Multiple sequence alignment - TraesCS2A01G405000

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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 TraesCS2A01G405000 chr2A 100.000 6223 0 0 1 6223 660556894 660563116 0.000000e+00 11492.0
1 TraesCS2A01G405000 chr2A 90.672 536 24 9 1 527 392851907 392852425 0.000000e+00 689.0
2 TraesCS2A01G405000 chr2A 87.763 523 47 13 11 527 316793196 316793707 4.150000e-166 595.0
3 TraesCS2A01G405000 chr2A 90.000 50 5 0 5333 5382 779498107 779498156 1.450000e-06 65.8
4 TraesCS2A01G405000 chr2B 95.668 3024 88 16 2289 5298 608475472 608478466 0.000000e+00 4819.0
5 TraesCS2A01G405000 chr2B 93.853 911 37 4 1376 2273 608474582 608475486 0.000000e+00 1354.0
6 TraesCS2A01G405000 chr2B 88.470 451 19 13 530 958 608473601 608474040 1.200000e-141 514.0
7 TraesCS2A01G405000 chr2B 94.366 213 10 2 5931 6143 608478473 608478683 6.020000e-85 326.0
8 TraesCS2A01G405000 chr2B 98.315 178 3 0 980 1157 608474104 608474281 4.680000e-81 313.0
9 TraesCS2A01G405000 chr2D 91.825 3009 172 41 2291 5255 516829250 516832228 0.000000e+00 4126.0
10 TraesCS2A01G405000 chr2D 91.583 1794 57 31 530 2273 516827513 516829262 0.000000e+00 2390.0
11 TraesCS2A01G405000 chr2D 87.121 132 12 4 5930 6059 516832379 516832507 1.810000e-30 145.0
12 TraesCS2A01G405000 chr5A 92.222 540 28 6 1 527 105675686 105675148 0.000000e+00 752.0
13 TraesCS2A01G405000 chr5A 91.993 537 29 7 1 527 213325236 213325768 0.000000e+00 741.0
14 TraesCS2A01G405000 chr5A 87.743 514 32 23 1 495 631651159 631651660 7.000000e-159 571.0
15 TraesCS2A01G405000 chr5A 84.177 316 26 14 5371 5668 679377362 679377671 1.020000e-72 285.0
16 TraesCS2A01G405000 chr3A 91.728 544 25 10 1 527 703588049 703587509 0.000000e+00 737.0
17 TraesCS2A01G405000 chr3A 87.845 543 44 11 1 527 720254320 720253784 8.860000e-173 617.0
18 TraesCS2A01G405000 chr3A 85.455 55 8 0 5541 5595 526570161 526570107 2.420000e-04 58.4
19 TraesCS2A01G405000 chr6A 91.481 540 32 7 1 527 548410100 548409562 0.000000e+00 730.0
20 TraesCS2A01G405000 chr6A 100.000 29 0 0 5540 5568 196336820 196336792 3.000000e-03 54.7
21 TraesCS2A01G405000 chrUn 100.000 392 0 0 3534 3925 479715306 479714915 0.000000e+00 725.0
22 TraesCS2A01G405000 chr6D 83.243 734 98 13 2996 3718 132763995 132764714 0.000000e+00 651.0
23 TraesCS2A01G405000 chr3D 82.111 777 117 19 2955 3718 81040252 81041019 0.000000e+00 645.0
24 TraesCS2A01G405000 chr4B 81.877 778 114 21 2955 3716 535144547 535145313 1.140000e-176 630.0
25 TraesCS2A01G405000 chr4B 100.000 29 0 0 5423 5451 7504694 7504722 3.000000e-03 54.7
26 TraesCS2A01G405000 chr1A 87.684 544 38 19 1 527 513425177 513425708 1.920000e-169 606.0
27 TraesCS2A01G405000 chr1A 89.565 345 31 4 5325 5668 471257293 471257633 3.450000e-117 433.0
28 TraesCS2A01G405000 chr1A 91.065 291 24 2 5632 5921 471257569 471257858 5.850000e-105 392.0
29 TraesCS2A01G405000 chr1A 80.663 181 31 3 3326 3506 45637148 45636972 3.030000e-28 137.0
30 TraesCS2A01G405000 chr7A 91.908 346 23 5 5318 5660 207471893 207472236 4.360000e-131 479.0
31 TraesCS2A01G405000 chr7A 89.189 296 28 4 5632 5926 207472179 207472471 3.540000e-97 366.0
32 TraesCS2A01G405000 chr7A 85.938 64 9 0 5332 5395 6424900 6424963 1.120000e-07 69.4
33 TraesCS2A01G405000 chr7D 86.087 345 43 5 5604 5945 309441225 309440883 3.540000e-97 366.0
34 TraesCS2A01G405000 chr7D 85.556 360 32 7 5324 5668 309441486 309441132 5.930000e-95 359.0
35 TraesCS2A01G405000 chr7D 81.768 181 29 3 3326 3506 528074392 528074216 1.400000e-31 148.0
36 TraesCS2A01G405000 chr5D 86.120 317 43 1 2955 3271 82365437 82365122 2.150000e-89 340.0
37 TraesCS2A01G405000 chr1D 78.275 313 45 12 3337 3648 486700951 486700661 4.960000e-41 180.0
38 TraesCS2A01G405000 chr1D 80.663 181 31 3 3326 3506 12281370 12281546 3.030000e-28 137.0
39 TraesCS2A01G405000 chr6B 75.576 217 27 9 1693 1885 85845263 85845477 4.000000e-12 84.2
40 TraesCS2A01G405000 chr5B 76.978 139 19 7 5325 5461 370237322 370237195 4.030000e-07 67.6
41 TraesCS2A01G405000 chr5B 76.259 139 20 7 5325 5461 370186848 370186721 1.870000e-05 62.1


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 TraesCS2A01G405000 chr2A 660556894 660563116 6222 False 11492.000000 11492 100.000000 1 6223 1 chr2A.!!$F3 6222
1 TraesCS2A01G405000 chr2A 392851907 392852425 518 False 689.000000 689 90.672000 1 527 1 chr2A.!!$F2 526
2 TraesCS2A01G405000 chr2A 316793196 316793707 511 False 595.000000 595 87.763000 11 527 1 chr2A.!!$F1 516
3 TraesCS2A01G405000 chr2B 608473601 608478683 5082 False 1465.200000 4819 94.134400 530 6143 5 chr2B.!!$F1 5613
