Multiple sequence alignment - TraesCS7D01G407000

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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 TraesCS7D01G407000 chr7D 100.000 6892 0 0 1 6892 524318741 524325632 0.000000e+00 12728
1 TraesCS7D01G407000 chr7A 88.675 2490 184 53 3464 5872 604393036 604395508 0.000000e+00 2946
2 TraesCS7D01G407000 chr7A 86.457 1905 144 51 1620 3431 604391003 604392886 0.000000e+00 1984
3 TraesCS7D01G407000 chr7A 94.797 1057 41 4 5846 6892 604395545 604396597 0.000000e+00 1635
4 TraesCS7D01G407000 chr7A 89.253 1312 98 26 369 1660 604389703 604390991 0.000000e+00 1602
5 TraesCS7D01G407000 chr7A 86.239 218 19 6 12 227 604383135 604383343 6.960000e-55 226
6 TraesCS7D01G407000 chr7A 88.430 121 10 3 2753 2873 729362965 729362849 7.210000e-30 143
7 TraesCS7D01G407000 chr7A 88.333 120 10 3 2754 2873 729340398 729340283 2.590000e-29 141
8 TraesCS7D01G407000 chr7B 91.417 1934 128 22 3970 5872 560529031 560530957 0.000000e+00 2617
9 TraesCS7D01G407000 chr7B 86.716 2183 127 64 8 2093 560524587 560526703 0.000000e+00 2274
10 TraesCS7D01G407000 chr7B 90.544 1692 107 17 2215 3858 560526988 560528674 0.000000e+00 2189
11 TraesCS7D01G407000 chr7B 88.447 1056 93 13 5846 6892 560530994 560532029 0.000000e+00 1247
12 TraesCS7D01G407000 chr7B 94.355 124 7 0 2093 2216 560526835 560526958 2.540000e-44 191
13 TraesCS7D01G407000 chr6B 86.777 121 12 3 2753 2873 32297502 32297386 1.560000e-26 132
14 TraesCS7D01G407000 chr2D 79.394 165 23 4 2546 2709 385168335 385168181 9.450000e-19 106


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 TraesCS7D01G407000 chr7D 524318741 524325632 6891 False 12728.00 12728 100.0000 1 6892 1 chr7D.!!$F1 6891
1 TraesCS7D01G407000 chr7A 604389703 604396597 6894 False 2041.75 2946 89.7955 369 6892 4 chr7A.!!$F2 6523
2 TraesCS7D01G407000 chr7B 560524587 560532029 7442 False 1703.60 2617 90.2958 8 6892 5 chr7B.!!$F1 6884

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
593 648 0.039764 CCCCTTTCTTCTTCCCCACC 59.960 60.0 0.00 0.0 0.00 4.61 F
594 649 0.039764 CCCTTTCTTCTTCCCCACCC 59.960 60.0 0.00 0.0 0.00 4.61 F
596 651 0.039764 CTTTCTTCTTCCCCACCCCC 59.960 60.0 0.00 0.0 0.00 5.40 F
1106 1201 0.373024 GCTCTGCTGCATTCTCGTTC 59.627 55.0 1.31 0.0 0.00 3.95 F
1575 1681 0.608035 TTGGACGGATGGCTGAAACC 60.608 55.0 0.00 0.0 0.00 3.27 F
3228 3633 0.110295 TTGGCCATGTAGCACACACT 59.890 50.0 6.09 0.0 40.86 3.55 F
4024 4837 0.250338 GACTCCAACCTCGCCACTTT 60.250 55.0 0.00 0.0 0.00 2.66 F
4088 4901 0.736053 TGTTTTGTTGCGAGGGTCAC 59.264 50.0 0.00 0.0 0.00 3.67 F
5625 6477 0.478072 TTCTTTTCCAGAGCCAGCCA 59.522 50.0 0.00 0.0 31.12 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1681 0.030638 CAAACCAGAAACTGCCCACG 59.969 55.0 0.00 0.0 0.00 4.94 R
2388 2730 0.540597 AGGCCAGAAGGGTTTTCAGC 60.541 55.0 5.01 0.0 39.65 4.26 R
2500 2856 1.315257 GGTGTGCTGCCTATTGGTGG 61.315 60.0 0.00 0.0 35.27 4.61 R
2865 3256 0.320771 AGTCACGGGCAGCTTGTTAG 60.321 55.0 0.00 0.0 0.00 2.34 R
3500 4023 0.189574 CCTCCTCCTCTGCTGGGATA 59.810 60.0 0.00 0.0 31.89 2.59 R
4066 4879 0.031994 ACCCTCGCAACAAAACATGC 59.968 50.0 0.00 0.0 39.17 4.06 R
5270 6116 0.394488 TCAGTGGTTGCCCGTTCAAA 60.394 50.0 0.00 0.0 0.00 2.69 R
5727 6607 1.516161 TCAAGCATGCACAGACAGTC 58.484 50.0 21.98 0.0 0.00 3.51 R
6840 7802 0.108898 CCGAGGAGAAGAGTGCAGTG 60.109 60.0 0.00 0.0 0.00 3.66 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
76 77 4.526970 AGAAACTGGTGTGTCTGAAACAT 58.473 39.130 3.60 0.00 39.20 2.71
95 96 7.647318 TGAAACATATATAATGCGCCTTTTGTG 59.353 33.333 4.18 1.83 0.00 3.33
98 99 7.581476 ACATATATAATGCGCCTTTTGTGTAC 58.419 34.615 4.18 0.00 0.00 2.90
99 100 7.227711 ACATATATAATGCGCCTTTTGTGTACA 59.772 33.333 4.18 0.00 0.00 2.90
101 102 7.737972 ATATAATGCGCCTTTTGTGTACATA 57.262 32.000 4.18 0.00 0.00 2.29
102 103 4.981806 AATGCGCCTTTTGTGTACATAT 57.018 36.364 4.18 0.00 0.00 1.78
103 104 7.737972 ATAATGCGCCTTTTGTGTACATATA 57.262 32.000 4.18 0.00 0.00 0.86
104 105 6.633500 AATGCGCCTTTTGTGTACATATAT 57.367 33.333 4.18 0.00 0.00 0.86
105 106 6.633500 ATGCGCCTTTTGTGTACATATATT 57.367 33.333 4.18 0.00 0.00 1.28
106 107 6.443934 TGCGCCTTTTGTGTACATATATTT 57.556 33.333 4.18 0.00 0.00 1.40
107 108 6.857956 TGCGCCTTTTGTGTACATATATTTT 58.142 32.000 4.18 0.00 0.00 1.82
108 109 7.986562 TGCGCCTTTTGTGTACATATATTTTA 58.013 30.769 4.18 0.00 0.00 1.52
144 145 7.232534 AGCCTATATTTTGTTCTTCACCAACAA 59.767 33.333 0.00 0.00 41.05 2.83
145 146 8.034804 GCCTATATTTTGTTCTTCACCAACAAT 58.965 33.333 0.00 0.00 42.04 2.71
166 167 3.207778 TCTGGTTTCTGTTTTACGGTGG 58.792 45.455 0.00 0.00 0.00 4.61
178 181 4.096003 CGGTGGTTGGATCGGGCT 62.096 66.667 0.00 0.00 0.00 5.19
182 185 1.097547 GTGGTTGGATCGGGCTGATG 61.098 60.000 14.83 0.00 37.47 3.07
186 189 1.130777 TTGGATCGGGCTGATGATCA 58.869 50.000 14.83 6.53 42.19 2.92
216 222 6.432936 CGAATATAGTGTGCATTTGCTTGAT 58.567 36.000 3.94 0.00 42.66 2.57
218 224 7.096763 CGAATATAGTGTGCATTTGCTTGATTG 60.097 37.037 3.94 0.00 42.66 2.67
221 227 4.053295 AGTGTGCATTTGCTTGATTGAAC 58.947 39.130 3.94 0.00 42.66 3.18
