Multiple sequence alignment - TraesCS4B01G171300

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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 TraesCS4B01G171300 chr4B 100.000 4376 0 0 1 4376 375140463 375136088 0.000000e+00 8082.0
1 TraesCS4B01G171300 chr4D 96.453 2312 79 3 1 2312 301302453 301300145 0.000000e+00 3812.0
2 TraesCS4B01G171300 chr4D 95.408 1677 60 9 2716 4376 301299883 301298208 0.000000e+00 2654.0
3 TraesCS4B01G171300 chr4A 95.772 2318 91 6 1 2314 180394996 180397310 0.000000e+00 3731.0
4 TraesCS4B01G171300 chr4A 93.680 981 43 9 2716 3677 180397561 180398541 0.000000e+00 1450.0
5 TraesCS4B01G171300 chr4A 97.441 508 13 0 3869 4376 180402528 180403035 0.000000e+00 867.0
6 TraesCS4B01G171300 chr2A 75.769 1300 271 30 1008 2282 57547254 57548534 2.240000e-172 616.0
7 TraesCS4B01G171300 chr2D 75.751 1299 270 32 1008 2282 56104814 56106091 2.890000e-171 612.0
8 TraesCS4B01G171300 chr2D 90.141 71 7 0 3715 3785 241661973 241661903 4.660000e-15 93.5
9 TraesCS4B01G171300 chr2B 75.615 1300 273 29 1008 2282 88839260 88840540 4.840000e-169 604.0
10 TraesCS4B01G171300 chr2B 96.970 165 4 1 2453 2617 664125201 664125038 4.310000e-70 276.0
11 TraesCS4B01G171300 chr2B 95.858 169 5 2 2450 2618 500939542 500939708 5.580000e-69 272.0
12 TraesCS4B01G171300 chr2B 93.820 178 9 2 2447 2624 713695791 713695966 2.590000e-67 267.0
13 TraesCS4B01G171300 chr7B 97.006 167 4 1 2451 2617 497576621 497576786 3.330000e-71 279.0
14 TraesCS4B01G171300 chr7B 95.294 170 7 1 2451 2620 155387826 155387658 7.210000e-68 268.0
15 TraesCS4B01G171300 chr5B 96.450 169 5 1 2454 2622 701551811 701551644 1.200000e-70 278.0
16 TraesCS4B01G171300 chr5B 75.648 193 40 7 3110 3297 24113558 24113368 6.030000e-14 89.8
17 TraesCS4B01G171300 chr5B 95.000 40 2 0 3671 3710 230883447 230883486 3.650000e-06 63.9
18 TraesCS4B01G171300 chr5B 88.889 45 5 0 3637 3681 636609486 636609442 6.110000e-04 56.5
19 TraesCS4B01G171300 chr7D 93.889 180 8 3 2450 2628 573953111 573953288 7.210000e-68 268.0
20 TraesCS4B01G171300 chr7D 96.364 55 2 0 3714 3768 593035235 593035289 1.680000e-14 91.6
21 TraesCS4B01G171300 chr1B 90.452 199 14 4 2430 2627 14094280 14094474 1.560000e-64 257.0
22 TraesCS4B01G171300 chr1B 89.950 199 15 4 2430 2627 14026087 14026281 7.270000e-63 252.0
23 TraesCS4B01G171300 chr1B 75.338 296 64 7 3014 3303 535143642 535143350 2.750000e-27 134.0
24 TraesCS4B01G171300 chr1B 91.667 72 6 0 3714 3785 70321282 70321211 2.780000e-17 100.0
25 TraesCS4B01G171300 chr1B 91.667 48 1 3 3666 3710 70321300 70321253 3.650000e-06 63.9
26 TraesCS4B01G171300 chr6A 78.395 162 29 6 3626 3785 532026778 532026621 2.780000e-17 100.0
27 TraesCS4B01G171300 chr6A 97.297 37 1 0 3674 3710 532026700 532026664 3.650000e-06 63.9
28 TraesCS4B01G171300 chr3D 92.754 69 5 0 3110 3178 323698839 323698907 2.780000e-17 100.0
29 TraesCS4B01G171300 chr3A 91.667 72 6 0 3110 3181 398881171 398881100 2.780000e-17 100.0
30 TraesCS4B01G171300 chr3B 92.647 68 5 0 3110 3177 395380212 395380145 1.000000e-16 99.0
31 TraesCS4B01G171300 chr5D 91.176 68 6 0 3110 3177 33022691 33022624 4.660000e-15 93.5
32 TraesCS4B01G171300 chr5D 94.545 55 3 0 3714 3768 215302563 215302617 7.800000e-13 86.1
33 TraesCS4B01G171300 chr5D 95.122 41 2 0 3670 3710 259536755 259536795 1.020000e-06 65.8
34 TraesCS4B01G171300 chr5D 87.719 57 3 4 3658 3710 215302536 215302592 3.650000e-06 63.9
35 TraesCS4B01G171300 chr7A 93.443 61 4 0 3708 3768 685583779 685583839 1.680000e-14 91.6
36 TraesCS4B01G171300 chr7A 95.000 40 2 0 3671 3710 718430942 718430981 3.650000e-06 63.9
37 TraesCS4B01G171300 chr5A 75.773 194 38 8 3110 3297 21431090 21430900 6.030000e-14 89.8
38 TraesCS4B01G171300 chr5A 77.419 155 28 6 3021 3170 415322226 415322378 7.800000e-13 86.1
39 TraesCS4B01G171300 chr5A 88.060 67 8 0 3716 3782 558315463 558315397 3.630000e-11 80.5
40 TraesCS4B01G171300 chr5A 95.122 41 2 0 3670 3710 346189556 346189516 1.020000e-06 65.8
41 TraesCS4B01G171300 chr6B 88.406 69 8 0 3714 3782 249443296 249443364 2.800000e-12 84.2
42 TraesCS4B01G171300 chr6B 100.000 35 0 0 3676 3710 249443291 249443325 1.020000e-06 65.8
43 TraesCS4B01G171300 chr6D 89.362 47 5 0 3023 3069 470961826 470961780 4.730000e-05 60.2


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 TraesCS4B01G171300 chr4B 375136088 375140463 4375 True 8082 8082 100.0000 1 4376 1 chr4B.!!$R1 4375
1 TraesCS4B01G171300 chr4D 301298208 301302453 4245 True 3233 3812 95.9305 1 4376 2 chr4D.!!$R1 4375
2 TraesCS4B01G171300 chr4A 180394996 180403035 8039 False 2016 3731 95.6310 1 4376 3 chr4A.!!$F1 4375
