Multiple sequence alignment - TraesCS3D01G096800

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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 TraesCS3D01G096800 chr3D 100.000 4054 0 0 1 4054 48864385 48868438 0.000000e+00 7487
1 TraesCS3D01G096800 chr3D 94.068 118 6 1 3528 3645 162449549 162449665 1.160000e-40 178
2 TraesCS3D01G096800 chr3A 91.991 2135 155 8 1395 3526 61347557 61349678 0.000000e+00 2981
3 TraesCS3D01G096800 chr3A 88.011 1126 123 7 2080 3203 61434812 61435927 0.000000e+00 1321
4 TraesCS3D01G096800 chr3A 87.564 973 79 22 418 1357 61346593 61347556 0.000000e+00 1088
5 TraesCS3D01G096800 chr3A 89.367 395 27 5 1 384 61346208 61346598 2.190000e-132 483
6 TraesCS3D01G096800 chr3A 96.313 217 6 2 3822 4038 61436179 61436393 4.980000e-94 355
7 TraesCS3D01G096800 chr3A 97.143 70 2 0 3688 3757 61436117 61436186 7.120000e-23 119
8 TraesCS3D01G096800 chr3B 92.992 1955 125 8 1584 3535 78397411 78399356 0.000000e+00 2841
9 TraesCS3D01G096800 chr3B 88.837 1487 86 29 1 1452 78395959 78397400 0.000000e+00 1753
10 TraesCS3D01G096800 chr3B 95.628 183 4 2 3872 4054 78521554 78521732 1.430000e-74 291
11 TraesCS3D01G096800 chr3B 95.946 148 6 0 3688 3835 78521404 78521551 1.460000e-59 241
12 TraesCS3D01G096800 chr3B 92.857 126 7 2 3520 3645 803756907 803757030 8.950000e-42 182
13 TraesCS3D01G096800 chr7B 96.460 113 4 0 3533 3645 64575793 64575681 1.920000e-43 187
14 TraesCS3D01G096800 chr7B 94.068 118 7 0 3528 3645 556825294 556825411 3.220000e-41 180
15 TraesCS3D01G096800 chr2D 96.460 113 4 0 3533 3645 204855801 204855913 1.920000e-43 187
16 TraesCS3D01G096800 chr5B 96.396 111 4 0 3533 3643 152231082 152231192 2.490000e-42 183
17 TraesCS3D01G096800 chr1D 95.575 113 5 0 3533 3645 15293275 15293387 8.950000e-42 182
18 TraesCS3D01G096800 chr1B 94.828 116 6 0 3530 3645 654508631 654508516 8.950000e-42 182
19 TraesCS3D01G096800 chr6D 94.068 118 7 0 3528 3645 110447188 110447305 3.220000e-41 180


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 TraesCS3D01G096800 chr3D 48864385 48868438 4053 False 7487.000000 7487 100.000000 1 4054 1 chr3D.!!$F1 4053
1 TraesCS3D01G096800 chr3A 61346208 61349678 3470 False 1517.333333 2981 89.640667 1 3526 3 chr3A.!!$F1 3525
2 TraesCS3D01G096800 chr3A 61434812 61436393 1581 False 598.333333 1321 93.822333 2080 4038 3 chr3A.!!$F2 1958
3 TraesCS3D01G096800 chr3B 78395959 78399356 3397 False 2297.000000 2841 90.914500 1 3535 2 chr3B.!!$F2 3534

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
382 406 0.325860 TACGGCCACCCCTGTTATCT 60.326 55.0 2.24 0.0 0.0 1.98 F
385 409 0.470341 GGCCACCCCTGTTATCTCTC 59.530 60.0 0.00 0.0 0.0 3.20 F
533 557 0.594602 TGCTGCTGATGTCTTGTTGC 59.405 50.0 0.00 0.0 0.0 4.17 F
2237 2300 0.532573 TGAAGTCTGAGGATGGCGAC 59.467 55.0 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1395 1.063174 GCTCCACGAACAATCAGATGC 59.937 52.381 0.00 0.0 0.00 3.91 R
2030 2093 1.536284 CCGAACTCAGAGCCGGATAAC 60.536 57.143 21.37 0.0 44.29 1.89 R
2427 2490 1.000955 AGTTGACGCGAACTCTCCATT 59.999 47.619 15.93 0.0 29.85 3.16 R
3562 3654 0.250793 TGGCAACCTGGGTATACGTG 59.749 55.000 0.00 0.0 0.00 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
82 83 3.933861 TTTCTTTCTATCCCCTGCCTC 57.066 47.619 0.00 0.00 0.00 4.70
105 106 1.394917 CGTGTAGTGCTCAGATTTGGC 59.605 52.381 0.00 0.00 0.00 4.52
138 139 3.596066 GAACAGAGCTGGCGCCTCA 62.596 63.158 29.70 7.24 36.60 3.86
239 241 2.842496 TCCTGCTCATCTGGAATCTGTT 59.158 45.455 0.00 0.00 39.49 3.16
269 281 3.691049 TGTTTCAGTTTCTTCAAGCCG 57.309 42.857 0.00 0.00 0.00 5.52
276 288 4.819630 TCAGTTTCTTCAAGCCGTGTTTAT 59.180 37.500 0.00 0.00 0.00 1.40
279 291 6.142320 CAGTTTCTTCAAGCCGTGTTTATTTC 59.858 38.462 0.00 0.00 0.00 2.17
286 298 4.929819 AGCCGTGTTTATTTCCTGTTTT 57.070 36.364 0.00 0.00 0.00 2.43
287 299 5.270893 AGCCGTGTTTATTTCCTGTTTTT 57.729 34.783 0.00 0.00 0.00 1.94
319 343 0.986527 TGCTCCCAAGATCTTGCAGA 59.013 50.000 27.01 22.72 39.16 4.26
335 359 1.280421 GCAGAGTTTCTCCAGGGATGT 59.720 52.381 0.00 0.00 0.00 3.06
340 364 3.753797 GAGTTTCTCCAGGGATGTTGTTC 59.246 47.826 0.00 0.00 0.00 3.18
356 380 4.821805 TGTTGTTCTCTTTTGATCTGGTCC 59.178 41.667 0.00 0.00 0.00 4.46
365 389 6.650120 TCTTTTGATCTGGTCCTGGTTATAC 58.350 40.000 0.00 0.00 0.00 1.47
367 391 2.963101 TGATCTGGTCCTGGTTATACGG 59.037 50.000 0.00 0.00 0.00 4.02
379 403 1.485895 GTTATACGGCCACCCCTGTTA 59.514 52.381 2.24 0.00 0.00 2.41
382 406 0.325860 TACGGCCACCCCTGTTATCT 60.326 55.000 2.24 0.00 0.00 1.98
384 408 1.338136 CGGCCACCCCTGTTATCTCT 61.338 60.000 2.24 0.00 0.00 3.10
385 409 0.470341 GGCCACCCCTGTTATCTCTC 59.530 60.000 0.00 0.00 0.00 3.20
386 410 1.501582 GCCACCCCTGTTATCTCTCT 58.498 55.000 0.00 0.00 0.00 3.10
387 411 1.840635 GCCACCCCTGTTATCTCTCTT 59.159 52.381 0.00 0.00 0.00 2.85
388 412 2.420687 GCCACCCCTGTTATCTCTCTTG 60.421 54.545 0.00 0.00 0.00 3.02
389 413 3.107601 CCACCCCTGTTATCTCTCTTGA 58.892 50.000 0.00 0.00 0.00 3.02
390 414 3.713764 CCACCCCTGTTATCTCTCTTGAT 59.286 47.826 0.00 0.00 0.00 2.57
