Multiple sequence alignment - TraesCS1B01G319200

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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 TraesCS1B01G319200 chr1B 100.000 3107 0 0 1 3107 543481821 543478715 0.000000e+00 5738.0
1 TraesCS1B01G319200 chr7A 99.175 970 6 2 2 970 256007204 256008172 0.000000e+00 1746.0
2 TraesCS1B01G319200 chr7A 98.632 950 11 2 1 948 24594429 24595378 0.000000e+00 1681.0
3 TraesCS1B01G319200 chr5B 98.967 968 9 1 1 967 415792858 415793825 0.000000e+00 1731.0
4 TraesCS1B01G319200 chr5B 98.657 968 12 1 1 967 580489340 580490307 0.000000e+00 1714.0
5 TraesCS1B01G319200 chr2B 98.865 969 9 2 1 967 512302928 512301960 0.000000e+00 1727.0
6 TraesCS1B01G319200 chr2B 98.244 968 16 1 1 967 680579477 680578510 0.000000e+00 1692.0
7 TraesCS1B01G319200 chr6B 98.663 972 12 1 1 971 715712611 715711640 0.000000e+00 1722.0
8 TraesCS1B01G319200 chr3B 98.762 969 10 2 1 967 814366344 814367312 0.000000e+00 1722.0
9 TraesCS1B01G319200 chr4B 98.660 970 11 2 1 968 115078924 115079893 0.000000e+00 1718.0
10 TraesCS1B01G319200 chr1D 91.910 890 47 14 968 1839 404067663 404066781 0.000000e+00 1221.0
11 TraesCS1B01G319200 chr1D 83.921 709 79 13 2117 2796 89597068 89596366 0.000000e+00 645.0
12 TraesCS1B01G319200 chr1D 91.703 229 16 3 1833 2060 404066285 404066059 6.470000e-82 315.0
13 TraesCS1B01G319200 chr1D 84.080 201 7 8 2932 3107 404066068 404065868 1.480000e-38 171.0
14 TraesCS1B01G319200 chr1A 90.887 812 41 16 1043 1839 499737071 499736278 0.000000e+00 1059.0
15 TraesCS1B01G319200 chr1A 91.416 233 14 4 1833 2060 499735860 499735629 6.470000e-82 315.0
16 TraesCS1B01G319200 chr1A 88.298 94 9 1 2970 3061 499735564 499735471 9.110000e-21 111.0
17 TraesCS1B01G319200 chr3D 80.000 145 17 5 2543 2675 487378270 487378126 2.550000e-16 97.1
18 TraesCS1B01G319200 chr4A 76.804 194 29 15 2475 2663 677211735 677211917 9.170000e-16 95.3
19 TraesCS1B01G319200 chr4A 76.804 194 29 15 2475 2663 677233532 677233714 9.170000e-16 95.3
20 TraesCS1B01G319200 chr3A 100.000 28 0 0 2699 2726 362546714 362546741 6.000000e-03 52.8


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 TraesCS1B01G319200 chr1B 543478715 543481821 3106 True 5738 5738 100.000000 1 3107 1 chr1B.!!$R1 3106
1 TraesCS1B01G319200 chr7A 256007204 256008172 968 False 1746 1746 99.175000 2 970 1 chr7A.!!$F2 968
2 TraesCS1B01G319200 chr7A 24594429 24595378 949 False 1681 1681 98.632000 1 948 1 chr7A.!!$F1 947
3 TraesCS1B01G319200 chr5B 415792858 415793825 967 False 1731 1731 98.967000 1 967 1 chr5B.!!$F1 966
4 TraesCS1B01G319200 chr5B 580489340 580490307 967 False 1714 1714 98.657000 1 967 1 chr5B.!!$F2 966
5 TraesCS1B01G319200 chr2B 512301960 512302928 968 True 1727 1727 98.865000 1 967 1 chr2B.!!$R1 966
6 TraesCS1B01G319200 chr2B 680578510 680579477 967 True 1692 1692 98.244000 1 967 1 chr2B.!!$R2 966
7 TraesCS1B01G319200 chr6B 715711640 715712611 971 True 1722 1722 98.663000 1 971 1 chr6B.!!$R1 970
8 TraesCS1B01G319200 chr3B 814366344 814367312 968 False 1722 1722 98.762000 1 967 1 chr3B.!!$F1 966
9 TraesCS1B01G319200 chr4B 115078924 115079893 969 False 1718 1718 98.660000 1 968 1 chr4B.!!$F1 967
10 TraesCS1B01G319200 chr1D 89596366 89597068 702 True 645 645 83.921000 2117 2796 1 chr1D.!!$R1 679
11 TraesCS1B01G319200 chr1D 404065868 404067663 1795 True 569 1221 89.231000 968 3107 3 chr1D.!!$R2 2139
12 TraesCS1B01G319200 chr1A 499735471 499737071 1600 True 495 1059 90.200333 1043 3061 3 chr1A.!!$R1 2018

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
317 319 0.966920 GGACGAGGACTTGGAAGACA 59.033 55.0 0.00 0.0 0.0 3.41 F
1037 1041 0.679505 CGTGACCACTGGAGGAGAAA 59.320 55.0 0.71 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1435 0.171903 GCAGGTACGCGTAGAAAGGA 59.828 55.0 21.25 0.0 0.0 3.36 R
2895 3473 0.034198 TGCCGACGGACAATCTGAAA 59.966 50.0 20.50 0.0 0.0 2.69 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
245 247 3.508793 CCCAGCACAAGTGATTTCTTCAT 59.491 43.478 4.04 0.00 36.54 2.57
317 319 0.966920 GGACGAGGACTTGGAAGACA 59.033 55.000 0.00 0.00 0.00 3.41
801 803 2.280524 CGCCACCCGACAAGTTCA 60.281 61.111 0.00 0.00 40.02 3.18
1037 1041 0.679505 CGTGACCACTGGAGGAGAAA 59.320 55.000 0.71 0.00 0.00 2.52
1224 1240 2.354072 GAATCTCGCCTCGCCTCG 60.354 66.667 0.00 0.00 0.00 4.63
1283 1302 4.003788 CCGAAGGCTGGTGGTCGT 62.004 66.667 4.99 0.00 46.14 4.34
1419 1438 3.692406 GACGCCGTCCAGGTTCCT 61.692 66.667 5.81 0.00 43.70 3.36
1428 1447 0.245539 TCCAGGTTCCTTTCTACGCG 59.754 55.000 3.53 3.53 0.00 6.01
1486 1506 3.616802 CGTACCTTCTCCAACCCTTCTTC 60.617 52.174 0.00 0.00 0.00 2.87
1487 1507 2.707554 ACCTTCTCCAACCCTTCTTCT 58.292 47.619 0.00 0.00 0.00 2.85
1491 1511 4.202514 CCTTCTCCAACCCTTCTTCTTCTT 60.203 45.833 0.00 0.00 0.00 2.52
1493 1513 4.235372 TCTCCAACCCTTCTTCTTCTTCT 58.765 43.478 0.00 0.00 0.00 2.85
1494 1514 4.660771 TCTCCAACCCTTCTTCTTCTTCTT 59.339 41.667 0.00 0.00 0.00 2.52
1495 1515 4.974399 TCCAACCCTTCTTCTTCTTCTTC 58.026 43.478 0.00 0.00 0.00 2.87
1496 1516 4.660771 TCCAACCCTTCTTCTTCTTCTTCT 59.339 41.667 0.00 0.00 0.00 2.85
1500 1520 4.530553 ACCCTTCTTCTTCTTCTTCTCCTC 59.469 45.833 0.00 0.00 0.00 3.71
1503 1523 5.105351 CCTTCTTCTTCTTCTTCTCCTCCTC 60.105 48.000 0.00 0.00 0.00 3.71
