Multiple sequence alignment - TraesCS1B01G241200

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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 TraesCS1B01G241200 chr1B 100.000 2686 0 0 1 2686 428800718 428803403 0.000000e+00 4961.0
1 TraesCS1B01G241200 chr1D 91.204 1512 86 25 7 1507 316677439 316678914 0.000000e+00 2012.0
2 TraesCS1B01G241200 chr1D 84.725 491 58 14 1973 2454 316679460 316679942 2.420000e-130 475.0
3 TraesCS1B01G241200 chr1D 85.536 401 31 17 1502 1895 316679025 316679405 6.970000e-106 394.0
4 TraesCS1B01G241200 chr1D 96.970 33 1 0 620 652 418766231 418766263 3.740000e-04 56.5
5 TraesCS1B01G241200 chr1A 89.791 911 53 21 897 1803 397769666 397770540 0.000000e+00 1131.0
6 TraesCS1B01G241200 chr1A 87.500 488 35 12 9 488 397769066 397769535 8.460000e-150 540.0
7 TraesCS1B01G241200 chr1A 78.800 750 75 39 1735 2454 397770550 397771245 6.870000e-116 427.0
8 TraesCS1B01G241200 chr1A 94.444 108 6 0 759 866 397769558 397769665 1.650000e-37 167.0
9 TraesCS1B01G241200 chr7D 95.238 231 6 3 2460 2686 616332994 616332765 7.070000e-96 361.0
10 TraesCS1B01G241200 chr7D 87.037 216 28 0 1275 1490 586783769 586783984 7.430000e-61 244.0
11 TraesCS1B01G241200 chr7D 86.111 216 30 0 1275 1490 586765905 586766120 1.610000e-57 233.0
12 TraesCS1B01G241200 chr7D 89.157 166 12 3 961 1120 586765671 586765836 4.530000e-48 202.0
13 TraesCS1B01G241200 chr7D 87.255 102 11 2 1575 1675 586766116 586766216 6.080000e-22 115.0
14 TraesCS1B01G241200 chr7D 87.255 102 11 2 1575 1675 586783980 586784080 6.080000e-22 115.0
15 TraesCS1B01G241200 chr3B 94.492 236 6 5 2456 2686 382000986 382001219 9.140000e-95 357.0
16 TraesCS1B01G241200 chr2B 94.372 231 8 3 2460 2686 412773941 412774170 1.530000e-92 350.0
17 TraesCS1B01G241200 chr2B 92.641 231 11 3 2461 2686 236049769 236049540 7.170000e-86 327.0
18 TraesCS1B01G241200 chr5B 91.837 245 13 5 2448 2686 622464022 622464265 4.280000e-88 335.0
19 TraesCS1B01G241200 chr5B 92.609 230 13 3 2460 2686 616722227 616722455 7.170000e-86 327.0
20 TraesCS1B01G241200 chr5B 97.321 112 3 0 997 1108 445173801 445173912 9.820000e-45 191.0
21 TraesCS1B01G241200 chr4B 92.704 233 10 3 2460 2686 14544228 14543997 1.990000e-86 329.0
22 TraesCS1B01G241200 chr4B 92.672 232 12 2 2460 2686 613380933 613380702 1.990000e-86 329.0
23 TraesCS1B01G241200 chr4B 92.576 229 13 4 2461 2686 4591601 4591828 2.580000e-85 326.0
24 TraesCS1B01G241200 chr4B 94.595 111 6 0 995 1105 5466074 5466184 3.560000e-39 172.0
25 TraesCS1B01G241200 chr7B 87.037 216 28 0 1275 1490 657479569 657479784 7.430000e-61 244.0
26 TraesCS1B01G241200 chr7B 87.037 216 28 0 1275 1490 657496503 657496718 7.430000e-61 244.0
27 TraesCS1B01G241200 chr7B 85.135 222 33 0 1269 1490 657500714 657500935 7.480000e-56 228.0
28 TraesCS1B01G241200 chr7B 85.294 102 13 2 1575 1675 657479780 657479880 1.320000e-18 104.0
29 TraesCS1B01G241200 chr7B 85.294 102 13 2 1575 1675 657496714 657496814 1.320000e-18 104.0
30 TraesCS1B01G241200 chr7B 85.294 102 13 2 1575 1675 657500931 657501031 1.320000e-18 104.0
31 TraesCS1B01G241200 chr7A 87.037 216 28 0 1275 1490 677871600 677871815 7.430000e-61 244.0
32 TraesCS1B01G241200 chr7A 94.309 123 7 0 998 1120 677871397 677871519 3.530000e-44 189.0
33 TraesCS1B01G241200 chr7A 86.275 102 12 2 1575 1675 677871811 677871911 2.830000e-20 110.0
34 TraesCS1B01G241200 chr5D 96.429 112 4 0 997 1108 373763089 373763200 4.570000e-43 185.0
35 TraesCS1B01G241200 chr2D 82.110 218 32 5 1279 1491 565586543 565586328 2.120000e-41 180.0
36 TraesCS1B01G241200 chr2D 87.209 86 11 0 1575 1660 565860989 565860904 6.120000e-17 99.0
37 TraesCS1B01G241200 chr4D 94.595 111 6 0 995 1105 3588706 3588596 3.560000e-39 172.0
38 TraesCS1B01G241200 chr4A 94.595 111 6 0 995 1105 601059805 601059915 3.560000e-39 172.0
39 TraesCS1B01G241200 chr3A 83.133 83 13 1 1987 2068 657398129 657398211 1.030000e-09 75.0


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 TraesCS1B01G241200 chr1B 428800718 428803403 2685 False 4961.000000 4961 100.00000 1 2686 1 chr1B.!!$F1 2685
1 TraesCS1B01G241200 chr1D 316677439 316679942 2503 False 960.333333 2012 87.15500 7 2454 3 chr1D.!!$F2 2447
2 TraesCS1B01G241200 chr1A 397769066 397771245 2179 False 566.250000 1131 87.63375 9 2454 4 chr1A.!!$F1 2445

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
685 699 0.250513 GGAGTGAGGAAAGATGCGGT 59.749 55.0 0.00 0.00 0.00 5.68 F
1224 1241 0.316204 ATGGTGAAGCAGCTGTTTGC 59.684 50.0 21.32 12.46 44.41 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1784 0.107752 CTCTTCTTGGGCCTCAGCTC 60.108 60.0 4.53 0.0 41.29 4.09 R
2604 2858 0.109179 CATTGTGCCGGTTGACATGG 60.109 55.0 1.90 0.0 0.00 3.66 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
45 47 2.414138 GGTTGTTATGTGTGGCGAGTAC 59.586 50.000 0.00 0.00 0.00 2.73
77 79 7.857569 TGTTTGTTGTCTAATTTAAGGACTCG 58.142 34.615 0.00 0.00 0.00 4.18
91 93 3.632333 AGGACTCGGACAACATGATCTA 58.368 45.455 0.00 0.00 0.00 1.98
97 99 6.231211 ACTCGGACAACATGATCTAAAAACT 58.769 36.000 0.00 0.00 0.00 2.66
231 235 9.166173 CTCAATTACTTGTGTTTCATCCTCATA 57.834 33.333 0.00 0.00 33.87 2.15
243 247 7.967854 TGTTTCATCCTCATAGTAATTTTTGCG 59.032 33.333 0.00 0.00 0.00 4.85
