Multiple sequence alignment - TraesCS6B01G300700

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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 TraesCS6B01G300700 chr6B 100.000 5382 0 0 927 6308 539173136 539178517 0.000000e+00 9939.0
1 TraesCS6B01G300700 chr6B 100.000 636 0 0 1 636 539172210 539172845 0.000000e+00 1175.0
2 TraesCS6B01G300700 chr6B 92.188 64 3 2 3470 3531 179356792 179356729 8.710000e-14 89.8
3 TraesCS6B01G300700 chr6D 92.554 2619 103 37 927 3484 357573361 357575948 0.000000e+00 3672.0
4 TraesCS6B01G300700 chr6D 93.090 1780 75 25 3535 5289 357575949 357577705 0.000000e+00 2562.0
5 TraesCS6B01G300700 chr6D 89.715 632 44 16 1 618 357572651 357573275 0.000000e+00 787.0
6 TraesCS6B01G300700 chr6D 87.097 620 43 14 5722 6308 357579386 357580001 0.000000e+00 667.0
7 TraesCS6B01G300700 chr6D 87.069 116 12 3 5460 5573 357578469 357578583 1.850000e-25 128.0
8 TraesCS6B01G300700 chr6D 100.000 52 0 0 3479 3530 457543837 457543786 5.210000e-16 97.1
9 TraesCS6B01G300700 chr6A 92.459 2599 109 25 927 3485 499651284 499653835 0.000000e+00 3633.0
10 TraesCS6B01G300700 chr6A 94.415 1683 62 17 3534 5199 499653835 499655502 0.000000e+00 2558.0
11 TraesCS6B01G300700 chr6A 86.370 763 72 16 5574 6308 499657952 499658710 0.000000e+00 804.0
12 TraesCS6B01G300700 chr6A 85.333 300 27 8 331 622 499650892 499651182 1.720000e-75 294.0
13 TraesCS6B01G300700 chr2A 87.736 106 12 1 162 267 736528460 736528356 8.590000e-24 122.0
14 TraesCS6B01G300700 chr3D 98.214 56 0 1 3477 3531 292887737 292887792 5.210000e-16 97.1
15 TraesCS6B01G300700 chr7D 93.750 64 2 2 3470 3531 621015869 621015932 1.870000e-15 95.3
16 TraesCS6B01G300700 chr5B 93.548 62 3 1 3471 3531 222371173 222371234 2.420000e-14 91.6
17 TraesCS6B01G300700 chr1A 93.651 63 1 3 3470 3531 506548697 506548637 2.420000e-14 91.6
18 TraesCS6B01G300700 chr3B 91.045 67 4 2 3465 3531 27864017 27863953 8.710000e-14 89.8
19 TraesCS6B01G300700 chr2B 92.188 64 4 1 3469 3531 672641791 672641854 8.710000e-14 89.8
20 TraesCS6B01G300700 chr5D 86.076 79 7 3 3457 3531 294634762 294634684 1.460000e-11 82.4


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 TraesCS6B01G300700 chr6B 539172210 539178517 6307 False 5557.00 9939 100.00000 1 6308 2 chr6B.!!$F1 6307
1 TraesCS6B01G300700 chr6D 357572651 357580001 7350 False 1563.20 3672 89.90500 1 6308 5 chr6D.!!$F1 6307
2 TraesCS6B01G300700 chr6A 499650892 499658710 7818 False 1822.25 3633 89.64425 331 6308 4 chr6A.!!$F1 5977

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
78 83 0.394762 TCATGCTTGCATCCCCAGTC 60.395 55.000 4.99 0.00 0.00 3.51 F
83 88 1.676746 CTTGCATCCCCAGTCATGAG 58.323 55.000 0.00 0.00 0.00 2.90 F
121 126 2.169769 AGTCAAACTTGTGAACGGAGGA 59.830 45.455 0.00 0.00 0.00 3.71 F
2150 2277 1.398041 GTGCTATGATTTGTGCGCTGA 59.602 47.619 9.73 0.00 33.71 4.26 F
2579 2710 0.455410 CGAACCTCTCTGAGCCTCAG 59.545 60.000 15.79 15.79 45.59 3.35 F
2670 2801 0.689080 ATCCTGCCATGACGAGGTCT 60.689 55.000 0.00 0.00 33.15 3.85 F
4642 4823 1.311859 TCTGTTGAAACCAGCAGCAG 58.688 50.000 0.00 0.00 43.31 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2050 2.819608 ACCAATTGTTCCGATGGTTCAG 59.180 45.455 4.43 0.00 43.47 3.02 R
2150 2277 2.210116 CAGCAAGTTACGAACTGGTGT 58.790 47.619 0.00 0.00 41.91 4.16 R
2191 2318 6.481134 CATGAACATGTTATGTACAGCAGAC 58.519 40.000 11.95 0.00 44.07 3.51 R
3263 3427 0.108186 TCAGCCATCACCGACATGTC 60.108 55.000 16.21 16.21 0.00 3.06 R
3748 3915 1.493311 CTTCAGCACGCTTCCGAAC 59.507 57.895 0.00 0.00 38.29 3.95 R
4712 4893 1.456296 CATTAGCTGGAGTGCTTGCA 58.544 50.000 0.00 0.00 43.74 4.08 R
5567 8224 0.036952 CACTCCGTTGATGCTGGACT 60.037 55.000 0.00 0.00 0.00 3.85 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
24 25 4.096081 GGTTCATCATGAGCCTTCTTTCTG 59.904 45.833 13.18 0.00 43.41 3.02
29 30 6.491062 TCATCATGAGCCTTCTTTCTGAAAAA 59.509 34.615 0.09 1.88 33.79 1.94
51 56 8.810652 AAAAACAATACATGTATGCGAGTTTT 57.189 26.923 26.04 26.04 42.99 2.43
53 58 6.735678 ACAATACATGTATGCGAGTTTTCA 57.264 33.333 18.94 0.00 41.63 2.69
54 59 7.320443 ACAATACATGTATGCGAGTTTTCAT 57.680 32.000 18.94 0.00 41.63 2.57
55 60 7.409697 ACAATACATGTATGCGAGTTTTCATC 58.590 34.615 18.94 0.00 41.63 2.92
56 61 4.520743 ACATGTATGCGAGTTTTCATCG 57.479 40.909 0.00 0.00 43.00 3.84
58 63 2.967362 TGTATGCGAGTTTTCATCGGT 58.033 42.857 0.00 0.00 40.50 4.69
74 79 1.818555 GGTTCATGCTTGCATCCCC 59.181 57.895 4.99 2.55 0.00 4.81
78 83 0.394762 TCATGCTTGCATCCCCAGTC 60.395 55.000 4.99 0.00 0.00 3.51
83 88 1.676746 CTTGCATCCCCAGTCATGAG 58.323 55.000 0.00 0.00 0.00 2.90
94 99 4.772100 CCCCAGTCATGAGGTTTACATTTT 59.228 41.667 0.00 0.00 0.00 1.82
104 109 9.653287 CATGAGGTTTACATTTTACTAGAGTCA 57.347 33.333 0.00 0.00 0.00 3.41
118 123 3.536956 AGAGTCAAACTTGTGAACGGA 57.463 42.857 0.00 0.00 0.00 4.69
120 125 2.544267 GAGTCAAACTTGTGAACGGAGG 59.456 50.000 0.00 0.00 0.00 4.30
121 126 2.169769 AGTCAAACTTGTGAACGGAGGA 59.830 45.455 0.00 0.00 0.00 3.71
