Multiple sequence alignment - TraesCS4A01G118100

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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 TraesCS4A01G118100 chr4A 100.000 2255 0 0 1 2255 144625448 144627702 0.000000e+00 4165.0
1 TraesCS4A01G118100 chr4D 92.944 1318 67 9 651 1963 326383904 326382608 0.000000e+00 1895.0
2 TraesCS4A01G118100 chr4D 88.280 529 39 12 1 512 326385071 326384549 1.480000e-171 612.0
3 TraesCS4A01G118100 chr4B 92.489 1318 73 9 651 1963 406392717 406391421 0.000000e+00 1862.0
4 TraesCS4A01G118100 chr4B 83.992 531 24 23 1 511 406393855 406393366 9.500000e-124 453.0
5 TraesCS4A01G118100 chr5D 86.291 1510 130 41 652 2139 524917022 524918476 0.000000e+00 1570.0
6 TraesCS4A01G118100 chr5D 97.778 135 3 0 518 652 448586029 448585895 1.350000e-57 233.0
7 TraesCS4A01G118100 chr5D 91.339 127 11 0 526 652 461438284 461438410 8.280000e-40 174.0
8 TraesCS4A01G118100 chr5A 88.657 1296 102 22 651 1935 651436686 651437947 0.000000e+00 1537.0
9 TraesCS4A01G118100 chr5A 86.301 73 4 5 1 69 10860617 10860547 8.640000e-10 75.0
10 TraesCS4A01G118100 chr5B 89.195 944 74 13 652 1595 659411218 659412133 0.000000e+00 1153.0
11 TraesCS4A01G118100 chr5B 89.103 312 24 3 1597 1907 659412226 659412528 1.630000e-101 379.0
12 TraesCS4A01G118100 chr1A 96.296 135 5 0 518 652 50920629 50920495 2.920000e-54 222.0
13 TraesCS4A01G118100 chr1A 93.496 123 8 0 530 652 561936198 561936076 1.380000e-42 183.0
14 TraesCS4A01G118100 chr3A 95.556 135 6 0 518 652 466243755 466243621 1.360000e-52 217.0
15 TraesCS4A01G118100 chr2A 96.032 126 4 1 528 652 174788961 174789086 1.060000e-48 204.0
16 TraesCS4A01G118100 chr2A 86.301 73 3 5 1 69 102679263 102679332 3.110000e-09 73.1
17 TraesCS4A01G118100 chr2A 79.130 115 11 13 1 108 102325363 102325471 1.450000e-07 67.6
18 TraesCS4A01G118100 chr6A 94.444 126 6 1 518 643 32652844 32652968 2.290000e-45 193.0
19 TraesCS4A01G118100 chr7B 89.844 128 12 1 526 652 178397734 178397861 1.790000e-36 163.0
20 TraesCS4A01G118100 chr2B 84.298 121 12 1 535 655 498864790 498864677 6.580000e-21 111.0
21 TraesCS4A01G118100 chr2B 82.203 118 18 3 1 117 140744205 140744320 5.130000e-17 99.0
22 TraesCS4A01G118100 chr2B 86.486 74 1 8 1 69 154906954 154907023 3.110000e-09 73.1
23 TraesCS4A01G118100 chr2D 86.301 73 3 7 1 69 99658632 99658563 3.110000e-09 73.1
24 TraesCS4A01G118100 chr2D 86.301 73 3 7 1 69 103147672 103147741 3.110000e-09 73.1


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 TraesCS4A01G118100 chr4A 144625448 144627702 2254 False 4165.0 4165 100.0000 1 2255 1 chr4A.!!$F1 2254
1 TraesCS4A01G118100 chr4D 326382608 326385071 2463 True 1253.5 1895 90.6120 1 1963 2 chr4D.!!$R1 1962
2 TraesCS4A01G118100 chr4B 406391421 406393855 2434 True 1157.5 1862 88.2405 1 1963 2 chr4B.!!$R1 1962
3 TraesCS4A01G118100 chr5D 524917022 524918476 1454 False 1570.0 1570 86.2910 652 2139 1 chr5D.!!$F2 1487
4 TraesCS4A01G118100 chr5A 651436686 651437947 1261 False 1537.0 1537 88.6570 651 1935 1 chr5A.!!$F1 1284
5 TraesCS4A01G118100 chr5B 659411218 659412528 1310 False 766.0 1153 89.1490 652 1907 2 chr5B.!!$F1 1255

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
550 689 0.03467 GGTTGGCTCTTCTGCAGGAT 60.035 55.0 15.13 0.0 34.04 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2623 0.034186 AATGGATGGTGCACCGACAT 60.034 50.0 30.07 27.28 39.43 3.06 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
69 70 2.755655 TCGCTCTCTTATATAGCCAGCC 59.244 50.000 0.00 0.00 32.50 4.85
123 124 1.946984 ACTATTGTCCCGGGTCTCAA 58.053 50.000 22.86 22.71 0.00 3.02
145 155 3.964875 CACCGGCAGCACCACAAC 61.965 66.667 0.00 0.00 39.03 3.32
153 171 2.043405 AGCACCACAACGCACAACA 61.043 52.632 0.00 0.00 0.00 3.33
154 172 1.871789 GCACCACAACGCACAACAC 60.872 57.895 0.00 0.00 0.00 3.32
203 225 2.094417 GCCGCATACAGACTTGAGTTTC 59.906 50.000 0.00 0.00 0.00 2.78
265 287 4.056125 CTCGCCTCTCCACGCACA 62.056 66.667 0.00 0.00 0.00 4.57
268 290 2.946762 GCCTCTCCACGCACAAAC 59.053 61.111 0.00 0.00 0.00 2.93
271 293 0.588252 CCTCTCCACGCACAAACAAG 59.412 55.000 0.00 0.00 0.00 3.16
272 294 0.040958 CTCTCCACGCACAAACAAGC 60.041 55.000 0.00 0.00 0.00 4.01
275 297 0.746204 TCCACGCACAAACAAGCAGA 60.746 50.000 0.00 0.00 0.00 4.26
276 298 0.592247 CCACGCACAAACAAGCAGAC 60.592 55.000 0.00 0.00 0.00 3.51
277 299 0.098552 CACGCACAAACAAGCAGACA 59.901 50.000 0.00 0.00 0.00 3.41
469 499 2.100216 CCCAAAGCCGAATTCGCG 59.900 61.111 22.36 15.81 38.18 5.87
518 654 4.895297 CCAATGCATTCTAACCCTGGTATT 59.105 41.667 9.53 0.00 0.00 1.89
524 663 5.239525 GCATTCTAACCCTGGTATTCACATC 59.760 44.000 0.00 0.00 0.00 3.06
525 664 5.367945 TTCTAACCCTGGTATTCACATCC 57.632 43.478 0.00 0.00 0.00 3.51
526 665 2.710096 AACCCTGGTATTCACATCCG 57.290 50.000 0.00 0.00 0.00 4.18
527 666 1.874129 ACCCTGGTATTCACATCCGA 58.126 50.000 0.00 0.00 0.00 4.55
528 667 2.193127 ACCCTGGTATTCACATCCGAA 58.807 47.619 0.00 0.00 0.00 4.30
529 668 2.170607 ACCCTGGTATTCACATCCGAAG 59.829 50.000 0.00 0.00 0.00 3.79
