Multiple sequence alignment - TraesCS3A01G407700

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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 TraesCS3A01G407700 chr3A 100.000 4256 0 0 1 4256 652819933 652824188 0.000000e+00 7860
1 TraesCS3A01G407700 chr3B 90.380 3420 180 52 100 3463 680255756 680252430 0.000000e+00 4355
2 TraesCS3A01G407700 chr3B 92.857 84 4 1 3 86 680255819 680255738 2.080000e-23 121
3 TraesCS3A01G407700 chr3D 90.238 2602 162 47 2 2562 516998818 517001368 0.000000e+00 3314
4 TraesCS3A01G407700 chr3D 91.459 925 45 17 2618 3516 517001389 517002305 0.000000e+00 1240
5 TraesCS3A01G407700 chr5D 87.521 585 53 3 3690 4256 106808705 106809287 0.000000e+00 658
6 TraesCS3A01G407700 chr5D 86.644 584 70 6 3680 4256 334980141 334980723 1.290000e-179 640
7 TraesCS3A01G407700 chr5D 87.328 363 46 0 3894 4256 468322622 468322260 2.370000e-112 416
8 TraesCS3A01G407700 chr5D 86.226 363 50 0 3894 4256 4340612 4340974 1.110000e-105 394
9 TraesCS3A01G407700 chr5A 87.328 363 46 0 3894 4256 100652115 100652477 2.370000e-112 416
10 TraesCS3A01G407700 chr5A 81.435 237 26 3 3680 3899 100651807 100652042 1.220000e-40 178
11 TraesCS3A01G407700 chr4D 87.328 363 45 1 3894 4256 95173674 95174035 8.510000e-112 414
12 TraesCS3A01G407700 chr7D 86.777 363 46 1 3894 4256 459754307 459754667 1.840000e-108 403
13 TraesCS3A01G407700 chr1D 85.950 363 51 0 3894 4256 455542747 455543109 5.160000e-104 388
14 TraesCS3A01G407700 chr1D 81.370 365 60 7 2859 3219 361037046 361037406 1.500000e-74 291
15 TraesCS3A01G407700 chr1D 75.897 585 125 10 1707 2276 361036122 361036705 6.970000e-73 285
16 TraesCS3A01G407700 chr1A 85.675 363 50 2 3894 4256 543410438 543410078 8.640000e-102 381
17 TraesCS3A01G407700 chr1A 76.280 586 121 11 1707 2276 460640299 460640882 3.220000e-76 296
18 TraesCS3A01G407700 chr1A 80.822 365 62 7 2859 3219 460641470 460641830 3.240000e-71 279
19 TraesCS3A01G407700 chrUn 82.075 424 55 11 3679 4083 87419124 87418703 4.070000e-90 342
20 TraesCS3A01G407700 chr1B 76.976 582 121 5 1707 2276 483291519 483292099 1.910000e-83 320
21 TraesCS3A01G407700 chr1B 80.495 364 65 4 2859 3219 483292451 483292811 1.510000e-69 274


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 TraesCS3A01G407700 chr3A 652819933 652824188 4255 False 7860.0 7860 100.0000 1 4256 1 chr3A.!!$F1 4255
1 TraesCS3A01G407700 chr3B 680252430 680255819 3389 True 2238.0 4355 91.6185 3 3463 2 chr3B.!!$R1 3460
2 TraesCS3A01G407700 chr3D 516998818 517002305 3487 False 2277.0 3314 90.8485 2 3516 2 chr3D.!!$F1 3514
3 TraesCS3A01G407700 chr5D 106808705 106809287 582 False 658.0 658 87.5210 3690 4256 1 chr5D.!!$F2 566
4 TraesCS3A01G407700 chr5D 334980141 334980723 582 False 640.0 640 86.6440 3680 4256 1 chr5D.!!$F3 576
5 TraesCS3A01G407700 chr5A 100651807 100652477 670 False 297.0 416 84.3815 3680 4256 2 chr5A.!!$F1 576
6 TraesCS3A01G407700 chr1D 361036122 361037406 1284 False 288.0 291 78.6335 1707 3219 2 chr1D.!!$F2 1512
7 TraesCS3A01G407700 chr1A 460640299 460641830 1531 False 287.5 296 78.5510 1707 3219 2 chr1A.!!$F1 1512
8 TraesCS3A01G407700 chr1B 483291519 483292811 1292 False 297.0 320 78.7355 1707 3219 2 chr1B.!!$F1 1512

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
137 138 0.039165 CTTGCTTGCCGTTTCCTTCC 60.039 55.0 0.00 0.0 0.00 3.46 F
352 366 0.107654 AAGGCCGTCCATAGCAGTTC 60.108 55.0 0.00 0.0 33.74 3.01 F
1273 1295 0.457851 CTCGTGGTGAGTGATCCTCC 59.542 60.0 8.25 0.0 39.65 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1520 0.687354 AAGGTGGACAGCTGACGAAT 59.313 50.000 23.35 0.00 39.39 3.34 R
1486 1524 2.079925 GAATCAAGGTGGACAGCTGAC 58.920 52.381 23.35 15.15 39.39 3.51 R
3271 3707 1.211212 CTCAGAACCCTGCCATGATCA 59.789 52.381 0.00 0.00 40.20 2.92 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
35 36 1.667830 GTTGCTGTGCACGCCTCTA 60.668 57.895 24.00 8.64 38.71 2.43
52 53 6.270156 GCCTCTAGCGGTTTATAGAAGTAT 57.730 41.667 0.00 0.00 0.00 2.12
80 81 0.326927 CAAGTAGAAGGGGCCGGAAA 59.673 55.000 5.05 0.00 0.00 3.13
89 90 1.072505 GGGCCGGAAACTCTGACAA 59.927 57.895 5.05 0.00 0.00 3.18
97 98 3.142174 GGAAACTCTGACAACTTCCAGG 58.858 50.000 0.00 0.00 36.39 4.45
98 99 3.433740 GGAAACTCTGACAACTTCCAGGT 60.434 47.826 0.00 0.00 36.39 4.00
134 135 1.827789 TGCTTGCTTGCCGTTTCCT 60.828 52.632 0.00 0.00 0.00 3.36
136 137 0.664466 GCTTGCTTGCCGTTTCCTTC 60.664 55.000 0.00 0.00 0.00 3.46
137 138 0.039165 CTTGCTTGCCGTTTCCTTCC 60.039 55.000 0.00 0.00 0.00 3.46
139 140 1.172180 TGCTTGCCGTTTCCTTCCAG 61.172 55.000 0.00 0.00 0.00 3.86
140 141 1.172812 GCTTGCCGTTTCCTTCCAGT 61.173 55.000 0.00 0.00 0.00 4.00
173 174 3.241530 TTCCACGGCTGCAGACCT 61.242 61.111 20.43 0.00 0.00 3.85
174 175 3.240134 TTCCACGGCTGCAGACCTC 62.240 63.158 20.43 0.00 0.00 3.85
175 176 4.767255 CCACGGCTGCAGACCTCC 62.767 72.222 20.43 8.07 0.00 4.30
176 177 4.007644 CACGGCTGCAGACCTCCA 62.008 66.667 20.43 0.00 0.00 3.86
177 178 3.241530 ACGGCTGCAGACCTCCAA 61.242 61.111 20.43 0.00 0.00 3.53
178 179 2.032528 CGGCTGCAGACCTCCAAA 59.967 61.111 20.43 0.00 0.00 3.28
179 180 2.037136 CGGCTGCAGACCTCCAAAG 61.037 63.158 20.43 0.00 0.00 2.77
180 181 2.338785 GGCTGCAGACCTCCAAAGC 61.339 63.158 20.43 0.00 0.00 3.51
181 182 1.303155 GCTGCAGACCTCCAAAGCT 60.303 57.895 20.43 0.00 0.00 3.74
