Multiple sequence alignment - TraesCS7A01G117100

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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 TraesCS7A01G117100 chr7A 100.000 3320 0 0 1 3320 75034321 75037640 0.000000e+00 6131.0
1 TraesCS7A01G117100 chr7A 88.462 156 15 3 3167 3320 36461374 36461220 5.660000e-43 185.0
2 TraesCS7A01G117100 chr7A 100.000 35 0 0 3073 3107 1854934 1854968 7.690000e-07 65.8
3 TraesCS7A01G117100 chr7D 94.917 2361 95 18 647 2991 69264911 69267262 0.000000e+00 3672.0
4 TraesCS7A01G117100 chr7D 91.126 293 21 5 1 289 69264287 69264578 3.100000e-105 392.0
5 TraesCS7A01G117100 chr7D 93.191 235 13 3 285 516 69264606 69264840 3.170000e-90 342.0
6 TraesCS7A01G117100 chr7D 89.610 77 5 2 553 626 69264837 69264913 9.810000e-16 95.3
7 TraesCS7A01G117100 chr7D 83.333 72 10 2 3060 3130 39671863 39671793 7.690000e-07 65.8
8 TraesCS7A01G117100 chr7B 93.271 2363 94 27 677 2991 11529507 11531852 0.000000e+00 3422.0
9 TraesCS7A01G117100 chr7B 87.984 258 29 2 2 258 11528938 11529194 1.500000e-78 303.0
10 TraesCS7A01G117100 chr7B 86.325 234 22 6 285 509 11529284 11529516 2.560000e-61 246.0
11 TraesCS7A01G117100 chr7B 87.662 154 17 2 3169 3320 723943906 723944059 9.460000e-41 178.0
12 TraesCS7A01G117100 chr6D 91.667 156 11 2 3167 3320 454674225 454674380 7.210000e-52 215.0
13 TraesCS7A01G117100 chr4D 91.558 154 11 2 3169 3320 469196435 469196282 9.330000e-51 211.0
14 TraesCS7A01G117100 chr4D 89.744 156 13 3 3167 3320 55273301 55273147 2.610000e-46 196.0
15 TraesCS7A01G117100 chr4D 97.619 42 1 0 3063 3104 426785109 426785068 4.590000e-09 73.1
16 TraesCS7A01G117100 chr3D 89.091 165 15 3 3159 3320 97615854 97615690 5.620000e-48 202.0
17 TraesCS7A01G117100 chr3D 90.323 155 13 2 3167 3320 114398489 114398642 5.620000e-48 202.0
18 TraesCS7A01G117100 chr5A 87.975 158 17 2 3165 3320 593226053 593225896 5.660000e-43 185.0
19 TraesCS7A01G117100 chr5A 86.885 61 6 2 3064 3124 667326207 667326149 2.140000e-07 67.6
20 TraesCS7A01G117100 chr6A 87.117 163 16 5 3162 3320 455409989 455410150 2.630000e-41 180.0
21 TraesCS7A01G117100 chr1D 84.146 82 13 0 3063 3144 414883262 414883181 2.750000e-11 80.5
22 TraesCS7A01G117100 chr2B 91.071 56 4 1 3057 3112 564441126 564441180 1.280000e-09 75.0
23 TraesCS7A01G117100 chr2A 82.927 82 14 0 3064 3145 769485830 769485911 1.280000e-09 75.0
24 TraesCS7A01G117100 chr6B 91.667 48 4 0 3059 3106 693944796 693944749 2.140000e-07 67.6
25 TraesCS7A01G117100 chr4A 89.130 46 5 0 3060 3105 41966340 41966295 1.290000e-04 58.4


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 TraesCS7A01G117100 chr7A 75034321 75037640 3319 False 6131.000000 6131 100.000000 1 3320 1 chr7A.!!$F2 3319
1 TraesCS7A01G117100 chr7D 69264287 69267262 2975 False 1125.325000 3672 92.211000 1 2991 4 chr7D.!!$F1 2990
2 TraesCS7A01G117100 chr7B 11528938 11531852 2914 False 1323.666667 3422 89.193333 2 2991 3 chr7B.!!$F2 2989

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
462 535 0.249447 CATCATCCGCGTTAGGCAGA 60.249 55.0 4.92 0.0 43.84 4.26 F
1374 1477 0.180406 CCTACATGGTAGGCGGCTTT 59.820 55.0 19.76 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1565 1.470890 CTTCTCCTTCTTCTCGACGCT 59.529 52.381 0.00 0.0 0.00 5.07 R
3221 3354 0.108963 GAGACTAGAGCGGAGGCCTA 59.891 60.000 4.42 0.0 41.24 3.93 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
23 24 0.393132 TGACCGTTCTGTTTGGCACA 60.393 50.000 0.00 0.00 0.00 4.57
38 39 3.699413 TGGCACATTCAATCAAGATGGA 58.301 40.909 0.00 0.00 0.00 3.41
59 60 5.163395 TGGACAACATGTCTACAACAGTGTA 60.163 40.000 0.00 0.00 46.19 2.90
74 75 8.677148 ACAACAGTGTAGAATAACATTGAAGT 57.323 30.769 0.00 2.44 38.88 3.01
145 147 8.225603 CCAATGTTGGCATTAACTCTTATAGT 57.774 34.615 0.00 0.00 42.91 2.12
183 185 1.852309 TGATGTTATGGCCCCACTCAT 59.148 47.619 0.00 0.00 0.00 2.90
212 214 2.795231 TGGAGAAGCCCTTCATTCTG 57.205 50.000 10.37 0.00 41.84 3.02
281 315 9.474313 TTTCAAAGCCAATTAGAATACTACCAT 57.526 29.630 0.00 0.00 0.00 3.55
413 483 3.279434 TCATTCGATCTCTTCTCCGTCA 58.721 45.455 0.00 0.00 0.00 4.35
414 484 3.694566 TCATTCGATCTCTTCTCCGTCAA 59.305 43.478 0.00 0.00 0.00 3.18
416 486 4.720649 TTCGATCTCTTCTCCGTCAATT 57.279 40.909 0.00 0.00 0.00 2.32
462 535 0.249447 CATCATCCGCGTTAGGCAGA 60.249 55.000 4.92 0.00 43.84 4.26
465 538 0.739462 CATCCGCGTTAGGCAGACAA 60.739 55.000 4.92 0.00 43.84 3.18
468 541 1.666553 CGCGTTAGGCAGACAACCA 60.667 57.895 0.00 0.00 43.84 3.67
487 564 3.193263 CCAGTCAGCATGTGTATCAGTC 58.807 50.000 0.00 0.00 37.40 3.51
516 593 5.063438 CGTGTGGGTAGAGACAACAATAATG 59.937 44.000 0.00 0.00 0.00 1.90
519 596 6.070481 TGTGGGTAGAGACAACAATAATGCTA 60.070 38.462 0.00 0.00 0.00 3.49
520 597 6.480320 GTGGGTAGAGACAACAATAATGCTAG 59.520 42.308 0.00 0.00 0.00 3.42
521 598 6.382859 TGGGTAGAGACAACAATAATGCTAGA 59.617 38.462 0.00 0.00 0.00 2.43
522 599 6.702282 GGGTAGAGACAACAATAATGCTAGAC 59.298 42.308 0.00 0.00 0.00 2.59
524 601 6.552445 AGAGACAACAATAATGCTAGACCT 57.448 37.500 0.00 0.00 0.00 3.85
525 602 7.661536 AGAGACAACAATAATGCTAGACCTA 57.338 36.000 0.00 0.00 0.00 3.08
526 603 7.493367 AGAGACAACAATAATGCTAGACCTAC 58.507 38.462 0.00 0.00 0.00 3.18
527 604 6.273825 AGACAACAATAATGCTAGACCTACG 58.726 40.000 0.00 0.00 0.00 3.51
