Multiple sequence alignment - TraesCS3A01G278000

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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 TraesCS3A01G278000 chr3A 100.000 3795 0 0 1 3795 507593906 507597700 0.000000e+00 7009.0
1 TraesCS3A01G278000 chr3A 100.000 346 0 0 4194 4539 507598099 507598444 1.380000e-179 640.0
2 TraesCS3A01G278000 chr3B 87.291 1975 129 30 1728 3646 501420261 501422169 0.000000e+00 2145.0
3 TraesCS3A01G278000 chr3B 92.761 1188 58 13 477 1652 501417346 501418517 0.000000e+00 1692.0
4 TraesCS3A01G278000 chr3B 88.859 368 19 10 4194 4539 693647772 693648139 2.510000e-117 433.0
5 TraesCS3A01G278000 chr3B 88.920 361 24 11 4194 4539 141706753 141706394 9.020000e-117 431.0
6 TraesCS3A01G278000 chr3B 96.491 57 2 0 3739 3795 171089486 171089542 1.340000e-15 95.3
7 TraesCS3A01G278000 chr3D 91.817 941 57 8 477 1407 385433256 385434186 0.000000e+00 1293.0
8 TraesCS3A01G278000 chr3D 90.928 970 55 14 2767 3734 385467927 385468865 0.000000e+00 1273.0
9 TraesCS3A01G278000 chr3D 87.952 415 33 9 52 461 385432868 385433270 1.480000e-129 473.0
10 TraesCS3A01G278000 chr3D 92.063 315 24 1 2068 2381 385438207 385438521 4.170000e-120 442.0
11 TraesCS3A01G278000 chr3D 93.701 254 11 3 1400 1652 385435043 385435292 4.290000e-100 375.0
12 TraesCS3A01G278000 chr3D 92.218 257 16 4 4284 4539 519601785 519602038 1.200000e-95 361.0
13 TraesCS3A01G278000 chr3D 94.286 175 6 2 2394 2567 385467092 385467263 9.680000e-67 265.0
14 TraesCS3A01G278000 chr3D 89.806 206 9 7 1833 2038 385437703 385437896 2.100000e-63 254.0
15 TraesCS3A01G278000 chr3D 85.165 182 13 2 2604 2771 385467486 385467667 1.680000e-39 174.0
16 TraesCS3A01G278000 chr3D 94.286 105 6 0 1728 1832 385437545 385437649 1.310000e-35 161.0
17 TraesCS3A01G278000 chr3D 78.067 269 36 15 59 319 498996791 498997044 1.020000e-31 148.0
18 TraesCS3A01G278000 chr2D 89.130 368 18 2 4194 4539 637373910 637373543 5.390000e-119 438.0
19 TraesCS3A01G278000 chr2D 85.246 366 32 5 4194 4537 639297017 639297382 1.550000e-94 357.0
20 TraesCS3A01G278000 chr2D 77.143 280 49 10 62 328 622832611 622832888 1.020000e-31 148.0
21 TraesCS3A01G278000 chr5A 88.315 368 21 8 4194 4539 709416204 709415837 5.430000e-114 422.0
22 TraesCS3A01G278000 chr5A 88.315 368 21 8 4194 4539 709419531 709419898 5.430000e-114 422.0
23 TraesCS3A01G278000 chr5A 85.393 89 12 1 3650 3737 546332853 546332765 1.740000e-14 91.6
24 TraesCS3A01G278000 chr6A 88.043 368 22 11 4194 4539 54007396 54007763 2.530000e-112 416.0
25 TraesCS3A01G278000 chr7B 86.685 368 26 6 4194 4539 13804824 13804458 1.980000e-103 387.0
26 TraesCS3A01G278000 chr7B 83.955 268 28 7 62 321 366823914 366824174 4.540000e-60 243.0
27 TraesCS3A01G278000 chr2B 86.957 345 42 3 4195 4537 13237401 13237058 7.120000e-103 385.0
28 TraesCS3A01G278000 chr2B 90.234 256 21 4 4285 4539 610601282 610601534 9.410000e-87 331.0
29 TraesCS3A01G278000 chr6B 86.179 369 28 11 4194 4539 308517677 308517309 1.190000e-100 377.0
30 TraesCS3A01G278000 chr6B 93.220 59 3 1 3738 3795 308517812 308517754 8.090000e-13 86.1
31 TraesCS3A01G278000 chr4B 87.308 260 22 5 62 321 182668924 182669172 2.070000e-73 287.0
32 TraesCS3A01G278000 chr4B 76.494 251 38 16 68 303 90638511 90638755 2.870000e-22 117.0
33 TraesCS3A01G278000 chr4B 77.778 162 23 10 62 212 172782518 172782359 2.250000e-13 87.9
34 TraesCS3A01G278000 chr1B 90.625 160 14 1 2431 2589 665276858 665277017 1.280000e-50 211.0
35 TraesCS3A01G278000 chr2A 76.259 278 44 17 56 315 380187483 380187210 1.330000e-25 128.0
36 TraesCS3A01G278000 chr6D 76.449 276 35 14 62 321 138382204 138381943 6.170000e-24 122.0
37 TraesCS3A01G278000 chr6D 77.711 166 28 7 150 315 27224157 27224001 4.830000e-15 93.5
38 TraesCS3A01G278000 chr5D 80.921 152 18 10 68 212 100076317 100076464 4.800000e-20 110.0
39 TraesCS3A01G278000 chr4D 77.301 163 25 11 63 217 438162361 438162519 8.090000e-13 86.1
40 TraesCS3A01G278000 chr4D 76.871 147 25 8 85 222 442760202 442760056 1.750000e-09 75.0
41 TraesCS3A01G278000 chr1A 85.526 76 4 5 133 205 4362976 4363047 6.300000e-09 73.1
42 TraesCS3A01G278000 chr5B 82.927 82 9 4 134 212 185515775 185515854 8.150000e-08 69.4
43 TraesCS3A01G278000 chr1D 100.000 28 0 0 3763 3790 52356152 52356125 8.000000e-03 52.8


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 TraesCS3A01G278000 chr3A 507593906 507598444 4538 False 3824.500000 7009 100.000000 1 4539 2 chr3A.!!$F1 4538
1 TraesCS3A01G278000 chr3B 501417346 501422169 4823 False 1918.500000 2145 90.026000 477 3646 2 chr3B.!!$F3 3169
2 TraesCS3A01G278000 chr3D 385467092 385468865 1773 False 570.666667 1273 90.126333 2394 3734 3 chr3D.!!$F4 1340
