Multiple sequence alignment - TraesCS2B01G627300

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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 TraesCS2B01G627300 chr2B 100.000 3697 0 0 1 3697 799253588 799249892 0.000000e+00 6828.0
1 TraesCS2B01G627300 chr2B 91.304 253 20 2 3265 3515 350312201 350311949 9.830000e-91 344.0
2 TraesCS2B01G627300 chr2B 85.246 244 21 5 2819 3054 799256252 799256488 1.720000e-58 237.0
3 TraesCS2B01G627300 chr2A 95.782 2513 87 8 770 3270 767570613 767573118 0.000000e+00 4036.0
4 TraesCS2B01G627300 chr2A 98.260 977 17 0 1833 2809 767789243 767788267 0.000000e+00 1711.0
5 TraesCS2B01G627300 chr2A 90.442 701 55 7 37 736 767569833 767570522 0.000000e+00 913.0
6 TraesCS2B01G627300 chr2A 90.000 710 61 7 902 1604 767791668 767790962 0.000000e+00 909.0
7 TraesCS2B01G627300 chr2A 76.136 1144 192 54 1393 2501 767561850 767562947 3.270000e-145 525.0
8 TraesCS2B01G627300 chr2A 85.333 375 37 6 1780 2152 767575061 767575419 4.510000e-99 372.0
9 TraesCS2B01G627300 chr2A 78.755 546 98 9 148 684 767792231 767791695 2.110000e-92 350.0
10 TraesCS2B01G627300 chr2A 78.519 540 90 16 844 1369 767560406 767560933 7.650000e-87 331.0
11 TraesCS2B01G627300 chr2A 77.838 555 97 16 844 1384 767485846 767485304 1.660000e-83 320.0
12 TraesCS2B01G627300 chr2A 86.806 288 26 4 2819 3100 767783821 767784102 9.970000e-81 311.0
13 TraesCS2B01G627300 chr2A 88.372 129 9 2 1640 1767 767789731 767789608 2.300000e-32 150.0
14 TraesCS2B01G627300 chr2A 87.387 111 6 5 2765 2875 767567190 767567088 1.800000e-23 121.0
15 TraesCS2B01G627300 chr2A 91.250 80 7 0 392 471 767444695 767444616 3.900000e-20 110.0
16 TraesCS2B01G627300 chr2A 80.833 120 18 3 1393 1512 767481224 767481110 5.090000e-14 89.8
17 TraesCS2B01G627300 chr2D 97.238 1086 29 1 1808 2893 642444889 642445973 0.000000e+00 1838.0
18 TraesCS2B01G627300 chr2D 90.840 1059 65 15 770 1814 642500327 642501367 0.000000e+00 1389.0
19 TraesCS2B01G627300 chr2D 94.437 737 41 0 1 737 642442853 642443589 0.000000e+00 1134.0
20 TraesCS2B01G627300 chr2D 88.261 690 76 5 51 738 642499554 642500240 0.000000e+00 821.0
21 TraesCS2B01G627300 chr2D 86.630 733 84 6 2152 2882 642501943 642502663 0.000000e+00 798.0
22 TraesCS2B01G627300 chr2D 82.305 989 87 35 1276 2234 642941106 642942036 0.000000e+00 776.0
23 TraesCS2B01G627300 chr2D 93.491 507 17 8 1314 1806 642444178 642444682 0.000000e+00 739.0
24 TraesCS2B01G627300 chr2D 92.731 509 31 3 770 1278 642443679 642444181 0.000000e+00 730.0
25 TraesCS2B01G627300 chr2D 92.411 448 18 4 3260 3697 651033073 651033514 3.130000e-175 625.0
26 TraesCS2B01G627300 chr2D 87.302 504 49 10 11 506 642932960 642933456 2.490000e-156 562.0
27 TraesCS2B01G627300 chr2D 92.602 392 18 1 2879 3270 642459438 642459818 1.500000e-153 553.0
28 TraesCS2B01G627300 chr2D 86.468 436 46 10 844 1277 642940588 642941012 2.010000e-127 466.0
29 TraesCS2B01G627300 chr2D 82.881 479 75 6 2224 2695 642954000 642954478 1.230000e-114 424.0
30 TraesCS2B01G627300 chr2D 89.254 335 23 7 2941 3272 642507858 642508182 1.240000e-109 407.0
31 TraesCS2B01G627300 chr2D 88.194 288 22 4 2819 3100 642873202 642873483 2.130000e-87 333.0
32 TraesCS2B01G627300 chr2D 81.509 411 64 10 845 1252 642240888 642240487 9.900000e-86 327.0
33 TraesCS2B01G627300 chr2D 89.024 164 15 2 576 738 642940431 642940592 2.250000e-47 200.0
34 TraesCS2B01G627300 chr2D 88.393 112 11 1 2765 2876 642873090 642873199 2.320000e-27 134.0
35 TraesCS2B01G627300 chr2D 84.615 117 8 6 2765 2879 642440293 642440185 1.400000e-19 108.0
36 TraesCS2B01G627300 chr2D 83.750 80 11 2 770 848 507044869 507044791 1.420000e-09 75.0
37 TraesCS2B01G627300 chrUn 95.115 1126 35 12 1840 2960 31527788 31526678 0.000000e+00 1757.0
38 TraesCS2B01G627300 chrUn 90.922 705 58 5 902 1604 31530491 31529791 0.000000e+00 942.0
39 TraesCS2B01G627300 chrUn 86.800 750 89 8 1955 2695 31552345 31553093 0.000000e+00 828.0
40 TraesCS2B01G627300 chrUn 78.188 596 113 7 148 737 31531070 31530486 7.550000e-97 364.0
41 TraesCS2B01G627300 chrUn 84.800 375 37 9 1780 2152 183069701 183069345 3.510000e-95 359.0
42 TraesCS2B01G627300 chrUn 90.667 150 14 0 1499 1648 31529677 31529528 2.250000e-47 200.0
43 TraesCS2B01G627300 chrUn 88.372 129 8 2 1640 1767 31528413 31528291 8.270000e-32 148.0
44 TraesCS2B01G627300 chrUn 87.500 112 5 3 2765 2876 31520206 31520308 1.800000e-23 121.0
45 TraesCS2B01G627300 chr1B 97.635 296 6 1 3336 3630 629504199 629503904 1.180000e-139 507.0
46 TraesCS2B01G627300 chr1B 93.902 246 13 2 3272 3515 601478855 601479100 1.620000e-98 370.0
47 TraesCS2B01G627300 chr1B 97.872 47 1 0 3272 3318 629504242 629504196 8.510000e-12 82.4
48 TraesCS2B01G627300 chr4B 91.532 248 19 2 3270 3515 5925530 5925283 1.270000e-89 340.0
49 TraesCS2B01G627300 chr4B 86.420 81 11 0 772 852 80678281 80678361 5.090000e-14 89.8