528 605 5.974108 ACAACAATAATGCTAGACCTACGT 58.026 37.500 0.00 0.00 0.00 3.57
529 606 7.067859 AGACAACAATAATGCTAGACCTACGTA 59.932 37.037 0.00 0.00 0.00 3.57
530 607 7.549839 ACAACAATAATGCTAGACCTACGTAA 58.450 34.615 0.00 0.00 0.00 3.18
531 608 8.202137 ACAACAATAATGCTAGACCTACGTAAT 58.798 33.333 0.00 0.00 0.00 1.89
532 609 8.700644 CAACAATAATGCTAGACCTACGTAATC 58.299 37.037 0.00 0.00 0.00 1.75
533 610 8.179509 ACAATAATGCTAGACCTACGTAATCT 57.820 34.615 12.35 12.35 0.00 2.40
534 611 8.082852 ACAATAATGCTAGACCTACGTAATCTG 58.917 37.037 15.90 9.15 0.00 2.90
535 612 7.762588 ATAATGCTAGACCTACGTAATCTGT 57.237 36.000 15.90 3.52 0.00 3.41
536 613 6.466885 AATGCTAGACCTACGTAATCTGTT 57.533 37.500 15.90 6.12 0.00 3.16
537 614 7.578310 AATGCTAGACCTACGTAATCTGTTA 57.422 36.000 15.90 5.55 0.00 2.41
538 615 6.369059 TGCTAGACCTACGTAATCTGTTAC 57.631 41.667 15.90 6.28 37.44 2.50
550 627 6.980051 GTAATCTGTTACGAAACATCCCTT 57.020 37.500 0.00 0.00 44.43 3.95
551 628 7.001695 GTAATCTGTTACGAAACATCCCTTC 57.998 40.000 0.00 0.00 44.43 3.46
552 629 4.884668 TCTGTTACGAAACATCCCTTCT 57.115 40.909 0.00 0.00 44.43 2.85
553 630 5.988310 TCTGTTACGAAACATCCCTTCTA 57.012 39.130 0.00 0.00 44.43 2.10
554 631 6.349243 TCTGTTACGAAACATCCCTTCTAA 57.651 37.500 0.00 0.00 44.43 2.10
555 632 6.942976 TCTGTTACGAAACATCCCTTCTAAT 58.057 36.000 0.00 0.00 44.43 1.73
556 633 7.039882 TCTGTTACGAAACATCCCTTCTAATC 58.960 38.462 0.00 0.00 44.43 1.75
557 634 6.110707 TGTTACGAAACATCCCTTCTAATCC 58.889 40.000 0.00 0.00 40.69 3.01
558 635 6.070424 TGTTACGAAACATCCCTTCTAATCCT 60.070 38.462 0.00 0.00 40.69 3.24
559 636 5.024785 ACGAAACATCCCTTCTAATCCTC 57.975 43.478 0.00 0.00 0.00 3.71
560 637 4.717280 ACGAAACATCCCTTCTAATCCTCT 59.283 41.667 0.00 0.00 0.00 3.69
561 638 5.163395 ACGAAACATCCCTTCTAATCCTCTC 60.163 44.000 0.00 0.00 0.00 3.20
562 639 4.946478 AACATCCCTTCTAATCCTCTCG 57.054 45.455 0.00 0.00 0.00 4.04
567 644 1.710816 CTTCTAATCCTCTCGCCCCT 58.289 55.000 0.00 0.00 0.00 4.79
586 665 3.356290 CCTTGATTTCAACTAGGGTGGG 58.644 50.000 0.00 0.00 0.00 4.61
615 694 6.203723 CCCTTTCGCTCTATCTCCAATAAAAG 59.796 42.308 0.00 0.00 0.00 2.27
623 702 9.561069 GCTCTATCTCCAATAAAAGAATACCAA 57.439 33.333 0.00 0.00 0.00 3.67
627 706 7.938140 TCTCCAATAAAAGAATACCAACTGG 57.062 36.000 0.00 0.00 42.17 4.00
628 707 6.377146 TCTCCAATAAAAGAATACCAACTGGC 59.623 38.462 0.00 0.00 39.32 4.85
629 708 6.252995 TCCAATAAAAGAATACCAACTGGCT 58.747 36.000 0.00 0.00 39.32 4.75
630 709 7.406916 TCCAATAAAAGAATACCAACTGGCTA 58.593 34.615 0.00 0.00 39.32 3.93
631 710 7.891183 TCCAATAAAAGAATACCAACTGGCTAA 59.109 33.333 0.00 0.00 39.32 3.09
632 711 8.695456 CCAATAAAAGAATACCAACTGGCTAAT 58.305 33.333 0.00 0.00 39.32 1.73
633 712 9.736023 CAATAAAAGAATACCAACTGGCTAATC 57.264 33.333 0.00 0.00 39.32 1.75
634 713 6.775594 AAAAGAATACCAACTGGCTAATCC 57.224 37.500 0.00 0.00 39.32 3.01
635 714 4.439253 AGAATACCAACTGGCTAATCCC 57.561 45.455 0.00 0.00 39.32 3.85
636 715 3.138468 AGAATACCAACTGGCTAATCCCC 59.862 47.826 0.00 0.00 39.32 4.81
637 716 1.218844 TACCAACTGGCTAATCCCCC 58.781 55.000 0.00 0.00 39.32 5.40
638 717 1.152963 CCAACTGGCTAATCCCCCG 60.153 63.158 0.00 0.00 0.00 5.73
639 718 1.607612 CAACTGGCTAATCCCCCGT 59.392 57.895 0.00 0.00 0.00 5.28
640 719 0.834612 CAACTGGCTAATCCCCCGTA 59.165 55.000 0.00 0.00 0.00 4.02
641 720 1.210967 CAACTGGCTAATCCCCCGTAA 59.789 52.381 0.00 0.00 0.00 3.18
642 721 1.587066 ACTGGCTAATCCCCCGTAAA 58.413 50.000 0.00 0.00 0.00 2.01
643 722 2.132686 ACTGGCTAATCCCCCGTAAAT 58.867 47.619 0.00 0.00 0.00 1.40
644 723 2.158667 ACTGGCTAATCCCCCGTAAATG 60.159 50.000 0.00 0.00 0.00 2.32
645 724 1.847737 TGGCTAATCCCCCGTAAATGT 59.152 47.619 0.00 0.00 0.00 2.71
651 730 6.290605 GCTAATCCCCCGTAAATGTACTTAA 58.709 40.000 0.00 0.00 0.00 1.85
656 735 7.628769 TCCCCCGTAAATGTACTTAATTTTC 57.371 36.000 0.00 0.00 0.00 2.29
658 737 6.458615 CCCCCGTAAATGTACTTAATTTTCCG 60.459 42.308 0.00 0.00 0.00 4.30
677 756 1.656652 GTGGATGTAGCATTGCTCGT 58.343 50.000 15.81 8.35 40.44 4.18
970 1056 4.141981 CCTCTCATCAGTTCAGCTGTGTAT 60.142 45.833 14.67 0.00 45.23 2.29
983 1069 5.300539 TCAGCTGTGTATCTTCATCTCTACC 59.699 44.000 14.67 0.00 0.00 3.18
984 1070 5.068329 CAGCTGTGTATCTTCATCTCTACCA 59.932 44.000 5.25 0.00 0.00 3.25
985 1071 5.837979 AGCTGTGTATCTTCATCTCTACCAT 59.162 40.000 0.00 0.00 0.00 3.55
986 1072 6.015519 AGCTGTGTATCTTCATCTCTACCATC 60.016 42.308 0.00 0.00 0.00 3.51
987 1073 6.239148 GCTGTGTATCTTCATCTCTACCATCA 60.239 42.308 0.00 0.00 0.00 3.07
988 1074 7.282332 TGTGTATCTTCATCTCTACCATCAG 57.718 40.000 0.00 0.00 0.00 2.90
989 1075 6.836007 TGTGTATCTTCATCTCTACCATCAGT 59.164 38.462 0.00 0.00 0.00 3.41
1128 1231 0.323178 TCCACCTCCTGTCCTACGTC 60.323 60.000 0.00 0.00 0.00 4.34
1143 1246 4.773117 GTCGACACGGCCGTCTCC 62.773 72.222 31.80 18.90 33.54 3.71
1167 1270 1.078426 GCAGCCCACCGTTGAGTAT 60.078 57.895 0.00 0.00 0.00 2.12
1182 1285 2.125472 TATTTCTTCGGCGGCGCA 60.125 55.556 34.36 16.33 0.00 6.09
1263 1366 1.028130 GGGACTACTACGGCCAGTAC 58.972 60.000 2.24 0.00 0.00 2.73
1264 1367 1.028130 GGACTACTACGGCCAGTACC 58.972 60.000 2.24 0.00 0.00 3.34
1265 1368 1.683011 GGACTACTACGGCCAGTACCA 60.683 57.143 2.24 0.00 0.00 3.25
1374 1477 0.180406 CCTACATGGTAGGCGGCTTT 59.820 55.000 19.76 0.00 0.00 3.51
