Multiple sequence alignment - TraesCS3B01G093800

Loading Multiple Alignment...

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 TraesCS3B01G093800 chr3B 100.000 5075 0 0 1 5075 62944292 62949366 0.000000e+00 9372.0
1 TraesCS3B01G093800 chr3D 91.564 2181 128 29 801 2949 39386312 39388468 0.000000e+00 2957.0
2 TraesCS3B01G093800 chr3D 89.206 2066 119 42 3079 5075 39388480 39390510 0.000000e+00 2484.0
3 TraesCS3B01G093800 chr3D 92.000 75 6 0 2266 2340 58090186 58090260 6.950000e-19 106.0
4 TraesCS3B01G093800 chr3A 93.101 1725 89 16 1246 2949 50888843 50890558 0.000000e+00 2499.0
5 TraesCS3B01G093800 chr3A 90.000 1290 73 17 1 1244 50887494 50888773 0.000000e+00 1616.0
6 TraesCS3B01G093800 chr3A 93.123 1047 58 11 3463 4500 50890924 50891965 0.000000e+00 1522.0
7 TraesCS3B01G093800 chr3A 90.705 667 39 12 4418 5075 50892082 50892734 0.000000e+00 867.0
8 TraesCS3B01G093800 chr3A 93.976 249 10 2 3073 3319 50890557 50890802 6.210000e-99 372.0
9 TraesCS3B01G093800 chr3A 97.710 131 3 0 2945 3075 644809126 644809256 5.110000e-55 226.0
10 TraesCS3B01G093800 chr3A 83.505 194 28 2 2266 2456 66921279 66921471 1.450000e-40 178.0
11 TraesCS3B01G093800 chr3A 82.990 194 29 2 2266 2456 67011901 67012093 6.760000e-39 172.0
12 TraesCS3B01G093800 chr6B 98.507 134 1 1 2948 3080 77322961 77323094 8.490000e-58 235.0
13 TraesCS3B01G093800 chr6B 90.698 43 1 2 222 264 651012549 651012588 3.000000e-03 54.7
14 TraesCS3B01G093800 chr7B 99.225 129 1 0 2946 3074 94759091 94758963 3.060000e-57 233.0
15 TraesCS3B01G093800 chr7B 99.219 128 1 0 2947 3074 705715804 705715677 1.100000e-56 231.0
16 TraesCS3B01G093800 chr2B 97.059 136 4 0 2947 3082 143487833 143487968 3.950000e-56 230.0
17 TraesCS3B01G093800 chr2B 97.015 134 3 1 2941 3074 551568001 551567869 1.840000e-54 224.0
18 TraesCS3B01G093800 chr2B 95.070 142 5 2 2941 3082 578606507 578606368 6.610000e-54 222.0
19 TraesCS3B01G093800 chr6D 95.620 137 6 0 2938 3074 410401797 410401933 2.380000e-53 220.0
20 TraesCS3B01G093800 chrUn 94.366 142 8 0 2946 3087 87981823 87981682 8.550000e-53 219.0
21 TraesCS3B01G093800 chr4D 93.333 45 2 1 224 268 448516702 448516745 1.180000e-06 65.8
22 TraesCS3B01G093800 chr4D 92.500 40 2 1 224 263 390855010 390854972 7.100000e-04 56.5
23 TraesCS3B01G093800 chr6A 91.489 47 0 3 222 268 578072031 578072073 1.530000e-05 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 TraesCS3B01G093800 chr3B 62944292 62949366 5074 False 9372.0 9372 100.000 1 5075 1 chr3B.!!$F1 5074
1 TraesCS3B01G093800 chr3D 39386312 39390510 4198 False 2720.5 2957 90.385 801 5075 2 chr3D.!!$F2 4274
2 TraesCS3B01G093800 chr3A 50887494 50892734 5240 False 1375.2 2499 92.181 1 5075 5 chr3A.!!$F4 5074

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
918 932 0.033208 TTTCCCATCCATCCCAGTGC 60.033 55.000 0.00 0.00 0.00 4.40 F
934 948 0.033504 GTGCGAACTCCCAGTGAGAA 59.966 55.000 0.00 0.00 44.42 2.87 F
1102 1144 0.756294 TGCCACCGTCTTCTCTTTCA 59.244 50.000 0.00 0.00 0.00 2.69 F
1676 1800 0.918258 TGGCAATAGGACATCAGGCA 59.082 50.000 0.00 0.00 0.00 4.75 F
2005 2136 1.227704 CGCCACAACACCACTGGTA 60.228 57.895 0.00 0.00 32.11 3.25 F
2031 2162 1.341383 GGTGGCTGGAAATGGTCTGAT 60.341 52.381 0.00 0.00 0.00 2.90 F
3070 3207 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2561 2697 0.035820 TACCACCCGTCTTGGCATTC 60.036 55.000 0.00 0.00 37.69 2.67 R
2573 2709 1.277273 GTTCCACTGTAGGTACCACCC 59.723 57.143 15.94 1.34 39.75 4.61 R
3051 3188 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12 R
3052 3189 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89 R
3053 3190 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40 R
3663 3864 0.391927 TGTAAATGAACTCGGGGGCG 60.392 55.000 0.00 0.00 0.00 6.13 R
4957 5396 0.038159 CGAGTTCCGAAAGACAGGCT 60.038 55.000 0.00 0.00 41.76 4.58 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
179 180 7.407393 TCATAGTGATTGGATGATTTTGCAA 57.593 32.000 0.00 0.00 0.00 4.08
220 221 9.179909 GATATTCTGGAGTCTATTTCGGATCTA 57.820 37.037 0.00 0.00 0.00 1.98
392 394 1.403647 CGGAATACCAGTGCTTCGTCA 60.404 52.381 0.00 0.00 35.59 4.35
411 413 8.744008 TTCGTCAGTGAAACAAACAAAATTAA 57.256 26.923 0.00 0.00 41.43 1.40
413 415 8.237949 TCGTCAGTGAAACAAACAAAATTAAGA 58.762 29.630 0.00 0.00 41.43 2.10
429 431 9.113876 CAAAATTAAGAGTACCATTTCGTGTTC 57.886 33.333 0.00 0.00 0.00 3.18
439 441 3.966218 CCATTTCGTGTTCGACTTGTTTC 59.034 43.478 0.00 0.00 46.03 2.78
459 461 7.327214 TGTTTCTTTTAACAGGTCAAAATGCT 58.673 30.769 0.00 0.00 33.31 3.79
462 464 9.877178 TTTCTTTTAACAGGTCAAAATGCTTAA 57.123 25.926 0.00 0.00 0.00 1.85
469 471 6.739112 ACAGGTCAAAATGCTTAAGTCTTTC 58.261 36.000 4.02 0.00 0.00 2.62
476 478 9.088987 TCAAAATGCTTAAGTCTTTCCCTAAAT 57.911 29.630 4.02 0.00 0.00 1.40
