Multiple sequence alignment - TraesCS4B01G055900

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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 TraesCS4B01G055900 chr4B 100.000 3585 0 0 1 3585 44953939 44950355 0.000000e+00 6621.0
1 TraesCS4B01G055900 chr4D 87.160 1433 98 47 7 1403 31434702 31436084 0.000000e+00 1548.0
2 TraesCS4B01G055900 chr4D 90.807 1153 42 17 2452 3585 31443600 31444707 0.000000e+00 1483.0
3 TraesCS4B01G055900 chr4D 86.502 852 47 22 1399 2223 31436117 31436927 0.000000e+00 874.0
4 TraesCS4B01G055900 chr4D 89.963 538 37 8 2329 2856 31437051 31437581 0.000000e+00 678.0
5 TraesCS4B01G055900 chr4D 89.506 162 15 1 2062 2223 31443204 31443363 1.690000e-48 204.0
6 TraesCS4B01G055900 chr4D 90.000 160 13 2 2221 2378 31443428 31443586 1.690000e-48 204.0
7 TraesCS4B01G055900 chr4A 86.441 1003 77 26 412 1401 571212239 571213195 0.000000e+00 1044.0
8 TraesCS4B01G055900 chr4A 85.904 830 63 21 1399 2200 571213230 571214033 0.000000e+00 835.0
9 TraesCS4B01G055900 chr4A 91.211 512 33 9 2329 2836 571214101 571214604 0.000000e+00 686.0
10 TraesCS4B01G055900 chr4A 85.792 366 13 12 14 353 571211870 571212222 5.690000e-93 351.0
11 TraesCS4B01G055900 chr4A 82.759 435 35 21 2402 2824 571220875 571221281 5.690000e-93 351.0
12 TraesCS4B01G055900 chr4A 90.741 162 13 1 2062 2223 571220539 571220698 7.800000e-52 215.0
13 TraesCS4B01G055900 chr4A 89.308 159 16 1 2221 2378 571220763 571220921 7.850000e-47 198.0
14 TraesCS4B01G055900 chr5D 84.151 530 62 9 2402 2919 501520438 501520957 8.940000e-136 494.0
15 TraesCS4B01G055900 chr5B 84.630 514 57 9 2417 2918 633115086 633114583 3.220000e-135 492.0
16 TraesCS4B01G055900 chr5B 82.959 534 65 10 2402 2919 625233179 625233702 3.260000e-125 459.0
17 TraesCS4B01G055900 chr5B 82.959 534 65 10 2402 2919 628832698 628833221 3.260000e-125 459.0
18 TraesCS4B01G055900 chr5B 96.517 201 7 0 2496 2696 600187331 600187531 2.060000e-87 333.0
19 TraesCS4B01G055900 chr5B 94.505 91 3 2 2018 2108 600187125 600187213 4.830000e-29 139.0
20 TraesCS4B01G055900 chr5B 87.879 66 7 1 3287 3352 142660662 142660726 3.840000e-10 76.8
21 TraesCS4B01G055900 chrUn 82.959 534 65 10 2402 2919 310639539 310640062 3.260000e-125 459.0
22 TraesCS4B01G055900 chr2D 92.647 68 4 1 3285 3352 74975997 74975931 2.950000e-16 97.1
23 TraesCS4B01G055900 chr1B 92.424 66 4 1 3287 3352 597156889 597156825 3.810000e-15 93.5
24 TraesCS4B01G055900 chr5A 90.909 66 5 1 3287 3352 148054099 148054163 1.770000e-13 87.9
25 TraesCS4B01G055900 chr2A 90.769 65 4 1 3288 3352 182008967 182009029 6.380000e-13 86.1
26 TraesCS4B01G055900 chr3B 88.060 67 7 1 3286 3352 556504587 556504522 1.070000e-10 78.7
27 TraesCS4B01G055900 chr3B 86.154 65 9 0 2839 2903 461309060 461309124 1.790000e-08 71.3
28 TraesCS4B01G055900 chr2B 88.060 67 7 1 3286 3352 255054163 255054228 1.070000e-10 78.7
29 TraesCS4B01G055900 chr1D 88.060 67 7 1 3286 3352 348128609 348128544 1.070000e-10 78.7


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 TraesCS4B01G055900 chr4B 44950355 44953939 3584 True 6621.000000 6621 100.000000 1 3585 1 chr4B.!!$R1 3584
1 TraesCS4B01G055900 chr4D 31434702 31437581 2879 False 1033.333333 1548 87.875000 7 2856 3 chr4D.!!$F1 2849
2 TraesCS4B01G055900 chr4D 31443204 31444707 1503 False 630.333333 1483 90.104333 2062 3585 3 chr4D.!!$F2 1523
3 TraesCS4B01G055900 chr4A 571211870 571214604 2734 False 729.000000 1044 87.337000 14 2836 4 chr4A.!!$F1 2822
4 TraesCS4B01G055900 chr4A 571220539 571221281 742 False 254.666667 351 87.602667 2062 2824 3 chr4A.!!$F2 762
5 TraesCS4B01G055900 chr5D 501520438 501520957 519 False 494.000000 494 84.151000 2402 2919 1 chr5D.!!$F1 517
6 TraesCS4B01G055900 chr5B 633114583 633115086 503 True 492.000000 492 84.630000 2417 2918 1 chr5B.!!$R1 501
7 TraesCS4B01G055900 chr5B 625233179 625233702 523 False 459.000000 459 82.959000 2402 2919 1 chr5B.!!$F2 517
8 TraesCS4B01G055900 chr5B 628832698 628833221 523 False 459.000000 459 82.959000 2402 2919 1 chr5B.!!$F3 517
9 TraesCS4B01G055900 chrUn 310639539 310640062 523 False 459.000000 459 82.959000 2402 2919 1 chrUn.!!$F1 517

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
170 186 0.038159 CTCCTCAAAACCGAGTCGCT 60.038 55.0 7.12 0.0 0.0 4.93 F
334 357 0.102481 CATCTTGACCCCTACGACCG 59.898 60.0 0.00 0.0 0.0 4.79 F