1570 1673 1.896339 TTGCACCTTCGATGCGTTCG 61.896 55.000 5.12 2.68 46.49 3.95
1750 1853 2.284405 GGGAGGACGGTGGAGGAA 60.284 66.667 0.00 0.00 0.00 3.36
2110 2213 3.119849 GCCACATCTACATGTTCAACACC 60.120 47.826 2.30 0.00 40.66 4.16
2118 2221 4.164843 ACATGTTCAACACCAAGGTAGT 57.835 40.909 0.00 0.00 0.00 2.73
2133 2237 2.626266 AGGTAGTCACATCGTCACAACA 59.374 45.455 0.00 0.00 0.00 3.33
2211 2321 6.704289 TCAAGATATGCAAAAGAAGGATGG 57.296 37.500 0.00 0.00 0.00 3.51
2223 2333 7.657354 GCAAAAGAAGGATGGTAATTTTCTTGT 59.343 33.333 0.96 0.00 37.93 3.16
2225 2335 9.764363 AAAAGAAGGATGGTAATTTTCTTGTTC 57.236 29.630 0.96 0.00 37.93 3.18
2342 2457 4.498241 CAGCTTGTTATCTAGTCACAGCA 58.502 43.478 0.00 0.00 0.00 4.41
2343 2458 4.565962 CAGCTTGTTATCTAGTCACAGCAG 59.434 45.833 0.00 0.00 0.00 4.24
2345 2460 4.382040 GCTTGTTATCTAGTCACAGCAGGA 60.382 45.833 0.00 0.00 0.00 3.86
2346 2461 4.991153 TGTTATCTAGTCACAGCAGGAG 57.009 45.455 0.00 0.00 0.00 3.69
2347 2462 3.131223 TGTTATCTAGTCACAGCAGGAGC 59.869 47.826 0.00 0.00 42.56 4.70
2396 2515 5.575987 GCTAGCTAGGGTTCCTGGATATCTA 60.576 48.000 22.10 0.00 32.88 1.98
2405 2528 6.670027 GGGTTCCTGGATATCTACATCAGTAT 59.330 42.308 0.00 0.00 0.00 2.12
2479 2611 3.316308 AGACATTGTCTGAGTGTTTTGGC 59.684 43.478 18.35 0.00 41.76 4.52
2502 2634 6.547510 GGCATCTGAATTCTTAGGGTTTGTAT 59.452 38.462 7.05 0.00 0.00 2.29
2557 2689 3.374042 TTCAGTTTGGACTTTGGACCA 57.626 42.857 0.00 0.00 35.65 4.02
2741 2873 9.304731 CAGATATTATTTTTGTGTGGTTGGATG 57.695 33.333 0.00 0.00 0.00 3.51
2742 2874 9.253832 AGATATTATTTTTGTGTGGTTGGATGA 57.746 29.630 0.00 0.00 0.00 2.92
2757 2889 7.067494 GTGGTTGGATGAGAGCTTAATTACAAT 59.933 37.037 0.00 0.00 0.00 2.71
2767 2899 9.130312 GAGAGCTTAATTACAATACCATACTCG 57.870 37.037 0.00 0.00 0.00 4.18
2783 2915 7.426410 ACCATACTCGAGTACAATATTCTGTG 58.574 38.462 26.87 16.11 32.72 3.66
2795 2927 5.105756 ACAATATTCTGTGCCCAAAAGTAGC 60.106 40.000 0.00 0.00 0.00 3.58
2835 2967 1.206072 GTTCAGCAAGCAGTCGCAG 59.794 57.895 0.00 0.00 42.27 5.18
2944 3076 2.589014 CTCGTCTTTGCCTGAATTTGC 58.411 47.619 0.00 0.00 0.00 3.68
2981 3114 2.232452 AGACTCGTGGTGAAGATTGGAG 59.768 50.000 0.00 0.00 0.00 3.86
2991 3124 6.321181 GTGGTGAAGATTGGAGGCAAATATTA 59.679 38.462 0.00 0.00 0.00 0.98
2992 3125 7.014615 GTGGTGAAGATTGGAGGCAAATATTAT 59.985 37.037 0.00 0.00 0.00 1.28
2993 3126 7.564660 TGGTGAAGATTGGAGGCAAATATTATT 59.435 33.333 0.00 0.00 0.00 1.40
2994 3127 8.424133 GGTGAAGATTGGAGGCAAATATTATTT 58.576 33.333 0.00 0.00 0.00 1.40
3003 3136 8.637986 TGGAGGCAAATATTATTTACATTGTCC 58.362 33.333 1.41 4.18 0.00 4.02
3004 3137 8.860088 GGAGGCAAATATTATTTACATTGTCCT 58.140 33.333 1.41 2.41 31.62 3.85
3005 3138 9.683069 GAGGCAAATATTATTTACATTGTCCTG 57.317 33.333 1.41 0.00 30.22 3.86
3006 3139 8.641541 AGGCAAATATTATTTACATTGTCCTGG 58.358 33.333 1.41 0.00 0.00 4.45
3007 3140 7.872483 GGCAAATATTATTTACATTGTCCTGGG 59.128 37.037 1.41 0.00 0.00 4.45
3008 3141 8.637986 GCAAATATTATTTACATTGTCCTGGGA 58.362 33.333 1.41 0.00 0.00 4.37
3012 3145 9.881773 ATATTATTTACATTGTCCTGGGAATGT 57.118 29.630 21.16 21.16 43.55 2.71
3013 3146 8.608185 ATTATTTACATTGTCCTGGGAATGTT 57.392 30.769 22.05 12.20 41.79 2.71
3014 3147 6.933514 ATTTACATTGTCCTGGGAATGTTT 57.066 33.333 22.05 10.79 41.79 2.83
3015 3148 9.535170 TTATTTACATTGTCCTGGGAATGTTTA 57.465 29.630 22.05 14.40 41.79 2.01
3016 3149 7.461182 TTTACATTGTCCTGGGAATGTTTAG 57.539 36.000 22.05 2.80 41.79 1.85
3017 3150 3.763897 ACATTGTCCTGGGAATGTTTAGC 59.236 43.478 15.25 0.00 39.27 3.09
3018 3151 3.517296 TTGTCCTGGGAATGTTTAGCA 57.483 42.857 0.00 0.00 0.00 3.49
3019 3152 3.737559 TGTCCTGGGAATGTTTAGCAT 57.262 42.857 0.00 0.00 40.03 3.79
3020 3153 3.620488 TGTCCTGGGAATGTTTAGCATC 58.380 45.455 0.00 0.00 36.67 3.91
3021 3154 3.010027 TGTCCTGGGAATGTTTAGCATCA 59.990 43.478 0.00 0.00 36.67 3.07
3022 3155 4.210331 GTCCTGGGAATGTTTAGCATCAT 58.790 43.478 0.00 0.00 36.67 2.45
3023 3156 5.104151 TGTCCTGGGAATGTTTAGCATCATA 60.104 40.000 0.00 0.00 36.67 2.15
3024 3157 5.239525 GTCCTGGGAATGTTTAGCATCATAC 59.760 44.000 0.00 0.00 36.67 2.39
3025 3158 5.104151 TCCTGGGAATGTTTAGCATCATACA 60.104 40.000 0.00 0.00 36.67 2.29
3026 3159 5.771666 CCTGGGAATGTTTAGCATCATACAT 59.228 40.000 0.00 0.00 36.67 2.29
3027 3160 6.294342 CCTGGGAATGTTTAGCATCATACATG 60.294 42.308 0.00 0.00 36.67 3.21
3028 3161 6.128486 TGGGAATGTTTAGCATCATACATGT 58.872 36.000 2.69 2.69 36.67 3.21
3029 3162 6.262944 TGGGAATGTTTAGCATCATACATGTC 59.737 38.462 0.00 0.00 36.67 3.06
3030 3163 6.294176 GGGAATGTTTAGCATCATACATGTCC 60.294 42.308 0.00 0.00 36.67 4.02
3031 3164 6.488006 GGAATGTTTAGCATCATACATGTCCT 59.512 38.462 0.00 0.00 36.67 3.85
3032 3165 7.661437 GGAATGTTTAGCATCATACATGTCCTA 59.339 37.037 0.00 0.00 36.67 2.94
3033 3166 9.224267 GAATGTTTAGCATCATACATGTCCTAT 57.776 33.333 0.00 0.00 36.67 2.57
3034 3167 8.783833 ATGTTTAGCATCATACATGTCCTATC 57.216 34.615 0.00 0.00 30.67 2.08
3035 3168 7.734942 TGTTTAGCATCATACATGTCCTATCA 58.265 34.615 0.00 0.00 0.00 2.15
3036 3169 8.377799 TGTTTAGCATCATACATGTCCTATCAT 58.622 33.333 0.00 0.00 0.00 2.45
3037 3170 9.224267 GTTTAGCATCATACATGTCCTATCATT 57.776 33.333 0.00 0.00 0.00 2.57
3038 3171 9.440773 TTTAGCATCATACATGTCCTATCATTC 57.559 33.333 0.00 0.00 0.00 2.67
