Multiple sequence alignment - TraesCS2A01G075800

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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 TraesCS2A01G075800 chr2A 100.000 7745 0 0 1 7745 33702785 33695041 0.000000e+00 14303.0
1 TraesCS2A01G075800 chr2A 86.607 448 54 3 4533 4975 448502301 448501855 2.510000e-134 490.0
2 TraesCS2A01G075800 chr2A 94.393 214 12 0 5832 6045 33696918 33696705 5.790000e-86 329.0
3 TraesCS2A01G075800 chr2A 94.393 214 12 0 5868 6081 33696954 33696741 5.790000e-86 329.0
4 TraesCS2A01G075800 chr2A 94.944 178 9 0 5832 6009 33696882 33696705 5.920000e-71 279.0
5 TraesCS2A01G075800 chr2D 94.685 5136 179 38 1885 6978 31810795 31805712 0.000000e+00 7886.0
6 TraesCS2A01G075800 chr2D 87.897 1008 68 20 874 1862 31811742 31810770 0.000000e+00 1136.0
7 TraesCS2A01G075800 chr2D 90.261 729 42 12 5899 6622 31823689 31824393 0.000000e+00 926.0
8 TraesCS2A01G075800 chr2D 89.680 688 48 4 7041 7726 592079577 592078911 0.000000e+00 856.0
9 TraesCS2A01G075800 chr2D 88.872 656 49 11 4998 5633 31822422 31823073 0.000000e+00 785.0
10 TraesCS2A01G075800 chr2D 81.575 749 100 20 1 734 31816980 31816255 1.120000e-162 584.0
11 TraesCS2A01G075800 chr2D 94.022 368 19 3 5646 6011 31823509 31823875 8.780000e-154 555.0
12 TraesCS2A01G075800 chr2D 93.458 214 14 0 5832 6045 31806816 31806603 1.250000e-82 318.0
13 TraesCS2A01G075800 chr2D 92.991 214 15 0 5868 6081 31806852 31806639 5.830000e-81 313.0
14 TraesCS2A01G075800 chr2D 93.889 180 11 0 5832 6011 31806780 31806601 9.900000e-69 272.0
15 TraesCS2A01G075800 chr2D 93.820 178 11 0 5904 6081 31806852 31806675 1.280000e-67 268.0
16 TraesCS2A01G075800 chr2D 92.973 185 11 1 5863 6045 31823689 31823873 1.280000e-67 268.0
17 TraesCS2A01G075800 chr2D 93.377 151 8 1 5825 5975 31823727 31823875 1.010000e-53 222.0
18 TraesCS2A01G075800 chr2D 94.366 142 8 0 5940 6081 31806852 31806711 1.310000e-52 219.0
19 TraesCS2A01G075800 chr2D 82.383 193 24 6 6786 6975 31826370 31826555 8.040000e-35 159.0
20 TraesCS2A01G075800 chr2D 84.034 119 12 5 4999 5113 331762576 331762691 2.960000e-19 108.0
21 TraesCS2A01G075800 chr2D 82.051 117 18 3 4999 5113 249880875 249880760 6.400000e-16 97.1
22 TraesCS2A01G075800 chr2B 93.206 4033 160 40 2739 6740 51891369 51887420 0.000000e+00 5825.0
23 TraesCS2A01G075800 chr2B 91.500 1953 89 30 828 2740 51893408 51891493 0.000000e+00 2615.0
24 TraesCS2A01G075800 chr2B 85.305 803 82 12 1 792 51938439 51937662 0.000000e+00 797.0
25 TraesCS2A01G075800 chr2B 86.607 448 54 3 4533 4975 338746089 338746535 2.510000e-134 490.0
26 TraesCS2A01G075800 chr2B 83.789 475 51 12 1 467 51896682 51896226 2.000000e-115 427.0
27 TraesCS2A01G075800 chr2B 88.854 314 25 4 827 1130 51937167 51936854 2.040000e-100 377.0
28 TraesCS2A01G075800 chr2B 85.806 310 27 7 6438 6740 51959111 51959410 5.830000e-81 313.0
29 TraesCS2A01G075800 chr2B 96.407 167 6 0 5757 5923 51955709 51955875 7.660000e-70 276.0
30 TraesCS2A01G075800 chr2B 83.920 199 20 6 6786 6978 51959415 51959607 6.170000e-41 180.0
31 TraesCS2A01G075800 chr5D 91.026 702 41 5 7041 7740 460227183 460226502 0.000000e+00 928.0
32 TraesCS2A01G075800 chr5D 86.932 704 51 14 7041 7740 543752867 543752201 0.000000e+00 752.0
33 TraesCS2A01G075800 chr3D 90.504 695 44 8 7048 7740 503748842 503748168 0.000000e+00 898.0
34 TraesCS2A01G075800 chr3D 89.235 706 53 4 7037 7740 191495751 191496435 0.000000e+00 861.0
35 TraesCS2A01G075800 chr4D 89.392 707 53 7 7041 7745 260694617 260693931 0.000000e+00 870.0
36 TraesCS2A01G075800 chr4D 87.110 706 52 11 7038 7740 56722996 56723665 0.000000e+00 763.0
37 TraesCS2A01G075800 chr7D 89.601 702 35 16 7041 7740 68912285 68912950 0.000000e+00 857.0
38 TraesCS2A01G075800 chr1D 87.714 700 56 11 7042 7740 3512942 3513612 0.000000e+00 789.0
39 TraesCS2A01G075800 chr1D 82.500 120 12 7 4999 5113 409490807 409490692 6.400000e-16 97.1
40 TraesCS2A01G075800 chr7A 87.624 703 52 13 7041 7740 113429732 113429062 0.000000e+00 784.0
41 TraesCS2A01G075800 chr7A 86.809 705 61 17 7039 7740 684123664 684122989 0.000000e+00 758.0
42 TraesCS2A01G075800 chr4B 92.531 482 33 3 7261 7740 635028474 635028954 0.000000e+00 688.0
43 TraesCS2A01G075800 chr4B 86.384 448 55 3 4533 4975 28227799 28228245 1.170000e-132 484.0
44 TraesCS2A01G075800 chr4B 83.193 119 12 6 4999 5113 242711769 242711655 1.370000e-17 102.0
45 TraesCS2A01G075800 chr7B 86.607 448 54 3 4533 4975 123769542 123769096 2.510000e-134 490.0
46 TraesCS2A01G075800 chr7B 86.607 448 54 3 4533 4975 450596511 450596957 2.510000e-134 490.0
47 TraesCS2A01G075800 chr7B 86.456 443 38 4 7042 7482 694261481 694261903 4.230000e-127 466.0
48 TraesCS2A01G075800 chr7B 78.788 165 25 10 5007 5167 263111247 263111089 1.370000e-17 102.0
49 TraesCS2A01G075800 chr5B 86.607 448 54 3 4533 4975 560435857 560436303 2.510000e-134 490.0
50 TraesCS2A01G075800 chr3B 86.384 448 55 3 4533 4975 141750788 141751234 1.170000e-132 484.0
51 TraesCS2A01G075800 chr3A 83.333 126 14 6 4999 5118 633772586 633772710 8.220000e-20 110.0


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 TraesCS2A01G075800 chr2A 33695041 33702785 7744 True 14303.000000 14303 100.000000 1 7745 1 chr2A.!!$R1 7744
1 TraesCS2A01G075800 chr2D 31805712 31810795 5083 True 7886.000000 7886 94.685000 1885 6978 1 chr2D.!!$R1 5093
