Multiple sequence alignment - TraesCS1B01G450600

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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 TraesCS1B01G450600 chr1B 100.000 5307 0 0 1 5307 668719328 668714022 0.000000e+00 9801.0
1 TraesCS1B01G450600 chr1B 91.148 305 23 3 315 618 191944320 191944019 1.380000e-110 411.0
2 TraesCS1B01G450600 chr1B 79.276 608 85 22 47 618 591562243 591561641 2.320000e-103 387.0
3 TraesCS1B01G450600 chr1B 88.690 168 13 3 3853 4016 667275473 667275638 3.240000e-47 200.0
4 TraesCS1B01G450600 chr1B 92.366 131 9 1 4281 4410 667275690 667275820 9.080000e-43 185.0
5 TraesCS1B01G450600 chr1B 98.246 57 0 1 1 56 28559750 28559694 1.220000e-16 99.0
6 TraesCS1B01G450600 chr1B 98.077 52 1 0 1 52 329378688 329378637 2.040000e-14 91.6
7 TraesCS1B01G450600 chr1D 92.825 3303 100 52 615 3850 480406316 480403084 0.000000e+00 4660.0
8 TraesCS1B01G450600 chr1D 95.447 615 16 3 3851 4454 480402113 480401500 0.000000e+00 970.0
9 TraesCS1B01G450600 chr1D 83.799 716 60 21 3851 4538 479107957 479108644 3.490000e-176 628.0
10 TraesCS1B01G450600 chr1D 93.367 392 17 4 4462 4852 480401197 480400814 5.960000e-159 571.0
11 TraesCS1B01G450600 chr1D 90.476 315 22 7 307 618 480407157 480406848 4.950000e-110 409.0
12 TraesCS1B01G450600 chr1D 93.827 243 11 2 4853 5095 480400170 480399932 3.910000e-96 363.0
13 TraesCS1B01G450600 chr1D 86.992 246 12 3 5055 5300 480399925 480399700 5.270000e-65 259.0
14 TraesCS1B01G450600 chr1D 96.364 55 0 2 1 54 95842463 95842410 7.320000e-14 89.8
15 TraesCS1B01G450600 chr1A 92.666 3218 117 41 615 3772 576669783 576666625 0.000000e+00 4525.0
16 TraesCS1B01G450600 chr1A 94.794 557 22 3 3851 4401 576666556 576666001 0.000000e+00 861.0
17 TraesCS1B01G450600 chr1A 88.760 605 35 10 2805 3394 588674357 588674943 0.000000e+00 710.0
18 TraesCS1B01G450600 chr1A 85.691 601 47 14 44 618 576670563 576669976 9.840000e-167 597.0
19 TraesCS1B01G450600 chr2D 88.969 417 13 10 833 1221 650043627 650044038 7.990000e-133 484.0
20 TraesCS1B01G450600 chr2D 79.564 597 75 20 47 618 64625039 64625613 3.000000e-102 383.0
21 TraesCS1B01G450600 chr2B 88.452 407 24 11 833 1221 574038588 574038989 2.240000e-128 470.0
22 TraesCS1B01G450600 chr2B 90.850 306 24 3 314 618 216950002 216950304 1.780000e-109 407.0
23 TraesCS1B01G450600 chr2B 90.523 306 25 3 314 618 4334539 4334237 8.280000e-108 401.0
24 TraesCS1B01G450600 chr2B 89.902 307 26 4 314 619 122704887 122704585 1.790000e-104 390.0
25 TraesCS1B01G450600 chr7B 90.850 306 24 3 314 618 75064894 75064592 1.780000e-109 407.0
26 TraesCS1B01G450600 chr7B 79.333 600 77 20 44 618 43962264 43962841 1.400000e-100 377.0
27 TraesCS1B01G450600 chr7B 89.836 305 15 9 833 1126 577806711 577807010 1.400000e-100 377.0
28 TraesCS1B01G450600 chr7B 95.652 46 2 0 1176 1221 577807021 577807066 2.050000e-09 75.0
29 TraesCS1B01G450600 chr7B 96.875 32 0 1 3170 3201 639086488 639086518 1.000000e-02 52.8
30 TraesCS1B01G450600 chr7A 90.850 306 24 3 314 618 697948416 697948718 1.780000e-109 407.0
31 TraesCS1B01G450600 chr3A 79.310 609 80 23 47 618 102870970 102870371 8.340000e-103 385.0
32 TraesCS1B01G450600 chr3A 79.189 567 72 19 44 586 746368176 746368720 8.460000e-93 351.0
33 TraesCS1B01G450600 chr3A 96.364 55 0 2 1 55 702912185 702912133 7.320000e-14 89.8
34 TraesCS1B01G450600 chrUn 79.553 582 73 19 47 604 1553557 1552998 1.800000e-99 374.0
35 TraesCS1B01G450600 chr7D 81.915 470 59 8 47 492 602084464 602083997 1.800000e-99 374.0
36 TraesCS1B01G450600 chr7D 78.694 582 78 19 47 604 360140387 360139828 3.930000e-91 346.0
37 TraesCS1B01G450600 chr7D 98.077 52 1 0 1 52 600971041 600971092 2.040000e-14 91.6
38 TraesCS1B01G450600 chr5D 81.607 473 61 8 44 492 502147551 502148021 8.400000e-98 368.0
39 TraesCS1B01G450600 chr6A 79.541 567 70 19 44 586 584517286 584517830 3.910000e-96 363.0
40 TraesCS1B01G450600 chr3B 82.781 151 15 5 3658 3797 259456745 259456895 2.010000e-24 124.0
41 TraesCS1B01G450600 chr4D 94.915 59 2 1 1 58 1403056 1402998 2.040000e-14 91.6
42 TraesCS1B01G450600 chr4B 100.000 49 0 0 1 49 148210499 148210547 2.040000e-14 91.6
43 TraesCS1B01G450600 chr6D 92.063 63 1 4 1 60 430998509 430998448 9.470000e-13 86.1
44 TraesCS1B01G450600 chr5B 94.643 56 2 1 1 56 364483399 364483345 9.470000e-13 86.1
45 TraesCS1B01G450600 chr3D 81.132 106 15 1 3413 3513 181111247 181111352 4.410000e-11 80.5


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 TraesCS1B01G450600 chr1B 668714022 668719328 5306 True 9801.000000 9801 100.000000 1 5307 1 chr1B.!!$R5 5306
1 TraesCS1B01G450600 chr1B 591561641 591562243 602 True 387.000000 387 79.276000 47 618 1 chr1B.!!$R4 571
2 TraesCS1B01G450600 chr1D 480399700 480407157 7457 True 1205.333333 4660 92.155667 307 5300 6 chr1D.!!$R2 4993