197 205 2.464157 AGCTCCTTTTGAGAAGGTCG 57.536 50.000 1.38 0.00 44.42 4.79
237 246 0.389391 TCCCGGAATTTTTGCGCAAA 59.611 45.000 30.63 30.63 43.53 3.68
247 256 6.892310 AATTTTTGCGCAAATTCCTCTATC 57.108 33.333 33.94 0.00 31.90 2.08
311 324 3.700038 TCTCGTAGGGAGAGATTGGTTTC 59.300 47.826 0.00 0.00 46.80 2.78
318 331 6.642733 AGGGAGAGATTGGTTTCTTGATAA 57.357 37.500 0.00 0.00 0.00 1.75
320 333 7.470192 AGGGAGAGATTGGTTTCTTGATAAAA 58.530 34.615 0.00 0.00 0.00 1.52
321 334 7.394641 AGGGAGAGATTGGTTTCTTGATAAAAC 59.605 37.037 0.00 0.00 36.18 2.43
325 339 9.280174 AGAGATTGGTTTCTTGATAAAACGTAA 57.720 29.630 0.00 0.00 37.46 3.18
352 366 0.107654 AAGGCCGTCCATAGCAGTTC 60.108 55.000 0.00 0.00 33.74 3.01
501 516 1.881973 GCATCACAAGAAACTCTGCCA 59.118 47.619 0.00 0.00 0.00 4.92
524 539 4.041198 ACGGAAGAGAACTCCATGGTTAAA 59.959 41.667 12.58 0.00 0.00 1.52
535 550 4.142790 TCCATGGTTAAACAACGGCTTAA 58.857 39.130 12.58 0.00 0.00 1.85
568 583 5.277297 GCCAACCAAAGAAATTAAAGCACAC 60.277 40.000 0.00 0.00 0.00 3.82
605 620 6.799926 AAACAAAGCAAAAGCAGAAAAGAA 57.200 29.167 0.00 0.00 0.00 2.52
617 632 8.648557 AAAGCAGAAAAGAAAAATCAAGTACC 57.351 30.769 0.00 0.00 0.00 3.34
619 634 6.262273 AGCAGAAAAGAAAAATCAAGTACCGA 59.738 34.615 0.00 0.00 0.00 4.69
622 637 6.262273 AGAAAAGAAAAATCAAGTACCGAGCA 59.738 34.615 0.00 0.00 0.00 4.26
625 640 6.385649 AGAAAAATCAAGTACCGAGCAAAA 57.614 33.333 0.00 0.00 0.00 2.44
695 711 1.201343 GCGTCTAGGTTCTCGATTGC 58.799 55.000 0.00 0.00 0.00 3.56
754 770 5.924475 AATCTTGCGGGTATTTATCTTCG 57.076 39.130 0.00 0.00 0.00 3.79
805 821 6.370186 AAAGTAGTAAGAACCCTACCTTGG 57.630 41.667 0.00 0.00 35.25 3.61
809 825 3.838903 AGTAAGAACCCTACCTTGGTCAG 59.161 47.826 0.00 0.00 34.15 3.51
870 889 2.307363 CAGTATGGTTTAGCGCCCG 58.693 57.895 2.29 0.00 0.00 6.13
886 905 0.986550 CCCGGGGAGGTTACTTGGAT 60.987 60.000 14.71 0.00 38.74 3.41
887 906 0.468648 CCGGGGAGGTTACTTGGATC 59.531 60.000 0.00 0.00 34.51 3.36
888 907 1.497161 CGGGGAGGTTACTTGGATCT 58.503 55.000 0.00 0.00 0.00 2.75
892 911 2.239907 GGGAGGTTACTTGGATCTTGCT 59.760 50.000 0.00 0.00 0.00 3.91
920 939 7.131498 ACGTTTTTGTTGCGGATACTTATTA 57.869 32.000 0.00 0.00 0.00 0.98
921 940 7.017055 ACGTTTTTGTTGCGGATACTTATTAC 58.983 34.615 0.00 0.00 0.00 1.89
922 941 7.095102 ACGTTTTTGTTGCGGATACTTATTACT 60.095 33.333 0.00 0.00 0.00 2.24
923 942 7.747357 CGTTTTTGTTGCGGATACTTATTACTT 59.253 33.333 0.00 0.00 0.00 2.24
996 1015 4.623932 ACTGAATGCAGGTTTCTCTGTA 57.376 40.909 5.47 0.00 46.60 2.74
1101 1123 1.868997 GACACAGAATGGTGGCACG 59.131 57.895 12.17 0.00 46.33 5.34
1206 1228 0.470766 TTGTAGCCTCCGGTGTTTGT 59.529 50.000 0.00 0.00 0.00 2.83
1242 1264 1.762460 ACTAGGATGGGGAGCCACG 60.762 63.158 0.00 0.00 0.00 4.94
1270 1292 1.134965 CCTTCTCGTGGTGAGTGATCC 60.135 57.143 0.00 0.00 45.46 3.36
1273 1295 0.457851 CTCGTGGTGAGTGATCCTCC 59.542 60.000 8.25 0.00 39.65 4.30
1283 1305 3.969312 TGAGTGATCCTCCATTCTGCATA 59.031 43.478 8.25 0.00 39.65 3.14
1290 1312 4.486839 TCCTCCATTCTGCATATCTCTCA 58.513 43.478 0.00 0.00 0.00 3.27
1299 1321 8.657729 CATTCTGCATATCTCTCATATGTGAAC 58.342 37.037 8.70 0.00 35.14 3.18
1303 1325 6.370718 TGCATATCTCTCATATGTGAACATGC 59.629 38.462 24.09 24.09 37.15 4.06
1342 1371 8.655651 TTACAAGATGGTTCAAAATTTTGGTC 57.344 30.769 26.45 19.36 38.66 4.02
1393 1423 1.740025 GCACAGCTTATCACTGGGTTC 59.260 52.381 0.00 0.00 40.82 3.62
1406 1436 4.159135 TCACTGGGTTCGTAGTTTAGATCC 59.841 45.833 0.00 0.00 0.00 3.36
1409 1439 5.105432 ACTGGGTTCGTAGTTTAGATCCTTC 60.105 44.000 0.00 0.00 0.00 3.46
1412 1442 6.096001 TGGGTTCGTAGTTTAGATCCTTCTAC 59.904 42.308 0.00 0.00 34.15 2.59
1443 1481 8.267183 TCAGTCATATGATGTATGTTGGAAGTT 58.733 33.333 9.02 0.00 0.00 2.66
1457 1495 3.286353 TGGAAGTTCACTGCAAATGTGA 58.714 40.909 5.01 3.31 41.94 3.58
1467 1505 7.094508 TCACTGCAAATGTGAAAACTTTCTA 57.905 32.000 4.89 0.00 40.89 2.10
1468 1506 7.542890 TCACTGCAAATGTGAAAACTTTCTAA 58.457 30.769 4.89 0.00 40.89 2.10
1474 1512 8.534778 GCAAATGTGAAAACTTTCTAAGTCAAG 58.465 33.333 3.98 0.00 41.91 3.02
1475 1513 9.573133 CAAATGTGAAAACTTTCTAAGTCAAGT 57.427 29.630 3.98 0.00 41.91 3.16
1498 1536 1.795768 TTGATTCGTCAGCTGTCCAC 58.204 50.000 14.67 3.58 0.00 4.02
1499 1537 0.037326 TGATTCGTCAGCTGTCCACC 60.037 55.000 14.67 0.99 0.00 4.61
1500 1538 0.247736 GATTCGTCAGCTGTCCACCT 59.752 55.000 14.67 0.00 0.00 4.00
1501 1539 0.687354 ATTCGTCAGCTGTCCACCTT 59.313 50.000 14.67 0.00 0.00 3.50
1502 1540 0.249868 TTCGTCAGCTGTCCACCTTG 60.250 55.000 14.67 0.00 0.00 3.61
1505 1543 1.609061 CGTCAGCTGTCCACCTTGATT 60.609 52.381 14.67 0.00 0.00 2.57
1506 1544 2.079925 GTCAGCTGTCCACCTTGATTC 58.920 52.381 14.67 0.00 0.00 2.52
1507 1545 1.980765 TCAGCTGTCCACCTTGATTCT 59.019 47.619 14.67 0.00 0.00 2.40
1508 1546 3.055819 GTCAGCTGTCCACCTTGATTCTA 60.056 47.826 14.67 0.00 0.00 2.10
1509 1547 3.196469 TCAGCTGTCCACCTTGATTCTAG 59.804 47.826 14.67 0.00 0.00 2.43
1510 1548 3.196469 CAGCTGTCCACCTTGATTCTAGA 59.804 47.826 5.25 0.00 0.00 2.43
1511 1549 3.840666 AGCTGTCCACCTTGATTCTAGAA 59.159 43.478 7.82 7.82 0.00 2.10
1512 1550 4.287067 AGCTGTCCACCTTGATTCTAGAAA 59.713 41.667 9.71 0.00 0.00 2.52
1513 1551 4.633565 GCTGTCCACCTTGATTCTAGAAAG 59.366 45.833 9.71 2.39 0.00 2.62
