Multiple sequence alignment - TraesCS2D01G382100

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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 TraesCS2D01G382100 chr2D 100.000 6769 0 0 1001 7769 486244713 486251481 0.000000e+00 12501.0
1 TraesCS2D01G382100 chr2D 100.000 542 0 0 1 542 486243713 486244254 0.000000e+00 1002.0
2 TraesCS2D01G382100 chr2D 92.754 138 9 1 6336 6473 62293433 62293297 1.710000e-46 198.0
3 TraesCS2D01G382100 chr2A 95.044 4701 135 36 1001 5634 631657179 631661848 0.000000e+00 7300.0
4 TraesCS2D01G382100 chr2A 98.429 700 10 1 5649 6348 631661832 631662530 0.000000e+00 1230.0
5 TraesCS2D01G382100 chr2A 92.806 695 42 7 6471 7159 631662528 631663220 0.000000e+00 1000.0
6 TraesCS2D01G382100 chr2A 90.185 540 40 8 7151 7686 631663378 631663908 0.000000e+00 691.0
7 TraesCS2D01G382100 chr2A 92.105 190 13 1 72 261 631655659 631655846 4.620000e-67 267.0
8 TraesCS2D01G382100 chr2A 85.030 167 8 3 253 418 631656620 631656770 3.750000e-33 154.0
9 TraesCS2D01G382100 chr2A 97.333 75 2 0 360 434 631656789 631656863 2.280000e-25 128.0
10 TraesCS2D01G382100 chr2A 88.542 96 1 4 452 538 631656948 631657042 2.960000e-19 108.0
11 TraesCS2D01G382100 chr2B 95.393 4168 107 28 1001 5127 571140872 571144995 0.000000e+00 6554.0
12 TraesCS2D01G382100 chr2B 94.532 695 31 7 6818 7510 571151950 571152639 0.000000e+00 1066.0
13 TraesCS2D01G382100 chr2B 95.609 501 19 3 5848 6346 571145707 571146206 0.000000e+00 800.0
14 TraesCS2D01G382100 chr2B 96.170 470 10 5 5172 5634 571144997 571145465 0.000000e+00 761.0
15 TraesCS2D01G382100 chr2B 93.103 435 24 5 19 451 571098659 571099089 3.960000e-177 632.0
16 TraesCS2D01G382100 chr2B 93.056 360 18 3 6473 6826 571146208 571146566 3.210000e-143 520.0
17 TraesCS2D01G382100 chr2B 91.324 219 9 2 7561 7769 571153595 571153813 2.740000e-74 291.0
18 TraesCS2D01G382100 chr2B 97.917 144 3 0 5649 5792 571145449 571145592 4.650000e-62 250.0
19 TraesCS2D01G382100 chr6D 83.268 257 34 5 7412 7665 460588019 460588269 2.180000e-55 228.0
20 TraesCS2D01G382100 chr6D 93.333 135 9 0 6339 6473 115044530 115044664 4.750000e-47 200.0
21 TraesCS2D01G382100 chr6D 92.754 138 9 1 6336 6473 403312406 403312270 1.710000e-46 198.0
22 TraesCS2D01G382100 chr6D 88.356 146 15 2 1947 2091 237068721 237068865 2.880000e-39 174.0
23 TraesCS2D01G382100 chr6D 88.276 145 15 2 1947 2091 235135453 235135311 1.040000e-38 172.0
24 TraesCS2D01G382100 chr5D 95.385 130 6 0 6344 6473 445810777 445810648 2.840000e-49 207.0
25 TraesCS2D01G382100 chr5D 81.783 258 36 7 7412 7665 180473809 180473559 1.020000e-48 206.0
26 TraesCS2D01G382100 chr5D 94.656 131 7 0 6343 6473 241844208 241844078 3.680000e-48 204.0
27 TraesCS2D01G382100 chr3B 82.072 251 35 6 7412 7658 249986167 249985923 1.020000e-48 206.0
28 TraesCS2D01G382100 chr7D 94.030 134 8 0 6340 6473 567712447 567712580 3.680000e-48 204.0
29 TraesCS2D01G382100 chr7D 92.754 138 9 1 6340 6477 576290194 576290330 1.710000e-46 198.0
30 TraesCS2D01G382100 chr1D 93.382 136 9 0 6338 6473 43298895 43298760 1.320000e-47 202.0
31 TraesCS2D01G382100 chr1D 81.569 255 33 9 7415 7663 96116060 96115814 1.710000e-46 198.0
32 TraesCS2D01G382100 chr1D 88.356 146 15 2 1947 2091 47851319 47851175 2.880000e-39 174.0
33 TraesCS2D01G382100 chr1D 88.276 145 16 1 1947 2091 204021654 204021797 1.040000e-38 172.0
34 TraesCS2D01G382100 chr6A 92.254 142 10 1 6339 6479 494467141 494467282 4.750000e-47 200.0
35 TraesCS2D01G382100 chr5A 81.395 258 37 7 7412 7665 211625388 211625138 4.750000e-47 200.0
36 TraesCS2D01G382100 chr5A 79.044 272 48 5 7387 7656 653289883 653289619 2.230000e-40 178.0
37 TraesCS2D01G382100 chr4A 91.034 145 12 1 1947 2091 374698148 374698005 2.210000e-45 195.0
38 TraesCS2D01G382100 chr4A 87.324 142 17 1 1950 2091 733554881 733554741 2.240000e-35 161.0
39 TraesCS2D01G382100 chr3D 89.041 146 14 2 1947 2091 523248752 523248608 6.190000e-41 180.0
40 TraesCS2D01G382100 chr3D 93.023 43 2 1 250 292 608503732 608503691 2.340000e-05 62.1
41 TraesCS2D01G382100 chr1A 78.462 260 46 6 7402 7657 522475546 522475799 2.240000e-35 161.0
42 TraesCS2D01G382100 chr6B 100.000 30 0 0 1496 1525 608307797 608307826 1.000000e-03 56.5


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 TraesCS2D01G382100 chr2D 486243713 486251481 7768 False 6751.50 12501 100.00000 1 7769 2 chr2D.!!$F1 7768
1 TraesCS2D01G382100 chr2A 631655659 631663908 8249 False 1359.75 7300 92.43425 72 7686 8 chr2A.!!$F1 7614
2 TraesCS2D01G382100 chr2B 571140872 571146566 5694 False 1777.00 6554 95.62900 1001 6826 5 chr2B.!!$F2 5825
3 TraesCS2D01G382100 chr2B 571151950 571153813 1863 False 678.50 1066 92.92800 6818 7769 2 chr2B.!!$F3 951

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
51 52 0.098905 TCGGAGAGAAGCGAACGATG 59.901 55.000 0.00 0.00 0.00 3.84 F
52 53 0.098905 CGGAGAGAAGCGAACGATGA 59.901 55.000 0.00 0.00 0.00 2.92 F
1789 2770 0.173481 GCCACTGTCTATGACTGCGA 59.827 55.000 4.84 0.00 35.41 5.10 F
2477 3481 0.731417 CAAGCTGAATTGGCTCGGAG 59.269 55.000 0.00 0.00 39.30 4.63 F
3756 4763 0.109532 TCAGGGTCATGAAACCGCAA 59.890 50.000 11.00 0.54 40.46 4.85 F
4369 5377 0.180406 GGTGGCATCCCAACGATACT 59.820 55.000 0.00 0.00 44.33 2.12 F
