Multiple sequence alignment - TraesCS5B01G240200

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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 TraesCS5B01G240200 chr5B 100.000 3035 0 0 1 3035 420385141 420388175 0.000000e+00 5605
1 TraesCS5B01G240200 chr5B 94.242 330 18 1 2375 2703 683663742 683663413 1.260000e-138 503
2 TraesCS5B01G240200 chr5B 93.902 328 19 1 2371 2697 232297773 232298100 7.560000e-136 494
3 TraesCS5B01G240200 chr5B 78.654 609 93 25 1095 1679 586916279 586916874 1.330000e-98 370
4 TraesCS5B01G240200 chr5B 80.729 384 57 14 1290 1663 420856666 420856290 1.780000e-72 283
5 TraesCS5B01G240200 chr5D 91.730 2104 79 37 1 2052 355675880 355677940 0.000000e+00 2833
6 TraesCS5B01G240200 chr5D 79.180 610 88 29 1095 1679 479194578 479195173 1.320000e-103 387
7 TraesCS5B01G240200 chr5D 90.753 292 21 5 2697 2985 355678237 355678525 4.750000e-103 385
8 TraesCS5B01G240200 chr5D 81.627 381 59 9 1290 1663 356189272 356189648 3.800000e-79 305
9 TraesCS5B01G240200 chr5D 82.748 313 20 11 2088 2378 355677942 355678242 6.500000e-62 248
10 TraesCS5B01G240200 chr5A 90.289 1452 54 26 620 2048 457540434 457539047 0.000000e+00 1820
11 TraesCS5B01G240200 chr5A 86.690 571 36 12 1 562 457540971 457540432 5.600000e-167 597
12 TraesCS5B01G240200 chr5A 93.393 333 21 1 2372 2703 399772065 399772397 2.720000e-135 492
13 TraesCS5B01G240200 chr5A 93.030 330 22 1 2706 3035 457538751 457538423 5.880000e-132 481
14 TraesCS5B01G240200 chr5A 79.966 594 83 29 1095 1669 597941094 597941670 3.640000e-109 405
15 TraesCS5B01G240200 chr5A 80.620 387 58 12 1290 1663 457881064 457881446 1.780000e-72 283
16 TraesCS5B01G240200 chr5A 84.158 202 19 8 2189 2380 457538957 457538759 1.860000e-42 183
17 TraesCS5B01G240200 chr3D 94.753 324 16 1 2375 2697 7428779 7429102 1.260000e-138 503
18 TraesCS5B01G240200 chr2B 93.958 331 19 1 2375 2704 484925587 484925917 1.620000e-137 499
19 TraesCS5B01G240200 chr7B 93.472 337 19 3 2370 2704 482636007 482636342 5.840000e-137 497
20 TraesCS5B01G240200 chr6D 93.656 331 20 1 2372 2701 309103613 309103943 7.560000e-136 494
21 TraesCS5B01G240200 chr2D 93.884 327 20 0 2375 2701 200295258 200295584 7.560000e-136 494
22 TraesCS5B01G240200 chr3A 92.647 340 22 3 2369 2707 666487901 666488238 1.260000e-133 486
23 TraesCS5B01G240200 chr2A 87.755 196 18 2 1797 1986 756837438 756837633 1.100000e-54 224


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 TraesCS5B01G240200 chr5B 420385141 420388175 3034 False 5605.000000 5605 100.000000 1 3035 1 chr5B.!!$F2 3034
1 TraesCS5B01G240200 chr5B 586916279 586916874 595 False 370.000000 370 78.654000 1095 1679 1 chr5B.!!$F3 584
2 TraesCS5B01G240200 chr5D 355675880 355678525 2645 False 1155.333333 2833 88.410333 1 2985 3 chr5D.!!$F3 2984
3 TraesCS5B01G240200 chr5D 479194578 479195173 595 False 387.000000 387 79.180000 1095 1679 1 chr5D.!!$F2 584
4 TraesCS5B01G240200 chr5A 457538423 457540971 2548 True 770.250000 1820 88.541750 1 3035 4 chr5A.!!$R1 3034
5 TraesCS5B01G240200 chr5A 597941094 597941670 576 False 405.000000 405 79.966000 1095 1669 1 chr5A.!!$F3 574

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
483 515 0.099436 GCATTCAATGGTCGCTGTCC 59.901 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2265 0.385098 CCCGAACGAAAGGCGAAAAC 60.385 55.0 0.0 0.0 44.57 2.43 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
41 46 4.199310 CTCACAGGAGGAACAAAACAAGA 58.801 43.478 0.00 0.00 37.51 3.02
43 48 3.694072 CACAGGAGGAACAAAACAAGACA 59.306 43.478 0.00 0.00 0.00 3.41
93 98 1.817740 CGTGAACACCACCCCATCTTT 60.818 52.381 0.00 0.00 42.76 2.52
95 100 2.698274 GTGAACACCACCCCATCTTTTT 59.302 45.455 0.00 0.00 39.86 1.94
181 211 4.351054 GGGTCCAGGGTGTGCAGG 62.351 72.222 0.00 0.00 0.00 4.85
184 214 3.259314 TCCAGGGTGTGCAGGCAT 61.259 61.111 0.00 0.00 0.00 4.40
230 260 3.706373 CCTGTGCGCCAGTAGGGT 61.706 66.667 19.93 0.00 39.74 4.34
301 332 4.459089 GGAGCGACTGAGGCCACC 62.459 72.222 5.01 0.00 0.00 4.61
302 333 4.459089 GAGCGACTGAGGCCACCC 62.459 72.222 5.01 0.00 0.00 4.61
404 436 0.905337 AGCCAGACCAGACCACCTAC 60.905 60.000 0.00 0.00 0.00 3.18
406 438 0.898789 CCAGACCAGACCACCTACGT 60.899 60.000 0.00 0.00 0.00 3.57
419 451 1.372997 CTACGTGAGGCAGCGTTGT 60.373 57.895 0.00 0.00 41.77 3.32
475 507 4.178214 CGCGCCGCATTCAATGGT 62.178 61.111 10.75 0.00 0.00 3.55
483 515 0.099436 GCATTCAATGGTCGCTGTCC 59.901 55.000 0.00 0.00 0.00 4.02
501 533 2.393557 CCATTGTCGCGCTAATGGT 58.606 52.632 30.04 4.22 45.23 3.55
510 542 0.744414 GCGCTAATGGTCTTGCAGGA 60.744 55.000 0.00 0.00 0.00 3.86
513 545 1.748591 GCTAATGGTCTTGCAGGAGGG 60.749 57.143 0.00 0.00 0.00 4.30
514 546 1.839994 CTAATGGTCTTGCAGGAGGGA 59.160 52.381 0.00 0.00 0.00 4.20
515 547 0.622665 AATGGTCTTGCAGGAGGGAG 59.377 55.000 0.00 0.00 0.00 4.30
516 548 0.548682 ATGGTCTTGCAGGAGGGAGT 60.549 55.000 0.00 0.00 0.00 3.85
586 633 4.134563 TGAAACCTGCTGTCTTTTCTACC 58.865 43.478 9.46 0.00 0.00 3.18
601 648 9.240159 GTCTTTTCTACCGATTCTCTATTTCTC 57.760 37.037 0.00 0.00 0.00 2.87
602 649 9.191479 TCTTTTCTACCGATTCTCTATTTCTCT 57.809 33.333 0.00 0.00 0.00 3.10
617 664 9.364989 CTCTATTTCTCTTTGTGAAAGGAGTAG 57.635 37.037 0.00 0.00 39.01 2.57
