Multiple sequence alignment - TraesCS2B01G103200

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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 TraesCS2B01G103200 chr2B 100.000 2939 0 0 1 2939 64091346 64088408 0.000000e+00 5428.0
1 TraesCS2B01G103200 chr2B 87.664 2059 225 16 3 2054 64191206 64193242 0.000000e+00 2368.0
2 TraesCS2B01G103200 chr2B 86.089 2056 233 21 1 2044 63864895 63862881 0.000000e+00 2163.0
3 TraesCS2B01G103200 chr2B 93.958 331 18 2 2041 2370 64193268 64193597 1.570000e-137 499.0
4 TraesCS2B01G103200 chr2A 86.158 2059 240 21 1 2044 41620632 41622660 0.000000e+00 2182.0
5 TraesCS2B01G103200 chr2D 84.896 2059 251 25 1 2044 36911261 36913274 0.000000e+00 2025.0
6 TraesCS2B01G103200 chr2D 83.237 2070 280 27 3 2044 36886274 36888304 0.000000e+00 1838.0
7 TraesCS2B01G103200 chr2D 87.652 494 48 6 2042 2527 36913310 36913798 1.980000e-156 562.0
8 TraesCS2B01G103200 chr2D 86.774 499 48 10 2042 2527 36888340 36888833 9.270000e-150 540.0
9 TraesCS2B01G103200 chr6A 86.304 460 54 8 2057 2509 555858182 555857725 2.630000e-135 492.0
10 TraesCS2B01G103200 chr3D 100.000 67 0 0 2526 2592 574388411 574388477 1.110000e-24 124.0
11 TraesCS2B01G103200 chr3D 90.588 85 3 5 2512 2595 341522535 341522615 1.110000e-19 108.0
12 TraesCS2B01G103200 chr7B 98.551 69 1 0 2527 2595 342715085 342715017 3.980000e-24 122.0
13 TraesCS2B01G103200 chr7B 95.946 74 2 1 2527 2600 745115083 745115011 5.150000e-23 119.0
14 TraesCS2B01G103200 chr4B 98.529 68 1 0 2528 2595 613051886 613051953 1.430000e-23 121.0
15 TraesCS2B01G103200 chr5D 93.671 79 5 0 2514 2592 335881577 335881655 5.150000e-23 119.0
16 TraesCS2B01G103200 chr5B 98.507 67 1 0 2527 2593 461616004 461616070 5.150000e-23 119.0
17 TraesCS2B01G103200 chr1D 97.101 69 2 0 2527 2595 490031330 490031262 1.850000e-22 117.0
18 TraesCS2B01G103200 chr7D 94.595 74 3 1 2522 2595 574810442 574810514 2.390000e-21 113.0
19 TraesCS2B01G103200 chr7D 86.000 50 7 0 2594 2643 602177325 602177276 1.000000e-03 54.7
20 TraesCS2B01G103200 chr4D 91.489 47 0 2 2444 2490 351700328 351700370 8.790000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G103200 chr2B 64088408 64091346 2938 True 5428.0 5428 100.0000 1 2939 1 chr2B.!!$R2 2938
1 TraesCS2B01G103200 chr2B 63862881 63864895 2014 True 2163.0 2163 86.0890 1 2044 1 chr2B.!!$R1 2043
2 TraesCS2B01G103200 chr2B 64191206 64193597 2391 False 1433.5 2368 90.8110 3 2370 2 chr2B.!!$F1 2367
3 TraesCS2B01G103200 chr2A 41620632 41622660 2028 False 2182.0 2182 86.1580 1 2044 1 chr2A.!!$F1 2043
4 TraesCS2B01G103200 chr2D 36911261 36913798 2537 False 1293.5 2025 86.2740 1 2527 2 chr2D.!!$F2 2526
5 TraesCS2B01G103200 chr2D 36886274 36888833 2559 False 1189.0 1838 85.0055 3 2527 2 chr2D.!!$F1 2524

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
199 200 0.032130 TCGTGTTCTTTCTGCTCGCT 59.968 50.0 0.0 0.0 0.0 4.93 F
861 879 0.107017 TCAGCATAGCAAAGCTCCCC 60.107 55.0 0.0 0.0 39.5 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1293 0.039035 TTCCTTTGTCCAATCCCCCG 59.961 55.0 0.0 0.0 0.00 5.73 R
2553 2639 0.179062 ATCGTTCTGATGCAGAGGCC 60.179 55.0 0.0 0.0 41.75 5.19 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
49 50 3.064987 CTCGCCTTCCACCGACGAT 62.065 63.158 0.00 0.00 31.59 3.73
74 75 2.596338 TCGACGGCCAGAGTGTCA 60.596 61.111 2.24 0.00 32.91 3.58
75 76 2.197605 TCGACGGCCAGAGTGTCAA 61.198 57.895 2.24 0.00 32.91 3.18
82 83 1.293498 CCAGAGTGTCAAGACCCCG 59.707 63.158 0.00 0.00 0.00 5.73
83 84 1.374758 CAGAGTGTCAAGACCCCGC 60.375 63.158 0.00 0.00 0.00 6.13
88 89 1.918293 TGTCAAGACCCCGCTGGAT 60.918 57.895 0.00 0.00 38.00 3.41
126 127 3.567797 GGTGGCTTCGCTCATCGC 61.568 66.667 0.00 0.00 38.27 4.58
160 161 4.114997 GCGGAATGGTTGGGCGTG 62.115 66.667 0.00 0.00 0.00 5.34
162 163 3.758931 GGAATGGTTGGGCGTGCC 61.759 66.667 1.16 1.16 0.00 5.01
184 185 1.463444 GGGAAAACGGTCTTCATCGTG 59.537 52.381 0.00 0.00 39.70 4.35
190 191 3.107642 ACGGTCTTCATCGTGTTCTTT 57.892 42.857 0.00 0.00 38.25 2.52
198 199 1.071605 ATCGTGTTCTTTCTGCTCGC 58.928 50.000 0.00 0.00 0.00 5.03
199 200 0.032130 TCGTGTTCTTTCTGCTCGCT 59.968 50.000 0.00 0.00 0.00 4.93
203 204 3.059868 CGTGTTCTTTCTGCTCGCTTTTA 60.060 43.478 0.00 0.00 0.00 1.52
234 235 0.739112 CTCAAGCTGGTCGCCTTCTC 60.739 60.000 0.00 0.00 40.39 2.87
245 246 2.587194 CCTTCTCCATGGCGAGCG 60.587 66.667 6.96 1.42 0.00 5.03
353 354 1.586028 GTGCCTCCGTACGTGGTTA 59.414 57.895 20.59 11.05 0.00 2.85
354 355 0.733909 GTGCCTCCGTACGTGGTTAC 60.734 60.000 20.59 16.70 0.00 2.50
461 477 3.036084 CACTCGACCGTGTGTGGC 61.036 66.667 14.19 0.00 35.61 5.01
511 527 1.079405 CAAGCGGCGGGAGTTAAGA 60.079 57.895 9.78 0.00 0.00 2.10
525 541 4.466726 GGAGTTAAGAGACCTCTGCCTTTA 59.533 45.833 0.00 0.00 40.36 1.85
526 542 5.129650 GGAGTTAAGAGACCTCTGCCTTTAT 59.870 44.000 0.00 0.00 40.36 1.40
547 563 2.334006 TCTCCCTCTTCAAGAGCCTT 57.666 50.000 9.14 0.00 40.98 4.35
557 573 2.266627 AAGAGCCTTCGTCGTCGGT 61.267 57.895 1.55 0.00 37.69 4.69
628 644 2.273449 CTCAGGGGCATGGACACC 59.727 66.667 0.00 0.00 0.00 4.16
683 699 4.914128 GGTTGTTCCGGGTCCTTT 57.086 55.556 0.00 0.00 0.00 3.11
802 819 0.244721 CATCATCGCCGGAGCTATCA 59.755 55.000 5.05 0.00 36.60 2.15
803 820 0.244994 ATCATCGCCGGAGCTATCAC 59.755 55.000 5.05 0.00 36.60 3.06