495 497 5.574815 AAATGTTTGCGAGCAACATTTAC 57.425 34.783 28.29 18.65 40.83 2.01
499 501 2.917701 TGCGAGCAACATTTACATGG 57.082 45.000 0.00 0.00 34.27 3.66
510 512 6.749118 GCAACATTTACATGGAAAGAGACATC 59.251 38.462 9.41 0.00 34.27 3.06
512 514 5.586243 ACATTTACATGGAAAGAGACATCCG 59.414 40.000 9.41 0.00 38.63 4.18
542 544 1.886542 ACTACGAGCCGCATATGATGA 59.113 47.619 6.97 0.00 0.00 2.92
543 545 2.254459 CTACGAGCCGCATATGATGAC 58.746 52.381 6.97 0.00 0.00 3.06
544 546 0.676184 ACGAGCCGCATATGATGACT 59.324 50.000 6.97 0.00 0.00 3.41
553 555 6.432162 AGCCGCATATGATGACTTTTATCAAT 59.568 34.615 6.97 0.00 38.01 2.57
557 559 8.715088 CGCATATGATGACTTTTATCAATCTCA 58.285 33.333 6.97 0.00 38.01 3.27
590 598 0.107945 GCTCAATCTCTTGGAGGCGT 60.108 55.000 0.00 0.00 32.95 5.68
593 601 1.623311 TCAATCTCTTGGAGGCGTTCA 59.377 47.619 0.00 0.00 32.95 3.18
611 619 4.310769 GTTCACAGAGTTAGAGTGTGCAT 58.689 43.478 0.00 0.00 41.17 3.96
613 621 3.321968 TCACAGAGTTAGAGTGTGCATGT 59.678 43.478 0.00 0.00 41.17 3.21
621 629 5.639506 AGTTAGAGTGTGCATGTATGTGTTC 59.360 40.000 0.00 0.00 0.00 3.18
641 649 7.039714 TGTGTTCAGAGTGATGAGTGTAAGTAT 60.040 37.037 0.00 0.00 0.00 2.12
803 814 4.634443 AGTAAAAAGGGTATAGCAACAGCG 59.366 41.667 4.02 0.00 0.00 5.18
855 869 2.017049 GCAGTGGAATTAATGGCGAGT 58.983 47.619 0.00 0.00 0.00 4.18
888 902 3.167414 CCCACCCGTTCCCTTCTT 58.833 61.111 0.00 0.00 0.00 2.52
893 907 0.178900 ACCCGTTCCCTTCTTCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
894 908 0.537653 CCCGTTCCCTTCTTCCTCTC 59.462 60.000 0.00 0.00 0.00 3.20
918 932 0.033208 TTTCCCATCCATCCCAGTGC 60.033 55.000 0.00 0.00 0.00 4.40
923 937 0.107508 CATCCATCCCAGTGCGAACT 60.108 55.000 0.00 0.00 0.00 3.01
924 938 0.179000 ATCCATCCCAGTGCGAACTC 59.821 55.000 0.00 0.00 0.00 3.01
925 939 1.450312 CCATCCCAGTGCGAACTCC 60.450 63.158 0.00 0.00 0.00 3.85
926 940 1.450312 CATCCCAGTGCGAACTCCC 60.450 63.158 0.00 0.00 0.00 4.30
927 941 1.918293 ATCCCAGTGCGAACTCCCA 60.918 57.895 0.00 0.00 0.00 4.37
928 942 1.903877 ATCCCAGTGCGAACTCCCAG 61.904 60.000 0.00 0.00 0.00 4.45
929 943 2.743718 CCAGTGCGAACTCCCAGT 59.256 61.111 0.00 0.00 0.00 4.00
934 948 0.033504 GTGCGAACTCCCAGTGAGAA 59.966 55.000 0.00 0.00 44.42 2.87
937 951 1.540363 GCGAACTCCCAGTGAGAACAA 60.540 52.381 0.00 0.00 44.42 2.83
1101 1143 1.270358 ACTGCCACCGTCTTCTCTTTC 60.270 52.381 0.00 0.00 0.00 2.62
1102 1144 0.756294 TGCCACCGTCTTCTCTTTCA 59.244 50.000 0.00 0.00 0.00 2.69
1119 1166 3.491766 TTCACCCCCTTCACTCTAGAT 57.508 47.619 0.00 0.00 0.00 1.98
1129 1176 6.252233 CCCTTCACTCTAGATAGATCCATGA 58.748 44.000 0.00 0.00 0.00 3.07
1131 1178 6.152661 CCTTCACTCTAGATAGATCCATGACC 59.847 46.154 0.00 0.00 0.00 4.02
1139 1186 2.885388 AGATCCATGACCTCTTCCCT 57.115 50.000 0.00 0.00 0.00 4.20
1218 1265 3.866327 GGAGTCGAGCTATTTTTCCTCAC 59.134 47.826 0.00 0.00 0.00 3.51
1244 1291 4.081697 TCGTCTGCAAGGTCTGATTGATAA 60.082 41.667 0.00 0.00 0.00 1.75
1247 1356 6.479990 CGTCTGCAAGGTCTGATTGATAATAA 59.520 38.462 0.00 0.00 0.00 1.40
1304 1420 6.412072 GCGCACACAAATCAGAAGATAAATAC 59.588 38.462 0.30 0.00 33.08 1.89
1305 1421 7.677276 GCGCACACAAATCAGAAGATAAATACT 60.677 37.037 0.30 0.00 33.08 2.12
1394 1510 1.302511 AAATCTGCGGCACCTCGTT 60.303 52.632 0.00 0.00 0.00 3.85
1421 1537 7.676043 CCCCCTATCTGATATATATACTGGTGG 59.324 44.444 0.00 0.00 0.00 4.61
1422 1538 7.179338 CCCCTATCTGATATATATACTGGTGGC 59.821 44.444 0.00 0.00 0.00 5.01
1423 1539 7.952930 CCCTATCTGATATATATACTGGTGGCT 59.047 40.741 0.00 0.00 0.00 4.75
1425 1541 7.609097 ATCTGATATATATACTGGTGGCTGG 57.391 40.000 0.00 0.00 0.00 4.85
1426 1542 6.503041 TCTGATATATATACTGGTGGCTGGT 58.497 40.000 0.00 0.00 0.00 4.00
1427 1543 6.381133 TCTGATATATATACTGGTGGCTGGTG 59.619 42.308 0.00 0.00 0.00 4.17
1428 1544 3.703001 ATATATACTGGTGGCTGGTGC 57.297 47.619 0.00 0.00 38.76 5.01
1429 1545 1.511613 ATATACTGGTGGCTGGTGCT 58.488 50.000 0.00 0.00 39.59 4.40
1431 1547 2.202236 ATACTGGTGGCTGGTGCTGG 62.202 60.000 0.00 0.00 39.59 4.85
1432 1548 4.275508 CTGGTGGCTGGTGCTGGT 62.276 66.667 0.00 0.00 39.59 4.00
1433 1549 4.584518 TGGTGGCTGGTGCTGGTG 62.585 66.667 0.00 0.00 39.59 4.17
1434 1550 4.586235 GGTGGCTGGTGCTGGTGT 62.586 66.667 0.00 0.00 39.59 4.16
1455 1575 1.394917 GCCACAACTATCAAGCGTCAG 59.605 52.381 0.00 0.00 0.00 3.51
1456 1576 1.394917 CCACAACTATCAAGCGTCAGC 59.605 52.381 0.00 0.00 45.58 4.26
1565 1688 6.461648 CCTGTCAGAAACCGATCATATGTACT 60.462 42.308 0.00 0.00 0.00 2.73
1660 1784 4.370917 TGCAAAGAAAGACAGAAATTGGC 58.629 39.130 0.00 0.00 33.75 4.52
1668 1792 5.904362 AAGACAGAAATTGGCAATAGGAC 57.096 39.130 14.05 5.57 37.23 3.85
1669 1793 4.922206 AGACAGAAATTGGCAATAGGACA 58.078 39.130 14.05 0.00 37.23 4.02
1674 1798 4.891756 AGAAATTGGCAATAGGACATCAGG 59.108 41.667 14.05 0.00 31.62 3.86
