Multiple sequence alignment - TraesCS3B01G039800

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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 TraesCS3B01G039800 chr3B 100.000 3232 0 0 1 3232 19263814 19260583 0.000000e+00 5969.0
1 TraesCS3B01G039800 chr3B 82.997 347 46 9 2620 2959 19251089 19250749 5.240000e-78 302.0
2 TraesCS3B01G039800 chr3B 88.235 102 9 3 779 878 385854115 385854215 5.660000e-23 119.0
3 TraesCS3B01G039800 chr3D 83.398 2325 196 106 991 3229 13307510 13305290 0.000000e+00 1980.0
4 TraesCS3B01G039800 chr3D 79.376 994 142 35 2267 3232 13296146 13295188 2.720000e-180 641.0
5 TraesCS3B01G039800 chr3D 89.901 406 13 9 1 397 13308428 13308042 6.230000e-137 497.0
6 TraesCS3B01G039800 chr3D 87.189 281 17 6 656 919 13307870 13307592 5.240000e-78 302.0
7 TraesCS3B01G039800 chr3A 84.820 863 75 26 1637 2492 23830792 23831605 0.000000e+00 817.0
8 TraesCS3B01G039800 chr3A 81.366 966 120 44 2295 3228 23839101 23840038 0.000000e+00 732.0
9 TraesCS3B01G039800 chr3A 84.187 683 72 24 2565 3232 23831648 23832309 5.880000e-177 630.0
10 TraesCS3B01G039800 chr3A 84.906 583 37 26 985 1546 23830163 23830715 2.840000e-150 542.0
11 TraesCS3B01G039800 chr3A 92.364 275 11 8 1 275 23828972 23829236 1.820000e-102 383.0
12 TraesCS3B01G039800 chr3A 77.172 587 75 31 746 1318 118413214 118413755 1.470000e-73 287.0
13 TraesCS3B01G039800 chr3A 83.333 240 10 12 671 890 23829543 23829772 9.150000e-46 195.0
14 TraesCS3B01G039800 chr3A 82.192 219 19 7 298 515 23829229 23829428 1.540000e-38 171.0
15 TraesCS3B01G039800 chr6D 78.365 587 58 32 779 1318 201578620 201578056 1.870000e-82 316.0
16 TraesCS3B01G039800 chr6D 84.862 218 14 14 1110 1318 10408054 10408261 5.470000e-48 202.0
17 TraesCS3B01G039800 chr6A 76.792 586 76 32 746 1317 341650227 341650766 1.140000e-69 274.0
18 TraesCS3B01G039800 chr6A 84.343 198 15 13 1126 1318 11906024 11906210 2.560000e-41 180.0
19 TraesCS3B01G039800 chr2A 76.661 587 78 31 746 1318 157140705 157141246 1.480000e-68 270.0
20 TraesCS3B01G039800 chr2A 76.950 577 70 35 756 1318 283479172 283478645 1.480000e-68 270.0
21 TraesCS3B01G039800 chr2A 76.909 563 74 35 779 1318 377020456 377019927 5.310000e-68 268.0
22 TraesCS3B01G039800 chr2A 94.340 53 3 0 672 724 283479234 283479182 7.430000e-12 82.4
23 TraesCS3B01G039800 chr2B 85.787 197 22 6 1126 1318 529045983 529045789 1.520000e-48 204.0
24 TraesCS3B01G039800 chr6B 82.128 235 32 7 1092 1318 233934369 233934601 3.290000e-45 193.0
25 TraesCS3B01G039800 chr2D 83.974 156 11 10 779 932 220707428 220707285 1.560000e-28 137.0
26 TraesCS3B01G039800 chr2D 97.674 43 1 0 682 724 220707872 220707830 1.240000e-09 75.0
27 TraesCS3B01G039800 chr1B 88.235 102 9 2 779 878 303874434 303874334 5.660000e-23 119.0
28 TraesCS3B01G039800 chr1B 94.643 56 3 0 667 722 80098539 80098484 1.600000e-13 87.9
29 TraesCS3B01G039800 chr7B 87.629 97 10 2 784 878 576358555 576358651 9.480000e-21 111.0
30 TraesCS3B01G039800 chr4B 87.838 74 7 2 785 856 230638780 230638707 5.750000e-13 86.1
31 TraesCS3B01G039800 chr5A 94.340 53 3 0 672 724 202427517 202427569 7.430000e-12 82.4


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 TraesCS3B01G039800 chr3B 19260583 19263814 3231 True 5969.000000 5969 100.000000 1 3232 1 chr3B.!!$R2 3231
1 TraesCS3B01G039800 chr3D 13305290 13308428 3138 True 926.333333 1980 86.829333 1 3229 3 chr3D.!!$R2 3228
2 TraesCS3B01G039800 chr3D 13295188 13296146 958 True 641.000000 641 79.376000 2267 3232 1 chr3D.!!$R1 965
3 TraesCS3B01G039800 chr3A 23839101 23840038 937 False 732.000000 732 81.366000 2295 3228 1 chr3A.!!$F1 933
4 TraesCS3B01G039800 chr3A 23828972 23832309 3337 False 456.333333 817 85.300333 1 3232 6 chr3A.!!$F3 3231
5 TraesCS3B01G039800 chr3A 118413214 118413755 541 False 287.000000 287 77.172000 746 1318 1 chr3A.!!$F2 572
6 TraesCS3B01G039800 chr6D 201578056 201578620 564 True 316.000000 316 78.365000 779 1318 1 chr6D.!!$R1 539
7 TraesCS3B01G039800 chr6A 341650227 341650766 539 False 274.000000 274 76.792000 746 1317 1 chr6A.!!$F2 571
8 TraesCS3B01G039800 chr2A 157140705 157141246 541 False 270.000000 270 76.661000 746 1318 1 chr2A.!!$F1 572
9 TraesCS3B01G039800 chr2A 377019927 377020456 529 True 268.000000 268 76.909000 779 1318 1 chr2A.!!$R1 539

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
630 658 0.108615 CCGCCTGAGGTGAGTACTTG 60.109 60.0 14.8 0.0 34.74 3.16 F
1376 1859 0.164647 CTTGACAGTTACAGCAGCGC 59.835 55.0 0.0 0.0 0.00 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 2081 0.039617 TTTTTCCTGTCAATGGCGCG 60.040 50.0 0.0 0.0 0.00 6.86 R
2232 2764 0.455464 TACACGCAATCGGTCGTCAG 60.455 55.0 0.0 0.0 40.69 3.51 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
41 42 4.096682 GCGTTTATACTGAGAGTGGAGAGT 59.903 45.833 0.00 0.00 0.00 3.24
95 96 5.768164 GGATAGGTCCTAGACAAAGAGAGAG 59.232 48.000 4.57 0.00 41.60 3.20
99 100 7.161715 AGGTCCTAGACAAAGAGAGAGATAT 57.838 40.000 0.00 0.00 33.68 1.63
100 101 8.282801 AGGTCCTAGACAAAGAGAGAGATATA 57.717 38.462 0.00 0.00 33.68 0.86
119 120 8.508883 AGATATACTTAGTTCGTCTGAGTTGT 57.491 34.615 11.24 5.98 41.97 3.32
135 136 5.571277 TGAGTTGTTTACCGTTTTTAGCAC 58.429 37.500 0.00 0.00 0.00 4.40
140 141 6.690194 TGTTTACCGTTTTTAGCACCTTTA 57.310 33.333 0.00 0.00 0.00 1.85
154 155 3.440522 GCACCTTTATCCCAAGACAGTTC 59.559 47.826 0.00 0.00 0.00 3.01