301 307 0.830648 CTCCCCTACATTTCGCTGGA 59.169 55.000 0.00 0.00 0.00 3.86
536 549 5.486063 TGACCCTGTTTAGCTATTTCCACTA 59.514 40.000 0.00 0.00 0.00 2.74
537 550 5.990668 ACCCTGTTTAGCTATTTCCACTAG 58.009 41.667 0.00 0.00 0.00 2.57
580 594 2.479566 AGTGCGTCACTCAATCCATT 57.520 45.000 6.67 0.00 41.21 3.16
601 615 9.389755 TCCATTGATATGAATCGAGTTAACAAA 57.610 29.630 8.61 0.00 34.60 2.83
613 627 6.444633 TCGAGTTAACAAAGAAGAGACGATT 58.555 36.000 8.61 0.00 0.00 3.34
614 628 6.921857 TCGAGTTAACAAAGAAGAGACGATTT 59.078 34.615 8.61 0.00 0.00 2.17
618 632 9.706691 AGTTAACAAAGAAGAGACGATTTCATA 57.293 29.630 8.61 0.00 0.00 2.15
642 656 2.208132 AACATGCGGTTGGATGGTTA 57.792 45.000 0.00 0.00 41.63 2.85
648 662 0.616371 CGGTTGGATGGTTAGGTGGA 59.384 55.000 0.00 0.00 0.00 4.02
657 671 2.187958 TGGTTAGGTGGACAGAGATGG 58.812 52.381 0.00 0.00 0.00 3.51
685 699 0.250513 GGAGTGAGGAAAGATGCGGT 59.749 55.000 0.00 0.00 0.00 5.68
688 702 0.798776 GTGAGGAAAGATGCGGTGTG 59.201 55.000 0.00 0.00 0.00 3.82
689 703 0.321564 TGAGGAAAGATGCGGTGTGG 60.322 55.000 0.00 0.00 0.00 4.17
694 708 0.327924 AAAGATGCGGTGTGGGATCA 59.672 50.000 0.00 0.00 37.24 2.92
699 713 0.908910 TGCGGTGTGGGATCAGTTAT 59.091 50.000 0.00 0.00 0.00 1.89
720 734 0.753262 AGAGGGGAAATCACGATCCG 59.247 55.000 0.00 0.00 36.54 4.18
721 735 0.750850 GAGGGGAAATCACGATCCGA 59.249 55.000 0.00 0.00 36.54 4.55
748 762 2.452295 TGACGGTGGTTACGCATTTA 57.548 45.000 0.00 0.00 34.00 1.40
752 766 4.215827 TGACGGTGGTTACGCATTTAAAAT 59.784 37.500 0.00 0.00 34.00 1.82
753 767 5.123805 ACGGTGGTTACGCATTTAAAATT 57.876 34.783 0.00 0.00 34.00 1.82
754 768 5.530712 ACGGTGGTTACGCATTTAAAATTT 58.469 33.333 0.00 0.00 34.00 1.82
755 769 5.984323 ACGGTGGTTACGCATTTAAAATTTT 59.016 32.000 8.75 8.75 34.00 1.82
858 872 1.466360 GGTTACTTTCGTAGCGAGCGA 60.466 52.381 0.00 0.00 37.14 4.93
963 980 1.222300 CCCACGACGATCAAACAACA 58.778 50.000 0.00 0.00 0.00 3.33
969 986 2.411547 CGACGATCAAACAACAGAAGCC 60.412 50.000 0.00 0.00 0.00 4.35
1128 1145 1.371022 CCGCCATCGACTGATCTCG 60.371 63.158 0.00 0.00 38.10 4.04
1183 1200 3.920196 CCGGCCGGCCTTACGTAT 61.920 66.667 41.01 0.00 0.00 3.06
1196 1213 3.615496 CCTTACGTATACACTGTGTTGGC 59.385 47.826 19.73 8.27 0.00 4.52
1197 1214 2.823924 ACGTATACACTGTGTTGGCA 57.176 45.000 19.73 0.60 0.00 4.92
1198 1215 3.114668 ACGTATACACTGTGTTGGCAA 57.885 42.857 19.73 0.00 0.00 4.52
1199 1216 3.670625 ACGTATACACTGTGTTGGCAAT 58.329 40.909 19.73 8.47 0.00 3.56
1200 1217 3.435327 ACGTATACACTGTGTTGGCAATG 59.565 43.478 19.73 8.20 0.00 2.82
1201 1218 3.181511 CGTATACACTGTGTTGGCAATGG 60.182 47.826 19.73 0.00 0.00 3.16
1202 1219 0.958091 TACACTGTGTTGGCAATGGC 59.042 50.000 19.73 0.00 40.13 4.40
1213 1230 3.446507 GCAATGGCCAATGGTGAAG 57.553 52.632 22.24 0.00 0.00 3.02
1214 1231 0.741927 GCAATGGCCAATGGTGAAGC 60.742 55.000 22.24 2.73 0.00 3.86
1216 1233 0.899720 AATGGCCAATGGTGAAGCAG 59.100 50.000 10.96 0.00 0.00 4.24
1217 1234 1.610554 ATGGCCAATGGTGAAGCAGC 61.611 55.000 10.96 0.00 0.00 5.25
1218 1235 1.980772 GGCCAATGGTGAAGCAGCT 60.981 57.895 0.00 0.00 32.61 4.24
1219 1236 1.214589 GCCAATGGTGAAGCAGCTG 59.785 57.895 10.11 10.11 32.61 4.24
1220 1237 1.530013 GCCAATGGTGAAGCAGCTGT 61.530 55.000 16.64 0.00 32.61 4.40
1221 1238 0.963962 CCAATGGTGAAGCAGCTGTT 59.036 50.000 16.64 6.37 32.61 3.16
1222 1239 1.342174 CCAATGGTGAAGCAGCTGTTT 59.658 47.619 16.33 16.33 32.61 2.83
1223 1240 2.400399 CAATGGTGAAGCAGCTGTTTG 58.600 47.619 21.32 0.87 32.61 2.93
1224 1241 0.316204 ATGGTGAAGCAGCTGTTTGC 59.684 50.000 21.32 12.46 44.41 3.68
1242 1259 4.560136 TTGCTTGTTTGCAATCGACTAA 57.440 36.364 0.00 0.00 46.43 2.24
1243 1260 3.884169 TGCTTGTTTGCAATCGACTAAC 58.116 40.909 0.00 0.00 40.29 2.34
1244 1261 3.234386 GCTTGTTTGCAATCGACTAACC 58.766 45.455 0.00 0.00 33.65 2.85
1245 1262 3.479006 CTTGTTTGCAATCGACTAACCG 58.521 45.455 0.00 0.00 33.65 4.44
1246 1263 1.195900 TGTTTGCAATCGACTAACCGC 59.804 47.619 0.00 0.00 0.00 5.68
1247 1264 0.440758 TTTGCAATCGACTAACCGCG 59.559 50.000 0.00 0.00 0.00 6.46
1248 1265 1.962092 TTGCAATCGACTAACCGCGC 61.962 55.000 0.00 0.00 0.00 6.86
1249 1266 2.449525 GCAATCGACTAACCGCGCA 61.450 57.895 8.75 0.00 0.00 6.09
1270 1287 5.691508 CATGCTAATGCTAAACTGTTTGC 57.308 39.130 15.69 15.77 40.48 3.68
1431 1451 1.551883 GGAGGCTACCTAAACGTGGAA 59.448 52.381 0.00 0.00 31.76 3.53
1513 1649 6.415206 ACGTGTATATATATACCCCATGCC 57.585 41.667 23.94 3.86 38.17 4.40
1538 1674 4.267214 GCATGAGTTCATATGATCGATCGG 59.733 45.833 20.03 9.87 34.26 4.18
1539 1675 3.838120 TGAGTTCATATGATCGATCGGC 58.162 45.455 20.03 8.58 0.00 5.54
1540 1676 3.182967 GAGTTCATATGATCGATCGGCC 58.817 50.000 20.03 7.96 0.00 6.13
1541 1677 1.920574 GTTCATATGATCGATCGGCCG 59.079 52.381 22.12 22.12 0.00 6.13
1690 1833 5.360714 TCAACAAGCTTTCCAACTGAAGATT 59.639 36.000 0.00 0.00 33.63 2.40
1694 1837 5.444663 AGCTTTCCAACTGAAGATTGAAC 57.555 39.130 0.00 0.00 33.63 3.18
1696 1839 4.037923 GCTTTCCAACTGAAGATTGAACCA 59.962 41.667 0.00 0.00 33.63 3.67
1704 1847 1.003233 GAAGATTGAACCAGGACGGGT 59.997 52.381 0.00 0.00 45.04 5.28
1721 1864 1.270907 GGTGAGAGAAGCAAGAGGGA 58.729 55.000 0.00 0.00 0.00 4.20
1735 1878 2.125633 GGGAAAGGACCGTCGCTC 60.126 66.667 7.71 0.00 0.00 5.03
1739 1882 0.721718 GAAAGGACCGTCGCTCAATG 59.278 55.000 0.00 0.00 0.00 2.82