4916 5930 1.408702 ACGGCAATTTCCCATATGCAC 59.591 47.619 0.00 0.00 40.51 4.57 F
6362 7446 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 2760 1.471501 GCAGGTGTCATCGCAGTCATA 60.472 52.381 0.00 0.00 0.00 2.15 R
1845 2826 1.555075 TGGTACAGAGGCATCAAGGAC 59.445 52.381 0.00 0.00 0.00 3.85 R
2642 3646 0.532573 ACGGCTTGTGTCTCGATGAT 59.467 50.000 0.00 0.00 0.00 2.45 R
3933 4940 0.455633 CGATTTCTGCCAGCTGTTGC 60.456 55.000 13.81 10.56 40.05 4.17 R
5653 6676 1.135402 GGAGGCGCCACTTACAAATTG 60.135 52.381 31.54 0.00 36.34 2.32 R
6347 7431 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85 R
6457 7541 0.042131 ACATTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37 R
7421 8684 1.147817 AGTTGGATCTGCCCCTTTGTT 59.852 47.619 0.00 0.00 34.97 2.83 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
24 25 2.109425 TCGGAGAGAAGTGATGACGA 57.891 50.000 0.00 0.00 0.00 4.20
25 26 1.738350 TCGGAGAGAAGTGATGACGAC 59.262 52.381 0.00 0.00 0.00 4.34
26 27 1.530031 CGGAGAGAAGTGATGACGACG 60.530 57.143 0.00 0.00 0.00 5.12
27 28 1.540407 GAGAGAAGTGATGACGACGC 58.460 55.000 0.00 0.00 0.00 5.19
28 29 0.179187 AGAGAAGTGATGACGACGCG 60.179 55.000 3.53 3.53 0.00 6.01
29 30 0.454620 GAGAAGTGATGACGACGCGT 60.455 55.000 13.85 13.85 45.10 6.01
30 31 0.729478 AGAAGTGATGACGACGCGTG 60.729 55.000 20.70 12.18 41.37 5.34
31 32 2.267227 GAAGTGATGACGACGCGTGC 62.267 60.000 20.70 7.65 41.37 5.34
32 33 2.749110 AAGTGATGACGACGCGTGCT 62.749 55.000 20.70 0.00 41.37 4.40
33 34 2.504026 TGATGACGACGCGTGCTC 60.504 61.111 20.70 11.49 41.37 4.26
34 35 3.598562 GATGACGACGCGTGCTCG 61.599 66.667 20.70 17.84 41.37 5.03
49 50 3.976758 TCGGAGAGAAGCGAACGA 58.023 55.556 0.00 0.00 0.00 3.85
50 51 2.478989 TCGGAGAGAAGCGAACGAT 58.521 52.632 0.00 0.00 0.00 3.73
51 52 0.098905 TCGGAGAGAAGCGAACGATG 59.901 55.000 0.00 0.00 0.00 3.84
52 53 0.098905 CGGAGAGAAGCGAACGATGA 59.901 55.000 0.00 0.00 0.00 2.92
53 54 1.551145 GGAGAGAAGCGAACGATGAC 58.449 55.000 0.00 0.00 0.00 3.06
54 55 1.135373 GGAGAGAAGCGAACGATGACA 60.135 52.381 0.00 0.00 0.00 3.58
55 56 2.480416 GGAGAGAAGCGAACGATGACAT 60.480 50.000 0.00 0.00 0.00 3.06
56 57 3.243101 GGAGAGAAGCGAACGATGACATA 60.243 47.826 0.00 0.00 0.00 2.29
57 58 4.541779 GAGAGAAGCGAACGATGACATAT 58.458 43.478 0.00 0.00 0.00 1.78
58 59 5.334957 GGAGAGAAGCGAACGATGACATATA 60.335 44.000 0.00 0.00 0.00 0.86
59 60 6.260870 AGAGAAGCGAACGATGACATATAT 57.739 37.500 0.00 0.00 0.00 0.86
60 61 6.089476 AGAGAAGCGAACGATGACATATATG 58.911 40.000 11.29 11.29 0.00 1.78
61 62 5.773575 AGAAGCGAACGATGACATATATGT 58.226 37.500 18.31 18.31 45.16 2.29
62 63 5.631096 AGAAGCGAACGATGACATATATGTG 59.369 40.000 22.93 10.78 41.95 3.21
63 64 3.675225 AGCGAACGATGACATATATGTGC 59.325 43.478 22.93 15.96 41.95 4.57
64 65 3.675225 GCGAACGATGACATATATGTGCT 59.325 43.478 22.93 9.53 41.95 4.40
65 66 4.857037 GCGAACGATGACATATATGTGCTA 59.143 41.667 22.93 9.42 41.95 3.49
66 67 5.220043 GCGAACGATGACATATATGTGCTAC 60.220 44.000 22.93 8.99 41.95 3.58
67 68 5.286320 CGAACGATGACATATATGTGCTACC 59.714 44.000 22.93 8.63 41.95 3.18
68 69 5.984695 ACGATGACATATATGTGCTACCT 57.015 39.130 22.93 1.73 41.95 3.08
69 70 5.955488 ACGATGACATATATGTGCTACCTC 58.045 41.667 22.93 9.60 41.95 3.85
70 71 5.030936 CGATGACATATATGTGCTACCTCG 58.969 45.833 22.93 16.41 41.95 4.63
73 74 2.094700 ACATATATGTGCTACCTCGGCG 60.095 50.000 17.60 0.00 40.03 6.46
97 98 5.352643 ACCTTTTATTCGTTGTAGTGTGC 57.647 39.130 0.00 0.00 0.00 4.57
98 99 4.084223 ACCTTTTATTCGTTGTAGTGTGCG 60.084 41.667 0.00 0.00 0.00 5.34
114 115 0.951525 TGCGTGTGGGGTATTTCGTG 60.952 55.000 0.00 0.00 0.00 4.35
127 128 1.163420 TTTCGTGTGTGCCGCTCAAT 61.163 50.000 0.00 0.00 0.00 2.57
129 130 2.606961 CGTGTGTGCCGCTCAATGT 61.607 57.895 0.00 0.00 0.00 2.71
228 229 1.003866 GTTAACCGCTCATGCCGAATC 60.004 52.381 7.10 0.00 35.36 2.52
233 234 0.939419 CGCTCATGCCGAATCATTGA 59.061 50.000 0.01 0.00 35.36 2.57
341 1124 1.876799 ACATTGCATTGACCGAACGAA 59.123 42.857 15.20 0.00 0.00 3.85
342 1125 2.241722 CATTGCATTGACCGAACGAAC 58.758 47.619 2.33 0.00 0.00 3.95
343 1126 0.233590 TTGCATTGACCGAACGAACG 59.766 50.000 0.00 0.00 0.00 3.95
352 1135 2.102474 CCGAACGAACGGTCTAGATC 57.898 55.000 10.40 0.00 46.70 2.75
353 1136 1.268437 CCGAACGAACGGTCTAGATCC 60.268 57.143 10.40 0.00 46.70 3.36
406 1267 7.036220 ACGGTCTAGATCTGACATTTAAACAG 58.964 38.462 19.98 0.00 36.26 3.16
416 1277 4.202620 TGACATTTAAACAGGGGTGGATGA 60.203 41.667 0.00 0.00 0.00 2.92
437 1298 3.446184 CTGCTTTCAGTTGACGCTTAG 57.554 47.619 4.79 0.00 35.61 2.18
438 1299 1.531149 TGCTTTCAGTTGACGCTTAGC 59.469 47.619 0.00 0.00 0.00 3.09
449 1310 3.134127 GCTTAGCGTGGGCCCAAG 61.134 66.667 31.24 31.24 41.24 3.61
515 1451 5.767816 AACACGCCTCTAGTTTGATTTTT 57.232 34.783 0.00 0.00 0.00 1.94
1115 2056 3.827898 CCCTCCGCCTCTCACGTC 61.828 72.222 0.00 0.00 0.00 4.34
1116 2057 4.180946 CCTCCGCCTCTCACGTCG 62.181 72.222 0.00 0.00 0.00 5.12
1117 2058 4.838486 CTCCGCCTCTCACGTCGC 62.838 72.222 0.00 0.00 0.00 5.19
1120 2061 4.838486 CGCCTCTCACGTCGCCTC 62.838 72.222 0.00 0.00 0.00 4.70
1273 2249 1.680522 CTGCCGGTGCACTAGATCCT 61.681 60.000 17.98 0.00 44.23 3.24
1623 2604 5.760253 CAGTGTGTCTGTTTCCAGTAAATCT 59.240 40.000 0.00 0.00 39.82 2.40
1756 2737 0.321671 GCACCAGCCTAGACACTTCA 59.678 55.000 0.00 0.00 33.58 3.02
1758 2739 0.603569 ACCAGCCTAGACACTTCACG 59.396 55.000 0.00 0.00 0.00 4.35