619 666 7.736447 ATTTCTCTTTGTGAAAGGAGTAGTG 57.264 36.000 0.00 0.00 39.01 2.74
645 692 1.298859 GACGAGAGGTTTGCGCCATT 61.299 55.000 4.18 0.00 0.00 3.16
646 693 1.135315 CGAGAGGTTTGCGCCATTG 59.865 57.895 4.18 0.00 0.00 2.82
665 712 1.180029 GCAGGCAGGAATTCATGTGT 58.820 50.000 20.25 6.28 0.00 3.72
706 753 1.291184 TGCGAGTGTGAATGAAGCGG 61.291 55.000 0.00 0.00 0.00 5.52
707 754 1.421485 CGAGTGTGAATGAAGCGGC 59.579 57.895 0.00 0.00 0.00 6.53
708 755 1.796796 GAGTGTGAATGAAGCGGCC 59.203 57.895 0.00 0.00 0.00 6.13
709 756 0.955428 GAGTGTGAATGAAGCGGCCA 60.955 55.000 2.24 0.00 0.00 5.36
710 757 0.537143 AGTGTGAATGAAGCGGCCAA 60.537 50.000 2.24 0.00 0.00 4.52
711 758 0.109597 GTGTGAATGAAGCGGCCAAG 60.110 55.000 2.24 0.00 0.00 3.61
712 759 1.153958 GTGAATGAAGCGGCCAAGC 60.154 57.895 2.24 0.00 37.41 4.01
713 760 2.100991 GAATGAAGCGGCCAAGCG 59.899 61.111 2.24 0.00 43.00 4.68
775 828 2.125106 CGGCGGGAAAGGGAGAAG 60.125 66.667 0.00 0.00 0.00 2.85
905 958 2.561885 CTCAAGCAGCAGCAGCAC 59.438 61.111 12.92 0.00 45.49 4.40
937 990 2.194212 ACACTCACGCCTCACTCGT 61.194 57.895 0.00 0.00 41.28 4.18
990 1045 4.787280 CTCCCCCGGAGCACCTCT 62.787 72.222 0.73 0.00 43.29 3.69
995 1050 4.767255 CCGGAGCACCTCTGCCAC 62.767 72.222 0.00 0.00 45.53 5.01
996 1051 3.699894 CGGAGCACCTCTGCCACT 61.700 66.667 0.00 0.00 45.53 4.00
1276 1358 3.949885 TACCTCCCGAGCTTCCGCA 62.950 63.158 0.00 0.00 39.10 5.69
1308 1390 0.834687 TGCCCGTCCTGGTCTACTTT 60.835 55.000 0.00 0.00 35.15 2.66
1527 1618 2.203728 TGGCTGTCCCAGTACGGT 60.204 61.111 3.61 0.00 39.18 4.83
1980 2080 2.434884 ACCAAGATGAGCACGCCG 60.435 61.111 0.00 0.00 0.00 6.46
2027 2127 4.520846 CGCCTTCATCAACCGCGC 62.521 66.667 0.00 0.00 36.02 6.86
2037 2137 3.367743 AACCGCGCCGACTAGTGA 61.368 61.111 0.00 0.00 0.00 3.41
2044 2144 2.799371 CCGACTAGTGACTCGCCC 59.201 66.667 0.00 0.00 0.00 6.13
2048 2148 3.812019 CTAGTGACTCGCCCGCGT 61.812 66.667 4.92 0.00 40.74 6.01
2049 2149 4.111016 TAGTGACTCGCCCGCGTG 62.111 66.667 4.92 9.29 40.74 5.34
2081 2181 3.053291 CGCCCGGCAGCAAGTAAA 61.053 61.111 10.77 0.00 0.00 2.01
2082 2182 2.566529 GCCCGGCAGCAAGTAAAC 59.433 61.111 3.91 0.00 0.00 2.01
2083 2183 2.867472 CCCGGCAGCAAGTAAACG 59.133 61.111 0.00 0.00 0.00 3.60
2084 2184 2.175811 CCGGCAGCAAGTAAACGC 59.824 61.111 0.00 0.00 0.00 4.84
2085 2185 2.612567 CCGGCAGCAAGTAAACGCA 61.613 57.895 0.00 0.00 0.00 5.24
2086 2186 1.154413 CGGCAGCAAGTAAACGCAG 60.154 57.895 0.00 0.00 0.00 5.18
2094 2194 3.350612 GTAAACGCAGCACCGCCA 61.351 61.111 0.00 0.00 0.00 5.69
2117 2217 2.887783 CCCGACATGAGTACTCTGCTAT 59.112 50.000 23.01 6.05 0.00 2.97
2122 2222 5.278022 CGACATGAGTACTCTGCTATGCTAA 60.278 44.000 23.01 0.00 0.00 3.09
2160 2265 1.135333 GTAGCGAGGAGGAAGGTCTTG 59.865 57.143 0.00 0.00 0.00 3.02
2167 2272 1.535896 GGAGGAAGGTCTTGTTTTCGC 59.464 52.381 0.00 0.00 0.00 4.70
2168 2273 1.535896 GAGGAAGGTCTTGTTTTCGCC 59.464 52.381 0.00 0.00 0.00 5.54
2169 2274 1.143073 AGGAAGGTCTTGTTTTCGCCT 59.857 47.619 0.00 0.00 0.00 5.52
2170 2275 1.954382 GGAAGGTCTTGTTTTCGCCTT 59.046 47.619 0.00 0.00 41.69 4.35
2171 2276 2.361119 GGAAGGTCTTGTTTTCGCCTTT 59.639 45.455 0.00 0.00 39.39 3.11
2172 2277 3.550233 GGAAGGTCTTGTTTTCGCCTTTC 60.550 47.826 0.00 0.00 39.39 2.62
2173 2278 1.602377 AGGTCTTGTTTTCGCCTTTCG 59.398 47.619 0.00 0.00 40.15 3.46
2174 2279 1.332686 GGTCTTGTTTTCGCCTTTCGT 59.667 47.619 0.00 0.00 39.67 3.85
2175 2280 2.223409 GGTCTTGTTTTCGCCTTTCGTT 60.223 45.455 0.00 0.00 39.67 3.85
2176 2281 3.033873 GTCTTGTTTTCGCCTTTCGTTC 58.966 45.455 0.00 0.00 39.67 3.95
2177 2282 2.034076 CTTGTTTTCGCCTTTCGTTCG 58.966 47.619 0.00 0.00 39.67 3.95
2178 2283 0.305313 TGTTTTCGCCTTTCGTTCGG 59.695 50.000 0.00 0.00 39.67 4.30
2195 2300 1.341852 TCGGGTCGATTTCTTGTGTCA 59.658 47.619 0.00 0.00 0.00 3.58
2340 2462 2.993899 CAGTAGTAGTTGGCCGTTTCTG 59.006 50.000 0.00 0.00 0.00 3.02
2380 2505 1.163554 CCGAGCCGTATACTACTCCC 58.836 60.000 13.42 0.00 0.00 4.30
2381 2506 1.271271 CCGAGCCGTATACTACTCCCT 60.271 57.143 13.42 0.00 0.00 4.20
2382 2507 2.075338 CGAGCCGTATACTACTCCCTC 58.925 57.143 13.42 4.71 0.00 4.30
2383 2508 2.435422 GAGCCGTATACTACTCCCTCC 58.565 57.143 9.69 0.00 0.00 4.30
2386 2511 3.117208 AGCCGTATACTACTCCCTCCTTT 60.117 47.826 0.56 0.00 0.00 3.11
2387 2512 3.255395 GCCGTATACTACTCCCTCCTTTC 59.745 52.174 0.56 0.00 0.00 2.62
2388 2513 3.825585 CCGTATACTACTCCCTCCTTTCC 59.174 52.174 0.56 0.00 0.00 3.13
2389 2514 3.501445 CGTATACTACTCCCTCCTTTCCG 59.499 52.174 0.56 0.00 0.00 4.30
2390 2515 2.449137 TACTACTCCCTCCTTTCCGG 57.551 55.000 0.00 0.00 0.00 5.14
2391 2516 0.412640 ACTACTCCCTCCTTTCCGGT 59.587 55.000 0.00 0.00 0.00 5.28
2392 2517 1.203275 ACTACTCCCTCCTTTCCGGTT 60.203 52.381 0.00 0.00 0.00 4.44
2393 2518 1.907255 CTACTCCCTCCTTTCCGGTTT 59.093 52.381 0.00 0.00 0.00 3.27
2394 2519 2.034436 ACTCCCTCCTTTCCGGTTTA 57.966 50.000 0.00 0.00 0.00 2.01
2395 2520 1.627329 ACTCCCTCCTTTCCGGTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
2396 2521 1.626825 CTCCCTCCTTTCCGGTTTACA 59.373 52.381 0.00 0.00 0.00 2.41
2397 2522 1.626825 TCCCTCCTTTCCGGTTTACAG 59.373 52.381 0.00 0.00 0.00 2.74