3 TraesCS3A01G278000 chr3D 385432868 385438521 5653 False 499.666667 1293 91.604167 52 2381 6 chr3D.!!$F3 2329
4 TraesCS3A01G278000 chr6B 308517309 308517812 503 True 231.550000 377 89.699500 3738 4539 2 chr6B.!!$R1 801

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
120 121 0.185901 AATCACCACAGCCACAAGGT 59.814 50.0 0.00 0.00 37.19 3.50 F
1361 1385 0.794981 CAAGAAGACGACGAGGCGAG 60.795 60.0 4.95 0.00 34.83 5.03 F
1556 2445 0.179936 AGGCAGCTCAAGAGTATGGC 59.820 55.0 17.17 17.17 40.46 4.40 F
3029 7962 0.105778 GGAAGGAGAGATGGCGAAGG 59.894 60.0 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1392 0.757188 TCCCGGAGAAGAGGATCAGC 60.757 60.0 0.73 0.0 37.82 4.26 R
3010 7943 0.105778 CCTTCGCCATCTCTCCTTCC 59.894 60.0 0.00 0.0 0.00 3.46 R
3080 8013 0.535102 CGATGATGGGGCTGGTTACC 60.535 60.0 0.00 0.0 0.00 2.85 R
4420 9383 0.832135 ACCGAAGCTGGAGAAGACCA 60.832 55.0 0.00 0.0 38.33 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 6.252967 GGTGGCCAAAATTTAAAATTGGAG 57.747 37.500 27.56 11.81 45.14 3.86
24 25 6.000840 GGTGGCCAAAATTTAAAATTGGAGA 58.999 36.000 27.56 16.06 45.14 3.71
25 26 6.072728 GGTGGCCAAAATTTAAAATTGGAGAC 60.073 38.462 27.56 22.42 45.14 3.36
26 27 6.000840 TGGCCAAAATTTAAAATTGGAGACC 58.999 36.000 27.56 21.52 45.14 3.85
27 28 6.183361 TGGCCAAAATTTAAAATTGGAGACCT 60.183 34.615 27.56 0.00 45.14 3.85
28 29 6.714810 GGCCAAAATTTAAAATTGGAGACCTT 59.285 34.615 27.56 0.23 45.14 3.50
29 30 7.880713 GGCCAAAATTTAAAATTGGAGACCTTA 59.119 33.333 27.56 0.00 45.14 2.69
30 31 9.278978 GCCAAAATTTAAAATTGGAGACCTTAA 57.721 29.630 27.56 0.00 45.14 1.85
43 44 7.391148 TGGAGACCTTAATTGATTGTTAAGC 57.609 36.000 0.00 0.00 37.67 3.09
44 45 6.945435 TGGAGACCTTAATTGATTGTTAAGCA 59.055 34.615 0.00 0.00 37.67 3.91
45 46 7.615365 TGGAGACCTTAATTGATTGTTAAGCAT 59.385 33.333 0.00 0.00 37.67 3.79
46 47 8.470002 GGAGACCTTAATTGATTGTTAAGCATT 58.530 33.333 0.00 0.00 37.67 3.56
79 80 4.846779 AGCTTACCGAAAAATGCTTTCA 57.153 36.364 0.00 0.00 0.00 2.69
80 81 5.391312 AGCTTACCGAAAAATGCTTTCAT 57.609 34.783 0.00 0.00 33.53 2.57
82 83 5.048083 AGCTTACCGAAAAATGCTTTCATCA 60.048 36.000 0.00 0.00 31.27 3.07
120 121 0.185901 AATCACCACAGCCACAAGGT 59.814 50.000 0.00 0.00 37.19 3.50
130 131 1.214424 AGCCACAAGGTACAACAAGGT 59.786 47.619 0.00 0.00 37.19 3.50
140 141 3.630312 GGTACAACAAGGTTCACACACAT 59.370 43.478 0.00 0.00 0.00 3.21
168 169 4.151689 GCAGCACGACAGATAGTACAAAAA 59.848 41.667 0.00 0.00 0.00 1.94
173 174 6.617953 GCACGACAGATAGTACAAAAAGGTTC 60.618 42.308 0.00 0.00 0.00 3.62
182 183 3.297134 ACAAAAAGGTTCTGCTGAGGA 57.703 42.857 0.00 0.00 0.00 3.71
196 197 2.141517 CTGAGGACACAGCTCAACAAG 58.858 52.381 0.00 0.00 0.00 3.16
252 254 1.464997 GAGCCGCAACAAGGAAACTAG 59.535 52.381 0.00 0.00 42.68 2.57
261 263 1.275291 CAAGGAAACTAGTCCGGCTCA 59.725 52.381 0.00 0.00 42.68 4.26
339 341 5.649831 AGCAATTAGGGAGCTTAAGTCTTTG 59.350 40.000 4.02 4.04 34.37 2.77
353 355 8.123575 GCTTAAGTCTTTGGCTAGCTTAATAAC 58.876 37.037 15.72 10.81 33.13 1.89
358 360 7.550906 AGTCTTTGGCTAGCTTAATAACAAGAG 59.449 37.037 15.72 8.49 0.00 2.85
360 362 4.451900 TGGCTAGCTTAATAACAAGAGGC 58.548 43.478 15.72 0.00 0.00 4.70
363 365 6.043243 TGGCTAGCTTAATAACAAGAGGCTAT 59.957 38.462 15.72 0.00 30.63 2.97
364 366 6.937465 GGCTAGCTTAATAACAAGAGGCTATT 59.063 38.462 15.72 0.00 31.80 1.73
366 368 8.927721 GCTAGCTTAATAACAAGAGGCTATTAC 58.072 37.037 7.70 0.00 31.80 1.89
368 370 8.664211 AGCTTAATAACAAGAGGCTATTACAC 57.336 34.615 0.00 0.00 0.00 2.90
369 371 7.715686 AGCTTAATAACAAGAGGCTATTACACC 59.284 37.037 0.00 0.00 0.00 4.16
370 372 7.715686 GCTTAATAACAAGAGGCTATTACACCT 59.284 37.037 0.00 0.00 39.65 4.00
371 373 8.958119 TTAATAACAAGAGGCTATTACACCTG 57.042 34.615 0.00 0.00 36.05 4.00
372 374 6.808321 ATAACAAGAGGCTATTACACCTGA 57.192 37.500 0.00 0.00 36.05 3.86
373 375 5.499004 AACAAGAGGCTATTACACCTGAA 57.501 39.130 0.00 0.00 36.05 3.02
395 398 7.599171 TGAATGTGTCTTCTTATCGTCTTGTA 58.401 34.615 0.00 0.00 0.00 2.41
411 417 4.079253 TCTTGTAGGGACTTTGGAATTGC 58.921 43.478 0.00 0.00 41.75 3.56
419 425 3.256558 GACTTTGGAATTGCAGGAATGC 58.743 45.455 0.00 0.00 0.00 3.56
420 426 2.901839 ACTTTGGAATTGCAGGAATGCT 59.098 40.909 0.00 0.00 35.49 3.79
421 427 3.056322 ACTTTGGAATTGCAGGAATGCTC 60.056 43.478 0.00 0.00 35.49 4.26
422 428 2.519771 TGGAATTGCAGGAATGCTCT 57.480 45.000 0.00 0.00 35.49 4.09
423 429 2.097036 TGGAATTGCAGGAATGCTCTG 58.903 47.619 0.00 0.00 35.49 3.35
424 430 2.097825 GGAATTGCAGGAATGCTCTGT 58.902 47.619 1.53 0.00 34.89 3.41
441 447 9.678260 AATGCTCTGTCTTCACTAATCTATTTT 57.322 29.630 0.00 0.00 0.00 1.82
466 472 8.706492 TTCTCAACATGCAATCATTTAAATCC 57.294 30.769 0.00 0.00 0.00 3.01
