Multiple sequence alignment - TraesCS4B01G289200

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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 TraesCS4B01G289200 chr4B 100.000 4146 0 0 1 4146 574177487 574173342 0.000000e+00 7657.0
1 TraesCS4B01G289200 chr4B 81.704 399 62 8 3302 3699 171021603 171021991 5.170000e-84 322.0
2 TraesCS4B01G289200 chr4D 90.498 1326 72 13 718 2036 459423408 459422130 0.000000e+00 1701.0
3 TraesCS4B01G289200 chr4D 89.627 1340 53 21 2368 3630 459390114 459388784 0.000000e+00 1626.0
4 TraesCS4B01G289200 chr4D 92.188 320 19 4 2041 2359 459390375 459390061 8.180000e-122 448.0
5 TraesCS4B01G289200 chr4D 87.212 391 35 9 3624 4000 459388402 459388013 8.230000e-117 431.0
6 TraesCS4B01G289200 chr4D 82.171 387 52 9 3312 3697 95672996 95672626 2.410000e-82 316.0
7 TraesCS4B01G289200 chr4D 91.358 162 13 1 3986 4146 459387364 459387203 1.940000e-53 220.0
8 TraesCS4B01G289200 chr4D 96.429 56 2 0 3095 3150 459389305 459389250 4.410000e-15 93.5
9 TraesCS4B01G289200 chr4A 92.227 1055 48 10 1305 2359 9397576 9398596 0.000000e+00 1463.0
10 TraesCS4B01G289200 chr4A 93.268 609 30 7 619 1217 9396943 9397550 0.000000e+00 887.0
11 TraesCS4B01G289200 chr4A 87.913 786 39 25 2414 3150 9398608 9399386 0.000000e+00 874.0
12 TraesCS4B01G289200 chr4A 79.195 596 77 25 82 637 9396326 9396914 1.820000e-98 370.0
13 TraesCS4B01G289200 chr4A 83.715 393 54 8 3312 3699 700959859 700960246 3.050000e-96 363.0
14 TraesCS4B01G289200 chr4A 86.697 218 25 4 3698 3914 83741144 83741358 5.360000e-59 239.0
15 TraesCS4B01G289200 chr2D 86.469 776 62 23 1002 1752 335121802 335121045 0.000000e+00 811.0
16 TraesCS4B01G289200 chr2D 85.788 774 60 22 2414 3151 335118230 335117471 0.000000e+00 774.0
17 TraesCS4B01G289200 chr2D 91.844 282 22 1 2077 2358 335118522 335118242 3.890000e-105 392.0
18 TraesCS4B01G289200 chr2D 80.000 105 16 5 188 291 634048547 634048447 5.750000e-09 73.1
19 TraesCS4B01G289200 chr2A 85.954 776 66 24 1002 1752 445715758 445715001 0.000000e+00 789.0
20 TraesCS4B01G289200 chr2A 85.751 772 64 19 2414 3151 445712248 445711489 0.000000e+00 774.0
21 TraesCS4B01G289200 chr2A 92.553 282 20 1 2077 2358 445712540 445712260 1.790000e-108 403.0
22 TraesCS4B01G289200 chr2A 84.884 172 23 3 3742 3911 745676904 745677074 1.980000e-38 171.0
23 TraesCS4B01G289200 chr2B 85.806 775 68 23 1002 1752 403092053 403091297 0.000000e+00 784.0
24 TraesCS4B01G289200 chr2B 88.947 380 35 5 2773 3151 403085422 403085049 2.920000e-126 462.0
25 TraesCS4B01G289200 chr2B 91.958 286 21 2 2074 2358 403086261 403085977 2.320000e-107 399.0
26 TraesCS4B01G289200 chr2B 83.508 382 27 11 2414 2762 403085965 403085587 1.440000e-84 324.0
27 TraesCS4B01G289200 chr5A 83.871 217 30 4 3699 3912 659502929 659502715 7.030000e-48 202.0
28 TraesCS4B01G289200 chr5A 80.349 229 32 8 3698 3914 338848205 338847978 1.190000e-35 161.0
29 TraesCS4B01G289200 chr3B 82.273 220 30 9 3700 3914 499814446 499814231 9.160000e-42 182.0
30 TraesCS4B01G289200 chr6D 85.465 172 17 5 3742 3912 379559459 379559295 5.510000e-39 172.0
31 TraesCS4B01G289200 chr5B 86.000 150 17 3 3763 3910 704984251 704984104 1.540000e-34 158.0
32 TraesCS4B01G289200 chr3D 77.727 220 41 6 3698 3914 576783279 576783065 1.210000e-25 128.0


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 TraesCS4B01G289200 chr4B 574173342 574177487 4145 True 7657.000000 7657 100.000000 1 4146 1 chr4B.!!$R1 4145
1 TraesCS4B01G289200 chr4D 459422130 459423408 1278 True 1701.000000 1701 90.498000 718 2036 1 chr4D.!!$R2 1318
2 TraesCS4B01G289200 chr4D 459387203 459390375 3172 True 563.700000 1626 91.362800 2041 4146 5 chr4D.!!$R3 2105
3 TraesCS4B01G289200 chr4A 9396326 9399386 3060 False 898.500000 1463 88.150750 82 3150 4 chr4A.!!$F3 3068
4 TraesCS4B01G289200 chr2D 335117471 335121802 4331 True 659.000000 811 88.033667 1002 3151 3 chr2D.!!$R2 2149
5 TraesCS4B01G289200 chr2A 445711489 445715758 4269 True 655.333333 789 88.086000 1002 3151 3 chr2A.!!$R1 2149
6 TraesCS4B01G289200 chr2B 403091297 403092053 756 True 784.000000 784 85.806000 1002 1752 1 chr2B.!!$R1 750
7 TraesCS4B01G289200 chr2B 403085049 403086261 1212 True 395.000000 462 88.137667 2074 3151 3 chr2B.!!$R2 1077

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
584 646 0.469917 ATAGGATCTGCCAACCACGG 59.530 55.0 0.00 0.0 40.02 4.94 F
1782 2124 0.242017 GTCTGGCAAACTGGTGCATC 59.758 55.0 7.71 0.0 46.81 3.91 F
2054 4485 1.407656 AACGACAGACCAGAAGGCCA 61.408 55.0 5.01 0.0 39.06 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 4441 0.951040 GTTGGCCTTCTGGTCTGTCG 60.951 60.0 3.32 0.0 39.11 4.35 R
2978 5685 0.902984 TCGGCCAGTTCCTCTGCTAA 60.903 55.0 2.24 0.0 42.38 3.09 R
4046 7914 0.251916 TTCAATTGGATCCGTCGGCT 59.748 50.0 6.34 0.0 0.00 5.52 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
36 37 7.769272 TTCAACAATTTCTTGGAATGTGAAC 57.231 32.000 0.00 0.00 36.64 3.18
37 38 6.871844 TCAACAATTTCTTGGAATGTGAACA 58.128 32.000 0.00 0.00 36.64 3.18
38 39 7.326454 TCAACAATTTCTTGGAATGTGAACAA 58.674 30.769 0.00 0.00 36.64 2.83
39 40 7.986320 TCAACAATTTCTTGGAATGTGAACAAT 59.014 29.630 0.00 0.00 36.64 2.71