1789 2770 0.173481 GCCACTGTCTATGACTGCGA 59.827 55.000 4.84 0.00 35.41 5.10
1804 2785 1.672356 GCGATGACACCTGCTGGTT 60.672 57.895 13.36 4.90 46.05 3.67
1845 2826 6.336566 CCTGATCTTCAGTAATATCATCGGG 58.663 44.000 4.00 0.00 42.80 5.14
1895 2876 2.289694 CCTGCTCAATAACCTATCCCCG 60.290 54.545 0.00 0.00 0.00 5.73
1922 2903 1.580942 CACCACCTGCCAAATCACG 59.419 57.895 0.00 0.00 0.00 4.35
2052 3033 2.561733 TCTCACCTTCGATTGCTACG 57.438 50.000 0.00 0.00 0.00 3.51
2148 3150 3.251004 GCGTTGGAGAAACTTCTGTGATT 59.749 43.478 0.00 0.00 37.73 2.57
2206 3210 6.942576 ACTTATCTGCAACTGAAATAAGTGGT 59.057 34.615 5.52 0.00 40.08 4.16
2477 3481 0.731417 CAAGCTGAATTGGCTCGGAG 59.269 55.000 0.00 0.00 39.30 4.63
2526 3530 5.880901 ACTACTGGGAAATCTGTTGTGAAT 58.119 37.500 0.00 0.00 0.00 2.57
2560 3564 4.520179 TCACAGTCATGATTTGGATCAGG 58.480 43.478 0.00 0.00 45.01 3.86
2642 3646 0.768221 ACCAGAGAAGGGCAGGTTGA 60.768 55.000 0.00 0.00 0.00 3.18
2767 3771 4.164221 CCTCTAATGGGCTGAAGGAAGTAA 59.836 45.833 0.00 0.00 0.00 2.24
2898 3902 2.367567 ACAAGTGGTTCGGAGAAAGCTA 59.632 45.455 0.00 0.00 45.90 3.32
3081 4085 5.539955 ACCAACAATAACAAAGAATGGAGCT 59.460 36.000 0.00 0.00 0.00 4.09
3385 4389 7.862512 AATGTGTGTTGGTTGAAATTGAATT 57.137 28.000 0.00 0.00 0.00 2.17
3454 4461 6.463995 AAACACTGAATTTGTAGAAGCCAA 57.536 33.333 0.00 0.00 0.00 4.52
3735 4742 3.036819 TCTGGATCTTCTGGACCATCTG 58.963 50.000 0.00 0.00 0.00 2.90
3756 4763 0.109532 TCAGGGTCATGAAACCGCAA 59.890 50.000 11.00 0.54 40.46 4.85
3933 4940 3.256558 TCATGTCTTGCATCTTCAGACG 58.743 45.455 10.16 0.00 35.19 4.18
4173 5180 7.734942 AGAAGAGGTAATTCTTGATCATCTCC 58.265 38.462 0.00 0.00 37.53 3.71
4369 5377 0.180406 GGTGGCATCCCAACGATACT 59.820 55.000 0.00 0.00 44.33 2.12
4383 5391 3.846360 ACGATACTGTAAGAACACCTGC 58.154 45.455 0.00 0.00 37.43 4.85
4463 5474 4.156556 TCACTATGCCTCTTTTTGATGCAC 59.843 41.667 0.00 0.00 46.17 4.57
4464 5475 3.445096 ACTATGCCTCTTTTTGATGCACC 59.555 43.478 0.00 0.00 46.17 5.01
4510 5521 3.305608 GCTTGCACATTAGCAGTTCCTTT 60.306 43.478 3.21 0.00 46.54 3.11
4556 5567 1.982612 GGCTTCTCAATTGCCGAAAC 58.017 50.000 0.00 1.88 37.11 2.78
4626 5637 6.119144 AGTATTTGTTAGTTTGGCTATGCG 57.881 37.500 0.00 0.00 0.00 4.73
4633 5644 1.737793 AGTTTGGCTATGCGTAAGTGC 59.262 47.619 0.00 0.00 41.68 4.40
4916 5930 1.408702 ACGGCAATTTCCCATATGCAC 59.591 47.619 0.00 0.00 40.51 4.57
4987 6002 8.765517 CCCTTGTAGTTCCTCTACCTTTAAATA 58.234 37.037 3.15 0.00 45.99 1.40
5392 6412 1.683917 CCTTATCAGAGAGGGTGTCCG 59.316 57.143 0.00 0.00 38.33 4.79
5624 6647 5.474825 TGCGCATATTCAACCTAATATCGA 58.525 37.500 5.66 0.00 31.17 3.59
5625 6648 6.106003 TGCGCATATTCAACCTAATATCGAT 58.894 36.000 5.66 2.16 31.17 3.59
5626 6649 6.593770 TGCGCATATTCAACCTAATATCGATT 59.406 34.615 5.66 0.00 31.17 3.34
5627 6650 7.119116 TGCGCATATTCAACCTAATATCGATTT 59.881 33.333 5.66 0.54 31.17 2.17
5628 6651 7.426456 GCGCATATTCAACCTAATATCGATTTG 59.574 37.037 1.71 0.55 31.17 2.32
5629 6652 8.443160 CGCATATTCAACCTAATATCGATTTGT 58.557 33.333 1.71 0.00 31.17 2.83
5877 6958 6.787085 AGATAAACTGTTTTCCGACTTGAG 57.213 37.500 11.48 0.00 0.00 3.02
5916 6997 4.660168 TCTTCTGGGTTCTCTACGTAGTT 58.340 43.478 21.53 0.00 37.78 2.24
5995 7077 8.288689 ACAAATGTTGAACACTTACTAAAGGT 57.711 30.769 0.00 0.00 37.01 3.50
6150 7233 7.883311 AGTACTTACATAGTGGCATCTGTTTTT 59.117 33.333 0.00 0.00 37.73 1.94
6178 7261 3.024547 TCTCCGTAAGAAGTCCTGATGG 58.975 50.000 0.00 0.00 43.02 3.51
6346 7430 3.895704 AACCCTTGTCCCTTGTTATGT 57.104 42.857 0.00 0.00 0.00 2.29
6347 7431 6.419791 CATAACCCTTGTCCCTTGTTATGTA 58.580 40.000 10.86 0.00 41.54 2.29
6348 7432 4.296621 ACCCTTGTCCCTTGTTATGTAC 57.703 45.455 0.00 0.00 0.00 2.90
6349 7433 3.914435 ACCCTTGTCCCTTGTTATGTACT 59.086 43.478 0.00 0.00 0.00 2.73
6350 7434 4.019591 ACCCTTGTCCCTTGTTATGTACTC 60.020 45.833 0.00 0.00 0.00 2.59
6351 7435 4.514401 CCTTGTCCCTTGTTATGTACTCC 58.486 47.826 0.00 0.00 0.00 3.85
6352 7436 4.514401 CTTGTCCCTTGTTATGTACTCCC 58.486 47.826 0.00 0.00 0.00 4.30
6353 7437 3.798515 TGTCCCTTGTTATGTACTCCCT 58.201 45.455 0.00 0.00 0.00 4.20
6354 7438 3.773119 TGTCCCTTGTTATGTACTCCCTC 59.227 47.826 0.00 0.00 0.00 4.30
6355 7439 3.134262 GTCCCTTGTTATGTACTCCCTCC 59.866 52.174 0.00 0.00 0.00 4.30
6356 7440 2.102588 CCCTTGTTATGTACTCCCTCCG 59.897 54.545 0.00 0.00 0.00 4.63
6357 7441 2.764572 CCTTGTTATGTACTCCCTCCGT 59.235 50.000 0.00 0.00 0.00 4.69
6358 7442 3.181478 CCTTGTTATGTACTCCCTCCGTC 60.181 52.174 0.00 0.00 0.00 4.79
6359 7443 2.381911 TGTTATGTACTCCCTCCGTCC 58.618 52.381 0.00 0.00 0.00 4.79
6360 7444 1.685517 GTTATGTACTCCCTCCGTCCC 59.314 57.143 0.00 0.00 0.00 4.46
6361 7445 0.928505 TATGTACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
6362 7446 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
6363 7447 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
6364 7448 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
6365 7449 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
6366 7450 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
6367 7451 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
6368 7452 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
6369 7453 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
