Multiple sequence alignment - TraesCS5D01G508400

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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 TraesCS5D01G508400 chr5D 100.000 4025 0 0 1 4025 533629504 533633528 0.000000e+00 7433.0
1 TraesCS5D01G508400 chr5D 100.000 514 0 0 634 1147 533575554 533576067 0.000000e+00 950.0
2 TraesCS5D01G508400 chr5D 86.371 653 64 11 6 639 533575439 533576085 0.000000e+00 689.0
3 TraesCS5D01G508400 chr5D 85.714 546 52 12 633 1172 533629623 533630148 1.630000e-153 553.0
4 TraesCS5D01G508400 chr5D 85.714 546 52 12 120 645 533630136 533630675 1.630000e-153 553.0
5 TraesCS5D01G508400 chr5D 82.012 517 71 12 10 515 533589891 533590396 1.730000e-113 420.0
6 TraesCS5D01G508400 chr5D 84.615 364 36 9 1312 1673 533576168 533576513 1.070000e-90 344.0
7 TraesCS5D01G508400 chr5D 80.929 409 65 4 633 1041 533590001 533590396 1.090000e-80 311.0
8 TraesCS5D01G508400 chr5D 84.783 276 42 0 10 285 533570597 533570872 1.100000e-70 278.0
9 TraesCS5D01G508400 chr5D 91.837 49 3 1 1469 1517 533545489 533545536 2.600000e-07 67.6
10 TraesCS5D01G508400 chr5D 89.796 49 4 1 3908 3955 537914083 537914131 1.210000e-05 62.1
11 TraesCS5D01G508400 chr4A 87.381 2948 185 90 649 3499 638222903 638220046 0.000000e+00 3210.0
12 TraesCS5D01G508400 chr4A 87.755 490 48 6 136 620 638222903 638222421 2.720000e-156 562.0
13 TraesCS5D01G508400 chr4A 93.617 329 13 3 3595 3923 638220044 638219724 6.050000e-133 484.0
14 TraesCS5D01G508400 chr4A 77.067 641 98 22 10 644 638244029 638243432 1.400000e-84 324.0
15 TraesCS5D01G508400 chr5B 89.638 2210 145 37 1766 3923 673680523 673682700 0.000000e+00 2736.0
16 TraesCS5D01G508400 chr5B 83.976 830 73 21 633 1455 673669668 673670444 0.000000e+00 741.0
17 TraesCS5D01G508400 chr5B 90.772 531 23 8 1198 1710 673679942 673680464 0.000000e+00 686.0
18 TraesCS5D01G508400 chr5B 85.290 639 49 19 10 631 673669558 673670168 5.720000e-173 617.0
19 TraesCS5D01G508400 chr5B 78.408 1093 109 67 634 1710 673635743 673636724 9.630000e-166 593.0
20 TraesCS5D01G508400 chr5B 82.720 625 60 23 10 627 673635632 673636215 2.770000e-141 512.0
21 TraesCS5D01G508400 chr5B 80.784 510 80 11 10 510 673631732 673632232 2.270000e-102 383.0
22 TraesCS5D01G508400 chr5B 81.725 487 55 13 31 514 673625013 673625468 3.800000e-100 375.0
23 TraesCS5D01G508400 chr5B 79.537 518 82 15 10 515 673665898 673666403 8.280000e-92 348.0
24 TraesCS5D01G508400 chr5B 81.796 401 60 6 636 1036 673631845 673632232 1.400000e-84 324.0
25 TraesCS5D01G508400 chr5B 84.420 276 42 1 10 285 673673290 673673564 1.840000e-68 270.0
26 TraesCS5D01G508400 chr5B 76.471 408 55 24 633 1040 673625102 673625468 2.470000e-42 183.0
27 TraesCS5D01G508400 chr5B 83.077 195 31 1 2949 3141 673656889 673657083 4.130000e-40 176.0
28 TraesCS5D01G508400 chr5B 95.122 82 4 0 1603 1684 673671527 673671608 3.260000e-26 130.0
29 TraesCS5D01G508400 chr5B 85.965 114 10 2 331 444 673679456 673679563 2.540000e-22 117.0
30 TraesCS5D01G508400 chr5B 85.321 109 15 1 3913 4020 281628121 281628229 1.180000e-20 111.0
31 TraesCS5D01G508400 chr5B 85.149 101 7 5 1982 2074 673638691 673638791 3.310000e-16 97.1
32 TraesCS5D01G508400 chr5B 100.000 29 0 0 1712 1740 673680493 673680521 2.000000e-03 54.7
33 TraesCS5D01G508400 chr6D 77.937 630 98 16 3316 3920 354067266 354066653 4.950000e-94 355.0
34 TraesCS5D01G508400 chr6D 87.879 99 11 1 3922 4019 226946360 226946262 9.140000e-22 115.0
35 TraesCS5D01G508400 chr7D 78.061 588 84 17 3342 3908 528908373 528908936 3.000000e-86 329.0
36 TraesCS5D01G508400 chr7D 80.882 408 59 11 3528 3920 529038114 529038517 1.820000e-78 303.0
37 TraesCS5D01G508400 chr7D 94.737 38 2 0 2687 2724 32644811 32644848 4.340000e-05 60.2
38 TraesCS5D01G508400 chr6B 81.019 432 54 15 3505 3920 392492463 392492044 6.490000e-83 318.0
39 TraesCS5D01G508400 chr6B 77.576 495 86 11 3446 3920 524338736 524339225 3.960000e-70 276.0
40 TraesCS5D01G508400 chr6B 89.796 98 10 0 3920 4017 259041530 259041627 4.220000e-25 126.0
41 TraesCS5D01G508400 chr7A 77.090 598 87 25 3327 3908 608678433 608678996 2.350000e-77 300.0
42 TraesCS5D01G508400 chr6A 75.578 606 104 18 3324 3920 530135999 530135429 3.990000e-65 259.0
43 TraesCS5D01G508400 chr4D 87.500 104 12 1 3922 4025 206664982 206664880 7.070000e-23 119.0
44 TraesCS5D01G508400 chr1D 86.869 99 12 1 3922 4019 431326183 431326085 4.250000e-20 110.0
45 TraesCS5D01G508400 chr1D 85.437 103 15 0 3920 4022 96918322 96918424 1.530000e-19 108.0
46 TraesCS5D01G508400 chr3B 84.615 104 16 0 3922 4025 629638501 629638398 1.980000e-18 104.0
