Multiple sequence alignment - TraesCS3A01G193200

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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 TraesCS3A01G193200 chr3A 100.000 7017 0 0 1 7017 261354747 261347731 0.000000e+00 12959.0
1 TraesCS3A01G193200 chr3A 91.433 2136 174 5 992 3122 249860852 249858721 0.000000e+00 2922.0
2 TraesCS3A01G193200 chr3A 92.268 582 40 2 3998 4579 249858024 249857448 0.000000e+00 821.0
3 TraesCS3A01G193200 chr3A 91.827 208 17 0 5810 6017 249854697 249854490 2.480000e-74 291.0
4 TraesCS3A01G193200 chr3A 86.861 137 11 6 5105 5239 249854914 249854783 5.670000e-31 147.0
5 TraesCS3A01G193200 chr3B 97.798 3905 64 12 827 4727 275345980 275342094 0.000000e+00 6715.0
6 TraesCS3A01G193200 chr3B 94.578 2324 87 13 4719 7016 275338804 275336494 0.000000e+00 3557.0
7 TraesCS3A01G193200 chr3B 90.393 2238 187 18 905 3122 274521404 274519175 0.000000e+00 2916.0
8 TraesCS3A01G193200 chr3B 91.753 582 43 2 3998 4579 274518415 274517839 0.000000e+00 804.0
9 TraesCS3A01G193200 chr3B 91.346 208 18 0 5810 6017 274517138 274516931 1.150000e-72 285.0
10 TraesCS3A01G193200 chr3B 86.861 137 11 6 5105 5239 274517355 274517224 5.670000e-31 147.0
11 TraesCS3A01G193200 chr3D 96.518 3418 90 13 3224 6628 190255955 190259356 0.000000e+00 5626.0
12 TraesCS3A01G193200 chr3D 98.143 2369 33 4 827 3191 190253594 190255955 0.000000e+00 4120.0
13 TraesCS3A01G193200 chr3D 90.259 2238 190 18 905 3122 189452255 189454484 0.000000e+00 2900.0
14 TraesCS3A01G193200 chr3D 93.519 540 35 0 3998 4537 189455245 189455784 0.000000e+00 804.0
15 TraesCS3A01G193200 chr3D 92.909 550 39 0 5 554 418110862 418110313 0.000000e+00 800.0
16 TraesCS3A01G193200 chr3D 91.346 208 18 0 5810 6017 189456519 189456726 1.150000e-72 285.0
17 TraesCS3A01G193200 chr3D 81.090 312 33 17 6401 6698 406835577 406835278 7.080000e-55 226.0
18 TraesCS3A01G193200 chr3D 91.589 107 7 2 5135 5239 189456327 189456433 5.670000e-31 147.0
19 TraesCS3A01G193200 chr4D 93.682 554 35 0 1 554 220528981 220529534 0.000000e+00 830.0
20 TraesCS3A01G193200 chr4D 93.490 553 36 0 1 553 284225305 284225857 0.000000e+00 822.0
21 TraesCS3A01G193200 chr4D 93.141 554 38 0 1 554 101510853 101510300 0.000000e+00 813.0
22 TraesCS3A01G193200 chr4D 92.238 554 42 1 1 554 22613889 22613337 0.000000e+00 784.0
23 TraesCS3A01G193200 chr4D 92.238 554 42 1 1 554 311499749 311499197 0.000000e+00 784.0
24 TraesCS3A01G193200 chr4D 92.166 217 14 2 555 771 418725800 418725587 3.180000e-78 303.0
25 TraesCS3A01G193200 chr1D 92.780 554 39 1 1 554 74523020 74522468 0.000000e+00 800.0
26 TraesCS3A01G193200 chr1D 92.252 555 41 2 1 554 356106814 356107367 0.000000e+00 785.0
27 TraesCS3A01G193200 chr5D 92.599 554 38 3 1 554 266111254 266111804 0.000000e+00 793.0
28 TraesCS3A01G193200 chr5D 80.000 610 99 12 6428 7017 432932101 432931495 5.030000e-116 429.0
29 TraesCS3A01G193200 chr5D 78.571 588 98 16 6455 7017 336336703 336337287 5.170000e-96 363.0
30 TraesCS3A01G193200 chr5D 77.778 594 106 12 6448 7017 336241709 336241118 6.740000e-90 342.0
31 TraesCS3A01G193200 chr6D 84.711 484 65 5 6403 6878 62620295 62620777 6.370000e-130 475.0
32 TraesCS3A01G193200 chr6D 90.196 51 5 0 6401 6451 358973904 358973954 4.540000e-07 67.6
33 TraesCS3A01G193200 chr1B 78.336 637 107 18 6401 7017 637526189 637526814 3.970000e-102 383.0
34 TraesCS3A01G193200 chr1B 90.654 107 10 0 3755 3861 301273502 301273396 7.340000e-30 143.0
35 TraesCS3A01G193200 chr2B 79.262 569 99 16 6458 7011 379146259 379146823 5.140000e-101 379.0
36 TraesCS3A01G193200 chr2B 80.545 514 73 14 6399 6889 157108689 157109198 3.090000e-98 370.0
37 TraesCS3A01G193200 chr2B 79.960 504 74 12 6399 6879 157112852 157113351 5.210000e-91 346.0
38 TraesCS3A01G193200 chr2B 91.705 217 18 0 555 771 611072110 611072326 1.140000e-77 302.0
39 TraesCS3A01G193200 chr6B 77.589 647 108 20 6403 7017 133701040 133701681 2.410000e-94 357.0
40 TraesCS3A01G193200 chr4B 94.521 219 11 1 555 772 599052278 599052496 3.140000e-88 337.0
41 TraesCS3A01G193200 chr4B 95.122 41 2 0 6403 6443 362136657 362136617 1.630000e-06 65.8
42 TraesCS3A01G193200 chr1A 94.037 218 13 0 555 772 549756462 549756679 1.460000e-86 331.0
43 TraesCS3A01G193200 chr1A 89.815 108 11 0 3755 3862 352174199 352174092 9.490000e-29 139.0
44 TraesCS3A01G193200 chr7A 93.088 217 15 0 555 771 43468904 43468688 1.140000e-82 318.0
45 TraesCS3A01G193200 chr7A 91.324 219 18 1 555 772 575610001 575610219 1.480000e-76 298.0
46 TraesCS3A01G193200 chr7A 90.385 104 10 0 3751 3854 554392258 554392361 3.410000e-28 137.0
47 TraesCS3A01G193200 chr2D 93.119 218 14 1 555 772 440613042 440612826 1.140000e-82 318.0
48 TraesCS3A01G193200 chr2D 90.909 55 3 2 6403 6457 625194091 625194039 9.760000e-09 73.1
49 TraesCS3A01G193200 chrUn 91.324 219 18 1 555 772 328254196 328254414 1.480000e-76 298.0
50 TraesCS3A01G193200 chr7D 91.244 217 19 0 555 771 489189340 489189124 5.320000e-76 296.0
51 TraesCS3A01G193200 chr7B 92.523 107 8 0 3754 3860 216938334 216938228 3.390000e-33 154.0
52 TraesCS3A01G193200 chr7B 88.991 109 11 1 3754 3861 740536725 740536617 4.420000e-27 134.0
53 TraesCS3A01G193200 chr5A 90.741 108 10 0 3755 3862 559809527 559809634 2.040000e-30 145.0