1514 1552 5.569630 GCTGTCCACCTTGATTCTAGAAAGA 60.570 44.000 9.71 0.00 0.00 2.52
1515 1553 6.433847 TGTCCACCTTGATTCTAGAAAGAA 57.566 37.500 9.71 4.46 45.63 2.52
1516 1554 6.231211 TGTCCACCTTGATTCTAGAAAGAAC 58.769 40.000 9.71 2.73 44.40 3.01
1517 1555 6.183361 TGTCCACCTTGATTCTAGAAAGAACA 60.183 38.462 9.71 5.25 44.40 3.18
1518 1556 6.710744 GTCCACCTTGATTCTAGAAAGAACAA 59.289 38.462 9.71 11.98 44.40 2.83
1519 1557 7.228706 GTCCACCTTGATTCTAGAAAGAACAAA 59.771 37.037 9.71 0.00 44.40 2.83
1520 1558 7.777910 TCCACCTTGATTCTAGAAAGAACAAAA 59.222 33.333 9.71 0.00 44.40 2.44
1521 1559 8.413229 CCACCTTGATTCTAGAAAGAACAAAAA 58.587 33.333 9.71 0.00 44.40 1.94
1576 1614 9.570468 AACTGCTCAATCAGATGATATATTTGT 57.430 29.630 0.00 0.00 37.51 2.83
2057 2103 2.125391 GCAGCATCCGACAGAGCA 60.125 61.111 0.00 0.00 0.00 4.26
2299 2359 5.739959 TGTTTGATCGATCTTATGTTCCCA 58.260 37.500 25.02 7.10 0.00 4.37
2300 2360 5.817296 TGTTTGATCGATCTTATGTTCCCAG 59.183 40.000 25.02 0.00 0.00 4.45
2394 2454 6.662234 TCTGCTCTGCTAAGGTAGTTTAACTA 59.338 38.462 0.03 0.03 0.00 2.24
2564 2631 5.484173 ACATTACATTACACGCATCCTTG 57.516 39.130 0.00 0.00 0.00 3.61
2565 2632 4.335315 ACATTACATTACACGCATCCTTGG 59.665 41.667 0.00 0.00 0.00 3.61
2570 2637 2.851263 TACACGCATCCTTGGACTTT 57.149 45.000 0.00 0.00 0.00 2.66
2571 2638 1.981256 ACACGCATCCTTGGACTTTT 58.019 45.000 0.00 0.00 0.00 2.27
2651 2720 2.424956 GCTTCTGCATCCTTTACCCTTG 59.575 50.000 0.00 0.00 39.41 3.61
2693 2762 6.543831 GTGCAACCTTCATACTTATCCAAGAT 59.456 38.462 0.00 0.00 35.60 2.40
2694 2763 6.767902 TGCAACCTTCATACTTATCCAAGATC 59.232 38.462 0.00 0.00 35.60 2.75
2695 2764 6.767902 GCAACCTTCATACTTATCCAAGATCA 59.232 38.462 0.00 0.00 35.60 2.92
2696 2765 7.283127 GCAACCTTCATACTTATCCAAGATCAA 59.717 37.037 0.00 0.00 35.60 2.57
2697 2766 8.834465 CAACCTTCATACTTATCCAAGATCAAG 58.166 37.037 0.00 0.00 35.60 3.02
2711 2780 4.283363 AGATCAAGTCAAGTGTGCTCAT 57.717 40.909 0.00 0.00 0.00 2.90
2716 2785 3.213206 AGTCAAGTGTGCTCATCCAAA 57.787 42.857 0.00 0.00 0.00 3.28
2871 3301 1.755959 TCTCCTTCTGCAGATGAGAGC 59.244 52.381 29.03 0.00 32.27 4.09
2898 3328 3.604667 CTTGCAAACGGCTGCCCA 61.605 61.111 14.12 1.25 45.15 5.36
3240 3676 2.060383 CGGGAGAGCCATCCTGTCA 61.060 63.158 5.61 0.00 40.37 3.58
3271 3707 0.838122 CTGAGGTCCCTCCCTGTGTT 60.838 60.000 10.77 0.00 42.09 3.32
3286 3722 1.203038 TGTGTTGATCATGGCAGGGTT 60.203 47.619 0.00 0.00 0.00 4.11
3287 3723 1.474077 GTGTTGATCATGGCAGGGTTC 59.526 52.381 0.00 0.00 0.00 3.62
3299 3735 2.066999 AGGGTTCTGAGATCCCGGC 61.067 63.158 20.04 0.39 44.09 6.13
3305 3742 3.839353 CTGAGATCCCGGCATGGCC 62.839 68.421 14.46 0.00 46.75 5.36
3333 3770 3.855379 TGTATCGTGTTGTATCAGCGAAC 59.145 43.478 0.00 0.00 35.20 3.95
3347 3784 1.850640 CGAACGTGAAGTGGAACCG 59.149 57.895 0.00 0.00 37.80 4.44
3349 3787 1.574134 GAACGTGAAGTGGAACCGAA 58.426 50.000 0.00 0.00 37.80 4.30
3403 3853 7.214467 TGGACATTAACAAAATGAGTTCTCC 57.786 36.000 4.82 2.06 0.00 3.71
3405 3855 6.148811 GGACATTAACAAAATGAGTTCTCCGA 59.851 38.462 4.82 0.00 0.00 4.55
3461 3928 2.881513 TCAGTTTTGTGTGTGTGTGTGT 59.118 40.909 0.00 0.00 0.00 3.72
3463 3930 2.621055 AGTTTTGTGTGTGTGTGTGTGT 59.379 40.909 0.00 0.00 0.00 3.72
3466 3933 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
3467 3934 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
3469 3936 3.504273 GTGTGTGTGTGTGCGCCA 61.504 61.111 4.18 0.00 0.00 5.69
3470 3937 3.504273 TGTGTGTGTGTGCGCCAC 61.504 61.111 18.49 18.49 44.78 5.01
3477 3944 4.367023 GTGTGCGCCACGGGACTA 62.367 66.667 4.18 0.00 37.14 2.59
3481 3948 3.755628 GCGCCACGGGACTAGTCA 61.756 66.667 23.91 0.00 0.00 3.41
3484 3951 1.028330 CGCCACGGGACTAGTCACTA 61.028 60.000 22.47 0.00 0.00 2.74
3485 3952 1.400737 GCCACGGGACTAGTCACTAT 58.599 55.000 22.47 8.19 0.00 2.12
3513 3981 1.891150 CAAAGCTGGCCTGAACTGATT 59.109 47.619 14.77 0.00 0.00 2.57
3516 3984 3.439857 AGCTGGCCTGAACTGATTTTA 57.560 42.857 14.77 0.00 0.00 1.52
3517 3985 3.973425 AGCTGGCCTGAACTGATTTTAT 58.027 40.909 14.77 0.00 0.00 1.40
3518 3986 4.347607 AGCTGGCCTGAACTGATTTTATT 58.652 39.130 14.77 0.00 0.00 1.40
3519 3987 5.509498 AGCTGGCCTGAACTGATTTTATTA 58.491 37.500 14.77 0.00 0.00 0.98
3520 3988 5.591877 AGCTGGCCTGAACTGATTTTATTAG 59.408 40.000 14.77 0.00 0.00 1.73
3521 3989 5.590259 GCTGGCCTGAACTGATTTTATTAGA 59.410 40.000 14.77 0.00 0.00 2.10
3522 3990 6.095440 GCTGGCCTGAACTGATTTTATTAGAA 59.905 38.462 14.77 0.00 0.00 2.10
3523 3991 7.630242 TGGCCTGAACTGATTTTATTAGAAG 57.370 36.000 3.32 0.00 0.00 2.85
3524 3992 7.402054 TGGCCTGAACTGATTTTATTAGAAGA 58.598 34.615 3.32 0.00 0.00 2.87
3525 3993 7.888021 TGGCCTGAACTGATTTTATTAGAAGAA 59.112 33.333 3.32 0.00 0.00 2.52
3526 3994 8.739972 GGCCTGAACTGATTTTATTAGAAGAAA 58.260 33.333 0.00 0.00 0.00 2.52
3527 3995 9.780413 GCCTGAACTGATTTTATTAGAAGAAAG 57.220 33.333 0.00 0.00 0.00 2.62
3528 3996 9.780413 CCTGAACTGATTTTATTAGAAGAAAGC 57.220 33.333 0.00 0.00 0.00 3.51
3545 4013 9.589111 AGAAGAAAGCTACAGTATTTACTAAGC 57.411 33.333 12.82 12.82 41.30 3.09
3547 4015 8.934507 AGAAAGCTACAGTATTTACTAAGCTG 57.065 34.615 19.49 4.69 45.96 4.24
3548 4016 8.750298 AGAAAGCTACAGTATTTACTAAGCTGA 58.250 33.333 19.49 0.00 45.96 4.26
3549 4017 8.934507 AAAGCTACAGTATTTACTAAGCTGAG 57.065 34.615 19.49 0.00 45.96 3.35
3550 4018 7.883391 AGCTACAGTATTTACTAAGCTGAGA 57.117 36.000 18.67 0.00 45.44 3.27