391 415 4.444022 CCACCCCTGTTATCTCTCTTGATG 60.444 50.000 0.00 0.00 0.00 3.07
392 416 3.135530 ACCCCTGTTATCTCTCTTGATGC 59.864 47.826 0.00 0.00 0.00 3.91
393 417 3.388308 CCCTGTTATCTCTCTTGATGCG 58.612 50.000 0.00 0.00 0.00 4.73
394 418 3.068732 CCCTGTTATCTCTCTTGATGCGA 59.931 47.826 0.00 0.00 0.00 5.10
395 419 4.047822 CCTGTTATCTCTCTTGATGCGAC 58.952 47.826 0.00 0.00 0.00 5.19
396 420 4.202101 CCTGTTATCTCTCTTGATGCGACT 60.202 45.833 0.00 0.00 0.00 4.18
397 421 4.676546 TGTTATCTCTCTTGATGCGACTG 58.323 43.478 0.00 0.00 0.00 3.51
398 422 4.158579 TGTTATCTCTCTTGATGCGACTGT 59.841 41.667 0.00 0.00 0.00 3.55
399 423 5.357032 TGTTATCTCTCTTGATGCGACTGTA 59.643 40.000 0.00 0.00 0.00 2.74
400 424 3.766676 TCTCTCTTGATGCGACTGTAC 57.233 47.619 0.00 0.00 0.00 2.90
401 425 3.348119 TCTCTCTTGATGCGACTGTACT 58.652 45.455 0.00 0.00 0.00 2.73
402 426 4.514401 TCTCTCTTGATGCGACTGTACTA 58.486 43.478 0.00 0.00 0.00 1.82
403 427 5.126779 TCTCTCTTGATGCGACTGTACTAT 58.873 41.667 0.00 0.00 0.00 2.12
404 428 6.289064 TCTCTCTTGATGCGACTGTACTATA 58.711 40.000 0.00 0.00 0.00 1.31
405 429 6.937465 TCTCTCTTGATGCGACTGTACTATAT 59.063 38.462 0.00 0.00 0.00 0.86
450 474 2.103432 TGGAACAGTAAAAGACGCCTGA 59.897 45.455 0.00 0.00 0.00 3.86
451 475 2.479275 GGAACAGTAAAAGACGCCTGAC 59.521 50.000 0.00 0.00 0.00 3.51
473 497 4.445385 ACGAATCATTGCTTTTCTGTTTGC 59.555 37.500 0.00 0.00 0.00 3.68
480 504 8.436046 TCATTGCTTTTCTGTTTGCTAAAAAT 57.564 26.923 0.00 0.00 0.00 1.82
493 517 7.015682 TGTTTGCTAAAAATGGGTTATCCTTGA 59.984 33.333 0.00 0.00 36.20 3.02
494 518 7.732222 TTGCTAAAAATGGGTTATCCTTGAT 57.268 32.000 0.00 0.00 36.20 2.57
521 545 5.124457 ACCACAGTAAGAAAATATGCTGCTG 59.876 40.000 0.00 0.00 33.21 4.41
533 557 0.594602 TGCTGCTGATGTCTTGTTGC 59.405 50.000 0.00 0.00 0.00 4.17
541 568 5.295045 TGCTGATGTCTTGTTGCACATATAG 59.705 40.000 0.00 0.00 33.22 1.31
544 571 5.882000 TGATGTCTTGTTGCACATATAGCTT 59.118 36.000 0.00 0.00 33.22 3.74
548 575 8.279970 TGTCTTGTTGCACATATAGCTTAATT 57.720 30.769 0.00 0.00 0.00 1.40
550 577 9.573133 GTCTTGTTGCACATATAGCTTAATTTT 57.427 29.630 0.00 0.00 0.00 1.82
604 643 6.583806 GCAATTTCTTGTTAGTTCATCACAGG 59.416 38.462 0.00 0.00 34.69 4.00
636 675 3.865745 AGCATTTATTTCTCGAGGACACG 59.134 43.478 13.56 0.00 0.00 4.49
638 677 3.947910 TTTATTTCTCGAGGACACGGT 57.052 42.857 13.56 0.00 0.00 4.83
639 678 5.345702 CATTTATTTCTCGAGGACACGGTA 58.654 41.667 13.56 0.00 0.00 4.02
640 679 4.627611 TTATTTCTCGAGGACACGGTAG 57.372 45.455 13.56 0.00 0.00 3.18
641 680 2.189594 TTTCTCGAGGACACGGTAGA 57.810 50.000 13.56 0.00 0.00 2.59
643 682 2.414994 TCTCGAGGACACGGTAGATT 57.585 50.000 13.56 0.00 0.00 2.40
645 684 2.681848 TCTCGAGGACACGGTAGATTTC 59.318 50.000 13.56 0.00 0.00 2.17
647 686 3.021695 TCGAGGACACGGTAGATTTCAT 58.978 45.455 0.00 0.00 0.00 2.57
650 689 4.201980 CGAGGACACGGTAGATTTCATACA 60.202 45.833 0.00 0.00 0.00 2.29
651 690 5.007385 AGGACACGGTAGATTTCATACAC 57.993 43.478 0.00 0.00 0.00 2.90
652 691 4.117685 GGACACGGTAGATTTCATACACC 58.882 47.826 0.00 0.00 0.00 4.16
653 692 4.382254 GGACACGGTAGATTTCATACACCA 60.382 45.833 0.00 0.00 0.00 4.17
654 693 5.155278 ACACGGTAGATTTCATACACCAA 57.845 39.130 0.00 0.00 0.00 3.67
674 723 8.361139 ACACCAATGTACTACTAGATGCTAATC 58.639 37.037 0.00 0.00 37.26 1.75
678 727 6.798315 TGTACTACTAGATGCTAATCGGAC 57.202 41.667 0.00 0.00 37.92 4.79
703 752 6.088173 GCCGTTCGTAAAAACTGGAAATAAT 58.912 36.000 0.00 0.00 0.00 1.28
705 754 7.115236 GCCGTTCGTAAAAACTGGAAATAATTT 59.885 33.333 0.00 0.00 0.00 1.82
706 755 9.609950 CCGTTCGTAAAAACTGGAAATAATTTA 57.390 29.630 0.00 0.00 0.00 1.40
741 790 3.177228 AGCAAGGACTAGAATGAGTGGT 58.823 45.455 0.00 0.00 0.00 4.16
849 898 2.224066 GCGCTATACTTCACCCTGATGT 60.224 50.000 0.00 0.00 38.20 3.06
1319 1379 7.039784 AGGTGCTTTTGATGTACATATGTTGTT 60.040 33.333 14.77 0.00 39.87 2.83
1320 1380 8.240682 GGTGCTTTTGATGTACATATGTTGTTA 58.759 33.333 14.77 0.00 39.87 2.41
1371 1431 4.747108 CGTGGAGCTAATGACTAGGAATTG 59.253 45.833 0.00 0.00 0.00 2.32
1390 1450 5.927281 ATTGGCAGCTGAGTAAATGAAAT 57.073 34.783 20.43 0.10 0.00 2.17
1420 1481 6.476706 CAGAAGTTTTGATGGTTTTCCTGTTC 59.523 38.462 0.00 0.00 41.38 3.18
1472 1533 4.053295 GACTGTTCATTGTGCATTTGCTT 58.947 39.130 3.94 0.00 42.66 3.91
1476 1537 4.508492 TGTTCATTGTGCATTTGCTTCAAG 59.492 37.500 14.77 9.68 42.66 3.02
1478 1539 5.142061 TCATTGTGCATTTGCTTCAAGAT 57.858 34.783 14.77 2.67 42.66 2.40
1479 1540 5.543714 TCATTGTGCATTTGCTTCAAGATT 58.456 33.333 14.77 2.18 42.66 2.40
1480 1541 5.992829 TCATTGTGCATTTGCTTCAAGATTT 59.007 32.000 14.77 1.94 42.66 2.17
1486 1547 5.858049 TGCATTTGCTTCAAGATTTAAGACG 59.142 36.000 3.94 0.00 42.66 4.18
1488 1549 6.250104 GCATTTGCTTCAAGATTTAAGACGAG 59.750 38.462 0.00 0.00 38.21 4.18
1491 1552 4.690748 TGCTTCAAGATTTAAGACGAGTGG 59.309 41.667 0.00 0.00 0.00 4.00
1498 1559 9.932207 TCAAGATTTAAGACGAGTGGTAAATAA 57.068 29.630 0.00 0.00 0.00 1.40
1529 1590 5.129980 TGATGCTTCCATAGTCAAGTGAGAT 59.870 40.000 0.00 0.00 0.00 2.75
1534 1595 7.496920 TGCTTCCATAGTCAAGTGAGATAAATG 59.503 37.037 0.00 0.00 0.00 2.32