6370 7454 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
6371 7455 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
6372 7456 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
6373 7457 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
6374 7458 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
6375 7459 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
6376 7460 5.566469 TCCGTCCCAAAATTCTTGTCTTAT 58.434 37.500 0.00 0.00 0.00 1.73
6377 7461 6.713276 TCCGTCCCAAAATTCTTGTCTTATA 58.287 36.000 0.00 0.00 0.00 0.98
6378 7462 7.343357 TCCGTCCCAAAATTCTTGTCTTATAT 58.657 34.615 0.00 0.00 0.00 0.86
6379 7463 7.832187 TCCGTCCCAAAATTCTTGTCTTATATT 59.168 33.333 0.00 0.00 0.00 1.28
6380 7464 8.466798 CCGTCCCAAAATTCTTGTCTTATATTT 58.533 33.333 0.00 0.00 0.00 1.40
6381 7465 9.289303 CGTCCCAAAATTCTTGTCTTATATTTG 57.711 33.333 0.00 0.00 0.00 2.32
6382 7466 9.087424 GTCCCAAAATTCTTGTCTTATATTTGC 57.913 33.333 0.00 0.00 0.00 3.68
6383 7467 8.257306 TCCCAAAATTCTTGTCTTATATTTGCC 58.743 33.333 0.00 0.00 0.00 4.52
6384 7468 8.260114 CCCAAAATTCTTGTCTTATATTTGCCT 58.740 33.333 0.00 0.00 0.00 4.75
6385 7469 9.090692 CCAAAATTCTTGTCTTATATTTGCCTG 57.909 33.333 0.00 0.00 0.00 4.85
6386 7470 9.090692 CAAAATTCTTGTCTTATATTTGCCTGG 57.909 33.333 0.00 0.00 0.00 4.45
6387 7471 8.593945 AAATTCTTGTCTTATATTTGCCTGGA 57.406 30.769 0.00 0.00 0.00 3.86
6388 7472 8.773033 AATTCTTGTCTTATATTTGCCTGGAT 57.227 30.769 0.00 0.00 0.00 3.41
6389 7473 9.866655 AATTCTTGTCTTATATTTGCCTGGATA 57.133 29.630 0.00 0.00 0.00 2.59
6390 7474 8.677148 TTCTTGTCTTATATTTGCCTGGATAC 57.323 34.615 0.00 0.00 0.00 2.24
6391 7475 6.929049 TCTTGTCTTATATTTGCCTGGATACG 59.071 38.462 0.00 0.00 42.51 3.06
6392 7476 5.547465 TGTCTTATATTTGCCTGGATACGG 58.453 41.667 0.00 0.00 45.15 4.02
6412 7496 8.792831 ATACGGATGTATCTAACACTAAAACG 57.207 34.615 0.00 0.00 42.09 3.60
6413 7497 6.624423 ACGGATGTATCTAACACTAAAACGT 58.376 36.000 0.00 0.00 42.09 3.99
6414 7498 7.761409 ACGGATGTATCTAACACTAAAACGTA 58.239 34.615 0.00 0.00 42.09 3.57
6415 7499 8.243426 ACGGATGTATCTAACACTAAAACGTAA 58.757 33.333 0.00 0.00 42.09 3.18
6416 7500 8.526681 CGGATGTATCTAACACTAAAACGTAAC 58.473 37.037 0.00 0.00 42.09 2.50
6417 7501 9.578439 GGATGTATCTAACACTAAAACGTAACT 57.422 33.333 0.00 0.00 42.09 2.24
6428 7512 9.669353 ACACTAAAACGTAACTATATACATCCG 57.331 33.333 0.00 0.00 0.00 4.18
6429 7513 9.669353 CACTAAAACGTAACTATATACATCCGT 57.331 33.333 0.00 0.00 0.00 4.69
6447 7531 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
6448 7532 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
6449 7533 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
6450 7534 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
6451 7535 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
6452 7536 7.380065 CCGTATCTAGACAAATCTAAGACAAGC 59.620 40.741 0.00 0.00 36.98 4.01
6453 7537 7.915923 CGTATCTAGACAAATCTAAGACAAGCA 59.084 37.037 0.00 0.00 36.98 3.91
6454 7538 9.757227 GTATCTAGACAAATCTAAGACAAGCAT 57.243 33.333 0.00 0.00 36.98 3.79
6456 7540 9.678260 ATCTAGACAAATCTAAGACAAGCATTT 57.322 29.630 0.00 0.00 36.98 2.32
6457 7541 9.507329 TCTAGACAAATCTAAGACAAGCATTTT 57.493 29.630 0.00 0.00 36.98 1.82
6458 7542 9.552114 CTAGACAAATCTAAGACAAGCATTTTG 57.448 33.333 0.00 0.00 36.98 2.44
6459 7543 7.373493 AGACAAATCTAAGACAAGCATTTTGG 58.627 34.615 0.00 0.00 31.46 3.28
6460 7544 6.458210 ACAAATCTAAGACAAGCATTTTGGG 58.542 36.000 0.00 0.00 0.00 4.12
6461 7545 6.267471 ACAAATCTAAGACAAGCATTTTGGGA 59.733 34.615 0.00 0.00 0.00 4.37
6462 7546 5.904362 ATCTAAGACAAGCATTTTGGGAC 57.096 39.130 0.00 0.00 0.00 4.46
6463 7547 3.751175 TCTAAGACAAGCATTTTGGGACG 59.249 43.478 0.00 0.00 0.00 4.79
6464 7548 1.247567 AGACAAGCATTTTGGGACGG 58.752 50.000 0.00 0.00 0.00 4.79
6465 7549 1.202879 AGACAAGCATTTTGGGACGGA 60.203 47.619 0.00 0.00 0.00 4.69
6466 7550 1.200020 GACAAGCATTTTGGGACGGAG 59.800 52.381 0.00 0.00 0.00 4.63
6467 7551 0.527565 CAAGCATTTTGGGACGGAGG 59.472 55.000 0.00 0.00 0.00 4.30
6468 7552 0.611896 AAGCATTTTGGGACGGAGGG 60.612 55.000 0.00 0.00 0.00 4.30
6469 7553 1.001393 GCATTTTGGGACGGAGGGA 60.001 57.895 0.00 0.00 0.00 4.20
6470 7554 1.032114 GCATTTTGGGACGGAGGGAG 61.032 60.000 0.00 0.00 0.00 4.30
6571 7655 1.270550 CCTGTTTGCAAGTGTGGGATC 59.729 52.381 0.00 0.00 0.00 3.36
6581 7665 4.759782 CAAGTGTGGGATCACTAGTTAGG 58.240 47.826 0.00 0.00 46.25 2.69
6690 7774 1.046472 ATCGTATCGGAGGGTTGCCA 61.046 55.000 0.00 0.00 0.00 4.92
6816 7906 6.199937 ACTTGATATTCAACAACTGGCATC 57.800 37.500 0.00 0.00 32.21 3.91
6824 7914 3.072330 TCAACAACTGGCATCTAGTTCCA 59.928 43.478 0.00 0.00 36.29 3.53
6858 7948 3.126073 TGCTTGTCAGATATGATGTCGC 58.874 45.455 0.00 0.00 0.00 5.19
6870 7960 2.642427 TGATGTCGCAATACCATTGCT 58.358 42.857 18.68 3.28 42.87 3.91
6894 7984 7.275779 GCTAGATTAACGAGAACACATTGAAGA 59.724 37.037 0.00 0.00 0.00 2.87
6896 7986 8.553459 AGATTAACGAGAACACATTGAAGATT 57.447 30.769 0.00 0.00 0.00 2.40
6996 8090 7.977904 CAGAGTTGCATGATACTGTTATTTCA 58.022 34.615 0.00 0.00 0.00 2.69
7090 8185 7.875327 AACTACCTGAAGTTTTGTATGTGTT 57.125 32.000 0.00 0.00 36.26 3.32
7141 8236 2.869801 CGTAGTGTTGAGGTTGAAAGCA 59.130 45.455 0.00 0.00 0.00 3.91
7194 8455 9.758651 AAAATTGTAGTTTCTGGGTTGAAATAC 57.241 29.630 0.00 0.00 38.09 1.89
