Multiple sequence alignment - TraesCS2B01G230900

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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 TraesCS2B01G230900 chr2B 100.000 5851 0 0 1001 6851 227076518 227082368 0.000000e+00 10805.0
1 TraesCS2B01G230900 chr2B 100.000 649 0 0 1 649 227075518 227076166 0.000000e+00 1199.0
2 TraesCS2B01G230900 chr2B 92.742 124 5 1 1 120 702748552 702748429 7.060000e-40 176.0
3 TraesCS2B01G230900 chr2B 97.059 34 1 0 80 113 439023871 439023904 2.670000e-04 58.4
4 TraesCS2B01G230900 chr2A 95.365 5070 155 30 1001 6047 179664329 179669341 0.000000e+00 7987.0
5 TraesCS2B01G230900 chr2A 84.598 448 42 15 188 635 179663800 179664220 2.950000e-113 420.0
6 TraesCS2B01G230900 chr2A 83.516 364 45 12 6490 6851 179670155 179670505 6.630000e-85 326.0
7 TraesCS2B01G230900 chr2A 89.744 117 10 1 6175 6291 744975832 744975718 1.540000e-31 148.0
8 TraesCS2B01G230900 chr2A 84.043 94 11 2 6033 6122 711885158 711885065 3.400000e-13 87.9
9 TraesCS2B01G230900 chr2A 81.053 95 13 5 6037 6128 729564176 729564084 3.430000e-08 71.3
10 TraesCS2B01G230900 chr2A 81.053 95 9 8 6038 6127 717943949 717944039 4.430000e-07 67.6
11 TraesCS2B01G230900 chr2A 83.824 68 7 4 5927 5992 535219858 535219793 2.060000e-05 62.1
12 TraesCS2B01G230900 chr2D 93.351 3083 124 25 1001 4019 170453850 170450785 0.000000e+00 4482.0
13 TraesCS2B01G230900 chr2D 95.447 1208 43 8 4012 5211 170450415 170449212 0.000000e+00 1916.0
14 TraesCS2B01G230900 chr2D 95.572 542 18 3 5315 5851 170449168 170448628 0.000000e+00 863.0
15 TraesCS2B01G230900 chr2D 89.122 524 45 7 117 635 170454473 170453957 5.790000e-180 641.0
16 TraesCS2B01G230900 chr2D 91.818 110 9 0 6560 6669 371919250 371919359 3.310000e-33 154.0
17 TraesCS2B01G230900 chr5B 85.380 171 25 0 6499 6669 617173962 617173792 1.960000e-40 178.0
18 TraesCS2B01G230900 chr3D 94.545 110 6 0 6560 6669 15953742 15953633 3.290000e-38 171.0
19 TraesCS2B01G230900 chr3D 93.694 111 6 1 6560 6669 48419581 48419691 1.530000e-36 165.0
20 TraesCS2B01G230900 chr3D 93.694 111 6 1 6560 6669 603421917 603421807 1.530000e-36 165.0
21 TraesCS2B01G230900 chr3D 89.744 117 10 2 6175 6291 537905148 537905034 1.540000e-31 148.0
22 TraesCS2B01G230900 chr3D 96.970 33 1 0 6680 6712 45959321 45959289 1.000000e-03 56.5
23 TraesCS2B01G230900 chr1D 94.545 110 5 1 6560 6669 409816763 409816871 1.180000e-37 169.0
24 TraesCS2B01G230900 chr1D 89.916 119 10 1 6173 6291 110982588 110982704 1.190000e-32 152.0
25 TraesCS2B01G230900 chr1D 86.408 103 12 2 5221 5322 354565944 354566045 2.020000e-20 111.0
26 TraesCS2B01G230900 chr1D 80.808 99 17 1 6030 6126 216728386 216728484 7.370000e-10 76.8
27 TraesCS2B01G230900 chr3A 93.694 111 7 0 6560 6670 8602617 8602507 4.250000e-37 167.0
28 TraesCS2B01G230900 chr3A 88.333 60 3 4 5933 5990 621323072 621323015 1.230000e-07 69.4
29 TraesCS2B01G230900 chr3A 78.505 107 16 6 6038 6140 416192253 416192356 5.740000e-06 63.9
30 TraesCS2B01G230900 chr5D 93.636 110 7 0 6560 6669 458686726 458686835 1.530000e-36 165.0
31 TraesCS2B01G230900 chr5D 92.308 117 5 4 6175 6290 414230176 414230063 5.500000e-36 163.0
32 TraesCS2B01G230900 chr4D 88.722 133 11 4 6560 6690 504225947 504225817 7.110000e-35 159.0
33 TraesCS2B01G230900 chr7B 90.598 117 10 1 6175 6291 332644181 332644066 3.310000e-33 154.0
34 TraesCS2B01G230900 chr7B 85.593 118 11 3 1 112 721333956 721333839 1.210000e-22 119.0
35 TraesCS2B01G230900 chr7B 86.598 97 13 0 5225 5321 220135116 220135212 2.610000e-19 108.0
36 TraesCS2B01G230900 chr4B 89.076 119 11 2 6173 6291 534404957 534404841 5.540000e-31 147.0
37 TraesCS2B01G230900 chr4B 96.970 33 1 0 6680 6712 645456584 645456552 1.000000e-03 56.5
38 TraesCS2B01G230900 chr3B 88.618 123 11 3 6169 6291 206273350 206273231 5.540000e-31 147.0
39 TraesCS2B01G230900 chr3B 93.814 97 6 0 5226 5322 421902958 421903054 5.540000e-31 147.0
40 TraesCS2B01G230900 chr3B 87.200 125 14 2 6167 6291 243240494 243240616 2.580000e-29 141.0
41 TraesCS2B01G230900 chr3B 89.899 99 10 0 5224 5322 330797987 330798085 2.010000e-25 128.0
42 TraesCS2B01G230900 chr7D 88.333 120 12 2 6172 6291 63379821 63379938 7.160000e-30 143.0
43 TraesCS2B01G230900 chr7D 90.816 98 8 1 5226 5323 554684043 554683947 5.580000e-26 130.0
44 TraesCS2B01G230900 chr1B 86.585 82 11 0 5226 5307 535907317 535907398 2.630000e-14 91.6
45 TraesCS2B01G230900 chr6D 81.633 98 13 5 6030 6123 455101323 455101227 7.370000e-10 76.8
46 TraesCS2B01G230900 chr6D 85.135 74 8 3 6040 6111 390725825 390725753 9.530000e-09 73.1
47 TraesCS2B01G230900 chr6D 82.558 86 10 5 5224 5307 444661622 444661704 3.430000e-08 71.3
48 TraesCS2B01G230900 chr4A 81.915 94 12 5 6038 6128 669384961 669384870 2.650000e-09 75.0
49 TraesCS2B01G230900 chr4A 81.720 93 13 4 6035 6124 710784491 710784400 2.650000e-09 75.0
50 TraesCS2B01G230900 chrUn 89.655 58 4 1 5268 5323 83720185 83720128 9.530000e-09 73.1