54 TraesCS3A01G193200 chr5B 90.291 103 10 0 3760 3862 501957055 501956953 1.230000e-27 135.0
55 TraesCS3A01G193200 chr6A 88.136 59 5 2 6390 6446 33536126 33536184 1.260000e-07 69.4


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 TraesCS3A01G193200 chr3A 261347731 261354747 7016 True 12959.00 12959 100.00000 1 7017 1 chr3A.!!$R1 7016
1 TraesCS3A01G193200 chr3A 249854490 249860852 6362 True 1045.25 2922 90.59725 992 6017 4 chr3A.!!$R2 5025
2 TraesCS3A01G193200 chr3B 275336494 275345980 9486 True 5136.00 6715 96.18800 827 7016 2 chr3B.!!$R2 6189
3 TraesCS3A01G193200 chr3B 274516931 274521404 4473 True 1038.00 2916 90.08825 905 6017 4 chr3B.!!$R1 5112
4 TraesCS3A01G193200 chr3D 190253594 190259356 5762 False 4873.00 5626 97.33050 827 6628 2 chr3D.!!$F2 5801
5 TraesCS3A01G193200 chr3D 189452255 189456726 4471 False 1034.00 2900 91.67825 905 6017 4 chr3D.!!$F1 5112
6 TraesCS3A01G193200 chr3D 418110313 418110862 549 True 800.00 800 92.90900 5 554 1 chr3D.!!$R2 549
7 TraesCS3A01G193200 chr4D 220528981 220529534 553 False 830.00 830 93.68200 1 554 1 chr4D.!!$F1 553
8 TraesCS3A01G193200 chr4D 284225305 284225857 552 False 822.00 822 93.49000 1 553 1 chr4D.!!$F2 552
9 TraesCS3A01G193200 chr4D 101510300 101510853 553 True 813.00 813 93.14100 1 554 1 chr4D.!!$R2 553
10 TraesCS3A01G193200 chr4D 22613337 22613889 552 True 784.00 784 92.23800 1 554 1 chr4D.!!$R1 553
11 TraesCS3A01G193200 chr4D 311499197 311499749 552 True 784.00 784 92.23800 1 554 1 chr4D.!!$R3 553
12 TraesCS3A01G193200 chr1D 74522468 74523020 552 True 800.00 800 92.78000 1 554 1 chr1D.!!$R1 553
13 TraesCS3A01G193200 chr1D 356106814 356107367 553 False 785.00 785 92.25200 1 554 1 chr1D.!!$F1 553
14 TraesCS3A01G193200 chr5D 266111254 266111804 550 False 793.00 793 92.59900 1 554 1 chr5D.!!$F1 553
15 TraesCS3A01G193200 chr5D 432931495 432932101 606 True 429.00 429 80.00000 6428 7017 1 chr5D.!!$R2 589
16 TraesCS3A01G193200 chr5D 336336703 336337287 584 False 363.00 363 78.57100 6455 7017 1 chr5D.!!$F2 562
17 TraesCS3A01G193200 chr5D 336241118 336241709 591 True 342.00 342 77.77800 6448 7017 1 chr5D.!!$R1 569
18 TraesCS3A01G193200 chr1B 637526189 637526814 625 False 383.00 383 78.33600 6401 7017 1 chr1B.!!$F1 616
19 TraesCS3A01G193200 chr2B 379146259 379146823 564 False 379.00 379 79.26200 6458 7011 1 chr2B.!!$F1 553
20 TraesCS3A01G193200 chr2B 157108689 157113351 4662 False 358.00 370 80.25250 6399 6889 2 chr2B.!!$F3 490
21 TraesCS3A01G193200 chr6B 133701040 133701681 641 False 357.00 357 77.58900 6403 7017 1 chr6B.!!$F1 614

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
721 723 0.030101 GCTAGCCTACGAGCAGACTG 59.970 60.000 2.29 0.0 43.38 3.51 F
2063 2078 0.462047 CGTAATGTGGAGGAGGTGGC 60.462 60.000 0.00 0.0 0.00 5.01 F
3053 3071 1.163554 CACCTCAAGAGCAGAAAGGC 58.836 55.000 0.00 0.0 0.00 4.35 F
3727 3867 3.244976 GTGAAATGGACCAATTGCTTCG 58.755 45.455 0.00 0.0 0.00 3.79 F
4486 4627 1.337354 TGCGCAGATGTTACTTTCCGA 60.337 47.619 5.66 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2127 0.037605 GACGGTACTCACCACCCTTG 60.038 60.000 0.00 0.00 46.14 3.61 R
3118 3137 0.459063 GCCAGCTGCCAATTAAGCAC 60.459 55.000 8.66 3.21 42.06 4.40 R
3932 4072 1.133458 GCAGCACGCTAGCAAGTTC 59.867 57.895 16.45 0.00 37.77 3.01 R
4758 8198 5.633473 TGGGGGATATAAGTCTATGACCT 57.367 43.478 0.00 0.00 32.18 3.85 R
6316 12103 0.981183 AATGGAGGTCGGTAGCACAA 59.019 50.000 0.00 0.00 0.00 3.33 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
304 306 5.411361 TCGTTGATCAAAGATGGTTAAGGTG 59.589 40.000 18.50 0.00 0.00 4.00
341 343 4.153958 TGTGTTGTCATTTGATAACGGC 57.846 40.909 13.29 10.04 45.39 5.68
343 345 3.911964 GTGTTGTCATTTGATAACGGCAC 59.088 43.478 13.29 5.15 45.39 5.01
356 358 0.107214 ACGGCACCACATCATTAGGG 60.107 55.000 0.00 0.00 0.00 3.53
414 416 7.698130 GCTTAGCATAATGATCGTTCAGTTTTT 59.302 33.333 2.72 0.00 34.73 1.94
438 440 5.556355 TGCTATTGCTTTCTTCATGTCAG 57.444 39.130 0.00 0.00 40.48 3.51
441 443 6.183360 TGCTATTGCTTTCTTCATGTCAGATG 60.183 38.462 0.00 0.00 40.48 2.90
459 461 7.176690 TGTCAGATGCATATTCCTTCGACTATA 59.823 37.037 0.00 0.00 0.00 1.31
522 524 6.148645 TGTGCTATCAAATGTCACAACGTAAT 59.851 34.615 0.00 0.00 35.08 1.89
571 573 9.959721 ATAGGTATCATTATTGGACATTGTACC 57.040 33.333 0.00 0.00 0.00 3.34
572 574 7.811282 AGGTATCATTATTGGACATTGTACCA 58.189 34.615 0.00 0.52 32.37 3.25
573 575 7.719633 AGGTATCATTATTGGACATTGTACCAC 59.280 37.037 0.00 0.00 35.81 4.16
574 576 7.500892 GGTATCATTATTGGACATTGTACCACA 59.499 37.037 0.00 0.00 35.81 4.17
575 577 6.751514 TCATTATTGGACATTGTACCACAC 57.248 37.500 0.00 0.00 35.81 3.82
576 578 6.480763 TCATTATTGGACATTGTACCACACT 58.519 36.000 0.00 0.00 35.81 3.55
577 579 6.945435 TCATTATTGGACATTGTACCACACTT 59.055 34.615 0.00 0.00 35.81 3.16
578 580 7.450014 TCATTATTGGACATTGTACCACACTTT 59.550 33.333 0.00 0.00 35.81 2.66
579 581 8.735315 CATTATTGGACATTGTACCACACTTTA 58.265 33.333 0.00 0.00 35.81 1.85
580 582 8.871629 TTATTGGACATTGTACCACACTTTAT 57.128 30.769 0.00 0.00 35.81 1.40
581 583 7.775053 ATTGGACATTGTACCACACTTTATT 57.225 32.000 0.00 0.00 35.81 1.40
582 584 7.589958 TTGGACATTGTACCACACTTTATTT 57.410 32.000 0.00 0.00 35.81 1.40
583 585 7.209471 TGGACATTGTACCACACTTTATTTC 57.791 36.000 0.00 0.00 0.00 2.17