47 TraesCS5D01G508400 chr3A 97.059 34 1 0 3922 3955 692313934 692313901 1.560000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G508400 chr5D 533629504 533633528 4024 False 2846.333333 7433 90.476000 1 4025 3 chr5D.!!$F6 4024
1 TraesCS5D01G508400 chr5D 533575439 533576513 1074 False 661.000000 950 90.328667 6 1673 3 chr5D.!!$F4 1667
2 TraesCS5D01G508400 chr5D 533589891 533590396 505 False 365.500000 420 81.470500 10 1041 2 chr5D.!!$F5 1031
3 TraesCS5D01G508400 chr4A 638219724 638222903 3179 True 1418.666667 3210 89.584333 136 3923 3 chr4A.!!$R2 3787
4 TraesCS5D01G508400 chr4A 638243432 638244029 597 True 324.000000 324 77.067000 10 644 1 chr4A.!!$R1 634
5 TraesCS5D01G508400 chr5B 673679456 673682700 3244 False 898.425000 2736 91.593750 331 3923 4 chr5B.!!$F6 3592
6 TraesCS5D01G508400 chr5B 673665898 673673564 7666 False 421.200000 741 85.669000 10 1684 5 chr5B.!!$F5 1674
7 TraesCS5D01G508400 chr5B 673631732 673638791 7059 False 381.820000 593 81.771400 10 2074 5 chr5B.!!$F4 2064
8 TraesCS5D01G508400 chr6D 354066653 354067266 613 True 355.000000 355 77.937000 3316 3920 1 chr6D.!!$R2 604
9 TraesCS5D01G508400 chr7D 528908373 528908936 563 False 329.000000 329 78.061000 3342 3908 1 chr7D.!!$F2 566
10 TraesCS5D01G508400 chr7A 608678433 608678996 563 False 300.000000 300 77.090000 3327 3908 1 chr7A.!!$F1 581
11 TraesCS5D01G508400 chr6A 530135429 530135999 570 True 259.000000 259 75.578000 3324 3920 1 chr6A.!!$R1 596

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
232 233 0.030908 GATCCCATCCGTGACTCGAC 59.969 60.000 0.00 0.0 42.86 4.20 F
627 635 0.042731 AACCTCTCTTCATCCCCCGA 59.957 55.000 0.00 0.0 0.00 5.14 F
630 638 0.461961 CTCTCTTCATCCCCCGACAC 59.538 60.000 0.00 0.0 0.00 3.67 F
1228 4810 0.596577 CCGTACGTCCATCGATCCAT 59.403 55.000 15.21 0.0 42.86 3.41 F
1692 6227 1.003233 GGAGGTCGCCTTCAAGCTT 60.003 57.895 0.00 0.0 31.76 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 5020 0.229247 TTAACACGACGCCGAAAACG 59.771 50.000 0.00 0.0 39.50 3.60 R
1810 8722 0.319297 GAAAGGCAGCAGCAACAAGG 60.319 55.000 2.65 0.0 44.61 3.61 R
1811 8723 0.672342 AGAAAGGCAGCAGCAACAAG 59.328 50.000 2.65 0.0 44.61 3.16 R
2792 10346 0.247695 GAGCGAGTTAATTGGTGCGC 60.248 55.000 0.00 0.0 44.22 6.09 R
3598 11268 1.134371 GGGGAGGAGATTTTGAGTCGG 60.134 57.143 0.00 0.0 0.00 4.79 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
29 30 3.308595 CGTACATGTTGTATCCGCACAAT 59.691 43.478 2.30 0.00 40.36 2.71
85 86 4.141181 CCAGAAATTACCCATGGATCCTCA 60.141 45.833 15.22 0.00 32.55 3.86
103 104 2.768527 CTCAAGGGAGTGAATAGCAGGA 59.231 50.000 0.00 0.00 36.36 3.86
129 130 1.126846 GTTCGCTCGATGGTTCACAAG 59.873 52.381 0.00 0.00 0.00 3.16
145 146 2.022129 AAGAAGCAACGCCGACGAG 61.022 57.895 0.00 0.00 43.93 4.18
163 164 3.439540 GAAATCGCCGGCTGCCAA 61.440 61.111 26.68 4.74 36.24 4.52
189 190 3.496155 GCAAGTTTCTGCTGCTACAATC 58.504 45.455 0.00 0.00 39.34 2.67
190 191 3.058016 GCAAGTTTCTGCTGCTACAATCA 60.058 43.478 0.00 0.00 39.34 2.57
191 192 4.380233 GCAAGTTTCTGCTGCTACAATCAT 60.380 41.667 0.00 0.00 39.34 2.45
198 199 3.011818 TGCTGCTACAATCATTGAGTGG 58.988 45.455 17.47 2.99 31.53 4.00
199 200 2.223433 GCTGCTACAATCATTGAGTGGC 60.223 50.000 17.47 12.38 39.77 5.01
232 233 0.030908 GATCCCATCCGTGACTCGAC 59.969 60.000 0.00 0.00 42.86 4.20
236 237 1.500396 CATCCGTGACTCGACGTGA 59.500 57.895 3.58 0.00 42.86 4.35
237 238 0.109919 CATCCGTGACTCGACGTGAA 60.110 55.000 3.58 0.00 42.86 3.18
241 242 1.082300 GTGACTCGACGTGAAGCGA 60.082 57.895 3.58 0.00 44.77 4.93
255 256 2.045926 GCGACCTGCACCTTCCAT 60.046 61.111 0.00 0.00 45.45 3.41
259 260 1.003355 ACCTGCACCTTCCATCGTG 60.003 57.895 0.00 0.00 0.00 4.35
277 278 3.443045 GAGTGCCACAATGCCGGG 61.443 66.667 2.18 0.00 0.00 5.73
290 291 2.045926 CCGGGGAAAGCAGGACAG 60.046 66.667 0.00 0.00 0.00 3.51
300 301 2.436292 CAGGACAGGCAGCAGCTC 60.436 66.667 0.00 0.00 41.70 4.09
312 313 2.816958 CAGCTCAACGCATCCGCT 60.817 61.111 0.00 0.00 42.61 5.52
316 317 3.386867 CTCAACGCATCCGCTTGGC 62.387 63.158 0.00 0.00 38.22 4.52
321 322 2.517875 GCATCCGCTTGGCCATCT 60.518 61.111 6.09 0.00 34.30 2.90
325 326 0.536687 ATCCGCTTGGCCATCTGATG 60.537 55.000 6.09 10.71 0.00 3.07
326 327 1.153107 CCGCTTGGCCATCTGATGA 60.153 57.895 18.92 0.00 0.00 2.92
341 342 6.154021 CCATCTGATGAAAGTCCCTGAAAATT 59.846 38.462 18.92 0.00 0.00 1.82
345 346 4.335400 TGAAAGTCCCTGAAAATTTGGC 57.665 40.909 0.00 0.00 0.00 4.52
348 349 0.613260 GTCCCTGAAAATTTGGCCCC 59.387 55.000 0.00 0.00 0.00 5.80
