Multiple sequence alignment - TraesCS5D01G519600

Loading Multiple Alignment...

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 TraesCS5D01G519600 chr5D 100.000 3404 0 0 1 3404 540283819 540287222 0.000000e+00 6287.0
1 TraesCS5D01G519600 chr5D 88.800 1250 123 11 1129 2362 540340197 540341445 0.000000e+00 1517.0
2 TraesCS5D01G519600 chr5D 96.867 383 12 0 1 383 102512533 102512151 2.860000e-180 641.0
3 TraesCS5D01G519600 chr5D 94.286 385 22 0 1 385 381171659 381171275 1.050000e-164 590.0
4 TraesCS5D01G519600 chr5D 95.918 245 10 0 704 948 102512157 102511913 6.840000e-107 398.0
5 TraesCS5D01G519600 chr5D 96.667 150 5 0 816 965 381171131 381170982 2.030000e-62 250.0
6 TraesCS5D01G519600 chr5D 94.286 35 1 1 938 971 102511907 102511873 6.000000e-03 52.8
7 TraesCS5D01G519600 chr4A 93.386 1527 73 9 966 2465 628327296 628328821 0.000000e+00 2235.0
8 TraesCS5D01G519600 chr4A 88.482 1285 128 11 1129 2394 628483855 628485138 0.000000e+00 1535.0
9 TraesCS5D01G519600 chr4A 91.968 249 13 3 3157 3404 628328858 628329100 3.250000e-90 342.0
10 TraesCS5D01G519600 chr5B 91.835 1531 94 13 966 2465 682696220 682697750 0.000000e+00 2106.0
11 TraesCS5D01G519600 chr5B 88.969 1251 119 13 1129 2362 682817821 682819069 0.000000e+00 1528.0
12 TraesCS5D01G519600 chr5B 80.253 395 32 13 2562 2916 682697921 682698309 4.360000e-64 255.0
13 TraesCS5D01G519600 chr5B 92.568 148 7 1 3257 3404 682698799 682698942 3.440000e-50 209.0
14 TraesCS5D01G519600 chr5B 90.683 161 7 5 3100 3258 682698563 682698717 1.240000e-49 207.0
15 TraesCS5D01G519600 chr5B 97.297 74 2 0 2920 2993 27816167 27816094 3.570000e-25 126.0
16 TraesCS5D01G519600 chr7D 97.143 385 11 0 1 385 237654642 237655026 0.000000e+00 651.0
17 TraesCS5D01G519600 chr7D 95.325 385 18 0 1 385 237713029 237712645 2.250000e-171 612.0
18 TraesCS5D01G519600 chr7D 95.114 307 14 1 385 690 203402129 203402435 1.840000e-132 483.0
19 TraesCS5D01G519600 chr7D 92.879 323 21 2 382 703 165533575 165533896 5.140000e-128 468.0
20 TraesCS5D01G519600 chr7D 96.735 245 8 0 704 948 237655018 237655262 3.160000e-110 409.0
21 TraesCS5D01G519600 chr7D 95.918 245 10 0 704 948 237712653 237712409 6.840000e-107 398.0
22 TraesCS5D01G519600 chr7D 95.294 85 4 0 2915 2999 78412142 78412226 5.930000e-28 135.0
23 TraesCS5D01G519600 chr7D 100.000 28 0 0 938 965 237655268 237655295 6.000000e-03 52.8
24 TraesCS5D01G519600 chr7D 94.286 35 1 1 938 971 237712403 237712369 6.000000e-03 52.8
25 TraesCS5D01G519600 chr6B 96.114 386 14 1 1 385 168822447 168822062 2.230000e-176 628.0
26 TraesCS5D01G519600 chr6B 96.774 186 6 0 764 949 168822052 168821867 9.170000e-81 311.0
27 TraesCS5D01G519600 chr6B 100.000 30 0 0 938 967 168821862 168821833 4.750000e-04 56.5
28 TraesCS5D01G519600 chr7A 95.078 386 18 1 1 385 463931282 463930897 1.040000e-169 606.0
29 TraesCS5D01G519600 chr7A 96.327 245 9 0 704 948 463930905 463930661 1.470000e-108 403.0
30 TraesCS5D01G519600 chr7A 90.541 74 6 1 2921 2994 310221637 310221565 2.800000e-16 97.1
31 TraesCS5D01G519600 chr7A 100.000 28 0 0 938 965 463930655 463930628 6.000000e-03 52.8
32 TraesCS5D01G519600 chr1D 92.208 385 30 0 1 385 364389918 364390302 2.310000e-151 545.0
33 TraesCS5D01G519600 chr1D 92.208 385 30 0 1 385 364391289 364391673 2.310000e-151 545.0
34 TraesCS5D01G519600 chr1D 94.855 311 14 2 381 690 480712397 480712088 5.110000e-133 484.0
35 TraesCS5D01G519600 chr1D 91.628 215 5 1 734 948 364390391 364390592 5.560000e-73 285.0
36 TraesCS5D01G519600 chr1D 97.647 85 2 0 2915 2999 6193187 6193103 2.740000e-31 147.0
37 TraesCS5D01G519600 chr1D 100.000 28 0 0 938 965 364390598 364390625 6.000000e-03 52.8
38 TraesCS5D01G519600 chr2D 93.846 325 19 1 384 707 545049092 545048768 3.950000e-134 488.0
39 TraesCS5D01G519600 chr6D 95.130 308 14 1 385 691 8563180 8562873 5.110000e-133 484.0
40 TraesCS5D01G519600 chr6D 93.210 324 21 1 384 706 291249725 291250048 3.070000e-130 475.0
41 TraesCS5D01G519600 chr7B 94.805 308 15 1 385 691 414158236 414158543 2.380000e-131 479.0
42 TraesCS5D01G519600 chr7B 88.785 214 24 0 736 949 327572120 327572333 2.600000e-66 263.0
43 TraesCS5D01G519600 chr3B 94.516 310 16 1 383 691 658462139 658461830 8.550000e-131 477.0
44 TraesCS5D01G519600 chr2B 93.478 322 20 1 385 705 117897834 117898155 8.550000e-131 477.0
45 TraesCS5D01G519600 chr2B 85.859 99 14 0 850 948 150427819 150427721 4.650000e-19 106.0
46 TraesCS5D01G519600 chr1A 94.074 270 16 0 1 270 310974258 310974527 8.790000e-111 411.0
47 TraesCS5D01G519600 chr1A 93.333 195 13 0 754 948 310975697 310975891 4.300000e-74 289.0
48 TraesCS5D01G519600 chr1A 95.370 108 4 1 262 369 310975591 310975697 1.620000e-38 171.0
49 TraesCS5D01G519600 chr2A 79.769 173 27 6 796 967 737473856 737473691 5.970000e-23 119.0
50 TraesCS5D01G519600 chr6A 84.694 98 15 0 851 948 489898544 489898447 7.770000e-17 99.0


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 TraesCS5D01G519600 chr5D 540283819 540287222 3403 False 6287.000000 6287 100.000000 1 3404 1 chr5D.!!$F1 3403
1 TraesCS5D01G519600 chr5D 540340197 540341445 1248 False 1517.000000 1517 88.800000 1129 2362 1 chr5D.!!$F2 1233
2 TraesCS5D01G519600 chr5D 381170982 381171659 677 True 420.000000 590 95.476500 1 965 2 chr5D.!!$R2 964
