Multiple sequence alignment - TraesCS4B01G222900

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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 TraesCS4B01G222900 chr4B 100.000 2541 0 0 1 2541 467713732 467711192 0.000000e+00 4693.0
1 TraesCS4B01G222900 chr3B 95.841 2092 66 8 2 2091 781725677 781723605 0.000000e+00 3362.0
2 TraesCS4B01G222900 chr3B 75.093 269 59 8 518 782 819939556 819939292 4.440000e-23 119.0
3 TraesCS4B01G222900 chr3B 95.745 47 1 1 2493 2538 249930464 249930510 9.750000e-10 75.0
4 TraesCS4B01G222900 chr3B 100.000 32 0 0 2141 2172 727008181 727008212 2.730000e-05 60.2
5 TraesCS4B01G222900 chr3B 94.286 35 2 0 2149 2183 389034280 389034246 1.000000e-03 54.7
6 TraesCS4B01G222900 chr6D 95.761 401 16 1 1784 2184 306059073 306058674 0.000000e+00 645.0
7 TraesCS4B01G222900 chr4D 96.273 322 9 3 2185 2505 380285820 380285501 2.240000e-145 525.0
8 TraesCS4B01G222900 chr4A 94.569 313 16 1 2195 2507 83575413 83575724 1.370000e-132 483.0
9 TraesCS4B01G222900 chr6A 92.520 254 11 7 1784 2036 440691822 440691576 8.640000e-95 357.0
10 TraesCS4B01G222900 chr6A 92.453 159 7 1 2025 2183 440691313 440691160 3.290000e-54 222.0
11 TraesCS4B01G222900 chr7A 81.818 143 25 1 2041 2183 634913728 634913587 4.440000e-23 119.0
12 TraesCS4B01G222900 chr1B 83.077 130 22 0 2054 2183 515360837 515360708 4.440000e-23 119.0
13 TraesCS4B01G222900 chr1B 73.597 303 72 8 510 807 565899514 565899215 2.670000e-20 110.0
14 TraesCS4B01G222900 chr1B 100.000 32 0 0 2149 2180 35409996 35410027 2.730000e-05 60.2
15 TraesCS4B01G222900 chr7B 72.603 292 66 13 524 807 122724464 122724749 1.620000e-12 84.2
16 TraesCS4B01G222900 chr7B 100.000 41 0 0 2501 2541 98938055 98938015 2.710000e-10 76.8
17 TraesCS4B01G222900 chr7B 97.674 43 1 0 2499 2541 341850628 341850670 9.750000e-10 75.0
18 TraesCS4B01G222900 chr7B 100.000 37 0 0 2505 2541 505388175 505388139 4.540000e-08 69.4
19 TraesCS4B01G222900 chr6B 97.826 46 1 0 2496 2541 550406082 550406037 2.100000e-11 80.5
20 TraesCS4B01G222900 chr6B 95.556 45 2 0 2497 2541 25332358 25332402 3.510000e-09 73.1
21 TraesCS4B01G222900 chr2B 97.778 45 0 1 2498 2541 261550322 261550278 2.710000e-10 76.8
22 TraesCS4B01G222900 chr2B 97.297 37 1 0 2150 2186 93932220 93932256 2.110000e-06 63.9
23 TraesCS4B01G222900 chr5B 95.652 46 2 0 2496 2541 142014584 142014629 9.750000e-10 75.0
24 TraesCS4B01G222900 chr5A 97.674 43 1 0 2499 2541 367589500 367589458 9.750000e-10 75.0
25 TraesCS4B01G222900 chr2A 100.000 32 0 0 2149 2180 83715479 83715510 2.730000e-05 60.2


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 TraesCS4B01G222900 chr4B 467711192 467713732 2540 True 4693.0 4693 100.0000 1 2541 1 chr4B.!!$R1 2540
1 TraesCS4B01G222900 chr3B 781723605 781725677 2072 True 3362.0 3362 95.8410 2 2091 1 chr3B.!!$R2 2089
2 TraesCS4B01G222900 chr6A 440691160 440691822 662 True 289.5 357 92.4865 1784 2183 2 chr6A.!!$R1 399

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
567 568 0.398318 AGCAAAGGAGTGTCTGGGTC 59.602 55.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 2699 0.030235 CATGGCAATGACGCATCAGG 59.97 55.0 0.0 0.0 38.57 3.86 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
90 91 4.134563 AGGCGTATGACTTTGACAACTTT 58.865 39.130 0.00 0.00 0.00 2.66
139 140 2.168521 TGGTATGGCAAGAGTAGACTGC 59.831 50.000 0.00 0.00 0.00 4.40
172 173 5.352569 AGAACCAATTTAGTGCAAGAGATCG 59.647 40.000 0.00 0.00 0.00 3.69
176 177 5.580691 CCAATTTAGTGCAAGAGATCGTGTA 59.419 40.000 0.00 0.00 0.00 2.90
182 183 2.131183 GCAAGAGATCGTGTATGGCTC 58.869 52.381 0.00 0.00 0.00 4.70
186 187 4.052159 AGAGATCGTGTATGGCTCTTTG 57.948 45.455 0.00 0.00 32.35 2.77
242 243 2.035832 TCGATGACAGTGCTTTCTGACA 59.964 45.455 10.13 10.10 42.03 3.58
325 326 2.094234 AGTTTTGAGTGGGTGTTTGCAC 60.094 45.455 0.00 0.00 44.53 4.57
396 397 4.261447 GGTTTTGCACTGTACTAACTTGGG 60.261 45.833 0.00 0.00 0.00 4.12
434 435 9.158233 CATTTCTGGTTTTCTTGCATTTGATAT 57.842 29.630 0.00 0.00 0.00 1.63
455 456 9.151471 TGATATAGCTGACTAGTTGTTTTTGAC 57.849 33.333 0.00 0.00 0.00 3.18
567 568 0.398318 AGCAAAGGAGTGTCTGGGTC 59.602 55.000 0.00 0.00 0.00 4.46
677 678 5.914033 TCAGGTATGCTGTTGGATAAGTAC 58.086 41.667 0.00 0.00 0.00 2.73
761 762 5.803020 CTTACTTCAAGGGTGTATTCTGC 57.197 43.478 0.00 0.00 0.00 4.26
791 792 2.033602 GGCACCCAACTTAGCGGT 59.966 61.111 0.00 0.00 0.00 5.68
793 794 0.743345 GGCACCCAACTTAGCGGTAG 60.743 60.000 0.00 0.00 0.00 3.18
819 820 3.939740 ATCACATGGTTCAGTAGGCAT 57.060 42.857 0.00 0.00 0.00 4.40
848 849 2.044555 CAGGTCTCGGGTAGCGTGA 61.045 63.158 0.00 0.00 0.00 4.35
893 894 5.369685 TGCTTCAGTGAATGCGATTTTTA 57.630 34.783 5.91 0.00 0.00 1.52
900 901 7.508965 TCAGTGAATGCGATTTTTAAAATTGC 58.491 30.769 26.92 26.92 37.51 3.56
929 930 1.565390 TTATGCCAGGCAGGAGCACT 61.565 55.000 21.51 3.17 43.65 4.40
937 938 3.629398 CCAGGCAGGAGCACTATAAAAAG 59.371 47.826 0.00 0.00 44.61 2.27
939 940 3.523564 AGGCAGGAGCACTATAAAAAGGA 59.476 43.478 0.00 0.00 44.61 3.36
940 941 4.166919 AGGCAGGAGCACTATAAAAAGGAT 59.833 41.667 0.00 0.00 44.61 3.24
941 942 4.276926 GGCAGGAGCACTATAAAAAGGATG 59.723 45.833 0.00 0.00 44.61 3.51
942 943 4.276926 GCAGGAGCACTATAAAAAGGATGG 59.723 45.833 0.00 0.00 41.58 3.51
943 944 5.440610 CAGGAGCACTATAAAAAGGATGGT 58.559 41.667 0.00 0.00 0.00 3.55
