Multiple sequence alignment - TraesCS7D01G551500

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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 TraesCS7D01G551500 chr7D 100.000 5813 0 0 1 5813 634895333 634889521 0.000000e+00 10735.0
1 TraesCS7D01G551500 chr7D 92.407 2318 101 30 524 2789 635395076 635397370 0.000000e+00 3236.0
2 TraesCS7D01G551500 chr7D 94.784 1227 43 13 3229 4453 635397871 635399078 0.000000e+00 1892.0
3 TraesCS7D01G551500 chr7D 98.297 411 7 0 5403 5813 635400217 635400627 0.000000e+00 721.0
4 TraesCS7D01G551500 chr7D 92.553 376 22 5 2855 3227 635397464 635397836 8.570000e-148 534.0
5 TraesCS7D01G551500 chr7D 84.464 560 25 18 4568 5082 635399105 635399647 4.050000e-136 496.0
6 TraesCS7D01G551500 chr7D 86.413 368 21 16 5081 5437 635399678 635400027 5.500000e-100 375.0
7 TraesCS7D01G551500 chr7D 93.889 180 7 4 2535 2711 636665209 636665031 9.600000e-68 268.0
8 TraesCS7D01G551500 chr7D 93.043 115 8 0 927 1041 635393592 635393706 1.000000e-37 169.0
9 TraesCS7D01G551500 chr7D 90.000 90 8 1 5179 5268 635421805 635421893 1.320000e-21 115.0
10 TraesCS7D01G551500 chr7D 89.362 47 5 0 4 50 217616468 217616422 6.290000e-05 60.2
11 TraesCS7D01G551500 chr7B 92.194 1960 104 22 3164 5085 741244281 741242333 0.000000e+00 2726.0
12 TraesCS7D01G551500 chr7B 89.114 1332 67 28 538 1849 741246526 741245253 0.000000e+00 1585.0
13 TraesCS7D01G551500 chr7B 96.386 913 22 3 1861 2770 741245198 741244294 0.000000e+00 1493.0
14 TraesCS7D01G551500 chr7B 90.541 740 55 7 5081 5813 741242305 741241574 0.000000e+00 965.0
15 TraesCS7D01G551500 chr7B 85.856 403 52 5 3 401 741246928 741246527 1.940000e-114 424.0
16 TraesCS7D01G551500 chr7B 88.182 330 39 0 5451 5780 740916586 740916257 1.520000e-105 394.0
17 TraesCS7D01G551500 chr7B 81.346 520 58 20 3233 3739 739642890 739643383 2.540000e-103 387.0
18 TraesCS7D01G551500 chr7B 85.561 187 21 4 864 1044 741247157 741246971 2.140000e-44 191.0
19 TraesCS7D01G551500 chr7B 76.829 246 40 13 4 240 560804293 560804056 7.910000e-24 122.0
20 TraesCS7D01G551500 chr7A 93.929 1120 42 7 1677 2770 730712926 730711807 0.000000e+00 1668.0
21 TraesCS7D01G551500 chr7A 96.075 1019 34 5 3438 4453 730711231 730710216 0.000000e+00 1655.0
22 TraesCS7D01G551500 chr7A 85.571 797 56 29 4568 5309 730710189 730709397 0.000000e+00 780.0
23 TraesCS7D01G551500 chr7A 93.103 435 18 6 2804 3230 730711806 730711376 1.380000e-175 627.0
24 TraesCS7D01G551500 chr7A 87.052 363 36 3 5452 5813 730709403 730709051 3.260000e-107 399.0
25 TraesCS7D01G551500 chr7A 90.074 272 24 3 5167 5437 730598953 730598684 3.330000e-92 350.0
26 TraesCS7D01G551500 chr7A 90.234 256 14 6 1404 1651 730713173 730712921 2.020000e-84 324.0
27 TraesCS7D01G551500 chr7A 81.892 370 21 20 810 1160 730713607 730713265 2.670000e-68 270.0
28 TraesCS7D01G551500 chr7A 90.323 186 11 6 2535 2717 729612601 729612782 2.710000e-58 237.0
29 TraesCS7D01G551500 chr7A 90.323 186 11 6 2535 2717 729638005 729638186 2.710000e-58 237.0
30 TraesCS7D01G551500 chr7A 96.460 113 3 1 3232 3343 730711341 730711229 9.950000e-43 185.0
31 TraesCS7D01G551500 chr7A 93.750 96 4 2 1192 1286 730713268 730713174 6.070000e-30 143.0
32 TraesCS7D01G551500 chrUn 82.056 535 57 21 3233 3754 373778145 373778653 2.500000e-113 420.0
33 TraesCS7D01G551500 chrUn 81.869 535 58 21 3233 3754 159048873 159048365 1.170000e-111 414.0
34 TraesCS7D01G551500 chrUn 81.346 520 58 20 3233 3739 287874115 287874608 2.540000e-103 387.0
35 TraesCS7D01G551500 chrUn 81.346 520 58 20 3233 3739 307004175 307004668 2.540000e-103 387.0
36 TraesCS7D01G551500 chrUn 84.969 326 35 8 3233 3545 391122739 391123063 9.400000e-83 318.0
37 TraesCS7D01G551500 chrUn 95.210 167 6 1 4899 5063 50447813 50447979 4.470000e-66 263.0
38 TraesCS7D01G551500 chrUn 92.982 114 5 2 5081 5194 50448061 50448171 4.660000e-36 163.0
39 TraesCS7D01G551500 chrUn 89.381 113 12 0 4413 4525 19227927 19227815 6.070000e-30 143.0
40 TraesCS7D01G551500 chr4A 95.210 167 6 1 4899 5063 708069002 708069168 4.470000e-66 263.0
41 TraesCS7D01G551500 chr4A 92.982 114 5 2 5081 5194 708069249 708069359 4.660000e-36 163.0
42 TraesCS7D01G551500 chr4A 92.982 114 5 2 5081 5194 708091904 708092014 4.660000e-36 163.0
43 TraesCS7D01G551500 chr2A 79.221 231 36 8 4 227 550567472 550567697 3.630000e-32 150.0
44 TraesCS7D01G551500 chr2A 79.464 112 21 2 10 119 562728079 562727968 1.740000e-10 78.7
45 TraesCS7D01G551500 chr3B 92.308 104 8 0 2881 2984 812340357 812340460 1.310000e-31 148.0
46 TraesCS7D01G551500 chr3B 88.793 116 13 0 4411 4526 157237627 157237742 6.070000e-30 143.0
47 TraesCS7D01G551500 chr6A 91.346 104 9 0 2881 2984 502244228 502244331 6.070000e-30 143.0
48 TraesCS7D01G551500 chr4B 86.923 130 14 3 4402 4530 215918447 215918320 6.070000e-30 143.0
49 TraesCS7D01G551500 chr4B 94.595 37 2 0 13 49 596643967 596643931 2.260000e-04 58.4
50 TraesCS7D01G551500 chr1D 90.000 110 11 0 4413 4522 407673008 407673117 6.070000e-30 143.0
