Multiple sequence alignment - TraesCS1A01G357300

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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 TraesCS1A01G357300 chr1A 100.000 5502 0 0 934 6435 539969083 539963582 0.000000e+00 10161.0
1 TraesCS1A01G357300 chr1A 100.000 798 0 0 1 798 539970016 539969219 0.000000e+00 1474.0
2 TraesCS1A01G357300 chr1A 86.598 97 8 4 216 310 85909910 85909817 1.140000e-17 102.0
3 TraesCS1A01G357300 chr1A 83.673 98 6 5 3214 3310 490312117 490312205 4.130000e-12 84.2
4 TraesCS1A01G357300 chr1B 94.529 3802 148 26 1996 5754 604314494 604310710 0.000000e+00 5814.0
5 TraesCS1A01G357300 chr1B 87.414 723 47 19 934 1622 604317401 604316689 0.000000e+00 791.0
6 TraesCS1A01G357300 chr1B 92.537 335 17 4 1669 1997 604314856 604314524 2.100000e-129 473.0
7 TraesCS1A01G357300 chr1B 93.478 46 3 0 3214 3259 509149862 509149817 1.160000e-07 69.4
8 TraesCS1A01G357300 chr1D 93.736 3225 127 28 1996 5180 444338736 444335547 0.000000e+00 4767.0
9 TraesCS1A01G357300 chr1D 87.727 1100 66 23 934 1983 444339866 444338786 0.000000e+00 1219.0
10 TraesCS1A01G357300 chr1D 92.389 565 29 1 5206 5756 444335551 444334987 0.000000e+00 793.0
11 TraesCS1A01G357300 chr1D 86.286 700 47 22 5771 6435 444335002 444334317 0.000000e+00 715.0
12 TraesCS1A01G357300 chr1D 86.498 237 12 5 1 227 444340640 444340414 6.450000e-60 243.0
13 TraesCS1A01G357300 chr1D 82.639 288 22 5 255 515 444340413 444340127 5.020000e-56 230.0
14 TraesCS1A01G357300 chr1D 83.858 254 14 9 533 783 444340139 444339910 3.910000e-52 217.0
15 TraesCS1A01G357300 chr4A 88.889 99 7 2 213 310 38657164 38657259 1.130000e-22 119.0
16 TraesCS1A01G357300 chr3B 83.654 104 6 6 3209 3311 621148530 621148623 3.200000e-13 87.9
17 TraesCS1A01G357300 chr3B 82.105 95 6 7 3214 3307 126580149 126580065 3.220000e-08 71.3
18 TraesCS1A01G357300 chr3B 95.556 45 1 1 3214 3257 241680509 241680465 3.220000e-08 71.3
19 TraesCS1A01G357300 chr3B 88.679 53 5 1 3265 3316 224311020 224311072 5.390000e-06 63.9
20 TraesCS1A01G357300 chr3A 95.455 44 1 1 3215 3257 203994037 203993994 1.160000e-07 69.4
21 TraesCS1A01G357300 chr6D 91.837 49 2 2 3211 3257 166762400 166762448 4.160000e-07 67.6
22 TraesCS1A01G357300 chr5D 95.349 43 1 1 3265 3307 530425981 530426022 4.160000e-07 67.6
23 TraesCS1A01G357300 chr5A 95.349 43 1 1 3265 3307 658671550 658671591 4.160000e-07 67.6


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 TraesCS1A01G357300 chr1A 539963582 539970016 6434 True 5817.500000 10161 100.000000 1 6435 2 chr1A.!!$R2 6434
1 TraesCS1A01G357300 chr1B 604310710 604317401 6691 True 2359.333333 5814 91.493333 934 5754 3 chr1B.!!$R2 4820
2 TraesCS1A01G357300 chr1D 444334317 444340640 6323 True 1169.142857 4767 87.590429 1 6435 7 chr1D.!!$R1 6434

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
558 595 0.033228 CACATGGCGGCAAAAGGAAA 59.967 50.000 18.31 0.0 0.00 3.13 F
563 600 0.320683 GGCGGCAAAAGGAAAATGCT 60.321 50.000 3.07 0.0 39.94 3.79 F
1489 1556 0.528017 ACGATCTGCTCTGCTTCGAA 59.472 50.000 0.00 0.0 33.28 3.71 F
2124 4059 0.031178 GCTGCTGTTGGGAACACAAG 59.969 55.000 0.00 0.0 42.67 3.16 F
2563 4503 2.147958 GGTAAGCCATTCGTTGACACA 58.852 47.619 0.00 0.0 34.09 3.72 F
2564 4504 2.550606 GGTAAGCCATTCGTTGACACAA 59.449 45.455 0.00 0.0 34.09 3.33 F
2770 4730 2.818130 TTGGCCTTTTTGACAGCATC 57.182 45.000 3.32 0.0 0.00 3.91 F
4310 6281 0.466543 TAGGCGCGATGGGTTACATT 59.533 50.000 12.10 0.0 40.72 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 3600 0.541392 ATTAGCAGCCGGACATCACA 59.459 50.000 5.05 0.0 0.00 3.58 R
1853 3734 0.944386 GCAGGCTTTGAGACGAAACA 59.056 50.000 0.00 0.0 0.00 2.83 R
2564 4504 0.773644 ACCCAGGTCAAACAGATGCT 59.226 50.000 0.00 0.0 0.00 3.79 R
3968 5939 0.178992 CAGGCCTTTCCAAGTGACCA 60.179 55.000 0.00 0.0 37.29 4.02 R
4069 6040 1.867233 TGAAAGACGCAGAAGCTGTTC 59.133 47.619 0.00 0.0 39.10 3.18 R
4214 6185 3.994392 CCCACACCGAAAGATATATTCCG 59.006 47.826 0.00 0.0 0.00 4.30 R
4577 6548 5.512942 TTCCATCCTTTTCACCAGATGTA 57.487 39.130 0.00 0.0 35.42 2.29 R
5478 7479 0.034756 TGCGCCTTGAGCTAAGAACA 59.965 50.000 4.18 0.0 38.76 3.18 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 3.718434 AGGCTGATTGAGGTGGATTATGA 59.282 43.478 0.00 0.00 0.00 2.15
72 73 5.474876 ACAATCCAGTTCTTCCAATCAGTTC 59.525 40.000 0.00 0.00 0.00 3.01
88 95 7.380602 CCAATCAGTTCTTTGTCAATTGTTCTC 59.619 37.037 5.13 0.00 0.00 2.87
99 106 5.827797 TGTCAATTGTTCTCTTTGGCTAACT 59.172 36.000 5.13 0.00 0.00 2.24
119 127 7.491696 GCTAACTAGATAATTGGTTTCACGACT 59.508 37.037 0.00 0.00 0.00 4.18
120 128 7.596749 AACTAGATAATTGGTTTCACGACTG 57.403 36.000 0.00 0.00 0.00 3.51
175 186 4.944619 AGTATAGTATGCTGCAGCTCAA 57.055 40.909 36.61 19.72 42.66 3.02
181 192 0.596577 ATGCTGCAGCTCAACAACTG 59.403 50.000 36.61 0.00 42.66 3.16
187 198 2.565210 CAGCTCAACAACTGCAAACA 57.435 45.000 0.00 0.00 0.00 2.83
216 227 2.364632 TGCATTTCCCGTCGAATCATT 58.635 42.857 0.00 0.00 0.00 2.57
237 248 1.834188 TTTTCGATCAAAGGGGAGCC 58.166 50.000 0.00 0.00 0.00 4.70
238 249 0.034477 TTTCGATCAAAGGGGAGCCC 60.034 55.000 0.00 0.00 45.90 5.19
293 304 5.382303 CACGACAACCATACAAAACATCTC 58.618 41.667 0.00 0.00 0.00 2.75
320 331 0.178990 ACCAGGTTCTGAAAGCCACC 60.179 55.000 0.00 0.00 37.30 4.61
