Multiple sequence alignment - TraesCS2A01G147900

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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 TraesCS2A01G147900 chr2A 100.000 3350 0 0 1 3350 94206174 94202825 0.000000e+00 6187.0
1 TraesCS2A01G147900 chr2A 88.396 1241 76 29 789 2024 94275416 94276593 0.000000e+00 1432.0
2 TraesCS2A01G147900 chr2A 82.032 807 140 5 1423 2227 94162156 94161353 0.000000e+00 682.0
3 TraesCS2A01G147900 chr2D 91.620 2494 145 32 2 2469 95656300 95653845 0.000000e+00 3389.0
4 TraesCS2A01G147900 chr2D 85.935 1749 143 44 689 2396 95666914 95668600 0.000000e+00 1772.0
5 TraesCS2A01G147900 chr2D 89.918 1220 79 29 647 1836 95683611 95684816 0.000000e+00 1531.0
6 TraesCS2A01G147900 chr2D 89.039 593 36 12 1826 2393 95685838 95686426 0.000000e+00 708.0
7 TraesCS2A01G147900 chr2D 82.404 807 137 5 1423 2227 95649043 95648240 0.000000e+00 699.0
8 TraesCS2A01G147900 chr2D 83.871 589 88 7 2510 3093 112538233 112538819 3.780000e-154 555.0
9 TraesCS2A01G147900 chr2D 90.805 87 7 1 389 475 95683378 95683463 7.600000e-22 115.0
10 TraesCS2A01G147900 chr2D 93.023 43 3 0 652 694 95683494 95683536 2.790000e-06 63.9
11 TraesCS2A01G147900 chr2B 88.966 2021 132 46 491 2469 147286756 147284785 0.000000e+00 2412.0
12 TraesCS2A01G147900 chr2B 86.524 1217 90 28 689 1891 147409077 147407921 0.000000e+00 1271.0
13 TraesCS2A01G147900 chr2B 81.605 810 138 9 1423 2227 146996625 146995822 0.000000e+00 660.0
14 TraesCS2A01G147900 chr2B 89.341 516 37 9 2 515 147287398 147286899 1.700000e-177 632.0
15 TraesCS2A01G147900 chr2B 92.401 329 25 0 1884 2212 147405301 147404973 1.410000e-128 470.0
16 TraesCS2A01G147900 chr2B 85.366 123 11 2 2278 2396 147431491 147431610 1.630000e-23 121.0
17 TraesCS2A01G147900 chr2B 85.714 84 8 1 2278 2357 147431127 147431210 5.960000e-13 86.1
18 TraesCS2A01G147900 chr2B 85.484 62 9 0 2204 2265 147431233 147431294 7.760000e-07 65.8
19 TraesCS2A01G147900 chr7D 86.441 590 77 3 2503 3089 251355416 251354827 0.000000e+00 643.0
20 TraesCS2A01G147900 chr7D 83.333 600 90 10 2505 3098 595869660 595869065 2.270000e-151 545.0
21 TraesCS2A01G147900 chr7A 85.762 597 81 4 2497 3091 393325158 393325752 2.190000e-176 628.0
22 TraesCS2A01G147900 chr4D 85.304 592 80 7 2497 3086 421546000 421546586 3.700000e-169 604.0
23 TraesCS2A01G147900 chr4D 85.663 558 73 7 2539 3092 42574053 42574607 6.230000e-162 580.0
24 TraesCS2A01G147900 chr6B 84.950 598 84 6 2497 3091 508533430 508532836 4.780000e-168 601.0
25 TraesCS2A01G147900 chr5B 83.362 589 94 4 2505 3090 446454719 446455306 2.940000e-150 542.0
26 TraesCS2A01G147900 chr7B 83.419 585 92 5 2505 3086 748331676 748331094 3.800000e-149 538.0


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 TraesCS2A01G147900 chr2A 94202825 94206174 3349 True 6187.000 6187 100.00000 1 3350 1 chr2A.!!$R2 3349
1 TraesCS2A01G147900 chr2A 94275416 94276593 1177 False 1432.000 1432 88.39600 789 2024 1 chr2A.!!$F1 1235
2 TraesCS2A01G147900 chr2A 94161353 94162156 803 True 682.000 682 82.03200 1423 2227 1 chr2A.!!$R1 804
3 TraesCS2A01G147900 chr2D 95653845 95656300 2455 True 3389.000 3389 91.62000 2 2469 1 chr2D.!!$R2 2467
4 TraesCS2A01G147900 chr2D 95666914 95668600 1686 False 1772.000 1772 85.93500 689 2396 1 chr2D.!!$F1 1707
5 TraesCS2A01G147900 chr2D 95648240 95649043 803 True 699.000 699 82.40400 1423 2227 1 chr2D.!!$R1 804
6 TraesCS2A01G147900 chr2D 95683378 95686426 3048 False 604.475 1531 90.69625 389 2393 4 chr2D.!!$F3 2004
7 TraesCS2A01G147900 chr2D 112538233 112538819 586 False 555.000 555 83.87100 2510 3093 1 chr2D.!!$F2 583
8 TraesCS2A01G147900 chr2B 147284785 147287398 2613 True 1522.000 2412 89.15350 2 2469 2 chr2B.!!$R2 2467
9 TraesCS2A01G147900 chr2B 147404973 147409077 4104 True 870.500 1271 89.46250 689 2212 2 chr2B.!!$R3 1523
10 TraesCS2A01G147900 chr2B 146995822 146996625 803 True 660.000 660 81.60500 1423 2227 1 chr2B.!!$R1 804
11 TraesCS2A01G147900 chr7D 251354827 251355416 589 True 643.000 643 86.44100 2503 3089 1 chr7D.!!$R1 586
12 TraesCS2A01G147900 chr7D 595869065 595869660 595 True 545.000 545 83.33300 2505 3098 1 chr7D.!!$R2 593
13 TraesCS2A01G147900 chr7A 393325158 393325752 594 False 628.000 628 85.76200 2497 3091 1 chr7A.!!$F1 594
14 TraesCS2A01G147900 chr4D 421546000 421546586 586 False 604.000 604 85.30400 2497 3086 1 chr4D.!!$F2 589
15 TraesCS2A01G147900 chr4D 42574053 42574607 554 False 580.000 580 85.66300 2539 3092 1 chr4D.!!$F1 553
16 TraesCS2A01G147900 chr6B 508532836 508533430 594 True 601.000 601 84.95000 2497 3091 1 chr6B.!!$R1 594
17 TraesCS2A01G147900 chr5B 446454719 446455306 587 False 542.000 542 83.36200 2505 3090 1 chr5B.!!$F1 585
18 TraesCS2A01G147900 chr7B 748331094 748331676 582 True 538.000 538 83.41900 2505 3086 1 chr7B.!!$R1 581