7208 8469 3.885358 TGAAATACGGATCGTCTCATCG 58.115 45.455 0.00 0.00 41.54 3.84
7321 8583 2.286772 GCGAGTTTTGACCGTTGTTGAT 60.287 45.455 0.00 0.00 0.00 2.57
7357 8620 0.387565 AACAACGGGGTTGAACATGC 59.612 50.000 14.79 0.00 45.28 4.06
7496 8759 5.065090 CCAACGACATAGATTGCTCAAATGA 59.935 40.000 0.00 0.00 0.00 2.57
7521 8784 3.432252 AGCGCTCAACATGTTTAGTGTAC 59.568 43.478 26.06 15.23 29.68 2.90
7554 8817 5.943416 TCACACCAAATACAAACCTCCATAG 59.057 40.000 0.00 0.00 0.00 2.23
7556 8819 6.603201 CACACCAAATACAAACCTCCATAGAT 59.397 38.462 0.00 0.00 0.00 1.98
7557 8820 7.122650 CACACCAAATACAAACCTCCATAGATT 59.877 37.037 0.00 0.00 0.00 2.40
7558 8821 7.122650 ACACCAAATACAAACCTCCATAGATTG 59.877 37.037 0.00 0.00 0.00 2.67
7559 8822 6.096846 ACCAAATACAAACCTCCATAGATTGC 59.903 38.462 0.00 0.00 0.00 3.56
7563 9731 4.922206 ACAAACCTCCATAGATTGCTCAA 58.078 39.130 0.00 0.00 0.00 3.02
7735 9913 1.376295 CGGGGTTCGGTTTACAGGG 60.376 63.158 0.00 0.00 34.75 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.453793 ATCACTTCTCTCCGAGCACG 59.546 55.000 0.00 0.00 39.43 5.34
1 2 1.474478 TCATCACTTCTCTCCGAGCAC 59.526 52.381 0.00 0.00 0.00 4.40
2 3 1.474478 GTCATCACTTCTCTCCGAGCA 59.526 52.381 0.00 0.00 0.00 4.26
3 4 1.532921 CGTCATCACTTCTCTCCGAGC 60.533 57.143 0.00 0.00 0.00 5.03
4 5 2.010497 TCGTCATCACTTCTCTCCGAG 58.990 52.381 0.00 0.00 0.00 4.63
5 6 1.738350 GTCGTCATCACTTCTCTCCGA 59.262 52.381 0.00 0.00 0.00 4.55
6 7 1.530031 CGTCGTCATCACTTCTCTCCG 60.530 57.143 0.00 0.00 0.00 4.63
7 8 1.795889 GCGTCGTCATCACTTCTCTCC 60.796 57.143 0.00 0.00 0.00 3.71
8 9 1.540407 GCGTCGTCATCACTTCTCTC 58.460 55.000 0.00 0.00 0.00 3.20
9 10 0.179187 CGCGTCGTCATCACTTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
10 11 0.454620 ACGCGTCGTCATCACTTCTC 60.455 55.000 5.58 0.00 33.69 2.87
11 12 0.729478 CACGCGTCGTCATCACTTCT 60.729 55.000 9.86 0.00 38.32 2.85
12 13 1.696644 CACGCGTCGTCATCACTTC 59.303 57.895 9.86 0.00 38.32 3.01
13 14 2.372690 GCACGCGTCGTCATCACTT 61.373 57.895 9.86 0.00 38.32 3.16
14 15 2.805353 GCACGCGTCGTCATCACT 60.805 61.111 9.86 0.00 38.32 3.41
15 16 2.778997 GAGCACGCGTCGTCATCAC 61.779 63.158 9.86 0.00 38.32 3.06
16 17 2.504026 GAGCACGCGTCGTCATCA 60.504 61.111 9.86 0.00 38.32 3.07
17 18 3.598562 CGAGCACGCGTCGTCATC 61.599 66.667 9.86 1.95 38.32 2.92
23 24 3.324099 TTCTCTCCGAGCACGCGTC 62.324 63.158 9.86 4.43 38.29 5.19
24 25 3.329688 CTTCTCTCCGAGCACGCGT 62.330 63.158 5.58 5.58 38.29 6.01
25 26 2.578178 CTTCTCTCCGAGCACGCG 60.578 66.667 3.53 3.53 38.29 6.01
26 27 2.883253 GCTTCTCTCCGAGCACGC 60.883 66.667 0.00 0.00 38.29 5.34
27 28 2.529005 TTCGCTTCTCTCCGAGCACG 62.529 60.000 0.00 0.00 34.68 5.34
28 29 1.073768 GTTCGCTTCTCTCCGAGCAC 61.074 60.000 0.00 0.00 35.26 4.40
29 30 1.213013 GTTCGCTTCTCTCCGAGCA 59.787 57.895 0.00 0.00 35.26 4.26
30 31 1.870016 CGTTCGCTTCTCTCCGAGC 60.870 63.158 0.00 0.00 34.68 5.03
31 32 0.378962 ATCGTTCGCTTCTCTCCGAG 59.621 55.000 0.00 0.00 34.68 4.63
32 33 0.098905 CATCGTTCGCTTCTCTCCGA 59.901 55.000 0.00 0.00 0.00 4.55
33 34 0.098905 TCATCGTTCGCTTCTCTCCG 59.901 55.000 0.00 0.00 0.00 4.63
34 35 1.135373 TGTCATCGTTCGCTTCTCTCC 60.135 52.381 0.00 0.00 0.00 3.71
35 36 2.264109 TGTCATCGTTCGCTTCTCTC 57.736 50.000 0.00 0.00 0.00 3.20
36 37 2.949451 ATGTCATCGTTCGCTTCTCT 57.051 45.000 0.00 0.00 0.00 3.10
37 38 5.859114 ACATATATGTCATCGTTCGCTTCTC 59.141 40.000 12.75 0.00 35.87 2.87
38 39 5.631096 CACATATATGTCATCGTTCGCTTCT 59.369 40.000 15.60 0.00 39.39 2.85
39 40 5.666427 GCACATATATGTCATCGTTCGCTTC 60.666 44.000 15.60 0.00 39.39 3.86
40 41 4.150627 GCACATATATGTCATCGTTCGCTT 59.849 41.667 15.60 0.00 39.39 4.68
41 42 3.675225 GCACATATATGTCATCGTTCGCT 59.325 43.478 15.60 0.00 39.39 4.93
42 43 3.675225 AGCACATATATGTCATCGTTCGC 59.325 43.478 15.60 12.82 39.39 4.70
43 44 5.286320 GGTAGCACATATATGTCATCGTTCG 59.714 44.000 15.60 3.56 39.39 3.95
44 45 6.390721 AGGTAGCACATATATGTCATCGTTC 58.609 40.000 15.60 3.36 39.39 3.95
45 46 6.346477 AGGTAGCACATATATGTCATCGTT 57.654 37.500 15.60 5.58 39.39 3.85
46 47 5.392057 CGAGGTAGCACATATATGTCATCGT 60.392 44.000 21.54 12.83 39.39 3.73
47 48 5.030936 CGAGGTAGCACATATATGTCATCG 58.969 45.833 15.60 17.41 39.39 3.84
48 49 5.344066 CCGAGGTAGCACATATATGTCATC 58.656 45.833 15.60 10.41 39.39 2.92
49 50 4.382040 GCCGAGGTAGCACATATATGTCAT 60.382 45.833 15.60 9.57 39.39 3.06
50 51 3.056821 GCCGAGGTAGCACATATATGTCA 60.057 47.826 15.60 1.62 39.39 3.58
51 52 3.512680 GCCGAGGTAGCACATATATGTC 58.487 50.000 15.60 10.53 39.39 3.06
52 53 2.094700 CGCCGAGGTAGCACATATATGT 60.095 50.000 12.75 12.75 42.84 2.29
53 54 2.163613 TCGCCGAGGTAGCACATATATG 59.836 50.000 11.29 11.29 0.00 1.78
54 55 2.443416 TCGCCGAGGTAGCACATATAT 58.557 47.619 0.00 0.00 0.00 0.86
55 56 1.900245 TCGCCGAGGTAGCACATATA 58.100 50.000 0.00 0.00 0.00 0.86
56 57 1.037493 TTCGCCGAGGTAGCACATAT 58.963 50.000 0.00 0.00 0.00 1.78
57 58 0.101759 GTTCGCCGAGGTAGCACATA 59.898 55.000 0.00 0.00 0.00 2.29
58 59 1.153628 GTTCGCCGAGGTAGCACAT 60.154 57.895 0.00 0.00 0.00 3.21
59 60 2.260434 GTTCGCCGAGGTAGCACA 59.740 61.111 0.00 0.00 0.00 4.57
60 61 2.502692 AAGGTTCGCCGAGGTAGCAC 62.503 60.000 0.00 0.00 43.66 4.40
61 62 1.823169 AAAGGTTCGCCGAGGTAGCA 61.823 55.000 0.00 0.00 43.66 3.49
62 63 0.672711 AAAAGGTTCGCCGAGGTAGC 60.673 55.000 0.00 0.00 43.66 3.58