339 351 0.881796 CGAGGCAAGGGAAAGGAAAC 59.118 55.000 0.00 0.00 0.00 2.78
347 359 3.223674 AGGGAAAGGAAACGACAACAT 57.776 42.857 0.00 0.00 0.00 2.71
350 362 3.316868 GGGAAAGGAAACGACAACATCAA 59.683 43.478 0.00 0.00 0.00 2.57
361 373 1.073125 ACAACATCAACCATCCCGTCA 59.927 47.619 0.00 0.00 0.00 4.35
378 415 1.798813 GTCAATGTCGTGTGGGTCTTC 59.201 52.381 0.00 0.00 0.00 2.87
389 426 1.067776 GTGGGTCTTCCGTGTACTCTG 60.068 57.143 0.00 0.00 38.76 3.35
411 448 7.148641 TCTGTTTTTCTTTAAATTATGCCGCA 58.851 30.769 0.00 0.00 0.00 5.69
412 449 7.328249 TCTGTTTTTCTTTAAATTATGCCGCAG 59.672 33.333 0.00 0.00 0.00 5.18
425 462 2.171940 CGCAGTTCTGCTTCGCAC 59.828 61.111 20.12 0.00 33.79 5.34
428 465 1.831389 GCAGTTCTGCTTCGCACGAA 61.831 55.000 16.29 5.26 33.79 3.85
444 481 3.053831 ACGAAACGTGGGAATGAAGAT 57.946 42.857 0.00 0.00 39.18 2.40
445 482 4.196626 ACGAAACGTGGGAATGAAGATA 57.803 40.909 0.00 0.00 39.18 1.98
446 483 4.766375 ACGAAACGTGGGAATGAAGATAT 58.234 39.130 0.00 0.00 39.18 1.63
453 490 8.924511 AACGTGGGAATGAAGATATATTTGAT 57.075 30.769 0.00 0.00 0.00 2.57
497 534 1.069227 CAGCAACAAAGTACGCCTTCC 60.069 52.381 0.00 0.00 31.27 3.46
501 538 2.875933 CAACAAAGTACGCCTTCCTGAA 59.124 45.455 0.00 0.00 31.27 3.02
502 539 3.418684 ACAAAGTACGCCTTCCTGAAT 57.581 42.857 0.00 0.00 31.27 2.57
503 540 3.074412 ACAAAGTACGCCTTCCTGAATG 58.926 45.455 0.00 0.00 31.27 2.67
504 541 3.244422 ACAAAGTACGCCTTCCTGAATGA 60.244 43.478 0.00 0.00 31.27 2.57
505 542 3.695830 AAGTACGCCTTCCTGAATGAA 57.304 42.857 0.00 0.00 0.00 2.57
506 543 3.695830 AGTACGCCTTCCTGAATGAAA 57.304 42.857 0.00 0.00 0.00 2.69
507 544 4.222124 AGTACGCCTTCCTGAATGAAAT 57.778 40.909 0.00 0.00 0.00 2.17
508 545 3.941483 AGTACGCCTTCCTGAATGAAATG 59.059 43.478 0.00 0.00 0.00 2.32
509 546 1.474077 ACGCCTTCCTGAATGAAATGC 59.526 47.619 0.00 0.00 0.00 3.56
510 547 1.473677 CGCCTTCCTGAATGAAATGCA 59.526 47.619 0.00 0.00 0.00 3.96
511 548 2.733227 CGCCTTCCTGAATGAAATGCAC 60.733 50.000 0.00 0.00 0.00 4.57
512 549 2.231964 GCCTTCCTGAATGAAATGCACA 59.768 45.455 0.00 0.00 0.00 4.57
513 550 3.118884 GCCTTCCTGAATGAAATGCACAT 60.119 43.478 0.00 0.00 0.00 3.21
514 551 4.430007 CCTTCCTGAATGAAATGCACATG 58.570 43.478 0.00 0.00 0.00 3.21
515 552 4.081862 CCTTCCTGAATGAAATGCACATGT 60.082 41.667 0.00 0.00 0.00 3.21
516 553 5.471556 TTCCTGAATGAAATGCACATGTT 57.528 34.783 0.00 0.00 0.00 2.71
517 554 5.063180 TCCTGAATGAAATGCACATGTTC 57.937 39.130 0.00 0.00 0.00 3.18
518 555 4.768448 TCCTGAATGAAATGCACATGTTCT 59.232 37.500 0.00 0.00 0.00 3.01
519 556 5.945191 TCCTGAATGAAATGCACATGTTCTA 59.055 36.000 0.00 0.00 0.00 2.10
520 557 6.433716 TCCTGAATGAAATGCACATGTTCTAA 59.566 34.615 0.00 0.00 0.00 2.10
521 558 7.039853 TCCTGAATGAAATGCACATGTTCTAAA 60.040 33.333 0.00 0.00 0.00 1.85
522 559 7.599621 CCTGAATGAAATGCACATGTTCTAAAA 59.400 33.333 0.00 0.00 0.00 1.52
523 560 8.883954 TGAATGAAATGCACATGTTCTAAAAA 57.116 26.923 0.00 0.00 0.00 1.94
555 592 2.432972 GCACATGGCGGCAAAAGG 60.433 61.111 18.31 8.78 0.00 3.11
558 595 0.033228 CACATGGCGGCAAAAGGAAA 59.967 50.000 18.31 0.00 0.00 3.13
559 596 0.755686 ACATGGCGGCAAAAGGAAAA 59.244 45.000 18.31 0.00 0.00 2.29
562 599 0.602372 TGGCGGCAAAAGGAAAATGC 60.602 50.000 10.22 0.00 39.33 3.56
563 600 0.320683 GGCGGCAAAAGGAAAATGCT 60.321 50.000 3.07 0.00 39.94 3.79
573 610 7.360353 GGCAAAAGGAAAATGCTGAAAATACTC 60.360 37.037 0.00 0.00 39.94 2.59
574 611 7.619982 GCAAAAGGAAAATGCTGAAAATACTCG 60.620 37.037 0.00 0.00 37.12 4.18
582 619 3.188460 TGCTGAAAATACTCGAAACCAGC 59.812 43.478 0.00 0.00 44.11 4.85
596 633 4.143305 CGAAACCAGCTCGTAGAAGAAAAG 60.143 45.833 0.00 0.00 34.09 2.27
597 634 4.602340 AACCAGCTCGTAGAAGAAAAGA 57.398 40.909 0.00 0.00 34.09 2.52
602 639 6.136743 CCAGCTCGTAGAAGAAAAGAAAAAC 58.863 40.000 0.00 0.00 34.09 2.43
722 761 0.804989 CGGTTAGGAGCAAGGCAAAG 59.195 55.000 0.00 0.00 0.00 2.77
724 763 1.539157 GTTAGGAGCAAGGCAAAGCT 58.461 50.000 0.00 0.00 45.25 3.74
737 776 4.718961 AGGCAAAGCTGTTAAGAAAGAGA 58.281 39.130 0.00 0.00 0.00 3.10
780 819 4.208686 GCCGGTACTCCTCGCTGG 62.209 72.222 1.90 0.00 37.10 4.85
781 820 4.208686 CCGGTACTCCTCGCTGGC 62.209 72.222 0.00 0.00 35.26 4.85
782 821 3.141488 CGGTACTCCTCGCTGGCT 61.141 66.667 0.00 0.00 35.26 4.75
783 822 2.809010 GGTACTCCTCGCTGGCTC 59.191 66.667 0.00 0.00 35.26 4.70
784 823 2.409651 GTACTCCTCGCTGGCTCG 59.590 66.667 0.00 0.00 35.26 5.03
785 824 3.518998 TACTCCTCGCTGGCTCGC 61.519 66.667 0.00 0.00 35.26 5.03
786 825 3.997400 TACTCCTCGCTGGCTCGCT 62.997 63.158 0.00 0.00 35.26 4.93
787 826 2.604299 TACTCCTCGCTGGCTCGCTA 62.604 60.000 0.00 0.00 35.26 4.26
1028 1067 1.599667 GCAGACAAGTCACGACGAGAA 60.600 52.381 0.00 0.00 36.20 2.87
1054 1094 4.473520 CGGCAATGGCGTCCTCCT 62.474 66.667 21.27 0.00 46.33 3.69
1055 1095 2.514824 GGCAATGGCGTCCTCCTC 60.515 66.667 0.00 0.00 42.47 3.71
1100 1140 1.361668 CGACCTTGGCAAGATGACCG 61.362 60.000 28.18 17.57 0.00 4.79
1208 1251 4.135306 AGCTTGTGATAGATTGCTGATGG 58.865 43.478 0.00 0.00 0.00 3.51
1209 1252 3.881688 GCTTGTGATAGATTGCTGATGGT 59.118 43.478 0.00 0.00 0.00 3.55
1210 1253 4.337555 GCTTGTGATAGATTGCTGATGGTT 59.662 41.667 0.00 0.00 0.00 3.67
1215 1272 5.587844 GTGATAGATTGCTGATGGTTCTTGT 59.412 40.000 0.00 0.00 0.00 3.16
1223 1280 3.635331 CTGATGGTTCTTGTTTGTGCTG 58.365 45.455 0.00 0.00 0.00 4.41
