Multiple sequence alignment - TraesCS1B01G099600

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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 TraesCS1B01G099600 chr1B 100.000 5252 0 0 1 5252 107132328 107137579 0.000000e+00 9699.0
1 TraesCS1B01G099600 chr1B 90.164 61 5 1 1555 1614 561188291 561188231 1.570000e-10 78.7
2 TraesCS1B01G099600 chr1A 92.171 2248 125 33 1614 3826 65262839 65265070 0.000000e+00 3129.0
3 TraesCS1B01G099600 chr1A 86.507 1586 110 45 4 1556 65261333 65262847 0.000000e+00 1648.0
4 TraesCS1B01G099600 chr1A 89.757 742 52 14 3923 4660 65265093 65265814 0.000000e+00 928.0
5 TraesCS1B01G099600 chr1A 90.309 485 39 8 4774 5252 65266256 65266738 3.450000e-176 628.0
6 TraesCS1B01G099600 chr1A 78.710 465 48 27 490 945 158973194 158973616 4.030000e-66 263.0
7 TraesCS1B01G099600 chr1A 83.966 237 35 3 2592 2828 147166543 147166776 1.900000e-54 224.0
8 TraesCS1B01G099600 chr1A 97.297 37 1 0 4725 4761 65266181 65266217 4.390000e-06 63.9
9 TraesCS1B01G099600 chr1D 95.693 1927 57 9 1624 3538 66556352 66558264 0.000000e+00 3075.0
10 TraesCS1B01G099600 chr1D 90.101 1586 84 26 4 1556 66554807 66556352 0.000000e+00 1991.0
11 TraesCS1B01G099600 chr1D 92.569 619 35 7 3923 4535 66558690 66559303 0.000000e+00 878.0
12 TraesCS1B01G099600 chr1D 88.488 582 47 10 4678 5252 66560621 66561189 0.000000e+00 686.0
13 TraesCS1B01G099600 chr1D 95.076 264 12 1 3563 3826 66558406 66558668 1.050000e-111 414.0
14 TraesCS1B01G099600 chr1D 85.387 349 46 2 2969 3317 356417081 356417424 1.800000e-94 357.0
15 TraesCS1B01G099600 chr1D 91.525 118 6 2 4528 4645 66560445 66560558 5.440000e-35 159.0
16 TraesCS1B01G099600 chr1D 100.000 35 0 0 3531 3565 66558269 66558303 1.220000e-06 65.8
17 TraesCS1B01G099600 chr3A 81.555 759 118 12 2560 3317 511213071 511212334 1.620000e-169 606.0
18 TraesCS1B01G099600 chr6A 81.447 760 117 14 2560 3317 474453069 474452332 7.530000e-168 601.0
19 TraesCS1B01G099600 chr2A 80.000 760 126 17 2560 3317 603917405 603916670 5.980000e-149 538.0
20 TraesCS1B01G099600 chr2A 93.617 94 1 3 3836 3927 632952904 632952994 9.170000e-28 135.0
21 TraesCS1B01G099600 chr7A 82.631 593 82 12 2715 3306 47777152 47776580 6.070000e-139 505.0
22 TraesCS1B01G099600 chr7A 78.901 455 47 21 499 945 320366444 320366031 4.030000e-66 263.0
23 TraesCS1B01G099600 chr5B 81.532 509 71 12 2811 3317 203498605 203498118 1.060000e-106 398.0
24 TraesCS1B01G099600 chr5B 79.431 457 42 24 499 945 555729091 555728677 5.180000e-70 276.0
25 TraesCS1B01G099600 chr5B 89.720 107 4 5 3836 3940 140966019 140965918 4.270000e-26 130.0
26 TraesCS1B01G099600 chr2D 83.377 379 58 2 2939 3317 21436999 21436626 3.890000e-91 346.0
27 TraesCS1B01G099600 chr6B 79.741 464 44 23 490 945 518611326 518611747 1.850000e-74 291.0
28 TraesCS1B01G099600 chr6B 92.553 94 1 5 3836 3927 233032502 233032413 4.270000e-26 130.0
29 TraesCS1B01G099600 chr6B 90.196 102 5 4 3838 3937 13827613 13827515 1.540000e-25 128.0
30 TraesCS1B01G099600 chr2B 79.780 455 42 23 499 945 306176563 306176151 8.610000e-73 285.0
31 TraesCS1B01G099600 chr2B 79.310 464 46 23 490 945 190629171 190629592 4.010000e-71 279.0
32 TraesCS1B01G099600 chr2B 91.803 61 4 1 1555 1614 4731748 4731688 3.370000e-12 84.2
33 TraesCS1B01G099600 chr4A 79.431 457 42 24 499 945 375967557 375967143 5.180000e-70 276.0
34 TraesCS1B01G099600 chr7B 78.808 453 48 26 499 945 595719816 595719406 1.450000e-65 261.0
35 TraesCS1B01G099600 chr5D 89.720 107 4 5 3836 3939 128577677 128577575 4.270000e-26 130.0
36 TraesCS1B01G099600 chr5D 88.182 110 6 5 3828 3935 331118934 331119038 1.990000e-24 124.0
37 TraesCS1B01G099600 chr3B 87.611 113 6 7 3840 3950 113917150 113917044 1.990000e-24 124.0
38 TraesCS1B01G099600 chr4D 89.320 103 4 6 3841 3941 245478338 245478435 7.140000e-24 122.0
39 TraesCS1B01G099600 chr6D 87.273 110 8 4 3836 3942 380136975 380137081 2.570000e-23 121.0
40 TraesCS1B01G099600 chr6D 91.667 60 5 0 1555 1614 28626974 28626915 3.370000e-12 84.2
41 TraesCS1B01G099600 chr3D 85.470 117 10 5 3815 3931 197182409 197182300 1.200000e-21 115.0
42 TraesCS1B01G099600 chr4B 85.437 103 8 6 3841 3941 345265766 345265669 3.350000e-17 100.0
43 TraesCS1B01G099600 chr4B 84.314 102 9 5 3841 3939 445238649 445238552 5.600000e-15 93.5


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 TraesCS1B01G099600 chr1B 107132328 107137579 5251 False 9699.00 9699 100.000000 1 5252 1 chr1B.!!$F1 5251
1 TraesCS1B01G099600 chr1A 65261333 65266738 5405 False 1279.38 3129 91.208200 4 5252 5 chr1A.!!$F3 5248
2 TraesCS1B01G099600 chr1D 66554807 66561189 6382 False 1038.40 3075 93.350286 4 5252 7 chr1D.!!$F2 5248
3 TraesCS1B01G099600 chr3A 511212334 511213071 737 True 606.00 606 81.555000 2560 3317 1 chr3A.!!$R1 757
