Multiple sequence alignment - TraesCS4B01G138700

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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 TraesCS4B01G138700 chr4B 100.000 2702 0 0 1 2702 182673486 182676187 0.000000e+00 4990.0
1 TraesCS4B01G138700 chr4B 100.000 34 0 0 2040 2073 182675330 182675297 2.250000e-06 63.9
2 TraesCS4B01G138700 chr4B 100.000 34 0 0 1812 1845 182675558 182675525 2.250000e-06 63.9
3 TraesCS4B01G138700 chr4D 93.308 1554 54 14 200 1727 119825492 119827021 0.000000e+00 2248.0
4 TraesCS4B01G138700 chr4D 89.685 349 32 3 2353 2701 119827446 119827790 2.470000e-120 442.0
5 TraesCS4B01G138700 chr4D 93.119 218 5 1 1 208 119823984 119824201 7.260000e-81 311.0
6 TraesCS4B01G138700 chr4D 75.862 377 82 9 2313 2688 393629193 393628825 1.650000e-42 183.0
7 TraesCS4B01G138700 chr4D 92.553 94 7 0 1842 1935 119827071 119827164 4.690000e-28 135.0
8 TraesCS4B01G138700 chr4A 93.120 1279 53 14 485 1743 450793425 450794688 0.000000e+00 1842.0
9 TraesCS4B01G138700 chr4A 92.607 514 19 4 1 495 450792734 450793247 0.000000e+00 721.0
10 TraesCS4B01G138700 chr4A 83.858 254 30 10 2353 2605 450795463 450795706 5.820000e-57 231.0
11 TraesCS4B01G138700 chr4A 76.720 378 75 13 2313 2687 714427074 714426707 5.900000e-47 198.0
12 TraesCS4B01G138700 chr3D 79.733 375 68 6 2315 2688 374944697 374945064 5.740000e-67 265.0
13 TraesCS4B01G138700 chr5A 79.404 369 68 6 2321 2688 326065208 326064847 1.240000e-63 254.0
14 TraesCS4B01G138700 chr5A 81.494 308 23 23 1429 1713 337820304 337820008 3.500000e-54 222.0
15 TraesCS4B01G138700 chr5D 78.649 370 69 8 2321 2688 230490721 230491082 1.250000e-58 237.0
16 TraesCS4B01G138700 chr5D 81.046 306 25 23 1429 1713 254519340 254519047 2.110000e-51 213.0
17 TraesCS4B01G138700 chr6B 76.501 383 68 19 2313 2688 320542807 320542440 3.550000e-44 189.0
18 TraesCS4B01G138700 chr5B 79.677 310 25 21 1429 1713 288330014 288330310 3.550000e-44 189.0
19 TraesCS4B01G138700 chr3B 76.316 380 75 15 2313 2688 814498745 814498377 3.550000e-44 189.0
20 TraesCS4B01G138700 chr2B 76.316 380 75 14 2313 2688 51079462 51079830 3.550000e-44 189.0
21 TraesCS4B01G138700 chr2B 77.895 190 31 11 2313 2501 518793119 518792940 1.020000e-19 108.0
22 TraesCS4B01G138700 chr7B 75.328 381 72 16 2313 2688 234914908 234915271 2.150000e-36 163.0
23 TraesCS4B01G138700 chr7A 73.107 383 87 16 2313 2688 275974375 275974748 3.650000e-24 122.0


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 TraesCS4B01G138700 chr4B 182673486 182676187 2701 False 4990.000000 4990 100.000000 1 2702 1 chr4B.!!$F1 2701
1 TraesCS4B01G138700 chr4D 119823984 119827790 3806 False 784.000000 2248 92.166250 1 2701 4 chr4D.!!$F1 2700
2 TraesCS4B01G138700 chr4A 450792734 450795706 2972 False 931.333333 1842 89.861667 1 2605 3 chr4A.!!$F1 2604

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
373 1687 0.184933 AGGGCCTGTTTGTTGCTGTA 59.815 50.0 4.5 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 3755 0.11456 AGGGACGTGGGAGAGAGAAA 59.885 55.0 0.0 0.0 0.0 2.52 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
54 59 1.132262 CTCCACTGAAGTCTCGAGAGC 59.868 57.143 17.22 10.96 0.00 4.09
115 130 6.931840 ACAAAGTCTAATCAAGGACTGTCTTC 59.068 38.462 7.85 0.00 41.28 2.87
128 143 2.620115 ACTGTCTTCCACACTTGCATTG 59.380 45.455 0.00 0.00 0.00 2.82
214 1528 6.638873 CAGTTTTGGACATAAATAAACACGCA 59.361 34.615 0.00 0.00 32.58 5.24
373 1687 0.184933 AGGGCCTGTTTGTTGCTGTA 59.815 50.000 4.50 0.00 0.00 2.74
380 1694 4.396166 GCCTGTTTGTTGCTGTATAGTCAT 59.604 41.667 0.00 0.00 0.00 3.06
437 1756 7.765819 GCTGAAAAGAAAGGCATATGGTTTTAT 59.234 33.333 4.56 0.00 0.00 1.40
622 2130 1.750206 GCATGTATTGGTGATGGTGCA 59.250 47.619 0.00 0.00 0.00 4.57
762 2274 6.153851 TGTTCCAGGAAAGATAGAATCGTGTA 59.846 38.462 2.45 0.00 0.00 2.90
824 2339 3.015327 CGCACAAGGTAGTAGTAGGTCT 58.985 50.000 0.00 0.00 0.00 3.85
929 2454 9.331466 ACATATATAGAGTGGTTGATCTCCATT 57.669 33.333 11.99 8.76 37.30 3.16
997 2522 1.538204 GCACGAGTCCAAGACAGTTGA 60.538 52.381 0.00 0.00 34.60 3.18
999 2524 3.614150 GCACGAGTCCAAGACAGTTGATA 60.614 47.826 0.00 0.00 34.60 2.15
1164 2698 1.557099 ACTACTCCCAGTCGATGCAA 58.443 50.000 0.00 0.00 0.00 4.08
1329 2872 2.812011 GGTACGTTGATCTTTGGCAGTT 59.188 45.455 0.00 0.00 0.00 3.16
1349 2892 2.396955 CGTCGTCTGGTCGGTAGCT 61.397 63.158 0.00 0.00 0.00 3.32
1350 2893 1.086067 CGTCGTCTGGTCGGTAGCTA 61.086 60.000 0.00 0.00 0.00 3.32
1351 2894 0.656785 GTCGTCTGGTCGGTAGCTAG 59.343 60.000 0.00 0.00 0.00 3.42
1352 2895 0.251354 TCGTCTGGTCGGTAGCTAGT 59.749 55.000 0.00 0.00 0.00 2.57
1353 2896 1.482182 TCGTCTGGTCGGTAGCTAGTA 59.518 52.381 0.00 0.00 0.00 1.82
1354 2897 1.596727 CGTCTGGTCGGTAGCTAGTAC 59.403 57.143 0.00 0.00 0.00 2.73
1355 2898 2.741228 CGTCTGGTCGGTAGCTAGTACT 60.741 54.545 0.00 0.00 0.00 2.73
1356 2899 3.491619 CGTCTGGTCGGTAGCTAGTACTA 60.492 52.174 1.89 1.89 0.00 1.82