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
457 462 0.034670 ACAGGGCATGGAAGAAGAGC 60.035 55.0 3.46 0.00 0.00 4.09 F
1410 1660 0.110823 CGAGCACGTGGTTAACAAGC 60.111 55.0 22.78 5.99 34.56 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 1891 1.067060 CCGGCATCTTGTAGTCGATCA 59.933 52.381 0.0 0.0 0.0 2.92 R
3256 7225 0.179124 TGCAAAAGCAACGTGGAACC 60.179 50.000 0.0 0.0 0.0 3.62 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
29 30 1.151810 AGCCCTCCAACTCCTCCAA 60.152 57.895 0.00 0.00 0.00 3.53
41 42 2.985282 CTCCAAAAGCAGCCCGCA 60.985 61.111 0.00 0.00 46.13 5.69
45 46 4.603535 AAAAGCAGCCCGCACCCT 62.604 61.111 0.00 0.00 46.13 4.34
63 64 0.933097 CTGATCAGGACATTTCGCCG 59.067 55.000 15.38 0.00 0.00 6.46
64 65 0.461870 TGATCAGGACATTTCGCCGG 60.462 55.000 0.00 0.00 0.00 6.13
65 66 1.153168 ATCAGGACATTTCGCCGGG 60.153 57.895 2.18 0.00 0.00 5.73
66 67 2.608970 ATCAGGACATTTCGCCGGGG 62.609 60.000 13.31 13.31 0.00 5.73
103 105 1.132500 GCTAGAGGGGGTGTAAGCAT 58.868 55.000 0.00 0.00 34.77 3.79
110 112 0.897863 GGGGTGTAAGCATTGTGGCA 60.898 55.000 0.00 0.00 34.77 4.92
241 245 1.444917 ATCGCTAGCATCACGACCGA 61.445 55.000 16.45 0.23 38.85 4.69
323 327 4.384056 CAGATCTAGCCCATCGACAATTT 58.616 43.478 0.00 0.00 0.00 1.82
344 348 8.829612 CAATTTTAAGGCATTATCCATCAAACC 58.170 33.333 0.00 0.00 0.00 3.27
370 374 3.177487 CACGATCGATCCATGCATAGAG 58.823 50.000 24.34 4.14 0.00 2.43
415 420 8.052141 TCCTTTTCTTTTCCCATGAACAAATTT 58.948 29.630 0.00 0.00 0.00 1.82
455 460 3.432186 CGATTACAGGGCATGGAAGAAGA 60.432 47.826 2.26 0.00 34.35 2.87
457 462 0.034670 ACAGGGCATGGAAGAAGAGC 60.035 55.000 3.46 0.00 0.00 4.09
484 496 2.085320 CTCCCCGACGACCTATCTATG 58.915 57.143 0.00 0.00 0.00 2.23
499 669 8.546083 ACCTATCTATGTATGATCATCCTTCC 57.454 38.462 12.53 0.00 0.00 3.46
525 695 3.135712 TGGACTTTTGAGCTCACTGGTTA 59.864 43.478 18.03 0.00 0.00 2.85
563 740 0.389296 TTGCGTACACCATCGTCCAG 60.389 55.000 0.00 0.00 0.00 3.86
566 743 1.076533 CGTACACCATCGTCCAGTGC 61.077 60.000 0.00 0.00 34.83 4.40
609 786 0.984230 AGGCCCTCTTGAAACGATCA 59.016 50.000 0.00 0.00 35.85 2.92
631 808 3.674997 AGATGTCGTTTACCATGTGCTT 58.325 40.909 0.00 0.00 0.00 3.91
633 810 5.242434 AGATGTCGTTTACCATGTGCTTTA 58.758 37.500 0.00 0.00 0.00 1.85
634 811 5.880332 AGATGTCGTTTACCATGTGCTTTAT 59.120 36.000 0.00 0.00 0.00 1.40
635 812 7.045416 AGATGTCGTTTACCATGTGCTTTATA 58.955 34.615 0.00 0.00 0.00 0.98
699 878 5.007136 GGAGACATCAAATTCAGACGGAATC 59.993 44.000 1.11 0.00 45.46 2.52
723 906 3.879892 GCTAATTTAACCTCAGCTGGGAG 59.120 47.826 17.43 7.93 34.62 4.30
866 1075 0.681733 TTCCTTCAAGTCAGCGCTCT 59.318 50.000 7.13 0.00 0.00 4.09
868 1077 0.320247 CCTTCAAGTCAGCGCTCTGT 60.320 55.000 7.13 0.00 41.10 3.41
884 1093 0.387202 CTGTAGCTCGAGGGGATGTG 59.613 60.000 15.58 0.00 0.00 3.21
923 1133 3.949885 TTCCTGCGGCGTCTAGGGA 62.950 63.158 20.86 13.46 32.39 4.20
924 1134 3.905678 CCTGCGGCGTCTAGGGAG 61.906 72.222 9.37 0.00 0.00 4.30
925 1135 3.141488 CTGCGGCGTCTAGGGAGT 61.141 66.667 9.37 0.00 0.00 3.85
965 1178 3.304559 CGATTAAGAAACGCAGACAGGAG 59.695 47.826 0.00 0.00 0.00 3.69
966 1179 4.495422 GATTAAGAAACGCAGACAGGAGA 58.505 43.478 0.00 0.00 0.00 3.71
967 1180 2.447244 AAGAAACGCAGACAGGAGAG 57.553 50.000 0.00 0.00 0.00 3.20
990 1204 0.627986 CCCCTGCCAATTCTCCTTCT 59.372 55.000 0.00 0.00 0.00 2.85
1065 1298 0.179045 ACGACTGCAGCTTCCACTTT 60.179 50.000 15.27 0.00 0.00 2.66
1074 1307 1.001406 AGCTTCCACTTTCAGTCTCCG 59.999 52.381 0.00 0.00 0.00 4.63
1080 1314 1.122019 ACTTTCAGTCTCCGGCCACT 61.122 55.000 2.24 0.00 0.00 4.00
1086 1320 1.668151 GTCTCCGGCCACTCAACAC 60.668 63.158 2.24 0.00 0.00 3.32
1109 1352 0.471191 TCGGCTCTAGTGGGTCGATA 59.529 55.000 5.93 0.00 0.00 2.92
1256 1501 2.121538 CGGAGAGCATCGTCAGGGA 61.122 63.158 0.00 0.00 42.67 4.20
1410 1660 0.110823 CGAGCACGTGGTTAACAAGC 60.111 55.000 22.78 5.99 34.56 4.01
1411 1661 0.941542 GAGCACGTGGTTAACAAGCA 59.058 50.000 22.78 0.00 36.38 3.91
1412 1662 0.944386 AGCACGTGGTTAACAAGCAG 59.056 50.000 15.81 0.00 39.94 4.24
1632 1890 1.002868 TTCTTCCTCAGCAGCAGCC 60.003 57.895 0.00 0.00 43.56 4.85
1633 1891 1.486997 TTCTTCCTCAGCAGCAGCCT 61.487 55.000 0.00 0.00 43.56 4.58
1706 1965 3.123620 GAGGCGCTGCAGTTCCTG 61.124 66.667 26.43 9.82 34.12 3.86
1931 5849 1.599797 CTTCACCAACGACCCCACC 60.600 63.158 0.00 0.00 0.00 4.61
2171 6089 0.820871 GCGAGATCAGGAGGAACTGT 59.179 55.000 0.00 0.00 41.55 3.55
2175 6093 3.685835 CGAGATCAGGAGGAACTGTAGGA 60.686 52.174 0.00 0.00 41.55 2.94
2230 6154 2.094539 CACTCGAACGTGCATGCG 59.905 61.111 14.09 2.45 37.94 4.73
2245 6174 0.951558 ATGCGTTCGGTTCTTTTGCT 59.048 45.000 0.00 0.00 0.00 3.91
2246 6175 0.028770 TGCGTTCGGTTCTTTTGCTG 59.971 50.000 0.00 0.00 0.00 4.41
2247 6176 1.268778 GCGTTCGGTTCTTTTGCTGC 61.269 55.000 0.00 0.00 0.00 5.25