51 TraesCS7D01G551500 chr6B 89.286 112 12 0 4411 4522 42775738 42775627 2.180000e-29 141.0
52 TraesCS7D01G551500 chr6B 88.235 119 13 1 4407 4525 506389422 506389305 2.180000e-29 141.0
53 TraesCS7D01G551500 chr6B 87.931 116 14 0 4408 4523 637025253 637025368 2.820000e-28 137.0
54 TraesCS7D01G551500 chr5B 88.793 116 11 2 2880 2994 681080413 681080527 2.180000e-29 141.0
55 TraesCS7D01G551500 chr3D 91.346 104 7 2 2881 2984 604669409 604669510 2.180000e-29 141.0
56 TraesCS7D01G551500 chr3D 89.091 110 12 0 2881 2990 463716865 463716974 2.820000e-28 137.0
57 TraesCS7D01G551500 chr3D 87.500 120 13 2 4408 4526 578617987 578617869 2.820000e-28 137.0
58 TraesCS7D01G551500 chr1A 89.815 108 11 0 2881 2988 28705748 28705641 7.850000e-29 139.0
59 TraesCS7D01G551500 chr2D 88.496 113 13 0 2881 2993 473292199 473292311 2.820000e-28 137.0
60 TraesCS7D01G551500 chr2B 76.923 247 47 5 4 244 52937293 52937535 1.310000e-26 132.0
61 TraesCS7D01G551500 chr2B 100.000 28 0 0 136 163 15632223 15632250 1.100000e-02 52.8
62 TraesCS7D01G551500 chr5D 78.070 114 19 4 10 119 385696406 385696295 3.760000e-07 67.6
63 TraesCS7D01G551500 chr4D 91.111 45 4 0 4 48 297387867 297387911 1.750000e-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 TraesCS7D01G551500 chr7D 634889521 634895333 5812 True 10735.000000 10735 100.000000 1 5813 1 chr7D.!!$R2 5812
1 TraesCS7D01G551500 chr7D 635393592 635400627 7035 False 1060.428571 3236 91.708714 524 5813 7 chr7D.!!$F2 5289
2 TraesCS7D01G551500 chr7B 741241574 741247157 5583 True 1230.666667 2726 89.942000 3 5813 6 chr7B.!!$R3 5810
3 TraesCS7D01G551500 chr7A 730709051 730713607 4556 True 672.333333 1668 90.896222 810 5813 9 chr7A.!!$R2 5003
4 TraesCS7D01G551500 chrUn 373778145 373778653 508 False 420.000000 420 82.056000 3233 3754 1 chrUn.!!$F3 521
5 TraesCS7D01G551500 chrUn 159048365 159048873 508 True 414.000000 414 81.869000 3233 3754 1 chrUn.!!$R2 521

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
115 343 0.034767 ATAGGTGTGTCTCCGACGGA 60.035 55.000 17.28 17.28 34.95 4.69 F
796 1836 0.178926 TACTCCACCGAACCCCTTGA 60.179 55.000 0.00 0.00 0.00 3.02 F
1629 2714 0.105246 TTGGCTTTGTGGAATGGGGT 60.105 50.000 0.00 0.00 0.00 4.95 F
2417 3558 1.002544 GGCTTGTACAGGAAGCTGACT 59.997 52.381 15.69 0.00 44.44 3.41 F
3773 5008 0.240145 CTCGACACAAGTACAGGCGA 59.760 55.000 0.00 0.35 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 2460 0.107654 AGCTGCTCGGACCAAATACC 60.108 55.000 0.00 0.0 0.00 2.73 R
2039 3180 0.684479 ACAGCAGACAGAGCCGGATA 60.684 55.000 5.05 0.0 0.00 2.59 R
2498 3647 3.181491 GGAGACTCGGATGAGAAGAACAG 60.181 52.174 0.00 0.0 45.57 3.16 R
4270 5507 0.179034 GCTGCTGGGGGTTATCTGAG 60.179 60.000 0.00 0.0 0.00 3.35 R
4888 6170 0.242825 CGTTCTACAGGGTTCTGCGA 59.757 55.000 0.00 0.0 44.59 5.10 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
31 259 2.283529 GGTGACGGCTCCCTGAAGA 61.284 63.158 0.00 0.00 0.00 2.87
43 271 5.242615 GGCTCCCTGAAGATGGAATAAAATC 59.757 44.000 0.00 0.00 0.00 2.17
48 276 5.772169 CCTGAAGATGGAATAAAATCCTCCC 59.228 44.000 0.00 0.00 40.35 4.30
50 278 5.436374 TGAAGATGGAATAAAATCCTCCCCT 59.564 40.000 0.00 0.00 40.35 4.79
91 319 1.658686 CTCTAGCGCTGTCGAAGGGT 61.659 60.000 22.90 0.00 40.91 4.34
115 343 0.034767 ATAGGTGTGTCTCCGACGGA 60.035 55.000 17.28 17.28 34.95 4.69
121 349 1.025812 GTGTCTCCGACGGATCTCAT 58.974 55.000 18.71 0.00 34.95 2.90
139 367 1.966901 ATGGCATTCCGACGGTGCTA 61.967 55.000 23.77 20.11 38.83 3.49
142 370 1.146358 GCATTCCGACGGTGCTAGTC 61.146 60.000 19.23 0.00 36.02 2.59
146 374 1.226323 CCGACGGTGCTAGTCTTCG 60.226 63.158 5.48 0.00 36.53 3.79
156 384 1.751924 GCTAGTCTTCGGTGGATCTGT 59.248 52.381 0.00 0.00 0.00 3.41
159 387 4.142227 GCTAGTCTTCGGTGGATCTGTTTA 60.142 45.833 0.00 0.00 0.00 2.01
174 402 5.344743 TCTGTTTAGATCCAATCTTCGCT 57.655 39.130 0.00 0.00 40.76 4.93
180 408 3.600388 AGATCCAATCTTCGCTTTCGTT 58.400 40.909 0.00 0.00 35.76 3.85
192 420 2.121786 GCTTTCGTTCGTGTGTCTACA 58.878 47.619 0.00 0.00 0.00 2.74
227 455 9.349713 ACTTTCGATCTATACTTCTCTTCATCT 57.650 33.333 0.00 0.00 0.00 2.90
234 462 3.584406 ACTTCTCTTCATCTGTGACGG 57.416 47.619 0.00 0.00 33.11 4.79
235 463 2.266554 CTTCTCTTCATCTGTGACGGC 58.733 52.381 0.00 0.00 33.11 5.68
238 466 2.434185 TTCATCTGTGACGGCGGC 60.434 61.111 13.24 9.67 33.11 6.53
240 468 1.600511 TTCATCTGTGACGGCGGCTA 61.601 55.000 16.45 1.43 33.11 3.93
268 496 2.436115 GTGGGGCCTTAGCACGAC 60.436 66.667 0.84 0.00 46.55 4.34
277 505 2.683968 CCTTAGCACGACAACTTGCTA 58.316 47.619 0.00 0.00 46.95 3.49
279 507 3.989104 AGCACGACAACTTGCTAGT 57.011 47.368 0.00 0.00 46.95 2.57
300 528 1.111277 GTCCACAACAAGTTTGGCCT 58.889 50.000 3.32 0.00 0.00 5.19
337 565 2.435586 CTCTCGCCCCAGTGCTTG 60.436 66.667 0.00 0.00 0.00 4.01
347 575 2.334838 CCCAGTGCTTGTAGTCGTTAC 58.665 52.381 0.00 0.00 0.00 2.50
354 582 3.822735 TGCTTGTAGTCGTTACTAGGTGT 59.177 43.478 0.00 0.00 38.89 4.16