1357 2900 3.807071 GTCTGGTCGGTAGCTAGTACTAC 59.193 52.174 0.00 0.00 41.54 2.73
1358 2901 3.708631 TCTGGTCGGTAGCTAGTACTACT 59.291 47.826 0.00 4.58 41.88 2.57
1359 2902 4.895889 TCTGGTCGGTAGCTAGTACTACTA 59.104 45.833 0.00 3.65 41.88 1.82
1409 2958 2.624316 TACTCATCGTCGTGTCAACC 57.376 50.000 0.00 0.00 0.00 3.77
1421 2970 1.400494 GTGTCAACCCTGTGTGTTGTC 59.600 52.381 0.00 0.00 42.82 3.18
1427 2976 3.080300 ACCCTGTGTGTTGTCTTTTGA 57.920 42.857 0.00 0.00 0.00 2.69
1430 2979 4.097892 ACCCTGTGTGTTGTCTTTTGATTC 59.902 41.667 0.00 0.00 0.00 2.52
1432 2981 5.506317 CCCTGTGTGTTGTCTTTTGATTCTC 60.506 44.000 0.00 0.00 0.00 2.87
1530 3079 2.124983 GCAGCAGATCAGCCGGAA 60.125 61.111 5.05 0.00 34.23 4.30
1534 3083 0.106335 AGCAGATCAGCCGGAAGATG 59.894 55.000 5.05 0.00 34.23 2.90
1543 3092 2.949678 CGGAAGATGCGACGACGG 60.950 66.667 9.67 0.00 40.15 4.79
1545 3094 3.607987 GAAGATGCGACGACGGCG 61.608 66.667 21.02 21.02 44.79 6.46
1585 3134 4.228567 TGGTCAACGACGCCAGCA 62.229 61.111 0.00 0.00 32.65 4.41
1748 3300 8.978874 ACTCTCATCGATCTATATAGCTCAAT 57.021 34.615 12.77 0.00 0.00 2.57
1749 3301 8.839343 ACTCTCATCGATCTATATAGCTCAATG 58.161 37.037 12.77 10.27 0.00 2.82
1750 3302 8.970859 TCTCATCGATCTATATAGCTCAATGA 57.029 34.615 13.81 13.81 0.00 2.57
1751 3303 9.571816 TCTCATCGATCTATATAGCTCAATGAT 57.428 33.333 14.55 7.00 0.00 2.45
1760 3312 9.348476 TCTATATAGCTCAATGATCTAATCGCT 57.652 33.333 4.75 0.00 0.00 4.93
1761 3313 9.611284 CTATATAGCTCAATGATCTAATCGCTC 57.389 37.037 0.00 0.00 0.00 5.03
1762 3314 4.870123 AGCTCAATGATCTAATCGCTCT 57.130 40.909 0.00 0.00 0.00 4.09
1763 3315 5.212532 AGCTCAATGATCTAATCGCTCTT 57.787 39.130 0.00 0.00 0.00 2.85
1764 3316 6.338214 AGCTCAATGATCTAATCGCTCTTA 57.662 37.500 0.00 0.00 0.00 2.10
1765 3317 6.934056 AGCTCAATGATCTAATCGCTCTTAT 58.066 36.000 0.00 0.00 0.00 1.73
1766 3318 8.060931 AGCTCAATGATCTAATCGCTCTTATA 57.939 34.615 0.00 0.00 0.00 0.98
1767 3319 8.694540 AGCTCAATGATCTAATCGCTCTTATAT 58.305 33.333 0.00 0.00 0.00 0.86
1768 3320 9.958234 GCTCAATGATCTAATCGCTCTTATATA 57.042 33.333 0.00 0.00 0.00 0.86
1847 3399 9.452065 GACAAGTATTTTCTTTTGGTTTCTCTC 57.548 33.333 0.00 0.00 0.00 3.20
1877 3432 4.227197 AGCTGGCTATATGTACTGGAACT 58.773 43.478 0.00 0.00 0.00 3.01
1883 3438 3.560636 ATATGTACTGGAACTGCCACC 57.439 47.619 0.00 0.00 43.33 4.61
1886 3441 0.605589 GTACTGGAACTGCCACCACC 60.606 60.000 0.00 0.00 43.33 4.61
1890 3445 0.827089 TGGAACTGCCACCACCATTG 60.827 55.000 0.00 0.00 43.33 2.82
1892 3447 0.598065 GAACTGCCACCACCATTGTC 59.402 55.000 0.00 0.00 0.00 3.18
1919 3474 8.781404 CACGTGTTTATGTTAATATCAAAACGG 58.219 33.333 19.59 9.62 31.19 4.44
1935 3490 4.766404 AAACGGCCAACTAAGAAGATTG 57.234 40.909 2.24 0.00 0.00 2.67
1936 3491 3.418684 ACGGCCAACTAAGAAGATTGT 57.581 42.857 2.24 0.00 0.00 2.71
1937 3492 3.751518 ACGGCCAACTAAGAAGATTGTT 58.248 40.909 2.24 0.00 0.00 2.83
1938 3493 4.142038 ACGGCCAACTAAGAAGATTGTTT 58.858 39.130 2.24 0.00 0.00 2.83
1939 3494 4.583073 ACGGCCAACTAAGAAGATTGTTTT 59.417 37.500 2.24 0.00 0.00 2.43
1940 3495 5.154222 CGGCCAACTAAGAAGATTGTTTTC 58.846 41.667 2.24 0.00 0.00 2.29
1941 3496 5.470368 GGCCAACTAAGAAGATTGTTTTCC 58.530 41.667 0.00 0.00 0.00 3.13
1942 3497 5.243954 GGCCAACTAAGAAGATTGTTTTCCT 59.756 40.000 0.00 0.00 0.00 3.36
1943 3498 6.239317 GGCCAACTAAGAAGATTGTTTTCCTT 60.239 38.462 0.00 0.00 0.00 3.36
1944 3499 6.863645 GCCAACTAAGAAGATTGTTTTCCTTC 59.136 38.462 0.00 0.00 37.23 3.46
1945 3500 7.078228 CCAACTAAGAAGATTGTTTTCCTTCG 58.922 38.462 0.00 0.00 40.71 3.79
1946 3501 7.041372 CCAACTAAGAAGATTGTTTTCCTTCGA 60.041 37.037 0.00 0.00 40.71 3.71
1947 3502 8.342634 CAACTAAGAAGATTGTTTTCCTTCGAA 58.657 33.333 0.00 0.00 40.71 3.71
1948 3503 8.446599 ACTAAGAAGATTGTTTTCCTTCGAAA 57.553 30.769 0.00 0.00 40.71 3.46
1949 3504 8.343366 ACTAAGAAGATTGTTTTCCTTCGAAAC 58.657 33.333 0.00 0.00 40.71 2.78
1950 3505 6.944234 AGAAGATTGTTTTCCTTCGAAACT 57.056 33.333 0.00 0.00 40.71 2.66
1951 3506 8.446599 AAGAAGATTGTTTTCCTTCGAAACTA 57.553 30.769 0.00 0.00 40.71 2.24
1952 3507 8.446599 AGAAGATTGTTTTCCTTCGAAACTAA 57.553 30.769 0.00 0.00 40.71 2.24
1953 3508 8.560374 AGAAGATTGTTTTCCTTCGAAACTAAG 58.440 33.333 0.00 0.00 40.71 2.18
1954 3509 8.446599 AAGATTGTTTTCCTTCGAAACTAAGA 57.553 30.769 0.00 0.00 37.72 2.10
1955 3510 8.446599 AGATTGTTTTCCTTCGAAACTAAGAA 57.553 30.769 0.00 0.00 37.72 2.52
1956 3511 8.560374 AGATTGTTTTCCTTCGAAACTAAGAAG 58.440 33.333 0.00 0.00 42.42 2.85
1957 3512 7.852971 TTGTTTTCCTTCGAAACTAAGAAGA 57.147 32.000 0.00 0.00 44.76 2.87
1958 3513 7.478520 TGTTTTCCTTCGAAACTAAGAAGAG 57.521 36.000 0.00 0.00 44.76 2.85
1991 3546 7.959175 ACACGTGTTAGGACATATATAATGGT 58.041 34.615 17.22 0.00 38.23 3.55
1992 3547 9.081204 ACACGTGTTAGGACATATATAATGGTA 57.919 33.333 17.22 0.00 38.23 3.25
2026 3581 6.758416 GCAGTGTCACATAGAATATCTGTCAA 59.242 38.462 5.62 0.00 0.00 3.18