2248 6177 0.028770 CGTTCGGTTCTTTTGCTGCA 59.971 50.000 0.00 0.00 0.00 4.41
2249 6178 1.334960 CGTTCGGTTCTTTTGCTGCAT 60.335 47.619 1.84 0.00 0.00 3.96
2250 6179 2.742774 GTTCGGTTCTTTTGCTGCATT 58.257 42.857 1.84 0.00 0.00 3.56
2251 6180 2.704725 TCGGTTCTTTTGCTGCATTC 57.295 45.000 1.84 0.00 0.00 2.67
2252 6181 1.952990 TCGGTTCTTTTGCTGCATTCA 59.047 42.857 1.84 0.00 0.00 2.57
2253 6182 2.557924 TCGGTTCTTTTGCTGCATTCAT 59.442 40.909 1.84 0.00 0.00 2.57
2276 6234 5.710613 TGCATTTTGTTTCTTTCGTTTCC 57.289 34.783 0.00 0.00 0.00 3.13
2320 6278 4.638865 AGGTTGTAATTCGATTAACAGGGC 59.361 41.667 0.00 0.00 0.00 5.19
2398 6360 5.227569 TCCAGTCATCTACTTTCTTTGCA 57.772 39.130 0.00 0.00 35.76 4.08
2469 6434 5.545063 TTGCATTAGATCTCCGGTTCATA 57.455 39.130 0.00 0.00 0.00 2.15
2470 6435 5.745312 TGCATTAGATCTCCGGTTCATAT 57.255 39.130 0.00 0.00 0.00 1.78
2471 6436 5.482006 TGCATTAGATCTCCGGTTCATATG 58.518 41.667 0.00 0.00 0.00 1.78
2472 6437 4.872691 GCATTAGATCTCCGGTTCATATGG 59.127 45.833 0.00 0.00 0.00 2.74
2473 6438 4.537135 TTAGATCTCCGGTTCATATGGC 57.463 45.455 0.00 0.00 0.00 4.40
2474 6439 1.625818 AGATCTCCGGTTCATATGGCC 59.374 52.381 0.00 0.00 0.00 5.36
2475 6440 1.625818 GATCTCCGGTTCATATGGCCT 59.374 52.381 3.32 0.00 0.00 5.19
2476 6441 1.048601 TCTCCGGTTCATATGGCCTC 58.951 55.000 3.32 0.00 0.00 4.70
2477 6442 1.051812 CTCCGGTTCATATGGCCTCT 58.948 55.000 3.32 0.00 0.00 3.69
2478 6443 1.417890 CTCCGGTTCATATGGCCTCTT 59.582 52.381 3.32 0.00 0.00 2.85
2479 6444 1.416401 TCCGGTTCATATGGCCTCTTC 59.584 52.381 3.32 0.00 0.00 2.87
2480 6445 1.543429 CCGGTTCATATGGCCTCTTCC 60.543 57.143 3.32 0.00 0.00 3.46
2481 6446 1.543429 CGGTTCATATGGCCTCTTCCC 60.543 57.143 3.32 0.00 0.00 3.97
2482 6447 1.202940 GGTTCATATGGCCTCTTCCCC 60.203 57.143 3.32 0.00 0.00 4.81
2483 6448 1.494721 GTTCATATGGCCTCTTCCCCA 59.505 52.381 3.32 0.00 35.21 4.96
2484 6449 1.905839 TCATATGGCCTCTTCCCCAA 58.094 50.000 3.32 0.00 34.25 4.12
2485 6450 1.776667 TCATATGGCCTCTTCCCCAAG 59.223 52.381 3.32 0.00 34.25 3.61
2486 6451 1.776667 CATATGGCCTCTTCCCCAAGA 59.223 52.381 3.32 0.00 37.11 3.02
2487 6452 1.979809 TATGGCCTCTTCCCCAAGAA 58.020 50.000 3.32 0.00 38.23 2.52
2488 6453 1.084018 ATGGCCTCTTCCCCAAGAAA 58.916 50.000 3.32 0.00 38.23 2.52
2489 6454 0.405585 TGGCCTCTTCCCCAAGAAAG 59.594 55.000 3.32 0.00 38.23 2.62
2490 6455 0.698818 GGCCTCTTCCCCAAGAAAGA 59.301 55.000 0.00 0.00 38.23 2.52
2491 6456 1.286257 GGCCTCTTCCCCAAGAAAGAT 59.714 52.381 0.00 0.00 38.23 2.40
2492 6457 2.291865 GGCCTCTTCCCCAAGAAAGATT 60.292 50.000 0.00 0.00 38.23 2.40
2493 6458 3.053619 GGCCTCTTCCCCAAGAAAGATTA 60.054 47.826 0.00 0.00 38.23 1.75
2494 6459 4.203226 GCCTCTTCCCCAAGAAAGATTAG 58.797 47.826 0.00 0.00 38.23 1.73
2495 6460 4.786425 CCTCTTCCCCAAGAAAGATTAGG 58.214 47.826 0.00 0.00 38.23 2.69
2501 6466 3.564352 CCCCAAGAAAGATTAGGGTTGCT 60.564 47.826 0.00 0.00 37.84 3.91
2508 6473 2.463752 AGATTAGGGTTGCTGTCGGTA 58.536 47.619 0.00 0.00 0.00 4.02
2621 6587 7.924541 TGAGTATTGTTAGGGTTTGTATCCTT 58.075 34.615 0.00 0.00 34.75 3.36
2626 6592 7.899648 TTGTTAGGGTTTGTATCCTTTTCAA 57.100 32.000 0.00 0.00 34.75 2.69
2718 6684 0.314302 GCATAGCATCGTCGGTAGGT 59.686 55.000 0.00 0.00 0.00 3.08
2772 6740 0.464373 TGGATCTGCTCGGATTTGGC 60.464 55.000 0.00 0.00 0.00 4.52
2788 6756 2.417339 TGGCTATCGTTCGTCTATGC 57.583 50.000 0.00 0.00 0.00 3.14
2807 6775 1.400494 GCTCGTGTGTTTTCAGGTTGT 59.600 47.619 0.00 0.00 0.00 3.32
2862 6830 1.823470 TTGCTGTTCTGGTGCGCTT 60.823 52.632 9.73 0.00 0.00 4.68
2879 6847 2.298610 GCTTGTCTTATGGGGCCTTAC 58.701 52.381 0.84 0.00 0.00 2.34
2947 6915 1.202545 GGTAAGGAAGAGGCGATGACC 60.203 57.143 0.00 0.00 0.00 4.02
2990 6959 0.387367 AGTGCTTGTAGTCGTCGCTG 60.387 55.000 0.00 0.00 0.00 5.18
3005 6974 2.364324 GTCGCTGGGTGGTCTATGAATA 59.636 50.000 0.00 0.00 0.00 1.75
3055 7024 3.507786 TCGTTGTACCGTCATGATTGAG 58.492 45.455 0.00 0.00 30.85 3.02
3065 7034 4.934001 CCGTCATGATTGAGGATGAATAGG 59.066 45.833 0.00 0.00 39.56 2.57
3080 7049 4.495422 TGAATAGGTCAGAAGTTTCTCGC 58.505 43.478 0.00 0.00 34.74 5.03
3086 7055 4.035684 GGTCAGAAGTTTCTCGCAAAAAC 58.964 43.478 0.00 0.00 34.74 2.43
3094 7063 5.752712 AGTTTCTCGCAAAAACAAGATCTC 58.247 37.500 0.00 0.00 38.73 2.75
3095 7064 5.529060 AGTTTCTCGCAAAAACAAGATCTCT 59.471 36.000 0.00 0.00 38.73 3.10
3096 7065 6.706270 AGTTTCTCGCAAAAACAAGATCTCTA 59.294 34.615 0.00 0.00 38.73 2.43
3097 7066 6.712241 TTCTCGCAAAAACAAGATCTCTAG 57.288 37.500 0.00 0.00 0.00 2.43
3098 7067 5.784177 TCTCGCAAAAACAAGATCTCTAGT 58.216 37.500 0.00 0.00 0.00 2.57
3099 7068 6.223852 TCTCGCAAAAACAAGATCTCTAGTT 58.776 36.000 0.00 0.00 0.00 2.24
3100 7069 6.366332 TCTCGCAAAAACAAGATCTCTAGTTC 59.634 38.462 0.00 0.00 0.00 3.01
3101 7070 5.989168 TCGCAAAAACAAGATCTCTAGTTCA 59.011 36.000 0.00 0.00 0.00 3.18
3102 7071 6.650807 TCGCAAAAACAAGATCTCTAGTTCAT 59.349 34.615 0.00 0.00 0.00 2.57