356 584 5.473162 TGCTTGTAGTCGTTACTAGGTGTTA 59.527 40.000 0.00 0.00 38.89 2.41
358 586 6.471519 GCTTGTAGTCGTTACTAGGTGTTATG 59.528 42.308 0.00 0.00 38.89 1.90
359 587 6.441093 TGTAGTCGTTACTAGGTGTTATGG 57.559 41.667 0.00 0.00 38.89 2.74
360 588 6.179756 TGTAGTCGTTACTAGGTGTTATGGA 58.820 40.000 0.00 0.00 38.89 3.41
361 589 5.573337 AGTCGTTACTAGGTGTTATGGAC 57.427 43.478 0.00 0.00 32.84 4.02
363 591 5.655532 AGTCGTTACTAGGTGTTATGGACAT 59.344 40.000 0.00 0.00 35.77 3.06
364 592 5.747197 GTCGTTACTAGGTGTTATGGACATG 59.253 44.000 0.00 0.00 41.10 3.21
366 594 6.602803 TCGTTACTAGGTGTTATGGACATGTA 59.397 38.462 0.00 0.00 41.10 2.29
367 595 7.286087 TCGTTACTAGGTGTTATGGACATGTAT 59.714 37.037 0.00 0.00 41.10 2.29
368 596 7.381408 CGTTACTAGGTGTTATGGACATGTATG 59.619 40.741 0.00 0.00 41.10 2.39
369 597 5.611374 ACTAGGTGTTATGGACATGTATGC 58.389 41.667 0.00 0.00 41.10 3.14
370 598 4.502105 AGGTGTTATGGACATGTATGCA 57.498 40.909 0.00 0.00 41.10 3.96
371 599 4.854173 AGGTGTTATGGACATGTATGCAA 58.146 39.130 0.00 0.00 41.10 4.08
373 601 5.125417 AGGTGTTATGGACATGTATGCAAAC 59.875 40.000 0.00 1.11 41.10 2.93
377 605 7.598493 GTGTTATGGACATGTATGCAAACTTTT 59.402 33.333 0.00 0.00 41.10 2.27
378 606 7.598118 TGTTATGGACATGTATGCAAACTTTTG 59.402 33.333 0.00 0.00 35.85 2.44
383 611 7.812191 TGGACATGTATGCAAACTTTTGTTATC 59.188 33.333 0.00 0.00 42.67 1.75
385 613 9.410556 GACATGTATGCAAACTTTTGTTATCTT 57.589 29.630 0.00 0.00 42.67 2.40
390 618 9.848172 GTATGCAAACTTTTGTTATCTTTTGTG 57.152 29.630 0.00 0.00 42.67 3.33
391 619 7.897575 TGCAAACTTTTGTTATCTTTTGTGT 57.102 28.000 3.74 0.00 42.67 3.72
393 621 8.439286 TGCAAACTTTTGTTATCTTTTGTGTTC 58.561 29.630 3.74 0.00 42.67 3.18
408 636 8.783093 TCTTTTGTGTTCTTTATACTGTCATGG 58.217 33.333 0.00 0.00 0.00 3.66
409 637 6.494893 TTGTGTTCTTTATACTGTCATGGC 57.505 37.500 0.00 0.00 0.00 4.40
410 638 5.555966 TGTGTTCTTTATACTGTCATGGCA 58.444 37.500 0.00 0.00 0.00 4.92
411 639 5.411361 TGTGTTCTTTATACTGTCATGGCAC 59.589 40.000 0.00 0.00 0.00 5.01
429 657 6.321821 TGGCACAATAAATAGGTAGAAGGT 57.678 37.500 0.00 0.00 31.92 3.50
430 658 6.727394 TGGCACAATAAATAGGTAGAAGGTT 58.273 36.000 0.00 0.00 31.92 3.50
431 659 6.826741 TGGCACAATAAATAGGTAGAAGGTTC 59.173 38.462 0.00 0.00 31.92 3.62
432 660 6.262496 GGCACAATAAATAGGTAGAAGGTTCC 59.738 42.308 0.00 0.00 0.00 3.62
433 661 6.262496 GCACAATAAATAGGTAGAAGGTTCCC 59.738 42.308 0.00 0.00 0.00 3.97
436 664 8.053355 ACAATAAATAGGTAGAAGGTTCCCTTG 58.947 37.037 0.00 0.00 44.82 3.61
437 665 8.272173 CAATAAATAGGTAGAAGGTTCCCTTGA 58.728 37.037 0.00 0.00 44.82 3.02
438 666 6.713731 AAATAGGTAGAAGGTTCCCTTGAA 57.286 37.500 0.00 0.00 44.82 2.69
441 669 5.397553 AGGTAGAAGGTTCCCTTGAAAAA 57.602 39.130 0.00 0.00 44.82 1.94
476 704 8.637099 ACGGAAATCCTAGTTAAAGTATCTACC 58.363 37.037 0.00 0.00 0.00 3.18
477 705 8.087136 CGGAAATCCTAGTTAAAGTATCTACCC 58.913 40.741 0.00 0.00 0.00 3.69
479 707 9.156940 GAAATCCTAGTTAAAGTATCTACCCCT 57.843 37.037 0.00 0.00 0.00 4.79
481 709 7.477345 TCCTAGTTAAAGTATCTACCCCTCT 57.523 40.000 0.00 0.00 0.00 3.69
482 710 8.587202 TCCTAGTTAAAGTATCTACCCCTCTA 57.413 38.462 0.00 0.00 0.00 2.43
483 711 9.192129 TCCTAGTTAAAGTATCTACCCCTCTAT 57.808 37.037 0.00 0.00 0.00 1.98
484 712 9.465199 CCTAGTTAAAGTATCTACCCCTCTATC 57.535 40.741 0.00 0.00 0.00 2.08
485 713 9.465199 CTAGTTAAAGTATCTACCCCTCTATCC 57.535 40.741 0.00 0.00 0.00 2.59
486 714 7.247500 AGTTAAAGTATCTACCCCTCTATCCC 58.753 42.308 0.00 0.00 0.00 3.85
487 715 4.696040 AAGTATCTACCCCTCTATCCCC 57.304 50.000 0.00 0.00 0.00 4.81
489 717 5.065516 AGTATCTACCCCTCTATCCCCTA 57.934 47.826 0.00 0.00 0.00 3.53
491 719 6.053317 AGTATCTACCCCTCTATCCCCTATT 58.947 44.000 0.00 0.00 0.00 1.73
492 720 5.924001 ATCTACCCCTCTATCCCCTATTT 57.076 43.478 0.00 0.00 0.00 1.40
494 722 6.064618 TCTACCCCTCTATCCCCTATTTTT 57.935 41.667 0.00 0.00 0.00 1.94
524 752 9.739276 AGAAGAGTTTTGTACATATTCATTGGA 57.261 29.630 0.00 0.00 0.00 3.53
535 1567 5.245301 ACATATTCATTGGATTGGATGCCTG 59.755 40.000 0.00 0.00 0.00 4.85
536 1568 2.832643 TCATTGGATTGGATGCCTGT 57.167 45.000 0.00 0.00 0.00 4.00
701 1741 9.689976 TGTGTAATTTCAAGACACATATTTTGG 57.310 29.630 6.97 0.00 46.36 3.28
702 1742 8.647226 GTGTAATTTCAAGACACATATTTTGGC 58.353 33.333 4.00 0.00 42.45 4.52
704 1744 9.202273 GTAATTTCAAGACACATATTTTGGCAA 57.798 29.630 0.00 0.00 0.00 4.52
708 1748 5.538053 TCAAGACACATATTTTGGCAAGGAA 59.462 36.000 0.00 0.00 0.00 3.36
709 1749 6.211184 TCAAGACACATATTTTGGCAAGGAAT 59.789 34.615 0.00 0.98 0.00 3.01
711 1751 5.088680 ACACATATTTTGGCAAGGAATGG 57.911 39.130 16.83 8.61 0.00 3.16
712 1752 4.776837 ACACATATTTTGGCAAGGAATGGA 59.223 37.500 16.83 0.00 0.00 3.41
713 1753 5.426185 ACACATATTTTGGCAAGGAATGGAT 59.574 36.000 16.83 6.51 0.00 3.41
715 1755 3.918294 ATTTTGGCAAGGAATGGATGG 57.082 42.857 0.00 0.00 0.00 3.51
716 1756 2.619697 TTTGGCAAGGAATGGATGGA 57.380 45.000 0.00 0.00 0.00 3.41
718 1758 0.396139 TGGCAAGGAATGGATGGAGC 60.396 55.000 0.00 0.00 0.00 4.70
764 1804 5.106555 GCAGAGCAGAGCAAAAACAATACTA 60.107 40.000 0.00 0.00 0.00 1.82
