Multiple sequence alignment - TraesCS6D01G231300

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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 TraesCS6D01G231300 chr6D 100.000 3179 0 0 1 3179 324782145 324785323 0.000000e+00 5871.0
1 TraesCS6D01G231300 chr6D 76.303 1228 205 51 994 2184 324599424 324598246 7.650000e-161 577.0
2 TraesCS6D01G231300 chr6D 95.364 151 7 0 2680 2830 253748542 253748692 1.140000e-59 241.0
3 TraesCS6D01G231300 chr6D 94.805 154 8 0 2677 2830 266773284 266773131 1.140000e-59 241.0
4 TraesCS6D01G231300 chr6D 95.364 151 7 0 2680 2830 296863425 296863575 1.140000e-59 241.0
5 TraesCS6D01G231300 chr6A 92.228 2123 84 32 438 2525 462225307 462227383 0.000000e+00 2931.0
6 TraesCS6D01G231300 chr6A 87.611 339 36 3 1852 2184 461986876 461986538 3.850000e-104 388.0
7 TraesCS6D01G231300 chr6A 87.761 335 31 6 2849 3179 462227371 462227699 1.790000e-102 383.0
8 TraesCS6D01G231300 chr6A 74.427 786 130 41 994 1750 461987718 461986975 4.040000e-69 272.0
9 TraesCS6D01G231300 chr6A 87.719 57 7 0 79 135 462225254 462225310 2.050000e-07 67.6
10 TraesCS6D01G231300 chr6B 93.522 1976 77 22 570 2518 498544484 498542533 0.000000e+00 2892.0
11 TraesCS6D01G231300 chr6B 87.786 524 40 9 1 503 498552512 498551992 2.730000e-165 592.0
12 TraesCS6D01G231300 chr6B 89.877 326 22 8 2854 3179 498542538 498542224 2.950000e-110 409.0
13 TraesCS6D01G231300 chr6B 87.463 335 36 2 1853 2181 498852564 498852898 6.430000e-102 381.0
14 TraesCS6D01G231300 chr6B 87.568 185 23 0 2643 2827 630530183 630530367 6.910000e-52 215.0
15 TraesCS6D01G231300 chr6B 74.268 478 78 26 994 1460 498851680 498852123 3.280000e-35 159.0
16 TraesCS6D01G231300 chr6B 85.030 167 9 5 2526 2681 264059475 264059314 4.250000e-34 156.0
17 TraesCS6D01G231300 chr3D 89.435 1505 111 18 865 2350 580521643 580523118 0.000000e+00 1855.0
18 TraesCS6D01G231300 chr3D 81.447 318 29 12 2868 3179 580523310 580523603 1.910000e-57 233.0
19 TraesCS6D01G231300 chr3D 83.832 167 24 3 527 693 580520686 580520849 4.250000e-34 156.0
20 TraesCS6D01G231300 chr3D 84.431 167 10 5 2526 2681 453280587 453280426 1.980000e-32 150.0
21 TraesCS6D01G231300 chr3D 92.063 63 4 1 757 818 580521171 580521233 1.570000e-13 87.9
22 TraesCS6D01G231300 chr3A 89.112 1497 116 16 865 2342 715973647 715975115 0.000000e+00 1818.0
23 TraesCS6D01G231300 chr3A 81.562 320 29 14 2868 3179 715975331 715975628 1.470000e-58 237.0
24 TraesCS6D01G231300 chr3A 84.024 169 13 9 2524 2681 654404196 654404031 1.980000e-32 150.0
25 TraesCS6D01G231300 chr3B 88.654 1516 116 27 865 2350 775735414 775736903 0.000000e+00 1796.0
26 TraesCS6D01G231300 chr3B 81.588 277 23 10 2908 3178 775737106 775737360 1.490000e-48 204.0
27 TraesCS6D01G231300 chr3B 84.431 167 10 5 2526 2681 424849783 424849622 1.980000e-32 150.0
28 TraesCS6D01G231300 chr3B 84.431 167 10 5 2526 2681 666176113 666175952 1.980000e-32 150.0
29 TraesCS6D01G231300 chr3B 90.385 52 4 1 768 818 775735015 775735066 2.050000e-07 67.6
30 TraesCS6D01G231300 chr7D 96.026 151 6 0 2680 2830 163563479 163563629 2.450000e-61 246.0
31 TraesCS6D01G231300 chr4B 94.771 153 8 0 2678 2830 338425781 338425933 4.100000e-59 239.0
32 TraesCS6D01G231300 chr7B 94.737 152 8 0 2679 2830 460329556 460329707 1.470000e-58 237.0
33 TraesCS6D01G231300 chr2B 80.707 311 41 16 2522 2828 9033273 9033568 1.150000e-54 224.0
34 TraesCS6D01G231300 chr2B 84.431 167 12 6 2526 2681 778699922 778699759 5.490000e-33 152.0
35 TraesCS6D01G231300 chr5A 82.879 257 32 5 2580 2830 706668928 706668678 1.480000e-53 220.0
36 TraesCS6D01G231300 chr2D 85.455 165 10 9 2529 2681 609579806 609579644 3.280000e-35 159.0
37 TraesCS6D01G231300 chr1B 84.431 167 10 6 2526 2681 239055659 239055820 1.980000e-32 150.0


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 TraesCS6D01G231300 chr6D 324782145 324785323 3178 False 5871.000 5871 100.000000 1 3179 1 chr6D.!!$F3 3178
1 TraesCS6D01G231300 chr6D 324598246 324599424 1178 True 577.000 577 76.303000 994 2184 1 chr6D.!!$R2 1190
2 TraesCS6D01G231300 chr6A 462225254 462227699 2445 False 1127.200 2931 89.236000 79 3179 3 chr6A.!!$F1 3100
3 TraesCS6D01G231300 chr6A 461986538 461987718 1180 True 330.000 388 81.019000 994 2184 2 chr6A.!!$R1 1190
4 TraesCS6D01G231300 chr6B 498542224 498544484 2260 True 1650.500 2892 91.699500 570 3179 2 chr6B.!!$R3 2609
5 TraesCS6D01G231300 chr6B 498551992 498552512 520 True 592.000 592 87.786000 1 503 1 chr6B.!!$R2 502
6 TraesCS6D01G231300 chr6B 498851680 498852898 1218 False 270.000 381 80.865500 994 2181 2 chr6B.!!$F2 1187
7 TraesCS6D01G231300 chr3D 580520686 580523603 2917 False 582.975 1855 86.694250 527 3179 4 chr3D.!!$F1 2652
8 TraesCS6D01G231300 chr3A 715973647 715975628 1981 False 1027.500 1818 85.337000 865 3179 2 chr3A.!!$F1 2314
9 TraesCS6D01G231300 chr3B 775735015 775737360 2345 False 689.200 1796 86.875667 768 3178 3 chr3B.!!$F1 2410

