Multiple sequence alignment - TraesCS3B01G158500

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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 TraesCS3B01G158500 chr3B 100.000 3741 0 0 1 3741 153811512 153807772 0.000000e+00 6909.0
1 TraesCS3B01G158500 chr3D 91.077 2813 108 49 109 2869 103234557 103231836 0.000000e+00 3672.0
2 TraesCS3B01G158500 chr3D 91.298 724 38 8 2871 3583 103231731 103231022 0.000000e+00 965.0
3 TraesCS3B01G158500 chr3D 88.679 212 8 6 2289 2484 546711186 546710975 1.040000e-60 244.0
4 TraesCS3B01G158500 chr3D 85.463 227 15 7 1877 2095 546711524 546711308 1.750000e-53 220.0
5 TraesCS3B01G158500 chr3D 92.806 139 9 1 1669 1807 546783936 546783799 2.280000e-47 200.0
6 TraesCS3B01G158500 chr3D 84.091 176 14 2 3580 3741 103195245 103195070 1.390000e-34 158.0
7 TraesCS3B01G158500 chr3A 87.240 3362 195 103 211 3463 552801807 552805043 0.000000e+00 3616.0
8 TraesCS3B01G158500 chr3A 86.047 301 17 8 1881 2177 683452755 683452476 2.180000e-77 300.0
9 TraesCS3B01G158500 chr4D 90.137 365 29 4 1457 1820 489235502 489235860 5.660000e-128 468.0
10 TraesCS3B01G158500 chr4D 82.680 485 81 1 2252 2733 489236491 489236975 9.600000e-116 427.0
11 TraesCS3B01G158500 chr4D 94.444 36 2 0 3701 3736 314018738 314018703 5.220000e-04 56.5
12 TraesCS3B01G158500 chr4B 88.187 364 42 1 1457 1819 52967814 52968177 2.060000e-117 433.0
13 TraesCS3B01G158500 chr4B 96.875 32 1 0 3705 3736 484146280 484146249 2.000000e-03 54.7
14 TraesCS3B01G158500 chr7A 78.878 303 56 8 1519 1817 547569541 547569839 8.200000e-47 198.0
15 TraesCS3B01G158500 chr7A 96.774 31 1 0 3705 3735 286244021 286243991 7.000000e-03 52.8
16 TraesCS3B01G158500 chr7D 78.618 304 55 9 1519 1817 448340150 448339852 3.810000e-45 193.0
17 TraesCS3B01G158500 chr7B 78.618 304 55 9 1519 1817 465592735 465592437 3.810000e-45 193.0
18 TraesCS3B01G158500 chr7B 76.389 360 61 22 1472 1816 731101464 731101814 4.970000e-39 172.0
19 TraesCS3B01G158500 chr7B 100.000 30 0 0 3707 3736 569109061 569109090 5.220000e-04 56.5
20 TraesCS3B01G158500 chr7B 96.875 32 1 0 3705 3736 163385242 163385211 2.000000e-03 54.7
21 TraesCS3B01G158500 chr5B 78.188 298 61 4 2265 2560 5053982 5053687 1.770000e-43 187.0
22 TraesCS3B01G158500 chr5B 100.000 28 0 0 3705 3732 162565732 162565759 7.000000e-03 52.8
23 TraesCS3B01G158500 chr5D 77.592 299 61 6 2265 2560 3567041 3566746 3.840000e-40 176.0
24 TraesCS3B01G158500 chr5A 77.113 284 61 4 2265 2546 2409766 2409485 1.080000e-35 161.0
25 TraesCS3B01G158500 chr1A 100.000 31 0 0 3706 3736 588810893 588810923 1.450000e-04 58.4
26 TraesCS3B01G158500 chr6A 96.970 33 1 0 3704 3736 281816721 281816689 5.220000e-04 56.5
27 TraesCS3B01G158500 chr2A 96.875 32 1 0 3705 3736 226775850 226775819 2.000000e-03 54.7


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 TraesCS3B01G158500 chr3B 153807772 153811512 3740 True 6909.0 6909 100.0000 1 3741 1 chr3B.!!$R1 3740
1 TraesCS3B01G158500 chr3D 103231022 103234557 3535 True 2318.5 3672 91.1875 109 3583 2 chr3D.!!$R3 3474
2 TraesCS3B01G158500 chr3D 546710975 546711524 549 True 232.0 244 87.0710 1877 2484 2 chr3D.!!$R4 607
3 TraesCS3B01G158500 chr3A 552801807 552805043 3236 False 3616.0 3616 87.2400 211 3463 1 chr3A.!!$F1 3252
4 TraesCS3B01G158500 chr4D 489235502 489236975 1473 False 447.5 468 86.4085 1457 2733 2 chr4D.!!$F1 1276

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
52 53 0.042431 CACCCCATTCCCATCCCAAA 59.958 55.0 0.00 0.00 0.0 3.28 F
53 54 0.042581 ACCCCATTCCCATCCCAAAC 59.957 55.0 0.00 0.00 0.0 2.93 F
79 80 0.179067 TTTCTGGACAAAGCGGACGT 60.179 50.0 0.00 0.00 0.0 4.34 F
80 81 0.599204 TTCTGGACAAAGCGGACGTC 60.599 55.0 7.13 7.13 0.0 4.34 F
839 905 0.676782 CCGGCCGATTCCTTTTGTCT 60.677 55.0 30.73 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1384 1.002087 AGGAACAGGAACACGGTGATC 59.998 52.381 16.29 12.66 0.00 2.92 R
1857 1962 1.129437 GAGATCGTGTCAAGCAAAGCC 59.871 52.381 0.00 0.00 0.00 4.35 R
2016 2151 1.229529 AGGCGGGGAAGAAGGAGAA 60.230 57.895 0.00 0.00 0.00 2.87 R
2053 2188 1.927895 CCGTCAGTTCCAGCTCATAC 58.072 55.000 0.00 0.00 0.00 2.39 R
2814 3204 0.848305 ACGTCGAAGGAAACGAAACG 59.152 50.000 0.00 0.00 41.29 3.60 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
17 18 2.922503 TCAGGGCTGCACTTCGGA 60.923 61.111 0.00 0.00 0.00 4.55
18 19 2.032528 CAGGGCTGCACTTCGGAA 59.967 61.111 0.00 0.00 0.00 4.30
19 20 2.032681 AGGGCTGCACTTCGGAAC 59.967 61.111 0.00 0.00 0.00 3.62
34 35 1.448985 GGAACGCTGACTATTTGCCA 58.551 50.000 0.00 0.00 0.00 4.92
35 36 1.130561 GGAACGCTGACTATTTGCCAC 59.869 52.381 0.00 0.00 0.00 5.01
36 37 1.130561 GAACGCTGACTATTTGCCACC 59.869 52.381 0.00 0.00 0.00 4.61
37 38 0.676782 ACGCTGACTATTTGCCACCC 60.677 55.000 0.00 0.00 0.00 4.61
38 39 1.376609 CGCTGACTATTTGCCACCCC 61.377 60.000 0.00 0.00 0.00 4.95
39 40 0.323360 GCTGACTATTTGCCACCCCA 60.323 55.000 0.00 0.00 0.00 4.96
40 41 1.686115 GCTGACTATTTGCCACCCCAT 60.686 52.381 0.00 0.00 0.00 4.00
41 42 2.738743 CTGACTATTTGCCACCCCATT 58.261 47.619 0.00 0.00 0.00 3.16
42 43 2.689983 CTGACTATTTGCCACCCCATTC 59.310 50.000 0.00 0.00 0.00 2.67
43 44 2.031870 GACTATTTGCCACCCCATTCC 58.968 52.381 0.00 0.00 0.00 3.01
44 45 1.342975 ACTATTTGCCACCCCATTCCC 60.343 52.381 0.00 0.00 0.00 3.97
