Multiple sequence alignment - TraesCS2D01G133800

Loading Multiple Alignment...

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 TraesCS2D01G133800 chr2D 100.000 4466 0 0 1 4466 78755009 78759474 0.000000e+00 8248.0
1 TraesCS2D01G133800 chr2D 76.394 538 83 23 25 528 560191350 560190823 2.670000e-62 250.0
2 TraesCS2D01G133800 chr2B 94.819 3146 112 21 607 3741 122013265 122016370 0.000000e+00 4859.0
3 TraesCS2D01G133800 chr2B 91.266 790 52 7 2664 3446 159479398 159480177 0.000000e+00 1061.0
4 TraesCS2D01G133800 chr2B 91.336 681 55 2 1836 2516 159368531 159369207 0.000000e+00 928.0
5 TraesCS2D01G133800 chr2B 81.075 428 59 10 45 459 122012712 122013130 5.570000e-84 322.0
6 TraesCS2D01G133800 chr2B 90.132 152 14 1 2518 2669 159390596 159390746 3.520000e-46 196.0
7 TraesCS2D01G133800 chr2B 91.892 74 5 1 4053 4125 122054770 122054843 7.900000e-18 102.0
8 TraesCS2D01G133800 chr2A 93.642 3067 111 30 764 3798 79171912 79174926 0.000000e+00 4506.0
9 TraesCS2D01G133800 chr2A 84.449 463 40 14 2360 2809 23372745 23372302 1.150000e-115 427.0
10 TraesCS2D01G133800 chr2A 82.258 248 27 13 269 510 79171125 79171361 9.800000e-47 198.0
11 TraesCS2D01G133800 chr2A 84.038 213 16 9 3850 4045 79174939 79175150 5.900000e-44 189.0
12 TraesCS2D01G133800 chr2A 87.970 133 7 3 4335 4466 79175526 79175650 1.000000e-31 148.0
13 TraesCS2D01G133800 chr2A 88.235 119 8 3 2299 2417 23372915 23372803 2.170000e-28 137.0
14 TraesCS2D01G133800 chr2A 92.857 70 2 1 4185 4254 79175339 79175405 1.020000e-16 99.0
15 TraesCS2D01G133800 chr2A 97.059 34 1 0 609 642 79171709 79171742 1.740000e-04 58.4
16 TraesCS2D01G133800 chr4D 85.726 2396 281 32 1036 3408 118818146 118820503 0.000000e+00 2473.0
17 TraesCS2D01G133800 chr4D 80.000 545 98 10 2860 3397 334154719 334154179 4.190000e-105 392.0
18 TraesCS2D01G133800 chr4D 75.351 499 93 27 1119 1605 334156520 334156040 3.500000e-51 213.0
19 TraesCS2D01G133800 chr3B 90.826 1853 141 9 1553 3400 612929605 612931433 0.000000e+00 2453.0
20 TraesCS2D01G133800 chr3B 89.200 500 48 5 1063 1557 612912140 612912638 1.760000e-173 619.0
21 TraesCS2D01G133800 chr4A 86.078 2320 264 36 1113 3408 454121514 454123798 0.000000e+00 2440.0
22 TraesCS2D01G133800 chr4A 75.050 497 96 26 1120 1605 139537802 139538281 5.860000e-49 206.0
23 TraesCS2D01G133800 chr4B 85.362 2391 292 36 1036 3408 181251083 181253433 0.000000e+00 2423.0
24 TraesCS2D01G133800 chr4B 80.000 545 98 10 2860 3397 412181830 412181290 4.190000e-105 392.0
25 TraesCS2D01G133800 chr1B 86.059 538 60 9 1335 1858 664770619 664771155 8.390000e-157 564.0
26 TraesCS2D01G133800 chr1B 94.203 69 4 0 4046 4114 52352704 52352636 6.110000e-19 106.0
27 TraesCS2D01G133800 chr7A 85.992 514 42 15 2299 2809 671144004 671144490 1.420000e-144 523.0
28 TraesCS2D01G133800 chr3D 79.518 498 86 10 20 512 579595985 579596471 1.540000e-89 340.0
29 TraesCS2D01G133800 chr6A 78.676 544 91 11 1 528 501798878 501798344 5.530000e-89 339.0
30 TraesCS2D01G133800 chr6A 84.906 106 12 4 15 119 453222707 453222809 2.200000e-18 104.0
31 TraesCS2D01G133800 chr5D 77.362 508 92 13 21 513 45055663 45055164 3.400000e-71 279.0
32 TraesCS2D01G133800 chr5D 75.458 546 97 23 1 528 8490395 8490921 9.660000e-57 231.0
33 TraesCS2D01G133800 chr7B 75.810 525 82 21 25 528 384090167 384089667 1.620000e-54 224.0
34 TraesCS2D01G133800 chr7B 78.808 151 22 7 274 423 425300148 425300289 4.760000e-15 93.5
35 TraesCS2D01G133800 chr6B 90.000 60 6 0 2069 2128 141661124 141661065 1.330000e-10 78.7
36 TraesCS2D01G133800 chr3A 97.368 38 1 0 376 413 515859817 515859854 1.040000e-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 TraesCS2D01G133800 chr2D 78755009 78759474 4465 False 8248.0 8248 100.000000 1 4466 1 chr2D.!!$F1 4465
1 TraesCS2D01G133800 chr2D 560190823 560191350 527 True 250.0 250 76.394000 25 528 1 chr2D.!!$R1 503
2 TraesCS2D01G133800 chr2B 122012712 122016370 3658 False 2590.5 4859 87.947000 45 3741 2 chr2B.!!$F5 3696
3 TraesCS2D01G133800 chr2B 159479398 159480177 779 False 1061.0 1061 91.266000 2664 3446 1 chr2B.!!$F4 782
4 TraesCS2D01G133800 chr2B 159368531 159369207 676 False 928.0 928 91.336000 1836 2516 1 chr2B.!!$F2 680
5 TraesCS2D01G133800 chr2A 79171125 79175650 4525 False 866.4 4506 89.637333 269 4466 6 chr2A.!!$F1 4197
6 TraesCS2D01G133800 chr2A 23372302 23372915 613 True 282.0 427 86.342000 2299 2809 2 chr2A.!!$R1 510
7 TraesCS2D01G133800 chr4D 118818146 118820503 2357 False 2473.0 2473 85.726000 1036 3408 1 chr4D.!!$F1 2372
8 TraesCS2D01G133800 chr4D 334154179 334156520 2341 True 302.5 392 77.675500 1119 3397 2 chr4D.!!$R1 2278
9 TraesCS2D01G133800 chr3B 612929605 612931433 1828 False 2453.0 2453 90.826000 1553 3400 1 chr3B.!!$F2 1847
10 TraesCS2D01G133800 chr4A 454121514 454123798 2284 False 2440.0 2440 86.078000 1113 3408 1 chr4A.!!$F2 2295
11 TraesCS2D01G133800 chr4B 181251083 181253433 2350 False 2423.0 2423 85.362000 1036 3408 1 chr4B.!!$F1 2372
12 TraesCS2D01G133800 chr4B 412181290 412181830 540 True 392.0 392 80.000000 2860 3397 1 chr4B.!!$R1 537
13 TraesCS2D01G133800 chr1B 664770619 664771155 536 False 564.0 564 86.059000 1335 1858 1 chr1B.!!$F1 523
14 TraesCS2D01G133800 chr6A 501798344 501798878 534 True 339.0 339 78.676000 1 528 1 chr6A.!!$R1 527