40 41 8.614346 CAACAATTTCTTGGAATGTGAACAATT 58.386 29.630 0.00 0.00 36.64 2.32
41 42 8.735692 ACAATTTCTTGGAATGTGAACAATTT 57.264 26.923 0.00 0.00 36.64 1.82
42 43 9.176460 ACAATTTCTTGGAATGTGAACAATTTT 57.824 25.926 0.00 0.00 36.64 1.82
83 84 7.602517 ATTTGAACAAAATTTTGGAACGTGA 57.397 28.000 29.37 12.87 42.34 4.35
84 85 7.421530 TTTGAACAAAATTTTGGAACGTGAA 57.578 28.000 29.37 14.37 42.34 3.18
85 86 6.396459 TGAACAAAATTTTGGAACGTGAAC 57.604 33.333 29.37 12.81 42.34 3.18
86 87 5.926542 TGAACAAAATTTTGGAACGTGAACA 59.073 32.000 29.37 14.64 42.34 3.18
87 88 6.591834 TGAACAAAATTTTGGAACGTGAACAT 59.408 30.769 29.37 6.22 42.34 2.71
88 89 6.976636 ACAAAATTTTGGAACGTGAACATT 57.023 29.167 29.37 6.04 42.34 2.71
150 151 9.579610 GGAACATAATTTTTGAAAATGTGAACG 57.420 29.630 15.69 0.00 38.53 3.95
159 160 9.752274 TTTTTGAAAATGTGAACGAATTTCAAG 57.248 25.926 10.64 0.00 46.09 3.02
163 164 7.221838 TGAAAATGTGAACGAATTTCAAGTTCC 59.778 33.333 11.99 6.67 46.09 3.62
172 173 4.320202 CGAATTTCAAGTTCCGGACAATGT 60.320 41.667 1.83 0.00 0.00 2.71
174 175 4.993029 TTTCAAGTTCCGGACAATGTTT 57.007 36.364 1.83 0.00 0.00 2.83
182 183 5.591067 AGTTCCGGACAATGTTTTTGAACTA 59.409 36.000 1.83 0.00 39.34 2.24
213 234 9.974980 AAAAATACACACCGAACATTTTCTTAT 57.025 25.926 0.00 0.00 30.58 1.73
267 289 9.927668 ACTGAACTTTTTGAAAATATATGGTGG 57.072 29.630 0.00 0.00 0.00 4.61
364 406 5.838531 TTTCCAATGTACGGTGAACTTTT 57.161 34.783 0.00 0.00 0.00 2.27
413 455 9.159470 TGAAAAACGTGAACAAATTTGAAAAAC 57.841 25.926 24.64 14.41 0.00 2.43
414 456 9.159470 GAAAAACGTGAACAAATTTGAAAAACA 57.841 25.926 24.64 12.63 0.00 2.83
418 460 8.195617 ACGTGAACAAATTTGAAAAACATGAT 57.804 26.923 24.64 9.33 0.00 2.45
433 475 7.642071 AAAACATGATCAATTCCTGAAAACG 57.358 32.000 0.00 0.00 37.67 3.60
441 483 5.336744 TCAATTCCTGAAAACGTGAACAAC 58.663 37.500 0.00 0.00 0.00 3.32
447 489 4.380023 CCTGAAAACGTGAACAACTTTGGA 60.380 41.667 0.00 0.00 0.00 3.53
448 490 5.122512 TGAAAACGTGAACAACTTTGGAA 57.877 34.783 0.00 0.00 0.00 3.53
468 510 9.709495 TTTGGAATTTCGATCATTTTCTGAAAT 57.291 25.926 3.31 0.00 40.05 2.17
475 517 9.539825 TTTCGATCATTTTCTGAAATTTTGGAA 57.460 25.926 3.31 0.00 37.44 3.53
476 518 9.709495 TTCGATCATTTTCTGAAATTTTGGAAT 57.291 25.926 3.31 0.00 37.44 3.01
477 519 9.709495 TCGATCATTTTCTGAAATTTTGGAATT 57.291 25.926 3.31 0.00 37.44 2.17
478 520 9.962759 CGATCATTTTCTGAAATTTTGGAATTC 57.037 29.630 3.31 0.00 37.44 2.17
534 585 8.893219 AAAAGGAGAAAATAAGCAGAAAAAGG 57.107 30.769 0.00 0.00 0.00 3.11
535 586 7.603180 AAGGAGAAAATAAGCAGAAAAAGGT 57.397 32.000 0.00 0.00 0.00 3.50
548 610 8.251750 AGCAGAAAAAGGTAAGAAAACAAAAC 57.748 30.769 0.00 0.00 0.00 2.43
563 625 4.065321 ACAAAACAATCCATTTTCGGCA 57.935 36.364 0.00 0.00 0.00 5.69
584 646 0.469917 ATAGGATCTGCCAACCACGG 59.530 55.000 0.00 0.00 40.02 4.94
615 677 3.443925 CCGACGAGCTCCTGCAGA 61.444 66.667 17.39 0.00 42.74 4.26
688 798 1.330655 CCGGGCTGAGGTCTGTACAT 61.331 60.000 0.00 0.00 0.00 2.29
693 803 2.033550 GGCTGAGGTCTGTACATAGTCG 59.966 54.545 0.00 0.00 0.00 4.18
695 805 2.946329 CTGAGGTCTGTACATAGTCGCT 59.054 50.000 0.00 0.00 0.00 4.93
697 807 1.405821 AGGTCTGTACATAGTCGCTGC 59.594 52.381 0.00 0.00 0.00 5.25
740 851 4.020617 CTCCTCTGCGCCCAACCA 62.021 66.667 4.18 0.00 0.00 3.67
819 933 9.665719 AATTTTATCGTTTTCTTGCCCAATAAT 57.334 25.926 0.00 0.00 0.00 1.28
900 1014 4.545610 TGGAACTCAATTTGATGCGTTTC 58.454 39.130 0.00 1.03 28.99 2.78
1065 1183 2.034558 AGAAAGGCGAATGGTGTTTGTG 59.965 45.455 0.00 0.00 0.00 3.33
1221 1339 3.827008 ACATCTGTCTCCGTATTGCAT 57.173 42.857 0.00 0.00 0.00 3.96
1342 1470 7.272144 AGTAGGGGAAGTCAGATAATGTTTT 57.728 36.000 0.00 0.00 0.00 2.43
1343 1471 7.112779 AGTAGGGGAAGTCAGATAATGTTTTG 58.887 38.462 0.00 0.00 0.00 2.44
1344 1472 5.892348 AGGGGAAGTCAGATAATGTTTTGT 58.108 37.500 0.00 0.00 0.00 2.83
1345 1473 6.314917 AGGGGAAGTCAGATAATGTTTTGTT 58.685 36.000 0.00 0.00 0.00 2.83
1346 1474 7.466804 AGGGGAAGTCAGATAATGTTTTGTTA 58.533 34.615 0.00 0.00 0.00 2.41
1347 1475 8.116026 AGGGGAAGTCAGATAATGTTTTGTTAT 58.884 33.333 0.00 0.00 0.00 1.89
1348 1476 8.406297 GGGGAAGTCAGATAATGTTTTGTTATC 58.594 37.037 0.00 0.00 38.33 1.75
1349 1477 9.178758 GGGAAGTCAGATAATGTTTTGTTATCT 57.821 33.333 3.27 3.27 45.21 1.98
1351 1479 9.907576 GAAGTCAGATAATGTTTTGTTATCTCG 57.092 33.333 5.63 3.56 43.49 4.04
1352 1480 9.436957 AAGTCAGATAATGTTTTGTTATCTCGT 57.563 29.630 5.63 0.00 43.49 4.18
1353 1481 9.088512 AGTCAGATAATGTTTTGTTATCTCGTC 57.911 33.333 5.63 1.62 43.49 4.20
1354 1482 8.869897 GTCAGATAATGTTTTGTTATCTCGTCA 58.130 33.333 5.63 0.00 43.49 4.35
1355 1483 9.087424 TCAGATAATGTTTTGTTATCTCGTCAG 57.913 33.333 5.63 0.00 43.49 3.51
1356 1484 8.331022 CAGATAATGTTTTGTTATCTCGTCAGG 58.669 37.037 5.63 0.00 43.49 3.86
1357 1485 8.041323 AGATAATGTTTTGTTATCTCGTCAGGT 58.959 33.333 3.27 0.00 42.35 4.00
1358 1486 6.877611 AATGTTTTGTTATCTCGTCAGGTT 57.122 33.333 0.00 0.00 0.00 3.50
1359 1487 6.877611 ATGTTTTGTTATCTCGTCAGGTTT 57.122 33.333 0.00 0.00 0.00 3.27
1360 1488 7.972832 ATGTTTTGTTATCTCGTCAGGTTTA 57.027 32.000 0.00 0.00 0.00 2.01
1361 1489 7.181143 TGTTTTGTTATCTCGTCAGGTTTAC 57.819 36.000 0.00 0.00 0.00 2.01
