Multiple sequence alignment - TraesCS5A01G541100

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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 TraesCS5A01G541100 chr5A 100.000 1697 0 0 933 2629 698101772 698100076 0.000000e+00 3134.0
1 TraesCS5A01G541100 chr5A 100.000 623 0 0 1 623 698102704 698102082 0.000000e+00 1151.0
2 TraesCS5A01G541100 chr5A 85.234 684 63 25 1496 2154 8233503 8234173 0.000000e+00 669.0
3 TraesCS5A01G541100 chr5A 96.218 238 9 0 1079 1316 588852195 588852432 8.820000e-105 390.0
4 TraesCS5A01G541100 chr7B 91.433 1424 116 3 970 2388 493133875 493132453 0.000000e+00 1949.0
5 TraesCS5A01G541100 chr7B 91.332 623 46 7 3 621 493134547 493133929 0.000000e+00 845.0
6 TraesCS5A01G541100 chr7B 95.614 228 9 1 933 1160 130903838 130903612 5.350000e-97 364.0
7 TraesCS5A01G541100 chr7D 89.587 605 56 7 9 610 573301588 573300988 0.000000e+00 761.0
8 TraesCS5A01G541100 chr7A 88.651 608 57 9 11 610 351154534 351155137 0.000000e+00 730.0
9 TraesCS5A01G541100 chr7A 86.943 628 61 15 5 621 151704826 151704209 0.000000e+00 686.0
10 TraesCS5A01G541100 chr4A 87.898 628 53 19 1 618 724421109 724421723 0.000000e+00 717.0
11 TraesCS5A01G541100 chr1D 90.602 532 43 7 3 531 465258551 465259078 0.000000e+00 699.0
12 TraesCS5A01G541100 chr5D 90.226 532 46 6 3 531 29627348 29627876 0.000000e+00 689.0
13 TraesCS5A01G541100 chr5D 81.514 925 78 39 1320 2199 10521074 10521950 0.000000e+00 675.0
14 TraesCS5A01G541100 chr5D 96.218 238 9 0 1079 1316 468651783 468652020 8.820000e-105 390.0
15 TraesCS5A01G541100 chr4D 89.907 535 46 7 3 531 332128848 332129380 0.000000e+00 682.0
16 TraesCS5A01G541100 chr4D 94.444 108 6 0 967 1074 210023814 210023921 1.620000e-37 167.0
17 TraesCS5A01G541100 chr2D 88.408 578 52 11 3 572 283962934 283963504 0.000000e+00 682.0
18 TraesCS5A01G541100 chr2D 94.444 108 6 0 967 1074 283963559 283963666 1.620000e-37 167.0
19 TraesCS5A01G541100 chr2D 94.444 108 6 0 967 1074 524268738 524268845 1.620000e-37 167.0
20 TraesCS5A01G541100 chr5B 96.218 238 9 0 1079 1316 575253049 575253286 8.820000e-105 390.0
21 TraesCS5A01G541100 chr5B 94.298 228 13 0 933 1160 89070765 89070538 1.500000e-92 350.0
22 TraesCS5A01G541100 chr3B 94.340 106 6 0 969 1074 782859001 782859106 2.090000e-36 163.0
23 TraesCS5A01G541100 chr6A 91.509 106 8 1 967 1071 60063411 60063306 7.580000e-31 145.0
24 TraesCS5A01G541100 chr4B 90.741 108 10 0 967 1074 580890934 580890827 7.580000e-31 145.0
25 TraesCS5A01G541100 chr3A 95.238 63 2 1 933 995 451512179 451512118 5.990000e-17 99.0
26 TraesCS5A01G541100 chrUn 97.059 34 1 0 933 966 81658502 81658469 1.020000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G541100 chr5A 698100076 698102704 2628 True 2142.5 3134 100.0000 1 2629 2 chr5A.!!$R1 2628
1 TraesCS5A01G541100 chr5A 8233503 8234173 670 False 669.0 669 85.2340 1496 2154 1 chr5A.!!$F1 658
2 TraesCS5A01G541100 chr7B 493132453 493134547 2094 True 1397.0 1949 91.3825 3 2388 2 chr7B.!!$R2 2385
3 TraesCS5A01G541100 chr7D 573300988 573301588 600 True 761.0 761 89.5870 9 610 1 chr7D.!!$R1 601
4 TraesCS5A01G541100 chr7A 351154534 351155137 603 False 730.0 730 88.6510 11 610 1 chr7A.!!$F1 599
5 TraesCS5A01G541100 chr7A 151704209 151704826 617 True 686.0 686 86.9430 5 621 1 chr7A.!!$R1 616
6 TraesCS5A01G541100 chr4A 724421109 724421723 614 False 717.0 717 87.8980 1 618 1 chr4A.!!$F1 617
7 TraesCS5A01G541100 chr1D 465258551 465259078 527 False 699.0 699 90.6020 3 531 1 chr1D.!!$F1 528
8 TraesCS5A01G541100 chr5D 29627348 29627876 528 False 689.0 689 90.2260 3 531 1 chr5D.!!$F2 528
9 TraesCS5A01G541100 chr5D 10521074 10521950 876 False 675.0 675 81.5140 1320 2199 1 chr5D.!!$F1 879
10 TraesCS5A01G541100 chr4D 332128848 332129380 532 False 682.0 682 89.9070 3 531 1 chr4D.!!$F2 528
11 TraesCS5A01G541100 chr2D 283962934 283963666 732 False 424.5 682 91.4260 3 1074 2 chr2D.!!$F2 1071

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
384 393 0.040204 CTGATTGGTTCAGGGGCCTT 59.96 55.0 0.84 0.00 46.89 4.35 F
1139 1168 0.110295 TGCCAAGGAGCTGCTTAACA 59.89 50.0 20.95 17.69 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1503 0.317854 CGTCAAGTGAGTCTCGTGCA 60.318 55.0 3.60 0.00 0.00 4.57 R
2388 2489 0.033894 ATCACCATCCAGCATGCACA 60.034 50.0 21.98 2.71 31.97 4.57 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
44 45 9.887629 ATTTGGTCAATTGTGCATTAAATATGA 57.112 25.926 5.13 0.00 0.00 2.15
258 267 7.279615 TCCTGACACAATGAGAAGTTCTTTTA 58.720 34.615 6.88 0.00 0.00 1.52