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
942 1608 0.032678 GCTTATCTAGCTCGCAGCCA 59.967 55.0 0.0 0.0 46.77 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 3470 0.175302 CCACAAACAAGGCAGCAACA 59.825 50.0 0.0 0.0 0.0 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
25 26 3.489355 TGGCAAAGCATAGATACCATGG 58.511 45.455 11.19 11.19 0.00 3.66
29 30 4.505566 GCAAAGCATAGATACCATGGGAGA 60.506 45.833 18.09 0.54 0.00 3.71
31 32 5.912149 AAGCATAGATACCATGGGAGAAA 57.088 39.130 18.09 0.00 0.00 2.52
123 125 9.057089 CCCATCTTTGGTTTTCTACTCATATAC 57.943 37.037 0.00 0.00 41.91 1.47
190 192 3.365969 GGAATTGTTTCGCTCGGTTGATT 60.366 43.478 0.00 0.00 32.28 2.57
192 194 4.600012 ATTGTTTCGCTCGGTTGATTAG 57.400 40.909 0.00 0.00 0.00 1.73
197 199 1.822990 TCGCTCGGTTGATTAGAACCT 59.177 47.619 0.00 0.00 42.97 3.50
209 211 7.808381 GGTTGATTAGAACCTTAAAGCTCAAAC 59.192 37.037 0.00 0.00 42.03 2.93
225 229 1.111277 AAACCCAGGTGAGTTTGTGC 58.889 50.000 0.00 0.00 34.97 4.57
232 236 2.031870 AGGTGAGTTTGTGCTTTTCCC 58.968 47.619 0.00 0.00 0.00 3.97
234 238 2.430694 GGTGAGTTTGTGCTTTTCCCTT 59.569 45.455 0.00 0.00 0.00 3.95
257 265 3.687698 GGCAATCTAAAACTGCCGAAGTA 59.312 43.478 0.00 0.00 45.72 2.24
271 279 6.693978 ACTGCCGAAGTAATTGTGTTTTTAAC 59.306 34.615 0.00 0.00 37.36 2.01
275 283 7.593644 GCCGAAGTAATTGTGTTTTTAACAGAT 59.406 33.333 0.00 0.00 43.10 2.90
341 349 6.005823 TGATGGATTTGTGTGTGATCTTCTT 58.994 36.000 0.00 0.00 0.00 2.52
344 352 6.738114 TGGATTTGTGTGTGATCTTCTTTTC 58.262 36.000 0.00 0.00 0.00 2.29
348 356 3.248363 TGTGTGTGATCTTCTTTTCAGCG 59.752 43.478 0.00 0.00 0.00 5.18
358 366 2.175184 CTTTTCAGCGTGCGGAGGTG 62.175 60.000 0.00 0.00 38.34 4.00
516 558 3.877508 GTCATAGCGGAGGCAAAATAGTT 59.122 43.478 0.00 0.00 43.41 2.24
522 564 2.420022 CGGAGGCAAAATAGTTGTCCTG 59.580 50.000 1.55 0.00 0.00 3.86
532 574 6.821616 AAATAGTTGTCCTGATCTCCTCAT 57.178 37.500 0.00 0.00 32.10 2.90
534 576 2.692557 AGTTGTCCTGATCTCCTCATCG 59.307 50.000 0.00 0.00 32.10 3.84
541 583 3.993081 CCTGATCTCCTCATCGCATTAAC 59.007 47.826 0.00 0.00 32.10 2.01
598 640 9.575783 GTCCATTAGCATTATAGCTACTTCTAC 57.424 37.037 0.00 0.00 46.07 2.59
658 700 5.404667 GCGCTTATAACAGGTCCAAGTATAC 59.595 44.000 0.00 0.00 0.00 1.47
709 751 7.064134 TGCGTTTTCCTATTGTACAATCTACTG 59.936 37.037 24.00 9.72 32.50 2.74
835 1162 1.098712 TCCCCAATAATTCGCCACGC 61.099 55.000 0.00 0.00 0.00 5.34
845 1172 4.059459 CGCCACGCACGTCTGAAC 62.059 66.667 0.00 0.00 0.00 3.18
942 1608 0.032678 GCTTATCTAGCTCGCAGCCA 59.967 55.000 0.00 0.00 46.77 4.75
944 1610 0.389391 TTATCTAGCTCGCAGCCACC 59.611 55.000 0.00 0.00 43.77 4.61
969 1639 1.970092 TTCGAGCTCCTAGTCCTAGC 58.030 55.000 8.47 0.00 36.48 3.42
1379 2073 2.412323 CGGCTACCAGACCGCTGTA 61.412 63.158 0.00 0.00 43.44 2.74
1510 2284 0.467290 AATGGTGCAAAGTGGTCGGT 60.467 50.000 0.00 0.00 0.00 4.69
1542 2327 4.886489 TCCTGACAAAATGTGTTGATGTGA 59.114 37.500 0.00 0.00 41.96 3.58
1835 2649 1.651240 ATGTGTGCTGATCTTGGCGC 61.651 55.000 0.00 0.00 39.13 6.53
1850 2664 1.065491 TGGCGCTCCTGTTAATCATGT 60.065 47.619 7.64 0.00 0.00 3.21
2185 3005 1.254954 GAACTACCCCTGAGTCACGT 58.745 55.000 0.00 0.00 0.00 4.49
2186 3006 1.201880 GAACTACCCCTGAGTCACGTC 59.798 57.143 0.00 0.00 0.00 4.34
2187 3007 0.111832 ACTACCCCTGAGTCACGTCA 59.888 55.000 0.00 0.00 0.00 4.35
2188 3008 0.526662 CTACCCCTGAGTCACGTCAC 59.473 60.000 0.00 0.00 0.00 3.67
2189 3009 0.178984 TACCCCTGAGTCACGTCACA 60.179 55.000 0.00 0.00 0.00 3.58
2208 3028 2.509548 ACAGCCATATTTACCTGCTCCA 59.490 45.455 0.00 0.00 0.00 3.86
2291 3113 1.133513 TCAGATGAGGAGGAGGAGCTC 60.134 57.143 4.71 4.71 0.00 4.09
2298 3120 0.107459 GGAGGAGGAGCTCGCAAAAT 60.107 55.000 7.83 0.00 0.00 1.82
2359 3190 8.212995 AGTGATGTATCATGTGTCATTAATCCA 58.787 33.333 0.00 0.00 39.30 3.41
2373 3204 7.505585 TGTCATTAATCCATCTGTAATTTCCCC 59.494 37.037 0.00 0.00 0.00 4.81
2457 3298 2.096417 GTCGATGTACCAAGTTGTGTGC 60.096 50.000 1.45 4.17 0.00 4.57
2514 3356 9.988350 AAATTTCACGATTACTACTTGCTTATG 57.012 29.630 0.00 0.00 0.00 1.90
2515 3357 7.534085 TTTCACGATTACTACTTGCTTATGG 57.466 36.000 0.00 0.00 0.00 2.74
2517 3359 6.869695 TCACGATTACTACTTGCTTATGGAA 58.130 36.000 0.00 0.00 0.00 3.53
2518 3360 6.978659 TCACGATTACTACTTGCTTATGGAAG 59.021 38.462 8.13 8.13 45.44 3.46
2519 3361 6.201044 CACGATTACTACTTGCTTATGGAAGG 59.799 42.308 13.30 0.96 44.45 3.46
2520 3362 5.696724 CGATTACTACTTGCTTATGGAAGGG 59.303 44.000 13.30 8.51 44.45 3.95
2522 3364 6.630203 TTACTACTTGCTTATGGAAGGGAA 57.370 37.500 13.30 0.00 44.45 3.97
2523 3365 5.514500 ACTACTTGCTTATGGAAGGGAAA 57.486 39.130 13.30 0.00 44.45 3.13
2526 3368 4.026052 ACTTGCTTATGGAAGGGAAATGG 58.974 43.478 13.30 0.00 44.45 3.16
2527 3369 3.030873 TGCTTATGGAAGGGAAATGGG 57.969 47.619 0.00 0.00 32.84 4.00
2528 3370 2.314549 TGCTTATGGAAGGGAAATGGGT 59.685 45.455 0.00 0.00 32.84 4.51
2530 3372 3.373110 GCTTATGGAAGGGAAATGGGTCT 60.373 47.826 0.00 0.00 32.84 3.85