1362 1490 6.987992 TGTTTTGTTATCTCGTCAGGTTTACT 59.012 34.615 0.00 0.00 0.00 2.24
1363 1491 8.143193 TGTTTTGTTATCTCGTCAGGTTTACTA 58.857 33.333 0.00 0.00 0.00 1.82
1364 1492 8.430828 GTTTTGTTATCTCGTCAGGTTTACTAC 58.569 37.037 0.00 0.00 0.00 2.73
1403 1579 8.203485 TGGATTTTTAATGGTGCTTATCAATCC 58.797 33.333 0.00 0.00 34.19 3.01
1457 1633 9.270640 GAGATCTATAACTGCTGATTTGACATT 57.729 33.333 0.00 0.00 0.00 2.71
1509 1685 8.366401 TGGAAAGAAATTGCATGAAGATGTTTA 58.634 29.630 0.00 0.00 34.05 2.01
1655 1831 3.646736 AGTTAAACAGGATAGGTGGCC 57.353 47.619 0.00 0.00 0.00 5.36
1721 1912 1.205064 CGCACTTCAGGCAAGTTCG 59.795 57.895 0.00 0.00 43.38 3.95
1770 2112 7.442364 GCTAACTATGATATTTGAAGTCTGGCA 59.558 37.037 0.00 0.00 0.00 4.92
1780 2122 0.395586 AAGTCTGGCAAACTGGTGCA 60.396 50.000 0.00 0.00 46.81 4.57
1782 2124 0.242017 GTCTGGCAAACTGGTGCATC 59.758 55.000 7.71 0.00 46.81 3.91
1817 2170 9.732130 AGTATTATAGGCTGAAATCCAGAATTC 57.268 33.333 0.00 0.00 45.78 2.17
1823 2176 4.201920 GGCTGAAATCCAGAATTCGGTTAC 60.202 45.833 13.59 6.79 45.78 2.50
1824 2177 4.394920 GCTGAAATCCAGAATTCGGTTACA 59.605 41.667 13.59 9.64 45.78 2.41
1825 2178 5.673818 GCTGAAATCCAGAATTCGGTTACAC 60.674 44.000 13.59 1.73 45.78 2.90
1826 2179 4.698304 TGAAATCCAGAATTCGGTTACACC 59.302 41.667 13.59 0.00 34.05 4.16
1872 2231 7.390718 GCATTATAAGGTAGAAATGAACCGGAT 59.609 37.037 9.46 0.00 32.29 4.18
1909 2268 5.068215 TGGAAAAATGGGGAACTAACTCA 57.932 39.130 0.00 0.00 0.00 3.41
2054 4485 1.407656 AACGACAGACCAGAAGGCCA 61.408 55.000 5.01 0.00 39.06 5.36
2131 4597 3.412981 TCAACGATTGTGGTTTGTGTG 57.587 42.857 0.00 0.00 0.00 3.82
2359 4825 6.680810 TGGAACAATACTTGAAGCAGATTTG 58.319 36.000 0.00 0.00 31.92 2.32
2360 4826 6.489700 TGGAACAATACTTGAAGCAGATTTGA 59.510 34.615 0.00 0.00 31.92 2.69
2362 4828 7.699812 GGAACAATACTTGAAGCAGATTTGATC 59.300 37.037 0.00 0.00 0.00 2.92
2363 4829 7.692460 ACAATACTTGAAGCAGATTTGATCA 57.308 32.000 0.00 0.00 0.00 2.92
2365 4831 8.242053 ACAATACTTGAAGCAGATTTGATCAAG 58.758 33.333 20.91 20.91 45.51 3.02
2366 4832 5.056894 ACTTGAAGCAGATTTGATCAAGC 57.943 39.130 21.77 8.67 44.78 4.01
2367 4833 4.521639 ACTTGAAGCAGATTTGATCAAGCA 59.478 37.500 21.77 1.61 44.78 3.91
2369 4835 6.376299 ACTTGAAGCAGATTTGATCAAGCATA 59.624 34.615 21.77 0.57 44.78 3.14
2370 4836 6.373186 TGAAGCAGATTTGATCAAGCATAG 57.627 37.500 16.86 6.45 35.76 2.23
2371 4837 6.117488 TGAAGCAGATTTGATCAAGCATAGA 58.883 36.000 16.86 0.00 35.76 1.98
2372 4838 6.771267 TGAAGCAGATTTGATCAAGCATAGAT 59.229 34.615 16.86 4.31 35.76 1.98
2373 4839 7.284716 TGAAGCAGATTTGATCAAGCATAGATT 59.715 33.333 16.86 9.28 35.76 2.40
2374 4840 7.584122 AGCAGATTTGATCAAGCATAGATTT 57.416 32.000 16.86 0.00 35.76 2.17
2375 4841 8.687292 AGCAGATTTGATCAAGCATAGATTTA 57.313 30.769 16.86 0.00 35.76 1.40
2376 4842 9.298250 AGCAGATTTGATCAAGCATAGATTTAT 57.702 29.630 16.86 1.69 35.76 1.40
2377 4843 9.909644 GCAGATTTGATCAAGCATAGATTTATT 57.090 29.630 8.41 0.00 34.19 1.40
2554 5036 6.096282 TCCCCTTTTGTAGTTTCAACTTCAAG 59.904 38.462 10.49 2.79 43.77 3.02
2593 5081 9.930693 CAAGAAGGAAATAAGTACTACAGACTT 57.069 33.333 0.00 0.00 40.27 3.01
2696 5197 4.430007 TGGCGTTAGTCATTAGTGATCAC 58.570 43.478 18.47 18.47 36.60 3.06
2771 5474 9.733556 TGTTGGAGAACTTGCTATATTTTAGAA 57.266 29.630 0.00 0.00 32.79 2.10
2916 5623 1.667212 CAGCATATTTGAGACGCTGCA 59.333 47.619 0.00 0.00 43.09 4.41
2962 5669 5.526479 CGTTGTGAATGAAGATCTGATGGAT 59.474 40.000 0.00 0.00 37.37 3.41
2974 5681 7.146715 AGATCTGATGGATAATCACCAAAGT 57.853 36.000 0.00 0.00 40.50 2.66
3039 5746 3.997064 ATCCACAGACGCTGCGAGC 62.997 63.158 30.47 19.21 38.02 5.03
3122 5829 2.183478 TGTGGCACTGATCAACGAAT 57.817 45.000 19.83 0.00 0.00 3.34
3123 5830 2.503331 TGTGGCACTGATCAACGAATT 58.497 42.857 19.83 0.00 0.00 2.17
3124 5831 2.884012 TGTGGCACTGATCAACGAATTT 59.116 40.909 19.83 0.00 0.00 1.82
3125 5832 3.058293 TGTGGCACTGATCAACGAATTTC 60.058 43.478 19.83 0.00 0.00 2.17
3126 5833 3.189287 GTGGCACTGATCAACGAATTTCT 59.811 43.478 11.13 0.00 0.00 2.52
3127 5834 3.820467 TGGCACTGATCAACGAATTTCTT 59.180 39.130 0.00 0.00 0.00 2.52
3128 5835 4.161333 GGCACTGATCAACGAATTTCTTG 58.839 43.478 0.00 0.00 0.00 3.02
3129 5836 4.161333 GCACTGATCAACGAATTTCTTGG 58.839 43.478 0.00 0.00 0.00 3.61
3130 5837 4.320494 GCACTGATCAACGAATTTCTTGGT 60.320 41.667 0.00 0.00 0.00 3.67
3131 5838 5.762045 CACTGATCAACGAATTTCTTGGTT 58.238 37.500 0.00 0.00 34.10 3.67
3132 5839 6.208644 CACTGATCAACGAATTTCTTGGTTT 58.791 36.000 0.00 0.00 31.79 3.27
3133 5840 6.697019 CACTGATCAACGAATTTCTTGGTTTT 59.303 34.615 0.00 0.00 31.79 2.43
3134 5841 6.918022 ACTGATCAACGAATTTCTTGGTTTTC 59.082 34.615 0.00 0.00 31.79 2.29
3135 5842 6.212955 TGATCAACGAATTTCTTGGTTTTCC 58.787 36.000 0.00 0.00 31.79 3.13
3136 5843 5.845391 TCAACGAATTTCTTGGTTTTCCT 57.155 34.783 0.00 0.00 41.38 3.36
3137 5844 5.587289 TCAACGAATTTCTTGGTTTTCCTG 58.413 37.500 0.00 0.00 41.38 3.86
3138 5845 5.126384 TCAACGAATTTCTTGGTTTTCCTGT 59.874 36.000 0.00 0.00 41.38 4.00
3139 5846 5.183014 ACGAATTTCTTGGTTTTCCTGTC 57.817 39.130 0.00 0.00 41.38 3.51
3140 5847 4.219033 CGAATTTCTTGGTTTTCCTGTCG 58.781 43.478 0.00 0.00 41.38 4.35
