Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017921.1 Corchorus olitorius cultivar O-4 contig17954, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 159834
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1320 original size:23 final size:23
Alignment explanation
Indices: 1267--1321 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1257 TTGTTTGTTC
* *
1267 TTATGGGCTTGTTTTTTTTTCTT
1 TTATGGGCTTGGTTTTTTTACTT
1290 TTGATGGGCTTGGTTTTTTTACTT
1 TT-ATGGGCTTGGTTTTTTTACTT
1314 ATT-TGGGC
1 -TTATGGGC
1322 CTTATGGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.25
24 19 0.68
25 2 0.07
ACGTcount: A:0.07, C:0.09, G:0.24, T:0.60
Consensus pattern (23 bp):
TTATGGGCTTGGTTTTTTTACTT
Found at i:10101 original size:17 final size:18
Alignment explanation
Indices: 10079--10116 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
10069 ACAGAGAAAA
*
10079 AAAAAACAGTTAC-AGAG
1 AAAAAACAATTACAAGAG
10096 AAAAAACAATTACAAGAG
1 AAAAAACAATTACAAGAG
10114 AAA
1 AAA
10117 GAGACTCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.66, C:0.11, G:0.13, T:0.11
Consensus pattern (18 bp):
AAAAAACAATTACAAGAG
Found at i:10700 original size:2 final size:2
Alignment explanation
Indices: 10693--10724 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
10683 GACGGACTTG
10693 CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
10725 AAAGTTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:15422 original size:21 final size:21
Alignment explanation
Indices: 15396--15445 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
15386 TGCTAGGAGT
15396 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
15417 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
15438 TCATTGGA
1 TCATTGGA
15446 ATTGCCTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:17946 original size:33 final size:33
Alignment explanation
Indices: 17893--17973 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
17883 GTGTTTTAGA
** *
17893 TGTTGTTTGCAATGATACTAAACCTAATTTGA-G
1 TGTTGTTTGTGATGACACTAAACCT-ATTTGAGG
* * *
17926 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 TGTTGTTTGTGATGACACTAAACCTATTTGAGG
17959 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
17974 AACAAATTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 4 0.10
33 37 0.90
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAACCTATTTGAGG
Found at i:17985 original size:33 final size:33
Alignment explanation
Indices: 17925--18021 Score: 117
Period size: 33 Copynumber: 2.9 Consensus size: 33
17915 CCTAATTTGA
*
17925 GTGTTGTTTGTGATGACACTAAA-TCTGTTTTAG
1 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTTAG
*
17958 GTGTTGTTTGTGATGAAACAAATTCTGTTTTCG
1 GTGTTGTTTGTGATGAAACAAATTCTGTTTTAG
* **
17991 ATGTTAATTGTGATGAAAACAAATT-TGTTTT
1 GTGTTGTTTGTGATG-AAACAAATTCTGTTTT
18022 GGTTGATCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 3 0.05
33 45 0.79
34 9 0.16
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.45
Consensus pattern (33 bp):
GTGTTGTTTGTGATGAAACAAATTCTGTTTTAG
Found at i:19322 original size:21 final size:21
Alignment explanation
Indices: 19296--19408 Score: 183
Period size: 21 Copynumber: 5.4 Consensus size: 21
19286 TGCTAGGAGT
19296 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
19317 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
19338 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
19359 TCATTGAAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
**
19380 TCATTGGAGAAGGTTTTAAGC
1 TCATTGGAGAAGGTTCCAAGC
19401 TCATTGGA
1 TCATTGGA
19409 ATTGCCTAAG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 2 0.02
21 85 0.98
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:30981 original size:5 final size:5
Alignment explanation
Indices: 30971--30999 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
30961 AATATTCAAT
30971 CAAAG CAAAG CAAAG CAAAG CAAAG CAAA
1 CAAAG CAAAG CAAAG CAAAG CAAAG CAAA
31000 AATTAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.21, G:0.17, T:0.00
Consensus pattern (5 bp):
CAAAG
Found at i:46398 original size:65 final size:64
Alignment explanation
Indices: 46117--46544 Score: 321
Period size: 68 Copynumber: 6.5 Consensus size: 64
46107 ACAAAGTTCG
* * * * * *
46117 CCCTTTGACCTAAAGGGCATTTTTGGAAAGTAGAA-TAAACTGAAATGCGGAAATGATGAAACTG
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGTAAAACTAAACT-AAATGC-AAAATGACGAAACTG
46181 A
64 A
* * *
46182 CCTCTTC-ACCGAAAGGGTATTTTTGGAAATTAAAAGTAAACTCAAATGCAAGAATGAC-AGAAT
1 CC-CTTCGACCGAAAGGGTATTTTTGGAAAGTAAAACTAAACT-AAATGCAA-AATGACGA-AAC
46245 TGA
62 TGA
* * * *
46248 CCCTTTGACCGAAAGGGTATTCTTTAGAAAG-AAAGACTAGACTTAAATGCAACAACCTGATGAA
1 CCCTTCGACCGAAAGGGTATT-TTTGGAAAGTAAA-ACTAAAC-TAAATGCAA-AA--TGACGAA
46312 ACTGA
60 ACTGA
* *
46317 CCCTTCGACCGGAAGGGTATTTTTGGAAAGTAAAACTAAAACTAAATGCAAAAAGACGAAACTGA
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGTAAAACT-AAACTAAATGCAAAATGACGAAACTGA
* * * * * * * *
46382 ACCTTCAACCGAAAGGGTATCTCTGGAAACGAAAATACTAAACTTGAATGCAAAAAGACCAAAAC
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-GTAAA-ACTAAAC-TAAATGCAAAATGA-CGAAAC
*
46447 CGA
62 TGA
* * * * * *
46450 CCCTTTGACCGAAAGGGTATTTCTGG-AACTCAAAATACTAAACTTGAATGCAAAAAGAC-AAGT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGT--AAA-ACTAAAC-TAAATGCAAAATGACGAA-A
46513 CTGA
61 CTGA
* *
46517 CCCTTTGAGCGAAAGGGTA-TTTTGGAAA
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA
46545 TTTGAAAATA
Statistics
Matches: 300, Mismatches: 42, Indels: 40
0.79 0.11 0.10
Matches are distributed among these distances:
65 65 0.22
66 59 0.20
67 66 0.22
68 76 0.25
69 33 0.11
70 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.23
Consensus pattern (64 bp):
CCCTTCGACCGAAAGGGTATTTTTGGAAAGTAAAACTAAACTAAATGCAAAATGACGAAACTGA
Found at i:46432 original size:135 final size:135
Alignment explanation
Indices: 46170--46434 Score: 333
Period size: 135 Copynumber: 2.0 Consensus size: 135
46160 AATGCGGAAA
* *
46170 TGATGAAACTGACCTCTTCACCGAAAGGGTATTTTTGGAAATTAAAAGTAAACTCAAATGCAAGA
1 TGATGAAACTGACCTCTTCACCGAAAGGGTATTTTTGGAAAGTAAAACTAAACTCAAATGCAAGA
* * * ** * *
46235 ATGACAGAATTGACCCTTTGACCGAAAGGGTATTCTTTAGAAAGAAAGACTAGACTTAAATGCAA