1819 2039 5.124138 TGTTCTAGCTAGCTAGTGTGAAGTC 59.876 44.000 38.27 23.77 44.59 3.01
1856 2076 1.664873 TACCTCAGAGTCGACGATGG 58.335 55.000 18.86 15.42 0.00 3.51
1901 2136 6.321181 ACATATTCTGTGGTCTTTTTGTGTGT 59.679 34.615 0.00 0.00 36.48 3.72
1916 2153 1.802365 GTGTGTGGGGAAATCGTGTAC 59.198 52.381 0.00 0.00 0.00 2.90
1923 2160 2.424956 GGGGAAATCGTGTACGTCTAGT 59.575 50.000 4.20 0.00 40.80 2.57
1945 2182 3.033368 TGCACTAGTTATTGCACGTCA 57.967 42.857 1.83 0.00 43.79 4.35
1955 2195 3.752412 ATTGCACGTCATGACTCAATG 57.248 42.857 24.30 17.95 0.00 2.82
1961 2201 2.738846 ACGTCATGACTCAATGAAGCAC 59.261 45.455 22.95 0.00 38.97 4.40
1962 2202 2.222663 CGTCATGACTCAATGAAGCACG 60.223 50.000 22.95 2.41 38.28 5.34
1972 2212 5.973565 ACTCAATGAAGCACGAAAAGAAAAG 59.026 36.000 0.00 0.00 0.00 2.27
2012 2252 7.041635 TGAATCACCGCATAAAATCAATGAT 57.958 32.000 0.00 0.00 0.00 2.45
2017 2257 9.671279 ATCACCGCATAAAATCAATGATATAGA 57.329 29.630 0.00 0.00 0.00 1.98
2051 2291 5.411977 TGCTATAGTTAGGACGCATCTAGAC 59.588 44.000 0.00 0.00 0.00 2.59
2052 2292 5.411977 GCTATAGTTAGGACGCATCTAGACA 59.588 44.000 0.00 0.00 0.00 3.41
2060 2300 3.491267 GGACGCATCTAGACATGCTTTAC 59.509 47.826 14.70 1.24 46.09 2.01
2065 2305 5.573146 GCATCTAGACATGCTTTACCAAAC 58.427 41.667 10.48 0.00 45.03 2.93
2066 2306 5.355350 GCATCTAGACATGCTTTACCAAACT 59.645 40.000 10.48 0.00 45.03 2.66
2067 2307 6.676456 GCATCTAGACATGCTTTACCAAACTG 60.676 42.308 10.48 0.00 45.03 3.16
2096 2338 0.797579 TATTCTAGGGGGCTAGGGGG 59.202 60.000 0.00 0.00 0.00 5.40
2103 2345 0.841158 GGGGGCTAGGGGGATAGAAC 60.841 65.000 0.00 0.00 0.00 3.01
2145 2387 1.228367 CAGCAAGACAAGGTGGGCT 60.228 57.895 0.00 0.00 0.00 5.19
2176 2420 3.966154 AGTGCATCCTAGTATCGAAACG 58.034 45.455 0.00 0.00 0.00 3.60
2245 2489 4.213270 CGAATGGCATATTAACCACGTGAT 59.787 41.667 19.30 8.16 39.19 3.06
2263 2509 8.137210 CACGTGATACATGTGGTAAATAATCA 57.863 34.615 10.90 4.05 44.71 2.57
2264 2510 8.061857 CACGTGATACATGTGGTAAATAATCAC 58.938 37.037 10.90 18.06 44.71 3.06
2305 2556 0.522626 TGGCGAATGACATGTTGCAG 59.477 50.000 0.00 0.00 0.00 4.41
2403 2656 6.268847 ACCCCTTTTTCATTACTTGCATAACA 59.731 34.615 0.00 0.00 0.00 2.41
2427 2680 5.458041 AAGTACAAAGTTACGGACAGCTA 57.542 39.130 0.00 0.00 0.00 3.32
2454 2708 4.216472 GGAAAAGAAGAAGCGAGTTGGATT 59.784 41.667 0.00 0.00 0.00 3.01
2455 2709 5.278512 GGAAAAGAAGAAGCGAGTTGGATTT 60.279 40.000 0.00 0.00 0.00 2.17
2456 2710 5.774498 AAAGAAGAAGCGAGTTGGATTTT 57.226 34.783 0.00 0.00 0.00 1.82
2457 2711 6.877611 AAAGAAGAAGCGAGTTGGATTTTA 57.122 33.333 0.00 0.00 0.00 1.52
2458 2712 5.864628 AGAAGAAGCGAGTTGGATTTTAC 57.135 39.130 0.00 0.00 0.00 2.01
2459 2713 5.552178 AGAAGAAGCGAGTTGGATTTTACT 58.448 37.500 0.00 0.00 0.00 2.24
2460 2714 5.998363 AGAAGAAGCGAGTTGGATTTTACTT 59.002 36.000 0.00 0.00 0.00 2.24
2461 2715 6.486993 AGAAGAAGCGAGTTGGATTTTACTTT 59.513 34.615 0.00 0.00 0.00 2.66
2462 2716 6.635030 AGAAGCGAGTTGGATTTTACTTTT 57.365 33.333 0.00 0.00 0.00 2.27
2463 2717 7.039313 AGAAGCGAGTTGGATTTTACTTTTT 57.961 32.000 0.00 0.00 0.00 1.94
2497 2751 4.891037 GCCCCTGGCCTCTGCATC 62.891 72.222 3.32 0.00 44.06 3.91
2498 2752 3.414193 CCCCTGGCCTCTGCATCA 61.414 66.667 3.32 0.00 40.13 3.07
2499 2753 2.764737 CCCCTGGCCTCTGCATCAT 61.765 63.158 3.32 0.00 40.13 2.45
2500 2754 1.528542 CCCTGGCCTCTGCATCATG 60.529 63.158 3.32 0.00 40.13 3.07
2501 2755 1.530283 CCTGGCCTCTGCATCATGA 59.470 57.895 3.32 0.00 40.13 3.07
2502 2756 0.110678 CCTGGCCTCTGCATCATGAT 59.889 55.000 3.32 1.18 40.13 2.45
2503 2757 1.239347 CTGGCCTCTGCATCATGATG 58.761 55.000 28.04 28.04 41.60 3.07
2504 2758 0.841289 TGGCCTCTGCATCATGATGA 59.159 50.000 34.65 19.93 41.20 2.92
2505 2759 1.423921 TGGCCTCTGCATCATGATGAT 59.576 47.619 34.65 1.25 41.20 2.45
2513 2767 2.262572 CATCATGATGATGCATGCGG 57.737 50.000 28.37 0.00 46.37 5.69
2514 2768 0.526211 ATCATGATGATGCATGCGGC 59.474 50.000 14.09 7.96 44.08 6.53
2515 2769 1.080772 CATGATGATGCATGCGGCC 60.081 57.895 14.09 5.01 43.89 6.13
2516 2770 1.529713 ATGATGATGCATGCGGCCA 60.530 52.632 14.09 10.90 43.89 5.36
2517 2771 0.898326 ATGATGATGCATGCGGCCAT 60.898 50.000 14.09 15.20 43.89 4.40
2518 2772 1.211969 GATGATGCATGCGGCCATC 59.788 57.895 22.22 22.22 43.89 3.51
2519 2773 1.228459 ATGATGCATGCGGCCATCT 60.228 52.632 14.09 0.00 43.89 2.90
2520 2774 0.826256 ATGATGCATGCGGCCATCTT 60.826 50.000 14.09 5.81 43.89 2.40
2521 2775 0.179023 TGATGCATGCGGCCATCTTA 60.179 50.000 14.09 0.00 43.89 2.10
2522 2776 1.171308 GATGCATGCGGCCATCTTAT 58.829 50.000 14.09 0.00 43.89 1.73
2523 2777 1.542915 GATGCATGCGGCCATCTTATT 59.457 47.619 14.09 0.00 43.89 1.40
2524 2778 2.268762 TGCATGCGGCCATCTTATTA 57.731 45.000 14.09 0.00 43.89 0.98
2525 2779 2.580962 TGCATGCGGCCATCTTATTAA 58.419 42.857 14.09 0.00 43.89 1.40
2526 2780 2.293122 TGCATGCGGCCATCTTATTAAC 59.707 45.455 14.09 0.00 43.89 2.01
2527 2781 2.293122 GCATGCGGCCATCTTATTAACA 59.707 45.455 0.00 0.00 36.11 2.41
2528 2782 3.243367 GCATGCGGCCATCTTATTAACAA 60.243 43.478 0.00 0.00 36.11 2.83
2529 2783 4.559300 GCATGCGGCCATCTTATTAACAAT 60.559 41.667 0.00 0.00 36.11 2.71
2530 2784 4.829064 TGCGGCCATCTTATTAACAATC 57.171 40.909 2.24 0.00 0.00 2.67
2531 2785 3.568007 TGCGGCCATCTTATTAACAATCC 59.432 43.478 2.24 0.00 0.00 3.01
2532 2786 3.568007 GCGGCCATCTTATTAACAATCCA 59.432 43.478 2.24 0.00 0.00 3.41
