Multiple sequence alignment - TraesCS7A01G531000

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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 TraesCS7A01G531000 chr7A 100.000 5556 0 0 1 5556 709813533 709807978 0.000000e+00 10261.0
1 TraesCS7A01G531000 chr7A 97.818 275 6 0 5027 5301 67504302 67504576 5.040000e-130 475.0
2 TraesCS7A01G531000 chr7A 95.266 169 8 0 4858 5026 709786178 709786010 9.170000e-68 268.0
3 TraesCS7A01G531000 chr7A 94.366 71 4 0 2107 2177 137821705 137821775 5.880000e-20 110.0
4 TraesCS7A01G531000 chr7D 96.302 2109 73 5 2511 4616 617081145 617079039 0.000000e+00 3458.0
5 TraesCS7A01G531000 chr7D 92.217 1182 36 16 2 1182 617082877 617081751 0.000000e+00 1622.0
6 TraesCS7A01G531000 chr7D 88.018 651 37 10 1666 2275 98876784 98876134 0.000000e+00 732.0
7 TraesCS7A01G531000 chr7D 94.541 458 23 2 1192 1649 617081702 617081247 0.000000e+00 706.0
8 TraesCS7A01G531000 chr7D 92.549 255 19 0 1666 1920 618266891 618266637 3.160000e-97 366.0
9 TraesCS7A01G531000 chr7D 94.619 223 12 0 4637 4859 617078438 617078216 4.120000e-91 346.0
10 TraesCS7A01G531000 chr7D 83.285 347 21 11 1666 1979 25205691 25205349 9.110000e-73 285.0
11 TraesCS7A01G531000 chr7D 93.785 177 11 0 2050 2226 618264734 618264558 3.300000e-67 267.0
12 TraesCS7A01G531000 chr7D 86.878 221 22 2 1666 1886 137844562 137844775 2.000000e-59 241.0
13 TraesCS7A01G531000 chr7D 90.141 142 8 2 4858 4994 617078180 617078040 4.420000e-41 180.0
14 TraesCS7A01G531000 chr7D 90.476 105 10 0 549 653 105999668 105999772 7.510000e-29 139.0
15 TraesCS7A01G531000 chr2B 92.740 1336 77 8 2617 3951 90259 91575 0.000000e+00 1912.0
16 TraesCS7A01G531000 chr2B 93.667 600 38 0 4010 4609 91573 92172 0.000000e+00 898.0
17 TraesCS7A01G531000 chr2B 91.055 436 37 2 1214 1649 87629 88062 6.200000e-164 588.0
18 TraesCS7A01G531000 chr2B 88.587 368 31 5 818 1182 86646 87005 2.380000e-118 436.0
19 TraesCS7A01G531000 chr4B 90.757 898 83 0 3672 4569 483513048 483513945 0.000000e+00 1199.0
20 TraesCS7A01G531000 chr4B 84.629 1145 137 25 2529 3664 483511882 483512996 0.000000e+00 1103.0
21 TraesCS7A01G531000 chr4B 87.342 395 47 3 1250 1642 483511261 483511654 3.050000e-122 449.0
22 TraesCS7A01G531000 chr4D 90.408 907 86 1 3672 4578 393709770 393708865 0.000000e+00 1192.0
23 TraesCS7A01G531000 chr4D 84.987 1139 132 21 2528 3659 393710932 393709826 0.000000e+00 1120.0
24 TraesCS7A01G531000 chr4D 87.133 443 48 6 1208 1645 393719538 393719100 1.390000e-135 494.0
25 TraesCS7A01G531000 chr4D 85.398 226 30 3 959 1181 393719847 393719622 1.200000e-56 231.0
26 TraesCS7A01G531000 chr4A 89.978 898 90 0 3672 4569 75257506 75258403 0.000000e+00 1160.0
27 TraesCS7A01G531000 chr4A 87.279 904 96 15 2768 3664 75256498 75257389 0.000000e+00 1014.0
28 TraesCS7A01G531000 chr4A 80.399 903 103 33 776 1642 75255624 75256488 2.200000e-173 619.0
29 TraesCS7A01G531000 chr4A 89.912 228 18 1 1666 1888 715601811 715601584 7.040000e-74 289.0
30 TraesCS7A01G531000 chr4A 90.000 50 5 0 3672 3721 75257441 75257490 1.290000e-06 65.8
31 TraesCS7A01G531000 chr6A 97.570 535 11 2 5022 5556 570453799 570453267 0.000000e+00 915.0
32 TraesCS7A01G531000 chr2A 97.552 531 13 0 5026 5556 202778615 202779145 0.000000e+00 909.0
33 TraesCS7A01G531000 chr2A 97.373 533 13 1 5024 5556 28784692 28784161 0.000000e+00 905.0
34 TraesCS7A01G531000 chr2A 96.998 533 14 2 5024 5556 120718692 120718162 0.000000e+00 894.0
35 TraesCS7A01G531000 chr2A 91.228 57 4 1 462 517 143210153 143210209 5.970000e-10 76.8
36 TraesCS7A01G531000 chr7B 97.180 532 15 0 5025 5556 317878861 317879392 0.000000e+00 900.0
37 TraesCS7A01G531000 chr7B 90.991 111 8 2 549 658 747370736 747370627 1.250000e-31 148.0
38 TraesCS7A01G531000 chr7B 94.545 55 2 1 463 517 482482216 482482269 3.570000e-12 84.2
39 TraesCS7A01G531000 chr5A 96.805 532 17 0 5025 5556 601644738 601644207 0.000000e+00 889.0
40 TraesCS7A01G531000 chr5B 88.735 648 32 10 1666 2273 6973221 6972575 0.000000e+00 754.0
41 TraesCS7A01G531000 chr5B 93.191 235 15 1 2273 2507 6972529 6972296 1.480000e-90 344.0
42 TraesCS7A01G531000 chr5B 92.157 102 8 0 555 656 600931269 600931370 1.610000e-30 145.0
43 TraesCS7A01G531000 chr5B 96.429 56 1 1 462 517 16100158 16100104 2.130000e-14 91.6
44 TraesCS7A01G531000 chr5D 88.326 651 32 10 1666 2273 505951541 505950892 0.000000e+00 741.0
45 TraesCS7A01G531000 chr5D 94.894 235 11 1 2273 2507 505950846 505950613 3.160000e-97 366.0
46 TraesCS7A01G531000 chr5D 81.503 173 30 2 1666 1836 544718125 544717953 2.090000e-29 141.0
47 TraesCS7A01G531000 chr2D 86.022 651 25 15 1666 2273 622865770 622866397 6.070000e-179 638.0
48 TraesCS7A01G531000 chr2D 94.043 235 13 1 2273 2507 622866443 622866676 6.850000e-94 355.0