944 945 6.591935 CAGGAGCACTATAAAAAGGATGGTA 58.408 40.000 0.00 0.00 0.00 3.25
945 946 6.483640 CAGGAGCACTATAAAAAGGATGGTAC 59.516 42.308 0.00 0.00 0.00 3.34
1040 1041 3.788227 TGGTGAAGCAAGTGGTAAGAT 57.212 42.857 0.00 0.00 0.00 2.40
1044 1045 4.092968 GGTGAAGCAAGTGGTAAGATAACG 59.907 45.833 0.00 0.00 0.00 3.18
1066 1067 1.792949 CGACGGGTGAAGTTTCAGAAG 59.207 52.381 0.00 0.00 37.98 2.85
1067 1068 2.545113 CGACGGGTGAAGTTTCAGAAGA 60.545 50.000 0.00 0.00 37.98 2.87
1088 1089 3.740513 AAAAAGACGACGGGTGGC 58.259 55.556 0.00 0.00 0.00 5.01
1089 1090 1.153127 AAAAAGACGACGGGTGGCA 60.153 52.632 0.00 0.00 0.00 4.92
1142 1143 6.825213 AGGTACGTTGACATACAGATAGTGTA 59.175 38.462 0.00 0.00 45.93 2.90
1258 1259 2.356535 GGTGAAGAGCAGTGGGATCAAT 60.357 50.000 0.00 0.00 33.23 2.57
1289 1290 7.278868 GGTGAGATCGTTATTCAGAAAGATTGT 59.721 37.037 0.00 0.00 29.20 2.71
1314 1315 3.119602 TGTCTTCTCTCGGACGGTATTTG 60.120 47.826 0.00 0.00 35.45 2.32
1380 1381 1.556911 TGAGGAGGAAGCATGGAAGAC 59.443 52.381 0.00 0.00 0.00 3.01
1414 1415 1.473434 GGGGAATCTAGCACGGTCAAG 60.473 57.143 0.00 0.00 0.00 3.02
1436 1437 2.492090 CGGGTGAGGAGAGCTTCG 59.508 66.667 0.00 0.00 0.00 3.79
1468 1469 1.595382 AGCCGGCGCAGTCATTATC 60.595 57.895 23.20 0.00 37.52 1.75
1469 1470 1.887242 GCCGGCGCAGTCATTATCA 60.887 57.895 12.58 0.00 34.03 2.15
1481 1482 5.050769 GCAGTCATTATCAACGATGTACCAG 60.051 44.000 0.00 0.00 0.00 4.00
1527 1530 4.525024 CTGAAAAGCTGGAGGAATCAGAT 58.475 43.478 0.00 0.00 35.91 2.90
1528 1531 5.678583 CTGAAAAGCTGGAGGAATCAGATA 58.321 41.667 0.00 0.00 35.91 1.98
1535 1538 4.478203 CTGGAGGAATCAGATACAGAGGA 58.522 47.826 0.00 0.00 34.36 3.71
1536 1539 4.478203 TGGAGGAATCAGATACAGAGGAG 58.522 47.826 0.00 0.00 0.00 3.69
1537 1540 4.168871 TGGAGGAATCAGATACAGAGGAGA 59.831 45.833 0.00 0.00 0.00 3.71
1550 1553 1.570501 AGAGGAGATGAGCAGAGGTCT 59.429 52.381 0.00 0.00 0.00 3.85
1561 1564 0.102120 CAGAGGTCTGGCTAAGCGAG 59.898 60.000 0.00 0.00 40.20 5.03
1568 1571 2.109181 GGCTAAGCGAGGGCGAAT 59.891 61.111 0.00 0.00 46.35 3.34
1661 1664 6.031471 ACGTTGTGTACTGATTTGTTTTTCC 58.969 36.000 0.00 0.00 0.00 3.13
1663 1666 6.259638 GTTGTGTACTGATTTGTTTTTCCGA 58.740 36.000 0.00 0.00 0.00 4.55
1665 1668 7.033530 TGTGTACTGATTTGTTTTTCCGATT 57.966 32.000 0.00 0.00 0.00 3.34
2046 2317 2.582226 GGCGGCCGCTTTAAATGC 60.582 61.111 45.23 25.20 41.60 3.56
2080 2351 9.448438 GCCCACAATATTTCTATATCACATACA 57.552 33.333 0.00 0.00 0.00 2.29
2122 2393 1.331756 CAACTTATGGCGCTGATCCAC 59.668 52.381 7.64 0.00 36.26 4.02
2131 2402 1.004595 CGCTGATCCACATGTGACTG 58.995 55.000 27.46 19.45 0.00 3.51
2145 2416 5.309020 ACATGTGACTGGATGGCTAAGATAT 59.691 40.000 0.00 0.00 0.00 1.63
2146 2417 5.474578 TGTGACTGGATGGCTAAGATATC 57.525 43.478 0.00 0.00 0.00 1.63
2147 2418 4.901250 TGTGACTGGATGGCTAAGATATCA 59.099 41.667 5.32 0.00 0.00 2.15
2148 2419 5.011431 TGTGACTGGATGGCTAAGATATCAG 59.989 44.000 5.32 0.00 0.00 2.90
2149 2420 4.529769 TGACTGGATGGCTAAGATATCAGG 59.470 45.833 5.32 0.00 0.00 3.86
2183 2454 3.429085 CGGGCTCAGAAATGAATTTTCG 58.571 45.455 0.00 0.00 46.89 3.46
2184 2455 3.731867 CGGGCTCAGAAATGAATTTTCGG 60.732 47.826 0.00 0.00 46.89 4.30
2185 2456 3.443681 GGGCTCAGAAATGAATTTTCGGA 59.556 43.478 1.97 1.97 46.89 4.55
2186 2457 4.082245 GGGCTCAGAAATGAATTTTCGGAA 60.082 41.667 3.29 0.00 46.89 4.30
2187 2458 5.394553 GGGCTCAGAAATGAATTTTCGGAAT 60.395 40.000 0.00 0.00 46.89 3.01
2188 2459 6.183360 GGGCTCAGAAATGAATTTTCGGAATA 60.183 38.462 0.00 0.00 46.89 1.75
2189 2460 7.257722 GGCTCAGAAATGAATTTTCGGAATAA 58.742 34.615 0.00 0.00 46.89 1.40
2190 2461 7.922811 GGCTCAGAAATGAATTTTCGGAATAAT 59.077 33.333 0.00 0.00 46.89 1.28
2191 2462 8.749499 GCTCAGAAATGAATTTTCGGAATAATG 58.251 33.333 0.00 0.00 46.89 1.90
2192 2463 9.241317 CTCAGAAATGAATTTTCGGAATAATGG 57.759 33.333 0.00 0.00 46.89 3.16
2193 2464 8.748412 TCAGAAATGAATTTTCGGAATAATGGT 58.252 29.630 0.00 0.00 46.89 3.55
2196 2467 8.871686 AAATGAATTTTCGGAATAATGGTAGC 57.128 30.769 0.00 0.00 0.00 3.58
2197 2468 7.581213 ATGAATTTTCGGAATAATGGTAGCA 57.419 32.000 0.00 0.00 0.00 3.49
2198 2469 7.581213 TGAATTTTCGGAATAATGGTAGCAT 57.419 32.000 0.40 0.40 0.00 3.79
2199 2470 8.006298 TGAATTTTCGGAATAATGGTAGCATT 57.994 30.769 22.63 22.63 0.00 3.56
2200 2471 8.474025 TGAATTTTCGGAATAATGGTAGCATTT 58.526 29.630 24.01 8.44 0.00 2.32
2201 2472 9.313118 GAATTTTCGGAATAATGGTAGCATTTT 57.687 29.630 24.01 14.36 0.00 1.82
2202 2473 8.647143 ATTTTCGGAATAATGGTAGCATTTTG 57.353 30.769 24.01 10.61 0.00 2.44
2203 2474 6.767524 TTCGGAATAATGGTAGCATTTTGT 57.232 33.333 24.01 10.62 0.00 2.83
2204 2475 7.867305 TTCGGAATAATGGTAGCATTTTGTA 57.133 32.000 24.01 7.81 0.00 2.41
2205 2476 8.458573 TTCGGAATAATGGTAGCATTTTGTAT 57.541 30.769 24.01 9.76 0.00 2.29
2206 2477 7.870826 TCGGAATAATGGTAGCATTTTGTATG 58.129 34.615 24.01 11.09 0.00 2.39
2207 2478 7.500892 TCGGAATAATGGTAGCATTTTGTATGT 59.499 33.333 24.01 2.58 0.00 2.29
2208 2479 8.134895 CGGAATAATGGTAGCATTTTGTATGTT 58.865 33.333 24.01 4.75 0.00 2.71
2209 2480 9.816354 GGAATAATGGTAGCATTTTGTATGTTT 57.184 29.630 24.01 1.22 0.00 2.83
2212 2483 9.965824 ATAATGGTAGCATTTTGTATGTTTAGC 57.034 29.630 24.01 0.00 0.00 3.09
2213 2484 6.825944 TGGTAGCATTTTGTATGTTTAGCA 57.174 33.333 0.00 0.00 0.00 3.49