3 TraesCS1B01G450600 chr1D 479107957 479108644 687 False 628.000000 628 83.799000 3851 4538 1 chr1D.!!$F1 687
4 TraesCS1B01G450600 chr1A 576666001 576670563 4562 True 1994.333333 4525 91.050333 44 4401 3 chr1A.!!$R1 4357
5 TraesCS1B01G450600 chr1A 588674357 588674943 586 False 710.000000 710 88.760000 2805 3394 1 chr1A.!!$F1 589
6 TraesCS1B01G450600 chr2D 64625039 64625613 574 False 383.000000 383 79.564000 47 618 1 chr2D.!!$F1 571
7 TraesCS1B01G450600 chr7B 43962264 43962841 577 False 377.000000 377 79.333000 44 618 1 chr7B.!!$F1 574
8 TraesCS1B01G450600 chr3A 102870371 102870970 599 True 385.000000 385 79.310000 47 618 1 chr3A.!!$R1 571
9 TraesCS1B01G450600 chr3A 746368176 746368720 544 False 351.000000 351 79.189000 44 586 1 chr3A.!!$F1 542
10 TraesCS1B01G450600 chrUn 1552998 1553557 559 True 374.000000 374 79.553000 47 604 1 chrUn.!!$R1 557
11 TraesCS1B01G450600 chr7D 360139828 360140387 559 True 346.000000 346 78.694000 47 604 1 chr7D.!!$R1 557
12 TraesCS1B01G450600 chr6A 584517286 584517830 544 False 363.000000 363 79.541000 44 586 1 chr6A.!!$F1 542

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
33 34 0.030369 CCTCCGACGAGTATTTCCGG 59.970 60.000 0.00 0.0 41.36 5.14 F
40 41 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.0 46.06 4.30 F
215 216 0.032267 TCACAACCGCATCGTGTGTA 59.968 50.000 8.91 0.0 32.42 2.90 F
1367 2058 0.099259 CGTACGTACGCTCCCATTCA 59.901 55.000 32.36 0.0 43.14 2.57 F
1371 2062 0.389391 CGTACGCTCCCATTCATCCT 59.611 55.000 0.52 0.0 0.00 3.24 F
1776 2477 1.173043 TTGCCACCGGAACATGATTC 58.827 50.000 9.46 0.0 0.00 2.52 F
2805 3508 1.227853 AACGGCCACCAACTCAGAC 60.228 57.895 2.24 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1956 0.249447 GCCAAGTTCTGCAACCCAAC 60.249 55.000 0.0 0.0 32.22 3.77 R
1803 2504 0.397941 TCCAGACCAGGCAAACAGAG 59.602 55.000 0.0 0.0 0.00 3.35 R
2055 2756 2.285083 CGAAGTTGACACCAAACCTCA 58.715 47.619 0.0 0.0 33.49 3.86 R
2245 2946 1.526887 CTATACAAAGGCCGACATGCG 59.473 52.381 0.0 0.0 40.47 4.73 R
2472 3173 2.014128 GTAAAGGCACCATACGCATGT 58.986 47.619 0.0 0.0 0.00 3.21 R
2899 3606 2.956333 TGTATCAGGGGTCTGTACATCG 59.044 50.000 0.0 0.0 41.59 3.84 R
4486 6511 0.319555 TCAGCAGCACCAGACGTTAC 60.320 55.000 0.0 0.0 0.00 2.50 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
22 23 2.558795 AGATACATCCATTCCTCCGACG 59.441 50.000 0.00 0.00 0.00 5.12
23 24 2.061509 TACATCCATTCCTCCGACGA 57.938 50.000 0.00 0.00 0.00 4.20
24 25 0.747255 ACATCCATTCCTCCGACGAG 59.253 55.000 0.00 0.00 35.72 4.18
25 26 0.747255 CATCCATTCCTCCGACGAGT 59.253 55.000 0.00 0.00 33.93 4.18
26 27 1.954382 CATCCATTCCTCCGACGAGTA 59.046 52.381 0.00 0.00 33.93 2.59
27 28 2.359981 TCCATTCCTCCGACGAGTAT 57.640 50.000 0.00 0.00 33.93 2.12
28 29 2.662866 TCCATTCCTCCGACGAGTATT 58.337 47.619 0.00 0.00 33.93 1.89
29 30 3.028850 TCCATTCCTCCGACGAGTATTT 58.971 45.455 0.00 0.00 33.93 1.40
30 31 3.067742 TCCATTCCTCCGACGAGTATTTC 59.932 47.826 0.00 0.00 33.93 2.17
31 32 3.381949 CATTCCTCCGACGAGTATTTCC 58.618 50.000 0.00 0.00 33.93 3.13
32 33 1.019673 TCCTCCGACGAGTATTTCCG 58.980 55.000 0.00 0.00 33.93 4.30
33 34 0.030369 CCTCCGACGAGTATTTCCGG 59.970 60.000 0.00 0.00 41.36 5.14
34 35 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
35 36 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
36 37 0.590732 CCGACGAGTATTTCCGGACG 60.591 60.000 1.83 5.89 42.49 4.79
37 38 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
38 39 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
39 40 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
40 41 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
41 42 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
42 43 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
56 57 6.290605 GGACGGAGGGAGTATATAGAGTATC 58.709 48.000 0.00 0.00 0.00 2.24
64 65 6.668283 GGGAGTATATAGAGTATCCTTTGCCA 59.332 42.308 0.00 0.00 33.66 4.92
66 67 8.200792 GGAGTATATAGAGTATCCTTTGCCATG 58.799 40.741 0.00 0.00 33.66 3.66
80 81 2.261729 TGCCATGTCACTAACCCTACA 58.738 47.619 0.00 0.00 0.00 2.74
100 101 6.707608 CCTACAATCCGATCTGATCAAATGAA 59.292 38.462 17.19 0.00 0.00 2.57
124 125 7.195374 AGCTTATTAGGTGATACAAGACCAA 57.805 36.000 0.00 0.00 34.36 3.67
177 178 2.899303 AGGTGTTATCCCCACAAAGG 57.101 50.000 0.00 0.00 34.46 3.11
215 216 0.032267 TCACAACCGCATCGTGTGTA 59.968 50.000 8.91 0.00 32.42 2.90
221 222 1.746787 ACCGCATCGTGTGTATGTCTA 59.253 47.619 0.00 0.00 0.00 2.59
244 245 4.442038 GCCTTTTCCTCAAGGGGG 57.558 61.111 1.74 0.00 43.42 5.40
284 285 7.694093 AGTATCTTTTGACTTGAATCCTTCCT 58.306 34.615 0.00 0.00 0.00 3.36
288 289 8.567285 TCTTTTGACTTGAATCCTTCCTTATC 57.433 34.615 0.00 0.00 0.00 1.75
312 337 5.805486 CACACATAAAGCGCTTAGTCTTCTA 59.195 40.000 25.33 10.61 0.00 2.10
346 372 0.383231 CTCCAAAGCCCGATTGATGC 59.617 55.000 0.00 0.00 0.00 3.91