2027 3582 7.042858 GCAGTGTCACATAGAATATCTGTCAAG 60.043 40.741 5.62 0.00 0.00 3.02
2028 3583 8.193438 CAGTGTCACATAGAATATCTGTCAAGA 58.807 37.037 5.62 0.00 36.69 3.02
2031 3600 8.917088 TGTCACATAGAATATCTGTCAAGATGA 58.083 33.333 0.00 0.00 43.27 2.92
2038 3607 8.729805 AGAATATCTGTCAAGATGAAGGAAAC 57.270 34.615 0.00 0.00 43.27 2.78
2055 3624 8.100164 TGAAGGAAACAGAAACCAAAAGAAAAT 58.900 29.630 0.00 0.00 0.00 1.82
2096 3665 7.184800 TGATGATAATTTTATCCGGTGAACG 57.815 36.000 0.00 0.00 38.98 3.95
2097 3666 6.764085 TGATGATAATTTTATCCGGTGAACGT 59.236 34.615 0.00 0.00 42.24 3.99
2098 3667 6.592798 TGATAATTTTATCCGGTGAACGTC 57.407 37.500 0.00 0.00 42.24 4.34
2100 3669 4.939509 AATTTTATCCGGTGAACGTCAG 57.060 40.909 0.00 0.00 42.24 3.51
2101 3670 1.717194 TTTATCCGGTGAACGTCAGC 58.283 50.000 0.00 0.00 41.16 4.26
2113 3682 2.811317 GTCAGCGGACGAGGCTTG 60.811 66.667 0.00 0.00 39.08 4.01
2114 3683 4.742201 TCAGCGGACGAGGCTTGC 62.742 66.667 0.37 0.00 39.08 4.01
2116 3685 4.087892 AGCGGACGAGGCTTGCAT 62.088 61.111 0.37 0.00 37.50 3.96
2118 3687 3.869272 CGGACGAGGCTTGCATGC 61.869 66.667 15.87 15.87 0.00 4.06
2119 3688 2.437359 GGACGAGGCTTGCATGCT 60.437 61.111 22.27 9.87 0.00 3.79
2121 3690 2.437359 ACGAGGCTTGCATGCTCC 60.437 61.111 22.27 16.51 0.00 4.70
2122 3691 3.207669 CGAGGCTTGCATGCTCCC 61.208 66.667 22.27 15.54 0.00 4.30
2143 3712 4.899239 CGCTCCCGTGCTCCCATC 62.899 72.222 0.00 0.00 0.00 3.51
2144 3713 4.554036 GCTCCCGTGCTCCCATCC 62.554 72.222 0.00 0.00 0.00 3.51
2145 3714 3.866582 CTCCCGTGCTCCCATCCC 61.867 72.222 0.00 0.00 0.00 3.85
2146 3715 4.414956 TCCCGTGCTCCCATCCCT 62.415 66.667 0.00 0.00 0.00 4.20
2149 3718 1.762460 CCGTGCTCCCATCCCTACT 60.762 63.158 0.00 0.00 0.00 2.57
2150 3719 1.742768 CGTGCTCCCATCCCTACTC 59.257 63.158 0.00 0.00 0.00 2.59
2151 3720 1.749334 CGTGCTCCCATCCCTACTCC 61.749 65.000 0.00 0.00 0.00 3.85
2153 3722 2.873525 GCTCCCATCCCTACTCCGC 61.874 68.421 0.00 0.00 0.00 5.54
2154 3723 2.520982 TCCCATCCCTACTCCGCG 60.521 66.667 0.00 0.00 0.00 6.46
2156 3725 4.301027 CCATCCCTACTCCGCGCC 62.301 72.222 0.00 0.00 0.00 6.53
2162 3731 3.823330 CTACTCCGCGCCGTTCCT 61.823 66.667 0.00 0.00 0.00 3.36
2163 3732 3.352338 CTACTCCGCGCCGTTCCTT 62.352 63.158 0.00 0.00 0.00 3.36
2164 3733 2.830704 CTACTCCGCGCCGTTCCTTT 62.831 60.000 0.00 0.00 0.00 3.11
2165 3734 3.788766 CTCCGCGCCGTTCCTTTG 61.789 66.667 0.00 0.00 0.00 2.77
2173 3742 2.331893 CCGTTCCTTTGGCATCGCA 61.332 57.895 0.00 0.00 0.00 5.10
2174 3743 1.154225 CGTTCCTTTGGCATCGCAC 60.154 57.895 0.00 0.00 0.00 5.34
2175 3744 1.154225 GTTCCTTTGGCATCGCACG 60.154 57.895 0.00 0.00 0.00 5.34
2176 3745 2.331893 TTCCTTTGGCATCGCACGG 61.332 57.895 0.00 0.00 0.00 4.94
2177 3746 4.481112 CCTTTGGCATCGCACGGC 62.481 66.667 0.00 0.00 0.00 5.68
2193 3762 1.281899 CGGCTCCGTCAATTTCTCTC 58.718 55.000 0.00 0.00 34.35 3.20
2194 3763 1.134965 CGGCTCCGTCAATTTCTCTCT 60.135 52.381 0.00 0.00 34.35 3.10
2195 3764 2.545731 GGCTCCGTCAATTTCTCTCTC 58.454 52.381 0.00 0.00 0.00 3.20
2198 3767 2.497675 CTCCGTCAATTTCTCTCTCCCA 59.502 50.000 0.00 0.00 0.00 4.37
2199 3768 2.233922 TCCGTCAATTTCTCTCTCCCAC 59.766 50.000 0.00 0.00 0.00 4.61
2200 3769 2.263077 CGTCAATTTCTCTCTCCCACG 58.737 52.381 0.00 0.00 0.00 4.94
2201 3770 2.352814 CGTCAATTTCTCTCTCCCACGT 60.353 50.000 0.00 0.00 0.00 4.49
2209 4069 1.348036 CTCTCTCCCACGTCCCTTTTT 59.652 52.381 0.00 0.00 0.00 1.94
2229 4089 5.738118 TTTTTCTGCCAAAAAGCAATCAG 57.262 34.783 0.42 0.00 43.52 2.90
2232 4092 3.495331 TCTGCCAAAAAGCAATCAGGTA 58.505 40.909 0.00 0.00 43.52 3.08
2234 4094 5.260424 TCTGCCAAAAAGCAATCAGGTATA 58.740 37.500 0.00 0.00 43.52 1.47
2235 4095 5.125417 TCTGCCAAAAAGCAATCAGGTATAC 59.875 40.000 0.00 0.00 43.52 1.47
2237 4097 4.159506 GCCAAAAAGCAATCAGGTATACCA 59.840 41.667 23.87 4.43 38.89 3.25
2239 4099 6.630188 GCCAAAAAGCAATCAGGTATACCAAT 60.630 38.462 23.87 13.50 38.89 3.16
2240 4100 7.330262 CCAAAAAGCAATCAGGTATACCAATT 58.670 34.615 23.87 18.19 38.89 2.32
2241 4101 7.823799 CCAAAAAGCAATCAGGTATACCAATTT 59.176 33.333 23.87 10.51 38.89 1.82
2248 4108 8.780249 GCAATCAGGTATACCAATTTATTACGT 58.220 33.333 23.87 0.00 38.89 3.57
2250 4110 9.498176 AATCAGGTATACCAATTTATTACGTCC 57.502 33.333 23.87 0.00 38.89 4.79
2251 4111 7.147312 TCAGGTATACCAATTTATTACGTCCG 58.853 38.462 23.87 0.00 38.89 4.79
2255 4115 3.345414 ACCAATTTATTACGTCCGCCAA 58.655 40.909 0.00 0.00 0.00 4.52
2256 4116 3.949113 ACCAATTTATTACGTCCGCCAAT 59.051 39.130 0.00 0.00 0.00 3.16
2257 4117 4.399934 ACCAATTTATTACGTCCGCCAATT 59.600 37.500 0.00 0.00 0.00 2.32
2259 4119 6.095160 ACCAATTTATTACGTCCGCCAATTTA 59.905 34.615 0.00 0.00 0.00 1.40
2260 4120 7.142680 CCAATTTATTACGTCCGCCAATTTAT 58.857 34.615 0.00 0.00 0.00 1.40
2261 4121 7.650104 CCAATTTATTACGTCCGCCAATTTATT 59.350 33.333 0.00 0.00 0.00 1.40
2264 4124 4.775440 TTACGTCCGCCAATTTATTACG 57.225 40.909 0.00 0.00 35.17 3.18
2265 4125 2.620242 ACGTCCGCCAATTTATTACGT 58.380 42.857 0.00 0.00 37.28 3.57