49 TraesCS7A01G531000 chr2D 94.737 57 2 1 462 518 380579350 380579295 2.760000e-13 87.9
50 TraesCS7A01G531000 chr6B 90.826 109 9 1 545 652 424084080 424084188 1.610000e-30 145.0
51 TraesCS7A01G531000 chr6B 90.826 109 9 1 545 652 424306778 424306886 1.610000e-30 145.0
52 TraesCS7A01G531000 chr6B 91.667 60 3 2 460 517 100709940 100709881 1.280000e-11 82.4
53 TraesCS7A01G531000 chr6B 91.667 60 3 2 460 517 100745185 100745126 1.280000e-11 82.4
54 TraesCS7A01G531000 chr1B 90.741 108 10 0 545 652 480762094 480761987 1.610000e-30 145.0
55 TraesCS7A01G531000 chr1B 92.857 98 7 0 555 652 301264580 301264483 5.800000e-30 143.0
56 TraesCS7A01G531000 chr1B 91.935 62 3 2 462 521 639046659 639046598 9.920000e-13 86.1
57 TraesCS7A01G531000 chr1B 92.000 50 4 0 471 520 329380369 329380320 2.780000e-08 71.3
58 TraesCS7A01G531000 chr1A 92.000 100 7 1 549 647 474641669 474641768 7.510000e-29 139.0
59 TraesCS7A01G531000 chr1A 91.935 62 3 2 462 521 555829626 555829565 9.920000e-13 86.1
60 TraesCS7A01G531000 chr1A 92.157 51 2 1 471 521 302923642 302923690 2.780000e-08 71.3
61 TraesCS7A01G531000 chr6D 96.226 53 2 0 466 518 109865746 109865694 2.760000e-13 87.9
62 TraesCS7A01G531000 chrUn 90.476 63 4 2 457 517 360547664 360547726 1.280000e-11 82.4
63 TraesCS7A01G531000 chr1D 92.857 56 2 2 471 526 249135883 249135936 4.610000e-11 80.5
64 TraesCS7A01G531000 chr1D 90.323 62 4 2 462 521 463868262 463868201 4.610000e-11 80.5


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 TraesCS7A01G531000 chr7A 709807978 709813533 5555 True 10261.0 10261 100.00000 1 5556 1 chr7A.!!$R2 5555
1 TraesCS7A01G531000 chr7D 617078040 617082877 4837 True 1262.4 3458 93.56400 2 4994 5 chr7D.!!$R3 4992
2 TraesCS7A01G531000 chr7D 98876134 98876784 650 True 732.0 732 88.01800 1666 2275 1 chr7D.!!$R2 609
3 TraesCS7A01G531000 chr7D 618264558 618266891 2333 True 316.5 366 93.16700 1666 2226 2 chr7D.!!$R4 560
4 TraesCS7A01G531000 chr2B 86646 92172 5526 False 958.5 1912 91.51225 818 4609 4 chr2B.!!$F1 3791
5 TraesCS7A01G531000 chr4B 483511261 483513945 2684 False 917.0 1199 87.57600 1250 4569 3 chr4B.!!$F1 3319
6 TraesCS7A01G531000 chr4D 393708865 393710932 2067 True 1156.0 1192 87.69750 2528 4578 2 chr4D.!!$R1 2050
7 TraesCS7A01G531000 chr4D 393719100 393719847 747 True 362.5 494 86.26550 959 1645 2 chr4D.!!$R2 686
8 TraesCS7A01G531000 chr4A 75255624 75258403 2779 False 714.7 1160 86.91400 776 4569 4 chr4A.!!$F1 3793
9 TraesCS7A01G531000 chr6A 570453267 570453799 532 True 915.0 915 97.57000 5022 5556 1 chr6A.!!$R1 534
10 TraesCS7A01G531000 chr2A 202778615 202779145 530 False 909.0 909 97.55200 5026 5556 1 chr2A.!!$F2 530
11 TraesCS7A01G531000 chr2A 28784161 28784692 531 True 905.0 905 97.37300 5024 5556 1 chr2A.!!$R1 532
12 TraesCS7A01G531000 chr2A 120718162 120718692 530 True 894.0 894 96.99800 5024 5556 1 chr2A.!!$R2 532
13 TraesCS7A01G531000 chr7B 317878861 317879392 531 False 900.0 900 97.18000 5025 5556 1 chr7B.!!$F1 531
14 TraesCS7A01G531000 chr5A 601644207 601644738 531 True 889.0 889 96.80500 5025 5556 1 chr5A.!!$R1 531
15 TraesCS7A01G531000 chr5B 6972296 6973221 925 True 549.0 754 90.96300 1666 2507 2 chr5B.!!$R2 841
16 TraesCS7A01G531000 chr5D 505950613 505951541 928 True 553.5 741 91.61000 1666 2507 2 chr5D.!!$R2 841
17 TraesCS7A01G531000 chr2D 622865770 622866676 906 False 496.5 638 90.03250 1666 2507 2 chr2D.!!$F1 841

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
84 85 0.035152 TGCAGCTCCATCCGTTTCAT 60.035 50.000 0.00 0.00 0.00 2.57 F
314 315 0.105709 CTCTCTCCCTCCCTCCCTTC 60.106 65.000 0.00 0.00 0.00 3.46 F
366 367 0.404040 CCCTCTCCCTCGCTCTCTAT 59.596 60.000 0.00 0.00 0.00 1.98 F
2057 4356 0.101759 AAGAATCACATGCATGCGCC 59.898 50.000 26.53 11.19 37.32 6.53 F
2297 5428 0.238289 CTTCAACCATCGTGTGCACC 59.762 55.000 15.69 4.74 0.00 5.01 F
2416 5547 1.609208 AGCTGATCCTGCAAAACGTT 58.391 45.000 0.00 0.00 0.00 3.99 F
2481 5612 2.897969 GGATAAGATTAGAGGGTGCCGA 59.102 50.000 0.00 0.00 0.00 5.54 F
4317 8910 1.213430 TGAATCTCCAGATGGCATGCA 59.787 47.619 21.36 6.13 34.49 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 3198 0.615331 GGATGGAGAGGCTGTGAACA 59.385 55.000 0.00 0.0 0.00 3.18 R
1991 4274 0.891373 CGAAAGGTGAGGAGAGAGCA 59.109 55.000 0.00 0.0 0.00 4.26 R
2290 5421 0.953471 GAAGGTGTATGCGGTGCACA 60.953 55.000 20.43 0.0 44.25 4.57 R
3371 7850 1.303317 AATTTCCGGCTGCCTTCGT 60.303 52.632 17.92 0.0 0.00 3.85 R
4217 8810 1.774894 TACTGGGGTCCTTGCCACAC 61.775 60.000 0.00 0.0 36.94 3.82 R
4317 8910 4.023707 GCGAGAATGCCATACATAAGCTTT 60.024 41.667 3.20 0.0 38.34 3.51 R
4519 9112 7.564793 TCTTACATTTGTACCTCATAGCACAT 58.435 34.615 0.00 0.0 0.00 3.21 R