1630 1657 2.028190 CTCTACGCGCCCATCCTG 59.972 66.667 5.73 0.00 0.00 3.86
1670 1697 2.117156 ATCCCGACCTCCGTACGTG 61.117 63.158 15.21 5.96 36.31 4.49
1678 1705 1.278238 CCTCCGTACGTGCATCTTTC 58.722 55.000 15.21 0.00 0.00 2.62
1681 1708 2.267426 TCCGTACGTGCATCTTTCATG 58.733 47.619 15.21 0.00 0.00 3.07
1682 1709 1.267532 CCGTACGTGCATCTTTCATGC 60.268 52.381 15.21 0.00 44.76 4.06
1685 1712 1.315257 ACGTGCATCTTTCATGCCCC 61.315 55.000 4.18 0.00 43.94 5.80
1697 1724 0.608130 CATGCCCCGATCGATCCTAA 59.392 55.000 18.66 1.93 0.00 2.69
1698 1725 0.898320 ATGCCCCGATCGATCCTAAG 59.102 55.000 18.66 5.49 0.00 2.18
1699 1726 1.079750 GCCCCGATCGATCCTAAGC 60.080 63.158 18.66 13.13 0.00 3.09
1700 1727 1.536943 GCCCCGATCGATCCTAAGCT 61.537 60.000 18.66 0.00 0.00 3.74
1706 1733 4.095185 CCCGATCGATCCTAAGCTACTAAG 59.905 50.000 18.66 0.83 0.00 2.18
1722 1754 6.148480 AGCTACTAAGTTTGCACTTCTTGATG 59.852 38.462 7.27 2.23 42.66 3.07
1743 1775 4.253685 TGGAGTTCATTCTCGTTTGGATC 58.746 43.478 0.00 0.00 35.52 3.36
1744 1776 3.623510 GGAGTTCATTCTCGTTTGGATCC 59.376 47.826 4.20 4.20 35.52 3.36
1902 2447 4.679654 GCTGGTTGTGCTTAATGTTAACAC 59.320 41.667 11.22 0.00 0.00 3.32
1930 2475 4.708177 AGCATAAAACATCACGAGGCTAT 58.292 39.130 0.00 0.00 0.00 2.97
1955 2500 6.667414 TGGGGAAATTAGATTTGTTGCTATGT 59.333 34.615 0.00 0.00 31.47 2.29
1969 2514 4.625972 TGCTATGTTGAATGCATGTCTG 57.374 40.909 0.00 0.00 0.00 3.51
2010 2555 0.817634 CCCAGCGTTCAAGACCAACA 60.818 55.000 0.00 0.00 0.00 3.33
2027 2576 1.632589 ACAAAATCCTTGGGGCAGTC 58.367 50.000 0.00 0.00 0.00 3.51
2030 2579 1.497309 AAATCCTTGGGGCAGTCGGA 61.497 55.000 0.00 0.00 0.00 4.55
2059 2608 4.935205 TCACTCTACGCTGCATTGTTTTAT 59.065 37.500 0.00 0.00 0.00 1.40
2060 2609 5.023920 CACTCTACGCTGCATTGTTTTATG 58.976 41.667 0.00 0.00 0.00 1.90
2061 2610 4.094887 ACTCTACGCTGCATTGTTTTATGG 59.905 41.667 0.00 0.00 0.00 2.74
2062 2611 4.257731 TCTACGCTGCATTGTTTTATGGA 58.742 39.130 0.00 0.00 0.00 3.41
2063 2612 3.932545 ACGCTGCATTGTTTTATGGAA 57.067 38.095 0.00 0.00 0.00 3.53
2064 2613 4.250116 ACGCTGCATTGTTTTATGGAAA 57.750 36.364 0.00 0.00 0.00 3.13
2065 2614 4.626042 ACGCTGCATTGTTTTATGGAAAA 58.374 34.783 0.00 0.00 32.00 2.29
2078 2627 7.589958 TTTTATGGAAAACTCTTAGTGCCAA 57.410 32.000 0.00 0.00 31.55 4.52
2079 2628 6.569179 TTATGGAAAACTCTTAGTGCCAAC 57.431 37.500 0.00 0.00 31.55 3.77
2080 2629 3.219281 TGGAAAACTCTTAGTGCCAACC 58.781 45.455 0.00 0.00 0.00 3.77
2081 2630 2.225727 GGAAAACTCTTAGTGCCAACCG 59.774 50.000 0.00 0.00 0.00 4.44
2082 2631 1.892209 AAACTCTTAGTGCCAACCGG 58.108 50.000 0.00 0.00 0.00 5.28
2092 2641 3.497879 CCAACCGGCGGATTTCTC 58.502 61.111 35.78 0.00 0.00 2.87
2093 2642 1.078426 CCAACCGGCGGATTTCTCT 60.078 57.895 35.78 4.66 0.00 3.10
2094 2643 1.090052 CCAACCGGCGGATTTCTCTC 61.090 60.000 35.78 0.00 0.00 3.20
2095 2644 1.153628 AACCGGCGGATTTCTCTCG 60.154 57.895 35.78 1.17 0.00 4.04
2096 2645 1.885163 AACCGGCGGATTTCTCTCGT 61.885 55.000 35.78 1.87 0.00 4.18
2097 2646 1.153628 CCGGCGGATTTCTCTCGTT 60.154 57.895 24.41 0.00 0.00 3.85
2098 2647 1.146358 CCGGCGGATTTCTCTCGTTC 61.146 60.000 24.41 0.00 0.00 3.95
2099 2648 0.457853 CGGCGGATTTCTCTCGTTCA 60.458 55.000 0.00 0.00 0.00 3.18
2100 2649 1.802880 CGGCGGATTTCTCTCGTTCAT 60.803 52.381 0.00 0.00 0.00 2.57
2101 2650 1.861575 GGCGGATTTCTCTCGTTCATC 59.138 52.381 0.00 0.00 0.00 2.92
2102 2651 1.861575 GCGGATTTCTCTCGTTCATCC 59.138 52.381 0.00 0.00 0.00 3.51
2104 2653 1.861575 GGATTTCTCTCGTTCATCCGC 59.138 52.381 0.00 0.00 0.00 5.54
2105 2654 1.861575 GATTTCTCTCGTTCATCCGCC 59.138 52.381 0.00 0.00 0.00 6.13
2106 2655 0.457853 TTTCTCTCGTTCATCCGCCG 60.458 55.000 0.00 0.00 0.00 6.46
2107 2656 2.884087 TTCTCTCGTTCATCCGCCGC 62.884 60.000 0.00 0.00 0.00 6.53
2108 2657 4.508128 TCTCGTTCATCCGCCGCC 62.508 66.667 0.00 0.00 0.00 6.13
2109 2658 4.514577 CTCGTTCATCCGCCGCCT 62.515 66.667 0.00 0.00 0.00 5.52
2110 2659 4.508128 TCGTTCATCCGCCGCCTC 62.508 66.667 0.00 0.00 0.00 4.70
2136 2685 3.741476 CGCTTTGGGTGCTGCCTC 61.741 66.667 0.00 0.00 37.43 4.70
2145 2694 0.251354 GGTGCTGCCTCATCTTCTCA 59.749 55.000 0.00 0.00 0.00 3.27
2147 2696 2.211806 GTGCTGCCTCATCTTCTCATC 58.788 52.381 0.00 0.00 0.00 2.92
2150 2699 1.685517 CTGCCTCATCTTCTCATCGGA 59.314 52.381 0.00 0.00 0.00 4.55
2164 2713 3.766591 CTCATCGGATTACTCCTAGCCAT 59.233 47.826 0.00 0.00 39.65 4.40
2167 2716 5.594725 TCATCGGATTACTCCTAGCCATATC 59.405 44.000 0.00 0.00 39.65 1.63
2200 2749 1.075536 GCCTTCTTCCTTTCTTCCCCA 59.924 52.381 0.00 0.00 0.00 4.96
2203 2752 3.829026 CCTTCTTCCTTTCTTCCCCAAAG 59.171 47.826 0.00 0.00 36.22 2.77
2211 2760 0.783206 TCTTCCCCAAAGCCATCCAA 59.217 50.000 0.00 0.00 34.76 3.53
2216 2765 0.040204 CCCAAAGCCATCCAACCTCT 59.960 55.000 0.00 0.00 0.00 3.69
2225 2774 3.285484 CCATCCAACCTCTTTCCATCAG 58.715 50.000 0.00 0.00 0.00 2.90
2248 2797 2.412525 CAAGCACAACAGCGCCAA 59.587 55.556 2.29 0.00 40.15 4.52
2256 2805 4.666253 ACAGCGCCAACCCATGCT 62.666 61.111 2.29 0.00 38.43 3.79
2260 2809 2.360350 CGCCAACCCATGCTCACT 60.360 61.111 0.00 0.00 0.00 3.41
2272 2843 4.823276 CTCACTAGCAAGCCTCCG 57.177 61.111 0.00 0.00 0.00 4.63
2278 2849 1.689233 TAGCAAGCCTCCGGTGGAT 60.689 57.895 26.61 18.05 0.00 3.41
2304 2875 1.380380 CCCTGCCATGTTCTTCCCC 60.380 63.158 0.00 0.00 0.00 4.81
2319 2890 4.047125 CCCAACCCAGCCACGGAT 62.047 66.667 0.00 0.00 0.00 4.18