2398 2523 1.339727 CCCTCCTTTCCGGTTTACAGG 60.340 57.143 0.00 2.82 0.00 4.00
2399 2524 1.350019 CCTCCTTTCCGGTTTACAGGT 59.650 52.381 0.00 0.00 32.79 4.00
2400 2525 2.614734 CCTCCTTTCCGGTTTACAGGTC 60.615 54.545 0.00 0.00 32.79 3.85
2401 2526 2.302157 CTCCTTTCCGGTTTACAGGTCT 59.698 50.000 0.00 0.00 32.79 3.85
2402 2527 2.707257 TCCTTTCCGGTTTACAGGTCTT 59.293 45.455 0.00 0.00 32.79 3.01
2403 2528 3.903090 TCCTTTCCGGTTTACAGGTCTTA 59.097 43.478 0.00 0.00 32.79 2.10
2404 2529 4.533311 TCCTTTCCGGTTTACAGGTCTTAT 59.467 41.667 0.00 0.00 32.79 1.73
2405 2530 4.874396 CCTTTCCGGTTTACAGGTCTTATC 59.126 45.833 0.00 0.00 32.79 1.75
2406 2531 5.338137 CCTTTCCGGTTTACAGGTCTTATCT 60.338 44.000 0.00 0.00 32.79 1.98
2407 2532 4.996788 TCCGGTTTACAGGTCTTATCTC 57.003 45.455 0.00 0.00 32.79 2.75
2408 2533 4.346730 TCCGGTTTACAGGTCTTATCTCA 58.653 43.478 0.00 0.00 32.79 3.27
2409 2534 4.773674 TCCGGTTTACAGGTCTTATCTCAA 59.226 41.667 0.00 0.00 32.79 3.02
2410 2535 5.246656 TCCGGTTTACAGGTCTTATCTCAAA 59.753 40.000 0.00 0.00 32.79 2.69
2411 2536 5.935789 CCGGTTTACAGGTCTTATCTCAAAA 59.064 40.000 0.00 0.00 0.00 2.44
2412 2537 6.598064 CCGGTTTACAGGTCTTATCTCAAAAT 59.402 38.462 0.00 0.00 0.00 1.82
2413 2538 7.120726 CCGGTTTACAGGTCTTATCTCAAAATT 59.879 37.037 0.00 0.00 0.00 1.82
2414 2539 8.512138 CGGTTTACAGGTCTTATCTCAAAATTT 58.488 33.333 0.00 0.00 0.00 1.82
2453 2578 9.995003 TTTATAATGCTCAATTTGGTTGTTTCT 57.005 25.926 0.00 0.00 38.95 2.52
2454 2579 9.638239 TTATAATGCTCAATTTGGTTGTTTCTC 57.362 29.630 0.00 0.00 38.95 2.87
2455 2580 4.998671 TGCTCAATTTGGTTGTTTCTCA 57.001 36.364 0.00 0.00 38.95 3.27
2456 2581 5.534207 TGCTCAATTTGGTTGTTTCTCAT 57.466 34.783 0.00 0.00 38.95 2.90
2457 2582 5.531634 TGCTCAATTTGGTTGTTTCTCATC 58.468 37.500 0.00 0.00 38.95 2.92
2458 2583 5.068855 TGCTCAATTTGGTTGTTTCTCATCA 59.931 36.000 0.00 0.00 38.95 3.07
2459 2584 5.403466 GCTCAATTTGGTTGTTTCTCATCAC 59.597 40.000 0.00 0.00 38.95 3.06
2460 2585 6.462552 TCAATTTGGTTGTTTCTCATCACA 57.537 33.333 0.00 0.00 38.95 3.58
2461 2586 7.053316 TCAATTTGGTTGTTTCTCATCACAT 57.947 32.000 0.00 0.00 38.95 3.21
2462 2587 6.924612 TCAATTTGGTTGTTTCTCATCACATG 59.075 34.615 0.00 0.00 38.95 3.21
2463 2588 5.850557 TTTGGTTGTTTCTCATCACATGT 57.149 34.783 0.00 0.00 0.00 3.21
2464 2589 5.850557 TTGGTTGTTTCTCATCACATGTT 57.149 34.783 0.00 0.00 0.00 2.71
2465 2590 5.437289 TGGTTGTTTCTCATCACATGTTC 57.563 39.130 0.00 0.00 0.00 3.18
2466 2591 4.886489 TGGTTGTTTCTCATCACATGTTCA 59.114 37.500 0.00 0.00 0.00 3.18
2467 2592 5.359292 TGGTTGTTTCTCATCACATGTTCAA 59.641 36.000 0.00 0.00 0.00 2.69
2468 2593 6.127507 TGGTTGTTTCTCATCACATGTTCAAA 60.128 34.615 0.00 0.00 0.00 2.69
2469 2594 6.925165 GGTTGTTTCTCATCACATGTTCAAAT 59.075 34.615 0.00 0.00 0.00 2.32
2470 2595 7.439056 GGTTGTTTCTCATCACATGTTCAAATT 59.561 33.333 0.00 0.00 0.00 1.82
2471 2596 8.819974 GTTGTTTCTCATCACATGTTCAAATTT 58.180 29.630 0.00 0.00 0.00 1.82
2472 2597 8.945481 TGTTTCTCATCACATGTTCAAATTTT 57.055 26.923 0.00 0.00 0.00 1.82
2476 2601 9.695526 TTCTCATCACATGTTCAAATTTTAAGG 57.304 29.630 0.00 0.00 0.00 2.69
2477 2602 8.859090 TCTCATCACATGTTCAAATTTTAAGGT 58.141 29.630 0.00 0.00 0.00 3.50
2478 2603 8.815141 TCATCACATGTTCAAATTTTAAGGTG 57.185 30.769 0.00 0.00 0.00 4.00
2479 2604 7.384660 TCATCACATGTTCAAATTTTAAGGTGC 59.615 33.333 0.00 0.00 0.00 5.01
2480 2605 6.577103 TCACATGTTCAAATTTTAAGGTGCA 58.423 32.000 0.00 0.00 0.00 4.57
2481 2606 7.215789 TCACATGTTCAAATTTTAAGGTGCAT 58.784 30.769 0.00 0.00 0.00 3.96
2482 2607 7.714377 TCACATGTTCAAATTTTAAGGTGCATT 59.286 29.630 0.00 0.00 0.00 3.56
2483 2608 8.986847 CACATGTTCAAATTTTAAGGTGCATTA 58.013 29.630 0.00 0.00 0.00 1.90
2484 2609 9.553064 ACATGTTCAAATTTTAAGGTGCATTAA 57.447 25.926 0.00 0.00 0.00 1.40
2493 2618 8.789825 ATTTTAAGGTGCATTAAATCATTGCA 57.210 26.923 6.16 0.00 43.63 4.08
2494 2619 8.789825 TTTTAAGGTGCATTAAATCATTGCAT 57.210 26.923 4.14 0.00 46.90 3.96
2495 2620 7.773864 TTAAGGTGCATTAAATCATTGCATG 57.226 32.000 4.14 0.00 46.90 4.06
2496 2621 4.124238 AGGTGCATTAAATCATTGCATGC 58.876 39.130 11.82 11.82 46.90 4.06
2497 2622 3.872182 GGTGCATTAAATCATTGCATGCA 59.128 39.130 18.46 18.46 46.90 3.96
2498 2623 4.333095 GGTGCATTAAATCATTGCATGCAA 59.667 37.500 33.57 33.57 46.90 4.08
2499 2624 5.498159 GTGCATTAAATCATTGCATGCAAG 58.502 37.500 34.15 25.40 46.90 4.01
2500 2625 5.064198 GTGCATTAAATCATTGCATGCAAGT 59.936 36.000 34.15 21.32 46.90 3.16
2501 2626 6.256104 GTGCATTAAATCATTGCATGCAAGTA 59.744 34.615 34.15 25.25 46.90 2.24
2502 2627 6.987404 TGCATTAAATCATTGCATGCAAGTAT 59.013 30.769 34.15 26.18 40.64 2.12
2503 2628 7.496263 TGCATTAAATCATTGCATGCAAGTATT 59.504 29.630 34.15 29.40 40.64 1.89
2504 2629 8.980610 GCATTAAATCATTGCATGCAAGTATTA 58.019 29.630 34.15 25.22 39.47 0.98
2509 2634 9.656040 AAATCATTGCATGCAAGTATTAAAAGA 57.344 25.926 34.15 20.12 39.47 2.52
2510 2635 9.656040 AATCATTGCATGCAAGTATTAAAAGAA 57.344 25.926 34.15 10.64 39.47 2.52
2511 2636 9.656040 ATCATTGCATGCAAGTATTAAAAGAAA 57.344 25.926 34.15 10.19 39.47 2.52
2512 2637 9.486497 TCATTGCATGCAAGTATTAAAAGAAAA 57.514 25.926 34.15 9.52 39.47 2.29
2516 2641 9.486497 TGCATGCAAGTATTAAAAGAAAATTGA 57.514 25.926 20.30 0.00 0.00 2.57
