Multiple sequence alignment - TraesCS4D01G267300

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 TraesCS4D01G267300 chr4D 100.000 4813 0 0 1 4813 437949617 437954429 0.000000e+00 8889
1 TraesCS4D01G267300 chr4B 92.147 2687 109 38 178 2811 541362464 541365101 0.000000e+00 3699
2 TraesCS4D01G267300 chr4B 89.506 648 48 8 3582 4223 541367194 541367827 0.000000e+00 802
3 TraesCS4D01G267300 chr4B 95.506 445 14 6 2811 3254 541365137 541365576 0.000000e+00 706
4 TraesCS4D01G267300 chr4B 85.987 471 35 17 4321 4776 541369489 541369943 4.360000e-130 475
5 TraesCS4D01G267300 chr4B 92.437 238 10 3 3355 3591 541365582 541365812 2.780000e-87 333
6 TraesCS4D01G267300 chr4B 87.179 195 10 2 1 180 541362233 541362427 1.760000e-49 207
7 TraesCS4D01G267300 chr4A 92.136 1526 68 23 1708 3207 30149286 30147787 0.000000e+00 2106
8 TraesCS4D01G267300 chr4A 87.210 1423 83 46 271 1630 30150703 30149317 0.000000e+00 1528
9 TraesCS4D01G267300 chr4A 91.547 769 41 13 3362 4123 30147780 30147029 0.000000e+00 1038
10 TraesCS4D01G267300 chr4A 86.480 429 39 11 4299 4709 30146863 30146436 2.040000e-123 453
11 TraesCS4D01G267300 chr4A 83.582 134 20 2 4670 4803 29073480 29073611 1.820000e-24 124
12 TraesCS4D01G267300 chr7B 92.453 106 5 3 3255 3357 42026929 42026824 1.080000e-31 148
13 TraesCS4D01G267300 chr7B 91.589 107 6 3 3255 3358 453316539 453316645 1.400000e-30 145
14 TraesCS4D01G267300 chr7A 90.654 107 7 3 3255 3358 26034456 26034562 6.500000e-29 139
15 TraesCS4D01G267300 chr5A 90.654 107 7 3 3255 3358 91852696 91852802 6.500000e-29 139
16 TraesCS4D01G267300 chr5A 90.654 107 7 3 3255 3358 601723204 601723098 6.500000e-29 139
17 TraesCS4D01G267300 chr3B 90.566 106 7 3 3255 3357 811312949 811312844 2.340000e-28 137
18 TraesCS4D01G267300 chr2D 90.566 106 7 3 3255 3357 629474328 629474433 2.340000e-28 137
19 TraesCS4D01G267300 chr3D 91.089 101 6 3 3260 3357 614914926 614915026 3.020000e-27 134
20 TraesCS4D01G267300 chr1D 89.091 110 9 3 3255 3361 334232706 334232597 3.020000e-27 134


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 TraesCS4D01G267300 chr4D 437949617 437954429 4812 False 8889.00 8889 100.000000 1 4813 1 chr4D.!!$F1 4812
1 TraesCS4D01G267300 chr4B 541362233 541369943 7710 False 1037.00 3699 90.460333 1 4776 6 chr4B.!!$F1 4775
2 TraesCS4D01G267300 chr4A 30146436 30150703 4267 True 1281.25 2106 89.343250 271 4709 4 chr4A.!!$R1 4438

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
90 98 0.099968 CGTGCATGCTTTGGATCCAG 59.900 55.0 20.33 5.51 0.00 3.86 F
1285 1413 0.036858 AGCTTCCTCTGCGTTCCTTC 60.037 55.0 0.00 0.00 35.28 3.46 F
2042 2183 0.179140 CACGGGGTTAATGCATGCAC 60.179 55.0 25.37 10.28 0.00 4.57 F
3256 3452 0.108041 TTGCCGGACGGGAAGTATTC 60.108 55.0 13.73 0.00 46.67 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1558 0.361184 GCGCGTGTACAGTAAACGAG 59.639 55.0 24.87 22.13 39.64 4.18 R
2156 2297 0.458543 GCTGGCGATCAGAGAAACGA 60.459 55.0 9.87 0.00 46.18 3.85 R
3342 3538 0.038892 GCACGTACTCCTCCGTTTCA 60.039 55.0 0.00 0.00 34.59 2.69 R
4742 7960 0.032678 ACCTGCTCGCCTGATAATCG 59.967 55.0 0.00 0.00 0.00 3.34 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
49 50 0.857935 CGCAGGCTCATTCGATCTTC 59.142 55.000 0.00 0.00 0.00 2.87
60 61 6.566564 GCTCATTCGATCTTCTGTCAAAACAA 60.567 38.462 0.00 0.00 34.24 2.83
63 64 8.352201 TCATTCGATCTTCTGTCAAAACAAAAT 58.648 29.630 0.00 0.00 34.24 1.82
64 65 8.971321 CATTCGATCTTCTGTCAAAACAAAATT 58.029 29.630 0.00 0.00 34.24 1.82
65 66 8.560576 TTCGATCTTCTGTCAAAACAAAATTC 57.439 30.769 0.00 0.00 34.24 2.17
66 67 7.138736 TCGATCTTCTGTCAAAACAAAATTCC 58.861 34.615 0.00 0.00 34.24 3.01
80 88 2.048444 AATTCCATCTCGTGCATGCT 57.952 45.000 20.33 0.00 0.00 3.79
90 98 0.099968 CGTGCATGCTTTGGATCCAG 59.900 55.000 20.33 5.51 0.00 3.86
97 105 1.026718 GCTTTGGATCCAGTGACCCG 61.027 60.000 15.53 1.08 0.00 5.28
141 149 2.563976 CGTCTGCAGAAACAACAATCG 58.436 47.619 20.19 10.60 0.00 3.34
180 196 4.204799 CCATCAAATCAGATCCAAGCTCA 58.795 43.478 0.00 0.00 0.00 4.26
181 197 4.827835 CCATCAAATCAGATCCAAGCTCAT 59.172 41.667 0.00 0.00 0.00 2.90
182 198 5.048643 CCATCAAATCAGATCCAAGCTCATC 60.049 44.000 0.00 0.00 0.00 2.92
184 200 4.165565 TCAAATCAGATCCAAGCTCATCCT 59.834 41.667 0.00 0.00 0.00 3.24
186 202 2.045524 TCAGATCCAAGCTCATCCTCC 58.954 52.381 0.00 0.00 0.00 4.30
187 203 1.047002 AGATCCAAGCTCATCCTCCG 58.953 55.000 0.00 0.00 0.00 4.63
189 205 1.053264 ATCCAAGCTCATCCTCCGCT 61.053 55.000 0.00 0.00 35.09 5.52
251 309 0.684535 CAATGACCCAAACCCAACCC 59.315 55.000 0.00 0.00 0.00 4.11
445 504 2.743126 CCGGAAGTCTATACGAGGCTAG 59.257 54.545 0.00 0.00 40.09 3.42
455 514 6.472808 GTCTATACGAGGCTAGTTTTCACTTG 59.527 42.308 5.36 0.00 34.06 3.16