3141 5848 4.024387 CGAATTTCTTGGTTTTCCTGTCGA 60.024 41.667 0.00 0.00 41.38 4.20
3142 5849 5.334879 CGAATTTCTTGGTTTTCCTGTCGAT 60.335 40.000 0.00 0.00 41.38 3.59
3143 5850 6.405278 AATTTCTTGGTTTTCCTGTCGATT 57.595 33.333 0.00 0.00 41.38 3.34
3144 5851 4.829064 TTCTTGGTTTTCCTGTCGATTG 57.171 40.909 0.00 0.00 41.38 2.67
3145 5852 4.079980 TCTTGGTTTTCCTGTCGATTGA 57.920 40.909 0.00 0.00 41.38 2.57
3146 5853 4.651778 TCTTGGTTTTCCTGTCGATTGAT 58.348 39.130 0.00 0.00 41.38 2.57
3147 5854 5.800296 TCTTGGTTTTCCTGTCGATTGATA 58.200 37.500 0.00 0.00 41.38 2.15
3148 5855 5.874810 TCTTGGTTTTCCTGTCGATTGATAG 59.125 40.000 0.00 0.00 41.38 2.08
3149 5856 5.160607 TGGTTTTCCTGTCGATTGATAGT 57.839 39.130 6.02 0.00 41.38 2.12
3150 5857 4.935205 TGGTTTTCCTGTCGATTGATAGTG 59.065 41.667 6.02 0.00 41.38 2.74
3151 5858 5.175859 GGTTTTCCTGTCGATTGATAGTGA 58.824 41.667 6.02 1.01 36.94 3.41
3152 5859 5.292101 GGTTTTCCTGTCGATTGATAGTGAG 59.708 44.000 6.02 0.00 36.94 3.51
3153 5860 4.655762 TTCCTGTCGATTGATAGTGAGG 57.344 45.455 6.02 0.00 31.86 3.86
3154 5861 2.362397 TCCTGTCGATTGATAGTGAGGC 59.638 50.000 6.02 0.00 31.86 4.70
3155 5862 2.546795 CCTGTCGATTGATAGTGAGGCC 60.547 54.545 0.00 0.00 31.86 5.19
3156 5863 2.101415 CTGTCGATTGATAGTGAGGCCA 59.899 50.000 5.01 0.00 0.00 5.36
3157 5864 2.101415 TGTCGATTGATAGTGAGGCCAG 59.899 50.000 5.01 0.00 0.00 4.85
3158 5865 2.101582 GTCGATTGATAGTGAGGCCAGT 59.898 50.000 5.01 0.00 0.00 4.00
3159 5866 2.766263 TCGATTGATAGTGAGGCCAGTT 59.234 45.455 5.01 0.00 0.00 3.16
3160 5867 2.868583 CGATTGATAGTGAGGCCAGTTG 59.131 50.000 5.01 0.00 0.00 3.16
3161 5868 3.679917 CGATTGATAGTGAGGCCAGTTGT 60.680 47.826 5.01 0.00 0.00 3.32
3162 5869 2.768253 TGATAGTGAGGCCAGTTGTG 57.232 50.000 5.01 0.00 0.00 3.33
3172 5879 3.327600 CCAGTTGTGGCACTGATCA 57.672 52.632 19.83 0.00 46.29 2.92
3173 5880 1.608055 CCAGTTGTGGCACTGATCAA 58.392 50.000 19.83 0.80 46.29 2.57
3174 5881 1.267806 CCAGTTGTGGCACTGATCAAC 59.732 52.381 19.83 13.87 46.29 3.18
3175 5882 1.069703 CAGTTGTGGCACTGATCAACG 60.070 52.381 19.83 7.16 46.29 4.10
3204 5911 4.160065 TGGTTTTCCCGTCGATTGATAGTA 59.840 41.667 0.00 0.00 39.73 1.82
3205 5912 4.505556 GGTTTTCCCGTCGATTGATAGTAC 59.494 45.833 0.00 0.00 0.00 2.73
3206 5913 4.987408 TTTCCCGTCGATTGATAGTACA 57.013 40.909 0.00 0.00 0.00 2.90
3207 5914 3.976793 TCCCGTCGATTGATAGTACAC 57.023 47.619 0.00 0.00 0.00 2.90
3208 5915 3.281158 TCCCGTCGATTGATAGTACACA 58.719 45.455 0.00 0.00 0.00 3.72
3230 5993 9.155975 ACACATTTTCTCTTCATGTAGATGTAC 57.844 33.333 2.17 0.00 29.78 2.90
3232 5995 9.593134 ACATTTTCTCTTCATGTAGATGTACTC 57.407 33.333 2.17 0.00 29.07 2.59
3278 6054 4.645535 AGTGCAGAGTTTAGATGCTTCAA 58.354 39.130 2.07 0.00 40.62 2.69
3295 6071 4.381505 GCTTCAACCTGTTTGGAACTGAAA 60.382 41.667 0.00 0.00 39.71 2.69
3303 6079 5.309323 TGTTTGGAACTGAAAGACACTTG 57.691 39.130 0.00 0.00 37.43 3.16
3321 6097 4.025480 CACTTGTTGATGAAAAAGCTTGCC 60.025 41.667 0.00 0.00 0.00 4.52
3339 6115 5.394553 GCTTGCCAGGCTTTTATTGATTAGT 60.395 40.000 14.15 0.00 0.00 2.24
3356 6132 9.995003 ATTGATTAGTTAAAATGTTTGCAGGAA 57.005 25.926 0.00 0.00 0.00 3.36
3358 6134 9.421806 TGATTAGTTAAAATGTTTGCAGGAATG 57.578 29.630 0.00 0.00 0.00 2.67
3366 6142 3.286353 TGTTTGCAGGAATGACAACTGA 58.714 40.909 8.75 0.00 34.21 3.41
3397 6173 1.002544 GTACCCAGCCATAGATGCCTC 59.997 57.143 0.00 0.00 0.00 4.70
3404 6180 1.875576 GCCATAGATGCCTCTCCAACG 60.876 57.143 0.00 0.00 32.66 4.10
3416 6192 3.307059 CCTCTCCAACGGAAGAGAAACAT 60.307 47.826 1.05 0.00 38.62 2.71
3431 6207 5.835819 AGAGAAACATCATACCTAGCTAGCA 59.164 40.000 18.83 5.50 0.00 3.49
3444 6220 4.021632 CCTAGCTAGCATGTGAGCTTCATA 60.022 45.833 23.09 9.06 46.99 2.15
3448 6224 4.025061 GCTAGCATGTGAGCTTCATAGTTG 60.025 45.833 10.63 0.00 43.70 3.16
3561 6365 8.819845 TCCAGCTCTTTGATGTATATGATGTAT 58.180 33.333 0.00 0.00 0.00 2.29
3568 6372 8.552083 TTTGATGTATATGATGTATCACCTGC 57.448 34.615 0.00 0.00 40.03 4.85
3577 6381 3.354948 TGTATCACCTGCTTGCAATCT 57.645 42.857 0.00 0.00 0.00 2.40
3589 6393 3.314553 CTTGCAATCTGAAGCAACTTGG 58.685 45.455 14.37 4.53 44.98 3.61
3612 6416 4.848357 AGGTGTACCATTCCAAGATCTTG 58.152 43.478 25.75 25.75 38.19 3.02
3673 6865 2.681976 CGTTGGAGGATCAATCAAGCCT 60.682 50.000 0.00 0.00 36.25 4.58
3713 6905 4.215109 AGAGCCCATTGTTGTAGTTTGTT 58.785 39.130 0.00 0.00 0.00 2.83
3715 6907 3.957497 AGCCCATTGTTGTAGTTTGTTGA 59.043 39.130 0.00 0.00 0.00 3.18
3730 6922 3.302906 TGTTGATCGCGATTTTGATCG 57.697 42.857 24.55 4.55 43.10 3.69
3740 6932 1.745087 GATTTTGATCGCTTCAGGGCA 59.255 47.619 0.00 0.00 35.27 5.36
3750 6942 2.733026 CGCTTCAGGGCATTTTTCTTTG 59.267 45.455 0.00 0.00 0.00 2.77
3755 6947 3.573967 TCAGGGCATTTTTCTTTGTCCTC 59.426 43.478 0.00 0.00 44.58 3.71
3768 6960 0.389391 TGTCCTCGCTTAGGCATAGC 59.611 55.000 0.00 1.23 46.10 2.97
3772 6964 2.963101 TCCTCGCTTAGGCATAGCTTTA 59.037 45.455 0.00 0.00 46.10 1.85
3775 6967 4.372656 CTCGCTTAGGCATAGCTTTAGTT 58.627 43.478 0.00 0.00 38.60 2.24
3800 6992 0.525761 TGACTTTGCTATTTGCCGGC 59.474 50.000 22.73 22.73 42.00 6.13
3808 7000 1.624487 CTATTTGCCGGCGGTTTTTC 58.376 50.000 28.82 10.91 0.00 2.29