2544 2669 4.618338 CATGTAATTTATGCGTGCATGC 57.382 40.909 24.20 24.20 37.82 4.06
2580 2705 8.761575 ATGCATTGGTAAACATACTTTTTGAG 57.238 30.769 0.00 0.00 0.00 3.02
2581 2706 7.946207 TGCATTGGTAAACATACTTTTTGAGA 58.054 30.769 0.00 0.00 0.00 3.27
2582 2707 8.417106 TGCATTGGTAAACATACTTTTTGAGAA 58.583 29.630 0.00 0.00 0.00 2.87
2583 2708 9.255304 GCATTGGTAAACATACTTTTTGAGAAA 57.745 29.630 0.00 0.00 0.00 2.52
2605 2730 9.822185 AGAAAAATAAGATCATTAATTGGGTGC 57.178 29.630 0.00 0.00 0.00 5.01
2606 2731 9.822185 GAAAAATAAGATCATTAATTGGGTGCT 57.178 29.630 0.00 0.00 0.00 4.40
2612 2737 7.716799 AGATCATTAATTGGGTGCTTTTACA 57.283 32.000 0.00 0.00 0.00 2.41
2613 2738 8.133024 AGATCATTAATTGGGTGCTTTTACAA 57.867 30.769 0.00 0.00 0.00 2.41
2614 2739 8.592809 AGATCATTAATTGGGTGCTTTTACAAA 58.407 29.630 0.00 0.00 0.00 2.83
2615 2740 7.954788 TCATTAATTGGGTGCTTTTACAAAC 57.045 32.000 0.00 0.00 0.00 2.93
2616 2741 7.731054 TCATTAATTGGGTGCTTTTACAAACT 58.269 30.769 0.00 0.00 0.00 2.66
2617 2742 8.861086 TCATTAATTGGGTGCTTTTACAAACTA 58.139 29.630 0.00 0.00 0.00 2.24
2618 2743 8.921670 CATTAATTGGGTGCTTTTACAAACTAC 58.078 33.333 0.00 0.00 0.00 2.73
2619 2744 6.472686 AATTGGGTGCTTTTACAAACTACA 57.527 33.333 0.00 0.00 0.00 2.74
2620 2745 5.916661 TTGGGTGCTTTTACAAACTACAA 57.083 34.783 0.00 0.00 0.00 2.41
2621 2746 5.916661 TGGGTGCTTTTACAAACTACAAA 57.083 34.783 0.00 0.00 0.00 2.83
2622 2747 6.282199 TGGGTGCTTTTACAAACTACAAAA 57.718 33.333 0.00 0.00 0.00 2.44
2623 2748 6.698380 TGGGTGCTTTTACAAACTACAAAAA 58.302 32.000 0.00 0.00 0.00 1.94
2624 2749 6.814146 TGGGTGCTTTTACAAACTACAAAAAG 59.186 34.615 0.00 0.00 40.33 2.27
2625 2750 6.814644 GGGTGCTTTTACAAACTACAAAAAGT 59.185 34.615 7.87 0.00 39.81 2.66
2626 2751 7.975058 GGGTGCTTTTACAAACTACAAAAAGTA 59.025 33.333 7.87 1.77 39.81 2.24
2627 2752 9.524106 GGTGCTTTTACAAACTACAAAAAGTAT 57.476 29.630 7.87 0.00 39.81 2.12
2634 2759 7.648039 ACAAACTACAAAAAGTATTCCACCA 57.352 32.000 0.00 0.00 30.93 4.17
2635 2760 7.485810 ACAAACTACAAAAAGTATTCCACCAC 58.514 34.615 0.00 0.00 30.93 4.16
2636 2761 7.340999 ACAAACTACAAAAAGTATTCCACCACT 59.659 33.333 0.00 0.00 30.93 4.00
2637 2762 7.506328 AACTACAAAAAGTATTCCACCACTC 57.494 36.000 0.00 0.00 30.93 3.51
2638 2763 6.597562 ACTACAAAAAGTATTCCACCACTCA 58.402 36.000 0.00 0.00 30.93 3.41
2639 2764 7.231467 ACTACAAAAAGTATTCCACCACTCAT 58.769 34.615 0.00 0.00 30.93 2.90
2640 2765 6.575162 ACAAAAAGTATTCCACCACTCATC 57.425 37.500 0.00 0.00 0.00 2.92
2641 2766 6.068010 ACAAAAAGTATTCCACCACTCATCA 58.932 36.000 0.00 0.00 0.00 3.07
2642 2767 6.721208 ACAAAAAGTATTCCACCACTCATCAT 59.279 34.615 0.00 0.00 0.00 2.45
2643 2768 7.094205 ACAAAAAGTATTCCACCACTCATCATC 60.094 37.037 0.00 0.00 0.00 2.92
2644 2769 5.965033 AAGTATTCCACCACTCATCATCT 57.035 39.130 0.00 0.00 0.00 2.90
2645 2770 7.437713 AAAGTATTCCACCACTCATCATCTA 57.562 36.000 0.00 0.00 0.00 1.98
2646 2771 7.623999 AAGTATTCCACCACTCATCATCTAT 57.376 36.000 0.00 0.00 0.00 1.98
2647 2772 7.238486 AGTATTCCACCACTCATCATCTATC 57.762 40.000 0.00 0.00 0.00 2.08
2648 2773 7.015680 AGTATTCCACCACTCATCATCTATCT 58.984 38.462 0.00 0.00 0.00 1.98
2649 2774 6.760440 ATTCCACCACTCATCATCTATCTT 57.240 37.500 0.00 0.00 0.00 2.40
2650 2775 5.541953 TCCACCACTCATCATCTATCTTG 57.458 43.478 0.00 0.00 0.00 3.02
2651 2776 4.346127 TCCACCACTCATCATCTATCTTGG 59.654 45.833 0.00 0.00 0.00 3.61
2652 2777 4.102210 CCACCACTCATCATCTATCTTGGT 59.898 45.833 0.00 0.00 36.53 3.67
2653 2778 5.397221 CCACCACTCATCATCTATCTTGGTT 60.397 44.000 0.00 0.00 33.77 3.67
2654 2779 5.526479 CACCACTCATCATCTATCTTGGTTG 59.474 44.000 0.00 0.00 33.77 3.77
2655 2780 5.061853 CCACTCATCATCTATCTTGGTTGG 58.938 45.833 0.00 0.00 0.00 3.77
2656 2781 5.397221 CCACTCATCATCTATCTTGGTTGGT 60.397 44.000 0.00 0.00 0.00 3.67
2657 2782 5.526479 CACTCATCATCTATCTTGGTTGGTG 59.474 44.000 0.00 0.00 0.00 4.17
2658 2783 5.426509 ACTCATCATCTATCTTGGTTGGTGA 59.573 40.000 0.00 0.00 0.00 4.02
2659 2784 5.922053 TCATCATCTATCTTGGTTGGTGAG 58.078 41.667 0.00 0.00 0.00 3.51
2660 2785 5.662657 TCATCATCTATCTTGGTTGGTGAGA 59.337 40.000 0.00 0.00 0.00 3.27
2661 2786 6.328410 TCATCATCTATCTTGGTTGGTGAGAT 59.672 38.462 0.00 0.00 34.67 2.75
2662 2787 6.566079 TCATCTATCTTGGTTGGTGAGATT 57.434 37.500 0.00 0.00 32.68 2.40
2663 2788 6.962182 TCATCTATCTTGGTTGGTGAGATTT 58.038 36.000 0.00 0.00 32.68 2.17
2664 2789 7.405292 TCATCTATCTTGGTTGGTGAGATTTT 58.595 34.615 0.00 0.00 32.68 1.82
2665 2790 7.890127 TCATCTATCTTGGTTGGTGAGATTTTT 59.110 33.333 0.00 0.00 32.68 1.94
2666 2791 7.452880 TCTATCTTGGTTGGTGAGATTTTTG 57.547 36.000 0.00 0.00 32.68 2.44
2667 2792 7.230747 TCTATCTTGGTTGGTGAGATTTTTGA 58.769 34.615 0.00 0.00 32.68 2.69
2668 2793 6.729690 ATCTTGGTTGGTGAGATTTTTGAA 57.270 33.333 0.00 0.00 0.00 2.69
2669 2794 6.729690 TCTTGGTTGGTGAGATTTTTGAAT 57.270 33.333 0.00 0.00 0.00 2.57
2670 2795 7.123355 TCTTGGTTGGTGAGATTTTTGAATT 57.877 32.000 0.00 0.00 0.00 2.17
2671 2796 6.985645 TCTTGGTTGGTGAGATTTTTGAATTG 59.014 34.615 0.00 0.00 0.00 2.32
2672 2797 6.477053 TGGTTGGTGAGATTTTTGAATTGA 57.523 33.333 0.00 0.00 0.00 2.57
2673 2798 6.514947 TGGTTGGTGAGATTTTTGAATTGAG 58.485 36.000 0.00 0.00 0.00 3.02
2674 2799 5.406477 GGTTGGTGAGATTTTTGAATTGAGC 59.594 40.000 0.00 0.00 0.00 4.26
