Multiple sequence alignment - TraesCS1D01G350900

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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 TraesCS1D01G350900 chr1D 100.000 2710 0 0 1 2710 436218203 436215494 0.000000e+00 5005
1 TraesCS1D01G350900 chr1A 86.408 2369 160 76 1 2279 533470098 533467802 0.000000e+00 2442
2 TraesCS1D01G350900 chr1A 94.902 255 12 1 2457 2710 533467609 533467355 5.440000e-107 398
3 TraesCS1D01G350900 chr1A 95.181 166 8 0 2292 2457 250067520 250067355 2.070000e-66 263
4 TraesCS1D01G350900 chr1A 93.373 166 11 0 2292 2457 284322620 284322785 2.080000e-61 246
5 TraesCS1D01G350900 chr1B 89.864 1401 71 29 660 2030 591235334 591233975 0.000000e+00 1735
6 TraesCS1D01G350900 chr1B 86.355 513 43 9 103 608 591235968 591235476 3.970000e-148 534
7 TraesCS1D01G350900 chr1B 95.181 166 8 0 2292 2457 423584272 423584107 2.070000e-66 263
8 TraesCS1D01G350900 chr7B 95.758 165 7 0 2292 2456 394149572 394149736 1.600000e-67 267
9 TraesCS1D01G350900 chr7B 94.578 166 9 0 2292 2457 424832526 424832361 9.630000e-65 257
10 TraesCS1D01G350900 chr2A 95.181 166 8 0 2292 2457 403801995 403801830 2.070000e-66 263
11 TraesCS1D01G350900 chr4A 93.939 165 10 0 2292 2456 63718068 63717904 1.610000e-62 250
12 TraesCS1D01G350900 chr4A 92.614 176 9 1 2292 2463 67022519 67022694 1.610000e-62 250
13 TraesCS1D01G350900 chr6B 92.899 169 12 0 2292 2460 144362929 144362761 2.080000e-61 246


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 TraesCS1D01G350900 chr1D 436215494 436218203 2709 True 5005.0 5005 100.0000 1 2710 1 chr1D.!!$R1 2709
1 TraesCS1D01G350900 chr1A 533467355 533470098 2743 True 1420.0 2442 90.6550 1 2710 2 chr1A.!!$R2 2709
2 TraesCS1D01G350900 chr1B 591233975 591235968 1993 True 1134.5 1735 88.1095 103 2030 2 chr1B.!!$R2 1927

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
105 106 0.037975 GCTTCACCCATGTTTGCCAG 60.038 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2271 1.066587 GCGACCCTCTTCTCCATCG 59.933 63.158 0.0 0.0 0.0 3.84 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
43 44 1.526686 CACACAGGAGCTGCAACCA 60.527 57.895 8.35 0.00 34.37 3.67
47 48 3.655211 AGGAGCTGCAACCAGGGG 61.655 66.667 8.35 0.00 39.54 4.79
92 93 1.457303 CGCACACTACAGAAGCTTCAC 59.543 52.381 27.57 2.86 0.00 3.18
100 101 2.949447 ACAGAAGCTTCACCCATGTTT 58.051 42.857 27.57 1.05 0.00 2.83
105 106 0.037975 GCTTCACCCATGTTTGCCAG 60.038 55.000 0.00 0.00 0.00 4.85
106 107 1.619654 CTTCACCCATGTTTGCCAGA 58.380 50.000 0.00 0.00 0.00 3.86
107 108 1.542915 CTTCACCCATGTTTGCCAGAG 59.457 52.381 0.00 0.00 0.00 3.35
109 110 0.896940 CACCCATGTTTGCCAGAGCT 60.897 55.000 0.00 0.00 40.80 4.09
110 111 0.896940 ACCCATGTTTGCCAGAGCTG 60.897 55.000 0.00 0.00 40.80 4.24
111 112 1.214589 CCATGTTTGCCAGAGCTGC 59.785 57.895 0.00 0.00 40.80 5.25
145 146 3.461061 CATCATCGGTGAATGCTACAGT 58.539 45.455 0.60 0.00 38.01 3.55
152 153 3.179830 GGTGAATGCTACAGTCGTACAG 58.820 50.000 0.00 0.00 30.57 2.74
171 172 2.553602 CAGTGCAAAAGCTACATCCACA 59.446 45.455 0.00 0.00 0.00 4.17
185 186 1.376424 CCACATTCGCCAGAGCTGT 60.376 57.895 0.00 0.00 36.60 4.40
190 191 0.613260 ATTCGCCAGAGCTGTAACCA 59.387 50.000 0.00 0.00 36.60 3.67
194 195 1.812571 CGCCAGAGCTGTAACCATTTT 59.187 47.619 0.00 0.00 36.60 1.82
196 197 2.819608 GCCAGAGCTGTAACCATTTTGA 59.180 45.455 0.00 0.00 35.50 2.69
268 269 0.248661 CTGCAAGCATGAGCATGAGC 60.249 55.000 14.27 13.37 41.78 4.26
300 301 2.914097 GCCCTTGCTGCAACCAGT 60.914 61.111 11.69 0.00 41.26 4.00
303 304 1.829533 CCTTGCTGCAACCAGTGGT 60.830 57.895 9.70 9.70 41.26 4.16
353 354 2.280797 GACTGCAACTGGTGGCGA 60.281 61.111 0.00 0.00 0.00 5.54
389 391 0.541392 CATGACCGATGGGGACTTCA 59.459 55.000 0.00 0.00 39.97 3.02
514 535 4.019231 GGAGAGAGATGGTTAAGTTTGGGT 60.019 45.833 0.00 0.00 0.00 4.51
515 536 5.515008 GGAGAGAGATGGTTAAGTTTGGGTT 60.515 44.000 0.00 0.00 0.00 4.11
539 560 3.145551 CCGGCGCCTAGTAGTGGT 61.146 66.667 26.68 0.00 0.00 4.16
541 562 2.412323 CGGCGCCTAGTAGTGGTCA 61.412 63.158 26.68 0.00 0.00 4.02
542 563 1.735376 CGGCGCCTAGTAGTGGTCAT 61.735 60.000 26.68 0.00 0.00 3.06
543 564 0.464452 GGCGCCTAGTAGTGGTCATT 59.536 55.000 22.15 0.00 0.00 2.57
544 565 1.134491 GGCGCCTAGTAGTGGTCATTT 60.134 52.381 22.15 0.00 0.00 2.32
545 566 2.629051 GCGCCTAGTAGTGGTCATTTT 58.371 47.619 0.00 0.00 0.00 1.82
546 567 3.007635 GCGCCTAGTAGTGGTCATTTTT 58.992 45.455 0.00 0.00 0.00 1.94
600 621 6.723298 TTCAATGGTTTCAATGGTGTTACT 57.277 33.333 0.00 0.00 0.00 2.24
636 765 0.538516 CCACCCGTGGTCATTTCCAA 60.539 55.000 5.66 0.00 45.53 3.53
647 776 0.318120 CATTTCCAAAAGCCAGCGGT 59.682 50.000 0.00 0.00 0.00 5.68
654 783 0.668535 AAAAGCCAGCGGTTGTTCTC 59.331 50.000 0.00 0.00 0.00 2.87
674 803 2.281484 TGGCGTTTGGGCTCTGAC 60.281 61.111 0.00 0.00 42.84 3.51
678 807 1.597854 CGTTTGGGCTCTGACTGCA 60.598 57.895 0.00 0.00 0.00 4.41
753 891 1.514443 CGTCGACTCTTTCTCGGGC 60.514 63.158 14.70 0.00 0.00 6.13
755 893 2.202623 CGACTCTTTCTCGGGCCG 60.203 66.667 22.51 22.51 0.00 6.13
756 894 2.697761 CGACTCTTTCTCGGGCCGA 61.698 63.158 29.14 29.14 0.00 5.54
954 1093 2.991540 GCAAACACCTGCTCCCCC 60.992 66.667 0.00 0.00 39.34 5.40
955 1094 2.520458 CAAACACCTGCTCCCCCA 59.480 61.111 0.00 0.00 0.00 4.96
