Multiple sequence alignment - TraesCS2B01G466100

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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 TraesCS2B01G466100 chr2B 100.000 5424 0 0 1 5424 661772982 661778405 0.000000e+00 10017.0
1 TraesCS2B01G466100 chr2B 87.619 210 18 5 5220 5424 661832940 661833146 2.530000e-58 237.0
2 TraesCS2B01G466100 chr2A 90.975 4000 227 64 1474 5408 694951431 694955361 0.000000e+00 5264.0
3 TraesCS2B01G466100 chr2A 86.648 719 49 22 718 1405 694950716 694951418 0.000000e+00 752.0
4 TraesCS2B01G466100 chr2A 86.469 303 20 9 5119 5408 694976082 694976376 4.080000e-81 313.0
5 TraesCS2B01G466100 chr2A 93.023 129 4 4 575 700 694950519 694950645 3.340000e-42 183.0
6 TraesCS2B01G466100 chr2D 95.750 1506 48 11 3099 4604 555221183 555222672 0.000000e+00 2412.0
7 TraesCS2B01G466100 chr2D 91.592 1558 91 15 1459 2995 555219304 555220842 0.000000e+00 2115.0
8 TraesCS2B01G466100 chr2D 90.334 1407 86 24 87 1466 555217965 555219348 0.000000e+00 1799.0
9 TraesCS2B01G466100 chr2D 85.007 767 51 22 4671 5408 555222770 555223501 0.000000e+00 721.0
10 TraesCS2B01G466100 chr2D 94.595 111 5 1 2992 3102 555220867 555220976 2.600000e-38 171.0
11 TraesCS2B01G466100 chr2D 90.566 106 7 3 5165 5268 555234707 555234811 2.630000e-28 137.0
12 TraesCS2B01G466100 chr2D 92.105 38 3 0 3182 3219 555230216 555230253 3.000000e-03 54.7
13 TraesCS2B01G466100 chr4A 89.530 468 41 8 87 550 48509755 48509292 2.180000e-163 586.0
14 TraesCS2B01G466100 chr4A 82.917 480 62 18 82 550 255052145 255052615 1.090000e-111 414.0
15 TraesCS2B01G466100 chr4A 94.737 38 1 1 3178 3214 501266141 501266104 2.110000e-04 58.4
16 TraesCS2B01G466100 chr4D 87.905 463 49 7 93 550 249205583 249206043 6.180000e-149 538.0
17 TraesCS2B01G466100 chr4B 86.207 435 52 6 95 524 263590058 263590489 1.060000e-126 464.0
18 TraesCS2B01G466100 chr7D 85.153 458 56 12 98 549 548615474 548615925 4.950000e-125 459.0
19 TraesCS2B01G466100 chr5D 83.542 480 59 17 87 553 326240061 326239589 1.080000e-116 431.0
20 TraesCS2B01G466100 chr5D 93.182 44 3 0 3181 3224 441906574 441906531 1.260000e-06 65.8
21 TraesCS2B01G466100 chr5D 100.000 33 0 0 3181 3213 291923168 291923136 1.630000e-05 62.1
22 TraesCS2B01G466100 chr1B 84.633 436 62 5 118 549 250870404 250869970 3.880000e-116 429.0
23 TraesCS2B01G466100 chr6D 83.023 483 65 16 78 552 62149088 62148615 6.500000e-114 422.0
24 TraesCS2B01G466100 chr3B 81.468 545 61 19 1611 2148 731481382 731480871 1.410000e-110 411.0
25 TraesCS2B01G466100 chr5B 77.600 375 49 15 1776 2148 509461142 509460801 1.540000e-45 195.0
26 TraesCS2B01G466100 chr5B 87.647 170 14 6 1611 1774 509462372 509462204 1.990000e-44 191.0
27 TraesCS2B01G466100 chr1D 95.349 43 2 0 3181 3223 53260617 53260575 9.750000e-08 69.4
28 TraesCS2B01G466100 chr5A 93.182 44 3 0 3181 3224 558300452 558300409 1.260000e-06 65.8
29 TraesCS2B01G466100 chr7B 95.000 40 1 1 3181 3219 11852655 11852616 1.630000e-05 62.1


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 TraesCS2B01G466100 chr2B 661772982 661778405 5423 False 10017.000000 10017 100.000000 1 5424 1 chr2B.!!$F1 5423
1 TraesCS2B01G466100 chr2A 694950519 694955361 4842 False 2066.333333 5264 90.215333 575 5408 3 chr2A.!!$F2 4833
2 TraesCS2B01G466100 chr2D 555217965 555223501 5536 False 1443.600000 2412 91.455600 87 5408 5 chr2D.!!$F3 5321
3 TraesCS2B01G466100 chr3B 731480871 731481382 511 True 411.000000 411 81.468000 1611 2148 1 chr3B.!!$R1 537

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
27 28 0.035439 TGGAAGAAGACCCATTCGCC 60.035 55.000 0.00 0.0 34.27 5.54 F
81 82 0.370273 GACGCACGATAAGTTGCCAG 59.630 55.000 0.00 0.0 0.00 4.85 F
928 989 0.886490 GGCGGATCCATTTCTCGCAT 60.886 55.000 13.41 0.0 46.95 4.73 F
1599 1695 0.320771 ATGTCGGCAGTGACTGGTTC 60.321 55.000 15.24 0.0 39.64 3.62 F
1952 2058 1.135460 GGCGGTGACTGTGAGTACTAC 60.135 57.143 0.00 0.0 0.00 2.73 F
2480 2589 1.755179 AGTGTGTGTTGCAGAGCTTT 58.245 45.000 0.00 0.0 0.00 3.51 F
4144 4513 1.080298 TTGCAAATACCGCGAACGAT 58.920 45.000 8.23 0.0 43.93 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1583 0.036732 CCTAGCCACAGGAGCAAACA 59.963 55.000 0.00 0.0 38.00 2.83 R
1492 1584 0.036875 ACCTAGCCACAGGAGCAAAC 59.963 55.000 3.73 0.0 39.18 2.93 R
2734 2858 0.463654 AGCTCGTCACCACTGCAAAA 60.464 50.000 0.00 0.0 0.00 2.44 R
3017 3170 2.050168 CAACACATGCACACGGGC 60.050 61.111 0.00 0.0 0.00 6.13 R
3556 3920 2.483363 CCTGCAACAGCAATCAAACCAA 60.483 45.455 0.00 0.0 37.91 3.67 R
4342 4711 0.528466 GAGACGCATCGCTGGAATCA 60.528 55.000 0.00 0.0 0.00 2.57 R
5323 5784 1.309950 TATGTCGAGCTTCGGAGGAG 58.690 55.000 0.00 0.0 40.88 3.69 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
18 19 3.542046 GGCAGAGGTGGAAGAAGAC 57.458 57.895 0.00 0.00 0.00 3.01
19 20 0.035915 GGCAGAGGTGGAAGAAGACC 60.036 60.000 0.00 0.00 0.00 3.85
20 21 0.035915 GCAGAGGTGGAAGAAGACCC 60.036 60.000 0.00 0.00 32.03 4.46
21 22 1.352083 CAGAGGTGGAAGAAGACCCA 58.648 55.000 0.00 0.00 32.03 4.51
22 23 1.912043 CAGAGGTGGAAGAAGACCCAT 59.088 52.381 0.00 0.00 34.58 4.00
23 24 2.307098 CAGAGGTGGAAGAAGACCCATT 59.693 50.000 0.00 0.00 34.58 3.16