225 226 5.568685 AATCCGTAGACTGATGATATCCG 57.431 43.478 0.00 0.00 0.00 4.18
229 230 4.142795 CCGTAGACTGATGATATCCGTGAG 60.143 50.000 0.00 0.00 0.00 3.51
245 246 2.159170 CGTGAGGAGGATGAGAAGGTTC 60.159 54.545 0.00 0.00 0.00 3.62
286 287 5.587844 CCTTGTGGACTGATTAGAAATCCTG 59.412 44.000 0.00 0.00 34.57 3.86
293 294 3.797039 TGATTAGAAATCCTGCCTGTCG 58.203 45.455 0.00 0.00 0.00 4.35
320 326 4.770010 TGGTCTGAGACAGTTTTGGTTTTT 59.230 37.500 15.33 0.00 33.68 1.94
350 356 8.682710 TCAAAAGTGCTGTTGAAACTTATTACT 58.317 29.630 2.53 0.00 33.09 2.24
387 396 6.695713 GGTTTGTGTTTTATCCACTTTCACTC 59.304 38.462 0.00 0.00 33.92 3.51
397 406 3.324846 TCCACTTTCACTCTGTATGCTGT 59.675 43.478 0.00 0.00 0.00 4.40
398 407 4.067896 CCACTTTCACTCTGTATGCTGTT 58.932 43.478 0.00 0.00 0.00 3.16
399 408 4.083643 CCACTTTCACTCTGTATGCTGTTG 60.084 45.833 0.00 0.00 0.00 3.33
400 409 4.751600 CACTTTCACTCTGTATGCTGTTGA 59.248 41.667 0.00 0.00 0.00 3.18
401 410 5.410746 CACTTTCACTCTGTATGCTGTTGAT 59.589 40.000 0.00 0.00 0.00 2.57
402 411 6.000219 ACTTTCACTCTGTATGCTGTTGATT 59.000 36.000 0.00 0.00 0.00 2.57
403 412 6.488006 ACTTTCACTCTGTATGCTGTTGATTT 59.512 34.615 0.00 0.00 0.00 2.17
404 413 7.661437 ACTTTCACTCTGTATGCTGTTGATTTA 59.339 33.333 0.00 0.00 0.00 1.40
405 414 7.977789 TTCACTCTGTATGCTGTTGATTTAA 57.022 32.000 0.00 0.00 0.00 1.52
406 415 8.565896 TTCACTCTGTATGCTGTTGATTTAAT 57.434 30.769 0.00 0.00 0.00 1.40
407 416 8.201554 TCACTCTGTATGCTGTTGATTTAATC 57.798 34.615 0.00 0.00 0.00 1.75
408 417 7.010460 TCACTCTGTATGCTGTTGATTTAATCG 59.990 37.037 0.23 0.00 0.00 3.34
409 418 6.818644 ACTCTGTATGCTGTTGATTTAATCGT 59.181 34.615 0.23 0.00 0.00 3.73
410 419 7.334421 ACTCTGTATGCTGTTGATTTAATCGTT 59.666 33.333 0.23 0.00 0.00 3.85
426 435 9.751542 ATTTAATCGTTTTGTGTTTTATCCACA 57.248 25.926 0.00 0.00 40.87 4.17
458 468 9.469807 TTTGTATGCTGTTGATTTAATCGTTTT 57.530 25.926 0.23 0.00 0.00 2.43
460 470 9.549509 TGTATGCTGTTGATTTAATCGTTTTAC 57.450 29.630 0.23 0.00 0.00 2.01
488 498 3.964031 ACTCTCTGGTGTTCTTCTCTTGT 59.036 43.478 0.00 0.00 0.00 3.16
524 540 2.592102 TTTTTGCAGGGAGATGAGCT 57.408 45.000 0.00 0.00 0.00 4.09
525 541 2.592102 TTTTGCAGGGAGATGAGCTT 57.408 45.000 0.00 0.00 0.00 3.74
526 542 2.119801 TTTGCAGGGAGATGAGCTTC 57.880 50.000 0.00 0.00 0.00 3.86
527 543 1.283347 TTGCAGGGAGATGAGCTTCT 58.717 50.000 0.00 0.00 0.00 2.85
528 544 0.540454 TGCAGGGAGATGAGCTTCTG 59.460 55.000 0.00 0.00 33.85 3.02
529 545 0.540923 GCAGGGAGATGAGCTTCTGT 59.459 55.000 0.00 0.00 33.50 3.41
530 546 1.065564 GCAGGGAGATGAGCTTCTGTT 60.066 52.381 0.00 0.00 33.50 3.16
531 547 2.630158 CAGGGAGATGAGCTTCTGTTG 58.370 52.381 0.00 0.00 0.00 3.33
532 548 2.235650 CAGGGAGATGAGCTTCTGTTGA 59.764 50.000 0.00 0.00 0.00 3.18
533 549 3.113824 AGGGAGATGAGCTTCTGTTGAT 58.886 45.455 0.00 0.00 0.00 2.57
536 552 5.190528 AGGGAGATGAGCTTCTGTTGATTTA 59.809 40.000 0.00 0.00 0.00 1.40
541 557 8.571461 AGATGAGCTTCTGTTGATTTATTTGA 57.429 30.769 0.00 0.00 0.00 2.69
542 558 8.457261 AGATGAGCTTCTGTTGATTTATTTGAC 58.543 33.333 0.00 0.00 0.00 3.18
546 562 4.335082 TCTGTTGATTTATTTGACGGCG 57.665 40.909 4.80 4.80 0.00 6.46
559 575 3.345808 CGGCGGTGTGTTGGTCTG 61.346 66.667 0.00 0.00 0.00 3.51
564 592 1.095228 CGGTGTGTTGGTCTGTTGCT 61.095 55.000 0.00 0.00 0.00 3.91
592 620 4.796110 ACTAACCATGGGATTGCATAGT 57.204 40.909 18.09 9.32 0.00 2.12
593 621 4.718961 ACTAACCATGGGATTGCATAGTC 58.281 43.478 18.09 0.00 0.00 2.59
594 622 2.664402 ACCATGGGATTGCATAGTCC 57.336 50.000 18.09 5.06 0.00 3.85
595 623 2.138542 ACCATGGGATTGCATAGTCCT 58.861 47.619 18.09 0.00 34.84 3.85
596 624 2.107204 ACCATGGGATTGCATAGTCCTC 59.893 50.000 18.09 4.80 34.84 3.71
600 628 1.419387 GGGATTGCATAGTCCTCTGCT 59.581 52.381 11.63 0.00 39.16 4.24
601 629 2.158696 GGGATTGCATAGTCCTCTGCTT 60.159 50.000 11.63 0.00 39.16 3.91
602 630 3.137533 GGATTGCATAGTCCTCTGCTTC 58.862 50.000 6.28 3.90 39.16 3.86
603 631 2.698855 TTGCATAGTCCTCTGCTTCC 57.301 50.000 6.28 0.00 39.16 3.46
604 632 1.871418 TGCATAGTCCTCTGCTTCCT 58.129 50.000 6.28 0.00 39.16 3.36
605 633 1.759445 TGCATAGTCCTCTGCTTCCTC 59.241 52.381 6.28 0.00 39.16 3.71
607 635 2.392662 CATAGTCCTCTGCTTCCTCCA 58.607 52.381 0.00 0.00 0.00 3.86
609 637 0.411452 AGTCCTCTGCTTCCTCCAGA 59.589 55.000 0.00 0.00 37.71 3.86
613 641 2.186384 CTGCTTCCTCCAGAGCCG 59.814 66.667 0.00 0.00 32.03 5.52
614 642 4.087892 TGCTTCCTCCAGAGCCGC 62.088 66.667 0.00 0.00 0.00 6.53
615 643 4.847444 GCTTCCTCCAGAGCCGCC 62.847 72.222 0.00 0.00 0.00 6.13
619 647 3.847602 CCTCCAGAGCCGCCTGAG 61.848 72.222 9.65 6.12 36.29 3.35
621 649 4.704103 TCCAGAGCCGCCTGAGGT 62.704 66.667 0.00 0.00 36.29 3.85
622 650 4.463879 CCAGAGCCGCCTGAGGTG 62.464 72.222 4.74 4.74 36.29 4.00
623 651 3.385384 CAGAGCCGCCTGAGGTGA 61.385 66.667 14.80 0.00 36.29 4.02
624 652 3.073735 AGAGCCGCCTGAGGTGAG 61.074 66.667 14.80 4.87 34.74 3.51
625 653 3.386237 GAGCCGCCTGAGGTGAGT 61.386 66.667 14.80 0.00 34.74 3.41
626 654 2.037367 AGCCGCCTGAGGTGAGTA 59.963 61.111 14.80 0.00 34.74 2.59
628 656 2.352032 GCCGCCTGAGGTGAGTACT 61.352 63.158 14.80 0.00 34.74 2.73
629 657 1.889530 GCCGCCTGAGGTGAGTACTT 61.890 60.000 14.80 0.00 34.74 2.24
630 658 0.108615 CCGCCTGAGGTGAGTACTTG 60.109 60.000 14.80 0.00 34.74 3.16
632 660 0.977395 GCCTGAGGTGAGTACTTGGT 59.023 55.000 0.00 0.00 0.00 3.67
634 662 2.565834 GCCTGAGGTGAGTACTTGGTAA 59.434 50.000 0.00 0.00 0.00 2.85
635 663 3.197983 GCCTGAGGTGAGTACTTGGTAAT 59.802 47.826 0.00 0.00 0.00 1.89