956 1095 1.604593 CAAACACCTGCTCCCCCAG 60.605 63.158 0.00 0.00 0.00 4.45
990 1145 4.664677 CCCGTCGATCCATCCCGC 62.665 72.222 0.00 0.00 0.00 6.13
1005 1160 2.496341 CGCTCTCTTCCGATGGCA 59.504 61.111 0.00 0.00 0.00 4.92
1202 1357 1.355916 GTAACAAACCACGCCGCAA 59.644 52.632 0.00 0.00 0.00 4.85
1211 1372 1.154225 CACGCCGCAAATCCTTGTC 60.154 57.895 0.00 0.00 34.79 3.18
1212 1373 2.332654 ACGCCGCAAATCCTTGTCC 61.333 57.895 0.00 0.00 34.79 4.02
1213 1374 2.331893 CGCCGCAAATCCTTGTCCA 61.332 57.895 0.00 0.00 34.79 4.02
1214 1375 1.656818 CGCCGCAAATCCTTGTCCAT 61.657 55.000 0.00 0.00 34.79 3.41
1215 1376 0.101219 GCCGCAAATCCTTGTCCATC 59.899 55.000 0.00 0.00 34.79 3.51
1216 1377 1.755179 CCGCAAATCCTTGTCCATCT 58.245 50.000 0.00 0.00 34.79 2.90
1218 1379 2.098117 CCGCAAATCCTTGTCCATCTTC 59.902 50.000 0.00 0.00 34.79 2.87
1220 1381 4.191544 CGCAAATCCTTGTCCATCTTCTA 58.808 43.478 0.00 0.00 34.79 2.10
1221 1382 4.272018 CGCAAATCCTTGTCCATCTTCTAG 59.728 45.833 0.00 0.00 34.79 2.43
1222 1383 5.189180 GCAAATCCTTGTCCATCTTCTAGT 58.811 41.667 0.00 0.00 34.79 2.57
1223 1384 5.295540 GCAAATCCTTGTCCATCTTCTAGTC 59.704 44.000 0.00 0.00 34.79 2.59
1243 1410 2.801111 TCGTTACTCTCCTCGATCGATG 59.199 50.000 19.78 16.34 0.00 3.84
1246 1413 0.665835 ACTCTCCTCGATCGATGTGC 59.334 55.000 19.78 0.00 0.00 4.57
1248 1415 1.336440 CTCTCCTCGATCGATGTGCTT 59.664 52.381 19.78 0.00 0.00 3.91
1254 1421 3.182182 CTCGATCGATGTGCTTCTTGAA 58.818 45.455 19.78 0.00 0.00 2.69
1262 1429 4.322804 CGATGTGCTTCTTGAATTTCTTGC 59.677 41.667 0.00 0.00 0.00 4.01
1263 1430 4.924305 TGTGCTTCTTGAATTTCTTGCT 57.076 36.364 0.00 0.00 0.00 3.91
1524 1694 3.665675 ATGTCGGAGAAGCACGGCC 62.666 63.158 0.00 0.00 39.69 6.13
1679 1849 4.803426 GTGGTCCTCGGCGCTCTG 62.803 72.222 7.64 0.00 0.00 3.35
1713 1883 0.859232 CGTCGTTGGGTTCTGAGTTG 59.141 55.000 0.00 0.00 0.00 3.16
1720 1890 0.954452 GGGTTCTGAGTTGCTGTTGG 59.046 55.000 0.00 0.00 0.00 3.77
1722 1892 2.024414 GGTTCTGAGTTGCTGTTGGTT 58.976 47.619 0.00 0.00 0.00 3.67
1723 1893 3.211045 GGTTCTGAGTTGCTGTTGGTTA 58.789 45.455 0.00 0.00 0.00 2.85
1724 1894 3.251004 GGTTCTGAGTTGCTGTTGGTTAG 59.749 47.826 0.00 0.00 0.00 2.34
1921 2111 2.288152 ACTTGGGCGTGCTGTTTATTTG 60.288 45.455 0.00 0.00 0.00 2.32
1942 2132 7.851387 TTTGCGTGATAAATAAGGTGATACA 57.149 32.000 0.00 0.00 0.00 2.29
1948 2144 7.273598 CGTGATAAATAAGGTGATACAGGATCG 59.726 40.741 0.00 0.00 37.38 3.69
1949 2145 7.063544 GTGATAAATAAGGTGATACAGGATCGC 59.936 40.741 0.00 0.00 43.29 4.58
1950 2146 4.955811 AATAAGGTGATACAGGATCGCA 57.044 40.909 8.51 0.00 45.44 5.10
1951 2147 4.955811 ATAAGGTGATACAGGATCGCAA 57.044 40.909 8.51 0.00 45.44 4.85
1952 2148 2.898729 AGGTGATACAGGATCGCAAG 57.101 50.000 8.51 0.00 45.44 4.01
1953 2149 2.111384 AGGTGATACAGGATCGCAAGT 58.889 47.619 8.51 0.00 45.44 3.16
1954 2150 3.296854 AGGTGATACAGGATCGCAAGTA 58.703 45.455 8.51 0.00 45.44 2.24
1955 2151 3.898123 AGGTGATACAGGATCGCAAGTAT 59.102 43.478 8.51 0.00 45.44 2.12
1956 2152 3.990469 GGTGATACAGGATCGCAAGTATG 59.010 47.826 8.51 0.00 45.44 2.39
1957 2153 3.990469 GTGATACAGGATCGCAAGTATGG 59.010 47.826 0.78 0.00 43.47 2.74
1958 2154 3.895041 TGATACAGGATCGCAAGTATGGA 59.105 43.478 0.00 0.00 37.38 3.41
1959 2155 4.528206 TGATACAGGATCGCAAGTATGGAT 59.472 41.667 0.00 0.00 37.38 3.41
1960 2156 5.714806 TGATACAGGATCGCAAGTATGGATA 59.285 40.000 0.00 0.00 37.38 2.59
2009 2210 6.026947 ACTGTACAAGTCTGTAACTGATCC 57.973 41.667 0.00 0.00 39.75 3.36
2016 2217 6.596888 ACAAGTCTGTAACTGATCCATTGATG 59.403 38.462 0.00 0.00 38.58 3.07
2061 2262 0.526524 CGCTACCACAGAGCACTAGC 60.527 60.000 0.00 0.00 40.09 3.42
2091 2292 2.754658 GGAGAAGAGGGTCGCCGA 60.755 66.667 0.00 0.00 0.00 5.54
2098 2299 3.718210 GAGGGTCGCCGATGTGGTC 62.718 68.421 0.00 0.00 41.21 4.02
2102 2303 1.449601 GTCGCCGATGTGGTCCAAT 60.450 57.895 0.00 0.00 41.21 3.16
2103 2304 1.449423 TCGCCGATGTGGTCCAATG 60.449 57.895 0.00 0.00 41.21 2.82
2117 2318 3.244422 GGTCCAATGTTGAGTACTCCACA 60.244 47.826 26.64 26.64 39.17 4.17
2118 2319 3.746492 GTCCAATGTTGAGTACTCCACAC 59.254 47.826 26.90 17.65 37.94 3.82
2119 2320 3.389656 TCCAATGTTGAGTACTCCACACA 59.610 43.478 26.90 21.79 37.94 3.72
2120 2321 3.748048 CCAATGTTGAGTACTCCACACAG 59.252 47.826 26.90 21.44 37.94 3.66
2121 2322 4.380531 CAATGTTGAGTACTCCACACAGT 58.619 43.478 26.90 18.90 37.94 3.55
2122 2323 4.689612 ATGTTGAGTACTCCACACAGTT 57.310 40.909 26.90 12.28 37.94 3.16
2123 2324 4.481368 TGTTGAGTACTCCACACAGTTT 57.519 40.909 22.30 0.00 31.38 2.66
2124 2325 4.188462 TGTTGAGTACTCCACACAGTTTG 58.812 43.478 22.30 0.00 31.38 2.93
2125 2326 2.833794 TGAGTACTCCACACAGTTTGC 58.166 47.619 20.11 0.00 0.00 3.68
2126 2327 2.169561 TGAGTACTCCACACAGTTTGCA 59.830 45.455 20.11 0.00 0.00 4.08
2127 2328 3.181455 TGAGTACTCCACACAGTTTGCAT 60.181 43.478 20.11 0.00 0.00 3.96
2200 2401 4.279671 TCCCAAACGTAATTGCAGAAACAT 59.720 37.500 0.00 0.00 0.00 2.71
2206 2407 4.214545 ACGTAATTGCAGAAACATCCGAAA 59.785 37.500 0.00 0.00 0.00 3.46
2208 2409 5.452302 CGTAATTGCAGAAACATCCGAAATC 59.548 40.000 0.00 0.00 0.00 2.17
2210 2411 4.844998 TTGCAGAAACATCCGAAATCAA 57.155 36.364 0.00 0.00 0.00 2.57
2211 2412 5.389859 TTGCAGAAACATCCGAAATCAAT 57.610 34.783 0.00 0.00 0.00 2.57