2531 3373 2.834638 ATGGAAGGGAAATGGGTCTG 57.165 50.000 0.00 0.00 0.00 3.51
2532 3374 1.455822 TGGAAGGGAAATGGGTCTGT 58.544 50.000 0.00 0.00 0.00 3.41
2533 3375 1.786441 TGGAAGGGAAATGGGTCTGTT 59.214 47.619 0.00 0.00 0.00 3.16
2534 3376 2.178984 TGGAAGGGAAATGGGTCTGTTT 59.821 45.455 0.00 0.00 0.00 2.83
2535 3377 3.399644 TGGAAGGGAAATGGGTCTGTTTA 59.600 43.478 0.00 0.00 0.00 2.01
2536 3378 4.017126 GGAAGGGAAATGGGTCTGTTTAG 58.983 47.826 0.00 0.00 0.00 1.85
2537 3379 3.739401 AGGGAAATGGGTCTGTTTAGG 57.261 47.619 0.00 0.00 0.00 2.69
2538 3380 3.265489 AGGGAAATGGGTCTGTTTAGGA 58.735 45.455 0.00 0.00 0.00 2.94
2539 3381 3.010250 AGGGAAATGGGTCTGTTTAGGAC 59.990 47.826 0.00 0.00 0.00 3.85
2543 3385 6.365520 GGAAATGGGTCTGTTTAGGACATAT 58.634 40.000 0.00 0.00 37.69 1.78
2544 3386 6.486993 GGAAATGGGTCTGTTTAGGACATATC 59.513 42.308 0.00 0.00 37.69 1.63
2545 3387 6.831664 AATGGGTCTGTTTAGGACATATCT 57.168 37.500 0.00 0.00 37.69 1.98
2546 3388 7.931015 AATGGGTCTGTTTAGGACATATCTA 57.069 36.000 0.00 0.00 37.69 1.98
2549 3391 7.306013 TGGGTCTGTTTAGGACATATCTAGAT 58.694 38.462 10.73 10.73 37.69 1.98
2550 3392 7.233553 TGGGTCTGTTTAGGACATATCTAGATG 59.766 40.741 15.79 3.53 37.69 2.90
2554 3396 8.851145 TCTGTTTAGGACATATCTAGATGTGAC 58.149 37.037 29.72 24.07 40.18 3.67
2555 3397 8.533569 TGTTTAGGACATATCTAGATGTGACA 57.466 34.615 29.72 20.47 40.18 3.58
2583 3425 8.976353 AGTTATGTCACATCTAACTTGATCTCT 58.024 33.333 0.00 0.00 33.10 3.10
2584 3426 9.593134 GTTATGTCACATCTAACTTGATCTCTT 57.407 33.333 0.00 0.00 0.00 2.85
2586 3428 7.895975 TGTCACATCTAACTTGATCTCTTTG 57.104 36.000 0.00 0.00 0.00 2.77
2587 3429 7.445121 TGTCACATCTAACTTGATCTCTTTGT 58.555 34.615 0.00 0.00 0.00 2.83
2588 3430 7.386025 TGTCACATCTAACTTGATCTCTTTGTG 59.614 37.037 0.00 0.00 0.00 3.33
2589 3431 6.875726 TCACATCTAACTTGATCTCTTTGTGG 59.124 38.462 0.00 0.00 0.00 4.17
2590 3432 6.652481 CACATCTAACTTGATCTCTTTGTGGT 59.348 38.462 0.00 0.00 0.00 4.16
2591 3433 6.876257 ACATCTAACTTGATCTCTTTGTGGTC 59.124 38.462 0.00 0.00 0.00 4.02
2592 3434 6.672266 TCTAACTTGATCTCTTTGTGGTCT 57.328 37.500 0.00 0.00 0.00 3.85
2593 3435 7.776618 TCTAACTTGATCTCTTTGTGGTCTA 57.223 36.000 0.00 0.00 0.00 2.59
2594 3436 8.367660 TCTAACTTGATCTCTTTGTGGTCTAT 57.632 34.615 0.00 0.00 0.00 1.98
2596 3438 9.442047 CTAACTTGATCTCTTTGTGGTCTATTT 57.558 33.333 0.00 0.00 0.00 1.40
2598 3440 8.697507 ACTTGATCTCTTTGTGGTCTATTTTT 57.302 30.769 0.00 0.00 0.00 1.94
2638 3480 3.608316 TTTTGTTTCTTGTTGCTGCCT 57.392 38.095 0.00 0.00 0.00 4.75
2639 3481 3.608316 TTTGTTTCTTGTTGCTGCCTT 57.392 38.095 0.00 0.00 0.00 4.35
2640 3482 2.582728 TGTTTCTTGTTGCTGCCTTG 57.417 45.000 0.00 0.00 0.00 3.61
2641 3483 1.824230 TGTTTCTTGTTGCTGCCTTGT 59.176 42.857 0.00 0.00 0.00 3.16
2642 3484 2.233431 TGTTTCTTGTTGCTGCCTTGTT 59.767 40.909 0.00 0.00 0.00 2.83
2644 3486 2.582728 TCTTGTTGCTGCCTTGTTTG 57.417 45.000 0.00 0.00 0.00 2.93
2645 3487 1.824230 TCTTGTTGCTGCCTTGTTTGT 59.176 42.857 0.00 0.00 0.00 2.83
2646 3488 1.928503 CTTGTTGCTGCCTTGTTTGTG 59.071 47.619 0.00 0.00 0.00 3.33
2647 3489 0.175302 TGTTGCTGCCTTGTTTGTGG 59.825 50.000 0.00 0.00 0.00 4.17
2648 3490 0.530431 GTTGCTGCCTTGTTTGTGGG 60.530 55.000 0.00 0.00 0.00 4.61
2649 3491 0.685785 TTGCTGCCTTGTTTGTGGGA 60.686 50.000 0.00 0.00 0.00 4.37
2650 3492 1.108727 TGCTGCCTTGTTTGTGGGAG 61.109 55.000 0.00 0.00 43.41 4.30
2651 3493 1.809567 GCTGCCTTGTTTGTGGGAGG 61.810 60.000 0.00 0.00 41.30 4.30
2652 3494 0.468029 CTGCCTTGTTTGTGGGAGGT 60.468 55.000 0.00 0.00 38.01 3.85
2654 3496 1.215673 TGCCTTGTTTGTGGGAGGTTA 59.784 47.619 0.00 0.00 0.00 2.85
2655 3497 1.886542 GCCTTGTTTGTGGGAGGTTAG 59.113 52.381 0.00 0.00 0.00 2.34
2656 3498 2.488347 GCCTTGTTTGTGGGAGGTTAGA 60.488 50.000 0.00 0.00 0.00 2.10
2657 3499 3.814316 GCCTTGTTTGTGGGAGGTTAGAT 60.814 47.826 0.00 0.00 0.00 1.98
2658 3500 3.758554 CCTTGTTTGTGGGAGGTTAGATG 59.241 47.826 0.00 0.00 0.00 2.90
2662 3504 4.042809 TGTTTGTGGGAGGTTAGATGTGAT 59.957 41.667 0.00 0.00 0.00 3.06
2664 3506 6.069673 TGTTTGTGGGAGGTTAGATGTGATAT 60.070 38.462 0.00 0.00 0.00 1.63
2665 3507 5.808366 TGTGGGAGGTTAGATGTGATATC 57.192 43.478 0.00 0.00 0.00 1.63
2667 3509 4.841246 GTGGGAGGTTAGATGTGATATCCT 59.159 45.833 0.00 0.00 0.00 3.24
2668 3510 5.308237 GTGGGAGGTTAGATGTGATATCCTT 59.692 44.000 0.00 0.00 0.00 3.36
2669 3511 6.497259 GTGGGAGGTTAGATGTGATATCCTTA 59.503 42.308 0.00 0.00 0.00 2.69
2670 3512 7.016268 GTGGGAGGTTAGATGTGATATCCTTAA 59.984 40.741 0.00 0.00 0.00 1.85
2671 3513 7.570982 TGGGAGGTTAGATGTGATATCCTTAAA 59.429 37.037 0.00 0.00 0.00 1.52
2672 3514 8.437575 GGGAGGTTAGATGTGATATCCTTAAAA 58.562 37.037 0.00 0.00 0.00 1.52
2673 3515 9.847224 GGAGGTTAGATGTGATATCCTTAAAAA 57.153 33.333 0.00 0.00 0.00 1.94
2693 3535 6.650427 AAAAACATCTACTCCCTTTGTTCC 57.350 37.500 0.00 0.00 30.62 3.62
2694 3536 5.584551 AAACATCTACTCCCTTTGTTCCT 57.415 39.130 0.00 0.00 30.62 3.36
2695 3537 4.559862 ACATCTACTCCCTTTGTTCCTG 57.440 45.455 0.00 0.00 0.00 3.86