3039 3172 6.104665 AGCATCATACATGTCCTATCATTCG 58.895 40.000 0.00 0.00 0.00 3.34
3040 3173 5.871524 GCATCATACATGTCCTATCATTCGT 59.128 40.000 0.00 0.00 0.00 3.85
3041 3174 6.035435 GCATCATACATGTCCTATCATTCGTC 59.965 42.308 0.00 0.00 0.00 4.20
3042 3175 6.648879 TCATACATGTCCTATCATTCGTCA 57.351 37.500 0.00 0.00 0.00 4.35
3043 3176 7.232118 TCATACATGTCCTATCATTCGTCAT 57.768 36.000 0.00 0.00 0.00 3.06
3044 3177 7.670364 TCATACATGTCCTATCATTCGTCATT 58.330 34.615 0.00 0.00 0.00 2.57
3045 3178 8.150296 TCATACATGTCCTATCATTCGTCATTT 58.850 33.333 0.00 0.00 0.00 2.32
3046 3179 6.851222 ACATGTCCTATCATTCGTCATTTC 57.149 37.500 0.00 0.00 0.00 2.17
3047 3180 6.586344 ACATGTCCTATCATTCGTCATTTCT 58.414 36.000 0.00 0.00 0.00 2.52
3048 3181 7.050377 ACATGTCCTATCATTCGTCATTTCTT 58.950 34.615 0.00 0.00 0.00 2.52
3049 3182 7.225538 ACATGTCCTATCATTCGTCATTTCTTC 59.774 37.037 0.00 0.00 0.00 2.87
3050 3183 6.878317 TGTCCTATCATTCGTCATTTCTTCT 58.122 36.000 0.00 0.00 0.00 2.85
3051 3184 7.331026 TGTCCTATCATTCGTCATTTCTTCTT 58.669 34.615 0.00 0.00 0.00 2.52
3052 3185 8.474831 TGTCCTATCATTCGTCATTTCTTCTTA 58.525 33.333 0.00 0.00 0.00 2.10
3053 3186 9.482627 GTCCTATCATTCGTCATTTCTTCTTAT 57.517 33.333 0.00 0.00 0.00 1.73
3054 3187 9.698309 TCCTATCATTCGTCATTTCTTCTTATC 57.302 33.333 0.00 0.00 0.00 1.75
3055 3188 9.481340 CCTATCATTCGTCATTTCTTCTTATCA 57.519 33.333 0.00 0.00 0.00 2.15
3073 3206 9.542462 TTCTTATCAAATTACATACTCCCTTCG 57.458 33.333 0.00 0.00 0.00 3.79
3074 3207 8.701895 TCTTATCAAATTACATACTCCCTTCGT 58.298 33.333 0.00 0.00 0.00 3.85
3075 3208 8.882415 TTATCAAATTACATACTCCCTTCGTC 57.118 34.615 0.00 0.00 0.00 4.20
3076 3209 6.540438 TCAAATTACATACTCCCTTCGTCT 57.460 37.500 0.00 0.00 0.00 4.18
3077 3210 6.570692 TCAAATTACATACTCCCTTCGTCTC 58.429 40.000 0.00 0.00 0.00 3.36
3078 3211 6.153851 TCAAATTACATACTCCCTTCGTCTCA 59.846 38.462 0.00 0.00 0.00 3.27
3079 3212 6.540438 AATTACATACTCCCTTCGTCTCAA 57.460 37.500 0.00 0.00 0.00 3.02
3080 3213 5.988310 TTACATACTCCCTTCGTCTCAAA 57.012 39.130 0.00 0.00 0.00 2.69
3081 3214 4.884668 ACATACTCCCTTCGTCTCAAAA 57.115 40.909 0.00 0.00 0.00 2.44
3082 3215 5.422214 ACATACTCCCTTCGTCTCAAAAT 57.578 39.130 0.00 0.00 0.00 1.82
3083 3216 6.540438 ACATACTCCCTTCGTCTCAAAATA 57.460 37.500 0.00 0.00 0.00 1.40
3084 3217 6.942976 ACATACTCCCTTCGTCTCAAAATAA 58.057 36.000 0.00 0.00 0.00 1.40
3085 3218 7.042335 ACATACTCCCTTCGTCTCAAAATAAG 58.958 38.462 0.00 0.00 0.00 1.73
3086 3219 5.485209 ACTCCCTTCGTCTCAAAATAAGT 57.515 39.130 0.00 0.00 0.00 2.24
3087 3220 6.600882 ACTCCCTTCGTCTCAAAATAAGTA 57.399 37.500 0.00 0.00 0.00 2.24
3088 3221 7.184067 ACTCCCTTCGTCTCAAAATAAGTAT 57.816 36.000 0.00 0.00 0.00 2.12
3089 3222 7.266400 ACTCCCTTCGTCTCAAAATAAGTATC 58.734 38.462 0.00 0.00 0.00 2.24
3090 3223 7.124448 ACTCCCTTCGTCTCAAAATAAGTATCT 59.876 37.037 0.00 0.00 0.00 1.98
3091 3224 7.490000 TCCCTTCGTCTCAAAATAAGTATCTC 58.510 38.462 0.00 0.00 0.00 2.75
3092 3225 7.123697 TCCCTTCGTCTCAAAATAAGTATCTCA 59.876 37.037 0.00 0.00 0.00 3.27
3093 3226 7.764443 CCCTTCGTCTCAAAATAAGTATCTCAA 59.236 37.037 0.00 0.00 0.00 3.02
3094 3227 8.596380 CCTTCGTCTCAAAATAAGTATCTCAAC 58.404 37.037 0.00 0.00 0.00 3.18
3095 3228 9.360093 CTTCGTCTCAAAATAAGTATCTCAACT 57.640 33.333 0.00 0.00 0.00 3.16
3096 3229 9.706691 TTCGTCTCAAAATAAGTATCTCAACTT 57.293 29.630 0.00 0.00 42.31 2.66
3097 3230 9.706691 TCGTCTCAAAATAAGTATCTCAACTTT 57.293 29.630 0.00 0.00 40.20 2.66
3128 3261 8.530269 AATTCTAGTGTAAAGTTGTACGAAGG 57.470 34.615 0.00 0.00 0.00 3.46
3129 3262 6.639632 TCTAGTGTAAAGTTGTACGAAGGT 57.360 37.500 0.00 0.00 0.00 3.50
3130 3263 6.672147 TCTAGTGTAAAGTTGTACGAAGGTC 58.328 40.000 0.00 0.00 0.00 3.85
3131 3264 5.266733 AGTGTAAAGTTGTACGAAGGTCA 57.733 39.130 0.00 0.00 0.00 4.02
3132 3265 5.663456 AGTGTAAAGTTGTACGAAGGTCAA 58.337 37.500 0.00 0.00 0.00 3.18
3133 3266 5.751990 AGTGTAAAGTTGTACGAAGGTCAAG 59.248 40.000 0.00 0.00 0.00 3.02
3134 3267 5.750067 GTGTAAAGTTGTACGAAGGTCAAGA 59.250 40.000 0.00 0.00 0.00 3.02
3135 3268 5.750067 TGTAAAGTTGTACGAAGGTCAAGAC 59.250 40.000 0.00 0.00 0.00 3.01
3136 3269 4.395959 AAGTTGTACGAAGGTCAAGACA 57.604 40.909 2.29 0.00 0.00 3.41
3137 3270 4.602340 AGTTGTACGAAGGTCAAGACAT 57.398 40.909 2.29 0.00 0.00 3.06
3138 3271 4.957296 AGTTGTACGAAGGTCAAGACATT 58.043 39.130 0.00 0.00 38.10 2.71
3139 3272 5.365619 AGTTGTACGAAGGTCAAGACATTT 58.634 37.500 1.42 0.00 35.27 2.32
3140 3273 5.820947 AGTTGTACGAAGGTCAAGACATTTT 59.179 36.000 1.42 0.00 35.27 1.82
3141 3274 6.317893 AGTTGTACGAAGGTCAAGACATTTTT 59.682 34.615 1.42 0.00 35.27 1.94
3164 3297 4.428615 TTAACCTTTTACATGCCTTCGC 57.571 40.909 0.00 0.00 0.00 4.70
3165 3298 2.200373 ACCTTTTACATGCCTTCGCT 57.800 45.000 0.00 0.00 35.36 4.93
3166 3299 3.343941 ACCTTTTACATGCCTTCGCTA 57.656 42.857 0.00 0.00 35.36 4.26
3167 3300 3.007635 ACCTTTTACATGCCTTCGCTAC 58.992 45.455 0.00 0.00 35.36 3.58
3168 3301 2.354821 CCTTTTACATGCCTTCGCTACC 59.645 50.000 0.00 0.00 35.36 3.18
3169 3302 2.032680 TTTACATGCCTTCGCTACCC 57.967 50.000 0.00 0.00 35.36 3.69
3170 3303 0.179468 TTACATGCCTTCGCTACCCC 59.821 55.000 0.00 0.00 35.36 4.95
3171 3304 1.692173 TACATGCCTTCGCTACCCCC 61.692 60.000 0.00 0.00 35.36 5.40
3172 3305 3.861797 ATGCCTTCGCTACCCCCG 61.862 66.667 0.00 0.00 35.36 5.73
3174 3307 4.832608 GCCTTCGCTACCCCCGTG 62.833 72.222 0.00 0.00 0.00 4.94
