Multiple sequence alignment - TraesCS2A01G103200

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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 TraesCS2A01G103200 chr2A 100.000 5678 0 0 887 6564 56923605 56917928 0.000000e+00 10486.0
1 TraesCS2A01G103200 chr2A 100.000 308 0 0 1 308 56924491 56924184 2.660000e-158 569.0
2 TraesCS2A01G103200 chr2A 87.662 462 24 13 1139 1576 44391856 44392308 2.110000e-139 507.0
3 TraesCS2A01G103200 chr2A 94.355 124 2 2 177 295 44391324 44391447 1.120000e-42 185.0
4 TraesCS2A01G103200 chr2A 93.204 103 5 2 86 187 44389502 44389603 4.100000e-32 150.0
5 TraesCS2A01G103200 chr2A 88.462 130 4 3 887 1016 44391515 44391633 5.300000e-31 147.0
6 TraesCS2A01G103200 chr2A 98.611 72 1 0 177 248 44390991 44391062 1.920000e-25 128.0
7 TraesCS2A01G103200 chr2A 93.023 86 5 1 2346 2431 56921868 56921784 2.490000e-24 124.0
8 TraesCS2A01G103200 chr2A 93.023 86 5 1 2624 2708 56922146 56922061 2.490000e-24 124.0
9 TraesCS2A01G103200 chr2D 95.796 3140 75 16 3124 6222 39827428 39830551 0.000000e+00 5014.0
10 TraesCS2A01G103200 chr2D 94.266 2930 103 27 3111 6007 55372302 55369405 0.000000e+00 4420.0
11 TraesCS2A01G103200 chr2D 92.461 1963 74 25 1164 3079 55374774 55372839 0.000000e+00 2737.0
12 TraesCS2A01G103200 chr2D 91.701 1952 89 28 1162 3057 39819606 39821540 0.000000e+00 2639.0
13 TraesCS2A01G103200 chr2D 97.222 216 3 1 4599 4814 55354907 55354695 4.840000e-96 363.0
14 TraesCS2A01G103200 chr2D 91.506 259 15 5 6308 6564 39830555 39830808 3.770000e-92 350.0
15 TraesCS2A01G103200 chr2D 93.363 226 9 6 72 297 55375603 55375384 4.910000e-86 329.0
16 TraesCS2A01G103200 chr2D 99.020 102 1 0 896 997 55375332 55375231 4.040000e-42 183.0
17 TraesCS2A01G103200 chr2D 83.838 198 20 5 6375 6564 55316829 55316636 1.880000e-40 178.0
18 TraesCS2A01G103200 chr2D 88.889 126 11 1 6439 6564 55356682 55356804 1.140000e-32 152.0
19 TraesCS2A01G103200 chr2D 96.471 85 3 0 3269 3353 55372384 55372300 2.470000e-29 141.0
20 TraesCS2A01G103200 chr2D 93.258 89 5 1 2621 2708 39820824 39820912 5.340000e-26 130.0
21 TraesCS2A01G103200 chr2D 92.135 89 6 1 2343 2431 39821104 39821191 2.490000e-24 124.0
22 TraesCS2A01G103200 chr2D 91.860 86 5 2 2624 2708 55373563 55373479 1.160000e-22 119.0
23 TraesCS2A01G103200 chr2B 93.919 2401 84 24 3933 6281 87845181 87842791 0.000000e+00 3568.0
24 TraesCS2A01G103200 chr2B 94.407 1323 49 11 2623 3931 87846695 87845384 0.000000e+00 2010.0
25 TraesCS2A01G103200 chr2B 88.467 1396 81 36 973 2329 87848268 87846914 0.000000e+00 1613.0
26 TraesCS2A01G103200 chr2B 94.964 139 7 0 2328 2466 87846832 87846694 1.110000e-52 219.0
27 TraesCS2A01G103200 chr2B 86.829 205 12 7 102 297 87848834 87848636 1.430000e-51 215.0
28 TraesCS2A01G103200 chr2B 86.826 167 18 3 2461 2624 578597700 578597865 4.040000e-42 183.0
29 TraesCS2A01G103200 chr2B 84.483 174 22 3 2455 2624 101288174 101288002 4.070000e-37 167.0
30 TraesCS2A01G103200 chr2B 91.765 85 6 1 2625 2708 87846813 87846729 4.160000e-22 117.0
31 TraesCS2A01G103200 chr2B 91.071 56 5 0 2328 2383 87846607 87846552 7.060000e-10 76.8
32 TraesCS2A01G103200 chr2B 97.368 38 1 0 2624 2661 87846589 87846552 1.530000e-06 65.8
33 TraesCS2A01G103200 chr4A 83.931 1338 141 34 4969 6241 520188859 520190187 0.000000e+00 1212.0
34 TraesCS2A01G103200 chr4A 77.390 1004 206 16 4031 5023 176598069 176597076 1.590000e-160 577.0
35 TraesCS2A01G103200 chr4A 90.526 95 9 0 6446 6540 529633649 529633743 6.910000e-25 126.0
36 TraesCS2A01G103200 chr4A 90.909 88 3 3 3790 3874 520188488 520188573 5.380000e-21 113.0
37 TraesCS2A01G103200 chr4D 86.124 1081 88 28 4975 6046 191269892 191270919 0.000000e+00 1109.0
38 TraesCS2A01G103200 chr4D 77.767 1003 202 14 4031 5023 303065740 303066731 1.220000e-166 597.0
39 TraesCS2A01G103200 chr4D 89.820 167 13 3 2464 2627 435010531 435010366 1.850000e-50 211.0
40 TraesCS2A01G103200 chr4D 83.929 224 9 3 6043 6241 191270944 191271165 8.690000e-44 189.0
41 TraesCS2A01G103200 chr4D 94.118 85 2 2 3793 3874 191269541 191269625 6.910000e-25 126.0
42 TraesCS2A01G103200 chr7D 88.550 917 84 13 5144 6046 559668816 559667907 0.000000e+00 1092.0
43 TraesCS2A01G103200 chr7D 80.822 219 16 9 6048 6241 559667877 559667660 1.470000e-31 148.0
44 TraesCS2A01G103200 chr7D 93.407 91 2 4 3790 3877 559671250 559671161 1.490000e-26 132.0
45 TraesCS2A01G103200 chr7B 84.098 1025 76 38 5272 6241 620579452 620580444 0.000000e+00 909.0
46 TraesCS2A01G103200 chr7B 88.321 274 26 5 4975 5243 620573622 620573894 2.280000e-84 324.0