2696 3538 4.168101 ACATCTACTCCCTTTGTTCCTGA 58.832 43.478 0.00 0.00 0.00 3.86
2697 3539 4.597507 ACATCTACTCCCTTTGTTCCTGAA 59.402 41.667 0.00 0.00 0.00 3.02
2698 3540 5.251700 ACATCTACTCCCTTTGTTCCTGAAT 59.748 40.000 0.00 0.00 0.00 2.57
2699 3541 6.443849 ACATCTACTCCCTTTGTTCCTGAATA 59.556 38.462 0.00 0.00 0.00 1.75
2700 3542 7.127955 ACATCTACTCCCTTTGTTCCTGAATAT 59.872 37.037 0.00 0.00 0.00 1.28
2701 3543 7.510675 TCTACTCCCTTTGTTCCTGAATATT 57.489 36.000 0.00 0.00 0.00 1.28
2702 3544 7.928873 TCTACTCCCTTTGTTCCTGAATATTT 58.071 34.615 0.00 0.00 0.00 1.40
2703 3545 6.840780 ACTCCCTTTGTTCCTGAATATTTG 57.159 37.500 0.00 0.00 0.00 2.32
2704 3546 6.314917 ACTCCCTTTGTTCCTGAATATTTGT 58.685 36.000 0.00 0.00 0.00 2.83
2705 3547 6.434340 ACTCCCTTTGTTCCTGAATATTTGTC 59.566 38.462 0.00 0.00 0.00 3.18
2706 3548 6.552008 TCCCTTTGTTCCTGAATATTTGTCT 58.448 36.000 0.00 0.00 0.00 3.41
2707 3549 7.010160 TCCCTTTGTTCCTGAATATTTGTCTT 58.990 34.615 0.00 0.00 0.00 3.01
2708 3550 7.508977 TCCCTTTGTTCCTGAATATTTGTCTTT 59.491 33.333 0.00 0.00 0.00 2.52
2709 3551 7.814587 CCCTTTGTTCCTGAATATTTGTCTTTC 59.185 37.037 0.00 0.00 0.00 2.62
2710 3552 8.579863 CCTTTGTTCCTGAATATTTGTCTTTCT 58.420 33.333 0.00 0.00 0.00 2.52
2713 3555 8.792830 TGTTCCTGAATATTTGTCTTTCTAGG 57.207 34.615 0.00 0.00 0.00 3.02
2714 3556 7.336931 TGTTCCTGAATATTTGTCTTTCTAGGC 59.663 37.037 0.00 0.00 0.00 3.93
2715 3557 6.957631 TCCTGAATATTTGTCTTTCTAGGCA 58.042 36.000 0.00 0.00 33.22 4.75
2716 3558 7.577303 TCCTGAATATTTGTCTTTCTAGGCAT 58.423 34.615 0.00 0.00 35.56 4.40
2717 3559 8.055181 TCCTGAATATTTGTCTTTCTAGGCATT 58.945 33.333 0.00 0.00 35.56 3.56
2718 3560 8.689972 CCTGAATATTTGTCTTTCTAGGCATTT 58.310 33.333 0.00 0.00 35.56 2.32
2725 3567 9.657419 ATTTGTCTTTCTAGGCATTTTAAATGG 57.343 29.630 17.89 3.11 35.56 3.16
2726 3568 7.169158 TGTCTTTCTAGGCATTTTAAATGGG 57.831 36.000 17.89 0.00 29.10 4.00
2727 3569 6.042777 GTCTTTCTAGGCATTTTAAATGGGC 58.957 40.000 17.89 11.30 0.00 5.36
2728 3570 5.719085 TCTTTCTAGGCATTTTAAATGGGCA 59.281 36.000 17.89 3.90 0.00 5.36
2729 3571 5.337578 TTCTAGGCATTTTAAATGGGCAC 57.662 39.130 17.89 2.75 0.00 5.01
2730 3572 4.348486 TCTAGGCATTTTAAATGGGCACA 58.652 39.130 17.89 0.00 0.00 4.57
2731 3573 4.774726 TCTAGGCATTTTAAATGGGCACAA 59.225 37.500 17.89 3.00 0.00 3.33
2732 3574 3.673902 AGGCATTTTAAATGGGCACAAC 58.326 40.909 17.89 1.13 0.00 3.32
2733 3575 3.072184 AGGCATTTTAAATGGGCACAACA 59.928 39.130 17.89 0.00 0.00 3.33
2734 3576 4.009002 GGCATTTTAAATGGGCACAACAT 58.991 39.130 17.89 0.00 0.00 2.71
2735 3577 5.046014 AGGCATTTTAAATGGGCACAACATA 60.046 36.000 17.89 0.00 0.00 2.29
2736 3578 5.064579 GGCATTTTAAATGGGCACAACATAC 59.935 40.000 17.89 0.00 0.00 2.39
2737 3579 5.220378 GCATTTTAAATGGGCACAACATACG 60.220 40.000 17.89 0.00 0.00 3.06
2738 3580 4.442375 TTTAAATGGGCACAACATACGG 57.558 40.909 0.00 0.00 0.00 4.02
2739 3581 2.208132 AAATGGGCACAACATACGGA 57.792 45.000 0.00 0.00 0.00 4.69
2740 3582 2.435372 AATGGGCACAACATACGGAT 57.565 45.000 0.00 0.00 0.00 4.18
2741 3583 1.679139 ATGGGCACAACATACGGATG 58.321 50.000 5.94 5.94 39.16 3.51
2743 3585 1.555533 TGGGCACAACATACGGATGTA 59.444 47.619 15.10 0.00 45.93 2.29
2744 3586 2.171659 TGGGCACAACATACGGATGTAT 59.828 45.455 15.10 2.23 45.93 2.29
2782 3624 5.674052 AGTGTAGATTCACTCATCTTGCT 57.326 39.130 0.00 0.00 44.07 3.91
2783 3625 5.659463 AGTGTAGATTCACTCATCTTGCTC 58.341 41.667 0.00 0.00 44.07 4.26
2784 3626 4.808364 GTGTAGATTCACTCATCTTGCTCC 59.192 45.833 0.00 0.00 35.08 4.70
2785 3627 3.176552 AGATTCACTCATCTTGCTCCG 57.823 47.619 0.00 0.00 28.19 4.63
2786 3628 2.499289 AGATTCACTCATCTTGCTCCGT 59.501 45.455 0.00 0.00 28.19 4.69
2787 3629 3.701542 AGATTCACTCATCTTGCTCCGTA 59.298 43.478 0.00 0.00 28.19 4.02
2788 3630 4.343526 AGATTCACTCATCTTGCTCCGTAT 59.656 41.667 0.00 0.00 28.19 3.06
2789 3631 3.443099 TCACTCATCTTGCTCCGTATG 57.557 47.619 0.00 0.00 0.00 2.39
2790 3632 2.760650 TCACTCATCTTGCTCCGTATGT 59.239 45.455 0.00 0.00 0.00 2.29
2791 3633 3.951680 TCACTCATCTTGCTCCGTATGTA 59.048 43.478 0.00 0.00 0.00 2.29
2792 3634 4.036852 TCACTCATCTTGCTCCGTATGTAG 59.963 45.833 0.00 0.00 0.00 2.74
2793 3635 3.954904 ACTCATCTTGCTCCGTATGTAGT 59.045 43.478 0.00 0.00 0.00 2.73
2794 3636 4.036971 ACTCATCTTGCTCCGTATGTAGTC 59.963 45.833 0.00 0.00 0.00 2.59
2795 3637 3.951680 TCATCTTGCTCCGTATGTAGTCA 59.048 43.478 0.00 0.00 0.00 3.41
2796 3638 4.584743 TCATCTTGCTCCGTATGTAGTCAT 59.415 41.667 0.00 0.00 38.00 3.06
2797 3639 5.069119 TCATCTTGCTCCGTATGTAGTCATT 59.931 40.000 0.00 0.00 35.70 2.57
2798 3640 5.339008 TCTTGCTCCGTATGTAGTCATTT 57.661 39.130 0.00 0.00 35.70 2.32
2799 3641 5.109210 TCTTGCTCCGTATGTAGTCATTTG 58.891 41.667 0.00 0.00 35.70 2.32
2800 3642 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
2801 3643 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
2802 3644 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