3175 3308 3.387947 CCTTCGCTACCCCCGTGT 61.388 66.667 0.00 0.00 0.00 4.49
3176 3309 2.660802 CTTCGCTACCCCCGTGTT 59.339 61.111 0.00 0.00 0.00 3.32
3177 3310 1.740296 CTTCGCTACCCCCGTGTTG 60.740 63.158 0.00 0.00 0.00 3.33
3178 3311 3.887335 TTCGCTACCCCCGTGTTGC 62.887 63.158 0.00 0.00 34.32 4.17
3180 3313 4.338710 GCTACCCCCGTGTTGCCA 62.339 66.667 0.00 0.00 31.98 4.92
3181 3314 2.046314 CTACCCCCGTGTTGCCAG 60.046 66.667 0.00 0.00 0.00 4.85
3182 3315 4.338710 TACCCCCGTGTTGCCAGC 62.339 66.667 0.00 0.00 0.00 4.85
3235 3368 2.521479 CCCTAGGCCTCCGCTCTA 59.479 66.667 9.68 0.00 34.44 2.43
3236 3369 1.605165 CCCTAGGCCTCCGCTCTAG 60.605 68.421 9.68 0.00 36.45 2.43
3237 3370 1.151908 CCTAGGCCTCCGCTCTAGT 59.848 63.158 9.68 0.00 35.64 2.57
3238 3371 0.891904 CCTAGGCCTCCGCTCTAGTC 60.892 65.000 9.68 0.00 35.64 2.59
3239 3372 0.109723 CTAGGCCTCCGCTCTAGTCT 59.890 60.000 9.68 0.00 34.09 3.24
3240 3373 0.108963 TAGGCCTCCGCTCTAGTCTC 59.891 60.000 9.68 0.00 34.44 3.36
3241 3374 2.197605 GGCCTCCGCTCTAGTCTCC 61.198 68.421 0.00 0.00 34.44 3.71
3242 3375 2.197605 GCCTCCGCTCTAGTCTCCC 61.198 68.421 0.00 0.00 0.00 4.30
3243 3376 1.529713 CCTCCGCTCTAGTCTCCCC 60.530 68.421 0.00 0.00 0.00 4.81
3244 3377 1.529713 CTCCGCTCTAGTCTCCCCC 60.530 68.421 0.00 0.00 0.00 5.40
3245 3378 2.002018 CTCCGCTCTAGTCTCCCCCT 62.002 65.000 0.00 0.00 0.00 4.79
3246 3379 1.529713 CCGCTCTAGTCTCCCCCTC 60.530 68.421 0.00 0.00 0.00 4.30
3247 3380 1.529713 CGCTCTAGTCTCCCCCTCC 60.530 68.421 0.00 0.00 0.00 4.30
3248 3381 1.935191 GCTCTAGTCTCCCCCTCCT 59.065 63.158 0.00 0.00 0.00 3.69
3249 3382 0.469144 GCTCTAGTCTCCCCCTCCTG 60.469 65.000 0.00 0.00 0.00 3.86
3250 3383 0.469144 CTCTAGTCTCCCCCTCCTGC 60.469 65.000 0.00 0.00 0.00 4.85
3251 3384 0.926720 TCTAGTCTCCCCCTCCTGCT 60.927 60.000 0.00 0.00 0.00 4.24
3252 3385 0.758685 CTAGTCTCCCCCTCCTGCTG 60.759 65.000 0.00 0.00 0.00 4.41
3253 3386 2.880629 TAGTCTCCCCCTCCTGCTGC 62.881 65.000 0.00 0.00 0.00 5.25
3289 3422 2.707902 GCATAGCCTGGCCAGTAAC 58.292 57.895 30.63 19.33 0.00 2.50
3290 3423 1.160329 GCATAGCCTGGCCAGTAACG 61.160 60.000 30.63 16.64 0.00 3.18
3291 3424 0.532862 CATAGCCTGGCCAGTAACGG 60.533 60.000 30.63 17.57 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.619973 TGATTGAATGTGCCAAACAGAAC 58.380 39.130 0.00 0.00 43.64 3.01
11 12 4.583907 TCTTGATTGAATGTGCCAAACAGA 59.416 37.500 0.00 0.00 43.64 3.41
23 24 6.845758 ACATGTTGTCCATCTTGATTGAAT 57.154 33.333 0.00 0.00 0.00 2.57
74 75 2.832643 ATGCCAAGGTGATCCATTGA 57.167 45.000 9.30 0.00 35.89 2.57
138 140 3.060325 CCGGAGGCAGTGCAACTATAAG 61.060 54.545 18.61 0.00 46.86 1.73
212 214 0.175989 CCTTTCTCTAGCCGACCCAC 59.824 60.000 0.00 0.00 0.00 4.61
281 315 8.861086 GGATGGAGTAGTTATCTTTCATGAGTA 58.139 37.037 0.00 0.00 0.00 2.59
356 425 9.807921 TTTCTAAAGGATAAGATTTGTTGTCCT 57.192 29.630 0.63 0.63 46.84 3.85
462 535 2.928801 TACACATGCTGACTGGTTGT 57.071 45.000 0.00 0.00 0.00 3.32
465 538 2.568956 ACTGATACACATGCTGACTGGT 59.431 45.455 0.00 0.00 0.00 4.00
468 541 5.738495 GCATAGACTGATACACATGCTGACT 60.738 44.000 0.00 0.00 29.98 3.41
471 544 3.427863 CGCATAGACTGATACACATGCTG 59.572 47.826 0.00 0.00 30.28 4.41
487 564 1.749063 TGTCTCTACCCACACGCATAG 59.251 52.381 0.00 0.00 0.00 2.23
527 604 6.817140 AGAAGGGATGTTTCGTAACAGATTAC 59.183 38.462 13.17 0.00 46.71 1.89
528 605 6.942976 AGAAGGGATGTTTCGTAACAGATTA 58.057 36.000 13.17 0.00 46.71 1.75
529 606 5.805728 AGAAGGGATGTTTCGTAACAGATT 58.194 37.500 13.17 5.36 46.71 2.40
530 607 5.422214 AGAAGGGATGTTTCGTAACAGAT 57.578 39.130 13.17 0.00 46.71 2.90
531 608 4.884668 AGAAGGGATGTTTCGTAACAGA 57.115 40.909 13.17 0.00 46.71 3.41
532 609 6.258068 GGATTAGAAGGGATGTTTCGTAACAG 59.742 42.308 13.17 0.00 46.71 3.16
534 611 6.346896 AGGATTAGAAGGGATGTTTCGTAAC 58.653 40.000 0.00 0.00 34.75 2.50
535 612 6.383147 AGAGGATTAGAAGGGATGTTTCGTAA 59.617 38.462 0.00 0.00 0.00 3.18
536 613 5.897824 AGAGGATTAGAAGGGATGTTTCGTA 59.102 40.000 0.00 0.00 0.00 3.43
537 614 4.717280 AGAGGATTAGAAGGGATGTTTCGT 59.283 41.667 0.00 0.00 0.00 3.85
538 615 5.283457 AGAGGATTAGAAGGGATGTTTCG 57.717 43.478 0.00 0.00 0.00 3.46
539 616 5.293560 CGAGAGGATTAGAAGGGATGTTTC 58.706 45.833 0.00 0.00 0.00 2.78
540 617 4.443598 GCGAGAGGATTAGAAGGGATGTTT 60.444 45.833 0.00 0.00 0.00 2.83
541 618 3.070302 GCGAGAGGATTAGAAGGGATGTT 59.930 47.826 0.00 0.00 0.00 2.71
542 619 2.630580 GCGAGAGGATTAGAAGGGATGT 59.369 50.000 0.00 0.00 0.00 3.06
543 620 2.028567 GGCGAGAGGATTAGAAGGGATG 60.029 54.545 0.00 0.00 0.00 3.51
544 621 2.252714 GGCGAGAGGATTAGAAGGGAT 58.747 52.381 0.00 0.00 0.00 3.85
545 622 1.705873 GGCGAGAGGATTAGAAGGGA 58.294 55.000 0.00 0.00 0.00 4.20
546 623 0.682292 GGGCGAGAGGATTAGAAGGG 59.318 60.000 0.00 0.00 0.00 3.95
547 624 0.682292 GGGGCGAGAGGATTAGAAGG 59.318 60.000 0.00 0.00 0.00 3.46
548 625 1.710816 AGGGGCGAGAGGATTAGAAG 58.289 55.000 0.00 0.00 0.00 2.85
549 626 1.762957 CAAGGGGCGAGAGGATTAGAA 59.237 52.381 0.00 0.00 0.00 2.10
550 627 1.063190 TCAAGGGGCGAGAGGATTAGA 60.063 52.381 0.00 0.00 0.00 2.10
551 628 1.414158 TCAAGGGGCGAGAGGATTAG 58.586 55.000 0.00 0.00 0.00 1.73
552 629 2.103153 ATCAAGGGGCGAGAGGATTA 57.897 50.000 0.00 0.00 0.00 1.75
553 630 1.216990 AATCAAGGGGCGAGAGGATT 58.783 50.000 0.00 0.00 0.00 3.01