786 1826 1.752683 ACTACTCTGCTACTCCACCG 58.247 55.000 0.00 0.00 0.00 4.94
796 1836 0.178926 TACTCCACCGAACCCCTTGA 60.179 55.000 0.00 0.00 0.00 3.02
1151 2214 1.466025 AACTCCGTGGTAACCTCGCA 61.466 55.000 0.00 0.00 38.90 5.10
1211 2280 0.478072 TCACACTGAACCCATGGCTT 59.522 50.000 6.09 0.00 0.00 4.35
1369 2444 0.727793 CTTTTGCGCCGCGTTAATGT 60.728 50.000 15.34 0.00 0.00 2.71
1380 2455 2.591133 GCGTTAATGTTCACCGCATTT 58.409 42.857 0.00 0.00 43.53 2.32
1381 2456 2.592459 GCGTTAATGTTCACCGCATTTC 59.408 45.455 0.00 0.00 43.53 2.17
1385 2460 0.442310 ATGTTCACCGCATTTCGTCG 59.558 50.000 0.00 0.00 36.19 5.12
1469 2545 5.733676 AGGATTTGCCATTTTTACCATGTC 58.266 37.500 0.00 0.00 40.02 3.06
1479 2555 6.143758 CCATTTTTACCATGTCTTTCGTTGTG 59.856 38.462 0.00 0.00 0.00 3.33
1500 2576 2.744202 GACCAGCATTGTGTGAACCTAG 59.256 50.000 0.00 0.00 0.00 3.02
1515 2592 6.883756 TGTGAACCTAGATGCATAATGACAAA 59.116 34.615 0.00 0.00 0.00 2.83
1551 2628 4.040217 TGTTCATTGCTGGGCATTTACTTT 59.960 37.500 0.00 0.00 38.76 2.66
1602 2686 0.593128 CAAGGTTTCCGTGCCAGAAG 59.407 55.000 0.00 0.00 0.00 2.85
1629 2714 0.105246 TTGGCTTTGTGGAATGGGGT 60.105 50.000 0.00 0.00 0.00 4.95
1642 2727 1.571773 ATGGGGTGGTAGGGAAGTGC 61.572 60.000 0.00 0.00 0.00 4.40
1723 2813 1.135402 GCATTTACTTTGACCGGCCAG 60.135 52.381 0.00 0.00 0.00 4.85
1827 2920 4.534794 TTTACTTCGACCGACCAAAAAC 57.465 40.909 0.00 0.00 0.00 2.43
1851 2944 2.603021 TGCATTTCCTTTTAGTGCCCA 58.397 42.857 0.00 0.00 35.03 5.36
1853 2946 2.353704 GCATTTCCTTTTAGTGCCCACC 60.354 50.000 0.00 0.00 0.00 4.61
1856 2949 2.757894 TCCTTTTAGTGCCCACCAAA 57.242 45.000 0.00 0.00 0.00 3.28
1857 2950 2.312390 TCCTTTTAGTGCCCACCAAAC 58.688 47.619 0.00 0.00 0.00 2.93
1858 2951 1.343142 CCTTTTAGTGCCCACCAAACC 59.657 52.381 0.00 0.00 0.00 3.27
2039 3180 6.238648 CCACAAGGTACAACTCTTCGAAATTT 60.239 38.462 0.00 0.00 0.00 1.82
2417 3558 1.002544 GGCTTGTACAGGAAGCTGACT 59.997 52.381 15.69 0.00 44.44 3.41
2439 3580 6.192044 ACTCAAAAGTTTCCCAAGAAAGGTA 58.808 36.000 0.00 0.00 42.60 3.08
2440 3581 6.839134 ACTCAAAAGTTTCCCAAGAAAGGTAT 59.161 34.615 0.00 0.00 42.60 2.73
2441 3582 7.049799 TCAAAAGTTTCCCAAGAAAGGTATG 57.950 36.000 0.00 0.00 42.60 2.39
2482 3626 1.913451 TTTGTATTTGGTCGCGCCCG 61.913 55.000 15.40 0.00 36.04 6.13
2483 3627 4.232248 GTATTTGGTCGCGCCCGC 62.232 66.667 15.40 1.98 36.04 6.13
2484 3628 4.460683 TATTTGGTCGCGCCCGCT 62.461 61.111 15.40 0.00 39.32 5.52
2498 3647 1.000052 GCCCGCTCTACTCTGGTTATC 60.000 57.143 0.00 0.00 0.00 1.75
2789 3938 7.738437 ATATTGGGGGCATTATAGGAAATTG 57.262 36.000 0.00 0.00 0.00 2.32
2790 3939 4.551215 TGGGGGCATTATAGGAAATTGT 57.449 40.909 0.00 0.00 0.00 2.71
2792 3941 4.653341 TGGGGGCATTATAGGAAATTGTTG 59.347 41.667 0.00 0.00 0.00 3.33
2793 3942 4.653801 GGGGGCATTATAGGAAATTGTTGT 59.346 41.667 0.00 0.00 0.00 3.32
2795 3944 6.280643 GGGGCATTATAGGAAATTGTTGTTC 58.719 40.000 0.00 0.00 0.00 3.18
2796 3945 6.127196 GGGGCATTATAGGAAATTGTTGTTCA 60.127 38.462 0.00 0.00 0.00 3.18
2797 3946 6.756542 GGGCATTATAGGAAATTGTTGTTCAC 59.243 38.462 0.00 0.00 0.00 3.18
2799 3948 8.682710 GGCATTATAGGAAATTGTTGTTCACTA 58.317 33.333 0.00 0.00 0.00 2.74
2815 3964 9.330063 GTTGTTCACTAATCATCATATCTTGGA 57.670 33.333 0.00 0.00 0.00 3.53
2876 4053 5.473504 TCAAGCCATTTCTGAGTAACCTTTC 59.526 40.000 0.00 0.00 0.00 2.62
2877 4054 5.248380 AGCCATTTCTGAGTAACCTTTCT 57.752 39.130 0.00 0.00 0.00 2.52
2879 4056 6.779860 AGCCATTTCTGAGTAACCTTTCTTA 58.220 36.000 0.00 0.00 0.00 2.10
2880 4057 7.406104 AGCCATTTCTGAGTAACCTTTCTTAT 58.594 34.615 0.00 0.00 0.00 1.73
2881 4058 8.548877 AGCCATTTCTGAGTAACCTTTCTTATA 58.451 33.333 0.00 0.00 0.00 0.98
2882 4059 8.613482 GCCATTTCTGAGTAACCTTTCTTATAC 58.387 37.037 0.00 0.00 0.00 1.47
2883 4060 9.892130 CCATTTCTGAGTAACCTTTCTTATACT 57.108 33.333 0.00 0.00 0.00 2.12
2974 4154 5.276395 CCGTTTGAGCGACAACTAATATGAG 60.276 44.000 0.00 0.00 38.29 2.90
2977 4157 5.576447 TGAGCGACAACTAATATGAGACA 57.424 39.130 0.00 0.00 0.00 3.41
2984 4164 6.620877 ACAACTAATATGAGACAGTGGGAA 57.379 37.500 0.00 0.00 0.00 3.97
3227 4412 5.725110 ATGCACTCGAAACAGATACATTC 57.275 39.130 0.00 0.00 0.00 2.67
3520 4753 9.884636 TCAATATAGGGTGAATTATGAATACGG 57.115 33.333 0.00 0.00 0.00 4.02
3773 5008 0.240145 CTCGACACAAGTACAGGCGA 59.760 55.000 0.00 0.35 0.00 5.54
3977 5212 8.664211 GGTAACTCTTATCTTTTGATACCTGG 57.336 38.462 0.00 0.00 40.77 4.45
4001 5236 4.875536 TCATGACTAAATGACAACATCCCG 59.124 41.667 0.00 0.00 35.50 5.14
4006 5241 6.432783 TGACTAAATGACAACATCCCGAATTT 59.567 34.615 0.00 0.00 35.50 1.82
4047 5282 9.436957 TGTCCTTCTACTTTGTTAAATGAGATC 57.563 33.333 0.00 0.00 0.00 2.75
4144 5381 2.099756 TGAGTCATCATCGAAGCGACAT 59.900 45.455 11.06 0.00 39.18 3.06
4172 5409 7.159372 TGAACAGATAGAAAGTCAACCTTACC 58.841 38.462 0.00 0.00 31.48 2.85
4270 5507 1.071605 GTGCATCGTCCTCACAACTC 58.928 55.000 0.00 0.00 0.00 3.01
4424 5663 5.013183 ACATGCCAAATATAGTACTCCCTCC 59.987 44.000 0.00 0.00 0.00 4.30