2214 2485 6.616947 TGGTAGCATTTTGTATGTTTAGCAC 58.383 36.000 0.00 0.00 0.00 4.40
2215 2486 6.207614 TGGTAGCATTTTGTATGTTTAGCACA 59.792 34.615 0.00 0.00 40.71 4.57
2216 2487 7.087639 GGTAGCATTTTGTATGTTTAGCACAA 58.912 34.615 0.00 0.00 39.50 3.33
2217 2488 7.759433 GGTAGCATTTTGTATGTTTAGCACAAT 59.241 33.333 0.00 0.00 39.50 2.71
2218 2489 7.585286 AGCATTTTGTATGTTTAGCACAATG 57.415 32.000 0.00 0.00 39.50 2.82
2219 2490 6.591062 AGCATTTTGTATGTTTAGCACAATGG 59.409 34.615 0.00 0.00 39.50 3.16
2220 2491 6.589523 GCATTTTGTATGTTTAGCACAATGGA 59.410 34.615 0.00 0.00 39.50 3.41
2221 2492 7.117523 GCATTTTGTATGTTTAGCACAATGGAA 59.882 33.333 0.00 0.00 39.50 3.53
2222 2493 8.649841 CATTTTGTATGTTTAGCACAATGGAAG 58.350 33.333 0.00 0.00 39.50 3.46
2223 2494 6.892658 TTGTATGTTTAGCACAATGGAAGT 57.107 33.333 0.00 0.00 39.50 3.01
2224 2495 6.494893 TGTATGTTTAGCACAATGGAAGTC 57.505 37.500 0.00 0.00 39.50 3.01
2225 2496 6.237901 TGTATGTTTAGCACAATGGAAGTCT 58.762 36.000 0.00 0.00 39.50 3.24
2226 2497 6.714810 TGTATGTTTAGCACAATGGAAGTCTT 59.285 34.615 0.00 0.00 39.50 3.01
2227 2498 7.880713 TGTATGTTTAGCACAATGGAAGTCTTA 59.119 33.333 0.00 0.00 39.50 2.10
2228 2499 7.944729 ATGTTTAGCACAATGGAAGTCTTAT 57.055 32.000 0.00 0.00 39.50 1.73
2229 2500 7.144722 TGTTTAGCACAATGGAAGTCTTATG 57.855 36.000 0.00 0.00 29.87 1.90
2230 2501 5.818136 TTAGCACAATGGAAGTCTTATGC 57.182 39.130 0.00 0.00 0.00 3.14
2231 2502 3.960571 AGCACAATGGAAGTCTTATGCT 58.039 40.909 0.00 0.00 37.34 3.79
2232 2503 3.944015 AGCACAATGGAAGTCTTATGCTC 59.056 43.478 0.00 0.00 37.63 4.26
2233 2504 3.065925 GCACAATGGAAGTCTTATGCTCC 59.934 47.826 0.00 0.00 0.00 4.70
2234 2505 4.264253 CACAATGGAAGTCTTATGCTCCA 58.736 43.478 0.00 0.00 0.00 3.86
2235 2506 4.885907 CACAATGGAAGTCTTATGCTCCAT 59.114 41.667 0.00 0.00 39.38 3.41
2236 2507 6.057533 CACAATGGAAGTCTTATGCTCCATA 58.942 40.000 3.86 0.00 37.02 2.74
2237 2508 6.713903 CACAATGGAAGTCTTATGCTCCATAT 59.286 38.462 3.86 0.00 37.02 1.78
2238 2509 6.939163 ACAATGGAAGTCTTATGCTCCATATC 59.061 38.462 3.86 0.00 37.02 1.63
2239 2510 6.692849 ATGGAAGTCTTATGCTCCATATCA 57.307 37.500 1.74 0.00 36.34 2.15
2240 2511 5.858381 TGGAAGTCTTATGCTCCATATCAC 58.142 41.667 0.00 0.00 0.00 3.06
2241 2512 5.366477 TGGAAGTCTTATGCTCCATATCACA 59.634 40.000 0.00 0.00 0.00 3.58
2242 2513 6.043590 TGGAAGTCTTATGCTCCATATCACAT 59.956 38.462 0.00 0.00 0.00 3.21
2243 2514 6.939163 GGAAGTCTTATGCTCCATATCACATT 59.061 38.462 0.00 0.00 0.00 2.71
2244 2515 7.446625 GGAAGTCTTATGCTCCATATCACATTT 59.553 37.037 0.00 0.00 0.00 2.32
2245 2516 8.757982 AAGTCTTATGCTCCATATCACATTTT 57.242 30.769 0.00 0.00 0.00 1.82
2246 2517 8.757982 AGTCTTATGCTCCATATCACATTTTT 57.242 30.769 0.00 0.00 0.00 1.94
2247 2518 9.851686 AGTCTTATGCTCCATATCACATTTTTA 57.148 29.630 0.00 0.00 0.00 1.52
2263 2534 9.545105 TCACATTTTTAAATCAATTTGCAGTCT 57.455 25.926 0.00 0.00 0.00 3.24
2282 2553 9.332502 TGCAGTCTTTTAAGTAAAGTAATGACA 57.667 29.630 0.00 0.00 43.12 3.58
2283 2554 9.595357 GCAGTCTTTTAAGTAAAGTAATGACAC 57.405 33.333 0.00 0.00 43.12 3.67
2302 2573 9.480053 AATGACACATTTTAACCTTTTGATCAG 57.520 29.630 0.00 0.00 0.00 2.90
2303 2574 8.006298 TGACACATTTTAACCTTTTGATCAGT 57.994 30.769 0.00 0.00 0.00 3.41
2304 2575 9.126151 TGACACATTTTAACCTTTTGATCAGTA 57.874 29.630 0.00 0.00 0.00 2.74
2306 2577 9.912634 ACACATTTTAACCTTTTGATCAGTATG 57.087 29.630 0.00 0.00 37.54 2.39
2344 2615 7.412137 AGAAGCATACAAAAGTTTGAATTGC 57.588 32.000 10.66 13.82 40.55 3.56
2345 2616 6.985645 AGAAGCATACAAAAGTTTGAATTGCA 59.014 30.769 20.89 0.00 40.55 4.08
2346 2617 7.495279 AGAAGCATACAAAAGTTTGAATTGCAA 59.505 29.630 20.89 0.00 40.55 4.08
2347 2618 7.733402 AGCATACAAAAGTTTGAATTGCAAT 57.267 28.000 20.89 5.99 40.55 3.56
2348 2619 7.799784 AGCATACAAAAGTTTGAATTGCAATC 58.200 30.769 13.38 7.13 40.55 2.67
2349 2620 7.658575 AGCATACAAAAGTTTGAATTGCAATCT 59.341 29.630 13.38 1.77 40.55 2.40
2350 2621 7.953710 GCATACAAAAGTTTGAATTGCAATCTC 59.046 33.333 13.38 12.57 40.55 2.75
2351 2622 8.980610 CATACAAAAGTTTGAATTGCAATCTCA 58.019 29.630 13.38 14.88 40.55 3.27
2352 2623 9.715121 ATACAAAAGTTTGAATTGCAATCTCAT 57.285 25.926 13.38 0.00 40.55 2.90
2353 2624 7.857569 ACAAAAGTTTGAATTGCAATCTCATG 58.142 30.769 13.38 13.30 40.55 3.07
2354 2625 6.476243 AAAGTTTGAATTGCAATCTCATGC 57.524 33.333 13.38 12.72 46.58 4.06
2355 2626 5.401531 AGTTTGAATTGCAATCTCATGCT 57.598 34.783 13.38 14.33 46.54 3.79
2356 2627 6.519679 AGTTTGAATTGCAATCTCATGCTA 57.480 33.333 13.38 1.78 46.54 3.49
2357 2628 7.108841 AGTTTGAATTGCAATCTCATGCTAT 57.891 32.000 13.38 0.00 46.54 2.97
2359 2630 7.491372 AGTTTGAATTGCAATCTCATGCTATTG 59.509 33.333 13.38 12.83 46.61 1.90
2360 2631 6.702716 TGAATTGCAATCTCATGCTATTGA 57.297 33.333 13.38 3.23 46.61 2.57
2361 2632 7.102847 TGAATTGCAATCTCATGCTATTGAA 57.897 32.000 13.38 9.33 46.61 2.69
2362 2633 7.548967 TGAATTGCAATCTCATGCTATTGAAA 58.451 30.769 13.38 15.71 46.61 2.69
2363 2634 8.035984 TGAATTGCAATCTCATGCTATTGAAAA 58.964 29.630 13.38 13.36 46.61 2.29
2364 2635 8.780846 AATTGCAATCTCATGCTATTGAAAAA 57.219 26.923 13.38 11.66 45.52 1.94
2365 2636 7.821595 TTGCAATCTCATGCTATTGAAAAAG 57.178 32.000 18.55 0.00 46.54 2.27
2366 2637 7.160547 TGCAATCTCATGCTATTGAAAAAGA 57.839 32.000 18.55 1.00 46.54 2.52
2367 2638 7.031372 TGCAATCTCATGCTATTGAAAAAGAC 58.969 34.615 18.55 5.01 46.54 3.01