230 236 2.805671 TGCTTGATTGAACACTACACCG 59.194 45.455 0.00 0.00 0.00 4.94
232 238 3.684788 GCTTGATTGAACACTACACCGAT 59.315 43.478 0.00 0.00 0.00 4.18
237 253 9.093970 CTTGATTGAACACTACACCGATTATTA 57.906 33.333 0.00 0.00 0.00 0.98
282 301 4.350245 AGGTGTATGTGTTCTACTGCCTA 58.650 43.478 0.00 0.00 0.00 3.93
290 309 4.253685 GTGTTCTACTGCCTATTTGCTGA 58.746 43.478 0.00 0.00 34.63 4.26
297 316 4.911390 ACTGCCTATTTGCTGAAAGTACT 58.089 39.130 0.00 0.00 35.30 2.73
299 318 5.182001 ACTGCCTATTTGCTGAAAGTACTTG 59.818 40.000 9.34 0.00 35.30 3.16
303 322 6.183360 GCCTATTTGCTGAAAGTACTTGCATA 60.183 38.462 16.87 13.12 35.30 3.14
304 323 7.469181 GCCTATTTGCTGAAAGTACTTGCATAT 60.469 37.037 16.87 18.25 35.30 1.78
317 352 7.668492 AGTACTTGCATATAACTAACCCTAGC 58.332 38.462 0.00 0.00 0.00 3.42
352 387 2.235016 TGGTCAATCCAAACCCTTTCG 58.765 47.619 0.00 0.00 44.12 3.46
358 393 4.941263 TCAATCCAAACCCTTTCGATAGTG 59.059 41.667 2.13 0.00 37.40 2.74
363 398 5.239963 TCCAAACCCTTTCGATAGTGTTTTC 59.760 40.000 12.32 0.00 37.40 2.29
404 439 3.193267 AGCGATCTATGAGAATCTCCAGC 59.807 47.826 7.91 3.23 34.92 4.85
415 450 0.779997 ATCTCCAGCCCACCAAAACT 59.220 50.000 0.00 0.00 0.00 2.66
419 454 1.063266 TCCAGCCCACCAAAACTTTCT 60.063 47.619 0.00 0.00 0.00 2.52
491 538 0.907486 AAGCCTCATCACTAGCAGCA 59.093 50.000 0.00 0.00 0.00 4.41
515 562 3.561241 GAATCCGGGCCCTCCTCC 61.561 72.222 22.43 2.03 0.00 4.30
537 592 1.153086 CCGCTTTCTCCCCATCCAG 60.153 63.158 0.00 0.00 0.00 3.86
543 598 0.178876 TTCTCCCCATCCAGACCACA 60.179 55.000 0.00 0.00 0.00 4.17
544 599 0.909610 TCTCCCCATCCAGACCACAC 60.910 60.000 0.00 0.00 0.00 3.82
546 601 2.230653 CCCCATCCAGACCACACCA 61.231 63.158 0.00 0.00 0.00 4.17
547 602 1.002134 CCCATCCAGACCACACCAC 60.002 63.158 0.00 0.00 0.00 4.16
548 603 1.760527 CCATCCAGACCACACCACA 59.239 57.895 0.00 0.00 0.00 4.17
549 604 0.606401 CCATCCAGACCACACCACAC 60.606 60.000 0.00 0.00 0.00 3.82
550 605 0.606401 CATCCAGACCACACCACACC 60.606 60.000 0.00 0.00 0.00 4.16
551 606 1.059584 ATCCAGACCACACCACACCA 61.060 55.000 0.00 0.00 0.00 4.17
552 607 1.525995 CCAGACCACACCACACCAC 60.526 63.158 0.00 0.00 0.00 4.16
553 608 1.223211 CAGACCACACCACACCACA 59.777 57.895 0.00 0.00 0.00 4.17
554 609 1.095228 CAGACCACACCACACCACAC 61.095 60.000 0.00 0.00 0.00 3.82
555 610 1.822186 GACCACACCACACCACACC 60.822 63.158 0.00 0.00 0.00 4.16
556 611 2.273776 CCACACCACACCACACCA 59.726 61.111 0.00 0.00 0.00 4.17
557 612 2.118404 CCACACCACACCACACCAC 61.118 63.158 0.00 0.00 0.00 4.16
558 613 1.077787 CACACCACACCACACCACT 60.078 57.895 0.00 0.00 0.00 4.00
559 614 0.679640 CACACCACACCACACCACTT 60.680 55.000 0.00 0.00 0.00 3.16
560 615 0.679640 ACACCACACCACACCACTTG 60.680 55.000 0.00 0.00 0.00 3.16
561 616 1.752694 ACCACACCACACCACTTGC 60.753 57.895 0.00 0.00 0.00 4.01
562 617 1.453745 CCACACCACACCACTTGCT 60.454 57.895 0.00 0.00 0.00 3.91
563 618 1.447317 CCACACCACACCACTTGCTC 61.447 60.000 0.00 0.00 0.00 4.26
564 619 1.152963 ACACCACACCACTTGCTCC 60.153 57.895 0.00 0.00 0.00 4.70
565 620 2.111043 ACCACACCACTTGCTCCG 59.889 61.111 0.00 0.00 0.00 4.63
592 647 1.004862 CTCCCCTTTCTTCTTCCCCAC 59.995 57.143 0.00 0.00 0.00 4.61
593 648 0.039764 CCCCTTTCTTCTTCCCCACC 59.960 60.000 0.00 0.00 0.00 4.61
594 649 0.039764 CCCTTTCTTCTTCCCCACCC 59.960 60.000 0.00 0.00 0.00 4.61
595 650 0.039764 CCTTTCTTCTTCCCCACCCC 59.960 60.000 0.00 0.00 0.00 4.95
596 651 0.039764 CTTTCTTCTTCCCCACCCCC 59.960 60.000 0.00 0.00 0.00 5.40
807 864 3.680196 ACCCCGTCCCAGCCTCTA 61.680 66.667 0.00 0.00 0.00 2.43
808 865 2.122813 CCCCGTCCCAGCCTCTAT 60.123 66.667 0.00 0.00 0.00 1.98
811 868 2.210711 CCGTCCCAGCCTCTATCCC 61.211 68.421 0.00 0.00 0.00 3.85
812 869 2.565645 CGTCCCAGCCTCTATCCCG 61.566 68.421 0.00 0.00 0.00 5.14
813 870 2.524394 TCCCAGCCTCTATCCCGC 60.524 66.667 0.00 0.00 0.00 6.13
814 871 3.631046 CCCAGCCTCTATCCCGCC 61.631 72.222 0.00 0.00 0.00 6.13
815 872 3.996124 CCAGCCTCTATCCCGCCG 61.996 72.222 0.00 0.00 0.00 6.46
816 873 3.227276 CAGCCTCTATCCCGCCGT 61.227 66.667 0.00 0.00 0.00 5.68
817 874 2.444140 AGCCTCTATCCCGCCGTT 60.444 61.111 0.00 0.00 0.00 4.44
934 993 2.614983 GTTGCTTGTTCGGTTGTTCCTA 59.385 45.455 0.00 0.00 0.00 2.94
935 994 2.215196 TGCTTGTTCGGTTGTTCCTAC 58.785 47.619 0.00 0.00 0.00 3.18
1106 1201 0.373024 GCTCTGCTGCATTCTCGTTC 59.627 55.000 1.31 0.00 0.00 3.95
1125 1220 5.241506 TCGTTCATTTTTCTGCTGATTCCTT 59.758 36.000 0.00 0.00 0.00 3.36
1129 1224 4.503741 TTTTTCTGCTGATTCCTTTCCG 57.496 40.909 0.00 0.00 0.00 4.30
1169 1265 3.592898 AGGTCAATATATCATGCGCGA 57.407 42.857 12.10 0.00 0.00 5.87
1171 1267 2.993220 GGTCAATATATCATGCGCGACA 59.007 45.455 12.10 8.22 0.00 4.35
1192 1288 3.220507 TGTGCTATTGCTTGTTGATGC 57.779 42.857 0.00 0.00 40.48 3.91
1482 1588 9.374838 ACTTGGTAATGGTCTTTACTTTATACG 57.625 33.333 6.68 0.00 33.49 3.06
1489 1595 6.927416 TGGTCTTTACTTTATACGCTCAGAA 58.073 36.000 0.00 0.00 0.00 3.02
1504 1610 6.451393 ACGCTCAGAAATATCTTTAGCCTAG 58.549 40.000 0.00 0.00 38.23 3.02
1515 1621 5.968528 TCTTTAGCCTAGTAGCTATGAGC 57.031 43.478 0.00 0.00 44.56 4.26