636 664 4.759782 CCTGAGGTGAGTACTTGGTAATG 58.240 47.826 0.00 0.00 0.00 1.90
637 665 4.383118 CCTGAGGTGAGTACTTGGTAATGG 60.383 50.000 0.00 0.00 0.00 3.16
639 667 2.093658 AGGTGAGTACTTGGTAATGGCG 60.094 50.000 0.00 0.00 0.00 5.69
641 669 1.296727 GAGTACTTGGTAATGGCGGC 58.703 55.000 0.00 0.00 0.00 6.53
727 779 1.153939 CGGCGACTGAGGTGAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
761 827 1.448497 GTGGTGAACCTGGACGGAA 59.552 57.895 0.00 0.00 36.82 4.30
890 982 4.656112 ACTCAATCCTTCCTACCATACCAG 59.344 45.833 0.00 0.00 0.00 4.00
891 983 4.890988 TCAATCCTTCCTACCATACCAGA 58.109 43.478 0.00 0.00 0.00 3.86
892 984 5.476983 TCAATCCTTCCTACCATACCAGAT 58.523 41.667 0.00 0.00 0.00 2.90
906 1288 1.210478 ACCAGATACCACATCACAGCC 59.790 52.381 0.00 0.00 0.00 4.85
983 1416 3.936203 GCGACTCCACCACCACCA 61.936 66.667 0.00 0.00 0.00 4.17
988 1421 2.445085 TCCACCACCACCACGACT 60.445 61.111 0.00 0.00 0.00 4.18
989 1422 1.152504 TCCACCACCACCACGACTA 60.153 57.895 0.00 0.00 0.00 2.59
1076 1540 0.461548 CAGCTTCGCTACCATCCTCA 59.538 55.000 0.00 0.00 36.40 3.86
1122 1587 1.968703 CTTCTCGCTTGCTGCTGCTC 61.969 60.000 17.00 5.24 40.48 4.26
1333 1813 3.071206 ACTCGCCACTCTCGCCAT 61.071 61.111 0.00 0.00 0.00 4.40
1336 1816 1.729470 CTCGCCACTCTCGCCATACT 61.729 60.000 0.00 0.00 0.00 2.12
1357 1840 6.685527 ACTCTCTTTTCTTTTCACCAAGAC 57.314 37.500 0.00 0.00 32.28 3.01
1361 1844 6.884295 TCTCTTTTCTTTTCACCAAGACTTGA 59.116 34.615 16.99 0.00 32.28 3.02
1367 1850 6.411376 TCTTTTCACCAAGACTTGACAGTTA 58.589 36.000 16.99 0.00 31.22 2.24
1370 1853 4.693283 TCACCAAGACTTGACAGTTACAG 58.307 43.478 16.99 0.00 31.22 2.74
1371 1854 3.248602 CACCAAGACTTGACAGTTACAGC 59.751 47.826 16.99 0.00 31.22 4.40
1372 1855 3.118408 ACCAAGACTTGACAGTTACAGCA 60.118 43.478 16.99 0.00 31.22 4.41
1373 1856 3.496130 CCAAGACTTGACAGTTACAGCAG 59.504 47.826 16.99 0.00 31.22 4.24
1374 1857 2.760374 AGACTTGACAGTTACAGCAGC 58.240 47.619 0.00 0.00 31.22 5.25
1376 1859 0.164647 CTTGACAGTTACAGCAGCGC 59.835 55.000 0.00 0.00 0.00 5.92
1404 1889 3.204827 GCCTCGCAACGCCATGAT 61.205 61.111 0.00 0.00 0.00 2.45
1413 1898 2.351641 GCAACGCCATGATTTGACTGAA 60.352 45.455 0.00 0.00 0.00 3.02
1415 1900 4.487948 CAACGCCATGATTTGACTGAATT 58.512 39.130 0.00 0.00 0.00 2.17
1417 1902 6.267817 CAACGCCATGATTTGACTGAATTAT 58.732 36.000 0.00 0.00 0.00 1.28
1420 1905 5.174398 CGCCATGATTTGACTGAATTATTGC 59.826 40.000 0.00 0.00 0.00 3.56
1421 1906 6.278363 GCCATGATTTGACTGAATTATTGCT 58.722 36.000 0.00 0.00 0.00 3.91
1423 1908 7.042925 GCCATGATTTGACTGAATTATTGCTTC 60.043 37.037 0.00 0.00 0.00 3.86
1546 2043 1.366111 CCAACATCGTAAGCCCACCG 61.366 60.000 0.00 0.00 37.18 4.94
1547 2044 1.743995 AACATCGTAAGCCCACCGC 60.744 57.895 0.00 0.00 37.98 5.68
1548 2045 2.895372 CATCGTAAGCCCACCGCC 60.895 66.667 0.00 0.00 38.78 6.13
1549 2046 4.171103 ATCGTAAGCCCACCGCCC 62.171 66.667 0.00 0.00 38.78 6.13
1572 2069 3.779738 CCCCTCATTCCTCTTTCTCTTCT 59.220 47.826 0.00 0.00 0.00 2.85
1575 2072 4.716287 CCTCATTCCTCTTTCTCTTCTCCT 59.284 45.833 0.00 0.00 0.00 3.69
1576 2073 5.163416 CCTCATTCCTCTTTCTCTTCTCCTC 60.163 48.000 0.00 0.00 0.00 3.71
1577 2074 4.714308 TCATTCCTCTTTCTCTTCTCCTCC 59.286 45.833 0.00 0.00 0.00 4.30
1578 2075 2.729194 TCCTCTTTCTCTTCTCCTCCG 58.271 52.381 0.00 0.00 0.00 4.63
1600 2097 2.745884 CCGCGCCATTGACAGGAA 60.746 61.111 0.00 0.00 0.00 3.36
1601 2098 2.331893 CCGCGCCATTGACAGGAAA 61.332 57.895 0.00 0.00 0.00 3.13
1602 2099 1.578926 CGCGCCATTGACAGGAAAA 59.421 52.632 0.00 0.00 0.00 2.29
1603 2100 0.039617 CGCGCCATTGACAGGAAAAA 60.040 50.000 0.00 0.00 0.00 1.94
1623 2120 4.373156 AAAACACTCACCTGCTTATCCT 57.627 40.909 0.00 0.00 0.00 3.24
1624 2121 3.618690 AACACTCACCTGCTTATCCTC 57.381 47.619 0.00 0.00 0.00 3.71
1625 2122 1.478510 ACACTCACCTGCTTATCCTCG 59.521 52.381 0.00 0.00 0.00 4.63
1626 2123 1.478510 CACTCACCTGCTTATCCTCGT 59.521 52.381 0.00 0.00 0.00 4.18
1627 2124 1.478510 ACTCACCTGCTTATCCTCGTG 59.521 52.381 0.00 0.00 0.00 4.35
1628 2125 0.175760 TCACCTGCTTATCCTCGTGC 59.824 55.000 0.00 0.00 0.00 5.34
1629 2126 0.811616 CACCTGCTTATCCTCGTGCC 60.812 60.000 0.00 0.00 0.00 5.01
1630 2127 0.978146 ACCTGCTTATCCTCGTGCCT 60.978 55.000 0.00 0.00 0.00 4.75
1631 2128 0.179000 CCTGCTTATCCTCGTGCCTT 59.821 55.000 0.00 0.00 0.00 4.35
1632 2129 1.407437 CCTGCTTATCCTCGTGCCTTT 60.407 52.381 0.00 0.00 0.00 3.11
1633 2130 1.936547 CTGCTTATCCTCGTGCCTTTC 59.063 52.381 0.00 0.00 0.00 2.62
1634 2131 0.931005 GCTTATCCTCGTGCCTTTCG 59.069 55.000 0.00 0.00 0.00 3.46
1635 2132 1.571919 CTTATCCTCGTGCCTTTCGG 58.428 55.000 0.00 0.00 0.00 4.30
1785 2286 1.587054 GAGGTCACCACTCCTCACG 59.413 63.158 0.00 0.00 46.59 4.35
1786 2287 1.152525 AGGTCACCACTCCTCACGT 60.153 57.895 0.00 0.00 0.00 4.49
1792 2293 1.068194 CACCACTCCTCACGTTCTCTC 60.068 57.143 0.00 0.00 0.00 3.20
1799 2300 3.653344 TCCTCACGTTCTCTCAATGTTG 58.347 45.455 0.00 0.00 0.00 3.33
1806 2326 6.929049 TCACGTTCTCTCAATGTTGAATACTT 59.071 34.615 0.00 0.00 36.64 2.24
1814 2334 5.221880 TCAATGTTGAATACTTGCAGCAAC 58.778 37.500 2.83 0.00 39.29 4.17
1817 2337 3.243367 TGTTGAATACTTGCAGCAACACC 60.243 43.478 2.83 0.00 42.49 4.16
1820 2340 3.004629 TGAATACTTGCAGCAACACCAAG 59.995 43.478 2.83 0.00 41.20 3.61
1828 2348 2.813754 GCAGCAACACCAAGATTCAGTA 59.186 45.455 0.00 0.00 0.00 2.74
1829 2349 3.365364 GCAGCAACACCAAGATTCAGTAC 60.365 47.826 0.00 0.00 0.00 2.73
1830 2350 3.189287 CAGCAACACCAAGATTCAGTACC 59.811 47.826 0.00 0.00 0.00 3.34