45 46 0.712979 TATTTGCCACCCCATTCCCA 59.287 50.000 0.00 0.00 0.00 4.37
46 47 0.044549 ATTTGCCACCCCATTCCCAT 59.955 50.000 0.00 0.00 0.00 4.00
47 48 0.617249 TTTGCCACCCCATTCCCATC 60.617 55.000 0.00 0.00 0.00 3.51
48 49 2.123295 GCCACCCCATTCCCATCC 60.123 66.667 0.00 0.00 0.00 3.51
49 50 2.608759 CCACCCCATTCCCATCCC 59.391 66.667 0.00 0.00 0.00 3.85
50 51 2.323758 CCACCCCATTCCCATCCCA 61.324 63.158 0.00 0.00 0.00 4.37
51 52 1.702840 CACCCCATTCCCATCCCAA 59.297 57.895 0.00 0.00 0.00 4.12
52 53 0.042431 CACCCCATTCCCATCCCAAA 59.958 55.000 0.00 0.00 0.00 3.28
53 54 0.042581 ACCCCATTCCCATCCCAAAC 59.957 55.000 0.00 0.00 0.00 2.93
54 55 1.042559 CCCCATTCCCATCCCAAACG 61.043 60.000 0.00 0.00 0.00 3.60
55 56 1.042559 CCCATTCCCATCCCAAACGG 61.043 60.000 0.00 0.00 0.00 4.44
57 58 1.102978 CATTCCCATCCCAAACGGAC 58.897 55.000 0.00 0.00 46.09 4.79
58 59 0.393808 ATTCCCATCCCAAACGGACG 60.394 55.000 0.00 0.00 46.09 4.79
59 60 1.481901 TTCCCATCCCAAACGGACGA 61.482 55.000 0.00 0.00 46.09 4.20
60 61 1.223487 CCCATCCCAAACGGACGAT 59.777 57.895 0.00 0.00 46.09 3.73
61 62 0.393808 CCCATCCCAAACGGACGATT 60.394 55.000 0.00 0.00 46.09 3.34
62 63 1.459450 CCATCCCAAACGGACGATTT 58.541 50.000 0.00 0.00 46.09 2.17
63 64 1.400494 CCATCCCAAACGGACGATTTC 59.600 52.381 0.00 0.00 46.09 2.17
64 65 2.356135 CATCCCAAACGGACGATTTCT 58.644 47.619 0.00 0.00 46.09 2.52
65 66 1.803334 TCCCAAACGGACGATTTCTG 58.197 50.000 0.00 0.00 34.86 3.02
66 67 0.802494 CCCAAACGGACGATTTCTGG 59.198 55.000 0.00 0.00 34.44 3.86
67 68 1.609580 CCCAAACGGACGATTTCTGGA 60.610 52.381 0.00 0.00 34.44 3.86
68 69 1.463444 CCAAACGGACGATTTCTGGAC 59.537 52.381 0.00 0.00 34.44 4.02
69 70 2.139917 CAAACGGACGATTTCTGGACA 58.860 47.619 0.00 0.00 34.44 4.02
70 71 2.536761 AACGGACGATTTCTGGACAA 57.463 45.000 0.00 0.00 34.44 3.18
71 72 2.536761 ACGGACGATTTCTGGACAAA 57.463 45.000 0.00 0.00 34.44 2.83
72 73 2.413837 ACGGACGATTTCTGGACAAAG 58.586 47.619 0.00 0.00 34.44 2.77
73 74 1.128692 CGGACGATTTCTGGACAAAGC 59.871 52.381 0.00 0.00 0.00 3.51
75 76 1.128692 GACGATTTCTGGACAAAGCGG 59.871 52.381 8.27 0.00 46.76 5.52
76 77 1.270625 ACGATTTCTGGACAAAGCGGA 60.271 47.619 8.27 0.00 46.76 5.54
77 78 1.128692 CGATTTCTGGACAAAGCGGAC 59.871 52.381 0.00 0.00 40.59 4.79
78 79 1.128692 GATTTCTGGACAAAGCGGACG 59.871 52.381 0.00 0.00 0.00 4.79
79 80 0.179067 TTTCTGGACAAAGCGGACGT 60.179 50.000 0.00 0.00 0.00 4.34
80 81 0.599204 TTCTGGACAAAGCGGACGTC 60.599 55.000 7.13 7.13 0.00 4.34
95 96 2.027751 GTCCGGACGGCATCTAGC 59.972 66.667 20.85 0.00 44.65 3.42
113 114 2.906354 AGCATTGGAGTTAGCCTAACG 58.094 47.619 8.88 0.00 43.29 3.18
133 134 2.161012 CGTCGTACTGCTCCTAGTTTGA 59.839 50.000 0.00 0.00 32.19 2.69
136 137 2.230508 CGTACTGCTCCTAGTTTGACCA 59.769 50.000 0.00 0.00 32.19 4.02
140 141 3.073062 ACTGCTCCTAGTTTGACCAATGT 59.927 43.478 0.00 0.00 0.00 2.71
161 162 1.136884 CGTCGCGTGAAAGAAGAACTG 60.137 52.381 5.77 0.00 0.00 3.16
166 167 4.082625 TCGCGTGAAAGAAGAACTGGTATA 60.083 41.667 5.77 0.00 0.00 1.47
174 175 4.810345 AGAAGAACTGGTATAGAGAGGGG 58.190 47.826 0.00 0.00 0.00 4.79
178 179 5.600749 AGAACTGGTATAGAGAGGGGAAAA 58.399 41.667 0.00 0.00 0.00 2.29
191 196 1.065709 GGGGAAAATAGAGTCCGTGCA 60.066 52.381 0.00 0.00 34.47 4.57
389 409 2.404215 CACTCCGCCCGAATATGTTAG 58.596 52.381 0.00 0.00 0.00 2.34
402 428 7.148306 CCCGAATATGTTAGTGCTTGTTTAGTT 60.148 37.037 0.00 0.00 0.00 2.24
532 568 6.645884 TCTACTCTCCCTTACTTTCTCTCT 57.354 41.667 0.00 0.00 0.00 3.10
534 570 4.606210 ACTCTCCCTTACTTTCTCTCTCC 58.394 47.826 0.00 0.00 0.00 3.71
581 633 3.754965 TCATCCTCTTCTTGGTTGGTTG 58.245 45.455 0.00 0.00 0.00 3.77
582 634 3.394274 TCATCCTCTTCTTGGTTGGTTGA 59.606 43.478 0.00 0.00 0.00 3.18
583 635 4.043310 TCATCCTCTTCTTGGTTGGTTGAT 59.957 41.667 0.00 0.00 0.00 2.57
584 636 4.453480 TCCTCTTCTTGGTTGGTTGATT 57.547 40.909 0.00 0.00 0.00 2.57
620 675 1.289109 CGAAGGTGCCGTCGTTGATT 61.289 55.000 16.29 0.00 41.56 2.57
643 698 5.727434 TGATTGATGGATTGATCGATCGAT 58.273 37.500 29.76 29.76 44.08 3.59
644 699 6.271396 GATTGATGGATTGATCGATCGATC 57.729 41.667 38.90 38.90 46.29 3.69
670 725 4.578928 GTGTTCCAACAACTGGTCAATAGT 59.421 41.667 0.00 0.00 46.51 2.12
678 733 4.848357 CAACTGGTCAATAGTTGGGATCT 58.152 43.478 9.40 0.00 46.97 2.75
680 735 5.104259 ACTGGTCAATAGTTGGGATCTTC 57.896 43.478 0.00 0.00 0.00 2.87
834 900 2.045340 CCACCGGCCGATTCCTTT 60.045 61.111 30.73 0.00 0.00 3.11
839 905 0.676782 CCGGCCGATTCCTTTTGTCT 60.677 55.000 30.73 0.00 0.00 3.41
840 906 1.406341 CCGGCCGATTCCTTTTGTCTA 60.406 52.381 30.73 0.00 0.00 2.59
843 909 2.544267 GGCCGATTCCTTTTGTCTATCG 59.456 50.000 0.00 0.00 38.19 2.92
845 911 2.218759 CCGATTCCTTTTGTCTATCGCG 59.781 50.000 0.00 0.00 37.39 5.87
856 922 3.444916 TGTCTATCGCGACAAGGAATTC 58.555 45.455 12.93 0.00 40.69 2.17
857 923 3.130516 TGTCTATCGCGACAAGGAATTCT 59.869 43.478 12.93 0.00 40.69 2.40
859 925 4.207429 GTCTATCGCGACAAGGAATTCTTC 59.793 45.833 12.93 0.00 32.41 2.87
861 927 3.040147 TCGCGACAAGGAATTCTTCTT 57.960 42.857 3.71 0.00 32.41 2.52
1093 1169 2.035312 AGCAGTACTCCCCGTCGT 59.965 61.111 0.00 0.00 0.00 4.34
1223 1308 4.803426 GTCGTCCCTGCTGCCGAG 62.803 72.222 0.00 0.00 0.00 4.63
1245 1330 4.681978 GGCGTGTCGTCCCTGCTT 62.682 66.667 0.00 0.00 0.00 3.91
1494 1597 1.676678 GGCTGGCGTACCTCATCTCA 61.677 60.000 0.00 0.00 36.63 3.27