1448 1515 5.410067 CCATCTCTTCTCTTCTTCAGTGAC 58.590 45.833 0.00 0.00 0.00 3.67
1474 1541 2.114670 CCCATTTCCTGCGCACGAT 61.115 57.895 5.66 0.00 0.00 3.73
1476 1543 1.091771 CCATTTCCTGCGCACGATCT 61.092 55.000 5.66 0.00 0.00 2.75
1489 1556 0.528017 ACGATCTGCTCTGCTTCGAA 59.472 50.000 0.00 0.00 33.28 3.71
1490 1557 1.198767 CGATCTGCTCTGCTTCGAAG 58.801 55.000 21.02 21.02 31.73 3.79
1563 1639 1.594862 GAATTCGCAACGCAGATAGCT 59.405 47.619 0.00 0.00 42.61 3.32
1575 1651 4.202253 ACGCAGATAGCTTCACAATGGATA 60.202 41.667 0.00 0.00 42.61 2.59
1599 1685 2.028839 TGCCAGCTCAATTGTTCATTGG 60.029 45.455 5.13 8.67 42.52 3.16
1696 3577 1.961394 GAGTGCCGTATGGGTCATCTA 59.039 52.381 2.41 0.00 38.44 1.98
1719 3600 2.362503 TCGATGGCGACCTCCACT 60.363 61.111 0.00 0.00 42.51 4.00
1759 3640 0.532862 CACTTTCTGCAGACCACCGT 60.533 55.000 18.03 6.33 0.00 4.83
1813 3694 4.529716 TTAACCAGGAGAAAGGTTTGGT 57.470 40.909 1.84 0.00 45.46 3.67
1936 3828 2.751837 CCTTTTCGAGGCTGCCCC 60.752 66.667 16.57 1.39 39.09 5.80
1940 3832 1.178534 TTTTCGAGGCTGCCCCTTTG 61.179 55.000 16.57 0.66 46.60 2.77
1970 3864 3.849527 AGGGGAAAAGAGCAAAGAATGT 58.150 40.909 0.00 0.00 0.00 2.71
1983 3877 9.066892 AGAGCAAAGAATGTCTGTTAATTTGTA 57.933 29.630 0.00 0.00 0.00 2.41
1984 3878 9.118236 GAGCAAAGAATGTCTGTTAATTTGTAC 57.882 33.333 0.00 0.00 0.00 2.90
1991 3885 5.126779 TGTCTGTTAATTTGTACTGTGCCA 58.873 37.500 0.00 0.00 0.00 4.92
2003 3934 5.995446 TGTACTGTGCCATGTAAATCCATA 58.005 37.500 0.00 0.00 0.00 2.74
2021 3952 5.359756 TCCATAGCGCTTTATATGCATAGG 58.640 41.667 18.68 1.59 0.00 2.57
2056 3987 8.115520 GCTTAAATCTGCAGATTGATATCGATC 58.884 37.037 36.16 21.20 43.41 3.69
2124 4059 0.031178 GCTGCTGTTGGGAACACAAG 59.969 55.000 0.00 0.00 42.67 3.16
2210 4145 9.958180 TGTTATCTCATTTGTTGGAGAAGAATA 57.042 29.630 0.00 0.00 42.90 1.75
2561 4501 2.552599 TGGTAAGCCATTCGTTGACA 57.447 45.000 0.00 0.00 40.46 3.58
2563 4503 2.147958 GGTAAGCCATTCGTTGACACA 58.852 47.619 0.00 0.00 34.09 3.72
2564 4504 2.550606 GGTAAGCCATTCGTTGACACAA 59.449 45.455 0.00 0.00 34.09 3.33
2565 4505 3.364964 GGTAAGCCATTCGTTGACACAAG 60.365 47.826 0.00 0.00 34.09 3.16
2718 4678 4.320567 CGATGTCGCTGAACTCAGGTATAT 60.321 45.833 8.74 0.00 43.94 0.86
2719 4679 5.106673 CGATGTCGCTGAACTCAGGTATATA 60.107 44.000 8.74 0.00 43.94 0.86
2720 4680 5.690997 TGTCGCTGAACTCAGGTATATAG 57.309 43.478 8.74 0.00 43.94 1.31
2721 4681 4.023107 TGTCGCTGAACTCAGGTATATAGC 60.023 45.833 8.74 3.65 43.94 2.97
2722 4682 4.216687 GTCGCTGAACTCAGGTATATAGCT 59.783 45.833 8.67 8.67 43.94 3.32
2723 4683 5.411977 GTCGCTGAACTCAGGTATATAGCTA 59.588 44.000 13.91 0.00 43.94 3.32
2724 4684 5.644206 TCGCTGAACTCAGGTATATAGCTAG 59.356 44.000 13.91 13.22 43.94 3.42
2725 4685 5.644206 CGCTGAACTCAGGTATATAGCTAGA 59.356 44.000 13.91 12.26 43.94 2.43
2767 4727 2.888834 TCTTTGGCCTTTTTGACAGC 57.111 45.000 3.32 0.00 0.00 4.40
2770 4730 2.818130 TTGGCCTTTTTGACAGCATC 57.182 45.000 3.32 0.00 0.00 3.91
2811 4773 9.461312 TGTGGTTACTGAAATAAAAGCTCATAT 57.539 29.630 0.00 0.00 0.00 1.78
2841 4803 8.253810 TGGTTTCTGTCACATAAAACATTTCAA 58.746 29.630 14.57 0.00 34.15 2.69
2898 4860 8.622948 ACAATTAGGCTAATAAATGCTACTCC 57.377 34.615 19.53 0.00 0.00 3.85
2899 4861 7.665974 ACAATTAGGCTAATAAATGCTACTCCC 59.334 37.037 19.53 0.00 0.00 4.30
2900 4862 7.575499 ATTAGGCTAATAAATGCTACTCCCT 57.425 36.000 17.92 0.00 0.00 4.20
2901 4863 5.491323 AGGCTAATAAATGCTACTCCCTC 57.509 43.478 0.00 0.00 0.00 4.30
2902 4864 4.021016 AGGCTAATAAATGCTACTCCCTCG 60.021 45.833 0.00 0.00 0.00 4.63
2905 4867 5.047519 GCTAATAAATGCTACTCCCTCGGTA 60.048 44.000 0.00 0.00 0.00 4.02
2906 4868 5.881923 AATAAATGCTACTCCCTCGGTAA 57.118 39.130 0.00 0.00 0.00 2.85
2907 4869 5.881923 ATAAATGCTACTCCCTCGGTAAA 57.118 39.130 0.00 0.00 0.00 2.01
3068 5030 6.577427 GGTAAATCACTGCTAACAAACTTTCG 59.423 38.462 0.00 0.00 0.00 3.46
3162 5125 6.183361 ACAATCTGACATAGGCATAGCAGTTA 60.183 38.462 5.86 0.00 0.00 2.24
3176 5139 6.183360 GCATAGCAGTTACAATCTTGGGAAAT 60.183 38.462 0.00 0.00 0.00 2.17
3289 5253 7.541091 TGACAGTGTCAGAAAACGTCTTATATC 59.459 37.037 22.06 0.00 37.67 1.63
3315 5283 5.482878 AGTTACGGAGGGAGTATCTGAAAAA 59.517 40.000 0.00 0.00 33.73 1.94
3345 5313 5.047235 GGTTATCGGCTGGTATCTAATCAGT 60.047 44.000 0.00 0.00 0.00 3.41
3401 5371 5.375417 TGGCTAAGATGTGATTTGTTGTG 57.625 39.130 0.00 0.00 0.00 3.33
3423 5393 4.082300 TGGTGCACTACTGCCATTATTTTG 60.082 41.667 17.98 0.00 43.51 2.44
3471 5442 3.942130 ATTAAAGCCACAGTTCAAGCC 57.058 42.857 0.00 0.00 0.00 4.35
3653 5624 8.396272 AGATATGTCCATATAAACCAAAGCAC 57.604 34.615 0.00 0.00 34.36 4.40
3656 5627 6.266168 TGTCCATATAAACCAAAGCACAAG 57.734 37.500 0.00 0.00 0.00 3.16
3817 5788 7.705325 AGTTACTAATGATAGTGGCGTTTGTAG 59.295 37.037 0.00 0.00 42.37 2.74
3902 5873 6.458888 GCAAGATGCTTCCAGTAAATACTTCC 60.459 42.308 0.00 0.00 40.96 3.46
3968 5939 3.513515 TGAAAGAACCAAACAACCAAGCT 59.486 39.130 0.00 0.00 0.00 3.74
4032 6003 7.062322 ACAATTGGATATGCAGGTTCATCTTA 58.938 34.615 10.83 0.00 0.00 2.10
4037 6008 6.712095 TGGATATGCAGGTTCATCTTATTCAC 59.288 38.462 0.00 0.00 0.00 3.18
4069 6040 5.109662 TCAGTTACTTCAGTGAAGACTCG 57.890 43.478 34.16 21.23 41.71 4.18
4093 6064 3.316308 ACAGCTTCTGCGTCTTTCAAATT 59.684 39.130 0.00 0.00 45.42 1.82