3 TraesCS4B01G171300 chr2A 57547254 57548534 1280 False 616 616 75.7690 1008 2282 1 chr2A.!!$F1 1274
4 TraesCS4B01G171300 chr2D 56104814 56106091 1277 False 612 612 75.7510 1008 2282 1 chr2D.!!$F1 1274
5 TraesCS4B01G171300 chr2B 88839260 88840540 1280 False 604 604 75.6150 1008 2282 1 chr2B.!!$F1 1274

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
692 693 1.679977 ATGGCATGACAGTGTGGGC 60.680 57.895 7.63 2.98 0.00 5.36 F
1056 1061 0.391263 TGCTCTGTCTGCATCTGCTG 60.391 55.000 3.53 3.22 42.66 4.41 F
2784 2859 0.611896 CCCCATTGGACTGGAACACC 60.612 60.000 3.62 0.00 38.69 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1757 1.000385 CCATGTCGTGGCAATGTTTGT 60.000 47.619 0.00 0.0 42.12 2.83 R
2814 2889 0.533032 CATGGATGTGTGCAATGCCA 59.467 50.000 1.53 0.0 0.00 4.92 R
4040 7933 2.671396 CGTGAGAAGTTATTGTTCCCGG 59.329 50.000 0.00 0.0 0.00 5.73 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
45 46 2.481289 AGTTAAGCTGAGCCCACTTC 57.519 50.000 0.00 0.00 0.00 3.01
191 192 4.141846 TGCTCATCTTGGAGACCAGTATTC 60.142 45.833 0.00 0.00 37.05 1.75
346 347 4.970662 TCTCATGCTTGTATTGCCTTTC 57.029 40.909 0.00 0.00 0.00 2.62
439 440 3.256383 TGTGATTTGACAATGCTTCAGGG 59.744 43.478 0.00 0.00 0.00 4.45
526 527 3.151912 AGAGGCTTCCCATGCATAATC 57.848 47.619 0.00 0.00 0.00 1.75
543 544 7.729116 TGCATAATCTCTGATCATTCACACTA 58.271 34.615 0.00 0.00 0.00 2.74
684 685 2.583024 TGGTCTTTCATGGCATGACA 57.417 45.000 28.83 21.64 39.39 3.58
692 693 1.679977 ATGGCATGACAGTGTGGGC 60.680 57.895 7.63 2.98 0.00 5.36
848 849 8.129840 TGCTTGCAGTTTTATAACGAGTTAAAA 58.870 29.630 0.00 0.00 39.31 1.52
946 947 5.750067 CAGCTGTTTGATTATTACATTGGCC 59.250 40.000 5.25 0.00 0.00 5.36
992 993 4.703645 TTAGTGACATTGACTCCGAGAG 57.296 45.455 1.33 0.00 35.52 3.20
996 997 3.129462 GTGACATTGACTCCGAGAGATCA 59.871 47.826 1.33 0.00 33.32 2.92
1056 1061 0.391263 TGCTCTGTCTGCATCTGCTG 60.391 55.000 3.53 3.22 42.66 4.41
1077 1082 5.709164 GCTGCTATCACTATTCATCCCATTT 59.291 40.000 0.00 0.00 0.00 2.32
1212 1217 0.744281 TAACATGCGCAGAGGATCGA 59.256 50.000 18.32 0.00 42.67 3.59
1353 1358 3.996921 AGCATTCCTTCTGATGTCACT 57.003 42.857 0.00 0.00 0.00 3.41
1552 1557 7.510675 AATTCTTTGTCTGGACCTATTCCTA 57.489 36.000 0.00 0.00 46.10 2.94
1643 1648 6.768381 CCCTTCCTCCAAGTATTCTCAAATAC 59.232 42.308 1.00 1.00 45.09 1.89
1689 1694 1.075674 TGGGCCTCCTCTAGCTGAG 60.076 63.158 4.53 0.96 42.30 3.35
1719 1745 4.796231 CCTTCGCCGACACCCTCG 62.796 72.222 0.00 0.00 42.54 4.63
1725 1751 2.180017 CCGACACCCTCGTTACCG 59.820 66.667 0.00 0.00 41.18 4.02
1727 1753 2.968206 GACACCCTCGTTACCGCT 59.032 61.111 0.00 0.00 0.00 5.52
1731 1757 1.904865 ACCCTCGTTACCGCTGTCA 60.905 57.895 0.00 0.00 0.00 3.58
1788 1814 1.336240 GGATTTATCATTGCGGCTGCC 60.336 52.381 16.57 9.11 41.78 4.85
1994 2020 2.237143 TCTTGGAGGGATGCAGTTACAG 59.763 50.000 0.00 0.00 0.00 2.74
2299 2325 1.326548 GTACGCTATTGCCTTTCACCG 59.673 52.381 0.00 0.00 35.36 4.94
2302 2328 0.811281 GCTATTGCCTTTCACCGCTT 59.189 50.000 0.00 0.00 0.00 4.68
2306 2332 1.327303 TTGCCTTTCACCGCTTCATT 58.673 45.000 0.00 0.00 0.00 2.57
2309 2335 2.102252 TGCCTTTCACCGCTTCATTTTT 59.898 40.909 0.00 0.00 0.00 1.94
2350 2376 6.817765 TTGATTACTTTGCAAGTTAGGAGG 57.182 37.500 0.00 0.00 42.81 4.30
2356 2382 5.325239 ACTTTGCAAGTTAGGAGGCTAAAT 58.675 37.500 0.00 0.00 39.04 1.40
2388 2414 7.935520 TGTTTTGTTAGCATGAGACAAACATA 58.064 30.769 16.33 5.18 41.42 2.29
2393 2419 6.816640 TGTTAGCATGAGACAAACATACCTAC 59.183 38.462 0.00 0.00 0.00 3.18
2395 2421 3.555956 GCATGAGACAAACATACCTACCG 59.444 47.826 0.00 0.00 0.00 4.02
2401 2427 2.498885 ACAAACATACCTACCGTCCCTC 59.501 50.000 0.00 0.00 0.00 4.30
2425 2456 5.620417 CGCAAAATTTACATGCACAAAAAGG 59.380 36.000 12.50 0.00 40.04 3.11
2459 2490 6.678568 AGCAAAGCTATGATATGTACTCCT 57.321 37.500 0.00 0.00 36.99 3.69
2460 2491 7.072263 AGCAAAGCTATGATATGTACTCCTT 57.928 36.000 0.00 0.00 36.99 3.36
2461 2492 7.158021 AGCAAAGCTATGATATGTACTCCTTC 58.842 38.462 0.00 0.00 36.99 3.46
2462 2493 6.370166 GCAAAGCTATGATATGTACTCCTTCC 59.630 42.308 0.00 0.00 0.00 3.46
2463 2494 5.906113 AGCTATGATATGTACTCCTTCCG 57.094 43.478 0.00 0.00 0.00 4.30
2464 2495 5.326069 AGCTATGATATGTACTCCTTCCGT 58.674 41.667 0.00 0.00 0.00 4.69
2465 2496 5.775701 AGCTATGATATGTACTCCTTCCGTT 59.224 40.000 0.00 0.00 0.00 4.44
2466 2497 6.071840 AGCTATGATATGTACTCCTTCCGTTC 60.072 42.308 0.00 0.00 0.00 3.95
2467 2498 4.931661 TGATATGTACTCCTTCCGTTCC 57.068 45.455 0.00 0.00 0.00 3.62
2468 2499 4.543689 TGATATGTACTCCTTCCGTTCCT 58.456 43.478 0.00 0.00 0.00 3.36