51 TraesCS2B01G230900 chr6B 97.619 42 1 0 5246 5287 437165204 437165163 9.530000e-09 73.1


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 TraesCS2B01G230900 chr2B 227075518 227082368 6850 False 6002.0 10805 100.000000 1 6851 2 chr2B.!!$F2 6850
1 TraesCS2B01G230900 chr2A 179663800 179670505 6705 False 2911.0 7987 87.826333 188 6851 3 chr2A.!!$F2 6663
2 TraesCS2B01G230900 chr2D 170448628 170454473 5845 True 1975.5 4482 93.373000 117 5851 4 chr2D.!!$R1 5734

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
110 111 0.108329 ACGCGTGGGGTTTCATCTAG 60.108 55.000 12.93 0.00 0.00 2.43 F
111 112 0.108329 CGCGTGGGGTTTCATCTAGT 60.108 55.000 0.00 0.00 0.00 2.57 F
410 411 0.965439 AATGGCAGCGCTTAACCAAA 59.035 45.000 23.19 5.68 35.41 3.28 F
1405 1436 1.066454 GTTGCTGGTTTTGCGTTAGGT 59.934 47.619 0.00 0.00 0.00 3.08 F
1440 1471 1.784525 CCTCGTCCAAGTCAGTTGAC 58.215 55.000 4.09 4.09 45.08 3.18 F
1926 1972 1.923899 TGTTACTCACGTTTGTCGCA 58.076 45.000 0.00 0.00 44.19 5.10 F
2660 2722 1.463444 CATCGTTTTTCCGACTCCACC 59.537 52.381 0.00 0.00 40.08 4.61 F
3590 3688 2.296792 TCGAGATGAGAAGAGCTCTGG 58.703 52.381 19.06 0.00 44.27 3.86 F
5240 5723 0.105039 GCAATACTCCCTCCGTCCTG 59.895 60.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1387 0.186630 TCCCGTTCCTCGATATCCCA 59.813 55.000 0.00 0.00 42.86 4.37 R
1474 1505 0.580104 CGTAACGGGGCGATGAAATC 59.420 55.000 0.00 0.00 40.89 2.17 R
1754 1791 1.002142 TGTTCCACGATATACGCTCCG 60.002 52.381 0.00 0.00 46.94 4.63 R
2423 2473 1.135859 GGAACTCAAAGCATCTGCACG 60.136 52.381 4.79 0.00 45.16 5.34 R
2644 2694 1.520494 GAGGGTGGAGTCGGAAAAAC 58.480 55.000 0.00 0.00 0.00 2.43 R
3590 3688 0.469070 AGCATGACTGGCCTGAGATC 59.531 55.000 17.64 4.19 0.00 2.75 R
4375 4851 3.957671 ATAAACATGATGCAGTGCTCG 57.042 42.857 17.60 2.63 0.00 5.03 R
5523 6006 4.446889 GGCCTCATCCATCTCCAAGTATTT 60.447 45.833 0.00 0.00 0.00 1.40 R
6395 7203 0.037232 CCTCCTCACCCAAACTCGAC 60.037 60.000 0.00 0.00 0.00 4.20 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
20 21 2.858745 TGCACCTACCAAAGAGTTTCC 58.141 47.619 0.00 0.00 0.00 3.13
21 22 2.441750 TGCACCTACCAAAGAGTTTCCT 59.558 45.455 0.00 0.00 0.00 3.36
22 23 3.649023 TGCACCTACCAAAGAGTTTCCTA 59.351 43.478 0.00 0.00 0.00 2.94
23 24 4.288626 TGCACCTACCAAAGAGTTTCCTAT 59.711 41.667 0.00 0.00 0.00 2.57
24 25 5.486063 TGCACCTACCAAAGAGTTTCCTATA 59.514 40.000 0.00 0.00 0.00 1.31
25 26 6.157994 TGCACCTACCAAAGAGTTTCCTATAT 59.842 38.462 0.00 0.00 0.00 0.86
26 27 7.346175 TGCACCTACCAAAGAGTTTCCTATATA 59.654 37.037 0.00 0.00 0.00 0.86
27 28 8.376270 GCACCTACCAAAGAGTTTCCTATATAT 58.624 37.037 0.00 0.00 0.00 0.86
78 79 7.414436 TCTTATCCATAAAAATGTACGCAAGC 58.586 34.615 0.00 0.00 45.62 4.01
79 80 5.574891 ATCCATAAAAATGTACGCAAGCA 57.425 34.783 0.00 0.00 45.62 3.91
80 81 5.574891 TCCATAAAAATGTACGCAAGCAT 57.425 34.783 0.00 0.00 45.62 3.79
81 82 5.960113 TCCATAAAAATGTACGCAAGCATT 58.040 33.333 0.00 0.00 45.62 3.56
82 83 6.033341 TCCATAAAAATGTACGCAAGCATTC 58.967 36.000 0.00 0.00 45.62 2.67
83 84 5.231991 CCATAAAAATGTACGCAAGCATTCC 59.768 40.000 0.00 0.00 45.62 3.01
84 85 2.939460 AAATGTACGCAAGCATTCCC 57.061 45.000 0.00 0.00 45.62 3.97
85 86 0.732571 AATGTACGCAAGCATTCCCG 59.267 50.000 0.00 0.00 45.62 5.14
86 87 1.714899 ATGTACGCAAGCATTCCCGC 61.715 55.000 0.00 0.00 45.62 6.13
87 88 2.046796 TACGCAAGCATTCCCGCA 60.047 55.556 0.00 0.00 45.62 5.69
88 89 2.106074 TACGCAAGCATTCCCGCAG 61.106 57.895 0.00 0.00 45.62 5.18
89 90 4.842091 CGCAAGCATTCCCGCAGC 62.842 66.667 0.00 0.00 33.46 5.25
90 91 3.751246 GCAAGCATTCCCGCAGCA 61.751 61.111 0.00 0.00 35.87 4.41
91 92 2.964174 CAAGCATTCCCGCAGCAA 59.036 55.556 0.00 0.00 0.00 3.91
92 93 1.444895 CAAGCATTCCCGCAGCAAC 60.445 57.895 0.00 0.00 0.00 4.17
93 94 2.981560 AAGCATTCCCGCAGCAACG 61.982 57.895 0.00 0.00 0.00 4.10
103 104 3.591835 CAGCAACGCGTGGGGTTT 61.592 61.111 14.98 0.00 36.59 3.27
104 105 3.284449 AGCAACGCGTGGGGTTTC 61.284 61.111 14.98 0.00 36.59 2.78
105 106 3.587933 GCAACGCGTGGGGTTTCA 61.588 61.111 14.98 0.00 36.59 2.69
106 107 2.914908 GCAACGCGTGGGGTTTCAT 61.915 57.895 14.98 0.00 36.59 2.57
107 108 1.209127 CAACGCGTGGGGTTTCATC 59.791 57.895 14.98 0.00 36.59 2.92
108 109 1.072505 AACGCGTGGGGTTTCATCT 59.927 52.632 14.98 0.00 35.18 2.90
109 110 0.322322 AACGCGTGGGGTTTCATCTA 59.678 50.000 14.98 0.00 35.18 1.98
110 111 0.108329 ACGCGTGGGGTTTCATCTAG 60.108 55.000 12.93 0.00 0.00 2.43
111 112 0.108329 CGCGTGGGGTTTCATCTAGT 60.108 55.000 0.00 0.00 0.00 2.57
112 113 1.674817 CGCGTGGGGTTTCATCTAGTT 60.675 52.381 0.00 0.00 0.00 2.24
113 114 2.417651 CGCGTGGGGTTTCATCTAGTTA 60.418 50.000 0.00 0.00 0.00 2.24
114 115 3.602483 GCGTGGGGTTTCATCTAGTTAA 58.398 45.455 0.00 0.00 0.00 2.01
115 116 4.196971 GCGTGGGGTTTCATCTAGTTAAT 58.803 43.478 0.00 0.00 0.00 1.40
141 142 4.637483 AACCAGATGTTTGTTGTGTCAG 57.363 40.909 0.00 0.00 31.47 3.51
288 289 8.786826 ATATCATCACAAAAACGAGGAAGTTA 57.213 30.769 0.00 0.00 33.41 2.24