4214 6185 5.215160 CGGATAATAAGCAAGCAAATGGTC 58.785 41.667 0.00 0.00 0.00 4.02
4310 6281 0.466543 TAGGCGCGATGGGTTACATT 59.533 50.000 12.10 0.00 40.72 2.71
4385 6356 3.792956 GCATTCATTTGTACTTCATGCCG 59.207 43.478 0.00 0.00 0.00 5.69
4528 6499 2.039480 TGCTCCAGGGATCAATATCAGC 59.961 50.000 0.00 0.00 33.41 4.26
4577 6548 4.744795 TTGTTTTGTATGTTGCCACCTT 57.255 36.364 0.00 0.00 0.00 3.50
4776 6747 7.644945 TCATTTTCTCAATTGCTTACATATGCG 59.355 33.333 1.58 0.00 0.00 4.73
4989 6960 4.072131 TGACAGCTAAAATGGGAACTGAC 58.928 43.478 0.00 0.00 0.00 3.51
5095 7066 3.307379 GGGTGACGAGCCAATATCC 57.693 57.895 0.00 0.00 39.79 2.59
5098 7069 0.529773 GTGACGAGCCAATATCCGCA 60.530 55.000 0.00 0.00 0.00 5.69
5176 7177 8.892723 TGTTTCGCACATTTAATCTGATAAGAT 58.107 29.630 0.00 0.00 0.00 2.40
5177 7178 9.374960 GTTTCGCACATTTAATCTGATAAGATC 57.625 33.333 0.00 0.00 0.00 2.75
5178 7179 7.658179 TCGCACATTTAATCTGATAAGATCC 57.342 36.000 0.00 0.00 0.00 3.36
5179 7180 7.216494 TCGCACATTTAATCTGATAAGATCCA 58.784 34.615 0.00 0.00 0.00 3.41
5180 7181 7.879677 TCGCACATTTAATCTGATAAGATCCAT 59.120 33.333 0.00 0.00 0.00 3.41
5181 7182 8.173775 CGCACATTTAATCTGATAAGATCCATC 58.826 37.037 0.00 0.00 0.00 3.51
5182 7183 9.006839 GCACATTTAATCTGATAAGATCCATCA 57.993 33.333 7.25 7.25 0.00 3.07
5189 7190 7.974730 ATCTGATAAGATCCATCATAGCTCA 57.025 36.000 7.79 0.00 32.18 4.26
5190 7191 7.974730 TCTGATAAGATCCATCATAGCTCAT 57.025 36.000 7.79 0.00 32.18 2.90
5191 7192 7.783042 TCTGATAAGATCCATCATAGCTCATG 58.217 38.462 7.79 0.00 32.18 3.07
5192 7193 7.399478 TCTGATAAGATCCATCATAGCTCATGT 59.601 37.037 7.79 0.00 35.96 3.21
5193 7194 7.914859 TGATAAGATCCATCATAGCTCATGTT 58.085 34.615 0.00 0.00 35.96 2.71
5194 7195 8.380867 TGATAAGATCCATCATAGCTCATGTTT 58.619 33.333 0.00 0.00 35.96 2.83
5195 7196 6.879276 AAGATCCATCATAGCTCATGTTTG 57.121 37.500 0.00 0.00 35.96 2.93
5196 7197 5.314529 AGATCCATCATAGCTCATGTTTGG 58.685 41.667 0.00 5.71 38.91 3.28
5197 7198 3.824133 TCCATCATAGCTCATGTTTGGG 58.176 45.455 17.16 10.17 38.48 4.12
5242 7243 4.617253 TGTTGCATACTTCTGTAGGTGT 57.383 40.909 0.00 0.00 33.48 4.16
5265 7266 7.173907 GTGTGATCGGATTCTTTCATATGGAAT 59.826 37.037 2.13 4.24 34.91 3.01
5365 7366 3.254657 CCGAGGTTGAAGTTTTATGCCAA 59.745 43.478 0.00 0.00 0.00 4.52
5377 7378 8.962884 AAGTTTTATGCCAAAGAAAGTTTCAT 57.037 26.923 17.65 2.71 0.00 2.57
5419 7420 7.512058 ACCAATGTAGAGGTAGATGATCATCTT 59.488 37.037 36.46 22.75 45.31 2.40
5469 7470 1.694696 GAAGAACCCTGGACTGTGAGT 59.305 52.381 0.00 0.00 0.00 3.41
5478 7479 1.417517 TGGACTGTGAGTGAACATGCT 59.582 47.619 0.00 0.00 0.00 3.79
5582 7598 3.573967 GCATAATAGGGATTGGGTTGTGG 59.426 47.826 0.00 0.00 0.00 4.17
5700 7716 4.713814 ACAGGATCTGCAGAGAAATGAGTA 59.286 41.667 22.96 0.00 34.37 2.59
5708 7724 6.592994 TCTGCAGAGAAATGAGTAATGTTCTG 59.407 38.462 13.74 0.00 35.20 3.02
5712 7728 5.045286 AGAGAAATGAGTAATGTTCTGCCCT 60.045 40.000 0.00 0.00 30.56 5.19
5726 7742 5.710099 TGTTCTGCCCTTTTTCTTTATCGAT 59.290 36.000 2.16 2.16 0.00 3.59
5741 7757 2.736144 TCGATGTACCGTTCTTGCTT 57.264 45.000 0.00 0.00 0.00 3.91
5742 7758 2.602878 TCGATGTACCGTTCTTGCTTC 58.397 47.619 0.00 0.00 0.00 3.86
5743 7759 2.230508 TCGATGTACCGTTCTTGCTTCT 59.769 45.455 0.00 0.00 0.00 2.85
5744 7760 2.993899 CGATGTACCGTTCTTGCTTCTT 59.006 45.455 0.00 0.00 0.00 2.52
5745 7761 3.432252 CGATGTACCGTTCTTGCTTCTTT 59.568 43.478 0.00 0.00 0.00 2.52
5746 7762 4.084013 CGATGTACCGTTCTTGCTTCTTTT 60.084 41.667 0.00 0.00 0.00 2.27
5747 7763 5.560183 CGATGTACCGTTCTTGCTTCTTTTT 60.560 40.000 0.00 0.00 0.00 1.94
5815 7831 2.998316 AGCCACTGAAGATAAGAGCC 57.002 50.000 0.00 0.00 0.00 4.70
5830 7846 4.421952 GCCGGAGCTGCTAAGTAC 57.578 61.111 5.05 0.00 35.50 2.73
5832 7848 0.105039 GCCGGAGCTGCTAAGTACAT 59.895 55.000 5.05 0.00 35.50 2.29
5835 7851 2.604855 CCGGAGCTGCTAAGTACATACG 60.605 54.545 0.15 0.00 0.00 3.06
5838 7854 3.066342 GGAGCTGCTAAGTACATACGTGA 59.934 47.826 0.15 0.00 0.00 4.35
5842 7858 5.929992 AGCTGCTAAGTACATACGTGAAAAA 59.070 36.000 0.00 0.00 0.00 1.94
5866 7901 5.391312 AAAGTATTTCAGACCACATTGGC 57.609 39.130 0.00 0.00 34.95 4.52
5888 7923 5.818136 CGAAGCTGAAATTTCCTGGATTA 57.182 39.130 15.48 0.00 0.00 1.75
5890 7925 6.030228 CGAAGCTGAAATTTCCTGGATTAAC 58.970 40.000 15.48 0.80 0.00 2.01
5891 7926 5.567138 AGCTGAAATTTCCTGGATTAACG 57.433 39.130 15.48 0.00 0.00 3.18
5912 7947 5.482908 ACGATTCAGAAGCATCTTGTTACT 58.517 37.500 0.00 0.00 32.03 2.24
5926 7961 7.095774 GCATCTTGTTACTTTCGAACTTGAGTA 60.096 37.037 0.00 0.00 0.00 2.59
5927 7962 7.925703 TCTTGTTACTTTCGAACTTGAGTAG 57.074 36.000 0.00 0.00 0.00 2.57
5928 7963 7.709947 TCTTGTTACTTTCGAACTTGAGTAGA 58.290 34.615 0.00 0.00 0.00 2.59
5929 7964 7.861372 TCTTGTTACTTTCGAACTTGAGTAGAG 59.139 37.037 0.00 3.57 0.00 2.43
5937 7972 0.901124 ACTTGAGTAGAGCAGGGCAG 59.099 55.000 0.00 0.00 0.00 4.85
5970 8005 9.057089 AGTAAGTTCCTTCAGACAACATAAAAG 57.943 33.333 0.00 0.00 0.00 2.27
6073 8108 5.924356 TCATCACTCTGTCAGTAACCAAAA 58.076 37.500 0.00 0.00 32.21 2.44
6074 8109 6.353323 TCATCACTCTGTCAGTAACCAAAAA 58.647 36.000 0.00 0.00 32.21 1.94
6083 8118 8.402472 TCTGTCAGTAACCAAAAATACAAACAG 58.598 33.333 0.00 0.00 37.73 3.16
6087 8122 8.740906 TCAGTAACCAAAAATACAAACAGAACA 58.259 29.630 0.00 0.00 0.00 3.18
6110 8145 6.828273 ACATAATTAGCAGAACCTATGCAACA 59.172 34.615 0.00 0.00 46.31 3.33