382 408 3.708220 CTTCTCCACGGCCTCGAGC 62.708 68.421 6.99 2.33 40.11 5.03
403 429 2.233922 CCCCTCTAATGCCATACCTACG 59.766 54.545 0.00 0.00 0.00 3.51
457 483 7.802738 GTGTAAAAGACATACACTGCAATGTA 58.197 34.615 10.86 10.86 46.09 2.29
546 583 5.301045 TGAAAACCGAACTTACAGAGAGAGA 59.699 40.000 0.00 0.00 0.00 3.10
547 584 5.379732 AAACCGAACTTACAGAGAGAGAG 57.620 43.478 0.00 0.00 0.00 3.20
563 600 5.788450 AGAGAGAGGTATGTTTGTGTTCTG 58.212 41.667 0.00 0.00 0.00 3.02
588 625 1.913419 TGGTGTACCAAATCCTCCCTC 59.087 52.381 0.24 0.00 44.35 4.30
623 1208 3.346315 TGCAGTCATGGATTGGTGTAAG 58.654 45.455 0.00 0.00 0.00 2.34
631 1216 8.424918 AGTCATGGATTGGTGTAAGATTACTAG 58.575 37.037 4.50 0.00 34.77 2.57
632 1217 8.204836 GTCATGGATTGGTGTAAGATTACTAGT 58.795 37.037 0.00 0.00 34.77 2.57
633 1218 8.204160 TCATGGATTGGTGTAAGATTACTAGTG 58.796 37.037 5.39 0.00 34.77 2.74
659 1245 4.842139 ATCTGTTAAGACGCACGATTTC 57.158 40.909 0.00 0.00 34.48 2.17
684 1270 2.606587 GGGGCTGAGAGCAAAGGGA 61.607 63.158 0.00 0.00 44.75 4.20
685 1271 1.377856 GGGCTGAGAGCAAAGGGAC 60.378 63.158 0.00 0.00 44.75 4.46
686 1272 1.743252 GGCTGAGAGCAAAGGGACG 60.743 63.158 0.00 0.00 44.75 4.79
687 1273 1.743252 GCTGAGAGCAAAGGGACGG 60.743 63.158 0.00 0.00 41.89 4.79
742 1331 6.688385 CACAAGATATGTTGCCTTTATGAACG 59.312 38.462 12.27 0.00 41.46 3.95
743 1332 6.183360 ACAAGATATGTTGCCTTTATGAACGG 60.183 38.462 12.27 0.00 40.06 4.44
744 1333 4.821805 AGATATGTTGCCTTTATGAACGGG 59.178 41.667 0.00 0.00 0.00 5.28
791 1389 0.672091 TTTCATAGCGCGCACCTGAA 60.672 50.000 35.10 30.59 0.00 3.02
822 1435 4.059459 GCACGCACACGAGTTCCG 62.059 66.667 0.00 0.00 43.93 4.30
898 1511 2.922234 CCCCCTGCCCAGATCTTC 59.078 66.667 0.00 0.00 0.00 2.87
899 1512 2.761465 CCCCCTGCCCAGATCTTCC 61.761 68.421 0.00 0.00 0.00 3.46
900 1513 2.507944 CCCTGCCCAGATCTTCCG 59.492 66.667 0.00 0.00 0.00 4.30
901 1514 2.203126 CCTGCCCAGATCTTCCGC 60.203 66.667 0.00 0.00 0.00 5.54
902 1515 2.203126 CTGCCCAGATCTTCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
903 1516 3.764160 CTGCCCAGATCTTCCGCCC 62.764 68.421 0.00 0.00 0.00 6.13
904 1517 3.483869 GCCCAGATCTTCCGCCCT 61.484 66.667 0.00 0.00 0.00 5.19
1251 1926 0.392461 TATCCTGCCCGTCAAACTGC 60.392 55.000 0.00 0.00 0.00 4.40
1267 1946 2.054799 ACTGCACCTCCCTCTGTTTTA 58.945 47.619 0.00 0.00 0.00 1.52
1273 1952 4.082733 GCACCTCCCTCTGTTTTATTTGAC 60.083 45.833 0.00 0.00 0.00 3.18
1274 1953 5.070001 CACCTCCCTCTGTTTTATTTGACA 58.930 41.667 0.00 0.00 0.00 3.58
1275 1954 5.711976 CACCTCCCTCTGTTTTATTTGACAT 59.288 40.000 0.00 0.00 0.00 3.06
1276 1955 5.711976 ACCTCCCTCTGTTTTATTTGACATG 59.288 40.000 0.00 0.00 0.00 3.21
1277 1956 5.126061 CCTCCCTCTGTTTTATTTGACATGG 59.874 44.000 0.00 0.00 0.00 3.66
1279 1958 6.074648 TCCCTCTGTTTTATTTGACATGGTT 58.925 36.000 0.00 0.00 0.00 3.67
1280 1959 6.015519 TCCCTCTGTTTTATTTGACATGGTTG 60.016 38.462 0.00 0.00 0.00 3.77
1330 2021 2.224378 GCATTACTCTAGCTGGATGGCA 60.224 50.000 0.00 0.00 34.17 4.92
1366 2057 2.864028 CGTACGTACGCTCCCATTC 58.136 57.895 32.36 0.00 43.14 2.67
1367 2058 0.099259 CGTACGTACGCTCCCATTCA 59.901 55.000 32.36 0.00 43.14 2.57
1371 2062 0.389391 CGTACGCTCCCATTCATCCT 59.611 55.000 0.52 0.00 0.00 3.24
1393 2084 5.808540 CCTCAAACATATCATTTGCTTGGTG 59.191 40.000 4.67 0.00 37.05 4.17
1554 2255 1.585214 GTAACCGATTACCTTCACGCG 59.415 52.381 3.53 3.53 35.56 6.01
1558 2259 2.049228 CCGATTACCTTCACGCGTATC 58.951 52.381 13.44 8.77 0.00 2.24
1609 2310 4.563976 GGTTAATGTGAATGTGCATTGAGC 59.436 41.667 1.77 0.00 45.96 4.26
1622 2323 1.998315 CATTGAGCTCCGAGTGACAAG 59.002 52.381 12.15 0.00 0.00 3.16
1729 2430 1.448540 CCTAAGTGGCCGACTGCAG 60.449 63.158 13.48 13.48 43.89 4.41
1776 2477 1.173043 TTGCCACCGGAACATGATTC 58.827 50.000 9.46 0.00 0.00 2.52
1825 2526 2.027192 TCTGTTTGCCTGGTCTGGATAC 60.027 50.000 0.00 0.00 0.00 2.24
1843 2544 6.688578 TGGATACTTTCACTGTGACTACTTC 58.311 40.000 10.56 5.48 37.61 3.01
1851 2552 6.710597 TCACTGTGACTACTTCAGTTTACT 57.289 37.500 6.36 0.00 39.89 2.24
1852 2553 7.108841 TCACTGTGACTACTTCAGTTTACTT 57.891 36.000 6.36 0.00 39.89 2.24
1853 2554 6.978659 TCACTGTGACTACTTCAGTTTACTTG 59.021 38.462 6.36 0.00 39.89 3.16
1854 2555 6.757010 CACTGTGACTACTTCAGTTTACTTGT 59.243 38.462 0.32 0.00 39.89 3.16
1855 2556 6.757010 ACTGTGACTACTTCAGTTTACTTGTG 59.243 38.462 0.00 0.00 39.00 3.33
1856 2557 6.869695 TGTGACTACTTCAGTTTACTTGTGA 58.130 36.000 0.00 0.00 37.72 3.58
1857 2558 7.324935 TGTGACTACTTCAGTTTACTTGTGAA 58.675 34.615 0.00 0.00 37.72 3.18
1903 2604 8.926710 CCTCTATATCGTTTGACATATGTTTCC 58.073 37.037 10.30 0.00 0.00 3.13
1904 2605 9.698309 CTCTATATCGTTTGACATATGTTTCCT 57.302 33.333 10.30 0.00 0.00 3.36
1905 2606 9.476202 TCTATATCGTTTGACATATGTTTCCTG 57.524 33.333 10.30 1.18 0.00 3.86
1906 2607 9.261180 CTATATCGTTTGACATATGTTTCCTGT 57.739 33.333 10.30 0.00 0.00 4.00