1535 1596 7.041508 GCTTCCATAGTCAAGTGAGATAAATGG 60.042 40.741 0.00 0.00 0.00 3.16
1573 1634 3.083122 AGCAGAAATTGGCAGTGAGAT 57.917 42.857 0.00 0.00 0.00 2.75
1578 1639 5.327091 CAGAAATTGGCAGTGAGATAAACG 58.673 41.667 0.00 0.00 0.00 3.60
1609 1670 9.696917 AAATGTTGATACTTTCCTTGACAATTC 57.303 29.630 0.00 0.00 0.00 2.17
1706 1769 5.241662 GGATTGGGCAGATAGATTGTAGTC 58.758 45.833 0.00 0.00 0.00 2.59
1748 1811 5.751028 GTCCATGCTACTGTTATCTGTTCTC 59.249 44.000 0.00 0.00 0.00 2.87
1928 1991 0.603707 CAGTGCTCGTCACCCATGTT 60.604 55.000 6.89 0.00 46.81 2.71
2030 2093 0.533755 GGATGCAGTCCCAAGGATCG 60.534 60.000 0.00 0.00 41.50 3.69
2237 2300 0.532573 TGAAGTCTGAGGATGGCGAC 59.467 55.000 0.00 0.00 0.00 5.19
2397 2460 7.605449 CGATTATATGGAAAATGGAAATGGCT 58.395 34.615 0.00 0.00 0.00 4.75
2409 2472 1.534595 GAAATGGCTCCGATCATGCTC 59.465 52.381 0.00 0.00 0.00 4.26
2427 2490 4.661222 TGCTCCCAAAATTACAGACATCA 58.339 39.130 0.00 0.00 0.00 3.07
2455 2518 2.095161 AGTTCGCGTCAACTAAGGAGAG 60.095 50.000 11.11 0.00 34.70 3.20
2485 2548 4.380531 TCTTCACAAGTGGAGATCAACAC 58.619 43.478 7.11 10.74 40.16 3.32
2519 2582 0.390078 TCGAGGACGCCGCAATTTTA 60.390 50.000 0.00 0.00 39.58 1.52
2573 2636 2.751806 CAAGGGACTGGAAGCTGAAATC 59.248 50.000 0.00 0.00 40.86 2.17
2603 2666 1.457346 AGGAAGAAATGGCTTCAGCG 58.543 50.000 0.00 0.00 44.71 5.18
2639 2702 2.452105 GACAAACTATCCGAGAGCGAC 58.548 52.381 0.00 0.00 40.82 5.19
2741 2804 1.002544 GTGGGTAAGCTGCAAGAGACT 59.997 52.381 1.02 0.00 34.07 3.24
2752 2815 2.625314 TGCAAGAGACTATCCGGATCAG 59.375 50.000 23.08 18.12 0.00 2.90
2768 2831 3.684990 AGCAGTCGCGAGCTGGAA 61.685 61.111 27.82 0.00 45.49 3.53
2801 2864 2.903798 GAGAAATCTCTGGTGGAGCAG 58.096 52.381 3.16 0.00 41.60 4.24
2900 2963 1.340248 TCGGAGGACAAGTTCAGACAC 59.660 52.381 0.00 0.00 0.00 3.67
3115 3178 8.294954 AGTAAACTAGCAGTGCTATCTCTTTA 57.705 34.615 24.66 18.24 40.54 1.85
3227 3298 1.463214 AGGTGATGGGTGGTGGTCA 60.463 57.895 0.00 0.00 0.00 4.02
3253 3339 5.402270 GGTGTATGAAACATTTGCACTGAAC 59.598 40.000 2.57 0.00 41.10 3.18
3274 3364 3.993736 ACGCATTTCCTTTGGCAATAAAC 59.006 39.130 0.00 0.00 0.00 2.01
3278 3368 5.106987 GCATTTCCTTTGGCAATAAACTGTG 60.107 40.000 0.00 0.33 0.00 3.66
3281 3371 3.572255 TCCTTTGGCAATAAACTGTGTCC 59.428 43.478 0.00 0.00 0.00 4.02
3282 3372 3.564511 CTTTGGCAATAAACTGTGTCCG 58.435 45.455 0.00 0.00 0.00 4.79
3283 3373 2.552599 TGGCAATAAACTGTGTCCGA 57.447 45.000 0.00 0.00 0.00 4.55
3284 3374 3.066291 TGGCAATAAACTGTGTCCGAT 57.934 42.857 0.00 0.00 0.00 4.18
3285 3375 2.746904 TGGCAATAAACTGTGTCCGATG 59.253 45.455 0.00 0.00 0.00 3.84
3286 3376 3.006940 GGCAATAAACTGTGTCCGATGA 58.993 45.455 0.00 0.00 0.00 2.92
3287 3377 3.063997 GGCAATAAACTGTGTCCGATGAG 59.936 47.826 0.00 0.00 0.00 2.90
3329 3419 4.572795 GCTAAGTTCTGAACTCCTAATGCC 59.427 45.833 22.24 3.58 41.91 4.40
3402 3492 0.327867 TTCCTGGAGGCATCATCCCT 60.328 55.000 0.00 0.00 35.86 4.20
3463 3554 3.440415 GCGCCCCAGCTTACAACC 61.440 66.667 0.00 0.00 36.60 3.77
3475 3566 2.548480 GCTTACAACCTCCACAGAACAC 59.452 50.000 0.00 0.00 0.00 3.32
3484 3575 0.027979 CCACAGAACACAACACTGCG 59.972 55.000 0.00 0.00 35.38 5.18
3487 3578 1.290203 CAGAACACAACACTGCGACT 58.710 50.000 0.00 0.00 0.00 4.18
3494 3585 1.526887 ACAACACTGCGACTTTCATCG 59.473 47.619 0.00 0.00 45.09 3.84
3495 3586 1.792367 CAACACTGCGACTTTCATCGA 59.208 47.619 0.00 0.00 45.13 3.59
3496 3587 1.419374 ACACTGCGACTTTCATCGAC 58.581 50.000 0.00 0.00 45.13 4.20
3531 3623 9.163899 AGCTTCATTTATCTAGCATGTCATATG 57.836 33.333 0.00 0.00 36.11 1.78
3538 3630 5.984695 TCTAGCATGTCATATGTACTCCC 57.015 43.478 1.90 0.00 0.00 4.30
3539 3631 5.645201 TCTAGCATGTCATATGTACTCCCT 58.355 41.667 1.90 0.00 0.00 4.20
3540 3632 4.881019 AGCATGTCATATGTACTCCCTC 57.119 45.455 1.90 0.00 0.00 4.30
3541 3633 3.580458 AGCATGTCATATGTACTCCCTCC 59.420 47.826 1.90 0.00 0.00 4.30
3542 3634 3.615110 GCATGTCATATGTACTCCCTCCG 60.615 52.174 1.90 0.00 0.00 4.63
3543 3635 3.308035 TGTCATATGTACTCCCTCCGT 57.692 47.619 1.90 0.00 0.00 4.69
3544 3636 3.638860 TGTCATATGTACTCCCTCCGTT 58.361 45.455 1.90 0.00 0.00 4.44
3545 3637 4.028131 TGTCATATGTACTCCCTCCGTTT 58.972 43.478 1.90 0.00 0.00 3.60
3546 3638 4.098960 TGTCATATGTACTCCCTCCGTTTC 59.901 45.833 1.90 0.00 0.00 2.78
3547 3639 4.098960 GTCATATGTACTCCCTCCGTTTCA 59.901 45.833 1.90 0.00 0.00 2.69
3548 3640 4.341235 TCATATGTACTCCCTCCGTTTCAG 59.659 45.833 1.90 0.00 0.00 3.02
3549 3641 2.005370 TGTACTCCCTCCGTTTCAGT 57.995 50.000 0.00 0.00 0.00 3.41
3550 3642 2.322658 TGTACTCCCTCCGTTTCAGTT 58.677 47.619 0.00 0.00 0.00 3.16
3551 3643 2.701951 TGTACTCCCTCCGTTTCAGTTT 59.298 45.455 0.00 0.00 0.00 2.66
3552 3644 3.896888 TGTACTCCCTCCGTTTCAGTTTA 59.103 43.478 0.00 0.00 0.00 2.01
3553 3645 4.529377 TGTACTCCCTCCGTTTCAGTTTAT 59.471 41.667 0.00 0.00 0.00 1.40
3554 3646 5.716228 TGTACTCCCTCCGTTTCAGTTTATA 59.284 40.000 0.00 0.00 0.00 0.98
3555 3647 5.750352 ACTCCCTCCGTTTCAGTTTATAA 57.250 39.130 0.00 0.00 0.00 0.98
3556 3648 5.731591 ACTCCCTCCGTTTCAGTTTATAAG 58.268 41.667 0.00 0.00 0.00 1.73