122 127 3.139077 GTCAAACTTGTGAACGGAGGAT 58.861 45.455 0.00 0.00 0.00 3.24
123 128 3.186613 GTCAAACTTGTGAACGGAGGATC 59.813 47.826 0.00 0.00 0.00 3.36
124 129 3.071023 TCAAACTTGTGAACGGAGGATCT 59.929 43.478 0.00 0.00 33.73 2.75
140 145 5.221126 GGAGGATCTGTTGTGGCAATAATTC 60.221 44.000 0.00 0.00 33.73 2.17
142 147 5.359009 AGGATCTGTTGTGGCAATAATTCTG 59.641 40.000 0.00 0.00 0.00 3.02
146 151 4.496360 TGTTGTGGCAATAATTCTGCATG 58.504 39.130 12.93 0.00 41.78 4.06
150 155 5.353111 TGTGGCAATAATTCTGCATGATTG 58.647 37.500 12.93 0.00 41.78 2.67
160 165 6.615264 ATTCTGCATGATTGACTATGTGTC 57.385 37.500 0.00 0.00 45.54 3.67
197 203 2.479566 ATGAAACGACTGTGGATGCT 57.520 45.000 0.00 0.00 0.00 3.79
200 206 2.289631 TGAAACGACTGTGGATGCTGAT 60.290 45.455 0.00 0.00 0.00 2.90
209 215 5.028802 ACTGTGGATGCTGATATAGGCTAT 58.971 41.667 12.41 12.41 0.00 2.97
210 216 5.105023 ACTGTGGATGCTGATATAGGCTATG 60.105 44.000 17.24 1.30 0.00 2.23
238 244 7.878036 CATAAATGCATGAATATGTGGAGTCA 58.122 34.615 0.00 0.00 36.65 3.41
253 259 2.694109 GGAGTCAGGGTATAGCGAGTTT 59.306 50.000 0.00 0.00 0.00 2.66
254 260 3.887716 GGAGTCAGGGTATAGCGAGTTTA 59.112 47.826 0.00 0.00 0.00 2.01
409 421 5.634859 GGCGGATTTAAATCATAGGCATTTG 59.365 40.000 25.55 6.67 37.15 2.32
510 526 6.346896 GGTTAACTAGGTTAGTCATCCTTGG 58.653 44.000 5.42 0.00 38.26 3.61
544 563 7.551974 TCTCTTTCCTCTGCATTTATCTTCTTG 59.448 37.037 0.00 0.00 0.00 3.02
1342 1458 4.342772 CCGCGTAAGATTTCAAATTCAGG 58.657 43.478 4.92 0.00 43.02 3.86
1355 1471 6.271488 TCAAATTCAGGTCCATGAAACATC 57.729 37.500 0.00 0.00 42.21 3.06
1367 1483 4.742167 CCATGAAACATCTGCTAGTCTACG 59.258 45.833 0.00 0.00 0.00 3.51
1400 1520 8.462016 AGCAACATGAATTCACCTTATTTAGTC 58.538 33.333 11.07 0.00 0.00 2.59
1401 1521 8.243426 GCAACATGAATTCACCTTATTTAGTCA 58.757 33.333 11.07 0.00 0.00 3.41
1467 1589 3.371591 GTGTCTGAAACCACAACGTGTTA 59.628 43.478 0.00 0.00 0.00 2.41
1500 1622 3.380004 TGAATAGTTAGCGCAATTTGGGG 59.620 43.478 11.47 0.00 0.00 4.96
1525 1647 6.073003 GGAAGTCCTATTGTGTCAAACTGAAG 60.073 42.308 0.00 0.00 0.00 3.02
1592 1716 8.845413 ACAAATTTGCTGCTTCCATTATTTTA 57.155 26.923 18.12 0.00 0.00 1.52
1638 1762 3.847542 TCATTTGATCAACCAATTGCGG 58.152 40.909 7.89 0.00 35.63 5.69
1707 1831 3.442273 TGCTCAAAATAGCCGGTTAAAGG 59.558 43.478 0.79 0.00 42.05 3.11
1921 2046 7.039152 TGCTAAATCCTGTCATTTCATCCAAAA 60.039 33.333 0.00 0.00 0.00 2.44
1925 2050 9.657419 AAATCCTGTCATTTCATCCAAAATTAC 57.343 29.630 0.00 0.00 0.00 1.89
2103 2228 9.662947 GTAGCATCCCGGTAATTTAATTACTAT 57.337 33.333 22.19 11.42 43.53 2.12
2150 2277 1.398041 GTGCTATGATTTGTGCGCTGA 59.602 47.619 9.73 0.00 33.71 4.26
2191 2318 0.667993 AAATATTCCATGTGGCCGCG 59.332 50.000 12.58 0.00 34.44 6.46
2201 2328 4.735132 TGGCCGCGTCTGCTGTAC 62.735 66.667 4.92 0.00 39.65 2.90
2207 2334 1.624487 CGCGTCTGCTGTACATAACA 58.376 50.000 0.00 0.00 39.65 2.41
2395 2522 2.632996 ACAGGGAAACTCACAGATCGAA 59.367 45.455 0.00 0.00 0.00 3.71
2403 2530 6.590292 GGAAACTCACAGATCGAATCAAGTAA 59.410 38.462 0.00 0.00 0.00 2.24
2472 2599 1.272769 AGGCCTAACTCTTCACACGAC 59.727 52.381 1.29 0.00 0.00 4.34
2473 2600 1.272769 GGCCTAACTCTTCACACGACT 59.727 52.381 0.00 0.00 0.00 4.18
2474 2601 2.288886 GGCCTAACTCTTCACACGACTT 60.289 50.000 0.00 0.00 0.00 3.01
2475 2602 2.987821 GCCTAACTCTTCACACGACTTC 59.012 50.000 0.00 0.00 0.00 3.01
2476 2603 3.552273 GCCTAACTCTTCACACGACTTCA 60.552 47.826 0.00 0.00 0.00 3.02
2477 2604 3.982058 CCTAACTCTTCACACGACTTCAC 59.018 47.826 0.00 0.00 0.00 3.18
2478 2605 3.520290 AACTCTTCACACGACTTCACA 57.480 42.857 0.00 0.00 0.00 3.58
2479 2606 2.810650 ACTCTTCACACGACTTCACAC 58.189 47.619 0.00 0.00 0.00 3.82
2480 2607 1.781429 CTCTTCACACGACTTCACACG 59.219 52.381 0.00 0.00 0.00 4.49
2481 2608 1.402613 TCTTCACACGACTTCACACGA 59.597 47.619 0.00 0.00 0.00 4.35
2530 2657 1.270147 CCATCTCTCATGCATCAGCGA 60.270 52.381 0.00 0.00 46.23 4.93
2538 2665 2.437359 GCATCAGCGAGGGTTGCT 60.437 61.111 0.00 0.00 45.31 3.91
2579 2710 0.455410 CGAACCTCTCTGAGCCTCAG 59.545 60.000 15.79 15.79 45.59 3.35
2670 2801 0.689080 ATCCTGCCATGACGAGGTCT 60.689 55.000 0.00 0.00 33.15 3.85
2891 3022 3.578282 AGCAGGGTGGAAAATCGATTTTT 59.422 39.130 30.92 18.06 39.86 1.94
2968 3099 6.942005 AGTGTTTGTTCATGATCTGGATGTTA 59.058 34.615 0.00 0.00 0.00 2.41
3138 3292 1.597195 TGTGTTCATCTGTTCGTGTGC 59.403 47.619 0.00 0.00 0.00 4.57
3171 3325 5.799213 ACTCAGGCCTAGAAATATGTATGC 58.201 41.667 3.98 0.00 0.00 3.14
3210 3364 4.338964 CCCATTCTGCAATTACTGTATGCA 59.661 41.667 13.65 13.65 46.97 3.96
3243 3397 3.555917 ACCTCGTCTTCAGTACTTTCG 57.444 47.619 0.00 0.00 0.00 3.46
3270 3434 2.287788 CCAAGTGCAGTTTGGACATGTC 60.288 50.000 20.32 17.91 46.42 3.06
3354 3520 4.457949 CACAAAGTTATTAAGCCCTTCCGT 59.542 41.667 0.00 0.00 0.00 4.69
3408 3574 3.214328 GAACGGTTGATATGGCTGGATT 58.786 45.455 0.00 0.00 0.00 3.01
3448 3614 7.448777 CCAAGTGCAGATCCTATACTAGTCTTA 59.551 40.741 0.00 0.00 0.00 2.10
3493 3659 9.609346 TCTTTTTCTTTATTATTACTCCCTCCG 57.391 33.333 0.00 0.00 0.00 4.63