6112 8147 9.002600 CATAATTAGCAGAACCTATGCAACATA 57.997 33.333 0.00 0.00 46.31 2.29
6120 8155 5.418840 AGAACCTATGCAACATAAGGGTTTG 59.581 40.000 10.74 0.00 35.99 2.93
6144 8179 3.580458 AGTGTTAGAACTCATGACCAGCT 59.420 43.478 0.00 0.00 0.00 4.24
6145 8180 3.929610 GTGTTAGAACTCATGACCAGCTC 59.070 47.826 0.00 0.00 0.00 4.09
6182 8217 8.531982 AGAAAAGCTATATCATAATCGTGGCTA 58.468 33.333 0.00 0.00 0.00 3.93
6191 8226 2.097110 AATCGTGGCTATGTCCCCTA 57.903 50.000 0.00 0.00 0.00 3.53
6197 8232 3.244561 CGTGGCTATGTCCCCTATGAATT 60.245 47.826 0.00 0.00 0.00 2.17
6200 8235 4.202567 TGGCTATGTCCCCTATGAATTTCC 60.203 45.833 0.00 0.00 0.00 3.13
6205 8240 4.792068 TGTCCCCTATGAATTTCCATGAC 58.208 43.478 0.00 0.00 0.00 3.06
6211 8248 7.043565 CCCCTATGAATTTCCATGACAAAAAG 58.956 38.462 0.00 0.00 0.00 2.27
6226 8263 6.361433 TGACAAAAAGGAATGGAAGTACTGA 58.639 36.000 0.00 0.00 0.00 3.41
6230 8267 9.362151 ACAAAAAGGAATGGAAGTACTGAATAA 57.638 29.630 0.00 0.00 0.00 1.40
6279 8330 2.504367 ACATGCCAACTGAGTTACACC 58.496 47.619 0.00 0.00 0.00 4.16
6296 8347 8.647143 AGTTACACCTTTGACAATTGATTTTG 57.353 30.769 13.59 2.45 0.00 2.44
6299 8350 5.294060 ACACCTTTGACAATTGATTTTGCAC 59.706 36.000 13.59 0.00 0.00 4.57
6352 8403 5.398603 AAGTTCATCTATCTAGCATCGGG 57.601 43.478 0.00 0.00 0.00 5.14
6356 8407 4.407365 TCATCTATCTAGCATCGGGACAA 58.593 43.478 0.00 0.00 0.00 3.18
6359 8410 5.808366 TCTATCTAGCATCGGGACAATTT 57.192 39.130 0.00 0.00 0.00 1.82
6412 8463 7.588497 AATGCTTAAGAAGAAGAACAAAGGT 57.412 32.000 6.67 0.00 0.00 3.50
6413 8464 8.691661 AATGCTTAAGAAGAAGAACAAAGGTA 57.308 30.769 6.67 0.00 0.00 3.08
6414 8465 7.492352 TGCTTAAGAAGAAGAACAAAGGTAC 57.508 36.000 6.67 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.990526 ACTGATTGGAAGAACTGGATTGT 58.009 39.130 0.00 0.00 0.00 2.71
72 73 5.594926 AGCCAAAGAGAACAATTGACAAAG 58.405 37.500 13.59 0.00 0.00 2.77
88 95 8.956426 TGAAACCAATTATCTAGTTAGCCAAAG 58.044 33.333 0.00 0.00 0.00 2.77
99 106 7.972832 AAACAGTCGTGAAACCAATTATCTA 57.027 32.000 0.00 0.00 0.00 1.98
146 157 8.421784 AGCTGCAGCATACTATACTAAACTTAA 58.578 33.333 38.24 0.00 45.16 1.85
163 174 2.027325 CAGTTGTTGAGCTGCAGCA 58.973 52.632 38.24 18.36 45.16 4.41
175 186 2.638480 TAGGCTCTGTTTGCAGTTGT 57.362 45.000 0.00 0.00 43.05 3.32
181 192 3.515330 AATGCATTAGGCTCTGTTTGC 57.485 42.857 11.02 0.00 45.15 3.68
182 193 4.427312 GGAAATGCATTAGGCTCTGTTTG 58.573 43.478 13.39 0.00 45.15 2.93
183 194 3.448660 GGGAAATGCATTAGGCTCTGTTT 59.551 43.478 13.39 0.00 45.15 2.83
184 195 3.026694 GGGAAATGCATTAGGCTCTGTT 58.973 45.455 13.39 0.00 45.15 3.16
185 196 2.659428 GGGAAATGCATTAGGCTCTGT 58.341 47.619 13.39 0.00 45.15 3.41
186 197 1.605710 CGGGAAATGCATTAGGCTCTG 59.394 52.381 13.39 2.54 45.15 3.35
187 198 1.212935 ACGGGAAATGCATTAGGCTCT 59.787 47.619 13.39 0.00 45.15 4.09
188 199 1.604278 GACGGGAAATGCATTAGGCTC 59.396 52.381 13.39 6.33 45.15 4.70
189 200 1.680338 GACGGGAAATGCATTAGGCT 58.320 50.000 13.39 0.00 45.15 4.58
190 201 0.307760 CGACGGGAAATGCATTAGGC 59.692 55.000 13.39 6.16 45.13 3.93
238 249 3.420482 AAATGGAGCCTCCCGGGG 61.420 66.667 23.50 6.77 35.03 5.73
239 250 1.999634 ATGAAATGGAGCCTCCCGGG 62.000 60.000 16.85 16.85 35.03 5.73
240 251 0.764890 TATGAAATGGAGCCTCCCGG 59.235 55.000 8.62 0.00 35.03 5.73
241 252 1.694150 TCTATGAAATGGAGCCTCCCG 59.306 52.381 8.62 0.00 35.03 5.14
242 253 3.864789 TTCTATGAAATGGAGCCTCCC 57.135 47.619 8.62 0.00 34.41 4.30
243 254 3.561725 CGTTTCTATGAAATGGAGCCTCC 59.438 47.826 2.98 2.98 34.41 4.30
244 255 4.442706 TCGTTTCTATGAAATGGAGCCTC 58.557 43.478 10.98 0.00 34.41 4.70
245 256 4.487714 TCGTTTCTATGAAATGGAGCCT 57.512 40.909 10.98 0.00 34.41 4.58
246 257 5.332707 GTTTCGTTTCTATGAAATGGAGCC 58.667 41.667 10.98 0.00 40.40 4.70
247 258 5.106317 TGGTTTCGTTTCTATGAAATGGAGC 60.106 40.000 10.98 5.86 40.40 4.70
248 259 6.314784 GTGGTTTCGTTTCTATGAAATGGAG 58.685 40.000 10.98 0.00 40.40 3.86
249 260 5.106869 CGTGGTTTCGTTTCTATGAAATGGA 60.107 40.000 10.98 1.69 40.40 3.41
250 261 5.086058 CGTGGTTTCGTTTCTATGAAATGG 58.914 41.667 10.98 1.66 40.40 3.16
251 262 5.788531 GTCGTGGTTTCGTTTCTATGAAATG 59.211 40.000 6.05 6.05 40.40 2.32
252 263 5.467399 TGTCGTGGTTTCGTTTCTATGAAAT 59.533 36.000 0.00 0.00 40.40 2.17
253 264 4.809958 TGTCGTGGTTTCGTTTCTATGAAA 59.190 37.500 0.00 0.00 37.03 2.69
293 304 4.319549 GCTTTCAGAACCTGGTTTTAGTCG 60.320 45.833 14.28 3.35 31.51 4.18
320 331 0.881796 GTTTCCTTTCCCTTGCCTCG 59.118 55.000 0.00 0.00 0.00 4.63
330 342 4.201970 TGGTTGATGTTGTCGTTTCCTTTC 60.202 41.667 0.00 0.00 0.00 2.62
339 351 0.726827 CGGGATGGTTGATGTTGTCG 59.273 55.000 0.00 0.00 0.00 4.35
347 359 1.674519 CGACATTGACGGGATGGTTGA 60.675 52.381 0.46 0.00 0.00 3.18
350 362 0.391130 CACGACATTGACGGGATGGT 60.391 55.000 12.76 0.00 36.15 3.55
361 373 0.320421 CGGAAGACCCACACGACATT 60.320 55.000 0.00 0.00 34.14 2.71
389 426 7.346208 ACTGCGGCATAATTTAAAGAAAAAC 57.654 32.000 1.75 0.00 0.00 2.43
425 462 7.421530 AATATATCTTCATTCCCACGTTTCG 57.578 36.000 0.00 0.00 0.00 3.46
428 465 8.786898 CATCAAATATATCTTCATTCCCACGTT 58.213 33.333 0.00 0.00 0.00 3.99
468 505 7.170998 AGGCGTACTTTGTTGCTGTATATATTC 59.829 37.037 0.00 0.00 0.00 1.75
474 511 3.053831 AGGCGTACTTTGTTGCTGTAT 57.946 42.857 0.00 0.00 0.00 2.29