554 631 1.141858 GAAATCAAGGGGCGAGAGGAT 59.858 52.381 0.00 0.00 0.00 3.24
555 632 0.541863 GAAATCAAGGGGCGAGAGGA 59.458 55.000 0.00 0.00 0.00 3.71
556 633 0.253044 TGAAATCAAGGGGCGAGAGG 59.747 55.000 0.00 0.00 0.00 3.69
557 634 1.740025 GTTGAAATCAAGGGGCGAGAG 59.260 52.381 0.00 0.00 36.39 3.20
558 635 1.351017 AGTTGAAATCAAGGGGCGAGA 59.649 47.619 0.00 0.00 36.39 4.04
559 636 1.826385 AGTTGAAATCAAGGGGCGAG 58.174 50.000 0.00 0.00 36.39 5.03
560 637 2.355716 CCTAGTTGAAATCAAGGGGCGA 60.356 50.000 0.00 0.00 36.39 5.54
561 638 2.017049 CCTAGTTGAAATCAAGGGGCG 58.983 52.381 0.00 0.00 36.39 6.13
562 639 2.291605 ACCCTAGTTGAAATCAAGGGGC 60.292 50.000 18.48 0.00 40.94 5.80
567 644 3.245122 GGACCCACCCTAGTTGAAATCAA 60.245 47.826 0.00 0.00 0.00 2.57
586 665 1.341852 GAGATAGAGCGAAAGGGGGAC 59.658 57.143 0.00 0.00 0.00 4.46
615 694 3.487372 GGGGATTAGCCAGTTGGTATTC 58.513 50.000 0.00 0.00 38.95 1.75
619 698 1.921869 CGGGGGATTAGCCAGTTGGT 61.922 60.000 0.00 0.00 38.95 3.67
623 702 1.587066 TTTACGGGGGATTAGCCAGT 58.413 50.000 0.00 0.00 38.95 4.00
624 703 2.158667 ACATTTACGGGGGATTAGCCAG 60.159 50.000 0.00 0.00 38.95 4.85
625 704 1.847737 ACATTTACGGGGGATTAGCCA 59.152 47.619 0.00 0.00 38.95 4.75
626 705 2.651382 ACATTTACGGGGGATTAGCC 57.349 50.000 0.00 0.00 0.00 3.93
627 706 4.347360 AGTACATTTACGGGGGATTAGC 57.653 45.455 0.00 0.00 32.93 3.09
628 707 8.913487 AATTAAGTACATTTACGGGGGATTAG 57.087 34.615 0.00 0.00 32.93 1.73
629 708 9.697990 AAAATTAAGTACATTTACGGGGGATTA 57.302 29.630 0.00 0.00 32.93 1.75
630 709 8.598202 AAAATTAAGTACATTTACGGGGGATT 57.402 30.769 0.00 0.00 32.93 3.01
631 710 7.286087 GGAAAATTAAGTACATTTACGGGGGAT 59.714 37.037 0.00 0.00 32.93 3.85
632 711 6.602803 GGAAAATTAAGTACATTTACGGGGGA 59.397 38.462 0.00 0.00 32.93 4.81
633 712 6.458615 CGGAAAATTAAGTACATTTACGGGGG 60.459 42.308 0.00 0.00 32.93 5.40
634 713 6.093909 ACGGAAAATTAAGTACATTTACGGGG 59.906 38.462 13.45 0.00 32.61 5.73
635 714 6.962678 CACGGAAAATTAAGTACATTTACGGG 59.037 38.462 13.45 8.29 32.61 5.28
636 715 6.962678 CCACGGAAAATTAAGTACATTTACGG 59.037 38.462 13.45 6.22 32.61 4.02
637 716 7.741198 TCCACGGAAAATTAAGTACATTTACG 58.259 34.615 0.00 3.72 33.64 3.18
638 717 9.498307 CATCCACGGAAAATTAAGTACATTTAC 57.502 33.333 0.00 0.00 0.00 2.01
639 718 9.233649 ACATCCACGGAAAATTAAGTACATTTA 57.766 29.630 0.00 0.00 0.00 1.40
640 719 8.117813 ACATCCACGGAAAATTAAGTACATTT 57.882 30.769 0.00 0.00 0.00 2.32
641 720 7.696992 ACATCCACGGAAAATTAAGTACATT 57.303 32.000 0.00 0.00 0.00 2.71
642 721 7.012044 GCTACATCCACGGAAAATTAAGTACAT 59.988 37.037 0.00 0.00 0.00 2.29
643 722 6.314400 GCTACATCCACGGAAAATTAAGTACA 59.686 38.462 0.00 0.00 0.00 2.90
644 723 6.314400 TGCTACATCCACGGAAAATTAAGTAC 59.686 38.462 0.00 0.00 0.00 2.73
645 724 6.408035 TGCTACATCCACGGAAAATTAAGTA 58.592 36.000 0.00 0.00 0.00 2.24
651 730 3.181487 GCAATGCTACATCCACGGAAAAT 60.181 43.478 0.00 0.00 0.00 1.82
656 735 0.940126 GAGCAATGCTACATCCACGG 59.060 55.000 8.12 0.00 39.88 4.94
658 737 1.656652 ACGAGCAATGCTACATCCAC 58.343 50.000 8.12 0.00 39.88 4.02
970 1056 4.219115 GGGACTGATGGTAGAGATGAAGA 58.781 47.826 0.00 0.00 0.00 2.87
987 1073 3.041946 GTGATACATCTTCAGGGGGACT 58.958 50.000 0.00 0.00 0.00 3.85
988 1074 2.104963 GGTGATACATCTTCAGGGGGAC 59.895 54.545 0.00 0.00 0.00 4.46
989 1075 2.293519 TGGTGATACATCTTCAGGGGGA 60.294 50.000 0.00 0.00 0.00 4.81
1095 1198 1.294659 GGTGGAAGTTGAGCTCTGCG 61.295 60.000 16.19 0.00 0.00 5.18
1167 1270 4.673298 TCTGCGCCGCCGAAGAAA 62.673 61.111 6.63 0.00 45.91 2.52
1462 1565 1.470890 CTTCTCCTTCTTCTCGACGCT 59.529 52.381 0.00 0.00 0.00 5.07
1570 1673 6.358558 TGCGACGAATTAAAAACAAGATGAAC 59.641 34.615 0.00 0.00 0.00 3.18
1750 1853 3.231889 CTCCACCAGCAGCGTCAGT 62.232 63.158 0.00 0.00 0.00 3.41
1823 1926 4.181010 CCCATCTCCGGCCACCAG 62.181 72.222 2.24 0.00 0.00 4.00
1837 1940 3.324930 CCTGCAGAGCACTCCCCA 61.325 66.667 17.39 0.00 33.79 4.96
2110 2213 3.297830 TGTGACGATGTGACTACCTTG 57.702 47.619 0.00 0.00 0.00 3.61
2118 2221 3.507622 AGAGATCTGTTGTGACGATGTGA 59.492 43.478 0.00 0.00 0.00 3.58
2158 2263 2.076100 ACACTGAACGTACATGCATGG 58.924 47.619 29.41 14.96 0.00 3.66
2223 2333 6.430616 TCTGCATACACATCAACAAATGAGAA 59.569 34.615 0.00 0.00 42.53 2.87
2225 2335 6.185852 TCTGCATACACATCAACAAATGAG 57.814 37.500 0.00 0.00 42.53 2.90
2342 2457 3.944055 ATATAGAAACGCATCGCTCCT 57.056 42.857 0.00 0.00 0.00 3.69
2343 2458 3.423645 GCAATATAGAAACGCATCGCTCC 60.424 47.826 0.00 0.00 0.00 4.70
2345 2460 3.393800 AGCAATATAGAAACGCATCGCT 58.606 40.909 0.00 0.00 0.00 4.93
2346 2461 3.795561 AGCAATATAGAAACGCATCGC 57.204 42.857 0.00 0.00 0.00 4.58
2347 2462 4.623167 AGCTAGCAATATAGAAACGCATCG 59.377 41.667 18.83 0.00 0.00 3.84
2418 2541 9.626045 GGATCAAACAGTCCAAAATTAAAGTAG 57.374 33.333 0.00 0.00 34.57 2.57
2420 2543 8.017418 TGGATCAAACAGTCCAAAATTAAAGT 57.983 30.769 0.00 0.00 41.36 2.66
2460 2589 3.713858 TGCCAAAACACTCAGACAATG 57.286 42.857 0.00 0.00 0.00 2.82
2479 2611 9.177608 TCAATACAAACCCTAAGAATTCAGATG 57.822 33.333 8.44 0.00 0.00 2.90
2741 2873 9.130312 CGAGTATGGTATTGTAATTAAGCTCTC 57.870 37.037 0.00 0.00 0.00 3.20
2742 2874 8.857098 TCGAGTATGGTATTGTAATTAAGCTCT 58.143 33.333 0.00 0.00 0.00 4.09
2757 2889 8.565416 CACAGAATATTGTACTCGAGTATGGTA 58.435 37.037 27.02 18.73 32.54 3.25
