Multiple sequence alignment - TraesCS4A01G102400

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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 TraesCS4A01G102400 chr4A 100.000 3382 0 0 1 3382 115283984 115280603 0.000000e+00 6246.0
1 TraesCS4A01G102400 chr4D 92.690 1368 37 24 1126 2461 349575328 349576664 0.000000e+00 1914.0
2 TraesCS4A01G102400 chr4D 95.427 831 22 2 1 831 349574014 349574828 0.000000e+00 1310.0
3 TraesCS4A01G102400 chr4D 84.360 422 23 14 2977 3382 349577028 349577422 1.150000e-99 374.0
4 TraesCS4A01G102400 chr4D 83.062 307 32 10 836 1126 349574995 349575297 9.310000e-66 261.0
5 TraesCS4A01G102400 chr4D 77.406 239 27 14 2719 2942 349576720 349576946 2.130000e-22 117.0
6 TraesCS4A01G102400 chr4B 88.420 1373 53 36 1126 2462 432823226 432824528 0.000000e+00 1557.0
7 TraesCS4A01G102400 chr4B 94.775 555 21 2 1 555 432820750 432821296 0.000000e+00 857.0
8 TraesCS4A01G102400 chr4B 88.909 559 39 11 586 1126 432822642 432823195 0.000000e+00 667.0
9 TraesCS4A01G102400 chr4B 84.466 412 32 14 2977 3382 432824887 432825272 8.860000e-101 377.0
10 TraesCS4A01G102400 chr4B 83.424 368 35 15 2624 2977 432824461 432824816 5.450000e-83 318.0
11 TraesCS4A01G102400 chr5D 82.468 154 19 4 2470 2615 344567269 344567422 9.850000e-26 128.0
12 TraesCS4A01G102400 chr3B 81.250 160 19 10 2467 2615 263795933 263796092 5.930000e-23 119.0
13 TraesCS4A01G102400 chr3B 80.000 155 23 3 2470 2616 452424753 452424599 1.280000e-19 108.0
14 TraesCS4A01G102400 chr5B 95.588 68 2 1 2549 2615 639835546 639835479 1.280000e-19 108.0
15 TraesCS4A01G102400 chr1B 90.000 80 5 3 2544 2623 615485683 615485759 2.150000e-17 100.0
16 TraesCS4A01G102400 chr1B 95.000 40 2 0 2569 2608 599221559 599221520 2.820000e-06 63.9
17 TraesCS4A01G102400 chr5A 81.690 71 13 0 2545 2615 456090092 456090162 3.640000e-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 TraesCS4A01G102400 chr4A 115280603 115283984 3381 True 6246.0 6246 100.0000 1 3382 1 chr4A.!!$R1 3381
1 TraesCS4A01G102400 chr4D 349574014 349577422 3408 False 795.2 1914 86.5890 1 3382 5 chr4D.!!$F1 3381
2 TraesCS4A01G102400 chr4B 432820750 432825272 4522 False 755.2 1557 87.9988 1 3382 5 chr4B.!!$F1 3381

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
505 506 0.543410 TGGGAGAGGAGCCGTTTACA 60.543 55.0 0.0 0.0 0.00 2.41 F
1226 2793 0.322906 GCCTCCAAGACAAGGGAAGG 60.323 60.0 0.0 0.0 32.98 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 3886 0.263172 TTGGGCTAGAGGAGGAGGAG 59.737 60.0 0.0 0.0 0.0 3.69 R
2650 4235 0.101759 ACGCCGATAATGCTACACGT 59.898 50.0 0.0 0.0 0.0 4.49 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
121 122 2.825264 GATCGCCCTCCTCCAAGG 59.175 66.667 0.00 0.00 36.46 3.61
331 332 2.832672 GCAAAGGCTCGAATAGTTGG 57.167 50.000 0.00 0.00 36.96 3.77
369 370 3.006967 ACTGAAGATCGGGGTATGTATGC 59.993 47.826 0.00 0.00 0.00 3.14
406 407 7.715249 ACATAGTTGTGGTGTACATTATGATCC 59.285 37.037 0.00 0.00 38.34 3.36
415 416 6.347725 GGTGTACATTATGATCCGCTTCATTC 60.348 42.308 0.00 0.00 37.51 2.67
436 437 2.558795 CTCTCCTCGAAGACTTGTTGGA 59.441 50.000 0.00 0.00 0.00 3.53
493 494 2.941064 CACTGCACATATGTTGGGAGAG 59.059 50.000 17.88 8.98 0.00 3.20
505 506 0.543410 TGGGAGAGGAGCCGTTTACA 60.543 55.000 0.00 0.00 0.00 2.41
555 556 7.544566 AGTGAAATTGACCATACTTGTAGTACG 59.455 37.037 0.00 0.00 32.84 3.67
556 557 7.330208 GTGAAATTGACCATACTTGTAGTACGT 59.670 37.037 0.00 0.00 32.84 3.57
557 558 8.522003 TGAAATTGACCATACTTGTAGTACGTA 58.478 33.333 0.00 0.00 32.84 3.57
558 559 8.693542 AAATTGACCATACTTGTAGTACGTAC 57.306 34.615 18.10 18.10 32.84 3.67
560 561 6.668541 TGACCATACTTGTAGTACGTACTC 57.331 41.667 30.53 21.12 37.73 2.59
561 562 5.291858 TGACCATACTTGTAGTACGTACTCG 59.708 44.000 30.53 18.88 43.34 4.18
596 1912 2.777692 TCCAGTGAAAAGTCAACCTCCT 59.222 45.455 0.00 0.00 34.87 3.69
597 1913 2.880890 CCAGTGAAAAGTCAACCTCCTG 59.119 50.000 0.00 0.00 34.87 3.86
866 2350 2.168496 TCGTCTCCTCAGTTTACTGGG 58.832 52.381 9.82 6.42 44.00 4.45
885 2369 1.377536 GGCTTCATCCTGAGTTGAGC 58.622 55.000 0.00 0.00 0.00 4.26
980 2464 6.066032 GCTCAAATCTCTCTACCCTACTACT 58.934 44.000 0.00 0.00 0.00 2.57
982 2466 7.255346 GCTCAAATCTCTCTACCCTACTACTTC 60.255 44.444 0.00 0.00 0.00 3.01
984 2468 9.000978 TCAAATCTCTCTACCCTACTACTTCTA 57.999 37.037 0.00 0.00 0.00 2.10
986 2470 8.571460 AATCTCTCTACCCTACTACTTCTAGT 57.429 38.462 0.00 0.00 37.04 2.57
987 2471 7.993349 TCTCTCTACCCTACTACTTCTAGTT 57.007 40.000 0.00 0.00 34.79 2.24
989 2473 8.923270 TCTCTCTACCCTACTACTTCTAGTTAC 58.077 40.741 0.00 0.00 34.79 2.50