530 669 2.434336 CCCTGGTATTCACATCCGAAGA 59.566 50.000 0.00 0.00 0.00 2.87
531 670 3.493350 CCCTGGTATTCACATCCGAAGAG 60.493 52.174 0.00 0.00 0.00 2.85
532 671 3.493350 CCTGGTATTCACATCCGAAGAGG 60.493 52.174 0.00 0.00 42.97 3.69
533 672 3.104512 TGGTATTCACATCCGAAGAGGT 58.895 45.455 0.00 0.00 41.99 3.85
534 673 3.517901 TGGTATTCACATCCGAAGAGGTT 59.482 43.478 0.00 0.00 41.99 3.50
536 675 2.472695 TTCACATCCGAAGAGGTTGG 57.527 50.000 0.00 0.00 42.63 3.77
537 676 0.036388 TCACATCCGAAGAGGTTGGC 60.036 55.000 0.00 0.00 42.63 4.52
539 678 0.250513 ACATCCGAAGAGGTTGGCTC 59.749 55.000 0.00 0.00 42.63 4.70
540 679 0.539051 CATCCGAAGAGGTTGGCTCT 59.461 55.000 0.00 0.00 41.99 4.09
541 680 1.065854 CATCCGAAGAGGTTGGCTCTT 60.066 52.381 0.00 0.00 43.09 2.85
545 684 3.641017 AAGAGGTTGGCTCTTCTGC 57.359 52.632 0.00 0.00 36.54 4.26
546 685 0.767375 AAGAGGTTGGCTCTTCTGCA 59.233 50.000 0.00 0.00 36.54 4.41
547 686 0.324285 AGAGGTTGGCTCTTCTGCAG 59.676 55.000 7.63 7.63 34.04 4.41
550 689 0.034670 GGTTGGCTCTTCTGCAGGAT 60.035 55.000 15.13 0.00 34.04 3.24
552 691 0.694771 TTGGCTCTTCTGCAGGATGT 59.305 50.000 15.13 0.00 39.31 3.06
564 703 4.118410 CTGCAGGATGTAGCTTTAGTCTG 58.882 47.826 5.57 0.00 43.16 3.51
565 704 2.869192 GCAGGATGTAGCTTTAGTCTGC 59.131 50.000 12.77 12.77 39.31 4.26
568 707 4.569966 CAGGATGTAGCTTTAGTCTGCAAG 59.430 45.833 0.00 0.00 30.37 4.01
569 708 3.311048 GGATGTAGCTTTAGTCTGCAAGC 59.689 47.826 9.57 9.57 44.96 4.01
570 709 3.401033 TGTAGCTTTAGTCTGCAAGCA 57.599 42.857 16.79 0.00 46.70 3.91
571 710 3.329386 TGTAGCTTTAGTCTGCAAGCAG 58.671 45.455 15.67 15.67 46.70 4.24
572 711 1.163554 AGCTTTAGTCTGCAAGCAGC 58.836 50.000 16.89 11.87 46.70 5.25
590 1063 0.317436 GCACGTTGCGTCAATTTGGA 60.317 50.000 0.00 0.00 38.32 3.53
591 1064 1.862008 GCACGTTGCGTCAATTTGGAA 60.862 47.619 0.00 0.00 38.32 3.53
593 1066 1.268845 ACGTTGCGTCAATTTGGAACC 60.269 47.619 0.00 0.00 33.69 3.62
594 1067 1.268794 CGTTGCGTCAATTTGGAACCA 60.269 47.619 0.00 0.00 33.45 3.67
595 1068 2.606795 CGTTGCGTCAATTTGGAACCAT 60.607 45.455 0.00 0.00 33.45 3.55
608 1081 2.723273 GGAACCATCCAAACCTAGGTG 58.277 52.381 17.14 3.44 45.79 4.00
609 1082 2.620627 GGAACCATCCAAACCTAGGTGG 60.621 54.545 17.14 13.88 45.79 4.61
610 1083 0.331616 ACCATCCAAACCTAGGTGGC 59.668 55.000 17.14 0.00 40.22 5.01
611 1084 0.331278 CCATCCAAACCTAGGTGGCA 59.669 55.000 17.14 4.28 40.22 4.92
612 1085 1.683011 CCATCCAAACCTAGGTGGCAG 60.683 57.143 17.14 8.79 40.22 4.85
613 1086 1.004745 CATCCAAACCTAGGTGGCAGT 59.995 52.381 17.14 0.00 40.22 4.40
614 1087 1.145571 TCCAAACCTAGGTGGCAGTT 58.854 50.000 17.14 2.00 40.22 3.16
615 1088 1.202879 TCCAAACCTAGGTGGCAGTTG 60.203 52.381 17.14 15.24 40.22 3.16
616 1089 1.247567 CAAACCTAGGTGGCAGTTGG 58.752 55.000 17.14 0.00 40.22 3.77
617 1090 1.145571 AAACCTAGGTGGCAGTTGGA 58.854 50.000 17.14 0.00 40.22 3.53
618 1091 0.693049 AACCTAGGTGGCAGTTGGAG 59.307 55.000 17.14 0.00 40.22 3.86
619 1092 1.078143 CCTAGGTGGCAGTTGGAGC 60.078 63.158 0.00 0.00 0.00 4.70
620 1093 1.679311 CTAGGTGGCAGTTGGAGCA 59.321 57.895 0.00 0.00 0.00 4.26
621 1094 0.674895 CTAGGTGGCAGTTGGAGCAC 60.675 60.000 0.00 0.00 0.00 4.40
623 1096 2.985847 GTGGCAGTTGGAGCACCC 60.986 66.667 0.00 0.00 34.81 4.61
624 1097 4.641645 TGGCAGTTGGAGCACCCG 62.642 66.667 0.00 0.00 37.93 5.28
625 1098 4.643387 GGCAGTTGGAGCACCCGT 62.643 66.667 0.00 0.00 37.93 5.28
626 1099 3.050275 GCAGTTGGAGCACCCGTC 61.050 66.667 0.00 0.00 37.93 4.79
627 1100 2.358737 CAGTTGGAGCACCCGTCC 60.359 66.667 0.00 0.00 37.93 4.79
628 1101 2.847234 AGTTGGAGCACCCGTCCA 60.847 61.111 0.00 0.00 42.62 4.02
629 1102 2.668550 GTTGGAGCACCCGTCCAC 60.669 66.667 0.00 0.00 44.06 4.02
630 1103 3.948719 TTGGAGCACCCGTCCACC 61.949 66.667 0.00 0.00 44.06 4.61
637 1110 3.688159 ACCCGTCCACCGTGTAGC 61.688 66.667 0.00 0.00 33.66 3.58
638 1111 4.789075 CCCGTCCACCGTGTAGCG 62.789 72.222 0.00 0.00 40.95 4.26
639 1112 4.047059 CCGTCCACCGTGTAGCGT 62.047 66.667 0.00 0.00 39.32 5.07
640 1113 2.049802 CGTCCACCGTGTAGCGTT 60.050 61.111 0.00 0.00 39.32 4.84
642 1115 1.300388 GTCCACCGTGTAGCGTTGT 60.300 57.895 0.00 0.00 39.32 3.32
643 1116 0.039256 GTCCACCGTGTAGCGTTGTA 60.039 55.000 0.00 0.00 39.32 2.41
644 1117 0.039256 TCCACCGTGTAGCGTTGTAC 60.039 55.000 0.00 0.00 39.32 2.90
645 1118 0.318869 CCACCGTGTAGCGTTGTACA 60.319 55.000 0.00 0.00 39.32 2.90
647 1120 1.454276 CACCGTGTAGCGTTGTACAAG 59.546 52.381 8.98 4.70 39.32 3.16
648 1121 0.437295 CCGTGTAGCGTTGTACAAGC 59.563 55.000 8.98 14.23 39.32 4.01
649 1122 0.437295 CGTGTAGCGTTGTACAAGCC 59.563 55.000 19.73 10.56 34.69 4.35
729 1269 4.404715 GTGGATGCTAGTAGTTGGGACTTA 59.595 45.833 0.00 0.00 37.33 2.24
730 1270 4.404715 TGGATGCTAGTAGTTGGGACTTAC 59.595 45.833 0.00 0.00 37.33 2.34
806 1346 6.552445 ATCACTCTATCTTTACCTGCAAGT 57.448 37.500 0.00 0.00 0.00 3.16
835 1375 7.288810 ACTTCAGCCATAAAATTGAAGACAA 57.711 32.000 17.12 0.00 45.82 3.18
933 1473 8.899427 TTCCTTCTTGATTGCTATCTGATAAG 57.101 34.615 9.55 4.96 0.00 1.73
1056 1598 0.888736 CTTGGACATGGGACGCACAA 60.889 55.000 0.00 0.00 0.00 3.33