66 AAGACAGAACTGAACCTTCAACCGAAAGGGTATTCTCTAGAAAGAAAGACTAAACTTAAATGCAA
46300 CAACC
131 CAACC
*
46305 TGATGAAACTGACC-CTTCGACCGGAAGGGTATTTTTGGAAAGTAAAACTAAAACT-AAATGCAA
1 TGATGAAACTGACCTCTTC-ACCGAAAGGGTATTTTTGGAAAGTAAAACT-AAACTCAAATGCAA
* * *
46368 -AAAGAC-GAAACTGAACCTTCAACCGAAAGGGTA-TCTCTGGAAACGAAAATACTAAACTTGAA
64 GAAAGACAG-AACTGAACCTTCAACCGAAAGGGTATTCTCTAGAAA-G-AAAGACTAAACTTAAA
46430 TGCAA
126 TGCAA
46435 AAAGACCAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
133 9 0.08
134 31 0.28
135 67 0.60
136 5 0.04
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (135 bp):
TGATGAAACTGACCTCTTCACCGAAAGGGTATTTTTGGAAAGTAAAACTAAACTCAAATGCAAGA
AAGACAGAACTGAACCTTCAACCGAAAGGGTATTCTCTAGAAAGAAAGACTAAACTTAAATGCAA
CAACC
Found at i:46530 original size:135 final size:133
Alignment explanation
Indices: 46310--46558 Score: 290
Period size: 135 Copynumber: 1.8 Consensus size: 133
46300 CAACCTGATG
* * * *
46310 AAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAGTAAAACTAAAACTAAATGCAAAAAGACG
1 AAACCGACCCTTCGACCGAAAGGGTATTTCTGGAAACTAAAACTAAAACTAAATGCAAAAAGACG
46375 AAACTGAACCTTCAACCGAAAGGGTATCTCTGGAAA-CGAAAATACTAAACTTGAATGCAAAAAG
66 AAACTGAACCTTCAACCGAAAGGGTAT-TCTGGAAATCGAAAATACTAAACTTGAATGCAAAAAG
46439 ACCA
130 ACCA
* *
46443 AAACCGACCCTTTGACCGAAAGGGTATTTCTGG-AACTCAAAA-TACTAAACTTGAATGCAAAAA
1 AAACCGACCCTTCGACCGAAAGGGTATTTCTGGAAACT-AAAACTA--AAAC-TAAATGCAAAAA
* * ** * * *
46506 GAC-AAGTCTGACCCTTTGAGCGAAAGGGTATTTTGGAAATTTGAAAATACTAA
62 GACGAA-ACTGAACCTTCAACCGAAAGGGTATTCTGGAAA-TCGAAAATACTAA
46559 CAACCTTTGG
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
132 5 0.05
133 33 0.34
134 13 0.14
135 34 0.35
136 11 0.11
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (133 bp):
AAACCGACCCTTCGACCGAAAGGGTATTTCTGGAAACTAAAACTAAAACTAAATGCAAAAAGACG
AAACTGAACCTTCAACCGAAAGGGTATTCTGGAAATCGAAAATACTAAACTTGAATGCAAAAAGA
CCA
Found at i:47529 original size:6 final size:6
Alignment explanation
Indices: 47489--47528 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
47479 AACCTAGCAT
* *
47489 TTTTTG TTCTT- TTTTTG TTTTTG TTTTTG TTTTTC TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
47529 CATCAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:50573 original size:17 final size:17
Alignment explanation
Indices: 50542--50575 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
50532 GAATTGATTA
* *
50542 AAAGAAAAGATCCAAAT
1 AAAGAAAAAACCCAAAT
50559 AAAGAAAAAACCCAAAT
1 AAAGAAAAAACCCAAAT
50576 GCCCACAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.15, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAGAAAAAACCCAAAT
Found at i:51107 original size:90 final size:90
Alignment explanation
Indices: 50913--51235 Score: 433
Period size: 90 Copynumber: 3.6 Consensus size: 90
50903 TAGCTTGATC
* * *
50913 CACCAAA-T-CAATCCTTGAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAA
1 CACCAAATTCCAAT-CTTGAAGAAATAATGCACCTCATCAAATTGATTCACCGAATCA-CCTGAA
* * *
50976 CTGTTTGAAAATGTGCTGCACCCAGCT
64 CTGTTTGAGAATATGCTGCACCGAGCT
* *
51003 CACCGAATCCCAATCTTGAAGAAATAATGCACCTCATCAAATTGATTCACCGAATCACCTGAACT
1 CACCAAATTCCAATCTTGAAGAAATAATGCACCTCATCAAATTGATTCACCGAATCACCTGAACT
51068 GTTTGAGAATATGCTGCACCGAGCT
66 GTTTGAGAATATGCTGCACCGAGCT
* *
51093 CACCAAATTCCAATCTTGAAGAAATATTGCA-CT--TCAAATTTATTCACCGAATCACCTGAACT
1 CACCAAATTCCAATCTTGAAGAAATAATGCACCTCATCAAATTGATTCACCGAATCACCTGAACT
*
51155 ATTTGAGAATATGCTGCACCGAGCT
66 GTTTGAGAATATGCTGCACCGAGCT
* * * * * *
51180 CACCGAATTCC-ATCTTGAAGAAATAACGCACCACATTAACTTGATTAACCGAATCA
1 CACCAAATTCCAATCTTGAAGAAATAATGCACCTCATCAAATTGATTCACCGAATCA
51236 ATTTTGAACT
Statistics
Matches: 207, Mismatches: 21, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
86 17 0.08
87 63 0.30
89 19 0.09
90 64 0.31
91 40 0.19
92 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (90 bp):
CACCAAATTCCAATCTTGAAGAAATAATGCACCTCATCAAATTGATTCACCGAATCACCTGAACT
GTTTGAGAATATGCTGCACCGAGCT
Found at i:51322 original size:36 final size:36
Alignment explanation
Indices: 51275--51348 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
51265 AAGTTAATTT
* *
51275 GATTCACCGAATCACACTTTGAAGAAATGCTGCACC
1 GATTCACCGAATCAAACTTTGAAGAAATACTGCACC
51311 GATTCACCGAATCAAACTTTGAAGAAATACTGCACC
1 GATTCACCGAATCAAACTTTGAAGAAATACTGCACC
51347 GA
1 GA
51349 GTTAATTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (36 bp):
GATTCACCGAATCAAACTTTGAAGAAATACTGCACC
Found at i:51338 original size:135 final size:136
Alignment explanation
Indices: 51156--51423 Score: 366
Period size: 135 Copynumber: 2.0 Consensus size: 136
51146 ACCTGAACTA
* *
51156 TTTGAGAATATGCTGCACCGAGCTCACCGAATTCCATCTTGAAGAAATAAC-GCACC-ACATTAA
1 TTTGAGAATATGCTGCACCGAGCTCACCGAATTCAAACTTGAAGAAAT-ACTGCACCGA-ATTAA
*
51219 CTTGATTAACCGAATCAATTTTGAACTGTCTAAAAAGTACGGCACCAAGTTAATTTGATTCACCG
64 CTTGATTAACCGAATCAATCTTGAACTGTCTAAAAAGTACGGCACCAAGTTAATTTGATTCACCG
51284 AATCACAC
129 AATCACAC
* *
51292 TTTGAAGAA-ATGCTGCACCGA-TTCACCGAA-TCAAACTTTGAAGAAATACTGCACCGAGTTAA
1 TTTG-AGAATATGCTGCACCGAGCTCACCGAATTCAAAC-TTGAAGAAATACTGCACCGAATTAA
* * * * * *
51354 TTTGATTCACCGAATCAATCTTGAACTGTTTAAAAAGTACTGCACCGAGTTAATTTGATTCCCCG
64 CTTGATTAACCGAATCAATCTTGAACTGTCTAAAAAGTACGGCACCAAGTTAATTTGATTCACCG
51419 AATCA
129 AATCA
51424 ATCTTGAACT
Statistics
Matches: 117, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
134 6 0.05
135 90 0.77
136 17 0.15
137 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (136 bp):
TTTGAGAATATGCTGCACCGAGCTCACCGAATTCAAACTTGAAGAAATACTGCACCGAATTAACT
TGATTAACCGAATCAATCTTGAACTGTCTAAAAAGTACGGCACCAAGTTAATTTGATTCACCGAA
TCACAC
Found at i:51400 original size:53 final size:53
Alignment explanation
Indices: 51338--51476 Score: 260
Period size: 53 Copynumber: 2.6 Consensus size: 53
51328 TTTGAAGAAA
*
51338 TACTGCACCGAGTTAATTTGATTCACCGAATCAATCTTGAACTGTTTAAAAAG
1 TACTGCACCGAGTTAATTTGATTCACCGAATCAATCTTGAACTGTCTAAAAAG
*
51391 TACTGCACCGAGTTAATTTGATTCCCCGAATCAATCTTGAACTGTCTAAAAAG
1 TACTGCACCGAGTTAATTTGATTCACCGAATCAATCTTGAACTGTCTAAAAAG
51444 TACTGCACCGAGTTAATTTGATTCACCGAATCA
1 TACTGCACCGAGTTAATTTGATTCACCGAATCA
51477 CTGAAAACTT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 83 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (53 bp):