584 586 7.001674 TGGACATTGTACCACACTTTATTTCT 58.998 34.615 0.00 0.00 0.00 2.52
585 587 7.504238 TGGACATTGTACCACACTTTATTTCTT 59.496 33.333 0.00 0.00 0.00 2.52
586 588 8.357402 GGACATTGTACCACACTTTATTTCTTT 58.643 33.333 0.00 0.00 0.00 2.52
587 589 9.744468 GACATTGTACCACACTTTATTTCTTTT 57.256 29.630 0.00 0.00 0.00 2.27
590 592 8.844441 TTGTACCACACTTTATTTCTTTTTCG 57.156 30.769 0.00 0.00 0.00 3.46
591 593 7.419204 TGTACCACACTTTATTTCTTTTTCGG 58.581 34.615 0.00 0.00 0.00 4.30
592 594 6.459670 ACCACACTTTATTTCTTTTTCGGT 57.540 33.333 0.00 0.00 0.00 4.69
593 595 6.869695 ACCACACTTTATTTCTTTTTCGGTT 58.130 32.000 0.00 0.00 0.00 4.44
594 596 6.976349 ACCACACTTTATTTCTTTTTCGGTTC 59.024 34.615 0.00 0.00 0.00 3.62
595 597 6.141685 CCACACTTTATTTCTTTTTCGGTTCG 59.858 38.462 0.00 0.00 0.00 3.95
596 598 6.908284 CACACTTTATTTCTTTTTCGGTTCGA 59.092 34.615 0.00 0.00 0.00 3.71
597 599 6.908820 ACACTTTATTTCTTTTTCGGTTCGAC 59.091 34.615 0.00 0.00 34.89 4.20
598 600 6.908284 CACTTTATTTCTTTTTCGGTTCGACA 59.092 34.615 0.00 0.00 34.89 4.35
599 601 7.589954 CACTTTATTTCTTTTTCGGTTCGACAT 59.410 33.333 0.00 0.00 34.89 3.06
600 602 7.589954 ACTTTATTTCTTTTTCGGTTCGACATG 59.410 33.333 0.00 0.00 34.89 3.21
601 603 4.886247 TTTCTTTTTCGGTTCGACATGT 57.114 36.364 0.00 0.00 34.89 3.21
602 604 4.461992 TTCTTTTTCGGTTCGACATGTC 57.538 40.909 16.21 16.21 34.89 3.06
618 620 6.345920 GACATGTCGGTAGGAACTTAAATG 57.654 41.667 10.69 0.00 41.75 2.32
619 621 5.801380 ACATGTCGGTAGGAACTTAAATGT 58.199 37.500 0.00 0.00 41.75 2.71
620 622 5.642063 ACATGTCGGTAGGAACTTAAATGTG 59.358 40.000 0.00 0.00 41.75 3.21
621 623 3.998341 TGTCGGTAGGAACTTAAATGTGC 59.002 43.478 0.00 0.00 41.75 4.57
622 624 3.373130 GTCGGTAGGAACTTAAATGTGCC 59.627 47.826 0.00 0.00 41.75 5.01
623 625 2.350498 CGGTAGGAACTTAAATGTGCCG 59.650 50.000 0.00 0.00 40.60 5.69
624 626 2.681344 GGTAGGAACTTAAATGTGCCGG 59.319 50.000 0.00 0.00 40.60 6.13
625 627 1.173913 AGGAACTTAAATGTGCCGGC 58.826 50.000 22.73 22.73 40.60 6.13
626 628 0.172578 GGAACTTAAATGTGCCGGCC 59.827 55.000 26.77 16.24 0.00 6.13
627 629 0.172578 GAACTTAAATGTGCCGGCCC 59.827 55.000 26.77 14.61 0.00 5.80
628 630 0.540830 AACTTAAATGTGCCGGCCCA 60.541 50.000 26.77 21.41 0.00 5.36
629 631 0.324275 ACTTAAATGTGCCGGCCCAT 60.324 50.000 26.77 22.99 0.00 4.00
630 632 0.385390 CTTAAATGTGCCGGCCCATC 59.615 55.000 25.07 12.46 0.00 3.51
631 633 0.323816 TTAAATGTGCCGGCCCATCA 60.324 50.000 25.07 17.58 0.00 3.07
632 634 1.034838 TAAATGTGCCGGCCCATCAC 61.035 55.000 25.07 15.79 0.00 3.06
633 635 2.786512 AAATGTGCCGGCCCATCACT 62.787 55.000 25.07 6.82 0.00 3.41
634 636 4.720902 TGTGCCGGCCCATCACTG 62.721 66.667 26.77 0.00 0.00 3.66
635 637 4.722700 GTGCCGGCCCATCACTGT 62.723 66.667 26.77 0.00 0.00 3.55
636 638 4.720902 TGCCGGCCCATCACTGTG 62.721 66.667 26.77 0.17 0.00 3.66
638 640 4.415150 CCGGCCCATCACTGTGCT 62.415 66.667 2.12 0.00 0.00 4.40
639 641 2.821366 CGGCCCATCACTGTGCTC 60.821 66.667 2.12 0.00 0.00 4.26
640 642 2.352422 GGCCCATCACTGTGCTCA 59.648 61.111 2.12 0.00 0.00 4.26
641 643 1.748122 GGCCCATCACTGTGCTCAG 60.748 63.158 14.08 14.08 46.18 3.35
642 644 2.404995 GCCCATCACTGTGCTCAGC 61.405 63.158 15.50 0.00 44.77 4.26
643 645 2.104859 CCCATCACTGTGCTCAGCG 61.105 63.158 15.50 6.58 44.77 5.18
644 646 1.375140 CCATCACTGTGCTCAGCGT 60.375 57.895 15.50 0.00 44.77 5.07
645 647 1.632948 CCATCACTGTGCTCAGCGTG 61.633 60.000 15.50 8.54 44.77 5.34
646 648 2.031516 ATCACTGTGCTCAGCGTGC 61.032 57.895 15.50 0.00 44.77 5.34
647 649 3.720193 CACTGTGCTCAGCGTGCC 61.720 66.667 15.50 0.00 44.77 5.01
648 650 3.933722 ACTGTGCTCAGCGTGCCT 61.934 61.111 15.50 0.00 44.77 4.75
649 651 3.420606 CTGTGCTCAGCGTGCCTG 61.421 66.667 2.32 0.00 43.17 4.85
650 652 4.240103 TGTGCTCAGCGTGCCTGT 62.240 61.111 0.00 0.00 42.38 4.00
651 653 2.048222 GTGCTCAGCGTGCCTGTA 60.048 61.111 0.00 0.00 42.38 2.74
652 654 2.048222 TGCTCAGCGTGCCTGTAC 60.048 61.111 0.00 0.00 42.38 2.90
653 655 3.181967 GCTCAGCGTGCCTGTACG 61.182 66.667 3.32 3.32 46.28 3.67
659 661 4.185413 CGTGCCTGTACGCTTGAT 57.815 55.556 0.00 0.00 37.24 2.57
660 662 1.709760 CGTGCCTGTACGCTTGATG 59.290 57.895 0.00 0.00 37.24 3.07
661 663 1.695893 CGTGCCTGTACGCTTGATGG 61.696 60.000 0.00 0.00 37.24 3.51
662 664 1.078497 TGCCTGTACGCTTGATGGG 60.078 57.895 0.00 0.00 0.00 4.00
663 665 1.220749 GCCTGTACGCTTGATGGGA 59.779 57.895 0.00 0.00 0.00 4.37
664 666 1.090052 GCCTGTACGCTTGATGGGAC 61.090 60.000 0.00 0.00 0.00 4.46
665 667 0.806102 CCTGTACGCTTGATGGGACG 60.806 60.000 0.00 0.00 0.00 4.79
666 668 0.806102 CTGTACGCTTGATGGGACGG 60.806 60.000 0.00 0.00 0.00 4.79
667 669 1.252215 TGTACGCTTGATGGGACGGA 61.252 55.000 0.00 0.00 0.00 4.69
668 670 0.104304 GTACGCTTGATGGGACGGAT 59.896 55.000 0.00 0.00 0.00 4.18
669 671 1.338973 GTACGCTTGATGGGACGGATA 59.661 52.381 0.00 0.00 0.00 2.59
670 672 0.389391 ACGCTTGATGGGACGGATAG 59.611 55.000 0.00 0.00 0.00 2.08
671 673 0.389391 CGCTTGATGGGACGGATAGT 59.611 55.000 0.00 0.00 0.00 2.12
672 674 1.202533 CGCTTGATGGGACGGATAGTT 60.203 52.381 0.00 0.00 0.00 2.24
673 675 2.213499 GCTTGATGGGACGGATAGTTG 58.787 52.381 0.00 0.00 0.00 3.16
674 676 2.838736 CTTGATGGGACGGATAGTTGG 58.161 52.381 0.00 0.00 0.00 3.77
675 677 0.468226 TGATGGGACGGATAGTTGGC 59.532 55.000 0.00 0.00 0.00 4.52