4 TraesCS2A01G405000 chr2D 516827513 516832507 4994 False 2220.333333 4126 90.176333 530 6059 3 chr2D.!!$F1 5529
5 TraesCS2A01G405000 chr5A 105675148 105675686 538 True 752.000000 752 92.222000 1 527 1 chr5A.!!$R1 526
6 TraesCS2A01G405000 chr5A 213325236 213325768 532 False 741.000000 741 91.993000 1 527 1 chr5A.!!$F1 526
7 TraesCS2A01G405000 chr5A 631651159 631651660 501 False 571.000000 571 87.743000 1 495 1 chr5A.!!$F2 494
8 TraesCS2A01G405000 chr3A 703587509 703588049 540 True 737.000000 737 91.728000 1 527 1 chr3A.!!$R2 526
9 TraesCS2A01G405000 chr3A 720253784 720254320 536 True 617.000000 617 87.845000 1 527 1 chr3A.!!$R3 526
10 TraesCS2A01G405000 chr6A 548409562 548410100 538 True 730.000000 730 91.481000 1 527 1 chr6A.!!$R2 526
11 TraesCS2A01G405000 chr6D 132763995 132764714 719 False 651.000000 651 83.243000 2996 3718 1 chr6D.!!$F1 722
12 TraesCS2A01G405000 chr3D 81040252 81041019 767 False 645.000000 645 82.111000 2955 3718 1 chr3D.!!$F1 763
13 TraesCS2A01G405000 chr4B 535144547 535145313 766 False 630.000000 630 81.877000 2955 3716 1 chr4B.!!$F2 761
14 TraesCS2A01G405000 chr1A 513425177 513425708 531 False 606.000000 606 87.684000 1 527 1 chr1A.!!$F1 526
15 TraesCS2A01G405000 chr1A 471257293 471257858 565 False 412.500000 433 90.315000 5325 5921 2 chr1A.!!$F2 596
16 TraesCS2A01G405000 chr7A 207471893 207472471 578 False 422.500000 479 90.548500 5318 5926 2 chr7A.!!$F2 608
17 TraesCS2A01G405000 chr7D 309440883 309441486 603 True 362.500000 366 85.821500 5324 5945 2 chr7D.!!$R2 621

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
618 715 0.306533 AAAAGCGGTTAGTGTGCGTG 59.693 50.0 0.0 0.0 0.0 5.34 F
1201 1365 0.675837 GTTCCTGGTACGCTTTCCCC 60.676 60.0 0.0 0.0 0.0 4.81 F
2662 2939 0.303493 TGACACGAAAACGCTTCTGC 59.697 50.0 0.0 0.0 0.0 4.26 F
3436 3722 0.471022 ACTTTGGGGGTGGCGAAATT 60.471 50.0 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1785 1.137825 CTTCGACGTCCAGAGCTCC 59.862 63.158 10.93 0.0 0.0 4.70 R
2785 3062 1.552337 TGCTTTGCCAGAACAACCAAA 59.448 42.857 0.00 0.0 0.0 3.28 R
4631 4942 0.179081 GGCAATGTACTCCCTCCGTC 60.179 60.000 0.00 0.0 0.0 4.79 R
5320 5755 0.037590 ACGCATAGCAGTCCCCAAAA 59.962 50.000 0.00 0.0 0.0 2.44 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
90 105 2.821366 GCGTGCCTATGTGCTGCT 60.821 61.111 0.00 0.00 32.83 4.24
99 114 0.592637 TATGTGCTGCTTGTGTGTGC 59.407 50.000 0.00 0.00 0.00 4.57
106 121 2.051614 CTTGTGTGTGCTGCTGCG 60.052 61.111 11.21 0.00 43.34 5.18
107 122 2.823593 TTGTGTGTGCTGCTGCGT 60.824 55.556 11.21 0.00 43.34 5.24
108 123 2.976881 CTTGTGTGTGCTGCTGCGTG 62.977 60.000 11.21 0.00 43.34 5.34
111 126 3.576356 GTGTGCTGCTGCGTGTGT 61.576 61.111 11.21 0.00 43.34 3.72
116 131 2.243957 GCTGCTGCGTGTGTGTGTA 61.244 57.895 0.00 0.00 0.00 2.90
159 236 3.130160 TTGCTGCGTGTGTGTGCA 61.130 55.556 0.00 0.00 39.13 4.57
305 402 2.156343 TGTGTATGTGTTGCTGCGTA 57.844 45.000 0.00 0.00 0.00 4.42
321 418 1.405526 GCGTATGTTCTCTTGCCCTCA 60.406 52.381 0.00 0.00 0.00 3.86
330 427 1.002888 CTCTTGCCCTCACACTGATGT 59.997 52.381 0.00 0.00 40.80 3.06
342 439 3.933900 CTGATGTTGCGTGCGTGCC 62.934 63.158 0.00 0.00 0.00 5.01
343 440 3.726517 GATGTTGCGTGCGTGCCT 61.727 61.111 0.00 0.00 0.00 4.75
376 473 1.281867 CACACATACCACATGAGGGGT 59.718 52.381 14.11 12.85 41.21 4.95
397 494 6.040504 GGGGTAAAAGAGTCTTTTCATGTGTT 59.959 38.462 29.47 10.18 0.00 3.32
571 668 7.564793 TGCATTGGATTAGATTAGTGTGTACT 58.435 34.615 0.00 0.00 40.99 2.73
572 669 8.700973 TGCATTGGATTAGATTAGTGTGTACTA 58.299 33.333 0.00 0.00 38.36 1.82
573 670 9.712305 GCATTGGATTAGATTAGTGTGTACTAT 57.288 33.333 0.00 0.00 39.08 2.12
617 714 1.868469 TAAAAGCGGTTAGTGTGCGT 58.132 45.000 0.00 0.00 0.00 5.24
618 715 0.306533 AAAAGCGGTTAGTGTGCGTG 59.693 50.000 0.00 0.00 0.00 5.34
674 771 7.213678 ACCCACTGGTGTTGTTTATTTATTTG 58.786 34.615 0.00 0.00 45.58 2.32
686 783 5.862678 TTATTTATTTGCTTGTAGCCCCC 57.137 39.130 0.00 0.00 41.51 5.40
751 848 3.306502 CGCTAGTAGTCTAGGAGGAGGAG 60.307 56.522 0.00 0.00 42.66 3.69
788 885 2.599082 GCCGTCTCATCGTTTTCTACTG 59.401 50.000 0.00 0.00 0.00 2.74
841 938 1.029681 ACGAAACAAAAGCCTGGACC 58.970 50.000 0.00 0.00 0.00 4.46
904 1012 3.284449 ACCAAAACCCGCACGCTC 61.284 61.111 0.00 0.00 0.00 5.03
905 1013 4.383602 CCAAAACCCGCACGCTCG 62.384 66.667 0.00 0.00 0.00 5.03
906 1014 3.342627 CAAAACCCGCACGCTCGA 61.343 61.111 0.00 0.00 0.00 4.04
907 1015 2.358247 AAAACCCGCACGCTCGAT 60.358 55.556 0.00 0.00 0.00 3.59
908 1016 2.388232 AAAACCCGCACGCTCGATC 61.388 57.895 0.00 0.00 0.00 3.69
909 1017 3.583276 AAACCCGCACGCTCGATCA 62.583 57.895 0.00 0.00 0.00 2.92
912 1020 4.829518 CCGCACGCTCGATCACGA 62.830 66.667 9.27 0.00 46.56 4.35