1859 2379 3.671928 GTGCATTGTCTGAATGTTCTTGC 59.328 43.478 0.00 0.00 0.00 4.01
1905 2425 5.819991 ACATGTATGGTCCTTCAATCTTGT 58.180 37.500 0.00 0.00 0.00 3.16
1907 2427 4.009675 TGTATGGTCCTTCAATCTTGTGC 58.990 43.478 0.00 0.00 0.00 4.57
1935 2455 2.173519 CCTGGCATTGTGAGGATGTTT 58.826 47.619 0.00 0.00 0.00 2.83
1977 2497 1.457643 CGCCTGGATCCACCTCCTA 60.458 63.158 11.44 0.00 39.86 2.94
2018 2538 1.534729 AGGTCAGTCGGCCATTTTTC 58.465 50.000 2.24 0.00 0.00 2.29
2024 2544 2.095263 CAGTCGGCCATTTTTCGTTCAT 60.095 45.455 2.24 0.00 0.00 2.57
2028 2548 4.210328 GTCGGCCATTTTTCGTTCATTTTT 59.790 37.500 2.24 0.00 0.00 1.94
2030 2550 5.631512 TCGGCCATTTTTCGTTCATTTTTAG 59.368 36.000 2.24 0.00 0.00 1.85
2050 2570 2.159043 AGGTGTATGCGATTGTGAGGAG 60.159 50.000 0.00 0.00 0.00 3.69
2051 2571 2.205074 GTGTATGCGATTGTGAGGAGG 58.795 52.381 0.00 0.00 0.00 4.30
2052 2572 1.831106 TGTATGCGATTGTGAGGAGGT 59.169 47.619 0.00 0.00 0.00 3.85
2053 2573 3.028130 TGTATGCGATTGTGAGGAGGTA 58.972 45.455 0.00 0.00 0.00 3.08
2055 2575 1.847328 TGCGATTGTGAGGAGGTAGA 58.153 50.000 0.00 0.00 0.00 2.59
2056 2576 1.476891 TGCGATTGTGAGGAGGTAGAC 59.523 52.381 0.00 0.00 0.00 2.59
2057 2577 1.476891 GCGATTGTGAGGAGGTAGACA 59.523 52.381 0.00 0.00 0.00 3.41
2058 2578 2.735762 GCGATTGTGAGGAGGTAGACAC 60.736 54.545 0.00 0.00 0.00 3.67
2093 2625 2.133281 TTCCTTGATGGTGATGCAGG 57.867 50.000 0.00 0.00 37.07 4.85
2105 2637 1.202867 TGATGCAGGCAAGTGTACCAA 60.203 47.619 0.00 0.00 0.00 3.67
2150 2682 1.425428 CAGGCATTCGGTTTCGCTC 59.575 57.895 0.00 0.00 36.13 5.03
2232 2764 1.670087 CCACAGGTCGATCACACTGAC 60.670 57.143 12.74 2.51 35.08 3.51
2233 2765 1.270826 CACAGGTCGATCACACTGACT 59.729 52.381 12.74 0.00 35.08 3.41
2234 2766 1.270826 ACAGGTCGATCACACTGACTG 59.729 52.381 12.74 5.26 35.08 3.51
2235 2767 1.541588 CAGGTCGATCACACTGACTGA 59.458 52.381 0.00 0.00 32.86 3.41
2263 2795 3.390521 CGTGTAGGCAGGCTCCCA 61.391 66.667 0.00 0.00 0.00 4.37
2295 2827 4.026052 TGGCTCAGATAGTGTGATTCAGA 58.974 43.478 0.00 0.00 0.00 3.27
2296 2828 4.652881 TGGCTCAGATAGTGTGATTCAGAT 59.347 41.667 0.00 0.00 0.00 2.90
2342 2874 5.221048 GGTGCACCATTTGTTCCATATAGAC 60.221 44.000 31.23 0.00 35.64 2.59
2343 2875 5.356751 GTGCACCATTTGTTCCATATAGACA 59.643 40.000 5.22 0.00 0.00 3.41
2366 2898 7.905265 ACATCACATTGATTATTTTCACCCAA 58.095 30.769 0.00 0.00 34.28 4.12
2422 2954 3.118075 TCGCCATCATGGGTTCATAGAAA 60.118 43.478 5.62 0.00 38.19 2.52
2429 2961 4.968719 TCATGGGTTCATAGAAAGGCTAGA 59.031 41.667 0.00 0.00 31.33 2.43
2431 2963 5.099042 TGGGTTCATAGAAAGGCTAGAAC 57.901 43.478 0.00 0.00 36.98 3.01
2432 2964 4.783227 TGGGTTCATAGAAAGGCTAGAACT 59.217 41.667 0.00 0.00 37.38 3.01
2433 2965 5.119694 GGGTTCATAGAAAGGCTAGAACTG 58.880 45.833 0.00 0.00 37.38 3.16
2435 2967 5.423886 GTTCATAGAAAGGCTAGAACTGCT 58.576 41.667 0.00 0.00 36.01 4.24
2437 2969 4.711846 TCATAGAAAGGCTAGAACTGCTGA 59.288 41.667 0.00 0.00 31.33 4.26
2438 2970 5.365025 TCATAGAAAGGCTAGAACTGCTGAT 59.635 40.000 0.00 0.00 31.33 2.90
2439 2971 4.566426 AGAAAGGCTAGAACTGCTGATT 57.434 40.909 0.00 0.00 0.00 2.57
2466 2998 9.201989 TGATTTGTACTATCTGAGTCCTGTTAT 57.798 33.333 0.00 0.00 39.81 1.89
2509 3042 7.718334 TTTATATAGGATCTCGGATCAGCAA 57.282 36.000 13.59 0.79 0.00 3.91
2543 3078 5.942236 TGTGAAGGAATCAAAGAAGATGAGG 59.058 40.000 0.00 0.00 40.50 3.86
2548 3084 5.948758 AGGAATCAAAGAAGATGAGGGAAAC 59.051 40.000 0.00 0.00 0.00 2.78
2563 3099 5.998981 TGAGGGAAACTAAAACATCGCTTTA 59.001 36.000 0.00 0.00 35.52 1.85
2614 3175 9.383519 TGTTCAAGCAAATAGACTAATAAGAGG 57.616 33.333 0.00 0.00 0.00 3.69
2615 3176 8.831550 GTTCAAGCAAATAGACTAATAAGAGGG 58.168 37.037 0.00 0.00 0.00 4.30
2616 3177 8.090788 TCAAGCAAATAGACTAATAAGAGGGT 57.909 34.615 0.00 0.00 0.00 4.34
2617 3178 8.548877 TCAAGCAAATAGACTAATAAGAGGGTT 58.451 33.333 0.00 0.00 0.00 4.11
2618 3179 9.178758 CAAGCAAATAGACTAATAAGAGGGTTT 57.821 33.333 0.00 0.00 0.00 3.27
2619 3180 8.738645 AGCAAATAGACTAATAAGAGGGTTTG 57.261 34.615 0.00 0.00 0.00 2.93
2620 3181 8.329502 AGCAAATAGACTAATAAGAGGGTTTGT 58.670 33.333 0.00 0.00 0.00 2.83
2621 3182 9.609346 GCAAATAGACTAATAAGAGGGTTTGTA 57.391 33.333 0.00 0.00 0.00 2.41
2637 3198 6.097696 AGGGTTTGTATTGCAACTTTACAACT 59.902 34.615 18.95 12.57 36.01 3.16
2639 3200 7.921745 GGGTTTGTATTGCAACTTTACAACTAA 59.078 33.333 18.95 6.83 36.01 2.24
2655 3216 9.691362 TTTACAACTAATGAATTTCTGAAAGCC 57.309 29.630 8.95 3.72 0.00 4.35
2678 3239 1.308998 CCAAGGTTGCGTGACTCTTT 58.691 50.000 0.00 0.00 0.00 2.52
2679 3240 2.489971 CCAAGGTTGCGTGACTCTTTA 58.510 47.619 0.00 0.00 0.00 1.85
2680 3241 3.074412 CCAAGGTTGCGTGACTCTTTAT 58.926 45.455 0.00 0.00 0.00 1.40
2687 3248 7.272978 AGGTTGCGTGACTCTTTATATTACAT 58.727 34.615 0.00 0.00 0.00 2.29
2710 3272 8.333235 ACATAATGGTAAACCTATTGAAGTGGA 58.667 33.333 0.02 0.00 36.82 4.02
2733 3298 2.281484 ATCAAACGGCGTGGCAGT 60.281 55.556 15.70 0.00 38.82 4.40
2749 3314 1.290203 CAGTGGCAGCTACAATACCG 58.710 55.000 12.02 0.00 0.00 4.02
2750 3315 1.134818 CAGTGGCAGCTACAATACCGA 60.135 52.381 12.02 0.00 0.00 4.69
2751 3316 1.762957 AGTGGCAGCTACAATACCGAT 59.237 47.619 12.02 0.00 0.00 4.18
2752 3317 2.170607 AGTGGCAGCTACAATACCGATT 59.829 45.455 12.02 0.00 0.00 3.34
2753 3318 2.943033 GTGGCAGCTACAATACCGATTT 59.057 45.455 3.57 0.00 0.00 2.17
2754 3319 3.377172 GTGGCAGCTACAATACCGATTTT 59.623 43.478 3.57 0.00 0.00 1.82
2755 3320 4.013728 TGGCAGCTACAATACCGATTTTT 58.986 39.130 0.00 0.00 0.00 1.94