2340 2911 0.471191 TCCATGGAGGTAGCATGCAG 59.529 55.000 21.98 0.00 39.02 4.41
2341 2912 1.170919 CCATGGAGGTAGCATGCAGC 61.171 60.000 21.98 15.04 46.19 5.25
2367 2938 2.723273 GCTAGGGGCTACAACAACAAT 58.277 47.619 0.00 0.00 38.06 2.71
2424 2995 2.046314 CTGGCGACGGGAATTGGT 60.046 61.111 0.00 0.00 0.00 3.67
2437 3008 1.978455 AATTGGTGGCGCTCGGGATA 61.978 55.000 7.64 0.00 0.00 2.59
2441 3012 2.443203 TGGCGCTCGGGATAGGAA 60.443 61.111 7.64 0.00 0.00 3.36
2445 3016 1.283181 CGCTCGGGATAGGAACTCG 59.717 63.158 0.00 0.00 41.75 4.18
2449 3020 0.822532 TCGGGATAGGAACTCGGAGC 60.823 60.000 4.58 0.00 41.75 4.70
2476 3047 3.747521 CTTGGGGTTGGTGGCCACA 62.748 63.158 35.78 19.85 37.69 4.17
2500 3071 1.672356 GAACGATGGTGGTGCTGCT 60.672 57.895 0.00 0.00 0.00 4.24
2502 3073 2.046988 CGATGGTGGTGCTGCTGA 60.047 61.111 0.00 0.00 0.00 4.26
2506 3077 0.892358 ATGGTGGTGCTGCTGACAAG 60.892 55.000 0.00 0.00 0.00 3.16
2509 3080 0.607489 GTGGTGCTGCTGACAAGGAT 60.607 55.000 0.00 0.00 0.00 3.24
2515 3086 1.198637 GCTGCTGACAAGGATGTTGAC 59.801 52.381 0.00 0.00 40.74 3.18
2520 3091 3.243068 GCTGACAAGGATGTTGACGTTTT 60.243 43.478 0.00 0.00 40.74 2.43
2523 3094 3.443976 ACAAGGATGTTGACGTTTTTGC 58.556 40.909 0.00 0.00 35.91 3.68
2541 3112 9.483062 CGTTTTTGCAACTTAATTTTCATTGAA 57.517 25.926 0.00 0.00 0.00 2.69
2556 3130 8.434733 TTTTCATTGAATTTTCTGCAACATCA 57.565 26.923 0.00 0.00 0.00 3.07
2559 3133 6.814644 TCATTGAATTTTCTGCAACATCATCC 59.185 34.615 0.00 0.00 0.00 3.51
2560 3134 4.735985 TGAATTTTCTGCAACATCATCCG 58.264 39.130 0.00 0.00 0.00 4.18
2571 3145 3.724508 ACATCATCCGTGTTGCAAAAA 57.275 38.095 0.00 0.00 0.00 1.94
2579 3153 2.857748 CCGTGTTGCAAAAACTTCTTCC 59.142 45.455 0.00 0.00 29.63 3.46
2589 3163 5.332280 GCAAAAACTTCTTCCGCAATAACAC 60.332 40.000 0.00 0.00 0.00 3.32
2592 3166 2.224670 ACTTCTTCCGCAATAACACCCA 60.225 45.455 0.00 0.00 0.00 4.51
2604 3178 1.636148 AACACCCATGCTGCAGAAAT 58.364 45.000 20.43 7.26 0.00 2.17
2605 3179 1.636148 ACACCCATGCTGCAGAAATT 58.364 45.000 20.43 0.00 0.00 1.82
2606 3180 1.274167 ACACCCATGCTGCAGAAATTG 59.726 47.619 20.43 2.51 0.00 2.32
2607 3181 1.546923 CACCCATGCTGCAGAAATTGA 59.453 47.619 20.43 0.00 0.00 2.57
2608 3182 2.028839 CACCCATGCTGCAGAAATTGAA 60.029 45.455 20.43 0.00 0.00 2.69
2609 3183 2.232941 ACCCATGCTGCAGAAATTGAAG 59.767 45.455 20.43 0.86 35.31 3.02
2610 3184 2.494471 CCCATGCTGCAGAAATTGAAGA 59.506 45.455 20.43 0.00 33.87 2.87
2652 3227 6.639632 ACACATCTATGTTGCAAAAGTTCT 57.360 33.333 0.00 0.00 39.39 3.01
2664 3239 3.555547 GCAAAAGTTCTTTCCGCAACAAT 59.444 39.130 11.91 0.00 0.00 2.71
2738 3316 4.514441 TGTTGCAAAAATTCATTCCGCAAT 59.486 33.333 0.00 0.00 39.11 3.56
2741 3319 6.981762 TGCAAAAATTCATTCCGCAATAAT 57.018 29.167 0.00 0.00 0.00 1.28
2752 3330 6.862608 TCATTCCGCAATAATATCAATGTTGC 59.137 34.615 0.00 0.00 41.15 4.17
2757 3335 6.696583 CCGCAATAATATCAATGTTGCAGAAA 59.303 34.615 8.79 0.00 43.87 2.52
2767 3345 6.198687 TCAATGTTGCAGAAAAGTAAAGACG 58.801 36.000 0.00 0.00 0.00 4.18
2768 3346 6.037720 TCAATGTTGCAGAAAAGTAAAGACGA 59.962 34.615 0.00 0.00 0.00 4.20
2809 3387 7.100458 ACACTAATGTTGCAAAAGAGTTTCT 57.900 32.000 0.00 0.00 34.46 2.52
2810 3388 8.220755 ACACTAATGTTGCAAAAGAGTTTCTA 57.779 30.769 0.00 0.00 34.46 2.10
2811 3389 8.850156 ACACTAATGTTGCAAAAGAGTTTCTAT 58.150 29.630 0.00 0.00 34.46 1.98
2817 3395 9.630098 ATGTTGCAAAAGAGTTTCTATAACATG 57.370 29.630 0.00 0.00 34.76 3.21
2818 3396 8.629158 TGTTGCAAAAGAGTTTCTATAACATGT 58.371 29.630 0.00 0.00 0.00 3.21
2819 3397 8.905702 GTTGCAAAAGAGTTTCTATAACATGTG 58.094 33.333 0.00 0.00 0.00 3.21
2820 3398 7.083858 TGCAAAAGAGTTTCTATAACATGTGC 58.916 34.615 0.00 0.00 0.00 4.57
2821 3399 7.040478 TGCAAAAGAGTTTCTATAACATGTGCT 60.040 33.333 0.00 0.00 0.00 4.40
2822 3400 7.483059 GCAAAAGAGTTTCTATAACATGTGCTC 59.517 37.037 0.00 0.00 0.00 4.26
2823 3401 8.725148 CAAAAGAGTTTCTATAACATGTGCTCT 58.275 33.333 0.00 0.47 32.90 4.09
2824 3402 9.944376 AAAAGAGTTTCTATAACATGTGCTCTA 57.056 29.630 0.00 0.00 31.52 2.43
2827 3405 9.539825 AGAGTTTCTATAACATGTGCTCTATTG 57.460 33.333 0.00 0.00 0.00 1.90
2828 3406 8.147642 AGTTTCTATAACATGTGCTCTATTGC 57.852 34.615 0.00 0.00 0.00 3.56
2829 3407 7.770433 AGTTTCTATAACATGTGCTCTATTGCA 59.230 33.333 0.00 0.00 41.05 4.08
2830 3408 8.397906 GTTTCTATAACATGTGCTCTATTGCAA 58.602 33.333 0.00 0.00 45.12 4.08
2831 3409 8.681486 TTCTATAACATGTGCTCTATTGCAAT 57.319 30.769 17.56 17.56 45.12 3.56
2832 3410 8.091385 TCTATAACATGTGCTCTATTGCAATG 57.909 34.615 22.27 11.73 45.12 2.82
2833 3411 6.947644 ATAACATGTGCTCTATTGCAATGA 57.052 33.333 22.27 15.09 45.12 2.57
2834 3412 5.847111 AACATGTGCTCTATTGCAATGAT 57.153 34.783 22.27 0.00 45.12 2.45
2835 3413 5.183014 ACATGTGCTCTATTGCAATGATG 57.817 39.130 22.27 11.64 45.12 3.07
2836 3414 4.885325 ACATGTGCTCTATTGCAATGATGA 59.115 37.500 22.27 14.95 45.12 2.92
2837 3415 5.535030 ACATGTGCTCTATTGCAATGATGAT 59.465 36.000 22.27 0.00 45.12 2.45
2838 3416 5.432885 TGTGCTCTATTGCAATGATGATG 57.567 39.130 22.27 11.23 45.12 3.07
2839 3417 5.127491 TGTGCTCTATTGCAATGATGATGA 58.873 37.500 22.27 8.96 45.12 2.92
2840 3418 5.008316 TGTGCTCTATTGCAATGATGATGAC 59.992 40.000 22.27 14.39 45.12 3.06
2841 3419 4.212636 TGCTCTATTGCAATGATGATGACG 59.787 41.667 22.27 6.80 40.29 4.35