1857 1962 6.583050 TCAGCAAAACCGTTTAAAATATTCCG 59.417 34.615 0.00 0.00 0.00 4.30
1859 1964 5.444877 GCAAAACCGTTTAAAATATTCCGGC 60.445 40.000 11.37 0.00 38.99 6.13
1860 1965 5.648178 AAACCGTTTAAAATATTCCGGCT 57.352 34.783 11.37 0.00 38.99 5.52
1909 2016 3.693085 TCGAATCCGCTGACTAACTAACT 59.307 43.478 0.00 0.00 35.37 2.24
1910 2017 3.791887 CGAATCCGCTGACTAACTAACTG 59.208 47.826 0.00 0.00 0.00 3.16
1911 2018 2.649331 TCCGCTGACTAACTAACTGC 57.351 50.000 0.00 0.00 0.00 4.40
1912 2019 1.135489 TCCGCTGACTAACTAACTGCG 60.135 52.381 0.00 0.00 45.94 5.18
1913 2020 1.269166 CGCTGACTAACTAACTGCGG 58.731 55.000 0.00 0.00 43.95 5.69
1914 2021 1.000145 GCTGACTAACTAACTGCGGC 59.000 55.000 0.00 0.00 0.00 6.53
1915 2022 1.269166 CTGACTAACTAACTGCGGCG 58.731 55.000 0.51 0.51 0.00 6.46
1916 2023 0.883153 TGACTAACTAACTGCGGCGA 59.117 50.000 12.98 0.00 0.00 5.54
1917 2024 1.266466 GACTAACTAACTGCGGCGAC 58.734 55.000 12.98 2.02 0.00 5.19
2031 2166 1.208293 CTTCCTTCTCCTTCTTCCCCG 59.792 57.143 0.00 0.00 0.00 5.73
2095 2453 1.533965 GCGAGCGACTGTGTCATGATA 60.534 52.381 0.00 0.00 32.09 2.15
2653 3041 4.767255 GCCGAGGACTGGGTGCTG 62.767 72.222 2.31 0.00 33.56 4.41
2751 3139 0.175760 TGCAAGTAGCTAAGCTCGGG 59.824 55.000 13.26 0.00 45.94 5.14
2815 3205 3.323000 CACTGTGTGGTGTGCTCG 58.677 61.111 0.00 0.00 33.04 5.03
2816 3206 1.521457 CACTGTGTGGTGTGCTCGT 60.521 57.895 0.00 0.00 33.04 4.18
2817 3207 1.089481 CACTGTGTGGTGTGCTCGTT 61.089 55.000 0.00 0.00 33.04 3.85
2936 3435 4.373348 AGAGAGCTTCGTGGTACATTAC 57.627 45.455 0.00 0.00 44.52 1.89
2938 3437 5.191426 AGAGAGCTTCGTGGTACATTACTA 58.809 41.667 0.00 0.00 44.52 1.82
2942 3441 5.648572 AGCTTCGTGGTACATTACTAGTTC 58.351 41.667 0.00 0.00 44.52 3.01
2976 3475 1.537202 CTTACTCTGGTTTGCTGGTGC 59.463 52.381 0.00 0.00 40.20 5.01
2986 3485 1.302752 TGCTGGTGCATGGACTCAC 60.303 57.895 17.44 5.00 45.31 3.51
3013 3521 6.151144 AGGAGGAAAATGTTTTAACTGATCCG 59.849 38.462 0.00 0.00 0.00 4.18
3051 3559 6.705302 AGATGAACTCATGCTGTTCTTCTTA 58.295 36.000 25.72 12.96 46.88 2.10
3054 3562 6.705302 TGAACTCATGCTGTTCTTCTTATCT 58.295 36.000 22.58 0.00 42.86 1.98
3176 3708 8.290663 GAAGGATTCAATTGAAAAACACAGAG 57.709 34.615 23.91 0.00 46.62 3.35
3221 3756 3.777106 AAGAAACTGATGCCAGAGTCA 57.223 42.857 0.00 0.00 43.02 3.41
3274 3809 2.352342 GGAGACCTCGACTCTTAACTCG 59.648 54.545 2.02 0.00 35.10 4.18
3308 3843 1.672356 CAGAAGGGTTGCTGTCGGG 60.672 63.158 0.00 0.00 0.00 5.14
3343 3880 2.669133 CGGGAGGAGGATGTTGGCA 61.669 63.158 0.00 0.00 0.00 4.92
3346 3883 1.685148 GGAGGAGGATGTTGGCAATC 58.315 55.000 1.92 0.00 0.00 2.67
3349 3886 1.134280 AGGAGGATGTTGGCAATCGAG 60.134 52.381 1.92 0.00 0.00 4.04
3355 3892 2.689553 TGTTGGCAATCGAGCATCTA 57.310 45.000 1.92 0.00 35.83 1.98
3385 3926 2.358737 CCGAGCTTTCCGTTGCCT 60.359 61.111 0.00 0.00 0.00 4.75
3504 4048 1.378882 AAGATACGCCGACACGCCTA 61.379 55.000 0.00 0.00 36.19 3.93
3507 4051 0.103572 ATACGCCGACACGCCTAAAT 59.896 50.000 0.00 0.00 36.19 1.40
3508 4052 0.737804 TACGCCGACACGCCTAAATA 59.262 50.000 0.00 0.00 36.19 1.40
3509 4053 0.108709 ACGCCGACACGCCTAAATAA 60.109 50.000 0.00 0.00 36.19 1.40
3532 4076 7.449934 AAAATTTCGATCAAATTCATACGGC 57.550 32.000 12.96 0.00 42.86 5.68
3555 4099 3.064207 CCCTCGAGATTTTGACGTTTCA 58.936 45.455 15.71 0.00 0.00 2.69
3572 4116 0.325933 TCAAGTGGGATGTGCCTCAG 59.674 55.000 0.00 0.00 36.66 3.35
3579 4123 0.543277 GGATGTGCCTCAGGTCATGA 59.457 55.000 8.00 0.00 36.21 3.07
3592 4136 2.947448 GTCATGACCAGGCCAATTTC 57.053 50.000 15.31 0.00 0.00 2.17
3593 4137 1.478105 GTCATGACCAGGCCAATTTCC 59.522 52.381 15.31 0.00 0.00 3.13
3594 4138 1.076841 TCATGACCAGGCCAATTTCCA 59.923 47.619 5.01 0.00 0.00 3.53
3595 4139 1.901159 CATGACCAGGCCAATTTCCAA 59.099 47.619 5.01 0.00 0.00 3.53
3596 4140 2.094100 TGACCAGGCCAATTTCCAAA 57.906 45.000 5.01 0.00 0.00 3.28
3597 4141 2.402564 TGACCAGGCCAATTTCCAAAA 58.597 42.857 5.01 0.00 0.00 2.44
3598 4142 2.774234 TGACCAGGCCAATTTCCAAAAA 59.226 40.909 5.01 0.00 0.00 1.94
3599 4143 3.138304 GACCAGGCCAATTTCCAAAAAC 58.862 45.455 5.01 0.00 0.00 2.43
3600 4144 2.507471 ACCAGGCCAATTTCCAAAAACA 59.493 40.909 5.01 0.00 0.00 2.83
3601 4145 3.140623 CCAGGCCAATTTCCAAAAACAG 58.859 45.455 5.01 0.00 0.00 3.16
3602 4146 3.181456 CCAGGCCAATTTCCAAAAACAGA 60.181 43.478 5.01 0.00 0.00 3.41
3603 4147 4.505390 CCAGGCCAATTTCCAAAAACAGAT 60.505 41.667 5.01 0.00 0.00 2.90
3604 4148 5.279910 CCAGGCCAATTTCCAAAAACAGATA 60.280 40.000 5.01 0.00 0.00 1.98
3605 4149 6.229733 CAGGCCAATTTCCAAAAACAGATAA 58.770 36.000 5.01 0.00 0.00 1.75
3606 4150 6.709846 CAGGCCAATTTCCAAAAACAGATAAA 59.290 34.615 5.01 0.00 0.00 1.40
3607 4151 7.391275 CAGGCCAATTTCCAAAAACAGATAAAT 59.609 33.333 5.01 0.00 0.00 1.40
3608 4152 8.601546 AGGCCAATTTCCAAAAACAGATAAATA 58.398 29.630 5.01 0.00 0.00 1.40
3609 4153 8.882736 GGCCAATTTCCAAAAACAGATAAATAG 58.117 33.333 0.00 0.00 0.00 1.73
3610 4154 8.390354 GCCAATTTCCAAAAACAGATAAATAGC 58.610 33.333 0.00 0.00 0.00 2.97
3611 4155 9.434420 CCAATTTCCAAAAACAGATAAATAGCA 57.566 29.630 0.00 0.00 0.00 3.49
3613 4157 9.657419 AATTTCCAAAAACAGATAAATAGCAGG 57.343 29.630 0.00 0.00 0.00 4.85
3614 4158 8.415950 TTTCCAAAAACAGATAAATAGCAGGA 57.584 30.769 0.00 0.00 0.00 3.86
3615 4159 7.630242 TCCAAAAACAGATAAATAGCAGGAG 57.370 36.000 0.00 0.00 0.00 3.69
