.00 0.00 0.00 2.87
3540 6813 3.499918 CCACACAGCAGTTTTAGGAAGAG 59.500 47.826 0.00 0.00 0.00 2.85
3541 6814 4.380531 CACACAGCAGTTTTAGGAAGAGA 58.619 43.478 0.00 0.00 0.00 3.10
3542 6815 4.450419 CACACAGCAGTTTTAGGAAGAGAG 59.550 45.833 0.00 0.00 0.00 3.20
3543 6816 4.345257 ACACAGCAGTTTTAGGAAGAGAGA 59.655 41.667 0.00 0.00 0.00 3.10
3544 6817 5.163301 ACACAGCAGTTTTAGGAAGAGAGAA 60.163 40.000 0.00 0.00 0.00 2.87
3545 6818 5.407995 CACAGCAGTTTTAGGAAGAGAGAAG 59.592 44.000 0.00 0.00 0.00 2.85
3546 6819 4.934602 CAGCAGTTTTAGGAAGAGAGAAGG 59.065 45.833 0.00 0.00 0.00 3.46
3547 6820 4.841246 AGCAGTTTTAGGAAGAGAGAAGGA 59.159 41.667 0.00 0.00 0.00 3.36
3548 6821 5.487131 AGCAGTTTTAGGAAGAGAGAAGGAT 59.513 40.000 0.00 0.00 0.00 3.24
3549 6822 6.012945 AGCAGTTTTAGGAAGAGAGAAGGATT 60.013 38.462 0.00 0.00 0.00 3.01
3550 6823 6.657117 GCAGTTTTAGGAAGAGAGAAGGATTT 59.343 38.462 0.00 0.00 0.00 2.17
3551 6824 7.175816 GCAGTTTTAGGAAGAGAGAAGGATTTT 59.824 37.037 0.00 0.00 0.00 1.82
3552 6825 8.510505 CAGTTTTAGGAAGAGAGAAGGATTTTG 58.489 37.037 0.00 0.00 0.00 2.44
3553 6826 7.175816 AGTTTTAGGAAGAGAGAAGGATTTTGC 59.824 37.037 0.00 0.00 0.00 3.68
3554 6827 3.604582 AGGAAGAGAGAAGGATTTTGCG 58.395 45.455 0.00 0.00 0.00 4.85
3555 6828 2.096657 GGAAGAGAGAAGGATTTTGCGC 59.903 50.000 0.00 0.00 0.00 6.09
3556 6829 1.743996 AGAGAGAAGGATTTTGCGCC 58.256 50.000 4.18 0.00 0.00 6.53
3557 6830 0.735471 GAGAGAAGGATTTTGCGCCC 59.265 55.000 4.18 0.00 0.00 6.13
3622 6896 3.128068 CCCGGTTTGTAGCAATCCTTTAC 59.872 47.826 0.00 0.00 0.00 2.01
3643 6917 9.612620 CTTTACAGCCTTTCAATTAAGTTACTG 57.387 33.333 0.00 0.00 0.00 2.74
3699 6973 4.455877 CACTAAGCTAACCCTTGAAACCAG 59.544 45.833 0.00 0.00 0.00 4.00
3710 6984 0.179020 TGAAACCAGGACACTGCCAG 60.179 55.000 0.00 0.00 43.53 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 2.931320 GCTACTAGCTTTCGTGTGCCTT 60.931 50.000 0.00 0.00 38.45 4.35
76 78 3.596743 CGCGCAGAGGGCTAGCTA 61.597 66.667 15.72 0.00 41.67 3.32
99 101 2.279937 GAAAGCTCGTAACAGCGCCG 62.280 60.000 2.29 0.00 44.82 6.46
101 103 0.721718 ATGAAAGCTCGTAACAGCGC 59.278 50.000 0.00 0.00 44.82 5.92
119 122 9.725206 TTTAGGACCAGAAGTAATAAGTAGGAT 57.275 33.333 0.00 0.00 0.00 3.24
146 149 5.580691 GGGCTAGTTAATGTTTGCCATTTTC 59.419 40.000 0.00 0.00 41.01 2.29
166 169 1.289160 TGCATGTTAGGAGAAGGGCT 58.711 50.000 0.00 0.00 0.00 5.19
181 184 3.343941 TTAGCTACGGGTCTTTTGCAT 57.656 42.857 0.00 0.00 0.00 3.96
289 300 9.193806 ACATGCATGGAAAATTAAAGATCTACT 57.806 29.630 29.41 0.00 0.00 2.57
292 303 8.533657 TCAACATGCATGGAAAATTAAAGATCT 58.466 29.630 29.41 0.48 0.00 2.75