814 831 0.614979 AGCTATCACCGTGGGAGTGT 60.615 55.000 0.00 0.00 36.58 3.55
818 835 2.358322 ATCACCGTGGGAGTGTTTTT 57.642 45.000 0.00 0.00 36.58 1.94
851 869 2.032178 GGGTGATCGTTTTCAGCATAGC 59.968 50.000 13.76 0.00 44.08 2.97
852 870 2.677836 GGTGATCGTTTTCAGCATAGCA 59.322 45.455 9.09 0.00 42.34 3.49
853 871 3.126858 GGTGATCGTTTTCAGCATAGCAA 59.873 43.478 9.09 0.00 42.34 3.91
857 875 2.813754 TCGTTTTCAGCATAGCAAAGCT 59.186 40.909 0.00 0.00 42.94 3.74
861 879 0.107017 TCAGCATAGCAAAGCTCCCC 60.107 55.000 0.00 0.00 39.50 4.81
864 882 0.821301 GCATAGCAAAGCTCCCCTCC 60.821 60.000 0.00 0.00 40.44 4.30
866 884 0.691078 ATAGCAAAGCTCCCCTCCGA 60.691 55.000 0.00 0.00 40.44 4.55
871 889 3.864983 AAGCTCCCCTCCGACCCAA 62.865 63.158 0.00 0.00 0.00 4.12
874 892 4.304413 TCCCCTCCGACCCAACGA 62.304 66.667 0.00 0.00 35.09 3.85
875 893 3.315949 CCCCTCCGACCCAACGAA 61.316 66.667 0.00 0.00 35.09 3.85
876 894 2.264794 CCCTCCGACCCAACGAAG 59.735 66.667 0.00 0.00 35.09 3.79
877 895 2.264794 CCTCCGACCCAACGAAGG 59.735 66.667 0.00 0.00 35.09 3.46
878 896 2.434359 CTCCGACCCAACGAAGGC 60.434 66.667 0.00 0.00 35.09 4.35
879 897 4.367023 TCCGACCCAACGAAGGCG 62.367 66.667 0.00 0.00 44.79 5.52
886 904 4.735132 CAACGAAGGCGCTCCCGA 62.735 66.667 18.89 0.00 42.48 5.14
944 962 4.021925 GTTCCTCCTGCTGGCCGT 62.022 66.667 4.42 0.00 0.00 5.68
948 966 2.202987 CTCCTGCTGGCCGTCATC 60.203 66.667 4.42 0.00 0.00 2.92
1005 1023 0.251297 CCAACTGGACCAAGATGGCA 60.251 55.000 6.86 0.00 42.67 4.92
1023 1041 1.601162 GCATTGCTCGGCCAATACATG 60.601 52.381 2.24 0.00 33.86 3.21
1025 1043 1.378531 TTGCTCGGCCAATACATGAC 58.621 50.000 2.24 0.00 0.00 3.06
1126 1150 2.227089 GATCGGGCAGAACTCGGTGT 62.227 60.000 0.00 0.00 0.00 4.16
1167 1191 2.034066 CGGCCAGGGCTTTTCTCA 59.966 61.111 12.03 0.00 41.60 3.27
1173 1197 2.815589 GCCAGGGCTTTTCTCAGAGAAA 60.816 50.000 19.96 19.96 42.00 2.52
1176 1200 3.501445 CAGGGCTTTTCTCAGAGAAACTG 59.499 47.826 22.97 20.85 43.25 3.16
1177 1201 3.137360 AGGGCTTTTCTCAGAGAAACTGT 59.863 43.478 22.97 5.99 43.25 3.55
1178 1202 4.348168 AGGGCTTTTCTCAGAGAAACTGTA 59.652 41.667 22.97 9.49 43.25 2.74
1179 1203 4.452795 GGGCTTTTCTCAGAGAAACTGTAC 59.547 45.833 22.97 15.06 43.25 2.90
1180 1204 4.150804 GGCTTTTCTCAGAGAAACTGTACG 59.849 45.833 22.97 9.95 43.25 3.67
1181 1205 4.150804 GCTTTTCTCAGAGAAACTGTACGG 59.849 45.833 22.97 0.00 43.25 4.02
1182 1206 3.936372 TTCTCAGAGAAACTGTACGGG 57.064 47.619 10.68 0.00 45.86 5.28
1183 1207 2.168496 TCTCAGAGAAACTGTACGGGG 58.832 52.381 6.65 0.00 45.86 5.73
1184 1208 0.606604 TCAGAGAAACTGTACGGGGC 59.393 55.000 6.65 0.00 45.86 5.80
1255 1279 4.101448 ATGCGGTGCTCAGGTCCC 62.101 66.667 0.00 0.00 0.00 4.46
1265 1289 1.202330 CTCAGGTCCCTCAAGAGCAT 58.798 55.000 0.00 0.00 36.71 3.79
1266 1290 0.907486 TCAGGTCCCTCAAGAGCATG 59.093 55.000 0.00 0.00 36.71 4.06
1269 1293 1.834263 AGGTCCCTCAAGAGCATGTAC 59.166 52.381 0.00 0.00 36.71 2.90
1276 1300 0.469917 CAAGAGCATGTACGGGGGAT 59.530 55.000 0.00 0.00 0.00 3.85
1292 1316 2.460669 GGGATTGGACAAAGGAAGCAT 58.539 47.619 0.00 0.00 0.00 3.79
1334 1358 2.154798 CTCGGAGGCAAGGTCGACAA 62.155 60.000 18.91 0.00 0.00 3.18
1440 1473 0.526211 AGATCAAGTACTCGCACGCA 59.474 50.000 0.00 0.00 0.00 5.24
1503 1536 1.989864 CATTTGTCGTACTACTGCGCA 59.010 47.619 10.98 10.98 0.00 6.09
1561 1594 2.281208 CGGCCTGGACGGACAAAA 60.281 61.111 15.83 0.00 43.06 2.44
1569 1602 3.207778 CTGGACGGACAAAAGGTACAAA 58.792 45.455 0.00 0.00 0.00 2.83
1580 1613 3.945640 AAGGTACAAAGAAGTGGTGGT 57.054 42.857 0.00 0.00 0.00 4.16
1581 1614 5.376756 AAAGGTACAAAGAAGTGGTGGTA 57.623 39.130 0.00 0.00 0.00 3.25
1588 1621 0.317479 AGAAGTGGTGGTAGACGTGC 59.683 55.000 0.00 0.00 0.00 5.34
1845 1878 3.771160 GTCGAGGCCATGGGTCGT 61.771 66.667 15.13 0.00 35.22 4.34
1863 1896 3.998672 GGCGGGGAGTTCGTCACA 61.999 66.667 0.00 0.00 31.94 3.58
1866 1899 1.870055 GCGGGGAGTTCGTCACACTA 61.870 60.000 0.00 0.00 0.00 2.74
1941 1974 1.405933 GGTACTGGCGTCCCGTAATTT 60.406 52.381 0.00 0.00 0.00 1.82
1942 1975 2.349590 GTACTGGCGTCCCGTAATTTT 58.650 47.619 2.70 0.00 0.00 1.82
1943 1976 1.900245 ACTGGCGTCCCGTAATTTTT 58.100 45.000 0.00 0.00 0.00 1.94
1956 1990 8.468399 GTCCCGTAATTTTTAACATGGGAAATA 58.532 33.333 5.37 0.00 45.63 1.40
2022 2058 6.750039 CGTTTTAGAAGCTTCTTTTGTTTCCA 59.250 34.615 32.70 9.92 38.70 3.53
2105 2180 9.897744 TCATTTCTAGCATGAAAAACTACTTTG 57.102 29.630 0.00 1.47 39.08 2.77
2294 2376 7.825331 TGTGATGGTTTTTCCTACAAACATA 57.175 32.000 0.00 0.00 36.07 2.29
2305 2387 5.172934 TCCTACAAACATAGCCAAACTACG 58.827 41.667 0.00 0.00 32.32 3.51
2316 2398 0.446222 CAAACTACGCACCGATTGGG 59.554 55.000 3.39 0.00 43.87 4.12
2405 2491 6.072893 TGCAATGGATAATGATCTTCATGACG 60.073 38.462 0.00 0.00 37.15 4.35
2416 2502 5.584649 TGATCTTCATGACGGACATAAAACC 59.415 40.000 0.00 0.00 37.46 3.27
2431 2517 1.145571 AAACCTGCAACTCCACCCTA 58.854 50.000 0.00 0.00 0.00 3.53
2445 2531 2.904434 CCACCCTACTGACAAGTTAGGT 59.096 50.000 0.00 0.00 39.81 3.08
2457 2543 6.231211 TGACAAGTTAGGTCCTCTTTGATTC 58.769 40.000 13.84 5.72 34.36 2.52
2468 2554 4.095334 TCCTCTTTGATTCGCATGATTGTG 59.905 41.667 0.00 0.00 34.56 3.33
2481 2567 4.270084 GCATGATTGTGAAAATGCATGGAG 59.730 41.667 0.00 0.00 43.84 3.86
2483 2569 5.725325 TGATTGTGAAAATGCATGGAGAA 57.275 34.783 0.00 0.00 0.00 2.87