259 268 7.773224 TCCTGACACAATGAGAAGTTCTTTTAA 59.227 33.333 6.88 0.00 0.00 1.52
260 269 8.405531 CCTGACACAATGAGAAGTTCTTTTAAA 58.594 33.333 6.88 0.00 0.00 1.52
374 383 6.318648 ACATGTATAATGCGTTCTGATTGGTT 59.681 34.615 0.00 0.00 0.00 3.67
384 393 0.040204 CTGATTGGTTCAGGGGCCTT 59.960 55.000 0.84 0.00 46.89 4.35
412 421 2.612212 GGATCGTGCATAATTCACCGTT 59.388 45.455 0.00 0.00 0.00 4.44
434 443 0.982852 ATGCTCCTGGATCCAACGGA 60.983 55.000 19.08 19.08 35.55 4.69
435 444 0.982852 TGCTCCTGGATCCAACGGAT 60.983 55.000 20.18 0.00 46.28 4.18
460 469 1.229336 CTCACCCTCTCACCCACCT 60.229 63.158 0.00 0.00 0.00 4.00
621 637 3.700350 CCTCTCCCCTCCCCACCT 61.700 72.222 0.00 0.00 0.00 4.00
1022 1051 1.755008 GGGAGTCCTGGTCCTCTCG 60.755 68.421 9.58 0.00 34.16 4.04
1121 1150 3.554692 GCCTGGCGTCGATCGTTG 61.555 66.667 15.94 9.87 42.13 4.10
1135 1164 2.263741 CGTTGCCAAGGAGCTGCTT 61.264 57.895 15.60 15.60 0.00 3.91
1138 1167 1.068264 GTTGCCAAGGAGCTGCTTAAC 60.068 52.381 20.95 16.91 0.00 2.01
1139 1168 0.110295 TGCCAAGGAGCTGCTTAACA 59.890 50.000 20.95 17.69 0.00 2.41
1148 1177 3.422303 TGCTTAACAGGCAGCGCG 61.422 61.111 0.00 0.00 39.04 6.86
1174 1203 2.026879 GTCCGCTGCGAGGAGATC 59.973 66.667 25.45 3.62 38.65 2.75
1188 1217 2.106938 GATCTGCATGTCCGGCGA 59.893 61.111 9.30 0.00 0.00 5.54
1204 1233 2.182030 GACCTCGTCCGCCAGAAG 59.818 66.667 0.00 0.00 0.00 2.85
1210 1239 0.173481 TCGTCCGCCAGAAGATGAAG 59.827 55.000 0.00 0.00 0.00 3.02
1216 1245 2.482142 CCGCCAGAAGATGAAGTACCTC 60.482 54.545 0.00 0.00 0.00 3.85
1218 1247 2.501723 GCCAGAAGATGAAGTACCTCCA 59.498 50.000 0.00 0.00 0.00 3.86
1256 1285 2.351924 GAACACCAAGCCCTCCCACA 62.352 60.000 0.00 0.00 0.00 4.17
1291 1320 4.570874 GCCCCGGCCAAGATCCTC 62.571 72.222 2.24 0.00 34.56 3.71
1318 1347 3.063704 ATCCGCGGGTACGTCACA 61.064 61.111 27.83 1.69 43.45 3.58
1402 1431 1.998530 CCCATGCTCCTGGTAACCA 59.001 57.895 0.00 0.00 34.23 3.67
1408 1437 1.972660 GCTCCTGGTAACCATCGGCT 61.973 60.000 0.00 0.00 30.82 5.52
1421 1450 1.131638 ATCGGCTGCCTTATTCCTCA 58.868 50.000 17.92 0.00 0.00 3.86
1440 1469 0.984230 ACCTTCTGATTCCGCTTCCA 59.016 50.000 0.00 0.00 0.00 3.53
1461 1496 1.426251 TTCATGGTGCAGGGTCCTGT 61.426 55.000 17.28 0.00 45.24 4.00
1483 1518 1.005630 GGCTGCACGAGACTCACTT 60.006 57.895 0.50 0.00 0.00 3.16
1486 1521 1.413382 CTGCACGAGACTCACTTGAC 58.587 55.000 2.82 0.00 34.31 3.18
1576 1640 2.352032 CCGCTCCTCCTCCGTTTCT 61.352 63.158 0.00 0.00 0.00 2.52
1635 1699 1.812571 CAGATTGGTTTCGGTTCTGGG 59.187 52.381 0.00 0.00 32.14 4.45
1754 1826 4.113354 AGTATTAGCGAGCTTAGTGTTGC 58.887 43.478 1.86 0.00 0.00 4.17
1806 1881 4.460263 TCTGCTCTGGTTTTGTATTGTGT 58.540 39.130 0.00 0.00 0.00 3.72
1816 1891 1.141645 TGTATTGTGTCGTTCCGTGC 58.858 50.000 0.00 0.00 0.00 5.34
1852 1930 5.542635 AGTCTTACTTACACTTGGGACATGA 59.457 40.000 0.00 0.00 39.30 3.07
1943 2035 0.690762 TCTGGCCTACCTGTTCAACC 59.309 55.000 3.32 0.00 36.34 3.77
1958 2050 0.179020 CAACCCAACTGGACAGCTCA 60.179 55.000 0.00 0.00 37.39 4.26
1987 2079 3.805422 CACACTTTCAGTTTGCAATGCAT 59.195 39.130 9.39 0.00 38.76 3.96
2008 2100 1.021390 GCTATGCTTGCTCACGGTGT 61.021 55.000 8.17 0.00 0.00 4.16
2049 2141 7.751732 TCTGATGGACGAGTTTAATTTGATTG 58.248 34.615 0.00 0.00 0.00 2.67
2247 2347 1.202627 TGTGCTTTTCCAAATGCCACC 60.203 47.619 7.29 0.00 38.03 4.61
2290 2391 0.955178 CCACCGCAATGTAAACCACA 59.045 50.000 0.00 0.00 42.69 4.17
2303 2404 0.317160 AACCACAGCTTGATCGACGA 59.683 50.000 0.00 0.00 0.00 4.20
2307 2408 2.534298 CACAGCTTGATCGACGATTCT 58.466 47.619 12.40 4.64 0.00 2.40
2308 2409 2.280971 CACAGCTTGATCGACGATTCTG 59.719 50.000 12.40 17.02 0.00 3.02
2317 2418 1.611977 TCGACGATTCTGTTGTCCTGT 59.388 47.619 0.00 0.00 37.88 4.00
2325 2426 1.134521 TCTGTTGTCCTGTCGCACTTT 60.135 47.619 0.00 0.00 0.00 2.66
2365 2466 5.625311 GCTTCGTTTGGAAACTGATGTAAAG 59.375 40.000 1.04 0.00 36.77 1.85
2368 2469 4.556233 GTTTGGAAACTGATGTAAAGGGC 58.444 43.478 0.00 0.00 36.03 5.19
2378 2479 3.500680 TGATGTAAAGGGCGAACTTGTTC 59.499 43.478 3.60 3.60 0.00 3.18
2379 2480 1.868498 TGTAAAGGGCGAACTTGTTCG 59.132 47.619 25.63 25.63 46.34 3.95
2399 2500 2.508743 CACGTTTTGTGCATGCTGG 58.491 52.632 20.33 2.72 42.70 4.85
2400 2501 0.030504 CACGTTTTGTGCATGCTGGA 59.969 50.000 20.33 1.00 42.70 3.86
2401 2502 0.961019 ACGTTTTGTGCATGCTGGAT 59.039 45.000 20.33 0.00 0.00 3.41
2402 2503 1.336148 ACGTTTTGTGCATGCTGGATG 60.336 47.619 20.33 4.63 34.84 3.51
2403 2504 1.717194 GTTTTGTGCATGCTGGATGG 58.283 50.000 20.33 0.00 31.99 3.51