TACTGCACCGAGTTAATTTGATTCACCGAATCAATCTTGAACTGTCTAAAAAG
Found at i:51595 original size:54 final size:54
Alignment explanation
Indices: 51537--51643 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
51527 GATCTTACTG
* *
51537 GATTACTTGAAGATAAATTTAAACCACTGTAAACTTTCTTGATTGACCTCACTA
1 GATTACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTA
* * *
51591 GATTACTTGAAGATAAGCTTAAACCACTGGAAACTTTCTTGAATGACCGCACT
1 GATTACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACT
51644 GTTAAACTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (54 bp):
GATTACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTA
Found at i:51724 original size:96 final size:96
Alignment explanation
Indices: 51550--51725 Score: 280
Period size: 96 Copynumber: 1.8 Consensus size: 96
51540 TACTTGAAGA
* * * * *
51550 TAAATTTAAACCACTGTAAACTTTCTTGATTGACCTCACTAGATTACTTGAAGATAAGCTTAAAC
1 TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTAGATCACTTGAAGATAAACTTAAAC
51615 CACTGGAAACTTTCTTGAATGACCGCACTGT
66 CACTGGAAACTTTCTTGAATGACCGCACTGT
*
51646 TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTAGATCACTTGAAGATAAACTTGAAC
1 TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTAGATCACTTGAAGATAAACTTAAAC
* *
51711 CACTGTAATCTTTCT
66 CACTGGAAACTTTCT
51726 GACAGGCCGC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 72 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (96 bp):
TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTAGATCACTTGAAGATAAACTTAAAC
CACTGGAAACTTTCTTGAATGACCGCACTGT
Found at i:51829 original size:104 final size:105
Alignment explanation
Indices: 51646--51876 Score: 270
Period size: 104 Copynumber: 2.2 Consensus size: 105
51636 ACCGCACTGT
* *
51646 TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTAGATCACTTGAAGATAAACTTGAAC
1 TAAACTTAAACCACTGGAAA--TTCTTGATTGACCGCAATAGATCACTTGAAGATAAACTTAAAC
* * *
51711 CACTGTAATCTTTCTGACAGGCCGCACCGGATCTCTTGAAGA
64 CACTGGAATCTTTCTGACAGACCGCAACGGATCTCTTGAAGA
* * * *
51753 TAAACTTAAACCACTGTAAA-T-TTGATTGATCGCAATGGATCCCTTTGAAGATAAACTTAAACC
1 TAAACTTAAACCACTGGAAATTCTTGATTGACCGCAATAGATCAC-TTGAAGATAAACTTAAACC
* * * *
51816 ATTGGGAA-CTTTCTGGCCGACCGCAATGGATCTCTTGAAGA
65 ACT-GGAATCTTTCTGACAGACCGCAACGGATCTCTTGAAGA
* *
51857 TAAACTTAAGCCACTTGAAA
1 TAAACTTAAACCACTGGAAA
51877 GTTTTTGACT
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
103 18 0.17
104 66 0.62
105 3 0.03
107 19 0.18
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (105 bp):
TAAACTTAAACCACTGGAAATTCTTGATTGACCGCAATAGATCACTTGAAGATAAACTTAAACCA
CTGGAATCTTTCTGACAGACCGCAACGGATCTCTTGAAGA
Found at i:51899 original size:53 final size:52
Alignment explanation
Indices: 51646--51900 Score: 214
Period size: 53 Copynumber: 4.8 Consensus size: 52
51636 ACCGCACTGT
* * * *
51646 TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTAGATCACTTGAAGA
1 TAAACTTAAACCACTTGAAA-TTT-TTGACTGACCGCACTGGATCTCTTGAAGA
* * * * *
51700 TAAACTTGAACCAC-TGTAATCTTTCTGACAGGCCGCACCGGATCTCTTGAAGA
1 TAAACTTAAACCACTTGAAAT-TTT-TGACTGACCGCACTGGATCTCTTGAAGA
* * * *
51753 TAAACTTAAACCAC-TGTAAA--TTTGATTGATCGCAATGGATCCCTTTGAAGA
1 TAAACTTAAACCACTTG-AAATTTTTGACTGACCGCACTGGATCTC-TTGAAGA
* * * * *
51804 TAAACTTAAACCA-TTGGGAACTTTCTGGCCGACCGCAATGGATCTCTTGAAGA
1 TAAACTTAAACCACTT--GAAATTTTTGACTGACCGCACTGGATCTCTTGAAGA
* *
51857 TAAACTTAAGCCACTTGAAAGTTTTTGACTGACTGCACTGGATC
1 TAAACTTAAACCACTTGAAA-TTTTTGACTGACCGCACTGGATC
51901 ATTAAAGTAA
Statistics
Matches: 158, Mismatches: 32, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
50 14 0.09
51 23 0.15
52 7 0.04
53 80 0.51
54 34 0.22
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (52 bp):
TAAACTTAAACCACTTGAAATTTTTGACTGACCGCACTGGATCTCTTGAAGA
Found at i:51957 original size:16 final size:16
Alignment explanation
Indices: 51936--52012 Score: 75
Period size: 16 Copynumber: 4.8 Consensus size: 16
51926 AATGGAAGCT
51936 TTGAAGCATTGAATAA
1 TTGAAGCATTGAATAA
* *
51952 TTGAAGCTTTGAATAC
1 TTGAAGCATTGAATAA
** * *
51968 TTGAAAAACTGAAGT-T
1 TTGAAGCATTGAA-TAA
51984 TTGAAGCATTGAATAA
1 TTGAAGCATTGAATAA
*
52000 TTGAAGCTTTGAA
1 TTGAAGCATTGAA
52013 GTATTGAAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
15 1 0.02
16 45 0.96
17 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (16 bp):
TTGAAGCATTGAATAA
Found at i:52018 original size:24 final size:24
Alignment explanation
Indices: 51912--52027 Score: 121
Period size: 24 Copynumber: 4.9 Consensus size: 24
51902 TTAAAGTAAA
* * * *
51912 TTGAAGCATCGGAGAATGGAAGCT
1 TTGAAGCATTGAATAATTGAAGCT
51936 TTGAAGCATTGAATAATTGAAGCT
1 TTGAAGCATTGAATAATTGAAGCT
* * * *
51960 TTGAA-TACTTGAAAAACTGAAGTT
1 TTGAAGCA-TTGAATAATTGAAGCT
51984 TTGAAGCATTGAATAATTGAAGCT
1 TTGAAGCATTGAATAATTGAAGCT
*
52008 TTGAAGTATTG-A-AATTGAAG
1 TTGAAGCATTGAATAATTGAAG
52028 AAAGGCCACC
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
22 8 0.10
23 2 0.03
24 66 0.86
25 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (24 bp):
TTGAAGCATTGAATAATTGAAGCT
Found at i:52103 original size:26 final size:25
Alignment explanation
Indices: 52056--52114 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
52046 TTCTAAAATA
*
52056 AATTGAAGAAAGACCACCCTGCGTC
1 AATTGAAGAAAGACCACCCTGCATC
* * *
52081 AACTTGAAGAAAGATCGCTCTGCATC
1 AA-TTGAAGAAAGACCACCCTGCATC
52107 AATTGAAG
1 AATTGAAG
52115 TAAACTGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (25 bp):
AATTGAAGAAAGACCACCCTGCATC
Found at i:52132 original size:35 final size:35
Alignment explanation
Indices: 52085--52162 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
52075 TGCGTCAACT
*
52085 TGAAGAAAGATCGCTCTGCATCAATTGAAG-TAAAC
1 TGAAGAAAGATCGCCCTGCATCAATTGAAGCT-AAC
* * * *
52120 TGAAGAATGATCGCCCTGGATCAGTTGCAGCTAAC
1 TGAAGAAAGATCGCCCTGCATCAATTGAAGCTAAC
52155 TGAAGAAA
1 TGAAGAAA
52163 AACCGCCTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (35 bp):
TGAAGAAAGATCGCCCTGCATCAATTGAAGCTAAC
Found at i:52178 original size:96 final size:97
Alignment explanation
Indices: 52059--52240 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 97
52049 TAAAATAAAT
* *
52059 TGAAGAAAGACCACCCTGCGTCAACTTGAAGAAAGATCGCTCTGCATCAATTG-AAGTAAACTGA
1 TGAAGAAAAACCACCCTGCGTCAACTTGAAGAAAGATCGCTCTGCATCAATTGAAACT-AACTGA
* *
52123 AG-AATGATCGCCCTGGATCAGTTGCAGCTAAC