2469 2500 5.698104 TGATATGTACTCCTTCCGTTCCTA 58.302 41.667 0.00 0.00 0.00 2.94
2470 2501 6.131264 TGATATGTACTCCTTCCGTTCCTAA 58.869 40.000 0.00 0.00 0.00 2.69
2471 2502 6.608405 TGATATGTACTCCTTCCGTTCCTAAA 59.392 38.462 0.00 0.00 0.00 1.85
2472 2503 5.952347 ATGTACTCCTTCCGTTCCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
2473 2504 5.080969 TGTACTCCTTCCGTTCCTAAATG 57.919 43.478 0.00 0.00 0.00 2.32
2474 2505 4.529377 TGTACTCCTTCCGTTCCTAAATGT 59.471 41.667 0.00 0.00 0.00 2.71
2475 2506 5.716228 TGTACTCCTTCCGTTCCTAAATGTA 59.284 40.000 0.00 0.00 0.00 2.29
2476 2507 5.750352 ACTCCTTCCGTTCCTAAATGTAA 57.250 39.130 0.00 0.00 0.00 2.41
2477 2508 5.731591 ACTCCTTCCGTTCCTAAATGTAAG 58.268 41.667 0.00 0.00 0.00 2.34
2478 2509 5.247792 ACTCCTTCCGTTCCTAAATGTAAGT 59.752 40.000 0.00 0.00 0.00 2.24
2479 2510 5.727434 TCCTTCCGTTCCTAAATGTAAGTC 58.273 41.667 0.00 0.00 0.00 3.01
2480 2511 5.482878 TCCTTCCGTTCCTAAATGTAAGTCT 59.517 40.000 0.00 0.00 0.00 3.24
2481 2512 6.013984 TCCTTCCGTTCCTAAATGTAAGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
2482 2513 6.653740 CCTTCCGTTCCTAAATGTAAGTCTTT 59.346 38.462 0.00 0.00 0.00 2.52
2483 2514 7.360946 CCTTCCGTTCCTAAATGTAAGTCTTTG 60.361 40.741 0.00 0.00 0.00 2.77
2484 2515 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
2485 2516 7.669427 TCCGTTCCTAAATGTAAGTCTTTGTA 58.331 34.615 0.00 0.00 0.00 2.41
2486 2517 7.816031 TCCGTTCCTAAATGTAAGTCTTTGTAG 59.184 37.037 0.00 0.00 0.00 2.74
2487 2518 7.816031 CCGTTCCTAAATGTAAGTCTTTGTAGA 59.184 37.037 0.00 0.00 0.00 2.59
2488 2519 8.861101 CGTTCCTAAATGTAAGTCTTTGTAGAG 58.139 37.037 0.00 0.00 0.00 2.43
2489 2520 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
2495 2526 8.779354 AATGTAAGTCTTTGTAGAGATTCCAC 57.221 34.615 0.00 0.00 0.00 4.02
2496 2527 7.540474 TGTAAGTCTTTGTAGAGATTCCACT 57.460 36.000 0.00 0.00 0.00 4.00
2497 2528 8.645814 TGTAAGTCTTTGTAGAGATTCCACTA 57.354 34.615 0.00 0.00 0.00 2.74
2498 2529 9.256228 TGTAAGTCTTTGTAGAGATTCCACTAT 57.744 33.333 0.00 0.00 0.00 2.12
2506 2537 8.718102 TTGTAGAGATTCCACTATAAAACTGC 57.282 34.615 0.00 0.00 0.00 4.40
2507 2538 7.847096 TGTAGAGATTCCACTATAAAACTGCA 58.153 34.615 0.00 0.00 0.00 4.41
2508 2539 8.486210 TGTAGAGATTCCACTATAAAACTGCAT 58.514 33.333 0.00 0.00 0.00 3.96
2509 2540 9.982651 GTAGAGATTCCACTATAAAACTGCATA 57.017 33.333 0.00 0.00 0.00 3.14
2510 2541 8.894768 AGAGATTCCACTATAAAACTGCATAC 57.105 34.615 0.00 0.00 0.00 2.39
2511 2542 7.653713 AGAGATTCCACTATAAAACTGCATACG 59.346 37.037 0.00 0.00 0.00 3.06
2512 2543 6.706270 AGATTCCACTATAAAACTGCATACGG 59.294 38.462 0.00 0.00 0.00 4.02
2513 2544 5.601583 TCCACTATAAAACTGCATACGGA 57.398 39.130 0.00 0.00 0.00 4.69
2514 2545 6.169557 TCCACTATAAAACTGCATACGGAT 57.830 37.500 0.00 0.00 0.00 4.18
2515 2546 5.989168 TCCACTATAAAACTGCATACGGATG 59.011 40.000 2.22 2.22 36.02 3.51
2516 2547 5.758296 CCACTATAAAACTGCATACGGATGT 59.242 40.000 9.90 0.00 35.30 3.06
2517 2548 6.926826 CCACTATAAAACTGCATACGGATGTA 59.073 38.462 9.90 3.37 35.30 2.29
2518 2549 7.602644 CCACTATAAAACTGCATACGGATGTAT 59.397 37.037 9.90 0.56 42.03 2.29
2519 2550 9.634163 CACTATAAAACTGCATACGGATGTATA 57.366 33.333 9.90 1.75 39.28 1.47
2525 2556 8.932945 AAACTGCATACGGATGTATATAGATG 57.067 34.615 9.90 0.00 39.28 2.90
2526 2557 6.507900 ACTGCATACGGATGTATATAGATGC 58.492 40.000 9.90 0.00 39.28 3.91
2527 2558 6.096846 ACTGCATACGGATGTATATAGATGCA 59.903 38.462 9.90 7.54 39.28 3.96
2528 2559 7.054491 TGCATACGGATGTATATAGATGCAT 57.946 36.000 9.90 0.00 40.68 3.96
2529 2560 7.500141 TGCATACGGATGTATATAGATGCATT 58.500 34.615 9.90 1.23 38.38 3.56
2530 2561 7.986889 TGCATACGGATGTATATAGATGCATTT 59.013 33.333 9.90 0.00 38.38 2.32
2531 2562 8.830580 GCATACGGATGTATATAGATGCATTTT 58.169 33.333 9.90 0.00 38.38 1.82
2535 2566 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
2557 2588 8.992835 AAGTTTAGATTCATTCATTTTGCTCC 57.007 30.769 0.00 0.00 0.00 4.70
2558 2589 7.253422 AGTTTAGATTCATTCATTTTGCTCCG 58.747 34.615 0.00 0.00 0.00 4.63
2559 2590 6.757897 TTAGATTCATTCATTTTGCTCCGT 57.242 33.333 0.00 0.00 0.00 4.69
2560 2591 7.857734 TTAGATTCATTCATTTTGCTCCGTA 57.142 32.000 0.00 0.00 0.00 4.02
2561 2592 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
2562 2593 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
2563 2594 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
2564 2595 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
2565 2596 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
2566 2597 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
