Multiple sequence alignment - TraesCS2D01G135800

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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 TraesCS2D01G135800 chr2D 100.000 4525 0 0 1 4525 79882791 79878267 0.000000e+00 8357.0
1 TraesCS2D01G135800 chr2D 93.880 2745 122 27 1807 4525 42884298 42887022 0.000000e+00 4096.0
2 TraesCS2D01G135800 chr2D 98.039 51 1 0 503 553 17142722 17142772 6.230000e-14 89.8
3 TraesCS2D01G135800 chr2B 93.652 3560 144 40 632 4157 131294401 131290890 0.000000e+00 5247.0
4 TraesCS2D01G135800 chr2B 97.043 372 6 2 4154 4525 131290788 131290422 4.970000e-174 621.0
5 TraesCS2D01G135800 chr2B 82.684 231 30 3 37 258 131295610 131295381 3.570000e-46 196.0
6 TraesCS2D01G135800 chr2A 92.083 2602 124 38 681 3260 80483508 80480967 0.000000e+00 3589.0
7 TraesCS2D01G135800 chr2A 92.344 1267 68 17 3258 4520 80480844 80479603 0.000000e+00 1775.0
8 TraesCS2D01G135800 chr2A 81.975 405 44 16 33 411 80484156 80483755 2.630000e-82 316.0
9 TraesCS2D01G135800 chr2A 96.078 51 2 0 503 553 18623115 18623165 2.900000e-12 84.2
10 TraesCS2D01G135800 chr3A 90.169 590 41 7 1426 2005 592136674 592136092 0.000000e+00 752.0
11 TraesCS2D01G135800 chr3A 87.064 688 46 16 1426 2103 592201375 592200721 0.000000e+00 737.0
12 TraesCS2D01G135800 chr3A 94.915 59 3 0 2045 2103 592136078 592136020 4.820000e-15 93.5
13 TraesCS2D01G135800 chr7D 98.077 52 1 0 504 555 526495537 526495588 1.730000e-14 91.6
14 TraesCS2D01G135800 chr7D 94.340 53 3 0 503 555 34754065 34754117 1.040000e-11 82.4
15 TraesCS2D01G135800 chr7D 94.444 54 2 1 502 555 104453471 104453523 1.040000e-11 82.4
16 TraesCS2D01G135800 chr7D 94.340 53 3 0 503 555 596643512 596643460 1.040000e-11 82.4
17 TraesCS2D01G135800 chr4D 96.226 53 2 0 503 555 508008780 508008832 2.240000e-13 87.9
18 TraesCS2D01G135800 chr6B 97.959 49 1 0 509 557 18659393 18659345 8.070000e-13 86.1
19 TraesCS2D01G135800 chr3D 96.154 52 1 1 504 555 358187594 358187544 2.900000e-12 84.2
20 TraesCS2D01G135800 chr7B 80.392 102 14 4 425 521 609749191 609749091 6.280000e-09 73.1


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 TraesCS2D01G135800 chr2D 79878267 79882791 4524 True 8357.000000 8357 100.000000 1 4525 1 chr2D.!!$R1 4524
1 TraesCS2D01G135800 chr2D 42884298 42887022 2724 False 4096.000000 4096 93.880000 1807 4525 1 chr2D.!!$F2 2718
2 TraesCS2D01G135800 chr2B 131290422 131295610 5188 True 2021.333333 5247 91.126333 37 4525 3 chr2B.!!$R1 4488
3 TraesCS2D01G135800 chr2A 80479603 80484156 4553 True 1893.333333 3589 88.800667 33 4520 3 chr2A.!!$R1 4487
4 TraesCS2D01G135800 chr3A 592200721 592201375 654 True 737.000000 737 87.064000 1426 2103 1 chr3A.!!$R1 677
5 TraesCS2D01G135800 chr3A 592136020 592136674 654 True 422.750000 752 92.542000 1426 2103 2 chr3A.!!$R2 677

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
205 224 0.036388 ATTGCATTCCACGACGACCT 60.036 50.0 0.00 0.00 0.00 3.85 F
735 1591 0.179067 AACAGCCACCGAAAACGAGA 60.179 50.0 0.00 0.00 0.00 4.04 F
1355 2234 0.242825 TGTTCGAACTGGAGTAGCCG 59.757 55.0 27.32 0.00 40.66 5.52 F
2005 2908 0.026285 GCATCGACGCGTTAAATGCT 59.974 50.0 30.52 4.48 39.62 3.79 F
2793 3735 0.409092 ACCCCCATTGAAGCATCACA 59.591 50.0 0.00 0.00 34.61 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2876 0.036105 TCGATGCAGCACAGATGGTT 60.036 50.000 1.53 0.00 33.06 3.67 R
1976 2879 1.634753 CGTCGATGCAGCACAGATG 59.365 57.895 1.53 1.66 0.00 2.90 R
3104 4048 4.001652 TGCGGACCAAAATTGAACGTATA 58.998 39.130 0.00 0.00 0.00 1.47 R
3404 4478 0.674895 CCTCCAGAACAAAGCCCTCG 60.675 60.000 0.00 0.00 0.00 4.63 R
3946 5021 1.281899 GCAATCTGACTACGCCTCAC 58.718 55.000 0.00 0.00 0.00 3.51 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
19 20 4.308458 CGACTCGGCCACACCCAA 62.308 66.667 2.24 0.00 33.26 4.12
20 21 2.358737 GACTCGGCCACACCCAAG 60.359 66.667 2.24 0.00 33.26 3.61
21 22 4.643387 ACTCGGCCACACCCAAGC 62.643 66.667 2.24 0.00 33.26 4.01
27 28 4.722700 CCACACCCAAGCCCTCCG 62.723 72.222 0.00 0.00 0.00 4.63
28 29 4.722700 CACACCCAAGCCCTCCGG 62.723 72.222 0.00 0.00 0.00 5.14
52 53 2.864343 CTGTCCTTTAAATACTCCGGCG 59.136 50.000 0.00 0.00 0.00 6.46
83 86 0.326927 AACCCCCACTCAATACCACG 59.673 55.000 0.00 0.00 0.00 4.94
124 142 2.426023 GTCCAACTCCGCCACTGT 59.574 61.111 0.00 0.00 0.00 3.55
128 146 1.594293 CAACTCCGCCACTGTCGTT 60.594 57.895 0.00 0.00 0.00 3.85
137 155 0.456221 CCACTGTCGTTAGATCGCCT 59.544 55.000 0.00 0.00 0.00 5.52
142 160 2.086094 TGTCGTTAGATCGCCTACACA 58.914 47.619 0.00 0.00 0.00 3.72
158 176 2.688507 ACACATTTTCGACGAGCTCAT 58.311 42.857 15.40 0.00 0.00 2.90