3494 3660 9.392259 CTTTTTCTTTATTATTACTCCCTCCGT 57.608 33.333 0.00 0.00 0.00 4.69
3495 3661 8.953368 TTTTCTTTATTATTACTCCCTCCGTC 57.047 34.615 0.00 0.00 0.00 4.79
3496 3662 6.661304 TCTTTATTATTACTCCCTCCGTCC 57.339 41.667 0.00 0.00 0.00 4.79
3497 3663 5.541484 TCTTTATTATTACTCCCTCCGTCCC 59.459 44.000 0.00 0.00 0.00 4.46
3498 3664 2.852714 TTATTACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
3499 3665 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
3500 3666 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3501 3667 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
3502 3668 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3503 3669 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3504 3670 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3505 3671 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3506 3672 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3507 3673 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3508 3674 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3509 3675 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3510 3676 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3511 3677 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
3512 3678 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3513 3679 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3514 3680 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3515 3681 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3516 3682 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3517 3683 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3518 3684 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3519 3685 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3520 3686 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3521 3687 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3522 3688 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3528 3694 8.788325 AAGTGTCTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
3529 3695 9.880157 AAGTGTCTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
3530 3696 9.530633 AGTGTCTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
3531 3697 8.762426 GTGTCTCAACTTTGTACTAACTTTAGG 58.238 37.037 0.00 0.00 35.08 2.69
3532 3698 7.929785 TGTCTCAACTTTGTACTAACTTTAGGG 59.070 37.037 0.00 0.00 35.08 3.53
3533 3699 8.146412 GTCTCAACTTTGTACTAACTTTAGGGA 58.854 37.037 0.00 0.00 35.08 4.20
3625 3791 2.878406 GGCCATGTGCGTATAAGTCAAT 59.122 45.455 0.00 0.00 42.61 2.57
3748 3915 7.070074 ACCACCTACCTACAAGAATCTAATCAG 59.930 40.741 0.00 0.00 0.00 2.90
4181 4351 7.900299 GACTTAAGTCAGTTTCTTTCTTTGC 57.100 36.000 27.12 0.00 44.18 3.68
4187 4357 3.038710 CAGTTTCTTTCTTTGCTGCGTC 58.961 45.455 0.00 0.00 0.00 5.19
4583 4761 7.814264 ATATAATTTCCAGGTTGAAGAGCAG 57.186 36.000 0.00 0.00 0.00 4.24
4613 4791 4.201724 GCACGAGATGGTAAGCTTTACTTG 60.202 45.833 3.20 4.29 39.58 3.16
4625 4803 8.188799 GGTAAGCTTTACTTGTTTCTGTTTTCT 58.811 33.333 3.20 0.00 39.58 2.52
4641 4822 1.761449 TTCTGTTGAAACCAGCAGCA 58.239 45.000 0.00 0.00 41.02 4.41
4642 4823 1.311859 TCTGTTGAAACCAGCAGCAG 58.688 50.000 0.00 0.00 43.31 4.24
4672 4853 3.696051 ACTGAATTGAATACTTGCGCCAT 59.304 39.130 4.18 0.00 0.00 4.40
4712 4893 0.110486 ATGCAGGTCGTTCAAAGGGT 59.890 50.000 0.00 0.00 0.00 4.34
4753 4934 4.123506 GGCCAGTAAGTTTCAGATAGCTC 58.876 47.826 0.00 0.00 0.00 4.09
4771 4952 2.610479 GCTCTGCCTAAAAACTTTGGCC 60.610 50.000 0.00 0.00 44.32 5.36
4791 4972 3.564511 CCCGTGCAGTGATTAACAAAAG 58.435 45.455 0.00 0.00 0.00 2.27
4792 4973 2.979813 CCGTGCAGTGATTAACAAAAGC 59.020 45.455 0.00 0.00 0.00 3.51
4793 4974 3.549827 CCGTGCAGTGATTAACAAAAGCA 60.550 43.478 0.00 0.00 32.38 3.91
4874 5065 1.456705 GCGTCCTGGAGGGAGAGAT 60.457 63.158 17.33 0.00 46.10 2.75
4966 5157 5.452078 TCAGGCATCTTTTAACTTTGTGG 57.548 39.130 0.00 0.00 0.00 4.17
4968 5159 3.897505 AGGCATCTTTTAACTTTGTGGCT 59.102 39.130 0.00 0.00 36.37 4.75
4980 5171 3.244700 ACTTTGTGGCTGCATCTAGTTCT 60.245 43.478 0.50 0.00 0.00 3.01
5042 5233 1.737735 GCAAATCCAAACCAGCGCC 60.738 57.895 2.29 0.00 0.00 6.53
5088 5279 0.452184 CAGCTCATCTGCTTGCTTGG 59.548 55.000 0.00 0.00 41.98 3.61
5100 5291 4.090057 GCTTGGGCGTGCGTCTTC 62.090 66.667 0.00 0.00 0.00 2.87
5101 5292 3.777925 CTTGGGCGTGCGTCTTCG 61.778 66.667 0.00 0.00 40.37 3.79
5161 5352 6.986904 AAGGTAGCAGCAAGTTAATTAGAC 57.013 37.500 0.00 0.00 0.00 2.59
5162 5353 6.049955 AGGTAGCAGCAAGTTAATTAGACA 57.950 37.500 0.00 0.00 0.00 3.41
5182 5374 5.009010 AGACATGAAAAGTTGTGTGGACATC 59.991 40.000 0.00 0.00 30.13 3.06
5188 5380 5.443185 AAAGTTGTGTGGACATCATTCTG 57.557 39.130 0.00 0.00 30.13 3.02
5195 7215 5.008911 TGTGTGGACATCATTCTGTTTCTTG 59.991 40.000 0.00 0.00 0.00 3.02
5260 7281 2.111999 CTTGCCCTGGTTCTCGGTGA 62.112 60.000 0.00 0.00 0.00 4.02
5261 7282 1.488705 TTGCCCTGGTTCTCGGTGAT 61.489 55.000 0.00 0.00 0.00 3.06
5290 7336 4.159135 CCCTGGTCTGGATCATTCTTTTTG 59.841 45.833 0.00 0.00 0.00 2.44