1258 1800 1.064389 GGCAGTTCAAGGGCTAAGGAT 60.064 52.381 0.00 0.00 0.00 3.24
1259 1801 2.019984 GCAGTTCAAGGGCTAAGGATG 58.980 52.381 0.00 0.00 0.00 3.51
1360 1902 1.266989 GTTGTCTTGTAAGTGCCCTGC 59.733 52.381 0.00 0.00 0.00 4.85
1375 1917 2.648059 CCCTGCCATACTTTCTGGAAG 58.352 52.381 0.00 0.00 38.95 3.46
1382 1924 4.565652 GCCATACTTTCTGGAAGTCAGGAA 60.566 45.833 18.59 0.00 45.40 3.36
1383 1925 5.749462 CCATACTTTCTGGAAGTCAGGAAT 58.251 41.667 4.21 0.00 45.40 3.01
1406 1948 4.023536 TGTCGGCATCTTTTAAGTGAAACC 60.024 41.667 0.00 0.00 37.80 3.27
1407 1949 4.023536 GTCGGCATCTTTTAAGTGAAACCA 60.024 41.667 0.00 0.00 37.80 3.67
1428 1970 0.957888 GAGACCTTTGAGCCACAGCC 60.958 60.000 0.00 0.00 41.25 4.85
1457 1999 3.698539 TCTTTTCAAGTTGTGACCATGCA 59.301 39.130 2.11 0.00 35.39 3.96
1462 2004 5.021033 TCAAGTTGTGACCATGCAAAATT 57.979 34.783 2.11 0.00 0.00 1.82
1563 2106 5.238583 CCTCCCATGTAGTAATTCGATTCC 58.761 45.833 0.00 0.00 0.00 3.01
1702 2344 1.477553 TGATGAGCATTTTCCAGGCC 58.522 50.000 0.00 0.00 0.00 5.19
1724 2366 8.145767 AGGCCATAAATTGAAATGTATCACATG 58.854 33.333 5.01 0.00 37.97 3.21
1784 2426 5.220796 CCAATTATGCCAGCAGATATCATCG 60.221 44.000 5.32 0.00 0.00 3.84
1798 2440 7.041508 GCAGATATCATCGAGACTTGGATTTTT 60.042 37.037 5.32 0.00 0.00 1.94
1945 2592 1.055849 TTGAGTAGCAACCTGCCAGA 58.944 50.000 0.00 0.00 46.52 3.86
1947 2594 1.270839 TGAGTAGCAACCTGCCAGAAC 60.271 52.381 0.00 0.00 46.52 3.01
1964 2611 8.060931 TGCCAGAACTATATCTAGCATCTAAG 57.939 38.462 0.00 0.00 38.79 2.18
1975 2622 9.717942 ATATCTAGCATCTAAGACAAAATGGAC 57.282 33.333 0.00 0.00 0.00 4.02
1976 2623 6.946340 TCTAGCATCTAAGACAAAATGGACA 58.054 36.000 0.00 0.00 0.00 4.02
1977 2624 7.568349 TCTAGCATCTAAGACAAAATGGACAT 58.432 34.615 0.00 0.00 0.00 3.06
1978 2625 6.446781 AGCATCTAAGACAAAATGGACATG 57.553 37.500 0.00 0.00 0.00 3.21
1980 2627 6.094603 AGCATCTAAGACAAAATGGACATGTC 59.905 38.462 17.91 17.91 42.91 3.06
1981 2628 6.481134 CATCTAAGACAAAATGGACATGTCG 58.519 40.000 19.33 7.16 46.19 4.35
1982 2629 4.935205 TCTAAGACAAAATGGACATGTCGG 59.065 41.667 19.33 7.14 46.19 4.79
1983 2630 3.140325 AGACAAAATGGACATGTCGGT 57.860 42.857 19.33 7.72 46.19 4.69
1984 2631 2.813754 AGACAAAATGGACATGTCGGTG 59.186 45.455 19.33 13.74 46.19 4.94
1985 2632 1.269448 ACAAAATGGACATGTCGGTGC 59.731 47.619 19.33 6.34 0.00 5.01
1986 2633 1.269174 CAAAATGGACATGTCGGTGCA 59.731 47.619 19.33 11.89 43.39 4.57
1987 2634 0.881118 AAATGGACATGTCGGTGCAC 59.119 50.000 19.33 8.80 42.02 4.57
1988 2635 0.960364 AATGGACATGTCGGTGCACC 60.960 55.000 26.78 26.78 42.02 5.01
1989 2636 2.031919 GGACATGTCGGTGCACCA 59.968 61.111 34.16 19.11 35.14 4.17
1990 2637 1.377202 GGACATGTCGGTGCACCAT 60.377 57.895 34.16 18.47 35.14 3.55
1991 2638 1.369091 GGACATGTCGGTGCACCATC 61.369 60.000 34.16 24.92 35.14 3.51
1992 2639 1.369091 GACATGTCGGTGCACCATCC 61.369 60.000 34.16 20.94 35.14 3.51
1993 2640 1.377072 CATGTCGGTGCACCATCCA 60.377 57.895 34.16 25.49 35.14 3.41
1994 2641 0.749091 CATGTCGGTGCACCATCCAT 60.749 55.000 34.16 26.43 35.14 3.41
1995 2642 0.034186 ATGTCGGTGCACCATCCATT 60.034 50.000 34.16 11.59 35.14 3.16
1996 2643 0.251121 TGTCGGTGCACCATCCATTT 60.251 50.000 34.16 0.00 35.14 2.32
1997 2644 0.451783 GTCGGTGCACCATCCATTTC 59.548 55.000 34.16 11.40 35.14 2.17
2002 2649 2.183409 GCACCATCCATTTCGTGCT 58.817 52.632 3.88 0.00 46.32 4.40
2048 2695 7.865706 TTGAGTTACTCAAAAAGCTTCTTCT 57.134 32.000 23.50 0.00 45.84 2.85
2063 2710 8.940768 AAGCTTCTTCTTTAGATATCTGTGTC 57.059 34.615 15.79 0.00 31.54 3.67
2069 2718 6.798427 TCTTTAGATATCTGTGTCTTGCCT 57.202 37.500 15.79 0.00 0.00 4.75
2077 2726 4.574674 TCTGTGTCTTGCCTGGATAAAT 57.425 40.909 0.00 0.00 0.00 1.40
2078 2727 5.692115 TCTGTGTCTTGCCTGGATAAATA 57.308 39.130 0.00 0.00 0.00 1.40
2089 2738 5.880332 TGCCTGGATAAATAGTGACTTGAAC 59.120 40.000 0.00 0.00 0.00 3.18
2090 2739 5.880332 GCCTGGATAAATAGTGACTTGAACA 59.120 40.000 0.00 0.00 0.00 3.18
2091 2740 6.543831 GCCTGGATAAATAGTGACTTGAACAT 59.456 38.462 0.00 0.00 0.00 2.71
2095 2744 7.888021 TGGATAAATAGTGACTTGAACATTGGT 59.112 33.333 0.00 0.00 0.00 3.67
2096 2745 8.184192 GGATAAATAGTGACTTGAACATTGGTG 58.816 37.037 0.00 0.00 0.00 4.17
2109 2758 4.778213 ACATTGGTGCCTGTAGTGATAT 57.222 40.909 0.00 0.00 0.00 1.63
2110 2759 4.708177 ACATTGGTGCCTGTAGTGATATC 58.292 43.478 0.00 0.00 0.00 1.63
2111 2760 3.838244 TTGGTGCCTGTAGTGATATCC 57.162 47.619 0.00 0.00 0.00 2.59
2112 2761 2.758130 TGGTGCCTGTAGTGATATCCA 58.242 47.619 0.00 0.00 0.00 3.41
2113 2762 3.317406 TGGTGCCTGTAGTGATATCCAT 58.683 45.455 0.00 0.00 0.00 3.41
2118 2767 6.350277 GGTGCCTGTAGTGATATCCATACTAC 60.350 46.154 18.39 18.39 44.29 2.73
2133 2782 4.949856 CCATACTACAGGCATTTGACCTTT 59.050 41.667 0.00 0.00 34.42 3.11
2139 2788 1.070601 AGGCATTTGACCTTTGGTTGC 59.929 47.619 3.34 3.34 35.25 4.17
2140 2789 1.070601 GGCATTTGACCTTTGGTTGCT 59.929 47.619 9.91 0.00 36.37 3.91
2141 2790 2.298729 GGCATTTGACCTTTGGTTGCTA 59.701 45.455 9.91 0.00 36.37 3.49
2142 2791 3.578688 GCATTTGACCTTTGGTTGCTAG 58.421 45.455 4.46 0.00 35.25 3.42