2767 2899 6.151144 ACTTTTGGGCACAGAATATTGTACTC 59.849 38.462 0.00 0.00 0.00 2.59
2783 2915 2.742589 GTGTACTGAGCTACTTTTGGGC 59.257 50.000 0.00 0.00 0.00 5.36
2981 3114 7.872483 CCCAGGACAATGTAAATAATATTTGCC 59.128 37.037 8.39 0.47 0.00 4.52
2991 3124 6.933514 AAACATTCCCAGGACAATGTAAAT 57.066 33.333 14.26 4.99 41.42 1.40
2992 3125 6.071616 GCTAAACATTCCCAGGACAATGTAAA 60.072 38.462 14.26 7.34 41.42 2.01
2993 3126 5.417580 GCTAAACATTCCCAGGACAATGTAA 59.582 40.000 14.26 7.59 41.42 2.41
2994 3127 4.947388 GCTAAACATTCCCAGGACAATGTA 59.053 41.667 14.26 3.19 41.42 2.29
2995 3128 3.763897 GCTAAACATTCCCAGGACAATGT 59.236 43.478 9.85 9.85 43.61 2.71
2996 3129 3.763360 TGCTAAACATTCCCAGGACAATG 59.237 43.478 8.81 8.81 36.28 2.82
2997 3130 4.046286 TGCTAAACATTCCCAGGACAAT 57.954 40.909 0.00 0.00 0.00 2.71
2998 3131 3.517296 TGCTAAACATTCCCAGGACAA 57.483 42.857 0.00 0.00 0.00 3.18
2999 3132 3.010027 TGATGCTAAACATTCCCAGGACA 59.990 43.478 0.00 0.00 39.84 4.02
3000 3133 3.620488 TGATGCTAAACATTCCCAGGAC 58.380 45.455 0.00 0.00 39.84 3.85
3001 3134 4.524802 ATGATGCTAAACATTCCCAGGA 57.475 40.909 0.00 0.00 39.84 3.86
3002 3135 5.132502 TGTATGATGCTAAACATTCCCAGG 58.867 41.667 0.00 0.00 39.84 4.45
3003 3136 6.263842 ACATGTATGATGCTAAACATTCCCAG 59.736 38.462 0.00 0.00 39.84 4.45
3004 3137 6.128486 ACATGTATGATGCTAAACATTCCCA 58.872 36.000 0.00 0.00 39.84 4.37
3005 3138 6.294176 GGACATGTATGATGCTAAACATTCCC 60.294 42.308 0.00 0.00 39.84 3.97
3006 3139 6.488006 AGGACATGTATGATGCTAAACATTCC 59.512 38.462 0.00 0.00 39.84 3.01
3007 3140 7.502120 AGGACATGTATGATGCTAAACATTC 57.498 36.000 0.00 0.00 39.84 2.67
3008 3141 9.224267 GATAGGACATGTATGATGCTAAACATT 57.776 33.333 0.00 0.00 39.84 2.71
3009 3142 8.377799 TGATAGGACATGTATGATGCTAAACAT 58.622 33.333 0.00 0.00 43.54 2.71
3010 3143 7.734942 TGATAGGACATGTATGATGCTAAACA 58.265 34.615 0.00 0.00 0.00 2.83
3011 3144 8.783833 ATGATAGGACATGTATGATGCTAAAC 57.216 34.615 0.00 0.00 0.00 2.01
3012 3145 9.440773 GAATGATAGGACATGTATGATGCTAAA 57.559 33.333 0.00 0.00 0.00 1.85
3013 3146 7.761249 CGAATGATAGGACATGTATGATGCTAA 59.239 37.037 0.00 0.00 0.00 3.09
3014 3147 7.093771 ACGAATGATAGGACATGTATGATGCTA 60.094 37.037 0.00 0.00 0.00 3.49
3015 3148 6.104665 CGAATGATAGGACATGTATGATGCT 58.895 40.000 0.00 0.00 0.00 3.79
3016 3149 5.871524 ACGAATGATAGGACATGTATGATGC 59.128 40.000 0.00 0.00 0.00 3.91
3017 3150 7.092716 TGACGAATGATAGGACATGTATGATG 58.907 38.462 0.00 0.00 0.00 3.07
3018 3151 7.232118 TGACGAATGATAGGACATGTATGAT 57.768 36.000 0.00 0.00 0.00 2.45
3019 3152 6.648879 TGACGAATGATAGGACATGTATGA 57.351 37.500 0.00 0.00 0.00 2.15
3020 3153 7.895975 AATGACGAATGATAGGACATGTATG 57.104 36.000 0.00 0.00 0.00 2.39
3021 3154 8.370940 AGAAATGACGAATGATAGGACATGTAT 58.629 33.333 0.00 0.00 0.00 2.29
3022 3155 7.726216 AGAAATGACGAATGATAGGACATGTA 58.274 34.615 0.00 0.00 0.00 2.29
3023 3156 6.586344 AGAAATGACGAATGATAGGACATGT 58.414 36.000 0.00 0.00 0.00 3.21
3024 3157 7.440556 AGAAGAAATGACGAATGATAGGACATG 59.559 37.037 0.00 0.00 0.00 3.21
3025 3158 7.504403 AGAAGAAATGACGAATGATAGGACAT 58.496 34.615 0.00 0.00 0.00 3.06
3026 3159 6.878317 AGAAGAAATGACGAATGATAGGACA 58.122 36.000 0.00 0.00 0.00 4.02
3027 3160 7.778470 AAGAAGAAATGACGAATGATAGGAC 57.222 36.000 0.00 0.00 0.00 3.85
3028 3161 9.698309 GATAAGAAGAAATGACGAATGATAGGA 57.302 33.333 0.00 0.00 0.00 2.94
3029 3162 9.481340 TGATAAGAAGAAATGACGAATGATAGG 57.519 33.333 0.00 0.00 0.00 2.57
3047 3180 9.542462 CGAAGGGAGTATGTAATTTGATAAGAA 57.458 33.333 0.00 0.00 0.00 2.52
3048 3181 8.701895 ACGAAGGGAGTATGTAATTTGATAAGA 58.298 33.333 0.00 0.00 0.00 2.10
3049 3182 8.888579 ACGAAGGGAGTATGTAATTTGATAAG 57.111 34.615 0.00 0.00 0.00 1.73
3050 3183 8.701895 AGACGAAGGGAGTATGTAATTTGATAA 58.298 33.333 0.00 0.00 0.00 1.75
3051 3184 8.246430 AGACGAAGGGAGTATGTAATTTGATA 57.754 34.615 0.00 0.00 0.00 2.15
3052 3185 7.125792 AGACGAAGGGAGTATGTAATTTGAT 57.874 36.000 0.00 0.00 0.00 2.57
3053 3186 6.153851 TGAGACGAAGGGAGTATGTAATTTGA 59.846 38.462 0.00 0.00 0.00 2.69
3054 3187 6.338146 TGAGACGAAGGGAGTATGTAATTTG 58.662 40.000 0.00 0.00 0.00 2.32
3055 3188 6.540438 TGAGACGAAGGGAGTATGTAATTT 57.460 37.500 0.00 0.00 0.00 1.82
3056 3189 6.540438 TTGAGACGAAGGGAGTATGTAATT 57.460 37.500 0.00 0.00 0.00 1.40
3057 3190 6.540438 TTTGAGACGAAGGGAGTATGTAAT 57.460 37.500 0.00 0.00 0.00 1.89
3058 3191 5.988310 TTTGAGACGAAGGGAGTATGTAA 57.012 39.130 0.00 0.00 0.00 2.41
3059 3192 5.988310 TTTTGAGACGAAGGGAGTATGTA 57.012 39.130 0.00 0.00 0.00 2.29
3060 3193 4.884668 TTTTGAGACGAAGGGAGTATGT 57.115 40.909 0.00 0.00 0.00 2.29
3061 3194 7.042335 ACTTATTTTGAGACGAAGGGAGTATG 58.958 38.462 0.00 0.00 0.00 2.39
3062 3195 7.184067 ACTTATTTTGAGACGAAGGGAGTAT 57.816 36.000 0.00 0.00 0.00 2.12
3063 3196 6.600882 ACTTATTTTGAGACGAAGGGAGTA 57.399 37.500 0.00 0.00 0.00 2.59
3064 3197 5.485209 ACTTATTTTGAGACGAAGGGAGT 57.515 39.130 0.00 0.00 0.00 3.85
3065 3198 7.493367 AGATACTTATTTTGAGACGAAGGGAG 58.507 38.462 0.00 0.00 0.00 4.30
3066 3199 7.123697 TGAGATACTTATTTTGAGACGAAGGGA 59.876 37.037 0.00 0.00 0.00 4.20
3067 3200 7.265673 TGAGATACTTATTTTGAGACGAAGGG 58.734 38.462 0.00 0.00 0.00 3.95
3068 3201 8.596380 GTTGAGATACTTATTTTGAGACGAAGG 58.404 37.037 0.00 0.00 0.00 3.46
3069 3202 9.360093 AGTTGAGATACTTATTTTGAGACGAAG 57.640 33.333 0.00 0.00 0.00 3.79