24 25 2.573915 AGAGGTGGAAGAAGACCCATTC 59.426 50.000 0.00 0.00 34.58 2.67
25 26 1.279271 AGGTGGAAGAAGACCCATTCG 59.721 52.381 0.00 0.00 34.58 3.34
26 27 1.087501 GTGGAAGAAGACCCATTCGC 58.912 55.000 0.00 0.00 34.58 4.70
27 28 0.035439 TGGAAGAAGACCCATTCGCC 60.035 55.000 0.00 0.00 34.27 5.54
28 29 0.748367 GGAAGAAGACCCATTCGCCC 60.748 60.000 0.00 0.00 34.27 6.13
29 30 0.748367 GAAGAAGACCCATTCGCCCC 60.748 60.000 0.00 0.00 34.27 5.80
30 31 1.208165 AAGAAGACCCATTCGCCCCT 61.208 55.000 0.00 0.00 34.27 4.79
31 32 1.452108 GAAGACCCATTCGCCCCTG 60.452 63.158 0.00 0.00 0.00 4.45
32 33 2.893682 GAAGACCCATTCGCCCCTGG 62.894 65.000 0.00 0.00 0.00 4.45
33 34 3.728373 GACCCATTCGCCCCTGGT 61.728 66.667 0.00 0.00 0.00 4.00
34 35 3.995506 GACCCATTCGCCCCTGGTG 62.996 68.421 0.00 0.00 33.99 4.17
35 36 4.820744 CCCATTCGCCCCTGGTGG 62.821 72.222 0.00 0.00 33.43 4.61
45 46 3.801997 CCTGGTGGGCTGGGCTAG 61.802 72.222 0.00 0.00 0.00 3.42
56 57 2.074729 CTGGGCTAGCTACCTACAGT 57.925 55.000 15.72 0.00 0.00 3.55
57 58 1.683917 CTGGGCTAGCTACCTACAGTG 59.316 57.143 15.72 0.00 0.00 3.66
58 59 0.389757 GGGCTAGCTACCTACAGTGC 59.610 60.000 15.72 1.49 0.00 4.40
59 60 1.404843 GGCTAGCTACCTACAGTGCT 58.595 55.000 15.72 0.00 36.93 4.40
60 61 2.584236 GGCTAGCTACCTACAGTGCTA 58.416 52.381 15.72 0.00 35.41 3.49
61 62 2.554893 GGCTAGCTACCTACAGTGCTAG 59.445 54.545 15.72 14.28 45.79 3.42
62 63 2.554893 GCTAGCTACCTACAGTGCTAGG 59.445 54.545 18.45 13.93 44.61 3.02
63 64 3.748027 GCTAGCTACCTACAGTGCTAGGA 60.748 52.174 19.52 0.00 44.61 2.94
64 65 2.657143 AGCTACCTACAGTGCTAGGAC 58.343 52.381 19.52 6.22 37.35 3.85
65 66 1.334243 GCTACCTACAGTGCTAGGACG 59.666 57.143 19.52 6.70 37.35 4.79
66 67 1.334243 CTACCTACAGTGCTAGGACGC 59.666 57.143 19.52 0.00 37.35 5.19
67 68 0.611062 ACCTACAGTGCTAGGACGCA 60.611 55.000 19.52 0.00 37.35 5.24
74 75 3.938653 TGCTAGGACGCACGATAAG 57.061 52.632 0.00 0.00 34.44 1.73
75 76 1.100510 TGCTAGGACGCACGATAAGT 58.899 50.000 0.00 0.00 34.44 2.24
76 77 1.475280 TGCTAGGACGCACGATAAGTT 59.525 47.619 0.00 0.00 34.44 2.66
77 78 1.852895 GCTAGGACGCACGATAAGTTG 59.147 52.381 0.00 0.00 0.00 3.16
78 79 1.852895 CTAGGACGCACGATAAGTTGC 59.147 52.381 0.00 0.00 0.00 4.17
79 80 0.739813 AGGACGCACGATAAGTTGCC 60.740 55.000 0.00 0.00 0.00 4.52
80 81 1.017177 GGACGCACGATAAGTTGCCA 61.017 55.000 0.00 0.00 0.00 4.92
81 82 0.370273 GACGCACGATAAGTTGCCAG 59.630 55.000 0.00 0.00 0.00 4.85
82 83 1.019278 ACGCACGATAAGTTGCCAGG 61.019 55.000 0.00 0.00 0.00 4.45
83 84 1.019278 CGCACGATAAGTTGCCAGGT 61.019 55.000 0.00 0.00 0.00 4.00
84 85 1.737696 CGCACGATAAGTTGCCAGGTA 60.738 52.381 0.00 0.00 0.00 3.08
85 86 2.561569 GCACGATAAGTTGCCAGGTAT 58.438 47.619 0.00 0.00 0.00 2.73
113 114 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
127 128 8.062065 TCTCTCTCTCTCCTATTTCTGTTTTC 57.938 38.462 0.00 0.00 0.00 2.29
338 339 4.096984 CCAGGATGACCTAGAAAAATGTGC 59.903 45.833 0.00 0.00 45.94 4.57
369 370 7.945033 TTTTGCAGAGATTGTAAACCAATTC 57.055 32.000 0.00 0.00 43.87 2.17
377 378 8.992073 AGAGATTGTAAACCAATTCAAAAATGC 58.008 29.630 0.00 0.00 43.87 3.56
389 390 7.853929 CCAATTCAAAAATGCTGAACTTTTCTG 59.146 33.333 0.00 0.00 35.70 3.02
452 453 2.532250 AATTCAAAGGGGTGCTAGGG 57.468 50.000 0.00 0.00 0.00 3.53
456 457 1.203001 TCAAAGGGGTGCTAGGGTTTG 60.203 52.381 0.00 0.00 0.00 2.93
471 472 4.033009 AGGGTTTGATCAATCCCCATTTC 58.967 43.478 35.86 19.34 46.70 2.17
546 549 4.402155 CAGGCAATTATTTTAGGGCTGTGA 59.598 41.667 0.00 0.00 44.32 3.58
550 553 6.162777 GCAATTATTTTAGGGCTGTGACAAA 58.837 36.000 0.00 0.00 0.00 2.83
553 556 9.520204 CAATTATTTTAGGGCTGTGACAAATAG 57.480 33.333 0.00 0.00 0.00 1.73
571 574 9.220767 GACAAATAGTCCTTTATTGAACTCAGT 57.779 33.333 0.00 0.00 41.56 3.41
713 765 2.365635 GGCTGAGCCCCTGGACTA 60.366 66.667 13.77 0.00 44.06 2.59
927 988 1.523711 GGCGGATCCATTTCTCGCA 60.524 57.895 13.41 0.00 46.95 5.10
928 989 0.886490 GGCGGATCCATTTCTCGCAT 60.886 55.000 13.41 0.00 46.95 4.73
959 1020 1.901159 TCCCGTTTCCCGATTCAAGTA 59.099 47.619 0.00 0.00 39.56 2.24
1095 1168 2.483714 GGCTCTTGATCTGGATTGCGTA 60.484 50.000 0.00 0.00 0.00 4.42
1101 1174 4.271696 TGATCTGGATTGCGTATTAGGG 57.728 45.455 0.00 0.00 0.00 3.53
1121 1195 2.631062 GGTTTAGAAACAGGGGTTTGGG 59.369 50.000 7.40 0.00 46.84 4.12
1125 1199 2.840511 AGAAACAGGGGTTTGGGTTTT 58.159 42.857 0.00 0.00 46.84 2.43
1130 1204 1.074395 GGGGTTTGGGTTTTGGGGA 60.074 57.895 0.00 0.00 0.00 4.81
1165 1239 2.232452 GCATACGCTGTCCTGGATAGAT 59.768 50.000 22.89 12.57 34.30 1.98
1174 1249 6.558909 GCTGTCCTGGATAGATTTTTCTTTG 58.441 40.000 22.89 0.00 0.00 2.77
1215 1290 8.579682 CAAAGGTTGGAGAACTAAGATTTTTG 57.420 34.615 0.00 0.00 32.15 2.44
1216 1291 6.901081 AGGTTGGAGAACTAAGATTTTTGG 57.099 37.500 0.00 0.00 32.15 3.28
1218 1293 5.243954 GGTTGGAGAACTAAGATTTTTGGCT 59.756 40.000 0.00 0.00 32.15 4.75
1220 1295 5.010282 TGGAGAACTAAGATTTTTGGCTCC 58.990 41.667 0.00 0.00 36.39 4.70
1221 1296 5.222130 TGGAGAACTAAGATTTTTGGCTCCT 60.222 40.000 16.11 0.00 36.58 3.69
1223 1298 4.938226 AGAACTAAGATTTTTGGCTCCTCG 59.062 41.667 0.00 0.00 0.00 4.63
1225 1300 1.177401 AAGATTTTTGGCTCCTCGGC 58.823 50.000 0.00 0.00 38.97 5.54
1226 1301 1.026718 AGATTTTTGGCTCCTCGGCG 61.027 55.000 0.00 0.00 42.02 6.46