3103 7072 6.958193 CGCAAAAACAAGATCTCTAGTTCATC 59.042 38.462 0.00 0.00 0.00 2.92
3104 7073 7.360353 CGCAAAAACAAGATCTCTAGTTCATCA 60.360 37.037 0.00 0.00 0.00 3.07
3105 7074 8.457261 GCAAAAACAAGATCTCTAGTTCATCAT 58.543 33.333 0.00 0.00 0.00 2.45
3108 7077 9.730705 AAAACAAGATCTCTAGTTCATCATTCA 57.269 29.630 0.00 0.00 0.00 2.57
3109 7078 9.730705 AAACAAGATCTCTAGTTCATCATTCAA 57.269 29.630 0.00 0.00 0.00 2.69
3110 7079 9.730705 AACAAGATCTCTAGTTCATCATTCAAA 57.269 29.630 0.00 0.00 0.00 2.69
3111 7080 9.730705 ACAAGATCTCTAGTTCATCATTCAAAA 57.269 29.630 0.00 0.00 0.00 2.44
3113 7082 8.961294 AGATCTCTAGTTCATCATTCAAAAGG 57.039 34.615 0.00 0.00 0.00 3.11
3114 7083 8.547173 AGATCTCTAGTTCATCATTCAAAAGGT 58.453 33.333 0.00 0.00 0.00 3.50
3115 7084 9.171877 GATCTCTAGTTCATCATTCAAAAGGTT 57.828 33.333 0.00 0.00 0.00 3.50
3116 7085 8.924511 TCTCTAGTTCATCATTCAAAAGGTTT 57.075 30.769 0.00 0.00 0.00 3.27
3122 7091 9.971922 AGTTCATCATTCAAAAGGTTTAGAAAG 57.028 29.630 0.00 0.00 0.00 2.62
3123 7092 9.965824 GTTCATCATTCAAAAGGTTTAGAAAGA 57.034 29.630 0.00 0.00 0.00 2.52
3125 7094 8.299570 TCATCATTCAAAAGGTTTAGAAAGAGC 58.700 33.333 0.00 0.00 0.00 4.09
3126 7095 6.981722 TCATTCAAAAGGTTTAGAAAGAGCC 58.018 36.000 0.00 0.00 0.00 4.70
3127 7096 6.549364 TCATTCAAAAGGTTTAGAAAGAGCCA 59.451 34.615 0.00 0.00 0.00 4.75
3128 7097 6.783708 TTCAAAAGGTTTAGAAAGAGCCAA 57.216 33.333 0.00 0.00 0.00 4.52
3129 7098 6.976934 TCAAAAGGTTTAGAAAGAGCCAAT 57.023 33.333 0.00 0.00 0.00 3.16
3130 7099 8.472007 TTCAAAAGGTTTAGAAAGAGCCAATA 57.528 30.769 0.00 0.00 0.00 1.90
3131 7100 7.882179 TCAAAAGGTTTAGAAAGAGCCAATAC 58.118 34.615 0.00 0.00 0.00 1.89
3132 7101 7.504238 TCAAAAGGTTTAGAAAGAGCCAATACA 59.496 33.333 0.00 0.00 0.00 2.29
3133 7102 7.833285 AAAGGTTTAGAAAGAGCCAATACAA 57.167 32.000 0.00 0.00 0.00 2.41
3134 7103 7.833285 AAGGTTTAGAAAGAGCCAATACAAA 57.167 32.000 0.00 0.00 0.00 2.83
3135 7104 8.422577 AAGGTTTAGAAAGAGCCAATACAAAT 57.577 30.769 0.00 0.00 0.00 2.32
3136 7105 8.422577 AGGTTTAGAAAGAGCCAATACAAATT 57.577 30.769 0.00 0.00 0.00 1.82
3137 7106 8.870116 AGGTTTAGAAAGAGCCAATACAAATTT 58.130 29.630 0.00 0.00 0.00 1.82
3138 7107 8.925700 GGTTTAGAAAGAGCCAATACAAATTTG 58.074 33.333 16.67 16.67 0.00 2.32
3139 7108 9.691362 GTTTAGAAAGAGCCAATACAAATTTGA 57.309 29.630 24.64 8.78 0.00 2.69
3143 7112 9.428097 AGAAAGAGCCAATACAAATTTGATTTC 57.572 29.630 24.64 16.11 0.00 2.17
3144 7113 7.816945 AAGAGCCAATACAAATTTGATTTCG 57.183 32.000 24.64 10.69 0.00 3.46
3145 7114 6.332630 AGAGCCAATACAAATTTGATTTCGG 58.667 36.000 24.64 16.76 0.00 4.30
3146 7115 4.869861 AGCCAATACAAATTTGATTTCGGC 59.130 37.500 24.64 23.84 0.00 5.54
3147 7116 4.869861 GCCAATACAAATTTGATTTCGGCT 59.130 37.500 24.64 2.15 0.00 5.52
3148 7117 5.351189 GCCAATACAAATTTGATTTCGGCTT 59.649 36.000 24.64 1.42 0.00 4.35
3149 7118 6.128309 GCCAATACAAATTTGATTTCGGCTTT 60.128 34.615 24.64 0.68 0.00 3.51
3150 7119 7.455447 CCAATACAAATTTGATTTCGGCTTTC 58.545 34.615 24.64 0.00 0.00 2.62
3151 7120 7.412891 CCAATACAAATTTGATTTCGGCTTTCC 60.413 37.037 24.64 0.00 0.00 3.13
3152 7121 4.954875 ACAAATTTGATTTCGGCTTTCCA 58.045 34.783 24.64 0.00 0.00 3.53
3153 7122 5.363939 ACAAATTTGATTTCGGCTTTCCAA 58.636 33.333 24.64 0.00 0.00 3.53
3154 7123 5.819901 ACAAATTTGATTTCGGCTTTCCAAA 59.180 32.000 24.64 0.00 0.00 3.28
3155 7124 6.317391 ACAAATTTGATTTCGGCTTTCCAAAA 59.683 30.769 24.64 0.00 0.00 2.44
3156 7125 6.934048 AATTTGATTTCGGCTTTCCAAAAA 57.066 29.167 0.00 0.00 0.00 1.94
3182 7151 8.868522 AATTGATTTCAGACATTTAGAGGACA 57.131 30.769 0.00 0.00 0.00 4.02
3183 7152 8.868522 ATTGATTTCAGACATTTAGAGGACAA 57.131 30.769 0.00 0.00 0.00 3.18
3184 7153 8.690203 TTGATTTCAGACATTTAGAGGACAAA 57.310 30.769 0.00 0.00 0.00 2.83
3185 7154 8.868522 TGATTTCAGACATTTAGAGGACAAAT 57.131 30.769 0.00 0.00 0.00 2.32
3186 7155 9.300681 TGATTTCAGACATTTAGAGGACAAATT 57.699 29.630 0.00 0.00 0.00 1.82
3230 7199 7.939784 AATTTAGTTGTGAAATACTCCCTCC 57.060 36.000 0.00 0.00 0.00 4.30
3231 7200 3.611766 AGTTGTGAAATACTCCCTCCG 57.388 47.619 0.00 0.00 0.00 4.63
3232 7201 2.904434 AGTTGTGAAATACTCCCTCCGT 59.096 45.455 0.00 0.00 0.00 4.69
3233 7202 4.091549 AGTTGTGAAATACTCCCTCCGTA 58.908 43.478 0.00 0.00 0.00 4.02
3234 7203 4.081807 AGTTGTGAAATACTCCCTCCGTAC 60.082 45.833 0.00 0.00 0.00 3.67
3235 7204 3.433343 TGTGAAATACTCCCTCCGTACA 58.567 45.455 0.00 0.00 0.00 2.90
3236 7205 4.028131 TGTGAAATACTCCCTCCGTACAT 58.972 43.478 0.00 0.00 0.00 2.29
3237 7206 4.468510 TGTGAAATACTCCCTCCGTACATT 59.531 41.667 0.00 0.00 0.00 2.71
3238 7207 5.657745 TGTGAAATACTCCCTCCGTACATTA 59.342 40.000 0.00 0.00 0.00 1.90
3239 7208 6.154877 TGTGAAATACTCCCTCCGTACATTAA 59.845 38.462 0.00 0.00 0.00 1.40
3240 7209 7.147620 TGTGAAATACTCCCTCCGTACATTAAT 60.148 37.037 0.00 0.00 0.00 1.40
3241 7210 8.362639 GTGAAATACTCCCTCCGTACATTAATA 58.637 37.037 0.00 0.00 0.00 0.98