65 AGAAAAGACCGCCCTGGATCAGTTGCAGCTAAC
* * * * * * *
52155 TGAAGAAAAACCGCCTTGGGTCAACTTGAAGCAAGATTGCTCTGGATCGATTGAAACTAACTGAA
1 TGAAGAAAAACCACCCTGCGTCAACTTGAAGAAAGATCGCTCTGCATCAATTGAAACTAACTGAA
*
52220 GAAAAGACCGCTCTGGATCAG
66 GAAAAGACCGCCCTGGATCAG
52241 CTTGAACCAA
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
96 53 0.74
97 19 0.26
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (97 bp):
TGAAGAAAAACCACCCTGCGTCAACTTGAAGAAAGATCGCTCTGCATCAATTGAAACTAACTGAA
GAAAAGACCGCCCTGGATCAGTTGCAGCTAAC
Found at i:52281 original size:62 final size:61
Alignment explanation
Indices: 52128--52271 Score: 184
Period size: 62 Copynumber: 2.3 Consensus size: 61
52118 ACTGAAGAAT
* * * * *
52128 GATCGCCCTGGATC-AGTTGCAGCTAACTGAAGAAAAACCGCCTTGGGTCAACTTGAAGCAA
1 GATCGCTCTGGATCGA-TTGAAACTAACTGAAGAAAAACCGCCTTGGATCAACTTGAACCAA
* *
52189 GATTGCTCTGGATCGATTGAAACTAACTGAAGAAAAGACCG-CTCTGGATCAGCTTGAACCAA
1 GATCGCTCTGGATCGATTGAAACTAACTGAAGAAAA-ACCGCCT-TGGATCAACTTGAACCAA
52251 GATCGCTCTGGATCGATTGAA
1 GATCGCTCTGGATCGATTGAA
52272 GTAAACTGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
61 32 0.44
62 40 0.56
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (61 bp):
GATCGCTCTGGATCGATTGAAACTAACTGAAGAAAAACCGCCTTGGATCAACTTGAACCAA
Found at i:52314 original size:35 final size:35
Alignment explanation
Indices: 52261--52334 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
52251 GATCGCTCTG
* *
52261 GATCGATTGAAGTAAACTGAA-AAATGATCACCCTA
1 GATCGATTGAACTAAACTGAATAAA-GACCACCCTA
*
52296 GATCGATTGAAACT-AACTGAATAGAGACCACCCTA
1 GATCGATTG-AACTAAACTGAATAAAGACCACCCTA
52331 GATC
1 GATC
52335 TATCATGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 29 0.85
36 5 0.15
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (35 bp):
GATCGATTGAACTAAACTGAATAAAGACCACCCTA
Found at i:53234 original size:13 final size:13
Alignment explanation
Indices: 53216--53241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53206 GGAATGCAAT
53216 TCATTTTCAAAAC
1 TCATTTTCAAAAC
53229 TCATTTTCAAAAC
1 TCATTTTCAAAAC
53242 ATTTACAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
TCATTTTCAAAAC
Found at i:53672 original size:21 final size:20
Alignment explanation
Indices: 53636--53679 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
53626 TCTAAAACCT
*
53636 TTTTGAGAAAACATTTTTTC
1 TTTTGAAAAAACATTTTTTC
* *
53656 TTTTGAAAAAACAATTTTTA
1 TTTTGAAAAAACATTTTTTC
53676 TTTT
1 TTTT
53680 AGGGACTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTTGAAAAAACATTTTTTC
Found at i:54346 original size:14 final size:13
Alignment explanation
Indices: 54321--54365 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
54311 TTAAAAACTC
54321 AAAACC-TTTTTG
1 AAAACCATTTTTG
54333 AAAACTCATTTTTG
1 AAAAC-CATTTTTG
*
54347 AAAACCTTTTCTTG
1 AAAACCATTT-TTG
54361 AAAAC
1 AAAAC
54366 ACTTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 5 0.17
13 5 0.17
14 19 0.66
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (13 bp):
AAAACCATTTTTG
Found at i:54371 original size:26 final size:25
Alignment explanation
Indices: 54321--54371 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
54311 TTAAAAACTC
*
54321 AAAACCTTTTTGAAAACTCATTTTTG
1 AAAACCTTTTTGAAAAC-CACTTTTG
54347 AAAACCTTTTCTTGAAAA-CACTTTT
1 AAAACC-TTT-TTGAAAACCACTTTT
54372 TTTTTTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 12 0.55
27 3 0.14
28 7 0.32
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (25 bp):
AAAACCTTTTTGAAAACCACTTTTG
Found at i:57245 original size:65 final size:65
Alignment explanation
Indices: 57158--57389 Score: 202
Period size: 66 Copynumber: 3.5 Consensus size: 65
57148 ACAAAGTTCG
* * * *
57158 CCCTTTGACCTAAAGGGCATTTTTGGAAAGTAGAATAAACTAAAATGCGGA-AATGATGAAAATG
1 CCCTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTAAAATGC-AACAATGATGAAAATG
57222 A
65 A
* * * * *
57223 CCCTTTCACCGAAAGGGTATTTTTGGAAA-TCAAAAGTAAACTCAAATGCAAGAATGA-CAGAAT
1 CCCTTTCACCGAAAGGGTATTTTTGGAAAGT-AGAA-TAAACTAAAATGCAACAATGATGA-AAA
57286 TGA
63 TGA
* * ** * *
57289 CCCTTTGACCGAAAGGGTATTCTTTGGAAAGAATGGCTAGACTTAAATGCAACAACCTGATGAAA
1 CCCTTTCACCGAAAGGGTATT-TTTGGAAAGTA-GAATAAACTAAAATGCAACAA--TGATGAAA
*
57354 CTGA
62 ATGA
*
57358 CCC-TTCGACCGGAAGGGTATTTTTGGAAAGTA
1 CCCTTTC-ACCGAAAGGGTATTTTTGGAAAGTA
57390 AAACTACAAC
Statistics
Matches: 135, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
64 1 0.01
65 31 0.23
66 42 0.31
67 24 0.18
68 12 0.09
69 24 0.18
70 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (65 bp):
CCCTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTAAAATGCAACAATGATGAAAATGA
Found at i:57514 original size:68 final size:68
Alignment explanation
Indices: 57427--57582 Score: 221
Period size: 68 Copynumber: 2.3 Consensus size: 68
57417 ACTGACTATC
57427 TCTGGAAA-CGAAAATACTAAACTTGAAA-GCAAAAAGACCAAAACCGACCCTTTGACCGAAAGG
1 TCTGGAAATCGAAAATACTAAACTT-AAATGCAAAAAGA-CAAAACCGACCCTTTGACCGAAAGG
57490 ATATT
64 ATATT
* * *
57495 TCTGGAAATC-AAAATACTAAACTTAAATGCAAAAAGACAAGACTGACCCTTTGACCGAAAGGGT
1 TCTGGAAATCGAAAATACTAAACTTAAATGCAAAAAGACAAAACCGACCCTTTGACCGAAAGGAT
57559 ATT
66 ATT
*
57562 T-TGGAAATTTGAAAATACTAA
1 TCTGGAAA-TCGAAAATACTAA
57583 CAACCTTTGG
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
66 6 0.08
67 32 0.40
68 41 0.51
69 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (68 bp):
TCTGGAAATCGAAAATACTAAACTTAAATGCAAAAAGACAAAACCGACCCTTTGACCGAAAGGAT
ATT
Found at i:58928 original size:12 final size:12
Alignment explanation
Indices: 58911--58936 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58901 AGTATTAAGA
58911 ATTTAGCTACTC
1 ATTTAGCTACTC
58923 ATTTAGCTACTC
1 ATTTAGCTACTC
58935 AT
1 AT
58937 GGATTTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTTAGCTACTC
Found at i:72007 original size:37 final size:36
Alignment explanation
Indices: 71956--72139 Score: 208
Period size: 37 Copynumber: 4.8 Consensus size: 36
71946 GCACAATGGT
*
71956 AATAGTAATCAGTAAAGAATAAAAGAGTAATCAGTAA
1 AATAGTAATCAGTAAAGAGT-AAAGAGTAATCAGTAA
71993 AATAGTAA-CAAGTAAAAGAGTAAAGAGTAATCAGTAA
1 AATAGTAATC-AGT-AAAGAGTAAAGAGTAATCAGTAA
*
72030 AATAGTAATCAGTGAAAGAGTAAAGAGAAATCAGTAAAAGA
1 AATAGTAATCAGT-AAAGAGTAAAGAGTAATCAGT---A-A
*
