Multiple sequence alignment - TraesCS3D01G214000

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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 TraesCS3D01G214000 chr3D 100.000 4575 0 0 1 4575 288552225 288547651 0.000000e+00 8449.0
1 TraesCS3D01G214000 chr3D 84.247 146 20 3 499 643 23768155 23768298 6.170000e-29 139.0
2 TraesCS3D01G214000 chr3D 100.000 28 0 0 4055 4082 68326554 68326581 8.000000e-03 52.8
3 TraesCS3D01G214000 chr3B 95.328 2226 74 8 1575 3798 381481665 381479468 0.000000e+00 3507.0
4 TraesCS3D01G214000 chr3B 93.027 674 24 5 892 1564 381482399 381481748 0.000000e+00 963.0
5 TraesCS3D01G214000 chr3B 90.085 353 32 3 4074 4425 381476967 381476617 5.400000e-124 455.0
6 TraesCS3D01G214000 chr3B 93.380 287 14 4 3792 4076 381477640 381477357 1.970000e-113 420.0
7 TraesCS3D01G214000 chr3B 88.889 144 5 4 4413 4553 381466054 381465919 2.830000e-37 167.0
8 TraesCS3D01G214000 chr3A 89.784 2036 131 34 2054 4058 378812353 378810364 0.000000e+00 2536.0
9 TraesCS3D01G214000 chr3A 91.584 808 27 11 757 1564 378815038 378814272 0.000000e+00 1077.0
10 TraesCS3D01G214000 chr3A 83.576 688 72 19 48 726 378815775 378815120 1.410000e-169 606.0
11 TraesCS3D01G214000 chr3A 88.599 421 25 10 4140 4553 378810365 378809961 1.480000e-134 490.0
12 TraesCS3D01G214000 chr3A 97.209 215 6 0 1630 1844 378814153 378813939 9.350000e-97 364.0
13 TraesCS3D01G214000 chr3A 97.260 146 4 0 1845 1990 378812482 378812337 9.830000e-62 248.0
14 TraesCS3D01G214000 chr3A 85.106 141 21 0 501 641 641335779 641335639 1.330000e-30 145.0
15 TraesCS3D01G214000 chr3A 83.333 144 24 0 500 643 600312956 600313099 2.870000e-27 134.0
16 TraesCS3D01G214000 chr3A 97.368 38 1 0 1575 1612 378814189 378814152 1.060000e-06 65.8
17 TraesCS3D01G214000 chr7D 96.154 156 4 2 1620 1774 74596046 74596200 2.110000e-63 254.0
18 TraesCS3D01G214000 chr7D 92.398 171 11 2 1605 1773 535326648 535326818 4.570000e-60 243.0
19 TraesCS3D01G214000 chr7D 97.778 45 0 1 906 950 188163563 188163606 4.910000e-10 76.8
20 TraesCS3D01G214000 chr4D 96.104 154 6 0 1615 1768 74079351 74079504 7.600000e-63 252.0
21 TraesCS3D01G214000 chr4D 98.571 70 1 0 1984 2053 497502144 497502213 1.730000e-24 124.0
22 TraesCS3D01G214000 chr4D 96.053 76 1 2 1978 2053 253934921 253934994 6.220000e-24 122.0
23 TraesCS3D01G214000 chr4D 92.500 40 1 2 4055 4093 259493148 259493186 6.390000e-04 56.5
24 TraesCS3D01G214000 chr2D 95.541 157 6 1 1612 1768 79056164 79056319 2.730000e-62 250.0
25 TraesCS3D01G214000 chr2D 81.633 98 14 4 2554 2648 635142581 635142677 1.360000e-10 78.7
26 TraesCS3D01G214000 chr6D 93.210 162 10 1 1612 1772 303059850 303060011 2.130000e-58 237.0
27 TraesCS3D01G214000 chr6D 83.942 137 22 0 503 639 38244748 38244612 1.030000e-26 132.0
28 TraesCS3D01G214000 chr7B 92.683 164 11 1 1617 1780 245994268 245994106 7.650000e-58 235.0
29 TraesCS3D01G214000 chr7B 86.897 145 19 0 499 643 329852352 329852208 3.660000e-36 163.0
30 TraesCS3D01G214000 chr7B 100.000 68 0 0 1986 2053 420072292 420072225 4.810000e-25 126.0
31 TraesCS3D01G214000 chr7B 96.000 75 1 2 1986 2060 361150497 361150425 2.240000e-23 121.0
32 TraesCS3D01G214000 chr7B 90.244 41 4 0 413 453 70535744 70535784 2.000000e-03 54.7
33 TraesCS3D01G214000 chr6A 93.168 161 10 1 1612 1772 411770250 411770409 7.650000e-58 235.0
34 TraesCS3D01G214000 chr6A 88.652 141 16 0 501 641 123454784 123454924 6.090000e-39 172.0
35 TraesCS3D01G214000 chr6B 88.811 143 14 1 501 641 684417737 684417879 1.690000e-39 174.0
36 TraesCS3D01G214000 chr6B 98.571 70 1 0 1984 2053 142069035 142068966 1.730000e-24 124.0
37 TraesCS3D01G214000 chr5A 89.655 116 11 1 528 643 32933378 32933492 3.690000e-31 147.0
38 TraesCS3D01G214000 chr7A 85.075 134 18 2 501 633 21440341 21440473 7.980000e-28 135.0
39 TraesCS3D01G214000 chr7A 96.000 75 1 2 1986 2060 552975550 552975478 2.240000e-23 121.0
40 TraesCS3D01G214000 chr2B 97.333 75 2 0 1979 2053 717816994 717817068 1.340000e-25 128.0