2675 2800 5.138125 TGGTGAGATTTTTGAATTGAGCC 57.862 39.130 0.00 0.00 0.00 4.70
2676 2801 4.834496 TGGTGAGATTTTTGAATTGAGCCT 59.166 37.500 0.00 0.00 0.00 4.58
2677 2802 5.305128 TGGTGAGATTTTTGAATTGAGCCTT 59.695 36.000 0.00 0.00 0.00 4.35
2678 2803 6.493115 TGGTGAGATTTTTGAATTGAGCCTTA 59.507 34.615 0.00 0.00 0.00 2.69
2679 2804 7.178983 TGGTGAGATTTTTGAATTGAGCCTTAT 59.821 33.333 0.00 0.00 0.00 1.73
2680 2805 8.686334 GGTGAGATTTTTGAATTGAGCCTTATA 58.314 33.333 0.00 0.00 0.00 0.98
2684 2809 9.875691 AGATTTTTGAATTGAGCCTTATAAACC 57.124 29.630 0.00 0.00 0.00 3.27
2685 2810 8.702163 ATTTTTGAATTGAGCCTTATAAACCG 57.298 30.769 0.00 0.00 0.00 4.44
2686 2811 5.828299 TTGAATTGAGCCTTATAAACCGG 57.172 39.130 0.00 0.00 0.00 5.28
2687 2812 5.105567 TGAATTGAGCCTTATAAACCGGA 57.894 39.130 9.46 0.00 0.00 5.14
2688 2813 5.502079 TGAATTGAGCCTTATAAACCGGAA 58.498 37.500 9.46 0.00 0.00 4.30
2689 2814 5.946972 TGAATTGAGCCTTATAAACCGGAAA 59.053 36.000 9.46 0.00 0.00 3.13
2690 2815 6.094881 TGAATTGAGCCTTATAAACCGGAAAG 59.905 38.462 9.46 3.38 0.00 2.62
2692 2817 3.520317 TGAGCCTTATAAACCGGAAAGGA 59.480 43.478 9.46 0.00 45.00 3.36
2693 2818 4.127907 GAGCCTTATAAACCGGAAAGGAG 58.872 47.826 9.46 0.00 45.00 3.69
2694 2819 3.118000 AGCCTTATAAACCGGAAAGGAGG 60.118 47.826 9.46 9.29 45.00 4.30
2695 2820 3.816994 CCTTATAAACCGGAAAGGAGGG 58.183 50.000 9.46 0.00 45.00 4.30
2696 2821 3.457012 CCTTATAAACCGGAAAGGAGGGA 59.543 47.826 9.46 0.00 45.00 4.20
2697 2822 4.449131 CTTATAAACCGGAAAGGAGGGAC 58.551 47.826 9.46 0.00 45.00 4.46
2699 2824 2.034436 AAACCGGAAAGGAGGGACTA 57.966 50.000 9.46 0.00 41.55 2.59
2700 2825 1.273759 AACCGGAAAGGAGGGACTAC 58.726 55.000 9.46 0.00 41.55 2.73
2720 2845 6.701145 CTACTATGGTAGTGTCACTGTCAT 57.299 41.667 16.03 18.34 40.21 3.06
2787 2912 0.393537 GCTGCTATGGTGAACTGGCT 60.394 55.000 0.00 0.00 0.00 4.75
2796 2921 1.609208 GTGAACTGGCTGTGTGGAAT 58.391 50.000 0.00 0.00 0.00 3.01
2812 2937 4.021280 TGTGGAATTGGAATGGTGTGATTG 60.021 41.667 0.00 0.00 0.00 2.67
2834 2959 4.202223 TGAGTATTATCCGAGCTGGTTTCC 60.202 45.833 0.00 0.00 39.52 3.13
2835 2960 3.967987 AGTATTATCCGAGCTGGTTTCCT 59.032 43.478 0.00 0.00 39.52 3.36
2902 3028 2.444624 CGGCGGAGAATGTGTGTCG 61.445 63.158 0.00 0.00 0.00 4.35
2981 3107 2.370445 CCGGCATTCAGGGGACTCT 61.370 63.158 0.00 0.00 40.21 3.24
2985 3111 1.680249 GGCATTCAGGGGACTCTGTTC 60.680 57.143 0.00 0.00 40.21 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.492088 TCCTGTGAGTAATCGTGTCTGG 59.508 50.000 0.00 0.00 0.00 3.86
41 46 1.252904 GGCAGTGGCATTGATGGTGT 61.253 55.000 14.75 0.00 43.71 4.16
43 48 2.048023 CGGCAGTGGCATTGATGGT 61.048 57.895 17.80 0.00 43.71 3.55
93 98 1.587933 GCGGTCACGGGGCATAAAAA 61.588 55.000 0.00 0.00 41.36 1.94
95 100 2.437002 GCGGTCACGGGGCATAAA 60.437 61.111 0.00 0.00 41.36 1.40
98 103 3.936772 AATTGCGGTCACGGGGCAT 62.937 57.895 0.00 0.00 41.36 4.40
100 105 3.810896 GAATTGCGGTCACGGGGC 61.811 66.667 0.00 0.00 41.36 5.80
198 228 4.140599 AGGAAGAGCCGCAGCGAG 62.141 66.667 18.75 7.72 46.67 5.03
230 260 4.179361 CCAAGGCAAGGCACTGAA 57.821 55.556 0.00 0.00 40.86 3.02
301 332 1.526575 GGCAATCAGTGTGGGTGTGG 61.527 60.000 0.00 0.00 0.00 4.17
302 333 1.855213 CGGCAATCAGTGTGGGTGTG 61.855 60.000 0.00 0.00 0.00 3.82
303 334 1.600636 CGGCAATCAGTGTGGGTGT 60.601 57.895 0.00 0.00 0.00 4.16
304 335 2.334946 CCGGCAATCAGTGTGGGTG 61.335 63.158 0.00 0.00 0.00 4.61
404 436 2.967076 ACACAACGCTGCCTCACG 60.967 61.111 0.00 0.00 0.00 4.35
406 438 2.591429 CCACACAACGCTGCCTCA 60.591 61.111 0.00 0.00 0.00 3.86
500 532 0.398318 ACAACTCCCTCCTGCAAGAC 59.602 55.000 0.00 0.00 34.07 3.01
501 533 0.397941 CACAACTCCCTCCTGCAAGA 59.602 55.000 0.00 0.00 34.07 3.02
510 542 2.174639 TCACCAATTCACACAACTCCCT 59.825 45.455 0.00 0.00 0.00 4.20
513 545 4.097892 AGGTTTCACCAATTCACACAACTC 59.902 41.667 0.00 0.00 41.95 3.01
514 546 4.023291 AGGTTTCACCAATTCACACAACT 58.977 39.130 0.00 0.00 41.95 3.16
515 547 4.111916 CAGGTTTCACCAATTCACACAAC 58.888 43.478 0.00 0.00 41.95 3.32
516 548 4.019858 TCAGGTTTCACCAATTCACACAA 58.980 39.130 0.00 0.00 41.95 3.33
558 605 0.819259 GACAGCAGGTTTCAGGCACA 60.819 55.000 0.00 0.00 0.00 4.57
586 633 8.386606 CCTTTCACAAAGAGAAATAGAGAATCG 58.613 37.037 0.00 0.00 39.83 3.34
601 648 7.494625 TCTTTACACACTACTCCTTTCACAAAG 59.505 37.037 0.00 0.00 38.24 2.77
602 649 7.279313 GTCTTTACACACTACTCCTTTCACAAA 59.721 37.037 0.00 0.00 0.00 2.83
617 664 3.059800 GCAAACCTCTCGTCTTTACACAC 60.060 47.826 0.00 0.00 0.00 3.82
619 666 2.155155 CGCAAACCTCTCGTCTTTACAC 59.845 50.000 0.00 0.00 0.00 2.90
645 692 1.179152 CACATGAATTCCTGCCTGCA 58.821 50.000 10.29 0.00 0.00 4.41
646 693 1.135199 CACACATGAATTCCTGCCTGC 60.135 52.381 10.29 0.00 0.00 4.85
665 712 0.167908 CGCATACTCGCCAAAAAGCA 59.832 50.000 0.00 0.00 0.00 3.91
691 738 0.537143 TTGGCCGCTTCATTCACACT 60.537 50.000 0.00 0.00 0.00 3.55
937 990 0.529773 GCGTGGAGTGTGACTGTGAA 60.530 55.000 0.00 0.00 0.00 3.18
992 1047 4.489771 GGGACGCCATGGGAGTGG 62.490 72.222 15.13 0.00 35.49 4.00
1087 1166 1.758440 AACTTGACCTGCGAGCTGGA 61.758 55.000 24.46 3.45 38.26 3.86
1527 1618 2.203788 AAGAGGCGGGACAGGTCA 60.204 61.111 1.41 0.00 0.00 4.02