2368 2639 6.474751 GCAATCTCATGCTATTGAAAAAGACC 59.525 38.462 18.55 1.36 43.06 3.85
2369 2640 6.705863 ATCTCATGCTATTGAAAAAGACCC 57.294 37.500 0.00 0.00 0.00 4.46
2370 2641 5.569355 TCTCATGCTATTGAAAAAGACCCA 58.431 37.500 0.00 0.00 0.00 4.51
2371 2642 6.189859 TCTCATGCTATTGAAAAAGACCCAT 58.810 36.000 0.00 0.00 0.00 4.00
2372 2643 6.664816 TCTCATGCTATTGAAAAAGACCCATT 59.335 34.615 0.00 0.00 0.00 3.16
2373 2644 7.178983 TCTCATGCTATTGAAAAAGACCCATTT 59.821 33.333 0.00 0.00 0.00 2.32
2374 2645 7.678837 TCATGCTATTGAAAAAGACCCATTTT 58.321 30.769 0.00 0.00 33.86 1.82
2375 2646 8.156165 TCATGCTATTGAAAAAGACCCATTTTT 58.844 29.630 0.00 0.00 43.28 1.94
2392 2663 3.363341 TTTTTGTCCTGCGATGGTTTC 57.637 42.857 0.00 0.00 0.00 2.78
2393 2664 1.974265 TTTGTCCTGCGATGGTTTCA 58.026 45.000 0.00 0.00 0.00 2.69
2394 2665 2.198827 TTGTCCTGCGATGGTTTCAT 57.801 45.000 0.00 0.00 36.09 2.57
2395 2666 1.452110 TGTCCTGCGATGGTTTCATG 58.548 50.000 0.00 0.00 32.98 3.07
2396 2667 0.099436 GTCCTGCGATGGTTTCATGC 59.901 55.000 0.00 0.00 32.98 4.06
2397 2668 0.322366 TCCTGCGATGGTTTCATGCA 60.322 50.000 0.00 0.00 36.62 3.96
2398 2669 0.742505 CCTGCGATGGTTTCATGCAT 59.257 50.000 0.00 0.00 37.07 3.96
2399 2670 1.535226 CCTGCGATGGTTTCATGCATG 60.535 52.381 21.07 21.07 37.07 4.06
2400 2671 1.402613 CTGCGATGGTTTCATGCATGA 59.597 47.619 25.42 25.42 37.07 3.07
2401 2672 2.025898 TGCGATGGTTTCATGCATGAT 58.974 42.857 29.13 14.70 36.56 2.45
2402 2673 2.427812 TGCGATGGTTTCATGCATGATT 59.572 40.909 29.13 12.34 36.56 2.57
2403 2674 3.119065 TGCGATGGTTTCATGCATGATTT 60.119 39.130 29.13 12.67 36.56 2.17
2404 2675 3.866910 GCGATGGTTTCATGCATGATTTT 59.133 39.130 29.13 13.01 36.56 1.82
2405 2676 4.260051 GCGATGGTTTCATGCATGATTTTG 60.260 41.667 29.13 15.90 36.56 2.44
2406 2677 4.865925 CGATGGTTTCATGCATGATTTTGT 59.134 37.500 29.13 15.67 36.56 2.83
2407 2678 5.005012 CGATGGTTTCATGCATGATTTTGTC 59.995 40.000 29.13 21.16 36.56 3.18
2408 2679 5.211174 TGGTTTCATGCATGATTTTGTCA 57.789 34.783 29.13 17.63 42.06 3.58
2409 2680 6.411376 ATGGTTTCATGCATGATTTTGTCAT 58.589 32.000 29.13 20.91 38.99 3.06
2410 2681 6.932947 TGGTTTCATGCATGATTTTGTCATA 58.067 32.000 29.13 8.97 45.76 2.15
2411 2682 7.384477 TGGTTTCATGCATGATTTTGTCATAA 58.616 30.769 29.13 14.47 45.76 1.90
2412 2683 7.331440 TGGTTTCATGCATGATTTTGTCATAAC 59.669 33.333 29.13 23.48 45.76 1.89
2413 2684 7.546667 GGTTTCATGCATGATTTTGTCATAACT 59.453 33.333 29.13 0.00 45.76 2.24
2414 2685 8.377681 GTTTCATGCATGATTTTGTCATAACTG 58.622 33.333 29.13 0.00 45.76 3.16
2415 2686 6.566141 TCATGCATGATTTTGTCATAACTGG 58.434 36.000 25.42 0.00 45.76 4.00
2416 2687 6.377712 TCATGCATGATTTTGTCATAACTGGA 59.622 34.615 25.42 0.00 45.76 3.86
2417 2688 6.778834 TGCATGATTTTGTCATAACTGGAT 57.221 33.333 0.00 0.00 45.76 3.41
2418 2689 6.566141 TGCATGATTTTGTCATAACTGGATG 58.434 36.000 0.00 0.00 45.76 3.51
2419 2690 5.461078 GCATGATTTTGTCATAACTGGATGC 59.539 40.000 0.00 0.00 45.76 3.91
2420 2691 6.682113 GCATGATTTTGTCATAACTGGATGCT 60.682 38.462 0.00 0.00 45.76 3.79
2421 2692 7.469043 GCATGATTTTGTCATAACTGGATGCTA 60.469 37.037 0.00 0.00 45.76 3.49
2422 2693 8.573885 CATGATTTTGTCATAACTGGATGCTAT 58.426 33.333 0.00 0.00 45.76 2.97
2423 2694 8.523915 TGATTTTGTCATAACTGGATGCTATT 57.476 30.769 0.00 0.00 0.00 1.73
2424 2695 8.970020 TGATTTTGTCATAACTGGATGCTATTT 58.030 29.630 0.00 0.00 0.00 1.40
2425 2696 9.241317 GATTTTGTCATAACTGGATGCTATTTG 57.759 33.333 0.00 0.00 0.00 2.32
2426 2697 7.701539 TTTGTCATAACTGGATGCTATTTGT 57.298 32.000 0.00 0.00 0.00 2.83
2427 2698 7.701539 TTGTCATAACTGGATGCTATTTGTT 57.298 32.000 0.00 0.00 0.00 2.83
2428 2699 7.320443 TGTCATAACTGGATGCTATTTGTTC 57.680 36.000 0.00 0.00 0.00 3.18
2429 2700 6.318648 TGTCATAACTGGATGCTATTTGTTCC 59.681 38.462 0.00 0.00 0.00 3.62
2430 2701 6.543831 GTCATAACTGGATGCTATTTGTTCCT 59.456 38.462 0.00 0.00 0.00 3.36
2431 2702 6.543465 TCATAACTGGATGCTATTTGTTCCTG 59.457 38.462 0.00 0.00 34.44 3.86
2432 2703 4.574674 ACTGGATGCTATTTGTTCCTGA 57.425 40.909 0.00 0.00 33.06 3.86
2433 2704 5.121380 ACTGGATGCTATTTGTTCCTGAT 57.879 39.130 0.00 0.00 33.06 2.90
2434 2705 4.885907 ACTGGATGCTATTTGTTCCTGATG 59.114 41.667 0.00 0.00 33.06 3.07
2435 2706 3.633525 TGGATGCTATTTGTTCCTGATGC 59.366 43.478 0.00 0.00 0.00 3.91
2436 2707 3.304257 GGATGCTATTTGTTCCTGATGCG 60.304 47.826 0.00 0.00 0.00 4.73
2437 2708 2.710377 TGCTATTTGTTCCTGATGCGT 58.290 42.857 0.00 0.00 0.00 5.24
2438 2709 2.677836 TGCTATTTGTTCCTGATGCGTC 59.322 45.455 0.00 0.00 0.00 5.19
2439 2710 2.677836 GCTATTTGTTCCTGATGCGTCA 59.322 45.455 8.64 8.64 0.00 4.35
2440 2711 3.313526 GCTATTTGTTCCTGATGCGTCAT 59.686 43.478 9.53 0.00 32.98 3.06
2441 2712 4.201950 GCTATTTGTTCCTGATGCGTCATT 60.202 41.667 9.53 0.00 32.98 2.57
2442 2713 3.557577 TTTGTTCCTGATGCGTCATTG 57.442 42.857 9.53 4.18 32.98 2.82
2443 2714 0.804364 TGTTCCTGATGCGTCATTGC 59.196 50.000 9.53 1.39 32.98 3.56
2444 2715 0.099436 GTTCCTGATGCGTCATTGCC 59.901 55.000 9.53 0.00 32.98 4.52
2445 2716 0.322366 TTCCTGATGCGTCATTGCCA 60.322 50.000 9.53 0.00 32.98 4.92
2446 2717 0.107066 TCCTGATGCGTCATTGCCAT 60.107 50.000 9.53 0.00 32.98 4.40
2447 2718 0.030235 CCTGATGCGTCATTGCCATG 59.970 55.000 9.53 0.00 32.98 3.66
2448 2719 1.018910 CTGATGCGTCATTGCCATGA 58.981 50.000 9.53 0.00 37.05 3.07