498 557 2.182537 CCGCTGCTGAAAATGGGC 59.817 61.111 0.00 0.00 0.00 5.36
499 558 2.345760 CCGCTGCTGAAAATGGGCT 61.346 57.895 0.00 0.00 0.00 5.19
501 560 1.447314 GCTGCTGAAAATGGGCTGC 60.447 57.895 0.00 0.00 41.82 5.25
502 561 1.217244 CTGCTGAAAATGGGCTGCC 59.783 57.895 11.05 11.05 0.00 4.85
526 593 1.484356 CGGGTCGAGTAAATAAGGCG 58.516 55.000 0.00 0.00 0.00 5.52
539 606 6.920210 AGTAAATAAGGCGACGGTAATTACTC 59.080 38.462 15.05 5.32 31.41 2.59
540 607 2.199291 AAGGCGACGGTAATTACTCG 57.801 50.000 18.10 18.10 0.00 4.18
544 614 1.202177 GCGACGGTAATTACTCGACCA 60.202 52.381 23.74 0.00 32.39 4.02
559 629 4.637489 CCAGGCGATCGAGGCGAG 62.637 72.222 21.57 1.37 39.91 5.03
577 647 2.348591 CGAGACGGTGAAAACTGAAAGC 60.349 50.000 0.00 0.00 37.60 3.51
581 651 1.676006 CGGTGAAAACTGAAAGCTGGT 59.324 47.619 0.00 0.00 37.60 4.00
582 652 2.541588 CGGTGAAAACTGAAAGCTGGTG 60.542 50.000 0.00 0.00 37.60 4.17
583 653 2.463876 GTGAAAACTGAAAGCTGGTGC 58.536 47.619 0.00 0.00 37.60 5.01
584 654 2.098614 TGAAAACTGAAAGCTGGTGCA 58.901 42.857 0.00 0.00 42.74 4.57
610 681 1.304713 AGATACACGGACGGGTGGT 60.305 57.895 10.24 0.00 42.23 4.16
611 682 1.153706 GATACACGGACGGGTGGTG 60.154 63.158 10.24 3.19 42.23 4.17
612 683 2.567564 GATACACGGACGGGTGGTGG 62.568 65.000 10.24 0.00 42.23 4.61
623 694 3.315949 GTGGTGGGACGGGTGCTA 61.316 66.667 0.00 0.00 0.00 3.49
684 760 0.109873 ACTACACGTAGCAGTGACGC 60.110 55.000 12.78 0.00 44.43 5.19
685 761 1.126421 CTACACGTAGCAGTGACGCG 61.126 60.000 3.53 3.53 44.43 6.01
688 764 3.536394 CGTAGCAGTGACGCGCTG 61.536 66.667 5.73 6.98 43.89 5.18
693 769 4.360027 CAGTGACGCGCTGTGTGC 62.360 66.667 5.73 0.00 37.23 4.57
703 779 2.010670 GCTGTGTGCGTGTGTGTAA 58.989 52.632 0.00 0.00 0.00 2.41
704 780 0.375454 GCTGTGTGCGTGTGTGTAAA 59.625 50.000 0.00 0.00 0.00 2.01
705 781 1.594518 GCTGTGTGCGTGTGTGTAAAG 60.595 52.381 0.00 0.00 0.00 1.85
706 782 1.930503 CTGTGTGCGTGTGTGTAAAGA 59.069 47.619 0.00 0.00 0.00 2.52
707 783 2.347731 TGTGTGCGTGTGTGTAAAGAA 58.652 42.857 0.00 0.00 0.00 2.52
708 784 2.350192 TGTGTGCGTGTGTGTAAAGAAG 59.650 45.455 0.00 0.00 0.00 2.85
709 785 2.605818 GTGTGCGTGTGTGTAAAGAAGA 59.394 45.455 0.00 0.00 0.00 2.87
713 789 3.067601 TGCGTGTGTGTAAAGAAGAGAGA 59.932 43.478 0.00 0.00 0.00 3.10
971 1095 1.190643 GTTGCAGCTAGGGAGAGAGT 58.809 55.000 0.00 0.00 0.00 3.24
995 1119 1.813178 TGAGTGAGTAGTGAGGCGAAG 59.187 52.381 0.00 0.00 0.00 3.79
1245 1369 2.109126 GCTGCGCCTCAAAGGTAGG 61.109 63.158 4.18 0.00 37.80 3.18
1284 1412 0.321122 CAGCTTCCTCTGCGTTCCTT 60.321 55.000 0.00 0.00 35.28 3.36
1285 1413 0.036858 AGCTTCCTCTGCGTTCCTTC 60.037 55.000 0.00 0.00 35.28 3.46
1286 1414 1.021920 GCTTCCTCTGCGTTCCTTCC 61.022 60.000 0.00 0.00 0.00 3.46
1287 1415 0.610687 CTTCCTCTGCGTTCCTTCCT 59.389 55.000 0.00 0.00 0.00 3.36
1297 1425 1.266989 CGTTCCTTCCTGGTCTTTTGC 59.733 52.381 0.00 0.00 37.07 3.68
1414 1545 0.249868 TCGTGGTCTTGCAAGAGGTG 60.250 55.000 29.13 18.22 35.32 4.00
1415 1546 0.249868 CGTGGTCTTGCAAGAGGTGA 60.250 55.000 29.13 10.59 35.32 4.02
1416 1547 1.810031 CGTGGTCTTGCAAGAGGTGAA 60.810 52.381 29.13 10.45 35.32 3.18
1417 1548 2.508526 GTGGTCTTGCAAGAGGTGAAT 58.491 47.619 29.13 0.00 35.32 2.57
1427 1558 4.547367 AGGTGAATAGGCGCCGGC 62.547 66.667 23.20 19.07 43.18 6.13
1445 1576 0.361184 GCTCGTTTACTGTACACGCG 59.639 55.000 18.73 14.84 33.85 6.01
1641 1778 5.297547 TCTTCCGGTAATCATCATGCTAAC 58.702 41.667 0.00 0.00 0.00 2.34
1710 1847 1.752498 TGGCTTGCATGAATCATGACC 59.248 47.619 25.77 19.00 43.81 4.02
1723 1860 5.125900 TGAATCATGACCCATGTAAAGCAAG 59.874 40.000 0.00 0.00 41.98 4.01
1775 1914 7.503566 CCATGGGATACTGTGATAACTTCATTT 59.496 37.037 2.85 0.00 36.54 2.32
1902 2043 3.056465 AGAGAGGAGCTGGTAAAACGAAG 60.056 47.826 0.00 0.00 0.00 3.79
1904 2045 3.830755 AGAGGAGCTGGTAAAACGAAGTA 59.169 43.478 0.00 0.00 45.00 2.24
1905 2046 3.922910 AGGAGCTGGTAAAACGAAGTAC 58.077 45.455 0.00 0.00 45.00 2.73
1906 2047 3.577415 AGGAGCTGGTAAAACGAAGTACT 59.423 43.478 0.00 0.00 45.00 2.73
1907 2048 3.925299 GGAGCTGGTAAAACGAAGTACTC 59.075 47.826 0.00 0.00 45.00 2.59
1933 2074 3.214696 ACAGCAGCTTCTTACACCTTT 57.785 42.857 0.00 0.00 0.00 3.11
1953 2094 0.817634 CACGTTCCCTTTCTGCACCA 60.818 55.000 0.00 0.00 0.00 4.17
1995 2136 2.799126 TATCACCCAACGGCTCAAAT 57.201 45.000 0.00 0.00 0.00 2.32
2008 2149 2.550180 GGCTCAAATCGCTAGAATTCCC 59.450 50.000 0.65 0.00 0.00 3.97
2013 2154 4.081142 TCAAATCGCTAGAATTCCCACTCA 60.081 41.667 0.65 0.00 0.00 3.41
2042 2183 0.179140 CACGGGGTTAATGCATGCAC 60.179 55.000 25.37 10.28 0.00 4.57
2097 2238 5.009911 TGCAATGCAGTGTCTGAAGTAAAAT 59.990 36.000 16.47 0.00 33.32 1.82
2153 2294 5.298276 GTGGTGACTGTCCAACTAATTTTCA 59.702 40.000 5.17 0.00 36.68 2.69