3616 4160 6.603201 TCCAAAAACAGATAAATAGCAGGAGG 59.397 38.462 0.00 0.00 0.00 4.30
3617 4161 6.603201 CCAAAAACAGATAAATAGCAGGAGGA 59.397 38.462 0.00 0.00 0.00 3.71
3618 4162 7.286316 CCAAAAACAGATAAATAGCAGGAGGAT 59.714 37.037 0.00 0.00 0.00 3.24
3619 4163 8.689972 CAAAAACAGATAAATAGCAGGAGGATT 58.310 33.333 0.00 0.00 0.00 3.01
3620 4164 8.829373 AAAACAGATAAATAGCAGGAGGATTT 57.171 30.769 0.00 0.00 0.00 2.17
3621 4165 8.829373 AAACAGATAAATAGCAGGAGGATTTT 57.171 30.769 0.00 0.00 0.00 1.82
3622 4166 8.829373 AACAGATAAATAGCAGGAGGATTTTT 57.171 30.769 0.00 0.00 0.00 1.94
3623 4167 9.920946 AACAGATAAATAGCAGGAGGATTTTTA 57.079 29.630 0.00 0.00 0.00 1.52
3629 4173 8.608185 AAATAGCAGGAGGATTTTTATTTGGA 57.392 30.769 0.00 0.00 0.00 3.53
3630 4174 8.608185 AATAGCAGGAGGATTTTTATTTGGAA 57.392 30.769 0.00 0.00 0.00 3.53
3631 4175 6.286240 AGCAGGAGGATTTTTATTTGGAAC 57.714 37.500 0.00 0.00 0.00 3.62
3632 4176 5.102313 GCAGGAGGATTTTTATTTGGAACG 58.898 41.667 0.00 0.00 0.00 3.95
3633 4177 5.102313 CAGGAGGATTTTTATTTGGAACGC 58.898 41.667 0.00 0.00 0.00 4.84
3634 4178 4.159693 AGGAGGATTTTTATTTGGAACGCC 59.840 41.667 0.00 0.00 0.00 5.68
3635 4179 4.430007 GAGGATTTTTATTTGGAACGCCC 58.570 43.478 0.00 0.00 0.00 6.13
3636 4180 3.196901 AGGATTTTTATTTGGAACGCCCC 59.803 43.478 0.00 0.00 0.00 5.80
3637 4181 3.055747 GGATTTTTATTTGGAACGCCCCA 60.056 43.478 0.00 0.00 0.00 4.96
3638 4182 4.563786 GGATTTTTATTTGGAACGCCCCAA 60.564 41.667 5.13 5.13 43.90 4.12
3639 4183 3.388345 TTTTATTTGGAACGCCCCAAC 57.612 42.857 8.43 0.00 45.13 3.77
3640 4184 0.882474 TTATTTGGAACGCCCCAACG 59.118 50.000 8.43 0.00 45.13 4.10
3647 4191 2.506962 ACGCCCCAACGTTCAAGA 59.493 55.556 0.00 0.00 45.75 3.02
3648 4192 1.072505 ACGCCCCAACGTTCAAGAT 59.927 52.632 0.00 0.00 45.75 2.40
3649 4193 0.536460 ACGCCCCAACGTTCAAGATT 60.536 50.000 0.00 0.00 45.75 2.40
3650 4194 0.596082 CGCCCCAACGTTCAAGATTT 59.404 50.000 0.00 0.00 0.00 2.17
3651 4195 1.665735 CGCCCCAACGTTCAAGATTTG 60.666 52.381 0.00 0.00 0.00 2.32
3652 4196 1.611491 GCCCCAACGTTCAAGATTTGA 59.389 47.619 0.00 0.00 38.04 2.69
3653 4197 2.607038 GCCCCAACGTTCAAGATTTGAC 60.607 50.000 0.00 0.00 39.87 3.18
3654 4198 2.884639 CCCCAACGTTCAAGATTTGACT 59.115 45.455 0.00 0.00 39.87 3.41
3655 4199 3.058224 CCCCAACGTTCAAGATTTGACTC 60.058 47.826 0.00 0.00 39.87 3.36
3656 4200 3.363970 CCCAACGTTCAAGATTTGACTCG 60.364 47.826 0.00 11.32 39.87 4.18
3657 4201 3.247648 CCAACGTTCAAGATTTGACTCGT 59.752 43.478 0.00 12.22 45.42 4.18
3660 4204 5.479716 ACGTTCAAGATTTGACTCGTTTT 57.520 34.783 12.22 0.00 43.03 2.43
3661 4205 5.499047 ACGTTCAAGATTTGACTCGTTTTC 58.501 37.500 12.22 0.00 43.03 2.29
3662 4206 4.603146 CGTTCAAGATTTGACTCGTTTTCG 59.397 41.667 0.00 0.00 39.87 3.46
3663 4207 5.555631 CGTTCAAGATTTGACTCGTTTTCGA 60.556 40.000 0.00 0.00 44.20 3.71
3664 4208 6.363473 GTTCAAGATTTGACTCGTTTTCGAT 58.637 36.000 0.00 0.00 42.72 3.59
3665 4209 5.915857 TCAAGATTTGACTCGTTTTCGATG 58.084 37.500 0.00 0.00 42.36 3.84
3666 4210 5.107104 TCAAGATTTGACTCGTTTTCGATGG 60.107 40.000 0.00 0.00 42.36 3.51
3667 4211 8.469821 TCAAGATTTGACTCGTTTTCGATGGC 62.470 42.308 0.00 0.00 42.36 4.40
3679 4223 6.389622 GTTTTCGATGGCAATTTTAGGAAC 57.610 37.500 0.00 0.00 0.00 3.62
3680 4224 4.349663 TTCGATGGCAATTTTAGGAACG 57.650 40.909 0.00 0.00 0.00 3.95
3681 4225 3.340034 TCGATGGCAATTTTAGGAACGT 58.660 40.909 0.00 0.00 0.00 3.99
3682 4226 3.754323 TCGATGGCAATTTTAGGAACGTT 59.246 39.130 0.00 0.00 0.00 3.99
3683 4227 4.936411 TCGATGGCAATTTTAGGAACGTTA 59.064 37.500 0.00 0.00 0.00 3.18
3684 4228 5.587043 TCGATGGCAATTTTAGGAACGTTAT 59.413 36.000 0.00 0.00 0.00 1.89
3685 4229 5.681105 CGATGGCAATTTTAGGAACGTTATG 59.319 40.000 0.00 0.00 0.00 1.90
3686 4230 6.457663 CGATGGCAATTTTAGGAACGTTATGA 60.458 38.462 0.00 0.00 0.00 2.15
3687 4231 6.767524 TGGCAATTTTAGGAACGTTATGAT 57.232 33.333 0.00 0.00 0.00 2.45
3688 4232 6.791303 TGGCAATTTTAGGAACGTTATGATC 58.209 36.000 0.00 0.00 0.00 2.92
3689 4233 5.907391 GGCAATTTTAGGAACGTTATGATCG 59.093 40.000 0.00 0.00 0.00 3.69
3690 4234 5.395486 GCAATTTTAGGAACGTTATGATCGC 59.605 40.000 0.00 0.00 0.00 4.58
3691 4235 6.482835 CAATTTTAGGAACGTTATGATCGCA 58.517 36.000 0.00 0.00 0.00 5.10
3692 4236 6.671614 ATTTTAGGAACGTTATGATCGCAA 57.328 33.333 0.00 0.00 0.00 4.85
3693 4237 6.671614 TTTTAGGAACGTTATGATCGCAAT 57.328 33.333 0.00 0.00 0.00 3.56
3694 4238 6.671614 TTTAGGAACGTTATGATCGCAATT 57.328 33.333 0.00 0.00 0.00 2.32
3695 4239 6.671614 TTAGGAACGTTATGATCGCAATTT 57.328 33.333 0.00 0.00 0.00 1.82
3696 4240 5.560966 AGGAACGTTATGATCGCAATTTT 57.439 34.783 0.00 0.00 0.00 1.82
3697 4241 6.671614 AGGAACGTTATGATCGCAATTTTA 57.328 33.333 0.00 0.00 0.00 1.52
3698 4242 6.715464 AGGAACGTTATGATCGCAATTTTAG 58.285 36.000 0.00 0.00 0.00 1.85
3699 4243 6.315393 AGGAACGTTATGATCGCAATTTTAGT 59.685 34.615 0.00 0.00 0.00 2.24
3700 4244 6.964934 GGAACGTTATGATCGCAATTTTAGTT 59.035 34.615 0.00 0.00 0.00 2.24
3701 4245 8.117988 GGAACGTTATGATCGCAATTTTAGTTA 58.882 33.333 0.00 0.00 0.00 2.24
3702 4246 8.816204 AACGTTATGATCGCAATTTTAGTTAC 57.184 30.769 0.00 0.00 0.00 2.50
3703 4247 7.404203 ACGTTATGATCGCAATTTTAGTTACC 58.596 34.615 0.00 0.00 0.00 2.85
3704 4248 7.064847 ACGTTATGATCGCAATTTTAGTTACCA 59.935 33.333 0.00 0.00 0.00 3.25