350 351 1.061711 GTGCTCGTGTCATCTTCATGC 59.938 52.381 0.00 0.00 0.00 4.06
410 411 0.965439 AATGGCAGCGCTTAACCAAA 59.035 45.000 23.19 5.68 35.41 3.28
581 587 8.999431 ACACACAAAAATATAATCTCGTGAACT 58.001 29.630 0.00 0.00 0.00 3.01
1020 1040 1.232792 CAGGGAGGAGAGAGAGGGG 59.767 68.421 0.00 0.00 0.00 4.79
1195 1221 2.037641 CACCATCATTAGATCGGAGCCA 59.962 50.000 0.00 0.00 30.20 4.75
1201 1227 2.292794 TTAGATCGGAGCCACACGCC 62.293 60.000 0.00 0.00 38.78 5.68
1230 1256 2.097466 CGAATGGACCGGGAATCAAAAG 59.903 50.000 6.32 0.00 0.00 2.27
1269 1295 1.679898 CTCCTCTTTTCAGGCGGGT 59.320 57.895 0.00 0.00 32.91 5.28
1301 1327 2.537560 CCGGCGTGGATCTGCAATC 61.538 63.158 6.01 0.00 42.00 2.67
1303 1329 1.521457 GGCGTGGATCTGCAATCGA 60.521 57.895 7.29 0.00 0.00 3.59
1377 1407 1.954382 TGACTGGGATATCGAGGAACG 59.046 52.381 0.00 0.00 44.09 3.95
1405 1436 1.066454 GTTGCTGGTTTTGCGTTAGGT 59.934 47.619 0.00 0.00 0.00 3.08
1440 1471 1.784525 CCTCGTCCAAGTCAGTTGAC 58.215 55.000 4.09 4.09 45.08 3.18
1474 1505 4.019919 CCATTCGGCAGTTTGATTGTAG 57.980 45.455 0.00 0.00 0.00 2.74
1485 1516 5.967674 CAGTTTGATTGTAGATTTCATCGCC 59.032 40.000 0.00 0.00 0.00 5.54
1574 1605 7.123247 TGCTTCATAGTATCTGCTGCTCATATA 59.877 37.037 0.00 0.00 0.00 0.86
1591 1622 2.390225 ATACCTTGGGGCACAAAACA 57.610 45.000 2.72 0.00 38.91 2.83
1651 1688 7.201444 GCATTCTATTATGTATGTCTACGGTGC 60.201 40.741 0.00 0.00 0.00 5.01
1657 1694 3.349927 TGTATGTCTACGGTGCAGTAGT 58.650 45.455 11.63 3.90 43.31 2.73
1664 1701 4.872691 GTCTACGGTGCAGTAGTACTCTAA 59.127 45.833 11.63 0.00 43.31 2.10
1754 1791 6.572519 TCAATTTTGTGCCTCCTATATTTGC 58.427 36.000 0.00 0.00 0.00 3.68
1756 1793 2.254546 TGTGCCTCCTATATTTGCGG 57.745 50.000 0.00 0.00 0.00 5.69
1790 1827 5.646360 CGTGGAACAGAAGGGTTATAACATT 59.354 40.000 17.16 10.85 41.80 2.71
1903 1940 5.764686 TGTTGCAATCACACTCTTCTGTTAT 59.235 36.000 0.59 0.00 0.00 1.89
1904 1941 5.868043 TGCAATCACACTCTTCTGTTATG 57.132 39.130 0.00 0.00 0.00 1.90
1905 1942 4.154737 TGCAATCACACTCTTCTGTTATGC 59.845 41.667 0.00 0.00 0.00 3.14
1906 1943 4.154737 GCAATCACACTCTTCTGTTATGCA 59.845 41.667 0.00 0.00 30.34 3.96
1907 1944 5.163683 GCAATCACACTCTTCTGTTATGCAT 60.164 40.000 3.79 3.79 30.34 3.96
1908 1945 6.255950 CAATCACACTCTTCTGTTATGCATG 58.744 40.000 10.16 0.00 0.00 4.06
1909 1946 4.898320 TCACACTCTTCTGTTATGCATGT 58.102 39.130 10.16 0.00 0.00 3.21
1910 1947 5.308014 TCACACTCTTCTGTTATGCATGTT 58.692 37.500 10.16 0.00 0.00 2.71
1911 1948 6.463360 TCACACTCTTCTGTTATGCATGTTA 58.537 36.000 10.16 0.00 0.00 2.41
1916 1962 6.591834 ACTCTTCTGTTATGCATGTTACTCAC 59.408 38.462 10.16 0.00 0.00 3.51
1926 1972 1.923899 TGTTACTCACGTTTGTCGCA 58.076 45.000 0.00 0.00 44.19 5.10
1946 1992 3.853307 GCATAGCGTTTATGACCCATTGC 60.853 47.826 11.64 0.00 0.00 3.56
2116 2162 9.825109 TTTATGTTACCGATAGATTTGACATGA 57.175 29.630 0.00 0.00 39.76 3.07
2297 2343 3.064207 GCACGCGGGAATAGATTTATCA 58.936 45.455 15.48 0.00 0.00 2.15
2416 2466 4.896482 GCTAGTCTTTTCCCTCTATCTCCA 59.104 45.833 0.00 0.00 0.00 3.86
2423 2473 5.359194 TTTCCCTCTATCTCCATTCACAC 57.641 43.478 0.00 0.00 0.00 3.82
2458 2508 5.739752 TGAGTTCCATTTCTATGCATTCG 57.260 39.130 3.54 0.00 0.00 3.34
2644 2694 5.496387 GTCAGTGACTAATCATTTGCATCG 58.504 41.667 16.26 0.00 37.14 3.84
2660 2722 1.463444 CATCGTTTTTCCGACTCCACC 59.537 52.381 0.00 0.00 40.08 4.61
2666 2728 3.881019 TTCCGACTCCACCCTCGCT 62.881 63.158 0.00 0.00 0.00 4.93
2765 2827 5.760253 GTGAAGAACTTTCAGGACAATCTGA 59.240 40.000 0.00 0.00 41.51 3.27
3590 3688 2.296792 TCGAGATGAGAAGAGCTCTGG 58.703 52.381 19.06 0.00 44.27 3.86
4551 5027 3.908103 AGAAAGTAAGGCCCAGTCTACAA 59.092 43.478 0.00 0.00 0.00 2.41
4972 5449 2.761465 GCCTTCCCATAGCTGGCCT 61.761 63.158 3.32 0.00 41.64 5.19
5240 5723 0.105039 GCAATACTCCCTCCGTCCTG 59.895 60.000 0.00 0.00 0.00 3.86
5243 5726 2.074729 ATACTCCCTCCGTCCTGAAG 57.925 55.000 0.00 0.00 0.00 3.02
5264 5747 6.759827 TGAAGTAAGTGTCTCAACTTTGTACC 59.240 38.462 0.00 0.00 40.77 3.34
5373 5856 0.253894 TCTGATGCCATCTGTGGGTG 59.746 55.000 6.21 0.00 46.14 4.61
5534 6017 5.902613 TGAATGGCTTGAAATACTTGGAG 57.097 39.130 0.00 0.00 0.00 3.86
5736 6223 6.058833 TGTTACAGTGATGCCAAAGAACTTA 58.941 36.000 0.00 0.00 0.00 2.24
5802 6290 2.747446 CAGGGTGTAGTTGCAATACCAC 59.253 50.000 19.77 16.89 33.10 4.16
5871 6359 8.567104 TGTGTTCCATATATGTGATTGTATTGC 58.433 33.333 11.73 0.00 0.00 3.56
5884 6372 0.447801 GTATTGCTGTGACTTGCCCG 59.552 55.000 0.00 0.00 0.00 6.13
5887 6375 1.723608 TTGCTGTGACTTGCCCGTTG 61.724 55.000 0.00 0.00 0.00 4.10
5888 6376 2.186826 GCTGTGACTTGCCCGTTGT 61.187 57.895 0.00 0.00 0.00 3.32
5889 6377 1.724582 GCTGTGACTTGCCCGTTGTT 61.725 55.000 0.00 0.00 0.00 2.83
5895 6383 1.591327 CTTGCCCGTTGTTTGCACC 60.591 57.895 0.00 0.00 34.16 5.01
5931 6419 4.396357 TGGTATCCTTTGATGGGTTTGT 57.604 40.909 0.00 0.00 32.18 2.83
5958 6446 5.807520 AGTTATTGCACATCTAAGTGACTCG 59.192 40.000 0.00 0.00 42.05 4.18