1196 1360 2.047560 GCCGTTCCTGGTACGCTT 60.048 61.111 18.90 0.00 37.67 4.68
1197 1361 1.670083 GCCGTTCCTGGTACGCTTT 60.670 57.895 18.90 0.00 37.67 3.51
1199 1363 1.017701 CCGTTCCTGGTACGCTTTCC 61.018 60.000 18.90 0.00 37.67 3.13
1201 1365 0.675837 GTTCCTGGTACGCTTTCCCC 60.676 60.000 0.00 0.00 0.00 4.81
1202 1366 0.838987 TTCCTGGTACGCTTTCCCCT 60.839 55.000 0.00 0.00 0.00 4.79
1203 1367 1.221021 CCTGGTACGCTTTCCCCTC 59.779 63.158 0.00 0.00 0.00 4.30
1214 1378 2.826128 GCTTTCCCCTCCTAACAAAAGG 59.174 50.000 0.00 0.00 38.06 3.11
1275 1439 0.802222 TGCTCTCCGATTTTCGCTCG 60.802 55.000 0.00 0.00 38.82 5.03
1308 1472 1.317613 TGCCGATTCTGTTTGCTGTT 58.682 45.000 0.00 0.00 0.00 3.16
1309 1473 1.680735 TGCCGATTCTGTTTGCTGTTT 59.319 42.857 0.00 0.00 0.00 2.83
1310 1474 2.100584 TGCCGATTCTGTTTGCTGTTTT 59.899 40.909 0.00 0.00 0.00 2.43
1311 1475 3.123050 GCCGATTCTGTTTGCTGTTTTT 58.877 40.909 0.00 0.00 0.00 1.94
1312 1476 3.182372 GCCGATTCTGTTTGCTGTTTTTC 59.818 43.478 0.00 0.00 0.00 2.29
1313 1477 3.735746 CCGATTCTGTTTGCTGTTTTTCC 59.264 43.478 0.00 0.00 0.00 3.13
1314 1478 4.499696 CCGATTCTGTTTGCTGTTTTTCCT 60.500 41.667 0.00 0.00 0.00 3.36
1315 1479 4.676924 CGATTCTGTTTGCTGTTTTTCCTC 59.323 41.667 0.00 0.00 0.00 3.71
1316 1480 5.506317 CGATTCTGTTTGCTGTTTTTCCTCT 60.506 40.000 0.00 0.00 0.00 3.69
1317 1481 4.900635 TCTGTTTGCTGTTTTTCCTCTC 57.099 40.909 0.00 0.00 0.00 3.20
1318 1482 3.632145 TCTGTTTGCTGTTTTTCCTCTCC 59.368 43.478 0.00 0.00 0.00 3.71
1625 1892 1.269448 TGCAGCAATTTCGTTCCCTTC 59.731 47.619 0.00 0.00 0.00 3.46
1631 1898 3.872771 GCAATTTCGTTCCCTTCCGTATA 59.127 43.478 0.00 0.00 0.00 1.47
1684 1951 1.125021 CATTGCTCGTGTTCGTGTCTC 59.875 52.381 0.00 0.00 38.33 3.36
1701 1968 2.161808 GTCTCACTGCTCGCTAACAGTA 59.838 50.000 0.00 0.00 45.15 2.74
1707 1974 4.211374 CACTGCTCGCTAACAGTAAAGTTT 59.789 41.667 0.00 0.00 45.15 2.66
1804 2072 0.389948 CAGCGAACAGGGGTGAGTAC 60.390 60.000 0.00 0.00 34.96 2.73
1823 2091 1.154413 GAACGAACGTGCTGCCATG 60.154 57.895 0.00 0.00 0.00 3.66
1826 2094 2.100031 CGAACGTGCTGCCATGCTA 61.100 57.895 0.00 0.00 0.00 3.49
1987 2255 3.686726 GGTTTCGCAATGATGAGACTCTT 59.313 43.478 3.68 0.00 34.94 2.85
1988 2256 4.436584 GGTTTCGCAATGATGAGACTCTTG 60.437 45.833 3.68 1.11 34.94 3.02
1989 2257 2.897436 TCGCAATGATGAGACTCTTGG 58.103 47.619 3.68 0.00 29.81 3.61
1990 2258 1.938577 CGCAATGATGAGACTCTTGGG 59.061 52.381 3.68 4.65 0.00 4.12
1991 2259 1.674962 GCAATGATGAGACTCTTGGGC 59.325 52.381 3.68 0.00 0.00 5.36
1992 2260 2.683152 GCAATGATGAGACTCTTGGGCT 60.683 50.000 3.68 0.00 34.86 5.19
2273 2548 3.442977 ACTTGCCAATTCTGATCTTGAGC 59.557 43.478 0.00 0.00 0.00 4.26
2274 2549 3.361281 TGCCAATTCTGATCTTGAGCT 57.639 42.857 0.00 0.00 0.00 4.09
2275 2550 3.693807 TGCCAATTCTGATCTTGAGCTT 58.306 40.909 0.00 0.00 0.00 3.74
2276 2551 4.084287 TGCCAATTCTGATCTTGAGCTTT 58.916 39.130 0.00 0.00 0.00 3.51
2277 2552 5.255687 TGCCAATTCTGATCTTGAGCTTTA 58.744 37.500 0.00 0.00 0.00 1.85
2278 2553 5.711506 TGCCAATTCTGATCTTGAGCTTTAA 59.288 36.000 0.00 0.00 0.00 1.52
2279 2554 6.379133 TGCCAATTCTGATCTTGAGCTTTAAT 59.621 34.615 0.00 0.00 0.00 1.40
2280 2555 7.557358 TGCCAATTCTGATCTTGAGCTTTAATA 59.443 33.333 0.00 0.00 0.00 0.98
2281 2556 8.408601 GCCAATTCTGATCTTGAGCTTTAATAA 58.591 33.333 0.00 0.00 0.00 1.40
2324 2599 7.054124 TGAGTAATCTGAACAACTTCCAGTTT 58.946 34.615 0.00 0.00 36.03 2.66
2327 2602 6.966534 AATCTGAACAACTTCCAGTTTGAT 57.033 33.333 0.00 0.00 36.03 2.57
2345 2620 8.939929 CAGTTTGATATCATAGTGTGTGTTTCT 58.060 33.333 17.98 0.00 0.00 2.52
2359 2634 5.758296 TGTGTGTTTCTTTGACCTATGAGTC 59.242 40.000 0.00 0.00 37.28 3.36
2369 2644 5.541953 TGACCTATGAGTCATCAATCTGG 57.458 43.478 9.42 6.32 41.78 3.86
2395 2670 3.243234 ACTTCCAGTTCGAGATCATAGCG 60.243 47.826 0.00 0.00 0.00 4.26
2413 2688 3.067106 AGCGTGTGTTTCTTGACCTATG 58.933 45.455 0.00 0.00 0.00 2.23
2477 2753 2.290641 AGCGTGTGTTTCTTGACCAATC 59.709 45.455 0.00 0.00 0.00 2.67
2522 2799 5.940470 GCGGGTATCCAGATAATCAATTCTT 59.060 40.000 0.00 0.00 0.00 2.52
2662 2939 0.303493 TGACACGAAAACGCTTCTGC 59.697 50.000 0.00 0.00 0.00 4.26
3310 3595 7.272978 TCATTGCTCTTCACCTAAGGTAATAC 58.727 38.462 0.00 0.00 35.75 1.89
3368 3654 2.863809 AGCGAATTTTCTTCACCCACT 58.136 42.857 0.00 0.00 0.00 4.00
3400 3686 2.097629 CAGATTTGAGCCTGACATGCTG 59.902 50.000 10.18 0.00 39.69 4.41
3436 3722 0.471022 ACTTTGGGGGTGGCGAAATT 60.471 50.000 0.00 0.00 0.00 1.82
3984 4285 3.890756 TGCCTGCATATTCAAATACCCTG 59.109 43.478 0.00 0.00 0.00 4.45
3989 4290 7.255942 GCCTGCATATTCAAATACCCTGTAAAT 60.256 37.037 0.00 0.00 0.00 1.40
4539 4849 5.879223 ACTGCAGAATTTATCTTCTCCTGTG 59.121 40.000 23.35 0.00 35.73 3.66