306 317 1.771565 ATCCACCTCAACATGCATGG 58.228 50.000 29.41 14.59 0.00 3.66
343 354 5.588648 GTCGATGGAGATTTACCAATTCCAA 59.411 40.000 0.00 0.00 40.96 3.53
344 355 5.104527 AGTCGATGGAGATTTACCAATTCCA 60.105 40.000 0.00 0.00 41.75 3.53
347 358 5.989477 TCAGTCGATGGAGATTTACCAATT 58.011 37.500 0.00 0.00 40.93 2.32
362 373 9.656040 ACGATTATAGTATAAGTCTCAGTCGAT 57.344 33.333 19.22 7.43 0.00 3.59
489 519 4.947388 TCATGTAAACAAAGGGATGGCTAC 59.053 41.667 0.00 0.00 0.00 3.58
496 526 5.887598 CCATCTCATCATGTAAACAAAGGGA 59.112 40.000 0.00 0.00 0.00 4.20
497 527 5.450965 GCCATCTCATCATGTAAACAAAGGG 60.451 44.000 0.00 0.00 0.00 3.95
498 528 5.125900 TGCCATCTCATCATGTAAACAAAGG 59.874 40.000 0.00 0.00 0.00 3.11
500 530 6.153170 ACATGCCATCTCATCATGTAAACAAA 59.847 34.615 5.41 0.00 46.10 2.83
501 531 5.653330 ACATGCCATCTCATCATGTAAACAA 59.347 36.000 5.41 0.00 46.10 2.83
585 651 3.009723 CTCCTACCGTTTGTTGATGCAT 58.990 45.455 0.00 0.00 0.00 3.96
586 652 2.224426 ACTCCTACCGTTTGTTGATGCA 60.224 45.455 0.00 0.00 0.00 3.96
598 664 6.696441 AGAACAAAGACTATACTCCTACCG 57.304 41.667 0.00 0.00 0.00 4.02
613 679 4.470462 GCAGTCATGTTGCTAGAACAAAG 58.530 43.478 14.79 7.64 38.51 2.77
671 737 3.179265 CGTGCATCGTCGTGGGAC 61.179 66.667 0.00 0.00 39.89 4.46
672 738 3.336715 CTCGTGCATCGTCGTGGGA 62.337 63.158 8.22 0.00 40.80 4.37
673 739 2.880879 CTCGTGCATCGTCGTGGG 60.881 66.667 8.22 0.00 40.80 4.61
674 740 1.869574 CTCTCGTGCATCGTCGTGG 60.870 63.158 8.22 0.00 40.80 4.94
675 741 1.128724 GTCTCTCGTGCATCGTCGTG 61.129 60.000 8.22 0.27 40.80 4.35
676 742 1.134901 GTCTCTCGTGCATCGTCGT 59.865 57.895 8.22 0.00 40.80 4.34
677 743 1.930188 CGTCTCTCGTGCATCGTCG 60.930 63.158 8.22 0.00 40.80 5.12
678 744 0.587737 CTCGTCTCTCGTGCATCGTC 60.588 60.000 8.22 0.00 40.80 4.20
679 745 1.425825 CTCGTCTCTCGTGCATCGT 59.574 57.895 8.22 0.00 40.80 3.73
680 746 4.276945 CTCGTCTCTCGTGCATCG 57.723 61.111 0.00 0.00 40.80 3.84
685 751 4.838486 GCCGGCTCGTCTCTCGTG 62.838 72.222 22.15 0.00 40.80 4.35
687 753 4.544689 CTGCCGGCTCGTCTCTCG 62.545 72.222 29.70 0.57 41.41 4.04
688 754 4.863925 GCTGCCGGCTCGTCTCTC 62.864 72.222 29.70 3.61 38.06 3.20
876 949 2.616765 GGAGGAAGAGTTGGAGAAAGGC 60.617 54.545 0.00 0.00 0.00 4.35
885 958 3.071602 TGAGAAGTTGGGAGGAAGAGTTG 59.928 47.826 0.00 0.00 0.00 3.16
890 963 1.338200 CGGTGAGAAGTTGGGAGGAAG 60.338 57.143 0.00 0.00 0.00 3.46
918 991 0.037790 TTTTTATTGGTGCAGCCGGC 60.038 50.000 21.89 21.89 45.13 6.13
919 992 1.272212 AGTTTTTATTGGTGCAGCCGG 59.728 47.619 14.36 0.00 41.21 6.13