2567 2598 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
2568 2599 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
2569 2600 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2570 2601 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
2571 2602 1.108776 TGCTCCGTATGTAGTCCACC 58.891 55.000 0.00 0.00 0.00 4.61
2572 2603 1.341679 TGCTCCGTATGTAGTCCACCT 60.342 52.381 0.00 0.00 0.00 4.00
2573 2604 2.092267 TGCTCCGTATGTAGTCCACCTA 60.092 50.000 0.00 0.00 0.00 3.08
2574 2605 2.553172 GCTCCGTATGTAGTCCACCTAG 59.447 54.545 0.00 0.00 0.00 3.02
2575 2606 3.818180 CTCCGTATGTAGTCCACCTAGT 58.182 50.000 0.00 0.00 0.00 2.57
2576 2607 3.548770 TCCGTATGTAGTCCACCTAGTG 58.451 50.000 0.00 0.00 0.00 2.74
2590 2621 5.176407 CACCTAGTGGAATCTCTACGAAG 57.824 47.826 0.00 0.00 32.72 3.79
2591 2622 4.882427 CACCTAGTGGAATCTCTACGAAGA 59.118 45.833 0.00 0.00 32.72 2.87
2592 2623 4.883006 ACCTAGTGGAATCTCTACGAAGAC 59.117 45.833 0.00 0.00 32.72 3.01
2593 2624 5.127491 CCTAGTGGAATCTCTACGAAGACT 58.873 45.833 0.00 0.00 32.72 3.24
2594 2625 5.591067 CCTAGTGGAATCTCTACGAAGACTT 59.409 44.000 0.00 0.00 32.72 3.01
2595 2626 6.766944 CCTAGTGGAATCTCTACGAAGACTTA 59.233 42.308 0.00 0.00 32.72 2.24
2596 2627 6.439675 AGTGGAATCTCTACGAAGACTTAC 57.560 41.667 0.00 0.00 32.72 2.34
2597 2628 5.944599 AGTGGAATCTCTACGAAGACTTACA 59.055 40.000 0.00 0.00 32.72 2.41
2598 2629 6.603997 AGTGGAATCTCTACGAAGACTTACAT 59.396 38.462 0.00 0.00 32.72 2.29
2599 2630 7.122948 AGTGGAATCTCTACGAAGACTTACATT 59.877 37.037 0.00 0.00 32.72 2.71
2600 2631 7.760340 GTGGAATCTCTACGAAGACTTACATTT 59.240 37.037 0.00 0.00 0.00 2.32
2601 2632 8.963725 TGGAATCTCTACGAAGACTTACATTTA 58.036 33.333 0.00 0.00 0.00 1.40
2602 2633 9.453325 GGAATCTCTACGAAGACTTACATTTAG 57.547 37.037 0.00 0.00 0.00 1.85
2603 2634 9.453325 GAATCTCTACGAAGACTTACATTTAGG 57.547 37.037 0.00 0.00 0.00 2.69
2604 2635 8.749026 ATCTCTACGAAGACTTACATTTAGGA 57.251 34.615 0.00 0.00 0.00 2.94
2605 2636 8.571461 TCTCTACGAAGACTTACATTTAGGAA 57.429 34.615 0.00 0.00 0.00 3.36
2606 2637 8.457261 TCTCTACGAAGACTTACATTTAGGAAC 58.543 37.037 0.00 0.00 0.00 3.62
2607 2638 7.246311 TCTACGAAGACTTACATTTAGGAACG 58.754 38.462 0.00 0.00 0.00 3.95
2608 2639 5.166398 ACGAAGACTTACATTTAGGAACGG 58.834 41.667 0.00 0.00 0.00 4.44
2609 2640 5.047802 ACGAAGACTTACATTTAGGAACGGA 60.048 40.000 0.00 0.00 0.00 4.69
2610 2641 5.515626 CGAAGACTTACATTTAGGAACGGAG 59.484 44.000 0.00 0.00 0.00 4.63
2611 2642 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2612 2643 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2613 2644 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2629 2660 5.711036 ACGGAGGGAGTAGAATATACACATC 59.289 44.000 0.00 0.00 0.00 3.06
2648 2679 8.048534 ACACATCCATGAACTTCATTTTCTAG 57.951 34.615 1.17 0.00 34.28 2.43
2670 2701 8.088981 TCTAGTTCTGTTAAGAGGACATTGTTC 58.911 37.037 13.25 0.00 32.79 3.18
2675 2706 9.739276 TTCTGTTAAGAGGACATTGTTCATTAT 57.261 29.630 0.00 0.00 32.79 1.28
2688 2719 6.801539 TTGTTCATTATCCACTCACTGAAC 57.198 37.500 6.34 6.34 41.61 3.18
2689 2720 4.929211 TGTTCATTATCCACTCACTGAACG 59.071 41.667 8.24 0.00 43.24 3.95
2704 2735 3.498397 ACTGAACGTGGCTCTAATTGTTG 59.502 43.478 0.00 0.00 0.00 3.33
2706 2737 4.323417 TGAACGTGGCTCTAATTGTTGAT 58.677 39.130 0.00 0.00 0.00 2.57
2708 2739 2.930040 ACGTGGCTCTAATTGTTGATCG 59.070 45.455 0.00 0.00 0.00 3.69
2710 2741 3.804325 CGTGGCTCTAATTGTTGATCGAT 59.196 43.478 0.00 0.00 0.00 3.59
2712 2743 5.635280 CGTGGCTCTAATTGTTGATCGATAT 59.365 40.000 0.00 0.00 0.00 1.63
2714 2745 5.863935 TGGCTCTAATTGTTGATCGATATCG 59.136 40.000 19.14 19.14 41.45 2.92
2730 2805 5.690409 TCGATATCGGTTCTGATTAAAGTGC 59.310 40.000 24.12 0.00 40.29 4.40
2751 2826 3.624777 CTGATGAACAGGCATTAAGGGT 58.375 45.455 0.00 0.00 42.39 4.34
2781 2856 0.698818 AGACCCCATTGGACTGGAAC 59.301 55.000 3.62 0.00 37.76 3.62
2784 2859 0.611896 CCCCATTGGACTGGAACACC 60.612 60.000 3.62 0.00 38.69 4.16
2796 2871 3.960571 CTGGAACACCAGGATGAAGATT 58.039 45.455 8.23 0.00 45.18 2.40
2814 2889 7.112122 TGAAGATTATACTTGGAACAGCACAT 58.888 34.615 0.00 0.00 42.39 3.21
2958 3033 1.191489 TGAGCCTCCCGATCAACACA 61.191 55.000 0.00 0.00 0.00 3.72
2980 3055 3.001406 GGGTGGTGGTCGGCTACT 61.001 66.667 2.79 0.00 0.00 2.57
2997 3072 4.397832 TGCGCCCCGGAAACCTAC 62.398 66.667 0.73 0.00 0.00 3.18
3003 3078 1.138247 CCCGGAAACCTACGAGTCG 59.862 63.158 11.85 11.85 0.00 4.18
3006 3081 1.081892 CGGAAACCTACGAGTCGAGA 58.918 55.000 21.50 5.61 0.00 4.04
3030 3105 1.954146 CACCCACAAGTCGGACGTG 60.954 63.158 20.11 20.11 33.76 4.49
3096 3171 4.020617 CTCCAGTCGCAGGGGCAA 62.021 66.667 0.00 0.00 41.24 4.52