3811 7003 1.668101 TTTGCCGGCGGTTTTTCTGT 61.668 50.000 28.82 0.00 0.00 3.41
3812 7004 2.050442 GCCGGCGGTTTTTCTGTG 60.050 61.111 28.82 0.00 0.00 3.66
3822 7014 2.865551 GGTTTTTCTGTGTGTGCATTGG 59.134 45.455 0.00 0.00 0.00 3.16
3831 7023 0.958091 GTGTGCATTGGTGTTGGCTA 59.042 50.000 0.00 0.00 0.00 3.93
3833 7025 1.818060 TGTGCATTGGTGTTGGCTATC 59.182 47.619 0.00 0.00 0.00 2.08
3835 7027 3.278574 GTGCATTGGTGTTGGCTATCTA 58.721 45.455 0.00 0.00 0.00 1.98
3843 7041 5.155161 TGGTGTTGGCTATCTACATCCTAT 58.845 41.667 0.00 0.00 32.48 2.57
3855 7053 6.146140 TCTACATCCTATCTATGCAGAGGT 57.854 41.667 8.78 3.37 33.22 3.85
3856 7054 6.184068 TCTACATCCTATCTATGCAGAGGTC 58.816 44.000 8.78 0.00 33.22 3.85
3858 7056 3.510531 TCCTATCTATGCAGAGGTCGT 57.489 47.619 8.78 0.00 33.22 4.34
3863 7061 2.718563 TCTATGCAGAGGTCGTGTGTA 58.281 47.619 8.78 0.00 0.00 2.90
3870 7068 1.202582 AGAGGTCGTGTGTATGCTCAC 59.797 52.381 5.99 5.99 38.63 3.51
3888 7086 4.757149 GCTCACTGTGTTTGTATCCTCTTT 59.243 41.667 7.79 0.00 0.00 2.52
3978 7182 0.970937 ATCTCGGTCCCGACACACAT 60.971 55.000 3.90 0.00 44.01 3.21
3981 7185 1.446099 CGGTCCCGACACACATCAG 60.446 63.158 0.00 0.00 42.83 2.90
4000 7868 4.260985 TCAGCAGTTGTACCCACATTATG 58.739 43.478 0.00 0.00 33.76 1.90
4031 7899 3.558931 ATCCCAGCGTCAACATTGATA 57.441 42.857 0.00 0.00 39.73 2.15
4034 7902 4.269183 TCCCAGCGTCAACATTGATATTT 58.731 39.130 0.00 0.00 39.73 1.40
4037 7905 7.220740 TCCCAGCGTCAACATTGATATTTATA 58.779 34.615 0.00 0.00 39.73 0.98
4055 7923 1.186917 TAAAACCCTCAGCCGACGGA 61.187 55.000 20.50 0.00 0.00 4.69
4056 7924 1.838073 AAAACCCTCAGCCGACGGAT 61.838 55.000 20.50 9.11 0.00 4.18
4057 7925 2.240162 AAACCCTCAGCCGACGGATC 62.240 60.000 20.50 0.00 0.00 3.36
4059 7927 3.147595 CCTCAGCCGACGGATCCA 61.148 66.667 20.50 0.00 0.00 3.41
4061 7929 1.443407 CTCAGCCGACGGATCCAAT 59.557 57.895 20.50 0.00 0.00 3.16
4063 7931 0.461870 TCAGCCGACGGATCCAATTG 60.462 55.000 20.50 0.00 0.00 2.32
4064 7932 0.461870 CAGCCGACGGATCCAATTGA 60.462 55.000 20.50 0.00 0.00 2.57
4066 7934 0.657840 GCCGACGGATCCAATTGAAG 59.342 55.000 20.50 0.00 0.00 3.02
4086 7955 0.321122 GTCTGGTGAGCTTGTCCAGG 60.321 60.000 23.11 11.48 45.97 4.45
4095 7964 2.061220 CTTGTCCAGGAGCTGTCCA 58.939 57.895 0.00 0.00 46.80 4.02
4120 7989 1.398390 GGATGTTCTGGTCGCACATTC 59.602 52.381 0.00 0.00 29.40 2.67
4128 7997 0.517316 GGTCGCACATTCAGTTGGTC 59.483 55.000 0.00 0.00 0.00 4.02
4131 8000 0.518636 CGCACATTCAGTTGGTCCAG 59.481 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.474920 GTTCACATTCCAAGAAATTGTTGAATA 57.525 29.630 4.31 0.00 0.00 1.75
11 12 7.986320 TGTTCACATTCCAAGAAATTGTTGAAT 59.014 29.630 4.31 0.68 0.00 2.57
12 13 7.326454 TGTTCACATTCCAAGAAATTGTTGAA 58.674 30.769 4.31 0.00 0.00 2.69
13 14 6.871844 TGTTCACATTCCAAGAAATTGTTGA 58.128 32.000 4.31 0.00 0.00 3.18
14 15 7.536895 TTGTTCACATTCCAAGAAATTGTTG 57.463 32.000 0.00 0.00 0.00 3.33
15 16 8.735692 AATTGTTCACATTCCAAGAAATTGTT 57.264 26.923 0.00 0.00 0.00 2.83
16 17 8.735692 AAATTGTTCACATTCCAAGAAATTGT 57.264 26.923 0.00 0.00 0.00 2.71
58 59 8.034058 TCACGTTCCAAAATTTTGTTCAAATT 57.966 26.923 25.25 4.94 45.50 1.82
59 60 7.602517 TCACGTTCCAAAATTTTGTTCAAAT 57.397 28.000 25.25 7.39 36.57 2.32
60 61 7.042051 TGTTCACGTTCCAAAATTTTGTTCAAA 60.042 29.630 25.25 13.30 36.45 2.69
61 62 6.423905 TGTTCACGTTCCAAAATTTTGTTCAA 59.576 30.769 25.25 14.20 36.45 2.69
62 63 5.926542 TGTTCACGTTCCAAAATTTTGTTCA 59.073 32.000 25.25 9.59 36.45 3.18
63 64 6.396459 TGTTCACGTTCCAAAATTTTGTTC 57.604 33.333 25.25 15.29 36.45 3.18
64 65 6.976636 ATGTTCACGTTCCAAAATTTTGTT 57.023 29.167 25.25 5.55 36.45 2.83
65 66 6.976636 AATGTTCACGTTCCAAAATTTTGT 57.023 29.167 25.25 7.53 36.45 2.83
66 67 8.666580 AAAAATGTTCACGTTCCAAAATTTTG 57.333 26.923 21.65 21.65 37.90 2.44
124 125 9.579610 CGTTCACATTTTCAAAAATTATGTTCC 57.420 29.630 0.00 0.00 36.52 3.62
150 151 5.121221 ACATTGTCCGGAACTTGAAATTC 57.879 39.130 5.23 0.00 0.00 2.17
153 154 4.993029 AAACATTGTCCGGAACTTGAAA 57.007 36.364 5.23 0.00 0.00 2.69
159 160 4.678622 AGTTCAAAAACATTGTCCGGAAC 58.321 39.130 5.23 0.59 37.88 3.62
163 164 7.922505 TTTCATAGTTCAAAAACATTGTCCG 57.077 32.000 0.00 0.00 37.88 4.79
199 220 9.417284 GTTCACCGTATAATAAGAAAATGTTCG 57.583 33.333 0.00 0.00 38.90 3.95
242 263 9.927668 ACCACCATATATTTTCAAAAAGTTCAG 57.072 29.630 0.00 0.00 0.00 3.02
371 413 9.919348 CACGTTTTTCAAATTTTGATCAGATTT 57.081 25.926 12.39 11.31 39.84 2.17
374 416 8.591312 GTTCACGTTTTTCAAATTTTGATCAGA 58.409 29.630 12.39 0.00 39.84 3.27
376 418 8.244494 TGTTCACGTTTTTCAAATTTTGATCA 57.756 26.923 12.39 0.00 39.84 2.92
377 419 9.535270 TTTGTTCACGTTTTTCAAATTTTGATC 57.465 25.926 12.39 4.09 39.84 2.92
379 421 9.884465 AATTTGTTCACGTTTTTCAAATTTTGA 57.116 22.222 17.11 7.74 42.24 2.69
384 426 9.884465 TTTCAAATTTGTTCACGTTTTTCAAAT 57.116 22.222 17.47 10.10 39.38 2.32
387 429 9.159470 GTTTTTCAAATTTGTTCACGTTTTTCA 57.841 25.926 17.47 0.00 0.00 2.69
388 430 9.159470 TGTTTTTCAAATTTGTTCACGTTTTTC 57.841 25.926 17.47 0.52 0.00 2.29
389 431 9.670719 ATGTTTTTCAAATTTGTTCACGTTTTT 57.329 22.222 17.47 0.00 0.00 1.94
408 450 7.710475 ACGTTTTCAGGAATTGATCATGTTTTT 59.290 29.630 0.00 0.00 40.66 1.94