349 350 0.192064 TCCCTGAAAATTTGGCCCCA 59.808 50.000 0.00 0.00 0.00 4.96
350 351 0.614812 CCCTGAAAATTTGGCCCCAG 59.385 55.000 0.00 0.00 0.00 4.45
354 355 1.357137 GAAAATTTGGCCCCAGGGAA 58.643 50.000 7.25 0.00 37.50 3.97
355 356 1.278985 GAAAATTTGGCCCCAGGGAAG 59.721 52.381 7.25 0.00 37.50 3.46
356 357 1.200760 AAATTTGGCCCCAGGGAAGC 61.201 55.000 7.25 1.80 37.50 3.86
389 390 1.015109 GCTCGGTCGTGTAGATCTCA 58.985 55.000 0.00 0.00 0.00 3.27
390 391 1.003331 GCTCGGTCGTGTAGATCTCAG 60.003 57.143 0.00 0.00 0.00 3.35
391 392 1.003331 CTCGGTCGTGTAGATCTCAGC 60.003 57.143 0.00 0.00 0.00 4.26
393 394 1.003331 CGGTCGTGTAGATCTCAGCTC 60.003 57.143 0.00 0.00 0.00 4.09
394 395 1.003331 GGTCGTGTAGATCTCAGCTCG 60.003 57.143 0.00 4.38 0.00 5.03
395 396 1.934525 GTCGTGTAGATCTCAGCTCGA 59.065 52.381 0.00 6.71 0.00 4.04
396 397 2.546368 GTCGTGTAGATCTCAGCTCGAT 59.454 50.000 16.32 0.00 31.36 3.59
397 398 3.002862 GTCGTGTAGATCTCAGCTCGATT 59.997 47.826 16.32 0.00 31.36 3.34
399 400 3.971871 CGTGTAGATCTCAGCTCGATTTC 59.028 47.826 0.00 0.00 0.00 2.17
400 401 4.295051 GTGTAGATCTCAGCTCGATTTCC 58.705 47.826 0.00 0.00 0.00 3.13
401 402 2.791383 AGATCTCAGCTCGATTTCCG 57.209 50.000 0.00 0.00 40.25 4.30
402 403 1.339610 AGATCTCAGCTCGATTTCCGG 59.660 52.381 0.00 0.00 39.14 5.14
403 404 1.067821 GATCTCAGCTCGATTTCCGGT 59.932 52.381 0.00 0.00 39.14 5.28
404 405 0.895530 TCTCAGCTCGATTTCCGGTT 59.104 50.000 0.00 0.00 39.14 4.44
405 406 1.135083 TCTCAGCTCGATTTCCGGTTC 60.135 52.381 0.00 0.00 39.14 3.62
406 407 0.606096 TCAGCTCGATTTCCGGTTCA 59.394 50.000 0.00 0.00 39.14 3.18
407 408 1.002366 CAGCTCGATTTCCGGTTCAG 58.998 55.000 0.00 0.10 39.14 3.02
408 409 0.741221 AGCTCGATTTCCGGTTCAGC 60.741 55.000 0.00 9.14 39.14 4.26
434 435 0.389817 GATGCGGGGGCTTTTTGTTC 60.390 55.000 0.00 0.00 0.00 3.18
435 436 1.826340 ATGCGGGGGCTTTTTGTTCC 61.826 55.000 0.00 0.00 0.00 3.62
437 438 1.964448 CGGGGGCTTTTTGTTCCTC 59.036 57.895 0.00 0.00 0.00 3.71
438 439 1.862602 CGGGGGCTTTTTGTTCCTCG 61.863 60.000 0.00 0.00 36.90 4.63
439 440 0.826256 GGGGGCTTTTTGTTCCTCGT 60.826 55.000 0.00 0.00 0.00 4.18
440 441 1.037493 GGGGCTTTTTGTTCCTCGTT 58.963 50.000 0.00 0.00 0.00 3.85
442 443 2.545113 GGGGCTTTTTGTTCCTCGTTTC 60.545 50.000 0.00 0.00 0.00 2.78
443 444 2.381589 GGCTTTTTGTTCCTCGTTTCG 58.618 47.619 0.00 0.00 0.00 3.46
445 446 2.793237 GCTTTTTGTTCCTCGTTTCGCA 60.793 45.455 0.00 0.00 0.00 5.10
446 447 2.461897 TTTTGTTCCTCGTTTCGCAC 57.538 45.000 0.00 0.00 0.00 5.34
447 448 1.370609 TTTGTTCCTCGTTTCGCACA 58.629 45.000 0.00 0.00 0.00 4.57
448 449 1.370609 TTGTTCCTCGTTTCGCACAA 58.629 45.000 0.00 0.00 0.00 3.33
449 450 1.370609 TGTTCCTCGTTTCGCACAAA 58.629 45.000 0.00 0.00 0.00 2.83
450 451 1.329292 TGTTCCTCGTTTCGCACAAAG 59.671 47.619 0.00 0.00 0.00 2.77
452 453 1.214367 TCCTCGTTTCGCACAAAGAC 58.786 50.000 0.00 0.00 0.00 3.01
499 507 2.472909 CGCAATCCCCGCTCTTTCC 61.473 63.158 0.00 0.00 0.00 3.13
510 518 1.219393 CTCTTTCCGGCTCCACTCC 59.781 63.158 0.00 0.00 0.00 3.85
512 520 0.836400 TCTTTCCGGCTCCACTCCTT 60.836 55.000 0.00 0.00 0.00 3.36
513 521 0.391793 CTTTCCGGCTCCACTCCTTC 60.392 60.000 0.00 0.00 0.00 3.46
514 522 2.167398 TTTCCGGCTCCACTCCTTCG 62.167 60.000 0.00 0.00 0.00 3.79
516 524 2.182030 CGGCTCCACTCCTTCGTC 59.818 66.667 0.00 0.00 0.00 4.20
517 525 2.579738 GGCTCCACTCCTTCGTCC 59.420 66.667 0.00 0.00 0.00 4.79
519 527 1.513622 GCTCCACTCCTTCGTCCTC 59.486 63.158 0.00 0.00 0.00 3.71
520 528 1.950973 GCTCCACTCCTTCGTCCTCC 61.951 65.000 0.00 0.00 0.00 4.30
523 531 1.658686 CCACTCCTTCGTCCTCCTCG 61.659 65.000 0.00 0.00 0.00 4.63
525 533 1.077644 CTCCTTCGTCCTCCTCGGA 60.078 63.158 0.00 0.00 40.30 4.55
526 534 0.680280 CTCCTTCGTCCTCCTCGGAA 60.680 60.000 0.00 0.00 45.32 4.30
527 535 0.964358 TCCTTCGTCCTCCTCGGAAC 60.964 60.000 0.00 0.00 45.32 3.62
528 536 1.511768 CTTCGTCCTCCTCGGAACC 59.488 63.158 0.00 0.00 45.32 3.62
530 538 4.493747 CGTCCTCCTCGGAACCGC 62.494 72.222 8.48 0.00 45.32 5.68
550 558 4.787280 CTCCCGCTCCCACTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
551 559 4.779733 TCCCGCTCCCACTCCCTC 62.780 72.222 0.00 0.00 0.00 4.30
552 560 4.787280 CCCGCTCCCACTCCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
553 561 3.151022 CCGCTCCCACTCCCTCTC 61.151 72.222 0.00 0.00 0.00 3.20
555 563 3.844090 GCTCCCACTCCCTCTCGC 61.844 72.222 0.00 0.00 0.00 5.03
556 564 3.151022 CTCCCACTCCCTCTCGCC 61.151 72.222 0.00 0.00 0.00 5.54
558 566 3.151022 CCCACTCCCTCTCGCCTC 61.151 72.222 0.00 0.00 0.00 4.70
559 567 3.522731 CCACTCCCTCTCGCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