41 TraesCS3D01G214000 chr1B 100.000 68 0 0 1986 2053 574238132 574238065 4.810000e-25 126.0


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 TraesCS3D01G214000 chr3D 288547651 288552225 4574 True 8449.000000 8449 100.000000 1 4575 1 chr3D.!!$R1 4574
1 TraesCS3D01G214000 chr3B 381476617 381482399 5782 True 1336.250000 3507 92.955000 892 4425 4 chr3B.!!$R2 3533
2 TraesCS3D01G214000 chr3A 378809961 378815775 5814 True 769.542857 2536 92.197143 48 4553 7 chr3A.!!$R2 4505

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
589 596 0.032403 TGCAATTGTGTTGCTGCTCC 59.968 50.0 13.17 0.0 45.13 4.7 F
1015 1075 0.326264 CAGGATGGGCTACCTATGGC 59.674 60.0 0.00 0.0 37.76 4.4 F
2406 4012 1.241315 CGAAATTGGGCGGAACAGGT 61.241 55.0 0.00 0.0 0.00 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 3985 1.438814 GCCCAATTTCGGCCATCTG 59.561 57.895 2.24 0.0 40.78 2.90 R
2759 4378 1.948145 GCTGAATCTTCATCCTGCCAG 59.052 52.381 0.00 0.0 36.46 4.85 R
4308 8195 0.250338 AAACACCAGGCCTCGAAGAC 60.250 55.000 0.00 0.0 0.00 3.01 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
57 58 8.951787 AAACCAGTTAAAACCAGGAATAAAAC 57.048 30.769 0.00 0.00 0.00 2.43
60 61 8.541234 ACCAGTTAAAACCAGGAATAAAACAAA 58.459 29.630 0.00 0.00 0.00 2.83
195 198 8.669946 ACAAAAAGAAACCAAAAGAAAGAACA 57.330 26.923 0.00 0.00 0.00 3.18
196 199 9.114952 ACAAAAAGAAACCAAAAGAAAGAACAA 57.885 25.926 0.00 0.00 0.00 2.83
197 200 9.943163 CAAAAAGAAACCAAAAGAAAGAACAAA 57.057 25.926 0.00 0.00 0.00 2.83
201 204 8.322906 AGAAACCAAAAGAAAGAACAAAAAGG 57.677 30.769 0.00 0.00 0.00 3.11
202 205 8.154203 AGAAACCAAAAGAAAGAACAAAAAGGA 58.846 29.630 0.00 0.00 0.00 3.36
203 206 8.684386 AAACCAAAAGAAAGAACAAAAAGGAA 57.316 26.923 0.00 0.00 0.00 3.36
204 207 8.684386 AACCAAAAGAAAGAACAAAAAGGAAA 57.316 26.923 0.00 0.00 0.00 3.13
205 208 8.684386 ACCAAAAGAAAGAACAAAAAGGAAAA 57.316 26.923 0.00 0.00 0.00 2.29
206 209 8.564574 ACCAAAAGAAAGAACAAAAAGGAAAAC 58.435 29.630 0.00 0.00 0.00 2.43
207 210 8.020819 CCAAAAGAAAGAACAAAAAGGAAAACC 58.979 33.333 0.00 0.00 0.00 3.27
219 222 9.126151 ACAAAAAGGAAAACCAAAAAGAAAGAA 57.874 25.926 0.00 0.00 0.00 2.52
230 233 8.785329 ACCAAAAAGAAAGAAACTATGCAAAA 57.215 26.923 0.00 0.00 0.00 2.44
247 250 3.723542 GCAAAACAGTGAAAAACAACGCC 60.724 43.478 0.00 0.00 0.00 5.68
248 251 2.287393 AACAGTGAAAAACAACGCCC 57.713 45.000 0.00 0.00 0.00 6.13
249 252 1.178276 ACAGTGAAAAACAACGCCCA 58.822 45.000 0.00 0.00 0.00 5.36
251 254 2.952978 ACAGTGAAAAACAACGCCCATA 59.047 40.909 0.00 0.00 0.00 2.74
252 255 3.243267 ACAGTGAAAAACAACGCCCATAC 60.243 43.478 0.00 0.00 0.00 2.39
253 256 2.031508 AGTGAAAAACAACGCCCATACG 60.032 45.455 0.00 0.00 39.50 3.06
254 257 1.267261 TGAAAAACAACGCCCATACGG 59.733 47.619 0.00 0.00 37.37 4.02
255 258 1.536331 GAAAAACAACGCCCATACGGA 59.464 47.619 0.00 0.00 37.37 4.69
258 261 0.390735 AACAACGCCCATACGGAGTC 60.391 55.000 0.00 0.00 45.13 3.36
259 262 1.520787 CAACGCCCATACGGAGTCC 60.521 63.158 0.00 0.00 45.13 3.85
260 263 1.985662 AACGCCCATACGGAGTCCA 60.986 57.895 10.49 0.00 45.13 4.02
265 270 1.686325 CCCATACGGAGTCCACCCAG 61.686 65.000 10.49 0.00 43.93 4.45
270 275 0.178941 ACGGAGTCCACCCAGTACTT 60.179 55.000 10.49 0.00 29.74 2.24
278 283 2.835764 TCCACCCAGTACTTTAGCGATT 59.164 45.455 0.00 0.00 0.00 3.34
279 284 3.262405 TCCACCCAGTACTTTAGCGATTT 59.738 43.478 0.00 0.00 0.00 2.17
294 299 1.399791 CGATTTGAGGAAGCTTCAGGC 59.600 52.381 27.02 15.55 42.19 4.85
312 317 2.475200 GCGAGGCCATGTTACATTTC 57.525 50.000 5.01 0.00 0.00 2.17
315 320 2.285220 CGAGGCCATGTTACATTTCTCG 59.715 50.000 19.21 19.21 37.21 4.04
316 321 2.614057 GAGGCCATGTTACATTTCTCGG 59.386 50.000 5.01 0.00 0.00 4.63
322 327 4.260212 CCATGTTACATTTCTCGGTAAGCG 60.260 45.833 0.00 0.00 30.70 4.68
328 333 5.455056 ACATTTCTCGGTAAGCGAGATAT 57.545 39.130 0.00 0.00 41.36 1.63
345 350 5.901884 CGAGATATAACCATGACGCAAAAAC 59.098 40.000 0.00 0.00 0.00 2.43