47 TraesCS2A01G103200 chr7A 82.936 838 97 31 2995 3826 352983471 352982674 0.000000e+00 713.0
48 TraesCS2A01G103200 chr7A 88.024 167 17 2 2460 2624 534325467 534325632 1.870000e-45 195.0
49 TraesCS2A01G103200 chr7A 86.207 174 16 5 2460 2627 717441153 717441324 1.450000e-41 182.0
50 TraesCS2A01G103200 chr4B 77.888 1004 201 16 4031 5023 377789899 377790892 7.280000e-169 604.0
51 TraesCS2A01G103200 chr1B 90.964 166 10 2 2464 2624 515918594 515918429 1.110000e-52 219.0
52 TraesCS2A01G103200 chr5D 92.053 151 10 1 2476 2624 377988152 377988002 1.850000e-50 211.0
53 TraesCS2A01G103200 chr5D 90.123 162 14 1 2468 2627 529218324 529218163 6.670000e-50 209.0
54 TraesCS2A01G103200 chr5D 92.045 88 4 2 3790 3874 482214814 482214901 3.210000e-23 121.0
55 TraesCS2A01G103200 chr5A 89.412 170 15 2 2465 2631 426896741 426896910 1.850000e-50 211.0
56 TraesCS2A01G103200 chr1D 89.697 165 15 1 2462 2624 286378485 286378321 6.670000e-50 209.0
57 TraesCS2A01G103200 chr6B 88.068 176 16 4 2455 2627 633056576 633056403 3.100000e-48 204.0
58 TraesCS2A01G103200 chr3D 93.182 88 3 2 3790 3874 12627987 12628074 6.910000e-25 126.0
59 TraesCS2A01G103200 chr3D 93.023 86 2 3 3796 3877 253557853 253557768 8.940000e-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 TraesCS2A01G103200 chr2A 56917928 56924491 6563 True 2825.750000 10486 96.511500 1 6564 4 chr2A.!!$R1 6563
1 TraesCS2A01G103200 chr2A 44389502 44392308 2806 False 223.400000 507 92.458800 86 1576 5 chr2A.!!$F1 1490
2 TraesCS2A01G103200 chr2D 39827428 39830808 3380 False 2682.000000 5014 93.651000 3124 6564 2 chr2D.!!$F3 3440
3 TraesCS2A01G103200 chr2D 55369405 55375603 6198 True 1321.500000 4420 94.573500 72 6007 6 chr2D.!!$R3 5935
4 TraesCS2A01G103200 chr2D 39819606 39821540 1934 False 964.333333 2639 92.364667 1162 3057 3 chr2D.!!$F2 1895
5 TraesCS2A01G103200 chr2B 87842791 87848834 6043 True 985.575000 3568 92.348750 102 6281 8 chr2B.!!$R2 6179
6 TraesCS2A01G103200 chr4A 520188488 520190187 1699 False 662.500000 1212 87.420000 3790 6241 2 chr4A.!!$F2 2451
7 TraesCS2A01G103200 chr4A 176597076 176598069 993 True 577.000000 577 77.390000 4031 5023 1 chr4A.!!$R1 992
8 TraesCS2A01G103200 chr4D 303065740 303066731 991 False 597.000000 597 77.767000 4031 5023 1 chr4D.!!$F1 992
9 TraesCS2A01G103200 chr4D 191269541 191271165 1624 False 474.666667 1109 88.057000 3793 6241 3 chr4D.!!$F2 2448
10 TraesCS2A01G103200 chr7D 559667660 559671250 3590 True 457.333333 1092 87.593000 3790 6241 3 chr7D.!!$R1 2451
11 TraesCS2A01G103200 chr7B 620579452 620580444 992 False 909.000000 909 84.098000 5272 6241 1 chr7B.!!$F2 969
12 TraesCS2A01G103200 chr7A 352982674 352983471 797 True 713.000000 713 82.936000 2995 3826 1 chr7A.!!$R1 831
13 TraesCS2A01G103200 chr4B 377789899 377790892 993 False 604.000000 604 77.888000 4031 5023 1 chr4B.!!$F1 992

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
19 20 1.335935 CCATCGCGCGAAATGTTTTT 58.664 45.000 38.07 15.27 0.00 1.94 F
117 118 2.222027 GAACTGAGTTGGTTCCTGGTG 58.778 52.381 0.90 0.00 37.63 4.17 F
192 1928 2.352617 GGCAATTTGGCAAAGACGATGA 60.353 45.455 18.61 0.00 43.14 2.92 F
1138 3247 2.612251 CCCCTCCCTCTCCCTCTC 59.388 72.222 0.00 0.00 0.00 3.20 F
1148 3257 0.047176 TCTCCCTCTCTCTCCCCTCT 59.953 60.000 0.00 0.00 0.00 3.69 F
1154 3263 0.047176 TCTCTCTCCCCTCTCCCTCT 59.953 60.000 0.00 0.00 0.00 3.69 F
1156 3265 0.047176 TCTCTCCCCTCTCCCTCTCT 59.953 60.000 0.00 0.00 0.00 3.10 F
1159 3268 0.105709 CTCCCCTCTCCCTCTCTTCC 60.106 65.000 0.00 0.00 0.00 3.46 F
2024 4354 0.544697 ATAACCCGGTGCCCAGTTAG 59.455 55.000 0.00 0.00 29.50 2.34 F
2630 5071 2.028385 GGAACGGAGGAAGTAGAAGCAA 60.028 50.000 0.00 0.00 0.00 3.91 F
3595 6555 1.344763 GCCCGCTCATACTATCCAAGT 59.655 52.381 0.00 0.00 42.62 3.16 F
4546 9712 2.418609 GGCATGAAATACTGGTTTGCCC 60.419 50.000 0.00 0.00 34.18 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 3238 0.047176 AGAGGGGAGAGAGAGGGAGA 59.953 60.000 0.00 0.00 0.00 3.71 R
1137 3246 0.047176 AGAGAGGGAGAGGGGAGAGA 59.953 60.000 0.00 0.00 0.00 3.10 R
1140 3249 0.105709 GGAAGAGAGGGAGAGGGGAG 60.106 65.000 0.00 0.00 0.00 4.30 R
2508 4937 0.179084 TTGCTCAGTATGTAGCCCGC 60.179 55.000 0.00 0.00 38.10 6.13 R
2961 5408 1.106944 CCCTTCACAACCTTTGGCGT 61.107 55.000 0.00 0.00 34.12 5.68 R
2971 5418 5.047566 TCTTTCAGTTGATCCCTTCACAA 57.952 39.130 0.00 0.00 32.84 3.33 R
2988 5435 5.147162 CAGAAGGCGTACAATTGTTCTTTC 58.853 41.667 17.78 16.35 0.00 2.62 R
3023 5470 5.705905 AGCCCAGTTCTGAAAAATACAGTAC 59.294 40.000 1.00 0.00 36.44 2.73 R