3242 7211 9.096823 TGAAATACTCCCTCCGTACATTAATAT 57.903 33.333 0.00 0.00 0.00 1.28
3248 7217 8.680903 ACTCCCTCCGTACATTAATATAATACG 58.319 37.037 11.12 11.12 38.62 3.06
3249 7218 8.579850 TCCCTCCGTACATTAATATAATACGT 57.420 34.615 14.49 0.00 37.51 3.57
3250 7219 8.461222 TCCCTCCGTACATTAATATAATACGTG 58.539 37.037 0.00 9.33 37.51 4.49
3251 7220 8.246180 CCCTCCGTACATTAATATAATACGTGT 58.754 37.037 0.00 0.00 37.51 4.49
3252 7221 9.630098 CCTCCGTACATTAATATAATACGTGTT 57.370 33.333 2.29 2.29 37.51 3.32
3255 7224 9.519905 CCGTACATTAATATAATACGTGTTTGC 57.480 33.333 1.91 0.00 37.51 3.68
3256 7225 9.230583 CGTACATTAATATAATACGTGTTTGCG 57.769 33.333 1.91 0.00 35.17 4.85
3257 7226 9.519905 GTACATTAATATAATACGTGTTTGCGG 57.480 33.333 1.91 0.00 35.98 5.69
3258 7227 8.145316 ACATTAATATAATACGTGTTTGCGGT 57.855 30.769 1.91 0.00 35.98 5.68
3259 7228 8.614346 ACATTAATATAATACGTGTTTGCGGTT 58.386 29.630 1.91 0.00 35.98 4.44
3260 7229 9.098746 CATTAATATAATACGTGTTTGCGGTTC 57.901 33.333 1.91 0.00 35.98 3.62
3261 7230 5.662211 ATATAATACGTGTTTGCGGTTCC 57.338 39.130 1.91 0.00 35.98 3.62
3262 7231 1.595466 AATACGTGTTTGCGGTTCCA 58.405 45.000 0.00 0.00 35.98 3.53
3263 7232 0.869730 ATACGTGTTTGCGGTTCCAC 59.130 50.000 0.00 0.00 35.98 4.02
3264 7233 2.052590 CGTGTTTGCGGTTCCACG 60.053 61.111 0.00 0.00 43.70 4.94
3265 7234 2.815298 CGTGTTTGCGGTTCCACGT 61.815 57.895 0.00 0.00 44.04 4.49
3266 7235 1.430228 GTGTTTGCGGTTCCACGTT 59.570 52.632 0.00 0.00 35.98 3.99
3267 7236 0.863957 GTGTTTGCGGTTCCACGTTG 60.864 55.000 0.00 0.00 35.98 4.10
3268 7237 1.942223 GTTTGCGGTTCCACGTTGC 60.942 57.895 0.00 0.00 35.98 4.17
3269 7238 2.115911 TTTGCGGTTCCACGTTGCT 61.116 52.632 0.00 0.00 35.98 3.91
3270 7239 1.658686 TTTGCGGTTCCACGTTGCTT 61.659 50.000 0.00 0.00 35.98 3.91
3271 7240 1.658686 TTGCGGTTCCACGTTGCTTT 61.659 50.000 0.00 0.00 35.98 3.51
3272 7241 1.065109 GCGGTTCCACGTTGCTTTT 59.935 52.632 0.00 0.00 35.98 2.27
3273 7242 1.206115 GCGGTTCCACGTTGCTTTTG 61.206 55.000 0.00 0.00 35.98 2.44
3317 7286 9.926158 TTTGAACTGCAAAAATGTGTCATATAT 57.074 25.926 0.00 0.00 43.18 0.86
3343 7312 8.874744 AATTAGTGTACAGAGGTAGTAACAGA 57.125 34.615 0.00 0.00 0.00 3.41
3344 7313 9.476928 AATTAGTGTACAGAGGTAGTAACAGAT 57.523 33.333 0.00 0.00 0.00 2.90
3346 7315 7.862512 AGTGTACAGAGGTAGTAACAGATAC 57.137 40.000 0.00 0.00 34.52 2.24
3347 7316 6.538021 AGTGTACAGAGGTAGTAACAGATACG 59.462 42.308 0.00 0.00 39.62 3.06
3348 7317 6.314896 GTGTACAGAGGTAGTAACAGATACGT 59.685 42.308 0.00 0.00 39.62 3.57
3349 7318 7.492669 GTGTACAGAGGTAGTAACAGATACGTA 59.507 40.741 0.00 0.00 39.62 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.461870 CCGGCGAAATGTCCTGATCA 60.462 55.000 9.30 0.00 0.00 2.92
83 85 0.042731 TGCTTACACCCCCTCTAGCT 59.957 55.000 0.00 0.00 0.00 3.32
91 93 0.897863 TGCCACAATGCTTACACCCC 60.898 55.000 0.00 0.00 0.00 4.95
103 105 0.605319 CGAAACCCTAGCTGCCACAA 60.605 55.000 0.00 0.00 0.00 3.33
110 112 1.602327 GGTCGACCGAAACCCTAGCT 61.602 60.000 20.85 0.00 0.00 3.32
241 245 2.025226 TCGATCCCTACTTCACCAGTCT 60.025 50.000 0.00 0.00 36.88 3.24
323 327 4.582656 CCGGTTTGATGGATAATGCCTTAA 59.417 41.667 0.00 0.00 0.00 1.85
344 348 1.300156 ATGGATCGATCGTGCACCG 60.300 57.895 18.81 9.55 38.13 4.94
370 374 4.068599 AGGAAAGAAGAAAGCTAGTGTGC 58.931 43.478 0.00 0.00 0.00 4.57
377 381 7.268586 GGAAAAGAAAAGGAAAGAAGAAAGCT 58.731 34.615 0.00 0.00 0.00 3.74
383 387 7.054491 TCATGGGAAAAGAAAAGGAAAGAAG 57.946 36.000 0.00 0.00 0.00 2.85
415 420 2.203084 TGCAAACCGACGCCTCAA 60.203 55.556 0.00 0.00 0.00 3.02
475 480 7.286546 ACGGAAGGATGATCATACATAGATAGG 59.713 40.741 20.23 3.51 0.00 2.57
484 496 3.069586 TCCACACGGAAGGATGATCATAC 59.930 47.826 10.19 10.19 38.83 2.39
499 669 1.261619 GTGAGCTCAAAAGTCCACACG 59.738 52.381 20.19 0.00 31.59 4.49
525 695 5.123820 ACGCAATGACAAAAGTACTGCATAT 59.876 36.000 0.00 0.00 0.00 1.78
563 740 2.125952 GGCGAATTTGCTGGGCAC 60.126 61.111 17.19 0.00 38.71 5.01
566 743 2.179018 CACGGCGAATTTGCTGGG 59.821 61.111 26.73 21.24 45.70 4.45
609 786 3.674997 AGCACATGGTAAACGACATCTT 58.325 40.909 0.00 0.00 0.00 2.40
631 808 7.201661 GGCGACATGTTTGTTTACTCCATATAA 60.202 37.037 0.00 0.00 35.79 0.98
633 810 5.065988 GGCGACATGTTTGTTTACTCCATAT 59.934 40.000 0.00 0.00 35.79 1.78
634 811 4.393680 GGCGACATGTTTGTTTACTCCATA 59.606 41.667 0.00 0.00 35.79 2.74
635 812 3.190535 GGCGACATGTTTGTTTACTCCAT 59.809 43.478 0.00 0.00 35.79 3.41
699 878 3.629398 CCCAGCTGAGGTTAAATTAGCAG 59.371 47.826 17.39 0.00 36.87 4.24
723 906 2.552031 GTGGACGGATAGGCTTTTCTC 58.448 52.381 0.00 0.00 0.00 2.87
866 1075 0.324368 ACACATCCCCTCGAGCTACA 60.324 55.000 6.99 0.00 0.00 2.74
868 1077 1.676678 GCACACATCCCCTCGAGCTA 61.677 60.000 6.99 0.00 0.00 3.32
876 1085 0.250901 ACAACTCAGCACACATCCCC 60.251 55.000 0.00 0.00 0.00 4.81