920 993 2.723124 AGTTTTTATTGGTGCAGCCG 57.277 45.000 14.36 0.00 41.21 5.52
924 997 3.551863 CGGCTCAAGTTTTTATTGGTGCA 60.552 43.478 0.00 0.00 32.89 4.57
966 1039 2.953648 GCTACTAGAGGGTCTGGAGAAC 59.046 54.545 0.00 0.00 0.00 3.01
967 1040 2.853707 AGCTACTAGAGGGTCTGGAGAA 59.146 50.000 0.00 0.00 0.00 2.87
975 1048 1.394618 CTTGCGAGCTACTAGAGGGT 58.605 55.000 0.00 0.00 0.00 4.34
1130 1207 3.770040 CCCTCGCGTCCATGTCCA 61.770 66.667 5.77 0.00 0.00 4.02
1230 1310 2.114616 GCTGATCTCTTCTTCCTCCCA 58.885 52.381 0.00 0.00 0.00 4.37
1388 1542 3.629142 AGTAATTCCAAACGGAGGGAG 57.371 47.619 0.00 0.00 34.02 4.30
1390 1544 3.418047 ACAAGTAATTCCAAACGGAGGG 58.582 45.455 0.00 0.00 32.88 4.30
1391 1545 3.124636 CGACAAGTAATTCCAAACGGAGG 59.875 47.826 0.00 0.00 32.88 4.30
1393 1547 2.481185 GCGACAAGTAATTCCAAACGGA 59.519 45.455 0.00 0.00 0.00 4.69
1394 1548 2.723618 CGCGACAAGTAATTCCAAACGG 60.724 50.000 0.00 0.00 0.00 4.44
1395 1549 2.492001 CGCGACAAGTAATTCCAAACG 58.508 47.619 0.00 0.00 0.00 3.60
1396 1550 2.481185 TCCGCGACAAGTAATTCCAAAC 59.519 45.455 8.23 0.00 0.00 2.93
1397 1551 2.768698 TCCGCGACAAGTAATTCCAAA 58.231 42.857 8.23 0.00 0.00 3.28
1398 1552 2.459060 TCCGCGACAAGTAATTCCAA 57.541 45.000 8.23 0.00 0.00 3.53
1399 1553 2.459060 TTCCGCGACAAGTAATTCCA 57.541 45.000 8.23 0.00 0.00 3.53
1400 1554 3.486875 CCATTTCCGCGACAAGTAATTCC 60.487 47.826 8.23 0.00 0.00 3.01
1401 1555 3.372822 TCCATTTCCGCGACAAGTAATTC 59.627 43.478 8.23 0.00 0.00 2.17
1402 1556 3.340034 TCCATTTCCGCGACAAGTAATT 58.660 40.909 8.23 0.00 0.00 1.40
1403 1557 2.980568 TCCATTTCCGCGACAAGTAAT 58.019 42.857 8.23 0.00 0.00 1.89
1404 1558 2.459060 TCCATTTCCGCGACAAGTAA 57.541 45.000 8.23 0.00 0.00 2.24
1405 1559 2.684001 ATCCATTTCCGCGACAAGTA 57.316 45.000 8.23 0.00 0.00 2.24
1406 1560 2.684001 TATCCATTTCCGCGACAAGT 57.316 45.000 8.23 0.00 0.00 3.16
1407 1561 4.055360 TGTATATCCATTTCCGCGACAAG 58.945 43.478 8.23 0.00 0.00 3.16
1408 1562 4.061357 TGTATATCCATTTCCGCGACAA 57.939 40.909 8.23 0.00 0.00 3.18
1409 1563 3.737032 TGTATATCCATTTCCGCGACA 57.263 42.857 8.23 0.00 0.00 4.35
1410 1564 4.842139 GATGTATATCCATTTCCGCGAC 57.158 45.455 8.23 0.00 0.00 5.19
1422 1576 4.242475 TGTCGCGGAAATGGATGTATATC 58.758 43.478 6.13 0.00 0.00 1.63
1423 1577 4.265904 TGTCGCGGAAATGGATGTATAT 57.734 40.909 6.13 0.00 0.00 0.86
1424 1578 3.737032 TGTCGCGGAAATGGATGTATA 57.263 42.857 6.13 0.00 0.00 1.47
1425 1579 2.613026 TGTCGCGGAAATGGATGTAT 57.387 45.000 6.13 0.00 0.00 2.29
1426 1580 2.276201 CTTGTCGCGGAAATGGATGTA 58.724 47.619 6.13 0.00 0.00 2.29
1427 1581 1.086696 CTTGTCGCGGAAATGGATGT 58.913 50.000 6.13 0.00 0.00 3.06