2154 2295 6.016276 GTGGTGACTGTCCAACTAATTTTCAT 60.016 38.462 5.17 0.00 36.68 2.57
2155 2296 6.549364 TGGTGACTGTCCAACTAATTTTCATT 59.451 34.615 5.17 0.00 31.50 2.57
2156 2297 7.069331 TGGTGACTGTCCAACTAATTTTCATTT 59.931 33.333 5.17 0.00 31.50 2.32
2157 2298 7.595130 GGTGACTGTCCAACTAATTTTCATTTC 59.405 37.037 5.17 0.00 0.00 2.17
2179 2320 2.279120 CTCTGATCGCCAGCCGTC 60.279 66.667 0.53 0.00 42.62 4.79
2275 2416 2.430244 AAGCAGTACGTGGACGCG 60.430 61.111 3.53 3.53 44.43 6.01
2650 2791 4.933064 GGCGCGGAGGATGACGAG 62.933 72.222 8.83 0.00 0.00 4.18
2746 2890 1.141665 CATCATCGTGGACAGCGGA 59.858 57.895 0.00 0.00 0.00 5.54
2861 3045 4.215330 CGTTCGTCACGTGTAGCA 57.785 55.556 16.51 0.00 44.49 3.49
2911 3099 4.013267 AGTGAGCTGCAGTAGTTTTGAT 57.987 40.909 16.64 0.00 0.00 2.57
2921 3109 5.207768 GCAGTAGTTTTGATTGACACTGTG 58.792 41.667 6.19 6.19 35.49 3.66
2998 3186 8.733458 CATTATAATTAGGGTCATGTCATGTGG 58.267 37.037 12.54 0.00 0.00 4.17
3096 3288 6.030228 GTCCTGCGAAATTGATAGGAAAAAG 58.970 40.000 0.00 0.00 39.11 2.27
3097 3289 4.800471 CCTGCGAAATTGATAGGAAAAAGC 59.200 41.667 0.00 0.00 0.00 3.51
3098 3290 5.393461 CCTGCGAAATTGATAGGAAAAAGCT 60.393 40.000 0.00 0.00 0.00 3.74
3193 3386 2.492484 CTGTTCACGGTTCTAGCTAGGT 59.508 50.000 20.58 7.69 0.00 3.08
3254 3450 3.716381 TTGCCGGACGGGAAGTAT 58.284 55.556 13.73 0.00 40.69 2.12
3255 3451 1.984817 TTGCCGGACGGGAAGTATT 59.015 52.632 13.73 0.00 40.69 1.89
3256 3452 0.108041 TTGCCGGACGGGAAGTATTC 60.108 55.000 13.73 0.00 46.67 1.75
3274 3470 9.887406 GAAGTATTCGGAATTACTTGTCAAAAA 57.113 29.630 20.31 0.00 34.17 1.94
3344 3540 7.737972 TCCACTTTCGAGACAAATAATTTGA 57.262 32.000 0.00 0.00 43.26 2.69
3345 3541 8.160521 TCCACTTTCGAGACAAATAATTTGAA 57.839 30.769 0.00 0.00 43.26 2.69
3346 3542 8.625651 TCCACTTTCGAGACAAATAATTTGAAA 58.374 29.630 0.00 0.00 43.26 2.69
3347 3543 8.690840 CCACTTTCGAGACAAATAATTTGAAAC 58.309 33.333 0.00 0.00 43.26 2.78
3348 3544 8.409690 CACTTTCGAGACAAATAATTTGAAACG 58.590 33.333 0.00 0.00 43.26 3.60
3349 3545 7.589954 ACTTTCGAGACAAATAATTTGAAACGG 59.410 33.333 0.00 0.00 43.26 4.44
3350 3546 6.788684 TCGAGACAAATAATTTGAAACGGA 57.211 33.333 0.00 0.00 43.26 4.69
3351 3547 6.827641 TCGAGACAAATAATTTGAAACGGAG 58.172 36.000 0.00 0.00 43.26 4.63
3352 3548 6.021596 CGAGACAAATAATTTGAAACGGAGG 58.978 40.000 0.00 0.00 43.26 4.30
3353 3549 6.128391 CGAGACAAATAATTTGAAACGGAGGA 60.128 38.462 0.00 0.00 43.26 3.71
3406 3602 1.399440 CATGGATTCTCGTTGGCTGTG 59.601 52.381 0.00 0.00 0.00 3.66
3407 3603 0.396435 TGGATTCTCGTTGGCTGTGT 59.604 50.000 0.00 0.00 0.00 3.72
3408 3604 0.798776 GGATTCTCGTTGGCTGTGTG 59.201 55.000 0.00 0.00 0.00 3.82
3573 3773 2.851534 GAAAGTGCCTTTCACATACGC 58.148 47.619 17.61 0.00 46.23 4.42
3626 5217 0.321034 GCTGTCATCACTGTGCTCCA 60.321 55.000 2.12 0.00 0.00 3.86
3629 5220 2.483106 CTGTCATCACTGTGCTCCAAAG 59.517 50.000 2.12 0.00 0.00 2.77
3682 5276 6.292488 GCTGAGAATGGTTTTGTGTTTGAATG 60.292 38.462 0.00 0.00 0.00 2.67
3748 5342 0.902516 GATGAGAGGATCGGAGGGGG 60.903 65.000 0.00 0.00 42.67 5.40
3819 5413 1.510844 CAACACAAATAGGCCGGCC 59.489 57.895 39.29 39.29 0.00 6.13
3820 5414 2.043980 AACACAAATAGGCCGGCCG 61.044 57.895 38.88 26.54 41.95 6.13
3821 5415 3.209097 CACAAATAGGCCGGCCGG 61.209 66.667 40.26 40.26 41.95 6.13
3822 5416 3.723922 ACAAATAGGCCGGCCGGT 61.724 61.111 42.53 28.17 41.95 5.28
3840 5434 0.389391 GTGCCTCGGCTTAGCTATCA 59.611 55.000 9.65 0.00 42.51 2.15
3864 5458 2.996249 TAATCTCTGCTTGAGCCAGG 57.004 50.000 0.00 0.00 42.38 4.45
3898 5492 6.702716 ATAGTTCTAGTAGCAGGAGTGTTC 57.297 41.667 0.00 0.00 0.00 3.18
3933 5527 0.673437 GTGTTGTGGACCATGGGTTG 59.327 55.000 18.09 0.00 35.25 3.77
3948 5542 0.817229 GGTTGGCATGGAGAGCTAGC 60.817 60.000 6.62 6.62 0.00 3.42
4003 5603 2.560542 ACGCATGGCACTTAATTTTGGA 59.439 40.909 0.00 0.00 0.00 3.53
4143 5749 6.034591 CACGTTCCTTGATACTACCTAACAG 58.965 44.000 0.00 0.00 0.00 3.16
4144 5750 5.713861 ACGTTCCTTGATACTACCTAACAGT 59.286 40.000 0.00 0.00 0.00 3.55
4155 5761 9.176460 GATACTACCTAACAGTATCCATAGTCC 57.824 40.741 10.16 0.00 44.74 3.85
4169 5775 5.661458 TCCATAGTCCGACTTCTCAAATTC 58.339 41.667 6.31 0.00 0.00 2.17
4170 5776 4.504461 CCATAGTCCGACTTCTCAAATTCG 59.496 45.833 6.31 0.00 37.32 3.34
4183 5789 2.415168 TCAAATTCGCCACTGATCGAAC 59.585 45.455 7.82 0.00 45.68 3.95
4185 5791 2.093306 ATTCGCCACTGATCGAACAA 57.907 45.000 0.00 0.00 45.68 2.83
4186 5792 1.428448 TTCGCCACTGATCGAACAAG 58.572 50.000 0.00 0.00 39.43 3.16
4193 5821 3.428725 CCACTGATCGAACAAGAGAGAGG 60.429 52.174 0.00 0.00 0.00 3.69
4209 5837 3.117888 AGAGAGGAGCAAAAAGTTGACCA 60.118 43.478 0.00 0.00 36.83 4.02
4223 5851 0.930726 TGACCAAACCAAACCCCTCT 59.069 50.000 0.00 0.00 0.00 3.69
