Multiple sequence alignment - TraesCS5A01G178400

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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 TraesCS5A01G178400 chr5A 100.000 6924 0 0 2871 9794 376103160 376096237 0.000000e+00 12787.0
1 TraesCS5A01G178400 chr5A 100.000 2565 0 0 1 2565 376106030 376103466 0.000000e+00 4737.0
2 TraesCS5A01G178400 chr5A 74.857 350 60 19 1 325 698154028 698154374 6.170000e-27 134.0
3 TraesCS5A01G178400 chr5D 96.376 2318 75 6 7113 9428 284182261 284179951 0.000000e+00 3807.0
4 TraesCS5A01G178400 chr5D 97.063 1941 50 4 5180 7117 284185284 284183348 0.000000e+00 3262.0
5 TraesCS5A01G178400 chr5D 93.544 2029 81 15 2871 4879 284187286 284185288 0.000000e+00 2976.0
6 TraesCS5A01G178400 chr5D 94.807 1733 57 17 789 2509 284189330 284187619 0.000000e+00 2671.0
7 TraesCS5A01G178400 chr5D 89.954 657 58 5 1 651 284190421 284189767 0.000000e+00 841.0
8 TraesCS5A01G178400 chr5D 90.463 367 21 6 9429 9794 284179606 284179253 1.150000e-128 472.0
9 TraesCS5A01G178400 chr5D 96.825 126 2 2 651 775 284189440 284189316 9.970000e-50 209.0
10 TraesCS5A01G178400 chr5B 95.821 2321 84 9 7113 9428 322142314 322140002 0.000000e+00 3736.0
11 TraesCS5A01G178400 chr5B 93.341 2463 117 16 2871 5311 322149454 322147017 0.000000e+00 3596.0
12 TraesCS5A01G178400 chr5B 97.367 1595 29 5 5530 7117 322146503 322144915 0.000000e+00 2700.0
13 TraesCS5A01G178400 chr5B 95.556 1575 60 6 949 2516 322151420 322149849 0.000000e+00 2512.0
14 TraesCS5A01G178400 chr5B 84.826 547 53 13 230 773 322153192 322152673 3.130000e-144 523.0
15 TraesCS5A01G178400 chr5B 87.466 367 22 7 9429 9794 322139660 322139317 1.530000e-107 401.0
16 TraesCS5A01G178400 chr5B 93.657 268 13 2 5167 5430 322147027 322146760 1.980000e-106 398.0
17 TraesCS5A01G178400 chr5B 97.500 120 3 0 5415 5534 322146745 322146626 1.290000e-48 206.0
18 TraesCS5A01G178400 chrUn 75.581 344 58 18 1 324 378442140 378441803 7.930000e-31 147.0
19 TraesCS5A01G178400 chr4A 75.153 326 61 13 1 309 730551083 730551405 1.720000e-27 135.0
20 TraesCS5A01G178400 chr4A 75.153 326 61 13 1 309 730602977 730603299 1.720000e-27 135.0
21 TraesCS5A01G178400 chr4A 74.769 325 64 11 1 309 730471113 730471435 7.980000e-26 130.0
22 TraesCS5A01G178400 chr1B 75.563 311 56 16 1 296 603520989 603521294 1.720000e-27 135.0
23 TraesCS5A01G178400 chr7D 74.269 342 70 15 2 327 3694998 3694659 2.870000e-25 128.0
24 TraesCS5A01G178400 chr6D 84.921 126 12 7 1 121 4899589 4899712 4.800000e-23 121.0
25 TraesCS5A01G178400 chr3D 76.531 196 35 9 482 670 455851981 455851790 8.100000e-16 97.1
26 TraesCS5A01G178400 chr7A 90.000 50 5 0 620 669 526150657 526150608 2.280000e-06 65.8


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 TraesCS5A01G178400 chr5A 376096237 376106030 9793 True 8762 12787 100.000000 1 9794 2 chr5A.!!$R1 9793
1 TraesCS5A01G178400 chr5D 284179253 284190421 11168 True 2034 3807 94.147429 1 9794 7 chr5D.!!$R1 9793
2 TraesCS5A01G178400 chr5B 322139317 322153192 13875 True 1759 3736 93.191750 230 9794 8 chr5B.!!$R1 9564

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
324 326 0.106708 ATGGCCTGACGTATCGCAAT 59.893 50.000 3.32 0.0 0.00 3.56 F
1031 2590 0.025256 CTCACGCTCGTCTCGTAGAC 59.975 60.000 0.00 5.3 41.71 2.59 F
1308 2876 1.004440 GCCTCTGACCTTTCGCAGT 60.004 57.895 0.00 0.0 33.90 4.40 F
1830 3398 1.004745 TGATCTTTGAACCCCAGGCTC 59.995 52.381 0.00 0.0 0.00 4.70 F
1832 3400 1.065410 TCTTTGAACCCCAGGCTCCA 61.065 55.000 0.00 0.0 0.00 3.86 F
3506 5127 2.148446 TACCACCAGGCGTATACTGT 57.852 50.000 0.56 0.0 39.06 3.55 F
4435 6073 2.119801 AGCTGTATTGGTTGCCAGAG 57.880 50.000 0.00 0.0 33.81 3.35 F
4656 6294 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
4662 6300 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
4663 6301 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82 F
6554 8493 0.903454 GACCTCGAAGACCCTTCCCA 60.903 60.000 0.00 0.0 0.00 4.37 F
8143 12893 0.319728 CTCCATCTGCCCCAGTATCG 59.680 60.000 0.00 0.0 32.61 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 3393 0.696501 ATTTGGTTACGGTGGAGCCT 59.303 50.000 0.00 0.00 34.25 4.58 R
2527 4104 2.322658 ACGGAAAGTCAGGGAGTTACA 58.677 47.619 0.00 0.00 0.00 2.41 R
3115 4734 1.514678 GAACTTGTCATGGGCGCACA 61.515 55.000 18.16 18.16 0.00 4.57 R
3364 4984 0.598065 ATTGGTCTGTCAAAAGCCGC 59.402 50.000 0.00 0.00 0.00 6.53 R
3653 5274 0.819582 CCAATCAACCTCCCACATGC 59.180 55.000 0.00 0.00 0.00 4.06 R
4631 6269 0.392327 TGTGTGTGTGTGTGACAGGG 60.392 55.000 0.00 0.00 34.28 4.45 R
6143 8082 1.000938 CTTCCAACTTCTGCTGCAACC 60.001 52.381 3.02 0.00 0.00 3.77 R
6502 8441 1.774110 ACTGTGCCATGGTGTTTCAA 58.226 45.000 14.67 0.00 0.00 2.69 R
6554 8493 3.958798 CTGCATCCCAAGAATCTTCCAAT 59.041 43.478 0.00 0.00 0.00 3.16 R
6716 8655 0.034186 TGGGGTGTGCATCATCTTCC 60.034 55.000 0.00 0.00 0.00 3.46 R
8218 12968 0.036732 TGTTTGAGCTGCCTACTGGG 59.963 55.000 0.00 0.00 38.36 4.45 R
9645 14747 2.178273 CACGATGCGACGAGGACA 59.822 61.111 0.00 0.00 37.03 4.02 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
31 32 0.516322 CGTGTCGCAACTTGCATACG 60.516 55.000 14.10 14.91 45.36 3.06