2143 2792 3.005791 GCATTTGACCTTTGGTTGCTAGT 59.994 43.478 4.46 0.00 35.25 2.57
2144 2793 4.217550 GCATTTGACCTTTGGTTGCTAGTA 59.782 41.667 4.46 0.00 35.25 1.82
2145 2794 5.619981 GCATTTGACCTTTGGTTGCTAGTAG 60.620 44.000 4.46 0.00 35.25 2.57
2146 2795 4.699925 TTGACCTTTGGTTGCTAGTAGT 57.300 40.909 0.00 0.00 35.25 2.73
2147 2796 4.699925 TGACCTTTGGTTGCTAGTAGTT 57.300 40.909 0.00 0.00 35.25 2.24
2148 2797 5.043737 TGACCTTTGGTTGCTAGTAGTTT 57.956 39.130 0.00 0.00 35.25 2.66
2149 2798 4.819630 TGACCTTTGGTTGCTAGTAGTTTG 59.180 41.667 0.00 0.00 35.25 2.93
2150 2799 4.788679 ACCTTTGGTTGCTAGTAGTTTGT 58.211 39.130 0.00 0.00 27.29 2.83
2151 2800 5.932455 ACCTTTGGTTGCTAGTAGTTTGTA 58.068 37.500 0.00 0.00 27.29 2.41
2152 2801 6.540083 ACCTTTGGTTGCTAGTAGTTTGTAT 58.460 36.000 0.00 0.00 27.29 2.29
2153 2802 6.430000 ACCTTTGGTTGCTAGTAGTTTGTATG 59.570 38.462 0.00 0.00 27.29 2.39
2154 2803 6.128007 CCTTTGGTTGCTAGTAGTTTGTATGG 60.128 42.308 0.00 0.00 0.00 2.74
2155 2804 4.839121 TGGTTGCTAGTAGTTTGTATGGG 58.161 43.478 0.00 0.00 0.00 4.00
2156 2805 4.287585 TGGTTGCTAGTAGTTTGTATGGGT 59.712 41.667 0.00 0.00 0.00 4.51
2157 2806 4.634443 GGTTGCTAGTAGTTTGTATGGGTG 59.366 45.833 0.00 0.00 0.00 4.61
2158 2807 5.484715 GTTGCTAGTAGTTTGTATGGGTGA 58.515 41.667 0.00 0.00 0.00 4.02
2159 2808 5.950544 TGCTAGTAGTTTGTATGGGTGAT 57.049 39.130 0.00 0.00 0.00 3.06
2160 2809 7.270047 GTTGCTAGTAGTTTGTATGGGTGATA 58.730 38.462 0.00 0.00 0.00 2.15
2161 2810 7.050970 TGCTAGTAGTTTGTATGGGTGATAG 57.949 40.000 0.00 0.00 0.00 2.08
2162 2811 6.610020 TGCTAGTAGTTTGTATGGGTGATAGT 59.390 38.462 0.00 0.00 0.00 2.12
2163 2812 7.125204 TGCTAGTAGTTTGTATGGGTGATAGTT 59.875 37.037 0.00 0.00 0.00 2.24
2164 2813 7.985752 GCTAGTAGTTTGTATGGGTGATAGTTT 59.014 37.037 0.00 0.00 0.00 2.66
2167 2816 9.043548 AGTAGTTTGTATGGGTGATAGTTTAGT 57.956 33.333 0.00 0.00 0.00 2.24
2168 2817 9.095065 GTAGTTTGTATGGGTGATAGTTTAGTG 57.905 37.037 0.00 0.00 0.00 2.74
2169 2818 7.913789 AGTTTGTATGGGTGATAGTTTAGTGA 58.086 34.615 0.00 0.00 0.00 3.41
2170 2819 8.548877 AGTTTGTATGGGTGATAGTTTAGTGAT 58.451 33.333 0.00 0.00 0.00 3.06
2171 2820 9.826574 GTTTGTATGGGTGATAGTTTAGTGATA 57.173 33.333 0.00 0.00 0.00 2.15
2177 2826 8.190326 TGGGTGATAGTTTAGTGATATAGTGG 57.810 38.462 0.00 0.00 0.00 4.00
2178 2827 7.234782 TGGGTGATAGTTTAGTGATATAGTGGG 59.765 40.741 0.00 0.00 0.00 4.61
2179 2828 7.453752 GGGTGATAGTTTAGTGATATAGTGGGA 59.546 40.741 0.00 0.00 0.00 4.37
2180 2829 9.036980 GGTGATAGTTTAGTGATATAGTGGGAT 57.963 37.037 0.00 0.00 0.00 3.85
2185 2834 7.897864 AGTTTAGTGATATAGTGGGATACTGC 58.102 38.462 0.00 0.00 40.65 4.40
2186 2835 7.509318 AGTTTAGTGATATAGTGGGATACTGCA 59.491 37.037 0.00 0.00 40.65 4.41
2187 2836 7.849322 TTAGTGATATAGTGGGATACTGCAA 57.151 36.000 0.00 0.00 40.65 4.08
2188 2837 6.942163 AGTGATATAGTGGGATACTGCAAT 57.058 37.500 0.00 0.00 40.65 3.56
2189 2838 9.541884 TTAGTGATATAGTGGGATACTGCAATA 57.458 33.333 0.00 0.00 40.65 1.90
2190 2839 8.435931 AGTGATATAGTGGGATACTGCAATAA 57.564 34.615 0.00 0.00 40.65 1.40
2191 2840 8.880244 AGTGATATAGTGGGATACTGCAATAAA 58.120 33.333 0.00 0.00 40.65 1.40
2192 2841 9.155975 GTGATATAGTGGGATACTGCAATAAAG 57.844 37.037 0.00 0.00 40.65 1.85
2193 2842 9.100197 TGATATAGTGGGATACTGCAATAAAGA 57.900 33.333 0.00 0.00 40.65 2.52
2194 2843 9.944376 GATATAGTGGGATACTGCAATAAAGAA 57.056 33.333 0.00 0.00 40.65 2.52
2196 2845 8.682936 ATAGTGGGATACTGCAATAAAGAAAG 57.317 34.615 0.00 0.00 40.65 2.62
2197 2846 5.888161 AGTGGGATACTGCAATAAAGAAAGG 59.112 40.000 0.00 0.00 38.49 3.11
2198 2847 5.652452 GTGGGATACTGCAATAAAGAAAGGT 59.348 40.000 0.00 0.00 0.00 3.50
2199 2848 6.152831 GTGGGATACTGCAATAAAGAAAGGTT 59.847 38.462 0.00 0.00 0.00 3.50
2200 2849 6.152661 TGGGATACTGCAATAAAGAAAGGTTG 59.847 38.462 0.00 0.00 0.00 3.77
2201 2850 6.152831 GGGATACTGCAATAAAGAAAGGTTGT 59.847 38.462 0.00 0.00 0.00 3.32
2202 2851 7.029563 GGATACTGCAATAAAGAAAGGTTGTG 58.970 38.462 0.00 0.00 0.00 3.33
2203 2852 5.200368 ACTGCAATAAAGAAAGGTTGTGG 57.800 39.130 0.00 0.00 0.00 4.17
2204 2853 3.988819 TGCAATAAAGAAAGGTTGTGGC 58.011 40.909 0.00 0.00 0.00 5.01
2205 2854 3.386078 TGCAATAAAGAAAGGTTGTGGCA 59.614 39.130 0.00 0.00 0.00 4.92
2206 2855 4.141846 TGCAATAAAGAAAGGTTGTGGCAA 60.142 37.500 0.00 0.00 0.00 4.52
2207 2856 4.996758 GCAATAAAGAAAGGTTGTGGCAAT 59.003 37.500 0.00 0.00 0.00 3.56
2208 2857 6.162777 GCAATAAAGAAAGGTTGTGGCAATA 58.837 36.000 0.00 0.00 0.00 1.90
2209 2858 6.818142 GCAATAAAGAAAGGTTGTGGCAATAT 59.182 34.615 0.00 0.00 0.00 1.28
2210 2859 7.334171 GCAATAAAGAAAGGTTGTGGCAATATT 59.666 33.333 0.00 0.00 0.00 1.28
2211 2860 8.872845 CAATAAAGAAAGGTTGTGGCAATATTC 58.127 33.333 0.00 0.00 0.00 1.75
2212 2861 6.670695 AAAGAAAGGTTGTGGCAATATTCT 57.329 33.333 0.00 0.00 0.00 2.40
2213 2862 6.670695 AAGAAAGGTTGTGGCAATATTCTT 57.329 33.333 0.00 0.00 32.64 2.52
2214 2863 7.775053 AAGAAAGGTTGTGGCAATATTCTTA 57.225 32.000 12.95 0.00 34.96 2.10
2215 2864 7.775053 AGAAAGGTTGTGGCAATATTCTTAA 57.225 32.000 0.00 0.00 0.00 1.85
2216 2865 7.602753 AGAAAGGTTGTGGCAATATTCTTAAC 58.397 34.615 0.00 0.00 0.00 2.01