3705 4249 8.067784 CGTTATGATCGCAATTTTAGTTACCAT 58.932 33.333 0.00 0.00 0.00 3.55
3706 4250 9.169468 GTTATGATCGCAATTTTAGTTACCATG 57.831 33.333 0.00 0.00 0.00 3.66
3707 4251 6.751514 TGATCGCAATTTTAGTTACCATGT 57.248 33.333 0.00 0.00 0.00 3.21
3708 4252 6.550843 TGATCGCAATTTTAGTTACCATGTG 58.449 36.000 0.00 0.00 0.00 3.21
3709 4253 5.950758 TCGCAATTTTAGTTACCATGTGT 57.049 34.783 0.00 0.00 0.00 3.72
3710 4254 6.320494 TCGCAATTTTAGTTACCATGTGTT 57.680 33.333 0.00 0.00 0.00 3.32
3711 4255 6.375377 TCGCAATTTTAGTTACCATGTGTTC 58.625 36.000 0.00 0.00 0.00 3.18
3712 4256 6.017026 TCGCAATTTTAGTTACCATGTGTTCA 60.017 34.615 0.00 0.00 0.00 3.18
3713 4257 6.087555 CGCAATTTTAGTTACCATGTGTTCAC 59.912 38.462 0.00 0.00 0.00 3.18
3714 4258 6.920758 GCAATTTTAGTTACCATGTGTTCACA 59.079 34.615 8.09 8.09 0.00 3.58
3715 4259 7.096230 GCAATTTTAGTTACCATGTGTTCACAC 60.096 37.037 7.82 2.93 46.59 3.82
3726 4270 3.773591 GTTCACACACGAACACGTC 57.226 52.632 0.00 0.00 43.89 4.34
3727 4271 0.993532 GTTCACACACGAACACGTCA 59.006 50.000 0.00 0.00 43.89 4.35
3728 4272 0.993532 TTCACACACGAACACGTCAC 59.006 50.000 0.00 0.00 38.21 3.67
3729 4273 0.802994 TCACACACGAACACGTCACC 60.803 55.000 0.00 0.00 38.21 4.02
3730 4274 1.874915 ACACACGAACACGTCACCG 60.875 57.895 0.00 0.00 38.21 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.515979 TTCCGAAGTGCAGCCCTGA 61.516 57.895 0.00 0.00 0.00 3.86
2 3 2.032681 GTTCCGAAGTGCAGCCCT 59.967 61.111 0.00 0.00 0.00 5.19
6 7 1.664649 TCAGCGTTCCGAAGTGCAG 60.665 57.895 7.76 1.01 0.00 4.41
7 8 1.954146 GTCAGCGTTCCGAAGTGCA 60.954 57.895 7.76 0.00 0.00 4.57
8 9 0.388134 TAGTCAGCGTTCCGAAGTGC 60.388 55.000 0.00 0.00 0.00 4.40
9 10 2.279582 ATAGTCAGCGTTCCGAAGTG 57.720 50.000 0.00 0.00 0.00 3.16
10 11 2.993899 CAAATAGTCAGCGTTCCGAAGT 59.006 45.455 0.00 0.00 0.00 3.01
11 12 2.222819 GCAAATAGTCAGCGTTCCGAAG 60.223 50.000 0.00 0.00 0.00 3.79
12 13 1.730064 GCAAATAGTCAGCGTTCCGAA 59.270 47.619 0.00 0.00 0.00 4.30
13 14 1.355971 GCAAATAGTCAGCGTTCCGA 58.644 50.000 0.00 0.00 0.00 4.55
14 15 0.373716 GGCAAATAGTCAGCGTTCCG 59.626 55.000 0.00 0.00 0.00 4.30
15 16 1.130561 GTGGCAAATAGTCAGCGTTCC 59.869 52.381 0.00 0.00 28.23 3.62
16 17 1.130561 GGTGGCAAATAGTCAGCGTTC 59.869 52.381 0.00 0.00 40.90 3.95
17 18 1.165270 GGTGGCAAATAGTCAGCGTT 58.835 50.000 0.00 0.00 40.90 4.84
18 19 2.854522 GGTGGCAAATAGTCAGCGT 58.145 52.632 0.00 0.00 40.90 5.07
21 22 2.442236 ATGGGGTGGCAAATAGTCAG 57.558 50.000 0.00 0.00 28.23 3.51
22 23 2.622977 GGAATGGGGTGGCAAATAGTCA 60.623 50.000 0.00 0.00 0.00 3.41
23 24 2.031870 GGAATGGGGTGGCAAATAGTC 58.968 52.381 0.00 0.00 0.00 2.59
24 25 1.342975 GGGAATGGGGTGGCAAATAGT 60.343 52.381 0.00 0.00 0.00 2.12
25 26 1.342874 TGGGAATGGGGTGGCAAATAG 60.343 52.381 0.00 0.00 0.00 1.73
26 27 0.712979 TGGGAATGGGGTGGCAAATA 59.287 50.000 0.00 0.00 0.00 1.40
27 28 0.044549 ATGGGAATGGGGTGGCAAAT 59.955 50.000 0.00 0.00 0.00 2.32
28 29 0.617249 GATGGGAATGGGGTGGCAAA 60.617 55.000 0.00 0.00 0.00 3.68
29 30 1.001503 GATGGGAATGGGGTGGCAA 59.998 57.895 0.00 0.00 0.00 4.52
30 31 2.689175 GATGGGAATGGGGTGGCA 59.311 61.111 0.00 0.00 0.00 4.92
31 32 2.123295 GGATGGGAATGGGGTGGC 60.123 66.667 0.00 0.00 0.00 5.01
32 33 1.884456 TTGGGATGGGAATGGGGTGG 61.884 60.000 0.00 0.00 0.00 4.61
33 34 0.042431 TTTGGGATGGGAATGGGGTG 59.958 55.000 0.00 0.00 0.00 4.61
34 35 0.042581 GTTTGGGATGGGAATGGGGT 59.957 55.000 0.00 0.00 0.00 4.95
35 36 1.042559 CGTTTGGGATGGGAATGGGG 61.043 60.000 0.00 0.00 0.00 4.96
36 37 1.042559 CCGTTTGGGATGGGAATGGG 61.043 60.000 0.00 0.00 38.47 4.00
37 38 0.033601 TCCGTTTGGGATGGGAATGG 60.034 55.000 0.00 0.00 40.94 3.16
38 39 3.586843 TCCGTTTGGGATGGGAATG 57.413 52.632 0.00 0.00 40.94 2.67
46 47 1.609580 CCAGAAATCGTCCGTTTGGGA 60.610 52.381 0.00 0.00 44.68 4.37
47 48 0.802494 CCAGAAATCGTCCGTTTGGG 59.198 55.000 0.00 0.00 35.24 4.12
48 49 1.463444 GTCCAGAAATCGTCCGTTTGG 59.537 52.381 0.00 0.00 0.00 3.28
49 50 2.139917 TGTCCAGAAATCGTCCGTTTG 58.860 47.619 0.00 0.00 0.00 2.93
50 51 2.536761 TGTCCAGAAATCGTCCGTTT 57.463 45.000 0.00 0.00 0.00 3.60
51 52 2.536761 TTGTCCAGAAATCGTCCGTT 57.463 45.000 0.00 0.00 0.00 4.44
52 53 2.413837 CTTTGTCCAGAAATCGTCCGT 58.586 47.619 0.00 0.00 0.00 4.69
53 54 1.128692 GCTTTGTCCAGAAATCGTCCG 59.871 52.381 0.00 0.00 0.00 4.79
54 55 1.128692 CGCTTTGTCCAGAAATCGTCC 59.871 52.381 0.00 0.00 0.00 4.79
55 56 1.128692 CCGCTTTGTCCAGAAATCGTC 59.871 52.381 0.00 0.00 0.00 4.20
56 57 1.156736 CCGCTTTGTCCAGAAATCGT 58.843 50.000 0.00 0.00 0.00 3.73
57 58 1.128692 GTCCGCTTTGTCCAGAAATCG 59.871 52.381 0.00 0.00 0.00 3.34
58 59 1.128692 CGTCCGCTTTGTCCAGAAATC 59.871 52.381 0.00 0.00 0.00 2.17
59 60 1.156736 CGTCCGCTTTGTCCAGAAAT 58.843 50.000 0.00 0.00 0.00 2.17
60 61 0.179067 ACGTCCGCTTTGTCCAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
61 62 0.599204 GACGTCCGCTTTGTCCAGAA 60.599 55.000 3.51 0.00 0.00 3.02
62 63 1.006571 GACGTCCGCTTTGTCCAGA 60.007 57.895 3.51 0.00 0.00 3.86
63 64 3.550656 GACGTCCGCTTTGTCCAG 58.449 61.111 3.51 0.00 0.00 3.86
78 79 2.027751 GCTAGATGCCGTCCGGAC 59.972 66.667 25.28 25.28 37.50 4.79
79 80 1.399744 AATGCTAGATGCCGTCCGGA 61.400 55.000 10.46 0.00 42.00 5.14
80 81 1.069765 AATGCTAGATGCCGTCCGG 59.930 57.895 0.24 0.24 42.00 5.14
81 82 1.224069 CCAATGCTAGATGCCGTCCG 61.224 60.000 0.00 0.00 42.00 4.79