2842 3420 4.378149 GCTCTATTGCAATGATGATGACGG 60.378 45.833 22.27 6.50 0.00 4.79
2843 3421 4.067192 TCTATTGCAATGATGATGACGGG 58.933 43.478 22.27 0.00 0.00 5.28
2844 3422 1.391577 TTGCAATGATGATGACGGGG 58.608 50.000 0.00 0.00 0.00 5.73
2845 3423 0.255604 TGCAATGATGATGACGGGGT 59.744 50.000 0.00 0.00 0.00 4.95
2846 3424 1.340893 TGCAATGATGATGACGGGGTT 60.341 47.619 0.00 0.00 0.00 4.11
2847 3425 1.066002 GCAATGATGATGACGGGGTTG 59.934 52.381 0.00 0.00 0.00 3.77
2848 3426 2.642427 CAATGATGATGACGGGGTTGA 58.358 47.619 0.00 0.00 0.00 3.18
2849 3427 2.615447 CAATGATGATGACGGGGTTGAG 59.385 50.000 0.00 0.00 0.00 3.02
2850 3428 0.107703 TGATGATGACGGGGTTGAGC 60.108 55.000 0.00 0.00 0.00 4.26
2851 3429 0.815615 GATGATGACGGGGTTGAGCC 60.816 60.000 0.00 0.00 0.00 4.70
2852 3430 2.511600 GATGACGGGGTTGAGCCG 60.512 66.667 0.00 0.00 38.44 5.52
2853 3431 3.310860 GATGACGGGGTTGAGCCGT 62.311 63.158 0.00 0.00 42.98 5.68
2854 3432 2.798148 GATGACGGGGTTGAGCCGTT 62.798 60.000 0.00 0.00 40.33 4.44
2855 3433 2.741211 GACGGGGTTGAGCCGTTC 60.741 66.667 0.00 0.00 40.33 3.95
2856 3434 4.675029 ACGGGGTTGAGCCGTTCG 62.675 66.667 0.00 0.00 36.80 3.95
2857 3435 4.367023 CGGGGTTGAGCCGTTCGA 62.367 66.667 0.00 0.00 38.44 3.71
2858 3436 2.267961 GGGGTTGAGCCGTTCGAT 59.732 61.111 0.00 0.00 38.44 3.59
2859 3437 2.106683 GGGGTTGAGCCGTTCGATG 61.107 63.158 0.00 0.00 38.44 3.84
2860 3438 2.106683 GGGTTGAGCCGTTCGATGG 61.107 63.158 0.00 0.00 38.44 3.51
2861 3439 1.375523 GGTTGAGCCGTTCGATGGT 60.376 57.895 6.14 0.00 0.00 3.55
2862 3440 1.635663 GGTTGAGCCGTTCGATGGTG 61.636 60.000 6.14 0.00 0.00 4.17
2863 3441 2.032634 TTGAGCCGTTCGATGGTGC 61.033 57.895 6.14 0.00 0.00 5.01
2864 3442 3.195698 GAGCCGTTCGATGGTGCC 61.196 66.667 6.14 0.00 0.00 5.01
2865 3443 3.950794 GAGCCGTTCGATGGTGCCA 62.951 63.158 6.14 0.00 0.00 4.92
2866 3444 3.053291 GCCGTTCGATGGTGCCAA 61.053 61.111 6.14 0.00 0.00 4.52
2867 3445 2.622011 GCCGTTCGATGGTGCCAAA 61.622 57.895 6.14 0.00 0.00 3.28
2868 3446 1.933115 GCCGTTCGATGGTGCCAAAT 61.933 55.000 6.14 0.00 0.00 2.32
2869 3447 0.098728 CCGTTCGATGGTGCCAAATC 59.901 55.000 0.00 0.00 0.00 2.17
2870 3448 1.086696 CGTTCGATGGTGCCAAATCT 58.913 50.000 0.00 0.00 0.00 2.40
2871 3449 2.276201 CGTTCGATGGTGCCAAATCTA 58.724 47.619 0.00 0.00 0.00 1.98
2872 3450 2.675844 CGTTCGATGGTGCCAAATCTAA 59.324 45.455 0.00 0.00 0.00 2.10
2873 3451 3.485216 CGTTCGATGGTGCCAAATCTAAC 60.485 47.826 0.00 0.00 0.00 2.34
2874 3452 2.276201 TCGATGGTGCCAAATCTAACG 58.724 47.619 0.00 0.00 0.00 3.18
2875 3453 1.330521 CGATGGTGCCAAATCTAACGG 59.669 52.381 0.00 0.00 0.00 4.44
2876 3454 2.365582 GATGGTGCCAAATCTAACGGT 58.634 47.619 0.00 0.00 0.00 4.83
2877 3455 1.816074 TGGTGCCAAATCTAACGGTC 58.184 50.000 0.00 0.00 0.00 4.79
2878 3456 1.072489 TGGTGCCAAATCTAACGGTCA 59.928 47.619 0.00 0.00 0.00 4.02
2879 3457 1.467342 GGTGCCAAATCTAACGGTCAC 59.533 52.381 0.00 0.00 0.00 3.67
2880 3458 2.423577 GTGCCAAATCTAACGGTCACT 58.576 47.619 0.00 0.00 0.00 3.41
2881 3459 2.159627 GTGCCAAATCTAACGGTCACTG 59.840 50.000 0.00 0.00 0.00 3.66
2882 3460 2.037902 TGCCAAATCTAACGGTCACTGA 59.962 45.455 0.00 0.00 0.00 3.41
2883 3461 2.673368 GCCAAATCTAACGGTCACTGAG 59.327 50.000 0.00 0.00 0.00 3.35
2884 3462 3.262420 CCAAATCTAACGGTCACTGAGG 58.738 50.000 0.00 0.00 0.00 3.86
2885 3463 3.056107 CCAAATCTAACGGTCACTGAGGA 60.056 47.826 0.00 0.00 0.00 3.71
2886 3464 4.177026 CAAATCTAACGGTCACTGAGGAG 58.823 47.826 0.00 0.00 0.00 3.69
2887 3465 1.835494 TCTAACGGTCACTGAGGAGG 58.165 55.000 0.00 0.00 0.00 4.30
2888 3466 1.075050 TCTAACGGTCACTGAGGAGGT 59.925 52.381 0.00 0.00 0.00 3.85
2889 3467 1.202582 CTAACGGTCACTGAGGAGGTG 59.797 57.143 0.00 0.00 36.17 4.00
2890 3468 1.472662 AACGGTCACTGAGGAGGTGG 61.473 60.000 0.00 0.00 35.61 4.61
2891 3469 1.606601 CGGTCACTGAGGAGGTGGA 60.607 63.158 0.00 0.00 35.61 4.02
2892 3470 0.972983 CGGTCACTGAGGAGGTGGAT 60.973 60.000 0.00 0.00 35.61 3.41
2893 3471 0.827368 GGTCACTGAGGAGGTGGATC 59.173 60.000 0.00 0.00 35.61 3.36
2894 3472 1.621072 GGTCACTGAGGAGGTGGATCT 60.621 57.143 0.00 0.00 35.61 2.75
2895 3473 2.183679 GTCACTGAGGAGGTGGATCTT 58.816 52.381 0.00 0.00 35.61 2.40
2896 3474 2.569404 GTCACTGAGGAGGTGGATCTTT 59.431 50.000 0.00 0.00 35.61 2.52
2897 3475 3.008485 GTCACTGAGGAGGTGGATCTTTT 59.992 47.826 0.00 0.00 35.61 2.27
2898 3476 3.261897 TCACTGAGGAGGTGGATCTTTTC 59.738 47.826 0.00 0.00 35.61 2.29
2899 3477 3.008375 CACTGAGGAGGTGGATCTTTTCA 59.992 47.826 0.00 0.00 0.00 2.69
2900 3478 3.262915 ACTGAGGAGGTGGATCTTTTCAG 59.737 47.826 0.00 0.00 35.51 3.02
2901 3479 3.517100 CTGAGGAGGTGGATCTTTTCAGA 59.483 47.826 0.00 0.00 33.35 3.27
2902 3480 4.107072 TGAGGAGGTGGATCTTTTCAGAT 58.893 43.478 0.00 0.00 43.03 2.90
2903 3481 4.537688 TGAGGAGGTGGATCTTTTCAGATT 59.462 41.667 0.00 0.00 40.14 2.40
2904 3482 4.853007 AGGAGGTGGATCTTTTCAGATTG 58.147 43.478 0.00 0.00 40.14 2.67
2905 3483 4.290722 AGGAGGTGGATCTTTTCAGATTGT 59.709 41.667 0.00 0.00 40.14 2.71
2906 3484 4.637977 GGAGGTGGATCTTTTCAGATTGTC 59.362 45.833 0.00 0.00 40.14 3.18
2907 3485 4.593956 AGGTGGATCTTTTCAGATTGTCC 58.406 43.478 0.00 0.00 40.14 4.02
2908 3486 3.375299 GGTGGATCTTTTCAGATTGTCCG 59.625 47.826 0.00 0.00 40.14 4.79
2909 3487 4.003648 GTGGATCTTTTCAGATTGTCCGT 58.996 43.478 0.00 0.00 40.14 4.69
2910 3488 4.093556 GTGGATCTTTTCAGATTGTCCGTC 59.906 45.833 0.00 0.00 40.14 4.79