5291 7337 4.768968 CCTGGTCTGGATCATTCTTTTTGT 59.231 41.667 0.00 0.00 0.00 2.83
5293 7339 4.523943 TGGTCTGGATCATTCTTTTTGTGG 59.476 41.667 0.00 0.00 0.00 4.17
5299 7345 4.280677 GGATCATTCTTTTTGTGGTGTGGA 59.719 41.667 0.00 0.00 0.00 4.02
5302 7348 4.892345 TCATTCTTTTTGTGGTGTGGATCA 59.108 37.500 0.00 0.00 0.00 2.92
5303 7349 5.362143 TCATTCTTTTTGTGGTGTGGATCAA 59.638 36.000 0.00 0.00 0.00 2.57
5305 7351 4.277476 TCTTTTTGTGGTGTGGATCAAGT 58.723 39.130 0.00 0.00 0.00 3.16
5307 7353 5.888724 TCTTTTTGTGGTGTGGATCAAGTTA 59.111 36.000 0.00 0.00 0.00 2.24
5308 7354 6.549364 TCTTTTTGTGGTGTGGATCAAGTTAT 59.451 34.615 0.00 0.00 0.00 1.89
5309 7355 6.723298 TTTTGTGGTGTGGATCAAGTTATT 57.277 33.333 0.00 0.00 0.00 1.40
5310 7356 7.825331 TTTTGTGGTGTGGATCAAGTTATTA 57.175 32.000 0.00 0.00 0.00 0.98
5311 7357 7.825331 TTTGTGGTGTGGATCAAGTTATTAA 57.175 32.000 0.00 0.00 0.00 1.40
5315 7364 9.173021 TGTGGTGTGGATCAAGTTATTAATAAG 57.827 33.333 8.18 0.00 0.00 1.73
5338 7387 5.055144 GGGTAAAAAGGATGGAGTCGATAC 58.945 45.833 0.00 0.00 0.00 2.24
5339 7388 5.395990 GGGTAAAAAGGATGGAGTCGATACA 60.396 44.000 0.00 0.00 0.00 2.29
5343 7392 0.669077 GGATGGAGTCGATACACGCT 59.331 55.000 0.00 0.00 42.26 5.07
5350 7399 5.893687 TGGAGTCGATACACGCTTATAAAA 58.106 37.500 0.00 0.00 42.26 1.52
5356 7405 6.353582 GTCGATACACGCTTATAAAACATTGC 59.646 38.462 0.00 0.00 42.26 3.56
5360 7409 6.630676 ACACGCTTATAAAACATTGCAATG 57.369 33.333 32.74 32.74 42.10 2.82
5364 7413 6.527722 ACGCTTATAAAACATTGCAATGACAG 59.472 34.615 38.99 23.50 39.67 3.51
5368 7417 9.206870 CTTATAAAACATTGCAATGACAGGTTT 57.793 29.630 38.99 28.16 39.67 3.27
5376 7425 4.681744 TGCAATGACAGGTTTTCTTTGAC 58.318 39.130 0.00 0.00 32.47 3.18
5378 7427 4.733523 GCAATGACAGGTTTTCTTTGACGT 60.734 41.667 0.00 0.00 32.47 4.34
5383 7457 5.403166 TGACAGGTTTTCTTTGACGTATACG 59.597 40.000 23.24 23.24 46.33 3.06
5401 7475 8.635986 CGTATACGTACATATTTTCAATTGCC 57.364 34.615 17.16 0.00 34.11 4.52
5405 7479 4.732923 CGTACATATTTTCAATTGCCGTGG 59.267 41.667 0.00 0.00 0.00 4.94
5406 7480 3.520569 ACATATTTTCAATTGCCGTGGC 58.479 40.909 3.30 3.30 42.35 5.01
5417 7491 2.985282 CCGTGGCAGCATGGTTGT 60.985 61.111 0.00 0.00 35.86 3.32
5440 7514 6.037720 TGTGTTGACGATTGTGTTTGAACTAT 59.962 34.615 0.00 0.00 0.00 2.12
5446 7520 8.613482 TGACGATTGTGTTTGAACTATTTTGTA 58.387 29.630 0.00 0.00 0.00 2.41
5447 7521 9.607285 GACGATTGTGTTTGAACTATTTTGTAT 57.393 29.630 0.00 0.00 0.00 2.29
5483 8140 4.468713 TGTTGGGATCTGAATTGTGTTCA 58.531 39.130 0.00 0.00 0.00 3.18
5490 8147 6.458210 GGATCTGAATTGTGTTCAAAATGGT 58.542 36.000 0.00 0.00 37.11 3.55
5491 8148 6.366877 GGATCTGAATTGTGTTCAAAATGGTG 59.633 38.462 0.00 0.00 37.11 4.17
5495 8152 7.605691 TCTGAATTGTGTTCAAAATGGTGTTTT 59.394 29.630 0.00 0.00 37.11 2.43
5496 8153 7.524912 TGAATTGTGTTCAAAATGGTGTTTTG 58.475 30.769 6.86 6.86 39.90 2.44
5499 8156 4.932200 TGTGTTCAAAATGGTGTTTTGGAC 59.068 37.500 14.66 14.66 44.28 4.02
5502 8159 6.487689 GTTCAAAATGGTGTTTTGGACAAA 57.512 33.333 16.01 0.00 43.76 2.83
5511 8168 6.176183 TGGTGTTTTGGACAAATTGTTTCAT 58.824 32.000 0.00 0.00 40.65 2.57
5524 8181 9.609950 ACAAATTGTTTCATTGTGTTTTTGAAG 57.390 25.926 0.00 0.00 36.03 3.02
5525 8182 9.063739 CAAATTGTTTCATTGTGTTTTTGAAGG 57.936 29.630 0.00 0.00 31.54 3.46
5570 8227 2.764439 GGTGACCCTGGAACTAAGTC 57.236 55.000 0.00 0.00 0.00 3.01
5571 8228 1.278413 GGTGACCCTGGAACTAAGTCC 59.722 57.143 0.00 0.00 38.27 3.85
5572 8229 1.975680 GTGACCCTGGAACTAAGTCCA 59.024 52.381 0.00 0.00 45.72 4.02
5594 8287 2.609459 GCATCAACGGAGTGTTATCCAG 59.391 50.000 0.00 0.00 45.00 3.86
5595 8288 3.678806 GCATCAACGGAGTGTTATCCAGA 60.679 47.826 0.00 0.00 45.00 3.86
5596 8289 3.587797 TCAACGGAGTGTTATCCAGAC 57.412 47.619 0.00 0.00 45.00 3.51
5597 8290 2.232941 TCAACGGAGTGTTATCCAGACC 59.767 50.000 0.00 0.00 45.00 3.85
5599 8292 1.825474 ACGGAGTGTTATCCAGACCAG 59.175 52.381 0.00 0.00 42.51 4.00
5600 8293 2.100197 CGGAGTGTTATCCAGACCAGA 58.900 52.381 0.00 0.00 39.53 3.86
5601 8294 2.099921 CGGAGTGTTATCCAGACCAGAG 59.900 54.545 0.00 0.00 39.53 3.35
5602 8295 3.366396 GGAGTGTTATCCAGACCAGAGA 58.634 50.000 0.00 0.00 39.34 3.10
5603 8296 3.383185 GGAGTGTTATCCAGACCAGAGAG 59.617 52.174 0.00 0.00 39.34 3.20
5604 8297 2.763448 AGTGTTATCCAGACCAGAGAGC 59.237 50.000 0.00 0.00 0.00 4.09
5605 8298 1.751351 TGTTATCCAGACCAGAGAGCG 59.249 52.381 0.00 0.00 0.00 5.03
5606 8299 2.025155 GTTATCCAGACCAGAGAGCGA 58.975 52.381 0.00 0.00 0.00 4.93
5607 8300 2.625790 GTTATCCAGACCAGAGAGCGAT 59.374 50.000 0.00 0.00 0.00 4.58
5608 8301 1.786937 ATCCAGACCAGAGAGCGATT 58.213 50.000 0.00 0.00 0.00 3.34
5609 8302 2.437085 TCCAGACCAGAGAGCGATTA 57.563 50.000 0.00 0.00 0.00 1.75
5624 8317 1.683917 CGATTAGGCAGTCCAGCTAGT 59.316 52.381 0.00 0.00 33.74 2.57
5651 8344 4.021192 TGGGATTAAAGGCTTGCAGAAAAG 60.021 41.667 0.00 0.00 0.00 2.27
5652 8345 4.498241 GGATTAAAGGCTTGCAGAAAAGG 58.502 43.478 0.00 0.00 0.00 3.11
5667 8360 0.323178 AAAGGGAGTGCAGGCTCATG 60.323 55.000 6.66 0.00 37.24 3.07