2803 3645 4.868171 GCTCCGTATGTAGTCATTTGTTGA 59.132 41.667 0.00 0.00 35.70 3.18
2804 3646 5.350365 GCTCCGTATGTAGTCATTTGTTGAA 59.650 40.000 0.00 0.00 35.70 2.69
2805 3647 6.128391 GCTCCGTATGTAGTCATTTGTTGAAA 60.128 38.462 0.00 0.00 35.70 2.69
2806 3648 7.414098 GCTCCGTATGTAGTCATTTGTTGAAAT 60.414 37.037 0.00 0.00 35.70 2.17
2807 3649 7.970384 TCCGTATGTAGTCATTTGTTGAAATC 58.030 34.615 0.00 0.00 35.70 2.17
2808 3650 7.822334 TCCGTATGTAGTCATTTGTTGAAATCT 59.178 33.333 0.00 0.00 35.70 2.40
2809 3651 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
2810 3652 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
2814 3656 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
2837 3679 9.927668 AGAAAAACAAATATTTGGGTAGATGTG 57.072 29.630 27.43 4.32 42.34 3.21
2838 3680 9.921637 GAAAAACAAATATTTGGGTAGATGTGA 57.078 29.630 27.43 0.00 42.34 3.58
2848 3690 8.877864 ATTTGGGTAGATGTGAATTAGACAAA 57.122 30.769 0.00 0.00 0.00 2.83
2849 3691 8.877864 TTTGGGTAGATGTGAATTAGACAAAT 57.122 30.769 0.00 0.00 0.00 2.32
2850 3692 8.877864 TTGGGTAGATGTGAATTAGACAAATT 57.122 30.769 0.00 0.00 40.59 1.82
2851 3693 8.279970 TGGGTAGATGTGAATTAGACAAATTG 57.720 34.615 0.00 0.00 37.93 2.32
2852 3694 8.106462 TGGGTAGATGTGAATTAGACAAATTGA 58.894 33.333 0.00 0.00 37.93 2.57
2856 3698 8.868522 AGATGTGAATTAGACAAATTGAAGGA 57.131 30.769 0.00 0.00 37.93 3.36
2880 3722 7.061789 GGAAAATTAGTGAAGGTGCAAATTACG 59.938 37.037 0.00 0.00 0.00 3.18
2885 3727 5.250200 AGTGAAGGTGCAAATTACGGATAA 58.750 37.500 0.00 0.00 0.00 1.75
2899 3741 7.762588 ATTACGGATAATCTGTACTAGCACT 57.237 36.000 0.00 0.00 37.91 4.40
2900 3742 7.578310 TTACGGATAATCTGTACTAGCACTT 57.422 36.000 0.00 0.00 37.91 3.16
2906 3750 8.202137 GGATAATCTGTACTAGCACTTTTACCA 58.798 37.037 0.00 0.00 0.00 3.25
3064 3916 6.949352 ACTGATTGCCCTACTCAATTATTG 57.051 37.500 0.00 0.00 34.59 1.90
3116 3968 4.689612 TGAAGGAGCTTCAGTTGTAAGT 57.310 40.909 0.00 0.00 44.27 2.24
3117 3969 5.801531 TGAAGGAGCTTCAGTTGTAAGTA 57.198 39.130 0.00 0.00 44.27 2.24
3118 3970 5.539048 TGAAGGAGCTTCAGTTGTAAGTAC 58.461 41.667 0.00 0.00 44.27 2.73
3122 3974 5.094134 GGAGCTTCAGTTGTAAGTACGTAG 58.906 45.833 0.00 0.00 0.00 3.51
3124 3976 6.128172 GGAGCTTCAGTTGTAAGTACGTAGTA 60.128 42.308 2.72 0.00 45.11 1.82
3139 3995 3.310774 ACGTAGTAGTACACATGTAGGCG 59.689 47.826 0.00 0.00 41.94 5.52
3158 4014 2.576406 CGCTACTCTATAAGTCTGCGC 58.424 52.381 0.00 0.00 46.35 6.09
3159 4015 2.576406 GCTACTCTATAAGTCTGCGCG 58.424 52.381 0.00 0.00 39.55 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 3.962718 CCAAAGATGGGTGGCAAATAGAT 59.037 43.478 0.00 0.00 43.51 1.98
123 125 6.823689 AGTTGCTGGAGGTAAGTAATATGTTG 59.176 38.462 0.00 0.00 0.00 3.33
125 127 6.561519 AGTTGCTGGAGGTAAGTAATATGT 57.438 37.500 0.00 0.00 0.00 2.29
167 169 1.535462 CAACCGAGCGAAACAATTCCT 59.465 47.619 0.00 0.00 31.52 3.36
174 176 3.181523 GGTTCTAATCAACCGAGCGAAAC 60.182 47.826 0.00 0.00 36.69 2.78
175 177 2.997986 GGTTCTAATCAACCGAGCGAAA 59.002 45.455 0.00 0.00 36.69 3.46
190 192 5.313280 TGGGTTTGAGCTTTAAGGTTCTA 57.687 39.130 0.00 0.00 0.00 2.10
192 194 3.255888 CCTGGGTTTGAGCTTTAAGGTTC 59.744 47.826 0.00 0.00 0.00 3.62
197 199 3.117663 ACTCACCTGGGTTTGAGCTTTAA 60.118 43.478 11.53 0.00 42.67 1.52
209 211 1.402787 AAAGCACAAACTCACCTGGG 58.597 50.000 0.00 0.00 0.00 4.45
225 229 5.928264 CAGTTTTAGATTGCCAAGGGAAAAG 59.072 40.000 0.00 0.00 0.00 2.27
296 304 3.026630 TGTAGCTCGGAAGACAACTTG 57.973 47.619 0.00 0.00 36.39 3.16
297 305 3.258372 TCATGTAGCTCGGAAGACAACTT 59.742 43.478 0.00 0.00 39.24 2.66
299 307 3.232213 TCATGTAGCTCGGAAGACAAC 57.768 47.619 0.00 0.00 35.39 3.32
303 311 2.666317 TCCATCATGTAGCTCGGAAGA 58.334 47.619 0.00 0.00 39.12 2.87
307 315 3.249320 CACAAATCCATCATGTAGCTCGG 59.751 47.826 0.00 0.00 0.00 4.63
308 316 3.873361 ACACAAATCCATCATGTAGCTCG 59.127 43.478 0.00 0.00 0.00 5.03
309 317 4.637534 ACACACAAATCCATCATGTAGCTC 59.362 41.667 0.00 0.00 0.00 4.09
310 318 4.397103 CACACACAAATCCATCATGTAGCT 59.603 41.667 0.00 0.00 0.00 3.32
341 349 2.664851 CACCTCCGCACGCTGAAA 60.665 61.111 0.00 0.00 0.00 2.69
362 370 2.515523 ATCATGCTCCGCCACTGC 60.516 61.111 0.00 0.00 0.00 4.40
516 558 1.035923 GCGATGAGGAGATCAGGACA 58.964 55.000 0.00 0.00 42.53 4.02
522 564 4.876125 TCTGTTAATGCGATGAGGAGATC 58.124 43.478 0.00 0.00 0.00 2.75
532 574 4.404394 TGTAATCCTCCTCTGTTAATGCGA 59.596 41.667 0.00 0.00 0.00 5.10
534 576 5.880332 TGTTGTAATCCTCCTCTGTTAATGC 59.120 40.000 0.00 0.00 0.00 3.56
541 583 9.838339 ATATAACTTTGTTGTAATCCTCCTCTG 57.162 33.333 0.00 0.00 0.00 3.35
598 640 7.216973 AGGTCAAACTTACTGTCTGTACTAG 57.783 40.000 0.00 0.00 0.00 2.57
658 700 2.670414 GCTGAGAAGTTCAATCTGGACG 59.330 50.000 5.50 0.00 34.81 4.79
753 1039 7.113684 CGAACTATTACTAATCTGCAGTACAGC 59.886 40.741 14.67 2.82 46.76 4.40
755 1041 7.067859 ACCGAACTATTACTAATCTGCAGTACA 59.932 37.037 14.67 0.00 0.00 2.90
835 1162 3.584868 GACCGGGGGTTCAGACGTG 62.585 68.421 6.32 0.00 35.25 4.49