2212 2413 4.985413 TGCAGAAACATCCGAAATCAATC 58.015 39.130 0.00 0.00 0.00 2.67
2213 2414 4.701651 TGCAGAAACATCCGAAATCAATCT 59.298 37.500 0.00 0.00 0.00 2.40
2214 2415 5.163723 TGCAGAAACATCCGAAATCAATCTC 60.164 40.000 0.00 0.00 0.00 2.75
2215 2416 5.731686 GCAGAAACATCCGAAATCAATCTCC 60.732 44.000 0.00 0.00 0.00 3.71
2216 2417 5.355071 CAGAAACATCCGAAATCAATCTCCA 59.645 40.000 0.00 0.00 0.00 3.86
2217 2418 5.945784 AGAAACATCCGAAATCAATCTCCAA 59.054 36.000 0.00 0.00 0.00 3.53
2218 2419 6.434028 AGAAACATCCGAAATCAATCTCCAAA 59.566 34.615 0.00 0.00 0.00 3.28
2219 2420 5.567138 ACATCCGAAATCAATCTCCAAAC 57.433 39.130 0.00 0.00 0.00 2.93
2220 2421 5.009631 ACATCCGAAATCAATCTCCAAACA 58.990 37.500 0.00 0.00 0.00 2.83
2221 2422 5.476599 ACATCCGAAATCAATCTCCAAACAA 59.523 36.000 0.00 0.00 0.00 2.83
2222 2423 6.015519 ACATCCGAAATCAATCTCCAAACAAA 60.016 34.615 0.00 0.00 0.00 2.83
2223 2424 6.588719 TCCGAAATCAATCTCCAAACAAAT 57.411 33.333 0.00 0.00 0.00 2.32
2224 2425 6.389091 TCCGAAATCAATCTCCAAACAAATG 58.611 36.000 0.00 0.00 0.00 2.32
2225 2426 6.208402 TCCGAAATCAATCTCCAAACAAATGA 59.792 34.615 0.00 0.00 0.00 2.57
2226 2427 6.867816 CCGAAATCAATCTCCAAACAAATGAA 59.132 34.615 0.00 0.00 0.00 2.57
2227 2428 7.062605 CCGAAATCAATCTCCAAACAAATGAAG 59.937 37.037 0.00 0.00 0.00 3.02
2228 2429 7.411157 CGAAATCAATCTCCAAACAAATGAAGC 60.411 37.037 0.00 0.00 0.00 3.86
2229 2430 6.600882 ATCAATCTCCAAACAAATGAAGCT 57.399 33.333 0.00 0.00 0.00 3.74
2230 2431 6.409524 TCAATCTCCAAACAAATGAAGCTT 57.590 33.333 0.00 0.00 0.00 3.74
2231 2432 6.819284 TCAATCTCCAAACAAATGAAGCTTT 58.181 32.000 0.00 0.00 0.00 3.51
2232 2433 6.702723 TCAATCTCCAAACAAATGAAGCTTTG 59.297 34.615 0.00 0.00 41.02 2.77
2233 2434 4.370917 TCTCCAAACAAATGAAGCTTTGC 58.629 39.130 0.00 0.00 39.26 3.68
2247 2448 3.748083 AGCTTTGCATCAGAGTTCAGAA 58.252 40.909 0.00 0.00 0.00 3.02
2248 2449 3.501445 AGCTTTGCATCAGAGTTCAGAAC 59.499 43.478 5.00 5.00 0.00 3.01
2250 2451 4.023365 GCTTTGCATCAGAGTTCAGAACTT 60.023 41.667 17.19 4.91 43.03 2.66
2252 2453 6.455360 TTTGCATCAGAGTTCAGAACTTTT 57.545 33.333 17.19 6.37 43.03 2.27
2253 2454 7.566760 TTTGCATCAGAGTTCAGAACTTTTA 57.433 32.000 17.19 3.77 43.03 1.52
2254 2455 6.545504 TGCATCAGAGTTCAGAACTTTTAC 57.454 37.500 17.19 4.55 43.03 2.01
2255 2456 5.470098 TGCATCAGAGTTCAGAACTTTTACC 59.530 40.000 17.19 4.18 43.03 2.85
2257 2458 4.628074 TCAGAGTTCAGAACTTTTACCCG 58.372 43.478 17.19 0.05 43.03 5.28
2279 2502 6.074569 CCCGCACACTTTTTGTACTTTTAATG 60.075 38.462 0.00 0.00 35.67 1.90
2280 2503 6.474102 CCGCACACTTTTTGTACTTTTAATGT 59.526 34.615 0.00 0.00 35.67 2.71
2281 2504 7.009723 CCGCACACTTTTTGTACTTTTAATGTT 59.990 33.333 0.00 0.00 35.67 2.71
2308 2531 7.642669 ACACAAATGTTGTAGACTCAGAATTG 58.357 34.615 0.00 0.00 43.23 2.32
2309 2532 7.283127 ACACAAATGTTGTAGACTCAGAATTGT 59.717 33.333 0.00 0.00 43.23 2.71
2310 2533 7.588854 CACAAATGTTGTAGACTCAGAATTGTG 59.411 37.037 0.00 0.00 43.23 3.33
2311 2534 5.869753 ATGTTGTAGACTCAGAATTGTGC 57.130 39.130 0.00 0.00 0.00 4.57
2312 2535 4.065088 TGTTGTAGACTCAGAATTGTGCC 58.935 43.478 0.00 0.00 0.00 5.01
2313 2536 4.202357 TGTTGTAGACTCAGAATTGTGCCT 60.202 41.667 0.00 0.00 0.00 4.75
2314 2537 4.193826 TGTAGACTCAGAATTGTGCCTC 57.806 45.455 0.00 0.00 0.00 4.70
2315 2538 2.777832 AGACTCAGAATTGTGCCTCC 57.222 50.000 0.00 0.00 0.00 4.30
2317 2540 2.079925 GACTCAGAATTGTGCCTCCAC 58.920 52.381 0.00 0.00 42.40 4.02
2318 2541 1.271597 ACTCAGAATTGTGCCTCCACC 60.272 52.381 0.00 0.00 41.35 4.61
2319 2542 1.004044 CTCAGAATTGTGCCTCCACCT 59.996 52.381 0.00 0.00 41.35 4.00
2321 2544 2.237143 TCAGAATTGTGCCTCCACCTAG 59.763 50.000 0.00 0.00 41.35 3.02
2322 2545 1.561542 AGAATTGTGCCTCCACCTAGG 59.438 52.381 7.41 7.41 41.35 3.02
2323 2546 1.282157 GAATTGTGCCTCCACCTAGGT 59.718 52.381 9.21 9.21 41.35 3.08
2324 2547 2.263895 ATTGTGCCTCCACCTAGGTA 57.736 50.000 15.80 0.00 41.35 3.08
2327 2550 2.986492 TGCCTCCACCTAGGTACAC 58.014 57.895 15.80 3.40 39.02 2.90
2328 2551 0.968901 TGCCTCCACCTAGGTACACG 60.969 60.000 15.80 1.48 39.02 4.49
2329 2552 0.969409 GCCTCCACCTAGGTACACGT 60.969 60.000 15.80 0.00 39.02 4.49
2330 2553 1.683011 GCCTCCACCTAGGTACACGTA 60.683 57.143 15.80 0.00 39.02 3.57
2331 2554 2.019984 CCTCCACCTAGGTACACGTAC 58.980 57.143 15.80 0.00 39.02 3.67
2332 2555 2.356535 CCTCCACCTAGGTACACGTACT 60.357 54.545 15.80 0.00 39.02 2.73
2333 2556 3.350833 CTCCACCTAGGTACACGTACTT 58.649 50.000 15.80 2.48 39.02 2.24
2334 2557 4.517285 CTCCACCTAGGTACACGTACTTA 58.483 47.826 15.80 3.52 39.02 2.24
2335 2558 4.517285 TCCACCTAGGTACACGTACTTAG 58.483 47.826 15.80 15.84 42.15 2.18
2336 2559 3.065925 CCACCTAGGTACACGTACTTAGC 59.934 52.174 15.80 0.00 41.56 3.09
2337 2560 3.691118 CACCTAGGTACACGTACTTAGCA 59.309 47.826 15.80 0.00 41.56 3.49
2338 2561 3.691609 ACCTAGGTACACGTACTTAGCAC 59.308 47.826 14.41 0.00 41.56 4.40
2339 2562 3.065925 CCTAGGTACACGTACTTAGCACC 59.934 52.174 16.88 0.00 41.56 5.01
2341 2564 1.200020 GGTACACGTACTTAGCACCGT 59.800 52.381 7.25 0.00 36.36 4.83
2343 2566 2.514205 ACACGTACTTAGCACCGTTT 57.486 45.000 0.00 0.00 0.00 3.60
2344 2567 2.397549 ACACGTACTTAGCACCGTTTC 58.602 47.619 0.00 0.00 0.00 2.78
2345 2568 2.035066 ACACGTACTTAGCACCGTTTCT 59.965 45.455 0.00 0.00 0.00 2.52