1953 2053 3.055819 TGCTCATCTTGGTGAGGAAGTAC 60.056 47.826 12.19 0.00 42.52 2.73
2027 2127 2.799371 GGGCGAGTCACTAGTCGG 59.201 66.667 0.00 0.00 46.53 4.79
2064 2164 3.053291 TTTACTTGCTGCCGGGCG 61.053 61.111 15.40 10.40 34.52 6.13
2065 2165 2.566529 GTTTACTTGCTGCCGGGC 59.433 61.111 13.32 13.32 0.00 6.13
2066 2166 2.867472 CGTTTACTTGCTGCCGGG 59.133 61.111 2.18 0.00 0.00 5.73
2067 2167 2.175811 GCGTTTACTTGCTGCCGG 59.824 61.111 0.00 0.00 0.00 6.13
2068 2168 1.154413 CTGCGTTTACTTGCTGCCG 60.154 57.895 0.00 0.00 0.00 5.69
2069 2169 1.442688 GCTGCGTTTACTTGCTGCC 60.443 57.895 0.00 0.00 46.40 4.85
2070 2170 4.137145 GCTGCGTTTACTTGCTGC 57.863 55.556 0.00 0.00 46.19 5.25
2071 2171 0.385974 GGTGCTGCGTTTACTTGCTG 60.386 55.000 0.00 0.00 0.00 4.41
2072 2172 1.841663 CGGTGCTGCGTTTACTTGCT 61.842 55.000 0.00 0.00 0.00 3.91
2073 2173 1.440353 CGGTGCTGCGTTTACTTGC 60.440 57.895 0.00 0.00 0.00 4.01
2074 2174 1.440353 GCGGTGCTGCGTTTACTTG 60.440 57.895 0.00 0.00 0.00 3.16
2075 2175 2.613506 GGCGGTGCTGCGTTTACTT 61.614 57.895 0.00 0.00 35.06 2.24
2076 2176 3.047877 GGCGGTGCTGCGTTTACT 61.048 61.111 0.00 0.00 35.06 2.24
2077 2177 3.350612 TGGCGGTGCTGCGTTTAC 61.351 61.111 0.00 0.00 35.06 2.01
2078 2178 3.350612 GTGGCGGTGCTGCGTTTA 61.351 61.111 0.00 0.00 35.06 2.01
2094 2194 1.475403 CAGAGTACTCATGTCGGGGT 58.525 55.000 24.44 0.00 0.00 4.95
2135 2237 1.376543 CTTCCTCCTCGCTACGTACA 58.623 55.000 0.00 0.00 0.00 2.90
2160 2265 0.385098 CCCGAACGAAAGGCGAAAAC 60.385 55.000 0.00 0.00 44.57 2.43
2167 2272 1.392510 GAAATCGACCCGAACGAAAGG 59.607 52.381 0.00 0.00 42.80 3.11
2168 2273 2.334838 AGAAATCGACCCGAACGAAAG 58.665 47.619 0.00 0.00 42.80 2.62
2169 2274 2.443887 AGAAATCGACCCGAACGAAA 57.556 45.000 0.00 0.00 42.80 3.46
2170 2275 2.063266 CAAGAAATCGACCCGAACGAA 58.937 47.619 0.00 0.00 42.80 3.85
2171 2276 1.000060 ACAAGAAATCGACCCGAACGA 60.000 47.619 0.00 0.00 39.99 3.85
2172 2277 1.126113 CACAAGAAATCGACCCGAACG 59.874 52.381 0.00 0.00 39.99 3.95
2173 2278 2.140717 ACACAAGAAATCGACCCGAAC 58.859 47.619 0.00 0.00 39.99 3.95
2174 2279 2.224090 TGACACAAGAAATCGACCCGAA 60.224 45.455 0.00 0.00 39.99 4.30
2175 2280 1.341852 TGACACAAGAAATCGACCCGA 59.658 47.619 0.00 0.00 41.13 5.14
2176 2281 1.459592 GTGACACAAGAAATCGACCCG 59.540 52.381 0.00 0.00 0.00 5.28
2177 2282 1.804748 GGTGACACAAGAAATCGACCC 59.195 52.381 8.08 0.00 0.00 4.46
2178 2283 2.489971 TGGTGACACAAGAAATCGACC 58.510 47.619 8.08 0.00 33.40 4.79
2195 2300 2.649034 CGCACTCTACACCGTGGT 59.351 61.111 3.03 0.00 0.00 4.16
2220 2325 1.583054 GGGAGGAACCGAATTCATCG 58.417 55.000 6.22 0.00 46.88 3.84
2222 2327 1.212935 CTGGGGAGGAACCGAATTCAT 59.787 52.381 6.22 0.00 39.30 2.57
2223 2328 0.618458 CTGGGGAGGAACCGAATTCA 59.382 55.000 6.22 0.00 39.30 2.57
2225 2330 1.303282 GCTGGGGAGGAACCGAATT 59.697 57.895 0.00 0.00 40.11 2.17
2270 2375 4.063967 CGGTGGTAGAGCACGGCA 62.064 66.667 5.82 0.00 0.00 5.69
2310 2429 3.122445 GCCAACTACTACTGCGTTAACAC 59.878 47.826 6.39 0.00 0.00 3.32
2311 2430 3.319755 GCCAACTACTACTGCGTTAACA 58.680 45.455 6.39 0.00 0.00 2.41
2350 2475 1.009829 ACGGCTCGGTAGTTACTACG 58.990 55.000 15.28 11.07 37.79 3.51
2380 2505 2.302157 AGACCTGTAAACCGGAAAGGAG 59.698 50.000 9.46 0.00 45.00 3.69
2381 2506 2.332117 AGACCTGTAAACCGGAAAGGA 58.668 47.619 9.46 0.00 45.00 3.36
2383 2508 5.731591 AGATAAGACCTGTAAACCGGAAAG 58.268 41.667 9.46 0.00 0.00 2.62
2386 2511 4.346730 TGAGATAAGACCTGTAAACCGGA 58.653 43.478 9.46 0.00 0.00 5.14
2387 2512 4.730949 TGAGATAAGACCTGTAAACCGG 57.269 45.455 0.00 0.00 0.00 5.28
2388 2513 7.611213 ATTTTGAGATAAGACCTGTAAACCG 57.389 36.000 0.00 0.00 0.00 4.44
2427 2552 9.995003 AGAAACAACCAAATTGAGCATTATAAA 57.005 25.926 0.00 0.00 41.23 1.40
2428 2553 9.638239 GAGAAACAACCAAATTGAGCATTATAA 57.362 29.630 0.00 0.00 41.23 0.98
2429 2554 8.801299 TGAGAAACAACCAAATTGAGCATTATA 58.199 29.630 0.00 0.00 41.23 0.98
2430 2555 7.669427 TGAGAAACAACCAAATTGAGCATTAT 58.331 30.769 0.00 0.00 41.23 1.28
2431 2556 7.048629 TGAGAAACAACCAAATTGAGCATTA 57.951 32.000 0.00 0.00 41.23 1.90
2432 2557 5.916318 TGAGAAACAACCAAATTGAGCATT 58.084 33.333 0.00 0.00 41.23 3.56
2433 2558 5.534207 TGAGAAACAACCAAATTGAGCAT 57.466 34.783 0.00 0.00 41.23 3.79
2434 2559 4.998671 TGAGAAACAACCAAATTGAGCA 57.001 36.364 0.00 0.00 41.23 4.26
2435 2560 5.403466 GTGATGAGAAACAACCAAATTGAGC 59.597 40.000 0.00 0.00 41.23 4.26
2436 2561 6.506147 TGTGATGAGAAACAACCAAATTGAG 58.494 36.000 0.00 0.00 41.23 3.02
2437 2562 6.462552 TGTGATGAGAAACAACCAAATTGA 57.537 33.333 0.00 0.00 41.23 2.57
2438 2563 6.702723 ACATGTGATGAGAAACAACCAAATTG 59.297 34.615 0.00 0.00 44.60 2.32
2439 2564 6.819284 ACATGTGATGAGAAACAACCAAATT 58.181 32.000 0.00 0.00 0.00 1.82
2440 2565 6.409524 ACATGTGATGAGAAACAACCAAAT 57.590 33.333 0.00 0.00 0.00 2.32
2441 2566 5.850557 ACATGTGATGAGAAACAACCAAA 57.149 34.783 0.00 0.00 0.00 3.28
2442 2567 5.359292 TGAACATGTGATGAGAAACAACCAA 59.641 36.000 0.00 0.00 0.00 3.67
2443 2568 4.886489 TGAACATGTGATGAGAAACAACCA 59.114 37.500 0.00 0.00 0.00 3.67
2444 2569 5.437289 TGAACATGTGATGAGAAACAACC 57.563 39.130 0.00 0.00 0.00 3.77
2445 2570 7.935338 ATTTGAACATGTGATGAGAAACAAC 57.065 32.000 0.00 0.00 0.00 3.32
2446 2571 8.945481 AAATTTGAACATGTGATGAGAAACAA 57.055 26.923 0.00 0.00 0.00 2.83