2404 2505 1.001181 GTTTTGTGCATGCTGGATGGT 59.999 47.619 20.33 0.00 31.99 3.55
2405 2506 0.604073 TTTGTGCATGCTGGATGGTG 59.396 50.000 20.33 0.00 31.99 4.17
2406 2507 0.251253 TTGTGCATGCTGGATGGTGA 60.251 50.000 20.33 0.00 31.99 4.02
2407 2508 0.033894 TGTGCATGCTGGATGGTGAT 60.034 50.000 20.33 0.00 31.99 3.06
2408 2509 1.108776 GTGCATGCTGGATGGTGATT 58.891 50.000 20.33 0.00 31.99 2.57
2409 2510 1.107945 TGCATGCTGGATGGTGATTG 58.892 50.000 20.33 0.00 31.99 2.67
2410 2511 0.249322 GCATGCTGGATGGTGATTGC 60.249 55.000 11.37 0.00 31.99 3.56
2411 2512 0.387929 CATGCTGGATGGTGATTGCC 59.612 55.000 0.63 0.00 0.00 4.52
2412 2513 0.260816 ATGCTGGATGGTGATTGCCT 59.739 50.000 0.00 0.00 0.00 4.75
2413 2514 0.040058 TGCTGGATGGTGATTGCCTT 59.960 50.000 0.00 0.00 0.00 4.35
2414 2515 1.188863 GCTGGATGGTGATTGCCTTT 58.811 50.000 0.00 0.00 0.00 3.11
2415 2516 1.134907 GCTGGATGGTGATTGCCTTTG 60.135 52.381 0.00 0.00 0.00 2.77
2416 2517 2.173519 CTGGATGGTGATTGCCTTTGT 58.826 47.619 0.00 0.00 0.00 2.83
2417 2518 1.894466 TGGATGGTGATTGCCTTTGTG 59.106 47.619 0.00 0.00 0.00 3.33
2418 2519 1.404583 GGATGGTGATTGCCTTTGTGC 60.405 52.381 0.00 0.00 0.00 4.57
2419 2520 1.547372 GATGGTGATTGCCTTTGTGCT 59.453 47.619 0.00 0.00 0.00 4.40
2420 2521 1.412079 TGGTGATTGCCTTTGTGCTT 58.588 45.000 0.00 0.00 0.00 3.91
2421 2522 1.761784 TGGTGATTGCCTTTGTGCTTT 59.238 42.857 0.00 0.00 0.00 3.51
2422 2523 2.170187 TGGTGATTGCCTTTGTGCTTTT 59.830 40.909 0.00 0.00 0.00 2.27
2423 2524 2.545106 GGTGATTGCCTTTGTGCTTTTG 59.455 45.455 0.00 0.00 0.00 2.44
2424 2525 3.197265 GTGATTGCCTTTGTGCTTTTGT 58.803 40.909 0.00 0.00 0.00 2.83
2425 2526 3.001533 GTGATTGCCTTTGTGCTTTTGTG 59.998 43.478 0.00 0.00 0.00 3.33
2426 2527 1.367659 TTGCCTTTGTGCTTTTGTGC 58.632 45.000 0.00 0.00 0.00 4.57
2427 2528 0.248565 TGCCTTTGTGCTTTTGTGCA 59.751 45.000 0.00 0.00 41.05 4.57
2428 2529 1.134461 TGCCTTTGTGCTTTTGTGCAT 60.134 42.857 0.00 0.00 45.23 3.96
2429 2530 1.262151 GCCTTTGTGCTTTTGTGCATG 59.738 47.619 0.00 0.00 45.23 4.06
2430 2531 2.553086 CCTTTGTGCTTTTGTGCATGT 58.447 42.857 0.00 0.00 45.23 3.21
2431 2532 2.937799 CCTTTGTGCTTTTGTGCATGTT 59.062 40.909 0.00 0.00 45.23 2.71
2432 2533 3.242478 CCTTTGTGCTTTTGTGCATGTTG 60.242 43.478 0.00 0.00 45.23 3.33
2433 2534 1.288350 TGTGCTTTTGTGCATGTTGC 58.712 45.000 0.00 0.00 45.23 4.17
2434 2535 1.134759 TGTGCTTTTGTGCATGTTGCT 60.135 42.857 0.00 0.00 45.31 3.91
2435 2536 2.100418 TGTGCTTTTGTGCATGTTGCTA 59.900 40.909 0.00 0.00 45.31 3.49
2436 2537 2.727798 GTGCTTTTGTGCATGTTGCTAG 59.272 45.455 0.00 0.00 45.31 3.42
2437 2538 2.361757 TGCTTTTGTGCATGTTGCTAGT 59.638 40.909 0.00 0.00 45.31 2.57
2438 2539 3.567585 TGCTTTTGTGCATGTTGCTAGTA 59.432 39.130 0.00 0.00 45.31 1.82
2439 2540 4.161333 GCTTTTGTGCATGTTGCTAGTAG 58.839 43.478 0.00 0.00 45.31 2.57
2440 2541 4.320494 GCTTTTGTGCATGTTGCTAGTAGT 60.320 41.667 0.00 0.00 45.31 2.73
2441 2542 5.106712 GCTTTTGTGCATGTTGCTAGTAGTA 60.107 40.000 0.00 0.00 45.31 1.82
2442 2543 6.480524 TTTTGTGCATGTTGCTAGTAGTAG 57.519 37.500 0.00 0.00 45.31 2.57
2455 2556 5.365403 CTAGTAGTAGCAGCACTATGGTC 57.635 47.826 0.00 0.00 33.71 4.02
2456 2557 3.632333 AGTAGTAGCAGCACTATGGTCA 58.368 45.455 0.00 0.00 33.71 4.02
2457 2558 4.219115 AGTAGTAGCAGCACTATGGTCAT 58.781 43.478 0.00 0.00 33.71 3.06
2458 2559 3.465742 AGTAGCAGCACTATGGTCATG 57.534 47.619 0.00 0.00 32.15 3.07
2459 2560 3.033909 AGTAGCAGCACTATGGTCATGA 58.966 45.455 0.00 0.00 32.15 3.07
2460 2561 2.616634 AGCAGCACTATGGTCATGAG 57.383 50.000 0.00 0.00 0.00 2.90
2461 2562 0.942962 GCAGCACTATGGTCATGAGC 59.057 55.000 18.01 18.01 0.00 4.26
2462 2563 1.744798 GCAGCACTATGGTCATGAGCA 60.745 52.381 28.28 28.28 43.48 4.26
2463 2564 2.210961 CAGCACTATGGTCATGAGCAG 58.789 52.381 29.35 20.18 42.52 4.24
2464 2565 0.942962 GCACTATGGTCATGAGCAGC 59.057 55.000 29.35 23.15 42.52 5.25
2465 2566 1.474677 GCACTATGGTCATGAGCAGCT 60.475 52.381 29.35 18.01 42.52 4.24
2466 2567 2.224137 GCACTATGGTCATGAGCAGCTA 60.224 50.000 29.35 18.15 42.52 3.32
2467 2568 3.388308 CACTATGGTCATGAGCAGCTAC 58.612 50.000 29.35 1.81 42.52 3.58
2468 2569 2.366916 ACTATGGTCATGAGCAGCTACC 59.633 50.000 29.35 11.66 42.52 3.18
2469 2570 1.504912 ATGGTCATGAGCAGCTACCT 58.495 50.000 29.35 11.68 42.52 3.08
2470 2571 2.159179 TGGTCATGAGCAGCTACCTA 57.841 50.000 23.20 0.00 34.41 3.08
2471 2572 2.034878 TGGTCATGAGCAGCTACCTAG 58.965 52.381 23.20 0.00 34.41 3.02
2490 2591 5.275067 CTAGCATAGGATAGGATCTTGGC 57.725 47.826 0.00 0.00 34.22 4.52