3571 6531 0.679505 GATAGTATGAGCGGGCCACA 59.320 55.000 4.39 0.24 0.00 4.17 R
3604 6564 0.957888 GTGCCTCCTGTCCTTGAAGC 60.958 60.000 0.00 0.00 0.00 3.86 R
5028 10231 2.624838 AGCATGAAACCAACAGACAAGG 59.375 45.455 0.00 0.00 0.00 3.61 R
5635 10908 0.826715 GAGCTACAGGCATCCAGTCA 59.173 55.000 0.00 0.00 44.79 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.763593 CCATCGCGCGAAATGTTT 57.236 50.000 38.07 17.01 0.00 2.83
18 19 3.014369 CCATCGCGCGAAATGTTTT 57.986 47.368 38.07 16.14 0.00 2.43
19 20 1.335935 CCATCGCGCGAAATGTTTTT 58.664 45.000 38.07 15.27 0.00 1.94
117 118 2.222027 GAACTGAGTTGGTTCCTGGTG 58.778 52.381 0.90 0.00 37.63 4.17
192 1928 2.352617 GGCAATTTGGCAAAGACGATGA 60.353 45.455 18.61 0.00 43.14 2.92
297 2047 3.700350 CACTCCCTCCCCTCCCCT 61.700 72.222 0.00 0.00 0.00 4.79
298 2048 3.369388 ACTCCCTCCCCTCCCCTC 61.369 72.222 0.00 0.00 0.00 4.30
1137 3246 3.039526 CCCCCTCCCTCTCCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
1138 3247 2.612251 CCCCTCCCTCTCCCTCTC 59.388 72.222 0.00 0.00 0.00 3.20
1139 3248 2.018086 CCCCTCCCTCTCCCTCTCT 61.018 68.421 0.00 0.00 0.00 3.10
1140 3249 1.541672 CCCTCCCTCTCCCTCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
1141 3250 0.998945 CCCTCCCTCTCCCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1142 3251 0.478507 CCTCCCTCTCCCTCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1143 3252 0.478507 CTCCCTCTCCCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
1144 3253 0.996762 TCCCTCTCCCTCTCTCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
1145 3254 1.541672 CCTCTCCCTCTCTCTCCCC 59.458 68.421 0.00 0.00 0.00 4.81
1146 3255 0.998945 CCTCTCCCTCTCTCTCCCCT 60.999 65.000 0.00 0.00 0.00 4.79
1147 3256 0.478507 CTCTCCCTCTCTCTCCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
1148 3257 0.047176 TCTCCCTCTCTCTCCCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
1149 3258 0.478507 CTCCCTCTCTCTCCCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1150 3259 0.996762 TCCCTCTCTCTCCCCTCTCC 60.997 65.000 0.00 0.00 0.00 3.71
1151 3260 1.541672 CCTCTCTCTCCCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
1152 3261 0.998945 CCTCTCTCTCCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
1153 3262 0.478507 CTCTCTCTCCCCTCTCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
1154 3263 0.047176 TCTCTCTCCCCTCTCCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
1155 3264 0.478507 CTCTCTCCCCTCTCCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1156 3265 0.047176 TCTCTCCCCTCTCCCTCTCT 59.953 60.000 0.00 0.00 0.00 3.10
1157 3266 0.933700 CTCTCCCCTCTCCCTCTCTT 59.066 60.000 0.00 0.00 0.00 2.85
1158 3267 0.930726 TCTCCCCTCTCCCTCTCTTC 59.069 60.000 0.00 0.00 0.00 2.87
1159 3268 0.105709 CTCCCCTCTCCCTCTCTTCC 60.106 65.000 0.00 0.00 0.00 3.46
1160 3269 1.074850 CCCCTCTCCCTCTCTTCCC 60.075 68.421 0.00 0.00 0.00 3.97
1250 3548 3.323979 TCTCTGGATTATTAACCGCCTCC 59.676 47.826 0.00 0.00 0.00 4.30
1316 3615 2.666190 CGACAGGTGTGGCACTGG 60.666 66.667 19.83 7.91 34.40 4.00
1473 3775 2.501610 GCTGTCGATCCAGTCCCC 59.498 66.667 5.09 0.00 34.84 4.81
1497 3800 1.636148 AAGTAGCGGTACAGGTTGGA 58.364 50.000 25.28 0.00 0.00 3.53
1577 3883 1.079405 TTCCGTGATGGCGACCTTC 60.079 57.895 0.00 0.00 37.80 3.46
1605 3911 5.289595 TGTCTAGTCATCATCGTTTATGGC 58.710 41.667 0.00 0.00 36.15 4.40
1611 3917 0.927537 TCATCGTTTATGGCGCTTCG 59.072 50.000 7.64 3.82 36.15 3.79
1649 3955 4.945246 ACTCGGAATTAAGCATATGACGT 58.055 39.130 6.97 0.00 0.00 4.34
1655 3976 6.373779 GGAATTAAGCATATGACGTTCATGG 58.626 40.000 6.97 4.75 37.70 3.66
1664 3985 2.234143 TGACGTTCATGGAATGGCAAA 58.766 42.857 4.30 0.00 42.72 3.68
1666 3987 2.228822 GACGTTCATGGAATGGCAAACT 59.771 45.455 0.00 0.00 46.73 2.66
1693 4014 2.899976 TGGTGTAGTGTCTGTTGTGTG 58.100 47.619 0.00 0.00 0.00 3.82
1694 4015 2.235155 TGGTGTAGTGTCTGTTGTGTGT 59.765 45.455 0.00 0.00 0.00 3.72
1695 4016 3.267483 GGTGTAGTGTCTGTTGTGTGTT 58.733 45.455 0.00 0.00 0.00 3.32
1696 4017 4.081586 TGGTGTAGTGTCTGTTGTGTGTTA 60.082 41.667 0.00 0.00 0.00 2.41
1697 4018 4.506654 GGTGTAGTGTCTGTTGTGTGTTAG 59.493 45.833 0.00 0.00 0.00 2.34
1698 4019 4.506654 GTGTAGTGTCTGTTGTGTGTTAGG 59.493 45.833 0.00 0.00 0.00 2.69
1699 4020 2.561569 AGTGTCTGTTGTGTGTTAGGC 58.438 47.619 0.00 0.00 0.00 3.93
1700 4021 2.170607 AGTGTCTGTTGTGTGTTAGGCT 59.829 45.455 0.00 0.00 0.00 4.58
1736 4059 9.968870 GTTGAGATACCGTTCTCTTCTTATAAT 57.031 33.333 8.25 0.00 42.22 1.28
1738 4061 9.575868 TGAGATACCGTTCTCTTCTTATAATCT 57.424 33.333 8.25 0.00 42.22 2.40