2533 2787 4.218417 GCGGCCATCTTATTAACAATCCAT 59.782 41.667 2.24 0.00 0.00 3.41
2534 2788 5.414454 GCGGCCATCTTATTAACAATCCATA 59.586 40.000 2.24 0.00 0.00 2.74
2535 2789 6.072175 GCGGCCATCTTATTAACAATCCATAA 60.072 38.462 2.24 0.00 0.00 1.90
2536 2790 7.362920 GCGGCCATCTTATTAACAATCCATAAT 60.363 37.037 2.24 0.00 0.00 1.28
2537 2791 8.184192 CGGCCATCTTATTAACAATCCATAATC 58.816 37.037 2.24 0.00 0.00 1.75
2538 2792 9.023962 GGCCATCTTATTAACAATCCATAATCA 57.976 33.333 0.00 0.00 0.00 2.57
2560 2814 9.624373 AATCATCATAAAAGTCTTACAGCTCAT 57.376 29.630 0.00 0.00 0.00 2.90
2565 2819 8.869897 TCATAAAAGTCTTACAGCTCATAAACG 58.130 33.333 0.00 0.00 0.00 3.60
2566 2820 6.481954 AAAAGTCTTACAGCTCATAAACGG 57.518 37.500 0.00 0.00 0.00 4.44
2567 2821 5.401531 AAGTCTTACAGCTCATAAACGGA 57.598 39.130 0.00 0.00 0.00 4.69
2568 2822 5.000012 AGTCTTACAGCTCATAAACGGAG 58.000 43.478 0.00 0.00 35.47 4.63
2579 2833 6.910536 CTCATAAACGGAGCAGAATAAAGT 57.089 37.500 0.00 0.00 0.00 2.66
2581 2835 8.594881 CTCATAAACGGAGCAGAATAAAGTAT 57.405 34.615 0.00 0.00 0.00 2.12
2582 2836 8.589335 TCATAAACGGAGCAGAATAAAGTATC 57.411 34.615 0.00 0.00 0.00 2.24
2583 2837 8.201464 TCATAAACGGAGCAGAATAAAGTATCA 58.799 33.333 0.00 0.00 0.00 2.15
2584 2838 8.826710 CATAAACGGAGCAGAATAAAGTATCAA 58.173 33.333 0.00 0.00 0.00 2.57
2585 2839 7.681939 AAACGGAGCAGAATAAAGTATCAAA 57.318 32.000 0.00 0.00 0.00 2.69
2586 2840 7.681939 AACGGAGCAGAATAAAGTATCAAAA 57.318 32.000 0.00 0.00 0.00 2.44
2587 2841 7.308782 ACGGAGCAGAATAAAGTATCAAAAG 57.691 36.000 0.00 0.00 0.00 2.27
2588 2842 6.316390 ACGGAGCAGAATAAAGTATCAAAAGG 59.684 38.462 0.00 0.00 0.00 3.11
2589 2843 6.538742 CGGAGCAGAATAAAGTATCAAAAGGA 59.461 38.462 0.00 0.00 0.00 3.36
2590 2844 7.065803 CGGAGCAGAATAAAGTATCAAAAGGAA 59.934 37.037 0.00 0.00 0.00 3.36
2591 2845 8.739972 GGAGCAGAATAAAGTATCAAAAGGAAA 58.260 33.333 0.00 0.00 0.00 3.13
2605 2859 8.831715 ATCAAAAGGAAAAATACATGTGAACC 57.168 30.769 9.11 3.66 0.00 3.62
2606 2860 7.786030 TCAAAAGGAAAAATACATGTGAACCA 58.214 30.769 9.11 0.00 0.00 3.67
2607 2861 8.428063 TCAAAAGGAAAAATACATGTGAACCAT 58.572 29.630 9.11 0.00 0.00 3.55
2615 2869 2.617250 CATGTGAACCATGTCAACCG 57.383 50.000 0.00 0.00 44.96 4.44
2616 2870 1.199789 CATGTGAACCATGTCAACCGG 59.800 52.381 0.00 0.00 44.96 5.28
2617 2871 1.169661 TGTGAACCATGTCAACCGGC 61.170 55.000 0.00 0.00 0.00 6.13
2618 2872 1.149401 TGAACCATGTCAACCGGCA 59.851 52.632 0.00 0.00 0.00 5.69
2619 2873 1.169661 TGAACCATGTCAACCGGCAC 61.170 55.000 0.00 0.00 0.00 5.01
2620 2874 1.152860 AACCATGTCAACCGGCACA 60.153 52.632 0.00 1.89 0.00 4.57
2621 2875 0.753479 AACCATGTCAACCGGCACAA 60.753 50.000 0.00 0.00 0.00 3.33
2622 2876 0.539438 ACCATGTCAACCGGCACAAT 60.539 50.000 0.00 0.00 0.00 2.71
2623 2877 0.109179 CCATGTCAACCGGCACAATG 60.109 55.000 0.00 0.00 0.00 2.82
2624 2878 0.880441 CATGTCAACCGGCACAATGA 59.120 50.000 0.00 0.00 0.00 2.57
2625 2879 1.269174 CATGTCAACCGGCACAATGAA 59.731 47.619 0.00 0.00 0.00 2.57
2626 2880 0.950836 TGTCAACCGGCACAATGAAG 59.049 50.000 0.00 0.00 0.00 3.02
2627 2881 1.234821 GTCAACCGGCACAATGAAGA 58.765 50.000 0.00 0.00 0.00 2.87
2628 2882 1.812571 GTCAACCGGCACAATGAAGAT 59.187 47.619 0.00 0.00 0.00 2.40
2629 2883 3.006940 GTCAACCGGCACAATGAAGATA 58.993 45.455 0.00 0.00 0.00 1.98
2630 2884 3.438781 GTCAACCGGCACAATGAAGATAA 59.561 43.478 0.00 0.00 0.00 1.75
2631 2885 4.075682 TCAACCGGCACAATGAAGATAAA 58.924 39.130 0.00 0.00 0.00 1.40
2632 2886 4.520874 TCAACCGGCACAATGAAGATAAAA 59.479 37.500 0.00 0.00 0.00 1.52
2633 2887 5.010112 TCAACCGGCACAATGAAGATAAAAA 59.990 36.000 0.00 0.00 0.00 1.94
2634 2888 5.059404 ACCGGCACAATGAAGATAAAAAG 57.941 39.130 0.00 0.00 0.00 2.27
2635 2889 4.082245 ACCGGCACAATGAAGATAAAAAGG 60.082 41.667 0.00 0.00 0.00 3.11
2636 2890 4.157656 CCGGCACAATGAAGATAAAAAGGA 59.842 41.667 0.00 0.00 0.00 3.36
2637 2891 5.163519 CCGGCACAATGAAGATAAAAAGGAT 60.164 40.000 0.00 0.00 0.00 3.24
2638 2892 6.039270 CCGGCACAATGAAGATAAAAAGGATA 59.961 38.462 0.00 0.00 0.00 2.59
2639 2893 7.416213 CCGGCACAATGAAGATAAAAAGGATAA 60.416 37.037 0.00 0.00 0.00 1.75
2640 2894 7.645340 CGGCACAATGAAGATAAAAAGGATAAG 59.355 37.037 0.00 0.00 0.00 1.73
2641 2895 7.436376 GGCACAATGAAGATAAAAAGGATAAGC 59.564 37.037 0.00 0.00 0.00 3.09
2642 2896 8.193438 GCACAATGAAGATAAAAAGGATAAGCT 58.807 33.333 0.00 0.00 0.00 3.74
2643 2897 9.727627 CACAATGAAGATAAAAAGGATAAGCTC 57.272 33.333 0.00 0.00 0.00 4.09
2644 2898 9.692325 ACAATGAAGATAAAAAGGATAAGCTCT 57.308 29.630 0.00 0.00 0.00 4.09
2651 2905 9.654919 AGATAAAAAGGATAAGCTCTCTAGACT 57.345 33.333 0.00 0.00 0.00 3.24
2652 2906 9.908152 GATAAAAAGGATAAGCTCTCTAGACTC 57.092 37.037 0.00 0.00 0.00 3.36
2653 2907 6.724893 AAAAGGATAAGCTCTCTAGACTCC 57.275 41.667 0.00 0.00 0.00 3.85
2654 2908 5.663158 AAGGATAAGCTCTCTAGACTCCT 57.337 43.478 0.00 0.00 33.37 3.69
2655 2909 6.773583 AAGGATAAGCTCTCTAGACTCCTA 57.226 41.667 0.00 0.00 31.77 2.94
2656 2910 6.970165 AGGATAAGCTCTCTAGACTCCTAT 57.030 41.667 0.00 0.00 30.26 2.57
2657 2911 6.958767 AGGATAAGCTCTCTAGACTCCTATC 58.041 44.000 0.00 0.00 30.26 2.08
2658 2912 6.069615 AGGATAAGCTCTCTAGACTCCTATCC 60.070 46.154 9.56 9.56 34.83 2.59
2659 2913 6.069615 GGATAAGCTCTCTAGACTCCTATCCT 60.070 46.154 9.99 0.00 32.82 3.24