990 2474 8.852671 TCTCTACCCTACTACTTCTAGTTACT 57.147 38.462 0.00 0.00 34.79 2.24
991 2475 9.278011 TCTCTACCCTACTACTTCTAGTTACTT 57.722 37.037 0.00 0.00 34.79 2.24
992 2476 9.904198 CTCTACCCTACTACTTCTAGTTACTTT 57.096 37.037 0.00 0.00 34.79 2.66
1029 2513 4.286707 ACACAGGCAGGAGTACATACATA 58.713 43.478 0.00 0.00 0.00 2.29
1030 2514 4.099573 ACACAGGCAGGAGTACATACATAC 59.900 45.833 0.00 0.00 0.00 2.39
1032 2516 4.714802 ACAGGCAGGAGTACATACATACAA 59.285 41.667 0.00 0.00 0.00 2.41
1033 2517 5.163405 ACAGGCAGGAGTACATACATACAAG 60.163 44.000 0.00 0.00 0.00 3.16
1034 2518 5.069119 CAGGCAGGAGTACATACATACAAGA 59.931 44.000 0.00 0.00 0.00 3.02
1039 2539 8.141909 GCAGGAGTACATACATACAAGATACAA 58.858 37.037 0.00 0.00 0.00 2.41
1119 2631 4.617762 GGAGTACCAGCAAGTGTACTACAC 60.618 50.000 10.90 10.90 45.69 2.90
1159 2702 5.067273 CGAAGGTCATCTGATCTACTAGGT 58.933 45.833 0.00 0.00 33.65 3.08
1165 2721 3.885976 TCTGATCTACTAGGTGGGAGG 57.114 52.381 0.00 0.00 0.00 4.30
1223 2790 0.473694 TCAGCCTCCAAGACAAGGGA 60.474 55.000 0.00 0.00 32.98 4.20
1224 2791 0.401738 CAGCCTCCAAGACAAGGGAA 59.598 55.000 0.00 0.00 32.98 3.97
1225 2792 0.695347 AGCCTCCAAGACAAGGGAAG 59.305 55.000 0.00 0.00 32.98 3.46
1226 2793 0.322906 GCCTCCAAGACAAGGGAAGG 60.323 60.000 0.00 0.00 32.98 3.46
1326 2893 6.293900 CCTTGCCCATAATTTTTGTTCAAACC 60.294 38.462 0.00 0.00 0.00 3.27
1372 2942 3.632645 CCCTCTATTAACTCACTCCCCCA 60.633 52.174 0.00 0.00 0.00 4.96
1402 2972 4.717629 TTGCGACCGTCGGAGCAG 62.718 66.667 27.66 14.39 42.14 4.24
1435 3005 2.413371 GCTCGACCAGCTTGTTGAATTC 60.413 50.000 9.08 0.00 45.83 2.17
1869 3454 3.343788 GACCTGGTGCTCCGACGAG 62.344 68.421 2.82 0.00 39.33 4.18
2040 3625 1.227497 GCGGGAGAAGCTGATGGAG 60.227 63.158 0.00 0.00 0.00 3.86
2299 3884 3.248248 TTCCGTGCCCCCTCCTAGT 62.248 63.158 0.00 0.00 0.00 2.57
2300 3885 3.155167 CCGTGCCCCCTCCTAGTC 61.155 72.222 0.00 0.00 0.00 2.59
2301 3886 3.155167 CGTGCCCCCTCCTAGTCC 61.155 72.222 0.00 0.00 0.00 3.85
2312 3897 1.423921 CTCCTAGTCCTCCTCCTCCTC 59.576 61.905 0.00 0.00 0.00 3.71
2336 3921 1.679032 CCCAATTCCTTCCCGTCAGAC 60.679 57.143 0.00 0.00 0.00 3.51
2342 3927 1.472662 CCTTCCCGTCAGACCTGTGT 61.473 60.000 0.00 0.00 0.00 3.72
2343 3928 1.254026 CTTCCCGTCAGACCTGTGTA 58.746 55.000 0.00 0.00 0.00 2.90
2344 3929 1.202582 CTTCCCGTCAGACCTGTGTAG 59.797 57.143 0.00 0.00 0.00 2.74
2345 3930 0.111832 TCCCGTCAGACCTGTGTAGT 59.888 55.000 0.00 0.00 0.00 2.73
2346 3931 1.352017 TCCCGTCAGACCTGTGTAGTA 59.648 52.381 0.00 0.00 0.00 1.82
2347 3932 1.471684 CCCGTCAGACCTGTGTAGTAC 59.528 57.143 0.00 0.00 0.00 2.73
2348 3933 2.434428 CCGTCAGACCTGTGTAGTACT 58.566 52.381 0.00 0.00 0.00 2.73
2349 3934 2.161808 CCGTCAGACCTGTGTAGTACTG 59.838 54.545 5.39 0.00 0.00 2.74
2379 3964 2.855963 GTGCATGAAAAATGGCTGATCG 59.144 45.455 0.00 0.00 0.00 3.69
2382 3967 4.157472 TGCATGAAAAATGGCTGATCGTAA 59.843 37.500 0.00 0.00 0.00 3.18
2383 3968 5.163530 TGCATGAAAAATGGCTGATCGTAAT 60.164 36.000 0.00 0.00 0.00 1.89
2384 3969 6.039159 TGCATGAAAAATGGCTGATCGTAATA 59.961 34.615 0.00 0.00 0.00 0.98
2385 3970 7.086376 GCATGAAAAATGGCTGATCGTAATAT 58.914 34.615 0.00 0.00 0.00 1.28
2426 4011 7.968956 TGAAGTGTCTCTTTCATTCTACGTATC 59.031 37.037 0.00 0.00 36.40 2.24
2427 4012 6.487960 AGTGTCTCTTTCATTCTACGTATCG 58.512 40.000 0.00 0.00 0.00 2.92
2428 4013 5.171695 GTGTCTCTTTCATTCTACGTATCGC 59.828 44.000 0.00 0.00 0.00 4.58
2429 4014 5.163693 TGTCTCTTTCATTCTACGTATCGCA 60.164 40.000 0.00 0.00 0.00 5.10
2430 4015 5.915758 GTCTCTTTCATTCTACGTATCGCAT 59.084 40.000 0.00 0.00 0.00 4.73
2431 4016 6.418226 GTCTCTTTCATTCTACGTATCGCATT 59.582 38.462 0.00 0.00 0.00 3.56
2432 4017 7.590322 GTCTCTTTCATTCTACGTATCGCATTA 59.410 37.037 0.00 0.00 0.00 1.90
2433 4018 8.297426 TCTCTTTCATTCTACGTATCGCATTAT 58.703 33.333 0.00 0.00 0.00 1.28
2434 4019 8.449085 TCTTTCATTCTACGTATCGCATTATC 57.551 34.615 0.00 0.00 0.00 1.75
2435 4020 8.079809 TCTTTCATTCTACGTATCGCATTATCA 58.920 33.333 0.00 0.00 0.00 2.15
2436 4021 7.796958 TTCATTCTACGTATCGCATTATCAG 57.203 36.000 0.00 0.00 0.00 2.90
2437 4022 5.800438 TCATTCTACGTATCGCATTATCAGC 59.200 40.000 0.00 0.00 0.00 4.26
2451 4036 7.943735 GCATTATCAGCGTCAATTATATGTG 57.056 36.000 0.00 0.00 0.00 3.21
2452 4037 7.521529 GCATTATCAGCGTCAATTATATGTGT 58.478 34.615 0.00 0.00 0.00 3.72
2453 4038 8.017373 GCATTATCAGCGTCAATTATATGTGTT 58.983 33.333 0.00 0.00 0.00 3.32
2454 4039 9.882996 CATTATCAGCGTCAATTATATGTGTTT 57.117 29.630 0.00 0.00 0.00 2.83
2456 4041 7.792374 ATCAGCGTCAATTATATGTGTTTCT 57.208 32.000 0.00 0.00 0.00 2.52
2457 4042 7.609760 TCAGCGTCAATTATATGTGTTTCTT 57.390 32.000 0.00 0.00 0.00 2.52