2266 4126 2.604462 ACGTCCGCCAATTTATTACGTC 59.396 45.455 0.00 0.00 37.53 4.34
2267 4127 2.033492 CGTCCGCCAATTTATTACGTCC 60.033 50.000 0.00 0.00 0.00 4.79
2268 4128 2.033492 GTCCGCCAATTTATTACGTCCG 60.033 50.000 0.00 0.00 0.00 4.79
2269 4129 1.333435 CCGCCAATTTATTACGTCCGC 60.333 52.381 0.00 0.00 0.00 5.54
2273 4133 4.318903 CGCCAATTTATTACGTCCGCAATA 60.319 41.667 0.00 0.00 0.00 1.90
2275 4135 5.049954 GCCAATTTATTACGTCCGCAATAGA 60.050 40.000 0.00 0.00 0.00 1.98
2281 4141 2.995482 GTCCGCAATAGACGCACG 59.005 61.111 0.00 0.00 0.00 5.34
2284 4144 1.058748 CCGCAATAGACGCACGTTG 59.941 57.895 0.00 0.00 0.00 4.10
2286 4146 0.162933 CGCAATAGACGCACGTTGTT 59.837 50.000 0.00 0.00 0.00 2.83
2287 4147 1.591248 GCAATAGACGCACGTTGTTG 58.409 50.000 0.00 4.71 0.00 3.33
2288 4148 1.193650 GCAATAGACGCACGTTGTTGA 59.806 47.619 15.45 0.00 0.00 3.18
2289 4149 2.349060 GCAATAGACGCACGTTGTTGAA 60.349 45.455 15.45 0.00 0.00 2.69
2291 4151 3.515071 ATAGACGCACGTTGTTGAAAC 57.485 42.857 0.00 0.00 0.00 2.78
2292 4152 0.375803 AGACGCACGTTGTTGAAACC 59.624 50.000 0.00 0.00 0.00 3.27
2293 4153 0.375803 GACGCACGTTGTTGAAACCT 59.624 50.000 0.00 0.00 0.00 3.50
2294 4154 0.375803 ACGCACGTTGTTGAAACCTC 59.624 50.000 0.00 0.00 0.00 3.85
2295 4155 0.316689 CGCACGTTGTTGAAACCTCC 60.317 55.000 0.00 0.00 0.00 4.30
2296 4156 1.021968 GCACGTTGTTGAAACCTCCT 58.978 50.000 0.00 0.00 0.00 3.69
2297 4157 1.404035 GCACGTTGTTGAAACCTCCTT 59.596 47.619 0.00 0.00 0.00 3.36
2298 4158 2.540973 GCACGTTGTTGAAACCTCCTTC 60.541 50.000 0.00 0.00 0.00 3.46
2299 4159 2.032924 CACGTTGTTGAAACCTCCTTCC 59.967 50.000 0.00 0.00 0.00 3.46
2300 4160 1.263217 CGTTGTTGAAACCTCCTTCCG 59.737 52.381 0.00 0.00 0.00 4.30
2301 4161 1.001706 GTTGTTGAAACCTCCTTCCGC 60.002 52.381 0.00 0.00 0.00 5.54
2302 4162 0.536460 TGTTGAAACCTCCTTCCGCC 60.536 55.000 0.00 0.00 0.00 6.13
2303 4163 0.536460 GTTGAAACCTCCTTCCGCCA 60.536 55.000 0.00 0.00 0.00 5.69
2304 4164 0.183971 TTGAAACCTCCTTCCGCCAA 59.816 50.000 0.00 0.00 0.00 4.52
2305 4165 0.404040 TGAAACCTCCTTCCGCCAAT 59.596 50.000 0.00 0.00 0.00 3.16
2306 4166 1.631388 TGAAACCTCCTTCCGCCAATA 59.369 47.619 0.00 0.00 0.00 1.90
2307 4167 2.014857 GAAACCTCCTTCCGCCAATAC 58.985 52.381 0.00 0.00 0.00 1.89
2308 4168 0.988832 AACCTCCTTCCGCCAATACA 59.011 50.000 0.00 0.00 0.00 2.29
2309 4169 1.213296 ACCTCCTTCCGCCAATACAT 58.787 50.000 0.00 0.00 0.00 2.29
2310 4170 1.141053 ACCTCCTTCCGCCAATACATC 59.859 52.381 0.00 0.00 0.00 3.06
2311 4171 1.140852 CCTCCTTCCGCCAATACATCA 59.859 52.381 0.00 0.00 0.00 3.07
2318 4178 5.163519 CCTTCCGCCAATACATCAAGAAAAT 60.164 40.000 0.00 0.00 0.00 1.82
2324 4184 6.857964 CGCCAATACATCAAGAAAATACATCC 59.142 38.462 0.00 0.00 0.00 3.51
2336 4196 1.464376 ATACATCCACCGAGCCCGAG 61.464 60.000 0.00 0.00 38.22 4.63
2337 4197 2.561467 TACATCCACCGAGCCCGAGA 62.561 60.000 0.00 0.00 38.22 4.04
2339 4199 1.153061 ATCCACCGAGCCCGAGATA 59.847 57.895 0.00 0.00 38.22 1.98
2341 4201 2.565645 CCACCGAGCCCGAGATAGG 61.566 68.421 0.00 0.00 38.22 2.57
2349 4209 3.057749 CCCGAGATAGGGCATGAGA 57.942 57.895 0.00 0.00 45.72 3.27
2350 4210 0.605589 CCCGAGATAGGGCATGAGAC 59.394 60.000 0.00 0.00 45.72 3.36
2351 4211 1.626686 CCGAGATAGGGCATGAGACT 58.373 55.000 0.00 0.00 0.00 3.24
2352 4212 2.555448 CCCGAGATAGGGCATGAGACTA 60.555 54.545 0.00 0.00 45.72 2.59
2353 4213 2.752354 CCGAGATAGGGCATGAGACTAG 59.248 54.545 0.00 0.00 0.00 2.57
2354 4214 2.163412 CGAGATAGGGCATGAGACTAGC 59.837 54.545 0.00 0.00 0.00 3.42
2358 4218 3.538614 GGCATGAGACTAGCCCGA 58.461 61.111 0.00 0.00 42.58 5.14
2359 4219 1.068250 GGCATGAGACTAGCCCGAC 59.932 63.158 0.00 0.00 42.58 4.79
2360 4220 1.395826 GGCATGAGACTAGCCCGACT 61.396 60.000 0.00 0.00 42.58 4.18
2361 4221 0.461961 GCATGAGACTAGCCCGACTT 59.538 55.000 0.00 0.00 0.00 3.01
2362 4222 1.134670 GCATGAGACTAGCCCGACTTT 60.135 52.381 0.00 0.00 0.00 2.66
2363 4223 2.678190 GCATGAGACTAGCCCGACTTTT 60.678 50.000 0.00 0.00 0.00 2.27
2364 4224 2.743636 TGAGACTAGCCCGACTTTTG 57.256 50.000 0.00 0.00 0.00 2.44
2372 4232 5.310451 ACTAGCCCGACTTTTGATTAACAA 58.690 37.500 0.00 0.00 36.65 2.83
2401 4261 2.124411 ACCGGCCAGGATTACAAGTAT 58.876 47.619 18.74 0.00 45.00 2.12
2409 4269 4.056050 CAGGATTACAAGTATACGCCCAC 58.944 47.826 0.00 0.00 0.00 4.61
2411 4271 4.347000 AGGATTACAAGTATACGCCCACAT 59.653 41.667 0.00 0.00 0.00 3.21
2422 4282 0.813184 CGCCCACATGCAAAGAGAAT 59.187 50.000 0.00 0.00 0.00 2.40
2432 4292 7.201626 CCACATGCAAAGAGAATGAAAAACAAA 60.202 33.333 0.00 0.00 0.00 2.83
2433 4293 7.849026 CACATGCAAAGAGAATGAAAAACAAAG 59.151 33.333 0.00 0.00 0.00 2.77
2438 4298 4.610945 AGAGAATGAAAAACAAAGCGGTG 58.389 39.130 0.00 0.00 0.00 4.94
2444 4304 5.759506 TGAAAAACAAAGCGGTGAGATAA 57.240 34.783 0.00 0.00 0.00 1.75
2449 4309 5.957842 AACAAAGCGGTGAGATAAAATGA 57.042 34.783 0.00 0.00 0.00 2.57
2450 4310 5.296813 ACAAAGCGGTGAGATAAAATGAC 57.703 39.130 0.00 0.00 0.00 3.06