2756 3321 4.142491 TGGCAGCTACAATACCGATTTTTG 60.142 41.667 0.00 0.00 0.00 2.44
2768 3333 1.129811 CGATTTTTGTCCAGCCCGTAC 59.870 52.381 0.00 0.00 0.00 3.67
2777 3346 1.965643 TCCAGCCCGTACATATACACC 59.034 52.381 0.00 0.00 0.00 4.16
2799 3373 9.379791 ACACCTTTTGTACAAGTATAGCTATTC 57.620 33.333 12.39 6.92 36.32 1.75
2805 3379 9.745880 TTTGTACAAGTATAGCTATTCTACTGC 57.254 33.333 12.39 5.20 0.00 4.40
2831 3408 5.512082 CGTATAACGGCATAGTATCAGCTTC 59.488 44.000 0.00 0.00 38.08 3.86
2832 3409 5.730296 ATAACGGCATAGTATCAGCTTCT 57.270 39.130 0.00 0.00 0.00 2.85
2935 3512 5.050091 CGGGTGAAGTAATAATCATCTGCAC 60.050 44.000 0.00 0.00 36.17 4.57
2940 3517 8.834465 GTGAAGTAATAATCATCTGCACTTCAT 58.166 33.333 14.99 0.00 46.90 2.57
2959 3545 4.523083 TCATAGGAGTTGCCAACCATTAC 58.477 43.478 3.45 0.00 40.02 1.89
2962 3548 2.042979 AGGAGTTGCCAACCATTACCAT 59.957 45.455 3.45 0.00 40.02 3.55
2989 3590 6.422776 GCAAAATGCATACTACTACTGTGT 57.577 37.500 0.00 0.00 44.26 3.72
2990 3591 6.842163 GCAAAATGCATACTACTACTGTGTT 58.158 36.000 0.00 0.00 44.26 3.32
2991 3592 6.742718 GCAAAATGCATACTACTACTGTGTTG 59.257 38.462 0.00 0.00 44.26 3.33
2999 3600 8.440833 GCATACTACTACTGTGTTGGTTTTTAG 58.559 37.037 0.00 0.00 0.00 1.85
3018 3619 7.801716 TTTTAGAAGTACTGCTGTGAACATT 57.198 32.000 14.19 0.00 0.00 2.71
3020 3621 4.067896 AGAAGTACTGCTGTGAACATTGG 58.932 43.478 1.28 0.00 0.00 3.16
3081 3690 1.773496 GCGTAGTTGCACGACAGAC 59.227 57.895 0.00 0.00 44.69 3.51
3114 3723 3.490759 CGTAGCTGCAAGGCGTGG 61.491 66.667 1.02 0.00 37.29 4.94
3115 3724 3.127533 GTAGCTGCAAGGCGTGGG 61.128 66.667 1.02 0.00 37.29 4.61
3160 3774 9.146984 CAAATCTTGTGATCAAATTAGTTGCAT 57.853 29.630 0.00 0.00 37.13 3.96
3162 3776 7.451501 TCTTGTGATCAAATTAGTTGCATGA 57.548 32.000 0.00 0.00 37.13 3.07
3163 3777 7.532571 TCTTGTGATCAAATTAGTTGCATGAG 58.467 34.615 0.00 0.00 37.13 2.90
3164 3778 6.822667 TGTGATCAAATTAGTTGCATGAGT 57.177 33.333 0.00 0.00 37.13 3.41
3174 3790 3.079578 AGTTGCATGAGTCATGAACTGG 58.920 45.455 32.61 9.18 43.81 4.00
3175 3791 1.456296 TGCATGAGTCATGAACTGGC 58.544 50.000 32.61 18.36 43.81 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.096682 ACTCTCCACTCTCAGTATAAACGC 59.903 45.833 0.00 0.00 0.00 4.84
41 42 4.960332 TCTTTATTTCTCTCCCCTCTCCA 58.040 43.478 0.00 0.00 0.00 3.86
95 96 9.570488 AAACAACTCAGACGAACTAAGTATATC 57.430 33.333 0.00 0.00 0.00 1.63
99 100 7.141363 GGTAAACAACTCAGACGAACTAAGTA 58.859 38.462 0.00 0.00 0.00 2.24
100 101 5.981915 GGTAAACAACTCAGACGAACTAAGT 59.018 40.000 0.00 0.00 0.00 2.24
119 120 6.072008 GGGATAAAGGTGCTAAAAACGGTAAA 60.072 38.462 0.00 0.00 0.00 2.01
135 136 4.518249 GAGGAACTGTCTTGGGATAAAGG 58.482 47.826 0.00 0.00 41.55 3.11
140 141 1.912043 CAGGAGGAACTGTCTTGGGAT 59.088 52.381 0.00 0.00 41.55 3.85
220 221 3.491342 CTTCTCATCCTCCTCACGGATA 58.509 50.000 0.00 0.00 39.20 2.59
221 222 2.315176 CTTCTCATCCTCCTCACGGAT 58.685 52.381 0.00 0.00 41.88 4.18
222 223 1.686428 CCTTCTCATCCTCCTCACGGA 60.686 57.143 0.00 0.00 37.82 4.69
223 224 0.749649 CCTTCTCATCCTCCTCACGG 59.250 60.000 0.00 0.00 0.00 4.94
224 225 1.479709 ACCTTCTCATCCTCCTCACG 58.520 55.000 0.00 0.00 0.00 4.35
225 226 2.159170 CGAACCTTCTCATCCTCCTCAC 60.159 54.545 0.00 0.00 0.00 3.51
229 230 0.466124 CCCGAACCTTCTCATCCTCC 59.534 60.000 0.00 0.00 0.00 4.30
230 231 0.179070 GCCCGAACCTTCTCATCCTC 60.179 60.000 0.00 0.00 0.00 3.71
231 232 1.627297 GGCCCGAACCTTCTCATCCT 61.627 60.000 0.00 0.00 0.00 3.24
265 266 4.517285 GCAGGATTTCTAATCAGTCCACA 58.483 43.478 2.24 0.00 0.00 4.17
286 287 0.946221 CTCAGACCAACACGACAGGC 60.946 60.000 0.00 0.00 0.00 4.85
293 294 3.065371 CCAAAACTGTCTCAGACCAACAC 59.935 47.826 1.24 0.00 35.18 3.32
350 356 6.767524 AAAACACAAACCAACAGAGACATA 57.232 33.333 0.00 0.00 0.00 2.29
387 396 8.577939 CAAAACGATTAAATCAACAGCATACAG 58.422 33.333 0.00 0.00 0.00 2.74
398 407 9.967346 TGGATAAAACACAAAACGATTAAATCA 57.033 25.926 0.00 0.00 0.00 2.57
400 409 9.751542 TGTGGATAAAACACAAAACGATTAAAT 57.248 25.926 0.00 0.00 45.05 1.40
425 434 7.878477 AAATCAACAGCATACAAAGTGAATG 57.122 32.000 0.00 0.00 0.00 2.67
458 468 3.635373 AGAACACCAGAGAGTGAAACGTA 59.365 43.478 0.00 0.00 45.86 3.57
459 469 2.431057 AGAACACCAGAGAGTGAAACGT 59.569 45.455 0.00 0.00 45.86 3.99
460 470 3.099267 AGAACACCAGAGAGTGAAACG 57.901 47.619 0.00 0.00 45.86 3.60
505 521 2.592102 AGCTCATCTCCCTGCAAAAA 57.408 45.000 0.00 0.00 0.00 1.94
506 522 2.040813 AGAAGCTCATCTCCCTGCAAAA 59.959 45.455 0.00 0.00 0.00 2.44
507 523 1.632409 AGAAGCTCATCTCCCTGCAAA 59.368 47.619 0.00 0.00 0.00 3.68
508 524 1.065636 CAGAAGCTCATCTCCCTGCAA 60.066 52.381 0.00 0.00 0.00 4.08
509 525 0.540454 CAGAAGCTCATCTCCCTGCA 59.460 55.000 0.00 0.00 0.00 4.41
510 526 0.540923 ACAGAAGCTCATCTCCCTGC 59.459 55.000 0.00 0.00 32.18 4.85
511 527 2.235650 TCAACAGAAGCTCATCTCCCTG 59.764 50.000 0.00 0.00 33.96 4.45
512 528 2.544721 TCAACAGAAGCTCATCTCCCT 58.455 47.619 0.00 0.00 0.00 4.20
513 529 3.557228 ATCAACAGAAGCTCATCTCCC 57.443 47.619 0.00 0.00 0.00 4.30
514 530 7.565323 AATAAATCAACAGAAGCTCATCTCC 57.435 36.000 0.00 0.00 0.00 3.71
515 531 8.671921 TCAAATAAATCAACAGAAGCTCATCTC 58.328 33.333 0.00 0.00 0.00 2.75
516 532 8.457261 GTCAAATAAATCAACAGAAGCTCATCT 58.543 33.333 0.00 0.00 0.00 2.90
517 533 7.427606 CGTCAAATAAATCAACAGAAGCTCATC 59.572 37.037 0.00 0.00 0.00 2.92
518 534 7.246311 CGTCAAATAAATCAACAGAAGCTCAT 58.754 34.615 0.00 0.00 0.00 2.90