2 TraesCS2A01G075800 chr2D 592078911 592079577 666 True 856.000000 856 89.680000 7041 7726 1 chr2D.!!$R4 685
3 TraesCS2A01G075800 chr2D 31816255 31816980 725 True 584.000000 584 81.575000 1 734 1 chr2D.!!$R2 733
4 TraesCS2A01G075800 chr2D 31822422 31826555 4133 False 485.833333 926 90.314667 4998 6975 6 chr2D.!!$F2 1977
5 TraesCS2A01G075800 chr2D 31806601 31811742 5141 True 421.000000 1136 92.736833 874 6081 6 chr2D.!!$R5 5207
6 TraesCS2A01G075800 chr2B 51887420 51896682 9262 True 2955.666667 5825 89.498333 1 6740 3 chr2B.!!$R1 6739
7 TraesCS2A01G075800 chr2B 51936854 51938439 1585 True 587.000000 797 87.079500 1 1130 2 chr2B.!!$R2 1129
8 TraesCS2A01G075800 chr2B 51955709 51959607 3898 False 256.333333 313 88.711000 5757 6978 3 chr2B.!!$F2 1221
9 TraesCS2A01G075800 chr5D 460226502 460227183 681 True 928.000000 928 91.026000 7041 7740 1 chr5D.!!$R1 699
10 TraesCS2A01G075800 chr5D 543752201 543752867 666 True 752.000000 752 86.932000 7041 7740 1 chr5D.!!$R2 699
11 TraesCS2A01G075800 chr3D 503748168 503748842 674 True 898.000000 898 90.504000 7048 7740 1 chr3D.!!$R1 692
12 TraesCS2A01G075800 chr3D 191495751 191496435 684 False 861.000000 861 89.235000 7037 7740 1 chr3D.!!$F1 703
13 TraesCS2A01G075800 chr4D 260693931 260694617 686 True 870.000000 870 89.392000 7041 7745 1 chr4D.!!$R1 704
14 TraesCS2A01G075800 chr4D 56722996 56723665 669 False 763.000000 763 87.110000 7038 7740 1 chr4D.!!$F1 702
15 TraesCS2A01G075800 chr7D 68912285 68912950 665 False 857.000000 857 89.601000 7041 7740 1 chr7D.!!$F1 699
16 TraesCS2A01G075800 chr1D 3512942 3513612 670 False 789.000000 789 87.714000 7042 7740 1 chr1D.!!$F1 698
17 TraesCS2A01G075800 chr7A 113429062 113429732 670 True 784.000000 784 87.624000 7041 7740 1 chr7A.!!$R1 699
18 TraesCS2A01G075800 chr7A 684122989 684123664 675 True 758.000000 758 86.809000 7039 7740 1 chr7A.!!$R2 701

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
822 3337 0.593773 TGCAAAAACCGCTCGCTTTC 60.594 50.000 0.00 0.00 0.00 2.62 F
1397 4005 0.036765 GACGTTGGTGCCATGGTCTA 60.037 55.000 14.67 2.22 0.00 2.59 F
1674 4290 0.457851 CGAATGGAGGAAGACGAGCT 59.542 55.000 0.00 0.00 0.00 4.09 F
2864 5615 1.547820 TGTAGCAGTGCCTCAAGAGAG 59.452 52.381 12.58 0.00 41.72 3.20 F
3874 6638 2.143122 TCTGTGCAATCGTTGGTCTTC 58.857 47.619 0.00 0.00 0.00 2.87 F
5168 7973 0.533308 GCCCAACACCTACACACGAA 60.533 55.000 0.00 0.00 0.00 3.85 F
5254 8061 0.981183 TGTACTCTCCCATTTGGCGT 59.019 50.000 0.00 0.00 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 4285 0.321671 TCCCCTGTTTCTTCAGCTCG 59.678 55.000 0.00 0.0 34.47 5.03 R
2989 5740 0.250858 CACACAGCCCCTTCACATCA 60.251 55.000 0.00 0.0 0.00 3.07 R
3586 6344 4.598062 GTGTCAGTCAAAGCAGTAAAACC 58.402 43.478 0.00 0.0 0.00 3.27 R
4519 7310 0.403453 ATAGCCAGGCCCCATACCTT 60.403 55.000 8.22 0.0 34.42 3.50 R
5772 9026 0.032678 ACCGAGGATTCATGCTAGCG 59.967 55.000 10.77 0.0 0.00 4.26 R
6371 12180 0.247814 ATTTTCTCGCTCGCGCATTG 60.248 50.000 8.75 0.0 39.59 2.82 R
7015 14911 0.961753 CCAGACCACCAAAAAGAGGC 59.038 55.000 0.00 0.0 0.00 4.70 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
65 66 1.876849 ATGCACTCATCAGACTCCCT 58.123 50.000 0.00 0.00 0.00 4.20
106 108 6.231211 GTGAAGACTCCTCTTGGAATACAAA 58.769 40.000 0.00 0.00 42.66 2.83
110 112 5.073144 AGACTCCTCTTGGAATACAAAACCA 59.927 40.000 0.00 0.00 42.66 3.67
146 148 7.570607 AGGATTTGGAGATCAAACTATCCTACT 59.429 37.037 13.74 0.00 44.36 2.57
152 154 8.041323 TGGAGATCAAACTATCCTACTTTTGTC 58.959 37.037 0.00 0.00 32.79 3.18
178 180 2.286365 TCCCCATCAAAGTGTTGGAC 57.714 50.000 6.87 0.00 39.08 4.02
255 269 5.536161 TGGATTTCCTCTTTTGTTCTCCTTG 59.464 40.000 0.00 0.00 36.82 3.61
258 272 3.820557 TCCTCTTTTGTTCTCCTTGTGG 58.179 45.455 0.00 0.00 0.00 4.17
261 275 4.036852 CCTCTTTTGTTCTCCTTGTGGTTC 59.963 45.833 0.00 0.00 34.23 3.62
263 277 5.261216 TCTTTTGTTCTCCTTGTGGTTCTT 58.739 37.500 0.00 0.00 34.23 2.52
264 278 4.981806 TTTGTTCTCCTTGTGGTTCTTG 57.018 40.909 0.00 0.00 34.23 3.02
265 279 3.924114 TGTTCTCCTTGTGGTTCTTGA 57.076 42.857 0.00 0.00 34.23 3.02
268 282 4.821805 TGTTCTCCTTGTGGTTCTTGATTC 59.178 41.667 0.00 0.00 34.23 2.52
270 284 3.084786 CTCCTTGTGGTTCTTGATTCCC 58.915 50.000 0.00 0.00 34.23 3.97
271 285 2.716424 TCCTTGTGGTTCTTGATTCCCT 59.284 45.455 0.00 0.00 34.23 4.20
272 286 3.140144 TCCTTGTGGTTCTTGATTCCCTT 59.860 43.478 0.00 0.00 34.23 3.95
273 287 3.256631 CCTTGTGGTTCTTGATTCCCTTG 59.743 47.826 0.00 0.00 0.00 3.61
274 288 3.593442 TGTGGTTCTTGATTCCCTTGT 57.407 42.857 0.00 0.00 0.00 3.16
275 289 3.221771 TGTGGTTCTTGATTCCCTTGTG 58.778 45.455 0.00 0.00 0.00 3.33
276 290 3.222603 GTGGTTCTTGATTCCCTTGTGT 58.777 45.455 0.00 0.00 0.00 3.72
277 291 3.636764 GTGGTTCTTGATTCCCTTGTGTT 59.363 43.478 0.00 0.00 0.00 3.32
278 292 4.099419 GTGGTTCTTGATTCCCTTGTGTTT 59.901 41.667 0.00 0.00 0.00 2.83
303 317 3.758554 CCCATTTCTTCGTGTTCATCCTT 59.241 43.478 0.00 0.00 0.00 3.36
309 323 2.839486 TCGTGTTCATCCTTGAGCTT 57.161 45.000 0.00 0.00 34.45 3.74
334 348 2.025131 TCCAATTCATGATCAGGCCACA 60.025 45.455 5.01 0.00 0.00 4.17
335 349 2.963101 CCAATTCATGATCAGGCCACAT 59.037 45.455 5.01 1.94 0.00 3.21
336 350 3.005472 CCAATTCATGATCAGGCCACATC 59.995 47.826 5.01 6.22 0.00 3.06
337 351 2.353357 TTCATGATCAGGCCACATCC 57.647 50.000 5.01 0.00 0.00 3.51
419 434 2.618241 TCAACAAGCATTCTTTGAGCGT 59.382 40.909 0.00 0.00 0.00 5.07
423 438 2.975851 CAAGCATTCTTTGAGCGTGTTC 59.024 45.455 0.00 0.00 33.95 3.18