3 TraesCS5D01G519600 chr5D 102511873 102512533 660 True 363.933333 641 95.690333 1 971 3 chr5D.!!$R1 970
4 TraesCS5D01G519600 chr4A 628483855 628485138 1283 False 1535.000000 1535 88.482000 1129 2394 1 chr4A.!!$F1 1265
5 TraesCS5D01G519600 chr4A 628327296 628329100 1804 False 1288.500000 2235 92.677000 966 3404 2 chr4A.!!$F2 2438
6 TraesCS5D01G519600 chr5B 682817821 682819069 1248 False 1528.000000 1528 88.969000 1129 2362 1 chr5B.!!$F1 1233
7 TraesCS5D01G519600 chr5B 682696220 682698942 2722 False 694.250000 2106 88.834750 966 3404 4 chr5B.!!$F2 2438
8 TraesCS5D01G519600 chr7D 237654642 237655295 653 False 370.933333 651 97.959333 1 965 3 chr7D.!!$F4 964
9 TraesCS5D01G519600 chr7D 237712369 237713029 660 True 354.266667 612 95.176333 1 971 3 chr7D.!!$R1 970
10 TraesCS5D01G519600 chr6B 168821833 168822447 614 True 331.833333 628 97.629333 1 967 3 chr6B.!!$R1 966
11 TraesCS5D01G519600 chr7A 463930628 463931282 654 True 353.933333 606 97.135000 1 965 3 chr7A.!!$R2 964
12 TraesCS5D01G519600 chr1D 364389918 364391673 1755 False 356.950000 545 94.011000 1 965 4 chr1D.!!$F1 964
13 TraesCS5D01G519600 chr1A 310974258 310975891 1633 False 290.333333 411 94.259000 1 948 3 chr1A.!!$F1 947

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
509 1583 0.032540 GTTTTGAGCCCAACAGCAGG 59.967 55.0 0.0 0.0 34.23 4.85 F
538 1612 0.105408 GGCTTGGGCTTGGCATATTG 59.895 55.0 0.0 0.0 38.73 1.90 F
540 1614 0.105408 CTTGGGCTTGGCATATTGGC 59.895 55.0 0.0 0.0 44.03 4.52 F
561 1635 0.323087 TTTTAAGGAAGAGGCCCGGC 60.323 55.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 2911 0.040336 TCGTGAGCGTGACTGTCTTC 60.040 55.000 9.51 1.84 39.49 2.87 R
1803 3004 1.138883 CTCCGCGTAGTTGCTGCTA 59.861 57.895 4.92 0.00 0.00 3.49 R
2352 3553 1.372997 CGCGTTAGTGGTGCTGACT 60.373 57.895 0.00 0.00 32.19 3.41 R
2492 3733 3.869832 GGGTTAACCGTTCTGAATAGCTC 59.130 47.826 18.39 0.00 36.71 4.09 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
77 78 1.786937 ATCCCAACCACACAAGCAAA 58.213 45.000 0.00 0.00 0.00 3.68
81 82 1.204467 CCAACCACACAAGCAAACAGT 59.796 47.619 0.00 0.00 0.00 3.55
239 240 5.163663 TGCATTCTTGAAACGTGAAAGAAGT 60.164 36.000 19.22 9.79 41.74 3.01
348 1422 0.036306 GGTATTGACCGGCCCATAGG 59.964 60.000 0.00 0.00 35.52 2.57
387 1461 3.339093 GCCTGGGTTGGGGCTAGT 61.339 66.667 0.00 0.00 44.48 2.57
388 1462 2.998949 CCTGGGTTGGGGCTAGTC 59.001 66.667 0.00 0.00 0.00 2.59
389 1463 2.680370 CCTGGGTTGGGGCTAGTCC 61.680 68.421 4.21 4.21 0.00 3.85
390 1464 1.616628 CTGGGTTGGGGCTAGTCCT 60.617 63.158 14.34 0.00 34.39 3.85
391 1465 1.915078 CTGGGTTGGGGCTAGTCCTG 61.915 65.000 14.34 0.00 34.39 3.86
392 1466 2.680370 GGGTTGGGGCTAGTCCTGG 61.680 68.421 14.34 0.00 34.39 4.45
393 1467 2.272471 GTTGGGGCTAGTCCTGGC 59.728 66.667 14.34 0.00 36.25 4.85
400 1474 2.833244 GCTAGTCCTGGCCATCTCT 58.167 57.895 5.51 7.44 0.00 3.10
401 1475 0.392336 GCTAGTCCTGGCCATCTCTG 59.608 60.000 5.51 0.00 0.00 3.35
402 1476 1.047002 CTAGTCCTGGCCATCTCTGG 58.953 60.000 5.51 3.08 46.17 3.86
443 1517 2.277404 GGCCGGCCCTAAAATCCA 59.723 61.111 36.64 0.00 0.00 3.41
444 1518 1.828224 GGCCGGCCCTAAAATCCAG 60.828 63.158 36.64 0.00 0.00 3.86
445 1519 1.828224 GCCGGCCCTAAAATCCAGG 60.828 63.158 18.11 0.00 0.00 4.45
451 1525 2.959465 CCCTAAAATCCAGGGCCTAG 57.041 55.000 5.28 0.00 46.27 3.02
452 1526 1.425448 CCCTAAAATCCAGGGCCTAGG 59.575 57.143 5.28 10.90 46.27 3.02
453 1527 1.202940 CCTAAAATCCAGGGCCTAGGC 60.203 57.143 26.55 26.55 41.06 3.93
496 1570 2.732289 GCTTGGGCCTGAGTTTTGA 58.268 52.632 4.53 0.00 0.00 2.69
497 1571 0.600057 GCTTGGGCCTGAGTTTTGAG 59.400 55.000 4.53 0.00 0.00 3.02
498 1572 0.600057 CTTGGGCCTGAGTTTTGAGC 59.400 55.000 4.53 0.00 0.00 4.26
499 1573 0.827507 TTGGGCCTGAGTTTTGAGCC 60.828 55.000 4.53 0.00 43.09 4.70
500 1574 3.686760 GGCCTGAGTTTTGAGCCC 58.313 61.111 0.00 0.00 37.66 5.19
501 1575 1.228552 GGCCTGAGTTTTGAGCCCA 60.229 57.895 0.00 0.00 37.66 5.36
502 1576 0.827507 GGCCTGAGTTTTGAGCCCAA 60.828 55.000 0.00 0.00 37.66 4.12
503 1577 0.315251 GCCTGAGTTTTGAGCCCAAC 59.685 55.000 0.00 0.00 30.88 3.77
504 1578 1.691196 CCTGAGTTTTGAGCCCAACA 58.309 50.000 0.00 0.00 30.88 3.33
505 1579 1.610522 CCTGAGTTTTGAGCCCAACAG 59.389 52.381 0.00 0.00 30.88 3.16
506 1580 1.000938 CTGAGTTTTGAGCCCAACAGC 60.001 52.381 0.00 0.00 30.88 4.40
507 1581 1.032014 GAGTTTTGAGCCCAACAGCA 58.968 50.000 0.00 0.00 34.23 4.41
508 1582 1.000938 GAGTTTTGAGCCCAACAGCAG 60.001 52.381 0.00 0.00 34.23 4.24
509 1583 0.032540 GTTTTGAGCCCAACAGCAGG 59.967 55.000 0.00 0.00 34.23 4.85
515 1589 3.970410 CCCAACAGCAGGGCCTGA 61.970 66.667 37.07 0.00 39.96 3.86
516 1590 2.115910 CCAACAGCAGGGCCTGAA 59.884 61.111 37.07 0.00 36.67 3.02
517 1591 2.270986 CCAACAGCAGGGCCTGAAC 61.271 63.158 37.07 19.98 36.67 3.18
518 1592 2.281761 AACAGCAGGGCCTGAACG 60.282 61.111 37.07 24.08 36.67 3.95
519 1593 3.850098 AACAGCAGGGCCTGAACGG 62.850 63.158 37.07 21.78 36.67 4.44
528 1602 4.351054 CCTGAACGGGCTTGGGCT 62.351 66.667 0.00 0.00 38.73 5.19
529 1603 2.282462 CTGAACGGGCTTGGGCTT 60.282 61.111 0.00 0.00 38.73 4.35
530 1604 2.597217 TGAACGGGCTTGGGCTTG 60.597 61.111 0.00 0.00 38.73 4.01
531 1605 3.373565 GAACGGGCTTGGGCTTGG 61.374 66.667 0.00 0.00 38.73 3.61
535 1609 2.043046 GGGCTTGGGCTTGGCATA 60.043 61.111 0.00 0.00 38.73 3.14