1789 4112 7.432252 ACTCGATTTTCACTTTGTTTCATGTTC 59.568 33.333 0.00 0.00 0.00 3.18
1824 4152 9.349713 TGAAGGATAACAAAGTATTTCAACAGT 57.650 29.630 0.00 0.00 35.03 3.55
1840 4168 2.936202 ACAGTGCAGTTCAAGAATGGT 58.064 42.857 0.00 0.00 0.00 3.55
1868 4196 1.858091 CATCTGCGATACCTCACACC 58.142 55.000 0.00 0.00 0.00 4.16
1877 4206 4.142881 GCGATACCTCACACCTTCTTTTTC 60.143 45.833 0.00 0.00 0.00 2.29
2006 4335 5.609533 AGGTACCGCATAGTAACAGAAAT 57.390 39.130 6.18 0.00 32.01 2.17
2024 4354 0.544697 ATAACCCGGTGCCCAGTTAG 59.455 55.000 0.00 0.00 29.50 2.34
2031 4362 2.496111 CGGTGCCCAGTTAGTTTTGTA 58.504 47.619 0.00 0.00 0.00 2.41
2036 4368 6.285224 GGTGCCCAGTTAGTTTTGTATTTTT 58.715 36.000 0.00 0.00 0.00 1.94
2037 4369 6.201997 GGTGCCCAGTTAGTTTTGTATTTTTG 59.798 38.462 0.00 0.00 0.00 2.44
2038 4370 6.759356 GTGCCCAGTTAGTTTTGTATTTTTGT 59.241 34.615 0.00 0.00 0.00 2.83
2039 4371 6.981559 TGCCCAGTTAGTTTTGTATTTTTGTC 59.018 34.615 0.00 0.00 0.00 3.18
2040 4372 7.147811 TGCCCAGTTAGTTTTGTATTTTTGTCT 60.148 33.333 0.00 0.00 0.00 3.41
2081 4413 5.468072 AGTGAATCAGTGAAAGTGTTGCTAG 59.532 40.000 0.00 0.00 38.75 3.42
2158 4490 8.459911 ACATGGTATACTTATTAGCAAAACCC 57.540 34.615 2.25 0.00 0.00 4.11
2185 4519 3.402628 TTGTGCCTTTGAGGTCTACTC 57.597 47.619 0.00 0.00 46.78 2.59
2269 4615 7.559335 TGATAATGTGATATGCCCTAAGACT 57.441 36.000 0.00 0.00 0.00 3.24
2493 4922 8.925338 TCCCTCTGTTCCTAAATATAAGTCTTC 58.075 37.037 0.00 0.00 0.00 2.87
2512 4941 5.007136 GTCTTCTTAGAGATTTCAATGCGGG 59.993 44.000 0.00 0.00 0.00 6.13
2630 5071 2.028385 GGAACGGAGGAAGTAGAAGCAA 60.028 50.000 0.00 0.00 0.00 3.91
2631 5072 3.369576 GGAACGGAGGAAGTAGAAGCAAT 60.370 47.826 0.00 0.00 0.00 3.56
2632 5073 3.983044 ACGGAGGAAGTAGAAGCAATT 57.017 42.857 0.00 0.00 0.00 2.32
2633 5074 4.287766 ACGGAGGAAGTAGAAGCAATTT 57.712 40.909 0.00 0.00 0.00 1.82
2634 5075 5.416271 ACGGAGGAAGTAGAAGCAATTTA 57.584 39.130 0.00 0.00 0.00 1.40
2635 5076 5.990668 ACGGAGGAAGTAGAAGCAATTTAT 58.009 37.500 0.00 0.00 0.00 1.40
2636 5077 6.415573 ACGGAGGAAGTAGAAGCAATTTATT 58.584 36.000 0.00 0.00 0.00 1.40
2637 5078 6.539103 ACGGAGGAAGTAGAAGCAATTTATTC 59.461 38.462 0.00 0.00 0.00 1.75
2638 5079 6.763610 CGGAGGAAGTAGAAGCAATTTATTCT 59.236 38.462 7.02 7.02 39.13 2.40
2639 5080 7.926555 CGGAGGAAGTAGAAGCAATTTATTCTA 59.073 37.037 5.41 5.41 37.05 2.10
2803 5244 3.903530 ACAACCTCCCTTTCTTTGGAT 57.096 42.857 0.00 0.00 0.00 3.41
2889 5331 5.133221 GGTCTTTTATCCTGTATGGTGCAT 58.867 41.667 0.00 0.00 37.07 3.96
2926 5373 7.547370 AGCTTTACATCTGACTCAGTAATTGAC 59.453 37.037 5.94 0.00 32.61 3.18
2961 5408 3.388676 TCTTCCGGTACCAAGAACTGAAA 59.611 43.478 13.54 0.00 0.00 2.69
2971 5418 2.052782 AGAACTGAAACGCCAAAGGT 57.947 45.000 0.00 0.00 0.00 3.50
2988 5435 3.146104 AGGTTGTGAAGGGATCAACTG 57.854 47.619 0.00 0.00 40.50 3.16
3023 5470 4.297299 ACGCCTTCTGCATTCAAATATG 57.703 40.909 0.00 0.00 41.33 1.78
3097 5544 8.887717 TGTTTAGTCAACAAAATGGAAATTTGG 58.112 29.630 0.00 0.00 42.76 3.28
3098 5545 8.341903 GTTTAGTCAACAAAATGGAAATTTGGG 58.658 33.333 0.00 0.00 41.08 4.12
3099 5546 5.375773 AGTCAACAAAATGGAAATTTGGGG 58.624 37.500 0.00 0.00 41.08 4.96
3100 5547 4.518590 GTCAACAAAATGGAAATTTGGGGG 59.481 41.667 0.00 0.00 41.08 5.40
3363 6323 4.897670 CCTCCCCTTATCTTTGCATCAATT 59.102 41.667 0.00 0.00 0.00 2.32
3571 6531 8.141909 GTGAAAAGGCTAAAAGACCAACTATTT 58.858 33.333 0.00 0.00 0.00 1.40
3595 6555 1.344763 GCCCGCTCATACTATCCAAGT 59.655 52.381 0.00 0.00 42.62 3.16
3697 6657 2.629051 TCTGCTGTTGATGCTGATCTG 58.371 47.619 0.00 0.00 34.36 2.90
3740 6700 9.583765 ACATTTTTAACGGTTAAGCTTTTGTTA 57.416 25.926 3.20 6.37 0.00 2.41
3748 6708 6.854381 ACGGTTAAGCTTTTGTTATCTTTTCG 59.146 34.615 3.20 0.00 0.00 3.46
4546 9712 2.418609 GGCATGAAATACTGGTTTGCCC 60.419 50.000 0.00 0.00 34.18 5.36
4984 10169 7.969690 TTGGATAAATGGAGGAAGCATAAAA 57.030 32.000 0.00 0.00 0.00 1.52
5028 10231 5.066117 GCTCCTTAAACAGGTTGGTATAAGC 59.934 44.000 0.00 0.00 44.37 3.09
5032 10237 6.127730 CCTTAAACAGGTTGGTATAAGCCTTG 60.128 42.308 0.00 0.00 37.99 3.61
5036 10241 3.941483 CAGGTTGGTATAAGCCTTGTCTG 59.059 47.826 0.00 0.00 0.00 3.51
5168 10378 3.748083 CATGGAATAGGTAGCATGCTGT 58.252 45.455 30.42 16.39 0.00 4.40
5580 10836 3.579709 CGTAGCACACTTGATCAGAACT 58.420 45.455 0.00 0.00 0.00 3.01
5596 10852 5.838529 TCAGAACTATCGACAACAGTTTGA 58.161 37.500 0.00 0.68 36.48 2.69
5614 10870 0.980231 GAGACATCCACTGGCCTCCT 60.980 60.000 3.32 0.00 30.62 3.69
5619 10875 0.551131 ATCCACTGGCCTCCTCCTTT 60.551 55.000 3.32 0.00 0.00 3.11