676 678 0.759346 GATGGGACGGATAGTTGGCT 59.241 55.000 0.00 0.00 0.00 4.75
677 679 1.968493 GATGGGACGGATAGTTGGCTA 59.032 52.381 0.00 0.00 0.00 3.93
678 680 1.410004 TGGGACGGATAGTTGGCTAG 58.590 55.000 0.00 0.00 0.00 3.42
679 681 1.342674 TGGGACGGATAGTTGGCTAGT 60.343 52.381 0.00 0.00 0.00 2.57
680 682 1.761198 GGGACGGATAGTTGGCTAGTT 59.239 52.381 0.00 0.00 0.00 2.24
681 683 2.483188 GGGACGGATAGTTGGCTAGTTG 60.483 54.545 0.00 0.00 0.00 3.16
682 684 2.167900 GGACGGATAGTTGGCTAGTTGT 59.832 50.000 0.00 0.00 0.00 3.32
683 685 3.369157 GGACGGATAGTTGGCTAGTTGTT 60.369 47.826 0.00 0.00 0.00 2.83
684 686 4.142093 GGACGGATAGTTGGCTAGTTGTTA 60.142 45.833 0.00 0.00 0.00 2.41
685 687 5.007385 ACGGATAGTTGGCTAGTTGTTAG 57.993 43.478 0.00 0.00 0.00 2.34
697 699 3.595190 AGTTGTTAGCCCAGTTTTCCT 57.405 42.857 0.00 0.00 0.00 3.36
698 700 4.717279 AGTTGTTAGCCCAGTTTTCCTA 57.283 40.909 0.00 0.00 0.00 2.94
699 701 4.395625 AGTTGTTAGCCCAGTTTTCCTAC 58.604 43.478 0.00 0.00 0.00 3.18
700 702 3.048337 TGTTAGCCCAGTTTTCCTACG 57.952 47.619 0.00 0.00 0.00 3.51
701 703 2.369532 TGTTAGCCCAGTTTTCCTACGT 59.630 45.455 0.00 0.00 0.00 3.57
702 704 2.740447 GTTAGCCCAGTTTTCCTACGTG 59.260 50.000 0.00 0.00 0.00 4.49
703 705 0.605589 AGCCCAGTTTTCCTACGTGC 60.606 55.000 0.00 0.00 0.00 5.34
704 706 0.605589 GCCCAGTTTTCCTACGTGCT 60.606 55.000 0.00 0.00 0.00 4.40
705 707 1.338389 GCCCAGTTTTCCTACGTGCTA 60.338 52.381 0.00 0.00 0.00 3.49
706 708 2.618053 CCCAGTTTTCCTACGTGCTAG 58.382 52.381 0.00 0.00 0.00 3.42
707 709 2.000447 CCAGTTTTCCTACGTGCTAGC 59.000 52.381 8.10 8.10 0.00 3.42
708 710 2.000447 CAGTTTTCCTACGTGCTAGCC 59.000 52.381 13.29 2.49 0.00 3.93
709 711 1.900486 AGTTTTCCTACGTGCTAGCCT 59.100 47.619 13.29 0.00 0.00 4.58
710 712 3.094572 AGTTTTCCTACGTGCTAGCCTA 58.905 45.455 13.29 0.00 0.00 3.93
711 713 3.119209 AGTTTTCCTACGTGCTAGCCTAC 60.119 47.826 13.29 3.43 0.00 3.18
712 714 1.019673 TTCCTACGTGCTAGCCTACG 58.980 55.000 21.93 21.93 45.19 3.51
713 715 0.178767 TCCTACGTGCTAGCCTACGA 59.821 55.000 28.10 14.14 42.54 3.43
714 716 0.587285 CCTACGTGCTAGCCTACGAG 59.413 60.000 28.10 20.34 42.54 4.18
715 717 0.041135 CTACGTGCTAGCCTACGAGC 60.041 60.000 28.10 0.00 44.10 5.03
720 722 2.410466 GCTAGCCTACGAGCAGACT 58.590 57.895 2.29 0.00 43.38 3.24
721 723 0.030101 GCTAGCCTACGAGCAGACTG 59.970 60.000 2.29 0.00 43.38 3.51
722 724 1.384525 CTAGCCTACGAGCAGACTGT 58.615 55.000 3.99 0.00 34.23 3.55
723 725 2.562635 CTAGCCTACGAGCAGACTGTA 58.437 52.381 3.99 0.00 34.23 2.74
724 726 1.835494 AGCCTACGAGCAGACTGTAA 58.165 50.000 3.99 0.00 34.23 2.41
725 727 1.473278 AGCCTACGAGCAGACTGTAAC 59.527 52.381 3.99 0.00 34.23 2.50
726 728 1.469423 GCCTACGAGCAGACTGTAACC 60.469 57.143 3.99 0.00 0.00 2.85
727 729 1.202154 CCTACGAGCAGACTGTAACCG 60.202 57.143 3.99 5.51 0.00 4.44
728 730 1.736126 CTACGAGCAGACTGTAACCGA 59.264 52.381 3.99 0.00 0.00 4.69
729 731 1.174783 ACGAGCAGACTGTAACCGAT 58.825 50.000 3.99 0.00 0.00 4.18
730 732 1.544691 ACGAGCAGACTGTAACCGATT 59.455 47.619 3.99 0.00 0.00 3.34
731 733 2.029290 ACGAGCAGACTGTAACCGATTT 60.029 45.455 3.99 0.00 0.00 2.17
732 734 2.993899 CGAGCAGACTGTAACCGATTTT 59.006 45.455 3.99 0.00 0.00 1.82
733 735 3.432252 CGAGCAGACTGTAACCGATTTTT 59.568 43.478 3.99 0.00 0.00 1.94
734 736 4.666655 CGAGCAGACTGTAACCGATTTTTG 60.667 45.833 3.99 0.00 0.00 2.44
735 737 4.134563 AGCAGACTGTAACCGATTTTTGT 58.865 39.130 3.99 0.00 0.00 2.83
736 738 4.578928 AGCAGACTGTAACCGATTTTTGTT 59.421 37.500 3.99 0.00 0.00 2.83
737 739 5.761234 AGCAGACTGTAACCGATTTTTGTTA 59.239 36.000 3.99 0.00 0.00 2.41
738 740 6.430000 AGCAGACTGTAACCGATTTTTGTTAT 59.570 34.615 3.99 0.00 30.35 1.89
739 741 7.040686 AGCAGACTGTAACCGATTTTTGTTATT 60.041 33.333 3.99 0.00 30.35 1.40
740 742 8.231837 GCAGACTGTAACCGATTTTTGTTATTA 58.768 33.333 3.99 0.00 30.35 0.98
766 768 9.627123 ATGAATAAGGTCCTAAATTCGATGAAA 57.373 29.630 16.55 4.62 32.23 2.69
767 769 9.456147 TGAATAAGGTCCTAAATTCGATGAAAA 57.544 29.630 16.55 1.85 32.23 2.29
789 791 5.806955 AAAAACTCATATTCCCCTACCCA 57.193 39.130 0.00 0.00 0.00 4.51
790 792 5.806955 AAAACTCATATTCCCCTACCCAA 57.193 39.130 0.00 0.00 0.00 4.12
791 793 5.806955 AAACTCATATTCCCCTACCCAAA 57.193 39.130 0.00 0.00 0.00 3.28
792 794 6.355588 AAACTCATATTCCCCTACCCAAAT 57.644 37.500 0.00 0.00 0.00 2.32
793 795 5.324832 ACTCATATTCCCCTACCCAAATG 57.675 43.478 0.00 0.00 0.00 2.32
794 796 4.731929 ACTCATATTCCCCTACCCAAATGT 59.268 41.667 0.00 0.00 0.00 2.71
795 797 5.195756 ACTCATATTCCCCTACCCAAATGTT 59.804 40.000 0.00 0.00 0.00 2.71
796 798 6.098716 TCATATTCCCCTACCCAAATGTTT 57.901 37.500 0.00 0.00 0.00 2.83
797 799 7.091720 ACTCATATTCCCCTACCCAAATGTTTA 60.092 37.037 0.00 0.00 0.00 2.01
798 800 7.064229 TCATATTCCCCTACCCAAATGTTTAC 58.936 38.462 0.00 0.00 0.00 2.01
799 801 3.743092 TCCCCTACCCAAATGTTTACC 57.257 47.619 0.00 0.00 0.00 2.85
800 802 2.994581 TCCCCTACCCAAATGTTTACCA 59.005 45.455 0.00 0.00 0.00 3.25
801 803 3.401683 TCCCCTACCCAAATGTTTACCAA 59.598 43.478 0.00 0.00 0.00 3.67
802 804 4.140758 TCCCCTACCCAAATGTTTACCAAA 60.141 41.667 0.00 0.00 0.00 3.28
803 805 4.020928 CCCCTACCCAAATGTTTACCAAAC 60.021 45.833 0.00 0.00 41.73 2.93
814 816 4.830826 GTTTACCAAACAAGCTGCTAGT 57.169 40.909 0.90 0.00 41.04 2.57