15 TraesCS2D01G133800 chr5D 8490395 8490921 526 False 231.0 231 75.458000 1 528 1 chr5D.!!$F1 527
16 TraesCS2D01G133800 chr7B 384089667 384090167 500 True 224.0 224 75.810000 25 528 1 chr7B.!!$R1 503

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
743 1155 0.106708 TCCATCCATTAGCTCGTGCC 59.893 55.0 5.73 0.00 40.8 5.01 F
990 1409 0.107643 TTCCATTCGTGCACAGACCA 59.892 50.0 18.64 1.85 0.0 4.02 F
1575 1997 1.194781 ACTCCACCAAGCTCATCCGT 61.195 55.0 0.00 0.00 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1997 1.301716 GTTGCGGCTGAGGTTGAGA 60.302 57.895 0.00 0.00 0.00 3.27 R
2196 2927 2.620112 CCCGGCGATGATCAATGCC 61.620 63.158 24.49 24.49 44.09 4.40 R
3471 4430 0.693622 TAATTCACCCAAGTCGGCCA 59.306 50.000 2.24 0.00 0.00 5.36 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
33 34 4.980903 GTTGCCGGCGTGCACAAG 62.981 66.667 23.90 6.94 41.88 3.16
53 54 1.227853 GGTGTCTTGCCCACTTCGT 60.228 57.895 0.00 0.00 33.31 3.85
83 84 2.527374 TCCCCCGTCCCGAAAACT 60.527 61.111 0.00 0.00 0.00 2.66
104 105 0.324614 ACCATGATCCGTGCTTCACA 59.675 50.000 0.00 0.00 33.40 3.58
131 132 2.581354 GCCACTCTGATGAGCGGT 59.419 61.111 0.00 0.00 42.80 5.68
157 158 1.785647 GGACATAGGGAAGGTACGGT 58.214 55.000 0.00 0.00 0.00 4.83
192 193 2.208132 TCTTCTCCTCTCGCTGAAGT 57.792 50.000 0.00 0.00 37.67 3.01
201 202 3.192422 CCTCTCGCTGAAGTATATCCCTG 59.808 52.174 0.00 0.00 0.00 4.45
223 224 0.759346 GGGTATCCGGCAATCTGACT 59.241 55.000 0.00 0.00 0.00 3.41
227 228 1.123077 ATCCGGCAATCTGACTAGCA 58.877 50.000 0.00 0.00 0.00 3.49
228 229 1.123077 TCCGGCAATCTGACTAGCAT 58.877 50.000 0.00 0.00 0.00 3.79
229 230 2.316108 TCCGGCAATCTGACTAGCATA 58.684 47.619 0.00 0.00 0.00 3.14
249 250 0.549950 CTGCTGGACATGGGGAAGAT 59.450 55.000 0.00 0.00 0.00 2.40
266 288 1.129058 GATATGTCAACGGAGGGGGT 58.871 55.000 0.00 0.00 0.00 4.95
268 290 0.252330 TATGTCAACGGAGGGGGTGA 60.252 55.000 0.00 0.00 0.00 4.02
269 291 0.914417 ATGTCAACGGAGGGGGTGAT 60.914 55.000 0.00 0.00 0.00 3.06
271 293 1.229368 TCAACGGAGGGGGTGATGA 60.229 57.895 0.00 0.00 0.00 2.92
281 303 4.540715 GAGGGGGTGATGATTCATTTTCT 58.459 43.478 0.00 0.00 33.56 2.52
310 332 4.547367 CCGGACGAAGATGGGCCC 62.547 72.222 17.59 17.59 0.00 5.80
314 336 2.285368 ACGAAGATGGGCCCTGGA 60.285 61.111 25.70 2.00 0.00 3.86
315 337 1.910580 GACGAAGATGGGCCCTGGAA 61.911 60.000 25.70 1.52 0.00 3.53
317 339 0.323360 CGAAGATGGGCCCTGGAAAA 60.323 55.000 25.70 0.07 0.00 2.29
318 340 1.686115 CGAAGATGGGCCCTGGAAAAT 60.686 52.381 25.70 6.53 0.00 1.82
319 341 1.758862 GAAGATGGGCCCTGGAAAATG 59.241 52.381 25.70 0.00 0.00 2.32
320 342 0.688749 AGATGGGCCCTGGAAAATGC 60.689 55.000 25.70 1.41 0.00 3.56
321 343 0.977108 GATGGGCCCTGGAAAATGCA 60.977 55.000 25.70 0.00 0.00 3.96
322 344 0.326808 ATGGGCCCTGGAAAATGCAT 60.327 50.000 25.70 0.00 0.00 3.96
340 362 2.014128 CATCCGGCGGTCATTTTAGTT 58.986 47.619 27.32 0.00 0.00 2.24
350 372 6.403964 GGCGGTCATTTTAGTTTAGGTTTAGG 60.404 42.308 0.00 0.00 0.00 2.69
413 436 8.934507 TTGTTTCGGTTTAGATGAAAAACATT 57.065 26.923 0.00 0.00 39.56 2.71
513 567 5.189928 TGAAATGTAAACCGGACATATGCT 58.810 37.500 9.46 0.00 36.50 3.79
515 569 6.995686 TGAAATGTAAACCGGACATATGCTAT 59.004 34.615 9.46 0.00 36.50 2.97
528 582 6.881065 GGACATATGCTATTAGCTTTGGATGA 59.119 38.462 16.29 0.00 42.97 2.92
530 584 8.277490 ACATATGCTATTAGCTTTGGATGATG 57.723 34.615 16.29 11.16 42.97 3.07
531 585 7.338703 ACATATGCTATTAGCTTTGGATGATGG 59.661 37.037 16.29 0.59 42.97 3.51
532 586 5.052693 TGCTATTAGCTTTGGATGATGGT 57.947 39.130 16.29 0.00 42.97 3.55
533 587 4.823442 TGCTATTAGCTTTGGATGATGGTG 59.177 41.667 16.29 0.00 42.97 4.17
535 589 5.049129 GCTATTAGCTTTGGATGATGGTGTC 60.049 44.000 8.47 0.00 38.45 3.67
536 590 2.134789 AGCTTTGGATGATGGTGTCC 57.865 50.000 0.00 0.00 35.02 4.02
537 591 1.106285 GCTTTGGATGATGGTGTCCC 58.894 55.000 0.00 0.00 33.45 4.46
538 592 1.382522 CTTTGGATGATGGTGTCCCG 58.617 55.000 0.00 0.00 33.45 5.14
541 595 0.469494 TGGATGATGGTGTCCCGATG 59.531 55.000 0.00 0.00 33.45 3.84
542 596 0.886490 GGATGATGGTGTCCCGATGC 60.886 60.000 0.00 0.00 0.00 3.91
543 597 0.179048 GATGATGGTGTCCCGATGCA 60.179 55.000 0.00 0.00 0.00 3.96
561 615 2.034939 TGCAGGACTGAATTTGCAAGTG 59.965 45.455 3.00 0.00 42.96 3.16
562 616 2.294233 GCAGGACTGAATTTGCAAGTGA 59.706 45.455 3.00 0.00 36.59 3.41
563 617 3.243501 GCAGGACTGAATTTGCAAGTGAA 60.244 43.478 3.00 0.00 36.59 3.18
564 618 4.543692 CAGGACTGAATTTGCAAGTGAAG 58.456 43.478 0.00 0.94 0.00 3.02
565 619 4.276678 CAGGACTGAATTTGCAAGTGAAGA 59.723 41.667 0.00 0.00 0.00 2.87
566 620 5.048224 CAGGACTGAATTTGCAAGTGAAGAT 60.048 40.000 0.00 0.00 0.00 2.40
567 621 5.048224 AGGACTGAATTTGCAAGTGAAGATG 60.048 40.000 0.00 0.00 0.00 2.90
568 622 5.130292 ACTGAATTTGCAAGTGAAGATGG 57.870 39.130 0.00 0.00 0.00 3.51
569 623 3.916761 TGAATTTGCAAGTGAAGATGGC 58.083 40.909 0.00 0.00 0.00 4.40
570 624 3.256558 GAATTTGCAAGTGAAGATGGCC 58.743 45.455 0.00 0.00 0.00 5.36
604 659 1.361668 GCGTCGACGTACAGGAGGTA 61.362 60.000 35.48 0.00 42.22 3.08
605 660 0.649475 CGTCGACGTACAGGAGGTAG 59.351 60.000 29.08 0.00 31.13 3.18
655 972 2.376538 CCGCATACGTGTCGTTGCA 61.377 57.895 19.71 0.00 40.71 4.08
667 984 2.316867 CGTTGCACCGCAGACATCA 61.317 57.895 0.00 0.00 40.61 3.07
684 1001 4.334552 ACATCATGTACACTTTGCATCCA 58.665 39.130 0.00 0.00 0.00 3.41