413 455 5.941733 TCACGTTTTCAGGAATTGATCATG 58.058 37.500 0.00 0.00 41.18 3.07
414 456 6.016360 TGTTCACGTTTTCAGGAATTGATCAT 60.016 34.615 0.00 0.00 35.27 2.45
418 460 5.124776 AGTTGTTCACGTTTTCAGGAATTGA 59.875 36.000 0.00 0.00 0.00 2.57
424 466 3.857093 CCAAAGTTGTTCACGTTTTCAGG 59.143 43.478 0.00 0.00 0.00 3.86
433 475 6.205784 TGATCGAAATTCCAAAGTTGTTCAC 58.794 36.000 0.00 0.00 0.00 3.18
441 483 8.746922 TTCAGAAAATGATCGAAATTCCAAAG 57.253 30.769 0.00 0.00 37.89 2.77
448 490 9.709495 TCCAAAATTTCAGAAAATGATCGAAAT 57.291 25.926 0.00 0.00 37.89 2.17
513 564 8.793592 TCTTACCTTTTTCTGCTTATTTTCTCC 58.206 33.333 0.00 0.00 0.00 3.71
532 583 9.679661 AAAATGGATTGTTTTGTTTTCTTACCT 57.320 25.926 0.00 0.00 0.00 3.08
534 585 9.631639 CGAAAATGGATTGTTTTGTTTTCTTAC 57.368 29.630 0.00 0.00 34.89 2.34
535 586 8.821894 CCGAAAATGGATTGTTTTGTTTTCTTA 58.178 29.630 0.00 0.00 34.89 2.10
548 610 5.261209 TCCTATTTGCCGAAAATGGATTG 57.739 39.130 7.98 0.00 38.64 2.67
563 625 2.643551 CGTGGTTGGCAGATCCTATTT 58.356 47.619 6.91 0.00 35.26 1.40
586 648 4.849329 CGTCGGCTAGGTCGTGCC 62.849 72.222 0.00 0.00 45.25 5.01
599 661 2.202544 GTCTGCAGGAGCTCGTCG 60.203 66.667 15.13 3.90 42.74 5.12
670 780 1.338337 CTATGTACAGACCTCAGCCCG 59.662 57.143 0.33 0.00 0.00 6.13
683 793 1.536284 GGTGGAGCAGCGACTATGTAC 60.536 57.143 0.00 0.00 0.00 2.90
737 848 4.752879 CGCGGATTCGTGGGTGGT 62.753 66.667 0.00 0.00 42.54 4.16
917 1035 5.648092 CCATATTCCTCAACTCGGTTTTCTT 59.352 40.000 0.00 0.00 0.00 2.52
925 1043 3.819564 TCACCCATATTCCTCAACTCG 57.180 47.619 0.00 0.00 0.00 4.18
1065 1183 3.314541 AAACATGTCGTCCCTACTGTC 57.685 47.619 0.00 0.00 0.00 3.51
1221 1339 6.053005 ACGAAACCACACAAAGAGAATAGAA 58.947 36.000 0.00 0.00 0.00 2.10
1342 1470 6.624423 GCAGTAGTAAACCTGACGAGATAACA 60.624 42.308 0.00 0.00 0.00 2.41
1343 1471 5.742926 GCAGTAGTAAACCTGACGAGATAAC 59.257 44.000 0.00 0.00 0.00 1.89
1344 1472 5.416639 TGCAGTAGTAAACCTGACGAGATAA 59.583 40.000 0.00 0.00 0.00 1.75
1345 1473 4.945543 TGCAGTAGTAAACCTGACGAGATA 59.054 41.667 0.00 0.00 0.00 1.98
1346 1474 3.762288 TGCAGTAGTAAACCTGACGAGAT 59.238 43.478 0.00 0.00 0.00 2.75
1347 1475 3.151554 TGCAGTAGTAAACCTGACGAGA 58.848 45.455 0.00 0.00 0.00 4.04
1348 1476 3.570926 TGCAGTAGTAAACCTGACGAG 57.429 47.619 0.00 0.00 0.00 4.18
1349 1477 3.305813 CCTTGCAGTAGTAAACCTGACGA 60.306 47.826 0.00 0.00 0.00 4.20
1350 1478 2.993899 CCTTGCAGTAGTAAACCTGACG 59.006 50.000 0.00 0.00 0.00 4.35
1351 1479 4.246458 CTCCTTGCAGTAGTAAACCTGAC 58.754 47.826 0.00 0.00 0.00 3.51
1352 1480 3.901844 ACTCCTTGCAGTAGTAAACCTGA 59.098 43.478 0.00 0.00 0.00 3.86
1353 1481 4.273148 ACTCCTTGCAGTAGTAAACCTG 57.727 45.455 0.00 0.00 0.00 4.00
1354 1482 6.407202 CATTACTCCTTGCAGTAGTAAACCT 58.593 40.000 16.64 3.93 38.72 3.50
1355 1483 5.585047 CCATTACTCCTTGCAGTAGTAAACC 59.415 44.000 16.64 0.00 38.72 3.27
1356 1484 6.403878 TCCATTACTCCTTGCAGTAGTAAAC 58.596 40.000 16.64 0.00 38.72 2.01
1357 1485 6.614694 TCCATTACTCCTTGCAGTAGTAAA 57.385 37.500 16.64 3.93 38.72 2.01
1358 1486 6.808321 ATCCATTACTCCTTGCAGTAGTAA 57.192 37.500 15.61 15.61 39.36 2.24
1359 1487 6.808321 AATCCATTACTCCTTGCAGTAGTA 57.192 37.500 1.91 1.91 30.40 1.82
1360 1488 5.700402 AATCCATTACTCCTTGCAGTAGT 57.300 39.130 3.58 3.58 30.40 2.73
1361 1489 7.396540 AAAAATCCATTACTCCTTGCAGTAG 57.603 36.000 0.00 0.00 30.40 2.57
1362 1490 8.871629 TTAAAAATCCATTACTCCTTGCAGTA 57.128 30.769 0.00 0.00 0.00 2.74
1363 1491 7.775053 TTAAAAATCCATTACTCCTTGCAGT 57.225 32.000 0.00 0.00 0.00 4.40
1364 1492 7.707893 CCATTAAAAATCCATTACTCCTTGCAG 59.292 37.037 0.00 0.00 0.00 4.41
1403 1579 9.941664 GTTGATCAAATACTATGTCCATTTCAG 57.058 33.333 10.35 0.00 0.00 3.02
1421 1597 7.924947 CAGCAGTTATAGATCTCAGTTGATCAA 59.075 37.037 3.38 3.38 43.76 2.57
1457 1633 5.815581 AGCAATGAACAATCTACCACCTAA 58.184 37.500 0.00 0.00 0.00 2.69
1509 1685 6.942005 TCTAAGGATGTCACAATTTGTCACAT 59.058 34.615 17.51 17.51 0.00 3.21
1692 1870 2.489329 CCTGAAGTGCGGACAATCAATT 59.511 45.455 10.52 0.00 0.00 2.32
1823 2176 5.672819 GCATAAAAGCCTAACTGTAACGGTG 60.673 44.000 0.00 0.00 0.00 4.94
1824 2177 4.393990 GCATAAAAGCCTAACTGTAACGGT 59.606 41.667 0.00 0.00 0.00 4.83
1825 2178 4.393680 TGCATAAAAGCCTAACTGTAACGG 59.606 41.667 0.00 0.00 0.00 4.44
1826 2179 5.539582 TGCATAAAAGCCTAACTGTAACG 57.460 39.130 0.00 0.00 0.00 3.18
1830 2183 8.850156 CCTTATAATGCATAAAAGCCTAACTGT 58.150 33.333 0.00 0.00 0.00 3.55
1858 2216 6.001449 TCCTTCATTATCCGGTTCATTTCT 57.999 37.500 0.00 0.00 0.00 2.52
1872 2231 7.288389 CCCATTTTTCCATCAGATCCTTCATTA 59.712 37.037 0.00 0.00 0.00 1.90
2036 4440 1.407656 TTGGCCTTCTGGTCTGTCGT 61.408 55.000 3.32 0.00 39.11 4.34
2037 4441 0.951040 GTTGGCCTTCTGGTCTGTCG 60.951 60.000 3.32 0.00 39.11 4.35
2087 4553 3.386768 TGGTACAGTGAAGCAGAAGAC 57.613 47.619 0.00 0.00 0.00 3.01
2395 4861 9.880157 CAAAGGATTTTTCTCATATTGTTCCAT 57.120 29.630 0.00 0.00 35.03 3.41
2396 4862 8.313292 CCAAAGGATTTTTCTCATATTGTTCCA 58.687 33.333 0.00 0.00 35.03 3.53
2397 4863 7.278646 GCCAAAGGATTTTTCTCATATTGTTCC 59.721 37.037 0.00 0.00 35.03 3.62
2398 4864 7.278646 GGCCAAAGGATTTTTCTCATATTGTTC 59.721 37.037 0.00 0.00 35.03 3.18