815 817 5.934935 GTTTACCAAACAAGCTGCTAGTA 57.065 39.130 0.90 0.00 41.04 1.82
816 818 6.496338 GTTTACCAAACAAGCTGCTAGTAT 57.504 37.500 0.90 0.00 41.04 2.12
817 819 7.605410 GTTTACCAAACAAGCTGCTAGTATA 57.395 36.000 0.90 0.00 41.04 1.47
818 820 8.036273 GTTTACCAAACAAGCTGCTAGTATAA 57.964 34.615 0.90 0.00 41.04 0.98
819 821 8.508875 GTTTACCAAACAAGCTGCTAGTATAAA 58.491 33.333 0.90 0.02 41.04 1.40
820 822 6.496338 ACCAAACAAGCTGCTAGTATAAAC 57.504 37.500 0.90 0.00 0.00 2.01
821 823 6.238648 ACCAAACAAGCTGCTAGTATAAACT 58.761 36.000 0.90 0.00 39.91 2.66
822 824 6.715264 ACCAAACAAGCTGCTAGTATAAACTT 59.285 34.615 0.90 0.00 37.15 2.66
823 825 7.230712 ACCAAACAAGCTGCTAGTATAAACTTT 59.769 33.333 0.90 0.00 37.15 2.66
824 826 8.082242 CCAAACAAGCTGCTAGTATAAACTTTT 58.918 33.333 0.90 0.00 37.15 2.27
825 827 9.463443 CAAACAAGCTGCTAGTATAAACTTTTT 57.537 29.630 0.90 0.00 37.15 1.94
1338 1353 0.901580 ACCCCAACGAGTACATCCGT 60.902 55.000 0.00 0.00 41.14 4.69
1688 1703 0.676184 GCCGCAGTAGATCTCATCCA 59.324 55.000 0.00 0.00 0.00 3.41
1709 1724 4.344865 GGTCTGCCGCCCTCCAAA 62.345 66.667 0.00 0.00 0.00 3.28
1710 1725 3.056328 GTCTGCCGCCCTCCAAAC 61.056 66.667 0.00 0.00 0.00 2.93
1711 1726 4.344865 TCTGCCGCCCTCCAAACC 62.345 66.667 0.00 0.00 0.00 3.27
2063 2078 0.462047 CGTAATGTGGAGGAGGTGGC 60.462 60.000 0.00 0.00 0.00 5.01
2112 2127 1.271597 ACACAATCAGGGGAGCTTGAC 60.272 52.381 0.00 0.00 0.00 3.18
2273 2288 4.084066 TGTGTTATTTGTGCGTGAGATCAC 60.084 41.667 2.78 2.78 43.15 3.06
2896 2914 3.829948 CTTTGCAACACTGGTGATGATC 58.170 45.455 13.72 0.00 35.69 2.92
3053 3071 1.163554 CACCTCAAGAGCAGAAAGGC 58.836 55.000 0.00 0.00 0.00 4.35
3244 3269 8.553459 AAGTTATTGCATAGCATATGGAGTAC 57.447 34.615 4.56 0.00 38.76 2.73
3312 3337 4.337555 AGTCAGCATTTGTATCTTGCATCC 59.662 41.667 0.00 0.00 38.84 3.51
3313 3338 4.096833 GTCAGCATTTGTATCTTGCATCCA 59.903 41.667 0.00 0.00 38.84 3.41
3315 3340 3.635373 AGCATTTGTATCTTGCATCCAGG 59.365 43.478 0.00 0.00 38.84 4.45
3316 3341 3.797865 GCATTTGTATCTTGCATCCAGGC 60.798 47.826 0.00 0.00 36.40 4.85
3627 3755 9.937876 TTGTCTAGATTTTTCTAGGAGGATAGA 57.062 33.333 9.50 0.00 39.95 1.98
3727 3867 3.244976 GTGAAATGGACCAATTGCTTCG 58.755 45.455 0.00 0.00 0.00 3.79
3863 4003 4.836125 TTTCCCGACGGATGTAGTATAC 57.164 45.455 17.49 0.00 38.24 1.47
3932 4072 2.646930 TGGTGAGCTCATAATTGCCAG 58.353 47.619 21.47 0.00 0.00 4.85
4486 4627 1.337354 TGCGCAGATGTTACTTTCCGA 60.337 47.619 5.66 0.00 0.00 4.55
4630 4771 9.362539 CAGCTGATTACAAAATTTGCTTAATCT 57.637 29.630 20.15 6.89 34.13 2.40
4844 8285 6.209391 AGTTATTTGCTGAAATACTGTTGCCT 59.791 34.615 0.00 0.00 34.41 4.75
4861 8302 3.832527 TGCCTTTTTAGCTTCTGACCTT 58.167 40.909 0.00 0.00 0.00 3.50
4863 8304 5.381757 TGCCTTTTTAGCTTCTGACCTTTA 58.618 37.500 0.00 0.00 0.00 1.85
4917 8358 9.308000 ACTTTGTGGGTTATTTCTTATCAATCA 57.692 29.630 0.00 0.00 0.00 2.57
5272 11026 1.462616 TCGTATGCTGCCTTGCAAAT 58.537 45.000 0.00 0.00 46.61 2.32
5622 11386 5.846203 ACTGAGCATAAAATTGCACAAACT 58.154 33.333 0.00 0.00 45.23 2.66
5784 11556 6.209192 TGTGCAGTCCATTGTTTATCTGATTT 59.791 34.615 0.00 0.00 0.00 2.17
5933 11720 1.009829 CGATGGCAAGCTTAGTGGTC 58.990 55.000 0.00 0.00 0.00 4.02
5971 11758 0.320771 AGACACAAGGAATCGCGCTT 60.321 50.000 5.56 0.00 0.00 4.68
6062 11849 4.764823 ACACCGGATTGTATGACATGTTTT 59.235 37.500 9.46 0.00 0.00 2.43
6132 11919 9.468532 GGATTGATTGAATTAATTACAGGAAGC 57.531 33.333 0.00 0.00 0.00 3.86
6144 11931 6.952773 ATTACAGGAAGCTTTTGTGTACAA 57.047 33.333 21.19 11.72 0.00 2.41
6232 12019 2.910688 TCTTGACACTTCCTTTCGCT 57.089 45.000 0.00 0.00 0.00 4.93
6321 12108 9.224267 ACAGGTAGATCAATTATGATATTGTGC 57.776 33.333 0.00 0.00 46.30 4.57
6445 12252 2.504367 CAAATCTGACCCCTCAAACGT 58.496 47.619 0.00 0.00 0.00 3.99
6497 12309 7.447594 AGCCTCAAATTTTCAATCTCACAATT 58.552 30.769 0.00 0.00 0.00 2.32
6501 12313 9.431887 CTCAAATTTTCAATCTCACAATTGGAT 57.568 29.630 10.83 0.00 37.27 3.41
6634 16636 5.397360 TGGCTATGGTAGAGAAGATCATCA 58.603 41.667 0.10 0.00 0.00 3.07
6636 16638 6.499699 TGGCTATGGTAGAGAAGATCATCAAT 59.500 38.462 0.10 0.00 0.00 2.57
6655 16661 3.185203 ACTGCCCTTGCCCTTCCA 61.185 61.111 0.00 0.00 36.33 3.53
6714 16720 4.322049 CGAAGACACAGTAGGGATCAAGTT 60.322 45.833 0.00 0.00 0.00 2.66
6734 16740 1.649815 GATCTGCTCGTCGTCGGAT 59.350 57.895 1.55 9.99 37.69 4.18
6735 16741 0.029567 GATCTGCTCGTCGTCGGATT 59.970 55.000 1.55 0.00 37.69 3.01
6817 16824 2.496341 CGATTCTGCTCTCGGGCA 59.504 61.111 0.00 0.00 40.15 5.36
6879 16886 2.032860 GCGCAGATGGCTTCCTCCTA 62.033 60.000 0.30 0.00 41.67 2.94
6918 16935 3.381983 ATCAGCCGTCGCCTGTCA 61.382 61.111 2.83 0.00 34.57 3.58
6948 16965 2.193248 GCCTCGGCTGCCCTTATT 59.807 61.111 14.12 0.00 38.26 1.40
6963 16980 3.976654 CCCTTATTCTCTCCTTCCCATGA 59.023 47.826 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.334583 ACACCAATAGTTCACATCGCT 57.665 42.857 0.00 0.00 0.00 4.93
107 109 3.137360 GGGCATATTTCCTTCAGTCTCCT 59.863 47.826 0.00 0.00 0.00 3.69
241 243 3.592059 TCACTAGGAACACGGTATTTGC 58.408 45.455 0.00 0.00 0.00 3.68
304 306 5.488341 ACAACACATGTCTATGGTTAGGAC 58.512 41.667 0.00 0.00 37.96 3.85
356 358 3.629398 GGTCTTGTCCATCACATCATTCC 59.371 47.826 0.00 0.00 33.90 3.01
414 416 6.207221 TCTGACATGAAGAAAGCAATAGCAAA 59.793 34.615 0.00 0.00 45.49 3.68