1025 1091 0.106419 AGTAAGGAGAGCGGGGAGAG 60.106 60.0 0.00 0.0 0.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2178 0.103937 TTTGACGGCAAAAAGGGCAG 59.896 50.0 15.59 0.0 40.82 4.85 R
2031 2179 0.755686 ATTTGACGGCAAAAAGGGCA 59.244 45.0 22.36 0.0 46.19 5.36 R
2589 2820 0.171231 CGATCACGAGCTCAGGACAA 59.829 55.0 15.40 0.0 42.66 3.18 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
80 81 2.664424 CGTCACGTTTGCCGATTCAAAT 60.664 45.455 0.00 0.00 38.12 2.32
91 92 4.140963 GCCGATTCAAATTTCAAAAACGC 58.859 39.130 0.00 0.00 0.00 4.84
92 93 4.373557 CCGATTCAAATTTCAAAAACGCG 58.626 39.130 3.53 3.53 0.00 6.01
93 94 4.147306 CCGATTCAAATTTCAAAAACGCGA 59.853 37.500 15.93 0.00 0.00 5.87
144 160 4.222124 TCTTCTACCCAGAAAGATTGCC 57.778 45.455 0.00 0.00 40.28 4.52
145 161 2.691409 TCTACCCAGAAAGATTGCCG 57.309 50.000 0.00 0.00 0.00 5.69
146 162 1.906574 TCTACCCAGAAAGATTGCCGT 59.093 47.619 0.00 0.00 0.00 5.68
147 163 2.009774 CTACCCAGAAAGATTGCCGTG 58.990 52.381 0.00 0.00 0.00 4.94
170 186 0.038159 CTCCTCAAAACCGAGTCGCT 60.038 55.000 7.12 0.00 0.00 4.93
175 191 3.314553 CTCAAAACCGAGTCGCTAGAAA 58.685 45.455 7.12 0.00 0.00 2.52
263 279 4.173971 GGTACGTACAACCCTGCG 57.826 61.111 26.02 0.00 0.00 5.18
334 357 0.102481 CATCTTGACCCCTACGACCG 59.898 60.000 0.00 0.00 0.00 4.79
357 417 0.596083 CACGCGATCACATCTCCCTC 60.596 60.000 15.93 0.00 0.00 4.30
360 420 1.118356 GCGATCACATCTCCCTCCCT 61.118 60.000 0.00 0.00 0.00 4.20
366 426 0.397816 ACATCTCCCTCCCTTCTCCG 60.398 60.000 0.00 0.00 0.00 4.63
378 438 0.386113 CTTCTCCGCCTGCTACTACC 59.614 60.000 0.00 0.00 0.00 3.18
379 439 1.041447 TTCTCCGCCTGCTACTACCC 61.041 60.000 0.00 0.00 0.00 3.69
380 440 2.443390 TCCGCCTGCTACTACCCC 60.443 66.667 0.00 0.00 0.00 4.95
381 441 2.444140 CCGCCTGCTACTACCCCT 60.444 66.667 0.00 0.00 0.00 4.79
382 442 2.797278 CCGCCTGCTACTACCCCTG 61.797 68.421 0.00 0.00 0.00 4.45
383 443 2.058595 CGCCTGCTACTACCCCTGT 61.059 63.158 0.00 0.00 0.00 4.00
384 444 1.522569 GCCTGCTACTACCCCTGTG 59.477 63.158 0.00 0.00 0.00 3.66
385 445 1.265454 GCCTGCTACTACCCCTGTGT 61.265 60.000 0.00 0.00 0.00 3.72
386 446 0.537188 CCTGCTACTACCCCTGTGTG 59.463 60.000 0.00 0.00 0.00 3.82
387 447 1.267121 CTGCTACTACCCCTGTGTGT 58.733 55.000 0.00 0.00 0.00 3.72
388 448 1.623811 CTGCTACTACCCCTGTGTGTT 59.376 52.381 0.00 0.00 0.00 3.32
389 449 2.829720 CTGCTACTACCCCTGTGTGTTA 59.170 50.000 0.00 0.00 0.00 2.41
390 450 2.564062 TGCTACTACCCCTGTGTGTTAC 59.436 50.000 0.00 0.00 0.00 2.50
391 451 2.830321 GCTACTACCCCTGTGTGTTACT 59.170 50.000 0.00 0.00 0.00 2.24
392 452 3.119209 GCTACTACCCCTGTGTGTTACTC 60.119 52.174 0.00 0.00 0.00 2.59
393 453 3.255634 ACTACCCCTGTGTGTTACTCT 57.744 47.619 0.00 0.00 0.00 3.24
394 454 3.584294 ACTACCCCTGTGTGTTACTCTT 58.416 45.455 0.00 0.00 0.00 2.85
395 455 4.744237 ACTACCCCTGTGTGTTACTCTTA 58.256 43.478 0.00 0.00 0.00 2.10
396 456 4.525874 ACTACCCCTGTGTGTTACTCTTAC 59.474 45.833 0.00 0.00 0.00 2.34
397 457 3.584294 ACCCCTGTGTGTTACTCTTACT 58.416 45.455 0.00 0.00 0.00 2.24
398 458 3.577415 ACCCCTGTGTGTTACTCTTACTC 59.423 47.826 0.00 0.00 0.00 2.59
399 459 3.056035 CCCCTGTGTGTTACTCTTACTCC 60.056 52.174 0.00 0.00 0.00 3.85
400 460 3.576982 CCCTGTGTGTTACTCTTACTCCA 59.423 47.826 0.00 0.00 0.00 3.86
401 461 4.557205 CCTGTGTGTTACTCTTACTCCAC 58.443 47.826 0.00 0.00 0.00 4.02
402 462 4.227538 CTGTGTGTTACTCTTACTCCACG 58.772 47.826 0.00 0.00 0.00 4.94
403 463 3.884693 TGTGTGTTACTCTTACTCCACGA 59.115 43.478 0.00 0.00 0.00 4.35
404 464 4.023450 TGTGTGTTACTCTTACTCCACGAG 60.023 45.833 0.00 0.00 35.52 4.18
405 465 4.023365 GTGTGTTACTCTTACTCCACGAGT 60.023 45.833 0.00 0.00 45.54 4.18
406 466 4.581824 TGTGTTACTCTTACTCCACGAGTT 59.418 41.667 0.00 0.00 40.28 3.01
407 467 5.152804 GTGTTACTCTTACTCCACGAGTTC 58.847 45.833 0.00 0.00 40.28 3.01
408 468 4.083643 TGTTACTCTTACTCCACGAGTTCG 60.084 45.833 0.00 0.00 40.28 3.95
437 497 4.147449 CGCCCTGTCATCGGCTCA 62.147 66.667 8.91 0.00 43.38 4.26
463 524 2.657237 CTTCCTCGCGTGAACCCT 59.343 61.111 10.21 0.00 0.00 4.34
475 536 0.468226 TGAACCCTGTCGCAAACTCT 59.532 50.000 0.00 0.00 0.00 3.24
498 559 4.114997 TCGATCACGAGCGCTGCA 62.115 61.111 18.48 0.00 43.81 4.41
549 613 2.968206 CAGGAGCCTGCAAAAGCC 59.032 61.111 3.18 0.00 37.24 4.35
592 656 0.461961 CGAGGCCTTTCCGAGATTCT 59.538 55.000 6.77 0.00 40.77 2.40
595 659 2.169561 GAGGCCTTTCCGAGATTCTCTT 59.830 50.000 6.77 0.00 40.77 2.85
610 674 3.524095 TCTCTTGCCCAAGGAAATGAA 57.476 42.857 8.06 0.00 38.88 2.57