476 513 1.602377 GAAGGCGTACTTTGTTGCTGT 59.398 47.619 0.00 0.00 40.21 4.40
479 516 1.069227 CAGGAAGGCGTACTTTGTTGC 60.069 52.381 0.00 0.00 40.21 4.17
497 534 8.523523 TTTTAGAACATGTGCATTTCATTCAG 57.476 30.769 6.60 0.00 0.00 3.02
524 561 4.152759 CGCCATGTGCATTTCATTCTTTTT 59.847 37.500 0.00 0.00 41.33 1.94
525 562 3.680937 CGCCATGTGCATTTCATTCTTTT 59.319 39.130 0.00 0.00 41.33 2.27
526 563 3.255725 CGCCATGTGCATTTCATTCTTT 58.744 40.909 0.00 0.00 41.33 2.52
527 564 2.417651 CCGCCATGTGCATTTCATTCTT 60.418 45.455 0.00 0.00 41.33 2.52
528 565 1.135527 CCGCCATGTGCATTTCATTCT 59.864 47.619 0.00 0.00 41.33 2.40
529 566 1.563111 CCGCCATGTGCATTTCATTC 58.437 50.000 0.00 0.00 41.33 2.67
530 567 0.460635 GCCGCCATGTGCATTTCATT 60.461 50.000 0.00 0.00 41.33 2.57
531 568 1.142314 GCCGCCATGTGCATTTCAT 59.858 52.632 0.00 0.00 41.33 2.57
554 591 6.308041 GGTTTCGAGTATTTTCAGCATTTTCC 59.692 38.462 0.00 0.00 0.00 3.13
555 592 6.861055 TGGTTTCGAGTATTTTCAGCATTTTC 59.139 34.615 0.00 0.00 0.00 2.29
558 595 5.619981 GCTGGTTTCGAGTATTTTCAGCATT 60.620 40.000 0.00 0.00 43.82 3.56
559 596 4.142600 GCTGGTTTCGAGTATTTTCAGCAT 60.143 41.667 0.00 0.00 43.82 3.79
562 599 4.201628 CGAGCTGGTTTCGAGTATTTTCAG 60.202 45.833 0.00 0.00 40.36 3.02
563 600 3.678072 CGAGCTGGTTTCGAGTATTTTCA 59.322 43.478 0.00 0.00 40.36 2.69
573 610 2.631418 TCTTCTACGAGCTGGTTTCG 57.369 50.000 6.71 0.00 43.38 3.46
574 611 4.989168 TCTTTTCTTCTACGAGCTGGTTTC 59.011 41.667 6.71 0.00 0.00 2.78
582 619 7.527516 CGACATGTTTTTCTTTTCTTCTACGAG 59.472 37.037 0.00 0.00 0.00 4.18
679 718 9.265901 CCGTATCATTATCTCATCTCTGTTTTT 57.734 33.333 0.00 0.00 0.00 1.94
680 719 8.424918 ACCGTATCATTATCTCATCTCTGTTTT 58.575 33.333 0.00 0.00 0.00 2.43
681 720 7.957002 ACCGTATCATTATCTCATCTCTGTTT 58.043 34.615 0.00 0.00 0.00 2.83
682 721 7.531857 ACCGTATCATTATCTCATCTCTGTT 57.468 36.000 0.00 0.00 0.00 3.16
683 722 7.531857 AACCGTATCATTATCTCATCTCTGT 57.468 36.000 0.00 0.00 0.00 3.41
684 723 8.187480 CCTAACCGTATCATTATCTCATCTCTG 58.813 40.741 0.00 0.00 0.00 3.35
685 724 8.110271 TCCTAACCGTATCATTATCTCATCTCT 58.890 37.037 0.00 0.00 0.00 3.10
686 725 8.282455 TCCTAACCGTATCATTATCTCATCTC 57.718 38.462 0.00 0.00 0.00 2.75
687 726 7.147983 GCTCCTAACCGTATCATTATCTCATCT 60.148 40.741 0.00 0.00 0.00 2.90
688 727 6.975772 GCTCCTAACCGTATCATTATCTCATC 59.024 42.308 0.00 0.00 0.00 2.92
689 728 6.437477 TGCTCCTAACCGTATCATTATCTCAT 59.563 38.462 0.00 0.00 0.00 2.90
690 729 5.773176 TGCTCCTAACCGTATCATTATCTCA 59.227 40.000 0.00 0.00 0.00 3.27
691 730 6.268825 TGCTCCTAACCGTATCATTATCTC 57.731 41.667 0.00 0.00 0.00 2.75
692 731 6.295349 CCTTGCTCCTAACCGTATCATTATCT 60.295 42.308 0.00 0.00 0.00 1.98
722 761 2.662156 CCGTCGTCTCTTTCTTAACAGC 59.338 50.000 0.00 0.00 0.00 4.40
724 763 2.608752 GCCCGTCGTCTCTTTCTTAACA 60.609 50.000 0.00 0.00 0.00 2.41
768 807 2.604299 TAGCGAGCCAGCGAGGAGTA 62.604 60.000 2.12 0.00 43.00 2.59
1082 1122 1.026718 CCGGTCATCTTGCCAAGGTC 61.027 60.000 4.30 0.00 0.00 3.85
1142 1182 1.842381 AACCAGTACCTGCTCCTGCC 61.842 60.000 0.00 0.00 38.71 4.85
1145 1185 1.625818 CAAGAACCAGTACCTGCTCCT 59.374 52.381 0.00 0.00 0.00 3.69
1208 1251 2.111756 CTTCGCAGCACAAACAAGAAC 58.888 47.619 0.00 0.00 0.00 3.01
1209 1252 1.065401 CCTTCGCAGCACAAACAAGAA 59.935 47.619 0.00 0.00 0.00 2.52
1210 1253 0.662619 CCTTCGCAGCACAAACAAGA 59.337 50.000 0.00 0.00 0.00 3.02
1215 1272 2.597217 CCCCCTTCGCAGCACAAA 60.597 61.111 0.00 0.00 0.00 2.83
1390 1447 3.126225 GGCTCCTCGTCGTCGTCT 61.126 66.667 1.33 0.00 38.33 4.18
1448 1515 1.311059 CAGGAAATGGGGGAAGGGG 59.689 63.158 0.00 0.00 0.00 4.79
1563 1639 4.025360 AGCTGGCAATTATCCATTGTGAA 58.975 39.130 0.00 0.00 43.95 3.18
1575 1651 4.546829 ATGAACAATTGAGCTGGCAATT 57.453 36.364 13.59 7.40 46.35 2.32
1599 1685 1.980156 GAACTCAGACGAGAAAGCGAC 59.020 52.381 0.00 0.00 42.34 5.19
1719 3600 0.541392 ATTAGCAGCCGGACATCACA 59.459 50.000 5.05 0.00 0.00 3.58
1813 3694 2.903784 TGGAATCCTCAAACTCCTCGAA 59.096 45.455 0.00 0.00 0.00 3.71
1853 3734 0.944386 GCAGGCTTTGAGACGAAACA 59.056 50.000 0.00 0.00 0.00 2.83
1935 3827 2.220653 TCCCCTTTCTGCATCAAAGG 57.779 50.000 22.44 22.44 46.71 3.11
1936 3828 4.281688 TCTTTTCCCCTTTCTGCATCAAAG 59.718 41.667 10.15 10.15 0.00 2.77
1940 3832 2.165234 GCTCTTTTCCCCTTTCTGCATC 59.835 50.000 0.00 0.00 0.00 3.91
1991 3885 7.336679 TGCATATAAAGCGCTATGGATTTACAT 59.663 33.333 12.05 0.00 33.00 2.29
2003 3934 7.390440 TGAATAAACCTATGCATATAAAGCGCT 59.610 33.333 2.64 2.64 33.85 5.92
2021 3952 9.017669 CAATCTGCAGATTTAAGCTGAATAAAC 57.982 33.333 34.17 0.00 42.41 2.01
2056 3987 2.604914 GGCAGTCAGAACACGTATGATG 59.395 50.000 0.00 0.00 0.00 3.07
2124 4059 4.679373 TCTCCTTTCCTCATCATACAGC 57.321 45.455 0.00 0.00 0.00 4.40
2210 4145 4.343526 TGCCAACAACTGTTTTGTCCATAT 59.656 37.500 11.62 0.00 35.83 1.78
2283 4218 6.199937 CCTATTTGCTGGCATGGATATAAC 57.800 41.667 0.00 0.00 0.00 1.89
2402 4341 3.396560 AGCCAGACCGTTTGTACTTTAC 58.603 45.455 0.00 0.00 0.00 2.01
2408 4347 3.472283 TGTAAAGCCAGACCGTTTGTA 57.528 42.857 0.00 0.00 0.00 2.41
2459 4398 4.016444 TCCAGGTGCTTCCAAATTATCAC 58.984 43.478 1.79 0.00 39.02 3.06
2518 4457 7.485277 CCAAACAGTCGTTTATGTAACAAAACA 59.515 33.333 0.00 0.00 43.57 2.83
2561 4501 2.233271 CCAGGTCAAACAGATGCTTGT 58.767 47.619 0.00 0.00 0.00 3.16