1575 1681 0.608035 TTGGACGGATGGCTGAAACC 60.608 55.000 0.00 0.00 0.00 3.27
1583 1689 3.365265 GGCTGAAACCGTGGGCAG 61.365 66.667 0.00 0.00 0.00 4.85
1746 1905 6.992063 TTTGACCTCTCAGAATTCATTAGC 57.008 37.500 8.44 0.00 0.00 3.09
1753 1912 9.282569 ACCTCTCAGAATTCATTAGCATAATTC 57.717 33.333 8.44 0.00 39.04 2.17
1829 1988 5.534654 GCCTCCTTATGTATTTATGCCAACA 59.465 40.000 0.00 0.00 0.00 3.33
2098 2404 6.615264 TGATAACAGACCTACTAAGTAGCG 57.385 41.667 0.00 0.00 35.06 4.26
2356 2697 2.046292 TCAATGTGACTCACCTGGTGA 58.954 47.619 26.79 26.79 40.50 4.02
2416 2758 2.509964 ACCCTTCTGGCCTACATAAAGG 59.490 50.000 3.32 7.74 39.69 3.11
2466 2822 4.776349 TCTGTGTTGGAGCTTTAGTTTGA 58.224 39.130 0.00 0.00 0.00 2.69
2486 2842 7.227512 AGTTTGACTTAGGTGAGTGAATCAAAG 59.772 37.037 0.00 0.00 40.43 2.77
2500 2856 7.931275 AGTGAATCAAAGACTGTTTCCTTAAC 58.069 34.615 0.00 0.00 34.19 2.01
2598 2954 3.797353 CGGCTGGCATGTAGGGGT 61.797 66.667 1.08 0.00 0.00 4.95
2654 3013 2.936498 CAGTAAATCGGCTACTTGGTGG 59.064 50.000 0.00 0.00 0.00 4.61
2693 3052 6.757897 TTAATTGGCCAGTTAACTGATCTG 57.242 37.500 32.50 18.60 46.59 2.90
2709 3068 6.355397 CTGATCTGTCAGCGAATATTTTGT 57.645 37.500 0.00 0.00 44.86 2.83
2714 3073 5.350365 TCTGTCAGCGAATATTTTGTACACC 59.650 40.000 0.00 0.00 0.00 4.16
2733 3092 6.024552 ACACCGCTCATTTTCATTACAATT 57.975 33.333 0.00 0.00 0.00 2.32
2757 3148 6.530120 TGCTAGTGAAGTTTGAGTGGAAATA 58.470 36.000 0.00 0.00 0.00 1.40
2771 3162 8.006298 TGAGTGGAAATACAACATTCAGTTTT 57.994 30.769 0.00 0.00 38.74 2.43
2878 3269 3.408634 TGTAAGTTCTAACAAGCTGCCC 58.591 45.455 0.00 0.00 0.00 5.36
2906 3297 6.012745 ACTTTCTGAACTGGCAATAGGATTT 58.987 36.000 0.00 0.00 0.00 2.17
2918 3309 7.957002 TGGCAATAGGATTTTGTTACTGAAAA 58.043 30.769 0.00 0.00 0.00 2.29
2933 3331 8.286800 TGTTACTGAAAATGCATGTGTAACTAC 58.713 33.333 20.79 8.75 39.03 2.73
2961 3359 3.281727 TGGGACACAAAGCTCCATATC 57.718 47.619 0.00 0.00 0.00 1.63
3044 3442 0.307760 CTTGTGGTGACCGACTTTGC 59.692 55.000 0.00 0.00 0.00 3.68
3068 3467 6.538742 GCTCATAACTCTTAACACTTATGGCA 59.461 38.462 0.00 0.00 30.84 4.92
3228 3633 0.110295 TTGGCCATGTAGCACACACT 59.890 50.000 6.09 0.00 40.86 3.55
3254 3660 3.892284 TCTTTCCACTTGCACCACTAAA 58.108 40.909 0.00 0.00 0.00 1.85
3255 3661 3.882888 TCTTTCCACTTGCACCACTAAAG 59.117 43.478 0.00 0.00 0.00 1.85
3256 3662 3.290948 TTCCACTTGCACCACTAAAGT 57.709 42.857 0.00 0.00 34.52 2.66
3257 3663 4.425180 TTCCACTTGCACCACTAAAGTA 57.575 40.909 0.00 0.00 32.96 2.24
3261 3667 6.112734 TCCACTTGCACCACTAAAGTATATG 58.887 40.000 0.00 0.00 32.96 1.78
3286 3692 6.238484 GCTAAATGTGTTCAGTTCACAACTCT 60.238 38.462 2.99 0.00 46.47 3.24
3413 3819 9.801873 GCAAGATTAAATAATCAAAGGCAGTAA 57.198 29.630 13.94 0.00 43.43 2.24
3431 3837 6.316390 GGCAGTAAGATTAAAGTATGCACTGT 59.684 38.462 0.00 0.00 34.36 3.55
3472 3985 5.670485 AGTCACAACATGTACAGAACAGAA 58.330 37.500 0.00 0.00 42.70 3.02
3485 4008 3.562973 CAGAACAGAAGAGCTTTGCAGAA 59.437 43.478 0.00 0.00 0.00 3.02
3500 4023 4.924305 TGCAGAAAAAGAAACAGAGCAT 57.076 36.364 0.00 0.00 0.00 3.79
3504 4027 6.032717 GCAGAAAAAGAAACAGAGCATATCC 58.967 40.000 0.00 0.00 0.00 2.59
3573 4104 1.905894 AGGAAGAGGCAGGAAGAAGAC 59.094 52.381 0.00 0.00 0.00 3.01
3576 4107 1.274712 AGAGGCAGGAAGAAGACAGG 58.725 55.000 0.00 0.00 0.00 4.00
3596 4127 3.767044 GAGGAGGAGGAGGGAGGGC 62.767 73.684 0.00 0.00 0.00 5.19
3632 4163 4.648626 TTGGCGCTGAAGCTGGCT 62.649 61.111 7.64 0.00 39.42 4.75
3681 4212 1.143813 GTGGATCAGTGGATGGGGAT 58.856 55.000 0.00 0.00 32.67 3.85
3685 4216 1.776667 GATCAGTGGATGGGGATGGAA 59.223 52.381 0.00 0.00 32.67 3.53
3686 4217 1.216064 TCAGTGGATGGGGATGGAAG 58.784 55.000 0.00 0.00 0.00 3.46
3694 4225 2.597903 GGGATGGAAGGAGGTGGC 59.402 66.667 0.00 0.00 0.00 5.01
3731 4262 3.393970 CTGGAGCTGGGCGGAGAA 61.394 66.667 0.00 0.00 0.00 2.87
3736 4270 2.435059 GCTGGGCGGAGAAGTGAC 60.435 66.667 0.00 0.00 0.00 3.67
3737 4271 3.059982 CTGGGCGGAGAAGTGACA 58.940 61.111 0.00 0.00 0.00 3.58
3748 4282 1.614413 AGAAGTGACAGACGGGAAGAC 59.386 52.381 0.00 0.00 0.00 3.01
3749 4283 1.340248 GAAGTGACAGACGGGAAGACA 59.660 52.381 0.00 0.00 0.00 3.41
3779 4313 2.359975 GGAACTGGGCGGAACTGG 60.360 66.667 0.00 0.00 0.00 4.00
3794 4328 1.697394 CTGGATGGGGGATGGTGGA 60.697 63.158 0.00 0.00 0.00 4.02
3797 4331 0.562674 GGATGGGGGATGGTGGAAAT 59.437 55.000 0.00 0.00 0.00 2.17
3800 4334 2.295269 TGGGGGATGGTGGAAATAGA 57.705 50.000 0.00 0.00 0.00 1.98
3801 4335 2.800656 TGGGGGATGGTGGAAATAGAT 58.199 47.619 0.00 0.00 0.00 1.98
3806 4340 2.549754 GGATGGTGGAAATAGATGTGCG 59.450 50.000 0.00 0.00 0.00 5.34
3837 4371 0.979665 CAAGGTCAGAGAGAAGCCCA 59.020 55.000 0.00 0.00 0.00 5.36
3838 4372 1.349026 CAAGGTCAGAGAGAAGCCCAA 59.651 52.381 0.00 0.00 0.00 4.12
3861 4407 2.487265 GGCCGATTCTCTCTCTCTCTCT 60.487 54.545 0.00 0.00 0.00 3.10
3865 4411 4.039730 CCGATTCTCTCTCTCTCTCTCTCT 59.960 50.000 0.00 0.00 0.00 3.10
3869 4415 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3873 4419 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3877 4423 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3881 4427 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3883 4429 3.963374 TCTCTCTCTCTCTCTCTCTCTGG 59.037 52.174 0.00 0.00 0.00 3.86