63 64 2.660189 TAAAAGGTTCGCCGAGGTAG 57.340 50.000 0.00 0.00 43.66 3.18
64 65 3.524541 GAATAAAAGGTTCGCCGAGGTA 58.475 45.455 0.00 0.00 43.66 3.08
65 66 2.353323 GAATAAAAGGTTCGCCGAGGT 58.647 47.619 0.00 0.00 43.66 3.85
66 67 1.326548 CGAATAAAAGGTTCGCCGAGG 59.673 52.381 0.00 0.00 41.43 4.63
67 68 2.713927 CGAATAAAAGGTTCGCCGAG 57.286 50.000 0.00 0.00 41.43 4.63
73 74 5.849604 GCACACTACAACGAATAAAAGGTTC 59.150 40.000 0.00 0.00 0.00 3.62
93 94 0.951525 CGAAATACCCCACACGCACA 60.952 55.000 0.00 0.00 0.00 4.57
97 98 0.793861 CACACGAAATACCCCACACG 59.206 55.000 0.00 0.00 0.00 4.49
98 99 1.533731 CACACACGAAATACCCCACAC 59.466 52.381 0.00 0.00 0.00 3.82
114 115 0.661187 CAACACATTGAGCGGCACAC 60.661 55.000 1.45 0.00 38.15 3.82
127 128 8.659925 AAAATGAGCAAAATAATCACAACACA 57.340 26.923 0.00 0.00 0.00 3.72
155 156 3.550678 GGGAGTCGTTCAGCTAATTAACG 59.449 47.826 13.52 13.52 45.46 3.18
164 165 2.171341 AAAGAAGGGAGTCGTTCAGC 57.829 50.000 6.63 0.00 39.47 4.26
171 172 6.567891 CGGTCAACAATAAAAAGAAGGGAGTC 60.568 42.308 0.00 0.00 0.00 3.36
175 176 5.447624 ACGGTCAACAATAAAAAGAAGGG 57.552 39.130 0.00 0.00 0.00 3.95
305 1088 4.072131 GCAATGTTGGACTCTCTAACCAA 58.928 43.478 0.00 0.00 37.09 3.67
306 1089 3.072330 TGCAATGTTGGACTCTCTAACCA 59.928 43.478 0.00 0.00 37.09 3.67
342 1125 6.213677 TCATTTAAATGACGGATCTAGACCG 58.786 40.000 23.86 23.59 43.89 4.79
343 1126 6.647067 CCTCATTTAAATGACGGATCTAGACC 59.353 42.308 26.41 0.00 40.32 3.85
344 1127 7.210873 ACCTCATTTAAATGACGGATCTAGAC 58.789 38.462 31.74 0.00 40.32 2.59
345 1128 7.361457 ACCTCATTTAAATGACGGATCTAGA 57.639 36.000 31.74 12.95 40.32 2.43
346 1129 7.710907 TCAACCTCATTTAAATGACGGATCTAG 59.289 37.037 31.74 19.88 40.32 2.43
347 1130 7.561251 TCAACCTCATTTAAATGACGGATCTA 58.439 34.615 31.74 20.00 40.32 1.98
348 1131 6.414732 TCAACCTCATTTAAATGACGGATCT 58.585 36.000 31.74 20.96 40.32 2.75
349 1132 6.677781 TCAACCTCATTTAAATGACGGATC 57.322 37.500 31.74 0.00 40.32 3.36
350 1133 6.017934 CGATCAACCTCATTTAAATGACGGAT 60.018 38.462 31.74 25.56 40.32 4.18
351 1134 5.293324 CGATCAACCTCATTTAAATGACGGA 59.707 40.000 31.74 23.40 40.32 4.69
352 1135 5.293324 TCGATCAACCTCATTTAAATGACGG 59.707 40.000 27.55 27.55 40.32 4.79
353 1136 6.344572 TCGATCAACCTCATTTAAATGACG 57.655 37.500 23.86 21.87 40.32 4.35
354 1137 6.682863 CGTTCGATCAACCTCATTTAAATGAC 59.317 38.462 23.86 12.97 40.32 3.06
355 1138 6.592220 TCGTTCGATCAACCTCATTTAAATGA 59.408 34.615 25.44 25.44 42.78 2.57
406 1267 0.038166 TGAAAGCAGTCATCCACCCC 59.962 55.000 0.00 0.00 0.00 4.95
434 1295 1.498264 TATACTTGGGCCCACGCTAA 58.502 50.000 28.70 12.77 34.44 3.09
436 1297 1.623811 CTATATACTTGGGCCCACGCT 59.376 52.381 28.70 16.59 34.44 5.07
437 1298 1.346722 ACTATATACTTGGGCCCACGC 59.653 52.381 28.70 0.00 0.00 5.34
438 1299 2.631062 TGACTATATACTTGGGCCCACG 59.369 50.000 28.70 27.24 0.00 4.94
441 1302 5.562298 TTTCTGACTATATACTTGGGCCC 57.438 43.478 17.59 17.59 0.00 5.80
486 1414 5.355910 TCAAACTAGAGGCGTGTTTCTTTTT 59.644 36.000 0.00 0.00 32.42 1.94
1522 2498 8.060689 AGATGGATACTCTATGCTAGTCATCAT 58.939 37.037 0.00 0.00 35.26 2.45
1623 2604 6.764379 TCAACAGTTCCAACATATCACAGTA 58.236 36.000 0.00 0.00 0.00 2.74
1779 2760 1.471501 GCAGGTGTCATCGCAGTCATA 60.472 52.381 0.00 0.00 0.00 2.15
1804 2785 1.613630 GGGAGGTCAGGGCAGAGAA 60.614 63.158 0.00 0.00 0.00 2.87
1845 2826 1.555075 TGGTACAGAGGCATCAAGGAC 59.445 52.381 0.00 0.00 0.00 3.85
1922 2903 2.036256 ACACCCTGGCAATGGCTC 59.964 61.111 8.59 0.00 40.87 4.70
2148 3150 9.804758 CCCTTAACTTTTACATGTAAAAACACA 57.195 29.630 32.56 20.75 42.39 3.72
2206 3210 6.545666 GTGTTCATGTCAACCATATTATCCCA 59.454 38.462 0.00 0.00 30.71 4.37
2477 3481 4.028993 TCTAACTTTGGTGGGGACAATC 57.971 45.455 0.00 0.00 46.06 2.67
2526 3530 1.852157 ACTGTGAGCCCCATTCCCA 60.852 57.895 0.00 0.00 0.00 4.37
2560 3564 1.997606 GTGATTTGAAATGCTGCTGCC 59.002 47.619 13.47 0.00 38.71 4.85
2642 3646 0.532573 ACGGCTTGTGTCTCGATGAT 59.467 50.000 0.00 0.00 0.00 2.45
2898 3902 4.156008 GGAGAAATACAACCATTTCGCACT 59.844 41.667 12.27 0.00 45.52 4.40
3104 4108 3.067106 GTTCTGAACTTCTCGGATGCAA 58.933 45.455 13.13 0.00 39.28 4.08
3183 4187 7.093992 CCTTGTTGTTTAAACCTTCAGAACAA 58.906 34.615 21.43 21.43 37.73 2.83
3353 4357 6.471233 TCAACCAACACACATTAAAATCCA 57.529 33.333 0.00 0.00 0.00 3.41
3385 4389 7.575414 TGCACTAAAAACTTTATGAACTCCA 57.425 32.000 0.00 0.00 0.00 3.86
3735 4742 1.017387 GCGGTTTCATGACCCTGATC 58.983 55.000 0.00 0.00 36.28 2.92
3756 4763 6.072286 CCAAATGAGTTATTGCTGTCTTCTGT 60.072 38.462 0.00 0.00 0.00 3.41
3933 4940 0.455633 CGATTTCTGCCAGCTGTTGC 60.456 55.000 13.81 10.56 40.05 4.17
4173 5180 2.552315 ACACAAATACAAGGTGCGGAAG 59.448 45.455 0.00 0.00 36.00 3.46
4261 5269 6.866010 ACGATTGCATCAATCTGCTTTATA 57.134 33.333 15.05 0.00 45.48 0.98
4369 5377 1.045407 ACGAGGCAGGTGTTCTTACA 58.955 50.000 0.00 0.00 0.00 2.41
4463 5474 2.230130 TTGGAGCAACATAAAGGGGG 57.770 50.000 0.00 0.00 0.00 5.40
4464 5475 2.233676 GGTTTGGAGCAACATAAAGGGG 59.766 50.000 0.00 0.00 0.00 4.79
4553 5564 5.338953 GGCACTACCCCTATAACTTCAGTTT 60.339 44.000 0.00 0.00 39.31 2.66
4556 5567 4.338379 GGCACTACCCCTATAACTTCAG 57.662 50.000 0.00 0.00 0.00 3.02
4605 5616 7.334921 ACTTACGCATAGCCAAACTAACAAATA 59.665 33.333 0.00 0.00 33.57 1.40
4626 5637 4.981806 TTTAGCATGAATGGGCACTTAC 57.018 40.909 0.00 0.00 0.00 2.34