192 211 3.133464 CCGCCACCACGATTGCAT 61.133 61.111 0.00 0.00 34.06 3.96
205 224 0.036388 ATTGCATTCCACGACGACCT 60.036 50.000 0.00 0.00 0.00 3.85
249 268 3.550656 GCCCAACGACAACGAGAG 58.449 61.111 0.00 0.00 42.66 3.20
292 317 3.545481 CGCCGCTCACGTCATGTC 61.545 66.667 0.00 0.00 37.70 3.06
398 1010 7.764331 ACTTCCTACGTGTAAAAACAACAATT 58.236 30.769 0.00 0.00 0.00 2.32
436 1048 8.752766 ACAATTTTGCTAAGTCTCAATTGATG 57.247 30.769 8.96 3.70 35.88 3.07
437 1049 8.362639 ACAATTTTGCTAAGTCTCAATTGATGT 58.637 29.630 8.96 2.27 35.88 3.06
438 1050 9.199982 CAATTTTGCTAAGTCTCAATTGATGTT 57.800 29.630 8.96 5.56 34.80 2.71
439 1051 8.752766 ATTTTGCTAAGTCTCAATTGATGTTG 57.247 30.769 8.96 0.00 0.00 3.33
440 1052 5.300969 TGCTAAGTCTCAATTGATGTTGC 57.699 39.130 8.96 9.43 0.00 4.17
441 1053 4.761227 TGCTAAGTCTCAATTGATGTTGCA 59.239 37.500 8.96 11.71 0.00 4.08
442 1054 5.416639 TGCTAAGTCTCAATTGATGTTGCAT 59.583 36.000 8.96 0.00 0.00 3.96
443 1055 5.742453 GCTAAGTCTCAATTGATGTTGCATG 59.258 40.000 8.96 0.00 0.00 4.06
444 1056 4.106029 AGTCTCAATTGATGTTGCATGC 57.894 40.909 11.82 11.82 0.00 4.06
445 1057 3.119245 AGTCTCAATTGATGTTGCATGCC 60.119 43.478 16.68 0.28 0.00 4.40
446 1058 3.093814 TCTCAATTGATGTTGCATGCCT 58.906 40.909 16.68 0.00 0.00 4.75
447 1059 3.512329 TCTCAATTGATGTTGCATGCCTT 59.488 39.130 16.68 0.00 0.00 4.35
448 1060 4.020928 TCTCAATTGATGTTGCATGCCTTT 60.021 37.500 16.68 0.00 0.00 3.11
449 1061 3.997681 TCAATTGATGTTGCATGCCTTTG 59.002 39.130 16.68 7.78 0.00 2.77
450 1062 3.965379 ATTGATGTTGCATGCCTTTGA 57.035 38.095 16.68 0.00 0.00 2.69
451 1063 3.965379 TTGATGTTGCATGCCTTTGAT 57.035 38.095 16.68 0.00 0.00 2.57
452 1064 3.513680 TGATGTTGCATGCCTTTGATC 57.486 42.857 16.68 9.85 0.00 2.92
453 1065 3.093814 TGATGTTGCATGCCTTTGATCT 58.906 40.909 16.68 0.00 0.00 2.75
454 1066 3.512329 TGATGTTGCATGCCTTTGATCTT 59.488 39.130 16.68 0.00 0.00 2.40
455 1067 3.306917 TGTTGCATGCCTTTGATCTTG 57.693 42.857 16.68 0.00 0.00 3.02
456 1068 1.997606 GTTGCATGCCTTTGATCTTGC 59.002 47.619 16.68 0.00 34.96 4.01
457 1069 1.258676 TGCATGCCTTTGATCTTGCA 58.741 45.000 16.68 0.00 39.83 4.08
458 1070 1.828595 TGCATGCCTTTGATCTTGCAT 59.171 42.857 16.68 0.29 44.79 3.96
462 1074 3.861276 TGCCTTTGATCTTGCATGAAG 57.139 42.857 6.36 0.00 0.00 3.02
463 1075 3.423749 TGCCTTTGATCTTGCATGAAGA 58.576 40.909 6.36 3.41 45.03 2.87
471 1083 3.062122 TCTTGCATGAAGATCAGTGCA 57.938 42.857 0.00 9.35 38.31 4.57
472 1084 3.414269 TCTTGCATGAAGATCAGTGCAA 58.586 40.909 19.08 19.08 42.58 4.08
473 1085 3.822167 TCTTGCATGAAGATCAGTGCAAA 59.178 39.130 20.00 12.53 43.30 3.68
474 1086 4.278919 TCTTGCATGAAGATCAGTGCAAAA 59.721 37.500 20.00 10.54 43.30 2.44
475 1087 4.794278 TGCATGAAGATCAGTGCAAAAT 57.206 36.364 10.55 0.00 37.68 1.82
476 1088 5.142061 TGCATGAAGATCAGTGCAAAATT 57.858 34.783 10.55 0.00 37.68 1.82
477 1089 5.543714 TGCATGAAGATCAGTGCAAAATTT 58.456 33.333 10.55 0.00 37.68 1.82
478 1090 5.992829 TGCATGAAGATCAGTGCAAAATTTT 59.007 32.000 10.55 0.00 37.68 1.82
479 1091 7.153315 TGCATGAAGATCAGTGCAAAATTTTA 58.847 30.769 2.44 0.00 37.68 1.52
480 1092 7.820386 TGCATGAAGATCAGTGCAAAATTTTAT 59.180 29.630 2.44 0.00 37.68 1.40
481 1093 8.662141 GCATGAAGATCAGTGCAAAATTTTATT 58.338 29.630 2.44 0.00 33.88 1.40
484 1096 9.985730 TGAAGATCAGTGCAAAATTTTATTCTT 57.014 25.926 2.44 4.90 0.00 2.52
518 1130 9.457436 CTCTCTTTCTTATATACTACTCCCTCC 57.543 40.741 0.00 0.00 0.00 4.30
519 1131 8.102047 TCTCTTTCTTATATACTACTCCCTCCG 58.898 40.741 0.00 0.00 0.00 4.63
520 1132 7.753630 TCTTTCTTATATACTACTCCCTCCGT 58.246 38.462 0.00 0.00 0.00 4.69
521 1133 8.884323 TCTTTCTTATATACTACTCCCTCCGTA 58.116 37.037 0.00 0.00 0.00 4.02
522 1134 9.512588 CTTTCTTATATACTACTCCCTCCGTAA 57.487 37.037 0.00 0.00 0.00 3.18
523 1135 9.866655 TTTCTTATATACTACTCCCTCCGTAAA 57.133 33.333 0.00 0.00 0.00 2.01
524 1136 8.854614 TCTTATATACTACTCCCTCCGTAAAC 57.145 38.462 0.00 0.00 0.00 2.01
525 1137 8.664079 TCTTATATACTACTCCCTCCGTAAACT 58.336 37.037 0.00 0.00 0.00 2.66
526 1138 9.950496 CTTATATACTACTCCCTCCGTAAACTA 57.050 37.037 0.00 0.00 0.00 2.24
533 1145 9.646522 ACTACTCCCTCCGTAAACTAATATAAA 57.353 33.333 0.00 0.00 0.00 1.40
536 1148 9.605275 ACTCCCTCCGTAAACTAATATAAAAAC 57.395 33.333 0.00 0.00 0.00 2.43
537 1149 8.647143 TCCCTCCGTAAACTAATATAAAAACG 57.353 34.615 0.00 0.00 0.00 3.60
538 1150 8.257306 TCCCTCCGTAAACTAATATAAAAACGT 58.743 33.333 0.00 0.00 0.00 3.99
539 1151 8.882736 CCCTCCGTAAACTAATATAAAAACGTT 58.117 33.333 0.00 0.00 0.00 3.99
560 1172 8.530269 ACGTTTAGATCACTACTTTACAAAGG 57.470 34.615 6.66 0.00 40.31 3.11