625 689 1.618861 ATGAAACGCTCGTCTTCTCG 58.381 50.000 13.79 0.00 0.00 4.04
626 690 0.386858 TGAAACGCTCGTCTTCTCGG 60.387 55.000 13.79 0.00 0.00 4.63
627 691 1.675524 GAAACGCTCGTCTTCTCGGC 61.676 60.000 0.00 0.00 0.00 5.54
628 692 2.143594 AAACGCTCGTCTTCTCGGCT 62.144 55.000 0.00 0.00 0.00 5.52
629 693 2.143594 AACGCTCGTCTTCTCGGCTT 62.144 55.000 0.00 0.00 0.00 4.35
630 694 1.870016 CGCTCGTCTTCTCGGCTTC 60.870 63.158 0.00 0.00 0.00 3.86
631 695 1.509004 GCTCGTCTTCTCGGCTTCT 59.491 57.895 0.00 0.00 0.00 2.85
632 696 0.524604 GCTCGTCTTCTCGGCTTCTC 60.525 60.000 0.00 0.00 0.00 2.87
633 697 0.247894 CTCGTCTTCTCGGCTTCTCG 60.248 60.000 0.00 0.00 0.00 4.04
649 714 4.741781 CGCGCAAGAAGCAACGGG 62.742 66.667 8.75 0.00 46.13 5.28
778 844 1.000993 TCAGTGAGAGAGGGAGGGC 59.999 63.158 0.00 0.00 0.00 5.19
779 845 2.043450 AGTGAGAGAGGGAGGGCG 60.043 66.667 0.00 0.00 0.00 6.13
780 846 3.151022 GTGAGAGAGGGAGGGCGG 61.151 72.222 0.00 0.00 0.00 6.13
838 904 2.314647 CCGCGGCTTTCTTTCGTGA 61.315 57.895 14.67 0.00 36.65 4.35
853 919 2.282391 TGAATGCCAAGCCAGCGT 60.282 55.556 0.00 0.00 0.00 5.07
927 993 1.608717 TTTCTCCTCTCTCGGCTGGC 61.609 60.000 0.00 0.00 0.00 4.85
943 1009 2.506957 GGCTGGGTTGGTTGGTTGG 61.507 63.158 0.00 0.00 0.00 3.77
944 1010 1.760480 GCTGGGTTGGTTGGTTGGT 60.760 57.895 0.00 0.00 0.00 3.67
945 1011 1.334384 GCTGGGTTGGTTGGTTGGTT 61.334 55.000 0.00 0.00 0.00 3.67
946 1012 0.463620 CTGGGTTGGTTGGTTGGTTG 59.536 55.000 0.00 0.00 0.00 3.77
949 1015 0.906066 GGTTGGTTGGTTGGTTGGTT 59.094 50.000 0.00 0.00 0.00 3.67
950 1016 1.134640 GGTTGGTTGGTTGGTTGGTTC 60.135 52.381 0.00 0.00 0.00 3.62
951 1017 0.818296 TTGGTTGGTTGGTTGGTTCG 59.182 50.000 0.00 0.00 0.00 3.95
952 1018 0.323542 TGGTTGGTTGGTTGGTTCGT 60.324 50.000 0.00 0.00 0.00 3.85
953 1019 1.064906 TGGTTGGTTGGTTGGTTCGTA 60.065 47.619 0.00 0.00 0.00 3.43
954 1020 1.605232 GGTTGGTTGGTTGGTTCGTAG 59.395 52.381 0.00 0.00 0.00 3.51
976 1042 0.250209 TAGTAGGTAGGCGAGGCGAG 60.250 60.000 0.00 0.00 0.00 5.03
977 1043 2.203308 TAGGTAGGCGAGGCGAGG 60.203 66.667 0.00 0.00 0.00 4.63
1008 1074 2.711922 GCCGTCGGTGATGGAGAGT 61.712 63.158 13.94 0.00 40.94 3.24
1025 1091 0.106419 AGTAAGGAGAGCGGGGAGAG 60.106 60.000 0.00 0.00 0.00 3.20
1213 1279 0.321653 GGACTGCATCAAGAACCGGT 60.322 55.000 0.00 0.00 0.00 5.28
1293 1359 4.416601 CCCCCTCCTCCCCGTTCT 62.417 72.222 0.00 0.00 0.00 3.01
1295 1361 2.284699 CCCTCCTCCCCGTTCTGT 60.285 66.667 0.00 0.00 0.00 3.41
1325 1394 1.268899 CTCCTGCTTTGCCTTGTTCTG 59.731 52.381 0.00 0.00 0.00 3.02
1330 1399 1.603931 GCTTTGCCTTGTTCTGCTTCC 60.604 52.381 0.00 0.00 0.00 3.46
1334 1403 1.251251 GCCTTGTTCTGCTTCCATGT 58.749 50.000 0.00 0.00 0.00 3.21
1335 1404 1.615392 GCCTTGTTCTGCTTCCATGTT 59.385 47.619 0.00 0.00 0.00 2.71
1379 1452 1.006571 CGTACGTGTCCTGTGCCTT 60.007 57.895 7.22 0.00 0.00 4.35
1483 1593 4.217754 TGTTACGAAATGTTGCCACTTC 57.782 40.909 0.00 0.00 0.00 3.01
1484 1594 3.223157 GTTACGAAATGTTGCCACTTCG 58.777 45.455 9.78 9.78 44.69 3.79
1485 1595 1.305201 ACGAAATGTTGCCACTTCGT 58.695 45.000 10.85 10.85 46.51 3.85
1486 1596 2.399396 CGAAATGTTGCCACTTCGTT 57.601 45.000 4.69 0.00 36.72 3.85
1488 1598 2.719046 CGAAATGTTGCCACTTCGTTTC 59.281 45.455 4.69 0.00 36.72 2.78
1493 1604 2.002018 TTGCCACTTCGTTTCCCCCT 62.002 55.000 0.00 0.00 0.00 4.79
1528 1639 3.270027 TCGGAATGCATGTTCTTGTAGG 58.730 45.455 0.00 0.00 0.00 3.18
1535 1646 3.932710 TGCATGTTCTTGTAGGAATCGTC 59.067 43.478 0.00 0.00 0.00 4.20
1551 1662 5.009710 GGAATCGTCCTGTTTTCTTTTCCTT 59.990 40.000 0.00 0.00 41.24 3.36
1552 1663 6.461092 GGAATCGTCCTGTTTTCTTTTCCTTT 60.461 38.462 0.00 0.00 41.24 3.11
1553 1664 5.907866 TCGTCCTGTTTTCTTTTCCTTTT 57.092 34.783 0.00 0.00 0.00 2.27
1554 1665 5.646606 TCGTCCTGTTTTCTTTTCCTTTTG 58.353 37.500 0.00 0.00 0.00 2.44
1555 1666 5.184287 TCGTCCTGTTTTCTTTTCCTTTTGT 59.816 36.000 0.00 0.00 0.00 2.83
1556 1667 5.867174 CGTCCTGTTTTCTTTTCCTTTTGTT 59.133 36.000 0.00 0.00 0.00 2.83
1557 1668 6.183360 CGTCCTGTTTTCTTTTCCTTTTGTTG 60.183 38.462 0.00 0.00 0.00 3.33
1558 1669 6.649141 GTCCTGTTTTCTTTTCCTTTTGTTGT 59.351 34.615 0.00 0.00 0.00 3.32
1559 1670 7.172532 GTCCTGTTTTCTTTTCCTTTTGTTGTT 59.827 33.333 0.00 0.00 0.00 2.83
1563 1674 8.678199 TGTTTTCTTTTCCTTTTGTTGTTGTTT 58.322 25.926 0.00 0.00 0.00 2.83
1564 1675 8.952979 GTTTTCTTTTCCTTTTGTTGTTGTTTG 58.047 29.630 0.00 0.00 0.00 2.93
1565 1676 7.793927 TTCTTTTCCTTTTGTTGTTGTTTGT 57.206 28.000 0.00 0.00 0.00 2.83