884 1093 2.246739 TGCGAGCACAACTCAGCAC 61.247 57.895 0.00 0.00 46.63 4.40
923 1133 0.543749 GGCAGAGCATGTTCCCTACT 59.456 55.000 5.87 0.00 0.00 2.57
924 1134 0.464554 GGGCAGAGCATGTTCCCTAC 60.465 60.000 5.87 0.00 34.19 3.18
925 1135 1.915228 GGGCAGAGCATGTTCCCTA 59.085 57.895 5.87 0.00 34.19 3.53
990 1204 0.876777 CCATTTATACGCGCGGGACA 60.877 55.000 35.22 16.34 0.00 4.02
1065 1298 1.533033 TTGAGTGGCCGGAGACTGA 60.533 57.895 5.05 0.00 0.00 3.41
1074 1307 1.507141 CCGAGTTGTGTTGAGTGGCC 61.507 60.000 0.00 0.00 0.00 5.36
1080 1314 1.961394 ACTAGAGCCGAGTTGTGTTGA 59.039 47.619 0.00 0.00 0.00 3.18
1086 1320 0.173708 GACCCACTAGAGCCGAGTTG 59.826 60.000 0.00 0.00 0.00 3.16
1109 1352 1.694048 CCCTACCCATCCTTGAGCTCT 60.694 57.143 16.19 0.00 0.00 4.09
1188 1433 2.445845 CTCACCCTATGCCCCGGA 60.446 66.667 0.73 0.00 0.00 5.14
1347 1592 3.685836 AAAAACAGTTGACAGTACGGC 57.314 42.857 0.00 0.00 0.00 5.68
1632 1890 2.389059 CGGCATCTTGTAGTCGATCAG 58.611 52.381 0.00 0.00 0.00 2.90
1633 1891 1.067060 CCGGCATCTTGTAGTCGATCA 59.933 52.381 0.00 0.00 0.00 2.92
1682 1941 1.962822 CTGCAGCGCCTCAGTTTCA 60.963 57.895 15.85 0.00 0.00 2.69
1685 1944 2.111878 AACTGCAGCGCCTCAGTT 59.888 55.556 28.40 28.40 45.57 3.16
1706 1965 4.360405 TTGAAGAAGGGCGGGGGC 62.360 66.667 0.00 0.00 0.00 5.80
1844 3135 2.284405 ATGTCGGAGGGGTTCGGT 60.284 61.111 0.00 0.00 0.00 4.69
1931 5849 2.048222 ACGATGTCCTGCACCACG 60.048 61.111 0.00 0.00 0.00 4.94
2171 6089 5.424757 CAACCCTATTTGTTGACGATCCTA 58.575 41.667 0.00 0.00 44.57 2.94
2175 6093 3.440173 CAGCAACCCTATTTGTTGACGAT 59.560 43.478 7.28 0.00 44.57 3.73
2230 6154 2.422276 ATGCAGCAAAAGAACCGAAC 57.578 45.000 0.00 0.00 0.00 3.95
2232 6156 1.952990 TGAATGCAGCAAAAGAACCGA 59.047 42.857 0.00 0.00 0.00 4.69
2233 6157 2.420628 TGAATGCAGCAAAAGAACCG 57.579 45.000 0.00 0.00 0.00 4.44
2247 6176 7.346695 ACGAAAGAAACAAAATGCAATGAATG 58.653 30.769 0.00 0.00 0.00 2.67
2248 6177 7.481275 ACGAAAGAAACAAAATGCAATGAAT 57.519 28.000 0.00 0.00 0.00 2.57
2249 6178 6.900568 ACGAAAGAAACAAAATGCAATGAA 57.099 29.167 0.00 0.00 0.00 2.57
2250 6179 6.900568 AACGAAAGAAACAAAATGCAATGA 57.099 29.167 0.00 0.00 0.00 2.57
2251 6180 6.628461 GGAAACGAAAGAAACAAAATGCAATG 59.372 34.615 0.00 0.00 0.00 2.82
2252 6181 6.538381 AGGAAACGAAAGAAACAAAATGCAAT 59.462 30.769 0.00 0.00 0.00 3.56
2253 6182 5.872070 AGGAAACGAAAGAAACAAAATGCAA 59.128 32.000 0.00 0.00 0.00 4.08
2398 6360 5.296748 GTCGCCCCATAAATTAATGCATTT 58.703 37.500 18.75 2.40 0.00 2.32
2422 6385 1.156736 CACCTAAACCTTCGGTGCAG 58.843 55.000 0.00 0.00 41.39 4.41
2469 6434 1.006400 CTTTCTTGGGGAAGAGGCCAT 59.994 52.381 5.01 0.00 35.16 4.40
2470 6435 0.405585 CTTTCTTGGGGAAGAGGCCA 59.594 55.000 5.01 0.00 35.16 5.36
2471 6436 0.698818 TCTTTCTTGGGGAAGAGGCC 59.301 55.000 0.00 0.00 35.16 5.19
2472 6437 2.816777 ATCTTTCTTGGGGAAGAGGC 57.183 50.000 0.00 0.00 35.16 4.70
2473 6438 4.786425 CCTAATCTTTCTTGGGGAAGAGG 58.214 47.826 0.00 0.00 35.16 3.69
2480 6445 3.445096 CAGCAACCCTAATCTTTCTTGGG 59.555 47.826 0.00 0.00 43.26 4.12
2481 6446 4.082125 ACAGCAACCCTAATCTTTCTTGG 58.918 43.478 0.00 0.00 0.00 3.61
2482 6447 4.142816 CGACAGCAACCCTAATCTTTCTTG 60.143 45.833 0.00 0.00 0.00 3.02
2483 6448 4.003648 CGACAGCAACCCTAATCTTTCTT 58.996 43.478 0.00 0.00 0.00 2.52
2484 6449 3.600388 CGACAGCAACCCTAATCTTTCT 58.400 45.455 0.00 0.00 0.00 2.52
2485 6450 2.678336 CCGACAGCAACCCTAATCTTTC 59.322 50.000 0.00 0.00 0.00 2.62
2486 6451 2.039879 ACCGACAGCAACCCTAATCTTT 59.960 45.455 0.00 0.00 0.00 2.52
2487 6452 1.628846 ACCGACAGCAACCCTAATCTT 59.371 47.619 0.00 0.00 0.00 2.40
2488 6453 1.276622 ACCGACAGCAACCCTAATCT 58.723 50.000 0.00 0.00 0.00 2.40
2489 6454 2.547826 GTACCGACAGCAACCCTAATC 58.452 52.381 0.00 0.00 0.00 1.75
2490 6455 1.134907 CGTACCGACAGCAACCCTAAT 60.135 52.381 0.00 0.00 0.00 1.73
2491 6456 0.244450 CGTACCGACAGCAACCCTAA 59.756 55.000 0.00 0.00 0.00 2.69
2492 6457 1.885157 CGTACCGACAGCAACCCTA 59.115 57.895 0.00 0.00 0.00 3.53
2493 6458 2.654877 CGTACCGACAGCAACCCT 59.345 61.111 0.00 0.00 0.00 4.34
2494 6459 3.116531 GCGTACCGACAGCAACCC 61.117 66.667 0.00 0.00 0.00 4.11
2495 6460 3.116531 GGCGTACCGACAGCAACC 61.117 66.667 0.00 0.00 33.63 3.77
2501 6466 1.607148 CATAGATGAGGCGTACCGACA 59.393 52.381 0.00 0.00 42.76 4.35
2508 6473 1.447643 GCCACCATAGATGAGGCGT 59.552 57.895 9.28 0.00 38.39 5.68
2519 6484 4.860835 ATGGTCCTAGGCCACCAT 57.139 55.556 23.52 23.52 46.46 3.55
2537 6503 3.083997 GGGATCCACCGCACTCCT 61.084 66.667 15.23 0.00 40.11 3.69
2570 6536 7.544804 AGAACCATCTAAAAATGAAGCCTTT 57.455 32.000 0.00 0.00 32.88 3.11
2572 6538 7.233348 TCAAAGAACCATCTAAAAATGAAGCCT 59.767 33.333 0.00 0.00 33.77 4.58
2601 6567 8.485578 TTGAAAAGGATACAAACCCTAACAAT 57.514 30.769 0.00 0.00 41.41 2.71
2621 6587 0.949105 GCCGTCTCGCCTTCTTGAAA 60.949 55.000 0.00 0.00 0.00 2.69