845 1172 3.562732 GAACACTTGGGACCGGGGG 62.563 68.421 6.32 0.00 0.00 5.40
942 1608 4.254492 GACTAGGAGCTCGAAAATTTGGT 58.746 43.478 7.83 0.00 0.00 3.67
944 1610 4.508662 AGGACTAGGAGCTCGAAAATTTG 58.491 43.478 7.83 0.00 0.00 2.32
1421 2115 2.124570 CCCGCCATGAACAGAGGG 60.125 66.667 0.00 0.00 0.00 4.30
1510 2284 0.181587 TTTTGTCAGGACCAGCCGAA 59.818 50.000 0.00 0.00 43.43 4.30
1542 2327 1.461897 GTGCATTTAACCTGCGTACGT 59.538 47.619 17.90 0.00 42.62 3.57
1850 2664 0.322456 GTACTTGCATGGCACCCTGA 60.322 55.000 4.44 0.00 38.71 3.86
2013 2827 4.704103 AGAGCGCCCCAGTCCTGA 62.704 66.667 2.29 0.00 0.00 3.86
2028 2842 1.073025 ATTGTTGAGGCGCCACAGA 59.927 52.632 31.54 18.06 0.00 3.41
2185 3005 3.433598 GGAGCAGGTAAATATGGCTGTGA 60.434 47.826 0.00 0.00 34.44 3.58
2186 3006 2.880890 GGAGCAGGTAAATATGGCTGTG 59.119 50.000 0.00 0.00 34.44 3.66
2187 3007 2.509548 TGGAGCAGGTAAATATGGCTGT 59.490 45.455 0.00 0.00 34.44 4.40
2188 3008 3.213206 TGGAGCAGGTAAATATGGCTG 57.787 47.619 0.00 0.00 34.44 4.85
2189 3009 3.139025 ACATGGAGCAGGTAAATATGGCT 59.861 43.478 0.00 0.00 37.56 4.75
2208 3028 7.485418 TTCGCGGTATATAAAATTCACACAT 57.515 32.000 6.13 0.00 0.00 3.21
2291 3113 3.244976 GAGGGAACATCACAATTTTGCG 58.755 45.455 0.00 0.00 0.00 4.85
2298 3120 0.698238 CCAGGGAGGGAACATCACAA 59.302 55.000 0.00 0.00 0.00 3.33
2514 3356 2.604912 AACAGACCCATTTCCCTTCC 57.395 50.000 0.00 0.00 0.00 3.46
2515 3357 4.017126 CCTAAACAGACCCATTTCCCTTC 58.983 47.826 0.00 0.00 0.00 3.46
2517 3359 3.010250 GTCCTAAACAGACCCATTTCCCT 59.990 47.826 0.00 0.00 0.00 4.20
2518 3360 3.245122 TGTCCTAAACAGACCCATTTCCC 60.245 47.826 0.00 0.00 33.09 3.97
2519 3361 4.028993 TGTCCTAAACAGACCCATTTCC 57.971 45.455 0.00 0.00 33.09 3.13
2520 3362 7.283329 AGATATGTCCTAAACAGACCCATTTC 58.717 38.462 0.00 0.00 42.37 2.17
2522 3364 6.831664 AGATATGTCCTAAACAGACCCATT 57.168 37.500 0.00 0.00 42.37 3.16
2523 3365 7.306013 TCTAGATATGTCCTAAACAGACCCAT 58.694 38.462 0.00 0.00 42.37 4.00
2526 3368 8.085296 CACATCTAGATATGTCCTAAACAGACC 58.915 40.741 4.54 0.00 42.37 3.85
2527 3369 8.851145 TCACATCTAGATATGTCCTAAACAGAC 58.149 37.037 10.72 0.00 42.37 3.51
2528 3370 8.851145 GTCACATCTAGATATGTCCTAAACAGA 58.149 37.037 10.72 0.00 42.37 3.41
2530 3372 8.533569 TGTCACATCTAGATATGTCCTAAACA 57.466 34.615 10.72 4.19 43.51 2.83
2535 3377 8.948401 AACTATGTCACATCTAGATATGTCCT 57.052 34.615 10.72 1.66 38.01 3.85
2557 3399 8.976353 AGAGATCAAGTTAGATGTGACATAACT 58.024 33.333 7.69 7.69 40.55 2.24
2558 3400 9.593134 AAGAGATCAAGTTAGATGTGACATAAC 57.407 33.333 0.00 0.15 0.00 1.89
2561 3403 8.099537 ACAAAGAGATCAAGTTAGATGTGACAT 58.900 33.333 0.00 0.00 0.00 3.06
2562 3404 7.386025 CACAAAGAGATCAAGTTAGATGTGACA 59.614 37.037 0.00 0.00 0.00 3.58
2563 3405 7.148507 CCACAAAGAGATCAAGTTAGATGTGAC 60.149 40.741 0.00 0.00 0.00 3.67
2564 3406 6.875726 CCACAAAGAGATCAAGTTAGATGTGA 59.124 38.462 0.00 0.00 0.00 3.58
2565 3407 6.652481 ACCACAAAGAGATCAAGTTAGATGTG 59.348 38.462 0.00 0.00 0.00 3.21
2567 3409 7.102346 AGACCACAAAGAGATCAAGTTAGATG 58.898 38.462 0.00 0.00 0.00 2.90
2568 3410 7.251321 AGACCACAAAGAGATCAAGTTAGAT 57.749 36.000 0.00 0.00 0.00 1.98
2569 3411 6.672266 AGACCACAAAGAGATCAAGTTAGA 57.328 37.500 0.00 0.00 0.00 2.10
2570 3412 9.442047 AAATAGACCACAAAGAGATCAAGTTAG 57.558 33.333 0.00 0.00 0.00 2.34
2571 3413 9.793259 AAAATAGACCACAAAGAGATCAAGTTA 57.207 29.630 0.00 0.00 0.00 2.24
2572 3414 8.697507 AAAATAGACCACAAAGAGATCAAGTT 57.302 30.769 0.00 0.00 0.00 2.66
2573 3415 8.697507 AAAAATAGACCACAAAGAGATCAAGT 57.302 30.769 0.00 0.00 0.00 3.16
2618 3460 3.608316 AGGCAGCAACAAGAAACAAAA 57.392 38.095 0.00 0.00 0.00 2.44
2620 3462 2.233431 ACAAGGCAGCAACAAGAAACAA 59.767 40.909 0.00 0.00 0.00 2.83
2623 3465 3.260740 CAAACAAGGCAGCAACAAGAAA 58.739 40.909 0.00 0.00 0.00 2.52
2624 3466 2.233431 ACAAACAAGGCAGCAACAAGAA 59.767 40.909 0.00 0.00 0.00 2.52
2625 3467 1.824230 ACAAACAAGGCAGCAACAAGA 59.176 42.857 0.00 0.00 0.00 3.02
2626 3468 1.928503 CACAAACAAGGCAGCAACAAG 59.071 47.619 0.00 0.00 0.00 3.16
2627 3469 1.405256 CCACAAACAAGGCAGCAACAA 60.405 47.619 0.00 0.00 0.00 2.83
2628 3470 0.175302 CCACAAACAAGGCAGCAACA 59.825 50.000 0.00 0.00 0.00 3.33
2629 3471 0.530431 CCCACAAACAAGGCAGCAAC 60.530 55.000 0.00 0.00 0.00 4.17
2630 3472 0.685785 TCCCACAAACAAGGCAGCAA 60.686 50.000 0.00 0.00 0.00 3.91
2632 3474 1.662044 CTCCCACAAACAAGGCAGC 59.338 57.895 0.00 0.00 0.00 5.25
2635 3477 1.886542 CTAACCTCCCACAAACAAGGC 59.113 52.381 0.00 0.00 31.79 4.35
2636 3478 3.502123 TCTAACCTCCCACAAACAAGG 57.498 47.619 0.00 0.00 34.94 3.61
2637 3479 4.216257 CACATCTAACCTCCCACAAACAAG 59.784 45.833 0.00 0.00 0.00 3.16
2638 3480 4.141287 CACATCTAACCTCCCACAAACAA 58.859 43.478 0.00 0.00 0.00 2.83
2639 3481 3.392947 TCACATCTAACCTCCCACAAACA 59.607 43.478 0.00 0.00 0.00 2.83
2640 3482 4.015872 TCACATCTAACCTCCCACAAAC 57.984 45.455 0.00 0.00 0.00 2.93
2641 3483 4.927267 ATCACATCTAACCTCCCACAAA 57.073 40.909 0.00 0.00 0.00 2.83