1569 1695 6.927294 TTCCTTTTGTTGTTGTTTGTTGTT 57.073 29.167 0.00 0.00 0.00 2.83
1571 1697 5.817816 TCCTTTTGTTGTTGTTTGTTGTTGT 59.182 32.000 0.00 0.00 0.00 3.32
1636 1762 1.069204 GCACGGAGAAGCATCTGGATA 59.931 52.381 0.00 0.00 35.54 2.59
1638 1764 3.797039 CACGGAGAAGCATCTGGATAAA 58.203 45.455 0.00 0.00 35.54 1.40
1640 1766 4.212847 CACGGAGAAGCATCTGGATAAATG 59.787 45.833 0.00 0.00 35.54 2.32
1706 1836 4.691175 TGGTGAAAACAACCATGTGAATG 58.309 39.130 0.00 0.00 42.82 2.67
1707 1837 4.161189 TGGTGAAAACAACCATGTGAATGT 59.839 37.500 0.00 0.00 42.82 2.71
1708 1838 4.507388 GGTGAAAACAACCATGTGAATGTG 59.493 41.667 0.00 0.00 40.46 3.21
1709 1839 5.347342 GTGAAAACAACCATGTGAATGTGA 58.653 37.500 0.00 0.00 40.46 3.58
1710 1840 5.984926 GTGAAAACAACCATGTGAATGTGAT 59.015 36.000 0.00 0.00 40.46 3.06
1711 1841 5.984323 TGAAAACAACCATGTGAATGTGATG 59.016 36.000 0.00 0.00 40.46 3.07
1712 1842 5.787953 AAACAACCATGTGAATGTGATGA 57.212 34.783 0.00 0.00 40.46 2.92
1733 1863 1.888215 AGTGCAGTGTGGATGAAGTG 58.112 50.000 0.00 0.00 0.00 3.16
1751 1881 2.128035 GTGGCGATTCGTAGATCCTTG 58.872 52.381 8.03 0.00 35.04 3.61
1760 1890 4.978083 TCGTAGATCCTTGGACACTTAC 57.022 45.455 0.00 0.00 0.00 2.34
1783 1913 0.690192 TTCCCTCACGCATTTGGAGA 59.310 50.000 0.00 0.00 0.00 3.71
1787 1917 2.098117 CCCTCACGCATTTGGAGATTTC 59.902 50.000 0.00 0.00 0.00 2.17
1792 1922 5.460646 TCACGCATTTGGAGATTTCTTTTC 58.539 37.500 0.00 0.00 0.00 2.29
1876 2007 1.134220 TGTACAGGCATCCGGATTTCC 60.134 52.381 16.19 18.58 0.00 3.13
1902 2033 2.173782 TCTTGCTGTCAAAGTTGGGGTA 59.826 45.455 0.00 0.00 0.00 3.69
1960 2091 8.200792 GTCAGTCTCTGTCCATGTAGATTTATT 58.799 37.037 0.00 0.00 32.61 1.40
1961 2092 8.762645 TCAGTCTCTGTCCATGTAGATTTATTT 58.237 33.333 0.00 0.00 32.61 1.40
1962 2093 9.388506 CAGTCTCTGTCCATGTAGATTTATTTT 57.611 33.333 0.00 0.00 0.00 1.82
1963 2094 9.606631 AGTCTCTGTCCATGTAGATTTATTTTC 57.393 33.333 0.00 0.00 0.00 2.29
1964 2095 9.383519 GTCTCTGTCCATGTAGATTTATTTTCA 57.616 33.333 0.00 0.00 0.00 2.69
1965 2096 9.605275 TCTCTGTCCATGTAGATTTATTTTCAG 57.395 33.333 0.00 0.00 0.00 3.02
1966 2097 9.388506 CTCTGTCCATGTAGATTTATTTTCAGT 57.611 33.333 0.00 0.00 0.00 3.41
1967 2098 9.739276 TCTGTCCATGTAGATTTATTTTCAGTT 57.261 29.630 0.00 0.00 0.00 3.16
1971 2102 9.638239 TCCATGTAGATTTATTTTCAGTTTTGC 57.362 29.630 0.00 0.00 0.00 3.68
1972 2103 9.643693 CCATGTAGATTTATTTTCAGTTTTGCT 57.356 29.630 0.00 0.00 0.00 3.91
1974 2105 9.643693 ATGTAGATTTATTTTCAGTTTTGCTGG 57.356 29.630 0.00 0.00 45.08 4.85
1975 2106 8.855110 TGTAGATTTATTTTCAGTTTTGCTGGA 58.145 29.630 0.00 0.00 45.08 3.86
1976 2107 9.346725 GTAGATTTATTTTCAGTTTTGCTGGAG 57.653 33.333 0.00 0.00 45.08 3.86
1977 2108 8.181904 AGATTTATTTTCAGTTTTGCTGGAGA 57.818 30.769 0.00 0.00 45.08 3.71
1978 2109 8.810041 AGATTTATTTTCAGTTTTGCTGGAGAT 58.190 29.630 0.00 0.00 45.08 2.75
1979 2110 9.428097 GATTTATTTTCAGTTTTGCTGGAGATT 57.572 29.630 0.00 0.00 45.08 2.40
1991 2139 5.314923 TGCTGGAGATTATCTTTTGCAAC 57.685 39.130 0.00 0.00 0.00 4.17
2029 2177 9.312904 TGTTCAGAAATTTATTCTTGGAATCCT 57.687 29.630 0.00 0.00 0.00 3.24
2030 2178 9.794685 GTTCAGAAATTTATTCTTGGAATCCTC 57.205 33.333 0.00 0.00 0.00 3.71
2031 2179 9.759473 TTCAGAAATTTATTCTTGGAATCCTCT 57.241 29.630 0.00 0.00 0.00 3.69
2035 2183 2.744352 ATTCTTGGAATCCTCTGCCC 57.256 50.000 0.00 0.00 0.00 5.36
2065 2218 4.400845 CGTCAAATGCTTGTGATCTCTTG 58.599 43.478 0.00 0.00 33.94 3.02
2095 2248 5.570589 GCTGTACTACTTGTTACAGTAACCG 59.429 44.000 18.94 12.90 41.26 4.44
2126 2279 4.813161 GTGCTCTGATGCTATGTGTTGTAT 59.187 41.667 0.00 0.00 0.00 2.29
2204 2357 3.991121 GGATTCTGTTCTTATAGCGGCTC 59.009 47.826 5.39 0.00 0.00 4.70
2205 2358 4.262249 GGATTCTGTTCTTATAGCGGCTCT 60.262 45.833 5.39 0.00 0.00 4.09
2236 2456 7.053498 TGCATATGATTTGCTCTGGTTACTAA 58.947 34.615 6.97 0.00 40.77 2.24
2238 2458 8.233190 GCATATGATTTGCTCTGGTTACTAATC 58.767 37.037 6.97 0.00 37.14 1.75
2245 2465 3.561725 GCTCTGGTTACTAATCATGCCAC 59.438 47.826 0.00 0.00 0.00 5.01
2247 2467 3.118038 TCTGGTTACTAATCATGCCACCC 60.118 47.826 0.00 0.00 0.00 4.61
2266 2486 3.569701 ACCCATTGTAGTTTCTTGCTGTG 59.430 43.478 0.00 0.00 0.00 3.66
2279 2499 4.136796 TCTTGCTGTGCTTCTGTATTTGT 58.863 39.130 0.00 0.00 0.00 2.83
2342 2562 7.847711 TTCTGTTCTAAATTTCCCAATTCCA 57.152 32.000 0.00 0.00 30.80 3.53
2364 2584 5.105187 CCAATAGCCTATCTGCTGCTATGTA 60.105 44.000 0.00 0.00 45.10 2.29