4 TraesCS1B01G099600 chr6A 474452332 474453069 737 True 601.00 601 81.447000 2560 3317 1 chr6A.!!$R1 757
5 TraesCS1B01G099600 chr2A 603916670 603917405 735 True 538.00 538 80.000000 2560 3317 1 chr2A.!!$R1 757
6 TraesCS1B01G099600 chr7A 47776580 47777152 572 True 505.00 505 82.631000 2715 3306 1 chr7A.!!$R1 591

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
360 380 0.033920 TCACTCGCAAGTCACAGCAT 59.966 50.000 0.00 0.00 31.71 3.79 F
1592 1647 0.178975 AGAGATGTAGAGGCCGAGGG 60.179 60.000 0.00 0.00 0.00 4.30 F
1593 1648 0.468400 GAGATGTAGAGGCCGAGGGT 60.468 60.000 0.00 0.00 0.00 4.34 F
1594 1649 0.851469 AGATGTAGAGGCCGAGGGTA 59.149 55.000 0.00 0.00 0.00 3.69 F
1598 1653 0.967662 GTAGAGGCCGAGGGTATTCC 59.032 60.000 0.00 0.00 0.00 3.01 F
1608 1663 1.232909 AGGGTATTCCTCCTCCTCGA 58.767 55.000 0.00 0.00 44.06 4.04 F
2420 2481 1.272147 GGCCACTGGACCAGAGATTTT 60.272 52.381 28.56 0.77 35.18 1.82 F
4129 4339 0.541063 TTTCGCCTCCTTTTTCCCCC 60.541 55.000 0.00 0.00 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2335 0.038744 ATAGCAGCACAGCCTTTGGT 59.961 50.000 0.00 0.0 34.23 3.67 R
3267 3336 1.075601 TTGACTCTCCATTGGGGCTT 58.924 50.000 2.09 0.0 36.21 4.35 R
3374 3443 6.267496 AGTTAGGAAATGCGCTGTAAAAAT 57.733 33.333 9.73 0.0 0.00 1.82 R
3683 3883 2.953466 AACTCAATCACATGCCATGC 57.047 45.000 4.17 0.0 0.00 4.06 R
3700 3900 8.394121 TCAATGTAATTTGCTTTCCAACAAAAC 58.606 29.630 0.00 0.0 39.09 2.43 R
3720 3920 7.775120 AGAAGAACAAACAATGAAGTCAATGT 58.225 30.769 0.00 0.0 41.36 2.71 R
4147 4358 0.245539 CTGCAAGGGTTCATGGCAAG 59.754 55.000 0.00 0.0 33.58 4.01 R
5045 6745 1.511305 CGGAGGTATCGTGTGTGCT 59.489 57.895 0.00 0.0 0.00 4.40 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
102 113 3.900892 CCCGATGTCTCCGACCCG 61.901 72.222 0.00 0.00 0.00 5.28
142 153 1.303236 CCAATCCAGCCACCGACAA 60.303 57.895 0.00 0.00 0.00 3.18
192 203 2.277373 GAGCGACACGTAGCTCGG 60.277 66.667 19.26 0.00 45.53 4.63
196 207 1.061570 CGACACGTAGCTCGGTACC 59.938 63.158 0.16 0.16 44.69 3.34
208 219 4.439472 GGTACCGCGCACGCTTTG 62.439 66.667 13.70 4.15 39.32 2.77
323 343 1.082954 CCTTTCCCCCTCCTCCTCA 59.917 63.158 0.00 0.00 0.00 3.86
351 371 3.175240 CGCCGTCTCACTCGCAAG 61.175 66.667 0.00 0.00 0.00 4.01
352 372 2.049063 GCCGTCTCACTCGCAAGT 60.049 61.111 0.00 0.00 35.60 3.16
354 374 1.285950 CCGTCTCACTCGCAAGTCA 59.714 57.895 0.00 0.00 31.71 3.41
355 375 1.004277 CCGTCTCACTCGCAAGTCAC 61.004 60.000 0.00 0.00 31.71 3.67
356 376 0.317854 CGTCTCACTCGCAAGTCACA 60.318 55.000 0.00 0.00 31.71 3.58
357 377 1.413382 GTCTCACTCGCAAGTCACAG 58.587 55.000 0.00 0.00 31.71 3.66
358 378 0.319040 TCTCACTCGCAAGTCACAGC 60.319 55.000 0.00 0.00 31.71 4.40
359 379 0.598419 CTCACTCGCAAGTCACAGCA 60.598 55.000 0.00 0.00 31.71 4.41
360 380 0.033920 TCACTCGCAAGTCACAGCAT 59.966 50.000 0.00 0.00 31.71 3.79
394 416 0.251634 CTCTTGGGAGAGTTGGGAGC 59.748 60.000 0.00 0.00 43.66 4.70
403 426 4.821589 GTTGGGAGCGGAGGAGCG 62.822 72.222 0.00 0.00 43.00 5.03
485 512 7.418337 TTCTGCTTCTATGTGGTTAGTGATA 57.582 36.000 0.00 0.00 0.00 2.15
488 515 7.778382 TCTGCTTCTATGTGGTTAGTGATACTA 59.222 37.037 0.00 0.00 0.00 1.82
494 521 5.324784 TGTGGTTAGTGATACTAGCAGTG 57.675 43.478 5.44 0.00 34.15 3.66
550 577 2.371841 ACACATCAGTTGGGCTGTTAGA 59.628 45.455 0.00 0.00 45.23 2.10
551 578 3.005554 CACATCAGTTGGGCTGTTAGAG 58.994 50.000 0.00 0.00 45.23 2.43
553 580 2.839486 TCAGTTGGGCTGTTAGAGTG 57.161 50.000 0.00 0.00 45.23 3.51
554 581 2.047061 TCAGTTGGGCTGTTAGAGTGT 58.953 47.619 0.00 0.00 45.23 3.55
555 582 2.438021 TCAGTTGGGCTGTTAGAGTGTT 59.562 45.455 0.00 0.00 45.23 3.32
556 583 3.644265 TCAGTTGGGCTGTTAGAGTGTTA 59.356 43.478 0.00 0.00 45.23 2.41
563 590 4.323562 GGGCTGTTAGAGTGTTAGGTTCAT 60.324 45.833 0.00 0.00 0.00 2.57
627 655 4.703897 TGCTAGTACTTGCTGTTGTTCTT 58.296 39.130 25.89 0.00 32.65 2.52
628 656 4.511454 TGCTAGTACTTGCTGTTGTTCTTG 59.489 41.667 25.89 0.00 32.65 3.02
629 657 4.083802 GCTAGTACTTGCTGTTGTTCTTGG 60.084 45.833 20.15 0.00 0.00 3.61
630 658 4.150897 AGTACTTGCTGTTGTTCTTGGA 57.849 40.909 0.00 0.00 0.00 3.53
666 696 1.031235 TGTGTTGTGTGATTGGCCTG 58.969 50.000 3.32 0.00 0.00 4.85
667 697 1.032014 GTGTTGTGTGATTGGCCTGT 58.968 50.000 3.32 0.00 0.00 4.00
726 759 0.792640 CTGCTGTGGTTTCTACTGCG 59.207 55.000 9.50 0.00 43.33 5.18
766 799 5.065090 TGAATCTGCAATAAACCTGATGACG 59.935 40.000 0.00 0.00 0.00 4.35
772 805 5.064579 TGCAATAAACCTGATGACGTACATG 59.935 40.000 5.41 0.00 39.56 3.21
773 806 5.293324 GCAATAAACCTGATGACGTACATGA 59.707 40.000 0.00 0.00 39.56 3.07
776 809 8.487970 CAATAAACCTGATGACGTACATGATAC 58.512 37.037 0.00 0.00 39.56 2.24
777 810 5.592104 AACCTGATGACGTACATGATACA 57.408 39.130 0.00 0.00 39.56 2.29
778 811 4.933330 ACCTGATGACGTACATGATACAC 58.067 43.478 0.00 0.00 39.56 2.90
779 812 4.645136 ACCTGATGACGTACATGATACACT 59.355 41.667 0.00 0.00 39.56 3.55