72071 GTAATAGTAATCAGTAAAGAGTAAAGATTAATCAGTAA
1 --AATAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAA
* **
72109 AAGAGTAAAGAGTAAAGAGTAAAAGAGTAAT
1 AATAGTAATCAGTAAAGAGT-AAAGAGTAAT
72140 AATGGTCAGT
Statistics
Matches: 128, Mismatches: 9, Indels: 20
0.82 0.06 0.13
Matches are distributed among these distances:
36 18 0.14
37 67 0.52
38 8 0.06
39 1 0.01
40 1 0.01
41 1 0.01
42 19 0.15
43 13 0.10
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.20
Consensus pattern (36 bp):
AATAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAA
Found at i:72063 original size:22 final size:22
Alignment explanation
Indices: 72036--72138 Score: 122
Period size: 22 Copynumber: 4.8 Consensus size: 22
72026 GTAAAATAGT
*
72036 AATCAGTGAAAGAGTAAAGAGA
1 AATCAGTAAAAGAGTAAAGAGA
* *
72058 AATCAGTAAAAGAGT-AATAGT
1 AATCAGTAAAAGAGTAAAGAGA
**
72079 AATCAGT-AAAGAGTAAAGATT
1 AATCAGTAAAAGAGTAAAGAGA
72100 AATCAGTAAAAGAGTAAAGAGTA
1 AATCAGTAAAAGAGTAAAGAG-A
*
72123 AA-GAGTAAAAGAGTAA
1 AATCAGTAAAAGAGTAA
72139 TAATGGTCAG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.10
21 22 0.31
22 39 0.56
23 2 0.03
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.18
Consensus pattern (22 bp):
AATCAGTAAAAGAGTAAAGAGA
Found at i:72115 original size:64 final size:64
Alignment explanation
Indices: 72033--72168 Score: 202
Period size: 64 Copynumber: 2.1 Consensus size: 64
72023 TCAGTAAAAT
* *
72033 AGTAATCAGTGAAAGAGTAAAGAG-AAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAGTAAAG
1 AGTAATCAGTAAAAGAGTAAAGAGTAAA-CAGTAAAAGAGTAATAATAATCAGTAAAGAGTAAAG
* * **
72097 ATTAATCAGTAAAAGAGTAAAGAGTAAAGAGTAAAAGAGTAATAATGGTCAGTAAAGAGTAAAG
1 AGTAATCAGTAAAAGAGTAAAGAGTAAACAGTAAAAGAGTAATAATAATCAGTAAAGAGTAAAG
72161 AGTAATCA
1 AGTAATCA
72169 AGGAAGAGTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
64 61 0.95
65 3 0.05
ACGTcount: A:0.53, C:0.04, G:0.23, T:0.20
Consensus pattern (64 bp):
AGTAATCAGTAAAAGAGTAAAGAGTAAACAGTAAAAGAGTAATAATAATCAGTAAAGAGTAAAG
Found at i:72178 original size:28 final size:29
Alignment explanation
Indices: 72116--72179 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
72106 TAAAAGAGTA
72116 AAGAGTAAAGAGTAAAAGAGTAATAATGG
1 AAGAGTAAAGAGTAAAAGAGTAATAATGG
**
72145 -TCAGTAAAGAGT-AAAGAGTAATCAA-GG
1 AAGAGTAAAGAGTAAAAGAGTAAT-AATGG
72172 AAGAGTAA
1 AAGAGTAA
72180 TAGTAATTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.53, C:0.03, G:0.27, T:0.17
Consensus pattern (29 bp):
AAGAGTAAAGAGTAAAAGAGTAATAATGG
Found at i:72214 original size:84 final size:85
Alignment explanation
Indices: 72058--72253 Score: 215
Period size: 84 Copynumber: 2.3 Consensus size: 85
72048 AGTAAAGAGA
* *
72058 AATCAGTAAAAGAGT-AATAGTAATC-AGTAAAGAGTAAAGATTAATCAGTAAAAGAGTAAAGAG
1 AATCAGT-AAAGAGTAAAGAGTAATCAAGTAAAGAGTAAAGA-TAATCAGTAAAAGAGTAAACAG
*
72121 TAAAGAGTAAAA-GAGTAATAAT
64 TAAACAGTAAAATGA-TAATAAT
** * *
72143 GGTCAGTAAAGAGTAAAGAGTAATCAAG-GAAGAGTAATAG-TAATTAGTAAAAGAGTAAACAGT
1 AATCAGTAAAGAGTAAAGAGTAATCAAGTAAAGAGTAA-AGATAATCAGTAAAAGAGTAAACAGT
* *
72206 GAACAGTAAAATGATAATAGT
65 AAACAGTAAAATGATAATAAT
*
72227 AATCAATAAAGAGTAAATG-GTAATCAA
1 AATCAGTAAAGAGTAAA-GAGTAATCAA
72254 TAATTAAAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
84 65 0.69
85 25 0.27
86 4 0.04
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (85 bp):
AATCAGTAAAGAGTAAAGAGTAATCAAGTAAAGAGTAAAGATAATCAGTAAAAGAGTAAACAGTA
AACAGTAAAATGATAATAAT
Found at i:72341 original size:36 final size:35
Alignment explanation
Indices: 72298--72366 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
72288 ATTAAAAAAT
* *
72298 TAAAAATGGCATTCAGTAATTAAAGTGAAAAAAGAG
1 TAAAAATGGCACTCAATAATTAAAGT-AAAAAAGAG
*
72334 TAAAAATGGTACTCAATAATTAAAGTAAAAAAG
1 TAAAAATGGCACTCAATAATTAAAGTAAAAAAG
72367 GCAAAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 7 0.23
36 23 0.77
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.23
Consensus pattern (35 bp):
TAAAAATGGCACTCAATAATTAAAGTAAAAAAGAG
Found at i:72374 original size:35 final size:36
Alignment explanation
Indices: 72299--72377 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
72289 TTAAAAAATT
* * *
72299 AAAAATGGCATTCAGTAATTAAAGTGAAAAAAGAGT
1 AAAAATGGCACTCAATAATTAAAGTGAAAAAAGAGA
*
72335 AAAAATGGTACTCAATAATTAAAGT-AAAAAAG-GCA
1 AAAAATGGCACTCAATAATTAAAGTGAAAAAAGAG-A
72370 AAAAATGG
1 AAAAATGG
72378 AAACCAGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.03
35 15 0.39
36 22 0.58
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (36 bp):
AAAAATGGCACTCAATAATTAAAGTGAAAAAAGAGA
Found at i:72416 original size:29 final size:27
Alignment explanation
Indices: 72358--72447 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
72348 AATAATTAAA
* * * *
72358 GTAAAAAAG-GCAAAAAATGGAAACCA
1 GTAAAAAAGAGTAAAAAATGGTAATCG
* *
72384 GTAAAAAATAGGTAAGAAAATGGTAATCT
1 GTAAAAAAGA-GTAA-AAAATGGTAATCG
*
72413 GTAAAAAAGAGTAAAAATTGGTAATCG
1 GTAAAAAAGAGTAAAAAATGGTAATCG
72440 GTAAAAAA
1 GTAAAAAA
72448 AAAGAGTAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 8 0.15
27 19 0.36
28 7 0.13
29 19 0.36
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.18
Consensus pattern (27 bp):
GTAAAAAAGAGTAAAAAATGGTAATCG
Found at i:73621 original size:30 final size:31
Alignment explanation
Indices: 73551--73624 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
73541 TCATTTGTCC
* * *
73551 ATATCCTAAAATGACACAAGTCGATAACGTT
1 ATATCCTGAATTGACACAAGTCGATAACGGT
*
73582 ATATTCTGAATTGACACAAGTCG-TAACGGT
1 ATATCCTGAATTGACACAAGTCGATAACGGT
*
73612 GTATCCTGAATTG
1 ATATCCTGAATTG
73625 CATTTTCGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 17 0.46
31 20 0.54
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (31 bp):
ATATCCTGAATTGACACAAGTCGATAACGGT
Found at i:75471 original size:52 final size:51
Alignment explanation
Indices: 75408--75710 Score: 464
Period size: 52 Copynumber: 5.8 Consensus size: 51
75398 AAAATGCTGT
* * *
75408 TTGAATGCTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAATATCTAAA
1 TTGAAT-CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
75460 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
1 TTGAAT-CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
*
75512 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