4595 4906 9.085645 TCTTACAGAAGAAGACAGGTAAATACA 57.914 33.333 0.00 0.00 38.80 2.29
4596 4907 9.706691 CTTACAGAAGAAGACAGGTAAATACAA 57.293 33.333 0.00 0.00 34.25 2.41
4610 4921 9.341899 CAGGTAAATACAAAATACTTGACTTGC 57.658 33.333 0.00 0.00 30.67 4.01
4622 4933 8.487313 AATACTTGACTTGCGTAAATGATACA 57.513 30.769 0.00 0.00 0.00 2.29
4623 4934 6.795098 ACTTGACTTGCGTAAATGATACAA 57.205 33.333 0.00 0.00 0.00 2.41
4624 4935 7.197071 ACTTGACTTGCGTAAATGATACAAA 57.803 32.000 0.00 0.00 0.00 2.83
4625 4936 7.644490 ACTTGACTTGCGTAAATGATACAAAA 58.356 30.769 0.00 0.00 0.00 2.44
4626 4937 8.296713 ACTTGACTTGCGTAAATGATACAAAAT 58.703 29.630 0.00 0.00 0.00 1.82
4627 4938 9.767684 CTTGACTTGCGTAAATGATACAAAATA 57.232 29.630 0.00 0.00 0.00 1.40
4628 4939 9.549509 TTGACTTGCGTAAATGATACAAAATAC 57.450 29.630 0.00 0.00 0.00 1.89
4629 4940 8.941977 TGACTTGCGTAAATGATACAAAATACT 58.058 29.630 0.00 0.00 0.00 2.12
4630 4941 9.769093 GACTTGCGTAAATGATACAAAATACTT 57.231 29.630 0.00 0.00 0.00 2.24
4631 4942 9.554724 ACTTGCGTAAATGATACAAAATACTTG 57.445 29.630 0.00 0.00 0.00 3.16
4632 4943 9.767684 CTTGCGTAAATGATACAAAATACTTGA 57.232 29.630 0.00 0.00 0.00 3.02
4633 4944 9.549509 TTGCGTAAATGATACAAAATACTTGAC 57.450 29.630 0.00 0.00 0.00 3.18
4634 4945 7.900864 TGCGTAAATGATACAAAATACTTGACG 59.099 33.333 0.00 0.00 0.00 4.35
4635 4946 7.372396 GCGTAAATGATACAAAATACTTGACGG 59.628 37.037 0.00 0.00 0.00 4.79
4636 4947 8.597227 CGTAAATGATACAAAATACTTGACGGA 58.403 33.333 0.00 0.00 0.00 4.69
4637 4948 9.916397 GTAAATGATACAAAATACTTGACGGAG 57.084 33.333 0.00 0.00 0.00 4.63
4638 4949 7.553881 AATGATACAAAATACTTGACGGAGG 57.446 36.000 0.00 0.00 0.00 4.30
4639 4950 5.424757 TGATACAAAATACTTGACGGAGGG 58.575 41.667 0.00 0.00 0.00 4.30
4640 4951 5.188163 TGATACAAAATACTTGACGGAGGGA 59.812 40.000 0.00 0.00 0.00 4.20
4644 4955 4.732672 AAATACTTGACGGAGGGAGTAC 57.267 45.455 0.00 0.00 0.00 2.73
4662 4973 6.346096 GGAGTACATTGCCTTTATACACTGA 58.654 40.000 0.00 0.00 0.00 3.41
4716 5027 3.436704 TGATCTTCACGTTTGATTCTGGC 59.563 43.478 0.00 0.00 0.00 4.85
4881 5192 5.007430 CAGCAATCTGATACTCCACATGTTC 59.993 44.000 0.00 0.00 42.95 3.18
4949 5264 2.349590 CATTTGACTGGTCTGCATCGA 58.650 47.619 2.38 0.00 0.00 3.59
5041 5357 2.829003 GCGCTAGCCCCTTTTCCC 60.829 66.667 9.66 0.00 37.42 3.97
5045 5361 1.891011 CGCTAGCCCCTTTTCCCTTTT 60.891 52.381 9.66 0.00 0.00 2.27
5082 5428 9.114952 TGATGTAATGTTACAGTGAGTTCAAAA 57.885 29.630 10.90 0.00 45.80 2.44
5131 5477 8.367660 ACATAACTTAGAACATGAAGAGGAGA 57.632 34.615 0.00 0.00 0.00 3.71
5160 5506 9.206870 GAAAGAATGAAAATTTTATCCAGCACA 57.793 29.630 2.75 0.00 0.00 4.57
5196 5542 0.458669 TCGTTGGATAGTTCGGAGCC 59.541 55.000 0.00 0.00 0.00 4.70
5335 5770 6.780198 TCCTAATATTTTGGGGACTGCTAT 57.220 37.500 0.00 0.00 34.36 2.97
5344 5779 2.105128 GACTGCTATGCGTCGGCT 59.895 61.111 0.00 0.00 40.82 5.52
5365 5800 5.410924 GCTGGCGGATCTTTTTAAAAGATT 58.589 37.500 27.12 15.07 37.14 2.40
5372 5807 4.759516 TCTTTTTAAAAGATTCGCCGCT 57.240 36.364 15.24 0.00 0.00 5.52
5494 5943 6.800543 TGTTGTAACATAAGTTGTGTTGCAT 58.199 32.000 27.63 8.14 46.40 3.96
5836 6288 3.143728 TGCGAGGCGTAGAATCTATACA 58.856 45.455 0.00 0.00 0.00 2.29
5863 6315 5.007234 CACGTGGACTGTTTGATCAAAAGTA 59.993 40.000 22.07 10.87 31.33 2.24
5910 6362 3.069980 GAGAGCACGATCCGCTGGT 62.070 63.158 8.93 0.00 40.63 4.00
5922 6374 1.141254 TCCGCTGGTTGAAAGGTAACA 59.859 47.619 0.00 0.00 41.41 2.41
5926 6378 4.500716 CCGCTGGTTGAAAGGTAACATTTT 60.501 41.667 0.00 0.00 41.41 1.82
5927 6379 5.047188 CGCTGGTTGAAAGGTAACATTTTT 58.953 37.500 0.00 0.00 41.41 1.94
5931 6383 7.923878 GCTGGTTGAAAGGTAACATTTTTCTAA 59.076 33.333 0.00 0.00 41.41 2.10
5963 6417 6.014584 TCTCTTAGAATTGACAACTGTAGGCA 60.015 38.462 0.00 0.00 0.00 4.75
6014 6468 8.650143 AAAGAAAGATAGAAAGCCATTTGGTA 57.350 30.769 0.00 0.00 37.57 3.25
6080 6534 1.503542 GCAGTCACATTGAAGGGCG 59.496 57.895 0.00 0.00 0.00 6.13
6084 6538 2.035626 CACATTGAAGGGCGGGGT 59.964 61.111 0.00 0.00 0.00 4.95
6143 6597 8.999431 TCTCTTAGCAAAATTAGATGTTTCGTT 58.001 29.630 0.00 0.00 0.00 3.85
6144 6598 9.612620 CTCTTAGCAAAATTAGATGTTTCGTTT 57.387 29.630 0.00 0.00 0.00 3.60
6145 6599 9.393249 TCTTAGCAAAATTAGATGTTTCGTTTG 57.607 29.630 0.00 0.00 0.00 2.93
6146 6600 9.393249 CTTAGCAAAATTAGATGTTTCGTTTGA 57.607 29.630 0.00 0.00 0.00 2.69
6147 6601 7.623268 AGCAAAATTAGATGTTTCGTTTGAC 57.377 32.000 0.00 0.00 0.00 3.18
6148 6602 6.359617 AGCAAAATTAGATGTTTCGTTTGACG 59.640 34.615 0.00 0.00 44.19 4.35
6149 6603 6.504821 CAAAATTAGATGTTTCGTTTGACGC 58.495 36.000 0.00 0.00 42.21 5.19
6150 6604 3.799137 TTAGATGTTTCGTTTGACGCC 57.201 42.857 0.00 0.00 42.21 5.68
6151 6605 1.878953 AGATGTTTCGTTTGACGCCT 58.121 45.000 0.00 0.00 42.21 5.52