688 1005 4.696877 TCATGTACACTTTGCATCCAGAAG 59.303 41.667 0.00 0.00 0.00 2.85
689 1006 4.350368 TGTACACTTTGCATCCAGAAGA 57.650 40.909 2.16 0.00 0.00 2.87
690 1007 4.910195 TGTACACTTTGCATCCAGAAGAT 58.090 39.130 2.16 0.00 34.66 2.40
691 1008 5.316167 TGTACACTTTGCATCCAGAAGATT 58.684 37.500 2.16 0.00 30.59 2.40
693 1010 5.382618 ACACTTTGCATCCAGAAGATTTC 57.617 39.130 2.16 0.00 30.59 2.17
695 1012 5.048224 ACACTTTGCATCCAGAAGATTTCAG 60.048 40.000 2.16 0.00 30.59 3.02
724 1136 0.395724 GCCGTTGGGAGGGAATCAAT 60.396 55.000 0.00 0.00 34.06 2.57
743 1155 0.106708 TCCATCCATTAGCTCGTGCC 59.893 55.000 5.73 0.00 40.80 5.01
990 1409 0.107643 TTCCATTCGTGCACAGACCA 59.892 50.000 18.64 1.85 0.00 4.02
1512 1934 2.429236 CTGCAGTCGTTCGACGCT 60.429 61.111 26.83 10.77 42.21 5.07
1575 1997 1.194781 ACTCCACCAAGCTCATCCGT 61.195 55.000 0.00 0.00 0.00 4.69
1746 2180 4.675404 CGGAAAGAAGCCGTCACT 57.325 55.556 0.00 0.00 43.66 3.41
1985 2716 1.498865 CTCACCGCAACGCTCAAGTT 61.499 55.000 0.00 0.00 34.15 2.66
2049 2780 2.982744 GCTCGCCCAGAAGTTTGGC 61.983 63.158 0.00 0.00 41.85 4.52
2236 2967 1.300233 GTGATCGGCGTCCTCATCC 60.300 63.158 6.85 0.00 0.00 3.51
2749 3622 2.328099 GCCTTCTTGCACGGTGAGG 61.328 63.158 13.29 10.25 0.00 3.86
3317 4258 2.811317 GGACACGCTCAAGCTCGG 60.811 66.667 0.00 0.00 39.32 4.63
3446 4405 2.409870 GCGAGGAAGGCCATGTTGG 61.410 63.158 5.01 0.00 41.55 3.77
3468 4427 0.718343 CTGCAAGCAACGAGTAGAGC 59.282 55.000 0.00 0.00 0.00 4.09
3469 4428 0.033366 TGCAAGCAACGAGTAGAGCA 59.967 50.000 0.00 0.00 0.00 4.26
3470 4429 0.718343 GCAAGCAACGAGTAGAGCAG 59.282 55.000 0.00 0.00 0.00 4.24
3471 4430 1.937108 GCAAGCAACGAGTAGAGCAGT 60.937 52.381 0.00 0.00 0.00 4.40
3472 4431 1.723542 CAAGCAACGAGTAGAGCAGTG 59.276 52.381 0.00 0.00 0.00 3.66
3473 4432 0.244994 AGCAACGAGTAGAGCAGTGG 59.755 55.000 0.00 0.00 0.00 4.00
3474 4433 1.355066 GCAACGAGTAGAGCAGTGGC 61.355 60.000 0.00 0.00 41.61 5.01
3475 4434 0.737715 CAACGAGTAGAGCAGTGGCC 60.738 60.000 0.00 0.00 42.56 5.36
3476 4435 2.103143 CGAGTAGAGCAGTGGCCG 59.897 66.667 0.00 0.00 42.56 6.13
3477 4436 2.407428 CGAGTAGAGCAGTGGCCGA 61.407 63.158 0.00 0.00 42.56 5.54
3478 4437 1.139947 GAGTAGAGCAGTGGCCGAC 59.860 63.158 0.00 0.00 42.56 4.79
3479 4438 1.304547 AGTAGAGCAGTGGCCGACT 60.305 57.895 0.00 0.00 42.56 4.18
3480 4439 0.900647 AGTAGAGCAGTGGCCGACTT 60.901 55.000 0.00 0.00 42.56 3.01
3481 4440 0.737715 GTAGAGCAGTGGCCGACTTG 60.738 60.000 0.00 0.00 42.56 3.16
3482 4441 1.888436 TAGAGCAGTGGCCGACTTGG 61.888 60.000 0.00 0.00 42.56 3.61
3488 4447 1.303317 GTGGCCGACTTGGGTGAAT 60.303 57.895 0.00 0.00 38.63 2.57
3502 4461 6.216456 ACTTGGGTGAATTAGAGAGGAAAGAT 59.784 38.462 0.00 0.00 0.00 2.40
3532 4497 9.616156 TGTTACATTGAGGTTTAGTAGTTTTGA 57.384 29.630 0.00 0.00 0.00 2.69
3556 4521 9.571810 TGATTGATAATTCTTTGATTCGTTTGG 57.428 29.630 0.00 0.00 0.00 3.28
3675 4649 7.185565 TGTCAGGAATTCCAAACCCATATAAA 58.814 34.615 26.22 3.00 38.89 1.40
3708 4683 3.969117 TGTCAAAGCTGTTGATCACAC 57.031 42.857 12.42 0.00 0.00 3.82
3711 4691 4.398988 TGTCAAAGCTGTTGATCACACTTT 59.601 37.500 12.42 0.27 37.28 2.66
3713 4693 5.807011 GTCAAAGCTGTTGATCACACTTTTT 59.193 36.000 12.42 0.00 35.92 1.94
3721 4701 8.694394 GCTGTTGATCACACTTTTTAATTTCTC 58.306 33.333 0.00 0.00 0.00 2.87
3741 4721 1.220206 CAGCCTGCTTCCTCGTCAT 59.780 57.895 0.00 0.00 0.00 3.06
3744 4724 1.086634 GCCTGCTTCCTCGTCATGTC 61.087 60.000 0.00 0.00 0.00 3.06
3759 4739 6.602179 TCGTCATGTCATTCAGAATTTCAAC 58.398 36.000 0.00 0.00 0.00 3.18
3760 4740 6.427853 TCGTCATGTCATTCAGAATTTCAACT 59.572 34.615 0.00 0.00 0.00 3.16
3761 4741 6.522165 CGTCATGTCATTCAGAATTTCAACTG 59.478 38.462 0.00 0.00 35.72 3.16
3762 4742 7.571798 CGTCATGTCATTCAGAATTTCAACTGA 60.572 37.037 0.00 0.00 40.66 3.41
3798 4782 2.180432 AAGCGGTTCCAGTAAACCTC 57.820 50.000 0.00 0.00 45.45 3.85
3799 4783 0.037605 AGCGGTTCCAGTAAACCTCG 60.038 55.000 4.46 0.00 45.45 4.63
3800 4784 1.632948 GCGGTTCCAGTAAACCTCGC 61.633 60.000 4.46 0.00 45.45 5.03
3802 4786 1.154197 GGTTCCAGTAAACCTCGCAC 58.846 55.000 0.00 0.00 44.45 5.34
3803 4787 1.270678 GGTTCCAGTAAACCTCGCACT 60.271 52.381 0.00 0.00 44.45 4.40
3804 4788 2.067013 GTTCCAGTAAACCTCGCACTC 58.933 52.381 0.00 0.00 0.00 3.51
3806 4790 1.968493 TCCAGTAAACCTCGCACTCTT 59.032 47.619 0.00 0.00 0.00 2.85
3807 4791 2.029290 TCCAGTAAACCTCGCACTCTTC 60.029 50.000 0.00 0.00 0.00 2.87
3810 4794 2.633481 AGTAAACCTCGCACTCTTCCTT 59.367 45.455 0.00 0.00 0.00 3.36
3811 4795 2.171341 AAACCTCGCACTCTTCCTTC 57.829 50.000 0.00 0.00 0.00 3.46
3812 4796 1.343069 AACCTCGCACTCTTCCTTCT 58.657 50.000 0.00 0.00 0.00 2.85
3813 4797 0.605589 ACCTCGCACTCTTCCTTCTG 59.394 55.000 0.00 0.00 0.00 3.02
3814 4798 0.891373 CCTCGCACTCTTCCTTCTGA 59.109 55.000 0.00 0.00 0.00 3.27
3815 4799 1.273606 CCTCGCACTCTTCCTTCTGAA 59.726 52.381 0.00 0.00 0.00 3.02
3831 4815 6.831976 CCTTCTGAAGGTAGCCTAATTATGT 58.168 40.000 25.13 0.00 43.95 2.29
3832 4816 6.931840 CCTTCTGAAGGTAGCCTAATTATGTC 59.068 42.308 25.13 0.00 43.95 3.06
3833 4817 6.420913 TCTGAAGGTAGCCTAATTATGTCC 57.579 41.667 0.00 0.00 31.13 4.02
3834 4818 5.903010 TCTGAAGGTAGCCTAATTATGTCCA 59.097 40.000 0.00 0.00 31.13 4.02
3835 4819 6.042093 TCTGAAGGTAGCCTAATTATGTCCAG 59.958 42.308 0.00 0.00 31.13 3.86
3836 4820 5.665812 TGAAGGTAGCCTAATTATGTCCAGT 59.334 40.000 0.00 0.00 31.13 4.00