3557 3649 5.247792 ACTCCCTCCGTTTCAGTTTATAAGT 59.752 40.000 0.00 0.00 0.00 2.24
3558 3650 5.727434 TCCCTCCGTTTCAGTTTATAAGTC 58.273 41.667 0.00 0.00 0.00 3.01
3559 3651 4.874396 CCCTCCGTTTCAGTTTATAAGTCC 59.126 45.833 0.00 0.00 0.00 3.85
3560 3652 5.338137 CCCTCCGTTTCAGTTTATAAGTCCT 60.338 44.000 0.00 0.00 0.00 3.85
3561 3653 6.127253 CCCTCCGTTTCAGTTTATAAGTCCTA 60.127 42.308 0.00 0.00 0.00 2.94
3562 3654 6.755607 CCTCCGTTTCAGTTTATAAGTCCTAC 59.244 42.308 0.00 0.00 0.00 3.18
3563 3655 7.230849 TCCGTTTCAGTTTATAAGTCCTACA 57.769 36.000 0.00 0.00 0.00 2.74
3564 3656 7.092716 TCCGTTTCAGTTTATAAGTCCTACAC 58.907 38.462 0.00 0.00 0.00 2.90
3565 3657 6.034256 CCGTTTCAGTTTATAAGTCCTACACG 59.966 42.308 0.00 0.00 0.00 4.49
3566 3658 6.583806 CGTTTCAGTTTATAAGTCCTACACGT 59.416 38.462 0.00 0.00 0.00 4.49
3567 3659 7.750458 CGTTTCAGTTTATAAGTCCTACACGTA 59.250 37.037 0.00 0.00 0.00 3.57
3568 3660 9.578439 GTTTCAGTTTATAAGTCCTACACGTAT 57.422 33.333 0.00 0.00 34.44 3.06
3571 3663 8.840321 TCAGTTTATAAGTCCTACACGTATACC 58.160 37.037 0.00 0.00 33.24 2.73
3572 3664 8.078596 CAGTTTATAAGTCCTACACGTATACCC 58.921 40.741 0.00 0.00 33.24 3.69
3573 3665 7.779798 AGTTTATAAGTCCTACACGTATACCCA 59.220 37.037 0.00 0.00 33.24 4.51
3574 3666 7.750229 TTATAAGTCCTACACGTATACCCAG 57.250 40.000 0.00 0.00 33.24 4.45
3575 3667 2.941480 AGTCCTACACGTATACCCAGG 58.059 52.381 0.00 0.00 0.00 4.45
3576 3668 2.243221 AGTCCTACACGTATACCCAGGT 59.757 50.000 0.00 0.00 0.00 4.00
3577 3669 3.026694 GTCCTACACGTATACCCAGGTT 58.973 50.000 0.00 0.00 0.00 3.50
3578 3670 3.025978 TCCTACACGTATACCCAGGTTG 58.974 50.000 0.00 0.00 0.00 3.77
3579 3671 2.482490 CCTACACGTATACCCAGGTTGC 60.482 54.545 0.00 0.00 0.00 4.17
3580 3672 0.251073 ACACGTATACCCAGGTTGCC 59.749 55.000 0.00 0.00 0.00 4.52
3581 3673 0.250793 CACGTATACCCAGGTTGCCA 59.749 55.000 0.00 0.00 0.00 4.92
3582 3674 0.985760 ACGTATACCCAGGTTGCCAA 59.014 50.000 0.00 0.00 0.00 4.52
3583 3675 1.562475 ACGTATACCCAGGTTGCCAAT 59.438 47.619 0.00 0.00 0.00 3.16
3584 3676 2.025699 ACGTATACCCAGGTTGCCAATT 60.026 45.455 0.00 0.00 0.00 2.32
3585 3677 3.020984 CGTATACCCAGGTTGCCAATTT 58.979 45.455 0.00 0.00 0.00 1.82
3586 3678 3.445805 CGTATACCCAGGTTGCCAATTTT 59.554 43.478 0.00 0.00 0.00 1.82
3587 3679 4.641094 CGTATACCCAGGTTGCCAATTTTA 59.359 41.667 0.00 0.00 0.00 1.52
3588 3680 5.300792 CGTATACCCAGGTTGCCAATTTTAT 59.699 40.000 0.00 0.00 0.00 1.40
3589 3681 3.979101 ACCCAGGTTGCCAATTTTATG 57.021 42.857 0.00 0.00 0.00 1.90
3590 3682 3.515562 ACCCAGGTTGCCAATTTTATGA 58.484 40.909 0.00 0.00 0.00 2.15
3591 3683 3.260632 ACCCAGGTTGCCAATTTTATGAC 59.739 43.478 0.00 0.00 0.00 3.06
3592 3684 3.369366 CCCAGGTTGCCAATTTTATGACC 60.369 47.826 0.00 0.00 0.00 4.02
3593 3685 3.369366 CCAGGTTGCCAATTTTATGACCC 60.369 47.826 0.00 0.00 0.00 4.46
3594 3686 3.515104 CAGGTTGCCAATTTTATGACCCT 59.485 43.478 0.00 0.00 0.00 4.34
3595 3687 4.709397 CAGGTTGCCAATTTTATGACCCTA 59.291 41.667 0.00 0.00 0.00 3.53
3596 3688 5.186797 CAGGTTGCCAATTTTATGACCCTAA 59.813 40.000 0.00 0.00 0.00 2.69
3597 3689 5.963865 AGGTTGCCAATTTTATGACCCTAAT 59.036 36.000 0.00 0.00 0.00 1.73
3598 3690 7.069331 CAGGTTGCCAATTTTATGACCCTAATA 59.931 37.037 0.00 0.00 0.00 0.98
3599 3691 7.789349 AGGTTGCCAATTTTATGACCCTAATAT 59.211 33.333 0.00 0.00 0.00 1.28
3600 3692 9.084533 GGTTGCCAATTTTATGACCCTAATATA 57.915 33.333 0.00 0.00 0.00 0.86
3681 3773 8.265165 GGGAACGAAAATAGAACATCTAAAGT 57.735 34.615 0.00 0.00 31.96 2.66
3682 3774 8.727910 GGGAACGAAAATAGAACATCTAAAGTT 58.272 33.333 0.00 0.00 31.96 2.66
3734 3826 5.305644 TCAGGAGGTTCCTTAATGATCTAGC 59.694 44.000 0.00 0.00 46.91 3.42
3757 3849 1.618837 TCGTGGAGTCCCTTTTCTCTG 59.381 52.381 6.74 0.00 0.00 3.35
3758 3850 1.338200 CGTGGAGTCCCTTTTCTCTGG 60.338 57.143 6.74 0.00 0.00 3.86
3759 3851 1.978580 GTGGAGTCCCTTTTCTCTGGA 59.021 52.381 6.74 0.00 0.00 3.86
3763 3855 2.081725 GTCCCTTTTCTCTGGACGAC 57.918 55.000 0.00 0.00 39.22 4.34
3764 3856 0.601558 TCCCTTTTCTCTGGACGACG 59.398 55.000 0.00 0.00 0.00 5.12
3765 3857 1.014564 CCCTTTTCTCTGGACGACGC 61.015 60.000 0.00 0.00 0.00 5.19
3766 3858 0.038159 CCTTTTCTCTGGACGACGCT 60.038 55.000 0.00 0.00 0.00 5.07
3767 3859 1.605712 CCTTTTCTCTGGACGACGCTT 60.606 52.381 0.00 0.00 0.00 4.68
3768 3860 2.352421 CCTTTTCTCTGGACGACGCTTA 60.352 50.000 0.00 0.00 0.00 3.09
3769 3861 2.631418 TTTCTCTGGACGACGCTTAG 57.369 50.000 0.00 0.00 0.00 2.18
3770 3862 0.170561 TTCTCTGGACGACGCTTAGC 59.829 55.000 0.00 0.00 0.00 3.09
3782 3874 3.153024 GCTTAGCGTGGTCCAATGA 57.847 52.632 0.00 0.00 0.00 2.57
3783 3875 1.009829 GCTTAGCGTGGTCCAATGAG 58.990 55.000 0.00 0.00 0.00 2.90
3784 3876 1.009829 CTTAGCGTGGTCCAATGAGC 58.990 55.000 0.00 0.00 39.48 4.26
3785 3877 0.739462 TTAGCGTGGTCCAATGAGCG 60.739 55.000 0.00 0.00 41.98 5.03
3786 3878 4.166011 GCGTGGTCCAATGAGCGC 62.166 66.667 7.91 7.91 44.12 5.92
3787 3879 2.434884 CGTGGTCCAATGAGCGCT 60.435 61.111 11.27 11.27 45.10 5.92
3788 3880 2.034879 CGTGGTCCAATGAGCGCTT 61.035 57.895 13.26 0.00 45.10 4.68
3789 3881 1.503542 GTGGTCCAATGAGCGCTTG 59.496 57.895 13.26 5.87 44.17 4.01