4633 5644 5.745294 CGTTCTGATTTTTAGCATGAATGGG 59.255 40.000 0.00 0.00 0.00 4.00
4916 5930 3.366679 CCAAAGTTACTGGAGCTGCATTG 60.367 47.826 8.91 9.16 35.85 2.82
5169 6185 7.286087 TCGTAGTAGGAAGGCATATAACTTTCA 59.714 37.037 0.00 0.00 0.00 2.69
5171 6187 7.592885 TCGTAGTAGGAAGGCATATAACTTT 57.407 36.000 0.00 0.00 0.00 2.66
5645 6668 6.312672 GGCGCCACTTACAAATTGATATTTTT 59.687 34.615 24.80 0.00 31.63 1.94
5646 6669 5.810074 GGCGCCACTTACAAATTGATATTTT 59.190 36.000 24.80 0.00 31.63 1.82
5647 6670 5.127031 AGGCGCCACTTACAAATTGATATTT 59.873 36.000 31.54 0.00 34.29 1.40
5648 6671 4.644685 AGGCGCCACTTACAAATTGATATT 59.355 37.500 31.54 0.00 0.00 1.28
5649 6672 4.207165 AGGCGCCACTTACAAATTGATAT 58.793 39.130 31.54 0.00 0.00 1.63
5650 6673 3.616219 AGGCGCCACTTACAAATTGATA 58.384 40.909 31.54 0.00 0.00 2.15
5651 6674 2.423538 GAGGCGCCACTTACAAATTGAT 59.576 45.455 31.54 0.89 0.00 2.57
5652 6675 1.810151 GAGGCGCCACTTACAAATTGA 59.190 47.619 31.54 0.00 0.00 2.57
5653 6676 1.135402 GGAGGCGCCACTTACAAATTG 60.135 52.381 31.54 0.00 36.34 2.32
5654 6677 1.173913 GGAGGCGCCACTTACAAATT 58.826 50.000 31.54 2.38 36.34 1.82
5877 6958 7.824779 ACCCAGAAGAGTAAATCAAAGATACAC 59.175 37.037 0.00 0.00 0.00 2.90
6178 7261 7.492352 TGACTGTAAAAGAAAAAGGACTAGC 57.508 36.000 0.00 0.00 0.00 3.42
6346 7430 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
6347 7431 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
6348 7432 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
6349 7433 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
6350 7434 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
6351 7435 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
6352 7436 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
6353 7437 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
6354 7438 5.897377 ATAAGACAAGAATTTTGGGACGG 57.103 39.130 0.00 0.00 0.00 4.79
6355 7439 9.289303 CAAATATAAGACAAGAATTTTGGGACG 57.711 33.333 5.68 0.00 0.00 4.79
6356 7440 9.087424 GCAAATATAAGACAAGAATTTTGGGAC 57.913 33.333 0.00 0.00 0.00 4.46
6357 7441 8.257306 GGCAAATATAAGACAAGAATTTTGGGA 58.743 33.333 0.00 0.00 0.00 4.37
6358 7442 8.260114 AGGCAAATATAAGACAAGAATTTTGGG 58.740 33.333 0.00 0.00 0.00 4.12
6359 7443 9.090692 CAGGCAAATATAAGACAAGAATTTTGG 57.909 33.333 0.00 0.00 0.00 3.28
6360 7444 9.090692 CCAGGCAAATATAAGACAAGAATTTTG 57.909 33.333 0.00 0.00 0.00 2.44
6361 7445 9.034800 TCCAGGCAAATATAAGACAAGAATTTT 57.965 29.630 0.00 0.00 0.00 1.82
6362 7446 8.593945 TCCAGGCAAATATAAGACAAGAATTT 57.406 30.769 0.00 0.00 0.00 1.82
6363 7447 8.773033 ATCCAGGCAAATATAAGACAAGAATT 57.227 30.769 0.00 0.00 0.00 2.17
6364 7448 9.289782 GTATCCAGGCAAATATAAGACAAGAAT 57.710 33.333 0.00 0.00 0.00 2.40
6365 7449 7.441157 CGTATCCAGGCAAATATAAGACAAGAA 59.559 37.037 0.00 0.00 0.00 2.52
6366 7450 6.929049 CGTATCCAGGCAAATATAAGACAAGA 59.071 38.462 0.00 0.00 0.00 3.02
6367 7451 6.147821 CCGTATCCAGGCAAATATAAGACAAG 59.852 42.308 0.00 0.00 0.00 3.16
6368 7452 5.995282 CCGTATCCAGGCAAATATAAGACAA 59.005 40.000 0.00 0.00 0.00 3.18
6369 7453 5.305902 TCCGTATCCAGGCAAATATAAGACA 59.694 40.000 0.00 0.00 0.00 3.41
6370 7454 5.790593 TCCGTATCCAGGCAAATATAAGAC 58.209 41.667 0.00 0.00 0.00 3.01
6371 7455 6.013725 ACATCCGTATCCAGGCAAATATAAGA 60.014 38.462 0.00 0.00 0.00 2.10
6372 7456 6.173339 ACATCCGTATCCAGGCAAATATAAG 58.827 40.000 0.00 0.00 0.00 1.73
6373 7457 6.121776 ACATCCGTATCCAGGCAAATATAA 57.878 37.500 0.00 0.00 0.00 0.98
6374 7458 5.755409 ACATCCGTATCCAGGCAAATATA 57.245 39.130 0.00 0.00 0.00 0.86
6375 7459 4.640771 ACATCCGTATCCAGGCAAATAT 57.359 40.909 0.00 0.00 0.00 1.28
6376 7460 5.730550 GATACATCCGTATCCAGGCAAATA 58.269 41.667 1.87 0.00 45.67 1.40
6377 7461 4.579869 GATACATCCGTATCCAGGCAAAT 58.420 43.478 1.87 0.00 45.67 2.32
6378 7462 4.002906 GATACATCCGTATCCAGGCAAA 57.997 45.455 1.87 0.00 45.67 3.68
6379 7463 3.678056 GATACATCCGTATCCAGGCAA 57.322 47.619 1.87 0.00 45.67 4.52
6387 7471 8.408601 ACGTTTTAGTGTTAGATACATCCGTAT 58.591 33.333 0.00 0.00 41.16 3.06
6388 7472 7.761409 ACGTTTTAGTGTTAGATACATCCGTA 58.239 34.615 0.00 0.00 39.39 4.02
6389 7473 6.624423 ACGTTTTAGTGTTAGATACATCCGT 58.376 36.000 0.00 0.00 39.39 4.69
6390 7474 8.526681 GTTACGTTTTAGTGTTAGATACATCCG 58.473 37.037 0.00 0.00 39.39 4.18
6391 7475 9.578439 AGTTACGTTTTAGTGTTAGATACATCC 57.422 33.333 0.00 0.00 39.39 3.51
6402 7486 9.669353 CGGATGTATATAGTTACGTTTTAGTGT 57.331 33.333 0.00 0.00 0.00 3.55
6403 7487 9.669353 ACGGATGTATATAGTTACGTTTTAGTG 57.331 33.333 0.00 0.00 0.00 2.74
6421 7505 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
6422 7506 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
6423 7507 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
6424 7508 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
6425 7509 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
6426 7510 7.380065 GCTTGTCTTAGATTTGTCTAGATACGG 59.620 40.741 0.00 0.00 0.00 4.02
6427 7511 7.915923 TGCTTGTCTTAGATTTGTCTAGATACG 59.084 37.037 0.00 0.00 0.00 3.06
6428 7512 9.757227 ATGCTTGTCTTAGATTTGTCTAGATAC 57.243 33.333 0.00 0.00 0.00 2.24
6430 7514 9.678260 AAATGCTTGTCTTAGATTTGTCTAGAT 57.322 29.630 0.00 0.00 0.00 1.98
6431 7515 9.507329 AAAATGCTTGTCTTAGATTTGTCTAGA 57.493 29.630 0.00 0.00 0.00 2.43