346 351 6.456315 CGAGATATAACCATGACGCAAAAACA 60.456 38.462 0.00 0.00 0.00 2.83
349 354 7.915397 AGATATAACCATGACGCAAAAACAATC 59.085 33.333 0.00 0.00 0.00 2.67
350 355 3.025287 ACCATGACGCAAAAACAATCC 57.975 42.857 0.00 0.00 0.00 3.01
351 356 2.363680 ACCATGACGCAAAAACAATCCA 59.636 40.909 0.00 0.00 0.00 3.41
357 362 1.526464 CGCAAAAACAATCCAGGCAAC 59.474 47.619 0.00 0.00 0.00 4.17
358 363 1.872952 GCAAAAACAATCCAGGCAACC 59.127 47.619 0.00 0.00 37.17 3.77
359 364 2.744494 GCAAAAACAATCCAGGCAACCA 60.744 45.455 0.00 0.00 37.17 3.67
360 365 3.539604 CAAAAACAATCCAGGCAACCAA 58.460 40.909 0.00 0.00 37.17 3.67
361 366 3.922171 AAAACAATCCAGGCAACCAAA 57.078 38.095 0.00 0.00 37.17 3.28
362 367 4.436113 AAAACAATCCAGGCAACCAAAT 57.564 36.364 0.00 0.00 37.17 2.32
363 368 5.559148 AAAACAATCCAGGCAACCAAATA 57.441 34.783 0.00 0.00 37.17 1.40
364 369 5.559148 AAACAATCCAGGCAACCAAATAA 57.441 34.783 0.00 0.00 37.17 1.40
365 370 4.806640 ACAATCCAGGCAACCAAATAAG 57.193 40.909 0.00 0.00 37.17 1.73
377 382 6.017357 GGCAACCAAATAAGTACATAGGCTAC 60.017 42.308 0.00 0.00 0.00 3.58
387 392 1.249407 CATAGGCTACGGACCTCCTC 58.751 60.000 0.00 0.00 38.81 3.71
398 403 1.410882 GGACCTCCTCTGTGCTATCAC 59.589 57.143 0.00 0.00 43.40 3.06
411 416 3.057315 GTGCTATCACACACTTGCCAAAT 60.057 43.478 0.00 0.00 42.66 2.32
455 461 1.021390 CCATCGCCACACTCTTCCAC 61.021 60.000 0.00 0.00 0.00 4.02
465 471 1.080705 CTCTTCCACGTCGTGACCC 60.081 63.158 26.53 0.00 35.23 4.46
466 472 1.524863 CTCTTCCACGTCGTGACCCT 61.525 60.000 26.53 0.00 35.23 4.34
467 473 1.372997 CTTCCACGTCGTGACCCTG 60.373 63.158 26.53 9.46 35.23 4.45
478 484 3.701040 GTCGTGACCCTGTAAACCCTATA 59.299 47.826 0.00 0.00 0.00 1.31
483 489 4.141574 TGACCCTGTAAACCCTATATGTGC 60.142 45.833 0.00 0.00 0.00 4.57
487 493 5.003804 CCTGTAAACCCTATATGTGCATCC 58.996 45.833 0.00 0.00 0.00 3.51
497 503 6.266558 CCCTATATGTGCATCCTCCTATACTC 59.733 46.154 0.00 0.00 0.00 2.59
521 527 1.188219 TGCCTGTTCGGAAGCTCTCT 61.188 55.000 0.00 0.00 33.16 3.10
535 541 4.216411 AGCTCTCTAGTCTCGAAACTCT 57.784 45.455 0.00 0.00 0.00 3.24
542 548 1.061485 GTCTCGAAACTCTGTTCCGC 58.939 55.000 0.00 0.00 0.00 5.54
543 549 0.386858 TCTCGAAACTCTGTTCCGCG 60.387 55.000 0.00 0.00 0.00 6.46
544 550 0.663568 CTCGAAACTCTGTTCCGCGT 60.664 55.000 4.92 0.00 0.00 6.01
545 551 0.937699 TCGAAACTCTGTTCCGCGTG 60.938 55.000 4.92 0.00 0.00 5.34
546 552 1.213094 CGAAACTCTGTTCCGCGTGT 61.213 55.000 4.92 0.00 0.00 4.49
547 553 0.232303 GAAACTCTGTTCCGCGTGTG 59.768 55.000 4.92 0.00 0.00 3.82
548 554 1.157870 AAACTCTGTTCCGCGTGTGG 61.158 55.000 4.92 0.00 0.00 4.17
580 587 0.609662 GCCAATCCCTGCAATTGTGT 59.390 50.000 7.40 0.00 33.22 3.72
583 590 2.070783 CAATCCCTGCAATTGTGTTGC 58.929 47.619 7.40 5.85 45.11 4.17
586 593 0.947180 CCCTGCAATTGTGTTGCTGC 60.947 55.000 13.17 0.00 45.13 5.25
587 594 0.032952 CCTGCAATTGTGTTGCTGCT 59.967 50.000 13.17 0.00 45.13 4.24
589 596 0.032403 TGCAATTGTGTTGCTGCTCC 59.968 50.000 13.17 0.00 45.13 4.70
592 599 1.342174 CAATTGTGTTGCTGCTCCCTT 59.658 47.619 0.00 0.00 0.00 3.95
594 601 1.165907 TTGTGTTGCTGCTCCCTTCG 61.166 55.000 0.00 0.00 0.00 3.79
595 602 2.669569 TGTTGCTGCTCCCTTCGC 60.670 61.111 0.00 0.00 0.00 4.70
596 603 2.359230 GTTGCTGCTCCCTTCGCT 60.359 61.111 0.00 0.00 0.00 4.93
598 605 3.612247 TTGCTGCTCCCTTCGCTCC 62.612 63.158 0.00 0.00 0.00 4.70
600 607 4.521062 CTGCTCCCTTCGCTCCGG 62.521 72.222 0.00 0.00 0.00 5.14
615 622 3.052082 CGGGAGCTGCAGTTGTGG 61.052 66.667 16.64 0.00 0.00 4.17
622 629 2.031012 TGCAGTTGTGGAGCGGAG 59.969 61.111 0.00 0.00 0.00 4.63
679 686 1.704641 ACTCCTGGTTTTTGCTTCCC 58.295 50.000 0.00 0.00 0.00 3.97
683 690 0.969149 CTGGTTTTTGCTTCCCCCTC 59.031 55.000 0.00 0.00 0.00 4.30
701 708 3.057315 CCCTCATCGATTGCAACTTTTGT 60.057 43.478 0.00 0.00 0.00 2.83
789 847 4.856664 AGATGATCTCGATTGCAATTTGC 58.143 39.130 14.33 14.49 45.29 3.68
797 855 5.643348 TCTCGATTGCAATTTGCTTTCTCTA 59.357 36.000 21.19 0.00 45.31 2.43
815 873 5.592054 TCTCTAAATTATGTCTCAGGCACG 58.408 41.667 0.00 0.00 0.00 5.34