2387 2607 8.787852 TGTACTGATGCATCTGAATAGTAGTAG 58.212 37.037 32.64 17.60 0.00 2.57
2388 2608 7.831691 ACTGATGCATCTGAATAGTAGTAGT 57.168 36.000 32.64 18.17 0.00 2.73
2389 2609 8.926092 ACTGATGCATCTGAATAGTAGTAGTA 57.074 34.615 32.64 6.35 0.00 1.82
2433 2654 1.009829 GGCCAATCTGCTACTGTTCG 58.990 55.000 0.00 0.00 0.00 3.95
2454 2685 1.667724 CTGATGCGTCTGGTTGAATCC 59.332 52.381 7.58 0.00 0.00 3.01
2457 2688 0.389817 TGCGTCTGGTTGAATCCGAG 60.390 55.000 0.00 0.00 0.00 4.63
2589 2820 0.607620 GCTGAGACTCAGTGAAGGCT 59.392 55.000 28.76 0.00 45.94 4.58
2590 2821 1.001860 GCTGAGACTCAGTGAAGGCTT 59.998 52.381 28.76 0.00 45.94 4.35
2667 2898 0.461548 TGCGAGGTCTTATCAGCCTG 59.538 55.000 0.00 0.00 31.89 4.85
2668 2899 0.249657 GCGAGGTCTTATCAGCCTGG 60.250 60.000 0.00 0.00 31.89 4.45
2669 2900 1.403814 CGAGGTCTTATCAGCCTGGA 58.596 55.000 0.00 0.00 31.89 3.86
2670 2901 1.339610 CGAGGTCTTATCAGCCTGGAG 59.660 57.143 0.00 0.00 31.89 3.86
2700 2933 0.934496 CGCTTTGTCCTTGTGTTCGA 59.066 50.000 0.00 0.00 0.00 3.71
2710 2947 2.413837 CTTGTGTTCGACTAGTTGGGG 58.586 52.381 10.33 0.00 0.00 4.96
2754 3000 3.666902 CGCATTGTAAAAGACCCGTTCTG 60.667 47.826 0.00 0.00 33.46 3.02
2835 3092 4.619973 TGTTTTGCCATCATCTGTGTTTC 58.380 39.130 0.00 0.00 0.00 2.78
3048 3318 4.398988 TGATTTGGTAGCCATTCATCACAC 59.601 41.667 0.00 0.00 31.53 3.82
3070 3340 9.219603 CACACTCTCCTTCTATGTTTCAAATTA 57.780 33.333 0.00 0.00 0.00 1.40
3133 3403 5.302823 GCCCAATAAGCAAGTCCAGAATATT 59.697 40.000 0.00 0.00 0.00 1.28
3134 3404 6.736794 GCCCAATAAGCAAGTCCAGAATATTG 60.737 42.308 0.00 0.00 0.00 1.90
3358 3628 6.760161 ACTGCAAAAACGTCTTAGTAGTAC 57.240 37.500 0.00 0.00 0.00 2.73
3404 3674 6.727394 AGAGGAGTTGAGTTCTATGACTACT 58.273 40.000 0.00 0.00 34.31 2.57
3469 3739 1.661112 GCGCCTTCATCAAGTACAGAC 59.339 52.381 0.00 0.00 0.00 3.51
3503 3773 8.055181 TGAGGATCTATATATTGGGAATTTGGC 58.945 37.037 0.00 0.00 34.92 4.52
3530 3800 2.330216 ACTGCAACCCACTAGAACTCT 58.670 47.619 0.00 0.00 0.00 3.24
3531 3801 2.037772 ACTGCAACCCACTAGAACTCTG 59.962 50.000 0.00 0.00 0.00 3.35
3532 3802 1.347707 TGCAACCCACTAGAACTCTGG 59.652 52.381 0.00 0.00 0.00 3.86
3533 3803 1.946283 GCAACCCACTAGAACTCTGGC 60.946 57.143 0.00 0.00 0.00 4.85
3534 3804 1.625818 CAACCCACTAGAACTCTGGCT 59.374 52.381 0.00 0.00 0.00 4.75
3535 3805 1.562783 ACCCACTAGAACTCTGGCTC 58.437 55.000 0.00 0.00 0.00 4.70
3536 3806 1.077993 ACCCACTAGAACTCTGGCTCT 59.922 52.381 0.00 0.00 0.00 4.09
3537 3807 2.183679 CCCACTAGAACTCTGGCTCTT 58.816 52.381 0.00 0.00 0.00 2.85
3538 3808 2.569404 CCCACTAGAACTCTGGCTCTTT 59.431 50.000 0.00 0.00 0.00 2.52
3539 3809 3.008485 CCCACTAGAACTCTGGCTCTTTT 59.992 47.826 0.00 0.00 0.00 2.27
3540 3810 4.223032 CCCACTAGAACTCTGGCTCTTTTA 59.777 45.833 0.00 0.00 0.00 1.52
3541 3811 5.104735 CCCACTAGAACTCTGGCTCTTTTAT 60.105 44.000 0.00 0.00 0.00 1.40
3542 3812 6.410540 CCACTAGAACTCTGGCTCTTTTATT 58.589 40.000 0.00 0.00 0.00 1.40
3543 3813 6.536941 CCACTAGAACTCTGGCTCTTTTATTC 59.463 42.308 0.00 0.00 0.00 1.75
3556 3826 7.154656 GGCTCTTTTATTCCAACTTGACATTT 58.845 34.615 0.00 0.00 0.00 2.32
3574 3844 7.147312 TGACATTTGAAAAGCTTTCGATTCAT 58.853 30.769 13.10 0.00 32.35 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.593909 CGGGCATCTCTATCTCATCTATCTT 59.406 44.000 0.00 0.00 0.00 2.40
43 44 2.560542 GTGACGGGCATCTCTATCTCAT 59.439 50.000 0.00 0.00 0.00 2.90
45 46 1.068885 CGTGACGGGCATCTCTATCTC 60.069 57.143 0.00 0.00 0.00 2.75
80 81 0.723129 CGGCGATCGCGTTTTTGAAA 60.723 50.000 31.76 0.00 43.06 2.69
134 150 0.179179 GAGCAGCACGGCAATCTTTC 60.179 55.000 0.00 0.00 35.83 2.62
144 160 1.576421 GGTTTTGAGGAGCAGCACG 59.424 57.895 0.00 0.00 0.00 5.34
145 161 0.884704 TCGGTTTTGAGGAGCAGCAC 60.885 55.000 0.00 0.00 0.00 4.40
146 162 0.603707 CTCGGTTTTGAGGAGCAGCA 60.604 55.000 0.00 0.00 32.18 4.41
147 163 0.603975 ACTCGGTTTTGAGGAGCAGC 60.604 55.000 0.00 0.00 40.39 5.25
334 357 0.872021 GAGATGTGATCGCGTGACCC 60.872 60.000 5.77 0.00 0.00 4.46
357 417 0.755698 TAGTAGCAGGCGGAGAAGGG 60.756 60.000 0.00 0.00 0.00 3.95
360 420 1.041447 GGGTAGTAGCAGGCGGAGAA 61.041 60.000 1.13 0.00 0.00 2.87
366 426 1.265454 ACACAGGGGTAGTAGCAGGC 61.265 60.000 1.13 0.00 0.00 4.85
378 438 3.576982 TGGAGTAAGAGTAACACACAGGG 59.423 47.826 0.00 0.00 0.00 4.45
379 439 4.557205 GTGGAGTAAGAGTAACACACAGG 58.443 47.826 0.00 0.00 31.40 4.00
380 440 4.023450 TCGTGGAGTAAGAGTAACACACAG 60.023 45.833 0.00 0.00 31.40 3.66