3551 4019 8.472007 AGCTACAGTATTTACTAAGCTGAGAT 57.528 34.615 18.67 0.00 45.44 2.75
3552 4020 9.575868 AGCTACAGTATTTACTAAGCTGAGATA 57.424 33.333 18.67 0.00 45.44 1.98
3561 4029 8.466617 TTTACTAAGCTGAGATAACTAGAGGG 57.533 38.462 4.63 0.00 0.00 4.30
3562 4030 5.390387 ACTAAGCTGAGATAACTAGAGGGG 58.610 45.833 4.63 0.00 0.00 4.79
3563 4031 4.544564 AAGCTGAGATAACTAGAGGGGA 57.455 45.455 0.00 0.00 0.00 4.81
3564 4032 3.839778 AGCTGAGATAACTAGAGGGGAC 58.160 50.000 0.00 0.00 0.00 4.46
3566 4034 3.572255 GCTGAGATAACTAGAGGGGACTG 59.428 52.174 0.00 0.00 44.43 3.51
3567 4035 4.690261 GCTGAGATAACTAGAGGGGACTGA 60.690 50.000 0.00 0.00 44.43 3.41
3568 4036 5.055265 TGAGATAACTAGAGGGGACTGAG 57.945 47.826 0.00 0.00 44.43 3.35
3569 4037 4.727332 TGAGATAACTAGAGGGGACTGAGA 59.273 45.833 0.00 0.00 44.43 3.27
3570 4038 5.163141 TGAGATAACTAGAGGGGACTGAGAG 60.163 48.000 0.00 0.00 44.43 3.20
3571 4039 4.729881 AGATAACTAGAGGGGACTGAGAGT 59.270 45.833 0.00 0.00 44.43 3.24
3572 4040 2.818751 ACTAGAGGGGACTGAGAGTG 57.181 55.000 0.00 0.00 44.43 3.51
3573 4041 1.341581 ACTAGAGGGGACTGAGAGTGC 60.342 57.143 0.00 0.00 44.43 4.40
3574 4042 0.394488 TAGAGGGGACTGAGAGTGCG 60.394 60.000 0.00 0.00 44.43 5.34
3575 4043 1.679305 GAGGGGACTGAGAGTGCGA 60.679 63.158 0.00 0.00 44.43 5.10
3576 4044 1.228894 AGGGGACTGAGAGTGCGAA 60.229 57.895 0.00 0.00 37.44 4.70
3577 4045 1.216710 GGGGACTGAGAGTGCGAAG 59.783 63.158 0.00 0.00 37.44 3.79
3591 4059 3.280532 CGAAGCAGAATCACAACGC 57.719 52.632 0.00 0.00 0.00 4.84
3592 4060 0.179215 CGAAGCAGAATCACAACGCC 60.179 55.000 0.00 0.00 0.00 5.68
3593 4061 0.169009 GAAGCAGAATCACAACGCCC 59.831 55.000 0.00 0.00 0.00 6.13
3594 4062 1.244019 AAGCAGAATCACAACGCCCC 61.244 55.000 0.00 0.00 0.00 5.80
3595 4063 2.700773 GCAGAATCACAACGCCCCC 61.701 63.158 0.00 0.00 0.00 5.40
3609 4077 4.388499 CCCCCGGTGTCAACCTCG 62.388 72.222 0.00 0.00 45.17 4.63
3611 4079 4.003788 CCCGGTGTCAACCTCGCT 62.004 66.667 0.00 0.00 45.17 4.93
3612 4080 2.432628 CCGGTGTCAACCTCGCTC 60.433 66.667 0.00 0.00 45.17 5.03
3613 4081 2.805353 CGGTGTCAACCTCGCTCG 60.805 66.667 0.00 0.00 45.17 5.03
3614 4082 2.432628 GGTGTCAACCTCGCTCGG 60.433 66.667 0.00 0.00 43.84 4.63
3615 4083 2.432628 GTGTCAACCTCGCTCGGG 60.433 66.667 0.00 0.00 0.00 5.14
3616 4084 4.373116 TGTCAACCTCGCTCGGGC 62.373 66.667 0.00 0.00 0.00 6.13
3634 4102 4.475527 GGCGCCCGATCCTTATTT 57.524 55.556 18.11 0.00 0.00 1.40
3635 4103 2.244946 GGCGCCCGATCCTTATTTC 58.755 57.895 18.11 0.00 0.00 2.17
3636 4104 1.235281 GGCGCCCGATCCTTATTTCC 61.235 60.000 18.11 0.00 0.00 3.13
3637 4105 1.235281 GCGCCCGATCCTTATTTCCC 61.235 60.000 0.00 0.00 0.00 3.97
3638 4106 0.949105 CGCCCGATCCTTATTTCCCG 60.949 60.000 0.00 0.00 0.00 5.14
3639 4107 0.395312 GCCCGATCCTTATTTCCCGA 59.605 55.000 0.00 0.00 0.00 5.14
3640 4108 1.876837 GCCCGATCCTTATTTCCCGAC 60.877 57.143 0.00 0.00 0.00 4.79
3641 4109 1.604693 CCCGATCCTTATTTCCCGACG 60.605 57.143 0.00 0.00 0.00 5.12
3642 4110 1.338973 CCGATCCTTATTTCCCGACGA 59.661 52.381 0.00 0.00 0.00 4.20
3643 4111 2.391879 CGATCCTTATTTCCCGACGAC 58.608 52.381 0.00 0.00 0.00 4.34
3644 4112 2.752121 GATCCTTATTTCCCGACGACC 58.248 52.381 0.00 0.00 0.00 4.79
3645 4113 0.826062 TCCTTATTTCCCGACGACCC 59.174 55.000 0.00 0.00 0.00 4.46
3646 4114 0.828677 CCTTATTTCCCGACGACCCT 59.171 55.000 0.00 0.00 0.00 4.34
3647 4115 1.208776 CCTTATTTCCCGACGACCCTT 59.791 52.381 0.00 0.00 0.00 3.95
3648 4116 2.431782 CCTTATTTCCCGACGACCCTTA 59.568 50.000 0.00 0.00 0.00 2.69
3649 4117 3.451526 CTTATTTCCCGACGACCCTTAC 58.548 50.000 0.00 0.00 0.00 2.34
3650 4118 1.565067 ATTTCCCGACGACCCTTACT 58.435 50.000 0.00 0.00 0.00 2.24
3651 4119 2.214376 TTTCCCGACGACCCTTACTA 57.786 50.000 0.00 0.00 0.00 1.82
3652 4120 1.463674 TTCCCGACGACCCTTACTAC 58.536 55.000 0.00 0.00 0.00 2.73
3653 4121 0.327924 TCCCGACGACCCTTACTACA 59.672 55.000 0.00 0.00 0.00 2.74
3654 4122 0.737219 CCCGACGACCCTTACTACAG 59.263 60.000 0.00 0.00 0.00 2.74
3655 4123 0.100146 CCGACGACCCTTACTACAGC 59.900 60.000 0.00 0.00 0.00 4.40
3656 4124 0.247974 CGACGACCCTTACTACAGCG 60.248 60.000 0.00 0.00 0.00 5.18
3657 4125 0.525029 GACGACCCTTACTACAGCGC 60.525 60.000 0.00 0.00 0.00 5.92
3658 4126 1.246056 ACGACCCTTACTACAGCGCA 61.246 55.000 11.47 0.00 0.00 6.09
3659 4127 0.102481 CGACCCTTACTACAGCGCAT 59.898 55.000 11.47 0.00 0.00 4.73
3660 4128 1.335810 CGACCCTTACTACAGCGCATA 59.664 52.381 11.47 0.00 0.00 3.14
3661 4129 2.030185 CGACCCTTACTACAGCGCATAT 60.030 50.000 11.47 0.00 0.00 1.78
3662 4130 3.576648 GACCCTTACTACAGCGCATATC 58.423 50.000 11.47 0.00 0.00 1.63
3663 4131 3.231818 ACCCTTACTACAGCGCATATCT 58.768 45.455 11.47 0.00 0.00 1.98
3664 4132 3.256136 ACCCTTACTACAGCGCATATCTC 59.744 47.826 11.47 0.00 0.00 2.75
3665 4133 3.255888 CCCTTACTACAGCGCATATCTCA 59.744 47.826 11.47 0.00 0.00 3.27
3666 4134 4.081972 CCCTTACTACAGCGCATATCTCAT 60.082 45.833 11.47 0.00 0.00 2.90
3667 4135 5.473931 CCTTACTACAGCGCATATCTCATT 58.526 41.667 11.47 0.00 0.00 2.57
3668 4136 5.928839 CCTTACTACAGCGCATATCTCATTT 59.071 40.000 11.47 0.00 0.00 2.32
3669 4137 6.425114 CCTTACTACAGCGCATATCTCATTTT 59.575 38.462 11.47 0.00 0.00 1.82
3670 4138 7.598869 CCTTACTACAGCGCATATCTCATTTTA 59.401 37.037 11.47 0.00 0.00 1.52