438 440 9.593134 AATCTTATAGTCGAAGGAATATGCATC 57.407 33.333 0.19 0.00 34.57 3.91
459 461 5.063880 GGTATTCGGGAGTTGCATAATCTT 58.936 41.667 0.00 0.00 0.00 2.40
492 494 5.062528 TGTGACATTTGATAGCACACAAGA 58.937 37.500 0.00 0.00 34.85 3.02
554 556 7.775053 AAAGTGTGGTACAATGTCCAATAAT 57.225 32.000 6.21 0.00 44.16 1.28
555 557 8.871629 ATAAAGTGTGGTACAATGTCCAATAA 57.128 30.769 6.21 0.00 44.16 1.40
556 558 8.871629 AATAAAGTGTGGTACAATGTCCAATA 57.128 30.769 6.21 0.00 44.16 1.90
557 559 7.775053 AATAAAGTGTGGTACAATGTCCAAT 57.225 32.000 6.21 0.00 44.16 3.16
558 560 7.504238 AGAAATAAAGTGTGGTACAATGTCCAA 59.496 33.333 6.21 0.00 44.16 3.53
559 561 7.001674 AGAAATAAAGTGTGGTACAATGTCCA 58.998 34.615 0.00 0.00 44.16 4.02
560 562 7.448748 AGAAATAAAGTGTGGTACAATGTCC 57.551 36.000 0.00 0.00 44.16 4.02
561 563 9.744468 AAAAGAAATAAAGTGTGGTACAATGTC 57.256 29.630 0.00 0.00 44.16 3.06
564 566 9.458374 CGAAAAAGAAATAAAGTGTGGTACAAT 57.542 29.630 0.00 0.00 44.16 2.71
565 567 7.916450 CCGAAAAAGAAATAAAGTGTGGTACAA 59.084 33.333 0.00 0.00 44.16 2.41
566 568 7.067251 ACCGAAAAAGAAATAAAGTGTGGTACA 59.933 33.333 0.00 0.00 0.00 2.90
567 569 7.420002 ACCGAAAAAGAAATAAAGTGTGGTAC 58.580 34.615 0.00 0.00 0.00 3.34
568 570 7.571080 ACCGAAAAAGAAATAAAGTGTGGTA 57.429 32.000 0.00 0.00 0.00 3.25
569 571 6.459670 ACCGAAAAAGAAATAAAGTGTGGT 57.540 33.333 0.00 0.00 0.00 4.16
570 572 6.141685 CGAACCGAAAAAGAAATAAAGTGTGG 59.858 38.462 0.00 0.00 0.00 4.17
571 573 6.908284 TCGAACCGAAAAAGAAATAAAGTGTG 59.092 34.615 0.00 0.00 31.06 3.82
572 574 6.908820 GTCGAACCGAAAAAGAAATAAAGTGT 59.091 34.615 0.00 0.00 37.72 3.55
573 575 6.908284 TGTCGAACCGAAAAAGAAATAAAGTG 59.092 34.615 0.00 0.00 37.72 3.16
574 576 7.018635 TGTCGAACCGAAAAAGAAATAAAGT 57.981 32.000 0.00 0.00 37.72 2.66
575 577 7.589954 ACATGTCGAACCGAAAAAGAAATAAAG 59.410 33.333 0.00 0.00 37.72 1.85
576 578 7.419204 ACATGTCGAACCGAAAAAGAAATAAA 58.581 30.769 0.00 0.00 37.72 1.40
577 579 6.961576 ACATGTCGAACCGAAAAAGAAATAA 58.038 32.000 0.00 0.00 37.72 1.40
578 580 6.548441 ACATGTCGAACCGAAAAAGAAATA 57.452 33.333 0.00 0.00 37.72 1.40
579 581 5.432885 ACATGTCGAACCGAAAAAGAAAT 57.567 34.783 0.00 0.00 37.72 2.17
580 582 4.839796 GACATGTCGAACCGAAAAAGAAA 58.160 39.130 10.69 0.00 37.72 2.52
581 583 4.461992 GACATGTCGAACCGAAAAAGAA 57.538 40.909 10.69 0.00 37.72 2.52
595 597 5.873164 ACATTTAAGTTCCTACCGACATGTC 59.127 40.000 16.21 16.21 0.00 3.06
596 598 5.642063 CACATTTAAGTTCCTACCGACATGT 59.358 40.000 0.00 0.00 0.00 3.21
597 599 5.447279 GCACATTTAAGTTCCTACCGACATG 60.447 44.000 0.00 0.00 0.00 3.21
598 600 4.634443 GCACATTTAAGTTCCTACCGACAT 59.366 41.667 0.00 0.00 0.00 3.06
599 601 3.998341 GCACATTTAAGTTCCTACCGACA 59.002 43.478 0.00 0.00 0.00 4.35
600 602 3.373130 GGCACATTTAAGTTCCTACCGAC 59.627 47.826 0.00 0.00 0.00 4.79
601 603 3.602483 GGCACATTTAAGTTCCTACCGA 58.398 45.455 0.00 0.00 0.00 4.69
602 604 2.350498 CGGCACATTTAAGTTCCTACCG 59.650 50.000 0.00 0.00 0.00 4.02
603 605 2.681344 CCGGCACATTTAAGTTCCTACC 59.319 50.000 0.00 0.00 0.00 3.18
604 606 2.096980 GCCGGCACATTTAAGTTCCTAC 59.903 50.000 24.80 0.00 0.00 3.18
605 607 2.361789 GCCGGCACATTTAAGTTCCTA 58.638 47.619 24.80 0.00 0.00 2.94
606 608 1.173913 GCCGGCACATTTAAGTTCCT 58.826 50.000 24.80 0.00 0.00 3.36
607 609 0.172578 GGCCGGCACATTTAAGTTCC 59.827 55.000 30.85 0.98 0.00 3.62
608 610 0.172578 GGGCCGGCACATTTAAGTTC 59.827 55.000 30.85 5.46 0.00 3.01
609 611 0.540830 TGGGCCGGCACATTTAAGTT 60.541 50.000 31.83 0.00 0.00 2.66
610 612 0.324275 ATGGGCCGGCACATTTAAGT 60.324 50.000 38.42 17.45 36.54 2.24
611 613 0.385390 GATGGGCCGGCACATTTAAG 59.615 55.000 42.70 0.00 40.62 1.85
612 614 0.323816 TGATGGGCCGGCACATTTAA 60.324 50.000 42.70 28.47 40.62 1.52
613 615 1.034838 GTGATGGGCCGGCACATTTA 61.035 55.000 42.70 31.21 40.62 1.40
614 616 2.037049 TGATGGGCCGGCACATTT 59.963 55.556 42.70 26.22 40.62 2.32
615 617 2.755469 GTGATGGGCCGGCACATT 60.755 61.111 42.70 27.38 40.62 2.71
616 618 3.731728 AGTGATGGGCCGGCACAT 61.732 61.111 43.45 43.45 43.66 3.21
617 619 4.720902 CAGTGATGGGCCGGCACA 62.721 66.667 37.41 37.41 35.08 4.57
618 620 4.722700 ACAGTGATGGGCCGGCAC 62.723 66.667 30.85 28.40 0.00 5.01
619 621 4.720902 CACAGTGATGGGCCGGCA 62.721 66.667 30.85 9.36 0.00 5.69
621 623 4.415150 AGCACAGTGATGGGCCGG 62.415 66.667 4.15 0.00 39.45 6.13
622 624 2.821366 GAGCACAGTGATGGGCCG 60.821 66.667 4.15 0.00 39.45 6.13
623 625 1.748122 CTGAGCACAGTGATGGGCC 60.748 63.158 4.15 0.00 39.45 5.80
624 626 2.404995 GCTGAGCACAGTGATGGGC 61.405 63.158 12.89 0.48 45.04 5.36
625 627 3.900855 GCTGAGCACAGTGATGGG 58.099 61.111 12.89 0.00 45.04 4.00
631 633 3.933722 AGGCACGCTGAGCACAGT 61.934 61.111 12.89 0.00 45.04 3.55
632 634 2.770132 TACAGGCACGCTGAGCACAG 62.770 60.000 4.88 6.80 45.91 3.66
633 635 2.866726 TACAGGCACGCTGAGCACA 61.867 57.895 4.88 0.00 0.00 4.57
634 636 2.048222 TACAGGCACGCTGAGCAC 60.048 61.111 4.88 0.00 0.00 4.40
635 637 2.048222 GTACAGGCACGCTGAGCA 60.048 61.111 4.88 0.00 0.00 4.26
636 638 3.181967 CGTACAGGCACGCTGAGC 61.182 66.667 0.00 0.00 34.78 4.26
642 644 1.695893 CCATCAAGCGTACAGGCACG 61.696 60.000 0.00 0.00 44.71 5.34
643 645 1.369091 CCCATCAAGCGTACAGGCAC 61.369 60.000 0.00 0.00 34.64 5.01
644 646 1.078497 CCCATCAAGCGTACAGGCA 60.078 57.895 0.00 0.00 34.64 4.75