869 927 1.555075 CCCAGCTGGTAGCACTCTTTA 59.445 52.381 30.63 0.00 45.56 1.85
990 1050 1.922570 GAGCAAATCGGCGACTAAGA 58.077 50.000 13.76 0.00 39.27 2.10
991 1051 2.268298 GAGCAAATCGGCGACTAAGAA 58.732 47.619 13.76 0.00 39.27 2.52
1015 1075 0.326264 CAGGATGGGCTACCTATGGC 59.674 60.000 0.00 0.00 37.76 4.40
1375 1435 4.759516 TCTGGTGTTAAATTCTTTCGCC 57.240 40.909 0.00 0.00 0.00 5.54
1564 1624 3.350219 TCTGATTTACCTGGGTGCTTC 57.650 47.619 2.07 0.00 0.00 3.86
1618 1767 8.824159 ATGTACTGATGACTTTGCATATACTC 57.176 34.615 0.00 0.00 0.00 2.59
1619 1768 7.210174 TGTACTGATGACTTTGCATATACTCC 58.790 38.462 0.00 0.00 0.00 3.85
1620 1769 5.615289 ACTGATGACTTTGCATATACTCCC 58.385 41.667 0.00 0.00 0.00 4.30
1621 1770 4.973168 TGATGACTTTGCATATACTCCCC 58.027 43.478 0.00 0.00 0.00 4.81
1622 1771 3.857157 TGACTTTGCATATACTCCCCC 57.143 47.619 0.00 0.00 0.00 5.40
1886 3491 6.673154 AAAATAACTCGTACAATAGGGTGC 57.327 37.500 0.00 0.00 0.00 5.01
1996 3601 3.988379 GAGCATCTCCAACAACAACAA 57.012 42.857 0.00 0.00 0.00 2.83
1997 3602 3.632189 GAGCATCTCCAACAACAACAAC 58.368 45.455 0.00 0.00 0.00 3.32
1998 3603 3.023119 AGCATCTCCAACAACAACAACA 58.977 40.909 0.00 0.00 0.00 3.33
1999 3604 3.446873 AGCATCTCCAACAACAACAACAA 59.553 39.130 0.00 0.00 0.00 2.83
2000 3605 3.551485 GCATCTCCAACAACAACAACAAC 59.449 43.478 0.00 0.00 0.00 3.32
2001 3606 4.742417 CATCTCCAACAACAACAACAACA 58.258 39.130 0.00 0.00 0.00 3.33
2002 3607 4.855715 TCTCCAACAACAACAACAACAA 57.144 36.364 0.00 0.00 0.00 2.83
2003 3608 4.551388 TCTCCAACAACAACAACAACAAC 58.449 39.130 0.00 0.00 0.00 3.32
2004 3609 4.038042 TCTCCAACAACAACAACAACAACA 59.962 37.500 0.00 0.00 0.00 3.33
2005 3610 4.693283 TCCAACAACAACAACAACAACAA 58.307 34.783 0.00 0.00 0.00 2.83
2006 3611 4.508124 TCCAACAACAACAACAACAACAAC 59.492 37.500 0.00 0.00 0.00 3.32
2007 3612 4.271049 CCAACAACAACAACAACAACAACA 59.729 37.500 0.00 0.00 0.00 3.33
2008 3613 5.220662 CCAACAACAACAACAACAACAACAA 60.221 36.000 0.00 0.00 0.00 2.83
2084 3689 4.021192 TCTCCAACAGATGCCCAAAAATTC 60.021 41.667 0.00 0.00 0.00 2.17
2085 3690 3.007831 TCCAACAGATGCCCAAAAATTCC 59.992 43.478 0.00 0.00 0.00 3.01
2088 3693 2.029110 ACAGATGCCCAAAAATTCCGTG 60.029 45.455 0.00 0.00 0.00 4.94
2093 3698 1.551452 CCCAAAAATTCCGTGCCCTA 58.449 50.000 0.00 0.00 0.00 3.53
2127 3732 5.941948 AGGTGACGAATTAGAAGGTTTTG 57.058 39.130 0.00 0.00 0.00 2.44
2181 3787 3.708451 CCCTAAAACTGGTGCCCTAAAT 58.292 45.455 0.00 0.00 0.00 1.40
2264 3870 3.792736 GGTAGCATGGGGACGGCA 61.793 66.667 0.00 0.00 35.88 5.69
2325 3931 2.668550 GTGGTGCTTGGGGACGAC 60.669 66.667 0.00 0.00 35.76 4.34
2328 3934 2.264794 GTGCTTGGGGACGACGAT 59.735 61.111 0.00 0.00 0.00 3.73
2379 3985 2.046892 ATGGTGTGGAGCGCAGTC 60.047 61.111 11.47 0.00 0.00 3.51
2380 3986 2.786539 GATGGTGTGGAGCGCAGTCA 62.787 60.000 11.47 0.94 0.00 3.41
2406 4012 1.241315 CGAAATTGGGCGGAACAGGT 61.241 55.000 0.00 0.00 0.00 4.00
2759 4378 2.562298 TCCAAACCAGCAATTGTCCATC 59.438 45.455 7.40 0.00 0.00 3.51
3044 4664 5.329399 AGTTTGCCAACTTATTGTATGGGA 58.671 37.500 0.00 0.00 40.66 4.37
3138 4761 3.748048 CAGCCGAACCTGGATATATTGTG 59.252 47.826 0.00 0.00 0.00 3.33
3142 4765 2.185004 ACCTGGATATATTGTGCGCC 57.815 50.000 4.18 0.00 0.00 6.53
3257 4880 5.302568 TGATCCTTGTGATGTTTCTGCTTTT 59.697 36.000 0.00 0.00 32.41 2.27
3478 5108 1.741028 TCCAGGTGGAGGATGTCAAA 58.259 50.000 0.00 0.00 39.78 2.69
3778 5409 5.536538 TCGTTAATGAGTCAGCCTATCTCAT 59.463 40.000 0.00 5.38 46.54 2.90
3820 7285 6.138761 GTCTTCCATCAATATGTTCGCAATC 58.861 40.000 0.00 0.00 0.00 2.67
3838 7303 8.926715 TCGCAATCGATATAGCAAGTTTATAT 57.073 30.769 14.99 0.00 40.21 0.86
3886 7351 5.012239 AGCATTTTATCAGCTTTCCTGTGA 58.988 37.500 0.00 0.00 42.38 3.58
3997 7490 6.154203 TGATCTGACAGGTGAGATTGTATC 57.846 41.667 1.81 0.00 33.72 2.24
4062 7556 7.558444 TCTTGTTGTTTGTTACCAATTACTCCT 59.442 33.333 0.00 0.00 0.00 3.69
4064 7558 7.708998 TGTTGTTTGTTACCAATTACTCCTTC 58.291 34.615 0.00 0.00 0.00 3.46