1676 1800 0.918258 TGGCAATAGGACATCAGGCA 59.082 50.000 0.00 0.00 0.00 4.75
2000 2131 4.307908 GCGTCGCCACAACACCAC 62.308 66.667 5.75 0.00 0.00 4.16
2005 2136 1.227704 CGCCACAACACCACTGGTA 60.228 57.895 0.00 0.00 32.11 3.25
2031 2162 1.341383 GGTGGCTGGAAATGGTCTGAT 60.341 52.381 0.00 0.00 0.00 2.90
2178 2309 2.104281 ACTTACCGGAAAGAAGTGTGCT 59.896 45.455 9.46 0.00 32.25 4.40
2224 2360 4.690748 TGATGAATCACGGTGAGTCTTTTC 59.309 41.667 30.92 24.65 41.56 2.29
2249 2385 7.608761 TCTGGTAACACTGAAGTACTTTTGTTT 59.391 33.333 24.51 17.00 46.17 2.83
2266 2402 7.481169 ACTTTTGTTTCGTTGCATGAAAATTTG 59.519 29.630 14.14 8.14 35.16 2.32
2299 2435 3.997021 CAGTCTGACACCCACTGATTTAC 59.003 47.826 10.88 0.00 40.07 2.01
2300 2436 3.646162 AGTCTGACACCCACTGATTTACA 59.354 43.478 10.88 0.00 0.00 2.41
2312 2448 6.127054 CCCACTGATTTACACCAGAAGATAGA 60.127 42.308 0.00 0.00 34.65 1.98
2366 2502 4.449131 TCATAGTCCTCATCGTCGTAAGT 58.551 43.478 0.00 0.00 39.48 2.24
2381 2517 3.509967 TCGTAAGTGGCTTGATTCTCTCA 59.490 43.478 0.00 0.00 39.48 3.27
2390 2526 3.683822 GCTTGATTCTCTCAACCACTCTG 59.316 47.826 0.00 0.00 38.97 3.35
2573 2709 2.824041 CCCGGGAATGCCAAGACG 60.824 66.667 18.48 0.00 35.15 4.18
2648 2784 4.344679 AGATTGAAGAGATCCAGCCTACAG 59.655 45.833 0.00 0.00 0.00 2.74
2717 2853 7.671302 TCTATCATCCTAATTTAGTGGCTGTC 58.329 38.462 2.88 0.00 0.00 3.51
2759 2895 1.591619 GGCGACCGCTTTATTGTCTAC 59.408 52.381 14.25 0.00 41.60 2.59
2768 2904 5.107220 CCGCTTTATTGTCTACGAGTTTGTT 60.107 40.000 0.00 0.00 0.00 2.83
2916 3052 5.398603 TGTCTCTTCCACTCTGAGAAATC 57.601 43.478 12.44 0.00 38.39 2.17
2956 3093 8.030913 TCTATTTGGAAAGTAATACTCCCTCC 57.969 38.462 11.34 9.88 0.00 4.30
2957 3094 4.748277 TTGGAAAGTAATACTCCCTCCG 57.252 45.455 11.34 0.00 29.04 4.63
2958 3095 3.716431 TGGAAAGTAATACTCCCTCCGT 58.284 45.455 11.34 0.00 29.04 4.69
2959 3096 3.703052 TGGAAAGTAATACTCCCTCCGTC 59.297 47.826 11.34 0.00 29.04 4.79
2960 3097 3.069300 GGAAAGTAATACTCCCTCCGTCC 59.931 52.174 0.00 0.00 0.00 4.79
2961 3098 1.978454 AGTAATACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
2962 3099 1.492176 AGTAATACTCCCTCCGTCCGA 59.508 52.381 0.00 0.00 0.00 4.55
2963 3100 2.092212 AGTAATACTCCCTCCGTCCGAA 60.092 50.000 0.00 0.00 0.00 4.30
2964 3101 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
2965 3102 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2966 3103 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2967 3104 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2968 3105 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2969 3106 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2970 3107 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2971 3108 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2972 3109 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2973 3110 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2974 3111 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2975 3112 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2976 3113 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2977 3114 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2978 3115 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2979 3116 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2980 3117 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2981 3118 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2982 3119 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2983 3120 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2984 3121 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2985 3122 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
2993 3130 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
3031 3168 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
3038 3175 8.980832 ACATCTAGATACATCCCCTTTTATCT 57.019 34.615 4.54 0.00 35.79 1.98
3045 3182 9.225682 AGATACATCCCCTTTTATCTAGTTTGA 57.774 33.333 0.00 0.00 30.95 2.69
3047 3184 9.799106 ATACATCCCCTTTTATCTAGTTTGATG 57.201 33.333 0.00 0.00 33.80 3.07
3048 3185 7.872138 ACATCCCCTTTTATCTAGTTTGATGA 58.128 34.615 0.00 0.00 32.39 2.92
3049 3186 7.775561 ACATCCCCTTTTATCTAGTTTGATGAC 59.224 37.037 0.00 0.00 32.39 3.06
3050 3187 7.265599 TCCCCTTTTATCTAGTTTGATGACA 57.734 36.000 0.00 0.00 0.00 3.58
3051 3188 7.695055 TCCCCTTTTATCTAGTTTGATGACAA 58.305 34.615 0.00 0.00 0.00 3.18
3052 3189 7.829211 TCCCCTTTTATCTAGTTTGATGACAAG 59.171 37.037 0.00 0.00 37.32 3.16
3053 3190 7.611855 CCCCTTTTATCTAGTTTGATGACAAGT 59.388 37.037 0.00 0.00 37.32 3.16
3054 3191 9.667107 CCCTTTTATCTAGTTTGATGACAAGTA 57.333 33.333 0.00 0.00 37.32 2.24
3060 3197 7.827819 TCTAGTTTGATGACAAGTATTTCCG 57.172 36.000 0.00 0.00 37.32 4.30