645 647 1.090052 GTCCCATCAAGCGTACAGGC 61.090 60.000 0.00 0.00 0.00 4.85
646 648 0.806102 CGTCCCATCAAGCGTACAGG 60.806 60.000 0.00 0.00 0.00 4.00
647 649 0.806102 CCGTCCCATCAAGCGTACAG 60.806 60.000 0.00 0.00 0.00 2.74
648 650 1.216977 CCGTCCCATCAAGCGTACA 59.783 57.895 0.00 0.00 0.00 2.90
649 651 0.104304 ATCCGTCCCATCAAGCGTAC 59.896 55.000 0.00 0.00 0.00 3.67
650 652 1.611977 CTATCCGTCCCATCAAGCGTA 59.388 52.381 0.00 0.00 0.00 4.42
651 653 0.389391 CTATCCGTCCCATCAAGCGT 59.611 55.000 0.00 0.00 0.00 5.07
652 654 0.389391 ACTATCCGTCCCATCAAGCG 59.611 55.000 0.00 0.00 0.00 4.68
653 655 2.213499 CAACTATCCGTCCCATCAAGC 58.787 52.381 0.00 0.00 0.00 4.01
654 656 2.838736 CCAACTATCCGTCCCATCAAG 58.161 52.381 0.00 0.00 0.00 3.02
655 657 1.134220 GCCAACTATCCGTCCCATCAA 60.134 52.381 0.00 0.00 0.00 2.57
656 658 0.468226 GCCAACTATCCGTCCCATCA 59.532 55.000 0.00 0.00 0.00 3.07
657 659 0.759346 AGCCAACTATCCGTCCCATC 59.241 55.000 0.00 0.00 0.00 3.51
658 660 1.971357 CTAGCCAACTATCCGTCCCAT 59.029 52.381 0.00 0.00 0.00 4.00
659 661 1.342674 ACTAGCCAACTATCCGTCCCA 60.343 52.381 0.00 0.00 0.00 4.37
660 662 1.411041 ACTAGCCAACTATCCGTCCC 58.589 55.000 0.00 0.00 0.00 4.46
661 663 2.167900 ACAACTAGCCAACTATCCGTCC 59.832 50.000 0.00 0.00 0.00 4.79
662 664 3.521947 ACAACTAGCCAACTATCCGTC 57.478 47.619 0.00 0.00 0.00 4.79
663 665 3.975168 AACAACTAGCCAACTATCCGT 57.025 42.857 0.00 0.00 0.00 4.69
664 666 3.802685 GCTAACAACTAGCCAACTATCCG 59.197 47.826 0.00 0.00 46.46 4.18
675 677 4.652822 AGGAAAACTGGGCTAACAACTAG 58.347 43.478 0.00 0.00 0.00 2.57
676 678 4.717279 AGGAAAACTGGGCTAACAACTA 57.283 40.909 0.00 0.00 0.00 2.24
677 679 3.595190 AGGAAAACTGGGCTAACAACT 57.405 42.857 0.00 0.00 0.00 3.16
678 680 3.187842 CGTAGGAAAACTGGGCTAACAAC 59.812 47.826 0.00 0.00 0.00 3.32
679 681 3.181452 ACGTAGGAAAACTGGGCTAACAA 60.181 43.478 0.00 0.00 0.00 2.83
680 682 2.369532 ACGTAGGAAAACTGGGCTAACA 59.630 45.455 0.00 0.00 0.00 2.41
681 683 2.740447 CACGTAGGAAAACTGGGCTAAC 59.260 50.000 0.00 0.00 0.00 2.34
682 684 2.872842 GCACGTAGGAAAACTGGGCTAA 60.873 50.000 0.00 0.00 0.00 3.09
683 685 1.338389 GCACGTAGGAAAACTGGGCTA 60.338 52.381 0.00 0.00 0.00 3.93
684 686 0.605589 GCACGTAGGAAAACTGGGCT 60.606 55.000 0.00 0.00 0.00 5.19
685 687 0.605589 AGCACGTAGGAAAACTGGGC 60.606 55.000 0.00 0.00 0.00 5.36
686 688 2.618053 CTAGCACGTAGGAAAACTGGG 58.382 52.381 0.00 0.00 0.00 4.45
687 689 2.000447 GCTAGCACGTAGGAAAACTGG 59.000 52.381 10.63 0.00 0.00 4.00
688 690 2.000447 GGCTAGCACGTAGGAAAACTG 59.000 52.381 18.24 0.00 0.00 3.16
689 691 1.900486 AGGCTAGCACGTAGGAAAACT 59.100 47.619 18.24 0.00 0.00 2.66
690 692 2.381725 AGGCTAGCACGTAGGAAAAC 57.618 50.000 18.24 0.00 0.00 2.43
691 693 2.159338 CGTAGGCTAGCACGTAGGAAAA 60.159 50.000 18.24 0.00 33.56 2.29
692 694 1.402968 CGTAGGCTAGCACGTAGGAAA 59.597 52.381 18.24 0.00 33.56 3.13
693 695 1.019673 CGTAGGCTAGCACGTAGGAA 58.980 55.000 18.24 0.00 33.56 3.36
694 696 0.178767 TCGTAGGCTAGCACGTAGGA 59.821 55.000 22.33 15.17 39.18 2.94
695 697 0.587285 CTCGTAGGCTAGCACGTAGG 59.413 60.000 22.33 13.49 39.18 3.18
696 698 0.041135 GCTCGTAGGCTAGCACGTAG 60.041 60.000 22.33 18.70 39.18 3.51
697 699 0.745486 TGCTCGTAGGCTAGCACGTA 60.745 55.000 22.33 11.54 43.56 3.57
698 700 1.994507 CTGCTCGTAGGCTAGCACGT 61.995 60.000 22.33 7.89 43.56 4.49
699 701 1.298713 CTGCTCGTAGGCTAGCACG 60.299 63.158 18.24 18.47 43.56 5.34
700 702 0.248702 GTCTGCTCGTAGGCTAGCAC 60.249 60.000 18.24 6.06 43.56 4.40
701 703 0.394488 AGTCTGCTCGTAGGCTAGCA 60.394 55.000 18.24 9.89 46.11 3.49
702 704 0.030101 CAGTCTGCTCGTAGGCTAGC 59.970 60.000 6.04 6.04 39.25 3.42
703 705 1.384525 ACAGTCTGCTCGTAGGCTAG 58.615 55.000 0.00 0.00 29.98 3.42
704 706 2.681848 GTTACAGTCTGCTCGTAGGCTA 59.318 50.000 0.00 0.00 29.98 3.93
705 707 1.473278 GTTACAGTCTGCTCGTAGGCT 59.527 52.381 0.00 0.00 31.53 4.58
706 708 1.469423 GGTTACAGTCTGCTCGTAGGC 60.469 57.143 0.00 0.00 0.00 3.93
707 709 1.202154 CGGTTACAGTCTGCTCGTAGG 60.202 57.143 0.00 0.00 0.00 3.18
708 710 1.736126 TCGGTTACAGTCTGCTCGTAG 59.264 52.381 0.00 0.00 0.00 3.51
709 711 1.812235 TCGGTTACAGTCTGCTCGTA 58.188 50.000 0.00 0.00 0.00 3.43
710 712 1.174783 ATCGGTTACAGTCTGCTCGT 58.825 50.000 0.00 0.00 0.00 4.18
711 713 2.279582 AATCGGTTACAGTCTGCTCG 57.720 50.000 0.00 0.00 0.00 5.03
712 714 4.213482 ACAAAAATCGGTTACAGTCTGCTC 59.787 41.667 0.00 0.00 0.00 4.26
713 715 4.134563 ACAAAAATCGGTTACAGTCTGCT 58.865 39.130 0.00 0.00 0.00 4.24
714 716 4.483476 ACAAAAATCGGTTACAGTCTGC 57.517 40.909 0.00 0.00 0.00 4.26
740 742 9.627123 TTTCATCGAATTTAGGACCTTATTCAT 57.373 29.630 20.44 13.59 0.00 2.57
741 743 9.456147 TTTTCATCGAATTTAGGACCTTATTCA 57.544 29.630 20.44 12.51 0.00 2.57
767 769 5.806955 TGGGTAGGGGAATATGAGTTTTT 57.193 39.130 0.00 0.00 0.00 1.94
768 770 5.806955 TTGGGTAGGGGAATATGAGTTTT 57.193 39.130 0.00 0.00 0.00 2.43
769 771 5.806955 TTTGGGTAGGGGAATATGAGTTT 57.193 39.130 0.00 0.00 0.00 2.66
770 772 5.195756 ACATTTGGGTAGGGGAATATGAGTT 59.804 40.000 0.00 0.00 0.00 3.01
771 773 4.731929 ACATTTGGGTAGGGGAATATGAGT 59.268 41.667 0.00 0.00 0.00 3.41
772 774 5.324832 ACATTTGGGTAGGGGAATATGAG 57.675 43.478 0.00 0.00 0.00 2.90
773 775 5.742562 AACATTTGGGTAGGGGAATATGA 57.257 39.130 0.00 0.00 0.00 2.15