1 TTGAA-TCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
* * *
75564 GTGAACGCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAATACCTAAA
1 TTGAA-TCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
* *
75616 TTGAACTCTCTGAAAACTTGATGGGAACTATCCCACTTTGAAAAGACCTAAA
1 TTGAA-TCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
75668 TTGAACTCTTTG-AAACTTGATGGGAACTTTCCCACTTTGAAAA
1 TTGAA-TCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
75711 CTTTGAAGGG
Statistics
Matches: 235, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
51 30 0.13
52 205 0.87
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (51 bp):
TTGAATCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
Found at i:75654 original size:156 final size:155
Alignment explanation
Indices: 75409--75710 Score: 525
Period size: 156 Copynumber: 1.9 Consensus size: 155
75399 AAATGCTGTT
* * *
75409 TGAATGCTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAATATCTAAATTGAATACTTTGAA
1 TGAACGCTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAATACCTAAATTGAATACTCTGAA
*
75474 AACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACACTTTGAAAACTTGATGGGAA
66 AACTTGATGGGAACTATCCCACTTTGAAAAGACCTAAATTGAACACTTTG-AAACTTGATGGGAA
75539 CTTTCCCACTTTGAAAAGACCTAAAG
130 CTTTCCCACTTTGAAAAGACCTAAAG
*
75565 TGAACGCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAATACCTAAATTGAACT-CTCTGA
1 TGAACGCTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAATACCTAAATTGAA-TACTCTGA
*
75629 AAACTTGATGGGAACTATCCCACTTTGAAAAGACCTAAATTGAACTCTTTGAAACTTGATGGGAA
65 AAACTTGATGGGAACTATCCCACTTTGAAAAGACCTAAATTGAACACTTTGAAACTTGATGGGAA
75694 CTTTCCCACTTTGAAAA
130 CTTTCCCACTTTGAAAA
75711 CTTTGAAGGG
Statistics
Matches: 139, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
155 31 0.22
156 107 0.77
157 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (155 bp):
TGAACGCTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAATACCTAAATTGAATACTCTGAA
AACTTGATGGGAACTATCCCACTTTGAAAAGACCTAAATTGAACACTTTGAAACTTGATGGGAAC
TTTCCCACTTTGAAAAGACCTAAAG
Found at i:78364 original size:53 final size:53
Alignment explanation
Indices: 78277--78383 Score: 121
Period size: 53 Copynumber: 2.0 Consensus size: 53
78267 TATGAGGTAC
* * *
78277 GAGTTATTTTTTATAGAATTAAGTATAGTTGAAATTGTTTTTTTATAC-TTGTT
1 GAGTTATTTTTTATAGAATTAAGTATAGTCGAAATTG-ATTCTTATACTTTGTT
* *
78330 GAGTTATTTTTTATAGAATTGAG--TGGCTGCGAAATTGATTCTTATACTTTGTT
1 GAGTTATTTTTTATAGAATTAAGTATAG-T-CGAAATTGATTCTTATACTTTGTT
78383 G
1 G
78384 TGCAATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
51 2 0.04
52 9 0.20
53 35 0.76
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (53 bp):
GAGTTATTTTTTATAGAATTAAGTATAGTCGAAATTGATTCTTATACTTTGTT
Found at i:86775 original size:22 final size:22
Alignment explanation
Indices: 86725--86777 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
86715 TTTATTCTGA
*
86725 TTAATTGTTTTCTTTCATTTTC
1 TTAATTGTTTTCTTTCATATTC
*
86747 TTGATTGTTTTCTTAT-ATAATT-
1 TTAATTGTTTTCTT-TCAT-ATTC
86769 TTAATTGTT
1 TTAATTGTT
86778 AGTTTGCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.66
Consensus pattern (22 bp):
TTAATTGTTTTCTTTCATATTC
Found at i:98991 original size:88 final size:88
Alignment explanation
Indices: 98842--99014 Score: 337
Period size: 88 Copynumber: 2.0 Consensus size: 88
98832 GCTTGAACTC
98842 ATCTTCTAAATAATAAAGATGGCCATCGAGCGGTGGATTCTTGTCTTTTAAGTTCAAACTTGACT
1 ATCTTCTAAATAATAAAGATGGCCATCGAGCGGTGGATTCTTGTCTTTTAAGTTCAAACTTGACT
98907 CGACGAATCAATATTATAAGTCT
66 CGACGAATCAATATTATAAGTCT
*
98930 ATCTTCTAGATAATAAAGATGGCCATCGAGCGGTGGATTCTTGTCTTTTAAGTTCAAACTTGACT
1 ATCTTCTAAATAATAAAGATGGCCATCGAGCGGTGGATTCTTGTCTTTTAAGTTCAAACTTGACT
98995 CGACGAATCAATATTATAAG
66 CGACGAATCAATATTATAAG
99015 CCTGGAATTT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (88 bp):
ATCTTCTAAATAATAAAGATGGCCATCGAGCGGTGGATTCTTGTCTTTTAAGTTCAAACTTGACT
CGACGAATCAATATTATAAGTCT
Found at i:102532 original size:2 final size:2
Alignment explanation
Indices: 102527--102561 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
102517 ACACAGAATA
*
102527 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
102562 AATTCAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:104444 original size:2 final size:2
Alignment explanation
Indices: 104437--104477 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
104427 ATGTAAGTCA
104437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
104478 AGTGATATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:106956 original size:3 final size:3
Alignment explanation
Indices: 106943--106972 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
106933 ATGAAATGGG
*
106943 ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
106973 TTAAAAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:118171 original size:3 final size:3
Alignment explanation
Indices: 118163--118214 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
118153 AAAACCAATA
118163 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
118211 TAT T
1 TAT T
118215 TAGAATTTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:118242 original size:13 final size:13
Alignment explanation
Indices: 118224--118248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
118214 TTAGAATTTC
118224 AAATAATATTTAT
1 AAATAATATTTAT
118237 AAATAATATTTA
1 AAATAATATTTA
118249 AAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:121635 original size:14 final size:14
Alignment explanation
Indices: 121612--121669 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
121602 TCAAATTTTT
121612 TAAAATTAAAATGG
1 TAAAATTAAAATGG
* **
121626 TAAAAATAAAATATTTT
1 T-AAAATTAAA-A-TGG
121643 TAAAATTAAAATGG
1 TAAAATTAAAATGG
121657 TAAAATTAAAATG
1 TAAAATTAAAATG
121670 ATATTTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 15 0.43
15 9 0.26
16 9 0.26
17 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (14 bp):
TAAAATTAAAATGG
Found at i:121644 original size:31 final size:30
Alignment explanation
Indices: 121604--121668 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 30
121594 AAAAAGTCTC
121604 AAATTTTTTAAAATTAAAATGGTAAAAATA
1 AAATTTTTTAAAATTAAAATGGTAAAAATA
*
121634 AAATATTTTTAAAATTAAAATGGTAAAATTA