3837 4821 6.842280 TGAAGGTAGCCTAATTATGTCCAGTA 59.158 38.462 0.00 0.00 31.13 2.74
3838 4822 7.346175 TGAAGGTAGCCTAATTATGTCCAGTAA 59.654 37.037 0.00 0.00 31.13 2.24
3839 4823 7.685849 AGGTAGCCTAATTATGTCCAGTAAA 57.314 36.000 0.00 0.00 28.47 2.01
3840 4824 8.276453 AGGTAGCCTAATTATGTCCAGTAAAT 57.724 34.615 0.00 0.00 28.47 1.40
3841 4825 9.388672 AGGTAGCCTAATTATGTCCAGTAAATA 57.611 33.333 0.00 0.00 28.47 1.40
3842 4826 9.654663 GGTAGCCTAATTATGTCCAGTAAATAG 57.345 37.037 0.00 0.00 0.00 1.73
3868 4852 9.322773 GTAATACTCCAGTAACTTGGATTAACC 57.677 37.037 0.00 0.00 45.80 2.85
3901 4892 4.872691 GCAGGTATGGATAATCAATCTCCG 59.127 45.833 0.00 0.00 34.75 4.63
3914 4905 4.489737 TCAATCTCCGGATATACCAACCT 58.510 43.478 3.57 0.00 38.90 3.50
3915 4906 5.647230 TCAATCTCCGGATATACCAACCTA 58.353 41.667 3.57 0.00 38.90 3.08
3932 4923 4.213564 ACCTACAAGGAAGAATGCTCAG 57.786 45.455 0.00 0.00 37.67 3.35
3936 4927 2.005451 CAAGGAAGAATGCTCAGGACG 58.995 52.381 0.00 0.00 0.00 4.79
3946 4937 5.540337 AGAATGCTCAGGACGAATAATCCTA 59.460 40.000 0.00 0.00 45.25 2.94
3960 4951 9.046296 ACGAATAATCCTATTTGCAGTAAGAAG 57.954 33.333 0.00 0.00 33.62 2.85
3961 4952 8.012241 CGAATAATCCTATTTGCAGTAAGAAGC 58.988 37.037 0.00 0.00 0.00 3.86
3962 4953 7.751768 ATAATCCTATTTGCAGTAAGAAGCC 57.248 36.000 0.00 0.00 0.00 4.35
3963 4954 4.844349 TCCTATTTGCAGTAAGAAGCCT 57.156 40.909 0.00 0.00 0.00 4.58
3964 4955 4.770795 TCCTATTTGCAGTAAGAAGCCTC 58.229 43.478 0.00 0.00 0.00 4.70
3983 4975 3.703052 CCTCCTAGCATGCCAAAATTCTT 59.297 43.478 15.66 0.00 0.00 2.52
3984 4976 4.202090 CCTCCTAGCATGCCAAAATTCTTC 60.202 45.833 15.66 0.00 0.00 2.87
3985 4977 4.603131 TCCTAGCATGCCAAAATTCTTCT 58.397 39.130 15.66 0.00 0.00 2.85
3988 4980 2.498885 AGCATGCCAAAATTCTTCTCCC 59.501 45.455 15.66 0.00 0.00 4.30
3989 4981 2.234414 GCATGCCAAAATTCTTCTCCCA 59.766 45.455 6.36 0.00 0.00 4.37
3990 4982 3.677976 GCATGCCAAAATTCTTCTCCCAG 60.678 47.826 6.36 0.00 0.00 4.45
4004 5002 2.507058 TCTCCCAGACCAATCCAATCTG 59.493 50.000 0.00 0.00 39.70 2.90
4049 5047 8.301252 AGCAATTTAAAAGGGATATTAACCGT 57.699 30.769 0.00 0.00 0.00 4.83
4050 5048 8.410912 AGCAATTTAAAAGGGATATTAACCGTC 58.589 33.333 0.00 0.00 0.00 4.79
4051 5049 8.192110 GCAATTTAAAAGGGATATTAACCGTCA 58.808 33.333 0.00 0.00 0.00 4.35
4056 5054 9.517868 TTAAAAGGGATATTAACCGTCAAAGAA 57.482 29.630 0.00 0.00 0.00 2.52
4070 5068 7.275920 ACCGTCAAAGAAGCATATTAGAGATT 58.724 34.615 0.00 0.00 0.00 2.40
4071 5069 7.225538 ACCGTCAAAGAAGCATATTAGAGATTG 59.774 37.037 0.00 0.00 0.00 2.67
4072 5070 7.225538 CCGTCAAAGAAGCATATTAGAGATTGT 59.774 37.037 0.00 0.00 0.00 2.71
4073 5071 8.607459 CGTCAAAGAAGCATATTAGAGATTGTT 58.393 33.333 0.00 0.00 0.00 2.83
4076 5074 9.727627 CAAAGAAGCATATTAGAGATTGTTTCC 57.272 33.333 0.00 0.00 31.94 3.13
4077 5075 7.721286 AGAAGCATATTAGAGATTGTTTCCG 57.279 36.000 0.00 0.00 31.94 4.30
4078 5076 7.275920 AGAAGCATATTAGAGATTGTTTCCGT 58.724 34.615 0.00 0.00 31.94 4.69
4079 5077 7.770897 AGAAGCATATTAGAGATTGTTTCCGTT 59.229 33.333 0.00 0.00 31.94 4.44
4080 5078 7.484035 AGCATATTAGAGATTGTTTCCGTTC 57.516 36.000 0.00 0.00 0.00 3.95
4081 5079 7.047891 AGCATATTAGAGATTGTTTCCGTTCA 58.952 34.615 0.00 0.00 0.00 3.18
4082 5080 7.552687 AGCATATTAGAGATTGTTTCCGTTCAA 59.447 33.333 0.00 0.00 0.00 2.69
4083 5081 8.181573 GCATATTAGAGATTGTTTCCGTTCAAA 58.818 33.333 0.00 0.00 0.00 2.69
4089 5087 8.335532 AGAGATTGTTTCCGTTCAAAATATCA 57.664 30.769 0.00 0.00 0.00 2.15
4090 5088 8.960591 AGAGATTGTTTCCGTTCAAAATATCAT 58.039 29.630 0.00 0.00 0.00 2.45
4091 5089 9.226345 GAGATTGTTTCCGTTCAAAATATCATC 57.774 33.333 0.00 0.00 0.00 2.92
4092 5090 8.190784 AGATTGTTTCCGTTCAAAATATCATCC 58.809 33.333 0.00 0.00 0.00 3.51
4093 5091 6.825944 TGTTTCCGTTCAAAATATCATCCA 57.174 33.333 0.00 0.00 0.00 3.41
4123 5121 9.733556 ACAAACAGAGTGGTTATATATGTTCAA 57.266 29.630 0.00 0.00 0.00 2.69
4144 5142 8.589629 GTTCAAAAATATCATGCTGATGTTGTC 58.410 33.333 8.40 0.00 37.24 3.18
4145 5143 7.828712 TCAAAAATATCATGCTGATGTTGTCA 58.171 30.769 8.40 0.00 37.24 3.58
4147 5145 9.738832 CAAAAATATCATGCTGATGTTGTCATA 57.261 29.630 8.40 0.00 37.24 2.15
4164 5264 2.835764 TCATACTAGTTTGCCCTTCGGT 59.164 45.455 0.00 0.00 0.00 4.69
4172 5272 2.060050 TTGCCCTTCGGTCAGAAAAA 57.940 45.000 0.00 0.00 38.57 1.94
4173 5273 1.314730 TGCCCTTCGGTCAGAAAAAC 58.685 50.000 0.00 0.00 38.57 2.43
4174 5274 1.314730 GCCCTTCGGTCAGAAAAACA 58.685 50.000 0.00 0.00 38.57 2.83
4175 5275 1.001706 GCCCTTCGGTCAGAAAAACAC 60.002 52.381 0.00 0.00 38.57 3.32
4176 5276 2.572290 CCCTTCGGTCAGAAAAACACT 58.428 47.619 0.00 0.00 38.57 3.55
4177 5277 3.735591 CCCTTCGGTCAGAAAAACACTA 58.264 45.455 0.00 0.00 38.57 2.74
4178 5278 4.131596 CCCTTCGGTCAGAAAAACACTAA 58.868 43.478 0.00 0.00 38.57 2.24
4179 5279 4.024302 CCCTTCGGTCAGAAAAACACTAAC 60.024 45.833 0.00 0.00 38.57 2.34
4180 5280 4.573201 CCTTCGGTCAGAAAAACACTAACA 59.427 41.667 0.00 0.00 38.57 2.41
4181 5281 5.238650 CCTTCGGTCAGAAAAACACTAACAT 59.761 40.000 0.00 0.00 38.57 2.71
4182 5282 5.666969 TCGGTCAGAAAAACACTAACATG 57.333 39.130 0.00 0.00 0.00 3.21
4183 5283 4.024387 TCGGTCAGAAAAACACTAACATGC 60.024 41.667 0.00 0.00 0.00 4.06
4216 5316 1.604378 CGCCCCAATCTCACCTTCT 59.396 57.895 0.00 0.00 0.00 2.85
4217 5317 0.035056 CGCCCCAATCTCACCTTCTT 60.035 55.000 0.00 0.00 0.00 2.52