561 1173 7.601508 ACGTTTAGATCACTACTTTACAAAGGG 59.398 37.037 6.66 2.04 40.31 3.95
562 1174 7.816031 CGTTTAGATCACTACTTTACAAAGGGA 59.184 37.037 6.66 0.00 40.31 4.20
563 1175 9.152595 GTTTAGATCACTACTTTACAAAGGGAG 57.847 37.037 6.66 5.73 40.31 4.30
564 1176 6.936968 AGATCACTACTTTACAAAGGGAGT 57.063 37.500 6.66 6.27 40.31 3.85
565 1177 9.537852 TTAGATCACTACTTTACAAAGGGAGTA 57.462 33.333 6.66 0.00 40.31 2.59
566 1178 8.611051 AGATCACTACTTTACAAAGGGAGTAT 57.389 34.615 6.66 4.65 40.31 2.12
567 1179 8.478877 AGATCACTACTTTACAAAGGGAGTATG 58.521 37.037 6.66 0.49 40.31 2.39
568 1180 7.549147 TCACTACTTTACAAAGGGAGTATGT 57.451 36.000 6.66 0.00 40.31 2.29
569 1181 7.609056 TCACTACTTTACAAAGGGAGTATGTC 58.391 38.462 6.66 0.00 40.31 3.06
570 1182 7.453752 TCACTACTTTACAAAGGGAGTATGTCT 59.546 37.037 6.66 0.00 40.31 3.41
571 1183 8.095169 CACTACTTTACAAAGGGAGTATGTCTT 58.905 37.037 6.66 0.00 40.31 3.01
572 1184 8.095169 ACTACTTTACAAAGGGAGTATGTCTTG 58.905 37.037 6.66 0.00 40.31 3.02
573 1185 7.074653 ACTTTACAAAGGGAGTATGTCTTGA 57.925 36.000 6.66 0.00 40.31 3.02
574 1186 6.935208 ACTTTACAAAGGGAGTATGTCTTGAC 59.065 38.462 6.66 0.00 40.31 3.18
575 1187 6.681729 TTACAAAGGGAGTATGTCTTGACT 57.318 37.500 2.35 0.00 0.00 3.41
576 1188 7.786046 TTACAAAGGGAGTATGTCTTGACTA 57.214 36.000 2.35 0.00 0.00 2.59
577 1189 6.681729 ACAAAGGGAGTATGTCTTGACTAA 57.318 37.500 2.35 0.00 0.00 2.24
578 1190 6.702329 ACAAAGGGAGTATGTCTTGACTAAG 58.298 40.000 2.35 0.00 35.16 2.18
579 1191 6.497259 ACAAAGGGAGTATGTCTTGACTAAGA 59.503 38.462 2.35 0.00 40.53 2.10
588 1200 1.749634 TCTTGACTAAGACCTAGCCGC 59.250 52.381 0.00 0.00 37.99 6.53
589 1201 1.476891 CTTGACTAAGACCTAGCCGCA 59.523 52.381 0.00 0.00 35.92 5.69
590 1202 1.776662 TGACTAAGACCTAGCCGCAT 58.223 50.000 0.00 0.00 0.00 4.73
591 1203 1.681793 TGACTAAGACCTAGCCGCATC 59.318 52.381 0.00 0.00 0.00 3.91
651 1465 1.134907 AGTAGACATTAACACGGCCGG 60.135 52.381 31.76 20.69 0.00 6.13
672 1486 5.470845 GGACATCACCGATTTAAAGTCAG 57.529 43.478 0.00 0.00 0.00 3.51
674 1488 5.063564 GGACATCACCGATTTAAAGTCAGTC 59.936 44.000 0.00 0.00 0.00 3.51
675 1489 5.547465 ACATCACCGATTTAAAGTCAGTCA 58.453 37.500 0.00 0.00 0.00 3.41
676 1490 5.408604 ACATCACCGATTTAAAGTCAGTCAC 59.591 40.000 0.00 0.00 0.00 3.67
677 1491 4.312443 TCACCGATTTAAAGTCAGTCACC 58.688 43.478 0.00 0.00 0.00 4.02
678 1492 3.122948 CACCGATTTAAAGTCAGTCACCG 59.877 47.826 0.00 0.00 0.00 4.94
679 1493 3.006110 ACCGATTTAAAGTCAGTCACCGA 59.994 43.478 0.00 0.00 0.00 4.69
698 1554 4.165779 CCGAAAATGTGGGAGAAAATTCG 58.834 43.478 0.00 0.00 38.41 3.34
735 1591 0.179067 AACAGCCACCGAAAACGAGA 60.179 50.000 0.00 0.00 0.00 4.04
773 1630 3.126000 GCAAATGAGAAGGAAACGGAGAG 59.874 47.826 0.00 0.00 0.00 3.20
793 1655 2.006888 GATTTCGAGACGCAATTGGGA 58.993 47.619 27.32 4.96 0.00 4.37
797 1659 2.432444 TCGAGACGCAATTGGGAAAAT 58.568 42.857 27.32 6.28 0.00 1.82
932 1796 2.554893 CACCTAATACGCTCTCCTCTCC 59.445 54.545 0.00 0.00 0.00 3.71
1053 1920 2.520741 GCGGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1290 2169 2.015227 CTCTTCCGCTCTCCTCCTGC 62.015 65.000 0.00 0.00 0.00 4.85
1295 2174 3.394836 GCTCTCCTCCTGCCGGTT 61.395 66.667 1.90 0.00 0.00 4.44
1296 2175 2.581354 CTCTCCTCCTGCCGGTTG 59.419 66.667 1.90 0.00 0.00 3.77
1298 2177 4.785453 CTCCTCCTGCCGGTTGCC 62.785 72.222 1.90 0.00 40.16 4.52
1312 2191 0.598065 GTTGCCTTGATTGCTCCGTT 59.402 50.000 0.00 0.00 0.00 4.44
1338 2217 3.343788 GACTGCGCTCGCCTAGTGT 62.344 63.158 9.73 3.22 41.09 3.55
1350 2229 1.272769 GCCTAGTGTTCGAACTGGAGT 59.727 52.381 27.32 13.67 30.63 3.85
1355 2234 0.242825 TGTTCGAACTGGAGTAGCCG 59.757 55.000 27.32 0.00 40.66 5.52
1441 2324 3.418684 TTCCTTTCCTTTTCCTCTCCG 57.581 47.619 0.00 0.00 0.00 4.63
1522 2409 2.202544 GACCAGCGAGTGAGCGAG 60.203 66.667 0.00 0.00 43.00 5.03
1599 2487 3.137484 TGCTGTCACGGCAATAGTC 57.863 52.632 9.50 0.00 43.23 2.59
1621 2509 0.896019 TGGATAGCTCCTCGGCTAGC 60.896 60.000 6.04 6.04 46.13 3.42
1664 2552 5.209977 CAACATGGCAATCAGATAATGTCG 58.790 41.667 0.00 0.00 0.00 4.35
1705 2600 6.051717 GCTGACATGTATCACTTCCAGTAAT 58.948 40.000 0.00 0.00 0.00 1.89
1706 2601 7.210174 GCTGACATGTATCACTTCCAGTAATA 58.790 38.462 0.00 0.00 0.00 0.98
1707 2602 7.383572 GCTGACATGTATCACTTCCAGTAATAG 59.616 40.741 0.00 0.00 0.00 1.73
1744 2639 5.169992 TCTGGATGGGATAATGTGCTATG 57.830 43.478 0.00 0.00 0.00 2.23
1870 2767 4.240096 GCAACCAAACATCTGAATTCTGG 58.760 43.478 11.89 8.91 0.00 3.86
1881 2778 2.227388 CTGAATTCTGGAACCAGCACAC 59.773 50.000 15.20 8.04 43.31 3.82
1903 2801 5.466728 CACCTCTGTATGATAATCCAAACCG 59.533 44.000 0.00 0.00 0.00 4.44