780 813 5.826208 ACCTGATGACGTACATGATACACTA 59.174 40.000 0.00 0.00 39.56 2.74
781 814 6.017026 ACCTGATGACGTACATGATACACTAG 60.017 42.308 0.00 0.00 39.56 2.57
880 923 5.395990 GGGTTCTATGTCCTGAAATAACGGA 60.396 44.000 0.00 0.00 0.00 4.69
885 928 8.014070 TCTATGTCCTGAAATAACGGAACATA 57.986 34.615 0.00 0.00 0.00 2.29
1079 1127 3.567797 GCACGATGCTTCCTCGCC 61.568 66.667 0.00 0.00 40.96 5.54
1092 1140 1.395045 CCTCGCCTGATGGACTGCTA 61.395 60.000 0.00 0.00 34.57 3.49
1137 1185 3.181456 GCTTGACCTATGAATCTCTGGCT 60.181 47.826 0.00 0.00 0.00 4.75
1221 1269 1.460504 TCGTGCCTCTTGTCGACTAT 58.539 50.000 17.92 0.00 0.00 2.12
1308 1356 3.322466 ACCGGGAGCTCCAACCTG 61.322 66.667 33.29 17.90 37.91 4.00
1369 1423 5.036737 CCGCAGATTTACCAAATTCATGTC 58.963 41.667 0.00 0.00 0.00 3.06
1385 1439 3.072330 TCATGTCTGCTTTAACCTGTGGA 59.928 43.478 0.00 0.00 0.00 4.02
1388 1442 3.135712 TGTCTGCTTTAACCTGTGGAAGA 59.864 43.478 0.00 0.00 0.00 2.87
1517 1572 4.500375 GCAGATGGTATGATTTGCCTTTCC 60.500 45.833 0.00 0.00 29.25 3.13
1521 1576 4.277476 TGGTATGATTTGCCTTTCCGAAT 58.723 39.130 0.00 0.00 0.00 3.34
1556 1611 4.627900 TGTTTGCGCTATTCACGAGATTAA 59.372 37.500 9.73 0.00 0.00 1.40
1557 1612 5.120986 TGTTTGCGCTATTCACGAGATTAAA 59.879 36.000 9.73 0.00 0.00 1.52
1558 1613 5.984233 TTGCGCTATTCACGAGATTAAAT 57.016 34.783 9.73 0.00 0.00 1.40
1559 1614 5.328886 TGCGCTATTCACGAGATTAAATG 57.671 39.130 9.73 0.00 0.00 2.32
1560 1615 4.211164 TGCGCTATTCACGAGATTAAATGG 59.789 41.667 9.73 0.00 0.00 3.16
1561 1616 4.702392 CGCTATTCACGAGATTAAATGGC 58.298 43.478 0.00 0.00 33.72 4.40
1562 1617 4.449068 CGCTATTCACGAGATTAAATGGCT 59.551 41.667 0.00 0.00 34.56 4.75
1563 1618 5.613360 CGCTATTCACGAGATTAAATGGCTG 60.613 44.000 0.00 0.00 34.56 4.85
1564 1619 5.237344 GCTATTCACGAGATTAAATGGCTGT 59.763 40.000 0.00 0.00 34.10 4.40
1565 1620 4.944962 TTCACGAGATTAAATGGCTGTG 57.055 40.909 0.00 0.00 0.00 3.66
1566 1621 3.937814 TCACGAGATTAAATGGCTGTGT 58.062 40.909 0.00 0.00 0.00 3.72
1567 1622 3.684305 TCACGAGATTAAATGGCTGTGTG 59.316 43.478 0.00 0.00 0.00 3.82
1568 1623 2.420022 ACGAGATTAAATGGCTGTGTGC 59.580 45.455 0.00 0.00 41.94 4.57
1569 1624 2.419673 CGAGATTAAATGGCTGTGTGCA 59.580 45.455 0.00 0.00 45.15 4.57
1570 1625 3.065786 CGAGATTAAATGGCTGTGTGCAT 59.934 43.478 0.00 0.00 45.15 3.96
1571 1626 4.604976 GAGATTAAATGGCTGTGTGCATC 58.395 43.478 0.00 0.00 45.15 3.91
1572 1627 4.018490 AGATTAAATGGCTGTGTGCATCA 58.982 39.130 0.00 0.00 45.15 3.07
1573 1628 4.463539 AGATTAAATGGCTGTGTGCATCAA 59.536 37.500 0.00 0.00 45.15 2.57
1574 1629 2.736144 AAATGGCTGTGTGCATCAAG 57.264 45.000 0.00 0.00 45.15 3.02
1575 1630 1.913778 AATGGCTGTGTGCATCAAGA 58.086 45.000 0.00 0.00 45.15 3.02
1576 1631 1.460504 ATGGCTGTGTGCATCAAGAG 58.539 50.000 0.00 0.00 45.15 2.85
1577 1632 0.397564 TGGCTGTGTGCATCAAGAGA 59.602 50.000 0.00 0.00 45.15 3.10
1578 1633 1.003928 TGGCTGTGTGCATCAAGAGAT 59.996 47.619 0.00 0.00 45.15 2.75
1588 1643 3.023946 CATCAAGAGATGTAGAGGCCG 57.976 52.381 0.00 0.00 45.28 6.13
1589 1644 2.437085 TCAAGAGATGTAGAGGCCGA 57.563 50.000 0.00 0.00 0.00 5.54
1590 1645 2.302260 TCAAGAGATGTAGAGGCCGAG 58.698 52.381 0.00 0.00 0.00 4.63
1591 1646 1.339610 CAAGAGATGTAGAGGCCGAGG 59.660 57.143 0.00 0.00 0.00 4.63
1592 1647 0.178975 AGAGATGTAGAGGCCGAGGG 60.179 60.000 0.00 0.00 0.00 4.30
1593 1648 0.468400 GAGATGTAGAGGCCGAGGGT 60.468 60.000 0.00 0.00 0.00 4.34
1594 1649 0.851469 AGATGTAGAGGCCGAGGGTA 59.149 55.000 0.00 0.00 0.00 3.69
1595 1650 1.429687 AGATGTAGAGGCCGAGGGTAT 59.570 52.381 0.00 0.00 0.00 2.73
1596 1651 2.158295 AGATGTAGAGGCCGAGGGTATT 60.158 50.000 0.00 0.00 0.00 1.89
1597 1652 1.700955 TGTAGAGGCCGAGGGTATTC 58.299 55.000 0.00 0.00 0.00 1.75
1598 1653 0.967662 GTAGAGGCCGAGGGTATTCC 59.032 60.000 0.00 0.00 0.00 3.01
1607 1662 3.852558 AGGGTATTCCTCCTCCTCG 57.147 57.895 0.00 0.00 44.06 4.63
1608 1663 1.232909 AGGGTATTCCTCCTCCTCGA 58.767 55.000 0.00 0.00 44.06 4.04
1609 1664 1.574339 AGGGTATTCCTCCTCCTCGAA 59.426 52.381 0.00 0.00 44.06 3.71
1610 1665 2.023307 AGGGTATTCCTCCTCCTCGAAA 60.023 50.000 0.00 0.00 44.06 3.46
1611 1666 2.770232 GGGTATTCCTCCTCCTCGAAAA 59.230 50.000 0.00 0.00 0.00 2.29
1612 1667 3.199289 GGGTATTCCTCCTCCTCGAAAAA 59.801 47.826 0.00 0.00 0.00 1.94
1680 1735 8.937634 ATTATTCAGGTGAGATTTGCAAAATC 57.062 30.769 17.19 16.94 0.00 2.17
1895 1955 5.540911 AGTGTTAGTTTTATCGTCGGGAAA 58.459 37.500 0.00 0.00 0.00 3.13
1974 2034 6.807708 CAGTATGGTACGTCATCAAGTTAC 57.192 41.667 0.00 0.00 0.00 2.50
1982 2042 4.084287 ACGTCATCAAGTTACCTAGACCA 58.916 43.478 0.00 0.00 0.00 4.02
1983 2043 4.082354 ACGTCATCAAGTTACCTAGACCAC 60.082 45.833 0.00 0.00 0.00 4.16
1988 2048 5.209818 TCAAGTTACCTAGACCACTTGTG 57.790 43.478 19.21 0.00 44.34 3.33
2049 2109 5.652014 TGAACAAGTCCATTCTCTTTTGTGT 59.348 36.000 0.00 0.00 0.00 3.72