519 535 6.348458 CCGTCAAATAAATCAACAGAAGCTCA 60.348 38.462 0.00 0.00 0.00 4.26
520 536 6.024049 CCGTCAAATAAATCAACAGAAGCTC 58.976 40.000 0.00 0.00 0.00 4.09
521 537 5.619981 GCCGTCAAATAAATCAACAGAAGCT 60.620 40.000 0.00 0.00 0.00 3.74
522 538 4.558860 GCCGTCAAATAAATCAACAGAAGC 59.441 41.667 0.00 0.00 0.00 3.86
523 539 4.788100 CGCCGTCAAATAAATCAACAGAAG 59.212 41.667 0.00 0.00 0.00 2.85
524 540 4.378978 CCGCCGTCAAATAAATCAACAGAA 60.379 41.667 0.00 0.00 0.00 3.02
525 541 3.126171 CCGCCGTCAAATAAATCAACAGA 59.874 43.478 0.00 0.00 0.00 3.41
526 542 3.119990 ACCGCCGTCAAATAAATCAACAG 60.120 43.478 0.00 0.00 0.00 3.16
527 543 2.814919 ACCGCCGTCAAATAAATCAACA 59.185 40.909 0.00 0.00 0.00 3.33
528 544 3.168193 CACCGCCGTCAAATAAATCAAC 58.832 45.455 0.00 0.00 0.00 3.18
529 545 2.814919 ACACCGCCGTCAAATAAATCAA 59.185 40.909 0.00 0.00 0.00 2.57
530 546 2.160615 CACACCGCCGTCAAATAAATCA 59.839 45.455 0.00 0.00 0.00 2.57
531 547 2.160813 ACACACCGCCGTCAAATAAATC 59.839 45.455 0.00 0.00 0.00 2.17
532 548 2.156098 ACACACCGCCGTCAAATAAAT 58.844 42.857 0.00 0.00 0.00 1.40
533 549 1.595466 ACACACCGCCGTCAAATAAA 58.405 45.000 0.00 0.00 0.00 1.40
536 552 1.652012 CAACACACCGCCGTCAAAT 59.348 52.632 0.00 0.00 0.00 2.32
541 557 3.857038 AGACCAACACACCGCCGT 61.857 61.111 0.00 0.00 0.00 5.68
542 558 3.345808 CAGACCAACACACCGCCG 61.346 66.667 0.00 0.00 0.00 6.46
546 562 0.381801 CAGCAACAGACCAACACACC 59.618 55.000 0.00 0.00 0.00 4.16
577 605 3.409570 CAGAGGACTATGCAATCCCATG 58.590 50.000 10.55 6.93 35.38 3.66
578 606 2.224719 GCAGAGGACTATGCAATCCCAT 60.225 50.000 13.51 0.00 46.17 4.00
587 615 2.364970 CTGGAGGAAGCAGAGGACTATG 59.635 54.545 0.00 0.00 0.00 2.23
588 616 2.246067 TCTGGAGGAAGCAGAGGACTAT 59.754 50.000 0.00 0.00 0.00 2.12
589 617 1.641192 TCTGGAGGAAGCAGAGGACTA 59.359 52.381 0.00 0.00 0.00 2.59
592 620 0.975040 GCTCTGGAGGAAGCAGAGGA 60.975 60.000 2.39 0.00 41.84 3.71
593 621 1.521616 GCTCTGGAGGAAGCAGAGG 59.478 63.158 2.39 0.00 41.84 3.69
594 622 1.521616 GGCTCTGGAGGAAGCAGAG 59.478 63.158 0.00 0.00 43.74 3.35
595 623 2.354401 CGGCTCTGGAGGAAGCAGA 61.354 63.158 0.00 0.00 0.00 4.26
596 624 2.186384 CGGCTCTGGAGGAAGCAG 59.814 66.667 0.00 0.00 0.00 4.24
600 628 3.393970 CAGGCGGCTCTGGAGGAA 61.394 66.667 9.32 0.00 0.00 3.36
601 629 4.382541 TCAGGCGGCTCTGGAGGA 62.383 66.667 9.32 0.00 35.58 3.71
602 630 3.847602 CTCAGGCGGCTCTGGAGG 61.848 72.222 9.32 0.00 35.58 4.30
603 631 3.847602 CCTCAGGCGGCTCTGGAG 61.848 72.222 18.38 16.89 35.58 3.86
604 632 4.704103 ACCTCAGGCGGCTCTGGA 62.704 66.667 26.55 14.09 35.58 3.86
605 633 4.463879 CACCTCAGGCGGCTCTGG 62.464 72.222 20.62 20.62 35.58 3.86
607 635 2.500815 TACTCACCTCAGGCGGCTCT 62.501 60.000 9.32 0.00 0.00 4.09
609 637 2.037367 TACTCACCTCAGGCGGCT 59.963 61.111 5.25 5.25 0.00 5.52
610 638 1.889530 AAGTACTCACCTCAGGCGGC 61.890 60.000 0.00 0.00 0.00 6.53
611 639 0.108615 CAAGTACTCACCTCAGGCGG 60.109 60.000 0.00 0.00 0.00 6.13
613 641 0.977395 ACCAAGTACTCACCTCAGGC 59.023 55.000 0.00 0.00 0.00 4.85
614 642 4.383118 CCATTACCAAGTACTCACCTCAGG 60.383 50.000 0.00 0.00 0.00 3.86
615 643 4.759782 CCATTACCAAGTACTCACCTCAG 58.240 47.826 0.00 0.00 0.00 3.35
619 647 2.277084 CGCCATTACCAAGTACTCACC 58.723 52.381 0.00 0.00 0.00 4.02
621 649 1.406341 GCCGCCATTACCAAGTACTCA 60.406 52.381 0.00 0.00 0.00 3.41
622 650 1.296727 GCCGCCATTACCAAGTACTC 58.703 55.000 0.00 0.00 0.00 2.59
623 651 0.107361 GGCCGCCATTACCAAGTACT 60.107 55.000 3.91 0.00 0.00 2.73
624 652 0.393267 TGGCCGCCATTACCAAGTAC 60.393 55.000 8.43 0.00 0.00 2.73
625 653 0.393267 GTGGCCGCCATTACCAAGTA 60.393 55.000 16.96 0.00 35.28 2.24
626 654 1.677633 GTGGCCGCCATTACCAAGT 60.678 57.895 16.96 0.00 35.28 3.16
628 656 2.748251 CGTGGCCGCCATTACCAA 60.748 61.111 16.96 0.00 35.28 3.67
629 657 4.023234 ACGTGGCCGCCATTACCA 62.023 61.111 16.96 0.00 35.28 3.25
630 658 3.505184 CACGTGGCCGCCATTACC 61.505 66.667 16.96 0.99 35.28 2.85
632 660 2.435234 GACACGTGGCCGCCATTA 60.435 61.111 21.57 0.00 35.28 1.90
641 669 4.778415 CTCCTCGCCGACACGTGG 62.778 72.222 21.57 2.78 45.62 4.94
663 693 2.266055 GAGCCTTGACTGGGACGG 59.734 66.667 0.00 0.00 42.99 4.79
710 762 1.216710 CCTTCTCACCTCAGTCGCC 59.783 63.158 0.00 0.00 0.00 5.54
727 779 6.463472 GGTTCACCACCCATTATAGTAGTACC 60.463 46.154 0.00 0.00 40.19 3.34
817 909 2.521958 ATCTTGGGAACGGCAGGTCG 62.522 60.000 0.00 0.00 34.09 4.79
826 918 2.507407 TGCCTTACCATCTTGGGAAC 57.493 50.000 0.00 0.00 43.37 3.62
890 982 0.532862 CCGGGCTGTGATGTGGTATC 60.533 60.000 0.00 0.00 0.00 2.24
891 983 1.526887 CCGGGCTGTGATGTGGTAT 59.473 57.895 0.00 0.00 0.00 2.73
892 984 2.986290 CCGGGCTGTGATGTGGTA 59.014 61.111 0.00 0.00 0.00 3.25
945 1370 1.916777 TGTTCCGGGAAGGGGAGAC 60.917 63.158 10.35 0.00 41.52 3.36
946 1371 1.916777 GTGTTCCGGGAAGGGGAGA 60.917 63.158 10.35 0.00 41.52 3.71
983 1416 0.108329 CATTTCCAGCCGGTAGTCGT 60.108 55.000 1.90 0.00 37.11 4.34
988 1421 2.124901 CGCCATTTCCAGCCGGTA 60.125 61.111 1.90 0.00 0.00 4.02
1076 1540 4.500375 GCAGAAAGAAGTCAACAAAGGCAT 60.500 41.667 0.00 0.00 0.00 4.40
1333 1813 7.565680 AGTCTTGGTGAAAAGAAAAGAGAGTA 58.434 34.615 0.00 0.00 37.90 2.59
1336 1816 6.884295 TCAAGTCTTGGTGAAAAGAAAAGAGA 59.116 34.615 12.66 0.00 37.90 3.10
1357 1840 0.164647 GCGCTGCTGTAACTGTCAAG 59.835 55.000 0.00 0.00 0.00 3.02
1361 1844 2.358737 GGGCGCTGCTGTAACTGT 60.359 61.111 7.64 0.00 0.00 3.55
1387 1872 2.270297 AAATCATGGCGTTGCGAGGC 62.270 55.000 10.25 10.25 35.97 4.70