4065 7559 7.558444 TGTTGTTTGTTACCAATTACTCCTTCT 59.442 33.333 0.00 0.00 0.00 2.85
4113 7999 5.796350 AAGCTATGTTAGGCTTGTAAACG 57.204 39.130 0.00 0.00 45.49 3.60
4125 8011 9.724839 TTAGGCTTGTAAACGATATTATTTTGC 57.275 29.630 0.00 0.00 0.00 3.68
4129 8015 6.922247 TGTAAACGATATTATTTTGCGGGA 57.078 33.333 0.00 0.00 0.00 5.14
4167 8053 6.811253 TTTATTAAATCCTGTCGTGCTGTT 57.189 33.333 0.00 0.00 0.00 3.16
4208 8095 3.068024 TGAGTGAATTTGGTTTGTGAGGC 59.932 43.478 0.00 0.00 0.00 4.70
4303 8190 1.004044 CTGGCATTCTTGGGAGTCTGT 59.996 52.381 0.00 0.00 0.00 3.41
4308 8195 2.526304 TTCTTGGGAGTCTGTCAACG 57.474 50.000 0.00 0.00 0.00 4.10
4394 8281 3.861886 GCAATGTCACACCCTTCCATTTG 60.862 47.826 0.00 0.00 0.00 2.32
4395 8282 1.327303 TGTCACACCCTTCCATTTGC 58.673 50.000 0.00 0.00 0.00 3.68
4411 8298 4.081531 CCATTTGCAGGTGTGGTTGAATAT 60.082 41.667 0.00 0.00 0.00 1.28
4457 8347 4.703093 GCTCTGGATAGGGTATGAGTACTC 59.297 50.000 16.32 16.32 0.00 2.59
4476 8366 1.811965 TCACCAATTCATGCTTCCACG 59.188 47.619 0.00 0.00 0.00 4.94
4477 8367 1.811965 CACCAATTCATGCTTCCACGA 59.188 47.619 0.00 0.00 0.00 4.35
4478 8368 1.812571 ACCAATTCATGCTTCCACGAC 59.187 47.619 0.00 0.00 0.00 4.34
4479 8369 2.086869 CCAATTCATGCTTCCACGACT 58.913 47.619 0.00 0.00 0.00 4.18
4480 8370 2.096496 CCAATTCATGCTTCCACGACTC 59.904 50.000 0.00 0.00 0.00 3.36
4481 8371 2.029838 ATTCATGCTTCCACGACTCC 57.970 50.000 0.00 0.00 0.00 3.85
4482 8372 0.684535 TTCATGCTTCCACGACTCCA 59.315 50.000 0.00 0.00 0.00 3.86
4483 8373 0.037326 TCATGCTTCCACGACTCCAC 60.037 55.000 0.00 0.00 0.00 4.02
4484 8374 1.079819 ATGCTTCCACGACTCCACG 60.080 57.895 0.00 0.00 39.31 4.94
4486 8376 1.300697 GCTTCCACGACTCCACGTT 60.301 57.895 0.00 0.00 44.76 3.99
4489 8379 1.538512 CTTCCACGACTCCACGTTCTA 59.461 52.381 0.00 0.00 44.76 2.10
4571 8465 9.872721 ATTGCATATACTCATATGAAGAGAGTG 57.127 33.333 6.90 3.57 44.70 3.51
4572 8466 7.834803 TGCATATACTCATATGAAGAGAGTGG 58.165 38.462 6.90 0.00 44.70 4.00
4573 8467 7.671398 TGCATATACTCATATGAAGAGAGTGGA 59.329 37.037 6.90 1.03 44.70 4.02
4574 8468 8.526978 GCATATACTCATATGAAGAGAGTGGAA 58.473 37.037 6.90 0.00 44.70 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.961264 TTTTATTCCTGGTTTTAACTGGTTTTT 57.039 25.926 0.00 0.00 0.00 1.94
31 32 9.386010 GTTTTATTCCTGGTTTTAACTGGTTTT 57.614 29.630 0.00 0.00 0.00 2.43
32 33 8.541234 TGTTTTATTCCTGGTTTTAACTGGTTT 58.459 29.630 0.00 0.00 0.00 3.27
33 34 8.080363 TGTTTTATTCCTGGTTTTAACTGGTT 57.920 30.769 0.00 0.00 0.00 3.67
34 35 7.663043 TGTTTTATTCCTGGTTTTAACTGGT 57.337 32.000 0.00 0.00 0.00 4.00
35 36 8.950208 TTTGTTTTATTCCTGGTTTTAACTGG 57.050 30.769 0.00 0.00 0.00 4.00
136 139 5.411361 GGTTTTCTTTGCCTGTTTGTTTTCT 59.589 36.000 0.00 0.00 0.00 2.52
177 180 8.317891 TCCTTTTTGTTCTTTCTTTTGGTTTC 57.682 30.769 0.00 0.00 0.00 2.78
183 186 8.684386 TGGTTTTCCTTTTTGTTCTTTCTTTT 57.316 26.923 0.00 0.00 41.38 2.27
195 198 9.959749 GTTTCTTTCTTTTTGGTTTTCCTTTTT 57.040 25.926 0.00 0.00 41.38 1.94
196 199 9.349713 AGTTTCTTTCTTTTTGGTTTTCCTTTT 57.650 25.926 0.00 0.00 41.38 2.27
197 200 8.918202 AGTTTCTTTCTTTTTGGTTTTCCTTT 57.082 26.923 0.00 0.00 41.38 3.11
199 202 9.599866 CATAGTTTCTTTCTTTTTGGTTTTCCT 57.400 29.630 0.00 0.00 41.38 3.36
200 203 8.335356 GCATAGTTTCTTTCTTTTTGGTTTTCC 58.665 33.333 0.00 0.00 41.14 3.13
201 204 8.878769 TGCATAGTTTCTTTCTTTTTGGTTTTC 58.121 29.630 0.00 0.00 0.00 2.29
202 205 8.785329 TGCATAGTTTCTTTCTTTTTGGTTTT 57.215 26.923 0.00 0.00 0.00 2.43
203 206 8.785329 TTGCATAGTTTCTTTCTTTTTGGTTT 57.215 26.923 0.00 0.00 0.00 3.27
204 207 8.785329 TTTGCATAGTTTCTTTCTTTTTGGTT 57.215 26.923 0.00 0.00 0.00 3.67
205 208 8.664798 GTTTTGCATAGTTTCTTTCTTTTTGGT 58.335 29.630 0.00 0.00 0.00 3.67
206 209 8.663911 TGTTTTGCATAGTTTCTTTCTTTTTGG 58.336 29.630 0.00 0.00 0.00 3.28
207 210 9.693157 CTGTTTTGCATAGTTTCTTTCTTTTTG 57.307 29.630 0.00 0.00 0.00 2.44
219 222 7.411372 CGTTGTTTTTCACTGTTTTGCATAGTT 60.411 33.333 0.00 0.00 0.00 2.24