1904 2802 4.997395 CCTCTGTATGATAATCCAAACCGG 59.003 45.833 0.00 0.00 0.00 5.28
1954 2857 3.391296 AGTAACTCAAAGTTGCTCTGGGA 59.609 43.478 4.83 0.00 45.89 4.37
1973 2876 7.350382 TCTGGGATTTTAGTATTATGGTGCAA 58.650 34.615 0.00 0.00 0.00 4.08
1976 2879 7.147811 TGGGATTTTAGTATTATGGTGCAAACC 60.148 37.037 0.00 0.00 0.00 3.27
2005 2908 0.026285 GCATCGACGCGTTAAATGCT 59.974 50.000 30.52 4.48 39.62 3.79
2007 2910 2.285371 GCATCGACGCGTTAAATGCTTA 60.285 45.455 30.52 7.24 39.62 3.09
2008 2911 3.603857 GCATCGACGCGTTAAATGCTTAT 60.604 43.478 30.52 8.82 39.62 1.73
2009 2912 3.562781 TCGACGCGTTAAATGCTTATG 57.437 42.857 15.53 0.00 0.00 1.90
2010 2913 2.026990 CGACGCGTTAAATGCTTATGC 58.973 47.619 15.53 0.00 40.20 3.14
2021 2924 2.284754 TGCTTATGCACTTGGTTCCA 57.715 45.000 0.00 0.00 45.31 3.53
2022 2925 1.885887 TGCTTATGCACTTGGTTCCAC 59.114 47.619 0.00 0.00 45.31 4.02
2023 2926 1.885887 GCTTATGCACTTGGTTCCACA 59.114 47.619 0.00 0.00 39.41 4.17
2024 2927 2.493278 GCTTATGCACTTGGTTCCACAT 59.507 45.455 0.00 0.00 39.41 3.21
2025 2928 3.056607 GCTTATGCACTTGGTTCCACATT 60.057 43.478 0.00 0.00 39.41 2.71
2026 2929 4.561326 GCTTATGCACTTGGTTCCACATTT 60.561 41.667 0.00 0.00 39.41 2.32
2027 2930 2.886862 TGCACTTGGTTCCACATTTG 57.113 45.000 0.00 0.00 0.00 2.32
2028 2931 2.382882 TGCACTTGGTTCCACATTTGA 58.617 42.857 0.00 0.00 0.00 2.69
2029 2932 2.964464 TGCACTTGGTTCCACATTTGAT 59.036 40.909 0.00 0.00 0.00 2.57
2030 2933 3.387374 TGCACTTGGTTCCACATTTGATT 59.613 39.130 0.00 0.00 0.00 2.57
2031 2934 4.141756 TGCACTTGGTTCCACATTTGATTT 60.142 37.500 0.00 0.00 0.00 2.17
2032 2935 4.815846 GCACTTGGTTCCACATTTGATTTT 59.184 37.500 0.00 0.00 0.00 1.82
2033 2936 5.050159 GCACTTGGTTCCACATTTGATTTTC 60.050 40.000 0.00 0.00 0.00 2.29
2034 2937 6.047870 CACTTGGTTCCACATTTGATTTTCA 58.952 36.000 0.00 0.00 0.00 2.69
2035 2938 6.018832 CACTTGGTTCCACATTTGATTTTCAC 60.019 38.462 0.00 0.00 0.00 3.18
2036 2939 5.867903 TGGTTCCACATTTGATTTTCACT 57.132 34.783 0.00 0.00 0.00 3.41
2037 2940 6.968263 TGGTTCCACATTTGATTTTCACTA 57.032 33.333 0.00 0.00 0.00 2.74
2038 2941 6.744112 TGGTTCCACATTTGATTTTCACTAC 58.256 36.000 0.00 0.00 0.00 2.73
2039 2942 6.549364 TGGTTCCACATTTGATTTTCACTACT 59.451 34.615 0.00 0.00 0.00 2.57
2040 2943 7.069331 TGGTTCCACATTTGATTTTCACTACTT 59.931 33.333 0.00 0.00 0.00 2.24
2041 2944 7.382218 GGTTCCACATTTGATTTTCACTACTTG 59.618 37.037 0.00 0.00 0.00 3.16
2042 2945 7.581213 TCCACATTTGATTTTCACTACTTGT 57.419 32.000 0.00 0.00 0.00 3.16
2043 2946 8.684386 TCCACATTTGATTTTCACTACTTGTA 57.316 30.769 0.00 0.00 0.00 2.41
2066 3005 3.805422 TGAACGTTGTGTCCTATTGTGTC 59.195 43.478 5.00 0.00 0.00 3.67
2177 3116 2.898705 AGAGTTTAGGATGCGCTTCTG 58.101 47.619 21.05 0.00 0.00 3.02
2542 3481 4.905429 TCATGCTACAGTGGCTTTCTAAA 58.095 39.130 10.64 0.00 0.00 1.85
2578 3517 8.076178 GTCTATTGACAACACTTTGCTTAATGT 58.924 33.333 2.19 0.00 42.48 2.71
2580 3519 6.449635 TTGACAACACTTTGCTTAATGTCT 57.550 33.333 0.00 0.00 37.27 3.41
2639 3578 6.380274 TGGACTCTTTGATGGTAAGTAGGTAG 59.620 42.308 0.00 0.00 0.00 3.18
2654 3593 6.054860 AGTAGGTAGCATTCTGTCATTGTT 57.945 37.500 0.00 0.00 0.00 2.83
2666 3605 9.748708 CATTCTGTCATTGTTTCTTTTCCTTAA 57.251 29.630 0.00 0.00 0.00 1.85
2793 3735 0.409092 ACCCCCATTGAAGCATCACA 59.591 50.000 0.00 0.00 34.61 3.58
2805 3747 3.572632 AGCATCACATACAGCCTCATT 57.427 42.857 0.00 0.00 0.00 2.57
2812 3754 4.225042 TCACATACAGCCTCATTTACACCT 59.775 41.667 0.00 0.00 0.00 4.00
2813 3755 4.572389 CACATACAGCCTCATTTACACCTC 59.428 45.833 0.00 0.00 0.00 3.85
2924 3868 7.711772 TGGTACGAGTTTGAATAAGTTTCTTCA 59.288 33.333 0.00 0.00 0.00 3.02
2934 3878 9.453572 TTGAATAAGTTTCTTCATAGTGCAGAT 57.546 29.630 0.00 0.00 31.83 2.90
3104 4048 9.419297 ACGTATTAGTATTATGTCAATTCGCAT 57.581 29.630 0.00 0.00 0.00 4.73
3249 4194 5.680619 TGTAGTCAACACCACTGAATTTCT 58.319 37.500 0.00 0.00 31.43 2.52
3264 4337 7.499438 CTGAATTTCTCAGTAGTGTAGTTCG 57.501 40.000 0.00 0.00 45.76 3.95
3383 4457 1.070289 GTCTTCGACCCTGTTCCACTT 59.930 52.381 0.00 0.00 0.00 3.16
3404 4478 1.834263 ACTGAGAGTGGTAGATTGCCC 59.166 52.381 0.00 0.00 0.00 5.36
3491 4565 4.408182 AACAGGGATAGATTCTCCAACG 57.592 45.455 0.00 0.00 34.24 4.10
3775 4850 6.462909 GGAACAGAATTTGTCCCAGTTTCATT 60.463 38.462 0.00 0.00 39.73 2.57
3808 4883 9.836864 GGAATAGGAAAGAAATTGCCATTATTT 57.163 29.630 0.00 0.00 0.00 1.40
3901 4976 6.099269 TGGTATGTTCTGGGTTTCTAGGTATC 59.901 42.308 0.00 0.00 0.00 2.24
3960 5035 3.565902 TGAGATATGTGAGGCGTAGTCAG 59.434 47.826 0.00 0.00 0.00 3.51
3973 5048 2.738846 CGTAGTCAGATTGCAAGTTGCT 59.261 45.455 27.17 9.42 45.31 3.91