3884 4430 2.435805 TCTCTCTCTCTCTCTCTCTGGC 59.564 54.545 0.00 0.00 0.00 4.85
3906 4452 3.071312 CCAGAGAGAAGGATGATTCCCTG 59.929 52.174 0.00 0.00 43.76 4.45
3914 4460 1.906990 GATGATTCCCTGCCATCCTG 58.093 55.000 0.00 0.00 32.68 3.86
3939 4485 1.776662 TTCTCGTACCTGGCTGCTAT 58.223 50.000 0.00 0.00 0.00 2.97
3942 4488 2.100916 TCTCGTACCTGGCTGCTATTTC 59.899 50.000 0.00 0.00 0.00 2.17
3961 4507 2.935481 CTCCCACCCCTGCTTCCA 60.935 66.667 0.00 0.00 0.00 3.53
3965 4511 1.153756 CCACCCCTGCTTCCACTTT 59.846 57.895 0.00 0.00 0.00 2.66
3968 4514 1.360393 ACCCCTGCTTCCACTTTCCA 61.360 55.000 0.00 0.00 0.00 3.53
3980 4793 1.467734 CACTTTCCATGCACTCTGCTC 59.532 52.381 0.00 0.00 45.31 4.26
3984 4797 1.375140 CCATGCACTCTGCTCGTGT 60.375 57.895 0.00 0.00 45.31 4.49
3998 4811 2.084101 CGTGTCGTCGGAAATCGCA 61.084 57.895 0.00 0.00 39.05 5.10
4003 4816 2.159352 TGTCGTCGGAAATCGCATAAGA 60.159 45.455 0.00 0.00 39.05 2.10
4024 4837 0.250338 GACTCCAACCTCGCCACTTT 60.250 55.000 0.00 0.00 0.00 2.66
4037 4850 3.755905 TCGCCACTTTGATTGCAAATAGA 59.244 39.130 1.71 0.00 42.66 1.98
4039 4852 4.615682 CGCCACTTTGATTGCAAATAGACA 60.616 41.667 1.71 0.00 42.66 3.41
4052 4865 2.996249 ATAGACACCATGCCTCTGTG 57.004 50.000 0.00 0.00 36.11 3.66
4053 4866 0.904649 TAGACACCATGCCTCTGTGG 59.095 55.000 4.42 0.00 41.35 4.17
4087 4900 1.336440 CATGTTTTGTTGCGAGGGTCA 59.664 47.619 0.00 0.00 0.00 4.02
4088 4901 0.736053 TGTTTTGTTGCGAGGGTCAC 59.264 50.000 0.00 0.00 0.00 3.67
4114 4927 3.749981 CCTTGACAGGCACCACAC 58.250 61.111 0.00 0.00 31.53 3.82
4135 4948 5.131475 ACACCGGTATTATCCTTGTTATGGT 59.869 40.000 6.87 0.00 0.00 3.55
4157 4971 3.837731 TGACGAGATGGGATGCCATAATA 59.162 43.478 19.96 0.09 0.00 0.98
4190 5011 6.335471 TGGGTGGTATGTAACTGTATATCG 57.665 41.667 0.00 0.00 0.00 2.92
4288 5116 2.542411 GCATGAAATCGCCTCATTGGTC 60.542 50.000 0.00 0.00 38.35 4.02
4289 5117 1.750193 TGAAATCGCCTCATTGGTCC 58.250 50.000 0.00 0.00 38.35 4.46
4345 5184 2.500392 TATGCACTTTGGGGGTACAC 57.500 50.000 0.00 0.00 0.00 2.90
4347 5186 1.071814 GCACTTTGGGGGTACACGA 59.928 57.895 0.00 0.00 0.00 4.35
4385 5224 2.619074 CCACAACTTCAAGGATCCCCTC 60.619 54.545 8.55 0.00 43.48 4.30
4397 5236 2.354805 GGATCCCCTCGTATATTGCACC 60.355 54.545 0.00 0.00 0.00 5.01
4421 5260 6.363473 CCTTCGTAGAAATGTGTGTTTCTTC 58.637 40.000 7.14 2.42 43.90 2.87
4697 5540 2.829741 AGAGCTTTCTGTGGTGTCTC 57.170 50.000 0.00 0.00 0.00 3.36
4716 5559 5.991606 TGTCTCTTTGTCTTTATCTGGTGTG 59.008 40.000 0.00 0.00 0.00 3.82
4762 5605 9.840427 CCATTTAAGTAATGTAGAAACAAGTGG 57.160 33.333 0.00 0.00 41.74 4.00
4780 5626 8.474710 ACAAGTGGAAAGTAGTCTCTAACTTA 57.525 34.615 0.00 0.00 39.55 2.24
4848 5694 1.355720 AGGGCTATGTTTGTTGCCTCT 59.644 47.619 0.00 0.00 44.36 3.69
4858 5704 1.250328 TGTTGCCTCTGCTTTCCATG 58.750 50.000 0.00 0.00 38.71 3.66
4859 5705 1.251251 GTTGCCTCTGCTTTCCATGT 58.749 50.000 0.00 0.00 38.71 3.21
4881 5727 7.920160 TGTTGTATTGACTTGCTGATCAATA 57.080 32.000 10.94 10.94 42.41 1.90
4930 5776 5.047377 TCCTTGTTTCAGTGAAGCAAAACTT 60.047 36.000 28.02 0.00 40.88 2.66
4978 5824 1.340088 TCTGCAATGCCAAATGGTGT 58.660 45.000 1.53 0.00 37.57 4.16
4988 5834 1.404449 CCAAATGGTGTGATGCGCAAT 60.404 47.619 17.11 2.42 0.00 3.56
5033 5879 4.783560 TGGAACATCATCTGGTGATCAT 57.216 40.909 0.00 0.00 45.76 2.45
5060 5906 9.253832 TCAATTTATGGTGGTAAAGACATTCAT 57.746 29.630 0.00 0.00 0.00 2.57
5073 5919 7.437713 AAAGACATTCATGGTCCTCATAGTA 57.562 36.000 0.00 0.00 35.89 1.82
5075 5921 5.011533 AGACATTCATGGTCCTCATAGTAGC 59.988 44.000 0.00 0.00 35.89 3.58
5108 5954 1.599518 CAACGTGCTACCAGCCCAA 60.600 57.895 0.00 0.00 41.51 4.12
5270 6116 2.573462 TGGTTCCTTTAGCAGCTCAGAT 59.427 45.455 0.00 0.00 0.00 2.90
5384 6230 4.597507 TCAGACTTAACAGAGGGGTTCAAT 59.402 41.667 0.00 0.00 32.29 2.57
5428 6280 4.522022 AGGAGAGAGTTTTCCATTGCTTTG 59.478 41.667 0.00 0.00 35.88 2.77
5431 6283 6.225981 AGAGAGTTTTCCATTGCTTTGTTT 57.774 33.333 0.00 0.00 0.00 2.83
5457 6309 9.910267 TTTTTAGTACCTTTTCACCTAAAGTCT 57.090 29.630 0.00 0.00 34.11 3.24
5471 6323 7.343574 TCACCTAAAGTCTATTGGCTGTATACA 59.656 37.037 5.25 5.25 0.00 2.29
5508 6360 7.230510 ACCATTTTGTTGTCTGCAGAAGTATTA 59.769 33.333 20.19 1.95 0.00 0.98
5526 6378 6.692486 AGTATTAGAGAATTATGGCAGGTCG 58.308 40.000 0.00 0.00 0.00 4.79
5614 6466 5.452777 CATTTTCGTCCAGTCTTCTTTTCC 58.547 41.667 0.00 0.00 0.00 3.13
5624 6476 1.172175 CTTCTTTTCCAGAGCCAGCC 58.828 55.000 0.00 0.00 31.12 4.85
5625 6477 0.478072 TTCTTTTCCAGAGCCAGCCA 59.522 50.000 0.00 0.00 31.12 4.75
5665 6517 2.026636 GCCACCACCTCCACTGTAATTA 60.027 50.000 0.00 0.00 0.00 1.40
5666 6518 3.606687 CCACCACCTCCACTGTAATTAC 58.393 50.000 8.75 8.75 0.00 1.89
5667 6519 3.263425 CCACCACCTCCACTGTAATTACT 59.737 47.826 16.33 0.00 0.00 2.24
5668 6520 4.263331 CCACCACCTCCACTGTAATTACTT 60.263 45.833 16.33 1.17 0.00 2.24
5669 6521 4.935808 CACCACCTCCACTGTAATTACTTC 59.064 45.833 16.33 0.00 0.00 3.01