560 568 2.438614 CACTCCCTCTCGCCTCGA 60.439 66.667 0.00 0.00 0.00 4.04
561 569 1.826054 CACTCCCTCTCGCCTCGAT 60.826 63.158 0.00 0.00 34.61 3.59
562 570 1.527380 ACTCCCTCTCGCCTCGATC 60.527 63.158 0.00 0.00 34.61 3.69
564 572 1.228003 TCCCTCTCGCCTCGATCTC 60.228 63.158 0.00 0.00 34.61 2.75
566 574 1.228124 CCTCTCGCCTCGATCTCCT 60.228 63.158 0.00 0.00 34.61 3.69
567 575 1.234615 CCTCTCGCCTCGATCTCCTC 61.235 65.000 0.00 0.00 34.61 3.71
568 576 1.228003 TCTCGCCTCGATCTCCTCC 60.228 63.158 0.00 0.00 34.61 4.30
569 577 2.203365 TCGCCTCGATCTCCTCCC 60.203 66.667 0.00 0.00 0.00 4.30
570 578 3.299190 CGCCTCGATCTCCTCCCC 61.299 72.222 0.00 0.00 0.00 4.81
571 579 2.123251 GCCTCGATCTCCTCCCCA 60.123 66.667 0.00 0.00 0.00 4.96
572 580 2.503382 GCCTCGATCTCCTCCCCAC 61.503 68.421 0.00 0.00 0.00 4.61
573 581 1.834822 CCTCGATCTCCTCCCCACC 60.835 68.421 0.00 0.00 0.00 4.61
574 582 1.834822 CTCGATCTCCTCCCCACCC 60.835 68.421 0.00 0.00 0.00 4.61
576 584 2.372688 GATCTCCTCCCCACCCCA 59.627 66.667 0.00 0.00 0.00 4.96
577 585 2.042930 ATCTCCTCCCCACCCCAC 59.957 66.667 0.00 0.00 0.00 4.61
578 586 2.553438 GATCTCCTCCCCACCCCACT 62.553 65.000 0.00 0.00 0.00 4.00
580 588 4.348495 TCCTCCCCACCCCACTCC 62.348 72.222 0.00 0.00 0.00 3.85
581 589 4.675303 CCTCCCCACCCCACTCCA 62.675 72.222 0.00 0.00 0.00 3.86
582 590 3.330720 CTCCCCACCCCACTCCAC 61.331 72.222 0.00 0.00 0.00 4.02
583 591 4.995058 TCCCCACCCCACTCCACC 62.995 72.222 0.00 0.00 0.00 4.61
585 593 3.650950 CCCACCCCACTCCACCAG 61.651 72.222 0.00 0.00 0.00 4.00
586 594 3.650950 CCACCCCACTCCACCAGG 61.651 72.222 0.00 0.00 0.00 4.45
587 595 4.351054 CACCCCACTCCACCAGGC 62.351 72.222 0.00 0.00 33.74 4.85
592 600 4.624364 CACTCCACCAGGCGCACA 62.624 66.667 10.83 0.00 33.74 4.57
594 602 3.052082 CTCCACCAGGCGCACAAG 61.052 66.667 10.83 0.00 33.74 3.16
596 604 3.357079 CCACCAGGCGCACAAGTC 61.357 66.667 10.83 0.00 0.00 3.01
597 605 2.591429 CACCAGGCGCACAAGTCA 60.591 61.111 10.83 0.00 0.00 3.41
598 606 2.591715 ACCAGGCGCACAAGTCAC 60.592 61.111 10.83 0.00 0.00 3.67
603 611 3.947841 GCGCACAAGTCACGCCAA 61.948 61.111 0.30 0.00 46.63 4.52
604 612 2.945984 CGCACAAGTCACGCCAAT 59.054 55.556 0.00 0.00 0.00 3.16
607 615 1.069568 CGCACAAGTCACGCCAATAAA 60.070 47.619 0.00 0.00 0.00 1.40
609 617 3.376540 GCACAAGTCACGCCAATAAAAA 58.623 40.909 0.00 0.00 0.00 1.94
610 618 3.181575 GCACAAGTCACGCCAATAAAAAC 59.818 43.478 0.00 0.00 0.00 2.43
611 619 3.733727 CACAAGTCACGCCAATAAAAACC 59.266 43.478 0.00 0.00 0.00 3.27
612 620 3.634910 ACAAGTCACGCCAATAAAAACCT 59.365 39.130 0.00 0.00 0.00 3.50
613 621 4.226761 CAAGTCACGCCAATAAAAACCTC 58.773 43.478 0.00 0.00 0.00 3.85
614 622 3.751518 AGTCACGCCAATAAAAACCTCT 58.248 40.909 0.00 0.00 0.00 3.69
615 623 3.751698 AGTCACGCCAATAAAAACCTCTC 59.248 43.478 0.00 0.00 0.00 3.20
616 624 3.751698 GTCACGCCAATAAAAACCTCTCT 59.248 43.478 0.00 0.00 0.00 3.10
617 625 4.215613 GTCACGCCAATAAAAACCTCTCTT 59.784 41.667 0.00 0.00 0.00 2.85
618 626 4.454504 TCACGCCAATAAAAACCTCTCTTC 59.545 41.667 0.00 0.00 0.00 2.87
620 628 5.010282 ACGCCAATAAAAACCTCTCTTCAT 58.990 37.500 0.00 0.00 0.00 2.57
621 629 5.123979 ACGCCAATAAAAACCTCTCTTCATC 59.876 40.000 0.00 0.00 0.00 2.92
622 630 5.449177 CGCCAATAAAAACCTCTCTTCATCC 60.449 44.000 0.00 0.00 0.00 3.51
623 631 5.163509 GCCAATAAAAACCTCTCTTCATCCC 60.164 44.000 0.00 0.00 0.00 3.85
624 632 5.360999 CCAATAAAAACCTCTCTTCATCCCC 59.639 44.000 0.00 0.00 0.00 4.81
625 633 3.458044 AAAAACCTCTCTTCATCCCCC 57.542 47.619 0.00 0.00 0.00 5.40
626 634 0.912486 AAACCTCTCTTCATCCCCCG 59.088 55.000 0.00 0.00 0.00 5.73
627 635 0.042731 AACCTCTCTTCATCCCCCGA 59.957 55.000 0.00 0.00 0.00 5.14
628 636 0.688087 ACCTCTCTTCATCCCCCGAC 60.688 60.000 0.00 0.00 0.00 4.79
629 637 0.687757 CCTCTCTTCATCCCCCGACA 60.688 60.000 0.00 0.00 0.00 4.35
630 638 0.461961 CTCTCTTCATCCCCCGACAC 59.538 60.000 0.00 0.00 0.00 3.67
631 639 0.976073 TCTCTTCATCCCCCGACACC 60.976 60.000 0.00 0.00 0.00 4.16
1218 4800 4.849329 CTGCTCCGCCGTACGTCC 62.849 72.222 15.21 3.78 41.42 4.79
1226 4808 1.371389 GCCGTACGTCCATCGATCC 60.371 63.158 15.21 0.00 42.86 3.36
1227 4809 2.027325 CCGTACGTCCATCGATCCA 58.973 57.895 15.21 0.00 42.86 3.41
1228 4810 0.596577 CCGTACGTCCATCGATCCAT 59.403 55.000 15.21 0.00 42.86 3.41
1229 4811 1.401148 CCGTACGTCCATCGATCCATC 60.401 57.143 15.21 0.00 42.86 3.51
1408 4994 5.117897 CGTATACAATACATACGCATGCACA 59.882 40.000 19.57 4.37 43.14 4.57
1462 5049 2.028404 GGCGTCGTGTTAATTAACTCGG 59.972 50.000 34.37 25.82 46.75 4.63
1467 5288 5.442390 CGTCGTGTTAATTAACTCGGAACTG 60.442 44.000 34.37 23.24 46.75 3.16