4455 5697 3.308438 ACTTGTTGCTCAAATGGATGC 57.692 42.857 0.00 0.00 35.48 3.91
4458 5700 4.463539 ACTTGTTGCTCAAATGGATGCATA 59.536 37.500 0.00 0.00 35.48 3.14
4463 5705 6.016860 TGTTGCTCAAATGGATGCATATAGAC 60.017 38.462 0.00 0.00 35.27 2.59
4467 5709 6.536582 GCTCAAATGGATGCATATAGACGTAT 59.463 38.462 0.00 0.00 0.00 3.06
4470 5712 9.283768 TCAAATGGATGCATATAGACGTATTTT 57.716 29.630 0.00 0.00 0.00 1.82
4486 5728 9.069082 AGACGTATTTTAGTGCTAGATACATCT 57.931 33.333 0.00 0.00 40.86 2.90
4492 5734 7.539712 TTTAGTGCTAGATACATCTGTTTGC 57.460 36.000 1.88 2.69 37.76 3.68
4523 5765 4.676799 AATATGGATCGGAGGGAGTAGA 57.323 45.455 0.00 0.00 0.00 2.59
4540 5782 6.402226 GGGAGTAGAATCAAAACGTTCATCAC 60.402 42.308 0.00 0.00 0.00 3.06
4553 5795 2.363788 TCATCACGTTCCGGAAAGAG 57.636 50.000 32.65 25.55 0.00 2.85
4558 5800 0.320508 ACGTTCCGGAAAGAGAAGGC 60.321 55.000 32.65 11.65 32.48 4.35
4560 5802 1.876416 CGTTCCGGAAAGAGAAGGCAA 60.876 52.381 23.81 0.00 0.00 4.52
4608 5850 0.610174 TCATCCTGTCTGTCTGCACC 59.390 55.000 0.00 0.00 0.00 5.01
4617 5875 2.030946 GTCTGTCTGCACCGCATTATTC 59.969 50.000 0.00 0.00 38.13 1.75
4623 5881 0.730265 GCACCGCATTATTCCGACAA 59.270 50.000 0.00 0.00 0.00 3.18
4669 5927 7.444299 ACTTTTAATGTTCAAATGAGGTGCAT 58.556 30.769 0.00 0.00 39.43 3.96
4713 5971 5.303747 TGGTATGTTTTGTATTTCAGCCG 57.696 39.130 0.00 0.00 0.00 5.52
4833 6115 6.542005 TCTGACTGAGTTAAGCAATTTTGTCA 59.458 34.615 0.00 0.00 0.00 3.58
4837 6119 6.318648 ACTGAGTTAAGCAATTTTGTCACAGA 59.681 34.615 0.00 0.00 0.00 3.41
4888 6170 1.959985 TCAATGTTGTTTCGGCCATGT 59.040 42.857 2.24 0.00 0.00 3.21
4889 6171 2.030363 TCAATGTTGTTTCGGCCATGTC 60.030 45.455 2.24 0.00 0.00 3.06
4906 6188 1.000506 TGTCGCAGAACCCTGTAGAAC 59.999 52.381 0.00 0.00 42.35 3.01
4919 6201 1.677052 TGTAGAACGGGTTTTGGTTGC 59.323 47.619 0.00 0.00 0.00 4.17
4956 6241 2.887152 GTTCACTCTTGCCTTCAATGGT 59.113 45.455 0.00 0.00 0.00 3.55
5015 6310 8.726870 TTAACTGTTGTGCCTTACTATAATCC 57.273 34.615 2.69 0.00 0.00 3.01
5070 6377 9.681062 TTATGGAATATATTTAGCCCTTGTAGC 57.319 33.333 0.00 0.00 0.00 3.58
5088 6430 5.496556 TGTAGCCAGCATACAGTGTAAATT 58.503 37.500 7.16 0.00 0.00 1.82
5095 6437 5.877012 CAGCATACAGTGTAAATTGAGAGGT 59.123 40.000 7.16 0.00 0.00 3.85
5226 6570 2.640184 GAGACCAATTTAAGACCCCCG 58.360 52.381 0.00 0.00 0.00 5.73
5251 6595 6.640907 GCAAATTGGTCGTCACTTATTTCTTT 59.359 34.615 0.00 0.00 0.00 2.52
5253 6597 9.840427 CAAATTGGTCGTCACTTATTTCTTTAT 57.160 29.630 0.00 0.00 0.00 1.40
5288 6632 6.674066 TCTTTACCAAATTAACTTGAAGCCG 58.326 36.000 0.00 0.00 0.00 5.52
5291 6635 4.616953 ACCAAATTAACTTGAAGCCGTTG 58.383 39.130 0.00 0.00 0.00 4.10
5292 6636 4.098807 ACCAAATTAACTTGAAGCCGTTGT 59.901 37.500 0.00 0.00 0.00 3.32
5294 6638 5.051106 CCAAATTAACTTGAAGCCGTTGTTG 60.051 40.000 0.00 0.00 0.00 3.33
5296 6640 6.380095 AATTAACTTGAAGCCGTTGTTGTA 57.620 33.333 0.00 0.00 0.00 2.41
5297 6641 6.569179 ATTAACTTGAAGCCGTTGTTGTAT 57.431 33.333 0.00 0.00 0.00 2.29
5298 6642 4.483476 AACTTGAAGCCGTTGTTGTATC 57.517 40.909 0.00 0.00 0.00 2.24
5299 6643 3.472652 ACTTGAAGCCGTTGTTGTATCA 58.527 40.909 0.00 0.00 0.00 2.15
5300 6644 3.250040 ACTTGAAGCCGTTGTTGTATCAC 59.750 43.478 0.00 0.00 0.00 3.06
5303 6649 2.831685 AGCCGTTGTTGTATCACTGA 57.168 45.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.436998 GGGAGCCGTCACCGTCTG 62.437 72.222 0.00 0.00 0.00 3.51
14 242 0.460987 CATCTTCAGGGAGCCGTCAC 60.461 60.000 0.00 0.00 0.00 3.67
24 252 5.772169 GGGAGGATTTTATTCCATCTTCAGG 59.228 44.000 0.00 0.00 38.32 3.86
25 253 5.772169 GGGGAGGATTTTATTCCATCTTCAG 59.228 44.000 0.00 0.00 38.32 3.02
31 259 3.402708 GGGAGGGGAGGATTTTATTCCAT 59.597 47.826 0.00 0.00 38.32 3.41
43 271 1.153132 AGAATAGGATGGGAGGGGAGG 59.847 57.143 0.00 0.00 0.00 4.30
48 276 2.694397 TCACCAGAATAGGATGGGAGG 58.306 52.381 0.00 0.00 41.13 4.30
50 278 2.373169 GCATCACCAGAATAGGATGGGA 59.627 50.000 0.00 0.00 41.13 4.37
80 308 2.758979 ACCTATACACACCCTTCGACAG 59.241 50.000 0.00 0.00 0.00 3.51
81 309 2.494471 CACCTATACACACCCTTCGACA 59.506 50.000 0.00 0.00 0.00 4.35
91 319 3.076079 TCGGAGACACACCTATACACA 57.924 47.619 0.00 0.00 0.00 3.72
115 343 0.250038 CCGTCGGAATGCCATGAGAT 60.250 55.000 4.91 0.00 0.00 2.75
121 349 2.572095 CTAGCACCGTCGGAATGCCA 62.572 60.000 20.51 6.55 40.33 4.92
139 367 4.087182 TCTAAACAGATCCACCGAAGACT 58.913 43.478 0.00 0.00 0.00 3.24
156 384 5.175859 ACGAAAGCGAAGATTGGATCTAAA 58.824 37.500 0.00 0.00 34.86 1.85
159 387 3.252974 ACGAAAGCGAAGATTGGATCT 57.747 42.857 0.00 0.00 34.86 2.75
172 400 2.121786 TGTAGACACACGAACGAAAGC 58.878 47.619 0.14 0.00 0.00 3.51
174 402 2.099592 ACCTGTAGACACACGAACGAAA 59.900 45.455 0.14 0.00 0.00 3.46
180 408 4.521639 AGTATTCAACCTGTAGACACACGA 59.478 41.667 0.00 0.00 0.00 4.35
192 420 9.968870 GAAGTATAGATCGAAAGTATTCAACCT 57.031 33.333 0.00 0.00 35.15 3.50
227 455 2.185867 GGAATAGCCGCCGTCACA 59.814 61.111 0.00 0.00 0.00 3.58
238 466 1.611673 GGCCCCACATCATCGGAATAG 60.612 57.143 0.00 0.00 0.00 1.73