2660 2914 4.640771 AGCTCTCTAGACTCCTATCCTG 57.359 50.000 0.00 0.00 0.00 3.86
2661 2915 3.980698 AGCTCTCTAGACTCCTATCCTGT 59.019 47.826 0.00 0.00 0.00 4.00
2662 2916 4.415512 AGCTCTCTAGACTCCTATCCTGTT 59.584 45.833 0.00 0.00 0.00 3.16
2663 2917 5.609284 AGCTCTCTAGACTCCTATCCTGTTA 59.391 44.000 0.00 0.00 0.00 2.41
2664 2918 6.274672 AGCTCTCTAGACTCCTATCCTGTTAT 59.725 42.308 0.00 0.00 0.00 1.89
2665 2919 6.374333 GCTCTCTAGACTCCTATCCTGTTATG 59.626 46.154 0.00 0.00 0.00 1.90
2666 2920 6.242396 TCTCTAGACTCCTATCCTGTTATGC 58.758 44.000 0.00 0.00 0.00 3.14
2667 2921 5.004448 TCTAGACTCCTATCCTGTTATGCG 58.996 45.833 0.00 0.00 0.00 4.73
2668 2922 3.833732 AGACTCCTATCCTGTTATGCGA 58.166 45.455 0.00 0.00 0.00 5.10
2669 2923 3.823873 AGACTCCTATCCTGTTATGCGAG 59.176 47.826 0.00 0.00 0.00 5.03
2670 2924 2.297597 ACTCCTATCCTGTTATGCGAGC 59.702 50.000 0.00 0.00 0.00 5.03
2671 2925 1.269723 TCCTATCCTGTTATGCGAGCG 59.730 52.381 0.00 0.00 0.00 5.03
2672 2926 1.063806 CTATCCTGTTATGCGAGCGC 58.936 55.000 8.08 8.08 42.35 5.92
2673 2927 0.319555 TATCCTGTTATGCGAGCGCC 60.320 55.000 12.70 0.00 41.09 6.53
2674 2928 2.310327 ATCCTGTTATGCGAGCGCCA 62.310 55.000 12.70 0.00 41.09 5.69
2675 2929 1.889105 CCTGTTATGCGAGCGCCAT 60.889 57.895 12.70 2.83 41.09 4.40
2676 2930 1.566563 CTGTTATGCGAGCGCCATC 59.433 57.895 12.70 0.00 41.09 3.51
2677 2931 1.835483 CTGTTATGCGAGCGCCATCC 61.835 60.000 12.70 0.00 41.09 3.51
2678 2932 2.661537 TTATGCGAGCGCCATCCG 60.662 61.111 12.70 4.03 41.09 4.18
2679 2933 3.145422 TTATGCGAGCGCCATCCGA 62.145 57.895 12.70 0.00 41.09 4.55
2680 2934 2.636778 TTATGCGAGCGCCATCCGAA 62.637 55.000 12.70 0.00 41.09 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.608761 ACCTAGTACTTAATCATCGGATCTCTC 59.391 40.741 0.00 0.00 31.88 3.20
1 2 7.463431 ACCTAGTACTTAATCATCGGATCTCT 58.537 38.462 0.00 0.00 31.88 3.10
2 3 7.690952 ACCTAGTACTTAATCATCGGATCTC 57.309 40.000 0.00 0.00 31.88 2.75
3 4 7.506261 ACAACCTAGTACTTAATCATCGGATCT 59.494 37.037 0.00 0.00 31.88 2.75
4 5 7.659186 ACAACCTAGTACTTAATCATCGGATC 58.341 38.462 0.00 0.00 31.88 3.36
5 6 7.598759 ACAACCTAGTACTTAATCATCGGAT 57.401 36.000 0.00 0.00 34.43 4.18
6 7 7.414222 AACAACCTAGTACTTAATCATCGGA 57.586 36.000 0.00 0.00 0.00 4.55
7 8 9.193133 CATAACAACCTAGTACTTAATCATCGG 57.807 37.037 0.00 0.00 0.00 4.18
77 79 7.744715 CGTGTAAGTTTTTAGATCATGTTGTCC 59.255 37.037 0.00 0.00 0.00 4.02
91 93 2.359848 GAGGTTGGCCGTGTAAGTTTTT 59.640 45.455 0.00 0.00 40.50 1.94
97 99 0.320073 CGAAGAGGTTGGCCGTGTAA 60.320 55.000 0.00 0.00 40.50 2.41
202 205 7.458397 AGGATGAAACACAAGTAATTGAGGTA 58.542 34.615 10.35 0.00 0.00 3.08
231 235 4.657436 TTTGGTGTCCGCAAAAATTACT 57.343 36.364 0.00 0.00 0.00 2.24
243 247 3.437049 GTGAGCTGACTATTTTGGTGTCC 59.563 47.826 0.00 0.00 0.00 4.02
508 521 5.104652 GGAAATAGCTAAACAGGGTCAGGTA 60.105 44.000 0.00 0.00 0.00 3.08
536 549 2.750141 ATGATCATCCTTTGCCTGCT 57.250 45.000 1.18 0.00 0.00 4.24
537 550 3.304257 CGTTATGATCATCCTTTGCCTGC 60.304 47.826 12.53 0.00 0.00 4.85
574 588 9.559732 TTGTTAACTCGATTCATATCAATGGAT 57.440 29.630 7.22 0.00 33.69 3.41
580 594 9.869757 TCTTCTTTGTTAACTCGATTCATATCA 57.130 29.630 7.22 0.00 0.00 2.15
601 615 9.877178 ATGTTAGTTTATGAAATCGTCTCTTCT 57.123 29.630 0.00 0.00 0.00 2.85
613 627 5.004448 TCCAACCGCATGTTAGTTTATGAA 58.996 37.500 0.00 0.00 34.69 2.57
614 628 4.580868 TCCAACCGCATGTTAGTTTATGA 58.419 39.130 0.00 0.00 34.69 2.15
618 632 2.491693 CCATCCAACCGCATGTTAGTTT 59.508 45.455 0.00 0.00 34.69 2.66
642 656 0.251832 ACGACCATCTCTGTCCACCT 60.252 55.000 0.00 0.00 0.00 4.00
648 662 2.755655 CTCCTAACACGACCATCTCTGT 59.244 50.000 0.00 0.00 0.00 3.41
657 671 3.255149 TCTTTCCTCACTCCTAACACGAC 59.745 47.826 0.00 0.00 0.00 4.34
685 699 3.041211 CCCTCTGATAACTGATCCCACA 58.959 50.000 0.00 0.00 33.07 4.17
688 702 2.977808 TCCCCTCTGATAACTGATCCC 58.022 52.381 0.00 0.00 33.07 3.85
689 703 5.072329 TGATTTCCCCTCTGATAACTGATCC 59.928 44.000 0.00 0.00 33.07 3.36
694 708 4.030913 TCGTGATTTCCCCTCTGATAACT 58.969 43.478 0.00 0.00 0.00 2.24
699 713 1.762957 GGATCGTGATTTCCCCTCTGA 59.237 52.381 0.00 0.00 0.00 3.27
720 734 3.795101 CGTAACCACCGTCATTATCTGTC 59.205 47.826 0.00 0.00 0.00 3.51
721 735 3.777478 CGTAACCACCGTCATTATCTGT 58.223 45.455 0.00 0.00 0.00 3.41
758 772 9.179552 GAAACCGTAACCACGTTTATTTTTAAT 57.820 29.630 0.00 0.00 46.96 1.40
759 773 7.645735 GGAAACCGTAACCACGTTTATTTTTAA 59.354 33.333 0.00 0.00 46.96 1.52
760 774 7.135467 GGAAACCGTAACCACGTTTATTTTTA 58.865 34.615 0.00 0.00 46.96 1.52
829 843 0.678684 CGAAAGTAACCCGCCCCAAT 60.679 55.000 0.00 0.00 0.00 3.16
963 980 2.930562 AACCGCTCCCTGGCTTCT 60.931 61.111 0.00 0.00 0.00 2.85
969 986 0.598680 GATCGATCAACCGCTCCCTG 60.599 60.000 20.52 0.00 0.00 4.45
1035 1052 2.791927 TCGACCTCGAGCGTGATG 59.208 61.111 6.99 0.00 44.22 3.07
1115 1132 3.471680 TGAGATGACGAGATCAGTCGAT 58.528 45.455 10.96 8.14 41.91 3.59
1169 1186 0.386838 AGTGTATACGTAAGGCCGGC 59.613 55.000 21.18 21.18 46.39 6.13
1171 1188 2.159338 ACACAGTGTATACGTAAGGCCG 60.159 50.000 3.69 0.00 46.39 6.13
1172 1189 3.515330 ACACAGTGTATACGTAAGGCC 57.485 47.619 3.69 0.00 46.39 5.19
1176 1193 4.254402 TGCCAACACAGTGTATACGTAA 57.746 40.909 6.63 0.00 0.00 3.18
1177 1194 3.938289 TGCCAACACAGTGTATACGTA 57.062 42.857 6.63 0.00 0.00 3.57