536 1610 1.458209 GGGCTTGGGCTTGGCATAT 60.458 57.895 0.00 0.00 38.73 1.78
537 1611 1.050421 GGGCTTGGGCTTGGCATATT 61.050 55.000 0.00 0.00 38.73 1.28
538 1612 0.105408 GGCTTGGGCTTGGCATATTG 59.895 55.000 0.00 0.00 38.73 1.90
539 1613 0.105408 GCTTGGGCTTGGCATATTGG 59.895 55.000 0.00 0.00 35.22 3.16
540 1614 0.105408 CTTGGGCTTGGCATATTGGC 59.895 55.000 0.00 0.00 44.03 4.52
553 1627 6.160576 GGCATATTGGCATTTTAAGGAAGA 57.839 37.500 0.00 0.00 43.14 2.87
554 1628 6.218746 GGCATATTGGCATTTTAAGGAAGAG 58.781 40.000 0.00 0.00 43.14 2.85
555 1629 6.218746 GCATATTGGCATTTTAAGGAAGAGG 58.781 40.000 0.00 0.00 0.00 3.69
556 1630 4.743057 ATTGGCATTTTAAGGAAGAGGC 57.257 40.909 0.00 0.00 0.00 4.70
557 1631 2.456577 TGGCATTTTAAGGAAGAGGCC 58.543 47.619 0.00 0.00 40.51 5.19
558 1632 1.757118 GGCATTTTAAGGAAGAGGCCC 59.243 52.381 0.00 0.00 34.17 5.80
559 1633 1.405463 GCATTTTAAGGAAGAGGCCCG 59.595 52.381 0.00 0.00 0.00 6.13
560 1634 2.024414 CATTTTAAGGAAGAGGCCCGG 58.976 52.381 0.00 0.00 0.00 5.73
561 1635 0.323087 TTTTAAGGAAGAGGCCCGGC 60.323 55.000 0.00 0.00 0.00 6.13
595 1669 3.732048 CCCTAAGGGCTTTTTACCAGA 57.268 47.619 0.00 0.00 35.35 3.86
596 1670 4.251103 CCCTAAGGGCTTTTTACCAGAT 57.749 45.455 0.00 0.00 35.35 2.90
597 1671 3.954258 CCCTAAGGGCTTTTTACCAGATG 59.046 47.826 0.00 0.00 35.35 2.90
598 1672 3.954258 CCTAAGGGCTTTTTACCAGATGG 59.046 47.826 0.00 0.00 42.17 3.51
599 1673 2.532250 AGGGCTTTTTACCAGATGGG 57.468 50.000 3.48 0.00 44.81 4.00
600 1674 0.824109 GGGCTTTTTACCAGATGGGC 59.176 55.000 3.48 0.00 42.05 5.36
601 1675 0.824109 GGCTTTTTACCAGATGGGCC 59.176 55.000 3.48 0.00 42.05 5.80
602 1676 0.455815 GCTTTTTACCAGATGGGCCG 59.544 55.000 3.48 0.00 42.05 6.13
603 1677 1.102978 CTTTTTACCAGATGGGCCGG 58.897 55.000 0.00 0.00 42.05 6.13
604 1678 0.323908 TTTTTACCAGATGGGCCGGG 60.324 55.000 2.18 0.00 42.05 5.73
605 1679 2.847366 TTTTACCAGATGGGCCGGGC 62.847 60.000 22.00 22.00 42.05 6.13
606 1680 4.815973 TACCAGATGGGCCGGGCT 62.816 66.667 28.80 9.11 42.05 5.19
617 1691 2.600173 CCGGGCTTGGGCTTGAAA 60.600 61.111 0.00 0.00 38.73 2.69
618 1692 2.206536 CCGGGCTTGGGCTTGAAAA 61.207 57.895 0.00 0.00 38.73 2.29
631 1705 2.017049 CTTGAAAAGTAGGCCCGATGG 58.983 52.381 0.00 0.00 39.70 3.51
632 1706 0.988832 TGAAAAGTAGGCCCGATGGT 59.011 50.000 0.00 0.00 0.00 3.55
633 1707 2.189676 TGAAAAGTAGGCCCGATGGTA 58.810 47.619 0.00 0.00 0.00 3.25
634 1708 2.169769 TGAAAAGTAGGCCCGATGGTAG 59.830 50.000 0.00 0.00 0.00 3.18
635 1709 1.129058 AAAGTAGGCCCGATGGTAGG 58.871 55.000 0.00 0.00 0.00 3.18
641 1715 3.560251 CCCGATGGTAGGGCCTGG 61.560 72.222 18.53 7.41 42.77 4.45
642 1716 3.560251 CCGATGGTAGGGCCTGGG 61.560 72.222 18.53 3.75 38.35 4.45
643 1717 2.445845 CGATGGTAGGGCCTGGGA 60.446 66.667 18.53 0.00 38.35 4.37
644 1718 2.511452 CGATGGTAGGGCCTGGGAG 61.511 68.421 18.53 0.00 38.35 4.30
645 1719 2.039405 ATGGTAGGGCCTGGGAGG 60.039 66.667 18.53 0.00 38.80 4.30
646 1720 3.739080 ATGGTAGGGCCTGGGAGGG 62.739 68.421 18.53 0.00 35.37 4.30
662 1736 4.249513 GGCTGGGCCTCAGATTTC 57.750 61.111 21.37 6.70 46.69 2.17
663 1737 1.611965 GGCTGGGCCTCAGATTTCT 59.388 57.895 21.37 0.00 46.69 2.52
664 1738 0.750911 GGCTGGGCCTCAGATTTCTG 60.751 60.000 21.37 0.97 46.69 3.02
665 1739 1.382692 GCTGGGCCTCAGATTTCTGC 61.383 60.000 21.37 6.47 46.18 4.26
666 1740 0.750911 CTGGGCCTCAGATTTCTGCC 60.751 60.000 14.21 1.18 46.18 4.85
667 1741 1.821332 GGGCCTCAGATTTCTGCCG 60.821 63.158 0.84 0.00 43.46 5.69
668 1742 1.078143 GGCCTCAGATTTCTGCCGT 60.078 57.895 0.00 0.00 43.46 5.68
669 1743 1.372087 GGCCTCAGATTTCTGCCGTG 61.372 60.000 0.00 0.00 43.46 4.94
670 1744 1.372087 GCCTCAGATTTCTGCCGTGG 61.372 60.000 2.60 4.18 43.46 4.94
671 1745 0.745845 CCTCAGATTTCTGCCGTGGG 60.746 60.000 2.60 0.00 43.46 4.61
692 1766 3.274601 TTTTTAGGCCCGACCCATG 57.725 52.632 0.00 0.00 40.58 3.66
693 1767 0.323908 TTTTTAGGCCCGACCCATGG 60.324 55.000 4.14 4.14 40.58 3.66
700 1774 3.087253 CCGACCCATGGCCAGGTA 61.087 66.667 16.33 0.00 36.17 3.08
701 1775 2.452064 CCGACCCATGGCCAGGTAT 61.452 63.158 16.33 3.32 36.17 2.73
702 1776 1.125093 CCGACCCATGGCCAGGTATA 61.125 60.000 16.33 0.00 36.17 1.47
743 1884 5.041951 TGGACGCTTCACACAAAATAATC 57.958 39.130 0.00 0.00 0.00 1.75
794 1935 5.244785 ACGTGTATATGTCTATATGGCCG 57.755 43.478 0.00 0.00 31.97 6.13
867 2008 2.394506 CCCATGCCCTACCCACCAT 61.395 63.158 0.00 0.00 0.00 3.55
1096 2279 1.996292 CTGCCGTCGAAGAAAGATGA 58.004 50.000 0.00 0.00 39.69 2.92
1233 2422 2.435938 GCGGCCAATTCGACCTCA 60.436 61.111 2.24 0.00 0.00 3.86
1263 2452 0.326264 CCAACTCCACCTTCTCCCTG 59.674 60.000 0.00 0.00 0.00 4.45
1398 2587 2.835431 CGCCTCTCATCCTCCGGT 60.835 66.667 0.00 0.00 0.00 5.28
1419 2608 0.403271 ATCTGCAGCTGGTCAAAGGT 59.597 50.000 17.12 0.00 0.00 3.50
1505 2694 3.414700 CGGCAACCTCGTGCTCAC 61.415 66.667 0.00 0.00 44.31 3.51
1569 2758 1.369692 GGACACCGTGGTCATGTCA 59.630 57.895 3.03 0.00 43.73 3.58
1632 2824 2.979197 CTTCGCCGTCGACAGGTCT 61.979 63.158 17.16 0.00 45.43 3.85
1716 2908 1.157870 ACAACAACTCCTTCACCGCG 61.158 55.000 0.00 0.00 0.00 6.46
1803 3004 3.580193 CCCGTCGTCGTCGCCTAT 61.580 66.667 6.36 0.00 36.96 2.57
1817 3018 1.140816 GCCTATAGCAGCAACTACGC 58.859 55.000 0.00 0.00 42.97 4.42
1818 3019 1.409412 CCTATAGCAGCAACTACGCG 58.591 55.000 3.53 3.53 36.85 6.01
2372 3577 1.663388 TCAGCACCACTAACGCGTG 60.663 57.895 14.98 3.05 34.71 5.34