2346 2569 3.054878 CACGTACTTAGCACCGTTTCTT 58.945 45.455 0.00 0.00 0.00 2.52
2347 2570 3.120782 CACGTACTTAGCACCGTTTCTTC 59.879 47.826 0.00 0.00 0.00 2.87
2348 2571 2.665052 CGTACTTAGCACCGTTTCTTCC 59.335 50.000 0.00 0.00 0.00 3.46
2349 2572 2.180432 ACTTAGCACCGTTTCTTCCC 57.820 50.000 0.00 0.00 0.00 3.97
2350 2573 1.076332 CTTAGCACCGTTTCTTCCCG 58.924 55.000 0.00 0.00 0.00 5.14
2355 2578 2.046604 CCGTTTCTTCCCGGGGTC 60.047 66.667 23.50 4.11 40.54 4.46
2356 2579 2.745037 CGTTTCTTCCCGGGGTCA 59.255 61.111 23.50 3.93 0.00 4.02
2358 2581 1.303074 GTTTCTTCCCGGGGTCACC 60.303 63.158 23.50 0.40 0.00 4.02
2359 2582 1.770927 TTTCTTCCCGGGGTCACCA 60.771 57.895 23.50 0.00 40.22 4.17
2360 2583 1.137594 TTTCTTCCCGGGGTCACCAT 61.138 55.000 23.50 0.00 40.22 3.55
2361 2584 0.252789 TTCTTCCCGGGGTCACCATA 60.253 55.000 23.50 0.00 40.22 2.74
2362 2585 0.979187 TCTTCCCGGGGTCACCATAC 60.979 60.000 23.50 0.00 40.22 2.39
2363 2586 0.981277 CTTCCCGGGGTCACCATACT 60.981 60.000 23.50 0.00 40.22 2.12
2364 2587 0.339162 TTCCCGGGGTCACCATACTA 59.661 55.000 23.50 0.00 40.22 1.82
2365 2588 0.397535 TCCCGGGGTCACCATACTAC 60.398 60.000 23.50 0.00 40.22 2.73
2366 2589 0.398098 CCCGGGGTCACCATACTACT 60.398 60.000 14.71 0.00 40.22 2.57
2367 2590 1.038280 CCGGGGTCACCATACTACTC 58.962 60.000 0.00 0.00 40.22 2.59
2368 2591 1.411216 CCGGGGTCACCATACTACTCT 60.411 57.143 0.00 0.00 40.22 3.24
2369 2592 1.955080 CGGGGTCACCATACTACTCTC 59.045 57.143 0.00 0.00 40.22 3.20
2371 2594 3.224269 GGGGTCACCATACTACTCTCTC 58.776 54.545 0.00 0.00 39.85 3.20
2373 2596 4.139038 GGGTCACCATACTACTCTCTCTC 58.861 52.174 0.00 0.00 36.50 3.20
2377 2600 6.354130 GTCACCATACTACTCTCTCTCTTCT 58.646 44.000 0.00 0.00 0.00 2.85
2378 2601 6.826741 GTCACCATACTACTCTCTCTCTTCTT 59.173 42.308 0.00 0.00 0.00 2.52
2380 2603 8.549731 TCACCATACTACTCTCTCTCTTCTTAA 58.450 37.037 0.00 0.00 0.00 1.85
2381 2604 8.617809 CACCATACTACTCTCTCTCTTCTTAAC 58.382 40.741 0.00 0.00 0.00 2.01
2382 2605 8.554011 ACCATACTACTCTCTCTCTTCTTAACT 58.446 37.037 0.00 0.00 0.00 2.24
2385 2608 9.774413 ATACTACTCTCTCTCTTCTTAACTAGC 57.226 37.037 0.00 0.00 0.00 3.42
2386 2609 7.626390 ACTACTCTCTCTCTTCTTAACTAGCA 58.374 38.462 0.00 0.00 0.00 3.49
2388 2611 7.333528 ACTCTCTCTCTTCTTAACTAGCATG 57.666 40.000 0.00 0.00 0.00 4.06
2390 2613 5.068460 TCTCTCTCTTCTTAACTAGCATGCC 59.932 44.000 15.66 0.00 0.00 4.40
2391 2614 4.711846 TCTCTCTTCTTAACTAGCATGCCA 59.288 41.667 15.66 0.00 0.00 4.92
2392 2615 4.759782 TCTCTTCTTAACTAGCATGCCAC 58.240 43.478 15.66 0.00 0.00 5.01
2393 2616 4.222810 TCTCTTCTTAACTAGCATGCCACA 59.777 41.667 15.66 0.00 0.00 4.17
2394 2617 5.102953 TCTTCTTAACTAGCATGCCACAT 57.897 39.130 15.66 0.00 0.00 3.21
2395 2618 5.118990 TCTTCTTAACTAGCATGCCACATC 58.881 41.667 15.66 0.00 0.00 3.06
2396 2619 4.486125 TCTTAACTAGCATGCCACATCA 57.514 40.909 15.66 0.00 0.00 3.07
2397 2620 4.445453 TCTTAACTAGCATGCCACATCAG 58.555 43.478 15.66 4.60 0.00 2.90
2398 2621 4.162131 TCTTAACTAGCATGCCACATCAGA 59.838 41.667 15.66 7.08 0.00 3.27
2399 2622 2.322355 ACTAGCATGCCACATCAGAC 57.678 50.000 15.66 0.00 0.00 3.51
2403 2626 2.522185 AGCATGCCACATCAGACTTTT 58.478 42.857 15.66 0.00 0.00 2.27
2404 2627 2.895404 AGCATGCCACATCAGACTTTTT 59.105 40.909 15.66 0.00 0.00 1.94
2405 2628 2.991190 GCATGCCACATCAGACTTTTTG 59.009 45.455 6.36 0.00 0.00 2.44
2406 2629 2.798976 TGCCACATCAGACTTTTTGC 57.201 45.000 0.00 0.00 0.00 3.68
2407 2630 2.309613 TGCCACATCAGACTTTTTGCT 58.690 42.857 0.00 0.00 0.00 3.91
2408 2631 2.694628 TGCCACATCAGACTTTTTGCTT 59.305 40.909 0.00 0.00 0.00 3.91
2409 2632 3.888323 TGCCACATCAGACTTTTTGCTTA 59.112 39.130 0.00 0.00 0.00 3.09
2410 2633 4.022935 TGCCACATCAGACTTTTTGCTTAG 60.023 41.667 0.00 0.00 0.00 2.18
2411 2634 4.022849 GCCACATCAGACTTTTTGCTTAGT 60.023 41.667 0.00 0.00 0.00 2.24
2412 2635 5.507985 GCCACATCAGACTTTTTGCTTAGTT 60.508 40.000 0.00 0.00 0.00 2.24
2414 2637 5.916883 CACATCAGACTTTTTGCTTAGTTGG 59.083 40.000 0.00 0.00 0.00 3.77
2415 2638 4.568152 TCAGACTTTTTGCTTAGTTGGC 57.432 40.909 0.00 0.00 0.00 4.52
2416 2639 3.951037 TCAGACTTTTTGCTTAGTTGGCA 59.049 39.130 0.00 0.00 37.97 4.92
2417 2640 4.400884 TCAGACTTTTTGCTTAGTTGGCAA 59.599 37.500 0.00 0.00 46.12 4.52
2426 2649 1.537202 CTTAGTTGGCAACCTCAGCAC 59.463 52.381 25.81 0.00 0.00 4.40
2428 2651 1.529244 GTTGGCAACCTCAGCACCT 60.529 57.895 19.57 0.00 0.00 4.00
2429 2652 1.529010 TTGGCAACCTCAGCACCTG 60.529 57.895 0.00 0.00 0.00 4.00
2430 2653 2.113986 GGCAACCTCAGCACCTGT 59.886 61.111 0.00 0.00 32.61 4.00
2431 2654 1.374947 GGCAACCTCAGCACCTGTA 59.625 57.895 0.00 0.00 32.61 2.74
2432 2655 0.955919 GGCAACCTCAGCACCTGTAC 60.956 60.000 0.00 0.00 32.61 2.90
2435 2658 2.146342 CAACCTCAGCACCTGTACAAG 58.854 52.381 0.00 0.00 32.61 3.16
2446 2669 2.086869 CCTGTACAAGGTGGAGCATTG 58.913 52.381 0.00 0.00 43.74 2.82
2447 2670 2.086869 CTGTACAAGGTGGAGCATTGG 58.913 52.381 0.00 0.00 42.57 3.16
2449 2672 1.004277 GTACAAGGTGGAGCATTGGGA 59.996 52.381 0.00 0.00 42.57 4.37
2450 2673 0.038744 ACAAGGTGGAGCATTGGGAG 59.961 55.000 0.00 0.00 42.57 4.30
2451 2674 0.682209 CAAGGTGGAGCATTGGGAGG 60.682 60.000 0.00 0.00 35.45 4.30
2452 2675 1.867595 AAGGTGGAGCATTGGGAGGG 61.868 60.000 0.00 0.00 0.00 4.30