2454 4314 3.120792 GCGGTGAGATAAAATGACGCTA 58.879 45.455 0.00 0.00 42.18 4.26
2463 4323 7.386573 TGAGATAAAATGACGCTAGACAACAAA 59.613 33.333 0.00 0.00 0.00 2.83
2507 4367 5.995282 ACGAACAATGAAGATAAACACTGGA 59.005 36.000 0.00 0.00 0.00 3.86
2538 4398 3.069318 GACGCCGAGGTCCTCCTT 61.069 66.667 13.54 0.00 45.24 3.36
2570 4430 1.811965 CATCGGGAACAAGAACATGCA 59.188 47.619 0.00 0.00 0.00 3.96
2577 4437 3.338249 GAACAAGAACATGCAGGCTCTA 58.662 45.455 4.49 0.00 0.00 2.43
2634 4494 0.953960 CACCAAGCAACTACGGACCC 60.954 60.000 0.00 0.00 0.00 4.46
2635 4495 1.376812 CCAAGCAACTACGGACCCC 60.377 63.158 0.00 0.00 0.00 4.95
2687 4547 1.376037 GAAGGCCACAACCTCCTCG 60.376 63.158 5.01 0.00 39.93 4.63
2691 4551 1.235281 GGCCACAACCTCCTCGTTTC 61.235 60.000 0.00 0.00 0.00 2.78
2694 4554 1.137513 CACAACCTCCTCGTTTCGAC 58.862 55.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 59 9.239002 CTACTATCATTACCTTCGAAAGTGAAG 57.761 37.037 9.69 0.00 43.98 3.02
128 143 3.261580 TGATGACCATTGATCGACACAC 58.738 45.455 0.00 0.00 0.00 3.82
208 223 2.616842 CAAAGGTAAAGGTCTTGCGTGT 59.383 45.455 0.00 0.00 0.00 4.49
214 1528 2.501261 GGACGCAAAGGTAAAGGTCTT 58.499 47.619 0.00 0.00 0.00 3.01
373 1687 4.520111 TGTGCTCAACTTGCAAATGACTAT 59.480 37.500 9.82 0.00 42.41 2.12
380 1694 1.469595 GCACTGTGCTCAACTTGCAAA 60.470 47.619 24.68 0.00 42.41 3.68
437 1756 1.518367 ACTCTTCCCACTCAAACCCA 58.482 50.000 0.00 0.00 0.00 4.51
730 2239 9.927081 ATTCTATCTTTCCTGGAACAACAATAT 57.073 29.630 9.04 0.00 38.70 1.28
762 2274 5.403897 CGATATAAAGTCGTGGCAAACAT 57.596 39.130 0.00 0.00 34.56 2.71
824 2339 5.273170 CGCAAGTCAACTCTGATTTGAAAA 58.727 37.500 11.40 0.00 46.79 2.29
988 2513 7.423844 TCCAGTGATACATTATCAACTGTCT 57.576 36.000 16.23 3.13 45.91 3.41
997 2522 5.221521 ACGATGTGCTCCAGTGATACATTAT 60.222 40.000 0.00 0.00 31.92 1.28
999 2524 3.118629 ACGATGTGCTCCAGTGATACATT 60.119 43.478 0.00 0.00 31.92 2.71
1053 2581 3.575506 CAAGGGACCATTGCTGCTA 57.424 52.632 5.85 0.00 0.00 3.49
1135 2666 3.027412 ACTGGGAGTAGTAGTGATGCTG 58.973 50.000 0.00 0.00 0.00 4.41
1136 2667 3.292460 GACTGGGAGTAGTAGTGATGCT 58.708 50.000 0.00 0.00 0.00 3.79
1137 2668 2.033550 CGACTGGGAGTAGTAGTGATGC 59.966 54.545 0.00 0.00 0.00 3.91
1138 2669 3.542648 TCGACTGGGAGTAGTAGTGATG 58.457 50.000 0.00 0.00 0.00 3.07
1139 2670 3.928005 TCGACTGGGAGTAGTAGTGAT 57.072 47.619 0.00 0.00 0.00 3.06
1140 2671 3.542648 CATCGACTGGGAGTAGTAGTGA 58.457 50.000 0.00 0.00 0.00 3.41
1329 2872 1.915614 GCTACCGACCAGACGACGAA 61.916 60.000 0.00 0.00 35.09 3.85
1352 2895 5.597806 GTGGCATGCATTGTACTAGTAGTA 58.402 41.667 21.36 5.90 0.00 1.82
1353 2896 4.442706 GTGGCATGCATTGTACTAGTAGT 58.557 43.478 21.36 8.14 0.00 2.73
1354 2897 3.490896 CGTGGCATGCATTGTACTAGTAG 59.509 47.826 21.36 0.00 0.00 2.57
1355 2898 3.118920 ACGTGGCATGCATTGTACTAGTA 60.119 43.478 21.36 0.00 0.00 1.82
1356 2899 2.279741 CGTGGCATGCATTGTACTAGT 58.720 47.619 21.36 0.00 0.00 2.57
1357 2900 2.279741 ACGTGGCATGCATTGTACTAG 58.720 47.619 21.36 2.36 0.00 2.57
1358 2901 2.394930 ACGTGGCATGCATTGTACTA 57.605 45.000 21.36 0.00 0.00 1.82
1359 2902 1.533625 AACGTGGCATGCATTGTACT 58.466 45.000 21.36 0.00 0.00 2.73
1360 2903 3.119990 ACTTAACGTGGCATGCATTGTAC 60.120 43.478 21.36 8.87 0.00 2.90
1385 2934 5.271625 GTTGACACGACGATGAGTATACAT 58.728 41.667 0.00 0.00 0.00 2.29
1395 2944 0.319555 CACAGGGTTGACACGACGAT 60.320 55.000 0.00 0.00 0.00 3.73
1409 2958 5.066375 TGAGAATCAAAAGACAACACACAGG 59.934 40.000 0.00 0.00 45.97 4.00
1427 2976 0.460284 CCGGCAAGCGTACTGAGAAT 60.460 55.000 0.00 0.00 0.00 2.40
1430 2979 1.078759 CTTCCGGCAAGCGTACTGAG 61.079 60.000 0.00 0.00 0.00 3.35
1432 2981 1.080093 TCTTCCGGCAAGCGTACTG 60.080 57.895 0.00 0.00 31.26 2.74
1549 3098 1.664965 GAGACATATCCGCCGCCAC 60.665 63.158 0.00 0.00 0.00 5.01
1550 3099 1.832608 AGAGACATATCCGCCGCCA 60.833 57.895 0.00 0.00 0.00 5.69
1552 3101 1.373497 CCAGAGACATATCCGCCGC 60.373 63.158 0.00 0.00 0.00 6.53
1561 3110 0.388649 GCGTCGTTGACCAGAGACAT 60.389 55.000 0.00 0.00 33.56 3.06
1819 3371 9.803315 GAGAAACCAAAAGAAAATACTTGTCTT 57.197 29.630 0.00 0.00 33.01 3.01
1820 3372 9.190317 AGAGAAACCAAAAGAAAATACTTGTCT 57.810 29.630 0.00 0.00 0.00 3.41
1821 3373 9.452065 GAGAGAAACCAAAAGAAAATACTTGTC 57.548 33.333 0.00 0.00 0.00 3.18
1822 3374 9.190317 AGAGAGAAACCAAAAGAAAATACTTGT 57.810 29.630 0.00 0.00 0.00 3.16
1823 3375 9.670719 GAGAGAGAAACCAAAAGAAAATACTTG 57.329 33.333 0.00 0.00 0.00 3.16
1824 3376 9.408648 TGAGAGAGAAACCAAAAGAAAATACTT 57.591 29.630 0.00 0.00 0.00 2.24
1825 3377 8.980481 TGAGAGAGAAACCAAAAGAAAATACT 57.020 30.769 0.00 0.00 0.00 2.12
1826 3378 9.452065 GTTGAGAGAGAAACCAAAAGAAAATAC 57.548 33.333 0.00 0.00 0.00 1.89
1827 3379 9.184523 TGTTGAGAGAGAAACCAAAAGAAAATA 57.815 29.630 0.00 0.00 0.00 1.40
1828 3380 8.066612 TGTTGAGAGAGAAACCAAAAGAAAAT 57.933 30.769 0.00 0.00 0.00 1.82
1829 3381 7.461182 TGTTGAGAGAGAAACCAAAAGAAAA 57.539 32.000 0.00 0.00 0.00 2.29