5959 6447 2.654749 TGCACATCTAAGTGACTCGG 57.345 50.000 0.00 0.00 42.05 4.63
5964 6452 4.556233 CACATCTAAGTGACTCGGTCAAA 58.444 43.478 8.09 0.00 44.49 2.69
5974 6462 5.465724 AGTGACTCGGTCAAACATAAAAGAC 59.534 40.000 8.09 0.00 44.49 3.01
6011 6499 6.655078 AAAAAGATTACACCTGCACAATCT 57.345 33.333 0.00 0.00 38.95 2.40
6047 6535 9.255304 GATCAATGACATAAGAAGTACTTCCTC 57.745 37.037 28.05 16.33 40.33 3.71
6048 6536 7.556844 TCAATGACATAAGAAGTACTTCCTCC 58.443 38.462 28.05 14.05 40.33 4.30
6049 6537 5.578005 TGACATAAGAAGTACTTCCTCCG 57.422 43.478 28.05 18.11 40.33 4.63
6050 6538 5.014858 TGACATAAGAAGTACTTCCTCCGT 58.985 41.667 28.05 20.72 40.33 4.69
6051 6539 5.125097 TGACATAAGAAGTACTTCCTCCGTC 59.875 44.000 28.05 26.06 40.33 4.79
6052 6540 4.401837 ACATAAGAAGTACTTCCTCCGTCC 59.598 45.833 28.05 5.39 40.33 4.79
6053 6541 1.849977 AGAAGTACTTCCTCCGTCCC 58.150 55.000 28.05 4.69 40.33 4.46
6054 6542 1.076677 AGAAGTACTTCCTCCGTCCCA 59.923 52.381 28.05 0.00 40.33 4.37
6055 6543 2.108970 GAAGTACTTCCTCCGTCCCAT 58.891 52.381 22.74 0.00 33.64 4.00
6056 6544 3.053095 AGAAGTACTTCCTCCGTCCCATA 60.053 47.826 28.05 0.00 40.33 2.74
6057 6545 3.393426 AGTACTTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
6058 6546 3.924922 AGTACTTCCTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
6059 6547 5.070823 AGTACTTCCTCCGTCCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
6060 6548 5.652324 AGTACTTCCTCCGTCCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
6061 6549 6.797707 AGTACTTCCTCCGTCCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
6062 6550 7.243824 AGTACTTCCTCCGTCCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
6063 6551 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
6064 6552 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
6065 6553 6.960542 ACTTCCTCCGTCCCATAATATAAGAT 59.039 38.462 0.00 0.00 0.00 2.40
6066 6554 7.458170 ACTTCCTCCGTCCCATAATATAAGATT 59.542 37.037 0.00 0.00 0.00 2.40
6067 6555 7.182817 TCCTCCGTCCCATAATATAAGATTG 57.817 40.000 0.00 0.00 0.00 2.67
6068 6556 6.729100 TCCTCCGTCCCATAATATAAGATTGT 59.271 38.462 0.00 0.00 0.00 2.71
6069 6557 7.236847 TCCTCCGTCCCATAATATAAGATTGTT 59.763 37.037 0.00 0.00 0.00 2.83
6070 6558 7.883311 CCTCCGTCCCATAATATAAGATTGTTT 59.117 37.037 0.00 0.00 0.00 2.83
6071 6559 8.842358 TCCGTCCCATAATATAAGATTGTTTC 57.158 34.615 0.00 0.00 0.00 2.78
6113 6718 8.169977 TGAAAAGATCTTATATTGTGGGATGC 57.830 34.615 8.75 0.00 0.00 3.91
6115 6720 8.537728 AAAAGATCTTATATTGTGGGATGCAA 57.462 30.769 8.75 0.00 0.00 4.08
6140 6745 8.657387 AGGAGTAGCATATGTGATAACATAGT 57.343 34.615 8.88 0.00 36.21 2.12
6195 6808 5.163195 GCATACTCCCTCCATCCTTAAAAGA 60.163 44.000 0.00 0.00 0.00 2.52
6196 6809 6.529220 CATACTCCCTCCATCCTTAAAAGAG 58.471 44.000 0.00 0.00 0.00 2.85
6204 6817 7.168905 CCTCCATCCTTAAAAGAGTGTACTTT 58.831 38.462 0.00 0.00 41.09 2.66
6205 6818 7.665974 CCTCCATCCTTAAAAGAGTGTACTTTT 59.334 37.037 0.00 0.00 46.94 2.27
6322 7128 1.131126 GTGTTGCCATGGTCTGATTCG 59.869 52.381 14.67 0.00 0.00 3.34
6323 7129 1.003003 TGTTGCCATGGTCTGATTCGA 59.997 47.619 14.67 0.00 0.00 3.71
6325 7131 2.684881 GTTGCCATGGTCTGATTCGATT 59.315 45.455 14.67 0.00 0.00 3.34
6337 7143 6.257193 GGTCTGATTCGATTAACGTTAATGGT 59.743 38.462 32.38 18.70 43.13 3.55
6356 7162 0.546122 TATCACCTTTGGCGAGCCAT 59.454 50.000 18.32 3.48 46.64 4.40
6357 7163 0.323725 ATCACCTTTGGCGAGCCATT 60.324 50.000 18.32 0.05 46.64 3.16
6358 7164 0.326595 TCACCTTTGGCGAGCCATTA 59.673 50.000 18.32 8.31 46.64 1.90
6359 7165 0.734889 CACCTTTGGCGAGCCATTAG 59.265 55.000 18.32 16.65 46.64 1.73
6362 7170 1.134401 CCTTTGGCGAGCCATTAGAGA 60.134 52.381 18.32 0.00 46.64 3.10
6394 7202 0.464373 CATACCAGCAATGGAGCCGT 60.464 55.000 0.31 0.00 34.23 5.68
6395 7203 0.464373 ATACCAGCAATGGAGCCGTG 60.464 55.000 0.31 0.00 34.23 4.94
6398 7206 2.434884 AGCAATGGAGCCGTGTCG 60.435 61.111 0.00 0.00 34.23 4.35
6400 7208 2.456119 GCAATGGAGCCGTGTCGAG 61.456 63.158 0.00 0.00 0.00 4.04
6402 7210 0.670546 CAATGGAGCCGTGTCGAGTT 60.671 55.000 0.00 0.00 0.00 3.01
6403 7211 0.034896 AATGGAGCCGTGTCGAGTTT 59.965 50.000 0.00 0.00 0.00 2.66
6414 7222 0.037232 GTCGAGTTTGGGTGAGGAGG 60.037 60.000 0.00 0.00 0.00 4.30
6420 7228 1.351017 GTTTGGGTGAGGAGGTGATCA 59.649 52.381 0.00 0.00 0.00 2.92
6421 7229 1.971149 TTGGGTGAGGAGGTGATCAT 58.029 50.000 0.00 0.00 0.00 2.45
6422 7230 1.500474 TGGGTGAGGAGGTGATCATC 58.500 55.000 0.00 0.00 39.23 2.92
6423 7231 1.273781 TGGGTGAGGAGGTGATCATCA 60.274 52.381 9.06 0.00 46.04 3.07
6430 7238 5.195940 TGAGGAGGTGATCATCATTTTTCC 58.804 41.667 9.06 5.92 43.51 3.13
6434 7242 6.154021 AGGAGGTGATCATCATTTTTCCTTTG 59.846 38.462 9.06 0.00 0.00 2.77
6438 7247 6.295236 GGTGATCATCATTTTTCCTTTGGTGA 60.295 38.462 0.00 0.00 35.16 4.02
6445 7254 8.960591 CATCATTTTTCCTTTGGTGACTACTAT 58.039 33.333 0.00 0.00 0.00 2.12
6451 7260 3.270877 CTTTGGTGACTACTATGGTGGC 58.729 50.000 0.00 0.00 0.00 5.01