1619 6144 8.715088 ACACTGACGGTAGTAAATAAAATTGAC 58.285 33.333 0.00 0.00 0.00 3.18
1692 6227 1.003233 GGAGGTCGCCTTCAAGCTT 60.003 57.895 0.00 0.00 31.76 3.74
1717 7059 4.943705 TCTCCGAGGTACAGTACGTAATTT 59.056 41.667 5.90 0.00 0.00 1.82
1832 8744 1.527034 TGTTGCTGCTGCCTTTCTAG 58.473 50.000 13.47 0.00 38.71 2.43
2055 9205 5.669430 GCGCGATTCAATTCAATTCAATTTG 59.331 36.000 12.10 0.00 0.00 2.32
2057 9207 7.108630 CGCGATTCAATTCAATTCAATTTGAG 58.891 34.615 0.00 0.00 36.97 3.02
2108 9258 3.134127 GGCGGTCATGTTGCCTCC 61.134 66.667 15.27 7.42 45.40 4.30
2160 9312 7.837863 ACTGTACTGTACTGTATATTTGTGCT 58.162 34.615 23.50 0.91 38.78 4.40
2184 9341 1.595982 CGTGGCGTGCATTTCGTTTG 61.596 55.000 0.00 0.00 0.00 2.93
2641 10121 4.194720 CGGCCGTTCGAGGAGGAG 62.195 72.222 19.50 0.00 0.00 3.69
2792 10346 0.390078 CTCACAGGCTCACAGCAGAG 60.390 60.000 0.00 0.00 44.75 3.35
2816 10370 4.159120 GCACCAATTAACTCGCTCTTTTC 58.841 43.478 0.00 0.00 0.00 2.29
2854 10408 5.415077 AGTCAGATTCTCATTTTGAAGCAGG 59.585 40.000 0.00 0.00 32.89 4.85
2962 10541 5.163784 CCACTTCTCATAATTCACACTGCAG 60.164 44.000 13.48 13.48 0.00 4.41
3020 10599 6.889177 TGTAATGGATGATAAAGCAAACCAGA 59.111 34.615 0.00 0.00 33.95 3.86
3042 10622 9.337091 CCAGATTTTTAGTGGTTAACAATTACG 57.663 33.333 8.10 0.00 0.00 3.18
3209 10789 9.683069 GAAAGCAGATAAAAGAAAATCAGACAA 57.317 29.630 0.00 0.00 0.00 3.18
3215 10795 8.887717 AGATAAAAGAAAATCAGACAATCCTCG 58.112 33.333 0.00 0.00 0.00 4.63
3357 11013 0.616891 GGTACCCACGAACCCTTCAT 59.383 55.000 0.00 0.00 0.00 2.57
3447 11110 3.476419 CCCATCGGGTAAGGCGGT 61.476 66.667 0.00 0.00 38.25 5.68
3448 11111 2.135581 CCCATCGGGTAAGGCGGTA 61.136 63.158 0.00 0.00 38.25 4.02
3449 11112 1.366366 CCATCGGGTAAGGCGGTAG 59.634 63.158 0.00 0.00 0.00 3.18
3450 11113 1.366366 CATCGGGTAAGGCGGTAGG 59.634 63.158 0.00 0.00 0.00 3.18
3451 11114 2.505167 ATCGGGTAAGGCGGTAGGC 61.505 63.158 0.00 0.00 44.19 3.93
3462 11125 3.841758 GGTAGGCGGGTACGGGTG 61.842 72.222 0.00 0.00 41.36 4.61
3475 11138 2.342650 CGGGTGTGGGAAGGCAATG 61.343 63.158 0.00 0.00 0.00 2.82
3518 11181 6.625300 GCATACCCATATACTAGTTCCGTCTG 60.625 46.154 0.00 0.00 0.00 3.51
3530 11193 2.557490 GTTCCGTCTGACAAGTAGGTCT 59.443 50.000 8.73 0.00 38.61 3.85
3598 11268 3.486252 CTGACGTAGCCGCTAGCCC 62.486 68.421 9.66 0.00 45.47 5.19
3627 11297 2.918774 ATCTCCTCCCCTTACCCATT 57.081 50.000 0.00 0.00 0.00 3.16
3849 11551 7.940137 TCCCTAAAAACTTCACTTACATGCTAA 59.060 33.333 0.00 0.00 0.00 3.09
3893 11595 6.403636 GGACATTGTTTAGTGCCATCTAGTTG 60.404 42.308 0.00 0.00 0.00 3.16
3932 11634 9.775854 ATCCACTTCTGAAATAACTAGATGATG 57.224 33.333 0.00 0.00 0.00 3.07
3933 11635 7.712639 TCCACTTCTGAAATAACTAGATGATGC 59.287 37.037 0.00 0.00 0.00 3.91
3934 11636 7.041508 CCACTTCTGAAATAACTAGATGATGCC 60.042 40.741 0.00 0.00 0.00 4.40
3935 11637 6.995091 ACTTCTGAAATAACTAGATGATGCCC 59.005 38.462 0.00 0.00 0.00 5.36
3936 11638 5.869579 TCTGAAATAACTAGATGATGCCCC 58.130 41.667 0.00 0.00 0.00 5.80
3937 11639 4.641396 TGAAATAACTAGATGATGCCCCG 58.359 43.478 0.00 0.00 0.00 5.73
3938 11640 2.770164 ATAACTAGATGATGCCCCGC 57.230 50.000 0.00 0.00 0.00 6.13
3939 11641 0.317160 TAACTAGATGATGCCCCGCG 59.683 55.000 0.00 0.00 0.00 6.46
3940 11642 2.740055 CTAGATGATGCCCCGCGC 60.740 66.667 0.00 0.00 38.31 6.86
3941 11643 4.662961 TAGATGATGCCCCGCGCG 62.663 66.667 25.67 25.67 42.08 6.86
3960 11662 4.961637 TGCTGCGGCATTCATAGT 57.038 50.000 18.37 0.00 44.28 2.12
3961 11663 2.396700 TGCTGCGGCATTCATAGTG 58.603 52.632 18.37 0.00 44.28 2.74
3962 11664 1.009222 GCTGCGGCATTCATAGTGC 60.009 57.895 14.08 0.00 41.78 4.40
3963 11665 1.717791 GCTGCGGCATTCATAGTGCA 61.718 55.000 14.08 0.00 44.25 4.57
3964 11666 0.734309 CTGCGGCATTCATAGTGCAA 59.266 50.000 1.75 0.00 44.25 4.08
3965 11667 1.335810 CTGCGGCATTCATAGTGCAAT 59.664 47.619 1.75 0.00 44.25 3.56
3966 11668 1.750206 TGCGGCATTCATAGTGCAATT 59.250 42.857 0.00 0.00 44.25 2.32
3967 11669 2.166050 TGCGGCATTCATAGTGCAATTT 59.834 40.909 0.00 0.00 44.25 1.82
3968 11670 3.189285 GCGGCATTCATAGTGCAATTTT 58.811 40.909 0.00 0.00 44.25 1.82
3969 11671 3.618150 GCGGCATTCATAGTGCAATTTTT 59.382 39.130 0.00 0.00 44.25 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.870411 GGATACAACATGTACGGCCTTC 59.130 50.000 0.00 0.00 35.42 3.46
3 4 1.202486 CGGATACAACATGTACGGCCT 60.202 52.381 0.00 0.00 35.42 5.19
4 5 1.214367 CGGATACAACATGTACGGCC 58.786 55.000 0.00 0.00 35.42 6.13
8 9 4.875544 ATTGTGCGGATACAACATGTAC 57.124 40.909 0.00 0.00 42.74 2.90
29 30 5.492895 TGCCTAAACTGATTCAAATCCGTA 58.507 37.500 1.01 0.00 32.68 4.02