5687 8380 8.238631 GCTCATGCCAATTTTGTTTTATTTCAT 58.761 29.630 0.00 0.00 0.00 2.57
5715 8408 9.646427 TGTAAAACAAAGACAAGCTAAAAACAT 57.354 25.926 0.00 0.00 0.00 2.71
5742 9057 8.984482 CTCATAATCTGAGCAAATTAAAGACG 57.016 34.615 0.00 0.00 44.73 4.18
5770 9098 7.750655 TGGTACATGGGCAGAACATAAATATA 58.249 34.615 0.00 0.00 0.00 0.86
5777 9105 6.947733 TGGGCAGAACATAAATATATTCAGGG 59.052 38.462 0.00 0.00 0.00 4.45
5780 9108 8.299570 GGCAGAACATAAATATATTCAGGGTTG 58.700 37.037 0.00 0.00 0.00 3.77
5798 9126 3.412624 GACCCTCTGCATCCAGCCC 62.413 68.421 0.00 0.00 44.83 5.19
5818 9146 2.941333 CTTGCACACAGGTCAGCG 59.059 61.111 0.00 0.00 0.00 5.18
5822 9150 2.737180 CACACAGGTCAGCGGTCT 59.263 61.111 0.00 0.00 0.00 3.85
5827 9155 0.603569 ACAGGTCAGCGGTCTAACTG 59.396 55.000 9.41 9.41 35.15 3.16
5840 9168 4.092968 CGGTCTAACTGCATAAACACCTTC 59.907 45.833 0.00 0.00 0.00 3.46
5844 9182 7.244192 GTCTAACTGCATAAACACCTTCAATC 58.756 38.462 0.00 0.00 0.00 2.67
5858 9196 3.924686 CCTTCAATCAAGCAAACTCATGC 59.075 43.478 0.00 0.00 46.78 4.06
5909 9251 2.323968 GAGTCTGCTCAAGGGATTCC 57.676 55.000 0.00 0.00 41.29 3.01
5930 9272 3.579709 CTCACTTGTACTGCCAGTAGTG 58.420 50.000 16.65 16.65 34.98 2.74
5959 9301 1.281419 TTGGAGATCCCGGTAGCAAA 58.719 50.000 0.00 0.00 37.93 3.68
5967 9309 1.648467 CCCGGTAGCAAAGAAGCAGC 61.648 60.000 0.00 0.00 36.85 5.25
5971 9313 0.238289 GTAGCAAAGAAGCAGCGCAA 59.762 50.000 11.47 0.00 36.85 4.85
6008 9350 0.036732 CTGGTAGCTTGGCAACTCCA 59.963 55.000 0.00 7.95 44.85 3.86
6068 9410 1.122019 ACATATCGGTGCCCTCCCTC 61.122 60.000 0.00 0.00 0.00 4.30
6098 9440 5.772825 TGTAGACGACATCATCATCATCA 57.227 39.130 0.00 0.00 31.20 3.07
6131 9473 2.112815 GGTGGGGTAAGACATGCGC 61.113 63.158 0.00 0.00 0.00 6.09
6252 9599 4.853050 AGCATCGAGGCTGCCAGC 62.853 66.667 25.65 8.55 43.89 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.139896 TGAAAACTCGCATACATGTATTGTT 57.860 32.000 15.85 14.19 39.87 2.83
31 32 6.571154 CGATGAAAACTCGCATACATGTATTG 59.429 38.462 15.85 11.40 0.00 1.90
36 41 3.309682 ACCGATGAAAACTCGCATACATG 59.690 43.478 0.00 0.00 34.84 3.21
44 49 2.416547 AGCATGAACCGATGAAAACTCG 59.583 45.455 0.00 0.00 35.92 4.18
51 56 1.672363 GATGCAAGCATGAACCGATGA 59.328 47.619 12.94 0.00 36.70 2.92
53 58 1.027357 GGATGCAAGCATGAACCGAT 58.973 50.000 12.94 0.00 36.70 4.18
54 59 1.031571 GGGATGCAAGCATGAACCGA 61.032 55.000 12.94 0.00 36.70 4.69
55 60 1.434696 GGGATGCAAGCATGAACCG 59.565 57.895 12.94 0.00 36.70 4.44
56 61 0.971959 TGGGGATGCAAGCATGAACC 60.972 55.000 12.94 11.47 36.70 3.62
58 63 0.040058 ACTGGGGATGCAAGCATGAA 59.960 50.000 12.94 0.00 36.70 2.57
74 79 9.653287 TCTAGTAAAATGTAAACCTCATGACTG 57.347 33.333 0.00 0.00 0.00 3.51
78 83 9.653287 TGACTCTAGTAAAATGTAAACCTCATG 57.347 33.333 0.00 0.00 0.00 3.07
94 99 5.300034 TCCGTTCACAAGTTTGACTCTAGTA 59.700 40.000 0.00 0.00 0.00 1.82
104 109 3.181454 ACAGATCCTCCGTTCACAAGTTT 60.181 43.478 0.00 0.00 0.00 2.66
118 123 5.359009 CAGAATTATTGCCACAACAGATCCT 59.641 40.000 0.00 0.00 0.00 3.24
120 125 5.039333 GCAGAATTATTGCCACAACAGATC 58.961 41.667 3.59 0.00 35.54 2.75
121 126 4.463539 TGCAGAATTATTGCCACAACAGAT 59.536 37.500 10.83 0.00 40.81 2.90
122 127 3.825585 TGCAGAATTATTGCCACAACAGA 59.174 39.130 10.83 0.00 40.81 3.41
123 128 4.177165 TGCAGAATTATTGCCACAACAG 57.823 40.909 10.83 0.00 40.81 3.16
124 129 4.220163 TCATGCAGAATTATTGCCACAACA 59.780 37.500 10.83 0.00 40.81 3.33
125 130 4.746729 TCATGCAGAATTATTGCCACAAC 58.253 39.130 10.83 0.00 40.81 3.32
126 131 5.601583 ATCATGCAGAATTATTGCCACAA 57.398 34.783 10.83 0.00 40.81 3.33
127 132 5.127356 TCAATCATGCAGAATTATTGCCACA 59.873 36.000 10.83 0.00 40.81 4.17
128 133 5.461078 GTCAATCATGCAGAATTATTGCCAC 59.539 40.000 10.83 0.00 40.81 5.01
129 134 5.361571 AGTCAATCATGCAGAATTATTGCCA 59.638 36.000 10.83 2.01 40.81 4.92
173 179 5.030295 GCATCCACAGTCGTTTCATATTTG 58.970 41.667 0.00 0.00 0.00 2.32
179 185 1.069978 TCAGCATCCACAGTCGTTTCA 59.930 47.619 0.00 0.00 0.00 2.69
180 186 1.795768 TCAGCATCCACAGTCGTTTC 58.204 50.000 0.00 0.00 0.00 2.78
184 190 3.842820 CCTATATCAGCATCCACAGTCG 58.157 50.000 0.00 0.00 0.00 4.18
185 191 3.260380 AGCCTATATCAGCATCCACAGTC 59.740 47.826 0.26 0.00 0.00 3.51
186 192 3.246301 AGCCTATATCAGCATCCACAGT 58.754 45.455 0.26 0.00 0.00 3.55
188 194 5.025453 TCATAGCCTATATCAGCATCCACA 58.975 41.667 0.26 0.00 0.00 4.17
189 195 5.599732 CTCATAGCCTATATCAGCATCCAC 58.400 45.833 0.26 0.00 0.00 4.02
222 228 6.070538 GCTATACCCTGACTCCACATATTCAT 60.071 42.308 0.00 0.00 0.00 2.57
229 235 1.064240 TCGCTATACCCTGACTCCACA 60.064 52.381 0.00 0.00 0.00 4.17
231 237 1.214673 ACTCGCTATACCCTGACTCCA 59.785 52.381 0.00 0.00 0.00 3.86
232 238 1.984066 ACTCGCTATACCCTGACTCC 58.016 55.000 0.00 0.00 0.00 3.85
234 240 6.481434 AATTAAACTCGCTATACCCTGACT 57.519 37.500 0.00 0.00 0.00 3.41
235 241 7.549615 AAAATTAAACTCGCTATACCCTGAC 57.450 36.000 0.00 0.00 0.00 3.51
236 242 9.841295 AATAAAATTAAACTCGCTATACCCTGA 57.159 29.630 0.00 0.00 0.00 3.86
306 318 7.865706 AGCACTCTTGTTAAATAATAGGGTG 57.134 36.000 11.14 11.14 0.00 4.61