5626 10899 0.922626 GGCCTCCTCCTTTGAATCCT 59.077 55.000 0.00 0.00 0.00 3.24
5635 10908 4.224818 CCTCCTTTGAATCCTTCTCTGTCT 59.775 45.833 0.00 0.00 0.00 3.41
5813 11089 3.067180 CAGATTGATTGATGGTTTCGGGG 59.933 47.826 0.00 0.00 0.00 5.73
6098 11418 1.457346 CAGTGTCCATGGCTCCTTTC 58.543 55.000 6.96 0.00 0.00 2.62
6145 11490 1.741528 TGGCATGTATCAGTGCACTG 58.258 50.000 36.07 36.07 43.00 3.66
6222 11567 0.310854 CGTGGAACTGAAACTTGGGC 59.689 55.000 0.00 0.00 31.75 5.36
6228 11573 1.021968 ACTGAAACTTGGGCAACGAC 58.978 50.000 0.00 0.00 37.60 4.34
6245 11595 3.713288 ACGACGAATCTGAAACTGACAA 58.287 40.909 0.00 0.00 0.00 3.18
6261 11611 3.044305 AACAACGAGCCAGCGAGC 61.044 61.111 0.00 0.00 34.83 5.03
6281 11631 2.674852 GCAATCACTCGAGCAGATCAAA 59.325 45.455 13.61 0.00 0.00 2.69
6282 11632 3.484886 GCAATCACTCGAGCAGATCAAAC 60.485 47.826 13.61 3.81 0.00 2.93
6283 11633 1.982612 TCACTCGAGCAGATCAAACG 58.017 50.000 13.61 0.00 0.00 3.60
6284 11634 1.539827 TCACTCGAGCAGATCAAACGA 59.460 47.619 13.61 0.00 0.00 3.85
6285 11635 1.651138 CACTCGAGCAGATCAAACGAC 59.349 52.381 13.61 0.00 0.00 4.34
6286 11636 1.272781 CTCGAGCAGATCAAACGACC 58.727 55.000 0.00 0.00 0.00 4.79
6287 11637 0.601057 TCGAGCAGATCAAACGACCA 59.399 50.000 0.00 0.00 0.00 4.02
6288 11638 1.000394 TCGAGCAGATCAAACGACCAA 60.000 47.619 0.00 0.00 0.00 3.67
6289 11639 2.002586 CGAGCAGATCAAACGACCAAT 58.997 47.619 0.00 0.00 0.00 3.16
6290 11640 2.222886 CGAGCAGATCAAACGACCAATG 60.223 50.000 0.00 0.00 0.00 2.82
6291 11641 2.086869 AGCAGATCAAACGACCAATGG 58.913 47.619 0.00 0.00 0.00 3.16
6292 11642 1.468054 GCAGATCAAACGACCAATGGC 60.468 52.381 0.00 0.00 0.00 4.40
6293 11643 2.086869 CAGATCAAACGACCAATGGCT 58.913 47.619 0.00 0.00 0.00 4.75
6294 11644 2.086869 AGATCAAACGACCAATGGCTG 58.913 47.619 0.00 0.00 0.00 4.85
6295 11645 2.083774 GATCAAACGACCAATGGCTGA 58.916 47.619 0.00 0.00 0.00 4.26
6296 11646 2.198827 TCAAACGACCAATGGCTGAT 57.801 45.000 0.00 0.00 0.00 2.90
6297 11647 2.513753 TCAAACGACCAATGGCTGATT 58.486 42.857 0.00 0.00 0.00 2.57
6298 11648 2.228582 TCAAACGACCAATGGCTGATTG 59.771 45.455 0.00 3.63 41.20 2.67
6299 11649 2.198827 AACGACCAATGGCTGATTGA 57.801 45.000 0.00 0.00 43.87 2.57
6300 11650 2.198827 ACGACCAATGGCTGATTGAA 57.801 45.000 0.00 0.00 43.87 2.69
6301 11651 2.086869 ACGACCAATGGCTGATTGAAG 58.913 47.619 0.00 4.60 43.87 3.02
6302 11652 2.290260 ACGACCAATGGCTGATTGAAGA 60.290 45.455 0.00 0.00 43.87 2.87
6303 11653 2.749076 CGACCAATGGCTGATTGAAGAA 59.251 45.455 0.00 0.00 43.87 2.52
6304 11654 3.181503 CGACCAATGGCTGATTGAAGAAG 60.182 47.826 0.00 0.00 43.87 2.85
6305 11655 2.494870 ACCAATGGCTGATTGAAGAAGC 59.505 45.455 0.00 0.00 43.87 3.86
6306 11656 2.494471 CCAATGGCTGATTGAAGAAGCA 59.506 45.455 9.71 0.00 43.87 3.91
6319 11669 5.329035 TGAAGAAGCAATCAAATAAGCCC 57.671 39.130 0.00 0.00 0.00 5.19
6347 11697 9.594478 AAGGAACAAATTAACTTGTAAACCTTG 57.406 29.630 22.56 0.00 41.01 3.61
6386 11736 7.949690 AAAATTTGGTCATCATCTCATCTGA 57.050 32.000 0.00 0.00 0.00 3.27
6387 11737 7.949690 AAATTTGGTCATCATCTCATCTGAA 57.050 32.000 0.00 0.00 0.00 3.02
6388 11738 7.949690 AATTTGGTCATCATCTCATCTGAAA 57.050 32.000 0.00 0.00 0.00 2.69
6389 11739 6.748333 TTTGGTCATCATCTCATCTGAAAC 57.252 37.500 0.00 0.00 0.00 2.78
6390 11740 4.436332 TGGTCATCATCTCATCTGAAACG 58.564 43.478 0.00 0.00 0.00 3.60
6391 11741 3.247173 GGTCATCATCTCATCTGAAACGC 59.753 47.826 0.00 0.00 0.00 4.84
6392 11742 3.867493 GTCATCATCTCATCTGAAACGCA 59.133 43.478 0.00 0.00 0.00 5.24
6393 11743 4.510711 GTCATCATCTCATCTGAAACGCAT 59.489 41.667 0.00 0.00 0.00 4.73
6394 11744 4.510340 TCATCATCTCATCTGAAACGCATG 59.490 41.667 0.00 0.00 0.00 4.06
6395 11745 3.200483 TCATCTCATCTGAAACGCATGG 58.800 45.455 0.00 0.00 0.00 3.66
6403 11753 5.237127 TCATCTGAAACGCATGGATGTATTC 59.763 40.000 0.00 0.00 36.27 1.75
6410 11760 5.845985 ACGCATGGATGTATTCGAAATAG 57.154 39.130 0.00 0.00 0.00 1.73
6436 11786 3.795623 TTCCAACATCCTACGTAGCTC 57.204 47.619 17.41 0.00 0.00 4.09
6444 11794 4.894114 ACATCCTACGTAGCTCCTATTGTT 59.106 41.667 17.41 0.00 0.00 2.83
6506 11856 1.060729 TCCCCTCGTCCACAATGAAA 58.939 50.000 0.00 0.00 0.00 2.69
6526 11876 0.531974 TAGGCAAACGGATGATCGGC 60.532 55.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.335935 AAAAACATTTCGCGCGATGG 58.664 45.000 35.21 26.13 0.00 3.51
70 71 5.368989 ACAGTTTCCCAACAACAACAAAAA 58.631 33.333 0.00 0.00 35.05 1.94
71 72 4.962155 ACAGTTTCCCAACAACAACAAAA 58.038 34.783 0.00 0.00 35.05 2.44
72 73 4.608948 ACAGTTTCCCAACAACAACAAA 57.391 36.364 0.00 0.00 35.05 2.83