1907 2608 6.817765 ATCGTTTGACATATGTTTCCTGTT 57.182 33.333 10.30 0.00 0.00 3.16
1956 2657 8.779354 TTTTTGCTGTTTTGTTTATACAGGTT 57.221 26.923 0.00 0.00 39.66 3.50
1989 2690 7.606135 TGTCGATAACTGGGATATAAGGAAA 57.394 36.000 0.00 0.00 0.00 3.13
2044 2745 2.351544 GCTTCTCTGCTTCTTTTGCCAG 60.352 50.000 0.00 0.00 0.00 4.85
2067 2768 4.170468 AGAATTCACTGAGGTTTGGTGT 57.830 40.909 8.44 0.00 33.30 4.16
2074 2775 3.065371 CACTGAGGTTTGGTGTCAACTTC 59.935 47.826 0.00 0.00 31.78 3.01
2076 2777 1.602377 GAGGTTTGGTGTCAACTTCGG 59.398 52.381 0.00 0.00 31.78 4.30
2157 2858 1.756538 CTTGACCCCTTTTTGTGCAGT 59.243 47.619 0.00 0.00 0.00 4.40
2253 2954 3.740044 AGGTAATGAAAACGCATGTCG 57.260 42.857 7.79 7.79 45.38 4.35
2451 3152 2.969821 TGTACCTTTGTGGCTCCATT 57.030 45.000 0.00 0.00 40.22 3.16
2472 3173 2.105649 TGTTCCAAGTGTGTCTATGGCA 59.894 45.455 0.00 0.00 32.87 4.92
2611 3312 6.755206 TGCACTTAGTTATCACAGTACTTGT 58.245 36.000 0.00 0.00 41.94 3.16
2739 3442 7.985184 TCAGGATGGACAACAACTATGTTATAC 59.015 37.037 0.00 0.00 41.98 1.47
2805 3508 1.227853 AACGGCCACCAACTCAGAC 60.228 57.895 2.24 0.00 0.00 3.51
2899 3606 4.438744 CGGTAGTTTCCAGCCATTTCAATC 60.439 45.833 0.00 0.00 0.00 2.67
2921 3628 3.574396 CGATGTACAGACCCCTGATACAT 59.426 47.826 0.33 14.42 42.84 2.29
2932 3640 7.821359 CAGACCCCTGATACATGAGTATATTTG 59.179 40.741 0.00 0.00 43.02 2.32
3422 4139 7.039313 TGCCATATACTGCTATCTAATACCG 57.961 40.000 0.00 0.00 0.00 4.02
3694 4411 9.710818 AGTATTAACTGATCAAGGGAACTACTA 57.289 33.333 0.00 0.00 34.79 1.82
3775 4493 4.082026 AGGGCAAACAATGAGAATACTTGC 60.082 41.667 0.00 0.00 37.54 4.01
3776 4494 4.082026 GGGCAAACAATGAGAATACTTGCT 60.082 41.667 0.00 0.00 38.17 3.91
3777 4495 5.125417 GGGCAAACAATGAGAATACTTGCTA 59.875 40.000 0.00 0.00 38.17 3.49
3778 4496 6.030228 GGCAAACAATGAGAATACTTGCTAC 58.970 40.000 0.00 0.00 38.17 3.58
3779 4497 6.349280 GGCAAACAATGAGAATACTTGCTACA 60.349 38.462 0.00 0.00 38.17 2.74
3780 4498 6.744537 GCAAACAATGAGAATACTTGCTACAG 59.255 38.462 0.00 0.00 35.85 2.74
3781 4499 7.361201 GCAAACAATGAGAATACTTGCTACAGA 60.361 37.037 0.00 0.00 35.85 3.41
3782 4500 8.671921 CAAACAATGAGAATACTTGCTACAGAT 58.328 33.333 0.00 0.00 0.00 2.90
3783 4501 7.783090 ACAATGAGAATACTTGCTACAGATG 57.217 36.000 0.00 0.00 0.00 2.90
3787 4505 6.341316 TGAGAATACTTGCTACAGATGGTTC 58.659 40.000 0.00 0.00 0.00 3.62
3822 4540 6.854496 TCTTTGTGTGTACTTGGTATGAAC 57.146 37.500 0.00 0.00 0.00 3.18
4068 5759 1.228094 TGCCGATTCCTGCAACACA 60.228 52.632 0.00 0.00 33.87 3.72
4297 6015 0.948623 TGAGCACCCGATGTTTGACG 60.949 55.000 0.00 0.00 0.00 4.35
4327 6048 8.746922 TTTAGTTATTATACATACGGAAGGCG 57.253 34.615 0.00 0.00 0.00 5.52
4425 6154 1.150536 GAAGCCTGGTGACCCACAA 59.849 57.895 0.00 0.00 35.17 3.33
4432 6161 1.069513 CTGGTGACCCACAACGTTCTA 59.930 52.381 0.00 0.00 39.39 2.10
4451 6181 7.021196 CGTTCTATGAAAATCGTGTGGAATTT 58.979 34.615 0.00 0.00 30.46 1.82
4471 6496 0.890683 CATGGGGGAGTCAGTTTTGC 59.109 55.000 0.00 0.00 0.00 3.68
4531 6556 9.472361 AACAATACTAACCGTTAGCATACATAG 57.528 33.333 16.73 3.79 36.71 2.23
4611 6636 0.253327 TGCGGTGCCATATGGTTGTA 59.747 50.000 22.79 7.37 37.57 2.41
4633 6658 3.256383 ACTTGCAGCAAATTCTACATGCA 59.744 39.130 9.65 0.00 42.45 3.96
4694 6720 0.667993 CTGGAACACGGCAACATTGT 59.332 50.000 0.00 0.00 34.00 2.71
4725 6751 3.876914 TGTTTTTCTGTCGAGCTGAATGT 59.123 39.130 0.00 0.00 35.47 2.71
4734 6760 3.076621 TCGAGCTGAATGTTGATGCTTT 58.923 40.909 0.00 0.00 33.83 3.51
4735 6761 3.503363 TCGAGCTGAATGTTGATGCTTTT 59.497 39.130 0.00 0.00 33.83 2.27
4736 6762 4.694982 TCGAGCTGAATGTTGATGCTTTTA 59.305 37.500 0.00 0.00 33.83 1.52
4737 6763 5.355071 TCGAGCTGAATGTTGATGCTTTTAT 59.645 36.000 0.00 0.00 33.83 1.40
4738 6764 6.538381 TCGAGCTGAATGTTGATGCTTTTATA 59.462 34.615 0.00 0.00 33.83 0.98
4823 6849 6.200475 GGTTAATCCTTACTACGCATCTTCAC 59.800 42.308 0.00 0.00 0.00 3.18
4883 7551 8.578448 TCAATCATTCAGAATGGATAACAACA 57.422 30.769 20.91 1.15 39.38 3.33
4955 7623 6.201615 ACACATATATCTGTTGCAAGACGATG 59.798 38.462 0.00 2.31 0.00 3.84
5016 7684 2.022195 ACCATCAGCAATGCATCTCAC 58.978 47.619 8.35 0.00 33.71 3.51
5018 7686 0.661552 ATCAGCAATGCATCTCACGC 59.338 50.000 8.35 0.00 0.00 5.34
5019 7687 0.674269 TCAGCAATGCATCTCACGCA 60.674 50.000 8.35 0.00 44.94 5.24
5020 7688 0.248094 CAGCAATGCATCTCACGCAG 60.248 55.000 8.35 0.00 43.88 5.18
5032 7700 0.859232 TCACGCAGTTCGCTCTTTTC 59.141 50.000 0.00 0.00 41.61 2.29
5037 7705 2.499896 GCAGTTCGCTCTTTTCGAATG 58.500 47.619 0.00 0.00 45.84 2.67
5053 7721 8.703604 TTTTCGAATGTTGTGGTTTCATTTTA 57.296 26.923 0.00 0.00 32.90 1.52
5061 7729 7.776107 TGTTGTGGTTTCATTTTAAGATGTCA 58.224 30.769 5.93 0.00 0.00 3.58
5064 7732 7.377398 TGTGGTTTCATTTTAAGATGTCATGG 58.623 34.615 5.93 0.00 0.00 3.66
5104 7819 4.523943 ACTTGCACCAAATTCTTGCTGATA 59.476 37.500 7.24 0.00 37.16 2.15