2489 2575 8.899427 TTGTGAAAATGCATGGAGAATAAAAA 57.101 26.923 0.00 0.00 0.00 1.94
2493 2579 7.930325 TGAAAATGCATGGAGAATAAAAACACA 59.070 29.630 0.00 0.00 0.00 3.72
2504 2590 9.190317 GGAGAATAAAAACACAGGAAGGAATAT 57.810 33.333 0.00 0.00 0.00 1.28
2511 2597 5.894298 ACACAGGAAGGAATATCATGCTA 57.106 39.130 0.00 0.00 32.09 3.49
2515 2601 7.446625 ACACAGGAAGGAATATCATGCTAATTC 59.553 37.037 0.00 0.00 32.09 2.17
2564 2650 4.247380 CTCCCCGGCCTCTGCATC 62.247 72.222 0.00 0.00 40.13 3.91
2566 2652 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
2567 2653 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
2568 2654 2.586245 CCGGCCTCTGCATCAGAA 59.414 61.111 0.00 0.00 40.18 3.02
2569 2655 1.817099 CCGGCCTCTGCATCAGAAC 60.817 63.158 0.00 0.00 40.18 3.01
2570 2656 2.169789 CGGCCTCTGCATCAGAACG 61.170 63.158 0.00 0.63 40.18 3.95
2571 2657 1.219124 GGCCTCTGCATCAGAACGA 59.781 57.895 0.00 0.00 40.18 3.85
2572 2658 0.179062 GGCCTCTGCATCAGAACGAT 60.179 55.000 0.00 0.00 40.18 3.73
2581 2667 1.193203 CATCAGAACGATGCATACGGC 59.807 52.381 18.34 11.86 44.95 5.68
2582 2668 0.529773 TCAGAACGATGCATACGGCC 60.530 55.000 18.34 0.00 43.89 6.13
2583 2669 0.809636 CAGAACGATGCATACGGCCA 60.810 55.000 18.34 0.00 43.89 5.36
2584 2670 0.810031 AGAACGATGCATACGGCCAC 60.810 55.000 18.34 9.37 43.89 5.01
2585 2671 1.772063 GAACGATGCATACGGCCACC 61.772 60.000 18.34 0.00 43.89 4.61
2586 2672 2.108976 CGATGCATACGGCCACCT 59.891 61.111 2.24 0.00 43.89 4.00
2587 2673 1.523711 CGATGCATACGGCCACCTT 60.524 57.895 2.24 0.00 43.89 3.50
2588 2674 1.095228 CGATGCATACGGCCACCTTT 61.095 55.000 2.24 0.00 43.89 3.11
2589 2675 1.808512 CGATGCATACGGCCACCTTTA 60.809 52.381 2.24 0.00 43.89 1.85
2590 2676 2.504367 GATGCATACGGCCACCTTTAT 58.496 47.619 2.24 0.00 43.89 1.40
2591 2677 3.670625 GATGCATACGGCCACCTTTATA 58.329 45.455 2.24 0.00 43.89 0.98
2592 2678 3.120321 TGCATACGGCCACCTTTATAG 57.880 47.619 2.24 0.00 43.89 1.31
2593 2679 2.701423 TGCATACGGCCACCTTTATAGA 59.299 45.455 2.24 0.00 43.89 1.98
2594 2680 3.326588 TGCATACGGCCACCTTTATAGAT 59.673 43.478 2.24 0.00 43.89 1.98
2595 2681 4.202419 TGCATACGGCCACCTTTATAGATT 60.202 41.667 2.24 0.00 43.89 2.40
2596 2682 4.392138 GCATACGGCCACCTTTATAGATTC 59.608 45.833 2.24 0.00 36.11 2.52
2597 2683 5.547465 CATACGGCCACCTTTATAGATTCA 58.453 41.667 2.24 0.00 0.00 2.57
2598 2684 4.497291 ACGGCCACCTTTATAGATTCAA 57.503 40.909 2.24 0.00 0.00 2.69
2599 2685 4.850680 ACGGCCACCTTTATAGATTCAAA 58.149 39.130 2.24 0.00 0.00 2.69
2600 2686 5.445964 ACGGCCACCTTTATAGATTCAAAT 58.554 37.500 2.24 0.00 0.00 2.32
2601 2687 5.891551 ACGGCCACCTTTATAGATTCAAATT 59.108 36.000 2.24 0.00 0.00 1.82
2602 2688 6.039382 ACGGCCACCTTTATAGATTCAAATTC 59.961 38.462 2.24 0.00 0.00 2.17
2603 2689 6.263168 CGGCCACCTTTATAGATTCAAATTCT 59.737 38.462 2.24 0.00 0.00 2.40
2604 2690 7.444183 CGGCCACCTTTATAGATTCAAATTCTA 59.556 37.037 2.24 0.00 0.00 2.10
2605 2691 8.568794 GGCCACCTTTATAGATTCAAATTCTAC 58.431 37.037 0.00 0.00 0.00 2.59
2606 2692 9.120538 GCCACCTTTATAGATTCAAATTCTACA 57.879 33.333 0.00 0.00 0.00 2.74
2615 2701 7.636150 AGATTCAAATTCTACATGACTTGGG 57.364 36.000 0.00 0.00 0.00 4.12
2616 2702 7.177878 AGATTCAAATTCTACATGACTTGGGT 58.822 34.615 0.00 0.00 0.00 4.51
2617 2703 7.671398 AGATTCAAATTCTACATGACTTGGGTT 59.329 33.333 0.00 0.00 0.00 4.11
2618 2704 7.595819 TTCAAATTCTACATGACTTGGGTTT 57.404 32.000 0.00 0.00 0.00 3.27
2619 2705 6.980593 TCAAATTCTACATGACTTGGGTTTG 58.019 36.000 0.00 2.51 0.00 2.93
2620 2706 6.549364 TCAAATTCTACATGACTTGGGTTTGT 59.451 34.615 0.00 0.00 0.00 2.83
2621 2707 6.976934 AATTCTACATGACTTGGGTTTGTT 57.023 33.333 0.00 0.00 0.00 2.83
2622 2708 6.976934 ATTCTACATGACTTGGGTTTGTTT 57.023 33.333 0.00 0.00 0.00 2.83
2623 2709 5.766150 TCTACATGACTTGGGTTTGTTTG 57.234 39.130 0.00 0.00 0.00 2.93
2624 2710 5.441500 TCTACATGACTTGGGTTTGTTTGA 58.558 37.500 0.00 0.00 0.00 2.69
2625 2711 6.068010 TCTACATGACTTGGGTTTGTTTGAT 58.932 36.000 0.00 0.00 0.00 2.57
2626 2712 5.612725 ACATGACTTGGGTTTGTTTGATT 57.387 34.783 0.00 0.00 0.00 2.57
2627 2713 5.358922 ACATGACTTGGGTTTGTTTGATTG 58.641 37.500 0.00 0.00 0.00 2.67
2628 2714 3.791245 TGACTTGGGTTTGTTTGATTGC 58.209 40.909 0.00 0.00 0.00 3.56
2629 2715 3.196469 TGACTTGGGTTTGTTTGATTGCA 59.804 39.130 0.00 0.00 0.00 4.08
2630 2716 4.141756 TGACTTGGGTTTGTTTGATTGCAT 60.142 37.500 0.00 0.00 0.00 3.96
2631 2717 4.379652 ACTTGGGTTTGTTTGATTGCATC 58.620 39.130 0.00 0.00 0.00 3.91
2632 2718 4.141756 ACTTGGGTTTGTTTGATTGCATCA 60.142 37.500 0.00 0.00 37.55 3.07
2633 2719 3.726607 TGGGTTTGTTTGATTGCATCAC 58.273 40.909 0.00 0.00 39.39 3.06
2634 2720 3.133542 TGGGTTTGTTTGATTGCATCACA 59.866 39.130 0.00 0.00 39.39 3.58
2635 2721 4.202336 TGGGTTTGTTTGATTGCATCACAT 60.202 37.500 0.00 0.00 39.39 3.21
2636 2722 4.152759 GGGTTTGTTTGATTGCATCACATG 59.847 41.667 0.00 0.00 39.39 3.21
2637 2723 4.989797 GGTTTGTTTGATTGCATCACATGA 59.010 37.500 0.00 0.00 39.39 3.07
2638 2724 5.466058 GGTTTGTTTGATTGCATCACATGAA 59.534 36.000 0.00 0.00 39.39 2.57
2639 2725 6.018098 GGTTTGTTTGATTGCATCACATGAAA 60.018 34.615 0.00 0.00 39.39 2.69
2640 2726 7.408123 GTTTGTTTGATTGCATCACATGAAAA 58.592 30.769 0.00 0.00 39.39 2.29
2641 2727 7.549615 TTGTTTGATTGCATCACATGAAAAA 57.450 28.000 0.00 0.00 39.39 1.94