82 83 0.106708 TCCAATGCTAGATGCCGTCC 59.893 55.000 0.00 0.00 42.00 4.79
83 84 1.202580 ACTCCAATGCTAGATGCCGTC 60.203 52.381 0.00 0.00 42.00 4.79
84 85 0.833287 ACTCCAATGCTAGATGCCGT 59.167 50.000 0.00 0.00 42.00 5.68
85 86 1.959042 AACTCCAATGCTAGATGCCG 58.041 50.000 0.00 0.00 42.00 5.69
86 87 2.810852 GCTAACTCCAATGCTAGATGCC 59.189 50.000 0.00 0.00 42.00 4.40
87 88 2.810852 GGCTAACTCCAATGCTAGATGC 59.189 50.000 0.00 0.00 43.25 3.91
88 89 4.348863 AGGCTAACTCCAATGCTAGATG 57.651 45.455 0.00 0.00 0.00 2.90
89 90 5.509840 CGTTAGGCTAACTCCAATGCTAGAT 60.510 44.000 29.08 0.00 36.54 1.98
90 91 4.202121 CGTTAGGCTAACTCCAATGCTAGA 60.202 45.833 29.08 0.00 36.54 2.43
91 92 4.051922 CGTTAGGCTAACTCCAATGCTAG 58.948 47.826 29.08 10.55 36.54 3.42
92 93 3.449737 ACGTTAGGCTAACTCCAATGCTA 59.550 43.478 29.08 0.00 36.54 3.49
93 94 2.236395 ACGTTAGGCTAACTCCAATGCT 59.764 45.455 29.08 6.47 36.54 3.79
94 95 2.608090 GACGTTAGGCTAACTCCAATGC 59.392 50.000 29.08 10.93 36.54 3.56
95 96 2.858344 CGACGTTAGGCTAACTCCAATG 59.142 50.000 29.08 17.60 36.54 2.82
96 97 2.494870 ACGACGTTAGGCTAACTCCAAT 59.505 45.455 29.08 13.24 36.54 3.16
97 98 1.888512 ACGACGTTAGGCTAACTCCAA 59.111 47.619 29.08 0.00 36.54 3.53
98 99 1.538047 ACGACGTTAGGCTAACTCCA 58.462 50.000 29.08 0.00 36.54 3.86
99 100 2.680339 AGTACGACGTTAGGCTAACTCC 59.320 50.000 29.08 20.41 36.54 3.85
100 101 3.678662 CAGTACGACGTTAGGCTAACTC 58.321 50.000 29.08 23.30 36.54 3.01
101 102 2.159462 GCAGTACGACGTTAGGCTAACT 60.159 50.000 29.08 18.70 36.54 2.24
102 103 2.159462 AGCAGTACGACGTTAGGCTAAC 60.159 50.000 24.27 24.27 35.37 2.34
103 104 2.086869 AGCAGTACGACGTTAGGCTAA 58.913 47.619 5.50 2.04 0.00 3.09
104 105 1.667724 GAGCAGTACGACGTTAGGCTA 59.332 52.381 16.46 0.00 0.00 3.93
105 106 0.450983 GAGCAGTACGACGTTAGGCT 59.549 55.000 16.44 16.44 0.00 4.58
106 107 0.525029 GGAGCAGTACGACGTTAGGC 60.525 60.000 5.50 7.58 0.00 3.93
107 108 1.093159 AGGAGCAGTACGACGTTAGG 58.907 55.000 5.50 0.00 0.00 2.69
113 114 3.500014 GTCAAACTAGGAGCAGTACGAC 58.500 50.000 0.00 0.00 0.00 4.34
133 134 0.876777 TTTCACGCGACGACATTGGT 60.877 50.000 15.93 0.00 0.00 3.67
136 137 1.455786 CTTCTTTCACGCGACGACATT 59.544 47.619 15.93 0.00 0.00 2.71
140 141 1.126079 GTTCTTCTTTCACGCGACGA 58.874 50.000 15.93 5.90 0.00 4.20
161 162 6.438108 GGACTCTATTTTCCCCTCTCTATACC 59.562 46.154 0.00 0.00 0.00 2.73
166 167 3.301274 CGGACTCTATTTTCCCCTCTCT 58.699 50.000 0.00 0.00 0.00 3.10
174 175 4.553547 GCATCATGCACGGACTCTATTTTC 60.554 45.833 4.20 0.00 44.26 2.29
178 179 1.603931 CGCATCATGCACGGACTCTAT 60.604 52.381 11.00 0.00 45.36 1.98
191 196 0.723414 CGTTGCTTCTGTCGCATCAT 59.277 50.000 0.00 0.00 37.22 2.45
298 313 1.591768 ACCCCGAAATACCATCCACT 58.408 50.000 0.00 0.00 0.00 4.00
389 409 2.350484 GCGGGAGAAACTAAACAAGCAC 60.350 50.000 0.00 0.00 0.00 4.40
402 428 2.096980 CGATATATAGTGCGCGGGAGAA 59.903 50.000 8.83 0.00 0.00 2.87
550 594 2.487762 AGAAGAGGATGATCGATCGAGC 59.512 50.000 25.65 25.65 30.87 5.03
551 595 4.475028 CAAGAAGAGGATGATCGATCGAG 58.525 47.826 23.84 0.31 30.87 4.04
552 596 3.254411 CCAAGAAGAGGATGATCGATCGA 59.746 47.826 21.86 21.86 30.87 3.59
553 597 3.005261 ACCAAGAAGAGGATGATCGATCG 59.995 47.826 20.03 9.36 30.87 3.69
554 598 4.599047 ACCAAGAAGAGGATGATCGATC 57.401 45.455 18.72 18.72 0.00 3.69
562 606 4.664688 ATCAACCAACCAAGAAGAGGAT 57.335 40.909 0.00 0.00 0.00 3.24
581 633 4.686972 TCGTCACAGAGGATGATGAAATC 58.313 43.478 0.00 0.00 45.83 2.17
582 634 4.743057 TCGTCACAGAGGATGATGAAAT 57.257 40.909 0.00 0.00 38.79 2.17
583 635 4.498241 CTTCGTCACAGAGGATGATGAAA 58.502 43.478 10.06 0.00 46.36 2.69
584 636 3.118992 CCTTCGTCACAGAGGATGATGAA 60.119 47.826 8.82 8.82 45.47 2.57
620 675 5.138125 TCGATCGATCAATCCATCAATCA 57.862 39.130 24.40 0.00 0.00 2.57
670 725 0.530744 CAGACGACCGAAGATCCCAA 59.469 55.000 0.00 0.00 0.00 4.12
678 733 1.136774 CGATGAGCAGACGACCGAA 59.863 57.895 0.00 0.00 0.00 4.30
852 918 5.067805 ACGAGGTGCAAAGAAAAGAAGAATT 59.932 36.000 0.00 0.00 0.00 2.17
856 922 3.971032 ACGAGGTGCAAAGAAAAGAAG 57.029 42.857 0.00 0.00 0.00 2.85
857 923 4.454504 GGATACGAGGTGCAAAGAAAAGAA 59.545 41.667 0.00 0.00 0.00 2.52
859 925 4.003648 AGGATACGAGGTGCAAAGAAAAG 58.996 43.478 0.00 0.00 46.39 2.27
861 927 3.695830 AGGATACGAGGTGCAAAGAAA 57.304 42.857 0.00 0.00 46.39 2.52
918 990 1.676746 TTCTCCCGAGGATCACGTAG 58.323 55.000 9.86 7.44 33.17 3.51
1060 1136 3.827898 CTCGTCTCCGCCACCTCC 61.828 72.222 0.00 0.00 0.00 4.30
1061 1137 4.500116 GCTCGTCTCCGCCACCTC 62.500 72.222 0.00 0.00 0.00 3.85
1179 1264 2.811317 CTCGGCAGCAAGGACGAC 60.811 66.667 0.00 0.00 44.82 4.34
1228 1313 4.681978 AAGCAGGGACGACACGCC 62.682 66.667 0.00 0.00 0.00 5.68
1229 1314 3.112709 GAAGCAGGGACGACACGC 61.113 66.667 0.00 0.00 0.00 5.34
1230 1315 2.432628 GGAAGCAGGGACGACACG 60.433 66.667 0.00 0.00 0.00 4.49
1231 1316 2.432628 CGGAAGCAGGGACGACAC 60.433 66.667 0.00 0.00 0.00 3.67
1232 1317 2.599281 TCGGAAGCAGGGACGACA 60.599 61.111 0.00 0.00 0.00 4.35
1233 1318 2.182030 CTCGGAAGCAGGGACGAC 59.818 66.667 0.00 0.00 0.00 4.34
1299 1384 1.002087 AGGAACAGGAACACGGTGATC 59.998 52.381 16.29 12.66 0.00 2.92
1674 1777 3.642938 GTAGGTCACCATGTTGGCA 57.357 52.632 0.00 0.00 42.67 4.92
1710 1813 3.357079 GCGTGCAGGGTGTTGGAG 61.357 66.667 8.72 0.00 0.00 3.86