2399 4865 7.038088 AGGCCAAAGGATTTTTCTCATATTGTT 60.038 33.333 5.01 0.00 35.03 2.83
2400 4866 6.441604 AGGCCAAAGGATTTTTCTCATATTGT 59.558 34.615 5.01 0.00 35.03 2.71
2401 4867 6.881570 AGGCCAAAGGATTTTTCTCATATTG 58.118 36.000 5.01 0.00 35.03 1.90
2402 4868 8.645110 CATAGGCCAAAGGATTTTTCTCATATT 58.355 33.333 5.01 0.00 35.03 1.28
2403 4869 7.786464 ACATAGGCCAAAGGATTTTTCTCATAT 59.214 33.333 5.01 0.00 35.03 1.78
2404 4870 7.125391 ACATAGGCCAAAGGATTTTTCTCATA 58.875 34.615 5.01 0.00 35.03 2.15
2405 4871 5.960202 ACATAGGCCAAAGGATTTTTCTCAT 59.040 36.000 5.01 0.00 35.03 2.90
2406 4872 5.332743 ACATAGGCCAAAGGATTTTTCTCA 58.667 37.500 5.01 0.00 35.03 3.27
2407 4873 5.921962 ACATAGGCCAAAGGATTTTTCTC 57.078 39.130 5.01 0.00 35.03 2.87
2408 4874 9.660544 AATATACATAGGCCAAAGGATTTTTCT 57.339 29.630 5.01 0.00 35.03 2.52
2409 4875 9.696917 CAATATACATAGGCCAAAGGATTTTTC 57.303 33.333 5.01 0.00 35.03 2.29
2410 4876 8.650490 CCAATATACATAGGCCAAAGGATTTTT 58.350 33.333 5.01 0.00 35.03 1.94
2411 4877 7.789349 ACCAATATACATAGGCCAAAGGATTTT 59.211 33.333 5.01 0.00 35.03 1.82
2412 4878 7.305246 ACCAATATACATAGGCCAAAGGATTT 58.695 34.615 5.01 0.00 40.26 2.17
2531 4998 6.863275 ACTTGAAGTTGAAACTACAAAAGGG 58.137 36.000 0.00 0.00 38.57 3.95
2593 5081 9.337396 AGTAATGGACATATTTCGAAATGCTAA 57.663 29.630 29.20 12.86 0.00 3.09
2696 5197 2.673368 GCAACTACAAGTCCTGATTCCG 59.327 50.000 0.00 0.00 0.00 4.30
2783 5486 7.807907 CGACAGCATATTATTTTTCATAACCCC 59.192 37.037 0.00 0.00 0.00 4.95
2916 5623 1.407437 CGATAAGAGGCTTGCCCAGTT 60.407 52.381 8.17 2.34 35.39 3.16
2974 5681 1.276421 GCCAGTTCCTCTGCTAACTCA 59.724 52.381 0.00 0.00 42.38 3.41
2978 5685 0.902984 TCGGCCAGTTCCTCTGCTAA 60.903 55.000 2.24 0.00 42.38 3.09
3039 5746 2.629050 ATCCATCGCCTCGACGGTTG 62.629 60.000 1.29 0.00 40.28 3.77
3040 5747 2.351336 GATCCATCGCCTCGACGGTT 62.351 60.000 1.29 0.00 40.28 4.44
3076 5783 1.067821 CTCGCCTCTCCTGGAATGTAC 59.932 57.143 0.00 0.00 0.00 2.90
3122 5829 4.884744 TCAATCGACAGGAAAACCAAGAAA 59.115 37.500 0.00 0.00 0.00 2.52
3123 5830 4.456535 TCAATCGACAGGAAAACCAAGAA 58.543 39.130 0.00 0.00 0.00 2.52
3124 5831 4.079980 TCAATCGACAGGAAAACCAAGA 57.920 40.909 0.00 0.00 0.00 3.02
3125 5832 5.643777 ACTATCAATCGACAGGAAAACCAAG 59.356 40.000 0.00 0.00 0.00 3.61
3126 5833 5.411361 CACTATCAATCGACAGGAAAACCAA 59.589 40.000 0.00 0.00 0.00 3.67
3127 5834 4.935205 CACTATCAATCGACAGGAAAACCA 59.065 41.667 0.00 0.00 0.00 3.67
3128 5835 5.175859 TCACTATCAATCGACAGGAAAACC 58.824 41.667 0.00 0.00 0.00 3.27
3129 5836 5.292101 CCTCACTATCAATCGACAGGAAAAC 59.708 44.000 0.00 0.00 0.00 2.43
3130 5837 5.419542 CCTCACTATCAATCGACAGGAAAA 58.580 41.667 0.00 0.00 0.00 2.29
3131 5838 4.680708 GCCTCACTATCAATCGACAGGAAA 60.681 45.833 0.00 0.00 0.00 3.13
3132 5839 3.181475 GCCTCACTATCAATCGACAGGAA 60.181 47.826 0.00 0.00 0.00 3.36
3133 5840 2.362397 GCCTCACTATCAATCGACAGGA 59.638 50.000 0.00 0.00 0.00 3.86
3134 5841 2.546795 GGCCTCACTATCAATCGACAGG 60.547 54.545 0.00 0.00 0.00 4.00
3135 5842 2.101415 TGGCCTCACTATCAATCGACAG 59.899 50.000 3.32 0.00 0.00 3.51
3136 5843 2.101415 CTGGCCTCACTATCAATCGACA 59.899 50.000 3.32 0.00 0.00 4.35
3137 5844 2.101582 ACTGGCCTCACTATCAATCGAC 59.898 50.000 3.32 0.00 0.00 4.20
3138 5845 2.388735 ACTGGCCTCACTATCAATCGA 58.611 47.619 3.32 0.00 0.00 3.59
3139 5846 2.868583 CAACTGGCCTCACTATCAATCG 59.131 50.000 3.32 0.00 0.00 3.34
3140 5847 3.624861 CACAACTGGCCTCACTATCAATC 59.375 47.826 3.32 0.00 0.00 2.67
3141 5848 3.614092 CACAACTGGCCTCACTATCAAT 58.386 45.455 3.32 0.00 0.00 2.57
3142 5849 2.290260 CCACAACTGGCCTCACTATCAA 60.290 50.000 3.32 0.00 0.00 2.57
3143 5850 1.278985 CCACAACTGGCCTCACTATCA 59.721 52.381 3.32 0.00 0.00 2.15
3144 5851 2.029838 CCACAACTGGCCTCACTATC 57.970 55.000 3.32 0.00 0.00 2.08
3154 5861 1.267806 GTTGATCAGTGCCACAACTGG 59.732 52.381 14.76 0.00 46.27 4.00
3156 5863 1.229428 CGTTGATCAGTGCCACAACT 58.771 50.000 17.62 0.00 39.92 3.16
3157 5864 0.944386 ACGTTGATCAGTGCCACAAC 59.056 50.000 0.00 13.10 39.08 3.32
3158 5865 1.674359 AACGTTGATCAGTGCCACAA 58.326 45.000 0.00 0.00 0.00 3.33
3159 5866 1.601903 GAAACGTTGATCAGTGCCACA 59.398 47.619 0.00 0.00 0.00 4.17
3160 5867 1.873591 AGAAACGTTGATCAGTGCCAC 59.126 47.619 0.00 0.00 0.00 5.01
3161 5868 2.254546 AGAAACGTTGATCAGTGCCA 57.745 45.000 0.00 0.00 0.00 4.92
3162 5869 2.350772 CCAAGAAACGTTGATCAGTGCC 60.351 50.000 0.00 0.00 0.00 5.01
3163 5870 2.290641 ACCAAGAAACGTTGATCAGTGC 59.709 45.455 0.00 0.00 0.00 4.40
3164 5871 4.552166 AACCAAGAAACGTTGATCAGTG 57.448 40.909 0.00 0.00 0.00 3.66
3165 5872 5.449999 GGAAAACCAAGAAACGTTGATCAGT 60.450 40.000 0.00 0.00 0.00 3.41
3166 5873 4.976116 GGAAAACCAAGAAACGTTGATCAG 59.024 41.667 0.00 0.00 0.00 2.90
3167 5874 4.202070 GGGAAAACCAAGAAACGTTGATCA 60.202 41.667 0.00 0.00 39.85 2.92
3168 5875 4.295870 GGGAAAACCAAGAAACGTTGATC 58.704 43.478 0.00 0.00 39.85 2.92
3169 5876 3.243267 CGGGAAAACCAAGAAACGTTGAT 60.243 43.478 0.00 0.00 40.22 2.57
3170 5877 2.097791 CGGGAAAACCAAGAAACGTTGA 59.902 45.455 0.00 0.00 40.22 3.18
3171 5878 2.159352 ACGGGAAAACCAAGAAACGTTG 60.159 45.455 0.00 0.00 40.22 4.10
3172 5879 2.093890 ACGGGAAAACCAAGAAACGTT 58.906 42.857 0.00 0.00 40.22 3.99