774 776 6.266786 GGTAAACATTTGGGTAGGGGAATATG 59.733 42.308 0.00 0.00 0.00 1.78
775 777 6.068140 TGGTAAACATTTGGGTAGGGGAATAT 60.068 38.462 0.00 0.00 0.00 1.28
776 778 5.255679 TGGTAAACATTTGGGTAGGGGAATA 59.744 40.000 0.00 0.00 0.00 1.75
777 779 4.046103 TGGTAAACATTTGGGTAGGGGAAT 59.954 41.667 0.00 0.00 0.00 3.01
778 780 3.401683 TGGTAAACATTTGGGTAGGGGAA 59.598 43.478 0.00 0.00 0.00 3.97
779 781 2.994581 TGGTAAACATTTGGGTAGGGGA 59.005 45.455 0.00 0.00 0.00 4.81
780 782 3.459710 TGGTAAACATTTGGGTAGGGG 57.540 47.619 0.00 0.00 0.00 4.79
781 783 4.589374 TGTTTGGTAAACATTTGGGTAGGG 59.411 41.667 3.20 0.00 45.79 3.53
782 784 5.793030 TGTTTGGTAAACATTTGGGTAGG 57.207 39.130 3.20 0.00 45.79 3.18
793 795 4.830826 ACTAGCAGCTTGTTTGGTAAAC 57.169 40.909 0.00 0.00 41.73 2.01
794 796 8.508875 GTTTATACTAGCAGCTTGTTTGGTAAA 58.491 33.333 14.96 11.72 0.00 2.01
795 797 7.881232 AGTTTATACTAGCAGCTTGTTTGGTAA 59.119 33.333 14.96 7.13 31.21 2.85
796 798 7.391620 AGTTTATACTAGCAGCTTGTTTGGTA 58.608 34.615 14.96 0.00 31.21 3.25
797 799 6.238648 AGTTTATACTAGCAGCTTGTTTGGT 58.761 36.000 14.96 2.65 31.21 3.67
798 800 6.743575 AGTTTATACTAGCAGCTTGTTTGG 57.256 37.500 14.96 0.00 31.21 3.28
799 801 9.463443 AAAAAGTTTATACTAGCAGCTTGTTTG 57.537 29.630 14.96 0.00 33.17 2.93
867 869 8.674925 TGTTCCTATATATATTCCTTTCGGGT 57.325 34.615 0.00 0.00 36.25 5.28
868 870 9.379791 GTTGTTCCTATATATATTCCTTTCGGG 57.620 37.037 0.00 0.00 0.00 5.14
875 877 8.625467 AGGGGAGTTGTTCCTATATATATTCC 57.375 38.462 0.00 0.00 45.98 3.01
887 890 0.328592 GGGAAGAGGGGAGTTGTTCC 59.671 60.000 0.00 0.00 46.00 3.62
2063 2078 3.868077 CACCTCCTTCTTGAGATAAAGCG 59.132 47.826 0.00 0.00 34.11 4.68
2112 2127 0.037605 GACGGTACTCACCACCCTTG 60.038 60.000 0.00 0.00 46.14 3.61
2273 2288 3.055530 ACACAGCTTGGGATTAGTCTCAG 60.056 47.826 0.00 0.00 35.91 3.35
2735 2753 4.499696 CCTTGTTTGCTTCAACCTTCGATT 60.500 41.667 0.00 0.00 0.00 3.34
2850 2868 3.181445 ACCTCACACAAAGCACAATCCTA 60.181 43.478 0.00 0.00 0.00 2.94
2883 2901 2.102757 CCTCCTCAGATCATCACCAGTG 59.897 54.545 0.00 0.00 0.00 3.66
2896 2914 2.205022 TGCAACCAAATCCTCCTCAG 57.795 50.000 0.00 0.00 0.00 3.35
3118 3137 0.459063 GCCAGCTGCCAATTAAGCAC 60.459 55.000 8.66 3.21 42.06 4.40
3244 3269 3.204306 TGCCTGGATGCAAGATAAGAG 57.796 47.619 0.00 0.00 38.56 2.85
3302 3327 2.092049 TCATTCTGCCTGGATGCAAGAT 60.092 45.455 0.00 0.00 41.51 2.40
3312 3337 4.923871 GGTATACACGTATCATTCTGCCTG 59.076 45.833 5.01 0.00 0.00 4.85
3313 3338 4.587262 TGGTATACACGTATCATTCTGCCT 59.413 41.667 5.01 0.00 0.00 4.75
3315 3340 5.926542 ACATGGTATACACGTATCATTCTGC 59.073 40.000 5.01 0.00 0.00 4.26
3316 3341 7.327032 CAGACATGGTATACACGTATCATTCTG 59.673 40.741 5.01 9.15 0.00 3.02
3863 4003 7.909121 CAGATAATTTCTACTGAAGCTTTGCTG 59.091 37.037 0.00 0.00 33.83 4.41
3907 4047 3.252701 GCAATTATGAGCTCACCATCCAG 59.747 47.826 20.97 7.27 0.00 3.86
3932 4072 1.133458 GCAGCACGCTAGCAAGTTC 59.867 57.895 16.45 0.00 37.77 3.01
4486 4627 3.642848 ACTCAAATTCTGCCCACATGTTT 59.357 39.130 0.00 0.00 0.00 2.83
4757 8197 6.746456 TGGGGGATATAAGTCTATGACCTA 57.254 41.667 0.00 0.00 32.18 3.08
4758 8198 5.633473 TGGGGGATATAAGTCTATGACCT 57.367 43.478 0.00 0.00 32.18 3.85
4759 8199 6.697641 TTTGGGGGATATAAGTCTATGACC 57.302 41.667 0.00 0.00 32.18 4.02
4844 8285 7.230510 TCAGCAATAAAGGTCAGAAGCTAAAAA 59.769 33.333 0.00 0.00 31.54 1.94
4917 8358 8.043113 TCTGATATAAAGAACTCACACAAGCAT 58.957 33.333 0.00 0.00 0.00 3.79
5665 11429 9.205513 AGAATAATGAAAACTGATGCCCTATTT 57.794 29.630 0.00 0.00 0.00 1.40
5784 11556 4.459390 TCGGAAATTCCATTACAGACGA 57.541 40.909 13.04 0.00 35.91 4.20
5933 11720 5.064452 GTGTCTTGCTCCTTATTCTGATGTG 59.936 44.000 0.00 0.00 0.00 3.21
5971 11758 5.727630 AGGGTAATCTTATCTCCCAAGCTA 58.272 41.667 0.00 0.00 40.48 3.32
6062 11849 2.639347 TGGCAAGTGGATCTCTTGAAGA 59.361 45.455 24.29 0.00 43.17 2.87
6232 12019 7.506114 ACGCCATTTATCAAGAAAGACCTATA 58.494 34.615 0.00 0.00 0.00 1.31
6316 12103 0.981183 AATGGAGGTCGGTAGCACAA 59.019 50.000 0.00 0.00 0.00 3.33
6320 12107 3.963428 ATATGAATGGAGGTCGGTAGC 57.037 47.619 0.00 0.00 0.00 3.58
6321 12108 8.191446 CAGTATTATATGAATGGAGGTCGGTAG 58.809 40.741 0.00 0.00 0.00 3.18
6497 12309 7.797121 TGAGATATGCTAATTGAGGTATCCA 57.203 36.000 0.00 0.00 0.00 3.41
6501 12313 8.659527 TGGATTTGAGATATGCTAATTGAGGTA 58.340 33.333 0.00 0.00 0.00 3.08
6621 16623 4.444591 GGGCAGTCATTGATGATCTTCTCT 60.445 45.833 9.75 0.00 39.30 3.10
6634 16636 0.613012 GAAGGGCAAGGGCAGTCATT 60.613 55.000 0.00 0.00 43.71 2.57
6636 16638 2.436109 GAAGGGCAAGGGCAGTCA 59.564 61.111 0.00 0.00 43.71 3.41
6698 16704 4.163078 CAGATCCAACTTGATCCCTACTGT 59.837 45.833 0.00 0.00 41.73 3.55
6714 16720 2.761195 CCGACGACGAGCAGATCCA 61.761 63.158 9.28 0.00 42.66 3.41
6734 16740 0.176219 ACAACGACGGTGAGGACAAA 59.824 50.000 21.82 0.00 0.00 2.83
6735 16741 0.249155 GACAACGACGGTGAGGACAA 60.249 55.000 21.82 0.00 0.00 3.18
6793 16800 2.892425 GAGCAGAATCGGGCGGTG 60.892 66.667 0.00 0.00 34.54 4.94
6918 16935 2.586792 GAGGCCCGTCTCATTGCT 59.413 61.111 0.00 0.00 34.13 3.91
6948 16965 2.901975 CCGTCATGGGAAGGAGAGA 58.098 57.895 0.00 0.00 44.47 3.10
6982 16999 0.680061 GGGGCAGACTATAACTCCCG 59.320 60.000 0.00 0.00 34.63 5.14


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

AutoCloner maintained by Alex Coulton.