50 TraesCS2B01G627300 chr3B 88.000 75 9 0 770 844 489979100 489979026 5.090000e-14 89.8
51 TraesCS2B01G627300 chr7B 87.838 74 9 0 771 844 73212056 73211983 1.830000e-13 87.9
52 TraesCS2B01G627300 chr1D 87.013 77 6 3 770 844 461421377 461421451 2.370000e-12 84.2
53 TraesCS2B01G627300 chr7D 83.544 79 13 0 775 853 581298959 581298881 1.420000e-09 75.0


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 TraesCS2B01G627300 chr2B 799249892 799253588 3696 True 6828.000000 6828 100.000000 1 3697 1 chr2B.!!$R2 3696
1 TraesCS2B01G627300 chr2A 767569833 767575419 5586 False 1773.666667 4036 90.519000 37 3270 3 chr2A.!!$F3 3233
2 TraesCS2B01G627300 chr2A 767788267 767792231 3964 True 780.000000 1711 88.846750 148 2809 4 chr2A.!!$R5 2661
3 TraesCS2B01G627300 chr2A 767560406 767562947 2541 False 428.000000 525 77.327500 844 2501 2 chr2A.!!$F2 1657
4 TraesCS2B01G627300 chr2A 767485304 767485846 542 True 320.000000 320 77.838000 844 1384 1 chr2A.!!$R3 540
5 TraesCS2B01G627300 chr2D 642442853 642445973 3120 False 1110.250000 1838 94.474250 1 2893 4 chr2D.!!$F6 2892
6 TraesCS2B01G627300 chr2D 642499554 642502663 3109 False 1002.666667 1389 88.577000 51 2882 3 chr2D.!!$F7 2831
7 TraesCS2B01G627300 chr2D 642940431 642942036 1605 False 480.666667 776 85.932333 576 2234 3 chr2D.!!$F9 1658
8 TraesCS2B01G627300 chrUn 31552345 31553093 748 False 828.000000 828 86.800000 1955 2695 1 chrUn.!!$F2 740
9 TraesCS2B01G627300 chrUn 31526678 31531070 4392 True 682.200000 1757 88.652800 148 2960 5 chrUn.!!$R2 2812

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
294 305 0.106708 AGCGTCATAATGCCGATGGT 59.893 50.0 0.00 0.0 38.23 3.55 F
382 393 0.690762 GGTGAGTTTGCCCTACCTCA 59.309 55.0 0.00 0.0 0.00 3.86 F
1704 4140 0.591170 TGCACTGGCGCTTAAAAGAC 59.409 50.0 7.64 0.0 45.35 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1170 2.736670 AGAGTGGCCACTTCAAGTTT 57.263 45.000 37.98 15.12 42.66 2.66 R
1764 4202 3.287312 TGCTTTTTACTGACATGCTGC 57.713 42.857 0.00 0.00 0.00 5.25 R
3312 6717 0.035152 TAGGCGGTTAGACGAGTCCA 60.035 55.000 0.00 0.00 35.47 4.02 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 1.598132 CGAGAGCAATCATCTTGGCTG 59.402 52.381 0.00 0.00 36.59 4.85
133 144 3.349927 CAAAAGATGCAGATGGACAGGA 58.650 45.455 0.00 0.00 0.00 3.86
253 264 2.556459 CGGGATCTGGCGACGATCT 61.556 63.158 18.25 0.00 39.07 2.75
283 294 6.406692 AGAAGGCTTATCTAAAGCGTCATA 57.593 37.500 0.00 0.00 43.89 2.15
294 305 0.106708 AGCGTCATAATGCCGATGGT 59.893 50.000 0.00 0.00 38.23 3.55
306 317 1.346062 CCGATGGTGATGGGAGATCT 58.654 55.000 0.00 0.00 28.75 2.75
327 338 3.802948 ATATCACCTCAGTTGGTCGAC 57.197 47.619 7.13 7.13 38.45 4.20
382 393 0.690762 GGTGAGTTTGCCCTACCTCA 59.309 55.000 0.00 0.00 0.00 3.86
383 394 1.809684 GTGAGTTTGCCCTACCTCAC 58.190 55.000 0.00 0.00 44.75 3.51
415 428 3.160047 AGGCCCTGGATCTGCTCG 61.160 66.667 0.00 0.00 0.00 5.03
422 435 2.887568 GGATCTGCTCGTGCACGG 60.888 66.667 36.41 27.12 45.31 4.94
551 564 3.464833 AGGATCTCCAAAACCATAGCCAT 59.535 43.478 0.00 0.00 38.89 4.40
561 574 1.426215 ACCATAGCCATGCATGGATCA 59.574 47.619 43.18 28.10 44.64 2.92
565 578 0.754217 AGCCATGCATGGATCACCAC 60.754 55.000 43.18 25.65 44.64 4.16
746 794 5.797434 GCTTTGCTCCTTTTTAGAGAATTCG 59.203 40.000 0.00 0.00 32.86 3.34
762 810 8.637196 AGAGAATTCGATATGGACTACATACA 57.363 34.615 0.00 0.00 44.41 2.29
765 813 8.735315 AGAATTCGATATGGACTACATACAGAG 58.265 37.037 0.00 0.00 44.41 3.35
768 816 5.412904 TCGATATGGACTACATACAGAGCAG 59.587 44.000 0.00 0.00 44.41 4.24
888 958 9.774742 CATGTCTCAATCTATGCAATCATAATG 57.225 33.333 0.00 0.00 34.97 1.90
917 987 6.486253 TGCTTTGCTTCTTGTATAGTGAAG 57.514 37.500 0.00 0.00 39.88 3.02
947 1017 5.552870 TCTAGCCCCTTGATTTACTGATC 57.447 43.478 0.00 0.00 0.00 2.92
958 1028 9.618890 CCTTGATTTACTGATCTCCAGATTTAA 57.381 33.333 0.00 0.00 45.78 1.52
1098 1170 9.142014 TCCTTCAAAATCTTTGACCTAAATGAA 57.858 29.630 1.37 0.00 0.00 2.57
1337 1515 7.663493 AGCTAGTTCTGAAGTAAGAAAAGCATT 59.337 33.333 17.72 3.58 43.41 3.56
1376 1557 3.068590 ACTTGGCTGAAAACAACCTGATG 59.931 43.478 0.00 0.00 0.00 3.07
1427 2501 7.575720 GCTGCTACATTTCACAATTCTACCTTT 60.576 37.037 0.00 0.00 0.00 3.11
1544 2841 8.686334 CAATTAGGTATTTGATGCCTTTGTACT 58.314 33.333 2.91 0.00 43.28 2.73
1704 4140 0.591170 TGCACTGGCGCTTAAAAGAC 59.409 50.000 7.64 0.00 45.35 3.01
1764 4202 6.749923 ATAAAAGTTCTAGCAGGAGCAAAG 57.250 37.500 0.00 0.00 45.49 2.77
1767 4205 1.736681 GTTCTAGCAGGAGCAAAGCAG 59.263 52.381 0.00 0.00 45.49 4.24
1769 4207 0.675837 CTAGCAGGAGCAAAGCAGCA 60.676 55.000 0.00 0.00 45.49 4.41
1770 4208 0.034767 TAGCAGGAGCAAAGCAGCAT 60.035 50.000 0.00 0.00 45.49 3.79
1773 4211 0.170561 CAGGAGCAAAGCAGCATGTC 59.829 55.000 0.00 0.00 39.31 3.06
1838 5198 9.686683 GCATCCCAGTAAATAAGTAATATCCAT 57.313 33.333 0.00 0.00 0.00 3.41