2128 2188 2.241176 TGGCTTAACCGGGATTCTGATT 59.759 45.455 6.32 0.00 43.94 2.57
2349 2409 5.349817 CCCAACAGTATGCATCGATATCTTC 59.650 44.000 0.19 0.00 42.53 2.87
2420 2481 1.272147 GGCCACTGGACCAGAGATTTT 60.272 52.381 28.56 0.77 35.18 1.82
2688 2749 3.226777 CCAGTACGGAGAGATGATCCTT 58.773 50.000 0.00 0.00 36.56 3.36
2713 2774 7.946207 TGAATTGTTAATAGCACAGGTTTGAA 58.054 30.769 0.00 0.00 0.00 2.69
2976 3039 8.277197 TGCCCTCTCAGTACTACTATTAAACTA 58.723 37.037 0.00 0.00 0.00 2.24
3098 3164 4.641396 CTGTTGTGTGGATAGAGAACCAA 58.359 43.478 0.00 0.00 37.94 3.67
3125 3191 5.336744 CGTGAAAACAAAACAAAGGAGCTA 58.663 37.500 0.00 0.00 0.00 3.32
3137 3203 9.586435 AAAACAAAGGAGCTAATATTGCAATAC 57.414 29.630 21.10 8.80 0.00 1.89
3173 3239 2.585330 TCCTTTGTGATCTGCTTTGCA 58.415 42.857 0.00 0.00 36.92 4.08
3174 3240 3.159472 TCCTTTGTGATCTGCTTTGCAT 58.841 40.909 0.00 0.00 38.13 3.96
3246 3315 8.424918 TGGTGACAAGATTTTTGCCTTTTATTA 58.575 29.630 0.00 0.00 37.44 0.98
3255 3324 3.848272 TGCCTTTTATTACAGCTGTGC 57.152 42.857 29.57 20.41 0.00 4.57
3267 3336 2.566529 CTGTGCGAGCGTCTACCA 59.433 61.111 0.00 0.00 0.00 3.25
3676 3876 4.155709 AGATCGAGATTTAGGATGAGGCA 58.844 43.478 0.00 0.00 0.00 4.75
3683 3883 6.146837 CGAGATTTAGGATGAGGCAATTAGTG 59.853 42.308 0.00 0.00 0.00 2.74
3700 3900 1.749063 AGTGCATGGCATGTGATTGAG 59.251 47.619 26.94 1.03 41.91 3.02
3720 3920 8.729805 ATTGAGTTTTGTTGGAAAGCAAATTA 57.270 26.923 0.00 0.00 34.99 1.40
3760 3960 6.458232 TGTTCTTCTCTATTCTACTCTGCC 57.542 41.667 0.00 0.00 0.00 4.85
3848 4058 6.593268 ACTTCTGAAGTTTAGTACTCCCTC 57.407 41.667 17.00 0.00 39.04 4.30
3849 4059 6.316513 ACTTCTGAAGTTTAGTACTCCCTCT 58.683 40.000 17.00 0.00 39.04 3.69
3850 4060 7.468496 ACTTCTGAAGTTTAGTACTCCCTCTA 58.532 38.462 17.00 0.00 39.04 2.43
3851 4061 7.949006 ACTTCTGAAGTTTAGTACTCCCTCTAA 59.051 37.037 17.00 0.00 39.04 2.10
3852 4062 8.716674 TTCTGAAGTTTAGTACTCCCTCTAAA 57.283 34.615 0.00 0.00 35.54 1.85
3853 4063 8.350852 TCTGAAGTTTAGTACTCCCTCTAAAG 57.649 38.462 0.00 0.00 36.99 1.85
3854 4064 8.168725 TCTGAAGTTTAGTACTCCCTCTAAAGA 58.831 37.037 0.00 0.00 36.99 2.52
3855 4065 8.716674 TGAAGTTTAGTACTCCCTCTAAAGAA 57.283 34.615 0.00 0.00 36.99 2.52
3856 4066 9.151177 TGAAGTTTAGTACTCCCTCTAAAGAAA 57.849 33.333 0.00 0.00 36.99 2.52
3865 4075 9.917129 GTACTCCCTCTAAAGAAATATAAGAGC 57.083 37.037 0.00 0.00 33.80 4.09
3866 4076 7.662897 ACTCCCTCTAAAGAAATATAAGAGCG 58.337 38.462 0.00 0.00 33.80 5.03
3867 4077 7.288158 ACTCCCTCTAAAGAAATATAAGAGCGT 59.712 37.037 0.00 0.00 33.80 5.07
3868 4078 8.019656 TCCCTCTAAAGAAATATAAGAGCGTT 57.980 34.615 0.00 0.00 33.80 4.84
3869 4079 8.483758 TCCCTCTAAAGAAATATAAGAGCGTTT 58.516 33.333 0.00 0.00 33.80 3.60
3870 4080 9.760077 CCCTCTAAAGAAATATAAGAGCGTTTA 57.240 33.333 0.00 0.00 33.80 2.01
3884 4094 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
3885 4095 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
3899 4109 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
3900 4110 7.251994 ACTAAAGTAGTGATCTAAACGCTCTG 58.748 38.462 0.00 0.00 37.69 3.35
3901 4111 5.899120 AAGTAGTGATCTAAACGCTCTGA 57.101 39.130 0.00 0.00 0.00 3.27
3902 4112 6.458232 AAGTAGTGATCTAAACGCTCTGAT 57.542 37.500 0.00 0.00 0.00 2.90
3903 4113 7.569639 AAGTAGTGATCTAAACGCTCTGATA 57.430 36.000 0.00 0.00 0.00 2.15
3904 4114 7.753309 AGTAGTGATCTAAACGCTCTGATAT 57.247 36.000 0.00 0.00 0.00 1.63
3905 4115 8.172352 AGTAGTGATCTAAACGCTCTGATATT 57.828 34.615 0.00 0.00 0.00 1.28
3906 4116 8.634444 AGTAGTGATCTAAACGCTCTGATATTT 58.366 33.333 0.00 0.00 0.00 1.40
3907 4117 9.894783 GTAGTGATCTAAACGCTCTGATATTTA 57.105 33.333 0.00 0.00 0.00 1.40
3908 4118 8.804688 AGTGATCTAAACGCTCTGATATTTAC 57.195 34.615 0.00 0.00 0.00 2.01
3909 4119 8.634444 AGTGATCTAAACGCTCTGATATTTACT 58.366 33.333 0.00 0.00 0.00 2.24
3910 4120 9.250624 GTGATCTAAACGCTCTGATATTTACTT 57.749 33.333 0.00 0.00 0.00 2.24
3919 4129 9.900710 ACGCTCTGATATTTACTTATTACAGAG 57.099 33.333 0.85 0.85 46.94 3.35
3920 4130 9.347934 CGCTCTGATATTTACTTATTACAGAGG 57.652 37.037 18.05 8.22 45.44 3.69
3921 4131 9.646427 GCTCTGATATTTACTTATTACAGAGGG 57.354 37.037 18.05 1.06 45.44 4.30
3969 4179 3.144506 CATCTCCATGCATCCTTACACC 58.855 50.000 0.00 0.00 0.00 4.16
3979 4189 3.758554 GCATCCTTACACCATGTGAAACT 59.241 43.478 0.49 0.00 38.04 2.66
4004 4214 3.437395 TGTTGCAGTACGTTGTGAAACTT 59.563 39.130 17.24 0.00 38.04 2.66
4091 4301 2.896044 TCCTCTCTGGTATGCAGCATAG 59.104 50.000 15.81 6.33 37.07 2.23
4125 4335 3.756963 ACCTACATTTCGCCTCCTTTTTC 59.243 43.478 0.00 0.00 0.00 2.29
4127 4337 1.893137 ACATTTCGCCTCCTTTTTCCC 59.107 47.619 0.00 0.00 0.00 3.97
4128 4338 1.204704 CATTTCGCCTCCTTTTTCCCC 59.795 52.381 0.00 0.00 0.00 4.81
4129 4339 0.541063 TTTCGCCTCCTTTTTCCCCC 60.541 55.000 0.00 0.00 0.00 5.40
4147 4358 1.341209 CCCCCTCTTTCAGTGCAAAAC 59.659 52.381 0.00 0.00 0.00 2.43