2217 2866 6.909550 AAGGTTGTGGCAATATTCTTAACA 57.090 33.333 0.00 0.00 0.00 2.41
2218 2867 7.480760 AAGGTTGTGGCAATATTCTTAACAT 57.519 32.000 0.00 0.00 0.00 2.71
2219 2868 7.100458 AGGTTGTGGCAATATTCTTAACATC 57.900 36.000 0.00 0.00 0.00 3.06
2220 2869 6.891908 AGGTTGTGGCAATATTCTTAACATCT 59.108 34.615 0.00 0.00 0.00 2.90
2221 2870 6.974622 GGTTGTGGCAATATTCTTAACATCTG 59.025 38.462 0.00 0.00 0.00 2.90
2222 2871 7.148086 GGTTGTGGCAATATTCTTAACATCTGA 60.148 37.037 0.00 0.00 0.00 3.27
2223 2872 7.558161 TGTGGCAATATTCTTAACATCTGAG 57.442 36.000 0.00 0.00 0.00 3.35
2224 2873 7.337938 TGTGGCAATATTCTTAACATCTGAGA 58.662 34.615 0.00 0.00 0.00 3.27
2225 2874 7.828717 TGTGGCAATATTCTTAACATCTGAGAA 59.171 33.333 0.00 0.00 34.27 2.87
2226 2875 8.341173 GTGGCAATATTCTTAACATCTGAGAAG 58.659 37.037 0.00 0.00 33.37 2.85
2227 2876 8.049117 TGGCAATATTCTTAACATCTGAGAAGT 58.951 33.333 0.00 0.00 33.37 3.01
2228 2877 9.547753 GGCAATATTCTTAACATCTGAGAAGTA 57.452 33.333 0.00 0.00 33.37 2.24
2233 2882 8.885494 ATTCTTAACATCTGAGAAGTAGCATC 57.115 34.615 0.00 0.00 33.37 3.91
2234 2883 7.410120 TCTTAACATCTGAGAAGTAGCATCA 57.590 36.000 0.00 0.00 0.00 3.07
2235 2884 7.840931 TCTTAACATCTGAGAAGTAGCATCAA 58.159 34.615 0.00 0.00 0.00 2.57
2236 2885 8.481314 TCTTAACATCTGAGAAGTAGCATCAAT 58.519 33.333 0.00 0.00 0.00 2.57
2237 2886 8.654230 TTAACATCTGAGAAGTAGCATCAATC 57.346 34.615 0.00 0.00 0.00 2.67
2238 2887 6.231258 ACATCTGAGAAGTAGCATCAATCA 57.769 37.500 0.00 0.00 0.00 2.57
2239 2888 6.828788 ACATCTGAGAAGTAGCATCAATCAT 58.171 36.000 0.00 0.00 0.00 2.45
2240 2889 6.706716 ACATCTGAGAAGTAGCATCAATCATG 59.293 38.462 0.00 0.00 35.29 3.07
2241 2890 6.231258 TCTGAGAAGTAGCATCAATCATGT 57.769 37.500 0.00 0.00 34.56 3.21
2242 2891 6.279123 TCTGAGAAGTAGCATCAATCATGTC 58.721 40.000 0.00 0.00 34.56 3.06
2243 2892 5.981174 TGAGAAGTAGCATCAATCATGTCA 58.019 37.500 0.00 0.00 34.56 3.58
2244 2893 5.814188 TGAGAAGTAGCATCAATCATGTCAC 59.186 40.000 0.00 0.00 34.56 3.67
2245 2894 5.987098 AGAAGTAGCATCAATCATGTCACT 58.013 37.500 0.00 0.00 34.56 3.41
2246 2895 7.117285 AGAAGTAGCATCAATCATGTCACTA 57.883 36.000 0.00 0.00 34.56 2.74
2247 2896 7.208777 AGAAGTAGCATCAATCATGTCACTAG 58.791 38.462 0.00 0.00 34.56 2.57
2248 2897 6.477053 AGTAGCATCAATCATGTCACTAGT 57.523 37.500 0.00 0.00 34.56 2.57
2249 2898 6.882656 AGTAGCATCAATCATGTCACTAGTT 58.117 36.000 0.00 0.00 34.56 2.24
2250 2899 7.334090 AGTAGCATCAATCATGTCACTAGTTT 58.666 34.615 0.00 0.00 34.56 2.66
2251 2900 6.432607 AGCATCAATCATGTCACTAGTTTG 57.567 37.500 0.00 0.00 34.56 2.93
2252 2901 6.175471 AGCATCAATCATGTCACTAGTTTGA 58.825 36.000 6.41 6.41 34.56 2.69
2253 2902 6.827251 AGCATCAATCATGTCACTAGTTTGAT 59.173 34.615 9.79 9.79 34.02 2.57
2254 2903 7.012138 AGCATCAATCATGTCACTAGTTTGATC 59.988 37.037 11.86 8.53 32.38 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.049433 AGCGAGAACGAACGGGTG 60.049 61.111 0.00 0.00 42.66 4.61
123 124 2.045926 GGTGCTGCCGGTGAGAAT 60.046 61.111 1.90 0.00 0.00 2.40
145 155 2.121564 CTGGGCTGAAGTGTTGTGCG 62.122 60.000 0.00 0.00 0.00 5.34
146 164 1.656441 CTGGGCTGAAGTGTTGTGC 59.344 57.895 0.00 0.00 0.00 4.57
187 209 2.354805 GGGCCGAAACTCAAGTCTGTAT 60.355 50.000 0.00 0.00 0.00 2.29
203 225 2.900337 GGCGTAAAGGATGGGCCG 60.900 66.667 0.00 0.00 43.43 6.13
265 287 0.468226 TCCGGTCTGTCTGCTTGTTT 59.532 50.000 0.00 0.00 0.00 2.83
268 290 0.668706 CACTCCGGTCTGTCTGCTTG 60.669 60.000 0.00 0.00 0.00 4.01
271 293 1.214062 CTCACTCCGGTCTGTCTGC 59.786 63.158 0.00 0.00 0.00 4.26
272 294 0.523966 GACTCACTCCGGTCTGTCTG 59.476 60.000 0.00 0.00 0.00 3.51
275 297 0.956410 CTCGACTCACTCCGGTCTGT 60.956 60.000 0.00 0.00 0.00 3.41
276 298 0.956410 ACTCGACTCACTCCGGTCTG 60.956 60.000 0.00 0.00 0.00 3.51
277 299 0.956410 CACTCGACTCACTCCGGTCT 60.956 60.000 0.00 0.00 0.00 3.85
346 376 3.692406 GCCGTCGACCTCCCTTGT 61.692 66.667 10.58 0.00 0.00 3.16
469 499 0.108520 TACAATTGTCGAGGTCGCCC 60.109 55.000 15.85 0.00 39.60 6.13
482 512 6.108015 AGAATGCATTGGCGATTTTACAATT 58.892 32.000 18.59 0.00 45.35 2.32
483 513 5.663456 AGAATGCATTGGCGATTTTACAAT 58.337 33.333 18.59 0.00 45.35 2.71
518 654 0.036388 GCCAACCTCTTCGGATGTGA 60.036 55.000 0.00 0.00 33.93 3.58
529 668 0.676151 CCTGCAGAAGAGCCAACCTC 60.676 60.000 17.39 0.00 41.07 3.85
530 669 1.130054 TCCTGCAGAAGAGCCAACCT 61.130 55.000 17.39 0.00 0.00 3.50
531 670 0.034670 ATCCTGCAGAAGAGCCAACC 60.035 55.000 17.39 0.00 0.00 3.77
532 671 1.093159 CATCCTGCAGAAGAGCCAAC 58.907 55.000 17.39 0.00 0.00 3.77
533 672 0.694771 ACATCCTGCAGAAGAGCCAA 59.305 50.000 17.39 0.00 0.00 4.52
534 673 1.483827 CTACATCCTGCAGAAGAGCCA 59.516 52.381 17.39 0.00 0.00 4.75
536 675 1.138661 AGCTACATCCTGCAGAAGAGC 59.861 52.381 17.39 15.46 0.00 4.09
537 676 3.540314 AAGCTACATCCTGCAGAAGAG 57.460 47.619 17.39 6.02 0.00 2.85
539 678 4.764172 ACTAAAGCTACATCCTGCAGAAG 58.236 43.478 17.39 6.89 0.00 2.85
540 679 4.467795 AGACTAAAGCTACATCCTGCAGAA 59.532 41.667 17.39 0.00 0.00 3.02
541 680 4.026744 AGACTAAAGCTACATCCTGCAGA 58.973 43.478 17.39 1.21 0.00 4.26
542 681 4.118410 CAGACTAAAGCTACATCCTGCAG 58.882 47.826 6.78 6.78 0.00 4.41