5670 6522 4.844655 ACCACCTCCACTGTAATTACTTCT 59.155 41.667 16.33 0.00 0.00 2.85
5671 6523 5.309806 ACCACCTCCACTGTAATTACTTCTT 59.690 40.000 16.33 0.00 0.00 2.52
5727 6607 0.456653 GCATTAGTTTGGTGCCTGCG 60.457 55.000 0.00 0.00 32.88 5.18
5729 6609 1.135689 CATTAGTTTGGTGCCTGCGAC 60.136 52.381 0.00 0.00 0.00 5.19
5730 6610 0.107831 TTAGTTTGGTGCCTGCGACT 59.892 50.000 0.00 0.00 0.00 4.18
5731 6611 0.602638 TAGTTTGGTGCCTGCGACTG 60.603 55.000 0.00 0.00 0.00 3.51
5732 6612 2.186826 GTTTGGTGCCTGCGACTGT 61.187 57.895 0.00 0.00 0.00 3.55
5744 6624 1.572085 GCGACTGTCTGTGCATGCTT 61.572 55.000 20.33 0.00 0.00 3.91
5905 6853 3.719121 CTGAGCAGCTACCCACCT 58.281 61.111 0.00 0.00 0.00 4.00
5960 6908 4.584638 TTCATGCTAGCCTTTTCCCTTA 57.415 40.909 13.29 0.00 0.00 2.69
6200 7148 6.552859 TTAATTTCAAGTGAATGCTGACGA 57.447 33.333 0.00 0.00 33.54 4.20
6268 7216 7.065216 ACATACATCAGTTTCATATATGCGC 57.935 36.000 7.92 0.00 0.00 6.09
6332 7280 4.382040 GCAAACAGGCACTAGAGAGACATA 60.382 45.833 0.00 0.00 36.02 2.29
6429 7380 3.132111 TCAACAAGGGGAAGAAAAACAGC 59.868 43.478 0.00 0.00 0.00 4.40
6477 7428 1.153706 CCGTCGAAGCCGTGGTTAT 60.154 57.895 0.00 0.00 37.05 1.89
6487 7438 3.914312 AGCCGTGGTTATGATAGAATCG 58.086 45.455 0.00 0.00 0.00 3.34
6489 7440 4.220821 AGCCGTGGTTATGATAGAATCGAT 59.779 41.667 0.00 0.00 0.00 3.59
6515 7466 2.885135 ATCAGTGGCATGGAGAACAA 57.115 45.000 0.00 0.00 0.00 2.83
6556 7507 5.365021 AGGAAAACATCATCTCCAGGTAG 57.635 43.478 0.00 0.00 0.00 3.18
6557 7508 4.164988 AGGAAAACATCATCTCCAGGTAGG 59.835 45.833 0.00 0.00 39.47 3.18
6558 7509 4.080299 GGAAAACATCATCTCCAGGTAGGT 60.080 45.833 0.00 0.00 39.02 3.08
6559 7510 5.130477 GGAAAACATCATCTCCAGGTAGGTA 59.870 44.000 0.00 0.00 39.02 3.08
6633 7587 0.886490 CTTTGAGCTTGCCGGTGAGT 60.886 55.000 1.90 0.00 0.00 3.41
6718 7672 1.818674 TGATGTCGCTCTTGCTCACTA 59.181 47.619 0.00 0.00 36.97 2.74
6728 7682 4.319118 GCTCTTGCTCACTACAACAAGAAC 60.319 45.833 5.86 0.00 45.63 3.01
6778 7740 1.474478 TCTTCCAGTGCTAGAGCGAAG 59.526 52.381 9.38 9.38 45.83 3.79
6840 7802 1.016653 GCGAGGAGTTGAAGCTGTCC 61.017 60.000 0.00 0.00 0.00 4.02
6843 7805 1.346068 GAGGAGTTGAAGCTGTCCACT 59.654 52.381 0.00 0.00 34.97 4.00
6846 7808 0.181114 AGTTGAAGCTGTCCACTGCA 59.819 50.000 10.75 0.00 42.33 4.41
6858 7820 0.108898 CCACTGCACTCTTCTCCTCG 60.109 60.000 0.00 0.00 0.00 4.63
6859 7821 0.108898 CACTGCACTCTTCTCCTCGG 60.109 60.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.864334 CATCCTCCTGCACCGGCC 62.864 72.222 0.00 0.00 40.13 6.13
4 5 4.864334 CCATCCTCCTGCACCGGC 62.864 72.222 0.00 0.00 41.68 6.13
5 6 1.121407 TATCCATCCTCCTGCACCGG 61.121 60.000 0.00 0.00 0.00 5.28
6 7 0.034059 GTATCCATCCTCCTGCACCG 59.966 60.000 0.00 0.00 0.00 4.94
9 10 1.620323 CGATGTATCCATCCTCCTGCA 59.380 52.381 0.00 0.00 43.87 4.41
10 11 1.674221 GCGATGTATCCATCCTCCTGC 60.674 57.143 0.00 0.00 43.87 4.85
11 12 1.620323 TGCGATGTATCCATCCTCCTG 59.380 52.381 0.00 0.00 43.87 3.86
12 13 1.898472 CTGCGATGTATCCATCCTCCT 59.102 52.381 0.00 0.00 43.87 3.69
13 14 1.674221 GCTGCGATGTATCCATCCTCC 60.674 57.143 0.00 0.00 43.87 4.30
14 15 1.001293 TGCTGCGATGTATCCATCCTC 59.999 52.381 0.00 0.00 43.87 3.71
15 16 1.051008 TGCTGCGATGTATCCATCCT 58.949 50.000 0.00 0.00 43.87 3.24
76 77 7.737972 ATGTACACAAAAGGCGCATTATATA 57.262 32.000 8.12 0.00 0.00 0.86
114 115 7.093945 TGGTGAAGAACAAAATATAGGCTTTCC 60.094 37.037 0.00 0.00 0.00 3.13
124 125 7.432869 CCAGATTGTTGGTGAAGAACAAAATA 58.567 34.615 0.00 0.00 44.32 1.40
144 145 3.818773 CCACCGTAAAACAGAAACCAGAT 59.181 43.478 0.00 0.00 0.00 2.90
145 146 3.207778 CCACCGTAAAACAGAAACCAGA 58.792 45.455 0.00 0.00 0.00 3.86
166 167 1.202687 TGATCATCAGCCCGATCCAAC 60.203 52.381 0.00 0.00 37.77 3.77
178 181 1.044611 TATTCGGCCCGTGATCATCA 58.955 50.000 1.63 0.00 0.00 3.07
182 185 2.029290 ACACTATATTCGGCCCGTGATC 60.029 50.000 1.63 0.00 0.00 2.92
186 189 0.249741 GCACACTATATTCGGCCCGT 60.250 55.000 1.63 0.00 0.00 5.28
237 253 7.285401 ACCTCTGTGTTTCAGTGTCAAAATAAT 59.715 33.333 0.00 0.00 43.97 1.28
240 256 4.949856 ACCTCTGTGTTTCAGTGTCAAAAT 59.050 37.500 0.00 0.00 43.97 1.82
242 258 3.689161 CACCTCTGTGTTTCAGTGTCAAA 59.311 43.478 0.00 0.00 43.97 2.69
259 275 3.195825 AGGCAGTAGAACACATACACCTC 59.804 47.826 0.00 0.00 30.39 3.85
268 284 4.253685 TCAGCAAATAGGCAGTAGAACAC 58.746 43.478 0.00 0.00 35.83 3.32
274 290 6.049955 AGTACTTTCAGCAAATAGGCAGTA 57.950 37.500 0.00 0.00 35.83 2.74
282 301 8.960591 AGTTATATGCAAGTACTTTCAGCAAAT 58.039 29.630 19.36 9.51 38.85 2.32
297 316 6.654959 TGTTGCTAGGGTTAGTTATATGCAA 58.345 36.000 0.00 0.00 35.88 4.08
299 318 6.289064 ACTGTTGCTAGGGTTAGTTATATGC 58.711 40.000 0.00 0.00 0.00 3.14
303 322 7.248743 TGTTACTGTTGCTAGGGTTAGTTAT 57.751 36.000 0.00 0.00 0.00 1.89
304 323 6.669125 TGTTACTGTTGCTAGGGTTAGTTA 57.331 37.500 0.00 0.00 0.00 2.24
317 352 4.566545 TTGACCAAGCATGTTACTGTTG 57.433 40.909 0.00 0.00 0.00 3.33
363 398 9.436957 AGATCGCTGTAAATAAATAATAGTGGG 57.563 33.333 0.00 0.00 0.00 4.61
404 439 3.868661 CGGAAAAAGAAAGTTTTGGTGGG 59.131 43.478 0.00 0.00 30.87 4.61
415 450 6.016610 CCTCAAACATACTCCGGAAAAAGAAA 60.017 38.462 5.23 0.00 0.00 2.52