381 441 3.884693 TCGTGGAGTAAGAGTAACACACA 59.115 43.478 0.00 0.00 31.40 3.72
382 442 4.023365 ACTCGTGGAGTAAGAGTAACACAC 60.023 45.833 0.00 0.00 44.66 3.82
383 443 4.139786 ACTCGTGGAGTAAGAGTAACACA 58.860 43.478 0.00 0.00 44.66 3.72
384 444 4.762956 ACTCGTGGAGTAAGAGTAACAC 57.237 45.455 0.00 0.00 44.66 3.32
385 445 4.083643 CGAACTCGTGGAGTAAGAGTAACA 60.084 45.833 0.00 0.00 45.55 2.41
386 446 4.401714 CGAACTCGTGGAGTAAGAGTAAC 58.598 47.826 0.00 0.00 45.55 2.50
387 447 4.675190 CGAACTCGTGGAGTAAGAGTAA 57.325 45.455 0.00 0.00 45.55 2.24
401 461 2.879462 GCCCAGCGTACGAACTCG 60.879 66.667 21.65 0.00 46.33 4.18
402 462 2.508663 GGCCCAGCGTACGAACTC 60.509 66.667 21.65 0.11 0.00 3.01
403 463 4.078516 GGGCCCAGCGTACGAACT 62.079 66.667 21.65 4.24 0.00 3.01
422 482 0.387202 CTACTGAGCCGATGACAGGG 59.613 60.000 0.00 0.00 36.17 4.45
437 497 2.896443 GCGAGGAAGGCTGCTACT 59.104 61.111 0.00 0.00 0.00 2.57
592 656 2.295909 CGTTTCATTTCCTTGGGCAAGA 59.704 45.455 0.00 0.00 40.79 3.02
595 659 0.316841 GCGTTTCATTTCCTTGGGCA 59.683 50.000 0.00 0.00 0.00 5.36
610 674 2.126424 GCCGAGAAGACGAGCGTT 60.126 61.111 0.00 0.00 35.09 4.84
625 689 2.781300 CTTCTTGCGCGAGAAGCC 59.219 61.111 40.48 0.00 44.23 4.35
628 692 1.569493 GTTGCTTCTTGCGCGAGAA 59.431 52.632 32.62 32.62 46.63 2.87
629 693 2.657757 CGTTGCTTCTTGCGCGAGA 61.658 57.895 23.66 23.66 46.63 4.04
630 694 2.202096 CGTTGCTTCTTGCGCGAG 60.202 61.111 19.15 19.15 46.63 5.03
631 695 3.711842 CCGTTGCTTCTTGCGCGA 61.712 61.111 12.10 0.00 46.63 5.87
632 696 4.741781 CCCGTTGCTTCTTGCGCG 62.742 66.667 0.00 0.00 46.63 6.86
633 697 2.400896 TTTCCCGTTGCTTCTTGCGC 62.401 55.000 0.00 0.00 46.63 6.09
649 714 1.067974 CGGGGTTTTGTCAGGGTTTTC 59.932 52.381 0.00 0.00 0.00 2.29
838 904 3.064324 GGACGCTGGCTTGGCATT 61.064 61.111 0.00 0.00 0.00 3.56
853 919 0.032130 CGCTTTATAGCTCAGCCGGA 59.968 55.000 5.05 0.00 45.51 5.14
857 923 1.144136 GGCTCGCTTTATAGCTCAGC 58.856 55.000 13.99 13.99 45.51 4.26
858 924 1.069204 TGGGCTCGCTTTATAGCTCAG 59.931 52.381 3.62 0.93 44.16 3.35
859 925 1.069204 CTGGGCTCGCTTTATAGCTCA 59.931 52.381 3.62 0.00 46.77 4.26
860 926 1.789506 CTGGGCTCGCTTTATAGCTC 58.210 55.000 3.62 0.00 45.51 4.09
861 927 0.250081 GCTGGGCTCGCTTTATAGCT 60.250 55.000 3.62 0.00 45.51 3.32
894 960 1.197949 GGAGAAAGCTTTTCGTGCTCC 59.802 52.381 21.51 21.51 40.22 4.70
901 967 3.258228 CCGAGAGAGGAGAAAGCTTTTC 58.742 50.000 14.05 12.10 0.00 2.29
903 969 1.066502 GCCGAGAGAGGAGAAAGCTTT 60.067 52.381 12.53 12.53 0.00 3.51
927 993 0.463620 CAACCAACCAACCAACCCAG 59.536 55.000 0.00 0.00 0.00 4.45
943 1009 4.773323 ACCTACTACACTACGAACCAAC 57.227 45.455 0.00 0.00 0.00 3.77
944 1010 4.943705 CCTACCTACTACACTACGAACCAA 59.056 45.833 0.00 0.00 0.00 3.67
945 1011 4.517285 CCTACCTACTACACTACGAACCA 58.483 47.826 0.00 0.00 0.00 3.67
946 1012 3.313803 GCCTACCTACTACACTACGAACC 59.686 52.174 0.00 0.00 0.00 3.62
949 1015 2.430694 TCGCCTACCTACTACACTACGA 59.569 50.000 0.00 0.00 0.00 3.43
950 1016 2.799412 CTCGCCTACCTACTACACTACG 59.201 54.545 0.00 0.00 0.00 3.51
951 1017 3.137533 CCTCGCCTACCTACTACACTAC 58.862 54.545 0.00 0.00 0.00 2.73
952 1018 2.486191 GCCTCGCCTACCTACTACACTA 60.486 54.545 0.00 0.00 0.00 2.74
953 1019 1.749983 GCCTCGCCTACCTACTACACT 60.750 57.143 0.00 0.00 0.00 3.55
954 1020 0.667453 GCCTCGCCTACCTACTACAC 59.333 60.000 0.00 0.00 0.00 2.90
991 1057 1.065701 CTTACTCTCCATCACCGACGG 59.934 57.143 13.61 13.61 0.00 4.79
1008 1074 1.230497 CCTCTCCCCGCTCTCCTTA 59.770 63.158 0.00 0.00 0.00 2.69
1025 1091 0.543749 CACCTCCACCTTCTCCATCC 59.456 60.000 0.00 0.00 0.00 3.51
1230 1296 3.055530 AGCTGGTCTTGTTGGAGATGTAG 60.056 47.826 0.00 0.00 0.00 2.74
1325 1394 1.425412 CAGCAAGCAAACATGGAAGC 58.575 50.000 0.00 0.00 0.00 3.86
1379 1452 4.402192 GCACGATCTAGCGAGCAA 57.598 55.556 5.21 0.00 45.11 3.91
1448 1558 1.261989 GTAACAGCACGCGACGAATA 58.738 50.000 15.93 0.00 0.00 1.75
1483 1593 1.611977 GAGGAACAAAAGGGGGAAACG 59.388 52.381 0.00 0.00 0.00 3.60
1484 1594 1.611977 CGAGGAACAAAAGGGGGAAAC 59.388 52.381 0.00 0.00 0.00 2.78
1485 1595 1.479757 CCGAGGAACAAAAGGGGGAAA 60.480 52.381 0.00 0.00 0.00 3.13
1486 1596 0.111639 CCGAGGAACAAAAGGGGGAA 59.888 55.000 0.00 0.00 0.00 3.97
1488 1598 0.331616 ATCCGAGGAACAAAAGGGGG 59.668 55.000 0.00 0.00 0.00 5.40
1493 1604 2.843401 TTCCGATCCGAGGAACAAAA 57.157 45.000 0.00 0.00 42.33 2.44
1528 1639 5.690997 AGGAAAAGAAAACAGGACGATTC 57.309 39.130 0.00 0.00 0.00 2.52