6152 6606 1.798813 AGATGTTTCGTTTGACGCCTC 59.201 47.619 0.00 0.00 42.21 4.70
6153 6607 0.872388 ATGTTTCGTTTGACGCCTCC 59.128 50.000 0.00 0.00 42.21 4.30
6154 6608 0.462225 TGTTTCGTTTGACGCCTCCA 60.462 50.000 0.00 0.00 42.21 3.86
6155 6609 0.658897 GTTTCGTTTGACGCCTCCAA 59.341 50.000 0.00 0.00 42.21 3.53
6156 6610 1.064357 GTTTCGTTTGACGCCTCCAAA 59.936 47.619 0.00 0.00 42.21 3.28
6157 6611 0.658897 TTCGTTTGACGCCTCCAAAC 59.341 50.000 0.00 0.00 45.81 2.93
6161 6615 0.741915 TTTGACGCCTCCAAACAACC 59.258 50.000 0.00 0.00 0.00 3.77
6162 6616 0.394488 TTGACGCCTCCAAACAACCA 60.394 50.000 0.00 0.00 0.00 3.67
6163 6617 1.098712 TGACGCCTCCAAACAACCAC 61.099 55.000 0.00 0.00 0.00 4.16
6164 6618 1.077357 ACGCCTCCAAACAACCACA 60.077 52.632 0.00 0.00 0.00 4.17
6165 6619 1.358759 CGCCTCCAAACAACCACAC 59.641 57.895 0.00 0.00 0.00 3.82
6166 6620 1.739667 GCCTCCAAACAACCACACC 59.260 57.895 0.00 0.00 0.00 4.16
6167 6621 1.744320 GCCTCCAAACAACCACACCC 61.744 60.000 0.00 0.00 0.00 4.61
6168 6622 1.452145 CCTCCAAACAACCACACCCG 61.452 60.000 0.00 0.00 0.00 5.28
6169 6623 0.464735 CTCCAAACAACCACACCCGA 60.465 55.000 0.00 0.00 0.00 5.14
6170 6624 0.034380 TCCAAACAACCACACCCGAA 60.034 50.000 0.00 0.00 0.00 4.30
6171 6625 0.383949 CCAAACAACCACACCCGAAG 59.616 55.000 0.00 0.00 0.00 3.79
6186 6640 2.629051 CCGAAGGTATCCTTTGTCACC 58.371 52.381 12.90 0.00 44.82 4.02
6187 6641 2.027561 CCGAAGGTATCCTTTGTCACCA 60.028 50.000 12.90 0.00 44.82 4.17
6188 6642 3.370527 CCGAAGGTATCCTTTGTCACCAT 60.371 47.826 12.90 0.00 44.82 3.55
6189 6643 3.871594 CGAAGGTATCCTTTGTCACCATC 59.128 47.826 2.48 0.00 44.82 3.51
6190 6644 3.933861 AGGTATCCTTTGTCACCATCC 57.066 47.619 0.00 0.00 33.27 3.51
6191 6645 2.509964 AGGTATCCTTTGTCACCATCCC 59.490 50.000 0.00 0.00 33.27 3.85
6192 6646 2.422945 GGTATCCTTTGTCACCATCCCC 60.423 54.545 0.00 0.00 0.00 4.81
6193 6647 0.255890 ATCCTTTGTCACCATCCCCG 59.744 55.000 0.00 0.00 0.00 5.73
6194 6648 0.838554 TCCTTTGTCACCATCCCCGA 60.839 55.000 0.00 0.00 0.00 5.14
6195 6649 0.676782 CCTTTGTCACCATCCCCGAC 60.677 60.000 0.00 0.00 0.00 4.79
6196 6650 0.676782 CTTTGTCACCATCCCCGACC 60.677 60.000 0.00 0.00 0.00 4.79
6197 6651 1.419720 TTTGTCACCATCCCCGACCA 61.420 55.000 0.00 0.00 0.00 4.02
6198 6652 1.419720 TTGTCACCATCCCCGACCAA 61.420 55.000 0.00 0.00 0.00 3.67
6199 6653 1.377229 GTCACCATCCCCGACCAAA 59.623 57.895 0.00 0.00 0.00 3.28
6200 6654 0.958876 GTCACCATCCCCGACCAAAC 60.959 60.000 0.00 0.00 0.00 2.93
6201 6655 1.131303 TCACCATCCCCGACCAAACT 61.131 55.000 0.00 0.00 0.00 2.66
6202 6656 0.676782 CACCATCCCCGACCAAACTC 60.677 60.000 0.00 0.00 0.00 3.01
6203 6657 1.449601 CCATCCCCGACCAAACTCG 60.450 63.158 0.00 0.00 0.00 4.18
6204 6658 1.594833 CATCCCCGACCAAACTCGA 59.405 57.895 0.00 0.00 35.58 4.04
6205 6659 0.460284 CATCCCCGACCAAACTCGAG 60.460 60.000 11.84 11.84 35.58 4.04
6206 6660 2.240162 ATCCCCGACCAAACTCGAGC 62.240 60.000 13.61 0.00 35.58 5.03
6207 6661 2.342279 CCCGACCAAACTCGAGCA 59.658 61.111 13.61 0.00 35.58 4.26
6208 6662 1.301401 CCCGACCAAACTCGAGCAA 60.301 57.895 13.61 0.00 35.58 3.91
6209 6663 1.291877 CCCGACCAAACTCGAGCAAG 61.292 60.000 13.61 1.67 35.58 4.01
6210 6664 0.319555 CCGACCAAACTCGAGCAAGA 60.320 55.000 13.61 0.00 35.58 3.02
6211 6665 0.784778 CGACCAAACTCGAGCAAGAC 59.215 55.000 13.61 0.00 35.58 3.01
6212 6666 1.603172 CGACCAAACTCGAGCAAGACT 60.603 52.381 13.61 0.00 35.58 3.24
6213 6667 2.484889 GACCAAACTCGAGCAAGACTT 58.515 47.619 13.61 0.00 0.00 3.01
6214 6668 2.872858 GACCAAACTCGAGCAAGACTTT 59.127 45.455 13.61 1.11 0.00 2.66
6215 6669 2.872858 ACCAAACTCGAGCAAGACTTTC 59.127 45.455 13.61 0.00 0.00 2.62
6216 6670 2.096713 CCAAACTCGAGCAAGACTTTCG 60.097 50.000 13.61 3.37 35.76 3.46
6217 6671 1.140816 AACTCGAGCAAGACTTTCGC 58.859 50.000 13.61 0.00 34.52 4.70
6218 6672 0.667792 ACTCGAGCAAGACTTTCGCC 60.668 55.000 13.61 0.00 34.52 5.54
6219 6673 1.355066 CTCGAGCAAGACTTTCGCCC 61.355 60.000 0.00 0.00 34.52 6.13
6220 6674 2.730672 CGAGCAAGACTTTCGCCCG 61.731 63.158 0.00 0.00 0.00 6.13
6221 6675 2.358737 AGCAAGACTTTCGCCCGG 60.359 61.111 0.00 0.00 0.00 5.73
6222 6676 2.358247 GCAAGACTTTCGCCCGGA 60.358 61.111 0.73 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 105 2.823593 ACGCAGCAGCACACACAA 60.824 55.556 0.82 0.00 42.27 3.33
99 114 0.164432 CATACACACACACGCAGCAG 59.836 55.000 0.00 0.00 0.00 4.24
106 121 2.538737 GCACACACACATACACACACAC 60.539 50.000 0.00 0.00 0.00 3.82
107 122 1.668237 GCACACACACATACACACACA 59.332 47.619 0.00 0.00 0.00 3.72
108 123 1.939934 AGCACACACACATACACACAC 59.060 47.619 0.00 0.00 0.00 3.82
111 126 0.943673 GCAGCACACACACATACACA 59.056 50.000 0.00 0.00 0.00 3.72