43 44 2.102070 TGCATACGGTGTCGGAATTT 57.898 45.000 0.00 0.00 41.39 1.82
55 56 4.502645 GTGTCGGAATTTGTTCAAACCTTG 59.497 41.667 0.00 0.00 0.00 3.61
115 117 3.735720 TGGGTCATTTCATGGATGTCA 57.264 42.857 9.01 5.32 0.00 3.58
116 118 4.044946 TGGGTCATTTCATGGATGTCAA 57.955 40.909 9.01 0.00 0.00 3.18
143 145 3.324108 GGGTGTTCGGGTAGGCCA 61.324 66.667 5.01 0.00 36.17 5.36
147 149 0.535553 GTGTTCGGGTAGGCCACAAA 60.536 55.000 5.01 0.00 36.17 2.83
153 155 1.765074 GGTAGGCCACAAAGGTCCA 59.235 57.895 5.01 0.00 45.84 4.02
181 183 1.271876 CATGTCTGTGGTCGACATCG 58.728 55.000 18.91 2.47 46.15 3.84
192 194 2.307934 TCGACATCGATCAAATGGCA 57.692 45.000 10.63 0.00 44.22 4.92
199 201 5.909477 ACATCGATCAAATGGCATCAATTT 58.091 33.333 0.00 0.00 0.00 1.82
224 226 3.957288 GTGGCCTTGTATCACCAGT 57.043 52.632 3.32 0.00 31.46 4.00
251 253 2.877168 GCACCATGCCAAATTGTTTGAA 59.123 40.909 4.11 0.00 40.50 2.69
324 326 0.106708 ATGGCCTGACGTATCGCAAT 59.893 50.000 3.32 0.00 0.00 3.56
372 374 1.325355 GCATCTAACATGGGCATGCT 58.675 50.000 18.92 0.00 42.39 3.79
382 384 2.345760 GGGCATGCTCACTTGGTGG 61.346 63.158 18.92 0.00 33.87 4.61
435 437 8.858186 CGAATAATGTGTTTGATTTGCAACATA 58.142 29.630 0.00 0.00 35.91 2.29
467 469 4.570930 TCCATTACAAACACATACGCTCA 58.429 39.130 0.00 0.00 0.00 4.26
478 480 3.920412 CACATACGCTCATACATACGCAT 59.080 43.478 0.00 0.00 0.00 4.73
494 496 1.733912 CGCATTGCACATACACTCACT 59.266 47.619 9.69 0.00 0.00 3.41
506 508 5.594725 ACATACACTCACTCCTATGAACGAT 59.405 40.000 0.00 0.00 0.00 3.73
513 515 0.459899 TCCTATGAACGATGCGCACT 59.540 50.000 14.90 1.12 0.00 4.40
516 518 2.287608 CCTATGAACGATGCGCACTCTA 60.288 50.000 14.90 0.00 0.00 2.43
553 555 1.140312 ACCTCCAAGAAACTGAGCCA 58.860 50.000 0.00 0.00 0.00 4.75
560 562 3.508793 CCAAGAAACTGAGCCATCACATT 59.491 43.478 0.00 0.00 0.00 2.71
563 565 6.127535 CCAAGAAACTGAGCCATCACATTATT 60.128 38.462 0.00 0.00 0.00 1.40
569 571 9.995003 AAACTGAGCCATCACATTATTTTAAAA 57.005 25.926 2.51 2.51 0.00 1.52
586 588 2.867456 AAATTAACGAAGTCACCGCG 57.133 45.000 0.00 0.00 45.00 6.46
609 615 0.172578 TCGTAGTCAGCGGGAATGTG 59.827 55.000 0.00 0.00 0.00 3.21
770 1104 0.601558 CCACAGTACGTGCACCTAGT 59.398 55.000 12.15 6.16 44.91 2.57
771 1105 1.000506 CCACAGTACGTGCACCTAGTT 59.999 52.381 12.15 0.00 44.91 2.24
772 1106 2.547218 CCACAGTACGTGCACCTAGTTT 60.547 50.000 12.15 0.00 44.91 2.66
773 1107 3.128349 CACAGTACGTGCACCTAGTTTT 58.872 45.455 12.15 0.00 39.19 2.43
774 1108 3.558418 CACAGTACGTGCACCTAGTTTTT 59.442 43.478 12.15 0.00 39.19 1.94
828 2383 5.491982 CCTGACTAGCAAAATCCAGTAACT 58.508 41.667 0.00 0.00 0.00 2.24
838 2393 2.088950 TCCAGTAACTGTTAAGGCGC 57.911 50.000 0.00 0.00 0.00 6.53
839 2394 0.719465 CCAGTAACTGTTAAGGCGCG 59.281 55.000 0.00 0.00 0.00 6.86
842 2397 1.000060 AGTAACTGTTAAGGCGCGACA 60.000 47.619 17.71 5.98 0.00 4.35
869 2424 3.689649 AGCCCGTAATAAAGCAGTGAAAG 59.310 43.478 0.00 0.00 0.00 2.62
870 2425 3.439129 GCCCGTAATAAAGCAGTGAAAGT 59.561 43.478 0.00 0.00 0.00 2.66
872 2427 5.628134 CCCGTAATAAAGCAGTGAAAGTTC 58.372 41.667 0.00 0.00 0.00 3.01
873 2428 5.411669 CCCGTAATAAAGCAGTGAAAGTTCT 59.588 40.000 0.00 0.00 0.00 3.01
875 2430 6.147164 CCGTAATAAAGCAGTGAAAGTTCTGA 59.853 38.462 0.00 0.00 34.02 3.27
876 2431 7.148407 CCGTAATAAAGCAGTGAAAGTTCTGAT 60.148 37.037 0.00 0.00 34.02 2.90
877 2432 8.230486 CGTAATAAAGCAGTGAAAGTTCTGATT 58.770 33.333 0.00 0.00 41.10 2.57
928 2483 4.240103 CATCGGCCGCCTCATCCA 62.240 66.667 23.51 0.00 0.00 3.41
1031 2590 0.025256 CTCACGCTCGTCTCGTAGAC 59.975 60.000 0.00 5.30 41.71 2.59
1059 2618 2.098293 GATGGAATCGCGGTTTGCT 58.902 52.632 5.86 0.00 43.27 3.91
1158 2726 3.483869 GGGGGAGATTCAGCGGCT 61.484 66.667 0.00 0.00 0.00 5.52
1308 2876 1.004440 GCCTCTGACCTTTCGCAGT 60.004 57.895 0.00 0.00 33.90 4.40
1403 2971 4.521062 GAGCAGGACGCCATCGCT 62.521 66.667 7.01 7.01 44.04 4.93
1494 3062 1.674651 GTTGAACTTCCTCCCGCCC 60.675 63.158 0.00 0.00 0.00 6.13
1638 3206 3.515562 ACCAAGTCTCAGGAGTCAAGAT 58.484 45.455 0.00 0.00 0.00 2.40
1751 3319 9.135189 TGTGCATGATAAATAAAATAGAAGGCT 57.865 29.630 0.00 0.00 0.00 4.58
1782 3350 8.665643 TTCTTTTGAATGATGCAAAACTTCAT 57.334 26.923 7.22 0.00 43.14 2.57
1825 3393 3.609853 CGAAGATGATCTTTGAACCCCA 58.390 45.455 15.83 0.00 39.68 4.96
1826 3394 3.624861 CGAAGATGATCTTTGAACCCCAG 59.375 47.826 15.83 0.00 39.68 4.45
1828 3396 2.027385 GATGATCTTTGAACCCCAGGC 58.973 52.381 0.00 0.00 0.00 4.85
1829 3397 1.075601 TGATCTTTGAACCCCAGGCT 58.924 50.000 0.00 0.00 0.00 4.58
1830 3398 1.004745 TGATCTTTGAACCCCAGGCTC 59.995 52.381 0.00 0.00 0.00 4.70
1832 3400 1.065410 TCTTTGAACCCCAGGCTCCA 61.065 55.000 0.00 0.00 0.00 3.86
1887 3456 2.436417 GCATCAGCAACCCTTTACAGA 58.564 47.619 0.00 0.00 41.58 3.41
1956 3525 6.699575 ATCAACAATTATCACAGCTTACCC 57.300 37.500 0.00 0.00 0.00 3.69
1957 3526 5.565509 TCAACAATTATCACAGCTTACCCA 58.434 37.500 0.00 0.00 0.00 4.51
2032 3601 5.689819 CACGATAAAACCTCCAAAAGACAG 58.310 41.667 0.00 0.00 0.00 3.51
2190 3762 4.859304 AAATTGTGCTGCATGAGAGAAA 57.141 36.364 5.27 0.00 0.00 2.52
2199 3771 7.147966 TGTGCTGCATGAGAGAAATGAATATTT 60.148 33.333 5.27 0.00 39.16 1.40