1830 3382 7.461182 TTGTTGAGAGAGAAACCAAAAGAAA 57.539 32.000 0.00 0.00 0.00 2.52
1831 3383 7.461182 TTTGTTGAGAGAGAAACCAAAAGAA 57.539 32.000 0.00 0.00 0.00 2.52
1832 3384 6.404734 GCTTTGTTGAGAGAGAAACCAAAAGA 60.405 38.462 0.00 0.00 28.27 2.52
1833 3385 5.745769 GCTTTGTTGAGAGAGAAACCAAAAG 59.254 40.000 0.00 0.00 0.00 2.27
1834 3386 5.418840 AGCTTTGTTGAGAGAGAAACCAAAA 59.581 36.000 0.00 0.00 0.00 2.44
1835 3387 4.949856 AGCTTTGTTGAGAGAGAAACCAAA 59.050 37.500 0.00 0.00 0.00 3.28
1836 3388 4.336433 CAGCTTTGTTGAGAGAGAAACCAA 59.664 41.667 0.00 0.00 0.00 3.67
1837 3389 3.879295 CAGCTTTGTTGAGAGAGAAACCA 59.121 43.478 0.00 0.00 0.00 3.67
1838 3390 3.251972 CCAGCTTTGTTGAGAGAGAAACC 59.748 47.826 0.00 0.00 0.00 3.27
1839 3391 3.304324 GCCAGCTTTGTTGAGAGAGAAAC 60.304 47.826 0.00 0.00 0.00 2.78
1840 3392 2.880890 GCCAGCTTTGTTGAGAGAGAAA 59.119 45.455 0.00 0.00 0.00 2.52
1847 3399 6.018425 CAGTACATATAGCCAGCTTTGTTGAG 60.018 42.308 0.00 0.00 0.00 3.02
1877 3432 1.530419 GTGGACAATGGTGGTGGCA 60.530 57.895 0.00 0.00 0.00 4.92
1883 3438 3.252215 ACATAAACACGTGGACAATGGTG 59.748 43.478 21.57 9.53 36.50 4.17
1886 3441 9.433317 GATATTAACATAAACACGTGGACAATG 57.567 33.333 21.57 18.21 0.00 2.82
1890 3445 9.828852 TTTTGATATTAACATAAACACGTGGAC 57.171 29.630 21.57 0.00 0.00 4.02
1892 3447 8.781404 CGTTTTGATATTAACATAAACACGTGG 58.219 33.333 21.57 3.64 0.00 4.94
1919 3474 6.332735 AGGAAAACAATCTTCTTAGTTGGC 57.667 37.500 0.00 0.00 0.00 4.52
1935 3490 7.479897 ACTCTTCTTAGTTTCGAAGGAAAAC 57.520 36.000 0.00 0.00 43.39 2.43
1936 3491 8.502105 AAACTCTTCTTAGTTTCGAAGGAAAA 57.498 30.769 0.00 0.00 44.43 2.29
1937 3492 8.502105 AAAACTCTTCTTAGTTTCGAAGGAAA 57.498 30.769 0.00 0.00 46.40 3.13
1938 3493 8.502105 AAAAACTCTTCTTAGTTTCGAAGGAA 57.498 30.769 0.00 0.00 46.40 3.36
1985 3540 9.674068 TGTGACACTGCTAAAATAATACCATTA 57.326 29.630 7.20 0.00 0.00 1.90
1988 3543 9.325198 CTATGTGACACTGCTAAAATAATACCA 57.675 33.333 7.20 0.00 0.00 3.25
1989 3544 9.542462 TCTATGTGACACTGCTAAAATAATACC 57.458 33.333 7.20 0.00 0.00 2.73
1996 3551 9.317936 CAGATATTCTATGTGACACTGCTAAAA 57.682 33.333 7.20 0.00 0.00 1.52
1998 3553 8.011844 ACAGATATTCTATGTGACACTGCTAA 57.988 34.615 7.20 0.00 0.00 3.09
1999 3554 7.285401 TGACAGATATTCTATGTGACACTGCTA 59.715 37.037 7.20 0.00 0.00 3.49
2000 3555 6.097412 TGACAGATATTCTATGTGACACTGCT 59.903 38.462 7.20 0.00 0.00 4.24
2001 3556 6.276091 TGACAGATATTCTATGTGACACTGC 58.724 40.000 7.20 0.00 0.00 4.40
2026 3581 6.607198 TCTTTTGGTTTCTGTTTCCTTCATCT 59.393 34.615 0.00 0.00 0.00 2.90
2027 3582 6.805713 TCTTTTGGTTTCTGTTTCCTTCATC 58.194 36.000 0.00 0.00 0.00 2.92
2028 3583 6.790232 TCTTTTGGTTTCTGTTTCCTTCAT 57.210 33.333 0.00 0.00 0.00 2.57
2031 3600 9.378551 GTATTTTCTTTTGGTTTCTGTTTCCTT 57.621 29.630 0.00 0.00 0.00 3.36
2038 3607 9.586435 AAGACAAGTATTTTCTTTTGGTTTCTG 57.414 29.630 0.00 0.00 0.00 3.02
2070 3639 8.289618 CGTTCACCGGATAAAATTATCATCATT 58.710 33.333 9.46 0.00 40.98 2.57
2072 3641 6.764085 ACGTTCACCGGATAAAATTATCATCA 59.236 34.615 9.46 0.00 40.98 3.07
2073 3642 7.042321 TGACGTTCACCGGATAAAATTATCATC 60.042 37.037 9.46 0.00 40.98 2.92
2074 3643 6.764085 TGACGTTCACCGGATAAAATTATCAT 59.236 34.615 9.46 0.00 40.98 2.45
2076 3645 6.592798 TGACGTTCACCGGATAAAATTATC 57.407 37.500 9.46 4.86 42.24 1.75
2077 3646 5.007332 GCTGACGTTCACCGGATAAAATTAT 59.993 40.000 9.46 0.00 42.24 1.28
2078 3647 4.330620 GCTGACGTTCACCGGATAAAATTA 59.669 41.667 9.46 0.00 42.24 1.40
2079 3648 3.126343 GCTGACGTTCACCGGATAAAATT 59.874 43.478 9.46 0.00 42.24 1.82
2080 3649 2.676342 GCTGACGTTCACCGGATAAAAT 59.324 45.455 9.46 0.00 42.24 1.82
2081 3650 2.070783 GCTGACGTTCACCGGATAAAA 58.929 47.619 9.46 0.00 42.24 1.52
2082 3651 1.717194 GCTGACGTTCACCGGATAAA 58.283 50.000 9.46 0.00 42.24 1.40
2083 3652 0.457166 CGCTGACGTTCACCGGATAA 60.457 55.000 9.46 0.00 42.24 1.75
2084 3653 1.138036 CGCTGACGTTCACCGGATA 59.862 57.895 9.46 0.00 42.24 2.59
2086 3655 4.351938 CCGCTGACGTTCACCGGA 62.352 66.667 9.46 0.00 45.79 5.14
2087 3656 4.351938 TCCGCTGACGTTCACCGG 62.352 66.667 0.00 0.00 44.65 5.28
2088 3657 3.103911 GTCCGCTGACGTTCACCG 61.104 66.667 0.00 0.00 44.03 4.94
2096 3665 2.811317 CAAGCCTCGTCCGCTGAC 60.811 66.667 0.00 0.00 36.47 3.51
2097 3666 4.742201 GCAAGCCTCGTCCGCTGA 62.742 66.667 0.00 0.00 36.47 4.26
2100 3669 3.869272 CATGCAAGCCTCGTCCGC 61.869 66.667 0.00 0.00 0.00 5.54
2101 3670 3.869272 GCATGCAAGCCTCGTCCG 61.869 66.667 14.21 0.00 0.00 4.79
2102 3671 2.437359 AGCATGCAAGCCTCGTCC 60.437 61.111 21.98 0.00 34.23 4.79
2103 3672 2.467826 GGAGCATGCAAGCCTCGTC 61.468 63.158 21.98 5.57 34.23 4.20
2104 3673 2.437359 GGAGCATGCAAGCCTCGT 60.437 61.111 21.98 0.00 34.23 4.18
2105 3674 3.207669 GGGAGCATGCAAGCCTCG 61.208 66.667 21.98 0.00 34.23 4.63
2126 3695 4.899239 GATGGGAGCACGGGAGCG 62.899 72.222 0.00 0.00 40.15 5.03
2127 3696 4.554036 GGATGGGAGCACGGGAGC 62.554 72.222 0.00 0.00 0.00 4.70