427 442 3.558505 CATTCTTTGAGCGTGTTCAAGG 58.441 45.455 2.80 2.80 38.25 3.61
433 448 2.279741 TGAGCGTGTTCAAGGCATATC 58.720 47.619 0.00 0.00 42.28 1.63
454 469 4.404640 TCGGGTCTCATCCGTCTATTTAT 58.595 43.478 2.42 0.00 46.82 1.40
455 470 4.831155 TCGGGTCTCATCCGTCTATTTATT 59.169 41.667 2.42 0.00 46.82 1.40
456 471 5.303589 TCGGGTCTCATCCGTCTATTTATTT 59.696 40.000 2.42 0.00 46.82 1.40
457 472 6.491062 TCGGGTCTCATCCGTCTATTTATTTA 59.509 38.462 2.42 0.00 46.82 1.40
469 1345 9.632969 CCGTCTATTTATTTAGATTTGTTGACG 57.367 33.333 0.00 0.00 40.07 4.35
497 1373 8.656806 TCAAGAGGGTCTTAAAGAAATGAAGTA 58.343 33.333 0.00 0.00 33.78 2.24
536 1412 1.830486 AATCAGGGCATCCATCCTCT 58.170 50.000 0.00 0.00 34.83 3.69
552 1428 4.035612 TCCTCTCAGCTAGGCGTTATAT 57.964 45.455 0.00 0.00 33.84 0.86
598 1474 2.874701 CCATTTCGAGATGGTGTGGATC 59.125 50.000 23.53 0.00 41.37 3.36
599 1475 2.691409 TTTCGAGATGGTGTGGATCC 57.309 50.000 4.20 4.20 0.00 3.36
693 1573 5.173774 ACACAAGAAGTTACATTGCACAG 57.826 39.130 0.00 0.00 0.00 3.66
701 1581 2.558359 GTTACATTGCACAGGGCTTCTT 59.442 45.455 0.00 0.00 45.15 2.52
705 1585 3.640967 ACATTGCACAGGGCTTCTTTTTA 59.359 39.130 0.00 0.00 45.15 1.52
706 1586 4.100808 ACATTGCACAGGGCTTCTTTTTAA 59.899 37.500 0.00 0.00 45.15 1.52
722 1602 6.668323 TCTTTTTAAAGCAATCCAAGAGACG 58.332 36.000 0.00 0.00 35.99 4.18
724 1604 5.607119 TTTAAAGCAATCCAAGAGACGAC 57.393 39.130 0.00 0.00 0.00 4.34
735 1615 3.194861 CAAGAGACGACACACCAAGAAA 58.805 45.455 0.00 0.00 0.00 2.52
743 1623 5.816919 ACGACACACCAAGAAAATTTACAG 58.183 37.500 0.00 0.00 0.00 2.74
747 1627 7.176589 ACACACCAAGAAAATTTACAGGAAA 57.823 32.000 0.00 0.00 0.00 3.13
750 1630 5.689961 CACCAAGAAAATTTACAGGAAACCG 59.310 40.000 0.00 0.00 0.00 4.44
754 1634 2.296073 AATTTACAGGAAACCGCCCA 57.704 45.000 0.00 0.00 0.00 5.36
758 1640 1.320507 TACAGGAAACCGCCCAAAAC 58.679 50.000 0.00 0.00 0.00 2.43
773 1655 5.673286 CGCCCAAAACGAAATTTTACAAAAC 59.327 36.000 0.00 0.00 38.50 2.43
777 1659 8.231161 CCCAAAACGAAATTTTACAAAACAGTT 58.769 29.630 0.00 0.00 38.50 3.16
779 1661 9.256715 CAAAACGAAATTTTACAAAACAGTTCC 57.743 29.630 0.00 0.00 38.50 3.62
786 1668 7.761038 ATTTTACAAAACAGTTCCTCTAGGG 57.239 36.000 0.00 0.00 35.41 3.53
792 1674 3.130734 ACAGTTCCTCTAGGGCCATAA 57.869 47.619 6.18 0.00 35.41 1.90
794 1676 3.456277 ACAGTTCCTCTAGGGCCATAAAG 59.544 47.826 6.18 0.00 35.41 1.85
795 1677 3.456277 CAGTTCCTCTAGGGCCATAAAGT 59.544 47.826 6.18 0.00 35.41 2.66
796 1678 3.456277 AGTTCCTCTAGGGCCATAAAGTG 59.544 47.826 6.18 0.00 35.41 3.16
805 2104 1.749063 GGCCATAAAGTGTACCCTTGC 59.251 52.381 0.00 0.00 0.00 4.01
811 3326 5.694458 CCATAAAGTGTACCCTTGCAAAAAC 59.306 40.000 0.00 0.00 0.00 2.43
822 3337 0.593773 TGCAAAAACCGCTCGCTTTC 60.594 50.000 0.00 0.00 0.00 2.62
823 3338 1.275471 GCAAAAACCGCTCGCTTTCC 61.275 55.000 0.00 0.00 0.00 3.13
825 3340 1.441732 AAAAACCGCTCGCTTTCCGT 61.442 50.000 0.00 0.00 38.35 4.69
857 3427 4.643387 GCCTCACGTGCCACCCTT 62.643 66.667 11.67 0.00 0.00 3.95
1126 3710 4.463788 CCAATGGCCACCCCCTCC 62.464 72.222 8.16 0.00 0.00 4.30
1127 3711 4.820744 CAATGGCCACCCCCTCCG 62.821 72.222 8.16 0.00 0.00 4.63
1332 3925 2.668632 CAGGTTCGCCCCTGCTTA 59.331 61.111 7.18 0.00 45.19 3.09
1344 3942 0.610174 CCTGCTTACTCTGTCCTGCA 59.390 55.000 0.00 0.00 0.00 4.41
1396 4004 1.302511 GACGTTGGTGCCATGGTCT 60.303 57.895 14.67 0.00 0.00 3.85
1397 4005 0.036765 GACGTTGGTGCCATGGTCTA 60.037 55.000 14.67 2.22 0.00 2.59
1398 4006 0.618458 ACGTTGGTGCCATGGTCTAT 59.382 50.000 14.67 0.00 0.00 1.98
1399 4007 1.834896 ACGTTGGTGCCATGGTCTATA 59.165 47.619 14.67 0.00 0.00 1.31
1434 4042 8.091449 CGATTCCTAGCTAATTGGAGTAGATTT 58.909 37.037 0.00 0.00 34.11 2.17
1437 4045 8.554490 TCCTAGCTAATTGGAGTAGATTTCTT 57.446 34.615 0.00 0.00 0.00 2.52
1438 4046 9.656323 TCCTAGCTAATTGGAGTAGATTTCTTA 57.344 33.333 0.00 0.00 0.00 2.10
1442 4050 9.207868 AGCTAATTGGAGTAGATTTCTTAGTCT 57.792 33.333 0.00 0.00 0.00 3.24
1471 4083 7.092079 TGACAAGATTGCTTTCATATGGTTTG 58.908 34.615 2.13 0.00 30.14 2.93
1472 4084 6.996509 ACAAGATTGCTTTCATATGGTTTGT 58.003 32.000 2.13 0.00 30.14 2.83
1473 4085 7.444299 ACAAGATTGCTTTCATATGGTTTGTT 58.556 30.769 2.13 0.00 30.14 2.83
1474 4086 8.584157 ACAAGATTGCTTTCATATGGTTTGTTA 58.416 29.630 2.13 0.00 30.14 2.41
1475 4087 9.421806 CAAGATTGCTTTCATATGGTTTGTTAA 57.578 29.630 2.13 0.00 30.14 2.01
1536 4148 6.600032 ACTGTGTTTCATGTTTTGTGGTACTA 59.400 34.615 0.00 0.00 0.00 1.82
1547 4159 6.095580 TGTTTTGTGGTACTAATTTGTCAGCA 59.904 34.615 0.00 0.00 0.00 4.41
1549 4161 5.682943 TGTGGTACTAATTTGTCAGCAAC 57.317 39.130 0.00 0.00 33.82 4.17
1550 4162 5.373222 TGTGGTACTAATTTGTCAGCAACT 58.627 37.500 0.00 0.00 33.82 3.16
1610 4226 1.552792 CCCACAGAGAGAAGGAAGACC 59.447 57.143 0.00 0.00 0.00 3.85
1647 4263 0.659957 GCCTTGGATGACGATGAAGC 59.340 55.000 0.00 0.00 0.00 3.86
1674 4290 0.457851 CGAATGGAGGAAGACGAGCT 59.542 55.000 0.00 0.00 0.00 4.09
1818 4434 2.811514 ATGGTGATGGCGGCTCGAT 61.812 57.895 11.43 0.00 0.00 3.59
1851 4467 2.504175 TCCCCTACTCTGTTTGTATGCC 59.496 50.000 0.00 0.00 0.00 4.40
1856 4472 3.402628 ACTCTGTTTGTATGCCGAACT 57.597 42.857 0.00 0.00 38.16 3.01
1900 4516 6.567959 TCTATTATCATGCTTCTATGCCGAG 58.432 40.000 0.00 0.00 0.00 4.63
2036 4654 8.426489 ACACTGGACTACACAGAGTTATTAAAA 58.574 33.333 0.00 0.00 36.58 1.52
2037 4655 9.268268 CACTGGACTACACAGAGTTATTAAAAA 57.732 33.333 0.00 0.00 39.24 1.94