2911 3489 3.307242 GGATCTTTTCAGATTGTCCGTCG 59.693 47.826 0.00 0.00 40.14 5.12
2912 3490 2.683968 TCTTTTCAGATTGTCCGTCGG 58.316 47.619 4.39 4.39 0.00 4.79
2913 3491 1.128692 CTTTTCAGATTGTCCGTCGGC 59.871 52.381 6.34 2.31 0.00 5.54
2914 3492 0.034198 TTTCAGATTGTCCGTCGGCA 59.966 50.000 6.34 5.28 0.00 5.69
2915 3493 0.389817 TTCAGATTGTCCGTCGGCAG 60.390 55.000 6.34 0.00 0.00 4.85
2916 3494 1.215382 CAGATTGTCCGTCGGCAGA 59.785 57.895 6.34 0.00 0.00 4.26
2917 3495 1.078759 CAGATTGTCCGTCGGCAGAC 61.079 60.000 6.34 6.95 43.72 3.51
2925 3503 2.874780 GTCGGCAGACACGTAGCG 60.875 66.667 12.41 0.00 46.32 4.26
2926 3504 4.771356 TCGGCAGACACGTAGCGC 62.771 66.667 0.00 0.00 0.00 5.92
2927 3505 4.778415 CGGCAGACACGTAGCGCT 62.778 66.667 17.26 17.26 0.00 5.92
2928 3506 3.181967 GGCAGACACGTAGCGCTG 61.182 66.667 22.90 6.70 0.00 5.18
2929 3507 3.843240 GCAGACACGTAGCGCTGC 61.843 66.667 22.90 19.41 45.64 5.25
2930 3508 3.181967 CAGACACGTAGCGCTGCC 61.182 66.667 22.90 9.69 0.00 4.85
2931 3509 4.436998 AGACACGTAGCGCTGCCC 62.437 66.667 22.90 6.84 0.00 5.36
2952 3530 5.529060 GCCCTTGTTTTATATGTCCTCTGAG 59.471 44.000 0.00 0.00 0.00 3.35
2955 3533 8.432805 CCCTTGTTTTATATGTCCTCTGAGTAT 58.567 37.037 3.66 0.00 0.00 2.12
2964 3542 4.673968 TGTCCTCTGAGTATGTAGGTGTT 58.326 43.478 3.66 0.00 0.00 3.32
3061 3700 6.346096 TGAAGGAGGAAATACAGTTAATCCG 58.654 40.000 0.00 0.00 35.31 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
317 319 0.035439 CCATAGCCGGTTCAGGTTGT 60.035 55.000 1.90 0.00 0.00 3.32
801 803 3.334691 TGGAGAAGAATCGCACGATTTT 58.665 40.909 18.36 10.94 43.98 1.82
1026 1030 0.036294 GTTCCCGGTTTCTCCTCCAG 60.036 60.000 0.00 0.00 0.00 3.86
1027 1031 1.486145 GGTTCCCGGTTTCTCCTCCA 61.486 60.000 0.00 0.00 0.00 3.86
1302 1321 0.458716 CCTTCTCGTCCGCCTTCTTC 60.459 60.000 0.00 0.00 0.00 2.87
1409 1428 0.245539 CGCGTAGAAAGGAACCTGGA 59.754 55.000 0.00 0.00 0.00 3.86
1416 1435 0.171903 GCAGGTACGCGTAGAAAGGA 59.828 55.000 21.25 0.00 0.00 3.36
1419 1438 0.179181 CGAGCAGGTACGCGTAGAAA 60.179 55.000 21.25 0.00 36.85 2.52
1469 1488 4.632327 AGAAGAAGAAGGGTTGGAGAAG 57.368 45.455 0.00 0.00 0.00 2.85
1486 1506 3.031013 GGAGGAGGAGGAGAAGAAGAAG 58.969 54.545 0.00 0.00 0.00 2.85
1487 1507 2.657459 AGGAGGAGGAGGAGAAGAAGAA 59.343 50.000 0.00 0.00 0.00 2.52
1491 1511 0.930726 GGAGGAGGAGGAGGAGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
1493 1513 0.930726 GAGGAGGAGGAGGAGGAGAA 59.069 60.000 0.00 0.00 0.00 2.87
1494 1514 0.996762 GGAGGAGGAGGAGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
1495 1515 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1496 1516 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1500 1520 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
1503 1523 2.520741 GAGCGGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
1603 1630 3.851128 GCGTAGAGGGGGCTGTCC 61.851 72.222 0.00 0.00 0.00 4.02
1612 1639 3.227276 AGGATGGGCGCGTAGAGG 61.227 66.667 8.43 0.00 0.00 3.69
1670 1697 0.595095 GATCGGGGCATGAAAGATGC 59.405 55.000 0.00 0.00 43.85 3.91
1678 1705 0.608130 TTAGGATCGATCGGGGCATG 59.392 55.000 18.81 0.00 0.00 4.06
1681 1708 1.079750 GCTTAGGATCGATCGGGGC 60.080 63.158 18.81 15.28 0.00 5.80
1682 1709 1.473278 GTAGCTTAGGATCGATCGGGG 59.527 57.143 18.81 9.96 0.00 5.73
1685 1712 5.866335 ACTTAGTAGCTTAGGATCGATCG 57.134 43.478 18.81 9.36 0.00 3.69
1697 1724 5.611374 TCAAGAAGTGCAAACTTAGTAGCT 58.389 37.500 10.28 0.00 0.00 3.32
1698 1725 5.924475 TCAAGAAGTGCAAACTTAGTAGC 57.076 39.130 0.00 3.26 0.00 3.58
1699 1726 6.650807 TCCATCAAGAAGTGCAAACTTAGTAG 59.349 38.462 0.00 0.00 0.00 2.57
1700 1727 6.530120 TCCATCAAGAAGTGCAAACTTAGTA 58.470 36.000 0.00 0.00 0.00 1.82
1706 1733 4.036734 TGAACTCCATCAAGAAGTGCAAAC 59.963 41.667 0.00 0.00 0.00 2.93
1722 1754 3.623510 GGATCCAAACGAGAATGAACTCC 59.376 47.826 6.95 0.00 33.83 3.85
1744 1776 1.129058 GTACCACAGATACCCCTGGG 58.871 60.000 5.50 5.50 38.44 4.45
1902 2447 5.740569 CCTCGTGATGTTTTATGCTCAATTG 59.259 40.000 0.00 0.00 0.00 2.32
1930 2475 6.667414 ACATAGCAACAAATCTAATTTCCCCA 59.333 34.615 0.00 0.00 0.00 4.96
1955 2500 2.161855 GGTCACCAGACATGCATTCAA 58.838 47.619 0.00 0.00 46.80 2.69
1969 2514 1.625818 AGAGACAAGGACATGGTCACC 59.374 52.381 0.00 0.00 33.68 4.02
2010 2555 0.611896 CCGACTGCCCCAAGGATTTT 60.612 55.000 0.00 0.00 33.47 1.82
2027 2576 1.402259 AGCGTAGAGTGACAAGATCCG 59.598 52.381 0.00 0.00 0.00 4.18
2030 2579 1.546029 TGCAGCGTAGAGTGACAAGAT 59.454 47.619 0.00 0.00 0.00 2.40
2059 2608 3.219281 GGTTGGCACTAAGAGTTTTCCA 58.781 45.455 0.00 0.00 0.00 3.53
2060 2609 2.225727 CGGTTGGCACTAAGAGTTTTCC 59.774 50.000 0.00 0.00 0.00 3.13
2061 2610 2.225727 CCGGTTGGCACTAAGAGTTTTC 59.774 50.000 0.00 0.00 0.00 2.29
2062 2611 2.227194 CCGGTTGGCACTAAGAGTTTT 58.773 47.619 0.00 0.00 0.00 2.43
2063 2612 1.892209 CCGGTTGGCACTAAGAGTTT 58.108 50.000 0.00 0.00 0.00 2.66
2064 2613 3.625745 CCGGTTGGCACTAAGAGTT 57.374 52.632 0.00 0.00 0.00 3.01
2075 2624 1.078426 AGAGAAATCCGCCGGTTGG 60.078 57.895 1.63 5.83 38.77 3.77
2076 2625 1.421410 CGAGAGAAATCCGCCGGTTG 61.421 60.000 1.63 0.00 0.00 3.77
2077 2626 1.153628 CGAGAGAAATCCGCCGGTT 60.154 57.895 1.63 0.00 0.00 4.44
2078 2627 1.885163 AACGAGAGAAATCCGCCGGT 61.885 55.000 1.63 0.00 0.00 5.28
2079 2628 1.146358 GAACGAGAGAAATCCGCCGG 61.146 60.000 0.00 0.00 0.00 6.13