5441 10657 3.248024 TGGAGGACCTACACTCAATTGT 58.752 45.455 0.75 0.0 35.45 2.71 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
48 49 5.711976 GTGCATTATTGTAGGGCCATAGATT 59.288 40.000 6.18 0.00 0.00 2.40
59 60 4.008330 GGGCCATAGATTGAGACATCATG 58.992 47.826 4.39 0.00 34.73 3.07
82 83 1.372087 CCTGCAGCTCCATCCGTTTC 61.372 60.000 8.66 0.00 0.00 2.78
84 85 0.035152 TGCAGCTCCATCCGTTTCAT 60.035 50.000 0.00 0.00 0.00 2.57
106 107 6.820656 TCATGTTATCTTCTTCCTCTTGCTTC 59.179 38.462 0.00 0.00 0.00 3.86
107 108 5.491982 TGTTATCTTCTTCCTCTTGCTTCC 58.508 41.667 0.00 0.00 0.00 3.46
108 109 5.249393 TGTTATCTTCTTCCTCTTGCTTCCT 59.751 40.000 0.00 0.00 0.00 3.36
120 121 4.526970 TCTTGCTTCCTCTCTTGTTTTGT 58.473 39.130 0.00 0.00 0.00 2.83
292 293 3.172050 CTCATCACGAGAGGTTTGTACG 58.828 50.000 0.00 0.00 45.45 3.67
304 305 1.819903 GTTTGTACGCTCTCTCTCCCT 59.180 52.381 0.00 0.00 0.00 4.20
305 306 1.752683 TTGTACGCTCTCTCTCCCTC 58.247 55.000 0.00 0.00 0.00 4.30
306 307 0.107116 TGTACGCTCTCTCTCCCTCC 60.107 60.000 0.00 0.00 0.00 4.30
307 308 0.820482 GTACGCTCTCTCTCCCTCCC 60.820 65.000 0.00 0.00 0.00 4.30
308 309 0.989212 TACGCTCTCTCTCCCTCCCT 60.989 60.000 0.00 0.00 0.00 4.20
309 310 1.528309 CGCTCTCTCTCCCTCCCTC 60.528 68.421 0.00 0.00 0.00 4.30
310 311 1.152546 GCTCTCTCTCCCTCCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
311 312 1.541672 CTCTCTCTCCCTCCCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
312 313 0.998945 CTCTCTCTCCCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
313 314 0.556380 TCTCTCTCCCTCCCTCCCTT 60.556 60.000 0.00 0.00 0.00 3.95
314 315 0.105709 CTCTCTCCCTCCCTCCCTTC 60.106 65.000 0.00 0.00 0.00 3.46
315 316 1.074850 CTCTCCCTCCCTCCCTTCC 60.075 68.421 0.00 0.00 0.00 3.46
316 317 1.550374 TCTCCCTCCCTCCCTTCCT 60.550 63.158 0.00 0.00 0.00 3.36
317 318 1.074850 CTCCCTCCCTCCCTTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
318 319 1.550374 TCCCTCCCTCCCTTCCTCT 60.550 63.158 0.00 0.00 0.00 3.69
319 320 1.074850 CCCTCCCTCCCTTCCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
320 321 1.598856 CCCTCCCTCCCTTCCTCTCT 61.599 65.000 0.00 0.00 0.00 3.10
347 348 2.362397 TCTCTCTCTCTCTCGCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
354 355 0.535102 CTCTCGCTCTCTCCCTCTCC 60.535 65.000 0.00 0.00 0.00 3.71
355 356 1.528309 CTCGCTCTCTCCCTCTCCC 60.528 68.421 0.00 0.00 0.00 4.30
356 357 1.994885 CTCGCTCTCTCCCTCTCCCT 61.995 65.000 0.00 0.00 0.00 4.20
357 358 1.528309 CGCTCTCTCCCTCTCCCTC 60.528 68.421 0.00 0.00 0.00 4.30
358 359 1.528309 GCTCTCTCCCTCTCCCTCG 60.528 68.421 0.00 0.00 0.00 4.63
359 360 1.528309 CTCTCTCCCTCTCCCTCGC 60.528 68.421 0.00 0.00 0.00 5.03
360 361 1.994885 CTCTCTCCCTCTCCCTCGCT 61.995 65.000 0.00 0.00 0.00 4.93
361 362 1.528309 CTCTCCCTCTCCCTCGCTC 60.528 68.421 0.00 0.00 0.00 5.03
362 363 1.994885 CTCTCCCTCTCCCTCGCTCT 61.995 65.000 0.00 0.00 0.00 4.09
363 364 1.528309 CTCCCTCTCCCTCGCTCTC 60.528 68.421 0.00 0.00 0.00 3.20
364 365 1.994885 CTCCCTCTCCCTCGCTCTCT 61.995 65.000 0.00 0.00 0.00 3.10
365 366 0.694783 TCCCTCTCCCTCGCTCTCTA 60.695 60.000 0.00 0.00 0.00 2.43
366 367 0.404040 CCCTCTCCCTCGCTCTCTAT 59.596 60.000 0.00 0.00 0.00 1.98
367 368 1.613255 CCCTCTCCCTCGCTCTCTATC 60.613 61.905 0.00 0.00 0.00 2.08
368 369 1.351017 CCTCTCCCTCGCTCTCTATCT 59.649 57.143 0.00 0.00 0.00 1.98
369 370 2.615493 CCTCTCCCTCGCTCTCTATCTC 60.615 59.091 0.00 0.00 0.00 2.75
370 371 1.349688 TCTCCCTCGCTCTCTATCTCC 59.650 57.143 0.00 0.00 0.00 3.71
394 395 1.689813 TCTTCCGGCAACAGTGTCTTA 59.310 47.619 0.00 0.00 0.00 2.10
395 396 2.103432 TCTTCCGGCAACAGTGTCTTAA 59.897 45.455 0.00 0.00 0.00 1.85
396 397 2.851263 TCCGGCAACAGTGTCTTAAT 57.149 45.000 0.00 0.00 0.00 1.40
442 443 5.102953 TGCTTAGTTACCTGATGAAGCAT 57.897 39.130 3.13 0.00 43.08 3.79
449 450 1.141657 ACCTGATGAAGCATGCCGTAT 59.858 47.619 15.66 5.94 0.00 3.06
457 458 7.264221 TGATGAAGCATGCCGTATTAAATTTT 58.736 30.769 15.66 0.00 0.00 1.82
475 476 4.647424 TTTTAAACTTGTGCTCTGGTGG 57.353 40.909 0.00 0.00 0.00 4.61
479 480 1.392589 ACTTGTGCTCTGGTGGTTTG 58.607 50.000 0.00 0.00 0.00 2.93
550 551 7.473735 TTCCAAACCATGTGCATATTCTTAA 57.526 32.000 0.00 0.00 0.00 1.85
579 580 5.043762 ACTCCCTCCATCCCAAAATAACTA 58.956 41.667 0.00 0.00 0.00 2.24
647 648 3.118519 GGCACTTATTTTAGGACGGAGGA 60.119 47.826 0.00 0.00 0.00 3.71
747 748 3.727726 TGAGTTTCTGACAGCATCGAAA 58.272 40.909 0.00 0.00 31.68 3.46
794 795 7.922811 GGTTTCAAAGAACATCTGTTTTGAGAT 59.077 33.333 9.09 0.00 36.63 2.75
935 938 7.011763 GCACATTTCTCTATTGCTACATCTTCA 59.988 37.037 0.00 0.00 0.00 3.02
936 939 8.886719 CACATTTCTCTATTGCTACATCTTCAA 58.113 33.333 0.00 0.00 0.00 2.69
1100 1109 6.408662 GCCTCCTTCTTAATCATAGGTCAGTT 60.409 42.308 0.00 0.00 0.00 3.16
1206 1289 3.378427 AGAAAACACTTCACACTCAAGCC 59.622 43.478 0.00 0.00 0.00 4.35