2545 5935 3.931907 AGTTGCCATACAAGCCTATGA 57.068 42.857 0.00 0.00 39.50 2.15
2565 5955 1.048724 GGGATCTGACCGTCCATCCA 61.049 60.000 20.66 0.00 37.18 3.41
2898 6303 1.223187 ACTTTCGGTTGCTTGGTACG 58.777 50.000 0.00 0.00 0.00 3.67
2916 6321 8.774890 TTGGTACGTCTAGTGCATTTAATTTA 57.225 30.769 0.00 0.00 37.18 1.40
3069 6474 2.297698 TTTAGAGGGTCCAGTGTCGA 57.702 50.000 0.00 0.00 0.00 4.20
3071 6476 0.680280 TAGAGGGTCCAGTGTCGAGC 60.680 60.000 0.00 0.00 0.00 5.03
3202 6607 3.953612 ACCACGGACACGGTTATTCTATA 59.046 43.478 0.00 0.00 46.48 1.31
3232 6637 7.005062 AGCAGCTCGTACATAACTTATTTTG 57.995 36.000 0.00 0.00 0.00 2.44
3272 6677 5.931441 ACTCAAAGACAAGTCACTAATGC 57.069 39.130 2.72 0.00 0.00 3.56
3274 6679 4.973168 TCAAAGACAAGTCACTAATGCCT 58.027 39.130 2.72 0.00 0.00 4.75
3275 6680 5.376625 TCAAAGACAAGTCACTAATGCCTT 58.623 37.500 2.72 0.00 0.00 4.35
3276 6681 5.827797 TCAAAGACAAGTCACTAATGCCTTT 59.172 36.000 2.72 0.00 0.00 3.11
3277 6682 6.321181 TCAAAGACAAGTCACTAATGCCTTTT 59.679 34.615 2.72 0.00 0.00 2.27
3278 6683 6.715347 AAGACAAGTCACTAATGCCTTTTT 57.285 33.333 2.72 0.00 0.00 1.94
3296 6701 4.893424 TTTTTGGATACGCAGGATTAGC 57.107 40.909 0.00 0.00 42.51 3.09
3297 6702 2.543777 TTGGATACGCAGGATTAGCC 57.456 50.000 0.00 0.00 42.51 3.93
3298 6703 0.317160 TGGATACGCAGGATTAGCCG 59.683 55.000 0.00 0.00 40.77 5.52
3304 6709 1.067212 ACGCAGGATTAGCCGAACTAG 59.933 52.381 0.00 0.00 43.43 2.57
3306 6711 2.481449 CGCAGGATTAGCCGAACTAGTT 60.481 50.000 8.13 8.13 43.43 2.24
3307 6712 3.532542 GCAGGATTAGCCGAACTAGTTT 58.467 45.455 10.02 0.00 43.43 2.66
3308 6713 3.939592 GCAGGATTAGCCGAACTAGTTTT 59.060 43.478 10.02 0.00 43.43 2.43
3309 6714 5.114081 GCAGGATTAGCCGAACTAGTTTTA 58.886 41.667 10.02 0.00 43.43 1.52
3310 6715 5.006455 GCAGGATTAGCCGAACTAGTTTTAC 59.994 44.000 10.02 2.23 43.43 2.01
3311 6716 5.231568 CAGGATTAGCCGAACTAGTTTTACG 59.768 44.000 10.02 8.80 43.43 3.18
3312 6717 5.105063 GGATTAGCCGAACTAGTTTTACGT 58.895 41.667 10.02 0.00 30.79 3.57
3314 6719 2.680577 AGCCGAACTAGTTTTACGTGG 58.319 47.619 10.02 6.58 0.00 4.94
3315 6720 2.297033 AGCCGAACTAGTTTTACGTGGA 59.703 45.455 10.02 0.00 0.00 4.02
3316 6721 2.409715 GCCGAACTAGTTTTACGTGGAC 59.590 50.000 10.02 0.00 0.00 4.02
3317 6722 3.858503 GCCGAACTAGTTTTACGTGGACT 60.859 47.826 10.02 1.70 0.00 3.85
3318 6723 3.916776 CCGAACTAGTTTTACGTGGACTC 59.083 47.826 10.02 0.00 0.00 3.36
3319 6724 3.601211 CGAACTAGTTTTACGTGGACTCG 59.399 47.826 10.02 0.04 0.00 4.18
3320 6725 4.540824 GAACTAGTTTTACGTGGACTCGT 58.459 43.478 10.02 4.80 45.97 4.18
3321 6726 4.152607 ACTAGTTTTACGTGGACTCGTC 57.847 45.455 0.00 0.00 43.12 4.20
3322 6727 3.817647 ACTAGTTTTACGTGGACTCGTCT 59.182 43.478 0.00 0.00 43.12 4.18
3324 6729 4.836125 AGTTTTACGTGGACTCGTCTAA 57.164 40.909 0.00 0.00 43.12 2.10
3325 6730 4.540824 AGTTTTACGTGGACTCGTCTAAC 58.459 43.478 0.00 8.68 43.12 2.34
3327 6732 1.078709 TACGTGGACTCGTCTAACCG 58.921 55.000 0.00 0.00 43.12 4.44
3331 6736 0.035152 TGGACTCGTCTAACCGCCTA 60.035 55.000 0.00 0.00 0.00 3.93
3333 6738 1.202234 GGACTCGTCTAACCGCCTAAC 60.202 57.143 0.00 0.00 0.00 2.34
3334 6739 1.470098 GACTCGTCTAACCGCCTAACA 59.530 52.381 0.00 0.00 0.00 2.41
3335 6740 1.471684 ACTCGTCTAACCGCCTAACAG 59.528 52.381 0.00 0.00 0.00 3.16
3337 6742 1.470098 TCGTCTAACCGCCTAACAGAC 59.530 52.381 0.00 0.00 33.78 3.51
3338 6743 1.471684 CGTCTAACCGCCTAACAGACT 59.528 52.381 0.00 0.00 34.74 3.24
3339 6744 2.679837 CGTCTAACCGCCTAACAGACTA 59.320 50.000 0.00 0.00 34.74 2.59
3341 6746 4.379813 CGTCTAACCGCCTAACAGACTAAA 60.380 45.833 0.00 0.00 34.74 1.85
3342 6747 4.861462 GTCTAACCGCCTAACAGACTAAAC 59.139 45.833 0.00 0.00 34.21 2.01
3343 6748 2.756840 ACCGCCTAACAGACTAAACC 57.243 50.000 0.00 0.00 0.00 3.27
3344 6749 2.254508 ACCGCCTAACAGACTAAACCT 58.745 47.619 0.00 0.00 0.00 3.50
3345 6750 2.636403 ACCGCCTAACAGACTAAACCTT 59.364 45.455 0.00 0.00 0.00 3.50
3346 6751 3.000727 CCGCCTAACAGACTAAACCTTG 58.999 50.000 0.00 0.00 0.00 3.61
3347 6752 3.556423 CCGCCTAACAGACTAAACCTTGT 60.556 47.826 0.00 0.00 0.00 3.16
3348 6753 4.062991 CGCCTAACAGACTAAACCTTGTT 58.937 43.478 0.00 0.00 0.00 2.83
3349 6754 4.514066 CGCCTAACAGACTAAACCTTGTTT 59.486 41.667 0.00 0.00 0.00 2.83
3350 6755 5.560183 CGCCTAACAGACTAAACCTTGTTTG 60.560 44.000 2.60 0.00 0.00 2.93
3352 6757 5.826208 CCTAACAGACTAAACCTTGTTTGGT 59.174 40.000 8.21 8.21 43.11 3.67
3356 6761 5.104235 ACAGACTAAACCTTGTTTGGTACCT 60.104 40.000 14.36 1.40 39.83 3.08
3358 6763 4.722220 ACTAAACCTTGTTTGGTACCTCC 58.278 43.478 14.36 1.20 39.83 4.30
3371 6776 4.594970 TGGTACCTCCAACAAATATGTGG 58.405 43.478 14.36 0.00 44.12 4.17
3372 6777 4.289934 TGGTACCTCCAACAAATATGTGGA 59.710 41.667 14.36 0.00 44.12 4.02
3373 6778 5.044476 TGGTACCTCCAACAAATATGTGGAT 60.044 40.000 14.36 0.00 44.12 3.41
3374 6779 6.158871 TGGTACCTCCAACAAATATGTGGATA 59.841 38.462 14.36 0.00 44.12 2.59
3377 6782 6.129179 ACCTCCAACAAATATGTGGATAAGG 58.871 40.000 0.00 2.05 40.46 2.69