3790 3882 2.334946 TGGTCCAATGAGCGCTTGC 61.335 57.895 13.26 0.00 41.98 4.01
3791 3883 2.334946 GGTCCAATGAGCGCTTGCA 61.335 57.895 13.26 6.25 42.66 4.08
3792 3884 1.136147 GTCCAATGAGCGCTTGCAG 59.864 57.895 13.26 2.25 42.66 4.41
3793 3885 2.202570 CCAATGAGCGCTTGCAGC 60.203 61.111 13.26 0.00 42.66 5.25
3794 3886 2.202570 CAATGAGCGCTTGCAGCC 60.203 61.111 13.26 0.00 42.66 4.85
3795 3887 2.674033 AATGAGCGCTTGCAGCCA 60.674 55.556 13.26 3.49 42.66 4.75
3796 3888 2.270257 AATGAGCGCTTGCAGCCAA 61.270 52.632 13.26 0.00 42.66 4.52
3797 3889 1.601419 AATGAGCGCTTGCAGCCAAT 61.601 50.000 13.26 0.00 42.66 3.16
3798 3890 0.749091 ATGAGCGCTTGCAGCCAATA 60.749 50.000 13.26 0.00 42.66 1.90
3799 3891 1.063166 GAGCGCTTGCAGCCAATAC 59.937 57.895 13.26 0.00 42.66 1.89
3800 3892 1.372087 GAGCGCTTGCAGCCAATACT 61.372 55.000 13.26 0.00 42.66 2.12
3801 3893 1.063166 GCGCTTGCAGCCAATACTC 59.937 57.895 0.00 0.00 38.18 2.59
3802 3894 1.647545 GCGCTTGCAGCCAATACTCA 61.648 55.000 0.00 0.00 38.18 3.41
3803 3895 0.097674 CGCTTGCAGCCAATACTCAC 59.902 55.000 0.00 0.00 38.18 3.51
3804 3896 0.453390 GCTTGCAGCCAATACTCACC 59.547 55.000 0.00 0.00 34.48 4.02
3805 3897 1.825090 CTTGCAGCCAATACTCACCA 58.175 50.000 0.00 0.00 0.00 4.17
3806 3898 2.161855 CTTGCAGCCAATACTCACCAA 58.838 47.619 0.00 0.00 0.00 3.67
3807 3899 1.825090 TGCAGCCAATACTCACCAAG 58.175 50.000 0.00 0.00 0.00 3.61
3808 3900 1.350684 TGCAGCCAATACTCACCAAGA 59.649 47.619 0.00 0.00 0.00 3.02
3809 3901 2.025981 TGCAGCCAATACTCACCAAGAT 60.026 45.455 0.00 0.00 0.00 2.40
3810 3902 3.019564 GCAGCCAATACTCACCAAGATT 58.980 45.455 0.00 0.00 0.00 2.40
3811 3903 3.181493 GCAGCCAATACTCACCAAGATTG 60.181 47.826 0.00 0.00 0.00 2.67
3812 3904 4.264253 CAGCCAATACTCACCAAGATTGA 58.736 43.478 0.00 0.00 32.16 2.57
3813 3905 4.095483 CAGCCAATACTCACCAAGATTGAC 59.905 45.833 0.00 0.00 32.16 3.18
3814 3906 3.378427 GCCAATACTCACCAAGATTGACC 59.622 47.826 0.00 0.00 32.16 4.02
3815 3907 3.623060 CCAATACTCACCAAGATTGACCG 59.377 47.826 0.00 0.00 32.16 4.79
3816 3908 4.503910 CAATACTCACCAAGATTGACCGA 58.496 43.478 0.00 0.00 32.16 4.69
3817 3909 5.118990 CAATACTCACCAAGATTGACCGAT 58.881 41.667 0.00 0.00 32.16 4.18
3818 3910 2.977914 ACTCACCAAGATTGACCGATG 58.022 47.619 0.00 0.00 0.00 3.84
3819 3911 2.303022 ACTCACCAAGATTGACCGATGT 59.697 45.455 0.00 0.00 0.00 3.06
3820 3912 3.244561 ACTCACCAAGATTGACCGATGTT 60.245 43.478 0.00 0.00 0.00 2.71
3821 3913 3.750371 TCACCAAGATTGACCGATGTTT 58.250 40.909 0.00 0.00 0.00 2.83
3822 3914 4.141287 TCACCAAGATTGACCGATGTTTT 58.859 39.130 0.00 0.00 0.00 2.43
3823 3915 4.582656 TCACCAAGATTGACCGATGTTTTT 59.417 37.500 0.00 0.00 0.00 1.94
3862 3954 5.246203 TGATGAGTACTTGCAGTTCTTACCT 59.754 40.000 0.00 0.00 0.00 3.08
3884 3976 6.424207 ACCTCGAGTAAGACATTCTTTTCAAC 59.576 38.462 12.31 0.00 37.89 3.18
4038 4130 9.431887 GTTATCCCTATATGCATAAACGAGAAA 57.568 33.333 11.13 0.00 0.00 2.52
4040 4132 8.723942 ATCCCTATATGCATAAACGAGAAATC 57.276 34.615 11.13 0.00 0.00 2.17
4041 4133 7.676004 TCCCTATATGCATAAACGAGAAATCA 58.324 34.615 11.13 0.00 0.00 2.57
4042 4134 8.321353 TCCCTATATGCATAAACGAGAAATCAT 58.679 33.333 11.13 0.00 0.00 2.45
4043 4135 9.599866 CCCTATATGCATAAACGAGAAATCATA 57.400 33.333 11.13 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 2.926200 CAAATCTGAGCACTACACGGAG 59.074 50.000 0.00 0.00 0.00 4.63
138 139 1.305297 TCGTCAGGATCCTGCACCT 60.305 57.895 33.39 0.00 43.31 4.00
203 205 1.949547 GCAGGAAGCATCAAGAGCACT 60.950 52.381 0.00 0.00 44.79 4.40
239 241 6.826231 TGAAGAAACTGAAACATACAACTGGA 59.174 34.615 0.00 0.00 0.00 3.86
286 298 1.004745 GGGAGCAACCATCTCTCCAAA 59.995 52.381 9.40 0.00 46.24 3.28
287 299 0.620556 GGGAGCAACCATCTCTCCAA 59.379 55.000 9.40 0.00 46.24 3.53
319 343 3.395941 AGAACAACATCCCTGGAGAAACT 59.604 43.478 0.00 0.00 0.00 2.66
335 359 5.065914 CAGGACCAGATCAAAAGAGAACAA 58.934 41.667 0.00 0.00 0.00 2.83
340 364 3.710209 ACCAGGACCAGATCAAAAGAG 57.290 47.619 0.00 0.00 0.00 2.85
356 380 1.147600 GGGGTGGCCGTATAACCAG 59.852 63.158 11.09 0.00 36.38 4.00
365 389 1.146263 GAGATAACAGGGGTGGCCG 59.854 63.158 0.00 0.00 0.00 6.13
367 391 1.501582 AGAGAGATAACAGGGGTGGC 58.498 55.000 0.00 0.00 0.00 5.01
379 403 3.951037 AGTACAGTCGCATCAAGAGAGAT 59.049 43.478 0.00 0.00 0.00 2.75
382 406 6.149640 GGATATAGTACAGTCGCATCAAGAGA 59.850 42.308 0.00 0.00 0.00 3.10
384 408 5.768164 TGGATATAGTACAGTCGCATCAAGA 59.232 40.000 0.00 0.00 0.00 3.02
385 409 5.859114 GTGGATATAGTACAGTCGCATCAAG 59.141 44.000 0.00 0.00 0.00 3.02
386 410 5.300792 TGTGGATATAGTACAGTCGCATCAA 59.699 40.000 0.00 0.00 0.00 2.57
387 411 4.825085 TGTGGATATAGTACAGTCGCATCA 59.175 41.667 0.00 0.00 0.00 3.07
388 412 5.154932 GTGTGGATATAGTACAGTCGCATC 58.845 45.833 0.00 0.00 0.00 3.91
389 413 4.320275 CGTGTGGATATAGTACAGTCGCAT 60.320 45.833 0.00 0.00 0.00 4.73
390 414 3.002965 CGTGTGGATATAGTACAGTCGCA 59.997 47.826 0.00 0.00 0.00 5.10
391 415 3.552541 CGTGTGGATATAGTACAGTCGC 58.447 50.000 0.00 0.00 0.00 5.19
392 416 3.250280 AGCGTGTGGATATAGTACAGTCG 59.750 47.826 0.00 0.00 0.00 4.18