2355 3932 6.040878 ACCCGATACTTTTTCTCAATACTCG 58.959 40.000 0.00 0.00 0.00 4.18
2360 3937 8.473016 CGATACTTTTTCTCAATACTCGTCATC 58.527 37.037 0.00 0.00 0.00 2.92
2402 3979 6.350027 CCTGTTATTGCAATGTGAACCATGTA 60.350 38.462 22.27 1.97 32.82 2.29
2457 4034 2.480419 GTGCTATGAACAGGACACACAC 59.520 50.000 0.00 0.00 36.90 3.82
2477 4054 8.077991 CACACACATTTATCTGACAGTTTCAAT 58.922 33.333 1.59 0.00 32.21 2.57
2516 4093 4.388485 TGTGCTATCAACAAGACACACAT 58.612 39.130 0.00 0.00 33.96 3.21
2517 4094 5.546526 TGTGCTATCAACAAGACACACATA 58.453 37.500 0.00 0.00 33.96 2.29
2518 4095 6.172630 TGTGCTATCAACAAGACACACATAT 58.827 36.000 0.00 0.00 33.96 1.78
2519 4096 6.654582 TGTGCTATCAACAAGACACACATATT 59.345 34.615 0.00 0.00 33.96 1.28
2520 4097 7.174772 TGTGCTATCAACAAGACACACATATTT 59.825 33.333 0.00 0.00 33.96 1.40
2521 4098 8.664798 GTGCTATCAACAAGACACACATATTTA 58.335 33.333 0.00 0.00 30.86 1.40
2522 4099 9.394767 TGCTATCAACAAGACACACATATTTAT 57.605 29.630 0.00 0.00 0.00 1.40
2523 4100 9.869844 GCTATCAACAAGACACACATATTTATC 57.130 33.333 0.00 0.00 0.00 1.75
2544 4121 9.886132 TTTATCTATTGTAACTCCCTGACTTTC 57.114 33.333 0.00 0.00 0.00 2.62
2545 4122 6.295719 TCTATTGTAACTCCCTGACTTTCC 57.704 41.667 0.00 0.00 0.00 3.13
2546 4123 3.396260 TTGTAACTCCCTGACTTTCCG 57.604 47.619 0.00 0.00 0.00 4.30
2547 4124 2.322658 TGTAACTCCCTGACTTTCCGT 58.677 47.619 0.00 0.00 0.00 4.69
2548 4125 3.499338 TGTAACTCCCTGACTTTCCGTA 58.501 45.455 0.00 0.00 0.00 4.02
2549 4126 3.896888 TGTAACTCCCTGACTTTCCGTAA 59.103 43.478 0.00 0.00 0.00 3.18
2550 4127 4.344679 TGTAACTCCCTGACTTTCCGTAAA 59.655 41.667 0.00 0.00 0.00 2.01
2551 4128 4.426736 AACTCCCTGACTTTCCGTAAAA 57.573 40.909 0.00 0.00 0.00 1.52
2552 4129 4.635699 ACTCCCTGACTTTCCGTAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
2553 4130 5.750352 ACTCCCTGACTTTCCGTAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
2554 4131 6.117975 ACTCCCTGACTTTCCGTAAAATAA 57.882 37.500 0.00 0.00 0.00 1.40
2555 4132 6.718294 ACTCCCTGACTTTCCGTAAAATAAT 58.282 36.000 0.00 0.00 0.00 1.28
2556 4133 7.173032 ACTCCCTGACTTTCCGTAAAATAATT 58.827 34.615 0.00 0.00 0.00 1.40
2557 4134 7.336176 ACTCCCTGACTTTCCGTAAAATAATTC 59.664 37.037 0.00 0.00 0.00 2.17
2558 4135 7.399634 TCCCTGACTTTCCGTAAAATAATTCT 58.600 34.615 0.00 0.00 0.00 2.40
2559 4136 7.886446 TCCCTGACTTTCCGTAAAATAATTCTT 59.114 33.333 0.00 0.00 0.00 2.52
2560 4137 8.520351 CCCTGACTTTCCGTAAAATAATTCTTT 58.480 33.333 0.00 0.00 0.00 2.52
2561 4138 9.556030 CCTGACTTTCCGTAAAATAATTCTTTC 57.444 33.333 0.00 0.00 0.00 2.62
2564 4141 9.556030 GACTTTCCGTAAAATAATTCTTTCTGG 57.444 33.333 0.00 0.00 0.00 3.86
2917 4534 5.938125 TCAATCAAGCTTCTTGGGTAGTTAC 59.062 40.000 15.03 0.00 0.00 2.50
2954 4573 7.846101 TCATTATCTGACATAGACACCATCT 57.154 36.000 0.00 0.00 38.49 2.90
3115 4734 9.271828 GTTAAAAACCAATGATCCAAAAGTGAT 57.728 29.630 0.00 0.00 0.00 3.06
3233 4852 4.280677 CCAAATGGAAAACAGAAGGCTACA 59.719 41.667 0.00 0.00 37.39 2.74
3242 4861 5.869649 AACAGAAGGCTACAATTTTGGTT 57.130 34.783 0.00 0.00 0.00 3.67
3243 4862 5.200368 ACAGAAGGCTACAATTTTGGTTG 57.800 39.130 0.00 0.00 35.25 3.77
3364 4984 2.443255 AGAAAGGGTATGGGCATAGGTG 59.557 50.000 0.00 0.00 0.00 4.00
3438 5058 4.184629 AGGTCTTGCATTTCTATGACGAC 58.815 43.478 0.00 0.00 33.37 4.34
3506 5127 2.148446 TACCACCAGGCGTATACTGT 57.852 50.000 0.56 0.00 39.06 3.55
3554 5175 8.177119 TGGATAAGTGCTGTTCTAAAATTTGT 57.823 30.769 0.00 0.00 0.00 2.83
3596 5217 5.491982 GTGGTCTTCTGTCTCCAATGTATT 58.508 41.667 0.00 0.00 0.00 1.89
3653 5274 6.600822 CCAAATAGGCTGGATATAATCACAGG 59.399 42.308 0.00 0.00 35.85 4.00
3786 5407 9.887629 ATCCTGCTATAATCACAATAGATGAAG 57.112 33.333 0.00 0.00 0.00 3.02
3796 5417 4.035324 CACAATAGATGAAGCAGCTCCTTG 59.965 45.833 0.00 0.00 32.64 3.61
3829 5450 4.974645 TGGAGACAAATGAGTACCTGTT 57.025 40.909 0.00 0.00 37.44 3.16
3945 5580 2.863809 ACAAAGAACTACCTTGCCTGG 58.136 47.619 0.00 0.00 0.00 4.45
4059 5695 6.166279 CAAGAAAGTAATAGACTGCAGGTGA 58.834 40.000 19.93 2.05 38.87 4.02
4080 5716 7.707035 AGGTGAACTAATTTCTGCTAATCTACG 59.293 37.037 0.00 0.00 34.97 3.51
4125 5761 5.939764 AAGCACTAACATGAGATACTGGA 57.060 39.130 0.00 0.00 0.00 3.86
4223 5859 9.765795 GATAGCTGACAGGTAAATACAATAAGT 57.234 33.333 17.73 0.00 31.35 2.24
4233 5869 7.041372 AGGTAAATACAATAAGTAAGCCATGCG 60.041 37.037 0.00 0.00 36.05 4.73
4378 6016 5.483583 CCAATGGGGAATCAAAACCTAAAGA 59.516 40.000 0.00 0.00 40.01 2.52
4404 6042 3.780294 AGAACTGTGGATAATGGTGGCTA 59.220 43.478 0.00 0.00 0.00 3.93
4435 6073 2.119801 AGCTGTATTGGTTGCCAGAG 57.880 50.000 0.00 0.00 33.81 3.35
4526 6164 5.567138 AACCAAATATAGCAGCACAAGTC 57.433 39.130 0.00 0.00 0.00 3.01
4539 6177 2.286418 GCACAAGTCACAGAAAACCTCG 60.286 50.000 0.00 0.00 0.00 4.63
4654 6292 1.152510 GTCACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
4655 6293 1.136085 GTCACACACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