2642 3484 5.071788 GGATATCACATCTAACCTCCCACAA 59.928 44.000 4.83 0.00 0.00 3.33
2644 3486 4.841246 AGGATATCACATCTAACCTCCCAC 59.159 45.833 4.83 0.00 0.00 4.61
2645 3487 5.093236 AGGATATCACATCTAACCTCCCA 57.907 43.478 4.83 0.00 0.00 4.37
2646 3488 7.554959 TTAAGGATATCACATCTAACCTCCC 57.445 40.000 4.83 0.00 0.00 4.30
2647 3489 9.847224 TTTTTAAGGATATCACATCTAACCTCC 57.153 33.333 4.83 0.00 0.00 4.30
2670 3512 6.265422 CAGGAACAAAGGGAGTAGATGTTTTT 59.735 38.462 0.00 0.00 34.59 1.94
2671 3513 5.770162 CAGGAACAAAGGGAGTAGATGTTTT 59.230 40.000 0.00 0.00 34.59 2.43
2672 3514 5.073144 TCAGGAACAAAGGGAGTAGATGTTT 59.927 40.000 0.00 0.00 34.59 2.83
2673 3515 4.597507 TCAGGAACAAAGGGAGTAGATGTT 59.402 41.667 0.00 0.00 36.96 2.71
2674 3516 4.168101 TCAGGAACAAAGGGAGTAGATGT 58.832 43.478 0.00 0.00 0.00 3.06
2675 3517 4.826274 TCAGGAACAAAGGGAGTAGATG 57.174 45.455 0.00 0.00 0.00 2.90
2676 3518 7.698163 ATATTCAGGAACAAAGGGAGTAGAT 57.302 36.000 0.00 0.00 0.00 1.98
2677 3519 7.510675 AATATTCAGGAACAAAGGGAGTAGA 57.489 36.000 0.00 0.00 0.00 2.59
2678 3520 7.611855 ACAAATATTCAGGAACAAAGGGAGTAG 59.388 37.037 0.00 0.00 0.00 2.57
2679 3521 7.466804 ACAAATATTCAGGAACAAAGGGAGTA 58.533 34.615 0.00 0.00 0.00 2.59
2680 3522 6.314917 ACAAATATTCAGGAACAAAGGGAGT 58.685 36.000 0.00 0.00 0.00 3.85
2681 3523 6.660949 AGACAAATATTCAGGAACAAAGGGAG 59.339 38.462 0.00 0.00 0.00 4.30
2682 3524 6.552008 AGACAAATATTCAGGAACAAAGGGA 58.448 36.000 0.00 0.00 0.00 4.20
2683 3525 6.840780 AGACAAATATTCAGGAACAAAGGG 57.159 37.500 0.00 0.00 0.00 3.95
2684 3526 8.579863 AGAAAGACAAATATTCAGGAACAAAGG 58.420 33.333 0.00 0.00 0.00 3.11
2687 3529 9.231297 CCTAGAAAGACAAATATTCAGGAACAA 57.769 33.333 0.00 0.00 0.00 2.83
2688 3530 7.336931 GCCTAGAAAGACAAATATTCAGGAACA 59.663 37.037 0.00 0.00 0.00 3.18
2689 3531 7.336931 TGCCTAGAAAGACAAATATTCAGGAAC 59.663 37.037 0.00 0.00 0.00 3.62
2690 3532 7.402054 TGCCTAGAAAGACAAATATTCAGGAA 58.598 34.615 0.00 0.00 0.00 3.36
2691 3533 6.957631 TGCCTAGAAAGACAAATATTCAGGA 58.042 36.000 0.00 0.00 0.00 3.86
2692 3534 7.814264 ATGCCTAGAAAGACAAATATTCAGG 57.186 36.000 0.00 0.00 0.00 3.86
2699 3541 9.657419 CCATTTAAAATGCCTAGAAAGACAAAT 57.343 29.630 0.00 0.00 0.00 2.32
2700 3542 8.093927 CCCATTTAAAATGCCTAGAAAGACAAA 58.906 33.333 0.00 0.00 0.00 2.83
2701 3543 7.610865 CCCATTTAAAATGCCTAGAAAGACAA 58.389 34.615 0.00 0.00 0.00 3.18
2702 3544 6.350949 GCCCATTTAAAATGCCTAGAAAGACA 60.351 38.462 0.00 0.00 0.00 3.41
2703 3545 6.042777 GCCCATTTAAAATGCCTAGAAAGAC 58.957 40.000 0.00 0.00 0.00 3.01
2704 3546 5.719085 TGCCCATTTAAAATGCCTAGAAAGA 59.281 36.000 0.00 0.00 0.00 2.52
2705 3547 5.812127 GTGCCCATTTAAAATGCCTAGAAAG 59.188 40.000 0.00 0.00 0.00 2.62
2706 3548 5.247110 TGTGCCCATTTAAAATGCCTAGAAA 59.753 36.000 0.00 0.00 0.00 2.52
2707 3549 4.774726 TGTGCCCATTTAAAATGCCTAGAA 59.225 37.500 0.00 0.00 0.00 2.10
2708 3550 4.348486 TGTGCCCATTTAAAATGCCTAGA 58.652 39.130 0.00 0.00 0.00 2.43
2709 3551 4.734398 TGTGCCCATTTAAAATGCCTAG 57.266 40.909 0.00 0.00 0.00 3.02
2710 3552 4.284490 TGTTGTGCCCATTTAAAATGCCTA 59.716 37.500 0.00 0.00 0.00 3.93
2711 3553 3.072184 TGTTGTGCCCATTTAAAATGCCT 59.928 39.130 0.00 0.00 0.00 4.75
2712 3554 3.406764 TGTTGTGCCCATTTAAAATGCC 58.593 40.909 0.00 0.00 0.00 4.40
2713 3555 5.220378 CGTATGTTGTGCCCATTTAAAATGC 60.220 40.000 0.00 0.00 0.00 3.56
2714 3556 5.290643 CCGTATGTTGTGCCCATTTAAAATG 59.709 40.000 0.00 0.00 0.00 2.32
2715 3557 5.186021 TCCGTATGTTGTGCCCATTTAAAAT 59.814 36.000 0.00 0.00 0.00 1.82
2716 3558 4.523173 TCCGTATGTTGTGCCCATTTAAAA 59.477 37.500 0.00 0.00 0.00 1.52
2717 3559 4.079970 TCCGTATGTTGTGCCCATTTAAA 58.920 39.130 0.00 0.00 0.00 1.52
2718 3560 3.687125 TCCGTATGTTGTGCCCATTTAA 58.313 40.909 0.00 0.00 0.00 1.52
2719 3561 3.351794 TCCGTATGTTGTGCCCATTTA 57.648 42.857 0.00 0.00 0.00 1.40
2720 3562 2.208132 TCCGTATGTTGTGCCCATTT 57.792 45.000 0.00 0.00 0.00 2.32
2721 3563 2.023673 CATCCGTATGTTGTGCCCATT 58.976 47.619 0.00 0.00 0.00 3.16
2722 3564 1.064758 ACATCCGTATGTTGTGCCCAT 60.065 47.619 0.00 0.00 44.07 4.00
2723 3565 0.326595 ACATCCGTATGTTGTGCCCA 59.673 50.000 0.00 0.00 44.07 5.36
2724 3566 2.319136 TACATCCGTATGTTGTGCCC 57.681 50.000 0.00 0.00 44.07 5.36
2725 3567 3.878086 CATACATCCGTATGTTGTGCC 57.122 47.619 0.00 0.00 46.70 5.01
2761 3603 4.808364 GGAGCAAGATGAGTGAATCTACAC 59.192 45.833 0.00 0.00 35.83 2.90
2762 3604 4.440663 CGGAGCAAGATGAGTGAATCTACA 60.441 45.833 0.00 0.00 35.83 2.74
2763 3605 4.047822 CGGAGCAAGATGAGTGAATCTAC 58.952 47.826 0.00 0.00 35.83 2.59
2764 3606 3.701542 ACGGAGCAAGATGAGTGAATCTA 59.298 43.478 0.00 0.00 35.83 1.98
2765 3607 2.499289 ACGGAGCAAGATGAGTGAATCT 59.501 45.455 0.00 0.00 38.59 2.40
2766 3608 2.898705 ACGGAGCAAGATGAGTGAATC 58.101 47.619 0.00 0.00 0.00 2.52
2767 3609 4.141846 ACATACGGAGCAAGATGAGTGAAT 60.142 41.667 0.00 0.00 0.00 2.57
2768 3610 3.195610 ACATACGGAGCAAGATGAGTGAA 59.804 43.478 0.00 0.00 0.00 3.18