1376 2024 3.764885 ACTTTGTTGCAGTCTGTTCAC 57.235 42.857 0.93 0.00 0.00 3.18
1393 2041 3.683365 TCACTCTGCTGTTATCTTGCA 57.317 42.857 0.00 0.00 35.30 4.08
1400 2048 6.705381 ACTCTGCTGTTATCTTGCATATTCTC 59.295 38.462 0.00 0.00 36.07 2.87
1543 2191 2.547855 CGTTGCCGATTCATATCTGGGA 60.548 50.000 0.00 0.00 35.63 4.37
1557 2205 0.974383 CTGGGAAAGTACCGGACAGT 59.026 55.000 9.46 0.00 36.43 3.55
1562 2210 3.469739 GGAAAGTACCGGACAGTTTTGA 58.530 45.455 9.46 0.00 0.00 2.69
1573 2221 1.888512 ACAGTTTTGAATCGCCTGCAT 59.111 42.857 0.00 0.00 0.00 3.96
1583 2231 3.637998 ATCGCCTGCATGATTTTCATC 57.362 42.857 0.00 0.00 34.28 2.92
1649 2297 9.734620 CAAAATAATCACAAAGAGTCAAAGACA 57.265 29.630 0.00 0.00 34.60 3.41
1650 2298 9.736023 AAAATAATCACAAAGAGTCAAAGACAC 57.264 29.630 0.00 0.00 34.60 3.67
1653 2301 3.199946 TCACAAAGAGTCAAAGACACCCT 59.800 43.478 0.00 0.00 34.60 4.34
1654 2302 3.313526 CACAAAGAGTCAAAGACACCCTG 59.686 47.826 0.00 0.00 34.60 4.45
1656 2304 3.933861 AAGAGTCAAAGACACCCTGTT 57.066 42.857 0.00 0.00 34.60 3.16
1657 2305 5.123227 CAAAGAGTCAAAGACACCCTGTTA 58.877 41.667 0.00 0.00 34.60 2.41
1659 2307 5.153950 AGAGTCAAAGACACCCTGTTATC 57.846 43.478 0.00 0.00 34.60 1.75
1660 2308 4.593206 AGAGTCAAAGACACCCTGTTATCA 59.407 41.667 0.00 0.00 34.60 2.15
1661 2309 5.249393 AGAGTCAAAGACACCCTGTTATCAT 59.751 40.000 0.00 0.00 34.60 2.45
1662 2310 5.880901 AGTCAAAGACACCCTGTTATCATT 58.119 37.500 0.00 0.00 34.60 2.57
1663 2311 5.940470 AGTCAAAGACACCCTGTTATCATTC 59.060 40.000 0.00 0.00 34.60 2.67
1664 2312 5.705441 GTCAAAGACACCCTGTTATCATTCA 59.295 40.000 0.00 0.00 32.09 2.57
1847 3141 1.204941 CTCCTGACCACCTACCGAAAG 59.795 57.143 0.00 0.00 0.00 2.62
1903 3198 4.023291 CCTGCTACCTTTCTTCTCTCTCT 58.977 47.826 0.00 0.00 0.00 3.10
2010 4296 0.891373 TGCTCTCTCCTCACCTTTCG 59.109 55.000 0.00 0.00 0.00 3.46
2011 4297 0.174617 GCTCTCTCCTCACCTTTCGG 59.825 60.000 0.00 0.00 0.00 4.30
2057 4356 0.101759 AAGAATCACATGCATGCGCC 59.898 50.000 26.53 11.19 37.32 6.53
2074 5157 1.403972 GCCGCGTGAACGAGTTAGAG 61.404 60.000 4.92 0.00 43.02 2.43
2112 5195 4.844349 ACTACAGTAGCCATTGACCAAT 57.156 40.909 7.57 0.00 0.00 3.16
2205 5288 1.274703 GCCATTGGGGTCTGAGGAGA 61.275 60.000 4.53 0.00 39.65 3.71
2290 5421 0.320421 CCGGTCACTTCAACCATCGT 60.320 55.000 0.00 0.00 36.53 3.73
2294 5425 1.069906 GTCACTTCAACCATCGTGTGC 60.070 52.381 0.00 0.00 0.00 4.57
2297 5428 0.238289 CTTCAACCATCGTGTGCACC 59.762 55.000 15.69 4.74 0.00 5.01
2409 5540 3.198417 TGACTAATCAAGCTGATCCTGCA 59.802 43.478 9.89 0.00 35.76 4.41
2416 5547 1.609208 AGCTGATCCTGCAAAACGTT 58.391 45.000 0.00 0.00 0.00 3.99
2463 5594 5.448768 CGAATCGTAATATAGCTGGACGGAT 60.449 44.000 0.00 0.00 34.38 4.18
2481 5612 2.897969 GGATAAGATTAGAGGGTGCCGA 59.102 50.000 0.00 0.00 0.00 5.54
2509 5640 4.162592 TGCTGTGGCACCTTTCTG 57.837 55.556 16.26 0.00 44.28 3.02
2554 5690 6.313164 AGTTCTGATATGATATGCGCATTCAG 59.687 38.462 29.11 29.11 35.12 3.02
2626 7099 8.831715 ATTGGAAGAAGAAATAAAAATTGCGT 57.168 26.923 0.00 0.00 0.00 5.24
2693 7171 9.549078 ACTTACCAAAACAAAACAAAAGAGAAA 57.451 25.926 0.00 0.00 0.00 2.52
2747 7225 3.891366 GCAACCAACCTATATGCCTGATT 59.109 43.478 0.00 0.00 0.00 2.57
2766 7244 6.095021 CCTGATTGCAAGAGATCAAAAGATCA 59.905 38.462 4.94 0.00 32.33 2.92
2862 7341 9.527157 TTTCATTCTGTTGTTTAGGGAATGATA 57.473 29.630 14.53 9.22 46.05 2.15
3065 7544 4.457603 CACCGATTATGTGGAGAAAACCAA 59.542 41.667 0.00 0.00 41.87 3.67
3090 7569 3.022406 GAGCTCCTTCTTCAATTGGCAT 58.978 45.455 0.87 0.00 0.00 4.40
3096 7575 6.820152 GCTCCTTCTTCAATTGGCATTATTTT 59.180 34.615 5.42 0.00 0.00 1.82
3107 7586 7.633193 ATTGGCATTATTTTGCAATCAATGT 57.367 28.000 20.36 6.61 44.59 2.71
3183 7662 3.576550 GGCTCTGGGGTTTTACAATTTCA 59.423 43.478 0.00 0.00 0.00 2.69
3190 7669 5.053811 GGGGTTTTACAATTTCAACACTGG 58.946 41.667 0.00 0.00 0.00 4.00
3425 7904 4.772624 TGGACTTGAGTAATACTCTGCTGT 59.227 41.667 19.76 12.84 45.27 4.40
3749 8342 6.603201 CCCATTCAGGTTCTTTGATAAAGCTA 59.397 38.462 0.00 0.00 35.43 3.32
3757 8350 9.515226 AGGTTCTTTGATAAAGCTACAATTGTA 57.485 29.630 17.16 17.16 38.39 2.41
4317 8910 1.213430 TGAATCTCCAGATGGCATGCA 59.787 47.619 21.36 6.13 34.49 3.96
4356 8949 2.066262 CTCGCTTGTTAACATGTCGGT 58.934 47.619 23.99 0.00 0.00 4.69
4551 9144 6.303839 TGAGGTACAAATGTAAGAAGGCTTT 58.696 36.000 0.00 0.00 35.56 3.51
4556 9149 7.121315 GGTACAAATGTAAGAAGGCTTTCTGAT 59.879 37.037 12.36 0.00 42.80 2.90
4580 9173 4.458397 CTCATTGACCTCTGCAATATGGT 58.542 43.478 0.00 0.00 34.41 3.55
4609 9202 5.333035 CGTGTGTAGAAATTGTACTGTGGTG 60.333 44.000 2.03 0.00 0.00 4.17
4610 9203 5.756347 GTGTGTAGAAATTGTACTGTGGTGA 59.244 40.000 2.03 0.00 0.00 4.02
4611 9204 6.426937 GTGTGTAGAAATTGTACTGTGGTGAT 59.573 38.462 2.03 0.00 0.00 3.06