2405 3610 0.178906 TCCGGCCTCCATGGATGATA 60.179 55.000 20.12 0.00 38.35 2.15
2412 3617 4.704057 GGCCTCCATGGATGATATCTTTTC 59.296 45.833 20.12 0.00 38.35 2.29
2487 3728 9.482627 TTGTACACCCTTTTAGCAAAAATAATG 57.517 29.630 0.00 0.00 34.18 1.90
2492 3733 9.139174 CACCCTTTTAGCAAAAATAATGTGTAG 57.861 33.333 0.00 0.00 34.18 2.74
2495 3736 9.076596 CCTTTTAGCAAAAATAATGTGTAGAGC 57.923 33.333 0.00 0.00 34.18 4.09
2632 3920 2.107141 CCGCACCGATCTCCTTCC 59.893 66.667 0.00 0.00 0.00 3.46
2633 3921 2.427245 CCGCACCGATCTCCTTCCT 61.427 63.158 0.00 0.00 0.00 3.36
2634 3922 1.517832 CGCACCGATCTCCTTCCTT 59.482 57.895 0.00 0.00 0.00 3.36
2635 3923 0.528684 CGCACCGATCTCCTTCCTTC 60.529 60.000 0.00 0.00 0.00 3.46
2636 3924 0.528684 GCACCGATCTCCTTCCTTCG 60.529 60.000 0.00 0.00 0.00 3.79
2670 3958 4.486125 TTGATCGTCTCCCAATTCATCA 57.514 40.909 0.00 0.00 0.00 3.07
2681 3985 2.159476 CCAATTCATCAGCACGGAGTTG 60.159 50.000 0.00 0.00 41.61 3.16
2685 3989 1.021390 CATCAGCACGGAGTTGGGTC 61.021 60.000 0.00 0.00 41.61 4.46
2701 4005 3.045142 TCCAGTGGGACGACGAAC 58.955 61.111 9.92 0.00 38.64 3.95
2707 4011 0.580104 GTGGGACGACGAACAAGTTG 59.420 55.000 0.00 0.00 0.00 3.16
2716 4020 1.021202 CGAACAAGTTGTTGGCCTCA 58.979 50.000 25.46 0.00 41.28 3.86
2718 4022 2.034558 CGAACAAGTTGTTGGCCTCAAT 59.965 45.455 25.46 0.00 41.28 2.57
2720 4024 1.608590 ACAAGTTGTTGGCCTCAATCG 59.391 47.619 14.80 9.97 38.07 3.34
2728 4032 0.109153 TGGCCTCAATCGGATCCATG 59.891 55.000 13.41 7.68 0.00 3.66
2729 4033 0.397941 GGCCTCAATCGGATCCATGA 59.602 55.000 13.41 11.66 0.00 3.07
2731 4035 1.788258 CCTCAATCGGATCCATGACG 58.212 55.000 13.41 3.54 0.00 4.35
2745 4049 2.202756 GACGATGGTGACGAGGGC 60.203 66.667 0.00 0.00 34.70 5.19
2747 4051 4.873129 CGATGGTGACGAGGGCGG 62.873 72.222 0.00 0.00 43.17 6.13
2797 4119 3.845625 GTGGGACGCAAAAAGAGTG 57.154 52.632 0.00 0.00 39.55 3.51
2798 4120 0.310854 GTGGGACGCAAAAAGAGTGG 59.689 55.000 0.00 0.00 39.55 4.00
2810 4132 2.292828 AAGAGTGGGGGTGAATTGTG 57.707 50.000 0.00 0.00 0.00 3.33
2841 4163 0.591659 GCTTCGAGTGGGGTTTTGAC 59.408 55.000 0.00 0.00 0.00 3.18
2844 4166 0.107831 TCGAGTGGGGTTTTGACTGG 59.892 55.000 0.00 0.00 0.00 4.00
2845 4167 0.889186 CGAGTGGGGTTTTGACTGGG 60.889 60.000 0.00 0.00 0.00 4.45
2863 4185 1.420138 GGGTCAAGACTGTTGGAGGAA 59.580 52.381 0.00 0.00 0.00 3.36
2928 4255 4.357279 GCTTGCCCTCAGCCCACT 62.357 66.667 0.00 0.00 42.71 4.00
2929 4256 2.360852 CTTGCCCTCAGCCCACTG 60.361 66.667 0.00 0.00 45.95 3.66
2963 4290 4.662961 CCACGCGTCAGTGAGCCA 62.663 66.667 9.86 0.00 44.43 4.75
3010 4345 1.450312 CGGCTCCAACAGGTCCATC 60.450 63.158 0.00 0.00 0.00 3.51
3036 4371 4.660938 GGCAAGGGCGTTGAGGGT 62.661 66.667 22.92 0.00 42.47 4.34
3037 4372 3.365265 GCAAGGGCGTTGAGGGTG 61.365 66.667 22.92 0.00 38.60 4.61
3038 4373 2.672996 CAAGGGCGTTGAGGGTGG 60.673 66.667 14.44 0.00 38.60 4.61
3039 4374 2.852075 AAGGGCGTTGAGGGTGGA 60.852 61.111 0.00 0.00 0.00 4.02
3040 4375 2.895424 AAGGGCGTTGAGGGTGGAG 61.895 63.158 0.00 0.00 0.00 3.86
3041 4376 3.319198 GGGCGTTGAGGGTGGAGA 61.319 66.667 0.00 0.00 0.00 3.71
3042 4377 2.266055 GGCGTTGAGGGTGGAGAG 59.734 66.667 0.00 0.00 0.00 3.20
3046 4381 2.206900 TTGAGGGTGGAGAGGGCA 59.793 61.111 0.00 0.00 0.00 5.36
3047 4382 1.463214 TTGAGGGTGGAGAGGGCAA 60.463 57.895 0.00 0.00 0.00 4.52
3048 4383 1.492133 TTGAGGGTGGAGAGGGCAAG 61.492 60.000 0.00 0.00 0.00 4.01
3050 4385 2.936032 GGGTGGAGAGGGCAAGGT 60.936 66.667 0.00 0.00 0.00 3.50
3052 4387 1.303643 GGTGGAGAGGGCAAGGTTG 60.304 63.158 0.00 0.00 0.00 3.77
3053 4388 1.303643 GTGGAGAGGGCAAGGTTGG 60.304 63.158 0.00 0.00 0.00 3.77
3054 4389 1.463214 TGGAGAGGGCAAGGTTGGA 60.463 57.895 0.00 0.00 0.00 3.53
3056 4391 1.761174 GAGAGGGCAAGGTTGGACA 59.239 57.895 0.00 0.00 0.00 4.02
3058 4393 1.303643 GAGGGCAAGGTTGGACAGG 60.304 63.158 0.00 0.00 0.00 4.00
3059 4394 1.774217 AGGGCAAGGTTGGACAGGA 60.774 57.895 0.00 0.00 0.00 3.86
3060 4395 1.152830 GGGCAAGGTTGGACAGGAA 59.847 57.895 0.00 0.00 0.00 3.36
3061 4396 0.469144 GGGCAAGGTTGGACAGGAAA 60.469 55.000 0.00 0.00 0.00 3.13
3062 4397 1.408969 GGCAAGGTTGGACAGGAAAA 58.591 50.000 0.00 0.00 0.00 2.29
3064 4399 2.306847 GCAAGGTTGGACAGGAAAAGA 58.693 47.619 0.00 0.00 0.00 2.52
3065 4400 2.294512 GCAAGGTTGGACAGGAAAAGAG 59.705 50.000 0.00 0.00 0.00 2.85
3067 4402 3.214696 AGGTTGGACAGGAAAAGAGTG 57.785 47.619 0.00 0.00 0.00 3.51
3068 4403 2.158608 AGGTTGGACAGGAAAAGAGTGG 60.159 50.000 0.00 0.00 0.00 4.00
3070 4405 0.771127 TGGACAGGAAAAGAGTGGGG 59.229 55.000 0.00 0.00 0.00 4.96
3072 4407 1.545651 GGACAGGAAAAGAGTGGGGTG 60.546 57.143 0.00 0.00 0.00 4.61
3073 4408 1.420138 GACAGGAAAAGAGTGGGGTGA 59.580 52.381 0.00 0.00 0.00 4.02
3074 4409 1.850345 ACAGGAAAAGAGTGGGGTGAA 59.150 47.619 0.00 0.00 0.00 3.18
3075 4410 2.447047 ACAGGAAAAGAGTGGGGTGAAT 59.553 45.455 0.00 0.00 0.00 2.57
3076 4411 3.117131 ACAGGAAAAGAGTGGGGTGAATT 60.117 43.478 0.00 0.00 0.00 2.17
3077 4412 3.256631 CAGGAAAAGAGTGGGGTGAATTG 59.743 47.826 0.00 0.00 0.00 2.32
3078 4413 3.117131 AGGAAAAGAGTGGGGTGAATTGT 60.117 43.478 0.00 0.00 0.00 2.71
3079 4414 3.255888 GGAAAAGAGTGGGGTGAATTGTC 59.744 47.826 0.00 0.00 0.00 3.18
3081 4416 3.593442 AAGAGTGGGGTGAATTGTCAA 57.407 42.857 0.00 0.00 34.87 3.18
3083 4418 2.174639 AGAGTGGGGTGAATTGTCAACA 59.825 45.455 0.00 0.00 43.92 3.33