3061 3198 5.880054 AGTTTGATGACAAGTATTTCCGG 57.120 39.130 0.00 0.00 37.32 5.14
3062 3199 5.556915 AGTTTGATGACAAGTATTTCCGGA 58.443 37.500 0.00 0.00 37.32 5.14
3063 3200 5.411669 AGTTTGATGACAAGTATTTCCGGAC 59.588 40.000 1.83 0.00 37.32 4.79
3064 3201 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3065 3202 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3066 3203 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3067 3204 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3068 3205 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3069 3206 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3070 3207 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3071 3208 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3072 3209 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3073 3210 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
3074 3211 0.682209 TTTCCGGACGGAGGGAGTAG 60.682 60.000 13.64 0.00 46.06 2.57
3075 3212 1.856539 TTCCGGACGGAGGGAGTAGT 61.857 60.000 13.64 0.00 46.06 2.73
3293 3445 2.408271 TTGCATAAGTCAGCTCTGGG 57.592 50.000 0.00 0.00 0.00 4.45
3341 3522 1.476891 AGAATGATTGCTGCAGCCTTG 59.523 47.619 34.64 0.00 41.18 3.61
3345 3526 3.280197 TGATTGCTGCAGCCTTGTATA 57.720 42.857 34.64 12.62 41.18 1.47
3346 3527 3.619419 TGATTGCTGCAGCCTTGTATAA 58.381 40.909 34.64 20.75 41.18 0.98
3347 3528 4.209538 TGATTGCTGCAGCCTTGTATAAT 58.790 39.130 34.64 24.31 41.18 1.28
3388 3569 5.538118 TCTCACATGTCGTTTGTGTTCTAT 58.462 37.500 0.00 0.00 43.86 1.98
3390 3571 5.984627 TCACATGTCGTTTGTGTTCTATTG 58.015 37.500 0.00 0.00 43.86 1.90
3396 3577 6.252281 TGTCGTTTGTGTTCTATTGAAACAC 58.748 36.000 11.20 11.20 36.12 3.32
3431 3618 0.467290 TTGGCTGTCTTTGTCCCCAC 60.467 55.000 0.00 0.00 0.00 4.61
3433 3620 0.890996 GGCTGTCTTTGTCCCCACAG 60.891 60.000 0.00 0.00 39.47 3.66
3434 3621 2.633860 CTGTCTTTGTCCCCACAGC 58.366 57.895 0.00 0.00 32.71 4.40
3449 3636 4.097892 CCCCACAGCCTTACATTTAATCAC 59.902 45.833 0.00 0.00 0.00 3.06
3496 3697 5.619981 CGGTGGTCTTTTGATTCCAGATTTC 60.620 44.000 0.00 0.00 0.00 2.17
3612 3813 1.391157 GGCTGTCCAAGTTTGTGCCA 61.391 55.000 0.00 0.00 38.79 4.92
3663 3864 1.779569 CGGCAACATACGGATACCTC 58.220 55.000 0.00 0.00 0.00 3.85
3705 3906 2.604046 ACGAGCTGACAACAAAGAGT 57.396 45.000 0.00 0.00 0.00 3.24
3777 3978 1.741770 AGCGCAGTCCGTTGAATCC 60.742 57.895 11.47 0.00 39.71 3.01
3780 3981 2.032634 GCAGTCCGTTGAATCCGCA 61.033 57.895 0.00 0.00 0.00 5.69
3798 3999 3.668447 CGCAGGATGGCAGACTATATTT 58.332 45.455 0.00 0.00 35.86 1.40
3807 4008 4.144297 GGCAGACTATATTTGAATGGGCA 58.856 43.478 0.00 0.00 0.00 5.36
4138 4344 3.876914 CCATTAGGTAGCGCATTTCTTGA 59.123 43.478 11.47 0.00 0.00 3.02
4158 4364 1.668151 GCGTGGAGTGACCCAAGAC 60.668 63.158 9.41 0.00 37.81 3.01
4161 4367 1.846124 TGGAGTGACCCAAGACCCC 60.846 63.158 0.00 0.00 38.00 4.95
4214 4420 2.168728 GGGCAAGTACTTAGGGAGAGTG 59.831 54.545 8.04 0.00 0.00 3.51
4220 4426 4.117632 AGTACTTAGGGAGAGTGAGGGTA 58.882 47.826 0.00 0.00 0.00 3.69
4226 4432 1.062810 GGGAGAGTGAGGGTACTGGAT 60.063 57.143 0.00 0.00 0.00 3.41
4335 4542 4.304110 AGCAAGCAACATGAATTGTTCAG 58.696 39.130 0.00 0.00 45.55 3.02
4343 4552 6.373779 CAACATGAATTGTTCAGTGTCTACC 58.626 40.000 0.00 0.00 45.55 3.18
4358 4567 3.510360 TGTCTACCCAGTAGAAGCTGTTC 59.490 47.826 6.05 0.00 45.12 3.18
4370 4579 9.539825 CAGTAGAAGCTGTTCATCTATGTATTT 57.460 33.333 0.00 0.00 34.82 1.40
4375 4584 7.256756 AGCTGTTCATCTATGTATTTTCTGC 57.743 36.000 0.00 0.00 0.00 4.26
4376 4585 6.018425 AGCTGTTCATCTATGTATTTTCTGCG 60.018 38.462 0.00 0.00 0.00 5.18
4381 4590 8.600625 GTTCATCTATGTATTTTCTGCGTGTTA 58.399 33.333 0.00 0.00 0.00 2.41
4385 4594 7.406553 TCTATGTATTTTCTGCGTGTTAATGC 58.593 34.615 0.00 0.00 38.92 3.56
4391 4600 0.874390 CTGCGTGTTAATGCCAGTGT 59.126 50.000 0.00 0.00 37.53 3.55
4392 4601 0.871722 TGCGTGTTAATGCCAGTGTC 59.128 50.000 0.00 0.00 37.53 3.67
4395 4604 2.412870 CGTGTTAATGCCAGTGTCTCA 58.587 47.619 0.00 0.00 0.00 3.27
4398 4607 4.002982 GTGTTAATGCCAGTGTCTCATGA 58.997 43.478 0.00 0.00 0.00 3.07
4405 4614 6.616237 ATGCCAGTGTCTCATGATATATCA 57.384 37.500 17.56 17.56 41.70 2.15
4409 4618 8.596293 TGCCAGTGTCTCATGATATATCATTTA 58.404 33.333 22.97 14.23 44.70 1.40
4435 4644 7.645402 TCAACTTATCGTCGAGCTTCATATTA 58.355 34.615 0.00 0.00 0.00 0.98
4443 4654 7.398746 TCGTCGAGCTTCATATTAACAATTTG 58.601 34.615 0.00 0.00 0.00 2.32
4449 4660 9.214953 GAGCTTCATATTAACAATTTGAGAACG 57.785 33.333 2.79 0.00 31.93 3.95
4488 4699 3.928754 TCATTCTAGGGCTACACTGGAT 58.071 45.455 0.00 0.00 0.00 3.41
4520 4923 6.921914 TGAAGTAACTAGTGAAGTAGAAGGC 58.078 40.000 0.00 0.00 37.50 4.35
4525 4928 5.652994 ACTAGTGAAGTAGAAGGCTCTTG 57.347 43.478 0.00 0.00 36.36 3.02
4537 4940 5.124645 AGAAGGCTCTTGATTAATCTGCAG 58.875 41.667 16.24 7.63 0.00 4.41