3671 4139 6.771188 ACTACAGCGCATATCTCATTTTAC 57.229 37.500 11.47 0.00 0.00 2.01
3672 4140 5.696724 ACTACAGCGCATATCTCATTTTACC 59.303 40.000 11.47 0.00 0.00 2.85
3673 4141 4.708177 ACAGCGCATATCTCATTTTACCT 58.292 39.130 11.47 0.00 0.00 3.08
3674 4142 4.752101 ACAGCGCATATCTCATTTTACCTC 59.248 41.667 11.47 0.00 0.00 3.85
3675 4143 3.990469 AGCGCATATCTCATTTTACCTCG 59.010 43.478 11.47 0.00 0.00 4.63
3676 4144 3.423645 GCGCATATCTCATTTTACCTCGC 60.424 47.826 0.30 0.00 0.00 5.03
3677 4145 3.990469 CGCATATCTCATTTTACCTCGCT 59.010 43.478 0.00 0.00 0.00 4.93
3678 4146 4.449068 CGCATATCTCATTTTACCTCGCTT 59.551 41.667 0.00 0.00 0.00 4.68
3681 4149 2.985896 TCTCATTTTACCTCGCTTGGG 58.014 47.619 0.00 0.00 0.00 4.12
3919 4482 3.225798 TGCTGCGGCTGCCTTTTT 61.226 55.556 25.79 0.00 41.78 1.94
3922 4485 2.904866 TGCGGCTGCCTTTTTCGT 60.905 55.556 16.57 0.00 41.78 3.85
3930 4493 0.459489 TGCCTTTTTCGTTGCTGCTT 59.541 45.000 0.00 0.00 0.00 3.91
3934 4497 2.350772 CCTTTTTCGTTGCTGCTTCGAT 60.351 45.455 16.73 0.00 33.72 3.59
3944 4507 0.384309 CTGCTTCGATAGGCGGTGTA 59.616 55.000 6.30 0.00 41.33 2.90
3956 4520 3.330720 GGTGTAGGGGCCTGCTGT 61.331 66.667 0.84 0.00 0.00 4.40
3973 4537 2.484264 GCTGTTGTGCTCGAATAAAGGT 59.516 45.455 0.00 0.00 0.00 3.50
3990 4554 1.988406 GTGGCGGTCCTAGGGTTCT 60.988 63.158 9.46 0.00 0.00 3.01
4023 4587 0.784778 CGAAGAGTTGCCTGACGTTC 59.215 55.000 0.00 0.00 0.00 3.95
4036 4600 1.616865 TGACGTTCGTCCTTCCTGATT 59.383 47.619 20.02 0.00 34.50 2.57
4057 4621 4.323477 CCGGAGTGGCGGGTTTCA 62.323 66.667 0.00 0.00 32.60 2.69
4069 4633 1.302511 GGTTTCAGAAGGCTCCGCA 60.303 57.895 0.00 0.00 0.00 5.69
4084 4648 2.268920 GCAGGCGAACTCCCATGA 59.731 61.111 0.00 0.00 0.00 3.07
4085 4649 1.377202 GCAGGCGAACTCCCATGAA 60.377 57.895 0.00 0.00 0.00 2.57
4089 4653 0.108520 GGCGAACTCCCATGAACGTA 60.109 55.000 0.00 0.00 0.00 3.57
4093 4657 3.489785 GCGAACTCCCATGAACGTATTAG 59.510 47.826 0.00 0.00 0.00 1.73
4095 4659 4.441079 CGAACTCCCATGAACGTATTAGGT 60.441 45.833 0.00 0.00 0.00 3.08
4113 4677 1.767681 GGTCTGGAGATTGCTGGATCT 59.232 52.381 0.00 0.00 39.04 2.75
4125 4689 0.833287 CTGGATCTGGTGGGATTCGT 59.167 55.000 0.00 0.00 0.00 3.85
4127 4691 1.633432 TGGATCTGGTGGGATTCGTTT 59.367 47.619 0.00 0.00 0.00 3.60
4150 4714 2.164338 GCCCATTGGTTCTCCGTTAAA 58.836 47.619 1.20 0.00 36.30 1.52
4183 4747 3.594134 GTGAAGCTCTGCTATCTGTTGT 58.406 45.455 0.00 0.00 38.25 3.32
4222 4786 2.836372 AGCTCCATGTTGATGTCAGAGA 59.164 45.455 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.741841 GGATCTTCTATACTTCTATAAACCGCT 58.258 37.037 0.00 0.00 0.00 5.52
52 53 3.967987 GCCCCTTCTACTTGGATCTTCTA 59.032 47.826 0.00 0.00 0.00 2.10
80 81 2.398588 TCACCTGGAAGTTGTCAGAGT 58.601 47.619 0.00 0.17 33.11 3.24
114 115 1.661509 GAAACGGCAAGCAAGCACC 60.662 57.895 2.78 0.00 35.83 5.01
116 117 1.391157 AAGGAAACGGCAAGCAAGCA 61.391 50.000 2.78 0.00 35.83 3.91
173 174 3.117512 ACCTTCTCAAAAGGAGCTTTGGA 60.118 43.478 10.68 0.00 43.70 3.53
174 175 3.225940 ACCTTCTCAAAAGGAGCTTTGG 58.774 45.455 10.68 0.00 43.70 3.28
175 176 3.058639 CGACCTTCTCAAAAGGAGCTTTG 60.059 47.826 10.68 0.00 43.70 2.77
176 177 3.142174 CGACCTTCTCAAAAGGAGCTTT 58.858 45.455 10.68 0.00 43.70 3.51
177 178 2.551071 CCGACCTTCTCAAAAGGAGCTT 60.551 50.000 10.68 0.00 43.70 3.74
178 179 1.002544 CCGACCTTCTCAAAAGGAGCT 59.997 52.381 10.68 0.00 43.70 4.09
179 180 1.443802 CCGACCTTCTCAAAAGGAGC 58.556 55.000 10.68 1.98 43.70 4.70
180 181 1.443802 GCCGACCTTCTCAAAAGGAG 58.556 55.000 10.68 4.42 45.49 3.69
181 182 0.320421 CGCCGACCTTCTCAAAAGGA 60.320 55.000 10.68 0.00 39.81 3.36
197 205 1.661112 GAGTGAACTCTGCATAACGCC 59.339 52.381 3.13 0.00 39.81 5.68
237 246 9.978740 GCAACTAGCAACTTCCGATAGAGGAAT 62.979 44.444 0.00 0.00 45.26 3.01
296 309 7.539436 GTTTTATCAAGAAACCAATCTCTCCC 58.461 38.462 0.00 0.00 32.26 4.30
311 324 8.283291 GCCTTAGGATCATTACGTTTTATCAAG 58.717 37.037 0.69 0.00 0.00 3.02
318 331 3.118519 ACGGCCTTAGGATCATTACGTTT 60.119 43.478 0.69 0.00 0.00 3.60
320 333 2.035576 GACGGCCTTAGGATCATTACGT 59.964 50.000 0.69 0.00 34.50 3.57
321 334 2.609737 GGACGGCCTTAGGATCATTACG 60.610 54.545 0.00 0.00 0.00 3.18
325 339 1.734655 ATGGACGGCCTTAGGATCAT 58.265 50.000 9.82 0.00 34.31 2.45
352 366 3.119459 TCAGCTAGAAGTGGCGTAAGAAG 60.119 47.826 0.00 0.00 43.02 2.85
394 408 6.459066 CACTAATCTCTCAAGTCAACCAGAA 58.541 40.000 0.00 0.00 0.00 3.02
399 414 5.233988 ACTGCACTAATCTCTCAAGTCAAC 58.766 41.667 0.00 0.00 0.00 3.18
501 516 1.645710 ACCATGGAGTTCTCTTCCGT 58.354 50.000 21.47 0.00 0.00 4.69
535 550 6.796785 ATTTCTTTGGTTGGCTTATGCTAT 57.203 33.333 0.13 0.00 39.59 2.97
554 569 3.896122 TCTTGCCGTGTGCTTTAATTTC 58.104 40.909 0.00 0.00 42.00 2.17
568 583 3.485051 GCTTTGTTTTGGTTTTCTTGCCG 60.485 43.478 0.00 0.00 0.00 5.69
625 640 4.515191 TGTCTCTTTGCTATGTTTCGCTTT 59.485 37.500 0.00 0.00 0.00 3.51
628 643 4.398247 CTTGTCTCTTTGCTATGTTTCGC 58.602 43.478 0.00 0.00 0.00 4.70
636 651 1.337823 GCCGTCCTTGTCTCTTTGCTA 60.338 52.381 0.00 0.00 0.00 3.49
695 711 6.127535 ACAAACAGAGGAATGGAGCAATAATG 60.128 38.462 0.00 0.00 0.00 1.90
805 821 4.038162 ACCGAGATCTAGCAATTACCTGAC 59.962 45.833 0.00 0.00 0.00 3.51
809 825 4.551388 CTCACCGAGATCTAGCAATTACC 58.449 47.826 0.00 0.00 0.00 2.85
870 889 2.684038 GCAAGATCCAAGTAACCTCCCC 60.684 54.545 0.00 0.00 0.00 4.81