1237 1329 1.067060 CTCCTCGGCGATGTAATGTGA 59.933 52.381 11.27 0.00 0.00 3.58
1240 1332 2.030457 CCTCGGCGATGTAATGTGAAAC 59.970 50.000 11.27 0.00 37.35 2.78
1297 1389 6.923199 ACCAATTGATTCCAGTGAAATCTT 57.077 33.333 7.12 0.00 33.32 2.40
1302 1394 5.246981 TGATTCCAGTGAAATCTTGTCCT 57.753 39.130 3.59 0.00 33.32 3.85
1303 1395 6.373005 TGATTCCAGTGAAATCTTGTCCTA 57.627 37.500 3.59 0.00 33.32 2.94
1325 1417 1.227263 CGGTCGGCATTCTACCTGG 60.227 63.158 0.00 0.00 0.00 4.45
1356 1448 1.480212 ATGGCCGGCGGATCTGAATA 61.480 55.000 33.44 5.71 0.00 1.75
1374 1466 4.202493 TGAATATGCTGCCCAGTCATGTAT 60.202 41.667 0.00 1.45 0.00 2.29
1385 1477 5.180117 GCCCAGTCATGTATAATGCTGTTAG 59.820 44.000 0.00 0.00 0.00 2.34
1429 1521 4.305989 GTTCTGAAATGAACAAGTGGCA 57.694 40.909 0.00 0.00 44.00 4.92
1430 1522 4.874970 GTTCTGAAATGAACAAGTGGCAT 58.125 39.130 0.00 0.00 44.00 4.40
1431 1523 5.291971 GTTCTGAAATGAACAAGTGGCATT 58.708 37.500 0.00 0.00 44.00 3.56
1432 1524 5.125100 TCTGAAATGAACAAGTGGCATTC 57.875 39.130 0.00 0.00 31.52 2.67
1433 1525 4.828939 TCTGAAATGAACAAGTGGCATTCT 59.171 37.500 0.00 0.00 31.52 2.40
1434 1526 6.003326 TCTGAAATGAACAAGTGGCATTCTA 58.997 36.000 0.00 0.00 31.52 2.10
1435 1527 6.489700 TCTGAAATGAACAAGTGGCATTCTAA 59.510 34.615 0.00 0.00 31.52 2.10
1436 1528 7.177216 TCTGAAATGAACAAGTGGCATTCTAAT 59.823 33.333 0.00 0.00 31.52 1.73
1437 1529 7.315142 TGAAATGAACAAGTGGCATTCTAATC 58.685 34.615 0.00 0.00 31.52 1.75
1438 1530 6.839124 AATGAACAAGTGGCATTCTAATCA 57.161 33.333 0.00 0.00 0.00 2.57
1439 1531 6.839124 ATGAACAAGTGGCATTCTAATCAA 57.161 33.333 0.00 0.00 0.00 2.57
1440 1532 6.839124 TGAACAAGTGGCATTCTAATCAAT 57.161 33.333 0.00 0.00 0.00 2.57
1441 1533 7.230849 TGAACAAGTGGCATTCTAATCAATT 57.769 32.000 0.00 0.00 0.00 2.32
1442 1534 7.315142 TGAACAAGTGGCATTCTAATCAATTC 58.685 34.615 0.00 0.00 0.00 2.17
1443 1535 6.839124 ACAAGTGGCATTCTAATCAATTCA 57.161 33.333 0.00 0.00 0.00 2.57
1444 1536 7.414222 ACAAGTGGCATTCTAATCAATTCAT 57.586 32.000 0.00 0.00 0.00 2.57
1445 1537 7.486647 ACAAGTGGCATTCTAATCAATTCATC 58.513 34.615 0.00 0.00 0.00 2.92
1446 1538 7.341256 ACAAGTGGCATTCTAATCAATTCATCT 59.659 33.333 0.00 0.00 0.00 2.90
1447 1539 8.843262 CAAGTGGCATTCTAATCAATTCATCTA 58.157 33.333 0.00 0.00 0.00 1.98
1448 1540 8.618702 AGTGGCATTCTAATCAATTCATCTAG 57.381 34.615 0.00 0.00 0.00 2.43
1449 1541 8.216423 AGTGGCATTCTAATCAATTCATCTAGT 58.784 33.333 0.00 0.00 0.00 2.57
1450 1542 8.844244 GTGGCATTCTAATCAATTCATCTAGTT 58.156 33.333 0.00 0.00 0.00 2.24
1451 1543 8.843262 TGGCATTCTAATCAATTCATCTAGTTG 58.157 33.333 0.00 0.00 0.00 3.16
1452 1544 8.844244 GGCATTCTAATCAATTCATCTAGTTGT 58.156 33.333 0.83 0.00 0.00 3.32
1464 1556 7.490962 TTCATCTAGTTGTTTGTTACTGTGG 57.509 36.000 0.83 0.00 0.00 4.17
1469 1561 4.932146 AGTTGTTTGTTACTGTGGCATTC 58.068 39.130 0.00 0.00 0.00 2.67
1488 1580 6.369005 GCATTCCAATCGATTCATCTAGTTG 58.631 40.000 7.92 0.00 0.00 3.16
1491 1583 7.921786 TTCCAATCGATTCATCTAGTTGTTT 57.078 32.000 7.92 0.00 0.00 2.83
1492 1584 7.307493 TCCAATCGATTCATCTAGTTGTTTG 57.693 36.000 7.92 0.00 0.00 2.93
1494 1586 7.390440 TCCAATCGATTCATCTAGTTGTTTGTT 59.610 33.333 7.92 0.00 0.00 2.83
1495 1587 8.023128 CCAATCGATTCATCTAGTTGTTTGTTT 58.977 33.333 7.92 0.00 0.00 2.83
1496 1588 8.843733 CAATCGATTCATCTAGTTGTTTGTTTG 58.156 33.333 7.92 3.37 0.00 2.93
1497 1589 6.370593 TCGATTCATCTAGTTGTTTGTTTGC 58.629 36.000 0.83 0.00 0.00 3.68
1498 1590 6.204688 TCGATTCATCTAGTTGTTTGTTTGCT 59.795 34.615 0.83 0.00 0.00 3.91
1499 1591 6.521133 CGATTCATCTAGTTGTTTGTTTGCTC 59.479 38.462 0.83 0.00 0.00 4.26
1513 1605 2.124942 GCTCCTGTGGCTAGGTGC 60.125 66.667 15.75 15.75 46.29 5.01
1555 1648 2.297315 CAGCCTTCCTTGACCCTTTTTC 59.703 50.000 0.00 0.00 0.00 2.29
1564 1657 3.535280 TGACCCTTTTTCTTTGGCAAC 57.465 42.857 0.00 0.00 0.00 4.17
1599 1695 0.320771 ATGTCGGCAGTGACTGGTTC 60.321 55.000 15.24 0.00 39.64 3.62
1613 1709 2.969821 TGGTTCAACCAGCCTGTATT 57.030 45.000 4.67 0.00 44.79 1.89
1615 1711 3.681593 TGGTTCAACCAGCCTGTATTAC 58.318 45.455 4.67 0.00 44.79 1.89
1617 1713 4.202524 TGGTTCAACCAGCCTGTATTACTT 60.203 41.667 4.67 0.00 44.79 2.24
1619 1715 3.950397 TCAACCAGCCTGTATTACTTGG 58.050 45.455 0.00 0.00 0.00 3.61
1621 1717 4.079253 CAACCAGCCTGTATTACTTGGTT 58.921 43.478 14.31 14.31 38.74 3.67
1692 1794 9.071276 AGTATTAGGTGCAAATGGATCTTATTG 57.929 33.333 0.00 0.00 0.00 1.90
1730 1833 7.040132 TGCATTGTGAACACCAAGAATGTTATA 60.040 33.333 13.27 1.98 40.36 0.98
1774 1880 3.006967 TGTGAGCCTTCTTTCTCCACTAC 59.993 47.826 0.00 0.00 0.00 2.73
1804 1910 8.325787 TCATAAAATGGTTATAGTGGTGTCAGT 58.674 33.333 0.00 0.00 0.00 3.41
1818 1924 5.701290 GTGGTGTCAGTAATAGCAAAAGAGT 59.299 40.000 0.00 0.00 0.00 3.24
1827 1933 1.609208 AGCAAAAGAGTGCCGATTGT 58.391 45.000 0.00 0.00 46.14 2.71
1899 2005 7.985752 GCACTGACTAGTAAAATATAGTTGGGT 59.014 37.037 0.00 0.00 34.74 4.51
1952 2058 1.135460 GGCGGTGACTGTGAGTACTAC 60.135 57.143 0.00 0.00 0.00 2.73
2169 2277 5.772825 TCCAGCCATTTTATATGAACAGC 57.227 39.130 0.00 0.00 0.00 4.40
2173 2281 6.376978 CAGCCATTTTATATGAACAGCTAGC 58.623 40.000 6.62 6.62 0.00 3.42
2203 2311 9.097257 CAATGTTGTCCAAAAAGATTAGTTTGT 57.903 29.630 0.00 0.00 33.71 2.83