2186 4804 9.994432 GAAGACAATAGAGGTCACAAATAAATG 57.006 33.333 0.00 0.00 37.74 2.32
2357 4975 6.251655 AGCTTCATGTGAGTGAGATTTTTC 57.748 37.500 0.00 0.00 0.00 2.29
2358 4976 5.766670 AGCTTCATGTGAGTGAGATTTTTCA 59.233 36.000 0.00 0.00 0.00 2.69
2360 4978 7.039923 AGCTTCATGTGAGTGAGATTTTTCAAT 60.040 33.333 0.00 0.00 0.00 2.57
2361 4979 7.061905 GCTTCATGTGAGTGAGATTTTTCAATG 59.938 37.037 0.00 0.00 0.00 2.82
2362 4980 7.514784 TCATGTGAGTGAGATTTTTCAATGT 57.485 32.000 0.00 0.00 0.00 2.71
2363 4981 7.587629 TCATGTGAGTGAGATTTTTCAATGTC 58.412 34.615 0.00 0.00 33.99 3.06
2364 4982 6.940831 TGTGAGTGAGATTTTTCAATGTCA 57.059 33.333 0.00 0.00 39.71 3.58
2380 4998 6.774084 TCAATGTCATCATGTGTTGATTACG 58.226 36.000 0.00 0.00 42.62 3.18
2472 5094 1.984026 TCAGAGCTGGGACGATGCA 60.984 57.895 0.00 0.00 0.00 3.96
2586 5211 5.575957 CAACTCAGATTTGTCCATATGTGC 58.424 41.667 1.24 0.00 0.00 4.57
2864 5615 1.547820 TGTAGCAGTGCCTCAAGAGAG 59.452 52.381 12.58 0.00 41.72 3.20
2885 5636 6.662755 AGAGTAGCCATCATTTTTACCATGA 58.337 36.000 0.00 0.00 35.12 3.07
2989 5740 6.950041 TGAATGAAGGGAAGATTTCTGAATGT 59.050 34.615 0.00 0.00 0.00 2.71
3382 6139 6.132791 TCTGTAATAAGCTACCTTCAGACG 57.867 41.667 0.00 0.00 28.79 4.18
3424 6181 4.873259 GCCTATCTTCCAAGAAGAAGTGTC 59.127 45.833 10.83 0.00 43.17 3.67
3554 6312 2.600790 CCCTAAAAACGGGGGAAAGTT 58.399 47.619 0.00 0.00 38.08 2.66
3569 6327 5.122396 GGGGAAAGTTCGCAGCTAATATATG 59.878 44.000 9.92 0.00 41.42 1.78
3609 6367 4.271687 GTTTTACTGCTTTGACTGACACG 58.728 43.478 0.00 0.00 0.00 4.49
3673 6431 8.429237 ACAAGGTCCAAAAATTATATTGACCA 57.571 30.769 8.34 0.00 33.22 4.02
3674 6432 9.045745 ACAAGGTCCAAAAATTATATTGACCAT 57.954 29.630 8.34 0.00 33.22 3.55
3730 6488 5.008911 TGTCATTGCTATTGGATGTACATGC 59.991 40.000 19.53 19.53 0.00 4.06
3739 6503 3.966979 TGGATGTACATGCACCTTCATT 58.033 40.909 24.34 0.00 34.14 2.57
3874 6638 2.143122 TCTGTGCAATCGTTGGTCTTC 58.857 47.619 0.00 0.00 0.00 2.87
3969 6733 8.961294 TCTCAGAGTATAGTTCCTACTGTTAC 57.039 38.462 0.00 0.00 35.78 2.50
3974 6738 7.774625 AGAGTATAGTTCCTACTGTTACTGGTC 59.225 40.741 0.00 0.00 36.03 4.02
4026 6790 8.347035 GGCACAGTTATACTACTTTTTGTTGAA 58.653 33.333 0.00 0.00 0.00 2.69
4027 6791 9.166126 GCACAGTTATACTACTTTTTGTTGAAC 57.834 33.333 0.00 0.00 0.00 3.18
4139 6927 7.765695 ATGTTTGGTCTGATCTTTGTTGTAT 57.234 32.000 0.00 0.00 0.00 2.29
4203 6991 4.644685 GCCCCTGCTTATTTCTGACATTAA 59.355 41.667 0.00 0.00 33.53 1.40
4227 7015 3.831323 TGTTGTTGATATGCTATGGGGG 58.169 45.455 0.00 0.00 0.00 5.40
4347 7138 9.708222 GCAGAATACAACAAGAATATTGTACTG 57.292 33.333 0.00 5.14 42.47 2.74
4414 7205 7.880160 ATTTTTATAGTACTCTTGCATGCCA 57.120 32.000 16.68 2.49 0.00 4.92
4516 7307 2.738587 TTTGTGCTTGGGAGGTGTTA 57.261 45.000 0.00 0.00 0.00 2.41
4519 7310 3.019799 TGTGCTTGGGAGGTGTTAAAA 57.980 42.857 0.00 0.00 0.00 1.52
4761 7554 2.635427 GAGGAAGTGACCCTTGAGAGTT 59.365 50.000 0.00 0.00 33.36 3.01
4773 7566 4.438744 CCCTTGAGAGTTTTGTGTGACAAC 60.439 45.833 0.00 0.00 37.90 3.32
5168 7973 0.533308 GCCCAACACCTACACACGAA 60.533 55.000 0.00 0.00 0.00 3.85
5200 8005 3.593442 TGAACTGAAAATCCTGGTGGT 57.407 42.857 0.00 0.00 34.23 4.16
5254 8061 0.981183 TGTACTCTCCCATTTGGCGT 59.019 50.000 0.00 0.00 0.00 5.68
5300 8122 8.013378 GCTGGAAACATTTGAATGAAATTGAAG 58.987 33.333 10.48 1.60 41.51 3.02
5311 8133 8.063200 TGAATGAAATTGAAGAAGATCTGCAT 57.937 30.769 2.79 0.00 36.07 3.96
5315 8138 7.088272 TGAAATTGAAGAAGATCTGCATGTTG 58.912 34.615 2.79 0.00 30.74 3.33
5317 8140 4.025040 TGAAGAAGATCTGCATGTTGGT 57.975 40.909 2.79 0.00 23.62 3.67
5514 8337 3.667497 TGTTCTACAGCAGTTCCTCTG 57.333 47.619 0.00 0.00 46.12 3.35
5648 8900 1.076332 AGCGGTCGATACAAGCAAAC 58.924 50.000 0.00 0.00 34.46 2.93
5725 8979 4.675114 CGTTGTGTGTTTCCTCTTTATTGC 59.325 41.667 0.00 0.00 0.00 3.56
5772 9026 2.439156 GCTCATGGTGGCACCTCC 60.439 66.667 34.69 12.06 39.58 4.30
5797 9051 1.134699 GCATGAATCCTCGGTCTGACA 60.135 52.381 10.38 0.00 0.00 3.58
6045 9299 9.220767 GAACCAATTAGTTCAGAGACTAACAAT 57.779 33.333 11.29 0.00 42.92 2.71
6081 9335 5.601313 ACCAACTAGTTCAGAGACTACCAAA 59.399 40.000 4.77 0.00 0.00 3.28
6231 11676 4.158025 TCGGATACTGAAACTGGAGAGAAC 59.842 45.833 0.00 0.00 0.00 3.01
6278 11723 4.942483 GGATAATGAGATGGAGAAGCATGG 59.058 45.833 0.00 0.00 0.00 3.66
6361 12170 4.508128 GAAGCACGGATCCGGCGA 62.508 66.667 35.87 0.00 44.69 5.54
6365 12174 3.822192 CACGGATCCGGCGACTGA 61.822 66.667 35.87 0.00 44.69 3.41
6367 12176 4.570663 CGGATCCGGCGACTGACC 62.571 72.222 26.95 3.44 35.56 4.02
6368 12177 4.222847 GGATCCGGCGACTGACCC 62.223 72.222 9.30 0.00 0.00 4.46
6545 12573 7.102346 TGAGAGGTAGTAGTACTGAGTTGTAC 58.898 42.308 13.29 1.02 42.09 2.90
6630 14514 3.296322 ACGTTGGTTTATGCAATGTGG 57.704 42.857 0.00 0.00 0.00 4.17
6690 14575 5.065218 AGCAAATGGACGAAGATCATTGTAC 59.935 40.000 0.00 0.00 35.10 2.90
6712 14599 1.066605 GATGCAACACATGATGCCTCC 59.933 52.381 11.11 0.00 42.26 4.30
6809 14696 8.617809 TCGATTTAGTTGAAGTTAAGCTGTTTT 58.382 29.630 0.00 0.00 0.00 2.43
6820 14707 1.021390 AGCTGTTTTCGATGGAGCGG 61.021 55.000 0.00 0.00 34.75 5.52
6824 14711 1.153353 GTTTTCGATGGAGCGGTCAA 58.847 50.000 17.59 5.30 0.00 3.18
6886 14780 1.670811 AGGTTGAGAAAACACACAGCG 59.329 47.619 0.00 0.00 0.00 5.18
6978 14874 4.882427 TCCCATAAAACAGAACAAACGTGA 59.118 37.500 0.00 0.00 0.00 4.35
6979 14875 5.357314 TCCCATAAAACAGAACAAACGTGAA 59.643 36.000 0.00 0.00 0.00 3.18