2700 6666 1.337071 ACACCTACCGACGATGCTATG 59.663 52.381 0.00 0.00 0.00 2.23
2701 6667 1.337071 CACACCTACCGACGATGCTAT 59.663 52.381 0.00 0.00 0.00 2.97
2772 6740 3.219189 CACGAGCATAGACGAACGATAG 58.781 50.000 0.14 0.00 46.19 2.08
2788 6756 5.236478 AGAATACAACCTGAAAACACACGAG 59.764 40.000 0.00 0.00 0.00 4.18
2862 6830 1.562475 GTGGTAAGGCCCCATAAGACA 59.438 52.381 0.00 0.00 33.76 3.41
2879 6847 2.126580 GTCGGGAAGTCGTCGTGG 60.127 66.667 0.00 0.00 0.00 4.94
2990 6959 9.520515 AATTACATTCATATTCATAGACCACCC 57.479 33.333 0.00 0.00 0.00 4.61
3029 6998 2.128821 CATGACGGTACAACGAACACA 58.871 47.619 0.00 0.00 37.61 3.72
3043 7012 5.545588 ACCTATTCATCCTCAATCATGACG 58.454 41.667 0.00 0.00 0.00 4.35
3055 7024 5.751028 CGAGAAACTTCTGACCTATTCATCC 59.249 44.000 0.00 0.00 37.73 3.51
3065 7034 4.658071 TGTTTTTGCGAGAAACTTCTGAC 58.342 39.130 0.00 0.00 37.73 3.51
3096 7065 9.971922 CTTTCTAAACCTTTTGAATGATGAACT 57.028 29.630 3.38 0.00 33.31 3.01
3097 7066 9.965824 TCTTTCTAAACCTTTTGAATGATGAAC 57.034 29.630 6.50 0.00 34.15 3.18
3099 7068 8.299570 GCTCTTTCTAAACCTTTTGAATGATGA 58.700 33.333 9.39 2.12 36.41 2.92
3100 7069 7.543520 GGCTCTTTCTAAACCTTTTGAATGATG 59.456 37.037 9.39 6.81 36.41 3.07
3101 7070 7.233348 TGGCTCTTTCTAAACCTTTTGAATGAT 59.767 33.333 9.39 0.00 36.41 2.45
3102 7071 6.549364 TGGCTCTTTCTAAACCTTTTGAATGA 59.451 34.615 8.91 8.91 35.48 2.57
3103 7072 6.748132 TGGCTCTTTCTAAACCTTTTGAATG 58.252 36.000 0.00 0.47 33.31 2.67
3104 7073 6.976934 TGGCTCTTTCTAAACCTTTTGAAT 57.023 33.333 0.00 0.00 33.31 2.57
3105 7074 6.783708 TTGGCTCTTTCTAAACCTTTTGAA 57.216 33.333 0.00 0.00 31.81 2.69
3106 7075 6.976934 ATTGGCTCTTTCTAAACCTTTTGA 57.023 33.333 0.00 0.00 0.00 2.69
3107 7076 7.657336 TGTATTGGCTCTTTCTAAACCTTTTG 58.343 34.615 0.00 0.00 0.00 2.44
3108 7077 7.833285 TGTATTGGCTCTTTCTAAACCTTTT 57.167 32.000 0.00 0.00 0.00 2.27
3109 7078 7.833285 TTGTATTGGCTCTTTCTAAACCTTT 57.167 32.000 0.00 0.00 0.00 3.11
3110 7079 7.833285 TTTGTATTGGCTCTTTCTAAACCTT 57.167 32.000 0.00 0.00 0.00 3.50
3111 7080 8.422577 AATTTGTATTGGCTCTTTCTAAACCT 57.577 30.769 0.00 0.00 0.00 3.50
3112 7081 8.925700 CAAATTTGTATTGGCTCTTTCTAAACC 58.074 33.333 10.15 0.00 0.00 3.27
3113 7082 9.691362 TCAAATTTGTATTGGCTCTTTCTAAAC 57.309 29.630 17.47 0.00 0.00 2.01
3117 7086 9.428097 GAAATCAAATTTGTATTGGCTCTTTCT 57.572 29.630 17.47 0.00 31.47 2.52
3118 7087 8.375465 CGAAATCAAATTTGTATTGGCTCTTTC 58.625 33.333 17.47 11.47 31.47 2.62
3119 7088 7.331687 CCGAAATCAAATTTGTATTGGCTCTTT 59.668 33.333 17.47 5.50 31.47 2.52
3120 7089 6.813152 CCGAAATCAAATTTGTATTGGCTCTT 59.187 34.615 17.47 1.67 31.47 2.85
3121 7090 6.332630 CCGAAATCAAATTTGTATTGGCTCT 58.667 36.000 17.47 2.26 31.47 4.09
3122 7091 5.005682 GCCGAAATCAAATTTGTATTGGCTC 59.994 40.000 26.79 16.08 31.47 4.70
3123 7092 4.869861 GCCGAAATCAAATTTGTATTGGCT 59.130 37.500 26.79 11.74 31.47 4.75
3124 7093 4.869861 AGCCGAAATCAAATTTGTATTGGC 59.130 37.500 26.78 26.78 31.47 4.52
3125 7094 6.966435 AAGCCGAAATCAAATTTGTATTGG 57.034 33.333 17.47 16.68 31.47 3.16
3126 7095 7.117523 TGGAAAGCCGAAATCAAATTTGTATTG 59.882 33.333 17.47 8.87 36.79 1.90
3127 7096 7.158021 TGGAAAGCCGAAATCAAATTTGTATT 58.842 30.769 17.47 13.16 36.79 1.89
3128 7097 6.696411 TGGAAAGCCGAAATCAAATTTGTAT 58.304 32.000 17.47 7.53 36.79 2.29
3129 7098 6.090483 TGGAAAGCCGAAATCAAATTTGTA 57.910 33.333 17.47 5.54 36.79 2.41
3130 7099 4.954875 TGGAAAGCCGAAATCAAATTTGT 58.045 34.783 17.47 3.04 36.79 2.83
3131 7100 5.921004 TTGGAAAGCCGAAATCAAATTTG 57.079 34.783 12.15 12.15 36.79 2.32
3132 7101 6.934048 TTTTGGAAAGCCGAAATCAAATTT 57.066 29.167 0.00 0.00 41.60 1.82
3133 7102 6.934048 TTTTTGGAAAGCCGAAATCAAATT 57.066 29.167 0.00 0.00 44.95 1.82
3156 7125 9.300681 TGTCCTCTAAATGTCTGAAATCAATTT 57.699 29.630 0.00 0.00 0.00 1.82
3157 7126 8.868522 TGTCCTCTAAATGTCTGAAATCAATT 57.131 30.769 0.00 0.00 0.00 2.32
3158 7127 8.868522 TTGTCCTCTAAATGTCTGAAATCAAT 57.131 30.769 0.00 0.00 0.00 2.57
3159 7128 8.690203 TTTGTCCTCTAAATGTCTGAAATCAA 57.310 30.769 0.00 0.00 0.00 2.57
3160 7129 8.868522 ATTTGTCCTCTAAATGTCTGAAATCA 57.131 30.769 0.00 0.00 0.00 2.57
3204 7173 9.457436 GGAGGGAGTATTTCACAACTAAATTTA 57.543 33.333 0.00 0.00 0.00 1.40
3205 7174 7.120726 CGGAGGGAGTATTTCACAACTAAATTT 59.879 37.037 0.00 0.00 0.00 1.82
3206 7175 6.598064 CGGAGGGAGTATTTCACAACTAAATT 59.402 38.462 0.00 0.00 0.00 1.82
3207 7176 6.113411 CGGAGGGAGTATTTCACAACTAAAT 58.887 40.000 0.00 0.00 0.00 1.40
3208 7177 5.012354 ACGGAGGGAGTATTTCACAACTAAA 59.988 40.000 0.00 0.00 0.00 1.85
3209 7178 4.529377 ACGGAGGGAGTATTTCACAACTAA 59.471 41.667 0.00 0.00 0.00 2.24
3210 7179 4.091549 ACGGAGGGAGTATTTCACAACTA 58.908 43.478 0.00 0.00 0.00 2.24
3211 7180 2.904434 ACGGAGGGAGTATTTCACAACT 59.096 45.455 0.00 0.00 0.00 3.16
3212 7181 3.329929 ACGGAGGGAGTATTTCACAAC 57.670 47.619 0.00 0.00 0.00 3.32