467 473 7.267128 TCTCAACATGCAATCATTTAAATCCC 58.733 34.615 0.00 0.00 0.00 3.85
468 474 6.347696 TCAACATGCAATCATTTAAATCCCC 58.652 36.000 0.00 0.00 0.00 4.81
469 475 5.954153 ACATGCAATCATTTAAATCCCCA 57.046 34.783 0.00 0.00 0.00 4.96
470 476 5.673514 ACATGCAATCATTTAAATCCCCAC 58.326 37.500 0.00 0.00 0.00 4.61
471 477 5.189342 ACATGCAATCATTTAAATCCCCACA 59.811 36.000 0.00 0.00 0.00 4.17
472 478 5.752036 TGCAATCATTTAAATCCCCACAA 57.248 34.783 0.00 0.00 0.00 3.33
473 479 6.119240 TGCAATCATTTAAATCCCCACAAA 57.881 33.333 0.00 0.00 0.00 2.83
474 480 6.537355 TGCAATCATTTAAATCCCCACAAAA 58.463 32.000 0.00 0.00 0.00 2.44
475 481 6.654161 TGCAATCATTTAAATCCCCACAAAAG 59.346 34.615 0.00 0.00 0.00 2.27
478 484 9.282569 CAATCATTTAAATCCCCACAAAAGAAA 57.717 29.630 0.00 0.00 0.00 2.52
700 714 0.809636 GCTTGGCCACAAAACACACC 60.810 55.000 3.88 0.00 35.89 4.16
705 719 0.936600 GCCACAAAACACACCAATGC 59.063 50.000 0.00 0.00 0.00 3.56
724 738 1.123928 CGGATTAGACAGCCCCTTCT 58.876 55.000 0.00 0.00 0.00 2.85
738 752 5.047377 CAGCCCCTTCTATTTACAAGCAAAA 60.047 40.000 0.00 0.00 0.00 2.44
739 753 5.542251 AGCCCCTTCTATTTACAAGCAAAAA 59.458 36.000 0.00 0.00 0.00 1.94
740 754 6.213397 AGCCCCTTCTATTTACAAGCAAAAAT 59.787 34.615 0.00 0.00 0.00 1.82
741 755 6.535150 GCCCCTTCTATTTACAAGCAAAAATC 59.465 38.462 0.00 0.00 0.00 2.17
742 756 7.041721 CCCCTTCTATTTACAAGCAAAAATCC 58.958 38.462 0.00 0.00 0.00 3.01
743 757 7.310361 CCCCTTCTATTTACAAGCAAAAATCCA 60.310 37.037 0.00 0.00 0.00 3.41
752 766 4.094739 ACAAGCAAAAATCCAAAGTGCAAC 59.905 37.500 0.00 0.00 37.68 4.17
768 782 5.185454 AGTGCAACAATCGAATTGATAGGA 58.815 37.500 12.53 3.30 42.83 2.94
773 787 6.460123 GCAACAATCGAATTGATAGGACCATT 60.460 38.462 12.53 0.00 42.83 3.16
774 788 6.867662 ACAATCGAATTGATAGGACCATTC 57.132 37.500 12.53 0.00 42.83 2.67
783 797 8.951614 AATTGATAGGACCATTCATGATTCAT 57.048 30.769 0.00 0.00 0.00 2.57
786 800 6.938596 TGATAGGACCATTCATGATTCATCAC 59.061 38.462 0.00 0.00 40.03 3.06
806 820 8.806146 TCATCACATATCCGAATCAGAGAAATA 58.194 33.333 0.00 0.00 0.00 1.40
807 821 9.597170 CATCACATATCCGAATCAGAGAAATAT 57.403 33.333 0.00 0.00 0.00 1.28
819 833 3.005684 CAGAGAAATATGAGAGCGCTCCT 59.994 47.826 32.94 19.91 40.55 3.69
876 897 2.238521 GCAATTTCCACCCTGTCTCAA 58.761 47.619 0.00 0.00 0.00 3.02
896 917 2.433145 TGTCAGCTAGCGCACTGC 60.433 61.111 11.47 10.91 46.98 4.40
926 947 4.570772 CCATACACGCTACAAATACAGCTT 59.429 41.667 0.00 0.00 35.57 3.74
944 965 1.827399 TTTGTCCGTCTCCTCCTGCC 61.827 60.000 0.00 0.00 0.00 4.85
963 984 1.743321 CTCTCCTCTCATCCACGCCC 61.743 65.000 0.00 0.00 0.00 6.13
1026 1050 4.015406 TGGGACGCGCTTGTGGAT 62.015 61.111 5.73 0.00 0.00 3.41
1255 1279 1.717194 CAGGAAAATGCATGCCACAC 58.283 50.000 16.68 2.90 0.00 3.82
1270 1294 1.935199 CCACACTTTTTGCTTGCTTGG 59.065 47.619 0.00 0.00 0.00 3.61
1361 1385 0.794981 CAAGAAGACGACGAGGCGAG 60.795 60.000 4.95 0.00 34.83 5.03
1476 2365 6.233905 TCATTTGCTATTAGGACTGTAGCA 57.766 37.500 13.64 13.64 46.42 3.49
1502 2391 2.464157 ACTCTGAACAAGCTACCTGC 57.536 50.000 0.00 0.00 43.29 4.85
1503 2392 1.002544 ACTCTGAACAAGCTACCTGCC 59.997 52.381 0.00 0.00 44.23 4.85
1504 2393 1.277557 CTCTGAACAAGCTACCTGCCT 59.722 52.381 0.00 0.00 44.23 4.75
1505 2394 1.002430 TCTGAACAAGCTACCTGCCTG 59.998 52.381 0.00 0.00 44.23 4.85
1556 2445 0.179936 AGGCAGCTCAAGAGTATGGC 59.820 55.000 17.17 17.17 40.46 4.40
1608 2497 4.328169 GCGGGTACACTACTTATCACAAAC 59.672 45.833 0.00 0.00 0.00 2.93
1629 2518 2.117423 TGGAGGAGTCACTGGCGA 59.883 61.111 0.00 0.00 0.00 5.54
1660 2549 4.547406 AAAAAGAGGTACAGCACGAAAC 57.453 40.909 0.00 0.00 0.00 2.78
1661 2550 2.902705 AAGAGGTACAGCACGAAACA 57.097 45.000 0.00 0.00 0.00 2.83
1663 2552 3.188159 AGAGGTACAGCACGAAACAAA 57.812 42.857 0.00 0.00 0.00 2.83
1664 2553 3.537580 AGAGGTACAGCACGAAACAAAA 58.462 40.909 0.00 0.00 0.00 2.44
1665 2554 3.311596 AGAGGTACAGCACGAAACAAAAC 59.688 43.478 0.00 0.00 0.00 2.43
1666 2555 3.011119 AGGTACAGCACGAAACAAAACA 58.989 40.909 0.00 0.00 0.00 2.83
1667 2556 3.064820 AGGTACAGCACGAAACAAAACAG 59.935 43.478 0.00 0.00 0.00 3.16
1668 2557 3.064271 GGTACAGCACGAAACAAAACAGA 59.936 43.478 0.00 0.00 0.00 3.41
1669 2558 4.261031 GGTACAGCACGAAACAAAACAGAT 60.261 41.667 0.00 0.00 0.00 2.90
1670 2559 5.049954 GGTACAGCACGAAACAAAACAGATA 60.050 40.000 0.00 0.00 0.00 1.98
1671 2560 5.689383 ACAGCACGAAACAAAACAGATAT 57.311 34.783 0.00 0.00 0.00 1.63
1676 2565 9.767684 CAGCACGAAACAAAACAGATATTATTA 57.232 29.630 0.00 0.00 0.00 0.98
1678 2567 8.721476 GCACGAAACAAAACAGATATTATTACG 58.279 33.333 0.00 0.00 0.00 3.18
1679 2568 8.721476 CACGAAACAAAACAGATATTATTACGC 58.279 33.333 0.00 0.00 0.00 4.42
1681 2570 8.933955 CGAAACAAAACAGATATTATTACGCTG 58.066 33.333 0.00 0.00 0.00 5.18