116 131 3.024784 CACGCAGCACACACACAT 58.975 55.556 0.00 0.00 0.00 3.21
159 236 1.356270 CAGCAACACACATGCACGT 59.644 52.632 0.00 0.00 46.22 4.49
305 402 1.701847 AGTGTGAGGGCAAGAGAACAT 59.298 47.619 0.00 0.00 0.00 2.71
321 418 1.887242 ACGCACGCAACATCAGTGT 60.887 52.632 0.00 0.00 41.28 3.55
330 427 1.208870 CAATAAGGCACGCACGCAA 59.791 52.632 0.00 0.00 0.00 4.85
342 439 2.198827 TGTGTGTGAGGGGCAATAAG 57.801 50.000 0.00 0.00 0.00 1.73
343 440 2.897271 ATGTGTGTGAGGGGCAATAA 57.103 45.000 0.00 0.00 0.00 1.40
397 494 9.352784 CATTTTCGTTCATTTTGAGCCTAAATA 57.647 29.630 0.00 0.00 0.00 1.40
511 608 7.333323 CCTCAAAAGCATTCCTTATTTGGATT 58.667 34.615 0.00 0.00 35.83 3.01
512 609 6.126968 CCCTCAAAAGCATTCCTTATTTGGAT 60.127 38.462 0.00 0.00 35.83 3.41
514 611 5.046376 ACCCTCAAAAGCATTCCTTATTTGG 60.046 40.000 0.00 0.00 32.20 3.28
527 624 2.995939 GCAAAGCATTACCCTCAAAAGC 59.004 45.455 0.00 0.00 0.00 3.51
528 625 4.255833 TGCAAAGCATTACCCTCAAAAG 57.744 40.909 0.00 0.00 31.71 2.27
617 714 1.043816 GGAGGATCAGAGCGAATCCA 58.956 55.000 10.83 0.00 36.25 3.41
618 715 1.043816 TGGAGGATCAGAGCGAATCC 58.956 55.000 0.00 0.00 36.25 3.01
656 753 8.432359 GCTACAAGCAAATAAATAAACAACACC 58.568 33.333 0.00 0.00 41.89 4.16
659 756 7.064134 GGGGCTACAAGCAAATAAATAAACAAC 59.936 37.037 0.78 0.00 44.75 3.32
662 759 6.046593 GGGGGCTACAAGCAAATAAATAAAC 58.953 40.000 0.78 0.00 44.75 2.01
674 771 0.621082 AAAGAGAGGGGGCTACAAGC 59.379 55.000 0.00 0.00 41.46 4.01
686 783 9.761504 ATCAATCATATATATCGCCAAAGAGAG 57.238 33.333 0.00 0.00 0.00 3.20
788 885 1.451028 ATTTGGCGAGAGAGCAGGC 60.451 57.895 0.00 0.00 39.27 4.85
824 921 1.613925 GGAGGTCCAGGCTTTTGTTTC 59.386 52.381 0.00 0.00 35.64 2.78
904 1012 4.147449 TGCTGGGCCTCGTGATCG 62.147 66.667 4.53 0.00 38.55 3.69
905 1013 2.202987 CTGCTGGGCCTCGTGATC 60.203 66.667 4.53 0.00 0.00 2.92
906 1014 3.790437 CCTGCTGGGCCTCGTGAT 61.790 66.667 4.53 0.00 0.00 3.06
908 1016 4.767255 GTCCTGCTGGGCCTCGTG 62.767 72.222 10.07 0.00 34.39 4.35
972 1094 3.057547 CTCCTCCTCCACTCACGCG 62.058 68.421 3.53 3.53 0.00 6.01
974 1096 2.055042 CCCTCCTCCTCCACTCACG 61.055 68.421 0.00 0.00 0.00 4.35
975 1097 1.687493 CCCCTCCTCCTCCACTCAC 60.687 68.421 0.00 0.00 0.00 3.51
976 1098 2.780693 CCCCTCCTCCTCCACTCA 59.219 66.667 0.00 0.00 0.00 3.41
978 1100 4.787280 CGCCCCTCCTCCTCCACT 62.787 72.222 0.00 0.00 0.00 4.00
1089 1253 4.406173 ACGACGACGAGCAGCAGG 62.406 66.667 15.32 0.00 42.66 4.85
1196 1360 1.271707 CGCCTTTTGTTAGGAGGGGAA 60.272 52.381 0.00 0.00 43.88 3.97
1197 1361 0.326927 CGCCTTTTGTTAGGAGGGGA 59.673 55.000 0.00 0.00 43.88 4.81
1199 1363 1.644786 CGCGCCTTTTGTTAGGAGGG 61.645 60.000 0.00 0.00 40.52 4.30
1201 1365 0.442699 GTCGCGCCTTTTGTTAGGAG 59.557 55.000 0.00 0.00 37.50 3.69
1202 1366 0.034337 AGTCGCGCCTTTTGTTAGGA 59.966 50.000 0.00 0.00 37.50 2.94
1203 1367 0.872388 AAGTCGCGCCTTTTGTTAGG 59.128 50.000 0.00 0.00 38.40 2.69
1243 1407 2.829914 GAGCATTGCATGGGCCGA 60.830 61.111 11.91 0.00 40.13 5.54
1247 1411 0.536687 ATCGGAGAGCATTGCATGGG 60.537 55.000 11.91 0.00 43.63 4.00
1275 1439 0.748005 TCGGCATTAAGGCAGGAAGC 60.748 55.000 14.82 0.00 44.47 3.86
1519 1785 1.137825 CTTCGACGTCCAGAGCTCC 59.862 63.158 10.93 0.00 0.00 4.70
1625 1892 9.623132 TTGTGAAGCAAAACAATCCGTATACGG 62.623 40.741 33.86 33.86 46.57 4.02
1631 1898 3.380004 TCTTGTGAAGCAAAACAATCCGT 59.620 39.130 0.00 0.00 35.82 4.69
1684 1951 3.318017 ACTTTACTGTTAGCGAGCAGTG 58.682 45.455 23.03 11.25 44.59 3.66
1701 1968 3.160269 CATCTGCTGAAGGGGAAACTTT 58.840 45.455 0.00 0.00 0.00 2.66
1707 1974 1.499913 TTGGCATCTGCTGAAGGGGA 61.500 55.000 1.70 0.00 41.70 4.81
1804 2072 2.667318 ATGGCAGCACGTTCGTTCG 61.667 57.895 0.00 1.21 0.00 3.95
1823 2091 1.308783 GGGACAAGCCAGCAACTAGC 61.309 60.000 0.00 0.00 46.19 3.42
1826 2094 2.926250 TGGGACAAGCCAGCAACT 59.074 55.556 0.00 0.00 38.95 3.16
1901 2169 8.540388 AGGCTATGTATACATGGAAATTACGAT 58.460 33.333 27.80 3.11 37.04 3.73
1990 2258 2.301346 ACTATTAGCACATGGCCAAGC 58.699 47.619 10.96 15.23 46.50 4.01
1991 2259 4.450976 TGTACTATTAGCACATGGCCAAG 58.549 43.478 10.96 8.43 46.50 3.61
1992 2260 4.495690 TGTACTATTAGCACATGGCCAA 57.504 40.909 10.96 0.00 46.50 4.52
2167 2442 8.706322 AACAAGAAAGGAATAAATACAGTGGT 57.294 30.769 0.00 0.00 0.00 4.16
2287 2562 9.730705 TGTTCAGATTACTCAAGATCAGAATTT 57.269 29.630 0.00 0.00 32.72 1.82
2288 2563 9.730705 TTGTTCAGATTACTCAAGATCAGAATT 57.269 29.630 0.00 0.00 32.72 2.17
2289 2564 9.160496 GTTGTTCAGATTACTCAAGATCAGAAT 57.840 33.333 0.00 0.00 32.72 2.40
2290 2565 8.370940 AGTTGTTCAGATTACTCAAGATCAGAA 58.629 33.333 0.00 0.00 0.00 3.02
2291 2566 7.901029 AGTTGTTCAGATTACTCAAGATCAGA 58.099 34.615 0.00 0.00 0.00 3.27