886 905 4.030753 CGCAACAAAAACGTAAAAGCAAGA 59.969 37.500 0.00 0.00 0.00 3.02
887 906 4.252130 CGCAACAAAAACGTAAAAGCAAG 58.748 39.130 0.00 0.00 0.00 4.01
888 907 3.060895 CCGCAACAAAAACGTAAAAGCAA 59.939 39.130 0.00 0.00 0.00 3.91
892 911 5.819059 AGTATCCGCAACAAAAACGTAAAA 58.181 33.333 0.00 0.00 0.00 1.52
953 972 4.691860 AGTGCAGCTATTAGCAAACTTG 57.308 40.909 17.59 7.81 45.56 3.16
996 1015 4.040706 ACCATCTGTGCATTGACCATTTTT 59.959 37.500 0.00 0.00 0.00 1.94
1101 1123 4.800554 CCTGACAAGGTGGTGTCC 57.199 61.111 3.06 0.00 46.13 4.02
1164 1186 1.129917 CCATCCTGTCATCTCCAGCT 58.870 55.000 0.00 0.00 0.00 4.24
1206 1228 4.460683 GCATCACGCCACCCGGTA 62.461 66.667 0.00 0.00 42.52 4.02
1242 1264 1.470890 CACCACGAGAAGGAGAGACTC 59.529 57.143 0.00 0.00 0.00 3.36
1270 1292 7.492994 CACATATGAGAGATATGCAGAATGGAG 59.507 40.741 10.38 0.00 42.42 3.86
1273 1295 8.657729 GTTCACATATGAGAGATATGCAGAATG 58.342 37.037 10.38 0.00 35.83 2.67
1283 1305 4.103627 TGGGCATGTTCACATATGAGAGAT 59.896 41.667 10.38 0.64 35.83 2.75
1290 1312 5.657745 TGAAGAATTGGGCATGTTCACATAT 59.342 36.000 0.00 0.00 34.26 1.78
1299 1321 5.389859 TGTAAACTGAAGAATTGGGCATG 57.610 39.130 0.00 0.00 0.00 4.06
1303 1325 6.209391 ACCATCTTGTAAACTGAAGAATTGGG 59.791 38.462 0.00 0.00 34.59 4.12
1342 1371 9.669353 GCCTACAAGTGACATTTCATAATTATG 57.331 33.333 17.82 17.82 33.11 1.90
1420 1458 8.338259 GTGAACTTCCAACATACATCATATGAC 58.662 37.037 7.78 0.00 0.00 3.06
1423 1461 7.012704 GCAGTGAACTTCCAACATACATCATAT 59.987 37.037 0.00 0.00 0.00 1.78
1430 1468 4.829064 TTGCAGTGAACTTCCAACATAC 57.171 40.909 0.00 0.00 0.00 2.39
1443 1481 5.964758 AGAAAGTTTTCACATTTGCAGTGA 58.035 33.333 3.31 3.31 43.72 3.41
1467 1505 6.428159 AGCTGACGAATCAAATTACTTGACTT 59.572 34.615 0.00 0.00 46.80 3.01
1468 1506 5.934625 AGCTGACGAATCAAATTACTTGACT 59.065 36.000 0.00 0.00 46.80 3.41
1474 1512 4.391830 TGGACAGCTGACGAATCAAATTAC 59.608 41.667 23.35 0.00 33.30 1.89
1475 1513 4.391830 GTGGACAGCTGACGAATCAAATTA 59.608 41.667 23.35 0.00 33.30 1.40
1482 1520 0.687354 AAGGTGGACAGCTGACGAAT 59.313 50.000 23.35 0.00 39.39 3.34
1486 1524 2.079925 GAATCAAGGTGGACAGCTGAC 58.920 52.381 23.35 15.15 39.39 3.51
1542 1580 7.031372 TCATCTGATTGAGCAGTTTTAATTGC 58.969 34.615 2.13 2.13 41.38 3.56
2299 2359 2.469274 CACCAGATTGTGCAGACTCT 57.531 50.000 0.00 0.00 0.00 3.24
2363 2423 2.266554 CCTTAGCAGAGCAGAGAAACG 58.733 52.381 0.00 0.00 0.00 3.60
2423 2483 7.360691 CCAGTCTCAGTTCTGATATTGTTTGTG 60.361 40.741 2.89 0.00 34.02 3.33
2424 2484 6.652481 CCAGTCTCAGTTCTGATATTGTTTGT 59.348 38.462 2.89 0.00 34.02 2.83
2425 2485 6.402983 GCCAGTCTCAGTTCTGATATTGTTTG 60.403 42.308 2.89 0.00 34.02 2.93
2426 2486 5.645497 GCCAGTCTCAGTTCTGATATTGTTT 59.355 40.000 2.89 0.00 34.02 2.83
2535 2602 5.922546 TGCGTGTAATGTAATGTTTGAGAC 58.077 37.500 0.00 0.00 0.00 3.36
2607 2674 6.547510 AGCAACTTAACAAAATCAGGAAGACT 59.452 34.615 0.00 0.00 0.00 3.24
2608 2675 6.739112 AGCAACTTAACAAAATCAGGAAGAC 58.261 36.000 0.00 0.00 0.00 3.01
2651 2720 2.035961 TGCACCTCAGAGAACAGTGTAC 59.964 50.000 0.00 0.00 0.00 2.90
2685 2754 3.755378 GCACACTTGACTTGATCTTGGAT 59.245 43.478 0.00 0.00 0.00 3.41
2693 2762 2.104622 TGGATGAGCACACTTGACTTGA 59.895 45.455 0.00 0.00 0.00 3.02
2694 2763 2.497138 TGGATGAGCACACTTGACTTG 58.503 47.619 0.00 0.00 0.00 3.16
2695 2764 2.936919 TGGATGAGCACACTTGACTT 57.063 45.000 0.00 0.00 0.00 3.01
2696 2765 2.936919 TTGGATGAGCACACTTGACT 57.063 45.000 0.00 0.00 0.00 3.41
2697 2766 4.510038 AATTTGGATGAGCACACTTGAC 57.490 40.909 0.00 0.00 0.00 3.18
2711 2780 5.073311 TCAACAACCGAAACAAATTTGGA 57.927 34.783 21.74 2.61 44.46 3.53
2716 2785 5.841810 ACATCATCAACAACCGAAACAAAT 58.158 33.333 0.00 0.00 0.00 2.32
2898 3328 3.953775 CCCAGGGAACGCAGGTGT 61.954 66.667 0.00 0.00 0.00 4.16
2964 3394 2.169789 CCTGATGCGGCTGTTCTCG 61.170 63.158 0.00 0.00 0.00 4.04
3054 3490 1.582968 GGTGCACTGGCTGATGTTG 59.417 57.895 17.98 0.00 41.91 3.33
3271 3707 1.211212 CTCAGAACCCTGCCATGATCA 59.789 52.381 0.00 0.00 40.20 2.92
3286 3722 2.811514 GCCATGCCGGGATCTCAGA 61.812 63.158 5.02 0.00 34.06 3.27
3287 3723 2.281345 GCCATGCCGGGATCTCAG 60.281 66.667 5.02 0.00 34.06 3.35
3299 3735 1.327460 CACGATACAAACTCGGCCATG 59.673 52.381 2.24 0.00 40.37 3.66
3305 3742 5.498700 GCTGATACAACACGATACAAACTCG 60.499 44.000 0.00 0.00 41.77 4.18
3333 3770 0.249741 ACCTTCGGTTCCACTTCACG 60.250 55.000 0.00 0.00 27.29 4.35
3347 3784 0.951040 CAGACTTCCACCGCACCTTC 60.951 60.000 0.00 0.00 0.00 3.46
3349 3787 2.140792 ACAGACTTCCACCGCACCT 61.141 57.895 0.00 0.00 0.00 4.00
3403 3853 3.201290 AGCAAGGCTCACATATTCTTCG 58.799 45.455 0.00 0.00 30.62 3.79
3405 3855 4.157289 CACAAGCAAGGCTCACATATTCTT 59.843 41.667 0.00 0.00 38.25 2.52
3437 3889 3.505680 ACACACACACACAAAACTGACAT 59.494 39.130 0.00 0.00 0.00 3.06
3461 3928 4.063967 CTAGTCCCGTGGCGCACA 62.064 66.667 10.83 1.22 33.40 4.57
3463 3930 3.755628 GACTAGTCCCGTGGCGCA 61.756 66.667 12.13 0.00 0.00 6.09
3466 3933 1.067212 CATAGTGACTAGTCCCGTGGC 59.933 57.143 20.11 3.93 0.00 5.01
3467 3934 1.681793 CCATAGTGACTAGTCCCGTGG 59.318 57.143 20.11 16.95 0.00 4.94
3469 3936 1.063867 AGCCATAGTGACTAGTCCCGT 60.064 52.381 20.11 7.14 0.00 5.28
3470 3937 1.693627 AGCCATAGTGACTAGTCCCG 58.306 55.000 20.11 4.08 0.00 5.14
3471 3938 3.158676 CCTAGCCATAGTGACTAGTCCC 58.841 54.545 20.11 8.98 33.09 4.46