3141 3216 3.799755 GTGCATTCCGTGGTCCGC 61.800 66.667 0.00 0.00 34.38 5.54
3189 3264 0.459899 TCGCGCTGATGAAGTACCAT 59.540 50.000 5.56 0.00 0.00 3.55
3210 3285 0.749649 ACATCGAGGATGAGCTGGTC 59.250 55.000 3.06 0.00 42.09 4.02
3388 3463 2.778679 CGTAAACGCTGGCTCTGC 59.221 61.111 0.00 0.00 0.00 4.26
3483 3572 3.425404 GCGTGCATGTTAATTGGTAGTG 58.575 45.455 7.93 0.00 0.00 2.74
3681 3775 9.131791 ACATAAGATGTTCTAACCTTTTTGTGT 57.868 29.630 0.00 0.00 41.63 3.72
3711 6561 6.892310 TCACTCATTTCAATCTGTATGTCG 57.108 37.500 0.00 0.00 0.00 4.35
3712 6562 5.812127 TCACTCATTTCAATCTGTATGTCGG 59.188 40.000 0.00 0.00 0.00 4.79
3743 6593 8.394971 TGTTCACTCATTTCAATCTGTATGTT 57.605 30.769 0.00 0.00 0.00 2.71
3746 6596 8.032952 TCACTCATTTCAATCTGTATGTTGTC 57.967 34.615 0.00 0.00 0.00 3.18
3803 6653 9.767684 TGTGATCGAAAAATGTTATGATACAAC 57.232 29.630 0.00 0.00 0.00 3.32
3804 6654 9.767684 GTGATCGAAAAATGTTATGATACAACA 57.232 29.630 0.00 0.00 40.01 3.33
3805 6655 9.767684 TGATCGAAAAATGTTATGATACAACAC 57.232 29.630 0.00 0.00 38.63 3.32
3806 6656 9.767684 GATCGAAAAATGTTATGATACAACACA 57.232 29.630 0.00 0.00 38.63 3.72
3807 6657 9.773328 ATCGAAAAATGTTATGATACAACACAG 57.227 29.630 0.00 0.00 38.63 3.66
3882 7773 4.684703 ACATCAGCGACACTTAACACTTAC 59.315 41.667 0.00 0.00 0.00 2.34
3884 7775 4.295870 TCAGCGACACTTAACACTTACAG 58.704 43.478 0.00 0.00 0.00 2.74
3885 7776 4.049186 CAGCGACACTTAACACTTACAGT 58.951 43.478 0.00 0.00 0.00 3.55
3886 7777 5.008911 TCAGCGACACTTAACACTTACAGTA 59.991 40.000 0.00 0.00 0.00 2.74
3939 7832 2.035961 CCGTATCACCCACATACCAGAG 59.964 54.545 0.00 0.00 0.00 3.35
4040 7933 5.938125 TCAGACAAAGCCCTCTTGTATAAAC 59.062 40.000 0.00 0.00 31.78 2.01
4131 8024 1.202639 CCGCCACTAATCACCATAGCA 60.203 52.381 0.00 0.00 0.00 3.49
4178 8071 1.305219 CCGTCCAACACATTCGCCAT 61.305 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.054166 CACATCATGTGGCACTTTGTTG 58.946 45.455 19.83 20.34 44.27 3.33
93 94 8.041323 CCACAAACCAAATATAGTCTAGACACT 58.959 37.037 24.44 13.16 0.00 3.55
191 192 4.142513 GCAAGGAGGAAACTAAAGCTCATG 60.143 45.833 0.00 0.00 44.43 3.07
293 294 9.169592 AGTTGCACAAGAAAGTAACTAAAAGTA 57.830 29.630 0.00 0.00 38.60 2.24
346 347 0.454957 CCAAAGAACGGCGCTCATTG 60.455 55.000 18.18 18.18 0.00 2.82
439 440 1.625818 ACGGAGATGATTCCCTATGCC 59.374 52.381 0.00 0.00 33.46 4.40
526 527 5.595885 ACCGAATAGTGTGAATGATCAGAG 58.404 41.667 0.09 0.00 35.88 3.35
692 693 2.689553 ACAAACCACAAAGGCAAAGG 57.310 45.000 0.00 0.00 43.14 3.11
848 849 7.539034 ACTTTAAACATAACTCCATTTGCCT 57.461 32.000 0.00 0.00 0.00 4.75
906 907 6.529463 AACAGCTGCAATAAAAATGAACAC 57.471 33.333 15.27 0.00 0.00 3.32
908 909 7.176285 TCAAACAGCTGCAATAAAAATGAAC 57.824 32.000 15.27 0.00 0.00 3.18
917 918 9.518906 CAATGTAATAATCAAACAGCTGCAATA 57.481 29.630 15.27 0.00 0.00 1.90
946 947 8.545229 AATGAGAGACAACTTCATCTGTTTAG 57.455 34.615 0.00 0.00 0.00 1.85
996 997 9.041354 CCTCTAAGATTTAGATAGCCCATTAGT 57.959 37.037 0.00 0.00 0.00 2.24
1056 1061 5.709164 AGCAAATGGGATGAATAGTGATAGC 59.291 40.000 0.00 0.00 0.00 2.97
1212 1217 5.560724 ACCCTAAGCGCAAATATATGTGAT 58.439 37.500 11.47 0.00 32.55 3.06
1353 1358 5.026038 TGGAACGTAAAGAAGGAAGTGAA 57.974 39.130 0.00 0.00 0.00 3.18
1428 1433 0.463833 GGTCAAGGGTAATGAGGCCG 60.464 60.000 0.00 0.00 0.00 6.13
1552 1557 6.772716 TGTCTTAAGCTTGGAAGTTTGAGATT 59.227 34.615 9.86 0.00 41.38 2.40
1643 1648 3.596362 GGGTTCCCCAGGAATGAAG 57.404 57.895 0.00 0.00 44.04 3.02
1689 1694 1.531578 GGCGAAGGAAGAACAGAACAC 59.468 52.381 0.00 0.00 0.00 3.32
1719 1745 3.296628 CAATGTTTGTGACAGCGGTAAC 58.703 45.455 0.00 0.00 42.62 2.50
1725 1751 1.490621 GTGGCAATGTTTGTGACAGC 58.509 50.000 0.00 0.00 42.62 4.40
1727 1753 1.064803 GTCGTGGCAATGTTTGTGACA 59.935 47.619 0.00 0.00 43.71 3.58
1731 1757 1.000385 CCATGTCGTGGCAATGTTTGT 60.000 47.619 0.00 0.00 42.12 2.83
1788 1814 1.453155 ATACAGCAAAGCCTCCAACG 58.547 50.000 0.00 0.00 0.00 4.10
1994 2020 5.057149 TCAGTAAGTCTTCCAAGTCAAAGC 58.943 41.667 0.00 0.00 0.00 3.51
2287 2313 1.327303 AATGAAGCGGTGAAAGGCAA 58.673 45.000 0.00 0.00 0.00 4.52
2335 2361 6.546034 GGATATTTAGCCTCCTAACTTGCAAA 59.454 38.462 0.00 0.00 33.43 3.68
2336 2362 6.062095 GGATATTTAGCCTCCTAACTTGCAA 58.938 40.000 0.00 0.00 33.43 4.08
2337 2363 5.131977 TGGATATTTAGCCTCCTAACTTGCA 59.868 40.000 0.00 0.00 33.43 4.08
2338 2364 5.621193 TGGATATTTAGCCTCCTAACTTGC 58.379 41.667 0.00 0.00 33.43 4.01
2339 2365 7.721399 ACAATGGATATTTAGCCTCCTAACTTG 59.279 37.037 0.00 0.00 33.43 3.16
2340 2366 7.816411 ACAATGGATATTTAGCCTCCTAACTT 58.184 34.615 0.00 0.00 33.43 2.66