3070 3203 9.706691 AAGTTGAGATACTTATTTTGAGACGAA 57.293 29.630 0.00 0.00 36.62 3.85
3071 3204 9.706691 AAAGTTGAGATACTTATTTTGAGACGA 57.293 29.630 0.00 0.00 37.37 4.20
3102 3235 9.630098 CCTTCGTACAACTTTACACTAGAATTA 57.370 33.333 0.00 0.00 0.00 1.40
3103 3236 8.146412 ACCTTCGTACAACTTTACACTAGAATT 58.854 33.333 0.00 0.00 0.00 2.17
3104 3237 7.664758 ACCTTCGTACAACTTTACACTAGAAT 58.335 34.615 0.00 0.00 0.00 2.40
3105 3238 7.042797 ACCTTCGTACAACTTTACACTAGAA 57.957 36.000 0.00 0.00 0.00 2.10
3106 3239 6.262944 TGACCTTCGTACAACTTTACACTAGA 59.737 38.462 0.00 0.00 0.00 2.43
3107 3240 6.441274 TGACCTTCGTACAACTTTACACTAG 58.559 40.000 0.00 0.00 0.00 2.57
3108 3241 6.389830 TGACCTTCGTACAACTTTACACTA 57.610 37.500 0.00 0.00 0.00 2.74
3109 3242 5.266733 TGACCTTCGTACAACTTTACACT 57.733 39.130 0.00 0.00 0.00 3.55
3110 3243 5.750067 TCTTGACCTTCGTACAACTTTACAC 59.250 40.000 0.00 0.00 0.00 2.90
3111 3244 5.750067 GTCTTGACCTTCGTACAACTTTACA 59.250 40.000 0.00 0.00 0.00 2.41
3112 3245 5.750067 TGTCTTGACCTTCGTACAACTTTAC 59.250 40.000 0.00 0.00 0.00 2.01
3113 3246 5.904941 TGTCTTGACCTTCGTACAACTTTA 58.095 37.500 0.00 0.00 0.00 1.85
3114 3247 4.761975 TGTCTTGACCTTCGTACAACTTT 58.238 39.130 0.00 0.00 0.00 2.66
3115 3248 4.395959 TGTCTTGACCTTCGTACAACTT 57.604 40.909 0.00 0.00 0.00 2.66
3116 3249 4.602340 ATGTCTTGACCTTCGTACAACT 57.398 40.909 0.00 0.00 0.00 3.16
3117 3250 5.668558 AAATGTCTTGACCTTCGTACAAC 57.331 39.130 0.00 0.00 0.00 3.32
3118 3251 6.687081 AAAAATGTCTTGACCTTCGTACAA 57.313 33.333 0.00 0.00 0.00 2.41
3140 3273 5.692654 GCGAAGGCATGTAAAAGGTTAAAAA 59.307 36.000 0.00 0.00 39.62 1.94
3141 3274 5.010213 AGCGAAGGCATGTAAAAGGTTAAAA 59.990 36.000 0.00 0.00 43.41 1.52
3142 3275 4.521256 AGCGAAGGCATGTAAAAGGTTAAA 59.479 37.500 0.00 0.00 43.41 1.52
3143 3276 4.076394 AGCGAAGGCATGTAAAAGGTTAA 58.924 39.130 0.00 0.00 43.41 2.01
3144 3277 3.681593 AGCGAAGGCATGTAAAAGGTTA 58.318 40.909 0.00 0.00 43.41 2.85
3145 3278 2.514803 AGCGAAGGCATGTAAAAGGTT 58.485 42.857 0.00 0.00 43.41 3.50
3146 3279 2.200373 AGCGAAGGCATGTAAAAGGT 57.800 45.000 0.00 0.00 43.41 3.50
3147 3280 2.354821 GGTAGCGAAGGCATGTAAAAGG 59.645 50.000 0.00 0.00 43.41 3.11
3148 3281 2.354821 GGGTAGCGAAGGCATGTAAAAG 59.645 50.000 0.00 0.00 43.41 2.27
3149 3282 2.361789 GGGTAGCGAAGGCATGTAAAA 58.638 47.619 0.00 0.00 43.41 1.52
3150 3283 1.407712 GGGGTAGCGAAGGCATGTAAA 60.408 52.381 0.00 0.00 43.41 2.01
3151 3284 0.179468 GGGGTAGCGAAGGCATGTAA 59.821 55.000 0.00 0.00 43.41 2.41
3152 3285 1.692173 GGGGGTAGCGAAGGCATGTA 61.692 60.000 0.00 0.00 43.41 2.29
3153 3286 2.590092 GGGGTAGCGAAGGCATGT 59.410 61.111 0.00 0.00 43.41 3.21
3154 3287 2.203209 GGGGGTAGCGAAGGCATG 60.203 66.667 0.00 0.00 43.41 4.06
3155 3288 3.861797 CGGGGGTAGCGAAGGCAT 61.862 66.667 0.00 0.00 43.41 4.40
3157 3290 4.832608 CACGGGGGTAGCGAAGGC 62.833 72.222 0.00 0.00 40.37 4.35
3158 3291 2.951101 AACACGGGGGTAGCGAAGG 61.951 63.158 0.00 0.00 0.00 3.46
3159 3292 1.740296 CAACACGGGGGTAGCGAAG 60.740 63.158 0.00 0.00 0.00 3.79
3160 3293 2.344500 CAACACGGGGGTAGCGAA 59.656 61.111 0.00 0.00 0.00 4.70
3161 3294 4.382320 GCAACACGGGGGTAGCGA 62.382 66.667 0.00 0.00 0.00 4.93
3163 3296 4.338710 TGGCAACACGGGGGTAGC 62.339 66.667 0.00 0.00 46.17 3.58
3164 3297 2.046314 CTGGCAACACGGGGGTAG 60.046 66.667 0.00 0.00 46.17 3.18
3165 3298 4.338710 GCTGGCAACACGGGGGTA 62.339 66.667 0.00 0.00 46.17 3.69
3218 3351 1.605165 CTAGAGCGGAGGCCTAGGG 60.605 68.421 4.42 0.00 41.24 3.53
3219 3352 0.891904 GACTAGAGCGGAGGCCTAGG 60.892 65.000 4.42 3.67 40.96 3.02
3220 3353 0.109723 AGACTAGAGCGGAGGCCTAG 59.890 60.000 4.42 3.81 41.69 3.02
3221 3354 0.108963 GAGACTAGAGCGGAGGCCTA 59.891 60.000 4.42 0.00 41.24 3.93
3222 3355 1.152839 GAGACTAGAGCGGAGGCCT 60.153 63.158 3.86 3.86 41.24 5.19
3223 3356 2.197605 GGAGACTAGAGCGGAGGCC 61.198 68.421 0.00 0.00 41.24 5.19
3224 3357 2.197605 GGGAGACTAGAGCGGAGGC 61.198 68.421 0.00 0.00 40.37 4.70
3225 3358 1.529713 GGGGAGACTAGAGCGGAGG 60.530 68.421 0.00 0.00 0.00 4.30
3226 3359 1.529713 GGGGGAGACTAGAGCGGAG 60.530 68.421 0.00 0.00 0.00 4.63
3227 3360 1.997256 GAGGGGGAGACTAGAGCGGA 61.997 65.000 0.00 0.00 0.00 5.54
3228 3361 1.529713 GAGGGGGAGACTAGAGCGG 60.530 68.421 0.00 0.00 0.00 5.52
3229 3362 1.529713 GGAGGGGGAGACTAGAGCG 60.530 68.421 0.00 0.00 0.00 5.03
3230 3363 0.469144 CAGGAGGGGGAGACTAGAGC 60.469 65.000 0.00 0.00 0.00 4.09
3231 3364 0.469144 GCAGGAGGGGGAGACTAGAG 60.469 65.000 0.00 0.00 0.00 2.43
3232 3365 0.926720 AGCAGGAGGGGGAGACTAGA 60.927 60.000 0.00 0.00 0.00 2.43
3233 3366 0.758685 CAGCAGGAGGGGGAGACTAG 60.759 65.000 0.00 0.00 0.00 2.57
3234 3367 1.311403 CAGCAGGAGGGGGAGACTA 59.689 63.158 0.00 0.00 0.00 2.59
3235 3368 2.040278 CAGCAGGAGGGGGAGACT 59.960 66.667 0.00 0.00 0.00 3.24
3236 3369 3.791586 GCAGCAGGAGGGGGAGAC 61.792 72.222 0.00 0.00 0.00 3.36
3271 3404 1.160329 CGTTACTGGCCAGGCTATGC 61.160 60.000 35.42 17.54 0.00 3.14
3272 3405 0.532862 CCGTTACTGGCCAGGCTATG 60.533 60.000 35.42 22.93 0.00 2.23
3273 3406 1.830145 CCGTTACTGGCCAGGCTAT 59.170 57.895 35.42 17.90 0.00 2.97
3274 3407 3.305314 CCGTTACTGGCCAGGCTA 58.695 61.111 35.42 17.93 0.00 3.93


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

AutoCloner maintained by Alex Coulton.