1682 2571 9.769093 GAAACAAAACAGATATTATTACGCTGT 57.231 29.630 0.00 0.00 41.19 4.40
1701 5735 8.920509 ACGCTGTTTTATTAAGTGTTTTCTTT 57.079 26.923 0.00 0.00 30.73 2.52
1724 5758 9.289303 CTTTACCTTTACATCGATTGATTTTGG 57.711 33.333 0.00 0.00 30.49 3.28
1731 5801 5.942872 ACATCGATTGATTTTGGTCACTTC 58.057 37.500 0.00 0.00 30.49 3.01
1751 5821 3.347216 TCTACAGGATTGCCTTCTTTGC 58.653 45.455 0.00 0.00 43.90 3.68
1787 5857 0.240945 CAAACACGGCCTTGATGACC 59.759 55.000 17.43 0.00 0.00 4.02
1853 5976 0.240678 CAGAGGATGAGAGGATCGCG 59.759 60.000 0.00 0.00 42.67 5.87
1949 6072 1.071605 CCTTCGTCTACAAGCACTGC 58.928 55.000 0.00 0.00 0.00 4.40
1992 6115 1.293924 GCTGTATGCATGCGTCTTCT 58.706 50.000 17.45 0.00 42.31 2.85
1993 6116 1.260033 GCTGTATGCATGCGTCTTCTC 59.740 52.381 17.45 4.10 42.31 2.87
1994 6117 2.819115 CTGTATGCATGCGTCTTCTCT 58.181 47.619 17.45 0.00 0.00 3.10
1995 6118 2.793790 CTGTATGCATGCGTCTTCTCTC 59.206 50.000 17.45 0.69 0.00 3.20
1996 6119 2.131183 GTATGCATGCGTCTTCTCTCC 58.869 52.381 17.45 0.00 0.00 3.71
1997 6120 0.829333 ATGCATGCGTCTTCTCTCCT 59.171 50.000 14.09 0.00 0.00 3.69
1998 6121 0.610174 TGCATGCGTCTTCTCTCCTT 59.390 50.000 14.09 0.00 0.00 3.36
1999 6122 1.002430 TGCATGCGTCTTCTCTCCTTT 59.998 47.619 14.09 0.00 0.00 3.11
2000 6123 2.233676 TGCATGCGTCTTCTCTCCTTTA 59.766 45.455 14.09 0.00 0.00 1.85
2001 6124 3.262420 GCATGCGTCTTCTCTCCTTTAA 58.738 45.455 0.00 0.00 0.00 1.52
2065 6445 4.315803 ACATACATATTTAGCCACGCCTC 58.684 43.478 0.00 0.00 0.00 4.70
2077 6481 1.127951 CCACGCCTCGATTTTGTGTAC 59.872 52.381 0.00 0.00 0.00 2.90
2100 6504 0.604578 TACGTACAGGTCCAGTTGCC 59.395 55.000 0.00 0.00 0.00 4.52
2102 6506 1.375523 GTACAGGTCCAGTTGCCCG 60.376 63.158 0.00 0.00 0.00 6.13
2126 6530 4.728534 TGGAAAAGAAAGTTGTTGTCACG 58.271 39.130 0.00 0.00 0.00 4.35
2129 6533 4.351131 AAAGAAAGTTGTTGTCACGGAC 57.649 40.909 0.00 0.00 0.00 4.79
2160 6568 4.207891 ACCTGCCACTGAATAAGTACTG 57.792 45.455 0.00 0.00 36.83 2.74
2177 6585 5.194432 AGTACTGTTGATATCTCCGTCAGT 58.806 41.667 3.98 12.22 38.10 3.41
2181 6589 7.113658 ACTGTTGATATCTCCGTCAGTATTT 57.886 36.000 3.98 0.00 33.78 1.40
2189 6597 5.824904 TCTCCGTCAGTATTTACACCTAC 57.175 43.478 0.00 0.00 0.00 3.18
2191 6599 6.653020 TCTCCGTCAGTATTTACACCTACTA 58.347 40.000 0.00 0.00 0.00 1.82
2192 6600 6.765036 TCTCCGTCAGTATTTACACCTACTAG 59.235 42.308 0.00 0.00 0.00 2.57
2195 6603 7.066284 TCCGTCAGTATTTACACCTACTAGTTC 59.934 40.741 0.00 0.00 0.00 3.01
2196 6604 7.066766 CCGTCAGTATTTACACCTACTAGTTCT 59.933 40.741 0.00 0.00 0.00 3.01
2235 6643 5.276461 TGCATATTGTGAGGGTACTACTG 57.724 43.478 0.00 0.00 0.00 2.74
2315 6731 0.394938 TTGCTCCGTTGCCTCAACTA 59.605 50.000 7.91 0.00 41.62 2.24
2371 6787 5.066764 TGGTCGTCGATGATGTTAGTATTCA 59.933 40.000 11.16 0.00 0.00 2.57
2386 6802 8.701895 TGTTAGTATTCATTTTATCCTCTCGGT 58.298 33.333 0.00 0.00 0.00 4.69
2388 6804 9.760077 TTAGTATTCATTTTATCCTCTCGGTTC 57.240 33.333 0.00 0.00 0.00 3.62
2408 6825 9.471084 TCGGTTCTTAAATTTTTCCAATCTTTC 57.529 29.630 0.00 0.00 0.00 2.62
2587 7208 6.207417 GTGGTTTCATAGCATGCAGGTAATAT 59.793 38.462 21.98 4.69 36.50 1.28
2588 7209 7.390440 GTGGTTTCATAGCATGCAGGTAATATA 59.610 37.037 21.98 0.43 36.50 0.86
2589 7210 8.108999 TGGTTTCATAGCATGCAGGTAATATAT 58.891 33.333 21.98 3.13 33.24 0.86
2590 7211 8.400947 GGTTTCATAGCATGCAGGTAATATATG 58.599 37.037 21.98 15.45 33.24 1.78
2591 7212 8.950210 GTTTCATAGCATGCAGGTAATATATGT 58.050 33.333 21.98 0.00 33.24 2.29
2592 7213 9.519191 TTTCATAGCATGCAGGTAATATATGTT 57.481 29.630 21.98 0.00 33.24 2.71
2619 7240 8.048534 TCTATACTGTACTCTTTAAGCACGTT 57.951 34.615 0.00 0.00 0.00 3.99
2620 7241 6.946229 ATACTGTACTCTTTAAGCACGTTG 57.054 37.500 0.00 0.00 0.00 4.10
2702 7331 7.222611 GGTTATGCCATACAACTGCAAAATTAG 59.777 37.037 0.00 0.00 38.69 1.73
2719 7348 7.312899 CAAAATTAGGATTGTAACTGACACCC 58.687 38.462 0.00 0.00 37.96 4.61
2751 7390 9.760077 TCTCAAAAATATTTATCTAGACCCGAC 57.240 33.333 0.01 0.00 0.00 4.79
2771 7674 4.498345 CGACTCTTATGGTCTGAGCCTTAC 60.498 50.000 4.17 0.00 0.00 2.34
2774 7677 3.380637 TCTTATGGTCTGAGCCTTACGAC 59.619 47.826 4.17 0.00 0.00 4.34
2777 7680 2.366533 TGGTCTGAGCCTTACGACTAG 58.633 52.381 4.17 0.00 0.00 2.57
2796 7699 1.965643 AGCTGTTTGCATTGTGGTGAT 59.034 42.857 0.00 0.00 45.94 3.06
2797 7700 2.029649 AGCTGTTTGCATTGTGGTGATC 60.030 45.455 0.00 0.00 45.94 2.92
2798 7701 2.587956 CTGTTTGCATTGTGGTGATCG 58.412 47.619 0.00 0.00 0.00 3.69
2799 7702 1.269174 TGTTTGCATTGTGGTGATCGG 59.731 47.619 0.00 0.00 0.00 4.18
2861 7764 4.531332 GCTCATTCATATTTTCGACAGCC 58.469 43.478 0.00 0.00 0.00 4.85
2870 7773 3.876589 TTCGACAGCCTTGCCGGTC 62.877 63.158 1.90 0.00 30.56 4.79