4224 5852 1.328279 GACCAAACCAAACCCCTCTG 58.672 55.000 0.00 0.00 0.00 3.35
4226 5854 1.503347 ACCAAACCAAACCCCTCTGAT 59.497 47.619 0.00 0.00 0.00 2.90
4229 5857 2.200373 AACCAAACCCCTCTGATTCG 57.800 50.000 0.00 0.00 0.00 3.34
4230 5858 1.358152 ACCAAACCCCTCTGATTCGA 58.642 50.000 0.00 0.00 0.00 3.71
4231 5859 1.702957 ACCAAACCCCTCTGATTCGAA 59.297 47.619 0.00 0.00 0.00 3.71
4232 5860 2.084546 CCAAACCCCTCTGATTCGAAC 58.915 52.381 0.00 0.00 0.00 3.95
4233 5861 2.084546 CAAACCCCTCTGATTCGAACC 58.915 52.381 0.00 0.00 0.00 3.62
4234 5862 0.618981 AACCCCTCTGATTCGAACCC 59.381 55.000 0.00 0.00 0.00 4.11
4235 5863 1.272554 ACCCCTCTGATTCGAACCCC 61.273 60.000 0.00 0.00 0.00 4.95
4236 5864 1.527370 CCCTCTGATTCGAACCCCC 59.473 63.158 0.00 0.00 0.00 5.40
4237 5865 0.983378 CCCTCTGATTCGAACCCCCT 60.983 60.000 0.00 0.00 0.00 4.79
4239 5867 1.195115 CTCTGATTCGAACCCCCTCA 58.805 55.000 0.00 0.00 0.00 3.86
4240 5868 1.555075 CTCTGATTCGAACCCCCTCAA 59.445 52.381 0.00 0.00 0.00 3.02
4241 5869 1.982226 TCTGATTCGAACCCCCTCAAA 59.018 47.619 0.00 0.00 0.00 2.69
4242 5870 2.027192 TCTGATTCGAACCCCCTCAAAG 60.027 50.000 0.00 0.00 0.00 2.77
4243 5871 1.702957 TGATTCGAACCCCCTCAAAGT 59.297 47.619 0.00 0.00 0.00 2.66
4244 5872 2.290071 TGATTCGAACCCCCTCAAAGTC 60.290 50.000 0.00 0.00 0.00 3.01
4246 5874 0.974383 TCGAACCCCCTCAAAGTCTC 59.026 55.000 0.00 0.00 0.00 3.36
4247 5875 0.036294 CGAACCCCCTCAAAGTCTCC 60.036 60.000 0.00 0.00 0.00 3.71
4263 6150 4.279145 AGTCTCCTTAAATGCTCGGACTA 58.721 43.478 0.00 0.00 32.12 2.59
4285 6172 5.808366 ATTCGCCACTCCTCTTATTCATA 57.192 39.130 0.00 0.00 0.00 2.15
4287 6174 5.139435 TCGCCACTCCTCTTATTCATATG 57.861 43.478 0.00 0.00 0.00 1.78
4289 6176 5.047731 TCGCCACTCCTCTTATTCATATGAG 60.048 44.000 5.39 0.00 35.48 2.90
4292 6179 6.817641 GCCACTCCTCTTATTCATATGAGATG 59.182 42.308 5.39 1.58 36.95 2.90
4293 6180 7.310299 GCCACTCCTCTTATTCATATGAGATGA 60.310 40.741 5.39 5.54 36.95 2.92
4294 6181 8.591940 CCACTCCTCTTATTCATATGAGATGAA 58.408 37.037 4.85 4.85 41.59 2.57
4306 6193 6.499699 TCATATGAGATGAATAGCCACTCCTT 59.500 38.462 0.00 0.00 0.00 3.36
4318 6205 9.561069 GAATAGCCACTCCTTTTATTTATCTCA 57.439 33.333 0.00 0.00 0.00 3.27
4347 7542 1.065928 GAGTATGAGTGACCGGGCG 59.934 63.158 6.32 0.00 0.00 6.13
4366 7561 2.422479 GCGTGTCTAGTCAGTGGTCATA 59.578 50.000 0.00 0.00 0.00 2.15
4367 7562 3.066900 GCGTGTCTAGTCAGTGGTCATAT 59.933 47.826 0.00 0.00 0.00 1.78
4371 7566 4.335594 TGTCTAGTCAGTGGTCATATGTCG 59.664 45.833 1.90 0.00 0.00 4.35
4399 7594 6.777091 CACATAGGATTGGACCCATCATAAAA 59.223 38.462 7.80 0.00 0.00 1.52
4408 7606 7.552050 TGGACCCATCATAAAACATCTTTTT 57.448 32.000 0.00 0.00 31.74 1.94
4455 7663 7.771826 TCTTCTTCTTCATCAATCACATGCATA 59.228 33.333 0.00 0.00 0.00 3.14
4460 7668 5.952526 TCATCAATCACATGCATATGACC 57.047 39.130 10.42 0.00 37.73 4.02
4463 7671 2.880268 CAATCACATGCATATGACCGGT 59.120 45.455 10.42 6.92 37.73 5.28
4464 7672 4.064388 CAATCACATGCATATGACCGGTA 58.936 43.478 10.42 0.00 37.73 4.02
4466 7674 3.727726 TCACATGCATATGACCGGTAAG 58.272 45.455 7.34 0.00 37.73 2.34
4496 7709 3.321039 TGAGGAATATGGCTGAGTGGAT 58.679 45.455 0.00 0.00 0.00 3.41
4497 7710 3.072038 TGAGGAATATGGCTGAGTGGATG 59.928 47.826 0.00 0.00 0.00 3.51
4499 7712 2.553904 GGAATATGGCTGAGTGGATGGG 60.554 54.545 0.00 0.00 0.00 4.00
4523 7741 0.250858 TAGGAAGACGGACACGACCA 60.251 55.000 0.00 0.00 44.60 4.02
4524 7742 1.080705 GGAAGACGGACACGACCAG 60.081 63.158 0.00 0.00 44.60 4.00
4621 7839 3.370315 GGAGTGAGGATTCAGACATGCTT 60.370 47.826 0.00 0.00 32.98 3.91
4638 7856 1.001181 GCTTGCATTTCCAGCCTTTGA 59.999 47.619 0.00 0.00 0.00 2.69
4686 7904 1.735571 GCATTTTCCCTGCTGCATTTG 59.264 47.619 1.31 0.00 36.68 2.32
4716 7934 3.143728 CATCTTGCTGCATATGCCTGTA 58.856 45.455 24.54 13.86 41.18 2.74
4717 7935 3.497103 TCTTGCTGCATATGCCTGTAT 57.503 42.857 24.54 0.00 41.18 2.29
4719 7937 4.209538 TCTTGCTGCATATGCCTGTATTT 58.790 39.130 24.54 0.00 41.18 1.40
4729 7947 6.459024 GCATATGCCTGTATTTGGTTTTCGTA 60.459 38.462 17.26 0.00 34.31 3.43
4732 7950 5.250200 TGCCTGTATTTGGTTTTCGTATCT 58.750 37.500 0.00 0.00 0.00 1.98
4776 7994 1.202651 GCAGGTCCATATACTGGCGTT 60.203 52.381 0.00 0.00 45.52 4.84
4777 7995 2.745152 GCAGGTCCATATACTGGCGTTT 60.745 50.000 0.00 0.00 45.52 3.60
4778 7996 3.131396 CAGGTCCATATACTGGCGTTTC 58.869 50.000 0.00 0.00 45.52 2.78
4779 7997 2.104281 AGGTCCATATACTGGCGTTTCC 59.896 50.000 0.00 0.00 45.52 3.13
4780 7998 2.104281 GGTCCATATACTGGCGTTTCCT 59.896 50.000 0.00 0.00 45.52 3.36
4781 7999 3.322828 GGTCCATATACTGGCGTTTCCTA 59.677 47.826 0.00 0.00 45.52 2.94
4782 8000 4.020485 GGTCCATATACTGGCGTTTCCTAT 60.020 45.833 0.00 0.00 45.52 2.57
4783 8001 5.169295 GTCCATATACTGGCGTTTCCTATC 58.831 45.833 0.00 0.00 45.52 2.08