1428 1582 1.086696 ACTTGTCGCGGAAATGGATG 58.913 50.000 6.13 0.00 0.00 3.51
1429 1583 2.684001 TACTTGTCGCGGAAATGGAT 57.316 45.000 6.13 0.00 0.00 3.41
1430 1584 2.459060 TTACTTGTCGCGGAAATGGA 57.541 45.000 6.13 0.00 0.00 3.41
1431 1585 3.486875 GGAATTACTTGTCGCGGAAATGG 60.487 47.826 6.13 0.00 0.00 3.16
1432 1586 3.126171 TGGAATTACTTGTCGCGGAAATG 59.874 43.478 6.13 0.00 0.00 2.32
1433 1587 3.340034 TGGAATTACTTGTCGCGGAAAT 58.660 40.909 6.13 0.00 0.00 2.17
1434 1588 2.768698 TGGAATTACTTGTCGCGGAAA 58.231 42.857 6.13 0.00 0.00 3.13
1435 1589 2.459060 TGGAATTACTTGTCGCGGAA 57.541 45.000 6.13 0.00 0.00 4.30
1436 1590 2.459060 TTGGAATTACTTGTCGCGGA 57.541 45.000 6.13 0.00 0.00 5.54
1437 1591 2.723618 CGTTTGGAATTACTTGTCGCGG 60.724 50.000 6.13 0.00 0.00 6.46
1438 1592 2.156117 TCGTTTGGAATTACTTGTCGCG 59.844 45.455 0.00 0.00 0.00 5.87
1439 1593 3.799137 TCGTTTGGAATTACTTGTCGC 57.201 42.857 0.00 0.00 0.00 5.19
1440 1594 4.378046 CCCTTCGTTTGGAATTACTTGTCG 60.378 45.833 0.00 0.00 33.26 4.35
1441 1595 4.758165 TCCCTTCGTTTGGAATTACTTGTC 59.242 41.667 0.00 0.00 33.26 3.18
1442 1596 4.721132 TCCCTTCGTTTGGAATTACTTGT 58.279 39.130 0.00 0.00 33.26 3.16
1443 1597 4.156008 CCTCCCTTCGTTTGGAATTACTTG 59.844 45.833 0.00 0.00 33.26 3.16
1444 1598 4.332828 CCTCCCTTCGTTTGGAATTACTT 58.667 43.478 0.00 0.00 33.26 2.24
1445 1599 3.308188 CCCTCCCTTCGTTTGGAATTACT 60.308 47.826 0.00 0.00 33.26 2.24
1446 1600 3.014623 CCCTCCCTTCGTTTGGAATTAC 58.985 50.000 0.00 0.00 33.26 1.89
1447 1601 2.914278 TCCCTCCCTTCGTTTGGAATTA 59.086 45.455 0.00 0.00 33.26 1.40
1448 1602 1.708551 TCCCTCCCTTCGTTTGGAATT 59.291 47.619 0.00 0.00 33.26 2.17
1449 1603 1.282157 CTCCCTCCCTTCGTTTGGAAT 59.718 52.381 0.00 0.00 33.26 3.01
1450 1604 0.690762 CTCCCTCCCTTCGTTTGGAA 59.309 55.000 0.00 0.00 0.00 3.53
1451 1605 0.473117 ACTCCCTCCCTTCGTTTGGA 60.473 55.000 0.00 0.00 0.00 3.53
1452 1606 1.207329 CTACTCCCTCCCTTCGTTTGG 59.793 57.143 0.00 0.00 0.00 3.28
1453 1607 1.900486 ACTACTCCCTCCCTTCGTTTG 59.100 52.381 0.00 0.00 0.00 2.93
1454 1608 2.322339 ACTACTCCCTCCCTTCGTTT 57.678 50.000 0.00 0.00 0.00 3.60
1455 1609 3.684408 ATACTACTCCCTCCCTTCGTT 57.316 47.619 0.00 0.00 0.00 3.85
1456 1610 3.684408 AATACTACTCCCTCCCTTCGT 57.316 47.619 0.00 0.00 0.00 3.85
1457 1611 6.667558 ATAAAATACTACTCCCTCCCTTCG 57.332 41.667 0.00 0.00 0.00 3.79
1512 1666 2.404186 GGCGCTTAAAGTTCCCCCG 61.404 63.158 7.64 0.00 0.00 5.73
1543 1697 3.001736 CAGAAGCAGCCTATACTTTTCGC 59.998 47.826 0.00 0.00 0.00 4.70
1613 1770 4.754618 CGTGCATGCCCAAGTAATCTTATA 59.245 41.667 16.68 0.00 32.07 0.98