4656 6294 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4657 6295 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4658 6296 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4659 6297 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4660 6298 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4661 6299 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4662 6300 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4663 6301 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4734 6372 4.036734 TCTGTTCAAATGTCCAGTGCTTTC 59.963 41.667 0.00 0.00 0.00 2.62
4852 6490 5.405269 GCCACAAACACATTGGAATTTCTAC 59.595 40.000 0.00 0.00 43.66 2.59
4907 6545 2.676839 CACATGTCTGTTCTGCCAGATC 59.323 50.000 0.00 0.00 43.03 2.75
4911 6549 2.125552 TGTTCTGCCAGATCGCGG 60.126 61.111 6.13 0.09 36.40 6.46
4912 6550 2.892425 GTTCTGCCAGATCGCGGG 60.892 66.667 6.13 0.00 35.72 6.13
4926 6564 1.439644 GCGGGCAAACAAAACCAGA 59.560 52.632 0.00 0.00 0.00 3.86
5006 6644 5.893897 ATTGAAATCTGCTGAGACTTTCC 57.106 39.130 12.73 1.02 31.47 3.13
5018 6656 4.537751 TGAGACTTTCCAGTATCGAGGAT 58.462 43.478 0.00 0.00 43.24 3.24
5049 6687 4.546674 TGGCTGAGTATTATCTGTCCTGA 58.453 43.478 0.00 0.00 0.00 3.86
5064 6702 5.954752 TCTGTCCTGAAATACTCTGATGACT 59.045 40.000 0.00 0.00 0.00 3.41
5105 6744 2.484594 GGACTTGCCCAAGATCTCTAGC 60.485 54.545 14.46 0.00 40.79 3.42
5115 6754 6.149142 GCCCAAGATCTCTAGCATTCATTTAG 59.851 42.308 0.00 0.00 0.00 1.85
5298 7075 1.683365 CTGTTCCCCATTGGCCTGG 60.683 63.158 3.32 3.69 35.95 4.45
5338 7115 4.379813 GCTTCCAATCATTCGTGAACATGT 60.380 41.667 0.00 0.00 0.00 3.21
5354 7131 4.974645 ACATGTCACTCCTTGGTCTAAA 57.025 40.909 0.00 0.00 0.00 1.85
5395 7172 5.336372 CCGAAAATAGGAAATTGGCTCACAA 60.336 40.000 0.00 0.00 44.54 3.33
5441 7248 2.099141 TCTGATTGGACTTGCTTCCG 57.901 50.000 0.00 0.00 38.69 4.30
5597 7531 2.732619 GGGAAGTCTACCTGGCCGG 61.733 68.421 3.88 3.88 39.35 6.13
5619 7558 5.459762 CGGTTGTTCTGTCTCGTTTAACTTA 59.540 40.000 0.00 0.00 0.00 2.24
5676 7615 7.931407 TGATTCTGTCTGTCTGCTTACTTTAAA 59.069 33.333 0.00 0.00 0.00 1.52
5835 7774 9.159364 CACAATCTTCTGATGAGAGACATTTTA 57.841 33.333 0.00 0.00 39.56 1.52
5859 7798 5.667539 TGAACATGGAAGAAAACACCAAA 57.332 34.783 0.00 0.00 37.24 3.28
5953 7892 2.200373 TTTCCTGCTGGTCTAAAGGC 57.800 50.000 9.73 0.00 34.23 4.35
6143 8082 6.662616 CATATGCTTTTCTCGTAATGAAGGG 58.337 40.000 0.00 0.00 0.00 3.95
6170 8109 3.070018 AGCAGAAGTTGGAAGATGTTCG 58.930 45.455 0.00 0.00 32.92 3.95
6222 8161 3.525537 CGTAGTGTTCGGTCTAGGTCTA 58.474 50.000 0.00 0.00 0.00 2.59
6554 8493 0.903454 GACCTCGAAGACCCTTCCCA 60.903 60.000 0.00 0.00 0.00 4.37
6898 8837 3.199508 CCTGAACATCATGGACCTCTTCT 59.800 47.826 0.00 0.00 0.00 2.85
6899 8838 4.324099 CCTGAACATCATGGACCTCTTCTT 60.324 45.833 0.00 0.00 0.00 2.52
6900 8839 4.836825 TGAACATCATGGACCTCTTCTTC 58.163 43.478 0.00 0.00 0.00 2.87
7148 11895 3.377253 TGAACCGAGGGAGTATGTAGT 57.623 47.619 0.00 0.00 0.00 2.73
7168 11915 8.462143 TGTAGTTCACTTCGATATTTGTTCTC 57.538 34.615 0.00 0.00 0.00 2.87
7177 11924 8.499162 ACTTCGATATTTGTTCTCTTCAACTTG 58.501 33.333 0.00 0.00 0.00 3.16
7237 11987 8.596380 GTCTAATTCTTTTCTGATAGTCAACCG 58.404 37.037 0.00 0.00 0.00 4.44
7268 12018 3.969899 CTGTTTTTCAGGCCTGACTTTC 58.030 45.455 35.26 23.60 39.66 2.62
7342 12092 0.613260 CTGCTAGCAGTTGGGTGGTA 59.387 55.000 32.46 0.00 39.10 3.25
7579 12329 1.202758 ACCTCTGCAAATCGTCAACCA 60.203 47.619 0.00 0.00 0.00 3.67
7648 12398 5.678361 CACTGATGTGAGTAGTCATGAGGAC 60.678 48.000 2.99 0.00 46.55 3.85
7869 12619 1.534717 AAGGCCAGCACCAGCAATT 60.535 52.632 5.01 0.00 45.49 2.32
7877 12627 1.980036 AGCACCAGCAATTCCCAAATT 59.020 42.857 0.00 0.00 45.49 1.82
7908 12658 5.948162 CCTCAGGATGGTCCAATAATAATGG 59.052 44.000 0.00 0.00 39.61 3.16
8069 12819 4.024387 GTGAAGCGTCAAACATGTCCTTAA 60.024 41.667 3.20 0.00 34.87 1.85
8074 12824 4.213482 GCGTCAAACATGTCCTTAACTTCT 59.787 41.667 0.00 0.00 0.00 2.85
8143 12893 0.319728 CTCCATCTGCCCCAGTATCG 59.680 60.000 0.00 0.00 32.61 2.92
8203 12953 1.555477 CACAACAAAACCAACGAGGC 58.445 50.000 0.00 0.00 43.14 4.70
8381 13131 2.320587 CCTGTCCACAACTCGCAGC 61.321 63.158 0.00 0.00 0.00 5.25
8418 13168 0.663153 GTCCCATCGCAATTACAGGC 59.337 55.000 0.00 0.00 0.00 4.85
8462 13212 1.804151 CACTACCATCAAACCCACACG 59.196 52.381 0.00 0.00 0.00 4.49
8483 13233 5.696270 CACGTTATGCTTCTAGCCAATGATA 59.304 40.000 0.00 0.00 41.51 2.15
8484 13234 6.369890 CACGTTATGCTTCTAGCCAATGATAT 59.630 38.462 0.00 0.00 41.51 1.63
8486 13236 7.445402 ACGTTATGCTTCTAGCCAATGATATTT 59.555 33.333 8.45 0.00 41.51 1.40
8487 13237 7.959651 CGTTATGCTTCTAGCCAATGATATTTC 59.040 37.037 0.00 0.00 41.51 2.17
8488 13238 9.007901 GTTATGCTTCTAGCCAATGATATTTCT 57.992 33.333 0.00 0.00 41.51 2.52
8496 13247 6.690194 AGCCAATGATATTTCTCTTGTCAC 57.310 37.500 0.00 0.00 0.00 3.67
8614 13365 1.559682 CCCCCTTTCAGCAGCTTACTA 59.440 52.381 0.00 0.00 0.00 1.82
8616 13367 2.237392 CCCCTTTCAGCAGCTTACTACT 59.763 50.000 0.00 0.00 0.00 2.57
8617 13368 3.307762 CCCCTTTCAGCAGCTTACTACTT 60.308 47.826 0.00 0.00 0.00 2.24
8618 13369 3.935828 CCCTTTCAGCAGCTTACTACTTC 59.064 47.826 0.00 0.00 0.00 3.01
8619 13370 4.323104 CCCTTTCAGCAGCTTACTACTTCT 60.323 45.833 0.00 0.00 0.00 2.85
8620 13371 5.105310 CCCTTTCAGCAGCTTACTACTTCTA 60.105 44.000 0.00 0.00 0.00 2.10