2491 2592 2.843113 AGCATAGGATAGGATCTTGGCC 59.157 50.000 0.00 0.00 0.00 5.36
2492 2593 2.843113 GCATAGGATAGGATCTTGGCCT 59.157 50.000 3.32 5.78 39.56 5.19
2493 2594 3.118445 GCATAGGATAGGATCTTGGCCTC 60.118 52.174 3.32 0.00 36.96 4.70
2494 2595 2.037385 AGGATAGGATCTTGGCCTCC 57.963 55.000 3.32 1.59 36.96 4.30
2495 2596 1.511747 AGGATAGGATCTTGGCCTCCT 59.488 52.381 15.18 15.18 44.18 3.69
2496 2597 2.089696 AGGATAGGATCTTGGCCTCCTT 60.090 50.000 15.96 5.14 42.03 3.36
2497 2598 2.304470 GGATAGGATCTTGGCCTCCTTC 59.696 54.545 15.96 12.45 42.03 3.46
2498 2599 2.568546 TAGGATCTTGGCCTCCTTCA 57.431 50.000 15.96 0.00 42.03 3.02
2499 2600 1.904440 AGGATCTTGGCCTCCTTCAT 58.096 50.000 3.32 0.00 38.81 2.57
2500 2601 1.493871 AGGATCTTGGCCTCCTTCATG 59.506 52.381 3.32 0.00 38.81 3.07
2501 2602 1.478288 GGATCTTGGCCTCCTTCATGG 60.478 57.143 3.32 0.00 37.10 3.66
2502 2603 0.554792 ATCTTGGCCTCCTTCATGGG 59.445 55.000 3.32 0.00 36.20 4.00
2503 2604 0.549902 TCTTGGCCTCCTTCATGGGA 60.550 55.000 3.32 0.00 36.20 4.37
2504 2605 0.394899 CTTGGCCTCCTTCATGGGAC 60.395 60.000 3.32 0.00 36.20 4.46
2516 2617 4.342427 TGGGACATGGCTGATTGC 57.658 55.556 0.00 0.00 41.94 3.56
2527 2628 1.602311 GCTGATTGCCCCATAGTCTG 58.398 55.000 0.00 0.00 35.15 3.51
2528 2629 1.141657 GCTGATTGCCCCATAGTCTGA 59.858 52.381 0.00 0.00 35.15 3.27
2529 2630 2.421952 GCTGATTGCCCCATAGTCTGAA 60.422 50.000 0.00 0.00 35.15 3.02
2530 2631 3.749954 GCTGATTGCCCCATAGTCTGAAT 60.750 47.826 0.00 0.00 35.15 2.57
2531 2632 4.467769 CTGATTGCCCCATAGTCTGAATT 58.532 43.478 0.00 0.00 0.00 2.17
2532 2633 5.624159 CTGATTGCCCCATAGTCTGAATTA 58.376 41.667 0.00 0.00 0.00 1.40
2533 2634 6.204852 TGATTGCCCCATAGTCTGAATTAT 57.795 37.500 0.00 0.00 0.00 1.28
2534 2635 6.005823 TGATTGCCCCATAGTCTGAATTATG 58.994 40.000 4.34 4.34 0.00 1.90
2535 2636 5.387113 TTGCCCCATAGTCTGAATTATGT 57.613 39.130 8.66 0.00 0.00 2.29
2536 2637 5.387113 TGCCCCATAGTCTGAATTATGTT 57.613 39.130 8.66 0.00 0.00 2.71
2537 2638 5.765510 TGCCCCATAGTCTGAATTATGTTT 58.234 37.500 8.66 0.00 0.00 2.83
2538 2639 5.827797 TGCCCCATAGTCTGAATTATGTTTC 59.172 40.000 8.66 0.00 0.00 2.78
2539 2640 5.827797 GCCCCATAGTCTGAATTATGTTTCA 59.172 40.000 8.66 0.00 34.55 2.69
2547 2648 5.281693 CTGAATTATGTTTCAGCACACGA 57.718 39.130 6.55 0.00 44.30 4.35
2548 2649 5.281693 TGAATTATGTTTCAGCACACGAG 57.718 39.130 0.00 0.00 32.07 4.18
2549 2650 3.747099 ATTATGTTTCAGCACACGAGC 57.253 42.857 0.00 0.00 0.00 5.03
2550 2651 1.067693 TATGTTTCAGCACACGAGCG 58.932 50.000 0.00 0.00 40.15 5.03
2551 2652 1.568612 ATGTTTCAGCACACGAGCGG 61.569 55.000 0.00 0.00 40.15 5.52
2552 2653 2.108157 TTTCAGCACACGAGCGGT 59.892 55.556 0.00 0.00 40.15 5.68
2553 2654 1.522806 TTTCAGCACACGAGCGGTT 60.523 52.632 0.00 0.00 40.15 4.44
2554 2655 1.092921 TTTCAGCACACGAGCGGTTT 61.093 50.000 0.00 0.00 40.15 3.27
2555 2656 0.249531 TTCAGCACACGAGCGGTTTA 60.250 50.000 0.00 0.00 40.15 2.01
2556 2657 0.037697 TCAGCACACGAGCGGTTTAT 60.038 50.000 0.00 0.00 40.15 1.40
2557 2658 0.796312 CAGCACACGAGCGGTTTATT 59.204 50.000 0.00 0.00 40.15 1.40
2558 2659 0.796312 AGCACACGAGCGGTTTATTG 59.204 50.000 0.00 0.00 40.15 1.90
2559 2660 0.515564 GCACACGAGCGGTTTATTGT 59.484 50.000 0.00 0.00 0.00 2.71
2560 2661 1.463528 GCACACGAGCGGTTTATTGTC 60.464 52.381 0.00 0.00 0.00 3.18
2561 2662 2.066262 CACACGAGCGGTTTATTGTCT 58.934 47.619 0.00 0.00 0.00 3.41
2562 2663 2.478894 CACACGAGCGGTTTATTGTCTT 59.521 45.455 0.00 0.00 0.00 3.01
2563 2664 2.735134 ACACGAGCGGTTTATTGTCTTC 59.265 45.455 0.00 0.00 0.00 2.87
2564 2665 2.734606 CACGAGCGGTTTATTGTCTTCA 59.265 45.455 0.00 0.00 0.00 3.02
2565 2666 3.370978 CACGAGCGGTTTATTGTCTTCAT 59.629 43.478 0.00 0.00 0.00 2.57
2566 2667 3.617263 ACGAGCGGTTTATTGTCTTCATC 59.383 43.478 0.00 0.00 0.00 2.92
2567 2668 3.865745 CGAGCGGTTTATTGTCTTCATCT 59.134 43.478 0.00 0.00 0.00 2.90
2568 2669 4.330074 CGAGCGGTTTATTGTCTTCATCTT 59.670 41.667 0.00 0.00 0.00 2.40
2569 2670 5.518847 CGAGCGGTTTATTGTCTTCATCTTA 59.481 40.000 0.00 0.00 0.00 2.10
2570 2671 6.035650 CGAGCGGTTTATTGTCTTCATCTTAA 59.964 38.462 0.00 0.00 0.00 1.85
2571 2672 7.308782 AGCGGTTTATTGTCTTCATCTTAAG 57.691 36.000 0.00 0.00 0.00 1.85
2572 2673 5.965918 GCGGTTTATTGTCTTCATCTTAAGC 59.034 40.000 0.00 0.00 0.00 3.09
2573 2674 6.403200 GCGGTTTATTGTCTTCATCTTAAGCA 60.403 38.462 0.00 0.00 0.00 3.91
2574 2675 7.526608 CGGTTTATTGTCTTCATCTTAAGCAA 58.473 34.615 0.00 0.00 31.70 3.91
2575 2676 8.184192 CGGTTTATTGTCTTCATCTTAAGCAAT 58.816 33.333 0.00 2.90 37.20 3.56