4218 5318 1.756430 GCCCCAATCTCACCTTCTTC 58.244 55.000 0.00 0.00 0.00 2.87
4225 5325 4.252073 CAATCTCACCTTCTTCAGTCAGG 58.748 47.826 0.00 0.00 0.00 3.86
4249 5349 1.352622 AACACTGGGCCTGAACCTCA 61.353 55.000 18.12 0.00 0.00 3.86
4254 5354 0.474854 TGGGCCTGAACCTCACCTTA 60.475 55.000 4.53 0.00 0.00 2.69
4255 5355 0.253327 GGGCCTGAACCTCACCTTAG 59.747 60.000 0.84 0.00 0.00 2.18
4256 5356 0.393132 GGCCTGAACCTCACCTTAGC 60.393 60.000 0.00 0.00 0.00 3.09
4258 5358 1.003696 GCCTGAACCTCACCTTAGCTT 59.996 52.381 0.00 0.00 0.00 3.74
4259 5359 2.937433 GCCTGAACCTCACCTTAGCTTC 60.937 54.545 0.00 0.00 0.00 3.86
4260 5360 2.303022 CCTGAACCTCACCTTAGCTTCA 59.697 50.000 0.00 0.00 0.00 3.02
4261 5361 3.594134 CTGAACCTCACCTTAGCTTCAG 58.406 50.000 0.00 0.00 31.39 3.02
4262 5362 2.972713 TGAACCTCACCTTAGCTTCAGT 59.027 45.455 0.00 0.00 0.00 3.41
4264 5364 4.777896 TGAACCTCACCTTAGCTTCAGTAT 59.222 41.667 0.00 0.00 0.00 2.12
4265 5365 5.248477 TGAACCTCACCTTAGCTTCAGTATT 59.752 40.000 0.00 0.00 0.00 1.89
4267 5367 4.532521 ACCTCACCTTAGCTTCAGTATTGT 59.467 41.667 0.00 0.00 0.00 2.71
4268 5368 4.872691 CCTCACCTTAGCTTCAGTATTGTG 59.127 45.833 0.00 0.00 0.00 3.33
4269 5369 4.253685 TCACCTTAGCTTCAGTATTGTGC 58.746 43.478 0.00 0.00 0.00 4.57
4270 5370 4.020218 TCACCTTAGCTTCAGTATTGTGCT 60.020 41.667 0.00 11.46 38.21 4.40
4272 5372 4.938226 ACCTTAGCTTCAGTATTGTGCTTC 59.062 41.667 11.83 0.00 36.86 3.86
4273 5373 5.181748 CCTTAGCTTCAGTATTGTGCTTCT 58.818 41.667 11.83 0.00 36.86 2.85
4274 5374 5.293079 CCTTAGCTTCAGTATTGTGCTTCTC 59.707 44.000 11.83 0.00 36.86 2.87
4276 5376 2.996621 GCTTCAGTATTGTGCTTCTCGT 59.003 45.455 0.00 0.00 0.00 4.18
4277 5377 4.082190 AGCTTCAGTATTGTGCTTCTCGTA 60.082 41.667 3.58 0.00 33.80 3.43
4281 5381 6.937436 TCAGTATTGTGCTTCTCGTATCTA 57.063 37.500 0.00 0.00 0.00 1.98
4282 5382 6.726230 TCAGTATTGTGCTTCTCGTATCTAC 58.274 40.000 0.00 0.00 0.00 2.59
4301 5401 1.217882 CGCCAGTCGTCTCAAAAGTT 58.782 50.000 0.00 0.00 0.00 2.66
4302 5402 1.070577 CGCCAGTCGTCTCAAAAGTTG 60.071 52.381 0.00 0.00 0.00 3.16
4303 5403 1.264288 GCCAGTCGTCTCAAAAGTTGG 59.736 52.381 0.00 0.00 0.00 3.77
4304 5404 1.264288 CCAGTCGTCTCAAAAGTTGGC 59.736 52.381 0.00 0.00 0.00 4.52
4305 5405 2.213499 CAGTCGTCTCAAAAGTTGGCT 58.787 47.619 0.00 0.00 0.00 4.75
4306 5406 2.614057 CAGTCGTCTCAAAAGTTGGCTT 59.386 45.455 0.00 0.00 36.30 4.35
4307 5407 2.872858 AGTCGTCTCAAAAGTTGGCTTC 59.127 45.455 0.00 0.00 33.01 3.86
4310 5410 2.031682 CGTCTCAAAAGTTGGCTTCAGG 60.032 50.000 0.00 0.00 33.01 3.86
4311 5411 2.952310 GTCTCAAAAGTTGGCTTCAGGT 59.048 45.455 0.00 0.00 33.01 4.00
4312 5412 3.381590 GTCTCAAAAGTTGGCTTCAGGTT 59.618 43.478 0.00 0.00 33.01 3.50
4313 5413 3.381272 TCTCAAAAGTTGGCTTCAGGTTG 59.619 43.478 0.00 0.00 33.01 3.77
4314 5414 2.159114 TCAAAAGTTGGCTTCAGGTTGC 60.159 45.455 0.00 0.00 33.01 4.17
4315 5415 1.780503 AAAGTTGGCTTCAGGTTGCT 58.219 45.000 0.00 0.00 33.01 3.91
4316 5416 2.656947 AAGTTGGCTTCAGGTTGCTA 57.343 45.000 0.00 0.00 0.00 3.49
4345 5485 4.674101 CGTCAAAGGTTGTGCTTGAGAAAA 60.674 41.667 0.00 0.00 30.00 2.29
4350 5490 4.122046 AGGTTGTGCTTGAGAAAATTTGC 58.878 39.130 0.00 0.00 0.00 3.68
4352 5492 3.110447 TGTGCTTGAGAAAATTTGCCC 57.890 42.857 0.00 0.00 0.00 5.36
4359 5499 2.364970 TGAGAAAATTTGCCCTGTGTGG 59.635 45.455 0.00 0.00 0.00 4.17
4368 5508 1.341482 TGCCCTGTGTGGAAACTTTCA 60.341 47.619 3.93 0.00 38.35 2.69
4369 5509 1.067060 GCCCTGTGTGGAAACTTTCAC 59.933 52.381 3.93 0.00 38.35 3.18
4414 5554 6.042552 TCCAAATTCTGGCCACTAATTTTCAA 59.957 34.615 22.80 13.18 45.98 2.69
4421 5561 5.546526 TGGCCACTAATTTTCAAACCATTC 58.453 37.500 0.00 0.00 0.00 2.67
4422 5562 4.625311 GGCCACTAATTTTCAAACCATTCG 59.375 41.667 0.00 0.00 0.00 3.34
4423 5563 4.091365 GCCACTAATTTTCAAACCATTCGC 59.909 41.667 0.00 0.00 0.00 4.70
4430 5570 2.760634 TCAAACCATTCGCAGCTAGA 57.239 45.000 0.00 0.00 0.00 2.43
4431 5571 2.346803 TCAAACCATTCGCAGCTAGAC 58.653 47.619 0.00 0.00 0.00 2.59
4432 5572 2.028112 TCAAACCATTCGCAGCTAGACT 60.028 45.455 0.00 0.00 0.00 3.24
4433 5573 3.194755 TCAAACCATTCGCAGCTAGACTA 59.805 43.478 0.00 0.00 0.00 2.59
4434 5574 2.873133 ACCATTCGCAGCTAGACTAC 57.127 50.000 0.00 0.00 0.00 2.73
4435 5575 1.409427 ACCATTCGCAGCTAGACTACC 59.591 52.381 0.00 0.00 0.00 3.18
4436 5576 1.269831 CCATTCGCAGCTAGACTACCC 60.270 57.143 0.00 0.00 0.00 3.69
4441 5581 2.158652 TCGCAGCTAGACTACCCACTAT 60.159 50.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.227823 CGAAGTGGGCAAGACACCA 60.228 57.895 0.00 0.00 39.63 4.17
53 54 2.836360 GGGGACGACGATGGCCTA 60.836 66.667 3.32 0.00 0.00 3.93
73 74 3.680475 CGGATCATGGTTAGTTTTCGGGA 60.680 47.826 0.00 0.00 0.00 5.14
77 78 3.689649 AGCACGGATCATGGTTAGTTTTC 59.310 43.478 0.00 0.00 0.00 2.29
83 84 2.027653 TGTGAAGCACGGATCATGGTTA 60.028 45.455 12.15 0.00 37.88 2.85
104 105 2.284258 AGAGTGGCCTCCGCTTCT 60.284 61.111 3.32 0.00 45.19 2.85
131 132 0.251916 CTTCCCTATGTCCGGTTGCA 59.748 55.000 0.00 0.00 0.00 4.08
157 158 0.472471 AAGAACAACCTCCGCTTCCA 59.528 50.000 0.00 0.00 0.00 3.53
201 202 0.886490 CAGATTGCCGGATACCCTGC 60.886 60.000 5.05 0.00 42.27 4.85
227 228 1.492176 CTTCCCCATGTCCAGCAGTAT 59.508 52.381 0.00 0.00 0.00 2.12
228 229 0.911769 CTTCCCCATGTCCAGCAGTA 59.088 55.000 0.00 0.00 0.00 2.74