1690 2028 1.600957 CTTCGACCTGCCATGCATAAG 59.399 52.381 0.00 0.00 38.13 1.73
1724 2062 0.807667 CGTCCTAGCAGTGACCATGC 60.808 60.000 0.00 0.00 44.18 4.06
1865 2333 5.615289 GGTTCTGCATTCATACTACCTCAT 58.385 41.667 0.00 0.00 0.00 2.90
1942 2519 4.373156 AGCTCAACTTACCACAAAGGAT 57.627 40.909 0.00 0.00 41.22 3.24
1943 2520 3.857157 AGCTCAACTTACCACAAAGGA 57.143 42.857 0.00 0.00 41.22 3.36
2060 2682 9.793252 CATATGCAAATTAGCTACAACTCTTTT 57.207 29.630 0.00 0.00 34.99 2.27
2061 2683 7.917505 GCATATGCAAATTAGCTACAACTCTTT 59.082 33.333 22.84 0.00 41.59 2.52
2062 2684 7.420800 GCATATGCAAATTAGCTACAACTCTT 58.579 34.615 22.84 0.00 41.59 2.85
2063 2685 6.963796 GCATATGCAAATTAGCTACAACTCT 58.036 36.000 22.84 0.00 41.59 3.24
2230 2852 3.243602 TGAAGAGTGATCGAAACGTGGAA 60.244 43.478 0.00 0.00 0.00 3.53
2296 2918 1.165270 TCGACGTGAAGCTGATGAGA 58.835 50.000 0.00 0.00 0.00 3.27
2360 3012 0.179094 ACCGCTTCTTTCACGACACA 60.179 50.000 0.00 0.00 0.00 3.72
2443 3095 4.008933 GAGCCGCTGGACACACCT 62.009 66.667 0.00 0.00 39.86 4.00
2630 3306 2.747855 GAACCCAAGGCTGCTCGG 60.748 66.667 0.00 0.00 0.00 4.63
2631 3307 1.377725 ATGAACCCAAGGCTGCTCG 60.378 57.895 0.00 0.00 0.00 5.03
2632 3308 0.610232 ACATGAACCCAAGGCTGCTC 60.610 55.000 0.00 0.00 0.00 4.26
2641 3317 2.668632 GAGCCCGACATGAACCCA 59.331 61.111 0.00 0.00 0.00 4.51
2668 3344 5.682862 GTCGTAAATGCTATTGCCAAATGAG 59.317 40.000 0.00 0.00 38.71 2.90
2682 3358 0.638746 CAGGTCGTCGTCGTAAATGC 59.361 55.000 1.33 0.00 38.33 3.56
2752 3434 2.944349 GTTAATGGGCCAATTTGCATGG 59.056 45.455 11.59 0.11 41.08 3.66
2754 3436 3.008813 TGTGTTAATGGGCCAATTTGCAT 59.991 39.130 11.59 0.00 0.00 3.96
2758 5575 2.028567 CCGTGTGTTAATGGGCCAATTT 60.029 45.455 11.59 3.42 0.00 1.82
2766 5583 0.170116 ATTGCGCCGTGTGTTAATGG 59.830 50.000 4.18 0.00 0.00 3.16
2840 5659 5.084818 TCTATCCACATGCCCAATATACG 57.915 43.478 0.00 0.00 0.00 3.06
2904 5754 9.487790 CATACAACCTAGTACTAGTACTACTCC 57.512 40.741 30.50 8.03 43.98 3.85
2924 5774 4.021280 TCGTACTGGCAAACCTACATACAA 60.021 41.667 0.00 0.00 36.63 2.41
2925 5775 3.510753 TCGTACTGGCAAACCTACATACA 59.489 43.478 0.00 0.00 36.63 2.29
2933 5789 2.460757 TAAGGTCGTACTGGCAAACC 57.539 50.000 0.00 0.00 0.00 3.27
3024 5899 5.297776 GGCATGAGTATTGGGATATATGCAC 59.702 44.000 6.56 0.00 35.92 4.57
3033 5909 1.284491 TGCAAGGCATGAGTATTGGGA 59.716 47.619 0.00 0.00 31.71 4.37
3254 6416 9.253832 TCATAAATAAAGCCATTCTCCTTTTCA 57.746 29.630 0.00 0.00 33.64 2.69
3286 6448 6.770785 ACTACTGCATAACTTTTCAGAACCAA 59.229 34.615 0.00 0.00 0.00 3.67