2128 3697 2.946988 TAGGGATGGGAGCACGGGAG 62.947 65.000 0.00 0.00 0.00 4.30
2129 3698 3.016613 TAGGGATGGGAGCACGGGA 62.017 63.158 0.00 0.00 0.00 5.14
2131 3700 1.749334 GAGTAGGGATGGGAGCACGG 61.749 65.000 0.00 0.00 0.00 4.94
2132 3701 1.742768 GAGTAGGGATGGGAGCACG 59.257 63.158 0.00 0.00 0.00 5.34
2134 3703 1.457643 CGGAGTAGGGATGGGAGCA 60.458 63.158 0.00 0.00 0.00 4.26
2135 3704 2.873525 GCGGAGTAGGGATGGGAGC 61.874 68.421 0.00 0.00 0.00 4.70
2137 3706 2.520982 CGCGGAGTAGGGATGGGA 60.521 66.667 0.00 0.00 0.00 4.37
2138 3707 4.301027 GCGCGGAGTAGGGATGGG 62.301 72.222 8.83 0.00 0.00 4.00
2139 3708 4.301027 GGCGCGGAGTAGGGATGG 62.301 72.222 8.83 0.00 0.00 3.51
2143 3712 4.867599 GAACGGCGCGGAGTAGGG 62.868 72.222 22.76 0.00 0.00 3.53
2144 3713 4.867599 GGAACGGCGCGGAGTAGG 62.868 72.222 22.76 0.00 0.00 3.18
2145 3714 2.830704 AAAGGAACGGCGCGGAGTAG 62.831 60.000 22.76 0.98 0.00 2.57
2146 3715 2.934570 AAAGGAACGGCGCGGAGTA 61.935 57.895 22.76 0.00 0.00 2.59
2156 3725 1.154225 GTGCGATGCCAAAGGAACG 60.154 57.895 0.00 0.00 0.00 3.95
2158 3727 2.331893 CCGTGCGATGCCAAAGGAA 61.332 57.895 0.00 0.00 0.00 3.36
2159 3728 2.745884 CCGTGCGATGCCAAAGGA 60.746 61.111 0.00 0.00 0.00 3.36
2162 3731 3.430862 GAGCCGTGCGATGCCAAA 61.431 61.111 0.00 0.00 0.00 3.28
2174 3743 1.134965 AGAGAGAAATTGACGGAGCCG 60.135 52.381 7.48 7.48 46.03 5.52
2175 3744 2.545731 GAGAGAGAAATTGACGGAGCC 58.454 52.381 0.00 0.00 0.00 4.70
2176 3745 2.545731 GGAGAGAGAAATTGACGGAGC 58.454 52.381 0.00 0.00 0.00 4.70
2177 3746 2.497675 TGGGAGAGAGAAATTGACGGAG 59.502 50.000 0.00 0.00 0.00 4.63
2180 3749 2.263077 CGTGGGAGAGAGAAATTGACG 58.737 52.381 0.00 0.00 0.00 4.35
2182 3751 2.233922 GGACGTGGGAGAGAGAAATTGA 59.766 50.000 0.00 0.00 0.00 2.57
2184 3753 1.555533 GGGACGTGGGAGAGAGAAATT 59.444 52.381 0.00 0.00 0.00 1.82
2185 3754 1.196012 GGGACGTGGGAGAGAGAAAT 58.804 55.000 0.00 0.00 0.00 2.17
2186 3755 0.114560 AGGGACGTGGGAGAGAGAAA 59.885 55.000 0.00 0.00 0.00 2.52
2187 3756 0.114560 AAGGGACGTGGGAGAGAGAA 59.885 55.000 0.00 0.00 0.00 2.87
2189 3758 0.977395 AAAAGGGACGTGGGAGAGAG 59.023 55.000 0.00 0.00 0.00 3.20
2209 4069 3.134442 ACCTGATTGCTTTTTGGCAGAAA 59.866 39.130 3.00 3.00 43.39 2.52
2214 4074 4.159506 TGGTATACCTGATTGCTTTTTGGC 59.840 41.667 22.41 0.00 36.82 4.52
2224 4084 9.498176 GGACGTAATAAATTGGTATACCTGATT 57.502 33.333 22.41 17.88 36.82 2.57
2225 4085 7.816031 CGGACGTAATAAATTGGTATACCTGAT 59.184 37.037 22.41 13.36 36.82 2.90
2229 4089 5.120674 GGCGGACGTAATAAATTGGTATACC 59.879 44.000 15.50 15.50 0.00 2.73
2232 4092 4.706035 TGGCGGACGTAATAAATTGGTAT 58.294 39.130 0.00 0.00 0.00 2.73
2234 4094 2.988570 TGGCGGACGTAATAAATTGGT 58.011 42.857 0.00 0.00 0.00 3.67
2235 4095 4.561735 ATTGGCGGACGTAATAAATTGG 57.438 40.909 0.00 0.00 0.00 3.16
2237 4097 9.667989 GTAATAAATTGGCGGACGTAATAAATT 57.332 29.630 0.00 0.00 0.00 1.82
2239 4099 7.010923 ACGTAATAAATTGGCGGACGTAATAAA 59.989 33.333 0.00 0.00 39.99 1.40
2240 4100 6.478344 ACGTAATAAATTGGCGGACGTAATAA 59.522 34.615 0.00 0.00 39.99 1.40
2241 4101 5.982516 ACGTAATAAATTGGCGGACGTAATA 59.017 36.000 0.00 0.00 39.99 0.98
2243 4103 4.180057 ACGTAATAAATTGGCGGACGTAA 58.820 39.130 0.00 0.00 39.99 3.18
2244 4104 3.779759 ACGTAATAAATTGGCGGACGTA 58.220 40.909 0.00 0.00 39.99 3.57
2245 4105 2.604462 GACGTAATAAATTGGCGGACGT 59.396 45.455 0.00 0.00 44.00 4.34
2246 4106 2.033492 GGACGTAATAAATTGGCGGACG 60.033 50.000 0.00 0.00 35.10 4.79
2248 4108 2.203401 CGGACGTAATAAATTGGCGGA 58.797 47.619 0.00 0.00 0.00 5.54
2250 4110 1.328069 TGCGGACGTAATAAATTGGCG 59.672 47.619 0.00 0.00 0.00 5.69
2251 4111 3.408288 TTGCGGACGTAATAAATTGGC 57.592 42.857 0.00 0.00 0.00 4.52
2264 4124 1.349259 AACGTGCGTCTATTGCGGAC 61.349 55.000 0.00 0.00 44.99 4.79
2265 4125 1.080366 AACGTGCGTCTATTGCGGA 60.080 52.632 0.00 0.00 34.24 5.54
2266 4126 1.058748 CAACGTGCGTCTATTGCGG 59.941 57.895 0.00 0.00 34.24 5.69
2267 4127 0.162933 AACAACGTGCGTCTATTGCG 59.837 50.000 0.00 0.00 34.24 4.85
2268 4128 1.193650 TCAACAACGTGCGTCTATTGC 59.806 47.619 0.00 0.00 0.00 3.56
2269 4129 3.513462 TTCAACAACGTGCGTCTATTG 57.487 42.857 0.00 3.86 0.00 1.90
2273 4133 0.375803 GGTTTCAACAACGTGCGTCT 59.624 50.000 0.00 0.00 0.00 4.18
2275 4135 0.375803 GAGGTTTCAACAACGTGCGT 59.624 50.000 0.00 0.00 0.00 5.24
2277 4137 1.021968 AGGAGGTTTCAACAACGTGC 58.978 50.000 0.00 0.00 0.00 5.34
2278 4138 2.032924 GGAAGGAGGTTTCAACAACGTG 59.967 50.000 0.00 0.00 0.00 4.49
2279 4139 2.294979 GGAAGGAGGTTTCAACAACGT 58.705 47.619 0.00 0.00 0.00 3.99
2281 4141 1.001706 GCGGAAGGAGGTTTCAACAAC 60.002 52.381 0.00 0.00 0.00 3.32
2284 4144 0.536460 TGGCGGAAGGAGGTTTCAAC 60.536 55.000 0.00 0.00 0.00 3.18
2286 4146 0.404040 ATTGGCGGAAGGAGGTTTCA 59.596 50.000 0.00 0.00 0.00 2.69
2287 4147 2.014857 GTATTGGCGGAAGGAGGTTTC 58.985 52.381 0.00 0.00 0.00 2.78
2288 4148 1.353022 TGTATTGGCGGAAGGAGGTTT 59.647 47.619 0.00 0.00 0.00 3.27