9032 13784 9.274206 GGTATCGCCTTTATCTATTTTTCTCTT 57.726 33.333 0.00 0.00 0.00 2.85
9042 13794 9.912634 TTATCTATTTTTCTCTTTGTTTGCTGG 57.087 29.630 0.00 0.00 0.00 4.85
9245 13997 4.748102 GGCCAATTGATGCATCTTTATGTG 59.252 41.667 26.32 14.85 35.38 3.21
9276 14028 7.227873 TCATGTTTATGGAGTAGTTTTGGTCA 58.772 34.615 0.00 0.00 34.97 4.02
9301 14053 4.764172 AGCTTAACATCTGGTGAGACATC 58.236 43.478 0.00 0.00 0.00 3.06
9354 14106 5.527511 TTGTCAACACATTTTGCAAACAG 57.472 34.783 12.39 9.86 30.55 3.16
9415 14167 2.939103 AGAAAACAGATATCGCCTGTGC 59.061 45.455 0.00 0.00 43.42 4.57
9479 14580 1.717032 TCCTCATAATCAGGGGTCGG 58.283 55.000 0.00 0.00 0.00 4.79
9487 14588 0.991920 ATCAGGGGTCGGTCATTTGT 59.008 50.000 0.00 0.00 0.00 2.83
9565 14667 2.304751 GCATGCAAAGCTATGCCTTT 57.695 45.000 14.21 0.00 45.83 3.11
9604 14706 6.624352 TGCTATGCAGGAAATCATTTACTC 57.376 37.500 0.00 0.00 29.18 2.59
9645 14747 1.694696 GAAGAGTTGACCAGGTGACCT 59.305 52.381 0.00 0.00 0.00 3.85
9666 14768 1.655654 CCTCGTCGCATCGTGCTAG 60.656 63.158 8.07 0.00 42.25 3.42
9720 14823 6.557568 TGTTAATCCCCATGTTCTAAACCTT 58.442 36.000 0.00 0.00 0.00 3.50
9724 14827 5.853572 TCCCCATGTTCTAAACCTTTACT 57.146 39.130 0.00 0.00 0.00 2.24
9728 14831 6.071560 CCCCATGTTCTAAACCTTTACTTTCC 60.072 42.308 0.00 0.00 0.00 3.13
9739 14842 4.653801 ACCTTTACTTTCCCAGCATTTTGT 59.346 37.500 0.00 0.00 0.00 2.83
9741 14844 6.054941 CCTTTACTTTCCCAGCATTTTGTTT 58.945 36.000 0.00 0.00 0.00 2.83
9742 14845 7.147637 ACCTTTACTTTCCCAGCATTTTGTTTA 60.148 33.333 0.00 0.00 0.00 2.01
9743 14846 7.713073 CCTTTACTTTCCCAGCATTTTGTTTAA 59.287 33.333 0.00 0.00 0.00 1.52
9744 14847 8.426881 TTTACTTTCCCAGCATTTTGTTTAAC 57.573 30.769 0.00 0.00 0.00 2.01
9745 14848 5.983540 ACTTTCCCAGCATTTTGTTTAACA 58.016 33.333 0.00 0.00 0.00 2.41
9746 14849 6.591001 ACTTTCCCAGCATTTTGTTTAACAT 58.409 32.000 0.00 0.00 0.00 2.71
9747 14850 7.053498 ACTTTCCCAGCATTTTGTTTAACATT 58.947 30.769 0.00 0.00 0.00 2.71
9748 14851 8.207545 ACTTTCCCAGCATTTTGTTTAACATTA 58.792 29.630 0.00 0.00 0.00 1.90
9749 14852 8.600449 TTTCCCAGCATTTTGTTTAACATTAG 57.400 30.769 0.00 0.00 0.00 1.73
9750 14853 7.296628 TCCCAGCATTTTGTTTAACATTAGT 57.703 32.000 0.00 0.00 0.00 2.24
9751 14854 7.151308 TCCCAGCATTTTGTTTAACATTAGTG 58.849 34.615 0.00 0.00 0.00 2.74
9757 14860 9.030301 GCATTTTGTTTAACATTAGTGAAGTGT 57.970 29.630 0.00 0.00 0.00 3.55
9782 14885 5.565592 AATGATTTTACTCGCAGCAATCA 57.434 34.783 6.15 6.15 38.04 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.660552 AAGTTGCGACACGTCCGG 60.661 61.111 6.90 0.00 0.00 5.14
31 32 3.067601 AGGTTTGAACAAATTCCGACACC 59.932 43.478 3.34 0.00 33.49 4.16
43 44 3.663995 CATCCATGCAAGGTTTGAACA 57.336 42.857 8.03 0.00 0.00 3.18
86 88 4.637387 ATGAAATGACCCAAATTTGCCA 57.363 36.364 12.92 10.05 0.00 4.92
124 126 2.599757 GGCCTACCCGAACACCCTT 61.600 63.158 0.00 0.00 0.00 3.95
143 145 3.228188 TGCTCTCAAATGGACCTTTGT 57.772 42.857 12.99 0.00 37.39 2.83
147 149 2.575279 AGACATGCTCTCAAATGGACCT 59.425 45.455 0.00 0.00 0.00 3.85
153 155 3.341823 GACCACAGACATGCTCTCAAAT 58.658 45.455 0.00 0.00 0.00 2.32
199 201 1.074084 TGATACAAGGCCACCGGAAAA 59.926 47.619 9.46 0.00 0.00 2.29
242 244 9.505995 GCAAAACTTGATGAAAATTCAAACAAT 57.494 25.926 14.60 4.43 41.13 2.71
251 253 9.111613 TGAGAAAATGCAAAACTTGATGAAAAT 57.888 25.926 0.00 0.00 0.00 1.82
324 326 6.993786 TTGAACGAATTCCAATAGCATACA 57.006 33.333 0.00 0.00 33.49 2.29
334 336 1.611491 GCCTGGTTTGAACGAATTCCA 59.389 47.619 0.00 0.00 33.49 3.53
335 337 1.611491 TGCCTGGTTTGAACGAATTCC 59.389 47.619 0.00 0.00 33.49 3.01
372 374 1.070786 GAAGTCGGCCACCAAGTGA 59.929 57.895 2.24 0.00 35.23 3.41
457 459 3.636282 TGCGTATGTATGAGCGTATGT 57.364 42.857 0.00 0.00 0.00 2.29
467 469 5.056480 AGTGTATGTGCAATGCGTATGTAT 58.944 37.500 0.00 0.00 0.00 2.29
478 480 4.466015 TCATAGGAGTGAGTGTATGTGCAA 59.534 41.667 0.00 0.00 0.00 4.08
494 496 0.459899 AGTGCGCATCGTTCATAGGA 59.540 50.000 15.91 0.00 0.00 2.94
506 508 3.006756 GCAGGGAGTAGAGTGCGCA 62.007 63.158 5.66 5.66 0.00 6.09
540 542 7.472334 AAATAATGTGATGGCTCAGTTTCTT 57.528 32.000 0.00 0.00 30.18 2.52
560 562 7.478044 CGCGGTGACTTCGTTAATTTTAAAATA 59.522 33.333 13.68 0.00 0.00 1.40
563 565 5.138788 CGCGGTGACTTCGTTAATTTTAAA 58.861 37.500 0.00 0.00 0.00 1.52
569 571 2.634982 TACGCGGTGACTTCGTTAAT 57.365 45.000 12.47 0.00 38.04 1.40
572 574 1.343506 GAATACGCGGTGACTTCGTT 58.656 50.000 12.47 0.00 38.04 3.85
584 586 0.933509 CCCGCTGACTACGAATACGC 60.934 60.000 0.00 0.00 43.96 4.42
586 588 2.857592 TTCCCGCTGACTACGAATAC 57.142 50.000 0.00 0.00 0.00 1.89
609 615 0.391597 TGTCCGTTCAGTGGGAGAAC 59.608 55.000 0.00 0.00 41.41 3.01
775 1109 5.790593 ACTAGGAGCACGTCTGATTAAAAA 58.209 37.500 0.00 0.00 0.00 1.94
776 1110 5.401531 ACTAGGAGCACGTCTGATTAAAA 57.598 39.130 0.00 0.00 0.00 1.52
777 1111 5.401531 AACTAGGAGCACGTCTGATTAAA 57.598 39.130 0.00 0.00 0.00 1.52
778 1112 5.401531 AAACTAGGAGCACGTCTGATTAA 57.598 39.130 0.00 0.00 0.00 1.40
779 1113 5.401531 AAAACTAGGAGCACGTCTGATTA 57.598 39.130 0.00 0.00 0.00 1.75
780 1114 3.963428 AAACTAGGAGCACGTCTGATT 57.037 42.857 0.00 0.00 0.00 2.57
781 1115 3.963428 AAAACTAGGAGCACGTCTGAT 57.037 42.857 0.00 0.00 0.00 2.90