2458 4043 7.684670 TCAGCGTCAATTATATGTGTTTCTTC 58.315 34.615 0.00 0.00 0.00 2.87
2459 4044 7.549134 TCAGCGTCAATTATATGTGTTTCTTCT 59.451 33.333 0.00 0.00 0.00 2.85
2460 4045 8.177663 CAGCGTCAATTATATGTGTTTCTTCTT 58.822 33.333 0.00 0.00 0.00 2.52
2461 4046 8.730680 AGCGTCAATTATATGTGTTTCTTCTTT 58.269 29.630 0.00 0.00 0.00 2.52
2462 4047 8.788813 GCGTCAATTATATGTGTTTCTTCTTTG 58.211 33.333 0.00 0.00 0.00 2.77
2468 4053 6.727824 ATATGTGTTTCTTCTTTGAGTCCG 57.272 37.500 0.00 0.00 0.00 4.79
2469 4054 4.131649 TGTGTTTCTTCTTTGAGTCCGA 57.868 40.909 0.00 0.00 0.00 4.55
2470 4055 4.119862 TGTGTTTCTTCTTTGAGTCCGAG 58.880 43.478 0.00 0.00 0.00 4.63
2471 4056 4.142026 TGTGTTTCTTCTTTGAGTCCGAGA 60.142 41.667 0.00 0.00 0.00 4.04
2472 4057 4.209495 GTGTTTCTTCTTTGAGTCCGAGAC 59.791 45.833 0.00 0.00 0.00 3.36
2473 4058 4.099573 TGTTTCTTCTTTGAGTCCGAGACT 59.900 41.667 6.29 6.29 46.42 3.24
2474 4059 4.939052 TTCTTCTTTGAGTCCGAGACTT 57.061 40.909 7.80 0.00 43.53 3.01
2475 4060 4.939052 TCTTCTTTGAGTCCGAGACTTT 57.061 40.909 7.80 0.00 43.53 2.66
2476 4061 4.621991 TCTTCTTTGAGTCCGAGACTTTG 58.378 43.478 7.80 1.22 43.53 2.77
2477 4062 4.099573 TCTTCTTTGAGTCCGAGACTTTGT 59.900 41.667 7.80 0.00 43.53 2.83
2478 4063 4.402056 TCTTTGAGTCCGAGACTTTGTT 57.598 40.909 7.80 0.00 43.53 2.83
2479 4064 5.524971 TCTTTGAGTCCGAGACTTTGTTA 57.475 39.130 7.80 0.00 43.53 2.41
2480 4065 6.097915 TCTTTGAGTCCGAGACTTTGTTAT 57.902 37.500 7.80 0.00 43.53 1.89
2481 4066 5.926542 TCTTTGAGTCCGAGACTTTGTTATG 59.073 40.000 7.80 0.00 43.53 1.90
2482 4067 4.866508 TGAGTCCGAGACTTTGTTATGT 57.133 40.909 7.80 0.00 43.53 2.29
2483 4068 4.806330 TGAGTCCGAGACTTTGTTATGTC 58.194 43.478 7.80 0.00 43.53 3.06
2484 4069 4.523173 TGAGTCCGAGACTTTGTTATGTCT 59.477 41.667 7.80 0.00 43.53 3.41
2491 4076 5.707242 AGACTTTGTTATGTCTCAGTCGA 57.293 39.130 0.00 0.00 39.04 4.20
2492 4077 6.274157 AGACTTTGTTATGTCTCAGTCGAT 57.726 37.500 0.00 0.00 39.04 3.59
2493 4078 6.096036 AGACTTTGTTATGTCTCAGTCGATG 58.904 40.000 0.00 0.00 39.04 3.84
2494 4079 5.784177 ACTTTGTTATGTCTCAGTCGATGT 58.216 37.500 0.00 0.00 0.00 3.06
2495 4080 6.223852 ACTTTGTTATGTCTCAGTCGATGTT 58.776 36.000 0.00 0.00 0.00 2.71
2496 4081 7.375834 ACTTTGTTATGTCTCAGTCGATGTTA 58.624 34.615 0.00 0.00 0.00 2.41
2497 4082 7.328737 ACTTTGTTATGTCTCAGTCGATGTTAC 59.671 37.037 0.00 0.00 0.00 2.50
2498 4083 6.262193 TGTTATGTCTCAGTCGATGTTACA 57.738 37.500 0.00 0.00 0.00 2.41
2499 4084 6.863275 TGTTATGTCTCAGTCGATGTTACAT 58.137 36.000 0.00 0.00 38.25 2.29
2500 4085 7.320399 TGTTATGTCTCAGTCGATGTTACATT 58.680 34.615 0.00 0.00 36.96 2.71
2501 4086 7.488150 TGTTATGTCTCAGTCGATGTTACATTC 59.512 37.037 0.00 0.00 36.96 2.67
2502 4087 5.644977 TGTCTCAGTCGATGTTACATTCT 57.355 39.130 0.00 0.00 0.00 2.40
2503 4088 6.025749 TGTCTCAGTCGATGTTACATTCTT 57.974 37.500 0.00 0.00 0.00 2.52
2504 4089 6.455647 TGTCTCAGTCGATGTTACATTCTTT 58.544 36.000 0.00 0.00 0.00 2.52
2505 4090 6.929049 TGTCTCAGTCGATGTTACATTCTTTT 59.071 34.615 0.00 0.00 0.00 2.27
2506 4091 7.095649 TGTCTCAGTCGATGTTACATTCTTTTG 60.096 37.037 0.00 0.00 0.00 2.44
2507 4092 7.116376 GTCTCAGTCGATGTTACATTCTTTTGA 59.884 37.037 0.00 0.71 0.00 2.69
2508 4093 7.819415 TCTCAGTCGATGTTACATTCTTTTGAT 59.181 33.333 0.00 0.00 0.00 2.57
2509 4094 8.322906 TCAGTCGATGTTACATTCTTTTGATT 57.677 30.769 0.00 0.00 0.00 2.57
2510 4095 8.783093 TCAGTCGATGTTACATTCTTTTGATTT 58.217 29.630 0.00 0.00 0.00 2.17
2511 4096 9.398170 CAGTCGATGTTACATTCTTTTGATTTT 57.602 29.630 0.00 0.00 0.00 1.82
2512 4097 9.398170 AGTCGATGTTACATTCTTTTGATTTTG 57.602 29.630 0.00 0.00 0.00 2.44
2513 4098 9.180678 GTCGATGTTACATTCTTTTGATTTTGT 57.819 29.630 0.00 0.00 0.00 2.83
2522 4107 9.696917 ACATTCTTTTGATTTTGTATGGAGTTC 57.303 29.630 0.00 0.00 0.00 3.01
2523 4108 9.695526 CATTCTTTTGATTTTGTATGGAGTTCA 57.304 29.630 0.00 0.00 0.00 3.18
2582 4167 8.387190 TGCTATATCATTTGATTGAGACTTGG 57.613 34.615 0.00 0.00 36.05 3.61
2583 4168 7.994911 TGCTATATCATTTGATTGAGACTTGGT 59.005 33.333 0.00 0.00 36.05 3.67
2584 4169 8.844244 GCTATATCATTTGATTGAGACTTGGTT 58.156 33.333 0.00 0.00 36.05 3.67
2588 4173 9.739276 TATCATTTGATTGAGACTTGGTTAAGT 57.261 29.630 0.00 0.00 41.41 2.24
2602 4187 8.608844 ACTTGGTTAAGTCTTAATTGACTGAG 57.391 34.615 8.27 3.79 43.53 3.35
2603 4188 8.429641 ACTTGGTTAAGTCTTAATTGACTGAGA 58.570 33.333 8.27 0.00 43.53 3.27
2604 4189 8.603242 TTGGTTAAGTCTTAATTGACTGAGAC 57.397 34.615 8.27 0.00 45.49 3.36
2605 4190 7.159372 TGGTTAAGTCTTAATTGACTGAGACC 58.841 38.462 8.27 13.31 45.49 3.85
2606 4191 7.016268 TGGTTAAGTCTTAATTGACTGAGACCT 59.984 37.037 8.27 6.03 45.49 3.85