6453 7262 0.529992 GGTGACTACTATGGTGGCGC 60.530 60.000 0.00 0.00 0.00 6.53
6476 7285 2.630580 AGAGGAGGTGTCAAGTTCAGAC 59.369 50.000 0.00 0.00 36.55 3.51
6477 7286 2.630580 GAGGAGGTGTCAAGTTCAGACT 59.369 50.000 0.00 0.00 36.94 3.24
6478 7287 3.041946 AGGAGGTGTCAAGTTCAGACTT 58.958 45.455 0.00 0.00 46.85 3.01
6479 7288 3.070302 AGGAGGTGTCAAGTTCAGACTTC 59.930 47.826 0.00 0.00 44.14 3.01
6480 7289 3.181465 GGAGGTGTCAAGTTCAGACTTCA 60.181 47.826 0.00 0.00 44.14 3.02
6481 7290 4.054671 GAGGTGTCAAGTTCAGACTTCAG 58.945 47.826 0.00 0.00 44.14 3.02
6482 7291 3.706594 AGGTGTCAAGTTCAGACTTCAGA 59.293 43.478 0.00 0.00 44.14 3.27
6483 7292 4.054671 GGTGTCAAGTTCAGACTTCAGAG 58.945 47.826 0.00 0.00 44.14 3.35
6484 7293 4.442192 GGTGTCAAGTTCAGACTTCAGAGT 60.442 45.833 0.00 0.00 44.14 3.24
6486 7295 6.451393 GTGTCAAGTTCAGACTTCAGAGTAT 58.549 40.000 0.00 0.00 44.14 2.12
6488 7297 7.439655 GTGTCAAGTTCAGACTTCAGAGTATTT 59.560 37.037 0.00 0.00 44.14 1.40
6490 7299 8.491950 GTCAAGTTCAGACTTCAGAGTATTTTC 58.508 37.037 0.00 0.00 44.14 2.29
6494 7303 7.757624 AGTTCAGACTTCAGAGTATTTTCGATC 59.242 37.037 0.00 0.00 35.88 3.69
6496 7305 5.038033 AGACTTCAGAGTATTTTCGATCGC 58.962 41.667 11.09 0.00 35.88 4.58
6506 7390 0.166597 TTTCGATCGCGTACGTGACT 59.833 50.000 31.70 20.59 41.18 3.41
6507 7391 0.247419 TTCGATCGCGTACGTGACTC 60.247 55.000 31.70 25.28 41.18 3.36
6526 7410 7.148390 CGTGACTCGTACTATGATCCTTATGAT 60.148 40.741 0.00 0.00 33.59 2.45
6527 7411 9.163899 GTGACTCGTACTATGATCCTTATGATA 57.836 37.037 0.00 0.00 32.41 2.15
6662 7546 9.545105 TTGTATAAACTCGGTTAAACTTTGAGA 57.455 29.630 1.46 0.00 0.00 3.27
6663 7547 9.715121 TGTATAAACTCGGTTAAACTTTGAGAT 57.285 29.630 1.46 0.00 0.00 2.75
6666 7550 9.939802 ATAAACTCGGTTAAACTTTGAGATAGT 57.060 29.630 1.46 0.00 0.00 2.12
6667 7551 8.672823 AAACTCGGTTAAACTTTGAGATAGTT 57.327 30.769 1.46 0.00 37.43 2.24
6668 7552 8.672823 AACTCGGTTAAACTTTGAGATAGTTT 57.327 30.769 0.00 0.00 45.19 2.66
6669 7553 9.768662 AACTCGGTTAAACTTTGAGATAGTTTA 57.231 29.630 0.00 0.00 42.39 2.01
6670 7554 9.939802 ACTCGGTTAAACTTTGAGATAGTTTAT 57.060 29.630 8.50 0.00 43.65 1.40
6706 7590 7.948357 ACTTTGAAATAGTTTAACCCTCCAAC 58.052 34.615 0.00 0.00 0.00 3.77
6710 7594 7.947282 TGAAATAGTTTAACCCTCCAACAAAG 58.053 34.615 0.00 0.00 0.00 2.77
6712 7596 8.999905 AAATAGTTTAACCCTCCAACAAAGTA 57.000 30.769 0.00 0.00 0.00 2.24
6713 7597 7.991084 ATAGTTTAACCCTCCAACAAAGTAC 57.009 36.000 0.00 0.00 0.00 2.73
6715 7599 5.591472 AGTTTAACCCTCCAACAAAGTACAC 59.409 40.000 0.00 0.00 0.00 2.90
6716 7600 3.945640 AACCCTCCAACAAAGTACACT 57.054 42.857 0.00 0.00 0.00 3.55
6717 7601 3.945640 ACCCTCCAACAAAGTACACTT 57.054 42.857 0.00 0.00 37.91 3.16
6719 7603 4.606210 ACCCTCCAACAAAGTACACTTTT 58.394 39.130 4.61 0.00 43.07 2.27
6720 7604 4.643334 ACCCTCCAACAAAGTACACTTTTC 59.357 41.667 4.61 0.00 43.07 2.29
6721 7605 4.037565 CCCTCCAACAAAGTACACTTTTCC 59.962 45.833 4.61 0.00 43.07 3.13
6723 7607 5.126384 CCTCCAACAAAGTACACTTTTCCAA 59.874 40.000 4.61 0.00 43.07 3.53
6724 7608 6.350612 CCTCCAACAAAGTACACTTTTCCAAA 60.351 38.462 4.61 0.00 43.07 3.28
6725 7609 6.626302 TCCAACAAAGTACACTTTTCCAAAG 58.374 36.000 4.61 0.00 43.07 2.77
6726 7610 6.434652 TCCAACAAAGTACACTTTTCCAAAGA 59.565 34.615 4.61 0.00 43.07 2.52
6728 7612 5.875930 ACAAAGTACACTTTTCCAAAGACG 58.124 37.500 4.61 0.00 43.07 4.18
6729 7613 5.163693 ACAAAGTACACTTTTCCAAAGACGG 60.164 40.000 4.61 0.00 43.07 4.79
6731 7615 4.773013 AGTACACTTTTCCAAAGACGGAA 58.227 39.130 3.24 0.00 43.43 4.30
6732 7616 4.814771 AGTACACTTTTCCAAAGACGGAAG 59.185 41.667 3.24 0.00 45.65 3.46
6733 7617 2.949644 ACACTTTTCCAAAGACGGAAGG 59.050 45.455 3.24 0.00 45.65 3.46
6779 7685 9.530129 GAAAATATATCAGCATTTACTACGTGC 57.470 33.333 0.00 0.00 39.10 5.34
6828 7734 4.263435 TGTGAATACCCCCGTGAAAATAC 58.737 43.478 0.00 0.00 0.00 1.89
6842 7748 7.011950 CCCGTGAAAATACATCAGCATTTACTA 59.988 37.037 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.441750 AGGAAACTCTTTGGTAGGTGCA 59.558 45.455 0.00 0.00 32.90 4.57
1 2 3.141767 AGGAAACTCTTTGGTAGGTGC 57.858 47.619 0.00 0.00 32.90 5.01
51 52 9.950680 CTTGCGTACATTTTTATGGATAAGATT 57.049 29.630 0.00 0.00 0.00 2.40
52 53 8.076178 GCTTGCGTACATTTTTATGGATAAGAT 58.924 33.333 0.00 0.00 0.00 2.40
53 54 7.066404 TGCTTGCGTACATTTTTATGGATAAGA 59.934 33.333 0.00 0.00 0.00 2.10
54 55 7.192913 TGCTTGCGTACATTTTTATGGATAAG 58.807 34.615 0.00 0.00 0.00 1.73
55 56 7.089770 TGCTTGCGTACATTTTTATGGATAA 57.910 32.000 0.00 0.00 0.00 1.75
56 57 6.685527 TGCTTGCGTACATTTTTATGGATA 57.314 33.333 0.00 0.00 0.00 2.59
57 58 5.574891 TGCTTGCGTACATTTTTATGGAT 57.425 34.783 0.00 0.00 0.00 3.41
58 59 5.574891 ATGCTTGCGTACATTTTTATGGA 57.425 34.783 0.00 0.00 0.00 3.41
59 60 5.231991 GGAATGCTTGCGTACATTTTTATGG 59.768 40.000 0.00 0.00 36.65 2.74
60 61 5.231991 GGGAATGCTTGCGTACATTTTTATG 59.768 40.000 0.00 0.00 36.65 1.90
61 62 5.348164 GGGAATGCTTGCGTACATTTTTAT 58.652 37.500 0.00 0.00 36.65 1.40