2449 2720 1.607148 CTGATGCGTCATTGCCATGAT 59.393 47.619 9.53 0.00 41.64 2.45
2450 2721 2.809696 CTGATGCGTCATTGCCATGATA 59.190 45.455 9.53 0.00 41.64 2.15
2451 2722 3.212685 TGATGCGTCATTGCCATGATAA 58.787 40.909 3.97 0.00 41.64 1.75
2452 2723 3.631227 TGATGCGTCATTGCCATGATAAA 59.369 39.130 3.97 0.00 41.64 1.40
2453 2724 4.097589 TGATGCGTCATTGCCATGATAAAA 59.902 37.500 3.97 0.00 41.64 1.52
2454 2725 4.031418 TGCGTCATTGCCATGATAAAAG 57.969 40.909 3.48 0.00 41.64 2.27
2455 2726 3.443329 TGCGTCATTGCCATGATAAAAGT 59.557 39.130 3.48 0.00 41.64 2.66
2456 2727 4.637977 TGCGTCATTGCCATGATAAAAGTA 59.362 37.500 3.48 0.00 41.64 2.24
2457 2728 5.299028 TGCGTCATTGCCATGATAAAAGTAT 59.701 36.000 3.48 0.00 41.64 2.12
2458 2729 6.484977 TGCGTCATTGCCATGATAAAAGTATA 59.515 34.615 3.48 0.00 41.64 1.47
2459 2730 6.797033 GCGTCATTGCCATGATAAAAGTATAC 59.203 38.462 3.48 0.00 41.64 1.47
2460 2731 7.519809 GCGTCATTGCCATGATAAAAGTATACA 60.520 37.037 3.48 0.00 41.64 2.29
2461 2732 8.506437 CGTCATTGCCATGATAAAAGTATACAT 58.494 33.333 3.48 0.00 41.64 2.29
2492 2763 9.768215 AAGAAAATATTCCCAGAATAAACTCCA 57.232 29.630 1.43 0.00 36.12 3.86
2493 2764 9.768215 AGAAAATATTCCCAGAATAAACTCCAA 57.232 29.630 1.43 0.00 36.12 3.53
2497 2768 9.942526 AATATTCCCAGAATAAACTCCAATTCT 57.057 29.630 1.43 0.00 41.92 2.40
2498 2769 9.942526 ATATTCCCAGAATAAACTCCAATTCTT 57.057 29.630 1.43 0.00 39.79 2.52
2499 2770 8.670521 ATTCCCAGAATAAACTCCAATTCTTT 57.329 30.769 0.00 0.00 39.79 2.52
2500 2771 8.491045 TTCCCAGAATAAACTCCAATTCTTTT 57.509 30.769 0.00 0.00 39.79 2.27
2501 2772 9.594936 TTCCCAGAATAAACTCCAATTCTTTTA 57.405 29.630 0.00 0.00 39.79 1.52
2502 2773 9.594936 TCCCAGAATAAACTCCAATTCTTTTAA 57.405 29.630 0.00 0.00 39.79 1.52
2525 2796 5.391312 AAAAGGGACATTTACATCTGTGC 57.609 39.130 0.00 0.00 33.46 4.57
2527 2798 2.024414 GGGACATTTACATCTGTGCCC 58.976 52.381 2.18 0.00 45.22 5.36
2528 2799 2.024414 GGACATTTACATCTGTGCCCC 58.976 52.381 0.00 0.00 0.00 5.80
2529 2800 2.357154 GGACATTTACATCTGTGCCCCT 60.357 50.000 0.00 0.00 0.00 4.79
2530 2801 3.118038 GGACATTTACATCTGTGCCCCTA 60.118 47.826 0.00 0.00 0.00 3.53
2531 2802 4.523083 GACATTTACATCTGTGCCCCTAA 58.477 43.478 0.00 0.00 0.00 2.69
2532 2803 4.270008 ACATTTACATCTGTGCCCCTAAC 58.730 43.478 0.00 0.00 0.00 2.34
2533 2804 4.018415 ACATTTACATCTGTGCCCCTAACT 60.018 41.667 0.00 0.00 0.00 2.24
2534 2805 3.906720 TTACATCTGTGCCCCTAACTC 57.093 47.619 0.00 0.00 0.00 3.01
2535 2806 0.537188 ACATCTGTGCCCCTAACTCG 59.463 55.000 0.00 0.00 0.00 4.18
2536 2807 0.824109 CATCTGTGCCCCTAACTCGA 59.176 55.000 0.00 0.00 0.00 4.04
2537 2808 1.207089 CATCTGTGCCCCTAACTCGAA 59.793 52.381 0.00 0.00 0.00 3.71
2538 2809 0.606604 TCTGTGCCCCTAACTCGAAC 59.393 55.000 0.00 0.00 0.00 3.95
2539 2810 0.391263 CTGTGCCCCTAACTCGAACC 60.391 60.000 0.00 0.00 0.00 3.62
2540 2811 1.078637 GTGCCCCTAACTCGAACCC 60.079 63.158 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.091220 ACACTCTTAGTAGGTTCTTCTGTAAAT 57.909 33.333 0.00 0.00 0.00 1.40
90 91 1.896660 GCCAACCTCCGCTGAACAA 60.897 57.895 0.00 0.00 0.00 2.83
139 140 5.065731 GCACTAAATTGGTTCTCTCAGGATG 59.934 44.000 0.00 0.00 37.54 3.51
172 173 3.055819 TCTCTCACCAAAGAGCCATACAC 60.056 47.826 0.00 0.00 42.15 2.90
176 177 5.643421 AATATCTCTCACCAAAGAGCCAT 57.357 39.130 0.00 0.00 42.15 4.40
182 183 7.439157 TGAACACAAATATCTCTCACCAAAG 57.561 36.000 0.00 0.00 0.00 2.77
186 187 7.044181 TCAGATGAACACAAATATCTCTCACC 58.956 38.462 0.00 0.00 0.00 4.02
285 286 1.986378 CTTTCTACTTGCTCGTCCGTG 59.014 52.381 0.00 0.00 0.00 4.94
325 326 7.506938 AGGTCCACCCATCATAATAAGAAATTG 59.493 37.037 0.00 0.00 36.42 2.32
396 397 2.362077 ACCAGAAATGAATATTGCCGCC 59.638 45.455 0.00 0.00 0.00 6.13
434 435 6.346096 ACTGTCAAAAACAACTAGTCAGCTA 58.654 36.000 0.00 0.00 37.45 3.32
567 568 3.189080 TCATTCTTCTTCATGCACAACGG 59.811 43.478 0.00 0.00 0.00 4.44
631 632 0.888619 AGCCTCAAACTCGTCGATCA 59.111 50.000 0.00 0.00 0.00 2.92
677 678 8.177663 GTCATATATGGATGCTTCCGTAAATTG 58.822 37.037 20.94 17.53 44.77 2.32
721 722 2.861147 AGGCTTCACCCACTTAGTTC 57.139 50.000 0.00 0.00 40.58 3.01
761 762 1.812922 GGTGCCTGTCATCTCAGCG 60.813 63.158 0.00 0.00 34.47 5.18
811 812 3.338249 CTGCACAAGTTGTATGCCTACT 58.662 45.455 8.49 0.00 38.63 2.57
819 820 1.270094 CCGAGACCTGCACAAGTTGTA 60.270 52.381 8.49 0.00 0.00 2.41
893 894 4.937015 GGCATAACAATCCACTGCAATTTT 59.063 37.500 0.00 0.00 34.56 1.82
900 901 1.406539 GCCTGGCATAACAATCCACTG 59.593 52.381 15.17 0.00 0.00 3.66
941 942 2.641197 CCAACTGGCTGGTTGTACC 58.359 57.895 17.49 0.00 43.36 3.34
948 949 1.691196 TTTGAGAACCAACTGGCTGG 58.309 50.000 0.00 0.00 42.68 4.85
949 950 2.689983 AGTTTTGAGAACCAACTGGCTG 59.310 45.455 0.00 0.00 39.32 4.85
950 951 3.018423 AGTTTTGAGAACCAACTGGCT 57.982 42.857 0.00 0.00 39.32 4.75
951 952 3.801114 AAGTTTTGAGAACCAACTGGC 57.199 42.857 0.00 0.00 39.32 4.85
952 953 5.072040 ACAAAGTTTTGAGAACCAACTGG 57.928 39.130 11.29 0.00 40.55 4.00
953 954 6.155827 TGAACAAAGTTTTGAGAACCAACTG 58.844 36.000 11.29 0.00 40.55 3.16
954 955 6.208599 TCTGAACAAAGTTTTGAGAACCAACT 59.791 34.615 11.29 0.00 40.55 3.16
964 965 5.401550 TGCTCTGTTCTGAACAAAGTTTTG 58.598 37.500 21.28 10.50 41.61 2.44
965 966 5.393461 CCTGCTCTGTTCTGAACAAAGTTTT 60.393 40.000 21.28 0.00 41.61 2.43