2453 2676 2.276740 GTGGAGCATTGGGAGGGG 59.723 66.667 0.00 0.00 0.00 4.79
2454 2677 3.743017 TGGAGCATTGGGAGGGGC 61.743 66.667 0.00 0.00 0.00 5.80
2455 2678 4.529731 GGAGCATTGGGAGGGGCC 62.530 72.222 0.00 0.00 0.00 5.80
2457 2680 2.044450 AGCATTGGGAGGGGCCTA 59.956 61.111 0.84 0.00 36.66 3.93
2458 2681 1.622442 AGCATTGGGAGGGGCCTAA 60.622 57.895 0.84 0.00 41.78 2.69
2459 2682 1.152673 GCATTGGGAGGGGCCTAAG 60.153 63.158 0.84 0.00 40.79 2.18
2460 2683 1.937924 GCATTGGGAGGGGCCTAAGT 61.938 60.000 0.84 0.00 40.79 2.24
2471 2710 4.490706 AGGGGCCTAAGTATACCTAACTG 58.509 47.826 0.84 0.00 0.00 3.16
2475 2714 5.364735 GGGCCTAAGTATACCTAACTGACAA 59.635 44.000 0.84 0.00 0.00 3.18
2486 2725 3.686726 CCTAACTGACAATGAAGCTGACC 59.313 47.826 0.00 0.00 0.00 4.02
2503 2742 3.570540 TGACCATTTCACCACCAAATGA 58.429 40.909 6.70 0.00 41.81 2.57
2504 2743 4.158786 TGACCATTTCACCACCAAATGAT 58.841 39.130 6.70 0.00 41.81 2.45
2568 2807 9.303116 CTTTTCCTATCCTCTAGCTTATCTACA 57.697 37.037 0.00 0.00 0.00 2.74
2668 2907 9.770097 TCTAAAATGTTTTGCATTGATTGGTAA 57.230 25.926 1.16 0.00 46.29 2.85
2684 2923 3.643159 GGTAACAAGCAAAACCTCCTG 57.357 47.619 0.00 0.00 0.00 3.86
2689 2928 2.695147 ACAAGCAAAACCTCCTGGAAAG 59.305 45.455 0.00 0.00 37.04 2.62
2700 2939 2.551459 CTCCTGGAAAGTTGCAGTCAAG 59.449 50.000 11.06 3.10 44.06 3.02
2702 2941 3.152341 CCTGGAAAGTTGCAGTCAAGAT 58.848 45.455 11.06 0.00 44.06 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.090658 GGTTATAGCATTCGCGACGATG 59.909 50.000 9.15 12.84 45.49 3.84
92 93 1.888018 CAGCTCTGGCAAACATGGG 59.112 57.895 0.00 0.00 41.70 4.00
100 101 2.281970 CTGGTTGCAGCTCTGGCA 60.282 61.111 0.00 0.00 41.70 4.92
133 134 3.833442 CACTGTACGACTGTAGCATTCA 58.167 45.455 0.00 0.00 0.00 2.57
171 172 0.613260 TGGTTACAGCTCTGGCGAAT 59.387 50.000 1.66 0.00 44.37 3.34
185 186 6.262496 TGGTTGTAACATCGTCAAAATGGTTA 59.738 34.615 0.00 0.00 0.00 2.85
190 191 6.325919 ACATGGTTGTAACATCGTCAAAAT 57.674 33.333 0.00 0.00 33.16 1.82
194 195 4.331443 GCATACATGGTTGTAACATCGTCA 59.669 41.667 0.00 0.00 41.51 4.35
196 197 3.625764 GGCATACATGGTTGTAACATCGT 59.374 43.478 0.00 0.00 41.51 3.73
266 267 3.036084 CGTCGGTTGCAACTCGCT 61.036 61.111 27.64 0.00 43.06 4.93
268 269 4.072088 GGCGTCGGTTGCAACTCG 62.072 66.667 27.64 26.21 0.00 4.18
334 335 2.113986 GCCACCAGTTGCAGTCCT 59.886 61.111 0.00 0.00 0.00 3.85
345 346 3.716195 CATCCACCCTCGCCACCA 61.716 66.667 0.00 0.00 0.00 4.17
374 375 2.670148 GGCTGAAGTCCCCATCGGT 61.670 63.158 0.00 0.00 0.00 4.69
554 575 4.714632 AGTCCGAGGATTCAAGTTCAAAA 58.285 39.130 0.00 0.00 0.00 2.44
636 765 1.507141 CGAGAACAACCGCTGGCTTT 61.507 55.000 0.00 0.00 0.00 3.51
647 776 1.646540 CAAACGCCAGCGAGAACAA 59.353 52.632 20.32 0.00 42.83 2.83
755 893 4.760220 TTGCCCTCCCCTCCCCTC 62.760 72.222 0.00 0.00 0.00 4.30
855 994 2.358984 GGCGGGCGGTCAAAGTAA 60.359 61.111 0.00 0.00 0.00 2.24
938 1077 1.604593 CTGGGGGAGCAGGTGTTTG 60.605 63.158 0.00 0.00 0.00 2.93
1202 1357 4.712337 ACGACTAGAAGATGGACAAGGATT 59.288 41.667 0.00 0.00 0.00 3.01
1211 1372 5.127491 AGGAGAGTAACGACTAGAAGATGG 58.873 45.833 0.00 0.00 35.45 3.51
1212 1373 5.050634 CGAGGAGAGTAACGACTAGAAGATG 60.051 48.000 0.00 0.00 35.45 2.90
1213 1374 5.051816 CGAGGAGAGTAACGACTAGAAGAT 58.948 45.833 0.00 0.00 35.45 2.40
1214 1375 4.159321 TCGAGGAGAGTAACGACTAGAAGA 59.841 45.833 0.00 0.00 35.45 2.87
1215 1376 4.431809 TCGAGGAGAGTAACGACTAGAAG 58.568 47.826 0.00 0.00 35.45 2.85
1216 1377 4.462508 TCGAGGAGAGTAACGACTAGAA 57.537 45.455 0.00 0.00 35.45 2.10
1218 1379 3.426191 CGATCGAGGAGAGTAACGACTAG 59.574 52.174 10.26 0.00 35.45 2.57
1220 1381 2.159128 TCGATCGAGGAGAGTAACGACT 60.159 50.000 15.15 0.00 39.20 4.18
1221 1382 2.200067 TCGATCGAGGAGAGTAACGAC 58.800 52.381 15.15 0.00 37.58 4.34
1222 1383 2.591571 TCGATCGAGGAGAGTAACGA 57.408 50.000 15.15 0.00 39.01 3.85
1223 1384 2.544686 ACATCGATCGAGGAGAGTAACG 59.455 50.000 33.72 9.40 0.00 3.18
1243 1410 5.981915 AGAAAGCAAGAAATTCAAGAAGCAC 59.018 36.000 0.00 0.00 0.00 4.40
1246 1413 8.208855 CGTAAGAAAGCAAGAAATTCAAGAAG 57.791 34.615 0.00 0.00 43.02 2.85
1352 1522 2.084681 GTTGCACCGGTCGTAGTCG 61.085 63.158 2.59 0.00 38.55 4.18
1713 1883 3.454812 TCCCTAAGATCCTAACCAACAGC 59.545 47.826 0.00 0.00 0.00 4.40
1720 1890 8.881262 TCAAATAATCCTCCCTAAGATCCTAAC 58.119 37.037 0.00 0.00 0.00 2.34
1722 1892 9.635284 AATCAAATAATCCTCCCTAAGATCCTA 57.365 33.333 0.00 0.00 0.00 2.94
1723 1893 8.531362 AATCAAATAATCCTCCCTAAGATCCT 57.469 34.615 0.00 0.00 0.00 3.24
1724 1894 9.898152 CTAATCAAATAATCCTCCCTAAGATCC 57.102 37.037 0.00 0.00 0.00 3.36
1921 2111 6.220930 TCCTGTATCACCTTATTTATCACGC 58.779 40.000 0.00 0.00 0.00 5.34
1942 2132 3.306364 GCTGTATCCATACTTGCGATCCT 60.306 47.826 0.00 0.00 34.41 3.24
1948 2144 6.867662 ATAACTTGCTGTATCCATACTTGC 57.132 37.500 0.00 4.03 35.58 4.01
1949 2145 8.131100 CCAAATAACTTGCTGTATCCATACTTG 58.869 37.037 0.00 0.00 32.61 3.16
1950 2146 7.201821 GCCAAATAACTTGCTGTATCCATACTT 60.202 37.037 0.00 0.00 32.61 2.24
1951 2147 6.263168 GCCAAATAACTTGCTGTATCCATACT 59.737 38.462 0.00 0.00 32.61 2.12
1952 2148 6.263168 AGCCAAATAACTTGCTGTATCCATAC 59.737 38.462 0.00 0.00 33.27 2.39
1953 2149 6.262944 CAGCCAAATAACTTGCTGTATCCATA 59.737 38.462 0.00 0.00 35.85 2.74