62 63 4.673061 CGGGAATGCTTGCGTACATTTTTA 60.673 41.667 0.00 0.00 36.65 1.52
63 64 3.584834 GGGAATGCTTGCGTACATTTTT 58.415 40.909 0.00 0.00 36.65 1.94
64 65 2.415357 CGGGAATGCTTGCGTACATTTT 60.415 45.455 0.00 0.00 36.65 1.82
65 66 1.132262 CGGGAATGCTTGCGTACATTT 59.868 47.619 0.00 0.00 36.65 2.32
66 67 0.732571 CGGGAATGCTTGCGTACATT 59.267 50.000 0.00 0.00 39.16 2.71
67 68 1.714899 GCGGGAATGCTTGCGTACAT 61.715 55.000 0.00 0.00 0.00 2.29
68 69 2.395360 GCGGGAATGCTTGCGTACA 61.395 57.895 0.00 0.00 0.00 2.90
69 70 2.309764 CTGCGGGAATGCTTGCGTAC 62.310 60.000 0.00 0.00 35.36 3.67
70 71 2.046796 TGCGGGAATGCTTGCGTA 60.047 55.556 0.00 0.00 35.36 4.42
71 72 3.434319 CTGCGGGAATGCTTGCGT 61.434 61.111 0.00 0.00 35.36 5.24
72 73 4.842091 GCTGCGGGAATGCTTGCG 62.842 66.667 0.00 0.00 35.36 4.85
73 74 3.285523 TTGCTGCGGGAATGCTTGC 62.286 57.895 0.00 0.00 36.25 4.01
74 75 1.444895 GTTGCTGCGGGAATGCTTG 60.445 57.895 1.67 0.00 35.36 4.01
75 76 2.964978 GTTGCTGCGGGAATGCTT 59.035 55.556 1.67 0.00 35.36 3.91
76 77 3.434319 CGTTGCTGCGGGAATGCT 61.434 61.111 6.02 0.00 35.36 3.79
86 87 3.536498 GAAACCCCACGCGTTGCTG 62.536 63.158 10.22 2.41 0.00 4.41
87 88 3.284449 GAAACCCCACGCGTTGCT 61.284 61.111 10.22 0.00 0.00 3.91
88 89 2.796245 GATGAAACCCCACGCGTTGC 62.796 60.000 10.22 0.00 0.00 4.17
89 90 1.209127 GATGAAACCCCACGCGTTG 59.791 57.895 10.22 6.05 0.00 4.10
90 91 0.322322 TAGATGAAACCCCACGCGTT 59.678 50.000 10.22 0.00 0.00 4.84
91 92 0.108329 CTAGATGAAACCCCACGCGT 60.108 55.000 5.58 5.58 0.00 6.01
92 93 0.108329 ACTAGATGAAACCCCACGCG 60.108 55.000 3.53 3.53 0.00 6.01
93 94 2.109425 AACTAGATGAAACCCCACGC 57.891 50.000 0.00 0.00 0.00 5.34
94 95 6.753107 AAATTAACTAGATGAAACCCCACG 57.247 37.500 0.00 0.00 0.00 4.94
97 98 9.865321 GGTTTTAAATTAACTAGATGAAACCCC 57.135 33.333 0.00 0.00 38.20 4.95
122 123 4.637483 AACTGACACAACAAACATCTGG 57.363 40.909 0.00 0.00 0.00 3.86
124 125 6.515272 AGAAAACTGACACAACAAACATCT 57.485 33.333 0.00 0.00 0.00 2.90
160 161 0.945099 TGTTTTGCGTCGCACCATTA 59.055 45.000 21.61 1.01 38.71 1.90
170 171 9.638239 ATTAACATCTGAATTATTGTTTTGCGT 57.362 25.926 0.00 0.00 34.39 5.24
199 200 8.735692 TTTTTAGGGTGTTAGTATATTTCCGG 57.264 34.615 0.00 0.00 0.00 5.14
225 226 5.026121 TCTGAGTCATGTTTATCCTCAGGT 58.974 41.667 13.29 0.00 45.79 4.00
228 229 5.622233 CGTGTCTGAGTCATGTTTATCCTCA 60.622 44.000 0.00 0.00 0.00 3.86
288 289 0.806868 TCGACACGCCTTCGATAGTT 59.193 50.000 0.00 0.00 40.51 2.24
329 330 1.322637 CATGAAGATGACACGAGCACG 59.677 52.381 0.76 0.76 45.75 5.34
350 351 7.550196 CCACAAATATGGAAATGGAAAAGGAAG 59.450 37.037 0.00 0.00 43.02 3.46
388 389 1.342819 TGGTTAAGCGCTGCCATTTTT 59.657 42.857 12.58 0.00 0.00 1.94
483 489 4.503007 CGACAGACCACGATTATAAACCAG 59.497 45.833 0.00 0.00 0.00 4.00
490 496 1.470979 GGCACGACAGACCACGATTAT 60.471 52.381 0.00 0.00 0.00 1.28
620 626 0.755327 GTGCCCTCCCTCTCTCTCTC 60.755 65.000 0.00 0.00 0.00 3.20
1028 1052 4.161295 CGCAGGGATTCGGGCTCA 62.161 66.667 0.00 0.00 0.00 4.26
1201 1227 2.802667 CGGTCCATTCGAAGCAGCG 61.803 63.158 3.35 7.44 0.00 5.18
1262 1288 3.793888 GGATCCCGAAACCCGCCT 61.794 66.667 0.00 0.00 36.84 5.52
1283 1309 2.514592 ATTGCAGATCCACGCCGG 60.515 61.111 0.00 0.00 0.00 6.13
1301 1327 3.419915 CTTGTCAGGAATCGCAAAATCG 58.580 45.455 0.00 0.00 0.00 3.34
1303 1329 3.855689 CCTTGTCAGGAATCGCAAAAT 57.144 42.857 0.00 0.00 44.19 1.82
1361 1387 0.186630 TCCCGTTCCTCGATATCCCA 59.813 55.000 0.00 0.00 42.86 4.37
1428 1459 3.407424 TCCCATCTGTCAACTGACTTG 57.593 47.619 10.99 6.31 44.99 3.16
1432 1463 2.677902 GCGATTCCCATCTGTCAACTGA 60.678 50.000 0.00 0.00 0.00 3.41
1434 1465 1.407437 GGCGATTCCCATCTGTCAACT 60.407 52.381 0.00 0.00 0.00 3.16
1440 1471 0.870393 CGAATGGCGATTCCCATCTG 59.130 55.000 14.89 0.00 44.68 2.90
1442 1473 2.247790 CCGAATGGCGATTCCCATC 58.752 57.895 14.89 0.00 44.68 3.51
1462 1493 5.066505 GGGCGATGAAATCTACAATCAAACT 59.933 40.000 0.00 0.00 42.58 2.66
1468 1499 2.158813 ACGGGGCGATGAAATCTACAAT 60.159 45.455 0.00 0.00 42.58 2.71
1474 1505 0.580104 CGTAACGGGGCGATGAAATC 59.420 55.000 0.00 0.00 40.89 2.17
1500 1531 1.203376 TGTAATCCCACCCAGGAGACA 60.203 52.381 0.00 0.00 39.95 3.41
1545 1576 2.730404 CAGCAGATACTATGAAGCAGCG 59.270 50.000 0.00 0.00 0.00 5.18
1574 1605 1.140652 CAATGTTTTGTGCCCCAAGGT 59.859 47.619 0.00 0.00 33.75 3.50
1591 1622 3.069158 CGAACGGGAGGGTATTACTCAAT 59.931 47.826 0.00 0.00 36.70 2.57
1628 1659 7.013942 ACTGCACCGTAGACATACATAATAGAA 59.986 37.037 0.00 0.00 31.76 2.10
1664 1701 5.335426 CGGCACCGTAGACATACTAACATAT 60.335 44.000 0.00 0.00 32.49 1.78
1754 1791 1.002142 TGTTCCACGATATACGCTCCG 60.002 52.381 0.00 0.00 46.94 4.63
1756 1793 3.620929 TCTGTTCCACGATATACGCTC 57.379 47.619 0.00 0.00 46.94 5.03
1790 1827 2.299013 AGACGGTGAGATTGCTTACACA 59.701 45.455 0.00 0.00 32.62 3.72
1926 1972 2.884639 GGCAATGGGTCATAAACGCTAT 59.115 45.455 0.00 0.00 41.27 2.97
1946 1992 8.208718 TGGAAATAAATGTAGACGAAGAATGG 57.791 34.615 0.00 0.00 0.00 3.16