2341 2367 7.394144 ACAATGGATATTTAGCCTCCTAACT 57.606 36.000 0.00 0.00 33.43 2.24
2342 2368 8.465273 AAACAATGGATATTTAGCCTCCTAAC 57.535 34.615 0.00 0.00 33.43 2.34
2343 2369 8.912988 CAAAACAATGGATATTTAGCCTCCTAA 58.087 33.333 0.00 0.00 31.73 2.69
2344 2370 8.058847 ACAAAACAATGGATATTTAGCCTCCTA 58.941 33.333 0.00 0.00 31.73 2.94
2345 2371 6.897413 ACAAAACAATGGATATTTAGCCTCCT 59.103 34.615 0.00 0.00 31.73 3.69
2346 2372 7.112452 ACAAAACAATGGATATTTAGCCTCC 57.888 36.000 0.00 0.00 31.73 4.30
2347 2373 9.736023 CTAACAAAACAATGGATATTTAGCCTC 57.264 33.333 0.00 0.00 31.73 4.70
2348 2374 8.197439 GCTAACAAAACAATGGATATTTAGCCT 58.803 33.333 0.00 0.00 31.73 4.58
2349 2375 7.978975 TGCTAACAAAACAATGGATATTTAGCC 59.021 33.333 12.41 0.00 33.61 3.93
2350 2376 8.925161 TGCTAACAAAACAATGGATATTTAGC 57.075 30.769 9.68 9.68 34.72 3.09
2356 2382 7.392953 TGTCTCATGCTAACAAAACAATGGATA 59.607 33.333 0.00 0.00 0.00 2.59
2377 2403 3.429960 GGGACGGTAGGTATGTTTGTCTC 60.430 52.174 0.00 0.00 0.00 3.36
2388 2414 1.474332 TTTTGCGAGGGACGGTAGGT 61.474 55.000 0.00 0.00 42.83 3.08
2393 2419 1.807742 TGTAAATTTTGCGAGGGACGG 59.192 47.619 0.00 0.00 42.83 4.79
2395 2421 3.179048 GCATGTAAATTTTGCGAGGGAC 58.821 45.455 0.00 0.00 0.00 4.46
2401 2427 5.620417 CCTTTTTGTGCATGTAAATTTTGCG 59.380 36.000 8.41 0.00 39.23 4.85
2441 2472 5.326069 ACGGAAGGAGTACATATCATAGCT 58.674 41.667 0.00 0.00 0.00 3.32
2452 2483 5.082251 ACATTTAGGAACGGAAGGAGTAC 57.918 43.478 0.00 0.00 0.00 2.73
2453 2484 6.438425 ACTTACATTTAGGAACGGAAGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
2454 2485 5.247792 ACTTACATTTAGGAACGGAAGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
2455 2486 5.731591 ACTTACATTTAGGAACGGAAGGAG 58.268 41.667 0.00 0.00 0.00 3.69
2456 2487 5.482878 AGACTTACATTTAGGAACGGAAGGA 59.517 40.000 0.00 0.00 0.00 3.36
2457 2488 5.731591 AGACTTACATTTAGGAACGGAAGG 58.268 41.667 0.00 0.00 0.00 3.46
2458 2489 7.172703 ACAAAGACTTACATTTAGGAACGGAAG 59.827 37.037 0.00 0.00 0.00 3.46
2459 2490 6.993902 ACAAAGACTTACATTTAGGAACGGAA 59.006 34.615 0.00 0.00 0.00 4.30
2460 2491 6.527423 ACAAAGACTTACATTTAGGAACGGA 58.473 36.000 0.00 0.00 0.00 4.69
2461 2492 6.796705 ACAAAGACTTACATTTAGGAACGG 57.203 37.500 0.00 0.00 0.00 4.44
2462 2493 8.752766 TCTACAAAGACTTACATTTAGGAACG 57.247 34.615 0.00 0.00 0.00 3.95
2463 2494 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
2469 2500 9.220767 GTGGAATCTCTACAAAGACTTACATTT 57.779 33.333 0.00 0.00 0.00 2.32
2470 2501 8.598041 AGTGGAATCTCTACAAAGACTTACATT 58.402 33.333 0.00 0.00 29.47 2.71
2471 2502 8.140112 AGTGGAATCTCTACAAAGACTTACAT 57.860 34.615 0.00 0.00 29.47 2.29
2472 2503 7.540474 AGTGGAATCTCTACAAAGACTTACA 57.460 36.000 0.00 0.00 29.47 2.41
2480 2511 9.162764 GCAGTTTTATAGTGGAATCTCTACAAA 57.837 33.333 0.00 0.00 29.47 2.83
2481 2512 8.318412 TGCAGTTTTATAGTGGAATCTCTACAA 58.682 33.333 0.00 0.00 29.47 2.41
2482 2513 7.847096 TGCAGTTTTATAGTGGAATCTCTACA 58.153 34.615 0.00 0.00 29.47 2.74
2483 2514 8.894768 ATGCAGTTTTATAGTGGAATCTCTAC 57.105 34.615 0.00 0.00 30.77 2.59
2484 2515 9.982651 GTATGCAGTTTTATAGTGGAATCTCTA 57.017 33.333 0.00 0.00 30.77 2.43
2485 2516 7.653713 CGTATGCAGTTTTATAGTGGAATCTCT 59.346 37.037 0.00 0.00 30.77 3.10
2486 2517 7.095607 CCGTATGCAGTTTTATAGTGGAATCTC 60.096 40.741 0.00 0.00 30.77 2.75
2487 2518 6.706270 CCGTATGCAGTTTTATAGTGGAATCT 59.294 38.462 0.00 0.00 30.77 2.40
2488 2519 6.704493 TCCGTATGCAGTTTTATAGTGGAATC 59.296 38.462 0.00 0.00 30.77 2.52
2489 2520 6.588204 TCCGTATGCAGTTTTATAGTGGAAT 58.412 36.000 0.00 0.00 30.77 3.01
2490 2521 5.979993 TCCGTATGCAGTTTTATAGTGGAA 58.020 37.500 0.00 0.00 30.77 3.53
2491 2522 5.601583 TCCGTATGCAGTTTTATAGTGGA 57.398 39.130 0.00 0.00 31.60 4.02
2492 2523 5.758296 ACATCCGTATGCAGTTTTATAGTGG 59.242 40.000 0.00 0.00 36.50 4.00
2493 2524 6.844696 ACATCCGTATGCAGTTTTATAGTG 57.155 37.500 0.00 0.00 36.50 2.74
2499 2530 9.371136 CATCTATATACATCCGTATGCAGTTTT 57.629 33.333 0.00 0.00 38.79 2.43
2500 2531 7.492669 GCATCTATATACATCCGTATGCAGTTT 59.507 37.037 0.00 0.00 38.79 2.66
2501 2532 6.980978 GCATCTATATACATCCGTATGCAGTT 59.019 38.462 0.00 0.00 38.79 3.16
2502 2533 6.096846 TGCATCTATATACATCCGTATGCAGT 59.903 38.462 0.00 0.00 38.79 4.40
2503 2534 6.507023 TGCATCTATATACATCCGTATGCAG 58.493 40.000 0.00 0.00 38.79 4.41
2504 2535 6.463995 TGCATCTATATACATCCGTATGCA 57.536 37.500 0.00 0.00 38.79 3.96
2505 2536 7.953158 AATGCATCTATATACATCCGTATGC 57.047 36.000 0.00 0.00 38.79 3.14
2509 2540 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
2532 2563 7.756722 CGGAGCAAAATGAATGAATCTAAACTT 59.243 33.333 0.00 0.00 0.00 2.66