409 421 9.277783 GCCATATGATAGTTATGTTATGGGATC 57.722 37.037 3.65 0.00 37.57 3.36
510 526 3.316308 TGCAGAGGAAAGAGAAAAAGTGC 59.684 43.478 0.00 0.00 0.00 4.40
1342 1458 4.764172 AGACTAGCAGATGTTTCATGGAC 58.236 43.478 0.00 0.00 0.00 4.02
1367 1483 4.092383 GGTGAATTCATGTTGCTTTCATGC 59.908 41.667 12.12 0.00 41.40 4.06
1400 1520 6.618287 TTCAGACTTGTATTGTTCTGGTTG 57.382 37.500 0.00 0.00 0.00 3.77
1401 1521 7.012421 GTCTTTCAGACTTGTATTGTTCTGGTT 59.988 37.037 0.00 0.00 41.88 3.67
1467 1589 4.694339 GCTAACTATTCACTCCACGGAAT 58.306 43.478 0.00 0.00 37.49 3.01
1500 1622 5.305585 TCAGTTTGACACAATAGGACTTCC 58.694 41.667 0.00 0.00 0.00 3.46
1525 1647 8.527567 TCCAAAATTTAATTCAATCACGGAAC 57.472 30.769 0.00 0.00 0.00 3.62
1638 1762 7.820648 ACATCATAGAAATCAGTTTTCACACC 58.179 34.615 6.71 0.00 45.19 4.16
1904 2029 9.132521 GTTCAGTAATTTTGGATGAAATGACAG 57.867 33.333 0.00 0.00 34.23 3.51
1921 2046 5.125417 CCAATTGTTCCGATGGTTCAGTAAT 59.875 40.000 4.43 0.00 0.00 1.89
1925 2050 2.819608 ACCAATTGTTCCGATGGTTCAG 59.180 45.455 4.43 0.00 43.47 3.02
2150 2277 2.210116 CAGCAAGTTACGAACTGGTGT 58.790 47.619 0.00 0.00 41.91 4.16
2191 2318 6.481134 CATGAACATGTTATGTACAGCAGAC 58.519 40.000 11.95 0.00 44.07 3.51
2207 2334 4.764823 ACCATCCAACGTTAACATGAACAT 59.235 37.500 0.00 0.00 0.00 2.71
2243 2370 1.432251 GATGTGTGGCTGCTGATGC 59.568 57.895 0.00 0.00 40.20 3.91
2347 2474 6.668645 AGTGAGACAACAGATATAGAGGACT 58.331 40.000 0.00 0.00 0.00 3.85
2395 2522 9.199982 CAAATGTCTTGCATCTTTTTACTTGAT 57.800 29.630 0.00 0.00 36.67 2.57
2473 2600 2.342279 CGAGGGGCTTCGTGTGAA 59.658 61.111 4.24 0.00 35.91 3.18
2479 2606 2.125512 CTGGAACGAGGGGCTTCG 60.126 66.667 9.72 9.72 45.70 3.79
2480 2607 2.436824 GCTGGAACGAGGGGCTTC 60.437 66.667 0.00 0.00 0.00 3.86
2481 2608 4.035102 GGCTGGAACGAGGGGCTT 62.035 66.667 0.00 0.00 0.00 4.35
2558 2685 0.968393 GAGGCTCAGAGAGGTTCGGT 60.968 60.000 10.25 0.00 0.00 4.69
2670 2801 4.124351 CACGAGAAGCCGGCGGTA 62.124 66.667 28.82 0.00 0.00 4.02
2689 2820 2.092968 TGGAAGAACAAGTGACAGCAGT 60.093 45.455 0.00 0.00 0.00 4.40
2691 2822 2.708216 TGGAAGAACAAGTGACAGCA 57.292 45.000 0.00 0.00 0.00 4.41
2968 3099 6.405397 CCATTCGAATTTTAAAACCCGATCCT 60.405 38.462 20.14 10.42 0.00 3.24
3120 3272 0.858583 CGCACACGAACAGATGAACA 59.141 50.000 0.00 0.00 43.93 3.18
3138 3292 2.335712 GGCCTGAGTTTTCCCAGCG 61.336 63.158 0.00 0.00 0.00 5.18
3210 3364 0.620556 ACGAGGTTCCTGCCATGAAT 59.379 50.000 0.00 0.00 0.00 2.57
3243 3397 1.880027 CCAAACTGCACTTGGTAGTCC 59.120 52.381 12.81 0.00 42.03 3.85
3263 3427 0.108186 TCAGCCATCACCGACATGTC 60.108 55.000 16.21 16.21 0.00 3.06
3270 3434 2.815211 CACCGTCAGCCATCACCG 60.815 66.667 0.00 0.00 0.00 4.94
3342 3508 0.690762 AGCAAGAACGGAAGGGCTTA 59.309 50.000 0.00 0.00 0.00 3.09
3354 3520 4.700213 GGCAAGGTACAGATTAAGCAAGAA 59.300 41.667 0.00 0.00 0.00 2.52
3408 3574 1.737735 CTTGGCGTGAGATCGTGCA 60.738 57.895 0.00 0.00 0.00 4.57
3448 3614 9.232473 GAAAAAGAGGACACCATAAAATAGAGT 57.768 33.333 0.00 0.00 0.00 3.24
3485 3651 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3486 3652 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3487 3653 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3488 3654 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3489 3655 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3490 3656 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
3491 3657 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
3492 3658 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
3493 3659 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3494 3660 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
3495 3661 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
3496 3662 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
3502 3668 9.880157 AAAGTTAGTACAAAGTTGAGACACTTA 57.120 29.630 0.00 0.00 35.87 2.24
3503 3669 8.788325 AAAGTTAGTACAAAGTTGAGACACTT 57.212 30.769 0.00 0.98 38.74 3.16
3504 3670 9.530633 CTAAAGTTAGTACAAAGTTGAGACACT 57.469 33.333 0.00 0.00 0.00 3.55
3505 3671 8.762426 CCTAAAGTTAGTACAAAGTTGAGACAC 58.238 37.037 0.00 0.00 0.00 3.67
3506 3672 7.929785 CCCTAAAGTTAGTACAAAGTTGAGACA 59.070 37.037 0.00 0.00 0.00 3.41
3507 3673 8.146412 TCCCTAAAGTTAGTACAAAGTTGAGAC 58.854 37.037 0.00 0.00 0.00 3.36
3508 3674 8.253867 TCCCTAAAGTTAGTACAAAGTTGAGA 57.746 34.615 0.00 0.00 0.00 3.27
3509 3675 8.148999 ACTCCCTAAAGTTAGTACAAAGTTGAG 58.851 37.037 0.00 0.00 0.00 3.02
3510 3676 8.026396 ACTCCCTAAAGTTAGTACAAAGTTGA 57.974 34.615 0.00 0.00 0.00 3.18
3511 3677 9.201127 GTACTCCCTAAAGTTAGTACAAAGTTG 57.799 37.037 7.67 0.00 42.41 3.16
3512 3678 8.927411 TGTACTCCCTAAAGTTAGTACAAAGTT 58.073 33.333 11.46 0.00 46.80 2.66
3513 3679 8.482852 TGTACTCCCTAAAGTTAGTACAAAGT 57.517 34.615 11.46 0.00 46.80 2.66
3524 3690 9.544579 AGAAGTTACTAATGTACTCCCTAAAGT 57.455 33.333 0.00 0.00 0.00 2.66
3530 3696 9.597170 CCTAAAAGAAGTTACTAATGTACTCCC 57.403 37.037 0.00 0.00 0.00 4.30