2664 2750 8.422577 AAAACAAAGGATTGCTTCTAATAGGT 57.577 30.769 0.00 0.00 40.34 3.08
2665 2751 7.631717 AACAAAGGATTGCTTCTAATAGGTC 57.368 36.000 0.00 0.00 40.34 3.85
2666 2752 5.817816 ACAAAGGATTGCTTCTAATAGGTCG 59.182 40.000 0.00 0.00 40.34 4.79
2667 2753 4.608948 AGGATTGCTTCTAATAGGTCGG 57.391 45.455 0.00 0.00 0.00 4.79
2668 2754 4.223953 AGGATTGCTTCTAATAGGTCGGA 58.776 43.478 0.00 0.00 0.00 4.55
2669 2755 4.654262 AGGATTGCTTCTAATAGGTCGGAA 59.346 41.667 0.00 0.00 0.00 4.30
2670 2756 5.308237 AGGATTGCTTCTAATAGGTCGGAAT 59.692 40.000 0.00 0.00 0.00 3.01
2671 2757 5.409826 GGATTGCTTCTAATAGGTCGGAATG 59.590 44.000 0.00 0.00 0.00 2.67
2672 2758 4.336889 TGCTTCTAATAGGTCGGAATGG 57.663 45.455 0.00 0.00 0.00 3.16
2673 2759 3.964688 TGCTTCTAATAGGTCGGAATGGA 59.035 43.478 0.00 0.00 0.00 3.41
2674 2760 4.593206 TGCTTCTAATAGGTCGGAATGGAT 59.407 41.667 0.00 0.00 0.00 3.41
2675 2761 4.932200 GCTTCTAATAGGTCGGAATGGATG 59.068 45.833 0.00 0.00 0.00 3.51
2676 2762 4.537135 TCTAATAGGTCGGAATGGATGC 57.463 45.455 0.00 0.00 0.00 3.91
2677 2763 4.160329 TCTAATAGGTCGGAATGGATGCT 58.840 43.478 0.00 0.00 0.00 3.79
2678 2764 5.330233 TCTAATAGGTCGGAATGGATGCTA 58.670 41.667 0.00 0.00 0.00 3.49
2679 2765 4.543590 AATAGGTCGGAATGGATGCTAG 57.456 45.455 0.00 0.00 0.00 3.42
2680 2766 2.088104 AGGTCGGAATGGATGCTAGA 57.912 50.000 0.00 0.00 0.00 2.43
2681 2767 2.398588 AGGTCGGAATGGATGCTAGAA 58.601 47.619 0.00 0.00 0.00 2.10
2682 2768 2.975489 AGGTCGGAATGGATGCTAGAAT 59.025 45.455 0.00 0.00 0.00 2.40
2683 2769 3.070018 GGTCGGAATGGATGCTAGAATG 58.930 50.000 0.00 0.00 0.00 2.67
2684 2770 3.495100 GGTCGGAATGGATGCTAGAATGT 60.495 47.826 0.00 0.00 0.00 2.71
2685 2771 4.262463 GGTCGGAATGGATGCTAGAATGTA 60.262 45.833 0.00 0.00 0.00 2.29
2686 2772 4.926238 GTCGGAATGGATGCTAGAATGTAG 59.074 45.833 0.00 0.00 0.00 2.74
2687 2773 4.588951 TCGGAATGGATGCTAGAATGTAGT 59.411 41.667 0.00 0.00 0.00 2.73
2688 2774 5.773176 TCGGAATGGATGCTAGAATGTAGTA 59.227 40.000 0.00 0.00 0.00 1.82
2689 2775 5.864474 CGGAATGGATGCTAGAATGTAGTAC 59.136 44.000 0.00 0.00 0.00 2.73
2690 2776 6.516693 CGGAATGGATGCTAGAATGTAGTACA 60.517 42.308 5.24 5.24 0.00 2.90
2691 2777 6.870965 GGAATGGATGCTAGAATGTAGTACAG 59.129 42.308 9.25 0.00 0.00 2.74
2692 2778 7.255977 GGAATGGATGCTAGAATGTAGTACAGA 60.256 40.741 9.25 0.00 0.00 3.41
2693 2779 7.789202 ATGGATGCTAGAATGTAGTACAGAT 57.211 36.000 9.25 0.01 0.00 2.90
2694 2780 6.986250 TGGATGCTAGAATGTAGTACAGATG 58.014 40.000 9.25 0.00 0.00 2.90
2695 2781 6.015095 TGGATGCTAGAATGTAGTACAGATGG 60.015 42.308 9.25 0.81 0.00 3.51
2696 2782 6.209589 GGATGCTAGAATGTAGTACAGATGGA 59.790 42.308 9.25 0.00 0.00 3.41
2697 2783 7.255977 GGATGCTAGAATGTAGTACAGATGGAA 60.256 40.741 9.25 0.00 0.00 3.53
2698 2784 7.043961 TGCTAGAATGTAGTACAGATGGAAG 57.956 40.000 9.25 3.09 0.00 3.46
2699 2785 6.833933 TGCTAGAATGTAGTACAGATGGAAGA 59.166 38.462 9.25 0.00 0.00 2.87
2700 2786 7.507277 TGCTAGAATGTAGTACAGATGGAAGAT 59.493 37.037 9.25 0.00 0.00 2.40
2701 2787 8.364142 GCTAGAATGTAGTACAGATGGAAGATT 58.636 37.037 9.25 0.00 0.00 2.40
2719 2805 7.967908 GGAAGATTTCCTATAGGAGTCAATCA 58.032 38.462 29.71 12.97 46.36 2.57
2720 2806 8.601546 GGAAGATTTCCTATAGGAGTCAATCAT 58.398 37.037 29.71 23.72 46.36 2.45
2728 2814 8.961634 TCCTATAGGAGTCAATCATAAGAATCG 58.038 37.037 18.00 0.00 39.78 3.34
2729 2815 8.961634 CCTATAGGAGTCAATCATAAGAATCGA 58.038 37.037 14.11 0.00 37.39 3.59
2732 2818 7.118496 AGGAGTCAATCATAAGAATCGAACT 57.882 36.000 0.00 0.00 30.18 3.01
2733 2819 8.239038 AGGAGTCAATCATAAGAATCGAACTA 57.761 34.615 0.00 0.00 30.18 2.24
2734 2820 8.138712 AGGAGTCAATCATAAGAATCGAACTAC 58.861 37.037 0.00 0.00 30.18 2.73
2735 2821 7.382759 GGAGTCAATCATAAGAATCGAACTACC 59.617 40.741 0.00 0.00 30.18 3.18
2736 2822 7.782049 AGTCAATCATAAGAATCGAACTACCA 58.218 34.615 0.00 0.00 0.00 3.25
2737 2823 8.258007 AGTCAATCATAAGAATCGAACTACCAA 58.742 33.333 0.00 0.00 0.00 3.67
2738 2824 8.328864 GTCAATCATAAGAATCGAACTACCAAC 58.671 37.037 0.00 0.00 0.00 3.77
2739 2825 7.222031 TCAATCATAAGAATCGAACTACCAACG 59.778 37.037 0.00 0.00 0.00 4.10
2740 2826 5.957798 TCATAAGAATCGAACTACCAACGT 58.042 37.500 0.00 0.00 0.00 3.99
2741 2827 7.087409 TCATAAGAATCGAACTACCAACGTA 57.913 36.000 0.00 0.00 0.00 3.57
2742 2828 7.709947 TCATAAGAATCGAACTACCAACGTAT 58.290 34.615 0.00 0.00 0.00 3.06
2743 2829 8.839343 TCATAAGAATCGAACTACCAACGTATA 58.161 33.333 0.00 0.00 0.00 1.47
2744 2830 9.114965 CATAAGAATCGAACTACCAACGTATAG 57.885 37.037 0.00 0.00 0.00 1.31
2745 2831 6.069684 AGAATCGAACTACCAACGTATAGG 57.930 41.667 0.00 0.00 0.00 2.57
2746 2832 4.843220 ATCGAACTACCAACGTATAGGG 57.157 45.455 6.57 0.96 0.00 3.53
2747 2833 3.884895 TCGAACTACCAACGTATAGGGA 58.115 45.455 6.57 0.00 0.00 4.20
2748 2834 4.269183 TCGAACTACCAACGTATAGGGAA 58.731 43.478 6.57 0.00 0.00 3.97
2749 2835 4.704540 TCGAACTACCAACGTATAGGGAAA 59.295 41.667 6.57 0.00 0.00 3.13
2750 2836 5.184864 TCGAACTACCAACGTATAGGGAAAA 59.815 40.000 6.57 0.00 0.00 2.29
2751 2837 6.044682 CGAACTACCAACGTATAGGGAAAAT 58.955 40.000 6.57 0.00 0.00 1.82
2752 2838 6.536224 CGAACTACCAACGTATAGGGAAAATT 59.464 38.462 6.57 0.00 0.00 1.82
2753 2839 7.064966 CGAACTACCAACGTATAGGGAAAATTT 59.935 37.037 6.57 0.00 0.00 1.82
2754 2840 9.382275 GAACTACCAACGTATAGGGAAAATTTA 57.618 33.333 6.57 0.00 0.00 1.40