2576 2677 9.508567 GGTTTATTGTCTTCATCTTAAGCAATC 57.491 33.333 0.00 0.00 36.07 2.67
2579 2680 7.934855 ATTGTCTTCATCTTAAGCAATCACT 57.065 32.000 0.00 0.00 32.61 3.41
2580 2681 6.732531 TGTCTTCATCTTAAGCAATCACTG 57.267 37.500 0.00 0.00 0.00 3.66
2581 2682 6.233434 TGTCTTCATCTTAAGCAATCACTGT 58.767 36.000 0.00 0.00 0.00 3.55
2582 2683 6.148315 TGTCTTCATCTTAAGCAATCACTGTG 59.852 38.462 0.17 0.17 0.00 3.66
2583 2684 5.645067 TCTTCATCTTAAGCAATCACTGTGG 59.355 40.000 8.11 0.00 0.00 4.17
2584 2685 4.910195 TCATCTTAAGCAATCACTGTGGT 58.090 39.130 8.11 0.00 0.00 4.16
2585 2686 5.316167 TCATCTTAAGCAATCACTGTGGTT 58.684 37.500 8.11 3.83 39.80 3.67
2586 2687 5.769662 TCATCTTAAGCAATCACTGTGGTTT 59.230 36.000 2.99 0.00 37.79 3.27
2587 2688 5.437289 TCTTAAGCAATCACTGTGGTTTG 57.563 39.130 2.99 11.02 37.79 2.93
2588 2689 2.514205 AAGCAATCACTGTGGTTTGC 57.486 45.000 27.15 27.15 43.64 3.68
2590 2691 2.056094 GCAATCACTGTGGTTTGCTC 57.944 50.000 27.14 11.34 40.90 4.26
2591 2692 1.337703 GCAATCACTGTGGTTTGCTCA 59.662 47.619 27.14 3.77 40.90 4.26
2592 2693 2.223782 GCAATCACTGTGGTTTGCTCAA 60.224 45.455 27.14 3.17 40.90 3.02
2593 2694 3.374745 CAATCACTGTGGTTTGCTCAAC 58.625 45.455 2.99 0.00 34.18 3.18
2601 2702 1.358759 GTTTGCTCAACCACACGGG 59.641 57.895 0.00 0.00 44.81 5.28
2613 2714 2.279851 CACGGGTGTGCTGTTCGA 60.280 61.111 0.00 0.00 39.67 3.71
2614 2715 1.667830 CACGGGTGTGCTGTTCGAT 60.668 57.895 0.00 0.00 39.67 3.59
2615 2716 1.070786 ACGGGTGTGCTGTTCGATT 59.929 52.632 0.00 0.00 0.00 3.34
2616 2717 0.949105 ACGGGTGTGCTGTTCGATTC 60.949 55.000 0.00 0.00 0.00 2.52
2617 2718 0.670546 CGGGTGTGCTGTTCGATTCT 60.671 55.000 0.00 0.00 0.00 2.40
2618 2719 0.798776 GGGTGTGCTGTTCGATTCTG 59.201 55.000 0.00 0.00 0.00 3.02
2619 2720 1.608025 GGGTGTGCTGTTCGATTCTGA 60.608 52.381 0.00 0.00 0.00 3.27
2620 2721 2.350522 GGTGTGCTGTTCGATTCTGAT 58.649 47.619 0.00 0.00 0.00 2.90
2621 2722 2.744202 GGTGTGCTGTTCGATTCTGATT 59.256 45.455 0.00 0.00 0.00 2.57
2622 2723 3.189287 GGTGTGCTGTTCGATTCTGATTT 59.811 43.478 0.00 0.00 0.00 2.17
2623 2724 4.398247 GTGTGCTGTTCGATTCTGATTTC 58.602 43.478 0.00 0.00 0.00 2.17
2624 2725 3.436704 TGTGCTGTTCGATTCTGATTTCC 59.563 43.478 0.00 0.00 0.00 3.13
2625 2726 3.009723 TGCTGTTCGATTCTGATTTCCC 58.990 45.455 0.00 0.00 0.00 3.97
2626 2727 3.274288 GCTGTTCGATTCTGATTTCCCT 58.726 45.455 0.00 0.00 0.00 4.20
2627 2728 3.311048 GCTGTTCGATTCTGATTTCCCTC 59.689 47.826 0.00 0.00 0.00 4.30
2628 2729 4.764172 CTGTTCGATTCTGATTTCCCTCT 58.236 43.478 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 242 6.382869 AAAAGAACTTCTCATTGTGTCAGG 57.617 37.500 0.00 0.00 0.00 3.86
374 383 4.697756 CGCGTGAAAGGCCCCTGA 62.698 66.667 0.00 0.00 46.79 3.86
399 408 4.214980 GAGCATCCAACGGTGAATTATG 57.785 45.455 0.00 1.16 0.00 1.90
434 443 2.039624 AGAGGGTGAGGTGCGGAT 59.960 61.111 0.00 0.00 0.00 4.18
435 444 2.680352 GAGAGGGTGAGGTGCGGA 60.680 66.667 0.00 0.00 0.00 5.54
603 619 4.026357 GGTGGGGAGGGGAGAGGT 62.026 72.222 0.00 0.00 0.00 3.85
1003 1032 1.755008 GAGAGGACCAGGACTCCCG 60.755 68.421 10.98 0.00 37.58 5.14
1007 1036 1.379309 GAGCGAGAGGACCAGGACT 60.379 63.158 0.00 0.00 0.00 3.85
1104 1133 3.554692 CAACGATCGACGCCAGGC 61.555 66.667 24.34 0.00 46.94 4.85
1108 1137 3.083600 CTTGGCAACGATCGACGCC 62.084 63.158 31.85 31.85 46.94 5.68
1118 1147 1.068264 GTTAAGCAGCTCCTTGGCAAC 60.068 52.381 0.00 0.00 34.17 4.17
1120 1149 0.110295 TGTTAAGCAGCTCCTTGGCA 59.890 50.000 0.00 0.00 34.17 4.92
1121 1150 0.807496 CTGTTAAGCAGCTCCTTGGC 59.193 55.000 0.00 0.00 38.52 4.52
1135 1164 4.308458 ACCACGCGCTGCCTGTTA 62.308 61.111 5.73 0.00 0.00 2.41
1164 1193 0.599728 GGACATGCAGATCTCCTCGC 60.600 60.000 0.00 0.00 0.00 5.03
1174 1203 4.457496 AGGTCGCCGGACATGCAG 62.457 66.667 5.05 0.00 45.28 4.41
1188 1217 1.682684 ATCTTCTGGCGGACGAGGT 60.683 57.895 8.57 0.00 0.00 3.85
1197 1226 2.501723 TGGAGGTACTTCATCTTCTGGC 59.498 50.000 7.35 0.00 40.34 4.85
1210 1239 1.255667 TGCGGAGGAAGTGGAGGTAC 61.256 60.000 0.00 0.00 0.00 3.34
1226 1255 1.466167 CTTGGTGTTCATCCTCTTGCG 59.534 52.381 0.00 0.00 0.00 4.85
1256 1285 4.115199 GCGGAAGTGGATGGGGCT 62.115 66.667 0.00 0.00 0.00 5.19
1306 1335 1.791662 GGCAATTGTGACGTACCCG 59.208 57.895 7.40 0.00 40.83 5.28
1313 1342 2.202349 GAGCGCGGCAATTGTGAC 60.202 61.111 8.83 0.00 0.00 3.67
1318 1347 2.709475 GAATCGAGCGCGGCAATT 59.291 55.556 10.69 2.12 38.28 2.32
1352 1381 0.550914 GAGAGGAGAGGAGAGGAGCA 59.449 60.000 0.00 0.00 0.00 4.26