3533 3699 9.433153 GCACCTAAAAGAAGTTACTAATGTACT 57.567 33.333 0.00 0.00 0.00 2.73
3552 3718 9.154632 TCAGTTATAAGATAGATTGGCACCTAA 57.845 33.333 0.00 0.00 0.00 2.69
3625 3791 3.880490 ACATGCGTGGACAGTAAGAAAAA 59.120 39.130 11.36 0.00 0.00 1.94
3748 3915 1.493311 CTTCAGCACGCTTCCGAAC 59.507 57.895 0.00 0.00 38.29 3.95
3845 4012 2.112279 AGACCCCCTAACAGTTGACA 57.888 50.000 0.00 0.00 0.00 3.58
3846 4013 2.638363 AGAAGACCCCCTAACAGTTGAC 59.362 50.000 0.00 0.00 0.00 3.18
3847 4014 2.904434 GAGAAGACCCCCTAACAGTTGA 59.096 50.000 0.00 0.00 0.00 3.18
3848 4015 2.907042 AGAGAAGACCCCCTAACAGTTG 59.093 50.000 0.00 0.00 0.00 3.16
4181 4351 7.520119 TGTTCAATATAAAGTACTGACGCAG 57.480 36.000 0.00 5.47 37.52 5.18
4583 4761 2.578163 TACCATCTCGTGCAGCCAGC 62.578 60.000 0.00 0.00 45.96 4.85
4592 4770 5.148651 ACAAGTAAAGCTTACCATCTCGT 57.851 39.130 0.00 0.00 35.27 4.18
4625 4803 1.985473 ATCTGCTGCTGGTTTCAACA 58.015 45.000 6.69 0.00 0.00 3.33
4712 4893 1.456296 CATTAGCTGGAGTGCTTGCA 58.544 50.000 0.00 0.00 43.74 4.08
4757 4938 1.067821 TGCACGGGCCAAAGTTTTTAG 59.932 47.619 7.46 0.00 40.13 1.85
4758 4939 1.067821 CTGCACGGGCCAAAGTTTTTA 59.932 47.619 7.46 0.00 40.13 1.52
4771 4952 2.979813 GCTTTTGTTAATCACTGCACGG 59.020 45.455 0.00 0.00 0.00 4.94
4793 4974 6.128172 CGAGATATCAGAAAAACAGGCAAACT 60.128 38.462 5.32 0.00 0.00 2.66
4829 5020 0.250727 TCTTTGGTTTCCCTCTGCCG 60.251 55.000 0.00 0.00 0.00 5.69
4874 5065 2.481276 CGATGGACGTATTCTCTTGCCA 60.481 50.000 0.00 0.00 37.22 4.92
4966 5157 5.814705 ACATAAAGACAGAACTAGATGCAGC 59.185 40.000 0.00 0.00 0.00 5.25
4968 5159 6.701340 ACACATAAAGACAGAACTAGATGCA 58.299 36.000 0.00 0.00 0.00 3.96
4980 5171 5.590530 AAAGGCAACAACACATAAAGACA 57.409 34.783 0.00 0.00 41.41 3.41
5014 5205 4.344679 TGGTTTGGATTTGCAAGAGAACAT 59.655 37.500 0.00 0.00 0.00 2.71
5042 5233 4.991687 GCCTAAAATACAGGAGATTCCTCG 59.008 45.833 0.00 0.00 45.66 4.63
5060 5251 1.126488 CAGATGAGCTGGGAGCCTAA 58.874 55.000 0.00 0.00 43.77 2.69
5062 5253 2.744243 GCAGATGAGCTGGGAGCCT 61.744 63.158 0.00 0.00 43.77 4.58
5063 5254 2.203181 GCAGATGAGCTGGGAGCC 60.203 66.667 0.00 0.00 43.77 4.70
5064 5255 1.096386 CAAGCAGATGAGCTGGGAGC 61.096 60.000 0.00 0.00 45.89 4.70
5065 5256 1.096386 GCAAGCAGATGAGCTGGGAG 61.096 60.000 0.00 0.00 45.89 4.30
5108 5299 4.570930 ACAAAGGGCAAAACGAAGAAAAA 58.429 34.783 0.00 0.00 0.00 1.94
5114 5305 4.657436 ATGTTACAAAGGGCAAAACGAA 57.343 36.364 0.00 0.00 0.00 3.85
5161 5352 5.185668 TGATGTCCACACAACTTTTCATG 57.814 39.130 0.00 0.00 35.64 3.07
5162 5353 6.266103 AGAATGATGTCCACACAACTTTTCAT 59.734 34.615 0.00 0.00 35.64 2.57
5203 7223 8.860088 AGCCAATGAGAGTTTAAAACAAGTTAT 58.140 29.630 0.00 0.00 0.00 1.89
5204 7224 8.134895 CAGCCAATGAGAGTTTAAAACAAGTTA 58.865 33.333 0.00 0.00 0.00 2.24
5205 7225 6.980397 CAGCCAATGAGAGTTTAAAACAAGTT 59.020 34.615 0.00 0.00 0.00 2.66
5223 7243 3.428045 GCAAGTTAATTCGCTCAGCCAAT 60.428 43.478 0.00 0.00 0.00 3.16
5260 7281 2.053244 GATCCAGACCAGGGATGTCAT 58.947 52.381 0.00 0.00 45.05 3.06
5261 7282 1.273781 TGATCCAGACCAGGGATGTCA 60.274 52.381 0.00 0.00 45.05 3.58
5290 7336 8.621286 CCTTATTAATAACTTGATCCACACCAC 58.379 37.037 3.71 0.00 0.00 4.16
5291 7337 7.777910 CCCTTATTAATAACTTGATCCACACCA 59.222 37.037 3.71 0.00 0.00 4.17
5293 7339 8.747538 ACCCTTATTAATAACTTGATCCACAC 57.252 34.615 3.71 0.00 0.00 3.82
5307 7353 9.642343 GACTCCATCCTTTTTACCCTTATTAAT 57.358 33.333 0.00 0.00 0.00 1.40
5308 7354 7.771826 CGACTCCATCCTTTTTACCCTTATTAA 59.228 37.037 0.00 0.00 0.00 1.40
5309 7355 7.126115 TCGACTCCATCCTTTTTACCCTTATTA 59.874 37.037 0.00 0.00 0.00 0.98
5310 7356 6.069847 TCGACTCCATCCTTTTTACCCTTATT 60.070 38.462 0.00 0.00 0.00 1.40
5311 7357 5.427481 TCGACTCCATCCTTTTTACCCTTAT 59.573 40.000 0.00 0.00 0.00 1.73
5315 7364 3.622166 TCGACTCCATCCTTTTTACCC 57.378 47.619 0.00 0.00 0.00 3.69
5331 7380 6.353582 GCAATGTTTTATAAGCGTGTATCGAC 59.646 38.462 0.00 0.00 42.86 4.20
5338 7387 6.307558 TGTCATTGCAATGTTTTATAAGCGTG 59.692 34.615 32.67 9.59 37.65 5.34
5339 7388 6.385843 TGTCATTGCAATGTTTTATAAGCGT 58.614 32.000 32.67 0.00 37.65 5.07
5343 7392 9.553064 AAAACCTGTCATTGCAATGTTTTATAA 57.447 25.926 32.67 13.89 34.52 0.98
5350 7399 4.942761 AGAAAACCTGTCATTGCAATGT 57.057 36.364 32.67 15.56 37.65 2.71
5356 7405 4.920376 ACGTCAAAGAAAACCTGTCATTG 58.080 39.130 0.00 0.00 0.00 2.82
5360 7409 5.840250 CGTATACGTCAAAGAAAACCTGTC 58.160 41.667 17.16 0.00 34.11 3.51
5376 7425 7.473104 CGGCAATTGAAAATATGTACGTATACG 59.527 37.037 23.24 23.24 46.33 3.06
5378 7427 8.277018 CACGGCAATTGAAAATATGTACGTATA 58.723 33.333 10.34 0.00 31.20 1.47
5383 7457 4.502645 GCCACGGCAATTGAAAATATGTAC 59.497 41.667 10.34 0.00 41.49 2.90
5401 7475 2.074230 AACACAACCATGCTGCCACG 62.074 55.000 0.00 0.00 0.00 4.94
5405 7479 0.661187 CGTCAACACAACCATGCTGC 60.661 55.000 0.00 0.00 0.00 5.25
5406 7480 0.943673 TCGTCAACACAACCATGCTG 59.056 50.000 0.00 0.00 0.00 4.41
5413 7487 4.407818 TCAAACACAATCGTCAACACAAC 58.592 39.130 0.00 0.00 0.00 3.32
5417 7491 4.955925 AGTTCAAACACAATCGTCAACA 57.044 36.364 0.00 0.00 0.00 3.33