1178 1195 2.823924 TGCCAACACAGTGTATACGT 57.176 45.000 6.63 0.00 0.00 3.57
1183 1200 0.958091 GCCATTGCCAACACAGTGTA 59.042 50.000 6.63 0.00 0.00 2.90
1196 1213 0.609151 TGCTTCACCATTGGCCATTG 59.391 50.000 18.83 18.83 0.00 2.82
1197 1214 0.899720 CTGCTTCACCATTGGCCATT 59.100 50.000 6.09 0.00 0.00 3.16
1198 1215 1.610554 GCTGCTTCACCATTGGCCAT 61.611 55.000 6.09 0.00 0.00 4.40
1199 1216 2.277591 GCTGCTTCACCATTGGCCA 61.278 57.895 0.00 0.00 0.00 5.36
1200 1217 1.980772 AGCTGCTTCACCATTGGCC 60.981 57.895 1.54 0.00 0.00 5.36
1201 1218 1.214589 CAGCTGCTTCACCATTGGC 59.785 57.895 0.00 0.00 0.00 4.52
1202 1219 0.963962 AACAGCTGCTTCACCATTGG 59.036 50.000 15.27 0.00 0.00 3.16
1203 1220 2.400399 CAAACAGCTGCTTCACCATTG 58.600 47.619 15.27 3.01 0.00 2.82
1204 1221 1.269936 GCAAACAGCTGCTTCACCATT 60.270 47.619 15.27 0.00 39.34 3.16
1205 1222 0.316204 GCAAACAGCTGCTTCACCAT 59.684 50.000 15.27 0.00 39.34 3.55
1206 1223 1.735360 GCAAACAGCTGCTTCACCA 59.265 52.632 15.27 0.00 39.34 4.17
1207 1224 4.641777 GCAAACAGCTGCTTCACC 57.358 55.556 15.27 0.00 39.34 4.02
1222 1239 3.304391 GGTTAGTCGATTGCAAACAAGCA 60.304 43.478 1.71 0.00 42.38 3.91
1223 1240 3.234386 GGTTAGTCGATTGCAAACAAGC 58.766 45.455 1.71 0.00 39.69 4.01
1224 1241 3.479006 CGGTTAGTCGATTGCAAACAAG 58.521 45.455 1.71 0.00 39.69 3.16
1225 1242 2.350007 GCGGTTAGTCGATTGCAAACAA 60.350 45.455 1.71 0.00 40.87 2.83
1226 1243 1.195900 GCGGTTAGTCGATTGCAAACA 59.804 47.619 1.71 0.00 0.00 2.83
1227 1244 1.785518 CGCGGTTAGTCGATTGCAAAC 60.786 52.381 1.71 0.00 0.00 2.93
1228 1245 0.440758 CGCGGTTAGTCGATTGCAAA 59.559 50.000 1.71 0.00 0.00 3.68
1229 1246 1.962092 GCGCGGTTAGTCGATTGCAA 61.962 55.000 8.83 0.00 0.00 4.08
1230 1247 2.449525 GCGCGGTTAGTCGATTGCA 61.450 57.895 8.83 0.00 0.00 4.08
1231 1248 1.762222 ATGCGCGGTTAGTCGATTGC 61.762 55.000 8.83 0.00 0.00 3.56
1232 1249 0.043053 CATGCGCGGTTAGTCGATTG 60.043 55.000 8.83 0.00 0.00 2.67
1233 1250 1.762222 GCATGCGCGGTTAGTCGATT 61.762 55.000 8.83 0.00 0.00 3.34
1234 1251 2.237751 GCATGCGCGGTTAGTCGAT 61.238 57.895 8.83 0.00 0.00 3.59
1235 1252 1.995646 TAGCATGCGCGGTTAGTCGA 61.996 55.000 13.01 0.00 45.49 4.20
1236 1253 1.143373 TTAGCATGCGCGGTTAGTCG 61.143 55.000 13.01 0.00 45.49 4.18
1237 1254 1.070577 CATTAGCATGCGCGGTTAGTC 60.071 52.381 13.01 0.00 45.49 2.59
1238 1255 0.937304 CATTAGCATGCGCGGTTAGT 59.063 50.000 13.01 0.00 45.49 2.24
1239 1256 0.384725 GCATTAGCATGCGCGGTTAG 60.385 55.000 13.01 1.18 46.45 2.34
1240 1257 1.646540 GCATTAGCATGCGCGGTTA 59.353 52.632 13.01 0.00 46.45 2.85
1241 1258 2.408835 GCATTAGCATGCGCGGTT 59.591 55.556 13.01 0.00 46.45 4.44
1248 1265 5.404946 AGCAAACAGTTTAGCATTAGCATG 58.595 37.500 17.38 0.00 45.49 4.06
1249 1266 5.649782 AGCAAACAGTTTAGCATTAGCAT 57.350 34.783 17.38 0.00 45.49 3.79
1342 1362 0.687920 TGGATGTTGTAGTCGGCCAA 59.312 50.000 2.24 0.00 0.00 4.52
1431 1451 0.392193 CGAGCTGCAGGAGATTTGGT 60.392 55.000 17.12 0.00 0.00 3.67
1513 1649 5.004535 CGATCGATCATATGAACTCATGCAG 59.995 44.000 24.40 0.00 37.15 4.41
1538 1674 4.226761 CAGGTTAACAACAAAGATTCGGC 58.773 43.478 8.10 0.00 0.00 5.54
1539 1675 5.212194 CACAGGTTAACAACAAAGATTCGG 58.788 41.667 8.10 0.00 0.00 4.30
1540 1676 5.212194 CCACAGGTTAACAACAAAGATTCG 58.788 41.667 8.10 0.00 0.00 3.34
1541 1677 5.977129 CACCACAGGTTAACAACAAAGATTC 59.023 40.000 8.10 0.00 31.02 2.52
1641 1784 0.107752 CTCTTCTTGGGCCTCAGCTC 60.108 60.000 4.53 0.00 41.29 4.09
1644 1787 0.695347 AACCTCTTCTTGGGCCTCAG 59.305 55.000 4.53 0.24 0.00 3.35
1646 1789 0.391793 CGAACCTCTTCTTGGGCCTC 60.392 60.000 4.53 0.00 0.00 4.70
1690 1833 1.152419 TCTCACCCGTCCTGGTTCA 60.152 57.895 0.00 0.00 36.12 3.18
1694 1837 1.893786 CTTCTCTCACCCGTCCTGG 59.106 63.158 0.00 0.00 37.55 4.45
1696 1839 0.832135 TTGCTTCTCTCACCCGTCCT 60.832 55.000 0.00 0.00 0.00 3.85
1704 1847 2.304180 CCTTTCCCTCTTGCTTCTCTCA 59.696 50.000 0.00 0.00 0.00 3.27
1721 1864 0.320374 TCATTGAGCGACGGTCCTTT 59.680 50.000 23.06 6.17 0.00 3.11
1735 1878 8.834465 TGATAAACCAAACCAAACAATTCATTG 58.166 29.630 0.00 0.00 43.26 2.82
1739 1882 8.432110 ACTTGATAAACCAAACCAAACAATTC 57.568 30.769 0.00 0.00 0.00 2.17
1819 2039 2.224113 GGTAATCATTGCATGGCTTGGG 60.224 50.000 2.33 0.00 0.00 4.12
1835 2055 2.619177 CCATCGTCGACTCTGAGGTAAT 59.381 50.000 14.70 0.00 0.00 1.89
1840 2060 1.599171 GCATCCATCGTCGACTCTGAG 60.599 57.143 14.70 2.45 0.00 3.35
1856 2076 3.569277 TGTGGGTAATACATGCATGCATC 59.431 43.478 30.07 17.20 33.90 3.91
1887 2107 1.770294 TCCCCACACACAAAAAGACC 58.230 50.000 0.00 0.00 0.00 3.85
1891 2126 2.761208 ACGATTTCCCCACACACAAAAA 59.239 40.909 0.00 0.00 0.00 1.94
1896 2131 1.802365 GTACACGATTTCCCCACACAC 59.198 52.381 0.00 0.00 0.00 3.82
1901 2136 1.259609 AGACGTACACGATTTCCCCA 58.740 50.000 9.04 0.00 43.02 4.96
1941 2178 2.222663 CGTGCTTCATTGAGTCATGACG 60.223 50.000 19.85 5.80 36.20 4.35
1942 2179 2.995939 TCGTGCTTCATTGAGTCATGAC 59.004 45.455 18.47 18.47 0.00 3.06
1945 2182 4.756642 TCTTTTCGTGCTTCATTGAGTCAT 59.243 37.500 0.00 0.00 0.00 3.06
1983 2223 3.696281 TTTATGCGGTGATTCATGCAG 57.304 42.857 17.72 0.00 41.19 4.41
1984 2224 4.097589 TGATTTTATGCGGTGATTCATGCA 59.902 37.500 15.88 15.88 42.22 3.96
1985 2225 4.609947 TGATTTTATGCGGTGATTCATGC 58.390 39.130 6.84 6.84 0.00 4.06
1988 2228 6.448207 TCATTGATTTTATGCGGTGATTCA 57.552 33.333 0.00 0.00 0.00 2.57