1040 1041 0.667993 AACTTCACCCGTCGTCGTTA 59.332 50.000 0.71 0.00 35.01 3.18
1044 1045 1.137513 CTGAAACTTCACCCGTCGTC 58.862 55.000 0.00 0.00 32.90 4.20
1088 1089 2.185350 CCCCTACGCTGCTCAGTG 59.815 66.667 8.73 8.73 44.11 3.66
1089 1090 3.775654 GCCCCTACGCTGCTCAGT 61.776 66.667 0.00 0.00 0.00 3.41
1099 1100 0.103208 CTCAGTGACATCGCCCCTAC 59.897 60.000 0.00 0.00 0.00 3.18
1142 1143 7.210174 CCATTGTACTGCTACATACTACACAT 58.790 38.462 0.00 0.00 32.70 3.21
1148 1149 3.492656 CGGCCATTGTACTGCTACATACT 60.493 47.826 2.24 0.00 32.70 2.12
1153 1154 1.396996 CAACGGCCATTGTACTGCTAC 59.603 52.381 2.64 0.00 0.00 3.58
1279 1280 6.155827 CGAGAGAAGACAAGACAATCTTTCT 58.844 40.000 0.00 0.00 33.78 2.52
1289 1290 1.166129 CCGTCCGAGAGAAGACAAGA 58.834 55.000 0.00 0.00 0.00 3.02
1314 1315 3.563808 TGTTGTTCATGTTACTGCCTGAC 59.436 43.478 0.00 0.00 0.00 3.51
1414 1415 4.154347 CTCTCCTCACCCGCCAGC 62.154 72.222 0.00 0.00 0.00 4.85
1453 1454 0.043053 CGTTGATAATGACTGCGCCG 60.043 55.000 4.18 0.00 0.00 6.46
1456 1457 4.085055 GGTACATCGTTGATAATGACTGCG 60.085 45.833 0.00 0.00 0.00 5.18
1468 1469 2.386661 AGAAGGCTGGTACATCGTTG 57.613 50.000 0.00 0.00 38.20 4.10
1469 1470 2.301870 TCAAGAAGGCTGGTACATCGTT 59.698 45.455 0.00 0.00 38.20 3.85
1481 1482 0.378610 GCCAACGCTATCAAGAAGGC 59.621 55.000 0.00 0.00 0.00 4.35
1509 1512 4.718774 TCTGTATCTGATTCCTCCAGCTTT 59.281 41.667 0.00 0.00 0.00 3.51
1527 1530 2.243478 ACCTCTGCTCATCTCCTCTGTA 59.757 50.000 0.00 0.00 0.00 2.74
1528 1531 1.006998 ACCTCTGCTCATCTCCTCTGT 59.993 52.381 0.00 0.00 0.00 3.41
1535 1538 0.325484 AGCCAGACCTCTGCTCATCT 60.325 55.000 0.00 0.00 42.47 2.90
1536 1539 1.407936 TAGCCAGACCTCTGCTCATC 58.592 55.000 0.00 0.00 42.47 2.92
1537 1540 1.761784 CTTAGCCAGACCTCTGCTCAT 59.238 52.381 0.00 0.00 42.47 2.90
1550 1553 2.252072 AATTCGCCCTCGCTTAGCCA 62.252 55.000 0.00 0.00 35.26 4.75
1561 1564 2.554032 CCATCTATGGTTCAATTCGCCC 59.446 50.000 0.49 0.00 43.05 6.13
1588 1591 2.213499 CGTTGCTATCTCCCCAACATC 58.787 52.381 0.00 0.00 38.92 3.06
1661 1664 7.148869 TGTCACGAATCAGTAAACAACTAATCG 60.149 37.037 0.00 0.00 40.11 3.34
1663 1666 7.095355 GGTGTCACGAATCAGTAAACAACTAAT 60.095 37.037 0.00 0.00 35.76 1.73
1665 1668 5.693104 GGTGTCACGAATCAGTAAACAACTA 59.307 40.000 0.00 0.00 35.76 2.24
1921 1924 1.674441 CGCTGAAATCTCCATGCATGT 59.326 47.619 24.58 5.40 0.00 3.21
2046 2317 3.822735 AGAAATATTGTGGGCCATCATCG 59.177 43.478 10.70 0.00 0.00 3.84
2091 2362 5.878116 AGCGCCATAAGTTGTATTCTAACAA 59.122 36.000 2.29 0.00 37.03 2.83
2112 2383 1.004595 CAGTCACATGTGGATCAGCG 58.995 55.000 25.16 4.27 0.00 5.18
2122 2393 3.548745 TCTTAGCCATCCAGTCACATG 57.451 47.619 0.00 0.00 0.00 3.21
2131 2402 3.008375 TGCACCTGATATCTTAGCCATCC 59.992 47.826 3.98 0.00 0.00 3.51
2145 2416 4.025858 GGGCTCAGCTGCACCTGA 62.026 66.667 20.21 11.20 39.42 3.86
2164 2435 4.701956 TCCGAAAATTCATTTCTGAGCC 57.298 40.909 0.00 0.00 44.35 4.70
2183 2454 9.816354 AAACATACAAAATGCTACCATTATTCC 57.184 29.630 0.00 0.00 40.69 3.01
2186 2457 9.965824 GCTAAACATACAAAATGCTACCATTAT 57.034 29.630 0.00 0.00 40.69 1.28
2187 2458 8.961634 TGCTAAACATACAAAATGCTACCATTA 58.038 29.630 0.00 0.00 40.69 1.90
2188 2459 7.759433 GTGCTAAACATACAAAATGCTACCATT 59.241 33.333 0.00 0.00 43.32 3.16
2189 2460 7.093988 TGTGCTAAACATACAAAATGCTACCAT 60.094 33.333 0.00 0.00 32.36 3.55
2190 2461 6.207614 TGTGCTAAACATACAAAATGCTACCA 59.792 34.615 0.00 0.00 32.36 3.25
2191 2462 6.616947 TGTGCTAAACATACAAAATGCTACC 58.383 36.000 0.00 0.00 32.36 3.18
2192 2463 8.586273 CATTGTGCTAAACATACAAAATGCTAC 58.414 33.333 0.00 0.00 38.99 3.58
2193 2464 7.758980 CCATTGTGCTAAACATACAAAATGCTA 59.241 33.333 0.00 0.00 38.99 3.49
2194 2465 6.591062 CCATTGTGCTAAACATACAAAATGCT 59.409 34.615 0.00 0.00 38.99 3.79
2195 2466 6.589523 TCCATTGTGCTAAACATACAAAATGC 59.410 34.615 0.00 0.00 38.99 3.56
2196 2467 8.531622 TTCCATTGTGCTAAACATACAAAATG 57.468 30.769 0.00 0.00 38.99 2.32
2197 2468 8.367156 ACTTCCATTGTGCTAAACATACAAAAT 58.633 29.630 0.00 0.00 38.99 1.82
2198 2469 7.721402 ACTTCCATTGTGCTAAACATACAAAA 58.279 30.769 0.00 0.00 38.99 2.44
2199 2470 7.230510 AGACTTCCATTGTGCTAAACATACAAA 59.769 33.333 0.00 0.00 38.99 2.83
2200 2471 6.714810 AGACTTCCATTGTGCTAAACATACAA 59.285 34.615 0.00 0.00 38.99 2.41
2201 2472 6.237901 AGACTTCCATTGTGCTAAACATACA 58.762 36.000 0.00 0.00 38.99 2.29
2202 2473 6.743575 AGACTTCCATTGTGCTAAACATAC 57.256 37.500 0.00 0.00 38.99 2.39
2203 2474 8.892723 CATAAGACTTCCATTGTGCTAAACATA 58.107 33.333 0.00 0.00 38.99 2.29
2204 2475 7.629222 GCATAAGACTTCCATTGTGCTAAACAT 60.629 37.037 0.00 0.00 39.56 2.71
2205 2476 6.349280 GCATAAGACTTCCATTGTGCTAAACA 60.349 38.462 0.00 0.00 39.56 2.83
2206 2477 6.030228 GCATAAGACTTCCATTGTGCTAAAC 58.970 40.000 0.00 0.00 39.56 2.01
2207 2478 6.194796 GCATAAGACTTCCATTGTGCTAAA 57.805 37.500 0.00 0.00 39.56 1.85
2208 2479 5.818136 GCATAAGACTTCCATTGTGCTAA 57.182 39.130 0.00 0.00 39.56 3.09
2210 2481 3.960571 AGCATAAGACTTCCATTGTGCT 58.039 40.909 3.71 3.71 45.44 4.40
2211 2482 3.065925 GGAGCATAAGACTTCCATTGTGC 59.934 47.826 0.00 0.00 42.00 4.57
2212 2483 4.264253 TGGAGCATAAGACTTCCATTGTG 58.736 43.478 0.00 0.00 0.00 3.33
2213 2484 4.574674 TGGAGCATAAGACTTCCATTGT 57.425 40.909 0.00 0.00 0.00 2.71
2214 2485 6.938596 TGATATGGAGCATAAGACTTCCATTG 59.061 38.462 10.24 0.00 38.68 2.82