2080 2629 0.457853 TGAACGAGAGAAATCCGCCG 60.458 55.000 0.00 0.00 0.00 6.46
2081 2630 1.861575 GATGAACGAGAGAAATCCGCC 59.138 52.381 0.00 0.00 0.00 6.13
2082 2631 1.861575 GGATGAACGAGAGAAATCCGC 59.138 52.381 0.00 0.00 31.85 5.54
2083 2632 2.120232 CGGATGAACGAGAGAAATCCG 58.880 52.381 7.88 7.88 46.13 4.18
2084 2633 1.861575 GCGGATGAACGAGAGAAATCC 59.138 52.381 0.00 0.00 35.79 3.01
2085 2634 1.861575 GGCGGATGAACGAGAGAAATC 59.138 52.381 0.00 0.00 35.47 2.17
2086 2635 1.802880 CGGCGGATGAACGAGAGAAAT 60.803 52.381 0.00 0.00 35.47 2.17
2087 2636 0.457853 CGGCGGATGAACGAGAGAAA 60.458 55.000 0.00 0.00 35.47 2.52
2088 2637 1.138883 CGGCGGATGAACGAGAGAA 59.861 57.895 0.00 0.00 35.47 2.87
2089 2638 2.798689 CGGCGGATGAACGAGAGA 59.201 61.111 0.00 0.00 35.47 3.10
2090 2639 2.956964 GCGGCGGATGAACGAGAG 60.957 66.667 9.78 0.00 35.47 3.20
2091 2640 4.508128 GGCGGCGGATGAACGAGA 62.508 66.667 9.78 0.00 35.47 4.04
2092 2641 4.514577 AGGCGGCGGATGAACGAG 62.515 66.667 9.78 0.00 35.47 4.18
2093 2642 4.508128 GAGGCGGCGGATGAACGA 62.508 66.667 9.78 0.00 35.47 3.85
2107 2656 2.361610 AAAGCGGTGCATGGGAGG 60.362 61.111 0.00 0.00 0.00 4.30
2108 2657 2.703798 CCAAAGCGGTGCATGGGAG 61.704 63.158 6.48 0.00 35.25 4.30
2109 2658 2.676121 CCAAAGCGGTGCATGGGA 60.676 61.111 6.48 0.00 35.25 4.37
2110 2659 3.762247 CCCAAAGCGGTGCATGGG 61.762 66.667 16.15 16.15 46.10 4.00
2111 2660 2.990967 ACCCAAAGCGGTGCATGG 60.991 61.111 7.23 7.23 37.48 3.66
2112 2661 2.259204 CACCCAAAGCGGTGCATG 59.741 61.111 0.00 0.00 46.52 4.06
2136 2685 5.720371 AGGAGTAATCCGATGAGAAGATG 57.280 43.478 3.06 0.00 34.28 2.90
2145 2694 5.772004 AGATATGGCTAGGAGTAATCCGAT 58.228 41.667 3.06 0.00 34.28 4.18
2147 2696 5.923733 AAGATATGGCTAGGAGTAATCCG 57.076 43.478 3.06 0.00 34.28 4.18
2173 2722 5.069119 GGAAGAAAGGAAGAAGGCAAGAAAA 59.931 40.000 0.00 0.00 0.00 2.29
2174 2723 4.584743 GGAAGAAAGGAAGAAGGCAAGAAA 59.415 41.667 0.00 0.00 0.00 2.52
2175 2724 4.145052 GGAAGAAAGGAAGAAGGCAAGAA 58.855 43.478 0.00 0.00 0.00 2.52
2200 2749 2.158325 TGGAAAGAGGTTGGATGGCTTT 60.158 45.455 0.00 0.00 0.00 3.51
2203 2752 2.027385 GATGGAAAGAGGTTGGATGGC 58.973 52.381 0.00 0.00 0.00 4.40
2211 2760 1.684248 GCATGCCTGATGGAAAGAGGT 60.684 52.381 6.36 0.00 34.57 3.85
2216 2765 0.533491 GCTTGCATGCCTGATGGAAA 59.467 50.000 16.68 0.00 41.41 3.13
2225 2774 2.025418 GCTGTTGTGCTTGCATGCC 61.025 57.895 20.65 12.79 0.00 4.40
2256 2805 3.298958 CCGGAGGCTTGCTAGTGA 58.701 61.111 0.00 0.00 46.14 3.41
2278 2849 0.480690 AACATGGCAGGGTTGTGGTA 59.519 50.000 3.46 0.00 0.00 3.25
2282 2853 1.620822 GAAGAACATGGCAGGGTTGT 58.379 50.000 11.47 5.49 0.00 3.32
2289 2860 0.541764 GGTTGGGGAAGAACATGGCA 60.542 55.000 0.00 0.00 0.00 4.92
2304 2875 2.034066 ACATCCGTGGCTGGGTTG 59.966 61.111 0.00 4.58 0.00 3.77
2318 2889 1.202855 GCATGCTACCTCCATGGACAT 60.203 52.381 11.44 9.72 40.24 3.06
2319 2890 0.181114 GCATGCTACCTCCATGGACA 59.819 55.000 11.44 7.46 40.24 4.02
2349 2920 3.560453 GGTGATTGTTGTTGTAGCCCCTA 60.560 47.826 0.00 0.00 0.00 3.53
2352 2923 1.544246 GGGTGATTGTTGTTGTAGCCC 59.456 52.381 0.00 0.00 0.00 5.19
2362 2933 2.308570 TGCTACTCCATGGGTGATTGTT 59.691 45.455 13.02 0.00 0.00 2.83
2367 2938 0.181114 GCATGCTACTCCATGGGTGA 59.819 55.000 13.02 0.00 42.18 4.02
2404 2975 1.501741 CAATTCCCGTCGCCAGTTG 59.498 57.895 0.00 0.00 0.00 3.16
2405 2976 1.674322 CCAATTCCCGTCGCCAGTT 60.674 57.895 0.00 0.00 0.00 3.16
2408 2979 2.359354 CACCAATTCCCGTCGCCA 60.359 61.111 0.00 0.00 0.00 5.69
2415 2986 3.508840 CGAGCGCCACCAATTCCC 61.509 66.667 2.29 0.00 0.00 3.97
2417 2988 3.508840 CCCGAGCGCCACCAATTC 61.509 66.667 2.29 0.00 0.00 2.17
2424 2995 2.443203 TTCCTATCCCGAGCGCCA 60.443 61.111 2.29 0.00 0.00 5.69
2437 3008 1.333636 CCATCCAGCTCCGAGTTCCT 61.334 60.000 0.00 0.00 0.00 3.36
2441 3012 3.474570 GGCCATCCAGCTCCGAGT 61.475 66.667 0.00 0.00 0.00 4.18
2445 3016 2.123982 CCAAGGCCATCCAGCTCC 60.124 66.667 5.01 0.00 33.74 4.70
2449 3020 1.683365 CAACCCCAAGGCCATCCAG 60.683 63.158 5.01 0.00 36.11 3.86
2473 3044 2.314647 ACCATCGTTCGCCGTTGTG 61.315 57.895 0.00 0.00 35.06 3.33
2476 3047 2.740826 CCACCATCGTTCGCCGTT 60.741 61.111 0.00 0.00 37.94 4.44
2486 3057 0.890542 TTGTCAGCAGCACCACCATC 60.891 55.000 0.00 0.00 0.00 3.51
2488 3059 1.526686 CTTGTCAGCAGCACCACCA 60.527 57.895 0.00 0.00 0.00 4.17
2489 3060 2.263741 CCTTGTCAGCAGCACCACC 61.264 63.158 0.00 0.00 0.00 4.61
2491 3062 0.607217 CATCCTTGTCAGCAGCACCA 60.607 55.000 0.00 0.00 0.00 4.17
2500 3071 4.667262 CAAAAACGTCAACATCCTTGTCA 58.333 39.130 0.00 0.00 34.06 3.58
2502 3073 3.119316 TGCAAAAACGTCAACATCCTTGT 60.119 39.130 0.00 0.00 37.82 3.16
2506 3077 3.443976 AGTTGCAAAAACGTCAACATCC 58.556 40.909 16.48 0.00 41.67 3.51
2509 3080 6.952935 AATTAAGTTGCAAAAACGTCAACA 57.047 29.167 16.48 0.45 41.67 3.33
2515 3086 9.483062 TTCAATGAAAATTAAGTTGCAAAAACG 57.517 25.926 0.00 0.00 0.00 3.60
2541 3112 3.507233 ACACGGATGATGTTGCAGAAAAT 59.493 39.130 0.00 0.00 0.00 1.82
2556 3130 4.359706 GAAGAAGTTTTTGCAACACGGAT 58.640 39.130 0.00 0.00 0.00 4.18
2559 3133 2.529894 CGGAAGAAGTTTTTGCAACACG 59.470 45.455 0.00 0.00 0.00 4.49
2560 3134 2.281498 GCGGAAGAAGTTTTTGCAACAC 59.719 45.455 0.00 0.00 0.00 3.32
2565 3139 4.742659 TGTTATTGCGGAAGAAGTTTTTGC 59.257 37.500 0.00 0.00 0.00 3.68