3400 6805 6.084326 GAAAACTCTATTTCCACAAAGCCA 57.916 37.500 0.00 0.00 34.03 4.75
3402 6807 3.690460 ACTCTATTTCCACAAAGCCAGG 58.310 45.455 0.00 0.00 0.00 4.45
3403 6808 3.330701 ACTCTATTTCCACAAAGCCAGGA 59.669 43.478 0.00 0.00 0.00 3.86
3408 6813 0.469144 TCCACAAAGCCAGGAAACCC 60.469 55.000 0.00 0.00 0.00 4.11
3409 6814 1.471829 CCACAAAGCCAGGAAACCCC 61.472 60.000 0.00 0.00 0.00 4.95
3410 6815 1.530655 ACAAAGCCAGGAAACCCCG 60.531 57.895 0.00 0.00 40.87 5.73
3411 6816 1.530655 CAAAGCCAGGAAACCCCGT 60.531 57.895 0.00 0.00 40.87 5.28
3412 6817 1.112916 CAAAGCCAGGAAACCCCGTT 61.113 55.000 0.00 0.00 40.87 4.44
3414 6819 0.397957 AAGCCAGGAAACCCCGTTTT 60.398 50.000 0.00 0.00 40.87 2.43
3415 6820 0.479378 AGCCAGGAAACCCCGTTTTA 59.521 50.000 0.00 0.00 40.87 1.52
3416 6821 1.076513 AGCCAGGAAACCCCGTTTTAT 59.923 47.619 0.00 0.00 40.87 1.40
3417 6822 1.203758 GCCAGGAAACCCCGTTTTATG 59.796 52.381 0.00 0.00 40.87 1.90
3418 6823 2.797786 CCAGGAAACCCCGTTTTATGA 58.202 47.619 0.00 0.00 40.87 2.15
3419 6824 3.158676 CCAGGAAACCCCGTTTTATGAA 58.841 45.455 0.00 0.00 40.87 2.57
3420 6825 3.574826 CCAGGAAACCCCGTTTTATGAAA 59.425 43.478 0.00 0.00 40.87 2.69
3422 6827 5.453480 CCAGGAAACCCCGTTTTATGAAAAA 60.453 40.000 0.00 0.00 40.87 1.94
3457 6862 8.919145 ACTTGTTTTTATGGAAACAGGATTACA 58.081 29.630 18.27 0.00 46.60 2.41
3458 6863 9.410556 CTTGTTTTTATGGAAACAGGATTACAG 57.589 33.333 10.42 1.74 46.60 2.74
3459 6864 9.137459 TTGTTTTTATGGAAACAGGATTACAGA 57.863 29.630 8.02 0.00 46.60 3.41
3465 6870 6.877611 TGGAAACAGGATTACAGAAAACTC 57.122 37.500 0.00 0.00 35.01 3.01
3466 6871 5.468746 TGGAAACAGGATTACAGAAAACTCG 59.531 40.000 0.00 0.00 35.01 4.18
3467 6872 5.699458 GGAAACAGGATTACAGAAAACTCGA 59.301 40.000 0.00 0.00 0.00 4.04
3469 6874 6.727824 AACAGGATTACAGAAAACTCGATG 57.272 37.500 0.00 0.00 0.00 3.84
3470 6875 5.794894 ACAGGATTACAGAAAACTCGATGT 58.205 37.500 0.00 0.00 0.00 3.06
3471 6876 6.931838 ACAGGATTACAGAAAACTCGATGTA 58.068 36.000 0.00 0.00 0.00 2.29
3474 6879 7.545965 CAGGATTACAGAAAACTCGATGTAACT 59.454 37.037 8.72 1.88 40.00 2.24
3475 6880 8.746530 AGGATTACAGAAAACTCGATGTAACTA 58.253 33.333 8.72 0.00 40.00 2.24
3476 6881 9.362539 GGATTACAGAAAACTCGATGTAACTAA 57.637 33.333 8.72 0.00 40.00 2.24
3479 6884 9.754382 TTACAGAAAACTCGATGTAACTAACTT 57.246 29.630 3.52 0.00 34.20 2.66
3480 6885 8.658499 ACAGAAAACTCGATGTAACTAACTTT 57.342 30.769 0.00 0.00 0.00 2.66
3481 6886 9.106070 ACAGAAAACTCGATGTAACTAACTTTT 57.894 29.630 0.00 0.00 0.00 2.27
3482 6887 9.931210 CAGAAAACTCGATGTAACTAACTTTTT 57.069 29.630 0.00 0.00 0.00 1.94
3504 6927 1.420138 GTTCCACTCCCTCCTCAACAA 59.580 52.381 0.00 0.00 0.00 2.83
3505 6928 1.814429 TCCACTCCCTCCTCAACAAA 58.186 50.000 0.00 0.00 0.00 2.83
3507 6930 1.421646 CCACTCCCTCCTCAACAAACT 59.578 52.381 0.00 0.00 0.00 2.66
3509 6932 2.104792 CACTCCCTCCTCAACAAACTCA 59.895 50.000 0.00 0.00 0.00 3.41
3512 6935 4.597507 ACTCCCTCCTCAACAAACTCATTA 59.402 41.667 0.00 0.00 0.00 1.90
3517 6940 2.483877 CCTCAACAAACTCATTAGCGCA 59.516 45.455 11.47 0.00 0.00 6.09
3518 6941 3.482786 CTCAACAAACTCATTAGCGCAC 58.517 45.455 11.47 0.00 0.00 5.34
3519 6942 2.225491 TCAACAAACTCATTAGCGCACC 59.775 45.455 11.47 0.00 0.00 5.01
3520 6943 2.185004 ACAAACTCATTAGCGCACCT 57.815 45.000 11.47 0.00 0.00 4.00
3522 6945 2.226437 ACAAACTCATTAGCGCACCTTG 59.774 45.455 11.47 1.25 0.00 3.61
3523 6946 0.804989 AACTCATTAGCGCACCTTGC 59.195 50.000 11.47 0.00 40.69 4.01
3525 6948 1.002746 TCATTAGCGCACCTTGCCA 60.003 52.632 11.47 0.00 41.12 4.92
3526 6949 1.137404 CATTAGCGCACCTTGCCAC 59.863 57.895 11.47 0.00 41.12 5.01
3546 6969 4.845580 CCAGCTCCTCGCGCCAAT 62.846 66.667 0.00 0.00 45.59 3.16
3548 6971 2.045926 AGCTCCTCGCGCCAATTT 60.046 55.556 0.00 0.00 45.59 1.82
3549 6972 1.675641 AGCTCCTCGCGCCAATTTT 60.676 52.632 0.00 0.00 45.59 1.82
3550 6973 1.212751 GCTCCTCGCGCCAATTTTT 59.787 52.632 0.00 0.00 0.00 1.94
3575 6998 8.521170 TTCATCCCTTCTATATATACCTGACG 57.479 38.462 0.00 0.00 0.00 4.35
3576 6999 6.546403 TCATCCCTTCTATATATACCTGACGC 59.454 42.308 0.00 0.00 0.00 5.19
3577 7000 6.075949 TCCCTTCTATATATACCTGACGCT 57.924 41.667 0.00 0.00 0.00 5.07
3579 7002 5.007823 CCCTTCTATATATACCTGACGCTCG 59.992 48.000 0.00 0.00 0.00 5.03
3580 7003 5.585445 CCTTCTATATATACCTGACGCTCGT 59.415 44.000 0.00 0.00 0.00 4.18
3581 7004 6.760298 CCTTCTATATATACCTGACGCTCGTA 59.240 42.308 0.00 0.00 0.00 3.43
3582 7005 7.254387 CCTTCTATATATACCTGACGCTCGTAC 60.254 44.444 0.00 0.00 0.00 3.67
3583 7006 6.633856 TCTATATATACCTGACGCTCGTACA 58.366 40.000 0.00 0.00 0.00 2.90
3584 7007 7.099120 TCTATATATACCTGACGCTCGTACAA 58.901 38.462 0.00 0.00 0.00 2.41
3585 7008 2.556534 ATACCTGACGCTCGTACAAC 57.443 50.000 0.00 0.00 0.00 3.32
3586 7009 1.237533 TACCTGACGCTCGTACAACA 58.762 50.000 0.00 0.00 0.00 3.33
3587 7010 0.386476 ACCTGACGCTCGTACAACAA 59.614 50.000 0.00 0.00 0.00 2.83