2533 2564 7.094205 ACGGAGCAAAATGAATGAATCTAAACT 60.094 33.333 0.00 0.00 0.00 2.66
2534 2565 7.029563 ACGGAGCAAAATGAATGAATCTAAAC 58.970 34.615 0.00 0.00 0.00 2.01
2535 2566 7.156876 ACGGAGCAAAATGAATGAATCTAAA 57.843 32.000 0.00 0.00 0.00 1.85
2536 2567 6.757897 ACGGAGCAAAATGAATGAATCTAA 57.242 33.333 0.00 0.00 0.00 2.10
2537 2568 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
2538 2569 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
2539 2570 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
2540 2571 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
2541 2572 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
2542 2573 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
2543 2574 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
2544 2575 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
2545 2576 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
2546 2577 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
2547 2578 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
2548 2579 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
2549 2580 3.592059 GTGGACTACATACGGAGCAAAA 58.408 45.455 0.00 0.00 0.00 2.44
2550 2581 2.093869 GGTGGACTACATACGGAGCAAA 60.094 50.000 0.00 0.00 0.00 3.68
2551 2582 1.479323 GGTGGACTACATACGGAGCAA 59.521 52.381 0.00 0.00 0.00 3.91
2552 2583 1.108776 GGTGGACTACATACGGAGCA 58.891 55.000 0.00 0.00 0.00 4.26
2553 2584 1.400737 AGGTGGACTACATACGGAGC 58.599 55.000 0.00 0.00 0.00 4.70
2554 2585 3.564644 CACTAGGTGGACTACATACGGAG 59.435 52.174 0.00 0.00 0.00 4.63
2555 2586 3.548770 CACTAGGTGGACTACATACGGA 58.451 50.000 0.00 0.00 0.00 4.69
2556 2587 3.984508 CACTAGGTGGACTACATACGG 57.015 52.381 0.00 0.00 0.00 4.02
2568 2599 4.882427 TCTTCGTAGAGATTCCACTAGGTG 59.118 45.833 0.00 0.00 38.43 4.00
2569 2600 4.883006 GTCTTCGTAGAGATTCCACTAGGT 59.117 45.833 0.00 0.00 38.43 3.08
2570 2601 5.127491 AGTCTTCGTAGAGATTCCACTAGG 58.873 45.833 0.00 0.00 38.43 3.02
2571 2602 6.687081 AAGTCTTCGTAGAGATTCCACTAG 57.313 41.667 0.00 0.00 38.43 2.57
2572 2603 7.108194 TGTAAGTCTTCGTAGAGATTCCACTA 58.892 38.462 0.00 0.00 38.43 2.74
2573 2604 5.944599 TGTAAGTCTTCGTAGAGATTCCACT 59.055 40.000 0.00 0.00 38.43 4.00
2574 2605 6.192234 TGTAAGTCTTCGTAGAGATTCCAC 57.808 41.667 0.00 0.00 38.43 4.02
2575 2606 7.406031 AATGTAAGTCTTCGTAGAGATTCCA 57.594 36.000 0.00 0.00 38.43 3.53
2576 2607 9.453325 CTAAATGTAAGTCTTCGTAGAGATTCC 57.547 37.037 0.00 0.00 38.43 3.01
2577 2608 9.453325 CCTAAATGTAAGTCTTCGTAGAGATTC 57.547 37.037 0.00 0.00 38.43 2.52
2578 2609 9.186837 TCCTAAATGTAAGTCTTCGTAGAGATT 57.813 33.333 0.00 0.00 38.43 2.40
2579 2610 8.749026 TCCTAAATGTAAGTCTTCGTAGAGAT 57.251 34.615 0.00 0.00 38.43 2.75
2580 2611 8.457261 GTTCCTAAATGTAAGTCTTCGTAGAGA 58.543 37.037 0.00 0.00 38.43 3.10
2581 2612 7.428761 CGTTCCTAAATGTAAGTCTTCGTAGAG 59.571 40.741 0.00 0.00 38.43 2.43
2582 2613 7.246311 CGTTCCTAAATGTAAGTCTTCGTAGA 58.754 38.462 0.00 0.00 0.00 2.59
2583 2614 6.471519 CCGTTCCTAAATGTAAGTCTTCGTAG 59.528 42.308 0.00 0.00 0.00 3.51
2584 2615 6.150976 TCCGTTCCTAAATGTAAGTCTTCGTA 59.849 38.462 0.00 0.00 0.00 3.43
2585 2616 5.047802 TCCGTTCCTAAATGTAAGTCTTCGT 60.048 40.000 0.00 0.00 0.00 3.85
2586 2617 5.404946 TCCGTTCCTAAATGTAAGTCTTCG 58.595 41.667 0.00 0.00 0.00 3.79
2587 2618 5.811100 CCTCCGTTCCTAAATGTAAGTCTTC 59.189 44.000 0.00 0.00 0.00 2.87
2588 2619 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2589 2620 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2590 2621 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2591 2622 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2592 2623 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2593 2624 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2594 2625 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2595 2626 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2596 2627 3.958798 TCTACTCCCTCCGTTCCTAAATG 59.041 47.826 0.00 0.00 0.00 2.32
2597 2628 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2598 2629 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2599 2630 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
2600 2631 3.967467 ATTCTACTCCCTCCGTTCCTA 57.033 47.619 0.00 0.00 0.00 2.94
2601 2632 2.850695 ATTCTACTCCCTCCGTTCCT 57.149 50.000 0.00 0.00 0.00 3.36
2602 2633 5.048154 GTGTATATTCTACTCCCTCCGTTCC 60.048 48.000 0.00 0.00 0.00 3.62
2603 2634 5.533903 TGTGTATATTCTACTCCCTCCGTTC 59.466 44.000 0.00 0.00 0.00 3.95
2604 2635 5.452255 TGTGTATATTCTACTCCCTCCGTT 58.548 41.667 0.00 0.00 0.00 4.44