3472 3939 2.559231 GCCTAGCCATAGTGACTAGTCC 59.441 54.545 20.11 11.29 33.09 3.85
3473 3940 3.223435 TGCCTAGCCATAGTGACTAGTC 58.777 50.000 16.32 16.32 33.09 2.59
3474 3941 3.314307 TGCCTAGCCATAGTGACTAGT 57.686 47.619 0.00 0.00 33.09 2.57
3475 3942 4.626042 CTTTGCCTAGCCATAGTGACTAG 58.374 47.826 0.00 0.00 34.44 2.57
3476 3943 3.181465 GCTTTGCCTAGCCATAGTGACTA 60.181 47.826 0.00 0.00 35.06 2.59
3477 3944 2.420687 GCTTTGCCTAGCCATAGTGACT 60.421 50.000 0.00 0.00 35.06 3.41
3481 3948 1.133976 CCAGCTTTGCCTAGCCATAGT 60.134 52.381 3.75 0.00 42.20 2.12
3484 3951 1.755783 GCCAGCTTTGCCTAGCCAT 60.756 57.895 3.75 0.00 42.20 4.40
3485 3952 2.361610 GCCAGCTTTGCCTAGCCA 60.362 61.111 3.75 0.00 42.20 4.75
3492 3959 1.174712 TCAGTTCAGGCCAGCTTTGC 61.175 55.000 5.01 0.00 0.00 3.68
3519 3987 9.589111 GCTTAGTAAATACTGTAGCTTTCTTCT 57.411 33.333 16.11 0.00 39.80 2.85
3520 3988 9.589111 AGCTTAGTAAATACTGTAGCTTTCTTC 57.411 33.333 18.52 0.56 45.22 2.87
3521 3989 9.372369 CAGCTTAGTAAATACTGTAGCTTTCTT 57.628 33.333 20.30 6.13 45.22 2.52
3522 3990 8.750298 TCAGCTTAGTAAATACTGTAGCTTTCT 58.250 33.333 20.30 6.38 45.22 2.52
3523 3991 8.928270 TCAGCTTAGTAAATACTGTAGCTTTC 57.072 34.615 20.30 0.00 45.22 2.62
3524 3992 8.750298 TCTCAGCTTAGTAAATACTGTAGCTTT 58.250 33.333 20.30 7.10 45.22 3.51
3525 3993 8.294954 TCTCAGCTTAGTAAATACTGTAGCTT 57.705 34.615 20.30 10.05 45.22 3.74
3526 3994 7.883391 TCTCAGCTTAGTAAATACTGTAGCT 57.117 36.000 18.52 18.52 46.80 3.32
3535 4003 9.084533 CCCTCTAGTTATCTCAGCTTAGTAAAT 57.915 37.037 0.00 0.00 0.00 1.40
3536 4004 7.506261 CCCCTCTAGTTATCTCAGCTTAGTAAA 59.494 40.741 0.00 0.00 0.00 2.01
3537 4005 7.005296 CCCCTCTAGTTATCTCAGCTTAGTAA 58.995 42.308 0.00 0.00 0.00 2.24
3538 4006 6.332103 TCCCCTCTAGTTATCTCAGCTTAGTA 59.668 42.308 0.00 0.00 0.00 1.82
3539 4007 5.134679 TCCCCTCTAGTTATCTCAGCTTAGT 59.865 44.000 0.00 0.00 0.00 2.24
3540 4008 5.475564 GTCCCCTCTAGTTATCTCAGCTTAG 59.524 48.000 0.00 0.00 0.00 2.18
3541 4009 5.134679 AGTCCCCTCTAGTTATCTCAGCTTA 59.865 44.000 0.00 0.00 0.00 3.09
3542 4010 4.078863 AGTCCCCTCTAGTTATCTCAGCTT 60.079 45.833 0.00 0.00 0.00 3.74
3543 4011 3.465588 AGTCCCCTCTAGTTATCTCAGCT 59.534 47.826 0.00 0.00 0.00 4.24
3544 4012 3.572255 CAGTCCCCTCTAGTTATCTCAGC 59.428 52.174 0.00 0.00 0.00 4.26
3545 4013 5.055265 TCAGTCCCCTCTAGTTATCTCAG 57.945 47.826 0.00 0.00 0.00 3.35
3546 4014 4.727332 TCTCAGTCCCCTCTAGTTATCTCA 59.273 45.833 0.00 0.00 0.00 3.27
3547 4015 5.163131 ACTCTCAGTCCCCTCTAGTTATCTC 60.163 48.000 0.00 0.00 0.00 2.75
3548 4016 4.729881 ACTCTCAGTCCCCTCTAGTTATCT 59.270 45.833 0.00 0.00 0.00 1.98
3549 4017 4.825085 CACTCTCAGTCCCCTCTAGTTATC 59.175 50.000 0.00 0.00 0.00 1.75
3550 4018 4.798882 CACTCTCAGTCCCCTCTAGTTAT 58.201 47.826 0.00 0.00 0.00 1.89
3551 4019 3.625211 GCACTCTCAGTCCCCTCTAGTTA 60.625 52.174 0.00 0.00 0.00 2.24
3552 4020 2.886391 GCACTCTCAGTCCCCTCTAGTT 60.886 54.545 0.00 0.00 0.00 2.24
3553 4021 1.341581 GCACTCTCAGTCCCCTCTAGT 60.342 57.143 0.00 0.00 0.00 2.57
3554 4022 1.398692 GCACTCTCAGTCCCCTCTAG 58.601 60.000 0.00 0.00 0.00 2.43
3555 4023 0.394488 CGCACTCTCAGTCCCCTCTA 60.394 60.000 0.00 0.00 0.00 2.43
3556 4024 1.680651 CGCACTCTCAGTCCCCTCT 60.681 63.158 0.00 0.00 0.00 3.69
3557 4025 1.251527 TTCGCACTCTCAGTCCCCTC 61.252 60.000 0.00 0.00 0.00 4.30
3558 4026 1.228894 TTCGCACTCTCAGTCCCCT 60.229 57.895 0.00 0.00 0.00 4.79
3559 4027 1.216710 CTTCGCACTCTCAGTCCCC 59.783 63.158 0.00 0.00 0.00 4.81
3560 4028 1.446966 GCTTCGCACTCTCAGTCCC 60.447 63.158 0.00 0.00 0.00 4.46
3561 4029 0.735632 CTGCTTCGCACTCTCAGTCC 60.736 60.000 0.00 0.00 33.79 3.85
3562 4030 0.242286 TCTGCTTCGCACTCTCAGTC 59.758 55.000 0.00 0.00 33.79 3.51
3563 4031 0.676184 TTCTGCTTCGCACTCTCAGT 59.324 50.000 0.00 0.00 33.79 3.41
3564 4032 1.925847 GATTCTGCTTCGCACTCTCAG 59.074 52.381 0.00 0.00 33.79 3.35
3565 4033 1.273327 TGATTCTGCTTCGCACTCTCA 59.727 47.619 0.00 0.00 33.79 3.27
3566 4034 1.658095 GTGATTCTGCTTCGCACTCTC 59.342 52.381 0.00 0.00 33.79 3.20
3567 4035 1.001293 TGTGATTCTGCTTCGCACTCT 59.999 47.619 0.00 0.00 33.79 3.24
3568 4036 1.432514 TGTGATTCTGCTTCGCACTC 58.567 50.000 0.00 0.00 33.79 3.51
3569 4037 1.532868 GTTGTGATTCTGCTTCGCACT 59.467 47.619 0.00 0.00 33.60 4.40
3570 4038 1.722751 CGTTGTGATTCTGCTTCGCAC 60.723 52.381 0.00 0.00 33.60 5.34
3571 4039 0.512518 CGTTGTGATTCTGCTTCGCA 59.487 50.000 0.00 0.00 36.92 5.10
3572 4040 0.790866 GCGTTGTGATTCTGCTTCGC 60.791 55.000 0.00 0.00 36.06 4.70
3573 4041 0.179215 GGCGTTGTGATTCTGCTTCG 60.179 55.000 0.00 0.00 0.00 3.79
3574 4042 0.169009 GGGCGTTGTGATTCTGCTTC 59.831 55.000 0.00 0.00 0.00 3.86
3575 4043 1.244019 GGGGCGTTGTGATTCTGCTT 61.244 55.000 0.00 0.00 0.00 3.91
3576 4044 1.675641 GGGGCGTTGTGATTCTGCT 60.676 57.895 0.00 0.00 0.00 4.24
3577 4045 2.700773 GGGGGCGTTGTGATTCTGC 61.701 63.158 0.00 0.00 0.00 4.26
3578 4046 3.590824 GGGGGCGTTGTGATTCTG 58.409 61.111 0.00 0.00 0.00 3.02
3597 4065 2.432628 CCGAGCGAGGTTGACACC 60.433 66.667 0.00 0.00 44.67 4.16
3598 4066 2.432628 CCCGAGCGAGGTTGACAC 60.433 66.667 0.00 0.00 0.00 3.67
3599 4067 4.373116 GCCCGAGCGAGGTTGACA 62.373 66.667 0.00 0.00 0.00 3.58
3617 4085 1.235281 GGAAATAAGGATCGGGCGCC 61.235 60.000 21.18 21.18 0.00 6.53
3618 4086 1.235281 GGGAAATAAGGATCGGGCGC 61.235 60.000 0.00 0.00 0.00 6.53