2116 2162 2.308866 ACAGCTGCCTACCAAAATAGGT 59.691 45.455 15.27 0.00 43.39 3.08
2297 2343 4.672587 AGCACTAATGATACATCCACGT 57.327 40.909 0.00 0.00 0.00 4.49
2384 2434 4.602294 AGGGAAAAGACTAGCCTAAAAGGT 59.398 41.667 0.00 0.00 37.80 3.50
2416 2466 1.527034 AAGCATCTGCACGTGTGAAT 58.473 45.000 18.38 5.18 45.16 2.57
2423 2473 1.135859 GGAACTCAAAGCATCTGCACG 60.136 52.381 4.79 0.00 45.16 5.34
2644 2694 1.520494 GAGGGTGGAGTCGGAAAAAC 58.480 55.000 0.00 0.00 0.00 2.43
2666 2728 4.648762 TCAATGAAGGACAAAGCTTTTCCA 59.351 37.500 27.51 16.07 0.00 3.53
2765 2827 5.116084 TGATAAAGAACCCTTAGCATGCT 57.884 39.130 25.99 25.99 31.15 3.79
3496 3594 7.971168 GTCCTCGTATCTATATTTCAGACATGG 59.029 40.741 0.00 0.00 0.00 3.66
3590 3688 0.469070 AGCATGACTGGCCTGAGATC 59.531 55.000 17.64 4.19 0.00 2.75
3863 3961 6.719370 AGAAACTTGCAACAGATAATAACCCA 59.281 34.615 0.00 0.00 0.00 4.51
4375 4851 3.957671 ATAAACATGATGCAGTGCTCG 57.042 42.857 17.60 2.63 0.00 5.03
4551 5027 7.277319 GTCTTTAAATAAGTCTTCGATTCCCGT 59.723 37.037 0.00 0.00 39.75 5.28
4972 5449 5.903010 TGCAGGGTTCTGATAACCTAGATTA 59.097 40.000 6.85 0.00 43.49 1.75
5240 5723 6.759827 TGGTACAAAGTTGAGACACTTACTTC 59.240 38.462 0.00 0.00 35.87 3.01
5243 5726 5.050295 GCTGGTACAAAGTTGAGACACTTAC 60.050 44.000 0.00 0.00 38.70 2.34
5307 5790 7.550597 TCATATCTAGTACTCCCTTCGTCTA 57.449 40.000 0.00 0.00 0.00 2.59
5313 5796 8.840200 TCTGTTTTCATATCTAGTACTCCCTT 57.160 34.615 0.00 0.00 0.00 3.95
5523 6006 4.446889 GGCCTCATCCATCTCCAAGTATTT 60.447 45.833 0.00 0.00 0.00 1.40
5618 6105 7.272978 AGGTGATGTAACTATGTATCCACAAC 58.727 38.462 0.00 0.00 38.42 3.32
5650 6137 1.339535 TGCCATATCCGCACTTGTTGA 60.340 47.619 0.00 0.00 0.00 3.18
5736 6223 3.500343 CCACAAGGGAATCCTCTGTTTT 58.500 45.455 0.00 0.00 44.07 2.43
5802 6290 8.160342 GGCGTACAATACAAAGTAATCGATATG 58.840 37.037 0.00 0.00 0.00 1.78
5871 6359 0.738389 AAACAACGGGCAAGTCACAG 59.262 50.000 0.00 0.00 0.00 3.66
5884 6372 0.524604 AAGCGTTCGGTGCAAACAAC 60.525 50.000 0.00 0.00 33.85 3.32
5887 6375 0.524604 AACAAGCGTTCGGTGCAAAC 60.525 50.000 0.00 0.00 33.85 2.93
5888 6376 0.171455 AAACAAGCGTTCGGTGCAAA 59.829 45.000 0.00 0.00 32.91 3.68
5889 6377 1.015109 TAAACAAGCGTTCGGTGCAA 58.985 45.000 0.00 0.00 32.91 4.08
5895 6383 4.331717 AGGATACCAATAAACAAGCGTTCG 59.668 41.667 0.00 0.00 31.93 3.95
5931 6419 8.067751 AGTCACTTAGATGTGCAATAACTAGA 57.932 34.615 0.00 0.00 37.81 2.43
5958 6446 8.710835 TTTCCTTTTGTCTTTTATGTTTGACC 57.289 30.769 0.00 0.00 0.00 4.02
5991 6479 6.449698 CAAAAGATTGTGCAGGTGTAATCTT 58.550 36.000 12.98 12.98 46.27 2.40
5993 6481 4.622740 GCAAAAGATTGTGCAGGTGTAATC 59.377 41.667 2.80 0.00 40.58 1.75
5994 6482 4.039004 TGCAAAAGATTGTGCAGGTGTAAT 59.961 37.500 6.32 0.00 45.52 1.89
5996 6484 2.954989 TGCAAAAGATTGTGCAGGTGTA 59.045 40.909 6.32 0.00 45.52 2.90
5997 6485 1.755959 TGCAAAAGATTGTGCAGGTGT 59.244 42.857 6.32 0.00 45.52 4.16
5998 6486 2.512485 TGCAAAAGATTGTGCAGGTG 57.488 45.000 6.32 0.00 45.52 4.00
6003 6491 7.490079 TCATTGATCTTATGCAAAAGATTGTGC 59.510 33.333 0.55 0.55 44.38 4.57
6004 6492 8.804743 GTCATTGATCTTATGCAAAAGATTGTG 58.195 33.333 0.00 2.11 44.38 3.33
6005 6493 8.525316 TGTCATTGATCTTATGCAAAAGATTGT 58.475 29.630 0.00 0.00 44.38 2.71
6006 6494 8.920509 TGTCATTGATCTTATGCAAAAGATTG 57.079 30.769 0.00 0.00 44.38 2.67
6047 6535 8.848474 AGAAACAATCTTATATTATGGGACGG 57.152 34.615 0.00 0.00 33.39 4.79
6048 6536 9.489084 TGAGAAACAATCTTATATTATGGGACG 57.511 33.333 0.00 0.00 38.96 4.79
6060 6548 9.944376 ACTAACATAGCTTGAGAAACAATCTTA 57.056 29.630 0.00 0.00 38.96 2.10
6061 6549 8.854614 ACTAACATAGCTTGAGAAACAATCTT 57.145 30.769 0.00 0.00 38.96 2.40
6062 6550 8.854614 AACTAACATAGCTTGAGAAACAATCT 57.145 30.769 0.00 0.00 42.61 2.40
6063 6551 9.334693 CAAACTAACATAGCTTGAGAAACAATC 57.665 33.333 0.00 0.00 34.61 2.67
6064 6552 9.066892 TCAAACTAACATAGCTTGAGAAACAAT 57.933 29.630 0.00 0.00 36.33 2.71
6065 6553 8.445275 TCAAACTAACATAGCTTGAGAAACAA 57.555 30.769 0.00 0.00 36.33 2.83
6066 6554 8.445275 TTCAAACTAACATAGCTTGAGAAACA 57.555 30.769 0.00 0.00 40.66 2.83
6067 6555 9.730420 TTTTCAAACTAACATAGCTTGAGAAAC 57.270 29.630 0.00 0.00 40.66 2.78
6068 6556 9.950680 CTTTTCAAACTAACATAGCTTGAGAAA 57.049 29.630 0.00 8.14 40.66 2.52
6069 6557 9.337396 TCTTTTCAAACTAACATAGCTTGAGAA 57.663 29.630 0.00 5.36 40.66 2.87
6070 6558 8.902540 TCTTTTCAAACTAACATAGCTTGAGA 57.097 30.769 0.00 0.00 40.66 3.27
6071 6559 9.766277 GATCTTTTCAAACTAACATAGCTTGAG 57.234 33.333 0.00 0.00 40.66 3.02
6093 6581 6.044754 TCCTTGCATCCCACAATATAAGATCT 59.955 38.462 0.00 0.00 0.00 2.75
6113 6718 9.363763 CTATGTTATCACATATGCTACTCCTTG 57.636 37.037 1.58 0.00 43.60 3.61
6115 6720 8.657387 ACTATGTTATCACATATGCTACTCCT 57.343 34.615 1.58 0.00 43.60 3.69
6150 6755 9.726438 GTATGCTACTTCCCACAATATAAGATT 57.274 33.333 0.00 0.00 0.00 2.40
6180 6793 8.622948 AAAAGTACACTCTTTTAAGGATGGAG 57.377 34.615 0.00 0.00 43.12 3.86
6322 7128 8.126700 CCAAAGGTGATACCATTAACGTTAATC 58.873 37.037 26.65 17.99 41.95 1.75