1394 1423 1.847798 AAGGCAGCCGATGGTTACCA 61.848 55.000 6.53 6.53 38.19 3.25
1402 1431 1.131638 TGAGGAATAAGGCAGCCGAT 58.868 50.000 5.55 0.19 0.00 4.18
1408 1437 3.181329 TCAGAAGGTGAGGAATAAGGCA 58.819 45.455 0.00 0.00 0.00 4.75
1421 1450 0.984230 TGGAAGCGGAATCAGAAGGT 59.016 50.000 0.00 0.00 0.00 3.50
1440 1469 1.136329 AGGACCCTGCACCATGAAGT 61.136 55.000 0.00 0.00 0.00 3.01
1468 1503 0.317854 CGTCAAGTGAGTCTCGTGCA 60.318 55.000 3.60 0.00 0.00 4.57
1576 1640 1.202177 GCTAGCAGCAAAATAAGCGCA 60.202 47.619 11.47 0.00 41.89 6.09
1635 1699 4.344237 CCACCTGGCAGGAATTCC 57.656 61.111 38.99 17.31 37.67 3.01
1745 1817 1.402259 CACCAACCAACGCAACACTAA 59.598 47.619 0.00 0.00 0.00 2.24
1747 1819 0.963355 ACACCAACCAACGCAACACT 60.963 50.000 0.00 0.00 0.00 3.55
1749 1821 1.244697 ACACACCAACCAACGCAACA 61.245 50.000 0.00 0.00 0.00 3.33
1754 1826 2.263945 GGAAAAACACACCAACCAACG 58.736 47.619 0.00 0.00 0.00 4.10
1852 1930 0.693092 TAGGCTACCCCGCAATCCTT 60.693 55.000 0.00 0.00 39.21 3.36
1896 1984 0.750182 CTTGTGTGGGGTTGGTTCGT 60.750 55.000 0.00 0.00 0.00 3.85
1943 2035 2.354259 GAATCTGAGCTGTCCAGTTGG 58.646 52.381 0.00 0.00 33.57 3.77
1987 2079 0.321564 ACCGTGAGCAAGCATAGCAA 60.322 50.000 0.00 0.00 0.00 3.91
2003 2095 3.443045 GATGGGGCAGCAACACCG 61.443 66.667 0.00 0.00 0.00 4.94
2008 2100 1.776063 TCAGATATGATGGGGCAGCAA 59.224 47.619 0.00 0.00 32.21 3.91
2049 2141 9.439500 CTAGTACTCCAAGGTCATAGTCTATAC 57.561 40.741 0.00 0.00 0.00 1.47
2054 2146 6.120905 TCACTAGTACTCCAAGGTCATAGTC 58.879 44.000 0.00 0.00 0.00 2.59
2290 2391 2.926200 CAACAGAATCGTCGATCAAGCT 59.074 45.455 8.45 1.47 0.00 3.74
2303 2404 1.070758 AGTGCGACAGGACAACAGAAT 59.929 47.619 0.00 0.00 41.52 2.40
2307 2408 1.295792 GAAAGTGCGACAGGACAACA 58.704 50.000 0.00 0.00 41.52 3.33
2308 2409 1.003866 GTGAAAGTGCGACAGGACAAC 60.004 52.381 0.00 0.00 41.52 3.32
2317 2418 1.465777 CTGCATGATGTGAAAGTGCGA 59.534 47.619 0.00 0.00 38.58 5.10
2383 2484 1.342555 CATCCAGCATGCACAAAACG 58.657 50.000 21.98 0.00 31.97 3.60
2388 2489 0.033894 ATCACCATCCAGCATGCACA 60.034 50.000 21.98 2.71 31.97 4.57
2389 2490 1.108776 AATCACCATCCAGCATGCAC 58.891 50.000 21.98 0.00 31.97 4.57
2390 2491 1.107945 CAATCACCATCCAGCATGCA 58.892 50.000 21.98 0.00 31.97 3.96
2391 2492 0.249322 GCAATCACCATCCAGCATGC 60.249 55.000 10.51 10.51 31.97 4.06
2392 2493 0.387929 GGCAATCACCATCCAGCATG 59.612 55.000 0.00 0.00 0.00 4.06
2393 2494 0.260816 AGGCAATCACCATCCAGCAT 59.739 50.000 0.00 0.00 0.00 3.79
2394 2495 0.040058 AAGGCAATCACCATCCAGCA 59.960 50.000 0.00 0.00 0.00 4.41
2395 2496 1.134907 CAAAGGCAATCACCATCCAGC 60.135 52.381 0.00 0.00 0.00 4.85
2396 2497 2.094390 CACAAAGGCAATCACCATCCAG 60.094 50.000 0.00 0.00 0.00 3.86
2397 2498 1.894466 CACAAAGGCAATCACCATCCA 59.106 47.619 0.00 0.00 0.00 3.41
2398 2499 1.404583 GCACAAAGGCAATCACCATCC 60.405 52.381 0.00 0.00 0.00 3.51
2399 2500 1.547372 AGCACAAAGGCAATCACCATC 59.453 47.619 0.00 0.00 35.83 3.51
2400 2501 1.636148 AGCACAAAGGCAATCACCAT 58.364 45.000 0.00 0.00 35.83 3.55
2401 2502 1.412079 AAGCACAAAGGCAATCACCA 58.588 45.000 0.00 0.00 35.83 4.17
2402 2503 2.531522 AAAGCACAAAGGCAATCACC 57.468 45.000 0.00 0.00 35.83 4.02
2403 2504 3.001533 CACAAAAGCACAAAGGCAATCAC 59.998 43.478 0.00 0.00 35.83 3.06
2404 2505 3.196463 CACAAAAGCACAAAGGCAATCA 58.804 40.909 0.00 0.00 35.83 2.57
2405 2506 2.032636 GCACAAAAGCACAAAGGCAATC 60.033 45.455 0.00 0.00 35.83 2.67
2406 2507 1.941975 GCACAAAAGCACAAAGGCAAT 59.058 42.857 0.00 0.00 35.83 3.56
2407 2508 1.338484 TGCACAAAAGCACAAAGGCAA 60.338 42.857 0.00 0.00 40.11 4.52
2408 2509 0.248565 TGCACAAAAGCACAAAGGCA 59.751 45.000 0.00 0.00 40.11 4.75
2409 2510 3.062585 TGCACAAAAGCACAAAGGC 57.937 47.368 0.00 0.00 40.11 4.35
2432 2533 3.570550 ACCATAGTGCTGCTACTACTAGC 59.429 47.826 12.07 0.00 45.19 3.42
2433 2534 4.822350 TGACCATAGTGCTGCTACTACTAG 59.178 45.833 12.07 0.00 36.09 2.57
2434 2535 4.788679 TGACCATAGTGCTGCTACTACTA 58.211 43.478 12.07 6.97 36.09 1.82
2435 2536 3.632333 TGACCATAGTGCTGCTACTACT 58.368 45.455 12.07 5.15 36.09 2.57
2436 2537 4.038042 TCATGACCATAGTGCTGCTACTAC 59.962 45.833 12.07 0.00 36.09 2.73
2437 2538 4.215109 TCATGACCATAGTGCTGCTACTA 58.785 43.478 12.16 12.16 37.54 1.82
2438 2539 3.033909 TCATGACCATAGTGCTGCTACT 58.966 45.455 0.00 5.63 31.59 2.57
2439 2540 3.388308 CTCATGACCATAGTGCTGCTAC 58.612 50.000 0.00 0.00 31.59 3.58
2440 2541 2.224137 GCTCATGACCATAGTGCTGCTA 60.224 50.000 0.00 0.00 0.00 3.49
2441 2542 1.474677 GCTCATGACCATAGTGCTGCT 60.475 52.381 0.00 0.00 0.00 4.24