782 1116 3.390135 CAAAAACTAGGAGCACGTCTGA 58.610 45.455 0.00 0.00 0.00 3.27
783 1117 2.096218 GCAAAAACTAGGAGCACGTCTG 60.096 50.000 0.00 0.00 0.00 3.51
784 1118 2.143925 GCAAAAACTAGGAGCACGTCT 58.856 47.619 0.00 0.00 0.00 4.18
785 1119 1.197036 GGCAAAAACTAGGAGCACGTC 59.803 52.381 0.00 0.00 0.00 4.34
786 1120 1.235724 GGCAAAAACTAGGAGCACGT 58.764 50.000 0.00 0.00 0.00 4.49
787 1121 0.521735 GGGCAAAAACTAGGAGCACG 59.478 55.000 0.00 0.00 0.00 5.34
788 1122 1.541588 CAGGGCAAAAACTAGGAGCAC 59.458 52.381 0.00 0.00 0.00 4.40
789 1123 1.423541 TCAGGGCAAAAACTAGGAGCA 59.576 47.619 0.00 0.00 0.00 4.26
790 1124 1.813178 GTCAGGGCAAAAACTAGGAGC 59.187 52.381 0.00 0.00 0.00 4.70
791 1125 3.425162 AGTCAGGGCAAAAACTAGGAG 57.575 47.619 0.00 0.00 0.00 3.69
792 1126 3.307480 GCTAGTCAGGGCAAAAACTAGGA 60.307 47.826 13.90 0.00 40.88 2.94
793 1127 3.010420 GCTAGTCAGGGCAAAAACTAGG 58.990 50.000 13.90 1.76 40.88 3.02
794 1128 3.674997 TGCTAGTCAGGGCAAAAACTAG 58.325 45.455 9.83 9.83 42.57 2.57
795 1129 3.780804 TGCTAGTCAGGGCAAAAACTA 57.219 42.857 0.00 0.00 35.40 2.24
796 1130 2.656947 TGCTAGTCAGGGCAAAAACT 57.343 45.000 0.00 0.00 35.40 2.66
828 2383 1.160946 TGCTTTGTCGCGCCTTAACA 61.161 50.000 0.00 0.00 0.00 2.41
838 2393 1.647346 TATTACGGGCTGCTTTGTCG 58.353 50.000 0.00 0.00 0.00 4.35
839 2394 3.730963 GCTTTATTACGGGCTGCTTTGTC 60.731 47.826 0.00 0.00 0.00 3.18
842 2397 2.423538 CTGCTTTATTACGGGCTGCTTT 59.576 45.455 0.00 0.00 0.00 3.51
876 2431 7.966204 GCACTTCCTTGTATTTTCGCTTAATAA 59.034 33.333 0.00 0.00 0.00 1.40
877 2432 7.414762 GGCACTTCCTTGTATTTTCGCTTAATA 60.415 37.037 0.00 0.00 0.00 0.98
1073 2632 1.071699 AGCTGCAAAGAAGTAACCCGA 59.928 47.619 1.02 0.00 0.00 5.14
1134 2702 3.502875 GAATCTCCCCCTGCCCCC 61.503 72.222 0.00 0.00 0.00 5.40
1295 2863 1.305201 GGAACAACTGCGAAAGGTCA 58.695 50.000 0.00 0.00 0.00 4.02
1695 3263 2.687935 GTGAGCCTGTTTTTGTTCTGGA 59.312 45.455 0.00 0.00 0.00 3.86
1751 3319 8.819974 GTTTTGCATCATTCAAAAGAAAGAAGA 58.180 29.630 0.00 0.00 42.08 2.87
1756 3324 8.489990 TGAAGTTTTGCATCATTCAAAAGAAA 57.510 26.923 0.00 0.00 42.08 2.52
1782 3350 4.520111 CGCAAGGAATCCAATTGATCCATA 59.480 41.667 20.16 0.00 31.61 2.74
1825 3393 0.696501 ATTTGGTTACGGTGGAGCCT 59.303 50.000 0.00 0.00 34.25 4.58
1826 3394 2.406596 TATTTGGTTACGGTGGAGCC 57.593 50.000 0.00 0.00 0.00 4.70
1828 3396 5.820423 TGATCATTATTTGGTTACGGTGGAG 59.180 40.000 0.00 0.00 0.00 3.86
1829 3397 5.587043 GTGATCATTATTTGGTTACGGTGGA 59.413 40.000 0.00 0.00 0.00 4.02
1830 3398 5.355630 TGTGATCATTATTTGGTTACGGTGG 59.644 40.000 0.00 0.00 27.60 4.61
1832 3400 7.227910 GGTATGTGATCATTATTTGGTTACGGT 59.772 37.037 0.00 0.00 35.70 4.83
1887 3456 9.569122 AACTATTTGTTTTCATAGTACACCTGT 57.431 29.630 0.00 0.00 34.84 4.00
1956 3525 4.400845 CAAATTGTCGAGCTGAGACATTG 58.599 43.478 18.74 16.72 46.44 2.82
1957 3526 3.438087 CCAAATTGTCGAGCTGAGACATT 59.562 43.478 18.74 13.79 46.44 2.71
2044 3613 4.832248 TCTCAAGCTAACATTGTACCTGG 58.168 43.478 0.00 0.00 0.00 4.45
2208 3780 3.131240 ACGCGCATCTTATTTTTGACC 57.869 42.857 5.73 0.00 0.00 4.02
2225 3802 3.679725 TGTTTCATATGCAATCGAACGC 58.320 40.909 0.00 2.63 0.00 4.84
2341 3918 7.811236 ACTTAACGATGACGAGTATTGAGAAAA 59.189 33.333 0.00 0.00 42.66 2.29
2350 3927 7.118245 TCTGAGTAAACTTAACGATGACGAGTA 59.882 37.037 0.00 0.00 42.66 2.59
2355 3932 6.308282 CAGGTCTGAGTAAACTTAACGATGAC 59.692 42.308 0.00 0.00 0.00 3.06
2360 3937 8.433126 CAATAACAGGTCTGAGTAAACTTAACG 58.567 37.037 4.84 0.00 0.00 3.18
2402 3979 6.752168 AGTAAAGCTGCAAATGATGTCTTTT 58.248 32.000 1.02 0.00 32.08 2.27
2457 4034 9.903682 AGAACAATTGAAACTGTCAGATAAATG 57.096 29.630 13.59 2.52 37.61 2.32
2477 4054 8.845227 TGATAGCACAAACAGAATAAAGAACAA 58.155 29.630 0.00 0.00 0.00 2.83
2518 4095 9.886132 GAAAGTCAGGGAGTTACAATAGATAAA 57.114 33.333 0.00 0.00 0.00 1.40
2519 4096 8.483758 GGAAAGTCAGGGAGTTACAATAGATAA 58.516 37.037 0.00 0.00 0.00 1.75
2520 4097 7.201884 CGGAAAGTCAGGGAGTTACAATAGATA 60.202 40.741 0.00 0.00 0.00 1.98
2521 4098 6.407074 CGGAAAGTCAGGGAGTTACAATAGAT 60.407 42.308 0.00 0.00 0.00 1.98
2522 4099 5.105473 CGGAAAGTCAGGGAGTTACAATAGA 60.105 44.000 0.00 0.00 0.00 1.98
2523 4100 5.109903 CGGAAAGTCAGGGAGTTACAATAG 58.890 45.833 0.00 0.00 0.00 1.73
2524 4101 4.529377 ACGGAAAGTCAGGGAGTTACAATA 59.471 41.667 0.00 0.00 0.00 1.90
2525 4102 3.326880 ACGGAAAGTCAGGGAGTTACAAT 59.673 43.478 0.00 0.00 0.00 2.71
2526 4103 2.701951 ACGGAAAGTCAGGGAGTTACAA 59.298 45.455 0.00 0.00 0.00 2.41
2527 4104 2.322658 ACGGAAAGTCAGGGAGTTACA 58.677 47.619 0.00 0.00 0.00 2.41
2528 4105 4.525912 TTACGGAAAGTCAGGGAGTTAC 57.474 45.455 0.00 0.00 0.00 2.50
2529 4106 5.549742 TTTTACGGAAAGTCAGGGAGTTA 57.450 39.130 0.00 0.00 0.00 2.24
2530 4107 4.426736 TTTTACGGAAAGTCAGGGAGTT 57.573 40.909 0.00 0.00 0.00 3.01
2531 4108 4.635699 ATTTTACGGAAAGTCAGGGAGT 57.364 40.909 0.00 0.00 0.00 3.85
2532 4109 7.553044 AGAATTATTTTACGGAAAGTCAGGGAG 59.447 37.037 0.00 0.00 0.00 4.30
2533 4110 7.399634 AGAATTATTTTACGGAAAGTCAGGGA 58.600 34.615 0.00 0.00 0.00 4.20
2534 4111 7.625828 AGAATTATTTTACGGAAAGTCAGGG 57.374 36.000 0.00 0.00 0.00 4.45