85 86 2.092699 GCTTCCTGCTATTCACTCCCTT 60.093 50.000 0.00 0.00 38.95 3.95
91 92 1.726853 ACACGCTTCCTGCTATTCAC 58.273 50.000 0.00 0.00 40.11 3.18
93 94 1.324736 CGAACACGCTTCCTGCTATTC 59.675 52.381 0.00 0.00 40.11 1.75
94 95 1.359848 CGAACACGCTTCCTGCTATT 58.640 50.000 0.00 0.00 40.11 1.73
121 122 0.657368 CGGCGTTGCTTCTTGTGAAC 60.657 55.000 0.00 0.00 0.00 3.18
129 130 3.479269 CCTCGTCGGCGTTGCTTC 61.479 66.667 10.18 0.00 39.49 3.86
155 156 3.741476 CTTGCGGAGTTGGCAGCC 61.741 66.667 3.66 3.66 42.12 4.85
168 169 3.058016 TGATTGTAGCAGCAGAAACTTGC 60.058 43.478 0.00 0.00 44.41 4.01
171 172 5.005740 TCAATGATTGTAGCAGCAGAAACT 58.994 37.500 4.93 0.00 0.00 2.66
189 190 3.113745 GCCGATGGCCACTCAATG 58.886 61.111 8.16 0.00 44.06 2.82
199 200 1.958205 GGATCGAAGCAGCCGATGG 60.958 63.158 10.83 0.00 45.49 3.51
232 233 3.414700 GGTGCAGGTCGCTTCACG 61.415 66.667 0.00 0.00 43.06 4.35
236 237 2.032681 GGAAGGTGCAGGTCGCTT 59.967 61.111 0.00 0.00 43.06 4.68
237 238 2.527951 GATGGAAGGTGCAGGTCGCT 62.528 60.000 0.00 0.00 43.06 4.93
241 242 1.003355 CACGATGGAAGGTGCAGGT 60.003 57.895 0.00 0.00 0.00 4.00
259 260 3.443045 CCGGCATTGTGGCACTCC 61.443 66.667 19.83 12.91 43.94 3.85
277 278 2.338785 GCTGCCTGTCCTGCTTTCC 61.339 63.158 0.00 0.00 0.00 3.13
278 279 1.584380 CTGCTGCCTGTCCTGCTTTC 61.584 60.000 0.00 0.00 0.00 2.62
312 313 2.621407 GGGACTTTCATCAGATGGCCAA 60.621 50.000 10.96 0.00 30.10 4.52
316 317 3.920231 TCAGGGACTTTCATCAGATGG 57.080 47.619 10.67 0.00 34.60 3.51
318 319 7.310237 CCAAATTTTCAGGGACTTTCATCAGAT 60.310 37.037 0.00 0.00 34.60 2.90
321 322 5.511202 GCCAAATTTTCAGGGACTTTCATCA 60.511 40.000 0.00 0.00 34.60 3.07
325 326 3.557054 GGGCCAAATTTTCAGGGACTTTC 60.557 47.826 4.39 0.00 34.60 2.62
326 327 2.371841 GGGCCAAATTTTCAGGGACTTT 59.628 45.455 4.39 0.00 34.60 2.66
341 342 3.983420 CTGCTTCCCTGGGGCCAA 61.983 66.667 14.00 0.00 34.68 4.52
345 346 2.673523 CTCACTGCTTCCCTGGGG 59.326 66.667 14.00 2.42 0.00 4.96
348 349 3.123620 GCGCTCACTGCTTCCCTG 61.124 66.667 0.00 0.00 40.11 4.45
349 350 4.749310 CGCGCTCACTGCTTCCCT 62.749 66.667 5.56 0.00 40.11 4.20
365 366 1.011019 CTACACGACCGAGCTAGCG 60.011 63.158 9.55 0.00 0.00 4.26
366 367 0.945813 ATCTACACGACCGAGCTAGC 59.054 55.000 6.62 6.62 0.00 3.42
369 370 1.301423 GAGATCTACACGACCGAGCT 58.699 55.000 0.00 0.00 0.00 4.09
379 380 3.003793 CGGAAATCGAGCTGAGATCTACA 59.996 47.826 0.00 0.00 42.43 2.74
389 390 0.741221 GCTGAACCGGAAATCGAGCT 60.741 55.000 9.46 0.00 42.43 4.09
390 391 1.019278 TGCTGAACCGGAAATCGAGC 61.019 55.000 9.46 14.34 42.43 5.03
391 392 1.002366 CTGCTGAACCGGAAATCGAG 58.998 55.000 9.46 5.30 42.43 4.04
393 394 0.721718 GTCTGCTGAACCGGAAATCG 59.278 55.000 9.46 1.67 38.88 3.34
394 395 0.721718 CGTCTGCTGAACCGGAAATC 59.278 55.000 9.46 3.81 0.00 2.17
395 396 1.298859 GCGTCTGCTGAACCGGAAAT 61.299 55.000 9.46 0.00 38.39 2.17
396 397 1.959226 GCGTCTGCTGAACCGGAAA 60.959 57.895 9.46 0.00 38.39 3.13
397 398 2.357034 GCGTCTGCTGAACCGGAA 60.357 61.111 9.46 0.00 38.39 4.30
399 400 3.989698 ATCGCGTCTGCTGAACCGG 62.990 63.158 5.77 0.00 39.65 5.28
400 401 2.507102 ATCGCGTCTGCTGAACCG 60.507 61.111 5.77 1.44 39.65 4.44
401 402 3.084579 CATCGCGTCTGCTGAACC 58.915 61.111 5.77 0.00 39.65 3.62
402 403 2.397252 GCATCGCGTCTGCTGAAC 59.603 61.111 22.82 1.17 39.65 3.18
421 422 1.037493 AACGAGGAACAAAAAGCCCC 58.963 50.000 0.00 0.00 0.00 5.80
434 435 0.234884 GGTCTTTGTGCGAAACGAGG 59.765 55.000 0.00 0.00 0.00 4.63
435 436 1.070577 CAGGTCTTTGTGCGAAACGAG 60.071 52.381 0.00 0.00 0.00 4.18
437 438 0.041312 CCAGGTCTTTGTGCGAAACG 60.041 55.000 0.00 0.00 0.00 3.60
438 439 0.317854 GCCAGGTCTTTGTGCGAAAC 60.318 55.000 0.00 0.00 0.00 2.78
439 440 0.749818 TGCCAGGTCTTTGTGCGAAA 60.750 50.000 0.00 0.00 0.00 3.46
440 441 1.153066 TGCCAGGTCTTTGTGCGAA 60.153 52.632 0.00 0.00 0.00 4.70
442 443 2.620112 CCTGCCAGGTCTTTGTGCG 61.620 63.158 1.39 0.00 0.00 5.34
443 444 2.924105 GCCTGCCAGGTCTTTGTGC 61.924 63.158 13.35 0.00 37.80 4.57
445 446 2.281761 CGCCTGCCAGGTCTTTGT 60.282 61.111 13.35 0.00 37.80 2.83
446 447 2.032528 TCGCCTGCCAGGTCTTTG 59.967 61.111 13.35 0.00 37.80 2.77
447 448 2.032681 GTCGCCTGCCAGGTCTTT 59.967 61.111 13.35 0.00 37.80 2.52
448 449 3.241530 TGTCGCCTGCCAGGTCTT 61.242 61.111 13.35 0.00 37.80 3.01
449 450 4.008933 GTGTCGCCTGCCAGGTCT 62.009 66.667 13.35 0.00 37.80 3.85
499 507 2.182030 GACGAAGGAGTGGAGCCG 59.818 66.667 0.00 0.00 0.00 5.52
533 541 4.787280 AGGGAGTGGGAGCGGGAG 62.787 72.222 0.00 0.00 0.00 4.30
534 542 4.779733 GAGGGAGTGGGAGCGGGA 62.780 72.222 0.00 0.00 0.00 5.14