6980 14876 6.037098 CCCATAAAACAGAACAAACGTGAAA 58.963 36.000 0.00 0.00 0.00 2.69
6981 14877 6.531948 CCCATAAAACAGAACAAACGTGAAAA 59.468 34.615 0.00 0.00 0.00 2.29
6982 14878 7.063544 CCCATAAAACAGAACAAACGTGAAAAA 59.936 33.333 0.00 0.00 0.00 1.94
6983 14879 7.895767 CCATAAAACAGAACAAACGTGAAAAAC 59.104 33.333 0.00 0.00 0.00 2.43
6984 14880 6.830114 AAAACAGAACAAACGTGAAAAACA 57.170 29.167 0.00 0.00 0.00 2.83
6985 14881 7.414814 AAAACAGAACAAACGTGAAAAACAT 57.585 28.000 0.00 0.00 0.00 2.71
6986 14882 8.522178 AAAACAGAACAAACGTGAAAAACATA 57.478 26.923 0.00 0.00 0.00 2.29
6987 14883 7.734538 AACAGAACAAACGTGAAAAACATAG 57.265 32.000 0.00 0.00 0.00 2.23
6988 14884 7.079182 ACAGAACAAACGTGAAAAACATAGA 57.921 32.000 0.00 0.00 0.00 1.98
6989 14885 7.703328 ACAGAACAAACGTGAAAAACATAGAT 58.297 30.769 0.00 0.00 0.00 1.98
6990 14886 7.855904 ACAGAACAAACGTGAAAAACATAGATC 59.144 33.333 0.00 0.00 0.00 2.75
6991 14887 7.058354 CAGAACAAACGTGAAAAACATAGATCG 59.942 37.037 0.00 0.00 0.00 3.69
6992 14888 6.533819 ACAAACGTGAAAAACATAGATCGA 57.466 33.333 0.00 0.00 0.00 3.59
6993 14889 6.950545 ACAAACGTGAAAAACATAGATCGAA 58.049 32.000 0.00 0.00 0.00 3.71
6994 14890 7.411274 ACAAACGTGAAAAACATAGATCGAAA 58.589 30.769 0.00 0.00 0.00 3.46
6995 14891 7.586300 ACAAACGTGAAAAACATAGATCGAAAG 59.414 33.333 0.00 0.00 0.00 2.62
6996 14892 6.165659 ACGTGAAAAACATAGATCGAAAGG 57.834 37.500 0.00 0.00 0.00 3.11
6997 14893 5.121768 ACGTGAAAAACATAGATCGAAAGGG 59.878 40.000 0.00 0.00 0.00 3.95
6998 14894 5.350365 CGTGAAAAACATAGATCGAAAGGGA 59.650 40.000 0.00 0.00 0.00 4.20
6999 14895 6.037172 CGTGAAAAACATAGATCGAAAGGGAT 59.963 38.462 0.00 0.00 0.00 3.85
7000 14896 7.414098 CGTGAAAAACATAGATCGAAAGGGATT 60.414 37.037 0.00 0.00 0.00 3.01
7001 14897 8.244113 GTGAAAAACATAGATCGAAAGGGATTT 58.756 33.333 0.00 0.00 0.00 2.17
7002 14898 9.456147 TGAAAAACATAGATCGAAAGGGATTTA 57.544 29.630 0.00 0.00 0.00 1.40
7003 14899 9.717892 GAAAAACATAGATCGAAAGGGATTTAC 57.282 33.333 0.00 0.00 0.00 2.01
7004 14900 9.462606 AAAAACATAGATCGAAAGGGATTTACT 57.537 29.630 0.00 0.00 0.00 2.24
7007 14903 9.765795 AACATAGATCGAAAGGGATTTACTAAG 57.234 33.333 0.00 0.00 0.00 2.18
7008 14904 7.873505 ACATAGATCGAAAGGGATTTACTAAGC 59.126 37.037 0.00 0.00 0.00 3.09
7009 14905 6.235231 AGATCGAAAGGGATTTACTAAGCA 57.765 37.500 0.00 0.00 0.00 3.91
7010 14906 6.831976 AGATCGAAAGGGATTTACTAAGCAT 58.168 36.000 0.00 0.00 0.00 3.79
7011 14907 7.963532 AGATCGAAAGGGATTTACTAAGCATA 58.036 34.615 0.00 0.00 0.00 3.14
7012 14908 8.598041 AGATCGAAAGGGATTTACTAAGCATAT 58.402 33.333 0.00 0.00 0.00 1.78
7013 14909 9.220767 GATCGAAAGGGATTTACTAAGCATATT 57.779 33.333 0.00 0.00 0.00 1.28
7014 14910 8.974060 TCGAAAGGGATTTACTAAGCATATTT 57.026 30.769 0.00 0.00 0.00 1.40
7015 14911 8.836413 TCGAAAGGGATTTACTAAGCATATTTG 58.164 33.333 0.00 0.00 0.00 2.32
7029 14925 3.934579 GCATATTTGCCTCTTTTTGGTGG 59.065 43.478 0.00 0.00 43.38 4.61
7030 14926 4.563374 GCATATTTGCCTCTTTTTGGTGGT 60.563 41.667 0.00 0.00 43.38 4.16
7031 14927 3.751479 ATTTGCCTCTTTTTGGTGGTC 57.249 42.857 0.00 0.00 0.00 4.02
7032 14928 2.452600 TTGCCTCTTTTTGGTGGTCT 57.547 45.000 0.00 0.00 0.00 3.85
7033 14929 1.691196 TGCCTCTTTTTGGTGGTCTG 58.309 50.000 0.00 0.00 0.00 3.51
7034 14930 0.961753 GCCTCTTTTTGGTGGTCTGG 59.038 55.000 0.00 0.00 0.00 3.86
7035 14931 1.754201 GCCTCTTTTTGGTGGTCTGGT 60.754 52.381 0.00 0.00 0.00 4.00
7062 14958 4.803426 CACGTCGCCCTCCTCTGC 62.803 72.222 0.00 0.00 0.00 4.26
7095 14991 3.314331 CTCCCAGCGACACCCACT 61.314 66.667 0.00 0.00 0.00 4.00
7173 15069 2.046023 CGGGCTTCAGTGATGGCA 60.046 61.111 26.98 0.00 34.76 4.92
7175 15071 1.001641 GGGCTTCAGTGATGGCAGT 60.002 57.895 26.98 0.00 34.76 4.40
7243 15140 2.765807 TAGCAGCTGGAGGAGGGC 60.766 66.667 17.12 0.00 0.00 5.19
7289 15186 0.610174 AGCTTCGATCTGGACTTGCA 59.390 50.000 0.00 0.00 0.00 4.08
7598 15512 1.144969 GACGATCCGTGCACAAGAAA 58.855 50.000 18.64 0.00 41.37 2.52
7616 15530 2.905415 AACTTGATGGAGGCCATTGA 57.095 45.000 5.01 0.00 45.26 2.57
7619 15533 3.716431 ACTTGATGGAGGCCATTGAAAT 58.284 40.909 5.01 0.00 45.26 2.17
7715 15835 0.723981 GAAGGCATCGCTGTTGAGAC 59.276 55.000 0.00 0.00 0.00 3.36
7716 15836 0.035317 AAGGCATCGCTGTTGAGACA 59.965 50.000 0.00 0.00 0.00 3.41
7741 15861 3.356290 CAGGCCACTATTTGCTACCTTT 58.644 45.455 5.01 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.659925 TTTTGTGTGACATTTTGCTTATCATT 57.340 26.923 0.00 0.00 0.00 2.57
25 26 6.482641 TGCATTTTGTGTGACATTTTGCTTAT 59.517 30.769 0.00 0.00 31.74 1.73
65 66 3.820425 CCAGTAGGTGGCCCTTCA 58.180 61.111 0.00 0.00 42.66 3.02
80 81 2.398754 TCCAAGAGGAGTCTTCACCA 57.601 50.000 4.93 0.00 41.40 4.17
106 108 6.012508 TCTCCAAATCCTAAGAGATTGTGGTT 60.013 38.462 11.62 0.00 36.59 3.67
110 112 7.443302 TGATCTCCAAATCCTAAGAGATTGT 57.557 36.000 3.12 0.00 44.18 2.71
146 148 6.953520 ACTTTGATGGGGAATAGATGACAAAA 59.046 34.615 0.00 0.00 0.00 2.44
152 154 5.068198 CCAACACTTTGATGGGGAATAGATG 59.932 44.000 0.00 0.00 36.75 2.90
178 180 2.038952 TCAACACAAGAGGTCTCATGGG 59.961 50.000 4.18 4.18 37.68 4.00
255 269 3.222603 ACACAAGGGAATCAAGAACCAC 58.777 45.455 0.00 0.00 0.00 4.16
258 272 4.262036 GGGAAACACAAGGGAATCAAGAAC 60.262 45.833 0.00 0.00 0.00 3.01
261 275 2.562738 GGGGAAACACAAGGGAATCAAG 59.437 50.000 0.00 0.00 0.00 3.02
263 277 1.203125 GGGGGAAACACAAGGGAATCA 60.203 52.381 0.00 0.00 32.66 2.57
264 278 1.203125 TGGGGGAAACACAAGGGAATC 60.203 52.381 0.00 0.00 32.66 2.52