4612 9205 7.601130 GTGTGTAGAAATTGTACTGTGGTGATA 59.399 37.037 2.03 0.00 0.00 2.15
4613 9206 8.318412 TGTGTAGAAATTGTACTGTGGTGATAT 58.682 33.333 2.03 0.00 0.00 1.63
4614 9207 9.811995 GTGTAGAAATTGTACTGTGGTGATATA 57.188 33.333 2.03 0.00 0.00 0.86
4619 9212 9.216117 GAAATTGTACTGTGGTGATATATACCC 57.784 37.037 6.25 2.35 37.40 3.69
4622 9215 4.891992 ACTGTGGTGATATATACCCTGC 57.108 45.455 6.25 0.00 37.40 4.85
4624 9217 2.565391 TGTGGTGATATATACCCTGCGG 59.435 50.000 6.25 0.00 37.40 5.69
4625 9218 1.553248 TGGTGATATATACCCTGCGGC 59.447 52.381 6.25 0.00 37.40 6.53
4627 9220 2.170607 GGTGATATATACCCTGCGGCAT 59.829 50.000 1.75 0.00 31.89 4.40
4628 9221 3.370527 GGTGATATATACCCTGCGGCATT 60.371 47.826 1.75 0.00 31.89 3.56
4630 9223 2.107950 TATATACCCTGCGGCATTGC 57.892 50.000 1.75 0.00 0.00 3.56
4633 9226 0.756442 ATACCCTGCGGCATTGCAAT 60.756 50.000 5.99 5.99 45.74 3.56
4634 9227 0.969917 TACCCTGCGGCATTGCAATT 60.970 50.000 9.83 0.00 45.74 2.32
4635 9228 0.969917 ACCCTGCGGCATTGCAATTA 60.970 50.000 9.83 0.00 45.74 1.40
4695 9867 5.332581 CGTTATCACATGTGATCGTGGAATC 60.333 44.000 37.89 20.10 46.57 2.52
4699 9871 2.103094 ACATGTGATCGTGGAATCGGAT 59.897 45.455 0.00 0.00 35.12 4.18
4701 9873 3.260475 TGTGATCGTGGAATCGGATTT 57.740 42.857 4.47 0.00 0.00 2.17
4704 9876 3.002348 GTGATCGTGGAATCGGATTTTCC 59.998 47.826 4.47 4.12 42.52 3.13
4717 9889 2.029470 GGATTTTCCGTCCATTTGCACA 60.029 45.455 0.00 0.00 35.76 4.57
4733 9905 2.169561 TGCACAATATGGACGCTAGGAA 59.830 45.455 0.00 0.00 0.00 3.36
4736 9908 4.188462 CACAATATGGACGCTAGGAAACA 58.812 43.478 0.00 0.00 0.00 2.83
4740 9912 2.163818 TGGACGCTAGGAAACAACAG 57.836 50.000 0.00 0.00 0.00 3.16
4772 9944 3.054802 AGGCCAAGTTTGTAGAGAGATGG 60.055 47.826 5.01 0.00 0.00 3.51
4861 10070 0.106519 ACCAATGTGCTAGGCATCCC 60.107 55.000 0.00 0.00 41.91 3.85
4870 10079 1.546548 GCTAGGCATCCCTGATTTCCC 60.547 57.143 0.00 0.00 42.90 3.97
4934 10143 9.178758 GAATAAATACAAGGAGTGGTTCTCAAT 57.821 33.333 0.00 0.00 44.40 2.57
4947 10156 4.844085 TGGTTCTCAATAAAGAGGAGTCCA 59.156 41.667 12.86 0.00 36.30 4.02
4973 10187 3.248602 GTGGAATCCGTAGCATGCTAAAG 59.751 47.826 28.44 23.05 0.00 1.85
5005 10219 4.839668 TTTGTTTTCCGACAACATAGGG 57.160 40.909 1.03 0.00 39.11 3.53
5006 10220 3.773418 TGTTTTCCGACAACATAGGGA 57.227 42.857 0.00 0.00 0.00 4.20
5007 10221 3.670625 TGTTTTCCGACAACATAGGGAG 58.329 45.455 0.00 0.00 0.00 4.30
5008 10222 2.396590 TTTCCGACAACATAGGGAGC 57.603 50.000 0.00 0.00 0.00 4.70
5009 10223 1.271856 TTCCGACAACATAGGGAGCA 58.728 50.000 0.00 0.00 0.00 4.26
5010 10224 0.824109 TCCGACAACATAGGGAGCAG 59.176 55.000 0.00 0.00 0.00 4.24
5011 10225 0.824109 CCGACAACATAGGGAGCAGA 59.176 55.000 0.00 0.00 0.00 4.26
5012 10226 1.202463 CCGACAACATAGGGAGCAGAG 60.202 57.143 0.00 0.00 0.00 3.35
5013 10227 1.804372 CGACAACATAGGGAGCAGAGC 60.804 57.143 0.00 0.00 0.00 4.09
5014 10228 0.543749 ACAACATAGGGAGCAGAGCC 59.456 55.000 0.00 0.00 0.00 4.70
5015 10229 0.543277 CAACATAGGGAGCAGAGCCA 59.457 55.000 0.00 0.00 0.00 4.75
5016 10230 1.065199 CAACATAGGGAGCAGAGCCAA 60.065 52.381 0.00 0.00 0.00 4.52
5017 10231 0.835941 ACATAGGGAGCAGAGCCAAG 59.164 55.000 0.00 0.00 0.00 3.61
5018 10232 0.534652 CATAGGGAGCAGAGCCAAGC 60.535 60.000 0.00 0.00 0.00 4.01
5019 10233 1.704007 ATAGGGAGCAGAGCCAAGCC 61.704 60.000 0.00 0.00 0.00 4.35
5021 10235 4.087892 GGAGCAGAGCCAAGCCGA 62.088 66.667 0.00 0.00 0.00 5.54
5022 10236 2.817396 GAGCAGAGCCAAGCCGAC 60.817 66.667 0.00 0.00 0.00 4.79
5183 10397 6.497624 AAGACATATGAGAGAGCAAGGAAT 57.502 37.500 10.38 0.00 0.00 3.01
5240 10454 5.079998 ACAAAGGAAGAGAAGGGGAAAAT 57.920 39.130 0.00 0.00 0.00 1.82
5325 10541 3.394274 TGTTGAGATGAGGAACTTCCCAA 59.606 43.478 4.01 0.00 41.55 4.12
5412 10628 1.761784 CAAGAGAGGCAGCTACAGGAT 59.238 52.381 0.00 0.00 0.00 3.24
5441 10657 4.829492 TCAGTGACATGAGAGTGAGAAGAA 59.171 41.667 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.249120 ATGATCGGTGCTCGTTCCAA 59.751 50.000 8.02 0.00 40.32 3.53
48 49 0.460811 GCAGGTCGCATGATGTCTCA 60.461 55.000 0.00 0.00 41.79 3.27
59 60 2.894387 GATGGAGCTGCAGGTCGC 60.894 66.667 32.99 26.35 43.03 5.19
82 83 6.038050 GGAAGCAAGAGGAAGAAGATAACATG 59.962 42.308 0.00 0.00 0.00 3.21
84 85 5.249393 AGGAAGCAAGAGGAAGAAGATAACA 59.751 40.000 0.00 0.00 0.00 2.41
106 107 4.274459 CAGGAAGACACAAAACAAGAGAGG 59.726 45.833 0.00 0.00 0.00 3.69
107 108 4.878397 ACAGGAAGACACAAAACAAGAGAG 59.122 41.667 0.00 0.00 0.00 3.20
108 109 4.843728 ACAGGAAGACACAAAACAAGAGA 58.156 39.130 0.00 0.00 0.00 3.10
120 121 6.127281 TGAGTTACAACTGTTACAGGAAGACA 60.127 38.462 17.21 3.97 39.88 3.41
169 170 0.538287 AGGTTTGGGAGCTGCTGAAC 60.538 55.000 7.01 10.10 34.08 3.18
279 280 2.750712 AGAGAGAGCGTACAAACCTCTC 59.249 50.000 17.06 17.06 46.10 3.20