2755 2841 9.910267 AACTACCAACGTATAGGGAAAATTTAT 57.090 29.630 6.57 0.00 0.00 1.40
2784 2870 9.485206 AGATTCAAATTCTGTGAAAATCCTTTG 57.515 29.630 0.00 0.00 38.44 2.77
2785 2871 9.480053 GATTCAAATTCTGTGAAAATCCTTTGA 57.520 29.630 0.00 0.00 38.44 2.69
2786 2872 9.835389 ATTCAAATTCTGTGAAAATCCTTTGAA 57.165 25.926 15.06 15.06 42.25 2.69
2787 2873 8.647143 TCAAATTCTGTGAAAATCCTTTGAAC 57.353 30.769 0.00 0.00 30.79 3.18
2788 2874 7.710475 TCAAATTCTGTGAAAATCCTTTGAACC 59.290 33.333 0.00 0.00 30.79 3.62
2789 2875 6.729690 ATTCTGTGAAAATCCTTTGAACCA 57.270 33.333 0.00 0.00 0.00 3.67
2790 2876 6.537453 TTCTGTGAAAATCCTTTGAACCAA 57.463 33.333 0.00 0.00 0.00 3.67
2791 2877 6.537453 TCTGTGAAAATCCTTTGAACCAAA 57.463 33.333 0.00 0.00 0.00 3.28
2798 2884 3.986970 CTTTGAACCAAAGGCACCC 57.013 52.632 10.65 0.00 44.75 4.61
2799 2885 1.413118 CTTTGAACCAAAGGCACCCT 58.587 50.000 10.65 0.00 44.75 4.34
2812 2898 4.788925 AGGCACCCTTTAATAGTATGCA 57.211 40.909 0.00 0.00 35.54 3.96
2813 2899 5.324832 AGGCACCCTTTAATAGTATGCAT 57.675 39.130 3.79 3.79 35.54 3.96
2814 2900 6.448369 AGGCACCCTTTAATAGTATGCATA 57.552 37.500 1.16 1.16 35.54 3.14
2815 2901 6.848069 AGGCACCCTTTAATAGTATGCATAA 58.152 36.000 8.28 0.00 35.54 1.90
2816 2902 7.294584 AGGCACCCTTTAATAGTATGCATAAA 58.705 34.615 8.28 0.00 35.54 1.40
2817 2903 7.782644 AGGCACCCTTTAATAGTATGCATAAAA 59.217 33.333 8.28 4.27 35.54 1.52
2818 2904 8.585018 GGCACCCTTTAATAGTATGCATAAAAT 58.415 33.333 8.28 2.08 35.54 1.82
2834 2920 8.543862 TGCATAAAATAATCAAAACACATGCA 57.456 26.923 0.00 0.00 41.78 3.96
2835 2921 9.163899 TGCATAAAATAATCAAAACACATGCAT 57.836 25.926 0.00 0.00 39.86 3.96
2844 2930 8.524870 AATCAAAACACATGCATAGAAACTTC 57.475 30.769 0.00 0.00 0.00 3.01
2845 2931 7.036996 TCAAAACACATGCATAGAAACTTCA 57.963 32.000 0.00 0.00 0.00 3.02
2846 2932 7.487484 TCAAAACACATGCATAGAAACTTCAA 58.513 30.769 0.00 0.00 0.00 2.69
2847 2933 7.648908 TCAAAACACATGCATAGAAACTTCAAG 59.351 33.333 0.00 0.00 0.00 3.02
2848 2934 6.882610 AACACATGCATAGAAACTTCAAGA 57.117 33.333 0.00 0.00 0.00 3.02
2849 2935 6.492007 ACACATGCATAGAAACTTCAAGAG 57.508 37.500 0.00 0.00 0.00 2.85
2850 2936 6.000219 ACACATGCATAGAAACTTCAAGAGT 59.000 36.000 0.00 0.00 41.47 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.185310 ATCCAGCGGGGTCTTGACAC 62.185 60.000 2.05 0.00 38.11 3.67
70 71 1.899437 GATCCAGCGGGGTCTTGACA 61.899 60.000 9.14 0.00 41.45 3.58
82 83 1.142748 CGTGACCAGGAGATCCAGC 59.857 63.158 0.92 0.00 38.89 4.85
83 84 1.405821 GTACGTGACCAGGAGATCCAG 59.594 57.143 0.00 0.00 38.89 3.86
88 89 2.338015 GGCGTACGTGACCAGGAGA 61.338 63.158 17.90 0.00 0.00 3.71
126 127 1.769098 CGCCTCAGGAATGCACATCG 61.769 60.000 0.00 0.00 0.00 3.84
162 163 1.084289 GATGAAGACCGTTTTCCCCG 58.916 55.000 0.00 0.00 0.00 5.73
166 167 3.493503 AGAACACGATGAAGACCGTTTTC 59.506 43.478 0.00 0.00 42.39 2.29
170 171 2.814280 AAGAACACGATGAAGACCGT 57.186 45.000 0.00 0.00 39.88 4.83
184 185 3.250040 TGGTAAAAGCGAGCAGAAAGAAC 59.750 43.478 0.00 0.00 0.00 3.01
190 191 1.071699 ACCTTGGTAAAAGCGAGCAGA 59.928 47.619 0.00 0.00 0.00 4.26
234 235 2.490148 TAGGAGTCGCTCGCCATGG 61.490 63.158 7.63 7.63 38.50 3.66
245 246 4.549516 GCCGACGGCGTAGGAGTC 62.550 72.222 37.68 19.49 39.62 3.36
334 335 2.198906 TAACCACGTACGGAGGCACG 62.199 60.000 23.64 0.00 43.84 5.34
343 344 1.475682 CTCTCCCCTGTAACCACGTAC 59.524 57.143 0.00 0.00 0.00 3.67
353 354 2.297129 GCTCCTTGCTCTCCCCTGT 61.297 63.158 0.00 0.00 38.95 4.00
354 355 2.296365 TGCTCCTTGCTCTCCCCTG 61.296 63.158 0.00 0.00 43.37 4.45
388 389 0.616395 TCTTGATGCGGTACCCCTGA 60.616 55.000 6.25 0.00 0.00 3.86
411 412 0.949105 GAGCTTGTTTTCGAGGGCGA 60.949 55.000 0.00 0.00 46.33 5.54
445 461 4.640855 CGCCACACACGGTCGAGT 62.641 66.667 0.00 0.00 0.00 4.18
511 527 3.201045 GGGAGAAATAAAGGCAGAGGTCT 59.799 47.826 0.00 0.00 0.00 3.85
525 541 3.188773 AGGCTCTTGAAGAGGGAGAAAT 58.811 45.455 22.47 0.00 42.54 2.17
526 542 2.625639 AGGCTCTTGAAGAGGGAGAAA 58.374 47.619 22.47 0.00 42.54 2.52
547 563 2.330372 CCCTGAGAACCGACGACGA 61.330 63.158 9.28 0.00 42.66 4.20
586 602 4.069232 TCGAGGGCGTTGCTGGAG 62.069 66.667 0.00 0.00 38.98 3.86
668 684 0.551879 TCCAAAAGGACCCGGAACAA 59.448 50.000 0.73 0.00 0.00 2.83
683 699 0.884704 GCAAACCAGAGCTCGTCCAA 60.885 55.000 8.37 0.00 0.00 3.53
818 835 4.286297 ACGATCACCCTTTTGAGATGAA 57.714 40.909 0.00 0.00 0.00 2.57
823 840 4.787598 CTGAAAACGATCACCCTTTTGAG 58.212 43.478 0.00 0.00 0.00 3.02
851 869 2.269241 GGTCGGAGGGGAGCTTTG 59.731 66.667 0.00 0.00 0.00 2.77
852 870 3.009714 GGGTCGGAGGGGAGCTTT 61.010 66.667 0.00 0.00 34.90 3.51
853 871 3.864983 TTGGGTCGGAGGGGAGCTT 62.865 63.158 0.00 0.00 34.90 3.74
857 875 3.831727 TTCGTTGGGTCGGAGGGGA 62.832 63.158 0.00 0.00 0.00 4.81
861 879 2.434359 GCCTTCGTTGGGTCGGAG 60.434 66.667 0.00 0.00 36.33 4.63
866 884 4.699522 GGAGCGCCTTCGTTGGGT 62.700 66.667 2.29 0.00 38.14 4.51
871 889 3.718210 GAATCGGGAGCGCCTTCGT 62.718 63.158 2.29 0.00 38.14 3.85
874 892 4.530857 CGGAATCGGGAGCGCCTT 62.531 66.667 2.29 0.00 0.00 4.35
877 895 4.508128 TGTCGGAATCGGGAGCGC 62.508 66.667 0.00 0.00 36.95 5.92
878 896 2.165301 GTTGTCGGAATCGGGAGCG 61.165 63.158 0.00 0.00 36.95 5.03
879 897 2.165301 CGTTGTCGGAATCGGGAGC 61.165 63.158 0.00 0.00 36.95 4.70
880 898 4.088421 CGTTGTCGGAATCGGGAG 57.912 61.111 0.00 0.00 36.95 4.30