224 227 3.120854 GCGTTGTTTTTCACTGTTTTGCA 60.121 39.130 0.00 0.00 0.00 4.08
230 233 1.178276 TGGGCGTTGTTTTTCACTGT 58.822 45.000 0.00 0.00 0.00 3.55
247 250 0.976073 ACTGGGTGGACTCCGTATGG 60.976 60.000 0.00 0.00 0.00 2.74
248 251 1.407979 GTACTGGGTGGACTCCGTATG 59.592 57.143 0.00 0.00 0.00 2.39
249 252 1.287146 AGTACTGGGTGGACTCCGTAT 59.713 52.381 0.00 0.00 0.00 3.06
251 254 0.178941 AAGTACTGGGTGGACTCCGT 60.179 55.000 0.00 0.00 0.00 4.69
252 255 0.974383 AAAGTACTGGGTGGACTCCG 59.026 55.000 0.00 0.00 0.00 4.63
253 256 2.093606 GCTAAAGTACTGGGTGGACTCC 60.094 54.545 0.00 0.00 0.00 3.85
254 257 2.416972 CGCTAAAGTACTGGGTGGACTC 60.417 54.545 0.00 0.00 0.00 3.36
255 258 1.549170 CGCTAAAGTACTGGGTGGACT 59.451 52.381 0.00 0.00 0.00 3.85
257 260 1.927487 TCGCTAAAGTACTGGGTGGA 58.073 50.000 0.00 0.00 0.00 4.02
258 261 2.981859 ATCGCTAAAGTACTGGGTGG 57.018 50.000 0.00 0.00 0.00 4.61
259 262 4.250464 TCAAATCGCTAAAGTACTGGGTG 58.750 43.478 0.00 0.00 0.00 4.61
260 263 4.504858 CTCAAATCGCTAAAGTACTGGGT 58.495 43.478 0.00 0.00 0.00 4.51
265 270 4.870991 AGCTTCCTCAAATCGCTAAAGTAC 59.129 41.667 0.00 0.00 0.00 2.73
270 275 3.935203 CTGAAGCTTCCTCAAATCGCTAA 59.065 43.478 23.42 0.00 0.00 3.09
278 283 0.036952 CTCGCCTGAAGCTTCCTCAA 60.037 55.000 23.42 3.99 40.39 3.02
279 284 1.593787 CTCGCCTGAAGCTTCCTCA 59.406 57.895 23.42 5.15 40.39 3.86
294 299 2.285220 CGAGAAATGTAACATGGCCTCG 59.715 50.000 3.32 0.00 36.74 4.63
302 307 4.177165 TCGCTTACCGAGAAATGTAACA 57.823 40.909 0.00 0.00 41.89 2.41
315 320 4.857588 CGTCATGGTTATATCTCGCTTACC 59.142 45.833 0.00 0.00 0.00 2.85
316 321 4.323868 GCGTCATGGTTATATCTCGCTTAC 59.676 45.833 0.00 0.00 39.43 2.34
322 327 6.781138 TGTTTTTGCGTCATGGTTATATCTC 58.219 36.000 0.00 0.00 0.00 2.75
328 333 4.038042 TGGATTGTTTTTGCGTCATGGTTA 59.962 37.500 0.00 0.00 0.00 2.85
345 350 4.806640 ACTTATTTGGTTGCCTGGATTG 57.193 40.909 0.00 0.00 0.00 2.67
346 351 5.329399 TGTACTTATTTGGTTGCCTGGATT 58.671 37.500 0.00 0.00 0.00 3.01
349 354 5.299279 CCTATGTACTTATTTGGTTGCCTGG 59.701 44.000 0.00 0.00 0.00 4.45
350 355 5.221048 GCCTATGTACTTATTTGGTTGCCTG 60.221 44.000 0.00 0.00 0.00 4.85
351 356 4.887655 GCCTATGTACTTATTTGGTTGCCT 59.112 41.667 0.00 0.00 0.00 4.75
357 362 5.924825 GTCCGTAGCCTATGTACTTATTTGG 59.075 44.000 0.00 0.00 0.00 3.28
358 363 5.924825 GGTCCGTAGCCTATGTACTTATTTG 59.075 44.000 0.00 0.00 0.00 2.32
359 364 5.837438 AGGTCCGTAGCCTATGTACTTATTT 59.163 40.000 0.00 0.00 33.97 1.40
360 365 5.392125 AGGTCCGTAGCCTATGTACTTATT 58.608 41.667 0.00 0.00 33.97 1.40
361 366 4.995536 AGGTCCGTAGCCTATGTACTTAT 58.004 43.478 0.00 0.00 33.97 1.73
362 367 4.392940 GAGGTCCGTAGCCTATGTACTTA 58.607 47.826 0.00 0.00 36.29 2.24
363 368 3.220940 GAGGTCCGTAGCCTATGTACTT 58.779 50.000 0.00 0.00 36.29 2.24
364 369 2.488710 GGAGGTCCGTAGCCTATGTACT 60.489 54.545 0.00 0.00 36.29 2.73
365 370 1.885233 GGAGGTCCGTAGCCTATGTAC 59.115 57.143 0.00 0.00 36.29 2.90
377 382 0.671251 GATAGCACAGAGGAGGTCCG 59.329 60.000 0.00 0.00 42.08 4.79
398 403 7.599630 AAATATAAGCAATTTGGCAAGTGTG 57.400 32.000 12.74 8.20 35.83 3.82
411 416 7.382898 GTGTTTGGGAGGAAAAATATAAGCAA 58.617 34.615 0.00 0.00 0.00 3.91
455 461 0.668401 GGGTTTACAGGGTCACGACG 60.668 60.000 0.00 0.00 0.00 5.12
465 471 5.869579 AGGATGCACATATAGGGTTTACAG 58.130 41.667 0.00 0.00 0.00 2.74
466 472 5.221843 GGAGGATGCACATATAGGGTTTACA 60.222 44.000 0.00 0.00 0.00 2.41
467 473 5.013183 AGGAGGATGCACATATAGGGTTTAC 59.987 44.000 0.00 0.00 0.00 2.01
478 484 4.139162 AGGAGTATAGGAGGATGCACAT 57.861 45.455 0.00 0.00 0.00 3.21
483 489 4.020543 GGCACTAGGAGTATAGGAGGATG 58.979 52.174 0.00 0.00 0.00 3.51
487 493 4.107127 ACAGGCACTAGGAGTATAGGAG 57.893 50.000 0.00 0.00 36.02 3.69
497 503 0.741221 GCTTCCGAACAGGCACTAGG 60.741 60.000 0.00 0.00 40.77 3.02
521 527 2.095364 GCGGAACAGAGTTTCGAGACTA 60.095 50.000 14.22 0.00 0.00 2.59
535 541 3.858868 GAGCTCCACACGCGGAACA 62.859 63.158 12.47 0.00 33.65 3.18
542 548 1.284982 CTCAAACCGAGCTCCACACG 61.285 60.000 8.47 0.00 34.18 4.49