2535 4112 9.556030 GAAAGAATTATTTTACGGAAAGTCAGG 57.444 33.333 0.00 0.00 0.00 3.86
2538 4115 9.556030 CCAGAAAGAATTATTTTACGGAAAGTC 57.444 33.333 0.00 0.00 0.00 3.01
2883 4500 4.338682 AGAAGCTTGATTGATTGATCAGCC 59.661 41.667 2.10 0.00 37.35 4.85
2917 4534 8.603242 TGTCAGATAATGAAGATCATCACATG 57.397 34.615 2.13 0.00 40.43 3.21
2947 4566 5.413833 GCATAAGGTGGAATCATAGATGGTG 59.586 44.000 0.00 0.00 0.00 4.17
2954 4573 6.942005 CAGTATTGGCATAAGGTGGAATCATA 59.058 38.462 0.00 0.00 0.00 2.15
2958 4577 4.473444 CCAGTATTGGCATAAGGTGGAAT 58.527 43.478 0.00 0.00 37.73 3.01
3079 4698 8.893563 ATCATTGGTTTTTAACTAGGAATCCA 57.106 30.769 0.61 0.00 0.00 3.41
3115 4734 1.514678 GAACTTGTCATGGGCGCACA 61.515 55.000 18.16 18.16 0.00 4.57
3233 4852 6.756542 GTCAAGCAACTACTTCAACCAAAATT 59.243 34.615 0.00 0.00 0.00 1.82
3364 4984 0.598065 ATTGGTCTGTCAAAAGCCGC 59.402 50.000 0.00 0.00 0.00 6.53
3421 5041 5.878332 AACATGTCGTCATAGAAATGCAA 57.122 34.783 0.00 0.00 38.99 4.08
3438 5058 8.517878 ACTGAAAAGATCTTCCATACAAACATG 58.482 33.333 8.78 0.00 0.00 3.21
3506 5127 8.977412 TCCATGACTAGTCAATGATGTAACTAA 58.023 33.333 28.43 0.89 43.58 2.24
3554 5175 3.952323 CCACCTGTTCTAGTCTAATCGGA 59.048 47.826 0.00 0.00 0.00 4.55
3596 5217 4.947645 ACGCTTACCGGCTAATTATACAA 58.052 39.130 0.00 0.00 42.52 2.41
3605 5226 1.545582 AGTTACAACGCTTACCGGCTA 59.454 47.619 0.00 0.00 42.52 3.93
3653 5274 0.819582 CCAATCAACCTCCCACATGC 59.180 55.000 0.00 0.00 0.00 4.06
3682 5303 9.787532 GCACAGTAATCAAAACATTATGTACAT 57.212 29.630 13.93 13.93 0.00 2.29
3736 5357 4.787551 ACTGTGTTACCATGTCCTGAAAA 58.212 39.130 0.00 0.00 0.00 2.29
3786 5407 4.926140 AATAATTAAGCCAAGGAGCTGC 57.074 40.909 0.00 0.00 44.11 5.25
3796 5417 8.470002 ACTCATTTGTCTCCAAATAATTAAGCC 58.530 33.333 0.74 0.00 46.91 4.35
3824 5445 9.173021 TGTTATTAATATGTCAACAGGAACAGG 57.827 33.333 0.00 0.00 0.00 4.00
3829 5450 9.183368 TGCAATGTTATTAATATGTCAACAGGA 57.817 29.630 6.82 0.00 33.04 3.86
3945 5580 0.247736 ACAATCCTGCACTCCTCGTC 59.752 55.000 0.00 0.00 0.00 4.20
4035 5671 6.166279 TCACCTGCAGTCTATTACTTTCTTG 58.834 40.000 13.81 0.00 35.76 3.02
4044 5680 7.335422 CAGAAATTAGTTCACCTGCAGTCTATT 59.665 37.037 13.81 0.00 38.86 1.73
4059 5695 7.120923 TCCCGTAGATTAGCAGAAATTAGTT 57.879 36.000 0.00 0.00 0.00 2.24
4080 5716 3.774766 AGGTTGGCATTTTTATTCCTCCC 59.225 43.478 0.00 0.00 0.00 4.30
4125 5761 5.094387 CTGTACCCTATCAGTATCCCCATT 58.906 45.833 0.00 0.00 0.00 3.16
4197 5833 9.765795 ACTTATTGTATTTACCTGTCAGCTATC 57.234 33.333 0.00 0.00 0.00 2.08
4223 5859 1.153107 ATCAGCTGCGCATGGCTTA 60.153 52.632 20.32 13.93 44.05 3.09
4233 5869 2.275318 GGTTACAGAGTCATCAGCTGC 58.725 52.381 9.47 0.00 33.03 5.25
4286 5922 0.338120 CACTCTCCCCTCCCTCTCTT 59.662 60.000 0.00 0.00 0.00 2.85
4378 6016 5.195940 CCACCATTATCCACAGTTCTCAAT 58.804 41.667 0.00 0.00 0.00 2.57
4404 6042 1.867363 ATACAGCTTCCCTTCCGTCT 58.133 50.000 0.00 0.00 0.00 4.18
4518 6156 2.286418 CGAGGTTTTCTGTGACTTGTGC 60.286 50.000 0.00 0.00 0.00 4.57
4526 6164 3.857052 TGTATAGCCGAGGTTTTCTGTG 58.143 45.455 0.00 0.00 0.00 3.66
4631 6269 0.392327 TGTGTGTGTGTGTGACAGGG 60.392 55.000 0.00 0.00 34.28 4.45
4654 6292 2.418368 AAGATGGTGTGTGTGTGTGT 57.582 45.000 0.00 0.00 0.00 3.72
4655 6293 2.682352 TCAAAGATGGTGTGTGTGTGTG 59.318 45.455 0.00 0.00 0.00 3.82
4656 6294 2.682856 GTCAAAGATGGTGTGTGTGTGT 59.317 45.455 0.00 0.00 0.00 3.72
4657 6295 2.033299 GGTCAAAGATGGTGTGTGTGTG 59.967 50.000 0.00 0.00 0.00 3.82
4658 6296 2.297701 GGTCAAAGATGGTGTGTGTGT 58.702 47.619 0.00 0.00 0.00 3.72
4659 6297 2.033299 GTGGTCAAAGATGGTGTGTGTG 59.967 50.000 0.00 0.00 0.00 3.82
4660 6298 2.092429 AGTGGTCAAAGATGGTGTGTGT 60.092 45.455 0.00 0.00 0.00 3.72
4661 6299 2.575532 AGTGGTCAAAGATGGTGTGTG 58.424 47.619 0.00 0.00 0.00 3.82
4662 6300 3.117888 AGAAGTGGTCAAAGATGGTGTGT 60.118 43.478 0.00 0.00 0.00 3.72
4663 6301 3.480470 AGAAGTGGTCAAAGATGGTGTG 58.520 45.455 0.00 0.00 0.00 3.82
4734 6372 1.067364 TGTGGCTCAAATGTTGCACAG 59.933 47.619 0.00 0.00 30.97 3.66
4747 6385 5.468072 CACATAATCCAAGATACTGTGGCTC 59.532 44.000 9.77 0.00 34.68 4.70
4907 6545 1.948635 CTGGTTTTGTTTGCCCGCG 60.949 57.895 0.00 0.00 0.00 6.46
4911 6549 6.327279 ACTATACTTCTGGTTTTGTTTGCC 57.673 37.500 0.00 0.00 0.00 4.52
4912 6550 9.908152 ATAAACTATACTTCTGGTTTTGTTTGC 57.092 29.630 0.00 0.00 36.35 3.68
4988 6626 4.363991 ACTGGAAAGTCTCAGCAGATTT 57.636 40.909 0.00 0.00 34.57 2.17
5006 6644 4.984785 CCAATGTGTACATCCTCGATACTG 59.015 45.833 0.00 0.00 35.10 2.74
5018 6656 6.986231 CAGATAATACTCAGCCAATGTGTACA 59.014 38.462 0.00 0.00 39.87 2.90
5049 6687 6.627087 TTCCTTCCAGTCATCAGAGTATTT 57.373 37.500 0.00 0.00 0.00 1.40
5064 6702 8.367156 CAAGTCCAAAGAATAATTTTCCTTCCA 58.633 33.333 0.00 0.00 0.00 3.53
5159 6798 1.468520 CCAGAGCATACAAACCCGTTG 59.531 52.381 0.00 0.00 43.43 4.10
5249 7026 4.963373 TCTGGAACGTAAGGATCAAAACA 58.037 39.130 0.00 0.00 46.39 2.83
5338 7115 1.628846 GCCCTTTAGACCAAGGAGTGA 59.371 52.381 0.77 0.00 45.79 3.41
5344 7121 4.937201 AAAACTTGCCCTTTAGACCAAG 57.063 40.909 0.00 0.00 40.26 3.61
5349 7126 5.666462 GGAAACAAAAACTTGCCCTTTAGA 58.334 37.500 0.00 0.00 0.00 2.10