1711 1814 4.947147 GGCGTGCAGGGTGTTGGA 62.947 66.667 8.72 0.00 0.00 3.53
1857 1962 1.129437 GAGATCGTGTCAAGCAAAGCC 59.871 52.381 0.00 0.00 0.00 4.35
1859 1964 4.505922 GGATAGAGATCGTGTCAAGCAAAG 59.494 45.833 0.00 0.00 32.28 2.77
1860 1965 4.081697 TGGATAGAGATCGTGTCAAGCAAA 60.082 41.667 0.00 0.00 32.28 3.68
2013 2148 1.265454 GCGGGGAAGAAGGAGAAGGA 61.265 60.000 0.00 0.00 0.00 3.36
2016 2151 1.229529 AGGCGGGGAAGAAGGAGAA 60.230 57.895 0.00 0.00 0.00 2.87
2042 2177 5.055642 TCCAGCTCATACGTAAATATCGG 57.944 43.478 0.00 0.00 0.00 4.18
2053 2188 1.927895 CCGTCAGTTCCAGCTCATAC 58.072 55.000 0.00 0.00 0.00 2.39
2080 2433 2.798847 CCTGCATATCATGACACAGTCG 59.201 50.000 0.00 0.00 34.95 4.18
2249 2615 2.567497 CCCACACCACGTACTCGGT 61.567 63.158 0.00 0.00 41.85 4.69
2751 3139 1.897398 GCACGACCGACCATGTCAAC 61.897 60.000 0.00 0.00 32.91 3.18
2813 3203 1.122849 CGTCGAAGGAAACGAAACGA 58.877 50.000 0.00 0.00 41.29 3.85
2814 3204 0.848305 ACGTCGAAGGAAACGAAACG 59.152 50.000 0.00 0.00 41.29 3.60
2815 3205 3.024313 CAAACGTCGAAGGAAACGAAAC 58.976 45.455 0.00 0.00 41.29 2.78
2816 3206 2.672381 ACAAACGTCGAAGGAAACGAAA 59.328 40.909 0.00 0.00 41.29 3.46
2817 3207 2.270047 ACAAACGTCGAAGGAAACGAA 58.730 42.857 0.00 0.00 41.29 3.85
2955 3454 2.851195 CACCAGCAAACCAGAGTAAGT 58.149 47.619 0.00 0.00 0.00 2.24
2976 3475 1.186200 TTCCTCCTCGTGAGTCCATG 58.814 55.000 0.00 0.00 39.65 3.66
2986 3485 6.554334 TCAGTTAAAACATTTTCCTCCTCG 57.446 37.500 0.00 0.00 0.00 4.63
3051 3559 8.432805 CCACATTAAACCACCTCTCTATTAGAT 58.567 37.037 0.00 0.00 32.41 1.98
3054 3562 7.181305 TGACCACATTAAACCACCTCTCTATTA 59.819 37.037 0.00 0.00 0.00 0.98
3061 3585 3.443681 CCATGACCACATTAAACCACCTC 59.556 47.826 0.00 0.00 34.15 3.85
3164 3692 6.974965 ACTTTCCATCATCTCTGTGTTTTTC 58.025 36.000 0.00 0.00 0.00 2.29
3175 3707 5.639506 CAGACGTGTTTACTTTCCATCATCT 59.360 40.000 0.00 0.00 0.00 2.90
3176 3708 5.637810 TCAGACGTGTTTACTTTCCATCATC 59.362 40.000 0.00 0.00 0.00 2.92
3221 3756 1.888436 TTCTTGCGAGATGGCGGTCT 61.888 55.000 3.98 0.00 35.06 3.85
3308 3843 2.830321 TCCCGTCTTTTACCTCTCTTCC 59.170 50.000 0.00 0.00 0.00 3.46
3343 3880 2.864097 GCGGTGATGTAGATGCTCGATT 60.864 50.000 0.00 0.00 0.00 3.34
3346 3883 0.031314 AGCGGTGATGTAGATGCTCG 59.969 55.000 0.00 0.00 0.00 5.03
3349 3886 1.221414 GGAAGCGGTGATGTAGATGC 58.779 55.000 0.00 0.00 0.00 3.91
3355 3892 2.579201 CTCGGGAAGCGGTGATGT 59.421 61.111 0.00 0.00 0.00 3.06
3507 4051 7.646130 GGCCGTATGAATTTGATCGAAATTTTA 59.354 33.333 13.50 8.93 43.12 1.52
3508 4052 6.475402 GGCCGTATGAATTTGATCGAAATTTT 59.525 34.615 13.50 0.08 43.12 1.82
3509 4053 5.977129 GGCCGTATGAATTTGATCGAAATTT 59.023 36.000 13.50 0.00 43.12 1.82
3532 4076 0.249398 ACGTCAAAATCTCGAGGGGG 59.751 55.000 13.56 0.00 0.00 5.40
3555 4099 1.136329 ACCTGAGGCACATCCCACTT 61.136 55.000 0.00 0.00 34.51 3.16
3579 4123 2.507471 TGTTTTTGGAAATTGGCCTGGT 59.493 40.909 3.32 0.00 0.00 4.00
3583 4127 7.686438 ATTTATCTGTTTTTGGAAATTGGCC 57.314 32.000 0.00 0.00 0.00 5.36
3584 4128 8.390354 GCTATTTATCTGTTTTTGGAAATTGGC 58.610 33.333 0.00 0.00 0.00 4.52
3585 4129 9.434420 TGCTATTTATCTGTTTTTGGAAATTGG 57.566 29.630 0.00 0.00 0.00 3.16
3587 4131 9.657419 CCTGCTATTTATCTGTTTTTGGAAATT 57.343 29.630 0.00 0.00 0.00 1.82
3588 4132 9.034800 TCCTGCTATTTATCTGTTTTTGGAAAT 57.965 29.630 0.00 0.00 0.00 2.17
3589 4133 8.415950 TCCTGCTATTTATCTGTTTTTGGAAA 57.584 30.769 0.00 0.00 0.00 3.13
3590 4134 7.122650 CCTCCTGCTATTTATCTGTTTTTGGAA 59.877 37.037 0.00 0.00 0.00 3.53
3591 4135 6.603201 CCTCCTGCTATTTATCTGTTTTTGGA 59.397 38.462 0.00 0.00 0.00 3.53
3592 4136 6.603201 TCCTCCTGCTATTTATCTGTTTTTGG 59.397 38.462 0.00 0.00 0.00 3.28
3593 4137 7.630242 TCCTCCTGCTATTTATCTGTTTTTG 57.370 36.000 0.00 0.00 0.00 2.44
3594 4138 8.829373 AATCCTCCTGCTATTTATCTGTTTTT 57.171 30.769 0.00 0.00 0.00 1.94
3595 4139 8.829373 AAATCCTCCTGCTATTTATCTGTTTT 57.171 30.769 0.00 0.00 0.00 2.43
3596 4140 8.829373 AAAATCCTCCTGCTATTTATCTGTTT 57.171 30.769 0.00 0.00 0.00 2.83
3597 4141 8.829373 AAAAATCCTCCTGCTATTTATCTGTT 57.171 30.769 0.00 0.00 0.00 3.16
3603 4147 9.707957 TCCAAATAAAAATCCTCCTGCTATTTA 57.292 29.630 0.00 0.00 0.00 1.40
3604 4148 8.608185 TCCAAATAAAAATCCTCCTGCTATTT 57.392 30.769 0.00 0.00 0.00 1.40
3605 4149 8.478066 GTTCCAAATAAAAATCCTCCTGCTATT 58.522 33.333 0.00 0.00 0.00 1.73
3606 4150 7.201821 CGTTCCAAATAAAAATCCTCCTGCTAT 60.202 37.037 0.00 0.00 0.00 2.97
3607 4151 6.094881 CGTTCCAAATAAAAATCCTCCTGCTA 59.905 38.462 0.00 0.00 0.00 3.49
3608 4152 5.105756 CGTTCCAAATAAAAATCCTCCTGCT 60.106 40.000 0.00 0.00 0.00 4.24
3609 4153 5.102313 CGTTCCAAATAAAAATCCTCCTGC 58.898 41.667 0.00 0.00 0.00 4.85
3610 4154 5.102313 GCGTTCCAAATAAAAATCCTCCTG 58.898 41.667 0.00 0.00 0.00 3.86
3611 4155 4.159693 GGCGTTCCAAATAAAAATCCTCCT 59.840 41.667 0.00 0.00 0.00 3.69
3612 4156 4.430007 GGCGTTCCAAATAAAAATCCTCC 58.570 43.478 0.00 0.00 0.00 4.30
3613 4157 4.430007 GGGCGTTCCAAATAAAAATCCTC 58.570 43.478 0.00 0.00 35.00 3.71
3614 4158 3.196901 GGGGCGTTCCAAATAAAAATCCT 59.803 43.478 0.00 0.00 37.22 3.24
3615 4159 3.055747 TGGGGCGTTCCAAATAAAAATCC 60.056 43.478 0.00 0.00 37.22 3.01
3616 4160 4.195225 TGGGGCGTTCCAAATAAAAATC 57.805 40.909 0.00 0.00 37.22 2.17
3617 4161 4.320023 GTTGGGGCGTTCCAAATAAAAAT 58.680 39.130 12.01 0.00 46.98 1.82