2571 3145 2.224670 TGGGTGTTATTGCGGAAGAAGT 60.225 45.455 0.00 0.00 0.00 3.01
2579 3153 0.526096 GCAGCATGGGTGTTATTGCG 60.526 55.000 0.00 0.00 40.00 4.85
2589 3163 2.494471 TCTTCAATTTCTGCAGCATGGG 59.506 45.455 9.47 0.00 35.86 4.00
2592 3166 3.076621 TCGTCTTCAATTTCTGCAGCAT 58.923 40.909 9.47 0.00 0.00 3.79
2632 3207 6.306356 CGGAAAGAACTTTTGCAACATAGATG 59.694 38.462 0.00 0.00 32.11 2.90
2664 3239 9.529325 CGTCTTCACTTTTCTACAATATGGATA 57.471 33.333 0.00 0.00 0.00 2.59
2710 3288 6.454186 GCGGAATGAATTTTTGCAACATAGAC 60.454 38.462 0.00 0.00 0.00 2.59
2741 3319 8.015087 CGTCTTTACTTTTCTGCAACATTGATA 58.985 33.333 0.00 0.00 0.00 2.15
2796 3374 7.308435 AGCACATGTTATAGAAACTCTTTTGC 58.692 34.615 0.00 0.00 0.00 3.68
2797 3375 8.725148 AGAGCACATGTTATAGAAACTCTTTTG 58.275 33.333 0.00 0.00 0.00 2.44
2798 3376 8.854614 AGAGCACATGTTATAGAAACTCTTTT 57.145 30.769 0.00 0.00 0.00 2.27
2801 3379 9.539825 CAATAGAGCACATGTTATAGAAACTCT 57.460 33.333 0.00 1.65 36.11 3.24
2802 3380 8.279103 GCAATAGAGCACATGTTATAGAAACTC 58.721 37.037 0.00 0.00 0.00 3.01
2803 3381 7.770433 TGCAATAGAGCACATGTTATAGAAACT 59.230 33.333 0.00 0.00 40.11 2.66
2804 3382 7.919690 TGCAATAGAGCACATGTTATAGAAAC 58.080 34.615 0.00 0.00 40.11 2.78
2805 3383 8.504812 TTGCAATAGAGCACATGTTATAGAAA 57.495 30.769 0.00 0.00 45.61 2.52
2806 3384 8.562052 CATTGCAATAGAGCACATGTTATAGAA 58.438 33.333 12.53 0.00 45.61 2.10
2807 3385 7.933033 TCATTGCAATAGAGCACATGTTATAGA 59.067 33.333 12.53 0.00 45.61 1.98
2808 3386 8.091385 TCATTGCAATAGAGCACATGTTATAG 57.909 34.615 12.53 0.00 45.61 1.31
2809 3387 8.508875 CATCATTGCAATAGAGCACATGTTATA 58.491 33.333 12.53 0.00 45.61 0.98
2810 3388 6.947644 TCATTGCAATAGAGCACATGTTAT 57.052 33.333 12.53 0.00 45.61 1.89
2811 3389 6.543100 TCATCATTGCAATAGAGCACATGTTA 59.457 34.615 12.53 0.00 45.61 2.41
2812 3390 5.358725 TCATCATTGCAATAGAGCACATGTT 59.641 36.000 12.53 0.00 45.61 2.71
2813 3391 4.885325 TCATCATTGCAATAGAGCACATGT 59.115 37.500 12.53 0.00 45.61 3.21
2814 3392 5.432885 TCATCATTGCAATAGAGCACATG 57.567 39.130 12.53 7.21 45.61 3.21
2815 3393 5.768164 TCATCATCATTGCAATAGAGCACAT 59.232 36.000 12.53 0.00 45.61 3.21
2816 3394 5.008316 GTCATCATCATTGCAATAGAGCACA 59.992 40.000 12.53 0.00 45.61 4.57
2817 3395 5.450171 GTCATCATCATTGCAATAGAGCAC 58.550 41.667 12.53 7.59 45.61 4.40
2818 3396 4.212636 CGTCATCATCATTGCAATAGAGCA 59.787 41.667 12.53 3.82 43.99 4.26
2819 3397 4.378149 CCGTCATCATCATTGCAATAGAGC 60.378 45.833 12.53 5.06 0.00 4.09
2820 3398 4.153655 CCCGTCATCATCATTGCAATAGAG 59.846 45.833 12.53 4.78 0.00 2.43
2821 3399 4.067192 CCCGTCATCATCATTGCAATAGA 58.933 43.478 12.53 12.24 0.00 1.98
2822 3400 3.189910 CCCCGTCATCATCATTGCAATAG 59.810 47.826 12.53 7.05 0.00 1.73
2823 3401 3.148412 CCCCGTCATCATCATTGCAATA 58.852 45.455 12.53 0.00 0.00 1.90
2824 3402 1.958579 CCCCGTCATCATCATTGCAAT 59.041 47.619 5.99 5.99 0.00 3.56
2825 3403 1.340893 ACCCCGTCATCATCATTGCAA 60.341 47.619 0.00 0.00 0.00 4.08
2826 3404 0.255604 ACCCCGTCATCATCATTGCA 59.744 50.000 0.00 0.00 0.00 4.08
2827 3405 1.066002 CAACCCCGTCATCATCATTGC 59.934 52.381 0.00 0.00 0.00 3.56
2828 3406 2.615447 CTCAACCCCGTCATCATCATTG 59.385 50.000 0.00 0.00 0.00 2.82
2829 3407 2.923121 CTCAACCCCGTCATCATCATT 58.077 47.619 0.00 0.00 0.00 2.57
2830 3408 1.475751 GCTCAACCCCGTCATCATCAT 60.476 52.381 0.00 0.00 0.00 2.45
2831 3409 0.107703 GCTCAACCCCGTCATCATCA 60.108 55.000 0.00 0.00 0.00 3.07
2832 3410 0.815615 GGCTCAACCCCGTCATCATC 60.816 60.000 0.00 0.00 0.00 2.92
2833 3411 1.224592 GGCTCAACCCCGTCATCAT 59.775 57.895 0.00 0.00 0.00 2.45
2834 3412 2.668632 GGCTCAACCCCGTCATCA 59.331 61.111 0.00 0.00 0.00 3.07
2835 3413 2.511600 CGGCTCAACCCCGTCATC 60.512 66.667 0.00 0.00 40.84 2.92
2841 3419 2.106683 CATCGAACGGCTCAACCCC 61.107 63.158 0.00 0.00 33.26 4.95
2842 3420 2.106683 CCATCGAACGGCTCAACCC 61.107 63.158 0.00 0.00 33.26 4.11
2843 3421 1.375523 ACCATCGAACGGCTCAACC 60.376 57.895 4.22 0.00 0.00 3.77
2844 3422 1.787847 CACCATCGAACGGCTCAAC 59.212 57.895 4.22 0.00 0.00 3.18
2845 3423 2.032634 GCACCATCGAACGGCTCAA 61.033 57.895 4.22 0.00 0.00 3.02
2846 3424 2.434185 GCACCATCGAACGGCTCA 60.434 61.111 4.22 0.00 0.00 4.26
2847 3425 3.195698 GGCACCATCGAACGGCTC 61.196 66.667 4.22 0.00 0.00 4.70
2848 3426 3.545124 TTGGCACCATCGAACGGCT 62.545 57.895 4.22 0.00 0.00 5.52
2849 3427 1.933115 ATTTGGCACCATCGAACGGC 61.933 55.000 4.22 0.00 0.00 5.68
2850 3428 0.098728 GATTTGGCACCATCGAACGG 59.901 55.000 2.80 2.80 0.00 4.44
2851 3429 1.086696 AGATTTGGCACCATCGAACG 58.913 50.000 0.00 0.00 0.00 3.95
2852 3430 3.485216 CGTTAGATTTGGCACCATCGAAC 60.485 47.826 16.02 16.02 32.95 3.95
2853 3431 2.675844 CGTTAGATTTGGCACCATCGAA 59.324 45.455 0.00 0.00 0.00 3.71
2854 3432 2.276201 CGTTAGATTTGGCACCATCGA 58.724 47.619 0.00 0.00 0.00 3.59
2855 3433 1.330521 CCGTTAGATTTGGCACCATCG 59.669 52.381 0.00 0.00 0.00 3.84
2856 3434 2.354821 GACCGTTAGATTTGGCACCATC 59.645 50.000 0.00 0.00 0.00 3.51
2857 3435 2.290641 TGACCGTTAGATTTGGCACCAT 60.291 45.455 0.00 0.00 0.00 3.55
2858 3436 1.072489 TGACCGTTAGATTTGGCACCA 59.928 47.619 0.00 0.00 0.00 4.17
2859 3437 1.467342 GTGACCGTTAGATTTGGCACC 59.533 52.381 0.00 0.00 0.00 5.01
2860 3438 2.159627 CAGTGACCGTTAGATTTGGCAC 59.840 50.000 0.00 0.00 33.12 5.01
2861 3439 2.037902 TCAGTGACCGTTAGATTTGGCA 59.962 45.455 0.00 0.00 0.00 4.92