1396 1881 5.174398 GCAATAATTCAGTCAAATCATGGCG 59.826 40.000 0.00 0.00 39.19 5.69
1403 1888 6.625740 CGTGGGAAGCAATAATTCAGTCAAAT 60.626 38.462 0.00 0.00 0.00 2.32
1404 1889 5.335583 CGTGGGAAGCAATAATTCAGTCAAA 60.336 40.000 0.00 0.00 0.00 2.69
1413 1898 3.541632 CCTGTACGTGGGAAGCAATAAT 58.458 45.455 0.00 0.00 0.00 1.28
1415 1900 2.684001 CCTGTACGTGGGAAGCAATA 57.316 50.000 0.00 0.00 0.00 1.90
1423 1908 2.264794 GACAGCCCTGTACGTGGG 59.735 66.667 16.81 16.81 45.05 4.61
1549 2046 2.486716 AGAGAAAGAGGAATGAGGGGG 58.513 52.381 0.00 0.00 0.00 5.40
1554 2051 4.714308 GGAGGAGAAGAGAAAGAGGAATGA 59.286 45.833 0.00 0.00 0.00 2.57
1556 2053 3.704061 CGGAGGAGAAGAGAAAGAGGAAT 59.296 47.826 0.00 0.00 0.00 3.01
1583 2080 1.861542 TTTTCCTGTCAATGGCGCGG 61.862 55.000 8.83 0.00 0.00 6.46
1584 2081 0.039617 TTTTTCCTGTCAATGGCGCG 60.040 50.000 0.00 0.00 0.00 6.86
1601 2098 4.729868 AGGATAAGCAGGTGAGTGTTTTT 58.270 39.130 0.00 0.00 0.00 1.94
1602 2099 4.327680 GAGGATAAGCAGGTGAGTGTTTT 58.672 43.478 0.00 0.00 0.00 2.43
1603 2100 3.617531 CGAGGATAAGCAGGTGAGTGTTT 60.618 47.826 0.00 0.00 0.00 2.83
1604 2101 2.093973 CGAGGATAAGCAGGTGAGTGTT 60.094 50.000 0.00 0.00 0.00 3.32
1605 2102 1.478510 CGAGGATAAGCAGGTGAGTGT 59.521 52.381 0.00 0.00 0.00 3.55
1606 2103 1.478510 ACGAGGATAAGCAGGTGAGTG 59.521 52.381 0.00 0.00 0.00 3.51
1607 2104 1.478510 CACGAGGATAAGCAGGTGAGT 59.521 52.381 0.00 0.00 0.00 3.41
1610 2107 0.811616 GGCACGAGGATAAGCAGGTG 60.812 60.000 0.00 0.00 0.00 4.00
1611 2108 0.978146 AGGCACGAGGATAAGCAGGT 60.978 55.000 0.00 0.00 0.00 4.00
1613 2110 1.936547 GAAAGGCACGAGGATAAGCAG 59.063 52.381 0.00 0.00 0.00 4.24
1614 2111 1.739035 CGAAAGGCACGAGGATAAGCA 60.739 52.381 0.00 0.00 0.00 3.91
1615 2112 0.931005 CGAAAGGCACGAGGATAAGC 59.069 55.000 0.00 0.00 0.00 3.09
1629 2126 1.710339 GCTTAGTCTGCGCCGAAAG 59.290 57.895 4.18 6.93 0.00 2.62
1630 2127 2.092291 CGCTTAGTCTGCGCCGAAA 61.092 57.895 4.18 0.00 46.72 3.46
1631 2128 2.506217 CGCTTAGTCTGCGCCGAA 60.506 61.111 4.18 0.00 46.72 4.30
1679 2176 3.597728 GCGTAGAGGAGGCCGAGG 61.598 72.222 0.00 0.00 32.56 4.63
1774 2271 1.248486 TGAGAGAACGTGAGGAGTGG 58.752 55.000 0.00 0.00 0.00 4.00
1777 2278 3.584406 ACATTGAGAGAACGTGAGGAG 57.416 47.619 0.00 0.00 0.00 3.69
1785 2286 6.902341 TGCAAGTATTCAACATTGAGAGAAC 58.098 36.000 0.00 0.00 38.61 3.01
1786 2287 6.348786 GCTGCAAGTATTCAACATTGAGAGAA 60.349 38.462 0.00 0.00 35.61 2.87
1792 2293 4.983538 TGTTGCTGCAAGTATTCAACATTG 59.016 37.500 16.53 0.00 41.12 2.82
1799 2300 3.253188 TCTTGGTGTTGCTGCAAGTATTC 59.747 43.478 16.53 4.09 35.30 1.75
1806 2326 1.610038 CTGAATCTTGGTGTTGCTGCA 59.390 47.619 0.00 0.00 0.00 4.41
1814 2334 3.057969 TGCTGGTACTGAATCTTGGTG 57.942 47.619 0.00 0.00 0.00 4.17
1817 2337 4.673580 GCACAATGCTGGTACTGAATCTTG 60.674 45.833 0.00 0.00 40.96 3.02
1820 2340 2.749076 TGCACAATGCTGGTACTGAATC 59.251 45.455 2.02 0.00 45.31 2.52
1828 2348 1.271379 CAGACAATGCACAATGCTGGT 59.729 47.619 2.02 0.00 45.31 4.00
1829 2349 1.542472 TCAGACAATGCACAATGCTGG 59.458 47.619 2.02 0.00 45.31 4.85
1830 2350 3.291809 TTCAGACAATGCACAATGCTG 57.708 42.857 2.02 1.68 45.31 4.41
1878 2398 8.906867 CAAGATTGAAGGACCATACATGTTATT 58.093 33.333 2.30 0.00 0.00 1.40
1888 2408 2.086869 CGCACAAGATTGAAGGACCAT 58.913 47.619 0.00 0.00 0.00 3.55
1893 2413 3.667960 GCAACTACGCACAAGATTGAAGG 60.668 47.826 0.00 0.00 0.00 3.46
1895 2415 2.225491 GGCAACTACGCACAAGATTGAA 59.775 45.455 0.00 0.00 0.00 2.69
1935 2455 3.396911 GACGGTCATCTCGCTCGCA 62.397 63.158 2.62 0.00 0.00 5.10
2018 2538 5.211266 TCGCATACACCTAAAAATGAACG 57.789 39.130 0.00 0.00 0.00 3.95
2024 2544 5.123186 CCTCACAATCGCATACACCTAAAAA 59.877 40.000 0.00 0.00 0.00 1.94
2028 2548 3.028130 TCCTCACAATCGCATACACCTA 58.972 45.455 0.00 0.00 0.00 3.08
2030 2550 2.205074 CTCCTCACAATCGCATACACC 58.795 52.381 0.00 0.00 0.00 4.16
2081 2613 0.251474 ACACTTGCCTGCATCACCAT 60.251 50.000 0.00 0.00 0.00 3.55
2093 2625 1.533625 TGCCATCTTGGTACACTTGC 58.466 50.000 0.00 0.00 40.46 4.01
2105 2637 3.376234 CGATGTTGTTCTTGATGCCATCT 59.624 43.478 6.21 0.00 0.00 2.90
2150 2682 2.438075 GGGCAGAAGAGCAGGCAG 60.438 66.667 0.00 0.00 35.83 4.85
2232 2764 0.455464 TACACGCAATCGGTCGTCAG 60.455 55.000 0.00 0.00 40.69 3.51
2233 2765 0.455464 CTACACGCAATCGGTCGTCA 60.455 55.000 0.00 0.00 40.69 4.35
2234 2766 1.138047 CCTACACGCAATCGGTCGTC 61.138 60.000 0.00 0.00 40.69 4.20
2235 2767 1.153901 CCTACACGCAATCGGTCGT 60.154 57.895 0.00 0.00 40.69 4.34
2263 2795 6.765036 CACACTATCTGAGCCATCTAAACAAT 59.235 38.462 0.00 0.00 0.00 2.71
2342 2874 8.951787 ATTGGGTGAAAATAATCAATGTGATG 57.048 30.769 0.00 0.00 37.15 3.07
2343 2875 8.984855 AGATTGGGTGAAAATAATCAATGTGAT 58.015 29.630 0.00 0.00 39.09 3.06
2366 2898 4.963318 TCTCGAGCCAATTCCAATAGAT 57.037 40.909 7.81 0.00 0.00 1.98
2422 2954 3.988976 TCAAATCAGCAGTTCTAGCCT 57.011 42.857 0.00 0.00 0.00 4.58
2429 2961 8.671921 CAGATAGTACAAATCAAATCAGCAGTT 58.328 33.333 9.97 0.00 0.00 3.16
2431 2963 8.429493 TCAGATAGTACAAATCAAATCAGCAG 57.571 34.615 9.97 0.00 0.00 4.24
2432 2964 8.043113 ACTCAGATAGTACAAATCAAATCAGCA 58.957 33.333 9.97 0.00 36.36 4.41
2433 2965 8.430801 ACTCAGATAGTACAAATCAAATCAGC 57.569 34.615 9.97 0.00 36.36 4.26
2435 2967 8.762645 AGGACTCAGATAGTACAAATCAAATCA 58.237 33.333 9.97 0.00 42.17 2.57
2437 2969 8.543774 ACAGGACTCAGATAGTACAAATCAAAT 58.456 33.333 9.97 0.00 42.17 2.32
2438 2970 7.907389 ACAGGACTCAGATAGTACAAATCAAA 58.093 34.615 9.97 0.00 42.17 2.69