6432 7516 9.552114 CAAAATGCTTGTCTTAGATTTGTCTAG 57.448 33.333 0.00 0.00 0.00 2.43
6433 7517 8.514594 CCAAAATGCTTGTCTTAGATTTGTCTA 58.485 33.333 0.00 0.00 0.00 2.59
6434 7518 7.373493 CCAAAATGCTTGTCTTAGATTTGTCT 58.627 34.615 0.00 0.00 0.00 3.41
6435 7519 6.587608 CCCAAAATGCTTGTCTTAGATTTGTC 59.412 38.462 0.00 0.00 0.00 3.18
6436 7520 6.267471 TCCCAAAATGCTTGTCTTAGATTTGT 59.733 34.615 0.00 0.00 0.00 2.83
6437 7521 6.587608 GTCCCAAAATGCTTGTCTTAGATTTG 59.412 38.462 0.00 0.00 0.00 2.32
6438 7522 6.570378 CGTCCCAAAATGCTTGTCTTAGATTT 60.570 38.462 0.00 0.00 0.00 2.17
6439 7523 5.106157 CGTCCCAAAATGCTTGTCTTAGATT 60.106 40.000 0.00 0.00 0.00 2.40
6440 7524 4.396166 CGTCCCAAAATGCTTGTCTTAGAT 59.604 41.667 0.00 0.00 0.00 1.98
6441 7525 3.751175 CGTCCCAAAATGCTTGTCTTAGA 59.249 43.478 0.00 0.00 0.00 2.10
6442 7526 3.119849 CCGTCCCAAAATGCTTGTCTTAG 60.120 47.826 0.00 0.00 0.00 2.18
6443 7527 2.817258 CCGTCCCAAAATGCTTGTCTTA 59.183 45.455 0.00 0.00 0.00 2.10
6444 7528 1.613437 CCGTCCCAAAATGCTTGTCTT 59.387 47.619 0.00 0.00 0.00 3.01
6445 7529 1.202879 TCCGTCCCAAAATGCTTGTCT 60.203 47.619 0.00 0.00 0.00 3.41
6446 7530 1.200020 CTCCGTCCCAAAATGCTTGTC 59.800 52.381 0.00 0.00 0.00 3.18
6447 7531 1.247567 CTCCGTCCCAAAATGCTTGT 58.752 50.000 0.00 0.00 0.00 3.16
6448 7532 0.527565 CCTCCGTCCCAAAATGCTTG 59.472 55.000 0.00 0.00 0.00 4.01
6449 7533 0.611896 CCCTCCGTCCCAAAATGCTT 60.612 55.000 0.00 0.00 0.00 3.91
6450 7534 1.000896 CCCTCCGTCCCAAAATGCT 60.001 57.895 0.00 0.00 0.00 3.79
6451 7535 1.001393 TCCCTCCGTCCCAAAATGC 60.001 57.895 0.00 0.00 0.00 3.56
6452 7536 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.000 0.00 0.00 0.00 2.32
6453 7537 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
6454 7538 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
6455 7539 1.557832 CATTACTCCCTCCGTCCCAAA 59.442 52.381 0.00 0.00 0.00 3.28
6456 7540 1.200519 CATTACTCCCTCCGTCCCAA 58.799 55.000 0.00 0.00 0.00 4.12
6457 7541 0.042131 ACATTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
6458 7542 0.464452 CACATTACTCCCTCCGTCCC 59.536 60.000 0.00 0.00 0.00 4.46
6459 7543 1.192428 ACACATTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
6460 7544 3.000727 CAAACACATTACTCCCTCCGTC 58.999 50.000 0.00 0.00 0.00 4.79
6461 7545 2.874457 GCAAACACATTACTCCCTCCGT 60.874 50.000 0.00 0.00 0.00 4.69
6462 7546 1.737793 GCAAACACATTACTCCCTCCG 59.262 52.381 0.00 0.00 0.00 4.63
6463 7547 2.790433 TGCAAACACATTACTCCCTCC 58.210 47.619 0.00 0.00 0.00 4.30
6464 7548 5.183904 AGAAATGCAAACACATTACTCCCTC 59.816 40.000 0.00 0.00 39.32 4.30
6465 7549 5.047802 CAGAAATGCAAACACATTACTCCCT 60.048 40.000 0.00 0.00 39.32 4.20
6466 7550 5.048083 TCAGAAATGCAAACACATTACTCCC 60.048 40.000 0.00 0.00 39.32 4.30
6467 7551 5.858581 GTCAGAAATGCAAACACATTACTCC 59.141 40.000 0.00 0.00 39.32 3.85
6468 7552 5.565259 CGTCAGAAATGCAAACACATTACTC 59.435 40.000 0.00 0.00 39.32 2.59
6469 7553 5.008613 ACGTCAGAAATGCAAACACATTACT 59.991 36.000 0.00 0.00 39.32 2.24
6470 7554 5.115472 CACGTCAGAAATGCAAACACATTAC 59.885 40.000 0.00 0.00 39.32 1.89
6571 7655 5.376854 AAAACTGCATTGCCTAACTAGTG 57.623 39.130 6.12 0.00 0.00 2.74
6581 7665 4.606012 GCACGAAAACTAAAACTGCATTGC 60.606 41.667 0.46 0.46 0.00 3.56
6690 7774 0.394352 GGCATTGGGAGAACACCGAT 60.394 55.000 0.00 0.00 32.15 4.18
6757 7842 1.953686 ACAGAAAATGGTGAACACGGG 59.046 47.619 0.00 0.00 0.00 5.28
6807 7897 2.639839 ACTGTGGAACTAGATGCCAGTT 59.360 45.455 0.00 0.00 38.92 3.16
6816 7906 3.599730 TCTCATGCACTGTGGAACTAG 57.400 47.619 5.98 4.51 38.04 2.57
6858 7948 7.946655 TCTCGTTAATCTAGCAATGGTATTG 57.053 36.000 0.00 0.00 0.00 1.90
6870 7960 9.653287 AATCTTCAATGTGTTCTCGTTAATCTA 57.347 29.630 0.00 0.00 0.00 1.98
6902 7992 4.723309 AGGCAATGTGTTCTCTCTCTTTT 58.277 39.130 0.00 0.00 0.00 2.27
6903 7993 4.363991 AGGCAATGTGTTCTCTCTCTTT 57.636 40.909 0.00 0.00 0.00 2.52
6906 7996 5.068987 AGAGATAGGCAATGTGTTCTCTCTC 59.931 44.000 0.00 0.00 36.14 3.20
6907 7997 4.961730 AGAGATAGGCAATGTGTTCTCTCT 59.038 41.667 0.00 0.00 36.14 3.10
6908 7998 5.275067 AGAGATAGGCAATGTGTTCTCTC 57.725 43.478 0.00 0.00 36.14 3.20
6988 8082 5.673337 TGCAGAAGTCACTGTGAAATAAC 57.327 39.130 12.81 0.00 39.73 1.89
6996 8090 3.482156 AGTTGATGCAGAAGTCACTGT 57.518 42.857 0.00 0.00 39.73 3.55
7208 8469 5.411781 ACATCGACTTTCTTCCTACATGTC 58.588 41.667 0.00 0.00 0.00 3.06
7321 8583 6.293462 CCCGTTGTTGTTTCCAAAAAGAAAAA 60.293 34.615 0.00 0.00 37.49 1.94
7421 8684 1.147817 AGTTGGATCTGCCCCTTTGTT 59.852 47.619 0.00 0.00 34.97 2.83
7496 8759 3.125829 CACTAAACATGTTGAGCGCTCAT 59.874 43.478 38.40 24.45 39.64 2.90
7536 8799 7.067372 TGAGCAATCTATGGAGGTTTGTATTTG 59.933 37.037 0.00 0.00 0.00 2.32
7554 8817 8.856490 ATTCCGTGTTAATTATTTGAGCAATC 57.144 30.769 0.00 0.00 0.00 2.67
7556 8819 8.300286 TGAATTCCGTGTTAATTATTTGAGCAA 58.700 29.630 2.27 0.00 0.00 3.91
7557 8820 7.821652 TGAATTCCGTGTTAATTATTTGAGCA 58.178 30.769 2.27 0.00 0.00 4.26
7558 8821 8.856490 ATGAATTCCGTGTTAATTATTTGAGC 57.144 30.769 2.27 0.00 0.00 4.26
7670 9840 6.530019 AAGTTGTCAAGGTTTTCACAATCT 57.470 33.333 0.00 0.00 31.65 2.40
7677 9847 6.311935 GGTTTACCAAAGTTGTCAAGGTTTTC 59.688 38.462 0.00 0.00 33.91 2.29
7735 9913 4.569719 ACCCCATGACCCGATTATTATC 57.430 45.455 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.