3588 7011 1.202440 ACCTGACGCTCGTACAACAAA 60.202 47.619 0.00 0.00 0.00 2.83
3590 7013 1.855978 CTGACGCTCGTACAACAAACA 59.144 47.619 0.00 0.00 0.00 2.83
3591 7014 2.475111 CTGACGCTCGTACAACAAACAT 59.525 45.455 0.00 0.00 0.00 2.71
3593 7016 2.473609 GACGCTCGTACAACAAACATGA 59.526 45.455 0.00 0.00 0.00 3.07
3594 7017 2.220133 ACGCTCGTACAACAAACATGAC 59.780 45.455 0.00 0.00 0.00 3.06
3595 7018 2.717595 CGCTCGTACAACAAACATGACG 60.718 50.000 0.00 0.00 0.00 4.35
3596 7019 2.473609 GCTCGTACAACAAACATGACGA 59.526 45.455 0.00 0.26 37.69 4.20
3597 7020 3.060138 GCTCGTACAACAAACATGACGAA 60.060 43.478 0.00 0.00 38.68 3.85
3598 7021 4.551217 GCTCGTACAACAAACATGACGAAA 60.551 41.667 0.00 0.00 38.68 3.46
3599 7022 4.824301 TCGTACAACAAACATGACGAAAC 58.176 39.130 0.00 0.00 36.48 2.78
3600 7023 4.329256 TCGTACAACAAACATGACGAAACA 59.671 37.500 0.00 0.00 36.48 2.83
3601 7024 5.022653 CGTACAACAAACATGACGAAACAA 58.977 37.500 0.00 0.00 32.20 2.83
3602 7025 5.508573 CGTACAACAAACATGACGAAACAAA 59.491 36.000 0.00 0.00 32.20 2.83
3605 7028 6.329496 ACAACAAACATGACGAAACAAATCT 58.671 32.000 0.00 0.00 0.00 2.40
3606 7029 6.253298 ACAACAAACATGACGAAACAAATCTG 59.747 34.615 0.00 0.00 0.00 2.90
3607 7030 5.280945 ACAAACATGACGAAACAAATCTGG 58.719 37.500 0.00 0.00 0.00 3.86
3609 7032 2.095768 ACATGACGAAACAAATCTGGCG 60.096 45.455 0.00 0.00 0.00 5.69
3610 7033 1.872388 TGACGAAACAAATCTGGCGA 58.128 45.000 0.00 0.00 0.00 5.54
3613 7036 1.156736 CGAAACAAATCTGGCGACCT 58.843 50.000 0.00 0.00 0.00 3.85
3614 7037 1.135972 CGAAACAAATCTGGCGACCTG 60.136 52.381 0.00 0.00 0.00 4.00
3616 7039 1.244019 AACAAATCTGGCGACCTGGC 61.244 55.000 0.00 0.00 45.12 4.85
3618 7041 0.962356 CAAATCTGGCGACCTGGCTT 60.962 55.000 0.00 0.00 45.14 4.35
3620 7043 0.251341 AATCTGGCGACCTGGCTTTT 60.251 50.000 0.00 0.00 45.14 2.27
3621 7044 0.962356 ATCTGGCGACCTGGCTTTTG 60.962 55.000 0.00 0.00 45.14 2.44
3622 7045 3.273080 CTGGCGACCTGGCTTTTGC 62.273 63.158 0.00 0.00 45.14 3.68
3634 7057 1.689959 GCTTTTGCAGTTCGTCCATG 58.310 50.000 0.00 0.00 46.58 3.66
3637 7060 0.537143 TTTGCAGTTCGTCCATGGCT 60.537 50.000 6.96 0.00 0.00 4.75
3638 7061 1.236616 TTGCAGTTCGTCCATGGCTG 61.237 55.000 6.96 9.43 0.00 4.85
3639 7062 2.401766 GCAGTTCGTCCATGGCTGG 61.402 63.158 6.96 0.00 44.64 4.85
3640 7063 2.045926 AGTTCGTCCATGGCTGGC 60.046 61.111 6.96 0.00 42.80 4.85
3641 7064 3.134127 GTTCGTCCATGGCTGGCC 61.134 66.667 6.96 4.43 42.80 5.36
3642 7065 4.776322 TTCGTCCATGGCTGGCCG 62.776 66.667 6.96 4.14 45.12 6.13
3653 7076 4.954970 CTGGCCGCCAACACCTGT 62.955 66.667 14.45 0.00 30.80 4.00
3654 7077 4.514585 TGGCCGCCAACACCTGTT 62.515 61.111 10.50 0.00 39.12 3.16
3664 7087 3.030652 CACCTGTTGTGTTCGCCC 58.969 61.111 0.00 0.00 40.26 6.13
3665 7088 1.525995 CACCTGTTGTGTTCGCCCT 60.526 57.895 0.00 0.00 40.26 5.19
3666 7089 1.525995 ACCTGTTGTGTTCGCCCTG 60.526 57.895 0.00 0.00 0.00 4.45
3667 7090 2.260869 CCTGTTGTGTTCGCCCTGG 61.261 63.158 0.00 0.00 0.00 4.45
3669 7092 3.670377 GTTGTGTTCGCCCTGGCC 61.670 66.667 1.86 0.00 37.98 5.36
3689 7112 3.637297 CCGTCGGTAGGCTAAGTTC 57.363 57.895 2.08 0.00 0.00 3.01
3691 7114 1.468736 CCGTCGGTAGGCTAAGTTCAC 60.469 57.143 2.08 0.00 0.00 3.18
3693 7116 2.731341 CGTCGGTAGGCTAAGTTCACAG 60.731 54.545 0.00 0.00 0.00 3.66
3695 7118 3.130693 GTCGGTAGGCTAAGTTCACAGAT 59.869 47.826 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.470278 TCCTACAGCTTTAGGGTTAACTTTC 58.530 40.000 22.90 0.00 39.46 2.62
99 109 2.030027 TCTTTTGGGCCTCTCTCTGA 57.970 50.000 4.53 0.00 0.00 3.27
104 114 1.101331 CTGCATCTTTTGGGCCTCTC 58.899 55.000 4.53 0.00 0.00 3.20
180 191 0.972983 ACCTCAGGATCTCACGGTGG 60.973 60.000 8.50 0.00 0.00 4.61
253 264 5.671493 CTTTAGATAAGCCTTCTTTCCGGA 58.329 41.667 0.00 0.00 33.85 5.14
283 294 0.179009 CTCCCATCACCATCGGCATT 60.179 55.000 0.00 0.00 0.00 3.56
294 305 6.157862 TGAGGTGATATAGATCTCCCATCA 57.842 41.667 13.49 9.65 43.89 3.07
306 317 3.635373 GGTCGACCAACTGAGGTGATATA 59.365 47.826 29.75 0.00 43.38 0.86
327 338 0.692476 TCTTGTGGAGGGACATGTGG 59.308 55.000 1.15 0.00 0.00 4.17
382 393 2.039084 GGGCCTCTTCATGATTATCCGT 59.961 50.000 0.84 0.00 0.00 4.69
383 394 2.304180 AGGGCCTCTTCATGATTATCCG 59.696 50.000 0.00 0.00 0.00 4.18
422 435 0.246360 GTAGGCCAATTTGTGTGCCC 59.754 55.000 5.01 0.00 41.85 5.36
551 564 2.821378 CAAGAAAGTGGTGATCCATGCA 59.179 45.455 0.00 0.00 46.20 3.96
561 574 5.684704 TCAGAAGATTCACAAGAAAGTGGT 58.315 37.500 0.00 0.00 39.93 4.16
565 578 6.403418 GCATCCTCAGAAGATTCACAAGAAAG 60.403 42.308 0.00 0.00 37.29 2.62
616 629 2.249139 AGTAGATTCCCAGCCGATACC 58.751 52.381 0.00 0.00 0.00 2.73
698 711 7.123247 AGCGTACTAACAAGAGGAAATTAGGTA 59.877 37.037 0.00 0.00 0.00 3.08
720 733 3.740115 TCTCTAAAAAGGAGCAAAGCGT 58.260 40.909 0.00 0.00 0.00 5.07
746 794 6.825944 TCTGCTCTGTATGTAGTCCATATC 57.174 41.667 0.00 0.00 38.29 1.63
888 958 1.137513 CAAGAAGCAAAGCAGCAAGC 58.862 50.000 0.00 0.00 46.19 4.01