4271 4482 2.289547 GAGGAGTCGAGAGCACTATGAC 59.710 54.545 7.62 7.62 34.14 3.06
4282 4493 2.230508 AGCACTATGACGTTTCCGAAGA 59.769 45.455 0.00 0.00 37.88 2.87
4429 4646 6.998968 AATGGATGATTCAACTCTGAAGAC 57.001 37.500 0.00 0.00 44.68 3.01
4452 4669 3.915437 AAAAGGCACGTTTGTATCCAG 57.085 42.857 0.00 0.00 38.83 3.86
4456 4673 5.347620 AAGGCACGTTTGTATCCAGTATA 57.652 39.130 0.00 0.00 0.00 1.47
4498 4715 1.891919 GGAGTGCTTGCACGGTGAA 60.892 57.895 18.32 0.00 0.00 3.18
4502 4719 0.100503 GTGCTTGCACGGTGAAAACT 59.899 50.000 13.29 0.00 0.00 2.66
4503 4720 0.814457 TGCTTGCACGGTGAAAACTT 59.186 45.000 13.29 0.00 0.00 2.66
4512 4729 5.006941 TGCACGGTGAAAACTTAGAGTAAAC 59.993 40.000 13.29 0.00 0.00 2.01
4580 5946 7.398746 ACATACGACGATGTAACAATCAATTG 58.601 34.615 0.00 0.00 38.29 2.32
4606 5972 9.202273 GAATATAGTATGCTTCTTTCTGGAGTG 57.798 37.037 0.00 0.00 0.00 3.51
4616 6057 5.359194 TCTTTCTGGAGTGTTTCTTCTGT 57.641 39.130 0.00 0.00 0.00 3.41
4621 6062 7.730364 TTCTGGAGTGTTTCTTCTGTATTTC 57.270 36.000 0.00 0.00 0.00 2.17
4631 6072 8.227791 TGTTTCTTCTGTATTTCGCTACAAATC 58.772 33.333 0.00 0.00 31.50 2.17
4723 6391 4.155826 TGGCGATTCTTCAGGTATTTTGTG 59.844 41.667 0.00 0.00 0.00 3.33
4752 6420 3.675225 CGTGTGTTTCTCTGTACATCTGG 59.325 47.826 0.00 0.00 0.00 3.86
4761 6429 6.665992 TCTCTGTACATCTGGTTGTTAGTT 57.334 37.500 0.00 0.00 0.00 2.24
4762 6430 6.455647 TCTCTGTACATCTGGTTGTTAGTTG 58.544 40.000 0.00 0.00 0.00 3.16
4765 6433 5.676552 TGTACATCTGGTTGTTAGTTGTGT 58.323 37.500 0.00 0.00 32.20 3.72
4766 6434 6.818233 TGTACATCTGGTTGTTAGTTGTGTA 58.182 36.000 0.00 0.00 32.20 2.90
4767 6435 6.926826 TGTACATCTGGTTGTTAGTTGTGTAG 59.073 38.462 0.00 0.00 32.20 2.74
4768 6436 6.169557 ACATCTGGTTGTTAGTTGTGTAGA 57.830 37.500 0.00 0.00 29.51 2.59
4769 6437 6.769512 ACATCTGGTTGTTAGTTGTGTAGAT 58.230 36.000 0.00 0.00 29.51 1.98
4770 6438 7.903145 ACATCTGGTTGTTAGTTGTGTAGATA 58.097 34.615 0.00 0.00 29.51 1.98
4772 6440 8.820933 CATCTGGTTGTTAGTTGTGTAGATATG 58.179 37.037 0.00 0.00 0.00 1.78
4810 6504 6.983307 GTGTAGATATGTTCAGATCAAGCAGT 59.017 38.462 9.54 0.00 0.00 4.40
4814 6508 4.761235 ATGTTCAGATCAAGCAGTGTTG 57.239 40.909 0.00 0.00 0.00 3.33
4832 6527 3.499537 TGTTGTTGTAGATGCTCTTGCTG 59.500 43.478 0.00 0.00 40.48 4.41
4833 6528 2.703416 TGTTGTAGATGCTCTTGCTGG 58.297 47.619 0.00 0.00 40.48 4.85
4837 6532 2.040278 TGTAGATGCTCTTGCTGGGTTT 59.960 45.455 0.00 0.00 40.48 3.27
4838 6533 1.831580 AGATGCTCTTGCTGGGTTTC 58.168 50.000 0.00 0.00 40.48 2.78
4839 6534 1.353694 AGATGCTCTTGCTGGGTTTCT 59.646 47.619 0.00 0.00 40.48 2.52
4842 6537 3.611955 TGCTCTTGCTGGGTTTCTCCC 62.612 57.143 0.00 0.00 46.06 4.30
4850 6547 2.189784 GGTTTCTCCCTAGGCCGC 59.810 66.667 2.05 0.00 0.00 6.53
4870 6570 3.039202 GCCTTCCAATGTCGTGCGG 62.039 63.158 0.00 0.00 0.00 5.69
4874 6574 3.803082 CCAATGTCGTGCGGCCAG 61.803 66.667 2.24 0.00 0.00 4.85
4992 6692 3.839432 CTTCGACCTCCTCCCGCC 61.839 72.222 0.00 0.00 0.00 6.13
5052 6752 2.048222 GCCTCGTAGCAGCACACA 60.048 61.111 0.00 0.00 0.00 3.72
5164 6864 3.756082 ATGCCTCTGTTATTTGGGGAA 57.244 42.857 0.00 0.00 0.00 3.97
5183 6883 5.629079 GGAATTTGTCCCTTGTGTCTTAG 57.371 43.478 0.00 0.00 41.10 2.18
5209 6909 4.040952 AGTTACCAGCAGATCTGTCAAGTT 59.959 41.667 23.38 6.74 41.25 2.66
5213 6913 3.436015 CCAGCAGATCTGTCAAGTTTCAG 59.564 47.826 23.38 1.85 41.25 3.02
5221 6921 4.009675 TCTGTCAAGTTTCAGCACACTTT 58.990 39.130 0.00 0.00 30.48 2.66
5231 6931 6.751888 AGTTTCAGCACACTTTAACATTTCAC 59.248 34.615 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 3.440356 GAGAATTGAAGGCGCGCGG 62.440 63.158 33.06 13.66 0.00 6.46
98 109 1.590147 GTGAGACGAATGGACGGGT 59.410 57.895 0.00 0.00 37.61 5.28
102 113 0.458025 GACGGGTGAGACGAATGGAC 60.458 60.000 0.00 0.00 34.93 4.02
208 219 0.809241 CGGAGGCAGCTGAGTTCATC 60.809 60.000 20.43 6.53 0.00 2.92
323 343 4.814294 GACGGCGGCGGAGTCAAT 62.814 66.667 35.05 12.66 35.19 2.57
351 371 2.125106 GACGGGGGATGCTGTGAC 60.125 66.667 0.00 0.00 0.00 3.67
352 372 2.284625 AGACGGGGGATGCTGTGA 60.285 61.111 0.00 0.00 0.00 3.58
354 374 4.101448 GCAGACGGGGGATGCTGT 62.101 66.667 0.00 0.00 37.00 4.40
357 377 1.004440 GATAGCAGACGGGGGATGC 60.004 63.158 0.00 0.00 40.29 3.91
358 378 0.605589 GAGATAGCAGACGGGGGATG 59.394 60.000 0.00 0.00 0.00 3.51
359 379 0.485099 AGAGATAGCAGACGGGGGAT 59.515 55.000 0.00 0.00 0.00 3.85
360 380 0.261991 AAGAGATAGCAGACGGGGGA 59.738 55.000 0.00 0.00 0.00 4.81
461 488 5.738619 TCACTAACCACATAGAAGCAGAA 57.261 39.130 0.00 0.00 0.00 3.02
468 495 7.013369 CACTGCTAGTATCACTAACCACATAGA 59.987 40.741 0.00 0.00 29.00 1.98
473 500 4.113354 GCACTGCTAGTATCACTAACCAC 58.887 47.826 0.00 0.00 29.00 4.16
475 502 4.363999 CAGCACTGCTAGTATCACTAACC 58.636 47.826 2.39 0.00 36.40 2.85
480 507 2.969628 ACCAGCACTGCTAGTATCAC 57.030 50.000 2.39 0.00 36.40 3.06
485 512 5.989477 TGATTTTATACCAGCACTGCTAGT 58.011 37.500 2.39 5.18 36.40 2.57