2920 7823 3.502191 TTGCCGATTTTCCATGCTTAC 57.498 42.857 0.00 0.00 0.00 2.34
2921 7824 2.722094 TGCCGATTTTCCATGCTTACT 58.278 42.857 0.00 0.00 0.00 2.24
2922 7825 2.423185 TGCCGATTTTCCATGCTTACTG 59.577 45.455 0.00 0.00 0.00 2.74
2923 7826 2.682856 GCCGATTTTCCATGCTTACTGA 59.317 45.455 0.00 0.00 0.00 3.41
2924 7827 3.128589 GCCGATTTTCCATGCTTACTGAA 59.871 43.478 0.00 0.00 0.00 3.02
2927 7830 5.447818 CCGATTTTCCATGCTTACTGAACTC 60.448 44.000 0.00 0.00 0.00 3.01
2966 7894 5.894393 TCCACCATCAGTTTTCCTTTTAACA 59.106 36.000 0.00 0.00 0.00 2.41
2978 7911 9.561270 GTTTTCCTTTTAACATGAGAGAATAGC 57.439 33.333 0.00 0.00 0.00 2.97
3010 7943 1.416813 GCTGCAATCCACGTCTCGAG 61.417 60.000 5.93 5.93 0.00 4.04
3029 7962 0.105778 GGAAGGAGAGATGGCGAAGG 59.894 60.000 0.00 0.00 0.00 3.46
3059 7992 0.727398 GGGAGCACGTGCAGTATTTC 59.273 55.000 39.21 26.45 45.16 2.17
3080 8013 2.478134 CGCTTCTCTGACCAAACTCAAG 59.522 50.000 0.00 0.00 0.00 3.02
3122 8055 2.405594 CTCGTCGGAAGCGAGGAG 59.594 66.667 1.62 1.62 46.40 3.69
3152 8085 0.908198 AGGCTCACAGGTTCCATCTC 59.092 55.000 0.00 0.00 0.00 2.75
3160 8093 2.808206 GGTTCCATCTCCCGCCGAT 61.808 63.158 0.00 0.00 0.00 4.18
3236 8174 1.673920 TGCTTCCCGTGTTTGAAACTC 59.326 47.619 9.69 4.85 0.00 3.01
3323 8261 5.118286 CCAACTCAAGCAGGTTTCAAATTT 58.882 37.500 0.00 0.00 0.00 1.82
3324 8262 5.234972 CCAACTCAAGCAGGTTTCAAATTTC 59.765 40.000 0.00 0.00 0.00 2.17
3335 8273 4.024387 GGTTTCAAATTTCGCCTTTTTCCC 60.024 41.667 0.00 0.00 0.00 3.97
3336 8274 4.681074 TTCAAATTTCGCCTTTTTCCCT 57.319 36.364 0.00 0.00 0.00 4.20
3337 8275 4.681074 TCAAATTTCGCCTTTTTCCCTT 57.319 36.364 0.00 0.00 0.00 3.95
3339 8277 3.401033 AATTTCGCCTTTTTCCCTTGG 57.599 42.857 0.00 0.00 0.00 3.61
3341 8279 0.757188 TTCGCCTTTTTCCCTTGGCA 60.757 50.000 0.00 0.00 45.13 4.92
3384 8322 6.041409 CCAGATAGGCAGAGTCTATTTCAAGA 59.959 42.308 0.00 0.00 29.95 3.02
3387 8325 7.563188 AGATAGGCAGAGTCTATTTCAAGAGAA 59.437 37.037 0.00 0.00 29.95 2.87
3412 8350 5.290493 TGACTGATTGTTGAACTACTGGT 57.710 39.130 0.00 0.00 0.00 4.00
3539 8477 7.320443 TGCGCTTCAGTTTCAAGATTATAAT 57.680 32.000 9.73 0.00 0.00 1.28
3540 8478 7.761409 TGCGCTTCAGTTTCAAGATTATAATT 58.239 30.769 9.73 0.00 0.00 1.40
3542 8480 9.884465 GCGCTTCAGTTTCAAGATTATAATTAT 57.116 29.630 0.00 2.97 0.00 1.28
3561 8499 9.772973 ATAATTATAAGCAACGACCACTATTCA 57.227 29.630 0.00 0.00 0.00 2.57
3608 8546 8.221100 CGTGTCACCACTATATATGTTTTATGC 58.779 37.037 0.00 0.00 39.55 3.14
3662 8601 5.279456 GGGTGATATAATTGGTTTGATGCCC 60.279 44.000 0.00 0.00 0.00 5.36
3741 8681 1.528129 CAAGTTGTCTTGCCTCCTCC 58.472 55.000 0.00 0.00 43.34 4.30
3749 8689 2.829639 CTTGCCTCCTCCCCCTCTCA 62.830 65.000 0.00 0.00 0.00 3.27
3754 8694 3.700350 CCTCCCCCTCTCACCCCT 61.700 72.222 0.00 0.00 0.00 4.79
4417 9380 4.824515 CGGCTCGGGAGGACCTCT 62.825 72.222 20.97 0.00 36.97 3.69
4420 9383 1.985116 GCTCGGGAGGACCTCTGTT 60.985 63.158 20.97 0.00 36.97 3.16
4422 9385 1.608717 CTCGGGAGGACCTCTGTTGG 61.609 65.000 20.97 6.48 36.97 3.77
4435 9398 2.038295 CTCTGTTGGTCTTCTCCAGCTT 59.962 50.000 0.00 0.00 39.04 3.74
4436 9399 2.037772 TCTGTTGGTCTTCTCCAGCTTC 59.962 50.000 0.00 0.00 39.04 3.86
4473 9436 4.101448 GATGGTGGCGGTGGAGCT 62.101 66.667 0.00 0.00 37.29 4.09
4518 9481 1.992519 GCCTGGTCTCATGGCTGGAT 61.993 60.000 0.00 0.00 43.05 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.000840 TCTCCAATTTTAAATTTTGGCCACC 58.999 36.000 3.88 0.00 39.79 4.61
1 2 6.072728 GGTCTCCAATTTTAAATTTTGGCCAC 60.073 38.462 3.88 16.71 39.79 5.01
3 4 6.237901 AGGTCTCCAATTTTAAATTTTGGCC 58.762 36.000 18.84 15.55 39.79 5.36
4 5 7.744087 AAGGTCTCCAATTTTAAATTTTGGC 57.256 32.000 18.84 9.87 39.79 4.52
17 18 8.470002 GCTTAACAATCAATTAAGGTCTCCAAT 58.530 33.333 6.63 0.00 39.19 3.16
18 19 7.450014 TGCTTAACAATCAATTAAGGTCTCCAA 59.550 33.333 6.63 0.00 39.19 3.53
19 20 6.945435 TGCTTAACAATCAATTAAGGTCTCCA 59.055 34.615 6.63 0.00 39.19 3.86
20 21 7.391148 TGCTTAACAATCAATTAAGGTCTCC 57.609 36.000 6.63 0.00 39.19 3.71
40 41 7.973944 CGGTAAGCTTCCTAATTTTTAATGCTT 59.026 33.333 0.00 0.00 40.59 3.91
41 42 7.338449 TCGGTAAGCTTCCTAATTTTTAATGCT 59.662 33.333 0.00 0.00 0.00 3.79
42 43 7.477494 TCGGTAAGCTTCCTAATTTTTAATGC 58.523 34.615 0.00 0.00 0.00 3.56
43 44 9.849166 TTTCGGTAAGCTTCCTAATTTTTAATG 57.151 29.630 0.00 0.00 0.00 1.90
47 48 9.203421 CATTTTTCGGTAAGCTTCCTAATTTTT 57.797 29.630 0.00 0.00 0.00 1.94
48 49 7.330946 GCATTTTTCGGTAAGCTTCCTAATTTT 59.669 33.333 0.00 0.00 0.00 1.82
49 50 6.811665 GCATTTTTCGGTAAGCTTCCTAATTT 59.188 34.615 0.00 0.00 0.00 1.82
50 51 6.152831 AGCATTTTTCGGTAAGCTTCCTAATT 59.847 34.615 0.00 0.00 0.00 1.40
57 58 5.195001 TGAAAGCATTTTTCGGTAAGCTT 57.805 34.783 3.48 3.48 39.27 3.74