3084 4419 2.955660 GAGTGGGGTGAATTGTCAACAA 59.044 45.455 0.00 0.00 43.92 2.83
3085 4420 2.693074 AGTGGGGTGAATTGTCAACAAC 59.307 45.455 0.00 0.00 43.92 3.32
3086 4421 2.693074 GTGGGGTGAATTGTCAACAACT 59.307 45.455 0.00 0.00 43.92 3.16
3088 4423 2.693074 GGGGTGAATTGTCAACAACTGT 59.307 45.455 0.00 0.00 43.92 3.55
3089 4424 3.490761 GGGGTGAATTGTCAACAACTGTG 60.491 47.826 0.00 0.00 43.92 3.66
3090 4425 3.380004 GGGTGAATTGTCAACAACTGTGA 59.620 43.478 0.00 0.00 43.92 3.58
3091 4426 4.498009 GGGTGAATTGTCAACAACTGTGAG 60.498 45.833 0.00 0.00 43.92 3.51
3092 4427 4.037690 GTGAATTGTCAACAACTGTGAGC 58.962 43.478 0.00 0.00 38.86 4.26
3093 4428 3.947196 TGAATTGTCAACAACTGTGAGCT 59.053 39.130 0.00 0.00 38.86 4.09
3094 4429 4.398988 TGAATTGTCAACAACTGTGAGCTT 59.601 37.500 0.00 0.00 38.86 3.74
3095 4430 4.989279 ATTGTCAACAACTGTGAGCTTT 57.011 36.364 0.00 0.00 38.86 3.51
3096 4431 4.355543 TTGTCAACAACTGTGAGCTTTC 57.644 40.909 0.00 0.00 0.00 2.62
3097 4432 3.342719 TGTCAACAACTGTGAGCTTTCA 58.657 40.909 0.00 0.00 0.00 2.69
3098 4433 3.374988 TGTCAACAACTGTGAGCTTTCAG 59.625 43.478 14.65 14.65 37.65 3.02
3103 4503 1.858091 ACTGTGAGCTTTCAGACGTG 58.142 50.000 20.60 1.47 35.84 4.49
3145 4545 3.760151 ACGGGCATCCATCATTATGAATG 59.240 43.478 0.00 0.03 40.28 2.67
3168 4667 5.372363 TGATCCAGGCATATAGGGAAGAAAA 59.628 40.000 0.00 0.00 32.25 2.29
3169 4668 5.725551 TCCAGGCATATAGGGAAGAAAAA 57.274 39.130 0.00 0.00 0.00 1.94
3178 4677 0.887933 GGGAAGAAAAATGAGCGCCA 59.112 50.000 2.29 1.52 0.00 5.69
3213 4712 5.509498 TCCCCAAGGAACTGAAATTCATAG 58.491 41.667 0.00 0.00 40.08 2.23
3264 4848 7.041098 ACTGCAATGCTAGGTTTATATAAGCAC 60.041 37.037 6.82 0.91 45.18 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.349033 GCAACAATAGGAATCGTTTACCAAGT 60.349 38.462 0.00 0.00 0.00 3.16
77 78 0.035881 ACACAGCTGCTGCATACTGT 59.964 50.000 28.39 24.46 43.92 3.55
81 82 4.576053 CCTATAAAACACAGCTGCTGCATA 59.424 41.667 28.39 14.52 42.74 3.14
239 240 1.745232 AACAACCAGCTTCACGTTCA 58.255 45.000 0.00 0.00 0.00 3.18
348 1422 1.949525 TCACTCAGAGTTTGCAAAGGC 59.050 47.619 13.26 7.61 41.68 4.35
350 1424 3.562505 GCATCACTCAGAGTTTGCAAAG 58.437 45.455 22.40 1.61 35.78 2.77
385 1459 4.063335 CCAGAGATGGCCAGGACT 57.937 61.111 13.05 10.74 0.00 3.85
426 1500 1.828224 CTGGATTTTAGGGCCGGCC 60.828 63.158 38.57 38.57 0.00 6.13
427 1501 1.828224 CCTGGATTTTAGGGCCGGC 60.828 63.158 21.18 21.18 0.00 6.13
428 1502 4.579127 CCTGGATTTTAGGGCCGG 57.421 61.111 0.00 0.00 0.00 6.13
433 1507 1.202940 GCCTAGGCCCTGGATTTTAGG 60.203 57.143 24.19 10.45 34.56 2.69
434 1508 2.278332 GCCTAGGCCCTGGATTTTAG 57.722 55.000 24.19 0.33 34.56 1.85
478 1552 0.600057 CTCAAAACTCAGGCCCAAGC 59.400 55.000 0.00 0.00 38.76 4.01
479 1553 0.600057 GCTCAAAACTCAGGCCCAAG 59.400 55.000 0.00 0.00 0.00 3.61
480 1554 0.827507 GGCTCAAAACTCAGGCCCAA 60.828 55.000 0.00 0.00 37.12 4.12
481 1555 1.228552 GGCTCAAAACTCAGGCCCA 60.229 57.895 0.00 0.00 37.12 5.36
482 1556 3.686760 GGCTCAAAACTCAGGCCC 58.313 61.111 0.00 0.00 37.12 5.80
484 1558 0.315251 GTTGGGCTCAAAACTCAGGC 59.685 55.000 0.00 0.00 34.28 4.85
485 1559 1.610522 CTGTTGGGCTCAAAACTCAGG 59.389 52.381 0.00 0.00 34.28 3.86
486 1560 1.000938 GCTGTTGGGCTCAAAACTCAG 60.001 52.381 0.00 5.33 34.28 3.35
487 1561 1.032014 GCTGTTGGGCTCAAAACTCA 58.968 50.000 0.00 0.00 34.28 3.41
488 1562 1.000938 CTGCTGTTGGGCTCAAAACTC 60.001 52.381 0.00 0.00 34.28 3.01
489 1563 1.035139 CTGCTGTTGGGCTCAAAACT 58.965 50.000 0.00 0.00 34.28 2.66
490 1564 0.032540 CCTGCTGTTGGGCTCAAAAC 59.967 55.000 0.00 0.00 34.28 2.43
491 1565 1.114722 CCCTGCTGTTGGGCTCAAAA 61.115 55.000 0.00 0.00 37.99 2.44
492 1566 1.531365 CCCTGCTGTTGGGCTCAAA 60.531 57.895 0.00 0.00 37.99 2.69
493 1567 2.115910 CCCTGCTGTTGGGCTCAA 59.884 61.111 0.00 0.00 37.99 3.02
499 1573 2.115910 TTCAGGCCCTGCTGTTGG 59.884 61.111 5.66 0.00 0.00 3.77
500 1574 2.620112 CGTTCAGGCCCTGCTGTTG 61.620 63.158 5.66 0.00 0.00 3.33
501 1575 2.281761 CGTTCAGGCCCTGCTGTT 60.282 61.111 5.66 0.00 0.00 3.16
502 1576 4.335647 CCGTTCAGGCCCTGCTGT 62.336 66.667 5.66 0.00 0.00 4.40
511 1585 3.868200 AAGCCCAAGCCCGTTCAGG 62.868 63.158 0.00 0.00 41.25 3.86
512 1586 2.282462 AAGCCCAAGCCCGTTCAG 60.282 61.111 0.00 0.00 41.25 3.02
513 1587 2.597217 CAAGCCCAAGCCCGTTCA 60.597 61.111 0.00 0.00 41.25 3.18
514 1588 3.373565 CCAAGCCCAAGCCCGTTC 61.374 66.667 0.00 0.00 41.25 3.95
518 1592 1.050421 AATATGCCAAGCCCAAGCCC 61.050 55.000 0.00 0.00 41.25 5.19
519 1593 0.105408 CAATATGCCAAGCCCAAGCC 59.895 55.000 0.00 0.00 41.25 4.35
520 1594 0.105408 CCAATATGCCAAGCCCAAGC 59.895 55.000 0.00 0.00 40.32 4.01
521 1595 0.105408 GCCAATATGCCAAGCCCAAG 59.895 55.000 0.00 0.00 0.00 3.61
522 1596 0.616964 TGCCAATATGCCAAGCCCAA 60.617 50.000 0.00 0.00 0.00 4.12
523 1597 0.398806 ATGCCAATATGCCAAGCCCA 60.399 50.000 0.00 0.00 0.00 5.36
524 1598 0.760572 AATGCCAATATGCCAAGCCC 59.239 50.000 0.00 0.00 0.00 5.19
525 1599 2.625695 AAATGCCAATATGCCAAGCC 57.374 45.000 0.00 0.00 0.00 4.35
526 1600 4.512571 CCTTAAAATGCCAATATGCCAAGC 59.487 41.667 0.00 0.00 0.00 4.01
527 1601 5.916318 TCCTTAAAATGCCAATATGCCAAG 58.084 37.500 0.00 0.00 0.00 3.61
528 1602 5.946942 TCCTTAAAATGCCAATATGCCAA 57.053 34.783 0.00 0.00 0.00 4.52
529 1603 5.660417 TCTTCCTTAAAATGCCAATATGCCA 59.340 36.000 0.00 0.00 0.00 4.92