2413 2522 3.128589 GCCATCGGTGTTGTTTATGTGAT 59.871 43.478 0.00 0.00 0.00 3.06
2421 2530 6.029607 GGTGTTGTTTATGTGATAGTGCATG 58.970 40.000 0.00 0.00 0.00 4.06
2422 2531 6.349280 GGTGTTGTTTATGTGATAGTGCATGT 60.349 38.462 0.00 0.00 0.00 3.21
2427 2536 7.973601 TGTTTATGTGATAGTGCATGTAAGTG 58.026 34.615 0.00 0.00 0.00 3.16
2480 2589 1.755179 AGTGTGTGTTGCAGAGCTTT 58.245 45.000 0.00 0.00 0.00 3.51
2482 2591 2.159338 AGTGTGTGTTGCAGAGCTTTTG 60.159 45.455 0.00 0.00 0.00 2.44
2773 2897 3.120060 GCTGTCTCAAGTTGCCTACATTG 60.120 47.826 0.00 0.00 0.00 2.82
2886 3011 4.026356 AGGATATATGGTTGCTTGAGCC 57.974 45.455 0.00 0.00 41.18 4.70
2897 3022 3.138884 TGCTTGAGCCTGTGAAATGTA 57.861 42.857 0.00 0.00 41.18 2.29
2948 3073 4.790878 CATGCACCAATATTCTCCATTCG 58.209 43.478 0.00 0.00 0.00 3.34
2998 3123 8.870160 TTACTATTCCAATGCAACATAAATGC 57.130 30.769 0.00 0.00 44.08 3.56
2999 3124 6.282930 ACTATTCCAATGCAACATAAATGCC 58.717 36.000 0.00 0.00 43.16 4.40
3000 3125 3.540314 TCCAATGCAACATAAATGCCC 57.460 42.857 0.00 0.00 43.16 5.36
3001 3126 2.836372 TCCAATGCAACATAAATGCCCA 59.164 40.909 0.00 0.00 43.16 5.36
3002 3127 3.262660 TCCAATGCAACATAAATGCCCAA 59.737 39.130 0.00 0.00 43.16 4.12
3003 3128 3.374678 CCAATGCAACATAAATGCCCAAC 59.625 43.478 0.00 0.00 43.16 3.77
3047 3200 8.116753 GTGTGCATGTGTTGAATATAGTACTTC 58.883 37.037 0.00 0.00 0.00 3.01
3084 3237 1.764571 TTGCTTACCTGCTCCACGGT 61.765 55.000 0.00 0.00 37.31 4.83
3290 3654 3.623906 AGTTGTGACCATGATCTCAGG 57.376 47.619 0.00 0.00 0.00 3.86
3466 3830 7.829725 AGATTTCTGTTTGCAAATACATAGCA 58.170 30.769 16.21 5.71 36.32 3.49
3494 3858 6.148315 TCACTGAATTGTGTCTATTTCTGCTG 59.852 38.462 0.00 0.00 38.90 4.41
3520 3884 7.433425 GCTTAATTGCTTTATACTTGCTGGAAG 59.567 37.037 7.41 7.41 37.73 3.46
3534 3898 1.902508 CTGGAAGCCTGGAACTACTCA 59.097 52.381 0.00 0.00 0.00 3.41
3556 3920 6.579865 TCATATGATGAATATCTGATGCGCT 58.420 36.000 9.73 0.00 36.11 5.92
3722 4086 4.567747 GGTCTTTGTCTGGTGGTAATGGAT 60.568 45.833 0.00 0.00 0.00 3.41
3838 4207 2.614057 GTTCATTCTTGGTAGGGATGCG 59.386 50.000 0.00 0.00 0.00 4.73
3859 4228 3.628017 GCTCGACAAAGCAAAAGCTTTA 58.372 40.909 13.10 0.00 42.05 1.85
3862 4231 4.844267 TCGACAAAGCAAAAGCTTTAGAC 58.156 39.130 13.10 5.04 37.86 2.59
3946 4315 2.822561 TCTGAGTGAGAAGATCAGCGTT 59.177 45.455 0.00 0.00 40.22 4.84
3964 4333 5.049680 CAGCGTTGGTACTTCAGTTGTAAAT 60.050 40.000 0.00 0.00 0.00 1.40
4012 4381 8.410141 CAGAAATATCTAGTTTCCGAGAAGACT 58.590 37.037 1.74 0.00 36.48 3.24
4048 4417 2.164865 CTGCTGAACAGGGCGTCTCT 62.165 60.000 3.99 0.00 43.19 3.10
4144 4513 1.080298 TTGCAAATACCGCGAACGAT 58.920 45.000 8.23 0.00 43.93 3.73
4174 4543 1.941325 AGGCGAAGGAGAAAATAGCG 58.059 50.000 0.00 0.00 0.00 4.26
4236 4605 1.869574 CTGACATGTCGGACGCTCG 60.870 63.158 27.59 1.97 38.21 5.03
4265 4634 2.381911 CCAGGGATTTGGATGGTGAAG 58.618 52.381 0.00 0.00 40.87 3.02
4342 4711 5.193679 GCAGTTTTCCCCATTACAGTAGAT 58.806 41.667 0.00 0.00 0.00 1.98
4376 4745 3.390521 CTCCACCACCGCCTGCTA 61.391 66.667 0.00 0.00 0.00 3.49
4387 4756 1.153269 GCCTGCTACTGCTCTTCCC 60.153 63.158 0.00 0.00 40.48 3.97
4455 4824 8.210265 TGGCTGATACATGAATGTAAATAGACA 58.790 33.333 7.21 10.51 45.40 3.41
4456 4825 9.224267 GGCTGATACATGAATGTAAATAGACAT 57.776 33.333 7.21 0.00 45.40 3.06
4495 4864 2.358737 AGGCTGTAGCGTTGTGGC 60.359 61.111 0.00 0.00 43.26 5.01
4555 4924 1.071699 TCAGGACCGAAAGAGTTTGGG 59.928 52.381 0.00 0.00 42.13 4.12
4578 4947 6.258507 GGGATTTGTAGCAGCCATTTTAATTG 59.741 38.462 0.00 0.00 0.00 2.32
4605 4974 6.692249 TCAAACAATATTATCATGCACTTGCG 59.308 34.615 0.00 0.00 45.83 4.85
4612 4981 0.817229 TCATGCACTTGCGGTGTCAA 60.817 50.000 10.54 0.00 46.86 3.18
4649 5018 8.659925 ATGATATTCACTTCTCTGATGTGTTC 57.340 34.615 11.50 7.19 38.37 3.18
4661 5031 6.042552 TCTCTGATGTGTTCTTTTCTTCTCCT 59.957 38.462 0.00 0.00 0.00 3.69
4806 5252 3.951775 TTTGTTGTTGCCAGAAGTGTT 57.048 38.095 0.00 0.00 0.00 3.32
4830 5280 2.152016 GTGCAAGAGTTCCCTTGGTAC 58.848 52.381 0.00 0.00 42.73 3.34
4886 5337 8.655092 TGAAAACAACTTCTTTTATGCTTTGTG 58.345 29.630 0.00 0.00 0.00 3.33
4889 5340 8.546597 AACAACTTCTTTTATGCTTTGTGTTT 57.453 26.923 0.00 0.00 0.00 2.83
4929 5385 1.819632 GGCCGAATGGAAGTGCGAT 60.820 57.895 0.00 0.00 37.49 4.58
4998 5456 2.709397 AGTAGGCCGCATTTTATACCCT 59.291 45.455 0.00 0.00 0.00 4.34
4999 5457 2.271944 AGGCCGCATTTTATACCCTC 57.728 50.000 0.00 0.00 0.00 4.30
5000 5458 1.774856 AGGCCGCATTTTATACCCTCT 59.225 47.619 0.00 0.00 0.00 3.69
5001 5459 2.174854 AGGCCGCATTTTATACCCTCTT 59.825 45.455 0.00 0.00 0.00 2.85
5002 5460 2.552743 GGCCGCATTTTATACCCTCTTC 59.447 50.000 0.00 0.00 0.00 2.87
5003 5461 3.211045 GCCGCATTTTATACCCTCTTCA 58.789 45.455 0.00 0.00 0.00 3.02
5004 5462 3.251004 GCCGCATTTTATACCCTCTTCAG 59.749 47.826 0.00 0.00 0.00 3.02
5082 5540 1.175983 GCACCGGACCATGAAACCAA 61.176 55.000 9.46 0.00 0.00 3.67
5083 5541 1.323412 CACCGGACCATGAAACCAAA 58.677 50.000 9.46 0.00 0.00 3.28
5084 5542 1.000717 CACCGGACCATGAAACCAAAC 60.001 52.381 9.46 0.00 0.00 2.93
5085 5543 0.601057 CCGGACCATGAAACCAAACC 59.399 55.000 0.00 0.00 0.00 3.27
5117 5575 6.519382 TGAGAACCATCAGAGCATTATACTG 58.481 40.000 0.00 0.00 0.00 2.74
5151 5609 4.433186 TGCGTTTTATTATTGCTGCAGT 57.567 36.364 16.64 1.92 0.00 4.40