1535 1646 7.041440 ACAACAACAAAAGGAAAAGAAAACAGG 60.041 33.333 0.00 0.00 0.00 4.00
1543 1654 7.413644 ACAACAAACAACAACAAAAGGAAAAG 58.586 30.769 0.00 0.00 0.00 2.27
1551 1662 6.422776 ACAACAACAACAAACAACAACAAA 57.577 29.167 0.00 0.00 0.00 2.83
1552 1663 6.292381 GCTACAACAACAACAAACAACAACAA 60.292 34.615 0.00 0.00 0.00 2.83
1553 1664 5.175856 GCTACAACAACAACAAACAACAACA 59.824 36.000 0.00 0.00 0.00 3.33
1554 1665 5.175856 TGCTACAACAACAACAAACAACAAC 59.824 36.000 0.00 0.00 0.00 3.32
1555 1666 5.289595 TGCTACAACAACAACAAACAACAA 58.710 33.333 0.00 0.00 0.00 2.83
1556 1667 4.871513 TGCTACAACAACAACAAACAACA 58.128 34.783 0.00 0.00 0.00 3.33
1557 1668 4.201580 GCTGCTACAACAACAACAAACAAC 60.202 41.667 0.00 0.00 0.00 3.32
1558 1669 3.923461 GCTGCTACAACAACAACAAACAA 59.077 39.130 0.00 0.00 0.00 2.83
1559 1670 3.506810 GCTGCTACAACAACAACAAACA 58.493 40.909 0.00 0.00 0.00 2.83
1563 1674 1.657822 TCGCTGCTACAACAACAACA 58.342 45.000 0.00 0.00 0.00 3.33
1564 1675 2.969443 ATCGCTGCTACAACAACAAC 57.031 45.000 0.00 0.00 0.00 3.32
1565 1676 3.980646 AAATCGCTGCTACAACAACAA 57.019 38.095 0.00 0.00 0.00 2.83
1569 1695 2.873170 CGAAAATCGCTGCTACAACA 57.127 45.000 0.00 0.00 31.14 3.33
1608 1734 1.294659 GCTTCTCCGTGCAGGACAAG 61.295 60.000 8.24 11.06 45.98 3.16
1636 1762 5.243060 GGAAGCACACCTACCTAAAACATTT 59.757 40.000 0.00 0.00 0.00 2.32
1638 1764 4.332828 GGAAGCACACCTACCTAAAACAT 58.667 43.478 0.00 0.00 0.00 2.71
1640 1766 2.740447 CGGAAGCACACCTACCTAAAAC 59.260 50.000 0.00 0.00 0.00 2.43
1684 1814 4.161189 ACATTCACATGGTTGTTTTCACCA 59.839 37.500 0.00 0.00 36.20 4.17
1704 1834 3.198417 TCCACACTGCACTATCATCACAT 59.802 43.478 0.00 0.00 0.00 3.21
1705 1835 2.566724 TCCACACTGCACTATCATCACA 59.433 45.455 0.00 0.00 0.00 3.58
1706 1836 3.251479 TCCACACTGCACTATCATCAC 57.749 47.619 0.00 0.00 0.00 3.06
1707 1837 3.451902 TCATCCACACTGCACTATCATCA 59.548 43.478 0.00 0.00 0.00 3.07
1708 1838 4.063998 TCATCCACACTGCACTATCATC 57.936 45.455 0.00 0.00 0.00 2.92
1709 1839 4.080695 ACTTCATCCACACTGCACTATCAT 60.081 41.667 0.00 0.00 0.00 2.45
1710 1840 3.261643 ACTTCATCCACACTGCACTATCA 59.738 43.478 0.00 0.00 0.00 2.15
1711 1841 3.620374 CACTTCATCCACACTGCACTATC 59.380 47.826 0.00 0.00 0.00 2.08
1712 1842 3.603532 CACTTCATCCACACTGCACTAT 58.396 45.455 0.00 0.00 0.00 2.12
1733 1863 1.340248 TCCAAGGATCTACGAATCGCC 59.660 52.381 1.15 0.00 0.00 5.54
1751 1881 3.497262 CGTGAGGGAAAAAGTAAGTGTCC 59.503 47.826 0.00 0.00 0.00 4.02
1760 1890 2.295909 TCCAAATGCGTGAGGGAAAAAG 59.704 45.455 0.00 0.00 0.00 2.27
1787 1917 8.122952 CCGTAAGCATAACAATCTTAGGAAAAG 58.877 37.037 0.00 0.00 32.83 2.27
1792 1922 6.046593 TGTCCGTAAGCATAACAATCTTAGG 58.953 40.000 0.00 0.00 0.00 2.69
1833 1964 8.548880 ACAGGTTAATCGCCACCTATATATAT 57.451 34.615 0.00 0.00 41.86 0.86
1834 1965 7.966339 ACAGGTTAATCGCCACCTATATATA 57.034 36.000 0.00 0.00 41.86 0.86
1835 1966 6.869206 ACAGGTTAATCGCCACCTATATAT 57.131 37.500 0.00 0.00 41.86 0.86
1836 1967 6.720748 TGTACAGGTTAATCGCCACCTATATA 59.279 38.462 0.00 0.00 41.86 0.86
1876 2007 4.543692 CCAACTTTGACAGCAAGAATCAG 58.456 43.478 0.00 0.00 35.04 2.90
1910 2041 0.801251 GCTTACAGAGGCAGCAACTG 59.199 55.000 14.06 14.06 37.62 3.16
1963 2094 6.309737 GCAAAAGATAATCTCCAGCAAAACTG 59.690 38.462 0.00 0.00 46.77 3.16
1964 2095 6.015180 TGCAAAAGATAATCTCCAGCAAAACT 60.015 34.615 0.00 0.00 0.00 2.66
1965 2096 6.158598 TGCAAAAGATAATCTCCAGCAAAAC 58.841 36.000 0.00 0.00 0.00 2.43
1966 2097 6.343716 TGCAAAAGATAATCTCCAGCAAAA 57.656 33.333 0.00 0.00 0.00 2.44
1967 2098 5.981088 TGCAAAAGATAATCTCCAGCAAA 57.019 34.783 0.00 0.00 0.00 3.68
1968 2099 5.243507 TGTTGCAAAAGATAATCTCCAGCAA 59.756 36.000 0.00 0.00 35.41 3.91
1969 2100 4.766373 TGTTGCAAAAGATAATCTCCAGCA 59.234 37.500 0.00 0.00 0.00 4.41
1970 2101 5.314923 TGTTGCAAAAGATAATCTCCAGC 57.685 39.130 0.00 0.00 0.00 4.85
1971 2102 7.219535 CGAAATGTTGCAAAAGATAATCTCCAG 59.780 37.037 0.00 0.00 0.00 3.86
1972 2103 7.028962 CGAAATGTTGCAAAAGATAATCTCCA 58.971 34.615 0.00 0.00 0.00 3.86
1973 2104 7.029563 ACGAAATGTTGCAAAAGATAATCTCC 58.970 34.615 0.00 0.00 0.00 3.71
1974 2105 7.218963 GGACGAAATGTTGCAAAAGATAATCTC 59.781 37.037 0.00 0.00 0.00 2.75
1975 2106 7.029563 GGACGAAATGTTGCAAAAGATAATCT 58.970 34.615 0.00 0.00 0.00 2.40
1976 2107 7.008628 CAGGACGAAATGTTGCAAAAGATAATC 59.991 37.037 0.00 0.00 0.00 1.75
1977 2108 6.808212 CAGGACGAAATGTTGCAAAAGATAAT 59.192 34.615 0.00 0.00 0.00 1.28