240 468 1.151450 GGCCCCACATCATCGGAAT 59.849 57.895 0.00 0.00 0.00 3.01
245 473 0.183492 TGCTAAGGCCCCACATCATC 59.817 55.000 0.00 0.00 37.74 2.92
279 507 1.205893 GGCCAAACTTGTTGTGGACAA 59.794 47.619 0.00 0.00 45.70 3.18
287 515 1.455383 CGAGCCAGGCCAAACTTGTT 61.455 55.000 8.22 0.00 0.00 2.83
300 528 2.363018 CCTCCCTCACTCGAGCCA 60.363 66.667 13.61 0.00 38.00 4.75
325 553 1.741770 CGACTACAAGCACTGGGGC 60.742 63.158 0.00 0.00 0.00 5.80
337 565 6.094048 TGTCCATAACACCTAGTAACGACTAC 59.906 42.308 0.00 0.00 32.97 2.73
347 575 5.610398 TGCATACATGTCCATAACACCTAG 58.390 41.667 0.00 0.00 41.75 3.02
354 582 7.665690 ACAAAAGTTTGCATACATGTCCATAA 58.334 30.769 0.00 0.00 41.79 1.90
356 584 6.100404 ACAAAAGTTTGCATACATGTCCAT 57.900 33.333 0.00 0.00 41.79 3.41
358 586 8.028938 AGATAACAAAAGTTTGCATACATGTCC 58.971 33.333 0.00 0.00 41.79 4.02
359 587 8.970691 AGATAACAAAAGTTTGCATACATGTC 57.029 30.769 0.00 0.00 41.79 3.06
360 588 9.762933 AAAGATAACAAAAGTTTGCATACATGT 57.237 25.926 10.02 2.69 41.79 3.21
363 591 9.593134 ACAAAAGATAACAAAAGTTTGCATACA 57.407 25.926 10.02 0.00 41.79 2.29
364 592 9.848172 CACAAAAGATAACAAAAGTTTGCATAC 57.152 29.630 3.68 0.00 41.79 2.39
366 594 8.491331 ACACAAAAGATAACAAAAGTTTGCAT 57.509 26.923 3.68 0.00 41.79 3.96
367 595 7.897575 ACACAAAAGATAACAAAAGTTTGCA 57.102 28.000 3.68 0.00 41.79 4.08
368 596 8.655970 AGAACACAAAAGATAACAAAAGTTTGC 58.344 29.630 3.68 0.00 41.79 3.68
383 611 7.538678 GCCATGACAGTATAAAGAACACAAAAG 59.461 37.037 0.00 0.00 0.00 2.27
385 613 6.488344 TGCCATGACAGTATAAAGAACACAAA 59.512 34.615 0.00 0.00 0.00 2.83
388 616 5.411361 TGTGCCATGACAGTATAAAGAACAC 59.589 40.000 0.00 0.00 0.00 3.32
390 618 6.494893 TTGTGCCATGACAGTATAAAGAAC 57.505 37.500 0.00 0.00 0.00 3.01
391 619 8.800370 TTATTGTGCCATGACAGTATAAAGAA 57.200 30.769 0.00 0.00 0.00 2.52
396 624 8.436778 ACCTATTTATTGTGCCATGACAGTATA 58.563 33.333 0.00 0.00 0.00 1.47
397 625 7.290061 ACCTATTTATTGTGCCATGACAGTAT 58.710 34.615 0.00 0.00 0.00 2.12
399 627 5.509498 ACCTATTTATTGTGCCATGACAGT 58.491 37.500 0.00 0.00 0.00 3.55
400 628 6.992123 TCTACCTATTTATTGTGCCATGACAG 59.008 38.462 0.00 0.00 0.00 3.51
402 630 7.041098 CCTTCTACCTATTTATTGTGCCATGAC 60.041 40.741 0.00 0.00 0.00 3.06
403 631 6.998074 CCTTCTACCTATTTATTGTGCCATGA 59.002 38.462 0.00 0.00 0.00 3.07
404 632 6.772716 ACCTTCTACCTATTTATTGTGCCATG 59.227 38.462 0.00 0.00 0.00 3.66
405 633 6.911308 ACCTTCTACCTATTTATTGTGCCAT 58.089 36.000 0.00 0.00 0.00 4.40
407 635 6.262496 GGAACCTTCTACCTATTTATTGTGCC 59.738 42.308 0.00 0.00 0.00 5.01
408 636 7.260558 GGAACCTTCTACCTATTTATTGTGC 57.739 40.000 0.00 0.00 0.00 4.57
450 678 8.637099 GGTAGATACTTTAACTAGGATTTCCGT 58.363 37.037 0.00 0.00 42.08 4.69
451 679 8.087136 GGGTAGATACTTTAACTAGGATTTCCG 58.913 40.741 0.00 0.00 42.08 4.30
452 680 8.373981 GGGGTAGATACTTTAACTAGGATTTCC 58.626 40.741 0.00 0.00 0.00 3.13
454 682 9.156940 GAGGGGTAGATACTTTAACTAGGATTT 57.843 37.037 0.00 0.00 0.00 2.17
457 685 7.477345 AGAGGGGTAGATACTTTAACTAGGA 57.523 40.000 0.00 0.00 0.00 2.94
458 686 9.465199 GATAGAGGGGTAGATACTTTAACTAGG 57.535 40.741 0.00 0.00 0.00 3.02
460 688 8.397172 GGGATAGAGGGGTAGATACTTTAACTA 58.603 40.741 0.00 0.00 0.00 2.24
461 689 7.247500 GGGATAGAGGGGTAGATACTTTAACT 58.753 42.308 0.00 0.00 0.00 2.24
462 690 6.440010 GGGGATAGAGGGGTAGATACTTTAAC 59.560 46.154 0.00 0.00 0.00 2.01
463 691 6.340199 AGGGGATAGAGGGGTAGATACTTTAA 59.660 42.308 0.00 0.00 0.00 1.52
464 692 5.867497 AGGGGATAGAGGGGTAGATACTTTA 59.133 44.000 0.00 0.00 0.00 1.85
465 693 4.680429 AGGGGATAGAGGGGTAGATACTTT 59.320 45.833 0.00 0.00 0.00 2.66
468 696 6.358443 AATAGGGGATAGAGGGGTAGATAC 57.642 45.833 0.00 0.00 0.00 2.24
469 697 7.386015 AAAATAGGGGATAGAGGGGTAGATA 57.614 40.000 0.00 0.00 0.00 1.98
470 698 5.924001 AAATAGGGGATAGAGGGGTAGAT 57.076 43.478 0.00 0.00 0.00 1.98
471 699 5.715444 AAAATAGGGGATAGAGGGGTAGA 57.285 43.478 0.00 0.00 0.00 2.59
498 726 9.739276 TCCAATGAATATGTACAAAACTCTTCT 57.261 29.630 0.00 0.00 0.00 2.85
502 730 9.520204 CCAATCCAATGAATATGTACAAAACTC 57.480 33.333 0.00 0.00 0.00 3.01
503 731 9.253832 TCCAATCCAATGAATATGTACAAAACT 57.746 29.630 0.00 0.00 0.00 2.66
507 735 7.255906 GGCATCCAATCCAATGAATATGTACAA 60.256 37.037 0.00 0.00 0.00 2.41
508 736 6.209192 GGCATCCAATCCAATGAATATGTACA 59.791 38.462 0.00 0.00 0.00 2.90
509 737 6.435277 AGGCATCCAATCCAATGAATATGTAC 59.565 38.462 0.00 0.00 0.00 2.90
511 739 5.245301 CAGGCATCCAATCCAATGAATATGT 59.755 40.000 0.00 0.00 0.00 2.29
514 742 4.806892 ACAGGCATCCAATCCAATGAATA 58.193 39.130 0.00 0.00 0.00 1.75
515 743 3.649843 ACAGGCATCCAATCCAATGAAT 58.350 40.909 0.00 0.00 0.00 2.57
516 744 3.104519 ACAGGCATCCAATCCAATGAA 57.895 42.857 0.00 0.00 0.00 2.57
517 745 2.832643 ACAGGCATCCAATCCAATGA 57.167 45.000 0.00 0.00 0.00 2.57
518 746 3.189910 CGATACAGGCATCCAATCCAATG 59.810 47.826 0.00 0.00 0.00 2.82
519 747 3.415212 CGATACAGGCATCCAATCCAAT 58.585 45.455 0.00 0.00 0.00 3.16
520 748 2.849942 CGATACAGGCATCCAATCCAA 58.150 47.619 0.00 0.00 0.00 3.53