543 549 2.533318 CTCAAACCGAGCTCCACAC 58.467 57.895 8.47 0.00 34.18 3.82
580 587 2.046892 GAGCGAAGGGAGCAGCAA 60.047 61.111 0.00 0.00 37.01 3.91
583 590 4.521062 CCGGAGCGAAGGGAGCAG 62.521 72.222 0.00 0.00 37.01 4.24
595 602 2.435586 CAACTGCAGCTCCCGGAG 60.436 66.667 15.27 10.41 0.00 4.63
596 603 3.241530 ACAACTGCAGCTCCCGGA 61.242 61.111 15.27 0.00 0.00 5.14
598 605 3.052082 CCACAACTGCAGCTCCCG 61.052 66.667 15.27 0.00 0.00 5.14
599 606 1.673665 CTCCACAACTGCAGCTCCC 60.674 63.158 15.27 0.00 0.00 4.30
600 607 2.331132 GCTCCACAACTGCAGCTCC 61.331 63.158 15.27 0.00 0.00 4.70
601 608 2.675056 CGCTCCACAACTGCAGCTC 61.675 63.158 15.27 0.00 0.00 4.09
615 622 2.491693 CCTATTCAGATCCTCTCCGCTC 59.508 54.545 0.00 0.00 0.00 5.03
619 626 1.905894 GGCCCTATTCAGATCCTCTCC 59.094 57.143 0.00 0.00 0.00 3.71
622 629 5.487131 AGAATAAGGCCCTATTCAGATCCTC 59.513 44.000 28.13 7.00 39.69 3.71
629 636 9.739276 CATTACAATAGAATAAGGCCCTATTCA 57.261 33.333 28.13 17.76 39.69 2.57
633 640 7.516209 AGTCCATTACAATAGAATAAGGCCCTA 59.484 37.037 0.00 0.00 0.00 3.53
635 642 6.543735 AGTCCATTACAATAGAATAAGGCCC 58.456 40.000 0.00 0.00 0.00 5.80
637 644 9.425577 GAGTAGTCCATTACAATAGAATAAGGC 57.574 37.037 0.00 0.00 0.00 4.35
638 645 9.930693 GGAGTAGTCCATTACAATAGAATAAGG 57.069 37.037 12.02 0.00 43.31 2.69
679 686 3.057315 ACAAAAGTTGCAATCGATGAGGG 60.057 43.478 0.59 0.00 0.00 4.30
763 821 7.572539 GCAAATTGCAATCGAGATCATCTATCA 60.573 37.037 13.38 0.00 44.26 2.15
789 847 7.254252 CGTGCCTGAGACATAATTTAGAGAAAG 60.254 40.741 0.00 0.00 0.00 2.62
797 855 3.009723 CCACGTGCCTGAGACATAATTT 58.990 45.455 10.91 0.00 0.00 1.82
844 902 4.537433 GCTACCAGCTGGGCCTCG 62.537 72.222 35.42 18.85 42.05 4.63
986 1046 1.645402 GCCCATCCTGCCCCTTCTTA 61.645 60.000 0.00 0.00 0.00 2.10
989 1049 2.078665 TAGCCCATCCTGCCCCTTC 61.079 63.158 0.00 0.00 0.00 3.46
990 1050 2.044450 TAGCCCATCCTGCCCCTT 59.956 61.111 0.00 0.00 0.00 3.95
991 1051 2.774351 GTAGCCCATCCTGCCCCT 60.774 66.667 0.00 0.00 0.00 4.79
1047 1107 3.760035 ACCGCTGAAGCCGTCGAT 61.760 61.111 0.00 0.00 37.91 3.59
1145 1205 2.322999 CTAAAAGGCGATGCGGGTGC 62.323 60.000 0.00 0.00 43.20 5.01
1146 1206 1.721487 CTAAAAGGCGATGCGGGTG 59.279 57.895 0.00 0.00 0.00 4.61
1147 1207 2.112815 GCTAAAAGGCGATGCGGGT 61.113 57.895 0.00 0.00 0.00 5.28
1148 1208 2.715624 GCTAAAAGGCGATGCGGG 59.284 61.111 0.00 0.00 0.00 6.13
1149 1209 2.715624 GGCTAAAAGGCGATGCGG 59.284 61.111 0.00 0.00 0.00 5.69
1159 1219 0.601057 GCAAAAGGAGCCGGCTAAAA 59.399 50.000 32.97 0.00 0.00 1.52
1237 1297 4.576463 AGAAATGGCTACATCAAATCGGAC 59.424 41.667 0.00 0.00 35.94 4.79
1375 1435 5.292101 GGAAATGGAGTTCTGATACAACGAG 59.708 44.000 0.00 0.00 0.00 4.18
1545 1605 3.012518 CAGAAGCACCCAGGTAAATCAG 58.987 50.000 0.00 0.00 0.00 2.90
1564 1624 8.674263 AATTCCTAGCTGAGAACATAAATCAG 57.326 34.615 0.00 0.00 42.70 2.90
1619 1768 5.130350 ACATCTTATATTTGTGAACGGGGG 58.870 41.667 0.00 0.00 0.00 5.40
1620 1769 6.542370 AGAACATCTTATATTTGTGAACGGGG 59.458 38.462 0.00 0.00 0.00 5.73
1621 1770 7.553881 AGAACATCTTATATTTGTGAACGGG 57.446 36.000 0.00 0.00 0.00 5.28
1622 1771 9.916397 GTTAGAACATCTTATATTTGTGAACGG 57.084 33.333 0.00 0.00 0.00 4.44
1662 1811 6.809689 CACTAAAACGTGTCTGTATACATCCA 59.190 38.462 5.91 3.35 0.00 3.41
1751 1900 2.635915 ACAAATACTCCCTCCGTTCACA 59.364 45.455 0.00 0.00 0.00 3.58
1802 1951 7.430441 ACTGAAGTCTAAAACTGACTCTTCTC 58.570 38.462 0.00 0.00 43.16 2.87
1886 3491 6.531594 TCTTTGTATACAATCAGCTTCAGACG 59.468 38.462 18.69 0.00 35.55 4.18
1994 3599 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
1995 3600 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
1996 3601 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
1997 3602 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
1998 3603 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
1999 3604 5.503194 GCTTTGTTGTTGTTGTTGTTGTTGT 60.503 36.000 0.00 0.00 0.00 3.32
2000 3605 4.903016 GCTTTGTTGTTGTTGTTGTTGTTG 59.097 37.500 0.00 0.00 0.00 3.33