4555 4958 1.067000 CAGAGCAGAGTGAACTGGAGG 60.067 57.143 0.00 0.00 38.22 4.30
4557 4960 0.972883 AGCAGAGTGAACTGGAGGTC 59.027 55.000 0.00 0.00 38.22 3.85
4558 4961 0.972883 GCAGAGTGAACTGGAGGTCT 59.027 55.000 0.00 0.00 38.22 3.85
4559 4962 2.171840 GCAGAGTGAACTGGAGGTCTA 58.828 52.381 0.00 0.00 38.22 2.59
4560 4963 2.563179 GCAGAGTGAACTGGAGGTCTAA 59.437 50.000 0.00 0.00 38.22 2.10
4561 4964 3.367910 GCAGAGTGAACTGGAGGTCTAAG 60.368 52.174 0.00 0.00 38.22 2.18
4562 4965 4.082845 CAGAGTGAACTGGAGGTCTAAGA 58.917 47.826 0.00 0.00 34.64 2.10
4563 4966 4.157656 CAGAGTGAACTGGAGGTCTAAGAG 59.842 50.000 0.00 0.00 34.64 2.85
4566 4969 3.082548 TGAACTGGAGGTCTAAGAGACG 58.917 50.000 0.73 0.00 45.96 4.18
4602 5005 2.814336 CCTGTTGAAGGTAGGTTTCAGC 59.186 50.000 0.00 0.00 41.74 4.26
4752 5161 3.160047 AGCCGCTCCAGGATCCTG 61.160 66.667 31.69 31.69 43.26 3.86
4931 5370 4.479993 CTTGGGCTGGCTCGGGAG 62.480 72.222 0.00 0.00 0.00 4.30
4946 5385 1.911471 GGAGCTTCTTCTCCCTGGG 59.089 63.158 6.33 6.33 45.40 4.45
4947 5386 0.912006 GGAGCTTCTTCTCCCTGGGT 60.912 60.000 13.56 0.00 45.40 4.51
4948 5387 0.988063 GAGCTTCTTCTCCCTGGGTT 59.012 55.000 13.56 0.00 0.00 4.11
4949 5388 0.695347 AGCTTCTTCTCCCTGGGTTG 59.305 55.000 13.56 7.37 0.00 3.77
4950 5389 0.322906 GCTTCTTCTCCCTGGGTTGG 60.323 60.000 13.56 4.77 0.00 3.77
4951 5390 0.322906 CTTCTTCTCCCTGGGTTGGC 60.323 60.000 13.56 0.00 0.00 4.52
4952 5391 0.772124 TTCTTCTCCCTGGGTTGGCT 60.772 55.000 13.56 0.00 0.00 4.75
4953 5392 1.001641 CTTCTCCCTGGGTTGGCTG 60.002 63.158 13.56 0.00 0.00 4.85
4954 5393 2.490270 CTTCTCCCTGGGTTGGCTGG 62.490 65.000 13.56 0.00 0.00 4.85
4955 5394 4.052518 CTCCCTGGGTTGGCTGGG 62.053 72.222 13.56 0.00 40.95 4.45
4989 5428 1.003839 AACTCGGAAAGGCGATGCA 60.004 52.632 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.470002 GGCATTATCAATAAAAGGGGTATCATC 58.530 37.037 0.00 0.00 0.00 2.92
131 132 6.005823 AGCTATGCCATGCTTGTATGAAATA 58.994 36.000 0.35 0.00 35.86 1.40
206 207 4.114015 TGCTCCCTAGATCCGAAATAGA 57.886 45.455 0.00 0.00 0.00 1.98
299 300 9.965824 AAAAATCTACACAACTAAAGAACATGG 57.034 29.630 0.00 0.00 0.00 3.66
365 366 4.010667 AGCACTGGTATTCCGTTACAAA 57.989 40.909 0.00 0.00 36.30 2.83
379 381 1.261619 GTTTCACTGACGAAGCACTGG 59.738 52.381 0.00 0.00 0.00 4.00
392 394 9.797556 GGTACTCTTAATTTTGTTTGTTTCACT 57.202 29.630 0.00 0.00 0.00 3.41
411 413 3.255149 AGTCGAACACGAAATGGTACTCT 59.745 43.478 0.00 0.00 37.78 3.24
413 415 3.655276 AGTCGAACACGAAATGGTACT 57.345 42.857 0.00 0.00 37.78 2.73
429 431 6.114221 TGACCTGTTAAAAGAAACAAGTCG 57.886 37.500 11.67 0.00 46.66 4.18
439 441 8.871686 ACTTAAGCATTTTGACCTGTTAAAAG 57.128 30.769 1.29 0.00 32.77 2.27
459 461 6.487331 TCGCAAACATTTAGGGAAAGACTTAA 59.513 34.615 0.00 0.00 0.00 1.85
462 464 4.394729 TCGCAAACATTTAGGGAAAGACT 58.605 39.130 0.00 0.00 0.00 3.24
469 471 2.030363 TGTTGCTCGCAAACATTTAGGG 60.030 45.455 5.83 0.00 37.70 3.53
476 478 3.699779 TGTAAATGTTGCTCGCAAACA 57.300 38.095 5.83 4.12 37.70 2.83
495 497 2.555199 GACCGGATGTCTCTTTCCATG 58.445 52.381 9.46 0.00 41.03 3.66
499 501 1.473278 AGTCGACCGGATGTCTCTTTC 59.527 52.381 9.46 0.00 42.13 2.62
543 545 9.160496 GCCCTATCATACTGAGATTGATAAAAG 57.840 37.037 9.24 2.64 33.29 2.27
544 546 7.819415 CGCCCTATCATACTGAGATTGATAAAA 59.181 37.037 9.24 0.00 33.29 1.52
553 555 1.203063 AGCCGCCCTATCATACTGAGA 60.203 52.381 0.00 0.00 0.00 3.27
557 559 1.717032 TTGAGCCGCCCTATCATACT 58.283 50.000 0.00 0.00 0.00 2.12
590 598 4.202253 ACATGCACACTCTAACTCTGTGAA 60.202 41.667 0.00 0.00 38.02 3.18
593 601 5.047021 ACATACATGCACACTCTAACTCTGT 60.047 40.000 0.00 0.00 0.00 3.41
611 619 5.011023 ACACTCATCACTCTGAACACATACA 59.989 40.000 0.00 0.00 0.00 2.29
613 621 5.728637 ACACTCATCACTCTGAACACATA 57.271 39.130 0.00 0.00 0.00 2.29
700 711 7.201393 CCGCGCATCAAAAATATTTTTCTACAA 60.201 33.333 20.71 7.24 38.23 2.41
701 712 6.252441 CCGCGCATCAAAAATATTTTTCTACA 59.748 34.615 20.71 8.00 38.23 2.74
702 713 6.291585 CCCGCGCATCAAAAATATTTTTCTAC 60.292 38.462 20.71 11.18 38.23 2.59
768 779 6.216801 ACCCTTTTTACTCCACAGTTTTTC 57.783 37.500 0.00 0.00 33.62 2.29
773 784 5.249852 TGCTATACCCTTTTTACTCCACAGT 59.750 40.000 0.00 0.00 36.55 3.55
803 814 4.106925 CCCTGCCTGCCTCCAGTC 62.107 72.222 0.00 0.00 37.38 3.51
855 869 2.288025 GGGCCCACCGTCTTGACTA 61.288 63.158 19.95 0.00 36.48 2.59
888 902 1.344496 GGATGGGAAAGGAGGAGAGGA 60.344 57.143 0.00 0.00 0.00 3.71
893 907 1.522900 GGATGGATGGGAAAGGAGGA 58.477 55.000 0.00 0.00 0.00 3.71
894 908 0.480252 GGGATGGATGGGAAAGGAGG 59.520 60.000 0.00 0.00 0.00 4.30
918 932 2.526304 TTGTTCTCACTGGGAGTTCG 57.474 50.000 6.84 0.00 44.40 3.95
923 937 1.768275 TCTGCTTTGTTCTCACTGGGA 59.232 47.619 0.00 0.00 0.00 4.37
924 938 2.260844 TCTGCTTTGTTCTCACTGGG 57.739 50.000 0.00 0.00 0.00 4.45