393 417 4.832590 AGCGTGTGGATATAGTACAGTC 57.167 45.455 0.00 0.00 0.00 3.51
394 418 6.896021 ATAAGCGTGTGGATATAGTACAGT 57.104 37.500 0.00 0.00 0.00 3.55
395 419 8.082852 AGAAATAAGCGTGTGGATATAGTACAG 58.917 37.037 0.00 0.00 0.00 2.74
396 420 7.948357 AGAAATAAGCGTGTGGATATAGTACA 58.052 34.615 0.00 0.00 0.00 2.90
397 421 8.813643 AAGAAATAAGCGTGTGGATATAGTAC 57.186 34.615 0.00 0.00 0.00 2.73
398 422 8.635328 TGAAGAAATAAGCGTGTGGATATAGTA 58.365 33.333 0.00 0.00 0.00 1.82
399 423 7.497595 TGAAGAAATAAGCGTGTGGATATAGT 58.502 34.615 0.00 0.00 0.00 2.12
400 424 7.946655 TGAAGAAATAAGCGTGTGGATATAG 57.053 36.000 0.00 0.00 0.00 1.31
401 425 7.387673 CCATGAAGAAATAAGCGTGTGGATATA 59.612 37.037 0.00 0.00 0.00 0.86
402 426 6.205464 CCATGAAGAAATAAGCGTGTGGATAT 59.795 38.462 0.00 0.00 0.00 1.63
403 427 5.527214 CCATGAAGAAATAAGCGTGTGGATA 59.473 40.000 0.00 0.00 0.00 2.59
404 428 4.336433 CCATGAAGAAATAAGCGTGTGGAT 59.664 41.667 0.00 0.00 0.00 3.41
405 429 3.689161 CCATGAAGAAATAAGCGTGTGGA 59.311 43.478 0.00 0.00 0.00 4.02
443 467 0.391661 AGCAATGATTCGTCAGGCGT 60.392 50.000 0.00 0.00 42.13 5.68
450 474 4.445385 GCAAACAGAAAAGCAATGATTCGT 59.555 37.500 0.00 0.00 0.00 3.85
451 475 4.682860 AGCAAACAGAAAAGCAATGATTCG 59.317 37.500 0.00 0.00 0.00 3.34
480 504 5.908831 ACTGTGGTATATCAAGGATAACCCA 59.091 40.000 0.00 8.21 37.41 4.51
493 517 9.003658 GCAGCATATTTTCTTACTGTGGTATAT 57.996 33.333 0.00 0.00 0.00 0.86
494 518 8.210946 AGCAGCATATTTTCTTACTGTGGTATA 58.789 33.333 0.00 0.00 0.00 1.47
541 568 8.632679 TCATCAGGTCAATGGATAAAATTAAGC 58.367 33.333 0.00 0.00 0.00 3.09
548 575 6.994496 GTCAGATCATCAGGTCAATGGATAAA 59.006 38.462 0.00 0.00 0.00 1.40
550 577 5.012458 GGTCAGATCATCAGGTCAATGGATA 59.988 44.000 0.00 0.00 0.00 2.59
604 643 9.643652 CTCGAGAAATAAATGCTTAAATCTCAC 57.356 33.333 6.58 0.00 35.02 3.51
636 675 9.257651 GTAGTACATTGGTGTATGAAATCTACC 57.742 37.037 0.00 0.00 42.43 3.18
643 682 8.141909 GCATCTAGTAGTACATTGGTGTATGAA 58.858 37.037 2.52 0.00 42.43 2.57
645 684 7.661968 AGCATCTAGTAGTACATTGGTGTATG 58.338 38.462 2.52 0.00 42.43 2.39
647 686 8.756486 TTAGCATCTAGTAGTACATTGGTGTA 57.244 34.615 2.52 0.00 39.77 2.90
650 689 7.309255 CCGATTAGCATCTAGTAGTACATTGGT 60.309 40.741 2.52 2.99 0.00 3.67
651 690 7.030165 CCGATTAGCATCTAGTAGTACATTGG 58.970 42.308 2.52 0.00 0.00 3.16
652 691 7.751348 GTCCGATTAGCATCTAGTAGTACATTG 59.249 40.741 2.52 0.00 0.00 2.82
653 692 7.361031 CGTCCGATTAGCATCTAGTAGTACATT 60.361 40.741 2.52 0.00 0.00 2.71
654 693 6.092396 CGTCCGATTAGCATCTAGTAGTACAT 59.908 42.308 2.52 0.00 0.00 2.29
703 752 8.989131 AGTCCTTGCTAGTTGGATAATACTAAA 58.011 33.333 4.34 0.00 32.03 1.85
705 754 9.298250 CTAGTCCTTGCTAGTTGGATAATACTA 57.702 37.037 4.34 0.00 35.08 1.82
706 755 8.005388 TCTAGTCCTTGCTAGTTGGATAATACT 58.995 37.037 4.34 0.00 39.44 2.12
707 756 8.179509 TCTAGTCCTTGCTAGTTGGATAATAC 57.820 38.462 4.34 0.00 39.44 1.89
721 770 3.618690 ACCACTCATTCTAGTCCTTGC 57.381 47.619 0.00 0.00 0.00 4.01
922 973 8.642935 TGGAAATGAAAATGTGTATGGTTAGA 57.357 30.769 0.00 0.00 0.00 2.10
939 990 7.541162 CAGATTCAAGCACTAAATGGAAATGA 58.459 34.615 0.00 0.00 0.00 2.57
941 992 6.154021 AGCAGATTCAAGCACTAAATGGAAAT 59.846 34.615 4.31 0.00 0.00 2.17
1319 1379 4.649218 TCAGATGCTGCTACTGTACCATTA 59.351 41.667 19.48 3.55 33.93 1.90
1320 1380 3.452264 TCAGATGCTGCTACTGTACCATT 59.548 43.478 19.48 0.00 33.93 3.16
1335 1395 1.063174 GCTCCACGAACAATCAGATGC 59.937 52.381 0.00 0.00 0.00 3.91
1371 1431 5.731686 GCTGTATTTCATTTACTCAGCTGCC 60.732 44.000 9.47 0.00 42.00 4.85
1390 1450 6.460953 GGAAAACCATCAAAACTTCTGCTGTA 60.461 38.462 0.00 0.00 0.00 2.74
1420 1481 4.261867 GGCTACCACACCAAAACCTAAAAG 60.262 45.833 0.00 0.00 0.00 2.27
1472 1533 9.932207 TTATTTACCACTCGTCTTAAATCTTGA 57.068 29.630 0.00 0.00 0.00 3.02
1478 1539 9.715121 ACAATCTTATTTACCACTCGTCTTAAA 57.285 29.630 0.00 0.00 0.00 1.52
1479 1540 9.715121 AACAATCTTATTTACCACTCGTCTTAA 57.285 29.630 0.00 0.00 0.00 1.85
1480 1541 9.146984 CAACAATCTTATTTACCACTCGTCTTA 57.853 33.333 0.00 0.00 0.00 2.10
1486 1547 7.989826 AGCATCAACAATCTTATTTACCACTC 58.010 34.615 0.00 0.00 0.00 3.51
1488 1549 7.702348 GGAAGCATCAACAATCTTATTTACCAC 59.298 37.037 0.00 0.00 0.00 4.16
1498 1559 5.748402 TGACTATGGAAGCATCAACAATCT 58.252 37.500 0.00 0.00 0.00 2.40
1499 1560 6.094603 ACTTGACTATGGAAGCATCAACAATC 59.905 38.462 0.00 0.00 0.00 2.67
1549 1610 4.216257 TCTCACTGCCAATTTCTGCTAAAC 59.784 41.667 0.00 0.00 0.00 2.01
1682 1745 3.131709 ACAATCTATCTGCCCAATCCG 57.868 47.619 0.00 0.00 0.00 4.18
1706 1769 2.031683 GGACAACACCTCAAACAACTCG 59.968 50.000 0.00 0.00 0.00 4.18
1928 1991 3.698040 GGTACATCCGGTAGAAGTTCTCA 59.302 47.826 9.12 0.00 31.13 3.27
2030 2093 1.536284 CCGAACTCAGAGCCGGATAAC 60.536 57.143 21.37 0.00 44.29 1.89
2397 2460 2.734755 ATTTTGGGAGCATGATCGGA 57.265 45.000 4.63 0.00 0.00 4.55
2409 2472 6.377996 TCTCCATTGATGTCTGTAATTTTGGG 59.622 38.462 0.00 0.00 0.00 4.12
2427 2490 1.000955 AGTTGACGCGAACTCTCCATT 59.999 47.619 15.93 0.00 29.85 3.16
2455 2518 3.674997 TCCACTTGTGAAGATTGTAGCC 58.325 45.455 1.89 0.00 0.00 3.93
2485 2548 2.483441 TCGAGCCTCCTTTCGAGAG 58.517 57.895 0.00 0.00 41.63 3.20