292 293 1.152546 GGAGGGAGGGAGAGAGAGC 60.153 68.421 0.00 0.00 0.00 4.09
304 305 0.930726 GAGAGAGAGGAAGGGAGGGA 59.069 60.000 0.00 0.00 0.00 4.20
305 306 0.933700 AGAGAGAGAGGAAGGGAGGG 59.066 60.000 0.00 0.00 0.00 4.30
306 307 1.852965 AGAGAGAGAGAGGAAGGGAGG 59.147 57.143 0.00 0.00 0.00 4.30
307 308 2.780010 AGAGAGAGAGAGAGGAAGGGAG 59.220 54.545 0.00 0.00 0.00 4.30
308 309 2.777692 GAGAGAGAGAGAGAGGAAGGGA 59.222 54.545 0.00 0.00 0.00 4.20
309 310 2.780010 AGAGAGAGAGAGAGAGGAAGGG 59.220 54.545 0.00 0.00 0.00 3.95
310 311 3.713764 AGAGAGAGAGAGAGAGAGGAAGG 59.286 52.174 0.00 0.00 0.00 3.46
311 312 4.653341 AGAGAGAGAGAGAGAGAGAGGAAG 59.347 50.000 0.00 0.00 0.00 3.46
312 313 4.624913 AGAGAGAGAGAGAGAGAGAGGAA 58.375 47.826 0.00 0.00 0.00 3.36
313 314 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
314 315 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
315 316 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
316 317 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
317 318 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
318 319 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
319 320 3.551863 GCGAGAGAGAGAGAGAGAGAGAG 60.552 56.522 0.00 0.00 0.00 3.20
320 321 2.362397 GCGAGAGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
347 348 0.404040 ATAGAGAGCGAGGGAGAGGG 59.596 60.000 0.00 0.00 0.00 4.30
354 355 1.351017 AGAGGGAGATAGAGAGCGAGG 59.649 57.143 0.00 0.00 0.00 4.63
355 356 2.303022 AGAGAGGGAGATAGAGAGCGAG 59.697 54.545 0.00 0.00 0.00 5.03
356 357 2.334977 AGAGAGGGAGATAGAGAGCGA 58.665 52.381 0.00 0.00 0.00 4.93
357 358 2.859165 AGAGAGGGAGATAGAGAGCG 57.141 55.000 0.00 0.00 0.00 5.03
358 359 3.421844 GGAAGAGAGGGAGATAGAGAGC 58.578 54.545 0.00 0.00 0.00 4.09
359 360 3.559171 CCGGAAGAGAGGGAGATAGAGAG 60.559 56.522 0.00 0.00 0.00 3.20
360 361 2.373836 CCGGAAGAGAGGGAGATAGAGA 59.626 54.545 0.00 0.00 0.00 3.10
361 362 2.790433 CCGGAAGAGAGGGAGATAGAG 58.210 57.143 0.00 0.00 0.00 2.43
362 363 1.202952 GCCGGAAGAGAGGGAGATAGA 60.203 57.143 5.05 0.00 0.00 1.98
363 364 1.253100 GCCGGAAGAGAGGGAGATAG 58.747 60.000 5.05 0.00 0.00 2.08
364 365 0.556258 TGCCGGAAGAGAGGGAGATA 59.444 55.000 5.05 0.00 0.00 1.98
365 366 0.325671 TTGCCGGAAGAGAGGGAGAT 60.326 55.000 5.05 0.00 0.00 2.75
366 367 1.078528 TTGCCGGAAGAGAGGGAGA 59.921 57.895 5.05 0.00 0.00 3.71
367 368 1.219393 GTTGCCGGAAGAGAGGGAG 59.781 63.158 5.05 0.00 0.00 4.30
368 369 1.535444 TGTTGCCGGAAGAGAGGGA 60.535 57.895 5.05 0.00 0.00 4.20
369 370 1.078848 CTGTTGCCGGAAGAGAGGG 60.079 63.158 5.05 0.00 0.00 4.30
370 371 0.671781 CACTGTTGCCGGAAGAGAGG 60.672 60.000 5.05 0.00 0.00 3.69
394 395 6.263617 TGGAAACCGTTTGCTTAGACTTAATT 59.736 34.615 15.49 0.00 31.65 1.40
395 396 5.766174 TGGAAACCGTTTGCTTAGACTTAAT 59.234 36.000 15.49 0.00 31.65 1.40
396 397 5.124645 TGGAAACCGTTTGCTTAGACTTAA 58.875 37.500 15.49 0.00 31.65 1.85
442 443 7.868415 AGCACAAGTTTAAAATTTAATACGGCA 59.132 29.630 0.00 0.00 0.00 5.69
449 450 7.708752 CCACCAGAGCACAAGTTTAAAATTTAA 59.291 33.333 0.00 0.00 0.00 1.52
457 458 3.290948 AACCACCAGAGCACAAGTTTA 57.709 42.857 0.00 0.00 0.00 2.01
550 551 6.606241 TTTTGGGATGGAGGGAGTATTAAT 57.394 37.500 0.00 0.00 0.00 1.40
563 564 8.697507 AGCTTAAGATAGTTATTTTGGGATGG 57.302 34.615 6.67 0.00 0.00 3.51
603 604 7.387122 GTGCCTTAACTTTGTACTAGCTTTAGT 59.613 37.037 0.00 0.00 0.00 2.24
607 608 5.866207 AGTGCCTTAACTTTGTACTAGCTT 58.134 37.500 0.00 0.00 0.00 3.74
613 614 9.836076 CCTAAAATAAGTGCCTTAACTTTGTAC 57.164 33.333 0.00 0.00 40.77 2.90
614 615 9.796180 TCCTAAAATAAGTGCCTTAACTTTGTA 57.204 29.630 0.00 0.00 40.77 2.41
615 616 8.573885 GTCCTAAAATAAGTGCCTTAACTTTGT 58.426 33.333 0.00 0.00 40.77 2.83
616 617 7.749126 CGTCCTAAAATAAGTGCCTTAACTTTG 59.251 37.037 0.00 0.00 40.77 2.77
617 618 7.094506 CCGTCCTAAAATAAGTGCCTTAACTTT 60.095 37.037 0.00 2.92 40.77 2.66
618 619 6.373495 CCGTCCTAAAATAAGTGCCTTAACTT 59.627 38.462 0.00 0.00 42.89 2.66
619 620 5.878669 CCGTCCTAAAATAAGTGCCTTAACT 59.121 40.000 0.00 0.00 29.35 2.24
620 621 5.876460 TCCGTCCTAAAATAAGTGCCTTAAC 59.124 40.000 0.00 0.00 29.35 2.01
621 622 6.052405 TCCGTCCTAAAATAAGTGCCTTAA 57.948 37.500 0.00 0.00 29.35 1.85
622 623 5.395990 CCTCCGTCCTAAAATAAGTGCCTTA 60.396 44.000 0.00 0.00 0.00 2.69
623 624 4.514401 CTCCGTCCTAAAATAAGTGCCTT 58.486 43.478 0.00 0.00 0.00 4.35
624 625 3.118371 CCTCCGTCCTAAAATAAGTGCCT 60.118 47.826 0.00 0.00 0.00 4.75
625 626 3.118519 TCCTCCGTCCTAAAATAAGTGCC 60.119 47.826 0.00 0.00 0.00 5.01
626 627 4.133013 TCCTCCGTCCTAAAATAAGTGC 57.867 45.455 0.00 0.00 0.00 4.40
747 748 3.181447 CCATGAGCCATCACCTGTCTATT 60.181 47.826 0.00 0.00 38.57 1.73
794 795 6.897986 TGGTTACAAACTGGGAGTAGTTTAA 58.102 36.000 3.84 0.00 46.19 1.52
902 905 9.787532 GTAGCAATAGAGAAATGTGCATTAAAA 57.212 29.630 0.00 0.00 37.68 1.52