925 939 3.879295 TCTTTCTGCTTTGTTCTCACTGG 59.121 43.478 0.00 0.00 0.00 4.00
926 940 5.490139 TTCTTTCTGCTTTGTTCTCACTG 57.510 39.130 0.00 0.00 0.00 3.66
927 941 5.447818 CGTTTCTTTCTGCTTTGTTCTCACT 60.448 40.000 0.00 0.00 0.00 3.41
928 942 4.730521 CGTTTCTTTCTGCTTTGTTCTCAC 59.269 41.667 0.00 0.00 0.00 3.51
929 943 4.730613 GCGTTTCTTTCTGCTTTGTTCTCA 60.731 41.667 0.00 0.00 0.00 3.27
934 948 1.268539 CGGCGTTTCTTTCTGCTTTGT 60.269 47.619 0.00 0.00 0.00 2.83
937 951 1.282875 GCGGCGTTTCTTTCTGCTT 59.717 52.632 9.37 0.00 0.00 3.91
1101 1143 4.186077 TCTATCTAGAGTGAAGGGGGTG 57.814 50.000 0.00 0.00 0.00 4.61
1102 1144 4.202738 GGATCTATCTAGAGTGAAGGGGGT 60.203 50.000 0.00 0.00 35.50 4.95
1119 1166 4.202727 CCTAGGGAAGAGGTCATGGATCTA 60.203 50.000 0.00 0.00 0.00 1.98
1129 1176 1.433592 ACACACTCCTAGGGAAGAGGT 59.566 52.381 9.46 1.73 35.40 3.85
1131 1178 2.498078 GGAACACACTCCTAGGGAAGAG 59.502 54.545 9.46 0.73 36.16 2.85
1139 1186 1.347707 CAAGGCAGGAACACACTCCTA 59.652 52.381 0.00 0.00 44.46 2.94
1185 1232 2.041115 TCGACTCCGAGCTGGTCAG 61.041 63.158 7.70 0.32 40.30 3.51
1218 1265 0.884514 TCAGACCTTGCAGACGAGAG 59.115 55.000 0.00 0.00 0.00 3.20
1260 1375 3.613910 GCGCCCTTTGCAAAGAAAAGATA 60.614 43.478 35.25 0.90 41.33 1.98
1304 1420 6.451064 AGCCGGGAGACAAATTTATTTAAG 57.549 37.500 2.18 0.00 0.00 1.85
1305 1421 6.403855 CGAAGCCGGGAGACAAATTTATTTAA 60.404 38.462 2.18 0.00 0.00 1.52
1394 1510 8.456940 CACCAGTATATATATCAGATAGGGGGA 58.543 40.741 0.00 0.00 0.00 4.81
1432 1548 1.155889 CGCTTGATAGTTGTGGCACA 58.844 50.000 17.96 17.96 0.00 4.57
1433 1549 1.128692 GACGCTTGATAGTTGTGGCAC 59.871 52.381 11.55 11.55 0.00 5.01
1434 1550 1.270571 TGACGCTTGATAGTTGTGGCA 60.271 47.619 0.00 0.00 0.00 4.92
1477 1597 8.376270 GCACTAGAGTAAACCATTAGGGAATAT 58.624 37.037 0.00 0.00 41.15 1.28
1521 1641 2.029470 AGGAGCATAATCTAGAGCGCAC 60.029 50.000 11.47 2.25 0.00 5.34
1565 1688 3.748048 CAGAAAGAGTCGAGCCATTTCAA 59.252 43.478 12.26 0.00 33.36 2.69
1654 1777 2.961062 GCCTGATGTCCTATTGCCAATT 59.039 45.455 0.00 0.00 0.00 2.32
1660 1784 5.874895 CATACATGCCTGATGTCCTATTG 57.125 43.478 0.00 0.00 41.91 1.90
1676 1800 7.226441 ACAGTTATACATGTGGATGCATACAT 58.774 34.615 16.33 12.10 39.98 2.29
1719 1847 2.922740 ATCATTGGATTGGCAATGGC 57.077 45.000 19.07 3.73 38.81 4.40
1722 1850 5.607592 TGGGAAATATCATTGGATTGGCAAT 59.392 36.000 13.54 13.54 34.89 3.56
1760 1891 5.855395 GCTGCAGAAAACAGAAAGTATTGAG 59.145 40.000 20.43 0.00 37.32 3.02
1794 1925 1.234821 GACTGATTTGCCAACCGTCA 58.765 50.000 0.00 0.00 0.00 4.35
2000 2131 0.606401 CCAGCCACCAACACTACCAG 60.606 60.000 0.00 0.00 0.00 4.00
2005 2136 1.331214 CATTTCCAGCCACCAACACT 58.669 50.000 0.00 0.00 0.00 3.55
2012 2143 2.134789 ATCAGACCATTTCCAGCCAC 57.865 50.000 0.00 0.00 0.00 5.01
2031 2162 5.159209 GTCTCGTTCCAAGAAGACGAATTA 58.841 41.667 0.00 0.00 44.09 1.40
2113 2244 0.652592 GTGCACATATCGTCACTGGC 59.347 55.000 13.17 0.00 0.00 4.85
2116 2247 3.002791 CCAAAGTGCACATATCGTCACT 58.997 45.455 21.04 0.00 37.50 3.41
2118 2249 2.741517 CACCAAAGTGCACATATCGTCA 59.258 45.455 21.04 0.00 37.14 4.35
2178 2309 2.439409 CAAATCAGCCCATGTGACTCA 58.561 47.619 0.00 0.00 0.00 3.41
2224 2360 6.920569 ACAAAAGTACTTCAGTGTTACCAG 57.079 37.500 8.95 0.00 0.00 4.00
2249 2385 3.247173 GCAACCAAATTTTCATGCAACGA 59.753 39.130 11.84 0.00 34.10 3.85
2266 2402 2.544267 GTGTCAGACTGTTAGTGCAACC 59.456 50.000 1.59 0.00 37.80 3.77
2299 2435 4.944619 TGGTAGCATCTATCTTCTGGTG 57.055 45.455 0.00 0.00 0.00 4.17
2300 2436 5.150715 TCATGGTAGCATCTATCTTCTGGT 58.849 41.667 3.96 0.00 0.00 4.00
2312 2448 1.491754 TGGCAGTGATCATGGTAGCAT 59.508 47.619 0.40 0.40 0.00 3.79
2381 2517 0.466189 CCACAACAGCCAGAGTGGTT 60.466 55.000 0.00 0.00 44.95 3.67
2390 2526 1.067916 CAGCCAAACCACAACAGCC 59.932 57.895 0.00 0.00 0.00 4.85
2474 2610 0.177141 TCCATAGCGGTGGCACTAAC 59.823 55.000 18.45 7.26 43.41 2.34
2561 2697 0.035820 TACCACCCGTCTTGGCATTC 60.036 55.000 0.00 0.00 37.69 2.67
2573 2709 1.277273 GTTCCACTGTAGGTACCACCC 59.723 57.143 15.94 1.34 39.75 4.61
2648 2784 7.616313 TCTCAGAGTAGAAATCCTTTTTCCTC 58.384 38.462 0.00 0.00 0.00 3.71
2717 2853 5.981315 GCCATGATCATAACAACATCCTTTG 59.019 40.000 8.15 0.00 0.00 2.77
2783 2919 3.503800 ATATGATGCAGCCACACATCT 57.496 42.857 0.00 0.00 42.57 2.90
2931 3068 7.201974 CGGAGGGAGTATTACTTTCCAAATAGA 60.202 40.741 16.58 0.00 32.50 1.98
2949 3086 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2950 3087 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2951 3088 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2952 3089 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2953 3090 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2954 3091 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2955 3092 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2956 3093 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2957 3094 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2958 3095 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2959 3096 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