2563 4503 1.145738 ACCCAGGTCAAACAGATGCTT 59.854 47.619 0.00 0.00 0.00 3.91
2564 4504 0.773644 ACCCAGGTCAAACAGATGCT 59.226 50.000 0.00 0.00 0.00 3.79
2565 4505 1.270550 CAACCCAGGTCAAACAGATGC 59.729 52.381 0.00 0.00 0.00 3.91
2659 4619 3.051081 AGTGTCTCTGAATTGCACCTC 57.949 47.619 0.00 0.00 0.00 3.85
2718 4678 7.653503 AGGGGAGCAATATATAAGTCTAGCTA 58.346 38.462 0.00 0.00 0.00 3.32
2719 4679 6.507568 AGGGGAGCAATATATAAGTCTAGCT 58.492 40.000 0.00 0.00 0.00 3.32
2720 4680 6.609616 AGAGGGGAGCAATATATAAGTCTAGC 59.390 42.308 0.00 0.00 0.00 3.42
2721 4681 8.602472 AAGAGGGGAGCAATATATAAGTCTAG 57.398 38.462 0.00 0.00 0.00 2.43
2723 4683 9.207868 GATAAGAGGGGAGCAATATATAAGTCT 57.792 37.037 0.00 0.00 0.00 3.24
2724 4684 9.207868 AGATAAGAGGGGAGCAATATATAAGTC 57.792 37.037 0.00 0.00 0.00 3.01
2725 4685 9.567702 AAGATAAGAGGGGAGCAATATATAAGT 57.432 33.333 0.00 0.00 0.00 2.24
2811 4773 3.500448 TTATGTGACAGAAACCAGGCA 57.500 42.857 0.00 0.00 0.00 4.75
2873 4835 7.665974 GGGAGTAGCATTTATTAGCCTAATTGT 59.334 37.037 1.63 0.00 0.00 2.71
2877 4839 6.295123 CGAGGGAGTAGCATTTATTAGCCTAA 60.295 42.308 0.00 0.00 0.00 2.69
2897 4859 2.122783 TGGAAGCAATTTACCGAGGG 57.877 50.000 0.00 0.00 0.00 4.30
2898 4860 2.163613 GGTTGGAAGCAATTTACCGAGG 59.836 50.000 0.00 0.00 0.00 4.63
2899 4861 3.081804 AGGTTGGAAGCAATTTACCGAG 58.918 45.455 0.00 0.00 0.00 4.63
2900 4862 3.149005 AGGTTGGAAGCAATTTACCGA 57.851 42.857 0.00 0.00 0.00 4.69
2901 4863 3.669557 CGAAGGTTGGAAGCAATTTACCG 60.670 47.826 0.00 0.00 0.00 4.02
2902 4864 3.504520 TCGAAGGTTGGAAGCAATTTACC 59.495 43.478 0.00 0.00 0.00 2.85
2905 4867 2.558359 CCTCGAAGGTTGGAAGCAATTT 59.442 45.455 0.00 0.00 0.00 1.82
2906 4868 2.162681 CCTCGAAGGTTGGAAGCAATT 58.837 47.619 0.00 0.00 0.00 2.32
2907 4869 1.826385 CCTCGAAGGTTGGAAGCAAT 58.174 50.000 0.00 0.00 0.00 3.56
3162 5125 7.874528 CAGCTTTTTAAGATTTCCCAAGATTGT 59.125 33.333 0.00 0.00 0.00 2.71
3176 5139 7.094205 GGATGATCCAGAAACAGCTTTTTAAGA 60.094 37.037 6.60 0.00 36.28 2.10
3289 5253 3.952323 TCAGATACTCCCTCCGTAACTTG 59.048 47.826 0.00 0.00 0.00 3.16
3315 5283 6.374417 AGATACCAGCCGATAACCAAATAT 57.626 37.500 0.00 0.00 0.00 1.28
3423 5393 3.542304 GCCATGGGCCTTTCATCC 58.458 61.111 15.13 0.00 44.06 3.51
3445 5416 7.095649 GGCTTGAACTGTGGCTTTAATAAAAAG 60.096 37.037 0.00 0.00 0.00 2.27
3446 5417 6.704050 GGCTTGAACTGTGGCTTTAATAAAAA 59.296 34.615 0.00 0.00 0.00 1.94
3471 5442 2.159382 ACTAAGGGAATGTTTGGTGCG 58.841 47.619 0.00 0.00 0.00 5.34
3653 5624 1.354040 GAGGATCGCTGACACACTTG 58.646 55.000 0.00 0.00 0.00 3.16
3656 5627 0.247736 AAGGAGGATCGCTGACACAC 59.752 55.000 0.00 0.00 34.37 3.82
3665 5636 2.988010 TTGATGGTGAAGGAGGATCG 57.012 50.000 0.00 0.00 34.37 3.69
3817 5788 5.698545 GCAGAGGTGGAGTATTCATATGTTC 59.301 44.000 1.90 0.00 0.00 3.18
3902 5873 2.224621 ACTTGAGTTGTGGGAGTGATGG 60.225 50.000 0.00 0.00 0.00 3.51
3968 5939 0.178992 CAGGCCTTTCCAAGTGACCA 60.179 55.000 0.00 0.00 37.29 4.02
4032 6003 2.462456 ACTGATGTGCTGTCGTGAAT 57.538 45.000 0.00 0.00 0.00 2.57
4037 6008 3.317150 TGAAGTAACTGATGTGCTGTCG 58.683 45.455 0.00 0.00 0.00 4.35
4069 6040 1.867233 TGAAAGACGCAGAAGCTGTTC 59.133 47.619 0.00 0.00 39.10 3.18
4093 6064 8.868522 AAAACCATTAGAATTCTCATGTCTCA 57.131 30.769 22.23 0.00 0.00 3.27
4214 6185 3.994392 CCCACACCGAAAGATATATTCCG 59.006 47.826 0.00 0.00 0.00 4.30
4355 6326 8.523523 TGAAGTACAAATGAATGCAAAATGAG 57.476 30.769 0.00 0.00 0.00 2.90
4385 6356 6.703165 AGGCAAGTCAATGAAATGAAAACTTC 59.297 34.615 1.32 0.00 0.00 3.01
4455 6426 8.570096 TTTTGTAAATCAGATAGTATCCGACG 57.430 34.615 6.53 0.00 0.00 5.12
4577 6548 5.512942 TTCCATCCTTTTCACCAGATGTA 57.487 39.130 0.00 0.00 35.42 2.29
4776 6747 8.953368 ATCTTTCTGAAATTTATGAAATGGCC 57.047 30.769 14.47 0.00 0.00 5.36
4989 6960 1.201877 CGTCAAATGTACGCCCTTTCG 60.202 52.381 0.00 0.00 33.04 3.46
5095 7066 1.129998 CATGCAGGTCTTCTTCTTGCG 59.870 52.381 0.00 0.00 0.00 4.85
5138 7109 1.202359 TGCGAAACAAAAAGGCAGGAC 60.202 47.619 0.00 0.00 0.00 3.85
5176 7177 3.824133 CCCAAACATGAGCTATGATGGA 58.176 45.455 20.41 0.00 43.60 3.41
5177 7178 2.295349 GCCCAAACATGAGCTATGATGG 59.705 50.000 0.00 16.31 42.10 3.51
5178 7179 2.953648 TGCCCAAACATGAGCTATGATG 59.046 45.455 0.00 4.71 39.21 3.07
5179 7180 3.301794 TGCCCAAACATGAGCTATGAT 57.698 42.857 0.00 0.00 39.21 2.45
5180 7181 2.804986 TGCCCAAACATGAGCTATGA 57.195 45.000 0.00 0.00 39.21 2.15
5181 7182 4.823442 TCTAATGCCCAAACATGAGCTATG 59.177 41.667 0.00 0.00 42.68 2.23
5182 7183 5.052693 TCTAATGCCCAAACATGAGCTAT 57.947 39.130 0.00 0.00 29.61 2.97
5183 7184 4.502105 TCTAATGCCCAAACATGAGCTA 57.498 40.909 0.00 0.00 29.61 3.32
5184 7185 3.370840 TCTAATGCCCAAACATGAGCT 57.629 42.857 0.00 0.00 29.61 4.09
5185 7186 3.429410 GGTTCTAATGCCCAAACATGAGC 60.429 47.826 0.00 0.00 29.61 4.26
5186 7187 3.131046 GGGTTCTAATGCCCAAACATGAG 59.869 47.826 0.00 0.00 44.23 2.90
5187 7188 3.096092 GGGTTCTAATGCCCAAACATGA 58.904 45.455 0.00 0.00 44.23 3.07
5188 7189 3.525268 GGGTTCTAATGCCCAAACATG 57.475 47.619 0.00 0.00 44.23 3.21
5195 7196 3.876309 TTATCCTGGGTTCTAATGCCC 57.124 47.619 0.00 0.00 45.04 5.36
5196 7197 7.833285 TTTATTTATCCTGGGTTCTAATGCC 57.167 36.000 0.00 0.00 0.00 4.40
5197 7198 8.860088 ACATTTATTTATCCTGGGTTCTAATGC 58.140 33.333 0.00 0.00 0.00 3.56
5200 7201 8.691797 GCAACATTTATTTATCCTGGGTTCTAA 58.308 33.333 0.00 0.00 0.00 2.10