1 AAAT-TTTTTAAAATTAAAATGGTAAAAATA
121665 AAAT
1 AAAT
121669 GATATTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (30 bp):
AAATTTTTTAAAATTAAAATGGTAAAAATA
Found at i:121984 original size:25 final size:24
Alignment explanation
Indices: 121940--122000 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 24
121930 ATTGTTGGTT
* *
121940 TATTATAT-TA-AATTATTATTAG
1 TATTATATATATAATAATTATTAA
121962 TATTATATATATAATAATATATTAA
1 TATTATATATATAATAAT-TATTAA
121987 TATATAATATATAT
1 TAT-T-ATATATAT
122001 GTAGTTGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 8 0.25
23 2 0.06
24 5 0.16
25 8 0.25
26 1 0.03
27 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTATATATATAATAATTATTAA
Found at i:122254 original size:11 final size:11
Alignment explanation
Indices: 122211--122248 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
122201 TTTCTATATA
*
122211 AAATAAATTAT
1 AAATTAATTAT
122222 CAAA-TAATTAT
1 -AAATTAATTAT
122233 AAATTAATTAT
1 AAATTAATTAT
122244 AAATT
1 AAATT
122249 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:122882 original size:6 final size:7
Alignment explanation
Indices: 122866--122891 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
122856 TTCTCACATA
122866 TTTTGAT
1 TTTTGAT
122873 TTTTGAT
1 TTTTGAT
122880 TTTTGAT
1 TTTTGAT
122887 TTTTG
1 TTTTG
122892 CATCTTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.73
Consensus pattern (7 bp):
TTTTGAT
Found at i:128335 original size:78 final size:77
Alignment explanation
Indices: 128180--128365 Score: 250
Period size: 78 Copynumber: 2.4 Consensus size: 77
128170 GCAATCTTAA
* *
128180 ACAACACCTTCCGATTGA-GAAGGGCAAA-TTGGTGAATGCTGACAACACCTTCCGGGGGGAAGG
1 ACAACACCTTCCGA-TGAGGAAGGGCAAACTAGAT--AT--TGACAACACCTTCCGGGGGGAAGG
128243 GCAAACTAAGGATGCTG
61 GCAAACTAAGGATGCTG
* * *
128260 ACAACACCTTCCTATGGGGAAGGGCAAACTAGATATTGACGACACCTTCCGGTGGGGAAGGGCAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTAGATATTGACAACACCTTCCGG-GGGGAAGGGCAA
*
128325 ACTGAGGATGCTG
65 ACTAAGGATGCTG
128338 ACAACACCTTCCGATGAGGAAGGGCAAA
1 ACAACACCTTCCGATGAGGAAGGGCAAA
128366 TTGTACAAAG
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
77 15 0.16
78 50 0.53
79 4 0.04
80 23 0.24
81 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.30, T:0.17
Consensus pattern (77 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTAGATATTGACAACACCTTCCGGGGGGAAGGGCAAA
CTAAGGATGCTG
Found at i:128424 original size:41 final size:40
Alignment explanation
Indices: 127854--128455 Score: 335
Period size: 40 Copynumber: 14.9 Consensus size: 40
127844 CAGGGATAGG
*
127854 AACAACACCTTCCGACGAGGAAGGGCAAACTGGGAAAAGTTG-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGG-AAA--TGC
* * * * * *
127896 AACAACGCCTTTC-AGTGGGGAAAGGCAGACTTGGG-AATGATA
1 AACAACACCTTCCGA-TGAGGAAGGGCAAAC-TGGGAAATG--C
* * *
127938 AATAACACCTTCCGATGAGGAAGGGCAAACTTGG-AATGTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG-C
* **
127978 AACAACACCTTCCGATGAGGAAGGGCAAACTGGTGAACTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAAATGC
* * *
128019 AACAAAACCTTCCGATGAGGATGGGCAAACTGGTAAACT-C
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAA-TGC
* * * ** *
128059 GACAACACCTTCTGATGAGGAAGGGCAAAGTGATAAGCT-C
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ATGC
* * *
128099 AACAACACCTTCCAATGAGGAAGGGCAGACTAGGAAACT-C
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAA-TGC
* * * * * **
128139 AACGACACCTCCCGATGAGGAAGGGC-AACTCGCAATCTTA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ATGC
*
128179 AACAACACCTTCCGATTGA-GAAGGGCAAATTGGTG-AATGC
1 AACAACACCTTCCGA-TGAGGAAGGGCAAACTGG-GAAATGC
* * * *
128219 TGACAACACCTTCCG-GGGGGAAGGGCAAACTAAGG--ATGC
1 -AACAACACCTTCCGATGAGGAAGGGCAAACT-GGGAAATGC
* * * * *
128258 TGACAACACCTTCCTATGGGGAAGGGCAAACT-AGATATTG-
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGGGA-AATGC
* * *
128298 -ACGACACCTTCCGGTGGGGAAGGGCAAACTGAGG--ATGC
1 AACAACACCTTCCGATGAGGAAGGGCAAACTG-GGAAATGC
* * ** *
128336 TGACAACACCTTCCGATGAGGAAGGGCAAATTGTACAAAGGC
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTG-GGAAATGC
* *
128378 AACAACACC-TCCGGATGAGGAAGGGCAAACTGGGAAAAGA
1 AACAACACCTTCC-GATGAGGAAGGGCAAACTGGGAAATGC
* * * *
128418 AGACAACACCTCCCAACCG-GGGAGGGCAAACTGGGAAA
1 A-ACAACACCTTCCGA-TGAGGAAGGGCAAACTGGGAAA
128456 CGTAAAGAAA
Statistics
Matches: 440, Mismatches: 86, Indels: 69
0.74 0.14 0.12
Matches are distributed among these distances:
37 2 0.00
38 28 0.06
39 28 0.06
40 204 0.46
41 121 0.28
42 52 0.12
43 5 0.01
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.15
Consensus pattern (40 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATGC
Found at i:128519 original size:46 final size:46
Alignment explanation
Indices: 128460--129022 Score: 628
Period size: 46 Copynumber: 12.7 Consensus size: 46
128450 GGGAAACGTA
** * * *
128460 AAGAAAACTGGGACCTTCCAACCGGGAAGGGGCATTTTCGGTAATG
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* ** * * *
128506 AAGAAGACGGGGACCTTTCAACCGGGAAGGGGCATTTTTGGAAATA
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* * *
128552 AAGAAGACGAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATA
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
*
128598 AAGAAAACAAAGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT-
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
*
128643 --GAAAACAAGGACCTTCCAATCAGGAAGGGGCATTTTTGGAAAT-
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* * *
128686 --GAAAATAGGGACCTTCCAACCAGGAAGGGGCATTTTT-GATAATA
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGA-AATG
** *
128730 AAGAAAACAACAACCTTCAAACCAGGAAGGGGCATTTTTGGAAAT-
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* *
128775 --GAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATA
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* * *
128819 AAGAACATAAGGACCTTCCAACCAAGAAGGGGCATTTTTGGAAAT-
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
** ** * * *
128864 --GAAAATTAGGACCTTCCAAATACGAATGGGCATTTTTGGAAATA
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* *
128908 AAGAAAATAAGGACCTTCCAACCAGGAAAGGGCA-TTTTGGAAAT-
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
*