2215 2486 6.939163 GTGATATGGAGCATAAGACTTCCATT 59.061 38.462 10.24 0.97 38.68 3.16
2216 2487 6.043590 TGTGATATGGAGCATAAGACTTCCAT 59.956 38.462 9.92 9.92 40.57 3.41
2217 2488 5.366477 TGTGATATGGAGCATAAGACTTCCA 59.634 40.000 0.00 0.00 29.74 3.53
2218 2489 5.858381 TGTGATATGGAGCATAAGACTTCC 58.142 41.667 0.00 0.00 29.74 3.46
2219 2490 7.976135 AATGTGATATGGAGCATAAGACTTC 57.024 36.000 0.00 0.00 29.74 3.01
2220 2491 8.757982 AAAATGTGATATGGAGCATAAGACTT 57.242 30.769 0.00 0.00 29.74 3.01
2221 2492 8.757982 AAAAATGTGATATGGAGCATAAGACT 57.242 30.769 0.00 0.00 29.74 3.24
2237 2508 9.545105 AGACTGCAAATTGATTTAAAAATGTGA 57.455 25.926 6.89 0.00 0.00 3.58
2256 2527 9.332502 TGTCATTACTTTACTTAAAAGACTGCA 57.667 29.630 4.59 0.00 46.44 4.41
2257 2528 9.595357 GTGTCATTACTTTACTTAAAAGACTGC 57.405 33.333 4.59 0.00 46.44 4.40
2276 2547 9.480053 CTGATCAAAAGGTTAAAATGTGTCATT 57.520 29.630 0.00 0.00 0.00 2.57
2277 2548 8.641541 ACTGATCAAAAGGTTAAAATGTGTCAT 58.358 29.630 0.00 0.00 0.00 3.06
2278 2549 8.006298 ACTGATCAAAAGGTTAAAATGTGTCA 57.994 30.769 0.00 0.00 0.00 3.58
2280 2551 9.912634 CATACTGATCAAAAGGTTAAAATGTGT 57.087 29.630 0.00 0.00 0.00 3.72
2318 2589 8.977505 GCAATTCAAACTTTTGTATGCTTCTAA 58.022 29.630 15.40 0.00 38.15 2.10
2319 2590 8.140628 TGCAATTCAAACTTTTGTATGCTTCTA 58.859 29.630 19.60 6.68 39.86 2.10
2320 2591 6.985645 TGCAATTCAAACTTTTGTATGCTTCT 59.014 30.769 19.60 0.00 39.86 2.85
2321 2592 7.176285 TGCAATTCAAACTTTTGTATGCTTC 57.824 32.000 19.60 4.50 39.86 3.86
2322 2593 7.551035 TTGCAATTCAAACTTTTGTATGCTT 57.449 28.000 19.60 0.00 39.86 3.91
2323 2594 7.658575 AGATTGCAATTCAAACTTTTGTATGCT 59.341 29.630 14.33 0.00 39.86 3.79
2324 2595 7.799784 AGATTGCAATTCAAACTTTTGTATGC 58.200 30.769 14.33 15.63 34.62 3.14
2325 2596 8.980610 TGAGATTGCAATTCAAACTTTTGTATG 58.019 29.630 14.33 1.96 37.84 2.39
2326 2597 9.715121 ATGAGATTGCAATTCAAACTTTTGTAT 57.285 25.926 14.33 0.00 37.84 2.29
2327 2598 8.980610 CATGAGATTGCAATTCAAACTTTTGTA 58.019 29.630 14.33 0.00 37.84 2.41
2328 2599 7.519328 GCATGAGATTGCAATTCAAACTTTTGT 60.519 33.333 14.33 0.02 42.31 2.83
2329 2600 6.795114 GCATGAGATTGCAATTCAAACTTTTG 59.205 34.615 14.33 12.64 42.31 2.44
2330 2601 6.708949 AGCATGAGATTGCAATTCAAACTTTT 59.291 30.769 14.33 1.29 45.23 2.27
2331 2602 6.228258 AGCATGAGATTGCAATTCAAACTTT 58.772 32.000 14.33 1.93 45.23 2.66
2332 2603 5.790593 AGCATGAGATTGCAATTCAAACTT 58.209 33.333 14.33 2.25 45.23 2.66
2333 2604 5.401531 AGCATGAGATTGCAATTCAAACT 57.598 34.783 14.33 15.27 45.23 2.66
2334 2605 7.490079 TCAATAGCATGAGATTGCAATTCAAAC 59.510 33.333 14.33 13.65 45.23 2.93
2335 2606 7.548967 TCAATAGCATGAGATTGCAATTCAAA 58.451 30.769 14.33 0.48 45.23 2.69
2336 2607 7.102847 TCAATAGCATGAGATTGCAATTCAA 57.897 32.000 14.33 2.36 45.23 2.69
2337 2608 6.702716 TCAATAGCATGAGATTGCAATTCA 57.297 33.333 14.33 17.68 45.23 2.57
2338 2609 7.997107 TTTCAATAGCATGAGATTGCAATTC 57.003 32.000 14.33 12.93 45.23 2.17
2339 2610 8.780846 TTTTTCAATAGCATGAGATTGCAATT 57.219 26.923 14.33 3.59 45.23 2.32
2340 2611 8.255206 TCTTTTTCAATAGCATGAGATTGCAAT 58.745 29.630 12.83 12.83 45.23 3.56
2341 2612 7.543172 GTCTTTTTCAATAGCATGAGATTGCAA 59.457 33.333 0.00 0.00 45.23 4.08
2342 2613 7.031372 GTCTTTTTCAATAGCATGAGATTGCA 58.969 34.615 12.75 2.76 45.23 4.08
2343 2614 6.474751 GGTCTTTTTCAATAGCATGAGATTGC 59.525 38.462 12.75 0.00 43.09 3.56
2344 2615 6.976925 GGGTCTTTTTCAATAGCATGAGATTG 59.023 38.462 11.78 11.78 34.89 2.67
2345 2616 6.664816 TGGGTCTTTTTCAATAGCATGAGATT 59.335 34.615 0.00 0.00 0.00 2.40
2346 2617 6.189859 TGGGTCTTTTTCAATAGCATGAGAT 58.810 36.000 0.00 0.00 0.00 2.75
2347 2618 5.569355 TGGGTCTTTTTCAATAGCATGAGA 58.431 37.500 0.00 0.00 0.00 3.27
2348 2619 5.902613 TGGGTCTTTTTCAATAGCATGAG 57.097 39.130 0.00 0.00 0.00 2.90
2349 2620 6.855763 AATGGGTCTTTTTCAATAGCATGA 57.144 33.333 0.00 0.00 0.00 3.07
2350 2621 7.910441 AAAATGGGTCTTTTTCAATAGCATG 57.090 32.000 0.00 0.00 0.00 4.06
2372 2643 2.690497 TGAAACCATCGCAGGACAAAAA 59.310 40.909 0.00 0.00 0.00 1.94
2373 2644 2.302260 TGAAACCATCGCAGGACAAAA 58.698 42.857 0.00 0.00 0.00 2.44
2374 2645 1.974265 TGAAACCATCGCAGGACAAA 58.026 45.000 0.00 0.00 0.00 2.83
2375 2646 1.811965 CATGAAACCATCGCAGGACAA 59.188 47.619 0.00 0.00 0.00 3.18
2376 2647 1.452110 CATGAAACCATCGCAGGACA 58.548 50.000 0.00 0.00 0.00 4.02
2377 2648 0.099436 GCATGAAACCATCGCAGGAC 59.901 55.000 0.00 0.00 0.00 3.85
2378 2649 0.322366 TGCATGAAACCATCGCAGGA 60.322 50.000 0.00 0.00 0.00 3.86
2379 2650 0.742505 ATGCATGAAACCATCGCAGG 59.257 50.000 0.00 0.00 34.29 4.85
2380 2651 1.402613 TCATGCATGAAACCATCGCAG 59.597 47.619 26.87 0.00 34.29 5.18
2381 2652 1.461559 TCATGCATGAAACCATCGCA 58.538 45.000 26.87 0.00 34.83 5.10
2382 2653 2.787601 ATCATGCATGAAACCATCGC 57.212 45.000 31.79 0.00 40.69 4.58
2383 2654 4.865925 ACAAAATCATGCATGAAACCATCG 59.134 37.500 31.79 18.19 40.69 3.84
2384 2655 5.870433 TGACAAAATCATGCATGAAACCATC 59.130 36.000 31.79 24.21 40.69 3.51
2385 2656 5.795972 TGACAAAATCATGCATGAAACCAT 58.204 33.333 31.79 17.90 40.69 3.55
2386 2657 5.211174 TGACAAAATCATGCATGAAACCA 57.789 34.783 31.79 19.56 40.69 3.67
2398 2669 8.523915 AATAGCATCCAGTTATGACAAAATCA 57.476 30.769 0.00 0.00 43.13 2.57
2399 2670 9.241317 CAAATAGCATCCAGTTATGACAAAATC 57.759 33.333 0.00 0.00 0.00 2.17