2605 2636 5.057843 TGTGTATATTCTACTCCCTCCGT 57.942 43.478 0.00 0.00 0.00 4.69
2606 2637 5.125739 GGATGTGTATATTCTACTCCCTCCG 59.874 48.000 0.00 0.00 0.00 4.63
2607 2638 6.017192 TGGATGTGTATATTCTACTCCCTCC 58.983 44.000 0.00 0.00 0.00 4.30
2608 2639 7.397476 TCATGGATGTGTATATTCTACTCCCTC 59.603 40.741 0.00 0.00 0.00 4.30
2609 2640 7.248976 TCATGGATGTGTATATTCTACTCCCT 58.751 38.462 0.00 0.00 0.00 4.20
2610 2641 7.482169 TCATGGATGTGTATATTCTACTCCC 57.518 40.000 0.00 0.00 0.00 4.30
2611 2642 8.589338 AGTTCATGGATGTGTATATTCTACTCC 58.411 37.037 0.00 0.00 0.00 3.85
2612 2643 9.988815 AAGTTCATGGATGTGTATATTCTACTC 57.011 33.333 0.00 0.00 0.00 2.59
2613 2644 9.988815 GAAGTTCATGGATGTGTATATTCTACT 57.011 33.333 0.00 0.00 0.00 2.57
2641 2672 9.273016 CAATGTCCTCTTAACAGAACTAGAAAA 57.727 33.333 0.00 0.00 0.00 2.29
2648 2679 6.861065 TGAACAATGTCCTCTTAACAGAAC 57.139 37.500 0.00 0.00 0.00 3.01
2688 2719 3.186909 TCGATCAACAATTAGAGCCACG 58.813 45.455 0.00 0.00 0.00 4.94
2689 2720 6.183360 CGATATCGATCAACAATTAGAGCCAC 60.183 42.308 20.50 0.00 43.02 5.01
2704 2735 7.410942 GCACTTTAATCAGAACCGATATCGATC 60.411 40.741 26.32 21.34 43.02 3.69
2706 2737 5.690409 GCACTTTAATCAGAACCGATATCGA 59.310 40.000 26.32 5.51 43.02 3.59
2708 2739 6.701841 TCAGCACTTTAATCAGAACCGATATC 59.298 38.462 0.00 0.00 0.00 1.63
2710 2741 5.972935 TCAGCACTTTAATCAGAACCGATA 58.027 37.500 0.00 0.00 0.00 2.92
2712 2743 4.265904 TCAGCACTTTAATCAGAACCGA 57.734 40.909 0.00 0.00 0.00 4.69
2714 2745 6.072508 TGTTCATCAGCACTTTAATCAGAACC 60.073 38.462 0.00 0.00 32.84 3.62
2730 2805 3.624777 ACCCTTAATGCCTGTTCATCAG 58.375 45.455 0.00 0.00 43.27 2.90
2751 2826 3.053693 CCAATGGGGTCTTCTCCACAATA 60.054 47.826 0.00 0.00 44.56 1.90
2781 2856 6.830912 TCCAAGTATAATCTTCATCCTGGTG 58.169 40.000 0.00 0.00 0.00 4.17
2784 2859 7.041508 GCTGTTCCAAGTATAATCTTCATCCTG 60.042 40.741 0.00 0.00 0.00 3.86
2796 2871 3.278574 GCCATGTGCTGTTCCAAGTATA 58.721 45.455 0.00 0.00 36.87 1.47
2814 2889 0.533032 CATGGATGTGTGCAATGCCA 59.467 50.000 1.53 0.00 0.00 4.92
2980 3055 4.397832 GTAGGTTTCCGGGGCGCA 62.398 66.667 10.83 0.00 0.00 6.09
2988 3063 3.565905 TTTCTCGACTCGTAGGTTTCC 57.434 47.619 0.00 0.00 0.00 3.13
2997 3072 2.412089 GTGGGTGAATTTTCTCGACTCG 59.588 50.000 0.00 0.00 0.00 4.18
3003 3078 3.058224 CCGACTTGTGGGTGAATTTTCTC 60.058 47.826 0.00 0.00 0.00 2.87
3006 3081 2.621526 GTCCGACTTGTGGGTGAATTTT 59.378 45.455 1.94 0.00 0.00 1.82
3030 3105 2.432628 AGCACGCCGAAGCTGTAC 60.433 61.111 7.90 0.00 40.13 2.90
3048 3123 0.879400 CGGTCAGCATCTCCATGAGC 60.879 60.000 0.00 0.00 37.93 4.26
3189 3264 2.362397 GACCAGCTCATCCTCGATGTTA 59.638 50.000 1.80 0.00 40.55 2.41
3210 3285 3.518998 GCCAGCTGCAGCATCTGG 61.519 66.667 38.24 32.74 46.73 3.86
3681 3775 7.099266 ACAGATTGAAATGAGTGAACAAACA 57.901 32.000 0.00 0.00 0.00 2.83
3711 6561 4.647424 TGAAATGAGTGAACAAACACCC 57.353 40.909 0.00 0.00 41.12 4.61
3712 6562 6.418819 CAGATTGAAATGAGTGAACAAACACC 59.581 38.462 0.00 0.00 41.12 4.16
3798 6648 5.826601 TGCATGTTTCTTTCTGTGTTGTA 57.173 34.783 0.00 0.00 0.00 2.41
3799 6649 4.717233 TGCATGTTTCTTTCTGTGTTGT 57.283 36.364 0.00 0.00 0.00 3.32
3800 6650 6.406093 TTTTGCATGTTTCTTTCTGTGTTG 57.594 33.333 0.00 0.00 0.00 3.33
3801 6651 6.650390 AGTTTTTGCATGTTTCTTTCTGTGTT 59.350 30.769 0.00 0.00 0.00 3.32
3803 6653 6.237915 GGAGTTTTTGCATGTTTCTTTCTGTG 60.238 38.462 0.00 0.00 0.00 3.66
3804 6654 5.812127 GGAGTTTTTGCATGTTTCTTTCTGT 59.188 36.000 0.00 0.00 0.00 3.41
3805 6655 5.811613 TGGAGTTTTTGCATGTTTCTTTCTG 59.188 36.000 0.00 0.00 0.00 3.02
3806 6656 5.976458 TGGAGTTTTTGCATGTTTCTTTCT 58.024 33.333 0.00 0.00 0.00 2.52
3807 6657 6.073602 GGATGGAGTTTTTGCATGTTTCTTTC 60.074 38.462 0.00 0.00 38.05 2.62
3882 7773 5.221204 GGTTATTACTCCCTCCGTTCTACTG 60.221 48.000 0.00 0.00 0.00 2.74
3884 7775 4.646492 TGGTTATTACTCCCTCCGTTCTAC 59.354 45.833 0.00 0.00 0.00 2.59
3885 7776 4.870636 TGGTTATTACTCCCTCCGTTCTA 58.129 43.478 0.00 0.00 0.00 2.10
3886 7777 3.716431 TGGTTATTACTCCCTCCGTTCT 58.284 45.455 0.00 0.00 0.00 3.01
3939 7832 5.428253 TGGTATGCCTTGTATTCTCTGAAC 58.572 41.667 0.16 0.00 35.27 3.18
3984 7877 3.813443 AGCTGTACTGGCCAGATTTATG 58.187 45.455 39.19 21.78 31.38 1.90
4040 7933 2.671396 CGTGAGAAGTTATTGTTCCCGG 59.329 50.000 0.00 0.00 0.00 5.73
4118 8011 7.634429 GCAGAGATATGGATGCTATGGTGATTA 60.634 40.741 0.00 0.00 35.78 1.75
4131 8024 5.837770 TTGGATTCTGCAGAGATATGGAT 57.162 39.130 17.43 5.45 0.00 3.41
4178 8071 8.092068 TGGAACTTCTTCGTAACATTAAGATGA 58.908 33.333 0.00 0.97 36.73 2.92


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

AutoCloner maintained by Alex Coulton.