5456 7530 8.821686 AACACAATTCAGATCCCAACATAATA 57.178 30.769 0.00 0.00 0.00 0.98
5483 8140 7.459795 AACAATTTGTCCAAAACACCATTTT 57.540 28.000 1.83 0.00 37.70 1.82
5490 8147 7.173907 ACACAATGAAACAATTTGTCCAAAACA 59.826 29.630 1.83 0.00 31.48 2.83
5491 8148 7.525759 ACACAATGAAACAATTTGTCCAAAAC 58.474 30.769 1.83 0.00 31.48 2.43
5495 8152 7.678947 AAAACACAATGAAACAATTTGTCCA 57.321 28.000 1.83 4.94 31.48 4.02
5496 8153 8.233190 TCAAAAACACAATGAAACAATTTGTCC 58.767 29.630 1.83 0.00 31.48 4.02
5499 8156 9.063739 CCTTCAAAAACACAATGAAACAATTTG 57.936 29.630 0.00 0.00 33.08 2.32
5502 8159 8.558973 TTCCTTCAAAAACACAATGAAACAAT 57.441 26.923 0.00 0.00 33.08 2.71
5511 8168 8.961294 AATCATGAATTCCTTCAAAAACACAA 57.039 26.923 0.00 0.00 44.29 3.33
5524 8181 5.047847 CAGCATGTCCAAATCATGAATTCC 58.952 41.667 0.00 0.00 43.47 3.01
5525 8182 4.506654 GCAGCATGTCCAAATCATGAATTC 59.493 41.667 0.00 0.00 43.47 2.17
5561 8218 2.673368 CCGTTGATGCTGGACTTAGTTC 59.327 50.000 0.00 0.00 0.00 3.01
5567 8224 0.036952 CACTCCGTTGATGCTGGACT 60.037 55.000 0.00 0.00 0.00 3.85
5568 8225 0.320771 ACACTCCGTTGATGCTGGAC 60.321 55.000 0.00 0.00 0.00 4.02
5570 8227 2.093306 TAACACTCCGTTGATGCTGG 57.907 50.000 0.00 0.00 38.63 4.85
5571 8228 2.609459 GGATAACACTCCGTTGATGCTG 59.391 50.000 0.00 0.00 38.63 4.41
5572 8229 2.236146 TGGATAACACTCCGTTGATGCT 59.764 45.455 0.00 0.00 38.63 3.79
5594 8287 0.747255 TGCCTAATCGCTCTCTGGTC 59.253 55.000 0.00 0.00 0.00 4.02
5595 8288 0.749649 CTGCCTAATCGCTCTCTGGT 59.250 55.000 0.00 0.00 0.00 4.00
5596 8289 0.749649 ACTGCCTAATCGCTCTCTGG 59.250 55.000 0.00 0.00 0.00 3.86
5597 8290 1.269517 GGACTGCCTAATCGCTCTCTG 60.270 57.143 0.00 0.00 0.00 3.35
5599 8292 0.747255 TGGACTGCCTAATCGCTCTC 59.253 55.000 0.00 0.00 34.31 3.20
5600 8293 0.749649 CTGGACTGCCTAATCGCTCT 59.250 55.000 0.00 0.00 34.31 4.09
5601 8294 0.878086 GCTGGACTGCCTAATCGCTC 60.878 60.000 0.00 0.00 34.31 5.03
5602 8295 1.144936 GCTGGACTGCCTAATCGCT 59.855 57.895 0.00 0.00 34.31 4.93
5603 8296 0.389391 TAGCTGGACTGCCTAATCGC 59.611 55.000 0.00 0.00 34.31 4.58
5604 8297 1.683917 ACTAGCTGGACTGCCTAATCG 59.316 52.381 3.17 0.00 34.31 3.34
5605 8298 3.133003 TGAACTAGCTGGACTGCCTAATC 59.867 47.826 3.17 0.00 34.31 1.75
5606 8299 3.107601 TGAACTAGCTGGACTGCCTAAT 58.892 45.455 3.17 0.00 34.31 1.73
5607 8300 2.536066 TGAACTAGCTGGACTGCCTAA 58.464 47.619 3.17 0.00 34.31 2.69
5608 8301 2.231716 TGAACTAGCTGGACTGCCTA 57.768 50.000 3.17 0.00 34.31 3.93
5609 8302 1.209019 CATGAACTAGCTGGACTGCCT 59.791 52.381 3.17 0.00 34.31 4.75
5624 8317 3.439154 TGCAAGCCTTTAATCCCATGAA 58.561 40.909 0.00 0.00 0.00 2.57
5651 8344 2.827642 GCATGAGCCTGCACTCCC 60.828 66.667 0.00 0.00 41.87 4.30
5685 8378 9.515020 TTTTAGCTTGTCTTTGTTTTACAGATG 57.485 29.630 0.00 0.00 0.00 2.90
5687 8380 9.349145 GTTTTTAGCTTGTCTTTGTTTTACAGA 57.651 29.630 0.00 0.00 0.00 3.41
5693 8386 9.516314 GAGTATGTTTTTAGCTTGTCTTTGTTT 57.484 29.630 0.00 0.00 0.00 2.83
5735 9050 2.912771 CCCATGTACCATGCGTCTTTA 58.087 47.619 0.00 0.00 0.00 1.85
5742 9057 0.740737 GTTCTGCCCATGTACCATGC 59.259 55.000 0.00 0.00 0.00 4.06
5753 9068 6.948309 ACCCTGAATATATTTATGTTCTGCCC 59.052 38.462 0.00 0.00 35.59 5.36
5754 9069 8.299570 CAACCCTGAATATATTTATGTTCTGCC 58.700 37.037 0.00 0.00 35.59 4.85
5777 9105 1.028868 GCTGGATGCAGAGGGTCAAC 61.029 60.000 19.59 0.00 42.31 3.18
5780 9108 2.191641 GGCTGGATGCAGAGGGTC 59.808 66.667 19.59 0.00 45.15 4.46
5786 9114 2.044252 AAGCTGGGCTGGATGCAG 60.044 61.111 10.32 10.32 45.15 4.41
5787 9115 2.361992 CAAGCTGGGCTGGATGCA 60.362 61.111 0.00 0.00 45.15 3.96
5790 9118 2.362120 GTGCAAGCTGGGCTGGAT 60.362 61.111 11.44 0.00 39.62 3.41
5792 9120 3.677648 GTGTGCAAGCTGGGCTGG 61.678 66.667 11.44 0.00 39.62 4.85
5798 9126 1.947013 CTGACCTGTGTGCAAGCTG 59.053 57.895 0.00 0.00 0.00 4.24
5818 9146 5.001232 TGAAGGTGTTTATGCAGTTAGACC 58.999 41.667 0.00 0.00 0.00 3.85
5822 9150 7.517614 TTGATTGAAGGTGTTTATGCAGTTA 57.482 32.000 0.00 0.00 0.00 2.24
5827 9155 4.808558 TGCTTGATTGAAGGTGTTTATGC 58.191 39.130 0.00 0.00 31.56 3.14
5840 9168 3.909430 AGTGCATGAGTTTGCTTGATTG 58.091 40.909 0.00 0.00 43.18 2.67
5844 9182 3.358707 TCAAGTGCATGAGTTTGCTTG 57.641 42.857 0.00 0.00 43.18 4.01
5858 9196 5.924254 AGATGCAAATGTTTGTCATCAAGTG 59.076 36.000 26.03 3.63 44.56 3.16
5890 9232 1.836802 AGGAATCCCTTGAGCAGACTC 59.163 52.381 0.00 0.00 40.78 3.36
5909 9251 3.005897 ACACTACTGGCAGTACAAGTGAG 59.994 47.826 37.14 25.21 35.42 3.51
5930 9272 2.939103 CGGGATCTCCAAACATCTCAAC 59.061 50.000 0.00 0.00 37.91 3.18
5980 9322 0.321653 CAAGCTACCAGACCACCACC 60.322 60.000 0.00 0.00 0.00 4.61
6095 9437 1.662760 CATGAGCGTCGCCGATGAT 60.663 57.895 14.86 2.81 35.63 2.45
6098 9440 3.838271 ACCATGAGCGTCGCCGAT 61.838 61.111 14.86 2.89 35.63 4.18
6112 9454 1.298340 CGCATGTCTTACCCCACCA 59.702 57.895 0.00 0.00 0.00 4.17
6272 9619 4.760047 ACGTGGAGCATGCCGGTC 62.760 66.667 15.66 5.36 41.64 4.79


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

AutoCloner maintained by Alex Coulton.