917 987 8.379331 AGTAAATCAAGGGGCTAGAATATTCTC 58.621 37.037 21.17 8.31 38.70 2.87
930 1000 4.410228 TCTGGAGATCAGTAAATCAAGGGG 59.590 45.833 0.00 0.00 43.76 4.79
947 1017 7.827236 TGTGGGTAGTGTTATTTAAATCTGGAG 59.173 37.037 3.39 0.00 0.00 3.86
958 1028 6.039717 GCATCATGAATGTGGGTAGTGTTATT 59.960 38.462 0.00 0.00 37.71 1.40
1098 1170 2.736670 AGAGTGGCCACTTCAAGTTT 57.263 45.000 37.98 15.12 42.66 2.66
1337 1515 7.555914 TCAGCCAAGTGTAATAATAATCAAGCA 59.444 33.333 0.00 0.00 0.00 3.91
1376 1557 7.031975 CCAGATAAAAGAAATGAGTTGCTTCC 58.968 38.462 0.00 0.00 0.00 3.46
1427 2501 6.540438 AGGAAATCTGTTCAGTATTACCGA 57.460 37.500 0.00 0.00 0.00 4.69
1544 2841 6.482973 TCGAGCATTCAAGTTGCATCATTATA 59.517 34.615 0.00 0.00 42.62 0.98
1546 2843 4.635324 TCGAGCATTCAAGTTGCATCATTA 59.365 37.500 0.00 0.00 42.62 1.90
1704 4140 4.566004 TCTTTATTTCTGTCCTGGACGTG 58.434 43.478 21.15 16.07 34.95 4.49
1764 4202 3.287312 TGCTTTTTACTGACATGCTGC 57.713 42.857 0.00 0.00 0.00 5.25
1767 4205 4.853743 GCTACTTGCTTTTTACTGACATGC 59.146 41.667 0.00 0.00 38.95 4.06
1769 4207 6.615088 CATGCTACTTGCTTTTTACTGACAT 58.385 36.000 0.00 0.00 43.37 3.06
1770 4208 5.562696 GCATGCTACTTGCTTTTTACTGACA 60.563 40.000 11.37 0.00 43.37 3.58
1773 4211 4.797471 TGCATGCTACTTGCTTTTTACTG 58.203 39.130 20.33 0.00 43.37 2.74
1838 5198 4.274147 TCACACAGGAAAGTTAGCCAAAA 58.726 39.130 0.00 0.00 0.00 2.44
2545 5935 0.760945 GGATGGACGGTCAGATCCCT 60.761 60.000 20.19 0.00 33.69 4.20
2565 5955 5.217400 AGGGAAGTAAAGAAGACCGGATAT 58.783 41.667 9.46 0.00 0.00 1.63
2876 6281 3.061697 CGTACCAAGCAACCGAAAGTATC 59.938 47.826 0.00 0.00 0.00 2.24
2898 6303 7.472543 CAGGTGGTAAATTAAATGCACTAGAC 58.527 38.462 0.00 0.00 0.00 2.59
2916 6321 0.968901 CATCAATGGCAGCAGGTGGT 60.969 55.000 0.86 0.00 0.00 4.16
3202 6607 2.751166 ATGTACGAGCTGCTTGAACT 57.249 45.000 23.27 3.87 0.00 3.01
3232 6637 9.691362 TCTTTGAGTAATAAATTTGAAGTTGCC 57.309 29.630 0.00 0.00 0.00 4.52
3275 6680 3.630312 GGCTAATCCTGCGTATCCAAAAA 59.370 43.478 0.00 0.00 0.00 1.94
3276 6681 3.211045 GGCTAATCCTGCGTATCCAAAA 58.789 45.455 0.00 0.00 0.00 2.44
3277 6682 2.805295 CGGCTAATCCTGCGTATCCAAA 60.805 50.000 0.00 0.00 0.00 3.28
3278 6683 1.270094 CGGCTAATCCTGCGTATCCAA 60.270 52.381 0.00 0.00 0.00 3.53
3279 6684 0.317160 CGGCTAATCCTGCGTATCCA 59.683 55.000 0.00 0.00 0.00 3.41
3280 6685 0.601558 TCGGCTAATCCTGCGTATCC 59.398 55.000 0.00 0.00 0.00 2.59
3281 6686 2.059541 GTTCGGCTAATCCTGCGTATC 58.940 52.381 0.00 0.00 0.00 2.24
3282 6687 1.687123 AGTTCGGCTAATCCTGCGTAT 59.313 47.619 0.00 0.00 0.00 3.06
3285 6690 1.067212 ACTAGTTCGGCTAATCCTGCG 59.933 52.381 0.00 0.00 0.00 5.18
3286 6691 2.892784 ACTAGTTCGGCTAATCCTGC 57.107 50.000 0.00 0.00 0.00 4.85
3288 6693 5.105595 ACGTAAAACTAGTTCGGCTAATCCT 60.106 40.000 8.95 0.00 0.00 3.24
3289 6694 5.005107 CACGTAAAACTAGTTCGGCTAATCC 59.995 44.000 8.95 0.00 0.00 3.01
3290 6695 5.005107 CCACGTAAAACTAGTTCGGCTAATC 59.995 44.000 8.95 0.00 0.00 1.75
3291 6696 4.866486 CCACGTAAAACTAGTTCGGCTAAT 59.134 41.667 8.95 0.00 0.00 1.73
3292 6697 4.022416 TCCACGTAAAACTAGTTCGGCTAA 60.022 41.667 8.95 0.00 0.00 3.09
3293 6698 3.505680 TCCACGTAAAACTAGTTCGGCTA 59.494 43.478 8.95 0.00 0.00 3.93
3294 6699 2.297033 TCCACGTAAAACTAGTTCGGCT 59.703 45.455 8.95 0.00 0.00 5.52
3295 6700 2.409715 GTCCACGTAAAACTAGTTCGGC 59.590 50.000 8.95 1.18 0.00 5.54
3296 6701 3.905784 AGTCCACGTAAAACTAGTTCGG 58.094 45.455 8.95 3.55 0.00 4.30
3297 6702 3.601211 CGAGTCCACGTAAAACTAGTTCG 59.399 47.826 8.95 10.90 0.00 3.95
3298 6703 4.540824 ACGAGTCCACGTAAAACTAGTTC 58.459 43.478 8.95 0.00 44.72 3.01
3304 6709 3.670523 GGTTAGACGAGTCCACGTAAAAC 59.329 47.826 0.00 0.00 46.52 2.43
3306 6711 2.095768 CGGTTAGACGAGTCCACGTAAA 60.096 50.000 0.00 0.00 46.52 2.01
3307 6712 1.464608 CGGTTAGACGAGTCCACGTAA 59.535 52.381 0.00 0.00 46.52 3.18
3308 6713 1.078709 CGGTTAGACGAGTCCACGTA 58.921 55.000 0.00 0.00 46.52 3.57
3310 6715 1.513586 GCGGTTAGACGAGTCCACG 60.514 63.158 0.00 1.59 39.31 4.94
3311 6716 1.153881 GGCGGTTAGACGAGTCCAC 60.154 63.158 0.00 0.00 35.47 4.02
3312 6717 0.035152 TAGGCGGTTAGACGAGTCCA 60.035 55.000 0.00 0.00 35.47 4.02
3314 6719 1.470098 TGTTAGGCGGTTAGACGAGTC 59.530 52.381 0.00 0.00 35.47 3.36
3315 6720 1.471684 CTGTTAGGCGGTTAGACGAGT 59.528 52.381 0.00 0.00 35.47 4.18
3316 6721 1.741706 TCTGTTAGGCGGTTAGACGAG 59.258 52.381 0.00 0.00 35.47 4.18
3317 6722 1.470098 GTCTGTTAGGCGGTTAGACGA 59.530 52.381 0.00 0.00 35.47 4.20
3318 6723 1.471684 AGTCTGTTAGGCGGTTAGACG 59.528 52.381 0.00 0.00 41.86 4.18
3319 6724 4.708726 TTAGTCTGTTAGGCGGTTAGAC 57.291 45.455 0.00 0.00 38.37 2.59
3320 6725 4.082026 GGTTTAGTCTGTTAGGCGGTTAGA 60.082 45.833 0.00 0.00 0.00 2.10
3321 6726 4.081807 AGGTTTAGTCTGTTAGGCGGTTAG 60.082 45.833 0.00 0.00 0.00 2.34
3322 6727 3.834231 AGGTTTAGTCTGTTAGGCGGTTA 59.166 43.478 0.00 0.00 0.00 2.85