128952 --GAAAACAGGGACCTTCCAACCAGGAAGGGGCA-TTTTGGAAAT-
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
*
128994 --GAAAATAAGGACCTTCCAACCAGGAAGGG
1 AAGAAAACAAGGACCTTCCAACCAGGAAGGG
129023 ACCTTCCAAA
Statistics
Matches: 462, Mismatches: 44, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
42 68 0.15
43 154 0.33
45 10 0.02
46 228 0.49
47 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (46 bp):
AAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
Found at i:128736 original size:89 final size:89
Alignment explanation
Indices: 128458--129022 Score: 727
Period size: 89 Copynumber: 6.4 Consensus size: 89
128448 CTGGGAAACG
** * * * *
128458 TAAAGAAAACTGGGACCTTCCAACCGGGAAGGGGCATTTTCGGTAATGAAGAAGACGGGGACCTT
1 TAAAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAA-AATA--GGGACCTT
* *
128523 TCAACCGGGAAGGGGCATTTTTGGAAA
63 CCAACCAGGAAGGGGCATTTTTGGAAA
* * * **
128550 TAAAGAAGACGAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAACAAAGACCTT
1 TAAAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT---GAAAATAGGGACCTT
128615 CCAACCAGGAAGGGGCATTTTTGGAAA
63 CCAACCAGGAAGGGGCATTTTTGGAAA
*
128642 T---GAAAACAAGGACCTTCCAATCAGGAAGGGGCATTTTTGGAAATGAAAATAGGGACCTTCCA
1 TAAAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAATAGGGACCTTCCA
128704 ACCAGGAAGGGGCATTTTT-GATAA
66 ACCAGGAAGGGGCATTTTTGGA-AA
** * *
128728 TAAAGAAAACAACAACCTTCAAACCAGGAAGGGGCATTTTTGGAAATGAAAATAAGGACCTTCCA
1 TAAAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAATAGGGACCTTCCA
128793 ACCAGGAAGGGGCATTTTTGGAAA
66 ACCAGGAAGGGGCATTTTTGGAAA
* * *
128817 TAAAGAACATAAGGACCTTCCAACCAAGAAGGGGCATTTTTGGAAATGAAAATTA-GGACCTTCC
1 TAAAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAA-TAGGGACCTTCC
** * *
128881 AAATACGAATGGGCATTTTTGGAAA
65 AACCAGGAAGGGGCATTTTTGGAAA
* * *
128906 TAAAGAAAATAAGGACCTTCCAACCAGGAAAGGGCA-TTTTGGAAATGAAAACAGGGACCTTCCA
1 TAAAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAATAGGGACCTTCCA
128970 ACCAGGAAGGGGCA-TTTTGGAAA
66 ACCAGGAAGGGGCATTTTTGGAAA
*
128993 T---GAAAATAAGGACCTTCCAACCAGGAAGGG
1 TAAAGAAAACAAGGACCTTCCAACCAGGAAGGG
129023 ACCTTCCAAA
Statistics
Matches: 422, Mismatches: 41, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
84 28 0.07
85 2 0.00
86 37 0.09
87 11 0.03
88 35 0.08
89 226 0.54
90 4 0.01
92 73 0.17
94 3 0.01
95 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (89 bp):
TAAAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAATAGGGACCTTCCA
ACCAGGAAGGGGCATTTTTGGAAA
Found at i:130531 original size:21 final size:22
Alignment explanation
Indices: 130489--130528 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
130479 TTAACTGGGG
130489 GTTTTGATTTTTTGGATTAAGT
1 GTTTTGATTTTTTGGATTAAGT
130511 GTTTTG-TTTTTTGG-TTAA
1 GTTTTGATTTTTTGGATTAA
130529 AGTATTTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (22 bp):
GTTTTGATTTTTTGGATTAAGT
Found at i:134260 original size:22 final size:22
Alignment explanation
Indices: 134235--134295 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
134225 AATATGCATG
*
134235 AAAATTCGAAATTTTATCTTCA
1 AAAATTCAAAATTTTATCTTCA
* *
134257 AAAA-TCCATATTTTATCTTCA
1 AAAATTCAAAATTTTATCTTCA
*
134278 ATTAATT-AAAATTTTATC
1 A-AAATTCAAAATTTTATC
134296 AAAAATTGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 16 0.50
22 15 0.47
23 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTCAAAATTTTATCTTCA
Found at i:135591 original size:17 final size:18
Alignment explanation
Indices: 135556--135593 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
135546 AATTAGTGTA
*
135556 AAAATTAAAAATAATAAT
1 AAAATCAAAAATAATAAT
*
135574 AAAATCAAAATTAA-AAT
1 AAAATCAAAAATAATAAT
135591 AAA
1 AAA
135594 TATGCAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATCAAAAATAATAAT
Found at i:140009 original size:19 final size:18
Alignment explanation
Indices: 139976--140011 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
139966 TGAAAATAAT
139976 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
139994 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
140012 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:142497 original size:76 final size:76
Alignment explanation
Indices: 142366--142657 Score: 458
Period size: 76 Copynumber: 3.8 Consensus size: 76
142356 AGATTAACAA
*
142366 GGGTGCCAATCTAGGCACTCAGCCGTCGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGG
1 GGGTGCCAATCTAGGCACTCAGCCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGG
**
142431 TGGTTGAACGG
66 TGAATGAACGG
* * * * *
142442 GGGTGCCAATCTAGGCATTCAGCTGTTGAGTGAGTGGCGTTTGTGTGGACACTCTGCCTCACTGG
1 GGGTGCCAATCTAGGCACTCAGCCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGG
142507 TGAATGAACGG
66 TGAATGAACGG
* * * * *
142518 GGGTGCCAATCTAGGCACTCAGTCGTTGAGTGAGTGGCGTTTGCGTGGATGCTATGCCTCACTGA
1 GGGTGCCAATCTAGGCACTCAGCCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGG
142583 TGAATGAACGG
66 TGAATGAACGG
*
142594 GGGTGCCAATCTAGGCACTTAGCCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTG
1 GGGTGCCAATCTAGGCACTCAGCCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTG
142658 ATGCTCTGAT
Statistics
Matches: 195, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 195 1.00
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (76 bp):
GGGTGCCAATCTAGGCACTCAGCCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGG
TGAATGAACGG
Found at i:153412 original size:15 final size:15
Alignment explanation
Indices: 153394--153424 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
153384 TTGTTTCTAG
153394 TTTAACTGTTTTCTT
1 TTTAACTGTTTTCTT
*
153409 TTTAATTGTTTTCTT
1 TTTAACTGTTTTCTT
153424 T
1 T
153425 CAACCTCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTAACTGTTTTCTT
Found at i:153791 original size:26 final size:26
Alignment explanation
Indices: 153762--153815 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
153752 TTAATTTTTT
153762 GAGTCTTGCGCTTTT-GAAAAAAAAAA
1 GAGT-TTGCGCTTTTCGAAAAAAAAAA
* *
153788 GAGTTTTCGGTTTTGCGAAAAAAAAAA
1 GAGTTTGCGCTTTT-CGAAAAAAAAAA
153815 G
1 G
153816 TTTTTGCGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 4 0.17
27 12 0.50
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (26 bp):
GAGTTTGCGCTTTTCGAAAAAAAAAA
Done.