530 1604 6.160576 TCTTCCTTAAAATGCCAATATGCC 57.839 37.500 0.00 0.00 0.00 4.40
531 1605 6.218746 CCTCTTCCTTAAAATGCCAATATGC 58.781 40.000 0.00 0.00 0.00 3.14
532 1606 6.218746 GCCTCTTCCTTAAAATGCCAATATG 58.781 40.000 0.00 0.00 0.00 1.78
533 1607 5.305386 GGCCTCTTCCTTAAAATGCCAATAT 59.695 40.000 0.00 0.00 37.58 1.28
534 1608 4.649218 GGCCTCTTCCTTAAAATGCCAATA 59.351 41.667 0.00 0.00 37.58 1.90
535 1609 3.452264 GGCCTCTTCCTTAAAATGCCAAT 59.548 43.478 0.00 0.00 37.58 3.16
536 1610 2.831526 GGCCTCTTCCTTAAAATGCCAA 59.168 45.455 0.00 0.00 37.58 4.52
537 1611 2.456577 GGCCTCTTCCTTAAAATGCCA 58.543 47.619 0.00 0.00 37.58 4.92
538 1612 1.757118 GGGCCTCTTCCTTAAAATGCC 59.243 52.381 0.84 0.00 36.92 4.40
539 1613 1.405463 CGGGCCTCTTCCTTAAAATGC 59.595 52.381 0.84 0.00 0.00 3.56
540 1614 2.024414 CCGGGCCTCTTCCTTAAAATG 58.976 52.381 0.84 0.00 0.00 2.32
541 1615 1.685180 GCCGGGCCTCTTCCTTAAAAT 60.685 52.381 8.12 0.00 0.00 1.82
542 1616 0.323087 GCCGGGCCTCTTCCTTAAAA 60.323 55.000 8.12 0.00 0.00 1.52
543 1617 1.301954 GCCGGGCCTCTTCCTTAAA 59.698 57.895 8.12 0.00 0.00 1.52
544 1618 2.676265 GGCCGGGCCTCTTCCTTAA 61.676 63.158 30.86 0.00 46.69 1.85
545 1619 3.087906 GGCCGGGCCTCTTCCTTA 61.088 66.667 30.86 0.00 46.69 2.69
576 1650 3.954258 CCATCTGGTAAAAAGCCCTTAGG 59.046 47.826 0.00 0.00 0.00 2.69
577 1651 3.954258 CCCATCTGGTAAAAAGCCCTTAG 59.046 47.826 0.00 0.00 0.00 2.18
578 1652 3.880117 GCCCATCTGGTAAAAAGCCCTTA 60.880 47.826 0.00 0.00 36.04 2.69
579 1653 2.820178 CCCATCTGGTAAAAAGCCCTT 58.180 47.619 0.00 0.00 0.00 3.95
580 1654 1.619704 GCCCATCTGGTAAAAAGCCCT 60.620 52.381 0.00 0.00 36.04 5.19
581 1655 0.824109 GCCCATCTGGTAAAAAGCCC 59.176 55.000 0.00 0.00 36.04 5.19
582 1656 0.824109 GGCCCATCTGGTAAAAAGCC 59.176 55.000 0.00 0.00 36.04 4.35
583 1657 0.455815 CGGCCCATCTGGTAAAAAGC 59.544 55.000 0.00 0.00 36.04 3.51
584 1658 1.102978 CCGGCCCATCTGGTAAAAAG 58.897 55.000 0.00 0.00 36.43 2.27
585 1659 0.323908 CCCGGCCCATCTGGTAAAAA 60.324 55.000 0.00 0.00 39.73 1.94
586 1660 1.304952 CCCGGCCCATCTGGTAAAA 59.695 57.895 0.00 0.00 39.73 1.52
587 1661 3.003230 CCCGGCCCATCTGGTAAA 58.997 61.111 0.00 0.00 39.73 2.01
588 1662 3.804329 GCCCGGCCCATCTGGTAA 61.804 66.667 0.00 0.00 39.73 2.85
589 1663 4.815973 AGCCCGGCCCATCTGGTA 62.816 66.667 5.55 0.00 39.73 3.25
600 1674 2.158561 CTTTTCAAGCCCAAGCCCGG 62.159 60.000 0.00 0.00 41.25 5.73
601 1675 1.290009 CTTTTCAAGCCCAAGCCCG 59.710 57.895 0.00 0.00 41.25 6.13
602 1676 1.546029 CTACTTTTCAAGCCCAAGCCC 59.454 52.381 0.00 0.00 41.25 5.19
603 1677 1.546029 CCTACTTTTCAAGCCCAAGCC 59.454 52.381 0.00 0.00 41.25 4.35
604 1678 1.067565 GCCTACTTTTCAAGCCCAAGC 60.068 52.381 0.00 0.00 40.32 4.01
605 1679 1.546029 GGCCTACTTTTCAAGCCCAAG 59.454 52.381 0.00 0.00 37.66 3.61
606 1680 1.627864 GGCCTACTTTTCAAGCCCAA 58.372 50.000 0.00 0.00 37.66 4.12
607 1681 3.356814 GGCCTACTTTTCAAGCCCA 57.643 52.632 0.00 0.00 37.66 5.36
609 1683 0.322187 TCGGGCCTACTTTTCAAGCC 60.322 55.000 0.84 0.00 43.09 4.35
610 1684 1.401905 CATCGGGCCTACTTTTCAAGC 59.598 52.381 0.84 0.00 0.00 4.01
611 1685 2.017049 CCATCGGGCCTACTTTTCAAG 58.983 52.381 0.84 0.00 0.00 3.02
612 1686 1.353022 ACCATCGGGCCTACTTTTCAA 59.647 47.619 0.84 0.00 37.90 2.69
613 1687 0.988832 ACCATCGGGCCTACTTTTCA 59.011 50.000 0.84 0.00 37.90 2.69
614 1688 2.484947 CCTACCATCGGGCCTACTTTTC 60.485 54.545 0.84 0.00 37.90 2.29
615 1689 1.489230 CCTACCATCGGGCCTACTTTT 59.511 52.381 0.84 0.00 37.90 2.27
616 1690 1.129058 CCTACCATCGGGCCTACTTT 58.871 55.000 0.84 0.00 37.90 2.66
617 1691 0.763223 CCCTACCATCGGGCCTACTT 60.763 60.000 0.84 0.00 37.90 2.24
618 1692 1.152312 CCCTACCATCGGGCCTACT 60.152 63.158 0.84 0.00 37.90 2.57
619 1693 3.468063 CCCTACCATCGGGCCTAC 58.532 66.667 0.84 0.00 37.90 3.18
624 1698 3.560251 CCAGGCCCTACCATCGGG 61.560 72.222 0.00 0.00 44.89 5.14
625 1699 3.560251 CCCAGGCCCTACCATCGG 61.560 72.222 0.00 0.00 43.14 4.18
626 1700 2.445845 TCCCAGGCCCTACCATCG 60.446 66.667 0.00 0.00 43.14 3.84
627 1701 2.150051 CCTCCCAGGCCCTACCATC 61.150 68.421 0.00 0.00 43.14 3.51
628 1702 2.039405 CCTCCCAGGCCCTACCAT 60.039 66.667 0.00 0.00 43.14 3.55
629 1703 4.431524 CCCTCCCAGGCCCTACCA 62.432 72.222 0.00 0.00 43.14 3.25
645 1719 0.750911 CAGAAATCTGAGGCCCAGCC 60.751 60.000 14.49 0.00 46.59 4.85
646 1720 1.382692 GCAGAAATCTGAGGCCCAGC 61.383 60.000 14.43 0.00 46.59 4.85
647 1721 0.750911 GGCAGAAATCTGAGGCCCAG 60.751 60.000 14.43 13.43 46.59 4.45
648 1722 1.304282 GGCAGAAATCTGAGGCCCA 59.696 57.895 14.43 0.00 46.59 5.36
649 1723 1.821332 CGGCAGAAATCTGAGGCCC 60.821 63.158 14.43 4.90 46.59 5.80
650 1724 1.078143 ACGGCAGAAATCTGAGGCC 60.078 57.895 14.43 7.32 46.59 5.19
651 1725 1.372087 CCACGGCAGAAATCTGAGGC 61.372 60.000 14.43 0.00 46.59 4.70
652 1726 0.745845 CCCACGGCAGAAATCTGAGG 60.746 60.000 14.43 9.03 46.59 3.86
653 1727 2.772739 CCCACGGCAGAAATCTGAG 58.227 57.895 14.43 9.22 46.59 3.35
674 1748 0.323908 CCATGGGTCGGGCCTAAAAA 60.324 55.000 2.85 0.00 37.43 1.94
675 1749 1.304952 CCATGGGTCGGGCCTAAAA 59.695 57.895 2.85 0.00 37.43 1.52
676 1750 3.003230 CCATGGGTCGGGCCTAAA 58.997 61.111 2.85 0.00 37.43 1.85
677 1751 3.804329 GCCATGGGTCGGGCCTAA 61.804 66.667 15.13 0.00 44.53 2.69
683 1757 1.125093 TATACCTGGCCATGGGTCGG 61.125 60.000 19.47 12.27 37.07 4.79
684 1758 0.321671 CTATACCTGGCCATGGGTCG 59.678 60.000 19.47 6.76 37.07 4.79