2607 4192 8.529476 GGTTAAGTCTTAATTGACTGAGACCTA 58.471 37.037 8.27 0.00 45.49 3.08
2608 4193 9.575783 GTTAAGTCTTAATTGACTGAGACCTAG 57.424 37.037 8.27 0.00 45.49 3.02
2609 4194 9.529823 TTAAGTCTTAATTGACTGAGACCTAGA 57.470 33.333 0.65 0.00 45.49 2.43
2610 4195 7.399245 AGTCTTAATTGACTGAGACCTAGAC 57.601 40.000 0.00 0.00 44.64 2.59
2611 4196 6.948886 AGTCTTAATTGACTGAGACCTAGACA 59.051 38.462 0.00 0.00 44.64 3.41
2612 4197 7.030768 GTCTTAATTGACTGAGACCTAGACAC 58.969 42.308 0.00 0.00 34.00 3.67
2613 4198 6.719829 TCTTAATTGACTGAGACCTAGACACA 59.280 38.462 0.00 0.00 0.00 3.72
2614 4199 4.792521 ATTGACTGAGACCTAGACACAC 57.207 45.455 0.00 0.00 0.00 3.82
2615 4200 3.510531 TGACTGAGACCTAGACACACT 57.489 47.619 0.00 0.00 0.00 3.55
2616 4201 4.635699 TGACTGAGACCTAGACACACTA 57.364 45.455 0.00 0.00 0.00 2.74
2617 4202 4.981812 TGACTGAGACCTAGACACACTAA 58.018 43.478 0.00 0.00 0.00 2.24
2618 4203 5.004448 TGACTGAGACCTAGACACACTAAG 58.996 45.833 0.00 0.00 0.00 2.18
2619 4204 4.988029 ACTGAGACCTAGACACACTAAGT 58.012 43.478 0.00 0.00 0.00 2.24
2620 4205 5.386924 ACTGAGACCTAGACACACTAAGTT 58.613 41.667 0.00 0.00 0.00 2.66
2621 4206 6.540995 ACTGAGACCTAGACACACTAAGTTA 58.459 40.000 0.00 0.00 0.00 2.24
2622 4207 7.002879 ACTGAGACCTAGACACACTAAGTTAA 58.997 38.462 0.00 0.00 0.00 2.01
2623 4208 7.504911 ACTGAGACCTAGACACACTAAGTTAAA 59.495 37.037 0.00 0.00 0.00 1.52
2624 4209 8.241497 TGAGACCTAGACACACTAAGTTAAAA 57.759 34.615 0.00 0.00 0.00 1.52
2625 4210 8.867097 TGAGACCTAGACACACTAAGTTAAAAT 58.133 33.333 0.00 0.00 0.00 1.82
2652 4237 8.864069 ATATGAAGTGTCTCTTTCATTCTACG 57.136 34.615 5.19 0.00 36.40 3.51
2653 4238 6.085555 TGAAGTGTCTCTTTCATTCTACGT 57.914 37.500 0.00 0.00 36.40 3.57
2654 4239 5.920840 TGAAGTGTCTCTTTCATTCTACGTG 59.079 40.000 0.00 0.00 36.40 4.49
2655 4240 5.455056 AGTGTCTCTTTCATTCTACGTGT 57.545 39.130 0.00 0.00 0.00 4.49
2656 4241 6.570672 AGTGTCTCTTTCATTCTACGTGTA 57.429 37.500 0.00 0.00 0.00 2.90
2681 4266 6.818644 AGCATTATCGGCGTCAATTATATCTT 59.181 34.615 6.85 0.00 36.08 2.40
2703 4288 8.874745 TCTTTTTATATTTCTGTTTCTTCGCG 57.125 30.769 0.00 0.00 0.00 5.87
2704 4289 7.960738 TCTTTTTATATTTCTGTTTCTTCGCGG 59.039 33.333 6.13 0.00 0.00 6.46
2705 4290 5.728351 TTATATTTCTGTTTCTTCGCGGG 57.272 39.130 6.13 0.00 0.00 6.13
2706 4291 1.892209 ATTTCTGTTTCTTCGCGGGT 58.108 45.000 6.13 0.00 0.00 5.28
2708 4293 1.503818 TTCTGTTTCTTCGCGGGTGC 61.504 55.000 6.13 0.00 37.91 5.01
2712 4326 1.525077 TTTCTTCGCGGGTGCAAGT 60.525 52.632 6.13 0.00 42.97 3.16
2713 4327 1.098712 TTTCTTCGCGGGTGCAAGTT 61.099 50.000 6.13 0.00 42.97 2.66
2723 4337 2.286772 CGGGTGCAAGTTGTACAAAGTC 60.287 50.000 23.06 7.44 34.53 3.01
2726 4340 3.064271 GGTGCAAGTTGTACAAAGTCGAA 59.936 43.478 23.06 0.00 34.53 3.71
2740 4354 9.155053 GTACAAAGTCGAAACAGTTATTTTGAG 57.845 33.333 8.68 0.00 33.52 3.02
2743 4357 9.107367 CAAAGTCGAAACAGTTATTTTGAGATC 57.893 33.333 0.00 0.00 33.52 2.75
2745 4359 6.866770 AGTCGAAACAGTTATTTTGAGATCGA 59.133 34.615 0.00 0.00 33.52 3.59
2746 4360 7.384115 AGTCGAAACAGTTATTTTGAGATCGAA 59.616 33.333 3.21 0.00 37.34 3.71
2763 4377 7.492669 TGAGATCGAAGGAGTATTTGTTTCATC 59.507 37.037 0.00 0.00 0.00 2.92
2764 4378 7.331026 AGATCGAAGGAGTATTTGTTTCATCA 58.669 34.615 0.00 0.00 0.00 3.07
2765 4379 6.968131 TCGAAGGAGTATTTGTTTCATCAG 57.032 37.500 0.00 0.00 0.00 2.90
2766 4380 6.697395 TCGAAGGAGTATTTGTTTCATCAGA 58.303 36.000 0.00 0.00 0.00 3.27
2767 4381 7.158697 TCGAAGGAGTATTTGTTTCATCAGAA 58.841 34.615 0.00 0.00 0.00 3.02
2768 4382 7.824289 TCGAAGGAGTATTTGTTTCATCAGAAT 59.176 33.333 0.00 0.00 32.89 2.40
2769 4383 8.119226 CGAAGGAGTATTTGTTTCATCAGAATC 58.881 37.037 0.00 0.00 32.89 2.52
2804 4418 1.937899 CCAAAACGAGACAAAGACGGT 59.062 47.619 0.00 0.00 0.00 4.83
2863 4477 0.670546 CTCCGACCGCACAGAATTGT 60.671 55.000 0.00 0.00 38.31 2.71
2931 4572 2.272146 CATCCACCCCTGAACCCG 59.728 66.667 0.00 0.00 0.00 5.28
2952 4593 4.435436 CAGCGCGGTAGCCAGTCA 62.435 66.667 11.92 0.00 41.18 3.41
2955 4596 2.507102 CGCGGTAGCCAGTCACTG 60.507 66.667 0.00 0.00 41.18 3.66
2958 4599 2.650116 CGGTAGCCAGTCACTGCCT 61.650 63.158 0.00 0.00 37.73 4.75
2959 4600 1.078848 GGTAGCCAGTCACTGCCTG 60.079 63.158 0.00 0.00 37.00 4.85
2984 4671 2.380410 CCGGCAACACGAGCTGTAC 61.380 63.158 0.00 0.00 36.64 2.90
3031 4743 0.101579 ACGCCAAAACAAAACCTCCG 59.898 50.000 0.00 0.00 0.00 4.63
3043 4755 4.765339 ACAAAACCTCCGGATTTCCTTAAG 59.235 41.667 3.57 0.00 0.00 1.85
3085 4797 2.430921 GTATCTCGGCGCGGATGG 60.431 66.667 18.58 7.97 0.00 3.51
3120 4833 1.102809 TGATTGACGGCATGATGGGC 61.103 55.000 0.00 0.00 0.00 5.36
3197 4915 3.803162 GAGGGGAGGGAGCCAAGC 61.803 72.222 0.00 0.00 0.00 4.01