3324 6729 2.254508 AGGTTTAGTCTGTTAGGCGGT 58.745 47.619 0.00 0.00 0.00 5.68
3325 6730 3.000727 CAAGGTTTAGTCTGTTAGGCGG 58.999 50.000 0.00 0.00 0.00 6.13
3327 6732 5.278315 CCAAACAAGGTTTAGTCTGTTAGGC 60.278 44.000 0.00 0.00 0.00 3.93
3331 6736 5.591472 GGTACCAAACAAGGTTTAGTCTGTT 59.409 40.000 7.15 0.00 43.08 3.16
3333 6738 5.374071 AGGTACCAAACAAGGTTTAGTCTG 58.626 41.667 15.94 0.00 43.08 3.51
3334 6739 5.455755 GGAGGTACCAAACAAGGTTTAGTCT 60.456 44.000 15.94 0.00 43.08 3.24
3335 6740 4.758674 GGAGGTACCAAACAAGGTTTAGTC 59.241 45.833 15.94 0.00 43.08 2.59
3337 6742 4.721132 TGGAGGTACCAAACAAGGTTTAG 58.279 43.478 15.94 0.00 46.75 1.85
3338 6743 4.792513 TGGAGGTACCAAACAAGGTTTA 57.207 40.909 15.94 0.00 46.75 2.01
3339 6744 3.673543 TGGAGGTACCAAACAAGGTTT 57.326 42.857 15.94 0.00 46.75 3.27
3350 6755 4.850680 TCCACATATTTGTTGGAGGTACC 58.149 43.478 2.73 2.73 32.34 3.34
3352 6757 7.128109 TCCTTATCCACATATTTGTTGGAGGTA 59.872 37.037 11.10 1.58 36.86 3.08
3356 6761 8.527810 GTTTTCCTTATCCACATATTTGTTGGA 58.472 33.333 8.90 8.90 37.41 3.53
3358 6763 9.573133 GAGTTTTCCTTATCCACATATTTGTTG 57.427 33.333 0.00 0.00 32.34 3.33
3377 6782 6.084326 TGGCTTTGTGGAAATAGAGTTTTC 57.916 37.500 0.00 0.00 35.34 2.29
3387 6792 1.760029 GGTTTCCTGGCTTTGTGGAAA 59.240 47.619 0.00 0.00 44.56 3.13
3388 6793 1.408969 GGTTTCCTGGCTTTGTGGAA 58.591 50.000 0.00 0.00 38.00 3.53
3395 6800 0.397957 AAAACGGGGTTTCCTGGCTT 60.398 50.000 0.00 0.00 43.79 4.35
3396 6801 0.479378 TAAAACGGGGTTTCCTGGCT 59.521 50.000 0.00 0.00 43.79 4.75
3397 6802 1.203758 CATAAAACGGGGTTTCCTGGC 59.796 52.381 0.00 0.00 43.79 4.85
3398 6803 2.797786 TCATAAAACGGGGTTTCCTGG 58.202 47.619 0.00 0.00 43.79 4.45
3399 6804 4.857509 TTTCATAAAACGGGGTTTCCTG 57.142 40.909 0.00 0.00 45.02 3.86
3400 6805 5.603596 GTTTTTCATAAAACGGGGTTTCCT 58.396 37.500 0.00 0.00 42.47 3.36
3431 6836 8.919145 TGTAATCCTGTTTCCATAAAAACAAGT 58.081 29.630 4.04 0.00 45.67 3.16
3432 6837 9.410556 CTGTAATCCTGTTTCCATAAAAACAAG 57.589 33.333 4.04 0.00 45.67 3.16
3434 6839 8.698973 TCTGTAATCCTGTTTCCATAAAAACA 57.301 30.769 2.60 2.60 44.59 2.83
3437 6842 9.974980 GTTTTCTGTAATCCTGTTTCCATAAAA 57.025 29.630 0.00 0.00 0.00 1.52
3439 6844 8.934023 AGTTTTCTGTAATCCTGTTTCCATAA 57.066 30.769 0.00 0.00 0.00 1.90
3440 6845 7.333423 CGAGTTTTCTGTAATCCTGTTTCCATA 59.667 37.037 0.00 0.00 0.00 2.74
3442 6847 5.468746 CGAGTTTTCTGTAATCCTGTTTCCA 59.531 40.000 0.00 0.00 0.00 3.53
3443 6848 5.699458 TCGAGTTTTCTGTAATCCTGTTTCC 59.301 40.000 0.00 0.00 0.00 3.13
3444 6849 6.780706 TCGAGTTTTCTGTAATCCTGTTTC 57.219 37.500 0.00 0.00 0.00 2.78
3445 6850 6.710744 ACATCGAGTTTTCTGTAATCCTGTTT 59.289 34.615 0.00 0.00 0.00 2.83
3446 6851 6.231211 ACATCGAGTTTTCTGTAATCCTGTT 58.769 36.000 0.00 0.00 0.00 3.16
3447 6852 5.794894 ACATCGAGTTTTCTGTAATCCTGT 58.205 37.500 0.00 0.00 0.00 4.00
3449 6854 7.612677 AGTTACATCGAGTTTTCTGTAATCCT 58.387 34.615 9.53 2.39 36.70 3.24
3450 6855 7.829378 AGTTACATCGAGTTTTCTGTAATCC 57.171 36.000 9.53 0.49 36.70 3.01
3452 6857 9.924650 AGTTAGTTACATCGAGTTTTCTGTAAT 57.075 29.630 9.53 3.73 36.70 1.89
3453 6858 9.754382 AAGTTAGTTACATCGAGTTTTCTGTAA 57.246 29.630 3.52 3.52 33.07 2.41
3454 6859 9.754382 AAAGTTAGTTACATCGAGTTTTCTGTA 57.246 29.630 0.00 0.00 0.00 2.74
3456 6861 9.931210 AAAAAGTTAGTTACATCGAGTTTTCTG 57.069 29.630 0.00 0.00 0.00 3.02
3479 6884 2.512056 TGAGGAGGGAGTGGAACAAAAA 59.488 45.455 0.00 0.00 44.16 1.94
3480 6885 2.131854 TGAGGAGGGAGTGGAACAAAA 58.868 47.619 0.00 0.00 44.16 2.44
3481 6886 1.814429 TGAGGAGGGAGTGGAACAAA 58.186 50.000 0.00 0.00 44.16 2.83
3482 6887 1.420138 GTTGAGGAGGGAGTGGAACAA 59.580 52.381 0.00 0.00 44.16 2.83
3483 6888 1.056660 GTTGAGGAGGGAGTGGAACA 58.943 55.000 0.00 0.00 41.43 3.18
3485 6890 1.814429 TTGTTGAGGAGGGAGTGGAA 58.186 50.000 0.00 0.00 0.00 3.53
3486 6891 1.420138 GTTTGTTGAGGAGGGAGTGGA 59.580 52.381 0.00 0.00 0.00 4.02
3489 6912 2.408565 TGAGTTTGTTGAGGAGGGAGT 58.591 47.619 0.00 0.00 0.00 3.85
3491 6914 4.565652 GCTAATGAGTTTGTTGAGGAGGGA 60.566 45.833 0.00 0.00 0.00 4.20
3492 6915 3.691609 GCTAATGAGTTTGTTGAGGAGGG 59.308 47.826 0.00 0.00 0.00 4.30
3497 6920 3.482786 GTGCGCTAATGAGTTTGTTGAG 58.517 45.455 9.73 0.00 0.00 3.02
3498 6921 2.225491 GGTGCGCTAATGAGTTTGTTGA 59.775 45.455 9.73 0.00 0.00 3.18
3504 6927 0.804989 GCAAGGTGCGCTAATGAGTT 59.195 50.000 9.73 0.00 31.71 3.01
3505 6928 1.026718 GGCAAGGTGCGCTAATGAGT 61.027 55.000 9.73 0.00 46.21 3.41
3507 6930 1.002746 TGGCAAGGTGCGCTAATGA 60.003 52.632 9.73 0.00 46.21 2.57
3509 6932 2.046285 GGTGGCAAGGTGCGCTAAT 61.046 57.895 9.73 0.00 46.21 1.73
3529 6952 4.845580 ATTGGCGCGAGGAGCTGG 62.846 66.667 12.10 0.00 45.59 4.85
3530 6953 1.926511 AAAATTGGCGCGAGGAGCTG 61.927 55.000 12.10 0.00 45.59 4.24
3531 6954 1.244019 AAAAATTGGCGCGAGGAGCT 61.244 50.000 12.10 0.00 45.59 4.09
3532 6955 1.212751 AAAAATTGGCGCGAGGAGC 59.787 52.632 12.10 0.00 43.95 4.70