4784 8002 4.836175 TCCATATACTGGCGTTTCCTATCA 59.164 41.667 0.00 0.00 45.52 2.15
4785 8003 5.047306 TCCATATACTGGCGTTTCCTATCAG 60.047 44.000 0.00 0.00 45.52 2.90
4786 8004 2.596904 TACTGGCGTTTCCTATCAGC 57.403 50.000 0.00 0.00 35.26 4.26
4789 8007 2.993539 GGCGTTTCCTATCAGCCTC 58.006 57.895 0.00 0.00 44.06 4.70
4790 8008 0.533085 GGCGTTTCCTATCAGCCTCC 60.533 60.000 0.00 0.00 44.06 4.30
4791 8009 0.533085 GCGTTTCCTATCAGCCTCCC 60.533 60.000 0.00 0.00 0.00 4.30
4792 8010 0.830648 CGTTTCCTATCAGCCTCCCA 59.169 55.000 0.00 0.00 0.00 4.37
4793 8011 1.209504 CGTTTCCTATCAGCCTCCCAA 59.790 52.381 0.00 0.00 0.00 4.12
4794 8012 2.644676 GTTTCCTATCAGCCTCCCAAC 58.355 52.381 0.00 0.00 0.00 3.77
4795 8013 1.965414 TTCCTATCAGCCTCCCAACA 58.035 50.000 0.00 0.00 0.00 3.33
4796 8014 1.965414 TCCTATCAGCCTCCCAACAA 58.035 50.000 0.00 0.00 0.00 2.83
4797 8015 1.839994 TCCTATCAGCCTCCCAACAAG 59.160 52.381 0.00 0.00 0.00 3.16
4798 8016 1.839994 CCTATCAGCCTCCCAACAAGA 59.160 52.381 0.00 0.00 0.00 3.02
4799 8017 2.441001 CCTATCAGCCTCCCAACAAGAT 59.559 50.000 0.00 0.00 0.00 2.40
4800 8018 3.648067 CCTATCAGCCTCCCAACAAGATA 59.352 47.826 0.00 0.00 0.00 1.98
4801 8019 4.288105 CCTATCAGCCTCCCAACAAGATAT 59.712 45.833 0.00 0.00 0.00 1.63
4802 8020 3.565764 TCAGCCTCCCAACAAGATATG 57.434 47.619 0.00 0.00 0.00 1.78
4803 8021 1.952296 CAGCCTCCCAACAAGATATGC 59.048 52.381 0.00 0.00 0.00 3.14
4804 8022 1.565759 AGCCTCCCAACAAGATATGCA 59.434 47.619 0.00 0.00 0.00 3.96
4805 8023 1.952296 GCCTCCCAACAAGATATGCAG 59.048 52.381 0.00 0.00 0.00 4.41
4806 8024 2.579873 CCTCCCAACAAGATATGCAGG 58.420 52.381 0.00 0.00 0.00 4.85
4807 8025 2.092212 CCTCCCAACAAGATATGCAGGT 60.092 50.000 0.00 0.00 0.00 4.00
4808 8026 3.209410 CTCCCAACAAGATATGCAGGTC 58.791 50.000 0.00 0.00 0.00 3.85
4809 8027 2.575735 TCCCAACAAGATATGCAGGTCA 59.424 45.455 0.00 0.00 0.00 4.02
4810 8028 3.202818 TCCCAACAAGATATGCAGGTCAT 59.797 43.478 0.00 0.00 39.17 3.06
4811 8029 4.411869 TCCCAACAAGATATGCAGGTCATA 59.588 41.667 0.00 0.00 41.52 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.555741 GATCGAATGAGCCTGCGAGC 61.556 60.000 0.00 0.00 36.12 5.03
49 50 6.142798 CACGAGATGGAATTTTGTTTTGACAG 59.857 38.462 0.00 0.00 0.00 3.51
60 61 2.372264 AGCATGCACGAGATGGAATTT 58.628 42.857 21.98 0.00 29.34 1.82
63 64 1.469703 CAAAGCATGCACGAGATGGAA 59.530 47.619 21.98 0.00 29.34 3.53
64 65 1.089112 CAAAGCATGCACGAGATGGA 58.911 50.000 21.98 0.00 0.00 3.41
65 66 0.099968 CCAAAGCATGCACGAGATGG 59.900 55.000 21.98 13.76 0.00 3.51
66 67 1.089112 TCCAAAGCATGCACGAGATG 58.911 50.000 21.98 8.72 0.00 2.90
80 88 1.002624 GCGGGTCACTGGATCCAAA 60.003 57.895 17.00 1.15 45.27 3.28
90 98 0.521735 CTTTAGCTTTGGCGGGTCAC 59.478 55.000 0.00 0.00 44.37 3.67
117 125 3.394674 TGTTGTTTCTGCAGACGGATA 57.605 42.857 18.03 0.00 0.00 2.59
180 196 1.110442 CTGAGACTTGAGCGGAGGAT 58.890 55.000 0.00 0.00 0.00 3.24
181 197 0.038310 TCTGAGACTTGAGCGGAGGA 59.962 55.000 0.00 0.00 0.00 3.71
182 198 1.110442 ATCTGAGACTTGAGCGGAGG 58.890 55.000 0.00 0.00 0.00 4.30
184 200 2.562738 TCAAATCTGAGACTTGAGCGGA 59.437 45.455 1.75 0.00 0.00 5.54
210 268 1.437986 GGGTCAAGCGCTAGTCGAT 59.562 57.895 12.05 0.00 41.67 3.59
357 416 2.800736 CAATAAGTGCGCCTGCCC 59.199 61.111 4.18 0.00 41.78 5.36
426 485 5.771153 AAACTAGCCTCGTATAGACTTCC 57.229 43.478 0.00 0.00 0.00 3.46
427 486 6.692249 GTGAAAACTAGCCTCGTATAGACTTC 59.308 42.308 0.00 0.00 0.00 3.01
455 514 3.945434 CACGCTCGATGCCATGGC 61.945 66.667 30.54 30.54 38.78 4.40
510 569 2.114825 CCGTCGCCTTATTTACTCGAC 58.885 52.381 0.00 0.00 44.01 4.20
523 590 1.470940 GTCGAGTAATTACCGTCGCC 58.529 55.000 17.78 7.28 32.41 5.54
526 593 2.797439 GCCTGGTCGAGTAATTACCGTC 60.797 54.545 19.24 15.56 35.98 4.79
539 606 4.933064 GCCTCGATCGCCTGGTCG 62.933 72.222 11.09 0.00 39.11 4.79
540 607 4.933064 CGCCTCGATCGCCTGGTC 62.933 72.222 11.09 7.82 0.00 4.02
544 614 3.587933 GTCTCGCCTCGATCGCCT 61.588 66.667 11.09 0.00 34.61 5.52
559 629 2.287009 CCAGCTTTCAGTTTTCACCGTC 60.287 50.000 0.00 0.00 0.00 4.79
577 647 2.302199 TATCTCGCCAGCTGCACCAG 62.302 60.000 8.66 0.39 41.33 4.00
581 651 1.153568 GTGTATCTCGCCAGCTGCA 60.154 57.895 8.66 0.00 41.33 4.41
582 652 2.233654 CGTGTATCTCGCCAGCTGC 61.234 63.158 8.66 2.87 0.00 5.25
583 653 1.589993 CCGTGTATCTCGCCAGCTG 60.590 63.158 6.78 6.78 0.00 4.24
584 654 1.753078 TCCGTGTATCTCGCCAGCT 60.753 57.895 0.00 0.00 0.00 4.24
610 681 2.589157 CCAACTAGCACCCGTCCCA 61.589 63.158 0.00 0.00 0.00 4.37
611 682 2.267961 CCAACTAGCACCCGTCCC 59.732 66.667 0.00 0.00 0.00 4.46
612 683 2.267961 CCCAACTAGCACCCGTCC 59.732 66.667 0.00 0.00 0.00 4.79
613 684 2.436115 GCCCAACTAGCACCCGTC 60.436 66.667 0.00 0.00 0.00 4.79