926 929 6.071672 TCGCCCATTGAATTTTTGAAGATGTA 60.072 34.615 0.00 0.00 0.00 2.29
935 938 7.555087 TGATAAATCTCGCCCATTGAATTTTT 58.445 30.769 0.00 0.00 0.00 1.94
936 939 7.111247 TGATAAATCTCGCCCATTGAATTTT 57.889 32.000 0.00 0.00 0.00 1.82
1146 1157 5.895534 AGCATCTAACCATCACATTTCCATT 59.104 36.000 0.00 0.00 0.00 3.16
1182 1193 5.402398 GCTTGAGTGTGAAGTGTTTTCTTT 58.598 37.500 0.00 0.00 0.00 2.52
1184 1195 3.378427 GGCTTGAGTGTGAAGTGTTTTCT 59.622 43.478 0.00 0.00 0.00 2.52
1185 1196 3.378427 AGGCTTGAGTGTGAAGTGTTTTC 59.622 43.478 0.00 0.00 0.00 2.29
1188 1199 2.717639 AGGCTTGAGTGTGAAGTGTT 57.282 45.000 0.00 0.00 0.00 3.32
1190 1273 2.564771 TGAAGGCTTGAGTGTGAAGTG 58.435 47.619 3.46 0.00 0.00 3.16
1271 1919 3.655276 TCAACTAGAGTTCCGTTCACC 57.345 47.619 0.00 0.00 35.83 4.02
1348 1996 3.066760 AGACTGCAACAAAGTAGTTTGCC 59.933 43.478 20.59 11.15 46.13 4.52
1376 2024 6.147492 GGAGAATATGCAAGATAACAGCAGAG 59.853 42.308 0.00 0.00 42.14 3.35
1417 2065 4.284490 AGGACTTTTGTGAGATAGCTGACA 59.716 41.667 0.00 0.00 36.44 3.58
1423 2071 8.660373 GTTTCATGTAGGACTTTTGTGAGATAG 58.340 37.037 0.00 0.00 0.00 2.08
1543 2191 4.212636 CGATTCAAAACTGTCCGGTACTTT 59.787 41.667 0.00 0.00 0.00 2.66
1557 2205 3.872511 AATCATGCAGGCGATTCAAAA 57.127 38.095 0.00 0.00 0.00 2.44
1562 2210 3.382227 TGATGAAAATCATGCAGGCGATT 59.618 39.130 0.00 0.00 37.20 3.34
1573 2221 5.565592 AGCGCTTACAATGATGAAAATCA 57.434 34.783 2.64 0.00 34.73 2.57
1649 2297 3.959495 AGGCATGAATGATAACAGGGT 57.041 42.857 0.00 0.00 0.00 4.34
1650 2298 4.999950 GTCTAGGCATGAATGATAACAGGG 59.000 45.833 0.00 0.00 0.00 4.45
1653 2301 5.368145 GGTGTCTAGGCATGAATGATAACA 58.632 41.667 0.00 0.00 0.00 2.41
1654 2302 4.757149 GGGTGTCTAGGCATGAATGATAAC 59.243 45.833 0.00 0.00 0.00 1.89
1656 2304 4.040829 CAGGGTGTCTAGGCATGAATGATA 59.959 45.833 0.00 0.00 0.00 2.15
1657 2305 3.051581 AGGGTGTCTAGGCATGAATGAT 58.948 45.455 0.00 0.00 0.00 2.45
1659 2307 2.092753 ACAGGGTGTCTAGGCATGAATG 60.093 50.000 0.00 0.22 0.00 2.67
1660 2308 2.200081 ACAGGGTGTCTAGGCATGAAT 58.800 47.619 0.00 0.00 0.00 2.57
1661 2309 1.656587 ACAGGGTGTCTAGGCATGAA 58.343 50.000 0.00 0.00 0.00 2.57
1662 2310 1.656587 AACAGGGTGTCTAGGCATGA 58.343 50.000 0.00 0.00 0.00 3.07
1663 2311 3.389329 AGATAACAGGGTGTCTAGGCATG 59.611 47.826 0.00 0.00 0.00 4.06
1664 2312 3.389329 CAGATAACAGGGTGTCTAGGCAT 59.611 47.826 0.00 0.00 0.00 4.40
1737 2385 4.273318 AGACCTGCTAATTGATTCCAACC 58.727 43.478 0.00 0.00 34.72 3.77
1903 3198 0.615331 GGATGGAGAGGCTGTGAACA 59.385 55.000 0.00 0.00 0.00 3.18
1991 4274 0.891373 CGAAAGGTGAGGAGAGAGCA 59.109 55.000 0.00 0.00 0.00 4.26
1992 4275 3.731295 CGAAAGGTGAGGAGAGAGC 57.269 57.895 0.00 0.00 0.00 4.09
2057 4356 1.959747 TTCTCTAACTCGTTCACGCG 58.040 50.000 3.53 3.53 39.60 6.01
2074 5157 5.638234 ACTGTAGTAAAGGCGAGATGTTTTC 59.362 40.000 0.00 0.00 0.00 2.29
2112 5195 1.690893 CCTAGGCTGCAGCAGATAGAA 59.309 52.381 37.63 14.45 44.36 2.10
2140 5223 5.215160 CAGGCAATTTACAGAGTCAAACAC 58.785 41.667 0.00 0.00 0.00 3.32
2290 5421 0.953471 GAAGGTGTATGCGGTGCACA 60.953 55.000 20.43 0.00 44.25 4.57
2294 5425 1.369091 GGCAGAAGGTGTATGCGGTG 61.369 60.000 0.00 0.00 40.90 4.94
2297 5428 1.091771 CCTGGCAGAAGGTGTATGCG 61.092 60.000 17.94 0.00 40.90 4.73
2328 5459 5.105756 GGTGTAGCATGCAGAAATAGGTTTT 60.106 40.000 21.98 0.00 0.00 2.43
2385 5516 4.378774 CAGGATCAGCTTGATTAGTCAGG 58.621 47.826 0.00 0.00 37.20 3.86
2409 5540 4.497340 CCACTGTACAGATGCAAACGTTTT 60.497 41.667 29.30 0.00 0.00 2.43
2416 5547 2.153645 CAAGCCACTGTACAGATGCAA 58.846 47.619 29.30 0.00 33.33 4.08
2420 5551 1.813513 GTGCAAGCCACTGTACAGAT 58.186 50.000 29.30 10.76 41.35 2.90
2422 5553 0.599991 TCGTGCAAGCCACTGTACAG 60.600 55.000 21.44 21.44 42.42 2.74
2463 5594 2.957006 GTCTCGGCACCCTCTAATCTTA 59.043 50.000 0.00 0.00 0.00 2.10
2481 5612 3.314331 CACAGCACCCGGGAGTCT 61.314 66.667 32.02 18.06 0.00 3.24
2554 5690 6.966632 TGCATGTTCGAGATAAAATAAAGTGC 59.033 34.615 0.00 0.00 0.00 4.40
2626 7099 3.671008 TTCGCAGGTGTTAGAGCTTTA 57.329 42.857 0.00 0.00 0.00 1.85
2702 7180 5.048013 GCTAGATTTGTTGGGCTGTTTAGTT 60.048 40.000 0.00 0.00 0.00 2.24
2705 7183 4.402829 TGCTAGATTTGTTGGGCTGTTTA 58.597 39.130 0.00 0.00 0.00 2.01
2721 7199 3.973973 AGGCATATAGGTTGGTTGCTAGA 59.026 43.478 0.00 0.00 33.86 2.43
3009 7488 3.000815 GGCTCCAAAAGACGTGACA 57.999 52.632 0.00 0.00 0.00 3.58
3065 7544 4.021632 GCCAATTGAAGAAGGAGCTCTTTT 60.022 41.667 12.88 8.07 35.76 2.27
3090 7569 8.618702 ATGAACCAACATTGATTGCAAAATAA 57.381 26.923 1.71 0.00 37.59 1.40
3107 7586 2.562298 GTCCCAGCAATCAATGAACCAA 59.438 45.455 0.00 0.00 0.00 3.67
3222 7701 6.499699 TCTGAAATCTATACATGATGGAGCCT 59.500 38.462 0.00 0.00 0.00 4.58
3232 7711 6.239829 CCTCCAGGCTTCTGAAATCTATACAT 60.240 42.308 0.00 0.00 40.86 2.29