265 279 0.863956 TGGGGGAAACACAAGGGAAT 59.136 50.000 0.00 0.00 32.66 3.01
268 282 1.623311 GAAATGGGGGAAACACAAGGG 59.377 52.381 0.00 0.00 32.66 3.95
270 284 3.305335 CGAAGAAATGGGGGAAACACAAG 60.305 47.826 0.00 0.00 32.66 3.16
271 285 2.625790 CGAAGAAATGGGGGAAACACAA 59.374 45.455 0.00 0.00 32.66 3.33
272 286 2.235016 CGAAGAAATGGGGGAAACACA 58.765 47.619 0.00 0.00 32.66 3.72
273 287 2.030274 CACGAAGAAATGGGGGAAACAC 60.030 50.000 0.00 0.00 0.00 3.32
274 288 2.235016 CACGAAGAAATGGGGGAAACA 58.765 47.619 0.00 0.00 0.00 2.83
275 289 2.235891 ACACGAAGAAATGGGGGAAAC 58.764 47.619 0.00 0.00 0.00 2.78
276 290 2.668144 ACACGAAGAAATGGGGGAAA 57.332 45.000 0.00 0.00 0.00 3.13
277 291 2.158593 TGAACACGAAGAAATGGGGGAA 60.159 45.455 0.00 0.00 0.00 3.97
278 292 1.422024 TGAACACGAAGAAATGGGGGA 59.578 47.619 0.00 0.00 0.00 4.81
303 317 4.842531 TCATGAATTGGAGGTAAGCTCA 57.157 40.909 0.00 0.00 0.00 4.26
309 323 3.181440 GGCCTGATCATGAATTGGAGGTA 60.181 47.826 0.00 0.00 0.00 3.08
334 348 6.792473 TGTGATATGGGGTGAACTATAAGGAT 59.208 38.462 0.00 0.00 0.00 3.24
335 349 6.147473 TGTGATATGGGGTGAACTATAAGGA 58.853 40.000 0.00 0.00 0.00 3.36
336 350 6.433847 TGTGATATGGGGTGAACTATAAGG 57.566 41.667 0.00 0.00 0.00 2.69
337 351 7.509546 ACTTGTGATATGGGGTGAACTATAAG 58.490 38.462 0.00 0.00 0.00 1.73
406 421 3.558505 CCTTGAACACGCTCAAAGAATG 58.441 45.455 0.00 0.00 34.96 2.67
419 434 1.837439 AGACCCGATATGCCTTGAACA 59.163 47.619 0.00 0.00 0.00 3.18
423 438 2.613977 GGATGAGACCCGATATGCCTTG 60.614 54.545 0.00 0.00 0.00 3.61
454 469 5.179368 CCTCTTGAGCGTCAACAAATCTAAA 59.821 40.000 0.00 0.00 32.21 1.85
455 470 4.690748 CCTCTTGAGCGTCAACAAATCTAA 59.309 41.667 0.00 0.00 32.21 2.10
456 471 4.245660 CCTCTTGAGCGTCAACAAATCTA 58.754 43.478 0.00 0.00 32.21 1.98
457 472 3.070018 CCTCTTGAGCGTCAACAAATCT 58.930 45.455 0.00 0.00 32.21 2.40
467 482 2.897969 TCTTTAAGACCCTCTTGAGCGT 59.102 45.455 0.00 0.00 37.29 5.07
469 1345 5.940470 TCATTTCTTTAAGACCCTCTTGAGC 59.060 40.000 0.00 0.00 37.29 4.26
497 1373 2.046285 CCCGCTCCGCCAAGAAATT 61.046 57.895 0.00 0.00 0.00 1.82
519 1395 0.030807 TGAGAGGATGGATGCCCTGA 60.031 55.000 0.00 0.00 31.84 3.86
536 1412 5.068591 TCAAAGACATATAACGCCTAGCTGA 59.931 40.000 0.00 0.00 0.00 4.26
552 1428 1.272092 CCCCAAGCTCCATCAAAGACA 60.272 52.381 0.00 0.00 0.00 3.41
598 1474 2.169352 ACCCAATGTGAGATCGAAGAGG 59.831 50.000 0.00 0.00 43.63 3.69
599 1475 3.533606 ACCCAATGTGAGATCGAAGAG 57.466 47.619 0.00 0.00 43.63 2.85
642 1522 9.793259 TGTGAGTATAAATGAGACCTTTCTTTT 57.207 29.630 0.00 0.00 29.47 2.27
643 1523 9.965902 ATGTGAGTATAAATGAGACCTTTCTTT 57.034 29.630 0.00 0.00 29.47 2.52
649 1529 8.758829 TGTGTTATGTGAGTATAAATGAGACCT 58.241 33.333 0.00 0.00 0.00 3.85
663 1543 7.535258 GCAATGTAACTTCTTGTGTTATGTGAG 59.465 37.037 0.00 0.00 33.29 3.51
677 1557 2.162681 AGCCCTGTGCAATGTAACTTC 58.837 47.619 0.00 0.00 44.83 3.01
693 1573 4.893608 TGGATTGCTTTAAAAAGAAGCCC 58.106 39.130 6.64 2.29 46.85 5.19
701 1581 5.529430 TGTCGTCTCTTGGATTGCTTTAAAA 59.471 36.000 0.00 0.00 0.00 1.52
705 1585 2.808543 GTGTCGTCTCTTGGATTGCTTT 59.191 45.455 0.00 0.00 0.00 3.51
706 1586 2.224281 TGTGTCGTCTCTTGGATTGCTT 60.224 45.455 0.00 0.00 0.00 3.91
722 1602 6.385649 TCCTGTAAATTTTCTTGGTGTGTC 57.614 37.500 0.00 0.00 0.00 3.67
724 1604 6.478673 GGTTTCCTGTAAATTTTCTTGGTGTG 59.521 38.462 0.00 0.00 0.00 3.82
735 1615 2.296073 TGGGCGGTTTCCTGTAAATT 57.704 45.000 0.00 0.00 0.00 1.82
743 1623 0.102663 TTTCGTTTTGGGCGGTTTCC 59.897 50.000 0.00 0.00 0.00 3.13
747 1627 2.605837 AAAATTTCGTTTTGGGCGGT 57.394 40.000 0.00 0.00 38.56 5.68
750 1630 6.543736 TGTTTTGTAAAATTTCGTTTTGGGC 58.456 32.000 0.00 0.00 40.17 5.36
754 1634 9.210329 AGGAACTGTTTTGTAAAATTTCGTTTT 57.790 25.926 0.00 0.00 39.68 2.43
758 1640 9.382244 CTAGAGGAACTGTTTTGTAAAATTTCG 57.618 33.333 0.00 0.00 41.55 3.46
773 1655 3.456277 ACTTTATGGCCCTAGAGGAACTG 59.544 47.826 0.00 0.00 41.55 3.16
777 1659 3.130734 ACACTTTATGGCCCTAGAGGA 57.869 47.619 0.00 0.00 38.24 3.71
779 1661 3.071167 GGGTACACTTTATGGCCCTAGAG 59.929 52.174 0.00 1.53 41.74 2.43
786 1668 2.442413 TGCAAGGGTACACTTTATGGC 58.558 47.619 7.90 9.30 0.00 4.40
792 1674 2.100087 CGGTTTTTGCAAGGGTACACTT 59.900 45.455 3.98 3.98 0.00 3.16
794 1676 1.866471 GCGGTTTTTGCAAGGGTACAC 60.866 52.381 0.00 0.00 0.00 2.90
795 1677 0.386113 GCGGTTTTTGCAAGGGTACA 59.614 50.000 0.00 0.00 0.00 2.90
796 1678 0.671796 AGCGGTTTTTGCAAGGGTAC 59.328 50.000 0.00 0.00 33.85 3.34
805 2104 0.996727 CGGAAAGCGAGCGGTTTTTG 60.997 55.000 19.11 11.90 44.45 2.44
997 3571 1.290324 GAGAGCAGAGTGTTCCGCA 59.710 57.895 0.00 0.00 0.00 5.69
1038 3622 3.551407 GAGGTGGGAGGGATCGGC 61.551 72.222 0.00 0.00 0.00 5.54
1332 3925 1.696336 ACAGTTCATGCAGGACAGAGT 59.304 47.619 0.00 0.00 0.00 3.24
1358 3956 2.157474 TCACGAATTTCAGCACATGACG 59.843 45.455 0.00 0.00 37.77 4.35
1364 3969 2.298300 CAACGTCACGAATTTCAGCAC 58.702 47.619 2.91 0.00 0.00 4.40
1396 4004 3.369471 GCTAGGAATCGCAAGCCCATATA 60.369 47.826 0.00 0.00 37.18 0.86
1397 4005 2.616510 GCTAGGAATCGCAAGCCCATAT 60.617 50.000 0.00 0.00 37.18 1.78
1398 4006 1.270839 GCTAGGAATCGCAAGCCCATA 60.271 52.381 0.00 0.00 37.18 2.74
1399 4007 0.536006 GCTAGGAATCGCAAGCCCAT 60.536 55.000 0.00 0.00 37.18 4.00
1441 4049 9.459640 CCATATGAAAGCAATCTTGTCAAATAG 57.540 33.333 3.65 0.00 31.78 1.73
1442 4050 8.970020 ACCATATGAAAGCAATCTTGTCAAATA 58.030 29.630 3.65 0.00 31.78 1.40