5116 7831 9.638176 AAATTCTTGCTGATAAGGTCTGATATT 57.362 29.630 0.00 0.00 0.00 1.28
5118 7833 9.717942 ATTCTTGCTGATAAGGTCTGATATTAC 57.282 33.333 0.00 0.00 0.00 1.89
5119 7834 8.250143 TCTTGCTGATAAGGTCTGATATTACA 57.750 34.615 0.00 0.00 0.00 2.41
5120 7835 8.704668 TCTTGCTGATAAGGTCTGATATTACAA 58.295 33.333 0.00 0.00 0.00 2.41
5121 7836 9.330063 CTTGCTGATAAGGTCTGATATTACAAA 57.670 33.333 0.00 0.00 0.00 2.83
5122 7837 8.662781 TGCTGATAAGGTCTGATATTACAAAC 57.337 34.615 0.00 0.00 0.00 2.93
5123 7838 7.715249 TGCTGATAAGGTCTGATATTACAAACC 59.285 37.037 0.00 0.00 31.69 3.27
5124 7839 7.715249 GCTGATAAGGTCTGATATTACAAACCA 59.285 37.037 0.00 0.00 33.75 3.67
5125 7840 9.784531 CTGATAAGGTCTGATATTACAAACCAT 57.215 33.333 0.00 0.00 33.75 3.55
5166 7881 6.494893 TTACCAACAAGATCACAGTATTGC 57.505 37.500 0.00 0.00 0.00 3.56
5167 7882 4.397420 ACCAACAAGATCACAGTATTGCA 58.603 39.130 0.00 0.00 0.00 4.08
5168 7883 4.826733 ACCAACAAGATCACAGTATTGCAA 59.173 37.500 0.00 0.00 0.00 4.08
5169 7884 5.301551 ACCAACAAGATCACAGTATTGCAAA 59.698 36.000 1.71 0.00 0.00 3.68
5170 7885 5.630680 CCAACAAGATCACAGTATTGCAAAC 59.369 40.000 1.71 3.36 0.00 2.93
5171 7886 5.376854 ACAAGATCACAGTATTGCAAACC 57.623 39.130 1.71 0.00 0.00 3.27
5172 7887 4.826733 ACAAGATCACAGTATTGCAAACCA 59.173 37.500 1.71 0.00 0.00 3.67
5173 7888 5.477984 ACAAGATCACAGTATTGCAAACCAT 59.522 36.000 1.71 0.00 0.00 3.55
5174 7889 5.824904 AGATCACAGTATTGCAAACCATC 57.175 39.130 1.71 0.00 0.00 3.51
5175 7890 4.641989 AGATCACAGTATTGCAAACCATCC 59.358 41.667 1.71 0.00 0.00 3.51
5176 7891 3.760738 TCACAGTATTGCAAACCATCCA 58.239 40.909 1.71 0.00 0.00 3.41
5177 7892 4.343231 TCACAGTATTGCAAACCATCCAT 58.657 39.130 1.71 0.00 0.00 3.41
5178 7893 4.771577 TCACAGTATTGCAAACCATCCATT 59.228 37.500 1.71 0.00 0.00 3.16
5247 7962 8.398665 AGAGTACAAAAGCTAGTGAAAAACTTG 58.601 33.333 3.67 0.00 40.56 3.16
5261 7976 2.838637 AACTTGAGGGAACACCCAAA 57.161 45.000 8.05 1.40 45.73 3.28
5297 8012 2.239654 CCTCAAGGGGTGATGCTTTCTA 59.760 50.000 0.00 0.00 35.07 2.10
5300 8015 3.055094 TCAAGGGGTGATGCTTTCTACTC 60.055 47.826 0.00 0.00 0.00 2.59
5301 8016 1.840635 AGGGGTGATGCTTTCTACTCC 59.159 52.381 0.00 0.00 0.00 3.85
5302 8017 1.134068 GGGGTGATGCTTTCTACTCCC 60.134 57.143 0.00 0.00 0.00 4.30
5303 8018 1.840635 GGGTGATGCTTTCTACTCCCT 59.159 52.381 0.00 0.00 0.00 4.20
5304 8019 2.158885 GGGTGATGCTTTCTACTCCCTC 60.159 54.545 0.00 0.00 0.00 4.30
5305 8020 2.769095 GGTGATGCTTTCTACTCCCTCT 59.231 50.000 0.00 0.00 0.00 3.69
5306 8021 3.431486 GGTGATGCTTTCTACTCCCTCTG 60.431 52.174 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.756963 CGTCGGAGGAATGGATGTATCTA 59.243 47.826 0.00 0.00 0.00 1.98
1 2 2.558795 CGTCGGAGGAATGGATGTATCT 59.441 50.000 0.00 0.00 0.00 1.98
2 3 2.557056 TCGTCGGAGGAATGGATGTATC 59.443 50.000 0.00 0.00 0.00 2.24
3 4 2.558795 CTCGTCGGAGGAATGGATGTAT 59.441 50.000 1.73 0.00 36.61 2.29
4 5 1.954382 CTCGTCGGAGGAATGGATGTA 59.046 52.381 1.73 0.00 36.61 2.29
5 6 0.747255 CTCGTCGGAGGAATGGATGT 59.253 55.000 1.73 0.00 36.61 3.06
6 7 0.747255 ACTCGTCGGAGGAATGGATG 59.253 55.000 1.73 0.00 44.93 3.51
7 8 2.359981 TACTCGTCGGAGGAATGGAT 57.640 50.000 1.73 0.00 44.93 3.41
8 9 2.359981 ATACTCGTCGGAGGAATGGA 57.640 50.000 1.73 0.00 44.93 3.41
9 10 3.381949 GAAATACTCGTCGGAGGAATGG 58.618 50.000 1.73 0.00 44.93 3.16
10 11 3.381949 GGAAATACTCGTCGGAGGAATG 58.618 50.000 1.73 0.00 44.93 2.67
11 12 2.034305 CGGAAATACTCGTCGGAGGAAT 59.966 50.000 1.73 0.00 44.93 3.01
12 13 1.402968 CGGAAATACTCGTCGGAGGAA 59.597 52.381 1.73 0.00 44.93 3.36
13 14 1.019673 CGGAAATACTCGTCGGAGGA 58.980 55.000 0.00 0.00 44.93 3.71
14 15 0.030369 CCGGAAATACTCGTCGGAGG 59.970 60.000 0.00 0.00 44.93 4.30
15 16 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
16 17 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
17 18 0.590732 CGTCCGGAAATACTCGTCGG 60.591 60.000 5.23 0.00 41.80 4.79
18 19 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
19 20 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
20 21 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
21 22 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
22 23 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
23 24 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
24 25 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
25 26 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
26 27 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
27 28 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
28 29 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
29 30 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
30 31 2.238144 TCTATATACTCCCTCCGTCCGG 59.762 54.545 0.00 0.00 0.00 5.14
31 32 3.055240 ACTCTATATACTCCCTCCGTCCG 60.055 52.174 0.00 0.00 0.00 4.79