5168 5626 3.007290 TGCAGTGAGATCAGTACAGCTTT 59.993 43.478 0.00 0.00 0.00 3.51
5218 5676 7.812669 AGAAAGAAAACAGAAAACGTTCACATT 59.187 29.630 0.00 0.00 36.09 2.71
5266 5727 2.423926 TCTTGAGCTCTTGTCACGAC 57.576 50.000 16.19 0.00 0.00 4.34
5365 5834 0.527385 GCAGACCAAAAACGCAGCAA 60.527 50.000 0.00 0.00 0.00 3.91
5408 5877 3.512680 AGCACAGCTGTATAAAGACGTC 58.487 45.455 21.20 7.70 37.57 4.34
5409 5878 2.603560 GCACAGCTGTATAAAGACGTCC 59.396 50.000 21.20 0.00 0.00 4.79
5410 5879 2.852413 CACAGCTGTATAAAGACGTCCG 59.148 50.000 21.20 0.00 0.00 4.79
5411 5880 2.490903 ACAGCTGTATAAAGACGTCCGT 59.509 45.455 20.16 2.51 0.00 4.69
5412 5881 3.057033 ACAGCTGTATAAAGACGTCCGTT 60.057 43.478 20.16 9.62 0.00 4.44
5413 5882 3.303495 CAGCTGTATAAAGACGTCCGTTG 59.697 47.826 13.01 0.00 0.00 4.10
5414 5883 2.028883 GCTGTATAAAGACGTCCGTTGC 59.971 50.000 13.01 2.80 0.00 4.17
5415 5884 3.247442 CTGTATAAAGACGTCCGTTGCA 58.753 45.455 13.01 4.14 0.00 4.08
5416 5885 3.852286 TGTATAAAGACGTCCGTTGCAT 58.148 40.909 13.01 1.42 0.00 3.96
5417 5886 3.615056 TGTATAAAGACGTCCGTTGCATG 59.385 43.478 13.01 0.00 0.00 4.06
5418 5887 0.793861 TAAAGACGTCCGTTGCATGC 59.206 50.000 13.01 11.82 0.00 4.06
5419 5888 1.163420 AAAGACGTCCGTTGCATGCA 61.163 50.000 18.46 18.46 0.00 3.96
5420 5889 0.955428 AAGACGTCCGTTGCATGCAT 60.955 50.000 23.37 3.89 0.00 3.96
5421 5890 0.955428 AGACGTCCGTTGCATGCATT 60.955 50.000 23.37 0.00 0.00 3.56
5422 5891 0.794229 GACGTCCGTTGCATGCATTG 60.794 55.000 23.37 16.52 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.035915 GGTCTTCTTCCACCTCTGCC 60.036 60.000 0.00 0.00 0.00 4.85
1 2 0.035915 GGGTCTTCTTCCACCTCTGC 60.036 60.000 0.00 0.00 32.69 4.26
2 3 1.352083 TGGGTCTTCTTCCACCTCTG 58.648 55.000 0.00 0.00 32.69 3.35
3 4 2.350863 ATGGGTCTTCTTCCACCTCT 57.649 50.000 0.00 0.00 35.67 3.69
4 5 2.678190 CGAATGGGTCTTCTTCCACCTC 60.678 54.545 0.00 0.00 35.67 3.85
5 6 1.279271 CGAATGGGTCTTCTTCCACCT 59.721 52.381 0.00 0.00 35.67 4.00
6 7 1.739067 CGAATGGGTCTTCTTCCACC 58.261 55.000 0.00 0.00 35.67 4.61
7 8 1.087501 GCGAATGGGTCTTCTTCCAC 58.912 55.000 0.00 0.00 35.67 4.02
8 9 0.035439 GGCGAATGGGTCTTCTTCCA 60.035 55.000 0.00 0.00 37.46 3.53
9 10 0.748367 GGGCGAATGGGTCTTCTTCC 60.748 60.000 0.00 0.00 0.00 3.46
10 11 0.748367 GGGGCGAATGGGTCTTCTTC 60.748 60.000 0.00 0.00 0.00 2.87
11 12 1.208165 AGGGGCGAATGGGTCTTCTT 61.208 55.000 0.00 0.00 0.00 2.52
12 13 1.616628 AGGGGCGAATGGGTCTTCT 60.617 57.895 0.00 0.00 0.00 2.85
13 14 1.452108 CAGGGGCGAATGGGTCTTC 60.452 63.158 0.00 0.00 0.00 2.87
14 15 2.677228 CAGGGGCGAATGGGTCTT 59.323 61.111 0.00 0.00 0.00 3.01
15 16 3.411517 CCAGGGGCGAATGGGTCT 61.412 66.667 0.00 0.00 32.63 3.85
16 17 3.728373 ACCAGGGGCGAATGGGTC 61.728 66.667 6.27 0.00 41.13 4.46
17 18 4.047125 CACCAGGGGCGAATGGGT 62.047 66.667 6.27 0.00 41.13 4.51
18 19 4.820744 CCACCAGGGGCGAATGGG 62.821 72.222 6.27 0.00 41.13 4.00
28 29 3.801997 CTAGCCCAGCCCACCAGG 61.802 72.222 0.00 0.00 39.47 4.45
29 30 4.496336 GCTAGCCCAGCCCACCAG 62.496 72.222 2.29 0.00 45.23 4.00
37 38 1.683917 CACTGTAGGTAGCTAGCCCAG 59.316 57.143 26.43 26.43 32.65 4.45
38 39 1.776662 CACTGTAGGTAGCTAGCCCA 58.223 55.000 19.06 14.58 0.00 5.36
39 40 0.389757 GCACTGTAGGTAGCTAGCCC 59.610 60.000 19.06 6.50 0.00 5.19
40 41 1.404843 AGCACTGTAGGTAGCTAGCC 58.595 55.000 19.06 11.24 33.13 3.93
41 42 2.554893 CCTAGCACTGTAGGTAGCTAGC 59.445 54.545 15.19 15.19 43.27 3.42
42 43 3.816523 GTCCTAGCACTGTAGGTAGCTAG 59.183 52.174 14.02 14.02 43.67 3.42
43 44 3.743584 CGTCCTAGCACTGTAGGTAGCTA 60.744 52.174 0.00 0.00 40.64 3.32
44 45 2.657143 GTCCTAGCACTGTAGGTAGCT 58.343 52.381 0.00 0.00 40.64 3.32
45 46 1.334243 CGTCCTAGCACTGTAGGTAGC 59.666 57.143 9.47 0.00 40.64 3.58
46 47 1.334243 GCGTCCTAGCACTGTAGGTAG 59.666 57.143 8.51 8.51 40.64 3.18
47 48 1.340308 TGCGTCCTAGCACTGTAGGTA 60.340 52.381 0.00 0.00 42.92 3.08
48 49 0.611062 TGCGTCCTAGCACTGTAGGT 60.611 55.000 0.00 0.00 42.92 3.08
49 50 2.189833 TGCGTCCTAGCACTGTAGG 58.810 57.895 0.00 0.00 42.92 3.18
56 57 1.100510 ACTTATCGTGCGTCCTAGCA 58.899 50.000 0.00 0.00 45.96 3.49
57 58 1.852895 CAACTTATCGTGCGTCCTAGC 59.147 52.381 0.00 0.00 37.71 3.42
58 59 1.852895 GCAACTTATCGTGCGTCCTAG 59.147 52.381 0.00 0.00 0.00 3.02
59 60 1.470285 GGCAACTTATCGTGCGTCCTA 60.470 52.381 0.00 0.00 0.00 2.94
60 61 0.739813 GGCAACTTATCGTGCGTCCT 60.740 55.000 0.00 0.00 0.00 3.85
61 62 1.017177 TGGCAACTTATCGTGCGTCC 61.017 55.000 0.00 0.00 37.61 4.79
62 63 0.370273 CTGGCAACTTATCGTGCGTC 59.630 55.000 0.00 0.00 37.61 5.19
63 64 1.019278 CCTGGCAACTTATCGTGCGT 61.019 55.000 0.00 0.00 37.61 5.24
64 65 1.019278 ACCTGGCAACTTATCGTGCG 61.019 55.000 0.00 0.00 37.61 5.34
65 66 2.018542 TACCTGGCAACTTATCGTGC 57.981 50.000 0.00 0.00 37.61 5.34
66 67 4.442706 AGAATACCTGGCAACTTATCGTG 58.557 43.478 0.00 0.00 37.61 4.35
67 68 4.406003 AGAGAATACCTGGCAACTTATCGT 59.594 41.667 0.00 0.00 37.61 3.73
68 69 4.950050 AGAGAATACCTGGCAACTTATCG 58.050 43.478 0.00 0.00 37.61 2.92
69 70 6.041523 AGAGAGAGAATACCTGGCAACTTATC 59.958 42.308 0.00 0.00 37.61 1.75
70 71 5.902431 AGAGAGAGAATACCTGGCAACTTAT 59.098 40.000 0.00 0.00 37.61 1.73
71 72 5.273208 AGAGAGAGAATACCTGGCAACTTA 58.727 41.667 0.00 0.00 37.61 2.24