3213 7182 3.833650 TGTACGGAGGGAGTATTTCACAA 59.166 43.478 0.00 0.00 0.00 3.33
3214 7183 3.433343 TGTACGGAGGGAGTATTTCACA 58.567 45.455 0.00 0.00 0.00 3.58
3215 7184 4.667519 ATGTACGGAGGGAGTATTTCAC 57.332 45.455 0.00 0.00 0.00 3.18
3216 7185 6.795144 TTAATGTACGGAGGGAGTATTTCA 57.205 37.500 0.00 0.00 0.00 2.69
3222 7191 8.680903 CGTATTATATTAATGTACGGAGGGAGT 58.319 37.037 0.00 0.00 35.71 3.85
3223 7192 8.680903 ACGTATTATATTAATGTACGGAGGGAG 58.319 37.037 19.26 2.37 41.57 4.30
3224 7193 8.461222 CACGTATTATATTAATGTACGGAGGGA 58.539 37.037 19.26 0.00 41.57 4.20
3225 7194 8.246180 ACACGTATTATATTAATGTACGGAGGG 58.754 37.037 19.26 12.47 41.57 4.30
3226 7195 9.630098 AACACGTATTATATTAATGTACGGAGG 57.370 33.333 19.26 13.90 41.57 4.30
3229 7198 9.519905 GCAAACACGTATTATATTAATGTACGG 57.480 33.333 19.26 13.90 41.57 4.02
3230 7199 9.230583 CGCAAACACGTATTATATTAATGTACG 57.769 33.333 16.17 16.17 42.58 3.67
3231 7200 9.519905 CCGCAAACACGTATTATATTAATGTAC 57.480 33.333 0.00 0.00 0.00 2.90
3232 7201 9.258826 ACCGCAAACACGTATTATATTAATGTA 57.741 29.630 0.00 0.00 0.00 2.29
3233 7202 8.145316 ACCGCAAACACGTATTATATTAATGT 57.855 30.769 0.00 0.00 0.00 2.71
3234 7203 8.996988 AACCGCAAACACGTATTATATTAATG 57.003 30.769 0.00 0.00 0.00 1.90
3235 7204 8.284693 GGAACCGCAAACACGTATTATATTAAT 58.715 33.333 0.00 0.00 0.00 1.40
3236 7205 7.279536 TGGAACCGCAAACACGTATTATATTAA 59.720 33.333 0.00 0.00 0.00 1.40
3237 7206 6.760298 TGGAACCGCAAACACGTATTATATTA 59.240 34.615 0.00 0.00 0.00 0.98
3238 7207 5.585445 TGGAACCGCAAACACGTATTATATT 59.415 36.000 0.00 0.00 0.00 1.28
3239 7208 5.006941 GTGGAACCGCAAACACGTATTATAT 59.993 40.000 0.00 0.00 0.00 0.86
3240 7209 4.329528 GTGGAACCGCAAACACGTATTATA 59.670 41.667 0.00 0.00 0.00 0.98
3241 7210 3.125658 GTGGAACCGCAAACACGTATTAT 59.874 43.478 0.00 0.00 0.00 1.28
3242 7211 2.479656 GTGGAACCGCAAACACGTATTA 59.520 45.455 0.00 0.00 0.00 0.98
3243 7212 1.264826 GTGGAACCGCAAACACGTATT 59.735 47.619 0.00 0.00 0.00 1.89
3244 7213 0.869730 GTGGAACCGCAAACACGTAT 59.130 50.000 0.00 0.00 0.00 3.06
3245 7214 2.309326 GTGGAACCGCAAACACGTA 58.691 52.632 0.00 0.00 0.00 3.57
3246 7215 3.103875 GTGGAACCGCAAACACGT 58.896 55.556 0.00 0.00 0.00 4.49
3248 7217 0.863957 CAACGTGGAACCGCAAACAC 60.864 55.000 5.27 0.00 0.00 3.32
3249 7218 1.429825 CAACGTGGAACCGCAAACA 59.570 52.632 5.27 0.00 0.00 2.83
3250 7219 1.942223 GCAACGTGGAACCGCAAAC 60.942 57.895 0.00 0.00 0.00 2.93
3251 7220 1.658686 AAGCAACGTGGAACCGCAAA 61.659 50.000 0.00 0.00 0.00 3.68
3252 7221 1.658686 AAAGCAACGTGGAACCGCAA 61.659 50.000 0.00 0.00 0.00 4.85
3253 7222 1.658686 AAAAGCAACGTGGAACCGCA 61.659 50.000 0.00 0.00 0.00 5.69
3254 7223 1.065109 AAAAGCAACGTGGAACCGC 59.935 52.632 0.00 0.00 0.00 5.68
3255 7224 1.206115 GCAAAAGCAACGTGGAACCG 61.206 55.000 0.00 0.00 0.00 4.44
3256 7225 0.179124 TGCAAAAGCAACGTGGAACC 60.179 50.000 0.00 0.00 0.00 3.62
3257 7226 1.851658 ATGCAAAAGCAACGTGGAAC 58.148 45.000 0.00 0.00 0.00 3.62
3258 7227 2.593346 AATGCAAAAGCAACGTGGAA 57.407 40.000 0.00 0.00 0.00 3.53
3259 7228 2.593346 AAATGCAAAAGCAACGTGGA 57.407 40.000 0.00 0.00 0.00 4.02
3260 7229 2.865551 AGAAAATGCAAAAGCAACGTGG 59.134 40.909 0.00 0.00 0.00 4.94
3261 7230 3.551082 TGAGAAAATGCAAAAGCAACGTG 59.449 39.130 0.00 0.00 0.00 4.49
3262 7231 3.779759 TGAGAAAATGCAAAAGCAACGT 58.220 36.364 0.00 0.00 0.00 3.99
3263 7232 4.977741 ATGAGAAAATGCAAAAGCAACG 57.022 36.364 0.00 0.00 0.00 4.10
3264 7233 7.974243 AAAAATGAGAAAATGCAAAAGCAAC 57.026 28.000 0.00 0.00 0.00 4.17
3285 7254 9.766277 GACACATTTTTGCAGTTCAAATAAAAA 57.234 25.926 0.00 0.00 43.53 1.94
3286 7255 8.939929 TGACACATTTTTGCAGTTCAAATAAAA 58.060 25.926 0.00 0.00 43.53 1.52
3287 7256 8.484641 TGACACATTTTTGCAGTTCAAATAAA 57.515 26.923 0.00 0.00 43.53 1.40
3288 7257 8.659925 ATGACACATTTTTGCAGTTCAAATAA 57.340 26.923 0.00 0.00 43.53 1.40
3289 7258 9.926158 ATATGACACATTTTTGCAGTTCAAATA 57.074 25.926 0.00 0.00 43.53 1.40
3290 7259 8.836268 ATATGACACATTTTTGCAGTTCAAAT 57.164 26.923 0.00 0.00 43.53 2.32
3291 7260 9.926158 ATATATGACACATTTTTGCAGTTCAAA 57.074 25.926 0.00 0.00 42.50 2.69
3317 7286 9.964354 TCTGTTACTACCTCTGTACACTAATTA 57.036 33.333 0.00 0.00 0.00 1.40
3318 7287 8.874744 TCTGTTACTACCTCTGTACACTAATT 57.125 34.615 0.00 0.00 0.00 1.40
3320 7289 9.388506 GTATCTGTTACTACCTCTGTACACTAA 57.611 37.037 0.00 0.00 0.00 2.24
3321 7290 7.708322 CGTATCTGTTACTACCTCTGTACACTA 59.292 40.741 0.00 0.00 0.00 2.74
3322 7291 6.538021 CGTATCTGTTACTACCTCTGTACACT 59.462 42.308 0.00 0.00 0.00 3.55
3323 7292 6.314896 ACGTATCTGTTACTACCTCTGTACAC 59.685 42.308 0.00 0.00 0.00 2.90
3324 7293 6.409704 ACGTATCTGTTACTACCTCTGTACA 58.590 40.000 0.00 0.00 0.00 2.90
3325 7294 6.917217 ACGTATCTGTTACTACCTCTGTAC 57.083 41.667 0.00 0.00 0.00 2.90



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

AutoCloner maintained by Alex Coulton.