2447 2572 8.945481 AAAATTTGAACATGTGATGAGAAACA 57.055 26.923 0.00 0.00 0.00 2.83
2450 2575 9.695526 CCTTAAAATTTGAACATGTGATGAGAA 57.304 29.630 0.00 0.00 0.00 2.87
2451 2576 8.859090 ACCTTAAAATTTGAACATGTGATGAGA 58.141 29.630 0.00 0.00 0.00 3.27
2452 2577 8.918658 CACCTTAAAATTTGAACATGTGATGAG 58.081 33.333 0.00 0.00 0.00 2.90
2453 2578 7.384660 GCACCTTAAAATTTGAACATGTGATGA 59.615 33.333 0.00 0.00 0.00 2.92
2454 2579 7.171167 TGCACCTTAAAATTTGAACATGTGATG 59.829 33.333 0.00 0.00 0.00 3.07
2455 2580 7.215789 TGCACCTTAAAATTTGAACATGTGAT 58.784 30.769 0.00 0.00 0.00 3.06
2456 2581 6.577103 TGCACCTTAAAATTTGAACATGTGA 58.423 32.000 0.00 0.00 0.00 3.58
2457 2582 6.841443 TGCACCTTAAAATTTGAACATGTG 57.159 33.333 0.00 0.00 0.00 3.21
2458 2583 9.553064 TTAATGCACCTTAAAATTTGAACATGT 57.447 25.926 0.00 0.00 0.00 3.21
2467 2592 9.228949 TGCAATGATTTAATGCACCTTAAAATT 57.771 25.926 8.82 3.95 44.52 1.82
2468 2593 8.789825 TGCAATGATTTAATGCACCTTAAAAT 57.210 26.923 8.82 2.32 44.52 1.82
2490 2615 9.486497 TCAATTTTCTTTTAATACTTGCATGCA 57.514 25.926 18.46 18.46 0.00 3.96
2522 2647 4.618338 CATGCACGCATAAATTACATGC 57.382 40.909 3.80 12.71 44.31 4.06
2523 2648 4.043073 TGCATGCACGCATAAATTACATG 58.957 39.130 18.46 0.00 36.86 3.21
2524 2649 4.304537 TGCATGCACGCATAAATTACAT 57.695 36.364 18.46 0.00 36.86 2.29
2525 2650 3.772060 TGCATGCACGCATAAATTACA 57.228 38.095 18.46 0.00 36.86 2.41
2554 2679 9.206870 CTCAAAAAGTATGTTTACCAATGCATT 57.793 29.630 5.99 5.99 0.00 3.56
2555 2680 8.584157 TCTCAAAAAGTATGTTTACCAATGCAT 58.416 29.630 0.00 0.00 0.00 3.96
2556 2681 7.946207 TCTCAAAAAGTATGTTTACCAATGCA 58.054 30.769 0.00 0.00 0.00 3.96
2557 2682 8.810652 TTCTCAAAAAGTATGTTTACCAATGC 57.189 30.769 0.00 0.00 0.00 3.56
2579 2704 9.822185 GCACCCAATTAATGATCTTATTTTTCT 57.178 29.630 0.00 0.00 0.00 2.52
2580 2705 9.822185 AGCACCCAATTAATGATCTTATTTTTC 57.178 29.630 0.00 0.00 0.00 2.29
2586 2711 9.249053 TGTAAAAGCACCCAATTAATGATCTTA 57.751 29.630 0.00 0.00 0.00 2.10
2587 2712 8.133024 TGTAAAAGCACCCAATTAATGATCTT 57.867 30.769 0.00 0.00 0.00 2.40
2588 2713 7.716799 TGTAAAAGCACCCAATTAATGATCT 57.283 32.000 0.00 0.00 0.00 2.75
2589 2714 8.655970 GTTTGTAAAAGCACCCAATTAATGATC 58.344 33.333 0.00 0.00 0.00 2.92
2590 2715 8.374743 AGTTTGTAAAAGCACCCAATTAATGAT 58.625 29.630 0.00 0.00 0.00 2.45
2591 2716 7.731054 AGTTTGTAAAAGCACCCAATTAATGA 58.269 30.769 0.00 0.00 0.00 2.57
2592 2717 7.961325 AGTTTGTAAAAGCACCCAATTAATG 57.039 32.000 0.00 0.00 0.00 1.90
2593 2718 8.643324 TGTAGTTTGTAAAAGCACCCAATTAAT 58.357 29.630 0.00 0.00 0.00 1.40
2594 2719 8.008513 TGTAGTTTGTAAAAGCACCCAATTAA 57.991 30.769 0.00 0.00 0.00 1.40
2595 2720 7.584122 TGTAGTTTGTAAAAGCACCCAATTA 57.416 32.000 0.00 0.00 0.00 1.40
2596 2721 6.472686 TGTAGTTTGTAAAAGCACCCAATT 57.527 33.333 0.00 0.00 0.00 2.32
2597 2722 6.472686 TTGTAGTTTGTAAAAGCACCCAAT 57.527 33.333 0.00 0.00 0.00 3.16
2598 2723 5.916661 TTGTAGTTTGTAAAAGCACCCAA 57.083 34.783 0.00 0.00 0.00 4.12
2599 2724 5.916661 TTTGTAGTTTGTAAAAGCACCCA 57.083 34.783 0.00 0.00 0.00 4.51
2600 2725 6.814644 ACTTTTTGTAGTTTGTAAAAGCACCC 59.185 34.615 0.00 0.00 39.83 4.61
2601 2726 7.821595 ACTTTTTGTAGTTTGTAAAAGCACC 57.178 32.000 0.00 0.00 39.83 5.01
2608 2733 9.186837 TGGTGGAATACTTTTTGTAGTTTGTAA 57.813 29.630 0.00 0.00 34.24 2.41
2609 2734 8.623030 GTGGTGGAATACTTTTTGTAGTTTGTA 58.377 33.333 0.00 0.00 34.24 2.41
2610 2735 7.340999 AGTGGTGGAATACTTTTTGTAGTTTGT 59.659 33.333 0.00 0.00 34.24 2.83
2611 2736 7.712797 AGTGGTGGAATACTTTTTGTAGTTTG 58.287 34.615 0.00 0.00 34.24 2.93
2612 2737 7.558444 TGAGTGGTGGAATACTTTTTGTAGTTT 59.442 33.333 0.00 0.00 34.24 2.66
2613 2738 7.057894 TGAGTGGTGGAATACTTTTTGTAGTT 58.942 34.615 0.00 0.00 34.24 2.24
2614 2739 6.597562 TGAGTGGTGGAATACTTTTTGTAGT 58.402 36.000 0.00 0.00 34.24 2.73
2615 2740 7.390440 TGATGAGTGGTGGAATACTTTTTGTAG 59.610 37.037 0.00 0.00 34.24 2.74
2616 2741 7.227873 TGATGAGTGGTGGAATACTTTTTGTA 58.772 34.615 0.00 0.00 35.37 2.41
2617 2742 6.068010 TGATGAGTGGTGGAATACTTTTTGT 58.932 36.000 0.00 0.00 0.00 2.83
2618 2743 6.573664 TGATGAGTGGTGGAATACTTTTTG 57.426 37.500 0.00 0.00 0.00 2.44
2619 2744 7.177878 AGATGATGAGTGGTGGAATACTTTTT 58.822 34.615 0.00 0.00 0.00 1.94
2620 2745 6.725364 AGATGATGAGTGGTGGAATACTTTT 58.275 36.000 0.00 0.00 0.00 2.27
2621 2746 6.319048 AGATGATGAGTGGTGGAATACTTT 57.681 37.500 0.00 0.00 0.00 2.66
2622 2747 5.965033 AGATGATGAGTGGTGGAATACTT 57.035 39.130 0.00 0.00 0.00 2.24
2623 2748 7.015680 AGATAGATGATGAGTGGTGGAATACT 58.984 38.462 0.00 0.00 0.00 2.12
2624 2749 7.238486 AGATAGATGATGAGTGGTGGAATAC 57.762 40.000 0.00 0.00 0.00 1.89
2625 2750 7.256439 CCAAGATAGATGATGAGTGGTGGAATA 60.256 40.741 0.00 0.00 0.00 1.75
2626 2751 6.465464 CCAAGATAGATGATGAGTGGTGGAAT 60.465 42.308 0.00 0.00 0.00 3.01
2627 2752 5.163269 CCAAGATAGATGATGAGTGGTGGAA 60.163 44.000 0.00 0.00 0.00 3.53
2628 2753 4.346127 CCAAGATAGATGATGAGTGGTGGA 59.654 45.833 0.00 0.00 0.00 4.02
2629 2754 4.102210 ACCAAGATAGATGATGAGTGGTGG 59.898 45.833 0.00 0.00 36.77 4.61
2630 2755 5.287674 ACCAAGATAGATGATGAGTGGTG 57.712 43.478 0.00 0.00 36.77 4.17
2631 2756 5.397221 CCAACCAAGATAGATGATGAGTGGT 60.397 44.000 0.00 0.00 39.79 4.16