5354 7131 2.104170 TCGGAAACAAAAACTTGCCCT 58.896 42.857 0.00 0.00 0.00 5.19
5395 7172 6.198639 ACTTCCCAAGTACTCTGATGTAGAT 58.801 40.000 0.00 0.00 40.69 1.98
5441 7248 7.546316 GGTGAGACTAAGAAATAACCTCAGTTC 59.454 40.741 0.00 0.00 37.42 3.01
5597 7531 7.633664 GTGTTAAGTTAAACGAGACAGAACAAC 59.366 37.037 0.00 0.00 31.76 3.32
5676 7615 2.504175 ACGGTGATACCAATACAAGGCT 59.496 45.455 0.00 0.00 38.47 4.58
5682 7621 4.525487 TGAGGGATACGGTGATACCAATAC 59.475 45.833 0.00 0.00 38.47 1.89
5835 7774 5.867903 TGGTGTTTTCTTCCATGTTCAAT 57.132 34.783 0.00 0.00 0.00 2.57
5855 7794 4.060205 CTGATTTTTCAGGGCTTGTTTGG 58.940 43.478 0.00 0.00 34.28 3.28
5859 7798 3.960102 TCAACTGATTTTTCAGGGCTTGT 59.040 39.130 7.80 0.00 41.76 3.16
5953 7892 1.370609 CCACAGAGCTGCTTCATCTG 58.629 55.000 13.22 13.22 44.81 2.90
6143 8082 1.000938 CTTCCAACTTCTGCTGCAACC 60.001 52.381 3.02 0.00 0.00 3.77
6170 8109 1.816679 GGAATACGGGGCAACGGAC 60.817 63.158 5.83 0.00 38.39 4.79
6222 8161 7.364144 GGCCTCAAAATCTTGGTCTTCAAATAT 60.364 37.037 0.00 0.00 34.56 1.28
6502 8441 1.774110 ACTGTGCCATGGTGTTTCAA 58.226 45.000 14.67 0.00 0.00 2.69
6554 8493 3.958798 CTGCATCCCAAGAATCTTCCAAT 59.041 43.478 0.00 0.00 0.00 3.16
6716 8655 0.034186 TGGGGTGTGCATCATCTTCC 60.034 55.000 0.00 0.00 0.00 3.46
6898 8837 3.261897 CCAGCTCCACTCTTCTTTAGGAA 59.738 47.826 0.00 0.00 0.00 3.36
6899 8838 2.834549 CCAGCTCCACTCTTCTTTAGGA 59.165 50.000 0.00 0.00 0.00 2.94
6900 8839 2.834549 TCCAGCTCCACTCTTCTTTAGG 59.165 50.000 0.00 0.00 0.00 2.69
7036 8978 6.936900 AGAGATGTTGTGTTAAATACTGCACT 59.063 34.615 0.00 0.00 33.44 4.40
7133 11880 4.496010 CGAAGTGAACTACATACTCCCTCG 60.496 50.000 0.00 0.00 0.00 4.63
7148 11895 8.495949 GTTGAAGAGAACAAATATCGAAGTGAA 58.504 33.333 0.00 0.00 0.00 3.18
7268 12018 0.108424 GTCCTAGCAGTGCAGTCCAG 60.108 60.000 19.20 5.86 0.00 3.86
7579 12329 2.019984 GGCATTTTCTCCGATGCTTCT 58.980 47.619 8.06 0.00 46.01 2.85
7648 12398 4.259356 TGAGTCTTCTCAATGCATCTTGG 58.741 43.478 0.00 0.00 46.17 3.61
7748 12498 7.158099 ACTTGTAAGGTGGAATAAAATCTGC 57.842 36.000 0.00 0.00 0.00 4.26
7869 12619 0.189574 TGAGGGCCACAAATTTGGGA 59.810 50.000 22.16 0.00 37.10 4.37
7877 12627 1.852157 ACCATCCTGAGGGCCACAA 60.852 57.895 6.18 0.00 35.25 3.33
7908 12658 2.359975 CGGAACCTGGACTTGGGC 60.360 66.667 0.00 0.00 0.00 5.36
8069 12819 4.351111 AGGTTGAGGTGGTTTCATAGAAGT 59.649 41.667 0.00 0.00 0.00 3.01
8074 12824 2.983192 TGGAGGTTGAGGTGGTTTCATA 59.017 45.455 0.00 0.00 0.00 2.15
8218 12968 0.036732 TGTTTGAGCTGCCTACTGGG 59.963 55.000 0.00 0.00 38.36 4.45
8418 13168 2.978010 GTATTGGCGGCGGATGGG 60.978 66.667 9.78 0.00 0.00 4.00
8462 13212 9.007901 AGAAATATCATTGGCTAGAAGCATAAC 57.992 33.333 0.00 0.00 44.75 1.89
8496 13247 2.552315 AGGTGGTAAATGCAAAGTCGTG 59.448 45.455 0.00 0.00 0.00 4.35
8614 13365 0.246635 ATTGACGCACCGCTAGAAGT 59.753 50.000 0.00 0.00 0.00 3.01
8616 13367 1.358725 GCATTGACGCACCGCTAGAA 61.359 55.000 0.00 0.00 0.00 2.10
8617 13368 1.809619 GCATTGACGCACCGCTAGA 60.810 57.895 0.00 0.00 0.00 2.43
8618 13369 1.634757 TTGCATTGACGCACCGCTAG 61.635 55.000 0.00 0.00 42.87 3.42
8619 13370 1.231296 TTTGCATTGACGCACCGCTA 61.231 50.000 0.00 0.00 42.87 4.26
8620 13371 2.551006 TTTGCATTGACGCACCGCT 61.551 52.632 0.00 0.00 42.87 5.52
8682 13433 0.247736 CTCCGTCAAGGTCTTCCTGG 59.752 60.000 0.00 0.00 44.35 4.45
9005 13756 7.599245 AGAGAAAAATAGATAAAGGCGATACCG 59.401 37.037 0.00 0.00 46.52 4.02
9032 13784 5.337169 GGCCAGATTTTATACCAGCAAACAA 60.337 40.000 0.00 0.00 0.00 2.83
9041 13793 3.891366 ACAGCATGGCCAGATTTTATACC 59.109 43.478 13.05 0.00 43.62 2.73
9042 13794 5.520376 AACAGCATGGCCAGATTTTATAC 57.480 39.130 13.05 0.00 43.62 1.47
9245 13997 5.665459 ACTACTCCATAAACATGAGTGAGC 58.335 41.667 0.00 0.00 0.00 4.26
9276 14028 4.284490 TGTCTCACCAGATGTTAAGCTTCT 59.716 41.667 0.00 0.00 32.54 2.85
9334 14086 4.388469 ACACTGTTTGCAAAATGTGTTGAC 59.612 37.500 29.78 13.19 34.93 3.18
9354 14106 2.648059 AGGGCTTATGAATCAGCACAC 58.352 47.619 1.83 0.00 42.39 3.82
9415 14167 5.349817 ACGTATATGACCGGTAGTTCTATCG 59.650 44.000 7.34 8.94 0.00 2.92
9479 14580 7.970614 GTCATTTCCTATCCTTGAACAAATGAC 59.029 37.037 15.17 15.17 45.33 3.06
9487 14588 7.403231 AGACCTAAGTCATTTCCTATCCTTGAA 59.597 37.037 0.00 0.00 46.15 2.69
9565 14667 4.680708 GCATAGCAGGCTCACTACTACAAA 60.681 45.833 0.00 0.00 27.96 2.83
9604 14706 8.301730 TCTTCTACGTGGTTTTACAAGTAATG 57.698 34.615 0.00 0.00 35.48 1.90
9617 14719 2.296471 CTGGTCAACTCTTCTACGTGGT 59.704 50.000 0.00 0.00 0.00 4.16
9618 14720 2.352814 CCTGGTCAACTCTTCTACGTGG 60.353 54.545 0.00 0.00 0.00 4.94
9619 14721 2.296471 ACCTGGTCAACTCTTCTACGTG 59.704 50.000 0.00 0.00 0.00 4.49
9645 14747 2.178273 CACGATGCGACGAGGACA 59.822 61.111 0.00 0.00 37.03 4.02
9720 14823 7.556844 TGTTAAACAAAATGCTGGGAAAGTAA 58.443 30.769 0.00 0.00 0.00 2.24
9724 14827 8.207545 ACTAATGTTAAACAAAATGCTGGGAAA 58.792 29.630 0.00 0.00 0.00 3.13
9728 14831 8.586570 TTCACTAATGTTAAACAAAATGCTGG 57.413 30.769 0.00 0.00 0.00 4.85
9757 14860 7.484641 GTGATTGCTGCGAGTAAAATCATTTTA 59.515 33.333 12.14 0.00 38.93 1.52


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

AutoCloner maintained by Alex Coulton.