1954 2150 5.068198 CAGCCAAATAACTTGCTGTATCCAT 59.932 40.000 0.00 0.00 35.85 3.41
1955 2151 4.398988 CAGCCAAATAACTTGCTGTATCCA 59.601 41.667 0.00 0.00 35.85 3.41
1956 2152 4.734695 GCAGCCAAATAACTTGCTGTATCC 60.735 45.833 11.47 0.00 39.43 2.59
1957 2153 4.142403 TGCAGCCAAATAACTTGCTGTATC 60.142 41.667 11.47 0.00 39.43 2.24
1958 2154 3.763360 TGCAGCCAAATAACTTGCTGTAT 59.237 39.130 11.47 0.00 39.43 2.29
1959 2155 3.057596 GTGCAGCCAAATAACTTGCTGTA 60.058 43.478 11.47 4.75 39.43 2.74
1960 2156 1.962807 TGCAGCCAAATAACTTGCTGT 59.037 42.857 11.47 0.00 39.43 4.40
2009 2210 2.943865 CGTCGTTTACTCGCATCAATG 58.056 47.619 0.00 0.00 0.00 2.82
2061 2262 1.429927 CTTCTCCATCGCTGCTGCAG 61.430 60.000 24.80 24.80 39.64 4.41
2062 2263 1.449070 CTTCTCCATCGCTGCTGCA 60.449 57.895 16.29 0.88 39.64 4.41
2070 2271 1.066587 GCGACCCTCTTCTCCATCG 59.933 63.158 0.00 0.00 0.00 3.84
2091 2292 4.565652 GGAGTACTCAACATTGGACCACAT 60.566 45.833 23.91 0.00 0.00 3.21
2098 2299 3.738982 TGTGTGGAGTACTCAACATTGG 58.261 45.455 31.00 0.00 44.55 3.16
2102 2303 4.188462 CAAACTGTGTGGAGTACTCAACA 58.812 43.478 26.24 26.24 40.98 3.33
2103 2304 3.002348 GCAAACTGTGTGGAGTACTCAAC 59.998 47.826 21.68 21.68 32.87 3.18
2117 2318 1.069049 GCCAACTGGAATGCAAACTGT 59.931 47.619 0.00 0.00 37.39 3.55
2118 2319 1.068895 TGCCAACTGGAATGCAAACTG 59.931 47.619 0.00 0.00 37.39 3.16
2119 2320 1.412079 TGCCAACTGGAATGCAAACT 58.588 45.000 0.00 0.00 37.39 2.66
2120 2321 2.237393 TTGCCAACTGGAATGCAAAC 57.763 45.000 0.00 0.00 40.46 2.93
2121 2322 3.488778 AATTGCCAACTGGAATGCAAA 57.511 38.095 0.00 0.00 45.71 3.68
2122 2323 3.488778 AAATTGCCAACTGGAATGCAA 57.511 38.095 0.00 0.00 46.51 4.08
2123 2324 3.488778 AAAATTGCCAACTGGAATGCA 57.511 38.095 0.00 0.00 37.39 3.96
2124 2325 5.063817 GTGATAAAATTGCCAACTGGAATGC 59.936 40.000 0.00 0.00 37.39 3.56
2125 2326 5.581874 GGTGATAAAATTGCCAACTGGAATG 59.418 40.000 0.00 0.00 37.39 2.67
2126 2327 5.338300 GGGTGATAAAATTGCCAACTGGAAT 60.338 40.000 0.00 0.00 37.39 3.01
2127 2328 4.020662 GGGTGATAAAATTGCCAACTGGAA 60.021 41.667 0.00 0.00 37.39 3.53
2163 2364 4.279671 ACGTTTGGGATGTTTCTGCAAATA 59.720 37.500 0.00 0.00 0.00 1.40
2164 2365 3.069443 ACGTTTGGGATGTTTCTGCAAAT 59.931 39.130 0.00 0.00 0.00 2.32
2165 2366 2.428890 ACGTTTGGGATGTTTCTGCAAA 59.571 40.909 0.00 0.00 0.00 3.68
2166 2367 2.028130 ACGTTTGGGATGTTTCTGCAA 58.972 42.857 0.00 0.00 0.00 4.08
2167 2368 1.686355 ACGTTTGGGATGTTTCTGCA 58.314 45.000 0.00 0.00 0.00 4.41
2200 2401 6.208402 TCATTTGTTTGGAGATTGATTTCGGA 59.792 34.615 0.00 0.00 0.00 4.55
2206 2407 6.600882 AGCTTCATTTGTTTGGAGATTGAT 57.399 33.333 0.00 0.00 0.00 2.57
2208 2409 6.565247 GCAAAGCTTCATTTGTTTGGAGATTG 60.565 38.462 0.00 0.00 41.31 2.67
2210 2411 4.992951 GCAAAGCTTCATTTGTTTGGAGAT 59.007 37.500 0.00 0.00 41.31 2.75
2211 2412 4.141981 TGCAAAGCTTCATTTGTTTGGAGA 60.142 37.500 0.00 0.00 41.31 3.71
2212 2413 4.121317 TGCAAAGCTTCATTTGTTTGGAG 58.879 39.130 0.00 0.00 41.31 3.86
2213 2414 4.134379 TGCAAAGCTTCATTTGTTTGGA 57.866 36.364 0.00 0.00 41.31 3.53
2214 2415 4.512198 TGATGCAAAGCTTCATTTGTTTGG 59.488 37.500 0.00 0.00 41.31 3.28
2215 2416 5.464057 TCTGATGCAAAGCTTCATTTGTTTG 59.536 36.000 0.00 0.00 40.83 2.93
2216 2417 5.603596 TCTGATGCAAAGCTTCATTTGTTT 58.396 33.333 0.00 0.00 40.83 2.83
2217 2418 5.204409 TCTGATGCAAAGCTTCATTTGTT 57.796 34.783 0.00 0.00 40.83 2.83
2218 2419 4.280174 ACTCTGATGCAAAGCTTCATTTGT 59.720 37.500 0.00 5.37 40.83 2.83
2219 2420 4.806330 ACTCTGATGCAAAGCTTCATTTG 58.194 39.130 0.00 0.00 40.83 2.32
2220 2421 5.010314 TGAACTCTGATGCAAAGCTTCATTT 59.990 36.000 0.00 3.25 40.83 2.32
2221 2422 4.521639 TGAACTCTGATGCAAAGCTTCATT 59.478 37.500 0.00 1.19 40.83 2.57
2222 2423 4.077108 TGAACTCTGATGCAAAGCTTCAT 58.923 39.130 0.00 0.00 40.83 2.57
2223 2424 3.479489 TGAACTCTGATGCAAAGCTTCA 58.521 40.909 0.00 7.26 39.73 3.02
2224 2425 3.750130 TCTGAACTCTGATGCAAAGCTTC 59.250 43.478 0.00 0.00 34.04 3.86
2225 2426 3.748083 TCTGAACTCTGATGCAAAGCTT 58.252 40.909 0.00 0.00 0.00 3.74
2226 2427 3.413846 TCTGAACTCTGATGCAAAGCT 57.586 42.857 0.00 0.00 0.00 3.74
2227 2428 3.501445 AGTTCTGAACTCTGATGCAAAGC 59.499 43.478 17.00 0.00 37.02 3.51
2228 2429 5.686159 AAGTTCTGAACTCTGATGCAAAG 57.314 39.130 22.24 0.00 41.91 2.77
2229 2430 6.455360 AAAAGTTCTGAACTCTGATGCAAA 57.545 33.333 22.24 0.00 41.91 3.68
2230 2431 6.017109 GGTAAAAGTTCTGAACTCTGATGCAA 60.017 38.462 22.24 1.81 41.91 4.08
2231 2432 5.470098 GGTAAAAGTTCTGAACTCTGATGCA 59.530 40.000 22.24 0.00 41.91 3.96
2232 2433 5.106515 GGGTAAAAGTTCTGAACTCTGATGC 60.107 44.000 22.24 12.15 41.91 3.91
2233 2434 5.120830 CGGGTAAAAGTTCTGAACTCTGATG 59.879 44.000 22.24 7.04 41.91 3.07
2247 2448 3.193903 ACAAAAAGTGTGCGGGTAAAAGT 59.806 39.130 0.00 0.00 39.72 2.66
2248 2449 3.776340 ACAAAAAGTGTGCGGGTAAAAG 58.224 40.909 0.00 0.00 39.72 2.27
2250 2451 3.946558 AGTACAAAAAGTGTGCGGGTAAA 59.053 39.130 0.00 0.00 46.59 2.01
2252 2453 3.196939 AGTACAAAAAGTGTGCGGGTA 57.803 42.857 0.00 0.00 46.59 3.69
2253 2454 2.047002 AGTACAAAAAGTGTGCGGGT 57.953 45.000 0.00 0.00 46.59 5.28
2254 2455 3.430333 AAAGTACAAAAAGTGTGCGGG 57.570 42.857 0.00 0.00 46.59 6.13
2255 2456 6.474102 ACATTAAAAGTACAAAAAGTGTGCGG 59.526 34.615 0.00 0.00 46.59 5.69