2504 2567 1.668751 TCTGATAAAATTGCGGCGTCC 59.331 47.619 9.37 0.00 0.00 4.79
2519 2582 2.694628 CAGCCTAGAGTGCTCTTCTGAT 59.305 50.000 7.05 0.00 40.93 2.90
2573 2636 3.681897 CCATTTCTTCCTTCAGACTGACG 59.318 47.826 4.15 2.94 0.00 4.35
2672 2735 3.154589 CAGCTTCTGAGATGCAGCA 57.845 52.632 20.41 0.00 44.52 4.41
2678 2741 0.107606 CCTGCAGCAGCTTCTGAGAT 60.108 55.000 18.08 0.00 42.74 2.75
2682 2745 0.321387 TTCTCCTGCAGCAGCTTCTG 60.321 55.000 17.81 9.21 42.74 3.02
2741 2804 1.660355 GCGACTGCTGATCCGGATA 59.340 57.895 19.15 0.00 38.39 2.59
2752 2815 1.841663 TTTTTCCAGCTCGCGACTGC 61.842 55.000 24.24 19.26 33.65 4.40
2799 2862 4.298009 CAGCTCCTTCACCTGCTG 57.702 61.111 0.00 0.00 45.15 4.41
2801 2864 1.078567 CTCCAGCTCCTTCACCTGC 60.079 63.158 0.00 0.00 0.00 4.85
2900 2963 0.735471 TCGTCAGGATCTCAGCTTCG 59.265 55.000 0.00 0.00 0.00 3.79
2976 3039 0.179045 AACCAGAGTTTCAGCAGCGT 60.179 50.000 0.00 0.00 29.61 5.07
3227 3298 5.243507 TCAGTGCAAATGTTTCATACACCAT 59.756 36.000 0.00 0.00 40.19 3.55
3253 3339 4.091800 CAGTTTATTGCCAAAGGAAATGCG 59.908 41.667 0.00 0.00 32.35 4.73
3274 3364 2.165234 ACTCATCACTCATCGGACACAG 59.835 50.000 0.00 0.00 0.00 3.66
3278 3368 1.134995 TGCACTCATCACTCATCGGAC 60.135 52.381 0.00 0.00 0.00 4.79
3281 3371 3.242641 CCAAATGCACTCATCACTCATCG 60.243 47.826 0.00 0.00 31.27 3.84
3282 3372 3.943381 TCCAAATGCACTCATCACTCATC 59.057 43.478 0.00 0.00 31.27 2.92
3283 3373 3.945921 CTCCAAATGCACTCATCACTCAT 59.054 43.478 0.00 0.00 31.27 2.90
3284 3374 3.340928 CTCCAAATGCACTCATCACTCA 58.659 45.455 0.00 0.00 31.27 3.41
3285 3375 2.681848 CCTCCAAATGCACTCATCACTC 59.318 50.000 0.00 0.00 31.27 3.51
3286 3376 2.719739 CCTCCAAATGCACTCATCACT 58.280 47.619 0.00 0.00 31.27 3.41
3287 3377 1.133790 GCCTCCAAATGCACTCATCAC 59.866 52.381 0.00 0.00 31.27 3.06
3329 3419 1.212616 GCTAGATACCAACAGCTGCG 58.787 55.000 15.27 5.03 0.00 5.18
3365 3455 5.656416 CCAGGAATGGTTTAATTCTGGCTAA 59.344 40.000 0.00 0.00 36.87 3.09
3376 3466 2.580322 TGATGCCTCCAGGAATGGTTTA 59.420 45.455 0.00 0.00 32.14 2.01
3402 3492 2.026542 ACAGCATCAGGATTCAGAGCAA 60.027 45.455 0.00 0.00 0.00 3.91
3454 3545 2.548480 GTGTTCTGTGGAGGTTGTAAGC 59.452 50.000 0.00 0.00 0.00 3.09
3463 3554 1.331756 GCAGTGTTGTGTTCTGTGGAG 59.668 52.381 0.00 0.00 0.00 3.86
3475 3566 1.792367 TCGATGAAAGTCGCAGTGTTG 59.208 47.619 0.00 0.00 41.22 3.33
3484 3575 2.159503 TGAGAGCTCGTCGATGAAAGTC 60.160 50.000 8.37 5.71 0.00 3.01
3487 3578 1.468224 GCTGAGAGCTCGTCGATGAAA 60.468 52.381 8.37 0.00 38.45 2.69
3531 3623 3.397849 AAACTGAAACGGAGGGAGTAC 57.602 47.619 0.00 0.00 0.00 2.73
3535 3627 5.337813 GGACTTATAAACTGAAACGGAGGGA 60.338 44.000 0.00 0.00 0.00 4.20
3536 3628 4.874396 GGACTTATAAACTGAAACGGAGGG 59.126 45.833 0.00 0.00 0.00 4.30
3537 3629 5.731591 AGGACTTATAAACTGAAACGGAGG 58.268 41.667 0.00 0.00 0.00 4.30
3538 3630 7.275123 GTGTAGGACTTATAAACTGAAACGGAG 59.725 40.741 0.00 0.00 0.00 4.63
3539 3631 7.092716 GTGTAGGACTTATAAACTGAAACGGA 58.907 38.462 0.00 0.00 0.00 4.69
3540 3632 6.034256 CGTGTAGGACTTATAAACTGAAACGG 59.966 42.308 0.00 0.00 0.00 4.44
3541 3633 6.583806 ACGTGTAGGACTTATAAACTGAAACG 59.416 38.462 0.00 0.00 0.00 3.60
3542 3634 7.880059 ACGTGTAGGACTTATAAACTGAAAC 57.120 36.000 0.00 0.00 0.00 2.78
3545 3637 8.840321 GGTATACGTGTAGGACTTATAAACTGA 58.160 37.037 0.00 0.00 0.00 3.41
3546 3638 8.078596 GGGTATACGTGTAGGACTTATAAACTG 58.921 40.741 0.00 0.00 0.00 3.16
3547 3639 7.779798 TGGGTATACGTGTAGGACTTATAAACT 59.220 37.037 0.00 0.00 0.00 2.66
3548 3640 7.940850 TGGGTATACGTGTAGGACTTATAAAC 58.059 38.462 0.00 0.00 0.00 2.01
3549 3641 7.231317 CCTGGGTATACGTGTAGGACTTATAAA 59.769 40.741 0.00 0.00 0.00 1.40
3550 3642 6.716628 CCTGGGTATACGTGTAGGACTTATAA 59.283 42.308 0.00 0.00 0.00 0.98
3551 3643 6.183361 ACCTGGGTATACGTGTAGGACTTATA 60.183 42.308 15.79 0.00 0.00 0.98
3552 3644 5.075493 CCTGGGTATACGTGTAGGACTTAT 58.925 45.833 0.00 0.00 0.00 1.73
3553 3645 4.079787 ACCTGGGTATACGTGTAGGACTTA 60.080 45.833 15.79 0.00 0.00 2.24
3554 3646 3.294214 CCTGGGTATACGTGTAGGACTT 58.706 50.000 0.00 0.00 0.00 3.01
3555 3647 2.243221 ACCTGGGTATACGTGTAGGACT 59.757 50.000 15.79 0.00 0.00 3.85
3556 3648 2.659428 ACCTGGGTATACGTGTAGGAC 58.341 52.381 15.79 0.00 0.00 3.85
3557 3649 3.025978 CAACCTGGGTATACGTGTAGGA 58.974 50.000 15.79 0.00 0.00 2.94
3558 3650 2.482490 GCAACCTGGGTATACGTGTAGG 60.482 54.545 0.00 0.00 0.00 3.18
3559 3651 2.482490 GGCAACCTGGGTATACGTGTAG 60.482 54.545 0.00 0.00 0.00 2.74
3560 3652 1.481772 GGCAACCTGGGTATACGTGTA 59.518 52.381 0.00 0.00 0.00 2.90
3561 3653 0.251073 GGCAACCTGGGTATACGTGT 59.749 55.000 0.00 0.00 0.00 4.49
3562 3654 0.250793 TGGCAACCTGGGTATACGTG 59.749 55.000 0.00 0.00 0.00 4.49
3563 3655 0.985760 TTGGCAACCTGGGTATACGT 59.014 50.000 0.00 0.00 0.00 3.57
3564 3656 2.341846 ATTGGCAACCTGGGTATACG 57.658 50.000 0.00 0.00 0.00 3.06
3565 3657 6.322712 TCATAAAATTGGCAACCTGGGTATAC 59.677 38.462 0.00 0.00 0.00 1.47
3566 3658 6.322712 GTCATAAAATTGGCAACCTGGGTATA 59.677 38.462 0.00 0.00 0.00 1.47