2289 4149 0.988832 TGTATTGGCGGAAGGAGGTT 59.011 50.000 0.00 0.00 0.00 3.50
2291 4151 1.140852 TGATGTATTGGCGGAAGGAGG 59.859 52.381 0.00 0.00 0.00 4.30
2292 4152 2.620251 TGATGTATTGGCGGAAGGAG 57.380 50.000 0.00 0.00 0.00 3.69
2293 4153 2.503765 TCTTGATGTATTGGCGGAAGGA 59.496 45.455 0.00 0.00 0.00 3.36
2294 4154 2.917933 TCTTGATGTATTGGCGGAAGG 58.082 47.619 0.00 0.00 0.00 3.46
2295 4155 4.963276 TTTCTTGATGTATTGGCGGAAG 57.037 40.909 0.00 0.00 0.00 3.46
2296 4156 5.913137 ATTTTCTTGATGTATTGGCGGAA 57.087 34.783 0.00 0.00 0.00 4.30
2297 4157 5.883115 TGTATTTTCTTGATGTATTGGCGGA 59.117 36.000 0.00 0.00 0.00 5.54
2298 4158 6.130298 TGTATTTTCTTGATGTATTGGCGG 57.870 37.500 0.00 0.00 0.00 6.13
2299 4159 6.857964 GGATGTATTTTCTTGATGTATTGGCG 59.142 38.462 0.00 0.00 0.00 5.69
2300 4160 7.649306 GTGGATGTATTTTCTTGATGTATTGGC 59.351 37.037 0.00 0.00 0.00 4.52
2301 4161 8.137437 GGTGGATGTATTTTCTTGATGTATTGG 58.863 37.037 0.00 0.00 0.00 3.16
2302 4162 7.857389 CGGTGGATGTATTTTCTTGATGTATTG 59.143 37.037 0.00 0.00 0.00 1.90
2303 4163 7.773224 TCGGTGGATGTATTTTCTTGATGTATT 59.227 33.333 0.00 0.00 0.00 1.89
2304 4164 7.279615 TCGGTGGATGTATTTTCTTGATGTAT 58.720 34.615 0.00 0.00 0.00 2.29
2305 4165 6.645306 TCGGTGGATGTATTTTCTTGATGTA 58.355 36.000 0.00 0.00 0.00 2.29
2306 4166 5.496556 TCGGTGGATGTATTTTCTTGATGT 58.503 37.500 0.00 0.00 0.00 3.06
2307 4167 5.504665 GCTCGGTGGATGTATTTTCTTGATG 60.505 44.000 0.00 0.00 0.00 3.07
2308 4168 4.576463 GCTCGGTGGATGTATTTTCTTGAT 59.424 41.667 0.00 0.00 0.00 2.57
2309 4169 3.938963 GCTCGGTGGATGTATTTTCTTGA 59.061 43.478 0.00 0.00 0.00 3.02
2310 4170 3.065371 GGCTCGGTGGATGTATTTTCTTG 59.935 47.826 0.00 0.00 0.00 3.02
2311 4171 3.279434 GGCTCGGTGGATGTATTTTCTT 58.721 45.455 0.00 0.00 0.00 2.52
2318 4178 2.043752 TCGGGCTCGGTGGATGTA 60.044 61.111 5.94 0.00 36.95 2.29
2324 4184 2.565645 CCCTATCTCGGGCTCGGTG 61.566 68.421 5.94 0.00 37.41 4.94
2341 4201 1.068250 GTCGGGCTAGTCTCATGCC 59.932 63.158 0.00 0.00 45.42 4.40
2342 4202 0.461961 AAGTCGGGCTAGTCTCATGC 59.538 55.000 0.00 0.00 0.00 4.06
2343 4203 2.932614 CAAAAGTCGGGCTAGTCTCATG 59.067 50.000 0.00 0.00 0.00 3.07
2344 4204 2.832129 TCAAAAGTCGGGCTAGTCTCAT 59.168 45.455 0.00 0.00 0.00 2.90
2345 4205 2.244695 TCAAAAGTCGGGCTAGTCTCA 58.755 47.619 0.00 0.00 0.00 3.27
2346 4206 3.528597 ATCAAAAGTCGGGCTAGTCTC 57.471 47.619 0.00 0.00 0.00 3.36
2347 4207 3.983044 AATCAAAAGTCGGGCTAGTCT 57.017 42.857 0.00 0.00 0.00 3.24
2348 4208 4.933400 TGTTAATCAAAAGTCGGGCTAGTC 59.067 41.667 0.00 0.00 0.00 2.59
2349 4209 4.901868 TGTTAATCAAAAGTCGGGCTAGT 58.098 39.130 0.00 0.00 0.00 2.57
2350 4210 5.873179 TTGTTAATCAAAAGTCGGGCTAG 57.127 39.130 0.00 0.00 32.64 3.42
2351 4211 5.335348 GCTTTGTTAATCAAAAGTCGGGCTA 60.335 40.000 8.92 0.00 44.08 3.93
2352 4212 4.558697 GCTTTGTTAATCAAAAGTCGGGCT 60.559 41.667 8.92 0.00 44.08 5.19
2353 4213 3.673338 GCTTTGTTAATCAAAAGTCGGGC 59.327 43.478 8.92 3.83 44.08 6.13
2354 4214 4.234574 GGCTTTGTTAATCAAAAGTCGGG 58.765 43.478 8.92 0.00 44.08 5.14
2355 4215 4.865776 TGGCTTTGTTAATCAAAAGTCGG 58.134 39.130 7.77 0.00 44.08 4.79
2356 4216 6.148948 TGATGGCTTTGTTAATCAAAAGTCG 58.851 36.000 7.77 0.00 44.08 4.18
2357 4217 7.095649 GGTTGATGGCTTTGTTAATCAAAAGTC 60.096 37.037 0.00 6.11 44.08 3.01
2358 4218 6.705825 GGTTGATGGCTTTGTTAATCAAAAGT 59.294 34.615 0.00 0.00 44.08 2.66
2359 4219 6.128849 CGGTTGATGGCTTTGTTAATCAAAAG 60.129 38.462 0.00 4.95 44.08 2.27
2360 4220 5.694006 CGGTTGATGGCTTTGTTAATCAAAA 59.306 36.000 0.00 0.00 44.08 2.44
2361 4221 5.226396 CGGTTGATGGCTTTGTTAATCAAA 58.774 37.500 0.00 4.07 39.89 2.69
2362 4222 4.321601 CCGGTTGATGGCTTTGTTAATCAA 60.322 41.667 0.00 0.00 36.85 2.57
2363 4223 3.192422 CCGGTTGATGGCTTTGTTAATCA 59.808 43.478 0.00 0.00 0.00 2.57
2364 4224 3.769536 CCGGTTGATGGCTTTGTTAATC 58.230 45.455 0.00 0.00 0.00 1.75
2401 4261 0.323302 TCTCTTTGCATGTGGGCGTA 59.677 50.000 0.00 0.00 36.28 4.42
2409 4269 6.849305 GCTTTGTTTTTCATTCTCTTTGCATG 59.151 34.615 0.00 0.00 0.00 4.06
2411 4271 5.005586 CGCTTTGTTTTTCATTCTCTTTGCA 59.994 36.000 0.00 0.00 0.00 4.08
2422 4282 5.759506 TTATCTCACCGCTTTGTTTTTCA 57.240 34.783 0.00 0.00 0.00 2.69
2432 4292 1.933853 GCGTCATTTTATCTCACCGCT 59.066 47.619 0.00 0.00 37.14 5.52
2433 4293 1.933853 AGCGTCATTTTATCTCACCGC 59.066 47.619 0.00 0.00 40.12 5.68
2438 4298 6.887376 TGTTGTCTAGCGTCATTTTATCTC 57.113 37.500 0.00 0.00 0.00 2.75
2463 4323 2.256117 AGCGTGTGAGGCTTAGTTTT 57.744 45.000 0.00 0.00 35.57 2.43
2507 4367 2.042831 GCGTCTTTGGCTCCATGCT 61.043 57.895 0.00 0.00 42.39 3.79
2518 4378 2.647158 GGAGGACCTCGGCGTCTTT 61.647 63.158 15.46 0.00 33.07 2.52
2552 4412 1.522668 CTGCATGTTCTTGTTCCCGA 58.477 50.000 0.00 0.00 0.00 5.14
2577 4437 1.075698 TGTCGGTCTTCCTCTCTCCTT 59.924 52.381 0.00 0.00 0.00 3.36
2593 4453 1.338674 TGGCATTCCCAACTAGTGTCG 60.339 52.381 0.00 0.00 41.82 4.35


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

AutoCloner maintained by Alex Coulton.