3619 4087 0.949105 CGGGAAATAAGGATCGGGCG 60.949 60.000 0.00 0.00 0.00 6.13
3620 4088 0.395312 TCGGGAAATAAGGATCGGGC 59.605 55.000 0.00 0.00 0.00 6.13
3621 4089 1.604693 CGTCGGGAAATAAGGATCGGG 60.605 57.143 0.00 0.00 0.00 5.14
3622 4090 1.338973 TCGTCGGGAAATAAGGATCGG 59.661 52.381 0.00 0.00 0.00 4.18
3623 4091 2.391879 GTCGTCGGGAAATAAGGATCG 58.608 52.381 0.00 0.00 0.00 3.69
3624 4092 2.547430 GGGTCGTCGGGAAATAAGGATC 60.547 54.545 0.00 0.00 0.00 3.36
3625 4093 1.415289 GGGTCGTCGGGAAATAAGGAT 59.585 52.381 0.00 0.00 0.00 3.24
3626 4094 0.826062 GGGTCGTCGGGAAATAAGGA 59.174 55.000 0.00 0.00 0.00 3.36
3627 4095 0.828677 AGGGTCGTCGGGAAATAAGG 59.171 55.000 0.00 0.00 0.00 2.69
3628 4096 2.685850 AAGGGTCGTCGGGAAATAAG 57.314 50.000 0.00 0.00 0.00 1.73
3629 4097 3.099141 AGTAAGGGTCGTCGGGAAATAA 58.901 45.455 0.00 0.00 0.00 1.40
3630 4098 2.738743 AGTAAGGGTCGTCGGGAAATA 58.261 47.619 0.00 0.00 0.00 1.40
3631 4099 1.565067 AGTAAGGGTCGTCGGGAAAT 58.435 50.000 0.00 0.00 0.00 2.17
3632 4100 1.818674 GTAGTAAGGGTCGTCGGGAAA 59.181 52.381 0.00 0.00 0.00 3.13
3633 4101 1.271871 TGTAGTAAGGGTCGTCGGGAA 60.272 52.381 0.00 0.00 0.00 3.97
3634 4102 0.327924 TGTAGTAAGGGTCGTCGGGA 59.672 55.000 0.00 0.00 0.00 5.14
3635 4103 0.737219 CTGTAGTAAGGGTCGTCGGG 59.263 60.000 0.00 0.00 0.00 5.14
3636 4104 0.100146 GCTGTAGTAAGGGTCGTCGG 59.900 60.000 0.00 0.00 0.00 4.79
3637 4105 0.247974 CGCTGTAGTAAGGGTCGTCG 60.248 60.000 0.00 0.00 0.00 5.12
3638 4106 0.525029 GCGCTGTAGTAAGGGTCGTC 60.525 60.000 0.00 0.00 32.90 4.20
3639 4107 1.246056 TGCGCTGTAGTAAGGGTCGT 61.246 55.000 9.73 0.00 32.90 4.34
3640 4108 0.102481 ATGCGCTGTAGTAAGGGTCG 59.898 55.000 9.73 0.00 32.90 4.79
3641 4109 3.256136 AGATATGCGCTGTAGTAAGGGTC 59.744 47.826 9.73 0.00 32.90 4.46
3642 4110 3.231818 AGATATGCGCTGTAGTAAGGGT 58.768 45.455 9.73 0.00 32.90 4.34
3643 4111 3.255888 TGAGATATGCGCTGTAGTAAGGG 59.744 47.826 9.73 0.00 0.00 3.95
3644 4112 4.505313 TGAGATATGCGCTGTAGTAAGG 57.495 45.455 9.73 0.00 0.00 2.69
3645 4113 7.413475 AAAATGAGATATGCGCTGTAGTAAG 57.587 36.000 9.73 0.00 0.00 2.34
3646 4114 7.384115 GGTAAAATGAGATATGCGCTGTAGTAA 59.616 37.037 9.73 0.00 0.00 2.24
3647 4115 6.866770 GGTAAAATGAGATATGCGCTGTAGTA 59.133 38.462 9.73 0.00 0.00 1.82
3648 4116 5.696724 GGTAAAATGAGATATGCGCTGTAGT 59.303 40.000 9.73 0.00 0.00 2.73
3649 4117 5.928839 AGGTAAAATGAGATATGCGCTGTAG 59.071 40.000 9.73 0.00 0.00 2.74
3650 4118 5.853936 AGGTAAAATGAGATATGCGCTGTA 58.146 37.500 9.73 1.70 0.00 2.74
3651 4119 4.708177 AGGTAAAATGAGATATGCGCTGT 58.292 39.130 9.73 0.00 0.00 4.40
3652 4120 4.143242 CGAGGTAAAATGAGATATGCGCTG 60.143 45.833 9.73 0.00 0.00 5.18
3653 4121 3.990469 CGAGGTAAAATGAGATATGCGCT 59.010 43.478 9.73 0.00 0.00 5.92
3654 4122 3.423645 GCGAGGTAAAATGAGATATGCGC 60.424 47.826 0.00 0.00 0.00 6.09
3655 4123 3.990469 AGCGAGGTAAAATGAGATATGCG 59.010 43.478 0.00 0.00 0.00 4.73
3656 4124 5.334414 CCAAGCGAGGTAAAATGAGATATGC 60.334 44.000 0.00 0.00 0.00 3.14
3657 4125 5.180117 CCCAAGCGAGGTAAAATGAGATATG 59.820 44.000 0.00 0.00 0.00 1.78
3658 4126 5.308825 CCCAAGCGAGGTAAAATGAGATAT 58.691 41.667 0.00 0.00 0.00 1.63
3659 4127 4.703897 CCCAAGCGAGGTAAAATGAGATA 58.296 43.478 0.00 0.00 0.00 1.98
3660 4128 3.545703 CCCAAGCGAGGTAAAATGAGAT 58.454 45.455 0.00 0.00 0.00 2.75
3661 4129 2.939640 GCCCAAGCGAGGTAAAATGAGA 60.940 50.000 0.00 0.00 0.00 3.27
3662 4130 1.401905 GCCCAAGCGAGGTAAAATGAG 59.598 52.381 0.00 0.00 0.00 2.90
3663 4131 1.459450 GCCCAAGCGAGGTAAAATGA 58.541 50.000 0.00 0.00 0.00 2.57
3830 4315 2.511373 CGGCTACAAGCATCGCCA 60.511 61.111 0.78 0.00 44.75 5.69
3902 4465 3.211564 GAAAAAGGCAGCCGCAGCA 62.212 57.895 5.55 0.00 43.56 4.41
3917 4480 1.999735 CCTATCGAAGCAGCAACGAAA 59.000 47.619 15.69 0.00 39.38 3.46
3919 4482 0.806102 GCCTATCGAAGCAGCAACGA 60.806 55.000 14.45 14.45 40.18 3.85
3922 4485 1.521457 CCGCCTATCGAAGCAGCAA 60.521 57.895 0.00 0.00 41.67 3.91
3930 4493 1.529948 CCCCTACACCGCCTATCGA 60.530 63.158 0.00 0.00 41.67 3.59
3944 4507 4.982701 GCACAACAGCAGGCCCCT 62.983 66.667 0.00 0.00 0.00 4.79
3956 4520 1.810151 GCCACCTTTATTCGAGCACAA 59.190 47.619 0.00 0.00 0.00 3.33
3973 4537 1.229400 AAGAACCCTAGGACCGCCA 60.229 57.895 11.48 0.00 36.29 5.69
4023 4587 2.482326 GGCCAAATCAGGAAGGACG 58.518 57.895 0.00 0.00 0.00 4.79
4069 4633 1.079127 CGTTCATGGGAGTTCGCCT 60.079 57.895 0.00 0.00 0.00 5.52
4084 4648 4.406003 AGCAATCTCCAGACCTAATACGTT 59.594 41.667 0.00 0.00 0.00 3.99
4085 4649 3.961408 AGCAATCTCCAGACCTAATACGT 59.039 43.478 0.00 0.00 0.00 3.57
4089 4653 3.387962 TCCAGCAATCTCCAGACCTAAT 58.612 45.455 0.00 0.00 0.00 1.73
4093 4657 1.767681 AGATCCAGCAATCTCCAGACC 59.232 52.381 0.00 0.00 29.89 3.85
4095 4659 1.767088 CCAGATCCAGCAATCTCCAGA 59.233 52.381 0.00 0.00 33.68 3.86
4113 4677 1.175983 GGCACAAACGAATCCCACCA 61.176 55.000 0.00 0.00 0.00 4.17
4125 4689 1.337118 GGAGAACCAATGGGCACAAA 58.663 50.000 3.55 0.00 37.90 2.83
4127 4691 1.303236 CGGAGAACCAATGGGCACA 60.303 57.895 3.55 0.00 37.90 4.57
4163 4727 3.259123 TGACAACAGATAGCAGAGCTTCA 59.741 43.478 0.00 0.00 40.44 3.02
4183 4747 5.840693 TGGAGCTAAACATATCTCCTGATGA 59.159 40.000 8.39 0.00 44.09 2.92
4222 4786 1.407437 GGCTTCCATGACATTCTCCGT 60.407 52.381 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.