2292 2567 8.545229 AAGTTGTTCAGATTACTCAAGATCAG 57.455 34.615 0.00 0.00 0.00 2.90
2293 2568 7.604164 GGAAGTTGTTCAGATTACTCAAGATCA 59.396 37.037 0.00 0.00 33.93 2.92
2294 2569 7.604164 TGGAAGTTGTTCAGATTACTCAAGATC 59.396 37.037 0.00 0.00 33.93 2.75
2295 2570 7.453393 TGGAAGTTGTTCAGATTACTCAAGAT 58.547 34.615 0.00 0.00 33.93 2.40
2296 2571 6.826668 TGGAAGTTGTTCAGATTACTCAAGA 58.173 36.000 0.00 0.00 33.93 3.02
2297 2572 7.126726 CTGGAAGTTGTTCAGATTACTCAAG 57.873 40.000 0.00 0.00 33.93 3.02
2324 2599 8.935844 GTCAAAGAAACACACACTATGATATCA 58.064 33.333 8.10 8.10 0.00 2.15
2327 2602 7.450074 AGGTCAAAGAAACACACACTATGATA 58.550 34.615 0.00 0.00 0.00 2.15
2395 2670 7.097192 TCATACTCATAGGTCAAGAAACACAC 58.903 38.462 0.00 0.00 0.00 3.82
2413 2688 9.593134 AGTTGTTCAGATTGATAACTCATACTC 57.407 33.333 0.00 0.00 32.39 2.59
2477 2753 4.737279 CGCTCACAGTGATAACTCATACTG 59.263 45.833 2.97 0.00 33.72 2.74
2498 2775 5.491982 AGAATTGATTATCTGGATACCCGC 58.508 41.667 0.00 0.00 34.29 6.13
2522 2799 1.933181 CACGAGTCTGAGCACAAACAA 59.067 47.619 0.00 0.00 0.00 2.83
2589 2866 9.438163 AATGGGGAATATTATCATGACAAACTT 57.562 29.630 0.00 0.00 0.00 2.66
2785 3062 1.552337 TGCTTTGCCAGAACAACCAAA 59.448 42.857 0.00 0.00 0.00 3.28
3114 3398 4.203226 TGTTAGTTGAACAACCTGCATGA 58.797 39.130 13.07 0.00 45.23 3.07
3310 3595 9.437045 GCCAACACAAAATTTATTTGAAAGAAG 57.563 29.630 7.83 0.00 33.83 2.85
3368 3654 6.070251 TCAGGCTCAAATCTGTCATAGGTTAA 60.070 38.462 0.00 0.00 33.13 2.01
3400 3686 1.069935 GTAGCATCCCGAGAAGGCC 59.930 63.158 0.00 0.00 39.21 5.19
3436 3722 2.180276 GCACCTAGTTCCCTTCTCTCA 58.820 52.381 0.00 0.00 0.00 3.27
3955 4256 6.913873 ATTTGAATATGCAGGCAACAATTC 57.086 33.333 15.01 15.01 41.41 2.17
4112 4414 6.209192 ACATCTGAACTTTGGATGCAAATGTA 59.791 34.615 13.13 0.18 40.06 2.29
4610 4921 8.597227 TCCGTCAAGTATTTTGTATCATTTACG 58.403 33.333 0.00 0.00 0.00 3.18
4622 4933 4.529377 TGTACTCCCTCCGTCAAGTATTTT 59.471 41.667 0.00 0.00 0.00 1.82
4623 4934 4.091549 TGTACTCCCTCCGTCAAGTATTT 58.908 43.478 0.00 0.00 0.00 1.40
4624 4935 3.705051 TGTACTCCCTCCGTCAAGTATT 58.295 45.455 0.00 0.00 0.00 1.89
4625 4936 3.377253 TGTACTCCCTCCGTCAAGTAT 57.623 47.619 0.00 0.00 0.00 2.12
4626 4937 2.885135 TGTACTCCCTCCGTCAAGTA 57.115 50.000 0.00 0.00 0.00 2.24
4627 4938 2.233305 ATGTACTCCCTCCGTCAAGT 57.767 50.000 0.00 0.00 0.00 3.16
4628 4939 2.893637 CAATGTACTCCCTCCGTCAAG 58.106 52.381 0.00 0.00 0.00 3.02
4629 4940 1.066430 GCAATGTACTCCCTCCGTCAA 60.066 52.381 0.00 0.00 0.00 3.18
4630 4941 0.535335 GCAATGTACTCCCTCCGTCA 59.465 55.000 0.00 0.00 0.00 4.35
4631 4942 0.179081 GGCAATGTACTCCCTCCGTC 60.179 60.000 0.00 0.00 0.00 4.79
4632 4943 0.617820 AGGCAATGTACTCCCTCCGT 60.618 55.000 0.00 0.00 0.00 4.69
4633 4944 0.541863 AAGGCAATGTACTCCCTCCG 59.458 55.000 0.00 0.00 0.00 4.63
4634 4945 2.808906 AAAGGCAATGTACTCCCTCC 57.191 50.000 0.00 0.00 0.00 4.30
4635 4946 5.758784 GTGTATAAAGGCAATGTACTCCCTC 59.241 44.000 0.00 0.00 0.00 4.30
4636 4947 5.428783 AGTGTATAAAGGCAATGTACTCCCT 59.571 40.000 0.00 0.00 0.00 4.20
4637 4948 5.527582 CAGTGTATAAAGGCAATGTACTCCC 59.472 44.000 0.00 0.00 0.00 4.30
4638 4949 6.346096 TCAGTGTATAAAGGCAATGTACTCC 58.654 40.000 0.00 0.00 33.18 3.85
4639 4950 7.843490 TTCAGTGTATAAAGGCAATGTACTC 57.157 36.000 0.00 0.00 33.18 2.59
4640 4951 9.326413 GTATTCAGTGTATAAAGGCAATGTACT 57.674 33.333 0.00 0.00 33.18 2.73
4644 4955 7.498900 TGAGGTATTCAGTGTATAAAGGCAATG 59.501 37.037 0.00 0.00 32.74 2.82
4662 4973 8.462016 GTGCATAAGTTTCATCTTTGAGGTATT 58.538 33.333 0.00 0.00 32.27 1.89
4760 5071 6.330004 ACCGCATATCAAATGCATATTTCA 57.670 33.333 0.00 0.00 44.75 2.69
4767 5078 7.332926 ACAAAATTTAACCGCATATCAAATGCA 59.667 29.630 10.30 0.00 44.75 3.96
4807 5118 2.414138 GTCATGTTTCCGGTTAGGTTCG 59.586 50.000 0.00 0.00 41.99 3.95
4901 5215 7.607607 TGTACATTTGTCTTGCTCATACTGATT 59.392 33.333 0.00 0.00 0.00 2.57
4949 5264 6.534475 TCTTCTAATTTGCCAATCAGCATT 57.466 33.333 0.00 0.00 43.64 3.56
5067 5385 7.479980 CAGACCAAAATTTTGAACTCACTGTA 58.520 34.615 28.44 0.00 40.55 2.74
5082 5428 3.057315 CAGATTTCACGGCAGACCAAAAT 60.057 43.478 0.00 0.00 34.57 1.82
5152 5498 1.365999 CACGTACAGGTGTGCTGGA 59.634 57.895 0.00 0.00 33.24 3.86
5160 5506 0.109272 CGATGCTGACACGTACAGGT 60.109 55.000 18.83 0.34 36.09 4.00
5196 5542 1.448985 TGATTTCCCGAAAAGGAGCG 58.551 50.000 0.00 0.00 45.00 5.03
5266 5700 4.592485 ATCCTACTAATGAGCGTTCAGG 57.408 45.455 8.26 2.38 36.61 3.86
5309 5744 6.543735 AGCAGTCCCCAAAATATTAGGATAC 58.456 40.000 8.13 6.13 0.00 2.24
5314 5749 5.106555 CGCATAGCAGTCCCCAAAATATTAG 60.107 44.000 0.00 0.00 0.00 1.73
5316 5751 3.569701 CGCATAGCAGTCCCCAAAATATT 59.430 43.478 0.00 0.00 0.00 1.28