2017 2257 9.804758 GCGTCCTAACTATAGCATATCTAAATT 57.195 33.333 0.00 0.00 0.00 1.82
2034 2274 3.053455 GCATGTCTAGATGCGTCCTAAC 58.947 50.000 1.23 0.00 39.47 2.34
2037 2277 3.976339 GCATGTCTAGATGCGTCCT 57.024 52.632 1.23 0.00 39.47 3.85
2074 2316 3.542604 CCCCTAGCCCCCTAGAATAAAT 58.457 50.000 0.00 0.00 43.07 1.40
2096 2338 4.602995 CCTTCTCGTGCTGTAGTTCTATC 58.397 47.826 0.00 0.00 0.00 2.08
2103 2345 0.528017 TGAGCCTTCTCGTGCTGTAG 59.472 55.000 0.00 0.00 42.26 2.74
2145 2387 3.770933 ACTAGGATGCACTACGGGTAAAA 59.229 43.478 0.00 0.00 0.00 1.52
2176 2420 2.436417 TGCTATGTGGAGCCTTTGAAC 58.564 47.619 0.00 0.00 42.11 3.18
2219 2463 2.621055 GTGGTTAATATGCCATTCGCCA 59.379 45.455 0.00 0.00 37.09 5.69
2222 2466 3.558006 TCACGTGGTTAATATGCCATTCG 59.442 43.478 17.00 0.00 37.09 3.34
2228 2472 6.362686 CACATGTATCACGTGGTTAATATGC 58.637 40.000 17.00 4.78 39.36 3.14
2305 2556 6.458615 GCACATCCATTTAATTTCCCAATTGC 60.459 38.462 0.00 0.00 34.29 3.56
2403 2656 5.121105 AGCTGTCCGTAACTTTGTACTTTT 58.879 37.500 0.00 0.00 0.00 2.27
2407 2660 5.051891 TCTAGCTGTCCGTAACTTTGTAC 57.948 43.478 0.00 0.00 0.00 2.90
2427 2680 4.344359 ACTCGCTTCTTCTTTTCCTTCT 57.656 40.909 0.00 0.00 0.00 2.85
2460 2714 3.819902 GGCAATGCCTCCATTTTCAAAAA 59.180 39.130 18.47 0.00 46.69 1.94
2461 2715 3.410508 GGCAATGCCTCCATTTTCAAAA 58.589 40.909 18.47 0.00 46.69 2.44
2462 2716 3.056588 GGCAATGCCTCCATTTTCAAA 57.943 42.857 18.47 0.00 46.69 2.69
2463 2717 2.766345 GGCAATGCCTCCATTTTCAA 57.234 45.000 18.47 0.00 46.69 2.69
2464 2718 2.516149 GGGGCAATGCCTCCATTTTCA 61.516 52.381 24.77 0.00 44.86 2.69
2465 2719 0.178767 GGGGCAATGCCTCCATTTTC 59.821 55.000 24.77 4.19 44.86 2.29
2466 2720 2.299975 GGGGCAATGCCTCCATTTT 58.700 52.632 24.77 0.00 44.86 1.82
2467 2721 4.055178 GGGGCAATGCCTCCATTT 57.945 55.556 24.77 0.00 44.86 2.32
2481 2735 2.764737 ATGATGCAGAGGCCAGGGG 61.765 63.158 5.01 0.00 40.13 4.79
2482 2736 1.528542 CATGATGCAGAGGCCAGGG 60.529 63.158 5.01 0.00 40.13 4.45
2483 2737 0.110678 ATCATGATGCAGAGGCCAGG 59.889 55.000 7.59 0.00 40.13 4.45
2484 2738 1.202770 TCATCATGATGCAGAGGCCAG 60.203 52.381 27.68 3.62 40.13 4.85
2485 2739 0.841289 TCATCATGATGCAGAGGCCA 59.159 50.000 27.68 7.97 40.13 5.36
2486 2740 1.813178 CATCATCATGATGCAGAGGCC 59.187 52.381 27.68 0.00 46.37 5.19
2495 2749 0.526211 GCCGCATGCATCATCATGAT 59.474 50.000 19.57 1.18 44.94 2.45
2496 2750 1.520600 GGCCGCATGCATCATCATGA 61.521 55.000 19.57 0.00 44.94 3.07
2497 2751 1.080772 GGCCGCATGCATCATCATG 60.081 57.895 19.57 0.00 44.93 3.07
2498 2752 0.898326 ATGGCCGCATGCATCATCAT 60.898 50.000 19.57 10.37 43.89 2.45
2499 2753 1.520600 GATGGCCGCATGCATCATCA 61.521 55.000 26.33 15.35 43.89 3.07
2500 2754 1.211969 GATGGCCGCATGCATCATC 59.788 57.895 19.57 20.53 43.89 2.92
2501 2755 0.826256 AAGATGGCCGCATGCATCAT 60.826 50.000 19.57 16.63 43.89 2.45
2502 2756 0.179023 TAAGATGGCCGCATGCATCA 60.179 50.000 19.57 12.47 43.89 3.07
2503 2757 1.171308 ATAAGATGGCCGCATGCATC 58.829 50.000 19.57 12.80 43.89 3.91
2504 2758 1.624336 AATAAGATGGCCGCATGCAT 58.376 45.000 19.57 2.77 43.89 3.96
2505 2759 2.268762 TAATAAGATGGCCGCATGCA 57.731 45.000 19.57 0.00 43.89 3.96
2506 2760 2.293122 TGTTAATAAGATGGCCGCATGC 59.707 45.455 7.91 7.91 40.16 4.06
2507 2761 4.566545 TTGTTAATAAGATGGCCGCATG 57.433 40.909 0.00 0.00 0.00 4.06
2508 2762 4.218417 GGATTGTTAATAAGATGGCCGCAT 59.782 41.667 0.00 0.00 0.00 4.73
2509 2763 3.568007 GGATTGTTAATAAGATGGCCGCA 59.432 43.478 0.00 0.00 0.00 5.69
2510 2764 3.568007 TGGATTGTTAATAAGATGGCCGC 59.432 43.478 0.00 0.00 0.00 6.53
2511 2765 5.964958 ATGGATTGTTAATAAGATGGCCG 57.035 39.130 0.00 0.00 0.00 6.13
2512 2766 9.023962 TGATTATGGATTGTTAATAAGATGGCC 57.976 33.333 0.00 0.00 0.00 5.36
2534 2788 9.624373 ATGAGCTGTAAGACTTTTATGATGATT 57.376 29.630 0.00 0.00 34.07 2.57
2539 2793 8.869897 CGTTTATGAGCTGTAAGACTTTTATGA 58.130 33.333 0.00 0.00 34.07 2.15
2540 2794 8.116753 CCGTTTATGAGCTGTAAGACTTTTATG 58.883 37.037 0.00 0.00 34.07 1.90
2541 2795 8.038944 TCCGTTTATGAGCTGTAAGACTTTTAT 58.961 33.333 0.00 0.00 34.07 1.40
2542 2796 7.380536 TCCGTTTATGAGCTGTAAGACTTTTA 58.619 34.615 0.00 0.00 34.07 1.52
2543 2797 6.228258 TCCGTTTATGAGCTGTAAGACTTTT 58.772 36.000 0.00 0.00 34.07 2.27
2544 2798 5.790593 TCCGTTTATGAGCTGTAAGACTTT 58.209 37.500 0.00 0.00 34.07 2.66
2545 2799 5.401531 TCCGTTTATGAGCTGTAAGACTT 57.598 39.130 0.00 0.00 34.07 3.01
2546 2800 5.000012 CTCCGTTTATGAGCTGTAAGACT 58.000 43.478 0.00 0.00 34.07 3.24
2556 2810 6.910536 ACTTTATTCTGCTCCGTTTATGAG 57.089 37.500 0.00 0.00 0.00 2.90
2557 2811 8.201464 TGATACTTTATTCTGCTCCGTTTATGA 58.799 33.333 0.00 0.00 0.00 2.15
2558 2812 8.365399 TGATACTTTATTCTGCTCCGTTTATG 57.635 34.615 0.00 0.00 0.00 1.90
2559 2813 8.958119 TTGATACTTTATTCTGCTCCGTTTAT 57.042 30.769 0.00 0.00 0.00 1.40
2560 2814 8.780846 TTTGATACTTTATTCTGCTCCGTTTA 57.219 30.769 0.00 0.00 0.00 2.01
2561 2815 7.681939 TTTGATACTTTATTCTGCTCCGTTT 57.318 32.000 0.00 0.00 0.00 3.60
2562 2816 7.148239 CCTTTTGATACTTTATTCTGCTCCGTT 60.148 37.037 0.00 0.00 0.00 4.44
2563 2817 6.316390 CCTTTTGATACTTTATTCTGCTCCGT 59.684 38.462 0.00 0.00 0.00 4.69
2564 2818 6.538742 TCCTTTTGATACTTTATTCTGCTCCG 59.461 38.462 0.00 0.00 0.00 4.63
2565 2819 7.865706 TCCTTTTGATACTTTATTCTGCTCC 57.134 36.000 0.00 0.00 0.00 4.70