32 33 4.573021 ACTCTATATACTCCCTCCGTCC 57.427 50.000 0.00 0.00 0.00 4.79
33 34 6.290605 GGATACTCTATATACTCCCTCCGTC 58.709 48.000 0.00 0.00 0.00 4.79
34 35 6.251255 GGATACTCTATATACTCCCTCCGT 57.749 45.833 0.00 0.00 0.00 4.69
56 57 1.818674 GGGTTAGTGACATGGCAAAGG 59.181 52.381 0.58 0.00 0.00 3.11
64 65 4.028131 TCGGATTGTAGGGTTAGTGACAT 58.972 43.478 0.00 0.00 0.00 3.06
66 67 4.341520 AGATCGGATTGTAGGGTTAGTGAC 59.658 45.833 0.00 0.00 0.00 3.67
80 81 5.374921 AGCTTCATTTGATCAGATCGGATT 58.625 37.500 9.82 0.00 0.00 3.01
100 101 6.808321 TGGTCTTGTATCACCTAATAAGCT 57.192 37.500 0.00 0.00 33.36 3.74
124 125 2.982130 GGTCGAGCACCATGTCCT 59.018 61.111 10.30 0.00 45.98 3.85
177 178 4.580167 TGTGATGCCCATATCTTTGTTAGC 59.420 41.667 0.00 0.00 0.00 3.09
215 216 4.222145 TGAGGAAAAGGCGTAAGTAGACAT 59.778 41.667 0.00 0.00 41.68 3.06
221 222 2.552373 CCCTTGAGGAAAAGGCGTAAGT 60.552 50.000 0.00 0.00 44.69 2.24
244 245 3.301274 AGATACTAAGGAGACTGGTGCC 58.699 50.000 0.00 0.00 42.68 5.01
245 246 5.346181 AAAGATACTAAGGAGACTGGTGC 57.654 43.478 0.00 0.00 42.68 5.01
284 285 6.338146 AGACTAAGCGCTTTATGTGTGATAA 58.662 36.000 30.13 4.14 0.00 1.75
288 289 4.627467 AGAAGACTAAGCGCTTTATGTGTG 59.373 41.667 30.13 11.88 0.00 3.82
325 351 1.672881 CATCAATCGGGCTTTGGAGTC 59.327 52.381 0.00 0.00 0.00 3.36
346 372 4.122776 AGAAGTTCTACAAGGCATATGCG 58.877 43.478 21.04 10.32 43.26 4.73
382 408 2.233922 CGTAGGTATGGCATTAGAGGGG 59.766 54.545 4.78 0.00 0.00 4.79
403 429 4.156556 TGTGATGAGCATTTGAAGCCTAAC 59.843 41.667 0.00 0.00 0.00 2.34
457 483 6.707440 TGTGTGTATCATGGTTTGTTCTTT 57.293 33.333 0.00 0.00 0.00 2.52
529 566 5.587043 ACATACCTCTCTCTCTGTAAGTTCG 59.413 44.000 0.00 0.00 33.76 3.95
546 583 6.071051 ACCAAAAACAGAACACAAACATACCT 60.071 34.615 0.00 0.00 0.00 3.08
547 584 6.035542 CACCAAAAACAGAACACAAACATACC 59.964 38.462 0.00 0.00 0.00 2.73
606 644 8.204836 ACTAGTAATCTTACACCAATCCATGAC 58.795 37.037 0.00 0.00 36.12 3.06
607 645 8.204160 CACTAGTAATCTTACACCAATCCATGA 58.796 37.037 0.00 0.00 36.12 3.07
608 646 7.041780 GCACTAGTAATCTTACACCAATCCATG 60.042 40.741 0.00 0.00 36.12 3.66
609 647 6.992715 GCACTAGTAATCTTACACCAATCCAT 59.007 38.462 0.00 0.00 36.12 3.41
610 648 6.070481 TGCACTAGTAATCTTACACCAATCCA 60.070 38.462 0.00 0.00 36.12 3.41
611 649 6.346096 TGCACTAGTAATCTTACACCAATCC 58.654 40.000 0.00 0.00 36.12 3.01
613 651 8.630054 TTTTGCACTAGTAATCTTACACCAAT 57.370 30.769 0.00 0.00 36.12 3.16
623 1208 9.974750 GTCTTAACAGATTTTGCACTAGTAATC 57.025 33.333 7.69 7.69 0.00 1.75
631 1216 3.664025 GTGCGTCTTAACAGATTTTGCAC 59.336 43.478 0.00 0.00 38.47 4.57
632 1217 3.605922 CGTGCGTCTTAACAGATTTTGCA 60.606 43.478 0.00 0.00 0.00 4.08
633 1218 2.902484 CGTGCGTCTTAACAGATTTTGC 59.098 45.455 0.00 0.00 0.00 3.68
659 1245 2.415010 CTCTCAGCCCCACGATCG 59.585 66.667 14.88 14.88 0.00 3.69
684 1270 0.966875 TACTGTATCCGTGTGCCCGT 60.967 55.000 0.00 0.00 0.00 5.28
685 1271 0.387929 ATACTGTATCCGTGTGCCCG 59.612 55.000 0.00 0.00 0.00 6.13
686 1272 2.606308 CGTATACTGTATCCGTGTGCCC 60.606 54.545 3.09 0.00 0.00 5.36
687 1273 2.606308 CCGTATACTGTATCCGTGTGCC 60.606 54.545 11.08 0.00 0.00 5.01
742 1331 5.066893 AGTTTTTCTTTCTGGTTTACGTCCC 59.933 40.000 0.00 0.00 0.00 4.46
743 1332 6.127810 AGTTTTTCTTTCTGGTTTACGTCC 57.872 37.500 0.00 0.00 0.00 4.79
744 1333 5.900242 CGAGTTTTTCTTTCTGGTTTACGTC 59.100 40.000 0.00 0.00 0.00 4.34
803 1416 3.327754 GAACTCGTGTGCGTGCGT 61.328 61.111 0.00 0.00 39.49 5.24
805 1418 4.059459 CGGAACTCGTGTGCGTGC 62.059 66.667 0.00 0.00 39.49 5.34
806 1419 4.059459 GCGGAACTCGTGTGCGTG 62.059 66.667 0.00 0.00 41.72 5.34
807 1420 4.280494 AGCGGAACTCGTGTGCGT 62.280 61.111 0.00 0.00 41.72 5.24
811 1424 1.213094 CGTTTCAGCGGAACTCGTGT 61.213 55.000 0.00 0.00 41.72 4.49
812 1425 1.487231 CGTTTCAGCGGAACTCGTG 59.513 57.895 0.00 0.00 41.72 4.35
813 1426 2.308039 GCGTTTCAGCGGAACTCGT 61.308 57.895 18.47 0.00 41.72 4.18
814 1427 2.470286 GCGTTTCAGCGGAACTCG 59.530 61.111 15.11 15.11 42.76 4.18
890 1503 1.227380 CGGAAGGGCGGAAGATCTG 60.227 63.158 0.00 0.00 0.00 2.90
902 1515 4.168291 GAGCAGAGGGGCGGAAGG 62.168 72.222 0.00 0.00 39.27 3.46
903 1516 4.168291 GGAGCAGAGGGGCGGAAG 62.168 72.222 0.00 0.00 39.27 3.46
1251 1926 5.070001 TGTCAAATAAAACAGAGGGAGGTG 58.930 41.667 0.00 0.00 0.00 4.00
1267 1946 2.037511 CTGCAACCCAACCATGTCAAAT 59.962 45.455 0.00 0.00 0.00 2.32
1273 1952 1.331214 AGTTCTGCAACCCAACCATG 58.669 50.000 0.00 0.00 32.22 3.66
1274 1953 1.688197 CAAGTTCTGCAACCCAACCAT 59.312 47.619 0.00 0.00 32.22 3.55
1275 1954 1.110442 CAAGTTCTGCAACCCAACCA 58.890 50.000 0.00 0.00 32.22 3.67
1276 1955 0.389025 CCAAGTTCTGCAACCCAACC 59.611 55.000 0.00 0.00 32.22 3.77
1277 1956 0.249447 GCCAAGTTCTGCAACCCAAC 60.249 55.000 0.00 0.00 32.22 3.77
1279 1958 2.192861 CGCCAAGTTCTGCAACCCA 61.193 57.895 0.00 0.00 32.22 4.51
1280 1959 1.856265 CTCGCCAAGTTCTGCAACCC 61.856 60.000 0.00 0.00 32.22 4.11