3287 6449 6.296026 ACTACTGCATAACTTTTCAGAACCA 58.704 36.000 0.00 0.00 0.00 3.67
3288 6450 6.803154 ACTACTGCATAACTTTTCAGAACC 57.197 37.500 0.00 0.00 0.00 3.62
3323 6596 5.048713 GGTCCGATTTTTGTCACAGAAATCT 60.049 40.000 24.09 0.23 40.48 2.40
3333 6606 2.035321 TGCCTTTGGTCCGATTTTTGTC 59.965 45.455 0.00 0.00 0.00 3.18
3372 6645 5.369409 TGAGATCAAGCTTTCATCTCCAT 57.631 39.130 27.69 7.95 41.29 3.41
3387 6660 6.009589 TGGGTTTTAAATCTTGCTGAGATCA 58.990 36.000 0.00 0.00 44.41 2.92
3388 6661 6.515272 TGGGTTTTAAATCTTGCTGAGATC 57.485 37.500 4.06 0.00 44.41 2.75
3438 6711 9.802039 ACCTGTTTAAGTAATGGAAGTGATTTA 57.198 29.630 0.00 0.00 0.00 1.40
3439 6712 8.706322 ACCTGTTTAAGTAATGGAAGTGATTT 57.294 30.769 0.00 0.00 0.00 2.17
3440 6713 8.706322 AACCTGTTTAAGTAATGGAAGTGATT 57.294 30.769 0.00 0.00 0.00 2.57
3441 6714 7.942341 TGAACCTGTTTAAGTAATGGAAGTGAT 59.058 33.333 0.00 0.00 0.00 3.06
3442 6715 7.284074 TGAACCTGTTTAAGTAATGGAAGTGA 58.716 34.615 0.00 0.00 0.00 3.41
3443 6716 7.504924 TGAACCTGTTTAAGTAATGGAAGTG 57.495 36.000 0.00 0.00 0.00 3.16
3444 6717 8.706322 AATGAACCTGTTTAAGTAATGGAAGT 57.294 30.769 0.00 0.00 0.00 3.01
3446 6719 9.575868 TGTAATGAACCTGTTTAAGTAATGGAA 57.424 29.630 0.00 0.00 0.00 3.53
3447 6720 9.226606 CTGTAATGAACCTGTTTAAGTAATGGA 57.773 33.333 0.00 0.00 0.00 3.41
3448 6721 9.010029 ACTGTAATGAACCTGTTTAAGTAATGG 57.990 33.333 0.00 0.00 0.00 3.16
3450 6723 9.227777 GGACTGTAATGAACCTGTTTAAGTAAT 57.772 33.333 0.00 0.00 0.00 1.89
3451 6724 8.434392 AGGACTGTAATGAACCTGTTTAAGTAA 58.566 33.333 0.00 0.00 0.00 2.24
3452 6725 7.876068 CAGGACTGTAATGAACCTGTTTAAGTA 59.124 37.037 0.00 0.00 41.91 2.24
3453 6726 6.710744 CAGGACTGTAATGAACCTGTTTAAGT 59.289 38.462 0.00 0.00 41.91 2.24
3454 6727 6.348540 GCAGGACTGTAATGAACCTGTTTAAG 60.349 42.308 0.00 0.00 46.55 1.85
3455 6728 5.472137 GCAGGACTGTAATGAACCTGTTTAA 59.528 40.000 0.00 0.00 46.55 1.52
3456 6729 5.001232 GCAGGACTGTAATGAACCTGTTTA 58.999 41.667 0.00 0.00 46.55 2.01
3457 6730 3.821033 GCAGGACTGTAATGAACCTGTTT 59.179 43.478 0.00 0.00 46.55 2.83
3458 6731 3.073062 AGCAGGACTGTAATGAACCTGTT 59.927 43.478 0.00 0.00 46.55 3.16
3459 6732 2.639839 AGCAGGACTGTAATGAACCTGT 59.360 45.455 0.00 0.00 46.55 4.00
3461 6734 3.340814 CAGCAGGACTGTAATGAACCT 57.659 47.619 0.82 0.00 41.86 3.50
3479 6752 5.583457 TGATGAGATTAACATGCTGTGTCAG 59.417 40.000 0.00 0.00 41.14 3.51
3480 6753 5.490159 TGATGAGATTAACATGCTGTGTCA 58.510 37.500 0.00 0.00 41.14 3.58
3481 6754 5.007430 CCTGATGAGATTAACATGCTGTGTC 59.993 44.000 0.00 0.00 41.14 3.67