614 685 2.928396 AGCCCAACTAGCACCCGT 60.928 61.111 0.00 0.00 0.00 5.28
615 686 2.125106 GAGCCCAACTAGCACCCG 60.125 66.667 0.00 0.00 0.00 5.28
616 687 0.038310 AAAGAGCCCAACTAGCACCC 59.962 55.000 0.00 0.00 0.00 4.61
619 690 2.783135 CTCAAAAGAGCCCAACTAGCA 58.217 47.619 0.00 0.00 0.00 3.49
620 691 1.470494 GCTCAAAAGAGCCCAACTAGC 59.530 52.381 6.21 0.00 42.05 3.42
621 692 2.485814 GTGCTCAAAAGAGCCCAACTAG 59.514 50.000 14.22 0.00 46.96 2.57
622 693 2.504367 GTGCTCAAAAGAGCCCAACTA 58.496 47.619 14.22 0.00 46.96 2.24
623 694 1.322442 GTGCTCAAAAGAGCCCAACT 58.678 50.000 14.22 0.00 46.96 3.16
685 761 0.375454 TTTACACACACGCACACAGC 59.625 50.000 0.00 0.00 40.87 4.40
688 764 2.605818 TCTTCTTTACACACACGCACAC 59.394 45.455 0.00 0.00 0.00 3.82
693 769 5.049336 TCTCTCTCTCTTCTTTACACACACG 60.049 44.000 0.00 0.00 0.00 4.49
698 774 5.183140 ACTGCTCTCTCTCTCTTCTTTACAC 59.817 44.000 0.00 0.00 0.00 2.90
699 775 5.182950 CACTGCTCTCTCTCTCTTCTTTACA 59.817 44.000 0.00 0.00 0.00 2.41
700 776 5.393027 CCACTGCTCTCTCTCTCTTCTTTAC 60.393 48.000 0.00 0.00 0.00 2.01
701 777 4.704540 CCACTGCTCTCTCTCTCTTCTTTA 59.295 45.833 0.00 0.00 0.00 1.85
703 779 3.091545 CCACTGCTCTCTCTCTCTTCTT 58.908 50.000 0.00 0.00 0.00 2.52
704 780 2.308570 TCCACTGCTCTCTCTCTCTTCT 59.691 50.000 0.00 0.00 0.00 2.85
705 781 2.684881 CTCCACTGCTCTCTCTCTCTTC 59.315 54.545 0.00 0.00 0.00 2.87
706 782 2.726821 CTCCACTGCTCTCTCTCTCTT 58.273 52.381 0.00 0.00 0.00 2.85
707 783 1.683011 GCTCCACTGCTCTCTCTCTCT 60.683 57.143 0.00 0.00 0.00 3.10
708 784 0.740737 GCTCCACTGCTCTCTCTCTC 59.259 60.000 0.00 0.00 0.00 3.20
709 785 0.039472 TGCTCCACTGCTCTCTCTCT 59.961 55.000 0.00 0.00 0.00 3.10
713 789 1.624479 CCCATGCTCCACTGCTCTCT 61.624 60.000 0.00 0.00 0.00 3.10
971 1095 2.163509 GCCTCACTACTCACTCACTCA 58.836 52.381 0.00 0.00 0.00 3.41
1245 1369 1.078848 AGATGGAAGAGGTGCGTGC 60.079 57.895 0.00 0.00 0.00 5.34
1246 1370 1.364626 GCAGATGGAAGAGGTGCGTG 61.365 60.000 0.00 0.00 0.00 5.34
1247 1371 1.078848 GCAGATGGAAGAGGTGCGT 60.079 57.895 0.00 0.00 0.00 5.24
1248 1372 1.078918 TGCAGATGGAAGAGGTGCG 60.079 57.895 0.00 0.00 36.92 5.34
1284 1412 2.290323 GGCTAGAAGCAAAAGACCAGGA 60.290 50.000 0.00 0.00 44.75 3.86
1285 1413 2.087646 GGCTAGAAGCAAAAGACCAGG 58.912 52.381 0.00 0.00 44.75 4.45
1286 1414 2.783135 TGGCTAGAAGCAAAAGACCAG 58.217 47.619 0.00 0.00 44.75 4.00
1287 1415 2.949177 TGGCTAGAAGCAAAAGACCA 57.051 45.000 0.00 0.00 44.75 4.02
1414 1545 4.587189 ACGAGCCGGCGCCTATTC 62.587 66.667 26.68 16.96 34.57 1.75
1415 1546 2.300850 TAAACGAGCCGGCGCCTATT 62.301 55.000 26.68 17.99 34.57 1.73
1416 1547 2.788640 TAAACGAGCCGGCGCCTAT 61.789 57.895 26.68 12.66 34.57 2.57
1417 1548 3.451004 TAAACGAGCCGGCGCCTA 61.451 61.111 26.68 10.68 34.57 3.93
1427 1558 0.361184 GCGCGTGTACAGTAAACGAG 59.639 55.000 24.87 22.13 39.64 4.18
1445 1576 5.006358 ACATTTTCATGAGAATACGTACGGC 59.994 40.000 21.06 5.92 34.11 5.68
1641 1778 1.765314 CAGGTAAGTGATGGAGAGGGG 59.235 57.143 0.00 0.00 0.00 4.79
1710 1847 6.566197 AGAAGAAGTTCTTGCTTTACATGG 57.434 37.500 22.68 0.00 40.35 3.66
1723 1860 6.402222 TCATGCTAGGAAGAAGAAGAAGTTC 58.598 40.000 0.00 0.00 0.00 3.01
1902 2043 3.949113 AGAAGCTGCTGTAGGTAGAGTAC 59.051 47.826 1.35 0.00 35.72 2.73
1903 2044 4.237976 AGAAGCTGCTGTAGGTAGAGTA 57.762 45.455 1.35 0.00 35.72 2.59
1904 2045 3.094484 AGAAGCTGCTGTAGGTAGAGT 57.906 47.619 1.35 0.00 35.72 3.24
1905 2046 4.399618 TGTAAGAAGCTGCTGTAGGTAGAG 59.600 45.833 1.35 0.00 35.72 2.43
1906 2047 4.158025 GTGTAAGAAGCTGCTGTAGGTAGA 59.842 45.833 1.35 0.00 35.72 2.59
1907 2048 4.425520 GTGTAAGAAGCTGCTGTAGGTAG 58.574 47.826 1.35 0.00 35.72 3.18
1933 2074 0.534203 GGTGCAGAAAGGGAACGTGA 60.534 55.000 0.00 0.00 0.00 4.35
1995 2136 4.487714 AAATGAGTGGGAATTCTAGCGA 57.512 40.909 5.23 0.00 0.00 4.93
2025 2166 1.063972 CGTGCATGCATTAACCCCG 59.936 57.895 25.64 16.66 0.00 5.73
2097 2238 3.541996 TCTGCTGCGGATAAATTCAGA 57.458 42.857 7.16 0.00 0.00 3.27
2108 2249 1.374631 TGCTGTACTTCTGCTGCGG 60.375 57.895 0.95 0.95 40.79 5.69
2134 2275 7.360361 ACGAAATGAAAATTAGTTGGACAGTC 58.640 34.615 0.00 0.00 0.00 3.51
2153 2294 2.932614 CTGGCGATCAGAGAAACGAAAT 59.067 45.455 0.00 0.00 46.18 2.17
2154 2295 2.337583 CTGGCGATCAGAGAAACGAAA 58.662 47.619 0.00 0.00 46.18 3.46
2155 2296 1.996292 CTGGCGATCAGAGAAACGAA 58.004 50.000 0.00 0.00 46.18 3.85
2156 2297 0.458543 GCTGGCGATCAGAGAAACGA 60.459 55.000 9.87 0.00 46.18 3.85
2157 2298 1.424493 GGCTGGCGATCAGAGAAACG 61.424 60.000 9.87 0.00 46.18 3.60
2188 2329 4.760047 CGGAGGTGCTGGAACCGG 62.760 72.222 0.00 0.00 45.53 5.28
2696 2840 2.905935 TACTCCTTCTCCTCGGCCCG 62.906 65.000 0.00 0.00 0.00 6.13
2911 3099 0.682292 TATGCGTCCCACAGTGTCAA 59.318 50.000 0.00 0.00 0.00 3.18