685 1759 1.435256 ACTATACCTGGCCATGGGTC 58.565 55.000 19.47 0.00 37.07 4.46
686 1760 1.494721 CAACTATACCTGGCCATGGGT 59.505 52.381 19.76 19.76 39.40 4.51
687 1761 1.202927 CCAACTATACCTGGCCATGGG 60.203 57.143 20.97 16.10 0.00 4.00
688 1762 1.202927 CCCAACTATACCTGGCCATGG 60.203 57.143 5.51 13.05 0.00 3.66
689 1763 1.202927 CCCCAACTATACCTGGCCATG 60.203 57.143 5.51 6.06 0.00 3.66
690 1764 1.149101 CCCCAACTATACCTGGCCAT 58.851 55.000 5.51 0.00 0.00 4.40
691 1765 1.641552 GCCCCAACTATACCTGGCCA 61.642 60.000 4.71 4.71 32.74 5.36
692 1766 1.150764 GCCCCAACTATACCTGGCC 59.849 63.158 0.00 0.00 32.74 5.36
693 1767 0.179018 CAGCCCCAACTATACCTGGC 60.179 60.000 0.00 0.00 39.17 4.85
694 1768 1.141053 GTCAGCCCCAACTATACCTGG 59.859 57.143 0.00 0.00 0.00 4.45
695 1769 1.202533 CGTCAGCCCCAACTATACCTG 60.203 57.143 0.00 0.00 0.00 4.00
696 1770 1.120530 CGTCAGCCCCAACTATACCT 58.879 55.000 0.00 0.00 0.00 3.08
697 1771 0.106149 CCGTCAGCCCCAACTATACC 59.894 60.000 0.00 0.00 0.00 2.73
698 1772 0.828677 ACCGTCAGCCCCAACTATAC 59.171 55.000 0.00 0.00 0.00 1.47
699 1773 2.034124 GTACCGTCAGCCCCAACTATA 58.966 52.381 0.00 0.00 0.00 1.31
700 1774 0.828677 GTACCGTCAGCCCCAACTAT 59.171 55.000 0.00 0.00 0.00 2.12
701 1775 0.542467 TGTACCGTCAGCCCCAACTA 60.542 55.000 0.00 0.00 0.00 2.24
702 1776 1.198759 ATGTACCGTCAGCCCCAACT 61.199 55.000 0.00 0.00 0.00 3.16
743 1884 6.922980 CAGTGATCTAATTTTTGTGCACTG 57.077 37.500 19.41 0.00 43.74 3.66
761 1902 7.797038 AGACATATACACGTACATACAGTGA 57.203 36.000 15.85 5.51 35.89 3.41
794 1935 2.838736 ACCCGATTAGCATGACATGTC 58.161 47.619 19.27 19.27 0.00 3.06
898 2052 0.821517 TATGGGTCGTCATGTTCGCT 59.178 50.000 7.84 0.00 0.00 4.93
976 2146 2.683867 CGTCTTCCCTCGGCTATATAGG 59.316 54.545 11.72 0.00 0.00 2.57
1027 2197 1.527380 GGTGGTTGCACCGGAAGAA 60.527 57.895 9.46 0.00 42.58 2.52
1057 2240 1.153804 GAGGAAGAAGACCGCGGAC 60.154 63.158 35.90 27.70 0.00 4.79
1233 2422 2.264794 GAGTTGGGCGACGACCAT 59.735 61.111 26.08 10.02 42.18 3.55
1398 2587 1.612462 CCTTTGACCAGCTGCAGATCA 60.612 52.381 20.43 11.89 0.00 2.92
1525 2714 1.680735 GTGGTCAAATGACTGCCACAA 59.319 47.619 12.87 0.00 44.20 3.33
1632 2824 1.891919 GTTGAGCGTGAGGTTGCCA 60.892 57.895 0.00 0.00 45.11 4.92
1668 2860 1.988406 GAAGTAGGTGACGGGGGCT 60.988 63.158 0.00 0.00 0.00 5.19
1716 2908 2.055100 GTGAGCGTGACTGTCTTCTTC 58.945 52.381 9.51 3.21 0.00 2.87
1719 2911 0.040336 TCGTGAGCGTGACTGTCTTC 60.040 55.000 9.51 1.84 39.49 2.87
1803 3004 1.138883 CTCCGCGTAGTTGCTGCTA 59.861 57.895 4.92 0.00 0.00 3.49
1817 3018 3.989698 AACATGTCGCCGCTCTCCG 62.990 63.158 0.00 0.00 0.00 4.63
1818 3019 2.125512 AACATGTCGCCGCTCTCC 60.126 61.111 0.00 0.00 0.00 3.71
1843 3044 4.838486 GTCCGAGTCGAGGCGCAG 62.838 72.222 15.64 0.00 0.00 5.18
1902 3103 4.057428 GACCACTGCTCCGTCGCT 62.057 66.667 0.00 0.00 0.00 4.93
2352 3553 1.372997 CGCGTTAGTGGTGCTGACT 60.373 57.895 0.00 0.00 32.19 3.41
2412 3617 7.540474 TGCTAGTAGTATGATTTTAGAGGGG 57.460 40.000 0.00 0.00 0.00 4.79
2487 3728 4.373348 ACCGTTCTGAATAGCTCTACAC 57.627 45.455 0.00 0.00 0.00 2.90
2492 3733 3.869832 GGGTTAACCGTTCTGAATAGCTC 59.130 47.826 18.39 0.00 36.71 4.09
2538 3802 7.902920 ACATTCCTAATAACAGGATGCAATT 57.097 32.000 0.00 0.00 44.26 2.32
2539 3803 7.902920 AACATTCCTAATAACAGGATGCAAT 57.097 32.000 0.00 0.00 44.26 3.56
2586 3874 9.314321 GCGGCAATATATATTAGTGTACATCTT 57.686 33.333 7.65 0.00 0.00 2.40
2621 3909 0.390860 ATGGCGAAGGAAGGAGATCG 59.609 55.000 0.00 0.00 38.28 3.69
2636 3924 1.729881 GATCAAACGGCTGGATGGC 59.270 57.895 0.00 0.00 37.94 4.40
2670 3958 2.847234 TGGACCCAACTCCGTGCT 60.847 61.111 0.00 0.00 32.22 4.40
2685 3989 0.944311 CTTGTTCGTCGTCCCACTGG 60.944 60.000 0.00 0.00 0.00 4.00
2701 4005 1.068333 CCGATTGAGGCCAACAACTTG 60.068 52.381 15.67 9.49 34.72 3.16
2707 4011 0.107214 TGGATCCGATTGAGGCCAAC 60.107 55.000 5.01 0.00 34.72 3.77
2728 4032 2.202756 GCCCTCGTCACCATCGTC 60.203 66.667 0.00 0.00 0.00 4.20
2729 4033 4.129737 CGCCCTCGTCACCATCGT 62.130 66.667 0.00 0.00 0.00 3.73
2731 4035 4.530857 CCCGCCCTCGTCACCATC 62.531 72.222 0.00 0.00 0.00 3.51
2747 4051 4.530857 CCTCATCGTCACCGCCCC 62.531 72.222 0.00 0.00 0.00 5.80
2755 4059 1.395826 CCCTCTCCACCCTCATCGTC 61.396 65.000 0.00 0.00 0.00 4.20
2768 4090 4.083862 GTCCCACACCGCCCTCTC 62.084 72.222 0.00 0.00 0.00 3.20
2816 4138 2.286523 CCCCACTCGAAGCTCCTGT 61.287 63.158 0.00 0.00 0.00 4.00
2817 4139 1.831652 AACCCCACTCGAAGCTCCTG 61.832 60.000 0.00 0.00 0.00 3.86
2818 4140 1.128188 AAACCCCACTCGAAGCTCCT 61.128 55.000 0.00 0.00 0.00 3.69
2819 4141 0.250770 AAAACCCCACTCGAAGCTCC 60.251 55.000 0.00 0.00 0.00 4.70
2841 4163 1.271054 CCTCCAACAGTCTTGACCCAG 60.271 57.143 0.00 0.00 0.00 4.45
2844 4166 2.930826 TTCCTCCAACAGTCTTGACC 57.069 50.000 0.00 0.00 0.00 4.02
2845 4167 4.938226 CCTAATTCCTCCAACAGTCTTGAC 59.062 45.833 0.00 0.00 0.00 3.18
2855 4177 0.837272 CCGAGCCCTAATTCCTCCAA 59.163 55.000 0.00 0.00 0.00 3.53
2863 4185 3.489513 GGCCACCCGAGCCCTAAT 61.490 66.667 0.00 0.00 45.16 1.73
2947 4274 2.661537 TTGGCTCACTGACGCGTG 60.662 61.111 20.70 5.54 36.25 5.34
2961 4288 1.078497 TACTGCATCCTGCCGTTGG 60.078 57.895 1.58 0.00 44.23 3.77
2963 4290 1.447838 CGTACTGCATCCTGCCGTT 60.448 57.895 1.58 0.00 44.23 4.44
2975 4310 2.496817 GGCTCCTCTGCCGTACTG 59.503 66.667 0.00 0.00 43.74 2.74