1361 2052 7.384115 GCAAATGATATGTTTGAGGATGAATGG 59.616 37.037 12.18 0.00 38.51 3.16
1366 2057 6.700081 CCAAGCAAATGATATGTTTGAGGATG 59.300 38.462 12.18 6.33 40.22 3.51
1367 2058 6.381994 ACCAAGCAAATGATATGTTTGAGGAT 59.618 34.615 12.18 0.00 40.22 3.24
1371 2062 6.389091 GTCACCAAGCAAATGATATGTTTGA 58.611 36.000 12.18 0.00 40.22 2.69
1393 2084 1.663379 GCCGGCCAATTAACCAGGTC 61.663 60.000 18.11 0.00 0.00 3.85
1500 2191 5.350640 CCACTCGACAAAGGGATTAAAGTAC 59.649 44.000 0.00 0.00 0.00 2.73
1554 2255 4.961551 CCGCAATACAATCAAACACGATAC 59.038 41.667 0.00 0.00 0.00 2.24
1558 2259 2.908009 CACCGCAATACAATCAAACACG 59.092 45.455 0.00 0.00 0.00 4.49
1609 2310 1.261619 GCAACAACTTGTCACTCGGAG 59.738 52.381 2.83 2.83 0.00 4.63
1622 2323 4.320494 CCTCTACATCCACAAAGCAACAAC 60.320 45.833 0.00 0.00 0.00 3.32
1729 2430 7.274603 AGAAGAGGATATACGTACAGGTTTC 57.725 40.000 0.00 0.00 0.00 2.78
1803 2504 0.397941 TCCAGACCAGGCAAACAGAG 59.602 55.000 0.00 0.00 0.00 3.35
1825 2526 6.910536 AAACTGAAGTAGTCACAGTGAAAG 57.089 37.500 4.32 0.00 42.81 2.62
1843 2544 5.082059 GCATCACGATTCACAAGTAAACTG 58.918 41.667 0.00 0.00 0.00 3.16
1851 2552 3.563390 TGAAGTTGCATCACGATTCACAA 59.437 39.130 0.00 0.00 0.00 3.33
1852 2553 3.058983 GTGAAGTTGCATCACGATTCACA 60.059 43.478 16.66 0.00 43.65 3.58
1853 2554 3.482786 GTGAAGTTGCATCACGATTCAC 58.517 45.455 3.31 7.34 39.58 3.18
1854 2555 3.811722 GTGAAGTTGCATCACGATTCA 57.188 42.857 3.31 0.00 37.98 2.57
1956 2657 3.571571 CCAGTTATCGACAAGAACACGA 58.428 45.455 0.00 0.00 40.18 4.35
1989 2690 8.082242 GCCATTTTCAGATTAACTGTGTTAACT 58.918 33.333 7.22 3.40 45.86 2.24
2044 2745 4.580580 ACACCAAACCTCAGTGAATTCTTC 59.419 41.667 7.05 0.25 35.47 2.87
2055 2756 2.285083 CGAAGTTGACACCAAACCTCA 58.715 47.619 0.00 0.00 33.49 3.86
2067 2768 6.203338 GGTAGTAAACATCAAACCGAAGTTGA 59.797 38.462 0.00 0.00 35.77 3.18
2074 2775 6.489127 TTCATGGTAGTAAACATCAAACCG 57.511 37.500 0.00 0.00 0.00 4.44
2245 2946 1.526887 CTATACAAAGGCCGACATGCG 59.473 52.381 0.00 0.00 40.47 4.73
2428 3129 2.640332 TGGAGCCACAAAGGTACATACA 59.360 45.455 0.00 0.00 40.61 2.29
2429 3130 3.343941 TGGAGCCACAAAGGTACATAC 57.656 47.619 0.00 0.00 40.61 2.39
2430 3131 4.263727 ACAATGGAGCCACAAAGGTACATA 60.264 41.667 0.00 0.00 40.61 2.29
2431 3132 3.091545 CAATGGAGCCACAAAGGTACAT 58.908 45.455 0.00 0.00 40.61 2.29
2451 3152 2.105649 TGCCATAGACACACTTGGAACA 59.894 45.455 0.00 0.00 32.50 3.18
2472 3173 2.014128 GTAAAGGCACCATACGCATGT 58.986 47.619 0.00 0.00 0.00 3.21
2549 3250 8.651391 TTTCGTTAGTCATAAACAGAAGTTCA 57.349 30.769 5.50 0.00 36.84 3.18
2693 3396 5.453057 CCTGAATGGTTGGTTCAATTGACAA 60.453 40.000 7.89 7.51 35.36 3.18
2739 3442 7.438459 CCTCTCAAATTATTAGGAAGTACACCG 59.562 40.741 0.00 0.00 0.00 4.94
2740 3443 8.265764 ACCTCTCAAATTATTAGGAAGTACACC 58.734 37.037 0.00 0.00 0.00 4.16
2741 3444 9.099454 CACCTCTCAAATTATTAGGAAGTACAC 57.901 37.037 0.00 0.00 0.00 2.90
2742 3445 9.042450 TCACCTCTCAAATTATTAGGAAGTACA 57.958 33.333 0.00 0.00 0.00 2.90
2745 3448 8.997734 AGATCACCTCTCAAATTATTAGGAAGT 58.002 33.333 0.00 0.00 0.00 3.01
2805 3508 9.512588 ACCAAATCATAAGCAGAATTATAGAGG 57.487 33.333 0.00 0.00 0.00 3.69
2899 3606 2.956333 TGTATCAGGGGTCTGTACATCG 59.044 50.000 0.00 0.00 41.59 3.84
2921 3628 8.547481 TCAGTATCCCTTCACAAATATACTCA 57.453 34.615 0.00 0.00 29.90 3.41
2932 3640 5.344743 TGACATCTTCAGTATCCCTTCAC 57.655 43.478 0.00 0.00 0.00 3.18
3554 4271 5.445964 ACTGATTTACCTTCCTTGTGTGTT 58.554 37.500 0.00 0.00 0.00 3.32
3558 4275 5.643777 CCACTACTGATTTACCTTCCTTGTG 59.356 44.000 0.00 0.00 0.00 3.33
3694 4411 7.166691 ACCGAGTACAGACAATTATACAACT 57.833 36.000 0.00 0.00 0.00 3.16
3775 4493 8.936864 AGATTAAAAGTTTCGAACCATCTGTAG 58.063 33.333 0.00 0.00 0.00 2.74
3776 4494 8.842358 AGATTAAAAGTTTCGAACCATCTGTA 57.158 30.769 0.00 0.00 0.00 2.74
3777 4495 7.745620 AGATTAAAAGTTTCGAACCATCTGT 57.254 32.000 0.00 0.00 0.00 3.41
3778 4496 8.905702 CAAAGATTAAAAGTTTCGAACCATCTG 58.094 33.333 0.00 0.00 0.00 2.90
3779 4497 8.630037 ACAAAGATTAAAAGTTTCGAACCATCT 58.370 29.630 0.00 0.00 0.00 2.90
3780 4498 8.690840 CACAAAGATTAAAAGTTTCGAACCATC 58.309 33.333 0.00 0.00 0.00 3.51
3781 4499 8.194769 ACACAAAGATTAAAAGTTTCGAACCAT 58.805 29.630 0.00 0.00 0.00 3.55
3782 4500 7.486551 CACACAAAGATTAAAAGTTTCGAACCA 59.513 33.333 0.00 0.00 0.00 3.67
3783 4501 7.486870 ACACACAAAGATTAAAAGTTTCGAACC 59.513 33.333 0.00 0.00 0.00 3.62
3787 4505 9.498307 AAGTACACACAAAGATTAAAAGTTTCG 57.502 29.630 0.00 0.00 0.00 3.46
3822 4540 4.165779 GTTTTGTTTGTGATCTATGCCGG 58.834 43.478 0.00 0.00 0.00 6.13
4025 5716 2.674852 CGAATATGAATGGATCTGGGCG 59.325 50.000 0.00 0.00 0.00 6.13
4171 5862 2.855880 AAACCATTACGCGGCGCCTA 62.856 55.000 27.87 16.80 0.00 3.93
4327 6048 3.428413 TGTTAAACTAGGGGAAGCCAC 57.572 47.619 0.00 0.00 0.00 5.01