5201 7202 7.836685 TGCAACATTTATTTATCCTGGGTTCTA 59.163 33.333 0.00 0.00 0.00 2.10
5202 7203 6.667414 TGCAACATTTATTTATCCTGGGTTCT 59.333 34.615 0.00 0.00 0.00 3.01
5203 7204 6.872920 TGCAACATTTATTTATCCTGGGTTC 58.127 36.000 0.00 0.00 0.00 3.62
5204 7205 6.865834 TGCAACATTTATTTATCCTGGGTT 57.134 33.333 0.00 0.00 0.00 4.11
5205 7206 7.784550 AGTATGCAACATTTATTTATCCTGGGT 59.215 33.333 0.00 0.00 0.00 4.51
5242 7243 6.656270 CCATTCCATATGAAAGAATCCGATCA 59.344 38.462 3.65 0.00 36.33 2.92
5265 7266 1.002069 AGAATCCAACCTGATGCCCA 58.998 50.000 0.00 0.00 0.00 5.36
5365 7366 8.870075 ATGTTAGAGCCTTATGAAACTTTCTT 57.130 30.769 3.22 0.00 0.00 2.52
5419 7420 8.514594 CAACAAGTGCTTTATCTCTCCAATAAA 58.485 33.333 0.00 0.00 0.00 1.40
5433 7434 5.351458 GGTTCTTCATTCAACAAGTGCTTT 58.649 37.500 0.00 0.00 0.00 3.51
5478 7479 0.034756 TGCGCCTTGAGCTAAGAACA 59.965 50.000 4.18 0.00 38.76 3.18
5565 7581 1.287739 CACCCACAACCCAATCCCTAT 59.712 52.381 0.00 0.00 0.00 2.57
5582 7598 1.096416 TTTGGTCGGAAACACACACC 58.904 50.000 0.00 0.00 0.00 4.16
5700 7716 6.208599 TCGATAAAGAAAAAGGGCAGAACATT 59.791 34.615 0.00 0.00 0.00 2.71
5708 7724 5.503520 CGGTACATCGATAAAGAAAAAGGGC 60.504 44.000 0.00 0.00 0.00 5.19
5712 7728 7.894376 AGAACGGTACATCGATAAAGAAAAA 57.106 32.000 0.00 0.00 0.00 1.94
5793 7809 4.123506 GGCTCTTATCTTCAGTGGCTAAC 58.876 47.826 0.00 0.00 0.00 2.34
5797 7813 1.576356 CGGCTCTTATCTTCAGTGGC 58.424 55.000 0.00 0.00 0.00 5.01
5815 7831 2.033049 ACGTATGTACTTAGCAGCTCCG 59.967 50.000 0.00 0.00 0.00 4.63
5842 7858 6.223120 GCCAATGTGGTCTGAAATACTTTTT 58.777 36.000 0.00 0.00 40.46 1.94
5848 7864 3.342377 TCGCCAATGTGGTCTGAAATA 57.658 42.857 0.00 0.00 40.46 1.40
5850 7866 1.879380 CTTCGCCAATGTGGTCTGAAA 59.121 47.619 0.00 0.00 40.46 2.69
5852 7868 0.955428 GCTTCGCCAATGTGGTCTGA 60.955 55.000 0.00 0.00 40.46 3.27
5853 7869 0.957395 AGCTTCGCCAATGTGGTCTG 60.957 55.000 0.00 0.00 40.46 3.51
5855 7871 0.955428 TCAGCTTCGCCAATGTGGTC 60.955 55.000 0.00 0.00 40.46 4.02
5857 7873 0.597568 TTTCAGCTTCGCCAATGTGG 59.402 50.000 0.00 0.00 41.55 4.17
5859 7875 3.578688 GAAATTTCAGCTTCGCCAATGT 58.421 40.909 13.40 0.00 0.00 2.71
5860 7876 2.925563 GGAAATTTCAGCTTCGCCAATG 59.074 45.455 19.49 0.00 0.00 2.82
5866 7901 4.708726 AATCCAGGAAATTTCAGCTTCG 57.291 40.909 19.49 2.21 0.00 3.79
5874 7909 7.938140 TCTGAATCGTTAATCCAGGAAATTT 57.062 32.000 0.00 0.00 0.00 1.82
5888 7923 5.934625 AGTAACAAGATGCTTCTGAATCGTT 59.065 36.000 2.39 5.23 33.41 3.85
5890 7925 6.414408 AAGTAACAAGATGCTTCTGAATCG 57.586 37.500 2.39 0.00 33.41 3.34
5891 7926 6.958193 CGAAAGTAACAAGATGCTTCTGAATC 59.042 38.462 2.39 0.00 30.72 2.52
5912 7947 3.306088 CCCTGCTCTACTCAAGTTCGAAA 60.306 47.826 0.00 0.00 0.00 3.46
5926 7961 0.252479 CTGAACATCTGCCCTGCTCT 59.748 55.000 0.00 0.00 0.00 4.09
5927 7962 0.035630 ACTGAACATCTGCCCTGCTC 60.036 55.000 0.00 0.00 0.00 4.26
5928 7963 1.279496 TACTGAACATCTGCCCTGCT 58.721 50.000 0.00 0.00 0.00 4.24
5929 7964 2.012673 CTTACTGAACATCTGCCCTGC 58.987 52.381 0.00 0.00 0.00 4.85
5970 8005 6.757897 TTGGATCAATGTGGTCTGAAATAC 57.242 37.500 0.00 0.00 0.00 1.89
5997 8032 2.096819 TGCAGTTTTCACCGAGTTTGTC 59.903 45.455 0.00 0.00 0.00 3.18
6033 8068 9.136323 AGAGTGATGATTTTGTTTTCTTTAGGT 57.864 29.630 0.00 0.00 0.00 3.08
6083 8118 7.496529 TGCATAGGTTCTGCTAATTATGTTC 57.503 36.000 0.00 0.00 40.34 3.18
6087 8122 9.573166 TTATGTTGCATAGGTTCTGCTAATTAT 57.427 29.630 0.00 0.00 40.34 1.28
6110 8145 7.514721 TGAGTTCTAACACTTCAAACCCTTAT 58.485 34.615 0.00 0.00 0.00 1.73
6112 8147 5.751586 TGAGTTCTAACACTTCAAACCCTT 58.248 37.500 0.00 0.00 0.00 3.95
6120 8155 4.390297 GCTGGTCATGAGTTCTAACACTTC 59.610 45.833 0.00 0.00 0.00 3.01
6175 8210 1.338107 TCATAGGGGACATAGCCACG 58.662 55.000 0.00 0.00 36.10 4.94
6182 8217 5.103558 TGTCATGGAAATTCATAGGGGACAT 60.104 40.000 0.00 0.00 28.22 3.06
6191 8226 7.608761 CCATTCCTTTTTGTCATGGAAATTCAT 59.391 33.333 0.00 0.00 41.22 2.57
6197 8232 5.602145 ACTTCCATTCCTTTTTGTCATGGAA 59.398 36.000 10.68 10.68 46.94 3.53
6200 8235 7.040478 TCAGTACTTCCATTCCTTTTTGTCATG 60.040 37.037 0.00 0.00 0.00 3.07
6205 8240 9.626045 GTTATTCAGTACTTCCATTCCTTTTTG 57.374 33.333 0.00 0.00 0.00 2.44
6230 8267 8.107729 GGGGCCTTAAAGCTAGTAATATTATGT 58.892 37.037 0.84 0.00 0.00 2.29
6279 8330 9.424659 GTAAAAGTGCAAAATCAATTGTCAAAG 57.575 29.630 5.13 0.00 32.80 2.77
6296 8347 5.088739 CGGATGTCAAATGAGTAAAAGTGC 58.911 41.667 0.00 0.00 0.00 4.40
6299 8350 5.569059 GCAACGGATGTCAAATGAGTAAAAG 59.431 40.000 0.00 0.00 0.00 2.27
6329 8380 6.151312 GTCCCGATGCTAGATAGATGAACTTA 59.849 42.308 0.00 0.00 0.00 2.24
6332 8383 4.218635 TGTCCCGATGCTAGATAGATGAAC 59.781 45.833 0.00 0.00 0.00 3.18
6386 8437 9.131791 ACCTTTGTTCTTCTTCTTAAGCATTAA 57.868 29.630 0.00 0.00 38.42 1.40
6387 8438 8.691661 ACCTTTGTTCTTCTTCTTAAGCATTA 57.308 30.769 0.00 0.00 0.00 1.90
6388 8439 7.588497 ACCTTTGTTCTTCTTCTTAAGCATT 57.412 32.000 0.00 0.00 0.00 3.56
6389 8440 7.939588 AGTACCTTTGTTCTTCTTCTTAAGCAT 59.060 33.333 0.00 0.00 0.00 3.79
6390 8441 7.280356 AGTACCTTTGTTCTTCTTCTTAAGCA 58.720 34.615 0.00 0.00 0.00 3.91
6400 8451 9.880064 GTTTCTCAAATAGTACCTTTGTTCTTC 57.120 33.333 14.69 5.11 35.56 2.87


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

AutoCloner maintained by Alex Coulton.