73 74 4.158764 CCTACAGTTTCCCAACAACAACAA 59.841 41.667 0.00 0.00 35.05 2.83
74 75 3.697045 CCTACAGTTTCCCAACAACAACA 59.303 43.478 0.00 0.00 35.05 3.33
75 76 3.067601 CCCTACAGTTTCCCAACAACAAC 59.932 47.826 0.00 0.00 35.05 3.32
76 77 3.053544 TCCCTACAGTTTCCCAACAACAA 60.054 43.478 0.00 0.00 35.05 2.83
77 78 2.510382 TCCCTACAGTTTCCCAACAACA 59.490 45.455 0.00 0.00 35.05 3.33
78 79 3.217681 TCCCTACAGTTTCCCAACAAC 57.782 47.619 0.00 0.00 35.05 3.32
81 82 3.146847 CAGTTCCCTACAGTTTCCCAAC 58.853 50.000 0.00 0.00 0.00 3.77
85 86 4.065789 CAACTCAGTTCCCTACAGTTTCC 58.934 47.826 0.00 0.00 0.00 3.13
137 142 1.131826 CGATTGAAACGGGTCGTGC 59.868 57.895 0.00 0.00 39.99 5.34
1122 3112 0.998945 AGAGAGAGGGAGAGGGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
1125 3115 0.996762 GGGAGAGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
1128 3237 0.478507 GAGGGGAGAGAGAGGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
1129 3238 0.047176 AGAGGGGAGAGAGAGGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
1130 3239 0.478507 GAGAGGGGAGAGAGAGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
1131 3240 0.996762 GGAGAGGGGAGAGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
1132 3241 1.541672 GGAGAGGGGAGAGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
1133 3242 0.998945 AGGGAGAGGGGAGAGAGAGG 60.999 65.000 0.00 0.00 0.00 3.69
1134 3243 0.478507 GAGGGAGAGGGGAGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
1135 3244 0.047176 AGAGGGAGAGGGGAGAGAGA 59.953 60.000 0.00 0.00 0.00 3.10
1136 3245 0.478507 GAGAGGGAGAGGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
1137 3246 0.047176 AGAGAGGGAGAGGGGAGAGA 59.953 60.000 0.00 0.00 0.00 3.10
1138 3247 0.933700 AAGAGAGGGAGAGGGGAGAG 59.066 60.000 0.00 0.00 0.00 3.20
1139 3248 0.930726 GAAGAGAGGGAGAGGGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
1140 3249 0.105709 GGAAGAGAGGGAGAGGGGAG 60.106 65.000 0.00 0.00 0.00 4.30
1141 3250 1.595058 GGGAAGAGAGGGAGAGGGGA 61.595 65.000 0.00 0.00 0.00 4.81
1142 3251 1.074850 GGGAAGAGAGGGAGAGGGG 60.075 68.421 0.00 0.00 0.00 4.79
1143 3252 1.074850 GGGGAAGAGAGGGAGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
1144 3253 1.074850 GGGGGAAGAGAGGGAGAGG 60.075 68.421 0.00 0.00 0.00 3.69
1145 3254 1.456705 CGGGGGAAGAGAGGGAGAG 60.457 68.421 0.00 0.00 0.00 3.20
1146 3255 1.297409 ATCGGGGGAAGAGAGGGAGA 61.297 60.000 0.00 0.00 0.00 3.71
1147 3256 0.399233 AATCGGGGGAAGAGAGGGAG 60.399 60.000 0.00 0.00 0.00 4.30
1148 3257 0.691078 CAATCGGGGGAAGAGAGGGA 60.691 60.000 0.00 0.00 0.00 4.20
1149 3258 1.700042 CCAATCGGGGGAAGAGAGGG 61.700 65.000 0.00 0.00 0.00 4.30
1150 3259 1.832912 CCAATCGGGGGAAGAGAGG 59.167 63.158 0.00 0.00 0.00 3.69
1226 3510 4.704965 AGGCGGTTAATAATCCAGAGAAC 58.295 43.478 0.00 0.00 0.00 3.01
1250 3548 2.053627 GCATCGCAAACCAGTCAAAAG 58.946 47.619 0.00 0.00 0.00 2.27
1473 3775 1.068055 ACCTGTACCGCTACTTTGACG 60.068 52.381 0.00 0.00 0.00 4.35
1497 3800 0.336048 AAAGGGGTATGGCAGCACAT 59.664 50.000 0.00 0.00 34.90 3.21
1557 3863 2.047655 GGTCGCCATCACGGAACA 60.048 61.111 0.00 0.00 36.56 3.18
1605 3911 1.126846 GAATCTTCACACCACGAAGCG 59.873 52.381 0.00 0.00 39.80 4.68
1611 3917 3.192844 TCCGAGTAGAATCTTCACACCAC 59.807 47.826 0.00 0.00 0.00 4.16
1693 4014 4.755123 TCTCAACAAAGCTAACAGCCTAAC 59.245 41.667 0.00 0.00 43.77 2.34
1694 4015 4.968259 TCTCAACAAAGCTAACAGCCTAA 58.032 39.130 0.00 0.00 43.77 2.69
1695 4016 4.617253 TCTCAACAAAGCTAACAGCCTA 57.383 40.909 0.00 0.00 43.77 3.93
1696 4017 3.492102 TCTCAACAAAGCTAACAGCCT 57.508 42.857 0.00 0.00 43.77 4.58
1697 4018 4.095036 GGTATCTCAACAAAGCTAACAGCC 59.905 45.833 0.00 0.00 43.77 4.85
1698 4019 4.201724 CGGTATCTCAACAAAGCTAACAGC 60.202 45.833 0.00 0.00 42.84 4.40
1699 4020 4.929808 ACGGTATCTCAACAAAGCTAACAG 59.070 41.667 0.00 0.00 0.00 3.16
1700 4021 4.890088 ACGGTATCTCAACAAAGCTAACA 58.110 39.130 0.00 0.00 0.00 2.41
1736 4059 1.284785 CATTCCCCCTGGTGCTAAAGA 59.715 52.381 0.00 0.00 0.00 2.52
1738 4061 1.080638 ACATTCCCCCTGGTGCTAAA 58.919 50.000 0.00 0.00 0.00 1.85
1789 4112 9.784531 ATACTTTGTTATCCTTCATACTCCATG 57.215 33.333 0.00 0.00 35.81 3.66
1818 4146 3.067180 ACCATTCTTGAACTGCACTGTTG 59.933 43.478 0.00 0.00 0.00 3.33
1819 4147 3.290710 ACCATTCTTGAACTGCACTGTT 58.709 40.909 0.00 0.00 0.00 3.16
1824 4152 5.534207 AATTTGACCATTCTTGAACTGCA 57.466 34.783 0.00 0.00 0.00 4.41
1840 4168 3.947196 AGGTATCGCAGATGCAAATTTGA 59.053 39.130 22.31 7.50 45.12 2.69
1868 4196 5.414144 GTGGATCCTGAGAAGGAAAAAGAAG 59.586 44.000 14.23 0.00 41.90 2.85