72 73 4.100373 AGAGAGAGAATACCTGGCAACTT 58.900 43.478 0.00 0.00 37.61 2.66
73 74 3.704061 GAGAGAGAGAATACCTGGCAACT 59.296 47.826 0.00 0.00 37.61 3.16
74 75 3.704061 AGAGAGAGAGAATACCTGGCAAC 59.296 47.826 0.00 0.00 0.00 4.17
75 76 3.957497 GAGAGAGAGAGAATACCTGGCAA 59.043 47.826 0.00 0.00 0.00 4.52
76 77 3.204158 AGAGAGAGAGAGAATACCTGGCA 59.796 47.826 0.00 0.00 0.00 4.92
77 78 3.821033 GAGAGAGAGAGAGAATACCTGGC 59.179 52.174 0.00 0.00 0.00 4.85
78 79 5.072329 AGAGAGAGAGAGAGAGAATACCTGG 59.928 48.000 0.00 0.00 0.00 4.45
79 80 6.042552 AGAGAGAGAGAGAGAGAGAATACCTG 59.957 46.154 0.00 0.00 0.00 4.00
80 81 6.146760 AGAGAGAGAGAGAGAGAGAATACCT 58.853 44.000 0.00 0.00 0.00 3.08
81 82 6.268847 AGAGAGAGAGAGAGAGAGAGAATACC 59.731 46.154 0.00 0.00 0.00 2.73
82 83 7.232534 AGAGAGAGAGAGAGAGAGAGAGAATAC 59.767 44.444 0.00 0.00 0.00 1.89
83 84 7.301420 AGAGAGAGAGAGAGAGAGAGAGAATA 58.699 42.308 0.00 0.00 0.00 1.75
84 85 6.142498 AGAGAGAGAGAGAGAGAGAGAGAAT 58.858 44.000 0.00 0.00 0.00 2.40
85 86 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
195 196 6.371595 TGGAAATATTTCAAAAGTGCCCAT 57.628 33.333 25.55 0.00 38.92 4.00
214 215 0.550914 ACAGTTGAGGGCTGTTGGAA 59.449 50.000 0.00 0.00 43.87 3.53
316 317 4.701651 TGCACATTTTTCTAGGTCATCCTG 59.298 41.667 0.00 0.00 44.81 3.86
358 359 8.141835 AGTTCAGCATTTTTGAATTGGTTTAC 57.858 30.769 0.00 0.00 36.96 2.01
369 370 6.510638 GCCTTCAGAAAAGTTCAGCATTTTTG 60.511 38.462 0.00 0.00 0.00 2.44
377 378 5.464389 CCAAAATGCCTTCAGAAAAGTTCAG 59.536 40.000 0.00 0.00 0.00 3.02
389 390 4.270245 TCAATGAACCCAAAATGCCTTC 57.730 40.909 0.00 0.00 0.00 3.46
439 440 1.285078 GATCAAACCCTAGCACCCCTT 59.715 52.381 0.00 0.00 0.00 3.95
452 453 7.926674 AATTTGAAATGGGGATTGATCAAAC 57.073 32.000 13.09 9.88 38.95 2.93
456 457 9.447157 TTGTTAAATTTGAAATGGGGATTGATC 57.553 29.630 0.00 0.00 0.00 2.92
509 510 5.603170 AATTGCCTGCAAATAGTAGCATT 57.397 34.783 8.84 0.00 40.42 3.56
514 515 8.637986 CCCTAAAATAATTGCCTGCAAATAGTA 58.362 33.333 8.84 0.32 39.55 1.82
571 574 8.483307 AAAGCGAAGTTCGTAAAGGAAATATA 57.517 30.769 25.04 0.00 42.81 0.86
572 575 6.980051 AAGCGAAGTTCGTAAAGGAAATAT 57.020 33.333 25.04 0.00 42.81 1.28
654 658 9.657419 AAAGCACAAATATTCCTCATAAAAAGG 57.343 29.630 0.00 0.00 35.05 3.11
907 968 1.598130 CGAGAAATGGATCCGCCCC 60.598 63.158 7.39 0.00 34.97 5.80
908 969 2.254464 GCGAGAAATGGATCCGCCC 61.254 63.158 7.39 0.00 39.97 6.13
927 988 6.358991 TCGGGAAACGGGAAGAAAAATATAT 58.641 36.000 0.00 0.00 44.45 0.86
928 989 5.743117 TCGGGAAACGGGAAGAAAAATATA 58.257 37.500 0.00 0.00 44.45 0.86
959 1020 0.901580 TCTCCGAACCCTAACCGCTT 60.902 55.000 0.00 0.00 0.00 4.68
1095 1168 5.610429 AACCCCTGTTTCTAAACCCTAAT 57.390 39.130 3.27 0.00 38.11 1.73
1101 1174 3.302161 ACCCAAACCCCTGTTTCTAAAC 58.698 45.455 0.00 0.00 42.73 2.01
1121 1195 4.462834 CCCAAATCTAGAACTCCCCAAAAC 59.537 45.833 0.00 0.00 0.00 2.43
1125 1199 1.564348 GCCCAAATCTAGAACTCCCCA 59.436 52.381 0.00 0.00 0.00 4.96
1130 1204 3.134804 AGCGTATGCCCAAATCTAGAACT 59.865 43.478 2.51 0.00 44.31 3.01
1165 1239 5.584251 GCAGGACAAATTGACCAAAGAAAAA 59.416 36.000 16.05 0.00 34.63 1.94
1174 1249 3.030668 CTTTGGCAGGACAAATTGACC 57.969 47.619 6.37 6.37 39.39 4.02
1195 1270 6.332735 AGCCAAAAATCTTAGTTCTCCAAC 57.667 37.500 0.00 0.00 0.00 3.77
1200 1275 4.938226 CGAGGAGCCAAAAATCTTAGTTCT 59.062 41.667 0.00 0.00 0.00 3.01
1204 1279 2.356069 GCCGAGGAGCCAAAAATCTTAG 59.644 50.000 0.00 0.00 0.00 2.18
1211 1286 1.745115 CATCGCCGAGGAGCCAAAA 60.745 57.895 0.00 0.00 0.00 2.44
1212 1287 1.609635 TACATCGCCGAGGAGCCAAA 61.610 55.000 5.50 0.00 0.00 3.28
1215 1290 0.946221 CATTACATCGCCGAGGAGCC 60.946 60.000 5.50 0.00 0.00 4.70
1216 1291 0.249489 ACATTACATCGCCGAGGAGC 60.249 55.000 5.50 0.00 0.00 4.70
1218 1293 1.107945 TCACATTACATCGCCGAGGA 58.892 50.000 5.50 0.00 0.00 3.71
1220 1295 2.670905 TGTTTCACATTACATCGCCGAG 59.329 45.455 0.00 0.00 0.00 4.63
1221 1296 2.670905 CTGTTTCACATTACATCGCCGA 59.329 45.455 0.00 0.00 0.00 5.54
1223 1298 3.747193 CACTGTTTCACATTACATCGCC 58.253 45.455 0.00 0.00 0.00 5.54
1225 1300 4.403015 TGCACTGTTTCACATTACATCG 57.597 40.909 0.00 0.00 0.00 3.84
1226 1301 5.023920 CGATGCACTGTTTCACATTACATC 58.976 41.667 0.00 0.00 32.08 3.06
1237 1329 0.957395 CTGCCTCCGATGCACTGTTT 60.957 55.000 0.00 0.00 34.46 2.83
1240 1332 3.200593 GCTGCCTCCGATGCACTG 61.201 66.667 0.00 0.00 34.46 3.66
1271 1363 8.421249 AGATTTCACTGGAATCAATTGGTAAA 57.579 30.769 11.93 0.00 31.93 2.01
1286 1378 5.643777 ACCGAAATAGGACAAGATTTCACTG 59.356 40.000 7.80 0.00 40.55 3.66
1297 1389 0.828022 ATGCCGACCGAAATAGGACA 59.172 50.000 0.00 0.00 34.73 4.02
1302 1394 3.102052 GGTAGAATGCCGACCGAAATA 57.898 47.619 0.00 0.00 30.90 1.40
1303 1395 1.949465 GGTAGAATGCCGACCGAAAT 58.051 50.000 0.00 0.00 30.90 2.17
1325 1417 2.410469 GGCCATCGCACATTCAGC 59.590 61.111 0.00 0.00 36.38 4.26
1349 1441 1.839354 TGACTGGGCAGCATATTCAGA 59.161 47.619 0.00 0.00 0.00 3.27
1356 1448 3.862877 TTATACATGACTGGGCAGCAT 57.137 42.857 0.00 0.00 0.00 3.79
1374 1466 5.765576 TTTGAGTACCCCTAACAGCATTA 57.234 39.130 0.00 0.00 0.00 1.90
1385 1477 6.885922 ACATACTAAGTGATTTGAGTACCCC 58.114 40.000 0.00 0.00 0.00 4.95
1422 1514 7.893124 AGATGAATTGATTAGAATGCCACTT 57.107 32.000 0.00 0.00 0.00 3.16