419 454 4.076394 CCCTCAAACATACTCCGGAAAAA 58.924 43.478 5.23 0.00 0.00 1.94
491 538 0.104409 AGGGCCCGGATTCCTAATCT 60.104 55.000 18.44 0.00 38.01 2.40
537 592 1.822186 GGTGTGGTGTGGTGTGGTC 60.822 63.158 0.00 0.00 0.00 4.02
543 598 1.752694 GCAAGTGGTGTGGTGTGGT 60.753 57.895 0.00 0.00 0.00 4.16
544 599 1.447317 GAGCAAGTGGTGTGGTGTGG 61.447 60.000 0.00 0.00 0.00 4.17
546 601 1.152963 GGAGCAAGTGGTGTGGTGT 60.153 57.895 0.00 0.00 0.00 4.16
547 602 2.253758 CGGAGCAAGTGGTGTGGTG 61.254 63.158 0.00 0.00 0.00 4.17
548 603 2.111043 CGGAGCAAGTGGTGTGGT 59.889 61.111 0.00 0.00 0.00 4.16
549 604 1.961277 GACGGAGCAAGTGGTGTGG 60.961 63.158 0.00 0.00 0.00 4.17
550 605 2.310233 CGACGGAGCAAGTGGTGTG 61.310 63.158 0.00 0.00 0.00 3.82
551 606 2.029073 CGACGGAGCAAGTGGTGT 59.971 61.111 0.00 0.00 0.00 4.16
552 607 3.414700 GCGACGGAGCAAGTGGTG 61.415 66.667 0.00 0.00 37.05 4.17
553 608 3.575351 GAGCGACGGAGCAAGTGGT 62.575 63.158 7.12 0.00 40.15 4.16
554 609 2.811317 GAGCGACGGAGCAAGTGG 60.811 66.667 7.12 0.00 40.15 4.00
555 610 2.811317 GGAGCGACGGAGCAAGTG 60.811 66.667 7.12 0.00 40.15 3.16
556 611 2.992114 AGGAGCGACGGAGCAAGT 60.992 61.111 7.12 0.00 40.15 3.16
557 612 2.202676 GAGGAGCGACGGAGCAAG 60.203 66.667 7.12 0.00 40.15 4.01
558 613 3.760035 GGAGGAGCGACGGAGCAA 61.760 66.667 7.12 0.00 40.15 3.91
561 616 4.824515 AGGGGAGGAGCGACGGAG 62.825 72.222 0.00 0.00 0.00 4.63
562 617 3.899545 AAAGGGGAGGAGCGACGGA 62.900 63.158 0.00 0.00 0.00 4.69
563 618 3.372554 GAAAGGGGAGGAGCGACGG 62.373 68.421 0.00 0.00 0.00 4.79
564 619 1.889530 AAGAAAGGGGAGGAGCGACG 61.890 60.000 0.00 0.00 0.00 5.12
565 620 0.108089 GAAGAAAGGGGAGGAGCGAC 60.108 60.000 0.00 0.00 0.00 5.19
594 649 3.539593 AAAAGGGGGCCGGAAAGGG 62.540 63.158 5.05 0.00 41.48 3.95
595 650 1.982395 GAAAAGGGGGCCGGAAAGG 60.982 63.158 5.05 0.00 44.97 3.11
596 651 1.982395 GGAAAAGGGGGCCGGAAAG 60.982 63.158 5.05 0.00 0.00 2.62
603 658 2.363018 GAGCTGGGAAAAGGGGGC 60.363 66.667 0.00 0.00 0.00 5.80
811 868 0.675522 ATACCTCAAACCCAACGGCG 60.676 55.000 4.80 4.80 0.00 6.46
812 869 0.808755 CATACCTCAAACCCAACGGC 59.191 55.000 0.00 0.00 0.00 5.68
813 870 2.356135 CTCATACCTCAAACCCAACGG 58.644 52.381 0.00 0.00 0.00 4.44
814 871 1.737793 GCTCATACCTCAAACCCAACG 59.262 52.381 0.00 0.00 0.00 4.10
815 872 3.010420 GAGCTCATACCTCAAACCCAAC 58.990 50.000 9.40 0.00 0.00 3.77
816 873 2.354704 CGAGCTCATACCTCAAACCCAA 60.355 50.000 15.40 0.00 0.00 4.12
817 874 1.207089 CGAGCTCATACCTCAAACCCA 59.793 52.381 15.40 0.00 0.00 4.51
820 877 2.924290 GACACGAGCTCATACCTCAAAC 59.076 50.000 15.40 0.00 0.00 2.93
934 993 2.685380 CCTTCCGCTCTCCCTGGT 60.685 66.667 0.00 0.00 0.00 4.00
935 994 3.474570 CCCTTCCGCTCTCCCTGG 61.475 72.222 0.00 0.00 0.00 4.45
1106 1201 4.860907 CGGAAAGGAATCAGCAGAAAAATG 59.139 41.667 0.00 0.00 0.00 2.32
1125 1220 1.014044 CGCAGCTAGCTTGAACGGAA 61.014 55.000 16.46 0.00 42.61 4.30
1129 1224 2.754995 GGCCGCAGCTAGCTTGAAC 61.755 63.158 16.46 5.23 42.61 3.18
1146 1242 3.798878 CGCGCATGATATATTGACCTAGG 59.201 47.826 7.41 7.41 0.00 3.02
1169 1265 4.740268 CATCAACAAGCAATAGCACATGT 58.260 39.130 0.00 0.00 45.49 3.21
1171 1267 3.446161 AGCATCAACAAGCAATAGCACAT 59.554 39.130 0.00 0.00 45.49 3.21
1192 1288 1.400242 GCCTGCTACTTTGCGTTTCAG 60.400 52.381 0.00 0.00 35.36 3.02
1234 1331 2.520458 CTCCCCAACCCACAAGCA 59.480 61.111 0.00 0.00 0.00 3.91
1235 1332 2.991540 GCTCCCCAACCCACAAGC 60.992 66.667 0.00 0.00 0.00 4.01
1482 1588 7.544217 GCTACTAGGCTAAAGATATTTCTGAGC 59.456 40.741 10.22 10.22 39.44 4.26
1489 1595 8.691797 GCTCATAGCTACTAGGCTAAAGATATT 58.308 37.037 10.15 0.00 46.06 1.28
1549 1655 3.389656 TCAGCCATCCGTCCAATTACATA 59.610 43.478 0.00 0.00 0.00 2.29
1551 1657 1.557371 TCAGCCATCCGTCCAATTACA 59.443 47.619 0.00 0.00 0.00 2.41
1552 1658 2.325583 TCAGCCATCCGTCCAATTAC 57.674 50.000 0.00 0.00 0.00 1.89
1575 1681 0.030638 CAAACCAGAAACTGCCCACG 59.969 55.000 0.00 0.00 0.00 4.94
1753 1912 7.537715 TGCAAGATGTTTCCATTATGTTACAG 58.462 34.615 0.00 0.00 0.00 2.74
1755 1914 8.647226 GTTTGCAAGATGTTTCCATTATGTTAC 58.353 33.333 0.00 0.00 0.00 2.50
1829 1988 8.971073 CACAAATGGGAACTAGGAAATATTTCT 58.029 33.333 23.85 14.18 37.35 2.52
2098 2404 8.351495 ACATGTTCAAACATTTTCACATGTAC 57.649 30.769 20.19 0.00 46.95 2.90
2306 2647 2.814805 CACAGAAGTGGGATTGGGAT 57.185 50.000 0.00 0.00 42.13 3.85
2356 2697 5.852282 AAAAACATGGGCGCTATATCTTT 57.148 34.783 7.64 0.00 0.00 2.52
2385 2727 1.269778 GCCAGAAGGGTTTTCAGCAAC 60.270 52.381 0.00 0.00 39.65 4.17
2388 2730 0.540597 AGGCCAGAAGGGTTTTCAGC 60.541 55.000 5.01 0.00 39.65 4.26
2466 2822 6.183361 ACAGTCTTTGATTCACTCACCTAAGT 60.183 38.462 0.00 0.00 32.17 2.24
2486 2842 5.414765 CCTATTGGTGGTTAAGGAAACAGTC 59.585 44.000 0.00 0.00 40.08 3.51
2500 2856 1.315257 GGTGTGCTGCCTATTGGTGG 61.315 60.000 0.00 0.00 35.27 4.61
2598 2954 7.013274 GCATAACTGGCTGATTCACCTATTAAA 59.987 37.037 0.00 0.00 0.00 1.52
2637 2996 0.679960 GGCCACCAAGTAGCCGATTT 60.680 55.000 0.00 0.00 36.84 2.17
2654 3013 2.507407 TTAATCCCTGTTCAGTGGGC 57.493 50.000 0.00 0.00 43.04 5.36