3371 7850 1.303317 AATTTCCGGCTGCCTTCGT 60.303 52.632 17.92 0.00 0.00 3.85
3583 8067 7.681939 TCCATTTGTACCACAATAGAAGTTC 57.318 36.000 0.00 0.00 38.00 3.01
3749 8342 6.995686 TCACAGTCAGGTAATGTTACAATTGT 59.004 34.615 16.68 16.68 35.37 2.71
3757 8350 5.249393 AGGAGATTCACAGTCAGGTAATGTT 59.751 40.000 0.00 0.00 0.00 2.71
4023 8616 8.561738 TCTAATTACTGGAACAATGAGTTTCC 57.438 34.615 0.00 0.00 41.51 3.13
4217 8810 1.774894 TACTGGGGTCCTTGCCACAC 61.775 60.000 0.00 0.00 36.94 3.82
4317 8910 4.023707 GCGAGAATGCCATACATAAGCTTT 60.024 41.667 3.20 0.00 38.34 3.51
4519 9112 7.564793 TCTTACATTTGTACCTCATAGCACAT 58.435 34.615 0.00 0.00 0.00 3.21
4556 9149 4.445305 CCATATTGCAGAGGTCAATGAGGA 60.445 45.833 0.00 0.00 35.87 3.71
4580 9173 5.176774 CAGTACAATTTCTACACACGCTTCA 59.823 40.000 0.00 0.00 0.00 3.02
4619 9212 1.921887 CAAGTAATTGCAATGCCGCAG 59.078 47.619 13.82 0.00 44.14 5.18
4622 9215 2.176369 CGACAAGTAATTGCAATGCCG 58.824 47.619 13.82 1.63 0.00 5.69
4624 9217 3.820689 TCACGACAAGTAATTGCAATGC 58.179 40.909 13.82 9.33 0.00 3.56
4625 9218 4.263677 GCATCACGACAAGTAATTGCAATG 59.736 41.667 13.82 3.85 33.81 2.82
4627 9220 3.501828 AGCATCACGACAAGTAATTGCAA 59.498 39.130 0.00 0.00 35.15 4.08
4628 9221 3.073678 AGCATCACGACAAGTAATTGCA 58.926 40.909 2.17 0.00 35.15 4.08
4630 9223 6.588348 TCATAGCATCACGACAAGTAATTG 57.412 37.500 0.45 0.45 0.00 2.32
4633 9226 6.163476 AGTTTCATAGCATCACGACAAGTAA 58.837 36.000 0.00 0.00 0.00 2.24
4634 9227 5.720202 AGTTTCATAGCATCACGACAAGTA 58.280 37.500 0.00 0.00 0.00 2.24
4635 9228 4.569943 AGTTTCATAGCATCACGACAAGT 58.430 39.130 0.00 0.00 0.00 3.16
4699 9871 3.742433 ATTGTGCAAATGGACGGAAAA 57.258 38.095 0.00 0.00 39.39 2.29
4701 9873 3.130164 CCATATTGTGCAAATGGACGGAA 59.870 43.478 11.38 0.00 42.36 4.30
4717 9889 4.839121 TGTTGTTTCCTAGCGTCCATATT 58.161 39.130 0.00 0.00 0.00 1.28
4726 9898 3.067833 GACAGACCTGTTGTTTCCTAGC 58.932 50.000 3.98 0.00 45.05 3.42
4733 9905 1.810412 GCCTTCGACAGACCTGTTGTT 60.810 52.381 14.98 0.00 45.05 2.83
4736 9908 1.371558 GGCCTTCGACAGACCTGTT 59.628 57.895 3.98 0.00 45.05 3.16
4740 9912 0.250338 AACTTGGCCTTCGACAGACC 60.250 55.000 3.32 0.00 0.00 3.85
4772 9944 5.304686 TCAGAGGAGGAGAGATAAGAGTC 57.695 47.826 0.00 0.00 0.00 3.36
4786 9958 7.010160 AGACTAGATAAAATCCCTCAGAGGAG 58.990 42.308 19.21 8.28 39.95 3.69
4802 9974 2.098607 CCCGACGCACAAAGACTAGATA 59.901 50.000 0.00 0.00 0.00 1.98
4861 10070 2.292267 CAGGGTCAATCGGGAAATCAG 58.708 52.381 0.00 0.00 0.00 2.90
4896 10105 9.527157 TCCTTGTATTTATTCATTCAAGTGGAA 57.473 29.630 0.00 0.00 40.46 3.53
4947 10156 2.289694 GCATGCTACGGATTCCACCTAT 60.290 50.000 11.37 0.00 0.00 2.57
4962 10171 5.458041 AAAATGTGACACTTTAGCATGCT 57.542 34.783 25.99 25.99 0.00 3.79
4986 10200 3.670625 CTCCCTATGTTGTCGGAAAACA 58.329 45.455 15.67 15.67 41.50 2.83
4987 10201 2.418976 GCTCCCTATGTTGTCGGAAAAC 59.581 50.000 4.03 4.03 0.00 2.43
4991 10205 0.824109 CTGCTCCCTATGTTGTCGGA 59.176 55.000 0.00 0.00 0.00 4.55
4993 10207 1.804372 GCTCTGCTCCCTATGTTGTCG 60.804 57.143 0.00 0.00 0.00 4.35
4994 10208 1.474143 GGCTCTGCTCCCTATGTTGTC 60.474 57.143 0.00 0.00 0.00 3.18
4995 10209 0.543749 GGCTCTGCTCCCTATGTTGT 59.456 55.000 0.00 0.00 0.00 3.32
4996 10210 0.543277 TGGCTCTGCTCCCTATGTTG 59.457 55.000 0.00 0.00 0.00 3.33
4997 10211 1.211457 CTTGGCTCTGCTCCCTATGTT 59.789 52.381 0.00 0.00 0.00 2.71
4998 10212 0.835941 CTTGGCTCTGCTCCCTATGT 59.164 55.000 0.00 0.00 0.00 2.29
4999 10213 0.534652 GCTTGGCTCTGCTCCCTATG 60.535 60.000 0.00 0.00 0.00 2.23
5000 10214 1.704007 GGCTTGGCTCTGCTCCCTAT 61.704 60.000 0.00 0.00 0.00 2.57
5001 10215 2.370445 GGCTTGGCTCTGCTCCCTA 61.370 63.158 0.00 0.00 0.00 3.53
5002 10216 3.726144 GGCTTGGCTCTGCTCCCT 61.726 66.667 0.00 0.00 0.00 4.20
5004 10218 4.087892 TCGGCTTGGCTCTGCTCC 62.088 66.667 0.00 0.00 0.00 4.70
5005 10219 2.817396 GTCGGCTTGGCTCTGCTC 60.817 66.667 0.00 0.00 0.00 4.26
5006 10220 4.400961 GGTCGGCTTGGCTCTGCT 62.401 66.667 0.00 0.00 0.00 4.24
5007 10221 3.909086 AAGGTCGGCTTGGCTCTGC 62.909 63.158 0.00 0.00 0.00 4.26
5008 10222 0.890996 AAAAGGTCGGCTTGGCTCTG 60.891 55.000 0.00 0.00 0.00 3.35
5009 10223 0.178990 AAAAAGGTCGGCTTGGCTCT 60.179 50.000 0.00 0.00 0.00 4.09
5010 10224 2.341452 AAAAAGGTCGGCTTGGCTC 58.659 52.632 0.00 0.00 0.00 4.70
5011 10225 4.599036 AAAAAGGTCGGCTTGGCT 57.401 50.000 0.00 0.00 0.00 4.75
5107 10321 9.430623 GCAGTTCTTCTTTCTCTTTATTCTAGT 57.569 33.333 0.00 0.00 0.00 2.57
5325 10541 6.942576 TGCTTTTAGGAGAAAGTTGATAGCTT 59.057 34.615 0.00 0.00 38.56 3.74
5412 10628 6.604795 TCTCACTCTCATGTCACTGAATCATA 59.395 38.462 0.00 0.00 0.00 2.15
5441 10657 3.248024 TGGAGGACCTACACTCAATTGT 58.752 45.455 0.75 0.00 35.45 2.71


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

AutoCloner maintained by Alex Coulton.