2400 2671 8.752187 ACAAATAGCATCCAGTTATGACAAAAT 58.248 29.630 0.00 0.00 0.00 1.82
2401 2672 8.121305 ACAAATAGCATCCAGTTATGACAAAA 57.879 30.769 0.00 0.00 0.00 2.44
2402 2673 7.701539 ACAAATAGCATCCAGTTATGACAAA 57.298 32.000 0.00 0.00 0.00 2.83
2403 2674 7.148086 GGAACAAATAGCATCCAGTTATGACAA 60.148 37.037 0.00 0.00 32.08 3.18
2404 2675 6.318648 GGAACAAATAGCATCCAGTTATGACA 59.681 38.462 0.00 0.00 32.08 3.58
2405 2676 6.543831 AGGAACAAATAGCATCCAGTTATGAC 59.456 38.462 0.00 0.00 34.30 3.06
2406 2677 6.543465 CAGGAACAAATAGCATCCAGTTATGA 59.457 38.462 0.00 0.00 34.30 2.15
2407 2678 6.543465 TCAGGAACAAATAGCATCCAGTTATG 59.457 38.462 0.00 0.00 34.30 1.90
2408 2679 6.662755 TCAGGAACAAATAGCATCCAGTTAT 58.337 36.000 0.00 0.00 34.30 1.89
2409 2680 6.061022 TCAGGAACAAATAGCATCCAGTTA 57.939 37.500 0.00 0.00 34.30 2.24
2410 2681 4.922206 TCAGGAACAAATAGCATCCAGTT 58.078 39.130 0.00 0.00 34.30 3.16
2411 2682 4.574674 TCAGGAACAAATAGCATCCAGT 57.425 40.909 0.00 0.00 34.30 4.00
2412 2683 4.261489 GCATCAGGAACAAATAGCATCCAG 60.261 45.833 0.00 0.00 34.30 3.86
2413 2684 3.633525 GCATCAGGAACAAATAGCATCCA 59.366 43.478 0.00 0.00 34.30 3.41
2414 2685 3.304257 CGCATCAGGAACAAATAGCATCC 60.304 47.826 0.00 0.00 0.00 3.51
2415 2686 3.313526 ACGCATCAGGAACAAATAGCATC 59.686 43.478 0.00 0.00 0.00 3.91
2416 2687 3.282021 ACGCATCAGGAACAAATAGCAT 58.718 40.909 0.00 0.00 0.00 3.79
2417 2688 2.677836 GACGCATCAGGAACAAATAGCA 59.322 45.455 0.00 0.00 0.00 3.49
2418 2689 2.677836 TGACGCATCAGGAACAAATAGC 59.322 45.455 0.00 0.00 0.00 2.97
2419 2690 5.268544 CAATGACGCATCAGGAACAAATAG 58.731 41.667 0.00 0.00 38.57 1.73
2420 2691 4.438608 GCAATGACGCATCAGGAACAAATA 60.439 41.667 0.00 0.00 38.57 1.40
2421 2692 3.674138 GCAATGACGCATCAGGAACAAAT 60.674 43.478 0.00 0.00 38.57 2.32
2422 2693 2.351641 GCAATGACGCATCAGGAACAAA 60.352 45.455 0.00 0.00 38.57 2.83
2423 2694 1.199789 GCAATGACGCATCAGGAACAA 59.800 47.619 0.00 0.00 38.57 2.83
2424 2695 0.804364 GCAATGACGCATCAGGAACA 59.196 50.000 0.00 0.00 38.57 3.18
2425 2696 0.099436 GGCAATGACGCATCAGGAAC 59.901 55.000 0.00 0.00 38.57 3.62
2426 2697 0.322366 TGGCAATGACGCATCAGGAA 60.322 50.000 0.00 0.00 38.57 3.36
2427 2698 0.107066 ATGGCAATGACGCATCAGGA 60.107 50.000 0.00 0.00 38.57 3.86
2428 2699 0.030235 CATGGCAATGACGCATCAGG 59.970 55.000 0.00 0.00 38.57 3.86
2429 2700 1.018910 TCATGGCAATGACGCATCAG 58.981 50.000 0.00 0.00 37.91 2.90
2430 2701 1.682740 ATCATGGCAATGACGCATCA 58.317 45.000 5.74 0.00 45.51 3.07
2431 2702 3.902261 TTATCATGGCAATGACGCATC 57.098 42.857 5.74 0.00 45.51 3.91
2432 2703 4.098349 ACTTTTATCATGGCAATGACGCAT 59.902 37.500 5.74 0.00 45.51 4.73
2433 2704 3.443329 ACTTTTATCATGGCAATGACGCA 59.557 39.130 5.74 0.00 45.51 5.24
2434 2705 4.032703 ACTTTTATCATGGCAATGACGC 57.967 40.909 5.74 0.00 45.51 5.19
2435 2706 7.860613 TGTATACTTTTATCATGGCAATGACG 58.139 34.615 5.74 0.00 45.51 4.35
2466 2737 9.768215 TGGAGTTTATTCTGGGAATATTTTCTT 57.232 29.630 1.56 0.00 32.16 2.52
2467 2738 9.768215 TTGGAGTTTATTCTGGGAATATTTTCT 57.232 29.630 1.56 0.00 32.16 2.52
2471 2742 9.942526 AGAATTGGAGTTTATTCTGGGAATATT 57.057 29.630 0.00 0.00 39.11 1.28
2472 2743 9.942526 AAGAATTGGAGTTTATTCTGGGAATAT 57.057 29.630 0.00 0.00 39.53 1.28
2473 2744 9.768215 AAAGAATTGGAGTTTATTCTGGGAATA 57.232 29.630 0.00 0.00 39.53 1.75
2474 2745 8.670521 AAAGAATTGGAGTTTATTCTGGGAAT 57.329 30.769 0.00 0.00 39.53 3.01
2475 2746 8.491045 AAAAGAATTGGAGTTTATTCTGGGAA 57.509 30.769 0.00 0.00 39.53 3.97
2476 2747 9.594936 TTAAAAGAATTGGAGTTTATTCTGGGA 57.405 29.630 0.00 0.00 39.53 4.37
2502 2773 5.279456 GGCACAGATGTAAATGTCCCTTTTT 60.279 40.000 0.00 0.00 0.00 1.94
2503 2774 4.220602 GGCACAGATGTAAATGTCCCTTTT 59.779 41.667 0.00 0.00 0.00 2.27
2504 2775 3.763897 GGCACAGATGTAAATGTCCCTTT 59.236 43.478 0.00 0.00 0.00 3.11
2505 2776 3.356290 GGCACAGATGTAAATGTCCCTT 58.644 45.455 0.00 0.00 0.00 3.95
2506 2777 2.357154 GGGCACAGATGTAAATGTCCCT 60.357 50.000 0.00 0.00 35.56 4.20
2507 2778 2.024414 GGGCACAGATGTAAATGTCCC 58.976 52.381 0.00 0.00 33.00 4.46
2508 2779 2.024414 GGGGCACAGATGTAAATGTCC 58.976 52.381 0.00 0.00 36.03 4.02
2509 2780 3.004752 AGGGGCACAGATGTAAATGTC 57.995 47.619 0.00 0.00 0.00 3.06
2510 2781 4.018415 AGTTAGGGGCACAGATGTAAATGT 60.018 41.667 0.00 0.00 0.00 2.71
2511 2782 4.526970 AGTTAGGGGCACAGATGTAAATG 58.473 43.478 0.00 0.00 0.00 2.32
2512 2783 4.683400 CGAGTTAGGGGCACAGATGTAAAT 60.683 45.833 0.00 0.00 0.00 1.40
2513 2784 3.369052 CGAGTTAGGGGCACAGATGTAAA 60.369 47.826 0.00 0.00 0.00 2.01
2514 2785 2.167693 CGAGTTAGGGGCACAGATGTAA 59.832 50.000 0.00 0.00 0.00 2.41
2515 2786 1.754803 CGAGTTAGGGGCACAGATGTA 59.245 52.381 0.00 0.00 0.00 2.29
2516 2787 0.537188 CGAGTTAGGGGCACAGATGT 59.463 55.000 0.00 0.00 0.00 3.06
2517 2788 0.824109 TCGAGTTAGGGGCACAGATG 59.176 55.000 0.00 0.00 0.00 2.90
2518 2789 1.207329 GTTCGAGTTAGGGGCACAGAT 59.793 52.381 0.00 0.00 0.00 2.90
2519 2790 0.606604 GTTCGAGTTAGGGGCACAGA 59.393 55.000 0.00 0.00 0.00 3.41
2520 2791 0.391263 GGTTCGAGTTAGGGGCACAG 60.391 60.000 0.00 0.00 0.00 3.66
2521 2792 1.675219 GGTTCGAGTTAGGGGCACA 59.325 57.895 0.00 0.00 0.00 4.57
2522 2793 1.078637 GGGTTCGAGTTAGGGGCAC 60.079 63.158 0.00 0.00 0.00 5.01
2523 2794 3.395630 GGGTTCGAGTTAGGGGCA 58.604 61.111 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.