916 934 2.746362 GCAGGAGGAACAAAGTGATGAG 59.254 50.000 0.00 0.00 0.00 2.90
1005 1023 1.949525 GTCATGTATTGGCCGAGCAAT 59.050 47.619 0.00 0.00 0.00 3.56
1017 1035 4.433615 CCGTCTTACTGCTTGTCATGTAT 58.566 43.478 0.00 0.00 0.00 2.29
1023 1041 1.019805 GCCCCGTCTTACTGCTTGTC 61.020 60.000 0.00 0.00 0.00 3.18
1025 1043 2.100631 CGCCCCGTCTTACTGCTTG 61.101 63.158 0.00 0.00 0.00 4.01
1069 1093 3.114616 CGGCCTGAGACGCAACAG 61.115 66.667 0.00 0.00 0.00 3.16
1153 1177 2.816672 GTTTCTCTGAGAAAAGCCCTGG 59.183 50.000 28.83 0.00 44.84 4.45
1155 1179 3.137360 ACAGTTTCTCTGAGAAAAGCCCT 59.863 43.478 28.83 20.16 44.84 5.19
1167 1191 1.183676 ACGCCCCGTACAGTTTCTCT 61.184 55.000 0.00 0.00 38.73 3.10
1173 1197 2.428925 CCCATACGCCCCGTACAGT 61.429 63.158 0.00 0.00 45.07 3.55
1176 1200 4.955774 CGCCCATACGCCCCGTAC 62.956 72.222 0.00 0.00 45.07 3.67
1195 1219 2.060383 CCGACCTCATCAGCCCTGA 61.060 63.158 0.00 0.00 44.59 3.86
1255 1279 0.179073 CCCCCGTACATGCTCTTGAG 60.179 60.000 0.00 0.00 0.00 3.02
1265 1289 1.003812 CTTTGTCCAATCCCCCGTACA 59.996 52.381 0.00 0.00 0.00 2.90
1266 1290 1.680860 CCTTTGTCCAATCCCCCGTAC 60.681 57.143 0.00 0.00 0.00 3.67
1269 1293 0.039035 TTCCTTTGTCCAATCCCCCG 59.961 55.000 0.00 0.00 0.00 5.73
1276 1300 0.968405 GCCATGCTTCCTTTGTCCAA 59.032 50.000 0.00 0.00 0.00 3.53
1347 1371 4.379243 CTTCCGTCACCGCTGGCT 62.379 66.667 0.00 0.00 0.00 4.75
1372 1405 1.598130 GGATATGCTCCGTGGTGCC 60.598 63.158 10.19 0.00 33.29 5.01
1463 1496 1.068083 CAGGCGGCTATCATGTCGT 59.932 57.895 12.74 0.00 37.38 4.34
1472 1505 1.748879 GACAAATGGCAGGCGGCTA 60.749 57.895 12.74 3.26 44.01 3.93
1548 1581 2.536761 TGTACCTTTTGTCCGTCCAG 57.463 50.000 0.00 0.00 0.00 3.86
1554 1587 4.643334 ACCACTTCTTTGTACCTTTTGTCC 59.357 41.667 0.00 0.00 0.00 4.02
1560 1593 3.945640 ACCACCACTTCTTTGTACCTT 57.054 42.857 0.00 0.00 0.00 3.50
1561 1594 4.040095 GTCTACCACCACTTCTTTGTACCT 59.960 45.833 0.00 0.00 0.00 3.08
1569 1602 0.317479 GCACGTCTACCACCACTTCT 59.683 55.000 0.00 0.00 0.00 2.85
1588 1621 3.058160 CTTTCCCAGTGCCGCCTG 61.058 66.667 2.75 2.75 0.00 4.85
1845 1878 3.998672 GTGACGAACTCCCCGCCA 61.999 66.667 0.00 0.00 0.00 5.69
1863 1896 3.302347 GAGCAGCGCCCACACTAGT 62.302 63.158 2.29 0.00 0.00 2.57
1908 1941 2.259511 GTACCGTCACGTGTCCCC 59.740 66.667 16.51 1.50 0.00 4.81
2022 2058 7.506261 ACCCATACAACGATCTAGTCTAAAGAT 59.494 37.037 0.00 0.00 36.40 2.40
2105 2180 1.204146 TTCAGACATGGGGGAGTAGC 58.796 55.000 0.00 0.00 0.00 3.58
2138 2214 6.618287 TTCACTATTTGACTCCACACAAAG 57.382 37.500 0.00 0.00 38.94 2.77
2144 2220 7.259290 TCAAAGTTTCACTATTTGACTCCAC 57.741 36.000 0.00 0.00 37.86 4.02
2294 2376 0.321298 AATCGGTGCGTAGTTTGGCT 60.321 50.000 0.00 0.00 0.00 4.75
2336 2418 2.703007 CTCCCCCTGTCTCATAAGAAGG 59.297 54.545 0.00 0.00 31.93 3.46
2343 2425 4.561254 AATACTACTCCCCCTGTCTCAT 57.439 45.455 0.00 0.00 0.00 2.90
2349 2431 6.553852 ACATGTACTAAATACTACTCCCCCTG 59.446 42.308 0.00 0.00 34.56 4.45
2350 2432 6.690569 ACATGTACTAAATACTACTCCCCCT 58.309 40.000 0.00 0.00 34.56 4.79
2352 2434 8.015185 TGAACATGTACTAAATACTACTCCCC 57.985 38.462 0.00 0.00 34.56 4.81
2384 2470 6.169094 GTCCGTCATGAAGATCATTATCCAT 58.831 40.000 10.47 0.00 34.28 3.41
2405 2491 3.057526 GTGGAGTTGCAGGTTTTATGTCC 60.058 47.826 0.00 0.00 0.00 4.02
2416 2502 0.976641 TCAGTAGGGTGGAGTTGCAG 59.023 55.000 0.00 0.00 0.00 4.41
2431 2517 4.654262 TCAAAGAGGACCTAACTTGTCAGT 59.346 41.667 0.00 0.00 34.36 3.41
2445 2531 4.095334 CACAATCATGCGAATCAAAGAGGA 59.905 41.667 0.00 0.00 0.00 3.71
2457 2543 3.000825 CCATGCATTTTCACAATCATGCG 59.999 43.478 0.00 0.00 44.22 4.73
2468 2554 8.309163 TGTGTTTTTATTCTCCATGCATTTTC 57.691 30.769 0.00 0.00 0.00 2.29
2483 2569 8.416329 GCATGATATTCCTTCCTGTGTTTTTAT 58.584 33.333 0.00 0.00 0.00 1.40
2489 2575 4.785346 AGCATGATATTCCTTCCTGTGT 57.215 40.909 0.00 0.00 0.00 3.72
2493 2579 9.597681 ATTTGAATTAGCATGATATTCCTTCCT 57.402 29.630 0.00 0.00 0.00 3.36
2547 2633 4.247380 GATGCAGAGGCCGGGGAG 62.247 72.222 2.18 0.00 40.13 4.30
2549 2635 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
2550 2636 3.035173 TTCTGATGCAGAGGCCGGG 62.035 63.158 2.18 0.00 41.75 5.73
2551 2637 1.817099 GTTCTGATGCAGAGGCCGG 60.817 63.158 0.00 0.00 41.75 6.13
2552 2638 2.169789 CGTTCTGATGCAGAGGCCG 61.170 63.158 0.00 0.00 41.75 6.13
2553 2639 0.179062 ATCGTTCTGATGCAGAGGCC 60.179 55.000 0.00 0.00 41.75 5.19
2554 2640 3.376218 ATCGTTCTGATGCAGAGGC 57.624 52.632 0.00 0.00 41.75 4.70
2562 2648 1.502231 GCCGTATGCATCGTTCTGAT 58.498 50.000 0.19 0.00 40.77 2.90
2563 2649 0.529773 GGCCGTATGCATCGTTCTGA 60.530 55.000 0.19 0.00 43.89 3.27
2564 2650 0.809636 TGGCCGTATGCATCGTTCTG 60.810 55.000 0.19 0.00 43.89 3.02
2565 2651 0.810031 GTGGCCGTATGCATCGTTCT 60.810 55.000 0.19 0.00 43.89 3.01
2566 2652 1.641677 GTGGCCGTATGCATCGTTC 59.358 57.895 0.19 2.49 43.89 3.95
2567 2653 1.817941 GGTGGCCGTATGCATCGTT 60.818 57.895 0.19 0.00 43.89 3.85
2568 2654 2.203015 GGTGGCCGTATGCATCGT 60.203 61.111 0.19 0.00 43.89 3.73
2569 2655 1.095228 AAAGGTGGCCGTATGCATCG 61.095 55.000 0.19 7.03 43.89 3.84
2570 2656 1.961793 TAAAGGTGGCCGTATGCATC 58.038 50.000 0.19 0.00 43.89 3.91
2571 2657 2.656947 ATAAAGGTGGCCGTATGCAT 57.343 45.000 3.79 3.79 43.89 3.96
2572 2658 2.701423 TCTATAAAGGTGGCCGTATGCA 59.299 45.455 0.00 0.00 43.89 3.96