488 515 6.125029 AGATTGATTTTATACCAGCACTGCT 58.875 36.000 0.00 0.00 40.77 4.24
494 521 7.269477 AGCAAGAGATTGATTTTATACCAGC 57.731 36.000 0.00 0.00 0.00 4.85
508 535 1.160137 GTGACGGCAAGCAAGAGATT 58.840 50.000 0.00 0.00 0.00 2.40
550 577 5.701224 TCAAAAGGGAATGAACCTAACACT 58.299 37.500 0.00 0.00 37.35 3.55
551 578 5.535030 ACTCAAAAGGGAATGAACCTAACAC 59.465 40.000 0.00 0.00 37.35 3.32
553 580 6.490381 AGAACTCAAAAGGGAATGAACCTAAC 59.510 38.462 0.00 0.00 37.35 2.34
554 581 6.610830 AGAACTCAAAAGGGAATGAACCTAA 58.389 36.000 0.00 0.00 37.35 2.69
555 582 6.200878 AGAACTCAAAAGGGAATGAACCTA 57.799 37.500 0.00 0.00 37.35 3.08
556 583 5.066913 AGAACTCAAAAGGGAATGAACCT 57.933 39.130 0.00 0.00 40.96 3.50
563 590 3.204382 ACTCCCAAGAACTCAAAAGGGAA 59.796 43.478 0.00 0.00 44.19 3.97
604 631 4.310769 AGAACAACAGCAAGTACTAGCAG 58.689 43.478 0.00 0.00 0.00 4.24
627 655 1.078115 CCCATCCATCCATCCATCCA 58.922 55.000 0.00 0.00 0.00 3.41
628 656 1.078955 ACCCATCCATCCATCCATCC 58.921 55.000 0.00 0.00 0.00 3.51
629 657 1.426598 ACACCCATCCATCCATCCATC 59.573 52.381 0.00 0.00 0.00 3.51
630 658 1.146359 CACACCCATCCATCCATCCAT 59.854 52.381 0.00 0.00 0.00 3.41
666 696 4.457603 TGCACAAACCAACCTGACATATAC 59.542 41.667 0.00 0.00 0.00 1.47
667 697 4.657013 TGCACAAACCAACCTGACATATA 58.343 39.130 0.00 0.00 0.00 0.86
697 727 6.992063 AGAAACCACAGCAGTTTATATCAG 57.008 37.500 0.00 0.00 37.55 2.90
726 759 6.147821 TGCAGATTCAGTACAGTTTCTTTAGC 59.852 38.462 0.00 0.00 0.00 3.09
766 799 8.818057 GGAATTGACAACTAGTGTATCATGTAC 58.182 37.037 0.00 0.00 41.96 2.90
772 805 7.907214 ACAAGGAATTGACAACTAGTGTATC 57.093 36.000 0.00 0.00 41.96 2.24
773 806 8.691661 AAACAAGGAATTGACAACTAGTGTAT 57.308 30.769 0.00 0.00 41.96 2.29
776 809 8.076178 CCTAAAACAAGGAATTGACAACTAGTG 58.924 37.037 0.00 0.00 39.15 2.74
777 810 7.230712 CCCTAAAACAAGGAATTGACAACTAGT 59.769 37.037 0.00 0.00 39.15 2.57
778 811 7.309194 CCCCTAAAACAAGGAATTGACAACTAG 60.309 40.741 0.00 0.00 39.15 2.57
779 812 6.492087 CCCCTAAAACAAGGAATTGACAACTA 59.508 38.462 0.00 0.00 39.15 2.24
780 813 5.304357 CCCCTAAAACAAGGAATTGACAACT 59.696 40.000 0.00 0.00 39.15 3.16
781 814 5.303333 TCCCCTAAAACAAGGAATTGACAAC 59.697 40.000 0.00 0.00 39.15 3.32
880 923 9.453572 AGTCAAACAGTGATATGTTGATATGTT 57.546 29.630 0.00 0.00 42.49 2.71
885 928 6.942005 TGGAAGTCAAACAGTGATATGTTGAT 59.058 34.615 0.00 0.00 42.49 2.57
971 1015 5.501156 ACAGAAACTCAAAAGAGTCTGGTT 58.499 37.500 14.75 1.23 39.33 3.67
977 1021 7.201821 CCATGGTTTACAGAAACTCAAAAGAGT 60.202 37.037 2.57 0.00 43.83 3.24
978 1022 7.141363 CCATGGTTTACAGAAACTCAAAAGAG 58.859 38.462 2.57 0.00 43.83 2.85
994 1042 1.214305 AGCCTCTGCCCCATGGTTTA 61.214 55.000 11.73 0.00 38.69 2.01
995 1043 2.037847 GCCTCTGCCCCATGGTTT 59.962 61.111 11.73 0.00 0.00 3.27
996 1044 2.943265 AGCCTCTGCCCCATGGTT 60.943 61.111 11.73 0.00 38.69 3.67
1066 1114 0.883814 CCATCAGGCGAGGAAGCATC 60.884 60.000 0.00 0.00 39.27 3.91
1079 1127 4.125703 GTTGATCCTTAGCAGTCCATCAG 58.874 47.826 0.00 0.00 0.00 2.90
1092 1140 5.310409 TCTTCTTGTTCAGGTTGATCCTT 57.690 39.130 0.00 0.00 45.67 3.36
1351 1405 9.638239 TTAAAGCAGACATGAATTTGGTAAATC 57.362 29.630 0.00 0.00 0.00 2.17
1369 1423 3.744660 AGTCTTCCACAGGTTAAAGCAG 58.255 45.455 0.00 0.00 0.00 4.24
1517 1572 3.546815 GCAAACATGAGATCCCGAATTCG 60.547 47.826 20.92 20.92 39.44 3.34
1521 1576 1.368641 CGCAAACATGAGATCCCGAA 58.631 50.000 0.00 0.00 0.00 4.30
1556 1611 1.816835 CTCTTGATGCACACAGCCATT 59.183 47.619 0.00 0.00 44.83 3.16
1557 1612 1.003928 TCTCTTGATGCACACAGCCAT 59.996 47.619 0.00 0.00 44.83 4.40
1558 1613 0.397564 TCTCTTGATGCACACAGCCA 59.602 50.000 0.00 0.00 44.83 4.75
1559 1614 1.400846 CATCTCTTGATGCACACAGCC 59.599 52.381 0.00 0.00 42.83 4.85
1560 1615 2.826979 CATCTCTTGATGCACACAGC 57.173 50.000 0.00 0.00 42.83 4.40
1569 1624 2.890311 CTCGGCCTCTACATCTCTTGAT 59.110 50.000 0.00 0.00 0.00 2.57
1570 1625 2.302260 CTCGGCCTCTACATCTCTTGA 58.698 52.381 0.00 0.00 0.00 3.02
1571 1626 1.339610 CCTCGGCCTCTACATCTCTTG 59.660 57.143 0.00 0.00 0.00 3.02
1572 1627 1.698506 CCTCGGCCTCTACATCTCTT 58.301 55.000 0.00 0.00 0.00 2.85
1573 1628 0.178975 CCCTCGGCCTCTACATCTCT 60.179 60.000 0.00 0.00 0.00 3.10
1574 1629 0.468400 ACCCTCGGCCTCTACATCTC 60.468 60.000 0.00 0.00 0.00 2.75
1575 1630 0.851469 TACCCTCGGCCTCTACATCT 59.149 55.000 0.00 0.00 0.00 2.90
1576 1631 1.926108 ATACCCTCGGCCTCTACATC 58.074 55.000 0.00 0.00 0.00 3.06
1577 1632 2.249139 GAATACCCTCGGCCTCTACAT 58.751 52.381 0.00 0.00 0.00 2.29
1578 1633 1.700955 GAATACCCTCGGCCTCTACA 58.299 55.000 0.00 0.00 0.00 2.74
1579 1634 0.967662 GGAATACCCTCGGCCTCTAC 59.032 60.000 0.00 0.00 0.00 2.59
1580 1635 0.858369 AGGAATACCCTCGGCCTCTA 59.142 55.000 0.00 0.00 43.31 2.43
1581 1636 1.627019 AGGAATACCCTCGGCCTCT 59.373 57.895 0.00 0.00 43.31 3.69