2442 2543 0.942962 GCTCATGACCATAGTGCTGC 59.057 55.000 0.00 0.00 0.00 5.25
2443 2544 2.210961 CTGCTCATGACCATAGTGCTG 58.789 52.381 0.00 0.00 0.00 4.41
2444 2545 1.474677 GCTGCTCATGACCATAGTGCT 60.475 52.381 0.00 0.00 0.00 4.40
2445 2546 0.942962 GCTGCTCATGACCATAGTGC 59.057 55.000 0.00 0.00 0.00 4.40
2446 2547 2.616634 AGCTGCTCATGACCATAGTG 57.383 50.000 0.00 0.00 0.00 2.74
2447 2548 2.366916 GGTAGCTGCTCATGACCATAGT 59.633 50.000 4.91 0.00 0.00 2.12
2448 2549 2.632028 AGGTAGCTGCTCATGACCATAG 59.368 50.000 18.71 0.00 32.28 2.23
2449 2550 2.682594 AGGTAGCTGCTCATGACCATA 58.317 47.619 18.71 0.00 32.28 2.74
2450 2551 1.504912 AGGTAGCTGCTCATGACCAT 58.495 50.000 18.71 4.41 32.28 3.55
2451 2552 2.034878 CTAGGTAGCTGCTCATGACCA 58.965 52.381 18.71 6.67 32.28 4.02
2452 2553 1.270041 GCTAGGTAGCTGCTCATGACC 60.270 57.143 4.91 8.48 45.62 4.02
2453 2554 2.147436 GCTAGGTAGCTGCTCATGAC 57.853 55.000 4.91 0.00 45.62 3.06
2464 2565 6.549364 CCAAGATCCTATCCTATGCTAGGTAG 59.451 46.154 8.51 9.02 46.32 3.18
2465 2566 6.436027 CCAAGATCCTATCCTATGCTAGGTA 58.564 44.000 8.51 2.35 46.32 3.08
2466 2567 5.276440 CCAAGATCCTATCCTATGCTAGGT 58.724 45.833 8.51 1.53 46.32 3.08
2468 2569 4.100808 GGCCAAGATCCTATCCTATGCTAG 59.899 50.000 0.00 0.00 0.00 3.42
2469 2570 4.033709 GGCCAAGATCCTATCCTATGCTA 58.966 47.826 0.00 0.00 0.00 3.49
2470 2571 2.843113 GGCCAAGATCCTATCCTATGCT 59.157 50.000 0.00 0.00 0.00 3.79
2471 2572 2.843113 AGGCCAAGATCCTATCCTATGC 59.157 50.000 5.01 0.00 30.79 3.14
2472 2573 3.454082 GGAGGCCAAGATCCTATCCTATG 59.546 52.174 5.01 0.00 33.24 2.23
2473 2574 3.342517 AGGAGGCCAAGATCCTATCCTAT 59.657 47.826 9.51 0.00 44.28 2.57
2474 2575 2.730254 AGGAGGCCAAGATCCTATCCTA 59.270 50.000 9.51 0.00 44.28 2.94
2475 2576 1.511747 AGGAGGCCAAGATCCTATCCT 59.488 52.381 9.51 4.03 44.28 3.24
2476 2577 2.037385 AGGAGGCCAAGATCCTATCC 57.963 55.000 9.51 1.53 44.28 2.59
2477 2578 2.975489 TGAAGGAGGCCAAGATCCTATC 59.025 50.000 11.51 11.24 45.39 2.08
2478 2579 3.066208 TGAAGGAGGCCAAGATCCTAT 57.934 47.619 11.51 3.04 45.39 2.57
2479 2580 2.568546 TGAAGGAGGCCAAGATCCTA 57.431 50.000 11.51 0.00 45.39 2.94
2481 2582 1.478288 CCATGAAGGAGGCCAAGATCC 60.478 57.143 5.01 2.28 41.22 3.36
2482 2583 1.478288 CCCATGAAGGAGGCCAAGATC 60.478 57.143 5.01 0.00 41.22 2.75
2483 2584 0.554792 CCCATGAAGGAGGCCAAGAT 59.445 55.000 5.01 0.00 41.22 2.40
2484 2585 0.549902 TCCCATGAAGGAGGCCAAGA 60.550 55.000 5.01 0.00 41.22 3.02
2485 2586 0.394899 GTCCCATGAAGGAGGCCAAG 60.395 60.000 5.01 0.00 41.22 3.61
2486 2587 1.139498 TGTCCCATGAAGGAGGCCAA 61.139 55.000 5.01 0.00 41.22 4.52
2487 2588 0.920763 ATGTCCCATGAAGGAGGCCA 60.921 55.000 5.01 0.00 41.22 5.36
2488 2589 0.466922 CATGTCCCATGAAGGAGGCC 60.467 60.000 0.00 0.00 41.22 5.19
2489 2590 0.466922 CCATGTCCCATGAAGGAGGC 60.467 60.000 5.80 0.00 41.22 4.70
2490 2591 0.466922 GCCATGTCCCATGAAGGAGG 60.467 60.000 5.80 0.00 41.22 4.30
2491 2592 0.549950 AGCCATGTCCCATGAAGGAG 59.450 55.000 5.80 0.00 41.22 3.69
2492 2593 0.256752 CAGCCATGTCCCATGAAGGA 59.743 55.000 5.80 0.00 41.22 3.36
2493 2594 0.256752 TCAGCCATGTCCCATGAAGG 59.743 55.000 5.80 0.00 37.03 3.46
2494 2595 2.359981 ATCAGCCATGTCCCATGAAG 57.640 50.000 5.80 0.00 0.00 3.02
2495 2596 2.380941 CAATCAGCCATGTCCCATGAA 58.619 47.619 5.80 0.00 0.00 2.57
2496 2597 2.025344 GCAATCAGCCATGTCCCATGA 61.025 52.381 5.80 0.00 37.23 3.07
2497 2598 0.387929 GCAATCAGCCATGTCCCATG 59.612 55.000 0.00 0.00 37.23 3.66
2498 2599 2.816746 GCAATCAGCCATGTCCCAT 58.183 52.632 0.00 0.00 37.23 4.00
2499 2600 4.342427 GCAATCAGCCATGTCCCA 57.658 55.556 0.00 0.00 37.23 4.37
2508 2609 1.141657 TCAGACTATGGGGCAATCAGC 59.858 52.381 0.00 0.00 44.65 4.26
2509 2610 3.565764 TTCAGACTATGGGGCAATCAG 57.434 47.619 0.00 0.00 0.00 2.90
2510 2611 4.524802 AATTCAGACTATGGGGCAATCA 57.475 40.909 0.00 0.00 0.00 2.57
2511 2612 6.006449 ACATAATTCAGACTATGGGGCAATC 58.994 40.000 4.44 0.00 31.06 2.67
2512 2613 5.957132 ACATAATTCAGACTATGGGGCAAT 58.043 37.500 4.44 0.00 31.06 3.56
2513 2614 5.387113 ACATAATTCAGACTATGGGGCAA 57.613 39.130 4.44 0.00 31.06 4.52
2514 2615 5.387113 AACATAATTCAGACTATGGGGCA 57.613 39.130 4.44 0.00 31.06 5.36
2515 2616 5.827797 TGAAACATAATTCAGACTATGGGGC 59.172 40.000 4.44 0.00 34.50 5.80
2526 2627 4.378356 GCTCGTGTGCTGAAACATAATTCA 60.378 41.667 0.00 0.00 37.70 2.57
2527 2628 4.091424 GCTCGTGTGCTGAAACATAATTC 58.909 43.478 0.00 0.00 31.49 2.17
2528 2629 3.424829 CGCTCGTGTGCTGAAACATAATT 60.425 43.478 0.00 0.00 31.49 1.40