535 543 4.787280 AGAGGGAGTGGGAGCGGG 62.787 72.222 0.00 0.00 0.00 6.13
536 544 3.151022 GAGAGGGAGTGGGAGCGG 61.151 72.222 0.00 0.00 0.00 5.52
537 545 3.522731 CGAGAGGGAGTGGGAGCG 61.523 72.222 0.00 0.00 0.00 5.03
538 546 3.844090 GCGAGAGGGAGTGGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
539 547 3.151022 GGCGAGAGGGAGTGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
541 549 3.151022 GAGGCGAGAGGGAGTGGG 61.151 72.222 0.00 0.00 0.00 4.61
543 551 1.791103 GATCGAGGCGAGAGGGAGTG 61.791 65.000 0.00 0.00 39.91 3.51
545 553 1.228124 AGATCGAGGCGAGAGGGAG 60.228 63.158 0.00 0.00 39.91 4.30
546 554 1.228003 GAGATCGAGGCGAGAGGGA 60.228 63.158 0.00 0.00 39.91 4.20
547 555 2.265182 GGAGATCGAGGCGAGAGGG 61.265 68.421 0.00 0.00 39.91 4.30
548 556 1.228124 AGGAGATCGAGGCGAGAGG 60.228 63.158 0.00 0.00 39.91 3.69
549 557 1.234615 GGAGGAGATCGAGGCGAGAG 61.235 65.000 0.00 0.00 39.91 3.20
550 558 1.228003 GGAGGAGATCGAGGCGAGA 60.228 63.158 0.00 0.00 39.91 4.04
551 559 2.265182 GGGAGGAGATCGAGGCGAG 61.265 68.421 0.00 0.00 39.91 5.03
552 560 2.203365 GGGAGGAGATCGAGGCGA 60.203 66.667 0.00 0.00 41.13 5.54
553 561 3.299190 GGGGAGGAGATCGAGGCG 61.299 72.222 0.00 0.00 0.00 5.52
555 563 1.834822 GGTGGGGAGGAGATCGAGG 60.835 68.421 0.00 0.00 0.00 4.63
556 564 1.834822 GGGTGGGGAGGAGATCGAG 60.835 68.421 0.00 0.00 0.00 4.04
558 566 2.844839 GGGGTGGGGAGGAGATCG 60.845 72.222 0.00 0.00 0.00 3.69
559 567 2.073101 GTGGGGTGGGGAGGAGATC 61.073 68.421 0.00 0.00 0.00 2.75
560 568 2.042930 GTGGGGTGGGGAGGAGAT 59.957 66.667 0.00 0.00 0.00 2.75
561 569 3.208592 AGTGGGGTGGGGAGGAGA 61.209 66.667 0.00 0.00 0.00 3.71
562 570 2.689034 GAGTGGGGTGGGGAGGAG 60.689 72.222 0.00 0.00 0.00 3.69
564 572 4.675303 TGGAGTGGGGTGGGGAGG 62.675 72.222 0.00 0.00 0.00 4.30
566 574 4.995058 GGTGGAGTGGGGTGGGGA 62.995 72.222 0.00 0.00 0.00 4.81
568 576 3.650950 CTGGTGGAGTGGGGTGGG 61.651 72.222 0.00 0.00 0.00 4.61
569 577 3.650950 CCTGGTGGAGTGGGGTGG 61.651 72.222 0.00 0.00 34.57 4.61
570 578 4.351054 GCCTGGTGGAGTGGGGTG 62.351 72.222 0.00 0.00 34.57 4.61
576 584 3.832237 CTTGTGCGCCTGGTGGAGT 62.832 63.158 4.18 0.00 35.46 3.85
577 585 3.052082 CTTGTGCGCCTGGTGGAG 61.052 66.667 4.18 0.00 36.16 3.86
578 586 3.825160 GACTTGTGCGCCTGGTGGA 62.825 63.158 4.18 2.70 34.57 4.02
580 588 2.591429 TGACTTGTGCGCCTGGTG 60.591 61.111 4.18 2.05 0.00 4.17
581 589 2.591715 GTGACTTGTGCGCCTGGT 60.592 61.111 4.18 0.00 0.00 4.00
582 590 3.716006 CGTGACTTGTGCGCCTGG 61.716 66.667 4.18 0.00 0.00 4.45
583 591 4.374702 GCGTGACTTGTGCGCCTG 62.375 66.667 4.18 0.00 44.67 4.85
587 595 0.515127 TTATTGGCGTGACTTGTGCG 59.485 50.000 0.00 0.00 0.00 5.34
588 596 2.697431 TTTATTGGCGTGACTTGTGC 57.303 45.000 0.00 0.00 0.00 4.57
589 597 3.733727 GGTTTTTATTGGCGTGACTTGTG 59.266 43.478 0.00 0.00 0.00 3.33
591 599 4.023193 AGAGGTTTTTATTGGCGTGACTTG 60.023 41.667 0.00 0.00 0.00 3.16
592 600 4.142038 AGAGGTTTTTATTGGCGTGACTT 58.858 39.130 0.00 0.00 0.00 3.01
594 602 3.751698 AGAGAGGTTTTTATTGGCGTGAC 59.248 43.478 0.00 0.00 0.00 3.67
596 604 4.215399 TGAAGAGAGGTTTTTATTGGCGTG 59.785 41.667 0.00 0.00 0.00 5.34
597 605 4.394729 TGAAGAGAGGTTTTTATTGGCGT 58.605 39.130 0.00 0.00 0.00 5.68
598 606 5.449177 GGATGAAGAGAGGTTTTTATTGGCG 60.449 44.000 0.00 0.00 0.00 5.69
600 608 5.360999 GGGGATGAAGAGAGGTTTTTATTGG 59.639 44.000 0.00 0.00 0.00 3.16
603 611 4.385310 CGGGGGATGAAGAGAGGTTTTTAT 60.385 45.833 0.00 0.00 0.00 1.40
604 612 3.054655 CGGGGGATGAAGAGAGGTTTTTA 60.055 47.826 0.00 0.00 0.00 1.52
607 615 0.912486 CGGGGGATGAAGAGAGGTTT 59.088 55.000 0.00 0.00 0.00 3.27
609 617 0.688087 GTCGGGGGATGAAGAGAGGT 60.688 60.000 0.00 0.00 0.00 3.85
610 618 0.687757 TGTCGGGGGATGAAGAGAGG 60.688 60.000 0.00 0.00 0.00 3.69
611 619 0.461961 GTGTCGGGGGATGAAGAGAG 59.538 60.000 0.00 0.00 0.00 3.20
612 620 0.976073 GGTGTCGGGGGATGAAGAGA 60.976 60.000 0.00 0.00 0.00 3.10
613 621 0.978146 AGGTGTCGGGGGATGAAGAG 60.978 60.000 0.00 0.00 0.00 2.85
614 622 1.080354 AGGTGTCGGGGGATGAAGA 59.920 57.895 0.00 0.00 0.00 2.87
615 623 1.221840 CAGGTGTCGGGGGATGAAG 59.778 63.158 0.00 0.00 0.00 3.02
616 624 2.297895 CCAGGTGTCGGGGGATGAA 61.298 63.158 0.00 0.00 0.00 2.57
617 625 2.687200 CCAGGTGTCGGGGGATGA 60.687 66.667 0.00 0.00 0.00 2.92
618 626 2.536997 GAACCAGGTGTCGGGGGATG 62.537 65.000 0.00 0.00 32.25 3.51
620 628 2.926242 GAACCAGGTGTCGGGGGA 60.926 66.667 0.00 0.00 32.25 4.81
621 629 3.246112 TGAACCAGGTGTCGGGGG 61.246 66.667 0.00 0.00 32.25 5.40
622 630 2.032071 GTGAACCAGGTGTCGGGG 59.968 66.667 0.00 0.00 32.25 5.73
623 631 0.884704 CTTGTGAACCAGGTGTCGGG 60.885 60.000 0.00 0.00 0.00 5.14