521 749 1.543208 GCGATACAGGCATCCAATCCA 60.543 52.381 0.00 0.00 0.00 3.41
522 750 1.160137 GCGATACAGGCATCCAATCC 58.840 55.000 0.00 0.00 0.00 3.01
523 751 0.792640 CGCGATACAGGCATCCAATC 59.207 55.000 0.00 0.00 0.00 2.67
524 752 1.230635 GCGCGATACAGGCATCCAAT 61.231 55.000 12.10 0.00 0.00 3.16
525 753 1.887242 GCGCGATACAGGCATCCAA 60.887 57.895 12.10 0.00 0.00 3.53
526 754 2.280119 GCGCGATACAGGCATCCA 60.280 61.111 12.10 0.00 0.00 3.41
535 1567 5.385396 ACACTATTTTTACAGCGCGATAC 57.615 39.130 12.10 0.00 0.00 2.24
536 1568 7.703298 AATACACTATTTTTACAGCGCGATA 57.297 32.000 12.10 0.00 0.00 2.92
685 1725 5.389859 TCCTTGCCAAAATATGTGTCTTG 57.610 39.130 0.00 0.00 0.00 3.02
701 1741 1.030457 CTGCTCCATCCATTCCTTGC 58.970 55.000 0.00 0.00 0.00 4.01
702 1742 1.213678 TCCTGCTCCATCCATTCCTTG 59.786 52.381 0.00 0.00 0.00 3.61
704 1744 1.138568 CTCCTGCTCCATCCATTCCT 58.861 55.000 0.00 0.00 0.00 3.36
708 1748 1.350351 GCATACTCCTGCTCCATCCAT 59.650 52.381 0.00 0.00 39.12 3.41
709 1749 0.761187 GCATACTCCTGCTCCATCCA 59.239 55.000 0.00 0.00 39.12 3.41
711 1751 1.055040 AGGCATACTCCTGCTCCATC 58.945 55.000 0.00 0.00 41.95 3.51
712 1752 1.516110 AAGGCATACTCCTGCTCCAT 58.484 50.000 0.00 0.00 41.95 3.41
713 1753 1.289160 AAAGGCATACTCCTGCTCCA 58.711 50.000 0.00 0.00 41.95 3.86
715 1755 2.019984 CCAAAAGGCATACTCCTGCTC 58.980 52.381 0.00 0.00 41.95 4.26
716 1756 1.355720 ACCAAAAGGCATACTCCTGCT 59.644 47.619 0.00 0.00 41.95 4.24
718 1758 3.071874 TCACCAAAAGGCATACTCCTG 57.928 47.619 0.00 0.00 36.38 3.86
764 1804 3.682155 CGGTGGAGTAGCAGAGTAGTAGT 60.682 52.174 0.00 0.00 0.00 2.73
786 1826 0.609406 GGGAGCAAGTCAAGGGGTTC 60.609 60.000 0.00 0.00 0.00 3.62
796 1836 1.119684 GTTTGGGTTTGGGAGCAAGT 58.880 50.000 0.00 0.00 0.00 3.16
1092 2155 2.888863 CTGTCCTCCTCGGTGAGC 59.111 66.667 0.00 0.00 0.00 4.26
1161 2224 1.304617 GGCTTGGGAAAGAGAGGGG 59.695 63.158 0.00 0.00 0.00 4.79
1186 2249 1.053835 TGGGTTCAGTGTGAGCAGGA 61.054 55.000 0.00 0.00 28.47 3.86
1211 2280 3.325870 CACAGATTGGAACGAGCTAACA 58.674 45.455 0.00 0.00 0.00 2.41
1359 2434 4.336174 GCGGTGAACATTAACGCG 57.664 55.556 3.53 3.53 40.84 6.01
1369 2444 3.556625 CCGACGAAATGCGGTGAA 58.443 55.556 0.00 0.00 46.49 3.18
1385 2460 0.107654 AGCTGCTCGGACCAAATACC 60.108 55.000 0.00 0.00 0.00 2.73
1386 2461 1.009829 CAGCTGCTCGGACCAAATAC 58.990 55.000 0.00 0.00 0.00 1.89
1469 2545 2.033299 ACAATGCTGGTCACAACGAAAG 59.967 45.455 0.00 0.00 0.00 2.62
1479 2555 1.609208 AGGTTCACACAATGCTGGTC 58.391 50.000 0.00 0.00 0.00 4.02
1551 2628 6.646653 TGCATTTAAATACACGGCATTTTTCA 59.353 30.769 0.00 0.00 0.00 2.69
1602 2686 2.626840 TCCACAAAGCCAAAGCAAAAC 58.373 42.857 0.00 0.00 43.56 2.43
1629 2714 2.158385 ACAAAATGGCACTTCCCTACCA 60.158 45.455 0.00 0.00 36.43 3.25
1723 2813 2.614057 CACATTCCTACCTCCGCATTTC 59.386 50.000 0.00 0.00 0.00 2.17
1827 2920 3.438360 GCACTAAAAGGAAATGCATCCG 58.562 45.455 0.00 0.00 44.60 4.18
1857 2950 3.006430 GGTTAACACTCAAAACCATGGGG 59.994 47.826 18.09 2.52 41.89 4.96
1858 2951 3.305064 CGGTTAACACTCAAAACCATGGG 60.305 47.826 18.09 0.00 42.31 4.00
1956 3092 1.107114 TCTCAAGAGCCGAGTGATCC 58.893 55.000 0.00 0.00 0.00 3.36
1959 3095 1.270826 CTGTTCTCAAGAGCCGAGTGA 59.729 52.381 0.00 0.00 0.00 3.41
2013 3149 1.798813 CGAAGAGTTGTACCTTGTGGC 59.201 52.381 0.00 0.00 36.63 5.01
2039 3180 0.684479 ACAGCAGACAGAGCCGGATA 60.684 55.000 5.05 0.00 0.00 2.59
2417 3558 6.836527 TCATACCTTTCTTGGGAAACTTTTGA 59.163 34.615 0.00 0.00 36.63 2.69
2439 3580 7.818997 ATTGCTGTTCACTAATCATCATCAT 57.181 32.000 0.00 0.00 0.00 2.45
2440 3581 7.634671 AATTGCTGTTCACTAATCATCATCA 57.365 32.000 0.00 0.00 0.00 3.07
2441 3582 7.972277 ACAAATTGCTGTTCACTAATCATCATC 59.028 33.333 0.00 0.00 0.00 2.92
2482 3626 5.845391 AGAACAGATAACCAGAGTAGAGC 57.155 43.478 0.00 0.00 0.00 4.09
2483 3627 7.338196 TGAGAAGAACAGATAACCAGAGTAGAG 59.662 40.741 0.00 0.00 0.00 2.43
2484 3628 7.175797 TGAGAAGAACAGATAACCAGAGTAGA 58.824 38.462 0.00 0.00 0.00 2.59
2485 3629 7.397892 TGAGAAGAACAGATAACCAGAGTAG 57.602 40.000 0.00 0.00 0.00 2.57
2486 3630 7.068839 GGATGAGAAGAACAGATAACCAGAGTA 59.931 40.741 0.00 0.00 0.00 2.59
2498 3647 3.181491 GGAGACTCGGATGAGAAGAACAG 60.181 52.174 0.00 0.00 45.57 3.16
2696 3845 6.603201 GGGTGAATCAGAGAAAATACCATTCA 59.397 38.462 0.00 0.00 0.00 2.57
2789 3938 9.330063 TCCAAGATATGATGATTAGTGAACAAC 57.670 33.333 0.00 0.00 0.00 3.32
2790 3939 9.904198 TTCCAAGATATGATGATTAGTGAACAA 57.096 29.630 0.00 0.00 0.00 2.83
2815 3964 8.630037 CACTGAAGGGAGTATAACAAAAGTTTT 58.370 33.333 0.00 0.00 0.00 2.43
2881 4058 9.853177 CAAAAACTAATATGGAATAGAGGGAGT 57.147 33.333 0.00 0.00 28.50 3.85
2882 4059 8.787852 GCAAAAACTAATATGGAATAGAGGGAG 58.212 37.037 0.00 0.00 28.50 4.30
2883 4060 8.502738 AGCAAAAACTAATATGGAATAGAGGGA 58.497 33.333 0.00 0.00 28.50 4.20
2884 4061 8.571336 CAGCAAAAACTAATATGGAATAGAGGG 58.429 37.037 0.00 0.00 28.50 4.30
2885 4062 9.342308 TCAGCAAAAACTAATATGGAATAGAGG 57.658 33.333 0.00 0.00 28.50 3.69