4028 5103 7.383102 AGGCAAATATTCAGACTTTGTAGTG 57.617 36.000 0.00 0.00 33.84 2.74
4031 5106 6.955963 GCAAATATTCAGACTTTGTAGTGTCG 59.044 38.462 0.00 0.00 38.16 4.35
4050 5125 6.147821 AGTGTCGATTCTTTGTTACCAAGATG 59.852 38.462 0.00 0.00 0.00 2.90
4133 5208 2.624838 AGTTTGGCAATCACTGTTCAGG 59.375 45.455 10.67 0.00 0.00 3.86
4463 5648 5.592054 TGGCATAGATCTTCAGACTTAACG 58.408 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.308458 TTGGGTGTGGCCGAGTCG 62.308 66.667 5.29 5.29 38.44 4.18
3 4 2.358737 CTTGGGTGTGGCCGAGTC 60.359 66.667 0.00 0.00 38.44 3.36
4 5 4.643387 GCTTGGGTGTGGCCGAGT 62.643 66.667 0.00 0.00 38.44 4.18
10 11 4.722700 CGGAGGGCTTGGGTGTGG 62.723 72.222 0.00 0.00 0.00 4.17
23 24 0.326927 TTTAAAGGACAGGGCCGGAG 59.673 55.000 11.67 0.76 0.00 4.63
24 25 0.996583 ATTTAAAGGACAGGGCCGGA 59.003 50.000 11.67 0.00 0.00 5.14
25 26 2.092592 AGTATTTAAAGGACAGGGCCGG 60.093 50.000 0.79 0.79 0.00 6.13
26 27 3.203716 GAGTATTTAAAGGACAGGGCCG 58.796 50.000 0.00 0.00 0.00 6.13
27 28 3.552875 GGAGTATTTAAAGGACAGGGCC 58.447 50.000 0.00 0.00 0.00 5.80
28 29 3.203716 CGGAGTATTTAAAGGACAGGGC 58.796 50.000 5.97 0.00 0.00 5.19
29 30 3.805207 CCGGAGTATTTAAAGGACAGGG 58.195 50.000 0.00 1.30 0.00 4.45
30 31 3.203716 GCCGGAGTATTTAAAGGACAGG 58.796 50.000 5.05 6.76 0.00 4.00
31 32 2.864343 CGCCGGAGTATTTAAAGGACAG 59.136 50.000 5.05 0.00 0.00 3.51
35 36 0.942252 GGCGCCGGAGTATTTAAAGG 59.058 55.000 12.58 0.00 0.00 3.11
52 53 2.585153 GGGGTTTCGAGAGAGGGC 59.415 66.667 0.00 0.00 43.69 5.19
107 125 1.668151 GACAGTGGCGGAGTTGGAC 60.668 63.158 0.00 0.00 0.00 4.02
124 142 4.380841 AAATGTGTAGGCGATCTAACGA 57.619 40.909 0.00 0.00 35.09 3.85
128 146 4.357142 GTCGAAAATGTGTAGGCGATCTA 58.643 43.478 0.00 0.00 0.00 1.98
137 155 3.291809 TGAGCTCGTCGAAAATGTGTA 57.708 42.857 9.64 0.00 0.00 2.90
160 178 2.511600 CGGCTGGTCGAATGGGTC 60.512 66.667 0.00 0.00 0.00 4.46
185 204 0.373716 GGTCGTCGTGGAATGCAATC 59.626 55.000 0.00 0.00 0.00 2.67
192 211 1.588824 ATGCGTAGGTCGTCGTGGAA 61.589 55.000 0.00 0.00 42.13 3.53
205 224 1.775385 TGATGTCCAGGAGATGCGTA 58.225 50.000 3.14 0.00 0.00 4.42
242 261 1.893801 AGGGAAATCGACACTCTCGTT 59.106 47.619 0.00 0.00 43.45 3.85
246 265 1.205893 GCTCAGGGAAATCGACACTCT 59.794 52.381 0.00 0.00 0.00 3.24
248 267 0.250513 GGCTCAGGGAAATCGACACT 59.749 55.000 0.00 0.00 0.00 3.55
249 268 0.250513 AGGCTCAGGGAAATCGACAC 59.749 55.000 0.00 0.00 0.00 3.67
250 269 0.537188 GAGGCTCAGGGAAATCGACA 59.463 55.000 10.25 0.00 0.00 4.35
251 270 0.528684 CGAGGCTCAGGGAAATCGAC 60.529 60.000 15.95 0.00 32.13 4.20
253 272 1.884926 GCGAGGCTCAGGGAAATCG 60.885 63.158 15.95 0.00 0.00 3.34
254 273 1.524849 GGCGAGGCTCAGGGAAATC 60.525 63.158 15.95 0.00 0.00 2.17
255 274 2.300967 TGGCGAGGCTCAGGGAAAT 61.301 57.895 15.95 0.00 0.00 2.17
281 306 2.995939 GCAATTGAGAGACATGACGTGA 59.004 45.455 10.34 0.00 0.00 4.35
285 310 3.620374 ACGATGCAATTGAGAGACATGAC 59.380 43.478 10.34 0.00 0.00 3.06
286 311 3.619929 CACGATGCAATTGAGAGACATGA 59.380 43.478 10.34 0.00 0.00 3.07
292 317 3.434641 AGTGAACACGATGCAATTGAGAG 59.565 43.478 10.34 0.00 36.20 3.20
410 1022 9.199982 CATCAATTGAGACTTAGCAAAATTGTT 57.800 29.630 14.54 0.00 36.72 2.83
411 1023 8.362639 ACATCAATTGAGACTTAGCAAAATTGT 58.637 29.630 14.54 5.14 36.72 2.71
412 1024 8.752766 ACATCAATTGAGACTTAGCAAAATTG 57.247 30.769 14.54 4.52 36.70 2.32
413 1025 9.199982 CAACATCAATTGAGACTTAGCAAAATT 57.800 29.630 14.54 0.00 0.00 1.82
414 1026 7.330208 GCAACATCAATTGAGACTTAGCAAAAT 59.670 33.333 14.54 0.00 0.00 1.82
415 1027 6.642131 GCAACATCAATTGAGACTTAGCAAAA 59.358 34.615 14.54 0.00 0.00 2.44
416 1028 6.151691 GCAACATCAATTGAGACTTAGCAAA 58.848 36.000 14.54 0.00 0.00 3.68
417 1029 5.241285 TGCAACATCAATTGAGACTTAGCAA 59.759 36.000 14.54 2.53 0.00 3.91
418 1030 4.761227 TGCAACATCAATTGAGACTTAGCA 59.239 37.500 14.54 14.73 0.00 3.49
419 1031 5.300969 TGCAACATCAATTGAGACTTAGC 57.699 39.130 14.54 12.54 0.00 3.09
420 1032 5.742453 GCATGCAACATCAATTGAGACTTAG 59.258 40.000 14.21 3.08 0.00 2.18
421 1033 5.393352 GGCATGCAACATCAATTGAGACTTA 60.393 40.000 21.36 0.00 0.00 2.24
422 1034 4.491676 GCATGCAACATCAATTGAGACTT 58.508 39.130 14.21 2.06 0.00 3.01
423 1035 3.119245 GGCATGCAACATCAATTGAGACT 60.119 43.478 21.36 0.00 0.00 3.24
424 1036 3.119245 AGGCATGCAACATCAATTGAGAC 60.119 43.478 21.36 0.00 0.00 3.36
425 1037 3.093814 AGGCATGCAACATCAATTGAGA 58.906 40.909 21.36 0.00 0.00 3.27
426 1038 3.520290 AGGCATGCAACATCAATTGAG 57.480 42.857 21.36 8.57 0.00 3.02
427 1039 3.965379 AAGGCATGCAACATCAATTGA 57.035 38.095 21.36 11.26 0.00 2.57
428 1040 3.997681 TCAAAGGCATGCAACATCAATTG 59.002 39.130 21.36 11.38 0.00 2.32