624 632 0.105964 TCTTGTGAACCAGGTGTCGG 59.894 55.000 0.00 0.00 0.00 4.79
625 633 1.502231 CTCTTGTGAACCAGGTGTCG 58.498 55.000 0.00 0.00 0.00 4.35
626 634 1.884235 CCTCTTGTGAACCAGGTGTC 58.116 55.000 0.00 0.00 0.00 3.67
627 635 0.179018 GCCTCTTGTGAACCAGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
628 636 0.179020 TGCCTCTTGTGAACCAGGTG 60.179 55.000 0.00 0.00 0.00 4.00
629 637 0.550914 TTGCCTCTTGTGAACCAGGT 59.449 50.000 0.00 0.00 0.00 4.00
630 638 0.954452 GTTGCCTCTTGTGAACCAGG 59.046 55.000 0.00 0.00 0.00 4.45
631 639 0.588252 CGTTGCCTCTTGTGAACCAG 59.412 55.000 0.00 0.00 0.00 4.00
1408 4994 1.076632 AGCGAGGAGGACGAAGGAT 60.077 57.895 0.00 0.00 0.00 3.24
1434 5020 0.229247 TTAACACGACGCCGAAAACG 59.771 50.000 0.00 0.00 39.50 3.60
1461 5048 0.383231 GCCATACATGCAGCAGTTCC 59.617 55.000 0.00 0.00 0.00 3.62
1462 5049 1.097232 TGCCATACATGCAGCAGTTC 58.903 50.000 0.00 0.00 34.05 3.01
1692 6227 1.002430 ACGTACTGTACCTCGGAGACA 59.998 52.381 12.08 2.95 0.00 3.41
1717 7059 2.348104 ATGCGGAGAGGCGTGTGTA 61.348 57.895 0.00 0.00 35.06 2.90
1745 7087 3.009115 TAGCACTCCCCAGCCCAC 61.009 66.667 0.00 0.00 0.00 4.61
1750 7092 3.140325 TGAAAAAGTAGCACTCCCCAG 57.860 47.619 0.00 0.00 0.00 4.45
1751 7093 3.073798 TCATGAAAAAGTAGCACTCCCCA 59.926 43.478 0.00 0.00 0.00 4.96
1755 7097 8.857216 CAAAATCATCATGAAAAAGTAGCACTC 58.143 33.333 0.00 0.00 0.00 3.51
1756 7098 7.330208 GCAAAATCATCATGAAAAAGTAGCACT 59.670 33.333 0.00 0.00 0.00 4.40
1810 8722 0.319297 GAAAGGCAGCAGCAACAAGG 60.319 55.000 2.65 0.00 44.61 3.61
1811 8723 0.672342 AGAAAGGCAGCAGCAACAAG 59.328 50.000 2.65 0.00 44.61 3.16
1832 8744 1.268352 CTAGTATGCGGAGAGGAGTGC 59.732 57.143 0.00 0.00 0.00 4.40
1917 9029 3.336138 AACTTCCAATCTCTTCCCGTC 57.664 47.619 0.00 0.00 0.00 4.79
2097 9247 2.627791 TTGACGTGGAGGCAACATG 58.372 52.632 0.00 0.00 44.35 3.21
2138 9288 8.188799 TCAGAGCACAAATATACAGTACAGTAC 58.811 37.037 2.05 2.05 0.00 2.73
2139 9289 8.188799 GTCAGAGCACAAATATACAGTACAGTA 58.811 37.037 0.13 0.13 0.00 2.74
2140 9290 7.036220 GTCAGAGCACAAATATACAGTACAGT 58.964 38.462 0.00 0.00 0.00 3.55
2160 9312 1.565156 GAAATGCACGCCACGTCAGA 61.565 55.000 0.00 0.00 38.32 3.27
2792 10346 0.247695 GAGCGAGTTAATTGGTGCGC 60.248 55.000 0.00 0.00 44.22 6.09
2793 10347 1.359848 AGAGCGAGTTAATTGGTGCG 58.640 50.000 0.00 0.00 0.00 5.34
2816 10370 6.179040 AGAATCTGACTTCAAAATGAGAGGG 58.821 40.000 0.00 0.00 0.00 4.30
2854 10408 2.270047 GAGAATCTGTCTGTCTGCTGC 58.730 52.381 0.00 0.00 36.41 5.25
2865 10419 5.885465 AGGGACTTCAAAATGAGAATCTGT 58.115 37.500 0.00 0.00 27.25 3.41
3020 10599 8.848182 TGTCCGTAATTGTTAACCACTAAAAAT 58.152 29.630 2.48 0.00 29.87 1.82
3103 10683 4.137543 GGGGTGCGAATCTATTTCAAGAT 58.862 43.478 0.00 0.00 37.84 2.40
3107 10687 1.948104 CGGGGTGCGAATCTATTTCA 58.052 50.000 0.00 0.00 33.66 2.69
3435 11098 4.580551 CGCCTACCGCCTTACCCG 62.581 72.222 0.00 0.00 0.00 5.28
3438 11101 2.127232 TACCCGCCTACCGCCTTAC 61.127 63.158 0.00 0.00 35.03 2.34
3439 11102 2.127232 GTACCCGCCTACCGCCTTA 61.127 63.158 0.00 0.00 35.03 2.69
3445 11108 3.841758 CACCCGTACCCGCCTACC 61.842 72.222 0.00 0.00 0.00 3.18
3446 11109 3.070576 ACACCCGTACCCGCCTAC 61.071 66.667 0.00 0.00 0.00 3.18
3447 11110 3.069946 CACACCCGTACCCGCCTA 61.070 66.667 0.00 0.00 0.00 3.93
3451 11114 3.305177 CTTCCCACACCCGTACCCG 62.305 68.421 0.00 0.00 0.00 5.28
3518 11181 4.883083 TGACACAATGAGACCTACTTGTC 58.117 43.478 0.00 0.00 34.10 3.18
3561 11229 1.460504 GCCTTGGGTAAAGTGGCTAC 58.539 55.000 0.00 0.00 40.36 3.58
3598 11268 1.134371 GGGGAGGAGATTTTGAGTCGG 60.134 57.143 0.00 0.00 0.00 4.79
3627 11297 3.533547 GCATTTAAAGATGGCCATGCAA 58.466 40.909 26.56 8.38 37.54 4.08
3635 11305 6.267817 ACATGATCAACGCATTTAAAGATGG 58.732 36.000 0.00 0.00 0.00 3.51
3639 11309 7.786114 ACAAAACATGATCAACGCATTTAAAG 58.214 30.769 0.00 0.00 0.00 1.85
3722 11392 8.963725 TCTGCAACTTCTAAATGATCAAATGAT 58.036 29.630 0.00 0.00 37.51 2.45
3893 11595 7.792374 TCAGAAGTGGATAACAATAAGCATC 57.208 36.000 0.00 0.00 0.00 3.91
3923 11625 2.740055 GCGCGGGGCATCATCTAG 60.740 66.667 8.83 0.00 42.87 2.43
3924 11626 4.662961 CGCGCGGGGCATCATCTA 62.663 66.667 24.84 0.00 43.84 1.98
3944 11646 1.009222 GCACTATGAATGCCGCAGC 60.009 57.895 0.00 0.00 37.08 5.25
3945 11647 0.734309 TTGCACTATGAATGCCGCAG 59.266 50.000 0.00 0.00 42.69 5.18
3946 11648 1.391577 ATTGCACTATGAATGCCGCA 58.608 45.000 0.00 0.00 42.69 5.69
3947 11649 2.497107 AATTGCACTATGAATGCCGC 57.503 45.000 0.00 0.00 42.69 6.53


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

AutoCloner maintained by Alex Coulton.