4425 6154 4.562082 TCCACACGATTTTCATAGAACGT 58.438 39.130 0.00 0.00 34.40 3.99
4451 6181 1.547675 GCAAAACTGACTCCCCCATGA 60.548 52.381 0.00 0.00 0.00 3.07
4454 6184 1.152830 GGCAAAACTGACTCCCCCA 59.847 57.895 0.00 0.00 0.00 4.96
4486 6511 0.319555 TCAGCAGCACCAGACGTTAC 60.320 55.000 0.00 0.00 0.00 2.50
4531 6556 4.319177 AGACAGAGTGCCATGTAACTTTC 58.681 43.478 0.00 0.00 0.00 2.62
4578 6603 0.820074 ACCGCATGACGTCCCAAAAA 60.820 50.000 14.12 0.00 41.42 1.94
4579 6604 1.228003 ACCGCATGACGTCCCAAAA 60.228 52.632 14.12 0.00 41.42 2.44
4588 6613 0.819259 ACCATATGGCACCGCATGAC 60.819 55.000 22.18 0.00 39.32 3.06
4601 6626 5.920193 ATTTGCTGCAAGTACAACCATAT 57.080 34.783 15.39 0.00 35.30 1.78
4611 6636 3.256383 TGCATGTAGAATTTGCTGCAAGT 59.744 39.130 15.39 10.04 36.75 3.16
4633 6658 5.026790 AGGTTCTTGGAGCAGTAACTATCT 58.973 41.667 0.00 0.00 0.00 1.98
4650 6675 3.913163 ACAAGGAAATCAGAGGAGGTTCT 59.087 43.478 0.00 0.00 0.00 3.01
4653 6678 2.307098 CCACAAGGAAATCAGAGGAGGT 59.693 50.000 0.00 0.00 36.89 3.85
4694 6720 5.117897 GCTCGACAGAAAAACAAAAACAACA 59.882 36.000 0.00 0.00 0.00 3.33
4770 6796 3.888583 TGATATGCACTGAATGGAGCAA 58.111 40.909 0.00 0.00 40.76 3.91
4771 6797 3.564053 TGATATGCACTGAATGGAGCA 57.436 42.857 0.00 0.00 41.73 4.26
4772 6798 5.009310 TGAAATGATATGCACTGAATGGAGC 59.991 40.000 0.00 0.00 28.84 4.70
4842 6868 6.932356 ATGATTGATTAGAAATGCACGTCT 57.068 33.333 6.26 6.26 0.00 4.18
4843 6869 7.188834 TGAATGATTGATTAGAAATGCACGTC 58.811 34.615 0.00 0.00 0.00 4.34
4844 6870 7.066163 TCTGAATGATTGATTAGAAATGCACGT 59.934 33.333 0.00 0.00 0.00 4.49
4845 6871 7.412063 TCTGAATGATTGATTAGAAATGCACG 58.588 34.615 0.00 0.00 0.00 5.34
4846 6872 9.745880 ATTCTGAATGATTGATTAGAAATGCAC 57.254 29.630 1.31 0.00 0.00 4.57
4847 6873 9.744468 CATTCTGAATGATTGATTAGAAATGCA 57.256 29.630 22.75 0.00 41.46 3.96
4848 6874 9.193133 CCATTCTGAATGATTGATTAGAAATGC 57.807 33.333 27.42 0.00 41.46 3.56
4880 7548 8.147704 CAGGTTGTTAGGAAATTTACCATTGTT 58.852 33.333 0.00 0.00 0.00 2.83
4883 7551 7.947890 TCTCAGGTTGTTAGGAAATTTACCATT 59.052 33.333 0.00 0.00 0.00 3.16
4919 7587 5.047731 ACAGATATATGTGTCCATCCTCACG 60.048 44.000 9.62 0.00 37.38 4.35
4929 7597 5.748630 TCGTCTTGCAACAGATATATGTGTC 59.251 40.000 15.27 5.53 32.63 3.67
4936 7604 2.874701 GCCATCGTCTTGCAACAGATAT 59.125 45.455 0.00 0.00 0.00 1.63
5032 7700 7.922505 TCTTAAAATGAAACCACAACATTCG 57.077 32.000 0.00 0.00 33.90 3.34
5037 7705 8.702438 CATGACATCTTAAAATGAAACCACAAC 58.298 33.333 0.00 0.00 0.00 3.32
5053 7721 2.610438 AAAGCACCCCATGACATCTT 57.390 45.000 0.00 0.00 0.00 2.40
5061 7729 0.397535 CCAGCCATAAAGCACCCCAT 60.398 55.000 0.00 0.00 34.23 4.00
5064 7732 0.034089 AGTCCAGCCATAAAGCACCC 60.034 55.000 0.00 0.00 34.23 4.61
5104 7819 6.365520 GGGATGGTTTGTAATATCAGACCTT 58.634 40.000 7.66 2.32 41.35 3.50
5116 7831 0.930726 GGGGATGGGGATGGTTTGTA 59.069 55.000 0.00 0.00 0.00 2.41
5117 7832 1.152387 TGGGGATGGGGATGGTTTGT 61.152 55.000 0.00 0.00 0.00 2.83
5118 7833 0.265553 ATGGGGATGGGGATGGTTTG 59.734 55.000 0.00 0.00 0.00 2.93
5119 7834 1.026173 AATGGGGATGGGGATGGTTT 58.974 50.000 0.00 0.00 0.00 3.27
5120 7835 1.026173 AAATGGGGATGGGGATGGTT 58.974 50.000 0.00 0.00 0.00 3.67
5121 7836 1.934218 TAAATGGGGATGGGGATGGT 58.066 50.000 0.00 0.00 0.00 3.55
5122 7837 4.905566 ATATAAATGGGGATGGGGATGG 57.094 45.455 0.00 0.00 0.00 3.51
5123 7838 6.136155 GGTAATATAAATGGGGATGGGGATG 58.864 44.000 0.00 0.00 0.00 3.51
5124 7839 5.806007 TGGTAATATAAATGGGGATGGGGAT 59.194 40.000 0.00 0.00 0.00 3.85
5125 7840 5.181700 TGGTAATATAAATGGGGATGGGGA 58.818 41.667 0.00 0.00 0.00 4.81
5165 7880 3.253230 GTGCTTGTAATGGATGGTTTGC 58.747 45.455 0.00 0.00 0.00 3.68
5166 7881 3.057596 ACGTGCTTGTAATGGATGGTTTG 60.058 43.478 0.00 0.00 0.00 2.93
5167 7882 3.057596 CACGTGCTTGTAATGGATGGTTT 60.058 43.478 0.82 0.00 0.00 3.27
5168 7883 2.487762 CACGTGCTTGTAATGGATGGTT 59.512 45.455 0.82 0.00 0.00 3.67
5169 7884 2.083774 CACGTGCTTGTAATGGATGGT 58.916 47.619 0.82 0.00 0.00 3.55
5170 7885 2.355197 TCACGTGCTTGTAATGGATGG 58.645 47.619 11.67 0.00 0.00 3.51
5171 7886 3.181507 CCTTCACGTGCTTGTAATGGATG 60.182 47.826 11.67 0.00 0.00 3.51
5172 7887 3.009723 CCTTCACGTGCTTGTAATGGAT 58.990 45.455 11.67 0.00 0.00 3.41
5173 7888 2.422597 CCTTCACGTGCTTGTAATGGA 58.577 47.619 11.67 0.00 0.00 3.41
5174 7889 1.135689 GCCTTCACGTGCTTGTAATGG 60.136 52.381 11.67 5.49 0.00 3.16
5175 7890 1.535028 TGCCTTCACGTGCTTGTAATG 59.465 47.619 11.67 0.00 0.00 1.90
5176 7891 1.890876 TGCCTTCACGTGCTTGTAAT 58.109 45.000 11.67 0.00 0.00 1.89
5177 7892 1.601903 CTTGCCTTCACGTGCTTGTAA 59.398 47.619 11.67 6.07 0.00 2.41
5178 7893 1.225855 CTTGCCTTCACGTGCTTGTA 58.774 50.000 11.67 0.00 0.00 2.41
5261 7976 3.209410 CTTGAGGAGTTGTGTTGCTCTT 58.791 45.455 0.00 0.00 34.50 2.85


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

AutoCloner maintained by Alex Coulton.