1978 2109 6.148948 CAGGACGAAATGTTGCAAAAGATAA 58.851 36.000 0.00 0.00 0.00 1.75
1979 2110 5.240623 ACAGGACGAAATGTTGCAAAAGATA 59.759 36.000 0.00 0.00 0.00 1.98
1980 2111 4.037923 ACAGGACGAAATGTTGCAAAAGAT 59.962 37.500 0.00 0.00 0.00 2.40
1981 2112 3.380004 ACAGGACGAAATGTTGCAAAAGA 59.620 39.130 0.00 0.00 0.00 2.52
1982 2113 3.486841 CACAGGACGAAATGTTGCAAAAG 59.513 43.478 0.00 0.00 0.00 2.27
1991 2139 4.811555 TTTCTGAACACAGGACGAAATG 57.188 40.909 0.00 0.00 33.04 2.32
2029 2177 0.753479 TTGACGGCAAAAAGGGCAGA 60.753 50.000 0.00 0.00 0.00 4.26
2030 2178 0.103937 TTTGACGGCAAAAAGGGCAG 59.896 50.000 15.59 0.00 40.82 4.85
2031 2179 0.755686 ATTTGACGGCAAAAAGGGCA 59.244 45.000 22.36 0.00 46.19 5.36
2035 2183 2.865551 ACAAGCATTTGACGGCAAAAAG 59.134 40.909 22.36 17.18 46.19 2.27
2065 2218 5.227908 TGTAACAAGTAGTACAGCAAGCTC 58.772 41.667 2.52 0.00 0.00 4.09
2095 2248 2.005451 AGCATCAGAGCACGAAATGTC 58.995 47.619 0.00 0.00 36.85 3.06
2175 2328 6.092122 CGCTATAAGAACAGAATCCAACAACA 59.908 38.462 0.00 0.00 0.00 3.33
2236 2456 3.386932 AACTACAATGGGTGGCATGAT 57.613 42.857 0.00 0.00 0.00 2.45
2238 2458 3.091545 AGAAACTACAATGGGTGGCATG 58.908 45.455 0.00 0.00 0.00 4.06
2245 2465 3.612479 GCACAGCAAGAAACTACAATGGG 60.612 47.826 0.00 0.00 0.00 4.00
2247 2467 4.494350 AGCACAGCAAGAAACTACAATG 57.506 40.909 0.00 0.00 0.00 2.82
2266 2486 9.334693 CTGAATTAACAGAACAAATACAGAAGC 57.665 33.333 0.00 0.00 39.94 3.86
2342 2562 5.719085 AGTACATAGCAGCAGATAGGCTATT 59.281 40.000 8.71 0.00 45.81 1.73
2364 2584 7.831691 ACTACTACTATTCAGATGCATCAGT 57.168 36.000 27.81 22.10 0.00 3.41
2389 2609 9.244292 CCATCAGATTTCAGATTCCATCATAAT 57.756 33.333 0.00 0.00 0.00 1.28
2407 2627 2.709934 AGTAGCAGATTGGCCATCAGAT 59.290 45.455 6.09 4.93 33.75 2.90
2414 2634 1.009829 CGAACAGTAGCAGATTGGCC 58.990 55.000 0.00 0.00 0.00 5.36
2433 2654 1.063174 GATTCAACCAGACGCATCAGC 59.937 52.381 0.00 0.00 37.42 4.26
2589 2820 0.171231 CGATCACGAGCTCAGGACAA 59.829 55.000 15.40 0.00 42.66 3.18
2590 2821 0.960861 ACGATCACGAGCTCAGGACA 60.961 55.000 15.40 0.00 42.66 4.02
2667 2898 4.503007 GGACAAAGCGAAAAGAAAAACTCC 59.497 41.667 0.00 0.00 0.00 3.85
2668 2899 5.340803 AGGACAAAGCGAAAAGAAAAACTC 58.659 37.500 0.00 0.00 0.00 3.01
2669 2900 5.324784 AGGACAAAGCGAAAAGAAAAACT 57.675 34.783 0.00 0.00 0.00 2.66
2670 2901 5.347635 ACAAGGACAAAGCGAAAAGAAAAAC 59.652 36.000 0.00 0.00 0.00 2.43
2700 2933 1.923356 CAAACCATGCCCCAACTAGT 58.077 50.000 0.00 0.00 0.00 2.57
2742 2987 1.071471 CACAGCCAGAACGGGTCTT 59.929 57.895 0.00 0.00 44.26 3.01
2743 2988 2.743718 CACAGCCAGAACGGGTCT 59.256 61.111 0.00 0.00 44.26 3.85
2835 3092 3.875727 AGTGATCTTGCATTCCATTCGAG 59.124 43.478 0.00 0.00 0.00 4.04
3089 3359 1.754803 CGGAGGCACTTCTATACCACA 59.245 52.381 0.00 0.00 41.55 4.17
3206 3476 2.914059 ACAGTTGCCTAAAACGACACT 58.086 42.857 0.00 0.00 35.13 3.55
3212 3482 5.163754 CCATAGCACTACAGTTGCCTAAAAC 60.164 44.000 0.00 0.00 0.00 2.43
3338 3608 6.760161 ACAGTACTACTAAGACGTTTTTGC 57.240 37.500 0.00 0.00 0.00 3.68
3358 3628 7.925483 CCTCTCACATTTCCTTCTCTAATACAG 59.075 40.741 0.00 0.00 0.00 2.74
3404 3674 6.295249 TGACACATGAAAAGTGGATTAGTCA 58.705 36.000 0.00 0.00 41.21 3.41
3469 3739 7.387122 CCCAATATATAGATCCTCATGAATGCG 59.613 40.741 0.00 0.00 0.00 4.73
3503 3773 3.882888 TCTAGTGGGTTGCAGTTTTCTTG 59.117 43.478 0.00 0.00 0.00 3.02
3530 3800 5.136828 TGTCAAGTTGGAATAAAAGAGCCA 58.863 37.500 2.34 0.00 0.00 4.75
3531 3801 5.705609 TGTCAAGTTGGAATAAAAGAGCC 57.294 39.130 2.34 0.00 0.00 4.70
3532 3802 7.867403 TCAAATGTCAAGTTGGAATAAAAGAGC 59.133 33.333 2.34 0.00 32.26 4.09
3533 3803 9.748708 TTCAAATGTCAAGTTGGAATAAAAGAG 57.251 29.630 2.34 0.00 32.26 2.85
3537 3807 8.825745 GCTTTTCAAATGTCAAGTTGGAATAAA 58.174 29.630 2.34 0.00 29.36 1.40
3538 3808 8.203485 AGCTTTTCAAATGTCAAGTTGGAATAA 58.797 29.630 2.34 0.00 29.36 1.40
3539 3809 7.725251 AGCTTTTCAAATGTCAAGTTGGAATA 58.275 30.769 2.34 0.00 29.36 1.75
3540 3810 6.585416 AGCTTTTCAAATGTCAAGTTGGAAT 58.415 32.000 2.34 0.00 29.36 3.01
3541 3811 5.976458 AGCTTTTCAAATGTCAAGTTGGAA 58.024 33.333 2.34 0.00 32.26 3.53
3542 3812 5.596836 AGCTTTTCAAATGTCAAGTTGGA 57.403 34.783 2.34 0.00 32.26 3.53
3543 3813 6.508404 CGAAAGCTTTTCAAATGTCAAGTTGG 60.508 38.462 14.05 0.00 32.26 3.77
3556 3826 6.558771 TCTCAATGAATCGAAAGCTTTTCA 57.441 33.333 14.05 13.11 0.00 2.69


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

AutoCloner maintained by Alex Coulton.