3282 5014 2.826738 GTCGCGAGCCTCTCCTCT 60.827 66.667 10.24 0.00 0.00 3.69
3293 5025 0.735632 CTCTCCTCTTGCTGTGTCGC 60.736 60.000 0.00 0.00 0.00 5.19
3294 5026 1.181741 TCTCCTCTTGCTGTGTCGCT 61.182 55.000 0.00 0.00 0.00 4.93
3301 5033 4.314440 GCTGTGTCGCTGGGGTGA 62.314 66.667 0.00 0.00 0.00 4.02
3330 5070 2.730672 GCGCACATGACACGACTCC 61.731 63.158 0.30 0.00 0.00 3.85
3363 5103 0.461516 GTCTTACCTTACCGGCAGGC 60.462 60.000 18.48 0.39 42.76 4.85
3364 5104 0.905809 TCTTACCTTACCGGCAGGCA 60.906 55.000 18.48 4.70 42.76 4.75
3365 5105 0.462047 CTTACCTTACCGGCAGGCAG 60.462 60.000 18.48 11.68 42.76 4.85
3366 5106 1.906105 TTACCTTACCGGCAGGCAGG 61.906 60.000 18.48 17.30 43.67 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
267 268 4.397417 CCTTCAAGATCATCAAACTCCCAC 59.603 45.833 0.00 0.00 0.00 4.61
331 332 6.968131 TCTTCAGTGCTAATGATTGTACAC 57.032 37.500 0.00 0.00 0.00 2.90
390 391 4.377021 TGAAGCGGATCATAATGTACACC 58.623 43.478 0.00 0.00 0.00 4.16
406 407 2.098280 TCTTCGAGGAGAGAATGAAGCG 59.902 50.000 0.00 0.00 36.77 4.68
415 416 2.558795 TCCAACAAGTCTTCGAGGAGAG 59.441 50.000 0.00 0.00 0.00 3.20
436 437 0.745845 GCGACCTTCACAGGATGCAT 60.746 55.000 0.00 0.00 44.19 3.96
493 494 3.907894 TCAAACATTGTAAACGGCTCC 57.092 42.857 0.00 0.00 0.00 4.70
505 506 3.084039 AGATGTGGACGCATCAAACATT 58.916 40.909 23.17 3.56 45.58 2.71
555 556 3.001736 GGAGATGTACCACGTACGAGTAC 59.998 52.174 29.50 29.50 41.41 2.73
556 557 3.198068 GGAGATGTACCACGTACGAGTA 58.802 50.000 24.41 19.01 41.41 2.59
557 558 2.012673 GGAGATGTACCACGTACGAGT 58.987 52.381 24.41 20.05 41.41 4.18
558 559 2.011947 TGGAGATGTACCACGTACGAG 58.988 52.381 24.41 14.76 41.41 4.18
560 561 1.741706 ACTGGAGATGTACCACGTACG 59.258 52.381 15.01 15.01 41.41 3.67
561 562 2.751259 TCACTGGAGATGTACCACGTAC 59.249 50.000 0.00 0.00 39.24 3.67
563 564 1.919240 TCACTGGAGATGTACCACGT 58.081 50.000 0.00 0.00 33.57 4.49
564 565 3.313012 TTTCACTGGAGATGTACCACG 57.687 47.619 0.00 0.00 33.57 4.94
565 566 4.642429 ACTTTTCACTGGAGATGTACCAC 58.358 43.478 0.00 0.00 33.57 4.16
566 567 4.346709 TGACTTTTCACTGGAGATGTACCA 59.653 41.667 0.00 0.00 35.96 3.25
567 568 4.894784 TGACTTTTCACTGGAGATGTACC 58.105 43.478 0.00 0.00 0.00 3.34
596 1912 0.669318 CGCAGACGGGTAAAAGAGCA 60.669 55.000 0.00 0.00 34.97 4.26
597 1913 0.669625 ACGCAGACGGGTAAAAGAGC 60.670 55.000 0.00 0.00 46.04 4.09
790 2112 4.872691 AGAAAAAGAGCACGTATGGATCAG 59.127 41.667 0.00 0.00 0.00 2.90
831 2153 8.473358 TGAGGAGACGAATTATTACCTATGAA 57.527 34.615 0.00 0.00 0.00 2.57
834 2156 8.480133 AACTGAGGAGACGAATTATTACCTAT 57.520 34.615 0.00 0.00 0.00 2.57
885 2369 3.244105 CGCAAACGGTGTCAGGAG 58.756 61.111 0.00 0.00 34.97 3.69
917 2401 4.843220 ATGCATGAATAAAGCTACCAGC 57.157 40.909 0.00 0.00 42.84 4.85
989 2473 8.136800 TGCCTGTGTATTATTGCATGAATAAAG 58.863 33.333 0.00 0.00 39.46 1.85
990 2474 8.005192 TGCCTGTGTATTATTGCATGAATAAA 57.995 30.769 0.00 0.00 39.46 1.40
991 2475 7.255555 CCTGCCTGTGTATTATTGCATGAATAA 60.256 37.037 0.00 4.96 40.15 1.40
992 2476 6.207221 CCTGCCTGTGTATTATTGCATGAATA 59.793 38.462 0.00 0.00 0.00 1.75
993 2477 5.010314 CCTGCCTGTGTATTATTGCATGAAT 59.990 40.000 0.00 0.00 0.00 2.57
994 2478 4.338964 CCTGCCTGTGTATTATTGCATGAA 59.661 41.667 0.00 0.00 0.00 2.57
995 2479 3.884693 CCTGCCTGTGTATTATTGCATGA 59.115 43.478 0.00 0.00 0.00 3.07
996 2480 3.884693 TCCTGCCTGTGTATTATTGCATG 59.115 43.478 0.00 0.00 0.00 4.06
997 2481 4.139786 CTCCTGCCTGTGTATTATTGCAT 58.860 43.478 0.00 0.00 0.00 3.96
998 2482 3.054434 ACTCCTGCCTGTGTATTATTGCA 60.054 43.478 0.00 0.00 0.00 4.08
999 2483 3.545703 ACTCCTGCCTGTGTATTATTGC 58.454 45.455 0.00 0.00 0.00 3.56
1000 2484 5.670485 TGTACTCCTGCCTGTGTATTATTG 58.330 41.667 0.00 0.00 0.00 1.90
1001 2485 5.950544 TGTACTCCTGCCTGTGTATTATT 57.049 39.130 0.00 0.00 0.00 1.40
1002 2486 6.553476 TGTATGTACTCCTGCCTGTGTATTAT 59.447 38.462 0.00 0.00 0.00 1.28
1003 2487 5.894964 TGTATGTACTCCTGCCTGTGTATTA 59.105 40.000 0.00 0.00 0.00 0.98
1004 2488 4.714802 TGTATGTACTCCTGCCTGTGTATT 59.285 41.667 0.00 0.00 0.00 1.89
1029 2513 7.931948 AGCAAACAGTAACTAGTTGTATCTTGT 59.068 33.333 18.56 9.74 0.00 3.16
1030 2514 8.311650 AGCAAACAGTAACTAGTTGTATCTTG 57.688 34.615 18.56 15.21 0.00 3.02
1032 2516 7.815068 CAGAGCAAACAGTAACTAGTTGTATCT 59.185 37.037 18.56 8.21 0.00 1.98
1033 2517 7.599245 ACAGAGCAAACAGTAACTAGTTGTATC 59.401 37.037 18.56 6.17 0.00 2.24
1034 2518 7.385205 CACAGAGCAAACAGTAACTAGTTGTAT 59.615 37.037 18.56 0.89 0.00 2.29
1039 2539 5.050490 CACACAGAGCAAACAGTAACTAGT 58.950 41.667 0.00 0.00 0.00 2.57
1119 2631 3.746492 CCTTCGTTCCTAGTTGTTGAAGG 59.254 47.826 11.32 11.32 43.35 3.46