1877 4206 0.835941 CTGGGTGGATCCTGAGAAGG 59.164 60.000 14.23 0.00 36.25 3.46
1889 4218 2.489938 TTCGAAATCTTCCTGGGTGG 57.510 50.000 0.00 0.00 37.10 4.61
1941 4270 3.614806 GGGGGCGATCAATTTGCA 58.385 55.556 0.00 0.00 36.33 4.08
2031 4362 9.466497 TCCTATCTCAAAAGCATAGACAAAAAT 57.534 29.630 0.00 0.00 0.00 1.82
2036 4368 6.381133 TCACTCCTATCTCAAAAGCATAGACA 59.619 38.462 0.00 0.00 0.00 3.41
2037 4369 6.810911 TCACTCCTATCTCAAAAGCATAGAC 58.189 40.000 0.00 0.00 0.00 2.59
2038 4370 7.423844 TTCACTCCTATCTCAAAAGCATAGA 57.576 36.000 0.00 0.00 0.00 1.98
2039 4371 7.930325 TGATTCACTCCTATCTCAAAAGCATAG 59.070 37.037 0.00 0.00 0.00 2.23
2040 4372 7.795047 TGATTCACTCCTATCTCAAAAGCATA 58.205 34.615 0.00 0.00 0.00 3.14
2042 4374 6.053632 TGATTCACTCCTATCTCAAAAGCA 57.946 37.500 0.00 0.00 0.00 3.91
2158 4490 1.269413 CCTCAAAGGCACAAACAGCAG 60.269 52.381 0.00 0.00 0.00 4.24
2185 4519 3.752412 TCGTGATGTACACTTACCTCG 57.248 47.619 0.00 0.00 46.24 4.63
2190 4524 7.134163 CGTGGTATATTCGTGATGTACACTTA 58.866 38.462 0.00 0.00 46.24 2.24
2213 4547 3.057596 CACTGGTTTAAATCATGCCACGT 60.058 43.478 0.65 0.00 0.00 4.49
2269 4615 2.401583 AACCGAGATAGCACATGCAA 57.598 45.000 6.64 0.00 45.16 4.08
2493 4922 3.209410 AGCCCGCATTGAAATCTCTAAG 58.791 45.455 0.00 0.00 0.00 2.18
2508 4937 0.179084 TTGCTCAGTATGTAGCCCGC 60.179 55.000 0.00 0.00 38.10 6.13
2512 4941 5.582269 TCACTCATTTTGCTCAGTATGTAGC 59.418 40.000 0.00 0.00 38.93 3.58
2594 5025 7.949434 TCCTCCGTTCCTAAATATAAGTCTTC 58.051 38.462 0.00 0.00 0.00 2.87
2633 5074 9.983024 TCTGTTTGGAAATATTTGGGTAGAATA 57.017 29.630 5.17 0.00 0.00 1.75
2634 5075 8.749354 GTCTGTTTGGAAATATTTGGGTAGAAT 58.251 33.333 5.17 0.00 0.00 2.40
2635 5076 7.947890 AGTCTGTTTGGAAATATTTGGGTAGAA 59.052 33.333 5.17 0.00 0.00 2.10
2636 5077 7.466804 AGTCTGTTTGGAAATATTTGGGTAGA 58.533 34.615 5.17 0.00 0.00 2.59
2637 5078 7.703058 AGTCTGTTTGGAAATATTTGGGTAG 57.297 36.000 5.17 0.00 0.00 3.18
2638 5079 9.184523 CATAGTCTGTTTGGAAATATTTGGGTA 57.815 33.333 5.17 0.00 0.00 3.69
2639 5080 7.893302 TCATAGTCTGTTTGGAAATATTTGGGT 59.107 33.333 5.17 0.00 0.00 4.51
2724 5165 7.450014 TGTTTGGGTAGAATAAATTGCTTCTCA 59.550 33.333 6.14 0.00 33.83 3.27
2803 5244 8.440059 CGTAAAACAAAACATATAGACAGCTCA 58.560 33.333 0.00 0.00 0.00 4.26
2889 5331 7.715249 AGTCAGATGTAAAGCTAAACAAACAGA 59.285 33.333 5.26 3.62 0.00 3.41
2926 5373 1.860950 CCGGAAGAACTGCATATGTCG 59.139 52.381 0.00 0.00 0.00 4.35
2961 5408 1.106944 CCCTTCACAACCTTTGGCGT 61.107 55.000 0.00 0.00 34.12 5.68
2971 5418 5.047566 TCTTTCAGTTGATCCCTTCACAA 57.952 39.130 0.00 0.00 32.84 3.33
2988 5435 5.147162 CAGAAGGCGTACAATTGTTCTTTC 58.853 41.667 17.78 16.35 0.00 2.62
3023 5470 5.705905 AGCCCAGTTCTGAAAAATACAGTAC 59.294 40.000 1.00 0.00 36.44 2.73
3363 6323 6.614694 TTATAGCAAAACCACTGGACTCTA 57.385 37.500 0.71 0.00 0.00 2.43
3535 6495 8.157476 TCTTTTAGCCTTTTCACTACTGAATCT 58.843 33.333 0.00 0.00 36.26 2.40
3571 6531 0.679505 GATAGTATGAGCGGGCCACA 59.320 55.000 4.39 0.24 0.00 4.17
3595 6555 3.084039 CTGTCCTTGAAGCTTGGCAATA 58.916 45.455 2.10 0.00 0.00 1.90
3604 6564 0.957888 GTGCCTCCTGTCCTTGAAGC 60.958 60.000 0.00 0.00 0.00 3.86
3740 6700 7.161773 ACAATGGAATGAATGACGAAAAGAT 57.838 32.000 0.00 0.00 0.00 2.40
3938 9101 4.001652 GCAGGTTGGGTTTCTACTACTTC 58.998 47.826 0.00 0.00 0.00 3.01
3942 9105 5.968676 ATATGCAGGTTGGGTTTCTACTA 57.031 39.130 0.00 0.00 0.00 1.82
4449 9613 7.824289 TCCTACAAGAACAATAAGAACATCAGG 59.176 37.037 0.00 0.00 0.00 3.86
4546 9712 5.469479 AGGTGCCTTTTTGTATGAATTTCG 58.531 37.500 0.00 0.00 0.00 3.46
4984 10169 5.363939 GAGCAGCAGGTAATTCTCTGTTAT 58.636 41.667 0.00 0.00 33.81 1.89
5028 10231 2.624838 AGCATGAAACCAACAGACAAGG 59.375 45.455 0.00 0.00 0.00 3.61
5032 10237 3.815401 ACTGTAGCATGAAACCAACAGAC 59.185 43.478 7.24 0.00 38.14 3.51
5036 10241 5.880054 ATACACTGTAGCATGAAACCAAC 57.120 39.130 0.00 0.00 0.00 3.77
5135 10344 9.014297 GCTACCTATTCCATGCAAGTAATTATT 57.986 33.333 0.00 0.00 0.00 1.40
5168 10378 7.296628 ACTTGCCCAGTAACAAAAATGAATA 57.703 32.000 0.00 0.00 31.97 1.75
5580 10836 5.168569 GGATGTCTCAAACTGTTGTCGATA 58.831 41.667 0.00 0.00 36.07 2.92
5596 10852 0.980231 GAGGAGGCCAGTGGATGTCT 60.980 60.000 15.20 4.20 0.00 3.41
5626 10899 1.552337 GGCATCCAGTCAGACAGAGAA 59.448 52.381 2.66 0.00 0.00 2.87
5635 10908 0.826715 GAGCTACAGGCATCCAGTCA 59.173 55.000 0.00 0.00 44.79 3.41
5777 11052 4.459390 TCAATCTGTTCAATGCAATGGG 57.541 40.909 1.05 0.00 0.00 4.00
6098 11418 1.195448 GACACACCAATTCAGACGCAG 59.805 52.381 0.00 0.00 0.00 5.18
6145 11490 3.205784 AGAGGTGCTAATCATGCCTTC 57.794 47.619 0.00 0.00 0.00 3.46