98 99 0.388659 TTGTGGCTGTGGTGATTTGC 59.611 50.000 0.00 0.00 0.00 3.68
103 104 0.107831 GTACCTTGTGGCTGTGGTGA 59.892 55.000 0.00 0.00 36.63 4.02
120 121 5.676552 ACTATGTGTGTGAACCTTGTTGTA 58.323 37.500 0.00 0.00 0.00 2.41
130 131 3.325870 GTGCTGCTACTATGTGTGTGAA 58.674 45.455 0.00 0.00 0.00 3.18
140 141 3.542648 ACTATCTGTCGTGCTGCTACTA 58.457 45.455 0.00 0.00 0.00 1.82
168 169 0.683973 CTGTGTCCTCAGCAGAACCT 59.316 55.000 0.00 0.00 32.39 3.50
252 254 3.311110 TCACCACCTGAGCCGGAC 61.311 66.667 5.05 0.00 0.00 4.79
261 263 2.584391 GCTTCCTCCGTCACCACCT 61.584 63.158 0.00 0.00 0.00 4.00
303 305 1.061131 CTAATTGCTGACCTTCGTGCG 59.939 52.381 0.00 0.00 0.00 5.34
339 341 4.709250 AGCCTCTTGTTATTAAGCTAGCC 58.291 43.478 12.13 0.00 0.00 3.93
353 355 5.295292 CACATTCAGGTGTAATAGCCTCTTG 59.705 44.000 0.00 0.00 34.09 3.02
366 368 5.171476 ACGATAAGAAGACACATTCAGGTG 58.829 41.667 0.00 0.00 44.35 4.00
368 370 5.655488 AGACGATAAGAAGACACATTCAGG 58.345 41.667 0.00 0.00 0.00 3.86
369 371 6.587990 ACAAGACGATAAGAAGACACATTCAG 59.412 38.462 0.00 0.00 0.00 3.02
370 372 6.455647 ACAAGACGATAAGAAGACACATTCA 58.544 36.000 0.00 0.00 0.00 2.57
371 373 6.952935 ACAAGACGATAAGAAGACACATTC 57.047 37.500 0.00 0.00 0.00 2.67
372 374 7.036220 CCTACAAGACGATAAGAAGACACATT 58.964 38.462 0.00 0.00 0.00 2.71
373 375 6.405953 CCCTACAAGACGATAAGAAGACACAT 60.406 42.308 0.00 0.00 0.00 3.21
378 380 5.507637 AGTCCCTACAAGACGATAAGAAGA 58.492 41.667 0.00 0.00 39.31 2.87
395 398 1.428912 TCCTGCAATTCCAAAGTCCCT 59.571 47.619 0.00 0.00 0.00 4.20
411 417 3.331478 AGTGAAGACAGAGCATTCCTG 57.669 47.619 0.00 0.00 37.64 3.86
441 447 7.765360 GGGATTTAAATGATTGCATGTTGAGAA 59.235 33.333 5.17 0.00 34.26 2.87
461 467 5.046288 TGCATTTTCTTTTGTGGGGATTT 57.954 34.783 0.00 0.00 0.00 2.17
462 468 4.703379 TGCATTTTCTTTTGTGGGGATT 57.297 36.364 0.00 0.00 0.00 3.01
463 469 4.703379 TTGCATTTTCTTTTGTGGGGAT 57.297 36.364 0.00 0.00 0.00 3.85
464 470 4.102210 TGATTGCATTTTCTTTTGTGGGGA 59.898 37.500 0.00 0.00 0.00 4.81
465 471 4.387598 TGATTGCATTTTCTTTTGTGGGG 58.612 39.130 0.00 0.00 0.00 4.96
466 472 6.563222 AATGATTGCATTTTCTTTTGTGGG 57.437 33.333 0.00 0.00 41.87 4.61
501 507 3.818210 TGAATGTTCGCATGTTAAGGTGT 59.182 39.130 0.00 0.00 37.97 4.16
700 714 0.947244 GGGCTGTCTAATCCGCATTG 59.053 55.000 0.00 0.00 0.00 2.82
705 719 1.123928 AGAAGGGGCTGTCTAATCCG 58.876 55.000 0.00 0.00 0.00 4.18
724 738 7.712639 TGCACTTTGGATTTTTGCTTGTAAATA 59.287 29.630 0.00 0.00 34.18 1.40
738 752 4.582701 TTCGATTGTTGCACTTTGGATT 57.417 36.364 0.00 0.00 0.00 3.01
739 753 4.789012 ATTCGATTGTTGCACTTTGGAT 57.211 36.364 0.00 0.00 0.00 3.41
740 754 4.037327 TCAATTCGATTGTTGCACTTTGGA 59.963 37.500 0.00 0.00 41.02 3.53
741 755 4.297510 TCAATTCGATTGTTGCACTTTGG 58.702 39.130 0.00 0.00 41.02 3.28
742 756 6.252015 CCTATCAATTCGATTGTTGCACTTTG 59.748 38.462 0.00 0.00 41.02 2.77
743 757 6.150976 TCCTATCAATTCGATTGTTGCACTTT 59.849 34.615 0.00 0.00 41.02 2.66
752 766 6.866010 TGAATGGTCCTATCAATTCGATTG 57.134 37.500 0.00 0.00 41.57 2.67
768 782 6.373495 CGGATATGTGATGAATCATGAATGGT 59.627 38.462 0.00 0.00 39.30 3.55
773 787 7.388437 TGATTCGGATATGTGATGAATCATGA 58.612 34.615 0.00 0.00 45.82 3.07
774 788 7.605410 TGATTCGGATATGTGATGAATCATG 57.395 36.000 0.00 0.00 45.82 3.07
783 797 8.806146 TCATATTTCTCTGATTCGGATATGTGA 58.194 33.333 11.13 9.14 31.38 3.58
786 800 9.518906 CTCTCATATTTCTCTGATTCGGATATG 57.481 37.037 0.00 2.21 0.00 1.78
806 820 2.804167 CGACAGGAGCGCTCTCAT 59.196 61.111 34.46 20.63 41.13 2.90
819 833 1.904990 TTGGATCCGAATGGGCGACA 61.905 55.000 7.39 0.00 35.24 4.35
867 888 0.683973 AGCTGACACCTTGAGACAGG 59.316 55.000 0.00 0.00 40.23 4.00
876 897 2.262915 GTGCGCTAGCTGACACCT 59.737 61.111 13.93 0.00 45.42 4.00
896 917 3.446310 TGTAGCGTGTATGGTATGGTG 57.554 47.619 0.00 0.00 0.00 4.17
926 947 2.283529 GGCAGGAGGAGACGGACAA 61.284 63.158 0.00 0.00 0.00 3.18
944 965 1.739049 GGCGTGGATGAGAGGAGAG 59.261 63.158 0.00 0.00 0.00 3.20
1051 1075 0.861837 GTGTTGAACAGCAGTCTCCG 59.138 55.000 0.00 0.00 0.00 4.63
1255 1279 2.903798 TGGTTCCAAGCAAGCAAAAAG 58.096 42.857 0.00 0.00 32.80 2.27
1270 1294 6.237915 CGTAACCCGTTCATTTAGTATGGTTC 60.238 42.308 0.00 0.00 36.36 3.62
1298 1322 1.454276 AGAACAAACGCATGTACGACG 59.546 47.619 0.00 0.00 36.70 5.12
1299 1323 2.411031 CCAGAACAAACGCATGTACGAC 60.411 50.000 0.00 0.00 36.70 4.34
1300 1324 1.795872 CCAGAACAAACGCATGTACGA 59.204 47.619 0.00 0.00 36.70 3.43
1308 1332 2.414161 GCCATCTAACCAGAACAAACGC 60.414 50.000 0.00 0.00 33.50 4.84
1361 1385 2.376228 GAAGAGGATCAGCTCCCGGC 62.376 65.000 0.00 0.00 46.27 6.13
1368 1392 0.757188 TCCCGGAGAAGAGGATCAGC 60.757 60.000 0.73 0.00 37.82 4.26
1463 2352 4.836825 AGTACGTACTGCTACAGTCCTAA 58.163 43.478 26.87 0.00 41.21 2.69