429 1041 4.274602 TCAAAGGCATGCAACATCAATT 57.725 36.364 21.36 0.00 0.00 2.32
430 1042 3.965379 TCAAAGGCATGCAACATCAAT 57.035 38.095 21.36 0.00 0.00 2.57
431 1043 3.512329 AGATCAAAGGCATGCAACATCAA 59.488 39.130 21.36 0.00 0.00 2.57
432 1044 3.093814 AGATCAAAGGCATGCAACATCA 58.906 40.909 21.36 0.00 0.00 3.07
433 1045 3.795623 AGATCAAAGGCATGCAACATC 57.204 42.857 21.36 12.31 0.00 3.06
434 1046 3.857052 CAAGATCAAAGGCATGCAACAT 58.143 40.909 21.36 3.23 0.00 2.71
435 1047 2.610976 GCAAGATCAAAGGCATGCAACA 60.611 45.455 21.36 0.00 34.10 3.33
436 1048 1.997606 GCAAGATCAAAGGCATGCAAC 59.002 47.619 21.36 2.42 34.10 4.17
437 1049 1.619332 TGCAAGATCAAAGGCATGCAA 59.381 42.857 21.36 0.00 40.47 4.08
438 1050 1.258676 TGCAAGATCAAAGGCATGCA 58.741 45.000 21.36 0.00 41.08 3.96
439 1051 2.596904 ATGCAAGATCAAAGGCATGC 57.403 45.000 9.90 9.90 44.64 4.06
442 1054 3.423749 TCTTCATGCAAGATCAAAGGCA 58.576 40.909 0.00 0.00 36.08 4.75
451 1063 3.062122 TGCACTGATCTTCATGCAAGA 57.938 42.857 10.11 9.18 45.60 3.02
452 1064 3.842732 TTGCACTGATCTTCATGCAAG 57.157 42.857 16.98 0.00 41.36 4.01
453 1065 4.587584 TTTTGCACTGATCTTCATGCAA 57.412 36.364 16.98 16.98 42.83 4.08
454 1066 4.794278 ATTTTGCACTGATCTTCATGCA 57.206 36.364 8.91 8.91 38.31 3.96
455 1067 6.476243 AAAATTTTGCACTGATCTTCATGC 57.524 33.333 1.75 0.00 34.11 4.06
458 1070 9.985730 AAGAATAAAATTTTGCACTGATCTTCA 57.014 25.926 13.76 0.00 0.00 3.02
492 1104 9.457436 GGAGGGAGTAGTATATAAGAAAGAGAG 57.543 40.741 0.00 0.00 0.00 3.20
493 1105 8.102047 CGGAGGGAGTAGTATATAAGAAAGAGA 58.898 40.741 0.00 0.00 0.00 3.10
494 1106 7.884354 ACGGAGGGAGTAGTATATAAGAAAGAG 59.116 40.741 0.00 0.00 0.00 2.85
495 1107 7.753630 ACGGAGGGAGTAGTATATAAGAAAGA 58.246 38.462 0.00 0.00 0.00 2.52
496 1108 7.999450 ACGGAGGGAGTAGTATATAAGAAAG 57.001 40.000 0.00 0.00 0.00 2.62
497 1109 9.866655 TTTACGGAGGGAGTAGTATATAAGAAA 57.133 33.333 0.00 0.00 0.00 2.52
498 1110 9.289782 GTTTACGGAGGGAGTAGTATATAAGAA 57.710 37.037 0.00 0.00 0.00 2.52
499 1111 8.664079 AGTTTACGGAGGGAGTAGTATATAAGA 58.336 37.037 0.00 0.00 0.00 2.10
500 1112 8.860780 AGTTTACGGAGGGAGTAGTATATAAG 57.139 38.462 0.00 0.00 0.00 1.73
507 1119 9.646522 TTTATATTAGTTTACGGAGGGAGTAGT 57.353 33.333 0.00 0.00 0.00 2.73
510 1122 9.605275 GTTTTTATATTAGTTTACGGAGGGAGT 57.395 33.333 0.00 0.00 0.00 3.85
511 1123 8.758715 CGTTTTTATATTAGTTTACGGAGGGAG 58.241 37.037 0.00 0.00 0.00 4.30
512 1124 8.257306 ACGTTTTTATATTAGTTTACGGAGGGA 58.743 33.333 0.00 0.00 32.54 4.20
513 1125 8.424274 ACGTTTTTATATTAGTTTACGGAGGG 57.576 34.615 0.00 0.00 32.54 4.30
534 1146 8.985805 CCTTTGTAAAGTAGTGATCTAAACGTT 58.014 33.333 0.00 0.00 34.20 3.99
535 1147 7.601508 CCCTTTGTAAAGTAGTGATCTAAACGT 59.398 37.037 3.90 0.00 34.20 3.99
536 1148 7.816031 TCCCTTTGTAAAGTAGTGATCTAAACG 59.184 37.037 3.90 0.00 34.20 3.60
537 1149 9.152595 CTCCCTTTGTAAAGTAGTGATCTAAAC 57.847 37.037 3.90 0.00 34.20 2.01
538 1150 8.877195 ACTCCCTTTGTAAAGTAGTGATCTAAA 58.123 33.333 3.90 0.00 32.44 1.85
539 1151 8.431910 ACTCCCTTTGTAAAGTAGTGATCTAA 57.568 34.615 3.90 0.00 32.44 2.10
540 1152 9.710818 ATACTCCCTTTGTAAAGTAGTGATCTA 57.289 33.333 14.74 1.98 34.32 1.98
541 1153 6.936968 ACTCCCTTTGTAAAGTAGTGATCT 57.063 37.500 3.90 0.00 32.44 2.75
542 1154 8.258708 ACATACTCCCTTTGTAAAGTAGTGATC 58.741 37.037 14.74 0.00 34.32 2.92
543 1155 8.147244 ACATACTCCCTTTGTAAAGTAGTGAT 57.853 34.615 14.74 6.58 34.32 3.06
544 1156 7.453752 AGACATACTCCCTTTGTAAAGTAGTGA 59.546 37.037 14.74 3.19 34.32 3.41
545 1157 7.612677 AGACATACTCCCTTTGTAAAGTAGTG 58.387 38.462 14.74 6.22 34.32 2.74
546 1158 7.793948 AGACATACTCCCTTTGTAAAGTAGT 57.206 36.000 11.75 11.75 35.66 2.73
547 1159 8.311836 TCAAGACATACTCCCTTTGTAAAGTAG 58.688 37.037 3.90 3.79 34.20 2.57
548 1160 8.092687 GTCAAGACATACTCCCTTTGTAAAGTA 58.907 37.037 3.90 0.00 34.20 2.24
549 1161 6.935208 GTCAAGACATACTCCCTTTGTAAAGT 59.065 38.462 3.90 0.00 34.20 2.66
550 1162 7.162082 AGTCAAGACATACTCCCTTTGTAAAG 58.838 38.462 2.72 0.00 35.79 1.85
551 1163 7.074653 AGTCAAGACATACTCCCTTTGTAAA 57.925 36.000 2.72 0.00 0.00 2.01
552 1164 6.681729 AGTCAAGACATACTCCCTTTGTAA 57.318 37.500 2.72 0.00 0.00 2.41
553 1165 7.672660 TCTTAGTCAAGACATACTCCCTTTGTA 59.327 37.037 2.72 0.00 35.82 2.41
554 1166 6.497259 TCTTAGTCAAGACATACTCCCTTTGT 59.503 38.462 2.72 0.00 35.82 2.83
555 1167 6.936279 TCTTAGTCAAGACATACTCCCTTTG 58.064 40.000 2.72 0.00 35.82 2.77
568 1180 1.749634 GCGGCTAGGTCTTAGTCAAGA 59.250 52.381 0.00 0.00 38.49 3.02
569 1181 1.476891 TGCGGCTAGGTCTTAGTCAAG 59.523 52.381 0.00 0.00 33.41 3.02