1443 4051 7.844009 ACCATATGAAAGCAATCTTGTCAAAT 58.156 30.769 3.65 0.00 31.78 2.32
1508 4120 6.692486 ACCACAAAACATGAAACACAGTTTA 58.308 32.000 0.00 0.00 33.27 2.01
1547 4159 7.798596 CATGGATGCTAAATTAGACAGAGTT 57.201 36.000 3.88 0.00 0.00 3.01
1647 4263 3.799420 GTCTTCCTCCATTCGATTCTTCG 59.201 47.826 0.00 0.00 46.87 3.79
1665 4281 2.548920 CCCTGTTTCTTCAGCTCGTCTT 60.549 50.000 0.00 0.00 34.47 3.01
1669 4285 0.321671 TCCCCTGTTTCTTCAGCTCG 59.678 55.000 0.00 0.00 34.47 5.03
1674 4290 2.701551 TCTCCTTCCCCTGTTTCTTCA 58.298 47.619 0.00 0.00 0.00 3.02
1851 4467 3.778718 CGGAATCACGCAAATAAAGTTCG 59.221 43.478 0.00 0.00 0.00 3.95
1856 4472 5.811399 AGATTCGGAATCACGCAAATAAA 57.189 34.783 27.39 0.00 40.42 1.40
1900 4516 8.213518 ACATCAACATGGTCACAATAATAGAC 57.786 34.615 0.00 0.00 33.82 2.59
2059 4677 4.202441 CTCTTGGCATGTACTTGGCTAAT 58.798 43.478 28.03 0.00 42.34 1.73
2186 4804 2.732001 ACAACGAGAAAGCGACAAAC 57.268 45.000 0.00 0.00 34.83 2.93
2380 4998 6.917533 ACATTCAAGGAATCACATCTCAAAC 58.082 36.000 0.00 0.00 28.87 2.93
2472 5094 6.976934 AATCAACCTTGTACATTTTGTCCT 57.023 33.333 0.00 0.00 0.00 3.85
2586 5211 1.134670 GTAGCTGCACTAACCTCCCAG 60.135 57.143 1.02 0.00 30.90 4.45
2864 5615 6.460123 CCAGTCATGGTAAAAATGATGGCTAC 60.460 42.308 0.00 0.00 42.17 3.58
2885 5636 6.764560 ACGTAAAACTACAAAAGACATCCAGT 59.235 34.615 0.00 0.00 0.00 4.00
2989 5740 0.250858 CACACAGCCCCTTCACATCA 60.251 55.000 0.00 0.00 0.00 3.07
3382 6139 5.297569 AGGCATGTCTACTTATTTCTCCC 57.702 43.478 0.00 0.00 0.00 4.30
3479 6236 9.965902 CTCATAGGCCTAGTAATGGATAAAAAT 57.034 33.333 19.33 0.00 0.00 1.82
3554 6312 5.659440 TGGATGACATATATTAGCTGCGA 57.341 39.130 0.00 0.00 0.00 5.10
3569 6327 7.227512 CAGTAAAACCTTCCTATCATGGATGAC 59.772 40.741 0.00 0.00 40.03 3.06
3586 6344 4.598062 GTGTCAGTCAAAGCAGTAAAACC 58.402 43.478 0.00 0.00 0.00 3.27
3660 6418 9.592196 ACAAGCCTCAATATGGTCAATATAATT 57.408 29.630 0.00 0.00 30.84 1.40
3661 6419 9.592196 AACAAGCCTCAATATGGTCAATATAAT 57.408 29.630 0.00 0.00 30.84 1.28
3662 6420 8.995027 AACAAGCCTCAATATGGTCAATATAA 57.005 30.769 0.00 0.00 30.84 0.98
3663 6421 8.995027 AAACAAGCCTCAATATGGTCAATATA 57.005 30.769 0.00 0.00 30.84 0.86
3664 6422 7.781693 AGAAACAAGCCTCAATATGGTCAATAT 59.218 33.333 0.00 0.00 32.49 1.28
3665 6423 7.118723 AGAAACAAGCCTCAATATGGTCAATA 58.881 34.615 0.00 0.00 0.00 1.90
3666 6424 5.954150 AGAAACAAGCCTCAATATGGTCAAT 59.046 36.000 0.00 0.00 0.00 2.57
3667 6425 5.324409 AGAAACAAGCCTCAATATGGTCAA 58.676 37.500 0.00 0.00 0.00 3.18
3668 6426 4.922206 AGAAACAAGCCTCAATATGGTCA 58.078 39.130 0.00 0.00 0.00 4.02
3669 6427 6.116126 AGTAGAAACAAGCCTCAATATGGTC 58.884 40.000 0.00 0.00 0.00 4.02
3670 6428 6.067217 AGTAGAAACAAGCCTCAATATGGT 57.933 37.500 0.00 0.00 0.00 3.55
3671 6429 8.506168 TTTAGTAGAAACAAGCCTCAATATGG 57.494 34.615 0.00 0.00 0.00 2.74
3674 6432 9.733556 TCATTTTAGTAGAAACAAGCCTCAATA 57.266 29.630 0.00 0.00 0.00 1.90
3675 6433 8.635765 TCATTTTAGTAGAAACAAGCCTCAAT 57.364 30.769 0.00 0.00 0.00 2.57
3676 6434 8.635765 ATCATTTTAGTAGAAACAAGCCTCAA 57.364 30.769 0.00 0.00 0.00 3.02
3730 6488 9.612620 GAACACTTCTAAATTACAATGAAGGTG 57.387 33.333 0.00 0.00 38.60 4.00
3791 6555 5.673818 GCATTTTTCGAGGCTGGTAGTTAAG 60.674 44.000 0.00 0.00 0.00 1.85
3820 6584 2.396590 TCCCTGGTACTTTCAATCGC 57.603 50.000 0.00 0.00 0.00 4.58
3874 6638 6.371548 TCTGGTCATCAGGTAATTTCTTTTCG 59.628 38.462 0.00 0.00 43.53 3.46
3969 6733 6.294473 AGCTATCAAAATATCACCTGACCAG 58.706 40.000 0.00 0.00 0.00 4.00
3999 6763 7.717875 TCAACAAAAAGTAGTATAACTGTGCCT 59.282 33.333 0.00 0.00 0.00 4.75
4203 6991 6.011717 TCCCCCATAGCATATCAACAACATAT 60.012 38.462 0.00 0.00 0.00 1.78
4227 7015 2.283298 TCCTCGCTTGCTGATTTCATC 58.717 47.619 0.00 0.00 0.00 2.92
4320 7111 9.448438 AGTACAATATTCTTGTTGTATTCTGCA 57.552 29.630 0.00 0.00 40.25 4.41
4414 7205 3.952323 CTCCTGAAATCTCCATTGTGCAT 59.048 43.478 0.00 0.00 0.00 3.96
4483 7274 2.887152 AGCACAAATTCAACTCCCTGAC 59.113 45.455 0.00 0.00 0.00 3.51
4516 7307 0.617535 GCCAGGCCCCATACCTTTTT 60.618 55.000 0.00 0.00 34.42 1.94
4519 7310 0.403453 ATAGCCAGGCCCCATACCTT 60.403 55.000 8.22 0.00 34.42 3.50
4761 7554 3.616219 AGCTAACTGGTTGTCACACAAA 58.384 40.909 0.00 0.00 40.15 2.83
4773 7566 3.002348 GCCAACGCTTTATAGCTAACTGG 59.998 47.826 0.00 5.71 45.51 4.00
4794 7587 4.752661 TCACGTTAAACTGGGTTATTGC 57.247 40.909 0.00 0.00 0.00 3.56
4886 7679 0.321919 TGCCCAGAACTGACATGAGC 60.322 55.000 0.00 0.00 0.00 4.26
4938 7731 6.881067 ATGCCAAGATATAATCCTCTGCTA 57.119 37.500 0.00 0.00 0.00 3.49
4950 7743 4.569228 CCCTCTTGCCATATGCCAAGATAT 60.569 45.833 24.76 0.00 40.16 1.63
4986 7783 3.820557 ACCACTCTTGCTCTGCTAAAAA 58.179 40.909 0.00 0.00 0.00 1.94
5042 7839 0.034477 AGGCCCAATACCGGTTCAAG 60.034 55.000 15.04 0.00 0.00 3.02
5159 7964 0.598158 GCGGACCAGTTTCGTGTGTA 60.598 55.000 0.00 0.00 0.00 2.90
5168 7973 0.468226 TCAGTTCAAGCGGACCAGTT 59.532 50.000 0.00 0.00 0.00 3.16
5200 8005 0.913205 TGCCGGGAGCTACCAAATAA 59.087 50.000 17.35 0.00 44.23 1.40
5254 8061 8.018537 TCCAGCATTTATAGTAGCAAGTAGAA 57.981 34.615 0.00 0.00 0.00 2.10
5300 8122 4.771590 TTTGACCAACATGCAGATCTTC 57.228 40.909 0.00 0.00 0.00 2.87
5311 8133 3.635836 TGATGTGCAGATTTTGACCAACA 59.364 39.130 0.00 0.00 0.00 3.33
5315 8138 4.418392 GACATGATGTGCAGATTTTGACC 58.582 43.478 1.23 0.00 0.00 4.02
5317 8140 4.080687 TGGACATGATGTGCAGATTTTGA 58.919 39.130 15.95 0.00 43.78 2.69
5491 8314 4.629200 CAGAGGAACTGCTGTAGAACATTC 59.371 45.833 0.00 0.00 41.55 2.67