5318 5753 2.092646 ACGCATAGCAGTCCCCAAAATA 60.093 45.455 0.00 0.00 0.00 1.40
5319 5754 1.340991 ACGCATAGCAGTCCCCAAAAT 60.341 47.619 0.00 0.00 0.00 1.82
5320 5755 0.037590 ACGCATAGCAGTCCCCAAAA 59.962 50.000 0.00 0.00 0.00 2.44
5322 5757 1.220749 GACGCATAGCAGTCCCCAA 59.779 57.895 0.00 0.00 0.00 4.12
5344 5779 5.636837 CGAATCTTTTAAAAAGATCCGCCA 58.363 37.500 0.00 0.00 36.07 5.69
5372 5807 4.435436 AATCAGACGGCTCGCGCA 62.435 61.111 8.75 0.00 38.10 6.09
5410 5845 7.173390 GGTCTCTGTTGCAAAGTAGAGTAAAAT 59.827 37.037 24.35 0.00 38.66 1.82
5649 6099 9.979578 TCTGTTGCAAAAATAATTCTGTAACAT 57.020 25.926 0.00 0.00 41.44 2.71
5650 6100 9.979578 ATCTGTTGCAAAAATAATTCTGTAACA 57.020 25.926 0.00 1.37 40.53 2.41
5767 6218 6.546034 GCACCCACTGTATGTATTAGGATTTT 59.454 38.462 0.00 0.00 0.00 1.82
5836 6288 4.265904 TGATCAAACAGTCCACGTGTAT 57.734 40.909 15.65 0.00 0.00 2.29
5963 6417 2.159179 AGTTTCAGTGCTGGGGTTTT 57.841 45.000 0.00 0.00 0.00 2.43
6014 6468 4.037923 ACGCCAAGATTTTTGACAATGTCT 59.962 37.500 14.97 0.00 33.15 3.41
6125 6579 6.398517 GGCGTCAAACGAAACATCTAATTTTG 60.399 38.462 3.28 0.00 46.05 2.44
6136 6590 0.658897 TTGGAGGCGTCAAACGAAAC 59.341 50.000 8.91 0.00 46.05 2.78
6137 6591 1.064357 GTTTGGAGGCGTCAAACGAAA 59.936 47.619 17.78 0.00 46.05 3.46
6143 6597 0.394488 TGGTTGTTTGGAGGCGTCAA 60.394 50.000 8.91 0.00 0.00 3.18
6144 6598 1.098712 GTGGTTGTTTGGAGGCGTCA 61.099 55.000 8.91 0.00 0.00 4.35
6145 6599 1.098712 TGTGGTTGTTTGGAGGCGTC 61.099 55.000 0.00 0.00 0.00 5.19
6146 6600 1.077357 TGTGGTTGTTTGGAGGCGT 60.077 52.632 0.00 0.00 0.00 5.68
6147 6601 1.358759 GTGTGGTTGTTTGGAGGCG 59.641 57.895 0.00 0.00 0.00 5.52
6148 6602 1.739667 GGTGTGGTTGTTTGGAGGC 59.260 57.895 0.00 0.00 0.00 4.70
6149 6603 1.452145 CGGGTGTGGTTGTTTGGAGG 61.452 60.000 0.00 0.00 0.00 4.30
6150 6604 0.464735 TCGGGTGTGGTTGTTTGGAG 60.465 55.000 0.00 0.00 0.00 3.86
6151 6605 0.034380 TTCGGGTGTGGTTGTTTGGA 60.034 50.000 0.00 0.00 0.00 3.53
6152 6606 0.383949 CTTCGGGTGTGGTTGTTTGG 59.616 55.000 0.00 0.00 0.00 3.28
6153 6607 0.383949 CCTTCGGGTGTGGTTGTTTG 59.616 55.000 0.00 0.00 0.00 2.93
6154 6608 2.801859 CCTTCGGGTGTGGTTGTTT 58.198 52.632 0.00 0.00 0.00 2.83
6155 6609 4.571243 CCTTCGGGTGTGGTTGTT 57.429 55.556 0.00 0.00 0.00 2.83
6164 6618 2.027469 GTGACAAAGGATACCTTCGGGT 60.027 50.000 3.45 3.43 43.92 5.28
6165 6619 2.629051 GTGACAAAGGATACCTTCGGG 58.371 52.381 3.45 0.52 43.92 5.14
6166 6620 2.027561 TGGTGACAAAGGATACCTTCGG 60.028 50.000 3.45 2.74 43.92 4.30
6167 6621 3.328382 TGGTGACAAAGGATACCTTCG 57.672 47.619 3.45 0.00 43.92 3.79
6168 6622 4.200092 GGATGGTGACAAAGGATACCTTC 58.800 47.826 3.45 0.00 43.92 3.46
6181 6635 0.958876 GTTTGGTCGGGGATGGTGAC 60.959 60.000 0.00 0.00 0.00 3.67
6182 6636 1.131303 AGTTTGGTCGGGGATGGTGA 61.131 55.000 0.00 0.00 0.00 4.02
6183 6637 0.676782 GAGTTTGGTCGGGGATGGTG 60.677 60.000 0.00 0.00 0.00 4.17
6184 6638 1.683441 GAGTTTGGTCGGGGATGGT 59.317 57.895 0.00 0.00 0.00 3.55
6185 6639 1.449601 CGAGTTTGGTCGGGGATGG 60.450 63.158 0.00 0.00 36.26 3.51
6186 6640 0.460284 CTCGAGTTTGGTCGGGGATG 60.460 60.000 3.62 0.00 40.49 3.51
6187 6641 1.898154 CTCGAGTTTGGTCGGGGAT 59.102 57.895 3.62 0.00 40.49 3.85
6188 6642 2.939261 GCTCGAGTTTGGTCGGGGA 61.939 63.158 15.13 0.00 41.01 4.81
6189 6643 2.434359 GCTCGAGTTTGGTCGGGG 60.434 66.667 15.13 0.00 41.01 5.73
6190 6644 1.291877 CTTGCTCGAGTTTGGTCGGG 61.292 60.000 15.13 0.00 43.71 5.14
6191 6645 0.319555 TCTTGCTCGAGTTTGGTCGG 60.320 55.000 15.13 0.00 40.49 4.79
6192 6646 0.784778 GTCTTGCTCGAGTTTGGTCG 59.215 55.000 15.13 0.00 41.51 4.79
6193 6647 2.156343 AGTCTTGCTCGAGTTTGGTC 57.844 50.000 15.13 0.00 0.00 4.02
6194 6648 2.622064 AAGTCTTGCTCGAGTTTGGT 57.378 45.000 15.13 0.00 0.00 3.67
6195 6649 2.096713 CGAAAGTCTTGCTCGAGTTTGG 60.097 50.000 15.13 3.12 36.85 3.28
6196 6650 2.660362 GCGAAAGTCTTGCTCGAGTTTG 60.660 50.000 15.13 3.56 36.85 2.93
6197 6651 1.527311 GCGAAAGTCTTGCTCGAGTTT 59.473 47.619 15.13 5.20 38.80 2.66
6198 6652 1.140816 GCGAAAGTCTTGCTCGAGTT 58.859 50.000 15.13 0.00 34.52 3.01
6199 6653 0.667792 GGCGAAAGTCTTGCTCGAGT 60.668 55.000 15.13 0.00 34.52 4.18
6200 6654 1.355066 GGGCGAAAGTCTTGCTCGAG 61.355 60.000 8.45 8.45 34.52 4.04
6201 6655 1.374252 GGGCGAAAGTCTTGCTCGA 60.374 57.895 10.22 0.00 34.52 4.04
6202 6656 2.730672 CGGGCGAAAGTCTTGCTCG 61.731 63.158 3.10 3.10 46.98 5.03
6203 6657 2.391389 CCGGGCGAAAGTCTTGCTC 61.391 63.158 0.00 0.00 34.89 4.26
6204 6658 2.358737 CCGGGCGAAAGTCTTGCT 60.359 61.111 0.00 0.00 34.89 3.91
6205 6659 2.358247 TCCGGGCGAAAGTCTTGC 60.358 61.111 0.00 0.00 34.89 4.01


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

AutoCloner maintained by Alex Coulton.