2960 3097 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
2967 3104 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
3005 3142 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
3013 3150 8.980832 AGATAAAAGGGGATGTATCTAGATGT 57.019 34.615 15.79 1.25 32.73 3.06
3019 3156 9.225682 TCAAACTAGATAAAAGGGGATGTATCT 57.774 33.333 0.00 0.00 37.18 1.98
3021 3158 9.799106 CATCAAACTAGATAAAAGGGGATGTAT 57.201 33.333 0.00 0.00 0.00 2.29
3022 3159 8.998814 TCATCAAACTAGATAAAAGGGGATGTA 58.001 33.333 0.00 0.00 32.47 2.29
3023 3160 7.775561 GTCATCAAACTAGATAAAAGGGGATGT 59.224 37.037 0.00 0.00 32.47 3.06
3024 3161 7.775093 TGTCATCAAACTAGATAAAAGGGGATG 59.225 37.037 0.00 0.00 0.00 3.51
3025 3162 7.872138 TGTCATCAAACTAGATAAAAGGGGAT 58.128 34.615 0.00 0.00 0.00 3.85
3026 3163 7.265599 TGTCATCAAACTAGATAAAAGGGGA 57.734 36.000 0.00 0.00 0.00 4.81
3027 3164 7.611855 ACTTGTCATCAAACTAGATAAAAGGGG 59.388 37.037 0.00 0.00 32.87 4.79
3028 3165 8.567285 ACTTGTCATCAAACTAGATAAAAGGG 57.433 34.615 0.00 0.00 32.87 3.95
3034 3171 9.529325 CGGAAATACTTGTCATCAAACTAGATA 57.471 33.333 0.00 0.00 32.87 1.98
3035 3172 7.495934 CCGGAAATACTTGTCATCAAACTAGAT 59.504 37.037 0.00 0.00 32.87 1.98
3036 3173 6.816640 CCGGAAATACTTGTCATCAAACTAGA 59.183 38.462 0.00 0.00 32.87 2.43
3037 3174 6.816640 TCCGGAAATACTTGTCATCAAACTAG 59.183 38.462 0.00 0.00 32.87 2.57
3038 3175 6.592607 GTCCGGAAATACTTGTCATCAAACTA 59.407 38.462 5.23 0.00 32.87 2.24
3039 3176 5.411669 GTCCGGAAATACTTGTCATCAAACT 59.588 40.000 5.23 0.00 32.87 2.66
3040 3177 5.628134 GTCCGGAAATACTTGTCATCAAAC 58.372 41.667 5.23 0.00 32.87 2.93
3041 3178 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3042 3179 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3043 3180 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3044 3181 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3045 3182 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3046 3183 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3047 3184 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3048 3185 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3049 3186 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3050 3187 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3051 3188 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3052 3189 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3053 3190 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3054 3191 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3055 3192 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
3056 3193 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
3057 3194 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
3058 3195 1.379576 AACTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
3059 3196 0.679002 TCAACTACTCCCTCCGTCCG 60.679 60.000 0.00 0.00 0.00 4.79
3060 3197 1.777941 ATCAACTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
3061 3198 4.737055 GCTTTATCAACTACTCCCTCCGTC 60.737 50.000 0.00 0.00 0.00 4.79
3062 3199 3.132467 GCTTTATCAACTACTCCCTCCGT 59.868 47.826 0.00 0.00 0.00 4.69
3063 3200 3.132289 TGCTTTATCAACTACTCCCTCCG 59.868 47.826 0.00 0.00 0.00 4.63
3064 3201 4.443621 GTGCTTTATCAACTACTCCCTCC 58.556 47.826 0.00 0.00 0.00 4.30
3065 3202 4.162509 AGGTGCTTTATCAACTACTCCCTC 59.837 45.833 0.00 0.00 31.06 4.30
3066 3203 4.080863 CAGGTGCTTTATCAACTACTCCCT 60.081 45.833 0.00 0.00 31.06 4.20
3067 3204 4.192317 CAGGTGCTTTATCAACTACTCCC 58.808 47.826 0.00 0.00 31.06 4.30
3068 3205 4.631813 CACAGGTGCTTTATCAACTACTCC 59.368 45.833 0.00 0.00 31.06 3.85
3069 3206 4.631813 CCACAGGTGCTTTATCAACTACTC 59.368 45.833 0.00 0.00 31.06 2.59
3070 3207 4.041691 ACCACAGGTGCTTTATCAACTACT 59.958 41.667 0.00 0.00 32.98 2.57
3071 3208 4.324267 ACCACAGGTGCTTTATCAACTAC 58.676 43.478 0.00 0.00 32.98 2.73
3072 3209 4.286032 AGACCACAGGTGCTTTATCAACTA 59.714 41.667 0.00 0.00 35.25 2.24
3073 3210 3.073062 AGACCACAGGTGCTTTATCAACT 59.927 43.478 0.00 0.00 35.25 3.16
3074 3211 3.412386 AGACCACAGGTGCTTTATCAAC 58.588 45.455 0.00 0.00 35.25 3.18
3075 3212 3.788227 AGACCACAGGTGCTTTATCAA 57.212 42.857 0.00 0.00 35.25 2.57
3202 3346 7.989416 TTTCCCAAGAATTAAACGTCTGTAT 57.011 32.000 0.00 0.00 0.00 2.29
3209 3359 5.348451 CCAGCATTTTCCCAAGAATTAAACG 59.652 40.000 0.00 0.00 0.00 3.60
3293 3445 4.571984 ACCTACAACAGTAAAACGGTGAAC 59.428 41.667 0.00 0.00 0.00 3.18