545 684 4.128925 TGCAGACTAAAGCTACATCCTG 57.871 45.455 0.00 0.00 0.00 3.86
546 685 4.764172 CTTGCAGACTAAAGCTACATCCT 58.236 43.478 0.00 0.00 0.00 3.24
547 686 3.311048 GCTTGCAGACTAAAGCTACATCC 59.689 47.826 12.62 0.00 44.33 3.51
564 703 4.612536 ACGCAACGTGCTGCTTGC 62.613 61.111 13.27 13.27 42.25 4.01
565 704 2.425773 GACGCAACGTGCTGCTTG 60.426 61.111 10.30 0.00 42.25 4.01
568 707 0.934436 AAATTGACGCAACGTGCTGC 60.934 50.000 2.02 2.02 42.25 5.25
569 708 0.771756 CAAATTGACGCAACGTGCTG 59.228 50.000 0.00 0.00 42.25 4.41
570 709 0.317770 CCAAATTGACGCAACGTGCT 60.318 50.000 0.00 0.00 42.25 4.40
571 710 0.317436 TCCAAATTGACGCAACGTGC 60.317 50.000 0.00 0.00 41.37 5.34
572 711 1.778591 GTTCCAAATTGACGCAACGTG 59.221 47.619 0.00 0.00 41.37 4.49
574 713 1.268794 TGGTTCCAAATTGACGCAACG 60.269 47.619 0.00 0.00 0.00 4.10
575 714 2.500509 TGGTTCCAAATTGACGCAAC 57.499 45.000 0.00 0.00 0.00 4.17
576 715 2.029470 GGATGGTTCCAAATTGACGCAA 60.029 45.455 0.00 0.00 42.12 4.85
590 1063 1.272480 GCCACCTAGGTTTGGATGGTT 60.272 52.381 20.18 0.00 40.61 3.67
591 1064 0.331616 GCCACCTAGGTTTGGATGGT 59.668 55.000 20.18 0.00 40.61 3.55
593 1066 1.004745 ACTGCCACCTAGGTTTGGATG 59.995 52.381 20.18 13.64 40.61 3.51
594 1067 1.372501 ACTGCCACCTAGGTTTGGAT 58.627 50.000 20.18 4.03 40.61 3.41
595 1068 1.145571 AACTGCCACCTAGGTTTGGA 58.854 50.000 20.18 11.57 40.61 3.53
602 1075 0.674895 GTGCTCCAACTGCCACCTAG 60.675 60.000 0.00 0.00 0.00 3.02
604 1077 2.113986 GTGCTCCAACTGCCACCT 59.886 61.111 0.00 0.00 0.00 4.00
608 1081 4.643387 ACGGGTGCTCCAACTGCC 62.643 66.667 7.20 0.00 29.06 4.85
609 1082 3.050275 GACGGGTGCTCCAACTGC 61.050 66.667 7.20 0.00 29.06 4.40
610 1083 2.358737 GGACGGGTGCTCCAACTG 60.359 66.667 7.20 0.00 32.98 3.16
611 1084 2.847234 TGGACGGGTGCTCCAACT 60.847 61.111 7.20 0.00 34.70 3.16
612 1085 2.668550 GTGGACGGGTGCTCCAAC 60.669 66.667 7.20 0.00 39.60 3.77
613 1086 3.948719 GGTGGACGGGTGCTCCAA 61.949 66.667 7.20 0.00 39.60 3.53
631 1104 0.794473 GGGCTTGTACAACGCTACAC 59.206 55.000 21.39 10.52 0.00 2.90
632 1105 0.682852 AGGGCTTGTACAACGCTACA 59.317 50.000 21.39 0.00 0.00 2.74
633 1106 1.337447 TGAGGGCTTGTACAACGCTAC 60.337 52.381 21.39 16.63 0.00 3.58
634 1107 0.970640 TGAGGGCTTGTACAACGCTA 59.029 50.000 21.39 11.59 0.00 4.26
637 1110 1.808411 ACATGAGGGCTTGTACAACG 58.192 50.000 3.59 2.58 31.37 4.10
638 1111 4.379499 GCTTAACATGAGGGCTTGTACAAC 60.379 45.833 3.59 2.04 32.68 3.32
639 1112 3.756434 GCTTAACATGAGGGCTTGTACAA 59.244 43.478 8.28 8.28 32.68 2.41
640 1113 3.343617 GCTTAACATGAGGGCTTGTACA 58.656 45.455 0.00 0.00 32.68 2.90
642 1115 2.356741 GGGCTTAACATGAGGGCTTGTA 60.357 50.000 0.00 0.00 32.68 2.41
643 1116 1.616994 GGGCTTAACATGAGGGCTTGT 60.617 52.381 0.00 0.00 34.23 3.16
644 1117 1.106285 GGGCTTAACATGAGGGCTTG 58.894 55.000 0.00 0.00 0.00 4.01
645 1118 0.394352 CGGGCTTAACATGAGGGCTT 60.394 55.000 0.00 0.00 0.00 4.35
647 1120 2.481471 GCGGGCTTAACATGAGGGC 61.481 63.158 0.00 0.00 0.00 5.19
648 1121 1.823899 GGCGGGCTTAACATGAGGG 60.824 63.158 0.00 0.00 0.00 4.30
649 1122 1.823899 GGGCGGGCTTAACATGAGG 60.824 63.158 0.00 0.00 0.00 3.86
678 1217 2.813754 ACATGGTCAACACATTTCCTCG 59.186 45.455 0.00 0.00 0.00 4.63
806 1346 5.851720 TCAATTTTATGGCTGAAGTTGCAA 58.148 33.333 0.00 0.00 0.00 4.08
835 1375 6.176183 AGAACACATGCAGTATTAGCTTTCT 58.824 36.000 0.00 0.00 0.00 2.52
849 1389 8.986477 ATTAAATGGTCTAAAAGAACACATGC 57.014 30.769 0.00 0.00 45.96 4.06
877 1417 5.129485 AGACAGGAGAAGAGAAGTTTCACAA 59.871 40.000 0.00 0.00 0.00 3.33
878 1418 4.651503 AGACAGGAGAAGAGAAGTTTCACA 59.348 41.667 0.00 0.00 0.00 3.58
879 1419 4.987912 CAGACAGGAGAAGAGAAGTTTCAC 59.012 45.833 0.00 0.00 0.00 3.18
880 1420 4.502259 GCAGACAGGAGAAGAGAAGTTTCA 60.502 45.833 0.00 0.00 0.00 2.69
881 1421 3.993736 GCAGACAGGAGAAGAGAAGTTTC 59.006 47.826 0.00 0.00 0.00 2.78
882 1422 3.244387 GGCAGACAGGAGAAGAGAAGTTT 60.244 47.826 0.00 0.00 0.00 2.66
933 1473 6.182039 TGAGAACATTGTACTAATTGCAGC 57.818 37.500 0.00 0.00 0.00 5.25
1056 1598 3.181448 TGCATATGCCACATGTCTCATCT 60.181 43.478 24.54 1.96 41.18 2.90
1258 1800 6.266786 TCTTGGTACTGACATAGTTTGAGACA 59.733 38.462 0.00 0.00 40.89 3.41
1259 1801 6.688578 TCTTGGTACTGACATAGTTTGAGAC 58.311 40.000 0.00 0.00 40.89 3.36
1375 1917 2.029838 AAGATGCCGACATTCCTGAC 57.970 50.000 0.00 0.00 36.35 3.51
1382 1924 5.335661 GGTTTCACTTAAAAGATGCCGACAT 60.336 40.000 0.00 0.00 39.98 3.06
1383 1925 4.023536 GGTTTCACTTAAAAGATGCCGACA 60.024 41.667 0.00 0.00 0.00 4.35
1406 1948 2.082231 CTGTGGCTCAAAGGTCTCATG 58.918 52.381 0.00 0.00 0.00 3.07
1407 1949 1.612726 GCTGTGGCTCAAAGGTCTCAT 60.613 52.381 0.00 0.00 35.22 2.90
1485 2027 1.467734 GTCACAATCTCAGGCTGCTTG 59.532 52.381 10.34 14.83 0.00 4.01
1531 2074 2.043604 TACATGGGAGGCCATCTGCG 62.044 60.000 5.01 0.00 42.61 5.18
1676 2318 6.461927 GCCTGGAAAATGCTCATCAAATCATA 60.462 38.462 0.00 0.00 0.00 2.15
1695 2337 6.838090 TGATACATTTCAATTTATGGCCTGGA 59.162 34.615 3.32 0.00 0.00 3.86
1697 2339 7.490840 TGTGATACATTTCAATTTATGGCCTG 58.509 34.615 3.32 0.00 0.00 4.85