2693 3052 4.574759 CGGTGTACAAAATATTCGCTGAC 58.425 43.478 0.00 0.00 0.00 3.51
2699 3058 7.753132 TGAAAATGAGCGGTGTACAAAATATTC 59.247 33.333 0.00 0.00 0.00 1.75
2709 3068 6.751514 ATTGTAATGAAAATGAGCGGTGTA 57.248 33.333 0.00 0.00 0.00 2.90
2714 3073 6.968904 ACTAGCAATTGTAATGAAAATGAGCG 59.031 34.615 7.40 0.00 0.00 5.03
2733 3092 4.415881 TTCCACTCAAACTTCACTAGCA 57.584 40.909 0.00 0.00 0.00 3.49
2865 3256 0.320771 AGTCACGGGCAGCTTGTTAG 60.321 55.000 0.00 0.00 0.00 2.34
2878 3269 1.581934 TGCCAGTTCAGAAAGTCACG 58.418 50.000 0.00 0.00 0.00 4.35
2906 3297 7.711846 AGTTACACATGCATTTTCAGTAACAA 58.288 30.769 23.76 5.44 41.14 2.83
2918 3309 3.684908 TGCTTGGTAGTTACACATGCAT 58.315 40.909 0.00 0.00 39.40 3.96
2933 3331 0.670162 CTTTGTGTCCCACTGCTTGG 59.330 55.000 0.00 0.00 46.47 3.61
3044 3442 8.668510 ATGCCATAAGTGTTAAGAGTTATGAG 57.331 34.615 28.82 22.03 39.89 2.90
3068 3467 4.010349 TCTATGATGTCGCCTCGTCATAT 58.990 43.478 14.13 0.00 42.01 1.78
3228 3633 2.297701 GGTGCAAGTGGAAAGAAGACA 58.702 47.619 0.00 0.00 0.00 3.41
3254 3660 8.883731 GTGAACTGAACACATTTAGCATATACT 58.116 33.333 0.00 0.00 38.05 2.12
3255 3661 8.664798 TGTGAACTGAACACATTTAGCATATAC 58.335 33.333 0.00 0.00 42.20 1.47
3256 3662 8.785329 TGTGAACTGAACACATTTAGCATATA 57.215 30.769 0.00 0.00 42.20 0.86
3257 3663 7.686438 TGTGAACTGAACACATTTAGCATAT 57.314 32.000 0.00 0.00 42.20 1.78
3261 3667 5.821204 AGTTGTGAACTGAACACATTTAGC 58.179 37.500 0.00 0.00 45.52 3.09
3286 3692 3.952967 TGCTCATTGCTAATTGCCATGTA 59.047 39.130 11.13 2.58 43.06 2.29
3447 3864 6.811954 TCTGTTCTGTACATGTTGTGACTAA 58.188 36.000 2.30 0.00 35.85 2.24
3450 3867 5.753438 TCTTCTGTTCTGTACATGTTGTGAC 59.247 40.000 2.30 0.00 35.85 3.67
3472 3985 5.126061 TCTGTTTCTTTTTCTGCAAAGCTCT 59.874 36.000 0.00 0.00 34.26 4.09
3485 4008 4.400567 GCTGGGATATGCTCTGTTTCTTTT 59.599 41.667 0.00 0.00 0.00 2.27
3500 4023 0.189574 CCTCCTCCTCTGCTGGGATA 59.810 60.000 0.00 0.00 31.89 2.59
3504 4027 3.478274 GCCCTCCTCCTCTGCTGG 61.478 72.222 0.00 0.00 0.00 4.85
3573 4104 2.285180 CCTCCTCCTCCTCCCCTG 59.715 72.222 0.00 0.00 0.00 4.45
3576 4107 2.612251 CTCCCTCCTCCTCCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
3596 4127 1.102222 ACTCCGGCGAGGTAAGCTAG 61.102 60.000 9.30 0.00 40.77 3.42
3620 4151 1.449956 CTCTCCAGCCAGCTTCAGC 60.450 63.158 0.00 0.00 42.49 4.26
3632 4163 2.427320 GTGCAGCACACCTCTCCA 59.573 61.111 21.22 0.00 44.02 3.86
3681 4212 4.020617 CAGCGCCACCTCCTTCCA 62.021 66.667 2.29 0.00 0.00 3.53
3685 4216 4.479993 GCATCAGCGCCACCTCCT 62.480 66.667 2.29 0.00 0.00 3.69
3731 4262 0.674534 GTGTCTTCCCGTCTGTCACT 59.325 55.000 0.00 0.00 0.00 3.41
3736 4270 2.432628 GGCGTGTCTTCCCGTCTG 60.433 66.667 0.00 0.00 0.00 3.51
3737 4271 2.600769 AGGCGTGTCTTCCCGTCT 60.601 61.111 0.00 0.00 33.54 4.18
3771 4305 1.149174 CATCCCCCATCCAGTTCCG 59.851 63.158 0.00 0.00 0.00 4.30
3775 4309 2.008723 CCACCATCCCCCATCCAGT 61.009 63.158 0.00 0.00 0.00 4.00
3779 4313 2.716424 TCTATTTCCACCATCCCCCATC 59.284 50.000 0.00 0.00 0.00 3.51
3794 4328 4.141144 CGGCCCGCACATCTATTT 57.859 55.556 0.00 0.00 0.00 1.40
3837 4371 2.627699 GAGAGAGAGAGAATCGGCCATT 59.372 50.000 2.24 1.28 42.67 3.16
3838 4372 2.158475 AGAGAGAGAGAGAATCGGCCAT 60.158 50.000 2.24 0.00 42.67 4.40
3861 4407 3.963374 CCAGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
3865 4411 1.490490 GGCCAGAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
3869 4415 1.294041 TCTGGCCAGAGAGAGAGAGA 58.706 55.000 32.00 5.54 32.82 3.10
3881 4427 2.187239 ATCATCCTTCTCTCTGGCCA 57.813 50.000 4.71 4.71 0.00 5.36
3883 4429 2.224499 GGGAATCATCCTTCTCTCTGGC 60.224 54.545 0.00 0.00 45.77 4.85
3884 4430 3.071312 CAGGGAATCATCCTTCTCTCTGG 59.929 52.174 0.00 0.00 45.77 3.86
3895 4441 1.906990 CAGGATGGCAGGGAATCATC 58.093 55.000 0.00 0.00 37.23 2.92
3914 4460 1.413077 AGCCAGGTACGAGAAATAGCC 59.587 52.381 0.00 0.00 0.00 3.93
3927 4473 0.548510 GAGGGAAATAGCAGCCAGGT 59.451 55.000 0.00 0.00 0.00 4.00
3939 4485 3.264845 GCAGGGGTGGGAGGGAAA 61.265 66.667 0.00 0.00 0.00 3.13
3942 4488 3.732849 GAAGCAGGGGTGGGAGGG 61.733 72.222 0.00 0.00 0.00 4.30
3980 4793 1.410737 ATGCGATTTCCGACGACACG 61.411 55.000 0.00 0.00 41.76 4.49
3984 4797 2.456989 GTCTTATGCGATTTCCGACGA 58.543 47.619 0.00 0.00 41.76 4.20
3998 4811 1.134560 GCGAGGTTGGAGTCGTCTTAT 59.865 52.381 0.00 0.00 38.48 1.73
4003 4816 2.915659 TGGCGAGGTTGGAGTCGT 60.916 61.111 0.00 0.00 38.48 4.34
4024 4837 3.130869 GGCATGGTGTCTATTTGCAATCA 59.869 43.478 0.00 0.00 35.04 2.57
4066 4879 0.031994 ACCCTCGCAACAAAACATGC 59.968 50.000 0.00 0.00 39.17 4.06
4087 4900 1.071471 CTGTCAAGGCCAAGACGGT 59.929 57.895 21.90 0.00 37.58 4.83
4088 4901 1.672356 CCTGTCAAGGCCAAGACGG 60.672 63.158 22.78 22.78 40.11 4.79
4114 4927 5.699458 GTCACCATAACAAGGATAATACCGG 59.301 44.000 0.00 0.00 34.73 5.28
4135 4948 4.048696 TGGCATCCCATCTCGTCA 57.951 55.556 0.00 0.00 35.79 4.35
4157 4971 8.375506 CAGTTACATACCACCCATAATCATAGT 58.624 37.037 0.00 0.00 0.00 2.12
4226 5053 3.063316 GGTTGCACCAACACATTCAAAAC 59.937 43.478 9.93 0.00 45.11 2.43
4234 5061 0.393132 TCGAAGGTTGCACCAACACA 60.393 50.000 9.93 0.00 45.11 3.72