5514 8337 1.615392 AGGCCAAACAGAACATGAAGC 59.385 47.619 5.01 0.00 0.00 3.86
5648 8900 8.394877 TGTATAAAGTGCATATTGGTTCGAAAG 58.605 33.333 0.00 0.00 0.00 2.62
5725 8979 6.262273 ACATGGTAAGGTAAAATCATTAGGCG 59.738 38.462 0.00 0.00 0.00 5.52
5772 9026 0.032678 ACCGAGGATTCATGCTAGCG 59.967 55.000 10.77 0.00 0.00 4.26
5797 9051 5.240844 CGGTATTGACCCTCTTTTCTTTTGT 59.759 40.000 0.00 0.00 43.64 2.83
5934 9188 2.888834 TTGGTTCTTTGCCTTGCTTC 57.111 45.000 0.00 0.00 0.00 3.86
6041 9295 3.706086 AGTTGGTTCTTTGCCTTGATTGT 59.294 39.130 0.00 0.00 0.00 2.71
6045 9299 4.164843 ACTAGTTGGTTCTTTGCCTTGA 57.835 40.909 0.00 0.00 0.00 3.02
6099 9353 2.727916 CGTCTGCTTTGGTATTTTCCGC 60.728 50.000 0.00 0.00 0.00 5.54
6231 11676 0.804989 GGGCGTCTTCCTTTGACATG 59.195 55.000 0.00 0.00 34.37 3.21
6278 11723 1.818674 CCACTTCTTGGGTTGCCATAC 59.181 52.381 0.00 0.00 42.54 2.39
6359 12168 3.499737 GCATTGCCGGGTCAGTCG 61.500 66.667 2.18 0.00 0.00 4.18
6360 12169 3.499737 CGCATTGCCGGGTCAGTC 61.500 66.667 2.18 0.00 0.00 3.51
6370 12179 2.832818 TTTTCTCGCTCGCGCATTGC 62.833 55.000 8.75 7.24 39.59 3.56
6371 12180 0.247814 ATTTTCTCGCTCGCGCATTG 60.248 50.000 8.75 0.00 39.59 2.82
6548 12576 9.120538 GCACCTTTTTATTATCTGGTTCATCTA 57.879 33.333 0.00 0.00 0.00 1.98
6630 14514 8.487176 CCAAATAACTTAACACAAATGTCAAGC 58.513 33.333 0.00 0.00 38.45 4.01
6690 14575 1.749063 AGGCATCATGTGTTGCATCAG 59.251 47.619 15.55 0.00 41.26 2.90
6712 14599 6.648310 ACCTCGATGATATTCATTGCTTACAG 59.352 38.462 0.00 0.00 37.20 2.74
6774 14661 7.383102 ACTTCAACTAAATCGATCTGCAAAT 57.617 32.000 0.00 0.00 0.00 2.32
6782 14669 7.907214 ACAGCTTAACTTCAACTAAATCGAT 57.093 32.000 0.00 0.00 0.00 3.59
6797 14684 3.725010 CGCTCCATCGAAAACAGCTTAAC 60.725 47.826 0.00 0.00 0.00 2.01
6809 14696 1.153353 GTTTTTGACCGCTCCATCGA 58.847 50.000 0.00 0.00 0.00 3.59
6870 14763 2.548057 GGATTCGCTGTGTGTTTTCTCA 59.452 45.455 0.00 0.00 0.00 3.27
6886 14780 9.680315 TTTTGCATTTGATTCAAAATTGGATTC 57.320 25.926 15.34 0.12 36.90 2.52
6978 14874 9.462606 AGTAAATCCCTTTCGATCTATGTTTTT 57.537 29.630 0.00 0.00 0.00 1.94
6981 14877 9.765795 CTTAGTAAATCCCTTTCGATCTATGTT 57.234 33.333 0.00 0.00 0.00 2.71
6982 14878 7.873505 GCTTAGTAAATCCCTTTCGATCTATGT 59.126 37.037 0.00 0.00 0.00 2.29
6983 14879 7.872993 TGCTTAGTAAATCCCTTTCGATCTATG 59.127 37.037 0.00 0.00 0.00 2.23
6984 14880 7.963532 TGCTTAGTAAATCCCTTTCGATCTAT 58.036 34.615 0.00 0.00 0.00 1.98
6985 14881 7.356089 TGCTTAGTAAATCCCTTTCGATCTA 57.644 36.000 0.00 0.00 0.00 1.98
6986 14882 6.235231 TGCTTAGTAAATCCCTTTCGATCT 57.765 37.500 0.00 0.00 0.00 2.75
6987 14883 8.779354 ATATGCTTAGTAAATCCCTTTCGATC 57.221 34.615 0.00 0.00 0.00 3.69
6988 14884 9.574516 AAATATGCTTAGTAAATCCCTTTCGAT 57.425 29.630 0.00 0.00 0.00 3.59
6989 14885 8.836413 CAAATATGCTTAGTAAATCCCTTTCGA 58.164 33.333 0.00 0.00 0.00 3.71
7008 14904 5.047092 AGACCACCAAAAAGAGGCAAATATG 60.047 40.000 0.00 0.00 0.00 1.78
7009 14905 5.047092 CAGACCACCAAAAAGAGGCAAATAT 60.047 40.000 0.00 0.00 0.00 1.28
7010 14906 4.280677 CAGACCACCAAAAAGAGGCAAATA 59.719 41.667 0.00 0.00 0.00 1.40
7011 14907 3.070015 CAGACCACCAAAAAGAGGCAAAT 59.930 43.478 0.00 0.00 0.00 2.32
7012 14908 2.430332 CAGACCACCAAAAAGAGGCAAA 59.570 45.455 0.00 0.00 0.00 3.68
7013 14909 2.031120 CAGACCACCAAAAAGAGGCAA 58.969 47.619 0.00 0.00 0.00 4.52
7014 14910 1.691196 CAGACCACCAAAAAGAGGCA 58.309 50.000 0.00 0.00 0.00 4.75
7015 14911 0.961753 CCAGACCACCAAAAAGAGGC 59.038 55.000 0.00 0.00 0.00 4.70
7016 14912 2.364972 ACCAGACCACCAAAAAGAGG 57.635 50.000 0.00 0.00 0.00 3.69
7017 14913 3.316308 CAGAACCAGACCACCAAAAAGAG 59.684 47.826 0.00 0.00 0.00 2.85
7018 14914 3.053991 TCAGAACCAGACCACCAAAAAGA 60.054 43.478 0.00 0.00 0.00 2.52
7019 14915 3.066760 GTCAGAACCAGACCACCAAAAAG 59.933 47.826 0.00 0.00 0.00 2.27
7020 14916 3.020984 GTCAGAACCAGACCACCAAAAA 58.979 45.455 0.00 0.00 0.00 1.94
7021 14917 2.650322 GTCAGAACCAGACCACCAAAA 58.350 47.619 0.00 0.00 0.00 2.44
7022 14918 2.341846 GTCAGAACCAGACCACCAAA 57.658 50.000 0.00 0.00 0.00 3.28
7033 14929 2.346365 GACGTGGGGGTCAGAACC 59.654 66.667 0.00 0.00 45.65 3.62
7034 14930 2.048503 CGACGTGGGGGTCAGAAC 60.049 66.667 0.00 0.00 36.73 3.01
7035 14931 3.998672 GCGACGTGGGGGTCAGAA 61.999 66.667 0.00 0.00 36.73 3.02
7095 14991 2.041265 GAGGAGAAGGGGAGGGCA 59.959 66.667 0.00 0.00 0.00 5.36
7151 15047 1.982395 ATCACTGAAGCCCGTCCGA 60.982 57.895 0.00 0.00 0.00 4.55
7155 15051 2.045926 GCCATCACTGAAGCCCGT 60.046 61.111 0.00 0.00 0.00 5.28
7162 15058 1.376086 CCACCACTGCCATCACTGA 59.624 57.895 0.00 0.00 0.00 3.41
7245 15142 4.951963 CCCGATCGAAGCTCCCGC 62.952 72.222 18.66 0.00 0.00 6.13
7246 15143 4.951963 GCCCGATCGAAGCTCCCG 62.952 72.222 18.66 2.44 0.00 5.14
7247 15144 4.610714 GGCCCGATCGAAGCTCCC 62.611 72.222 18.66 3.07 0.00 4.30
7248 15145 4.951963 CGGCCCGATCGAAGCTCC 62.952 72.222 18.66 8.64 0.00 4.70
7598 15512 2.905415 TTCAATGGCCTCCATCAAGT 57.095 45.000 3.32 0.00 44.40 3.16
7616 15530 4.384647 GCAGGTCTTCACCCAGATCTATTT 60.385 45.833 0.00 0.00 45.12 1.40
7619 15533 2.111384 GCAGGTCTTCACCCAGATCTA 58.889 52.381 0.00 0.00 45.12 1.98
7667 15581 1.153901 CGACACCGAATAGTGCCGT 60.154 57.895 0.00 0.00 41.67 5.68
7715 15835 2.381911 AGCAAATAGTGGCCTGGAATG 58.618 47.619 3.32 0.00 0.00 2.67
7716 15836 2.834638 AGCAAATAGTGGCCTGGAAT 57.165 45.000 3.32 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.