3549 6972 8.967918 CGTCAGGTATATATAGAAGGGATGAAA 58.032 37.037 0.00 0.00 0.00 2.69
3550 6973 7.068348 GCGTCAGGTATATATAGAAGGGATGAA 59.932 40.741 0.00 0.00 0.00 2.57
3553 6976 6.674573 AGCGTCAGGTATATATAGAAGGGAT 58.325 40.000 0.00 0.00 0.00 3.85
3555 6978 5.007823 CGAGCGTCAGGTATATATAGAAGGG 59.992 48.000 0.00 0.00 0.00 3.95
3556 6979 5.585445 ACGAGCGTCAGGTATATATAGAAGG 59.415 44.000 0.00 0.00 0.00 3.46
3558 6981 7.099120 TGTACGAGCGTCAGGTATATATAGAA 58.901 38.462 0.00 0.00 0.00 2.10
3559 6982 6.633856 TGTACGAGCGTCAGGTATATATAGA 58.366 40.000 0.00 0.00 0.00 1.98
3560 6983 6.898912 TGTACGAGCGTCAGGTATATATAG 57.101 41.667 0.00 0.00 0.00 1.31
3561 6984 6.650390 TGTTGTACGAGCGTCAGGTATATATA 59.350 38.462 0.00 0.00 0.00 0.86
3562 6985 5.471116 TGTTGTACGAGCGTCAGGTATATAT 59.529 40.000 0.00 0.00 0.00 0.86
3563 6986 4.815846 TGTTGTACGAGCGTCAGGTATATA 59.184 41.667 0.00 0.00 0.00 0.86
3565 6988 3.009026 TGTTGTACGAGCGTCAGGTATA 58.991 45.455 0.00 0.00 0.00 1.47
3566 6989 1.814394 TGTTGTACGAGCGTCAGGTAT 59.186 47.619 0.00 0.00 0.00 2.73
3568 6991 0.386476 TTGTTGTACGAGCGTCAGGT 59.614 50.000 0.00 0.00 0.00 4.00
3569 6992 1.191647 GTTTGTTGTACGAGCGTCAGG 59.808 52.381 0.00 0.00 0.00 3.86
3571 6994 1.923899 TGTTTGTTGTACGAGCGTCA 58.076 45.000 0.00 0.00 0.00 4.35
3572 6995 2.473609 TCATGTTTGTTGTACGAGCGTC 59.526 45.455 0.00 0.00 0.00 5.19
3573 6996 2.220133 GTCATGTTTGTTGTACGAGCGT 59.780 45.455 0.00 0.00 0.00 5.07
3575 6998 2.473609 TCGTCATGTTTGTTGTACGAGC 59.526 45.455 0.00 0.00 34.74 5.03
3576 6999 4.702247 TTCGTCATGTTTGTTGTACGAG 57.298 40.909 0.00 0.00 40.06 4.18
3577 7000 4.329256 TGTTTCGTCATGTTTGTTGTACGA 59.671 37.500 0.00 0.00 37.56 3.43
3579 7002 6.856494 TTTGTTTCGTCATGTTTGTTGTAC 57.144 33.333 0.00 0.00 0.00 2.90
3580 7003 7.430793 CAGATTTGTTTCGTCATGTTTGTTGTA 59.569 33.333 0.00 0.00 0.00 2.41
3581 7004 6.253298 CAGATTTGTTTCGTCATGTTTGTTGT 59.747 34.615 0.00 0.00 0.00 3.32
3582 7005 6.291743 CCAGATTTGTTTCGTCATGTTTGTTG 60.292 38.462 0.00 0.00 0.00 3.33
3583 7006 5.748152 CCAGATTTGTTTCGTCATGTTTGTT 59.252 36.000 0.00 0.00 0.00 2.83
3584 7007 5.280945 CCAGATTTGTTTCGTCATGTTTGT 58.719 37.500 0.00 0.00 0.00 2.83
3585 7008 4.148696 GCCAGATTTGTTTCGTCATGTTTG 59.851 41.667 0.00 0.00 0.00 2.93
3586 7009 4.298332 GCCAGATTTGTTTCGTCATGTTT 58.702 39.130 0.00 0.00 0.00 2.83
3587 7010 3.609175 CGCCAGATTTGTTTCGTCATGTT 60.609 43.478 0.00 0.00 0.00 2.71
3588 7011 2.095768 CGCCAGATTTGTTTCGTCATGT 60.096 45.455 0.00 0.00 0.00 3.21
3590 7013 2.159627 GTCGCCAGATTTGTTTCGTCAT 59.840 45.455 0.00 0.00 0.00 3.06
3591 7014 1.529438 GTCGCCAGATTTGTTTCGTCA 59.471 47.619 0.00 0.00 0.00 4.35
3593 7016 0.872388 GGTCGCCAGATTTGTTTCGT 59.128 50.000 0.00 0.00 0.00 3.85
3594 7017 1.135972 CAGGTCGCCAGATTTGTTTCG 60.136 52.381 0.00 0.00 0.00 3.46
3595 7018 1.200020 CCAGGTCGCCAGATTTGTTTC 59.800 52.381 0.00 0.00 0.00 2.78
3596 7019 1.247567 CCAGGTCGCCAGATTTGTTT 58.752 50.000 0.00 0.00 0.00 2.83
3597 7020 1.244019 GCCAGGTCGCCAGATTTGTT 61.244 55.000 0.00 0.00 0.00 2.83
3598 7021 1.675641 GCCAGGTCGCCAGATTTGT 60.676 57.895 0.00 0.00 0.00 2.83
3599 7022 0.962356 AAGCCAGGTCGCCAGATTTG 60.962 55.000 0.00 0.00 0.00 2.32
3600 7023 0.251341 AAAGCCAGGTCGCCAGATTT 60.251 50.000 0.00 0.00 0.00 2.17
3601 7024 0.251341 AAAAGCCAGGTCGCCAGATT 60.251 50.000 0.00 0.00 0.00 2.40
3602 7025 0.962356 CAAAAGCCAGGTCGCCAGAT 60.962 55.000 0.00 0.00 0.00 2.90
3605 7028 3.294493 GCAAAAGCCAGGTCGCCA 61.294 61.111 0.00 0.00 0.00 5.69
3606 7029 3.273080 CTGCAAAAGCCAGGTCGCC 62.273 63.158 0.00 0.00 0.00 5.54
3607 7030 2.075426 AACTGCAAAAGCCAGGTCGC 62.075 55.000 0.00 0.00 34.65 5.19
3609 7032 0.040067 CGAACTGCAAAAGCCAGGTC 60.040 55.000 0.00 0.00 42.27 3.85
3610 7033 0.751643 ACGAACTGCAAAAGCCAGGT 60.752 50.000 0.00 0.00 34.65 4.00
3613 7036 0.749818 TGGACGAACTGCAAAAGCCA 60.750 50.000 0.00 0.00 0.00 4.75
3614 7037 0.598065 ATGGACGAACTGCAAAAGCC 59.402 50.000 0.00 0.00 0.00 4.35
3616 7039 1.666888 GCCATGGACGAACTGCAAAAG 60.667 52.381 18.40 0.00 0.00 2.27
3618 7041 0.537143 AGCCATGGACGAACTGCAAA 60.537 50.000 18.40 0.00 0.00 3.68
3620 7043 1.672030 CAGCCATGGACGAACTGCA 60.672 57.895 18.40 0.00 0.00 4.41
3621 7044 3.181367 CAGCCATGGACGAACTGC 58.819 61.111 18.40 0.00 0.00 4.40
3637 7060 4.514585 AACAGGTGTTGGCGGCCA 62.515 61.111 19.77 19.77 36.80 5.36
3649 7072 2.260869 CCAGGGCGAACACAACAGG 61.261 63.158 0.00 0.00 0.00 4.00
3652 7075 3.670377 GGCCAGGGCGAACACAAC 61.670 66.667 0.00 0.00 43.06 3.32
3671 7094 0.813184 TGAACTTAGCCTACCGACGG 59.187 55.000 13.61 13.61 0.00 4.79
3672 7095 1.200716 TGTGAACTTAGCCTACCGACG 59.799 52.381 0.00 0.00 0.00 5.12
3673 7096 2.490903 TCTGTGAACTTAGCCTACCGAC 59.509 50.000 0.00 0.00 0.00 4.79
3674 7097 2.799017 TCTGTGAACTTAGCCTACCGA 58.201 47.619 0.00 0.00 0.00 4.69
3675 7098 3.707793 GATCTGTGAACTTAGCCTACCG 58.292 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.