2632 2757 5.061853 CCAACCAAGATAGATGATGAGTGG 58.938 45.833 0.00 0.00 0.00 4.00
2633 2758 5.526479 CACCAACCAAGATAGATGATGAGTG 59.474 44.000 0.00 0.00 0.00 3.51
2634 2759 5.426509 TCACCAACCAAGATAGATGATGAGT 59.573 40.000 0.00 0.00 0.00 3.41
2635 2760 5.922053 TCACCAACCAAGATAGATGATGAG 58.078 41.667 0.00 0.00 0.00 2.90
2636 2761 5.662657 TCTCACCAACCAAGATAGATGATGA 59.337 40.000 0.00 0.00 0.00 2.92
2637 2762 5.922053 TCTCACCAACCAAGATAGATGATG 58.078 41.667 0.00 0.00 0.00 3.07
2638 2763 6.760440 ATCTCACCAACCAAGATAGATGAT 57.240 37.500 0.00 0.00 0.00 2.45
2639 2764 6.566079 AATCTCACCAACCAAGATAGATGA 57.434 37.500 0.00 0.00 0.00 2.92
2640 2765 7.636150 AAAATCTCACCAACCAAGATAGATG 57.364 36.000 0.00 0.00 0.00 2.90
2641 2766 7.890127 TCAAAAATCTCACCAACCAAGATAGAT 59.110 33.333 0.00 0.00 0.00 1.98
2642 2767 7.230747 TCAAAAATCTCACCAACCAAGATAGA 58.769 34.615 0.00 0.00 0.00 1.98
2643 2768 7.452880 TCAAAAATCTCACCAACCAAGATAG 57.547 36.000 0.00 0.00 0.00 2.08
2644 2769 7.831691 TTCAAAAATCTCACCAACCAAGATA 57.168 32.000 0.00 0.00 0.00 1.98
2645 2770 6.729690 TTCAAAAATCTCACCAACCAAGAT 57.270 33.333 0.00 0.00 0.00 2.40
2646 2771 6.729690 ATTCAAAAATCTCACCAACCAAGA 57.270 33.333 0.00 0.00 0.00 3.02
2647 2772 6.985645 TCAATTCAAAAATCTCACCAACCAAG 59.014 34.615 0.00 0.00 0.00 3.61
2648 2773 6.882656 TCAATTCAAAAATCTCACCAACCAA 58.117 32.000 0.00 0.00 0.00 3.67
2649 2774 6.477053 TCAATTCAAAAATCTCACCAACCA 57.523 33.333 0.00 0.00 0.00 3.67
2650 2775 5.406477 GCTCAATTCAAAAATCTCACCAACC 59.594 40.000 0.00 0.00 0.00 3.77
2651 2776 5.406477 GGCTCAATTCAAAAATCTCACCAAC 59.594 40.000 0.00 0.00 0.00 3.77
2652 2777 5.305128 AGGCTCAATTCAAAAATCTCACCAA 59.695 36.000 0.00 0.00 0.00 3.67
2653 2778 4.834496 AGGCTCAATTCAAAAATCTCACCA 59.166 37.500 0.00 0.00 0.00 4.17
2654 2779 5.397142 AGGCTCAATTCAAAAATCTCACC 57.603 39.130 0.00 0.00 0.00 4.02
2658 2783 9.875691 GGTTTATAAGGCTCAATTCAAAAATCT 57.124 29.630 0.00 0.00 0.00 2.40
2659 2784 8.807581 CGGTTTATAAGGCTCAATTCAAAAATC 58.192 33.333 0.00 0.00 0.00 2.17
2660 2785 7.763985 CCGGTTTATAAGGCTCAATTCAAAAAT 59.236 33.333 0.00 0.00 0.00 1.82
2661 2786 7.039644 TCCGGTTTATAAGGCTCAATTCAAAAA 60.040 33.333 0.00 0.00 0.00 1.94
2662 2787 6.434652 TCCGGTTTATAAGGCTCAATTCAAAA 59.565 34.615 0.00 0.00 0.00 2.44
2663 2788 5.946972 TCCGGTTTATAAGGCTCAATTCAAA 59.053 36.000 0.00 0.00 0.00 2.69
2664 2789 5.502079 TCCGGTTTATAAGGCTCAATTCAA 58.498 37.500 0.00 0.00 0.00 2.69
2665 2790 5.105567 TCCGGTTTATAAGGCTCAATTCA 57.894 39.130 0.00 0.00 0.00 2.57
2666 2791 6.445357 TTTCCGGTTTATAAGGCTCAATTC 57.555 37.500 0.00 0.00 0.00 2.17
2667 2792 5.359860 CCTTTCCGGTTTATAAGGCTCAATT 59.640 40.000 0.00 0.00 31.59 2.32
2668 2793 4.887655 CCTTTCCGGTTTATAAGGCTCAAT 59.112 41.667 0.00 0.00 31.59 2.57
2669 2794 4.019141 TCCTTTCCGGTTTATAAGGCTCAA 60.019 41.667 0.00 0.00 37.62 3.02
2670 2795 3.520317 TCCTTTCCGGTTTATAAGGCTCA 59.480 43.478 0.00 0.00 37.62 4.26
2671 2796 4.127907 CTCCTTTCCGGTTTATAAGGCTC 58.872 47.826 0.00 0.00 37.62 4.70
2672 2797 3.118000 CCTCCTTTCCGGTTTATAAGGCT 60.118 47.826 0.00 0.00 37.62 4.58
2673 2798 3.211865 CCTCCTTTCCGGTTTATAAGGC 58.788 50.000 0.00 0.00 37.62 4.35
2674 2799 3.457012 TCCCTCCTTTCCGGTTTATAAGG 59.543 47.826 0.00 8.36 38.78 2.69
2675 2800 4.163649 AGTCCCTCCTTTCCGGTTTATAAG 59.836 45.833 0.00 0.00 0.00 1.73
2676 2801 4.106324 AGTCCCTCCTTTCCGGTTTATAA 58.894 43.478 0.00 0.00 0.00 0.98
2677 2802 3.727948 AGTCCCTCCTTTCCGGTTTATA 58.272 45.455 0.00 0.00 0.00 0.98
2678 2803 2.558974 AGTCCCTCCTTTCCGGTTTAT 58.441 47.619 0.00 0.00 0.00 1.40
2679 2804 2.034436 AGTCCCTCCTTTCCGGTTTA 57.966 50.000 0.00 0.00 0.00 2.01
2680 2805 1.627329 GTAGTCCCTCCTTTCCGGTTT 59.373 52.381 0.00 0.00 0.00 3.27
2681 2806 1.203275 AGTAGTCCCTCCTTTCCGGTT 60.203 52.381 0.00 0.00 0.00 4.44
2682 2807 0.412640 AGTAGTCCCTCCTTTCCGGT 59.587 55.000 0.00 0.00 0.00 5.28
2683 2808 2.449137 TAGTAGTCCCTCCTTTCCGG 57.551 55.000 0.00 0.00 0.00 5.14
2684 2809 2.628657 CCATAGTAGTCCCTCCTTTCCG 59.371 54.545 0.00 0.00 0.00 4.30
2685 2810 3.655384 ACCATAGTAGTCCCTCCTTTCC 58.345 50.000 0.00 0.00 0.00 3.13
2698 2823 8.762481 ATAATGACAGTGACACTACCATAGTA 57.238 34.615 17.21 10.56 37.23 1.82
2699 2824 7.661536 ATAATGACAGTGACACTACCATAGT 57.338 36.000 17.21 7.72 40.28 2.12
2703 2828 9.811995 GTAAATATAATGACAGTGACACTACCA 57.188 33.333 8.02 9.46 0.00 3.25
2704 2829 9.257651 GGTAAATATAATGACAGTGACACTACC 57.742 37.037 8.02 3.76 0.00 3.18
2720 2845 7.214381 ACACTGCAATCGCTAGGTAAATATAA 58.786 34.615 0.00 0.00 39.64 0.98
2787 2912 2.627221 CACACCATTCCAATTCCACACA 59.373 45.455 0.00 0.00 0.00 3.72
2796 2921 7.502226 GGATAATACTCAATCACACCATTCCAA 59.498 37.037 0.00 0.00 0.00 3.53
2812 2937 4.039366 AGGAAACCAGCTCGGATAATACTC 59.961 45.833 8.91 0.00 38.63 2.59
2834 2959 2.205074 CTAACTAGATGCCGCCACAAG 58.795 52.381 0.00 0.00 0.00 3.16
2835 2960 1.742411 GCTAACTAGATGCCGCCACAA 60.742 52.381 0.00 0.00 0.00 3.33
2902 3028 1.395670 GTCGAAGAAAACAAAGGCGC 58.604 50.000 0.00 0.00 39.69 6.53
2981 3107 1.570813 CGCCGATGATGCTTAGAACA 58.429 50.000 0.00 0.00 0.00 3.18
2985 3111 2.849007 CGCGCCGATGATGCTTAG 59.151 61.111 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.