3371 3552 6.910433 GTGTTTCAATAGAACACAAACGACAT 59.090 34.615 13.46 0.00 36.58 3.06
3375 3556 5.260140 ACGTGTTTCAATAGAACACAAACG 58.740 37.500 17.14 8.05 36.47 3.60
3390 3571 8.159709 GCCAAATGAATTAATGTTACGTGTTTC 58.840 33.333 0.00 0.00 0.00 2.78
3396 3577 7.250569 AGACAGCCAAATGAATTAATGTTACG 58.749 34.615 0.00 0.00 0.00 3.18
3431 3618 6.266168 TGGTTGTGATTAAATGTAAGGCTG 57.734 37.500 0.00 0.00 0.00 4.85
3449 3636 6.590292 CCGGTAAGTATGCTCTAATATGGTTG 59.410 42.308 0.00 0.00 0.00 3.77
3461 3648 1.861982 AGACCACCGGTAAGTATGCT 58.138 50.000 6.87 0.00 35.25 3.79
3496 3697 0.524862 GGCTTCACCTTGTCATGCAG 59.475 55.000 0.00 0.00 34.51 4.41
3612 3813 2.158900 CCTCTCGTGCATTACTTCCCAT 60.159 50.000 0.00 0.00 0.00 4.00
3663 3864 0.391927 TGTAAATGAACTCGGGGGCG 60.392 55.000 0.00 0.00 0.00 6.13
3705 3906 1.211969 GCCGAAGCTGTAGACGTCA 59.788 57.895 19.50 0.48 35.50 4.35
3777 3978 3.325293 AATATAGTCTGCCATCCTGCG 57.675 47.619 0.00 0.00 0.00 5.18
3780 3981 6.243900 CCATTCAAATATAGTCTGCCATCCT 58.756 40.000 0.00 0.00 0.00 3.24
3807 4008 1.202758 TGTGATTGAACCAGAGGCGTT 60.203 47.619 0.00 0.00 0.00 4.84
3819 4020 0.392863 CCAGATGCCGGTGTGATTGA 60.393 55.000 1.90 0.00 0.00 2.57
4032 4233 0.541392 ATGGCAGCATCGGTGAAGTA 59.459 50.000 0.00 0.00 32.22 2.24
4138 4344 1.071471 CTTGGGTCACTCCACGCTT 59.929 57.895 0.00 0.00 36.38 4.68
4161 4367 0.671163 TTGCGCTTACGGTTACAGGG 60.671 55.000 9.73 0.00 40.57 4.45
4214 4420 3.134262 GGGTTTAGACATCCAGTACCCTC 59.866 52.174 0.00 0.00 40.43 4.30
4220 4426 2.537143 ACGAGGGTTTAGACATCCAGT 58.463 47.619 0.00 0.00 0.00 4.00
4226 4432 2.549349 GGCAAGAACGAGGGTTTAGACA 60.549 50.000 0.00 0.00 36.24 3.41
4259 4466 1.304879 GCTGGGGTACAAATGGCCA 60.305 57.895 8.56 8.56 0.00 5.36
4335 4542 2.826725 ACAGCTTCTACTGGGTAGACAC 59.173 50.000 6.88 3.35 43.65 3.67
4343 4552 5.911752 ACATAGATGAACAGCTTCTACTGG 58.088 41.667 0.00 0.00 42.21 4.00
4358 4567 9.373750 CATTAACACGCAGAAAATACATAGATG 57.626 33.333 0.00 0.00 0.00 2.90
4370 4579 1.535028 CACTGGCATTAACACGCAGAA 59.465 47.619 0.00 0.00 0.00 3.02
4375 4584 2.412870 TGAGACACTGGCATTAACACG 58.587 47.619 0.00 0.00 0.00 4.49
4376 4585 4.002982 TCATGAGACACTGGCATTAACAC 58.997 43.478 0.00 0.00 0.00 3.32
4381 4590 7.012661 TGATATATCATGAGACACTGGCATT 57.987 36.000 11.49 0.00 0.00 3.56
4405 4614 6.978659 TGAAGCTCGACGATAAGTTGATAAAT 59.021 34.615 0.00 0.00 42.10 1.40
4409 4618 4.371855 TGAAGCTCGACGATAAGTTGAT 57.628 40.909 0.00 0.00 42.10 2.57
4422 4631 9.214953 GTTCTCAAATTGTTAATATGAAGCTCG 57.785 33.333 0.00 0.00 0.00 5.03
4435 4644 7.543868 TCAACATGTTTTCGTTCTCAAATTGTT 59.456 29.630 8.77 0.00 0.00 2.83
4443 4654 8.443160 TGATATTCTCAACATGTTTTCGTTCTC 58.557 33.333 8.77 2.75 0.00 2.87
4488 4699 7.952671 ACTTCACTAGTTACTTCATGAGTTCA 58.047 34.615 0.00 0.00 39.86 3.18
4537 4940 0.972883 ACCTCCAGTTCACTCTGCTC 59.027 55.000 0.00 0.00 34.47 4.26
4546 4949 2.424246 CCGTCTCTTAGACCTCCAGTTC 59.576 54.545 1.63 0.00 42.12 3.01
4555 4958 1.910688 CGAAAGCCCGTCTCTTAGAC 58.089 55.000 0.00 0.00 41.71 2.59
4644 5047 2.815647 GTCAGTAGCACGCAGGCC 60.816 66.667 0.00 0.00 0.00 5.19
4645 5048 2.048222 TGTCAGTAGCACGCAGGC 60.048 61.111 0.00 0.00 0.00 4.85
4650 5053 1.733041 CGGTGGTGTCAGTAGCACG 60.733 63.158 0.00 0.00 46.93 5.34
4752 5161 0.528470 CACTGGACGAGAAGACCTCC 59.472 60.000 0.00 0.00 38.71 4.30
4931 5370 0.322906 CCAACCCAGGGAGAAGAAGC 60.323 60.000 14.54 0.00 0.00 3.86
4932 5371 0.322906 GCCAACCCAGGGAGAAGAAG 60.323 60.000 14.54 0.00 0.00 2.85
4933 5372 0.772124 AGCCAACCCAGGGAGAAGAA 60.772 55.000 14.54 0.00 0.00 2.52
4934 5373 1.151810 AGCCAACCCAGGGAGAAGA 60.152 57.895 14.54 0.00 0.00 2.87
4935 5374 1.001641 CAGCCAACCCAGGGAGAAG 60.002 63.158 14.54 0.00 0.00 2.85
4936 5375 2.538141 CCAGCCAACCCAGGGAGAA 61.538 63.158 14.54 0.00 0.00 2.87
4937 5376 2.935481 CCAGCCAACCCAGGGAGA 60.935 66.667 14.54 0.00 0.00 3.71
4938 5377 4.052518 CCCAGCCAACCCAGGGAG 62.053 72.222 14.54 3.82 44.30 4.30
4941 5380 4.052518 CTCCCCAGCCAACCCAGG 62.053 72.222 0.00 0.00 0.00 4.45
4942 5381 4.748144 GCTCCCCAGCCAACCCAG 62.748 72.222 0.00 0.00 40.14 4.45
4950 5389 1.377856 GAAAGACAGGCTCCCCAGC 60.378 63.158 0.00 0.00 46.06 4.85
4951 5390 1.078848 CGAAAGACAGGCTCCCCAG 60.079 63.158 0.00 0.00 0.00 4.45
4952 5391 2.592993 CCGAAAGACAGGCTCCCCA 61.593 63.158 0.00 0.00 0.00 4.96
4953 5392 1.838073 TTCCGAAAGACAGGCTCCCC 61.838 60.000 0.00 0.00 0.00 4.81
4954 5393 0.673956 GTTCCGAAAGACAGGCTCCC 60.674 60.000 0.00 0.00 0.00 4.30
4955 5394 0.321996 AGTTCCGAAAGACAGGCTCC 59.678 55.000 0.00 0.00 0.00 4.70
4956 5395 1.715993 GAGTTCCGAAAGACAGGCTC 58.284 55.000 0.00 0.00 0.00 4.70
4957 5396 0.038159 CGAGTTCCGAAAGACAGGCT 60.038 55.000 0.00 0.00 41.76 4.58


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

AutoCloner maintained by Alex Coulton.