570 1182 1.552578 TGCGGCTAGGTCTTAGTCAA 58.447 50.000 0.00 0.00 33.41 3.18
571 1183 1.681793 GATGCGGCTAGGTCTTAGTCA 59.318 52.381 0.00 0.00 33.41 3.41
572 1184 1.957877 AGATGCGGCTAGGTCTTAGTC 59.042 52.381 0.00 0.00 0.00 2.59
573 1185 2.074729 AGATGCGGCTAGGTCTTAGT 57.925 50.000 0.00 0.00 0.00 2.24
574 1186 3.460857 AAAGATGCGGCTAGGTCTTAG 57.539 47.619 0.00 0.00 31.16 2.18
575 1187 3.906720 AAAAGATGCGGCTAGGTCTTA 57.093 42.857 0.00 0.00 31.16 2.10
576 1188 2.789409 AAAAGATGCGGCTAGGTCTT 57.211 45.000 0.00 3.37 32.62 3.01
577 1189 2.789409 AAAAAGATGCGGCTAGGTCT 57.211 45.000 0.00 0.00 0.00 3.85
599 1211 4.162131 ACTGCACCTTGTTTTTCTTCCATT 59.838 37.500 0.00 0.00 0.00 3.16
601 1213 3.096092 ACTGCACCTTGTTTTTCTTCCA 58.904 40.909 0.00 0.00 0.00 3.53
651 1465 5.637810 TGACTGACTTTAAATCGGTGATGTC 59.362 40.000 13.46 5.37 35.77 3.06
667 1481 2.494059 CCACATTTTCGGTGACTGACT 58.506 47.619 0.00 0.00 38.54 3.41
670 1484 1.806542 CTCCCACATTTTCGGTGACTG 59.193 52.381 0.00 0.00 38.54 3.51
671 1485 1.697432 TCTCCCACATTTTCGGTGACT 59.303 47.619 0.00 0.00 38.54 3.41
672 1486 2.178912 TCTCCCACATTTTCGGTGAC 57.821 50.000 0.00 0.00 38.54 3.67
674 1488 4.519540 ATTTTCTCCCACATTTTCGGTG 57.480 40.909 0.00 0.00 36.03 4.94
675 1489 4.320935 CGAATTTTCTCCCACATTTTCGGT 60.321 41.667 0.00 0.00 33.15 4.69
676 1490 4.083003 TCGAATTTTCTCCCACATTTTCGG 60.083 41.667 0.00 0.00 36.36 4.30
677 1491 5.041951 TCGAATTTTCTCCCACATTTTCG 57.958 39.130 0.00 0.00 36.86 3.46
678 1492 4.859245 GCTCGAATTTTCTCCCACATTTTC 59.141 41.667 0.00 0.00 0.00 2.29
679 1493 4.321974 GGCTCGAATTTTCTCCCACATTTT 60.322 41.667 0.00 0.00 0.00 1.82
698 1554 0.800012 TTACCGCGATTTTGTGGCTC 59.200 50.000 8.23 0.00 43.47 4.70
735 1591 2.270352 TTGCTGACTTTTCCGATGGT 57.730 45.000 0.00 0.00 0.00 3.55
773 1630 2.006888 TCCCAATTGCGTCTCGAAATC 58.993 47.619 0.00 0.00 33.56 2.17
793 1655 2.859538 CAGCCGATGCGCATTTTATTTT 59.140 40.909 26.12 0.00 44.33 1.82
797 1659 1.726865 CCAGCCGATGCGCATTTTA 59.273 52.632 26.12 0.00 44.33 1.52
932 1796 0.764752 GAGGTGGGGGTGGATAGAGG 60.765 65.000 0.00 0.00 0.00 3.69
1217 2096 2.081425 GATCATGAGGAGGCGCGAGT 62.081 60.000 12.10 0.00 0.00 4.18
1290 2169 1.508088 GAGCAATCAAGGCAACCGG 59.492 57.895 0.00 0.00 37.17 5.28
1292 2171 1.244019 ACGGAGCAATCAAGGCAACC 61.244 55.000 0.00 0.00 37.17 3.77
1293 2172 0.598065 AACGGAGCAATCAAGGCAAC 59.402 50.000 0.00 0.00 0.00 4.17
1294 2173 0.597568 CAACGGAGCAATCAAGGCAA 59.402 50.000 0.00 0.00 0.00 4.52
1295 2174 0.250684 TCAACGGAGCAATCAAGGCA 60.251 50.000 0.00 0.00 0.00 4.75
1296 2175 0.449388 CTCAACGGAGCAATCAAGGC 59.551 55.000 0.00 0.00 33.67 4.35
1298 2177 1.391485 CGTCTCAACGGAGCAATCAAG 59.609 52.381 0.00 0.00 45.21 3.02
1299 2178 1.428448 CGTCTCAACGGAGCAATCAA 58.572 50.000 0.00 0.00 45.21 2.57
1312 2191 2.871099 GAGCGCAGTCTCGTCTCA 59.129 61.111 11.47 0.00 34.86 3.27
1338 2217 1.888018 CCGGCTACTCCAGTTCGAA 59.112 57.895 0.00 0.00 34.01 3.71
1350 2229 2.666862 CAACCAACACGCCGGCTA 60.667 61.111 26.68 0.00 0.00 3.93
1384 2263 1.226435 GAGAGACGAATGCGCGAGT 60.226 57.895 12.10 0.00 42.48 4.18
1452 2335 6.072286 ACAATCAAGCACCTATTTGAACAGAG 60.072 38.462 0.00 0.00 36.93 3.35
1455 2338 5.534278 TCACAATCAAGCACCTATTTGAACA 59.466 36.000 0.00 0.00 36.93 3.18
1522 2409 2.615912 AGCAGCTAATCCAAAAGATCGC 59.384 45.455 0.00 0.00 32.47 4.58
1556 2443 0.037326 GATCCCAACAGACGCTGACA 60.037 55.000 12.77 0.00 35.18 3.58
1664 2552 2.497675 TCAGCCTGTGGACTGATAGAAC 59.502 50.000 0.00 0.00 37.99 3.01
1705 2600 9.480861 CCCATCCAGAGTATAATTATCAGACTA 57.519 37.037 0.00 0.00 0.00 2.59
1706 2601 8.180165 TCCCATCCAGAGTATAATTATCAGACT 58.820 37.037 0.00 0.00 0.00 3.24
1707 2602 8.367660 TCCCATCCAGAGTATAATTATCAGAC 57.632 38.462 0.00 0.00 0.00 3.51
1744 2639 4.081642 TCACAGATTGCCTAACTGTAGACC 60.082 45.833 0.00 0.00 41.93 3.85
1870 2767 2.028112 TCATACAGAGGTGTGCTGGTTC 60.028 50.000 0.00 0.00 37.52 3.62
1881 2778 4.997395 CCGGTTTGGATTATCATACAGAGG 59.003 45.833 0.00 0.00 42.00 3.69
1973 2876 0.036105 TCGATGCAGCACAGATGGTT 60.036 50.000 1.53 0.00 33.06 3.67
1976 2879 1.634753 CGTCGATGCAGCACAGATG 59.365 57.895 1.53 1.66 0.00 2.90
2005 2908 4.586421 TCAAATGTGGAACCAAGTGCATAA 59.414 37.500 0.00 0.00 34.36 1.90
2007 2910 2.964464 TCAAATGTGGAACCAAGTGCAT 59.036 40.909 0.00 0.00 34.36 3.96
2008 2911 2.382882 TCAAATGTGGAACCAAGTGCA 58.617 42.857 0.00 0.00 34.36 4.57
2009 2912 3.665745 ATCAAATGTGGAACCAAGTGC 57.334 42.857 0.00 0.00 34.36 4.40
2010 2913 6.018832 GTGAAAATCAAATGTGGAACCAAGTG 60.019 38.462 0.00 0.00 34.36 3.16
2011 2914 6.048509 GTGAAAATCAAATGTGGAACCAAGT 58.951 36.000 0.00 0.00 34.36 3.16