1811 2453 4.517453 ACTTGTTCGCCTAAAACATGCTTA 59.483 37.500 0.00 0.00 36.57 3.09
1964 2611 2.668279 GCACCGACATGTCCATTTTGTC 60.668 50.000 20.03 0.00 37.10 3.18
1968 2615 0.881118 GTGCACCGACATGTCCATTT 59.119 50.000 20.03 0.00 0.00 2.32
1969 2616 0.960364 GGTGCACCGACATGTCCATT 60.960 55.000 22.49 1.46 0.00 3.16
1971 2618 2.031919 GGTGCACCGACATGTCCA 59.968 61.111 22.49 9.21 0.00 4.02
1972 2619 1.369091 GATGGTGCACCGACATGTCC 61.369 60.000 30.07 6.58 39.43 4.02
1973 2620 1.369091 GGATGGTGCACCGACATGTC 61.369 60.000 30.07 16.21 39.43 3.06
1974 2621 1.377202 GGATGGTGCACCGACATGT 60.377 57.895 30.07 11.90 39.43 3.21
1975 2622 0.749091 ATGGATGGTGCACCGACATG 60.749 55.000 30.07 0.00 39.43 3.21
1976 2623 0.034186 AATGGATGGTGCACCGACAT 60.034 50.000 30.07 27.28 39.43 3.06
1977 2624 0.251121 AAATGGATGGTGCACCGACA 60.251 50.000 30.07 26.38 39.43 4.35
1978 2625 0.451783 GAAATGGATGGTGCACCGAC 59.548 55.000 30.07 24.22 39.43 4.79
1980 2627 1.305219 ACGAAATGGATGGTGCACCG 61.305 55.000 30.07 16.91 39.43 4.94
1981 2628 0.171007 CACGAAATGGATGGTGCACC 59.829 55.000 29.67 29.67 0.00 5.01
1982 2629 3.700577 CACGAAATGGATGGTGCAC 57.299 52.632 8.80 8.80 0.00 4.57
1985 2632 3.627123 TCATAAGCACGAAATGGATGGTG 59.373 43.478 0.00 0.00 0.00 4.17
1986 2633 3.884895 TCATAAGCACGAAATGGATGGT 58.115 40.909 0.00 0.00 0.00 3.55
1987 2634 5.240183 AGAATCATAAGCACGAAATGGATGG 59.760 40.000 0.00 0.00 0.00 3.51
1988 2635 6.309712 AGAATCATAAGCACGAAATGGATG 57.690 37.500 0.00 0.00 0.00 3.51
1989 2636 7.220030 ACTAGAATCATAAGCACGAAATGGAT 58.780 34.615 0.00 0.00 0.00 3.41
1990 2637 6.582636 ACTAGAATCATAAGCACGAAATGGA 58.417 36.000 0.00 0.00 0.00 3.41
1991 2638 6.851222 ACTAGAATCATAAGCACGAAATGG 57.149 37.500 0.00 0.00 0.00 3.16
1992 2639 8.390354 TGAAACTAGAATCATAAGCACGAAATG 58.610 33.333 0.00 0.00 0.00 2.32
1993 2640 8.492673 TGAAACTAGAATCATAAGCACGAAAT 57.507 30.769 0.00 0.00 0.00 2.17
1994 2641 7.817478 TCTGAAACTAGAATCATAAGCACGAAA 59.183 33.333 0.00 0.00 0.00 3.46
1995 2642 7.320399 TCTGAAACTAGAATCATAAGCACGAA 58.680 34.615 0.00 0.00 0.00 3.85
1996 2643 6.863275 TCTGAAACTAGAATCATAAGCACGA 58.137 36.000 0.00 0.00 0.00 4.35
1997 2644 7.276658 AGTTCTGAAACTAGAATCATAAGCACG 59.723 37.037 0.00 0.00 43.98 5.34
2047 2694 5.757320 CCAGGCAAGACACAGATATCTAAAG 59.243 44.000 4.54 0.95 0.00 1.85
2048 2695 5.425217 TCCAGGCAAGACACAGATATCTAAA 59.575 40.000 4.54 0.00 0.00 1.85
2057 2704 5.295292 CACTATTTATCCAGGCAAGACACAG 59.705 44.000 0.00 0.00 0.00 3.66
2061 2708 5.675538 AGTCACTATTTATCCAGGCAAGAC 58.324 41.667 0.00 0.00 0.00 3.01
2063 2710 6.115446 TCAAGTCACTATTTATCCAGGCAAG 58.885 40.000 0.00 0.00 0.00 4.01
2069 2718 7.888021 ACCAATGTTCAAGTCACTATTTATCCA 59.112 33.333 0.00 0.00 0.00 3.41
2077 2726 3.146066 GGCACCAATGTTCAAGTCACTA 58.854 45.455 0.00 0.00 0.00 2.74
2078 2727 1.956477 GGCACCAATGTTCAAGTCACT 59.044 47.619 0.00 0.00 0.00 3.41
2089 2738 4.067896 GGATATCACTACAGGCACCAATG 58.932 47.826 4.83 0.00 0.00 2.82
2090 2739 3.716353 TGGATATCACTACAGGCACCAAT 59.284 43.478 4.83 0.00 0.00 3.16
2091 2740 3.111484 TGGATATCACTACAGGCACCAA 58.889 45.455 4.83 0.00 0.00 3.67
2095 2744 6.311735 TGTAGTATGGATATCACTACAGGCA 58.688 40.000 21.74 12.08 45.89 4.75
2096 2745 6.835819 TGTAGTATGGATATCACTACAGGC 57.164 41.667 21.74 10.44 45.89 4.85
2109 2758 3.780294 AGGTCAAATGCCTGTAGTATGGA 59.220 43.478 0.00 0.00 34.56 3.41
2110 2759 4.156455 AGGTCAAATGCCTGTAGTATGG 57.844 45.455 0.00 0.00 34.56 2.74
2111 2760 5.163622 CCAAAGGTCAAATGCCTGTAGTATG 60.164 44.000 0.00 0.00 36.30 2.39
2112 2761 4.949856 CCAAAGGTCAAATGCCTGTAGTAT 59.050 41.667 0.00 0.00 36.30 2.12
2113 2762 4.202524 ACCAAAGGTCAAATGCCTGTAGTA 60.203 41.667 0.00 0.00 36.30 1.82
2118 2767 2.758009 CAACCAAAGGTCAAATGCCTG 58.242 47.619 0.00 0.00 33.12 4.85
2133 2782 4.287585 ACCCATACAAACTACTAGCAACCA 59.712 41.667 0.00 0.00 0.00 3.67
2141 2790 9.043548 ACTAAACTATCACCCATACAAACTACT 57.956 33.333 0.00 0.00 0.00 2.57
2142 2791 9.095065 CACTAAACTATCACCCATACAAACTAC 57.905 37.037 0.00 0.00 0.00 2.73
2143 2792 9.038072 TCACTAAACTATCACCCATACAAACTA 57.962 33.333 0.00 0.00 0.00 2.24
2144 2793 7.913789 TCACTAAACTATCACCCATACAAACT 58.086 34.615 0.00 0.00 0.00 2.66
2145 2794 8.732746 ATCACTAAACTATCACCCATACAAAC 57.267 34.615 0.00 0.00 0.00 2.93
2151 2800 8.816894 CCACTATATCACTAAACTATCACCCAT 58.183 37.037 0.00 0.00 0.00 4.00
2152 2801 7.234782 CCCACTATATCACTAAACTATCACCCA 59.765 40.741 0.00 0.00 0.00 4.51
2153 2802 7.453752 TCCCACTATATCACTAAACTATCACCC 59.546 40.741 0.00 0.00 0.00 4.61
2154 2803 8.418597 TCCCACTATATCACTAAACTATCACC 57.581 38.462 0.00 0.00 0.00 4.02
2159 2808 9.021807 GCAGTATCCCACTATATCACTAAACTA 57.978 37.037 0.00 0.00 34.98 2.24
2160 2809 7.509318 TGCAGTATCCCACTATATCACTAAACT 59.491 37.037 0.00 0.00 34.98 2.66
2161 2810 7.667557 TGCAGTATCCCACTATATCACTAAAC 58.332 38.462 0.00 0.00 34.98 2.01
2162 2811 7.849322 TGCAGTATCCCACTATATCACTAAA 57.151 36.000 0.00 0.00 34.98 1.85
2163 2812 7.849322 TTGCAGTATCCCACTATATCACTAA 57.151 36.000 0.00 0.00 34.98 2.24
2164 2813 9.541884 TTATTGCAGTATCCCACTATATCACTA 57.458 33.333 0.00 0.00 34.98 2.74