1582 1637 4.297207 AGGAATACCCTCGGCCTC 57.703 61.111 0.00 0.00 43.31 4.70
1590 1645 2.083628 TTCGAGGAGGAGGAATACCC 57.916 55.000 0.00 0.00 36.73 3.69
1591 1646 4.482952 TTTTTCGAGGAGGAGGAATACC 57.517 45.455 0.00 0.00 0.00 2.73
1609 1664 9.774742 GATATTCAGCAATTTACTCTCGTTTTT 57.225 29.630 0.00 0.00 0.00 1.94
1610 1665 8.946085 TGATATTCAGCAATTTACTCTCGTTTT 58.054 29.630 0.00 0.00 0.00 2.43
1611 1666 8.492673 TGATATTCAGCAATTTACTCTCGTTT 57.507 30.769 0.00 0.00 0.00 3.60
1612 1667 8.668510 ATGATATTCAGCAATTTACTCTCGTT 57.331 30.769 0.00 0.00 0.00 3.85
1613 1668 9.935241 ATATGATATTCAGCAATTTACTCTCGT 57.065 29.630 0.00 0.00 0.00 4.18
1670 1725 6.164876 CCAGAACCATATGTGATTTTGCAAA 58.835 36.000 8.05 8.05 0.00 3.68
1680 1735 3.949754 AGATTGCACCAGAACCATATGTG 59.050 43.478 1.24 0.00 0.00 3.21
1853 1913 3.124466 CACTTGTTTCACGTGTTGTCTCA 59.876 43.478 16.51 5.16 30.59 3.27
1974 2034 4.929808 GTGATTGTACACAAGTGGTCTAGG 59.070 45.833 0.00 0.00 39.47 3.02
1988 2048 4.970662 AATGTGGCTGATGTGATTGTAC 57.029 40.909 0.00 0.00 0.00 2.90
2049 2109 1.239296 GCATGCTCAGCCTGTTGTCA 61.239 55.000 11.37 0.00 0.00 3.58
2128 2188 1.131638 AGCTCACCACCAGAAAGTGA 58.868 50.000 0.00 0.00 40.34 3.41
2193 2253 1.521681 GCGGCTCACAGGGACATAC 60.522 63.158 0.00 0.00 0.00 2.39
2275 2335 0.038744 ATAGCAGCACAGCCTTTGGT 59.961 50.000 0.00 0.00 34.23 3.67
2420 2481 1.621814 AGTAACTCCCGCTTAGCAACA 59.378 47.619 4.70 0.00 0.00 3.33
2688 2749 7.517614 TCAAACCTGTGCTATTAACAATTCA 57.482 32.000 0.00 0.00 0.00 2.57
2932 2995 3.565307 GGCAGGTTTATTCATGGATGGA 58.435 45.455 0.00 0.00 0.00 3.41
2933 2996 2.629617 GGGCAGGTTTATTCATGGATGG 59.370 50.000 0.00 0.00 0.00 3.51
2934 2997 3.569491 AGGGCAGGTTTATTCATGGATG 58.431 45.455 0.00 0.00 0.00 3.51
2935 2998 3.464833 AGAGGGCAGGTTTATTCATGGAT 59.535 43.478 0.00 0.00 0.00 3.41
3071 3137 3.264193 TCTCTATCCACACAACAGCCATT 59.736 43.478 0.00 0.00 0.00 3.16
3137 3203 3.329929 AAGGAAGTAACCTGGTTAGCG 57.670 47.619 19.25 0.00 40.49 4.26
3173 3239 7.893124 ACATAGCATCAGAGAATGGAAAAAT 57.107 32.000 0.00 0.00 0.00 1.82
3174 3240 8.806429 TTACATAGCATCAGAGAATGGAAAAA 57.194 30.769 0.00 0.00 0.00 1.94
3218 3285 2.036346 AGGCAAAAATCTTGTCACCAGC 59.964 45.455 0.00 0.00 0.00 4.85
3255 3324 2.202756 GGGCTTGGTAGACGCTCG 60.203 66.667 0.00 0.00 0.00 5.03
3267 3336 1.075601 TTGACTCTCCATTGGGGCTT 58.924 50.000 2.09 0.00 36.21 4.35
3374 3443 6.267496 AGTTAGGAAATGCGCTGTAAAAAT 57.733 33.333 9.73 0.00 0.00 1.82
3676 3876 4.403113 TCAATCACATGCCATGCACTAATT 59.597 37.500 4.17 0.00 43.04 1.40
3683 3883 2.953466 AACTCAATCACATGCCATGC 57.047 45.000 4.17 0.00 0.00 4.06
3700 3900 8.394121 TCAATGTAATTTGCTTTCCAACAAAAC 58.606 29.630 0.00 0.00 39.09 2.43
3720 3920 7.775120 AGAAGAACAAACAATGAAGTCAATGT 58.225 30.769 0.00 0.00 41.36 2.71
3840 4050 8.794553 CGCTCTTATATTTCTTTAGAGGGAGTA 58.205 37.037 0.00 0.00 44.18 2.59
3841 4051 7.288158 ACGCTCTTATATTTCTTTAGAGGGAGT 59.712 37.037 17.66 0.00 44.18 3.85
3842 4052 7.662897 ACGCTCTTATATTTCTTTAGAGGGAG 58.337 38.462 17.66 0.00 44.18 4.30
3843 4053 7.598759 ACGCTCTTATATTTCTTTAGAGGGA 57.401 36.000 17.66 0.00 44.18 4.20
3844 4054 8.664211 AAACGCTCTTATATTTCTTTAGAGGG 57.336 34.615 11.43 11.43 45.78 4.30
3858 4068 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
3859 4069 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
3860 4070 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
3861 4071 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
3875 4085 7.120873 TCAGAGCGTTTAGATCACTACTTTAGT 59.879 37.037 0.00 0.00 37.82 2.24
3876 4086 7.473366 TCAGAGCGTTTAGATCACTACTTTAG 58.527 38.462 0.00 0.00 37.82 1.85
3877 4087 7.387119 TCAGAGCGTTTAGATCACTACTTTA 57.613 36.000 0.00 0.00 37.82 1.85
3878 4088 6.268825 TCAGAGCGTTTAGATCACTACTTT 57.731 37.500 0.00 0.00 37.82 2.66
3879 4089 5.899120 TCAGAGCGTTTAGATCACTACTT 57.101 39.130 0.00 0.00 37.82 2.24
3880 4090 7.753309 ATATCAGAGCGTTTAGATCACTACT 57.247 36.000 0.00 0.00 37.82 2.57
3881 4091 8.804688 AAATATCAGAGCGTTTAGATCACTAC 57.195 34.615 0.00 0.00 37.82 2.73
3882 4092 9.894783 GTAAATATCAGAGCGTTTAGATCACTA 57.105 33.333 0.00 0.00 37.82 2.74
3883 4093 8.634444 AGTAAATATCAGAGCGTTTAGATCACT 58.366 33.333 0.00 0.00 37.82 3.41
3884 4094 8.804688 AGTAAATATCAGAGCGTTTAGATCAC 57.195 34.615 0.00 0.00 37.82 3.06
3893 4103 9.900710 CTCTGTAATAAGTAAATATCAGAGCGT 57.099 33.333 0.00 0.00 40.28 5.07
3894 4104 9.347934 CCTCTGTAATAAGTAAATATCAGAGCG 57.652 37.037 11.72 4.13 43.24 5.03
3895 4105 9.646427 CCCTCTGTAATAAGTAAATATCAGAGC 57.354 37.037 11.72 0.00 43.24 4.09
3905 4115 9.804977 GATAGGTACTCCCTCTGTAATAAGTAA 57.195 37.037 0.00 0.00 44.81 2.24
3906 4116 9.180282 AGATAGGTACTCCCTCTGTAATAAGTA 57.820 37.037 0.00 0.00 44.81 2.24
3907 4117 8.059565 AGATAGGTACTCCCTCTGTAATAAGT 57.940 38.462 0.00 0.00 44.81 2.24
3913 4123 9.347777 TGAATATAGATAGGTACTCCCTCTGTA 57.652 37.037 0.00 0.00 44.81 2.74