1424 1516 8.388484 ACTAGATGAATTGATTAGAATGCCAC 57.612 34.615 0.00 0.00 0.00 5.01
1425 1517 8.843262 CAACTAGATGAATTGATTAGAATGCCA 58.157 33.333 0.00 0.00 0.00 4.92
1426 1518 8.844244 ACAACTAGATGAATTGATTAGAATGCC 58.156 33.333 7.05 0.00 0.00 4.40
1436 1528 9.337396 ACAGTAACAAACAACTAGATGAATTGA 57.663 29.630 20.93 5.85 0.00 2.57
1437 1529 9.385902 CACAGTAACAAACAACTAGATGAATTG 57.614 33.333 7.05 12.76 0.00 2.32
1438 1530 8.567948 CCACAGTAACAAACAACTAGATGAATT 58.432 33.333 7.05 0.00 0.00 2.17
1439 1531 7.308589 GCCACAGTAACAAACAACTAGATGAAT 60.309 37.037 7.05 0.00 0.00 2.57
1440 1532 6.017440 GCCACAGTAACAAACAACTAGATGAA 60.017 38.462 7.05 0.00 0.00 2.57
1441 1533 5.468746 GCCACAGTAACAAACAACTAGATGA 59.531 40.000 7.05 0.00 0.00 2.92
1442 1534 5.238432 TGCCACAGTAACAAACAACTAGATG 59.762 40.000 0.00 0.00 0.00 2.90
1443 1535 5.373222 TGCCACAGTAACAAACAACTAGAT 58.627 37.500 0.00 0.00 0.00 1.98
1444 1536 4.771903 TGCCACAGTAACAAACAACTAGA 58.228 39.130 0.00 0.00 0.00 2.43
1445 1537 5.689383 ATGCCACAGTAACAAACAACTAG 57.311 39.130 0.00 0.00 0.00 2.57
1446 1538 5.009210 GGAATGCCACAGTAACAAACAACTA 59.991 40.000 0.00 0.00 0.00 2.24
1447 1539 4.202111 GGAATGCCACAGTAACAAACAACT 60.202 41.667 0.00 0.00 0.00 3.16
1448 1540 4.048504 GGAATGCCACAGTAACAAACAAC 58.951 43.478 0.00 0.00 0.00 3.32
1449 1541 3.701542 TGGAATGCCACAGTAACAAACAA 59.298 39.130 0.00 0.00 39.92 2.83
1450 1542 3.291584 TGGAATGCCACAGTAACAAACA 58.708 40.909 0.00 0.00 39.92 2.83
1451 1543 4.314740 TTGGAATGCCACAGTAACAAAC 57.685 40.909 0.00 0.00 45.94 2.93
1452 1544 4.320861 CGATTGGAATGCCACAGTAACAAA 60.321 41.667 0.00 0.00 45.94 2.83
1453 1545 3.190327 CGATTGGAATGCCACAGTAACAA 59.810 43.478 0.00 0.00 45.94 2.83
1454 1546 2.746904 CGATTGGAATGCCACAGTAACA 59.253 45.455 0.00 0.00 45.94 2.41
1455 1547 3.006940 TCGATTGGAATGCCACAGTAAC 58.993 45.455 0.00 0.00 45.94 2.50
1456 1548 3.342377 TCGATTGGAATGCCACAGTAA 57.658 42.857 0.00 0.00 45.94 2.24
1457 1549 3.558931 ATCGATTGGAATGCCACAGTA 57.441 42.857 0.00 0.00 45.94 2.74
1458 1550 2.425143 ATCGATTGGAATGCCACAGT 57.575 45.000 0.00 0.00 45.94 3.55
1459 1551 2.684374 TGAATCGATTGGAATGCCACAG 59.316 45.455 16.96 0.00 45.94 3.66
1460 1552 2.720915 TGAATCGATTGGAATGCCACA 58.279 42.857 16.96 0.55 45.94 4.17
1464 1556 6.017605 ACAACTAGATGAATCGATTGGAATGC 60.018 38.462 16.96 0.00 0.00 3.56
1469 1561 7.076842 ACAAACAACTAGATGAATCGATTGG 57.923 36.000 16.96 0.00 0.00 3.16
1488 1580 0.746659 AGCCACAGGAGCAAACAAAC 59.253 50.000 0.00 0.00 0.00 2.93
1491 1583 0.036732 CCTAGCCACAGGAGCAAACA 59.963 55.000 0.00 0.00 38.00 2.83
1492 1584 0.036875 ACCTAGCCACAGGAGCAAAC 59.963 55.000 3.73 0.00 39.18 2.93
1494 1586 1.679311 CACCTAGCCACAGGAGCAA 59.321 57.895 3.73 0.00 39.18 3.91
1495 1587 3.392228 CACCTAGCCACAGGAGCA 58.608 61.111 3.73 0.00 39.18 4.26
1496 1588 2.124942 GCACCTAGCCACAGGAGC 60.125 66.667 3.73 3.78 43.57 4.70
1513 1605 2.174363 TCATGGCTCACAAGTCACAG 57.826 50.000 0.00 0.00 40.66 3.66
1564 1657 5.095490 GCCGACATTAATCTCAACAAAAGG 58.905 41.667 0.00 0.00 0.00 3.11
1575 1668 2.609459 CCAGTCACTGCCGACATTAATC 59.391 50.000 0.00 0.00 38.43 1.75
1579 1672 0.108585 AACCAGTCACTGCCGACATT 59.891 50.000 0.00 0.00 38.43 2.71
1585 1681 0.465460 TGGTTGAACCAGTCACTGCC 60.465 55.000 14.05 0.00 44.79 4.85
1599 1695 3.686016 ACCAAGTAATACAGGCTGGTTG 58.314 45.455 20.34 11.26 0.00 3.77
1613 1709 5.535029 ACAGGGACAGGATATAACCAAGTA 58.465 41.667 1.42 0.00 0.00 2.24
1614 1710 4.371681 ACAGGGACAGGATATAACCAAGT 58.628 43.478 1.42 0.00 0.00 3.16
1615 1711 5.373812 AACAGGGACAGGATATAACCAAG 57.626 43.478 1.42 0.00 0.00 3.61
1617 1713 6.270000 CAGATAACAGGGACAGGATATAACCA 59.730 42.308 1.42 0.00 0.00 3.67
1619 1715 7.304497 ACAGATAACAGGGACAGGATATAAC 57.696 40.000 0.00 0.00 0.00 1.89
1621 1717 7.931015 AAACAGATAACAGGGACAGGATATA 57.069 36.000 0.00 0.00 0.00 0.86
1681 1779 7.037438 GCAATGAAAAGAAGCAATAAGATCCA 58.963 34.615 0.00 0.00 0.00 3.41
1692 1794 5.234757 TGTTCACAATGCAATGAAAAGAAGC 59.765 36.000 9.20 0.00 36.62 3.86
1730 1833 7.828717 TCACATTCACCATGTACTGATTGTTAT 59.171 33.333 7.33 0.00 45.06 1.89
1753 1858 2.849294 AGTGGAGAAAGAAGGCTCAC 57.151 50.000 0.00 0.00 32.83 3.51
1804 1910 4.941263 ACAATCGGCACTCTTTTGCTATTA 59.059 37.500 0.00 0.00 42.56 0.98
1818 1924 3.818210 ACTGTAAAATGACACAATCGGCA 59.182 39.130 0.00 0.00 0.00 5.69
1871 1977 9.378551 CCAACTATATTTTACTAGTCAGTGCAA 57.621 33.333 0.00 0.00 36.14 4.08
1899 2005 2.355197 CCGTGACAGGCATTGTATGAA 58.645 47.619 0.00 0.00 41.05 2.57
2169 2277 2.093306 TGGACAACATTGACCGCTAG 57.907 50.000 8.29 0.00 44.27 3.42
2173 2281 4.300189 TCTTTTTGGACAACATTGACCG 57.700 40.909 8.29 0.00 44.27 4.79
2306 2415 8.527810 GGGATTTCCTAATCAACATTACACAAA 58.472 33.333 0.00 0.00 41.62 2.83
2734 2858 0.463654 AGCTCGTCACCACTGCAAAA 60.464 50.000 0.00 0.00 0.00 2.44
2838 2962 4.893524 GGGGAAAGGAAGTTCTTTTCAGAA 59.106 41.667 30.30 0.00 42.20 3.02
2975 3100 6.282930 GGCATTTATGTTGCATTGGAATAGT 58.717 36.000 0.00 0.00 41.95 2.12
2976 3101 5.697633 GGGCATTTATGTTGCATTGGAATAG 59.302 40.000 0.00 0.00 41.95 1.73
3001 3126 3.058777 CACGGGCAATACAACGTAAAGTT 60.059 43.478 0.00 0.00 45.45 2.66
3002 3127 2.481185 CACGGGCAATACAACGTAAAGT 59.519 45.455 0.00 0.00 37.85 2.66