1132 2675 3.810310 AGATCAGATGACCTTCGTTCC 57.190 47.619 0.00 0.00 0.00 3.62
1159 2702 1.461268 TTGTGCTCACTCCCTCCCA 60.461 57.895 1.47 0.00 0.00 4.37
1417 2987 2.350772 GGTGAATTCAACAAGCTGGTCG 60.351 50.000 18.74 0.00 32.77 4.79
1637 3213 4.043200 GCGCCACCTTGTCCTTGC 62.043 66.667 0.00 0.00 0.00 4.01
1638 3214 3.365265 GGCGCCACCTTGTCCTTG 61.365 66.667 24.80 0.00 34.51 3.61
1909 3494 2.401766 CCTTGTCCCTGTCATGCGC 61.402 63.158 0.00 0.00 0.00 6.09
2040 3625 3.827898 CGGACGTGCTCCTCCTCC 61.828 72.222 5.27 0.00 36.80 4.30
2117 3702 4.717629 CGCACGAGTTCCTCCGCA 62.718 66.667 0.00 0.00 0.00 5.69
2292 3877 1.423921 GAGGAGGAGGAGGACTAGGAG 59.576 61.905 0.00 0.00 0.00 3.69
2299 3884 1.365105 GGGCTAGAGGAGGAGGAGGA 61.365 65.000 0.00 0.00 0.00 3.71
2300 3885 1.155155 GGGCTAGAGGAGGAGGAGG 59.845 68.421 0.00 0.00 0.00 4.30
2301 3886 0.263172 TTGGGCTAGAGGAGGAGGAG 59.737 60.000 0.00 0.00 0.00 3.69
2312 3897 0.546598 ACGGGAAGGAATTGGGCTAG 59.453 55.000 0.00 0.00 0.00 3.42
2336 3921 4.692625 ACACGTACTACAGTACTACACAGG 59.307 45.833 15.57 3.30 46.43 4.00
2342 3927 4.937015 TCATGCACACGTACTACAGTACTA 59.063 41.667 15.57 0.00 46.43 1.82
2343 3928 3.754850 TCATGCACACGTACTACAGTACT 59.245 43.478 15.57 0.00 46.43 2.73
2344 3929 4.087510 TCATGCACACGTACTACAGTAC 57.912 45.455 9.11 9.11 45.47 2.73
2345 3930 4.769859 TTCATGCACACGTACTACAGTA 57.230 40.909 0.00 0.00 0.00 2.74
2346 3931 3.653539 TTCATGCACACGTACTACAGT 57.346 42.857 0.00 0.00 0.00 3.55
2347 3932 4.983215 TTTTCATGCACACGTACTACAG 57.017 40.909 0.00 0.00 0.00 2.74
2348 3933 5.334491 CCATTTTTCATGCACACGTACTACA 60.334 40.000 0.00 0.00 0.00 2.74
2349 3934 5.086058 CCATTTTTCATGCACACGTACTAC 58.914 41.667 0.00 0.00 0.00 2.73
2427 4012 7.521529 ACACATATAATTGACGCTGATAATGC 58.478 34.615 0.00 0.00 0.00 3.56
2428 4013 9.882996 AAACACATATAATTGACGCTGATAATG 57.117 29.630 0.00 0.00 0.00 1.90
2430 4015 9.325198 AGAAACACATATAATTGACGCTGATAA 57.675 29.630 0.00 0.00 0.00 1.75
2431 4016 8.887036 AGAAACACATATAATTGACGCTGATA 57.113 30.769 0.00 0.00 0.00 2.15
2432 4017 7.792374 AGAAACACATATAATTGACGCTGAT 57.208 32.000 0.00 0.00 0.00 2.90
2433 4018 7.549134 AGAAGAAACACATATAATTGACGCTGA 59.451 33.333 0.00 0.00 0.00 4.26
2434 4019 7.688372 AGAAGAAACACATATAATTGACGCTG 58.312 34.615 0.00 0.00 0.00 5.18
2435 4020 7.849804 AGAAGAAACACATATAATTGACGCT 57.150 32.000 0.00 0.00 0.00 5.07
2436 4021 8.788813 CAAAGAAGAAACACATATAATTGACGC 58.211 33.333 0.00 0.00 0.00 5.19
2442 4027 8.883731 CGGACTCAAAGAAGAAACACATATAAT 58.116 33.333 0.00 0.00 0.00 1.28
2443 4028 8.092068 TCGGACTCAAAGAAGAAACACATATAA 58.908 33.333 0.00 0.00 0.00 0.98
2444 4029 7.608153 TCGGACTCAAAGAAGAAACACATATA 58.392 34.615 0.00 0.00 0.00 0.86
2445 4030 6.464222 TCGGACTCAAAGAAGAAACACATAT 58.536 36.000 0.00 0.00 0.00 1.78
2446 4031 5.849510 TCGGACTCAAAGAAGAAACACATA 58.150 37.500 0.00 0.00 0.00 2.29
2447 4032 4.703897 TCGGACTCAAAGAAGAAACACAT 58.296 39.130 0.00 0.00 0.00 3.21
2448 4033 4.119862 CTCGGACTCAAAGAAGAAACACA 58.880 43.478 0.00 0.00 0.00 3.72
2449 4034 4.209495 GTCTCGGACTCAAAGAAGAAACAC 59.791 45.833 0.00 0.00 0.00 3.32
2450 4035 4.099573 AGTCTCGGACTCAAAGAAGAAACA 59.900 41.667 1.23 0.00 38.71 2.83
2451 4036 4.623002 AGTCTCGGACTCAAAGAAGAAAC 58.377 43.478 1.23 0.00 38.71 2.78
2452 4037 4.939052 AGTCTCGGACTCAAAGAAGAAA 57.061 40.909 1.23 0.00 38.71 2.52
2453 4038 4.939052 AAGTCTCGGACTCAAAGAAGAA 57.061 40.909 6.96 0.00 42.59 2.52
2454 4039 4.099573 ACAAAGTCTCGGACTCAAAGAAGA 59.900 41.667 6.96 0.00 42.59 2.87
2455 4040 4.372656 ACAAAGTCTCGGACTCAAAGAAG 58.627 43.478 6.96 0.00 42.59 2.85
2456 4041 4.402056 ACAAAGTCTCGGACTCAAAGAA 57.598 40.909 6.96 0.00 42.59 2.52
2457 4042 4.402056 AACAAAGTCTCGGACTCAAAGA 57.598 40.909 6.96 0.00 42.59 2.52
2458 4043 5.696724 ACATAACAAAGTCTCGGACTCAAAG 59.303 40.000 6.96 1.95 42.59 2.77
2459 4044 5.607477 ACATAACAAAGTCTCGGACTCAAA 58.393 37.500 6.96 0.00 42.59 2.69
2460 4045 5.010719 AGACATAACAAAGTCTCGGACTCAA 59.989 40.000 6.96 0.00 42.59 3.02
2461 4046 4.523173 AGACATAACAAAGTCTCGGACTCA 59.477 41.667 6.96 0.00 42.59 3.41
2462 4047 5.061920 AGACATAACAAAGTCTCGGACTC 57.938 43.478 6.96 0.00 42.59 3.36
2470 4055 5.864474 ACATCGACTGAGACATAACAAAGTC 59.136 40.000 0.00 0.00 35.02 3.01
2471 4056 5.784177 ACATCGACTGAGACATAACAAAGT 58.216 37.500 0.00 0.00 0.00 2.66
2472 4057 6.712241 AACATCGACTGAGACATAACAAAG 57.288 37.500 0.00 0.00 0.00 2.77
2473 4058 7.149307 TGTAACATCGACTGAGACATAACAAA 58.851 34.615 0.00 0.00 0.00 2.83
2474 4059 6.683715 TGTAACATCGACTGAGACATAACAA 58.316 36.000 0.00 0.00 0.00 2.83
2475 4060 6.262193 TGTAACATCGACTGAGACATAACA 57.738 37.500 0.00 0.00 0.00 2.41