1476 2365 4.155644 GGTAGCTTGTTCAGAGTACGTACT 59.844 45.833 27.71 27.71 39.71 2.73
1478 2367 4.155462 CAGGTAGCTTGTTCAGAGTACGTA 59.845 45.833 0.00 0.00 0.00 3.57
1502 2391 2.557924 TGCACAAATTAGAGTTGCCAGG 59.442 45.455 0.00 0.00 0.00 4.45
1503 2392 3.921119 TGCACAAATTAGAGTTGCCAG 57.079 42.857 0.00 0.00 0.00 4.85
1504 2393 3.614630 GCATGCACAAATTAGAGTTGCCA 60.615 43.478 14.21 0.00 0.00 4.92
1505 2394 2.925563 GCATGCACAAATTAGAGTTGCC 59.074 45.455 14.21 0.00 0.00 4.52
1608 2497 1.978473 CCAGTGACTCCTCCACCAG 59.022 63.158 0.00 0.00 35.23 4.00
1652 2541 8.721476 CGTAATAATATCTGTTTTGTTTCGTGC 58.279 33.333 0.00 0.00 0.00 5.34
1653 2542 8.721476 GCGTAATAATATCTGTTTTGTTTCGTG 58.279 33.333 0.00 0.00 0.00 4.35
1656 2545 9.769093 ACAGCGTAATAATATCTGTTTTGTTTC 57.231 29.630 0.00 0.00 34.69 2.78
1676 2565 8.920509 AAAGAAAACACTTAATAAAACAGCGT 57.079 26.923 0.00 0.00 0.00 5.07
1688 5722 9.545105 TCGATGTAAAGGTAAAGAAAACACTTA 57.455 29.630 0.00 0.00 0.00 2.24
1690 5724 8.617290 ATCGATGTAAAGGTAAAGAAAACACT 57.383 30.769 0.00 0.00 0.00 3.55
1692 5726 9.058174 TCAATCGATGTAAAGGTAAAGAAAACA 57.942 29.630 0.00 0.00 0.00 2.83
1701 5735 7.608376 TGACCAAAATCAATCGATGTAAAGGTA 59.392 33.333 0.00 0.00 30.13 3.08
1706 5740 7.390440 AGAAGTGACCAAAATCAATCGATGTAA 59.610 33.333 0.00 0.00 30.13 2.41
1712 5746 6.402550 CCTGTAGAAGTGACCAAAATCAATCG 60.403 42.308 0.00 0.00 0.00 3.34
1723 5757 2.237392 AGGCAATCCTGTAGAAGTGACC 59.763 50.000 0.00 0.00 42.34 4.02
1724 5758 3.618690 AGGCAATCCTGTAGAAGTGAC 57.381 47.619 0.00 0.00 42.34 3.67
1731 5801 2.424956 GGCAAAGAAGGCAATCCTGTAG 59.575 50.000 0.00 0.00 43.40 2.74
1787 5857 3.506096 CTGATGCTGCCCAGTGCG 61.506 66.667 9.96 0.00 45.60 5.34
1853 5976 1.350193 TCAGCGCGTCTGAGAAAATC 58.650 50.000 23.20 0.00 46.34 2.17
1982 6105 5.119694 GGAATTAAAGGAGAGAAGACGCAT 58.880 41.667 0.00 0.00 0.00 4.73
1984 6107 4.504858 TGGAATTAAAGGAGAGAAGACGC 58.495 43.478 0.00 0.00 0.00 5.19
1985 6108 6.256757 GTGATGGAATTAAAGGAGAGAAGACG 59.743 42.308 0.00 0.00 0.00 4.18
1986 6109 6.540551 GGTGATGGAATTAAAGGAGAGAAGAC 59.459 42.308 0.00 0.00 0.00 3.01
1988 6111 6.541641 CAGGTGATGGAATTAAAGGAGAGAAG 59.458 42.308 0.00 0.00 0.00 2.85
1989 6112 6.418101 CAGGTGATGGAATTAAAGGAGAGAA 58.582 40.000 0.00 0.00 0.00 2.87
2065 6445 4.381270 TGTACGTAACGGTACACAAAATCG 59.619 41.667 11.87 0.00 45.68 3.34
2077 6481 0.883833 ACTGGACCTGTACGTAACGG 59.116 55.000 1.49 3.15 0.00 4.44
2100 6504 4.932146 ACAACAACTTTCTTTTCCATCGG 58.068 39.130 0.00 0.00 0.00 4.18
2102 6506 5.455525 CGTGACAACAACTTTCTTTTCCATC 59.544 40.000 0.00 0.00 0.00 3.51
2147 6554 8.353684 ACGGAGATATCAACAGTACTTATTCAG 58.646 37.037 5.32 0.00 0.00 3.02
2160 6568 7.381678 GGTGTAAATACTGACGGAGATATCAAC 59.618 40.741 5.32 0.00 0.00 3.18
2177 6585 8.591072 ACAAGCAAGAACTAGTAGGTGTAAATA 58.409 33.333 0.00 0.00 0.00 1.40
2181 6589 6.041182 TGAACAAGCAAGAACTAGTAGGTGTA 59.959 38.462 0.00 0.00 0.00 2.90
2189 6597 6.785488 TGTGTATGAACAAGCAAGAACTAG 57.215 37.500 0.00 0.00 37.36 2.57
2191 6599 5.563475 GCATGTGTATGAACAAGCAAGAACT 60.563 40.000 0.00 0.00 42.73 3.01
2192 6600 4.618489 GCATGTGTATGAACAAGCAAGAAC 59.382 41.667 0.00 0.00 42.73 3.01
2315 6731 7.151999 TCCATATTTGTTGCGTAATTTGACT 57.848 32.000 0.00 0.00 0.00 3.41
2412 6829 8.341903 CGCAATAGTGATAACCATTATTTGTCA 58.658 33.333 0.00 0.00 36.08 3.58
2430 6847 2.621055 TGTGCCTTGAAAACGCAATAGT 59.379 40.909 0.00 0.00 39.46 2.12
2431 6848 3.281341 TGTGCCTTGAAAACGCAATAG 57.719 42.857 0.00 0.00 39.46 1.73
2432 6849 3.573598 CATGTGCCTTGAAAACGCAATA 58.426 40.909 0.00 0.00 39.46 1.90
2551 6968 2.520741 AAACCACCCTGGCAACCG 60.521 61.111 0.00 0.00 42.67 4.44
2592 7213 9.334947 ACGTGCTTAAAGAGTACAGTATAGATA 57.665 33.333 0.00 0.00 40.60 1.98
2593 7214 8.223177 ACGTGCTTAAAGAGTACAGTATAGAT 57.777 34.615 0.00 0.00 40.60 1.98
2594 7215 7.621428 ACGTGCTTAAAGAGTACAGTATAGA 57.379 36.000 0.00 0.00 40.60 1.98
2595 7216 7.754027 ACAACGTGCTTAAAGAGTACAGTATAG 59.246 37.037 0.00 0.00 40.60 1.31
2596 7217 7.539710 CACAACGTGCTTAAAGAGTACAGTATA 59.460 37.037 0.00 0.00 40.60 1.47
2597 7218 6.365247 CACAACGTGCTTAAAGAGTACAGTAT 59.635 38.462 0.00 0.00 40.60 2.12
2598 7219 5.688621 CACAACGTGCTTAAAGAGTACAGTA 59.311 40.000 0.00 0.00 40.60 2.74
2599 7220 4.506654 CACAACGTGCTTAAAGAGTACAGT 59.493 41.667 0.00 0.00 40.60 3.55
2600 7221 4.506654 ACACAACGTGCTTAAAGAGTACAG 59.493 41.667 0.00 0.00 40.60 2.74
2601 7222 4.435425 ACACAACGTGCTTAAAGAGTACA 58.565 39.130 0.00 0.00 40.60 2.90
2602 7223 5.459762 TGTACACAACGTGCTTAAAGAGTAC 59.540 40.000 0.00 0.00 36.98 2.73
2603 7224 5.590145 TGTACACAACGTGCTTAAAGAGTA 58.410 37.500 0.00 0.00 36.98 2.59
2604 7225 4.435425 TGTACACAACGTGCTTAAAGAGT 58.565 39.130 0.00 0.00 36.98 3.24