2279 2502 8.138365 TCTGAGTCTACAACATTTGTGTTAAC 57.862 34.615 0.00 0.00 45.03 2.01
2280 2503 8.725405 TTCTGAGTCTACAACATTTGTGTTAA 57.275 30.769 1.73 0.00 45.03 2.01
2281 2504 8.902540 ATTCTGAGTCTACAACATTTGTGTTA 57.097 30.769 1.73 0.00 45.03 2.41
2284 2507 7.588854 CACAATTCTGAGTCTACAACATTTGTG 59.411 37.037 1.73 0.00 45.03 3.33
2286 2509 6.580041 GCACAATTCTGAGTCTACAACATTTG 59.420 38.462 0.00 0.00 0.00 2.32
2287 2510 6.294176 GGCACAATTCTGAGTCTACAACATTT 60.294 38.462 0.00 0.00 0.00 2.32
2288 2511 5.182001 GGCACAATTCTGAGTCTACAACATT 59.818 40.000 0.00 0.00 0.00 2.71
2289 2512 4.697352 GGCACAATTCTGAGTCTACAACAT 59.303 41.667 0.00 0.00 0.00 2.71
2291 2514 4.319177 AGGCACAATTCTGAGTCTACAAC 58.681 43.478 0.00 0.00 0.00 3.32
2293 2516 3.055819 GGAGGCACAATTCTGAGTCTACA 60.056 47.826 0.00 0.00 29.69 2.74
2296 2519 1.980765 TGGAGGCACAATTCTGAGTCT 59.019 47.619 0.00 0.00 30.02 3.24
2297 2520 2.079925 GTGGAGGCACAATTCTGAGTC 58.920 52.381 0.00 0.00 0.00 3.36
2298 2521 1.271597 GGTGGAGGCACAATTCTGAGT 60.272 52.381 0.00 0.00 0.00 3.41
2300 2523 1.067295 AGGTGGAGGCACAATTCTGA 58.933 50.000 0.00 0.00 0.00 3.27
2301 2524 2.636830 CTAGGTGGAGGCACAATTCTG 58.363 52.381 0.00 0.00 0.00 3.02
2302 2525 1.561542 CCTAGGTGGAGGCACAATTCT 59.438 52.381 0.00 0.00 38.35 2.40
2303 2526 1.282157 ACCTAGGTGGAGGCACAATTC 59.718 52.381 15.42 0.00 40.65 2.17
2304 2527 1.372501 ACCTAGGTGGAGGCACAATT 58.627 50.000 15.42 0.00 40.65 2.32
2305 2528 1.838077 GTACCTAGGTGGAGGCACAAT 59.162 52.381 25.33 0.00 40.65 2.71
2306 2529 1.272807 GTACCTAGGTGGAGGCACAA 58.727 55.000 25.33 0.00 40.65 3.33
2308 2531 0.535797 GTGTACCTAGGTGGAGGCAC 59.464 60.000 25.33 18.73 40.65 5.01
2309 2532 0.968901 CGTGTACCTAGGTGGAGGCA 60.969 60.000 25.33 11.93 40.65 4.75
2310 2533 0.969409 ACGTGTACCTAGGTGGAGGC 60.969 60.000 25.33 9.57 40.65 4.70
2311 2534 2.019984 GTACGTGTACCTAGGTGGAGG 58.980 57.143 25.33 17.01 42.89 4.30
2312 2535 2.996631 AGTACGTGTACCTAGGTGGAG 58.003 52.381 25.33 14.64 39.71 3.86
2313 2536 3.439857 AAGTACGTGTACCTAGGTGGA 57.560 47.619 25.33 7.67 39.71 4.02
2314 2537 3.065925 GCTAAGTACGTGTACCTAGGTGG 59.934 52.174 25.33 12.86 42.93 4.61
2315 2538 3.691118 TGCTAAGTACGTGTACCTAGGTG 59.309 47.826 25.33 10.11 36.75 4.00
2317 2540 3.065925 GGTGCTAAGTACGTGTACCTAGG 59.934 52.174 7.41 7.41 36.75 3.02
2318 2541 3.242543 CGGTGCTAAGTACGTGTACCTAG 60.243 52.174 16.00 10.21 36.75 3.02
2319 2542 2.677836 CGGTGCTAAGTACGTGTACCTA 59.322 50.000 16.00 0.00 36.75 3.08
2321 2544 1.200020 ACGGTGCTAAGTACGTGTACC 59.800 52.381 0.00 0.00 38.24 3.34
2322 2545 2.619013 ACGGTGCTAAGTACGTGTAC 57.381 50.000 0.00 1.90 38.24 2.90
2323 2546 3.253188 AGAAACGGTGCTAAGTACGTGTA 59.747 43.478 0.00 0.00 39.76 2.90
2324 2547 2.035066 AGAAACGGTGCTAAGTACGTGT 59.965 45.455 0.00 0.00 39.76 4.49
2325 2548 2.669364 AGAAACGGTGCTAAGTACGTG 58.331 47.619 0.00 0.00 39.76 4.49
2327 2550 2.665052 GGAAGAAACGGTGCTAAGTACG 59.335 50.000 0.00 0.00 0.00 3.67
2328 2551 2.998670 GGGAAGAAACGGTGCTAAGTAC 59.001 50.000 0.00 0.00 0.00 2.73
2329 2552 2.353011 CGGGAAGAAACGGTGCTAAGTA 60.353 50.000 0.00 0.00 0.00 2.24
2330 2553 1.607251 CGGGAAGAAACGGTGCTAAGT 60.607 52.381 0.00 0.00 0.00 2.24
2331 2554 1.076332 CGGGAAGAAACGGTGCTAAG 58.924 55.000 0.00 0.00 0.00 2.18
2332 2555 0.320946 CCGGGAAGAAACGGTGCTAA 60.321 55.000 0.00 0.00 44.85 3.09
2333 2556 1.294138 CCGGGAAGAAACGGTGCTA 59.706 57.895 0.00 0.00 44.85 3.49
2334 2557 2.032071 CCGGGAAGAAACGGTGCT 59.968 61.111 0.00 0.00 44.85 4.40
2339 2562 1.670083 GTGACCCCGGGAAGAAACG 60.670 63.158 26.32 5.39 0.00 3.60
2341 2564 1.137594 ATGGTGACCCCGGGAAGAAA 61.138 55.000 26.32 2.63 35.15 2.52
2343 2566 0.979187 GTATGGTGACCCCGGGAAGA 60.979 60.000 26.32 0.52 35.15 2.87
2344 2567 0.981277 AGTATGGTGACCCCGGGAAG 60.981 60.000 26.32 9.05 35.15 3.46
2345 2568 0.339162 TAGTATGGTGACCCCGGGAA 59.661 55.000 26.32 3.73 35.15 3.97
2346 2569 0.397535 GTAGTATGGTGACCCCGGGA 60.398 60.000 26.32 0.00 35.15 5.14
2347 2570 0.398098 AGTAGTATGGTGACCCCGGG 60.398 60.000 15.80 15.80 35.15 5.73
2348 2571 1.038280 GAGTAGTATGGTGACCCCGG 58.962 60.000 0.00 0.00 35.15 5.73
2349 2572 1.955080 GAGAGTAGTATGGTGACCCCG 59.045 57.143 0.00 0.00 35.15 5.73
2350 2573 3.117436 AGAGAGAGTAGTATGGTGACCCC 60.117 52.174 0.00 0.00 0.00 4.95
2351 2574 4.139038 GAGAGAGAGTAGTATGGTGACCC 58.861 52.174 0.00 0.00 0.00 4.46
2352 2575 5.043737 AGAGAGAGAGTAGTATGGTGACC 57.956 47.826 0.00 0.00 0.00 4.02
2353 2576 6.354130 AGAAGAGAGAGAGTAGTATGGTGAC 58.646 44.000 0.00 0.00 0.00 3.67
2355 2578 8.617809 GTTAAGAAGAGAGAGAGTAGTATGGTG 58.382 40.741 0.00 0.00 0.00 4.17
2356 2579 8.554011 AGTTAAGAAGAGAGAGAGTAGTATGGT 58.446 37.037 0.00 0.00 0.00 3.55
2359 2582 9.774413 GCTAGTTAAGAAGAGAGAGAGTAGTAT 57.226 37.037 0.00 0.00 0.00 2.12
2360 2583 8.760735 TGCTAGTTAAGAAGAGAGAGAGTAGTA 58.239 37.037 0.00 0.00 0.00 1.82
2361 2584 7.626390 TGCTAGTTAAGAAGAGAGAGAGTAGT 58.374 38.462 0.00 0.00 0.00 2.73
2362 2585 8.559536 CATGCTAGTTAAGAAGAGAGAGAGTAG 58.440 40.741 0.00 0.00 0.00 2.57
2363 2586 7.012894 GCATGCTAGTTAAGAAGAGAGAGAGTA 59.987 40.741 11.37 0.00 0.00 2.59
2364 2587 6.183360 GCATGCTAGTTAAGAAGAGAGAGAGT 60.183 42.308 11.37 0.00 0.00 3.24