3482 6755 4.880120 CCTGATGAGATTAACATGCTGTGT 59.120 41.667 0.00 0.00 44.84 3.72
3483 6756 4.880120 ACCTGATGAGATTAACATGCTGTG 59.120 41.667 0.00 0.00 0.00 3.66
3484 6757 5.108187 ACCTGATGAGATTAACATGCTGT 57.892 39.130 0.00 0.00 0.00 4.40
3485 6758 6.018425 GTGTACCTGATGAGATTAACATGCTG 60.018 42.308 0.00 0.00 0.00 4.41
3486 6759 6.051717 GTGTACCTGATGAGATTAACATGCT 58.948 40.000 0.00 0.00 0.00 3.79
3487 6760 5.237344 GGTGTACCTGATGAGATTAACATGC 59.763 44.000 0.00 0.00 0.00 4.06
3488 6761 6.586344 AGGTGTACCTGATGAGATTAACATG 58.414 40.000 2.06 0.00 46.55 3.21
3489 6762 6.814954 AGGTGTACCTGATGAGATTAACAT 57.185 37.500 2.06 0.00 46.55 2.71
3504 6777 3.660865 CTGTGTGGTTAAGAGGTGTACC 58.339 50.000 0.00 0.00 0.00 3.34
3505 6778 3.064931 GCTGTGTGGTTAAGAGGTGTAC 58.935 50.000 0.00 0.00 0.00 2.90
3506 6779 2.701423 TGCTGTGTGGTTAAGAGGTGTA 59.299 45.455 0.00 0.00 0.00 2.90
3507 6780 1.488812 TGCTGTGTGGTTAAGAGGTGT 59.511 47.619 0.00 0.00 0.00 4.16
3508 6781 2.146342 CTGCTGTGTGGTTAAGAGGTG 58.854 52.381 0.00 0.00 0.00 4.00
3509 6782 1.768870 ACTGCTGTGTGGTTAAGAGGT 59.231 47.619 0.00 0.00 0.00 3.85
3510 6783 2.550830 ACTGCTGTGTGGTTAAGAGG 57.449 50.000 0.00 0.00 0.00 3.69
3511 6784 4.900635 AAAACTGCTGTGTGGTTAAGAG 57.099 40.909 0.00 0.00 0.00 2.85
3512 6785 4.819630 CCTAAAACTGCTGTGTGGTTAAGA 59.180 41.667 0.00 0.00 0.00 2.10
3513 6786 4.819630 TCCTAAAACTGCTGTGTGGTTAAG 59.180 41.667 0.00 0.00 0.00 1.85
3514 6787 4.783055 TCCTAAAACTGCTGTGTGGTTAA 58.217 39.130 0.00 0.00 0.00 2.01
3515 6788 4.425180 TCCTAAAACTGCTGTGTGGTTA 57.575 40.909 0.00 0.00 0.00 2.85
3516 6789 3.290948 TCCTAAAACTGCTGTGTGGTT 57.709 42.857 0.00 0.00 0.00 3.67
3517 6790 3.118038 TCTTCCTAAAACTGCTGTGTGGT 60.118 43.478 0.00 0.00 0.00 4.16
3518 6791 3.476552 TCTTCCTAAAACTGCTGTGTGG 58.523 45.455 0.00 0.00 0.00 4.17
3519 6792 4.380531 TCTCTTCCTAAAACTGCTGTGTG 58.619 43.478 0.00 0.00 0.00 3.82
3520 6793 4.345257 TCTCTCTTCCTAAAACTGCTGTGT 59.655 41.667 0.00 0.00 0.00 3.72
3521 6794 4.887748 TCTCTCTTCCTAAAACTGCTGTG 58.112 43.478 0.00 0.00 0.00 3.66
3522 6795 5.512232 CCTTCTCTCTTCCTAAAACTGCTGT 60.512 44.000 0.00 0.00 0.00 4.40
3523 6796 4.934602 CCTTCTCTCTTCCTAAAACTGCTG 59.065 45.833 0.00 0.00 0.00 4.41
3524 6797 4.841246 TCCTTCTCTCTTCCTAAAACTGCT 59.159 41.667 0.00 0.00 0.00 4.24
3525 6798 5.153950 TCCTTCTCTCTTCCTAAAACTGC 57.846 43.478 0.00 0.00 0.00 4.40
3526 6799 8.510505 CAAAATCCTTCTCTCTTCCTAAAACTG 58.489 37.037 0.00 0.00 0.00 3.16
3527 6800 7.175816 GCAAAATCCTTCTCTCTTCCTAAAACT 59.824 37.037 0.00 0.00 0.00 2.66
3528 6801 7.309177 GCAAAATCCTTCTCTCTTCCTAAAAC 58.691 38.462 0.00 0.00 0.00 2.43