2619 7240 6.348498 CATGTTTCCTATCCATCTGTACACA 58.652 40.000 0.00 0.00 0.00 3.72
2620 7241 5.237344 GCATGTTTCCTATCCATCTGTACAC 59.763 44.000 0.00 0.00 0.00 2.90
2702 7331 2.754946 TCGGGTGTCAGTTACAATCC 57.245 50.000 0.00 0.00 40.63 3.01
2751 7390 3.632604 TCGTAAGGCTCAGACCATAAGAG 59.367 47.826 0.00 0.00 38.47 2.85
2771 7674 2.413239 CCACAATGCAAACAGCTAGTCG 60.413 50.000 0.00 0.00 45.94 4.18
2774 7677 2.553602 TCACCACAATGCAAACAGCTAG 59.446 45.455 0.00 0.00 45.94 3.42
2777 7680 2.331194 GATCACCACAATGCAAACAGC 58.669 47.619 0.00 0.00 45.96 4.40
2796 7699 0.975556 TTCCATCTAGTGCTGCCCGA 60.976 55.000 0.00 0.00 0.00 5.14
2797 7700 0.531532 CTTCCATCTAGTGCTGCCCG 60.532 60.000 0.00 0.00 0.00 6.13
2798 7701 0.833287 TCTTCCATCTAGTGCTGCCC 59.167 55.000 0.00 0.00 0.00 5.36
2799 7702 1.202627 CCTCTTCCATCTAGTGCTGCC 60.203 57.143 0.00 0.00 0.00 4.85
2870 7773 2.113139 ACAGAAGCAACCACGGGG 59.887 61.111 0.00 0.00 41.29 5.73
2920 7823 3.461061 TGCTCAGTTCAGTTGAGTTCAG 58.539 45.455 4.41 0.00 43.12 3.02
2921 7824 3.541996 TGCTCAGTTCAGTTGAGTTCA 57.458 42.857 4.41 0.00 43.12 3.18
2922 7825 3.434984 GGATGCTCAGTTCAGTTGAGTTC 59.565 47.826 4.41 2.66 43.12 3.01
2923 7826 3.181451 TGGATGCTCAGTTCAGTTGAGTT 60.181 43.478 4.41 0.00 43.12 3.01
2924 7827 2.369860 TGGATGCTCAGTTCAGTTGAGT 59.630 45.455 4.41 0.00 43.12 3.41
2927 7830 1.808945 GGTGGATGCTCAGTTCAGTTG 59.191 52.381 0.00 0.00 0.00 3.16
2966 7894 6.598503 TGAATCATGGTTGCTATTCTCTCAT 58.401 36.000 0.00 0.00 31.16 2.90
2978 7911 3.444916 GATTGCAGCTGAATCATGGTTG 58.555 45.455 20.43 0.00 31.26 3.77
3010 7943 0.105778 CCTTCGCCATCTCTCCTTCC 59.894 60.000 0.00 0.00 0.00 3.46
3029 7962 1.153549 GTGCTCCCAGATGACCGAC 60.154 63.158 0.00 0.00 0.00 4.79
3059 7992 2.154854 TGAGTTTGGTCAGAGAAGCG 57.845 50.000 0.00 0.00 0.00 4.68
3080 8013 0.535102 CGATGATGGGGCTGGTTACC 60.535 60.000 0.00 0.00 0.00 2.85
3152 8085 1.093496 GGTAGGAAAACATCGGCGGG 61.093 60.000 7.21 1.91 0.00 6.13
3160 8093 4.219115 TGAAGGCAAATGGTAGGAAAACA 58.781 39.130 0.00 0.00 0.00 2.83
3236 8174 1.134189 TCTCAGAAGATGCCTGCATGG 60.134 52.381 9.76 0.00 36.70 3.66
3323 8261 3.771978 GCCAAGGGAAAAAGGCGA 58.228 55.556 0.00 0.00 37.41 5.54
3335 8273 7.066887 TGGTTCACATACAGTATATTTGCCAAG 59.933 37.037 0.00 0.00 0.00 3.61
3336 8274 6.887002 TGGTTCACATACAGTATATTTGCCAA 59.113 34.615 0.00 0.00 0.00 4.52
3337 8275 6.418946 TGGTTCACATACAGTATATTTGCCA 58.581 36.000 0.00 0.00 0.00 4.92
3339 8277 7.786178 TCTGGTTCACATACAGTATATTTGC 57.214 36.000 0.00 0.00 34.02 3.68
3384 8322 8.562892 CAGTAGTTCAACAATCAGTCAATTTCT 58.437 33.333 0.00 0.00 0.00 2.52
3387 8325 6.772716 ACCAGTAGTTCAACAATCAGTCAATT 59.227 34.615 0.00 0.00 0.00 2.32
3393 8331 5.794894 ACCTACCAGTAGTTCAACAATCAG 58.205 41.667 4.23 0.00 0.00 2.90
3412 8350 5.126545 TGAGCTAAGAGTAATTCGCAACCTA 59.873 40.000 0.00 0.00 0.00 3.08
3539 8477 7.269316 TCATGAATAGTGGTCGTTGCTTATAA 58.731 34.615 0.00 0.00 0.00 0.98
3540 8478 6.811954 TCATGAATAGTGGTCGTTGCTTATA 58.188 36.000 0.00 0.00 0.00 0.98
3542 8480 5.079689 TCATGAATAGTGGTCGTTGCTTA 57.920 39.130 0.00 0.00 0.00 3.09
3543 8481 3.937814 TCATGAATAGTGGTCGTTGCTT 58.062 40.909 0.00 0.00 0.00 3.91
3544 8482 3.610040 TCATGAATAGTGGTCGTTGCT 57.390 42.857 0.00 0.00 0.00 3.91
3545 8483 7.652300 TTATATCATGAATAGTGGTCGTTGC 57.348 36.000 0.00 0.00 0.00 4.17
3628 8567 5.237779 CCAATTATATCACCCCGTGTTACAC 59.762 44.000 5.27 5.27 34.79 2.90
3637 8576 5.279456 GGCATCAAACCAATTATATCACCCC 60.279 44.000 0.00 0.00 0.00 4.95
3646 8585 5.709164 CCAATTTTGGGCATCAAACCAATTA 59.291 36.000 1.14 0.00 45.43 1.40
3702 8641 8.345565 CAACTTGATAATCAACCAATAGTAGCC 58.654 37.037 0.00 0.00 32.21 3.93
3734 8674 2.041405 GGTGAGAGGGGGAGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
3735 8675 2.041405 GGGTGAGAGGGGGAGGAG 60.041 72.222 0.00 0.00 0.00 3.69
3736 8676 3.695825 GGGGTGAGAGGGGGAGGA 61.696 72.222 0.00 0.00 0.00 3.71
3737 8677 3.700350 AGGGGTGAGAGGGGGAGG 61.700 72.222 0.00 0.00 0.00 4.30
3738 8678 2.366167 CAGGGGTGAGAGGGGGAG 60.366 72.222 0.00 0.00 0.00 4.30
3739 8679 4.741239 GCAGGGGTGAGAGGGGGA 62.741 72.222 0.00 0.00 0.00 4.81
4209 9149 1.142965 GAGCGGAGGAGGAAGAAGC 59.857 63.158 0.00 0.00 0.00 3.86
4417 9380 1.270305 CGAAGCTGGAGAAGACCAACA 60.270 52.381 0.00 0.00 39.59 3.33
4420 9383 0.832135 ACCGAAGCTGGAGAAGACCA 60.832 55.000 0.00 0.00 38.33 4.02
4422 9385 1.433534 CAACCGAAGCTGGAGAAGAC 58.566 55.000 0.00 0.00 0.00 3.01
4435 9398 2.221299 CCCCCAGAGAACCAACCGA 61.221 63.158 0.00 0.00 0.00 4.69
4436 9399 2.351276 CCCCCAGAGAACCAACCG 59.649 66.667 0.00 0.00 0.00 4.44
4473 9436 3.691342 CGACCACCCGAAGCCTCA 61.691 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.