2476 4061 7.702772 AGAATGTAACATCGACTGAGACATAAC 59.297 37.037 13.64 11.97 34.67 1.89
2477 4062 7.772166 AGAATGTAACATCGACTGAGACATAA 58.228 34.615 13.64 0.00 34.67 1.90
2478 4063 7.334844 AGAATGTAACATCGACTGAGACATA 57.665 36.000 13.64 0.00 34.67 2.29
2479 4064 6.214191 AGAATGTAACATCGACTGAGACAT 57.786 37.500 0.00 1.19 36.16 3.06
2480 4065 5.644977 AGAATGTAACATCGACTGAGACA 57.355 39.130 0.00 0.00 0.00 3.41
2481 4066 6.952935 AAAGAATGTAACATCGACTGAGAC 57.047 37.500 0.00 0.00 0.00 3.36
2482 4067 7.151976 TCAAAAGAATGTAACATCGACTGAGA 58.848 34.615 0.00 0.00 0.00 3.27
2483 4068 7.351414 TCAAAAGAATGTAACATCGACTGAG 57.649 36.000 0.00 0.00 0.00 3.35
2484 4069 7.905604 ATCAAAAGAATGTAACATCGACTGA 57.094 32.000 0.00 0.00 0.00 3.41
2485 4070 8.955061 AAATCAAAAGAATGTAACATCGACTG 57.045 30.769 0.00 0.00 0.00 3.51
2486 4071 9.398170 CAAAATCAAAAGAATGTAACATCGACT 57.602 29.630 0.00 0.00 0.00 4.18
2487 4072 9.180678 ACAAAATCAAAAGAATGTAACATCGAC 57.819 29.630 0.00 0.00 0.00 4.20
2496 4081 9.696917 GAACTCCATACAAAATCAAAAGAATGT 57.303 29.630 0.00 0.00 0.00 2.71
2497 4082 9.695526 TGAACTCCATACAAAATCAAAAGAATG 57.304 29.630 0.00 0.00 0.00 2.67
2556 4141 9.011095 CCAAGTCTCAATCAAATGATATAGCAT 57.989 33.333 0.00 0.00 33.73 3.79
2557 4142 7.994911 ACCAAGTCTCAATCAAATGATATAGCA 59.005 33.333 0.00 0.00 33.73 3.49
2558 4143 8.388484 ACCAAGTCTCAATCAAATGATATAGC 57.612 34.615 0.00 0.00 33.73 2.97
2562 4147 9.739276 ACTTAACCAAGTCTCAATCAAATGATA 57.261 29.630 0.00 0.00 41.25 2.15
2563 4148 8.641498 ACTTAACCAAGTCTCAATCAAATGAT 57.359 30.769 0.00 0.00 41.25 2.45
2577 4162 8.429641 TCTCAGTCAATTAAGACTTAACCAAGT 58.570 33.333 9.82 0.00 46.26 3.16
2578 4163 8.713271 GTCTCAGTCAATTAAGACTTAACCAAG 58.287 37.037 9.82 1.56 46.26 3.61
2579 4164 7.660208 GGTCTCAGTCAATTAAGACTTAACCAA 59.340 37.037 9.82 0.00 46.26 3.67
2580 4165 7.016268 AGGTCTCAGTCAATTAAGACTTAACCA 59.984 37.037 9.82 0.00 46.26 3.67
2581 4166 7.387643 AGGTCTCAGTCAATTAAGACTTAACC 58.612 38.462 9.82 3.92 46.26 2.85
2582 4167 9.575783 CTAGGTCTCAGTCAATTAAGACTTAAC 57.424 37.037 9.82 0.00 46.26 2.01
2583 4168 9.529823 TCTAGGTCTCAGTCAATTAAGACTTAA 57.470 33.333 10.02 10.02 46.26 1.85
2584 4169 8.958506 GTCTAGGTCTCAGTCAATTAAGACTTA 58.041 37.037 0.00 0.00 46.26 2.24
2585 4170 7.451877 TGTCTAGGTCTCAGTCAATTAAGACTT 59.548 37.037 0.00 0.00 46.26 3.01
2587 4172 7.030768 GTGTCTAGGTCTCAGTCAATTAAGAC 58.969 42.308 0.00 0.00 37.90 3.01
2588 4173 6.719829 TGTGTCTAGGTCTCAGTCAATTAAGA 59.280 38.462 0.00 0.00 0.00 2.10
2589 4174 6.809196 GTGTGTCTAGGTCTCAGTCAATTAAG 59.191 42.308 0.00 0.00 0.00 1.85
2590 4175 6.493802 AGTGTGTCTAGGTCTCAGTCAATTAA 59.506 38.462 0.00 0.00 0.00 1.40
2591 4176 6.010850 AGTGTGTCTAGGTCTCAGTCAATTA 58.989 40.000 0.00 0.00 0.00 1.40
2592 4177 4.835615 AGTGTGTCTAGGTCTCAGTCAATT 59.164 41.667 0.00 0.00 0.00 2.32
2593 4178 4.411927 AGTGTGTCTAGGTCTCAGTCAAT 58.588 43.478 0.00 0.00 0.00 2.57
2594 4179 3.833732 AGTGTGTCTAGGTCTCAGTCAA 58.166 45.455 0.00 0.00 0.00 3.18
2595 4180 3.510531 AGTGTGTCTAGGTCTCAGTCA 57.489 47.619 0.00 0.00 0.00 3.41
2596 4181 5.005094 ACTTAGTGTGTCTAGGTCTCAGTC 58.995 45.833 0.00 0.00 34.53 3.51
2597 4182 4.988029 ACTTAGTGTGTCTAGGTCTCAGT 58.012 43.478 0.00 0.00 34.53 3.41
2598 4183 5.968528 AACTTAGTGTGTCTAGGTCTCAG 57.031 43.478 0.00 0.00 37.86 3.35
2599 4184 7.828508 TTTAACTTAGTGTGTCTAGGTCTCA 57.171 36.000 0.00 0.00 37.86 3.27
2626 4211 9.307121 CGTAGAATGAAAGAGACACTTCATATT 57.693 33.333 0.00 0.00 37.93 1.28
2627 4212 8.470805 ACGTAGAATGAAAGAGACACTTCATAT 58.529 33.333 0.00 0.00 37.93 1.78
2628 4213 7.755373 CACGTAGAATGAAAGAGACACTTCATA 59.245 37.037 0.00 0.00 37.93 2.15
2629 4214 6.587990 CACGTAGAATGAAAGAGACACTTCAT 59.412 38.462 0.00 0.00 37.93 2.57
2630 4215 5.920840 CACGTAGAATGAAAGAGACACTTCA 59.079 40.000 0.00 0.00 37.93 3.02
2631 4216 5.921408 ACACGTAGAATGAAAGAGACACTTC 59.079 40.000 0.00 0.00 37.93 3.01
2632 4217 5.844004 ACACGTAGAATGAAAGAGACACTT 58.156 37.500 0.00 0.00 40.98 3.16
2633 4218 5.455056 ACACGTAGAATGAAAGAGACACT 57.545 39.130 0.00 0.00 0.00 3.55
2634 4219 5.286558 GCTACACGTAGAATGAAAGAGACAC 59.713 44.000 8.41 0.00 35.21 3.67
2635 4220 5.048294 TGCTACACGTAGAATGAAAGAGACA 60.048 40.000 8.41 0.00 35.21 3.41
2636 4221 5.399858 TGCTACACGTAGAATGAAAGAGAC 58.600 41.667 8.41 0.00 35.21 3.36
2637 4222 5.638596 TGCTACACGTAGAATGAAAGAGA 57.361 39.130 8.41 0.00 35.21 3.10
2638 4223 6.893958 AATGCTACACGTAGAATGAAAGAG 57.106 37.500 8.41 0.00 31.86 2.85
2639 4224 7.378728 CGATAATGCTACACGTAGAATGAAAGA 59.621 37.037 8.41 0.00 31.86 2.52
2640 4225 7.358435 CCGATAATGCTACACGTAGAATGAAAG 60.358 40.741 8.41 0.00 31.86 2.62