3618 4162 3.729966 GTTGGGGCGTTCCAAATAAAAA 58.270 40.909 12.01 0.00 46.98 1.94
3619 4163 2.288273 CGTTGGGGCGTTCCAAATAAAA 60.288 45.455 12.01 0.00 46.98 1.52
3620 4164 1.269998 CGTTGGGGCGTTCCAAATAAA 59.730 47.619 12.01 0.00 46.98 1.40
3621 4165 0.882474 CGTTGGGGCGTTCCAAATAA 59.118 50.000 12.01 0.00 46.98 1.40
3622 4166 0.250814 ACGTTGGGGCGTTCCAAATA 60.251 50.000 12.01 0.00 46.98 1.40
3623 4167 1.529713 ACGTTGGGGCGTTCCAAAT 60.530 52.632 12.01 3.13 46.98 2.32
3624 4168 2.124236 ACGTTGGGGCGTTCCAAA 60.124 55.556 12.01 0.00 46.98 3.28
3631 4175 0.596082 AAATCTTGAACGTTGGGGCG 59.404 50.000 5.00 0.00 37.94 6.13
3632 4176 1.611491 TCAAATCTTGAACGTTGGGGC 59.389 47.619 5.00 0.00 36.59 5.80
3633 4177 2.884639 AGTCAAATCTTGAACGTTGGGG 59.115 45.455 5.00 0.00 42.15 4.96
3634 4178 3.363970 CGAGTCAAATCTTGAACGTTGGG 60.364 47.826 5.00 0.00 42.15 4.12
3635 4179 3.247648 ACGAGTCAAATCTTGAACGTTGG 59.752 43.478 5.00 0.00 45.38 3.77
3636 4180 4.452890 ACGAGTCAAATCTTGAACGTTG 57.547 40.909 5.00 0.00 45.38 4.10
3639 4183 4.603146 CGAAAACGAGTCAAATCTTGAACG 59.397 41.667 12.40 12.40 42.15 3.95
3640 4184 5.734311 TCGAAAACGAGTCAAATCTTGAAC 58.266 37.500 0.00 0.00 42.15 3.18
3641 4185 5.977171 TCGAAAACGAGTCAAATCTTGAA 57.023 34.783 0.00 0.00 42.15 2.69
3642 4186 5.107104 CCATCGAAAACGAGTCAAATCTTGA 60.107 40.000 0.00 0.00 37.33 3.02
3643 4187 5.082059 CCATCGAAAACGAGTCAAATCTTG 58.918 41.667 0.00 0.00 0.00 3.02
3644 4188 4.378459 GCCATCGAAAACGAGTCAAATCTT 60.378 41.667 0.00 0.00 0.00 2.40
3645 4189 3.125316 GCCATCGAAAACGAGTCAAATCT 59.875 43.478 0.00 0.00 0.00 2.40
3646 4190 3.120338 TGCCATCGAAAACGAGTCAAATC 60.120 43.478 0.00 0.00 0.00 2.17
3647 4191 2.811431 TGCCATCGAAAACGAGTCAAAT 59.189 40.909 0.00 0.00 0.00 2.32
3648 4192 2.214347 TGCCATCGAAAACGAGTCAAA 58.786 42.857 0.00 0.00 0.00 2.69
3649 4193 1.872388 TGCCATCGAAAACGAGTCAA 58.128 45.000 0.00 0.00 0.00 3.18
3650 4194 1.872388 TTGCCATCGAAAACGAGTCA 58.128 45.000 0.00 0.00 0.00 3.41
3651 4195 3.471495 AATTGCCATCGAAAACGAGTC 57.529 42.857 0.00 0.00 0.00 3.36
3652 4196 3.915437 AAATTGCCATCGAAAACGAGT 57.085 38.095 0.00 0.00 0.00 4.18
3653 4197 4.793216 CCTAAAATTGCCATCGAAAACGAG 59.207 41.667 0.00 0.00 0.00 4.18
3654 4198 4.456222 TCCTAAAATTGCCATCGAAAACGA 59.544 37.500 0.00 0.00 0.00 3.85
3655 4199 4.728534 TCCTAAAATTGCCATCGAAAACG 58.271 39.130 0.00 0.00 0.00 3.60
3656 4200 5.060446 CGTTCCTAAAATTGCCATCGAAAAC 59.940 40.000 0.00 0.00 0.00 2.43
3657 4201 5.157781 CGTTCCTAAAATTGCCATCGAAAA 58.842 37.500 0.00 0.00 0.00 2.29
3658 4202 4.216687 ACGTTCCTAAAATTGCCATCGAAA 59.783 37.500 0.00 0.00 0.00 3.46
3659 4203 3.754323 ACGTTCCTAAAATTGCCATCGAA 59.246 39.130 0.00 0.00 0.00 3.71
3660 4204 3.340034 ACGTTCCTAAAATTGCCATCGA 58.660 40.909 0.00 0.00 0.00 3.59
3661 4205 3.757745 ACGTTCCTAAAATTGCCATCG 57.242 42.857 0.00 0.00 0.00 3.84
3662 4206 6.791303 TCATAACGTTCCTAAAATTGCCATC 58.209 36.000 2.82 0.00 0.00 3.51
3663 4207 6.767524 TCATAACGTTCCTAAAATTGCCAT 57.232 33.333 2.82 0.00 0.00 4.40
3664 4208 6.457663 CGATCATAACGTTCCTAAAATTGCCA 60.458 38.462 2.82 0.00 0.00 4.92
3665 4209 5.907391 CGATCATAACGTTCCTAAAATTGCC 59.093 40.000 2.82 0.00 0.00 4.52
3666 4210 5.395486 GCGATCATAACGTTCCTAAAATTGC 59.605 40.000 2.82 3.54 0.00 3.56
3667 4211 6.482835 TGCGATCATAACGTTCCTAAAATTG 58.517 36.000 2.82 0.00 0.00 2.32
3668 4212 6.671614 TGCGATCATAACGTTCCTAAAATT 57.328 33.333 2.82 0.00 0.00 1.82
3669 4213 6.671614 TTGCGATCATAACGTTCCTAAAAT 57.328 33.333 2.82 0.00 0.00 1.82
3670 4214 6.671614 ATTGCGATCATAACGTTCCTAAAA 57.328 33.333 2.82 0.00 0.00 1.52
3671 4215 6.671614 AATTGCGATCATAACGTTCCTAAA 57.328 33.333 2.82 0.00 0.00 1.85
3672 4216 6.671614 AAATTGCGATCATAACGTTCCTAA 57.328 33.333 2.82 0.00 0.00 2.69
3673 4217 6.671614 AAAATTGCGATCATAACGTTCCTA 57.328 33.333 2.82 0.00 0.00 2.94
3674 4218 5.560966 AAAATTGCGATCATAACGTTCCT 57.439 34.783 2.82 0.00 0.00 3.36
3675 4219 6.483687 ACTAAAATTGCGATCATAACGTTCC 58.516 36.000 2.82 0.00 0.00 3.62
3676 4220 7.948513 AACTAAAATTGCGATCATAACGTTC 57.051 32.000 2.82 0.00 0.00 3.95
3677 4221 7.906527 GGTAACTAAAATTGCGATCATAACGTT 59.093 33.333 5.88 5.88 0.00 3.99
3678 4222 7.064847 TGGTAACTAAAATTGCGATCATAACGT 59.935 33.333 0.00 0.00 37.61 3.99
3679 4223 7.403421 TGGTAACTAAAATTGCGATCATAACG 58.597 34.615 0.00 0.00 37.61 3.18
3680 4224 9.169468 CATGGTAACTAAAATTGCGATCATAAC 57.831 33.333 0.00 0.00 37.61 1.89
3681 4225 8.898761 ACATGGTAACTAAAATTGCGATCATAA 58.101 29.630 0.00 0.00 37.61 1.90
3682 4226 8.341903 CACATGGTAACTAAAATTGCGATCATA 58.658 33.333 0.00 0.00 37.61 2.15
3683 4227 7.148086 ACACATGGTAACTAAAATTGCGATCAT 60.148 33.333 0.00 0.00 37.61 2.45
3684 4228 6.150307 ACACATGGTAACTAAAATTGCGATCA 59.850 34.615 0.00 0.00 37.61 2.92
3685 4229 6.551736 ACACATGGTAACTAAAATTGCGATC 58.448 36.000 0.00 0.00 37.61 3.69
3686 4230 6.509418 ACACATGGTAACTAAAATTGCGAT 57.491 33.333 0.00 0.00 37.61 4.58
3687 4231 5.950758 ACACATGGTAACTAAAATTGCGA 57.049 34.783 0.00 0.00 37.61 5.10
3688 4232 6.087555 GTGAACACATGGTAACTAAAATTGCG 59.912 38.462 0.00 0.00 37.61 4.85
3689 4233 6.920758 TGTGAACACATGGTAACTAAAATTGC 59.079 34.615 3.39 0.00 36.21 3.56
3690 4234 8.280909 GTGTGAACACATGGTAACTAAAATTG 57.719 34.615 10.78 0.00 45.75 2.32


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

AutoCloner maintained by Alex Coulton.