3567 3659 5.128663 GTCATAAAATTGGCAACCTGGGTAT 59.871 40.000 0.00 0.00 0.00 2.73
3568 3660 4.464597 GTCATAAAATTGGCAACCTGGGTA 59.535 41.667 0.00 0.00 0.00 3.69
3569 3661 3.260632 GTCATAAAATTGGCAACCTGGGT 59.739 43.478 0.00 0.00 0.00 4.51
3570 3662 3.369366 GGTCATAAAATTGGCAACCTGGG 60.369 47.826 0.00 0.00 0.00 4.45
3571 3663 3.369366 GGGTCATAAAATTGGCAACCTGG 60.369 47.826 0.00 0.00 0.00 4.45
3572 3664 3.515104 AGGGTCATAAAATTGGCAACCTG 59.485 43.478 0.00 0.00 0.00 4.00
3573 3665 3.790126 AGGGTCATAAAATTGGCAACCT 58.210 40.909 0.00 0.00 0.00 3.50
3574 3666 5.669164 TTAGGGTCATAAAATTGGCAACC 57.331 39.130 0.00 0.00 0.00 3.77
3649 3741 4.832590 TCTATTTTCGTTCCCGCAAAAA 57.167 36.364 0.00 0.00 33.17 1.94
3650 3742 4.036498 TGTTCTATTTTCGTTCCCGCAAAA 59.964 37.500 0.00 0.00 33.17 2.44
3651 3743 3.564644 TGTTCTATTTTCGTTCCCGCAAA 59.435 39.130 0.00 0.00 33.92 3.68
3652 3744 3.139850 TGTTCTATTTTCGTTCCCGCAA 58.860 40.909 0.00 0.00 0.00 4.85
3653 3745 2.768698 TGTTCTATTTTCGTTCCCGCA 58.231 42.857 0.00 0.00 0.00 5.69
3654 3746 3.621715 AGATGTTCTATTTTCGTTCCCGC 59.378 43.478 0.00 0.00 0.00 6.13
3655 3747 6.897259 TTAGATGTTCTATTTTCGTTCCCG 57.103 37.500 0.00 0.00 0.00 5.14
3656 3748 8.265165 ACTTTAGATGTTCTATTTTCGTTCCC 57.735 34.615 0.00 0.00 0.00 3.97
3670 3762 9.609346 ACGCCTGTTATATAAACTTTAGATGTT 57.391 29.630 0.00 0.00 0.00 2.71
3677 3769 9.555727 ACATCATACGCCTGTTATATAAACTTT 57.444 29.630 0.00 0.00 0.00 2.66
3678 3770 8.988934 CACATCATACGCCTGTTATATAAACTT 58.011 33.333 0.00 0.00 0.00 2.66
3679 3771 8.364894 TCACATCATACGCCTGTTATATAAACT 58.635 33.333 0.00 0.00 0.00 2.66
3680 3772 8.528917 TCACATCATACGCCTGTTATATAAAC 57.471 34.615 0.00 0.00 0.00 2.01
3681 3773 9.549078 TTTCACATCATACGCCTGTTATATAAA 57.451 29.630 0.00 0.00 0.00 1.40
3682 3774 9.203421 CTTTCACATCATACGCCTGTTATATAA 57.797 33.333 0.00 0.00 0.00 0.98
3683 3775 8.364894 ACTTTCACATCATACGCCTGTTATATA 58.635 33.333 0.00 0.00 0.00 0.86
3684 3776 7.217200 ACTTTCACATCATACGCCTGTTATAT 58.783 34.615 0.00 0.00 0.00 0.86
3685 3777 6.578944 ACTTTCACATCATACGCCTGTTATA 58.421 36.000 0.00 0.00 0.00 0.98
3686 3778 5.428253 ACTTTCACATCATACGCCTGTTAT 58.572 37.500 0.00 0.00 0.00 1.89
3700 3792 3.756117 GGAACCTCCTGAACTTTCACAT 58.244 45.455 0.00 0.00 32.53 3.21
3734 3826 3.003480 GAGAAAAGGGACTCCACGATTG 58.997 50.000 0.00 0.00 38.49 2.67
3764 3856 1.009829 CTCATTGGACCACGCTAAGC 58.990 55.000 0.00 0.00 0.00 3.09
3765 3857 1.009829 GCTCATTGGACCACGCTAAG 58.990 55.000 0.00 0.00 0.00 2.18
3766 3858 0.739462 CGCTCATTGGACCACGCTAA 60.739 55.000 0.00 0.00 0.00 3.09
3767 3859 1.153647 CGCTCATTGGACCACGCTA 60.154 57.895 0.00 0.00 0.00 4.26
3768 3860 2.434884 CGCTCATTGGACCACGCT 60.435 61.111 0.00 0.00 0.00 5.07
3769 3861 4.166011 GCGCTCATTGGACCACGC 62.166 66.667 10.23 10.23 39.49 5.34
3770 3862 2.034879 AAGCGCTCATTGGACCACG 61.035 57.895 12.06 0.00 0.00 4.94
3771 3863 1.503542 CAAGCGCTCATTGGACCAC 59.496 57.895 12.06 0.00 0.00 4.16
3772 3864 2.334946 GCAAGCGCTCATTGGACCA 61.335 57.895 12.06 0.00 34.30 4.02
3773 3865 2.262471 CTGCAAGCGCTCATTGGACC 62.262 60.000 12.06 0.00 39.64 4.46
3774 3866 1.136147 CTGCAAGCGCTCATTGGAC 59.864 57.895 12.06 0.00 39.64 4.02
3775 3867 3.582148 CTGCAAGCGCTCATTGGA 58.418 55.556 12.06 5.89 39.64 3.53
3786 3878 1.825090 TGGTGAGTATTGGCTGCAAG 58.175 50.000 0.50 0.00 0.00 4.01
3787 3879 2.161855 CTTGGTGAGTATTGGCTGCAA 58.838 47.619 0.50 0.00 0.00 4.08
3788 3880 1.350684 TCTTGGTGAGTATTGGCTGCA 59.649 47.619 0.50 0.00 0.00 4.41
3789 3881 2.113860 TCTTGGTGAGTATTGGCTGC 57.886 50.000 0.00 0.00 0.00 5.25
3790 3882 4.095483 GTCAATCTTGGTGAGTATTGGCTG 59.905 45.833 0.00 0.00 32.53 4.85
3791 3883 4.265073 GTCAATCTTGGTGAGTATTGGCT 58.735 43.478 0.00 0.00 32.53 4.75
3792 3884 3.378427 GGTCAATCTTGGTGAGTATTGGC 59.622 47.826 0.00 0.00 34.08 4.52
3793 3885 3.623060 CGGTCAATCTTGGTGAGTATTGG 59.377 47.826 0.00 0.00 31.66 3.16
3794 3886 4.503910 TCGGTCAATCTTGGTGAGTATTG 58.496 43.478 0.00 0.00 0.00 1.90
3795 3887 4.819105 TCGGTCAATCTTGGTGAGTATT 57.181 40.909 0.00 0.00 0.00 1.89
3796 3888 4.162320 ACATCGGTCAATCTTGGTGAGTAT 59.838 41.667 0.00 0.00 0.00 2.12
3797 3889 3.513912 ACATCGGTCAATCTTGGTGAGTA 59.486 43.478 0.00 0.00 0.00 2.59
3798 3890 2.303022 ACATCGGTCAATCTTGGTGAGT 59.697 45.455 0.00 0.00 0.00 3.41
3799 3891 2.977914 ACATCGGTCAATCTTGGTGAG 58.022 47.619 0.00 0.00 0.00 3.51
3800 3892 3.417069 AACATCGGTCAATCTTGGTGA 57.583 42.857 0.00 0.00 0.00 4.02
3801 3893 4.503741 AAAACATCGGTCAATCTTGGTG 57.496 40.909 0.00 0.00 0.00 4.17
3862 3954 6.423905 CAGGTTGAAAAGAATGTCTTACTCGA 59.576 38.462 0.00 0.00 35.27 4.04
3899 3991 9.213799 CAGTGAGATAATAAGGAAATAAGGAGC 57.786 37.037 0.00 0.00 0.00 4.70
3965 4057 4.673968 TCACTACACTACCAAGACTGGAT 58.326 43.478 0.00 0.00 46.92 3.41
3966 4058 4.108501 TCACTACACTACCAAGACTGGA 57.891 45.455 0.00 0.00 46.92 3.86
3967 4059 6.071560 TGTAATCACTACACTACCAAGACTGG 60.072 42.308 0.00 0.00 41.05 4.00
4008 4100 8.372459 TCGTTTATGCATATAGGGATAACAGTT 58.628 33.333 10.39 0.00 31.89 3.16


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

AutoCloner maintained by Alex Coulton.