2579 2833 9.921637 GGTTCACATGTATTTTTCCTTTTGATA 57.078 29.630 0.00 0.00 0.00 2.15
2580 2834 8.428063 TGGTTCACATGTATTTTTCCTTTTGAT 58.572 29.630 0.00 0.00 0.00 2.57
2581 2835 7.786030 TGGTTCACATGTATTTTTCCTTTTGA 58.214 30.769 0.00 0.00 0.00 2.69
2582 2836 8.606040 ATGGTTCACATGTATTTTTCCTTTTG 57.394 30.769 0.00 0.00 38.70 2.44
2597 2851 1.533625 CCGGTTGACATGGTTCACAT 58.466 50.000 0.00 0.00 41.57 3.21
2598 2852 1.169661 GCCGGTTGACATGGTTCACA 61.170 55.000 1.90 0.00 0.00 3.58
2599 2853 1.169661 TGCCGGTTGACATGGTTCAC 61.170 55.000 1.90 0.00 0.00 3.18
2600 2854 1.149401 TGCCGGTTGACATGGTTCA 59.851 52.632 1.90 0.00 0.00 3.18
2601 2855 1.169661 TGTGCCGGTTGACATGGTTC 61.170 55.000 1.90 0.00 0.00 3.62
2602 2856 0.753479 TTGTGCCGGTTGACATGGTT 60.753 50.000 1.90 0.00 0.00 3.67
2603 2857 0.539438 ATTGTGCCGGTTGACATGGT 60.539 50.000 1.90 0.00 0.00 3.55
2604 2858 0.109179 CATTGTGCCGGTTGACATGG 60.109 55.000 1.90 0.00 0.00 3.66
2605 2859 0.880441 TCATTGTGCCGGTTGACATG 59.120 50.000 1.90 0.00 0.00 3.21
2606 2860 1.541147 CTTCATTGTGCCGGTTGACAT 59.459 47.619 1.90 0.00 0.00 3.06
2607 2861 0.950836 CTTCATTGTGCCGGTTGACA 59.049 50.000 1.90 0.50 0.00 3.58
2608 2862 1.234821 TCTTCATTGTGCCGGTTGAC 58.765 50.000 1.90 0.00 0.00 3.18
2609 2863 2.198827 ATCTTCATTGTGCCGGTTGA 57.801 45.000 1.90 0.00 0.00 3.18
2610 2864 4.433186 TTTATCTTCATTGTGCCGGTTG 57.567 40.909 1.90 0.00 0.00 3.77
2611 2865 5.461032 TTTTTATCTTCATTGTGCCGGTT 57.539 34.783 1.90 0.00 0.00 4.44
2612 2866 4.082245 CCTTTTTATCTTCATTGTGCCGGT 60.082 41.667 1.90 0.00 0.00 5.28
2613 2867 4.157656 TCCTTTTTATCTTCATTGTGCCGG 59.842 41.667 0.00 0.00 0.00 6.13
2614 2868 5.309323 TCCTTTTTATCTTCATTGTGCCG 57.691 39.130 0.00 0.00 0.00 5.69
2615 2869 7.436376 GCTTATCCTTTTTATCTTCATTGTGCC 59.564 37.037 0.00 0.00 0.00 5.01
2616 2870 8.193438 AGCTTATCCTTTTTATCTTCATTGTGC 58.807 33.333 0.00 0.00 0.00 4.57
2617 2871 9.727627 GAGCTTATCCTTTTTATCTTCATTGTG 57.272 33.333 0.00 0.00 0.00 3.33
2618 2872 9.692325 AGAGCTTATCCTTTTTATCTTCATTGT 57.308 29.630 0.00 0.00 0.00 2.71
2625 2879 9.654919 AGTCTAGAGAGCTTATCCTTTTTATCT 57.345 33.333 0.00 0.00 0.00 1.98
2626 2880 9.908152 GAGTCTAGAGAGCTTATCCTTTTTATC 57.092 37.037 0.00 0.00 0.00 1.75
2627 2881 8.866093 GGAGTCTAGAGAGCTTATCCTTTTTAT 58.134 37.037 0.00 0.00 0.00 1.40
2628 2882 8.062536 AGGAGTCTAGAGAGCTTATCCTTTTTA 58.937 37.037 0.00 0.00 31.97 1.52
2629 2883 6.900743 AGGAGTCTAGAGAGCTTATCCTTTTT 59.099 38.462 0.00 0.00 31.97 1.94
2630 2884 6.440354 AGGAGTCTAGAGAGCTTATCCTTTT 58.560 40.000 0.00 0.00 31.97 2.27
2631 2885 6.025793 AGGAGTCTAGAGAGCTTATCCTTT 57.974 41.667 0.00 0.00 31.97 3.11
2632 2886 5.663158 AGGAGTCTAGAGAGCTTATCCTT 57.337 43.478 0.00 0.00 31.97 3.36
2633 2887 6.069615 GGATAGGAGTCTAGAGAGCTTATCCT 60.070 46.154 19.73 14.05 36.68 3.24
2634 2888 6.069615 AGGATAGGAGTCTAGAGAGCTTATCC 60.070 46.154 19.56 19.56 38.11 2.59
2635 2889 6.823689 CAGGATAGGAGTCTAGAGAGCTTATC 59.176 46.154 0.00 1.84 0.00 1.75
2636 2890 6.274672 ACAGGATAGGAGTCTAGAGAGCTTAT 59.725 42.308 0.00 0.00 0.00 1.73
2637 2891 5.609284 ACAGGATAGGAGTCTAGAGAGCTTA 59.391 44.000 0.00 0.00 0.00 3.09
2638 2892 4.415512 ACAGGATAGGAGTCTAGAGAGCTT 59.584 45.833 0.00 0.00 0.00 3.74
2639 2893 3.980698 ACAGGATAGGAGTCTAGAGAGCT 59.019 47.826 0.00 0.00 0.00 4.09
2640 2894 4.367039 ACAGGATAGGAGTCTAGAGAGC 57.633 50.000 0.00 0.00 0.00 4.09
2641 2895 6.374333 GCATAACAGGATAGGAGTCTAGAGAG 59.626 46.154 0.00 0.00 0.00 3.20
2642 2896 6.242396 GCATAACAGGATAGGAGTCTAGAGA 58.758 44.000 0.00 0.00 0.00 3.10
2643 2897 5.123186 CGCATAACAGGATAGGAGTCTAGAG 59.877 48.000 0.00 0.00 0.00 2.43
2644 2898 5.004448 CGCATAACAGGATAGGAGTCTAGA 58.996 45.833 0.00 0.00 0.00 2.43
2645 2899 5.004448 TCGCATAACAGGATAGGAGTCTAG 58.996 45.833 0.00 0.00 0.00 2.43
2646 2900 4.981812 TCGCATAACAGGATAGGAGTCTA 58.018 43.478 0.00 0.00 0.00 2.59
2647 2901 3.823873 CTCGCATAACAGGATAGGAGTCT 59.176 47.826 0.00 0.00 0.00 3.24
2648 2902 3.612955 GCTCGCATAACAGGATAGGAGTC 60.613 52.174 0.00 0.00 0.00 3.36
2649 2903 2.297597 GCTCGCATAACAGGATAGGAGT 59.702 50.000 0.00 0.00 0.00 3.85
2650 2904 2.669670 CGCTCGCATAACAGGATAGGAG 60.670 54.545 0.00 0.00 0.00 3.69
2651 2905 1.269723 CGCTCGCATAACAGGATAGGA 59.730 52.381 0.00 0.00 0.00 2.94
2652 2906 1.702886 CGCTCGCATAACAGGATAGG 58.297 55.000 0.00 0.00 0.00 2.57
2653 2907 1.063806 GCGCTCGCATAACAGGATAG 58.936 55.000 9.59 0.00 41.49 2.08
2654 2908 0.319555 GGCGCTCGCATAACAGGATA 60.320 55.000 16.36 0.00 44.11 2.59
2655 2909 1.595382 GGCGCTCGCATAACAGGAT 60.595 57.895 16.36 0.00 44.11 3.24
2656 2910 2.202878 GGCGCTCGCATAACAGGA 60.203 61.111 16.36 0.00 44.11 3.86
2657 2911 1.835483 GATGGCGCTCGCATAACAGG 61.835 60.000 16.36 0.00 44.11 4.00
2658 2912 1.566563 GATGGCGCTCGCATAACAG 59.433 57.895 16.36 0.00 44.11 3.16
2659 2913 1.887242 GGATGGCGCTCGCATAACA 60.887 57.895 16.36 5.08 44.11 2.41
2660 2914 2.939022 GGATGGCGCTCGCATAAC 59.061 61.111 16.36 3.44 44.11 1.89
2661 2915 2.636778 TTCGGATGGCGCTCGCATAA 62.637 55.000 16.36 1.48 44.11 1.90
2662 2916 3.145422 TTCGGATGGCGCTCGCATA 62.145 57.895 16.36 4.84 44.11 3.14
2663 2917 4.529219 TTCGGATGGCGCTCGCAT 62.529 61.111 16.36 1.47 44.11 4.73


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

AutoCloner maintained by Alex Coulton.