3173 5880 1.672363 GACGGGAAAACCAAGAAACGT 59.328 47.619 0.00 0.00 40.22 3.99
3174 5881 1.333435 CGACGGGAAAACCAAGAAACG 60.333 52.381 0.00 0.00 40.22 3.60
3175 5882 1.941975 TCGACGGGAAAACCAAGAAAC 59.058 47.619 0.00 0.00 40.22 2.78
3204 5911 9.155975 GTACATCTACATGAAGAGAAAATGTGT 57.844 33.333 0.00 3.14 36.08 3.72
3205 5912 9.376075 AGTACATCTACATGAAGAGAAAATGTG 57.624 33.333 0.00 0.00 36.08 3.21
3206 5913 9.593134 GAGTACATCTACATGAAGAGAAAATGT 57.407 33.333 0.00 3.80 38.13 2.71
3207 5914 9.591792 TGAGTACATCTACATGAAGAGAAAATG 57.408 33.333 0.00 0.00 33.72 2.32
3278 6054 3.694566 GTGTCTTTCAGTTCCAAACAGGT 59.305 43.478 0.00 0.00 39.02 4.00
3295 6071 5.841957 AGCTTTTTCATCAACAAGTGTCT 57.158 34.783 0.00 0.00 0.00 3.41
3303 6079 3.062042 CCTGGCAAGCTTTTTCATCAAC 58.938 45.455 0.00 0.00 0.00 3.18
3339 6115 7.224362 CAGTTGTCATTCCTGCAAACATTTTAA 59.776 33.333 0.00 0.00 0.00 1.52
3349 6125 2.104622 TGACTCAGTTGTCATTCCTGCA 59.895 45.455 0.00 0.00 41.43 4.41
3358 6134 3.951775 ACTCCTCATGACTCAGTTGTC 57.048 47.619 0.00 0.00 37.47 3.18
3366 6142 1.490574 GCTGGGTACTCCTCATGACT 58.509 55.000 0.00 0.00 36.20 3.41
3397 6173 3.664107 TGATGTTTCTCTTCCGTTGGAG 58.336 45.455 0.00 0.00 31.21 3.86
3404 6180 6.168270 AGCTAGGTATGATGTTTCTCTTCC 57.832 41.667 0.00 0.00 0.00 3.46
3416 6192 3.256879 GCTCACATGCTAGCTAGGTATGA 59.743 47.826 22.10 9.82 35.80 2.15
3431 6207 3.276857 CTGCCAACTATGAAGCTCACAT 58.723 45.455 10.43 10.43 0.00 3.21
3444 6220 1.004440 GAACCTCGAGCTGCCAACT 60.004 57.895 6.99 0.00 0.00 3.16
3561 6365 2.156917 CTTCAGATTGCAAGCAGGTGA 58.843 47.619 18.24 9.24 0.00 4.02
3577 6381 2.486548 GGTACACCTCCAAGTTGCTTCA 60.487 50.000 0.00 0.00 0.00 3.02
3589 6393 4.878397 CAAGATCTTGGAATGGTACACCTC 59.122 45.833 25.14 0.00 37.90 3.85
3612 6416 1.604915 GAGGGTCTCTCTTTGGCCC 59.395 63.158 0.00 0.00 39.38 5.80
3613 6417 1.604915 GGAGGGTCTCTCTTTGGCC 59.395 63.158 0.00 0.00 42.10 5.36
3622 6426 2.191641 GCATGCAGGGAGGGTCTC 59.808 66.667 14.21 0.00 0.00 3.36
3655 6847 2.357465 CCAAGGCTTGATTGATCCTCCA 60.357 50.000 28.18 0.00 0.00 3.86
3657 6849 3.287867 TCCAAGGCTTGATTGATCCTC 57.712 47.619 28.18 0.00 0.00 3.71
3673 6865 5.112668 GGCTCTTCCATGTTGGTTATCCAA 61.113 45.833 0.86 0.86 41.99 3.53
3730 6922 3.732212 ACAAAGAAAAATGCCCTGAAGC 58.268 40.909 0.00 0.00 0.00 3.86
3755 6947 5.485662 AAAACTAAAGCTATGCCTAAGCG 57.514 39.130 0.00 0.00 44.87 4.68
3796 6988 1.008995 CACACAGAAAAACCGCCGG 60.009 57.895 0.00 0.00 0.00 6.13
3800 6992 2.490328 ATGCACACACAGAAAAACCG 57.510 45.000 0.00 0.00 0.00 4.44
3808 7000 1.536496 CCAACACCAATGCACACACAG 60.536 52.381 0.00 0.00 0.00 3.66
3811 7003 1.042003 AGCCAACACCAATGCACACA 61.042 50.000 0.00 0.00 0.00 3.72
3812 7004 0.958091 TAGCCAACACCAATGCACAC 59.042 50.000 0.00 0.00 0.00 3.82
3822 7014 6.597832 AGATAGGATGTAGATAGCCAACAC 57.402 41.667 0.00 0.00 0.00 3.32
3831 7023 6.740693 ACCTCTGCATAGATAGGATGTAGAT 58.259 40.000 0.00 0.00 42.68 1.98
3833 7025 5.065859 CGACCTCTGCATAGATAGGATGTAG 59.934 48.000 0.00 0.00 38.10 2.74
3835 7027 3.761218 CGACCTCTGCATAGATAGGATGT 59.239 47.826 0.00 0.00 31.21 3.06
3843 7041 1.545841 ACACACGACCTCTGCATAGA 58.454 50.000 0.00 0.00 0.00 1.98
3855 7053 1.339929 ACACAGTGAGCATACACACGA 59.660 47.619 7.81 0.00 41.66 4.35
3856 7054 1.783284 ACACAGTGAGCATACACACG 58.217 50.000 7.81 4.75 41.66 4.49
3858 7056 3.540617 ACAAACACAGTGAGCATACACA 58.459 40.909 7.81 0.00 42.45 3.72
3863 7061 4.019860 AGAGGATACAAACACAGTGAGCAT 60.020 41.667 7.81 0.00 41.41 3.79
3870 7068 6.992063 AGCATAAAGAGGATACAAACACAG 57.008 37.500 0.00 0.00 41.41 3.66
3945 7148 3.239449 ACCGAGATGGCACTTATATGGA 58.761 45.455 0.00 0.00 43.94 3.41
3978 7182 2.949177 AATGTGGGTACAACTGCTGA 57.051 45.000 0.00 0.00 40.84 4.26
3981 7185 4.457603 TGAACATAATGTGGGTACAACTGC 59.542 41.667 0.00 0.00 40.84 4.40
4000 7868 0.804989 CGCTGGGATTTCCACTGAAC 59.195 55.000 0.00 0.00 41.46 3.18
4031 7899 3.875134 CGTCGGCTGAGGGTTTTATAAAT 59.125 43.478 7.37 0.00 0.00 1.40
4034 7902 1.137479 CCGTCGGCTGAGGGTTTTATA 59.863 52.381 23.55 0.00 43.64 0.98
4037 7905 2.032071 CCGTCGGCTGAGGGTTTT 59.968 61.111 23.55 0.00 43.64 2.43
4045 7913 0.461870 TCAATTGGATCCGTCGGCTG 60.462 55.000 6.34 0.00 0.00 4.85
4046 7914 0.251916 TTCAATTGGATCCGTCGGCT 59.748 50.000 6.34 0.00 0.00 5.52
4055 7923 3.875369 GCTCACCAGACCTTCAATTGGAT 60.875 47.826 5.42 0.00 34.76 3.41
4056 7924 2.553028 GCTCACCAGACCTTCAATTGGA 60.553 50.000 5.42 0.00 34.76 3.53
4057 7925 1.815003 GCTCACCAGACCTTCAATTGG 59.185 52.381 5.42 0.00 36.76 3.16
4059 7927 3.152341 CAAGCTCACCAGACCTTCAATT 58.848 45.455 0.00 0.00 0.00 2.32
4061 7929 1.490490 ACAAGCTCACCAGACCTTCAA 59.510 47.619 0.00 0.00 0.00 2.69
4063 7931 1.609320 GGACAAGCTCACCAGACCTTC 60.609 57.143 0.00 0.00 0.00 3.46
4064 7932 0.398318 GGACAAGCTCACCAGACCTT 59.602 55.000 0.00 0.00 0.00 3.50
4066 7934 1.754745 TGGACAAGCTCACCAGACC 59.245 57.895 2.95 0.00 0.00 3.85
4095 7964 0.321653 GCGACCAGAACATCCCTTGT 60.322 55.000 0.00 0.00 41.53 3.16
4120 7989 5.089970 TCATAGATGAACTGGACCAACTG 57.910 43.478 0.00 0.00 33.08 3.16


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

AutoCloner maintained by Alex Coulton.