2013 2916 6.232581 AGTGAAAATCAAATGTGGAACCAA 57.767 33.333 0.00 0.00 34.36 3.67
2014 2917 5.867903 AGTGAAAATCAAATGTGGAACCA 57.132 34.783 0.00 0.00 34.36 3.67
2015 2918 6.981722 AGTAGTGAAAATCAAATGTGGAACC 58.018 36.000 0.00 0.00 34.36 3.62
2016 2919 7.920682 ACAAGTAGTGAAAATCAAATGTGGAAC 59.079 33.333 0.00 0.00 37.35 3.62
2018 2921 7.581213 ACAAGTAGTGAAAATCAAATGTGGA 57.419 32.000 0.00 0.00 0.00 4.02
2019 2922 9.345517 CATACAAGTAGTGAAAATCAAATGTGG 57.654 33.333 0.00 0.00 0.00 4.17
2023 2926 9.825972 CGTTCATACAAGTAGTGAAAATCAAAT 57.174 29.630 0.00 0.00 34.04 2.32
2024 2927 8.832521 ACGTTCATACAAGTAGTGAAAATCAAA 58.167 29.630 0.00 0.00 34.04 2.69
2025 2928 8.373048 ACGTTCATACAAGTAGTGAAAATCAA 57.627 30.769 0.00 0.00 34.04 2.57
2026 2929 7.956420 ACGTTCATACAAGTAGTGAAAATCA 57.044 32.000 0.00 0.00 34.04 2.57
2027 2930 8.280497 ACAACGTTCATACAAGTAGTGAAAATC 58.720 33.333 0.00 0.00 34.04 2.17
2028 2931 8.067784 CACAACGTTCATACAAGTAGTGAAAAT 58.932 33.333 0.00 0.00 34.04 1.82
2029 2932 7.064847 ACACAACGTTCATACAAGTAGTGAAAA 59.935 33.333 13.02 0.00 34.04 2.29
2030 2933 6.535865 ACACAACGTTCATACAAGTAGTGAAA 59.464 34.615 13.02 0.00 34.04 2.69
2031 2934 6.044046 ACACAACGTTCATACAAGTAGTGAA 58.956 36.000 13.02 0.00 0.00 3.18
2032 2935 5.593968 ACACAACGTTCATACAAGTAGTGA 58.406 37.500 13.02 0.00 0.00 3.41
2033 2936 5.107607 GGACACAACGTTCATACAAGTAGTG 60.108 44.000 0.00 2.00 0.00 2.74
2034 2937 4.986659 GGACACAACGTTCATACAAGTAGT 59.013 41.667 0.00 0.00 0.00 2.73
2035 2938 5.227908 AGGACACAACGTTCATACAAGTAG 58.772 41.667 0.00 0.00 0.00 2.57
2036 2939 5.204409 AGGACACAACGTTCATACAAGTA 57.796 39.130 0.00 0.00 0.00 2.24
2037 2940 4.067972 AGGACACAACGTTCATACAAGT 57.932 40.909 0.00 0.00 0.00 3.16
2038 2941 6.147164 ACAATAGGACACAACGTTCATACAAG 59.853 38.462 0.00 0.00 0.00 3.16
2039 2942 5.992829 ACAATAGGACACAACGTTCATACAA 59.007 36.000 0.00 0.00 0.00 2.41
2040 2943 5.407084 CACAATAGGACACAACGTTCATACA 59.593 40.000 0.00 0.00 0.00 2.29
2041 2944 5.407387 ACACAATAGGACACAACGTTCATAC 59.593 40.000 0.00 0.00 0.00 2.39
2042 2945 5.543714 ACACAATAGGACACAACGTTCATA 58.456 37.500 0.00 0.00 0.00 2.15
2043 2946 4.385825 ACACAATAGGACACAACGTTCAT 58.614 39.130 0.00 0.00 0.00 2.57
2066 3005 8.683550 TCTGTAACGAAACTATGACTAATGTG 57.316 34.615 0.00 0.00 0.00 3.21
2153 3092 4.342378 AGAAGCGCATCCTAAACTCTATCA 59.658 41.667 11.47 0.00 0.00 2.15
2177 3116 6.019779 AGTGTAATCATCGAGCCTAGATTC 57.980 41.667 0.00 0.00 33.22 2.52
2542 3481 9.561069 AAGTGTTGTCAATAGACTCAATACTTT 57.439 29.630 11.10 0.69 45.20 2.66
2578 3517 7.903995 AGAAATGCACAAAAAGAACAAAAGA 57.096 28.000 0.00 0.00 0.00 2.52
2639 3578 6.218746 AGGAAAAGAAACAATGACAGAATGC 58.781 36.000 0.00 0.00 42.53 3.56
2666 3605 4.328983 CGCGATGTTGAAGTAGTACCAAAT 59.671 41.667 0.00 0.00 0.00 2.32
2793 3735 8.671987 ATATAGAGGTGTAAATGAGGCTGTAT 57.328 34.615 0.00 0.00 0.00 2.29
2805 3747 9.595823 GCTGAACTTAACAATATAGAGGTGTAA 57.404 33.333 0.00 0.00 0.00 2.41
2812 3754 9.330063 CAGGAATGCTGAACTTAACAATATAGA 57.670 33.333 0.00 0.00 0.00 1.98
2813 3755 8.072567 GCAGGAATGCTGAACTTAACAATATAG 58.927 37.037 5.79 0.00 0.00 1.31
3104 4048 4.001652 TGCGGACCAAAATTGAACGTATA 58.998 39.130 0.00 0.00 0.00 1.47
3162 4107 5.067413 CCTATTCATGAGCAAGCAAACAGAT 59.933 40.000 0.00 0.00 0.00 2.90
3208 4153 6.145534 TGACTACACAAGTTAAAGCTCGAATG 59.854 38.462 0.00 0.00 39.07 2.67
3247 4192 7.126726 GTTCTTACGAACTACACTACTGAGA 57.873 40.000 4.91 0.00 44.80 3.27
3288 4361 8.976986 AAAATGATCATGCTAAAGTTCTGTTC 57.023 30.769 9.46 0.00 0.00 3.18
3383 4457 3.031736 GGGCAATCTACCACTCTCAGTA 58.968 50.000 0.00 0.00 0.00 2.74
3404 4478 0.674895 CCTCCAGAACAAAGCCCTCG 60.675 60.000 0.00 0.00 0.00 4.63
3491 4565 3.708563 TGCAACTTCAAGTGGCTTAAC 57.291 42.857 18.09 0.00 45.40 2.01
3775 4850 6.375455 GCAATTTCTTTCCTATTCCACAGAGA 59.625 38.462 0.00 0.00 0.00 3.10
3808 4883 6.237942 CCACGCAAACAAAAATACAATCAACA 60.238 34.615 0.00 0.00 0.00 3.33
3843 4918 5.930135 ACTCCTTCAACAAACTGATAGTGT 58.070 37.500 0.00 0.00 0.00 3.55
3856 4931 8.993121 CATACCACATGAATATACTCCTTCAAC 58.007 37.037 0.00 0.00 35.20 3.18
3859 4934 9.209175 GAACATACCACATGAATATACTCCTTC 57.791 37.037 0.00 0.00 0.00 3.46
3946 5021 1.281899 GCAATCTGACTACGCCTCAC 58.718 55.000 0.00 0.00 0.00 3.51
4002 5077 8.946085 CACTACAAAGTCTGAATATTTGCCTTA 58.054 33.333 9.76 0.00 37.42 2.69
4050 5125 7.159372 TGACTAACCAGGAGAATGAAACTTAC 58.841 38.462 0.00 0.00 0.00 2.34
4463 5648 7.736893 AGATAGGAAACTGTATGGTGTAATCC 58.263 38.462 0.00 0.00 43.88 3.01


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

AutoCloner maintained by Alex Coulton.