2439 2971 7.482169 ACAGGACTCAGATAGTACAAATCAA 57.518 36.000 9.97 0.00 42.17 2.57
2492 3024 2.036992 GTCATTGCTGATCCGAGATCCT 59.963 50.000 10.25 0.00 32.98 3.24
2495 3027 2.169144 TGTGTCATTGCTGATCCGAGAT 59.831 45.455 0.00 0.00 32.98 2.75
2500 3032 4.082625 TCACATTTGTGTCATTGCTGATCC 60.083 41.667 10.30 0.00 45.76 3.36
2504 3036 3.985279 CCTTCACATTTGTGTCATTGCTG 59.015 43.478 10.30 0.00 45.76 4.41
2506 3039 4.241590 TCCTTCACATTTGTGTCATTGC 57.758 40.909 10.30 0.00 45.76 3.56
2509 3042 6.653526 TTGATTCCTTCACATTTGTGTCAT 57.346 33.333 10.30 0.00 45.76 3.06
2522 3057 5.749462 TCCCTCATCTTCTTTGATTCCTTC 58.251 41.667 0.00 0.00 0.00 3.46
2530 3065 7.940850 TGTTTTAGTTTCCCTCATCTTCTTTG 58.059 34.615 0.00 0.00 0.00 2.77
2543 3078 7.358105 GCAGTTTAAAGCGATGTTTTAGTTTCC 60.358 37.037 0.00 0.00 0.00 3.13
2548 3084 6.142817 AGTGCAGTTTAAAGCGATGTTTTAG 58.857 36.000 0.00 0.00 0.00 1.85
2563 3099 4.470334 AACAAATCCACAAGTGCAGTTT 57.530 36.364 3.38 0.00 0.00 2.66
2607 3168 7.539034 AAAGTTGCAATACAAACCCTCTTAT 57.461 32.000 0.59 0.00 40.82 1.73
2608 3169 6.969993 AAAGTTGCAATACAAACCCTCTTA 57.030 33.333 0.59 0.00 40.82 2.10
2609 3170 5.869649 AAAGTTGCAATACAAACCCTCTT 57.130 34.783 0.59 0.00 40.82 2.85
2610 3171 5.830991 TGTAAAGTTGCAATACAAACCCTCT 59.169 36.000 0.59 0.00 40.82 3.69
2611 3172 6.079424 TGTAAAGTTGCAATACAAACCCTC 57.921 37.500 0.59 0.00 40.82 4.30
2612 3173 6.097696 AGTTGTAAAGTTGCAATACAAACCCT 59.902 34.615 20.23 13.22 40.19 4.34
2613 3174 6.277605 AGTTGTAAAGTTGCAATACAAACCC 58.722 36.000 20.23 11.67 40.19 4.11
2614 3175 8.859517 TTAGTTGTAAAGTTGCAATACAAACC 57.140 30.769 20.23 12.20 40.19 3.27
2623 3184 9.462174 CAGAAATTCATTAGTTGTAAAGTTGCA 57.538 29.630 0.00 0.00 0.00 4.08
2624 3185 9.677567 TCAGAAATTCATTAGTTGTAAAGTTGC 57.322 29.630 0.00 0.00 0.00 4.17
2637 3198 4.380444 GGCACGGCTTTCAGAAATTCATTA 60.380 41.667 0.00 0.00 0.00 1.90
2639 3200 2.094545 GGCACGGCTTTCAGAAATTCAT 60.095 45.455 0.00 0.00 0.00 2.57
2655 3216 3.276091 TCACGCAACCTTGGCACG 61.276 61.111 0.00 0.00 0.00 5.34
2687 3248 9.762381 ATTTCCACTTCAATAGGTTTACCATTA 57.238 29.630 1.13 0.00 38.89 1.90
2710 3272 1.668628 GCCACGCCGTTTGATCAATTT 60.669 47.619 9.40 0.00 0.00 1.82
2733 3298 3.275617 AAATCGGTATTGTAGCTGCCA 57.724 42.857 0.00 0.00 0.00 4.92
2749 3314 2.156098 TGTACGGGCTGGACAAAAATC 58.844 47.619 9.47 0.00 0.00 2.17
2750 3315 2.279935 TGTACGGGCTGGACAAAAAT 57.720 45.000 9.47 0.00 0.00 1.82
2751 3316 2.279935 ATGTACGGGCTGGACAAAAA 57.720 45.000 16.81 0.00 0.00 1.94
2752 3317 3.637911 ATATGTACGGGCTGGACAAAA 57.362 42.857 16.81 7.53 0.00 2.44
2753 3318 3.451540 TGTATATGTACGGGCTGGACAAA 59.548 43.478 16.81 1.29 33.36 2.83
2754 3319 3.032459 TGTATATGTACGGGCTGGACAA 58.968 45.455 16.81 5.75 33.36 3.18
2755 3320 2.363038 GTGTATATGTACGGGCTGGACA 59.637 50.000 15.03 15.03 33.36 4.02
2756 3321 2.288640 GGTGTATATGTACGGGCTGGAC 60.289 54.545 0.29 0.29 33.36 4.02
2799 3373 2.197792 TGCCGTTATACGTGCAGTAG 57.802 50.000 0.00 0.00 40.75 2.57
2805 3379 4.557690 GCTGATACTATGCCGTTATACGTG 59.442 45.833 0.00 0.00 40.58 4.49
2826 3400 6.879458 ACCGTATATTTGACAAGAAAGAAGCT 59.121 34.615 0.00 0.00 0.00 3.74
2831 3408 8.029642 ACTCAACCGTATATTTGACAAGAAAG 57.970 34.615 0.00 0.00 0.00 2.62
2832 3409 7.972832 ACTCAACCGTATATTTGACAAGAAA 57.027 32.000 0.00 0.00 0.00 2.52
2883 3460 1.734465 GTTGTGGAGAAGAGATTGGCG 59.266 52.381 0.00 0.00 0.00 5.69
2886 3463 2.350522 CCGGTTGTGGAGAAGAGATTG 58.649 52.381 0.00 0.00 0.00 2.67
2888 3465 0.905357 CCCGGTTGTGGAGAAGAGAT 59.095 55.000 0.00 0.00 0.00 2.75
2935 3512 3.071874 TGGTTGGCAACTCCTATGAAG 57.928 47.619 27.77 0.00 35.26 3.02
2940 3517 2.645297 TGGTAATGGTTGGCAACTCCTA 59.355 45.455 27.77 14.25 35.26 2.94
2959 3545 6.639632 AGTAGTATGCATTTTGCCTAATGG 57.360 37.500 3.54 0.00 44.23 3.16
2962 3548 7.279981 CACAGTAGTAGTATGCATTTTGCCTAA 59.720 37.037 3.54 0.00 44.23 2.69
2979 3580 9.533253 GTACTTCTAAAAACCAACACAGTAGTA 57.467 33.333 0.00 0.00 0.00 1.82
2980 3581 8.262933 AGTACTTCTAAAAACCAACACAGTAGT 58.737 33.333 0.00 0.00 0.00 2.73
2981 3582 8.548721 CAGTACTTCTAAAAACCAACACAGTAG 58.451 37.037 0.00 0.00 0.00 2.57
2982 3583 7.011669 GCAGTACTTCTAAAAACCAACACAGTA 59.988 37.037 0.00 0.00 0.00 2.74
2983 3584 6.183360 GCAGTACTTCTAAAAACCAACACAGT 60.183 38.462 0.00 0.00 0.00 3.55
2984 3585 6.038271 AGCAGTACTTCTAAAAACCAACACAG 59.962 38.462 0.00 0.00 0.00 3.66
2986 3587 6.183360 ACAGCAGTACTTCTAAAAACCAACAC 60.183 38.462 0.00 0.00 0.00 3.32
2987 3588 5.883673 ACAGCAGTACTTCTAAAAACCAACA 59.116 36.000 0.00 0.00 0.00 3.33
2988 3589 6.037830 TCACAGCAGTACTTCTAAAAACCAAC 59.962 38.462 0.00 0.00 0.00 3.77
2989 3590 6.116806 TCACAGCAGTACTTCTAAAAACCAA 58.883 36.000 0.00 0.00 0.00 3.67
2990 3591 5.676552 TCACAGCAGTACTTCTAAAAACCA 58.323 37.500 0.00 0.00 0.00 3.67
2991 3592 6.037830 TGTTCACAGCAGTACTTCTAAAAACC 59.962 38.462 0.00 0.00 0.00 3.27
2999 3600 3.365364 GCCAATGTTCACAGCAGTACTTC 60.365 47.826 0.00 0.00 0.00 3.01
3018 3619 1.306141 CCCTAGGAGGTCAGTGCCA 60.306 63.158 11.48 0.00 31.93 4.92
3020 3621 0.614979 TCACCCTAGGAGGTCAGTGC 60.615 60.000 11.48 0.00 38.39 4.40
3081 3690 2.500888 CTACGCGATCGAGAGCATAAG 58.499 52.381 25.85 8.40 39.41 1.73
3115 3724 8.539770 AGATTTGACATGATATGGTATCGAAC 57.460 34.615 0.00 0.00 33.60 3.95
3197 3815 4.568760 TGCGCAAACGAGTATGATTCATAA 59.431 37.500 8.16 0.00 43.93 1.90


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

AutoCloner maintained by Alex Coulton.