6323 7129 7.415877 GCCAAAGGTGATACCATTAACGTTAAT 60.416 37.037 24.43 24.43 41.95 1.40
6325 7131 5.354792 GCCAAAGGTGATACCATTAACGTTA 59.645 40.000 3.29 3.29 41.95 3.18
6337 7143 1.987213 TGGCTCGCCAAAGGTGATA 59.013 52.632 8.43 0.00 44.12 2.15
6356 7162 3.339253 TGCAGCTTTGCAGATCTCTAA 57.661 42.857 0.00 0.00 40.23 2.10
6358 7164 3.950869 TGCAGCTTTGCAGATCTCT 57.049 47.368 0.00 0.00 40.23 3.10
6379 7187 2.360350 ACACGGCTCCATTGCTGG 60.360 61.111 0.00 0.00 43.17 4.85
6383 7191 0.670546 AACTCGACACGGCTCCATTG 60.671 55.000 0.00 0.00 0.00 2.82
6394 7202 0.679505 CTCCTCACCCAAACTCGACA 59.320 55.000 0.00 0.00 0.00 4.35
6395 7203 0.037232 CCTCCTCACCCAAACTCGAC 60.037 60.000 0.00 0.00 0.00 4.20
6398 7206 1.056660 TCACCTCCTCACCCAAACTC 58.943 55.000 0.00 0.00 0.00 3.01
6400 7208 1.351017 TGATCACCTCCTCACCCAAAC 59.649 52.381 0.00 0.00 0.00 2.93
6402 7210 1.839994 GATGATCACCTCCTCACCCAA 59.160 52.381 0.00 0.00 0.00 4.12
6403 7211 1.273781 TGATGATCACCTCCTCACCCA 60.274 52.381 0.00 0.00 0.00 4.51
6414 7222 6.587608 GTCACCAAAGGAAAAATGATGATCAC 59.412 38.462 0.00 0.00 0.00 3.06
6420 7228 8.960591 CATAGTAGTCACCAAAGGAAAAATGAT 58.039 33.333 0.00 0.00 0.00 2.45
6421 7229 7.393234 CCATAGTAGTCACCAAAGGAAAAATGA 59.607 37.037 0.00 0.00 0.00 2.57
6422 7230 7.176690 ACCATAGTAGTCACCAAAGGAAAAATG 59.823 37.037 0.00 0.00 0.00 2.32
6423 7231 7.176690 CACCATAGTAGTCACCAAAGGAAAAAT 59.823 37.037 0.00 0.00 0.00 1.82
6424 7232 6.488683 CACCATAGTAGTCACCAAAGGAAAAA 59.511 38.462 0.00 0.00 0.00 1.94
6429 7237 3.873910 CCACCATAGTAGTCACCAAAGG 58.126 50.000 0.00 0.00 0.00 3.11
6430 7238 3.270877 GCCACCATAGTAGTCACCAAAG 58.729 50.000 0.00 0.00 0.00 2.77
6434 7242 0.529992 GCGCCACCATAGTAGTCACC 60.530 60.000 0.00 0.00 0.00 4.02
6438 7247 4.043859 TGGCGCCACCATAGTAGT 57.956 55.556 29.03 0.00 46.36 2.73
6451 7260 1.079543 CTTGACACCTCCTCTGGCG 60.080 63.158 0.00 0.00 0.00 5.69
6453 7262 1.694150 TGAACTTGACACCTCCTCTGG 59.306 52.381 0.00 0.00 0.00 3.86
6456 7265 2.630580 AGTCTGAACTTGACACCTCCTC 59.369 50.000 0.00 0.00 36.94 3.71
6460 7269 3.706594 TCTGAAGTCTGAACTTGACACCT 59.293 43.478 0.00 0.00 45.80 4.00
6476 7285 3.791887 ACGCGATCGAAAATACTCTGAAG 59.208 43.478 21.57 0.00 39.41 3.02
6477 7286 3.766151 ACGCGATCGAAAATACTCTGAA 58.234 40.909 21.57 0.00 39.41 3.02
6478 7287 3.416119 ACGCGATCGAAAATACTCTGA 57.584 42.857 21.57 0.00 39.41 3.27
6479 7288 3.115897 CGTACGCGATCGAAAATACTCTG 59.884 47.826 21.57 0.00 41.33 3.35
6480 7289 3.242543 ACGTACGCGATCGAAAATACTCT 60.243 43.478 26.56 5.59 42.00 3.24
6481 7290 3.031812 ACGTACGCGATCGAAAATACTC 58.968 45.455 26.56 0.00 42.00 2.59
6482 7291 2.780014 CACGTACGCGATCGAAAATACT 59.220 45.455 26.56 6.75 42.00 2.12
6483 7292 2.777845 TCACGTACGCGATCGAAAATAC 59.222 45.455 26.56 12.93 42.00 1.89
6484 7293 2.777845 GTCACGTACGCGATCGAAAATA 59.222 45.455 26.56 1.48 42.00 1.40
6486 7295 0.976963 GTCACGTACGCGATCGAAAA 59.023 50.000 26.56 12.98 42.00 2.29
6488 7297 0.247419 GAGTCACGTACGCGATCGAA 60.247 55.000 26.56 15.11 42.00 3.71
6490 7299 3.871651 GAGTCACGTACGCGATCG 58.128 61.111 15.93 19.18 42.00 3.69
6641 7525 9.768662 AACTATCTCAAAGTTTAACCGAGTTTA 57.231 29.630 6.66 1.99 33.39 2.01
6677 7561 9.903682 GGAGGGTTAAACTATTTCAAAGTTTAC 57.096 33.333 7.69 4.69 44.79 2.01
6678 7562 9.643735 TGGAGGGTTAAACTATTTCAAAGTTTA 57.356 29.630 4.71 4.71 43.54 2.01
6679 7563 8.541899 TGGAGGGTTAAACTATTTCAAAGTTT 57.458 30.769 6.47 6.47 46.23 2.66
6688 7572 8.000127 TGTACTTTGTTGGAGGGTTAAACTATT 59.000 33.333 0.00 0.00 0.00 1.73
6696 7580 3.945640 AGTGTACTTTGTTGGAGGGTT 57.054 42.857 0.00 0.00 0.00 4.11
6706 7590 5.065474 TCCGTCTTTGGAAAAGTGTACTTTG 59.935 40.000 10.48 0.00 44.69 2.77
6710 7594 4.024302 CCTTCCGTCTTTGGAAAAGTGTAC 60.024 45.833 0.00 0.00 46.95 2.90
6712 7596 2.949644 CCTTCCGTCTTTGGAAAAGTGT 59.050 45.455 0.00 0.00 46.95 3.55
6713 7597 3.211045 TCCTTCCGTCTTTGGAAAAGTG 58.789 45.455 0.00 0.00 46.95 3.16
6715 7599 6.151144 ACATATTCCTTCCGTCTTTGGAAAAG 59.849 38.462 0.00 0.00 46.95 2.27
6716 7600 6.007703 ACATATTCCTTCCGTCTTTGGAAAA 58.992 36.000 0.00 0.00 46.95 2.29
6717 7601 5.414454 CACATATTCCTTCCGTCTTTGGAAA 59.586 40.000 0.00 0.00 46.95 3.13
6719 7603 4.224147 TCACATATTCCTTCCGTCTTTGGA 59.776 41.667 0.00 0.00 35.83 3.53
6720 7604 4.513442 TCACATATTCCTTCCGTCTTTGG 58.487 43.478 0.00 0.00 0.00 3.28
6721 7605 6.683974 ATTCACATATTCCTTCCGTCTTTG 57.316 37.500 0.00 0.00 0.00 2.77
6723 7607 6.126883 TGGTATTCACATATTCCTTCCGTCTT 60.127 38.462 0.00 0.00 0.00 3.01
6724 7608 5.365605 TGGTATTCACATATTCCTTCCGTCT 59.634 40.000 0.00 0.00 0.00 4.18
6725 7609 5.465724 GTGGTATTCACATATTCCTTCCGTC 59.534 44.000 0.00 0.00 45.39 4.79
6726 7610 5.365619 GTGGTATTCACATATTCCTTCCGT 58.634 41.667 0.00 0.00 45.39 4.69
6778 7684 5.980715 GCTACTTCTCTTAAGGTACATCAGC 59.019 44.000 1.85 0.96 0.00 4.26
6779 7685 7.101652 TGCTACTTCTCTTAAGGTACATCAG 57.898 40.000 1.85 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.