2988 4323 3.959991 GACCTGTTGGAGCCGGCTC 62.960 68.421 42.46 42.46 42.04 4.70
2993 4328 1.450312 CGATGGACCTGTTGGAGCC 60.450 63.158 0.00 0.00 37.04 4.70
2994 4329 2.109126 GCGATGGACCTGTTGGAGC 61.109 63.158 0.00 0.00 37.04 4.70
3024 4359 3.316573 CTCTCCACCCTCAACGCCC 62.317 68.421 0.00 0.00 0.00 6.13
3025 4360 2.266055 CTCTCCACCCTCAACGCC 59.734 66.667 0.00 0.00 0.00 5.68
3027 4362 2.982130 CCCTCTCCACCCTCAACG 59.018 66.667 0.00 0.00 0.00 4.10
3028 4363 1.779061 TTGCCCTCTCCACCCTCAAC 61.779 60.000 0.00 0.00 0.00 3.18
3030 4365 1.920325 CTTGCCCTCTCCACCCTCA 60.920 63.158 0.00 0.00 0.00 3.86
3032 4367 2.612115 CCTTGCCCTCTCCACCCT 60.612 66.667 0.00 0.00 0.00 4.34
3036 4371 1.463214 TCCAACCTTGCCCTCTCCA 60.463 57.895 0.00 0.00 0.00 3.86
3037 4372 1.002011 GTCCAACCTTGCCCTCTCC 60.002 63.158 0.00 0.00 0.00 3.71
3038 4373 0.322008 CTGTCCAACCTTGCCCTCTC 60.322 60.000 0.00 0.00 0.00 3.20
3039 4374 1.763770 CTGTCCAACCTTGCCCTCT 59.236 57.895 0.00 0.00 0.00 3.69
3040 4375 1.303643 CCTGTCCAACCTTGCCCTC 60.304 63.158 0.00 0.00 0.00 4.30
3041 4376 1.360393 TTCCTGTCCAACCTTGCCCT 61.360 55.000 0.00 0.00 0.00 5.19
3042 4377 0.469144 TTTCCTGTCCAACCTTGCCC 60.469 55.000 0.00 0.00 0.00 5.36
3046 4381 3.555966 CACTCTTTTCCTGTCCAACCTT 58.444 45.455 0.00 0.00 0.00 3.50
3047 4382 2.158608 CCACTCTTTTCCTGTCCAACCT 60.159 50.000 0.00 0.00 0.00 3.50
3048 4383 2.230660 CCACTCTTTTCCTGTCCAACC 58.769 52.381 0.00 0.00 0.00 3.77
3050 4385 1.144913 CCCCACTCTTTTCCTGTCCAA 59.855 52.381 0.00 0.00 0.00 3.53
3052 4387 0.771755 ACCCCACTCTTTTCCTGTCC 59.228 55.000 0.00 0.00 0.00 4.02
3053 4388 1.420138 TCACCCCACTCTTTTCCTGTC 59.580 52.381 0.00 0.00 0.00 3.51
3054 4389 1.518367 TCACCCCACTCTTTTCCTGT 58.482 50.000 0.00 0.00 0.00 4.00
3056 4391 3.117131 ACAATTCACCCCACTCTTTTCCT 60.117 43.478 0.00 0.00 0.00 3.36
3058 4393 3.888930 TGACAATTCACCCCACTCTTTTC 59.111 43.478 0.00 0.00 0.00 2.29
3059 4394 3.909732 TGACAATTCACCCCACTCTTTT 58.090 40.909 0.00 0.00 0.00 2.27
3060 4395 3.593442 TGACAATTCACCCCACTCTTT 57.407 42.857 0.00 0.00 0.00 2.52
3061 4396 3.222603 GTTGACAATTCACCCCACTCTT 58.777 45.455 0.00 0.00 0.00 2.85
3062 4397 2.174639 TGTTGACAATTCACCCCACTCT 59.825 45.455 0.00 0.00 0.00 3.24
3064 4399 2.693074 GTTGTTGACAATTCACCCCACT 59.307 45.455 0.00 0.00 38.24 4.00
3065 4400 2.693074 AGTTGTTGACAATTCACCCCAC 59.307 45.455 0.00 0.00 38.24 4.61
3067 4402 2.693074 ACAGTTGTTGACAATTCACCCC 59.307 45.455 0.00 0.00 38.24 4.95
3068 4403 3.380004 TCACAGTTGTTGACAATTCACCC 59.620 43.478 0.00 0.00 38.24 4.61
3070 4405 4.037690 GCTCACAGTTGTTGACAATTCAC 58.962 43.478 0.00 0.00 38.24 3.18
3072 4407 4.558538 AGCTCACAGTTGTTGACAATTC 57.441 40.909 0.00 0.00 38.24 2.17
3073 4408 4.989279 AAGCTCACAGTTGTTGACAATT 57.011 36.364 0.00 0.00 38.24 2.32
3074 4409 4.398988 TGAAAGCTCACAGTTGTTGACAAT 59.601 37.500 0.00 0.00 38.24 2.71
3075 4410 3.755905 TGAAAGCTCACAGTTGTTGACAA 59.244 39.130 0.00 0.00 0.00 3.18
3076 4411 3.342719 TGAAAGCTCACAGTTGTTGACA 58.657 40.909 0.00 0.00 0.00 3.58
3077 4412 3.623060 TCTGAAAGCTCACAGTTGTTGAC 59.377 43.478 16.13 0.00 35.84 3.18
3078 4413 3.623060 GTCTGAAAGCTCACAGTTGTTGA 59.377 43.478 16.13 0.00 35.84 3.18
3079 4414 3.544834 CGTCTGAAAGCTCACAGTTGTTG 60.545 47.826 16.13 4.03 35.84 3.33
3081 4416 2.205074 CGTCTGAAAGCTCACAGTTGT 58.795 47.619 16.13 0.00 35.84 3.32
3083 4418 2.205074 CACGTCTGAAAGCTCACAGTT 58.795 47.619 16.13 0.00 35.84 3.16
3084 4419 1.858091 CACGTCTGAAAGCTCACAGT 58.142 50.000 16.13 0.61 35.84 3.55
3085 4420 0.510359 GCACGTCTGAAAGCTCACAG 59.490 55.000 12.14 12.14 35.72 3.66
3086 4421 0.179086 TGCACGTCTGAAAGCTCACA 60.179 50.000 0.00 0.00 0.00 3.58
3088 4423 1.330521 GTTTGCACGTCTGAAAGCTCA 59.669 47.619 0.00 0.00 0.00 4.26
3089 4424 1.334149 GGTTTGCACGTCTGAAAGCTC 60.334 52.381 0.00 0.00 0.00 4.09
3090 4425 0.663153 GGTTTGCACGTCTGAAAGCT 59.337 50.000 0.00 0.00 0.00 3.74
3091 4426 0.380378 TGGTTTGCACGTCTGAAAGC 59.620 50.000 0.00 0.00 0.00 3.51
3092 4427 1.670811 ACTGGTTTGCACGTCTGAAAG 59.329 47.619 0.00 0.00 0.00 2.62
3093 4428 1.668751 GACTGGTTTGCACGTCTGAAA 59.331 47.619 0.00 0.00 0.00 2.69
3094 4429 1.295792 GACTGGTTTGCACGTCTGAA 58.704 50.000 0.00 0.00 0.00 3.02
3095 4430 0.531974 GGACTGGTTTGCACGTCTGA 60.532 55.000 0.00 0.00 0.00 3.27
3096 4431 0.813610 TGGACTGGTTTGCACGTCTG 60.814 55.000 0.00 0.00 0.00 3.51
3097 4432 0.532862 CTGGACTGGTTTGCACGTCT 60.533 55.000 0.00 0.00 0.00 4.18
3098 4433 1.941812 CTGGACTGGTTTGCACGTC 59.058 57.895 0.00 0.00 0.00 4.34
3103 4503 1.187567 ATTGGGCTGGACTGGTTTGC 61.188 55.000 0.00 0.00 0.00 3.68
3145 4545 5.505181 TTTCTTCCCTATATGCCTGGATC 57.495 43.478 0.00 0.00 0.00 3.36
3152 4552 5.693814 CGCTCATTTTTCTTCCCTATATGC 58.306 41.667 0.00 0.00 0.00 3.14
3168 4667 1.896220 TTTCAACTCTGGCGCTCATT 58.104 45.000 7.64 0.00 0.00 2.57
3169 4668 1.896220 TTTTCAACTCTGGCGCTCAT 58.104 45.000 7.64 0.00 0.00 2.90
3178 4677 4.469469 TCCTTGGGGAATTTTCAACTCT 57.531 40.909 0.00 0.00 38.93 3.24
3213 4712 2.159170 AGACGAGATAACAGCCAGAAGC 60.159 50.000 0.00 0.00 44.25 3.86
3295 4879 7.265693 GAAAAGGACATAATCTTTTTCGTGC 57.734 36.000 8.04 0.00 46.92 5.34
3356 5197 2.027745 TGACCTCCTGATTTCTGTCTGC 60.028 50.000 0.00 0.00 0.00 4.26
3359 5200 4.543590 TCTTGACCTCCTGATTTCTGTC 57.456 45.455 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.