229 230 0.842030 TCTTCCCCATGTCCAGCAGT 60.842 55.000 0.00 0.00 0.00 4.40
249 250 0.252330 TCACCCCCTCCGTTGACATA 60.252 55.000 0.00 0.00 0.00 2.29
266 288 6.005066 TGAGCCCTAGAAAATGAATCATCA 57.995 37.500 0.00 0.00 40.57 3.07
268 290 5.773680 CCATGAGCCCTAGAAAATGAATCAT 59.226 40.000 0.00 0.00 0.00 2.45
269 291 5.135383 CCATGAGCCCTAGAAAATGAATCA 58.865 41.667 0.00 0.00 0.00 2.57
271 293 3.893813 GCCATGAGCCCTAGAAAATGAAT 59.106 43.478 0.00 0.00 34.35 2.57
297 319 1.497309 TTTCCAGGGCCCATCTTCGT 61.497 55.000 27.56 0.00 0.00 3.85
308 330 2.019897 GCCGGATGCATTTTCCAGGG 62.020 60.000 5.05 0.00 40.77 4.45
309 331 1.438814 GCCGGATGCATTTTCCAGG 59.561 57.895 5.05 6.04 40.77 4.45
310 332 1.064621 CGCCGGATGCATTTTCCAG 59.935 57.895 5.05 0.00 41.33 3.86
314 336 1.037030 ATGACCGCCGGATGCATTTT 61.037 50.000 11.71 0.00 41.33 1.82
315 337 1.037030 AATGACCGCCGGATGCATTT 61.037 50.000 11.71 0.00 41.33 2.32
317 339 1.037030 AAAATGACCGCCGGATGCAT 61.037 50.000 11.71 7.65 41.33 3.96
318 340 0.393132 TAAAATGACCGCCGGATGCA 60.393 50.000 11.71 5.23 41.33 3.96
319 341 0.307760 CTAAAATGACCGCCGGATGC 59.692 55.000 11.71 0.00 0.00 3.91
320 342 1.663695 ACTAAAATGACCGCCGGATG 58.336 50.000 11.71 0.00 0.00 3.51
321 343 2.413310 AACTAAAATGACCGCCGGAT 57.587 45.000 11.71 0.00 0.00 4.18
322 344 2.188062 AAACTAAAATGACCGCCGGA 57.812 45.000 11.71 0.00 0.00 5.14
340 362 5.134725 ACTAGATCGGACCCTAAACCTAA 57.865 43.478 0.00 0.00 0.00 2.69
350 372 5.875359 AGACATTTTTCAACTAGATCGGACC 59.125 40.000 0.00 0.00 0.00 4.46
436 478 5.975693 TTCAAACTCAAACAAACCAGACT 57.024 34.783 0.00 0.00 0.00 3.24
489 542 5.296780 AGCATATGTCCGGTTTACATTTCAG 59.703 40.000 12.05 2.92 38.49 3.02
513 567 5.376625 GGACACCATCATCCAAAGCTAATA 58.623 41.667 0.00 0.00 34.87 0.98
515 569 3.620488 GGACACCATCATCCAAAGCTAA 58.380 45.455 0.00 0.00 34.87 3.09
528 582 1.995066 TCCTGCATCGGGACACCAT 60.995 57.895 0.00 0.00 33.41 3.55
535 589 1.402968 CAAATTCAGTCCTGCATCGGG 59.597 52.381 0.00 0.00 0.00 5.14
536 590 1.202222 GCAAATTCAGTCCTGCATCGG 60.202 52.381 0.00 0.00 34.87 4.18
537 591 1.469703 TGCAAATTCAGTCCTGCATCG 59.530 47.619 0.00 0.00 39.77 3.84
538 592 3.057033 ACTTGCAAATTCAGTCCTGCATC 60.057 43.478 0.00 0.00 43.83 3.91
541 595 2.294233 TCACTTGCAAATTCAGTCCTGC 59.706 45.455 0.00 0.00 35.32 4.85
542 596 4.276678 TCTTCACTTGCAAATTCAGTCCTG 59.723 41.667 0.00 0.00 0.00 3.86
543 597 4.464008 TCTTCACTTGCAAATTCAGTCCT 58.536 39.130 0.00 0.00 0.00 3.85
547 601 3.924686 GCCATCTTCACTTGCAAATTCAG 59.075 43.478 0.00 0.00 0.00 3.02
549 603 3.256558 GGCCATCTTCACTTGCAAATTC 58.743 45.455 0.00 0.00 0.00 2.17
561 615 3.567797 GACAGCGCGGCCATCTTC 61.568 66.667 8.83 0.00 0.00 2.87
596 651 3.802685 GCGTTTGCTAATACTACCTCCTG 59.197 47.826 0.00 0.00 38.39 3.86
604 659 1.657094 CGTTCCGCGTTTGCTAATACT 59.343 47.619 4.92 0.00 39.65 2.12
605 660 1.655099 TCGTTCCGCGTTTGCTAATAC 59.345 47.619 4.92 0.00 42.13 1.89
642 959 3.031457 GCGGTGCAACGACACGTA 61.031 61.111 31.65 0.00 39.99 3.57
655 972 1.550524 AGTGTACATGATGTCTGCGGT 59.449 47.619 0.00 0.00 0.00 5.68
667 984 4.910195 TCTTCTGGATGCAAAGTGTACAT 58.090 39.130 0.00 0.00 0.00 2.29
684 1001 3.935828 GCTAGTTTCGGCTGAAATCTTCT 59.064 43.478 23.02 16.86 45.31 2.85
688 1005 1.327764 CGGCTAGTTTCGGCTGAAATC 59.672 52.381 23.02 15.97 45.31 2.17
689 1006 1.338769 ACGGCTAGTTTCGGCTGAAAT 60.339 47.619 23.02 14.21 45.31 2.17
690 1007 0.034337 ACGGCTAGTTTCGGCTGAAA 59.966 50.000 16.83 16.83 41.69 2.69
691 1008 0.034337 AACGGCTAGTTTCGGCTGAA 59.966 50.000 3.13 3.13 40.88 3.02
693 1010 1.635663 CCAACGGCTAGTTTCGGCTG 61.636 60.000 0.00 0.00 42.02 4.85
695 1012 2.396157 CCCAACGGCTAGTTTCGGC 61.396 63.158 0.00 0.00 42.02 5.54
724 1136 0.106708 GGCACGAGCTAATGGATGGA 59.893 55.000 4.48 0.00 41.70 3.41
743 1155 3.375443 TAGTCGAGGCAGGAGGGGG 62.375 68.421 0.00 0.00 0.00 5.40
1512 1934 2.307768 CCGGTGAGGAGATTACTGCTA 58.692 52.381 0.00 0.00 44.53 3.49
1575 1997 1.301716 GTTGCGGCTGAGGTTGAGA 60.302 57.895 0.00 0.00 0.00 3.27
1962 2693 2.665185 AGCGTTGCGGTGAGGTTC 60.665 61.111 0.00 0.00 35.85 3.62
1985 2716 4.365723 GTTGTTGTAGGAGACGTTGAAGA 58.634 43.478 0.00 0.00 0.00 2.87
2196 2927 2.620112 CCCGGCGATGATCAATGCC 61.620 63.158 24.49 24.49 44.09 4.40
2749 3622 6.646653 GGATGAACAATTTTGAAGGAAGGAAC 59.353 38.462 0.00 0.00 0.00 3.62
3426 4385 1.078143 AACATGGCCTTCCTCGCTC 60.078 57.895 3.32 0.00 0.00 5.03
3446 4405 2.404215 TCTACTCGTTGCTTGCAGAAC 58.596 47.619 0.00 0.00 0.00 3.01
3468 4427 2.669569 CACCCAAGTCGGCCACTG 60.670 66.667 2.24 1.35 34.56 3.66
3469 4428 1.779061 ATTCACCCAAGTCGGCCACT 61.779 55.000 2.24 2.32 36.64 4.00
3470 4429 0.893727 AATTCACCCAAGTCGGCCAC 60.894 55.000 2.24 0.00 0.00 5.01
3471 4430 0.693622 TAATTCACCCAAGTCGGCCA 59.306 50.000 2.24 0.00 0.00 5.36
3472 4431 1.065709 TCTAATTCACCCAAGTCGGCC 60.066 52.381 0.00 0.00 0.00 6.13
3473 4432 2.093658 TCTCTAATTCACCCAAGTCGGC 60.094 50.000 0.00 0.00 0.00 5.54
3474 4433 3.430929 CCTCTCTAATTCACCCAAGTCGG 60.431 52.174 0.00 0.00 0.00 4.79
3475 4434 3.447586 TCCTCTCTAATTCACCCAAGTCG 59.552 47.826 0.00 0.00 0.00 4.18
3476 4435 5.422214 TTCCTCTCTAATTCACCCAAGTC 57.578 43.478 0.00 0.00 0.00 3.01
3477 4436 5.548056 TCTTTCCTCTCTAATTCACCCAAGT 59.452 40.000 0.00 0.00 0.00 3.16
3478 4437 6.054860 TCTTTCCTCTCTAATTCACCCAAG 57.945 41.667 0.00 0.00 0.00 3.61