3529 6802 6.149474 CGCAAAATCCTTCTCTCTTCCTAAAA 59.851 38.462 0.00 0.00 0.00 1.52
3530 6803 5.643777 CGCAAAATCCTTCTCTCTTCCTAAA 59.356 40.000 0.00 0.00 0.00 1.85
3531 6804 5.178797 CGCAAAATCCTTCTCTCTTCCTAA 58.821 41.667 0.00 0.00 0.00 2.69
3532 6805 4.759782 CGCAAAATCCTTCTCTCTTCCTA 58.240 43.478 0.00 0.00 0.00 2.94
3533 6806 3.604582 CGCAAAATCCTTCTCTCTTCCT 58.395 45.455 0.00 0.00 0.00 3.36
3534 6807 2.096657 GCGCAAAATCCTTCTCTCTTCC 59.903 50.000 0.30 0.00 0.00 3.46
3535 6808 2.096657 GGCGCAAAATCCTTCTCTCTTC 59.903 50.000 10.83 0.00 0.00 2.87
3536 6809 2.087646 GGCGCAAAATCCTTCTCTCTT 58.912 47.619 10.83 0.00 0.00 2.85
3537 6810 1.680249 GGGCGCAAAATCCTTCTCTCT 60.680 52.381 10.83 0.00 0.00 3.10
3538 6811 0.735471 GGGCGCAAAATCCTTCTCTC 59.265 55.000 10.83 0.00 0.00 3.20
3539 6812 0.329596 AGGGCGCAAAATCCTTCTCT 59.670 50.000 10.83 0.00 0.00 3.10
3540 6813 2.038387 TAGGGCGCAAAATCCTTCTC 57.962 50.000 10.83 0.00 32.46 2.87
3541 6814 2.092323 GTTAGGGCGCAAAATCCTTCT 58.908 47.619 10.83 0.00 32.46 2.85
3542 6815 2.092323 AGTTAGGGCGCAAAATCCTTC 58.908 47.619 10.83 3.31 32.46 3.46
3543 6816 2.215942 AGTTAGGGCGCAAAATCCTT 57.784 45.000 10.83 0.00 32.46 3.36
3544 6817 2.238898 ACTAGTTAGGGCGCAAAATCCT 59.761 45.455 10.83 8.76 34.85 3.24
3545 6818 2.640184 ACTAGTTAGGGCGCAAAATCC 58.360 47.619 10.83 0.00 0.00 3.01
3546 6819 4.186159 TGTACTAGTTAGGGCGCAAAATC 58.814 43.478 10.83 0.00 0.00 2.17
3547 6820 4.210724 TGTACTAGTTAGGGCGCAAAAT 57.789 40.909 10.83 1.79 0.00 1.82
3548 6821 3.681593 TGTACTAGTTAGGGCGCAAAA 57.318 42.857 10.83 0.00 0.00 2.44
3549 6822 3.899052 ATGTACTAGTTAGGGCGCAAA 57.101 42.857 10.83 0.00 0.00 3.68
3550 6823 3.899052 AATGTACTAGTTAGGGCGCAA 57.101 42.857 10.83 0.00 0.00 4.85
3551 6824 5.111293 GTTTAATGTACTAGTTAGGGCGCA 58.889 41.667 10.83 0.00 0.00 6.09
3552 6825 5.111293 TGTTTAATGTACTAGTTAGGGCGC 58.889 41.667 0.00 0.00 0.00 6.53
3553 6826 7.781548 ATTGTTTAATGTACTAGTTAGGGCG 57.218 36.000 0.00 0.00 0.00 6.13
3554 6827 7.913821 GCAATTGTTTAATGTACTAGTTAGGGC 59.086 37.037 7.40 0.00 0.00 5.19
3555 6828 8.952278 TGCAATTGTTTAATGTACTAGTTAGGG 58.048 33.333 7.40 0.00 0.00 3.53
3556 6829 9.769093 GTGCAATTGTTTAATGTACTAGTTAGG 57.231 33.333 7.40 0.00 0.00 2.69
3622 6896 6.575162 ACCAGTAACTTAATTGAAAGGCTG 57.425 37.500 0.00 0.00 0.00 4.85
3667 6941 3.947834 GGGTTAGCTTAGTGACATGCATT 59.052 43.478 0.00 0.00 0.00 3.56
3699 6973 1.302832 CCCTTGTCTGGCAGTGTCC 60.303 63.158 15.27 2.06 0.00 4.02


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

AutoCloner maintained by Alex Coulton.