2573 2659 3.396260 TCTATAAAGGTGGCCGTATGC 57.604 47.619 0.00 0.00 40.16 3.14
2574 2660 5.547465 TGAATCTATAAAGGTGGCCGTATG 58.453 41.667 0.00 0.00 0.00 2.39
2575 2661 5.818678 TGAATCTATAAAGGTGGCCGTAT 57.181 39.130 0.00 0.00 0.00 3.06
2576 2662 5.617528 TTGAATCTATAAAGGTGGCCGTA 57.382 39.130 0.00 0.00 0.00 4.02
2577 2663 4.497291 TTGAATCTATAAAGGTGGCCGT 57.503 40.909 0.00 0.00 0.00 5.68
2578 2664 6.263168 AGAATTTGAATCTATAAAGGTGGCCG 59.737 38.462 0.00 0.00 0.00 6.13
2579 2665 7.588497 AGAATTTGAATCTATAAAGGTGGCC 57.412 36.000 0.00 0.00 0.00 5.36
2580 2666 9.120538 TGTAGAATTTGAATCTATAAAGGTGGC 57.879 33.333 0.00 0.00 32.37 5.01
2589 2675 9.347240 CCCAAGTCATGTAGAATTTGAATCTAT 57.653 33.333 0.00 0.00 31.02 1.98
2590 2676 8.328758 ACCCAAGTCATGTAGAATTTGAATCTA 58.671 33.333 0.00 0.00 31.02 1.98
2591 2677 7.177878 ACCCAAGTCATGTAGAATTTGAATCT 58.822 34.615 0.00 0.00 31.02 2.40
2592 2678 7.396540 ACCCAAGTCATGTAGAATTTGAATC 57.603 36.000 0.00 0.00 31.02 2.52
2593 2679 7.781324 AACCCAAGTCATGTAGAATTTGAAT 57.219 32.000 0.00 0.00 31.02 2.57
2594 2680 7.069331 ACAAACCCAAGTCATGTAGAATTTGAA 59.931 33.333 0.00 0.00 31.02 2.69
2595 2681 6.549364 ACAAACCCAAGTCATGTAGAATTTGA 59.451 34.615 0.00 0.00 31.02 2.69
2596 2682 6.748132 ACAAACCCAAGTCATGTAGAATTTG 58.252 36.000 0.00 0.00 31.02 2.32
2597 2683 6.976934 ACAAACCCAAGTCATGTAGAATTT 57.023 33.333 0.00 0.00 31.02 1.82
2598 2684 6.976934 AACAAACCCAAGTCATGTAGAATT 57.023 33.333 0.00 0.00 34.31 2.17
2599 2685 6.549364 TCAAACAAACCCAAGTCATGTAGAAT 59.451 34.615 0.00 0.00 0.00 2.40
2600 2686 5.888724 TCAAACAAACCCAAGTCATGTAGAA 59.111 36.000 0.00 0.00 0.00 2.10
2601 2687 5.441500 TCAAACAAACCCAAGTCATGTAGA 58.558 37.500 0.00 0.00 0.00 2.59
2602 2688 5.766150 TCAAACAAACCCAAGTCATGTAG 57.234 39.130 0.00 0.00 0.00 2.74
2603 2689 6.511416 CAATCAAACAAACCCAAGTCATGTA 58.489 36.000 0.00 0.00 0.00 2.29
2604 2690 5.358922 CAATCAAACAAACCCAAGTCATGT 58.641 37.500 0.00 0.00 0.00 3.21
2605 2691 4.211794 GCAATCAAACAAACCCAAGTCATG 59.788 41.667 0.00 0.00 0.00 3.07
2606 2692 4.141756 TGCAATCAAACAAACCCAAGTCAT 60.142 37.500 0.00 0.00 0.00 3.06
2607 2693 3.196469 TGCAATCAAACAAACCCAAGTCA 59.804 39.130 0.00 0.00 0.00 3.41
2608 2694 3.791245 TGCAATCAAACAAACCCAAGTC 58.209 40.909 0.00 0.00 0.00 3.01
2609 2695 3.902881 TGCAATCAAACAAACCCAAGT 57.097 38.095 0.00 0.00 0.00 3.16
2610 2696 4.996062 GATGCAATCAAACAAACCCAAG 57.004 40.909 0.00 0.00 44.70 3.61
2638 2724 8.870116 ACCTATTAGAAGCAATCCTTTGTTTTT 58.130 29.630 0.00 0.00 36.54 1.94
2639 2725 8.422577 ACCTATTAGAAGCAATCCTTTGTTTT 57.577 30.769 0.00 0.00 36.54 2.43
2640 2726 7.148239 CGACCTATTAGAAGCAATCCTTTGTTT 60.148 37.037 0.00 0.00 38.76 2.83
2641 2727 6.316390 CGACCTATTAGAAGCAATCCTTTGTT 59.684 38.462 0.00 0.00 35.17 2.83
2642 2728 5.817816 CGACCTATTAGAAGCAATCCTTTGT 59.182 40.000 0.00 0.00 35.17 2.83
2643 2729 5.237344 CCGACCTATTAGAAGCAATCCTTTG 59.763 44.000 0.00 0.00 32.78 2.77
2644 2730 5.130477 TCCGACCTATTAGAAGCAATCCTTT 59.870 40.000 0.00 0.00 32.78 3.11
2645 2731 4.654262 TCCGACCTATTAGAAGCAATCCTT 59.346 41.667 0.00 0.00 36.19 3.36
2646 2732 4.223953 TCCGACCTATTAGAAGCAATCCT 58.776 43.478 0.00 0.00 0.00 3.24
2647 2733 4.602340 TCCGACCTATTAGAAGCAATCC 57.398 45.455 0.00 0.00 0.00 3.01
2648 2734 5.409826 CCATTCCGACCTATTAGAAGCAATC 59.590 44.000 0.00 0.00 0.00 2.67
2649 2735 5.071788 TCCATTCCGACCTATTAGAAGCAAT 59.928 40.000 0.00 0.00 0.00 3.56
2650 2736 4.407621 TCCATTCCGACCTATTAGAAGCAA 59.592 41.667 0.00 0.00 0.00 3.91
2651 2737 3.964688 TCCATTCCGACCTATTAGAAGCA 59.035 43.478 0.00 0.00 0.00 3.91
2652 2738 4.602340 TCCATTCCGACCTATTAGAAGC 57.398 45.455 0.00 0.00 0.00 3.86
2653 2739 4.932200 GCATCCATTCCGACCTATTAGAAG 59.068 45.833 0.00 0.00 0.00 2.85
2654 2740 4.593206 AGCATCCATTCCGACCTATTAGAA 59.407 41.667 0.00 0.00 0.00 2.10
2655 2741 4.160329 AGCATCCATTCCGACCTATTAGA 58.840 43.478 0.00 0.00 0.00 2.10
2656 2742 4.543590 AGCATCCATTCCGACCTATTAG 57.456 45.455 0.00 0.00 0.00 1.73
2657 2743 5.330233 TCTAGCATCCATTCCGACCTATTA 58.670 41.667 0.00 0.00 0.00 0.98
2658 2744 4.160329 TCTAGCATCCATTCCGACCTATT 58.840 43.478 0.00 0.00 0.00 1.73
2659 2745 3.779444 TCTAGCATCCATTCCGACCTAT 58.221 45.455 0.00 0.00 0.00 2.57
2660 2746 3.238788 TCTAGCATCCATTCCGACCTA 57.761 47.619 0.00 0.00 0.00 3.08
2661 2747 2.088104 TCTAGCATCCATTCCGACCT 57.912 50.000 0.00 0.00 0.00 3.85
2662 2748 2.910688 TTCTAGCATCCATTCCGACC 57.089 50.000 0.00 0.00 0.00 4.79
2663 2749 3.733337 ACATTCTAGCATCCATTCCGAC 58.267 45.455 0.00 0.00 0.00 4.79
2664 2750 4.588951 ACTACATTCTAGCATCCATTCCGA 59.411 41.667 0.00 0.00 0.00 4.55
2665 2751 4.887748 ACTACATTCTAGCATCCATTCCG 58.112 43.478 0.00 0.00 0.00 4.30
2666 2752 6.759272 TGTACTACATTCTAGCATCCATTCC 58.241 40.000 0.00 0.00 0.00 3.01
2667 2753 7.661968 TCTGTACTACATTCTAGCATCCATTC 58.338 38.462 0.00 0.00 0.00 2.67
2668 2754 7.603180 TCTGTACTACATTCTAGCATCCATT 57.397 36.000 0.00 0.00 0.00 3.16
2669 2755 7.310299 CCATCTGTACTACATTCTAGCATCCAT 60.310 40.741 0.00 0.00 0.00 3.41
2670 2756 6.015095 CCATCTGTACTACATTCTAGCATCCA 60.015 42.308 0.00 0.00 0.00 3.41
2671 2757 6.209589 TCCATCTGTACTACATTCTAGCATCC 59.790 42.308 0.00 0.00 0.00 3.51
2672 2758 7.220741 TCCATCTGTACTACATTCTAGCATC 57.779 40.000 0.00 0.00 0.00 3.91