6190 11535 1.547372 GTTCCACGCCTAGGTACTCAA 59.453 52.381 11.31 0.00 41.75 3.02
6222 11567 3.489416 TGTCAGTTTCAGATTCGTCGTTG 59.511 43.478 0.00 0.00 0.00 4.10
6228 11573 4.026062 TCGTTGTTGTCAGTTTCAGATTCG 60.026 41.667 0.00 0.00 0.00 3.34
6245 11595 3.807631 TTGCTCGCTGGCTCGTTGT 62.808 57.895 0.00 0.00 0.00 3.32
6261 11611 3.241900 CGTTTGATCTGCTCGAGTGATTG 60.242 47.826 15.13 0.43 0.00 2.67
6281 11631 2.086869 CTTCAATCAGCCATTGGTCGT 58.913 47.619 4.26 0.00 42.18 4.34
6282 11632 2.358957 TCTTCAATCAGCCATTGGTCG 58.641 47.619 4.26 0.00 42.18 4.79
6283 11633 3.428589 GCTTCTTCAATCAGCCATTGGTC 60.429 47.826 4.26 0.00 42.18 4.02
6284 11634 2.494870 GCTTCTTCAATCAGCCATTGGT 59.505 45.455 4.26 0.00 42.18 3.67
6285 11635 2.494471 TGCTTCTTCAATCAGCCATTGG 59.506 45.455 0.00 0.00 42.18 3.16
6286 11636 3.861276 TGCTTCTTCAATCAGCCATTG 57.139 42.857 0.33 0.33 43.15 2.82
6295 11645 6.343703 GGGCTTATTTGATTGCTTCTTCAAT 58.656 36.000 0.00 0.00 39.20 2.57
6296 11646 5.622007 CGGGCTTATTTGATTGCTTCTTCAA 60.622 40.000 0.00 0.00 0.00 2.69
6297 11647 4.142403 CGGGCTTATTTGATTGCTTCTTCA 60.142 41.667 0.00 0.00 0.00 3.02
6298 11648 4.096382 TCGGGCTTATTTGATTGCTTCTTC 59.904 41.667 0.00 0.00 0.00 2.87
6299 11649 4.016444 TCGGGCTTATTTGATTGCTTCTT 58.984 39.130 0.00 0.00 0.00 2.52
6300 11650 3.620488 TCGGGCTTATTTGATTGCTTCT 58.380 40.909 0.00 0.00 0.00 2.85
6301 11651 4.354587 CTTCGGGCTTATTTGATTGCTTC 58.645 43.478 0.00 0.00 0.00 3.86
6302 11652 3.131046 CCTTCGGGCTTATTTGATTGCTT 59.869 43.478 0.00 0.00 0.00 3.91
6303 11653 2.689983 CCTTCGGGCTTATTTGATTGCT 59.310 45.455 0.00 0.00 0.00 3.91
6304 11654 2.687935 TCCTTCGGGCTTATTTGATTGC 59.312 45.455 0.00 0.00 34.44 3.56
6305 11655 4.157656 TGTTCCTTCGGGCTTATTTGATTG 59.842 41.667 0.00 0.00 34.44 2.67
6306 11656 4.340617 TGTTCCTTCGGGCTTATTTGATT 58.659 39.130 0.00 0.00 34.44 2.57
6312 11662 5.949952 AGTTAATTTGTTCCTTCGGGCTTAT 59.050 36.000 0.00 0.00 34.44 1.73
6319 11669 8.132995 AGGTTTACAAGTTAATTTGTTCCTTCG 58.867 33.333 19.79 0.00 41.31 3.79
6366 11716 5.352293 CGTTTCAGATGAGATGATGACCAAA 59.648 40.000 0.00 0.00 0.00 3.28
6367 11717 4.872124 CGTTTCAGATGAGATGATGACCAA 59.128 41.667 0.00 0.00 0.00 3.67
6369 11719 3.247173 GCGTTTCAGATGAGATGATGACC 59.753 47.826 0.00 0.00 0.00 4.02
6371 11721 4.127566 TGCGTTTCAGATGAGATGATGA 57.872 40.909 0.00 0.00 0.00 2.92
6372 11722 4.319549 CCATGCGTTTCAGATGAGATGATG 60.320 45.833 0.00 0.00 0.00 3.07
6373 11723 3.813724 CCATGCGTTTCAGATGAGATGAT 59.186 43.478 0.00 0.00 0.00 2.45
6374 11724 3.118665 TCCATGCGTTTCAGATGAGATGA 60.119 43.478 0.00 0.00 0.00 2.92
6375 11725 3.200483 TCCATGCGTTTCAGATGAGATG 58.800 45.455 0.00 0.00 0.00 2.90
6376 11726 3.548745 TCCATGCGTTTCAGATGAGAT 57.451 42.857 0.00 0.00 0.00 2.75
6378 11728 2.941064 ACATCCATGCGTTTCAGATGAG 59.059 45.455 11.35 0.00 38.15 2.90
6380 11730 5.428496 AATACATCCATGCGTTTCAGATG 57.572 39.130 4.83 4.83 40.12 2.90
6381 11731 4.212004 CGAATACATCCATGCGTTTCAGAT 59.788 41.667 0.00 0.00 0.00 2.90
6382 11732 3.555547 CGAATACATCCATGCGTTTCAGA 59.444 43.478 0.00 0.00 0.00 3.27
6383 11733 3.555547 TCGAATACATCCATGCGTTTCAG 59.444 43.478 0.00 0.00 0.00 3.02
6384 11734 3.526534 TCGAATACATCCATGCGTTTCA 58.473 40.909 0.00 0.00 0.00 2.69
6385 11735 4.530094 TTCGAATACATCCATGCGTTTC 57.470 40.909 0.00 0.00 0.00 2.78
6386 11736 4.955925 TTTCGAATACATCCATGCGTTT 57.044 36.364 0.00 0.00 0.00 3.60
6387 11737 5.179368 CCTATTTCGAATACATCCATGCGTT 59.821 40.000 0.00 0.00 0.00 4.84
6388 11738 4.690748 CCTATTTCGAATACATCCATGCGT 59.309 41.667 0.00 0.00 0.00 5.24
6389 11739 4.093408 CCCTATTTCGAATACATCCATGCG 59.907 45.833 0.00 0.00 0.00 4.73
6390 11740 4.396166 CCCCTATTTCGAATACATCCATGC 59.604 45.833 0.00 0.00 0.00 4.06
6391 11741 5.804639 TCCCCTATTTCGAATACATCCATG 58.195 41.667 0.00 0.00 0.00 3.66
6392 11742 6.448369 TTCCCCTATTTCGAATACATCCAT 57.552 37.500 0.00 0.00 0.00 3.41
6393 11743 5.897851 TTCCCCTATTTCGAATACATCCA 57.102 39.130 0.00 0.00 0.00 3.41
6394 11744 6.374613 GGAATTCCCCTATTTCGAATACATCC 59.625 42.308 14.03 0.00 0.00 3.51
6395 11745 6.940298 TGGAATTCCCCTATTTCGAATACATC 59.060 38.462 21.90 0.00 34.29 3.06
6403 11753 4.278419 GGATGTTGGAATTCCCCTATTTCG 59.722 45.833 21.90 0.00 34.29 3.46
6410 11760 2.092592 ACGTAGGATGTTGGAATTCCCC 60.093 50.000 21.90 14.56 34.29 4.81
6506 11856 1.878102 GCCGATCATCCGTTTGCCTAT 60.878 52.381 0.00 0.00 0.00 2.57
6526 11876 0.887387 ACCGGTGGTGGATTTTGTCG 60.887 55.000 6.12 0.00 32.98 4.35


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

AutoCloner maintained by Alex Coulton.