2365 2588 6.208644 GCATGCTAGTTAAGAAGAGAGAGAG 58.791 44.000 11.37 0.00 0.00 3.20
2366 2589 5.068460 GGCATGCTAGTTAAGAAGAGAGAGA 59.932 44.000 18.92 0.00 0.00 3.10
2367 2590 5.163468 TGGCATGCTAGTTAAGAAGAGAGAG 60.163 44.000 18.92 0.00 0.00 3.20
2368 2591 4.711846 TGGCATGCTAGTTAAGAAGAGAGA 59.288 41.667 18.92 0.00 0.00 3.10
2369 2592 4.808364 GTGGCATGCTAGTTAAGAAGAGAG 59.192 45.833 18.92 0.00 0.00 3.20
2371 2594 4.507710 TGTGGCATGCTAGTTAAGAAGAG 58.492 43.478 18.92 0.00 0.00 2.85
2373 2596 4.877823 TGATGTGGCATGCTAGTTAAGAAG 59.122 41.667 18.92 0.00 0.00 2.85
2377 2600 4.080919 AGTCTGATGTGGCATGCTAGTTAA 60.081 41.667 18.92 0.00 0.00 2.01
2378 2601 3.452264 AGTCTGATGTGGCATGCTAGTTA 59.548 43.478 18.92 1.05 0.00 2.24
2380 2603 1.836166 AGTCTGATGTGGCATGCTAGT 59.164 47.619 18.92 2.76 0.00 2.57
2381 2604 2.616634 AGTCTGATGTGGCATGCTAG 57.383 50.000 18.92 6.92 0.00 3.42
2382 2605 3.354948 AAAGTCTGATGTGGCATGCTA 57.645 42.857 18.92 9.16 0.00 3.49
2385 2608 2.991190 GCAAAAAGTCTGATGTGGCATG 59.009 45.455 0.00 0.00 0.00 4.06
2386 2609 2.895404 AGCAAAAAGTCTGATGTGGCAT 59.105 40.909 0.00 0.00 0.00 4.40
2388 2611 3.375782 AAGCAAAAAGTCTGATGTGGC 57.624 42.857 0.00 0.00 0.00 5.01
2390 2613 5.916883 CCAACTAAGCAAAAAGTCTGATGTG 59.083 40.000 0.00 0.00 0.00 3.21
2391 2614 5.507985 GCCAACTAAGCAAAAAGTCTGATGT 60.508 40.000 0.00 0.00 0.00 3.06
2392 2615 4.919754 GCCAACTAAGCAAAAAGTCTGATG 59.080 41.667 0.00 0.00 0.00 3.07
2393 2616 4.584325 TGCCAACTAAGCAAAAAGTCTGAT 59.416 37.500 0.00 0.00 37.28 2.90
2394 2617 3.951037 TGCCAACTAAGCAAAAAGTCTGA 59.049 39.130 0.00 0.00 37.28 3.27
2395 2618 4.305989 TGCCAACTAAGCAAAAAGTCTG 57.694 40.909 0.00 0.00 37.28 3.51
2404 2627 1.896220 CTGAGGTTGCCAACTAAGCA 58.104 50.000 7.62 0.54 38.81 3.91
2405 2628 0.523519 GCTGAGGTTGCCAACTAAGC 59.476 55.000 7.62 10.15 0.00 3.09
2406 2629 1.537202 GTGCTGAGGTTGCCAACTAAG 59.463 52.381 7.62 4.22 0.00 2.18
2407 2630 1.604604 GTGCTGAGGTTGCCAACTAA 58.395 50.000 7.62 0.00 0.00 2.24
2408 2631 0.250727 GGTGCTGAGGTTGCCAACTA 60.251 55.000 7.62 0.00 0.00 2.24
2409 2632 1.529244 GGTGCTGAGGTTGCCAACT 60.529 57.895 7.62 0.00 0.00 3.16
2410 2633 1.529244 AGGTGCTGAGGTTGCCAAC 60.529 57.895 0.00 0.00 0.00 3.77
2411 2634 1.529010 CAGGTGCTGAGGTTGCCAA 60.529 57.895 0.00 0.00 32.44 4.52
2412 2635 1.414866 TACAGGTGCTGAGGTTGCCA 61.415 55.000 0.00 0.00 35.18 4.92
2414 2637 0.250295 TGTACAGGTGCTGAGGTTGC 60.250 55.000 0.00 0.00 35.18 4.17
2415 2638 2.146342 CTTGTACAGGTGCTGAGGTTG 58.854 52.381 0.00 0.00 35.18 3.77
2416 2639 1.072331 CCTTGTACAGGTGCTGAGGTT 59.928 52.381 4.10 0.00 37.99 3.50
2417 2640 0.687354 CCTTGTACAGGTGCTGAGGT 59.313 55.000 4.10 0.00 37.99 3.85
2418 2641 3.540211 CCTTGTACAGGTGCTGAGG 57.460 57.895 4.10 0.00 37.99 3.86
2428 2651 1.271871 CCCAATGCTCCACCTTGTACA 60.272 52.381 0.00 0.00 0.00 2.90
2429 2652 1.004277 TCCCAATGCTCCACCTTGTAC 59.996 52.381 0.00 0.00 0.00 2.90
2430 2653 1.281867 CTCCCAATGCTCCACCTTGTA 59.718 52.381 0.00 0.00 0.00 2.41
2431 2654 0.038744 CTCCCAATGCTCCACCTTGT 59.961 55.000 0.00 0.00 0.00 3.16
2432 2655 0.682209 CCTCCCAATGCTCCACCTTG 60.682 60.000 0.00 0.00 0.00 3.61
2435 2658 2.276740 CCCTCCCAATGCTCCACC 59.723 66.667 0.00 0.00 0.00 4.61
2436 2659 2.276740 CCCCTCCCAATGCTCCAC 59.723 66.667 0.00 0.00 0.00 4.02
2437 2660 3.743017 GCCCCTCCCAATGCTCCA 61.743 66.667 0.00 0.00 0.00 3.86
2440 2663 1.622442 TTAGGCCCCTCCCAATGCT 60.622 57.895 0.00 0.00 34.51 3.79
2441 2664 1.152673 CTTAGGCCCCTCCCAATGC 60.153 63.158 0.00 0.00 34.51 3.56
2443 2666 2.533018 ATACTTAGGCCCCTCCCAAT 57.467 50.000 0.00 0.00 34.51 3.16
2446 2669 1.151627 AGGTATACTTAGGCCCCTCCC 59.848 57.143 0.00 0.00 34.51 4.30
2447 2670 2.717701 AGGTATACTTAGGCCCCTCC 57.282 55.000 0.00 0.00 0.00 4.30
2449 2672 4.171442 TCAGTTAGGTATACTTAGGCCCCT 59.829 45.833 0.00 0.00 0.00 4.79
2450 2673 4.282957 GTCAGTTAGGTATACTTAGGCCCC 59.717 50.000 0.00 0.00 0.00 5.80
2451 2674 4.897670 TGTCAGTTAGGTATACTTAGGCCC 59.102 45.833 0.00 0.00 0.00 5.80
2452 2675 6.475596 TTGTCAGTTAGGTATACTTAGGCC 57.524 41.667 2.25 0.00 0.00 5.19
2453 2676 7.723324 TCATTGTCAGTTAGGTATACTTAGGC 58.277 38.462 2.25 0.00 0.00 3.93
2454 2677 9.751542 CTTCATTGTCAGTTAGGTATACTTAGG 57.248 37.037 2.25 0.00 0.00 2.69
2455 2678 9.250624 GCTTCATTGTCAGTTAGGTATACTTAG 57.749 37.037 2.25 0.00 0.00 2.18
2457 2680 7.766278 CAGCTTCATTGTCAGTTAGGTATACTT 59.234 37.037 2.25 0.00 0.00 2.24
2458 2681 7.124298 TCAGCTTCATTGTCAGTTAGGTATACT 59.876 37.037 2.25 0.00 0.00 2.12
2459 2682 7.222999 GTCAGCTTCATTGTCAGTTAGGTATAC 59.777 40.741 0.00 0.00 0.00 1.47
2460 2683 7.265673 GTCAGCTTCATTGTCAGTTAGGTATA 58.734 38.462 0.00 0.00 0.00 1.47
2471 2710 4.479619 GTGAAATGGTCAGCTTCATTGTC 58.520 43.478 7.27 7.76 36.74 3.18
2486 2725 6.036300 GTGCAATATCATTTGGTGGTGAAATG 59.964 38.462 0.00 0.00 40.64 2.32
2557 2796 8.345565 CAAACAAACTTTCTGTGTAGATAAGCT 58.654 33.333 0.00 0.00 31.81 3.74
2568 2807 5.393461 CCTTCTCTGCAAACAAACTTTCTGT 60.393 40.000 0.00 0.00 0.00 3.41
2668 2907 2.452600 TTCCAGGAGGTTTTGCTTGT 57.547 45.000 0.00 0.00 35.89 3.16
2684 2923 2.294233 TGCATCTTGACTGCAACTTTCC 59.706 45.455 0.00 0.00 46.06 3.13


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

AutoCloner maintained by Alex Coulton.