2673 2759 7.507277 TCTTCCATCTGTACTACATTCTAGCAT 59.493 37.037 0.00 0.00 0.00 3.79
2674 2760 6.833933 TCTTCCATCTGTACTACATTCTAGCA 59.166 38.462 0.00 0.00 0.00 3.49
2675 2761 7.278461 TCTTCCATCTGTACTACATTCTAGC 57.722 40.000 0.00 0.00 0.00 3.42
2702 2788 8.961634 CGATTCTTATGATTGACTCCTATAGGA 58.038 37.037 20.53 20.53 43.08 2.94
2703 2789 8.961634 TCGATTCTTATGATTGACTCCTATAGG 58.038 37.037 13.07 13.07 0.00 2.57
2706 2792 8.865090 AGTTCGATTCTTATGATTGACTCCTAT 58.135 33.333 0.00 0.00 0.00 2.57
2707 2793 8.239038 AGTTCGATTCTTATGATTGACTCCTA 57.761 34.615 0.00 0.00 0.00 2.94
2708 2794 7.118496 AGTTCGATTCTTATGATTGACTCCT 57.882 36.000 0.00 0.00 0.00 3.69
2709 2795 7.382759 GGTAGTTCGATTCTTATGATTGACTCC 59.617 40.741 0.00 0.00 0.00 3.85
2710 2796 7.921214 TGGTAGTTCGATTCTTATGATTGACTC 59.079 37.037 0.00 0.00 0.00 3.36
2711 2797 7.782049 TGGTAGTTCGATTCTTATGATTGACT 58.218 34.615 0.00 0.00 0.00 3.41
2712 2798 8.328864 GTTGGTAGTTCGATTCTTATGATTGAC 58.671 37.037 0.00 0.00 0.00 3.18
2713 2799 7.222031 CGTTGGTAGTTCGATTCTTATGATTGA 59.778 37.037 0.00 0.00 0.00 2.57
2714 2800 7.010183 ACGTTGGTAGTTCGATTCTTATGATTG 59.990 37.037 0.00 0.00 0.00 2.67
2715 2801 7.039882 ACGTTGGTAGTTCGATTCTTATGATT 58.960 34.615 0.00 0.00 0.00 2.57
2716 2802 6.570692 ACGTTGGTAGTTCGATTCTTATGAT 58.429 36.000 0.00 0.00 0.00 2.45
2717 2803 5.957798 ACGTTGGTAGTTCGATTCTTATGA 58.042 37.500 0.00 0.00 0.00 2.15
2718 2804 7.925703 ATACGTTGGTAGTTCGATTCTTATG 57.074 36.000 0.00 0.00 30.81 1.90
2719 2805 8.295288 CCTATACGTTGGTAGTTCGATTCTTAT 58.705 37.037 0.00 0.00 30.81 1.73
2720 2806 7.255242 CCCTATACGTTGGTAGTTCGATTCTTA 60.255 40.741 0.00 0.00 30.81 2.10
2721 2807 6.460676 CCCTATACGTTGGTAGTTCGATTCTT 60.461 42.308 0.00 0.00 30.81 2.52
2722 2808 5.009410 CCCTATACGTTGGTAGTTCGATTCT 59.991 44.000 0.00 0.00 30.81 2.40
2723 2809 5.009010 TCCCTATACGTTGGTAGTTCGATTC 59.991 44.000 0.00 0.00 30.81 2.52
2724 2810 4.889409 TCCCTATACGTTGGTAGTTCGATT 59.111 41.667 0.00 0.00 30.81 3.34
2725 2811 4.464008 TCCCTATACGTTGGTAGTTCGAT 58.536 43.478 0.00 0.00 30.81 3.59
2726 2812 3.884895 TCCCTATACGTTGGTAGTTCGA 58.115 45.455 0.00 0.00 30.81 3.71
2727 2813 4.637483 TTCCCTATACGTTGGTAGTTCG 57.363 45.455 0.00 0.00 30.81 3.95
2728 2814 7.854557 AATTTTCCCTATACGTTGGTAGTTC 57.145 36.000 0.00 0.00 30.81 3.01
2729 2815 9.910267 ATAAATTTTCCCTATACGTTGGTAGTT 57.090 29.630 0.00 0.00 30.81 2.24
2758 2844 9.485206 CAAAGGATTTTCACAGAATTTGAATCT 57.515 29.630 0.00 0.00 35.03 2.40
2759 2845 9.480053 TCAAAGGATTTTCACAGAATTTGAATC 57.520 29.630 0.00 0.00 35.03 2.52
2760 2846 9.835389 TTCAAAGGATTTTCACAGAATTTGAAT 57.165 25.926 11.26 0.00 39.28 2.57
2761 2847 9.097257 GTTCAAAGGATTTTCACAGAATTTGAA 57.903 29.630 11.26 11.26 40.89 2.69
2762 2848 7.710475 GGTTCAAAGGATTTTCACAGAATTTGA 59.290 33.333 0.00 0.00 35.03 2.69
2763 2849 7.495279 TGGTTCAAAGGATTTTCACAGAATTTG 59.505 33.333 0.00 0.00 35.03 2.32
2764 2850 7.563906 TGGTTCAAAGGATTTTCACAGAATTT 58.436 30.769 0.00 0.00 35.03 1.82
2765 2851 7.123355 TGGTTCAAAGGATTTTCACAGAATT 57.877 32.000 0.00 0.00 35.03 2.17
2766 2852 6.729690 TGGTTCAAAGGATTTTCACAGAAT 57.270 33.333 0.00 0.00 35.03 2.40
2767 2853 6.537453 TTGGTTCAAAGGATTTTCACAGAA 57.463 33.333 0.00 0.00 35.03 3.02
2768 2854 6.537453 TTTGGTTCAAAGGATTTTCACAGA 57.463 33.333 0.00 0.00 35.03 3.41
2769 2855 6.833342 CTTTGGTTCAAAGGATTTTCACAG 57.167 37.500 11.36 0.00 44.75 3.66
2781 2867 1.872773 AAGGGTGCCTTTGGTTCAAA 58.127 45.000 0.00 0.00 41.69 2.69
2782 2868 3.625314 AAGGGTGCCTTTGGTTCAA 57.375 47.368 0.00 0.00 41.69 2.69
2791 2877 4.788925 TGCATACTATTAAAGGGTGCCT 57.211 40.909 0.00 0.00 38.32 4.75
2792 2878 7.519032 TTTATGCATACTATTAAAGGGTGCC 57.481 36.000 5.74 0.00 38.32 5.01
2808 2894 9.163899 TGCATGTGTTTTGATTATTTTATGCAT 57.836 25.926 3.79 3.79 41.27 3.96
2809 2895 8.543862 TGCATGTGTTTTGATTATTTTATGCA 57.456 26.923 0.00 0.00 43.12 3.96
2818 2904 9.624697 GAAGTTTCTATGCATGTGTTTTGATTA 57.375 29.630 10.16 0.00 0.00 1.75
2819 2905 8.143193 TGAAGTTTCTATGCATGTGTTTTGATT 58.857 29.630 10.16 0.00 0.00 2.57
2820 2906 7.660112 TGAAGTTTCTATGCATGTGTTTTGAT 58.340 30.769 10.16 0.00 0.00 2.57
2821 2907 7.036996 TGAAGTTTCTATGCATGTGTTTTGA 57.963 32.000 10.16 0.00 0.00 2.69
2822 2908 7.648908 TCTTGAAGTTTCTATGCATGTGTTTTG 59.351 33.333 10.16 0.00 0.00 2.44
2823 2909 7.715657 TCTTGAAGTTTCTATGCATGTGTTTT 58.284 30.769 10.16 0.00 0.00 2.43
2824 2910 7.013655 ACTCTTGAAGTTTCTATGCATGTGTTT 59.986 33.333 10.16 0.00 33.03 2.83
2825 2911 6.488006 ACTCTTGAAGTTTCTATGCATGTGTT 59.512 34.615 10.16 0.00 33.03 3.32
2826 2912 6.000219 ACTCTTGAAGTTTCTATGCATGTGT 59.000 36.000 10.16 0.00 33.03 3.72
2827 2913 6.492007 ACTCTTGAAGTTTCTATGCATGTG 57.508 37.500 10.16 2.07 33.03 3.21
2828 2914 6.569226 GCAACTCTTGAAGTTTCTATGCATGT 60.569 38.462 10.16 0.00 46.26 3.21
2829 2915 5.798934 GCAACTCTTGAAGTTTCTATGCATG 59.201 40.000 10.16 0.00 46.26 4.06
2830 2916 5.474532 TGCAACTCTTGAAGTTTCTATGCAT 59.525 36.000 3.79 3.79 46.26 3.96
2831 2917 4.821260 TGCAACTCTTGAAGTTTCTATGCA 59.179 37.500 0.00 0.00 46.26 3.96
2832 2918 5.362556 TGCAACTCTTGAAGTTTCTATGC 57.637 39.130 0.00 0.00 46.26 3.14
2836 2922 9.822185 AAAATTAATGCAACTCTTGAAGTTTCT 57.178 25.926 0.00 0.00 46.26 2.52


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

AutoCloner maintained by Alex Coulton.