3003 3128 2.481185 ACACGGGCAATACAACGTAAAG 59.519 45.455 0.00 0.00 37.85 1.85
3017 3170 2.050168 CAACACATGCACACGGGC 60.050 61.111 0.00 0.00 0.00 6.13
3047 3200 3.119316 AGCAACCTCACTCGTTATCTCTG 60.119 47.826 0.00 0.00 0.00 3.35
3107 3470 8.090214 TGTAGACCAGGTAAACAATACAAGTAC 58.910 37.037 4.31 0.00 0.00 2.73
3113 3476 5.484715 TGCTGTAGACCAGGTAAACAATAC 58.515 41.667 7.69 2.57 41.81 1.89
3206 3569 7.994334 AGTACTCCCAATTGTACTGTAAAAACA 59.006 33.333 4.43 0.00 45.05 2.83
3253 3616 7.081976 GTCACAACTTACATAACATGGTTTCC 58.918 38.462 0.00 0.00 33.60 3.13
3466 3830 7.361542 GCAGAAATAGACACAATTCAGTGACAT 60.362 37.037 3.12 0.00 42.05 3.06
3494 3858 6.795399 TCCAGCAAGTATAAAGCAATTAAGC 58.205 36.000 0.00 0.00 0.00 3.09
3520 3884 5.474578 TCATCATATGAGTAGTTCCAGGC 57.525 43.478 11.78 0.00 33.59 4.85
3521 3885 9.814899 GATATTCATCATATGAGTAGTTCCAGG 57.185 37.037 11.78 0.00 40.94 4.45
3534 3898 6.260271 CCAAGCGCATCAGATATTCATCATAT 59.740 38.462 11.47 0.00 33.21 1.78
3556 3920 2.483363 CCTGCAACAGCAATCAAACCAA 60.483 45.455 0.00 0.00 37.91 3.67
3722 4086 4.282957 TGGATGCAAAGCAATGTAAGGAAA 59.717 37.500 0.00 0.00 43.62 3.13
3946 4315 9.787435 ACTTTATCATTTACAACTGAAGTACCA 57.213 29.630 0.00 0.00 0.00 3.25
3964 4333 9.973661 TTCTGATCCATTTCCTTTACTTTATCA 57.026 29.630 0.00 0.00 0.00 2.15
4000 4369 2.093106 GCTGACCTAGTCTTCTCGGAA 58.907 52.381 0.00 0.00 33.15 4.30
4012 4381 2.061220 AGCTGCAAGTGCTGACCTA 58.939 52.632 13.64 0.00 41.71 3.08
4096 4465 1.000896 GGCACCAGTTACCCATGCT 60.001 57.895 0.00 0.00 36.52 3.79
4129 4498 0.918619 CGACATCGTTCGCGGTATTT 59.081 50.000 6.13 0.00 41.70 1.40
4144 4513 4.257654 TTCGCCTTTGCCCCGACA 62.258 61.111 0.00 0.00 0.00 4.35
4174 4543 3.991725 CTTGCCCTCCTGCTCAGCC 62.992 68.421 0.00 0.00 0.00 4.85
4236 4605 1.276138 CCAAATCCCTGGGCTTTTCAC 59.724 52.381 11.75 0.00 32.32 3.18
4265 4634 7.658179 TTTCAGAGACATGTATCTTTGTGAC 57.342 36.000 20.15 0.00 33.56 3.67
4342 4711 0.528466 GAGACGCATCGCTGGAATCA 60.528 55.000 0.00 0.00 0.00 2.57
4372 4741 1.644509 TCTTGGGAAGAGCAGTAGCA 58.355 50.000 0.00 0.00 45.49 3.49
4376 4745 1.543429 CGGTTTCTTGGGAAGAGCAGT 60.543 52.381 0.00 0.00 39.03 4.40
4387 4756 1.574428 CGCAGGTTCCGGTTTCTTG 59.426 57.895 0.00 1.21 0.00 3.02
4455 4824 6.607198 CCTGAATTAAACAACCCACCTCATAT 59.393 38.462 0.00 0.00 0.00 1.78
4456 4825 5.949354 CCTGAATTAAACAACCCACCTCATA 59.051 40.000 0.00 0.00 0.00 2.15
4462 4831 3.320826 ACAGCCTGAATTAAACAACCCAC 59.679 43.478 0.00 0.00 0.00 4.61
4495 4864 4.005650 ACAGGTGAATCACAATACAGCAG 58.994 43.478 15.86 0.00 35.86 4.24
4537 4906 1.430992 TCCCAAACTCTTTCGGTCCT 58.569 50.000 0.00 0.00 0.00 3.85
4555 4924 8.652810 ATCAATTAAAATGGCTGCTACAAATC 57.347 30.769 0.00 0.00 0.00 2.17
4578 4947 8.697067 GCAAGTGCATGATAATATTGTTTGATC 58.303 33.333 0.00 0.00 41.59 2.92
4605 4974 4.541779 TCATACGCAAACATTTTGACACC 58.458 39.130 2.80 0.00 0.00 4.16
4612 4981 8.677300 AGAAGTGAATATCATACGCAAACATTT 58.323 29.630 0.00 0.00 0.00 2.32
4649 5018 8.893727 TCTTGTAAAAACTCAGGAGAAGAAAAG 58.106 33.333 2.79 0.00 0.00 2.27
4718 5146 0.457035 CATTCAGTCCATTTGGGCCG 59.543 55.000 0.00 0.00 41.83 6.13
4752 5180 5.455056 AGGCAATACAAGTACTCCTATCG 57.545 43.478 0.00 0.00 0.00 2.92
4806 5252 2.281484 GGGAACTCTTGCACGCCA 60.281 61.111 0.00 0.00 0.00 5.69
4886 5337 7.965107 CCACTCTTCACAGCAGAATAAATAAAC 59.035 37.037 0.00 0.00 0.00 2.01
4889 5340 5.586243 GCCACTCTTCACAGCAGAATAAATA 59.414 40.000 0.00 0.00 0.00 1.40
4894 5345 1.612726 GGCCACTCTTCACAGCAGAAT 60.613 52.381 0.00 0.00 0.00 2.40
4897 5348 2.031516 CGGCCACTCTTCACAGCAG 61.032 63.158 2.24 0.00 0.00 4.24
4929 5385 2.409055 GCCTGATGTTGCCATGCGA 61.409 57.895 0.00 0.00 0.00 5.10
4933 5389 2.048023 CGGTGCCTGATGTTGCCAT 61.048 57.895 0.00 0.00 0.00 4.40
4946 5402 1.787847 CTCGACAAATGTCCGGTGC 59.212 57.895 0.00 0.00 41.86 5.01
4998 5456 5.466728 CCATTTCTTCGTTGAAGACTGAAGA 59.533 40.000 8.67 0.00 46.54 2.87
4999 5457 5.237344 ACCATTTCTTCGTTGAAGACTGAAG 59.763 40.000 8.67 0.00 46.54 3.02
5000 5458 5.123227 ACCATTTCTTCGTTGAAGACTGAA 58.877 37.500 8.67 2.31 46.54 3.02
5001 5459 4.703897 ACCATTTCTTCGTTGAAGACTGA 58.296 39.130 8.67 0.00 46.54 3.41
5002 5460 4.511454 TGACCATTTCTTCGTTGAAGACTG 59.489 41.667 8.67 9.26 46.54 3.51
5003 5461 4.703897 TGACCATTTCTTCGTTGAAGACT 58.296 39.130 8.67 0.00 46.54 3.24
5004 5462 4.750098 TCTGACCATTTCTTCGTTGAAGAC 59.250 41.667 8.67 0.00 46.54 3.01
5110 5568 4.266739 CGCATACAGAACGCAACAGTATAA 59.733 41.667 0.00 0.00 0.00 0.98
5111 5569 3.794564 CGCATACAGAACGCAACAGTATA 59.205 43.478 0.00 0.00 0.00 1.47
5112 5570 2.603110 CGCATACAGAACGCAACAGTAT 59.397 45.455 0.00 0.00 0.00 2.12
5117 5575 2.309898 AAACGCATACAGAACGCAAC 57.690 45.000 0.00 0.00 0.00 4.17
5266 5727 1.597461 GGACCAAGGAAGGAGACGG 59.403 63.158 0.00 0.00 0.00 4.79
5322 5783 1.388065 ATGTCGAGCTTCGGAGGAGG 61.388 60.000 0.00 0.00 40.88 4.30
5323 5784 1.309950 TATGTCGAGCTTCGGAGGAG 58.690 55.000 0.00 0.00 40.88 3.69
5324 5785 1.880675 GATATGTCGAGCTTCGGAGGA 59.119 52.381 0.00 0.00 40.88 3.71
5365 5834 2.683867 GCTGATTCTGAGCTCTGCATTT 59.316 45.455 16.19 0.05 36.63 2.32


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

AutoCloner maintained by Alex Coulton.