3479 4438 6.215431 TCATCTTTCCTCTCTAATTCACCCAA 59.785 38.462 0.00 0.00 0.00 4.12
3480 4439 5.726308 TCATCTTTCCTCTCTAATTCACCCA 59.274 40.000 0.00 0.00 0.00 4.51
3481 4440 6.240549 TCATCTTTCCTCTCTAATTCACCC 57.759 41.667 0.00 0.00 0.00 4.61
3482 4441 7.772757 ACAATCATCTTTCCTCTCTAATTCACC 59.227 37.037 0.00 0.00 0.00 4.02
3502 4461 9.787435 AACTACTAAACCTCAATGTAACAATCA 57.213 29.630 0.00 0.00 0.00 2.57
3530 4495 9.571810 CCAAACGAATCAAAGAATTATCAATCA 57.428 29.630 0.00 0.00 0.00 2.57
3531 4496 9.787532 TCCAAACGAATCAAAGAATTATCAATC 57.212 29.630 0.00 0.00 0.00 2.67
3675 4649 8.767085 CAACAGCTTTGACAAATCAATAATGTT 58.233 29.630 0.05 1.49 44.36 2.71
3689 4663 4.558538 AAGTGTGATCAACAGCTTTGAC 57.441 40.909 11.78 8.07 40.26 3.18
3708 4683 5.776744 AGCAGGCTGTGAGAAATTAAAAAG 58.223 37.500 17.16 0.00 0.00 2.27
3711 4691 4.218417 GGAAGCAGGCTGTGAGAAATTAAA 59.782 41.667 17.16 0.00 0.00 1.52
3713 4693 3.009473 AGGAAGCAGGCTGTGAGAAATTA 59.991 43.478 17.16 0.00 0.00 1.40
3721 4701 1.739562 GACGAGGAAGCAGGCTGTG 60.740 63.158 17.16 0.00 0.00 3.66
3759 4739 9.139174 ACCGCTTTTAAATGTATCAAAATTCAG 57.861 29.630 3.34 0.00 0.00 3.02
3760 4740 9.482627 AACCGCTTTTAAATGTATCAAAATTCA 57.517 25.926 3.34 0.00 0.00 2.57
3761 4741 9.952341 GAACCGCTTTTAAATGTATCAAAATTC 57.048 29.630 3.34 0.00 0.00 2.17
3762 4742 8.931775 GGAACCGCTTTTAAATGTATCAAAATT 58.068 29.630 3.34 0.00 0.00 1.82
3764 4744 7.434492 TGGAACCGCTTTTAAATGTATCAAAA 58.566 30.769 3.34 0.00 0.00 2.44
3765 4745 6.982852 TGGAACCGCTTTTAAATGTATCAAA 58.017 32.000 3.34 0.00 0.00 2.69
3768 4748 6.190954 ACTGGAACCGCTTTTAAATGTATC 57.809 37.500 3.34 0.00 0.00 2.24
3769 4749 7.690952 TTACTGGAACCGCTTTTAAATGTAT 57.309 32.000 3.34 0.00 0.00 2.29
3770 4750 7.361894 GTTTACTGGAACCGCTTTTAAATGTA 58.638 34.615 3.34 0.00 0.00 2.29
3772 4752 5.631929 GGTTTACTGGAACCGCTTTTAAATG 59.368 40.000 0.00 0.00 39.68 2.32
3810 4794 5.903010 TGGACATAATTAGGCTACCTTCAGA 59.097 40.000 0.00 0.00 34.61 3.27
3811 4795 6.174720 TGGACATAATTAGGCTACCTTCAG 57.825 41.667 0.00 0.00 34.61 3.02
3812 4796 5.665812 ACTGGACATAATTAGGCTACCTTCA 59.334 40.000 0.00 0.00 34.61 3.02
3813 4797 6.176014 ACTGGACATAATTAGGCTACCTTC 57.824 41.667 0.00 0.00 34.61 3.46
3814 4798 7.685849 TTACTGGACATAATTAGGCTACCTT 57.314 36.000 0.00 0.00 34.61 3.50
3815 4799 7.685849 TTTACTGGACATAATTAGGCTACCT 57.314 36.000 0.00 0.00 37.71 3.08
3816 4800 9.654663 CTATTTACTGGACATAATTAGGCTACC 57.345 37.037 0.00 0.00 0.00 3.18
3828 4812 9.435570 ACTGGAGTATTACTATTTACTGGACAT 57.564 33.333 0.00 0.00 0.00 3.06
3829 4813 8.834004 ACTGGAGTATTACTATTTACTGGACA 57.166 34.615 0.00 0.00 0.00 4.02
3867 4851 9.499479 GATTATCCATACCTGCATATATCTTGG 57.501 37.037 0.00 0.00 0.00 3.61
3878 4869 4.872691 CGGAGATTGATTATCCATACCTGC 59.127 45.833 0.00 0.00 33.45 4.85
3901 4892 6.742559 TCTTCCTTGTAGGTTGGTATATCC 57.257 41.667 0.00 0.00 36.53 2.59
3914 4905 3.368427 CGTCCTGAGCATTCTTCCTTGTA 60.368 47.826 0.00 0.00 0.00 2.41
3915 4906 2.613977 CGTCCTGAGCATTCTTCCTTGT 60.614 50.000 0.00 0.00 0.00 3.16
3932 4923 7.656137 TCTTACTGCAAATAGGATTATTCGTCC 59.344 37.037 0.00 0.00 35.94 4.79
3936 4927 8.293157 GGCTTCTTACTGCAAATAGGATTATTC 58.707 37.037 0.00 0.00 0.00 1.75
3945 4936 4.844349 AGGAGGCTTCTTACTGCAAATA 57.156 40.909 0.00 0.00 0.00 1.40
3946 4937 3.728385 AGGAGGCTTCTTACTGCAAAT 57.272 42.857 0.00 0.00 0.00 2.32
3960 4951 1.406903 ATTTTGGCATGCTAGGAGGC 58.593 50.000 18.92 12.89 0.00 4.70
3961 4952 3.294214 AGAATTTTGGCATGCTAGGAGG 58.706 45.455 18.92 0.00 0.00 4.30
3962 4953 4.643784 AGAAGAATTTTGGCATGCTAGGAG 59.356 41.667 18.92 0.00 0.00 3.69
3963 4954 4.603131 AGAAGAATTTTGGCATGCTAGGA 58.397 39.130 18.92 4.19 0.00 2.94
3964 4955 4.202090 GGAGAAGAATTTTGGCATGCTAGG 60.202 45.833 18.92 0.00 0.00 3.02
3983 4975 2.507058 CAGATTGGATTGGTCTGGGAGA 59.493 50.000 0.00 0.00 36.57 3.71
3984 4976 2.240667 ACAGATTGGATTGGTCTGGGAG 59.759 50.000 6.56 0.00 42.75 4.30
3985 4977 2.025981 CACAGATTGGATTGGTCTGGGA 60.026 50.000 6.56 0.00 44.25 4.37
3988 4980 4.330250 AGTTCACAGATTGGATTGGTCTG 58.670 43.478 0.00 0.00 43.76 3.51
3989 4981 4.647564 AGTTCACAGATTGGATTGGTCT 57.352 40.909 0.00 0.00 0.00 3.85
3990 4982 4.156739 GGAAGTTCACAGATTGGATTGGTC 59.843 45.833 5.01 0.00 0.00 4.02
4004 5002 8.910351 ATTGCTTATATAAGAGGGAAGTTCAC 57.090 34.615 23.84 0.00 35.33 3.18
4033 5031 6.095021 GCTTCTTTGACGGTTAATATCCCTTT 59.905 38.462 0.00 0.00 0.00 3.11
4034 5032 5.589050 GCTTCTTTGACGGTTAATATCCCTT 59.411 40.000 0.00 0.00 0.00 3.95
4035 5033 5.123936 GCTTCTTTGACGGTTAATATCCCT 58.876 41.667 0.00 0.00 0.00 4.20
4036 5034 4.879545 TGCTTCTTTGACGGTTAATATCCC 59.120 41.667 0.00 0.00 0.00 3.85
4037 5035 6.619801 ATGCTTCTTTGACGGTTAATATCC 57.380 37.500 0.00 0.00 0.00 2.59
4041 5039 8.958119 TCTAATATGCTTCTTTGACGGTTAAT 57.042 30.769 0.00 0.00 0.00 1.40
4042 5040 8.255206 TCTCTAATATGCTTCTTTGACGGTTAA 58.745 33.333 0.00 0.00 0.00 2.01
4043 5041 7.778083 TCTCTAATATGCTTCTTTGACGGTTA 58.222 34.615 0.00 0.00 0.00 2.85
4044 5042 6.640518 TCTCTAATATGCTTCTTTGACGGTT 58.359 36.000 0.00 0.00 0.00 4.44
4045 5043 6.222038 TCTCTAATATGCTTCTTTGACGGT 57.778 37.500 0.00 0.00 0.00 4.83
4046 5044 7.225538 ACAATCTCTAATATGCTTCTTTGACGG 59.774 37.037 0.00 0.00 0.00 4.79
4047 5045 8.136057 ACAATCTCTAATATGCTTCTTTGACG 57.864 34.615 0.00 0.00 0.00 4.35