4288 5116 4.578516 TGCCATAAATCATGTCCTTAACGG 59.421 41.667 0.00 0.00 32.21 4.44
4289 5117 5.065859 TGTGCCATAAATCATGTCCTTAACG 59.934 40.000 0.00 0.00 32.21 3.18
4345 5184 0.108945 GGGTGGTTCGTCTAGGTTCG 60.109 60.000 0.00 0.00 0.00 3.95
4347 5186 0.472352 TGGGGTGGTTCGTCTAGGTT 60.472 55.000 0.00 0.00 0.00 3.50
4385 5224 4.233123 TCTACGAAGGGTGCAATATACG 57.767 45.455 0.00 0.00 0.00 3.06
4397 5236 5.924475 AGAAACACACATTTCTACGAAGG 57.076 39.130 0.00 0.00 45.14 3.46
4421 5260 9.965824 ACAAAACATTAAGGAGAATAACAACAG 57.034 29.630 0.00 0.00 0.00 3.16
4441 5284 7.758495 TGGAAAGAACAGAGTAAGAACAAAAC 58.242 34.615 0.00 0.00 0.00 2.43
4697 5540 8.950210 ACATTATCACACCAGATAAAGACAAAG 58.050 33.333 0.00 0.00 42.07 2.77
4761 5604 9.012161 TCTTGAGTAAGTTAGAGACTACTTTCC 57.988 37.037 0.00 0.00 37.72 3.13
4848 5694 5.771469 CAAGTCAATACAACATGGAAAGCA 58.229 37.500 0.00 0.00 0.00 3.91
4858 5704 8.236586 TGTTATTGATCAGCAAGTCAATACAAC 58.763 33.333 13.72 12.85 43.31 3.32
4859 5705 8.334263 TGTTATTGATCAGCAAGTCAATACAA 57.666 30.769 13.72 0.00 43.31 2.41
4881 5727 9.423061 GAAAATAGCAGACCATGTTAAAATGTT 57.577 29.630 4.91 0.00 0.00 2.71
4930 5776 3.476552 CCAGACTCTGGTAAAAAGCACA 58.523 45.455 16.18 0.00 45.82 4.57
4978 5824 1.469703 CTGAACTTCCATTGCGCATCA 59.530 47.619 12.75 8.56 0.00 3.07
4988 5834 5.633655 TTACTAAACCACCTGAACTTCCA 57.366 39.130 0.00 0.00 0.00 3.53
5033 5879 9.083422 TGAATGTCTTTACCACCATAAATTGAA 57.917 29.630 0.00 0.00 0.00 2.69
5060 5906 3.328535 TCCATGCTACTATGAGGACCA 57.671 47.619 0.00 0.00 0.00 4.02
5075 5921 1.541147 ACGTTGGTTGAAGCATCCATG 59.459 47.619 0.00 0.00 33.86 3.66
5108 5954 1.835494 ACAGCAGAGCAGATGCATTT 58.165 45.000 0.00 0.00 46.31 2.32
5270 6116 0.394488 TCAGTGGTTGCCCGTTCAAA 60.394 50.000 0.00 0.00 0.00 2.69
5405 6251 4.379302 AAGCAATGGAAAACTCTCTCCT 57.621 40.909 0.00 0.00 32.51 3.69
5431 6283 9.910267 AGACTTTAGGTGAAAAGGTACTAAAAA 57.090 29.630 0.00 0.00 38.49 1.94
5438 6290 6.882678 GCCAATAGACTTTAGGTGAAAAGGTA 59.117 38.462 1.84 0.00 40.16 3.08
5478 6330 5.587289 TCTGCAGACAACAAAATGGTAAAC 58.413 37.500 13.74 0.00 0.00 2.01
5480 6332 5.359576 ACTTCTGCAGACAACAAAATGGTAA 59.640 36.000 18.03 0.00 0.00 2.85
5508 6360 2.246719 GCGACCTGCCATAATTCTCT 57.753 50.000 0.00 0.00 37.76 3.10
5526 6378 2.220313 GGCTCAGATGAGAGAAATGGC 58.780 52.381 13.98 0.00 44.74 4.40
5614 6466 2.634815 ATAACTCATGGCTGGCTCTG 57.365 50.000 2.00 0.42 0.00 3.35
5624 6476 4.392754 TGGCATGCGCTAATATAACTCATG 59.607 41.667 12.44 0.00 38.60 3.07
5625 6477 4.393062 GTGGCATGCGCTAATATAACTCAT 59.607 41.667 12.44 0.00 38.60 2.90
5694 6546 1.632018 TAATGCAAGAGGACCCGGGG 61.632 60.000 27.92 12.73 0.00 5.73
5727 6607 1.516161 TCAAGCATGCACAGACAGTC 58.484 50.000 21.98 0.00 0.00 3.51
5729 6609 1.810755 ACATCAAGCATGCACAGACAG 59.189 47.619 21.98 12.34 35.65 3.51
5730 6610 1.538075 CACATCAAGCATGCACAGACA 59.462 47.619 21.98 0.00 35.65 3.41
5731 6611 1.538512 ACACATCAAGCATGCACAGAC 59.461 47.619 21.98 0.00 35.65 3.51
5732 6612 1.900245 ACACATCAAGCATGCACAGA 58.100 45.000 21.98 14.51 35.65 3.41
5902 6850 8.739972 GTTCTCCATGAATATGTACAAAAAGGT 58.260 33.333 0.00 0.00 36.99 3.50
5960 6908 5.734720 ACATTACAAGACATCGGAACTGAT 58.265 37.500 0.00 0.00 0.00 2.90
6198 7146 4.436584 GCCATCACAAATCAAACTCTCTCG 60.437 45.833 0.00 0.00 0.00 4.04
6200 7148 4.660168 AGCCATCACAAATCAAACTCTCT 58.340 39.130 0.00 0.00 0.00 3.10
6266 7214 1.951130 CCGAGATTCCGATGTGGCG 60.951 63.158 0.00 0.00 37.80 5.69
6268 7216 1.154205 GCACCGAGATTCCGATGTGG 61.154 60.000 0.00 0.00 40.09 4.17
6429 7380 6.094048 ACAATCTGTTAGAATCACAATTCCCG 59.906 38.462 0.00 0.00 41.97 5.14
6477 7428 8.462016 CCACTGATACATGTATCGATTCTATCA 58.538 37.037 31.03 17.74 43.64 2.15
6487 7438 4.898320 TCCATGCCACTGATACATGTATC 58.102 43.478 30.80 30.80 39.62 2.24
6489 7440 3.966665 TCTCCATGCCACTGATACATGTA 59.033 43.478 8.27 8.27 39.62 2.29
6556 7507 4.708177 TGACGAGTACATACCTACCTACC 58.292 47.826 0.00 0.00 0.00 3.18
6557 7508 5.465056 GTCTGACGAGTACATACCTACCTAC 59.535 48.000 0.00 0.00 0.00 3.18
6558 7509 5.129320 TGTCTGACGAGTACATACCTACCTA 59.871 44.000 2.98 0.00 0.00 3.08
6559 7510 4.080695 TGTCTGACGAGTACATACCTACCT 60.081 45.833 2.98 0.00 0.00 3.08
6669 7623 1.226101 GTCGGCGTTCGTATCGTCA 60.226 57.895 6.85 0.00 40.32 4.35
6675 7629 1.081242 GTCCAAGTCGGCGTTCGTA 60.081 57.895 6.85 0.00 40.32 3.43
6718 7672 1.597663 CTCGCTTTCCGTTCTTGTTGT 59.402 47.619 0.00 0.00 38.35 3.32
6728 7682 1.212616 GGTGATCATCTCGCTTTCCG 58.787 55.000 0.00 0.00 34.65 4.30
6778 7740 7.548097 TCAGGTATGTACTTCTTCATCAGTTC 58.452 38.462 0.00 0.00 0.00 3.01
6840 7802 0.108898 CCGAGGAGAAGAGTGCAGTG 60.109 60.000 0.00 0.00 0.00 3.66
6843 7805 1.967535 CACCGAGGAGAAGAGTGCA 59.032 57.895 0.00 0.00 0.00 4.57
6846 7808 0.605589 CAAGCACCGAGGAGAAGAGT 59.394 55.000 0.00 0.00 0.00 3.24
6858 7820 1.002033 CAACAGTTCAGCTCAAGCACC 60.002 52.381 4.59 0.00 45.16 5.01
6859 7821 1.598924 GCAACAGTTCAGCTCAAGCAC 60.599 52.381 4.59 0.00 45.16 4.40


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

AutoCloner maintained by Alex Coulton.