2641 4226 6.419710 CCGATAATGCTACACGTAGAATGAAA 59.580 38.462 8.41 0.00 31.86 2.69
2642 4227 5.918576 CCGATAATGCTACACGTAGAATGAA 59.081 40.000 8.41 0.00 31.86 2.57
2643 4228 5.458015 CCGATAATGCTACACGTAGAATGA 58.542 41.667 8.41 0.00 31.86 2.57
2644 4229 4.090066 GCCGATAATGCTACACGTAGAATG 59.910 45.833 8.41 0.00 31.86 2.67
2645 4230 4.235360 GCCGATAATGCTACACGTAGAAT 58.765 43.478 8.41 0.00 32.82 2.40
2646 4231 3.635331 GCCGATAATGCTACACGTAGAA 58.365 45.455 8.41 0.00 35.21 2.10
2647 4232 2.350102 CGCCGATAATGCTACACGTAGA 60.350 50.000 8.41 0.00 35.21 2.59
2648 4233 1.976728 CGCCGATAATGCTACACGTAG 59.023 52.381 0.00 0.00 36.29 3.51
2649 4234 1.334556 ACGCCGATAATGCTACACGTA 59.665 47.619 0.00 0.00 0.00 3.57
2650 4235 0.101759 ACGCCGATAATGCTACACGT 59.898 50.000 0.00 0.00 0.00 4.49
2651 4236 0.776451 GACGCCGATAATGCTACACG 59.224 55.000 0.00 0.00 0.00 4.49
2652 4237 1.847818 TGACGCCGATAATGCTACAC 58.152 50.000 0.00 0.00 0.00 2.90
2653 4238 2.588027 TTGACGCCGATAATGCTACA 57.412 45.000 0.00 0.00 0.00 2.74
2654 4239 5.779806 ATAATTGACGCCGATAATGCTAC 57.220 39.130 0.00 0.00 0.00 3.58
2655 4240 7.489160 AGATATAATTGACGCCGATAATGCTA 58.511 34.615 0.00 0.00 0.00 3.49
2656 4241 6.341316 AGATATAATTGACGCCGATAATGCT 58.659 36.000 0.00 0.00 0.00 3.79
2681 4266 6.149807 ACCCGCGAAGAAACAGAAATATAAAA 59.850 34.615 8.23 0.00 0.00 1.52
2685 4270 3.374058 CACCCGCGAAGAAACAGAAATAT 59.626 43.478 8.23 0.00 0.00 1.28
2687 4272 1.535462 CACCCGCGAAGAAACAGAAAT 59.465 47.619 8.23 0.00 0.00 2.17
2693 4278 1.082104 CTTGCACCCGCGAAGAAAC 60.082 57.895 8.23 0.00 42.97 2.78
2694 4279 1.098712 AACTTGCACCCGCGAAGAAA 61.099 50.000 8.23 0.00 42.97 2.52
2695 4280 1.525077 AACTTGCACCCGCGAAGAA 60.525 52.632 8.23 0.00 42.97 2.52
2696 4281 2.110213 AACTTGCACCCGCGAAGA 59.890 55.556 8.23 0.00 42.97 2.87
2697 4282 1.225376 TACAACTTGCACCCGCGAAG 61.225 55.000 8.23 5.12 42.97 3.79
2699 4284 1.957186 GTACAACTTGCACCCGCGA 60.957 57.895 8.23 0.00 42.97 5.87
2700 4285 1.777030 TTGTACAACTTGCACCCGCG 61.777 55.000 3.59 0.00 42.97 6.46
2702 4287 1.673920 ACTTTGTACAACTTGCACCCG 59.326 47.619 8.07 0.00 0.00 5.28
2703 4288 2.286772 CGACTTTGTACAACTTGCACCC 60.287 50.000 8.07 0.00 0.00 4.61
2704 4289 2.610374 TCGACTTTGTACAACTTGCACC 59.390 45.455 8.07 0.00 0.00 5.01
2705 4290 3.936902 TCGACTTTGTACAACTTGCAC 57.063 42.857 8.07 0.00 0.00 4.57
2706 4291 4.154375 TGTTTCGACTTTGTACAACTTGCA 59.846 37.500 8.07 0.00 0.00 4.08
2708 4293 5.864986 ACTGTTTCGACTTTGTACAACTTG 58.135 37.500 8.07 4.45 0.00 3.16
2712 4326 9.279904 CAAAATAACTGTTTCGACTTTGTACAA 57.720 29.630 3.59 3.59 0.00 2.41
2713 4327 8.666573 TCAAAATAACTGTTTCGACTTTGTACA 58.333 29.630 0.00 0.00 0.00 2.90
2723 4337 6.955963 CCTTCGATCTCAAAATAACTGTTTCG 59.044 38.462 0.00 0.00 0.00 3.46
2726 4340 7.162082 ACTCCTTCGATCTCAAAATAACTGTT 58.838 34.615 0.00 0.00 0.00 3.16
2740 4354 7.492669 TCTGATGAAACAAATACTCCTTCGATC 59.507 37.037 0.00 0.00 0.00 3.69
2743 4357 6.968131 TCTGATGAAACAAATACTCCTTCG 57.032 37.500 0.00 0.00 0.00 3.79
2745 4359 8.868522 TGATTCTGATGAAACAAATACTCCTT 57.131 30.769 0.00 0.00 33.11 3.36
2746 4360 8.324306 TCTGATTCTGATGAAACAAATACTCCT 58.676 33.333 0.00 0.00 35.16 3.69
2789 4403 1.300697 GCCACCGTCTTTGTCTCGT 60.301 57.895 0.00 0.00 0.00 4.18
2863 4477 1.028905 CCGGCACTTGACCAGAAAAA 58.971 50.000 0.00 0.00 0.00 1.94
2935 4576 4.435436 TGACTGGCTACCGCGCTG 62.435 66.667 5.56 0.00 36.88 5.18
2947 4588 1.526686 TGTTGGCAGGCAGTGACTG 60.527 57.895 22.48 22.48 42.51 3.51
2952 4593 4.954970 CCGGTGTTGGCAGGCAGT 62.955 66.667 0.00 0.00 0.00 4.40
2984 4671 3.919197 CAGATCAGCAGCACATATCGTAG 59.081 47.826 0.00 0.00 0.00 3.51
3052 4764 2.431057 AGATACTCCAACACATCGACCC 59.569 50.000 0.00 0.00 0.00 4.46
3054 4766 3.364062 CGAGATACTCCAACACATCGAC 58.636 50.000 0.00 0.00 0.00 4.20
3271 5003 0.835543 ACACAGCAAGAGGAGAGGCT 60.836 55.000 0.00 0.00 36.99 4.58
3272 5004 0.390998 GACACAGCAAGAGGAGAGGC 60.391 60.000 0.00 0.00 0.00 4.70
3273 5005 0.108898 CGACACAGCAAGAGGAGAGG 60.109 60.000 0.00 0.00 0.00 3.69
3274 5006 0.735632 GCGACACAGCAAGAGGAGAG 60.736 60.000 0.00 0.00 37.05 3.20
3275 5007 1.181741 AGCGACACAGCAAGAGGAGA 61.182 55.000 0.00 0.00 40.15 3.71
3276 5008 1.013005 CAGCGACACAGCAAGAGGAG 61.013 60.000 0.00 0.00 40.15 3.69
3277 5009 1.005748 CAGCGACACAGCAAGAGGA 60.006 57.895 0.00 0.00 40.15 3.71
3282 5014 3.872603 ACCCCAGCGACACAGCAA 61.873 61.111 0.00 0.00 40.15 3.91
3330 5070 1.265905 GTAAGACCAAAACTGGCGGTG 59.734 52.381 0.00 0.00 31.63 4.94


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

AutoCloner maintained by Alex Coulton.