3914 4124 8.233349 TGAATATAGATAGGTACTCCCTCTGT 57.767 38.462 0.00 0.00 44.81 3.41
3915 4125 9.349713 GATGAATATAGATAGGTACTCCCTCTG 57.650 40.741 0.00 0.00 44.81 3.35
3916 4126 8.215050 CGATGAATATAGATAGGTACTCCCTCT 58.785 40.741 0.00 0.00 44.81 3.69
3917 4127 7.040961 GCGATGAATATAGATAGGTACTCCCTC 60.041 44.444 0.00 0.00 44.81 4.30
3919 4129 6.773685 AGCGATGAATATAGATAGGTACTCCC 59.226 42.308 0.00 0.00 41.75 4.30
3920 4130 7.644490 CAGCGATGAATATAGATAGGTACTCC 58.356 42.308 0.00 0.00 41.75 3.85
3921 4131 7.136119 GCAGCGATGAATATAGATAGGTACTC 58.864 42.308 4.02 0.00 41.75 2.59
3922 4132 6.603599 TGCAGCGATGAATATAGATAGGTACT 59.396 38.462 4.02 0.00 46.37 2.73
3923 4133 6.693545 GTGCAGCGATGAATATAGATAGGTAC 59.306 42.308 4.02 0.00 0.00 3.34
3969 4179 3.772932 ACTGCAACACAAGTTTCACATG 58.227 40.909 0.00 0.00 35.28 3.21
3979 4189 2.347731 TCACAACGTACTGCAACACAA 58.652 42.857 0.00 0.00 0.00 3.33
4004 4214 1.243342 CGGTTTGCCCTGATTGCTCA 61.243 55.000 0.00 0.00 0.00 4.26
4091 4301 2.781681 ATGTAGGTGGTGTAAGGTGC 57.218 50.000 0.00 0.00 0.00 5.01
4127 4337 1.341209 GTTTTGCACTGAAAGAGGGGG 59.659 52.381 0.00 0.00 37.43 5.40
4128 4338 2.310538 AGTTTTGCACTGAAAGAGGGG 58.689 47.619 0.00 0.00 37.43 4.79
4129 4339 3.709987 CAAGTTTTGCACTGAAAGAGGG 58.290 45.455 0.00 0.00 35.12 4.30
4147 4358 0.245539 CTGCAAGGGTTCATGGCAAG 59.754 55.000 0.00 0.00 33.58 4.01
4282 4493 4.613925 TCTAGGATACGTACGTGGAGAT 57.386 45.455 30.25 15.92 46.39 2.75
4452 4669 6.980978 TCTTCATTAGACAGCAACAGCTATAC 59.019 38.462 0.00 0.00 36.70 1.47
4456 4673 4.277515 TCTTCATTAGACAGCAACAGCT 57.722 40.909 0.00 0.00 39.75 4.24
4468 4685 4.397103 TGCAAGCACTCCATTCTTCATTAG 59.603 41.667 0.00 0.00 0.00 1.73
4498 4715 5.883673 TGTGTTGCCTGTTTACTCTAAGTTT 59.116 36.000 0.00 0.00 0.00 2.66
4502 4719 4.759693 CCATGTGTTGCCTGTTTACTCTAA 59.240 41.667 0.00 0.00 0.00 2.10
4503 4720 4.202419 ACCATGTGTTGCCTGTTTACTCTA 60.202 41.667 0.00 0.00 0.00 2.43
4512 4729 3.724508 TTACAAACCATGTGTTGCCTG 57.275 42.857 5.70 2.10 43.77 4.85
4555 5921 7.276878 TCAATTGATTGTTACATCGTCGTATGT 59.723 33.333 3.38 12.68 39.71 2.29
4580 5946 9.202273 CACTCCAGAAAGAAGCATACTATATTC 57.798 37.037 0.00 0.00 0.00 1.75
4587 5953 5.703130 AGAAACACTCCAGAAAGAAGCATAC 59.297 40.000 0.00 0.00 0.00 2.39
4588 5954 5.869579 AGAAACACTCCAGAAAGAAGCATA 58.130 37.500 0.00 0.00 0.00 3.14
4589 5955 4.723309 AGAAACACTCCAGAAAGAAGCAT 58.277 39.130 0.00 0.00 0.00 3.79
4606 5972 7.422746 CGATTTGTAGCGAAATACAGAAGAAAC 59.577 37.037 0.00 0.00 37.01 2.78
4621 6062 2.247637 TCTGACGTTCGATTTGTAGCG 58.752 47.619 0.00 0.00 33.70 4.26
4647 6088 4.955925 AACGTTCGATTTGCCATGATAA 57.044 36.364 0.00 0.00 0.00 1.75
4648 6089 4.955925 AAACGTTCGATTTGCCATGATA 57.044 36.364 0.00 0.00 0.00 2.15
4649 6090 3.848272 AAACGTTCGATTTGCCATGAT 57.152 38.095 0.00 0.00 0.00 2.45
4650 6091 3.634568 AAAACGTTCGATTTGCCATGA 57.365 38.095 0.00 0.00 0.00 3.07
4703 6184 9.329913 CTTTAACACAAAATACCTGAAGAATCG 57.670 33.333 0.00 0.00 0.00 3.34
4711 6192 5.398122 CACACGCTTTAACACAAAATACCTG 59.602 40.000 0.00 0.00 0.00 4.00
4723 6391 4.531659 ACAGAGAAACACACGCTTTAAC 57.468 40.909 0.00 0.00 0.00 2.01
4752 6420 8.656849 CCTGAACATATCTACACAACTAACAAC 58.343 37.037 0.00 0.00 0.00 3.32
4761 6429 7.817478 CACAACTAACCTGAACATATCTACACA 59.183 37.037 0.00 0.00 0.00 3.72
4762 6430 7.817962 ACACAACTAACCTGAACATATCTACAC 59.182 37.037 0.00 0.00 0.00 2.90
4765 6433 9.470399 TCTACACAACTAACCTGAACATATCTA 57.530 33.333 0.00 0.00 0.00 1.98
4766 6434 8.362464 TCTACACAACTAACCTGAACATATCT 57.638 34.615 0.00 0.00 0.00 1.98
4770 6438 8.540388 ACATATCTACACAACTAACCTGAACAT 58.460 33.333 0.00 0.00 0.00 2.71
4772 6440 8.773404 AACATATCTACACAACTAACCTGAAC 57.227 34.615 0.00 0.00 0.00 3.18
4833 6528 2.189784 GCGGCCTAGGGAGAAACC 59.810 66.667 11.72 0.37 38.08 3.27
4846 6543 3.056313 GACATTGGAAGGCAGCGGC 62.056 63.158 0.00 0.00 40.13 6.53
4850 6547 1.503542 GCACGACATTGGAAGGCAG 59.496 57.895 0.00 0.00 0.00 4.85
4885 6585 0.178533 AGAGATGAAGAGCCAGCAGC 59.821 55.000 0.00 0.00 44.25 5.25
4961 6661 4.752879 GAAGCGCGTGTGGCCCTA 62.753 66.667 8.43 0.00 38.94 3.53
4971 6671 4.856607 GGAGGAGGTCGAAGCGCG 62.857 72.222 0.00 0.00 42.69 6.86
4977 6677 4.816984 GAGGCGGGAGGAGGTCGA 62.817 72.222 0.00 0.00 0.00 4.20
5045 6745 1.511305 CGGAGGTATCGTGTGTGCT 59.489 57.895 0.00 0.00 0.00 4.40
5048 6748 2.890371 GGCGGAGGTATCGTGTGT 59.110 61.111 0.00 0.00 0.00 3.72
5164 6864 4.098914 TGCTAAGACACAAGGGACAAAT 57.901 40.909 0.00 0.00 0.00 2.32
5209 6909 6.449635 AGTGAAATGTTAAAGTGTGCTGAA 57.550 33.333 0.00 0.00 0.00 3.02
5213 6913 3.664025 GCGAGTGAAATGTTAAAGTGTGC 59.336 43.478 0.00 0.00 0.00 4.57
5221 6921 4.340894 GCTCAATGCGAGTGAAATGTTA 57.659 40.909 0.00 0.00 44.33 2.41


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

AutoCloner maintained by Alex Coulton.