2165 2814 6.942163 ATTGCAGTATCCCACTATATCACT 57.058 37.500 0.00 0.00 34.98 3.41
2166 2815 9.155975 CTTTATTGCAGTATCCCACTATATCAC 57.844 37.037 0.00 0.00 34.98 3.06
2167 2816 9.100197 TCTTTATTGCAGTATCCCACTATATCA 57.900 33.333 0.00 0.00 34.98 2.15
2168 2817 9.944376 TTCTTTATTGCAGTATCCCACTATATC 57.056 33.333 0.00 0.00 34.98 1.63
2170 2819 9.778741 CTTTCTTTATTGCAGTATCCCACTATA 57.221 33.333 0.00 0.00 34.98 1.31
2171 2820 7.721399 CCTTTCTTTATTGCAGTATCCCACTAT 59.279 37.037 0.00 0.00 34.98 2.12
2172 2821 7.054124 CCTTTCTTTATTGCAGTATCCCACTA 58.946 38.462 0.00 0.00 34.98 2.74
2173 2822 5.888161 CCTTTCTTTATTGCAGTATCCCACT 59.112 40.000 0.00 0.00 38.32 4.00
2174 2823 5.652452 ACCTTTCTTTATTGCAGTATCCCAC 59.348 40.000 0.00 0.00 0.00 4.61
2175 2824 5.826643 ACCTTTCTTTATTGCAGTATCCCA 58.173 37.500 0.00 0.00 0.00 4.37
2176 2825 6.152831 ACAACCTTTCTTTATTGCAGTATCCC 59.847 38.462 0.00 0.00 0.00 3.85
2177 2826 7.029563 CACAACCTTTCTTTATTGCAGTATCC 58.970 38.462 0.00 0.00 0.00 2.59
2178 2827 7.029563 CCACAACCTTTCTTTATTGCAGTATC 58.970 38.462 0.00 0.00 0.00 2.24
2179 2828 6.572314 GCCACAACCTTTCTTTATTGCAGTAT 60.572 38.462 0.00 0.00 0.00 2.12
2180 2829 5.278758 GCCACAACCTTTCTTTATTGCAGTA 60.279 40.000 0.00 0.00 0.00 2.74
2181 2830 4.501400 GCCACAACCTTTCTTTATTGCAGT 60.501 41.667 0.00 0.00 0.00 4.40
2182 2831 3.989817 GCCACAACCTTTCTTTATTGCAG 59.010 43.478 0.00 0.00 0.00 4.41
2183 2832 3.386078 TGCCACAACCTTTCTTTATTGCA 59.614 39.130 0.00 0.00 0.00 4.08
2184 2833 3.988819 TGCCACAACCTTTCTTTATTGC 58.011 40.909 0.00 0.00 0.00 3.56
2185 2834 8.776376 AATATTGCCACAACCTTTCTTTATTG 57.224 30.769 0.00 0.00 0.00 1.90
2186 2835 8.815912 AGAATATTGCCACAACCTTTCTTTATT 58.184 29.630 0.00 0.00 0.00 1.40
2187 2836 8.366359 AGAATATTGCCACAACCTTTCTTTAT 57.634 30.769 0.00 0.00 0.00 1.40
2188 2837 7.775053 AGAATATTGCCACAACCTTTCTTTA 57.225 32.000 0.00 0.00 0.00 1.85
2189 2838 6.670695 AGAATATTGCCACAACCTTTCTTT 57.329 33.333 0.00 0.00 0.00 2.52
2190 2839 6.670695 AAGAATATTGCCACAACCTTTCTT 57.329 33.333 0.00 7.57 0.00 2.52
2191 2840 7.232534 TGTTAAGAATATTGCCACAACCTTTCT 59.767 33.333 0.00 0.00 0.00 2.52
2192 2841 7.375053 TGTTAAGAATATTGCCACAACCTTTC 58.625 34.615 0.00 0.00 0.00 2.62
2193 2842 7.296628 TGTTAAGAATATTGCCACAACCTTT 57.703 32.000 0.00 0.00 0.00 3.11
2194 2843 6.909550 TGTTAAGAATATTGCCACAACCTT 57.090 33.333 0.00 0.00 0.00 3.50
2195 2844 6.891908 AGATGTTAAGAATATTGCCACAACCT 59.108 34.615 0.00 0.00 0.00 3.50
2196 2845 6.974622 CAGATGTTAAGAATATTGCCACAACC 59.025 38.462 0.00 0.00 0.00 3.77
2197 2846 7.761409 TCAGATGTTAAGAATATTGCCACAAC 58.239 34.615 0.00 0.00 0.00 3.32
2198 2847 7.828717 TCTCAGATGTTAAGAATATTGCCACAA 59.171 33.333 0.00 0.00 0.00 3.33
2199 2848 7.337938 TCTCAGATGTTAAGAATATTGCCACA 58.662 34.615 0.00 0.00 0.00 4.17
2200 2849 7.792374 TCTCAGATGTTAAGAATATTGCCAC 57.208 36.000 0.00 0.00 0.00 5.01
2201 2850 8.049117 ACTTCTCAGATGTTAAGAATATTGCCA 58.951 33.333 0.00 0.00 0.00 4.92
2202 2851 8.443953 ACTTCTCAGATGTTAAGAATATTGCC 57.556 34.615 0.00 0.00 0.00 4.52
2207 2856 9.973450 GATGCTACTTCTCAGATGTTAAGAATA 57.027 33.333 0.00 0.00 0.00 1.75
2208 2857 8.481314 TGATGCTACTTCTCAGATGTTAAGAAT 58.519 33.333 0.00 0.00 0.00 2.40
2209 2858 7.840931 TGATGCTACTTCTCAGATGTTAAGAA 58.159 34.615 0.00 0.00 0.00 2.52
2210 2859 7.410120 TGATGCTACTTCTCAGATGTTAAGA 57.590 36.000 0.00 0.00 0.00 2.10
2211 2860 8.659925 ATTGATGCTACTTCTCAGATGTTAAG 57.340 34.615 0.00 0.00 0.00 1.85
2212 2861 8.260114 TGATTGATGCTACTTCTCAGATGTTAA 58.740 33.333 0.00 0.00 0.00 2.01
2213 2862 7.785033 TGATTGATGCTACTTCTCAGATGTTA 58.215 34.615 0.00 0.00 0.00 2.41
2214 2863 6.647229 TGATTGATGCTACTTCTCAGATGTT 58.353 36.000 0.00 0.00 0.00 2.71
2215 2864 6.231258 TGATTGATGCTACTTCTCAGATGT 57.769 37.500 0.00 0.00 0.00 3.06
2216 2865 6.706716 ACATGATTGATGCTACTTCTCAGATG 59.293 38.462 0.00 0.00 35.15 2.90
2217 2866 6.828788 ACATGATTGATGCTACTTCTCAGAT 58.171 36.000 0.00 0.00 35.15 2.90
2218 2867 6.127253 TGACATGATTGATGCTACTTCTCAGA 60.127 38.462 0.00 0.00 35.15 3.27
2219 2868 6.018913 GTGACATGATTGATGCTACTTCTCAG 60.019 42.308 0.00 0.00 35.15 3.35
2220 2869 5.814188 GTGACATGATTGATGCTACTTCTCA 59.186 40.000 0.00 0.00 35.15 3.27
2221 2870 6.047870 AGTGACATGATTGATGCTACTTCTC 58.952 40.000 0.00 0.00 35.15 2.87
2222 2871 5.987098 AGTGACATGATTGATGCTACTTCT 58.013 37.500 0.00 0.00 35.15 2.85
2223 2872 6.983307 ACTAGTGACATGATTGATGCTACTTC 59.017 38.462 0.00 0.00 34.82 3.01
2224 2873 6.882656 ACTAGTGACATGATTGATGCTACTT 58.117 36.000 0.00 0.00 34.82 2.24
2225 2874 6.477053 ACTAGTGACATGATTGATGCTACT 57.523 37.500 0.00 0.00 36.24 2.57
2226 2875 7.278646 TCAAACTAGTGACATGATTGATGCTAC 59.721 37.037 0.00 0.00 35.15 3.58
2227 2876 7.330262 TCAAACTAGTGACATGATTGATGCTA 58.670 34.615 0.00 0.00 35.15 3.49
2228 2877 6.175471 TCAAACTAGTGACATGATTGATGCT 58.825 36.000 0.00 0.00 35.15 3.79
2229 2878 6.426980 TCAAACTAGTGACATGATTGATGC 57.573 37.500 0.00 0.00 35.15 3.91


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

AutoCloner maintained by Alex Coulton.