2862 3440 2.673368 CTCAGTGACCGTTAGATTTGGC 59.327 50.000 0.00 0.00 0.00 4.52
2863 3441 3.056107 TCCTCAGTGACCGTTAGATTTGG 60.056 47.826 0.00 0.00 0.00 3.28
2864 3442 4.177026 CTCCTCAGTGACCGTTAGATTTG 58.823 47.826 0.00 0.00 0.00 2.32
2865 3443 3.195825 CCTCCTCAGTGACCGTTAGATTT 59.804 47.826 0.00 0.00 0.00 2.17
2866 3444 2.761208 CCTCCTCAGTGACCGTTAGATT 59.239 50.000 0.00 0.00 0.00 2.40
2867 3445 2.291670 ACCTCCTCAGTGACCGTTAGAT 60.292 50.000 0.00 0.00 0.00 1.98
2868 3446 1.075050 ACCTCCTCAGTGACCGTTAGA 59.925 52.381 0.00 0.00 0.00 2.10
2869 3447 1.202582 CACCTCCTCAGTGACCGTTAG 59.797 57.143 0.00 0.00 37.42 2.34
2870 3448 1.254026 CACCTCCTCAGTGACCGTTA 58.746 55.000 0.00 0.00 37.42 3.18
2871 3449 1.472662 CCACCTCCTCAGTGACCGTT 61.473 60.000 0.00 0.00 37.42 4.44
2872 3450 1.908793 CCACCTCCTCAGTGACCGT 60.909 63.158 0.00 0.00 37.42 4.83
2873 3451 0.972983 ATCCACCTCCTCAGTGACCG 60.973 60.000 0.00 0.00 37.42 4.79
2874 3452 0.827368 GATCCACCTCCTCAGTGACC 59.173 60.000 0.00 0.00 37.42 4.02
2875 3453 1.859302 AGATCCACCTCCTCAGTGAC 58.141 55.000 0.00 0.00 37.42 3.67
2876 3454 2.630889 AAGATCCACCTCCTCAGTGA 57.369 50.000 0.00 0.00 37.42 3.41
2877 3455 3.008375 TGAAAAGATCCACCTCCTCAGTG 59.992 47.826 0.00 0.00 34.91 3.66
2878 3456 3.251484 TGAAAAGATCCACCTCCTCAGT 58.749 45.455 0.00 0.00 0.00 3.41
2879 3457 3.517100 TCTGAAAAGATCCACCTCCTCAG 59.483 47.826 0.00 0.00 0.00 3.35
2880 3458 3.520696 TCTGAAAAGATCCACCTCCTCA 58.479 45.455 0.00 0.00 0.00 3.86
2881 3459 4.769345 ATCTGAAAAGATCCACCTCCTC 57.231 45.455 0.00 0.00 0.00 3.71
2882 3460 4.290722 ACAATCTGAAAAGATCCACCTCCT 59.709 41.667 0.00 0.00 0.00 3.69
2883 3461 4.593956 ACAATCTGAAAAGATCCACCTCC 58.406 43.478 0.00 0.00 0.00 4.30
2884 3462 4.637977 GGACAATCTGAAAAGATCCACCTC 59.362 45.833 0.00 0.00 0.00 3.85
2885 3463 4.593956 GGACAATCTGAAAAGATCCACCT 58.406 43.478 0.00 0.00 0.00 4.00
2886 3464 3.375299 CGGACAATCTGAAAAGATCCACC 59.625 47.826 0.00 0.00 0.00 4.61
2887 3465 4.003648 ACGGACAATCTGAAAAGATCCAC 58.996 43.478 0.00 0.00 0.00 4.02
2888 3466 4.253685 GACGGACAATCTGAAAAGATCCA 58.746 43.478 0.00 0.00 0.00 3.41
2889 3467 3.307242 CGACGGACAATCTGAAAAGATCC 59.693 47.826 0.00 0.00 0.00 3.36
2890 3468 3.307242 CCGACGGACAATCTGAAAAGATC 59.693 47.826 8.64 0.00 0.00 2.75
2891 3469 3.262420 CCGACGGACAATCTGAAAAGAT 58.738 45.455 8.64 0.00 0.00 2.40
2892 3470 2.683968 CCGACGGACAATCTGAAAAGA 58.316 47.619 8.64 0.00 0.00 2.52
2893 3471 1.128692 GCCGACGGACAATCTGAAAAG 59.871 52.381 20.50 0.00 0.00 2.27
2894 3472 1.153353 GCCGACGGACAATCTGAAAA 58.847 50.000 20.50 0.00 0.00 2.29
2895 3473 0.034198 TGCCGACGGACAATCTGAAA 59.966 50.000 20.50 0.00 0.00 2.69
2896 3474 0.389817 CTGCCGACGGACAATCTGAA 60.390 55.000 20.50 0.00 0.00 3.02
2897 3475 1.215382 CTGCCGACGGACAATCTGA 59.785 57.895 20.50 0.00 0.00 3.27
2898 3476 1.215382 TCTGCCGACGGACAATCTG 59.785 57.895 20.50 3.47 0.00 2.90
2899 3477 3.694746 TCTGCCGACGGACAATCT 58.305 55.556 20.50 0.00 0.00 2.40
2905 3483 2.669229 TACGTGTCTGCCGACGGA 60.669 61.111 20.50 1.60 43.21 4.69
2906 3484 2.202440 CTACGTGTCTGCCGACGG 60.202 66.667 10.29 10.29 43.21 4.79
2907 3485 2.874780 GCTACGTGTCTGCCGACG 60.875 66.667 0.00 0.00 43.21 5.12
2908 3486 2.874780 CGCTACGTGTCTGCCGAC 60.875 66.667 0.00 0.64 40.64 4.79
2909 3487 4.771356 GCGCTACGTGTCTGCCGA 62.771 66.667 0.00 0.00 0.00 5.54
2910 3488 4.778415 AGCGCTACGTGTCTGCCG 62.778 66.667 8.99 0.00 0.00 5.69
2911 3489 3.181967 CAGCGCTACGTGTCTGCC 61.182 66.667 10.99 0.00 0.00 4.85
2912 3490 3.843240 GCAGCGCTACGTGTCTGC 61.843 66.667 10.99 3.36 43.95 4.26
2913 3491 3.181967 GGCAGCGCTACGTGTCTG 61.182 66.667 10.99 0.00 0.00 3.51
2914 3492 4.436998 GGGCAGCGCTACGTGTCT 62.437 66.667 10.99 0.00 0.00 3.41
2915 3493 3.934391 AAGGGCAGCGCTACGTGTC 62.934 63.158 10.99 0.00 0.00 3.67
2916 3494 4.003788 AAGGGCAGCGCTACGTGT 62.004 61.111 10.99 0.00 0.00 4.49
2917 3495 3.490759 CAAGGGCAGCGCTACGTG 61.491 66.667 10.99 8.56 0.00 4.49
2918 3496 3.530910 AACAAGGGCAGCGCTACGT 62.531 57.895 10.99 10.34 0.00 3.57
2919 3497 1.852067 AAAACAAGGGCAGCGCTACG 61.852 55.000 10.99 9.67 0.00 3.51
2920 3498 1.161843 TAAAACAAGGGCAGCGCTAC 58.838 50.000 10.99 3.45 0.00 3.58
2921 3499 2.122783 ATAAAACAAGGGCAGCGCTA 57.877 45.000 10.99 0.00 0.00 4.26
2922 3500 2.122783 TATAAAACAAGGGCAGCGCT 57.877 45.000 2.64 2.64 0.00 5.92
2923 3501 2.099098 ACATATAAAACAAGGGCAGCGC 59.901 45.455 0.00 0.00 0.00 5.92
2924 3502 3.243068 GGACATATAAAACAAGGGCAGCG 60.243 47.826 0.00 0.00 0.00 5.18
2925 3503 3.954258 AGGACATATAAAACAAGGGCAGC 59.046 43.478 0.00 0.00 0.00 5.25
2926 3504 5.297776 CAGAGGACATATAAAACAAGGGCAG 59.702 44.000 0.00 0.00 0.00 4.85
2927 3505 5.045213 TCAGAGGACATATAAAACAAGGGCA 60.045 40.000 0.00 0.00 0.00 5.36
2928 3506 5.437060 TCAGAGGACATATAAAACAAGGGC 58.563 41.667 0.00 0.00 0.00 5.19
2929 3507 6.653989 ACTCAGAGGACATATAAAACAAGGG 58.346 40.000 1.53 0.00 0.00 3.95
2930 3508 9.265901 CATACTCAGAGGACATATAAAACAAGG 57.734 37.037 1.53 0.00 0.00 3.61
2931 3509 9.823647 ACATACTCAGAGGACATATAAAACAAG 57.176 33.333 1.53 0.00 0.00 3.16
3010 3624 8.038351 TCCAAGATTGTATTTCTCGTGATTGTA 58.962 33.333 0.00 0.00 0.00 2.41
3061 3700 3.827302 TGAGTTGAGGAGAAGGTGTCTAC 59.173 47.826 0.00 0.00 36.41 2.59


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

AutoCloner maintained by Alex Coulton.