2906 4086 5.125578 ACGTCTAGATACATCTGTTTCAGCA 59.874 40.000 0.00 0.00 37.76 4.41
2915 4095 6.459024 GCACTGAAAGACGTCTAGATACATCT 60.459 42.308 20.39 0.00 38.01 2.90
2974 4154 7.736893 AGTCCATATTTACTATTCCCACTGTC 58.263 38.462 0.00 0.00 0.00 3.51
2977 4157 8.331931 TCAAGTCCATATTTACTATTCCCACT 57.668 34.615 0.00 0.00 0.00 4.00
3094 4274 4.202284 GGCCACCAATTCAAGAATATGCAT 60.202 41.667 3.79 3.79 0.00 3.96
3134 4318 4.681483 GCAGAATTCGGTCAAAAGGAAAAG 59.319 41.667 7.44 0.00 0.00 2.27
3144 4329 4.801330 TTCTAGAAGCAGAATTCGGTCA 57.199 40.909 0.00 0.00 34.27 4.02
3145 4330 4.330347 GGTTTCTAGAAGCAGAATTCGGTC 59.670 45.833 19.41 0.00 34.59 4.79
3146 4331 4.254492 GGTTTCTAGAAGCAGAATTCGGT 58.746 43.478 19.41 2.21 34.59 4.69
3148 4333 4.508662 AGGGTTTCTAGAAGCAGAATTCG 58.491 43.478 19.41 0.00 34.59 3.34
3149 4334 5.355630 GGAAGGGTTTCTAGAAGCAGAATTC 59.644 44.000 19.41 15.29 34.59 2.17
3227 4412 3.880047 TTATCCACACCACTTACGAGG 57.120 47.619 0.00 0.00 0.00 4.63
3404 4637 4.730966 TGGTACAATTAAGCCCTGTTGAA 58.269 39.130 0.00 0.00 31.92 2.69
3463 4696 4.935205 CGGACAGGAATACAGTCAATTTCA 59.065 41.667 0.00 0.00 34.04 2.69
3664 4898 8.397148 ACCTGCACATTTAGAAAACAAAAATTG 58.603 29.630 0.00 0.00 0.00 2.32
3666 4900 8.504812 AACCTGCACATTTAGAAAACAAAAAT 57.495 26.923 0.00 0.00 0.00 1.82
3672 4906 7.491048 TCTTTTGAACCTGCACATTTAGAAAAC 59.509 33.333 0.00 0.00 0.00 2.43
3773 5008 1.075374 TCAAATACTGGCTGCAGGGTT 59.925 47.619 17.12 0.00 0.00 4.11
3820 5055 6.095440 TGCAACCTTAGAATCTTAAATCCAGC 59.905 38.462 0.00 0.00 0.00 4.85
4001 5236 5.639931 GGACAGGAGAAGTCACTGTAAATTC 59.360 44.000 8.18 0.00 44.79 2.17
4006 5241 3.527507 AGGACAGGAGAAGTCACTGTA 57.472 47.619 8.18 0.00 44.79 2.74
4172 5409 2.071540 TGCTTGATCGAGAAAGTGCAG 58.928 47.619 14.59 0.00 0.00 4.41
4270 5507 0.179034 GCTGCTGGGGGTTATCTGAG 60.179 60.000 0.00 0.00 0.00 3.35
4424 5663 6.603237 TTGAGCAACAAGTAATATGGATCG 57.397 37.500 0.00 0.00 34.20 3.69
4463 5705 9.464714 AACAGATGTATCTAGCACTAAAATACG 57.535 33.333 0.00 0.00 34.85 3.06
4467 5709 7.201522 CGCAAACAGATGTATCTAGCACTAAAA 60.202 37.037 0.00 0.00 34.85 1.52
4470 5712 5.281727 CGCAAACAGATGTATCTAGCACTA 58.718 41.667 0.00 0.00 34.85 2.74
4486 5728 5.051153 TCCATATTACTTATCGCGCAAACA 58.949 37.500 8.75 0.00 0.00 2.83
4492 5734 4.916870 TCCGATCCATATTACTTATCGCG 58.083 43.478 0.00 0.00 38.43 5.87
4545 5787 1.461127 CGAAGTTGCCTTCTCTTTCCG 59.539 52.381 1.93 0.00 44.12 4.30
4560 5802 6.620733 GCAACTAATTACTGCATGAACGAAGT 60.621 38.462 0.00 0.00 38.15 3.01
4565 5807 6.381801 ACTTGCAACTAATTACTGCATGAAC 58.618 36.000 23.84 0.00 44.99 3.18
4566 5808 6.206438 TGACTTGCAACTAATTACTGCATGAA 59.794 34.615 23.84 15.01 44.99 2.57
4608 5850 3.124466 TGTTCAGTTGTCGGAATAATGCG 59.876 43.478 0.00 0.00 42.36 4.73
4617 5875 2.851824 GCTGTTTTTGTTCAGTTGTCGG 59.148 45.455 0.00 0.00 34.57 4.79
4623 5881 6.699575 AGTAGATTGCTGTTTTTGTTCAGT 57.300 33.333 0.00 0.00 34.57 3.41
4661 5919 6.158598 ACAATTCACAATAACAATGCACCTC 58.841 36.000 0.00 0.00 0.00 3.85
4669 5927 7.950512 ACCATCAAGACAATTCACAATAACAA 58.049 30.769 0.00 0.00 0.00 2.83
4888 6170 0.242825 CGTTCTACAGGGTTCTGCGA 59.757 55.000 0.00 0.00 44.59 5.10
4889 6171 0.736325 CCGTTCTACAGGGTTCTGCG 60.736 60.000 0.00 0.00 44.59 5.18
4906 6188 1.679153 AGTTACAGCAACCAAAACCCG 59.321 47.619 0.00 0.00 37.93 5.28
4956 6241 9.078990 GGGAGTCACATCCATCGATATATATTA 57.921 37.037 0.00 0.00 41.52 0.98
5070 6377 5.295292 CCTCTCAATTTACACTGTATGCTGG 59.705 44.000 0.00 0.00 0.00 4.85
5088 6430 8.985315 AGAATTGATATGCAAAATACCTCTCA 57.015 30.769 0.00 0.00 40.48 3.27
5203 6547 3.052869 GGGGGTCTTAAATTGGTCTCCAT 60.053 47.826 0.00 0.00 31.53 3.41
5212 6556 3.055458 CCAATTTGCGGGGGTCTTAAATT 60.055 43.478 0.00 0.00 32.82 1.82
5214 6558 1.896465 CCAATTTGCGGGGGTCTTAAA 59.104 47.619 0.00 0.00 0.00 1.52
5219 6563 2.696759 CGACCAATTTGCGGGGGTC 61.697 63.158 0.00 0.00 44.97 4.46
5221 6565 2.675075 ACGACCAATTTGCGGGGG 60.675 61.111 0.00 0.00 0.00 5.40
5226 6570 5.699839 AGAAATAAGTGACGACCAATTTGC 58.300 37.500 0.00 0.00 34.59 3.68
5288 6632 4.692625 AGCAGATGTCAGTGATACAACAAC 59.307 41.667 0.00 0.00 0.00 3.32
5291 6635 4.498241 TGAGCAGATGTCAGTGATACAAC 58.502 43.478 0.00 0.00 0.00 3.32
5292 6636 4.806640 TGAGCAGATGTCAGTGATACAA 57.193 40.909 0.00 0.00 0.00 2.41
5294 6638 4.931601 TGTTTGAGCAGATGTCAGTGATAC 59.068 41.667 0.00 0.00 0.00 2.24
5296 6640 4.011966 TGTTTGAGCAGATGTCAGTGAT 57.988 40.909 0.00 0.00 0.00 3.06
5297 6641 3.473923 TGTTTGAGCAGATGTCAGTGA 57.526 42.857 0.00 0.00 0.00 3.41
5298 6642 3.501062 ACATGTTTGAGCAGATGTCAGTG 59.499 43.478 0.00 0.00 0.00 3.66
5299 6643 3.748083 ACATGTTTGAGCAGATGTCAGT 58.252 40.909 0.00 0.00 0.00 3.41
5300 6644 6.432607 AATACATGTTTGAGCAGATGTCAG 57.567 37.500 2.30 0.00 31.56 3.51
5303 6649 4.641989 GGGAATACATGTTTGAGCAGATGT 59.358 41.667 2.30 0.00 33.64 3.06
5552 7129 1.153706 GTACGAGGCGGCAAAGCTA 60.154 57.895 13.08 0.00 37.29 3.32


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

AutoCloner maintained by Alex Coulton.