2529 2630 2.094258 CGCTCGTGTGCTGAAACATAAT 59.906 45.455 0.00 0.00 31.49 1.28
2530 2631 1.459209 CGCTCGTGTGCTGAAACATAA 59.541 47.619 0.00 0.00 31.49 1.90
2531 2632 1.067693 CGCTCGTGTGCTGAAACATA 58.932 50.000 0.00 0.00 31.49 2.29
2532 2633 1.568612 CCGCTCGTGTGCTGAAACAT 61.569 55.000 0.00 0.00 31.49 2.71
2533 2634 2.243957 CCGCTCGTGTGCTGAAACA 61.244 57.895 0.00 0.00 0.00 2.83
2534 2635 1.772063 AACCGCTCGTGTGCTGAAAC 61.772 55.000 0.00 0.00 0.00 2.78
2535 2636 1.092921 AAACCGCTCGTGTGCTGAAA 61.093 50.000 0.00 0.00 0.00 2.69
2536 2637 0.249531 TAAACCGCTCGTGTGCTGAA 60.250 50.000 0.00 0.00 0.00 3.02
2537 2638 0.037697 ATAAACCGCTCGTGTGCTGA 60.038 50.000 0.00 0.00 0.00 4.26
2538 2639 0.796312 AATAAACCGCTCGTGTGCTG 59.204 50.000 0.00 0.00 0.00 4.41
2539 2640 0.796312 CAATAAACCGCTCGTGTGCT 59.204 50.000 0.00 0.00 0.00 4.40
2540 2641 0.515564 ACAATAAACCGCTCGTGTGC 59.484 50.000 0.00 0.00 0.00 4.57
2541 2642 2.066262 AGACAATAAACCGCTCGTGTG 58.934 47.619 0.00 0.00 0.00 3.82
2542 2643 2.450609 AGACAATAAACCGCTCGTGT 57.549 45.000 0.00 0.00 0.00 4.49
2543 2644 2.734606 TGAAGACAATAAACCGCTCGTG 59.265 45.455 0.00 0.00 0.00 4.35
2544 2645 3.034721 TGAAGACAATAAACCGCTCGT 57.965 42.857 0.00 0.00 0.00 4.18
2545 2646 3.865745 AGATGAAGACAATAAACCGCTCG 59.134 43.478 0.00 0.00 0.00 5.03
2546 2647 5.803020 AAGATGAAGACAATAAACCGCTC 57.197 39.130 0.00 0.00 0.00 5.03
2547 2648 6.183360 GCTTAAGATGAAGACAATAAACCGCT 60.183 38.462 6.67 0.00 0.00 5.52
2548 2649 5.965918 GCTTAAGATGAAGACAATAAACCGC 59.034 40.000 6.67 0.00 0.00 5.68
2549 2650 7.072177 TGCTTAAGATGAAGACAATAAACCG 57.928 36.000 6.67 0.00 0.00 4.44
2550 2651 9.508567 GATTGCTTAAGATGAAGACAATAAACC 57.491 33.333 6.67 0.00 35.35 3.27
2553 2654 9.453572 AGTGATTGCTTAAGATGAAGACAATAA 57.546 29.630 6.67 0.00 35.35 1.40
2554 2655 8.886719 CAGTGATTGCTTAAGATGAAGACAATA 58.113 33.333 6.67 0.00 35.35 1.90
2555 2656 7.392673 ACAGTGATTGCTTAAGATGAAGACAAT 59.607 33.333 6.67 4.39 36.62 2.71
2556 2657 6.712095 ACAGTGATTGCTTAAGATGAAGACAA 59.288 34.615 6.67 0.00 31.61 3.18
2557 2658 6.148315 CACAGTGATTGCTTAAGATGAAGACA 59.852 38.462 6.67 0.00 0.00 3.41
2558 2659 6.402983 CCACAGTGATTGCTTAAGATGAAGAC 60.403 42.308 6.67 0.00 0.00 3.01
2559 2660 5.645067 CCACAGTGATTGCTTAAGATGAAGA 59.355 40.000 6.67 0.00 0.00 2.87
2560 2661 5.413833 ACCACAGTGATTGCTTAAGATGAAG 59.586 40.000 6.67 0.00 0.00 3.02
2561 2662 5.316167 ACCACAGTGATTGCTTAAGATGAA 58.684 37.500 6.67 0.00 0.00 2.57
2562 2663 4.910195 ACCACAGTGATTGCTTAAGATGA 58.090 39.130 6.67 0.00 0.00 2.92
2563 2664 5.633830 AACCACAGTGATTGCTTAAGATG 57.366 39.130 6.67 0.00 0.00 2.90
2564 2665 5.565439 GCAAACCACAGTGATTGCTTAAGAT 60.565 40.000 25.18 0.00 43.58 2.40
2565 2666 4.261572 GCAAACCACAGTGATTGCTTAAGA 60.262 41.667 25.18 0.00 43.58 2.10
2566 2667 3.983344 GCAAACCACAGTGATTGCTTAAG 59.017 43.478 25.18 0.00 43.58 1.85
2567 2668 3.976169 GCAAACCACAGTGATTGCTTAA 58.024 40.909 25.18 0.00 43.58 1.85
2568 2669 3.641437 GCAAACCACAGTGATTGCTTA 57.359 42.857 25.18 0.00 43.58 3.09
2569 2670 2.514205 GCAAACCACAGTGATTGCTT 57.486 45.000 25.18 2.98 43.58 3.91
2571 2672 1.337703 TGAGCAAACCACAGTGATTGC 59.662 47.619 25.13 25.13 46.43 3.56
2572 2673 3.374745 GTTGAGCAAACCACAGTGATTG 58.625 45.455 0.62 8.27 32.13 2.67
2573 2674 3.715628 GTTGAGCAAACCACAGTGATT 57.284 42.857 0.62 0.00 32.13 2.57
2583 2684 1.358759 CCCGTGTGGTTGAGCAAAC 59.641 57.895 0.00 0.00 38.12 2.93
2584 2685 3.834726 CCCGTGTGGTTGAGCAAA 58.165 55.556 0.00 0.00 0.00 3.68
2595 2696 2.377628 ATCGAACAGCACACCCGTGT 62.378 55.000 0.00 0.00 45.50 4.49
2596 2697 1.227999 AATCGAACAGCACACCCGTG 61.228 55.000 0.00 0.00 46.56 4.94
2597 2698 0.949105 GAATCGAACAGCACACCCGT 60.949 55.000 0.00 0.00 0.00 5.28
2598 2699 0.670546 AGAATCGAACAGCACACCCG 60.671 55.000 0.00 0.00 0.00 5.28
2599 2700 0.798776 CAGAATCGAACAGCACACCC 59.201 55.000 0.00 0.00 0.00 4.61
2600 2701 1.795768 TCAGAATCGAACAGCACACC 58.204 50.000 0.00 0.00 0.00 4.16
2601 2702 4.398247 GAAATCAGAATCGAACAGCACAC 58.602 43.478 0.00 0.00 0.00 3.82
2602 2703 3.436704 GGAAATCAGAATCGAACAGCACA 59.563 43.478 0.00 0.00 0.00 4.57
2603 2704 3.181506 GGGAAATCAGAATCGAACAGCAC 60.182 47.826 0.00 0.00 0.00 4.40
2604 2705 3.009723 GGGAAATCAGAATCGAACAGCA 58.990 45.455 0.00 0.00 0.00 4.41
2605 2706 3.274288 AGGGAAATCAGAATCGAACAGC 58.726 45.455 0.00 0.00 0.00 4.40
2606 2707 4.764172 AGAGGGAAATCAGAATCGAACAG 58.236 43.478 0.00 0.00 0.00 3.16
2607 2708 4.826274 AGAGGGAAATCAGAATCGAACA 57.174 40.909 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.