2001 3606 4.024472 GGCTTTGTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
2002 3607 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
2003 3608 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
2004 3609 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
2005 3610 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
2006 3611 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
2007 3612 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
2008 3613 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
2049 3654 4.977132 ATCTGTTGGAGATGCTCTTAAGCG 60.977 45.833 0.00 0.00 41.30 4.68
2084 3689 3.394674 AAAACCATTTTTAGGGCACGG 57.605 42.857 0.00 0.00 32.90 4.94
2093 3698 8.852135 TCTAATTCGTCACCTAAAACCATTTTT 58.148 29.630 0.00 0.00 38.51 1.94
2127 3732 2.874052 GCAAAACCTTTTATGGTGCCCC 60.874 50.000 0.00 0.00 40.73 5.80
2181 3787 2.942804 TGTTCCATGTGGCTCTCAAAA 58.057 42.857 0.00 0.00 34.44 2.44
2264 3870 2.283388 TGTCCCCGAGTTACCGCT 60.283 61.111 0.00 0.00 0.00 5.52
2325 3931 2.124570 CACCCCAAGCTCCCATCG 60.125 66.667 0.00 0.00 0.00 3.84
2379 3985 1.438814 GCCCAATTTCGGCCATCTG 59.561 57.895 2.24 0.00 40.78 2.90
2380 3986 2.120909 CGCCCAATTTCGGCCATCT 61.121 57.895 2.24 0.00 43.98 2.90
2759 4378 1.948145 GCTGAATCTTCATCCTGCCAG 59.052 52.381 0.00 0.00 36.46 4.85
3044 4664 3.828451 AGCTTGTTGGTAGTTCATTGCAT 59.172 39.130 0.00 0.00 0.00 3.96
3138 4761 0.242825 GGTTGGAAAAGTAAGGGCGC 59.757 55.000 0.00 0.00 0.00 6.53
3142 4765 2.572209 TCCCGGTTGGAAAAGTAAGG 57.428 50.000 0.00 0.00 41.40 2.69
3257 4880 5.982516 AGTTGCAACATCTAAATTCGCAAAA 59.017 32.000 30.11 0.00 39.36 2.44
3478 5108 7.811713 GCTTCATAGTGCTTTTCAGAAATTCTT 59.188 33.333 0.00 0.00 0.00 2.52
3778 5409 6.770303 TGGAAGACAGATCACAAACATAACAA 59.230 34.615 0.00 0.00 0.00 2.83
3843 7308 5.853936 TGCTCAACACACAGACTAGTAATT 58.146 37.500 0.00 0.00 0.00 1.40
3940 7406 8.791327 TTTGCACAAGAAGTTCATATATCAGA 57.209 30.769 5.50 0.00 0.00 3.27
4009 7502 8.512956 CATGATTTCCTTCATATGATCTGAACC 58.487 37.037 6.17 5.50 34.59 3.62
4014 7507 9.286170 CAAGACATGATTTCCTTCATATGATCT 57.714 33.333 6.17 0.00 34.59 2.75
4080 7966 6.036470 GCCTAACATAGCTTGGAAAACAATC 58.964 40.000 0.00 0.00 38.65 2.67
4100 7986 8.065407 CGCAAAATAATATCGTTTACAAGCCTA 58.935 33.333 0.00 0.00 0.00 3.93
4108 7994 5.050227 CCGTCCCGCAAAATAATATCGTTTA 60.050 40.000 0.00 0.00 0.00 2.01
4112 7998 3.061322 TCCGTCCCGCAAAATAATATCG 58.939 45.455 0.00 0.00 0.00 2.92
4113 7999 4.062991 ACTCCGTCCCGCAAAATAATATC 58.937 43.478 0.00 0.00 0.00 1.63
4125 8011 4.317671 AAATAATACTCACTCCGTCCCG 57.682 45.455 0.00 0.00 0.00 5.14
4208 8095 1.658114 CCTCGCCATCATGCAATGG 59.342 57.895 12.36 12.36 46.73 3.16
4303 8190 1.289066 CAGGCCTCGAAGACGTTGA 59.711 57.895 0.00 0.00 40.69 3.18
4308 8195 0.250338 AAACACCAGGCCTCGAAGAC 60.250 55.000 0.00 0.00 0.00 3.01
4359 8246 2.089980 GACATTGCACAGGCTGAGAAT 58.910 47.619 23.66 12.41 41.91 2.40
4394 8281 5.186198 AGACTTATATTCAACCACACCTGC 58.814 41.667 0.00 0.00 0.00 4.85
4395 8282 5.817816 GGAGACTTATATTCAACCACACCTG 59.182 44.000 0.00 0.00 0.00 4.00
4411 8298 5.775701 GCTGATATGGTAAGAGGGAGACTTA 59.224 44.000 0.00 0.00 0.00 2.24
4457 8347 1.811965 TCGTGGAAGCATGAATTGGTG 59.188 47.619 0.00 0.00 35.85 4.17
4476 8366 0.172803 ATGGCGTAGAACGTGGAGTC 59.827 55.000 0.00 0.00 44.73 3.36
4477 8367 0.108804 CATGGCGTAGAACGTGGAGT 60.109 55.000 0.00 0.00 44.73 3.85
4478 8368 0.108804 ACATGGCGTAGAACGTGGAG 60.109 55.000 0.00 0.00 44.73 3.86
4479 8369 1.175654 TACATGGCGTAGAACGTGGA 58.824 50.000 0.00 0.00 44.73 4.02
4480 8370 1.999048 TTACATGGCGTAGAACGTGG 58.001 50.000 0.00 0.00 44.73 4.94
4481 8371 2.347452 CCTTTACATGGCGTAGAACGTG 59.653 50.000 0.00 0.00 44.73 4.49
4482 8372 2.613691 CCTTTACATGGCGTAGAACGT 58.386 47.619 0.00 0.00 44.73 3.99
4483 8373 1.326548 GCCTTTACATGGCGTAGAACG 59.673 52.381 0.00 0.00 45.88 3.95


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

AutoCloner maintained by Alex Coulton.