2921 3109 0.468226 TGGGAACTCATATGCGTCCC 59.532 55.000 22.19 22.19 36.52 4.46
3078 3266 6.365789 TGCAAAGCTTTTTCCTATCAATTTCG 59.634 34.615 9.53 0.00 0.00 3.46
3079 3267 7.656707 TGCAAAGCTTTTTCCTATCAATTTC 57.343 32.000 9.53 0.00 0.00 2.17
3083 3271 4.931002 GCATGCAAAGCTTTTTCCTATCAA 59.069 37.500 14.21 0.00 0.00 2.57
3087 3275 4.247258 CATGCATGCAAAGCTTTTTCCTA 58.753 39.130 26.68 0.00 0.00 2.94
3244 3440 5.114081 CAAGTAATTCCGAATACTTCCCGT 58.886 41.667 10.54 0.00 31.15 5.28
3318 3514 9.443323 TCAAATTATTTGTCTCGAAAGTGGATA 57.557 29.630 16.06 0.00 41.36 2.59
3319 3515 8.335532 TCAAATTATTTGTCTCGAAAGTGGAT 57.664 30.769 16.06 0.00 41.36 3.41
3320 3516 7.737972 TCAAATTATTTGTCTCGAAAGTGGA 57.262 32.000 16.06 0.00 41.36 4.02
3321 3517 8.690840 GTTTCAAATTATTTGTCTCGAAAGTGG 58.309 33.333 16.06 0.00 41.36 4.00
3322 3518 8.409690 CGTTTCAAATTATTTGTCTCGAAAGTG 58.590 33.333 16.06 3.29 41.36 3.16
3323 3519 7.589954 CCGTTTCAAATTATTTGTCTCGAAAGT 59.410 33.333 16.06 0.00 41.36 2.66
3324 3520 7.801315 TCCGTTTCAAATTATTTGTCTCGAAAG 59.199 33.333 16.06 7.89 41.36 2.62
3325 3521 7.640852 TCCGTTTCAAATTATTTGTCTCGAAA 58.359 30.769 16.06 7.31 41.36 3.46
3326 3522 7.192148 TCCGTTTCAAATTATTTGTCTCGAA 57.808 32.000 16.06 1.81 41.36 3.71
3327 3523 6.128391 CCTCCGTTTCAAATTATTTGTCTCGA 60.128 38.462 16.06 7.12 41.36 4.04
3328 3524 6.021596 CCTCCGTTTCAAATTATTTGTCTCG 58.978 40.000 16.06 16.29 41.36 4.04
3329 3525 7.094762 ACTCCTCCGTTTCAAATTATTTGTCTC 60.095 37.037 16.06 7.73 41.36 3.36
3330 3526 6.715264 ACTCCTCCGTTTCAAATTATTTGTCT 59.285 34.615 16.06 0.00 41.36 3.41
3331 3527 6.909909 ACTCCTCCGTTTCAAATTATTTGTC 58.090 36.000 16.06 8.30 41.36 3.18
3332 3528 6.894339 ACTCCTCCGTTTCAAATTATTTGT 57.106 33.333 16.06 0.00 41.36 2.83
3333 3529 6.959311 CGTACTCCTCCGTTTCAAATTATTTG 59.041 38.462 11.12 11.12 41.96 2.32
3334 3530 6.652062 ACGTACTCCTCCGTTTCAAATTATTT 59.348 34.615 0.00 0.00 32.50 1.40
3335 3531 6.091713 CACGTACTCCTCCGTTTCAAATTATT 59.908 38.462 0.00 0.00 34.59 1.40
3336 3532 5.579511 CACGTACTCCTCCGTTTCAAATTAT 59.420 40.000 0.00 0.00 34.59 1.28
3337 3533 4.925054 CACGTACTCCTCCGTTTCAAATTA 59.075 41.667 0.00 0.00 34.59 1.40
3338 3534 3.744426 CACGTACTCCTCCGTTTCAAATT 59.256 43.478 0.00 0.00 34.59 1.82
3339 3535 3.323243 CACGTACTCCTCCGTTTCAAAT 58.677 45.455 0.00 0.00 34.59 2.32
3340 3536 2.746269 CACGTACTCCTCCGTTTCAAA 58.254 47.619 0.00 0.00 34.59 2.69
3341 3537 1.603678 GCACGTACTCCTCCGTTTCAA 60.604 52.381 0.00 0.00 34.59 2.69
3342 3538 0.038892 GCACGTACTCCTCCGTTTCA 60.039 55.000 0.00 0.00 34.59 2.69
3343 3539 1.069378 CGCACGTACTCCTCCGTTTC 61.069 60.000 0.00 0.00 34.59 2.78
3344 3540 1.080974 CGCACGTACTCCTCCGTTT 60.081 57.895 0.00 0.00 34.59 3.60
3345 3541 0.955428 TACGCACGTACTCCTCCGTT 60.955 55.000 0.00 0.00 34.59 4.44
3346 3542 1.375908 TACGCACGTACTCCTCCGT 60.376 57.895 0.00 0.00 37.90 4.69
3347 3543 1.061570 GTACGCACGTACTCCTCCG 59.938 63.158 22.45 0.00 45.30 4.63
3348 3544 1.061570 CGTACGCACGTACTCCTCC 59.938 63.158 25.53 4.40 46.22 4.30
3349 3545 4.659002 CGTACGCACGTACTCCTC 57.341 61.111 25.53 5.03 46.22 3.71
3379 3575 0.179062 ACGAGAATCCATGGAGCAGC 60.179 55.000 21.33 9.02 0.00 5.25
3406 3602 0.812412 AACGTACAGTGCACCACCAC 60.812 55.000 14.63 5.83 34.49 4.16
3407 3603 0.531090 GAACGTACAGTGCACCACCA 60.531 55.000 14.63 0.00 34.49 4.17
3408 3604 0.531090 TGAACGTACAGTGCACCACC 60.531 55.000 14.63 0.00 32.17 4.61
3541 3741 2.509336 ACTTTCGCCTGCCGATCG 60.509 61.111 8.51 8.51 46.81 3.69
3542 3742 3.093278 CACTTTCGCCTGCCGATC 58.907 61.111 0.00 0.00 46.81 3.69
3543 3743 3.127533 GCACTTTCGCCTGCCGAT 61.128 61.111 0.00 0.00 46.81 4.18
3748 5342 1.849823 CCCCTCATCATCCCCTCCC 60.850 68.421 0.00 0.00 0.00 4.30
3779 5373 4.039092 GGCTGCCTCTTCCTGCCA 62.039 66.667 12.43 0.00 44.05 4.92
3806 5400 3.209097 CACCGGCCGGCCTATTTG 61.209 66.667 43.58 28.61 39.32 2.32
3819 5413 2.088674 ATAGCTAAGCCGAGGCACCG 62.089 60.000 17.18 4.68 44.88 4.94
3820 5414 0.319986 GATAGCTAAGCCGAGGCACC 60.320 60.000 17.18 1.38 44.88 5.01
3821 5415 0.389391 TGATAGCTAAGCCGAGGCAC 59.611 55.000 17.18 2.80 44.88 5.01
3822 5416 1.069204 CTTGATAGCTAAGCCGAGGCA 59.931 52.381 17.18 0.00 44.88 4.75
3864 5458 7.883217 TGCTACTAGAACTATTACTACATGCC 58.117 38.462 0.00 0.00 0.00 4.40
3898 5492 4.060900 ACAACACACAAGTAGAGATGCTG 58.939 43.478 0.00 0.00 0.00 4.41
3933 5527 1.001860 CTAAGGCTAGCTCTCCATGCC 59.998 57.143 15.72 0.00 43.52 4.40
4003 5603 5.362717 TCACCGTTCACATAGACATAGGATT 59.637 40.000 0.00 0.00 0.00 3.01
4143 5749 5.769484 TTGAGAAGTCGGACTATGGATAC 57.231 43.478 11.71 0.64 0.00 2.24
4144 5750 6.978674 ATTTGAGAAGTCGGACTATGGATA 57.021 37.500 11.71 0.00 0.00 2.59
4148 5754 5.627802 CGAATTTGAGAAGTCGGACTATG 57.372 43.478 11.71 0.00 46.26 2.23