4050 5048 9.727627 GGAAACAATCTCTAATATGCTTCTTTG 57.272 33.333 0.00 0.00 0.00 2.77
4051 5049 8.616076 CGGAAACAATCTCTAATATGCTTCTTT 58.384 33.333 0.00 0.00 0.00 2.52
4056 5054 7.047891 TGAACGGAAACAATCTCTAATATGCT 58.952 34.615 0.00 0.00 0.00 3.79
4070 5068 6.825944 TGGATGATATTTTGAACGGAAACA 57.174 33.333 0.00 0.00 0.00 2.83
4071 5069 8.702163 AAATGGATGATATTTTGAACGGAAAC 57.298 30.769 0.00 0.00 0.00 2.78
4072 5070 9.796120 GTAAATGGATGATATTTTGAACGGAAA 57.204 29.630 0.00 0.00 0.00 3.13
4073 5071 8.961634 TGTAAATGGATGATATTTTGAACGGAA 58.038 29.630 0.00 0.00 0.00 4.30
4074 5072 8.512966 TGTAAATGGATGATATTTTGAACGGA 57.487 30.769 0.00 0.00 0.00 4.69
4075 5073 9.579768 TTTGTAAATGGATGATATTTTGAACGG 57.420 29.630 0.00 0.00 0.00 4.44
4083 5081 8.906867 CCACTCTGTTTGTAAATGGATGATATT 58.093 33.333 0.00 0.00 0.00 1.28
4084 5082 8.055181 ACCACTCTGTTTGTAAATGGATGATAT 58.945 33.333 0.00 0.00 0.00 1.63
4085 5083 7.402054 ACCACTCTGTTTGTAAATGGATGATA 58.598 34.615 0.00 0.00 0.00 2.15
4086 5084 6.248433 ACCACTCTGTTTGTAAATGGATGAT 58.752 36.000 0.00 0.00 0.00 2.45
4087 5085 5.630121 ACCACTCTGTTTGTAAATGGATGA 58.370 37.500 0.00 0.00 0.00 2.92
4088 5086 5.964958 ACCACTCTGTTTGTAAATGGATG 57.035 39.130 0.00 0.00 0.00 3.51
4089 5087 9.920946 ATATAACCACTCTGTTTGTAAATGGAT 57.079 29.630 0.00 0.00 0.00 3.41
4133 5131 5.447818 GGCAAACTAGTATGACAACATCAGC 60.448 44.000 0.00 0.00 41.91 4.26
4164 5264 4.037446 GTGGGCATGTTAGTGTTTTTCTGA 59.963 41.667 0.00 0.00 0.00 3.27
4180 5280 1.152610 GGCATCTCCATGTGGGCAT 60.153 57.895 0.00 0.00 36.21 4.40
4181 5281 2.276409 GGCATCTCCATGTGGGCA 59.724 61.111 0.00 0.00 36.21 5.36
4182 5282 2.903855 CGGCATCTCCATGTGGGC 60.904 66.667 0.00 0.00 36.21 5.36
4183 5283 2.903855 GCGGCATCTCCATGTGGG 60.904 66.667 0.00 0.00 35.41 4.61
4249 5349 4.559862 AGCACAATACTGAAGCTAAGGT 57.440 40.909 0.00 0.00 36.29 3.50
4254 5354 3.257393 CGAGAAGCACAATACTGAAGCT 58.743 45.455 0.00 0.00 38.48 3.74
4255 5355 2.996621 ACGAGAAGCACAATACTGAAGC 59.003 45.455 0.00 0.00 0.00 3.86
4256 5356 6.269315 AGATACGAGAAGCACAATACTGAAG 58.731 40.000 0.00 0.00 0.00 3.02
4258 5358 5.836821 AGATACGAGAAGCACAATACTGA 57.163 39.130 0.00 0.00 0.00 3.41
4259 5359 6.978024 GTAGATACGAGAAGCACAATACTG 57.022 41.667 0.00 0.00 0.00 2.74
4283 5383 1.264288 CCAACTTTTGAGACGACTGGC 59.736 52.381 0.00 0.00 0.00 4.85
4284 5384 1.264288 GCCAACTTTTGAGACGACTGG 59.736 52.381 0.00 0.00 0.00 4.00
4285 5385 2.213499 AGCCAACTTTTGAGACGACTG 58.787 47.619 0.00 0.00 0.00 3.51
4286 5386 2.622064 AGCCAACTTTTGAGACGACT 57.378 45.000 0.00 0.00 0.00 4.18
4287 5387 2.612212 TGAAGCCAACTTTTGAGACGAC 59.388 45.455 0.00 0.00 35.82 4.34
4288 5388 2.872245 CTGAAGCCAACTTTTGAGACGA 59.128 45.455 0.00 0.00 35.82 4.20
4290 5390 2.952310 ACCTGAAGCCAACTTTTGAGAC 59.048 45.455 0.00 0.00 35.82 3.36
4291 5391 3.297134 ACCTGAAGCCAACTTTTGAGA 57.703 42.857 0.00 0.00 35.82 3.27
4292 5392 3.709987 CAACCTGAAGCCAACTTTTGAG 58.290 45.455 0.00 0.00 35.82 3.02
4293 5393 2.159114 GCAACCTGAAGCCAACTTTTGA 60.159 45.455 0.00 0.00 35.82 2.69
4294 5394 2.159057 AGCAACCTGAAGCCAACTTTTG 60.159 45.455 0.00 0.00 35.82 2.44
4295 5395 2.110578 AGCAACCTGAAGCCAACTTTT 58.889 42.857 0.00 0.00 35.82 2.27
4296 5396 1.780503 AGCAACCTGAAGCCAACTTT 58.219 45.000 0.00 0.00 35.82 2.66
4297 5397 2.656947 TAGCAACCTGAAGCCAACTT 57.343 45.000 0.00 0.00 39.43 2.66
4299 5399 4.675408 GCTTAATAGCAACCTGAAGCCAAC 60.675 45.833 0.00 0.00 46.95 3.77
4301 5401 3.016736 GCTTAATAGCAACCTGAAGCCA 58.983 45.455 0.00 0.00 46.95 4.75
4302 5402 3.699779 GCTTAATAGCAACCTGAAGCC 57.300 47.619 0.00 0.00 46.95 4.35
4313 5413 4.403453 CACAACCTTTGACGCTTAATAGC 58.597 43.478 0.00 0.00 44.21 2.97
4314 5414 4.154195 AGCACAACCTTTGACGCTTAATAG 59.846 41.667 0.00 0.00 38.92 1.73
4315 5415 4.069304 AGCACAACCTTTGACGCTTAATA 58.931 39.130 0.00 0.00 38.92 0.98
4316 5416 2.884639 AGCACAACCTTTGACGCTTAAT 59.115 40.909 0.00 0.00 38.92 1.40
4345 5485 2.086610 AGTTTCCACACAGGGCAAAT 57.913 45.000 0.00 0.00 38.24 2.32
4350 5490 2.374184 TGTGAAAGTTTCCACACAGGG 58.626 47.619 13.01 0.00 38.26 4.45
4352 5492 4.997565 ACAATGTGAAAGTTTCCACACAG 58.002 39.130 17.44 15.34 44.79 3.66
4359 5499 7.269297 GCGAATTAGAGACAATGTGAAAGTTTC 59.731 37.037 8.75 8.75 0.00 2.78
4368 5508 5.112686 GGAAGAGCGAATTAGAGACAATGT 58.887 41.667 0.00 0.00 0.00 2.71
4369 5509 5.111989 TGGAAGAGCGAATTAGAGACAATG 58.888 41.667 0.00 0.00 0.00 2.82
4414 5554 2.159085 GGTAGTCTAGCTGCGAATGGTT 60.159 50.000 0.00 0.00 0.00 3.67
4421 5561 1.676746 TAGTGGGTAGTCTAGCTGCG 58.323 55.000 8.89 0.00 0.00 5.18
4422 5562 2.559231 GGATAGTGGGTAGTCTAGCTGC 59.441 54.545 8.89 0.00 0.00 5.25
4423 5563 3.823873 CTGGATAGTGGGTAGTCTAGCTG 59.176 52.174 8.89 0.00 0.00 4.24
4430 5570 0.642710 AGGGCTGGATAGTGGGTAGT 59.357 55.000 0.00 0.00 0.00 2.73
4431 5571 1.133009 AGAGGGCTGGATAGTGGGTAG 60.133 57.143 0.00 0.00 0.00 3.18
4432 5572 0.941963 AGAGGGCTGGATAGTGGGTA 59.058 55.000 0.00 0.00 0.00 3.69
4433 5573 0.399233 GAGAGGGCTGGATAGTGGGT 60.399 60.000 0.00 0.00 0.00 4.51
4434 5574 0.105246 AGAGAGGGCTGGATAGTGGG 60.105 60.000 0.00 0.00 0.00 4.61
4435 5575 1.337118 GAGAGAGGGCTGGATAGTGG 58.663 60.000 0.00 0.00 0.00 4.00
4436 5576 2.079170 TGAGAGAGGGCTGGATAGTG 57.921 55.000 0.00 0.00 0.00 2.74
4441 5581 0.633378 TGAGATGAGAGAGGGCTGGA 59.367 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.