2769 3611 2.760650 ACATACGGAGCAAGATGAGTGA 59.239 45.455 0.00 0.00 0.00 3.41
2770 3612 3.170791 ACATACGGAGCAAGATGAGTG 57.829 47.619 0.00 0.00 0.00 3.51
2771 3613 3.954904 ACTACATACGGAGCAAGATGAGT 59.045 43.478 0.00 0.00 0.00 3.41
2772 3614 4.036852 TGACTACATACGGAGCAAGATGAG 59.963 45.833 0.00 0.00 0.00 2.90
2773 3615 3.951680 TGACTACATACGGAGCAAGATGA 59.048 43.478 0.00 0.00 0.00 2.92
2774 3616 4.307443 TGACTACATACGGAGCAAGATG 57.693 45.455 0.00 0.00 0.00 2.90
2775 3617 5.537300 AATGACTACATACGGAGCAAGAT 57.463 39.130 0.00 0.00 35.50 2.40
2776 3618 5.109210 CAAATGACTACATACGGAGCAAGA 58.891 41.667 0.00 0.00 35.50 3.02
2777 3619 4.870426 ACAAATGACTACATACGGAGCAAG 59.130 41.667 0.00 0.00 35.50 4.01
2778 3620 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
2779 3621 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
2780 3622 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
2781 3623 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
2782 3624 7.822334 AGATTTCAACAAATGACTACATACGGA 59.178 33.333 0.00 0.00 37.92 4.69
2783 3625 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
2784 3626 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
2788 3630 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
2811 3653 9.927668 CACATCTACCCAAATATTTGTTTTTCT 57.072 29.630 23.24 4.97 36.45 2.52
2812 3654 9.921637 TCACATCTACCCAAATATTTGTTTTTC 57.078 29.630 23.24 0.00 36.45 2.29
2822 3664 9.967451 TTTGTCTAATTCACATCTACCCAAATA 57.033 29.630 0.00 0.00 0.00 1.40
2823 3665 8.877864 TTTGTCTAATTCACATCTACCCAAAT 57.122 30.769 0.00 0.00 0.00 2.32
2824 3666 8.877864 ATTTGTCTAATTCACATCTACCCAAA 57.122 30.769 0.00 0.00 0.00 3.28
2825 3667 8.739039 CAATTTGTCTAATTCACATCTACCCAA 58.261 33.333 0.00 0.00 34.19 4.12
2826 3668 8.106462 TCAATTTGTCTAATTCACATCTACCCA 58.894 33.333 0.00 0.00 34.19 4.51
2827 3669 8.506168 TCAATTTGTCTAATTCACATCTACCC 57.494 34.615 0.00 0.00 34.19 3.69
2828 3670 9.994432 CTTCAATTTGTCTAATTCACATCTACC 57.006 33.333 0.00 0.00 34.19 3.18
2829 3671 9.994432 CCTTCAATTTGTCTAATTCACATCTAC 57.006 33.333 0.00 0.00 34.19 2.59
2830 3672 9.958180 TCCTTCAATTTGTCTAATTCACATCTA 57.042 29.630 0.00 0.00 34.19 1.98
2831 3673 8.868522 TCCTTCAATTTGTCTAATTCACATCT 57.131 30.769 0.00 0.00 34.19 2.90
2832 3674 9.912634 TTTCCTTCAATTTGTCTAATTCACATC 57.087 29.630 0.00 0.00 34.19 3.06
2842 3684 9.971922 CTTCACTAATTTTCCTTCAATTTGTCT 57.028 29.630 0.00 0.00 30.32 3.41
2843 3685 9.196552 CCTTCACTAATTTTCCTTCAATTTGTC 57.803 33.333 0.00 0.00 30.32 3.18
2844 3686 8.704668 ACCTTCACTAATTTTCCTTCAATTTGT 58.295 29.630 0.00 0.00 32.12 2.83
2845 3687 8.981647 CACCTTCACTAATTTTCCTTCAATTTG 58.018 33.333 0.00 0.00 0.00 2.32
2846 3688 7.657354 GCACCTTCACTAATTTTCCTTCAATTT 59.343 33.333 0.00 0.00 0.00 1.82
2847 3689 7.154656 GCACCTTCACTAATTTTCCTTCAATT 58.845 34.615 0.00 0.00 0.00 2.32
2848 3690 6.267471 TGCACCTTCACTAATTTTCCTTCAAT 59.733 34.615 0.00 0.00 0.00 2.57
2849 3691 5.596361 TGCACCTTCACTAATTTTCCTTCAA 59.404 36.000 0.00 0.00 0.00 2.69
2850 3692 5.136828 TGCACCTTCACTAATTTTCCTTCA 58.863 37.500 0.00 0.00 0.00 3.02
2851 3693 5.705609 TGCACCTTCACTAATTTTCCTTC 57.294 39.130 0.00 0.00 0.00 3.46
2852 3694 6.478512 TTTGCACCTTCACTAATTTTCCTT 57.521 33.333 0.00 0.00 0.00 3.36
2856 3698 6.866248 CCGTAATTTGCACCTTCACTAATTTT 59.134 34.615 0.00 0.00 0.00 1.82
2863 3705 5.554822 TTATCCGTAATTTGCACCTTCAC 57.445 39.130 0.00 0.00 0.00 3.18
2880 3722 8.202137 TGGTAAAAGTGCTAGTACAGATTATCC 58.798 37.037 13.75 11.77 0.00 2.59
2885 3727 6.013639 AGGTTGGTAAAAGTGCTAGTACAGAT 60.014 38.462 13.75 1.14 0.00 2.90
2899 3741 2.423660 CCCAGTGTCCAGGTTGGTAAAA 60.424 50.000 0.00 0.00 39.03 1.52
2900 3742 1.144093 CCCAGTGTCCAGGTTGGTAAA 59.856 52.381 0.00 0.00 39.03 2.01
2906 3750 0.991355 TGGTTCCCAGTGTCCAGGTT 60.991 55.000 0.00 0.00 0.00 3.50
3114 3966 5.525378 GCCTACATGTGTACTACTACGTACT 59.475 44.000 9.11 0.00 40.25 2.73
3115 3967 5.557136 CGCCTACATGTGTACTACTACGTAC 60.557 48.000 9.11 0.00 40.06 3.67
3116 3968 4.507756 CGCCTACATGTGTACTACTACGTA 59.492 45.833 9.11 0.00 0.00 3.57
3117 3969 3.310774 CGCCTACATGTGTACTACTACGT 59.689 47.826 9.11 0.00 0.00 3.57
3118 3970 3.847467 GCGCCTACATGTGTACTACTACG 60.847 52.174 9.11 0.77 0.00 3.51
3122 3974 2.865343 AGCGCCTACATGTGTACTAC 57.135 50.000 9.11 0.00 0.00 2.73
3123 3975 3.548770 AGTAGCGCCTACATGTGTACTA 58.451 45.455 9.11 0.44 39.22 1.82
3124 3976 2.358267 GAGTAGCGCCTACATGTGTACT 59.642 50.000 9.11 1.13 39.22 2.73
3125 3977 2.358267 AGAGTAGCGCCTACATGTGTAC 59.642 50.000 9.11 0.00 39.22 2.90
3126 3978 2.651455 AGAGTAGCGCCTACATGTGTA 58.349 47.619 9.11 0.00 39.22 2.90
3127 3979 1.475403 AGAGTAGCGCCTACATGTGT 58.525 50.000 9.11 0.00 39.22 3.72
3128 3980 3.924918 ATAGAGTAGCGCCTACATGTG 57.075 47.619 9.11 0.00 39.22 3.21
3139 3995 2.576406 CGCGCAGACTTATAGAGTAGC 58.424 52.381 8.75 0.00 39.19 3.58
3158 4014 2.307049 GACACAACCGAAGATTTTGCG 58.693 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.