4169 5775 0.994995 CTCTTGTTCGATCAGTGGCG 59.005 55.000 0.00 0.00 0.00 5.69
4170 5776 2.094494 TCTCTCTTGTTCGATCAGTGGC 60.094 50.000 0.00 0.00 0.00 5.01
4183 5789 4.818546 TCAACTTTTTGCTCCTCTCTCTTG 59.181 41.667 0.00 0.00 32.17 3.02
4185 5791 4.384940 GTCAACTTTTTGCTCCTCTCTCT 58.615 43.478 0.00 0.00 32.17 3.10
4186 5792 3.500299 GGTCAACTTTTTGCTCCTCTCTC 59.500 47.826 0.00 0.00 32.17 3.20
4193 5821 3.855858 TGGTTTGGTCAACTTTTTGCTC 58.144 40.909 0.00 0.00 35.46 4.26
4209 5837 2.107552 TCGAATCAGAGGGGTTTGGTTT 59.892 45.455 0.00 0.00 0.00 3.27
4223 5851 1.702957 ACTTTGAGGGGGTTCGAATCA 59.297 47.619 11.19 2.30 0.00 2.57
4224 5852 2.027100 AGACTTTGAGGGGGTTCGAATC 60.027 50.000 0.00 0.00 0.00 2.52
4226 5854 1.346722 GAGACTTTGAGGGGGTTCGAA 59.653 52.381 0.00 0.00 0.00 3.71
4229 5857 1.363246 AGGAGACTTTGAGGGGGTTC 58.637 55.000 0.00 0.00 37.44 3.62
4230 5858 3.599037 AGGAGACTTTGAGGGGGTT 57.401 52.632 0.00 0.00 37.44 4.11
4242 5870 3.528597 AGTCCGAGCATTTAAGGAGAC 57.471 47.619 0.00 0.00 32.82 3.36
4243 5871 5.507482 CGAATAGTCCGAGCATTTAAGGAGA 60.507 44.000 0.00 0.00 32.82 3.71
4244 5872 4.681942 CGAATAGTCCGAGCATTTAAGGAG 59.318 45.833 0.00 0.00 32.82 3.69
4246 5874 3.184581 GCGAATAGTCCGAGCATTTAAGG 59.815 47.826 0.00 0.00 0.00 2.69
4247 5875 3.184581 GGCGAATAGTCCGAGCATTTAAG 59.815 47.826 0.00 0.00 0.00 1.85
4263 6150 4.696479 ATGAATAAGAGGAGTGGCGAAT 57.304 40.909 0.00 0.00 0.00 3.34
4285 6172 5.643421 AAAGGAGTGGCTATTCATCTCAT 57.357 39.130 0.00 0.00 0.00 2.90
4287 6174 8.457238 AAATAAAAGGAGTGGCTATTCATCTC 57.543 34.615 0.00 0.00 0.00 2.75
4292 6179 9.561069 TGAGATAAATAAAAGGAGTGGCTATTC 57.439 33.333 0.00 0.00 0.00 1.75
4294 6181 9.512588 CATGAGATAAATAAAAGGAGTGGCTAT 57.487 33.333 0.00 0.00 0.00 2.97
4295 6182 8.494433 ACATGAGATAAATAAAAGGAGTGGCTA 58.506 33.333 0.00 0.00 0.00 3.93
4296 6183 7.349598 ACATGAGATAAATAAAAGGAGTGGCT 58.650 34.615 0.00 0.00 0.00 4.75
4297 6184 7.573968 ACATGAGATAAATAAAAGGAGTGGC 57.426 36.000 0.00 0.00 0.00 5.01
4318 6205 6.072230 CGGTCACTCATACTCATCTCATACAT 60.072 42.308 0.00 0.00 0.00 2.29
4347 7542 5.583495 GACATATGACCACTGACTAGACAC 58.417 45.833 10.38 0.00 0.00 3.67
4367 7562 0.180171 CCAATCCTATGTGGCCGACA 59.820 55.000 9.93 9.93 39.53 4.35
4371 7566 0.178990 GGGTCCAATCCTATGTGGCC 60.179 60.000 0.00 0.00 34.68 5.36
4425 7623 9.856488 CATGTGATTGATGAAGAAGAAGAAAAT 57.144 29.630 0.00 0.00 0.00 1.82
4474 7687 3.321039 TCCACTCAGCCATATTCCTCAT 58.679 45.455 0.00 0.00 0.00 2.90
4482 7695 2.487746 TACCCATCCACTCAGCCATA 57.512 50.000 0.00 0.00 0.00 2.74
4496 7709 3.196254 GTGTCCGTCTTCCTATTTACCCA 59.804 47.826 0.00 0.00 0.00 4.51
4497 7710 3.736126 CGTGTCCGTCTTCCTATTTACCC 60.736 52.174 0.00 0.00 0.00 3.69
4499 7712 4.101235 GTCGTGTCCGTCTTCCTATTTAC 58.899 47.826 0.00 0.00 35.01 2.01
4523 7741 1.609208 AAACTGGAAATGCAGCGTCT 58.391 45.000 1.49 0.00 0.00 4.18
4524 7742 2.422276 AAAACTGGAAATGCAGCGTC 57.578 45.000 1.49 0.00 0.00 5.19
4548 7766 5.355910 GCAAATTGTAAATTACTCCCTCCGA 59.644 40.000 4.67 0.00 0.00 4.55
4621 7839 1.344114 GGTTCAAAGGCTGGAAATGCA 59.656 47.619 3.72 0.00 0.00 3.96
4638 7856 0.405973 GCAAAGAGGAAGGGGAGGTT 59.594 55.000 0.00 0.00 0.00 3.50
4717 7935 9.549509 CGAAATAATTCAGATACGAAAACCAAA 57.450 29.630 0.00 0.00 35.15 3.28
4719 7937 8.481974 TCGAAATAATTCAGATACGAAAACCA 57.518 30.769 0.00 0.00 35.15 3.67
4729 7947 7.819415 TCGCCTGATAATCGAAATAATTCAGAT 59.181 33.333 11.12 0.00 35.15 2.90
4732 7950 6.128553 GCTCGCCTGATAATCGAAATAATTCA 60.129 38.462 0.00 0.00 35.15 2.57
4742 7960 0.032678 ACCTGCTCGCCTGATAATCG 59.967 55.000 0.00 0.00 0.00 3.34
4776 7994 1.965414 TGTTGGGAGGCTGATAGGAA 58.035 50.000 0.00 0.00 0.00 3.36
4777 7995 1.839994 CTTGTTGGGAGGCTGATAGGA 59.160 52.381 0.00 0.00 0.00 2.94
4778 7996 1.839994 TCTTGTTGGGAGGCTGATAGG 59.160 52.381 0.00 0.00 0.00 2.57
4779 7997 3.853355 ATCTTGTTGGGAGGCTGATAG 57.147 47.619 0.00 0.00 0.00 2.08
4780 7998 4.505566 GCATATCTTGTTGGGAGGCTGATA 60.506 45.833 0.00 0.00 0.00 2.15
4781 7999 3.749954 GCATATCTTGTTGGGAGGCTGAT 60.750 47.826 0.00 0.00 0.00 2.90
4782 8000 2.421952 GCATATCTTGTTGGGAGGCTGA 60.422 50.000 0.00 0.00 0.00 4.26
4783 8001 1.952296 GCATATCTTGTTGGGAGGCTG 59.048 52.381 0.00 0.00 0.00 4.85
4784 8002 1.565759 TGCATATCTTGTTGGGAGGCT 59.434 47.619 0.00 0.00 0.00 4.58
4785 8003 1.952296 CTGCATATCTTGTTGGGAGGC 59.048 52.381 0.00 0.00 0.00 4.70
4786 8004 2.092212 ACCTGCATATCTTGTTGGGAGG 60.092 50.000 0.00 0.00 0.00 4.30
4787 8005 3.209410 GACCTGCATATCTTGTTGGGAG 58.791 50.000 0.00 0.00 0.00 4.30
4788 8006 2.575735 TGACCTGCATATCTTGTTGGGA 59.424 45.455 0.00 0.00 0.00 4.37
4789 8007 3.003394 TGACCTGCATATCTTGTTGGG 57.997 47.619 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.